Overview -------- For each unique event, we indicate the resolution of placement onto the great ape tree and the set of comparisons in which the event is detected. Event names (numbers 1-4017) correspond to the event identifiers used in all Supplementary Data files. The mutation cluster associated with each event is shown within the context of an EPO multiple alignment between the great apes (human sequence repeated to facilitate the display of all possible pairwise comparisons). The displayed multiple alignment also contains ancestral switch point annotations for each pairwise comparison in which the event was identified as significant; square brackets are used to mark the boundaries of the event-associated mutation cluster. The corresponding unidirectional and TSA pairHMM output is shown for each statistically significant comparison. The 4003 template switch events for which human genome sequence exists (event numbers 1-4003) are also described in Supplementary Data File 2, in BED format. Phylogenetic placement ---------------------- species tree consistent: event assigned to a lineage in a manner consistent with the species tree ILS consistent: event assigned to a lineage in a manner consistent with incomplete lineage sorting ambiguous, species tree consistent: event is consistent with the species tree but cannot be unambiguously assigned to a lineage ambiguous, species tree or ILS consistent: event is consistent either with the species tree or incomplete lineage sorting, but cannot be unambiguously assigned to a lineage ambiguous, missing/gapped/masked alignment block: event cannot be placed onto the hominid phylogeny due to missing, gapped or masked sequence in one species unresolved: event has an unresolved phylogenetic placement despite three complete sequences, possible false positive Comparisons ----------- Ancestral > Descendant 1 = Chimp > Human 2 = Human > Chimp 3 = Gorilla > Human 4 = Human > Gorilla 5 = Gorilla > Chimp 6 = Chimp > Gorilla ======= Event 1 ======= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: --------------------A--CTAA--------GTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCGCGACATTGTGAGCT Chimp: --------------------A--CTAA--------GTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCGCGACATTGTGAGCT Gorilla: --------------------A----GG--------CTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTTAGTACCCTCGACATTGTGAGCT ↓ 1 4 3 2 Human: --------------------A--CTAA--------GTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCGCGACATTGTGAGCT Cluster: [ ] Orangutan: GGTCAATATTTTTAATTAGTCCT--GAGTAGGAGGCTGGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCTCAACATTGTGAGCT Gorilla > Human --------------- chr10:108923936-108923940 Template switch process: F1: L TTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGA 1 F3: 4 TAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACT R RF: TTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGAGGCTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTTAG RR: AAACCATAAACCAGTTATAAAAATTAATCAGGACTCATCCTCCGATCGTATGAATACATCGGATCATAATGACCTTAATAATGAATC F2: 3 GAATC 2 Unidirectional alignment (log-probability: -26.5) TTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGA--CtaagTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACT TTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGAGGC----TAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACT Template switch alignment (log-probability: -16.4) TTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGA|CTAAG|TAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACT TTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGA|CTAAG|TAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACT ======= Event 2 ======= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGTGTTATTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--CTAA--------GTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCGCGACATTGTGAGCT Chimp: TAGTGTTATTTGGTATTTGGTTAATATTTGTAATTAGTCCTGAGTAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--CTAA--------GTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCGCGACATTGTGAGCT ↑ 1 4 3 2 Gorilla: TAGTGTTATTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----GG--------CTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTTAGTACCCTCGACATTGTGAGCT Human: TAGTGTTATTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--CTAA--------GTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCGCGACATTGTGAGCT Cluster: [ ] Orangutan: TAGTGTTATTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGAGGCTGGCATACTTATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTGGTTGTTGGGAAAGAAACTTTTGAGCAGTAGCTATTTTTTCTCTCAATTTCTCCGGAGCTCCAGTAAACCAGAGATGGAGAGCAtttttttttAGGGTTAGATCATCTCTCCACTCTGGAAAGTTTCGGTGTCATTACTATTCCAGAATATGTCATCTTTTGGGAGTAGTGTTATTTGGTATTTGGTCAATATTTTTAATTAGTCCT--GAGTAGGAGGCTGGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTCAGTACTCTCAACATTGTGAGCT Gorilla > Chimp --------------- chr10:110471891-110471895 Template switch process: F1: L ATATTATCATCTTTTGGGAGTAGTGTTATTTGGTATTTGGTTAATATTTGTAATTAGTCCTGAGTAGGA 1 F3: 4 TAGCATACTTATGTAG R RF: ATATTATCATCTTTTGGGAGTAGTGTTATTTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGAGGCTAGCATACTTATGTAGCCTAGTATTACTGGAATTATTACTTAG RR: TATAATAGTAGAAAACCCTCATCACAATAAACCATAAACCAGTTATAAAAATTAATCAGGACTCATCCTCCGATCGTATGAATACATCGGATCATAATGACCTTAATAATGAATC F2: 3 GAATC 2 Unidirectional alignment (log-probability: -37.6) TTGGTATTTGGTtAATATTTgTAATTAGTCCTGAGTAGGactaAG--TAGCATACTTATGTAG TTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGG----AGGCTAGCATACTTATGTAG Template switch alignment (log-probability: -27.5) TTGGTATTTGGTtAATATTTgTAATTAGTCCTGAGTAGGA|CTAAG|TAGCATACTTATGTAG TTGGTATTTGGTCAATATTTTTAATTAGTCCTGAGTAGGA|CTAAG|TAGCATACTTATGTAG ======= Event 3 ======= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCACTCATTTATAATATCACCTTTCAGAAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGGTGA ↑ 1 4 3 2 Chimp: TCACTCATTTATAATATCACC-TTCAG-AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGAC-TGTGA ↓ 1 4 3 2 Gorilla: TCACTCATTTATAATATCACCTTTCAGAAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGGTGA Human: TCACTCATTTATAATATCACCTTTCAGAAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGGTGA Cluster: [ ] Orangutan: TCACTCATTTATAATATCACCTTCCAGAAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGGTGA Chimp > Human ------------- chr10:102708304-102708308 Template switch process: F1: L TTCTATTAGCTATATTGCAATCACTCATTTATAATATCACCTT 1 F3: 4 AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGGT R RF: TTCTATTAGCTATATTGCAATCACTCATTTATAATATCACCTTCAGAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTG RR: AAGATAATCGATATAACGTTAGTGAGTAAATATTATAGTGGAAGTCTTTCATTTTTAATTTTAAGACTCTAGGAATCCCCTGAC F2: 3 AGACT 2 Unidirectional alignment (log-probability: -35.7) TATTAGCTATATTGCAATCACTCATTTATAATATCACCtTTCAGaAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGgT TATTAGCTATATTGCAATCACTCATTTATAATATCACC-TTCAG-AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTG-T Template switch alignment (log-probability: -26) TATTAGCTATATTGCAATCACTCATTTATAATATCACCTT|TCAGA|AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTggt TATTAGCTATATTGCAATCACTCATTTATAATATCACCTT|TCAGA|AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACT--G Chimp > Gorilla --------------- chr10:117385570-117385574 Template switch process: F1: L TTCTACTAGCTATATTGCAATCACTCATTTATAATATCACCTT 1 F3: 4 AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTGGT R RF: TTCTATTAGCTATATTGCAATCACTCATTTATAATATCACCTTCAGAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTG RR: AAGATAATCGATATAACGTTAGTGAGTAAATATTATAGTGGAAGTCTTTCATTTTTAATTTTAAGACTCTAGGAATCCCCTGAC F2: 3 AGACT 2 Unidirectional alignment (log-probability: -40.3) TAcTAGCTATATTGCAATCACTCATTTATAATATCACCtTTCAGaAAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTgGT TATTAGCTATATTGCAATCACTCATTTATAATATCACC-TTCAG-AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACT-GT Template switch alignment (log-probability: -31.5) TAcTAGCTATATTGCAATCACTCATTTATAATATCACCTT|TCAGA|AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACTggt TATTAGCTATATTGCAATCACTCATTTATAATATCACCTT|TCAGA|AAAGTAAAAATTAAAATTCTGAGATCCTTAGGGGACT--G ======= Event 4 ======= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATCCTCTGGACATAGTGGTGCAAACAGCGCCCTAGTGGACAGGTAAATTA Chimp: CATCCTCTGGACATAGTGGTGCAAACAGCGCCCTAGTGGACAGGTAAATTA ↓ 3 2 4 Gorilla: CATCCTCTGGACATAGTGGTGCA-ATTGCACCCTAGTGGACAGGTAAATTA ↑ 3 2 4 Human: CATCCTCTGGACATAGTGGTGCAAACAGCGCCCTAGTGGACAGGTAAATTA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr10:123881175-123881179 Template switch process: F1: L AGGCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA 1 F3: 4 CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA R RF: AGGCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAAACAGCGCCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA RR: TCCGTACTCGACTCGGGTGTAGGAGACCTGTATCACCACGTTTGTCGCGGGATCACCTGTCCATTTAATGTCTGGTCCCTATCGGTAT F2: 3 ACGTT 2 Unidirectional alignment (log-probability: -26.7) GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAAttgcA-----CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA----ACAGCGCCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA Template switch alignment (log-probability: -16.4) GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA|TTGCA|CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA|TTGCA|CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA Chimp > Gorilla --------------- chr10:123881175-123881179 Template switch process: F1: L AGGCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA 1 F3: 4 CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA R RF: AGGCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAAACAGCGCCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA RR: TCCGTACTCGACTCGGGTGTAGGAGACCTGTATCACCACGTTTGTCGCGGGATCACCTGTCCATTTAATGTCTGGTCCCTATCGGTAT F2: 3 ACGTT 2 Unidirectional alignment (log-probability: -26.7) GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAAttgcA-----CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA----ACAGCGCCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA Template switch alignment (log-probability: -16.4) GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA|TTGCA|CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA GCATGAGCTGAGCCCACATCCTCTGGACATAGTGGTGCAA|TTGCA|CCCTAGTGGACAGGTAAATTACAGACCAGGGATAGCCATA ======= Event 5 ======= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CTCTGGGGATCAGCACAGGCTGATGCAGTCTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTGCTGCTTAATGCTGGTAATTTCTGCTGCTTCACCTATTTCCACTTTGCTCATTTGACACTATCTAATAAGCACCTGCATGGGACGATTCATGCCACTGCTTATCTACTCATTCAGGAG ↑ 4 1 3 2 Chimp: CTCTGGAGATCAGCACAGGCT----------GATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTGCTGCTTAATGCTGGTAATTTCTGCTGCTTCACCTATTTCCACTTTGCTCATTTGACACTATCTAATAAGCACCTGCATGGGACGATTCATGCCACTGCTTATCTACTCATTCAGGAG Gorilla: CTCTGGGGATCAGCACAGGCTGACGCAGTCTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTGCTGCTTAATGCTGGTAATTTCTGCTTCTTCACCTATTTCCACTTTGCTCATTTGACACTATCTAATAAGCACCTGCATGGGACGATTCATGCCACTGCTTATCTACTCATTCAGGAG Human: CTCTGGGGATCAGCACAGGCTGATGCAGTCTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTGCTGCTTAATGCTGGTAATTTCTGCTGCTTCACCTATTTCCACTTTGCTCATTTGACACTATCTAATAAGCACCTGCATGGGACGATTCATGCCACTGCTTATCTACTCATTCAGGAG Cluster: [ ] Orangutan: CTCTGGGGATCAGCACAGGCTGACGCAGTCTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTGCTGCTTAATGCTGGTAATTTCTGCTGCTTCACCTATTTCCAATTTGCTCATTTGACACTATCTAATAAGCACCTGCATGGGACGATTCATGCCACTGCTTATCTACTCATTCAGGAG Chimp > Human ------------- chr10:122584371-122584374 Template switch process: F1: L AGAGGTGACCGGCCAGGGGGCTCTGGGGATCAGCACAGGCTGATG 1 F3: 4 CTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTG R RF: AGAGGTGACCGGCCAGGGGGCTCTGGAGATCAGCACAGGCTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCATTGCTGCTTAATGCTGGTAATTTCTGCTGCTTCACCTATTTCCACTTTGCTCATTTGACACTATCTAATAAGCACCTGCATGGGACGATTCATGCCACTG RR: TCTCCACTGGCCGGTCCCCCGAGACCTCTAGTCGTGTCCGACTACTTGGTCCACGAAGACGTCCAGAGTTGGGAGGGTAACGACGAATTACGACCATTAAAGACGACGAAGTGGATAAAGGTGAAACGAGTAAACTGTGATAGATTATTCGTGGACGTACCCTGCTAAGTACGGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -31.3) TGACCGGCCAGGGGGCTCTGGgGATCAGCACAGGctgatgcagtCTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCAT TGACCGGCCAGGGGGCTCTGGAGATCAGCACAGG----------CTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCAT Template switch alignment (log-probability: -21.9) TGACCGGCCAGGGGGCTCTGGgGATCAGCACAGGCTGATG|CAGT|CTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCAT TGACCGGCCAGGGGGCTCTGGAGATCAGCACAGGCTGATG|CAGT|CTGATGAACCAGGTGCTTCTGCAGGTCTCAACCCTCCCAT ======= Event 6 ======= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GTCCAAATGGCCAAGATCACAGAA-------GAGGGGC----TTCTGTGCACATTTCCACCaatcaac Chimp: GTCCAAATGGCCAAGATCACAGAA-------GA-GGGC----TTCTGTGCACGTTTCCACTaatcaac ↑ 3 1 2 4 Gorilla: GTCCAAATGGCCAAGATCACAGAAGCCCTAATA-GTACCAAAGTATATGCACGTTTCCACCaatcaac Human: GTCCAAATGGCCAAGATCACAGAA-------GAGGGGC----TTCTGTGCACATTTCCACCaatcaac Cluster: [ ] Orangutan: GTCCAAATGGCCAAGATTACAGAAGCCCCAGTG-GTACTAAAGTATATGCACGTTTCCACCAATC--- Gorilla > Chimp --------------- chr10:124613265-124613274 Template switch process: F1: L GCTAACTGGATGCTACAGTCCAAATGGCCAAGATCACAGAAG 1 F3: 4 TGCACGTTTCCACTAATCAACAGTTTCTTCCAGTGTTCTT R RF: GCTAACTGGATGCTATAGTCCAAATGGCCAAGATCACAGAAGCCCTAATAGTACCAAAGTATATGCACGTTTCCACCAATCAACAGTTTCTTCCAGTGTTCTT RR: CGATTGACCTACGATATCAGGTTTACCGGTTCTAGTGTCTTCGGGATTATCATGGTTTCATATACGTGCAAAGGTGGTTAGTTGTCAAAGAAGGTCACAAGAA F2: 3 GTCTTCGGGA 2 Unidirectional alignment (log-probability: -78) TAACTGGATGCTAcAGTCCAAATGGCCAAGATCACAGAAG--------------------AgggcttctgTGCACGTTTCCACtAATCAACAgtttcttccagtgttctt TAACTGGATGCTATAGTCCAAATGGCCAAGATCACAGAAGCCCTAATAGTACCAAAGTATA---------TGCACGTTTCCACCAATCAACA------------------ Template switch alignment (log-probability: -28.1) TAACTGGATGCTAcAGTCCAAATGGCCAAGATCACAGAAG|AGGGCTTCTG|TGCACGTTTCCACtAATCAACAGTTTCTTCCAGTGTTCTT TAACTGGATGCTATAGTCCAAATGGCCAAGATCACAGAAG|AGGGCTTCTG|TGCACGTTTCCACCAATCAACAGTTTCTTCCAGTGTTCTT ======= Event 7 ======= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GACTGGAACATGCCAGATCCTCCACTGGATCCAGAAGGGCAGGTTTTAACATTA Chimp: GACTGGAACATGCCAGATCCT---------CCAGAAGAGCAGGTTTTAACATTA ↓ 4 12 Gorilla: GACTGGAACATGCCAGATCCTCCACTGGATCCAGAAGAGCAGGTTTTAACATTA Human: GACTGGAACATGCCAGATCCTCCACTGGATCCAGAAGGGCAGGTTTTAACATTA Cluster: [ ] Orangutan: GACTGGAACATGCCAGATCCTCCACTGGATCCAGAAGAGCAGGTTTTAATATTA Chimp > Gorilla --------------- chr10:137371220-137371224 Template switch process: F1: L TGCAATAAATACTACAACTCGACTGGAACATGCCAGATCCTCCA 1 F3: 4 TCCAGAAGAGCAGGTTTTAACATTAGATTCCTTTTTTTTTT R RF: TGCAATAAATACTACAACTCGACTGGAACATGCCAGATCCTCCAGAAGAGCAGGTTTTAACATTAGATTCCTTTTTTTTTT RR: ACGTTATTTATGATGTTGAGCTGACCTTGTACGGTCTAGGAGGTCTTCTCGTCCAAAATTGTAATCTAAGGAAAAAAAAAA F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -34.8) ATAAATACTACAACTCGACTGGAACATGCCAGATCCtccactggaTCCAGAAGAGCAGGTTTTAACATTAGATTCCTTTTTTTtt ATAAATACTACAACTCGACTGGAACATGCCAGATCC---------TCCAGAAGAGCAGGTTTTAACATTAGATTCCTTTTTTT-- Template switch alignment (log-probability: -16.5) ATAAATACTACAACTCGACTGGAACATGCCAGATCCTCCA|CTGGA|TCCAGAAGAGCAGGTTTTAACATTAGATTCCTTTTTTTTT ATAAATACTACAACTCGACTGGAACATGCCAGATCCTCCA|CTGGA|TCCAGAAGAGCAGGTTTTAACATTAGATTCCTTTTTTTTT ======= Event 8 ======= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTCACAGGAGAGCGCTCTTTCATGCCATTCCCTGCCATGTACTCCAGATACCTTCTTTAGTCGTAGGAGAGCCAGGTTCCCAGATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCAGGGGTCTGACTCCTAGTGAGGGCACAGAGGACAGAGCTATTCCACTTCTCGaaaaaaaaa---aaaa-aaaaaGAGT-AGTTGTTAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCTTTTCTCTCCCA-GGACAGCACCTCTGACTACAAGGAGGTGAGTACAG--------------- Chimp: ACTCACAGGAGAGCGCTCTTTCATGCCATTCCCTGCCATGTACTCCAGATACCCTCTTTAGTCGTAGGAGAGCCAGGTTCCCAGATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCA-------------------GGGCACAGAGGACAGAGCTATTCCACTTCTCGCATGAAGTA-------TGAAAATCTTATGTTGTTAATACCAATTCCCTGAGCAAGCCAAAAGAATCAGGGCAAACTCACAGGATGAAGGCCGAAAAAGATCTAGGTACTTGACATTACACGGGAATTCATGACCCTTACTAAAAATCATAAGTCCTAAGATTCTGAGCTTTTTCGCATTTGCTTCATGGGTTAATATTACTTATGAGTTTTCTGGAATGAGTACTGTAGAGAGAAATATCTACAACAGCTCTCATAATTTAGAAGCCAATTTAAGTAAGAAATCCTCAGTTTTATATCAAACAAAGAAATCAATGGTGTTTGTTTTCTGGTGGCTCTTACTCCAAGTTCTTACTAACCTCTAGGCCCTGTGAATATGAGTTCTGTACCAAAGGTGAGTGGGCTCGTCCAAATCAATAGCTATAGAATGGAATGAATTATTAACGTTATTATCAAAAAATATTACAGATATCGCCCCTTCCG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTATATCCTTTCTCAGTGACACAAAGTCTGAA----------TAAGTACAGTAGAAAAGCGAAGAT ↑ 3 2 1 4 Gorilla: ACTCACAGGAGAGCGCTCTTTCATGCCATTCCCTGCCATGTACTCCAAATACCCTCTGTAGTCATAGGAGAGCCAGGTTCCCAGATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCAGGGGTCTGACTCCTAGTGAGAGCACAGAGGACAGAGCTATTCCACTTCTCGaaaaaaaa---------aaaaaTACT-AGTTGTTAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCTTTTCTCTCCCA-GGACAGCACCTCTGACTACAAGGAGGTGAGTACAG--------------- Human: ACTCACAGGAGAGCGCTCTTTCATGCCATTCCCTGCCATGTACTCCAGATACCTTCTTTAGTCGTAGGAGAGCCAGGTTCCCAGATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCAGGGGTCTGACTCCTAGTGAGGGCACAGAGGACAGAGCTATTCCACTTCTCGaaaaaaaaa---aaaa-aaaaaGAGT-AGTTGTTAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCTTTTCTCTCCCA-GGACAGCACCTCTGACTACAAGGAGGTGAGTACAG--------------- Cluster: [ ] Orangutan: ACTCACAGGAGAGCCCCCTTTCATGCCATTCCCTGCCATGTACTCCAGATACCCTCTTTAGTTGTAGGAGAGCCAGGTTCCCAGATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCAGGGGTCTGACTCCTAGTGAGGGCACAGAGGACAGAACTATTCCACTTCTCGGaaaaaaaaaaa-----aaaaaGAGT-AGTTGTTAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTTGTCTTTTCggccaggtgtggtggctcgtgcctgttgtcccagcactttgggaggccgaggcgggcagatcacgaggtcaagatatcgagactatcctgggggacaaggtgaaaccctgtctctactaaaaatacaaaaattagccgggcgtggtggtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggcggagcttgcaggtgagcgaagattgcgccactgcactccagcctaggtgacagagtgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaTTCTCTTTTCTCTCCCA-GGACAGCACCTTTGACTACAAGGAGGTGAGTACAG--------------- Gorilla > Chimp --------------- chr10:20443266-20443271 Template switch process: F1: L GATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCAGG-------------------GCACAGAGGACAGAGCTATTCCACTTCTCG 1 F3: 4 GTAT R RF: TTCATGCCATTCCCTGCCATGTACTCCAAATACCCTCTGTAGTCATAGGAGAGCCAGGTTCCCAGATGGAAAATGGGTTAATTCCCTATCTGGCAAGTCCATCCAGGGGTCTGACTCCTAGTGAGAGCACAGAGGACAGAGCTATTCCACTTCTCGAAAAAAAAAAAAATACTAGTTGTTAAAAGTTCTCTTTTCTCTCCCAGGACAGCACCTCTGACTACAAGGAGGTGAGTAC RR: AAGTACGGTAAGGGACGGTACATGAGGTTTATGGGAGACATCAGTATCCTCTCGGTCCAAGGGTCTACCTTTTACCCAATTAAGGGATAGACCGTTCAGGTAGGTCCCCAGACTGAGGATCACTCTCGTGTCTCCTGTCTCGATAAGGTGAAGAGCTTTTTTTTTTTTTATGATCAACAATTTTCAAGAGAAAAGAGAGGGTCCTGTCGTGGAGACTGATGTTCCTCCACTCATG F2: 3 AAGTAC 2 Unidirectional alignment (log-probability: -43) TCCATCCAGG-------------------GCACAGAGGACAGAGCTATTCCACTTCTCGcatgaagtat-------- TCCATCCAGGGGTCTGACTCCTAGTGAGAGCACAGAGGACAGAGCTATTCCACTTCTCG----------AAAAAAAA Template switch alignment (log-probability: -32.6) TCCATCCAGG-------------------GCACAGAGGACAGAGCTATTCCACTTCTCG|CATGAA|GTAt TCCATCCAGGGGTCTGACTCCTAGTGAGAGCACAGAGGACAGAGCTATTCCACTTCTCG|CATGAA|GTAC ======= Event 9 ======= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTGCATATTAGGTTTATGTGTTCAAATGTGTTTTCATTTGAACAAAAAATTTTACAACTCA ↑ 1 4 3 2 Chimp: TTTGCATATTAGGTTTATGTG------TCTGTTTTCATTTGAACAAAAAGTTTTACAACTCA Gorilla: TTTGCATATTAGGTTTATGTG------TCTGTTTTCATTTGAACAAAAAGTTTTACAACTCA Human: TTTGCATATTAGGTTTATGTGTTCAAATGTGTTTTCATTTGAACAAAAAATTTTACAACTCA Cluster: [ ] Orangutan: TTTGCATATTAGGTTTATGTG------TCTGTTTTCACGTGAACAAAAAGTTTTACAACTCA Chimp > Human ------------- chr10:119531567-119531573 Template switch process: F1: L TATTTCATACTCTAATCATTTTTGCATATTAGGTTTATGTGT 1 F3: 4 TGTTTTCATTTGAACAAAAAATTTTACAACTCAAAACACA R RF: TATTTCATACTCTAATCATTTTTGCATATTAGGTTTATGTGTCTGTTTTCATTTGAACAAAAAGTTTTACAACTCAAAACACA RR: ATAAAGTATGAGATTAGTAAAAACGTATAATCCAAATACACAGACAAAAGTAAACTTGTTTTTCAAAATGTTGAGTTTTGTGT F2: 3 GTAAACT 2 Unidirectional alignment (log-probability: -31.6) TTTCATACTCTAATCATTTTTGCATATTAGGTTTATGTGTtcaaatgTGTTTTCATTTGAACAAAAAaTTTTACAACTCAAAACACA TTTCATACTCTAATCATTTTTGCATATTAGGTTTATGTGT------CTGTTTTCATTTGAACAAAAAGTTTTACAACTCAAAACACA Template switch alignment (log-probability: -22.2) TTTCATACTCTAATCATTTTTGCATATTAGGTTTATGTGT|TCAAATG|TGTTTTCATTTGAACAAAAAaTTTTACAACTCAAAACACA TTTCATACTCTAATCATTTTTGCATATTAGGTTTATGTGT|TCAAATG|TGTTTTCATTTGAACAAAAAGTTTTACAACTCAAAACACA ======== Event 10 ======== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cgacatcactgttctggaaggca----ttttgacaatgtatacagcaagtgcctt Chimp: TGACATCACTGTTCTGGAAGGTGTCAAAATTGACAATGTATACAGCAAGTGCCTT ↑ 1 3 4 2 Gorilla: CGACATCACTGTTCTGGAAGGCA----TTTTGACAATGTATACAGCAAGTGCCTT Human: cgacatcactgttctggaaggca----ttttgacaatgtatacagcaagtgcctt Cluster: [ ] Orangutan: tgacatcactgttctggaaggca----ttttgacaatgtatacagcaagtgcctt Gorilla > Chimp --------------- chr10:12035453-12035460 Template switch process: F1: L CATGCCCTGGTGAGAGAAGTTGACATCACTGTTCTGGAAGG 1 F3: 4 TTGACAATGTATACAGCAAGTGCCTTTTGAAAGTACTAAC R RF: CATGCCCTGGTGAGAGAAGTCGACATCACTGTTCTGGAAGGCATTTTGACAATGTATACAGCAAGTGCCTTTTGAAAGTACTAAC RR: GTACGGGACCACTCTCTTCAGCTGTAGTGACAAGACCTTCCGTAAAACTGTTACATATGTCGTTCACGGAAAACTTTCATGATTG F2: 3 AAAACTGT 2 Unidirectional alignment (log-probability: -36.4) ATGCCCTGGTGAGAGAAGTtGACATCACTGTTCTGGAAGG---TgtcaaaaTTGACAATGTATACAGCAAGTGCCTTTTGAAAGTACTAAC ATGCCCTGGTGAGAGAAGTCGACATCACTGTTCTGGAAGGCATT-------TTGACAATGTATACAGCAAGTGCCTTTTGAAAGTACTAAC Template switch alignment (log-probability: -22.3) ATGCCCTGGTGAGAGAAGTtGACATCACTGTTCTGGAAGG|TGTCAAAA|TTGACAATGTATACAGCAAGTGCCTTTTGAAAGTACTAAC ATGCCCTGGTGAGAGAAGTCGACATCACTGTTCTGGAAGG|TGTCAAAA|TTGACAATGTATACAGCAAGTGCCTTTTGAAAGTACTAAC ======== Event 11 ======== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCATGCTAACACACACCCAAAAAA---TCCAAAGAGCATAATTCTTGTACGTTATTGCCAC ↓ 1 3 4 2 Chimp: CCATGCTAACACACACCCAAATTATGCTCTTTGGAGCATAATTCTTGTACGTTATTGCCAC ↑ 1 3 4 2 Gorilla: CTATGCTAACACACACCCAAAAAA---TCCAAAGAGCATAATTCTTGTACGTTATTGCCAC Human: CCATGCTAACACACACCCAAAAAA---TCCAAAGAGCATAATTCTTGTACGTTATTGCCAC Cluster: [ ] Orangutan: Human > Chimp ------------- chr10:123237104-123237115 Template switch process: F1: L CCAAACTCCATTTTTACTGACCATGCTAACACACACCCAAA 1 F3: 4 GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC R RF: CCAAACTCCATTTTTACTGACCATGCTAACACACACCCAAAAAATCCAAAGAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC RR: GGTTTGAGGTAAAAATGACTGGTACGATTGTGTGTGGGTTTTTTAGGTTTCTCGTATTAAGAACATGCAATAACGGTGTATGTCCTACAG F2: 3 GTTTCTCGTATT 2 Unidirectional alignment (log-probability: -38.9) CAAACTCCATTTTTACTGACCATGCTAACACACAC---------CCAAAttatgctctttgGAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC CAAACTCCATTTTTACTGACCATGCTAACACACACCCAAAAAATCCAAA------------GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC Template switch alignment (log-probability: -16.8) CAAACTCCATTTTTACTGACCATGCTAACACACACCCAAA|TTATGCTCTTTG|GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC CAAACTCCATTTTTACTGACCATGCTAACACACACCCAAA|TTATGCTCTTTG|GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC Gorilla > Chimp --------------- chr10:123237104-123237115 Template switch process: F1: L CCAAACTCCATTTTTACTGACCATGCTAACACACACCCAAA 1 F3: 4 GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC R RF: CCAAACTCCATTTTTACTGACTATGCTAACACACACCCAAAAAATCCAAAGAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC RR: GGTTTGAGGTAAAAATGACTGATACGATTGTGTGTGGGTTTTTTAGGTTTCTCGTATTAAGAACATGCAATAACGGTGTATGTCCTACAG F2: 3 GTTTCTCGTATT 2 Unidirectional alignment (log-probability: -43.9) CAAACTCCATTTTTACTGACcATGCTAACACACAC---------CCAAAttatgctctttgGAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC CAAACTCCATTTTTACTGACTATGCTAACACACACCCAAAAAATCCAAA------------GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC Template switch alignment (log-probability: -22.8) CAAACTCCATTTTTACTGACcATGCTAACACACACCCAAA|TTATGCTCTTTG|GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC CAAACTCCATTTTTACTGACTATGCTAACACACACCCAAA|TTATGCTCTTTG|GAGCATAATTCTTGTACGTTATTGCCACATACAGGATGTC ======== Event 12 ======== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GTTTTCCAGCTAAAACACTGCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAGTAGCTTCTTTTGAAGGGCAAGGAGGGTGATTTCAA ↑ 3 2 4 1 Chimp: GTTTTCCAGCTAAAACACTGCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTT---------------GAAGGGCAAGAAGGGTGATTTCAA ↓ 3 2 4 1 Gorilla: GTTTTCCAGCTAAAACACTGCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCTAAAACACAGTTTTCTTTTGAAGTAGCTTCTTTTGAAGGGCAAGGAGGGTGATTTCAA Human: GTTTTCCAGCTAAAACACTGCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAGTAGCTTCTTTTGAAGGGCAAGGAGGGTGATTTCAA Cluster: [ ] Orangutan: GTTTTCCAGCTAAAACACTGCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAGTAGCTTCTTTTGAAGGACAAGGAGGGTGATTTCAA Chimp > Human ------------- chr10:18931809-18931812 Template switch process: F1: L TGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAG 1 F3: 4 TTCTTTTGAAGGGCAAGGAGGGTGATTTCAACTCTTCAATGTCTAAA R RF: GCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAGGGCAAGAAGGGTGATTTCAACTCTTCAATGTCTAAA RR: CGATTTAAGAATTGTCAAACTTCGTCCAAAACCTGACCCCTAGGTTAATACGTAAGGGTTTTGTGTCAAAAGAAAACTTCCCGTTCTTCCCACTAAAGTTGAGAAGTTACAGATTT F2: 3 CGAT 2 Unidirectional alignment (log-probability: -38.5) ATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGaagtagcttcttttgAAGGGCAAGgAGGGTGATTTCAACTCTTCAAT ATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTG---------------AAGGGCAAGAAGGGTGATTTCAACTCTTCAAT Template switch alignment (log-probability: -22) ATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAG|TAGC|TTCTTTTGAAGGGCAAGgAGGGTGATTTCAACTCTTCAAT ATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAG|TAGC|TTCTTTTGAAGGGCAAGAAGGGTGATTTCAACTCTTCAAT Chimp > Gorilla --------------- chr10:18805163-18805166 Template switch process: F1: L TGGGGATCCAATTATGCATTCCTAAAACACAGTTTTCTTTTGAAG 1 F3: 4 TTCTTTTGAAGGGCAAGGAGGGTGATTTCAACTCTTCAATGTCTAAA R RF: GCTAAATTCTTAACAGTTTGAAGCAGGTTTTGGACTGGGGATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAGGGCAAGAAGGGTGATTTCAACTCTTCAATGTCTAAA RR: CGATTTAAGAATTGTCAAACTTCGTCCAAAACCTGACCCCTAGGTTAATACGTAAGGGTTTTGTGTCAAAAGAAAACTTCCCGTTCTTCCCACTAAAGTTGAGAAGTTACAGATTT F2: 3 CGAT 2 Unidirectional alignment (log-probability: -43.5) ATCCAATTATGCATTCCtAAAACACAGTTttcttttgaagtagcTTCTTTTGAAGGGCAAGgAGGGTGATTTCAACTCTTCAAT ATCCAATTATGCATTCCCAAAACACAGTT---------------TTCTTTTGAAGGGCAAGAAGGGTGATTTCAACTCTTCAAT Template switch alignment (log-probability: -27.5) ATCCAATTATGCATTCCtAAAACACAGTTTTCTTTTGAAG|TAGC|TTCTTTTGAAGGGCAAGgAGGGTGATTTCAACTCTTCAAT ATCCAATTATGCATTCCCAAAACACAGTTTTCTTTTGAAG|TAGC|TTCTTTTGAAGGGCAAGAAGGGTGATTTCAACTCTTCAAT ======== Event 13 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAAGATTTAATAATGCCAAATTCCTAGCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTT Chimp: ATAAGATTTAATAATGCCAAATTCCTAGCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTT ↑ 1 4 3 2 Gorilla: ATAAGATTTAATAATGCCAAAAAC--ATCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTT ↓ 1 4 3 2 Human: ATAAGATTTAATAATGCCAAATTCCTAGCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTT Cluster: [ ] Orangutan: ATAAGATTTAATAATGCCAAAAAC--ATCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTT Gorilla > Human --------------- chr10:17887570-17887576 Template switch process: F1: L ATTTACTTTATTTAGGGAAGATAAGATTTAATAATGCCAAA 1 F3: 4 CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC R RF: ATTTACTTTCCTTAGGGAAGATAAGATTTAATAATGCCAAAAACATCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC RR: TAAATGAAAGGAATCCCTTCTATTCTAAATTATTACGGTTTTTGTAGGAAGACCGATCCTTAGTGACTAGCGATGTTTCAATAGAG F2: 3 GATCCTT 2 Unidirectional alignment (log-probability: -40.5) TTTACTTTatTTAGGGAAGATAAGATTTAATAATGCCAA----ATtcctagCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC TTTACTTTCCTTAGGGAAGATAAGATTTAATAATGCCAAAAACAT------CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC Template switch alignment (log-probability: -27.7) TTTACTTTatTTAGGGAAGATAAGATTTAATAATGCCAAA|TTCCTAG|CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC TTTACTTTCCTTAGGGAAGATAAGATTTAATAATGCCAAA|TTCCTAG|CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC Gorilla > Chimp --------------- chr10:18278939-18278945 Template switch process: F1: L ATTTACTTTATTTAGGGAAGATAAGATTTAATAATGCCAAA 1 F3: 4 CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC R RF: ATTTACTTTCCTTAGGGAAGATAAGATTTAATAATGCCAAAAACATCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC RR: TAAATGAAAGGAATCCCTTCTATTCTAAATTATTACGGTTTTTGTAGGAAGACCGATCCTTAGTGACTAGCGATGTTTCAATAGAG F2: 3 GATCCTT 2 Unidirectional alignment (log-probability: -40.5) TTTACTTTatTTAGGGAAGATAAGATTTAATAATGCCAA----ATtcctagCCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC TTTACTTTCCTTAGGGAAGATAAGATTTAATAATGCCAAAAACAT------CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC Template switch alignment (log-probability: -27.7) TTTACTTTatTTAGGGAAGATAAGATTTAATAATGCCAAA|TTCCTAG|CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC TTTACTTTCCTTAGGGAAGATAAGATTTAATAATGCCAAA|TTCCTAG|CCTTCTGGCTAGGAATCACTGATCGCTACAAAGTTATCTC ======== Event 14 ======== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATGCTGGGATTTTACCCACC-----------AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCA ↓ 4 3 2 Chimp: GATGCTGGGATTTTACCCACCATCTGGGGGGAAGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCA ↑ 4 3 2 Gorilla: GATGCTGGGATTTTACCCACC-----------AGGCCTACATCCCCCCAGAATATCTGTTTGAAGTCATCA Human: GATGCTGGGATTTTACCCACC-----------AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCA Cluster: [ ] Orangutan: GATGCTGGGATTTTACCCGCC-----------AGGCCTATTTCCCTCCAGAATATCTATTTGAAGTCACCA Human > Chimp ------------- chr10:124156994-124157003 Template switch process: F1: L GGGCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACCA 1 F3: 4 AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAA R RF: GGGCCTTCAGGAGCAGCCTAGATGCTGGGATTTTACCCACCAGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAA RR: CCCGGAAGTCCTCGTCGGATCTACGACCCTAAAATGGGTGGTCCGGATGAAGGGGGGTCTTATAGATAAACTTCAGTAGTT F2: 3 AGGGGGGTCT 2 Unidirectional alignment (log-probability: -32.7) GCCTTCAGGAGCAGCCcAGATGCTGGGATTTTACCCACCatctggggggaAGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAA GCCTTCAGGAGCAGCCTAGATGCTGGGATTTTACCCACC-----------AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAA Template switch alignment (log-probability: -22.5) GCCTTCAGGAGCAGCCcAGATGCTGGGATTTTACCCACCA|TCTGGGGGGA|AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAA GCCTTCAGGAGCAGCCTAGATGCTGGGATTTTACCCACCA|TCTGGGGGGA|AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAA Gorilla > Chimp --------------- chr10:124156994-124157003 Template switch process: F1: L GGGCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACCA 1 F3: 4 AGGCCTACTTCCCCCCAGAATATCTATTTGAAGTCATCAAATATTTTAT R RF: GGGCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACCAGGCCTACATCCCCCCAGAATATCTGTTTGAAGTCATCAAATATTTTAT RR: CCCGGAAGTCCTCGTCGGGTCTACGACCCTAAAATGGGTGGTCCGGATGTAGGGGGGTCTTATAGACAAACTTCAGTAGTTTATAAAATA F2: 3 AGGGGGGTCT 2 Unidirectional alignment (log-probability: -37.9) GCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACCatctggggggaAGGCCTACtTCCCCCCAGAATATCTaTTTGAAGTCATCAA GCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACC-----------AGGCCTACATCCCCCCAGAATATCTGTTTGAAGTCATCAA Template switch alignment (log-probability: -28.3) GCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACCA|TCTGGGGGGA|AGGCCTACtTCCCCCCAGAATATCTaTTTGAAGTCATCAA GCCTTCAGGAGCAGCCCAGATGCTGGGATTTTACCCACCA|TCTGGGGGGA|AGGCCTACATCCCCCCAGAATATCTGTTTGAAGTCATCAA ======== Event 15 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTATATGAAGCAACAAATA---ATGATTCTTAAATAAAGCTCTAATTCTTGGGACTGATTCA ↓ 1 4 3 2 Chimp: TCCTATATGAAGCAACAAATAGAGCTTATTCTTAAAT-AAGCTCTAATTCTTGGGACTGATTCA Gorilla: TCCTATATGAAGCAACAAATA---ATGATTCTTAAATAAAGCTCTAATTCTTGGGACTGATTCA Human: TCCTATATGAAGCAACAAATA---ATGATTCTTAAATAAAGCTCTAATTCTTGGGACTGATTCA Cluster: [ ] Orangutan: TCCTATATGAAGCAACAAAAA---ATGATTCTTAAATAAAGCTCTAATTCTTGGGACAGATTCA Human > Chimp ------------- chr10:18766763-18766768 Template switch process: F1: L ACTTTACAATTCTCTGAGCTTCCTATATGAAGCAACAAATA 1 F3: 4 ATTCTTAAAT-AAGCTCTAATTCTTGGGACTGATTCAAAC R RF: ACTTTACAATTCTCTGAGCTTCCTATATGAAGCAACAAATAATGATTCTTAAATAAAGCTCTAATTCTTGGGACTGATTCAAAC RR: TGAAATGTTAAGAGACTCGAAGGATATACTTCGTTGTTTATTACTAAGAATTTATTTCGAGATTAAGAACCCTGACTAAGTTTG F2: 3 TTCGAG 2 Unidirectional alignment (log-probability: -37.5) CTTTACAATTCTCTGAGCTTCCTATATGAAGCAACAAATAgagcTtATTCTTAAATA-AGCTCTAATTCTTGGGACTGATTCAAAC CTTTACAATTCTCTGAGCTTCCTATATGAAGCAACAAATA---ATGATTCTTAAATAAAGCTCTAATTCTTGGGACTGATTCAAAC Template switch alignment (log-probability: -26.3) CTTTACAATTCTCTGAGCTTCCTATATGAAGCAACAAATA|GAGCTT|ATTCTTAAAT-AAGCTCTAATTCTTGGGACTGATTCAAAC CTTTACAATTCTCTGAGCTTCCTATATGAAGCAACAAATA|GAGCTT|ATTCTTAAATAAAGCTCTAATTCTTGGGACTGATTCAAAC ======== Event 16 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TATGGGAATTCAAAGAAGGCATTTGCCCAAT----GAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGACCCTTAAAAATT Chimp: TACGGGAATTCAAAGAAGGCAAATA-TCAAT--GAAAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGAGGGCCCTTAAAAATT Gorilla: TACGGGAATTCAAAGAAGGCAAATA-TCAATGA--AAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGACCCTTAAAAATT ↓ 1 4 3 2 Human: TATGGGAATTCAAAGAAGGCATTTGCCCAAT----GAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGACCCTTAAAAATT Cluster: [ ] Orangutan: TATGGGAATTCGAAGAAGGCAAATA-TCAATGA--AAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAAATGACCCTTAAAAATT Gorilla > Human --------------- chr10:18312821-18312831 Template switch process: F1: L ATAAATATAAGCTAAGATGCTATGGGAATTCAAAGAAGGCA 1 F3: 4 AGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGAC R RF: ATAAATATAAGCTAAGATGCTACGGGAATTCAAAGAAGGCAAATATCAATGAAAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGAC RR: TATTTATATTCGATTCTACGATGCCCTTAAGTTTCTTCCGTTTATAGTTACTTTCACCACAATTTCTTCGTGAGTAACCCTTTTATTCTACTG F2: 3 GTAACCCGTTT 2 Unidirectional alignment (log-probability: -42.2) TAAATATAAGCTAAGATGCTAtGGGAATTCAAAGAAGGCAtttgcccAAT--------gAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGAC TAAATATAAGCTAAGATGCTACGGGAATTCAAAGAAGGCA-------AATATCAATGAAAGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGAC Template switch alignment (log-probability: -28.2) TAAATATAAGCTAAGATGCTAtGGGAATTCAAAGAAGGCA|TTTgCCCAATG|AGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGAC TAAATATAAGCTAAGATGCTACGGGAATTCAAAGAAGGCA|TTTTCCCAATG|AGTGGTGTTAAAGAAGCACTCATTGGGAAAATAAGATGAC ======== Event 17 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGACCGAGGTGGGTTGTTCGGGGCA---CTTGAGGATTTTTCAATGCTTTCACTCTTTCAGATGAGCATGAAGCCTTCTGTTCTCATTCAGCTCCATCTCAAGCACTGAAGCAGGGATTCCCC Chimp: AGACCGAGGTGGGTTGTTCGGAGCA---CTTGAGGATTTTTCAATGCTTTCACTCTTTCAGATGAGCATGAAGCCTTCTGTTCTCATTCAGCTCCATCTCAAGCACTGAAGCAGGGATTCCCC ↑ 1 4 3 2 Gorilla: AGACCGAGGTGGGTTGTTCGGGGCA------ACGGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAGCCTTCTGTTCTCATTCAGCTCCATCTCAAGC-ATGAAGCAGGGATTcccc ↓ 1 4 3 2 Human: AGACCGAGGTGGGTTGTTCGGGGCA---CTTGAGGATTTTTCAATGCTTTCACTCTTTCAGATGAGCATGAAGCCTTCTGTTCTCATTCAGCTCCATCTCAAGCACTGAAGCAGGGATTCCCC Cluster: [ ] Orangutan: AGACCGAGGTGGGTTGTTCGGGGCACTT---GAGGATTTTTCAATGCTTTCACTCTTTCAGATGAGCGTGAAGCCTTCTGTTCTCATTCAGCCCCATCTCAAGCACTGAAGCAGGGATTCCCC Gorilla > Human --------------- chr10:117765201-117765205 Template switch process: F1: L ATTAAAAGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCA 1 F3: 4 GGATTTTTCAATGCTTTCACTCTTTCAGATGAGCATGAAG R RF: ATTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCAACGGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAGCCTTCTGTTCTCATTCAGCTCCATCTCAAG RR: TAATTTCCTCCACAAATCTGGCTCCACCCAACAAGCCCCGTTGCCTAAAAAGTTACGAAAGTGACAAAGTCTACTCGTACTTCGGAAGACAAGAGTAAGTCGAGGTAGAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -37.3) TTAAAaGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCActtgaGGATTTTTCAATGCTTTCACTcTTTCAGATGAGCATGAAG TTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCAAC---GGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAG Template switch alignment (log-probability: -27.4) TTAAAaGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCA|CTTGA|GGATTTTTCAATGCTTTCACTcTTTCAGATGAGCATGAAG TTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCA|CTTGA|GGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAG Gorilla > Chimp --------------- chr10:119534158-119534162 Template switch process: F1: L AGCTATTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGAGCA 1 F3: 4 GGATTTTTCAATGCTTTCACTCTTTCAGATGAGCATGAAG R RF: AGCTATTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCAACGGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAGCCTTCTGTTCTCATTCAGCTCCATCTCAAG RR: TCGATAATTTCCTCCACAAATCTGGCTCCACCCAACAAGCCCCGTTGCCTAAAAAGTTACGAAAGTGACAAAGTCTACTCGTACTTCGGAAGACAAGAGTAAGTCGAGGTAGAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -37.4) TTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGaGCActtgaGGATTTTTCAATGCTTTCACTcTTTCAGATGAGCATGAAG TTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCAAC---GGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAG Template switch alignment (log-probability: -27.5) TTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGaGCA|CTTGA|GGATTTTTCAATGCTTTCACTcTTTCAGATGAGCATGAAG TTAAAGGAGGTGTTTAGACCGAGGTGGGTTGTTCGGGGCA|CTTGA|GGATTTTTCAATGCTTTCACTGTTTCAGATGAGCATGAAG ======== Event 18 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAATGGGTGGAAGAGATAATGCA------------ATTCCTAGTGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGTTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAGGAAAGAGAC----ATCTGAA Chimp: GAATGGGTGGAAGAGATAATGCA------------ATTCCTAGTGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGTTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAGGAAAGAGAC--ATATCTGAA ↑ 4 1 3 2 Gorilla: GAATGGGTGGAAGAGATAATGCA------------------------ATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGTTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAGGAAAGAGACAT--ATCTGAA ↓ 4 1 3 2 Human: GAATGGGTGGAAGAGATAATGCA------------ATTCCTAGTGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGTTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAGGAAAGAGAC----ATCTGAA Cluster: [ ] Orangutan: GAATGGGTGGAAGGGATAATGCAATTCCTAGTGCA------------ATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGGTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAGGAAAGAGACAT--ATCTGAA Gorilla > Human --------------- chr10:13782543-13782546 Template switch process: F1: L TAAAGCAAGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTC 1 F3: 4 TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGA R RF: TAAAGCAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGTTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAG RR: ATTTCGTCCAAGTTTCGACTTACCCACCTTCTCTATTACGTTAAGAAAGGTGTACCCCGGTATCCTCCTCTCTTGTAGACTTGTGTGACGACAAGGAATCTGTGTGAGAAAAGTTCAACTTGTAAACGTGTCCTGTTACTGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -33.7) CAaGTTCAAAGCTGAATGGGTGGAAGAGATAAtgcaattcctagTGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT CAGGTTCAAAGCTGAATGGGTGGAAGAGATAA------------TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT Template switch alignment (log-probability: -21.9) CAaGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTC|CTAG|TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT CAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTC|CTAG|TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT Gorilla > Chimp --------------- chr10:14090670-14090673 Template switch process: F1: L TAAAGCAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTC 1 F3: 4 TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGA R RF: TAAAGCAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACATCTGAACACACTGCTGTTCCTTAGACACACTCTTTTCAAGTTGAACATTTGCACAGGACAATGACTAG RR: ATTTCGTCCAAGTTTCGACTTACCCACCTTCTCTATTACGTTAAGAAAGGTGTACCCCGGTATCCTCCTCTCTTGTAGACTTGTGTGACGACAAGGAATCTGTGTGAGAAAAGTTCAACTTGTAAACGTGTCCTGTTACTGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -28.1) CAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGcaattcctagtgCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT CAGGTTCAAAGCTGAATGGGTGGAAGAGATAATG------------CAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT Template switch alignment (log-probability: -16.4) CAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTC|CTAG|TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT CAGGTTCAAAGCTGAATGGGTGGAAGAGATAATGCAATTC|CTAG|TGCAATTCTTTCCACATGGGGCCATAGGAGGAGAGAACAT ======== Event 19 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTCTGGCCAAGTCTACCCTGCAACACGCTGGTAAAATGTAAAATTCCTTCGCACGAGAGTGAAGAGGATGATCCCCAGGTGCGTCTCTCCATTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTGCGCGGGGGCCACGCTCTCCCACTGGGA ↓ 3 2 1 4 Chimp: TTCTCTGGCCAAGTCTACCCTGCAACACGCTGGTAAAATGTAAAATTCCTTCGCACGAGAGTGAAGAGGATGATCCCCAGGTGCGTCTCTCCATTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTGTGCA-GGGCCACGCTctcccactg-ga Gorilla: TTCTCTGGCCAAGTCTACCCTGCAACACGCTGGTAAAATGTAAAATTCCTTCGCACGAGAGTGAAGAGGATGATCCCCAGGTGCGTCTCTCCATTCCTGGGTCCTAATGATTCCTCCTTAAGCCGGCTACCTGTGCGGGGGCCACGATCCCCCACTGGGA Human: TTCTCTGGCCAAGTCTACCCTGCAACACGCTGGTAAAATGTAAAATTCCTTCGCACGAGAGTGAAGAGGATGATCCCCAGGTGCGTCTCTCCATTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTGCGCGGGGGCCACGCTCTCCCACTGGGA Cluster: [ ] Orangutan: TTTTCTGGCCAAGTCTACCCTGCAACATGCTGGTAAAACGTAAAATTCCTTCGCACGAGAGCGAAGAGGATGATCCCCAGGTGCGTCTCTCCATTCCCGGGTCCTAACGATTGCTCTTTATGCGGGCTACCTGTGCGGGGGCCACGCTCTCTCACTGGGA Human > Chimp ------------- chr10:1287013-1287017 Template switch process: F1: L ATTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTG 1 F3: 4 GGCCACGCTCTCCCACTGGA R RF: CTGCAACACGCTGGTAAAATGTAAAATTCCTTCGCACGAGAGTGAAGAGGATGATCCCCAGGTGCGTCTCTCCATTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTGCGCGGGGGCCACGCTCTCCCACTGGG RR: GACGTTGTGCGACCATTTTACATTTTAAGGAAGCGTGCTCTCACTTCTCCTACTAGGGGTCCACGCAGAGAGGTAAGGGCCCAGGATTGCTAAGGAGGAATTCGGCCGATGGACGCGCCCCCGGTGCGAGAGGGTGACCC F2: 3 GACGT 2 Unidirectional alignment (log-probability: -37) TTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTGtGC-aGGGCCACGCTCTCCCACTGGa------------------- TTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTGCGCGGGGGCCACGCTCTCCCACTGGGAGGATGGTTTCTGGGACAT Template switch alignment (log-probability: -21.5) TTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTG|TGCAG|GGCCACGCTCTCCCACTGGa TTCCCGGGTCCTAACGATTCCTCCTTAAGCCGGCTACCTG|TGCAG|GGCCACGCTCTCCCACTGGG ======== Event 20 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAAAATTGCCAGTTAAGTAGGAGAAT---ACGCTTTCAGTGGTGCAAATAAGAACAGTAGTGGTCAAAG Chimp: TAAAAATTGCCAGTAAAGTAGGAGAAT---ACGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAG ↓ 1 4 3 2 Gorilla: TAAAAATTGCCAGTAAAGTAGCAATTTGTACCGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAG Human: TAAAAATTGCCAGTTAAGTAGGAGAAT---ACGCTTTCAGTGGTGCAAATAAGAACAGTAGTGGTCAAAG Cluster: [ ] Orangutan: TAAAAATTGCCAGTAAAGTAGGAGAAT---ACACTTGCAGTGGTACAAATAAGAACAGTAGTGGTCAAAG Chimp > Gorilla --------------- chr10:1443518-1443525 Template switch process: F1: L TATTTTTTAGTTGAGAAAATTAAAAATTGCCAGTAAAGTAGCA 1 F3: 4 CGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAGA R RF: TATTTTTTAGTTGAGAAAATTAAAAATTGCCAGTAAAGTAGGAGAATACGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAGA RR: ATAAAAAATCAACTCTTTTAATTTTTAACGGTCATTTCATCCTCTTATGCGAAAGTCACCATGTTTATTCTTGTCATCACCAGTTTCT F2: 3 CATGTTTA 2 Unidirectional alignment (log-probability: -35.4) TTTTTAGTTGAGAAAATTAAAAATTGCCAGTAAAGTAG-------caatttgtacCGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAGA TTTTTAGTTGAGAAAATTAAAAATTGCCAGTAAAGTAGGAGAATA----------CGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAGA Template switch alignment (log-probability: -22.3) TTTTTAGTTGAGAAAATTAAAAATTGCCAGTAAAGTAGcA|ATTTGTAC|CGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAGA TTTTTAGTTGAGAAAATTAAAAATTGCCAGTAAAGTAGGA|ATTTGTAC|CGCTTTCAGTGGTACAAATAAGAACAGTAGTGGTCAAAGA ======== Event 21 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGATTATGCAGTAGAAAGGAACAGGTCATGATATGTAAAATCATGACcctcctatgttctccatcttccccaccctgccgtgtggttttcatagctgtcaggcctctgagcccaagctaagccatcatatcccctgtgacctgcacgtatacatccagatggc Chimp: GGATTATGCAGTAGAAAGGAACAGGTCATGATATGTAAAATCATGACcctcctatgttctccatcttccccaccctgccgtgtggttttcatagctgtcatgcctctgagcaaaagctaagccatcatatcccctgtgacctgcacatatacatccagatggc ↑ 1 4 3 2 Gorilla: GGATTATGCAGTAGAAAGGAATCTGTGTTCATATGTAAAATCATGACcctcctatgttctccatcttccccaccctgccgtgtggttttcatagctgtcaggcctctgagcccaagctaagccatcatatcccctgtgacctgcacatatacatccagatggc ↓ 1 4 3 2 Human: GGATTATGCAGTAGAAAGGAACAGGTCATGATATGTAAAATCATGACcctcctatgttctccatcttccccaccctgccgtgtggttttcatagctgtcaggcctctgagcccaagctaagccatcatatcccctgtgacctgcacgtatacatccagatggc Cluster: [ ] Orangutan: GGATTATGCAGTAGAAAGGAACCTGTGTTCAtatgtaaaattgtgaccctcctatgttctccatcttccccaccctgccgtgtggttttcgtagctgtcaggcctctgagcccaagctaaaccatcacatcccctgtgacctgcacatatacatccagatggc Gorilla > Human --------------- chr10:13690321-13690327 Template switch process: F1: L CACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA 1 F3: 4 TGATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTCCC R RF: CACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAATCTGTGTTCATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTCCCCACCCTGCCGTGTGGTTTTCATAGCTGTCAGGCCTCTGAGCCCAAGCTAAGCCATCATATCCCCTGTGACCTG RR: GTGAAGGGACCCTTCATGACCCTAATACGTCATCTTTCCTTAGACACAAGTATACATTTTAGTACTGGGAGGATACAAGAGGTAGAAGGGGTGGGACGGCACACCAAAAGTATCGACAGTCCGGAGACTCGGGTTCGATTCGGTAGTATAGGGGACACTGGAC F2: 3 ACTGGAC 2 Unidirectional alignment (log-probability: -32.6) ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA--------CaggtcatgATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAATCTGTGTTC--------ATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC Template switch alignment (log-probability: -22.2) ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA|CAGGTCA|TgATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA|CAGGTCA|TCATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC Gorilla > Chimp --------------- chr10:13998522-13998528 Template switch process: F1: L CACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA 1 F3: 4 TGATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTCCC R RF: CACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAATCTGTGTTCATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTCCCCACCCTGCCGTGTGGTTTTCATAGCTGTCAGGCCTCTGAGCCCAAGCTAAGCCATCATATCCCCTGTGACCTG RR: GTGAAGGGACCCTTCATGACCCTAATACGTCATCTTTCCTTAGACACAAGTATACATTTTAGTACTGGGAGGATACAAGAGGTAGAAGGGGTGGGACGGCACACCAAAAGTATCGACAGTCCGGAGACTCGGGTTCGATTCGGTAGTATAGGGGACACTGGAC F2: 3 ACTGGAC 2 Unidirectional alignment (log-probability: -32.6) ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA--------CaggtcatgATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAATCTGTGTTC--------ATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC Template switch alignment (log-probability: -22.2) ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA|CAGGTCA|TgATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC ACTTCCCTGGGAAGTACTGGGATTATGCAGTAGAAAGGAA|CAGGTCA|TCATATGTAAAATCATGACCCTCCTATGTTCTCCATCTTC ======== Event 22 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATAACTCCTACTCCTTCCTCAGATTTCATCTCATCTTAGTTCCTCAAAATCTCTCTAATTAAACCTCCCTCTCCAACCCTCGTTAGTGGGGTCCTCTTTGTCCCTTCCCAGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCTTGCTGGGCTGAACttcttcttctt Chimp: CATAACTCCTACTCCTTCCTCAGATTTCATCTCATCTTAGTTCCTCAAAATCTCTCTAATTAAACCTCCCTCTCCAATCCTCGTTAGTGGGGTCCTCTTTGTCCCTTCCCAGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCTTGCTGGGCTGAACTTCTTCttctt ↓ 3 2 1 4 Gorilla: CATAACTCCTACTCCTTCCTCAGATTTCATCTCATCTTAGGTCTTCAAAATCTCTCCAATTAAACCTCCCTCTCCAACCCTCGTTAGTGGGGTCCTCTTTGTCCCTTCCCAGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCCTGATGGGCTGAACttcttcttctt Human: CATAACTCCTACTCCTTCCTCAGATTTCATCTCATCTTAGTTCCTCAAAATCTCTCTAATTAAACCTCCCTCTCCAACCCTCGTTAGTGGGGTCCTCTTTGTCCCTTCCCAGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCTTGCTGGGCTGAACttcttcttctt Cluster: [ ] Orangutan: GATAACTTCTACTCCTTCCTCAGATTTCATCTCATCTTAGTTCCTCAAAATTTCTCTAATTAAACCTCCCTCTCCAACCCTCTTTAGTGGGGTCCTCTTTGTCCCTTCCCAGTCCCTCCTCTTGGCCACTCTAATCCATCCTCTACACTCTTGCTGGGCTGAACttctttttt-- Chimp > Gorilla --------------- chr10:29690045-29690048 Template switch process: F1: L CAGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTC 1 F3: 4 TGGGCTGAACTTCTTCTTCTTTTTTTTTTTTTT R RF: TCAGATTTCATCTCATCTTAGTTCCTCAAAATCTCTCTAATTAAACCTCCCTCTCCAATCCTCGTTAGTGGGGTCCTCTTTGTCCCTTCCCAGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCTTGCTGGGCTGAACTTCTTCTTCTTTTTTTTTTTTTT RR: AGTCTAAAGTAGAGTAGAATCAAGGAGTTTTAGAGAGATTAATTTGGAGGGAGAGGTTAGGAGCAATCACCCCAGGAGAAACAGGGAAGGGTCAGGGAGGAGAACCTGTGAGATTAGGTAGGAGATGTAAGAACGACCCGACTTGAAGAAGAAGAAAAAAAAAAAAAA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -26) AGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCcTGaTGGGCTGAACTTCTTCTTCTTTTTTTTTttttt AGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTCTTGCTGGGCTGAACTTCTTCTTCTTTTTTTTT----- Template switch alignment (log-probability: -16) AGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTC|CTGA|TGGGCTGAACTTCTTCTTCTTTTTTTTTTTTTT AGTCCCTCCTCTTGGACACTCTAATCCATCCTCTACATTC|CTGA|TGGGCTGAACTTCTTCTTCTTTTTTTTTTTTTT ======== Event 23 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAACACACGCTCGAAAGTGCTCTGAAAGCACAAGATGTTCCACTGCTATTTCTCCTCCTTGGCACACCCCTGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCT----TCAGAGCCTGGGATCCTCCTGCAGGTCA Chimp: TAAACACACGCTCGAAAGTGCTCTGAAAGCACAAGATGTTCCACTGCTATTTCTCTTCCTTGGCACACCCCTGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCT----TCAGACACTGGGATCCTCCTGCAGGTCA ↓ 3 2 1 4 Gorilla: TAAACACACGCTCGAAAGTGCTCTGAAAGCACAAGATGTTCCACTGCTATTTCTCTTCCTTGGCACACCCCTGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCTTCATTCAGAGCCTGGGATCCTCCTGCAGGTCA Human: TAAACACACGCTCGAAAGTGCTCTGAAAGCACAAGATGTTCCACTGCTATTTCTCCTCCTTGGCACACCCCTGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCT----TCAGAGCCTGGGATCCTCCTGCAGGTCA Cluster: [ ] Orangutan: TAAACACACGCTCGAAAGTGCTCTGAAAGCACAAGATGTTCCACTGCTATTTCTCTTCCTTGGCACACCCCTGAGTCCGCCCTGGCCCCCAGCAAAGGGGAGAAGGCT----CCAGAGCCTGGGATCCTCCTGCAGGTCA Chimp > Gorilla --------------- chr10:118989531-118989538 Template switch process: F1: L CCCCTGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCTTCA 1 F3: 4 CTGGGATCCTCCTGCAGGTCAGGGGTTCCCTCTGACTCAC R RF: GCTCTGAAAGCACAAGATGTTCCACTGCTATTTCTCTTCCTTGGCACACCCCTGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCTTCAGACACTGGGATCCTCCTGCAGGTCAGGGGTTCCCTCTGACTCAC RR: CGAGACTTTCGTGTTCTACAAGGTGACGATAAAGAGAAGGAACCGTGTGGGGACTCAGGTGGGACCGGGGGTCGTTTCCCCTCTTCCGAAGTCTGTGACCCTAGGAGGACGTCCAGTCCCCAAGGGAGACTGAGTG F2: 3 CGAGACTT 2 Unidirectional alignment (log-probability: -27.8) TGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCttcaTTCAGAgcCTGGGATCCTCCTGCAGGTCAGGGGTTCCCTCTGACTCAC TGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGC----TTCAGACACTGGGATCCTCCTGCAGGTCAGGGGTTCCCTCTGACTCAC Template switch alignment (log-probability: -16.8) TGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCTTCA|TTCAGAGC|CTGGGATCCTCCTGCAGGTCAGGGGTTCCCTCTGACTCAC TGAGTCCACCCTGGCCCCCAGCAAAGGGGAGAAGGCTTCA|TTCAGAGC|CTGGGATCCTCCTGCAGGTCAGGGGTTCCCTCTGACTCAC ======== Event 24 ======== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGGGCTGCCATGGGTTGGGCAG---CAGCTGCTGGGATCAGAGAGGCTCTGAACCTG Chimp: AGGGGCTGCCATGGGTTGGGCAG---CAGCTGCTGGGAGCAGAGAGGCTCTGAACCTG ↓ 1 4 3 2 Gorilla: AGGGGCTGCCATGGGTTGGGCTCCCAGAGCTGCTGGGAGCAGAGAGGCTCTGAACCTG ↑ 1 4 3 2 Human: AGGGGCTGCCATGGGTTGGGCAG---CAGCTGCTGGGATCAGAGAGGCTCTGAACCTG Cluster: [ ] Orangutan: AGGGGCTGCCATGGATTGAACAG---CAGCTGCTGGGAGCAGAGAGGCTCTGAACCTG Human > Gorilla --------------- chr10:30303448-30303453 Template switch process: F1: L GAGGGGGAGGCCGCCACCCAAGGGGCTGCCATGGGTTGGGC 1 F3: 4 AGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC R RF: GAGGGGGAGGCCGCAACCCAAGGGGCTGCCATGGGTTGGGCAGCAGCTGCTGGGATCAGAGAGGCTCTGAACCTGCCAGCCTCC RR: CTCCCCCTCCGGCGTTGGGTTCCCCGACGGTACCCAACCCGTCGTCGACGACCCTAGTCTCTCCGAGACTTGGACGGTCGGAGG F2: 3 GACCCT 2 Unidirectional alignment (log-probability: -37.3) AGGGGGAGGCCGCcACCCAAGGGGCTGCCATGGGTTGGGCtcCcagAGCTGCTGGGAgCAGAGAGGCTCTGAACCTGCCAGCCTCC AGGGGGAGGCCGCAACCCAAGGGGCTGCCATGGGTTGGGCAGC---AGCTGCTGGGATCAGAGAGGCTCTGAACCTGCCAGCCTCC Template switch alignment (log-probability: -27.5) AGGGGGAGGCCGCcACCCAAGGGGCTGCCATGGGTTGGGC|TCCCAG|AGCTGCTGGGAgCAGAGAGGCTCTGAACCTGCCAGCCTCC AGGGGGAGGCCGCAACCCAAGGGGCTGCCATGGGTTGGGC|TCCCAG|AGCTGCTGGGATCAGAGAGGCTCTGAACCTGCCAGCCTCC Chimp > Gorilla --------------- chr10:30303448-30303453 Template switch process: F1: L GAGGGGGAGGCCGCCACCCAAGGGGCTGCCATGGGTTGGGC 1 F3: 4 AGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC R RF: GAGGGGGAGGCCGCAACCCAAGGGGCTGCCATGGGTTGGGCAGCAGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC RR: CTCCCCCTCCGGCGTTGGGTTCCCCGACGGTACCCAACCCGTCGTCGACGACCCTCGTCTCTCCGAGACTTGGACGGTCGGAGG F2: 3 GACCCT 2 Unidirectional alignment (log-probability: -31.8) AGGGGGAGGCCGCcACCCAAGGGGCTGCCATGGGTTGGGCtcCcagAGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC AGGGGGAGGCCGCAACCCAAGGGGCTGCCATGGGTTGGGCAGC---AGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC Template switch alignment (log-probability: -22) AGGGGGAGGCCGCcACCCAAGGGGCTGCCATGGGTTGGGC|TCCCAG|AGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC AGGGGGAGGCCGCAACCCAAGGGGCTGCCATGGGTTGGGC|TCCCAG|AGCTGCTGGGAGCAGAGAGGCTCTGAACCTGCCAGCCTCC ======== Event 25 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAACACTAACGGAGTACATGGTTA-------TTTGCATACCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAATGACCTAATTGAGAACTCAGGTCTATTTCTCTATACAAATACCCCTGTCTACCAGACTGGACT Chimp: TAAACACTAACGGGGTACATGGTTA-------TTTGCATACCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAATGACCTAATTGAGAACTCAGGTCTATTTCTCTATACAAATACCCCTGTCTACCAGACTGGACT Gorilla: TAAACACTAACGGAGTACATGCAAA--------------TCCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAATGACCTAATTGAGAACTCAGGTCTATTTCTCTATACAAATACCCTTGTCTACCAGACTGGACT ↓ 1 4 3 2 Human: TAAACACTAACGGAGTACATGGTTA-------TTTGCATACCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAATGACCTAATTGAGAACTCAGGTCTATTTCTCTATACAAATACCCCTGTCTACCAGACTGGACT Cluster: [ ] Orangutan: TAAACACTAATGGAGTACATGGTTATTTGCAC-------ACCCAGCTTAGAATTTTATATTGGGTGTTGAGAGTGGAAATGACCTAATTGAGAACTCAGGTCTATTTCTCTATACAAATACCCCTGTCTACCAGATTAGACT Gorilla > Human --------------- chr10:12167301-12167312 Template switch process: F1: L TTTTCTTTTTAACGCTGTTTTAAACACTAACGGAGTACATG 1 F3: 4 CCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAAT R RF: TTTTCTTTTTAACGCTGTTTTAAACACTAACGGAGTACATGCAAATCCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAATGACCTAATTGAGAACTCAGGTCTATTTCTCTATACAAATACC RR: AAAAGAAAAATTGCGACAAAATTTGTGATTGCCTCATGTACGTTTAGGGTCGAATCTTAAAATATAACCCCCAACTCTCACCTTTACTGGATTAACTCTTGAGTCCAGATAAAGAGATATGTTTATGG F2: 3 ATACGTTTATTG 2 Unidirectional alignment (log-probability: -37.6) TTTCTTTTTAACGCTGTTTTAAACACTAACGGAGTACATGgttATttgcataCCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAAT TTTCTTTTTAACGCTGTTTTAAACACTAACGGAGTACATGCAAAT-------CCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAAT Template switch alignment (log-probability: -28.3) TTTCTTTTTAACGCTGTTTTAAACACTAACGGAGTACATG|GtTATTTGcATA|CCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAAT TTTCTTTTTAACGCTGTTTTAAACACTAACGGAGTACATG|GGTATTTGTATA|CCCAGCTTAGAATTTTATATTGGGGGTTGAGAGTGGAAAT ======== Event 26 ======== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATCAAAAGTTAAAATTAAAAT-ACAATGGGGGTCCAGTTTTTCTTTGTTAAAGTCCTCATATTCTTTTT ↓ 13 24 ↑ 13 24 Chimp: ATCAAAAGTTAAAATTAAAATAACAAAGAAAAACTGGACCCCCATT-GTAAAGTCCTCATATTCTTTTT Gorilla: ATCAAAAGTTAAAATTAAAATAACAAAGAAAAACTGGACCCCCATT-GTAAAGCCCTCATAtttttttt Human: ATCAAAAGTTAAAATTAAAAT-ACAATGGGGGTCCAGTTTTTCTTTGTTAAAGTCCTCATATTCTTTTT Cluster: [ ] Orangutan: ATCAAAAGTTAAAATTAAAATAACA----AAAACTGGAACCCCATT-TTAAAGTCCTCATATTCTTTTT Chimp > Human ------------- chr10:27639112-27639136 Template switch process: F1: L TAGCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA 1 F3: 4 TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT R RF: TAGCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATAACAAAGAAAAACTGGACCCCCATTGTAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT RR: ATCGATCTTGTTACACCGAGTAGTTTTCAATTTTAATTTTATTGTTTCTTTTTGACCTGGGGGTAACATTTCAGGAGTATAAGAAAAAGAATTTTACGATTTTATAA F2: 3 TGTTTCTTTTTGACCTGGGGGTAAC 2 Unidirectional alignment (log-probability: -57) GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA--------------------CAaTGggggtccagtttttctttgtTAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATAACAAAGAAAAACTGGACCCCCATTG--------------------TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT Template switch alignment (log-probability: -18.4) GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA|CAATGGGGGTCCAGTTTTTCTTTGT|TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA|CAATGGGGGTCCAGTTTTTCTTTGT|TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT Human > Chimp ------------- chr10:28265534-28265558 Template switch process: F1: L TAGCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA 1 F3: 4 TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT R RF: TAGCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATACAATGGGGGTCCAGTTTTTCTTTGTTAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT RR: ATCGATCTTGTTACACCGAGTAGTTTTCAATTTTAATTTTATGTTACCCCCAGGTCAAAAAGAAACAATTTCAGGAGTATAAGAAAAAGAATTTTACGATTTTATAA F2: 3 GTTACCCCCAGGTCAAAAAGAAACA 2 Unidirectional alignment (log-probability: -57) GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATAacaaagaaaaactggaccccCAtTG--------------------TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA--------------------CAATGGGGGTCCAGTTTTTCTTTGTTAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT Template switch alignment (log-probability: -18.4) GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA|ACAAAGAAAAACTGGACCCCCATTG|TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT GCTAGAACAATGTGGCTCATCAAAAGTTAAAATTAAAATA|ACAAAGAAAAACTGGACCCCCATTG|TAAAGTCCTCATATTCTTTTTCTTAAAATGCTAAAATATT ======== Event 27 ======== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: --------CTGCCTTCTGGTG----GGTACCCCCTCCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGA Chimp: taaagcAACTGCCTTCTGGTG----GGTACCCCCTCCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGA Gorilla: --------CTGCCTTCTGGTG--------GCAGCTGCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGA ↑ 1 4 3 2 Human: --------CTGCCTTCTGGTG----GGTACCCCCTCCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGA Cluster: [ ] Orangutan: --------CTGCCTTCTAGTGGGTA----CCCCCTCCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGA Human > Gorilla --------------- chr10:19302015-19302020 Template switch process: F1: L ATTAAACAGGATAAAGTCTGTAAAGCAACTGCCTTCTGGTGG 1 F3: 4 CTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGAAGGA R RF: ATTAAACAGGATAAAGTCTGTAAAGCAACTGCCTTCTGGTGGGTACCCCCTCCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGAAGGA RR: TAATTTGTCCTATTTCAGACATTTCGTTGACGGAAGACCACCCATGGGGGAGGAAGAACAGAGTCGACCTCTTCGGGGACCACAAACTTCCT F2: 3 GTCGAC 2 Unidirectional alignment (log-probability: -27.7) TAAACAGGATAAAGTCTGTAAAGCAACTGCCTTCTGGTGG----CagCTgCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGAAGGA TAAACAGGATAAAGTCTGTAAAGCAACTGCCTTCTGGTGGGTACCCCCTCCTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGAAGGA Template switch alignment (log-probability: -16.5) TAAACAGGATAAAGTCTGTAAAGCAACTGCCTTCTGGTGG|CAGCTG|CTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGAAGGA TAAACAGGATAAAGTCTGTAAAGCAACTGCCTTCTGGTGG|CAGCTG|CTTCTTGTCTCAGCTGGAGAAGCCCCTGGTGTTTGAAGGA ======== Event 28 ======== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAACACTGGGTTAAGGGATTTTTAA-GGAACTTGCACAAACAATTAGCAAGTTCCTTAAAA ↓ 1 4 3 2 Chimp: AAACACTGGGTTAAGGGATTTGTGTGTGCACTTGCACAAACAATTAGCAAGTTCCTTAAAA Gorilla: AAACACTGGGTTAAGGGATTTGTGTGTGCACTTGCACAAACAATTAGCAAGTTCCTTAAAA ↑ 1 4 3 2 Human: AAACACTGGGTTAAGGGATTTTTAA-GGAACTTGCACAAACAATTAGCAAGTTCCTTAAAA Cluster: [ ] Orangutan: AAACACTGGGTTAAGGGATTTGTGTGTGCACTTGCACAAACAATTAGCAAGTTCCTTAAAA Human > Chimp ------------- chr10:28069274-28069282 Template switch process: F1: L GACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT 1 F3: 4 CTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA R RF: GACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTTTTAAGGAACTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA RR: CTGTGTAAACACAAGAACTGTTTGTGACCCAATTCCCTAAAAATTCCTTGAACGTGTTTGTTAATCGTTCAAGGAATTTTCGGTGTCT F2: 3 ACGTGTGTG 2 Unidirectional alignment (log-probability: -33) ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTTgtgtgtgc-------ACTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT--------TTAAGGAACTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA Template switch alignment (log-probability: -22.4) ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT|GTgTGTGCA|CTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT|GTTTGTGCA|CTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA Human > Gorilla --------------- chr10:27577980-27577988 Template switch process: F1: L GACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT 1 F3: 4 CTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA R RF: GACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTTTTAAGGAACTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA RR: CTGTGTAAACACAAGAACTGTTTGTGACCCAATTCCCTAAAAATTCCTTGAACGTGTTTGTTAATCGTTCAAGGAATTTTCGGTGTCT F2: 3 ACGTGTGTG 2 Unidirectional alignment (log-probability: -32.5) ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT-------gtgtgtgcACTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTTTTAAGGA--------ACTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA Template switch alignment (log-probability: -22.4) ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT|GTgTGTGCA|CTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA ACACATTTGTGTTCTTGACAAACACTGGGTTAAGGGATTT|GTTTGTGCA|CTTGCACAAACAATTAGCAAGTTCCTTAAAAGCCACAGA ======== Event 29 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAGTTTGTAACTTTGGAGTCAGGAGAGAAAGATGCAGATTATGGATGACAAATGTGAAGTGA--AAACATCGCTCCTTAACAGCTGTGAAAT Chimp: ATAGTTTGTAACTTTGGAGTCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAACTGAATGACAAATGCTCCTTAACAGCTGTGAAAT ↑ 3 2 4 1 Gorilla: ATAGTTTGTAACTTTGGAGTCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAAGTGA--AAACATCACTCCTTAACAGCTGTGAAAT Human: ATAGTTTGTAACTTTGGAGTCAGGAGAGAAAGATGCAGATTATGGATGACAAATGTGAAGTGA--AAACATCGCTCCTTAACAGCTGTGAAAT Cluster: [ ] Orangutan: ATAGTTTGTAACTTTGGAGTCAGGAGAGAAAGATGCGGATTATGGATGACAAACGTGAAGTCA--AAACATCGCTCCTTAACAGCTGTGAAAT Gorilla > Chimp --------------- chr10:28193623-28193626 Template switch process: F1: L GTCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAA 1 F3: 4 ATGACAAATG----------------CTCCTTAACAGCTGTGAAATCCCCTTTGACCCTCCTCCTA R RF: GTCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAAGTGAAAACATCACTCCTTAACAGCTGTGAAATCCCCTTTGACCCTCCTCCTA RR: CAGTCCTCTCTTTCTACGTATAATACCTACTGTTTACACTTCACTTTTGTAGTGAGGAATTGTCGACACTTTAGGGGAAACTGGGAGGAGGAT F2: 3 AGTC 2 Unidirectional alignment (log-probability: -39.5) TCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAAcTGA-------AtgacaaatgCTCCTTAACAGCTGTGAAATCCCCTTTGAC TCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAAGTGAAAACATCA---------CTCCTTAACAGCTGTGAAATCCCCTTTGAC Template switch alignment (log-probability: -27) TCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAA|CTGA|ATGACAAATG----------------CTCCTTAACAGCTGTGAAATCCCCTTTGAC TCAGGAGAGAAAGATGCATATTATGGATGACAAATGTGAA|CTGA|ATGACAAATGTGAAGTGAAAACATCACTCCTTAACAGCTGTGAAATCCCCTTTGAC ======== Event 30 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATGATACTGGAGTGTCTGCTTAGATGCACTGACTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAACTGGAGGCAAGATGAAGAAGCTTCTGGCAcaacacttctgaaacggaaatgtgggcatccatcacctgggatcttgttaaaatgcagatcctgattcaggaggtctgggctggacc-ta Chimp: AAATGATACTGGAGTGTCTGC--------------TCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAACTGGAGGCAAGATGAAGAAGCTTTTGGCAcaacacttctgaaatggaaatgtgggcatccatcacctgggatcttgttaaaatgcagatcctgattcaggaggtctgggctggacc-ta ↓ 4 1 3 2 Gorilla: AAATGATACTGGAGTGTCTGCTCAGATGCACTGACTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAACTGGAGGCAAGATGAAGAAGCTTTTGGCACAAGActtctgaaacggaaatgtgggcatccatcacctgggatcttgttaaaatgcagatcctgattcaggaggtctgggctggacc-aa Human: AAATGATACTGGAGTGTCTGCTTAGATGCACTGACTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAACTGGAGGCAAGATGAAGAAGCTTCTGGCAcaacacttctgaaacggaaatgtgggcatccatcacctgggatcttgttaaaatgcagatcctgattcaggaggtctgggctggacc-ta Cluster: [ ] Orangutan: AAATGATACTGGAGTGTCTGCTCAGATGCACTGACTCAGATGCCAAATGAGGGCGGCAATTCTGGGCACCCAACTGGAGGCAAGATGAAGAAGCTTTTGGCAcaacacttctgaaacagaaatgtgggcatccatcacctgggaccttgttaaaatgcagatcctgattcaggaggtttgggctggacctga Chimp > Gorilla --------------- chr10:15000430-15000433 Template switch process: F1: L CTTCACAGAGAGGTTTTCTTAAATGATACTGGAGTGTCTGCTCAGATGCA 1 F3: 4 CTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAACT R RF: CTTCATAGAGAGGTTTTCTTAAATGATACTGGAGTGTCTGCTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAACTGGAGGCAAGATGAAGAAGCTTTTGGCACAACACTTCTGAAATGGAAATGTGGGCATCCATCACCTGGGATCTTGTTAAAATGCAGATCCTGATTCAG RR: GAAGTATCTCTCCAAAAGAATTTACTATGACCTCACAGACGAGTCTACGGTTTACTCCCACCGTTAAGACCCGTGGGTTGACCTCCGTTCTACTTCTTCGAAAACCGTGTTGTGAAGACTTTACCTTTACACCCGTAGGTAGTGGACCCTAGAACAATTTTACGTCTAGGACTAAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -36.5) AGGTTTTCTTAAATGATACTGGAGTGTCTGctcagatgcactgaCTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAAC AGGTTTTCTTAAATGATACTGGAGTGTCTG--------------CTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAAC Template switch alignment (log-probability: -27.5) AGGTTTTCTTAAATGATACTGGAGTGTCTGCTCAGATGCa|CTGA|CTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAAC AGGTTTTCTTAAATGATACTGGAGTGTCTGCTCAGATGCC|CTGA|CTCAGATGCCAAATGAGGGTGGCAATTCTGGGCACCCAAC ======== Event 31 ======== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: CCATTTTTTGCATGATTGAATTAGTCATTGGAACATTTCTTGAGTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGACTCTTGGGAAGGTAGACATTGGGCAAAGGAGGGAGGATAGAAAGAGACTCACTAACCTCAAGGAGCCCAAGGGCTGAGTGTAGG ↓ 3 2 1 4 ↑ 1 4 3 2 Chimp: CCATTTTTTGCATGATTGAATTAGTCATTGGAACATGA-CTAATTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGACTCTTGGGAAGGTAGACATTGGGCAAACGAGGGAGGATAGAAAGAGACTCACTAACCTCAAGGAGCCCAAGGGCTGAGTGTAGG Gorilla: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: CCATTTTTTGCATGATTGAATTAGTCATTGGAACATTTCTTGAGTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGACTCTTGGGAAGGTAGACATTGGGCAAAGGAGGGAGGATAGAAAGAGACTCACTAACCTCAAGGAGCCCAAGGGCTGAGTGTAGG Cluster: [ ] Orangutan: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Chimp > Human ------------- chr10:12670581-12670588 Template switch process: F1: L TATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT 1 F3: 4 TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC R RF: TATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACATGACTAATTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGACTCTTGGGAAGGTAGACATTGGGCAAACGAGGGAGGATAGAAAGAGACTCACTAACCTCAAGGA RR: ATAGCGGTAAAAAACGTACTAACTTAATCAGTAACCTTGTACTGATTAACAGACGGTACAAAAACTGTTACAGGATCTATGACCTCTGAGAACCCTTCCATCTGTAACCCGTTTGCTCCCTCCTATCTTTCTCTGAGTGATTGGAGTTCCT F2: 3 GAGTTCTT 2 Unidirectional alignment (log-probability: -31.5) ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACATttcttgaG------TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT-------GACTAATTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC Template switch alignment (log-probability: -22.3) ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT|TtCTTGAG|TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT|TCCTTGAG|TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC Human > Chimp ------------- chr10:12951519-12951525 Template switch process: F1: L TATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT 1 F3: 4 TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC R RF: TATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACATTTCTTGAGTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC RR: ATAGCGGTAAAAAACGTACTAACTTAATCAGTAACCTTGTAAAGAACTCACAGACGGTACAAAAACTGTTACAGGATCTATGACCTCTG F2: 3 TAATCAG 2 Unidirectional alignment (log-probability: -30.1) ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACATgactaaT-------TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT------TTCTTGAGTGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC Template switch alignment (log-probability: -16.2) ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT|GACTAAT|TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC ATCGCCATTTTTTGCATGATTGAATTAGTCATTGGAACAT|GACTAAT|TGTCTGCCATGTTTTTGACAATGTCCTAGATACTGGAGAC ======== Event 32 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAAATCCATGCCTACTTCATGCAGTAGAAA--CGCATGTCCTCTTTTATCATTGGTca Chimp: TAAAATCCATGCCTACTTCATGCAGTAGAAA--CGCATGTCCTCTTTTATCATTGGTCa ↑ 3 2 1 4 Gorilla: TAAAATCCATGCCTACTTCATGCAGTAGAAA----CACGTCCTCTTTTATCATTGGTca ↓ 3 2 1 4 Human: TAAAATCCATGCCTACTTCATGCAGTAGAAA--CGCATGTCCTCTTTTATCATTGGTca Cluster: [ ] Orangutan: TAAAATCCATGCCTCCTTCATGCAGTAGAAATG--CATGTTCTCTTTTATCATTGGTaa Gorilla > Human --------------- chr10:12526641-12526644 Template switch process: F1: L CTCTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAAC 1 F3: 4 GTCCTCTTTTATCATTGGTCAAAACAAAAA R RF: CTCTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAACACGTCCTCTTTTATCATTGGTCAAAACAAAAA RR: GAGACGGAAAATTTTAGGTACGGATGAAGTACGTCATCTTTGTGCAGGAGAAAATAGTAACCAGTTTTGTTTTT F2: 3 TACG 2 Unidirectional alignment (log-probability: -26.4) CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAACgCatGTCCTCTTTTATCATTGGTCAAAACAAAAA---------- CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAACAC--GTCCTCTTTTATCATTGGTCAAAACAAAAAACAAAACAAA Template switch alignment (log-probability: -16) CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAAC|GCAT|GTCCTCTTTTATCATTGGTCAAAACAAAAA CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAAC|GCAT|GTCCTCTTTTATCATTGGTCAAAACAAAAA Gorilla > Chimp --------------- chr10:12807694-12807697 Template switch process: F1: L CTCTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAAC 1 F3: 4 GTCCTCTTTTATCATTGGTCAAAACAAAAA R RF: CTCTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAACACGTCCTCTTTTATCATTGGTCAAAACAAAAA RR: GAGACGGAAAATTTTAGGTACGGATGAAGTACGTCATCTTTGTGCAGGAGAAAATAGTAACCAGTTTTGTTTTT F2: 3 TACG 2 Unidirectional alignment (log-probability: -26.4) CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAACgCatGTCCTCTTTTATCATTGGTCAAAACAAAAA---------- CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAACAC--GTCCTCTTTTATCATTGGTCAAAACAAAAAACAAAACAAA Template switch alignment (log-probability: -16) CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAAC|GCAT|GTCCTCTTTTATCATTGGTCAAAACAAAAA CTGCCTTTTAAAATCCATGCCTACTTCATGCAGTAGAAAC|GCAT|GTCCTCTTTTATCATTGGTCAAAACAAAAA ======== Event 33 ======== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATATTGACTTATCCTTTTCAATG--AATGTTCTATGTTCTGGATTTCCAAGGATTAGAATACTGGGG Chimp: AATATTGACTTATCCTTTTCAATG--AAT-------GTTCTGGATTTCCAAGGATTAGAATACTGGGG ↓ 1 4 3 2 Gorilla: AATATTGACTTATCCTTTTCAGAAATCCT-------GTTCTGGATTTCCAAGGATTAGAATACTGGGG ↑ 1 4 3 2 Human: AATATTGACTTATCCTTTTCAATG--AATGTTCTATGTTCTGGATTTCCAAGGATTAGAATACTGGGG Cluster: [ ] Orangutan: AATATTGACTTATCCTTTTCAATG--AAT-------GTTCTGGATTTCCAAGGATTGGAATACTGGGG Human > Gorilla --------------- chr10:12219305-12219311 Template switch process: F1: L AGTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA 1 F3: 4 TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTTT R RF: AGTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCAATGAATGTTCTATGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTTT RR: TCAAATTTACTTAAGAAAATTTATAACTGAATAGGAAAAGTTACTTACAAGATACAAGACCTAAAGGTTCCTAATCTTATGACCCCCGAAGAAA F2: 3 CCTAAAG 2 Unidirectional alignment (log-probability: -31.3) GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTC------------AgaaatccTGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCAATGAATGTTCTA-------TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT Template switch alignment (log-probability: -16.6) GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA|GAAATCC|TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA|GAAATCC|TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT Chimp > Gorilla --------------- chr10:12219305-12219311 Template switch process: F1: L AGTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA 1 F3: 4 TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT R RF: AGTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCAATGAATGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT RR: TCAAATTTACTTAAGAAAATTTATAACTGAATAGGAAAAGTTACTTACAAGACCTAAAGGTTCCTAATCTTATGACCCCCGAAGAA F2: 3 CCTAAAG 2 Unidirectional alignment (log-probability: -26.5) GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA--GAAatccTGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCAATGAA----TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT Template switch alignment (log-probability: -16.6) GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA|GAAATCC|TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT GTTTAAATGAATTCTTTTAAATATTGACTTATCCTTTTCA|GAAATCC|TGTTCTGGATTTCCAAGGATTAGAATACTGGGGGCTTCTT ======== Event 34 ======== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGCTCAACAGCGCCTGCGAAG------------A--------GCCCCATGGCCAGCAGCACACTCAGCTC ↑ 1 3 2 4 Chimp: TGCTCAACGGCGCCTGCGAAG------CCATGGG----GCTCCTCCCAGGGCCAGCAGCACACTCAGCTC Gorilla: TGCTCAACGGCGCCTGCGAAGCCATGG------GGCTC----CTCCCAGGGCCAGCAGCACACTCAGCTC ↓ 1 3 2 4 Human: TGCTCAACAGCGCCTGCGAAG------------A--------GCCCCATGGCCAGCAGCACACTCAGCTC Cluster: [ ] Orangutan: TGCTCAACGGCGCCTGCGAAGCCATGA------GGCTC----CTCCCAGGGCCAGCAGCACACTCAGCTC Chimp > Human ------------- chr10:123995825-123995832 Template switch process: F1: L AGGGCACAGCCGGTCCCATCTGCTCAACAGCGCCTGCGAAG 1 F3: 4 GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG R RF: AGGGCACAGCCGGTCCCATCTGCTCAACGGCGCCTGCGAAGCCATGGGGCTCCTCCCAGGGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG RR: TCCCGTGTCGGCCAGGGTAGACGAGTTGCCGCGGACGCTTCGGTACCCCGAGGAGGGTCCCGGTCGTCGTGTGAGTCGAGCCGAGACCGGACGTCCCCC F2: 3 TACCCCGA 2 Unidirectional alignment (log-probability: -33.6) GGGCACAGCCGGTCCCATCTGCTCAACaGCGCCTGCGAAGagccCCATGG--------------CCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG GGGCACAGCCGGTCCCATCTGCTCAACGGCGCCTGCGAAG----CCATGGGGCTCCTCCCAGGGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG Template switch alignment (log-probability: -22.3) GGGCACAGCCGGTCCCATCTGCTCAACaGCGCCTGCGAAG|AGCCCCAT|GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG GGGCACAGCCGGTCCCATCTGCTCAACGGCGCCTGCGAAG|AGCCCCAT|GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG Gorilla > Human --------------- chr10:123995825-123995832 Template switch process: F1: L AGGGCACAGCCGGTCCCATCTGCTCAACAGCGCCTGCGAAG 1 F3: 4 GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG R RF: AGGGCACAGCCGGTCCCATCTGCTCAACGGCGCCTGCGAAGCCATGGGGCTCCTCCCAGGGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG RR: TCCCGTGTCGGCCAGGGTAGACGAGTTGCCGCGGACGCTTCGGTACCCCGAGGAGGGTCCCGGTCGTCGTGTGAGTCGAGCCGAGACCGGACGTCCCCC F2: 3 TACCCCGA 2 Unidirectional alignment (log-probability: -32.7) GGGCACAGCCGGTCCCATCTGCTCAACaGCGCCTGCGAAGagccCCAT--------------GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG GGGCACAGCCGGTCCCATCTGCTCAACGGCGCCTGCGAAG----CCATGGGGCTCCTCCCAGGGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG Template switch alignment (log-probability: -22.3) GGGCACAGCCGGTCCCATCTGCTCAACaGCGCCTGCGAAG|AGCCCCAT|GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG GGGCACAGCCGGTCCCATCTGCTCAACGGCGCCTGCGAAG|AGCCCCAT|GGCCAGCAGCACACTCAGCTCGGCTCTGGCCTGCAGGGGG ======== Event 35 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tctgtgttctctaaagtttcAGTGTGGCCTACTTCTTTAGTGATGAGGGGGACAGCtttttgt------tttgttttaagagatggtatcttactctgtcacccaaggtggagtgcagtggcatgatcatagctcactgcagcctcaaacttct Chimp: TCTGTGTTCTCTAAAGTTTCATTGCGGCCTACTTCTTTAGTGATGAGGGGGACAGCtttttgt------tttgttttaagagatgatatcttactctgtcacccaaggtggagtgcagtggcatgatgatagctcactgcaatctcaaacttcg ↓ 1 4 3 2 Gorilla: TCTGTGTTCTCTAAAGTTTCAGTGCAGCTTACTTCTTTAGTGATGAGGGGGACAGCtttttgt-tttgttttgttttaagagatggtatcttactctgtcacccaaggtggagtgcagtggcatggtcatagctcactgcagcctcaaacttct Human: tctgtgttctctaaagtttcAGTGTGGCCTACTTCTTTAGTGATGAGGGGGACAGCtttttgt------tttgttttaagagatggtatcttactctgtcacccaaggtggagtgcagtggcatgatcatagctcactgcagcctcaaacttct Cluster: [ ] Orangutan: tctgtgttctctaaagtttcAGTGCGGCCTACTTCTTTAGTGATGAAGGAGACAGCtttttgtttttgttttgttttaagagatggtatcttactctgtcacccaaggtggagtgcagtggcatgattatagctcactgcagcctcaaacttct Chimp > Gorilla --------------- chr10:136437667-136437670 Template switch process: F1: L ATTCTTTTCCGTTCTAATTTTCTGTGTTCTCTAAAGTTTCAGTGC 1 F3: 4 TACTTCTTTAGTGATGAGGGGGACAGCTTTTTGTTTTGTT R RF: ATTCTTTTCCATTCTAATTTTCTGTGTTCTCTAAAGTTTCATTGCGGCCTACTTCTTTAGTGATGAGGGGGACAGCTTTTTGTTTTGTTTTAAGAGATGATATCTTACTCTGTCACCCAAGGTGGAGTGCAGTGGCATGATGATAGCT RR: TAAGAAAAGGTAAGATTAAAAGACACAAGAGATTTCAAAGTAACGCCGGATGAAGAAATCACTACTCCCCCTGTCGAAAAACAAAACAAAATTCTCTACTATAGAATGAGACAGTGGGTTCCACCTCACGTCACCGTACTACTATCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -37.2) TTTCCgTTCTAATTTTCTGTGTTCTCTAAAGTTTCAgTGCaGCtTACTTCTTTAGTGATGAGGGGGACAGCTTTTTGTTttgtt TTTCCATTCTAATTTTCTGTGTTCTCTAAAGTTTCATTGCGGCCTACTTCTTTAGTGATGAGGGGGACAGCTTTTTGTT----- Template switch alignment (log-probability: -27.4) TTTCCgTTCTAATTTTCTGTGTTCTCTAAAGTTTCAgTGC|AGCT|TACTTCTTTAGTGATGAGGGGGACAGCTTTTTGTTTTGTT TTTCCATTCTAATTTTCTGTGTTCTCTAAAGTTTCATTGC|AGCT|TACTTCTTTAGTGATGAGGGGGACAGCTTTTTGTTTTGTT ======== Event 36 ======== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTATATCAGAAAGGATAACCATTAACAAATGGTTAGTCTAAGACCCACCAAAGC ↑ 3 1 4 2 Chimp: TTATATCAGAAAAGATAACCAT-------TTGTTAGTCTAAGACCCACCAAAGC Gorilla: TTATATCAGAAAGGATAACCAT-------TTGTTAGTCTAAGACCCACCAAAGC ↓ 3 1 4 2 Human: TTATATCAGAAAGGATAACCATTAACAAATGGTTAGTCTAAGACCCACCAAAGC Cluster: [ ] Orangutan: ------------------------------------------------------ Chimp > Human ------------- chr10:28980974-28980981 Template switch process: F1: L AGGCACATTCTATTTTTCCTTATATCAGAAAGGATAACCATT 1 F3: 4 GTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT R RF: AGGCACATTCTATTTTTCCTTATATCAGAAAAGATAACCATTTGTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT RR: TCCGTGTAAGATAAAAAGGAATATAGTCTTTTCTATTGGTAAACAATCAGATTCTGGGTGGTTTCGTCCTACTAGAGACTTTA F2: 3 GTAAACAA 2 Unidirectional alignment (log-probability: -33) GCACATTCTATTTTTCCTTATATCAGAAAgGATAACCATtaacaaaTgGTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT GCACATTCTATTTTTCCTTATATCAGAAAAGATAACCAT-------TTGTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT Template switch alignment (log-probability: -22.3) GCACATTCTATTTTTCCTTATATCAGAAAgGATAACCATT|AACAAATG|GTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT GCACATTCTATTTTTCCTTATATCAGAAAAGATAACCATT|AACAAATG|GTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT Gorilla > Human --------------- chr10:28980974-28980981 Template switch process: F1: L AGGCACATTCTATTTTTCCTTATATCAGAAAGGATAACCATT 1 F3: 4 GTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT R RF: AGGCACATTCTATTTTTCCTTATATCAGAAAGGATAACCATTTGTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT RR: TCCGTGTAAGATAAAAAGGAATATAGTCTTTCCTATTGGTAAACAATCAGATTCTGGGTGGTTTCGTCCTACTAGAGACTTTA F2: 3 GTAAACAA 2 Unidirectional alignment (log-probability: -26.5) GCACATTCTATTTTTCCTTATATCAGAAAGGATAACCATtaacaaaTgGTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT GCACATTCTATTTTTCCTTATATCAGAAAGGATAACCAT-------TTGTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT Template switch alignment (log-probability: -16.8) GCACATTCTATTTTTCCTTATATCAGAAAGGATAACCATT|AACAAATG|GTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT GCACATTCTATTTTTCCTTATATCAGAAAGGATAACCATT|AACAAATG|GTTAGTCTAAGACCCACCAAAGCAGGATGATCTCTGAAAT ======== Event 37 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCAAACACAGTTTCACTGCAGGTGTTTACCTGTTTTGTAAATGTCATTTGTCT Chimp: TTCAAACACAGTTTCACTGCAGGTGTTTACCTGTTTTGTAAATGTCATTTGTCT ↑ 3 1 2 4 Gorilla: TTCAAACACAGTTTCACTGCAGGT----AAACATTTTGTAAATGTCATTTGTCT ↓ 3 1 2 4 Human: TTCAAACACAGTTTCACTGCAGGTGTTTACCTGTTTTGTAAATGTCATTTGTCT Cluster: [ ] Orangutan: TTCAAACACAATTTCACTGCACGT----AAACATTTTGTAAATGTCATTTGTCT Gorilla > Human --------------- chr10:25172847-25172855 Template switch process: F1: L CTTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT 1 F3: 4 TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA R RF: CTTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGTAAACATTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA RR: GAAAGAATAATCTATTAAAGTTTGTGTCAAAGTGACGTCCATTTGTAAAACATTTACAGTAAACAGATATATTAATATTACATATT F2: 3 GTCCATTTG 2 Unidirectional alignment (log-probability: -33.8) TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT-----gtttacctgTTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGTAAACA---------TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA Template switch alignment (log-probability: -16.9) TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT|GTTTACCTG|TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT|GTTTACCTG|TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA Gorilla > Chimp --------------- chr10:25762293-25762301 Template switch process: F1: L CTTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT 1 F3: 4 TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA R RF: CTTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGTAAACATTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA RR: GAAAGAATAATCTATTAAAGTTTGTGTCAAAGTGACGTCCATTTGTAAAACATTTACAGTAAACAGATATATTAATATTACATATT F2: 3 GTCCATTTG 2 Unidirectional alignment (log-probability: -33.8) TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT-----gtttacctgTTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGTAAACA---------TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA Template switch alignment (log-probability: -16.9) TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT|GTTTACCTG|TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA TTTCTTATTAGATAATTTCAAACACAGTTTCACTGCAGGT|GTTTACCTG|TTTTGTAAATGTCATTTGTCTATATAATTATAATGTATAA ======== Event 38 ======== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CGGATAGAAGTATCCTTTATTTCATGGAGAAGACACCATGAAATACCATGAGGCCATGTCCCCA ↑ 3 2 1 4 Chimp: CGGATAGAAGTATCCTTTATTTCATGGGGAAGACACT-----GTACCATGAGGCCATGTCCCCA Gorilla: CGGATAGAAGTATCCTTTATTTGATGGAGAAGACACT-----GCACCATGAGGCCATGTCCCCA Human: CGGATAGAAGTATCCTTTATTTCATGGAGAAGACACCATGAAATACCATGAGGCCATGTCCCCA Cluster: [ ] Orangutan: TGGATAGAAGTATCCTTTATTTCATGGAGAAGACACT-----GTACCATGAGGCCATGTCCCCA Chimp > Human ------------- chr10:123312764-123312770 Template switch process: F1: L TGCACTGTGTTAACCGGATAGAAGTATCCTTTATTTCATGGAGAAGACAC 1 F3: 4 TACCATGAGGCCATGTCCCCACATGGGTGGTACTTGTGGA R RF: TGCACTGTGTTAACCGGATAGAAGTATCCTTTATTTCATGGGGAAGACACTGTACCATGAGGCCATGTCCCCACATGGGTGGTACTTGTGGA RR: ACGTGACACAATTGGCCTATCTTCATAGGAAATAAAGTACCCCTTCTGTGACATGGTACTCCGGTACAGGGGTGTACCCACCATGAACACCT F2: 3 AAAGTAC 2 Unidirectional alignment (log-probability: -34.4) TAACCGGATAGAAGTATCCTTTATTTCATGGaGAAGACACcaTGaaaTACCATGAGGCCATGTCCCCACATGGGTGGTACTTGTGGA TAACCGGATAGAAGTATCCTTTATTTCATGGGGAAGACAC--TG---TACCATGAGGCCATGTCCCCACATGGGTGGTACTTGTGGA Template switch alignment (log-probability: -22.3) TAACCGGATAGAAGTATCCTTTATTTCATGGaGAAGACAC|CATGAAA|TACCATGAGGCCATGTCCCCACATGGGTGGTACTTGTGGA TAACCGGATAGAAGTATCCTTTATTTCATGGGGAAGACAC|CATGAAA|TACCATGAGGCCATGTCCCCACATGGGTGGTACTTGTGGA ======== Event 39 ======== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTCTGCTTCATTTACAGCCCACCCCAGGACCTCACCCAGAGCTGAG--CCCTCCAGTGCCCAGTGGGGAGAGTGGT Chimp: CTCTGCTTCATTTACAGCCCACCCCAGGACCTCACCCAGAGCTGAG--CCCTCCAGTGCCCAGTGGGGAGAGTGGT Gorilla: CTCTGCTTCATTTACAGCCCATCCCAGGGGCTCAGCTCTGGGTGAG----GTCCATTGCCCAGTGGGGAGAGTGGT ↓ 3 4 ↑ 1 3 2 4 Human: CTCTGCTTCATTTACAGCCCACCCCAGGACCTCACCCAGAGCTGAG--CCCTCCAGTGCCCAGTGGGGAGAGTGGT Cluster: [ ] Orangutan: CTCTGCTTCATTTACAGCCCACCCCAGGACCTCACCCAGAGCTGAGCC--CTCCAGTGCCCAGTGGGGAGAGTGGT Gorilla > Human --------------- chr10:123252308-123252328 Template switch process: F1: L GAGGTCTCCCACCCAAGCATCTCTGCTTCATTTACAGCCCACCCCAGG 1 F3: 4 TCCAGTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGATGATAA R RF: GAGGTCTCCCACCCAAGCATCTCTGCTTCATTTACAGCCCATCCCAGGGGCTCAGCTCTGGGTGAGGTCCATTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGATGATAA RR: CTCCAGAGGGTGGGTTCGTAGAGACGAAGTAAATGTCGGGTAGGGTCCCCGAGTCGAGACCCACTCCAGGTAACGGGTCACCCCTCTCACCATTTTTTCTCTCCCTACTATT F2: 3 CCCGAGTCGAGACCCACTCCA 2 Unidirectional alignment (log-probability: -63) CCACCCAAGCATCTCTGCTTCATTTACAGCCCAcCCC-------------------AGGacctcacccagagctgagcccTCCAgTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT CCACCCAAGCATCTCTGCTTCATTTACAGCCCATCCCAGGGGCTCAGCTCTGGGTGAGG---------------------TCCATTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT Template switch alignment (log-probability: -29.7) CCACCCAAGCATCTCTGCTTCATTTACAGCCCAcCCCAGG|ACCTCACCCAGAGCTGAGCCC|TCCAgTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT CCACCCAAGCATCTCTGCTTCATTTACAGCCCATCCCAGG|ACCTCACCCAGAGCTGAGCCC|TCCATTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT Human > Gorilla --------------- chr10:138324182-138324200 Template switch process: F1: L GAGGTCTCCCACCCAAGCATCTCTGCTTCATTTACAGCCCATCCCAGG 1 F3: 4 TCCATTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGATGATAA R RF: GAGGTCTCCCACCCAAGCATCTCTGCTTCATTTACAGCCCACCCCAGGACCTCACCCAGAGCTGAGCCCTCCAGTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGATGATAA RR: CTCCAGAGGGTGGGTTCGTAGAGACGAAGTAAATGTCGGGTGGGGTCCTGGAGTGGGTCTCGACTCGGGAGGTCACGGGTCACCCCTCTCACCATTTTTTCTCTCCCTACTATT F2: 3 GGAGTGGGTCTCGACTCGG 2 Unidirectional alignment (log-probability: -60.2) CCACCCAAGCATCTCTGCTTCATTTACAGCCCAtCCCAGG---------------------ggctcagctctgggtgaggTCCAtTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT CCACCCAAGCATCTCTGCTTCATTTACAGCCCACCCCAGGACCTCACCCAGAGCTGAGCCC-------------------TCCAGTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT Template switch alignment (log-probability: -29.5) CCACCCAAGCATCTCTGCTTCATTTACAGCCCAtCCCAGG|GGCTCAGCTCTGGGTGAGG|TCCAtTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT CCACCCAAGCATCTCTGCTTCATTTACAGCCCACCCCAGG|GGCTCAGCTCTGGGTGAGG|TCCAGTGCCCAGTGGGGAGAGTGGTAAAAAAGAGAGGGAT ======== Event 40 ======== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCTGAAGGGTTGACCTGCAGAAG-TCAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCAAAATTCCTtgg---tggtagtggtggtggtggtggtggtggtgctagtgtggtTCAAATTAGTGTCTTAGTGCGTATGGACTGGCACTAAGGGCATGTGTAT ↑ 1 4 3 2 Chimp: CCTGAAGGGTTGACCTGCAGAGTACTAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCGAAATTCCTtgg---tg---------------gtggtggtggtgCTAGTGTGGTTGAAATTAGTGTCTTAGTGCTTATTGACTGGCACTAAGGGCATGTGTAT ↓ 1 4 3 2 Gorilla: CCTGAAGGGTTGACCTGCAGAAG-TCAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCAAAATTCCTTGG---------------------TGGTGGTGGTGCTAGTGTGGTTGAAATTAGTGTCTTAGTGCTTATTGACTGGCACTAAGGGCATGTGTAT Human: CCTGAAGGGTTGACCTGCAGAAG-TCAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCAAAATTCCTtgg---tggtagtggtggtggtggtggtggtggtgctagtgtggtTCAAATTAGTGTCTTAGTGCGTATGGACTGGCACTAAGGGCATGTGTAT Cluster: [ ] Orangutan: CCTGAAGGGTTGACCTGCAGAAG-TCAAGCCTGCCTTGAGAATATTAATTTAACCACTTATTTTCTAAATTCCTTGGTGG------------------TGGTGGTGGTGCTAGTGTGGTTGAAATTAGTGTCTTAGTGCTTATTGACTGGCACTAAGGGCATGTGTAT Chimp > Human ------------- chr10:16884289-16884292 Template switch process: F1: L TTGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA 1 F3: 4 AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCA R RF: TTGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGAGTACTAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCGAAATTCCTTGGTGGTGGTGGTGGTGCTAGTGTGGTTGAAATTAGTGTCTTAGTGCTTATTGACT RR: AACTTGCAGTGTCGAATAGTGGACTTCCCAACTGGACGTCTCATGATTCGGACGGAACTCTTATAATTAAATTGGCGAATAAAAGCTTTAAGGAACCACCACCACCACCACGATCACACCAACTTTAATCACAGAATCACGAATAACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -33.1) TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGAagtc-----AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCa TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA----GTACTAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCG Template switch alignment (log-probability: -21.8) TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA|AGTC|AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCa TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA|AGTC|AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCG Chimp > Gorilla --------------- chr10:16750938-16750941 Template switch process: F1: L TTGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA 1 F3: 4 AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCA R RF: TTGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGAGTACTAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCGAAATTCCTTGGTGGTGGTGGTGGTGCTAGTGTGGTTGAAATTAGTGTCTTAGTGCTTATTGACT RR: AACTTGCAGTGTCGAATAGTGGACTTCCCAACTGGACGTCTCATGATTCGGACGGAACTCTTATAATTAAATTGGCGAATAAAAGCTTTAAGGAACCACCACCACCACCACGATCACACCAACTTTAATCACAGAATCACGAATAACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -32.2) TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA-----agtcAAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCa TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGAGTACT----AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCG Template switch alignment (log-probability: -21.7) TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA|AGTC|AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCa TGAACGTCACAGCTTATCACCTGAAGGGTTGACCTGCAGA|AGTC|AAGCCTGCCTTGAGAATATTAATTTAACCGCTTATTTTCG ======== Event 41 ======== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCCACCTTCTTAAGCACTCAATACATGATAGTT------------------ATTCACTGGAAACAGTGAATAACTAGAATAACTATCATGTATTGAGTGCCTAAGAAGGTGGCTTt ↑ 3 1 2 4 Chimp: AGCCACCTTCTTAAGCACTCAATACATGATAGTT---------ATTCTAGTTATTCACTGTTTCCAGTGA---------ACAACTGTCACGTATTGAGTGCCTAAGAAGGTGGCTTt Gorilla: AGCCACCTTCTTAAGCACTCAATACATGATAGTTATTCTAGTT---------ATTCACTGTTTCCAGTGA---------ATAACTGTCACGTATTAAGTGCCTAAGAAGGTGGCTtt ↓ 3 1 2 4 Human: AGCCACCTTCTTAAGCACTCAATACATGATAGTT------------------ATTCACTGGAAACAGTGAATAACTAGAATAACTATCATGTATTGAGTGCCTAAGAAGGTGGCTTt Cluster: [ ] Orangutan: AGCCACCTTCTTACGCACTCAATACATGATAGTTATTCTCGTT---------ATTCACTGTTTCCAGTGA---------ATAACTGTCATGTATTGAGTGCCTAAGAAGGTGGCTTt Chimp > Human ------------- chr10:16286369-16286402 Template switch process: F1: L GGACAAAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC 1 F3: 4 GTATTGAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTGTTG R RF: GGACAAAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTCTAGTTATTCACTGTTTCCAGTGAACAACTGTCACGTATTGAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTATTG RR: CCTGTTTTCGGTGGAAGAATTCGTGAGTTATGTACTATCAATAAGATCAATAAGTGACAAAGGTCACTTGTTGACAGTGCATAACTCACGGATTCTTCCACCGAAAACAAACGGATAAC F2: 3 TACTATCAATAAGATCAATAAGTGACAAAGGTCA 2 Unidirectional alignment (log-probability: -71.9) AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC--------------------------ACTGgaaacagtgaataactagaataactaTCAtGTATTGAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTgTTG AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTCTAGTTATTCACTGTTTCCAGTGAACAACTG--------------------------TCACGTATTGAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTATTG Template switch alignment (log-probability: -25.5) AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC|ACTGGAAACAGTGAATAACTAGAATAACTATCAT|GTATTGAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTgTTG AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC|ACTGGAAACAGTGAATAACTAGAATAACTATCAT|GTATTGAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTATTG Gorilla > Human --------------- chr10:16286369-16286408 Template switch process: F1: L GGACAAAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC 1 F3: 4 AGTGCCTAAGAAGGTGGCTTTTGTTTGCCTGTTGGCTGTC R RF: GGACAAAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTCTAGTTATTCACTGTTTCCAGTGAATAACTGTCACGTATTAAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTATTGGCTGTC RR: CCTGTTTTCGGTGGAAGAATTCGTGAGTTATGTACTATCAATAAGATCAATAAGTGACAAAGGTCACTTATTGACAGTGCATAATTCACGGATTCTTCCACCGAAAACAAACGGATAACCGACAG F2: 3 GTTATGTACTATCAATAAGATCAATAAGTGACAAAGGTCA 2 Unidirectional alignment (log-probability: -71.3) AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTcactggaaacagtgaataaCTA-------------------GAATAACTaTCAtGTATTgAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTgTTGGCTGTC AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATT-------------------CTAGTTATTCACTGTTTCCAGTGAATAACTGTCACGTATTAAGTGCCTAAGAAGGTGGCTTTTGTTTGCCTATTGGCTGTC Template switch alignment (log-probability: -26.4) AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC|ACTGGAAACAGTGAATAACTAGAATAACTATCATGTATTG|AGTGCCTAAGAAGGTGGCTTTTGTTTGCCTgTTGGCTGTC AAAGCCACCTTCTTAAGCACTCAATACATGATAGTTATTC|ACTGGAAACAGTGAATAACTAGAATAACTATCATGTATTG|AGTGCCTAAGAAGGTGGCTTTTGTTTGCCTATTGGCTGTC ======== Event 42 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGATGCAACAGAAACCTCTGACCCCCCGCCCGGGGTCTCGCACCAAGGCCAGACAGCCCCGCTCCCGGGGTCACCCGAGGGTTACCTTTGGGTGCAGGCGCGGC--CTTTCTCCGAAGGGAGGGGCAGCTCCCCTGCCCCTGCAAAATGAAGGAGAAATGA ↓ 3 2 1 4 Chimp: TCTGACGCAACAGAAACCTCTGAC-CCCCGCCCGGGGTCTCGCAGCAAGGCCAGACAGCTCCGCTCCCGGGGCCACCCGAGGGTTACCTTTGGGTGCAGGCGCGGC--CTTTCTCCGAAGGGAGGGGCAGCTCCC---TCAGTGCAAAATGAAGGAGAAATGA Gorilla: TCTGATGCAACAGAAACCTCTGACCCCCCGCCCGGGGTCTCGAACCAAGGCCAGACAGCCCCGCTCCCGGGGTCACCCGAGGGTTACCTTTGGGTGCAGGCGCGGC--CTTTCTCCGAAGGGAGGGGCAGCTCCC---CCAGTGCAAAATGAAGGAGAAATGA Human: TCTGATGCAACAGAAACCTCTGACCCCCCGCCCGGGGTCTCGCACCAAGGCCAGACAGCCCCGCTCCCGGGGTCACCCGAGGGTTACCTTTGGGTGCAGGCGCGGC--CTTTCTCCGAAGGGAGGGGCAGCTCCCCTGCCCCTGCAAAATGAAGGAGAAATGA Cluster: [ ] Orangutan: TCTGATGCAACAGAAACCTCTGACTCCCCGCCCGGGGTCTCGCACCAAGGCCAGACAGCCCCGCTCCCGGGGTCACCCGAGGGTTACCTTTGGGTGCAGGCGCGGCCTCTTTCTCCGAAGGGAGGGGCAGCTCCC---CCAGTGCAAAATGAAGGAGAAATGA Human > Chimp ------------- chr10:17001205-17001208 Template switch process: F1: L GGTGCAGGCGCGGCCTTTCTCCGAAGGGAGGGGCAGCTCCC 1 F3: 4 TGCAAAATGAAGGAGAAATGATAAGCAGCGGTGAAACCGT R RF: CTGACCCCCCGCCCGGGGTCTCGCACCAAGGCCAGACAGCCCCGCTCCCGGGGTCACCCGAGGGTTACCTTTGGGTGCAGGCGCGGCCTTTCTCCGAAGGGAGGGGCAGCTCCCCTGCCCCTGCAAAATGAAGGAGAAATGATAAGCAGCGGTGAAACCGT RR: GACTGGGGGGCGGGCCCCAGAGCGTGGTTCCGGTCTGTCGGGGCGAGGGCCCCAGTGGGCTCCCAATGGAAACCCACGTCCGCGCCGGAAAGAGGCTTCCCTCCCCGTCGAGGGGACGGGGACGTTTTACTTCCTCTTTACTATTCGTCGCCACTTTGGCA F2: 3 GACT 2 Unidirectional alignment (log-probability: -27.2) GTGCAGGCGCGGCCTTTCTCCGAAGGGAGGGGCAGCTCCCtcag-------TGCAAAATGAAGGAGAAATGATAAGCAGCGGTGAAACCGT GTGCAGGCGCGGCCTTTCTCCGAAGGGAGGGGCAGCTCCC----CTGCCCCTGCAAAATGAAGGAGAAATGATAAGCAGCGGTGAAACCGT Template switch alignment (log-probability: -15.8) GTGCAGGCGCGGCCTTTCTCCGAAGGGAGGGGCAGCTCCC|TCAG|TGCAAAATGAAGGAGAAATGATAAGCAGCGGTGAAACCGT GTGCAGGCGCGGCCTTTCTCCGAAGGGAGGGGCAGCTCCC|TCAG|TGCAAAATGAAGGAGAAATGATAAGCAGCGGTGAAACCGT ======== Event 43 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAACAGAATACTGAAGAAAAGCTTCACAAAGG-------TTGGAGGTTGAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTACAATAGCTATCATTT ↓ 3 2 1 4 Chimp: AAACAGAATACTGAAGAAAAGCTCCACAAAGG----------AA----GCTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTACAATAGCTATCATTT Gorilla: AAACAGAATACTGAAGAAAAGCTCCACAAAGG-----TG---GAGGTTGAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTACAATAGCTATCATTT Human: AAACAGAATACTGAAGAAAAGCTTCACAAAGG-------TTGGAGGTTGAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTACAATAGCTATCATTT Cluster: [ ] Orangutan: AAACAGAATACTGAAAAAAAGCTCCACAAAGGGGTGG-----GAGCCTGAAATTTCTACCAAATAACTATCATTTTTCTGTGGTTTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGAAAGCTCCACAAAGGTGAGCTGAAATCTA-CATAGCTATCATTT Human > Chimp ------------- chr10:28946329-28946333 Template switch process: F1: L GGTGCCCAGAACCTGCAGAAACAGAATACTGAAGAAAAGCTCCACAAAGG 1 F3: 4 ATTCTACAATAGCTATCATTTCTGTGTTTCTGTGTTCATG R RF: GGTGCCCAGAACCTGCAGAAACAGAATACTGAAGAAAAGCTTCACAAAGGTTGGAGGTTGAAATTCTACAATAGCTATCATTTCTGTGTTTCTGTGTTCATG RR: CCACGGGTCTTGGACGTCTTTGTCTTATGACTTCTTTTCGAAGTGTTTCCAACCTCCAACTTTAAGATGTTATCGATAGTAAAGACACAAAGACACAAGTAC F2: 3 TCGAA 2 Unidirectional alignment (log-probability: -32.1) ACCTGCAGAAACAGAATACTGAAGAAAAGCTcCACAAAG----------GAAgctATTCTACAATAGCTATCATTTCTGTGTTTCTGTGTTCATG ACCTGCAGAAACAGAATACTGAAGAAAAGCTTCACAAAGGTTGGAGGTTGAA---ATTCTACAATAGCTATCATTTCTGTGTTTCTGTGTTCATG Template switch alignment (log-probability: -22.1) ACCTGCAGAAACAGAATACTGAAGAAAAGCTcCACAAAGG|AAGCT|ATTCTACAATAGCTATCATTTCTGTGTTTCTGTGTTCATG ACCTGCAGAAACAGAATACTGAAGAAAAGCTTCACAAAGG|AAGCT|ATTCTACAATAGCTATCATTTCTGTGTTTCTGTGTTCATG ======== Event 44 ======== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGAGTGTTCAAATGTGCAAG----------GCATAAGGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAATCAATGAGAGGATAAGTATTCAAAGCCCAGACACAAGAGATTATTATTGGAAAGGAAGAGGCAAGCAGCAATGCCCATATAATAAAACTGAACC ↑ 1 4 3 2 Chimp: AAGAGTGTTCAAATGTGCAAG-----TATTTACCCAAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAATCAATGAGAGGATAAGTATTGAAAGCCCAGACACAAGAGATTATTATTGGGAAGGAAGAGGCAAGCAGCAATGCCCAAATAATAAAACTGAACC Gorilla: AAGAGTGTTCAAATGTGCAAGTATTT-----ACCCAAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAATCAATGAGAGAATAAGTATTCAAAGCCCAGACACAAGATATTATTATTGGAAAGGAAGAGGCAAGCAGCAATGCCCAAATAATAAAACTGAACC ↓ 1 4 3 2 Human: AAGAGTGTTCAAATGTGCAAG----------GCATAAGGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAATCAATGAGAGGATAAGTATTCAAAGCCCAGACACAAGAGATTATTATTGGAAAGGAAGAGGCAAGCAGCAATGCCCATATAATAAAACTGAACC Cluster: [ ] Orangutan: Chimp > Human ------------- chr10:8877053-8877056 Template switch process: F1: L ATGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG 1 F3: 4 AAGGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAAT R RF: ATGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAGTATTTACCCAAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAATCAATGAGAGGATAAGTATTGAAAGCCCAGACACAAGAGATTATTATTGGGAAGGAAGAGGCAAGCAGCAATGC RR: TACAACACTACACTCCTCCATTCTCACAAGTTTACACGTTCATAAATGGGTTTCGTATTCACCTCGTGTTTATAAGGTTTAGCTTATGGTTTAGTTACTCTCCTATTCATAACTTTCGGGTCTGTGTTCTCTAATAATAACCCTTCCTTCTCCGTTCGTCGTTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -31.8) TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCaaggcatAAG------------GCATAAGTGGAGCACAAATATTCCAAATCGAATACCA TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGC-------AAGTATTTACCCAAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA Template switch alignment (log-probability: -21.8) TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG|GCAT|AAgGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG|GCAT|AAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA Gorilla > Human --------------- chr10:8877053-8877056 Template switch process: F1: L ATGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG 1 F3: 4 AAGGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAAT R RF: ATGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAGTATTTACCCAAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCAAATCAATGAGAGAATAAGTATTCAAAGCCCAGACACAAGATATTATTATTGGAAAGGAAGAGGCAAGCAGCAATGC RR: TACAACACTACACTCCTCCATTCTCACAAGTTTACACGTTCATAAATGGGTTTCGTATTCACCTCGTGTTTATAAGGTTTAGCTTATGGTTTAGTTACTCTCTTATTCATAAGTTTCGGGTCTGTGTTCTATAATAATAACCTTTCCTTCTCCGTTCGTCGTTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -30.9) TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAGgcaT--------AAgGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG---TATTTACCCAAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA Template switch alignment (log-probability: -21.8) TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG|GCAT|AAgGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA TGTTGTGATGTGAGGAGGTAAGAGTGTTCAAATGTGCAAG|GCAT|AAAGCATAAGTGGAGCACAAATATTCCAAATCGAATACCA ======== Event 45 ======== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGGTACTGCCTCTGACTCCAGTTCCCTGGAGGGGAACAAGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCTGGGGCCTGTGGGACCCCTGGCAGTGTGCCACCCACTGGGCAGCAGTGGTACTGCCTCTGCCTCTGCACTGCCGGAAGTttccctcccgccgc ↓ 1 4 3 2 Chimp: TCATGGTACTGCCTCTGACTCG---GCACT--------GCAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCTGGGGCCTGTGGGACCCCTGGCAGTGTGCCACCCACTGGGCAGCAGTGGTACTGCCTCTGCCTCTGCACTGCCGGAAGTTTCCctccagccgc ↑ 1 4 3 2 Gorilla: TCATGGTACTGCCTCTGACTCCAGTTCCCTGGAGGGGAACAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCTGGGGCCTGTGGGACCCCTGGCAGTGTGCCACCCACTGGGCAGCAGTGGTACTGCCTCTGCCTCTGCACTGCAGGAAGTTTCCctcccgccgc Human: TCATGGTACTGCCTCTGACTCCAGTTCCCTGGAGGGGAACAAGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCTGGGGCCTGTGGGACCCCTGGCAGTGTGCCACCCACTGGGCAGCAGTGGTACTGCCTCTGCCTCTGCACTGCCGGAAGTttccctcccgccgc Cluster: [ ] Orangutan: TCATGGTACTGCCTCTGACTCG---GCACT--------GCCGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGCGCGTGGGGCCTGTGGGACCCCTGGCAGTGTGCCACCCACTGGGCAGCAGTGGTATTGCCTCTGCCTCTGCACTGCCGGAAGTttccctccagccgc Human > Chimp ------------- chr10:8484008-8484017 Template switch process: F1: L AGTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC 1 F3: 4 GAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCT R RF: AGTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTCCAGTTCCCTGGAGGGGAACAAGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCTGGGGCCTGTGGGACCCCTGGCAGTGTGCCACCCACTGGGCAGCAGTGGTACTGCCTCTGCCTCTGCACTGCC RR: TCACGCGGGGGTCACCCGTCAGTACCATGACGGAGACTGAGGTCAAGGGACCTCCCCTTGTTCTTCAAAGGGAGGTCAAGGCAGAAGAGTCGACCACACGGACCCCGGACACCCTGGGGACCGTCACACGGTGGGTGACCCGTCGTCACCATGACGGAGACGGAGACGTGACGG F2: 3 GACGTCACGG 2 Unidirectional alignment (log-probability: -32.2) GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTCggcactgCAG------------------GAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCT GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC-------CAGTTCCCTGGAGGGGAACAAGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCT Template switch alignment (log-probability: -22.5) GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC|GGCAcTGCAG|GAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCT GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC|GGCAGTGCAG|GAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTGCCT Gorilla > Chimp --------------- chr10:8484008-8484014 Template switch process: F1: L AGTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC 1 F3: 4 CAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTG R RF: AGTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTCCAGTTCCCTGGAGGGGAACAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTG RR: TCACGCGGGGGTCACCCGTCAGTACCATGACGGAGACTGAGGTCAAGGGACCTCCCCTTGTCCTTCAAAGGGAGGTCAAGGCAGAAGAGTCGACCACAC F2: 3 GTCACGG 2 Unidirectional alignment (log-probability: -31.2) GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC--------------GGcActgCAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTG GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTCCAGTTCCCTGGAGGGGAA---CAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTG Template switch alignment (log-probability: -22.1) GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC|GGcACTG|CAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTG GTGCGCCCCCAGTGGGCAGTCATGGTACTGCCTCTGACTC|GGAACTG|CAGGAAGTTTCCCTCCAGTTCCGTCTTCTCAGCTGGTGTG ======== Event 46 ======== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCTGTTTCTGAGAGTGGTCATCGCAACAGCCACCACTGGAGAACT----GACACTCAGACCTCCTGGCCACCAAT Chimp: GGCTGTTTCTAAGAGTGGTCATCGCAACAGCCACCACTGGAGAACT----GACCCTCGGACCTCCTGGCCACCAAT Gorilla: GGCTATTTCTGAGAGTGGTCATCGCAACAGCCACCACTGTTGCGAT--------GTCAGACCTCCTGGCCACCAAT ↑ 3 2 1 4 Human: GGCTGTTTCTGAGAGTGGTCATCGCAACAGCCACCACTGGAGAACT----GACACTCAGACCTCCTGGCCACCAAT Cluster: [ ] Orangutan: GGCTGTTTCTGAGAGTGGTCATCGCAACAGCCACCACTGGAGAACTGACC----CTCCGACCTCCTGGCCACCAAT Human > Gorilla --------------- chr10:8530314-8530321 Template switch process: F1: L CAGGCTATTTCTGAGAGTGGTCATCGCAACAGCCACCACTG 1 F3: 4 TCAGACCTCCTGGCCACCAATCAGTGACCCACAGGTGGAA R RF: CAGGCTGTTTCTGAGAGTGGTCATCGCAACAGCCACCACTGGAGAACTGACACTCAGACCTCCTGGCCACCAATCAGTGACCCACAGGTGGAA RR: GTCCGACAAAGACTCTCACCAGTAGCGTTGTCGGTGGTGACCTCTTGACTGTGAGTCTGGAGGACCGGTGGTTAGTCACTGGGTGTCCACCTT F2: 3 GTAGCGTT 2 Unidirectional alignment (log-probability: -36.8) AGGCTaTTTCTGAGAGTGGTCATCGCAACAGCCACCACTGttgcgatG-----------TCAGACCTCCTGGCCACCAATCAGTGACCCACAGGTGGAA AGGCTGTTTCTGAGAGTGGTCATCGCAACAGCCACCACTG-------GAGAACTGACACTCAGACCTCCTGGCCACCAATCAGTGACCCACAGGTGGAA Template switch alignment (log-probability: -22.3) AGGCTaTTTCTGAGAGTGGTCATCGCAACAGCCACCACTG|TTGCGATG|TCAGACCTCCTGGCCACCAATCAGTGACCCACAGGTGGAA AGGCTGTTTCTGAGAGTGGTCATCGCAACAGCCACCACTG|TTGCGATG|TCAGACCTCCTGGCCACCAATCAGTGACCCACAGGTGGAA ======== Event 47 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGTTAAGGTTAGAGAACATTTTGGGCAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTGC ↓ 1 4 3 2 Chimp: TCATGTTAAGGTTAGAGAACAC-CTAGCCAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTGC Gorilla: TCATGTTAAGGTTAGAGAACATTTTGGGCAGGTGGCCGGCCTGGCTAGGATGGTTGCCACAGCTCCTGC Human: TCATGTTAAGGTTAGAGAACATTTTGGGCAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTGC Cluster: [ ] Orangutan: TCATGTTAAGGTTAGAGAACATTTTGGGCAGGTGGCCCGCCTGGCTAGGACGGTGGCCACAGCTCCTGC Human > Chimp ------------- chr10:9537829-9537834 Template switch process: F1: L AGAGCCCAAGTGGCCCAGGTTCATGTTAAGGTTAGAGAACA 1 F3: 4 CAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTG R RF: AGAGCCCAAGTGGCCCAGGTTCATGTTAAGGTTAGAGAACATTTTGGGCAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTG RR: TCTCGGGTTCACCGGGTCCAAGTACAATTCCAATCTCTTGTAAAACCCGTCCACCGGCCGGACCGATCCTGCCACCGGTGTCGAGGAC F2: 3 CGATCC 2 Unidirectional alignment (log-probability: -30.1) GAGCCCAAGTGGCCCAGGTTCATGTTAAGGTTAGAGAACAcctagc-------CAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTG GAGCCCAAGTGGCCCAGGTTCATGTTAAGGTTAGAGAACA------TTTTGGGCAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTG Template switch alignment (log-probability: -16) GAGCCCAAGTGGCCCAGGTTCATGTTAAGGTTAGAGAACA|CCTAGC|CAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTG GAGCCCAAGTGGCCCAGGTTCATGTTAAGGTTAGAGAACA|CCTAGC|CAGGTGGCCGGCCTGGCTAGGACGGTGGCCACAGCTCCTG ======== Event 48 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GCAGCCAGCTCCACAGCCATGCAC-CCTGCAGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATCCTAGATCGGCTGGCCACCCCACTGGGGGGAAACCCCTTCAGCACCCAGGCCACAGCTAGAAGGGACCTTGCAGGATGTCGGGAATCACGGTCCAGGA Chimp: GCAGCCAGCTCCACAGCCATGCAC-CCTGCAGCCCCTCGTCTTCCAGCTTTGTGCAAGGTGGCTGGAATCCTAGATCAGCTGGCCACCCCGCTGGGGGGAAACCCCTTCAGCACCCACGCCACAGCTAGAAGGGACCTTGCAGGATGTCGGGAATCACGGTCCAGGA Gorilla: GCAGCCAGCTCCACAGCCATGGAGCTGTGGAGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATCCTAGATCGGCTGGCCACCCCACTGGGGGGAAACCCCTTCAGCACCCAGGCCACAGCTAGAGGGGACCTTGCAGGATGTCGGGAATCACGGTCCAGGA ↓ 1 4 3 2 Human: GCAGCCAGCTCCACAGCCATGCAC-CCTGCAGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATCCTAGATCGGCTGGCCACCCCACTGGGGGGAAACCCCTTCAGCACCCAGGCCACAGCTAGAAGGGACCTTGCAGGATGTCGGGAATCACGGTCCAGGA Cluster: [ ] Orangutan: CCAGCCAGCTCCACAGCCACGCAC-CCTGCAGCCCCTCGTCTTCCAGCTTTGCGCAAGACGGCTGGAATCCTAGATCGGCTGGCCGCCCCGCTGG-GGGAAACCCCTTCAACACCCAGGCCCCAGCTAGAAGGGACCTTGCGGGACGTTGGGAATCACGGTCCAGGA Gorilla > Human --------------- chr10:9274045-9274052 Template switch process: F1: L GGGGCACTCTCCCTCCCGACGCAGCCAGCTCCACAGCCATG 1 F3: 4 AGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATC R RF: GGGGCACTCTCCCTCCAGACGCAGCCAGCTCCACAGCCATGGAGCTGTGGAGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATCCTAGATCGGCTGGCCACCCCACTGGGGGGAAACCCCTTCAGCACCCAGGCCACAGCTAGAGGGGACCTTGCAGGATG RR: CCCCGTGAGAGGGAGGTCTGCGTCGGTCGAGGTGTCGGTACCTCGACACCTCGGGGAGCAGAAGGTCGAAACACGTTCCGCCGACCTTAGGATCTAGCCGACCGGTGGGGTGACCCCCCTTTGGGGAAGTCGTGGGTCCGGTGTCGATCTCCCCTGGAACGTCCTAC F2: 3 CGTCCCAC 2 Unidirectional alignment (log-probability: -37.7) GGGCACTCTCCCTCCcGACGCAGCCAGCTCCACAGCCATGcAccctGC-----AGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATC GGGCACTCTCCCTCCAGACGCAGCCAGCTCCACAGCCATGGA----GCTGTGGAGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATC Template switch alignment (log-probability: -27.8) GGGCACTCTCCCTCCcGACGCAGCCAGCTCCACAGCCATG|CAcCCTGC|AGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATC GGGCACTCTCCCTCCAGACGCAGCCAGCTCCACAGCCATG|CATCCTGC|AGCCCCTCGTCTTCCAGCTTTGTGCAAGGCGGCTGGAATC ======== Event 49 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTGACAGCTGCCTCAGAAA----CAATtgtgtgtgtgtg------------tgtgtgtacg----------------tgtaagtgcgtgcacgtgtgcgtgcTCCGTACTAGAAGACCTTGGCTGAGGGCACGTCCCACAGCAGGACCAGTGGG Chimp: TCCTGACAGCTGCCTCAGAAA--CATAATtgtgtgtgtgtg------------tgtgtgtacgtgtaagtgcgtgcacgtgtaagtgcgtgcacgtgtgcgtgcTCCGTACTAGAAGACCTTGGCTGAGGGCACGTCCCACAGCAGGACCAGTGGG ↑ 1 4 3 2 Gorilla: TCCTGACAGCTGCCTCAGAAACA--TAATtgtgtgtgtgtg----tgtgtgtgtgtgtgtACG----------------TATAAGTGCGTGCACGTGTGCGTGCTCTGTACTAGAAGACCCTGGCTGAGGGCACGTCCCACAGCAGGACCAGTGGG Human: TCCTGACAGCTGCCTCAGAAA----CAATtgtgtgtgtgtg------------tgtgtgtacg----------------tgtaagtgcgtgcacgtgtgcgtgcTCCGTACTAGAAGACCTTGGCTGAGGGCACGTCCCACAGCAGGACCAGTGGG Cluster: [ ] Orangutan: TCCTGACAGCTGCCTCAGAAACA--CAATcgtgtgtgtgtatgtg--------tgtgtgtacg----------------tgtaagtgggtgcacgtgtgcgtgCTCCGTACTAGAAGACCTTGGCTGAGGGCACGTCCCGCAGCAGGACCAGTGGG Gorilla > Chimp --------------- chr10:9542264-9542268 Template switch process: F1: L CGCCTCTCGGCCTCTCAGACTCCTGACAGCTGCCTCAGAAACATAATTGTGTGTGTGTGTGTGTGT 1 F3: 4 TAAG R RF: CGCCTCTCGGCCTCTCAGACTCCTGACAGCTGCCTCAGAAACATAATTGTGTGTGTGTGTGTGTGTGTGTGTGTACGTATAAGTGCGTGCACGTGTGCGTGCTCTGTACTAGAAGACCCTGGCTGAGGGCACGT RR: GCGGAGAGCCGGAGAGTCTGAGGACTGTCGACGGAGTCTTTGTATTAACACACACACACACACACACACACACATGCATATTCACGCACGTGCACACGCACGAGACATGATCTTCTGGGACCGACTCCCGTGCA F2: 3 GTGCA 2 Unidirectional alignment (log-probability: -26.5) CAGCTGCCTCAGAAACATAATTGTGTGTGTGTG--------TGTGTGTACGtgtaag CAGCTGCCTCAGAAACATAATTGTGTGTGTGTGTGTGTGTGTGTGTGTACG------ Template switch alignment (log-probability: -16.1) CAGCTGCCTCAGAAACATAATTGTGTGTGTGTGTGTGTGT|ACGTG|TAAG CAGCTGCCTCAGAAACATAATTGTGTGTGTGTGTGTGTGT|ACGTG|TAAG ======== Event 50 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATCTACCAGCACTCTGGAAG-----TGAGTGTGAGCCTGGAAGGTTGCAGTGGCAGGTGG Chimp: CATCTACCAGCACTCTGGAAG-----TGAGTGTGAGCCTGGAAGGTTGCAGTGGCAGGTGG ↓ 1 3 4 2 Gorilla: CATCTACCAGCACTCTGGAAGGCTCACACTCGTGAGCCTGCAAGGTTGCAGTGGCAGGTGG Human: CATCTACCAGCACTCTGGAAG-----TGAGTGTGAGCCTGGAAGGTTGCAGTGGCAGGTGG Cluster: [ ] Orangutan: CACCTACCAGCACTCTGGAAG-----TGAGTGTGAGCCTCAAAGGTTGCAGTGGCAGGTGG Chimp > Gorilla --------------- chr10:9093170-9093179 Template switch process: F1: L AGCTCTTCGGGGTGAGCCCCCATCTACCAGCACTCTGGAAG 1 F3: 4 GTGAGCCTGCAAGGTTGCAGTGGCAGGTGGAGGGAAGGCCCCAGAGTGGA R RF: AGCTCTTCGGGGTGAGCCCCCATCTACCAGCACTCTGGAAGTGAGTGTGAGCCTGGAAGGTTGCAGTGGCAGGTGGAGGGAAGGCCCCAGAATAGA RR: TCGAGAAGCCCCACTCGGGGGTAGATGGTCGTGAGACCTTCACTCACACTCGGACCTTCCAACGTCACCGTCCACCTCCCTTCCGGGGTCTTATCT F2: 3 CTCACACTCG 2 Unidirectional alignment (log-probability: -52) GCTCTTCGGGGTGAGCCCCCATCTACCAGCACTCTGGAAG-----gctcacactcGTGAGCCTGcAAGGTTGCAGTGGCAGGTGGAGGGAAGGCC GCTCTTCGGGGTGAGCCCCCATCTACCAGCACTCTGGAAGTGAGT----------GTGAGCCTGGAAGGTTGCAGTGGCAGGTGGAGGGAAGGCC Template switch alignment (log-probability: -33.8) GCTCTTCGGGGTGAGCCCCCATCTACCAGCACTCTGGAAG|GCTCACACTC|GTGAGCCTGcAAGGTTGCAGTGGCAGGTGGAGGGAAGGCC GCTCTTCGGGGTGAGCCCCCATCTACCAGCACTCTGGAAG|GCTCACACTC|GTGAGCCTGGAAGGTTGCAGTGGCAGGTGGAGGGAAGGCC ======== Event 51 ======== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: GCTCTTTATGGCTAAGTGGCATAAAGAGTGGCttt-----ttttttttCCTT ↓ 1 3 42 Chimp: GCTCTTTATGGCTAAGTGGCAGCCA---CTGCttt-----ttttttttCCTT Gorilla: GCTCTTTATGGCTAAGTGGCAGCCA---CTGCttt----tttttttttCCTT Human: GCTCTTTATGGCTAAGTGGCATAAAGAGTGGCttt-----ttttttttCCTT Cluster: [ ] Orangutan: GCTCTTTATGGCTAAGTGGCAGCCA---CTGCttttttt-ttttttttCCTT Human > Chimp ------------- chr10:114221388-114221393 Template switch process: F1: L GCTATTTCTAACACGACTTTGCTCTTTATGGCTAAGTGGCA 1 F3: 4 GCTTTTTTTTTTTCCTTCTAAATTATGTGTTCTTGTTTCA R RF: GCTATTTCTAACACGACTTTGCTCTTTATGGCTAAGTGGCATAAAGAGTGGCTTTTTTTTTTTCCTTCTAAATTATGTGTTCTTGTTTCA RR: CGATAAAGATTGTGCTGAAACGAGAAATACCGATTCACCGTATTTCTCACCGAAAAAAAAAAAGGAAGATTTAATACACAAGAACAAAGT F2: 3 TCACCG 2 Unidirectional alignment (log-probability: -28.7) CTATTTCTAACACGACTTTGCTCTTTATGGCTAAGTGGCAgccacT--------GCTTTTTTTTTTTCCTTCTAAATTATGTGTTCTTGTTTCA CTATTTCTAACACGACTTTGCTCTTTATGGCTAAGTGGCA-----TAAAGAGTGGCTTTTTTTTTTTCCTTCTAAATTATGTGTTCTTGTTTCA Template switch alignment (log-probability: -16) CTATTTCTAACACGACTTTGCTCTTTATGGCTAAGTGGCA|GCCACT|GCTTTTTTTTTTTCCTTCTAAATTATGTGTTCTTGTTTCA CTATTTCTAACACGACTTTGCTCTTTATGGCTAAGTGGCA|GCCACT|GCTTTTTTTTTTTCCTTCTAAATTATGTGTTCTTGTTTCA ======== Event 52 ======== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: TAGCATTGATATAAATTGTTAAAAATAATGATCGTAGATAGATA-ATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATCAGAGTTTGGGCTCAGCC ↓ 13 24 ↑ 1 3 24 Chimp: TAGCATTGATATAAATTGTTAC-ATTATCTATCTACGATCATTATTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATCAGAGTTTGGGCTCAGCC Gorilla: ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: TAGCATTGATATAAATTGTTAAAAATAATGATCGTAGATAGATA-ATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATCAGAGTTTGGGCTCAGCC Cluster: [ ] Orangutan: ------------------------------------------------AAtttttttttAAAAGGCCTAATGNTTTACAACAAATTTGGGAGATACTTATATGCACTGCTAACTAGTGTTCTTTTGTGGTGTTTTAGAAATTCTGGCTTACTTGTATTTTTTGCTGGCCTTCTAATGATCTTACTCATCAATCAGAAAATATTTGTAGTGCCACCTCCCTGCTTCCTCTCCTGTGATCTTGTCTATTTCTTGGTTCCCattttagagttgacttagaagcctgcacaaaactggttggaatttccactgggattaaagtgataggtcatttttgggagacctttacaatactgaactttccaatccgtgaactttgcccatttattgtgtttgtttttggtAGATtacaaaattatatgatcactccaaaaattaccttgccctttatagtaaaaccttccattgtaaacttcgggcaatcactgatctgtgttcctctagcgttgcttttttttttcccagaatttttatacaaatggaatcgttcaggatgtagccttttgagtctggctactttcgtgtactgtatcaacagttactcctttttattgccaaatagtaatccattgtatagatactacatggtttgcttattggtttgtcattgggagaacatggactattttcactttttggtaaattataagtggattggaattcacaaagtgctttttgtctgggcataggttttcatttcacttgtgcaaatgcctaagggtagcattgccgagtcacatggtccgtgtacgtttgactttatcagaacctgccaaattgtcttccaaagtgctgcgccacttctgtttctttaataaatatagggatattcaagctgtttcttcttgagtttggtagtttgtctttcaaggatttgatctatttcacctaatttgtagaatttagaagcatatggttgtgtttatgttttgtttttgtagtatccattaggatttgtaataatattcctttcatctctggtattggtaatttgtgttttctcttcttgtcagtctgatggtcttcctcatttgattgatttccgcatcccaccaccccctgcaaataaccaactttggatttcattgaatttttttcccttactgttcttgtttaaatattactgatttagttttatttagtctgtcttttcttatgcctgatttgagtttatttggttctttttttacttaaagtagatgcctacattattgatttgatgcttcatttcatgagtatactttagtgctataaattgccctctcagcacatattttggtaagttgatgcatattcattaagttcaaactgttttccaatttttcttaagatgctctctttgacctgtgggccatttagaagtacgccgtttaacttctcatatttggggatgttctagaaatgttctagattcctagtttaattctgtcatcagagaacataattcactgaattttaattg--------------------- Chimp > Human ------------- chr10:125920600-125920625 Template switch process: F1: L GCTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA 1 F3: 4 TATCAGAGTTTGGGCTCAGCCGCTGTAGCTGCTGTTGACC R RF: GCTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTACATTATCTATCTACGATCATTATTTTTATCAGAGTTTGGGCTCAGCCGCGTAGCTGCTGTTGACC RR: CGAAGAGACACTGAATACCCATCGTAACTATATTTAACAATGTAATAGATAGATGCTAGTAATAAAAATAGTCTCAAACCCGAGTCGGCGCATCGACGACAACTGG F2: 3 GTAATAGATAGATGCTAGTAATAAAA 2 Unidirectional alignment (log-probability: -71.5) CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA--------------------------aaaataatgatcgtagatagataatgTATCAGAGTTTGGGCTCAGCCGCtGTAGCTGCTGTTGACC CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTACATTATCTATCTACGATCATTATTTT--------------------------TATCAGAGTTTGGGCTCAGCCGC-GTAGCTGCTGTTGACC Template switch alignment (log-probability: -30.1) CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA|AAAATAATGATCGTAGATAGATAATG|TATCAGAGTTTGGGCTCAGCCGCtGTAGCTGCTGTTGACC CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA|AAAATAATGATCGTAGATAGATAATG|TATCAGAGTTTGGGCTCAGCCGC-GTAGCTGCTGTTGACC Human > Chimp ------------- chr10:127842077-127842102 Template switch process: F1: L GCTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA 1 F3: 4 TATCAGAGTTTGGGCTCAGCCGC-GTAGCTGCTGTTGACC R RF: GCTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTAAAAATAATGATCGTAGATAGATAATGTATCAGAGTTTGGGCTCAGCCGCTGTAGCTGCTGTTGACC RR: CGAAGAGACACTGAATACCCATCGTAACTATATTTAACAATTTTTATTACTAGCATCTATCTATTACATAGTCTCAAACCCGAGTCGGCGACATCGACGACAACTGG F2: 3 TTTTATTACTAGCATCTATCTATTAC 2 Unidirectional alignment (log-probability: -70.1) CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA--------------------------cattatctatctacgatcattattttTATCAGAGTTTGGGCTCAGCCGC-GTAGCTGCTGTTGACC CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTAAAAATAATGATCGTAGATAGATAATG--------------------------TATCAGAGTTTGGGCTCAGCCGCTGTAGCTGCTGTTGACC Template switch alignment (log-probability: -28.7) CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA|CATTATCTATCTACGATCATTATTTT|TATCAGAGTTTGGGCTCAGCCGC-GTAGCTGCTGTTGACC CTTCTCTGTGACTTATGGGTAGCATTGATATAAATTGTTA|CATTATCTATCTACGATCATTATTTT|TATCAGAGTTTGGGCTCAGCCGCTGTAGCTGCTGTTGACC ======== Event 53 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAAGAACCACCAATTCACCCAAAGGTGAATTCAACACATTCAGTGTTGAATTCATCAGCACAAGCTCATGGT Chimp: TAAAGAACCACCAATTCAC--------CAATTCAACACTGAATGTGTTGAATTCATCAGCACAAGCTCATGGT ↑ 1 3 4 2 Gorilla: TAAAGAACCACCAATTCACCCAAAGGTGAATTCAACACATTCAGTGTTGAATTCATCAGCACAAGCTCATGGT Human: TAAAGAACCACCAATTCACCCAAAGGTGAATTCAACACATTCAGTGTTGAATTCATCAGCACAAGCTCATGGT Cluster: [ ] Orangutan: TAAAGAACCACCAATTCACCCAAAGGTGAATTCAACACATTCAGTGTTGAATTCATCAGCACAAGCTCATAGT Gorilla > Chimp --------------- chr10:127795125-127795139 Template switch process: F1: L ATCTAAAGAACCACCAATTCACC 1 F3: 4 GTGTTGAATTCATCAGCACAAGCTCATGGTTTTTAAGTTT R RF: ATCTAAAGAACCACCAATTCACCCAAAGGTGAATTCAACACATTCAGTGTTGAATTCATCAGCACAAGCTCATGGTTTTTAAGTTT RR: TAGATTTCTTGGTGGTTAAGTGGGTTTCCACTTAAGTTGTGTAAGTCACAACTTAAGTAGTCGTGTTCGAGTACCAAAAATTCAAA F2: 3 TAAGTCACAACTTAA 2 Unidirectional alignment (log-probability: -35.2) ATCTAAAGAACCACCAATTCACC--------AATTCAACACtgaAT---GTGTTGAATTCATCAGCACAAGCTCATGGTTTTTAAGTTT ATCTAAAGAACCACCAATTCACCCAAAGGTGAATTCAACAC---ATTCAGTGTTGAATTCATCAGCACAAGCTCATGGTTTTTAAGTTT Template switch alignment (log-probability: -17.2) ATCTAAAGAACCACCAATTCACC|AATTCAACACTGAAT|GTGTTGAATTCATCAGCACAAGCTCATGGTTTTTAAGTTT ATCTAAAGAACCACCAATTCACC|AATTCAACACTGAAT|GTGTTGAATTCATCAGCACAAGCTCATGGTTTTTAAGTTT ======== Event 54 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gcaaccatgcctggccCTTTGGCTCAGGTTTTGAGAAGACTTTTAGT-------------------AATACGAGAGAGAAcacttactgtctct Chimp: gcaaccatgcctggccCTTTGGCTCAGGTTTTGAGAAGACTTTTAGT-------------------AATACAAGGCAGAACACTTACTGTCtct ↓ 3 2 4 1 Gorilla: gcaaccatgcctggccCTTTGGCTCAGGTTTTGAGAAGACTTTTAGTAATACAAGCTGAGGCAAGTAATACAAGGCAGAACACTTACTGTCtct Human: gcaaccatgcctggccCTTTGGCTCAGGTTTTGAGAAGACTTTTAGT-------------------AATACGAGAGAGAAcacttactgtctct Cluster: [ ] Orangutan: gccaccatgcctggccCTTTGGCTCAGGTTTTGAGAAGACTTGGAGT-------------------AATACAAGGCAGAACACTTGCTGTCtct Chimp > Gorilla --------------- chr10:125374535-125374542 Template switch process: F1: L ATGCCTGGCCCTTTGGCTCAGGTTTTGAGAAGACTTTTAGTAATACAAG 1 F3: 4 AGTAATACAAGGCAGAACACTTACTGTCTCTCATAAGCTTCAC R RF: ATGCCTGGCCCTTTGGCTCAGGTTTTGAGAAGACTTTTAGTAATACAAGGCAGAACACTTACTGTCTCTCATAAGCTTCAC RR: TACGGACCGGGAAACCGAGTCCAAAACTCTTCTGAAAATCATTATGTTCCGTCTTGTGAATGACAGAGAGTATTCGAAGTG F2: 3 ACGGAGTC 2 Unidirectional alignment (log-probability: -38.2) CCTTTGGCTCAGGTTTTGAGAAGACTTTTAgtaatacaagctgaggcaaGTAATACAAGGCAGAACACTTACTGTCTCTCATAAGCTT CCTTTGGCTCAGGTTTTGAGAAGACTTTTA-------------------GTAATACAAGGCAGAACACTTACTGTCTCTCATAAGCTT Template switch alignment (log-probability: -22.5) CCTTTGGCTCAGGTTTTGAGAAGACTTTTAGTAATACAAG|CTGAGgCA|AGTAATACAAGGCAGAACACTTACTGTCTCTCATAAGCTT CCTTTGGCTCAGGTTTTGAGAAGACTTTTAGTAATACAAG|CTGAGCCA|AGTAATACAAGGCAGAACACTTACTGTCTCTCATAAGCTT ======== Event 55 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAAAGGTTAGGCCATCACTT----ATCAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATCAAAAGTGGGCTCATTGAATTCATAGAGCAAATCTATTGATACATTCAGttattcattcaaaataactatattcagcattcagttgtcctgggccctgacaatgaagcagtgcataaaa Chimp: GAAAAGGTTAGGCCATCACTT---AATCAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATCAAAAGTGGGCTCATTGAATTCATAGAGCAAATCTATCGATACATTCAGttattcattcaaaataactatattcagcattcagttgtcctgggctctgacaatgaagcagtgcataaaa ↓ 1 4 3 2 Gorilla: GAAAAGGTTAGGCCATCACTTATCAGACAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATCAAAAGTGGGCTCATTGAATTCATAGAGCAAATCTATCGATACATTCAGttattcattcaaaataactatattcagcattcagtcgtcctgggctctgacaatgaagcagtgcataaaa Human: GAAAAGGTTAGGCCATCACTT----ATCAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATCAAAAGTGGGCTCATTGAATTCATAGAGCAAATCTATTGATACATTCAGttattcattcaaaataactatattcagcattcagttgtcctgggccctgacaatgaagcagtgcataaaa Cluster: [ ] Orangutan: GAAAAGGTTAGGCCATCACTTATCAGACAAATTAGTATGTGCCAGACAATTTACTAGACACTGCATCAAAAGTGGGTTCATTGAATTCATAGAGCAAGTCTATCGATACATTCAGttattcattcaaaataactatattcagcattcagttgtcctgggctctgacaatgcagcagtgcataaaa Chimp > Gorilla --------------- chr10:22213992-22213996 Template switch process: F1: L TGGAGAGAGATAAGTAGACGGAAAAGGTTAGGCCATCACTTA 1 F3: 4 CAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATC R RF: TGGAGAGAGATAAGTAGAGGGAAAAGGTTAGGCCATCACTTAATCAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATCAAAAGTGGGCTCATTGAATTCATAGAGCAAATCTATCGATACATTCAGTTATTCATTCAAAATAACTATATTCAGCATTCAGTTGTCCTGGGCTCTGA RR: ACCTCTCTCTATTCATCTCCCTTTTCCAATCCGGTAGTGAATTAGTTTAATCCTACACGGTCTGTTAAATGATCTGTGACATAGTTTTCACCCGAGTAACTTAAGTATCTCGTTTAGATAGCTATGTAAGTCAATAAGTAAGTTTTATTGATATAAGTCGTAAGTCAACAGGACCCGAGACT F2: 3 AGACT 2 Unidirectional alignment (log-probability: -31.8) GAGAGAGATAAGTAGAcGGAAAAGGTTAGGCCATCACTTatcAgaCAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATC GAGAGAGATAAGTAGAGGGAAAAGGTTAGGCCATCACTT---AATCAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATC Template switch alignment (log-probability: -21.9) GAGAGAGATAAGTAGAcGGAAAAGGTTAGGCCATCACTTA|TCAGA|CAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATC GAGAGAGATAAGTAGAGGGAAAAGGTTAGGCCATCACTTA|TCAGA|CAAATTAGGATGTGCCAGACAATTTACTAGACACTGTATC ======== Event 56 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGTTGAGATTGGGAAGACATCCCTTGTTCT---------------CACTTCCAGCCCTCTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGAGGCTCACCGTGCTT Chimp: GGTTGAGATTGGGAAGACATCCCTTGTTCT---------------CACTTCCAGCCCTCTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGAGGCTCACCGTGCTT Gorilla: GGTTGAGATTGGGAAGACATCACTTGTTCT------------------------------CACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGAGGCTCACCGTGCTT ↓ 4 1 3 2 Human: GGTTGAGATTGGGAAGACATCCCTTGTTCT---------------CACTTCCAGCCCTCTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGAGGCTCACCGTGCTT Cluster: [ ] Orangutan: GGTTGAGATTGGGAAGACATCACTTGTTCTCTCTTCCTGCCCTCT---------------CACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGAGGCTCACAGTGCTT Gorilla > Human --------------- chr10:127291148-127291154 Template switch process: F1: L AGTCTGTGTACTCTGGCTTAGGTTGAGATTGGGAAGACATCCCTTGTTCTCACTTC 1 F3: 4 CTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGA R RF: AGTCTGTGTACTCTGGCTTAGGTTGAGATTGGGAAGACATCACTTGTTCTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACAGA RR: TCAGACACATGAGACCGAATCCAACTCTAACCCTTCTGTAGTGAACAAGAGTGAAGTCAGTTCTGAAAACGAATGTTTCCCGTCGTGTCT F2: 3 TCCCGAC 2 Unidirectional alignment (log-probability: -38.1) CTTAGGTTGAGATTGGGAAGACATCcCTTGTtctcacttccagcccTCTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACA CTTAGGTTGAGATTGGGAAGACATCACTTGT---------------TCTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACA Template switch alignment (log-probability: -28.1) CTTAGGTTGAGATTGGGAAGACATCcCTTGTTCTCACTTC|CaGCCCT|CTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACA CTTAGGTTGAGATTGGGAAGACATCACTTGTTCTCACTTC|CTGCCCT|CTCACTTCAGTCAAGACTTTTGCTTACAAAGGGCAGCACA ======== Event 57 ======== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTTGCC-CCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTCTAAACAGGCCCCTGGGCACAC ↓ 3 2 1 4 Chimp: TCCTTGCC-CCCTCTCTCCAAGGCTGCAGTCTCAGGCAGCCT-----TTAAACAGGCCCCTGGGCACAC ↑ 3 2 1 4 Gorilla: TCCTTGCC-TCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTCTAAACAGGCCCCTGGGCACAC Human: TCCTTGCC-CCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTCTAAACAGGCCCCTGGGCACAC Cluster: [ ] Orangutan: TCCTTGCCCCCCTCCTTCCAAGGCTGCCGTTTCAGGATCTCTTTCCTCTAAACAGGCCCCTGGGCACAC Human > Chimp ------------- chr10:132000028-132000034 Template switch process: F1: L CTCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGG 1 F3: 4 TAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC R RF: CTCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTCTAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC RR: GAGGAGAGGAACGGGGGAGAGAGGTTCCGACGTCAGAGTCCTAGAGAAAGGAGATTTGTCCGGGGACCCGTGTGGCGCAACGGGTGAGTCAAG F2: 3 TTCCGAC 2 Unidirectional alignment (log-probability: -30.3) TCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGG-----------CagccttTAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC TCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTC------TAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC Template switch alignment (log-probability: -16.2) TCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGG|CAGCCTT|TAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC TCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGG|CAGCCTT|TAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC Gorilla > Chimp --------------- chr10:132000028-132000034 Template switch process: F1: L CTCCTCTCCTTGCCCCCTCTCTCCAAGGCTGCAGTCTCAGG 1 F3: 4 TAAACAGGCCCCTGGGCACACCGCGTTGCCCACTCAGTTC R RF: CTCCTCTCCTTGCCTCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTCTAAACAGGCCCCTGGGCACACCGCGTTGCCCACCCAGTTC RR: GAGGAGAGGAACGGAGGAGAGAGGTTCCGACGTCAGAGTCCTAGAGAAAGGAGATTTGTCCGGGGACCCGTGTGGCGCAACGGGTGGGTCAAG F2: 3 TTCCGAC 2 Unidirectional alignment (log-probability: -40.9) TCCTCTCCTTGCCcCCTCTCTCCAAGGCTGCAGTCTCAGG-----------CagccttTAAACAGGCCCCTGGGCACACCGCGTTGCCCACtCAGTTC TCCTCTCCTTGCCTCCTCTCTCCAAGGCTGCAGTCTCAGGATCTCTTTCCTC------TAAACAGGCCCCTGGGCACACCGCGTTGCCCACCCAGTTC Template switch alignment (log-probability: -27.7) TCCTCTCCTTGCCcCCTCTCTCCAAGGCTGCAGTCTCAGG|CAGCCTT|TAAACAGGCCCCTGGGCACACCGCGTTGCCCACtCAGTTC TCCTCTCCTTGCCTCCTCTCTCCAAGGCTGCAGTCTCAGG|CAGCCTT|TAAACAGGCCCCTGGGCACACCGCGTTGCCCACCCAGTTC ======== Event 58 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTTGTCCTGTAGGAAAACCT------ACCTGGCT----------GGGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCATTTTTTTATTTGGAAAACAGAACTTTGGGTTGACCTTACTCCAACCCCCAAGCTTCCCTACCATTCTTCATTGCAGTCCCTGAAATGAGGTTGGAA Chimp: AGTTGTCCTGTAGGAAAACCTTATCTTCTCCTGCAGGCTTATCTGCAGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCATT-TTTTATTCGGAAAACAGAACTTAGGGTTGGCCTTACTCCAACCCCCAAGCTTCCCTACCATTCTTCATTGCAGTCCCTGAAATGAGGTTGGAA ↑ 4 1 3 2 Gorilla: AGTTGTCCTGTAGGAAAACCT------ACCCGGTT----------GGGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCATC-TTTTATTCGGAAAACAGAACTTTGGGTTGACCTTACTCCAACCCCCAAGCTTCCCTACCATTCTTCATTGCAGTCCCTGAAATGAGGTTGGAA Human: AGTTGTCCTGTAGGAAAACCT------ACCTGGCT----------GGGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCATTTTTTTATTTGGAAAACAGAACTTTGGGTTGACCTTACTCCAACCCCCAAGCTTCCCTACCATTCTTCATTGCAGTCCCTGAAATGAGGTTGGAA Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr10:2990838-2990842 Template switch process: F1: L GCTTAACATGCTTGGAGGCAAGTTGTCCTGTAGGAAAAC-----------------------CTTATCTTCTCCTGCAGGCTTAT 1 F3: 4 GGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCAT R RF: GCTTAACATGCTTGGAGGCAAGTTGTCCTGTAGGAAAACCTACCCGGTTGGGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCATCTTTTATTCGGAAAACAGAACTTTGGGTTGACCTTACTCCAACCCCCAAGCTTCCCTACCATTCTTCATTGCAG RR: CGAATTGTACGAACCTCCGTTCAACAGGACATCCTTTTGGATGGGCCAACCCCTTGCCCTCCGAATAGAAGAGGACGTCCGAAGAAAAGTAGAAAATAAGCCTTTTGTCTTGAAACCCAACTGGAATGAGGTTGGGGGTTCGAAGGGATGGTAAGAAGTAACGTC F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -57) TTGTCCTGTAGGAAAACCTtatcttctcctgcaggcttatctgcA---------GGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCAT TTGTCCTGTAGGAAAACCT-------------------------ACCCGGTTGGGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCAT Template switch alignment (log-probability: -33.3) TTGTCCTGTAGGAAAAC-----------------------CTTATCTTCTCCTGCAGGCTTaT|CTGCA|GGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCAT TTGTCCTGTAGGAAAACCTACCCGGTTGGGGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCT|CTGCA|GGAACGGGAGGCTTATCTTCTCCTGCAGGCTTCTTTTCAT ======== Event 59 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCATGGTGACTCTTACAAAAATGCAAAA-GT-GCACCTTTCAACAGGTAaaagaaaaaaatccccaaat Chimp: CCATGGTGACT--CATAAAAACGCAAAA-GT-GCACCTTTCAACAGGTAAAAGaaaaaaaTCCCCAAAT ↓ 1 4 3 2 Gorilla: CCATGGTGACT--CATAAAAATGCAATACCTGTTACCTTTCAACAGGTAaaagaaaaaaatccccaaat Human: CCATGGTGACTCTTACAAAAATGCAAAA-GT-GCACCTTTCAACAGGTAaaagaaaaaaatccccaaat Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr10:2865901-2865908 Template switch process: F1: L TCACGAGCATGAGCTATCATTACCATGGTGACTCATAAAAATGCAA 1 F3: 4 ACCTTTCAACAGGTAAAAGAAAAAAATCCCCAAATCTTAA R RF: TCACAAGCATGAGCTATCATTACCATGGTGACTCATAAAAACGCAAAAGTGCACCTTTCAACAGGTAAAAGAAAAAAATCCCCAAATCTTAA RR: AGTGTTCGTACTCGATAGTAATGGTACCACTGAGTATTTTTGCGTTTTCACGTGGAAAGTTGTCCATTTTCTTTTTTTAGGGGTTTAGAATT F2: 3 TTGTCCAT 2 Unidirectional alignment (log-probability: -41) GCATGAGCTATCATTACCATGGTGACTCATAAAAA--------TGCaatacctgttACCTTTCAACAGGTAAAAGAAAAAAATCCCCAAATCTTAA GCATGAGCTATCATTACCATGGTGACTCATAAAAACGCAAAAGTGC----------ACCTTTCAACAGGTAAAAGAAAAAAATCCCCAAATCTTAA Template switch alignment (log-probability: -27.9) GCATGAGCTATCATTACCATGGTGACTCATAAAAAtGCAA|TACCTGTT|ACCTTTCAACAGGTAAAAGAAAAAAATCCCCAAATCTTAA GCATGAGCTATCATTACCATGGTGACTCATAAAAACGCAA|TACCTGTT|ACCTTTCAACAGGTAAAAGAAAAAAATCCCCAAATCTTAA ======== Event 60 ======== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGGCCTGGTGATTGGGACTTCAAAGGTC-TGTGAAA-------CTGCTAAAGCTTCTGACAGTAGT ↓ 3 2 1 4 Chimp: TAGGCCTGGTGATTGGGACTTCAAAGGTC-TGTGAAGTCCTTTGAAGCTAAAGCTTCTGACAGTAGT ↑ 3 2 1 4 Gorilla: TAGGCCTGGTGATTGGGACTTCAAAGGTC-TGTGAAA-------CTGCTAAAGCTTCTGACAGTAGT Human: TAGGCCTGGTGATTGGGACTTCAAAGGTC-TGTGAAA-------CTGCTAAAGCTTCTGACAGTAGT Cluster: [ ] Orangutan: TAGGCCTGGTGATTGGGACTTCAAAGGTCTTGTGAAA-------CTGCTAAAGGTTCTGACAGTAGT Human > Chimp ------------- chr10:7243293-7243302 Template switch process: F1: L GACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAA 1 F3: 4 GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG R RF: GACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAAACTGCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG RR: CTGGGTATCCGGACCACTAACCCTGAAGTTTCCAGACACTTTGACGATTTCGAAGACTGTCATCAAACACACAAAGATACTCTC F2: 3 AAGTTTCCTG 2 Unidirectional alignment (log-probability: -34.2) ACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAagtcctttgAA--GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG ACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGA---------AACTGCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG Template switch alignment (log-probability: -22.5) ACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAA|GtCCTTTGAA|GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG ACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAA|GACCTTTGAA|GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG Gorilla > Chimp --------------- chr10:7243293-7243302 Template switch process: F1: L GACCCATAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAA 1 F3: 4 GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG R RF: GACCCTTAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAAACTGCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG RR: CTGGGAATCCGGACCACTAACCCTGAAGTTTCCAGACACTTTGACGATTTCGAAGACTGTCATCAAACACACAAAGATACTCTC F2: 3 AAGTTTCCTG 2 Unidirectional alignment (log-probability: -39.2) ACCCaTAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAagtcctttgAA--GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG ACCCTTAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGA---------AACTGCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG Template switch alignment (log-probability: -28) ACCCaTAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAA|GtCCTTTGAA|GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG ACCCTTAGGCCTGGTGATTGGGACTTCAAAGGTCTGTGAA|GACCTTTGAA|GCTAAAGCTTCTGACAGTAGTTTGTGTGTTTCTATGAGAG ======== Event 61 ======== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTGGGGGAGCTGCTCTGGGGTG-----------------GGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTTTTATCCTGCAGTGAACTTCGACCACTTCCAGATCCTTCGGGCCATTGGGAAGGGCAGCTTTGGCAAGGTAAGGCAGGGCCTGGGG Chimp: GGTGGGGGAGCTGCTCTGGAGTG-----------------GGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTTTTATCCTGCAGTGAACTTCGACCACTTCCAGATCCTTCGGGCCATTGGGAagggcagctttggcaaggtaaggcagggcctgggg Gorilla: GGTGGGAGAGCTGCTCTGGGGTGGGGCCTTGTGCCATGTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTTTTATCCTGCAGTGAACTTCGACCACTTCCAGATCCTTCGGGCCATTGGGAagggcagctttggcaaggtaaggcagggcctgggg ↑ 4 1 3 2 Human: GGTGGGGGAGCTGCTCTGGGGTG-----------------GGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTTTTATCCTGCAGTGAACTTCGACCACTTCCAGATCCTTCGGGCCATTGGGAAGGGCAGCTTTGGCAAGGTAAGGCAGGGCCTGGGG Cluster: [ ] Orangutan: GGTGGGGGAGCTACTCTGGGGTGGGGGCTTGTGCCATGTGGGGCCTTGCTGCCACCTCACCAGGTGTTCCTCTGTTTTATTCTGCAGTGAACTTCGACCACTTCCAGATCCTTCGGGCCATTGGGAAGGGCAGCTTTGGCAAGGTAAGGCAGGGCCTGGGG Human > Gorilla --------------- chr10:1523023-1523027 Template switch process: F1: L CGGGGTGGGGGATGTTGAGGTGGGAGAGCTGCTCTGGGGTGGGGCCTTG 1 F3: 4 TGTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTTTTAT R RF: CGGGGTGGGGGATGTTGAGGTGGGGGAGCTGCTCTGGGGTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTTTTATCCTGCAGTGAACTTCGACCACTTCCAGATCCTTCGGGCCATTGGGAAGGGCAGCTTTGGCA RR: GCCCCACCCCCTACAACTCCACCCCCTCGACGAGACCCCACCCCGGAACGACGGTGGAGTGGTCCACAGGGAGACAAAATAGGACGTCACTTGAAGCTGGTGAAGGTCTAGGAAGCCCGGTAACCCTTCCCGTCGAAACCGT F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -40.8) GGATGTTGAGGTGGGaGAGCTGCTCTGGGgtggggccttgtgccatGTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTT GGATGTTGAGGTGGGGGAGCTGCTCTGGG-----------------GTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTT Template switch alignment (log-probability: -27.7) GGATGTTGAGGTGGGaGAGCTGCTCTGGGGTGGGGCCTTG|TGCCA|tGTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTT GGATGTTGAGGTGGGGGAGCTGCTCTGGGGTGGGGCCTTG|TGCCA|GGTGGGGCCTTGCTGCCACCTCACCAGGTGTCCCTCTGTT ======== Event 62 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TATGGGGCTGGGGTCAGCACACGCATAGTGGG-CTCTTATGATCTTTCACTTAGATCCActct Chimp: TATGGGGCTGGGGTCAGCACATGCATAGTGGG-CTCTTATGATCTttcacttagatccactct ↓ 1 3 4 2 Gorilla: TATGGGGCTGGGGTCAGCACACGCATAGTGATCATAAGATGATCTttcacttagatccactct Human: TATGGGGCTGGGGTCAGCACACGCATAGTGGG-CTCTTATGATCTTTCACTTAGATCCActct Cluster: [ ] Orangutan: TATGGGGCTGGGGTCAGCACACGCGTAGTGGG-CTCTTATGATCTTTCACTTAGATccactct Chimp > Gorilla --------------- chr10:1496071-1496078 Template switch process: F1: L GGCAGCCCAGGCCCAGTCAGTATGGGGCTGGGGTCAGCACACGCATAGTG 1 F3: 4 ATGATCTTTCACTTAGATCCACTCTCATTCATTCACTCAC R RF: GGCAGCCCGGGCCCAGTCAGTATGGGGCTGGGGTCAGCACATGCATAGTGGGCTCTTATGATCTTTCACTTAGATCCACTCTCATTCATTCACTCAC RR: CCGTCGGGCCCGGGTCAGTCATACCCCGACCCCAGTCGTGTACGTATCACCCGAGAATACTAGAAAGTGAATCTAGGTGAGAGTAAGTAAGTGAGTG F2: 3 GAATACTA 2 Unidirectional alignment (log-probability: -57.5) GCCCAGTCAGTATGGGGCTGGGGTCAGCACAcGCATAGTGatcataaG------ATGATCTTTCACTTAGATCCACTCTCATTCATTCactcac GCCCAGTCAGTATGGGGCTGGGGTCAGCACATGCATAGTG-------GGCTCTTATGATCTTTCACTTAGATCCACTCTCATTCATTC------ Template switch alignment (log-probability: -28) GCCCAGTCAGTATGGGGCTGGGGTCAGCACAcGCATAGTG|ATCATAAG|ATGATCTTTCACTTAGATCCACTCTCATTCATTCACTCAC GCCCAGTCAGTATGGGGCTGGGGTCAGCACATGCATAGTG|ATCATAAG|ATGATCTTTCACTTAGATCCACTCTCATTCATTCACTCAC ======== Event 63 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GGCACGTTACAGGGAGGTAACAACGATCGGTGGATCGTTGTTGGAGCTGGAATCCCCC Chimp: GGCACGTTACAGGGAGGCAACAACGATCGGTGGATCGTTGTTGGAGCTGGAATCCCCC ↑ 1 3 4 2 Gorilla: GGCAGGTTACAGGGAGGCAAC-ATGACACACCGATCGTTGTTGGAGTTGGAATCCCCC Human: GGCACGTTACAGGGAGGTAACAACGATCGGTGGATCGTTGTTGGAGCTGGAATCCCCC Cluster: [ ] Orangutan: GGCACGTTACAGGGAGGCAAC-ATGACACACCGATCATTGTTGGAGTTAGAATCCCCC Gorilla > Chimp --------------- chr10:133537383-133537392 Template switch process: F1: L GTGCGTGCGTGTGTGGTGCTGGCACGTTACAGGGAGGCAACA 1 F3: 4 GATCGTTGTTGGAGCTGGAATCCCCCCAGCCTTGTGTGAC R RF: GTGCGTGCGTGTGTGGTGCTGGCAGGTTACAGGGAGGCAACATGACACACCGATCGTTGTTGGAGTTGGAATCCCCCCAGCCTTGTGTGAC RR: CACGCACGCACACACCACGACCGTCCAATGTCCCTCCGTTGTACTGTGTGGCTAGCAACAACCTCAACCTTAGGGGGGTCGGAACACACTG F2: 3 GTGGCTAGCA 2 Unidirectional alignment (log-probability: -43.6) GCGTGCGTGTGTGGTGCTGGCAcGTTACAGGGAGGCAACAacgatcggTG-------GATCGTTGTTGGAGcTGGAATCCCCCCAGCCTTGTGTGAC GCGTGCGTGTGTGGTGCTGGCAGGTTACAGGGAGGCAACA--------TGACACACCGATCGTTGTTGGAGTTGGAATCCCCCCAGCCTTGTGTGAC Template switch alignment (log-probability: -28.1) GCGTGCGTGTGTGGTGCTGGCAcGTTACAGGGAGGCAACA|ACGATCGGTG|GATCGTTGTTGGAGcTGGAATCCCCCCAGCCTTGTGTGAC GCGTGCGTGTGTGGTGCTGGCAGGTTACAGGGAGGCAACA|ACGATCGGTG|GATCGTTGTTGGAGTTGGAATCCCCCCAGCCTTGTGTGAC ======== Event 64 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCTAGCCGTAACCTAAAGTTACGACTAGAGATAGatttttgaatttttcttcctagagtt-----tattttttattttttattttttggagacagagtctcgctctgttgcccaggctggagtgcagtggtatgatctcagctcactgcaac Chimp: ATTCTAGCCGTAACCTAAAGTTACGACTAGAGATAGatttttgaatttttcttcctagagtt---tttatt-------ttttattttttggagacagagtctcgctctgttgcccaggctggagtgcagtggtacgatctcagctcactgcaac ↑ 1 4 3 2 Gorilla: ATTCTAGCTGTAACCTAAAGT----CTGAGAGATAGATTTTTGAATTTTTCTTCCTAGAGttt-t---tttttttattttttattttttggagacagagtctcgctctgttgcccaggctggagtgtagtggtatgatctcagctcactgcaac Human: ATTCTAGCCGTAACCTAAAGTTACGACTAGAGATAGatttttgaatttttcttcctagagtt-----tattttttattttttattttttggagacagagtctcgctctgttgcccaggctggagtgcagtggtatgatctcagctcactgcaac Cluster: [ ] Orangutan: AT-TTAGCTGTAACCTAAAGT----CTGAGAGATAGATTTTTGAATTTTTCTTCCTAGAGttatt--tattttttattttttattttttggagatggactcttgctctgttgcccaggctggagtgcagtggtacgatctcagctcactgcaac Gorilla > Chimp --------------- chr10:130308528-130308534 Template switch process: F1: L ATACTCTAACTCAAATTATCATTCTAGCCGTAACCTAAAGT 1 F3: 4 AGAGATAGATTTTTGAATTTTTCTTCCTAGAGTTTTTA R RF: ATACTCTAACTCAAATTATCATTCTAGCTGTAACCTAAAGTCTGAGAGATAGATTTTTGAATTTTTCTTCCTAGAGTTTTTTTTTTTATTTTTTATTTTTTGGAGACAGAGTCTCGCTCTGTTGCCCAGGCTGGAGTGTAGTGGTA RR: TATGAGATTGAGTTTAATAGTAAGATCGACATTGGATTTCAGACTCTCTATCTAAAAACTTAAAAAGAAGGATCTCAAAAAAAAAAATAAAAAATAAAAAACCTCTGTCTCAGAGCGAGACAACGGGTCCGACCTCACATCACCAT F2: 3 TCAGCAT 2 Unidirectional alignment (log-probability: -41.6) TACTCTAACTCAAATTATCATTCTAGCcGTAACCTAAAGTtacgaCT-AGAGATAGATTTTTGAATTTTTCTTCCTAGAGTTTTTa TACTCTAACTCAAATTATCATTCTAGCTGTAACCTAAAGT-----CTGAGAGATAGATTTTTGAATTTTTCTTCCTAGAGTTTTT- Template switch alignment (log-probability: -33.1) TACTCTAACTCAAATTATCATTCTAGCcGTAACCTAAAGT|TACgACT|AGAGATAGATTTTTGAATTTTTCTTCCTAGAGTTTTTa TACTCTAACTCAAATTATCATTCTAGCTGTAACCTAAAGT|TACCACT|AGAGATAGATTTTTGAATTTTTCTTCCTAGAGTTTTTT ======== Event 65 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: --GCATTGCAAGCTACCTATTTGttggaaaatacattggaaa-taca--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------t----ttccaaatacattgg Chimp: --GCATTGCAAGCTACCTATTCGTTGGAAAATACATTGGAAA-TACA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----Ttccacat--atg-- ↓ 3 4 2 1 Gorilla: --GCATTGCAAGCTACCTATTTGCTGGAAaatacattggaaa-taca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgtatttccaatacattgggaaatacaatgatgtatttccaatacattgggaaatacaatgatgtatttccaatacattgggaaatacaatgatgtatttccaatacgttgggaaatacaatgatgtatttccaatacgttgggaaatacaatgatgtatttccaatacattgggaaatacaatgatgtatttccaatacatttggaaatacat----ttccaaatacatGGG Human: --GCATTGCAAGCTACCTATTTGttggaaaatacattggaaa-taca--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------t----ttccaaatacattgg Cluster: [ ] Orangutan: aaacattggaaactacctatttgttcaaaaacacagggttagtgacataaactacagtgtgtccTACTGCCCCAGATTAGTGATTCTTAATCTGTGCCCATAAAAGCTTCTGGGTTGCCCTGGGGAGTCCCTTCAAGGGCCACAGGAGACCAACTTTGGGGATATTACTCTGATTTGATTTTATTGACATGAAAGTCTTAATTTGAACAAAACTTTTCCTCACTTTAATAAGGTTTAAGTCCACAATTGCAGAGAGATGTTTAATCACATGGAAAGTTGCCTGAGATATAGTTGTTTTAAAGACTGTTTATAAGATAATGCCCAATGTACAACTCTGTGGTCCTGAAGCACCGATCCTACAGCCCACAACTTCCACCCCTCCTGATGGCACCCTCCACTGGGATGATGTCCTCTCCTGCAGACCTGCCCTCCTCTGCCCACTGAGACCCCCAGCCCATGATCTGAGCATGCCTCCCCAGCACTGCTGCTagaagctgcacagtgtggggctcatgcctggggctcaaggctggatcctggcttcacctgctgttgcgcaagctcctctgtgcctcagtgtcctcattggcaaatgagtgtgctgacagctcctccttcctcaggtaactggggattaaacgagtgtatagatACTCAAATAATGCCATAGATATTTAAACATAGATACCCtcctcccttggtatgcatggggatttgtttccccacagataggaaaatccacagatgctcaagtcttttacatagaatggtgtagtatttgcatgtaacctacacacatcgtccccaaaactttaaaccatctctagattgcccgtaatagctaatacgctgtagatgttatgtaaataactgttatatcgtatcatttaggcaataatgacaagaaagaaaagcctgtacttgttcagtgcaaaagcaaaccatctactttttcctgaatatttttaatctcaggttgact---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gttgaacccacac--atg-- Chimp > Gorilla --------------- chr10:143216848-143216856 Template switch process: F1: L ACAGGTGTTTGCTGCAATGCTTGCATTGCAAGCTACCTATTTGCTGGAAAATACATTGGAAATACAT 1 F3: 4 AATACATT R RF: ACAGGTGTTTGCTGCAATGCTTGCATTGCAAGCTACCTATTCGTTGGAAAATACATTGGAAATACATGGAAATACA RR: TGTCCACAAACGACGTTACGAACGTAACGTTCGATGGATAAGCAACCTTTTATGTAACCTTTATGTACCTTTATGT F2: 3 CCTTTATGT 2 Unidirectional alignment (log-probability: -43.2) GCAAGCTACCTATTtGcTGGAAAATACATTGGAAATACATtgtatttccaatacatt GCAAGCTACCTATTCGTTGGAAAATACATTGGAAATACAT----------------- Template switch alignment (log-probability: -27.8) GCAAGCTACCTATTtGcTGGAAAATACATTGGAAATACAT|TGTATTTCC|AATACATT GCAAGCTACCTATTCGTTGGAAAATACATTGGAAATACAT|TGTATTTCC|AATACATT ======== Event 66 ======== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: GATGGTGAGCCCACGCCGCTGGCAGGGTGCCGACCCCACGCCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGACCGCCGTTGGGTATCCATGTGTCTGTGCAGGCTTTGGA Chimp: Gorilla: GATGGTGAGCCCACGCCGCTGGCAGGGTGCCGACCCCACGCCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGACTGCCATTGGGCATCCACGTGTCTGTGCAGGCTTTGGA ↑ 3 2 1 4 Human: GATGGTGAGCCCACGCCGCTGGCAGGGTGCCGACCCCACGCCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGACCGCCGTTGGGTATCCATGTGTCTGTGCAGGCTTTGGA Cluster: [ ] Orangutan: GATGGTGAGCTCACGCTGCTGGCAGGGTGCTGACCCCACGCAGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGGTCTGGACGGCCGTTGGGCATCCACGTGTCTGTGCAGGCTCTGGA Human > Gorilla --------------- chr10:881493-881497 Template switch process: F1: L GCCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGAC 1 F3: 4 TTGGGCATCCACGTGTCTGTGCAGGCTTTGGAGGCCAGGAGCCCCTGACGTG R RF: TGGCAGGGTGCCGACCCCACGCCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGACCGCCGTTGGGTATCCATGTGTCTGTGCAGGCTTTGGAGGCCAGGAGCCCCTGACGTG RR: ACCGTCCCACGGCTGGGGTGCGGCGAGGGGTCTCGAGACGAAGGACGAGGCACTAGACCTGGCGGCAACCCATAGGTACACAGACACGTCCGAAACCTCCGGTCCTCGGGGACTGCAC F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -38.7) CCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGACtGCCaTTGGGcATCCAcGTGTCTGTGCAGGCTTTGGAGGCCAGGA CCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGACCGCCGTTGGGTATCCATGTGTCTGTGCAGGCTTTGGAGGCCAGGA Template switch alignment (log-probability: -27.7) CCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGAC|TGCCA|TTGGGcATCCAcGTGTCTGTGCAGGCTTTGGAGGCCAGGA CCGCTCCCCAGAGCTCTGCTTCCTGCTCCGTGATCTGGAC|TGCCA|TTGGGTATCCATGTGTCTGTGCAGGCTTTGGAGGCCAGGA ======== Event 67 ======== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGTTGTGATGGCTTTAGAACACAGCAA------------TTGGACCCTGTCATTGGGCTCACGCTCACA Chimp: AAGGTGGTGATGGCTTTAGAACACAGCAA------------TTGGACCCTGTCATTGGGCTCACGCTCACA ↓ 34 2 Gorilla: AAGGTGGTGATGGCTTTAGAATACAGCAATCAGGGTCCAATTTGGACCCTGTCATTGGGCTCACGCTCACA ↑ 34 2 Human: AAGGTTGTGATGGCTTTAGAACACAGCAA------------TTGGACCCTGTCATTGGGCTCACGCTCACA Cluster: [ ] Orangutan: ----------------------------------------------------------------------- Human > Gorilla --------------- chr10:2019042-2019052 Template switch process: F1: L TATTGGAAAGTAAATCATCAAAGGTGGTGATGGCTTTAGAATACAGCAAT 1 F3: 4 TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA R RF: TATTGGAAAGTAAATCATCAAAGGTTGTGATGGCTTTAGAACACAGCAATTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA RR: ATAACCTTTCATTTAGTAGTTTCCAACACTACCGAAATCTTGTGTCGTTAACCTGGGACAGTAACCCGAGTGCGAGTGTCTCGTCTCGT F2: 3 TAACCTGGGAC 2 Unidirectional alignment (log-probability: -39.3) TAAATCATCAAAGGTgGTGATGGCTTTAGAAtACAGCAAtcagggtccaatTTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA TAAATCATCAAAGGTTGTGATGGCTTTAGAACACAGCAA------------TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA Template switch alignment (log-probability: -28.4) TAAATCATCAAAGGTgGTGATGGCTTTAGAAtACAGCAAT|CAGGGTCCAAT|TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA TAAATCATCAAAGGTTGTGATGGCTTTAGAACACAGCAAT|CAGGGTCCAAT|TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA Chimp > Gorilla --------------- chr10:2019042-2019052 Template switch process: F1: L TATTGGAAAGTAAATCATCAAAGGTGGTGATGGCTTTAGAATACAGCAAT 1 F3: 4 TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA R RF: GATTGGAAAGTAAATCATCAAAGGTGGTGATGGCTTTAGAACACAGCAATTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA RR: CTAACCTTTCATTTAGTAGTTTCCACCACTACCGAAATCTTGTGTCGTTAACCTGGGACAGTAACCCGAGTGCGAGTGTCTCGTCTCGT F2: 3 TAACCTGGGAC 2 Unidirectional alignment (log-probability: -39.3) TAAATCATCAAAGGTGGTGATGGCTTTAGAAtACAGCAAtcagggtccaatTTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA TAAATCATCAAAGGTGGTGATGGCTTTAGAACACAGCAA------------TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA Template switch alignment (log-probability: -28.4) TAAATCATCAAAGGTGGTGATGGCTTTAGAAtACAGCAAT|CAGGGTCCAAT|TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA TAAATCATCAAAGGTGGTGATGGCTTTAGAACACAGCAAT|CAGGGTCCAAT|TTGGACCCTGTCATTGGGCTCACGCTCACAGAGCAGAGCA ======== Event 68 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGCTGTAAATAATGCAATCCTGTGACTGCAAACTGCCCGGCCGGGAGGTGATGATGAGATGGGGGCCAGGCAGGTTCTGG--------------------------------TGGG------------CGGGGCAGTCACAGGGGCAGGCACAGGCAGGCTCTGAAGA Chimp: GGCTGTAAATAATGCAATCCTGTGACTGCAAACCGCCGGGCCAGGAGGTGATGATGAGATGGGGGCCAGGCAGGTTCTGG-------------CGGTGGTgggggggggggggggg------------CGGGGCAGTCACAGGGGCAGGCACAGGCAGGCTCTGAAGA Gorilla: GGCTGTAAATAATGCAATCCTGTGACTGCAAACCGCCCGGCCGGGAGGTGATGATGAGATGGGGGCCAGGCAGGTTCTGG-------TGGGGG-------------------AGGG------------------------CGGGGCAGGCACAGGCAGGCTCTGAAGA ↓ 3 2 4 1 Human: GGCTGTAAATAATGCAATCCTGTGACTGCAAACTGCCCGGCCGGGAGGTGATGATGAGATGGGGGCCAGGCAGGTTCTGG--------------------------------TGGG------------CGGGGCAGTCACAGGGGCAGGCACAGGCAGGCTCTGAAGA Cluster: [ ] Orangutan: GGCTGGAAATGATGCAATCCTGTGACTGCAAACTGCCCGGCCAGGAGGTGGTGATGAGATgggggccaggcaggttctgggagtggg-------------------------ggggcggggcagtcac------------gggggcaggcacaggcaggcTCTGAAGA Gorilla > Human --------------- chr10:132060335-132060340 Template switch process: F1: L GCCGGGAGGTGATGATGAGATGGGGGCCAGGCAGGTTCTGGTGG------GCGGGGCAG 1 F3: 4 GGGCAGGCACAGGCAGGCTCTGAAGAGACAGGGAGAGAA R RF: CTGTGACTGCAAACCGCCCGGCCGGGAGGTGATGATGAGATGGGGGCCAGGCAGGTTCTGGTGGGGGAGGGCGGGGCAGGCACAGGCAGGCTCTGAAGAGACAGGGAGAGAA RR: GACACTGACGTTTGGCGGGCCGGCCCTCCACTACTACTCTACCCCCGGTCCGTCCAAGACCACCCCCTCCCGCCCCGTCCGTGTCCGTCCGAGACTTCTCTGTCCCTCTCTT F2: 3 GACACT 2 Unidirectional alignment (log-probability: -36.4) GATGAGATGGGGGCCAGGCAGGTTCTGGTGGGcG-GGGCagtcacaGGGGCAGGCACAGGCAGGCTCTGAAGAGACAGGGAGAGAA GATGAGATGGGGGCCAGGCAGGTTCTGGTGGGGGAGGGC-------GGGGCAGGCACAGGCAGGCTCTGAAGAGACAGGGAGAGAA Template switch alignment (log-probability: -26.8) GATGAGATGGGGGCCAGGCAGGTTCTGGTGG------GCGGGGCAG|TCACAG|GGGCAGGCACAGGCAGGCTCTGAAGAGACAGGGAGAGAA GATGAGATGGGGGCCAGGCAGGTTCTGGTGGGGGAGGGCGGGGCAG|TCACAG|GGGCAGGCACAGGCAGGCTCTGAAGAGACAGGGAGAGAA ======== Event 69 ======== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTCCCAGCGACATGGAGGGTCTAAGCCTCAGCttagacaaggctgtcaccatcatc ↑ 3 4 2 Chimp: CCTCCCAGCGACATGGAGGGT--G-----AGGCttagacaaggctgtcaccatcatc Gorilla: CCTCCCAGCGACATGGAGGGT--G-----AGGCttagacaaggctgtcaccatcatc ↓ 3 4 2 Human: CCTCCCAGCGACATGGAGGGTCTAAGCCTCAGCttagacaaggctgtcaccatcatc Cluster: [ ] Orangutan: CCTCCCAGCGACATGGAGGGT--G-----AGGCTTAGACAaggctgtcaccatcatc Chimp > Human ------------- chr10:120558879-120558888 Template switch process: F1: L AAGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT 1 F3: 4 GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGG R RF: AAGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGTGAGGCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGA RR: TTCAACAAGTCCTTCTGGTAGGAGGGTCGCTGTACCTCCCACTCCGAATCTGTTCCGACAGTGGTAGTAGGCCCTCTCGTTACT F2: 3 ACTCCGAATC 2 Unidirectional alignment (log-probability: -41.7) AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT---ctaagcctcaGCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGg AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGTGAG----------GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGA Template switch alignment (log-probability: -22.5) AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT|CTAAGCCTCA|GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGg AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT|CTAAGCCTCA|GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGA Gorilla > Human --------------- chr10:120558879-120558888 Template switch process: F1: L AAGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT 1 F3: 4 GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGG R RF: AAGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGTGAGGCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGA RR: TTCAACAAGTCCTTCTGGTAGGAGGGTCGCTGTACCTCCCACTCCGAATCTGTTCCGACAGTGGTAGTAGGCCCTCTCGTTACT F2: 3 ACTCCGAATC 2 Unidirectional alignment (log-probability: -40.7) AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT---ctaagcctcaGCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGg AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGTGAG----------GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGA Template switch alignment (log-probability: -22.5) AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT|CTAAGCCTCA|GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGg AGTTGTTCAGGAAGACCATCCTCCCAGCGACATGGAGGGT|CTAAGCCTCA|GCTTAGACAAGGCTGTCACCATCATCCGGGAGAGCAATGA ======== Event 70 ======== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAACAACAAAGTCACCGAGTCAGATTCGCGTCCCTTATCTCCAGTTTCTCTCCACACCCGACGCCGCCACTCCAGCCTGGGCACCTCCCCCACACGGCTCTCTCCACGGCCTCACCCCTCCCGGTTTCCAATACTCCAACCAAAGGTCCTCACAAATC-----------TGTCCGTGGCTGCCGTTACC Chimp: CAACAACAAAGTCACCGAGTCAGATTCGCGTCCCTTATCTCCAGTTTCTCTCCACACCCGACGCCGCCACTCCAGCCTGGGCACCTCCCCCACACGGCTCTCTCCACGGCCTCACCCCTCCCGGTTTCCAATACTCCAACCAAGGGTCCTCACAAATC-------TGACTGTCCGTGGCTGCCGTTACC Gorilla: CGACAACAAAGTCACCGAGTCAGATTCGCGTCCCTTATCTCCAGTTTCTCTCCACACCCGACGCTGCCACTCCAGCCTGGGCACCTCCCCCACACGGCTCTCTCCACGGCCTCACCCCTCCCGGTTTCCAATACTCCAACCAACGGTCCCCAC-AATC---TGAC----TGTCCGTGGCTGCCGTTACC ↑ 3 2 1 4 Human: CAACAACAAAGTCACCGAGTCAGATTCGCGTCCCTTATCTCCAGTTTCTCTCCACACCCGACGCCGCCACTCCAGCCTGGGCACCTCCCCCACACGGCTCTCTCCACGGCCTCACCCCTCCCGGTTTCCAATACTCCAACCAAAGGTCCTCACAAATC-----------TGTCCGTGGCTGCCGTTACC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--------NNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr10:1132084-1132088 Template switch process: F1: L TCCACGGCCTCACCCCTCCCGGTTTCCAATACTCCAACCAACGGTCCCCACAA 1 F3: 4 CTGTCCGTGGCTGCCGTTACCCTGAGGATGAAGAAAGTCTG R RF: TCAGATTCGCGTCCCTTATCTCCAGTTTCTCTCCACACCCGACGCCGCCACTCCAGCCTGGGCACCTCCCCCACACGGCTCTCTCCACGGCCTCACCCCTCCCGGTTTCCAATACTCCAACCAAAGGTCCTCACAAATCTGTCCGTGGCTGCCGTTACCCTGAGGATGAAGAAAGTCTG RR: AGTCTAAGCGCAGGGAATAGAGGTCAAAGAGAGGTGTGGGCTGCGGCGGTGAGGTCGGACCCGTGGAGGGGGTGTGCCGAGAGAGGTGCCGGAGTGGGGAGGGCCAAAGGTTATGAGGTTGGTTTCCAGGAGTGTTTAGACAGGCACCGACGGCAATGGGACTCCTACTTCTTTCAGAC F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -37.5) CCCTCCCGGTTTCCAATACTCCAACCAAcGGTCCcCACAAtctgaCTGTCCGTGGCTGCCGTTACCCTGAGGATGAAGAAAGTCT CCCTCCCGGTTTCCAATACTCCAACCAAAGGTCCTCACAAA---TCTGTCCGTGGCTGCCGTTACCCTGAGGATGAAGAAAGTCT Template switch alignment (log-probability: -27.7) CCCTCCCGGTTTCCAATACTCCAACCAAcGGTCCcCACAA|TCTGA|CTGTCCGTGGCTGCCGTTACCCTGAGGATGAAGAAAGTCT CCCTCCCGGTTTCCAATACTCCAACCAAAGGTCCTCACAA|TCTGA|CTGTCCGTGGCTGCCGTTACCCTGAGGATGAAGAAAGTCT ======== Event 71 ======== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGCGTGGGAAG--GCGTG-CCGCCAGGG-------------------------AGAGT-GGTGGAGGGCGACGGGGCA-----------------------------------------CTGCGCCCTTGTCCTTCAGATCAACGA--GGCC----------TGGTGGCTTGAGGGCACCCCCGTCCCCGGGCCAGGCGCTGCCTGGCAGATGGACTTGC-ATGCAGGCCACTGACTTCAGGTGACCTTGCCCG Chimp: G-TCGTGGGAAAGGTCGTGCGCACCAGGG-----------AGGAAGCAGTTGGGAGAGTGGGTGGAGGGCGCGCGGGCA-----------------------------------------CTGCGCCCTTGTCCTTCAGATCAACGTAGTGCC---------TGGGTGGCTTGAGGGCAC-CCTGTCCCCGCGGCCAGCGCTGCCTTGC-AATGGACTTGCGTTGCAGGCCACTGACTCAGGATGTCCTTGCCCT Gorilla: GTGCGTGGGAAG--GCGTG-CTGCCAGGGAGAGCAGTGGG--------------AGAGT-GGTGGAGGGCGACGGGGCA-----------------------------------------CTGCGCCCTTGTCCTTCAGATCAACGA--GGCC----------TGGTGGCTTGAGGGCACCCCCGTCCCCAGGCCAGGCGCTGCCTGGCAGATGGACTTGC-ATGCAGGCCACTGACTTCAGGTGACCTTGCCCG ↑ 4 1 3 2 Human: GTGCGTGGGAAG--GCGTG-CCGCCAGGG-------------------------AGAGT-GGTGGAGGGCGACGGGGCA-----------------------------------------CTGCGCCCTTGTCCTTCAGATCAACGA--GGCC----------TGGTGGCTTGAGGGCACCCCCGTCCCCGGGCCAGGCGCTGCCTGGCAGATGGACTTGC-ATGCAGGCCACTGACTTCAGGTGACCTTGCCCG Cluster: [ ] Orangutan: GTGCGTGGGAAG--GCGTG-CCGCCAGGGAGAGCAGTGGG--------------AGAGT-GGTGGAGGGTGACGGGGCACACGTGCTCAGGACGTGCAGAAAAGCCCGAGACAGAATGGCCTGTGCCCTTGTCCTTCAGGTCAACAA--GGCCTGGCAGGAC-AGGTGGCTTGAGGGCACCCCCGTCCCCGGGCCAGGCGCTGCCTGGCAGATGGACTTGC-GTGCAGGCCACTGGCTTCGGGTGTCCTTGCCCT Human > Gorilla --------------- chr10:553095-553098 Template switch process: F1: L GCCCTTCGGGAAGGTAGGCTGTTGTGCGTGGGAAGGCGTGCTGCCAGGGAGAG 1 F3: 4 GGGAGAGTGGTGGAGGGCGACGGGGCACTGCGCCCTTGTCCTT R RF: GCCCTTCGGGAAGGTAGGCTGTTGTGCGTGGGAAGGCGTGCCGCCAGGGAGAGTGGTGGAGGGCGACGGGGCACTGCGCCCTTGTCCTTCAGATCAACGAGGCCTGGTGGCTTGAGGGCACCCCCGTCCCCGGGCCAGGCGCTGCCTGGCAGATGGACTTGCATGCAGGCCACTG RR: CGGGAAGCCCTTCCATCCGACAACACGCACCCTTCCGCACGGCGGTCCCTCTCACCACCTCCCGCTGCCCCGTGACGCGGGAACAGGAAGTCTAGTTGCTCCGGACCACCGAACTCCCGTGGGGGCAGGGGCCCGGTCCGCGACGGACCGTCTACCTGAACGTACGTCCGGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -32.3) GTAGGCTGTTGTGCGTGGGAAGGCGTGCtGCCAgggagagcagtGGGAGAGTGGTGGAGGGCGACGGGGCACTGCGCCCTTGTC GTAGGCTGTTGTGCGTGGGAAGGCGTGCCGCCA-----------GGGAGAGTGGTGGAGGGCGACGGGGCACTGCGCCCTTGTC Template switch alignment (log-probability: -22.1) GTAGGCTGTTGTGCGTGGGAAGGCGTGCtGCCAGGGAGAG|CAGT|GGGAGAGTGGTGGAGGGCGACGGGGCACTGCGCCCTTGTC GTAGGCTGTTGTGCGTGGGAAGGCGTGCCGCCAGGGAGAG|CAGT|GGGAGAGTGGTGGAGGGCGACGGGGCACTGCGCCCTTGTC ======== Event 72 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTGTAA-AAACCAAGGGTGCATTCAT-----TACCTGCAGTGCGTGGATCCCT ↓ 3 1 24 Chimp: TTTGTAA-AAACCAAGGGTGCATTAATGAATGCACCTGCAGTGCGTGGATCCCT Gorilla: GTTGTAAAAAACCAAGGGTGCATTCAT-----TACCTGCAGTGCGTGGATCCCT Human: TTTGTAA-AAACCAAGGGTGCATTCAT-----TACCTGCAGTGCGTGGATCCCT Cluster: [ ] Orangutan: GTTGTAA-AAACCAAGGGTGCATTCAT-----TACCTGCAGCACGTGGATCCCT Human > Chimp ------------- chr10:13573827-13573835 Template switch process: F1: L TCATCCCAACCACCATCATTTGTAAAAACCAAGGGTGCATT 1 F3: 4 ACCTGCAGTGCGTGGATCCCTGTGGTGCCATCATTATCAT R RF: TCATCCCAACCACCATCATTTGTAAAAACCAAGGGTGCATTCATTACCTGCAGTGCGTGGATCCCTGTGGTGCCATCATTATCAT RR: AGTAGGGTTGGTGGTAGTAAACATTTTTGGTTCCCACGTAAGTAATGGACGTCACGCACCTAGGGACACCACGGTAGTAATAGTA F2: 3 CGTAAGTAA 2 Unidirectional alignment (log-probability: -30.1) CATCCCAACCACCATCATTTGTAAAAACCAAGGGTGCATTaATgaatgcACCTGCAGTGCGTGGATCCCTGTGGTGCCATCATTATCAT CATCCCAACCACCATCATTTGTAAAAACCAAGGGTGCATTCAT-----TACCTGCAGTGCGTGGATCCCTGTGGTGCCATCATTATCAT Template switch alignment (log-probability: -16.4) CATCCCAACCACCATCATTTGTAAAAACCAAGGGTGCATT|AATGAATGC|ACCTGCAGTGCGTGGATCCCTGTGGTGCCATCATTATCAT CATCCCAACCACCATCATTTGTAAAAACCAAGGGTGCATT|AATGAATGC|ACCTGCAGTGCGTGGATCCCTGTGGTGCCATCATTATCAT ======== Event 73 ======== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGGTTGAAACCCATGGGCAGAGGCCTCCTGCCCCGAGAGCCATGTCCTCATCATCTCTGCATCCTGG ↓ 1 4 3 2 Chimp: AAGGCTGAAACCCATGGGCAGGGA---CATGCCCTGAGAGCCATGTCCTCATCATCTCTGCATCCTGG Gorilla: AAGGCTGAAACCCATGGGCAGGGGCCTCCTGCCCCGAGAGCCATCTCCTCATCATCTCTGCATCCTGG Human: AAGGTTGAAACCCATGGGCAGAGGCCTCCTGCCCCGAGAGCCATGTCCTCATCATCTCTGCATCCTGG Cluster: [ ] Orangutan: -------------------------------------------------------------------- Human > Chimp ------------- chr10:3518781-3518786 Template switch process: F1: L GAATGGAGCACAAGGTGGCCAAGGCTGAAACCCATGGGCAG 1 F3: 4 GCCCTGAGAGCCATGTCCTCATCATCTCTGCATCCTGGGTCACAG R RF: GAATGGAGCACAAGGTGGCCAAGGTTGAAACCCATGGGCAGAGGCCTCCTGCCCCGAGAGCCATGTCCTCATCATCTCTGCATCCTGGGTCACAG RR: CTTACCTCGTGTTCCACCGGTTCCAACTTTGGGTACCCGTCTCCGGAGGACGGGGCTCTCGGTACAGGAGTAGTAGAGACGTAGGACCCAGTGTC F2: 3 TACAGG 2 Unidirectional alignment (log-probability: -39.3) AATGGAGCACAAGGTGGCCAAGGcTGAAACCCATGGGCAGggacA-------TGCCCtGAGAGCCATGTCCTCATCATCTCTGCATCCTGGGT AATGGAGCACAAGGTGGCCAAGGTTGAAACCCATGGGCAG----AGGCCTCCTGCCCCGAGAGCCATGTCCTCATCATCTCTGCATCCTGGGT Template switch alignment (log-probability: -28.1) AATGGAGCACAAGGTGGCCAAGGcTGAAACCCATGGGCAG|GGACAT|GCCCtGAGAGCCATGTCCTCATCATCTCTGCATCCTGGGT AATGGAGCACAAGGTGGCCAAGGTTGAAACCCATGGGCAG|GGACAT|GCCCCGAGAGCCATGTCCTCATCATCTCTGCATCCTGGGT ======== Event 74 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGTTGCTCTCACCTAACATTAGAGCAGTTTGTAAAGACAAACTGCTCCGAGGCTCTAATTTGTAAT Chimp: TGGTTGCTCTCACCTAGCATTAGAGCGG-TGGTAAAGAAAAACTTCTCCGAGGCGCTAATTTGTAAT Gorilla: TGGTTGCTCTCACCTAACATT---------TGTCTTTACAAACTGCTCCGAGGCTCTAATTTGTAAT ↓ 1 3 4 2 Human: TGGTTGCTCTCACCTAACATTAGAGCAGTTTGTAAAGACAAACTGCTCCGAGGCTCTAATTTGTAAT Cluster: [ ] Orangutan: ------------------------------------------------------------------- Gorilla > Human --------------- chr10:3423044-3423057 Template switch process: F1: L CTGTGTCGAATATTTCACTGTGGTTGCTCTCACCTAACATTAG 1 F3: 4 ACAAACTGCTCCGAGGCTCTAATTTGTAATGATGTGCCAT R RF: CTGTGTCGAATATTTCACTGTGGTTGCTCTCACCTAACATTTGTCTTTACAAACTGCTCCGAGGCTCTAATTTGTAATGATGTGCCAT RR: GACACAGCTTATAAAGTGACACCAACGAGAGTGGATTGTAAACAGAAATGTTTGACGAGGCTCCGAGATTAAACATTACTACACGGTA F2: 3 GAAATGTTTGACGA 2 Unidirectional alignment (log-probability: -44) TGTCGAATATTTCACTGTGGTTGCTCTCACCTAACATTagagcagtttgtaaag-------ACAAACTGCTCCGAGGCTCTAATTTGTAATGATGTGCCAT TGTCGAATATTTCACTGTGGTTGCTCTCACCTAACATT----------------TGTCTTTACAAACTGCTCCGAGGCTCTAATTTGTAATGATGTGCCAT Template switch alignment (log-probability: -23.1) TGTCGAATATTTCACTGTGGTTGCTCTCACCTAACATTaG|AGCAGTTTGTAAAG|ACAAACTGCTCCGAGGCTCTAATTTGTAATGATGTGCCAT TGTCGAATATTTCACTGTGGTTGCTCTCACCTAACATTTG|AGCAGTTTGTAAAG|ACAAACTGCTCCGAGGCTCTAATTTGTAATGATGTGCCAT ======== Event 75 ======== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GGCTGCTGGGAAAGGGGAGCACCAGGCC---AGGCTTCAGGT-GGAGCGCGCAGGCCGGCG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGGGCT----GGGTGGAGGGGTGGGGCAGAGACGCTCTGCCCCATGCAGCCCCCACAGGAGCCCCTTTCTGAGCCCAGGGCTCCACAGACTTC ↓ 4 1 3 2 Chimp: ggctgcggggcctgttaggaaccaggctgcagggcaggaagtgggagggggcgggtgggcggcgaccaaactccatctgcatttacagtcgccgctgccactggcactcccacctgagccccgcctcccgtcccatcagcagctgcattccagtctcacaggagcgcgaaccctattgcgatcagcgcattccaaggatctaggccgcgtgctccttgcgagaattgaacacctgatgatctgaggtggaaacggtttcatcccgcgaccagcctccacccagccagtctgtggaaaaactgtctcccatgaaaccagtccctgggactgaaacagctgggacggctgGATGGTGTCTAAGTGTGAGATGGTCTTTCCCCACCCGCCCTCGCTAAAGAGAGTGTGGACTCTTCCTATGAGACTCTCGTTTCCGGAAGTCTGTGGAGCCCGGGGCTCAGAAAGGGGCTCCTGTGGGGGCTGCATGGGGCAGAGCGTCTCTGCCCCACCCCTCCACC--------------------------------------- Gorilla: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: GGCTGCTGGGAAAGGGGAGCACCAGGCC---AGGCTTCAGGT-GGAGCGCGCAGGCCGGCG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGGGCT----GGGTGGAGGGGTGGGGCAGAGACGCTCTGCCCCATGCAGCCCCCACAGGAGCCCCTTTCTGAGCCCAGGGCTCCACAGACTTC Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human > Chimp ------------- chr10:882762-882819 Template switch process: F1: L GG 1 F3: 4 CACC R RF: GGAGGCCAGGCTTCAGGTGGAGCGCGCAGGCCGGCGGGGGGCTGGGTGGAGGGGTGGGGCAGAGACGCTCTGCCCCATGCAGCCCCCACAGGAGCCCCTTTCTGAG RR: CCTCCGGTCCGAAGTCCACCTCGCGCGTCCGGCCGCCCCCCGACCCACCTCCCCACCCCGTCTCTGCGAGACGGGGTACGTCGGGGGTGTCCTCGGGGAAAGACTC F2: 3 CTCCCCACCCCGTCTCTGCGAGACGGGGTACGTCGGGGGTGTCCTCGGGGAAAGACTC 2 Unidirectional alignment (log-probability: -104) ggctcagaaaggggctcctgtGGGGGCT--------------------------------------------------------------GCatggggcagagcgtctctgccccacccctccacc ---------------------GGGGGCTGGGTGGAGGGGTGGGGCAGAGACGCTCTGCCCCATGCAGCCCCCACAGGAGCCCCTTTCTGAGC---------------------------------- Template switch alignment (log-probability: -20.9) GG|CTCAGAAAGGGGCTCCTGTGGGGGCTGCATGGGGCAGAGCGTCTCTGCCCCACCCCTC|CACC GG|CTCAGAAAGGGGCTCCTGTGGGGGCTGCATGGGGCAGAGCGTCTCTGCCCCACCCCTC|CACC ======== Event 76 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAGGGTATGTTAGTGGAATCAATCGTCATGGCCTTGCTTAAGGGGCTCCCTCCAggactgggccataggggcatctgag Chimp: CCAGGGTGTGTTAGTGGAATCCATCGTCATGGCCTTGCTTAAGGGGCTCCCTCCAggactggaccataggggcatctgag ↓ 1 4 3 2 Gorilla: CCAGGGTGTGTTAGTGGAATCAGTCCTCATGGCCTTGCTTAAGGGG---------------------------------- Human: CCAGGGTATGTTAGTGGAATCAATCGTCATGGCCTTGCTTAAGGGGCTCCCTCCAggactgggccataggggcatctgag Cluster: [ ] Orangutan: CCAGCGTGTGTTAGTGGAATCAATCCTCATGGCCTCGCTTCAGGGGCTCCCTCCAggactgggccagaggggcatctgag Chimp > Gorilla --------------- chr10:18074123-18074127 Template switch process: F1: L CCAGGTGCTCCCCATGTCTTCCAGGGTGTGTTAGTGGAATC 1 F3: 4 TCATGGCCTTGCTTAAGGGG R RF: CCAGGTGCTCCCTATGTCTTCCAGGGTGTGTTAGTGGAATCCATCGTCATGGCCTTGCTTAAGGGGCTCCCTCCAGGACT RR: GGTCCACGAGGGATACAGAAGGTCCCACACAATCACCTTAGGTAGCAGTACCGGAACGAATTCCCCGAGGGAGGTCCTGA F2: 3 CCTGA 2 Unidirectional alignment (log-probability: -30.8) CAGGTGCTCCCcATGTCTTCCAGGGTGTGTTAGTGGAATCagTCcTCATGGCCTTGCTTAAGGGG-------------------- CAGGTGCTCCCTATGTCTTCCAGGGTGTGTTAGTGGAATCCATCGTCATGGCCTTGCTTAAGGGGCTCCCTCCAGGACTGGACCA Template switch alignment (log-probability: -21.3) CAGGTGCTCCCcATGTCTTCCAGGGTGTGTTAGTGGAATC|AGTCC|TCATGGCCTTGCTTAAGGGG CAGGTGCTCCCTATGTCTTCCAGGGTGTGTTAGTGGAATC|AGTCC|TCATGGCCTTGCTTAAGGGG ======== Event 77 ======== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCTGTGAGAATTCAAAAACATGTCAACCTTGTTTAAATGGCATTGCGTAGTGTGCTGACTTTTTAATAAC ↓ 1 4 3 2 Chimp: GTCTGTGAGAATTCAAAAACAC-------TACGCAAAAAGGCATTGCGTAGTGTGCTGACTTTTTAATAAC ↑ 1 4 3 2 Gorilla: GTCTGTGAGAATTCAAAAACATGTCAACCTTGTTTAAATGGCATTGCGTAGTGTGCTGACTTTTTAATAAC Human: GTCTGTGAGAATTCAAAAACATGTCAACCTTGTTTAAATGGCATTGCGTAGTGTGCTGACTTTTTAATAAC Cluster: [ ] Orangutan: GTCTGTTAGAATTCAAAAACATGTCAACCTTGTTTAAATGGAATTGCGTAGTATGCTGACTTTTTAATAAC Human > Chimp ------------- chr10:18517187-18517193 Template switch process: F1: L CTTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACA 1 F3: 4 AAAAGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGGGCTG R RF: CTTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACATGTCAACCTTGTTTAAATGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGGGCTG RR: GAAAGTTACTACAAAAGATACAGACACTCTTAAGTTTTTGTACAGTTGGAACAAATTTACCGTAACGCATCACACGACTGAAAAATTATTGGACCCGAC F2: 3 ACGCATC 2 Unidirectional alignment (log-probability: -37.9) TTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACA------------------ctacgcaaaaaGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG TTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACATGTCAACCTTGTTTAAAT-----------GGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG Template switch alignment (log-probability: -22.2) TTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACA|CTACGCA|AAAaGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG TTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACA|CTACGCA|AAATGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG Gorilla > Chimp --------------- chr10:18517187-18517193 Template switch process: F1: L CTTTCAATGATGTTTTCTATGTCTGTGAGAATTCAAAAACA 1 F3: 4 AAAAGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGGGCTG R RF: CTTTCAATGATGTTTTCTTTGTCTGTGAGAATTCAAAAACATGTCAACCTTGTTTAAATGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGGGCTG RR: GAAAGTTACTACAAAAGAAACAGACACTCTTAAGTTTTTGTACAGTTGGAACAAATTTACCGTAACGCATCACACGACTGAAAAATTATTGGACCCGAC F2: 3 ACGCATC 2 Unidirectional alignment (log-probability: -42.5) TTTCAATGATGTTTTCTaTGTCTGTGAGAATTCAAAAACA--------------ctacgcaAAAaGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG TTTCAATGATGTTTTCTTTGTCTGTGAGAATTCAAAAACATGTCAACCTTGTTT-------AAATGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG Template switch alignment (log-probability: -27.8) TTTCAATGATGTTTTCTaTGTCTGTGAGAATTCAAAAACA|CTACGCA|AAAaGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG TTTCAATGATGTTTTCTTTGTCTGTGAGAATTCAAAAACA|CTACGCA|AAATGGCATTGCGTAGTGTGCTGACTTTTTAATAACCTGG ======== Event 78 ======== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCCCTCCTAAGTGAAGAGAAGTCAGATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT ↑ 1 4 3 2 Chimp: CTCCCTCCTAAGTGAAGAGAA-AAGGATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT Gorilla: CTCCCTCCTAAGTGAAGAGAA-AAGGATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT Human: CTCCCTCCTAAGTGAAGAGAAGTCAGATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT Cluster: [ ] Orangutan: CTCCCTCCTAAGTGAAGAGAA-AAGGATCAGGCTACTGTTCTGACGTGCACACCTCCTCTTCTGT Chimp > Human ------------- chr10:120086334-120086337 Template switch process: F1: L CCTGCTCCCTAGCTCACCCCCTCCCTCCTAAGTGAAGAGAA 1 F3: 4 GATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT R RF: CCTGCTCCCTAGCTCACCCCCTCCCTCCTAAGTGAAGAGAAAAGGATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT RR: GGACGAGGGATCGAGTGGGGGAGGGAGGATTCACTTCTCTTTTCCTAGTCCGATGACAAGACTGTACGTGTGGAAGAGAAGACA F2: 3 ACTG 2 Unidirectional alignment (log-probability: -25.6) CTGCTCCCTAGCTCACCCCCTCCCTCCTAAGTGAAGAGAAgtcA--GATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT CTGCTCCCTAGCTCACCCCCTCCCTCCTAAGTGAAGAGAA---AAGGATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT Template switch alignment (log-probability: -15.8) CTGCTCCCTAGCTCACCCCCTCCCTCCTAAGTGAAGAGAA|GTCA|GATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT CTGCTCCCTAGCTCACCCCCTCCCTCCTAAGTGAAGAGAA|GTCA|GATCAGGCTACTGTTCTGACATGCACACCTTCTCTTCTGT ======== Event 79 ======== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: ACCACTGCCTTTTGACCCTGTATTTTAAGCCCAAGGAGAAAAAGAAAAACATTTTGTTAGTTAAATG ↓ 13 24 ↑ 13 24 Chimp: ACCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAATAAACATTTTGTTAGTTAAATG Gorilla: ACCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAACAAACATTTTGTTAGTTAAATG ↓ 31 2 4 ↑ 1 3 42 Human: ACCACTGCCTTTTGACCCTGTATTTTAAGCCCAAGGAGAAAAAGAAAAACATTTTGTTAGTTAAATG Cluster: [ ] Orangutan: ATCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAATAAACATTTTGTTAGTTAAATG Chimp > Human ------------- chr10:118010376-118010400 Template switch process: F1: L TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT 1 F3: 4 AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG R RF: TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAATAAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG RR: ACAAAAGATAATAGACTACATGGTGACGGAAAACTGGGACAAAGAAAAAGAGGAACCCGAATTTTATTTGTAAAACAATCAATTTACGGAGTAAACAATTTAAGTC F2: 3 AAGAAAAAGAGGAACCCGAATTTTA 2 Unidirectional alignment (log-probability: -55.4) GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT-----------------------ATtttaagcccaaggagaaaaagaaAAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAAT-----------------------AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG Template switch alignment (log-probability: -18.4) GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT|ATTTTAAGCCCAAGGAGAAAAAGAA|AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT|ATTTTAAGCCCAAGGAGAAAAAGAA|AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG Human > Chimp ------------- chr10:119357653-119357677 Template switch process: F1: L TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT 1 F3: 4 AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG R RF: TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTATTTTAAGCCCAAGGAGAAAAAGAAAAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG RR: ACAAAAGATAATAGACTACATGGTGACGGAAAACTGGGACATAAAATTCGGGTTCCTCTTTTTCTTTTTGTAAAACAATCAATTTACGGAGTAAACAATTTAAGTC F2: 3 TAAAATTCGGGTTCCTCTTTTTCTT 2 Unidirectional alignment (log-probability: -55.4) GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTttctttttctccttgggcttaaaAT-----------------------AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT-----------------------ATTTTAAGCCCAAGGAGAAAAAGAAAAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG Template switch alignment (log-probability: -18.4) GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT|TTCTTTTTCTCCTTGGGCTTAAAAT|AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT|TTCTTTTTCTCCTTGGGCTTAAAAT|AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG Gorilla > Human --------------- chr10:118010378-118010400 Template switch process: F1: L TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTAT 1 F3: 4 AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG R RF: TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAACAAACATTTTGTTAGTTAAATGCCTTATTTGTTAAATTCAG RR: ACAAAAGATAATAGACTACATGGTGACGGAAAACTGGGACAAAGAAAAAGAGGAACCCGAATTTTGTTTGTAAAACAATCAATTTACGGAATAAACAATTTAAGTC F2: 3 AAGAAAAAGAGGAACCCGAATTT 2 Unidirectional alignment (log-probability: -63.4) TTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT-------------------------attttaagcccaaggagaaaaagaaAAACATTTTGTTAGTTAAATGCCTcATTTGTTAAATTCAG TTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTTTCTTTTTCTCCTTGGGCTTAAAAC-------------------------AAACATTTTGTTAGTTAAATGCCTTATTTGTTAAATTCAG Template switch alignment (log-probability: -29.7) TTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTaT|TTTAAGCCCAAGGAGAAAAAGAA|AAACATTTTGTTAGTTAAATGCCTcATTTGTTAAATTCAG TTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTTT|TTTAAGCCCAAGGAGAAAAAGAA|AAACATTTTGTTAGTTAAATGCCTTATTTGTTAAATTCAG Human > Gorilla --------------- chr10:132616502-132616524 Template switch process: F1: L TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT 1 F3: 4 ACAAACATTTTGTTAGTTAAATGCCTTATTTGTTAAATTCAG R RF: TGTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTATTTTAAGCCCAAGGAGAAAAAGAAAAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTCAG RR: ACAAAAGATAATAGACTACATGGTGACGGAAAACTGGGACATAAAATTCGGGTTCCTCTTTTTCTTTTTGTAAAACAATCAATTTACGGAGTAAACAATTTAAGTC F2: 3 AAATTCGGGTTCCTCTTTTTCTT 2 Unidirectional alignment (log-probability: -63.4) GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT-------------------------ttctttttctccttgggcttaaaacAAACATTTTGTTAGTTAAATGCCTtATTTGTTAAATTC GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGTATTTTAAGCCCAAGGAGAAAAAGAA-------------------------AAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTC Template switch alignment (log-probability: -29.7) GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT|TTCTTTTTCTCCTTGGGCTTAAA|AcAAACATTTTGTTAGTTAAATGCCTtATTTGTTAAATTC GTTTTCTATTATCTGATGTACCACTGCCTTTTGACCCTGT|TTCTTTTTCTCCTTGGGCTTAAA|AAAAACATTTTGTTAGTTAAATGCCTCATTTGTTAAATTC ======== Event 80 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCTATTAAGCCTTCCAAAAACAAAATGATCATAATGTGTATAGAT---------------------------------------------------------------TATCATATGATTCAATGACCATTTGCCAGATAATTGCCTTGA Chimp: ATTCTATTAAGCCTTCCAAAAACAAAATGATCATAATATGTATAGATTAGCATATGATTCAATGACCATATGCTAATCTATACATATTATGATCATTTTGTTTTATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAATTGCCTTGA ↑ 3 4 2 1 Gorilla: ATTCTATTAAGCCTTCCAAAAACAAAATCATCATAATATGTATAGAT---------------------------------------------------------------TAGCATATGATTCAATGACCATTTGCCAGAGAATTGCCTTGA Human: ATTCTATTAAGCCTTCCAAAAACAAAATGATCATAATGTGTATAGAT---------------------------------------------------------------TATCATATGATTCAATGACCATTTGCCAGATAATTGCCTTGA Cluster: [ ] Orangutan: ATTCTATTAAGACTTCCAAAAACAAAATGATCATATTATGTATAGAT---------------------------------------------------------------TATCATATGATTCAATGACCATTTGCCAGAGAATTGCCTTGA Gorilla > Chimp --------------- chr10:16363164-16363197 Template switch process: F1: L TTAAGCCTTCCAAAAACAAAATGATCATAATATGTATAGATTAGCATATGATTCAATGACCAT 1 F3: 4 TATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAATTGCCTT R RF: TTAAGCCTTCCAAAAACAAAATCATCATAATATGTATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAATTGCCTT RR: AATTCGGAAGGTTTTTGTTTTAGTAGTATTATACATATCTAATCGTATACTAAGTTACTGGTAAACGGTCTCTTAACGGAA F2: 3 TTTGTTTTACTAGTATTATACATATCTAATCGTA 2 Unidirectional alignment (log-probability: -107) ATCATAATATGtatagattagcatatgattcaatgaccatatgctaatctatacatattatgatcattttgtttTATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAA ATCATAATATG---------------------------------------------------------------TATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAA Template switch alignment (log-probability: -31.7) ATCATAATATGTATAGATTAGCATATGATTCAATGACCAT|ATGCTAATCTATACATATTATGATcATTTTGTTT|TATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAA ATCATAATATGTATAGATTAGCATATGATTCAATGACCAT|ATGCTAATCTATACATATTATGATGATTTTGTTT|TATAGATTAGCATATGATTCAATGACCATTTGCCAGAGAA ======== Event 81 ======== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: ggtgcagcccgatggattcgctgatggattggatgtgggtgtagaacagagataagccgaaggctgTGAGGTCAGCGTGGTTTTGGGGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGTGCAGAGATGGAGGAGCGGCTGGGCAAAGGCATGGA Chimp: Gorilla: GGTGCAGCCCGATggattcgctgatggattggacatgggtgtggaacagagataagccgaaggctgTGAGGTCAGCGTGGTTTTGGGGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGTTCAGCGATGGAGGAACGGCTGGGCAAAGGCATGGA ↑ 3 2 1 4 Human: ggtgcagcccgatggattcgctgatggattggatgtgggtgtagaacagagataagccgaaggctgTGAGGTCAGCGTGGTTTTGGGGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGTGCAGAGATGGAGGAGCGGCTGGGCAAAGGCATGGA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr10:148353022-148353026 Template switch process: F1: L GGGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGT 1 F3: 4 GATGGAGGAACGGCTGGGCAAAGGCATGGACACAGGCGTGTGGAGCAGGG R RF: GCTGATGGATTGGATGTGGGTGTAGAACAGAGATAAGCCGAAGGCTGTGAGGTCAGCGTGGTTTTGGGGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGTGCAGAGATGGAGGAGCGGCTGGGCAAAGGCATGGACACAGGCGTGTGGAGCAGGG RR: CGACTACCTAACCTACACCCACATCTTGTCTCTATTCGGCTTCCGACACTCCAGTCGCACCAAAACCCCCGACCCCCTTCAGCCTTCATTCCAAAACCCCACGTTCACGTCTCTACCTCCTCGCCGACCCGTTTCCGTACCTGTGTCCGCACACCTCGTCCC F2: 3 CGACT 2 Unidirectional alignment (log-probability: -46) GGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGTtCAGcGATGGAGGAaCGGCTGGGCAAAGGCATGGACACAGgcgtg GGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGTGCAGAGATGGAGGAGCGGCTGGGCAAAGGCATGGACACAG----- Template switch alignment (log-probability: -22.1) GGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGT|TCAGC|GATGGAGGAaCGGCTGGGCAAAGGCATGGACACAGGCGTG GGGCTGGGGGAAGTCGGAAGTAAGGTTTTGGGGTGCAAGT|TCAGC|GATGGAGGAGCGGCTGGGCAAAGGCATGGACACAGGCGTG ======== Event 82 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCTCTTACCTACTTATACCAGTATACTAAGATGTATACTACCATCTTAGTATACTGGTAGTTTTATCACAATAG Chimp: TCCTCTTACCTGCTTATACCAGTATACTAAGATGTATACTACCATCTTAGTATACTGGTAGTTTTATCACAATAG ↑ 1 4 3 2 Gorilla: TCCTCTTACCTACTTATACCAATA------------TACTACCATCTTAGTATACTGGTAGTTTTATCACAGTAG ↓ 1 4 3 2 Human: TCCTCTTACCTACTTATACCAGTATACTAAGATGTATACTACCATCTTAGTATACTGGTAGTTTTATCACAATAG Cluster: [ ] Orangutan: tcctcttacctacttataccagta------------tactaccatcttagtatactggtagttttatcacaatag Gorilla > Human --------------- chr10:116685999-116686011 Template switch process: F1: L AAACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCA 1 F3: 4 TATACTACCATCTTAGTATACTGGTAGTTTTATCACAATAGG R RF: AAACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCAATATACTACCATCTTAGTATACTGGTAGTTTTATCACAGTAGG RR: TTTGTCACGACGCCATCTGTAGGAGAATGGATGAATATGGTTATATGATGGTAGAATCATATGACCATCAAAATAGTGTCATCC F2: 3 GTAGAATCATATG 2 Unidirectional alignment (log-probability: -39.2) AACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCAgtatactaagatgTATACTACCATCTTAGTATACTGGTAGTTTTATCACAaTA AACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCA------------ATATACTACCATCTTAGTATACTGGTAGTTTTATCACAGTA Template switch alignment (log-probability: -23) AACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCA|GTATACTAAGATG|TATACTACCATCTTAGTATACTGGTAGTTTTATCACAaTA AACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCA|GTATACTAAGATG|TATACTACCATCTTAGTATACTGGTAGTTTTATCACAGTA Gorilla > Chimp --------------- chr10:118021159-118021171 Template switch process: F1: L AAACAGTGCTGCGGTAGACATCCTCTTACCTGCTTATACCA 1 F3: 4 TATACTACCATCTTAGTATACTGGTAGTTTTATCACAATAGG R RF: AAACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCAATATACTACCATCTTAGTATACTGGTAGTTTTATCACAGTAGG RR: TTTGTCACGACGCCATCTGTAGGAGAATGGATGAATATGGTTATATGATGGTAGAATCATATGACCATCAAAATAGTGTCATCC F2: 3 GTAGAATCATATG 2 Unidirectional alignment (log-probability: -44.7) AACAGTGCTGCGGTAGACATCCTCTTACCTgCTTATACCAgtatactaagatgTATACTACCATCTTAGTATACTGGTAGTTTTATCACAaTA AACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCA------------ATATACTACCATCTTAGTATACTGGTAGTTTTATCACAGTA Template switch alignment (log-probability: -28.5) AACAGTGCTGCGGTAGACATCCTCTTACCTgCTTATACCA|GTATACTAAGATG|TATACTACCATCTTAGTATACTGGTAGTTTTATCACAaTA AACAGTGCTGCGGTAGACATCCTCTTACCTACTTATACCA|GTATACTAAGATG|TATACTACCATCTTAGTATACTGGTAGTTTTATCACAGTA ======== Event 83 ======== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCCAAAGTAATATGGTTTCCAAGGAGTACAGAAACCTTACAGAACCAAAATAAAAGCATGTAttttttt--ttAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTCGGGCAATACAAGCCCTCTTTTTTTAAGCAGCACAAACATAAGTTTTCACATGAACTCAATTTAACTGCTAGTTAATG ↑ 1 4 3 2 Chimp: CCCAAAGTAATATGGTTTCCA-AGAGTATCGAAACCTTACAGAACCAAAATAAAAGCATGTAtt--ttt--ttAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTTGAGCAATACAAGCCCTCtttttttAAGCAGCACAAACAAAAGTTTTCACATGAACTCAATTTAACTGCTAGTTAATG ↓ 1 4 3 2 Gorilla: CCCAAAGTAATATGGTTTCCAAGGAGTACAGAAACCTTACAGAACCAAAATAAAAGCATGTAttttttt--ttAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTTGGGCAATACAAGCCCTCtttttttAAGCAGCACAAATATAAGTTTTCACATGAACTCAATTTAACTGCTAGTTAATG Human: CCCAAAGTAATATGGTTTCCAAGGAGTACAGAAACCTTACAGAACCAAAATAAAAGCATGTAttttttt--ttAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTCGGGCAATACAAGCCCTCTTTTTTTAAGCAGCACAAACATAAGTTTTCACATGAACTCAATTTAACTGCTAGTTAATG Cluster: [ ] Orangutan: CCCAAAGTAATACGGTTTCCAAGGAGTACAGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTAAAAAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTTGGGCAATACAAGCCCTCTTTTTTTAAGCAGCAGAAACATAAGTTTTCACATGAACTCAATTTAACTGCTAGTTAATG Chimp > Human ------------- chr10:117936113-117936119 Template switch process: F1: L TAACTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAG 1 F3: 4 GAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTT R RF: TAACTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAGAGTATCGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTTGAGCAATACAAGCCCTCTTTTTTTAAGCAGCACAAACAAAAGTTTTCACATGAACTC RR: ATTGATAACGTAATGACGTAGGGTTTCATTATACCAAAGGTTCTCATAGCTTTGGAATGTCTTGGTTTTATTTTCGTACATAAAAAAATTTAGTCTAAAACGGGAAAGCAAAATTTAAGTTTCGAACTCGTTATGTTCGGGAGAAAAAAATTCGTCGTGTTTGTTTTCAAAAGTGTACTTGAG F2: 3 ACATGAG 2 Unidirectional alignment (log-probability: -34.5) CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAgGAGTAcaGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTtt CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAA-GAGTATCGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTT-- Template switch alignment (log-probability: -28.2) CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAG|GAGTaCA|GAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTt CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAG|GAGTTCA|GAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTA Chimp > Gorilla --------------- chr10:132541539-132541545 Template switch process: F1: L TAACTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAG 1 F3: 4 GAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTT R RF: TAACTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAGAGTATCGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTAAATCAGATTTTGCCCTTTCGTTTTAAATTCAAAGCTTGAGCAATACAAGCCCTCTTTTTTTAAGCAGCACAAACAAAAGTTTTCACATGAACTC RR: ATTGATAACGTAATGACGTAGGGTTTCATTATACCAAAGGTTCTCATAGCTTTGGAATGTCTTGGTTTTATTTTCGTACATAAAAAAATTTAGTCTAAAACGGGAAAGCAAAATTTAAGTTTCGAACTCGTTATGTTCGGGAGAAAAAAATTCGTCGTGTTTGTTTTCAAAAGTGTACTTGAG F2: 3 ACATGAG 2 Unidirectional alignment (log-probability: -33.1) CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAgGAGTAcaGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTtt CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAA-GAGTATCGAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTT-- Template switch alignment (log-probability: -27.7) CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAG|GAGTaCA|GAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTt CTATTGCATTACTGCATCCCAAAGTAATATGGTTTCCAAG|GAGTTCA|GAAACCTTACAGAACCAAAATAAAAGCATGTATTTTTTTA ======== Event 84 ======== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTTTCATGCCCTGGGTTCTGCCCGCACAGACTG------------------------TGA-----GGGCAGAGGAAGTGAGGAAGTAAGAT Chimp: ATTTTCATGCCCTGGGTTCTGCCCGCACAGACTG------------------------TGA-----GGGCAGAGGAAGTGAGGAAGTAAGAT ↑ 3 2 1 4 Gorilla: ATTTTCATGCCCTGGGTTCTGCCCGCACAGACTCCCATCTCTGTAACTTCCTGGAGAGTGAATTCCTAGATGAGGAAGTGAGGAAATAAGAT ↓ 3 2 1 4 Human: ATTTTCATGCCCTGGGTTCTGCCCGCACAGACTG------------------------TGA-----GGGCAGAGGAAGTGAGGAAGTAAGAT Cluster: [ ] Orangutan: ATTTTCATGCCCTGGGTTCTGCCCACACAGACACCCATCTCTGTGACTTCCTGGAGAGTGAATTCCTAGATGAGGAAGTGAGGAAGTAAGAT Gorilla > Human --------------- chr10:117725878-117725886 Template switch process: F1: L CCTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACT 1 F3: 4 GAGGAAGTGAGGAAGTAAGATTCATCAAGGAGATAGGTGG R RF: CCTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACTCCCATCTCTGTAACTTCCTGGAGAGTGAATTCCTAGATGAGGAAGTGAGGAAATAAGATTCATCAAGGAGATAGGTGG RR: GGAAAAACTAAAAGTACGGGACCCAAGACGGGCGTGTCTGAGGGTAGAGACATTGAAGGACCTCTCACTTAAGGATCTACTCCTTCACTCCTTTATTCTAAGTAGTTCCTCTATCCACC F2: 3 ACGGGAGTG 2 Unidirectional alignment (log-probability: -41) CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGAC--------------------------------------TgtgagggcaGAGGAAGTGAGGAAgTAAGATTCATCAAGGAGATAGGTGG CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACTCCCATCTCTGTAACTTCCTGGAGAGTGAATTCCTAGAT---------GAGGAAGTGAGGAAATAAGATTCATCAAGGAGATAGGTGG Template switch alignment (log-probability: -27.9) CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACT|GTGaGGGCA|GAGGAAGTGAGGAAgTAAGATTCATCAAGGAGATAGGTGG CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACT|GTGCGGGCA|GAGGAAGTGAGGAAATAAGATTCATCAAGGAGATAGGTGG Gorilla > Chimp --------------- chr10:119070090-119070098 Template switch process: F1: L CCTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACT 1 F3: 4 GAGGAAGTGAGGAAGTAAGATTCATCAAGGAGATAGGTGG R RF: CCTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACTCCCATCTCTGTAACTTCCTGGAGAGTGAATTCCTAGATGAGGAAGTGAGGAAATAAGATTCATCAAGGAGATAGGTGG RR: GGAAAAACTAAAAGTACGGGACCCAAGACGGGCGTGTCTGAGGGTAGAGACATTGAAGGACCTCTCACTTAAGGATCTACTCCTTCACTCCTTTATTCTAAGTAGTTCCTCTATCCACC F2: 3 ACGGGAGTG 2 Unidirectional alignment (log-probability: -41) CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGAC--------------------------------------TgtgagggcaGAGGAAGTGAGGAAgTAAGATTCATCAAGGAGATAGGTGG CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACTCCCATCTCTGTAACTTCCTGGAGAGTGAATTCCTAGAT---------GAGGAAGTGAGGAAATAAGATTCATCAAGGAGATAGGTGG Template switch alignment (log-probability: -27.9) CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACT|GTGaGGGCA|GAGGAAGTGAGGAAgTAAGATTCATCAAGGAGATAGGTGG CTTTTTGATTTTCATGCCCTGGGTTCTGCCCGCACAGACT|GTGCGGGCA|GAGGAAGTGAGGAAATAAGATTCATCAAGGAGATAGGTGG ======== Event 85 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGATGAAAATCATCCCCACCC----------------------------------------------------------------------------------------------------CAGGTTGTTGGAGACACTGATCCAAACCGGTGGTGATCGTGATGCATTCGAAGGCTTGCTAGTAAGTCAATGCCTTTGAACCCGG Chimp: --AAGAAAATCATCCCCACCC--------------------------CGGGTTGTTGGAGACACTGATCCAAACCGGTGGTGATCTTACTAGCAAGCCTTCGAATGCATCACGATCACCACCGGGTTGTTGGAGACACTGATCCAAACCGGTGGTGATCGTGATGCATTCGAAGGCTTGCTAGTAAGTCAATGCCTTTGAACCCGG ↑ 4 3 1 2 Gorilla: GGAAGAAAATCATCCCCACCC----------------------------------------------------------------------------------------------------CGGGTTGTTGGAGACACTGGTCCAAACCGGTGGTGATCGTGATGCATTCGAAGGCTTGCTAGTAAGTCAATGCCTTTGAACCCGG Human: GGATGAAAATCATCCCCACCC----------------------------------------------------------------------------------------------------CAGGTTGTTGGAGACACTGATCCAAACCGGTGGTGATCGTGATGCATTCGAAGGCTTGCTAGTAAGTCAATGCCTTTGAACCCGG Cluster: [ ] Orangutan: GAAAGAAAATCATCCCCACCCCCGGTTGTTGGAGACACTGATCCAAA----------------------------------------------------------------------------------------------------CTGGTGGTGATCGTGATGCACTTGAAGGCTTGCTAGTAAGTCAATGCCTTTGAACCCAG Gorilla > Chimp --------------- chr10:2012676-2012710 Template switch process: F1: L TGTGACAGTGAAGAAAAT---GAAGAAAATCATCCCCACCCCGGGTTGTTGGAGACACTGATCCAAACCGGTGGTGATC 1 F3: 4 CCGGGTTGTTGGAGACACTGATCCAAACCGGTGGTGATCGT R RF: TGTGACAGTGAAGAAAATGAGGAAGAAAATCATCCCCACCCCGGGTTGTTGGAGACACTGGTCCAAACCGGTGGTGATCGTGATGCATTCGAAGGCTTGCTAGTAA RR: ACACTGTCACTTCTTTTACTCCTTCTTTTAGTAGGGGTGGGGCCCAACAACCTCTGTGACCAGGTTTGGCCACCACTAGCACTACGTAAGCTTCCGAACGATCATT F2: 3 ACCACTAGCACTACGTAAGCTTCCGAACGATCATT 2 Unidirectional alignment (log-probability: -133) CccgggttgttggagacactgatccaaaccggtggtgatcttactagcaagccttcgaatgcatcacgatcaccaCCGGGTTGTTGGAGACACTGaTCCAAACCGGTGGTGATCG C--------------------------------------------------------------------------CCGGGTTGTTGGAGACACTGGTCCAAACCGGTGGTGATCG Template switch alignment (log-probability: -41.9) CCCGGGTTGTTGGAGACACTGaTCCAAACCGGTGGTGATC|TTACTAGCAAGCCTTCGAATGCATCACGATCACCA|CCGGGTTGTTGGAGACACTGaTCCAAACCGGTGGTGATCG CCCGGGTTGTTGGAGACACTGGTCCAAACCGGTGGTGATC|TTACTAGCAAGCCTTCGAATGCATCACGATCACCA|CCGGGTTGTTGGAGACACTGGTCCAAACCGGTGGTGATCG ======== Event 86 ======== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GAGTTACCTTTATTCACATAATT------------------------------------------AAAAATTGTTTTCAGAtttcttttatctttaattttt ↓ 4 13 2 Chimp: GAGTTACCTTTATTCACATAATT---------------------AAAAATTATGTGAAAACAATTAAAAATTGTTTTCAGATTTCttttatctttgattttt Gorilla: GAGTTACCTTTATTCACATAATTAAAAATTATGTGAAAACAATT---------------------AAAAATTGTTTTCAGATTTCttttatctttgattttt ↑ 4 13 2 Human: GAGTTACCTTTATTCACATAATT------------------------------------------AAAAATTGTTTTCAGAtttcttttatctttaattttt Cluster: [ ] Orangutan: GATTTACCTTTATTCATATAATT------------------------------------------AAAAATTGTTTTCAGATTTCTTTTATGTTTGAttttt Human > Chimp ------------- chr10:22351215-22351224 Template switch process: F1: L TTATTTCTGCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATT 1 F3: 4 AATTAAAAATTGTTTTCAGATTTCTTTTATCTTTGATTTTTTTT R RF: TTATTTCTGCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATTGTTTTCAGATTTCTTTTATCTTTAATTTTTTTT RR: AATAAAGACGGTGGACCTCTCAATGGAAATAAGTGTATTAATTTTTAACAAAAGTCTAAAGAAAATAGAAATTAAAAAAAA F2: 3 CAAAAGTGTA 2 Unidirectional alignment (log-probability: -55.7) GCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAAttatgtgaaaacaattaaaaaTTGTTTTCAGATTTCTTTTATCTTTgATTTT GCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAA---------------------TTGTTTTCAGATTTCTTTTATCTTTAATTTT Template switch alignment (log-probability: -28.7) GCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATT|ATgTGAAAAC|AATTAAAAATTGTTTTCAGATTTCTTTTATCTTTgATTTT GCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATT|ATCTGAAAAC|AATTAAAAATTGTTTTCAGATTTCTTTTATCTTTAATTTT Human > Gorilla --------------- chr10:24372273-24372282 Template switch process: F1: L TTATTTCTGCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATT 1 F3: 4 AATTAAAAATTGTTTTCAGATTTCTTTTATCTTTGATTTTTTTT R RF: TTATTTCTGCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATTGTTTTCAGATTTCTTTTATCTTTAATTTTTTTT RR: AATAAAGACGGTGGACCTCTCAATGGAAATAAGTGTATTAATTTTTAACAAAAGTCTAAAGAAAATAGAAATTAAAAAAAA F2: 3 CAAAAGTGTA 2 Unidirectional alignment (log-probability: -54.8) GCCACCTGGAGAGTTACCTTTATTCACATAAttaaaaattatgtgaaaacaaTTAAAAATTGTTTTCAGATTTCTTTTATCTTTgATTTT GCCACCTGGAGAGTTACCTTTATTCACATAA---------------------TTAAAAATTGTTTTCAGATTTCTTTTATCTTTAATTTT Template switch alignment (log-probability: -28.3) GCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATT|ATgTGAAAAC|AATTAAAAATTGTTTTCAGATTTCTTTTATCTTTgATTTT GCCACCTGGAGAGTTACCTTTATTCACATAATTAAAAATT|ATCTGAAAAC|AATTAAAAATTGTTTTCAGATTTCTTTTATCTTTAATTTT ======== Event 87 ======== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AACACAGAAAATCTCAGTTAAC---CTAAA-------ATGTCTGCAATGTGGGGTGTTCTG Chimp: AACACAAAAAATCTCAGTTAAA---CTAAA-------ATGTCTGCAATGTGGGGTGTTCTG ↑ 1 3 4 Gorilla: AACACAGAAAATCTCAGTTAACCATTTTAGGTCATTTTAGTCTGCAATGTGGGGTGTTCTG Human: AACACAGAAAATCTCAGTTAAC---CTAAA-------ATGTCTGCAATGTGGGGTGTTCTG Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr10:114186686-114186694 Template switch process: F1: L GCTACATTAGTTCTCATGCAAACACAAAAAATCTCAGTTAA 1 F3: 4 TCTGCAATGTGGGGTGTTCTGGTAAACCAATTATTATAT R RF: GCTACATTAGTTCTCATGCAAACACAGAAAATCTCAGTTAACCATTTTAGGTCATTTTAGTCTGCAATGTGGGGTGTTCTGGTAAACCAATTATTATAT RR: CGATGTAATCAAGAGTACGTTTGTGTCTTTTAGAGTCAATTGGTAAAATCCAGTAAAATCAGACGTTACACCCCACAAGACCATTTGGTTAATAATATA F2: 3 GTAAAATCA 2 Unidirectional alignment (log-probability: -37.1) CTACATTAGTTCTCATGCAAACACAaAAAATCTCAGTTAA-----------------ActaaaatGTCTGCAATGTGGGGTGTTCTGGTAAACCAATTATTATAT CTACATTAGTTCTCATGCAAACACAGAAAATCTCAGTTAACCATTTTAGGTCATTTTA-------GTCTGCAATGTGGGGTGTTCTGGTAAACCAATTATTATAT Template switch alignment (log-probability: -22.4) CTACATTAGTTCTCATGCAAACACAaAAAATCTCAGTTAA|ACTAAAATG|TCTGCAATGTGGGGTGTTCTGGTAAACCAATTATTATAT CTACATTAGTTCTCATGCAAACACAGAAAATCTCAGTTAA|ACTAAAATG|TCTGCAATGTGGGGTGTTCTGGTAAACCAATTATTATAT ======== Event 88 ======== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AACTCCAGTACTGTAGATAAT---TTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTC Chimp: AACTCCAGTACTGTAGATAAT---TTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTC ↓ 13 24 ↑ 13 24 Gorilla: AACTCCAGTACTGTAGATAATCAGATTTCAGTTTTAA---AAATTATCACGGGGTATGCTCTC ↓ 13 24 ↑ 13 24 Human: AACTCCAGTACTGTAGATAAT---TTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTC Cluster: [ ] Orangutan: AGCTCCAGTACTGTAGATAATCAGATTTCAGTTTAAA---AAATTATCACAGGGTATG----T Gorilla > Human --------------- chr10:133552608-133552625 Template switch process: F1: L ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT 1 F3: 4 ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA R RF: ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATCAGATTTCAGTTTTAAAAATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA RR: TGAAGATAAGAGGAAATTAGTTGAGGTCATGACATCTATTAGTCTAAAGTCAAAATTTTTAATAGTGCCCCATACGAGAGACTAGATGTTTTTTAT F2: 3 GTCTAAAGTCAAATTTTT 2 Unidirectional alignment (log-probability: -48) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT----------TTTTtAAActgaaatctgATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA--- CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATCAGATTTCAGTTTTAAAA----------ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA Template switch alignment (log-probability: -23.5) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|TTTTtAAACTGAAATCTG|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|TTTTAAAACTGAAATCTG|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA Human > Gorilla --------------- chr10:148434849-148434866 Template switch process: F1: L ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT 1 F3: 4 ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA R RF: ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATTTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA RR: TGAAGATAAGAGGAAATTAGTTGAGGTCATGACATCTATTAAAAAATTTGACTTTAGACTAATAGTGCCCCATACGAGAGACTAGATGTTTTTTATTTT F2: 3 AAAATTTTGACTTTAGAC 2 Unidirectional alignment (log-probability: -52.2) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATcagatttcagTTTTaAAA----------ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAaaa CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT----------TTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA--- Template switch alignment (log-probability: -23.5) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|CAGATTTCAGTTTtAAAA|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|CAGATTTCAGTTTAAAAA|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA Gorilla > Chimp --------------- chr10:135700817-135700834 Template switch process: F1: L ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT 1 F3: 4 ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA R RF: ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATCAGATTTCAGTTTTAAAAATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA RR: TGAAGATAAGAGGAAATTAGTTGAGGTCATGACATCTATTAGTCTAAAGTCAAAATTTTTAATAGTGCCCCATACGAGAGACTAGATGTTTTTTAT F2: 3 GTCTAAAGTCAAATTTTT 2 Unidirectional alignment (log-probability: -48) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT----------TTTTtAAActgaaatctgATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA--- CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATCAGATTTCAGTTTTAAAA----------ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA Template switch alignment (log-probability: -23.5) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|TTTTtAAACTGAAATCTG|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|TTTTAAAACTGAAATCTG|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA Chimp > Gorilla --------------- chr10:148434849-148434866 Template switch process: F1: L ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT 1 F3: 4 ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA R RF: ACTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATTTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA RR: TGAAGATAAGAGGAAATTAGTTGAGGTCATGACATCTATTAAAAAATTTGACTTTAGACTAATAGTGCCCCATACGAGAGACTAGATGTTTTTTATTTT F2: 3 AAAATTTTGACTTTAGAC 2 Unidirectional alignment (log-probability: -52.2) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAATcagatttcagTTTTaAAA----------ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAaaa CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT----------TTTTTAAACTGAAATCTGATTATCACGGGGTATGCTCTCTGATCTACAAAAAATA--- Template switch alignment (log-probability: -23.5) CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|CAGATTTCAGTTTtAAAA|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA CTTCTATTCTCCTTTAATCAACTCCAGTACTGTAGATAAT|CAGATTTCAGTTTAAAAA|ATTATCACGGGGTATGCTCTCTGATCTACAAAAAATAAAA ======== Event 89 ======== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GGAGGAAGTACTTTGCTGTTGTAGTGGCAAATTACTCCAGATGACACTCTTTCAAGAGAAATACTCTTGAAAGAGTATTTCTAAACCATAAAGTATTCAGAGCTATTTGTGAAACACACTGATAGACTGATAACCATTCTGCATTTACATTAAAATCCATGATGCTAATGCAA Chimp: GGAGGAAGTACTTTGCTGTTGTTGTGGCAAATTACTCCAGATGACACT---------------CTCTTGAAAGAGTATTTCTAAACCATAAAGTATTCAGAGCTATTTGTGAAACACACTGATAGACTGATAACCATTCTGCATTTACATTAAAATCCATGATGCTAATGCAA ↓ 31 2 4 Gorilla: GGAGGAAGTACTTTGCTGTTGCAGTGGCAAATTACTCCAGATGACACTCTTTCAAGAGAAATACTCTTGAAAGAGTATTTCTAAACCATAAAGTATTCAGAGCTATTTGTGAAACACACTGATAGACTGATAACCATTCTGCATTTACATTAAAATCCATGATGCTAGTGCAA Human: GGAGGAAGTACTTTGCTGTTGTAGTGGCAAATTACTCCAGATGACACTCTTTCAAGAGAAATACTCTTGAAAGAGTATTTCTAAACCATAAAGTATTCAGAGCTATTTGTGAAACACACTGATAGACTGATAACCATTCTGCATTTACATTAAAATCCATGATGCTAATGCAA Cluster: [] Orangutan: GGAGGGAGTACTTTGCTGTCATAGTGGCAAATTACTCCAGATGATACT---------------CTCTTGAAGGAGTATTTCTAAACCATAAAGTATTCAGAGCTATTTGTGAAACACACTGATAGACTGATAACCATTCTGCATTTACATTAAAATCTATGATGCCAATGCAA Chimp > Gorilla --------------- chr10:125163617-125163623 Template switch process: F1: L TTAGCTCCATCCAGCTTGGGGGAGGAAGTACTTTGCTGTTGCAGTGGCAAATTACTCCAGATGACACTCT 1 F3: 4 GAAATA R RF: TTAGCTCCATCCAGCTTGGGGGAGGAAGTACTTTGCTGTTGTTGTGGCAAATTACTCCAGATGACACTCTCTTGAAAGAGTATTTCTAAACCATAAAGTATTCAGAGCTATTTGTGAAACA RR: AATCGAGGTAGGTCGAACCCCCTCCTTCATGAAACGACAACAACACCGTTTAATGAGGTCTACTGTGAGAGAACTTTCTCATAAAGATTTGGTATTTCATAAGTCTCGATAAACACTTTGT F2: 3 AGAACTT 2 Unidirectional alignment (log-probability: -40.3) CTTTGCTGTTGcaGTGGCAAATTACTCCAGATGACACTctttcaagagaaata CTTTGCTGTTGTTGTGGCAAATTACTCCAGATGACACT--------------- Template switch alignment (log-probability: -33) CTTTGCTGTTGcaGTGGCAAATTACTCCAGATGACACTCT|TTCAAGA|GAAAtA CTTTGCTGTTGTTGTGGCAAATTACTCCAGATGACACTCT|TTCAAGA|GAAACA ======== Event 90 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTTAAATGAATATGCAAATTCAATGAGT---GTTATTCAAATTGAATAAATACTATCAACCAACTAAATGACTA Chimp: AGTTAAATGAATATGCAAATTCAATGAGT---GATATTCAAATTGAATAAATACTATCAACCAACTAAATGACTA ↓ 1 3 4 2 Gorilla: AGTTAAATGAATATGCAAATTTAGTGAGAGTATTTATTCAATTTGAATA---ACAATCAACCAACTAAATGACTA Human: AGTTAAATGAATATGCAAATTCAATGAGT---GTTATTCAAATTGAATAAATACTATCAACCAACTAAATGACTA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr10:125284411-125284431 Template switch process: F1: L CAGTCCTGTGTGAGAGTGAAAGTTAAATGAATATGCAAATTTAGTGAG 1 F3: 4 ACAATCAACCAACTAAATGACTAAAATAATGAAATTACTAAAT R RF: CAGTCCTGTGTGAGAGTGAAAGTTAAATGAATATGCAAATTCAATGAGTGATATTCAAATTGAATAAATACTATCAACCAACTAAATGACTAAAATAATGAAATTACTAAAT RR: GTCAGGACACACTCTCACTTTCAATTTACTTATACGTTTAAGTTACTCACTATAAGTTTAACTTATTTATGATAGTTGGTTGATTTACTGATTTTATTACTTTAATGATTTA F2: 3 ATAAGTTTAACTTATTTATGA 2 Unidirectional alignment (log-probability: -57.7) TGTGAGAGTGAAAGTTAAATGAATATGCAAAT----TtAGTGAgagtattTATTCAAtTTGAATA---ACaATCAACCAACTAAATGACTAAAATAATGAAATTACTA TGTGAGAGTGAAAGTTAAATGAATATGCAAATTCAATGAGTGA-------TATTCAAATTGAATAAATACTATCAACCAACTAAATGACTAAAATAATGAAATTACTA Template switch alignment (log-probability: -35.2) TGTGAGAGTGAAAGTTAAATGAATATGCAAATTtAgTGAG|AGTATTTATTCAATTTGAATA|ACaATCAACCAACTAAATGACTAAAATAATGAAATTACTA TGTGAGAGTGAAAGTTAAATGAATATGCAAATTCAATGAG|AGTATTTATTCAATTTGAATA|ACTATCAACCAACTAAATGACTAAAATAATGAAATTACTA ======== Event 91 ======== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCAAAATGGACAGGTACAAGGCGAG----AGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCTTTGTACGTCAGTTTAGGGATACTAATGCG Chimp: GCAAAATGGACAGGTACAAGGTGAG----AGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCTTTGTACGTCAGTTTAGGGATACTAATGCC ↓ 1 4 3 2 Gorilla: GCAAAATGGACAGGTACAAGGCGAGGACGTATGTGGTACTCTCACTAAGAACGGAGACAATTCACTTAGCTTTGTACGTCAGTTTAGGGATACTAATGCA ↑ 1 4 3 2 Human: GCAAAATGGACAGGTACAAGGCGAG----AGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCTTTGTACGTCAGTTTAGGGATACTAATGCG Cluster: [ ] Orangutan: GCAAAATGGACAGGTACAAGGCGAGGACATATGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCTTTGCACGTCAGTTTAGGGATACTAATGCA Human > Gorilla --------------- chr10:146199363-146199368 Template switch process: F1: L CACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGAG 1 F3: 4 TGTGGTACTCTCACTAAGAACGGAGACAATTCACTTAGCT R RF: CACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGAGAGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCTTTGTACGTC RR: GTGAGAGGGACGGAGTCGTTTTACCTGTCCATGTTCCGCTCTCACACCATGAGAGTGATTCTTGCCTCTTTTAAGTGAATCGAAACATGCAG F2: 3 ATGCAG 2 Unidirectional alignment (log-probability: -33.2) ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGAggacGtaTGTGGTACTCTCACTAAGAACGGAGAcAATTCACTTAGCT ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGA----GAGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCT Template switch alignment (log-probability: -22) ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGAG|GACGTA|TGTGGTACTCTCACTAAGAACGGAGAcAATTCACTTAGCT ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGAG|GACGTA|TGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCT Chimp > Gorilla --------------- chr10:146199363-146199368 Template switch process: F1: L ACATCACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGCGAG 1 F3: 4 TGTGGTACTCTCACTAAGAACGGAGACAATTCACTTAGCT R RF: ACATCACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGTGAGAGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCTTTGTACGTC RR: TGTAGTGAGAGGGACGGAGTCGTTTTACCTGTCCATGTTCCACTCTCACACCATGAGAGTGATTCTTGCCTCTTTTAAGTGAATCGAAACATGCAG F2: 3 ATGCAG 2 Unidirectional alignment (log-probability: -38.8) ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGcGAggacGtaTGTGGTACTCTCACTAAGAACGGAGAcAATTCACTTAGCT ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGTGA----GAGTGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCT Template switch alignment (log-probability: -27.6) ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGcGAG|GACGTA|TGTGGTACTCTCACTAAGAACGGAGAcAATTCACTTAGCT ACTCTCCCTGCCTCAGCAAAATGGACAGGTACAAGGTGAG|GACGTA|TGTGGTACTCTCACTAAGAACGGAGAAAATTCACTTAGCT ======== Event 92 ======== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTAAGAATTTATATACACTTACATGCAGTGTGCCTTTAACACCACTCTAAAAACAGA Chimp: TTAAGAATTTATATACACTTACATGCAGTGTGCCTTTAACACCACTCTAAAAACAGA ↓ 13 24 ↑ 13 24 Gorilla: TTAAGAATTTATATACACTTAAAGGCACACTGCATGTAACACCACTCTAAAAACAGA ↓ 13 24 ↑ 13 24 Human: TTAAGAATTTATATACACTTACATGCAGTGTGCCTTTAACACCACTCTAAAAACAGA Cluster: [ ] Orangutan: TTAAGAATTTATATACACTTATATGCAGTGTGCCTTTAACACCACTCTAAAAACAGA Gorilla > Human --------------- chr10:112059462-112059476 Template switch process: F1: L CCACCACGCCCGGCCAGCATTTAAGAATTTATATACACTTA 1 F3: 4 TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC R RF: CCACCACACCCGGCCAGCATTTAAGAATTTATATACACTTAAAGGCACACTGCATGTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC RR: GGTGGTGTGGGCCGGTCGTAAATTCTTAAATATATGTGAATTTCCGTGTGACGTACATTGTGGTGAGATTTTTGTCTGACTTTTACTAGGTCTTAG F2: 3 TTCCGTGTGACGTAC 2 Unidirectional alignment (log-probability: -42.6) CACCACgCCCGGCCAGCATTTAAGAATTTATATACACTTA-----------CATGcagtgtgccttTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACACCCGGCCAGCATTTAAGAATTTATATACACTTAAAGGCACACTGCATG-----------TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Template switch alignment (log-probability: -23.2) CACCACgCCCGGCCAGCATTTAAGAATTTATATACACTTA|CATGCAGTGTGCCTT|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACACCCGGCCAGCATTTAAGAATTTATATACACTTA|CATGCAGTGTGCCTT|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Human > Gorilla --------------- chr10:124081538-124081552 Template switch process: F1: L CCACCACACCCGGCCAGCATTTAAGAATTTATATACACTTA 1 F3: 4 TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC R RF: CCACCACGCCCGGCCAGCATTTAAGAATTTATATACACTTACATGCAGTGTGCCTTTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC RR: GGTGGTGCGGGCCGGTCGTAAATTCTTAAATATATGTGAATGTACGTCACACGGAAATTGTGGTGAGATTTTTGTCTGACTTTTACTAGGTCTTAG F2: 3 GTACGTCACACGGAA 2 Unidirectional alignment (log-probability: -42.6) CACCACaCCCGGCCAGCATTTAAGAATTTATATACACTTAaaggcacactgCATG-----------TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACGCCCGGCCAGCATTTAAGAATTTATATACACTTA-----------CATGCAGTGTGCCTTTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Template switch alignment (log-probability: -23.2) CACCACaCCCGGCCAGCATTTAAGAATTTATATACACTTA|AAGGCACACTGCATG|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACGCCCGGCCAGCATTTAAGAATTTATATACACTTA|AAGGCACACTGCATG|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Gorilla > Chimp --------------- chr10:113381296-113381310 Template switch process: F1: L CCACCACGCCCGGCCAGCCTTTAAGAATTTATATACACTTA 1 F3: 4 TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC R RF: CCACCACACCCGGCCAGCATTTAAGAATTTATATACACTTAAAGGCACACTGCATGTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC RR: GGTGGTGTGGGCCGGTCGTAAATTCTTAAATATATGTGAATTTCCGTGTGACGTACATTGTGGTGAGATTTTTGTCTGACTTTTACTAGGTCTTAG F2: 3 TTCCGTGTGACGTAC 2 Unidirectional alignment (log-probability: -48.1) CACCACgCCCGGCCAGCcTTTAAGAATTTATATACACTTA-----------CATGcagtgtgccttTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACACCCGGCCAGCATTTAAGAATTTATATACACTTAAAGGCACACTGCATG-----------TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Template switch alignment (log-probability: -28.7) CACCACgCCCGGCCAGCcTTTAAGAATTTATATACACTTA|CATGCAGTGTGCCTT|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACACCCGGCCAGCATTTAAGAATTTATATACACTTA|CATGCAGTGTGCCTT|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Chimp > Gorilla --------------- chr10:124081538-124081552 Template switch process: F1: L CCACCACACCCGGCCAGCATTTAAGAATTTATATACACTTA 1 F3: 4 TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC R RF: CCACCACGCCCGGCCAGCCTTTAAGAATTTATATACACTTACATGCAGTGTGCCTTTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC RR: GGTGGTGCGGGCCGGTCGGAAATTCTTAAATATATGTGAATGTACGTCACACGGAAATTGTGGTGAGATTTTTGTCTGACTTTTACTAGGTCTTAG F2: 3 GTACGTCACACGGAA 2 Unidirectional alignment (log-probability: -48.1) CACCACaCCCGGCCAGCaTTTAAGAATTTATATACACTTAaaggcacactgCATG-----------TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACGCCCGGCCAGCCTTTAAGAATTTATATACACTTA-----------CATGCAGTGTGCCTTTAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC Template switch alignment (log-probability: -28.7) CACCACaCCCGGCCAGCaTTTAAGAATTTATATACACTTA|AAGGCACACTGCATG|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC CACCACGCCCGGCCAGCCTTTAAGAATTTATATACACTTA|AAGGCACACTGCATG|TAACACCACTCTAAAAACAGACTGAAAATGATCCAGAATC ======== Event 93 ======== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTTTCATTAAATTTAAAGTACATCTTTATGTACTACAGGGAGGGAAGCTACAGGAGTC ↑ 3 4 2 Chimp: TCCTTTCATTAAATTTAAAGTACA-----------TAAAGGGAGGGAAGCTACAGGAGTC Gorilla: TCCTTTCATTAAATTTAAAGTACA-----------TAAAGGGAGGGAAGCTACAGGAGTC ↓ 3 4 2 Human: TCCTTTCATTAAATTTAAAGTACATCTTTATGTACTACAGGGAGGGAAGCTACAGGAGTC Cluster: [ ] Orangutan: TCCTTTCATTAAATTTAAAGTACA-----------TAAAGGGAGGGAAGCTACAGGAGTC Chimp > Human ------------- chr10:131681640-131681649 Template switch process: F1: L GTTCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAT 1 F3: 4 TACAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATATGC R RF: GTTCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACATAAAGGGAGGGAAGCTACAGGAGTCTGAAAGAGCAGAATATGC RR: CAAGGTTTTAGGAGACGAGGAAAGTAATTTAAATTTCATGTATTTCCCTCCCTTCGATGTCCTCAGACTTTCTCGTCTTATACG F2: 3 CATGTATTTC 2 Unidirectional alignment (log-probability: -38.7) TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAtctttatgtacTAcAGGGAGGGAAGCTACAGGAGTCTGAAAcAGCAGAATA TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACA-----------TAAAGGGAGGGAAGCTACAGGAGTCTGAAAGAGCAGAATA Template switch alignment (log-probability: -28.6) TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAT|CTTTATGTAC|TAcAGGGAGGGAAGCTACAGGAGTCTGAAAcAGCAGAATA TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAT|CTTTATGTAC|TAAAGGGAGGGAAGCTACAGGAGTCTGAAAGAGCAGAATA Gorilla > Human --------------- chr10:131681640-131681649 Template switch process: F1: L GTTCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAT 1 F3: 4 TACAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATATGC R RF: GTTCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACATAAAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATATGC RR: CAAGGTTTTAGGAGACGAGGAAAGTAATTTAAATTTCATGTATTTCCCTCCCTTCGATGTCCTCAGACTTTGTCGTCTTATACG F2: 3 CATGTATTTC 2 Unidirectional alignment (log-probability: -32.3) TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAtctttatgtacTAcAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATA TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACA-----------TAAAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATA Template switch alignment (log-probability: -22.6) TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAT|CTTTATGTAC|TAcAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATA TCCAAAATCCTCTGCTCCTTTCATTAAATTTAAAGTACAT|CTTTATGTAC|TAAAGGGAGGGAAGCTACAGGAGTCTGAAACAGCAGAATA ======== Event 94 ======== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 256 Detected in comparisons: 1256 Multiple sequence alignment: Human: TTTAAACCATTGTTAAACTTTATTTTTAAATTATGAATGGTAAAGGAGCATTTCAAAATCATCT ↓ 13 24 Chimp: TTTAAACCATTGTTAAACTTTACCATTCAGAATTTAAAAATAAAGGAGCATTTCAAAATCATCT ↓ 13 24 ↑ 3 1 2 4 Gorilla: TTTAAACCATTGTTAAACTTTATTTTTAAATTCTGAATGGTACAGGAGCATTTCAAAATCATCT Human: TTTAAACCATTGTTAAACTTTATTTTTAAATTATGAATGGTAAAGGAGCATTTCAAAATCATCT Cluster: [ ] Orangutan: TTTAAACCATTGTTAAACTTTATTTTTAAATTCTGAATGGTAAAGGAGCATTTCAAAATCATCT Human > Chimp ------------- chr10:112792685-112792702 Template switch process: F1: L CATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA 1 F3: 4 TAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA R RF: CATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTATTTTTAAATTATGAATGGTAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA RR: GTAAAATTAGGTAAGACTTAAATTTGGTAACAATTTGAAATAAAAATTTAATACTTACCATTTCCTCGTAAAGTTTTAGTAGAGTTATTTGCTAGAAAT F2: 3 AAAAATTTAAGACTTACC 2 Unidirectional alignment (log-probability: -47.9) ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA------------------ccattcagaatttaaaaaTAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTATTTTTAAATTATGAATGG------------------TAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA Template switch alignment (log-probability: -23.5) ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA|CCATTCAgAATTTAAAAA|TAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA|CCATTCATAATTTAAAAA|TAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA Gorilla > Chimp --------------- chr10:112792685-112792705 Template switch process: F1: L CATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA 1 F3: 4 AGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA R RF: CATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTATTTTTAAATTCTGAATGGTACAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA RR: GTAAAATTAGGTAAGACTTAAATTTGGTAACAATTTGAAATAAAAATTTAAGACTTACCATGTCCTCGTAAAGTTTTAGTAGAGTTATTTGCTAGAAATTTT F2: 3 AATAAAAATTTAAGACTTACC 2 Unidirectional alignment (log-probability: -50.4) ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTT--------------------ACcattcagaatttaaaaataaAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTATTTTTAAATTCTGAATGGTAC--------------------AGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA Template switch alignment (log-probability: -18.4) ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA|CCATTCAGAATTTAAAAATAA|AGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA|CCATTCAGAATTTAAAAATAA|AGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA Chimp > Gorilla --------------- chr10:123489742-123489759 Template switch process: F1: L CATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA 1 F3: 4 TACAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA R RF: CATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTACCATTCAGAATTTAAAAATAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTAAAA RR: GTAAAATTAGGTAAGACTTAAATTTGGTAACAATTTGAAATGGTAAGTCTTAAATTTTTATTTCCTCGTAAAGTTTTAGTAGAGTTATTTGCTAGAAATTTT F2: 3 GGTAAGTCTTAAATTTTT 2 Unidirectional alignment (log-probability: -50.4) ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTtatttttaaattctgaatggTAC--------------------AGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTT--------------------TACCATTCAGAATTTAAAAATAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA Template switch alignment (log-probability: -23.6) ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA|TTTTTAAATTCTGAATGG|TAcAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA ATTTTAATCCATTCTGAATTTAAACCATTGTTAAACTTTA|TTTTTAAATTCTGAATGG|TAAAGGAGCATTTCAAAATCATCTCAATAAACGATCTTTA ======== Event 95 ======== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTAATGGGGACTTTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAGGAGAG---------CCCATGAAATGTGAAGGTATT Chimp: GCTAATGGGGACTTTGAAGAGAAGTGAACTCTCTGGGCCCAAGCAGAAGGCAGGAGAG---------CCCATGAAATGTGAAGGTATT Gorilla: GCTAATGGGGACTTTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCA-GAGAGTTCACTTCTGCCATGAAATGTGAAGGTATT ↑ 3 2 1 4 Human: GCTAATGGGGACTTTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAGGAGAG---------CCCATGAAATGTGAAGGTATT Cluster: [ ] Orangutan: GCTAATGGGGACTTTGAAGAGAAGTGAACCCTCTGGGCCCAAGCAGAAGGCGGGAGAG---------CCCATGAAATGTGAAGGTATT Human > Gorilla --------------- chr10:123182619-123182631 Template switch process: F1: L CTTTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAG 1 F3: 4 GCCATGAAATGTGAAGGTATTTGGATGGTGGCAGAATAGTG R RF: CTTTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAGGAGAGCCCATGAAATGTGAAGGTATTTGGATGGTGGCAGAATAGTG RR: GAAACTTCTCTTCACTTGAGAGACCCGGGTTCGCCTTCCGTCCTCTCGGGTACTTTACACTTCCATAAACCTACCACCGTCTTATCAC F2: 3 TCTTCACTTGAGA 2 Unidirectional alignment (log-probability: -39.2) TTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCA-GAGAGttcacttctgCCATGAAATGTGAAGGTATTTGGATGGTGGCAGAATAGT TTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAGGAGAG---------CCCATGAAATGTGAAGGTATTTGGATGGTGGCAGAATAGT Template switch alignment (log-probability: -23) TTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAG|AGAGTTCACTTCT|gCCATGAAATGTGAAGGTATTTGGATGGTGGCAGAATAGT TTGAAGAGAAGTGAACTCTCTGGGCCCAAGCGGAAGGCAG|AGAGTTCACTTCT|CCCATGAAATGTGAAGGTATTTGGATGGTGGCAGAATAGT ======== Event 96 ======== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: TCAAAATACATGTAAATTGATAAATTATGTGAGCTTTGTTCTCTTAA-TTATCAATAAGTAGAGAATGT ↓ 13 24 ↑ 13 24 Chimp: TCAAAATACATGTAAATTGAT-AATTAAGAGAACAAAGCTCACATAATTTATCAATAAGTAGAGAATGT Gorilla: TCAAAATACATGTAAATTGATAAATTATGTGGGCTTTGTTCTCTTAG-TTATCAATAAGTAGAGAATGT Human: TCAAAATACATGTAAATTGATAAATTATGTGAGCTTTGTTCTCTTAA-TTATCAATAAGTAGAGAATGT Cluster: [ ] Orangutan: TCAAAATAGATGTAAATTGATAAATTATGTGAGATTTGTTCTCTTAA-TTATCAATAAGTAGAGAATGT Chimp > Human ------------- chr10:108382618-108382641 Template switch process: F1: L ATTACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA 1 F3: 4 TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA R RF: ATTACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAATTAAGAGAACAAAGCTCACATAATTTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA RR: TAATGTTAACCTAAAAAACCAGTTTTATGTACATTTAACTATTAATTCTCTTGTTTCGAGTGTATTAAATAGTTATTCATCTCTTACATTATCCTTTGAGGCTTTCT F2: 3 AATTCTCTTGTTTCGAGTGTATTA 2 Unidirectional alignment (log-probability: -51) ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAAattatgtgagctttgttctcTTAA--------------------TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA--------------------TTAAGAGAACAAAGCTCACATAATTTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA Template switch alignment (log-probability: -18.3) ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA|ATTATGTGAGCTTTGTTCTCTTAA|TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA|ATTATGTGAGCTTTGTTCTCTTAA|TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA Human > Chimp ------------- chr10:109639973-109639996 Template switch process: F1: L ATTACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA 1 F3: 4 TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA R RF: ATTACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAAATTATGTGAGCTTTGTTCTCTTAATTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA RR: TAATGTTAACCTAAAAAACCAGTTTTATGTACATTTAACTATTTAATACACTCGAAACAAGAGAATTAATAGTTATTCATCTCTTACATTATCCTTTGAGGCTTTCT F2: 3 TAATACACTCGAAACAAGAGAATT 2 Unidirectional alignment (log-probability: -51) ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA--------------------TTAAgagaacaaagctcacataatTTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAAATTATGTGAGCTTTGTTCTCTTAA--------------------TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA Template switch alignment (log-probability: -18.3) ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA|TTAAGAGAACAAAGCTCACATAAT|TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA ACAATTGGATTTTTTGGTCAAAATACATGTAAATTGATAA|TTAAGAGAACAAAGCTCACATAAT|TTATCAATAAGTAGAGAATGTAATAGGAAACTCCGAAAGA ======== Event 97 ======== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: agtTGACAACGAAGTTGAACTTTGTCCTCTACGTATGAGAAGAAACTCATACGTAGAGGACAAAGTTCTACGCATGCTCAAAAGTC Chimp: agtTGACAACGAAGTTGAACTCTGTCCTCTACGTATGAGTTTCTTCTCATACGTAGGGGACAAAGTTCTACGCATGCCCAAAAGTC Gorilla: agtTAACAACGAAGTTGAACTTTGTCCTCTACGTATGAGTTTCTTCTCATACGTAGAGGACAAATTTCTACGCATGCCCAAAAGTC ↓ 3 1 2 4 Human: agtTGACAACGAAGTTGAACTTTGTCCTCTACGTATGAGAAGAAACTCATACGTAGAGGACAAAGTTCTACGCATGCTCAAAAGTC Cluster: [ ] Orangutan: agtTGACAATGAAGTTGAACTTTGTCCTCTACGTATGAGTTTCTTCTCATACATAGAGGACAAAGTTCTACGCATGCCCAAAAGTC Gorilla > Human --------------- chr10:15466422-15466447 Template switch process: F1: L TGAGTTGACAACGAAGTTGAACTTTGTCCTCTACGTATGAG 1 F3: 4 TTCTACGCATGCTCAAAAGT R RF: TGAGTTAACAACGAAGTTGAACTTTGTCCTCTACGTATGAGTTTCTTCTCATACGTAGAGGACAAATTTCTACGCATGCCCAAAAGT RR: ACTCAATTGTTGCTTCAACTTGAAACAGGAGATGCATACTCAAAGAAGAGTATGCATCTCCTGTTTAAAGATGCGTACGGGTTTTCA F2: 3 GAAACAGGAGATGCATACTCAAAGAA 2 Unidirectional alignment (log-probability: -46.1) GAGTTgACAACGAAGTTGAACTTTGTCCTCTACGTATGAG------aagaaaCTCATACGTAGAGGACAAAgTTCTACGCATGCtCAAAAGT GAGTTAACAACGAAGTTGAACTTTGTCCTCTACGTATGAGTTTCTT------CTCATACGTAGAGGACAAATTTCTACGCATGCCCAAAAGT Template switch alignment (log-probability: -29.6) GAGTTgACAACGAAGTTGAACTTTGTCCTCTACGTATGAG|AAGAAACTCATACGTAGAGGACAAAG|TTCTACGCATGCtCAAAAGT GAGTTAACAACGAAGTTGAACTTTGTCCTCTACGTATGAG|AAGAAACTCATACGTAGAGGACAAAG|TTCTACGCATGCCCAAAAGT ======== Event 98 ======== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CAAAGCAACTAGCTCATCAAT-ATT------ACA--TAGTCATTCGTTTTCCCCTAATTTTTACTTATTA Chimp: CAAAGCAACTAGCTCATCAAT-ATT------A--CATAGTCATCCGTTTTCCCCTAATTTTTACTTATTA ↓ 13 4 2 Gorilla: CAAAGCAACTAGCTCATCAATGACTATGTAATCA--TAGTCATCCATTTCCCCCTAATTTTTACTTATTA Human: CAAAGCAACTAGCTCATCAAT-ATT------ACA--TAGTCATTCGTTTTCCCCTAATTTTTACTTATTA Cluster: [ ] Orangutan: CAAAGCAACTAGCTCATCAAT-ATT------ACA--TAGTCATCAGTTTTCCCCTAATTTTTACTTACGA Chimp > Gorilla --------------- chr10:118995032-118995042 Template switch process: F1: L ATTTTTATTCTATTAGCATGCAAAGCAACTAGCTCATCAAT 1 F3: 4 CATAGTCATCCATTTCCCCCTAATTTTTACTTATTAGAATTTCTCAAAAGTTCTAC R RF: ATTTTTATTCTATTAGCATGCAAAGCAACTAGCTCATCAATATTACATAGTCATCCGTTTTCCCCTAATTTTTACTTATTAGAATTTCTCAAAAGTTCTAC RR: TAAAAATAAGATAATCGTACGTTTCGTTGATCGAGTAGTTATAATGTATCAGTAGGCAAAAGGGGATTAAAAATGAATAATCTTAAAGAGTTTTCAAGATG F2: 3 TAATGTATCAG 2 Unidirectional alignment (log-probability: -45) TTTTTATTCTATTAGCATGCAAAGCAACTAGCTCATCAATgactatgtaAT--CATAGTCATCCaTTTcCCCCTAATTTTTACTTATTAGAAT TTTTTATTCTATTAGCATGCAAAGCAACTAGCTCATCAAT---------ATTACATAGTCATCCGTTTTCCCCTAATTTTTACTTATTAGAAT Template switch alignment (log-probability: -28.6) TTTTTATTCTATTAGCATGCAAAGCAACTAGCTCATCAAT|GACTATGTAAT|CATAGTCATCCaTTTcCCCCTAATTTTTACTTATTAGAAT TTTTTATTCTATTAGCATGCAAAGCAACTAGCTCATCAAT|GACTATGTAAT|CATAGTCATCCGTTTTCCCCTAATTTTTACTTATTAGAAT ======== Event 99 ======== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTTCATTGACCTCTGCAGCCATTCAGGGGAATGGCTGTAG-TTGGAGACGTT ↑ 13 4 2 Chimp: ACTTCATTGACCTCTGCAGCCCC----CTGAATGGCTGTAGTTTGGAGACGTT Gorilla: ACTTCATTGACCTCTGCAGCCCC----CTGAATGGCTGTAGTTTGGAGACGTT Human: ACTTCATTGACCTCTGCAGCCATTCAGGGGAATGGCTGTAG-TTGGAGACGTT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr10:100667942-100667949 Template switch process: F1: L CACAAGCATTTTCAGACGTTACTTCATTGACCTCTGCAGCC 1 F3: 4 GAATGGCTGTAG-TTGGAGACGTTTGAATGCTCCGGCAGA R RF: CACAAGCATTTTCAGACGTTACTTCATTGACCTCTGCAGCCCCCTGAATGGCTGTAGTTTGGAGACGTTTGAATGCTCCGGCAGA RR: GTGTTCGTAAAAGTCTGCAATGAAGTAACTGGAGACGTCGGGGGACTTACCGACATCAAACCTCTGCAAACTTACGAGGCCGTCT F2: 3 GGGACTTA 2 Unidirectional alignment (log-probability: -43.1) ACAAGCATTTTCAGACGTTACTTCATTGACCTCTGCAGCCattcaggg----GAATGGCTGTAG-TTGGAGACGTTTGAATGCTCCGGCAGA ACAAGCATTTTCAGACGTTACTTCATTGACCTCTGCAGCC--------CCCTGAATGGCTGTAGTTTGGAGACGTTTGAATGCTCCGGCAGA Template switch alignment (log-probability: -26.5) ACAAGCATTTTCAGACGTTACTTCATTGACCTCTGCAGCC|ATTCAGGG|GAATGGCTGTAG-TTGGAGACGTTTGAATGCTCCGGCAGA ACAAGCATTTTCAGACGTTACTTCATTGACCTCTGCAGCC|ATTCAGGG|GAATGGCTGTAGTTTGGAGACGTTTGAATGCTCCGGCAGA ========= Event 100 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAACCAACAGCTATGCTCTGCCGGTTGATA-----ACTGAGTTGTTTACCACCTCAACC Chimp: TAAACCAACAGCTATGCTCTGCCGGTTGATA-----ACTGAGTTGTTTACCACCTCAACC Gorilla: TAAACCAACAGCTATGCTCTGCCGCTTTATCAAGCGGCAGAGTTGTTTACCACCTCAACC ↑ 3 1 2 4 Human: TAAACCAACAGCTATGCTCTGCCGGTTGATA-----ACTGAGTTGTTTACCACCTCAACC Cluster: [ ] Orangutan: TAAACCAACAGGTTTGCTCTGCTGGTTGATA-----ACTGAGTTGTTTACCACCTCAACC Human > Gorilla --------------- chr10:87653662-87653673 Template switch process: F1: L ACGGTTGACTTGAATTATAAACCAACAGCTATGCTCTGCCGCTT 1 F3: 4 GAGTTGTTTACCACCTCAACCAGAAGATGCAACGATTAGC R RF: ACGGTTGACTTGAATTATAAACCAACAGCTATGCTCTGCCGGTTGATAACTGAGTTGTTTACCACCTCAACCAGAAGATGCAACGATTAGC RR: TGCCAACTGAACTTAATATTTGGTTGTCGATACGAGACGGCCAACTATTGACTCAACAAATGGTGGAGTTGGTCTTCTACGTTGCTAATCG F2: 3 ACGGCGAACTAT 2 Unidirectional alignment (log-probability: -39.8) TTGACTTGAATTATAAACCAACAGCTATGCTCTGCCG--------CTttatcaagcggcaGAGTTGTTTACCACCTCAACCAGAAGATGCAACGATTAGC TTGACTTGAATTATAAACCAACAGCTATGCTCTGCCGGTTGATAACT-------------GAGTTGTTTACCACCTCAACCAGAAGATGCAACGATTAGC Template switch alignment (log-probability: -28.4) TTGACTTGAATTATAAACCAACAGCTATGCTCTGCCGcTT|TATCAAgCGGCA|GAGTTGTTTACCACCTCAACCAGAAGATGCAACGATTAGC TTGACTTGAATTATAAACCAACAGCTATGCTCTGCCGGTT|TATCAACCGGCA|GAGTTGTTTACCACCTCAACCAGAAGATGCAACGATTAGC ========= Event 101 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAAGCCATCCTTCCATACCATTGGA--GGTCTTCTC---AAGAAGCTGGTATGAAGTATCCTGAAGAGGC Chimp: CAAGCCATCCTTCCATACCATTGGA--GGTCTTCTC---AAGAAGCTGGTATGAAGTATCCTGAAGAGGG ↓ 1 3 4 2 Gorilla: CAAGCCATCCTTCCATACCATACCA----GCTTCTTAAGAAGAAGCTGGTATGAAGTATCCTGAAGAGGC ↑ 1 3 4 2 Human: CAAGCCATCCTTCCATACCATTGGA--GGTCTTCTC---AAGAAGCTGGTATGAAGTATCCTGAAGAGGC Cluster: [ ] Orangutan: CAAGCCATCCTTCCATACCATTGGAGG--TCTTCTC---AAGAAGCTGGTATGAAGTATCCTGAAGAGGC Human > Gorilla --------------- chr10:88395742-88395755 Template switch process: F1: L TCAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT 1 F3: 4 AAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAGT R RF: TCAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCATTGGAGGTCTTCTCAAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAAT RR: AGTCTTCGGTAATATTCGAAGTTCGGTAGGAAGGTATGGTAACCTCCAGAAGAGTTCTTCGACCATACTTCATAGGACTTCTCCGTATTCGTTA F2: 3 GAATTCTTCGACCA 2 Unidirectional alignment (log-probability: -46.9) CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT-------------accagcttcttaagAAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAgT CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCATTGGAGGTCTTCTC--------------AAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAAT Template switch alignment (log-probability: -28.5) CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT|ACCAGCTTCTTaAG|AAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAgT CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT|ACCAGCTTCTTGAG|AAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAAT Chimp > Gorilla --------------- chr10:88395742-88395755 Template switch process: F1: L TCAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT 1 F3: 4 AAGAAGCTGGTATGAAGTATCCTGAAGAGGCATAAGCAGT R RF: TCAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCATTGGAGGTCTTCTCAAGAAGCTGGTATGAAGTATCCTGAAGAGGGATAAGCAGT RR: AGTCTTCGGTAATATTCGAAGTTCGGTAGGAAGGTATGGTAACCTCCAGAAGAGTTCTTCGACCATACTTCATAGGACTTCTCCCTATTCGTCA F2: 3 GAATTCTTCGACCA 2 Unidirectional alignment (log-probability: -46.9) CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT-------------accagcttcttaagAAGAAGCTGGTATGAAGTATCCTGAAGAGGcATAAGCAGT CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCATTGGAGGTCTTCTC--------------AAGAAGCTGGTATGAAGTATCCTGAAGAGGGATAAGCAGT Template switch alignment (log-probability: -28.5) CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT|ACCAGCTTCTTaAG|AAGAAGCTGGTATGAAGTATCCTGAAGAGGcATAAGCAGT CAGAAGCCATTATAAGCTTCAAGCCATCCTTCCATACCAT|ACCAGCTTCTTGAG|AAGAAGCTGGTATGAAGTATCCTGAAGAGGGATAAGCAGT ========= Event 102 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: CTGTGAAACCATTGCCTGATGACACCCACATCTTTATGTCCAGAAGTACTATGAGAGCATCATCTGAGTAGCTCCTATGTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAACAGGGTGTACAATACACCCTGTACAAGAGTGTATGCATTT ↓ 3 2 1 4 Chimp: CTGTGAAACCATTGCCTGATGACACCCACATCTTTATGTCCAGAAGTACTATGAGAGCATCATCTGAGTAGCTCCTATGTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAACT--------GTCACACCCCGTACAAGAGTGTATGCATTT Gorilla: CTGTGAAACCATTGCCTGATGACACCCACATCTTTATGTCCAGAAGTACTATGAGAGCATCATCTGAGTAGCTCCTATGTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAACT--------GCCACACCCCGTACAAGAGTGTATGCATTT Human: CTGTGAAACCATTGCCTGATGACACCCACATCTTTATGTCCAGAAGTACTATGAGAGCATCATCTGAGTAGCTCCTATGTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAACAGGGTGTACAATACACCCTGTACAAGAGTGTATGCATTT Cluster: [ ] Orangutan: CTATGAAACCATTGCCTAATGACACCCATATCCTTATGTCCAGAAGTACTATCAGAGCATGATCTGAGTAGCTCCTATGTGGGTCAAGCTGAAACATCTTACTGTGGCCAATAATAACT--------GTCACACCCCAGACAAGAGTGTATGCATTT Human > Chimp ------------- chr10:34902244-34902248 Template switch process: F1: L TGTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAAC 1 F3: 4 CACCCCGTACAAGAGTGTATGCATTTAGGGAGACAATTTTTATCAA R RF: TGACACCCACATCTTTATGTCCAGAAGTACTATGAGAGCATCATCTGAGTAGCTCCTATGTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAACAGGGTGTACAATACACCCTGTACAAGAGTGTATGCATTTAGGGAGACAATTTTTATCAA RR: ACTGTGGGTGTAGAAATACAGGTCTTCATGATACTCTCGTAGTAGACTCATCGAGGATACACCCAGTTCGACTTTGTAGAGTGACACCGGTCATTATTGTCCCACATGTTATGTGGGACATGTTCTCACATACGTAAATCCCTCTGTTAAAAATAGTT F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -32.1) GTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAAC-----------TgtcACACCCcGTACAAGAGTGTATGCATTTAGGGAGACAATTTT GTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAACAGGGTGTACAAT---ACACCCTGTACAAGAGTGTATGCATTTAGGGAGACAATTTT Template switch alignment (log-probability: -22) GTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAAC|TGTCA|CACCCcGTACAAGAGTGTATGCATTTAGGGAGACAATTTT GTGGGTCAAGCTGAAACATCTCACTGTGGCCAGTAATAAC|TGTCA|CACCCTGTACAAGAGTGTATGCATTTAGGGAGACAATTTT ========= Event 103 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGGATTCCTGGAGCTTTATTTCA-GC------ATGGGGATGCTCCCA--TGCTGAA---CCTCCTCCCCAGTGTCTGGGC Chimp: TGGATTCCTGGAGCTTTATTTCA-GC------ATGGGGATGCTCCCA--TGCTGAA---CCTCCTCCCCAGTGTCTGGGC ↑ 3 2 1 4 Gorilla: TGGATTCCTGGAGCTTTATTTCA-GC------ATGGGGATGCTCCCAGTGTCTGGGCCCACTCCTCCCCAGTGTCTGGGC ↓ 3 2 1 4 Human: TGGATTCCTGGAGCTTTATTTCA-GC------ATGGGGATGCTCCCA--TGCTGAA---CCTCCTCCCCAGTGTCTGGGC Cluster: [ ] Orangutan: TGGATTCCTGGAGCACCAGGCTGGTCGTGCACCCCGGGACGCTCCCA--TTCTGAA---CCTCCTCCCCAGTGTCTGGGC Gorilla > Human --------------- chr10:102178658-102178664 Template switch process: F1: L CTGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCA 1 F3: 4 CCTCCTCCCCAGTGTCTGGGCCATTCAAGCCGGCGCGGGGC R RF: CTGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCAGTGTCTGGGCCCACTCCTCCCCAGTGTCTGGGCCATTCAAGCTGGCGCGGGGC RR: GACCTAAGGACCTCGAAATAAAGTCGTACCCCTACGAGGGTCACAGACCCGGGTGAGGAGGGGTCACAGACCCGGTAAGTTCGACCGCGCCCCG F2: 3 AAGTCGT 2 Unidirectional alignment (log-probability: -38.3) TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTC-------------CCAtgctgaacCTCCTCCCCAGTGTCTGGGCCATTCAAGCcGGCGCGGGG TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCAGTGTCTGGGCCCA--------CTCCTCCCCAGTGTCTGGGCCATTCAAGCTGGCGCGGGG Template switch alignment (log-probability: -27.7) TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCA|TGCTGAA|cCTCCTCCCCAGTGTCTGGGCCATTCAAGCcGGCGCGGGG TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCA|TGCTGAA|ACTCCTCCCCAGTGTCTGGGCCATTCAAGCTGGCGCGGGG Gorilla > Chimp --------------- chr10:103297850-103297856 Template switch process: F1: L CTGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCA 1 F3: 4 CCTCCTCCCCAGTGTCTGGGCCATTCAAGCCGGCGCGGGGC R RF: CTGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCAGTGTCTGGGCCCACTCCTCCCCAGTGTCTGGGCCATTCAAGCTGGCGCGGGGC RR: GACCTAAGGACCTCGAAATAAAGTCGTACCCCTACGAGGGTCACAGACCCGGGTGAGGAGGGGTCACAGACCCGGTAAGTTCGACCGCGCCCCG F2: 3 AAGTCGT 2 Unidirectional alignment (log-probability: -38.3) TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTC-------------CCAtgctgaacCTCCTCCCCAGTGTCTGGGCCATTCAAGCcGGCGCGGGG TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCAGTGTCTGGGCCCA--------CTCCTCCCCAGTGTCTGGGCCATTCAAGCTGGCGCGGGG Template switch alignment (log-probability: -27.7) TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCA|TGCTGAA|cCTCCTCCCCAGTGTCTGGGCCATTCAAGCcGGCGCGGGG TGGATTCCTGGAGCTTTATTTCAGCATGGGGATGCTCCCA|TGCTGAA|ACTCCTCCCCAGTGTCTGGGCCATTCAAGCTGGCGCGGGG ========= Event 104 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATGACTCTACAGTTTAAGG------ACTAAGGACT--AGCTAGCTATTGGAACATCAAAGTCACAGTTATGCtcattgaaatagaat Chimp: AAATGACTCTACAGTTTAAGG------ACTAAGGACT--AGCTAGCTATTGGAACATCAAAGTCACAGTTATGCtcatcgaaatagaat Gorilla: AAATGACTCTACAGTTTAAGG------------AACT----GTAGCTATTGGAATGTCAAAGTCACAGTTATGCtcattgaaatagaat ↑ 1 4 3 2 Human: AAATGACTCTACAGTTTAAGG------ACTAAGGACT--AGCTAGCTATTGGAACATCAAAGTCACAGTTATGCtcattgaaatagaat Cluster: [ ] Orangutan: AAATGACTCTACAGTTTAAGGACTAAG------GACTAG--CTAGCTATTGGAACATCAAAGTCACAGTTATGCttattgaaatagaat Human > Gorilla --------------- chr10:63146837-63146840 Template switch process: F1: L CCCTGATGCTGATCAGGAAAAAATGACTCTACAGTTTAAGGA 1 F3: 4 TAGCTATTGGAATGTCAAAGTCACAGTTATGCTCATTGAA R RF: CCCTGATGCTGATCAGGAAAAAATGACTCTACAGTTTAAGGACTAAGGACTAGCTAGCTATTGGAACATCAAAGTCACAGTTATGCTCATTGAA RR: GGGACTACGACTAGTCCTTTTTTACTGAGATGTCAAATTCCTGATTCCTGATCGATCGATAACCTTGTAGTTTCAGTGTCAATACGAGTAACTT F2: 3 GTCA 2 Unidirectional alignment (log-probability: -37.7) CTGATGCTGATCAGGAAAAAATGACTCTACAGTTTAAGGA------ACT--gTAGCTATTGGAAtgTCAAAGTCACAGTTATGCTCATTGAA CTGATGCTGATCAGGAAAAAATGACTCTACAGTTTAAGGACTAAGGACTAGCTAGCTATTGGAACATCAAAGTCACAGTTATGCTCATTGAA Template switch alignment (log-probability: -27.3) CTGATGCTGATCAGGAAAAAATGACTCTACAGTTTAAGGA|ACTG|TAGCTATTGGAAtgTCAAAGTCACAGTTATGCTCATTGAA CTGATGCTGATCAGGAAAAAATGACTCTACAGTTTAAGGA|ACTG|TAGCTATTGGAACATCAAAGTCACAGTTATGCTCATTGAA ========= Event 105 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CCACCTTTCTCTGTACTTTAGGGGCTTTCAGCCACTCCCCTCTACCTTCATTCCCAC ↑ 3 1 24 Chimp: CCACCTTTCTCTGTACTTTAGGGGCT-------GAACCCCTCTACCTTCATTCCCAC Gorilla: CCACCTTTCTCTGTACTTTAGGGGCTTCCAGCCACTCCCGTCTACCCTCATTCCCAC Human: CCACCTTTCTCTGTACTTTAGGGGCTTTCAGCCACTCCCCTCTACCTTCATTCCCAC Cluster: [ ] Orangutan: CCACCTTTCTCTGTACTTTAGGGGCTTTCATCCACTCCCGCCTACCCTCATTCCCAC Chimp > Human ------------- chr10:100573350-100573359 Template switch process: F1: L TGATTGTTGCCCACCCCACCTTTCTCTGTACTTTAGGGGCT 1 F3: 4 CCCCTCTACCTTCATTCCCACTTTGCTCCAGGAGTGCAGC R RF: TGATTGTTGCCCACCCCACCTTTCTCTGTACTTTAGGGGCTGAACCCCTCTACCTTCATTCCCACTTTGCTCCAGGAGTGCAGC RR: ACTAACAACGGGTGGGGTGGAAAGAGACATGAAATCCCCGACTTGGGGAGATGGAAGTAAGGGTGAAACGAGGTCCTCACGTCG F2: 3 TCACCGACTT 2 Unidirectional alignment (log-probability: -35.7) GATTGTTGCCCACCCCACCTTTCTCTGTACTTTAGGGGCT---ttcagccactCCCCTCTACCTTCATTCCCACTTTGCTCCAGGAGTGCAGC GATTGTTGCCCACCCCACCTTTCTCTGTACTTTAGGGGCTGAA----------CCCCTCTACCTTCATTCCCACTTTGCTCCAGGAGTGCAGC Template switch alignment (log-probability: -22.5) GATTGTTGCCCACCCCACCTTTCTCTGTACTTTAGGGGCT|TTCAGCCaCT|CCCCTCTACCTTCATTCCCACTTTGCTCCAGGAGTGCAGC GATTGTTGCCCACCCCACCTTTCTCTGTACTTTAGGGGCT|TTCAGCCCCT|CCCCTCTACCTTCATTCCCACTTTGCTCCAGGAGTGCAGC ========= Event 106 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACAAGGCAGCACCTTCACAG-------------TCCTACTTTTGTCTTGGGTTGTTTGCATGACTCT Chimp: CACAAGGCAGCACCTTCACAG-------------TCCTACTTTTGTCTTGGGTTGTTTGCATGACTCT ↓ 3 4 2 Gorilla: CACAAGGCAGCACCTTCACAGTAGACAAAAGTAGGACTACTTTTGTCTTGGGTTGTTTGCATGAGTCT ↑ 3 4 2 Human: CACAAGGCAGCACCTTCACAG-------------TCCTACTTTTGTCTTGGGTTGTTTGCATGACTCT Cluster: [ ] Orangutan: CACAAGGCAGCACCTTCACAG-------------TCCTACTTTTGTCTTGGGTTGTTTGCAAGACTCT Human > Gorilla --------------- chr10:87559421-87559434 Template switch process: F1: L CTCAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT 1 F3: 4 CTACTTTTGTCTTGGGTTGTTTGCATGAGTCTCCTCGGAT R RF: CTCAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGTCCTACTTTTGTCTTGGGTTGTTTGCATGACTCTCCTCGGAT RR: GAGTTTCGAGACTGTGTCCAGTGTTCCGTCGTGGAAGTGTCAGGATGAAAACAGAACCCAACAAACGTACTGAGAGGAGCCTA F2: 3 AGGATGAAAACAGA 2 Unidirectional alignment (log-probability: -40.6) CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGTagacaaaagtaggaCTACTTTTGTCTTGGGTTGTTTGCATGAgTCTCCTCGGAT CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT-------------CCTACTTTTGTCTTGGGTTGTTTGCATGACTCTCCTCGGAT Template switch alignment (log-probability: -23.1) CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT|AGACAAAAGTAGGA|CTACTTTTGTCTTGGGTTGTTTGCATGAgTCTCCTCGGAT CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT|AGACAAAAGTAGGA|CTACTTTTGTCTTGGGTTGTTTGCATGACTCTCCTCGGAT Chimp > Gorilla --------------- chr10:87559421-87559434 Template switch process: F1: L CTCAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT 1 F3: 4 CTACTTTTGTCTTGGGTTGTTTGCATGAGTCTCCTCGGAT R RF: CTCAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGTCCTACTTTTGTCTTGGGTTGTTTGCATGACTCTCCTCGGAT RR: GAGTTTCGAGACTGTGTCCAGTGTTCCGTCGTGGAAGTGTCAGGATGAAAACAGAACCCAACAAACGTACTGAGAGGAGCCTA F2: 3 AGGATGAAAACAGA 2 Unidirectional alignment (log-probability: -40.6) CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGTagacaaaagtaggaCTACTTTTGTCTTGGGTTGTTTGCATGAgTCTCCTCGGAT CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT-------------CCTACTTTTGTCTTGGGTTGTTTGCATGACTCTCCTCGGAT Template switch alignment (log-probability: -23.1) CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT|AGACAAAAGTAGGA|CTACTTTTGTCTTGGGTTGTTTGCATGAgTCTCCTCGGAT CAAAGCTCTGACACAGGTCACAAGGCAGCACCTTCACAGT|AGACAAAAGTAGGA|CTACTTTTGTCTTGGGTTGTTTGCATGACTCTCCTCGGAT ========= Event 107 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: aaa--aaaaaGGTAATAATGGAATTAATTCAGTCCTAATTACGTAGACCTAATATAGTA Chimp: aaa-aaaaaaGGTAATAATGGAATTAATTCAGTCCTAATTAGGTAGACCTAATATAGTA ↓ 3 1 2 4 ↑ 3 1 4 2 Gorilla: aaaa-aaaaaGGTAATAATGGACTGAATTAATTC-CAAATAGGTAGACCTAATATAGTA Human: aaa--aaaaaGGTAATAATGGAATTAATTCAGTCCTAATTACGTAGACCTAATATAGTA Cluster: [ ] Orangutan: AAA---AAAATGTAATGATGGACTGACTGAATTC-CAAATAGGTAGGCTTAACATAGTA Gorilla > Chimp --------------- chr10:116582807-116582819 Template switch process: F1: L GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGA 1 F3: 4 TAAT------TAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTTGCC R RF: GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGACTGAATTAATTCCAAATAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTTGCC RR: CCTCCATACTAAAAGATAGTTTTTTTTTCCATTATTACCTGACTTAATTAAGGTTTATCCATCTGGATTATATCATTCATACAGAAGGAGAAACGG F2: 3 CCTGACTTAATTA 2 Unidirectional alignment (log-probability: -39.2) GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATG----GAATTAATTcagtcCtAAtTAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTT GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGACTGAATTAATT-----CCAAATAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTT Template switch alignment (log-probability: -27.5) GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGA|ATTAATTCAGTCC|TAAT------TAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTT GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGA|ATTAATTCAGTCC|TAATTCCAAATAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTT Chimp > Gorilla --------------- chr10:129650093-129650105 Template switch process: F1: L GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGA 1 F3: 4 AAATAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTTGCC R RF: GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGAATTAATTCAGTCCTAATTAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTTGCC RR: CCTCCATACTAAAAGATAGTTTTTTTTTCCATTATTACCTTAATTAAGTCAGGATTAATCCATCTGGATTATATCATTCATACAGAAGGAGAAACGG F2: 3 CCTTAATTAAGTC 2 Unidirectional alignment (log-probability: -37.8) GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGactgAATTAATT-----CcAAaTAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTT GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGG----AATTAATTCAGTCCTAATTAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTT Template switch alignment (log-probability: -23) GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGA|CTGAATTAATTCC|AAaTAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTT GGAGGTATGATTTTCTATCAAAAAAAAAGGTAATAATGGA|CTGAATTAATTCC|AATTAGGTAGACCTAATATAGTAAGTATGTCTTCCTCTTT ========= Event 108 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGACTCACATTTCCAGCCTG----CATTTTATAAGACAAACTAATTGGAATGCATGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGAAACCCT Chimp: AAGACTCACATTTCCAGCCTG----CATTTTAGAAGACAAACTAATTGGAATGCATGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGAAACCCT ↑ 4 2 1 Gorilla: AAGACTCACATTTCCAGCCTG------------------------------------CATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGAAACCCT ↓ 4 2 1 Human: AAGACTCACATTTCCAGCCTG----CATTTTATAAGACAAACTAATTGGAATGCATGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGAAACCCT Cluster: [ ] Orangutan: AAGACTCACATTTCCAGCCTGCATG--------------------------------CATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGAAACCCT Gorilla > Human --------------- chr10:104847965-104847968 Template switch process: F1: L GCTGTGCTCGCTGGATCTTGAAGACTCACATTTCCAGCCTGCATTTTATAAGACAAACTAATTGGAA 1 F3: 4 TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGA R RF: GCTGTGCTCGCTGGATCTCGAAGACTCACATTTCCAGCCTGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGA RR: CGACACGAGCGACCTAGAGCTTCTGAGTGTAAAGGTCGGACGTAAAATCTTCTGTTTGATTAACCTTTAATTAACTCCTCT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -62.4) ACATTTCCAGCCtgcattttataagacaaactaattggaatgcaTGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA ACATTTCCAGCC--------------------------------TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA Template switch alignment (log-probability: -27.9) ACATTTCCAGCCTGCATTTTAtAAGACAAACTAATTGGAA|TGCA|TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA ACATTTCCAGCCTGCATTTTAGAAGACAAACTAATTGGAA|TGCA|TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA Gorilla > Chimp --------------- chr10:106000370-106000373 Template switch process: F1: L GCTGTGCTCGCTGGATCTCGAAGACTCACATTTCCAGCCTGCATTTTAGAAGACAAACTAATTGGAA 1 F3: 4 TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGA R RF: GCTGTGCTCGCTGGATCTCGAAGACTCACATTTCCAGCCTGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGAGA RR: CGACACGAGCGACCTAGAGCTTCTGAGTGTAAAGGTCGGACGTAAAATCTTCTGTTTGATTAACCTTTAATTAACTCCTCT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -56.9) ACATTTCCAGCCtgcattttagaagacaaactaattggaatgcaTGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA ACATTTCCAGCC--------------------------------TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA Template switch alignment (log-probability: -16.9) ACATTTCCAGCCTGCATTTTAGAAGACAAACTAATTGGAA|TGCA|TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA ACATTTCCAGCCTGCATTTTAGAAGACAAACTAATTGGAA|TGCA|TGCATTTTAGAAGACAAACTAATTGGAAATTAATTGAGGA ========= Event 109 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAGAGAGTCCTATAAACTCAGGCCT------------------GACTCTCAACTGGAGTGACCAAA Chimp: TGAGAGAGTCCTATAAACTCAGACCT---------GGTCAGGTCTGCTCTCAACTGGAGTGACCAAA Gorilla: TGAGAGAGTCCTATAAACTCAGACCTGGTCAGGCC---------TGCTCTCAACTGGAGTGACCAAA ↑ 3 1 4 Human: TGAGAGAGTCCTATAAACTCAGGCCT------------------GACTCTCAACTGGAGTGACCAAA Cluster: [ ] Orangutan: TG--AGAGTCCTATAAACTCAGACTGAGTCAGGCC---------TGCTCTCAACTGGAGTGACCAAA Human > Gorilla --------------- chr10:91937217-91937226 Template switch process: F1: L TTCTAGAGGATATGAGGAGTGAGAGAGTCCTATAAACTCAGACCTG 1 F3: 4 CTCTCAACTGGAGTGACCAAAACCTCATTCGATATCTACC R RF: TTCTAGAGGATATGAGGAGTGAGAGAGTCCTATAAACTCAGGCCTGACTCTCAACTGGAGTGACCAAAACCTCATTCGATATCTACC RR: AAGATCTCCTATACTCCTCACTCTCTCAGGATATTTGAGTCCGGACTGAGAGTTGACCTCACTGGTTTTGGAGTAAGCTATAGATGG F2: 3 GTCCGGACTG 2 Unidirectional alignment (log-probability: -34.9) AGGATATGAGGAGTGAGAGAGTCCTATAAACTCAGaCCTGgtcaggcctgCTCTCAACTGGAGTGACCAAAACCTCATTCGATATCTACC AGGATATGAGGAGTGAGAGAGTCCTATAAACTCAGGCCTG---------ACTCTCAACTGGAGTGACCAAAACCTCATTCGATATCTACC Template switch alignment (log-probability: -22.6) AGGATATGAGGAGTGAGAGAGTCCTATAAACTCAGaCCTG|GTCAGGCCTG|CTCTCAACTGGAGTGACCAAAACCTCATTCGATATCTACC AGGATATGAGGAGTGAGAGAGTCCTATAAACTCAGGCCTG|GTCAGGCCTG|CTCTCAACTGGAGTGACCAAAACCTCATTCGATATCTACC ========= Event 110 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AGCTAGGACAAATTCCTACATGCATCTGATGTTTTTGTTAATCAAAAGC Chimp: AGCTAGGACAAATTCCTACATGCATCTGATGTTTTTGTTAATCAAAAGC ↓ 13 24 ↑ 13 24 Gorilla: AGCTAGGACAAATTCCTACATCAGATGCATGTTTTTGTTAATCAAAAGC ↓ 13 24 ↑ 13 24 Human: AGCTAGGACAAATTCCTACATGCATCTGATGTTTTTGTTAATCAAAAGC Cluster: [ ] Orangutan: AGCTAGGACAAATTCCTACATGCATCTGATGTTTTTGTTCATCAAAAGC Gorilla > Human --------------- chr10:115402987-115402993 Template switch process: F1: L TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT 1 F3: 4 ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT R RF: TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACATCAGATGCATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT RR: ACAGACGAGTATTTTTCTTTTCGATCCTGTTTAAGGATGTAGTCTACGTACAAAAACAATTAGTTTTCGTATACAAAAAAGACAAACA F2: 3 GTCTACG 2 Unidirectional alignment (log-probability: -28.1) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTAC-----ATGCatctgATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACATCAGATGC-----ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Template switch alignment (log-probability: -16.6) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|GCATCTG|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|GCATCTG|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Human > Gorilla --------------- chr10:129765070-129765076 Template switch process: F1: L TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT 1 F3: 4 ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT R RF: TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACATGCATCTGATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT RR: ACAGACGAGTATTTTTCTTTTCGATCCTGTTTAAGGATGTACGTAGACTACAAAAACAATTAGTTTTCGTATACAAAAAAGACAAACA F2: 3 CGTAGAC 2 Unidirectional alignment (log-probability: -28.1) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACatcagATGC-----ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTAC-----ATGCATCTGATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Template switch alignment (log-probability: -16.6) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|CAGATGC|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|CAGATGC|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Gorilla > Chimp --------------- chr10:116698573-116698579 Template switch process: F1: L TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT 1 F3: 4 ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT R RF: TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACATCAGATGCATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT RR: ACAGACGAGTATTTTTCTTTTCGATCCTGTTTAAGGATGTAGTCTACGTACAAAAACAATTAGTTTTCGTATACAAAAAAGACAAACA F2: 3 GTCTACG 2 Unidirectional alignment (log-probability: -28.1) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTAC-----ATGCatctgATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACATCAGATGC-----ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Template switch alignment (log-probability: -16.6) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|GCATCTG|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|GCATCTG|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Chimp > Gorilla --------------- chr10:129765070-129765076 Template switch process: F1: L TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT 1 F3: 4 ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT R RF: TGTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACATGCATCTGATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT RR: ACAGACGAGTATTTTTCTTTTCGATCCTGTTTAAGGATGTACGTAGACTACAAAAACAATTAGTTTTCGTATACAAAAAAGACAAACA F2: 3 CGTAGAC 2 Unidirectional alignment (log-probability: -28.1) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACatcagATGC-----ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTAC-----ATGCATCTGATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT Template switch alignment (log-probability: -16.6) GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|CAGATGC|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT GTCTGCTCATAAAAAGAAAAGCTAGGACAAATTCCTACAT|CAGATGC|ATGTTTTTGTTAATCAAAAGCATATGTTTTTTCTGTTTGT ========= Event 111 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTGAAGTTTGTATTTTTGTGGTGTTACTTTAAGATTTCAAGCTGttttttt-------------- Chimp: CATTGAAgtttgtatttttgtggtgatactttaagatttccagctgtttttgt-------------- Gorilla: CATTGAAGTTTGTATTTTTGTAGTGATACTTTAAGATTTCCAGCttttttttttttttttttttgtt ↑ 1 3 24 Human: CATTGAAGTTTGTATTTTTGTGGTGTTACTTTAAGATTTCAAGCTGttttttt-------------- Cluster: [ ] Orangutan: CATTGAAGTTTGTATTTTTGTGGTGATACTTTAAGATTTCCAACttttttttt-------------- Human > Gorilla --------------- chr10:4581781-4581785 Template switch process: F1: L AAATGACTCTTTATGGCACTCATTGAAGTTTGTATTTTTGTAGTGATACTTTAAGATTTC 1 F3: 4 TTTTTTTTTTTTTTTTTTTGT R RF: AAATGACTCTTTATGGCACTCATTGAAGTTTGTATTTTTGTGGTGTTACTTTAAGATTTCAAGCTGTTTTTTTTTTTTTTTTTTTGA RR: TTTACTGAGAAATACCGTGAGTAACTTCAAACATAAAAACACCACAATGAAATTCTAAAGTTCGACAAAAAAAAAAAAAAAAAAACT F2: 3 TCGAC 2 Unidirectional alignment (log-probability: -48.5) CATTGAAGTTTGTATTTTTGTaGTGaTACTTTAAGATTTCcAGCTtTTTTTTTtttttttttttgt CATTGAAGTTTGTATTTTTGTGGTGTTACTTTAAGATTTCAAGCTGTTTTTTT------------- Template switch alignment (log-probability: -32.9) CATTGAAGTTTGTATTTTTGTaGTGaTACTTTAAGATTTC|CAGCT|TTTTTTTTTTTTTTTTTTTGt CATTGAAGTTTGTATTTTTGTGGTGTTACTTTAAGATTTC|CAGCT|TTTTTTTTTTTTTTTTTTTGA ========= Event 112 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GATAACGTTTTAAAAAATAAAA--------------------------GTAACCTAAGTATTGAACAAGCCCATTATAAATGA ↑ 1 3 2 4 Chimp: GATAACGTTTTAAAAAATAAA-TACTTAGGTTACTTTTAACAAGCCCATTATAATAAGCATTTAACAAGCCCATTATAAATGA Gorilla: ----------------------------------------------------------------------------------- Human: GATAACGTTTTAAAAAATAAAA--------------------------GTAACCTAAGTATTGAACAAGCCCATTATAAATGA Cluster: [ ] Orangutan: ----------------------------------------------------------------------------------- Chimp > Human ------------- chr10:596174-596185 Template switch process: F1: L TGAAAAGCTGAAAGGTCACAGATAACGTTTTAAAAAATAAA 1 F3: 4 ATTGAACAAGCCCATTATAAATGATAAAAAATGATATTAAGTTG R RF: TGAAAAGCTCAAAGGTCACAGATAACGTTTTAAAAAATAAATACTTAGGTTACTTTTAACAAGCCCATTATAATAAGCATTTAACAAGCCCATTATAAATGATAAAAAATGATATTAAGTTG RR: ACTTTTCGAGTTTCCAGTGTCTATTGCAAAATTTTTTATTTATGAATCCAATGAAAATTGTTCGGGTAATATTATTCGTAAATTGTTCGGGTAATATTTACTATTTTTTACTATAATTCAAC F2: 3 TGAATCCAATGA 2 Unidirectional alignment (log-probability: -49.4) GAAAAGCTgAAAGGTCACAGATAACGTTTTAAAAAATAA-------------------------------AAgtaaccTAAGtATTgAACAAGCCCATTATAAATGATAAAAAATGATATTAA GAAAAGCTCAAAGGTCACAGATAACGTTTTAAAAAATAAATACTTAGGTTACTTTTAACAAGCCCATTATAA------TAAGCATTTAACAAGCCCATTATAAATGATAAAAAATGATATTAA Template switch alignment (log-probability: -28.8) GAAAAGCTgAAAGGTCACAGATAACGTTTTAAAAAATAAA|AGTAACCTAAGT|ATTgAACAAGCCCATTATAAATGATAAAAAATGATATTAA GAAAAGCTCAAAGGTCACAGATAACGTTTTAAAAAATAAA|AGTAACCTAAGT|ATTTAACAAGCCCATTATAAATGATAAAAAATGATATTAA ========= Event 113 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGTTGCTGAACCACCGTTATTCAGCAG-----------CAAAAACGGCAGCAAATTCTAAAAT Chimp: CATTTGCTGAACCACCGTTATTCAGCAG-----------CAAAAACGGCAGCAAATTCTAAAAT ↓ 3 1 4 Gorilla: CAGTTGCTGAACCACCGTTATTCAGCAGCTTTTGCTGCTGAATAACGGCAGCAAATTCTAAAAT ↑ 3 1 4 Human: CAGTTGCTGAACCACCGTTATTCAGCAG-----------CAAAAACGGCAGCAAATTCTAAAAT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNN-----------NNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr10:376551-376564 Template switch process: F1: L TACAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGC 1 F3: 4 AACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC R RF: TACAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGCAAAAACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC RR: ATGTTCTTAAAGAGTCAACGACTTGGTGGCAATAAGTCGTCGTTTTTGCCGTCGTTTAAGATTTTAAAGAAAAAGAAGAGTACTG F2: 3 TAAGTCGTCGTTTT 2 Unidirectional alignment (log-probability: -32.3) CAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGCttttgctgctgAAtAACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC CAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGC-----------AAAAACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC Template switch alignment (log-probability: -17.5) CAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGC|TTTTGCTGCTGAAT|AACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC CAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGC|TTTTGCTGCTGAAT|AACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC Chimp > Gorilla --------------- chr10:376551-376564 Template switch process: F1: L TACAAGAATTTCTCAGTTGCTGAACCACCGTTATTCAGCAGC 1 F3: 4 AACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC R RF: TACGAGAATTTCTCATTTGCTGAACCACCGTTATTCAGCAGCAAAAACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC RR: ATGCTCTTAAAGAGTAAACGACTTGGTGGCAATAAGTCGTCGTTTTTGCCGTCGTTTAAGATTTTAAAGAAAAAGAAGAGTACTG F2: 3 TAAGTCGTCGTTTT 2 Unidirectional alignment (log-probability: -43.3) CaAGAATTTCTCAgTTGCTGAACCACCGTTATTCAGCAGCttttgctgctgAAtAACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC CGAGAATTTCTCATTTGCTGAACCACCGTTATTCAGCAGC-----------AAAAACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC Template switch alignment (log-probability: -28.6) CaAGAATTTCTCAgTTGCTGAACCACCGTTATTCAGCAGC|TTTTGCTGCTGAAT|AACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC CGAGAATTTCTCATTTGCTGAACCACCGTTATTCAGCAGC|TTTTGCTGCTGAAT|AACGGCAGCAAATTCTAAAATTTCTTTTTCTTCTCATGAC ========= Event 114 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGAGTATTCTGTTCCCATAATGTCCGACCAATTCTTGATGAGTACTGGCATTTTTAAATTTTTTAA Chimp: TAGAGTATTCTGTTCCCATAATGTCTGACCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTAA ↓ 1 4 3 2 Gorilla: TAGAGTATTCTGTTCCCATAAAGTACTCCCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTGA Human: TAGAGTATTCTGTTCCCATAATGTCCGACCAATTCTTGATGAGTACTGGCATTTTTAAATTTTTTAA Cluster: [ ] Orangutan: TAGAGTATTGTGTTCCCATAATGCCTGACCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTGA Chimp > Gorilla --------------- chr10:86128467-86128473 Template switch process: F1: L CCTAGATATCTGTTTAATATTAGAGTATTCTGTTCCCATAA 1 F3: 4 CCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTGAA R RF: CCTAGATTTCTGTTTAATATTAGAGTATTCTGTTCCCATAATGTCTGACCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTAAA RR: GGATCTAAAGACAAATTATAATCTCATAAGACAAGGGTATTACAGACTGGTTAAGAACTACTCATGACGGTAAAAATTTAAAAAATTT F2: 3 CTCATGA 2 Unidirectional alignment (log-probability: -39.9) CTAGATaTCTGTTTAATATTAGAGTATTCTGTTCCCATAAaGTactcCCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTgAA CTAGATTTCTGTTTAATATTAGAGTATTCTGTTCCCATAATGTCTGACCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTAAA Template switch alignment (log-probability: -27.7) CTAGATaTCTGTTTAATATTAGAGTATTCTGTTCCCATAA|AGTACTC|CCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTgAA CTAGATTTCTGTTTAATATTAGAGTATTCTGTTCCCATAA|AGTACTC|CCAATTCTTGATGAGTACTGCCATTTTTAAATTTTTTAAA ========= Event 115 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGCCAGAATTTCTTATACCTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGA-----------------------------------------------------------------------------------------------ATTTTATTTTTCTTACTATATA ↓ 3 4 2 1 Chimp: AGGCCAGAATTTCTTATACCTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAATAGTTGTCATTCATATCATAAAGGAGGTGGACATTTGGGTGCGAGGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAATTTTATTTTTCTTACTATATA ↑ 3 4 2 1 Gorilla: AGGCCAGAATTTCTTATACCTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGA-----------------------------------------------------------------------------------------------ATTTTATTTTTCTTACTATATA Human: AGGCCAGAATTTCTTATACCTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGA-----------------------------------------------------------------------------------------------ATTTTATTTTTCTTACTATATA Cluster: [ ] Orangutan: AGGCCAGAATTTCTTATACCTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGA-----------------------------------------------------------------------------------------------ATTTTATTTTTCTTACTATATA Human > Chimp ------------- chr10:99300068-99300111 Template switch process: F1: L ACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAAT 1 F3: 4 GAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAATTTTATTTTTCTTACTATATAGTTCTGATTTAAAAAACT R RF: CTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAATTTTATTTTTCTTACTATATAGTTCTGATTAAAAAAACT RR: GAGCGTGGGTTTACAGGTGGAGGAAATACTATACTTACTGTTGATAAAATCATCGACAAAAGTGGTACTTTATATCAGTTCTTAAAATAAAAAGAATGATATATCAAGACTAATTTTTTTGA F2: 3 GAGCGTGGGTTTACAGGTGGAGGAAATACTATACTTACTGTTGA 2 Unidirectional alignment (log-probability: -148) attttagtagctgttttcaccatgaaatatagtcaagaatagttgtcattcatatcataaaggaggtggacatttgggtgcgaggaatgacaACTATTTTAGTAGCTGTTTTCACCATGAAATA --------------------------------------------------------------------------------------------ACTATTTTAGTAGCTGTTTTCACCATGAAATA Template switch alignment (log-probability: -27.5) ATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAAT|AGTTGTCATTCATATCATAAAGGAGGTGGACATTTGGGTGCGAG|GAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATA ATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAAT|AGTTGTCATTCATATCATAAAGGAGGTGGACATTTGGGTGCGAG|GAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATA Gorilla > Chimp --------------- chr10:99300068-99300111 Template switch process: F1: L ACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAAT 1 F3: 4 GAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAATTTTATTTTTCTTACTATATAGTTCTGATTTAAAAAACT R RF: CTCGCACCCAAATGTCCACCTCCTTTATGATATGAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAATTTTATTTTTCTTACTATATAGTTCTGATTAAAAAAACT RR: GAGCGTGGGTTTACAGGTGGAGGAAATACTATACTTACTGTTGATAAAATCATCGACAAAAGTGGTACTTTATATCAGTTCTTAAAATAAAAAGAATGATATATCAAGACTAATTTTTTTGA F2: 3 GAGCGTGGGTTTACAGGTGGAGGAAATACTATACTTACTGTTGA 2 Unidirectional alignment (log-probability: -148) attttagtagctgttttcaccatgaaatatagtcaagaatagttgtcattcatatcataaaggaggtggacatttgggtgcgaggaatgacaACTATTTTAGTAGCTGTTTTCACCATGAAATA --------------------------------------------------------------------------------------------ACTATTTTAGTAGCTGTTTTCACCATGAAATA Template switch alignment (log-probability: -27.9) ATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAAT|AGTTGTCATTCATATCATAAAGGAGGTGGACATTTGGGTGCGAG|GAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATA ATTTTAGTAGCTGTTTTCACCATGAAATATAGTCAAGAAT|AGTTGTCATTCATATCATAAAGGAGGTGGACATTTGGGTGCGAG|GAATGACAACTATTTTAGTAGCTGTTTTCACCATGAAATA ========= Event 116 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAACAGGGATGAAAAGCCCTTTCTCCTCAGAA----AGGAGGAGGGGCCATCATGCTGG ↑ 3 1 2 4 Chimp: ATAACAGGGATGAAAAGCCCTTTCTGAGGAGAA--ACCTGAGGAGGGGCCATCATGCTGG Gorilla: ATAACAGGGATGAAAAGCCCTTTCTGAGGAGAAAC--CTGAGGAGGGGCCATCATGCTGG ↓ 3 1 2 4 Human: ATAACAGGGATGAAAAGCCCTTTCTCCTCAGAA----AGGAGGAGGGGCCATCATGCTGG Cluster: [ ] Orangutan: ATAACAGGGATGAAAAGCCCTTTCTGAGGAGAAAT--CTGAGGAGGGGCCATCATGCTGG Chimp > Human ------------- chr10:88325205-88325214 Template switch process: F1: L AGGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT 1 F3: 4 GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT R RF: AGGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCTGAGGAGAAACCTGAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT RR: TCCCATGTTCCTATACTATTGTCCCTACTTTTCGGGAAAGACTCCTCTTTGGACTCCTCCCCGGTAGTACGACCCAACCTTACACCCTCACAA F2: 3 GAAAGACTCC 2 Unidirectional alignment (log-probability: -31.7) GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT---------CCTcagaaagGAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCTGAGGAGAAACCT-------GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT Template switch alignment (log-probability: -16.5) GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT|CCTCAGAAAG|GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT|CCTCAGAAAG|GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT Gorilla > Human --------------- chr10:88325205-88325214 Template switch process: F1: L AGGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT 1 F3: 4 GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT R RF: AGGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCTGAGGAGAAACCTGAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT RR: TCCCATGTTCCTATACTATTGTCCCTACTTTTCGGGAAAGACTCCTCTTTGGACTCCTCCCCGGTAGTACGACCCAACCTTACACCCTCACAA F2: 3 GAAAGACTCC 2 Unidirectional alignment (log-probability: -31.2) GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT---------CCTcagaaagGAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCTGAGGAGAAACCT-------GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT Template switch alignment (log-probability: -17) GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT|CCTCAGAAAG|GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT GGGTACAAGGATATGATAACAGGGATGAAAAGCCCTTTCT|CCTCAGAAAG|GAGGAGGGGCCATCATGCTGGGTTGGAATGTGGGAGTGTT ========= Event 117 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CCCAGGTGTAACCAGAAACCACTAAGGCACTT--AGTGGCCACTTGCTGTATAGAAGCT Chimp: CCCAGGTGTAACCAGAAACCACTAAGGCATTT-GGGAGGCCACTTGCTGTATAGAAGCT ↓ 3 2 1 4 Gorilla: CCCAGGTGTAACCAGAAACCACTAAGGCACTT--AGTGGCCACTTGCTGTACAGAAGCT Human: CCCAGGTGTAACCAGAAACCACTAAGGCACTT--AGTGGCCACTTGCTGTATAGAAGCT Cluster: [ ] Orangutan: CCCAGGTGTAACCAGAAACCACTAAGGCATTTG-GGAGGCCACTTGCTGTATAGAAGCT Chimp > Gorilla --------------- chr10:64440602-64440608 Template switch process: F1: L AGGACCCTGTTCCCCAGGTGTAACCAGAAACCACTAAGGCA 1 F3: 4 GCCACTTGCTGTACAGAAGCTCAGTTCAGACTGATGCTG R RF: AGGACCCTGTTCCCCAGGTGTAACCAGAAACCACTAAGGCATTTGGGAGGCCACTTGCTGTATAGAAGCTCAGTTCAGACTGATGCTG RR: TCCTGGGACAAGGGGTCCACATTGGTCTTTGGTGATTCCGTAAACCCTCCGGTGAACGACATATCTTCGAGTCAAGTCTGACTACGAC F2: 3 GTGATTC 2 Unidirectional alignment (log-probability: -33.1) GGACCCTGTTCCCCAGGTGTAACCAGAAACCACTAAGGCAcTTa-GtGGCCACTTGCTGTAcAGAAGCTCAGTTCAGACTGATGCTG GGACCCTGTTCCCCAGGTGTAACCAGAAACCACTAAGGCATTTGGGAGGCCACTTGCTGTATAGAAGCTCAGTTCAGACTGATGCTG Template switch alignment (log-probability: -22.1) GGACCCTGTTCCCCAGGTGTAACCAGAAACCACTAAGGCA|CTTAGTG|GCCACTTGCTGTAcAGAAGCTCAGTTCAGACTGATGCTG GGACCCTGTTCCCCAGGTGTAACCAGAAACCACTAAGGCA|CTTAGTG|GCCACTTGCTGTATAGAAGCTCAGTTCAGACTGATGCTG ========= Event 118 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGAGAAAGAGAAGAGTTCTTTCTTCTGACTCTCTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAGGTGGCTGTAAGTGATGAAGAGAGTCAGAAAACCATGTGTCCAAGGTTCTGC Chimp: AAGAGAAAGAGAAGAGTTCTTGTTGAGA----ACTCTGACTCTCACCGTGTTCCTAGAGCCACCCCAGCAGAGGTGGCTGTAAGTGATGAAGAGAGTCAGAAAACCATGTGTCCAAGGTTCTGC Gorilla: AAGAGAAAGAGAAGAGTTCTTGTTGAGA----ACTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAGGTGGCTGTAAGTGATGAAGAGAGTCAGAAAACCATGTGTCCAAGGTTCTGC ↓ 1 4 3 2 Human: AAGAGAAAGAGAAGAGTTCTTTCTTCTGACTCTCTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAGGTGGCTGTAAGTGATGAAGAGAGTCAGAAAACCATGTGTCCAAGGTTCTGC Cluster: [ ] Orangutan: AAGACAACAAGAAGAGTTCTTGTTGAGA----ACTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAGGTGGCTGTAAGTGATGAAGAGAGTCAGAAAACCATGTGTCCAAGGTTCTGC Gorilla > Human --------------- chr10:89001433-89001444 Template switch process: F1: L GTTATACTTAAGAACATATGAAGAGAAAGAGAAGAGTTCTT 1 F3: 4 CTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAG R RF: GTTATACTTAAGAACATATGAAGAGAAAGAGAAGAGTTCTTGTTGAGAACTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAGGTGGCTGTAAGTGATGAAGAGAGTCAGAAAA RR: CAATATGAATTCTTGTATACTTCTCTTTCTCTTCTCAAGAACAACTCTTGAGACTGAGAGTGACACAAGGATCTCGGTGGGGTCGTCTCCACCGACATTCACTACTTCTCTCAGTCTTTT F2: 3 TCTCAGTCTTCT 2 Unidirectional alignment (log-probability: -38.3) TTATACTTAAGAACATATGAAGAGAAAGAGAAGAGTTCTT--------tcttctgactctCTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAG TTATACTTAAGAACATATGAAGAGAAAGAGAAGAGTTCTTGTTGAGAA------------CTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAG Template switch alignment (log-probability: -22.8) TTATACTTAAGAACATATGAAGAGAAAGAGAAGAGTTCTT|TcTTCTGACTCT|CTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAG TTATACTTAAGAACATATGAAGAGAAAGAGAAGAGTTCTT|TTTTCTGACTCT|CTCTGACTCTCACTGTGTTCCTAGAGCCACCCCAGCAGAG ========= Event 119 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCCGTCCAGAGCTCAGCATCAGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTCCCCTACCCCCCCTTAAGCTATTTGAAC Chimp: GGCCGTCCAGAGTTCAGCATCAGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTCCCCTAcccccccTTAAGCTACTTGAAC Gorilla: GGCCGTCCAGAGTTCAGCATCAGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTGCT-GACTCCCCCTTAAGCTATTTGAAC ↑ 3 2 1 4 Human: GGCCGTCCAGAGCTCAGCATCAGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTCCCCTACCCCCCCTTAAGCTATTTGAAC Cluster: [ ] Orangutan: GGCCGTCCAGAGTTCAGCATCAGTGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTCCCCTAC-CCACCTTAAGCTATTTGAAC Human > Gorilla --------------- chr10:81462390-81462394 Template switch process: F1: L CAGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACT 1 F3: 4 CTCCCCCTTAAGCTATTTGAACTTCTCACGCCCTCCACCTGC R RF: TCAGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTCCCCTACCCCCCCTTAAGCTATTTGAACTTCTCACGCCCTCCACCTGC RR: AGTCGCGAGGACCGTGTCTGGGGTGACGACTGAGGTAAGTGAGGGGATGGGGGGGAATTCGATAAACTTGAAGAGTGCGGGAGGTGGACG F2: 3 AGTCG 2 Unidirectional alignment (log-probability: -31.1) AGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACT--------gctgactCCCCCTTAAGCTATTTGAACTTCTCACGCCCTCCACCT AGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACTCCCCTACC-------CCCCCTTAAGCTATTTGAACTTCTCACGCCCTCCACCT Template switch alignment (log-probability: -21.9) AGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACT|GCTGA|CtCCCCCTTAAGCTATTTGAACTTCTCACGCCCTCCACCT AGCGCTCCTGGCACAGACCCCACTGCTGACTCCATTCACT|GCTGA|CCCCCCCTTAAGCTATTTGAACTTCTCACGCCCTCCACCT ========= Event 120 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACCAAGCTACTT-TCATTATGACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTTAGCAATATAAAGCAAAGTGTCC----CATTTAAAAATTGGTAAAACCTTATAATCAATATGCATTAAAAATTTT----------------TAGTATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATCATTATTAATGGCAAA---- Chimp: ACCAAGCTACTT-TCATTATGACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTTAACAATATAAAGCAAAGTGTCC----CATTTAAAAATTGGTAAAACCTTATAATCAATATGCATTAAAAATTTT----------------TAGTATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATCATTATTAATGGCAAA---- ↓ 1 3 2 4 ↑ 1 3 4 2 Gorilla: --TGGGATACTTTGCTTTATATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTGTCATAAT-GAAAGTAGCTTGGTATTTTCAAAATTGG------ATTCTAATTTCTGGCCAGTTAAAGTTCTCAAGGAGAAAAAATTTTAACAACAGAAGGTCTAAGGAATGCATGGTCAAAACAGGAAACACCCAGTGGGCAGGTGACACGGGCGGAACCTCCAGGGAAGGTCAGGCACGCTCAGACTTTGTTCTGCACCTGGCTGTGATCCCTGCTCCTTCTCATAATCCAGTGTGTCTTTTCTTTGACTTCTAGTCAGGTTCAATCTGTGAATTCAAGTACCAACTTTGTTTTTGTTTTCAAAATCTTGAACTCTGGACCACTTTAGGCATGCTGTTTTAAGAAAGTAGTTCACTTTCTGAAAATGGTTTTAATTACTTTGCTATTCACGTGGAAGCATAATTTGCACATTCAGCCAATTTTTGCAGATAACTTTCCTCTGTTTCATATTGTTTCAAGCCTAGAGGAATAATAATTTCTTGTTCCAGGAGATACTGTTTTCAGTCATTAATTGGTGATTTGATTAAAAAACAAATTCTGCCTTCTGCCTGGGTCATAGTGATCCCCAAGGGACTGTTCTgt------------------------------------------tgtttgcagatctgagatatcaatactctgtctccctaaaccttcaggagagtctgctgcatacacagtaacctgtatcaatgtctggcttctttctttgaaggtaaaaagagggtgtgctctgtgcctcatcaccatagtacagaacaggatggcccctgcagctcggtgagaagatcactaaactgaactaacttcataggatctggtttttggcagcagatgtaaccatgagactagaaggccccaggaattcataaacttcctggcattgagctgggctcctccatgggctgcggactgaattcaaacggatgcccctaggtctcaacaagcagagtaatcactgctgtctgacttgcaCTGCTAAGTTTTAAGTCTAATCTGAATTGGGGCTTACTGAATCTCAAAGATGTCAACCAAGTCATCAGAGAAACCAAAATTCTCCTAACCAAAAATTACCTACGCTAAGATTCACTAGCAGGCAAGTTTTAGCTCAAACTCACGGTGAAGTCCCTGCATTCTGGTTGCCAAGTGGCAGTGTGAGAAGGCAGCCAGCACCACTGCTGGCTAACAGGAGGGCTCACACCACAGTTTGATTTCCACAGGCTGAGGTCTCCTAGTTAGCTCCCTTCCTGGTCTCTGGTGTCACTGAAGGAAGCTTCACGGTGAGAGTAATTGTGGCTCTTTGAGTACCACTGGGCATAGCCAGTGTAAATCTATCCCCCAACTGGTCATCAGTGGGTGTGACCCTTCTTAATTCTCACCAAAGACAAAATCAagctgtgtcaggaatttattccttctggtgggttcttggtctcggtgacttcaagaatgaagctgtggacctcgcggtgagtgttacagctcttaaaggtgggcgtccggaatttgctccttcaggtgcgttcatggtctcgctgacttcaggagtgaagacgcagaccctccccttgagtgttacagctattaaacgtggcacggacccaaacagtgagcagcagcaagattcattatgaagagcaaaagaa ↓ 1 3 4 2 ↑ 1 3 2 4 Human: ACCAAGCTACTT-TCATTATGACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTTAGCAATATAAAGCAAAGTGTCC----CATTTAAAAATTGGTAAAACCTTATAATCAATATGCATTAAAAATTTT----------------TAGTATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATCATTATTAATGGCAAA---- Cluster: [ ] Orangutan: --CACTTTGCTT-TTATTG-----TTAAATATAAAACAATATAAACCAAATTTCGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTGTCATAAT-GAAAGTAGCTTGGTATTTTCAAAATTGG------ATTCTAATTTCTGGCCAGTTAAAGTTCTCAAGGAGAAAAAATTTTAACAACAGAAGGTCTAAGAAATGCATGGTCAAAAGAGG-AACACCCAGTGGGCAGGTGACACGGGCAGAACCTCCAGGGAAGGTCAGGCACGCTCAGACTTTGTTCTGCGCCTGGCTGTGATCCCTGCTCCTTCTCACAATTCAGTGTATCTTTTCTTTGACTTCTAGTTAGCTTCAATGTGTGAATTCAAGTACCAACTTTGTTTTTGTTTTCAAAATCTTGAACTCTGGACCACTTTCAGCATGCTGTTTTAAGAAAGTAGTTCACTTTCTGAAAATGATTTTAATTACTTTGCTATTCATGTGGAAGCATAATTTGCACATTCAGCCAATTTTTGTAAATAACTTTCCTCTGTTTCATATTGTTTCAAGCCTAGAGGAATAATAATTTCTTGTGCCAGGAGATACTGTTTTCAGTCATTAATGGGTGATTTGATTAAAAAACGAATTCTGCCTTCTGCCTGGGTCATAGTGATCCCCAAGGGGCTGTTCTGTTAAgtttgcagatctgagatatcaatactctagtctccctaa---------------------------------------accttcaggagagtctgctgcacacacagtaacctgtatcaatgtctggcttccttctttgaaggtaaaaagagggtgtgctctgtgcctcatcaccatggtacagaacaggatggcccctgcagcttggtg---agatcactaaactgaactaacttcataggatctggtttttggcagcagatgtaaccgtgagactagaaggccccaggaattcacaaacttcctggcattgagctgggctcgtccatggggtgcggactgaattcaaacggatgtccctaggtctcaacaagcagagtaatcactgctgTCTCACTTGCACTGATAGGTTTTAAGTCTAATCTGAATTGCGGCTTGCTGAATCTCGAAGATGTCAGCCACGTTATCAGAGAAACCAAAATTCTCCTAACCAAAAATTACCTATGCTAAGATTCACTAGCACGCAAGTTTTAGCTCAAACTCACGGTGAAGTCCCTGCATTCTGGTTGGCAACTGGCAGCGTGAGAAGGCAGCCAGCACCGCTGCTGGCTAACAGATGGGCTCACACCACAGTTTGATTTCCACACGCTGAGGTCTCCTAGTTAGCTCCCTTCCCGGTCTCTGGTTCCACTGAAGGAAGCTCCACAGTGAGAGTAATTGTGGCGCTCTGAGTACCACTGGGCATGGCCAGTGTAAATCTATCCCTCAACTGGTCATCCGTGGATGTGACCCTTCTTAATTCTCACCAAAGACAAAATCAagctgtgtccggaatttattccttctggtgggttcttggtctcggtgacttcaagaatgaagccgtggacctcacggtgagtgttacagctcttaaaggtgggcgtccataatttgctccttcaggtgcgttcatggtctcgctgacttcaggagtgaagacgcagaccctccccttgagtgttatagctcttaaacgtggcgcggacccaaacagtgagcagcagcaacattcattatgaagagcaaaagaa Gorilla > Human --------------- chr10:46500349-46500422 Template switch process: F1: L TAT 1 F3: 4 AGCAATAT R RF: TATATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTGTC RR: ATATAACAATTTATATTTTGTTATATTTTGTTTAAACCTGTTCCGACAGGTTTAAACCCATTATAAACGAATTGACGTCACAG F2: 3 TTTATATTTTGTTATATTTTGTTTAAACCTGTTCCGACAGGTTTAAACCCATTATAAACGAATTGACGTCACAG 2 Unidirectional alignment (log-probability: -128) tatgacactgcagttaagcaaatattacccaaatttggacagccttgtccaaatttgtttTATATTGTTttATATttAgCAATAT------------------------------------------------------------ ------------------------------------------------------------TATATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTGTCAT Template switch alignment (log-probability: -29) TAT|GACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTT|AgCAATAT TAT|GACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTT|AACAATAT Human > Gorilla --------------- chr10:63643592-63643669 Template switch process: F1: L TAT 1 F3: 4 TCAT R RF: TATGACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTTAGCAATATAAAGCAAAGTGTCCCATTTAAAAATTGGTAAAACCTTATAATCAATATGCATTAAAAATTTTTAGTATCACATCAT RR: ATACTGTGACGTCAATTCGTTTATAATGGGTTTAAACCTGTCGGAACAGGTTTAAACAAAATATAACAAAATATAAATCGTTATATTTCGTTTCACAGGGTAAATTTTTAACCATTTTGGAATATTAGTTATACGTAATTTTTAAAAATCATAGTGTAGTA F2: 3 GTGACGTCAATTCGTTTATAATGGGTTTAAACCTGTCGGAACAGGTTTAAACAAAATATAACAAAATATAAATTGTTA 2 Unidirectional alignment (log-probability: -128) TATATTGTTaaATATaaAaCAATATaaaacaaatttggacaaggctgtccaaatttgggtaatatttgcttaactgcagtgtcat TATATTGTTTTATATTTAGCAATAT------------------------------------------------------------ Template switch alignment (log-probability: -29.4) TAT|ATTGtTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTG|TCAT TAT|ATTGCTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTG|TCAT Gorilla > Chimp --------------- chr10:85224705-85224778 Template switch process: F1: L TAT 1 F3: 4 AACAATAT R RF: TATATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTGTC RR: ATATAACAATTTATATTTTGTTATATTTTGTTTAAACCTGTTCCGACAGGTTTAAACCCATTATAAACGAATTGACGTCACAG F2: 3 TTTATATTTTGTTATATTTTGTTTAAACCTGTTCCGACAGGTTTAAACCCATTATAAACGAATTGACGTCACAG 2 Unidirectional alignment (log-probability: -123) tatgacactgcagttaagcaaatattacccaaatttggacagccttgtccaaatttgtttTATATTGTTttATATttAACAATAT------------------------------------------------------------ ------------------------------------------------------------TATATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTGTCAT Template switch alignment (log-probability: -23.4) TAT|GACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTT|AACAATAT TAT|GACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTT|AACAATAT Chimp > Gorilla --------------- chr10:63643592-63643669 Template switch process: F1: L TAT 1 F3: 4 TCAT R RF: TATGACACTGCAGTTAAGCAAATATTACCCAAATTTGGACAGCCTTGTCCAAATTTGTTTTATATTGTTTTATATTTAACAATATAAAGCAAAGTGTCCCATTTAAAAATTGGTAAAACCTTATAATCAATATGCATTAAAAATTTTTAGTATCACATCAT RR: ATACTGTGACGTCAATTCGTTTATAATGGGTTTAAACCTGTCGGAACAGGTTTAAACAAAATATAACAAAATATAAATTGTTATATTTCGTTTCACAGGGTAAATTTTTAACCATTTTGGAATATTAGTTATACGTAATTTTTAAAAATCATAGTGTAGTA F2: 3 GTGACGTCAATTCGTTTATAATGGGTTTAAACCTGTCGGAACAGGTTTAAACAAAATATAACAAAATATAAATTGTTA 2 Unidirectional alignment (log-probability: -123) TATATTGTTaaATATaaAACAATATaaaacaaatttggacaaggctgtccaaatttgggtaatatttgcttaactgcagtgtcat TATATTGTTTTATATTTAACAATAT------------------------------------------------------------ Template switch alignment (log-probability: -23.9) TAT|ATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTG|TCAT TAT|ATTGTTAAATATAAAACAATATAAAACAAATTTGGACAAGGCTGTCCAAATTTGGGTAATATTTGCTTAACTGCAGTG|TCAT ========= Event 121 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAAATATGATAATTCCACTCATATAAATGTCCAATATTTCCTAATTAATCAAATATTGTTATCACTTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCC--------------------------------------------TCAAACACTTATGTGAGACTTCTGTGAGAGTATTCTTTCAAGCCTCAGGACACTTACCGAGTCTTATG Chimp: GGAAATATGATAATTCTACTCATATAAATGTCCAATATTTCCTAATTAATCAAATATTGTTATCACTTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCC--------------------------------------------TCAAACACTTATGTGAGACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTACCGAGTCTTATG ↑ 3 2 4 1 Gorilla: GGAAATATGATAATTCCACTCATATAAATGTCCAATATTTCCTAATTAATCAAATATTGTTATCACTTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCC----------------------------------------------------------------------------------------TCAAGACACTTACCGAGTCTTATG ↓ 3 2 4 1 Human: GGAAATATGATAATTCCACTCATATAAATGTCCAATATTTCCTAATTAATCAAATATTGTTATCACTTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCC--------------------------------------------TCAAACACTTATGTGAGACTTCTGTGAGAGTATTCTTTCAAGCCTCAGGACACTTACCGAGTCTTATG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNCTCATATAAATGTCCAATAATTCCTAATTAATCAAATATTGTTATCACTTTGGGATGAtgagacttctgtgagagtattctatcaagcctcaaacacttatgtgagacttctatgagagtattctttcaagcc--------------------------------------------ttaagacacttaCCGAGTCTTATG Gorilla > Human --------------- chr10:28503891-28503902 Template switch process: F1: L TTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA 1 F3: 4 GACTTCTGTGAGAGTATTCTTTCAAGCCTCAGGACACTTACCGAGTCTTATGTTTACTATGATGGAAGGTTT R RF: TCATATAAATGTCCAATATTTCCTAATTAATCAAATATTGTTATCACTTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTACCGAGTCTTATGTTTACTATGATGGAAGGTTT RR: AGTATATTTACAGGTTATAAAGGATTAATTAGTTTATAACAATAGTGAAACCCTACTACACTGAAGACACTCTCATAAGAAAGTTCGGAGTTCTGTGAATGGCTCAGAATACAAATGATACTACCTTCCAAA F2: 3 AGTGTATTCACA 2 Unidirectional alignment (log-probability: -74.2) GATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAAacacttatgtgagacttctgtgagagtattctttcaagcctcagGACACTTA GATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA--------------------------------------------GACACTTA Template switch alignment (log-probability: -34.6) GATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA|ACAcTTATgTGA|GACTTCTGTGAGAGTATTCTTTCAAGCCTCAgGACACTTA GATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA|ACATTTATATGA|GACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTA Gorilla > Chimp --------------- chr10:29460668-29460679 Template switch process: F1: L TTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA 1 F3: 4 GACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTACCGAGTCTTATGTTTACTATGATGGAAG R RF: TCATATAAATGTCCAATATTTCCTAATTAATCAAATATTGTTATCACTTTGGGATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTACCGAGTCTTATGTTTACTATGATGGAAG RR: AGTATATTTACAGGTTATAAAGGATTAATTAGTTTATAACAATAGTGAAACCCTACTACACTGAAGACACTCTCATAAGAAAGTTCGGAGTTCTGTGAATGGCTCAGAATACAAATGATACTACCTTC F2: 3 AGTGTATTCACA 2 Unidirectional alignment (log-probability: -74.1) GATGATGTgacttctgtgagagtattctttcaagcctcaaacacttatgtgaGACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTA GATGATGT--------------------------------------------GACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTA Template switch alignment (log-probability: -29) GATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA|ACAcTTATgTGA|GACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTA GATGATGTGACTTCTGTGAGAGTATTCTTTCAAGCCTCAA|ACATTTATATGA|GACTTCTGTGAGAGTATTCTTTCAAGCCTCAAGACACTTA ========= Event 122 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGGCAGGGCTTGGCTGCTGGGTCAAGGGTGAAGAGTGGAgtgtgtgtgtgtgtgtgtgt------gtgtgtgtgtgtgtgtgtgtTTGGTGAGGGTCAGGGGACATGCAATTC ↑ 1 4 3 2 Chimp: TTGGCAGGGCTTGGCTGCTGGCTCGAGGGTGAAGAGTGGAgtgtgtgtgtgtgtgt------------------gtgtgtgtgtgtTTGGTGACGGTCAGGGGACATGCAATTC Gorilla: TTGGCAGGGCTTGGCTGCTGGCTCGAGGGTGAAGAGTGGAgtgtgtgtgtgtgtgtgtgt--------gtgtgtgtgtgtatgtgtTTGGTGAGGGTCAGGGGACATGCAATTC Human: GTGGCAGGGCTTGGCTGCTGGGTCAAGGGTGAAGAGTGGAgtgtgtgtgtgtgtgtgtgt------gtgtgtgtgtgtgtgtgtgtTTGGTGAGGGTCAGGGGACATGCAATTC Cluster: [ ] Orangutan: TTGGCAGGGCTTGGCTGCTGGCTCGAGAGTGAGGAGTGGAgtgtgtgtgtgtgtgtgtgtgtgtgt--gtgtgtgtgtgtgtgtgtTTGGTGAGGGTCAGGGGACATGCAATTC Chimp > Human ------------- chr10:119325038-119325041 Template switch process: F1: L GGAGGGGTTTAGAGTTAAAAGTGGCAGGGCTTGGCTGCTGG 1 F3: 4 AGGGTGAAGAGTGGAGTGTGTGTGTGTGTGTGTGTGTGTG R RF: GGAGGGGTTTAGAGTTAAAATTGGCAGGGCTTGGCTGCTGGCTCGAGGGTGAAGAGTGGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGGTGAC RR: CCTCCCCAAATCTCAATTTTAACCGTCCCGAACCGACGACCGAGCTCCCACTTCTCACCTCACACACACACACACACACACACACACAAACCACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -38.8) GAGGGGTTTAGAGTTAAAAgTGGCAGGGCTTGGCTGCTGGgTCaAGGGTGAAGAGTGGAGTGTGTGTGTGTGTGTgtgtgtgtg GAGGGGTTTAGAGTTAAAATTGGCAGGGCTTGGCTGCTGGCTCGAGGGTGAAGAGTGGAGTGTGTGTGTGTGTGT--------- Template switch alignment (log-probability: -21.8) GAGGGGTTTAGAGTTAAAAgTGGCAGGGCTTGGCTGCTGG|GTCA|AGGGTGAAGAGTGGAGTGTGTGTGTGTGTGTGTGTGTGTG GAGGGGTTTAGAGTTAAAATTGGCAGGGCTTGGCTGCTGG|GTCA|AGGGTGAAGAGTGGAGTGTGTGTGTGTGTGTGTGTGTGTG ========= Event 123 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCTGGGCTTGCAGAGCCGGC--------------------AGTCAGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTG Chimp: GCCTGGGCTTGCAGAGCCGGC--------------------AGTCGGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTG ↓ 1 3 2 4 Gorilla: GCCTGGGCTTGCAGAGCCGGC----------------------------------------ACTGACTTCT-GACTGTTTTTCTTCAGTAATTG ↑ 1 3 2 4 Human: GCCTGGGCTTGCAGAGCCGGC--------------------AGTCAGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTG Cluster: [ ] Orangutan: GTCTGGGCTGGCAGAGCCGGCGGTCAGAAGTCAGTGCCGGC--------------------TTCGGCTTCTAAACTGTTTTTCTTCAGTAATTG Human > Gorilla --------------- chr10:145667711-145667720 Template switch process: F1: L GGACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA 1 F3: 4 ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA R RF: GGACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCAGTCAGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA RR: CCTGTGTGAGTTCTCGGTCGCGGACCCGAACGTCTCGGCCGTCAGTCTTCAGTCGCGGCCGAAACCGAAGATTTGACAAAAAGAAGTCATTAACGGTCCATTTGACGAAGAGT F2: 3 GTCTTCAGTC 2 Unidirectional alignment (log-probability: -35.1) ACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCActgacttctG------------------------------ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA ACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA---------GTCAGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA Template switch alignment (log-probability: -17) ACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA|CTGACTTCTG|ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA ACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA|CTGACTTCTG|ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA Chimp > Gorilla --------------- chr10:145667711-145667720 Template switch process: F1: L GGACACACTCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA 1 F3: 4 ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA R RF: GGACACACCCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCAGTCGGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA RR: CCTGTGTGGGTTCTCGGTCGCGGACCCGAACGTCTCGGCCGTCAGCCTTCAGTCGCGGCCGAAACCGAAGATTTGACAAAAAGAAGTCATTAACGGTCCATTTGACGAAGAGT F2: 3 GTCTTCAGTC 2 Unidirectional alignment (log-probability: -40.7) ACACACtCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCActgacttctG------------------------------ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA ACACACCCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA---------GTCGGAAGTCAGCGCCGGCTTTGGCTTCTAAACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA Template switch alignment (log-probability: -28.1) ACACACtCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA|CTGACTTCtG|ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA ACACACCCAAGAGCCAGCGCCTGGGCTTGCAGAGCCGGCA|CTGACTTCCG|ACTGTTTTTCTTCAGTAATTGCCAGGTAAACTGCTTCTCA ========= Event 124 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: attattagataagaagaggatcactgcaAAAACAAACAGATACTTGTT-TTTGCAGT-GATGGAGATAACATTGTTAATATT ↑ 3 2 1 4 Chimp: attattagataagaagaggatcactgcaAAAACAAACAGATACTTGATGGTCTCAGTACACGGAGATAACATTGTTAATATT Gorilla: attattagataagaagaggatcactgcaAAAACAAACAGATGCTTGATGGTCTCAGTACATGGAGATAACATTGTTAATATT ↓ 3 2 1 4 Human: attattagataagaagaggatcactgcaAAAACAAACAGATACTTGTT-TTTGCAGT-GATGGAGATAACATTGTTAATATT Cluster: [ ] Orangutan: attattagataagaagaggatcactacaAAA----ACAGATACTTGATGGTCTCAGTACATGGAGATAACATTGTTAATATT Chimp > Human ------------- chr10:50227340-50227352 Template switch process: F1: L TAGATAAGAAGAGGATCACTGCAAAAACAAACAGATACTTG 1 F3: 4 GGAGATAACATTGTTAATATTTTTATAGTATTTTAAAGCT R RF: TAGATAAGAAGAGGATCACTGCAAAAACAAACAGATACTTGATGGTCTCAGTACACGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAGCT RR: ATCTATTCTTCTCCTAGTGACGTTTTTGTTTGTCTATGAACTACCAGAGTCATGTGCCTCTATTGTAACAATTATAAAAATATCATAAAATTTCGA F2: 3 TAGTGACGTTTTT 2 Unidirectional alignment (log-probability: -37.6) AGATAAGAAGAGGATCACTGCAAAAACAAACAGATACTtgtttttgcagTGATG-------------GAGATAACATTGTTAATATTTTTATAGTATTTTAAAGCT AGATAAGAAGAGGATCACTGCAAAAACAAACAGATACT-----------TGATGGTCTCAGTACACGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAGCT Template switch alignment (log-probability: -16.9) AGATAAGAAGAGGATCACTGCAAAAACAAACAGATACTTG|TTTTTGCAGTGAT|GGAGATAACATTGTTAATATTTTTATAGTATTTTAAAGCT AGATAAGAAGAGGATCACTGCAAAAACAAACAGATACTTG|TTTTTGCAGTGAT|GGAGATAACATTGTTAATATTTTTATAGTATTTTAAAGCT Gorilla > Human --------------- chr10:50227340-50227350 Template switch process: F1: L ATTATTAGATAAGAAGAGGATCACTGCAAAAACAAACAGATACTTG 1 F3: 4 ATGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAG R RF: ATTATTAGATAAGAAGAGGATCACTGCAAAAACAAACAGATGCTTGATGGTCTCAGTACATGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAG RR: TAATAATCTATTCTTCTCCTAGTGACGTTTTTGTTTGTCTACGAACTACCAGAGTCATGTACCTCTATTGTAACAATTATAAAAATATCATAAAATTTC F2: 3 GTGACGTTTTT 2 Unidirectional alignment (log-probability: -41.6) AGATAAGAAGAGGATCACTGCAAAAACAAACAGA----------------TACttgtttttgcagtgATGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAG AGATAAGAAGAGGATCACTGCAAAAACAAACAGATGCTTGATGGTCTCAGTAC--------------ATGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAG Template switch alignment (log-probability: -22.8) AGATAAGAAGAGGATCACTGCAAAAACAAACAGATaCTTG|TTTTTGCAGTG|ATGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAG AGATAAGAAGAGGATCACTGCAAAAACAAACAGATGCTTG|TTTTTGCAGTG|ATGGAGATAACATTGTTAATATTTTTATAGTATTTTAAAG ========= Event 125 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: AATTTATTATTTTGAAAATACT--GTATTATGAAGCCATGTTCATA--AAGGTAAGAAAGGCAGATTCTACA Chimp: Gorilla: AATTTATTATTTTGAAAATACC----TTTATGAACATGGCTTCATAATATAGTAAGAAAGGCAGATTCTACA ↓ 1 3 24 ↑ 1 3 24 Human: AATTTATTATTTTGAAAATACT--GTATTATGAAGCCATGTTCATA--AAGGTAAGAAAGGCAGATTCTACA Cluster: [ ] Orangutan: AATTTATTATTTTGAAAATACTAT--ATTATGAAGCCACATTCATA--AAGGTAAGAAAGGCAGATTCTACA Gorilla > Human --------------- chr10:5107303-5107328 Template switch process: F1: L ATAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC 1 F3: 4 GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC R RF: ATAAGGGAATATGATTGAATAATTTATTATTTTGAAAATACCTTTATGAACATGGCTTCATAATATAGTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC RR: TATTCCCTTATACTAACTTATTAAATAATAAAACTTTTATGGAAATACTTGTACCGAAGTATTATATCATTCTTTCCGTCTAAGATGTTGATCAGTCTGTTGAATTG F2: 3 GAAATACTTGTACCGAAGTATTATGT 2 Unidirectional alignment (log-probability: -59) TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC----------------------TgTAttatgaagccatgttcataaagGTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATACCTTTATGAACATGGCTTCATAATATA----------------------GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC Template switch alignment (log-probability: -24.6) TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC|TgTATTATGAAGCCATGTTCATAAAG|GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC|TATATTATGAAGCCATGTTCATAAAG|GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC Human > Gorilla --------------- chr10:5163884-5163909 Template switch process: F1: L ATAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC 1 F3: 4 GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC R RF: ATAAGGGAATATGATTGAATAATTTATTATTTTGAAAATACTGTATTATGAAGCCATGTTCATAAAGGTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC RR: TATTCCCTTATACTAACTTATTAAATAATAAAACTTTTATGACATAATACTTCGGTACAAGTATTTCCATTCTTTCCGTCTAAGATGTTGATCAGTCTGTTGAATTG F2: 3 ATATAATACTTCGGTACAAGTATTTC 2 Unidirectional alignment (log-probability: -59) TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATACctttatgaacatggcttcataaTaTA----------------------GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC----------------------TGTATTATGAAGCCATGTTCATAAAGGTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC Template switch alignment (log-probability: -24.6) TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC|CTTTATGAACATGGCTTCATAATAtA|GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC TAAGGGAATATGATTGAATAATTTATTATTTTGAAAATAC|CTTTATGAACATGGCTTCATAATACA|GTAAGAAAGGCAGATTCTACAACTAGTCAGACAACTTAAC ========= Event 126 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCATGTGGAAAAATTAAAGTCACACTGGCATTTATTACGTGGGAACTGACTCACTTCAATAGACTCACCAGAATTCTCAATTGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGTGTGA-------------CCTTTGGATGAACCACATAAGTC Chimp: TTCATGTGGAAAAATTAAAGTCACACTGGCATTTATTACGTGGGAACTGACTCACTTCAATAGACTCACCAGAATTCTCAATTGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGTGTGA-------------CCTTTGGATGAACCACATAAGTC ↑ 3 2 1 4 Gorilla: TTCATGTGGAAAAATTAAAGTCACACTGGCATTTATTACGTGGGAACTGACTCACTTCAATAGACTCACCAGAATTCTCAATTGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGAATTATTTTACAATGAATTCATTGGATGAACCACATAAGCC ↓ 3 2 1 4 Human: TTCATGTGGAAAAATTAAAGTCACACTGGCATTTATTACGTGGGAACTGACTCACTTCAATAGACTCACCAGAATTCTCAATTGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGTGTGA-------------CCTTTGGATGAACCACATAAGTC Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------tatagaatatatatattgaat--atatatagaatata------------------------------------------- Gorilla > Human --------------- chr10:50947238-50947243 Template switch process: F1: L TGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG 1 F3: 4 CTTTGGATGAACCACATAAGTCGTCGCAAAGCTAATAAGGAT R RF: GTCACACTGGCATTTATTACGTGGGAACTGACTCACTTCAATAGACTCACCAGAATTCTCAATTGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGAATTATTTTACAATGAATTCATTGGATGAACCACATAAGCCGTCGCAAAGCTAATAAGGAT RR: CAGTGTGACCGTAAATAATGCACCCTTGACTGAGTGAAGTTATCTGAGTGGTCTTAAGAGTTAACACTTCTTACACCTGAAACTTAATAAAATGTCTGATCTACTTAATAAAATGTTACTTAAGTAACCTACTTGGTGTATTCGGCAGCGTTTCGATTATTCCTA F2: 3 CAGTGT 2 Unidirectional alignment (log-probability: -38.7) GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG---------------------tgtgacctTTGGATGAACCACATAAGtCGTCGCAAAGCTAATAAGG GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGAATTATTTTACAATGAATTCA--------TTGGATGAACCACATAAGCCGTCGCAAAGCTAATAAGG Template switch alignment (log-probability: -27.6) GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG|TGTGAC|CtTTGGATGAACCACATAAGtCGTCGCAAAGCTAATAAGG GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG|TGTGAC|CATTGGATGAACCACATAAGCCGTCGCAAAGCTAATAAGG Gorilla > Chimp --------------- chr10:51742451-51742456 Template switch process: F1: L TGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG 1 F3: 4 CTTTGGATGAACCACATAAGTCGTCGCAAAGCTAATAAGGAT R RF: GTCACACTGGCATTTATTACGTGGGAACTGACTCACTTCAATAGACTCACCAGAATTCTCAATTGTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGAATTATTTTACAATGAATTCATTGGATGAACCACATAAGCCGTCGCAAAGCTAATAAGGAT RR: CAGTGTGACCGTAAATAATGCACCCTTGACTGAGTGAAGTTATCTGAGTGGTCTTAAGAGTTAACACTTCTTACACCTGAAACTTAATAAAATGTCTGATCTACTTAATAAAATGTTACTTAAGTAACCTACTTGGTGTATTCGGCAGCGTTTCGATTATTCCTA F2: 3 CAGTGT 2 Unidirectional alignment (log-probability: -38.7) GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG---------------------tgtgacctTTGGATGAACCACATAAGtCGTCGCAAAGCTAATAAGG GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATGAATTATTTTACAATGAATTCA--------TTGGATGAACCACATAAGCCGTCGCAAAGCTAATAAGG Template switch alignment (log-probability: -27.6) GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG|TGTGAC|CtTTGGATGAACCACATAAGtCGTCGCAAAGCTAATAAGG GTGAAGAATGTGGACTTTGAATTATTTTACAGACTAGATG|TGTGAC|CATTGGATGAACCACATAAGCCGTCGCAAAGCTAATAAGG ========= Event 127 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTGGGAGCATGACCACTCTTTCTAGGTCTGA---------------------ATAGATAGAATAACCACCACCTCAGAAAATAGACTGTACAGCTTAAGACAGATGTTGAG Chimp: GCTGGGAGCATGACCACTCTTTCTAGGTCTGA---------------------ATAGATAGAATAACCACCACTTCAGAAAATAGAATGTATAGCTTAAGACAGATGTTGAG ↓ 3 1 2 4 Gorilla: GCTGGGAGCATGACCACTCTTTCTAGGTCTAT------------------------------------------TCAGACCTAGAAATGTATAGCTTAAGACAGATGTTGAG ↑ 3 1 2 4 Human: GCTGGGAGCATGACCACTCTTTCTAGGTCTGA---------------------ATAGATAGAATAACCACCACCTCAGAAAATAGACTGTACAGCTTAAGACAGATGTTGAG Cluster: [ ] Orangutan: GCTGGGAGCATGACCAGTCTTTCTAGGTCTGAATAGATAGAATAACCACCACC---------------------TCAGAAAAGAGAATGTATAG-CTAAGACAGATGTTGAG Human > Gorilla --------------- chr10:89857196-89857210 Template switch process: F1: L CACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT 1 F3: 4 TGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGATAAATCCT R RF: CACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCTGAATAGATAGAATAACCACCACCTCAGAAAATAGACTGTACAGCTTAAGACAGATGTTGAGGCATGAAGAAGATAAATCCT RR: GTGTTATAGAACGACCCTCGTACTGGTGAGAAAGATCCAGACTTATCTATCTTATTGGTGGTGGAGTCTTTTATCTGACATGTCGAATTCTGTCTACAACTCCGTACTTCTTCTATTTAGGA F2: 3 AAAGATCCAGACTTA 2 Unidirectional alignment (log-probability: -49.2) ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCTattcagacctaGA--------------------------------AaTGTAtAGCTTAAGACAGATGTTGAGGCATGAAGAAGATAA ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT-----------GAATAGATAGAATAACCACCACCTCAGAAAATAGACTGTACAGCTTAAGACAGATGTTGAGGCATGAAGAAGATAA Template switch alignment (log-probability: -23.3) ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT|ATTCAGACCTAGAAA|TGTAtAGCTTAAGACAGATGTTGAGGCATGAAGAAGATAA ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT|ATTCAGACCTAGAAA|TGTACAGCTTAAGACAGATGTTGAGGCATGAAGAAGATAA Chimp > Gorilla --------------- chr10:89857196-89857208 Template switch process: F1: L CACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT 1 F3: 4 AATGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGAT R RF: CACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCTGAATAGATAGAATAACCACCACTTCAGAAAATAGAATGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGAT RR: GTGTTATAGAACGACCCTCGTACTGGTGAGAAAGATCCAGACTTATCTATCTTATTGGTGGTGAAGTCTTTTATCTTACATATCGAATTCTGTCTACAACTCCGTACTTCTTCTA F2: 3 AGATCCAGACTTA 2 Unidirectional alignment (log-probability: -38.1) ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCTattcagacctaGA--------------------------------AATGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGAT ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT-----------GAATAGATAGAATAACCACCACTTCAGAAAATAGAATGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGAT Template switch alignment (log-probability: -17.4) ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT|ATTCAGACCTAGA|AATGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGAT ACAATATCTTGCTGGGAGCATGACCACTCTTTCTAGGTCT|ATTCAGACCTAGA|AATGTATAGCTTAAGACAGATGTTGAGGCATGAAGAAGAT ========= Event 128 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGTTGTTTCCTCTGCTTTTGAGTCACAGTTAATATTT-AGTGTG-------AGTAAAATTATACCATGGTA Chimp: CAGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTTAACTGTG-ACTCATGGTAAAATTATACCATGGTA ↑ 3 2 1 4 Gorilla: CTGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTT-AGTGT-G------GGTAAAATTATACCATGGTA Human: CAGTTGTTTCCTCTGCTTTTGAGTCACAGTTAATATTT-AGTGTG-------AGTAAAATTATACCATGGTA Cluster: [ ] Orangutan: CAGTTGTTTCCTCTGTTTTTGAATCACAGTTAATATTC-AGTGT-G------GGTAAAATTATACCATGGTA Gorilla > Chimp --------------- chr10:52927817-52927827 Template switch process: F1: L TTACAGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTTA 1 F3: 4 TGGTAAAATTATACCATGGTAGATGCACTAAATGATAAAGT R RF: TTACTGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTTAGTGTGGGTAAAATTATACCATGGTAGATGCACTAAATGATAAAGT RR: AATGACAACAAAGGAGACAAAAACTCAGTGTCAATTATAAATCACACCCATTTTAATATGGTACCATCTACGTGATTTACTATTTCA F2: 3 ACTCAGTGTCA 2 Unidirectional alignment (log-probability: -41.8) ACaGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTTaAcTGTGactcatGGTAAAATTATACCATGGTAGATGCACTAAATGATAAAG ACTGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTT-AGTGTG------GGTAAAATTATACCATGGTAGATGCACTAAATGATAAAG Template switch alignment (log-probability: -28.2) ACaGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTTA|ACTGTGACTCA|tGGTAAAATTATACCATGGTAGATGCACTAAATGATAAAG ACTGTTGTTTCCTCTGTTTTTGAGTCACAGTTAATATTTA|ACTGTGACTCA|GGGTAAAATTATACCATGGTAGATGCACTAAATGATAAAG ========= Event 129 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTAATTTTCATGTCTCGTAGATTTGGTAGCACCAAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTTGTTTCTGTTAAAAGCAGAAGAAAATTTACAGAAATAACAAAGAATGAGGATAATTTCAGGGGGATATTAATACTAGTTTAATTCATGCAGTAAGTAGAAATAAAGAG ↓ 1 4 3 2 Chimp: CTAATTTTCATGTCTCGTAGACATG-------AAAATAAGATTGTAAACACCTTGCACTTTGTTCTCCAACTTGTTTCTGTTAAAAGCAGAAGAAAATTTACAGAAATAACAAAGAATGAGGATAATTTCAGGGGGATATTAATACTAGTTTAATTCATGCAGTAAGTAGAAATAAAGAG Gorilla: CAAATTTTCATGTCTCGTAGATTTGGTAGCACCAAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTTGTTTCTGTTAAAAGCAGAAGAAAATTTACAAAAATAACAAAGAATGAGGATAATTTCAGGGGGATATTAATACTAGTTTAATTCATGCAGTAAGTAGAAATAAAGAG Human: CTAATTTTCATGTCTCGTAGATTTGGTAGCACCAAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTTGTTTCTGTTAAAAGCAGAAGAAAATTTACAGAAATAACAAAGAATGAGGATAATTTCAGGGGGATATTAATACTAGTTTAATTCATGCAGTAAGTAGAAATAAAGAG Cluster: [ ] Orangutan: CTAATTTTCATGTCTTATAGATTTGGTAGCACCAAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTTGCTTCTGTTAAAAGCAGAAGAAAATTTACAGAAATAACAAAGAATGAGGATAATTTCAGGGGGATATTAATTCTAGTTTAATTCATGCAGTAAGTAGAAATAAAGAG Human > Chimp ------------- chr10:29566026-29566030 Template switch process: F1: L AGGATTTTTAAGCCCTTCTGCTAATTTTCATGTCTCGTAGA 1 F3: 4 AAATAAGATTGTAAACACCTTGCACTTTGTTCTCCAACTTGTTTCTG R RF: AGGATTTTTAAGCCCTTCTGCTAATTTTCATGTCTCGTAGATTTGGTAGCACCAAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTTGTTTCTGTTAAAAGCAGAAGAAAATTTACAGAAATAACAAAGAATGAGGATAATTTCAGGGGGATATTAATACTAGTTTAATTCATG RR: TCCTAAAAATTCGGGAAGACGATTAAAAGTACAGAGCATCTAAACCATCGTGGTTTATTTTAACATTTGTGGAACGTGAAAGAAGAGGTTGAACAAAGACAATTTTCGTCTTCTTTTAAATGTCTTTATTGTTTCTTACTCCTATTAAAGTCCCCCTATAATTATGATCAAATTAAGTAC F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -39.5) GGATTTTTAAGCCCTTCTGCTAATTTTCATGTCTCGTAGA-----------CatgaAAATAAgATTGTAAACACCTTGCACTTTgTTCTCCAACTT GGATTTTTAAGCCCTTCTGCTAATTTTCATGTCTCGTAGATTTGGTAGCACC----AAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTT Template switch alignment (log-probability: -28) GGATTTTTAAGCCCTTCTGCTAATTTTCATGTCTCGTAGA|CATGA|AAATAAgATTGTAAACACCTTGCACTTTgTTCTCCAACTT GGATTTTTAAGCCCTTCTGCTAATTTTCATGTCTCGTAGA|CATGA|AAATAAAATTGTAAACACCTTGCACTTTCTTCTCCAACTT ========= Event 130 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ---------GACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAACACATCCTACGCGCTCTTCTTC ↓ 3 2 1 4 Chimp: ---------GACCTTTGTTATCTTGGACATAGGCATG-----TCCAAGATACATCCTACGCGCTCTTCTTC ↑ 3 2 1 4 Gorilla: ---------GACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAACACATCCTACGCGCTCTTCTTC Human: ---------GACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAACACATCCTACGCGCTCTTCTTC Cluster: [ ] Orangutan: GTTCTACTGTACCTTTGTTATCTTGGACACAGGCATGCAGGTCATAGAACACATCCTACTAGCTCTTCTTC Human > Chimp ------------- chr10:82226139-82226145 Template switch process: F1: L TCCCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT 1 F3: 4 ACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT R RF: TCCCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAACACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT RR: AGGGTAAACATGACTGGAAACAATAGAACCTGTATCCGTACATCCAGTGTCTTGTGTAGGATGCGCGAGAAGAAGGTAGCCCACCAGAGTTATA F2: 3 TAGAACC 2 Unidirectional alignment (log-probability: -30.3) CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT-----------CcaagatACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAAC------ACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT Template switch alignment (log-probability: -16.2) CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT|CCAAGAT|ACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT|CCAAGAT|ACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT Gorilla > Chimp --------------- chr10:82226139-82226145 Template switch process: F1: L TCCCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT 1 F3: 4 ACATCCTACGCGCTCTTCTTCCATCGGGTGGTCTCAATAT R RF: TCCCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAACACATCCTACGCGCTCTTCTTCCATCAGGTGGTCTCAATAT RR: AGGGTAAACATGACTGGAAACAATAGAACCTGTATCCGTACATCCAGTGTCTTGTGTAGGATGCGCGAGAAGAAGGTAGTCCACCAGAGTTATA F2: 3 TAGAACC 2 Unidirectional alignment (log-probability: -35.4) CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT-----------CcaagatACATCCTACGCGCTCTTCTTCCATCgGGTGGTCTCAATAT CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGTAGGTCACAGAAC------ACATCCTACGCGCTCTTCTTCCATCAGGTGGTCTCAATAT Template switch alignment (log-probability: -22.2) CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT|CCAAGAT|ACATCCTACGCGCTCTTCTTCCATCgGGTGGTCTCAATAT CCATTTGTACTGACCTTTGTTATCTTGGACATAGGCATGT|CCAAGAT|ACATCCTACGCGCTCTTCTTCCATCAGGTGGTCTCAATAT ========= Event 131 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTCATGAATATTATCGCATACTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACGGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGACGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATACAATTCAGTGTTTACTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATC----AAGATAATTTTTATGCACATAAAAGAATTATATTATCAACAAAG Chimp: TGTCATGAATGTTATCGCATACTGAATTGTAAACACTTTGCCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATACAATTCAGTGTTTACTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAAT----AATCAAGATAATTTTTATGCACATAAAAGAATTATATTATCAACAAAG ↑ 4 3 2 1 Gorilla: TGTCATGAATATTATCGCATATTGAATT---------------------------------------------------------------------------------------------------------------------------------------------------------GTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATC----AAGATAATTTTTATGCACATAAAAGA---GAATTATCAACAAAG ↓ 4 3 2 1 Human: TGTCATGAATATTATCGCATACTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACGGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGACGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATACAATTCAGTGTTTACTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATC----AAGATAATTTTTATGCACATAAAAGAATTATATTATCAACAAAG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr10:53346612-53346623 Template switch process: F1: L ACCAGCCAGGCTGTGAAGTTTGTCATGAATATTATCGCATACTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACGGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGACGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATACAA 1 F3: 4 TGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACAC R RF: ACCAGCCAGGCTGTGAAGTTTGTCATGAATATTATCGCATATTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATAAAA RR: TGGTCGGTCCGACACTTCAAACAGTACTTATAATAGCGTATAACTTAACATTTGTGAAATGGTGACATTTTTAATGACCTTTCTTGTGAAGTAATTGTCACGTGTAATGATTTTTTACTCGAGTCGTTACAATCTTCAGCTCCTGAAGAAAATTATTAGTTCTATTAAAAATACGTGTATTTT F2: 3 CATTTGTGACTT 2 Unidirectional alignment (log-probability: -233) acttcttttaataatcaagataatttttatgcacatacaattcagtgtttactgaattgtaaacactttaccactgtaaaaattactggaaa -------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -53.4) ACTTCTTTTAATAATCAAGATAATTTTTATGCACATAcAA|TtcAGTGTTTAC|TGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAA ACTTCTTTTAATAATCAAGATAATTTTTATGCACATAAAA|TAAAGTGTTTAC|TGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAA Gorilla > Chimp --------------- chr10:54174751-54174762 Template switch process: F1: L ACCAGCCAGGCTGTGAAGTTTGTCATGAATGTTATCGCATACTGAATTGTAAACACTTTGCCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATACAA 1 F3: 4 TGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACAC R RF: ACCAGCCAGGCTGTGAAGTTTGTCATGAATATTATCGCATATTGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAAGAACACTTCATTAACAGTGCACATTACTAAAAAATGAGCTCAGCAATGTTAGAAGTCGAGGACTTCTTTTAATAATCAAGATAATTTTTATGCACATAAAA RR: TGGTCGGTCCGACACTTCAAACAGTACTTATAATAGCGTATAACTTAACATTTGTGAAATGGTGACATTTTTAATGACCTTTCTTGTGAAGTAATTGTCACGTGTAATGATTTTTTACTCGAGTCGTTACAATCTTCAGCTCCTGAAGAAAATTATTAGTTCTATTAAAAATACGTGTATTTT F2: 3 CATTTGTGACTT 2 Unidirectional alignment (log-probability: -242) acttcttttaataatcaagataatttttatgcacatacaattcagtgtttactgaattgtaaacactttACCACTGTAAAAATTACTGGAAA ---------------------------------------------------------------------ACCACTGTAAAAATTACTGGAAA Template switch alignment (log-probability: -53.4) ACTTCTTTTAATAATCAAGATAATTTTTATGCACATAcAA|TtcAGTGTTTAC|TGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAA ACTTCTTTTAATAATCAAGATAATTTTTATGCACATAAAA|TAAAGTGTTTAC|TGAATTGTAAACACTTTACCACTGTAAAAATTACTGGAAA ========= Event 132 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTCAAGATAATAATAGCCAGGAAACTTCTGCTGGCCAAAGTCCATGAAGGTCTGTCTCTGCAATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCATCATCAG----TTTCCTGCTTGGACAGGGGAGGGGCTG Chimp: TTTCAAGATAATAATAGCCAGGAAACTTCTGCTGGCCAAAGTCCATGAAGGTCTGTCTCTGCAGTCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCATGATCAG----TTTCCTGCTTGGACAGGGGAGGGGCTG Gorilla: TTTCAAGATAATAATAGCCAGGAAACTTCTGCTGGCCAAAGTCCATGAAGCTCTGTCTCTGCAATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCATGGTGAG--------GGGCTTGGACAGGGGAGGGGCTG ↓ 3 2 1 4 Human: TTTCAAGATAATAATAGCCAGGAAACTTCTGCTGGCCAAAGTCCATGAAGGTCTGTCTCTGCAATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCATCATCAG----TTTCCTGCTTGGACAGGGGAGGGGCTG Cluster: [ ] Orangutan: TTTCAAGATAATAATAGCCAGGAAACTTCTGCTGGCCAAAGTCCATG-AGGTCTGTCTCTGCAATCATCCCAGTGTCCTGAGGGCAGAGCTTCTTTTGGCATGATCAGTTTC----CTGCTTGGACAGGGGAGGGGCTG Gorilla > Human --------------- chr10:80259721-80259732 Template switch process: F1: L CAATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCAT 1 F3: 4 GCTTGGACAGGGGAGGGGCTGCTAATCTCTTTAAGCCAGA R RF: AGGAAACTTCTGCTGGCCAAAGTCCATGAAGCTCTGTCTCTGCAATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCATGGTGAGGGGCTTGGACAGGGGAGGGGCTGCTAATCTCTTTAAGCCAGA RR: TCCTTTGAAGACGACCGGTTTCAGGTACTTCGAGACAGAGACGTTAGTAGGGTCACAGGACTCCCGTTTCAAAGAAAACCGTACCACTCCCCGAACCTGTCCCCTCCCCGACGATTAGAGAAATTCGGTCT F2: 3 TCCTTTGACTAC 2 Unidirectional alignment (log-probability: -38.3) AATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCAT--------catcagtttcctGCTTGGACAGGGGAGGGGCTGCTAATCTCTTTAAGCCAGA AATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCATGGTGAGGG------------GCTTGGACAGGGGAGGGGCTGCTAATCTCTTTAAGCCAGA Template switch alignment (log-probability: -28.3) AATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCAT|CAtcAGTTTCCT|GCTTGGACAGGGGAGGGGCTGCTAATCTCTTTAAGCCAGA AATCATCCCAGTGTCCTGAGGGCAAAGTTTCTTTTGGCAT|CAGAAGTTTCCT|GCTTGGACAGGGGAGGGGCTGCTAATCTCTTTAAGCCAGA ========= Event 133 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGTCTAAAGGCTTTTCTGATGTCAAAGTTTT------CACCTCTATAATGCCAGAATGAGG ↓ 3 2 1 4 Chimp: ATGTCTAAAGGCTTTTCTGATGTCAAAGTTTTCTTTGACATCTCTATAATGCCAGAATGAGG Gorilla: ATGTCTAAAGGCTTTTCTGATGTCAAAGTTTT------CACCTCTATAATGCCAGAATGAGG Human: ATGTCTAAAGGCTTTTCTGATGTCAAAGTTTT------CACCTCTATAATGCCAGAATGAGG Cluster: [ ] Orangutan: -------------------------------------------------------------- Human > Chimp ------------- chr10:81279013-81279020 Template switch process: F1: L ACCTTGCACATGTCTAAAGGCTTTTCTGATGTCAAAGTTTTC 1 F3: 4 CTCTATAATGCCAGAATGAGGACATTCAAATAAAGAGATA R RF: ACCTTGCACATGTCTAAAGGCTTTTCTGATGTCAAAGTTTTCACCTCTATAATGCCAGAATGAGGACATTCAAATGAAGAGATA RR: TGGAACGTGTACAGATTTCCGAAAAGACTACAGTTTCAAAAGTGGAGATATTACGGTCTTACTCCTGTAAGTTTACTTCTCTAT F2: 3 TACAGTTT 2 Unidirectional alignment (log-probability: -31.6) CTTGCACATGTCTAAAGGCTTTTCTGATGTCAAAGTTTTctttgaCAtCTCTATAATGCCAGAATGAGGACATTCAAATaAAGAGATA CTTGCACATGTCTAAAGGCTTTTCTGATGTCAAAGTTTT------CACCTCTATAATGCCAGAATGAGGACATTCAAATGAAGAGATA Template switch alignment (log-probability: -22.3) CTTGCACATGTCTAAAGGCTTTTCTGATGTCAAAGTTTTC|TTTGACAT|CTCTATAATGCCAGAATGAGGACATTCAAATaAAGAGATA CTTGCACATGTCTAAAGGCTTTTCTGATGTCAAAGTTTTC|TTTGACAT|CTCTATAATGCCAGAATGAGGACATTCAAATGAAGAGATA ========= Event 134 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ACAATGATTGCTAAAAGGGTAA-------------------------------ATTGCCAGAATATTTTCCACTTTCACTAGCATTCTTTCTTGCCAAAAGATTTATATTAATCCTACTTTAATTAAGTCATTAATCAAAGGCCAGGTTGTAAAGGTCTGCAATTTTCATAGTTCTATAACTGTG Chimp: ACAATGATTGCTAAAAGGGTAA-------------------------------ATTGCCAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAAAAGATTTATATTAATCCCACTTTAATTAAGTCATTAATCAAAGGCCAGGTTGTAAAGGTCTGCAATTTTCACAGTTCTATAATTGTG ↑ 1 4 3 2 Gorilla: ACAATAATTGCTAAAAGGGTATTTATTTTAGCAGAATAATTTATTTTAGCAGAAAAAGTAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAAAAGATTTATATTAATCCTACTTTAATTAAGTCATTAATCAAAGGCCAGGTTGTAAAGGTCTGCAATTTTCACAGTTCTACAACTGTG Human: ACAATGATTGCTAAAAGGGTAA-------------------------------ATTGCCAGAATATTTTCCACTTTCACTAGCATTCTTTCTTGCCAAAAGATTTATATTAATCCTACTTTAATTAAGTCATTAATCAAAGGCCAGGTTGTAAAGGTCTGCAATTTTCATAGTTCTATAACTGTG Cluster: [ ] Orangutan: ACAGTGACTGCTAAAAGGGTAG-------------------------------ATTGACAGAATATTTT---CTTTCACTAGCATTATTTCTTGCCAAAAGATTTATATTAATCCTACTTTAATTAAGTCATTAATCAAAGGCCAGGTTGTAAAGGTCTGCAATTTTCACAGTTCTATAACTGTG Gorilla > Chimp --------------- chr10:81262443-81262448 Template switch process: F1: L TCCTGTTATCAATGCCTCTTACAATGATTGCTAAAAGGGTA 1 F3: 4 CAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAAA R RF: TCCTGTTATCAATGCCTCTTACAATAATTGCTAAAAGGGTATTTATTTTAGCAGAATAATTTATTTTAGCAGAAAAAGTAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAAAAGATTTATATTAATCCTACTTTAATTAAGTCATTAATCAAAGGCCAGGTTGTAAAGGTCTGCAATT RR: AGGACAATAGTTACGGAGAATGTTATTAACGATTTTCCCATAAATAAAATCGTCTTATTAAATAAAATCGTCTTTTTCATCTTATAAAAGATGAAAGTGATCGTAAGAAAGAACGGTTTTCTAAATATAATTAGGATGAAATTAATTCAGTAATTAGTTTCCGGTCCAACATTTCCAGACGTTAA F2: 3 CGTTAA 2 Unidirectional alignment (log-probability: -37.8) CCTGTTATCAATGCCTCTTACAATgATTGCTAAAAGGGT----------------------------------AAAtTgccAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAA CCTGTTATCAATGCCTCTTACAATAATTGCTAAAAGGGTATTTATTTTAGCAGAATAATTTATTTTAGCAGAAAAAGT---AGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAA Template switch alignment (log-probability: -27.5) CCTGTTATCAATGCCTCTTACAATgATTGCTAAAAGGGTA|AATTGC|cAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAA CCTGTTATCAATGCCTCTTACAATAATTGCTAAAAGGGTA|AATTGC|TAGAATATTTTCTACTTTCACTAGCATTCTTTCTTGCCAA ========= Event 135 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ATACTTCTTCAAGAAATCTCACGTTGTATACAATGCCAAATCTAAACTACTCTAC Chimp: ATACTTCTTCAAGAAATCTCACATTGTATACAATGCCAAATCTAAACTA------ ↑ 1 4 3 2 Gorilla: ATACTTCTTCAAGAAATCTCATATCATATACAATGCCAAATCTAAACTACTCTAC Human: ATACTTCTTCAAGAAATCTCACGTTGTATACAATGCCAAATCTAAACTACTCTAC Cluster: [ ] Orangutan: ATACTTCTTCAAGAAATCTCATATTGTATACAATGCCAAATCTAAACTACTCTAC Gorilla > Chimp --------------- chr10:55032203-55032208 Template switch process: F1: L ATTTAAGGACCCAGTCTTTCATACTTCTTCAAGAAATCTCA 1 F3: 4 ATACAATGCCAAATCTAAACTA R RF: ATTTAAGGACCCAGTCTTTCATACTTCTTCAAGAAATCTCATATCATATACAATGCCAAATCTAAACTA RR: TAAATTCCTGGGTCAGAAAGTATGAAGAAGTTCTTTAGAGTATAGTATATGTTACGGTTTAGATTTGAT F2: 3 TGTTAC 2 Unidirectional alignment (log-probability: -25.1) TTTAAGGACCCAGTCTTTCATACTTCTTCAAGAAATCTCAcATtgTATACAATGCCAAATCTAAACTA----------------- TTTAAGGACCCAGTCTTTCATACTTCTTCAAGAAATCTCATATCATATACAATGCCAAATCTAAACTACTCTACATGCAAGGTAG Template switch alignment (log-probability: -16) TTTAAGGACCCAGTCTTTCATACTTCTTCAAGAAATCTCA|CATTGT|ATACAATGCCAAATCTAAACTA TTTAAGGACCCAGTCTTTCATACTTCTTCAAGAAATCTCA|CATTGT|ATACAATGCCAAATCTAAACTA ========= Event 136 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AATGGAAGCAAAATATTTATCATTAAAAATGCATGAAAATGTTAAACTGTCTTTGGGGAACTTATTAAATCAGAGTTCATCAGAAACCTCTGGCTGTAATGCCTAGGCTGCTGTTTTTGAAGAGTCTTGAAGCCTGAGAGCTCTTTCTGAAGACCACGGTTCTTTGAAATAGCGCATGTTGCCTTTCCTCCAGGGACA ↑ 4 1 3 2 Chimp: AATGGAAGCAAAATATTTATCGTTAAAA----------ATGTTAAAATGTCTTTGGGGAACTTATTAAATCAGAGTTCATCAGAAACCTCTGGCTGTAATGCTTAGGCTGCTGTTTTTGAAGAGTCTTGAAGCCTGAGAGCTCTTTCTGAAGACCACGGTTCTTTGAAATAGCACATGTTGCCTTTCCTCCAGGGACA Gorilla: AATGGAAGCAAAATATTTATCGTTAAAAATGCATGAAAATGTTAAAATGTCTTTGGGGAACTTATTAAATCTGAGTTCATCAGAAACCTCTGGCTGTAATGCCTAGGCTGCTGTTTTTGAAGAGTCTTGAAGCCTGAGAGCTCTTTCTGAAGACCACGGTTCTTTGAAATAGCGCATGTTGCCTTTTCTCCAGGGACG Human: AATGGAAGCAAAATATTTATCATTAAAAATGCATGAAAATGTTAAACTGTCTTTGGGGAACTTATTAAATCAGAGTTCATCAGAAACCTCTGGCTGTAATGCCTAGGCTGCTGTTTTTGAAGAGTCTTGAAGCCTGAGAGCTCTTTCTGAAGACCACGGTTCTTTGAAATAGCGCATGTTGCCTTTCCTCCAGGGACA Cluster: [ ] Orangutan: AATGGAAGCAAAATATTTATTGTTAAAAATGCATGAAAATGTTAAAATGTCTTTGGGGAACTTATTAAATCAGAGTTCATTAGAAGCCTCTGGCTGTAATGCTTAGGCTGCTGTTTTTGAAGAGTCTTGAAGCCTGAGAGCTCTTTCTGAAGACCACGGTTCTTTGAAATAGCGCATGTTGCCTTTCCTCCGGGGACA Chimp > Human ------------- chr10:28270714-28270717 Template switch process: F1: L TTCTTAAACATGCAGTAGGAAATGGAAGCAAAATATTTATCATTAAAAATG 1 F3: 4 AAAATGTTAAACTGTCTTTGGGGAACTTATTAAATCAGAGTTCATCAGAAAC R RF: TTCTTAAACATGCAGTAGGAAATGGAAGCAAAATATTTATCGTTAAAAATGTTAAAATGTCTTTGGGGAACTTATTAAATCAGAGTTCATCAGAAACCTCTGGCTGTAATGCTTAGGCTGCTGTTTTTGAAGAGTCTTGAAGCCTGAGAGCTCTTTCTGAAGACCACGGTTCTTTGAAATAGCACATG RR: AAGAATTTGTACGTCATCCTTTACCTTCGTTTTATAAATAGCAATTTTTACAATTTTACAGAAACCCCTTGAATAATTTAGTCTCAAGTAGTCTTTGGAGACCGACATTACGAATCCGACGACAAAAACTTCTCAGAACTTCGGACTCTCGAGAAAGACTTCTGGTGCCAAGAAACTTTATCGTGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -37.4) GCAGTAGGAAATGGAAGCAAAATATTTATCaTTAaaaatgcatgAAAATGTTAAAcTGTCTTTGGGGAACTTATTAAATCAGAG GCAGTAGGAAATGGAAGCAAAATATTTATCGTTA----------AAAATGTTAAAATGTCTTTGGGGAACTTATTAAATCAGAG Template switch alignment (log-probability: -28.2) GCAGTAGGAAATGGAAGCAAAATATTTATCaTTAAAAATG|CATG|AAAATGTTAAAcTGTCTTTGGGGAACTTATTAAATCAGAG GCAGTAGGAAATGGAAGCAAAATATTTATCGTTAAAAATG|CATG|AAAATGTTAAAATGTCTTTGGGGAACTTATTAAATCAGAG ========= Event 137 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTGTTTTAACATTATTTACATTGATATAGAATAAGATATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTT------AATATTTTCTACAAAGATATAGTAG Chimp: ATTGTTTTAACATTATTTACATTGATATAGAATAAGATATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTT---AACAATATTTTCTACAAAGATATAGTAG Gorilla: attgttttaacattattTACATTGATATAGAATAAGAAATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTTAAC---AATGTTTTCTACAAAGATATAGTAG ↑ 3 2 1 4 Human: ATTGTTTTAACATTATTTACATTGATATAGAATAAGATATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTT------AATATTTTCTACAAAGATATAGTAG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr10:55698760-55698764 Template switch process: F1: L AAGAAATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTTAA 1 F3: 4 TTTTCTACAAAGATATAGTAGATAATTCATTTTAAAAAA R RF: CATTGATATAGAATAAGATATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTTAATATTTTCTACAAAGATATAGTAGAGAATTCATTTTAAAAAA RR: GTAACTATATCTTATTCTATAAAAAAGAAGACATACGAAGAGATACTAGGATCAATTATAAAAGATGTTTCTATATCATCTCTTAAGTAAAATTTTTT F2: 3 GTAAC 2 Unidirectional alignment (log-probability: -40) AaATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTTaacAATgTTTTCTACAAAGATATAGTAGAtAATTCATTTTAAAAAa ATATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTT---AATATTTTCTACAAAGATATAGTAGAGAATTCATTTTAAAAA- Template switch alignment (log-probability: -27.4) AaATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTTAA|CAATG|TTTTCTACAAAGATATAGTAGAtAATTCATTTTAAAAAA ATATTTTTTCTTCTGTATGCTTCTCTATGATCCTAGTTAA|CAATG|TTTTCTACAAAGATATAGTAGAGAATTCATTTTAAAAAA ========= Event 138 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTCATTCTGGCATGACAAATATAGTACTTTGTGCATCAAACTTTTATAAGCTGTTTATTAACCTGTAGT-C-TAATTCAGCTTGAGAATATAAGT Chimp: GTTCATTCTGGCATGACAAATACAGTACTTTGTGCATCAAATTTTTATAAGCTGTTTATTAACCTGTAGT-C-TAATTCAGCTTGAGAATATAAGT ↓ 3 2 1 4 Gorilla: GTTCATTCTGGCATGACAAATACAGTACTTTGCGCATCAAACTTTTATAAGCTGTTTATTAACCTGTAGCTGTATATTCAGCTTGAGAATATAAGT Human: GTTCATTCTGGCATGACAAATATAGTACTTTGTGCATCAAACTTTTATAAGCTGTTTATTAACCTGTAGT-C-TAATTCAGCTTGAGAATATAAGT Cluster: [ ] Orangutan: GTTCATTCTGGCATGACAAATATAGTACTTTGCGCATCAAACTTTTATAAGCTGTTTATTAACCTGTAGT-C-TAATTCAGCTTGAAAATATAAGT Chimp > Gorilla --------------- chr10:96423975-96423980 Template switch process: F1: L TTTGCGCATCAAACTTTTATAAGCTGTTTATTAACCTGTAG 1 F3: 4 ATTCAGCTTGAGAATATAAGTTTTGTCCAAGGGGAAGAAG R RF: ATACAGTACTTTGTGCATCAAATTTTTATAAGCTGTTTATTAACCTGTAGTCTAATTCAGCTTGAGAATATAAGTTTTGTCCAAGGGGAAGAAG RR: TATGTCATGAAACACGTAGTTTAAAAATATTCGACAAATAATTGGACATCAGATTAAGTCGAACTCTTATATTCAAAACAGGTTCCCCTTCTTC F2: 3 TATGTC 2 Unidirectional alignment (log-probability: -39) TTGcGCATCAAAcTTTTATAAGCTGTTTATTAACCTGTAGctgtaT---ATTCAGCTTGAGAATATAAGTTTTGTCCAAGGGGAAGAAG TTGTGCATCAAATTTTTATAAGCTGTTTATTAACCTGTAG-----TCTAATTCAGCTTGAGAATATAAGTTTTGTCCAAGGGGAAGAAG Template switch alignment (log-probability: -27.5) TTGcGCATCAAAcTTTTATAAGCTGTTTATTAACCTGTAG|CTGTAT|ATTCAGCTTGAGAATATAAGTTTTGTCCAAGGGGAAGAAG TTGTGCATCAAATTTTTATAAGCTGTTTATTAACCTGTAG|CTGTAT|ATTCAGCTTGAGAATATAAGTTTTGTCCAAGGGGAAGAAG ========= Event 139 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGGAAGGAAGTCCTGGCAGA----------CCAGTTTTAAttctttttttttttttttttt--tttttttgagacggagtctggctctatcgcccaggctggagtgcagtggcgcgatctcggctta ↓ 14 3 2 Chimp: ATGGAAGGAAGTCCTGGCAGA-----CGCACTCAGTTTTAAttctttt--------------tttttttttgagacggagtctggctctatcacccaggctggagtacagtggcgcaatctcggctta Gorilla: ATGGAAGGAAGTCCTGGCAGACGCAC-----TCAGTTTTAAttctttt-----------------ttttttgagatggagtctggctctatcgcccaggctggagtgcagtggcgcgatctcggctta Human: ATGGAAGGAAGTCCTGGCAGA----------CCAGTTTTAAttctttttttttttttttttt--tttttttgagacggagtctggctctatcgcccaggctggagtgcagtggcgcgatctcggctta Cluster: [ ] Orangutan: Human > Chimp ------------- chr10:79646829-79646833 Template switch process: F1: L AAGAAACGACCATCGGGTGGATGGAAGGAAGTCCTGGCAGAC 1 F3: 4 CAGTTTTAATTCTTTTTTTTTTTTTG R RF: AAGAAACGACCATCGGGTGGATGGAAGGAAGTCCTGGCAGACCAGTTTTAATTCTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTGGCTCTATCGCCCAGGCTGGAGTGC RR: TTCTTTGCTGGTAGCCCACCTACCTTCCTTCAGGACCGTCTGGTCAAAATTAAGAAAAAAAAAAAAAAAAAAAAAAAAACTCTGCCTCAGACCGAGATAGCGGGTCCGACCTCACG F2: 3 TCACG 2 Unidirectional alignment (log-probability: -28.8) GAAACGACCATCGGGTGGATGGAAGGAAGTCCTGGCAGACgcactCAGTTTTAATTC------------TTTTTTTTTTTTTG GAAACGACCATCGGGTGGATGGAAGGAAGTCCTGGCAGAC-----CAGTTTTAATTCTTTTTTTTTTTTTTTTTTTTTTTTTG Template switch alignment (log-probability: -21.6) GAAACGACCATCGGGTGGATGGAAGGAAGTCCTGGCAGAC|GCACT|CAGTTTTAATTCTTTTTTTTTTTTTg GAAACGACCATCGGGTGGATGGAAGGAAGTCCTGGCAGAC|GCACT|CAGTTTTAATTCTTTTTTTTTTTTTT ========= Event 140 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: catctctagctctctaggactctaGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCA Chimp: catctctagctctctaggactctaGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCA ↓ 3 2 1 4 Gorilla: catctctagctctctaggactctaGGCACCTTTATAAAGTG----CCTAGAGTCATCAGGATAAACTCTTGCA ↑ 3 2 1 4 Human: catctctagctctctaggactctaGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr10:5641250-5641256 Template switch process: F1: L CATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG 1 F3: 4 TCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC R RF: CATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC RR: GTAGAGATCGAGAGATCCTGAGATCCGTGGAAATATTTCACCCCTTTATCTTAGTAGTCCTATTTGAGAACGTCTTTAGTAGTATGACCCCG F2: 3 GAGATCC 2 Unidirectional alignment (log-probability: -27.7) ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG----ccTAGAgTCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC Template switch alignment (log-probability: -16.6) ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG|CCTAGAG|TCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG|CCTAGAG|TCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC Chimp > Gorilla --------------- chr10:5641250-5641256 Template switch process: F1: L CATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG 1 F3: 4 TCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC R RF: CATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC RR: GTAGAGATCGAGAGATCCTGAGATCCGTGGAAATATTTCACCCCTTTATCTTAGTAGTCCTATTTGAGAACGTCTTTAGTAGTATGACCCCG F2: 3 GAGATCC 2 Unidirectional alignment (log-probability: -27.7) ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG----ccTAGAgTCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTGGGGAAATAGAATCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC Template switch alignment (log-probability: -16.6) ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG|CCTAGAG|TCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC ATCTCTAGCTCTCTAGGACTCTAGGCACCTTTATAAAGTG|CCTAGAG|TCATCAGGATAAACTCTTGCAGAAATCATCATACTGGGGC ========= Event 141 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: aatcacaaaGAGTAATAAATGCATAAAGTCAACATCCTTATAACTGCATCAAAATATAGACCAGAACTC ↑ 3 2 1 4 Chimp: aatcacaaagagtaataaatgcataaaGTCAACATCCTTATAACCACGTCAAAATATAGACCAGAACTC Gorilla: aatcacaaagagtaataaatgcataaaGTCAACATCCTTATAACCGCATCAAAATATAGACCAGAACTC Human: aatcacaaaGAGTAATAAATGCATAAAGTCAACATCCTTATAACTGCATCAAAATATAGACCAGAACTC Cluster: [ ] Orangutan: aatcacaaagagtaataaaTGCATAAAGTCAACATCCTTATAACCACATCAAAATATAGACCAGAATTC Chimp > Human ------------- chr10:57594114-57594117 Template switch process: F1: L CACAAAGAGTAATAAATGCATAAAGTCAACATCCTTATAAC 1 F3: 4 TCAAAATATAGACCAGAACTCTGATTATAA R RF: CACAAAGAGTAATAAATGCATAAAGTCAACATCCTTATAACCACGTCAAAATATAGACCAGAACTCTGATTATAA RR: GTGTTTCTCATTATTTACGTATTTCAGTTGTAGGAATATTGGTGCAGTTTTATATCTGGTCTTGAGACTAATATT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -26.4) ACAAAGAGTAATAAATGCATAAAGTCAACATCCTTATAACtgCaTCAAAATATAGACCAGAACTCTGATTATAA---------- ACAAAGAGTAATAAATGCATAAAGTCAACATCCTTATAACCACGTCAAAATATAGACCAGAACTCTGATTATAAACCTAAAACT Template switch alignment (log-probability: -15.6) ACAAAGAGTAATAAATGCATAAAGTCAACATCCTTATAAC|TGCA|TCAAAATATAGACCAGAACTCTGATTATAA ACAAAGAGTAATAAATGCATAAAGTCAACATCCTTATAAC|TGCA|TCAAAATATAGACCAGAACTCTGATTATAA ========= Event 142 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TACTTTAGCGATGGATACTGGTTGTCACATTTTTGCTCTTGCTAGCATGAATTATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATG-------------------------------------------------------------------------------------------GAAGAAATTTTGTTTTATTTCTCCTTC ↓ 3 4 2 1 Chimp: TACTTTAGCGATGGATACTGGTTGTCACATTTTTGCTCCTGCTAGCATGAATTATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAAATTCATGCTAGCAGGAGCAAAAATGTGACAACCAGAATGAATTATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAATTTTGTTTTATTTCTCCTTC Gorilla: TACTTTAGCGATGGATACTGGTTGTCACATTTTTGCTCTTGCTAGCATGAATTATCTTACCTCCAAAATCTTTAACATAAGACTCTACACTATG-------------------------------------------------------------------------------------------GAAGAAATTTTGTTTTATTTCTCCTTC Human: TACTTTAGCGATGGATACTGGTTGTCACATTTTTGCTCTTGCTAGCATGAATTATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATG-------------------------------------------------------------------------------------------GAAGAAATTTTGTTTTATTTCTCCTTC Cluster: [ ] Orangutan: TACTTTAGCGATGGATACTGGTTGTCACATTTTTACTCTTGCTAGTATGAATTATCTTACCTCCAAAATCTTTAACATAAGATTCTACACTACG-------------------------------------------------------------------------------------------GAAGAAATTTTGTTTTATTTCTCCTTC Human > Chimp ------------- chr10:65838696-65838728 Template switch process: F1: L ATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAA 1 F3: 4 AGAATGAATTATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAATTTTGTTTTATTTCTCCTTCATGGCCTCTCCTA R RF: GGTTGTCACATTTTTGCTCTTGCTAGCATGAATTATCTTACCTCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAATTTTGTTTTATTTCTCCTTCATGGCCTCTCCTA RR: CCAACAGTGTAAAAACGAGAACGATCGTACTTAATAGAATGGAGGTTTTAGAAATTGTACTCTAAGATGTGATACCTTCTTTAAAACAAAATAAAGAGGAAGTACCGGAGAGGAT F2: 3 CCAACAGTGTAAAAACGAGGACGATCGTACTTA 2 Unidirectional alignment (log-probability: -136) tccaaaatctttaacatgagattctacactatggaagaaaattcatgctagcaggagcaaaaatgtgacaaccagaatgaattATCTTACCTCCAAAATCTTTAACATGAGAT -----------------------------------------------------------------------------------ATCTTACCTCCAAAATCTTTAACATGAGAT Template switch alignment (log-probability: -32.3) TCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAA|ATTCATGCTAGCAgGAGCAAAAATGTGACAACC|AGaATGAATTATCTTACCTCCAAAATCTTTAACATGAGAT TCCAAAATCTTTAACATGAGATTCTACACTATGGAAGAAA|ATTCATGCTAGCAAGAGCAAAAATGTGACAACC|AGCATGAATTATCTTACCTCCAAAATCTTTAACATGAGAT ========= Event 143 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAATAGTAAACTGTGTACTAAGTATCTATAA----------CCTTTGTTGAATAAATTACTTGCTAA Chimp: ataaCAGTAAGCTGTGTACTAAGTATCTATAAGGTTATAGATACTTAGTTGAATAAATTACTTGCTAA ↑ 3 1 2 4 Gorilla: ataacAGTAAGCTGTGTACTAAGTATCTATAA----------CCTTTGTTGAATAAATTACTTGCTAA Human: ATAATAGTAAACTGTGTACTAAGTATCTATAA----------CCTTTGTTGAATAAATTACTTGCTAA Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr10:69392366-69392380 Template switch process: F1: L AACATAAGAATAACAGTAAGCTGTGTACTAAGTATCTATAA 1 F3: 4 GTTGAATAAATTACTTGCTAATAATAGACTTAACAATACC R RF: AACATA---ATAACAGTAAGCTGTGTACTAAGTATCTATAACCTTTGTTGAATAAATTACTTGCTAATAATAGACTTAACAATACC RR: TTGTAT---TATTGTCATTCGACACATGATTCATAGATATTGGAAACAACTTATTTAATGAACGATTATTATCTGAATTGTTATGG F2: 3 ATTCATAGATATTGG 2 Unidirectional alignment (log-probability: -50.4) ACATAagaATAACAGTAAGCTGTGTACTAAGTATCTATAAggttatagataCTTaGTTGAATAAATTACTTGCTAATAATAGACTTAACAATACC ACATA---ATAACAGTAAGCTGTGTACTAAGTATCTATAA----------CCTTTGTTGAATAAATTACTTGCTAATAATAGACTTAACAATACC Template switch alignment (log-probability: -31.7) ACATAagaATAACAGTAAGCTGTGTACTAAGTATCTATAA|GGTTATAGATACTTA|GTTGAATAAATTACTTGCTAATAATAGACTTAACAATACC ACATA---ATAACAGTAAGCTGTGTACTAAGTATCTATAA|GGTTATAGATACTTA|GTTGAATAAATTACTTGCTAATAATAGACTTAACAATACC ========= Event 144 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TATCTAATTTTAGATAAACAAGAAATAC----AGTAGTCCCATGGTAAGTCCAGAGGAAGTCTG Chimp: TATCTAATTTTAGATAAACAAGAAATAC----AGTAGTCCCACGGTAAGTCCAGAGGAAGTCTG ↓ 3 1 2 4 Gorilla: TATCTAATTTTAGATAAACAAGAAATGT--------ATTTCGTGGTAAGTCCAGAGGAAGTCTG Human: TATCTAATTTTAGATAAACAAGAAATAC----AGTAGTCCCATGGTAAGTCCAGAGGAAGTCTG Cluster: [ ] Orangutan: TATCTAATTTTAAATAAACAAGAAATACAGTA----GTCCTGTGGTAAGTCCAAAGGAAGTCTG Chimp > Gorilla --------------- chr10:36194875-36194883 Template switch process: F1: L GAAAGATACATTAAGTATCTAATTTTAGATAAACAAGAAAT 1 F3: 4 GGTAAGTCCAGAGGAAGTCTGATTCATGGCATTAGAGCCA R RF: GAAAGATACATTAAGTATCTAATTTTAGATAAACAAGAAATACAGTAGTCCCACGGTAAGTCCAGAGGAAGTCTGATTCATGGCATTAGAGCCA RR: CTTTCTATGTAATTCATAGATTAAAATCTATTTGTTCTTTATGTCATCAGGGTGCCATTCAGGTCTCCTTCAGACTAAGTACCGTAATCTCGGT F2: 3 TGCTTTATG 2 Unidirectional alignment (log-probability: -34.2) AAAGATACATTAAGTATCTAATTTTAGATAAACAAGAAAT-------------gtatttcgtGGTAAGTCCAGAGGAAGTCTGATTCATGGCATTAGAGCCA AAAGATACATTAAGTATCTAATTTTAGATAAACAAGAAATACAGTAGTCCCAC---------GGTAAGTCCAGAGGAAGTCTGATTCATGGCATTAGAGCCA Template switch alignment (log-probability: -22.4) AAAGATACATTAAGTATCTAATTTTAGATAAACAAGAAAT|GTATTTCgT|GGTAAGTCCAGAGGAAGTCTGATTCATGGCATTAGAGCCA AAAGATACATTAAGTATCTAATTTTAGATAAACAAGAAAT|GTATTTCTT|GGTAAGTCCAGAGGAAGTCTGATTCATGGCATTAGAGCCA ========= Event 145 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: taaaatttgaaagccaAATTTAGAGGTCCCTTAGAAGGGACCTCTAAGTCCCTTCTAACACCAAAAATCAAGTTCT ↑ 3 4 1 2 Chimp: taaaatttgaaagccaAATTTAGAG----------------------GTCCCTTCTAACACCAAAAATCAAGTTCT ↓ 3 4 1 2 Gorilla: taaaatttgaaagccaAATTTAGAGGTCCCTTAGAAGGGACCTCTAAGTCCCTTCTAACACCAAAAATCAAGTTCT Human: taaaatttgaaagccaAATTTAGAGGTCCCTTAGAAGGGACCTCTAAGTCCCTTCTAACACCAAAAATCAAGTTCT Cluster: [ ] Orangutan: taaaatttgaaagcca-GTATAATGG----------CAGACTTCTAAGTCCCTTCTAACACCAAAAATCAAGTTCT Chimp > Human ------------- chr10:61779641-61779655 Template switch process: F1: L TAATAGTTAAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTT 1 F3: 4 GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA R RF: TAATAGTTCAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA RR: ATTATCAAGTCATGAAATTTTAAACTTTCGGTTTAAATCTCCAGGGAAGATTGTGGTTTTTAGTTCAAGAAATTTCTTTTT F2: 3 AATCTCCAGGGAAGA 2 Unidirectional alignment (log-probability: -48.5) aAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCcttagaagggacctctaagtccCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA CAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCC----------------------CTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA Template switch alignment (log-probability: -23.3) aAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTT|AGAAGGGACCTCTAA|GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA CAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTT|AGAAGGGACCTCTAA|GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA Chimp > Gorilla --------------- chr10:100370745-100370759 Template switch process: F1: L TAATAGTTAAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTT 1 F3: 4 GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA R RF: TAATAGTTCAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA RR: ATTATCAAGTCATGAAATTTTAAACTTTCGGTTTAAATCTCCAGGGAAGATTGTGGTTTTTAGTTCAAGAAATTTCTTTTT F2: 3 AATCTCCAGGGAAGA 2 Unidirectional alignment (log-probability: -48) aAGTACTTTAAAATTTGAAAGCCAAATTTAGAGgtcccttagaagggacctctaaGTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA CAGTACTTTAAAATTTGAAAGCCAAATTTAGAG----------------------GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA Template switch alignment (log-probability: -23.3) aAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTT|AGAAGGGACCTCTAA|GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA CAGTACTTTAAAATTTGAAAGCCAAATTTAGAGGTCCCTT|AGAAGGGACCTCTAA|GTCCCTTCTAACACCAAAAATCAAGTTCTTTAAAGAAAAA ========= Event 146 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGTGAAAGAATAATTCTGACA-------TTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC Chimp: TAAGTGAAAGAATAATTCTGACA-------TTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC ↓ 1 4 3 2 Gorilla: TAAGTGAAAGAATAATTCTGAAGCTTCTAGATATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC ↑ 1 4 3 2 Human: TAAGTGAAAGAATAATTCTGACA-------TTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC Cluster: [ ] Orangutan: TAAGTGAAAGAATAATTCTGACT-------TTATCTTTTTATCTAGAAGCTTCAGATCAGGTCAATTTTAC Human > Gorilla --------------- chrCABD030158506:15177-15186 Template switch process: F1: L CTTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA 1 F3: 4 TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC R RF: CTTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGACATTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC RR: GAACCCAAAAGAATGGACCAATTCACTTTCTTATTAAGACTGTAATAGAAAAATAGATCTTCGAAGTCTAGTCCATTTAAAATG F2: 3 AGATCTTCGA 2 Unidirectional alignment (log-probability: -35.2) TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA---agcttctagaTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGACAT----------TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC Template switch alignment (log-probability: -17) TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA|AGCTTCTAGA|TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA|AGCTTCTAGA|TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC Chimp > Gorilla --------------- chrCABD030158506:15177-15186 Template switch process: F1: L CTTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA 1 F3: 4 TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC R RF: CTTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGACATTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC RR: GAACCCAAAAGAATGGACCAATTCACTTTCTTATTAAGACTGTAATAGAAAAATAGATCTTCGAAGTCTAGTCCATTTAAAATG F2: 3 AGATCTTCGA 2 Unidirectional alignment (log-probability: -35.2) TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA---agcttctagaTATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGACAT----------TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC Template switch alignment (log-probability: -17) TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA|AGCTTCTAGA|TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC TTGGGTTTTCTTACCTGGTTAAGTGAAAGAATAATTCTGA|AGCTTCTAGA|TATCTTTTTATCTAGAAGCTTCAGATCAGGTAAATTTTAC ========= Event 147 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: GATGGTAAAACTCTTCATTAAATGTCTTA---------AAATAGCAGAGTTGAAAGCCTAAT Chimp: -------------------------------------------------------------- Gorilla: GATGGTAAAACTCTTCATTAAATGTCTTATTTAAGCTATTTTAGCAGAGTTGAAAGCCTAAT ↑ 3 1 2 4 Human: GATGGTAAAACTCTTCATTAAATGTCTTA---------AAATAGCAGAGTTGAAAGCCTAAT Cluster: [ ] Orangutan: GATGGTAAAACTCTCCATTAAATGTCTTA---------AAATAGCAGAGTTGAAAGCCTAAT Human > Gorilla --------------- chr10:107562091-107562102 Template switch process: F1: L GGTGCTTATATTGATGGTAAAACTCTTCATTAAATGTCTTA 1 F3: 4 TAGCAGAGTTGAAAGCCTAATAAGCTGCGGAGTTAGAGCC R RF: GGTGCTTATATTGATGGTAAAACTCTTCATTAAATGTCTTAAAATAGCAGAGTTGAAAGCCTAATAAGCTGCGGAGTTAGAGCC RR: CCACGAATATAACTACCATTTTGAGAAGTAATTTACAGAATTTTATCGTCTCAACTTTCGGATTATTCGACGCCTCAATCTCGG F2: 3 TTTATCGAATTT 2 Unidirectional alignment (log-probability: -38) GTGCTTATATTGATGGTAAAACTCTTCATTAAATGTCTT---AtttaagctatttTAGCAGAGTTGAAAGCCTAATAAGCTGCGGAGTTAGAGCC GTGCTTATATTGATGGTAAAACTCTTCATTAAATGTCTTAAAA------------TAGCAGAGTTGAAAGCCTAATAAGCTGCGGAGTTAGAGCC Template switch alignment (log-probability: -28.3) GTGCTTATATTGATGGTAAAACTCTTCATTAAATGTCTTA|TTTAAGctATTT|TAGCAGAGTTGAAAGCCTAATAAGCTGCGGAGTTAGAGCC GTGCTTATATTGATGGTAAAACTCTTCATTAAATGTCTTA|TTTAAGACATTT|TAGCAGAGTTGAAAGCCTAATAAGCTGCGGAGTTAGAGCC ========= Event 148 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TACCAGAAGCATGTAGAGATT------TTAGGCAAAGGACTGAAATGTACACAGTAGCCTAggtgcggtggctta Chimp: TACCAGAAGCATGTAGAGATT------TTAGGCAAAAGACTGAAATGTACACAGTAGCCTAggcgcggtggctca ↓ 1 4 3 2 Gorilla: TACCAGAAGCATGTAGAGATT------------TACTGTGTGAAATGTACACAGTAGCCTAggcgcggtggctca Human: TACCAGAAGCATGTAGAGATT------TTAGGCAAAGGACTGAAATGTACACAGTAGCCTAggtgcggtggctta Cluster: [ ] Orangutan: TACCAGAAGCATGTAGGGATTTTAGGC------AAAGGATTGAAATGTACACAGTAggctaggcgcagtggctca Chimp > Gorilla --------------- chr10:107552306-107552311 Template switch process: F1: L TCAAAGCAGGCATCATCACATACCAGAAGCATGTAGAGATTT 1 F3: 4 TGAAATGTACACAGTAGCCTAGGCGCGGTGGCTCACGCCT R RF: TCAAAGCAGG---CATCACATACCAGAAGCATGTAGAGATTTTAGGCAAAAGACTGAAATGTACACAGTAGCCTAGGCGCGGTGGCTCACGCCT RR: AGTTTCGTCC---GTAGTGTATGGTCTTCGTACATCTCTAAAATCCGTTTTCTGACTTTACATGTGTCATCGGATCCGCGCCACCGAGTGCGGA F2: 3 GTGTCA 2 Unidirectional alignment (log-probability: -40.9) AAAGCAGGCatcATCACATACCAGAAGCATGTAGAGATTT----------ACtgtgTGAAATGTACACAGTAGCCTAGGCGCGGTGGCTCACGCCT AAAGCAGGC---ATCACATACCAGAAGCATGTAGAGATTTTAGGCAAAAGAC----TGAAATGTACACAGTAGCCTAGGCGCGGTGGCTCACGCCT Template switch alignment (log-probability: -30.5) AAAGCAGGcatCATCACATACCAGAAGCATGTAGAGATTT|ACTGTG|TGAAATGTACACAGTAGCCTAGGCGCGGTGGCTCACGCCT AAAGCAGG---CATCACATACCAGAAGCATGTAGAGATTT|ACTGTG|TGAAATGTACACAGTAGCCTAGGCGCGGTGGCTCACGCCT ========= Event 149 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGTGCAGAAATTCT-TTTTTACCTTACATGACTTTATTAGAAAttttttttGGATTGAAAGATAAATTGATTAAATATTAAACCCGATAAGTTTGAAACATGATAAAATAAAAGAAACAAGAAGAAAGGGCTTATAAGGTAAAAGAGAAATTAAGGAAAT Chimp: ATGTGCAGAAATTCT-TTTTTACCTTATACGCCTTTATTAGAAAtttttttAGGATTGAAAGATAAATTGATTAAATATTAAACACAATAAGTTTGAAACATGATGAAAT-----AAACAAGAAGAAAGGGCTTATAAGGTAAAAGAGAAATTAAGGAAAT ↑ 1 4 3 2 Gorilla: ATGTGCAGAAATTCtttttttACCTTACATAGCTTTATTAGAAAtttttttAGGATTGAAAGATAAATTGATTAAATATTAAATCCAATAAGTTTGAAACACGataaaataaaagaaacaagaagaaagggcttataaggtaaaagagaaattacggaaat Human: ATGTGCAGAAATTCT-TTTTTACCTTACATGACTTTATTAGAAAttttttttGGATTGAAAGATAAATTGATTAAATATTAAACCCGATAAGTTTGAAACATGATAAAATAAAAGAAACAAGAAGAAAGGGCTTATAAGGTAAAAGAGAAATTAAGGAAAT Cluster: [ ] Orangutan: ATGTGCAGAAATTCT-TTTTTAccttacatgactttattagaaatttttttaggattgaaagataaattgattaaatattaaacccaataagtttgaaacatgataaaataaaagaaacaagaagaaagggcttataaggtaaaagagaaattaaggaaat Gorilla > Chimp --------------- chr10:70327702-70327712 Template switch process: F1: L TCAGCTGTTAAGGAATGTGCAGAAATTCTTTTTT 1 F3: 4 CTTTATTAGAAATTTTTTTAGGATTGAAAGATAAATTGAT R RF: TCAGCTGTTAAGGAATGTGCAGAAATTCTTTTTTTACCTTACATAGCTTTATTAGAAATTTTTTTAGGATTGAAAGATAAATTGATTAAATATTAAATCCAATAAGTTTGAAACACGATAAAATAAAAGAAACAAGAAGAAAGGGCTTATAAGGT RR: AGTCGACAATTCCTTACACGTCTTTAAGAAAAAAATGGAATGTATCGAAATAATCTTTAAAAAAATCCTAACTTTCTATTTAACTAATTTATAATTTAGGTTATTCAAACTTTGTGCTATTTTATTTTCTTTGTTCTTCTTTCCCGAATATTCCA F2: 3 CGCATATTCCA 2 Unidirectional alignment (log-probability: -33.1) TCAGCTGTTAAGGAATGTGCAGAAATTCTTTTT-TACCTTAtAcgcCTTTATTAGAAATTTTTTTAGGATTGAAAGATAAATTGAT TCAGCTGTTAAGGAATGTGCAGAAATTCTTTTTTTACCTTACATAGCTTTATTAGAAATTTTTTTAGGATTGAAAGATAAATTGAT Template switch alignment (log-probability: -22.5) TCAGCTGTTAAGGAATGTGCAGAAATTCTTTTTT|ACCTTATAcGC|CTTTATTAGAAATTTTTTTAGGATTGAAAGATAAATTGAT TCAGCTGTTAAGGAATGTGCAGAAATTCTTTTTT|ACCTTATAAGC|CTTTATTAGAAATTTTTTTAGGATTGAAAGATAAATTGAT ========= Event 150 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAGCTTTTATAAAATATCT--------CAGTATTTTAAAATAATATGCGAATTG Chimp: AATAGCTTTTATAAAATATCT----CAAATAGTGTTTTAAAATAATATGCGAATTG Gorilla: AATAGCTTTTATAAAATATCTCAAA----TACTGTTTTAAAATAATATGTGAATTG ↑ 31 42 Human: AATAGCTTTTATAAAATATCT--------CAGTATTTTAAAATAATATGCGAATTG Cluster: [ ] Orangutan: AATAGCTTTTATAAAATATCTCAAA----TAGTGTTTTAAAATAATACACAAATGG Human > Gorilla --------------- chr10:52828720-52828726 Template switch process: F1: L CATCACAGATAAAAGCTATGAATAGCTTTTATAAAATATCTCA 1 F3: 4 TTTTAAAATAATATGTGAATTGGTACCATTTGCAATGTAG R RF: CATCACAGATAAAAGCTATGAATAGCTTTTATAAAATATCTCAGTATTTTAAAATAATATGCGAATTGGTACCATTTGCAATGTAG RR: GTAGTGTCTATTTTCGATACTTATCGAAAATATTTTATAGAGTCATAAAATTTTATTATACGCTTAACCATGGTAAACGTTACATC F2: 3 GTCATAA 2 Unidirectional alignment (log-probability: -33.3) CACAGATAAAAGCTATGAATAGCTTTTATAAAATATCTCaaatAcTgTTTTAAAATAATATGtGAATTGGTACCATTTGCAATGTAG CACAGATAAAAGCTATGAATAGCTTTTATAAAATATCTC----AGTATTTTAAAATAATATGCGAATTGGTACCATTTGCAATGTAG Template switch alignment (log-probability: -22.2) CACAGATAAAAGCTATGAATAGCTTTTATAAAATATCTCA|AATACTG|TTTTAAAATAATATGtGAATTGGTACCATTTGCAATGTAG CACAGATAAAAGCTATGAATAGCTTTTATAAAATATCTCA|AATACTG|TTTTAAAATAATATGCGAATTGGTACCATTTGCAATGTAG ========= Event 151 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGTTCCCAGAGCAGAGGGTGGCCAAGACCA-------GGTGCCCTTAAGTGGAATAGTACA Chimp: AGGTTCCCAGAGCAGAGGGTGGCCAAGACCA-------GGTGCCCTTGAGTGGAATGGTACA ↓ 3 2 1 4 Gorilla: AGGTTCCCAGAGCAGAGGGTGGCCAAGACCCTCTTGGCCATTCCCTTGAGTGGAATGGTACA Human: AGGTTCCCAGAGCAGAGGGTGGCCAAGACCA-------GGTGCCCTTAAGTGGAATAGTACA Cluster: [ ] Orangutan: AGGTTCCCAGAGCAGAGGGTGGCCAAGACTA-------GGTGCCCTTGAGTGGAATGGTACA Chimp > Gorilla --------------- chr10:99269259-99269267 Template switch process: F1: L TACCTGAGGACAGGTTCCCAGAGCAGAGGGTGGCCAAGACCC 1 F3: 4 TTCCCTTGAGTGGAATGGTACAGTTACAGTTCAGAGAAAGTA R RF: TACCTGAGGACAGGTTCCCAGAGCAGAGGGTGGCCAAGACCAGGTGCCCTTGAGTGGAATGGTACAGTTACAGTTCAGAGAAAGTA RR: ATGGACTCCTGTCCAAGGGTCTCGTCTCCCACCGGTTCTGGTCCACGGGAACTCACCTTACCATGTCAATGTCAAGTCTCTTTCAT F2: 3 ACCGGTTCT 2 Unidirectional alignment (log-probability: -38.1) CCTGAGGACAGGTTCCCAGAGCAGAGGGTGGCCAAGACC-----ctcttggccattCCCTTGAGTGGAATGGTACAGTTACAGTTCAGAGAAAG CCTGAGGACAGGTTCCCAGAGCAGAGGGTGGCCAAGACCAGGTG------------CCCTTGAGTGGAATGGTACAGTTACAGTTCAGAGAAAG Template switch alignment (log-probability: -28) CCTGAGGACAGGTTCCCAGAGCAGAGGGTGGCCAAGACCc|TCTTGGCCA|TtCCCTTGAGTGGAATGGTACAGTTACAGTTCAGAGAAAG CCTGAGGACAGGTTCCCAGAGCAGAGGGTGGCCAAGACCA|TCTTGGCCA|TGCCCTTGAGTGGAATGGTACAGTTACAGTTCAGAGAAAG ========= Event 152 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: tttttagttaccatctctttatggtacta-------ttggttcttcctctttttcctcct Chimp: TTTCTAGTTACCATCTCTTTATGGTACAATAGTACCATAGTTCTCCCTCTTTTTCCTCCT ↑ 3 1 2 4 Gorilla: TTTTTAGTTACCATCTCTTTATGGTACTA-------TTGGTTCTCCCTCTTTTTCCTCCT Human: tttttagttaccatctctttatggtacta-------ttggttcttcctctttttcctcct Cluster: [ ] Orangutan: tttatagttaccgtctctttatggtactg-------ttggttctccctctttttcctcct Gorilla > Chimp --------------- chr10:65464299-65464310 Template switch process: F1: L TTCACTATACTCATTTTCTAGTTACCATCTCTTTATGGTAC 1 F3: 4 GTTCTCCCTCTTTTTCCTCCTTCATTAAATGTCAGTAAAG R RF: TTCACTATACTCATTTTTTAGTTACCATCTCTTTATGGTACTATTGGTTCTCCCTCTTTTTCCTCCTTCATTAAATGTCAGTAAAG RR: AAGTGATATGAGTAAAAAATCAATGGTAGAGAAATACCATGATAACCAAGAGGGAGAAAAAGGAGGAAGTAATTTACAGTCATTTC F2: 3 ATACCATGATAA 2 Unidirectional alignment (log-probability: -37.6) TCACTATACTCATTTTcTAGTTACCATCTCTTTATGGTACaATagtaccaTaGTTCTCCCTCTTTTTCCTCCTTCATTAAATGTCAGTAAAG TCACTATACTCATTTTTTAGTTACCATCTCTTTATGGTACTAT-------TGGTTCTCCCTCTTTTTCCTCCTTCATTAAATGTCAGTAAAG Template switch alignment (log-probability: -22.8) TCACTATACTCATTTTcTAGTTACCATCTCTTTATGGTAC|AATAGTACCATA|GTTCTCCCTCTTTTTCCTCCTTCATTAAATGTCAGTAAAG TCACTATACTCATTTTTTAGTTACCATCTCTTTATGGTAC|AATAGTACCATA|GTTCTCCCTCTTTTTCCTCCTTCATTAAATGTCAGTAAAG ========= Event 153 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATTCCCACAACAAATATTTGGGGGAA-----AAGTAAAACCTCGTTCTTAATTGCC-TTGTCAGTTTgttggaaagctcaa Chimp: AATTCCCACAACAAATATTTGGGGGAA-----AAGTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTgttggaaagctcaa ↓ 4 3 2 1 Gorilla: AATTCCCACAACAAATATTTGTTGTAACGAGGTTGTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTgttggaaagctcaa Human: AATTCCCACAACAAATATTTGGGGGAA-----AAGTAAAACCTCGTTCTTAATTGCC-TTGTCAGTTTgttggaaagctcaa Cluster: [ ] Orangutan: AATTCCCACAACAAATATTTGGGGGAA-----AAGTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTgttggaaagctcaa Chimp > Gorilla --------------- chr10:100697977-100697985 Template switch process: F1: L ATCGCAAACTAGGGTCTGCTAATTCCCACAACAAATATTTG--------------------------------TTGT 1 F3: 4 GTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTGTTGGA R RF: ATCGCAAACTAGGGTCTGCTAATTCCCACAACAAATATTTGGGGGAAAAGTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTGTTGGA RR: TAGCGTTTGATCCCAGACGATTAAGGGTGTTGTTTATAAACCCCCTTTTCATTTTGGAGCAAGAATTAACGGAAACAGTCAAACAACCT F2: 3 TTGGAGCAA 2 Unidirectional alignment (log-probability: -39.7) AAACTAGGGTCTGCTAATTCCCACAACAAATATTTG--------ttgtaacgaggttGTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTGTTGGA AAACTAGGGTCTGCTAATTCCCACAACAAATATTTGGGGGAAAA-------------GTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTGTTGGA Template switch alignment (log-probability: -28.4) AAACTAGGGTCTGCTAATTCCCACAACAAATATTTG--------------------------------TTGT|AACGAGGTT|GTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTGTTGGA AAACTAGGGTCTGCTAATTCCCACAACAAATATTTGGGGGAAAAGTAAAACCTCGTTCTTAATTGCCTTTGT|AACGAGGTT|GTAAAACCTCGTTCTTAATTGCCTTTGTCAGTTTGTTGGA ========= Event 154 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: ATACAAGTTTTACCTATTCCATGAT-TTCATAAGTGTTCTTCTTTAGAAAACA ↓ 3 2 1 4 Chimp: ATACAAGTTTTACCTATTCCATGATTTTCATGAGTGTTCTTCTTTAGAAAACA Gorilla: ATACAAGTTTTACCTATTCCATGATTTTCATGAGTGTTCTTCTTTAGAAAACA Human: ATACAAGTTTTACCTATTCCATGAT-TTCATAAGTGTTCTTCTTTAGAAAACA Cluster: [ ] Orangutan: ATACAAGTTTTACCTATTCCATGATTTTCATGAGTGTTCTTCTTTAGAAAACA Human > Chimp ------------- chr10:67294648-67294652 Template switch process: F1: L CAGGAAGAGGTGCTGAATACAAGTTTTACCTATTCCATGATTT 1 F3: 4 AGTGTTCTTCTTTAGAAAACAGTTTTCTTTATTAATA R RF: CAGGAAGAGGTGCTGAATACAAGTTTTACCTATTCCATGATTTCATAAGTGTTCTTCTTTAGAAAACAGTTTTCTTTATTAATA RR: GTCCTTCTCCACGACTTATGTTCAAAATGGATAAGGTACTAAAGTATTCACAAGAAGAAATCTTTTGTCAAAAGAAATAATTAT F2: 3 GTACT 2 Unidirectional alignment (log-probability: -25.6) GAAGAGGTGCTGAATACAAGTTTTACCTATTCCATGAtTTTCATgAGTGTTCTTCTTTAGAAAACAGTTTTCTTTATTAATA- GAAGAGGTGCTGAATACAAGTTTTACCTATTCCATGA-TTTCATAAGTGTTCTTCTTTAGAAAACAGTTTTCTTTATTAATAA Template switch alignment (log-probability: -15.9) GAAGAGGTGCTGAATACAAGTTTTACCTATTCCATGATTT|TCATG|AGTGTTCTTCTTTAGAAAACAGTTTTCTTTATTAATA GAAGAGGTGCTGAATACAAGTTTTACCTATTCCATGATTT|TCATG|AGTGTTCTTCTTTAGAAAACAGTTTTCTTTATTAATA ========= Event 155 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTAGCAATTTGAGTATTTAACTAC-----------ATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTT Chimp: GGTAGCAATTTGAGTATTTAATTAC-----------ATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTT ↓ 1 4 3 2 Gorilla: GGTAGCAATTTGAGTATTTAACTACTCAAAGTACCACTAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTT ↑ 1 4 3 2 Human: GGTAGCAATTTGAGTATTTAACTAC-----------ATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTT Cluster: [ ] Orangutan: GGTAGCAATTTGAGTATTTAACTAC-----------ATAGGGTGGTACTTTGAAGGAAAAAGCGTTTTAAGTT Human > Gorilla --------------- chr10:46570894-46570905 Template switch process: F1: L TACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTAC 1 F3: 4 TAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC R RF: TACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTACATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC RR: ATGTATGATTTTCAAACCATCGTTAAACTCATAAATTGATGTATCCCACCATGAAACTTCCTTTTTCGTAAAATTCAACTCG F2: 3 CACCATGAAACT 2 Unidirectional alignment (log-probability: -32.2) ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTACtcaaagtaccacTAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTAC-----------ATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC Template switch alignment (log-probability: -17.3) ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTAC|TCAAAGTACCAC|TAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTAC|TCAAAGTACCAC|TAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC Chimp > Gorilla --------------- chr10:46570894-46570905 Template switch process: F1: L AATATACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAACTAC 1 F3: 4 TAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC R RF: AATATACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAATTACATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC RR: TTATATGTATGATTTTCAAACCATCGTTAAACTCATAAATTAATGTATCCCACCATGAAACTTCCTTTTTCGTAAAATTCAACTCG F2: 3 CACCATGAAACT 2 Unidirectional alignment (log-probability: -37.8) ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAAcTACtcaaagtaccacTAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAATTAC-----------ATAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC Template switch alignment (log-probability: -22.9) ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAAcTAC|TCAAAGTACCAC|TAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC ACATACTAAAAGTTTGGTAGCAATTTGAGTATTTAATTAC|TCAAAGTACCAC|TAGGGTGGTACTTTGAAGGAAAAAGCATTTTAAGTTGAGC ========= Event 156 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAATTACTTTATTCTCTGTGCTTATTTTCTAAA-CTGCCCAAATaattacaaaacttttc Chimp: ATAATTACTTTATTCTCTGTGCTTATTTTCTAAA-CTGCCCAAATAATTACGAAACTTTtc ↓ 3 2 1 4 Gorilla: ATAATTACTTTATTCTCTGTGCTTATTTTCTAAATAAGCACAAATAATTACAAAACTTTTC ↑ 3 2 1 4 Human: ATAATTACTTTATTCTCTGTGCTTATTTTCTAAA-CTGCCCAAATaattacaaaacttttc Cluster: [ ] Orangutan: ATAATTACTTTATTCTCTGTGCTTATTTTCTGAA-CTGCCCAAATaattacaaaacttttc Human > Gorilla --------------- chr10:102952773-102952778 Template switch process: F1: L ACTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA 1 F3: 4 CAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA R RF: ACTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAACTGCCCAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA RR: TGACTTGTATTAATGAAATAAGAGACACGAATAAAAGATTTGACGGGTTTATTAATGTTTTGAAAAGTATCTTAAAGTCACTTTCT F2: 3 ACGAAT 2 Unidirectional alignment (log-probability: -29) CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAAtaaGCaCAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA-CTGCCCAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA Template switch alignment (log-probability: -16.5) CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA|TAAGCA|CAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA|TAAGCA|CAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA Chimp > Gorilla --------------- chr10:102952773-102952778 Template switch process: F1: L ACTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA 1 F3: 4 CAAATAATTACAAAACTTTTCATAGAATTTCAGTGAAAGA R RF: ACTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAACTGCCCAAATAATTACGAAACTTTTCATAGAATTTCAGTGAAAGA RR: TGACTTGTATTAATGAAATAAGAGACACGAATAAAAGATTTGACGGGTTTATTAATGCTTTGAAAAGTATCTTAAAGTCACTTTCT F2: 3 ACGAAT 2 Unidirectional alignment (log-probability: -34.5) CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAAtaaGCaCAAATAATTACaAAACTTTTCATAGAATTTCAGTGAAAGA CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA-CTGCCCAAATAATTACGAAACTTTTCATAGAATTTCAGTGAAAGA Template switch alignment (log-probability: -22) CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA|TAAGCA|CAAATAATTACaAAACTTTTCATAGAATTTCAGTGAAAGA CTGAACATAATTACTTTATTCTCTGTGCTTATTTTCTAAA|TAAGCA|CAAATAATTACGAAACTTTTCATAGAATTTCAGTGAAAGA ========= Event 157 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGGATGTGGTGGGTTTGGTTTTTCAGATAGCTTTTTCAGGTagtgtctaattcaatggcttttagtatactcacagacttgtgaaccaccacgataaatgttagaacacttatatcaccccaaatagagatcccacacccactggctatcaccctccaacctcccatct Chimp: TTGGATGTGGTGGGTTTGGTTTTTCAGATAGCTTTTTCAGGTagtgtctaattcaatggcttttagtatactcacagacttgtgaaccaccacgataaattttagaacactt-aatcaccccaaatagagatcccacacccactggctatcatcctccaacctcccatcc ↑ 4 1 3 2 Gorilla: TTGGATGTGGTGGGTTTGGTTT-------------TTCAGGTagtgtctaattcaatggcttttagtatactcacagacttgtgaaccaccacgataaatgttagaacacttatatcaccccaaatagagatcccacacccactggctatcatcctccaacctcccatcc ↓ 4 1 3 2 Human: TTGGATGTGGTGGGTTTGGTTTTTCAGATAGCTTTTTCAGGTagtgtctaattcaatggcttttagtatactcacagacttgtgaaccaccacgataaatgttagaacacttatatcaccccaaatagagatcccacacccactggctatcaccctccaacctcccatct Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr10:79329952-79329956 Template switch process: F1: L ATAAGGGGTAGCCTGCTAATTGGATGTGGTGGGTTTGGTTTTTCAG 1 F3: 4 TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACTCAC R RF: ATAGGGGGTAGCCCGCTAATTGGATGTGGTGGGTTTGGTTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACTCACAGACTTGTGAACCACCACGATAAATGTTAGAACACTTATATCACCCCAAATAGAGATCCCACACCCACTGGCTAT RR: TATCCCCCATCGGGCGATTAACCTACACCACCCAAACCAAAAAGTCCATCACAGATTAAGTTACCGAAAATCATATGAGTGTCTGAACACTTGGTGGTGCTATTTACAATCTTGTGAATATAGTGGGGTTTATCTCTAGGGTGTGGGTGACCGATA F2: 3 CGATA 2 Unidirectional alignment (log-probability: -40.6) GGTAGCCtGCTAATTGGATGTGGTGGGTTTGGtttttcagatagcTTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT GGTAGCCCGCTAATTGGATGTGGTGGGTTTGG-------------TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT Template switch alignment (log-probability: -27.6) GGTAGCCtGCTAATTGGATGTGGTGGGTTTGGTTTTTCAG|ATAGC|TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT GGTAGCCCGCTAATTGGATGTGGTGGGTTTGGTTTTTCAG|ATAGC|TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT Gorilla > Chimp --------------- chr10:80611193-80611197 Template switch process: F1: L ATAGGGGGTAGCCTGCTAATTGGATGTGGTGGGTTTGGTTTTTCAG 1 F3: 4 TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACTCAC R RF: ATAGGGGGTAGCCCGCTAATTGGATGTGGTGGGTTTGGTTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACTCACAGACTTGTGAACCACCACGATAAATGTTAGAACACTTATATCACCCCAAATAGAGATCCCACACCCACTGGCTAT RR: TATCCCCCATCGGGCGATTAACCTACACCACCCAAACCAAAAAGTCCATCACAGATTAAGTTACCGAAAATCATATGAGTGTCTGAACACTTGGTGGTGCTATTTACAATCTTGTGAATATAGTGGGGTTTATCTCTAGGGTGTGGGTGACCGATA F2: 3 CGATA 2 Unidirectional alignment (log-probability: -35.1) GGTAGCCtGCTAATTGGATGTGGTGGGTTTGGtttttcagatagcTTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT GGTAGCCCGCTAATTGGATGTGGTGGGTTTGG-------------TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT Template switch alignment (log-probability: -22.1) GGTAGCCtGCTAATTGGATGTGGTGGGTTTGGTTTTTCAG|ATAGC|TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT GGTAGCCCGCTAATTGGATGTGGTGGGTTTGGTTTTTCAG|ATAGC|TTTTTCAGGTAGTGTCTAATTCAATGGCTTTTAGTATACT ========= Event 158 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCAGTCAGTTCTTTGGAGTGTAT-ATAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCATGATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGTGAGTTTGCGCCTCTTTCCATGTATGTTTCCAGTCTGCACACATGGATGGCGCT Chimp: ATCAGTCAGTTCTTTGGAGTGTAT-ATAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACGATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGTGAGTTTGCGCCTCTTTCCATGTATGTTTCCAGTCTGCACACATGGATGGCGCT ↓ 1 4 3 2 Gorilla: ATCAGTCAGTTCTTTGGAGTGACTGGAAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACAATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGCAAGTTTGCGCCTCTTTCCATGTATGTTTCCAGTCTGCACACACGGATGGCGCT ↑ 1 4 3 2 Human: ATCAGTCAGTTCTTTGGAGTGTAT-ATAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCATGATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGTGAGTTTGCGCCTCTTTCCATGTATGTTTCCAGTCTGCACACATGGATGGCGCT Cluster: [ ] Orangutan: ATCAGTCAGTTCTTTGGAGTGTAT-ATAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACAATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGCGAGTTTGTGCCTCTTTCCATGTATGTTTCCAGTCTGCACACATGGATGGTGCT Human > Gorilla --------------- chr10:118161647-118161652 Template switch process: F1: L TGGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG 1 F3: 4 AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACA R RF: TGGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTGTATATAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCATGATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGTGAGTTTGCGCCTCTTTCCATGTATGTTTCCAGT RR: ACCTGCAAAAGTGACTTAAGTAGTCAGTCAAGAAACCTCACATATATCTGTGTCGGAAGTACTTTTGCAACATTCCTGTAGAGTACTACACAAAGGTATTTAGACGAGTTAAATATTAGAGAACGCACACTCAAACGCGGAGAAAGGTACATACAAAGGTCA F2: 3 AGGTCA 2 Unidirectional alignment (log-probability: -40.5) GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG-----actggaAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCAca GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTGTATAT------AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCATG Template switch alignment (log-probability: -26.1) GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG|ACTGGA|AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCacA GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG|ACTGGA|AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTC--A Chimp > Gorilla --------------- chr10:118161647-118161652 Template switch process: F1: L TGGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG 1 F3: 4 AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACA R RF: TGGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTGTATATAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACGATGTGTTTCCATAAATCTGCTCAATTTATAATCTCTTGCGTGTGAGTTTGCGCCTCTTTCCATGTATGTTTCCAGT RR: ACCTGCAAAAGTGACTTAAGTAGTCAGTCAAGAAACCTCACATATATCTGTGTCGGAAGTACTTTTGCAACATTCCTGTAGAGTGCTACACAAAGGTATTTAGACGAGTTAAATATTAGAGAACGCACACTCAAACGCGGAGAAAGGTACATACAAAGGTCA F2: 3 AGGTCA 2 Unidirectional alignment (log-probability: -35) GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG-----actggaAGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACa GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTGTATAT------AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACG Template switch alignment (log-probability: -22) GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG|ACTGGA|AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACa GGACGTTTTCACTGAATTCATCAGTCAGTTCTTTGGAGTG|ACTGGA|AGACACAGCCTTCATGAAAACGTTGTAAGGACATCTCACG ========= Event 159 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gggtgggggttggggACAGCATGGGACATCCTG-CATA-TGGTATCTGAGAACAGCAGTGG Chimp: gggtgggggttggggACAGCATGGGACATCCTG-CATA-TGGTATCTGGGAACAGCAATGG ↓ 3 2 1 4 Gorilla: gggtgggggttggggACAGCATGGGACATCCTGTCCCATGGGTATCTGGGAACAGCAATGG Human: gggtgggggttggggACAGCATGGGACATCCTG-CATA-TGGTATCTGAGAACAGCAGTGG Cluster: [ ] Orangutan: gggtgggggttggggACAGCATGGGACATCCTG-CATA-TGGTGTCTGGGAACAGCAATGG Chimp > Gorilla --------------- chr10:117944729-117944735 Template switch process: F1: L GTTGAAGGGGGTGGGGGTTGGGGACAGCATGGGACATCCTG 1 F3: 4 GGTATCTGGGAACAGCAATGGAGCCTGGGGT-CATGACCC R RF: GTTGAAGGGGGTGGGGGTTGGGGACAGCATGGGACATCCTGCATATGGTATCTGGGAACAGCAATGGAGCCTGGGGTCCATGACCC RR: CAACTTCCCCCACCCCCAACCCCTGTCGTACCCTGTAGGACGTATACCATAGACCCTTGTCGTTACCTCGGACCCCAGGTACTGGG F2: 3 GTACCCT 2 Unidirectional alignment (log-probability: -39.3) TTGAAGGGGGTGGGGGTTGGGGACAGCATGGGACATCCTG----TcccatgGGTATCTGGGAACAGCAATGGAGCCTGGGGT-CATGACCC TTGAAGGGGGTGGGGGTTGGGGACAGCATGGGACATCCTGCATAT------GGTATCTGGGAACAGCAATGGAGCCTGGGGTCCATGACCC Template switch alignment (log-probability: -26.4) TTGAAGGGGGTGGGGGTTGGGGACAGCATGGGACATCCTG|TCCCATG|GGTATCTGGGAACAGCAATGGAGCCTGGGGT-CATGACCC TTGAAGGGGGTGGGGGTTGGGGACAGCATGGGACATCCTG|TCCCATG|GGTATCTGGGAACAGCAATGGAGCCTGGGGTCCATGACCC ========= Event 160 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAAGCATAGGCTCCAAATTCAAAATACATTTGTATTTTTAACATTTCAAAGTCCCCATGGCA----------TTAAA ↓ 1 4 3 2 Chimp: CAAAGCATAGGCTCCAAATTC--------ATGGGGACTTTAACATTTCAAAGTCCCCATGGCA----------TTAAA Gorilla: CAAAGCATAGGCTCCAAATTCAAAATACATTTGTATTTTTAACATTTCAAAGTCCCCATGGCA--------------- Human: CAAAGCATAGGCTCCAAATTCAAAATACATTTGTATTTTTAACATTTCAAAGTCCCCATGGCA----------TTAAA Cluster: [ ] Orangutan: CAAAGCATAGGCTCCAAATTCAAAATACATTTGTATTTTTAACATTTCAAAGTCCCCATGGCATTAAAGTTAC----- Human > Chimp ------------- chr10:67748297-67748303 Template switch process: F1: L ATTGCCTTGGGCAGAGATGACAAAGCATAGGCTCCAAATTCA 1 F3: 4 TTTAACATTTCAAAGTCCCCATGGCATTAAAGTTACTACA R RF: ATTGCCTTGGGCAGAGATGACAAAGCATAGGCTCCAAATTCAAAATACATTTGTATTTTTAACATTTCAAAGTCCCCATGGCATTAAAGTTACTACA RR: TAACGGAACCCGTCTCTACTGTTTCGTATCCGAGGTTTAAGTTTTATGTAAACATAAAAATTGTAAAGTTTCAGGGGTACCGTAATTTCAATGATGT F2: 3 CAGGGGT 2 Unidirectional alignment (log-probability: -30.5) TGCCTTGGGCAGAGATGACAAAGCATAGGCTCCAAATTCA--------------TggggacTTTAACATTTCAAAGTCCCCATGGCATTAAAGTTACTACA TGCCTTGGGCAGAGATGACAAAGCATAGGCTCCAAATTCAAAATACATTTGTATT------TTTAACATTTCAAAGTCCCCATGGCATTAAAGTTACTACA Template switch alignment (log-probability: -16.2) TGCCTTGGGCAGAGATGACAAAGCATAGGCTCCAAATTCA|TGGGGAC|TTTAACATTTCAAAGTCCCCATGGCATTAAAGTTACTACA TGCCTTGGGCAGAGATGACAAAGCATAGGCTCCAAATTCA|TGGGGAC|TTTAACATTTCAAAGTCCCCATGGCATTAAAGTTACTACA ========= Event 161 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGACCAGGGCTGTTGTCATATGGCTAAA-------------------------------------------------GGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACC Chimp: CCTGACCAGGGCTGTTGTCATATGGCTAAA-------------------------------------------------GGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACC ↓ 3 1 2 4 Gorilla: CCTGACCAGGGCTGTTGTCATATAGCCATA--------------------------------------------------------------------------------------------------TGACCAAGGCGGCCAAGGGACC ↑ 3 1 2 4 Human: CCTGACCAGGGCTGTTGTCATATGGCTAAA-------------------------------------------------GGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACC Cluster: [ ] Orangutan: CCTGACCAGAGCTGTTGTCATATGTCTAAAGGCAAGGCAGCATCCAGTGACCCACATTCCGAAGTGGAGGGGGTGACAG-------------------------------------------------GGACCAAGGCGGCCAAGGGACC Human > Gorilla --------------- chr10:142389785-142389792 Template switch process: F1: L TAGCAGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATAT 1 F3: 4 GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG R RF: TAGCGGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATATGGCTAAAGGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG RR: ATCGCCCCCGTCACCGAGGGACTGGTCCCGACAACAGTATACCGATTTCCGTCCTGTCGTAGGCCACTGGGTGTAAGGCTTCACCTCCCCCACTGTCCCTGGTTCCGCCGGTTCCCTGGGGTCGGAGAGAGTCCAGTC F2: 3 TATACCGA 2 Unidirectional alignment (log-probability: -39.8) AGCaGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATAT--------------------------AgCCAtAT-----------------------GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG AGCGGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATATGGCTAAAGGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG Template switch alignment (log-probability: -22.3) AGCaGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATAT|AGCCATAT|GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG AGCGGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATAT|AGCCATAT|GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG Chimp > Gorilla --------------- chr10:142389785-142389792 Template switch process: F1: L TAGCAGGGGCAGTGGCTCCCTGACCAGGGCTGTTGTCATAT 1 F3: 4 GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG R RF: TAGCGGGGGCAGCGGCTCCCTGACCAGGGCTGTTGTCATATGGCTAAAGGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG RR: ATCGCCCCCGTCGCCGAGGGACTGGTCCCGACAACAGTATACCGATTTCCGTCCTGTCGTAGGCCACTGGGTGTAAGGCTTCACCTCCCCCACTGTCCCTGGTTCCGCCGGTTCCCTGGGGTCGGAGAGAGTCCAGTC F2: 3 TATACCGA 2 Unidirectional alignment (log-probability: -45.3) AGCaGGGGCAGtGGCTCCCTGACCAGGGCTGTTGTCATAT--------------------------AgCCAtAT-----------------------GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG AGCGGGGGCAGCGGCTCCCTGACCAGGGCTGTTGTCATATGGCTAAAGGCAGGACAGCATCCGGTGACCCACATTCCGAAGTGGAGGGGGTGACAGGGACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG Template switch alignment (log-probability: -27.8) AGCaGGGGCAGtGGCTCCCTGACCAGGGCTGTTGTCATAT|AGCCATAT|GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG AGCGGGGGCAGCGGCTCCCTGACCAGGGCTGTTGTCATAT|AGCCATAT|GACCAAGGCGGCCAAGGGACCCCAGCCTCTCTCAGGTCAG ========= Event 162 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAAATAAACAAATAGCATT-----------------------------CACCTCCATGGTTCTCAGTCTTCCCACCTTTTCCTCCTTCTCTCCAGTC--------------------------------------TCCTTT Chimp: AATAAATAAACAAATAGCATT---------------CCCTCCCAGTCACTAACCTCCATG-------GTCTTCCCACCTTTTCCTCCTTCTCTCCAGTC-------------------TCAGAGCAGGAACACAATTTCCTTT ↓ 4 3 2 Gorilla: AATAAATAAACAAATAGCATTCCCTC-CCAGTCACT--------------CACCTCCATGGTTCTCAGTCTTCCCACCTTTTCCTCCTTCTCTCCAGTCTCAGAGCAGGAACACAATT-------------------TCCTTT Human: AATAAATAAACAAATAGCATT-----------------------------CACCTCCATGGTTCTCAGTCTTCCCACCTTTTCCTCCTTCTCTCCAGTC--------------------------------------TCCTTT Cluster: [ ] Orangutan: AATAAATAAACAAATAGCATTCCCTCCCCAGTCACT--------------CACCTCCATGGTTCTCAGCCTTCCCATCTTTTCCTCCTTCTCTCCAGTCTCAGAGCAGGAGCACAATT-------------------TCCTTT Chimp > Gorilla --------------- chr10:34685585-34685590 Template switch process: F1: L TGTTATATAAGTATTTGTCAAATAAATAAACAAATAGCATTCCCTCCCAGTCACTCACCTCCATGGT 1 F3: 4 TCTTCCCACCTTTTCCTCCTTCTCTCCAGTCTCAGAGCA R RF: TGTTATATAATTATTTGTCAAATAAATAAACAAATAGCATTCCCTCCCAGTCACTAACCTCCATGGTCTTCCCACCTTTTCCTCCTTCTCTCCAGTCTCAGAGCA RR: ACAATATATTAATAAACAGTTTATTTATTTGTTTATCGTAAGGGAGGGTCAGTGATTGGAGGTACCAGAAGGGTGGAAAAGGAGGAAGAGAGGTCAGAGTCTCGT F2: 3 GACTCT 2 Unidirectional alignment (log-probability: -50.5) AAACAAATAGCATTCCCTCCCAGTCACTcACCTCCATGgttctcaGTCTTCCCACCTTTTCCTCCTTCTCTCCAGTCtcagagca AAACAAATAGCATTCCCTCCCAGTCACTAACCTCCATG-------GTCTTCCCACCTTTTCCTCCTTCTCTCCAGTC-------- Template switch alignment (log-probability: -33.6) AAACAAATAGCATTCCCTCCCAGTCACTcACCTCCATGGT|TCTcAG|TCTTCCCACCTTTTCCTCCTTCTCTCCAGTCTCAGAGCA AAACAAATAGCATTCCCTCCCAGTCACTAACCTCCATGGT|TCTGAG|TCTTCCCACCTTTTCCTCCTTCTCTCCAGTCTCAGAGCA ========= Event 163 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 124 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCATTGCCCTCATTGACATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGCGGGCCCTCCGATGCCTGCCC ↓ 1 4 3 2 ↑ 43 2 1 Chimp: AAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCAGCTCC------AGCATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGCGGGCCCTCTGATGCCTGCCC Gorilla: AAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCAGCTCC------AGCATTGAAAGCGGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGCGGGCCCTCCGATGCCTGCCC ↑ 1 4 3 2 Human: AAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCATTGCCCTCATTGACATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGCGGGCCCTCCGATGCCTGCCC Cluster: [ ] Orangutan: AAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCAGCTCC------AGCATTGAAAGCGGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGCGGGCCCCCCGATGCCTGCCC Chimp > Human ------------- chr10:55667453-55667461 Template switch process: F1: L AGGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA 1 F3: 4 TTGA------------------CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA R RF: AGGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCAGCTCCAGCATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA RR: TCCTTTATTCGAACTGTTTCACCAACAACTCCCGTTACAGTCGAGGTCGTAACTTTCGTCTTCTCACCCACAACGACAACTTAAGCCT F2: 3 ACTCCCGTT 2 Unidirectional alignment (log-probability: -40.2) GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA-------ttgccctcattgaCATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATT GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCAGCTCCAG-------------CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATT Template switch alignment (log-probability: -27.6) GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA|TTGCCCTCA|TTGA------------------CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATT GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA|TTGCCCTCA|TTGAGGGCAATGTCAGCTCCAGCATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATT Human > Chimp ------------- chr10:56484283-56484289 Template switch process: F1: L AGGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA 1 F3: 4 CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA R RF: AGGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCATTGCCCTCATTGACATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGC RR: TCCTTTATTCGAACTGTTTCACCAACAACTCCCGTTACAGTAACGGGAGTAACTGTAACTTTCGTCTTCTCACCCACAACGACAACTTAAGCCTCCTCTGTTGGACCACGAGTCACATCGGGTCCTACGGGAACTCG F2: 3 GACCTCG 2 Unidirectional alignment (log-probability: -31.9) GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCAgctccag-------------CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA-------TTGCCCTCATTGACATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA Template switch alignment (log-probability: -22.1) GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA|GCTCcAG|CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA|GCTCAAG|CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA Human > Gorilla --------------- chr10:94302331-94302337 Template switch process: F1: L AGGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA 1 F3: 4 CATTGAAAGCGGAAGAGTGGGTGTTGCTGTTGAATTCGGA R RF: AGGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCATTGCCCTCATTGACATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGAGGAGACAACCTGGTGCTCAGTGTAGCCCAGGATGCCCTTGAGC RR: TCCTTTATTCGAACTGTTTCACCAACAACTCCCGTTACAGTAACGGGAGTAACTGTAACTTTCGTCTTCTCACCCACAACGACAACTTAAGCCTCCTCTGTTGGACCACGAGTCACATCGGGTCCTACGGGAACTCG F2: 3 GACCTCG 2 Unidirectional alignment (log-probability: -36.9) GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTC-------------AgctccagCATTGAAAGCgGAAGAGTGGGTGTTGCTGTTGAATTCGGA GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCATTGCCCTCATTGA-------CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA Template switch alignment (log-probability: -27.7) GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA|GCTCcAG|CATTGAAAGCgGAAGAGTGGGTGTTGCTGTTGAATTCGGA GGAAATAAGCTTGACAAAGTGGTTGTTGAGGGCAATGTCA|GCTCAAG|CATTGAAAGCAGAAGAGTGGGTGTTGCTGTTGAATTCGGA ========= Event 164 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: GGTCAACCTTTCCAGGTATGCTAATACCCTG-AAGAGACTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTCCATCTATTGACATCT ↓ 4 1 3 2 ↑ 1 4 3 2 Chimp: GGTCAACCTTTCCAGGTATGCTAATACCCAGCCTGCTAATGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTCCATCTATTGACATCT Gorilla: GGTCAACCTTTCCAGGTATGCTAATACCCTG-AAGAGACTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTCCATCTATTGACATCT Human: GGTCAACCTTTCCAGGTATGCTAATACCCTG-AAGAGACTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTCCATCTATTGACATCT Cluster: [ ] Orangutan: GGTCAACCTTTCCAGGTATGCTAATACGCTG-AAGAGACTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTCCATCTATTGACATCT Chimp > Human ------------- chr10:77252396-77252404 Template switch process: F1: L GCCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC 1 F3: 4 TGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC R RF: ACCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCCAGCCTGCTAATGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC RR: TGGACCGACGATCCAGTTGGAAAGGTCCATACGATTATGGGTCGGACGATTACGTCCGACTTCCCGTAACCTTCAGTCAGAGGAGTCACAG F2: 3 CAGAGAAGT 2 Unidirectional alignment (log-probability: -40.6) CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC----------tgaagagacTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCCAGCCTGCTAA---------TGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC Template switch alignment (log-probability: -28.4) CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC|TGAaGAGAC|TGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC|TGAGGAGAC|TGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC Human > Chimp ------------- chr10:78508043-78508047 Template switch process: F1: L ACCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC 1 F3: 4 GCTAAT--------------GCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC R RF: GCCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCCTGAAGAGACTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCAGTGTC RR: CGGACCGACGATCCAGTTGGAAAGGTCCATACGATTATGGGACTTCTCTGACGTCCGACTTCCCGTAACCTTCAGTCAGAGGAGTCACAG F2: 3 TCCGA 2 Unidirectional alignment (log-probability: -42) CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACC---------CagcctgctaaTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCA CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCCTGAAGAGAC----------TGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCA Template switch alignment (log-probability: -32.9) CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC|AGCCT|GCTAAT--------------GCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCA CCTGGCTGCTAGGTCAACCTTTCCAGGTATGCTAATACCC|AGCCT|GCTAATACCCTGAAGAGACTGCAGGCTGAAGGGCATTGGAAGTCAGTCTCCTCA ========= Event 165 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GTTAACTGTCCTCAACTCTGT----GAATATAGGCATATATTCATTCAATATATGCCTATTAATAAGCACCCATGCAGCA Chimp: GTTAACTGTTCTCAACTCTGT----GAATATAGGCATATATTCATTCAATATATGCTTATTAATAAGCACCCATGCAGCA Gorilla: GTTAACTGTCCTCAACTCTGT----------------GTATGCATTCAATATATGCCTATTAATAAGCACCCATGCAGCA ↓ 1 4 3 2 Human: GTTAACTGTCCTCAACTCTGT----GAATATAGGCATATATTCATTCAATATATGCCTATTAATAAGCACCCATGCAGCA Cluster: [ ] Orangutan: GTTAACTGTCCTCAACT----CCAT------------GTATTCATTCAATATATGCCTATTAATAAGCACCCATGCAGCA Gorilla > Human --------------- chr10:77488034-77488046 Template switch process: F1: L AGACACCTTCTGCAATATGGGTTAACTGTCCTCAACTCTGTGAAT 1 F3: 4 CATTCAATATATGCCTATTAATAAGCACCCATGCAGCAAA R RF: AGACACCTTCTGCAATATGGGTTAACTGTCCTCAACTCTGTGTATGCATTCAATATATGCCTATTAATAAGCACCCATGCAGCAAA RR: TCTGTGGAAGACGTTATACCCAATTGACAGGAGTTGAGACACATACGTAAGTTATATACGGATAATTATTCGTGGGTACGTCGTTT F2: 3 TTATATACGGATA 2 Unidirectional alignment (log-probability: -33.7) CCTTCTGCAATATGGGTTAACTGTCCTCAACTCTGTGaatataggcataTATtCATTCAATATATGCCTATTAATAAGCACCCATGCAGCAAA CCTTCTGCAATATGGGTTAACTGTCCTCAACTCTGTG------------TATGCATTCAATATATGCCTATTAATAAGCACCCATGCAGCAAA Template switch alignment (log-probability: -23) CCTTCTGCAATATGGGTTAACTGTCCTCAACTCTGTGaAT|ATAGGCATATATT|CATTCAATATATGCCTATTAATAAGCACCCATGCAGCAAA CCTTCTGCAATATGGGTTAACTGTCCTCAACTCTGTGTAT|ATAGGCATATATT|CATTCAATATATGCCTATTAATAAGCACCCATGCAGCAAA ========= Event 166 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCACTGGCATGTGTATTTTGCGGAATTATTTGGTTTGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC Chimp: TGCACTGGCATGTGTATTTTGTGGAATGATTTGGTTTGGCAACTACTCCTTGTCTAGAGATGGAGTTTAGAATTGTC ↓ 1 4 3 2 Gorilla: TGCACTGGCATGTGTATTTTGTGGAATGCTAGACAAAGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC ↑ 1 4 3 2 Human: TGCACTGGCATGTGTATTTTGCGGAATTATTTGGTTTGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC Cluster: [ ] Orangutan: TGCACTGGCATGTGTATTTTGCGGAATGATTTGGTTTGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC Human > Gorilla --------------- chr10:116454500-116454508 Template switch process: F1: L TTAAGACAAAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATG 1 F3: 4 GGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC R RF: TTAAGACAAAGAAAGGAAAATGCACTGGCATGTGTATTTTGCGGAATTATTTGGTTTGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC RR: AATTCTGTTTCTTTCCTTTTACGTGACCGTACACATAAAACGCCTTAATAAACCAAACCGTTGATGAGAAACAGATCTCTACCTCAAATCTTAACAG F2: 3 AAACAGATC 2 Unidirectional alignment (log-probability: -41.1) AAGAAAGGAAAATGCACTGGCATGTGTATTTTGtGGAA----------TgctagacaaaGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC AAGAAAGGAAAATGCACTGGCATGTGTATTTTGCGGAATTATTTGGTTT----------GGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC Template switch alignment (log-probability: -28.1) AAGAAAGGAAAATGCACTGGCATGTGTATTTTGtGGAATg|CTAGACAAA|GGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC AAGAAAGGAAAATGCACTGGCATGTGTATTTTGCGGAATT|CTAGACAAA|GGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC Chimp > Gorilla --------------- chr10:116454500-116454507 Template switch process: F1: L AAAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATG 1 F3: 4 AGGCAACTACTCTTTGTCTAGAGATGGAGTTTAGAATTGTC R RF: AAAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATGATTTGGTTTGGCAACTACTCCTTGTCTAGAGATGGAGTTTAGAATTGTC RR: TTTCTTTCCTTTTACGTGACCGTACACATAAAACACCTTACTAAACCAAACCGTTGATGAGGAACAGATCTCTACCTCAAATCTTAACAG F2: 3 AACAGATC 2 Unidirectional alignment (log-probability: -38.1) AAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATGctagacaaA--------GGCAACTACTCtTTGTCTAGAGATGGAGTTTAGAATTGT AAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATG--------ATTTGGTTTGGCAACTACTCCTTGTCTAGAGATGGAGTTTAGAATTGT Template switch alignment (log-probability: -27.8) AAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATG|CTAGACAA|aGGCAACTACTCtTTGTCTAGAGATGGAGTTTAGAATTGT AAGAAAGGAAAATGCACTGGCATGTGTATTTTGTGGAATG|CTAGACAA|TGGCAACTACTCCTTGTCTAGAGATGGAGTTTAGAATTGT ========= Event 167 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: ----GAAAGCTTGAGCTGG-ACTTTGTAGGATG-AAGAGGAGTTGACCCACTGTGGCCCTCTGCTCTGCCAAAG---------------------------------------------------GGCCACAGTAGGTCAACTCCTGTATATCCTACAAAGATCCTTCCCATCCTTTGAAAACCAACTGGGACATTCCCTCTGGGAAGCCTTCCTCACCTTTGCACTTGCATTCCTTGGCTCTGGTGCAAATATACAAAGTTCATGGGGGAGGGGTAACTTACAAGCAAAGAGGAGTTAGAGGTCATAGCATCTGCGACTTCTCTTTACCCTGCAGTTTAGACAGGGCATATGTGGACAGTATACTCTGGCCAATGTTCAAAAACAGAGGGAAGTTCCATTGTGAATCAGTTCTACGCATTTGCAGTTCTGGGGGTCCAGCACATCTACATGAC--TGTGACAATGGAAGCTTCCTGGTTGGGGAAATGGCCTTTTTAGAAAGGGGAGCTTCCGGAACTGAGCTAACTTGGACCCCTGGAGCCAGCTTTCTCGTAAGTACCCAAAT-AA-----------------GCCTCTGGACATCCTGATTTCTCATCTAACTACaatgccttataggaattatgtcatttaatccttcaacagccttatgaggcattctctattactcttcccattttacatatga--gcaactgagatatagagaagttaaaccactagcttatggtcagcaactagtaactgacagaccagggacttgacctcTATGATATAGTGCCTTTTAATACACAATCTTGggccgggcgcggtggctcacacctataatcccagcactttgggaggctgaggcaggcggatcacctgaggtcaggagttcaagagcagcctggccaacatggcaaaatcccgtctctactaaaaatacaaaaattagccacgcatggtgacgggcacctgtaatcccagctactcaggaggctgaggcaggagaatcacttgaacctgggaagcagaggctgcagtgagccatgattgcacccttgtacttcagcctgggtgacagagtaagactccatctccaaaaaaa-ataaaataaaataaaaCACGATCTTAAACCACACTACTAGCA------------------------------------------------------------TATATATATCTTGTAGATTGCTTCTAAAGTTTTACATATTTATCATTATTATTTTCTGCTACATATGTTTGTTGCCTATGCATAGTGTTGAATGCATGAAAATTTCGCAATAACCACTCTAATGGGTAAGAAAAATGAAGCTGAAAAAAGTTCCCTTAGCTACTCTGTTAATTTTTGCTCTCTGGTTTAAAGAACTAGGACTTTGAAGAAGGAGCCTGaaaa---------aaaaaaaTCCTTCAAGGATCCAGCGAGCCAGCAGCCCAGAATATTGCAGAAAAGAgtattttcagcactcagctccaagtaggcattcaataaatactcgctgaCTTGATAGAATTAAACAAACAGATTTTCCTGATTGACATGACATCCACTCTAATTGCA-AACCTATTTGAGGAACAACTTGATGAAGCAAAGCAAAATTAAATGTGCCGCTGTGAAAGCGGTATAACGGTATTAGAACCTTTTAGTTGCTGGGCTGGAAGGGAGCTGAGGAGAACGTTGTTAAGTGTGGAGAATGTACAGGCAAGGACCAAATAGAATTTCTTTGACTTAATAATTTTTGAAAACTATTTATACAATTCATATATTAAATGCTGTGGAAATTGTTTTGAGTC-TTGCGAGAGAGTTACTGCATTTAATCCCCACATAAATCTAGGT-----------A---CATTTGTAAGGCAATTGCAGCATACAGCAAACTTATAATAACTGCATCTCCCACATTTCTTATTTCAGCATTAAAATAAATAATATTTACGATTACATTTTTGAAAATGTTGTCGTACCAAGATGAAATCAAATAGTTAAGCTTCAGGGGAGAAAAGAGAAATAGACTGGGAAGGTGCTGTAACAAATGATGATGCTGAGTTGGTATTCTTGAGCAATAACTGTGATCTTTTCTATTTTCAATTGAAATGCAGCCCTCCGAGATTCTTCCAGTGTTTGGGAAGTCAAATTGTCTTATGAAATTGTGCAGAAATTGACAGATTCCAAACAAATAGAGACAGTAATCATTGGAGAATGCACAACAATCTGGCAATATGGAAATTACAAATTATAATATTTTCCCCCTGAGTAAATGAAATATGCAAAAGAACAACTGCATAATACAA--CACAGTTTGTGTAGTCCCTGGGTAGCTACTGTTAGCAAGCTATTTTATCACAGTTGTATACTTCCTTGGTTAATAATGAATGCACAAAATTAACTTTAAAATGAATTATAAAATTCTTTCAAAGTTCAATTTTTACATAAAATGCCATCGGGAAGTATCAAAATACGGTGGCAACCCATGACATAAATCTTTTAAAATGTCTGTGCACCTCACTGAACATTCTGCATTTTACTAACTCTTATTTATGTCAGGGAATTTTCCTAATCTGTTTTCATCCTATTACTGTACATAGTAATCTTGGCCCTAAAGAAATAGAAAAATTTAGCTCTGCCAGAAATATTTTTACAACCTTGATATTATCTTAATAAGATTGCATCTTACTGTGTTTATCTCTGGGATATAATATGGAAATCCAGTACTGGTAGCTATGATAATATTAATTCATTCTTTATTCAACAATACTTTGGTGAATGTTCTCTACTTATAAGCCCCTGAGCTCAGGGTTATGAGAGTATGTCATAAGCAGAGCACACAGATCTGCCTTTTAGGAGTTTACAGCCATCTAAAGAGCAGGTGGAATGAGACTTTTAAACATTGGTCGTGTTCTCTTTCTCAAAACTACCTTCACTGTGAGGTCAACATCCTTGGCCAACTGTTGATTACTCAGGAAGCTCACTCATCTTCTGGTCTTTGAAGTCGCTGCCTTGTTGATTTCACTGCTCATCACTTTCCCC---------------------------CACACTAAAAGGACACAAACCAGGGACAATTCACATCAATCAGGATGTGAGAAATTTGATAAAAGCTCTGTAGGGAAATGTCCGAACCTTGTGAGTGTTGAAGATTGCCTTCTTTCCTTCATGTGAGTAAGTTAGAATTGCCATATTTGGTGAACTGCTCATGTCCCAGATCTACCAGGTAACATCTGGTGTGGGCAAACAGTCTTTATTTATTATCATCTTGCAATAGCCAACTCTAGCTTTATTACTATTTCCTATAAAGCTTTGTGTAAATCTCAGTTTCTCCTCATATGAAATTGGAAACTTATGCTCTTCAACTACACATCTCCTAATGAAAATGAGTCAAATGATGTTTACAGAGATGGGATGTCAACCCAAAGGAAACTTCTGGAATGTAGAGA-CCAACAAGAGGCTGAGACTGAAAGACTATACCAGAGGGAACACTCACGGAACCAGGGCAAACCAAGTGGCCATGTCCTTGTAGTCAAGCAAGCCTGGAATGCTCAGGCAAGTACCAAGTGCCAGAGGAGGGTAAATGTGCTAA Chimp: ttttcaaaggatgggaaggatctttgtaggATA-TACAGGAGTTGACCTACTGTGGCCCGTTGGCAGAGCAGAG---------------------------------------------------GGCCACAGTGGGTcaactcctcttcatcctacaaa-gtccagctcaagcttt--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cacttccttg-tgacctccctggtgaccactgagcccaggcgcagcctctttctGAGAGAGagc-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ccctctcccagaacagggtgcacc------ ↓ 1 3 2 4 ↑ 1 3 4 2 Gorilla: ----gaaagcttgagctgg-actttgtaggatg-aagaggagttgaccCACTGTGGCCCTCTGCTCTGCCAAAG---------------------------------------------------GGCCACAGTAGGTCAACTCCTGTATATcctacaaagatccttcccatcctttgaaaaccaactgggacattccctctgggaagccttccTCACCTTTGCACTTGCATTCCTTGGCTCTGGTGCAAACATACAAAGTTCATGGGGGAGGGGTAACTTACAAGCAAAGAGGAGTTAGAGGTCATAGCATCTGCGACGTCTCTTTACCCTGCAGTTTAGACAGGGCATATGTGGACAGTATACTCTGGCCAATGTTCAAGAACAGAGGGAAGTTCCACTGTGAATCAGCTCTACGCATTTGCAGTTCTGGGGGTCCAGCACATCTACATGACTATGTGACAATGGAAGCC-TTTGGTTGGGGAAATGGCCTTTTTAGAAAGGGGAGCTTCCGGAACTGAGCTAACTTGGACCCCTGGAGCCAGCTTTCTCGTAAGTACCCAAAT-AA-----------------GCCTCTGGACATCCTGATTTCTCATCTAACTACaatgccttataggaattatgtcacttaatccttcaacagccttatgaggcattctctattactcttcccattttacatatga----tatagagatatagagaagttaaaccactagtttatggtcagcaactagtaactgacagaccagggacttgacctcTATGATACAGTGCCTCTTAATACACAATCTTGggccgggcgcggtggctcacacctataatcccagcactttgggaggctgaggcaggcggatcacctgaggtccggagttcaagaccagcctggccaacatggcaaaatcccgtctctactaaaaatacaaaaattagccatgcatggtgacgggcacctgtaatcccagctactcaggaggctgaggcaggagaatcacttgaacctgggaagcagaagctgcagtgagccatgattgcaccctcgtacttcagcctgggtgacagagtgagactccatctccaaaaaaaa------taaaataaaaCACGATCTTAAACCACACTACTAGCA------------------------------------------------------------TATATATATCTTGTAGATTTCTTCTAAAGTTTTACATATTTATCATTATTATTTTCTGCTACATACGTTTGTTGCCTAGGCATAGTGTTGAATGCATGAAAATTTCGCAATAACCACTCTAATGGGTAAGAAAAATGAAGCTGAAAAAAGTTCCCTTAGCTACTCTGTTAATTTGTGCTCTCTGGTTTAAAGAACTAGGACTTTGAAGAAGGAGCCTGaaaaa-------aaaaaaaaTCCTTCAAGGATCCAGCGAGCCAGCAGCCCAGAATATTGCAGAAAAGAGTATTTTcagcactcagctccaagtaggcattcaataaatactcgctgacttgatagaATTAAACAAACAGATTTTCCTGATTGACATGACATCCGCTCTAATTGCA-AACCTATTTGAGGAACAACTTGATGAAGCAAAGCAAAATTAAATGGGCCGCTGTGAAAGCAGTATAATGGTATTAGAACCTTTCAGTTGCTGGGCTGGAAGGGAGCTGAGGAGAATGTTGTTAAGTGTGGAGAATGTACAGGCAAGGACCAAATAGAATTTCTTTGACTTAATAATTTTTGAAAACTGTTTATACAATTCATATATTAAATGCTGTGGAAATTGTTTTGAGTC-TTGCGAGAGAGTTACTGCATTTAATCCCCACATAAACCTAGGT-----------G---CATTTGTAAGGCAATTGCAGCATACAGCAAACTTATAATAACTGCATCTCCCACATTTCTTATTTCAGCATTAAAATAAATAATATTTACGATTACATTTTTGAAAATGTTGTTTTACCAAGATGAAATCAAATAGTTAAGCTTCAGGGGAGAAAAGAGAAATAGACTGGGAAGGTGCTGTAACAAATGATGATGCTGAGTTGGTATTCTTGAGCAATAACTGTGATCTTTTCCATTTTCAATTGAAATGCAGCCCTCCGAGATTCTTCCAGTGTTTGGGAAGTCAAATTGTCTTATGAAATTGTGCAGAAATTGACAGATTCCAAACAAATAGAGAGAGTAATCATTGGAGAATGCACAACAATCTGGCAATATGGAAATTACAAATTATAATATTTTCCCCCTGAGTAAATGAAATATGCAAAAGCACAACTGCATAATACAA----CAGTTTGTGTAGTCCCTGGGTAGCTACTGTTAGCAAGCTATTTTATCACCGTTGTATACTTCCTTGGTTAATAATGAATGCACAAAATTAACTTTAAAATGAATTATAAAATTCTTTCAAAGTTCAATTTTTACATAAAATGCCATCAGGAAGTATCAAAATACGGTGGCAACCCATGACATAAATCTTTTAAAATGTCTGTGCACCTCACTGAACATTCTGCATTTTACTAACTCTTATTTATGTCAGGGAATTTTCCTAATCTGTTTTCATCCTATTACTGTACATACTAATCTTGGCCCTAAAGAAATAGAAAAATTTAGCTCTGCCAGAAATATTTTTACAACCTTGATATTATCTTAATAAGATTGCATCTTACTGTGTTTATCTTTGGGATATAATATGGAAATCCAGTACTGGTAGCTATGATAATACTAATTCATTCTTTATTCAATGATACTTTGGTGAATGTTCTCTACTTATAAGCCCCTGAGATCAGGGTTATGAGAGTATGTCATAAGCAGAGCACACAGATCTGCCTTTTAGGAGTTTACAGCCATCTAAAGAGCAGGTGGAATGAGACTTTTAAACATTGGTCGTGTTCTCTTTCTCAAAACTACCTTCACTGTGAGGTCAACATCCTTGGCCAACTGTTGATTACTCAGGAAGCTCACTCATCTTCTGGTCTTTGAAGTCGCTGCCTTGTTGATTTCACTGCTCATCACTTTCCCC---------------------------CACACTAAAAGGACACAAACCAGGGACAATTCACATCAATCAGGATGTGAGAAATTTGATAAAAGCTCTGTAGGGAAATGTCTGAACCTTGTGAGTGTTGAAGATTGCCTTCTTTCCTTCATGTGAGTAACTTAGAATTGCCATATTTGATGAACTGCTCATGTCCCAGATCTACCAGGTAACATCTGGTGTGGGAAAACAGTCTTTGttttttttCATCTTGCAATAGCCAACTCTAGCTTTATTACCATTTCCTATAAAGCTTTGTATAAATCTCAGTTTCTCCTCATATGAAATTGGAACCTTATGCTCTTCAACTACACATCTCCTAATGAAAATGAGTCACATGATGTTTACAGAGATGGGATGTCAACCCAAAGGAAACTCCTGGAATGCAGAGA-CCAACAAGAGGCTGAGACTGAAAGACTATACCAGAGGGAACACTCATGGAACGAGGGCAAACCAAGTGGCCATGTCCTTGTAGTCAAGCAAGCCTGGAATGCTCAGGCAAGTACCAAGTCCCAGAGGAGGGTAAATGTGCTAA Human: ----GAAAGCTTGAGCTGG-ACTTTGTAGGATG-AAGAGGAGTTGACCCACTGTGGCCCTCTGCTCTGCCAAAG---------------------------------------------------GGCCACAGTAGGTCAACTCCTGTATATCCTACAAAGATCCTTCCCATCCTTTGAAAACCAACTGGGACATTCCCTCTGGGAAGCCTTCCTCACCTTTGCACTTGCATTCCTTGGCTCTGGTGCAAATATACAAAGTTCATGGGGGAGGGGTAACTTACAAGCAAAGAGGAGTTAGAGGTCATAGCATCTGCGACTTCTCTTTACCCTGCAGTTTAGACAGGGCATATGTGGACAGTATACTCTGGCCAATGTTCAAAAACAGAGGGAAGTTCCATTGTGAATCAGTTCTACGCATTTGCAGTTCTGGGGGTCCAGCACATCTACATGAC--TGTGACAATGGAAGCTTCCTGGTTGGGGAAATGGCCTTTTTAGAAAGGGGAGCTTCCGGAACTGAGCTAACTTGGACCCCTGGAGCCAGCTTTCTCGTAAGTACCCAAAT-AA-----------------GCCTCTGGACATCCTGATTTCTCATCTAACTACaatgccttataggaattatgtcatttaatccttcaacagccttatgaggcattctctattactcttcccattttacatatga--gcaactgagatatagagaagttaaaccactagcttatggtcagcaactagtaactgacagaccagggacttgacctcTATGATATAGTGCCTTTTAATACACAATCTTGggccgggcgcggtggctcacacctataatcccagcactttgggaggctgaggcaggcggatcacctgaggtcaggagttcaagagcagcctggccaacatggcaaaatcccgtctctactaaaaatacaaaaattagccacgcatggtgacgggcacctgtaatcccagctactcaggaggctgaggcaggagaatcacttgaacctgggaagcagaggctgcagtgagccatgattgcacccttgtacttcagcctgggtgacagagtaagactccatctccaaaaaaa-ataaaataaaataaaaCACGATCTTAAACCACACTACTAGCA------------------------------------------------------------TATATATATCTTGTAGATTGCTTCTAAAGTTTTACATATTTATCATTATTATTTTCTGCTACATATGTTTGTTGCCTATGCATAGTGTTGAATGCATGAAAATTTCGCAATAACCACTCTAATGGGTAAGAAAAATGAAGCTGAAAAAAGTTCCCTTAGCTACTCTGTTAATTTTTGCTCTCTGGTTTAAAGAACTAGGACTTTGAAGAAGGAGCCTGaaaa---------aaaaaaaTCCTTCAAGGATCCAGCGAGCCAGCAGCCCAGAATATTGCAGAAAAGAgtattttcagcactcagctccaagtaggcattcaataaatactcgctgaCTTGATAGAATTAAACAAACAGATTTTCCTGATTGACATGACATCCACTCTAATTGCA-AACCTATTTGAGGAACAACTTGATGAAGCAAAGCAAAATTAAATGTGCCGCTGTGAAAGCGGTATAACGGTATTAGAACCTTTTAGTTGCTGGGCTGGAAGGGAGCTGAGGAGAACGTTGTTAAGTGTGGAGAATGTACAGGCAAGGACCAAATAGAATTTCTTTGACTTAATAATTTTTGAAAACTATTTATACAATTCATATATTAAATGCTGTGGAAATTGTTTTGAGTC-TTGCGAGAGAGTTACTGCATTTAATCCCCACATAAATCTAGGT-----------A---CATTTGTAAGGCAATTGCAGCATACAGCAAACTTATAATAACTGCATCTCCCACATTTCTTATTTCAGCATTAAAATAAATAATATTTACGATTACATTTTTGAAAATGTTGTCGTACCAAGATGAAATCAAATAGTTAAGCTTCAGGGGAGAAAAGAGAAATAGACTGGGAAGGTGCTGTAACAAATGATGATGCTGAGTTGGTATTCTTGAGCAATAACTGTGATCTTTTCTATTTTCAATTGAAATGCAGCCCTCCGAGATTCTTCCAGTGTTTGGGAAGTCAAATTGTCTTATGAAATTGTGCAGAAATTGACAGATTCCAAACAAATAGAGACAGTAATCATTGGAGAATGCACAACAATCTGGCAATATGGAAATTACAAATTATAATATTTTCCCCCTGAGTAAATGAAATATGCAAAAGAACAACTGCATAATACAA--CACAGTTTGTGTAGTCCCTGGGTAGCTACTGTTAGCAAGCTATTTTATCACAGTTGTATACTTCCTTGGTTAATAATGAATGCACAAAATTAACTTTAAAATGAATTATAAAATTCTTTCAAAGTTCAATTTTTACATAAAATGCCATCGGGAAGTATCAAAATACGGTGGCAACCCATGACATAAATCTTTTAAAATGTCTGTGCACCTCACTGAACATTCTGCATTTTACTAACTCTTATTTATGTCAGGGAATTTTCCTAATCTGTTTTCATCCTATTACTGTACATAGTAATCTTGGCCCTAAAGAAATAGAAAAATTTAGCTCTGCCAGAAATATTTTTACAACCTTGATATTATCTTAATAAGATTGCATCTTACTGTGTTTATCTCTGGGATATAATATGGAAATCCAGTACTGGTAGCTATGATAATATTAATTCATTCTTTATTCAACAATACTTTGGTGAATGTTCTCTACTTATAAGCCCCTGAGCTCAGGGTTATGAGAGTATGTCATAAGCAGAGCACACAGATCTGCCTTTTAGGAGTTTACAGCCATCTAAAGAGCAGGTGGAATGAGACTTTTAAACATTGGTCGTGTTCTCTTTCTCAAAACTACCTTCACTGTGAGGTCAACATCCTTGGCCAACTGTTGATTACTCAGGAAGCTCACTCATCTTCTGGTCTTTGAAGTCGCTGCCTTGTTGATTTCACTGCTCATCACTTTCCCC---------------------------CACACTAAAAGGACACAAACCAGGGACAATTCACATCAATCAGGATGTGAGAAATTTGATAAAAGCTCTGTAGGGAAATGTCCGAACCTTGTGAGTGTTGAAGATTGCCTTCTTTCCTTCATGTGAGTAAGTTAGAATTGCCATATTTGGTGAACTGCTCATGTCCCAGATCTACCAGGTAACATCTGGTGTGGGCAAACAGTCTTTATTTATTATCATCTTGCAATAGCCAACTCTAGCTTTATTACTATTTCCTATAAAGCTTTGTGTAAATCTCAGTTTCTCCTCATATGAAATTGGAAACTTATGCTCTTCAACTACACATCTCCTAATGAAAATGAGTCAAATGATGTTTACAGAGATGGGATGTCAACCCAAAGGAAACTTCTGGAATGTAGAGA-CCAACAAGAGGCTGAGACTGAAAGACTATACCAGAGGGAACACTCACGGAACCAGGGCAAACCAAGTGGCCATGTCCTTGTAGTCAAGCAAGCCTGGAATGCTCAGGCAAGTACCAAGTGCCAGAGGAGGGTAAATGTGCTAA Cluster: [ ] Orangutan: ----GAAAGCTTGAGCTGG-ACTTTGTAGGATGAAAGAGGANNNNNN-----NNNNTCGTTTAATATTCCAAAAGCTTTGGAAACCAAAATGTTGaaaaaaaaaaaGAGGAGGCTTTACGTTTACGGAC-AGGGAGGTCAACTCCTGTATATCCTACAAAGATCCTTCCCATCCTTTGAGAACCAACTGGGACCTCCCCTCTGGGAAGCCTTCCTCGCCTTTGCACTTGCATTGCTTGGCTCTGGTGCAAATACACACAGTTCATGCGGGA-GGGTGACTCACAAGCAAAGAGGAGTTAGAGGTCGCAGCATCTGCGACTTCTCTTTACCCTGCAGTTTAGACAGGGCATATGTGGACAGTATACTCTGGCCAACGTTCAAGAACAGAGGGAAGTTCCACCGTGAATCAGTTCTACGCATTTGCAGTTCTGTAGGTCCAGCACATCTACATGACTATGTGACAATGGAAGCTTCCTGGTTGGGGAAATGGCCTTTTTAGAAAGGAGAGCTTCCAGAACTGAGCTAACTTCGACCCCTGGAGCCAGCTTTCTCGTAAGTACCCAAAGTAAGTACTTACTCTCGTAAGTACTCTGGACATCCTGATTTGTCATCTAACTACaatgtcttataggaattatgtcatttaatccttcaacagccttatgaggcattctctattattcttcccattttacatatgagc--aactgagatatagagaagttaaacaactagcttatggtcagcaactagtaactgacagaccagggacttgacctctatgatatagtgcctcttaattcacaatcttgggccgggcacggtggctcacacctataacctcagcactttgggaggccgaggcaggcagatcacctgaggtcaggagttcaagaccagcctggccaacatggcaaaatcccgtctctactaaaaatacaaaaattagccaggcgtggtgacgggcacctgtaatcccagctactcaggaggctgaggcaggagaatcacttgaacctgagaagcagaggctgcagtgagccatgattgcacccttgcacttcagcctgggcgagagactgagactccatctccaaaaaaaa------taaaataaaacacaatcttaaaccacactactagCCtatatatatatatgctagtatgtatatatatatatatacacacatatatatgctagtatgtatatatatatGGTAGATTGCTTCTAAAGTTTTACATATTTATCACTATTATTTTCTGCTACATATGTTTGTTGCCTAGGCATAGTGTTGAATGCATGAAAATTTCTCAATAACGACTCTAATGGGTAAGAAAAATGAAGCTGAGAAAAGTTCCCTTAGCTACTCTGTTAATTTGTGCTCTCTGGTTTAAAGAACTAGGACTTTGAAGAAGGAGCCTGaaaaaaaaaaaaaaaaaaaaTCCTTCAAGGATCCAGCAAGCCAGCAGCCCAGAATATTGCAGAAAAGAgtattttcagcactcagctccaagtaggcattcaataaatacttgctgaCTTGATAGAATTAAACAAACAGATTTTCCTGATTGACATGACATCCGCTCTAATTGCAAAACCTATTTGAGGAACAACTTGATGAAGCAAAGCAAAATTAAATGGGCCGCTGTGAAAGCGGTATAATGGTATTAGAACCTTTCAGTTGCTGGGCTGGAAGGGAGCGGAGGAGAACACTGTAAAGTGTGGACAGTGTACAGGCAAGGACCAAATAGAATTTCTTTGACTTAATAATTTTTGGAAACTGTTTATACAATTCATATATTAAATGCTGTGGAAATTGTTTTGAGTCTTTGCAAGAGAGTTACTGCATTTAATCCCCACATAAATCTAGGGGATAAATCCCCACATAAATTGTAAGGCAATTGCAGCATACAGCAAACTTATAATAACTGCATCTCCCACATTTCTTATTTCAGCATTAAA----ATAATGTTTACGATTACATTTTTGAAGATGTTGTTGTACCAAGATGAAATCAAATAGTTAAGCTTCGGGGGAGAAAAGAGAAATAGACTGGGAAGGTGCTGTAACAAATGATGATGCGGAGTTGGTATTCTTGAGAAATAACTGTGATCTTTTCCATTTTCAATTGAAATGCAGCCCTCCGAGATTCTTCCGGTGTTTGGGAAGTCAAATTGTCTTATGAAATTGTGCAGAAATTGACAGATTCCAAACAAATAGAGAGAGTAATCATTGGAGAATGCACAACAATCTGGCAATATGGAAATTACAAATTATAATATTTTCCCCCTGAGTAAATGAAATATGCAAAAGAACAACTGCATAATACAACA--CAGTTTGTGTAGTCCCTGGGTAGCTACTGTTAGCAAGCTATTTTATCACAGTTGTTTACTTCCTTGGTTAATAATGAATGCACAAAATTAACTTTAAAATGAATTATAAAATTCTTTCAAAGTTCAATTTTTACGTAAAACGCCATCAGGAAGTATCAAAATATGGTGGCAACCCATGACATAAANNNN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNNNNNAACCTTTTGGATAACAGAGACCCAACAAGAGGCTGAGACTGAAAGACTGTGCCAGAGG-GACACTCACAGAACCAGGGCAAACCAGGTGGCCATGT-CTTGTAGTCAAGCAAGTCTGGAATGCTCAGGCAAGTACCAAGTCCCAGAGGAGGGTAAATGTGCTAA Gorilla > Chimp --------------- chr10:128554835-128554916 Template switch process: F1: L GGA 1 F3: 4 TACAAAGT R RF: GGACTTTGTAGGATGAAGAGGAGTTGACCCACTGTGGCCCTCTGCTCTGCCAAAGGGCCACAGTAGGTCAACTCCTGTATATCCTACAAAGATCCTTCCCATCCTTTGAAAACCAACTGGGACATTCCCTCTGGGAAGCCTTCCTCACCTTTGCACTTGCATTCCTTGGCTCTGGTGCAAACATACAAAGT RR: CCTGAAACATCCTACTTCTCCTCAACTGGGTGACACCGGGAGACGAGACGGTTTCCCGGTGTCATCCAGTTGAGGACATATAGGATGTTTCTAGGAAGGGTAGGAAACTTTTGGTTGACCCTGTAAGGGAGACCCTTCGGAAGGAGTGGAAACGTGAACGTAAGGAACCGAGACCACGTTTGTATGTTTCA F2: 3 CCTACTTCTCCTCAACTGGGTGACACCGGGAGACGAGACGGTTGCCCGGTGTCATCCAGTTGAGGACATATAGGATGTTTCT 2 Unidirectional alignment (log-probability: -105) GGAtCTTTGTAGGATatAcAGGAGTTGACCtACTGTGGCCCgttggcagagcag-------------AGGGCCACAGTgGGTCAACTCCTcTtcATCCTACAAAG-T GGA-CTTTGTAGGATGAAGAGGAGTTGACCCACTGTGGCCC-------------TCTGCTCTGCCAAAGGGCCACAGTAGGTCAACTCCTGTATATCCTACAAAGAT Template switch alignment (log-probability: -30) GGA|TCTTTGTAGGATATACAGGAGTTGACCTACTGTGGCCCgTTGGCAGAGCAGAGGGCCACAGTGGGTCAACTCCTCTTCATCC|TACAAAGT GGA|TCTTTGTAGGATATACAGGAGTTGACCTACTGTGGCCCTTTGGCAGAGCAGAGGGCCACAGTGGGTCAACTCCTCTTCATCC|TACAAAGT Chimp > Gorilla --------------- chr10:141426240-141426326 Template switch process: F1: L GGA 1 F3: 4 GAT R RF: GGATCTTTGTAGGATATACAGGAGTTGACCTACTGTGGCCCGTTGGCAGAGCAGAGGGCCACAGTGGGTCAACTCCTCTTCATCCTACAAAG RR: CCTAGAAACATCCTATATGTCCTCAACTGGATGACACCGGGCAACCGTCTCGTCTCCCGGTGTCACCCAGTTGAGGAGAAGTAGGATGTTTC F2: 3 AAACATCCTATATGTCCTCAACTGGATGACACCGGGAAACCGTCTCGTCTCCCGGTGTCACCCAGTTGAGGAGAAGTAGGATGTTTC 2 Unidirectional alignment (log-probability: -105) GGA-CTTTGTAGGATgaAgAGGAGTTGACCcACTGTGGCCCtctgctctgccaa-------------AGGGCCACAGTaGGTCAACTCCTgTatATCCTACAAAGaT GGATCTTTGTAGGATATACAGGAGTTGACCTACTGTGGCCC-------------GTTGGCAGAGCAGAGGGCCACAGTGGGTCAACTCCTCTTCATCCTACAAAG-T Template switch alignment (log-probability: -30.5) GGA|CTTTGTAGGATGAAGAGGAGTTGACCCACTGTGGCCCTCTGCTCTGCCAAaGGGCCACAGTAGGTCAACTCCTGTATATCCTACAAA|GAT GGA|CTTTGTAGGATGAAGAGGAGTTGACCCACTGTGGCCCTCTGCTCTGCCAACGGGCCACAGTAGGTCAACTCCTGTATATCCTACAAA|GAT ========= Event 168 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGCAGCACAGCACACACCCCGCCCAGGCCAGTGGGGGCTAGTCACCATGCTATTTCCC ↓ 1 3 2 4 Chimp: GTGCAGTACAGCACACACCCCAC-----------TGGCCTAGTCACCATGCTATTTCCC Gorilla: GTGCAGCACAGCACACACCCCACCCAGGCCAGTGGGGGCTAGTCACCATGCTATTTCCC Human: GTGCAGCACAGCACACACCCCGCCCAGGCCAGTGGGGGCTAGTCACCATGCTATTTCCC Cluster: [ ] Orangutan: GTGCAGCACAGCACGCACCCCGCCCAGCCCAGTGGGGGCTAGTCACTATGCTATTTCCC Human > Chimp ------------- chr10:73468458-73468463 Template switch process: F1: L CCAGCTGGCTATGGTTGTGGGTGCAGTACAGCACACACCCC 1 F3: 4 CTAGTCACCATGCTATTTCCCAAGGAGGTGGATGAAGTGG R RF: CCAGCTGGCTATGGTTGTGGGTGCAGCACAGCACACACCCCGCCCAGGCCAGTGGGGGCTAGTCACCATGCTATTTCCCAAGGAGGTGGATGAAGTGG RR: GGTCGACCGATACCAACACCCACGTCGTGTCGTGTGTGGGGCGGGTCCGGTCACCCCCGATCAGTGGTACGATAAAGGGTTCCTCCACCTACTTCACC F2: 3 CGGTCA 2 Unidirectional alignment (log-probability: -33.7) CAGCTGGCTATGGTTGTGGGTGCAGtACAGCACACACCCCactgGCC---------------TAGTCACCATGCTATTTCCCAAGGAGGTGGATGAAGTGG CAGCTGGCTATGGTTGTGGGTGCAGCACAGCACACACCCC----GCCCAGGCCAGTGGGGGCTAGTCACCATGCTATTTCCCAAGGAGGTGGATGAAGTGG Template switch alignment (log-probability: -22) CAGCTGGCTATGGTTGTGGGTGCAGtACAGCACACACCCC|ACTGGC|CTAGTCACCATGCTATTTCCCAAGGAGGTGGATGAAGTGG CAGCTGGCTATGGTTGTGGGTGCAGCACAGCACACACCCC|ACTGGC|CTAGTCACCATGCTATTTCCCAAGGAGGTGGATGAAGTGG ========= Event 169 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGCAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACA---------AATCTTAATGAATGAATGGAGAC Chimp: CAGCAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACA---------AATCTTAATGAATGAATGGAGAC ↓ 3 2 1 4 Gorilla: CAGCAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAACAGAGGACATTCTTAATGAATGAATGGAGAC ↑ 3 2 1 4 Human: CAGCAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACA---------AATCTTAATGAATGAATGGAGAC Cluster: [ ] Orangutan: CAGCAGGCTACTAGGAAATATGTTCTCTGTTGACATCTAGGACA---------AATCTTAATGAATGAATAGAGAC Human > Gorilla --------------- chr10:51588467-51588476 Template switch process: F1: L CAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAA 1 F3: 4 TCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG R RF: CAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAAATCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG RR: GTCCGATGATCCTTTATACAGGAGACAACTGCAGATCCTGTTTAGAATTACTTACTTACCTCTGACCCCAATAGATGGTCCTC F2: 3 TACAGGAGAC 2 Unidirectional alignment (log-probability: -29.4) GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAacagaggacAtTCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACA---------AATCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG Template switch alignment (log-probability: -17) GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAA|CAGAGGACAT|TCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAA|CAGAGGACAT|TCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG Chimp > Gorilla --------------- chr10:51588467-51588476 Template switch process: F1: L CAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAA 1 F3: 4 TCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG R RF: CAGGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAAATCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG RR: GTCCGATGATCCTTTATACAGGAGACAACTGCAGATCCTGTTTAGAATTACTTACTTACCTCTGACCCCAATAGATGGTCCTC F2: 3 TACAGGAGAC 2 Unidirectional alignment (log-probability: -29.4) GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAacagaggacAtTCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACA---------AATCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG Template switch alignment (log-probability: -17) GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAA|CAGAGGACAT|TCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG GGCTACTAGGAAATATGTCCTCTGTTGACGTCTAGGACAA|CAGAGGACAT|TCTTAATGAATGAATGGAGACTGGGGTTATCTACCAGGAG ========= Event 170 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CTGCAGTAGATTGCCCTAGGATCCCTTACCCCTCAGGGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCTGTGGTGCTGCTGGTCACTAACCTGTGGGAAAGCCTTGTGGGCCCGGGGCCAGTGTGGGCTCCTGAGTATGGAGACCCTTCATCAA ↑ 4 1 3 2 Chimp: TTGCAGTAGATTGCCCTAGGATCCCT------------------TACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCCGTGGTGCTGCTGATCACTAACCTGTGGGAAAGCCTTGTGGGCCCAGGGCCAGTGTGGGCTCCTGAGTATGGAGACCCTTCATCAA ↓ 4 1 3 2 Gorilla: CTGCAGTAGATTGCCCTAGGATCCCTTACCCCTCAGGGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCCGTGGTGCTGCTGGTCACTAACCTGTGGGAAAGCCTTGTGGGCCCGGGGCCAGTGTGGGCTCCTGAGTATGGAGACCCTTCATCAA Human: CTGCAGTAGATTGCCCTAGGATCCCTTACCCCTCAGGGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCTGTGGTGCTGCTGGTCACTAACCTGTGGGAAAGCCTTGTGGGCCCGGGGCCAGTGTGGGCTCCTGAGTATGGAGACCCTTCATCAA Cluster: [ ] Orangutan: Chimp > Human ------------- chr10:61973074-61973078 Template switch process: F1: L CTGCCATTTGGCCACCTGCAGTAGATTGCCCTAGGATCCCTTACCCC 1 F3: 4 GATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCTGTGG R RF: CTGCCATTTGGCCACTTGCAGTAGATTGCCCTAGGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCCGTGGTGCTGCTGATCACTAACCTGTGGGAAAGCCTTGTGGGCCCAGGGCCAGTGTGGGCTCCTGA RR: GACGGTAAACCGGTGAACGTCATCTAACGGGATCCTAGGGAATGGGGGGAATGAACCCGTCGGGACACAGAACAAGGCACCACGACGACTAGTGATTGGACACCCTTTCGGAACACCCGGGTCCCGGTCACACCCGAGGACT F2: 3 GGACT 2 Unidirectional alignment (log-probability: -48.8) TTGGCCACcTGCAGTAGATTGCCCTAGGATCCCTTACCcctcagggatcccttaccCCCCTTACTTGGGCAGCCCTGTGTCTTGT TTGGCCACTTGCAGTAGATTGCCCTAGGATCCCTTACC------------------CCCCTTACTTGGGCAGCCCTGTGTCTTGT Template switch alignment (log-probability: -28.1) TTGGCCACcTGCAGTAGATTGCCCTAGGATCCCTTACCCC|TCAGG|GATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGT TTGGCCACTTGCAGTAGATTGCCCTAGGATCCCTTACCCC|TCAGG|GATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGT Chimp > Gorilla --------------- chr10:38001287-38001291 Template switch process: F1: L CTGCCATTTGGCCACCTGCAGTAGATTGCCCTAGGATCCCTTACCCC 1 F3: 4 GATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCCGTGG R RF: CTGCCATTTGGCCACTTGCAGTAGATTGCCCTAGGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGTTCCGTGGTGCTGCTGATCACTAACCTGTGGGAAAGCCTTGTGGGCCCAGGGCCAGTGTGGGCTCCTGA RR: GACGGTAAACCGGTGAACGTCATCTAACGGGATCCTAGGGAATGGGGGGAATGAACCCGTCGGGACACAGAACAAGGCACCACGACGACTAGTGATTGGACACCCTTTCGGAACACCCGGGTCCCGGTCACACCCGAGGACT F2: 3 GGACT 2 Unidirectional alignment (log-probability: -42.3) TTGGCCACcTGCAGTAGATTGCCCTAggatcccttacccctcagGGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGT TTGGCCACTTGCAGTAGATTGCCCTA------------------GGATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGT Template switch alignment (log-probability: -22.2) TTGGCCACcTGCAGTAGATTGCCCTAGGATCCCTTACCCC|TCAGG|GATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGT TTGGCCACTTGCAGTAGATTGCCCTAGGATCCCTTACCCC|TCAGG|GATCCCTTACCCCCCTTACTTGGGCAGCCCTGTGTCTTGT ========= Event 171 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATGGGGAGGGTGACTGGTGACTTCTCC-----CTGTAGCTTAGGGCAGAAGGGGACATCAGG Chimp: TATGGGGAGGGTGACTGGTGACTTCTCC-----CTGTAGCTTAGGGCAGAAGGGGACATCAGG ↓ 3 2 1 4 Gorilla: TATGGGGAGGGTGACTGGTGACTTCTCC----------AGTCAGGGCAGAAGGGGACATCAGG ↑ 3 2 1 4 Human: TATGGGGAGGGTGACTGGTGACTTCTCC-----CTGTAGCTTAGGGCAGAAGGGGACATCAGG Cluster: [ ] Orangutan: TATGGGGAGGGTGACTGGTGACTTCTCCCTGTA-----GCTCAGGGCAGGAGGGGACATCAGG Human > Gorilla --------------- chr10:110307188-110307191 Template switch process: F1: L CTCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC 1 F3: 4 AGGGCAGAAGGGGACATCAGGGTCACTTCTGAGAAGGAAG R RF: CTCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCCCTGTAGCTTAGGGCAGAAGGGGACATCAGGATCACTTCTGAGAAGGAAG RR: GAGTAAGAACTCGATACCCCTCCCACTGACCACTGAAGAGGGACATCGAATCCCGTCTTCCCCTGTAGTCCTAGTGAAGACTCTTCCTTC F2: 3 CTGA 2 Unidirectional alignment (log-probability: -30.9) TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCCagtC--------AGGGCAGAAGGGGACATCAGGgTCACTTCTGAGAAGGAAG TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC---CTGTAGCTTAGGGCAGAAGGGGACATCAGGATCACTTCTGAGAAGGAAG Template switch alignment (log-probability: -21.7) TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC|AGTC|AGGGCAGAAGGGGACATCAGGgTCACTTCTGAGAAGGAAG TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC|AGTC|AGGGCAGAAGGGGACATCAGGATCACTTCTGAGAAGGAAG Chimp > Gorilla --------------- chr10:110307188-110307191 Template switch process: F1: L CTCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC 1 F3: 4 AGGGCAGAAGGGGACATCAGGGTCACTTCTGAGAAGGAAG R RF: CTCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCCCTGTAGCTTAGGGCAGAAGGGGACATCAGGATCACTTCTGAGAAGGAAG RR: GAGTAAGAACTCGATACCCCTCCCACTGACCACTGAAGAGGGACATCGAATCCCGTCTTCCCCTGTAGTCCTAGTGAAGACTCTTCCTTC F2: 3 CTGA 2 Unidirectional alignment (log-probability: -30.9) TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCCagtC--------AGGGCAGAAGGGGACATCAGGgTCACTTCTGAGAAGGAAG TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC---CTGTAGCTTAGGGCAGAAGGGGACATCAGGATCACTTCTGAGAAGGAAG Template switch alignment (log-probability: -21.7) TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC|AGTC|AGGGCAGAAGGGGACATCAGGgTCACTTCTGAGAAGGAAG TCATTCTTGAGCTATGGGGAGGGTGACTGGTGACTTCTCC|AGTC|AGGGCAGAAGGGGACATCAGGATCACTTCTGAGAAGGAAG ========= Event 172 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: tggcacctggcacCTGGAATGTCTTATCGCTGTAA----------------------TGACAGCCATGCATAGCAGCAGCCGCACC ↓ 1 3 4 2 ↑ 1 3 4 Chimp: tggcacctggcacCTGGAATG----TTGGCTGTCA-----------TTACAGCGATAAGACAGCCATGCATAGCAGCAGCCGCACC Gorilla: tggcacctggcacCTGGAATG----TTGGCTGTCATTACAGCGATA-----------AGACAGCCATGCATAGCAGCAGCCGCACC ↓ 1 3 4 ↑ 1 3 4 2 Human: tggcacctggcacCTGGAATGTCTTATCGCTGTAA----------------------TGACAGCCATGCATAGCAGCAGCCGCACC Cluster: [ ] Orangutan: tggcacctggcacCTGGAATG----TTGGCTGTCATTACAGCGATA-----------AGACAGCCATGCATAGCAGCAGCCGCACC Chimp > Human ------------- chr10:71684663-71684676 Template switch process: F1: L CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT 1 F3: 4 GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC R RF: CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTTGGCTGTCATTACAGCGATAAGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC RR: GACTTTACCCTAACACGTCCACCGTGGACCGTGGACCTTACAACCGACAGTAATGTCGCTATTCTGTCGGTACGTATCGTCGTCGGCGTGGGTACGGGGTCGG F2: 3 TAATGTCGCTATTC 2 Unidirectional alignment (log-probability: -39.5) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTcttaTcGCTGTaAT-----------GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT----TGGCTGTCATTACAGCGATAAGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Template switch alignment (log-probability: -17) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|CTTATCGCTGTAAT|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|CTTATCGCTGTAAT|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Human > Chimp ------------- chr10:72791859-72791879 Template switch process: F1: L CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT 1 F3: 4 GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC R RF: CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTCTTATCGCTGTAATGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC RR: GACTTTACCCTAACACGTCCACCGTGGACCGTGGACCTTACAGAATAGCGACATTACTGTCGGTACGTATCGTCGTCGGCGTGGGTACGGGGTCGG F2: 3 AATAGCGACATTACTGTCGGT 2 Unidirectional alignment (log-probability: -49.2) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT----TgGCTGTcATtacagcgataaGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTCTTATCGCTGTAAT-----------GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Template switch alignment (log-probability: -17.9) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|TGGCTGTCATTACAGCGATAA|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|TGGCTGTCATTACAGCGATAA|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Gorilla > Human --------------- chr10:71684663-71684676 Template switch process: F1: L CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT 1 F3: 4 GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC R RF: CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTTGGCTGTCATTACAGCGATAAGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC RR: GACTTTACCCTAACACGTCCACCGTGGACCGTGGACCTTACAACCGACAGTAATGTCGCTATTCTGTCGGTACGTATCGTCGTCGGCGTGGGTACGGGGTCGG F2: 3 TAATGTCGCTATTC 2 Unidirectional alignment (log-probability: -38.1) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTcttaTcGCTGTaAT-----------GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT----TGGCTGTCATTACAGCGATAAGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Template switch alignment (log-probability: -17.5) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|CTTATCGCTGTAAT|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|CTTATCGCTGTAAT|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Human > Gorilla --------------- chr10:110499912-110499932 Template switch process: F1: L CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT 1 F3: 4 GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC R RF: CTGAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTCTTATCGCTGTAATGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC RR: GACTTTACCCTAACACGTCCACCGTGGACCGTGGACCTTACAGAATAGCGACATTACTGTCGGTACGTATCGTCGTCGGCGTGGGTACGGGGTCGG F2: 3 AATAGCGACATTACTGTCGGT 2 Unidirectional alignment (log-probability: -47.8) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT----TgGCTGTcATtacagcgataaGACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGTCTTATCGCTGTAAT-----------GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC Template switch alignment (log-probability: -18.4) GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|TGGCTGTCATTACAGCGATAA|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC GAAATGGGATTGTGCAGGTGGCACCTGGCACCTGGAATGT|TGGCTGTCATTACAGCGATAA|GACAGCCATGCATAGCAGCAGCCGCACCCATGCCCCAGCC ========= Event 173 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: ccacgcccagccAAACATTTTTGATACAGACTATCAAAGCTTCTGTTTCCCTAAAT Chimp: Gorilla: ccacacccagccAAACATTTT---CACTCTGTATCAAAGCTTCTGTTTCCCTAAAT ↓ 1 3 4 2 Human: ccacgcccagccAAACATTTTTGATACAGACTATCAAAGCTTCTGTTTCCCTAAAT Cluster: [ ] Orangutan: ccacacccagccAAACATTTT---CACTCCGTATCAAAGCTTCTGTTTCCCTAAAT Gorilla > Human --------------- chr10:127409958-127409966 Template switch process: F1: L GGGATTACAGGCTTGAGCCGCCACGCCCAGCCAAACATTTT 1 F3: 4 CTATCAAAGCTTCTGTTTCCCTAAATCCCTAATTCTTTAAT R RF: GGGATTACAGGCTTGAGCCGCCACACCCAGCCAAACATTTTCACTCTGTATCAAAGCTTCTGTTTCCCTAAATCCCTAATTCTTTAAT RR: CCCTAATGTCCGAACTCGGCGGTGTGGGTCGGTTTGTAAAAGTGAGACATAGTTTCGAAGACAAAGGGATTTAGGGATTAAGAAATTA F2: 3 AGACATAGT 2 Unidirectional alignment (log-probability: -37.9) GGATTACAGGCTTGAGCCGCCACgCCCAGCCAAACATTTT-----TGatacagacTATCAAAGCTTCTGTTTCCCTAAATCCCTAATTCTTTAA GGATTACAGGCTTGAGCCGCCACACCCAGCCAAACATTTTCACTCTG--------TATCAAAGCTTCTGTTTCCCTAAATCCCTAATTCTTTAA Template switch alignment (log-probability: -27.9) GGATTACAGGCTTGAGCCGCCACgCCCAGCCAAACATTTT|TGATACAGA|cTATCAAAGCTTCTGTTTCCCTAAATCCCTAATTCTTTAA GGATTACAGGCTTGAGCCGCCACACCCAGCCAAACATTTT|TGATACAGA|GTATCAAAGCTTCTGTTTCCCTAAATCCCTAATTCTTTAA ========= Event 174 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGGCT----TATGCCAAAGCCAGTGGGATACA----GCTTAGTTAGTGGTCAGCACTTCTAGCT Chimp: TGGGCT----TATGCCAAAGCCAGTGAGACACA----GCCTAGTTAGTGGTCAGCACTTCTAGCT Gorilla: TGGGCT----TATGCCAAAGCCAGTGGGACACT--------GGCCAGTGGTCAGCACTTCTAGCT ↑ 3 2 1 4 Human: TGGGCT----TATGCCAAAGCCAGTGGGATACA----GCTTAGTTAGTGGTCAGCACTTCTAGCT Cluster: [ ] Orangutan: TGGGCTTATTTATGCCAAAGCCAGTGGGACACAGCCT----AGTTAGTGGTCAGCACTTCTAGCT Human > Gorilla --------------- chr10:115459740-115459746 Template switch process: F1: L ACGGAGTTATGAGACTTGGGCTTATGCCAAAGCCAGTGGGA 1 F3: 4 CAGTGGTCAGCACTTCTAGCTGTATGAAAGGCAGATTGCAG R RF: ACGGAGTTATGAGACTTGGGCTTATGCCAAAGCCAGTGGGATACAGCTTAGTTAGTGGTCAGCACTTCTAGCTGTATGAAATGCAGATTGCAG RR: TGCCTCAATACTCTGAACCCGAATACGGTTTCGGTCACCCTATGTCGAATCAATCACCAGTCGTGAAGATCGACATACTTTACGTCTAACGTC F2: 3 CGGTCAC 2 Unidirectional alignment (log-probability: -37.9) CGGAGTTATGAGACTTGGGCTTATGCCAAAGCCAGTGGGAcAC--------TggccAGTGGTCAGCACTTCTAGCTGTATGAAAgGCAGATTGCA CGGAGTTATGAGACTTGGGCTTATGCCAAAGCCAGTGGGATACAGCTTAGTT----AGTGGTCAGCACTTCTAGCTGTATGAAATGCAGATTGCA Template switch alignment (log-probability: -27.7) CGGAGTTATGAGACTTGGGCTTATGCCAAAGCCAGTGGGA|CACTGGC|cAGTGGTCAGCACTTCTAGCTGTATGAAAgGCAGATTGCA CGGAGTTATGAGACTTGGGCTTATGCCAAAGCCAGTGGGA|CACTGGC|TAGTGGTCAGCACTTCTAGCTGTATGAAATGCAGATTGCA ========= Event 175 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCCACCTCTTCG-CAACATAGCTATCAACAT----AGC---CTTCAGGTAATATAAGATGAGTGAGAC ↓ 3 2 1 4 Chimp: TGCCCACCTCTTCG-CAACATAGCTATCAACAT--ATAGC------TATGTAATATAAGATGAGTGAGAC Gorilla: TGCCCACCTCTTCG-CAACATAGCTATCAACATAC--AGC------TATGTAGTATAAGATGAGTGAGAC Human: TGCCCACCTCTTCG-CAACATAGCTATCAACAT----AGC---CTTCAGGTAATATAAGATGAGTGAGAC Cluster: [ ] Orangutan: TGCCTACCTCTTCTCAAACAGAGCCATCAACAT----AGCCTT---CAGGTAATATAAGATGAGTGACAC Human > Chimp ------------- chr10:79815361-79815367 Template switch process: F1: L ATCCTCACCTGCCCACCTCTTCGCAACATAGCTATCAACATA 1 F3: 4 GTAATATAAGATGAGTGAGACTGAGCTTTTGTGTTTAGCG R RF: ATCCTCACCTGCCCACCTCTTCGCAACATAGCTATCAACATAGCCTTCAGGTAATATAAGATGAGTGAGACTGAGCTTTTGTGTTTAGTG RR: TAGGAGTGGACGGGTGGAGAAGCGTTGTATCGATAGTTGTATCGGAAGTCCATTATATTCTACTCACTCTGACTCGAAAACACAAATCAC F2: 3 TATCGAT 2 Unidirectional alignment (log-probability: -37.6) CCTCACCTGCCCACCTCTTCGCAACATAGCTATCAACATAtagctat--------GTAATATAAGATGAGTGAGACTGAGCTTTTGTGTTTAGcG CCTCACCTGCCCACCTCTTCGCAACATAGCTATCAACATA-------GCCTTCAGGTAATATAAGATGAGTGAGACTGAGCTTTTGTGTTTAGTG Template switch alignment (log-probability: -22.2) CCTCACCTGCCCACCTCTTCGCAACATAGCTATCAACATA|TAGCTAT|GTAATATAAGATGAGTGAGACTGAGCTTTTGTGTTTAGcG CCTCACCTGCCCACCTCTTCGCAACATAGCTATCAACATA|TAGCTAT|GTAATATAAGATGAGTGAGACTGAGCTTTTGTGTTTAGTG ========= Event 176 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGTGACCCTTTTCTAACTT---CTATAGAAGAGCTCAAAGTAAACAAGGAAGATGACAAATT Chimp: AAGGTGACCCTTTTCTAACTT---CTATAGAAGAGCTCAAAGTAAAGAAGGAAGATGAAAAATT ↓ 1 4 3 2 Gorilla: AAGGTGACCCTTTTCTAACTTTACTTTGAGAAGAGCTCAAAGTAAAGAAGGAAGATGACAAATT ↑ 1 4 3 2 Human: AAGGTGACCCTTTTCTAACTT---CTATAGAAGAGCTCAAAGTAAACAAGGAAGATGACAAATT Cluster: [ ] Orangutan: AAGGTGACCCTTTTCTAACTT---CTATAGAAGAGCTCAAAGTAAAGAAGGAAGATGACAAATT Human > Gorilla --------------- chr10:99202278-99202284 Template switch process: F1: L AGACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT 1 F3: 4 AGAAGAGCTCAAAGTAAAGAAGGAAGATGACAAATTATTA R RF: AGACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTTCTATAGAAGAGCTCAAAGTAAACAAGGAAGATGACAAATTATTA RR: TCTGTCCTTTTCTACAAATATTCCACTGGGAAAAGATTGAAGATATCTTCTCGAGTTTCATTTGTTCCTTCTACTGTTTAATAAT F2: 3 GTTTCAT 2 Unidirectional alignment (log-probability: -34.9) GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT---TactttgAGAAGAGCTCAAAGTAAAgAAGGAAGATGACAAATTATTA GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTTCTAT------AGAAGAGCTCAAAGTAAACAAGGAAGATGACAAATTATTA Template switch alignment (log-probability: -22.1) GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT|TACTTTG|AGAAGAGCTCAAAGTAAAgAAGGAAGATGACAAATTATTA GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT|TACTTTG|AGAAGAGCTCAAAGTAAACAAGGAAGATGACAAATTATTA Chimp > Gorilla --------------- chr10:99202278-99202284 Template switch process: F1: L AGACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT 1 F3: 4 AGAAGAGCTCAAAGTAAAGAAGGAAGATGACAAATTATTA R RF: AGACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTTCTATAGAAGAGCTCAAAGTAAAGAAGGAAGATGAAAAATTATTA RR: TCTGTCCTTTTCTACAAATATTCCACTGGGAAAAGATTGAAGATATCTTCTCGAGTTTCATTTCTTCCTTCTACTTTTTAATAAT F2: 3 GTTTCAT 2 Unidirectional alignment (log-probability: -34.9) GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT---TactttgAGAAGAGCTCAAAGTAAAGAAGGAAGATGAcAAATTATTA GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTTCTAT------AGAAGAGCTCAAAGTAAAGAAGGAAGATGAAAAATTATTA Template switch alignment (log-probability: -22.1) GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT|TACTTTG|AGAAGAGCTCAAAGTAAAGAAGGAAGATGAcAAATTATTA GACAGGAAAAGATGTTTATAAGGTGACCCTTTTCTAACTT|TACTTTG|AGAAGAGCTCAAAGTAAAGAAGGAAGATGAAAAATTATTA ========= Event 177 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCAGGGCGGCCTCCAGCTCA--------GACACCTTGGTGTTGGCCTCCTTAACGGCC ↓ 3 4 2 Chimp: TGCAGGGCGGCCTCCAGCTCACCAAGGTGTCTACCTTGGTGTTGGCCTCCTTAACGGCC Gorilla: TGCACGGCGGCCTCCAGGTCA--------GACACCTTGGTGTTGGCCTCCTTAACGGCC Human: TGCAGGGCGGCCTCCAGCTCA--------GACACCTTGGTGTTGGCCTCCTTAACGGCC Cluster: [ ] Orangutan: TGCAGGGCGGCCTCCAGCTCA--------GACACCTTGGTGTTGGCCTCCTTAACGGCC Human > Chimp ------------- chr10:8769883-8769893 Template switch process: F1: L CCATGTCCTGCTTGACCCGCTGCAGGGCGGCCTCCAGCTCA 1 F3: 4 ACCTTGGTGTTGGCCTCCTTAACGGCCAGCTCCCCACGCT R RF: CCATGTCCTGCTTGACCCGCTGCAGGGCGGCCTCCAGCTCAGACACCTTGGTGTTGGCCTCCTTAACGGCCAGCTCCCCACGCT RR: GGTACAGGACGAACTGGGCGACGTCCCGCCGGAGGTCGAGTCTGTGGAACCACAACCGGAGGAATTGCCGGTCGAGGGGTGCGA F2: 3 TCTGTGGAACC 2 Unidirectional alignment (log-probability: -35.6) CATGTCCTGCTTGACCCGCTGCAGGGCGGCCTCCAGCTC--ACcaaggtgtctACCTTGGTGTTGGCCTCCTTAACGGCCAGCTCCCCACGCT CATGTCCTGCTTGACCCGCTGCAGGGCGGCCTCCAGCTCAGAC----------ACCTTGGTGTTGGCCTCCTTAACGGCCAGCTCCCCACGCT Template switch alignment (log-probability: -16.6) CATGTCCTGCTTGACCCGCTGCAGGGCGGCCTCCAGCTCA|CCAAGGTGTCT|ACCTTGGTGTTGGCCTCCTTAACGGCCAGCTCCCCACGCT CATGTCCTGCTTGACCCGCTGCAGGGCGGCCTCCAGCTCA|CCAAGGTGTCT|ACCTTGGTGTTGGCCTCCTTAACGGCCAGCTCCCCACGCT ========= Event 178 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CCTACTCCAAGGAGGGCCCCAGAGAGGTAGCTCAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGAGACAGGACCCCAACCTCTAATAAGGGCCTTTGGAAATTCTCCATCCATAAAGCtttgttttgctttatagggac Chimp: TGTACTCCAAGGAGGGCCCCAGAG-------------AGGTCTTAGAGAAGGCACTTTCAGGtttttttGGAGACAGAACCCCAACCTCTAATAAGGGCCTTTGGAAATTCTCCATCCATAAAGCtttgttttgctttatagtgac ↓ 4 1 3 2 Gorilla: TGTACTCCAAGGAGGGCCCCAGAGAGGTAGCTCAGAGAGGTCTTAGAGAAGGCACTTTCAGGtttttttGGAGACAGAACCCCAACCTCTAATAAGGGCCTTTGGAAATTCTCCATCCATAAAGCtttgttttgctttatagggac Human: CCTACTCCAAGGAGGGCCCCAGAGAGGTAGCTCAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGAGACAGGACCCCAACCTCTAATAAGGGCCTTTGGAAATTCTCCATCCATAAAGCtttgttttgctttatagggac Cluster: [ ] Orangutan: TGTACTCCAAGGAGGGCCCCAGAGAGGTAGCTCAGAGAGTTCTTAGAGAAGGCACTTTCAGGTTGTTTTGGAGACAGAACCCCAACCTCTAATAAGGGCCTTTGGAAATTCTCCATCCATAAAGCtttgttttgctttatagtgac Chimp > Gorilla --------------- chr10:98544141-98544144 Template switch process: F1: L CCCTCTCCTCAATGGACTGTACTCCAAGGAGGGCCCCAGAGAGGT 1 F3: 4 CAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGAGACAG R RF: CCCTCTCCTCAACGGACTGTACTCCAAGGAGGGCCCCAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGAGACAGAACCCCAACCTCTAATAAGGGCCTTTGGAAATTCTCCATCCATAAAGCT RR: GGGAGAGGAGTTGCCTGACATGAGGTTCCTCCCGGGGTCTCTCCAGAATCTCTTCCGTGAAAGTCCAAAAAAACCTCTGTCTTGGGGTTGGAGATTATTCCCGGAAACCTTTAAGAGGTAGGTATTTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -35.1) TCCTCAAtGGACTGTACTCCAAGGAGGGCCCcagagaggtagctCAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGA TCCTCAACGGACTGTACTCCAAGGAGGGCCC-------------CAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGA Template switch alignment (log-probability: -22) TCCTCAAtGGACTGTACTCCAAGGAGGGCCCCAGAGAGGT|AGCT|CAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGA TCCTCAACGGACTGTACTCCAAGGAGGGCCCCAGAGAGGT|AGCT|CAGAGAGGTCTTAGAGAAGGCACTTTCAGGTTTTTTTGGA ========= Event 179 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GCCTGTATGAGCTTTGCTACTCTATAGTAGCAGGACCTATTCCTGAAGATAGCTTCATGGTAT ↓ 1 3 2 4 Chimp: GCCTGTTTGAGCTTTGCTACTAT--A------------GGTCCTGAAGATAGCTTCATGGTAT Gorilla: GCCTGTATGAGCTTTGCTACTAT--A------------GGTCCTGAAGATAGCTTCATGGTAT ↑ 1 3 2 4 Human: GCCTGTATGAGCTTTGCTACTCTATAGTAGCAGGACCTATTCCTGAAGATAGCTTCATGGTAT Cluster: [ ] Orangutan: GCCTGTATGAGCTTCGCTACTAT--A------------GGTCCTGAAGATGGCTTCATGGTAT Human > Chimp ------------- chr10:84858963-84858969 Template switch process: F1: L CATACTGTCTTTAAATGAAAGCCTGTTTGAGCTTTGCTACT 1 F3: 4 CTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT R RF: CATACTGTCTTTAAATGAAAGCCTGTATGAGCTTTGCTACTCTATAGTAGCAGGACCTATTCCTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT RR: GTATGACAGAAATTTACTTTCGGACATACTCGAAACGATGAGATATCATCGTCCTGGATAAGGACTTCTATCGAAGTACCATATCCAGTGTGAACGTAGA F2: 3 CTGGATA 2 Unidirectional alignment (log-probability: -32.3) ATACTGTCTTTAAATGAAAGCCTGTtTGAGCTTTGCTA-----------------CTATaggTCCTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT ATACTGTCTTTAAATGAAAGCCTGTATGAGCTTTGCTACTCTATAGTAGCAGGACCTAT---TCCTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT Template switch alignment (log-probability: -22.1) ATACTGTCTTTAAATGAAAGCCTGTtTGAGCTTTGCTACT|ATAGGTC|CTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT ATACTGTCTTTAAATGAAAGCCTGTATGAGCTTTGCTACT|ATAGGTC|CTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT Human > Gorilla --------------- chr10:97877794-97877800 Template switch process: F1: L CATACTGTATTTAAATGAAAGCCTGTATGAGCTTTGCTACT 1 F3: 4 CTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT R RF: CATACTGTCTTTAAATGAAAGCCTGTATGAGCTTTGCTACTCTATAGTAGCAGGACCTATTCCTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT RR: GTATGACAGAAATTTACTTTCGGACATACTCGAAACGATGAGATATCATCGTCCTGGATAAGGACTTCTATCGAAGTACCATATCCAGTGTGAACGTAGA F2: 3 CTGGATA 2 Unidirectional alignment (log-probability: -31.4) ATACTGTaTTTAAATGAAAGCCTGTATGAGCTTTGCTA-----------------CTATaggTCCTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT ATACTGTCTTTAAATGAAAGCCTGTATGAGCTTTGCTACTCTATAGTAGCAGGACCTAT---TCCTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT Template switch alignment (log-probability: -22.1) ATACTGTaTTTAAATGAAAGCCTGTATGAGCTTTGCTACT|ATAGGTC|CTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT ATACTGTCTTTAAATGAAAGCCTGTATGAGCTTTGCTACT|ATAGGTC|CTGAAGATAGCTTCATGGTATAGGTCACACTTGCATCT ========= Event 180 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGACAGGAAAGAAATGACATCTT--ACTACTGCACATTTTGTTTTGGAAAGTGTGTATATTGGGAT Chimp: AGACAGGGAAGAAATGACATCTT--ACTACTGCACATTTTGTTTTGGAAATTGTGTATATCGGGAT Gorilla: AGACAGGAAAGAAATGACATCCAAAACAAAATGACATTTTGTTTTGGAAAGTGTGTATATTGGGAT ↑ 1 43 2 Human: AGACAGGAAAGAAATGACATCTT--ACTACTGCACATTTTGTTTTGGAAAGTGTGTATATTGGGAT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr10:93618471-93618482 Template switch process: F1: L AAGGGAATGAAGAATATAGGAGACAGGAAAGAAATGACATC 1 F3: 4 ACATTTTGTTTTGGAAAGTGTGTATATTGGGATGATAATT R RF: AAGGGAATGAAGAATATAGGAGACAGGAAAGAAATGACATCTTACTACTGCACATTTTGTTTTGGAAAGTGTGTATATTGGGATGATAATT RR: TTCCCTTACTTCTTATATCCTCTGTCCTTTCTTTACTGTAGAATGATGACGTGTAAAACAAAACCTTTCACACATATAACCCTACTATTAA F2: 3 GTAAAACAAAAC 2 Unidirectional alignment (log-probability: -36.9) AGGGAATGAAGAATATAGGAGACAGGAAAGAAATGACATC---------CaaaacaaaatgACATTTTGTTTTGGAAAGTGTGTATATTGGGATGATAATT AGGGAATGAAGAATATAGGAGACAGGAAAGAAATGACATCTTACTACTGC-----------ACATTTTGTTTTGGAAAGTGTGTATATTGGGATGATAATT Template switch alignment (log-probability: -17.3) AGGGAATGAAGAATATAGGAGACAGGAAAGAAATGACATC|CAAAACAAAATG|ACATTTTGTTTTGGAAAGTGTGTATATTGGGATGATAATT AGGGAATGAAGAATATAGGAGACAGGAAAGAAATGACATC|CAAAACAAAATG|ACATTTTGTTTTGGAAAGTGTGTATATTGGGATGATAATT ========= Event 181 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: ctctgccatgagaatggcatgt---cccagataa---ggataatggcatgtccttgagtgaggacgacacttaccatct Chimp: CTCTGCCATGAGAATGGCATGACTGCTCACTCAA-GGAGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCATCT ↑ 4 3 2 Gorilla: CTCTGCCATGAGAATGGCATGT---CC-------C--AGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCATCT Human: ctctgccatgagaatggcatgt---cccagataa---ggataatggcatgtccttgagtgaggacgacacttaccatct Cluster: [ ] Orangutan: ctctgccatgagaatggcatgt---cc-------c--agataaggaatgctccttgagtgaggacaacacttaccatct Gorilla > Chimp --------------- chr10:80127377-80127384 Template switch process: F1: L TTCTATCTTTGCTTTTTCTGCTCTGCCATGAGAATGGCATG------------ACTGCTC 1 F3: 4 AGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCAT R RF: TTCTATCTTTGCTTTTTCTGCTCTGCCATGAGAATGGCATGTCCCAGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCAT RR: AAGATAGAAACGAAAAAGACGAGACGGTACTCTTACCGTACAGGGTCTATTCCTGACGAGGAACTCACTCCTGTTGTGAATGGTA F2: 3 GGAACTCA 2 Unidirectional alignment (log-probability: -42) TTGCTTTTTCTGCTCTGCCATGAGAATGGCATGactgcTCaCtcaaggAGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCAT TTGCTTTTTCTGCTCTGCCATGAGAATGGCATG-----TCCC------AGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCAT Template switch alignment (log-probability: -27.3) TTGCTTTTTCTGCTCTGCCATGAGAATGGCATG------------ACTGCTC|ACTCAAGG|AGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCAT TTGCTTTTTCTGCTCTGCCATGAGAATGGCATGTCCCAGATAAGGACTGCTC|ACTCAAGG|AGATAAGGACTGCTCCTTGAGTGAGGACAACACTTACCAT ========= Event 182 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGGAAGATCAATAGGTCCTG---GGTTCAGCTGAGCcggctgagatgacttggcctttctctccacgtggtttccgtccttggttcttcagcgcctgcccagttcaggatggcgtccaagggaaca ↓ 1 4 3 2 Chimp: CTGGAAGATCAATAGGTCCTGGTGAACTCAGCTGAGCcggctgagatgacttggcctttctctccacgtggtttccgtccttggttcttcagcgcctgcccagttcaggatggcgtccaagggaaca ↑ 1 4 3 2 Gorilla: CTGGAAGATCAATAGGTCCTG---GGTTCAGCTGAGCTGgctgagatgacttggcctttctctccacgtggtttccgtccttggttcttcagcacctgcccagttcaggatggcgtccaagggaaca Human: CTGGAAGATCAATAGGTCCTG---GGTTCAGCTGAGCcggctgagatgacttggcctttctctccacgtggtttccgtccttggttcttcagcgcctgcccagttcaggatggcgtccaagggaaca Cluster: [ ] Orangutan: CTGGAAGATCAGTAGGTTCCG---GGTTCAGCTGAGCcggctgagatgacttggcctttctctccacgtggtttccgtccttggttcttcagcgcctgcccagttcaggatggcgtccaagggaaca Human > Chimp ------------- chr10:87061647-87061651 Template switch process: F1: L GCTCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGG 1 F3: 4 TCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCAC R RF: GCTCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGGGTTCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCACGTGGTTTCCGTCCTTGGTTCTTCAGCGCCTGCCCAGTTCA RR: CGAGGACCCTAAAGTAAGTCGACCTTCTAGTTATCCAGGACCCAAGTCGACTCGGCCGACTCTACTGAACCGGAAAGAGAGGTGCACCAAAGGCAGGAACCAAGAAGTCGCGGACGGGTCAAGT F2: 3 CAAGT 2 Unidirectional alignment (log-probability: -27) TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCT-GGTgaacTCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCAC TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGGGT----TCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCAC Template switch alignment (log-probability: -15.9) TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGG|TGAAC|TCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCAC TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGG|TGAAC|TCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCAC Gorilla > Chimp --------------- chr10:87061647-87061651 Template switch process: F1: L GCTCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGG 1 F3: 4 TCAGCTGAGCCGGCTGAGATGACTTGGCCTTTCTCTCCAC R RF: GCTCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGGGTTCAGCTGAGCTGGCTGAGATGACTTGGCCTTTCTCTCCACGTGGTTTCCGTCCTTGGTTCTTCAGCACCTGCCCAGTTCA RR: CGAGGACCCTAAAGTAAGTCGACCTTCTAGTTATCCAGGACCCAAGTCGACTCGACCGACTCTACTGAACCGGAAAGAGAGGTGCACCAAAGGCAGGAACCAAGAAGTCGTGGACGGGTCAAGT F2: 3 CAAGT 2 Unidirectional alignment (log-probability: -31.8) TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGGtgaacTCAGCTGAGCcGGCTGAGATGACTTGGCCTTTCTCTCCAC TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGGGT---TCAGCTGAGCTGGCTGAGATGACTTGGCCTTTCTCTCCAC Template switch alignment (log-probability: -21.9) TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGG|TGAAC|TCAGCTGAGCcGGCTGAGATGACTTGGCCTTTCTCTCCAC TCCTGGGATTTCATTCAGCTGGAAGATCAATAGGTCCTGG|TGAAC|TCAGCTGAGCTGGCTGAGATGACTTGGCCTTTCTCTCCAC ========= Event 183 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCTGAGCCATCACACTGCTGGAACG--------------------------------GGAGGAACATGGCCATAGGT------- Chimp: GGCTGAGCCATCACACTGCTGGAATG--------------------------------GGAGGAACATGGCCATAGGT------- Gorilla: GGCTGAGCCATCACACTGCTGGAACG----------------GGTTCCTCCTGTTCCAGGAGGAACATGGCCATAGGT------- ↑ 3 41 2 Human: GGCTGAGCCATCACACTGCTGGAACG--------------------------------GGAGGAACATGGCCATAGGT------- Cluster: [ ] Orangutan: GGCTGAGCCATCACACTGCT-GAACGGGTNNNNNNNNNNNNN----------------NNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr10:48017274-48017287 Template switch process: F1: L ATAAAGGCTTTGGAGGGCTGAGCCATCACACTGCTGGAACGGG 1 F3: 4 GGAGGAACATGGCCATAGGTGCCCTGGACAGTCCAGCAGT R RF: ATAAAGGCTTTGGAGGGCTGAGCCATCACACTGCTGGAACGGGAGGAACATGGCCATAGGTGCCCTGGACAGTCCAGCAGT RR: TATTTCCGAAACCTCCCGACTCGGTAGTGTGACGACCTTGCCCTCCTTGTACCGGTATCCACGGGACCTGTCAGGTCGTCA F2: 3 ACCTTGTCCTCCTT 2 Unidirectional alignment (log-probability: -33.9) AAGGCTTTGGAGGGCTGAGCCATCACACTGCTGGAACGggttcctcctgttccaGGAGGAACATGGCCATAGGTGCCCTGGACAGTCCAGCAGT AAGGCTTTGGAGGGCTGAGCCATCACACTGCTGGAACG----------------GGAGGAACATGGCCATAGGTGCCCTGGACAGTCCAGCAGT Template switch alignment (log-probability: -23.1) AAGGCTTTGGAGGGCTGAGCCATCACACTGCTGGAACGGG|TTCCTCCtGTTCCA|GGAGGAACATGGCCATAGGTGCCCTGGACAGTCCAGCAGT AAGGCTTTGGAGGGCTGAGCCATCACACTGCTGGAACGGG|TTCCTCCCGTTCCA|GGAGGAACATGGCCATAGGTGCCCTGGACAGTCCAGCAGT ========= Event 184 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCAAGGAGAAGCCAAGAACTGGCCTCACATGGGCTCCT-------------------GACACAAGGCTAGGAAACTGATCTTT Chimp: GCCAAAGAGAAGCCAAGAACTGGCCTCACATGGGCTCCT-------------------GACACAAGGCTAGGAAACTGATCTTT Gorilla: GCCAAGGAGAAGCCAAGAACTGGCCTCACATGGGCTCCTGACACAGTGAGAACAGCCTGACACAAGGCTAGGAAACTGATCTTT ↑ 3 2 4 1 Human: GCCAAGGAGAAGCCAAGAACTGGCCTCACATGGGCTCCT-------------------GACACAAGGCTAGGAAACTGATCTTT Cluster: [ ] Orangutan: GCCAAGGAGAAGCCAAGAACTGGCCTCACATGGGCTCCT-------------------GACACAAGGCTAGGAAACTGACCTTT Human > Gorilla --------------- chr10:46660241-46660250 Template switch process: F1: L CAGCCAAGGAGAAGCCAAGAACTGGCCTCACATGGGCTCCTGACACA 1 F3: 4 CCTGACACAAGGCTAGGAAACTGATCTTTCCTTTTCATGTAAA R RF: CAGCCAAGGAGAAGCCAAGAACTGGCCTCACATGGGCTCCTGACACAAGGCTAGGAAACTGATCTTTCCTTTTCATGTAAA RR: GTCGGTTCCTCTTCGGTTCTTGACCGGAGTGTACCCGAGGACTGTGTTCCGATCCTTTGACTAGAAAGGAAAAGTACATTT F2: 3 GACAAGAGTG 2 Unidirectional alignment (log-probability: -38.2) GGAGAAGCCAAGAACTGGCCTCACATGGGCTCctgacacagtgagaacagcCTGACACAAGGCTAGGAAACTGATCTTTCCTTTTCATGT GGAGAAGCCAAGAACTGGCCTCACATGGGCTC-------------------CTGACACAAGGCTAGGAAACTGATCTTTCCTTTTCATGT Template switch alignment (log-probability: -28.3) GGAGAAGCCAAGAACTGGCCTCACATGGGCTCCTGACACA|GTGAGaaCAG|CCTGACACAAGGCTAGGAAACTGATCTTTCCTTTTCATGT GGAGAAGCCAAGAACTGGCCTCACATGGGCTCCTGACACA|GTGAGGCCAG|CCTGACACAAGGCTAGGAAACTGATCTTTCCTTTTCATGT ========= Event 185 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAAAGAATTGCCATTGGCTTGAG-------TCATCCAATCTTTTAAAGCTTAGATATCTGCA Chimp: aaaaGAATTGCCATTGGCTTGAG-------TCATCCAATCTTTTAAAGCTTAGATATCTGCA ↓ 13 4 2 ↑ 13 2 4 Gorilla: aaaaGAATTGCCATTGGCTTGGATTGGATGACTTCCAATCT-TTAAAGCTTAGATATCGGCA Human: AAAAGAATTGCCATTGGCTTGAG-------TCATCCAATCTTTTAAAGCTTAGATATCTGCA Cluster: [ ] Orangutan: AAAAGAATTGCCATTGGCTTGAG-------TCATCCAATCTTTTAAAGCTTAGATATCTGCA Gorilla > Chimp --------------- chr10:47027548-47027559 Template switch process: F1: L ACACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG 1 F3: 4 TTTTAAAGCTTAGATATCTGCATTAAATGTCTGTCTTTTCAT R RF: ACACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTGGATTGGATGACTTCCAATCTTTAAAGCTTAGATATCGGCATTAAATGTCTGTCTTTTCAT RR: TGTGTTGACATTTAGTCTTTTTTTCTTAACGGTAACCGAACCTAACCTACTGAAGGTTAGAAATTTCGAATCTATAGCCGTAATTTACAGACAGAAAAGTA F2: 3 CTAACCTACTGA 2 Unidirectional alignment (log-probability: -44.7) CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG-------aGtCaTCCAATCtTTTAAAGCTTAGATATCtGCATTAAATGTCTGTCTTTTC CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTGGATTGGATGACTTCCAATC-TTTAAAGCTTAGATATCGGCATTAAATGTCTGTCTTTTC Template switch alignment (log-probability: -28.3) CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG|AGTCATCCAATC|tTTTAAAGCTTAGATATCtGCATTAAATGTCTGTCTTTTC CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG|AGTCATCCAATC|CTTTAAAGCTTAGATATCGGCATTAAATGTCTGTCTTTTC Chimp > Gorilla --------------- chr10:46668973-46668984 Template switch process: F1: L ACACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG 1 F3: 4 TCCAATC-TTTAAAGCTTAGATATCGGCATTAAATGTCTGTCTTTTCAT R RF: ACACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTGAGTCATCCAATCTTTTAAAGCTTAGATATCTGCATTAAATGTCTGTCTTTTCAT RR: TGTGTTGACATTTAGTCTTTTTTTCTTAACGGTAACCGAACTCAGTAGGTTAGAAAATTTCGAATCTATAGACGTAATTTACAGACAGAAAAGTA F2: 3 TCAGTAGGTTAG 2 Unidirectional alignment (log-probability: -53) CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTGgattggatGaCtTCCAATC-TTTAAAGCTTAGATATCgGCATTAAATGTCTGT CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG-------AGTCATCCAATCTTTTAAAGCTTAGATATCTGCATTAAATGTCTGT Template switch alignment (log-probability: -32.8) CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG|GATTGGATGACT|TCCAATC-TTTAAAGCTTAGATATCgGCATTAAATGTCTGT CACAACTGTAAATCAGAAAAAAAGAATTGCCATTGGCTTG|GATTGGATGACT|TCCAATCTTTTAAAGCTTAGATATCTGCATTAAATGTCTGT ========= Event 186 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAAAGACAGTGGAGCCCTCA-----CATTGTCTTTGCCTGTGCACAGCAGATAC ↓ 13 4 2 Chimp: TGAAAGACAGTGGAGCCCTCAAAGACAATGGTCTTTGCCTGTGCACAGCAGATAC ↑ 13 4 2 Gorilla: TGAAGGACAGTGGAGCCCTCA-----CATTGTCTTTGCCTGTGCACAGCAGATAC Human: TGAAAGACAGTGGAGCCCTCA-----CATTGTCTTTGCCTGTGCACAGCAGATAC Cluster: [ ] Orangutan: TGAAAGACAGTGGGGCCCTCA-----CATTGGCTTTGCCTGTGCACAGCAGATAC Human > Chimp ------------- chr10:90237113-90237121 Template switch process: F1: L CTTTCTTG--GAGAGAAATCTGAAAGACAGTGGAGCCCTCA 1 F3: 4 GTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG R RF: CTTTCTTGGAGAGAGAAATCTGAAAGACAGTGGAGCCCTCACATTGTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG RR: GAAAGAACCTCTCTCTTTAGACTTTCTGTCACCTCGGGAGTGTAACAGAAACGGACACGTGTCGTCTATGACGGTTAAAACCCAC F2: 3 GTAACAGAA 2 Unidirectional alignment (log-probability: -40.4) CTTTCTTG--GAGAGAAATCTGAAAGACAGTGGAGCCCTCAaagacaATgGTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG CTTTCTTGGAGAGAGAAATCTGAAAGACAGTGGAGCCCTCAC-----ATTGTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG Template switch alignment (log-probability: -26.7) CTTTCTTG--GAGAGAAATCTGAAAGACAGTGGAGCCCTCA|AAGACAATG|GTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG CTTTCTTGGAGAGAGAAATCTGAAAGACAGTGGAGCCCTCA|AAGACAATG|GTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG Gorilla > Chimp --------------- chr10:90237113-90237121 Template switch process: F1: L TGCTTTCTTGGAGAGAAATCTGAAAGACAGTGGAGCCCTCA 1 F3: 4 GTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG R RF: TGCTTTCTTGGAGAGAAATCTGAAGGACAGTGGAGCCCTCACATTGTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG RR: ACGAAAGAACCTCTCTTTAGACTTCCTGTCACCTCGGGAGTGTAACAGAAACGGACACGTGTCGTCTATGACGGTTAAAACCCAC F2: 3 GTAACAGAA 2 Unidirectional alignment (log-probability: -34.7) GCTTTCTTGGAGAGAAATCTGAAaGACAGTGGAGCCCTCAaagacaATgGTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG GCTTTCTTGGAGAGAAATCTGAAGGACAGTGGAGCCCTCAC-----ATTGTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG Template switch alignment (log-probability: -22.4) GCTTTCTTGGAGAGAAATCTGAAaGACAGTGGAGCCCTCA|AAGACAATG|GTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG GCTTTCTTGGAGAGAAATCTGAAGGACAGTGGAGCCCTCA|AAGACAATG|GTCTTTGCCTGTGCACAGCAGATACTGCCAATTTTGGGTG ========= Event 187 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTCCTTTGTGTCTGGCACTAAT---------------------------ATGTAATATGTATCTGTTAAAAGAATGAT ↓ 3 4 2 1 Chimp: CTGTCCTTTGTGTCTGGCACTAAT-------ATGTAATATTACATATTAGTTTGTAATATGTATCTGTTAAAAGAATGAT Gorilla: CTGTCCTTTGTGTCTGGCACTA--AGTTAGT--------------------TTGTAATATGTATCTGTTAAAAGAATGAT Human: CTGTCCTTTGTGTCTGGCACTAAT---------------------------ATGTAATATGTATCTGTTAAAAGAATGAT Cluster: [ ] Orangutan: CTGTCCTTTGTGTCTGGCACTA--AGTTAGT--------------------TTGTAATATGTATCTGTTAAAAGAATGAT Human > Chimp ------------- chr10:45568250-45568259 Template switch process: F1: L GACTGATGCTCATTTTTCTGTCCTTTGTGTCTGGCACTAATATGTAATAT 1 F3: 4 TTTGTAATATGTATCTGTTAAAAGAATGATTGAGTTGGCTCT R RF: GACTGATGCTCATTTTTCTGTCCTTTGTGTCTGGCACTAATATGTAATATGTATCTGTTAAAAGAATGATTGAGTTAGCTCT RR: CTGACTACGAGTAAAAAGACAGGAAACACAGACCGTGATTATACATTATACATAGACAATTTTCTTACTAACTCAATCGAGA F2: 3 GATTATACAT 2 Unidirectional alignment (log-probability: -45.7) CATTTTTCTGTCCTTTGTGTCTGGCACTAATATGTAATATtacatattagtttgtaatatGTATCTGTTAAAAGAATGATTGAGTTgGCT CATTTTTCTGTCCTTTGTGTCTGGCACTAATATGTAATAT--------------------GTATCTGTTAAAAGAATGATTGAGTTAGCT Template switch alignment (log-probability: -28.7) CATTTTTCTGTCCTTTGTGTCTGGCACTAATATGTAATAT|TACATATTAG|TtTGTAATATGTATCTGTTAAAAGAATGATTGAGTTgGCT CATTTTTCTGTCCTTTGTGTCTGGCACTAATATGTAATAT|TACATATTAG|TATGTAATATGTATCTGTTAAAAGAATGATTGAGTTAGCT ========= Event 188 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTAAGCATATTTGAAAATACTTGCATTTGGAAGAGCAAATGCAAGTACACAGATTTTTGTTGTTCCGT ↑ 3 2 1 4 Chimp: TCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTA-----CCACAGATTTTTGTTGTTCCGT Gorilla: TCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTA-----CCACAGATTTTTGTTGTTCCGT ↓ 3 2 1 4 Human: TCCTAAGCATATTTGAAAATACTTGCATTTGGAAGAGCAAATGCAAGTACACAGATTTTTGTTGTTCCGT Cluster: [ ] Orangutan: TCCCAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTA-----CCATAGATTTTTGTTGTTCCGT Chimp > Human ------------- chr10:43617897-43617905 Template switch process: F1: L GTAACTTTCTTCCTAAGCATATTTGAAAATACTTGCATTTGGAAGAGCAA 1 F3: 4 CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA R RF: GTAACTTTCTTCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTACCACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA RR: CATTGAAAGAAGGATTCGTATAAACTTTTATGAACGTAAACATTCTCGTTGATGGTGTCTAAAAACAACAAGGCACACATCATTCATGTAAAGT F2: 3 ATGAACGTA 2 Unidirectional alignment (log-probability: -36.2) TCCTAAGCATATTTGAAAATACTTGCATTTGgAAGAGCAAaTgCaagtaCACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA TCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTAC-----CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA Template switch alignment (log-probability: -22.6) TCCTAAGCATATTTGAAAATACTTGCATTTGgAAGAGCAA|ATGCAAGTA|CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA TCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAA|ATGCAAGTA|CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA Gorilla > Human --------------- chr10:43617897-43617905 Template switch process: F1: L GTAACTTTCTTCCTAAGCATATTTGAAAATACTTGCATTTGGAAGAGCAA 1 F3: 4 CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA R RF: GTAACTTTCTTCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTACCACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA RR: CATTGAAAGAAGGATTCGTATAAACTTTTATGAACGTAAACATTCTCGTTGATGGTGTCTAAAAACAACAAGGCACACATCATTCATGTAAAGT F2: 3 ATGAACGTA 2 Unidirectional alignment (log-probability: -34.8) TCCTAAGCATATTTGAAAATACTTGCATTTGgAAGAGCAAaTgCaagtaCACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA TCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAACTAC-----CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA Template switch alignment (log-probability: -22.6) TCCTAAGCATATTTGAAAATACTTGCATTTGgAAGAGCAA|ATGCAAGTA|CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA TCCTAAGCATATTTGAAAATACTTGCATTTGTAAGAGCAA|ATGCAAGTA|CACAGATTTTTGTTGTTCCGTGTGTAGTAAGTACATTTCA ========= Event 189 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTGAATCATGGCGTCCATGGGTTA----CGGACAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAG Chimp: ACTGAATCATGGCGTCCATGGGTTA----CGGACAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAG ↓ 1 4 3 2 Gorilla: ACTGAATCATGGCGTCCATGGAGTC--------CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAG ↑ 1 4 3 2 Human: ACTGAATCATGGCGTCCATGGGTTA----CGGACAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAG Cluster: [ ] Orangutan: ACTGAATCATGGCGTCCATGGGTTACGGA----CA-GAAAGATCCAGGACTCCCTGTGAAGTGTGACGAAG Human > Gorilla --------------- chr10:44440149-44440152 Template switch process: F1: L AAGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGG 1 F3: 4 CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA R RF: AAGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGGGTTACGGACAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA RR: TTCGGGGCCTGGAGGCGGTATGACTTAGTACCGCAGGTACCCAATGCCTGTCCTTTCTAGGTCCTGAGGGACACTTCACACTACTTCGT F2: 3 CTGA 2 Unidirectional alignment (log-probability: -25.3) AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCAT-------GGAgtcCAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGGGTTACGGA---CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA Template switch alignment (log-probability: -16.2) AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGG|AGTC|CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGG|AGTC|CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA Chimp > Gorilla --------------- chr10:44440149-44440152 Template switch process: F1: L AAGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGG 1 F3: 4 CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA R RF: AAGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGGGTTACGGACAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA RR: TTCGGGGCCTGGAGGCGGTATGACTTAGTACCGCAGGTACCCAATGCCTGTCCTTTCTAGGTCCTGAGGGACACTTCACACTACTTCGT F2: 3 CTGA 2 Unidirectional alignment (log-probability: -25.3) AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCAT-------GGAgtcCAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGGGTTACGGA---CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA Template switch alignment (log-probability: -16.2) AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGG|AGTC|CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA AGCCCCGGACCTCCGCCATACTGAATCATGGCGTCCATGG|AGTC|CAGGAAAGATCCAGGACTCCCTGTGAAGTGTGATGAAGCA ========= Event 190 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAACAATGGAAATAATAAAAAATATTTAGA ↑ 3 2 1 4 Chimp: ATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAAA--AGTAAATAATAAAAAATATTTAGA Gorilla: ATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAAA--AGTAAATAATAAAAAATATTTAGA Human: ATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAACAATGGAAATAATAAAAAATATTTAGA Cluster: [ ] Orangutan: ATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTGAA--AGTAAATAATAAAAAATATTTAGA Chimp > Human ------------- chr10:8866141-8866146 Template switch process: F1: L ACCATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAA 1 F3: 4 AAATAATAAAAAATATTTAGAAATATGTTCAAGCACAGGG R RF: ACCATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAAAAGTAAATAATAAAAAATATTTAGAAATATGTTCAAGCACAGGG RR: TGGTAAATAAAAGATTACATCAGGTAACAAAGGATAACATTTTCATTTATTATTTTTTATAAATCTTTATACAAGTTCGTGTCCC F2: 3 GGTAAC 2 Unidirectional alignment (log-probability: -25.8) CCATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAacAAtGgAAATAATAAAAAATATTTAGAAATATGTTCAAGCACAGGG CCATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTA--AAAGTAAATAATAAAAAATATTTAGAAATATGTTCAAGCACAGGG Template switch alignment (log-probability: -16) CCATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAA|CAATGG|AAATAATAAAAAATATTTAGAAATATGTTCAAGCACAGGG CCATTTATTTTCTAATGTAGTCCATTGTTTCCTATTGTAA|CAATGG|AAATAATAAAAAATATTTAGAAATATGTTCAAGCACAGGG ========= Event 191 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTTC-TTCATGGGTTCACCTTAGGGCCCTATTTATATCATT ↑ 3 2 1 4 Chimp: TTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTCCCAGCCCTGCTTCACCTTAGGGCCCTATTTATATCATT Gorilla: TTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTCCCAGCCCTGCTCCACCTCAGGGCCCTATTTATATCATT ↓ 3 2 1 4 Human: TTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTTC-TTCATGGGTTCACCTTAGGGCCCTATTTATATCATT Cluster: [ ] Orangutan: TTTAGTTCACCAGAGAGGAAACTCATGATGACTCCTCCCAGCCCTGCTTCACCTCAGGGCCCTATTTATATCATT Chimp > Human ------------- chr10:92085980-92085989 Template switch process: F1: L GGGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT 1 F3: 4 TTCACCTTAGGGCCCTATTTATATCATTTAATTATAATAC R RF: GGGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTCCCAGCCCTGCTTCACCTTAGGGCCCTATTTATATCATTTAATTATAATAC RR: CCCAGAAATCAAGTGGTCTCTCCTTTGGGTACTACTGAGGAGGGTCGGGACGAAGTGGAATCCCGGGATAAATATAGTAAATTAATATTATG F2: 3 GGGTACTTCT 2 Unidirectional alignment (log-probability: -36.1) GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT-----------tcttcatgggTTCACCTTAGGGCCCTATTTATATCATTTAATTATAATAC GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTCCCAGCCCTGC----------TTCACCTTAGGGCCCTATTTATATCATTTAATTATAATAC Template switch alignment (log-probability: -22.5) GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT|TCtTCATGGG|TTCACCTTAGGGCCCTATTTATATCATTTAATTATAATAC GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT|TCATCATGGG|TTCACCTTAGGGCCCTATTTATATCATTTAATTATAATAC Gorilla > Human --------------- chr10:92085980-92085991 Template switch process: F1: L GGGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT 1 F3: 4 CACCTTAGGGCCCTATTTATATCATTTAATTATAATACATTTCAAA R RF: GGGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTCCCAGCCCTGCTCCACCTCAGGGCCCTATTTATATCATTTAATTATAATACATTTCAAA RR: CCCAGAAATCAAGTGGTCTCTCCTTTGGGTACTACTGAGGAGGGTCGGGACGAGGTGGAGTCCCGGGATAAATATAGTAAATTAATATTATGTAAAGTTT F2: 3 TTGGGTACTTCT 2 Unidirectional alignment (log-probability: -41.2) GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT-----------TCttcatgggttCACCTtAGGGCCCTATTTATATCATTTAATTATAATACAT GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCTCCCAGCCCTGCTC----------CACCTCAGGGCCCTATTTATATCATTTAATTATAATACAT Template switch alignment (log-probability: -28.4) GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT|TCtTCATGGGTT|CACCTtAGGGCCCTATTTATATCATTTAATTATAATACAT GGTCTTTAGTTCACCAGAGAGGAAACCCATGATGACTCCT|TCATCATGGGTT|CACCTCAGGGCCCTATTTATATCATTTAATTATAATACAT ========= Event 192 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGCCACTATGGTATCACTGTTACCTTTGCAGGTAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTC ↑ 41 3 2 Chimp: TGGCCACTATGGTATCACTGT------------TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTC Gorilla: TGGCCACTATGGTATCACTGT------------TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTC ↓ 41 3 2 Human: TGGCCACTATGGTATCACTGTTACCTTTGCAGGTAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTC Cluster: [ ] Orangutan: TGGCCACTATGGTATCACTG-------------TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTC Chimp > Human ------------- chr10:93439184-93439193 Template switch process: F1: L CCCTCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTA 1 F3: 4 TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC R RF: CCCTCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC RR: GGGAGGGTGGAGACGTTGAGACCGGTGATACCATAGTGACAATTGTGGACGTTTCCCGACTCACCTTCGGGTCCAGAGGAG F2: 3 GGACGTTTCC 2 Unidirectional alignment (log-probability: -28.2) TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTtacctttgcaggTAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGT------------TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC Template switch alignment (log-probability: -16.6) TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTA|CCTTTGCAGG|TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTA|CCTTTGCAGG|TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC Gorilla > Human --------------- chr10:93439184-93439193 Template switch process: F1: L CCCTCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTA 1 F3: 4 TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC R RF: CCCTCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC RR: GGGAGGGTGGAGACGTTGAGACCGGTGATACCATAGTGACAATTGTGGACGTTTCCCGACTCACCTTCGGGTCCAGAGGAG F2: 3 GGACGTTTCC 2 Unidirectional alignment (log-probability: -28.1) TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTtacctttgcaggTAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGT------------TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC Template switch alignment (log-probability: -17.1) TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTA|CCTTTGCAGG|TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC TCCCACCTCTGCAACTCTGGCCACTATGGTATCACTGTTA|CCTTTGCAGG|TAACACCTGCAAAGGGCTGAGTGGAAGCCCAGGTCTCCTC ========= Event 193 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: aaaCCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGG----TTTTGAGTGTGTGGAGCATTTTT Chimp: aaaCCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGG----TTTTGAGTGTGTGGAGCATTTTT ↓ 3 2 1 4 Gorilla: aaaCCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGTGTGTCTACACTCTGAGTGTGTGGAGCATTTTT ↑ 3 2 1 4 Human: aaaCCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGG----TTTTGAGTGTGTGGAGCATTTTT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr10:106787389-106787399 Template switch process: F1: L AGAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG 1 F3: 4 TCTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTATCT R RF: AGAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGGTTTTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTATCT RR: TCTTTGGTATTTAACCTCAACCACATCTGTATTTCGGTCTCTTACCCAAAACTCACACACCTCGTAAAAAGTGACTCTTCACGAAATAGA F2: 3 CACATCTGTGT 2 Unidirectional alignment (log-probability: -38.3) GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG--------TgtgtctacactcTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGGTTT------------TGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT Template switch alignment (log-probability: -28.2) GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG|TgTGTCTACAC|TcTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG|TATGTCTACAC|TTTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT Chimp > Gorilla --------------- chr10:106787389-106787399 Template switch process: F1: L AGAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG 1 F3: 4 TCTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTATCT R RF: AGAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGGTTTTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTATCT RR: TCTTTGGTATTTAACCTCAACCACATCTGTATTTCGGTCTCTTACCCAAAACTCACACACCTCGTAAAAAGTGACTCTTCACGAAATAGA F2: 3 CACATCTGTGT 2 Unidirectional alignment (log-probability: -38.3) GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG--------TgtgtctacactcTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAGAATGGGTTT------------TGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT Template switch alignment (log-probability: -28.2) GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG|TgTGTCTACAC|TcTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT GAAACCATAAATTGGAGTTGGTGTAGACATAAAGCCAGAG|TATGTCTACAC|TTTGAGTGTGTGGAGCATTTTTCACTGAGAAGTGCTTTAT ========= Event 194 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tccag-ctgggccacagagtgaaactctgtctcaaaaa---aaaaaaTTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTT----TGTTTGTTTGTTGAGAC---------GGAGACTCAtgggattacagg Chimp: tccag-ctgggccacagagtgaaactctgtctcaaaaa---aaaaaaTTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTT----TGTTTGTTTGTTGAGAC---------GGAGTCTCAtgggattacagg ↓ 3 2 1 4 Gorilla: tccag-ctgggccacagagtgaaactctgtctcaaaaa--aaaaaaaTTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTT--------TGTTTGTTGAGACAGAGTCTCAGGAGTCTCATGGGATTACAGG ↑ 3 2 1 4 Human: tccag-ctgggccacagagtgaaactctgtctcaaaaa---aaaaaaTTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTT----TGTTTGTTTGTTGAGAC---------GGAGACTCAtgggattacagg Cluster: [ ] Orangutan: tccagcctgggccacagagtgagactctgcctcaaaaaag-aaaaaaTTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTATTTGTT----TGTTTGTTGAGACAGAGTCTCAGGAGTCTCAtgggattacagg Human > Gorilla --------------- chr10:36784672-36784685 Template switch process: F1: L TTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTT 1 F3: 4 GGAGTCTCATGGGATTAC R RF: TGAAACTCTGTCTCAAAAAAAAAAATTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTTTGTTGAGACGGAGACTCATGGGATTAC RR: ACTTTGAGACAGAGTTTTTTTTTTTAACGACTTTTCATAGGGTAACAGACGTCTATGTGTGAACAAACAAACAAACAACTCTGCCTCTGAGTACCCTAATG F2: 3 ACTCTGAGACAGAG 2 Unidirectional alignment (log-probability: -39.2) AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGT----TGAGACagagtctcaGGAGtCTCATGGGATTAC AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTTTGTTGAGAC---------GGAGACTCATGGGATTAC Template switch alignment (log-probability: -28.2) AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTT|GAGACAGAGTcTCA|GGAGtCTCATGGGATTAC AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTT|GAGACAGAGTTTCA|GGAGACTCATGGGATTAC Chimp > Gorilla --------------- chr10:36784672-36784685 Template switch process: F1: L TTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTT 1 F3: 4 GGAGTCTCATGGGATTAC R RF: TGAAACTCTGTCTCAAAAAAAAAAATTGCTGAAAAGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTTTGTTGAGACGGAGTCTCATGGGATTAC RR: ACTTTGAGACAGAGTTTTTTTTTTTAACGACTTTTCATAGGGTAACAGACGTCTATGTGTGAACAAACAAACAAACAACTCTGCCTCAGAGTACCCTAATG F2: 3 ACTCTGAGACAGAG 2 Unidirectional alignment (log-probability: -33.6) AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGT----TGAGACagagtctcaGGAGTCTCATGGGATTAC AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTTTGTTGAGAC---------GGAGTCTCATGGGATTAC Template switch alignment (log-probability: -22.7) AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTT|GAGACAGAGTcTCA|GGAGTCTCATGGGATTAC AGTATCCCATTGTCTGCAGATACACACTTGTTTGTTTGTT|GAGACAGAGTTTCA|GGAGTCTCATGGGATTAC ========= Event 195 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAATTATGGAACTCATTTTTCCAAGACTGCTATTCAGTCTTGGAATGTATGACAAAAGCTGGAAA ↑ 3 2 1 4 Chimp: AAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG---GGTGATGTATGACAAAAGCTGGAAA Gorilla: AAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG---GGTGATGTATGACAAAAGCTGGAAA ↓ 3 2 1 4 Human: AAATTATGGAACTCATTTTTCCAAGACTGCTATTCAGTCTTGGAATGTATGACAAAAGCTGGAAA Cluster: [ ] Orangutan: AAATTATGGAACTCATTTTTCCCAGACTGCTATTTAG---GGTGATGTATGACAAAAGCGGGAAA Chimp > Human ------------- chr10:33908400-33908406 Template switch process: F1: L TTTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG 1 F3: 4 ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT R RF: TTTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAGGGTGATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT RR: AAAGTTTAATACCTTGAGTAAAAAGGTTCTGACGATAAGTCCCACTACATACTGTTTTCGACCTTTCAAGACAGACAAGACTGAA F2: 3 AGGTTCT 2 Unidirectional alignment (log-probability: -31.4) TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAGtcttgga----ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG-------GGTGATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT Template switch alignment (log-probability: -16.2) TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG|TCTTGGA|ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG|TCTTGGA|ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT Gorilla > Human --------------- chr10:33908400-33908406 Template switch process: F1: L TTTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG 1 F3: 4 ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT R RF: TTTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAGGGTGATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT RR: AAAGTTTAATACCTTGAGTAAAAAGGTTCTGACGATAAGTCCCACTACATACTGTTTTCGACCTTTCAAGACAGACAAGACTGAA F2: 3 AGGTTCT 2 Unidirectional alignment (log-probability: -30.9) TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCA----GtcttggaATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAGGGTG-------ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT Template switch alignment (log-probability: -16.6) TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG|TCTTGGA|ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT TTCAAATTATGGAACTCATTTTTCCAAGACTGCTATTCAG|TCTTGGA|ATGTATGACAAAAGCTGGAAAGTTCTGTCTGTTCTGACTT ========= Event 196 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATCTGTGTAATTAAGTATTTATATATCTTAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATTTGCTGGGGCAATTCAATAGAAATAAATAATAAGCATTAC Chimp: TATCTGTGTAATTAAGTATTTATATAGCTCAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATTTGCTGGGGCAATTCAATAGAAATAAATAACAAGCATTAC ↓ 1 3 4 2 Gorilla: TATCTGTGTAATTAAGTATTTCTA------------TTGAATTGCCCCAGCAAATGTAAACACTATTACCTCTGCTGGGGCAATTCAATATAAATAAATAACAAGCATTAC ↑ 1 3 4 2 Human: TATCTGTGTAATTAAGTATTTATATATCTTAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATTTGCTGGGGCAATTCAATAGAAATAAATAATAAGCATTAC Cluster: [ ] Orangutan: Human > Gorilla --------------- chr1:106562032-106562070 Template switch process: F1: L TAATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTT 1 F3: 4 TGCTGGGGCAATTCAATATAAATAAATAACAAGCATTACC R RF: TAATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTTATATATCTTAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATTTGCTGGGGCAATTCAATAGAAATAAATAATAAGCATTACC RR: ATTAGGAAATATATTCCGTCATAGACACATTAATTCATAAATATATAGAATTCTCTAAATTTTCTTTATCGTCTCCATTATCACAAATGTAAACGACCCCGTTAAGTTATCTTTATTTATTATTCGTAATGG F2: 3 CTCCATTATCACAAATGTAAACGACCCCGTTAAGTTATC 2 Unidirectional alignment (log-probability: -88.5) AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTTcT----------------------------------------------ATTgaattgccccagcaaatgtaaacactattacctcTGCTGGGGCAATTCAATAtAAATAAATAAcAAGCATTACC AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTTATATATCTTAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATT----------------------------------TGCTGGGGCAATTCAATAGAAATAAATAATAAGCATTACC Template switch alignment (log-probability: -31.7) AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTT|CTATTGAATTGCCCCAGCAAATGTAAACACTATTACCTC|TGCTGGGGCAATTCAATAtAAATAAATAAcAAGCATTACC AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTT|CTATTGAATTGCCCCAGCAAATGTAAACACTATTACCTC|TGCTGGGGCAATTCAATAGAAATAAATAATAAGCATTACC Chimp > Gorilla --------------- chr1:106562032-106562070 Template switch process: F1: L TAATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTT 1 F3: 4 TGCTGGGGCAATTCAATATAAATAAATAACAAGCATTACC R RF: TAATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTTATATAGCTCAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATTTGCTGGGGCAATTCAATAGAAATAAATAACAAGCATTACC RR: ATTAGGAAATATATTCCGTCATAGACACATTAATTCATAAATATATCGAGTTCTCTAAATTTTCTTTATCGTCTCCATTATCACAAATGTAAACGACCCCGTTAAGTTATCTTTATTTATTGTTCGTAATGG F2: 3 CTCCATTATCACAAATGTAAACGACCCCGTTAAGTTATC 2 Unidirectional alignment (log-probability: -82.6) AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTTcTAttgaattgccccagcaaatgtaaacactatTAcCTC------------------------------------------TGCTGGGGCAATTCAATAtAAATAAATAACAAGCATTACC AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTTATA------------------------------TAGCTCAAGAGATTTAAAAGAAATAGCAGAGGTAATAGTGTTTACATTTGCTGGGGCAATTCAATAGAAATAAATAACAAGCATTACC Template switch alignment (log-probability: -26.2) AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTT|CTATTGAATTGCCCCAGCAAATGTAAACACTATTACCTC|TGCTGGGGCAATTCAATAtAAATAAATAACAAGCATTACC AATCCTTTATATAAGGCAGTATCTGTGTAATTAAGTATTT|CTATTGAATTGCCCCAGCAAATGTAAACACTATTACCTC|TGCTGGGGCAATTCAATAGAAATAAATAACAAGCATTACC ========= Event 197 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TAGCTAAAACAGTTTCATGAA----------------------GTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGACTATATAGAGATTATCATTTTACCC ↓ 4 1 3 2 Chimp: TAGCTAAAACAGTTTCATGAA-----------GTTTATAGTCAGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGACTATATAGAGATTATCATTTTACCC Gorilla: TAGCTAAAACAGTTTCATGAAGTTTATAGTCA-----------GTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGACTATATAGAGATTATCATTCTACCC ↑ 4 1 3 2 Human: TAGCTAAAACAGTTTCATGAA----------------------GTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGACTATATAGAGATTATCATTTTACCC Cluster: [ ] Orangutan: TAGCTAAAACAATTTCATGAAATTTGTAGTCA-----------GTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGTCTGTATAGAGATTATCATTTTACCC Human > Chimp ------------- chr1:106811232-106811238 Template switch process: F1: L TTATCACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTT 1 F3: 4 AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCA R RF: TTATCACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGACTATA RR: AATAGTGGAAGATCTTCCTTATCGATTTTGTCAAAGTACTTCAATATTTACTAAGTACAAAGGGATTCATTGAGTTTAGGTTTTCTATCTGATAT F2: 3 CTGATAT 2 Unidirectional alignment (log-probability: -26.7) CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAagtttatagtcAGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGA-----------AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC Template switch alignment (log-probability: -16.2) CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTT|TATAGTC|AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTT|TATAGTC|AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC Human > Gorilla --------------- chr1:107599152-107599158 Template switch process: F1: L TTATCACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTT 1 F3: 4 AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCA R RF: TTATCACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCCAAAAGATAGACTATA RR: AATAGTGGAAGATCTTCCTTATCGATTTTGTCAAAGTACTTCAATATTTACTAAGTACAAAGGGATTCATTGAGTTTAGGTTTTCTATCTGATAT F2: 3 CTGATAT 2 Unidirectional alignment (log-probability: -26.7) CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAagtttatagtcAGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGA-----------AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC Template switch alignment (log-probability: -16.7) CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTT|TATAGTC|AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC CACCTTCTAGAAGGAATAGCTAAAACAGTTTCATGAAGTT|TATAGTC|AGTTATAAATGATTCATGTTTCCCTAAGTAACTCAAATCC ========= Event 198 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGTTAAATGTCAACATTGGaaaaaaaaaaaGGTCTGTTTT Chimp: AGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGCTAAATGTCAACATTGGAA--ATAAAAAGGTCTGTTTT Gorilla: AGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGCTAAA---TAACATTGGaa--aaaaaaaGGTCTGTTTT ↓ 3 2 1 4 Human: AGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGTTAAATGTCAACATTGGaaaaaaaaaaaGGTCTGTTTT Cluster: [ ] Orangutan: AGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGCTAC------------aaa--aaaaaaaGCTCTGTTTT Gorilla > Human --------------- chr1:105980564-105980576 Template switch process: F1: L TTATAGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGTTAAAT 1 F3: 4 AAAAAAAAAGGTCTGTTTTTAGAAATAAAA R RF: TTATAGGTAAAACCCTACACTTCTTCCAATGTTGACATTAGCTAAATAACATTGGAAAAAAAAAGGTCTGTTTTTAGAAATAAAA RR: AATATCCATTTTGGGATGTGAAGAAGGTTACAACTGTAATCGATTTATTGTAACCTTTTTTTTTCCAGACAAAAATCTTTATTTT F2: 3 AAGGTTACAACTG 2 Unidirectional alignment (log-probability: -33.4) TAAAACCCTACACTTCTTCCAATGTTGACATTAGtTAAATgtcAACATTGGaaAAAAAAAAAGGTCTGTTTTTAGAAATAAAA TAAAACCCTACACTTCTTCCAATGTTGACATTAGCTAAAT---AACATTGG--AAAAAAAAAGGTCTGTTTTTAGAAATAAAA Template switch alignment (log-probability: -22.8) TAAAACCCTACACTTCTTCCAATGTTGACATTAGtTAAAT|GTCAACATTGGAA|AAAAAAAAAGGTCTGTTTTTAGAAATAAAA TAAAACCCTACACTTCTTCCAATGTTGACATTAGCTAAAT|GTCAACATTGGAA|AAAAAAAAAGGTCTGTTTTTAGAAATAAAA ========= Event 199 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ACATGTAATCCATTTATACTG-TAAGGAC----------------------------------TTGACAAAATGTTACTGCTTTTATATTC ↓ 3 4 2 1 Chimp: ACATGTAATCCATTTATACTG-TAAGGAT-----------------TTGACAAAGTCAAGTCCTTGACAAAATGTTACTGCTTTTATATTC Gorilla: ACATGTAATCCATTTATACTGTTAAGGACTTGACAAAGTCAAGTCC-----------------TTGACAAAATGTTACTGCTTTTATATTC ↑ 3 4 2 1 Human: ACATGTAATCCATTTATACTG-TAAGGAC----------------------------------TTGACAAAATGTTACTGCTTTTATATTC Cluster: [ ] Orangutan: ACATGTAATCCATTTATAGTG-TAAGGACTTGACAAAGTCAAGTCC-----------------CTGACAAAATATTACTGCTTTTATATTC Human > Chimp ------------- chr1:103767071-103767078 Template switch process: F1: L ACCAAATCAGATATACATGTAATCCATTTATACTGTAAGGATTTGACAAA 1 F3: 4 CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTAG R RF: ACCAAATCAGATATACATGTAATCCATTTATACTGTAAGGACTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTAG RR: TGGTTTAGTCTATATGTACATTAGGTAAATATGACATTCCTGAACTGTTTTACAATGACGAAAATATAAGTCTAAAAAAATC F2: 3 CTGAACTG 2 Unidirectional alignment (log-probability: -35.4) ATATACATGTAATCCATTTATACTGTAAGGAtttgacaaagtcaagtcCTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA ATATACATGTAATCCATTTATACTGTAAGGA-----------------CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA Template switch alignment (log-probability: -22.5) ATATACATGTAATCCATTTATACTGTAAGGAtTTGACAAA|GTCAAGTC|CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA ATATACATGTAATCCATTTATACTGTAAGGACTTGACAAA|GTCAAGTC|CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA Human > Gorilla --------------- chr1:104390339-104390346 Template switch process: F1: L ATTATTACCAAATCAGATATACATGTAATCCATTTATACTGTTAAGGACTTGACAAA 1 F3: 4 CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTAG R RF: ATTATTACCAAATCAGATATACATGTAATCCATTTATACTG-TAAGGACTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTAG RR: TAATAATGGTTTAGTCTATATGTACATTAGGTAAATATGAC-ATTCCTGAACTGTTTTACAATGACGAAAATATAAGTCTAAAAAAATC F2: 3 CTGAACTG 2 Unidirectional alignment (log-probability: -46.6) TATACATGTAATCCATTTATACTGtTAAGGActtgacaaagtcaagtcCTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA TATACATGTAATCCATTTATACTG-TAAGGA-----------------CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA Template switch alignment (log-probability: -28.3) TATACATGTAATCCATTTATACTGtTAAGGACTTGACAAA|GTCAAGTC|CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA TATACATGTAATCCATTTATACTG-TAAGGACTTGACAAA|GTCAAGTC|CTTGACAAAATGTTACTGCTTTTATATTCAGATTTTTTTA ========= Event 200 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: --------------------------------------CCTGTGACTTGCCTGGAGGGCG-AGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGG---CCTTGTGCAATG----------------------------------------------------------------------------------------------------- Chimp: --------------------------------------CCTGTGACTTGCCTGGAGGGCG-AGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGG---CCTTGTGCAATG----------------------------------------------------------------------------------------------------- ↑ 1 3 2 4 Gorilla: GGGATCTCCCTGCATGTCCTCTGAGTCGTTGCACAAGGCCTGTGTGCTGCCTGGAGGGGCTGGCCTGGGCCTGTGCTAGTGGAGAAGGTCGAAGGAGGAGCTTCTCTCCTCCCAGAGCCCCCTCCTC-GCCCTCCAGGCGAGTCACAGG------AGAGCCAGGACCAGCATCCTGAGGTCTGTGTCCTGGGGGTTTGTTGGGGTAGGGCGAGTAGGGGAGGGGAGAGACGGGTGAAGGATGTGAATGAAGTTGGAGAGGGGGTG ↓ 1 3 2 4 Human: --------------------------------------CCTGTGACTTGCCTGGAGGGCG-AGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGG---CCTTGTGCAATG----------------------------------------------------------------------------------------------------- Cluster: [ ] Orangutan: --------------------------------------CCTGTAACTCGCCTGGAGGGCG-AGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGGCCT---CATGCAATG----------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr1:10781145-10781259 Template switch process: F1: L CCT 1 F3: 4 AATG R RF: CCTCTGAGTCGTTGCACAAGGCCTGTGTGCTGCCTGGAGGGGCTGGCCTGGGCCTGTGCTAGTGGAGAAGGTCGAAGGAGGAGCTTCTCTCCTCCCAGAGCCCCCTCCTCGCCCTCCAGGCGAGTCACAGGAGAGCCAGGACCAGCATCCTGAGGTCTGTGTCCTGGGGGTTTGTTGGGGTAGGGCGAGTAGGGGAGGGGAGAGACGGGTGAAGGATGTGAATG RR: GGAGACTCAGCAACGTGTTCCGGACACACGACGGACCTCCCCGACCGGACCCGGACACGATCACCTCTTCCAGCTTCCTCCTCGAAGAGAGGAGGGTCTCGGGGGAGGAGCGGGAGGTCCGCTCAGTGTCCTCTCGGTCCTGGTCGTAGGACTCCAGACACAGGACCCCCAAACAACCCCATCCCGCTCATCCCCTCCCCTCTCTGCCCACTTCCTACACTTAC F2: 3 CGTGTTCCGGACACACGACGGACCTCCCCGACCGGACCCGGACACGATCACCTCTTCCAGCTTCCTCCTCGAAGAGAGGAGGGTCTCGGGGGAGGAGCGGGAGGTCCGTTCAGTG 2 Unidirectional alignment (log-probability: -189) CCTgTGAcT---------------------TGCCTGGAGGGcgaggagggggctctgggaggagagaagctcctccttcgaccttctccactagcacaggcccaggccagcccctccaggcagcacacaggccttgtgcaatG---------------------------------------------------------------------------------------------------------- CCTCTGAGTCGTTGCACAAGGCCTGTGTGCTGCCTGGAGGG-----------------------------------------------------------------------------------------------------GCTGGCCTGGGCCTGTGCTAGTGGAGAAGGTCGAAGGAGGAGCTTCTCTCCTCCCAGAGCCCCCTCCTCGCCCTCCAGGCGAGTCACAGGAGAGCCAGGACCAGCAT Template switch alignment (log-probability: -34.1) CCT|GTGACTtGCCTGGAGGGCGAGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGGCCTTGTGC|AATG CCT|GTGACTCGCCTGGAGGGCGAGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGGCCTTGTGC|AATG Gorilla > Chimp --------------- chr1:10233266-10233380 Template switch process: F1: L CCT 1 F3: 4 AATG R RF: CCTCTGAGTCGTTGCACAAGGCCTGTGTGCTGCCTGGAGGGGCTGGCCTGGGCCTGTGCTAGTGGAGAAGGTCGAAGGAGGAGCTTCTCTCCTCCCAGAGCCCCCTCCTCGCCCTCCAGGCGAGTCACAGGAGAGCCAGGACCAGCATCCTGAGGTCTGTGTCCTGGGGGTTTGTTGGGGTAGGGCGAGTAGGGGAGGGGAGAGACGGGTGAAGGATGTGAATG RR: GGAGACTCAGCAACGTGTTCCGGACACACGACGGACCTCCCCGACCGGACCCGGACACGATCACCTCTTCCAGCTTCCTCCTCGAAGAGAGGAGGGTCTCGGGGGAGGAGCGGGAGGTCCGCTCAGTGTCCTCTCGGTCCTGGTCGTAGGACTCCAGACACAGGACCCCCAAACAACCCCATCCCGCTCATCCCCTCCCCTCTCTGCCCACTTCCTACACTTAC F2: 3 CGTGTTCCGGACACACGACGGACCTCCCCGACCGGACCCGGACACGATCACCTCTTCCAGCTTCCTCCTCGAAGAGAGGAGGGTCTCGGGGGAGGAGCGGGAGGTCCGTTCAGTG 2 Unidirectional alignment (log-probability: -189) CCTgTGAcT---------------------TGCCTGGAGGGcgaggagggggctctgggaggagagaagctcctccttcgaccttctccactagcacaggcccaggccagcccctccaggcagcacacaggccttgtgcaatG---------------------------------------------------------------------------------------------------------- CCTCTGAGTCGTTGCACAAGGCCTGTGTGCTGCCTGGAGGG-----------------------------------------------------------------------------------------------------GCTGGCCTGGGCCTGTGCTAGTGGAGAAGGTCGAAGGAGGAGCTTCTCTCCTCCCAGAGCCCCCTCCTCGCCCTCCAGGCGAGTCACAGGAGAGCCAGGACCAGCAT Template switch alignment (log-probability: -34.1) CCT|GTGACTtGCCTGGAGGGCGAGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGGCCTTGTGC|AATG CCT|GTGACTCGCCTGGAGGGCGAGGAGGGGGCTCTGGGAGGAGAGAAGCTCCTCCTTCGACCTTCTCCACTAGCACAGGCCCAGGCCAGCCCCTCCAGGCAGCACACAGGCCTTGTGC|AATG ========= Event 201 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAGTATGGGTAACAATTACTATATTATTATTAGCTAATAATATATATTATTAGCTAGAAAgtcaaccttaaataac ↑ 4 3 1 2 Chimp: GAGTATGGGTAACAATTACTATA-----------------------TTATTAGCTAGAAAgtcaaccttaaataag Gorilla: GAGTATGGGTAACAATTACTATA-----------------------TTATTAGCTAGAAAgtcaaccttaaataac ↓ 4 3 1 2 Human: GAGTATGGGTAACAATTACTATATTATTATTAGCTAATAATATATATTATTAGCTAGAAAgtcaaccttaaataac Cluster: [ ] Orangutan: gagtatgagaaacaattaccata-----------------------ttattagctagaaagtcaaccctaaataac Chimp > Human ------------- chr1:101483094-101483105 Template switch process: F1: L AAGCACAAGAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAT 1 F3: 4 TATATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATTTAAA R RF: AAGCACAAGAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAGCTAGAAAGTCAACCTTAAATAAGAAAATTTAAA RR: TTCGTGTTCTTCTAAAACCTCATACCCATTGTTAATGATATAATAATCGATCTTTCAGTTGGAATTTATTCTTTTAAATTT F2: 3 ATAATAATCGAT 2 Unidirectional alignment (log-probability: -50) GAAGATTTTGGAGTATGGGTAACAATTACTATATTATTattagctaataatatatattattAGCTAGAAAGTCAACCTTAAATAAcAAAATT GAAGATTTTGGAGTATGGGTAACAATTACTATATTATT-----------------------AGCTAGAAAGTCAACCTTAAATAAGAAAATT Template switch alignment (log-probability: -29) GAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAt|TAGCTAATAATA|TATATTATTAGCTAGAAAGTCAACCTTAAATAAcAAAATT GAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAG|TAGCTAATAATA|TATATTATTAGCTAGAAAGTCAACCTTAAATAAGAAAATT Gorilla > Human --------------- chr1:101483094-101483105 Template switch process: F1: L AAGCACAAGAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAT 1 F3: 4 TATATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATTTAAA R RF: AAGCACAAGAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATTTAAA RR: TTCGTGTTCTTCTAAAACCTCATACCCATTGTTAATGATATAATAATCGATCTTTCAGTTGGAATTTATTGTTTTAAATTT F2: 3 ATAATAATCGAT 2 Unidirectional alignment (log-probability: -44) GAAGATTTTGGAGTATGGGTAACAATTACTAtattattattagctaataatataTATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATT GAAGATTTTGGAGTATGGGTAACAATTACTA-----------------------TATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATT Template switch alignment (log-probability: -23) GAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAt|TAGCTAATAATA|TATATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATT GAAGATTTTGGAGTATGGGTAACAATTACTATATTATTAG|TAGCTAATAATA|TATATTATTAGCTAGAAAGTCAACCTTAAATAACAAAATT ========= Event 202 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCCTCCCTTCTTTCCTAACAGGCACTTCCTGTGGCCCCAAGTGGAGGAGTCTATTGCCTGGTTTGCCTCTCTTTCAACTCTCCCTC-TGTCCCCAC--T-T-ATCCCTTGCTCCTGGCATCCTGTCTCT ↓ 3 1 2 4 Chimp: TTCCTCCCTTCTTTCCTAACAGGCACTTCGTGGGGA---CAGAGGGAGAGTTGACAGAGAGGCAAACCAGGCAATAGACTCCTCCACTTGGGGCCACAGGAAGTGCCTGTGCTCCTGGCTTCCTGTCTCT Gorilla: TTCCTCCCTTCTTTCCTAACAGGCACCTCCTGTGGCCCCAAGTGGAGGAGTCTATTGCCTGGTTTGCCTCTCCGTCAACTCTCCCTC-TGTCCCCAC--T-T-ATCCCTTGCTCCTGGCATCCTGTCTCT Human: TTCCTCCCTTCTTTCCTAACAGGCACTTCCTGTGGCCCCAAGTGGAGGAGTCTATTGCCTGGTTTGCCTCTCTTTCAACTCTCCCTC-TGTCCCCAC--T-T-ATCCCTTGCTCCTGGCATCCTGTCTCT Cluster: [ ] Orangutan: TTCCTCCCTTCTTTCCTAACAGGCACCTCCTGTGGCCCCAAGTGGAGGAGTCTATTGCCTGGTTTGCCTCTCTGTCAACTCTCCCTC-TGTCCCCAC--T-T-ATCCCTTGCTCCTGGCATCCTGGCTCT Human > Chimp ------------- chr1:102005985-102006061 Template switch process: F1: L GGTTTTCTGTCTTTCCTCCCTTCTTTCCTAACAGGCACTTC 1 F3: 4 TGCTCCTGGCTTCCTGTCTCTGCTCTGTGCTAAGTGATTT R RF: GGTTTTCTGTCTTTCCTCCCTTCTTTCCTAACAGGCACTTCCTGTGGCCCCAAGTGGAGGAGTCTATTGCCTGGTTTGCCTCTCTTTCAACTCTCCCTCTGTCCCCACTTATCCCTTGCTCCTGGCATCCTGTCTCTGCTCTGTGCTAAGTGATTT RR: CCAAAAGACAGAAAGGAGGGAAGAAAGGATTGTCCGTGAAGGACACCGGGGTTCACCTCCTCAGATAACGGACCAAACGGAGAGAAAGTTGAGAGGGAGACAGGGGTGAATAGGGAACGAGGACCGTAGGACAGAGACGAGACACGATTCACTAAA F2: 3 GTCCGTGAAGGACACCGGGGTTCACCTCCTCAGATAACGGACCAAACGGAGAGACAGTTGAGAGGGAGACAGGGGTG 2 Unidirectional alignment (log-probability: -137) GTTTTCTGTCTTTCCTCCCTTCTTTCCTAACAGGCACTTcgtggggacagagggagagttgacagagaggcaaaccaggcaatagactcctccacttggggccacaggaagtgCCTGT------------------------------------------------------------------------GCTCCTGGCtTCCTGTCTCTGCTCTGTGCTAAGTGATTT GTTTTCTGTCTTTCCTCCCTTCTTTCCTAACAGGCACTT--------------------------------------------------------------------------CCTGTGGCCCCAAGTGGAGGAGTCTATTGCCTGGTTTGCCTCTCTTTCAACTCTCCCTCTGTCCCCACTTATCCCTTGCTCCTGGCATCCTGTCTCTGCTCTGTGCTAAGTGATTT Template switch alignment (log-probability: -36.6) GTTTTCTGTCTTTCCTCCCTTCTTTCCTAACAGGCACTTC|GTGGGGACAGAGGGAGAGTTGAcAGAGAGGCAAACCAGGCAATAGACTCCTCCACTTGGGGCCACAGGAAGTGCCTG|TGCTCCTGGCtTCCTGTCTCTGCTCTGTGCTAAGTGATTT GTTTTCTGTCTTTCCTCCCTTCTTTCCTAACAGGCACTTC|GTGGGGACAGAGGGAGAGTTGAAAGAGAGGCAAACCAGGCAATAGACTCCTCCACTTGGGGCCACAGGAAGTGCCTG|TGCTCCTGGCATCCTGTCTCTGCTCTGTGCTAAGTGATTT ========= Event 203 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTCCCCTCTCAAGCTTGTGGTTCTGGGAGCTT Chimp: GTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTCACCTCTCAAGCTTGTGGTTCTGGGAGCTT Gorilla: GTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTCACAATGGGAGCTTGTGGTTCTGGGAGCTT ↑ 3 2 1 4 Human: GTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTCCCCTCTCAAGCTTGTGGTTCTGGGAGCTT Cluster: [ ] Orangutan: GTGCATCAGAAGCTATATACCCATTGTAGAGTCCGGTCACTTCTCAAGCATGTGGTTCTGGGAGCTT Human > Gorilla --------------- chr1:108250442-108250449 Template switch process: F1: L GCTGTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTC 1 F3: 4 AGCTTGTGGTTCTGGGAGCTTCCTTTAAGATAATAGCAGG R RF: GCTGTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTCCCCTCTCAAGCTTGTGGTTCTGGGAGCTTCCTTTAAGATAACAGCAGG RR: CGACACGTAGTCTTCGATGTATGGGTAACATCTCAGGTCAGGGGAGAGTTCGAACACCAAGACCCTCGAAGGAAATTCTATTGTCGTCC F2: 3 GGGTAACA 2 Unidirectional alignment (log-probability: -36.6) CTGTGCATCAGAAGCTACATACCCATTGTAGAGTCCAG-------TCAcaatgggAGCTTGTGGTTCTGGGAGCTTCCTTTAAGATAAtAGCAGG CTGTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTCCCCTCTCA-------AGCTTGTGGTTCTGGGAGCTTCCTTTAAGATAACAGCAGG Template switch alignment (log-probability: -22.3) CTGTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTC|ACAATGGG|AGCTTGTGGTTCTGGGAGCTTCCTTTAAGATAAtAGCAGG CTGTGCATCAGAAGCTACATACCCATTGTAGAGTCCAGTC|ACAATGGG|AGCTTGTGGTTCTGGGAGCTTCCTTTAAGATAACAGCAGG ========= Event 204 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCTGAACTGATCTTATAGCCTTAAACTTAAGGCTATACATTCAACTTTCAAAAT ↑ 3 1 24 Chimp: ATTCTGAACTGATCTTATAGCCTTA-------AGTTATACATTCAACTTTCAAAAT Gorilla: ATTCTGAACTAATCTTATAGCCTTA-------AGTTATACATTCAATTTTCAAAAT Human: ATTCTGAACTGATCTTATAGCCTTAAACTTAAGGCTATACATTCAACTTTCAAAAT Cluster: [ ] Orangutan: ATTCTGAACTGATCTTATAGCCTTA-------AGTTATACATTCAACTTTCAAAAT Chimp > Human ------------- chr1:107431249-107431257 Template switch process: F1: L ATTGTAAAACCTGATGATTCTGAACTGATCTTATAGCCTTAA 1 F3: 4 TATACATTCAACTTTCAAAATAGAAACTCATTATATGCGA R RF: ATTGTAAAACCTGATGATTCTGAACTGATCTTATAGCCTTAAGTTATACATTCAACTTTCAAAATAGAAACTCATTATATGGGA RR: TAACATTTTGGACTACTAAGACTTGACTAGAATATCGGAATTCAATATGTAAGTTGAAAGTTTTATCTTTGAGTAATATACCCT F2: 3 CGGAATTCA 2 Unidirectional alignment (log-probability: -33) TGTAAAACCTGATGATTCTGAACTGATCTTATAGCCTTAAacttaagGcTATACATTCAACTTTCAAAATAGAAACTCATTATATGcGA TGTAAAACCTGATGATTCTGAACTGATCTTATAGCCTTAA-------GTTATACATTCAACTTTCAAAATAGAAACTCATTATATGGGA Template switch alignment (log-probability: -22.4) TGTAAAACCTGATGATTCTGAACTGATCTTATAGCCTTAA|ACTTAAGGC|TATACATTCAACTTTCAAAATAGAAACTCATTATATGcGA TGTAAAACCTGATGATTCTGAACTGATCTTATAGCCTTAA|ACTTAAGGC|TATACATTCAACTTTCAAAATAGAAACTCATTATATGGGA ========= Event 205 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATATTTTCTAGATACTTTGAT----TGTAATACCTCCTTGTCAAAGTCTTGGACCCCAAAATCT ↓ 3 2 4 1 Chimp: CATATTTTCTAGATACTTTGACAAGAGGTATTA-----CAATCAAAGTCTTGGACCCCAAAATCT ↑ 3 2 4 1 Gorilla: CATATTTTCTAGATACTTTGAT----TGTAATACCTCCTTGTCAAAGTCTTGGACCCCAAAATCT Human: CATATTTTCTAGATACTTTGAT----TGTAATACCTCCTTGTCAAAGTCTTGGACCCCAAAATCT Cluster: [ ] Orangutan: CATATTTTCTAGATACTTTGAT----TGTAATACCTCCTTGTCAAAGTCTTGGACCCCAAAATCT Human > Chimp ------------- chr1:107992034-107992045 Template switch process: F1: L TGATTCATTCAGGATTATAACATATTTTCTAGATACTTTGA-----------------CAA 1 F3: 4 TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA R RF: TGATTCATTCAGGATTATAACATATTTTCTAGATACTTTGATTGTAATACCTCCTTGTCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA RR: ACTAAGTAAGTCCTAATATTGTATAAAAGATCTATGAAACTAACATTATGGAGGAACAGTTTCAGAACCTGGGGTTTTAGAGGTATTTGTATACTCT F2: 3 AACATTATGGAG 2 Unidirectional alignment (log-probability: -43.5) TCATTCAGGATTATAACATATTTTCTAGATACTTTGA----------------caagaggtattacaaTCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA TCATTCAGGATTATAACATATTTTCTAGATACTTTGATTGTAATACCTCCTTG---------------TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA Template switch alignment (log-probability: -27.9) TCATTCAGGATTATAACATATTTTCTAGATACTTTGA-----------------CAA|GAGGTATTACAA|TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA TCATTCAGGATTATAACATATTTTCTAGATACTTTGATTGTAATACCTCCTTGTCAA|GAGGTATTACAA|TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA Gorilla > Chimp --------------- chr1:107992034-107992045 Template switch process: F1: L TGATTCATTCAGGATTATAACATATTTTCTAGATACTTTGA-----------------CAA 1 F3: 4 TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA R RF: TGATTCATTCAGGATTATAACATATTTTCTAGATACTTTGATTGTAATACCTCCTTGTCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA RR: ACTAAGTAAGTCCTAATATTGTATAAAAGATCTATGAAACTAACATTATGGAGGAACAGTTTCAGAACCTGGGGTTTTAGAGGTATTTGTATACTCT F2: 3 AACATTATGGAG 2 Unidirectional alignment (log-probability: -43) TCATTCAGGATTATAACATATTTTCTAGATACTTTGA----------------caagaggtattacaaTCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA TCATTCAGGATTATAACATATTTTCTAGATACTTTGATTGTAATACCTCCTTG---------------TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA Template switch alignment (log-probability: -27.9) TCATTCAGGATTATAACATATTTTCTAGATACTTTGA-----------------CAA|GAGGTATTACAA|TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA TCATTCAGGATTATAACATATTTTCTAGATACTTTGATTGTAATACCTCCTTGTCAA|GAGGTATTACAA|TCAAAGTCTTGGACCCCAAAATCTCCATAAACATATGAGA ========= Event 206 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGCACCAGCACACAGCAGGTAGTAACCTGCCTAGGGCAACTTCATAGGATAAATTGTTTGTTTCCCTAGGTAGCCAT Chimp: TGGCACCAGCACACAGCAGGT----TACTGCCTAGGGCAACTTCATAGGAGAAATTGTTTGTTTCCCTAGGTAGCCAT Gorilla: TGGCACCAGCACACAGCAGGT----TACTGCCTAGGGCAACTTCATAGGAGAAATTGCTTGTTTCCCTAGGTAGCCAT ↓ 3 1 42 Human: TGGCACCAGCACACAGCAGGTAGTAACCTGCCTAGGGCAACTTCATAGGATAAATTGTTTGTTTCCCTAGGTAGCCAT Cluster: [ ] Orangutan: TGGCACCAGCACACAGCAGGT----TACTGCCTAGGGCAACTTCATAGGAGAAATTGTTTGTTTCCCTAGGTAGCCAT Gorilla > Human --------------- chr1:107175365-107175370 Template switch process: F1: L CACACAGCAGGT 1 F3: 4 CTGCCTAGGGCAACTTCATAGGATAAATTGTTTGTTTCCCTAGGTAGCCATCAGGATATTACTAGATTTCT R RF: CACACAGCAGGTTACTGCCTAGGGCAACTTCATAGGAGAAATTGCTTGTTTCCCTAGGTAGCCATCAGGATATTACTAGATTTCT RR: GTGTGTCGTCCAATGACGGATCCCGTTGAAGTATCCTCTTTAACGAACAAAGGGATCCATCGGTAGTCCTATAATGATCTAAAGA F2: 3 CAATGA 2 Unidirectional alignment (log-probability: -37.5) CACACAGCAGGTagTAacCTGCCTAGGGCAACTTCATAGGAtAAATTGtTTGTTTCCC CACACAGCAGGT--TA--CTGCCTAGGGCAACTTCATAGGAGAAATTGCTTGTTTCCC Template switch alignment (log-probability: -27.6) CACACAGCAGGT|AGTAAC|CTGCCTAGGGCAACTTCATAGGAtAAATTGtTTGTTTCCC CACACAGCAGGT|AGTAAC|CTGCCTAGGGCAACTTCATAGGAGAAATTGCTTGTTTCCC ========= Event 207 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CGGGACGCGACCGCCAGATCCACT--T--AGGACCCCGTCGTTCTGCGAAGCGG ↓ 3 1 2 4 Chimp: CGGGACGCGACCGCCAGATCCACTCCTAAGTGGCCCCGTCGTTCTGCGAAGCGG ↑ 3 1 4 Gorilla: CGGGACGCGACCGCCAGATCCACT--T--AGGGCCCCGTCGTTCTGCGAAGCGG Human: CGGGACGCGACCGCCAGATCCACT--T--AGGACCCCGTCGTTCTGCGAAGCGG Cluster: [ ] Orangutan: CGGGACGCGACCGCCAGATCCACT--T--AGGGCCCCGTCGTTCTGCGAAGCGG Human > Chimp ------------- chr10:36890027-36890035 Template switch process: F1: L CAGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT 1 F3: 4 CCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGGGG R RF: CAGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACTTAGGACCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGTCCCGGGG RR: GTCTCGGCCCCACGGTCGCCCTGCGCTGGCGGTCTAGGTGAATCCTGGGGCAGCAAGACGCTTCGCCGGTGCAGACTCAGGGCCCC F2: 3 GGTGAATCC 2 Unidirectional alignment (log-probability: -40.3) AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACTcctaagtgg-----CCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGcCCCGGGG AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT---------TAGGACCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGTCCCGGGG Template switch alignment (log-probability: -22.4) AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT|CCTAAGTGG|CCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGcCCCGGGG AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT|CCTAAGTGG|CCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGTCCCGGGG Gorilla > Chimp --------------- chr10:36890027-36890033 Template switch process: F1: L CAGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT 1 F3: 4 GGCCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGG R RF: CAGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACTTAGGGCCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGG RR: GTCTCGGCCCCACGGTCGCCCTGCGCTGGCGGTCTAGGTGAATCCCGGGGCAGCAAGACGCTTCGCCGGTGCAGACTCGGGGCC F2: 3 TGAATCC 2 Unidirectional alignment (log-probability: -29.4) AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACTcctaagT--GGCCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGG AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT------TAGGGCCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGG Template switch alignment (log-probability: -16.6) AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT|CCTAAGT|GGCCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGG AGAGCCGGGGTGCCAGCGGGACGCGACCGCCAGATCCACT|CCTAAGT|GGCCCCGTCGTTCTGCGAAGCGGCCACGTCTGAGCCCCGG ========= Event 208 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGGACAGCTCCCAACGCTGGCAATCAATCGTCGCCGGCCTCTACCAGCCACTTGCTG Chimp: CCTGGACAGCTCCCAACGCTGGCAATCAATCGTC----GCCTCTACCAGCCACTTGCTG ↓ 3 2 1 4 Gorilla: CCTGGACAGCTCCCAACGCTGGCAATCAATCATTGCCAGCCTCTACCAGCCACTTGCTG Human: CCTGGACAGCTCCCAACGCTGGCAATCAATCGTCGCCGGCCTCTACCAGCCACTTGCTG Cluster: [ ] Orangutan: CCTGGACAGCTCCCAAAGCTGGCAATCAATCATCACCGGCCTCTACCAGCCACTTGCTG Chimp > Gorilla --------------- chr10:112583601-112583607 Template switch process: F1: L GCGCTGGTGCCCTGGACAGCTCCCAACGCTGGCAATCAATC 1 F3: 4 GCCTCTACCAGCCACTTGCTGCCGTTTCCCCATCTCTGTT R RF: GCGCTGGTGCCCTGGACAGCTCCCAACGCTGGCAATCAATCGTCGCCTCTACCAGCCACTTGCTGCCGTTTCCCCATCTCTGTT RR: CGCGACCACGGGACCTGTCGAGGGTTGCGACCGTTAGTTAGCAGCGGAGATGGTCGGTGAACGACGGCAAAGGGGTAGAGACAA F2: 3 ACCGTTA 2 Unidirectional alignment (log-probability: -27.7) CGCTGGTGCCCTGGACAGCTCCCAACGCTGGCAATCAATCaTtgccaGCCTCTACCAGCCACTTGCTGCCGTTTCCCCATCTCTGTT CGCTGGTGCCCTGGACAGCTCCCAACGCTGGCAATCAATCGTC----GCCTCTACCAGCCACTTGCTGCCGTTTCCCCATCTCTGTT Template switch alignment (log-probability: -16.6) CGCTGGTGCCCTGGACAGCTCCCAACGCTGGCAATCAATC|ATTGCCA|GCCTCTACCAGCCACTTGCTGCCGTTTCCCCATCTCTGTT CGCTGGTGCCCTGGACAGCTCCCAACGCTGGCAATCAATC|ATTGCCA|GCCTCTACCAGCCACTTGCTGCCGTTTCCCCATCTCTGTT ========= Event 209 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: gaTTATGCTTAGTAATATTTTACCTG-TGCA--------------------------ATGCACAAAAGGATAACTATACAAGA Chimp: gaTTATGCTTAGTAATATTTTACCTATTGCA-------------AATGAAGCCCTAATTGCACAAAAGGATAACTATACAAGA Gorilla: gaTTATGCTTAGTAATATTTTGCCTATTGCAAATGAAGCCCTAA-------------TTGCACAAAAGGATAACTATACAAGA ↓ 1 34 2 Human: gaTTATGCTTAGTAATATTTTACCTG-TGCA--------------------------ATGCACAAAAGGATAACTATACAAGA Cluster: [ ] Orangutan: gaTCATGCTTAGTAATATTTTGCCTATTGCAAATGAAGCCCTAA-------------TTGCACAAAAGGATAACTATACAAGA Gorilla > Human --------------- chr1:10125176-10125181 Template switch process: F1: L AAGAAAAAGAAAAAGAAAAAGATTATGCTTAGTAATATTTTACCT 1 F3: 4 TGCACAAAAGGATAACTATACAAGAAAGTGTAATTATATT R RF: AAAAAAAAGAAAAAGAAAAAGATTATGCTTAGTAATATTTTGCCTATTGCAAATGAAGCCCTAATTGCACAAAAGGATAACTATACAAGAAAGTGTAATTATATT RR: TTTTTTTTCTTTTTCTTTTTCTAATACGAATCATTATAAAACGGATAACGTTTACTTCGGGATTAACGTGTTTTCCTATTGATATGTTCTTTCACATTAATATAA F2: 3 AACGTG 2 Unidirectional alignment (log-probability: -38) AAAGAAAAAGAAAAAGATTATGCTTAGTAATATTTTaCCT-gTGCAA-------------TGCACAAAAGGATAACTATACAAGAAAGTGTAATTATATT AAAGAAAAAGAAAAAGATTATGCTTAGTAATATTTTGCCTATTGCAAATGAAGCCCTAATTGCACAAAAGGATAACTATACAAGAAAGTGTAATTATATT Template switch alignment (log-probability: -27.6) AAAGAAAAAGAAAAAGATTATGCTTAGTAATATTTTaCCT|GTGCAA|TGCACAAAAGGATAACTATACAAGAAAGTGTAATTATATT AAAGAAAAAGAAAAAGATTATGCTTAGTAATATTTTGCCT|GTGCAA|TGCACAAAAGGATAACTATACAAGAAAGTGTAATTATATT ========= Event 210 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGTATTATCCATACCGAAAGATCTGGAATGGAGTGGATTTTAAGCCTCCTCGAAGTCAAA--------CAAGCTTAGAGCAAATGGCATGTCATATTTTCTGAGTAGCTGACATGGGGTTGCCAGATAAAATACAGAATgcatgttc ↑ 1 4 3 2 Chimp: CAGTATTATCCATACCGAAAGTT-CGGAATGGAGTGGATTTTAAGCCTCCTCAAAGTCAAA----CAGCCAAGCTTAGAGCAAATGGTATGTCATATTTTCTGAGTAGCTGACATGGGGTTGCCAGATAAAATACAGAATgcatgttc Gorilla: CAGTATTATCCATACCGAAAGATCTGGAATGGAATGGATTTTAAGCCTCCTCGAAGTCAAACAGC----CAAGCTTAGAGCAAATGGCATGTCATATTTTCTGAGTAGCTGACATGGGGTTGCCAGATAAAATACAGAATgcatgttc Human: CAGTATTATCCATACCGAAAGATCTGGAATGGAGTGGATTTTAAGCCTCCTCGAAGTCAAA--------CAAGCTTAGAGCAAATGGCATGTCATATTTTCTGAGTAGCTGACATGGGGTTGCCAGATAAAATACAGAATgcatgttc Cluster: [ ] Orangutan: CAGTATTATCCATACTGAAAGATCTGGAATGGAATGGATTTTGAGCCTCCTCGAAGTCTAACAAC----CAAGCTTAGAGCAAATGGCATGTCATATTTTCTGAGTAGCTGACATGGGGTTGCCAGATAAAATACAGAATgcatgctc Chimp > Human ------------- chr1:148492656-148492660 Template switch process: F1: L TAAAATATCTGGAATATTTCCAGTATTATCCATACCGAAAG 1 F3: 4 GAATGGAGTGGATTTTAAGCCTCCTCGAAGTCAAA R RF: TAAAATATCTGGAATATTTCCAGTATTATCCATACCGAAAGTTCGGAATGGAGTGGATTTTAAGCCTCCTCAAAGTCAAACAGCCAAGCTTAGAGCAAATGGTATGTCATATTTTCTGAGTAGCTGACATGGGGTTGCCAGAT RR: ATTTTATAGACCTTATAAAGGTCATAATAGGTATGGCTTTCAAGCCTTACCTCACCTAAAATTCGGAGGAGTTTCAGTTTGTCGGTTCGAATCTCGTTTACCATACAGTATAAAAGACTCATCGACTGTACCCCAACGGTCTA F2: 3 GTCTA 2 Unidirectional alignment (log-probability: -31.8) AAAATATCTGGAATATTTCCAGTATTATCCATACCGAAAGaTCtGGAATGGAGTGGATTTTAAGCCTCCTCgAAGTCAAA---- AAAATATCTGGAATATTTCCAGTATTATCCATACCGAAAGTTC-GGAATGGAGTGGATTTTAAGCCTCCTCAAAGTCAAACAGC Template switch alignment (log-probability: -21.8) AAAATATCTGGAATATTTCCAGTATTATCCATACCGAAAG|ATCTG|GAATGGAGTGGATTTTAAGCCTCCTCgAAGTCAAA AAAATATCTGGAATATTTCCAGTATTATCCATACCGAAAG|ATCTG|GAATGGAGTGGATTTTAAGCCTCCTCAAAGTCAAA ========= Event 211 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCTTGTCTTCCTTGAAGAGCATTTTTTAGTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGATTTGTTACTGTAAAA----AT Chimp: CTCTTGTCTTCCTTGAAGAGCATTTTTTAGTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGATTTGTTACTGTAAAA----AT ↓ 3 2 1 4 Gorilla: CTCTTGTCTTCCTTGAAGAGCATTTTTTAGTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGA-ATGCTTTGTTACTGTAAAA----AT ↑ 3 2 1 4 Human: CTCTTGTCTTCCTTGAAGAGCATTTTTTAGTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGATTTGTTACTGTAAAA----AT Cluster: [ ] Orangutan: CTCTTCTCTTCCTTGAAGAGCATTTTTTAGTGAGGGAAAAGAAATGGATACAAAGAAAGAATGAATAATGCTTTGATTTGTTACTGTAAAAATGAAT Human > Gorilla --------------- chr1:127435570-127435574 Template switch process: F1: L GTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATG 1 F3: 4 TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC R RF: GCATTTTTTAGTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGATTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC RR: CGTAAAAAATCACTCCCTTTTCTTTACCTACGTTTCTTTCTTACTTATTACGAAACTAAACAATGACATTTTTATACCATTGTTTCGGTTTTGTCTG F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -26.7) TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAA-----TGAatgcTTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGA----TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC Template switch alignment (log-probability: -16.4) TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATG|AATGC|TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATG|AATGC|TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC Chimp > Gorilla --------------- chr1:127435570-127435574 Template switch process: F1: L GTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATG 1 F3: 4 TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC R RF: GCATTTTTTAGTGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGATTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC RR: CGTAAAAAATCACTCCCTTTTCTTTACCTACGTTTCTTTCTTACTTATTACGAAACTAAACAATGACATTTTTATACCATTGTTTCGGTTTTGTCTG F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -26.7) TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAA-----TGAatgcTTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATGCTTTGA----TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC Template switch alignment (log-probability: -16.4) TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATG|AATGC|TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC TGAGGGAAAAGAAATGGATGCAAAGAAAGAATGAATAATG|AATGC|TTTGTTACTGTAAAAATATGGTAACAAAGCCAAAACAGAC ========= Event 212 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAG--------ATTATCTTCACACAGTGTACATTAGCCCTTACTC Chimp: ATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAG--------ATTATCTTCACACAGTGT---------------- Gorilla: ATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAC----------------TGAGTAGTGTACATTAGCCCTTACTC ↑ 3 2 1 4 Human: ATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAG--------ATTATCTTCACACAGTGTACATTAGCCCTTACTC Cluster: [ ] Orangutan: GTTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAGATTATCTT--------CACACAGTGTACATTAGCCCTTACTC Human > Gorilla --------------- chr10:113909654-113909659 Template switch process: F1: L AACCTCCTATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTA 1 F3: 4 AGTGTACATTAGCCCTTACTCACTGACTCATGAAAGGGTA R RF: AACCTCCTATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAGATTATCTTCACACAGTGTACATTAGCCCTTACTCACTGACTCATGAAAGGGTA RR: TTGGAGGATAAGTCATTTTCCTTTTCATGAGTCAGAGAGATCTAATAGAAGTGTGTCACATGTAATCGGGAATGAGTGACTGAGTACTTTCCCAT F2: 3 TGAGTC 2 Unidirectional alignment (log-probability: -28.5) ACCTCCTATTCAGTAAAAGGAAAAGTACTCAGTCTCTCT-------------ACtgagtAGTGTACATTAGCCCTTACTCACTGACTCATGAAAGGGTA ACCTCCTATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTAGATTATCTTCACAC-----AGTGTACATTAGCCCTTACTCACTGACTCATGAAAGGGTA Template switch alignment (log-probability: -16.5) ACCTCCTATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTA|CTGAGT|AGTGTACATTAGCCCTTACTCACTGACTCATGAAAGGGTA ACCTCCTATTCAGTAAAAGGAAAAGTACTCAGTCTCTCTA|CTGAGT|AGTGTACATTAGCCCTTACTCACTGACTCATGAAAGGGTA ========= Event 213 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: aaatgtctcatcaaaaatgtgcaaatatgaagtaaatggggcaaaatcttaataagaagtgaatgtaggtga------------------------GTGCTACTATTTAACATTTTTGGAGACTCAAAAATTTGCAAAATTAAAAATTGGGACAAAAGT ↑ 3 2 4 1 Chimp: aaatgtctcatcaaaaatgtgcaaatatgAAGTAAATGGGGCAAAATCTTAATAAGAAGTGAATATAGGTGA------------------------GTGCTACTATTTAACATTTTTGGAGACTCA----------AAATTAAAAATTGGGACAAAAGT Gorilla: aaatgtctcatcaaaaatgggcaaatatgAAGTAAATGGGGCAAAATCTTAATAAGAAGTGAATATAGGTGA------------------------GTGCTACTATTTAACATTTTTGGAGACTCAAACATTTGCAAAATTAAAAATTGGGACAAAAGT Human: aaatgtctcatcaaaaatgtgcaaatatgaagtaaatggggcaaaatcttaataagaagtgaatgtaggtga------------------------GTGCTACTATTTAACATTTTTGGAGACTCAAAAATTTGCAAAATTAAAAATTGGGACAAAAGT Cluster: [ ] Orangutan: aaatgtctcatcaaaaatgtgcaaatataaagtaaatggggcaaaatcttaataagaagtgagtataggtgagagatgtacaggtaggtgttcattgtgctactatttaacatttttggagactcaaaaatttgcaaaattaaaaATTGGGACAAAAGT Chimp > Human ------------- chr10:38571913-38571919 Template switch process: F1: L AATGTAGGTGAGTGCTACTATTTAACATTTTTGGAGACTCAAAA 1 F3: 4 AAATTAAAAATTGGGACAAAAGTATTTGGCAAATCATAAA R RF: TGCAAATATGAAGTAAATGGGGCAAAATCTTAATAAGAAGTGAATATAGGTGAGTGCTACTATTTAACATTTTTGGAGACTCAAAATTAAAAATTGGGACAAAAGTATTTGGCAAATCATAAA RR: ACGTTTATACTTCATTTACCCCGTTTTAGAATTATTCTTCACTTATATCCACTCACGATGATAAATTGTAAAAACCTCTGAGTTTTAATTTTTAACCCTGTTTTCATAAACCGTTTAGTATTT F2: 3 ACGTTTA 2 Unidirectional alignment (log-probability: -31.3) TAGGTGAGTGCTACTATTTAACATTTTTGGAGACTcaaaaatttgCAAAATTAAAAATTGGGACAAAAGTATTTGGCAAATCATAAA TAGGTGAGTGCTACTATTTAACATTTTTGGAGACT----------CAAAATTAAAAATTGGGACAAAAGTATTTGGCAAATCATAAA Template switch alignment (log-probability: -22.2) TAGGTGAGTGCTACTATTTAACATTTTTGGAGACTCAAAA|ATTTGCA|AAATTAAAAATTGGGACAAAAGTATTTGGCAAATCATAAA TAGGTGAGTGCTACTATTTAACATTTTTGGAGACTCAAAA|ATTTGCA|AAATTAAAAATTGGGACAAAAGTATTTGGCAAATCATAAA ========= Event 214 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGAACTGTTTCTGGCAACCTTATATAT----------GCAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG ↑ 1 4 3 2 Chimp: TGAACTGTTTCTGGCAACCTTTTATTC-----ACGTGTCAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG Gorilla: TGAACTGTTTCTGGCAACCTTTTATTCACGTG-----TCGAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG ↓ 1 4 3 2 Human: TGAACTGTTTCTGGCAACCTTATATAT----------GCAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG Cluster: [ ] Orangutan: TGAACTGTTTCTGGCAATCTTTTATTCACATG-----TCAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG Chimp > Human ------------- chr10:38183980-38183987 Template switch process: F1: L CCACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT 1 F3: 4 AAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATT R RF: CCACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTTTTATTCACGTGTCAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATT RR: GGTGTACCGTGATACGACTGACTTGACAAAGACCGTTGGAAAATAAGTGCACAGTTCCACAAGGGTTCGTATATAATAAAAAACCTAAACTAA F2: 3 CGTATATA 2 Unidirectional alignment (log-probability: -31.8) CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTTatatatg------------CAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATT CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT-------TTATTCACGTGTCAAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATT Template switch alignment (log-probability: -16.3) CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT|ATATATGC|AAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATT CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT|ATATATGC|AAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATT Gorilla > Human --------------- chr10:38183980-38183987 Template switch process: F1: L CCACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT 1 F3: 4 AAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG R RF: CCACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTTTTATTCACGTGTCGAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTTG RR: GGTGTACCGTGATACGACTGACTTGACAAAGACCGTTGGAAAATAAGTGCACAGCTCCACAAGGGTTCGTATATAATAAAAAACCTAAACTAAAC F2: 3 CGTATATA 2 Unidirectional alignment (log-probability: -33.9) CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTTaTAT----------atgcaAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTT CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTTTTATTCACGTGTCG-----AGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTT Template switch alignment (log-probability: -22.3) CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT|ATATATGC|aAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTT CACATGGCACTATGCTGACTGAACTGTTTCTGGCAACCTT|ATATATGC|GAGGTGTTCCCAAGCATATATTATTTTTTGGATTTGATTT ========= Event 215 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAATGCCATTAGAtcaagaaggcatattgagcacaggtatcaatcttatctttcacctaaaatcccatagttacagaaaaaa--tatATGTCTGTCTTTATCCACA------------------------------TTCATATCTATATACATATATTGAT ↓ 3 2 4 1 Chimp: GAAATGCCATTAGAtcaagaaggcatattgagcacaggtatcaatcttatctttcacctaaaatcccatagttacagaaaaaa--tatATGTCTGTCTTTATCCACA---------------TTCATTGCCATCACATTCATATCTATATACATATATTGAT Gorilla: GAAATGCCATTAGAtcaagaaggcatactgagcacaggtatcaatcttatctttcacctaaaatcccatagttacagaaaaaa----tatGTCTGTCTTTATCCACATTCATTGCCATCACA---------------TTCATATCTACATACATATATTGAT Human: GAAATGCCATTAGAtcaagaaggcatattgagcacaggtatcaatcttatctttcacctaaaatcccatagttacagaaaaaa--tatATGTCTGTCTTTATCCACA------------------------------TTCATATCTATATACATATATTGAT Cluster: [ ] Orangutan: GAAATGCTATTAGATCAAGAAGGCATATTGAGCACAGGTATCAATCTTATCTTTCACCTAAAATCCCACAGTTACAGAAAAAATC--TATGTCTGTCTTTATCCACATTCATTGCCATCACA---------------TTCATATCTATATACATATATTGAT Human > Chimp ------------- chr10:38668181-38668186 Template switch process: F1: L CCCATAGTTACAGAAAAAATATATGTCTGTCTTTATCCACATTCAT 1 F3: 4 CACATTCATATCTATATACATATATTGATAACTATCTTTATGGA R RF: AAGGCATATTGAGCACAGGTATCAATCTTATCTTTCACCTAAAATCCCATAGTTACAGAAAAAATATATGTCTGTCTTTATCCACATTCATATCTATATACATATATTGATAACTATCTTTATGGA RR: TTCCGTATAACTCGTGTCCATAGTTAGAATAGAAAGTGGATTTTAGGGTATCAATGTCTTTTTTATATACAGACAGAAATAGGTGTAAGTATAGATATATGTATATAACTATTGATAGAAATACCT F2: 3 TACCGT 2 Unidirectional alignment (log-probability: -32.5) GTTACAGAAAAAATATATGTCTGTCTTTATCCACATTCATtgccatcacattcatATCTATATACATATATTGATAACTATCTTTA GTTACAGAAAAAATATATGTCTGTCTTTATCCACATTCAT---------------ATCTATATACATATATTGATAACTATCTTTA Template switch alignment (log-probability: -22.2) GTTACAGAAAAAATATATGTCTGTCTTTATCCACATTCAT|TGCCaT|CACATTCATATCTATATACATATATTGATAACTATCTTTA GTTACAGAAAAAATATATGTCTGTCTTTATCCACATTCAT|TGCCTT|CACATTCATATCTATATACATATATTGATAACTATCTTTA ========= Event 216 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCATGA------AGAGTCATGCTCCATCCTTCCC Chimp: TATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCATGA------AGAGTCATGCTCCATCCTTCCC ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: TATTATCAGGGAACAATATTGTTTCATGGGTCACTGGCCCATGAAATAGAAAAGTCATGCTCCATCCTTCCC ↓ 3 1 2 4 ↑ 3 1 2 4 Human: TATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCATGA------AGAGTCATGCTCCATCCTTCCC Cluster: [ ] Orangutan: TATTATCAGGGAACAATATTGTTTCATGGGTCACTGGCCCATGAAATAGAAGAGTCATGCTCCATCCTTCCC Gorilla > Human --------------- chr10:37585163-37585174 Template switch process: F1: L ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG 1 F3: 4 GAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG R RF: ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGTCACTGGCCCATGAAATAGAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG RR: TAAGACCGTCTATAATAGTCCCTTGTTATAACAAAGTACCCAGTGACCGGGTACTTTATCTTTTCAGTACGAGGTAGGAAGGGATCTTGAGACAGAAGGACTC F2: 3 TACCCAGTGACC 2 Unidirectional alignment (log-probability: -33.5) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGcCAgTGaCCCAT------GAAgAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGTCACTGGCCCATGAAATAGAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Template switch alignment (log-probability: -22.9) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|CCAGTGACCCAT|GAAgAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|CCAGTGACCCAT|GAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Human > Gorilla --------------- chr10:37913764-37913781 Template switch process: F1: L ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG 1 F3: 4 GAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG R RF: ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCATGAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG RR: TAAGACCGTCTATAATAGTCCCTTGTTATAACAAAGTACCCGGTCACTGGGTACTTCTCAGTACGAGGTAGGAAGGGATCTTGAGACAGAAGGACTC F2: 3 ATAAAGTACCCGGTCACT 2 Unidirectional alignment (log-probability: -41.8) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGtCAcTGgCCCATgaaataGAAaAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCAT------GAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Template switch alignment (log-probability: -29.2) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|TCACTGGCCCATGAAAtA|GAAaAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|TCACTGGCCCATGAAACA|GAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Gorilla > Chimp --------------- chr10:38384205-38384216 Template switch process: F1: L ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG 1 F3: 4 GAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG R RF: ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGTCACTGGCCCATGAAATAGAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG RR: TAAGACCGTCTATAATAGTCCCTTGTTATAACAAAGTACCCAGTGACCGGGTACTTTATCTTTTCAGTACGAGGTAGGAAGGGATCTTGAGACAGAAGGACTC F2: 3 TACCCAGTGACC 2 Unidirectional alignment (log-probability: -33.5) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGcCAgTGaCCCAT------GAAgAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGTCACTGGCCCATGAAATAGAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Template switch alignment (log-probability: -22.9) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|CCAGTGACCCAT|GAAgAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|CCAGTGACCCAT|GAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Chimp > Gorilla --------------- chr10:37913764-37913781 Template switch process: F1: L ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG 1 F3: 4 GAAAAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG R RF: ATTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCATGAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCCTGAG RR: TAAGACCGTCTATAATAGTCCCTTGTTATAACAAAGTACCCGGTCACTGGGTACTTCTCAGTACGAGGTAGGAAGGGATCTTGAGACAGAAGGACTC F2: 3 ATAAAGTACCCGGTCACT 2 Unidirectional alignment (log-probability: -41.8) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGtCAcTGgCCCATgaaataGAAaAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGGCCAGTGACCCAT------GAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC Template switch alignment (log-probability: -29.2) TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|TCACTGGCCCATGAAAtA|GAAaAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC TTCTGGCAGATATTATCAGGGAACAATATTGTTTCATGGG|TCACTGGCCCATGAAACA|GAAGAGTCATGCTCCATCCTTCCCTAGAACTCTGTCTTCC ========= Event 217 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TTGAAGACAAAAGCAGCAAAAGT--CA--AAGAGCATAACTTTCCTGAGGGAGCACATGAAACAAAAACAGATGGTGAAGACTCTGCTGATAATTTCAGTTTCAGAGACTAAACTATGACTATAGAACTAATGTCACCTA Chimp: TTGAAGACAAAAGCAGCAAAACTTTTAAGGAAAGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGATGGTGAAGACTCTGCTGATAATTTCAGTTTCAGAGACTAAACTATGACTATAGAACTAATGTCACCTA ↓ 1 4 3 2 Gorilla: TTGAAGACAAAAGCAGCAAAAGT--CA--AAGAGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGATGGTGAAGACTCTGCTGATAATTTCAGTTTCAGAGACTAAACTATGACTATAGAACTAATGTCACCTA Human: TTGAAGACAAAAGCAGCAAAAGT--CA--AAGAGCATAACTTTCCTGAGGGAGCACATGAAACAAAAACAGATGGTGAAGACTCTGCTGATAATTTCAGTTTCAGAGACTAAACTATGACTATAGAACTAATGTCACCTA Cluster: [ ] Orangutan: TTGAAGACAGAAGCAGCAAAAGT--CA--AAGAGCATAACTTTCCTTAGGGAACACATGAAACAAAAACAGATGGTGAAGACTCTGCTGATAATTTCAGTTTCAGAGACTAAACTATGACGATAGAACTAATGTCACCTA Chimp > Gorilla --------------- chr1:110287478-110287484 Template switch process: F1: L AGTTTTTCAAACACTACTATTTGAAGACAAAAGCAGCAAAA 1 F3: 4 AGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGA R RF: AGTCTTTCAAACACTACTATTTGAAGACAAAAGCAGCAAAACTTTTAAGGAAAGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGATGGTGAAGACTCTGCTGATAATTTCAGTTTCAGAGACTAAACTATGAC RR: TCAGAAAGTTTGTGATGATAAACTTCTGTTTTCGTCGTTTTGAAAATTCCTTTCGTATTGAAAGGAATCCCTCGTGTACTTTGTTTTTGTCTACCACTTCTGAGACGACTATTAAAGTCAAAGTCTCTGATTTGATACTG F2: 3 GAAACTG 2 Unidirectional alignment (log-probability: -36.8) GTtTTTCAAACACTACTATTTGAAGACAAAAGCAGCAA-----------AAgtcaaagAGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGA GTCTTTCAAACACTACTATTTGAAGACAAAAGCAGCAAAACTTTTAAGGAA-------AGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGA Template switch alignment (log-probability: -27.7) GTtTTTCAAACACTACTATTTGAAGACAAAAGCAGCAAAA|GTCAaAG|AGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGA GTCTTTCAAACACTACTATTTGAAGACAAAAGCAGCAAAA|GTCATAG|AGCATAACTTTCCTTAGGGAGCACATGAAACAAAAACAGA ========= Event 218 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAAGTAAATTTCTATTGCTTGTAAGGGTTTCTGTAGAAACCCCTACTCCTACTTATTCTTCTCtaa ↑ 13 4 2 Chimp: AAAAGTAAATTTCTATTGCTT------------ACAGAAACCCCTACTCCTACTTATTCTTCTCtaa Gorilla: AAAAGTAAATTTCTATTGCTT------------ACAGAAACCCCTACTCCTACTTATTCTTCTCtaa ↓ 13 4 2 Human: AAAAGTAAATTTCTATTGCTTGTAAGGGTTTCTGTAGAAACCCCTACTCCTACTTATTCTTCTCtaa Cluster: [ ] Orangutan: AAAAGTAAATTTCTATTGCTT------------ACAGAAACCCCTACTCCTACTTATTCTTCTCtaa Chimp > Human ------------- chr1:139406360-139406373 Template switch process: F1: L CTCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTT 1 F3: 4 AGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA R RF: CTCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTTACAGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA RR: GAGTTTTTAGTTAACAAAATTTTTCATTTAAAGATAACGAATGTCTTTGGGGATGAGGATGAATAAGAAGAGATTACCTTTAT F2: 3 TGTCTTTGGGAATG 2 Unidirectional alignment (log-probability: -40.2) TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTTgtAagggtttctgtaGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTTACA------------GAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA Template switch alignment (log-probability: -23) TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTT|GTAaGGGTTTCTGT|AGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTT|GTAGGGGTTTCTGT|AGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA Gorilla > Human --------------- chr1:139406360-139406373 Template switch process: F1: L CTCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTT 1 F3: 4 AGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA R RF: CTCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTTACAGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA RR: GAGTTTTTAGTTAACAAAATTTTTCATTTAAAGATAACGAATGTCTTTGGGGATGAGGATGAATAAGAAGAGATTACCTTTAT F2: 3 TGTCTTTGGGAATG 2 Unidirectional alignment (log-probability: -39.2) TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTtgtaagggtttcTgtAGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCT------------TACAGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA Template switch alignment (log-probability: -23) TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTT|GTAaGGGTTTCTGT|AGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA TCAAAAATCAATTGTTTTAAAAAGTAAATTTCTATTGCTT|GTAGGGGTTTCTGT|AGAAACCCCTACTCCTACTTATTCTTCTCTAATGGAAATA ========= Event 219 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TCAGGTTAAAAAAACACCTGACTGGTACAACTAATGGTTGTGCTAATCATTAGTCGTGGTaaaa-a ↓ 1 4 3 2 Chimp: TCAGGTTaaaaaaaCACCTGATTAGCACAACTAATGGTTGTGCTAATCATTAGTCGTGGTaa--aa Gorilla: TCAGGTTaaaaaaaCACCTGATTAGTACAACTAATGGTTGTGCTAATCATTAGTCATGGTAA---A Human: TCAGGTTAAAAAAACACCTGACTGGTACAACTAATGGTTGTGCTAATCATTAGTCGTGGTaaaa-a Cluster: [ ] Orangutan: TCAGGTTAAAAAAACACCTGATTAGTGCAACTAATGGTTGTGCTAATCATTAGTCGTGGTAA---A Human > Chimp ------------- chr11:100331766-100331770 Template switch process: F1: L GTGTGTGTGTGTTGTATTAATCAGGTTAAAAAAACACCTGA 1 F3: 4 ACAACTAATGGTTGTGCTAATCATTAGTCGTGGTAAAA R RF: GTGTGTGTGTGTTGTATTAATCAGGTTAAAAAAACACCTGACTGGTACAACTAATGGTTGTGCTAATCATTAGTCGTGGTAAAA RR: CACACACACACAACATAATTAGTCCAATTTTTTTGTGGACTGACCATGTTGATTACCAACACGATTAGTAATCAGCACCATTTT F2: 3 CGATT 2 Unidirectional alignment (log-probability: -26) TGTGTGTGTGTTGTATTAATCAGGTTAAAAAAACACCTGAtTaGcACAACTAATGGTTGTGCTAATCATTAGTCGTGGTAAAA- TGTGTGTGTGTTGTATTAATCAGGTTAAAAAAACACCTGACTGGTACAACTAATGGTTGTGCTAATCATTAGTCGTGGTAAAAA Template switch alignment (log-probability: -15.9) TGTGTGTGTGTTGTATTAATCAGGTTAAAAAAACACCTGA|TTAGC|ACAACTAATGGTTGTGCTAATCATTAGTCGTGGTAAAA TGTGTGTGTGTTGTATTAATCAGGTTAAAAAAACACCTGA|TTAGC|ACAACTAATGGTTGTGCTAATCATTAGTCGTGGTAAAA ========= Event 220 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: gtGTTTCTTGCTAACTCACTGGACTGTGTCAGTGATAAAGAAACCACTAT ↓ 13 24 ↑ 13 24 Chimp: gtGTTTCTTGCTAACTCACTGACACAGTCCAGTGATAAAGAAACCACTAT ↓ 13 24 ↑ 13 24 Gorilla: gtGTTTCTTGCTAACTCACTGGACTGTGTCAGTGATAAAGAAACCACTAT Human: gtGTTTCTTGCTAACTCACTGGACTGTGTCAGTGATAAAGAAACCACTAT Cluster: [ ] Orangutan: gtGTTTCTTGCTAACTCACTGGACTGTGTCTGTGATAAAGAAACCACTAT Chimp > Human ------------- chr11:101048162-101048169 Template switch process: F1: L ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG 1 F3: 4 CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT R RF: ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGACACAGTCCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT RR: TGACCGATCTTCCTCGGACCCACAAAGAACGATTGAGTGACTGTGTCAGGTCACTATTTCTTTGGTGATAATATAATTCTACGATTAGA F2: 3 TGTGTCAG 2 Unidirectional alignment (log-probability: -33) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGgactgtgt--------CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG--------ACACAGTCCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Template switch alignment (log-probability: -16.3) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|GACTGTGT|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|GACTGTGT|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Human > Chimp ------------- chr11:101268749-101268756 Template switch process: F1: L ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG 1 F3: 4 CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT R RF: ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGGACTGTGTCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT RR: TGACCGATCTTCCTCGGACCCACAAAGAACGATTGAGTGACCTGACACAGTCACTATTTCTTTGGTGATAATATAATTCTACGATTAGA F2: 3 CTGACACA 2 Unidirectional alignment (log-probability: -33) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGacacagtc--------CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG--------GACTGTGTCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Template switch alignment (log-probability: -16.3) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|ACACAGTC|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|ACACAGTC|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Gorilla > Chimp --------------- chr11:101268749-101268756 Template switch process: F1: L ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG 1 F3: 4 CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT R RF: ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGGACTGTGTCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT RR: TGACCGATCTTCCTCGGACCCACAAAGAACGATTGAGTGACCTGACACAGTCACTATTTCTTTGGTGATAATATAATTCTACGATTAGA F2: 3 CTGACACA 2 Unidirectional alignment (log-probability: -32.5) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG--------acacagtcCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGGACTGTGT--------CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Template switch alignment (log-probability: -16.7) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|ACACAGTC|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|ACACAGTC|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Chimp > Gorilla --------------- chr11:100768527-100768534 Template switch process: F1: L ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG 1 F3: 4 CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT R RF: ACTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGACACAGTCCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT RR: TGACCGATCTTCCTCGGACCCACAAAGAACGATTGAGTGACTGTGTCAGGTCACTATTTCTTTGGTGATAATATAATTCTACGATTAGA F2: 3 TGTGTCAG 2 Unidirectional alignment (log-probability: -32.5) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG--------gactgtgtCAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTGACACAGTC--------CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT Template switch alignment (log-probability: -16.7) CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|GACTGTGT|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT CTGGCTAGAAGGAGCCTGGGTGTTTCTTGCTAACTCACTG|GACTGTGT|CAGTGATAAAGAAACCACTATTATATTAAGATGCTAATCT ========= Event 221 ========= Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GACCTCAATCAGAATTTGAACCAAATCTTTTACAGATTTGGTCTCTAGTAGATAAC Chimp: GACCTCAATCAGAGTTTGAAC----TCAGTAAAAGATTTGGTCTCTAGTAGATAAC Gorilla: GACCTCAATCAGAATTTGAAC----TCAGTAAAAGATTTGGTCTCTAGTAGATAAC ↑ 1 3 4 2 Human: GACCTCAATCAGAATTTGAACCAAATCTTTTACAGATTTGGTCTCTAGTAGATAAC Cluster: [ ] Orangutan: GACCTCAATCAGAATTTGAGT----TCAGTAAAAGATTTGGTCTCTAGTAGATAAC Human > Gorilla --------------- chr11:100162482-100162489 Template switch process: F1: L GTTCTCCCATAATCACTGATGACCTCAATCAGAATTTGAAC 1 F3: 4 AGATTTGGTCTCTAGTAGATAACACACCTCTACAATAAAA R RF: GTTCTCCCATAATCACTGATGACCTCAATCAGAATTTGAACCAAATCTTTTACAGATTTGGTCTCTAGTAGATAACACATCTCTACAATAAAA RR: CAAGAGGGTATTAGTGACTACTGGAGTTAGTCTTAAACTTGGTTTAGAAAATGTCTAAACCAGAGATCATCTATTGTGTAGAGATGTTATTTT F2: 3 AAATGACT 2 Unidirectional alignment (log-probability: -37.9) TTCTCCCATAATCACTGATGACCTCAATCAGAATTTGAACtcagtAAA--------AGATTTGGTCTCTAGTAGATAACACAcCTCTACAATAAAA TTCTCCCATAATCACTGATGACCTCAATCAGAATTTGAAC----CAAATCTTTTACAGATTTGGTCTCTAGTAGATAACACATCTCTACAATAAAA Template switch alignment (log-probability: -27.8) TTCTCCCATAATCACTGATGACCTCAATCAGAATTTGAAC|TCaGTAAA|AGATTTGGTCTCTAGTAGATAACACAcCTCTACAATAAAA TTCTCCCATAATCACTGATGACCTCAATCAGAATTTGAAC|TCTGTAAA|AGATTTGGTCTCTAGTAGATAACACATCTCTACAATAAAA ========= Event 222 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGTGCTTGGAGAGTGCATAAGCCTTC----ACATGGTTGAGTAATGATTTGAA Chimp: TTGTGCTTGGAGAGTGCATAAGCCTGAAGGCTTGTGGTTGAGTAATGATTTGAA ↑ 3 1 2 4 Gorilla: TTGTGCTTGGAGAGTGCATAAGCCTTC----ACATGGTTGAGTAATGATTTGAA Human: TTGTGCTTGGAGAGTGCATAAGCCTTC----ACATGGTTGAGTAATGATTTGAA Cluster: [ ] Orangutan: TTGTGCTTGGAGATTGCATAAGCCTTC----ACATGGTTGAGTAATGATTTGGA Gorilla > Chimp --------------- chr11:100432114-100432121 Template switch process: F1: L AATATGTAAGAGCCTATTGTGCTTGGAGAGTGCATAAGCCT 1 F3: 4 GTGGTTGAGTAATGATTTGAACGCAAAAGAGTCTCCAGTGA R RF: AATATGTAAGAGCCTATTGTGCTTGGAGAGTGCATAAGCCTTCACATGGTTGAGTAATGATTTGAATGCAAAAGAGTCTCCAGTGA RR: TTATACATTCTCGGATAACACGAACCTCTCACGTATTCGGAAGTGTACCAACTCATTACTAAACTTACGTTTTCTCAGAGGTCACT F2: 3 TTCGGAAG 2 Unidirectional alignment (log-probability: -39.3) ATATGTAAGAGCCTATTGTGCTTGGAGAGTGCATAAGCCT-----gaaggcttgTGGTTGAGTAATGATTTGAAcGCAAAAGAGTCTCCAGTG ATATGTAAGAGCCTATTGTGCTTGGAGAGTGCATAAGCCTTCACA---------TGGTTGAGTAATGATTTGAATGCAAAAGAGTCTCCAGTG Template switch alignment (log-probability: -27.8) ATATGTAAGAGCCTATTGTGCTTGGAGAGTGCATAAGCCT|GAAGGCTT|gTGGTTGAGTAATGATTTGAAcGCAAAAGAGTCTCCAGTG ATATGTAAGAGCCTATTGTGCTTGGAGAGTGCATAAGCCT|GAAGGCTT|ATGGTTGAGTAATGATTTGAATGCAAAAGAGTCTCCAGTG ========= Event 223 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGACAGTGACACAGACCCTCACCAGAACA ↑ 3 2 1 4 Chimp: GCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGAGG-GAACACAGACCCTCACCAGAACA Gorilla: GCCTTGCTGCCTACAAGTTGACTGTCTTGTTAGGGAGG-GAACACAGACCCTCACCAGAACA Human: GCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGACAGTGACACAGACCCTCACCAGAACA Cluster: [ ] Orangutan: GCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGAGG-GAACACAGACCCTCACCAGAACA Chimp > Human ------------- chr1:109885002-109885006 Template switch process: F1: L GCCAGGCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGA 1 F3: 4 ACACAGACCCTCACCAGAACAAGCTTAACACCACCGGGTG R RF: GCCAGGCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGAGGGAACACAGACCCTCACCAGAACAAGCTTAACACCACCGGGTG RR: CGGTCCGGAACGACGGATGTTCAAGTGACAGAACAATCCCTCCCTTGTGTCTGGGAGTGGTCTTGTTCGAATTGTGGTGGCCCAC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -27.1) CCAGGCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGAcagtG---ACACAGACCCTCACCAGAACAAGCTTAACACCACCGGGTG CCAGGCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGA----GGGAACACAGACCCTCACCAGAACAAGCTTAACACCACCGGGTG Template switch alignment (log-probability: -15.9) CCAGGCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGA|CAGTG|ACACAGACCCTCACCAGAACAAGCTTAACACCACCGGGTG CCAGGCCTTGCTGCCTACAAGTTCACTGTCTTGTTAGGGA|CAGTG|ACACAGACCCTCACCAGAACAAGCTTAACACCACCGGGTG ========= Event 224 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ttttttttttAGCTGTCGAAGCATAATGGGGGAAGCACC---TCCCCCGTTCTCCCCTTTCACCTAAA Chimp: ttttttttttAGCTGTCCAAGCATAATGGGGGAAGCACCATTATGCTCGTTCTCCCCTTTCACCTAAA ↑ 3 2 1 4 Gorilla: ttttttttttAGCTGTCCAAGCATAATGGGGGAAGCACC---TCCCCCGTTCTCCCCTTTCACCTAAA Human: ttttttttttAGCTGTCGAAGCATAATGGGGGAAGCACC---TCCCCCGTTCTCCCCTTTCACCTAAA Cluster: [ ] Orangutan: ttttttttttAGCTGTCCAAGCATAATGGGGCAAGCATC---TCCCCCACTCTCCCCTTTCACCTAAA Gorilla > Chimp --------------- chr1:125947064-125947071 Template switch process: F1: L TTTTTTTTTTTTAGCTGTCCAAGCATAATGGGGGAAGCACC 1 F3: 4 CGTTCTCCCCTTTCACCTAAAGGGGTTAGGGAAACTGGAT R RF: TTTTTTTTTTTTAGCTGTCCAAGCATAATGGGGGAAGCACCTCCCCCGTTCTCCCCTTTCACCTAAAGGGGTTAGGGAAACTGGAT RR: AAAAAAAAAAAATCGACAGGTTCGTATTACCCCCTTCGTGGAGGGGGCAAGAGGGGAAAGTGGATTTCCCCAATCCCTTTGACCTA F2: 3 TCGTATTA 2 Unidirectional alignment (log-probability: -30.9) TTTTTTTTTTTAGCTGTCCAAGCATAATGGGGGAAGCACcattatgCT----CGTTCTCCCCTTTCACCTAAAGGGGTTAGGGAAACTGGAT TTTTTTTTTTTAGCTGTCCAAGCATAATGGGGGAAGCAC-------CTCCCCCGTTCTCCCCTTTCACCTAAAGGGGTTAGGGAAACTGGAT Template switch alignment (log-probability: -16.7) TTTTTTTTTTTAGCTGTCCAAGCATAATGGGGGAAGCACC|ATTATGCT|CGTTCTCCCCTTTCACCTAAAGGGGTTAGGGAAACTGGAT TTTTTTTTTTTAGCTGTCCAAGCATAATGGGGGAAGCACC|ATTATGCT|CGTTCTCCCCTTTCACCTAAAGGGGTTAGGGAAACTGGAT ========= Event 225 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TGAAGCCTAGGACGCTTTCTTAGCATTTAGTGCAGAATTTTAG--------ATTGCCATCATTTTCTGAAAATTAGAA ↓ 13 24 ↑ 13 24 Chimp: TGAAGCCTAGGACGCTTTCTTGGCAA----TCTAAAATTCTGC----ACTAAATGCTATCATTTTCTGAAAATTAGAA Gorilla: TGAAGCCTGGGACGCTTTCTTGGCAA----TCTAAAATTCTGCACTA----AATGCTATCATTTTCTGAAAATTAGAA ↓ 13 24 ↑ 13 24 Human: TGAAGCCTAGGACGCTTTCTTAGCATTTAGTGCAGAATTTTAG--------ATTGCCATCATTTTCTGAAAATTAGAA Cluster: [ ] Orangutan: TGAAGCCTAGGACGCTTTCTTGGCAA----TCCAAAATTCTGCACTA----AATGCTATCATTTTCTGAAAATTAGAA Chimp > Human ------------- chr11:124536103-124536130 Template switch process: F1: L TATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT 1 F3: 4 ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA R RF: TATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTGGCAATCTAAAATTCTGCACTAAATGCTATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA RR: ATATAAAGATAAAATCAGAAACTTCGGATCCTGCGAAAGAACCGTTAGATTTTAAGACGTGATTTACGATAGTAAAAGACTTTTAATCTTAGGAAAAACTATTGAAGGT F2: 3 CCGTTAGATTTTAAGACGTGATTTACGA 2 Unidirectional alignment (log-probability: -60) ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTaGCAtttagtgcagaattttagAT------------------TGCcATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTGGCA------------------ATCTAAAATTCTGCACTAAATGCTATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Template switch alignment (log-probability: -18.7) ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT|AGCATTTAGTGCAGAATTTTAGATTGCC|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT|AGCATTTAGTGCAGAATTTTAGATTGCC|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Human > Chimp ------------- chr11:125335098-125335125 Template switch process: F1: L TATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT 1 F3: 4 ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA R RF: TATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTAGCATTTAGTGCAGAATTTTAGATTGCCATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA RR: ATATAAAGATAAAATCAGAAACTTCGGATCCTGCGAAAGAATCGTAAATCACGTCTTAAAATCTAACGGTAGTAAAAGACTTTTAATCTTAGGAAAAACTATTGAAGGT F2: 3 TCGTAAATCACGTCTTAAAATCTAACGG 2 Unidirectional alignment (log-probability: -60) ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTgGCA------------------ATctaaaattctgcactaaaTGCtATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTAGCATTTAGTGCAGAATTTTAGAT------------------TGCCATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Template switch alignment (log-probability: -18.7) ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT|GGCAATCTAAAATTCTGCACTAAATGCT|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT|GGCAATCTAAAATTCTGCACTAAATGCT|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Gorilla > Human --------------- chr11:124536103-124536130 Template switch process: F1: L TATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT 1 F3: 4 ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA R RF: TATATTTCTATTTTAGTCTTTGAAGCCTGGGACGCTTTCTTGGCAATCTAAAATTCTGCACTAAATGCTATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA RR: ATATAAAGATAAAATCAGAAACTTCGGACCCTGCGAAAGAACCGTTAGATTTTAAGACGTGATTTACGATAGTAAAAGACTTTTAATCTTAGGAAAAACTATTGAAGGT F2: 3 CCGTTAGATTTTAAGACGTGATTTACGA 2 Unidirectional alignment (log-probability: -64.1) ATATTTCTATTTTAGTCTTTGAAGCCTaGGACGCTTTCTTaGCAtttagtgcagaattttagAT------------------TGCcATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTGGGACGCTTTCTTGGCA------------------ATCTAAAATTCTGCACTAAATGCTATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Template switch alignment (log-probability: -24.8) ATATTTCTATTTTAGTCTTTGAAGCCTaGGACGCTTTCTT|AGCATTTAGTGCAGAATTTTAGATTGCC|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTGGGACGCTTTCTT|AGCATTTAGTGCAGAATTTTAGATTGCC|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Human > Gorilla --------------- chr11:124813317-124813344 Template switch process: F1: L TATATTTCTATTTTAGTCTTTGAAGCCTGGGACGCTTTCTT 1 F3: 4 ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA R RF: TATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTAGCATTTAGTGCAGAATTTTAGATTGCCATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA RR: ATATAAAGATAAAATCAGAAACTTCGGATCCTGCGAAAGAATCGTAAATCACGTCTTAAAATCTAACGGTAGTAAAAGACTTTTAATCTTAGGAAAAACTATTGAAGGT F2: 3 TCGTAAATCACGTCTTAAAATCTAACGG 2 Unidirectional alignment (log-probability: -64.1) ATATTTCTATTTTAGTCTTTGAAGCCTgGGACGCTTTCTTgGCA------------------ATctaaaattctgcactaaaTGCtATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTTAGCATTTAGTGCAGAATTTTAGAT------------------TGCCATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA Template switch alignment (log-probability: -24.8) ATATTTCTATTTTAGTCTTTGAAGCCTgGGACGCTTTCTT|GGCAATCTAAAATTCTGCACTAAATGCT|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ATATTTCTATTTTAGTCTTTGAAGCCTAGGACGCTTTCTT|GGCAATCTAAAATTCTGCACTAAATGCT|ATCATTTTCTGAAAATTAGAATCCTTTTTGATAACTTCCA ========= Event 226 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: catacacacatactgttgtgtacaca----cacacaacatgCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCT--------------CTGGGTGTGTACCTCTGGATAAATAAGATGCATGCCAAGCCA Chimp: catacacacatactgttgtgtacaca----cacacaacaTGCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCT--------------CTGGGTGTGTACCTCTGGATAGATAAGATGCATGCCAAGCCA ↑ 3 2 4 1 Gorilla: catacacacatactgttgtgtacacacatacacacaacatGCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCT----------------------------CTGGATAAATAAGATGCATGCCAAGCCA Human: catacacacatactgttgtgtacaca----cacacaacatgCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCT--------------CTGGGTGTGTACCTCTGGATAAATAAGATGCATGCCAAGCCA Cluster: [ ] Orangutan: CATACACACATACTGTTGTGCACACACATACACCCAACATGCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCTCTGGGTGTGTACCT--------------CTGCCTAAATAAGATGCATGCCAAGCCA Gorilla > Chimp --------------- chr11:125310010-125310017 Template switch process: F1: L CATGCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCTCTGG 1 F3: 4 CTCTGGATAGATAAGATGCATGCCAAGCCAACCCACAGATTTTCACTAGT R RF: GTACACACATACACACAACATGCCTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCTCTGGATAAATAAGATGCATGCCAAGCCAACCCACAGATTTTCACTAGT RR: CATGTGTGTATGTGTGTTGTACGGACACGTGTCTCGGTTGTTGGGAAGTTTTCACACGAGACCTATTTATTCTACGTACGGTTCGGTTGGGTGTCTAAAAGTGATCA F2: 3 CATGTGTG 2 Unidirectional alignment (log-probability: -36.6) CTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGctctgggtgtgtacCTCTGGATAgATAAGATGCATGCCAAGCCAACCCACAGAT CTGTGCACAGAGCCAACAACCCTTCAAAAGTGTG--------------CTCTGGATAAATAAGATGCATGCCAAGCCAACCCACAGAT Template switch alignment (log-probability: -22.6) CTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCTCTGG|GTGTGTAC|CTCTGGATAgATAAGATGCATGCCAAGCCAACCCACAGAT CTGTGCACAGAGCCAACAACCCTTCAAAAGTGTGCTCTGG|GTGTGTAC|CTCTGGATAAATAAGATGCATGCCAAGCCAACCCACAGAT ========= Event 227 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTCCTTCTCTGTCTATAACCAAGTCA----------------TTTTTGGTGCAAAAAACTGAGGTCCCTTTT ↑ 1 3 42 Chimp: TCTCCTTCTCTGTCTATAACCCTTTGA--------TCAAAAATGACTTGGTGCAAAAAACTGAGGTCCCATTT Gorilla: TCTCCTTCTCTGTCTATAACCCTTTGATCAAAAAT--------GACTTGGTGTAAAAAACTGAGGTCCCTTTT ↓ 1 3 42 Human: TCTCCTTCTCTGTCTATAACCAAGTCA----------------TTTTTGGTGCAAAAAACTGAGGTCCCTTTT Cluster: [ ] Orangutan: TTTCCTTCTCTGTCTATAACCCTTTGATCAAATAT--------GAGTTGGTGCAAAAAACTGAGGTCCCTTTT Chimp > Human ------------- chr11:103531277-103531285 Template switch process: F1: L CATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACC 1 F3: 4 TTGGTGCAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTA R RF: CATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACCCTTTGATCAAAAATGACTTGGTGCAAAAAACTGAGGTCCCATTTATGGAAAAGTGTA RR: GTAGTAAGGTATAGAGGAAGAGAGGAAGAGACAGATATTGGGAAACTAGTTTTTACTGAACCACGTTTTTTGACTCCAGGGTAAATACCTTTTCACAT F2: 3 TTTACTGAA 2 Unidirectional alignment (log-probability: -40.9) ATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACCaagtcattt-----------------TTGGTGCAAAAAACTGAGGTCCCtTTTATGGAAAAGTGTA ATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACC---------CTTTGATCAAAAATGACTTGGTGCAAAAAACTGAGGTCCCATTTATGGAAAAGTGTA Template switch alignment (log-probability: -22.4) ATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACC|AAGTCATTT|TTGGTGCAAAAAACTGAGGTCCCtTTTATGGAAAAGTGTA ATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACC|AAGTCATTT|TTGGTGCAAAAAACTGAGGTCCCATTTATGGAAAAGTGTA Gorilla > Human --------------- chr11:103531277-103531285 Template switch process: F1: L CATCATTCCATATCTCCTTCTCTCCTTCTCTGTCTATAACC 1 F3: 4 TTGGTGCAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTAGGTACTG R RF: CATCATTCCGTATCTCCTTCTCTCCTTCTCTGTCTATAACCCTTTGATCAAAAATGACTTGGTGTAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTAGGTACTG RR: GTAGTAAGGCATAGAGGAAGAGAGGAAGAGACAGATATTGGGAAACTAGTTTTTACTGAACCACATTTTTTGACTCCAGGGAAAATACCTTTTCACATCCATGAC F2: 3 TTTACTGAA 2 Unidirectional alignment (log-probability: -45.2) ATCATTCCaTATCTCCTTCTCTCCTTCTCTGTCTATAACcaagtCaTTT-------------TTGGTGcAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTA ATCATTCCGTATCTCCTTCTCTCCTTCTCTGTCTATAAC-----CCTTTGATCAAAAATGACTTGGTGTAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTA Template switch alignment (log-probability: -28.1) ATCATTCCaTATCTCCTTCTCTCCTTCTCTGTCTATAACC|AAGTCATTT|TTGGTGcAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTA ATCATTCCGTATCTCCTTCTCTCCTTCTCTGTCTATAACC|AAGTCATTT|TTGGTGTAAAAAACTGAGGTCCCTTTTATGGAAAAGTGTA ========= Event 228 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGAT ↓ 1 3 24 Chimp: TTTAGAATAGTAATGCTTGGG-----------CAGTACTATCATTCAACCTATATG-- ↑ 1 3 24 Gorilla: TTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGAT Human: TTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGAT Cluster: [ ] Orangutan: TTTAGAATGGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATG-- Human > Chimp ------------- chr11:103659110-103659114 Template switch process: F1: L TGTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG 1 F3: 4 CTATCATTCAACCTATATGATTAATTGAGGAGTAGG R RF: TGTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGATTAATTGAGGAGTAGG RR: ACAATTTCGTTTATTAGTCCAAATCTTATCATTACGAACCCAATATTTAATCATGACGATAGTAAGTTGGATATACTAATTAACTCCTCATCC F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -27.7) GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGGc--------AGTA---CTATCATTCAACCTATATGATTAATTGAGGAGTAGG GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGATTAATTGAGGAGTAGG Template switch alignment (log-probability: -15.8) GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG|CAGTA|CTATCATTCAACCTATATGATTAATTGAGGAGTAGG GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG|CAGTA|CTATCATTCAACCTATATGATTAATTGAGGAGTAGG Gorilla > Chimp --------------- chr11:103659110-103659114 Template switch process: F1: L TGTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG 1 F3: 4 CTATCATTCAACCTATATGATTAATTGAGGAGTAGG R RF: TGTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGATTAATTGAGGAGTAGG RR: ACAATTTCGTTTATTAGTCCAAATCTTATCATTACGAACCCAATATTTAATCATGACGATAGTAAGTTGGATATACTAATTAACTCCTCATCC F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -26.7) GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG--------cAGTA---CTATCATTCAACCTATATGATTAATTGAGGAGTAGG GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGGTTATAAATTAGTACTGCTATCATTCAACCTATATGATTAATTGAGGAGTAGG Template switch alignment (log-probability: -16.3) GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG|CAGTA|CTATCATTCAACCTATATGATTAATTGAGGAGTAGG GTTAAAGCAAATAATCAGGTTTAGAATAGTAATGCTTGGG|CAGTA|CTATCATTCAACCTATATGATTAATTGAGGAGTAGG ========= Event 229 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ttgcTAAATATGTCAAAGGAACAGAGAATTGTCAATCTCTGTTAGCAAAGTGATTTTCCTAAGT Chimp: TTGCTAAATATGTCAAAGGAACAGAGAATTGTCAATCTCTGTTAGCAAAGTGATTTTCCTAAGT ↑ 3 1 2 4 Gorilla: TTGCTAAATATGTCAAAGGAACAGAGAA-TGAC--------AGAGCAAAGTGATTTTCCTAAGT ↓ 3 1 2 4 Human: ttgcTAAATATGTCAAAGGAACAGAGAATTGTCAATCTCTGTTAGCAAAGTGATTTTCCTAAGT Cluster: [ ] Orangutan: ttgcTAAATATGTCAAAGGAACAGAGAA-TGAC--------AGAGCAAAGTGATTTTCCTAAGT Gorilla > Human --------------- chr11:30841958-30841971 Template switch process: F1: L GTGTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAT 1 F3: 4 AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA R RF: ATGTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAATGACAGAGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA RR: TACATTATTTAAAAACGATTTATACAGTTTCCTTGTCTCTTACTGTCTCGTTTCACTAAAAGGATTCATGTAAGGAAGAACGGTGGT F2: 3 TTGTCTCTAACTGT 2 Unidirectional alignment (log-probability: -46.5) GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAttgtcaatctctgtT-----AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAA--------------TGACAGAGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA Template switch alignment (log-probability: -28.6) GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAT|TGTCAaTCTCTGTT|AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAT|TGTCATTCTCTGTT|AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA Gorilla > Chimp --------------- chr11:31248161-31248174 Template switch process: F1: L ATGTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAT 1 F3: 4 AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA R RF: ATGTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAATGACAGAGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA RR: TACATTATTTAAAAACGATTTATACAGTTTCCTTGTCTCTTACTGTCTCGTTTCACTAAAAGGATTCATGTAAGGAAGAACGGTGGT F2: 3 TTGTCTCTAACTGT 2 Unidirectional alignment (log-probability: -41) GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAttgtcaatctctgtT-----AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAA--------------TGACAGAGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA Template switch alignment (log-probability: -23.1) GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAT|TGTCAaTCTCTGTT|AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA GTAATAAATTTTTGCTAAATATGTCAAAGGAACAGAGAAT|TGTCATTCTCTGTT|AGCAAAGTGATTTTCCTAAGTACATTCCTTCTTGCCACCA ========= Event 230 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTACCTAAGGGAAAACATTAGA ↓ 1 4 3 2 Chimp: TTCATTTCTGCCAGTAGTCACACTA------TGTGTAGTGCACATAGTACCTAAGGGAAAACATTAGA ↑ 1 4 3 2 Gorilla: TTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTAGCTAAGGGAAAACATTAGA Human: TTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTACCTAAGGGAAAACATTAGA Cluster: [ ] Orangutan: TTCATTTCTGCCAGTGGTCACTCTGTCCATAGTTGTAGTGCACATAGTACCTAAGGGAAAACATTAGA Human > Chimp ------------- chr11:31625117-31625123 Template switch process: F1: L TCCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCAC 1 F3: 4 GTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT R RF: TCCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT RR: AGGGTCTTAAGAGTGTACCCAAGTAAAGACGGTCATCAGTGAGACAGGTATCAACATCACGTGTATCATGGATTCCCTTTTGTAATCTTTTTA F2: 3 TGTATCA 2 Unidirectional alignment (log-probability: -29.3) CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCACaC------TAtgTGTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT Template switch alignment (log-probability: -16.1) CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCAC|ACTATGT|GTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCAC|ACTATGT|GTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT Gorilla > Chimp --------------- chr11:31625117-31625123 Template switch process: F1: L TCCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCAC 1 F3: 4 GTAGTGCACATAGTACCTAAGGGAAAACATTAGAAAAAT R RF: TCCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTAGCTAAGGGAAAACATTAGAAAAAT RR: AGGGTCTTAAGAGTGTACCCAAGTAAAGACGGTCATCAGTGAGACAGGTATCAACATCACGTGTATCATCGATTCCCTTTTGTAATCTTTTTA F2: 3 TGTATCA 2 Unidirectional alignment (log-probability: -33.4) CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCACaC------TAtgTGTAGTGCACATAGTAcCTAAGGGAAAACATTAGAAAAAT CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCACTCTGTCCATAGTTGTAGTGCACATAGTAGCTAAGGGAAAACATTAGAAAAAT Template switch alignment (log-probability: -22.1) CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCAC|ACTATGT|GTAGTGCACATAGTAcCTAAGGGAAAACATTAGAAAAAT CCCAGAATTCTCACATGGGTTCATTTCTGCCAGTAGTCAC|ACTATGT|GTAGTGCACATAGTAGCTAAGGGAAAACATTAGAAAAAT ========= Event 231 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTTTGGTAACGGTCCTTTGGAAC---TCTGTTCTACTCTTGTACTCACTCTG Chimp: TCTTTGGTAACGGTCCTTTGGAAC---TCTGTTCTACTCTTGTACTCACTCTG Gorilla: TCTTTGGTAACGGTCCTTTGGTAGTACAGAGTTCTACTCTTGTACTCACTCTG ↓ 1 3 42 Human: TCTTTGGTAACGGTCCTTTGGAAC---TCTGTTCTACTCTTGTACTCACTCTG Cluster: [ ] Orangutan: TCTTTGGTAACGGTCCTTTGGAAC---TCTGTTCTACTCTTGTACTCGCTCTG Gorilla > Human --------------- chr11:31100276-31100282 Template switch process: F1: L TTAAGTTTTTCAATCAGGTATCTTTGGTAACGGTCCTTTGG 1 F3: 4 TTCTACTCTTGTACTCACTCTGGCTCTAAGGAGACCTAG R RF: TTAAGTTTTTCGATCAGTTATCTTTGGTAACGGTCCTTTGGTAGTACAGAGTTCTACTCTTGTACTCACTCTGGCTCTAAGGAGACCTAG RR: AATTCAAAAAGCTAGTCAATAGAAACCATTGCCAGGAAACCATCATGTCTCAAGATGAGAACATGAGTGAGACCGAGATTCCTCTGGATC F2: 3 GTCTCAA 2 Unidirectional alignment (log-probability: -39.3) TAAGTTTTTCaATCAGgTATCTTTGGTAACGGTCCTTTGGaactcT--------GTTCTACTCTTGTACTCACTCTGGCTCTAAGGAGACCTAG TAAGTTTTTCGATCAGTTATCTTTGGTAACGGTCCTTTGG-----TAGTACAGAGTTCTACTCTTGTACTCACTCTGGCTCTAAGGAGACCTAG Template switch alignment (log-probability: -27.6) TAAGTTTTTCaATCAGgTATCTTTGGTAACGGTCCTTTGG|AACTCTG|TTCTACTCTTGTACTCACTCTGGCTCTAAGGAGACCTAG TAAGTTTTTCGATCAGTTATCTTTGGTAACGGTCCTTTGG|AACTCTG|TTCTACTCTTGTACTCACTCTGGCTCTAAGGAGACCTAG ========= Event 232 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 124 Detected in comparisons: 1234 Multiple sequence alignment: Human: CACATTGTCAAAAAATA-----AAATATGCATATTTTGTGTGCATACAACACACTTTC ↓ 13 42 ↑ 1 3 24 Chimp: CACATTGTCaaaaaataaaacaaaaTATGCAT---ATGTGTGCATACAACACACTTTC Gorilla: CACATTGTCaaaaaataaaacaaaaTATGCAT---ATGTGTGCATACAACACACTTTC ↑ 13 42 Human: CACATTGTCAAAAAATA-----AAATATGCATATTTTGTGTGCATACAACACACTTTC Cluster: [ ] Orangutan: CGCATTGTCAAAAAATAAAACAAAATATGCAT---ATGTGTGCATACAACATGCTTTC Chimp > Human ------------- chr11:104855126-104855136 Template switch process: F1: L GTGTATTTTCACATTGTCAAAAAATAAAA 1 F3: 4 TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA R RF: GTGTATTTTCACATTGTCAAAAAATAAAACAAAATATGCATATGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA RR: CACATAAAAGTGTAACAGTTTTTTATTTTGTTTTATACGTATACACACGTATGTTGTGTGAAAGATTATCGTTGACTTGTGT F2: 3 TTTATACGTAT 2 Unidirectional alignment (log-probability: -25.7) GTGTATTTTCACATTGTCAAAAAAT-----AAAATATGCATAtttTGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA GTGTATTTTCACATTGTCAAAAAATAAAACAAAATATGCATA---TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA Template switch alignment (log-probability: -16.4) GTGTATTTTCACATTGTCAAAAAATAAAA|TATGCATATTT|TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA GTGTATTTTCACATTGTCAAAAAATAAAA|TATGCATATTT|TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA Human > Chimp ------------- chr11:105129103-105129115 Template switch process: F1: L GTGTATTTTCACATTGTCAAAAAATAAAA 1 F3: 4 TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA R RF: GTGTATTTTCACATTGTCAAAAAATAAAATATGCATATTTTGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA RR: CACATAAAAGTGTAACAGTTTTTTATTTTATACGTATAAAACACACGTATGTTGTGTGAAAGATTATCGTTGACTTGTGT F2: 3 ATACGTATAAAAC 2 Unidirectional alignment (log-probability: -28.4) GTGTATTTTCACATTGTCAAAAAATaaaacAAAATATGCATA---TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA GTGTATTTTCACATTGTCAAAAAAT-----AAAATATGCATATTTTGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA Template switch alignment (log-probability: -16.7) GTGTATTTTCACATTGTCAAAAAATAAAA|CAAAATATGCATA|TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA GTGTATTTTCACATTGTCAAAAAATAAAA|CAAAATATGCATA|TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA Human > Gorilla --------------- chr11:104608369-104608381 Template switch process: F1: L GGGTATTTTCACATTGTCAAAAAATAAAA 1 F3: 4 TGTGTGCATACAACACACTTTCTAATAGCAGCTGAACACA R RF: GTGTATTTTCACATTGTCAAAAAATAAAATATGCATATTTTGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA RR: CACATAAAAGTGTAACAGTTTTTTATTTTATACGTATAAAACACACGTATGTTGTGTGAAAGATTATCGTTGACTTGTGT F2: 3 ATACGTATAAAAC 2 Unidirectional alignment (log-probability: -39) GgGTATTTTCACATTGTCAAAAAATaaaacAAAATATGCATA---TGTGTGCATACAACACACTTTCTAATAGCAgCTGAACACA GTGTATTTTCACATTGTCAAAAAAT-----AAAATATGCATATTTTGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA Template switch alignment (log-probability: -28.1) GgGTATTTTCACATTGTCAAAAAATAAAA|CAAAATATGCATA|TGTGTGCATACAACACACTTTCTAATAGCAgCTGAACACA GTGTATTTTCACATTGTCAAAAAATAAAA|CAAAATATGCATA|TGTGTGCATACAACACACTTTCTAATAGCAACTGAACACA ========= Event 233 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: atgaaaaTATTGGGTAACCCAATTCAAGTATTGAATTCAATACTTGAACAATTC-----------------------------AAGTATTGTTATCTGCTTATGTATAAAAGA Chimp: atgaaaaTATTGGGTAACCcaattcaagtattgaattcaatacttgaacaattcaagtattgaattcaatacttgaacaattcaagtattgTTATCTGCTTATGTATAAAAGA Gorilla: atgaaaaTATTGGGTAACCCAATTCA----------------------------------------------------------AGTATTGTTATCTGCTTATGTATAAAAGA ↓ 4 3 2 1 Human: atgaaaaTATTGGGTAACCCAATTCAAGTATTGAATTCAATACTTGAACAATTC-----------------------------AAGTATTGTTATCTGCTTATGTATAAAAGA Cluster: [ ] Orangutan: atgaaaaTATTGGGTAACCCAATTCA----------------------------------------------------------AGTATTGTTATCTGCTTATGTATAAAAGA Gorilla > Human --------------- chr11:114477787-114477797 Template switch process: F1: L ATAAAATTCTAGAACATGAAAATATTGGGTAACCCAATTCAAGTATTGAATT 1 F3: 4 CAATTCAAGTATTGTTATCTGCTTATGTATAAAAGAAAAAGAATCCC R RF: ATAAAATTCTAGAACATGAAAATATTGGGTAACCCAATTCAAGTATTG--TTATCTGCTTATGTATAAAAGAAAAAGAATCCC RR: TATTTTAAGATCTTGTACTTTTATAACCCATTGGGTTAAGTTCATAAC--AATAGACGAATACATATTTTCTTTTTCTTAGGG F2: 3 AAGTTCATAAC 2 Unidirectional alignment (log-probability: -52.6) AACATGAAAATATTGGGTAACCCAATTcaagtattgaattcaatacttgaacaattCAAGTATTGTTATCTGCTTATGTATAAAAGAAAAA AACATGAAAATATTGGGTAACCCAATT-----------------------------CAAGTATTGTTATCTGCTTATGTATAAAAGAAAAA Template switch alignment (log-probability: -30.1) AACATGAAAATATTGGGTAACCCAATTCAAGTATTGaaTT|CAATACTTGAA|CAATTCAAGTATTGTTATCTGCTTATGTATAAAAGAAAAA AACATGAAAATATTGGGTAACCCAATTCAAGTATTG--TT|CAATACTTGAA|CAATTCAAGTATTGTTATCTGCTTATGTATAAAAGAAAAA ========= Event 234 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGACGGGAGAATCTCCTACTTTACAGAATCAATAACTGTAGTT--------ATACTGTCATGTCATTTTTAAACAGTTTC Chimp: AGACGGGAGAATCTCCTACTTGAGAGT----ATAACTACAGTT----ATTGATTCTGTAATGTCATTTTTAAACAGTTTC Gorilla: AGACGGGAGAATCTCCTACTTGACAGT----ATAACTACAGTTATTG----ATTCTGTAATGTCATTTTTAAACAGTTTC ↓ 13 24 ↑ 13 24 Human: AGACGGGAGAATCTCCTACTTTACAGAATCAATAACTGTAGTT--------ATACTGTCATGTCATTTTTAAACAGTTTC Cluster: [ ] Orangutan: AGACAGGAGACTCTCCTACTTGACAGT----ATAA-CACAGTTATTG----ATTCTGTAACATCATTTTTAAACAGTTTC Gorilla > Human --------------- chr11:106805772-106805801 Template switch process: F1: L TAACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTT 1 F3: 4 ATGTCATTTTTAAACAGTTTCCACTCTTTGTTTCTATCAT R RF: TAACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTTGACAGTATAACTACAGTTATTGATTCTGTAATGTCATTTTTAAACAGTTTCCACCCTTTGTTTCTATCAT RR: ATTGTTTCTCTTTTCTACCGTCTGCCCTCTTAGAGGATGAACTGTCATATTGATGTCAATAACTAAGACATTACAGTAAAAATTTGTCAAAGGTGGGAAACAAAGATAGTA F2: 3 CTGTCATATTGATGTCAATAACTAAGACAT 2 Unidirectional alignment (log-probability: -61.2) AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTTtACAGaatcaataactgtagtTATA----------------CTGTcATGTCATTTTTAAACAGTTTCCACtCTTTGTTTCTATCAT AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTTGACAG----------------TATAACTACAGTTATTGATTCTGTAATGTCATTTTTAAACAGTTTCCACCCTTTGTTTCTATCAT Template switch alignment (log-probability: -25.1) AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTT|TACAGAATCAATAACTGTAGTTATACTGTC|ATGTCATTTTTAAACAGTTTCCACtCTTTGTTTCTATCAT AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTT|TACAGAATCAATAACTGTAGTTATACTGTC|ATGTCATTTTTAAACAGTTTCCACCCTTTGTTTCTATCAT Human > Gorilla --------------- chr11:106635854-106635883 Template switch process: F1: L TAACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTT 1 F3: 4 ATGTCATTTTTAAACAGTTTCCACCCTTTGTTTCTATCAT R RF: TAACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTTTACAGAATCAATAACTGTAGTTATACTGTCATGTCATTTTTAAACAGTTTCCACTCTTTGTTTCTATCAT RR: ATTGTTTCTCTTTTCTACCGTCTGCCCTCTTAGAGGATGAAATGTCTTAGTTATTGACATCAATATGACAGTACAGTAAAAATTTGTCAAAGGTGAGAAACAAAGATAGTA F2: 3 ATGTCTTAGTTATTGACATCAATATGACAG 2 Unidirectional alignment (log-probability: -61.2) AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTTgACAG----------------TATAactacagttattgattCTGTaATGTCATTTTTAAACAGTTTCCACcCTTTGTTTCTATCAT AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTTTACAGAATCAATAACTGTAGTTATA----------------CTGTCATGTCATTTTTAAACAGTTTCCACTCTTTGTTTCTATCAT Template switch alignment (log-probability: -25.1) AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTT|GACAGTATAACTACAGTTATTGATTCTGTA|ATGTCATTTTTAAACAGTTTCCACcCTTTGTTTCTATCAT AACAAAGAGAAAAGATGGCAGACGGGAGAATCTCCTACTT|GACAGTATAACTACAGTTATTGATTCTGTA|ATGTCATTTTTAAACAGTTTCCACTCTTTGTTTCTATCAT ========= Event 235 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: AATAGCTCAGAATTTGCTAGTAGACCTTAGCCATCTCACCTACAAAACCATTAT---TGTCTACCCCTCTATGACCCCGGATCCT Chimp: ------------------------------------------------------------------------------------- Gorilla: AATAACTCAGAATTTGCTAGTAGACCTTAGCAATCTCACCTACAAAACCATTAT------TTGTCCCTCTATGACCCCGGatcct ↓ 3 2 1 4 Human: AATAGCTCAGAATTTGCTAGTAGACCTTAGCCATCTCACCTACAAAACCATTAT---TGTCTACCCCTCTATGACCCCGGATCCT Cluster: [ ] Orangutan: AATAACTCAGAATTTGCTAGTAGACCTTAGCAATCTCACCTACAAAACCATTATTGT---CTGTCCCTCTATGACCCCGGATCCT Gorilla > Human --------------- chr11:20507899-20507904 Template switch process: F1: L TTGCTAGTAGACCTTAGCCATCTCACCTACAAAACCATTATT 1 F3: 4 CCCTCTATGACCCCGGATCCTGGCTCTCATCACTGAGAGA R RF: TTGCTAGTAGACCTTAGCAATCTCACCTACAAAACCATTATTTGTCCCTCTATGACCCCGGATCCTGGCTCTCATCACTGAGAGA RR: AACGATCATCTGGAATCGTTAGAGTGGATGTTTTGGTAATAAACAGGGAGATACTGGGGCCTAGGACCGAGAGTAGTGACTCTCT F2: 3 CATCTG 2 Unidirectional alignment (log-probability: -31.8) GCTAGTAGACCTTAGCcATCTCACCTACAAAACCATTATTgtcTacCCCTCTATGACCCCGGATCCTGGCTCTCATCACTGAGAGA GCTAGTAGACCTTAGCAATCTCACCTACAAAACCATTATT---TGTCCCTCTATGACCCCGGATCCTGGCTCTCATCACTGAGAGA Template switch alignment (log-probability: -22) GCTAGTAGACCTTAGCcATCTCACCTACAAAACCATTATT|GTCTAC|CCCTCTATGACCCCGGATCCTGGCTCTCATCACTGAGAGA GCTAGTAGACCTTAGCAATCTCACCTACAAAACCATTATT|GTCTAC|CCCTCTATGACCCCGGATCCTGGCTCTCATCACTGAGAGA ========= Event 236 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGACACTGATATAATGATAGTTATATCATAGCAGTAATCTCTGCCACACTGGTATATAATGATATAACTATCATTATATACCAGtgtggcagagattactgctgttcaatcttcctccaaaac ↑ 3 4 1 2 Chimp: AGACACTGATATAATGATAGTTATA---------------------------------------------TCATTATATACCAGtgtggcagagattactgctgttcaatcttcctccaaaac Gorilla: AGACACTGATATAATGATAGTTATA---------------------------------------------TCATTATATACCAGtgtggcagagattactgctgttcaatcttcctccaaaac ↓ 3 4 1 2 Human: AGACACTGATATAATGATAGTTATATCATAGCAGTAATCTCTGCCACACTGGTATATAATGATATAACTATCATTATATACCAGtgtggcagagattactgctgttcaatcttcctccaaaac Cluster: [ ] Orangutan: Chimp > Human ------------- chr11:10753302-10753340 Template switch process: F1: L ATTGATGATAATTGGCAGACACTGATATAATGATAGTTATATCAT 1 F3: 4 TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCAAT R RF: ATTGATGATAATTGGCAGACACTGATATAATGATAGTTATATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCAAT RR: TAACTACTATTAACCGTCTGTGACTATATTACTATCAATATAGTAATATATGGTCACACCGTCTCTAATGACGACAAGTTA F2: 3 CAATATAGTAATATATGGTCACACCGTCTCTAATGACGA 2 Unidirectional alignment (log-probability: -75.6) TGATAATTGGCAGACACTGATATAATGATAGTTAtatcatagcagtaatctctgccacactggtatataatgatataacTATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA TGATAATTGGCAGACACTGATATAATGATAGTTA---------------------------------------------TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA Template switch alignment (log-probability: -20.2) TGATAATTGGCAGACACTGATATAATGATAGTTATATCAT|AGCAGTAATCTCTGCCACACTGGTATATAATGATATAAC|TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA TGATAATTGGCAGACACTGATATAATGATAGTTATATCAT|AGCAGTAATCTCTGCCACACTGGTATATAATGATATAAC|TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA Gorilla > Human --------------- chr11:10753302-10753340 Template switch process: F1: L ATTGATGATAATTGGCAGACACTGATATAATGATAGTTATATCAT 1 F3: 4 TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCAAT R RF: ATTGATGATCATTGGCAGACACTGATATAATGATAGTTATATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCAAT RR: TAACTACTAGTAACCGTCTGTGACTATATTACTATCAATATAGTAATATATGGTCACACCGTCTCTAATGACGACAAGTTA F2: 3 CAATATAGTAATATATGGTCACACCGTCTCTAATGACGA 2 Unidirectional alignment (log-probability: -81.1) TGATaATTGGCAGACACTGATATAATGATAGTTAtatcatagcagtaatctctgccacactggtatataatgatataacTATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA TGATCATTGGCAGACACTGATATAATGATAGTTA---------------------------------------------TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA Template switch alignment (log-probability: -26.3) TGATaATTGGCAGACACTGATATAATGATAGTTATATCAT|AGCAGTAATCTCTGCCACACTGGTATATAATGATATAAC|TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA TGATCATTGGCAGACACTGATATAATGATAGTTATATCAT|AGCAGTAATCTCTGCCACACTGGTATATAATGATATAAC|TATCATTATATACCAGTGTGGCAGAGATTACTGCTGTTCA ========= Event 237 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: aaaa-------a--aaaaaaaaaGCTATC----------TTTTAAATTTCCCTTGGggctg Chimp: aaaa--------aaaaaaaaaaaGCTATC-----TTTTCTTTTAAATTTCCCTTGGggctg Gorilla: aaaa-----aaa--aaaaaaaaaGCTATCTTTTC-----TTTTAAATTTCCCTTGGGGCTG ↑ 3 1 4 2 Human: aaaa-------a--aaaaaaaaaGCTATC----------TTTTAAATTTCCCTTGGggctg Cluster: [ ] Orangutan: aaaaaaaaa--a--aaaaaaaaaGCTATCTTTTC-----TTTTAAATTTCCCTTGGggctg Human > Gorilla --------------- chr11:18069613-18069624 Template switch process: F1: L TTAGAGTGCTAGAGCTTAAAAAAAAAAAAAAAA 1 F3: 4 CTTTTAAATTTCCCTTGGGGCTGGGCACAGTGGCC R RF: TTAGAGTGCTAGAGCTTAAAAAAAAAAAAAAAAGCTATCTTTTAAATTTCCCTTGGGGCTGGGCACAGTGGCC RR: AATCTCACGATCTCGAATTTTTTTTTTTTTTTTCGATAGAAAATTTAAAGGGAACCCCGACCCGTGTCACCGG F2: 3 TTTTCTATCGAA 2 Unidirectional alignment (log-probability: -37.6) TTAGAGTGCTAGAGCTTAAAAAAAAAAAAaaAAAAGCTAtctttTCTTTTAAATTTCCCTTGGGGCTGGGCACAGTGGCC------ TTAGAGTGCTAGAGCTTAAAAAAAAAAAA--AAAAGCTA-----TCTTTTAAATTTCCCTTGGGGCTGGGCACAGTGGCCCATGCC Template switch alignment (log-probability: -28) TTAGAGTGCTAGAGCTTAAAAAAAAAAAAAAAA|AAGcTAtCTTTT|CTTTTAAATTTCCCTTGGGGCTGGGCACAGTGGCC TTAGAGTGCTAGAGCTTAAAAAAAAAAAAAAAA|AAGATAGCTTTT|CTTTTAAATTTCCCTTGGGGCTGGGCACAGTGGCC ========= Event 238 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTACATTCAACCCCTCCATTGTCCAGTGGCTGGACAGGGCCACTGGTCATTCTTTA Chimp: TCCTACATTCAACCCCTCCATG--AGAAAGGCTGGACAGGGCCACTGGTCATTCTTTA Gorilla: TCCTACATTCAACCCCTCCATG--AGAAAGGCTGGACAGGGCCACTGGTCATTCTTTA ↓ 1 4 3 2 Human: TCCTACATTCAACCCCTCCATTGTCCAGTGGCTGGACAGGGCCACTGGTCATTCTTTA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr11:123647504-123647510 Template switch process: F1: L CTTATCATCTTCTTAGGATCTCCTACATTCAACCCCTCCAT 1 F3: 4 TGGCTGGACAGGGCCACTGGTCATTCTTTAAAATTACTAGA R RF: CTTATCACCTTCTTAGGATCTCCTACATTCAACCCCTCCATGAGAAAGGCTGGACAGGGCCACTGGTCATTCTTTAAAATTACTAGA RR: GAATAGTGGAAGAATCCTAGAGGATGTAAGTTGGGGAGGTACTCTTTCCGACCTGTCCCGGTGACCAGTAAGAAATTTTAATGATCT F2: 3 GACCTGT 2 Unidirectional alignment (log-probability: -38) TTATCAtCTTCTTAGGATCTCCTACATTCAACCCCTCCAT------tgtccagtGGCTGGACAGGGCCACTGGTCATTCTTTAAAATTACTAG TTATCACCTTCTTAGGATCTCCTACATTCAACCCCTCCATGAGAAA--------GGCTGGACAGGGCCACTGGTCATTCTTTAAAATTACTAG Template switch alignment (log-probability: -27.7) TTATCAtCTTCTTAGGATCTCCTACATTCAACCCCTCCAT|TGTCCAG|tGGCTGGACAGGGCCACTGGTCATTCTTTAAAATTACTAG TTATCACCTTCTTAGGATCTCCTACATTCAACCCCTCCAT|TGTCCAG|AGGCTGGACAGGGCCACTGGTCATTCTTTAAAATTACTAG ========= Event 239 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: GGTATGATAATGATAACTTGTTTTGACTTGAATAAAG-TACTACATCAGTGTGGAAAAAAATT ↓ 13 24 ↑ 13 24 Chimp: GGTATGATAATGATAACTTGTAG-TACTTTATTCAAGTCAAAACATCAGTGTGGaaaaaaaTT Gorilla: Human: GGTATGATAATGATAACTTGTTTTGACTTGAATAAAG-TACTACATCAGTGTGGAAAAAAATT Cluster: [ ] Orangutan: Chimp > Human ------------- chr11:121307998-121308017 Template switch process: F1: L ATGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT 1 F3: 4 ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT R RF: ATGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGTAGTACTTTATTCAAGTCAAAACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT RR: TACCAATTAAGAAGTTGCAACCATACTATTACTATTGAACATCATGAAATAAGTTCAGTTTTGTAGTCACACCTTTTTTTAAGACTATGTAATCGTCGATA F2: 3 TCATGAAATAAGTTCAGTTT 2 Unidirectional alignment (log-probability: -42) TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGTtttgacttgaataaAGTACT--------------ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT--------------AGTACTTTATTCAAGTCAAAACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT Template switch alignment (log-probability: -17.8) TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT|TTTGACTTGAATAAAGTACT|ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT|TTTGACTTGAATAAAGTACT|ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT Human > Chimp ------------- chr11:121788725-121788744 Template switch process: F1: L ATGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT 1 F3: 4 ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT R RF: ATGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGTTTTGACTTGAATAAAGTACTACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT RR: TACCAATTAAGAAGTTGCAACCATACTATTACTATTGAACAAAACTGAACTTATTTCATGATGTAGTCACACCTTTTTTTAAGACTATGTAATCGTCGATA F2: 3 AAACTGAACTTATTTCATGA 2 Unidirectional alignment (log-probability: -42) TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT--------------AGTACTttattcaagtcaaaACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGTTTTGACTTGAATAAAGTACT--------------ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT Template switch alignment (log-probability: -17.8) TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT|AGTACTTTATTCAAGTCAAA|ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT TGGTTAATTCTTCAACGTTGGTATGATAATGATAACTTGT|AGTACTTTATTCAAGTCAAA|ACATCAGTGTGGAAAAAAATTCTGATACATTAGCAGCTAT ========= Event 240 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AGATCTATATAGATT-TTTTTGAGGCATTTCTATGTCAGGAGCTATCTAAGCCTCATCTAAAAATGTTGTTTTCCT ↓ 1 4 2 Chimp: AGATCTATATAGAttttttttGAGGCAT--------------AGATCTAAGCCTCATCTAAAAATGTTGTTTTCCT Gorilla: ---------------------------------------------------------------------------- Human: AGATCTATATAGATT-TTTTTGAGGCATTTCTATGTCAGGAGCTATCTAAGCCTCATCTAAAAATGTTGTTTTCCT Cluster: [ ] Orangutan: ---------------------------------------------------------------------------- Human > Chimp ------------- chr1:104885012-104885022 Template switch process: F1: L GATTTATTTAAATAGATCTATATAGATTTTTTT 1 F3: 4 TCTAAGCCTCATCTAAAAATGTTGTTTTCCTACCTTATG R RF: GATTTATTTAAATAGATCTATATAGATTTTTTTGAGGCATTTCTATGTCAGGAGCTATCTAAGCCTCATCTAAAAATGTTGTTTTCCTACCTTATG RR: CTAAATAAATTTATCTAGATATATCTAAAAAAACTCCGTAAAGATACAGTCCTCGATAGATTCGGAGTAGATTTTTACAACAAAAGGATGGAATAC F2: 3 AGATACGGAGT 2 Unidirectional alignment (log-probability: -33.5) GATTTATTTAAATAGATCTATATAGAtTTTTTTTGAGGCAT------------AG--ATCTAAGCCTCATCTAAAAATGTTGTTTTCCTACCTTATG GATTTATTTAAATAGATCTATATAGA-TTTTTTTGAGGCATTTCTATGTCAGGAGCTATCTAAGCCTCATCTAAAAATGTTGTTTTCCTACCTTATG Template switch alignment (log-probability: -22.5) GATTTATTTAAATAGATCTATATAGATTTTTTT|TGAGGCaTAGA|TCTAAGCCTCATCTAAAAATGTTGTTTTCCTACCTTATG GATTTATTTAAATAGATCTATATAGATTTTTTT|TGAGGCTTAGA|TCTAAGCCTCATCTAAAAATGTTGTTTTCCTACCTTATG ========= Event 241 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCTACTATTCCCAAATCCTGAGCCTGTCACACTATTTCTTGAATGTGACAGGCTCAGGATTTGGGAATAGTAGA Chimp: TCTACTATTCCCAAATCCTGAGCCTGTCACACTATTTCTTGAGTGTGACAGGCTCAGGATTTGGGAATAGTAGA ↓ 13 24 ↑ 1 3 4 2 Gorilla: TCTACTATTCCCAAATCCTGGGCCTGTCACACTCAAGAAATAGTGTGACAGGCTCAGGATTTGGGAATAGTAGA ↓ 1 3 4 2 ↑ 31 2 4 Human: TCTACTATTCCCAAATCCTGAGCCTGTCACACTATTTCTTGAATGTGACAGGCTCAGGATTTGGGAATAGTAGA Cluster: [ ] Orangutan: TCTACTATTCCCAAATCCTGAGCCTGTCACACTATTTCTTGAGTGTGACAGGCTCAGGATTTGGGAATAGCAGA Gorilla > Human --------------- chr1:112451354-112451374 Template switch process: F1: L CTGTCACATCTACTATTCCCAAATCCTG 1 F3: 4 AATGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA R RF: CTGTCACATCTACTATTCCCAAATCCTGGGCCTGTCACACTCAAGAAATAGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA RR: GACAGTGTAGATGATAAGGGTTTAGGACCCGGACAGTGTGAGTTCTTTATCACACTGTCCGAGTCCTAAACCCTTATCATCTACACTGTCT F2: 3 GTTCTTTATCACACTGTCCGA 2 Unidirectional alignment (log-probability: -40.7) CTGTCACATCTACTATTCCCAAATCCTGaGCCTGTCACACT------ATttcttgAaTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA CTGTCACATCTACTATTCCCAAATCCTGGGCCTGTCACACTCAAGAAAT------AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA Template switch alignment (log-probability: -23.7) CTGTCACATCTACTATTCCCAAATCCTG|AGCCTGTCACACTATTTCTTG|AaTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA CTGTCACATCTACTATTCCCAAATCCTG|AGCCTGTCACACTATTTCTTG|AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA Human > Gorilla --------------- chr1:113859331-113859340 Template switch process: F1: L CTGTCACATCTACTATTCCCAAATCCTGGGCCTGTCACACT 1 F3: 4 TGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA R RF: CTGTCACATCTACTATTCCCAAATCCTGAGCCTGTCACACTATTTCTTGAATGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA RR: GACAGTGTAGATGATAAGGGTTTAGGACTCGGACAGTGTGATAAAGAACTTACACTGTCCGAGTCCTAAACCCTTATCATCTACACTGTCT F2: 3 GATAAAGAAC 2 Unidirectional alignment (log-probability: -40.7) TGTCACATCTACTATTCCCAAATCCTGgGCCTGTCACACTcaagaaAT------AgTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA TGTCACATCTACTATTCCCAAATCCTGAGCCTGTCACACT------ATTTCTTGAATGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA Template switch alignment (log-probability: -22.5) TGTCACATCTACTATTCCCAAATCCTGgGCCTGTCACACT|CAAGAAATAG|TGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA TGTCACATCTACTATTCCCAAATCCTGAGCCTGTCACACT|CAAGAAATAG|TGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACAGA Gorilla > Chimp --------------- chr1:104930638-104930658 Template switch process: F1: L CTGTCACATCTACTATTCCCAAATCCTG 1 F3: 4 AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA R RF: CTGTCACATCTACTATTCCCAAATCCTGGGCCTGTCACACTCAAGAAATAGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA RR: GACAGTGTAGATGATAAGGGTTTAGGACCCGGACAGTGTGAGTTCTTTATCACACTGTCCGAGTCCTAAACCCTTATCATCTACACTGT F2: 3 GTTCTTTATCACACTGTCCGA 2 Unidirectional alignment (log-probability: -35.1) CTGTCACATCTACTATTCCCAAATCCTGaGCCTGTCACACT------ATttcttgAGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA CTGTCACATCTACTATTCCCAAATCCTGGGCCTGTCACACTCAAGAAAT------AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA Template switch alignment (log-probability: -18.1) CTGTCACATCTACTATTCCCAAATCCTG|AGCCTGTCACACTATTTCTTG|AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA CTGTCACATCTACTATTCCCAAATCCTG|AGCCTGTCACACTATTTCTTG|AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA Chimp > Gorilla --------------- chr1:113859331-113859338 Template switch process: F1: L CTGTCACATCTACTATTCCCAAATCCTGGGCCTGTCACACT 1 F3: 4 AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA R RF: CTGTCACATCTACTATTCCCAAATCCTGAGCCTGTCACACTATTTCTTGAGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA RR: GACAGTGTAGATGATAAGGGTTTAGGACTCGGACAGTGTGATAAAGAACTCACACTGTCCGAGTCCTAAACCCTTATCATCTACACTGT F2: 3 TAAAGAAC 2 Unidirectional alignment (log-probability: -35.1) TGTCACATCTACTATTCCCAAATCCTGgGCCTGTCACACTcaagaaAT------AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA TGTCACATCTACTATTCCCAAATCCTGAGCCTGTCACACT------ATTTCTTGAGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA Template switch alignment (log-probability: -22.3) TGTCACATCTACTATTCCCAAATCCTGgGCCTGTCACACT|CAAGAAAT|AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA TGTCACATCTACTATTCCCAAATCCTGAGCCTGTCACACT|CAAGAAAT|AGTGTGACAGGCTCAGGATTTGGGAATAGTAGATGTGACA ========= Event 242 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAGGCTTGGCCTGAGTGCCATGCCAGT----ACTTTGTACTTTGTGgaggtgacatg ↓ 1 3 4 2 Chimp: ttaggCTTGGCCTGAGTGCCAC-AAAGTACTGACTTTGTACTTTGTGgaggtgacatg ↑ 1 3 4 2 Gorilla: ttaggCTTGGCCTGAGTGCCATGCCAGT----ACTTTGTACTTTGTGgaggtgacatg Human: TTAGGCTTGGCCTGAGTGCCATGCCAGT----ACTTTGTACTTTGTGgaggtgacatg Cluster: [ ] Orangutan: TTAGGCTTGGCCTGAGTGCCATGCCAGT----GCTTTGTACTTTGTGgaggtgacatg Human > Chimp ------------- chr11:20981611-20981620 Template switch process: F1: L TAACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA 1 F3: 4 ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA R RF: TAACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCATGCCAGTACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA RR: ATTGTCCGACCTTTGTATCGAATCCGAACCGGACTCACGGTACGGTCATGAAACATGAAACACCTCCACTGTACTACATGGTGTTTGT F2: 3 GTCATGAAAC 2 Unidirectional alignment (log-probability: -32.9) AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCAcaaagtacTG-----ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA--------TGCCAGTACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA Template switch alignment (log-probability: -16.5) AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA|CAAAGTACTG|ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA|CAAAGTACTG|ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA Gorilla > Chimp --------------- chr11:20981611-20981620 Template switch process: F1: L TAACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA 1 F3: 4 ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA R RF: TAACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCATGCCAGTACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA RR: ATTGTCCGACCTTTGTATCGAATCCGAACCGGACTCACGGTACGGTCATGAAACATGAAACACCTCCACTGTACTACATGGTGTTTGT F2: 3 GTCATGAAAC 2 Unidirectional alignment (log-probability: -32.4) AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCAcaaagtacTG-----ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA--------TGCCAGTACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA Template switch alignment (log-probability: -17) AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA|CAAAGTACTG|ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA AACAGGCTGGAAACATAGCTTAGGCTTGGCCTGAGTGCCA|CAAAGTACTG|ACTTTGTACTTTGTGGAGGTGACATGATGTACCACAAACA ========= Event 243 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GATTATTCTTATAAAACTGCCGCCATTATTATTGTtaacataacaataatatg-ataataataaataatatgataataca---taattcaaattgttattattgttatattaacaataataatgataacaGCAGCCTGGTATGCAC ↓ 1 4 3 2 Chimp: GATTATTCTTATAAAACTGCCATCATTATTATTGTtaatataacaataatatg-at----------aatatgataataaa---taattcaaattgttattattgttatattaacaataataatgataaaaGCAGCCTGGTATGCAC Gorilla: GATTATTCTTATAAAACTGCCATCATTATTATTGTtaatataacaataatatg-ataataataaataatatgataataaa---taattcaaattgttattattgttatattaacaataataatgataaCAGCAGCCTGGTATGCAC Human: GATTATTCTTATAAAACTGCCGCCATTATTATTGTtaacataacaataatatg-ataataataaataatatgataataca---taattcaaattgttattattgttatattaacaataataatgataacaGCAGCCTGGTATGCAC Cluster: [] Orangutan: GATTATTCTTATAAAACTGCCATCATTATTATTGTtaatataacaataatatgaata-------ataatatgataataaataataattcaaattgttattattgttatattaacaataataatgataaaaGCAGCCTAGTATGCAC Human > Chimp ------------- chr11:20495949-20495966 Template switch process: F1: L TTCCAAGTTAAAAAAATAATGATTATTCTTATAAAACTGCC 1 F3: 4 ATAACAATAATATGAT R RF: TTCCAAGTTAAAAAAATAATGATTATTCTTATAAAACTGCCGCCATTATTATTGTTAACATAACAATAATATGATAATAATAAATAATATGATAATACATAATTCAAATTGTTATTATTGTTATATTAACAATAATAATGAT RR: AAGGTTCAATTTTTTTATTACTAATAAGAATATTTTGACGGCGGTAATAATAACAATTGTATTGTTATTATACTATTATTATTTATTATACTATTATGTATTAAGTTTAACAATAATAACAATATAATTGTTATTATTACTA F2: 3 TAATTGTTATTATTACTA 2 Unidirectional alignment (log-probability: -26.3) TCCAAGTTAAAAAAATAATGATTATTCTTATAAAACTGCCatCATTATTATTGTTAAtATAACAATAATATGAT-------- TCCAAGTTAAAAAAATAATGATTATTCTTATAAAACTGCCGCCATTATTATTGTTAACATAACAATAATATGATAATAATAA Template switch alignment (log-probability: -17) TCCAAGTTAAAAAAATAATGATTATTCTTATAAAACTGCC|ATCATTATTATTGTTAAT|ATAACAATAATATGAT TCCAAGTTAAAAAAATAATGATTATTCTTATAAAACTGCC|ATCATTATTATTGTTAAT|ATAACAATAATATGAT ========= Event 244 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAGGCAAGAGCCTGTGATCTCAGGTGACCTCAGGGTCAGGGCCGTGATGGTCCAGGCA ↑ 4 13 2 Chimp: AGAGGCAAGAGCCTGTGATCT----------CAGGGTCAGGGCCGTGATGGTCCAGGCA Gorilla: AGAGGCAAGAGCCTGTGATCTCAGGTGACCTCAGGGTCAGGGCCGTGATGGTCCAGGCA Human: AGAGGCAAGAGCCTGTGATCTCAGGTGACCTCAGGGTCAGGGCCGTGATGGTCCAGGCA Cluster: [ ] Orangutan: AGAGGCAAGAGCCTGTGTTCTCAGGTGACCTCAGGGTCAGGGCTGTGATGATCCAGGCA Chimp > Human ------------- chr11:17011410-17011413 Template switch process: F1: L GAGAGTTGGAAGTCTTGGGCAGAGGCAAGAGCCTGTGATCTCAGG 1 F3: 4 CTCAGGGTCAGGGCCGTGATGGTCCAGGCAGGCACCTCCCCA R RF: GAGAGTTGGAAGTCTTGGGCAGAGGCAAGAGCCTGTGATCTCAGGGTCAGGGCCGTGATGGTCCAGGCAGGCACCTCCCCA RR: CTCTCAACCTTCAGAACCCGTCTCCGTTCTCGGACACTAGAGTCCCAGTCCCGGCACTACCAGGTCCGTCCGTGGAGGGGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -25.3) TTGGAAGTCTTGGGCAGAGGCAAGAGCCTGTGATctcaggtgacCTCAGGGTCAGGGCCGTGATGGTCCAGGCAGGCACCTCCC TTGGAAGTCTTGGGCAGAGGCAAGAGCCTGTGAT----------CTCAGGGTCAGGGCCGTGATGGTCCAGGCAGGCACCTCCC Template switch alignment (log-probability: -15.9) TTGGAAGTCTTGGGCAGAGGCAAGAGCCTGTGATCTCAGG|TGAC|CTCAGGGTCAGGGCCGTGATGGTCCAGGCAGGCACCTCCC TTGGAAGTCTTGGGCAGAGGCAAGAGCCTGTGATCTCAGG|TGAC|CTCAGGGTCAGGGCCGTGATGGTCCAGGCAGGCACCTCCC ========= Event 245 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTTAATACACTGAGCTGATTGTACTTGGTGGTCTAACAAACTT-GCAGATTA-AAATGACAAACTGTTCACTATTGAGTC Chimp: TTTTAATACACTGAGCTGATTATACTTGGTGGTCTAACAAACTT-GCAGATTA-AAATGACAAACTGTTCAGTATTGAGTC ↓ 1 3 42 ↑ 13 24 Gorilla: TTTTAATTCACTGAGCTGATTGTCAT-TTTAATCT-GCAAGTTTGTTAGACCACCAAGTACAAACTGTTCAGTATTGAGTC ↓ 13 24 ↑ 13 24 Human: TTTTAATACACTGAGCTGATTGTACTTGGTGGTCTAACAAACTT-GCAGATTA-AAATGACAAACTGTTCACTATTGAGTC Cluster: [ ] Orangutan: TTTTAATACACTGAGCTGATTGTACT---TGGTCTAACAAACTT-GCAGATTA-AAATGACAAACTGTTGAGTATTGAGTC Gorilla > Human --------------- chr11:25706884-25706917 Template switch process: F1: L AATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATTGT 1 F3: 4 ACAAACTGTTCACTATTGAGTCTGTGAACACAGGGTTATT R RF: AATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATTGTCATTTTAATCTGCAAGTTTGTTAGACCACCAAGTACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT RR: TTAAAACAAGGACCCTTGAAAATTAAGTGACTCGACTAACAGTAAAATTAGACGTTCAAACAATCTGGTGGTTCATGTTTGACAAGTCATAACTCAGACACTTGTGTCCCAATAA F2: 3 GTAAAATTAGACGTTCAAACAATCTGGTGGTTCA 2 Unidirectional alignment (log-probability: -82.3) ATTTTGTTCCTGGGAACTTTTAATaCACTGAGCTGATTGTacttggtggtctaacaaacttgcagattaaaatg----------------------------------ACAAACTGTTCAcTATTGAGTCTGTGAACACAGGGTTATT ATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATTGT----------------------------------CATTTTAATCTGCAAGTTTGTTAGACCACCAAGTACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT Template switch alignment (log-probability: -31.1) ATTTTGTTCCTGGGAACTTTTAATaCACTGAGCTGATTGT|ACTTGGTGGTCTAACAAACTTGCAGATTAAAATG|ACAAACTGTTCAcTATTGAGTCTGTGAACACAGGGTTATT ATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATTGT|ACTTGGTGGTCTAACAAACTTGCAGATTAAAATG|ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT Human > Gorilla --------------- chr11:25933644-25933677 Template switch process: F1: L AATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATTGT 1 F3: 4 ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT R RF: AATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATTGTACTTGGTGGTCTAACAAACTTGCAGATTAAAATGACAAACTGTTCACTATTGAGTCTGTGAACACAGGGTTATT RR: TTAAAACAAGGACCCTTGAAAATTATGTGACTCGACTAACATGAACCACCAGATTGTTTGAACGTCTAATTTTACTGTTTGACAAGTGATAACTCAGACACTTGTGTCCCAATAA F2: 3 TGAACCACCAGATTGTTTGAACGTCTAATTTTAC 2 Unidirectional alignment (log-probability: -82.3) ATTTTGTTCCTGGGAACTTTTAATtCACTGAGCTGATTgtcattttaatctgcaagtttgttagaccaccaaGT----------------------------------ACAAACTGTTCAgTATTGAGTCTGTGAACACAGGGTTATT ATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATT----------------------------------GTACTTGGTGGTCTAACAAACTTGCAGATTAAAATGACAAACTGTTCACTATTGAGTCTGTGAACACAGGGTTATT Template switch alignment (log-probability: -31.1) ATTTTGTTCCTGGGAACTTTTAATtCACTGAGCTGATTGT|CATTTTAATCTGCAAGTTTGTTAGACCACCAAGT|ACAAACTGTTCAgTATTGAGTCTGTGAACACAGGGTTATT ATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATTGT|CATTTTAATCTGCAAGTTTGTTAGACCACCAAGT|ACAAACTGTTCACTATTGAGTCTGTGAACACAGGGTTATT Gorilla > Chimp --------------- chr11:26036489-26036522 Template switch process: F1: L GTAATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATTAT 1 F3: 4 ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT R RF: GTAATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATTGTCATTTTAATCTGCAAGTTTGTTAGACCACCAAGTACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT RR: CATTAAAACAAGGACCCTTGAAAATTAAGTGACTCGACTAACAGTAAAATTAGACGTTCAAACAATCTGGTGGTTCATGTTTGACAAGTCATAACTCAGACACTTGTGTCCCAATAA F2: 3 GTAAAATTAGACGTTCAAACAATCTGGTGGTTCA 2 Unidirectional alignment (log-probability: -89.3) ATTTTGTTCCTGGGAACTTTTAATaCACTGAGCTGATtatacttggtggtctaacaaacttgcagattaaaaTG-----------------------------------ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTatt ATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGAT-----------------------------------TGTCATTTTAATCTGCAAGTTTGTTAGACCACCAAGTACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTT--- Template switch alignment (log-probability: -31.1) ATTTTGTTCCTGGGAACTTTTAATaCACTGAGCTGATTaT|ACTTGGTGGTCTAACAAACTTGCAGATTAAAATG|ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT ATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATTGT|ACTTGGTGGTCTAACAAACTTGCAGATTAAAATG|ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT Chimp > Gorilla --------------- chr11:25933642-25933677 Template switch process: F1: L GTAATTTTGTTCCTGGGAACTTTTAATTCACTGAGCTGATT 1 F3: 4 ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTT R RF: GTAATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATTATACTTGGTGGTCTAACAAACTTGCAGATTAAAATGACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTT RR: CATTAAAACAAGGACCCTTGAAAATTATGTGACTCGACTAATATGAACCACCAGATTGTTTGAACGTCTAATTTTACTGTTTGACAAGTCATAACTCAGACACTTGTGTCCCAA F2: 3 TGAACCACCAGATTGTTTGAACGTCTAATTTTACTG 2 Unidirectional alignment (log-probability: -85.1) TAATTTTGTTCCTGGGAACTTTTAATtCACTGAGCTGAT-----------------------------------TGtcattttaatctgcaagtttgttagaccaccaagtACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTT--- TAATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATTATACTTGGTGGTCTAACAAACTTGCAGATTAAAATG-----------------------------------ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTTATT Template switch alignment (log-probability: -25.8) TAATTTTGTTCCTGGGAACTTTTAATtCACTGAGCTGATT|GTCATTTTAATCTGCAAGTTTGTTAGACCACCAAGT|ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTT TAATTTTGTTCCTGGGAACTTTTAATACACTGAGCTGATT|GTCATTTTAATCTGCAAGTTTGTTAGACCACCAAGT|ACAAACTGTTCAGTATTGAGTCTGTGAACACAGGGTT ========= Event 246 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCTGCTGAGCTAGTGCTGGGCTGA--ACTGTGCATGAAGTCAGCAAGACAAGCACGTTTC Chimp: CTTCTGCTGAGCTAGTGCTGGGCTGA--ACTGTGCATGAAGTCAGCAAGACAAACACGTTTC ↓ 1 3 4 2 Gorilla: CTTCTGCTGAGCTAGTGCTGGACTTCATGCACAGCATGAAGTCAGCAAGACAAACACGTTTC ↑ 1 3 4 2 Human: CTTCTGCTGAGCTAGTGCTGGGCTGA--ACTGTGCATGAAGTCAGCAAGACAAGCACGTTTC Cluster: [ ] Orangutan: cttctgctgagctagtgctgggctga--actgtgcatgaagtcagcaagacaaatacggttc Human > Gorilla --------------- chr11:19605886-19605897 Template switch process: F1: L CAGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGG 1 F3: 4 GCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG R RF: CAGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGGGCTGAACTGTGCATGAAGTCAGCAAGACAAGCACGTTTCTGCCCTCTGGG RR: GTCTAGGAAGTCAATAGGTGGAAGACGACTCGATCACGACCCGACTTGACACGTACTTCAGTCGTTCTGTTCGTGCAAAGACGGGAGACCC F2: 3 ACACGTACTTCA 2 Unidirectional alignment (log-probability: -43.5) AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGGaCT------TcatgcacaGCATGAAGTCAGCAAGACAAaCACGTTTCTGCCCTCTGGG AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGGGCTGAACTGT--------GCATGAAGTCAGCAAGACAAGCACGTTTCTGCCCTCTGGG Template switch alignment (log-probability: -22.8) AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGG|ACTTCATGCACA|GCATGAAGTCAGCAAGACAAaCACGTTTCTGCCCTCTGGG AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGG|ACTTCATGCACA|GCATGAAGTCAGCAAGACAAGCACGTTTCTGCCCTCTGGG Chimp > Gorilla --------------- chr11:19605886-19605897 Template switch process: F1: L CAGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGG 1 F3: 4 GCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG R RF: CAGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGGGCTGAACTGTGCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG RR: GTCTAGGAAGTCAATAGGTGGAAGACGACTCGATCACGACCCGACTTGACACGTACTTCAGTCGTTCTGTTTGTGCAAAGACGGGAGACCC F2: 3 ACACGTACTTCA 2 Unidirectional alignment (log-probability: -38) AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGGaCT------TcatgcacaGCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGGGCTGAACTGT--------GCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG Template switch alignment (log-probability: -17.3) AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGG|ACTTCATGCACA|GCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG AGATCCTTCAGTTATCCACCTTCTGCTGAGCTAGTGCTGG|ACTTCATGCACA|GCATGAAGTCAGCAAGACAAACACGTTTCTGCCCTCTGGG ========= Event 247 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGCCCATTGAATTGCATATTTATTTGCCATGCAGAATATAATTCTGCATGCCATTCATTAGTTCTCACA ↑ 13 4 2 Chimp: CAGCCCATTGAATTGCATATTTATTTGC--------CTA-TATTCTGCATGCCATTCATTAGTTCTCACA Gorilla: CAGCCCATTGAATTGCATATTAATTTGC--------CTA-TATTCTGCATGCCATTCATTAGTTCTCACA ↓ 13 4 2 Human: CAGCCCATTGAATTGCATATTTATTTGCCATGCAGAATATAATTCTGCATGCCATTCATTAGTTCTCACA Cluster: [ ] Orangutan: CAGCCCATTGAATTGCATATTAATTTGC--------CTA-TATTCTGCATGCCATTCATCAGTTCTCACA Chimp > Human ------------- chr11:118640215-118640226 Template switch process: F1: L TAGAGTGCCTGTGCAGCCCATTGAATTGCATATTTATTTGCC 1 F3: 4 ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC R RF: TAGAGTGCCTGGGCAGCCCATTGAATTGCATATTTATTTGCCTATATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC RR: ATCTCACGGACCCGTCGGGTAACTTAACGTATAAATAAACGGATATAAGACGTACGGTAAGTAATCAAGAGTGTTGTACGACCTG F2: 3 ATATAAGACGTA 2 Unidirectional alignment (log-probability: -40.1) GAGTGCCTGtGCAGCCCATTGAATTGCATATTTATTTGCCatgcagaaTATaATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC GAGTGCCTGGGCAGCCCATTGAATTGCATATTTATTTGCC--------TAT-ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC Template switch alignment (log-probability: -22.8) GAGTGCCTGtGCAGCCCATTGAATTGCATATTTATTTGCC|ATGCAGAATATA|ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC GAGTGCCTGGGCAGCCCATTGAATTGCATATTTATTTGCC|ATGCAGAATATA|ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC Gorilla > Human --------------- chr11:118640215-118640226 Template switch process: F1: L CATTCCATAGAGTGCCTGTGCAGCCCATTGAATTGCATATTTATTTGCC 1 F3: 4 ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC R RF: CATTCCATAGAGTGCCTGGGCAGCCCATTGAATTGCATATTAATTTGCCTATATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC RR: GTAAGGTATCTCACGGACCCGTCGGGTAACTTAACGTATAATTAAACGGATATAAGACGTACGGTAAGTAATCAAGAGTGTTGTACGACCTG F2: 3 ATATAAGACGTA 2 Unidirectional alignment (log-probability: -44.8) GAGTGCCTGtGCAGCCCATTGAATTGCATATTtATTTGCCatgcagaaTATaATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC GAGTGCCTGGGCAGCCCATTGAATTGCATATTAATTTGCC--------TAT-ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC Template switch alignment (log-probability: -28.5) GAGTGCCTGtGCAGCCCATTGAATTGCATATTtATTTGCC|ATGCAGAATATA|ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC GAGTGCCTGGGCAGCCCATTGAATTGCATATTAATTTGCC|ATGCAGAATATA|ATTCTGCATGCCATTCATTAGTTCTCACAACATGCTGGAC ========= Event 248 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGATTAAGGAGGGAAGAGGAAATGGTTTTCAGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTGTATACAGTTGGAGTTCAGTGATGATATTGTGAAGATCATT ↓ 1 4 3 2 Chimp: ATGATTAAGGAGGGAAGAGGACA-----CTGAGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTGTATACAGTTGGAGTTCAGTGATGATATTGTGAAGATCATT Gorilla: ATGATTAAGGAGGGAAGAGGAAATGGTTTTGAGAGCACACTGTTTTAAGAATAAATAACATTTTGTTTTTGTATACAGTTGGAGTTCAGTGATGATATTGTGAAGATCATT Human: ATGATTAAGGAGGGAAGAGGAAATGGTTTTCAGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTGTATACAGTTGGAGTTCAGTGATGATATTGTGAAGATCATT Cluster: [ ] Orangutan: ATGATTAGGGAGGGAAGAGGAAATGGTTTTGAGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTGTATACAGTTGGAGTTCAGTGATGATATTGTGAAGATCATT Human > Chimp ------------- chr11:118942792-118942797 Template switch process: F1: L CTGTTGGATCTCTGTGCTGGATGATTAAGGAGGGAAGAGGA 1 F3: 4 GAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTG R RF: CTGTTGGATCTCTGTGCTGGATGATTAAGGAGGGAAGAGGAAATGGTTTTCAGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTGTATACAGTTGGAGTTCAGTG RR: GACAACCTAGAGACACGACCTACTAATTCCTCCCTTCTCCTTTACCAAAAGTCTCGTGTGACAAAATTCTTATTAATTGTAAAACAAAAACATATGTCAACCTCAAGTCAC F2: 3 AGTCAC 2 Unidirectional alignment (log-probability: -27.4) TGTTGGATCTCTGTGCTGGATGATTAAGGAGGGAAGAGGA---------CactgAGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTG TGTTGGATCTCTGTGCTGGATGATTAAGGAGGGAAGAGGAAATGGTTTTC----AGAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTG Template switch alignment (log-probability: -16) TGTTGGATCTCTGTGCTGGATGATTAAGGAGGGAAGAGGA|CACTGA|GAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTG TGTTGGATCTCTGTGCTGGATGATTAAGGAGGGAAGAGGA|CACTGA|GAGCACACTGTTTTAAGAATAATTAACATTTTGTTTTTG ========= Event 249 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATTTCACCTTTCTCAAATGACAAAATG----------------------------------GCAGTCA-AAACTGCCATAAAATACACATTAAACAACAGTCACAGAACATACCACCTAATGAGTGAAGTTCT--CATGTGTTAATTTCATCTCAAATTAAGCAGTTATTTTAACTTTTCTTAA Chimp: TTATTTCACCTTTCTCAAATGACAAAATG------------GCTGCTCATTTTTGACAAAATGGCAGTCAAAAACTGCCATAAAATACACACTAAACAATAGTCACAGAACATACCACCTAATGAGTGAAGTTCT--CATGTGTTAATTTCATCTCAAATTAAGCAGTTATTTTAACTTTTCTTAA ↑ 4 1 3 2 Gorilla: TTATTTCACCTTTCTCAAATGACAAAATG----------------------------------GCAGTCAAAAACTGCCATAAAATACACACTAAACAATAGTCACAGAACATACCACCTAATGAGTGAAGTTCT----CGTGTTAATTTCATCTCAAATTAAGCAGTTATTTTAACTTTTCTTAA Human: TCATTTCACCTTTCTCAAATGACAAAATG----------------------------------GCAGTCA-AAACTGCCATAAAATACACATTAAACAACAGTCACAGAACATACCACCTAATGAGTGAAGTTCT--CATGTGTTAATTTCATCTCAAATTAAGCAGTTATTTTAACTTTTCTTAA Cluster: [ ] Orangutan: TTATTTCACCTTTCTCAAATGACAAAATGGCTGCTCATCTG------------------------TGTCAAAAACTGCCATAAAATACACACTAAACAACAGTCACAGACAATACCACCTAATGAGTGAAGTTCTCA--TGTGTTAATTTAATCTCAAATTGAGCAGTTACTTTAACTTTTCTTAA Gorilla > Chimp --------------- chr11:119221731-119221740 Template switch process: F1: L CAAAATAGTACTTTATTTCACCTTTCTCAAATGACAAAATGGC 1 F3: 4 TGACAAAATGGCAGTCAAAAACTGCCATAAAATACACACTAAACAATAGT R RF: CAAAATAGTACTTTATTTCACCTTTCTCAAATGACAAAATGGCAGTCAAAAACTGCCATAAAATACACACTAAACAATAGTCACAGAACATACCACCTAATGAGTGAAGTTCTCGTGTTAATTTCATCTCAAATTAAGCA RR: GTTTTATCATGAAATAAAGTGGAAAGAGTTTACTGTTTTACCGTCAGTTTTTGACGGTATTTTATGTGTGATTTGTTATCAGTGTCTTGTATGGTGGATTACTCACTTCAAGAGCACAATTAAAGTAGAGTTTAATTCGT F2: 3 TTTTACTCGT 2 Unidirectional alignment (log-probability: -42.5) AATAGTACTTTATTTCACCTTTCTCAAATGACAAAAtggctgctcatttttgacaaaaTGGCAGTCAAAAACTGCCATAAAATACACACT AATAGTACTTTATTTCACCTTTCTCAAATGACAAAA----------------------TGGCAGTCAAAAACTGCCATAAAATACACACT Template switch alignment (log-probability: -28.3) AATAGTACTTTATTTCACCTTTCTCAAATGACAAAATGGC|TGCTcAtTTT|TGACAAAATGGCAGTCAAAAACTGCCATAAAATACACACT AATAGTACTTTATTTCACCTTTCTCAAATGACAAAATGGC|TGCTTAATTT|TGACAAAATGGCAGTCAAAAACTGCCATAAAATACACACT ========= Event 250 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTGATATATCCCTCTATAGTAGGCATCATCTGAAAGAGATGACT------ACtttttt-ttttttttttttttt ↑ 3 1 2 4 Chimp: TTTGATATATCCCTCTATAGTAGGCATC-TCTT--TCAGATGCCT------ACtttttttttttttttttttttt Gorilla: TTTGATATATCCCTCTATAGTAGGCATC-TCTT--TCAGATGCCt------------tttttttttttttttttt Human: TTTGATATATCCCTCTATAGTAGGCATCATCTGAAAGAGATGACT------ACtttttt-ttttttttttttttt Cluster: [ ] Orangutan: TTTGATATATCCCTCTATAGTAGGCATC-TCTT--TCAGACGCCTACtttt---------ttttttttttttttt Chimp > Human ------------- chr11:123319550-123319568 Template switch process: F1: L TCCCCCTTGAAATTTTGATATATCCCTCTATAGTAGGCATC 1 F3: 4 TTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCT R RF: TCCCCCTTGAAATTTTGATATATCCCTCTATAGTAGGCATCTCTTTCAGATGCCTACTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCT RR: AGGGGGAACTTTAAAACTATATAGGGAGATATCATCCGTAGAGAAAGTCTACGGATGAAAAAAAAAAAAAAAAAAAAAAAACTCTGTCTCAGA F2: 3 CATCAGTAGAGAAAGTCTA 2 Unidirectional alignment (log-probability: -49.3) CCCCCTTGAAATTTTGATATATCCCTCTATAGTAGGCATC-----------------atctgaaagagatgactacTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCT CCCCCTTGAAATTTTGATATATCCCTCTATAGTAGGCATCTCTTTCAGATGCCTACT-------------------TTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCT Template switch alignment (log-probability: -23.5) CCCCCTTGAAATTTTGATATATCCCTCTATAGTAGGCATC|ATCTGAAAGAGATGaCTAC|TTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCT CCCCCTTGAAATTTTGATATATCCCTCTATAGTAGGCATC|ATCTGAAAGAGATGCCTAC|TTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCT ========= Event 251 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGAACATAAAAATGATTAAAGTAGATACAGCCATCTACTTTGATATGCCCTATATCTTTT Chimp: TGAACATAAAAATGATTAAAGTAGATACAGCTATCTACTTTGATATGCCCTATATCTTTT ↑ 3 1 2 4 Gorilla: TGAACATAAAAATGATTAAAGTAGAT------AGCTGACTTGATATGCCCTATATCTTTT ↓ 3 1 2 4 Human: TGAACATAAAAATGATTAAAGTAGATACAGCCATCTACTTTGATATGCCCTATATCTTTT Cluster: [ ] Orangutan: TGAACATAAAAATGATTAAAGTAGAC------AGCCAATTTGATATGCTCTATATCTTTT Gorilla > Human --------------- chr11:12999172-12999183 Template switch process: F1: L ATTAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATA 1 F3: 4 TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC R RF: ATTAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATAGCTGACTTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC RR: TAATTCACTTACTCTACTTGTATTTTTACTAATTTCATCTATCGACTGAACTATACGGGATATAGAAAATCATTAACCGGTTTCAAAG F2: 3 TCATCTACCGAC 2 Unidirectional alignment (log-probability: -36.7) TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGAT-----ACagccatctactTTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATAGCTGAC-----------TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC Template switch alignment (log-probability: -22.8) TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATA|CAGCcATCTACT|TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATA|CAGCTATCTACT|TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC Gorilla > Chimp --------------- chr11:13171212-13171223 Template switch process: F1: L ATTAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATA 1 F3: 4 TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC R RF: ATTAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATAGCTGACTTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC RR: TAATTCACTTACTCTACTTGTATTTTTACTAATTTCATCTATCGACTGAACTATACGGGATATAGAAAATCATTAACCGGTTTCAAAG F2: 3 TCATCTATCGAC 2 Unidirectional alignment (log-probability: -36.7) TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGAT-----ACagctatctactTTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATAGCTGAC-----------TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC Template switch alignment (log-probability: -17.3) TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATA|CAGCTATCTACT|TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC TAAGTGAATGAGATGAACATAAAAATGATTAAAGTAGATA|CAGCTATCTACT|TTGATATGCCCTATATCTTTTAGTAATTGGCCAAAGTTTC ========= Event 252 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTCTTTTCCAGCCCCGCTCCC----------------------------------------GCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCCCCGCCTCTGCCGGGGCCCCAGGAGGAATCTAAGAAAAGAGAGATGGAGGGAGGAAATGGCATCGCTTCAGGAAGGGGCAGGACCTCCAGGACC ↓ 4 1 3 2 Chimp: CCTCTTTTCCAGCCCCGCTCCC--------------------GCGCTGCCTGCCCGAAGCCCGCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCCCCGCCTCTGCCGGGTCCCCAGGAGGAATCTAAGAAAAGAGAGATGGAGGGAGGAAATGGCATCGCTTCAGGAAGGGGCAGGACCTCCAGGACC Gorilla: CCTCTTTTCCAGCCCCGCTCCCGCGCTGCCTGCCCGAAGCCC--------------------GCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCCCCGCCTCTGCCGGGGCCCCAGGAGGAATCTAAGAAAGGAGAGATGGAGGGAGGAAATGGCATCGCTTCAGGAAGGGGCAGGAC-CCCAGGACC Human: CCTCTTTTCCAGCCCCGCTCCC----------------------------------------GCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCCCCGCCTCTGCCGGGGCCCCAGGAGGAATCTAAGAAAAGAGAGATGGAGGGAGGAAATGGCATCGCTTCAGGAAGGGGCAGGACCTCCAGGACC Cluster: [ ] Orangutan: CCTCTTTTCCAGCCCCGCTCCCGCGCTGCCTGCCCGAAGCCC--------------------GCGCTGCCGCCGGAGAGGGACTCGGGGCCCAGCCGCCCCGCCTCTGCCGGGGCCCCAGGAGGAATCTAAGAAAGGAGAGATGGAGGGAGGAAATGGCATCGCTTCAGGAAGGGGCAGGACCTCCAGGACC Human > Chimp ------------- chr11:123491696-123491704 Template switch process: F1: L GCGGGGCGGCTCCCGGCGCCCTCTTTTCCAGCCCCGCTCCCGCGCTGCC 1 F3: 4 CCCGCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCCCCG R RF: GCGGGGCGGCTCCCGGCGCCCTCTTTTCCAGCCCCGCTCCCGCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCCCCGCCTCTGCCGGGGCCCCAGGAGGAATCTAAGAAAAGAGAGATGGAGGGAGGAAATGGCATCGCTTCAGGAA RR: CGCCCCGCCGAGGGCCGCGGGAGAAAAGGTCGGGGCGAGGGCGCGACGGCGGCCTCTCCCTGAGCCCCGCGTCGGCGGGGCGGAGACGGCCCCGGGGTCCTCCTTAGATTCTTTTCTCTCTACCTCCCTCCTTTACCGTAGCGAAGTCCTT F2: 3 GAAGCCCGT 2 Unidirectional alignment (log-probability: -39.7) CTCCCGGCGCCCTCTTTTCCAGCCCCGCTCCCGCGCTgcctgcccgaagcccgcgctGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCC CTCCCGGCGCCCTCTTTTCCAGCCCCGCTCCCGCGCT--------------------GCCGCCGGAGAGGGACTCGGGGCGCAGCCGCC Template switch alignment (log-probability: -28.6) CTCCCGGCGCCCTCTTTTCCAGCCCCGCTCCCGCGCTGCC|TgCCcGAAG|CCCGCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCC CTCCCGGCGCCCTCTTTTCCAGCCCCGCTCCCGCGCTGCC|TTCCTGAAG|CCCGCGCTGCCGCCGGAGAGGGACTCGGGGCGCAGCCGCC ========= Event 253 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGGGCTGGGCCATGGCTCTG--TGTCCTTAG-----AGAGTTATGAGACTTGACTGAGCCCCCGTTGGGACTGCTGTGAGAAAGAAGCGGGATAACATATTATAAACAATAGCATCTGCAGCTGGAGTGATGT Chimp: GTGGGCTGGGCCATGGCTCTG--TGTCCTTAG-----AGAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGTGAGAAAGAAGCGGGATAACACATTATAAACAATAGCATCTGCAGCTGGAGTGATGT ↓ 4 1 3 2 Gorilla: GTGGGCTGGGCCATGGCTCTG----TTATGAGAGCTATGAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGTGAGAAAGAAGCGGGATAACATATTATAAACAATAGCATCTGCAGCTGGAGTGATGT Human: GTGGGCTGGGCCATGGCTCTG--TGTCCTTAG-----AGAGTTATGAGACTTGACTGAGCCCCCGTTGGGACTGCTGTGAGAAAGAAGCGGGATAACATATTATAAACAATAGCATCTGCAGCTGGAGTGATGT Cluster: [ ] Orangutan: GTGGGCTGGGCCATGGCTCTGTG--TCCTTAG-----AGAGTTATCAGACTTGTCTGAGCCCCCGTTGGGAATGCTGTGAGAAAGAAGCGGGATAACATATTATAAATAATAGCATCTGCAGCTGGAGTAATGT Chimp > Gorilla --------------- chr11:122843171-122843175 Template switch process: F1: L ACACCAGAGTCCTGGGGAGTGTGGGCTGGGCCATGGCTCT-------------GTTATGAGA 1 F3: 4 GAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGT R RF: ACACCAGAGTCCTGGGGAGTGTGGGCTGGGCCATGGCTCTGTGTCCTTAGAGAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGTGAGAAAGAAGCGGGATAACACATTATAAACAATAGC RR: TGTGGTCTCAGGACCCCTCACACCCGACCCGGTACCGAGACACAGGAATCTCTCAATACTCTGAACAGACTCGGGGGCAACCCTGACGACACTCTTTCTTCGCCCTATTGTGTAATATTTGTTATCG F2: 3 TATCG 2 Unidirectional alignment (log-probability: -38.4) TCCTGGGGAGTGTGGGCTGGGCCATGGCTCTGT---------tatgagagctatGAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGT TCCTGGGGAGTGTGGGCTGGGCCATGGCTCTGTGTCCTTAGA------------GAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGT Template switch alignment (log-probability: -27) TCCTGGGGAGTGTGGGCTGGGCCATGGCTCT-------------GTTATGAGA|GCTAT|GAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGT TCCTGGGGAGTGTGGGCTGGGCCATGGCTCTGTGTCCTTAGAGAGTTATGAGA|GCTAT|GAGTTATGAGACTTGTCTGAGCCCCCGTTGGGACTGCTGT ========= Event 254 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: AGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCAT--GTGTTATCAGTGCAGCAGAGAATGTCA ↓ 13 24 ↑ 1 3 4 2 Chimp: AGCGAAACCTCTAGTTCTGATCAC--ACATGAGCCCACATGCTTGTTACCAGTGCAGCAGAGAATGTCA ↓ 1 3 4 2 ↑ 13 24 Gorilla: AGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCAT--GTGTTATCAGTGCAGCAGAGAATGTCA Human: AGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCAT--GTGTTATCAGTGCAGCAGAGAATGTCA Cluster: [ ] Orangutan: AGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCAT--GCGTTATCAGTACAGCAGAGAATGTCA Chimp > Human ------------- chr11:13415183-13415202 Template switch process: F1: L GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGAT 1 F3: 4 TGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG R RF: GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATCACACATGAGCCCACATGCTTGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG RR: CAGTCCCGTTCTACACCGGGTCGCTTTGGAGATCAAGACTAGTGTGTACTCGGGTGTACGAACAATGGTCACGTCGTCTCTTACAGTGACCCTGAAGGTCTGCCTCC F2: 3 GTACTCGGGTGTACGAACAA 2 Unidirectional alignment (log-probability: -51.1) TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATaACAagcatgtgggctCATG------------TGTTAtCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATCACA------------CATGAGCCCACATGCTTGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Template switch alignment (log-probability: -23.9) TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGAT|AACAAGCATGTGGGCTCATG|TGTTAtCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGAT|AACAAGCATGTGGGCTCATG|TGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Human > Chimp ------------- chr11:13598169-13598184 Template switch process: F1: L GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATCACA 1 F3: 4 TGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG R RF: GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCATGTGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG RR: CAGTCCCGTTCTACACCGGGTCGCTTTGGAGATCAAGACTATTGTTCGTACACCCGAGTACACAATAGTCACGTCGTCTCTTACAGTGACCCTGAAGGTCTGCCTCC F2: 3 TCGTACACCCGAGTAC 2 Unidirectional alignment (log-probability: -51.1) GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATcACA------------CATGagcccacatgctTGTTAcCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCATG------------TGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Template switch alignment (log-probability: -29.4) GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATcACA|CATGAGCCCACATGCT|TGTTAcCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATAACA|CATGAGCCCACATGCT|TGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Gorilla > Chimp --------------- chr11:13598169-13598184 Template switch process: F1: L GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATCACA 1 F3: 4 TGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG R RF: GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCATGTGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG RR: CAGTCCCGTTCTACACCGGGTCGCTTTGGAGATCAAGACTATTGTTCGTACACCCGAGTACACAATAGTCACGTCGTCTCTTACAGTGACCCTGAAGGTCTGCCTCC F2: 3 TCGTACACCCGAGTAC 2 Unidirectional alignment (log-probability: -49.7) GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATcACA------------CATGagcccacatgctTGTTAcCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATAACAAGCATGTGGGCTCATG------------TGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Template switch alignment (log-probability: -29) GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATcACA|CATGAGCCCACATGCT|TGTTAcCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA GGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATAACA|CATGAGCCCACATGCT|TGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Chimp > Gorilla --------------- chr11:13493271-13493290 Template switch process: F1: L GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGAT 1 F3: 4 TGTTATCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG R RF: GTCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATCACACATGAGCCCACATGCTTGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGACGGAGG RR: CAGTCCCGTTCTACACCGGGTCGCTTTGGAGATCAAGACTAGTGTGTACTCGGGTGTACGAACAATGGTCACGTCGTCTCTTACAGTGACCCTGAAGGTCTGCCTCC F2: 3 GTACTCGGGTGTACGAACAA 2 Unidirectional alignment (log-probability: -49.7) TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATaACAagcatgtgggctCATG------------TGTTAtCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGATCACA------------CATGAGCCCACATGCTTGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA Template switch alignment (log-probability: -23.9) TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGAT|AACAAGCATGTGGGCTCATG|TGTTAtCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA TCAGGGCAAGATGTGGCCCAGCGAAACCTCTAGTTCTGAT|AACAAGCATGTGGGCTCATG|TGTTACCAGTGCAGCAGAGAATGTCACTGGGACTTCCAGA ========= Event 255 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATATAAGACTGAGAAGTGAA--------CACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTG ↓ 1 4 3 2 Chimp: aaaTATAAGACTGAGAAGTGAACCATGGTTCTCTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTG ↑ 1 4 3 2 Gorilla: aaaTATAAGACTGAGAAGTGAG--------CACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTG Human: AAATATAAGACTGAGAAGTGAA--------CACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTG Cluster: [ ] Orangutan: AAATGTAAGACTGAGAATTGAA--------CGCTTGCTTGAGAACCATGTTGCATTGTTTACCTTTTTG Human > Chimp ------------- chr11:110436709-110436717 Template switch process: F1: L TTAAAAAACTAGAAAAGAAAAATATAAGACTGAGAAGTGAAC 1 F3: 4 CTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT R RF: TTAAAAAATTAGAAAAGAAAAATATAAGACTGAGAAGTGAACACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT RR: AATTTTTTAATCTTTTCTTTTTATATTCTGACTCTTCACTTGTGAACGAACTCTTGGTACAACATAACAAATGGAAGAACAAA F2: 3 TCTTGGTAC 2 Unidirectional alignment (log-probability: -34.4) AAAAAAcTAGAAAAGAAAAATATAAGACTGAGAAGTGAAccatggttCtCTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT AAAAAATTAGAAAAGAAAAATATAAGACTGAGAAGTGAA--------CACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT Template switch alignment (log-probability: -22.4) AAAAAAcTAGAAAAGAAAAATATAAGACTGAGAAGTGAAC|CATGGTTCT|CTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT AAAAAATTAGAAAAGAAAAATATAAGACTGAGAAGTGAAC|CATGGTTCT|CTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT Gorilla > Chimp --------------- chr11:110436709-110436717 Template switch process: F1: L ATTAAAAAACTAGAAAAGAAAAATATAAGACTGAGAAGTGAAC 1 F3: 4 CTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT R RF: ATTAAAAAATTAGAAAAGAAAAATATAAGACTGAGAAGTGAGCACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT RR: TAATTTTTTAATCTTTTCTTTTTATATTCTGACTCTTCACTCGTGAACGAACTCTTGGTACAACATAACAAATGGAAGAACAAA F2: 3 TCTTGGTAC 2 Unidirectional alignment (log-probability: -39) AAAAAAcTAGAAAAGAAAAATATAAGACTGAGAAGTGAaccatggttCtCTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT AAAAAATTAGAAAAGAAAAATATAAGACTGAGAAGTGA--------GCACTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT Template switch alignment (log-probability: -28) AAAAAAcTAGAAAAGAAAAATATAAGACTGAGAAGTGAaC|CATGGTTCT|CTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT AAAAAATTAGAAAAGAAAAATATAAGACTGAGAAGTGAGC|CATGGTTCT|CTTGCTTGAGAACCATGTTGTATTGTTTACCTTCTTGTTT ========= Event 256 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATTCTTGAGAAGCTTATCCTACA-----GGTATTTACATCAAAATTGAAGTA Chimp: ATATTCTTGAGAAGCTTATCCTACA-----GGTATTTACATCAAAATTGAAGTA ↓ 3 1 2 4 Gorilla: ATATTCTTGAGAAGCTTATCCTACACCTGTAGGATTTACATCAAAATTGAAGTA ↑ 3 1 2 4 Human: ATATTCTTGAGAAGCTTATCCTACA-----GGTATTTACATCAAAATTGAAGTA Cluster: [ ] Orangutan: ATATTCTTCAGAAGCTTATCCTACA-----GGTATTTACATCAAAATTGAAGTA Human > Gorilla --------------- chr11:110207985-110207992 Template switch process: F1: L TTGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA 1 F3: 4 ATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA R RF: TTGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACAGGTATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA RR: AACTTTTGAAAAAAAGTATAAGAACTCTTCGAATAGGATGTCCATAAATGTAGTTTTAACTTCATGAATCATACGGTAAACATT F2: 3 GGATGTCC 2 Unidirectional alignment (log-probability: -29.2) TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACAcctgtaGgATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA-----GGTATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA Template switch alignment (log-probability: -16.7) TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA|CCTGTAGG|ATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA|CCTGTAGG|ATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA Chimp > Gorilla --------------- chr11:110207985-110207992 Template switch process: F1: L TTGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA 1 F3: 4 ATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA R RF: TTGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACAGGTATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA RR: AACTTTTGAAAAAAAGTATAAGAACTCTTCGAATAGGATGTCCATAAATGTAGTTTTAACTTCATGAATCATACGGTAAACATT F2: 3 GGATGTCC 2 Unidirectional alignment (log-probability: -29.2) TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACAcctgtaGgATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA-----GGTATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA Template switch alignment (log-probability: -16.7) TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA|CCTGTAGG|ATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA TGAAAACTTTTTTTCATATTCTTGAGAAGCTTATCCTACA|CCTGTAGG|ATTTACATCAAAATTGAAGTACTTAGTATGCCATTTGTAA ========= Event 257 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGGGCATCCCTATGTATAAACATAAGACA------GTACTTCATGGTTGGGCAGAGAAGAAGG ↓ 3 1 2 4 Chimp: AAGGGCATCCCTATGTATAAACATAAGACTACTGTCTTATGTTATGGTTGGGCAGAGAAGAAGG Gorilla: AAGGTCATCCCTATGTATAAACATAAGGCA------GTACTTCATGGTTGGGCAGAGAAGAAGG Human: AAGGGCATCCCTATGTATAAACATAAGACA------GTACTTCATGGTTGGGCAGAGAAGAAGG Cluster: [ ] Orangutan: AAGTGCACCCCTATGTATAAACATAGGACA------ATACTTCATGTCTGGGCAGAGAAGAAGG Human > Chimp ------------- chr11:123511440-123511453 Template switch process: F1: L GAAGCCAGCTTAAAGGGCATCCCTATGTATAAACATAAGAC 1 F3: 4 ATGGTTGGGCAGAGAAGAAGGGTCTGAGTGTGGCCCCTCA R RF: GAAGCCAGCTTAAAGGGCATCCCTATGTATAAACATAAGACAGTACTTCATGGTTGGGCAGAGAAGAAGGGTCTGAGTGTGGCCCCCCA RR: CTTCGGTCGAATTTCCCGTAGGGATACATATTTGTATTCTGTCATGAAGTACCAACCCGTCTCTTCTTCCCAGACTCACACCGGGGGGT F2: 3 TTGTATTCTGTCAT 2 Unidirectional alignment (log-probability: -44.8) AAGCCAGCTTAAAGGGCATCCCTATGTATAAACATAAGAC--TACTgtcttatgTtATGGTTGGGCAGAGAAGAAGGGTCTGAGTGTGGCCCCtCA AAGCCAGCTTAAAGGGCATCCCTATGTATAAACATAAGACAGTACT--------TCATGGTTGGGCAGAGAAGAAGGGTCTGAGTGTGGCCCCCCA Template switch alignment (log-probability: -23) AAGCCAGCTTAAAGGGCATCCCTATGTATAAACATAAGAC|TACTGTCTTATGTT|ATGGTTGGGCAGAGAAGAAGGGTCTGAGTGTGGCCCCtCA AAGCCAGCTTAAAGGGCATCCCTATGTATAAACATAAGAC|TACTGTCTTATGTT|ATGGTTGGGCAGAGAAGAAGGGTCTGAGTGTGGCCCCCCA ========= Event 258 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCGTGGTAGCCTCTGGGTCATATTGGCTAGCTGGGACTggcggcagctagccaatatggtgtcttcaggtgaatt ↑ 1 4 3 2 Chimp: TCCGTGGTAGCCTCTGGGTCA--------TGATGGGACTggcggcagctagccaatatggtgtcttcaggtgaatt Gorilla: TCCGTGGTAGCCTCTGGGTCA--------TGATGGGACTggcggcagctagccaatatggtgtcttcaggtgaatt Human: TCCGTGGTAGCCTCTGGGTCATATTGGCTAGCTGGGACTggcggcagctagccaatatggtgtcttcaggtgaatt Cluster: [ ] Orangutan: TCCATGGTAGCTTCTGGGTCA--------TGATGGGACTggcggcagctagccaatatggtgtcttcaggtgaatt Chimp > Human ------------- chr11:8906667-8906676 Template switch process: F1: L AGCCTTAGCTGAACTTGGCCTCCGTGGTAGCCTCTGGGTCAT 1 F3: 4 TGGGACTGGCGGCAGCTAGCCAATATGGTGTCTTCAGGTG R RF: AGCCTTAGCCGAACTTGGCCTCCGTGGTAGCCTCTGGGTCATGATGGGACTGGCGGCAGCTAGCCAATATGGTGTCTTCAGGTG RR: TCGGAATCGGCTTGAACCGGAGGCACCATCGGAGACCCAGTACTACCCTGACCGCCGTCGATCGGTTATACCACAGAAGTCCAC F2: 3 CGATCGGTTA 2 Unidirectional alignment (log-probability: -34.4) CCTTAGCtGAACTTGGCCTCCGTGGTAGCCTCTGGGTCATattggctaGcTGGGACTGGCGGCAGCTAGCCAATATGGTGTCTTCAGGTG CCTTAGCCGAACTTGGCCTCCGTGGTAGCCTCTGGGTCAT--------GATGGGACTGGCGGCAGCTAGCCAATATGGTGTCTTCAGGTG Template switch alignment (log-probability: -22.5) CCTTAGCtGAACTTGGCCTCCGTGGTAGCCTCTGGGTCAT|ATTGGCTAGC|TGGGACTGGCGGCAGCTAGCCAATATGGTGTCTTCAGGTG CCTTAGCCGAACTTGGCCTCCGTGGTAGCCTCTGGGTCAT|ATTGGCTAGC|TGGGACTGGCGGCAGCTAGCCAATATGGTGTCTTCAGGTG ========= Event 259 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCCCAAGATGCCAGAGTTCC-------AGACACTCTTCTCAT------GGTGTCCTCTTCCTGCTCATGCCCTG Chimp: GCCCCAAGATGCCAGAGTTCC-------AGACACTCTTCTCAT------GGTGTCCTCTTCCTGCCCATGCCTTG ↑ 1 3 4 2 Gorilla: GCCCCAAGATGCCAGAGTTCC--------------TCTGGCATGAGAAGAGTGTCCTCTTCCTGCCCATGCCCTG ↓ 1 3 4 2 Human: GCCCCAAGATGCCAGAGTTCC-------AGACACTCTTCTCAT------GGTGTCCTCTTCCTGCTCATGCCCTG Cluster: [ ] Orangutan: GCCCCAAGATGCCAGAGCTCCAGGCACT-------CTTCTCAT------GGTGTTCTCTTCC--------CTGGG Gorilla > Human --------------- chr11:9011367-9011381 Template switch process: F1: L TTCTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCA 1 F3: 4 GTGTCCTCTTCCTGCTCATGCCCTGGTCCAGCCTCTCTCT R RF: TTCTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCTCTGGCATGAGAAGAGTGTCCTCTTCCTGCCCATGCCCTGGTCCAGCCTCTCTCT RR: AAGAAATCAGAGGATGGAGACGGGGTTCTACGGTCTCAAGGAGACCGTACTCTTCTCACAGGAGAAGGACGGGTACGGGACCAGGTCGGAGAGAGA F2: 3 GTACTCTTCTCACAG 2 Unidirectional alignment (log-probability: -45.5) CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCC------------AGAcactcttctcatgGTGTCCTCTTCCTGCtCATGCCCTGGTCCAGCCTCTCTCT CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCTCTGGCATGAGAAGA-------------GTGTCCTCTTCCTGCCCATGCCCTGGTCCAGCCTCTCTCT Template switch alignment (log-probability: -28.7) CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCa|GACACTCTTCTCATG|GTGTCCTCTTCCTGCtCATGCCCTGGTCCAGCCTCTCTCT CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCT|GACACTCTTCTCATG|GTGTCCTCTTCCTGCCCATGCCCTGGTCCAGCCTCTCTCT Gorilla > Chimp --------------- chr11:9155552-9155566 Template switch process: F1: L TTCTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCA 1 F3: 4 GTGTCCTCTTCCTGCCCATGCCTTGGTCCAGCCTCTCTCT R RF: TTCTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCTCTGGCATGAGAAGAGTGTCCTCTTCCTGCCCATGCCCTGGTCCAGCCTCTCTCT RR: AAGAAATCAGAGGATGGAGACGGGGTTCTACGGTCTCAAGGAGACCGTACTCTTCTCACAGGAGAAGGACGGGTACGGGACCAGGTCGGAGAGAGA F2: 3 GTACTCTTCTCACAG 2 Unidirectional alignment (log-probability: -45.5) CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCC------------AGAcactcttctcatgGTGTCCTCTTCCTGCCCATGCCtTGGTCCAGCCTCTCTCT CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCTCTGGCATGAGAAGA-------------GTGTCCTCTTCCTGCCCATGCCCTGGTCCAGCCTCTCTCT Template switch alignment (log-probability: -28.7) CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCa|GACACTCTTCTCATG|GTGTCCTCTTCCTGCCCATGCCtTGGTCCAGCCTCTCTCT CTTTAGTCTCCTACCTCTGCCCCAAGATGCCAGAGTTCCT|GACACTCTTCTCATG|GTGTCCTCTTCCTGCCCATGCCCTGGTCCAGCCTCTCTCT ========= Event 260 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: ctgtatctcacacaggctgtaGCTGTAAGGATACATACTAGAAAAAGCAGAAACCTTTGCTTTTTATGTAGGTAGAGGAGAGTGG ↓ 3 2 1 4 Chimp: ctgtatctcacacaggctgtaGCTGTAAGGATACATACTAGAAAAAGCAGAAACC--AG--CTATATGTAGGTAGAAGAGAGTGG Gorilla: CTGTATCTCACACAGGCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACC--AG--CTATATGTAGGTAGAAGAGAGTGG Human: ctgtatctcacacaggctgtaGCTGTAAGGATACATACTAGAAAAAGCAGAAACCTTTGCTTTTTATGTAGGTAGAGGAGAGTGG Cluster: [ ] Orangutan: CTGTATCTCACACAGGCTGTAGCTGTAAGGAAACATACTAGAAAAAGCAGAAACC--AG--CTATATGTAGGTAGAGAAGAGTGG Human > Chimp ------------- chr11:8060111-8060115 Template switch process: F1: L GGCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACC 1 F3: 4 TATGTAGGTAGAAGAGAGTGGCAGTAGGTATTTCATACTT R RF: GGCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACCTTTGCTTTTTATGTAGGTAGAGGAGAGTGGCAGTAGGTATTTCATACTT RR: CCGACATCGACATTCCTATGTATGATCTTTTTCGTCTTTGGAAACGAAAAATACATCCATCTCCTCTCACCGTCATCCATAAAGTATGAA F2: 3 ATCGA 2 Unidirectional alignment (log-probability: -34.8) GCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACCagcta---------TATGTAGGTAGAaGAGAGTGGCAGTAGGTATTTCATACTT GCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACC-----TTTGCTTTTTATGTAGGTAGAGGAGAGTGGCAGTAGGTATTTCATACTT Template switch alignment (log-probability: -21.9) GCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACC|AGCTA|TATGTAGGTAGAaGAGAGTGGCAGTAGGTATTTCATACTT GCTGTAGCTGTAAGGATACATACTAGAAAAAGCAGAAACC|AGCTA|TATGTAGGTAGAGGAGAGTGGCAGTAGGTATTTCATACTT ========= Event 261 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGGAGGACCAAGGGCAAGTTTGGGTCTAAACAACCCAGTCTGAAGGAAGGGGAGATGCTTGCTCCT Chimp: TGGGAGGACCAAGGGCAAGTTTGGGTCTAAACAACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCT ↓ 1 4 3 2 Gorilla: TGGGAGGACCAAGGGCAAGTT---CCCTC--AGACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCT ↑ 1 4 3 2 Human: TGGGAGGACCAAGGGCAAGTTTGGGTCTAAACAACCCAGTCTGAAGGAAGGGGAGATGCTTGCTCCT Cluster: [ ] Orangutan: ------------------------------------------------------------------- Human > Gorilla --------------- chr11:8120335-8120341 Template switch process: F1: L TAGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT 1 F3: 4 ACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA R RF: TAGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTTTGGGTCTAAACAACCCAGTCTGAAGGAAGGGGAGATGCTTGCTCCTCACAAA RR: ATCTCCCTTTATCGTCGTAAACCCTCCTGGTTCCCGTTCAAACCCAGATTTGTTGGGTCAGACTTCCTTCCCCTCTACGAACGAGGAGTGTTT F2: 3 GACTCCC 2 Unidirectional alignment (log-probability: -36.8) AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT------------ccctcagACCCAGTCTGAgGGAAGGGGAGATGCTTGCTCCTCACAAA AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTTTGGGTCTAAACA-------ACCCAGTCTGAAGGAAGGGGAGATGCTTGCTCCTCACAAA Template switch alignment (log-probability: -27.7) AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT|CCcTCAG|ACCCAGTCTGAgGGAAGGGGAGATGCTTGCTCCTCACAAA AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT|CCTTCAG|ACCCAGTCTGAAGGAAGGGGAGATGCTTGCTCCTCACAAA Chimp > Gorilla --------------- chr11:8120335-8120341 Template switch process: F1: L TAGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT 1 F3: 4 ACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA R RF: TAGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTTTGGGTCTAAACAACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA RR: ATCTCCCTTTATCGTCGTAAACCCTCCTGGTTCCCGTTCAAACCCAGATTTGTTGGGTCAGACTCCCTTCCCCTCTACGAACGAGGAGTGTTT F2: 3 GACTCCC 2 Unidirectional alignment (log-probability: -31.3) AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT------------ccctcagACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTTTGGGTCTAAACA-------ACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA Template switch alignment (log-probability: -16.6) AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT|CCCTCAG|ACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA AGAGGGAAATAGCAGCATTTGGGAGGACCAAGGGCAAGTT|CCCTCAG|ACCCAGTCTGAGGGAAGGGGAGATGCTTGCTCCTCACAAA ========= Event 262 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGGTTGCTGCAGAGCAGCAACTGGACCTTTCCAGCTGTCGCCATGTTCCTTCCA Chimp: GGGGTTGCTGCAGAGCAGCAACTGGACCTTTCCAGCTGTCCCCATGTTCCTTCCA ↑ 1 4 3 2 Gorilla: GGGGTTGCTGCAGAGCAGCAA-TCCCCCTTTCCAGCTGTCCCCATGTTCCTTCCA ↓ 1 4 3 2 Human: GGGGTTGCTGCAGAGCAGCAACTGGACCTTTCCAGCTGTCGCCATGTTCCTTCCA Cluster: [ ] Orangutan: GGGGTTGCTGCAGAGCAGCAACTGGACCTTTCCAGCTGCCCCCATGTTCCTTCCA Gorilla > Human --------------- chr11:119302673-119302677 Template switch process: F1: L TTTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA 1 F3: 4 CCTTTCCAGCTGTCGCCATGTTCCTTCCACTAAAGTAGAG R RF: TTTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAATCCCCCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG RR: AAAGGTTCGACGGAACAACGCCCCAACGACGTCTCGTCGTTAGGGGGAAAGGTCGACAGGGGTACAAGGAAGGTGATTTCATCTC F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -32.1) TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA---CtggaCCTTTCCAGCTGTCgCCATGTTCCTTCCACTAAAGTAGAG TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAATCCC----CCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG Template switch alignment (log-probability: -21.9) TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA|CTGGA|CCTTTCCAGCTGTCgCCATGTTCCTTCCACTAAAGTAGAG TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA|CTGGA|CCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG Gorilla > Chimp --------------- chr11:119775651-119775655 Template switch process: F1: L TTTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA 1 F3: 4 CCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG R RF: TTTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAATCCCCCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG RR: AAAGGTTCGACGGAACAACGCCCCAACGACGTCTCGTCGTTAGGGGGAAAGGTCGACAGGGGTACAAGGAAGGTGATTTCATCTC F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -26.5) TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA---CtggaCCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAATCCC----CCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG Template switch alignment (log-probability: -16.4) TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA|CTGGA|CCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG TTCCAAGCTGCCTTGTTGCGGGGTTGCTGCAGAGCAGCAA|CTGGA|CCTTTCCAGCTGTCCCCATGTTCCTTCCACTAAAGTAGAG ========= Event 263 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGAGAAACCCCGGCTGGGGCC-CAG---GGTCCCTAAGGACAGCATCCCGCGCCCCCTCCCACTCCCGCGGGCC Chimp: GGGAGAAACCCCGGCTGAGGCC-CAG---GGTCCCTAAGGACAGCATCCCGCGCCCCCTCCCACTCCCGCGGGCC Gorilla: GGGAGAAACCCCGGCTGGGGACCCTGGGCTGTCCCTAAGGACAGCGTCCCGCGCTCCCTCCCACTCCCGCGGGCC ↓ 13 2 4 Human: GGGAGAAACCCCGGCTGGGGCC-CAG---GGTCCCTAAGGACAGCATCCCGCGCCCCCTCCCACTCCCGCGGGCC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr11:133955339-133955346 Template switch process: F1: L GAAACCCCGGCTGGGG 1 F3: 4 CCCTAAGGACAGCATCCCGCGCCCCCTCCCACTCCCGCGGGCCTCGTCGCTCGCCCACCCTGG R RF: GAAACCCCGGCTGGGGACCCTGGGCTGTCCCTAAGGACAGCGTCCCGCGCTCCCTCCCACTCCCGCGGGCCTCGTCGCTCGCCCACCCTGG RR: CTTTGGGGCCGACCCCTGGGACCCGACAGGGATTCCTGTCGCAGGGCGCGAGGGAGGGTGAGGGCGCCCGGAGCAGCGAGCGGGTGGGACC F2: 3 TGGGACCC 2 Unidirectional alignment (log-probability: -37.5) GAAACCCCGGCTGGGG-CCCaGG---GTCCCTAAGGACAGCaTCCCGCGCcCCCTCCCACTCCCGCGG GAAACCCCGGCTGGGGACCCTGGGCTGTCCCTAAGGACAGCGTCCCGCGCTCCCTCCCACTCCCGCGG Template switch alignment (log-probability: -27.7) GAAACCCCGGCTGGGG|CCCAGGGT|CCCTAAGGACAGCaTCCCGCGCcCCCTCCCACTCCCGCGG GAAACCCCGGCTGGGG|CCCAGGGT|CCCTAAGGACAGCGTCCCGCGCTCCCTCCCACTCCCGCGG ========= Event 264 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GCCCCACGAGAAGGGCAGACAA----------------------------------TGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCA ↓ 4 3 1 2 Chimp: GCCCCACGAGAAGGGCAGACAT-----------------GGGCACCCCAACTGATTGGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCA Gorilla: GCCCCAAGAGAAGGGCAGACATGGGCACCCCAACTGATT-----------------GGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCA ↑ 4 3 1 2 Human: GCCCCACGAGAAGGGCAGACAA----------------------------------TGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCA Cluster: [ ] Orangutan: Human > Chimp ------------- chr11:124731128-124731134 Template switch process: F1: L TATTCCATCTGGCTTGTCCAGCCCCACGAGAAGGGCAGAC-ATGGGCACCCCAA 1 F3: 4 GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA R RF: TATTCCATCTGGCTTGTCCAGCCCCACGAGAAGGGCAGACAATGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA RR: ATAAGGTAGACCGAACAGGTCGGGGTGCTCTTCCCGTCTGTTACCCGTGGGGTTAGTCATCACGGTTGATGACCCCGTGGGGT F2: 3 GTTAGTC 2 Unidirectional alignment (log-probability: -45.6) TTGTCCAGCCCCACGAGAAGGGCAGACAtgggcaccccaactgATtgGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA TTGTCCAGCCCCACGAGAAGGGCAGACA---------------AT--GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA Template switch alignment (log-probability: -26.6) TTGTCCAGCCCCACGAGAAGGGCAGAC-ATGGGCACCCCAA|CTGATTG|GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA TTGTCCAGCCCCACGAGAAGGGCAGACAATGGGCACCCCAA|CTGATTG|GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA Human > Gorilla --------------- chr11:124231977-124231983 Template switch process: F1: L TATTCCATCTGGCTTGTCCAGCCCCAAGAGAAGGGCAGAC-ATGGGCACCCCAA 1 F3: 4 GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA R RF: TATTCCATCTGGCTTGTCCAGCCCCACGAGAAGGGCAGACAATGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA RR: ATAAGGTAGACCGAACAGGTCGGGGTGCTCTTCCCGTCTGTTACCCGTGGGGTTAGTCATCACGGTTGATGACCCCGTGGGGT F2: 3 GTTAGTC 2 Unidirectional alignment (log-probability: -50.6) TTGTCCAGCCCCAaGAGAAGGGCAGACAtgggcaccccaactgATtgGGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA TTGTCCAGCCCCACGAGAAGGGCAGACA---------------AT--GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA Template switch alignment (log-probability: -32.2) TTGTCCAGCCCCAaGAGAAGGGCAGAC-ATGGGCACCCCAA|CTGATTG|GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA TTGTCCAGCCCCACGAGAAGGGCAGACAATGGGCACCCCAA|CTGATTG|GGGCACCCCAATCAGTAGTGCCAACTACTGGGGCACCCCA ========= Event 265 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: -------------------TT---TCAGTAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGGAATTGAAGCCCCTGGATAT-AAGGGGACCCCAGGGGAACTATCCCACCTTCTCTTCATTGGTCTTCTGACATTTTGGAAGACTTCTGCTGAACAGAGGATCTGTGCTTTAA Chimp: -------------------TT---TCAGTAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGGAATTGAAGCCCCTGGATAT-AAGGGGACCCCAGGGGAACTATCCCACCTTCTCTTCATTGGTCTTCCGACATTTTGGAAGACTTCTGCTGAACACAGGATCTGTGCTTTAA Gorilla: -------------------TTCTGCCCTTAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGGAATTGAAGCCCCTGGATAT-AAGGGGACCCCAGGGGAACTATCCCACCTTCTCTTCATTGGTCTTCTGACATTTTGGAAGACTTCTGCTGAACACAGGATCTGTGCTTTAA ↓ 1 4 3 2 Human: -------------------TT---TCAGTAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGGAATTGAAGCCCCTGGATAT-AAGGGGACCCCAGGGGAACTATCCCACCTTCTCTTCATTGGTCTTCTGACATTTTGGAAGACTTCTGCTGAACAGAGGATCTGTGCTTTAA Cluster: [ ] Orangutan: GAAGCCAGGTCTGCCTAGAGT---TCAGTA-GTCTAGCTGTGGGAAATGAGAGCCCACAGGGCATGGGAATTGAAGCCCCTGGATATAAAGGGGACCCCAGGGGAACTATCCCA-CTTCTCTTCATTGGTCTTCTGACATTTTGGAAGACTTCTGCTGAACACAGGATCTGTACTTTAA Gorilla > Human --------------- chr11:123924735-123924738 Template switch process: F1: L TCTTGATCAGTGATGGAGAAGCCAGGTCTGCCCTTAGAGTT 1 F3: 4 TAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGG R RF: TCTTGATCAGTGTTGGAGAAGCCAGGTCTGCCCTTAGAGTTCTGCCCTTAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGGAATTGAAGCCCCTGGATATAAGGGGACCCCAGGGGAACTATCCCACCTTCTCTTCATTGGTCTTCTGACATTTTGGAAGACTTCTGCTGA RR: AGAACTAGTCACAACCTCTTCGGTCCAGACGGGAATCTCAAGACGGGAATCAAGATCGACACCCTTTACTCTCGGTGGTCCCGTATCCTTAACTTCGGGGACCTATATTCCCCTGGGGTCCCCTTGATAGGGTGGAAGAGAAGTAACCAGAAGACTGTAAAACCTTCTGAAGACGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -30.8) CTTGATCAGTGaTGGAGAAGCCAGGTCTGCCCTTAGAGTT------TcagTAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGG CTTGATCAGTGTTGGAGAAGCCAGGTCTGCCCTTAGAGTTCTGCCCT---TAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGG Template switch alignment (log-probability: -21.7) CTTGATCAGTGaTGGAGAAGCCAGGTCTGCCCTTAGAGTT|TCAG|TAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGG CTTGATCAGTGTTGGAGAAGCCAGGTCTGCCCTTAGAGTT|TCAG|TAGTTCTAGCTGTGGGAAATGAGAGCCACCAGGGCATAGG ========= Event 266 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGTGAAGGCCAGGGGCTTCCCACTGGGTTTAGGTTGGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATGCAATCAAATCCTATCTGG-AGA ↓ 1 4 3 2 Chimp: AAGTGAAGGCCAGGGGCTTCCTGC-----------AGGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATGCAATCAAATCCTATTTGGAGGA Gorilla: AAGTGAAGGCCCGGGGCTTCCCACTGGGTTTAGGTTGGAGCTGGCCTGCAGGATAGATTGTGTACTGGATGTCATGCAATCAAATCCTATTTGGAGGA Human: AAGTGAAGGCCAGGGGCTTCCCACTGGGTTTAGGTTGGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATGCAATCAAATCCTATCTGG-AGA Cluster: [ ] Orangutan: AAGTGAAGGCCAGGGGCTTCCCACTGGGTTTAGGTTGGAGCTGTCCTGCAGGATAGCTTATGTACTGGATGTCATGCAATCAAATACTATTTGGAGGA Human > Chimp ------------- chr11:128859296-128859299 Template switch process: F1: L TCTGGCTCTGCATCCCTTTAAAGTGAAGGCCAGGGGCTTCC 1 F3: 4 GGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATG R RF: TCTGGCTCTGCATCCCTTTTAAGTGAAGGCCAGGGGCTTCCCACTGGGTTTAGGTTGGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATGCA RR: AGACCGAGACGTAGGGAAAATTCACTTCCGGTCCCCGAAGGGTGACCCAAATCCAACCTCGACCGGACGTCCTATCTAACACATGACCTATAGTACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -30.7) CTGGCTCTGCATCCCTTTaAAGTGAAGGCCAGGGGCTTCCtgCA-------------GGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATG CTGGCTCTGCATCCCTTTTAAGTGAAGGCCAGGGGCTTCC--CACTGGGTTTAGGTTGGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATG Template switch alignment (log-probability: -21.8) CTGGCTCTGCATCCCTTTaAAGTGAAGGCCAGGGGCTTCC|TGCA|GGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATG CTGGCTCTGCATCCCTTTTAAGTGAAGGCCAGGGGCTTCC|TGCA|GGAGCTGGCCTGCAGGATAGATTGTGTACTGGATATCATG ========= Event 267 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GATATTACTTGGCCCAATTTGACCAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAG--------CATGGTCACAATGGGGAATGGGAAT----- Chimp: GATATCACTTGGCCCAATTTGACCAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAG--------CATGGTCACAATGGGGAATGGGAAT----- ↑ 3 2 41 Gorilla: GATATCACTTGGCCCAATTTGACCAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAG----------------CAatggggaatgggaataagat ↓ 3 2 41 Human: GATATTACTTGGCCCAATTTGACCAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAG--------CATGGTCACAATGGGGAATGGGAAT----- Cluster: [ ] Orangutan: GATATCACTTGGCCCAATTTGACCATGCACCATCTGCTGGACCAAAGAATGGTGGCCAGAGGAGCATGGTCA--------CAATGGGGAATGGGAAT----- Gorilla > Human --------------- chr11:128184305-128184310 Template switch process: F1: L CAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCA 1 F3: 4 CAATGGGGAATGGGAAT R RF: TGACCAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCAATGGGGAATGGGAAT RR: ACTGGTTCGTGGTAGATGACCTGGTTTATTACCACCGGTCTCTTCGTTACCCCTTACCCTTA F2: 3 ACTGGT 2 Unidirectional alignment (log-probability: -30) GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGcatggtcaCAATGGGGAATGGGAAT----------------------- GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAG--------CAATGGGGAATGGGAATAAGATGGGGATCATATGGGGAGT Template switch alignment (log-probability: -15.9) GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCA|TGGTCA|CAATGGGGAATGGGAAT GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCA|TGGTCA|CAATGGGGAATGGGAAT Gorilla > Chimp --------------- chr11:128736084-128736089 Template switch process: F1: L CAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCA 1 F3: 4 CAATGGGGAATGGGAAT R RF: TGACCAAGCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCAATGGGGAATGGGAAT RR: ACTGGTTCGTGGTAGATGACCTGGTTTATTACCACCGGTCTCTTCGTTACCCCTTACCCTTA F2: 3 ACTGGT 2 Unidirectional alignment (log-probability: -30) GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGcatggtcaCAATGGGGAATGGGAAT----------------------- GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAG--------CAATGGGGAATGGGAATAAGATGGGGATCATATGGGGAGT Template switch alignment (log-probability: -15.9) GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCA|TGGTCA|CAATGGGGAATGGGAAT GCACCATCTACTGGACCAAATAATGGTGGCCAGAGAAGCA|TGGTCA|CAATGGGGAATGGGAAT ========= Event 268 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAAACAGAAGTGGTGGAGAGGA--------------ATATTCT----------------CCTGGGGGAAAATATTC-----CTTTCTTGAGAAAATAATAAATAAATAT Chimp: AGAAACAGAAGTGGTGGAGAGGA-------ATACAGAATATTAT--------CAATTATGGCTGGGGGAAAATATTC-----CTTTCTTGAGAAAATAAT----AAATAT ↓ 3 2 1 4 Gorilla: AGAAACAGAAGTGGTGGAGAGGAATACAGA-------ATATTATCAATTATG--------GCTGGGGGAAAGTATTC----------CTGAGaaaataataaataaatgt Human: AGAAACAGAAGTGGTGGAGAGGA--------------ATATTCT----------------CCTGGGGGAAAATATTC-----CTTTCTTGAGAAAATAATAAATAAATAT Cluster: [ ] Orangutan: AGAAACAGAAGTGGTGGAGAGGAATACAGA-------ATATTATCAATTATG--------GCTGGGGGAAAATATTCCTTTC-----TTGAGAAAATAATAAATTAATAT Chimp > Gorilla --------------- chr11:128229466-128229473 Template switch process: F1: L AAGATGGTTAGAACTCTCAGAAACAGAAGTGGTGGAGAGGAATACAGAATATTATCAATTATGGCTGGGGGAAA 1 F3: 4 GAGAAAATAATAAATA R RF: AAGATGGTTAGAACTCTCAGAAACAGAAGTGGTGGAGAGGAATACAGAATATTATCAATTATGGCTGGGGGAAAATATTCCTTTCTTGAGAAAATAATAAATA RR: TTCTACCAATCTTGAGAGTCTTTGTCTTCACCACCTCTCCTTATGTCTTATAATAGTTAATACCGACCCCCTTTTATAAGGAAAGAACTCTTTTATTATTTAT F2: 3 TCCTTATG 2 Unidirectional alignment (log-probability: -29.3) GAGAGGAATACAGAATATTATCAATTATGGCTGGGGGAAAgTATTCC-----TGAGAAAATAATAaata GAGAGGAATACAGAATATTATCAATTATGGCTGGGGGAAAATATTCCTTTCTTGAGAAAATAATA---- Template switch alignment (log-probability: -17) GAGAGGAATACAGAATATTATCAATTATGGCTGGGGGAAA|GTATTCCT|GAGAAAATAATAAATA GAGAGGAATACAGAATATTATCAATTATGGCTGGGGGAAA|GTATTCCT|GAGAAAATAATAAATA ========= Event 269 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAACCACGGAAAGCTCAATGTCCCAGCACAGGCTGG----------GACATTATTAAGAAAAAGCTGCCA Chimp: AAACCATGGAAAGCTCAATGTCCCAGCACAGGCTGA-----GGCCTGAGATTATTAAGAAAAAGCTGCCA Gorilla: AAACCATGGAAAGCTCAATGTCCCAGCACAAGCGGAGGCCT-----GAGATTATTAAGAAAAAGCTGCCA ↓ 3 2 1 4 Human: AAACCACGGAAAGCTCAATGTCCCAGCACAGGCTGG----------GACATTATTAAGAAAAAGCTGCCA Cluster: [ ] Orangutan: AAACCATGGAAAGCTCAATGTCCCGGCACAGGCTGAGGCCT-----GAGATTATTAAGAAAAAGCTGCCA Gorilla > Human --------------- chr11:14120605-14120610 Template switch process: F1: L AGGCTTAAGTGAAACCACGGAAAGCTCAATGTCCCAGCACAGGC 1 F3: 4 ATTATTAAGAAAAAGCTGCCAAGAGGCTGGAAAACAACTA R RF: AGGCTTAAGTGAAACCATGGAAAGCTCAATGTCCCAGCACAAGCGGAGGCCTGAGATTATTAAGAAAAAGCTGCCAAGAGGCTGGAAAACAACTA RR: TCCGAATTCACTTTGGTACCTTTCGAGTTACAGGGTCGTGTTCGCCTCCGGACTCTAATAATTCTTTTTCGACGGTTCTCCGACCTTTTGTTGAT F2: 3 CAGGGT 2 Unidirectional alignment (log-probability: -38.3) TTAAGTGAAACCAcGGAAAGCTCAATGTCCCAGCAC-------------AGgctgggacATTATTAAGAAAAAGCTGCCAAGAGGCTGGAAAACAACTA TTAAGTGAAACCATGGAAAGCTCAATGTCCCAGCACAAGCGGAGGCCTGAG--------ATTATTAAGAAAAAGCTGCCAAGAGGCTGGAAAACAACTA Template switch alignment (log-probability: -27.6) TTAAGTGAAACCAcGGAAAGCTCAATGTCCCAGCACAgGC|TGGGAC|ATTATTAAGAAAAAGCTGCCAAGAGGCTGGAAAACAACTA TTAAGTGAAACCATGGAAAGCTCAATGTCCCAGCACAAGC|TGGGAC|ATTATTAAGAAAAAGCTGCCAAGAGGCTGGAAAACAACTA ========= Event 270 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTTCTGCACTGAGCTGCCCCAGACTCCAGCTCCCCCACCCACTGCCTCTGGGCTGGCTTACTCCTGGAGGGCACAGCCCACGGTAGCAATGTCCCCTCTGGCCTGGCGACCCTGGCTTAGTCATTATGCAGGGTTTCCAGTCTG--GGGCTGGCTCTCTGGTGCCAAA Chimp: ACTTCTGCACTGAGCTGCCCCAGACTCCAGCTCCCCCACCCACTGCCTCTGGGCTGGCTTACTCCTGGAGGGCACAGCCCATGGTAGCAATGTCCCCTCTGGCCTGGCGACTCTGGCTTAGTCATTATGCAGGGTTTCCAGTCTG--GGGCTGGCTCTCTGGTGCCAAA Gorilla: ACTTCTGCACTGAGCTGCCCCAGACTCCAGCTCCCCCACCCACTGCCTCTGGGCTGGCTTACTCCTGGAGGGCACAGCCCACGGTAGCAATGTCCCCTCTGGCCTGACGACCCTGGCTTAGTCATTATGCAGGGTTTCCT-GCTGGCTGGCTGGCTCTCTGGTGCCAAA ↓ 3 2 1 4 Human: ACTTCTGCACTGAGCTGCCCCAGACTCCAGCTCCCCCACCCACTGCCTCTGGGCTGGCTTACTCCTGGAGGGCACAGCCCACGGTAGCAATGTCCCCTCTGGCCTGGCGACCCTGGCTTAGTCATTATGCAGGGTTTCCAGTCTG--GGGCTGGCTCTCTGGTGCCAAA Cluster: [ ] Orangutan: ACTTCTGCACTGAGCTGCCCCAGACTCCAGCTCCCCCACCCACTGCCTCTGGGCTGGCTTACTCCTGGAGGGCACAGCCCACTTTAGCAATGTCCCCTCTGGCCTGGCGACCCTGGCTTAGTCATTATGCAGGGTTTCCAGTCTG--GGGCTGGCTCTCTGGTGCCAAA Gorilla > Human --------------- chr11:125225667-125225673 Template switch process: F1: L CTGGCCTGGCGACCCTGGCTTAGTCATTATGCAGGGTTTCC 1 F3: 4 GGCTGGCTCTCTGGTGCCAAATACTGTCCTCTGCCTGTGC R RF: CCAGACTCCAGCTCCCCCACCCACTGCCTCTGGGCTGGCTTACTCCTGGAGGGCACAGCCCACGGTAGCAATGTCCCCTCTGGCCTGACGACCCTGGCTTAGTCATTATGCAGGGTTTCCTGCTGGCTGGCTGGCTCTCTGGTGCCAAATACTGTCCTCTGCCTGTGC RR: GGTCTGAGGTCGAGGGGGTGGGTGACGGAGACCCGACCGAATGAGGACCTCCCGTGTCGGGTGCCATCGTTACAGGGGAGACCGGACTGCTGGGACCGAATCAGTAATACGTCCCAAAGGACGACCGACCGACCGAGAGACCACGGTTTATGACAGGAGACGGACACG F2: 3 GGTCTGA 2 Unidirectional alignment (log-probability: -33.3) TGGCCTGgCGACCCTGGCTTAGTCATTATGCAGGGTTTCCaGtCTGG--GGCTGGCTCTCTGGTGCCAAATACTGTCCTCTGCCTGTGC TGGCCTGACGACCCTGGCTTAGTCATTATGCAGGGTTTCCTG-CTGGCTGGCTGGCTCTCTGGTGCCAAATACTGTCCTCTGCCTGTGC Template switch alignment (log-probability: -22.1) TGGCCTGgCGACCCTGGCTTAGTCATTATGCAGGGTTTCC|AGTCTGG|GGCTGGCTCTCTGGTGCCAAATACTGTCCTCTGCCTGTGC TGGCCTGACGACCCTGGCTTAGTCATTATGCAGGGTTTCC|AGTCTGG|GGCTGGCTCTCTGGTGCCAAATACTGTCCTCTGCCTGTGC ========= Event 271 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCTAATAAGTGACTTTTCCCTTATTAGGGAAAAAAGTATAAAAGTATTACTTTTATACTTTATAGTATAAAGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATATATTCAAATAC Chimp: ACCTAATAAGTGACTTTTCCCTTATTAGGGaaaaaagtataaaagtattacttttatactttatagtataaagtaaaaactttatactatatTCAAGTACTGTAAGTAATATATTCAAATAC Gorilla: ACCTAATAAGTGACTTTTCCCCTACAG-------------------------------------------TAGTAAAAACTTTATACTATATTcaagtactgtaagtaatatattcaaatac ↑ 1 4 3 2 Human: ACCTAATAAGTGACTTTTCCCTTATTAGGGAAAAAAGTATAAAAGTATTACTTTTATACTTTATAGTATAAAGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATATATTCAAATAC Cluster: [ ] Orangutan: ACCTAATAAGTGACCTTTCCCCTACAG-------------------------------------------TAGTAAATACTTTATACTATATTCAAGTACTGTAAGTAATATATTAAAATAC Human > Gorilla --------------- chr11:23641407-23641410 Template switch process: F1: L AATTACACAAGTCTCCTGGTACCTAATAAGTGACTTTTCCCCTA 1 F3: 4 AGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATA R RF: AATTACACAAGTCTCCTGGTACCTAATAAGTGACTTTTCCCTTATTAGGGAAAAAAGTATAAAAGTATTACTTTTATACTTTATAGTATAAAGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATA RR: TTAATGTGTTCAGAGGACCATGGATTATTCACTGAAAAGGGAATAATCCCTTTTTTCATATTTTCATAATGAAAATATGAAATATCATATTTCATTTTTGAAATATGATATAAGTTCATGACATTCATTAT F2: 3 TGAC 2 Unidirectional alignment (log-probability: -31.8) ACACAAGTCTCCTGGTACCTAATAAGTGACTTTTCCCctacagT-------------------------------------------------AGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATA ACACAAGTCTCCTGGTACCTAATAAGTGACTTTTCCC------TTATTAGGGAAAAAAGTATAAAAGTATTACTTTTATACTTTATAGTATAAAGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATA Template switch alignment (log-probability: -21.8) ACACAAGTCTCCTGGTACCTAATAAGTGACTTTTCCCcTA|CAGT|AGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATA ACACAAGTCTCCTGGTACCTAATAAGTGACTTTTCCCTTA|CAGT|AGTAAAAACTTTATACTATATTCAAGTACTGTAAGTAATA ========= Event 272 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 14 Detected in comparisons: 1234 Multiple sequence alignment: Human: TATGAACACATTTGAAGTGTTTTAGAA-----CACTGGTAGGTGGTTCTAC----AACACTTC-----------------AAATGTGACTTAAGGTAGATTTTAGGAGAACAAGGTTCTCC ↑ 13 24 Chimp: TATGAACACATTTGAAGTGTTGTAGAACCACCTACCAG-----TGTTCTAA----AACACTTC-----------------AAATGTGACTTAAGGTAGATTTTAGGAGAACAAGGTTCTCC Gorilla: TATGAACACATTTGAAGTGTTTTAGAA-----CACTGGTAGGTGGTTCTAC--------CTAC----------------------------------CAGTTTAGGAGAACAAGTTTCTCC ↑ 3 2 1 4 Human: TATGAACACATTTGAAGTGTTTTAGAA-----CACTGGTAGGTGGTTCTAC----AACACTTC-----------------AAATGTGACTTAAGGTAGATTTTAGGAGAACAAGGTTCTCC Cluster: [ ] Orangutan: TTAAATCACATTTGAAGTGTTTTAGAA-----CACTGGTAGGTGGATTTACAACA----CTTCAAATGTGACTTAAGGGA-----------------GATTTTAGGAGAACAAGGTTCTCT Chimp > Human ------------- chr11:124837379-124837403 Template switch process: F1: L ACCATCTGGAACTCATTCCCTATGAACACATTTGAAGTGTT 1 F3: 4 AACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACA R RF: ACCATCTGGAACTCAATCCCTATGAACACATTTGAAGTGTTGTAGAACCACCTACCAGTGTTCTAAAACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACA RR: TGGTAGACCTTGAGTTAGGGATACTTGTGTAAACTTCACAACATCTTGGTGGATGGTCACAAGATTTTGTGAAGTTTACACTGAATTCCATCTAAAATCCTCTTGT F2: 3 CATCTTGGTGGATGGTCACAAGATT 2 Unidirectional alignment (log-probability: -55.6) CCATCTGGAACTCAtTCCCTATGAACACATTTGAAGTGTTtTAGAAC-----------actggtaggtgGTTCTAcAACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACA CCATCTGGAACTCAATCCCTATGAACACATTTGAAGTGTTGTAGAACCACCTACCAGT-----------GTTCTAAAACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACA Template switch alignment (log-probability: -24.4) CCATCTGGAACTCAtTCCCTATGAACACATTTGAAGTGTT|TTAGAACACTGGTAGGTGGTTCTAC|AACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACA CCATCTGGAACTCAATCCCTATGAACACATTTGAAGTGTT|TTAGAACACTGGTAGGTGGTTCTAC|AACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACA Human > Gorilla --------------- chr11:124977828-124977834 Template switch process: F1: L ACACATTTGAAGTGTTTTAGAACACTGGTAGGTGGTTCTAC 1 F3: 4 TTTAGGAGAACAAGTTTCTCCTAAAGAGGAAAGATAGCAC R RF: ACACATTTGAAGTGTTTTAGAACACTGGTAGGTGGTTCTACAACACTTCAAATGTGACTTAAGGTAGATTTTAGGAGAACAAGGTTCTCCTAAAGAGGAAAGATAGCAC RR: TGTGTAAACTTCACAAAATCTTGTGACCATCCACCAAGATGTTGTGAAGTTTACACTGAATTCCATCTAAAATCCTCTTGTTCCAAGAGGATTTCTCCTTTCTATCGTG F2: 3 GACCATC 2 Unidirectional alignment (log-probability: -37.6) CACATTTGAAGTGTTTTAGAACACTGGTAGGTGGTTCTAC----------------------------ctaccagTTTAGGAGAACAAGtTTCTCCTAAAGAGGAAAGATAGCAC CACATTTGAAGTGTTTTAGAACACTGGTAGGTGGTTCTACAACACTTCAAATGTGACTTAAGGTAGAT-------TTTAGGAGAACAAGGTTCTCCTAAAGAGGAAAGATAGCAC Template switch alignment (log-probability: -22.1) CACATTTGAAGTGTTTTAGAACACTGGTAGGTGGTTCTAC|CTACCAG|TTTAGGAGAACAAGtTTCTCCTAAAGAGGAAAGATAGCAC CACATTTGAAGTGTTTTAGAACACTGGTAGGTGGTTCTAC|CTACCAG|TTTAGGAGAACAAGGTTCTCCTAAAGAGGAAAGATAGCAC ========= Event 273 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTCCACCTCCA-----CTTCTGTTGTTTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTCTGCTTCATACTAACACTGTCTTGCCAGAGTGCAACTC--TAGTGTTTTCAGAGTCGGTTTATGGCCTAACCCTGTTCTGAAGGCAATGCCTGATATAGAAAGCAGGCC ↓ 1 4 3 2 Chimp: TCTCCACCTCCA-----CTTCCATTGCTTTTAGAACAGAATACTTTAGAAAATTCTACAAC--TCTGCTTCATACTAACACTGTCTTGCCAGAGTGCAACTC--TAGTGTTTTCAGAGTCGGTTTATGGCCTAACCCTGTTCTGAAGGCGATGCCTGATATAGAAAGCAGGCC Gorilla: TCTCCACCTCCAACAGTATTCTGTTGTTTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTCTGCTTCATACTAACACTGTCTTGCCAGAGTGCAACTC--TAGTGTTTTCAGAGTCGGTTTATGGCCTAACCCTATTCTGAAGGCAATGCCTGATATAGAAAGCAGGCC Human: TCTCCACCTCCA-----CTTCTGTTGTTTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTCTGCTTCATACTAACACTGTCTTGCCAGAGTGCAACTC--TAGTGTTTTCAGAGTCGGTTTATGGCCTAACCCTGTTCTGAAGGCAATGCCTGATATAGAAAGCAGGCC Cluster: [ ] Orangutan: TCTCCACCTCCA-----CTTTTGTTGTTTTTAGAAAAGAATACTTTAGAAAATTCTACAACTCTCTTCTTCATACTAACACCATCTTGCCAGAGTGCAACTCTACAGTGTTTTCAGAGTCGGTTTATGGCCTAACCCTGTTCTGAAGGCAATGCCTGATATAGAAAGCAGGCC Human > Chimp ------------- chr11:125621911-125621916 Template switch process: F1: L AATCAAGAAAAACCAAAGCATCCCCTCTCCACCTCCACTTC 1 F3: 4 TTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTG R RF: AATCAAGAAAAACCAAAGCATCCCCTCTCCACCTCCACTTCTGTTGTTTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTCTGCTTCATACTAACACTGTCTTGCCAGAGTGCAACTCTAGTGTTTTCAGAGTCGGTTTATGGCCTAACCCTGTTCTGAAGGCAATG RR: TTAGTTCTTTTTGGTTTCGTAGGGGAGAGGTGGAGGTGAAGACAACAAAAATCTTGTCTTATGAAATCTTTTAAGATGTTGAGAGACGAAGTATGATTGTGACAGAACGGTCTCACGTTGAGATCACAAAAGTCTCAGCCAAATACCGGATTGGGACAAGACTTCCGTTAC F2: 3 CGTTAC 2 Unidirectional alignment (log-probability: -29) ATCAAGAAAAACCAAAGCATCCCCTCTCCACCTCCACTTCcaTTGcTTTTAGAACAGAATACTTTAGAAAATTCTACAA--CTCTG ATCAAGAAAAACCAAAGCATCCCCTCTCCACCTCCACTTCTGTTGTTTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTCTG Template switch alignment (log-probability: -22) ATCAAGAAAAACCAAAGCATCCCCTCTCCACCTCCACTTC|CATTGC|TTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTg ATCAAGAAAAACCAAAGCATCCCCTCTCCACCTCCACTTC|CATTGC|TTTTAGAACAGAATACTTTAGAAAATTCTACAACTCTC ========= Event 274 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: CAGCTGAACAGATGGGTTTAAAAAAACTT-GAGATTATTTCACTCTCCAGAATCTCCAAGTCATTTTAT-ATGTTAT ↓ 13 24 ↑ 13 24 Chimp: CAGCTGAACAGATGGGTTTAATAAAACTTGGAGATTCTGGAGAGTGAAATAATC-TCAAGTCATTTTAT-ATGTTAT Gorilla: CAGCTGAACAGATGGGTTTAATAAAACTT-GAGATTATTTCACTCTCCAGAATCTCCAAGTCATTTTATATTGTTAT Human: CAGCTGAACAGATGGGTTTAAAAAAACTT-GAGATTATTTCACTCTCCAGAATCTCCAAGTCATTTTAT-ATGTTAT Cluster: [ ] Orangutan: CAGCTGAACAGATGGGTTTAATAAAACTT-GAGGTTATTTCACTCTCCAGAATCTCCAAGTCATTTTATATTGTTAC Chimp > Human ------------- chr11:106306990-106307014 Template switch process: F1: L CTCTGACTTGAAGAAGTGCACAGCTGAACAGATGGGTTTAAAAAAACTTG 1 F3: 4 CAAGTCATTTTATATGTTATTTCTAGGCCTTCCAAATACT R RF: CTCTGACTTGAAGAAGTGCACAGCTGAACAGATGGGTTTAATAAAACTTGGAGATTCTGGAGAGTGAAATAATCTCAAGTCATTTTATATGTTATTTCCAGGCCTTCCAAATACT RR: GAGACTGAACTTCTTCACGTGTCGACTTGTCTACCCAAATTATTTTGAACCTCTAAGACCTCTCACTTTATTAGAGTTCAGTAAAATATACAATAAAGGTCCGGAAGGTTTATGA F2: 3 CTCTAAGACCTCTCACTTTATTAGA 2 Unidirectional alignment (log-probability: -70.4) AAGAAGTGCACAGCTGAACAGATGGGTTTAAaAAAACTTG-------------------------agattatttcactctccagaatctcCAAGTCATTTTATATGTTATTTCtAGGCCTTCCAAATACT AAGAAGTGCACAGCTGAACAGATGGGTTTAATAAAACTTGGAGATTCTGGAGAGTGAAATAATCT-------------------------CAAGTCATTTTATATGTTATTTCCAGGCCTTCCAAATACT Template switch alignment (log-probability: -30.5) AAGAAGTGCACAGCTGAACAGATGGGTTTAAaAAAACTTG|AGATTATTTCACTCTCCAGAATCTC|CAAGTCATTTTATATGTTATTTCtAGGCCTTCCAAATACT AAGAAGTGCACAGCTGAACAGATGGGTTTAATAAAACTTG|AGATTATTTCACTCTCCAGAATCTC|CAAGTCATTTTATATGTTATTTCCAGGCCTTCCAAATACT Human > Chimp ------------- chr11:106545067-106545091 Template switch process: F1: L CTCTGACTTGAAGAAGTGCACAGCTGAACAGATGGGTTTAATAAAACTTG 1 F3: 4 CAAGTCATTTTATATGTTATTTCCAGGCCTTCCAAATACT R RF: CTCTGACTTGAAGAAGTGCACAGCTGAACAGATGGGTTTAAAAAAACTTGAGATTATTTCACTCTCCAGAATCTCCAAGTCATTTTATATGTTATTTCTAGGCCTTCCAAATACT RR: GAGACTGAACTTCTTCACGTGTCGACTTGTCTACCCAAATTTTTTTGAACTCTAATAAAGTGAGAGGTCTTAGAGGTTCAGTAAAATATACAATAAAGATCCGGAAGGTTTATGA F2: 3 TCTAATAAAGTGAGAGGTCTTAGAG 2 Unidirectional alignment (log-probability: -70.4) AAGAAGTGCACAGCTGAACAGATGGGTTTAAtAAAACTTG-------------------------gagattctggagagtgaaataatctCAAGTCATTTTATATGTTATTTCcAGGCCTTCCAAATACT AAGAAGTGCACAGCTGAACAGATGGGTTTAAAAAAACTTGAGATTATTTCACTCTCCAGAATCTC-------------------------CAAGTCATTTTATATGTTATTTCTAGGCCTTCCAAATACT Template switch alignment (log-probability: -30.5) AAGAAGTGCACAGCTGAACAGATGGGTTTAAtAAAACTTG|GAGATTCTGGAGAGTGAAATAATCT|CAAGTCATTTTATATGTTATTTCcAGGCCTTCCAAATACT AAGAAGTGCACAGCTGAACAGATGGGTTTAAAAAAACTTG|GAGATTCTGGAGAGTGAAATAATCT|CAAGTCATTTTATATGTTATTTCTAGGCCTTCCAAATACT ========= Event 275 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGTGGAAAAACCCACTCCTATTGCTCAGTTGGGCAGTTGCAA ↓ 3 2 1 4 Chimp: ATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGTTGGGAAA----------CTGCTCAGTTGGGCAGTTGCAA Gorilla: ATAACTTTCTCTTCAGGTCATTTCCCACAAAATTGGGTGGAAAAACCCACTCCTATTGCTCAGTTGGGCAGTTGCAA Human: ATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGTGGAAAAACCCACTCCTATTGCTCAGTTGGGCAGTTGCAA Cluster: [ ] Orangutan: ATAACTTTCTCTTCAGGTCATTTCCCACAAAATTGGGTGGAAAAACCCACTCCTATTGCTCAATTGGGCAGTTGCAA Human > Chimp ------------- chr11:112518054-112518061 Template switch process: F1: L AATATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGT 1 F3: 4 TGCTCAGTTGGGCAGTTGCAACGATGAGCTAAATCAATTG R RF: AATATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGTGGAAAAACCCACTCCTATTGCTCAGTTGGGCAGTTGCAACGATGAGCTAAATCAATTG RR: TTATATTGAAAGAGAAGTCCAGCAAAGGGTGTTTTAACCCACCTTTTTGGGTGAGGATAACGAGTCAACCCGTCAACGTTGCTACTCGATTTAGTTAAC F2: 3 CAAAGGGT 2 Unidirectional alignment (log-probability: -29.5) ATATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGTtGggAAAC----------TGCTCAGTTGGGCAGTTGCAACGATGAGCTAAATCAATTG ATATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGTGGAAAAACCCACTCCTATTGCTCAGTTGGGCAGTTGCAACGATGAGCTAAATCAATTG Template switch alignment (log-probability: -16.3) ATATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGT|TGGGAAAC|TGCTCAGTTGGGCAGTTGCAACGATGAGCTAAATCAATTG ATATAACTTTCTCTTCAGGTCGTTTCCCACAAAATTGGGT|TGGGAAAC|TGCTCAGTTGGGCAGTTGCAACGATGAGCTAAATCAATTG ========= Event 276 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGACGGAATCCCAGCAACATAT-CCCTAAGTTATTAGGGATAGTCCTTTAGGGCATCATT Chimp: AGACGGAATCCCAGCAACATAT-CCCTAAGTTATTAGGGATAGTCTTTTAGGGCATCATT ↑ 31 4 2 Gorilla: AGACGGAATCCCAGCAACATAA----------CTTAGGGATAGTCTTTTAGGGCATCATT ↓ 31 4 2 Human: AGACGGAATCCCAGCAACATAT-CCCTAAGTTATTAGGGATAGTCCTTTAGGGCATCATT Cluster: [ ] Orangutan: AGACGGAATCCCAGCAACAT--A---------ATTAGGGATAGTCTTTTAGGGCATCATT Gorilla > Human --------------- chr11:12626201-12626211 Template switch process: F1: L GGAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATA 1 F3: 4 TTAGGGATAGTCCTTTAGGGCATCATTTCTTCATTTGTCA R RF: GGAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATAACTTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA RR: CCTTCTGTAAGGGTGGGTAGTCTGCCTTAGGGTCGTTGTATTGAATCCCTATCAGAAAATCCCGTAGTAAAGAAGTAAACAGT F2: 3 ATTGAATCCCT 2 Unidirectional alignment (log-probability: -34.9) GAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATAtCcctaagttaTTAGGGATAGTCcTTTAGGGCATCATTTCTTCATTTGTCA GAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATAAC---------TTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA Template switch alignment (log-probability: -22.6) GAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATA|TCCCTAAGTTA|TTAGGGATAGTCcTTTAGGGCATCATTTCTTCATTTGTCA GAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATA|TCCCTAAGTTA|TTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA Gorilla > Chimp --------------- chr11:12511806-12511816 Template switch process: F1: L GGAAGACATTCCCACCGATCAGACGGAATCCCAGCAACATA 1 F3: 4 TTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA R RF: GGAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATAACTTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA RR: CCTTCTGTAAGGGTGGGTAGTCTGCCTTAGGGTCGTTGTATTGAATCCCTATCAGAAAATCCCGTAGTAAAGAAGTAAACAGT F2: 3 ATTGAATCCCT 2 Unidirectional alignment (log-probability: -34.9) GAAGACATTCCCACCgATCAGACGGAATCCCAGCAACATAtCcctaagttaTTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA GAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATAAC---------TTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA Template switch alignment (log-probability: -22.6) GAAGACATTCCCACCgATCAGACGGAATCCCAGCAACATA|TCCCTAAGTTA|TTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA GAAGACATTCCCACCCATCAGACGGAATCCCAGCAACATA|TCCCTAAGTTA|TTAGGGATAGTCTTTTAGGGCATCATTTCTTCATTTGTCA ========= Event 277 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGTGATTTGGGGAAAATTCTGG----------TGTTCAGATCAAATTCTACAATGCTTATAGTAACTGCTGCAACagatatcatttactgcaactttactgtatgccaggcccctggtgagtactttaaatgtattatttaatta Chimp: TTGTGATTTGGGGAAAATTCTGG----------TGTTCAGATCAAATTTTACAATGCTTATAGTAACTGCTGCAACagatatcatttactgcaactttactgtatgccaggcccctggtgagtactttaaatgtattatttaatta ↓ 1 4 3 2 Gorilla: TTGTGGTTTGGGGAAAATTCTTG--------------------TAGTACTACAATGCTTATAGTAACTGCTGCAACagatatcatttactgcaactttactgtatgccaggcccctggtgagtactttaaatgtattatttaatta Human: TTGTGATTTGGGGAAAATTCTGG----------TGTTCAGATCAAATTCTACAATGCTTATAGTAACTGCTGCAACagatatcatttactgcaactttactgtatgccaggcccctggtgagtactttaaatgtattatttaatta Cluster: [ ] Orangutan: TTGTGATTTGGGGAAAATTCTGGTGTTCAGATC----------AAATTTTACAATGCTTATAGTAACTGCTGCAACagatatcatttactgcaactttactatatgccaggcccctggtgagtagtttaaatgtattatttaatta Chimp > Gorilla --------------- chr11:12594033-12594037 Template switch process: F1: L TACATAGATAGTCTGCATGCTTGTGGTTTGGGGAAAATTCTTGT 1 F3: 4 TACAATGCTTATAGTAACTGCTGCAACAGATATCATTTAC R RF: TACATAGATAGTCTGCATGCTTGTGATTTGGGGAAAATTCTGGTGTTCAGATCAAATTTTACAATGCTTATAGTAACTGCTGCAACAGATATCATTTACTGCAACTTTACTGTATGCCAGGCCCCTGGTGAGTACT RR: ATGTATCTATCAGACGTACGAACACTAAACCCCTTTTAAGACCACAAGTCTAGTTTAAAATGTTACGAATATCATTGACGACGTTGTCTATAGTAAATGACGTTGAAATGACATACGGTCCGGGGACCACTCATGA F2: 3 CATGA 2 Unidirectional alignment (log-probability: -37.1) TAGATAGTCTGCATGCTTGTGgTTTGGGGAAAATTC-----------------TTgtagtacTACAATGCTTATAGTAACTGCTGCAACAGATATCATTTAC TAGATAGTCTGCATGCTTGTGATTTGGGGAAAATTCTGGTGTTCAGATCAAATTT-------TACAATGCTTATAGTAACTGCTGCAACAGATATCATTTAC Template switch alignment (log-probability: -27.5) TAGATAGTCTGCATGCTTGTGgTTTGGGGAAAATTCTtGT|AGTAC|TACAATGCTTATAGTAACTGCTGCAACAGATATCATTTAC TAGATAGTCTGCATGCTTGTGATTTGGGGAAAATTCTGGT|AGTAC|TACAATGCTTATAGTAACTGCTGCAACAGATATCATTTAC ========= Event 278 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCTCCTGAACACCTCTCAAGT---------CCCACTGATGGTGGGAGTGAGGCTAAATGTTCTACAGTC Chimp: CCTCCTGAACACCTCTCAAGT---------CCCACTGATGGTGGGAGTGAGGCTAAATGTTCTACAGTC ↓ 13 4 2 ↑ 1 3 4 2 Gorilla: CCTCCTGAACACCTCTCAAGTCACACCACTCCCACCGTCAGTGGGAGTGAGGCTAAATGTTCTACAGTC ↓ 1 3 4 2 Human: CCTCCTGAACACCTCTCAAGT---------CCCACTGATGGTGGGAGTGAGGCTAAATGTTCTACAGTC Cluster: [ ] Orangutan: CCTCCTGAACACCTCTCAAGTCACACCACTCCCACCATCAGTGGGAGCGAGGCTAAATGTTCCACAGTC Gorilla > Human --------------- chr11:14340778-14340787 Template switch process: F1: L GCAAAGGGGCTCATCACTACCCTCCTGAACACCTCTCAAGTC 1 F3: 4 TGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT R RF: GCAAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCACACCACTCCCACCGTCAGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT RR: CGTTTCCCCGAATAGTGATGGGAGGACTTGTGGAGAGTTCAGTGTGGTGAGGGTGGCAGTCACCCTCACTCCGATTTACAAGATGTCAGGTTTTGTTCGA F2: 3 GGTAGTCACC 2 Unidirectional alignment (log-probability: -39.1) AAAGGGGCTcATCACTACCCTCCTGAACACCTCTCAAG---------TCCCACtGatgGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT AAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCACACCACTCCCACCGTCAGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT Template switch alignment (log-probability: -28) AAAGGGGCTcATCACTACCCTCCTGAACACCTCTCAAGTC|CCACTGAtGG|TGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT AAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTC|CCACTGACGG|TGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT Gorilla > Chimp --------------- chr11:14539718-14539727 Template switch process: F1: L GCAAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTC 1 F3: 4 TGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT R RF: GCAAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCACACCACTCCCACCGTCAGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT RR: CGTTTCCCCGAATAGTGATGGGAGGACTTGTGGAGAGTTCAGTGTGGTGAGGGTGGCAGTCACCCTCACTCCGATTTACAAGATGTCAGGTTTTGTTCGA F2: 3 GGTAGTCACC 2 Unidirectional alignment (log-probability: -33.6) AAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAG---------TCCCACtGatgGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT AAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCACACCACTCCCACCGTCAGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT Template switch alignment (log-probability: -22.5) AAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTC|CCACTGAtGG|TGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT AAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTC|CCACTGACGG|TGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT Chimp > Gorilla --------------- chr11:14466979-14466992 Template switch process: F1: L GCAAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCACAC 1 F3: 4 GTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT R RF: GCAAAGGGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCCCACTGATGGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT RR: CGTTTCCCCGAATAGTGATGGGAGGACTTGTGGAGAGTTCAGGGTGACTACCACCCTCACTCCGATTTACAAGATGTCAGGTTTTGTTCGA F2: 3 ACTGCCACCCTCAC 2 Unidirectional alignment (log-probability: -46) GGGCTTATCACTACCCTCCTGAACACCTCTCAAGtcacaccacTCCCACcGtcaGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT GGGCTTATCACTACCCTCCTGAACACCTCTCAAG---------TCCCACTGATGGTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT Template switch alignment (log-probability: -28.7) GGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCaCAC|CACTCCCACCgTCA|GTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT GGGCTTATCACTACCCTCCTGAACACCTCTCAAGTCCCAC|CACTCCCACCATCA|GTGGGAGTGAGGCTAAATGTTCTACAGTCCAAAACAAGCT ========= Event 279 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GGCACTGCATGTGGGGTTAGA-----------------AAGACTTTAGTCTTGGCATTGTGGGAATGGGAGTAAT ↓ 1 3 4 2 Chimp: GGCACTGCATTTGGGGTTAGA----------AAGGGCCAAGACTAAAGTCTTGGCATTGTGGGAATGGGAGTAAT Gorilla: nnnnnnnnnnnnnnnnnnnnn-------nnn-------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Human: GGCACTGCATGTGGGGTTAGA-----------------AAGACTTTAGTCTTGGCATTGTGGGAATGGGAGTAAT Cluster: [ ] Orangutan: GGCACTGCATTTGCGGTTAGAAAGGGCC----------AAGACTAAAGTCTTGGCATTGTGGGAATGTGAGTAAT Human > Chimp ------------- chr11:130250756-130250766 Template switch process: F1: L GGACCTCAGGTGAATGATGAGGCACTGCATTTGGGGTTAGAAAGG 1 F3: 4 AGTCTTGGCATTGTGGGAATGGGAGTAATGCCTTTTTAGA R RF: GGACCTCAGGTGAATGATGAGGCACTGCATGTGGGGTTAGAAAGACTTTAGTCTTGGCATTGTGGGAATGGGAGTAATGCCTTTTTAGA RR: CCTGGAGTCCACTTACTACTCCGTGACGTACACCCCAATCTTTCTGAAATCAGAACCGTAACACCCTTACCCTCATTACGGAAAAATCT F2: 3 AATCAGAACCG 2 Unidirectional alignment (log-probability: -39) TCAGGTGAATGATGAGGCACTGCATtTGGGGTTAGAaagggccAAGACTaaAGTCTTGGCATTGTGGGAATGGGAGTAATGCCTTTTTAGA TCAGGTGAATGATGAGGCACTGCATGTGGGGTTAGA-------AAGACTTTAGTCTTGGCATTGTGGGAATGGGAGTAATGCCTTTTTAGA Template switch alignment (log-probability: -28.7) TCAGGTGAATGATGAGGCACTGCATtTGGGGTTAGAAAGg|GCCAAGACTAA|AGTCTTGGCATTGTGGGAATGGGAGTAATGCCTTTTTAGA TCAGGTGAATGATGAGGCACTGCATGTGGGGTTAGAAAGA|GCCAAGACTAA|AGTCTTGGCATTGTGGGAATGGGAGTAATGCCTTTTTAGA ========= Event 280 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTAATTAAATGAAAATTTATTAAATGT--ATATCTAT--TTATATCTATTGATATATTAACAGATGCCAGTGCATATCTATTAAAAGAGTAC Chimp: ACTAATTAAATGAAAATTTATTAAATGT--ATATCTAT--TTATATCTATTGATATATTAACAGATACCAGTGCATATCTATTAAAAGAGTAC ↓ 1 4 3 2 Gorilla: ACTAATTAAATGAAAATTTATCACTGGT----ATCTATTAATATATCTATTGATATATTAACAGATACCAGTGCATATCTATTAAAAGAGTAC Human: ACTAATTAAATGAAAATTTATTAAATGT--ATATCTAT--TTATATCTATTGATATATTAACAGATGCCAGTGCATATCTATTAAAAGAGTAC Cluster: [ ] Orangutan: actaattaaatgaaaatttattaaatgtat--atctat--tTATATCTATTGATATATTAACAGATACCAGTGCATATCTATTAAAAGAGTAC Chimp > Gorilla --------------- chr11:13177573-13177588 Template switch process: F1: L ATATCAGTTCACTAATGAATACTAATTAAATGAAAATTTAT 1 F3: 4 TATATCTATTGATATATTAACAGATACCAGTGCATATCTA R RF: ATATCAGTTCACTAATGAATACTAATTAAATGAAAATTTATTAAATGTATATCTATTTATATCTATTGATATATTAACAGATACCAGTGCATATCTA RR: TATAGTCAAGTGATTACTTATGATTAATTTACTTTTAAATAATTTACATATAGATAAATATAGATAACTATATAATTGTCTATGGTCACGTATAGAT F2: 3 AATTATCTATGGTCAC 2 Unidirectional alignment (log-probability: -40) TATCAGTTCACTAATGAATACTAATTAAATGAAAATTTatcactggtatctATTAA-------------TATATCTATTGATATATTAACAGATACCAGTGCATATCTA TATCAGTTCACTAATGAATACTAATTAAATGAAAATTT-------------ATTAAATGTATATCTATTTATATCTATTGATATATTAACAGATACCAGTGCATATCTA Template switch alignment (log-probability: -23.3) TATCAGTTCACTAATGAATACTAATTAAATGAAAATTTAT|CACTGGTATCTaTTAA|TATATCTATTGATATATTAACAGATACCAGTGCATATCTA TATCAGTTCACTAATGAATACTAATTAAATGAAAATTTAT|CACTGGTATCTGTTAA|TATATCTATTGATATATTAACAGATACCAGTGCATATCTA ========= Event 281 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAATAAGCAGCTTATCTGCTCGGAGA-----------AATCACCCCAGATCCTGAAGATCCT ↓ 3 1 42 Chimp: TCAATAAGCAGCTTATCTGCTCGGAGAATGATTTCTCTGAGCACCCCAGATCCTGAAGATCCT ↑ 3 1 42 Gorilla: TCAATAAGCAGCTTATCTGCTCGGAGA-----------AATCACCCCAGATCCTGAAGATCCT Human: TCAATAAGCAGCTTATCTGCTCGGAGA-----------AATCACCCCAGATCCTGAAGATCCT Cluster: [ ] Orangutan: TCAATAAGCAGCTTATCTGCTTGGAGA-----------AATCACCCCAGATCCTGAAGATCCC Human > Chimp ------------- chr11:4754206-4754218 Template switch process: F1: L TGCTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA 1 F3: 4 CACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT R RF: TGCTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAAATCACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT RR: ACGATGTCACTGAAAGTTATTCGTCGAATAGACGAGCCTCTTTAGTGGGGTCTAGGACTTCTAGGACCGAGGAAAGGACGTAAA F2: 3 GAGTCTCTTTAGT 2 Unidirectional alignment (log-probability: -32.8) CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAAtgatttctctgAgCACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA-----------ATCACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT Template switch alignment (log-probability: -22.9) CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA|TGATTTCTCtGAG|CACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA|TGATTTCTCCGAG|CACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT Gorilla > Chimp --------------- chr11:4754206-4754218 Template switch process: F1: L TGCTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA 1 F3: 4 CACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT R RF: TGCTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAAATCACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT RR: ACGATGTCACTGAAAGTTATTCGTCGAATAGACGAGCCTCTTTAGTGGGGTCTAGGACTTCTAGGACCGAGGAAAGGACGTAAA F2: 3 GAGTCTCTTTAGT 2 Unidirectional alignment (log-probability: -32.3) CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAAtgatttctctgAgCACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA-----------ATCACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT Template switch alignment (log-probability: -22.9) CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA|TGATTTCTCtGAG|CACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT CTACAGTGACTTTCAATAAGCAGCTTATCTGCTCGGAGAA|TGATTTCTCCGAG|CACCCCAGATCCTGAAGATCCTGGCTCCTTTCCTGCATTT ========= Event 282 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGGCCAGGGAGGCATTTTTGCCTCCCTGGAGATGGCAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACGGGCAAGATGGTAGCTTCTTTTTTGTAAGCCTGTCTTTCCGGGTCTTGCCCTCCCGGAAACACTAAGCAGTTCAAATACCCATTGTCAATTTCAGCATGCCATCCC ↓ 1 4 3 2 Chimp: GGGCCAGGGAGGCATTTTTGC-------ACGATG-GAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACGGGCAAGATGGTAGCTTCTTTTTTGTAAGCCTGTCTTTCCGGGTCTTGCCCTCCCGGAAACACTAAGCAGTTCAAATACCCATTGTCAATTTCAGCATGCCATCCC Gorilla: GGGCCAGGGAGGCATTTTTGC-------ACGATG-GAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACGGGCAAGATGGTAGCTTCTTTTTTGTAAGCCTGTCTTTCCGGGTCTTGCCCTCCCAGTAACACTAAGCAGTTCAAACACCCATTGTCAATTTCAGCATGCCATCCC ↑ 1 4 3 2 Human: GGGCCAGGGAGGCATTTTTGCCTCCCTGGAGATGGCAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACGGGCAAGATGGTAGCTTCTTTTTTGTAAGCCTGTCTTTCCGGGTCTTGCCCTCCCGGAAACACTAAGCAGTTCAAATACCCATTGTCAATTTCAGCATGCCATCCC Cluster: [ ] Orangutan: GGGTCACGGAGGCATTTTTGC-------ACTACG-GAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACAGGCAAGATGGTAGCTTCTTTTTTGAAAGCCTGTCTTTCCGGGTCTTGCCCTCCCAGAAACACTAAGCAGTTCAAACACCCATTGTCAATTTCAGCATGCCATCCC Human > Chimp ------------- chr11:131286164-131286170 Template switch process: F1: L AGCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC 1 F3: 4 AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT R RF: AGCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGCCTCCCTGGAGATGGCAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACGGGCAAGATGGTAGCTTCTTTTTTGTAAGCCTGTCTTTCCGGGTCTTGCCCTCCCGGAAACACTAAGCAGTTCAAATACCCATTGT RR: TCGATCTTGTCAGTGGGTTACCCGGTCCCTCCGTAAAAACGGAGGGACCTCTACCGTCTTACCCATTATGAGAGTTATATTGAAAGGACGGTAACAAGTGCCCGTTCTACCATCGAAGAAAAAACATTCGGACAGAAAGGCCCAGAACGGGAGGGCCTTTGTGATTCGTCAAGTTTATGGGTAACA F2: 3 GGTAGCA 2 Unidirectional alignment (log-probability: -32) GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGCacgatgg---------------AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC-------CTCCCTGGAGATGGCAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT Template switch alignment (log-probability: -22.1) GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC|ACgATGG|AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC|ACAATGG|AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT Human > Gorilla --------------- chr11:130914476-130914482 Template switch process: F1: L AGCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC 1 F3: 4 AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT R RF: AGCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGCCTCCCTGGAGATGGCAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGTTCACGGGCAAGATGGTAGCTTCTTTTTTGTAAGCCTGTCTTTCCGGGTCTTGCCCTCCCGGAAACACTAAGCAGTTCAAATACCCATTGT RR: TCGATCTTGTCAGTGGGTTACCCGGTCCCTCCGTAAAAACGGAGGGACCTCTACCGTCTTACCCATTATGAGAGTTATATTGAAAGGACGGTAACAAGTGCCCGTTCTACCATCGAAGAAAAAACATTCGGACAGAAAGGCCCAGAACGGGAGGGCCTTTGTGATTCGTCAAGTTTATGGGTAACA F2: 3 GGTAGCA 2 Unidirectional alignment (log-probability: -31.5) GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTG---------------CacgatggAGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGCCTCCCTGGAGATGGC-------AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT Template switch alignment (log-probability: -22.1) GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC|ACgATGG|AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT GCTAGAACAGTCACCCAATGGGCCAGGGAGGCATTTTTGC|ACAATGG|AGAATGGGTAATACTCTCAATATAACTTTCCTGCCATTGT ========= Event 283 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: aatgaactaatGAATCCAGGGATACA---GGC------------TGGGGCTGGGGCTGGGTGGG Chimp: aatgaactaatGAATCCAGGGATACA---GGC------------TGGGGCTGGGGCTGGGTGGG ↓ 3 1 2 4 Gorilla: aatgaactaatGAATCCAGGGATCTGTATCCC------------TGGGGCTGGGGCTGGGTGGG ↑ 3 1 2 4 Human: aatgaactaatGAATCCAGGGATACA---GGC------------TGGGGCTGGGGCTGGGTGGG Cluster: [ ] Orangutan: aatgaactaatGAATCCAGGGATACA---GGCTGGGTCTGAGGCTGGGGCCGGGGCTAGGTGGG Human > Gorilla --------------- chr11:3943784-3943791 Template switch process: F1: L CTCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT 1 F3: 4 CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG R RF: CTCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGATACAGGCTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG RR: GAGTCATTTATAAACAAGTTACTTGATTACTTAGGTCCCTATGTCCGACCCCGACCCCGACCCACCCTCGTAACCATTATCTCACC F2: 3 CCTATGTC 2 Unidirectional alignment (log-probability: -32.4) TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT-----ctgtatccCTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGATACAGG--------CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG Template switch alignment (log-probability: -16.7) TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT|CTGTATCC|CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT|CTGTATCC|CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG Chimp > Gorilla --------------- chr11:3943784-3943791 Template switch process: F1: L CTCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT 1 F3: 4 CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG R RF: CTCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGATACAGGCTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG RR: GAGTCATTTATAAACAAGTTACTTGATTACTTAGGTCCCTATGTCCGACCCCGACCCCGACCCACCCTCGTAACCATTATCTCACC F2: 3 CCTATGTC 2 Unidirectional alignment (log-probability: -32.4) TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT-----ctgtatccCTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGATACAGG--------CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG Template switch alignment (log-probability: -16.7) TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT|CTGTATCC|CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG TCAGTAAATATTTGTTCAATGAACTAATGAATCCAGGGAT|CTGTATCC|CTGGGGCTGGGGCTGGGTGGGAGCATTGGTAATAGAGTGG ========= Event 284 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGCATGGCTGGATTTACTCAAGTGCAGAATCAGCTGGGCCTGATTGGCCCCCACAGCCTTCGTGGTTAATGAGTTTTCTGATGGCAGCAATGGCGGGAGCACAGAA Chimp: GAGCATGGCTGGATTTACTCA-ATGCCAAATCAGCTGGGCCTGATTGGCCCCCACAGCCTTCGTGGTTAATGAGTTTTCTGATGGCAGCAATGGCGGGAGCACAGAA ↑ 1 4 3 2 Gorilla: GAGCATGGCTGGATTTACTCAAGAGCAGAATCAGCTGGGCCTGATTGGCCCCCTCAGCCTTCATGGTTAATGAGTTTTCTGATGGCAGCAATGGCGGGAGCACAGAA Human: GAGCATGGCTGGATTTACTCAAGTGCAGAATCAGCTGGGCCTGATTGGCCCCCACAGCCTTCGTGGTTAATGAGTTTTCTGATGGCAGCAATGGCGGGAGCACAGAA Cluster: [ ] Orangutan: GAGCATGGCTGGATTTACTCAAGTGCAGAATCAGCTGGGCCTGACTGGCCCCCACAGCCTTCATGGTTAATGAGTTTTCTGACGGCAGCAATGGCAGGAGCACAGAA Gorilla > Chimp --------------- chr11:3874389-3874393 Template switch process: F1: L TGAGCTAGCCACATTCCAAGGAGCATGGCTGGATTTACTCAA 1 F3: 4 AATCAGCTGGGCCTGATTGGCCCCCACAGCCTTCGTGGTT R RF: TGAGCTAGCCACATTCCAAGGAGCATGGCTGGATTTACTCAAGAGCAGAATCAGCTGGGCCTGATTGGCCCCCTCAGCCTTCATGGTTAATGAGTTTTCTGATGGCA RR: ACTCGATCGGTGTAAGGTTCCTCGTACCGACCTAAATGAGTTCTCGTCTTAGTCGACCCGGACTAACCGGGGGAGTCGGAAGTACCAATTACTCAAAAGACTACCGT F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -38.6) AGCTAGCCACATTCCAAGGAGCATGGCTGGATTTACTCAAt-GCcaAATCAGCTGGGCCTGATTGGCCCCCaCAGCCTTCgTGGTT AGCTAGCCACATTCCAAGGAGCATGGCTGGATTTACTCAAGAGCAGAATCAGCTGGGCCTGATTGGCCCCCTCAGCCTTCATGGTT Template switch alignment (log-probability: -27.4) AGCTAGCCACATTCCAAGGAGCATGGCTGGATTTACTCAA|TGCCA|AATCAGCTGGGCCTGATTGGCCCCCaCAGCCTTCgTGGTT AGCTAGCCACATTCCAAGGAGCATGGCTGGATTTACTCAA|TGCCA|AATCAGCTGGGCCTGATTGGCCCCCTCAGCCTTCATGGTT ========= Event 285 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAACTTACAAAGTGTTGGATGTCCCCCGTT--CGAACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGG Chimp: GAAACTTACAAAGTGTTGGATTTCCCCCGTT--GGAACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGG ↓ 1 4 3 2 Gorilla: GAAACTTACGAAGTGTTGGATTTCCCCTGCA----GTCTGAGGGACTGCAGACCGCCTCTGGGTAGCTGG ↑ 1 4 3 2 Human: GAAACTTACAAAGTGTTGGATGTCCCCCGTT--CGAACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGG Cluster: [ ] Orangutan: GAAACTTACAAAGTGTTGGATTTCCCCTGTTCG--AACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGG Human > Gorilla --------------- chr11:132122015-132122021 Template switch process: F1: L CCGGTGGCGAGCCCGGCTCCGAAACTTACGAAGTGTTGGATTTCCCC 1 F3: 4 TGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC R RF: CCGGTGGCGAGCCCGGCTCCGAAACTTACAAAGTGTTGGATGTCCCCCGTTCGAACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC RR: GGCCACCGCTCGGGCCGAGGCTTTGAATGTTTCACAACCTACAGGGGGCAAGCTTGACTCCCTGACGTCTGGCGGAGACCCATCGACCTACTTCG F2: 3 CTGACGT 2 Unidirectional alignment (log-probability: -40.8) CGAGCCCGGCTCCGAAACTTACgAAGTGTTGGATtTCCCCtgcagt--------CTGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC CGAGCCCGGCTCCGAAACTTACAAAGTGTTGGATGTCCCC------CGTTCGAACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC Template switch alignment (log-probability: -27.8) CGAGCCCGGCTCCGAAACTTACgAAGTGTTGGATtTCCCC|TGCAGTC|TGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC CGAGCCCGGCTCCGAAACTTACAAAGTGTTGGATGTCCCC|TGCAGTC|TGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC Chimp > Gorilla --------------- chr11:132122015-132122021 Template switch process: F1: L GCGAGCCCGGCTCCGAAACTTACGAAGTGTTGGATTTCCCC 1 F3: 4 TGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC R RF: GCGAGCCCGGCTCCGAAACTTACAAAGTGTTGGATTTCCCCCGTTGGAACTGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC RR: CGCTCGGGCCGAGGCTTTGAATGTTTCACAACCTAAAGGGGGCAACCTTGACTCCCTGACGTCTGGCGGAGACCCATCGACCTACTTCG F2: 3 CTGACGT 2 Unidirectional alignment (log-probability: -35.2) CGAGCCCGGCTCCGAAACTTACgAAGTGTTGGATTTCCCC--------tgcagtCTGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC CGAGCCCGGCTCCGAAACTTACAAAGTGTTGGATTTCCCCCGTTGGAA------CTGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC Template switch alignment (log-probability: -22.1) CGAGCCCGGCTCCGAAACTTACgAAGTGTTGGATTTCCCC|TGCAGTC|TGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC CGAGCCCGGCTCCGAAACTTACAAAGTGTTGGATTTCCCC|TGCAGTC|TGAGGGACTGCAGACCGCCTCTGGGTAGCTGGATGAAGC ========= Event 286 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ATGGGCCTCTCATTTGATGGT------------------------ATATTATCTCTTGTGATCTTCACAACAATATTCATAACAATAAATAACAGCTGAAGCGTTAGTGATCCCTGCCTGTTACTGAGGAATTTAAGAC-GGCACACTAGCCTTATGATTAGCATGTGATTGGCTAGTTAACTGTTGAG ↓ 4 1 3 2 Chimp: ACGGGCCTCTCATTTGATGGT------------ATTCACATGCTTATGTTATCTCTTGTGATCTTCACAACAATATTCATAACAATAAATAACAGCTGAAGTGTTAGTGATCCCTGCCTGTTACTGAGGAATTTAAGAC-GGCACACTAGCCTTATGATTAGCATGTGATTAGCTAGTTAACTGTTGAG Gorilla: ACGGGCCTCTCATTTGATGGTATTCACATGCTT------------ATATTATCTCTTGTGATCTTCACAACAATATTCATAACAATAAATAACAGCTGAAGTGTTAGTGATCCCTGCCTGTTACTGAGGAATTTAAGAT-GGCACACTAGCCTTATGATTAGCATGTGATTAGCTAGTTAACTGTTGAG ↑ 4 1 3 2 Human: ATGGGCCTCTCATTTGATGGT------------------------ATATTATCTCTTGTGATCTTCACAACAATATTCATAACAATAAATAACAGCTGAAGCGTTAGTGATCCCTGCCTGTTACTGAGGAATTTAAGAC-GGCACACTAGCCTTATGATTAGCATGTGATTGGCTAGTTAACTGTTGAG Cluster: [ ] Orangutan: ACAGGCCTCTCATTTGATGGTATTCACATGCTT------------ATATTATCTCTTGTGATTTTCACAACAATATTCATAACAATAAATAACAGCTGAAGTGTTAGTGATCCCTGCCTGTTACTGAGAAATTTAAGACGGGCACACTAGCCTTATGATTAGCATGTGATTAGCTAGTTAACCGTTGAG Human > Chimp ------------- chr11:133749576-133749584 Template switch process: F1: L GTTTGGTTAATTAACAACGCACGGGCCTCTCATTTGATGGTAT 1 F3: 4 TATGTTATCTCTTGTGATCTTCACAACAATATTCATAACAATAA R RF: GTTTGGTTAATTAACAACGCATGGGCCTCTCATTTGATGGTATATTATCTCTTGTGATCTTCACAACAATATTCATAACAATAAATAACAGCTGAAGCGTTAGTGATCCCTGCCTGTTACTGAGGAATTTAAGACGGCACACTAGCCTTATGATTAGCATGTGA RR: CAAACCAATTAATTGTTGCGTACCCGGAGAGTAAACTACCATATAATAGAGAACACTAGAAGTGTTGTTATAAGTATTGTTATTTATTGTCGACTTCGCAATCACTAGGGACGGACAATGACTCCTTAAATTCTGCCGTGTGATCGGAATACTAATCGTACACT F2: 3 TCGTACACT 2 Unidirectional alignment (log-probability: -40.2) TGGTTAATTAACAACGCAcGGGCCTCTCATTTGATGGTATtcacatgcttatgTTATCTCTTGTGATCTTCACAACAATATTCATAACA TGGTTAATTAACAACGCATGGGCCTCTCATTTGATGGTATA------------TTATCTCTTGTGATCTTCACAACAATATTCATAACA Template switch alignment (log-probability: -28.5) TGGTTAATTAACAACGCAcGGGCCTCTCATTTGATGGTAT|TCACATGCT|TATgTTATCTCTTGTGATCTTCACAACAATATTCATAACA TGGTTAATTAACAACGCATGGGCCTCTCATTTGATGGTAT|TCACATGCT|TATATTATCTCTTGTGATCTTCACAACAATATTCATAACA Human > Gorilla --------------- chr11:133314271-133314279 Template switch process: F1: L GTTTGGTTAATTAACAATGCACGGGCCTCTCATTTGATGGTAT 1 F3: 4 TATATTATCTCTTGTGATCTTCACAACAATATTCATAACAA R RF: GTTTGGTTAATTAACAACGCATGGGCCTCTCATTTGATGGTATATTATCTCTTGTGATCTTCACAACAATATTCATAACAATAAATAACAGCTGAAGCGTTAGTGATCCCTGCCTGTTACTGAGGAATTTAAGACGGCACACTAGCCTTATGATTAGCATGTGA RR: CAAACCAATTAATTGTTGCGTACCCGGAGAGTAAACTACCATATAATAGAGAACACTAGAAGTGTTGTTATAAGTATTGTTATTTATTGTCGACTTCGCAATCACTAGGGACGGACAATGACTCCTTAAATTCTGCCGTGTGATCGGAATACTAATCGTACACT F2: 3 TCGTACACT 2 Unidirectional alignment (log-probability: -39.2) TGGTTAATTAACAAtGCAcGGGCCTCTCATTTGATGGtattcacatgctTATATTATCTCTTGTGATCTTCACAACAATATTCATAACA TGGTTAATTAACAACGCATGGGCCTCTCATTTGATGG------------TATATTATCTCTTGTGATCTTCACAACAATATTCATAACA Template switch alignment (log-probability: -28) TGGTTAATTAACAAtGCAcGGGCCTCTCATTTGATGGTAT|TCACATGCT|TATATTATCTCTTGTGATCTTCACAACAATATTCATAACA TGGTTAATTAACAACGCATGGGCCTCTCATTTGATGGTAT|TCACATGCT|TATATTATCTCTTGTGATCTTCACAACAATATTCATAACA ========= Event 287 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACCCCTTGCCATCTTCCCATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCT Chimp: CTACCCCTTGCCATCTTCCCATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCT ↓ 1 4 3 2 Gorilla: CTACCCCTTGCCATCTTCCCACTG----ATGTCCATCAGAGCTGCTGCCTGTGTGCCCT ↑ 1 4 3 2 Human: CTACCCCTTGCCATCTTCCCATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCT Cluster: [ ] Orangutan: ----------------------------------------------------------- Human > Gorilla --------------- chr11:1416184-1416189 Template switch process: F1: L CTCCACTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCA 1 F3: 4 TCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA R RF: CTCCGCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA RR: GAGGCGAAAAGGGATGTCGAGATGGGGAACGGTAGAAGGGTAACGTGTGTCAGGTAGTCTCGACGACGGACACACGGGACGACAGAAAAT F2: 3 GTAGTC 2 Unidirectional alignment (log-probability: -32.3) TCCaCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCactgAT--------GTCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA TCCGCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCC----ATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA Template switch alignment (log-probability: -22) TCCaCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCA|CTGATG|TCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA TCCGCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCA|CTGATG|TCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA Chimp > Gorilla --------------- chr11:1416184-1416189 Template switch process: F1: L CTCCACTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCA 1 F3: 4 TCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA R RF: CTCCGCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA RR: GAGGCGAAAAGGGATGTCGAGATGGGGAACGGTAGAAGGGTAACGTGTGTCAGGTAGTCTCGACGACGGACACACGGGACGACAGAAAAT F2: 3 GTAGTC 2 Unidirectional alignment (log-probability: -32.3) TCCaCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCactgAT--------GTCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA TCCGCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCC----ATTGCACACAGTCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA Template switch alignment (log-probability: -22) TCCaCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCA|CTGATG|TCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA TCCGCTTTTCCCTACAGCTCTACCCCTTGCCATCTTCCCA|CTGATG|TCCATCAGAGCTGCTGCCTGTGTGCCCTGCTGTCTTTTA ========= Event 288 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ttctcatgcacacttatcttttgtgttaattgcgagtctaagtgtcttcatttcaatatccattatttctcctgtatagttaaattgctggtgttttttttgCTTTCATAGGGTCCAGAAAATATAGGAAGTTA---ACACTAACAACTCAGCTCTCAAAAAGTT Chimp: TTCTCATGCACACTTATCTTTTGTGTTAATTGCGAGTCTAAGTGTCTTCGTCTCAATATCCATTATTTCTCTTGTATAGTTAAATTGCTGGTGtt-tttttGCTTTCATAGGGTCCAGAAAATATAGGACCCTATATTTTCTCTCAACTCAGCTCTCAAAAAATT ↓ 3 2 1 4 Gorilla: TTCTCATGCACACTTATCTTTTGTGTTAATTGCGAGTCTAAGTGTCTTCGTCTCAATATCCATTATTTCTCTTGTATAGTTAAATTGCTGGTGtt-tttttGCTTTCATAGGGTCCAGAAAATATAGGAAGTTA---ACACTAACAACTCAGCTCTCAAAAAATT Human: ttctcatgcacacttatcttttgtgttaattgcgagtctaagtgtcttcatttcaatatccattatttctcctgtatagttaaattgctggtgttttttttgCTTTCATAGGGTCCAGAAAATATAGGAAGTTA---ACACTAACAACTCAGCTCTCAAAAAGTT Cluster: [ ] Orangutan: TCCTCATGCACACTTATCTTTTGTGTTAATTGCGAGTCTAAGTGTCTTCATTTCAATATCCATTATTTCTCTTGTATAGTTAAATTGCTGGTGTT-TTTTTGCTTTCATAGGGTCCAGAAAATATAGGAAGTC----ACACTAACAACTCAGCTCTCAAAAAATT Chimp > Gorilla --------------- chr1:114669074-114669085 Template switch process: F1: L CTGGTGTTTTTTTGCTTTCATAGGGTCCAGAAAATATAGGA 1 F3: 4 CAACTCAGCTCTCAAAAAATTCGTTTTTATAGTTAGCTTC R RF: TTTGTGTTAATTGCGAGTCTAAGTGTCTTCGTCTCAATATCCATTATTTCTCTTGTATAGTTAAATTGCTGGTGTTTTTTTGCTTTCATAGGGTCCAGAAAATATAGGACCCTATATTTTCTCTCAACTCAGCTCTCAAAAAATTCGTTTTTATAGTTAGCTTC RR: AAACACAATTAACGCTCAGATTCACAGAAGCAGAGTTATAGGTAATAAAGAGAACATATCAATTTAACGACCACAAAAAAACGAAAGTATCCCAGGTCTTTTATATCCTGGGATATAAAAGAGAGTTGAGTCGAGAGTTTTTTAAGCAAAAATATCAATCGAAG F2: 3 AATCACAATTGA 2 Unidirectional alignment (log-probability: -38.6) TGGTGTTTTTTTGCTTTCATAGGGTCCAGAAAATATAGGA---------------agttaacactaaCAACTCAGCTCTCAAAAAATTCGTTTTTATAGTTAGCTTC TGGTGTTTTTTTGCTTTCATAGGGTCCAGAAAATATAGGACCCTATATTTTCTCT------------CAACTCAGCTCTCAAAAAATTCGTTTTTATAGTTAGCTTC Template switch alignment (log-probability: -28.3) TGGTGTTTTTTTGCTTTCATAGGGTCCAGAAAATATAGGA|AgTTAACACtAA|CAACTCAGCTCTCAAAAAATTCGTTTTTATAGTTAGCTTC TGGTGTTTTTTTGCTTTCATAGGGTCCAGAAAATATAGGA|AATTAACACAAA|CAACTCAGCTCTCAAAAAATTCGTTTTTATAGTTAGCTTC ========= Event 289 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCTGCCCCAACTCACCACTCAGTCAGGGAGGCCCTGACTTCTGCCTGTGTGCCTCCCTC ↑ 1 34 2 Chimp: GCCTGCCCCAACTCACCACTCGGCC-----CGCCCTGACTTCTGCCTGTGTGCCTCCCTC Gorilla: GCCTGCCCCAACTCACCACTCGGCC-----TGCCCTGACTTCTGCCTGTGTGCCTCCCTC Human: GCCTGCCCCAACTCACCACTCAGTCAGGGAGGCCCTGACTTCTGCCTGTGTGCCTCCCTC Cluster: [ ] Orangutan: GCCTGCCCCAACTCACCACTCGGCC-----CGCCCTGACTTCTGCCTGTGTGCCTCCCTC Chimp > Human ------------- chr11:134409713-134409722 Template switch process: F1: L GGAACAGGGGGAGGCCCCCAGCCTGCCCCAACTCACCACTC 1 F3: 4 GCCCTGACTTCTGCCTGTGTGCCTCCCTCTGCTGTCCGCC R RF: GGAACAGGGGGAGGCCCCCAGCCTGCCCCAACTCACCACTCGGCCCGCCCTGACTTCTGCCTGTGTGCCTCCCTCTGCTGTCCGCC RR: CCTTGTCCCCCTCCGGGGGTCGGACGGGGTTGAGTGGTGAGCCGGGCGGGACTGAAGACGGACACACGGAGGGAGACGACAGGCGG F2: 3 GAGGGACTGA 2 Unidirectional alignment (log-probability: -34.3) GAACAGGGGGAGGCCCCCAGCCTGCCCCAACTCACCACTCagtcagggaGGCC----CTGACTTCTGCCTGTGTGCCTCCCTCTGCTGTCCGCC GAACAGGGGGAGGCCCCCAGCCTGCCCCAACTCACCACTC---------GGCCCGCCCTGACTTCTGCCTGTGTGCCTCCCTCTGCTGTCCGCC Template switch alignment (log-probability: -22.5) GAACAGGGGGAGGCCCCCAGCCTGCCCCAACTCACCACTC|AGTCAGGGaG|GCCCTGACTTCTGCCTGTGTGCCTCCCTCTGCTGTCCGCC GAACAGGGGGAGGCCCCCAGCCTGCCCCAACTCACCACTC|AGTCAGGGCG|GCCCTGACTTCTGCCTGTGTGCCTCCCTCTGCTGTCCGCC ========= Event 290 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAATATGGAGGCTGAGGGTTGCTTCCCCCACCCACAAATTGCCTAGGAGAGGAGGAAGAGGGGCCACAAGTACCTATAATCTAGCAGGAGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTG--------------GAAGCTGGAGGCCTTTGAATG Chimp: GAATATGGAGGCTGAGGGTTGCTTCCCCCACCCACAAATTGCCTAGGAGAGGAGGAAAAGGGGCCACAAGTACCTATAATCTAGCAGGAGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTG--------------GAAGCTGGAGGCCTTTGAATG ↓ 3 2 41 Gorilla: GAATATGGAGGCTGAGGGTTGCTTCCCCCACCCACAAATTGCCTAGGAGAGGAGGAAGAGGGGCCACAAGTACCTATAATCTAACAGGAGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGGGTGAGGGAAGCAGAAAGCTGGAGGCCTTTGAATG Human: GAATATGGAGGCTGAGGGTTGCTTCCCCCACCCACAAATTGCCTAGGAGAGGAGGAAGAGGGGCCACAAGTACCTATAATCTAGCAGGAGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTG--------------GAAGCTGGAGGCCTTTGAATG Cluster: [ ] Orangutan: GAATATGGAGGCTGAGGGTTGCTTCCCCTACCCACAAATTGCCTAGGAGAGGAGGAAGAGGGGCCACAAGTACCTATAATCTAGCAGGAGGTAGGACTCGAGTTCAGCGGGTGAGCGGGGAATGCTGGGTGAGGGAAGCAGAAAGCTGGAGGCCTTTGGATG Chimp > Gorilla --------------- chr1:11434828-11434839 Template switch process: F1: L GGAGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGG 1 F3: 4 GAAAGCTGGAGGCCTTTGAATGGGTGGGGCCTCTGATGAACT R RF: TGCTTCCCCCACCCACAAATTGCCTAGGAGAGGAGGAAAAGGGGCCACAAGTACCTATAATCTAGCAGGAGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGGAAGCTGGAGGCCTTTGAATGGGTGGGGCCTCTGATGAACT RR: ACGAAGGGGGTGGGTGTTTAACGGATCCTCTCCTCCTTTTCCCCGGTGTTCATGGATATTAGATCGTCCTCCATCCTGAGCTCAAGTCGTCCACTCGCCCCTTACGACCTTCGACCTCCGGAAACTTACCCACCCCGGAGACTACTTGA F2: 3 ACGAAGGGAGTG 2 Unidirectional alignment (log-probability: -66.2) AGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGGgtgagggaagcagaAAGCTGGAGGCCTTTGAATGggtggggcctctgatgaa AGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGG--------------AAGCTGGAGGCCTTTGAATG------------------ Template switch alignment (log-probability: -28.4) AGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGG|GTGaGGGAAGCA|GaAAGCTGGAGGCCTTTGAATGGGTGGGGCCTCTGATGAA AGGTAGGACTCGAGTTCAGCAGGTGAGCGGGGAATGCTGG|GTGGGGGAAGCA|GGAAGCTGGAGGCCTTTGAATGGGTGGGGCCTCTGATGAA ========= Event 291 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: --------------TCATCTT------CCAGTCCCTTCATT----------------TTTGTGTGttattttcctatcactttagtggggcttgaggaaggagttaagataaatgtatcaggtcaattcatcatg-tttaaccagaggtccactagcATTGA Chimp: --------------TCATCTT------CCAGTCCCTTCATT----------------TTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGGGAAGGAGTTAAGATAAATGTATCAGGTCAATTCATCATG-TTTAACCAGAGGTCCACTAGCATTGA ↓ 4 1 3 2 Gorilla: --------------TCATCTT------------CCTTCATTTTTGTGTGGTTATACTTTTGTGTGTTATtttcctatcactttagtggggcttggggaaggagttaagataaatgtatcaggtcaattcatcatg-tttagccagaggtcCACTAGCACTGA Human: --------------TCATCTT------CCAGTCCCTTCATT----------------TTTGTGTGttattttcctatcactttagtggggcttgaggaaggagttaagataaatgtatcaggtcaattcatcatg-tttaaccagaggtccactagcATTGA Cluster: [ ] Orangutan: cctgctgtagtctctcatcttccagtc------ccttcatttttgtgtggttatacttttgtgtgttattttcctatcactttagtggggcttggggaaggagttaagataaatgtatcaggtcaattcatcatgttttaaccagaggtcCACTAGCATTGA Chimp > Gorilla --------------- chr11:18248266-18248272 Template switch process: F1: L ATTTCTACTTTCCAAAGCATTGCTGGCAGACTTCTCATCTT------CCTTCATTTTTGTGTG 1 F3: 4 TTTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGGG R RF: ATTTCTACTTTCCAAAGCATTGCTGGCAGACTTCTCATCTTCCAGTCCCTTCATTTTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGGGAAGGAGTTAAGATAAATGTATCAGGTCAATTCATCATGTTTAAC RR: TAAAGATGAAAGGTTTCGTAACGACCGTCTGAAGAGTAGAAGGTCAGGGAAGTAAAAACACACAATAAAAGGATAGTGAAATCACCCCGAACCCCTTCCTCAATTCTATTTACATAGTCCAGTTAAGTAGTACAAATTG F2: 3 CATATTG 2 Unidirectional alignment (log-probability: -44.1) CATTGCTGGCAGACTTCTCATCTTCC------TTCATttttgtgtggttatacTTTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGG CATTGCTGGCAGACTTCTCATCTTCCAGTCCCTTCAT----------------TTTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGG Template switch alignment (log-probability: -32.6) CATTGCTGGCAGACTTCTCATCTT------CCTTCATTTTTGTGTG|GTTAtAC|TTTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGG CATTGCTGGCAGACTTCTCATCTTCCAGTCCCTTCATTTTTGTGTG|GTTAAAC|TTTTGTGTGTTATTTTCCTATCACTTTAGTGGGGCTTGGG ========= Event 292 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAG---GGTTGATTTCTCATT-CTTTAACA ↑ 3 2 1 4 Chimp: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACT-------------------------------------------------------------------------------------------------------------------------------------------------------TTGTTTGACAGAGGCTCTGATTTCTCATT-CTTTAACA Gorilla: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACT-------------------------------------------------------------------------------------------------------------------------------------------------------TTGTTTGACAGAGGCTCTGATTTCTCATT-CTTTAACA ↓ 3 2 1 4 Human: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAG---GGTTGATTTCTCATT-CTTTAACA Cluster: [ ] Orangutan: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATAAGGTCCTCTGCTTAATTTTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATGTTACTTCTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACCCTGCCCCAACATAAAGGTCCTCTGCATACTTGTTTGACAGAGACTCTGATGTCTCATTCGTTTAACA Chimp > Human ------------- chr1:128313257-128313262 Template switch process: F1: L TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG 1 F3: 4 TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA R RF: TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACTTTGTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATATTACTTCTCAAAAGCAA RR: AAAAGATGGACAGACATTGAGGTTGGGACGGGGTTGTACTCCAGGAGACACATGAAACAAACTGTCTCCGAGACTAAAGAGTAAGAAATTGTTATAATGAAGAGTTTTCGTT F2: 3 TGGGAC 2 Unidirectional alignment (log-probability: -35.8) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAggcagGGT-----------------------------TGATTTCTCATTCTTTAACAATgTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGA-----GGTCCTCTGTGTACTTTGTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATATTACTTCTCAAAAGCAA Template switch alignment (log-probability: -22) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATgTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATATTACTTCTCAAAAGCAA Gorilla > Human --------------- chr1:128313257-128313262 Template switch process: F1: L TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG 1 F3: 4 TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA R RF: TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACTTTGTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA RR: AAAAGATGGACAGACATTGAGGTTGGGACGGGGTTGTACTCCAGGAGACACATGAAACAAACTGTCTCCGAGACTAAAGAGTAAGAAATTGTTACAATGAAGAGTTTTCGTT F2: 3 TGGGAC 2 Unidirectional alignment (log-probability: -29.3) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG-----------------------------CagggtTGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACTTTGTTTGACAGAGGCTC-----TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA Template switch alignment (log-probability: -16.5) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA ========= Event 293 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTTTGAGGTCTATTTCATTT----AATCAGAAAACCTTCTCAGATAAACTTCTGTGAATAAAGTCAT ↓ 1 3 4 2 Chimp: ACTTTGAGGTCTATTTCATTTGCTTTATCTGAG--------AAGATAAACTTCTGTGAATAAAGTCAT Gorilla: ACTTTGAGGTCTAATTCATTT----AATCAGAAAACCTTCTCAGATAAACTTCTGTGAATAAAGTCAT Human: ACTTTGAGGTCTATTTCATTT----AATCAGAAAACCTTCTCAGATAAACTTCTGTGAATAAAGTCAT Cluster: [ ] Orangutan: ATTTTGAGGTCTATTTCATTT----AATCAGAAAACCTTCTCAGATAAACTTCTGTGAATAAAGTCAT Human > Chimp ------------- chr11:121035457-121035466 Template switch process: F1: L CCAAGAGATGTAAAGTTGATACTTTGAGGTCTATTTCATTTGCT 1 F3: 4 AGATAAACTTCTGTGAATAAAGTCATTAGGGATCTAGAGC R RF: CCAAGAGATGTAAAGTTGATACTTTGAGGTCTATTTCATTTAATCAGAAAACCTTCTCAGATAAACTTCTGTGAATAAAGTCATTAGGGATCTAGAGC RR: GGTTCTCTACATTTCAACTATGAAACTCCAGATAAAGTAAATTAGTCTTTTGGAAGAGTCTATTTGAAGACACTTATTTCAGTAATCCCTAGATCTCG F2: 3 AGAGTCTATT 2 Unidirectional alignment (log-probability: -39.2) GAGATGTAAAGTTGATACTTTGAGGTCTATTTCATTTgctttatctgagA----------------AGATAAACTTCTGTGAATAAAGTCATTAGGGATCTAGAGC GAGATGTAAAGTTGATACTTTGAGGTCTATTTCATTT------------AATCAGAAAACCTTCTCAGATAAACTTCTGTGAATAAAGTCATTAGGGATCTAGAGC Template switch alignment (log-probability: -28.6) GAGATGTAAAGTTGATACTTTGAGGTCTATTTCATTTgcT|TTATCTGAGA|AGATAAACTTCTGTGAATAAAGTCATTAGGGATCTAGAGC GAGATGTAAAGTTGATACTTTGAGGTCTATTTCATTTAAT|TTATCTGAGA|AGATAAACTTCTGTGAATAAAGTCATTAGGGATCTAGAGC ========= Event 294 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGAATTTGTGTTTCCCTTCTTCAGGACCTGTGACTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTCTGAAGGTGGTGGCAACCAGAAAGTAC ↑ 3 2 1 4 Chimp: CAGAATTTGTGTTTCCCTTCTTCAGGACCTGTGACTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTTT-CTGGTGGTGGCAACCAGAAAGTAC Gorilla: CAGAATTTGTGTTTCCCTTCTTCAGGACCTGTGACTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTCTGAAGGTGGTGGCAACCAGAAAGTAC Human: CAGAATTTGTGTTTCCCTTCTTCAGGACCTGTGACTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTCTGAAGGTGGTGGCAACCAGAAAGTAC Cluster: [ ] Orangutan: CAGAACTTGTGTTTCC-CTCTTCAGGATCTTTGACTGCTGTTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTCTGAAGGTGGTGGCAACCAGAAAGTAC Chimp > Human ------------- chr1:116242746-116242751 Template switch process: F1: L ACTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCT 1 F3: 4 GTGGTGGCAACCAGAAAGTACCTGGACTTTGACAGCACC R RF: CTTCAGGACCTGTGACTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTTTCTGGTGGTGGCAACCAGAAAGTACCTGGACTTTGACAGCACC RR: GAAGTCCTGGACACTGACGACCAAGAAGAGACTAGAGGTGGTCAGGTCGGAGGGAAAGACCACCACCGTTGGTCTTTCATGGACCTGAAACTGTCGTGG F2: 3 GAAGTC 2 Unidirectional alignment (log-probability: -25.6) CTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCC--TCTgaaGGTGGTGGCAACCAGAAAGTACCTGGACTTTGACAGCACC CTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCTTTCT---GGTGGTGGCAACCAGAAAGTACCTGGACTTTGACAGCACC Template switch alignment (log-probability: -16) CTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCT|CTGAAG|GTGGTGGCAACCAGAAAGTACCTGGACTTTGACAGCACC CTGCTGGTTCTTCTCTGATCTCCACCAGTCCAGCCTCCCT|CTGAAG|GTGGTGGCAACCAGAAAGTACCTGGACTTTGACAGCACC ========= Event 295 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCAAACACACATACATTTTACATATAGTTTATTTCTTTAT-------------------GAAATGCTAATCTTCAGCCCGTACC ↓ 3 2 4 1 Chimp: ATTCAAACACACATACATTTTACATATAGTTTATTTCTTTATGAAATAACTATATGTAAATGAAATGCTAATCTTCAGCCCGTACC ↑ 3 2 4 1 Gorilla: ATTCAAACACACATACATTTTACATATAGTTTATTTCTTTAT-------------------GAAATGCTAATCTTCAGCCCGTACC Human: ATTCAAACACACATACATTTTACATATAGTTTATTTCTTTAT-------------------GAAATGCTAATCTTCAGCCCGTACC Cluster: [ ] Orangutan: ATTCAAACACACATACATTTTACATATAGTTTATTTCTTTAT-------------------GAAATGCTAATCTTCAGCCCATACC Human > Chimp ------------- chr11:118832505-118832516 Template switch process: F1: L TTCAAACACACATACATTTTACATATAGTTTATTTCTTTATGAAAT 1 F3: 4 ATGAAATGCTAATCTTCAGCCCGTACCAAAAAAGTAGAGTGG R RF: TTCAAACACACATACATTTTACATATAGTTTATTTCTTTATGAAATGCTAATCTTCAGCCCGTACCAAAAAGTAGAGTGG RR: AAGTTTGTGTGTATGTAAAATGTATATCAAATAAAGAAATACTTTACGATTAGAAGTCGGGCATGGTTTTTCATCTCACC F2: 3 AATGTATATCAA 2 Unidirectional alignment (log-probability: -49.9) CACACATACATTTTACATATAGTTTATTTCTTTATGAAATaactatatgtaaatgaaatGCTAATCTTCAGCCCGTACCaAAAAAGTAGAGT CACACATACATTTTACATATAGTTTATTTCTTTATGAAAT-------------------GCTAATCTTCAGCCCGTACC-AAAAAGTAGAGT Template switch alignment (log-probability: -28.5) CACACATACATTTTACATATAGTTTATTTCTTTATGAAAT|AACTATATGTAA|ATGAAATGCTAATCTTCAGCCCGTACCaAAAAAGTAGAGT CACACATACATTTTACATATAGTTTATTTCTTTATGAAAT|AACTATATGTAA|ATGAAATGCTAATCTTCAGCCCGTACC-AAAAAGTAGAGT Gorilla > Chimp --------------- chr11:118832505-118832516 Template switch process: F1: L TTCAAACACACATACATTTTACATATAGTTTATTTCTTTATGAAAT 1 F3: 4 ATGAAATGCTAATCTTCAGCCCGTACCAAAAAAGTAGAGTGG R RF: TTCAAACACACATACATTTTACATATAGTTTATTTCTTTATGAAATGCTAATCTTCAGCCCGTACCAAAAAGTAGAGTGG RR: AAGTTTGTGTGTATGTAAAATGTATATCAAATAAAGAAATACTTTACGATTAGAAGTCGGGCATGGTTTTTCATCTCACC F2: 3 AATGTATATCAA 2 Unidirectional alignment (log-probability: -49.4) CACACATACATTTTACATATAGTTTATTTCTTTatgaaataactatatgtaaATGAAATGCTAATCTTCAGCCCGTACCaAAAAAGTAGAGT CACACATACATTTTACATATAGTTTATTTCTTT-------------------ATGAAATGCTAATCTTCAGCCCGTACC-AAAAAGTAGAGT Template switch alignment (log-probability: -28.6) CACACATACATTTTACATATAGTTTATTTCTTTATGAAAT|AACTATATGTAA|ATGAAATGCTAATCTTCAGCCCGTACCaAAAAAGTAGAGT CACACATACATTTTACATATAGTTTATTTCTTTATGAAAT|AACTATATGTAA|ATGAAATGCTAATCTTCAGCCCGTACC-AAAAAGTAGAGT ========= Event 296 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTACATCACCTCCAAATAAGAAAAAATATGGAGGCCAACAAttaaaactgaaggaaaaatattt ↓ 1 3 4 2 Chimp: TCCTACATCACCTCCAAATAAATA----ATTGTTGGCCTACAATTaaaactgaaggaaaaatattt Gorilla: TCCTACATCACCTCCaaataagaaaaaatatgtaggccaacaattaaaactgaaggaaaaatattt Human: TCCTACATCACCTCCAAATAAGAAAAAATATGGAGGCCAACAAttaaaactgaaggaaaaatattt Cluster: [ ] Orangutan: TTCTACATCACCTCCAAATAAGAAAAAATATGTAGGCCAACAATTaaaactgaaggaaaaatattt Human > Chimp ------------- chr1:111887392-111887404 Template switch process: F1: L TCAGTATAAGAGAAAGAAGGTCCTACATCACCTCCAAATAAA 1 F3: 4 ACAATTAAAACTGAAGGAAAAATATTTTTAAAAAGAAAGA R RF: TCAGTATAAGAGAAAGAAGGTCCTACATCACCTCCAAATAAGAAAAAATATGGAGGCCAACAATTAAAACTGAAGGAAAAATATTTTTAAAAAGAAAGA RR: AGTCATATTCTCTTTCTTCCAGGATGTAGTGGAGGTTTATTCTTTTTTATACCTCCGGTTGTTAATTTTGACTTCCTTTTTATAAAAATTTTTCTTTCT F2: 3 TCCGGTTGTTAAT 2 Unidirectional alignment (log-probability: -39.3) AGTATAAGAGAAAGAAGGTCCTACATCACCTCCAAATAA------------AtaattgttGGCCtACAATTAAAACTGAAGGAAAAATATTTTTAAAAAGAAAGA AGTATAAGAGAAAGAAGGTCCTACATCACCTCCAAATAAGAAAAAATATGGA--------GGCCAACAATTAAAACTGAAGGAAAAATATTTTTAAAAAGAAAGA Template switch alignment (log-probability: -22.9) AGTATAAGAGAAAGAAGGTCCTACATCACCTCCAAATAAa|TAATTGTTGGCCT|ACAATTAAAACTGAAGGAAAAATATTTTTAAAAAGAAAGA AGTATAAGAGAAAGAAGGTCCTACATCACCTCCAAATAAG|TAATTGTTGGCCT|ACAATTAAAACTGAAGGAAAAATATTTTTAAAAAGAAAGA ========= Event 297 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCGCTGGCTGACCCCTGCAGGCCCTCCAGGCCTCCTACGTCCAGTGTCAGCAGGAAATTC Chimp: GGCGCTGGCTGACCCCTGCAGGCCCTCCAGGCCTACTACGTCCAGTGTCAGCAGGAAATTC ↓ 3 1 2 4 Gorilla: GGCGCTGGCTGACCCCTGCAGGCCTGGAGGGCCTCCTACAACCAGTGTCAGCAGGAAATTC Human: GGCGCTGGCTGACCCCTGCAGGCCCTCCAGGCCTCCTACGTCCAGTGTCAGCAGGAAATTC Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr11:133339201-133339210 Template switch process: F1: L TGAGTGAGGGTCCTGGAGGCGCTGGCTGACCCCTGCAGGCC 1 F3: 4 CCTACAA---CCAGTGTCAGCAGGAAATTCCAGGCTGCAGTGGTCTTGGT R RF: TGAGTGAGGGTCCTGGAGGCGCTGGCTGACCCCTGCAGGCCCTCCAGGCCTACTACGTCCAGTGTCAGCAGGAAATTCCAGGCTGCAGTGGTCTTGGT RR: ACTCACTCCCAGGACCTCCGCGACCGACTGGGGACGTCCGGGAGGTCCGGATGATGCAGGTCACAGTCGTCCTTTAAGGTCCGACGTCACCAGAACCA F2: 3 TCCGGGAGGT 2 Unidirectional alignment (log-probability: -43.7) GAGTGAGGGTCCTGGAGGCGCTGGCTGACCCCTGCAGGCctggagggCCTC--------CTACaaCCAGTGTCAGCAGGAAATTCCAGGCTGCAGTGG GAGTGAGGGTCCTGGAGGCGCTGGCTGACCCCTGCAGGC--------CCTCCAGGCCTACTACGTCCAGTGTCAGCAGGAAATTCCAGGCTGCAGTGG Template switch alignment (log-probability: -32.6) GAGTGAGGGTCCTGGAGGCGCTGGCTGACCCCTGCAGGCC|TGGAGGGCCT|CCTACaA---CCAGTGTCAGCAGGAAATTCCAGGCTGCAGTGG GAGTGAGGGTCCTGGAGGCGCTGGCTGACCCCTGCAGGCC|TGGAGGGCCT|CCTACTACGTCCAGTGTCAGCAGGAAATTCCAGGCTGCAGTGG ========= Event 298 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: gtttggaaacaaTTGCTTTGCCTTATT---------GCTCCATCCAAGGCCAGCCAGGCT Chimp: GTTTGGAAATAAGTGCTTTGCCTTAGAGCAATAAGGCCTCCATCCAAGGCCAGCCAGGCT ↑ 3 1 4 2 Gorilla: GTTTGGAAATAATTGCTTTGCCTTATT---------GCTCCATCCAAGGCCAGCCAGGCT Human: gtttggaaacaaTTGCTTTGCCTTATT---------GCTCCATCCAAGGCCAGCCAGGCT Cluster: [ ] Orangutan: GTTTGGAAATAATTGCTTTGCCTTATT---------GCTCTATCCAAGGCCAGCCAGGCT Gorilla > Chimp --------------- chr11:118246578-118246589 Template switch process: F1: L CCCGTGAAGACATCCAGTTTGGAAATAAGTGCTTTGCCTTA 1 F3: 4 CTCCATCCAAGGCCAGCCAGGCTGGTCCTCAGGATCCCAG R RF: CCCGTGAAAACATCCAGTTTGGAAATAATTGCTTTGCCTTATTGCTCCATCCAAGGCCAGCCAGGCTGGTCCTCAGGATCCCAG RR: GGGCACTTTTGTAGGTCAAACCTTTATTAACGAAACGGAATAACGAGGTAGGTTCCGGTCGGTCCGACCAGGAGTCCTAGGGTC F2: 3 CGGAATAACGAG 2 Unidirectional alignment (log-probability: -45.9) CCGTGAAgACATCCAGTTTGGAAATAAgTGCTTTGCCTTAgaGcaataaggcCTCCATCCAAGGCCAGCCAGGCTGGTCCTCAGGATCCCAG CCGTGAAAACATCCAGTTTGGAAATAATTGCTTTGCCTTATTG---------CTCCATCCAAGGCCAGCCAGGCTGGTCCTCAGGATCCCAG Template switch alignment (log-probability: -28.3) CCGTGAAgACATCCAGTTTGGAAATAAgTGCTTTGCCTTA|GAGCAATAAGGC|CTCCATCCAAGGCCAGCCAGGCTGGTCCTCAGGATCCCAG CCGTGAAAACATCCAGTTTGGAAATAATTGCTTTGCCTTA|GAGCAATAAGGC|CTCCATCCAAGGCCAGCCAGGCTGGTCCTCAGGATCCCAG ========= Event 299 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGACTGGCATTGCCCTCAGTGACCACTTTGTTAAG--CTCATTTTCTCATATGATAATGAATT ↓ 3 2 1 4 Chimp: GGACTGGCATTGCTCTCAGTGACCACTTTGTTAAGTGGTCA-TTTCTCATATGATAATGAATT ↑ 3 2 1 4 Gorilla: GGACTGGCATTGCCCTCAGTGACCACTTTGTTAAG--CTCATTTTCTCATATGATAATGAATT Human: GGACTGGCATTGCCCTCAGTGACCACTTTGTTAAG--CTCATTTTCTCATATGATAATGAATT Cluster: [ ] Orangutan: GGACTGGCATTGCCCTCAGTGACCACTTTGTTAAG--CTCATTTTCTCATATGATAATGAATT Human > Chimp ------------- chr1:116161987-116161992 Template switch process: F1: L ATCCTGGGACTGGCATTGCTCTCAGTGACCACTTTGTTAAG 1 F3: 4 TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG R RF: ATCCTGGGACTGGCATTGCCCTCAGTGACCACTTTGTTAAGCTCATTTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG RR: TAGGACCCTGACCGTAACGGGAGTCACTGGTGAAACAATTCGAGTAAAAGAGTATACTATTACTTAAACCCATGTCGTTGTCCTAC F2: 3 ACTGGT 2 Unidirectional alignment (log-probability: -34.5) TCCTGGGACTGGCATTGCtCTCAGTGACCACTTTGTTAAG----TggtcaTTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG TCCTGGGACTGGCATTGCCCTCAGTGACCACTTTGTTAAGCTCAT-----TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG Template switch alignment (log-probability: -22) TCCTGGGACTGGCATTGCtCTCAGTGACCACTTTGTTAAG|TGGTCA|TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG TCCTGGGACTGGCATTGCCCTCAGTGACCACTTTGTTAAG|TGGTCA|TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG Gorilla > Chimp --------------- chr1:116161987-116161992 Template switch process: F1: L ATCCTGGGACTGGCATTGCTCTCAGTGACCACTTTGTTAAG 1 F3: 4 TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG R RF: ATCCTGGGACTGGCATTGCCCTCAGTGACCACTTTGTTAAGCTCATTTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG RR: TAGGACCCTGACCGTAACGGGAGTCACTGGTGAAACAATTCGAGTAAAAGAGTATACTATTACTTAAACCCATGTCGTTGTCCTAC F2: 3 ACTGGT 2 Unidirectional alignment (log-probability: -33.6) TCCTGGGACTGGCATTGCtCTCAGTGACCACTTTGTTAAG----TggtcaTTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG TCCTGGGACTGGCATTGCCCTCAGTGACCACTTTGTTAAGCTCAT-----TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG Template switch alignment (log-probability: -22) TCCTGGGACTGGCATTGCtCTCAGTGACCACTTTGTTAAG|TGGTCA|TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG TCCTGGGACTGGCATTGCCCTCAGTGACCACTTTGTTAAG|TGGTCA|TTTCTCATATGATAATGAATTTGGGTACAGCAACAGGATG ========= Event 300 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAAACTGTGGTGATGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTACCACCGCCAGGCACCTTTAAATCACCG--CAGAGTCTGCAGTGCGGAGGGGGCGGGAAGTCC ↑ 4 1 3 2 Chimp: CCGTACACTGCCCAAGCTCTGGGGGTG---------------------TCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTACCACCGCCAGGCACCTTTAAATCACCG--CAGAGTCTACAGTGCGGAGGGGGCGGGAAGTCC ↓ 4 1 3 2 Gorilla: CCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAGACTGTGGTGATGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTACCACCGCCAGGCACCTTTAAATCACCG----CAGTCTACAGTGCGGAGGGGGCGGGAAGTCC Human: CCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAAACTGTGGTGATGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTACCACCGCCAGGCACCTTTAAATCACCG--CAGAGTCTGCAGTGCGGAGGGGGCGGGAAGTCC Cluster: [ ] Orangutan: CCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAGACTGTGGTGATGTCACACTAGCTGGGATGACATTTTACAGTTGGATTCCGTACCACCGCCAGGCACCTTTAAATCACCGCG--GAGTCTACAGTGCGGAGGGGGCGGGAAGTCC Chimp > Human ------------- chr1:113929295-113929299 Template switch process: F1: L TAGGCACTGTCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTA 1 F3: 4 TGGTGATGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTA R RF: TAGGCACTGTCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTA RR: ATCCGTGACAGCAGGGCATGTGACGGGTTCGAGACCCCCACAGTGTGATCGACCCTACTGTAAAATGTCAACCTAGGGCAT F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -41.1) TCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACActaaactgtggtgatgtcacaCTAGCTGGGATGACATTTTACAGTTGG TCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACA---------------------CTAGCTGGGATGACATTTTACAGTTGG Template switch alignment (log-probability: -28.2) TCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTA|AACTG|TGGtGaTGTCACACTAGCTGGGATGACATTTTACAGTTGG TCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTA|AACTG|TGGGGGTGTCACACTAGCTGGGATGACATTTTACAGTTGG Chimp > Gorilla --------------- chr1:115397744-115397747 Template switch process: F1: L TAGGCACTGTCTTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAG 1 F3: 4 TGGTGATGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTA R RF: TAGGCACTGTCGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAGCTGGGATGACATTTTACAGTTGGATCCCGTACCACCGCCAGGCACCTTTAAATCACCGCAGAGTCTACAGT RR: ATCCGTGACAGCAGGGCATGTGACGGGTTCGAGACCCCCACAGTGTGATCGACCCTACTGTAAAATGTCAACCTAGGGCATGGTGGCGGTCCGTGGAAATTTAGTGGCGTCTCAGATGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -46.6) CtTCCCGTACACTGCCCAAGCTCTGGGGGtgtcacactagactgtggtgaTGTCACACTAGCTGGGATGACATTTTACAGTTGG CGTCCCGTACACTGCCCAAGCTCTGGGGG---------------------TGTCACACTAGCTGGGATGACATTTTACAGTTGG Template switch alignment (log-probability: -33.2) CtTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAG|ACTG|TGGtGaTGTCACACTAGCTGGGATGACATTTTACAGTTGG CGTCCCGTACACTGCCCAAGCTCTGGGGGTGTCACACTAG|ACTG|TGGGGGTGTCACACTAGCTGGGATGACATTTTACAGTTGG ========= Event 301 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTTGAAGGAGGACTAAAAGAAG------CCTATGCAGGTGAGAGTGAAGAAAGCCTAGAAAAG Chimp: ATTTGAAGGAGAACTAAAAGAGG------CCTATGCAGGTGAGGGTGAAGAAAGCCTAGAAAAG ↓ 13 4 2 Gorilla: ATTTGAAGGAGGACTAAAAGAGGCACCTGCATAGGCAGGTGAGGGTGAAGAAAGCCTAGAAAAG ↑ 13 4 2 Human: ATTTGAAGGAGGACTAAAAGAAG------CCTATGCAGGTGAGAGTGAAGAAAGCCTAGAAAAG Cluster: [ ] Orangutan: ATTTGAAG---GACTAAAAGAGG------CCTGTGCAGGTGAGGGTGAAGAAAGCCTAGAAAAG Human > Gorilla --------------- chr11:119900496-119900505 Template switch process: F1: L TGATGTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGAGGC 1 F3: 4 GCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGACCATGAAGAAG R RF: TGATGTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGAAGCCTATGCAGGTGAGAGTGAAGAAAGCCTAGAAAAGGAGTAGTGACCATGAAGAAG RR: ACTACAGGAAGTATAAACCTTAAACTTCCTCCTGATTTTCTTCGGATACGTCCACTCTCACTTCTTTCGGATCTTTTCCTCATCACTGGTACTTCTTC F2: 3 GATACGTCCA 2 Unidirectional alignment (log-probability: -41.8) GTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGAggcacctGCaTAgGCAGGTGAGgGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC GTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGA------AGCCTATGCAGGTGAGAGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC Template switch alignment (log-probability: -28.4) GTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGAgGC|ACCTGCATAG|GCAGGTGAGgGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC GTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGAAGC|ACCTGCATAG|GCAGGTGAGAGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC Chimp > Gorilla --------------- chr11:119900496-119900505 Template switch process: F1: L ATGTCCTTCATATTTGGAATTTGAAGGAGGACTAAAAGAGGC 1 F3: 4 GCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC R RF: ATGTCCTTCATATTTGGAATTTGAAGGAGAACTAAAAGAGGCCTATGCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC RR: TACAGGAAGTATAAACCTTAAACTTCCTCTTGATTTTCTCCGGATACGTCCACTCCCACTTCTTTCGGATCTTTTCCTCATCACTG F2: 3 GATACGTCCA 2 Unidirectional alignment (log-probability: -36.1) GTCCTTCATATTTGGAATTTGAAGGAGgACTAAAAGAGgcacctGCaTAgGCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC GTCCTTCATATTTGGAATTTGAAGGAGAACTAAAAGAG------GCCTATGCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC Template switch alignment (log-probability: -22.5) GTCCTTCATATTTGGAATTTGAAGGAGgACTAAAAGAGGC|ACCTGCATAG|GCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC GTCCTTCATATTTGGAATTTGAAGGAGAACTAAAAGAGGC|ACCTGCATAG|GCAGGTGAGGGTGAAGAAAGCCTAGAAAAGGAGTAGTGAC ========= Event 302 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAAGACCTGGCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGGGGCCAGCTGGCTCAATGTGCCCCACTCCAAAGGAAGCCAGC Chimp: AAAAGACCTGGCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGG---AAGAGG------GGTGCCCCACTCCAAAGGAAGCCAGC ↑ 3 2 1 4 Gorilla: AAAAGACCTGGCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGGGGCCAGCTGGCTCAATGTGTCCCACTCCAAAGGAAGCCAGC Human: AAAAGACCTGGCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGGGGCCAGCTGGCTCAATGTGCCCCACTCCAAAGGAAGCCAGC Cluster: [ ] Orangutan: AAGAGACCTGGCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGGGGCCAGCTGGCTCAATGTGCCCCACTCCAAAGGAGGCCAGC Gorilla > Chimp --------------- chr11:119983161-119983171 Template switch process: F1: L GCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGG 1 F3: 4 CCCACTCCAAAGGAAGCCAGCATCATGAAGAAGCAGGGAA R RF: GCCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGGGGCCAGCTGGCTCAATGTGTCCCACTCCAAAGGAAGCCAGCATCATGAAGAAGCAGGGAA RR: CGGGGTGAACGTGGGGAGAAGGAGGAGAGCCAATTCCACCCCCGGTCGACCGAGTTACACAGGGTGAGGTTTCCTTCGGTCGTAGTACTTCTTCGTCCCTT F2: 3 CGTGGGGAGAA 2 Unidirectional alignment (log-probability: -34.1) CCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGgaagaGGG--------------GTGcCCCACTCCAAAGGAAGCCAGCATCATGAAGAAGCAGGGAA CCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGG-----GGGCCAGCTGGCTCAATGTGTCCCACTCCAAAGGAAGCCAGCATCATGAAGAAGCAGGGAA Template switch alignment (log-probability: -17.1) CCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGG|AAGAGGGGTGC|CCCACTCCAAAGGAAGCCAGCATCATGAAGAAGCAGGGAA CCCCACTTGCACCCCTCTTCCTCCTCTCGGTTAAGGTGGG|AAGAGGGGTGC|CCCACTCCAAAGGAAGCCAGCATCATGAAGAAGCAGGGAA ========= Event 303 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGGCT-------CC-----------CGGAGAGACTGCTGATGTGTTGTCAGT ↑ 3 2 1 4 Chimp: AGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGGAG-----CAGT-----------CTCCTAGACTGCTGATGTGTTGTCCGT Gorilla: AGGTGCTGGGACGGTCAGCTCTCCGGGAGCTAGGAG---CA--GTCTCCTGGCTCCCGGAGAGACTGCTGATGTGTTGTCAGT Human: AGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGGCT-------CC-----------CGGAGAGACTGCTGATGTGTTGTCAGT Cluster: [ ] Orangutan: AGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGGAGCAG----CT-----------CAGCCAGTCTGCTGATGTGTTGTCAGT Chimp > Human ------------- chr11:134854753-134854762 Template switch process: F1: L TGCAGACAGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGG 1 F3: 4 GACTGCTGATGTGTTGTCAGTTAAAAAGAGGTGGCACCT R RF: TGCAGACAGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGGAGCAGTCTCCTAGACTGCTGATGTGTTGTCCGTTAAAAAGAGGTGGCACCT RR: ACGTCTGTCCACGACCCTGTCAGTCGAGAGGCCCTCGGTCCTCGTCAGAGGATCTGACGACTACACAACAGGCAATTTTTCTCCACCGTGGA F2: 3 AGAGGCCCTC 2 Unidirectional alignment (log-probability: -37.7) GCAGACAGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAggctcccGGAG---------AGACTGCTGATGTGTTGTCaGTTAAAAAGAGGTGGCACCT GCAGACAGGTGCTGGGACAGTCAGCTCTCCGGGAGCCA-------GGAGCAGTCTCCTAGACTGCTGATGTGTTGTCCGTTAAAAAGAGGTGGCACCT Template switch alignment (log-probability: -22.5) GCAGACAGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGG|CTCCCGGAGA|GACTGCTGATGTGTTGTCaGTTAAAAAGAGGTGGCACCT GCAGACAGGTGCTGGGACAGTCAGCTCTCCGGGAGCCAGG|CTCCCGGAGA|GACTGCTGATGTGTTGTCCGTTAAAAAGAGGTGGCACCT ========= Event 304 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGGAGCCCAGTGGACTGTAAATGTAACATC----------------------------------------------------------------CAGCCTGGGCCAGCCCCCC-GGGATTGGATGTTCCATCTCATCCTAGCAGTGTTGTT ↑ 1 4 3 2 Chimp: ATGGAGCCCAGTGGACTGTAATTGGGAACCC--------------------------------CACCCATGTCTAGCAAGAGTGGACTTGTCATCTAGCCTAGGCCAGCCCCCC-GGGATTGGATGTTCCATCTCATCCTAGCAGTGTTGTT Gorilla: ATGGAGCCCAGTGGACTGTAATTGGGAACCCAATCCATGTCTAGCAAGAGTGGACTTGTCACC--------------------------------AAGCCTGGGCCAGCCCCCCGGGGATTGGATGTTCCATCTCATCCTAGCAGTGTTGTT Human: ATGGAGCCCAGTGGACTGTAAATGTAACATC----------------------------------------------------------------CAGCCTGGGCCAGCCCCCC-GGGATTGGATGTTCCATCTCATCCTAGCAGTGTTGTT Cluster: [ ] Orangutan: ATGGAGCCCAGTGGGCTGTAATTGAGAACCCCACCCATGTCTAGCAAGAGTGGACTTGTCATC--------------------------------CAGCCTGGGCCAGCCCCCC-GGGATTGGATGTTCCATCGCATCCTAGCAGTGTTGTT Chimp > Human ------------- chr11:115864854-115864864 Template switch process: F1: L AATGACATTTTCCATGTTGGATGGAGCCCAGTGGACTGTAA 1 F3: 4 AGCCTGGGCCAGCCCCCCGGGATTGGATGTTCCATCTCATCCTAGC R RF: AATGACATTTTCCATGTTGGATGGAGCCCAGTGGACTGTAATTGGGAACCCCACCCATGTCTAGCAAGAGTGGACTTGTCATCTAGCCTAGGCCAGCCCCCCGGGATTGGATGTTCCATCTCATCCTAGC RR: TTACTGTAAAAGGTACAACCTACCTCGGGTCACCTGACATTAACCCTTGGGGTGGGTACAGATCGTTCTCACCTGAACAGTAGATCGGATCCGGTCGGGGGGCCCTAACCTACAAGGTAGAGTAGGATCG F2: 3 CCTACAATGTA 2 Unidirectional alignment (log-probability: -42.7) ATGACATTTTCCATGTTGGATGGAGCCCAGTGGACTGTAAaTG--------------------------------TaaCATCcAGCCTgGGCCAGCCCCCCGGGATTGGATGTTCCATCTCAT ATGACATTTTCCATGTTGGATGGAGCCCAGTGGACTGTAATTGGGAACCCCACCCATGTCTAGCAAGAGTGGACTTGTCATCTAGCCTAGGCCAGCCCCCCGGGATTGGATGTTCCATCTCAT Template switch alignment (log-probability: -28.7) ATGACATTTTCCATGTTGGATGGAGCCCAGTGGACTGTAA|ATGtAACATCC|AGCCTgGGCCAGCCCCCCGGGATTGGATGTTCCATCTCAT ATGACATTTTCCATGTTGGATGGAGCCCAGTGGACTGTAA|ATGGAACATCC|AGCCTAGGCCAGCCCCCCGGGATTGGATGTTCCATCTCAT ========= Event 305 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CGTATTTGATTCTGAATACCC-ATTCA----GGTTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCAAGT Chimp: CGTATTTTATTCTGAATACCCAAGTCA--TCTTTTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCAAGT Gorilla: CGTATTTTATTCTGAATACCCAAGTCATC--TTTTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCAAGT ↓ 1 4 3 2 Human: CGTATTTGATTCTGAATACCC-ATTCA----GGTTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCAAGT Cluster: [ ] Orangutan: CGTATCTTATTCTGAATACCCAAGTCATC--TTTTGGAAATCTCCTTCAACTTGAAGACCTATAATCAAGCCAAGT Gorilla > Human --------------- chr11:115708946-115708951 Template switch process: F1: L GTCTGTAAAATGGGCATGAACGTATTTGATTCTGAATACCCA 1 F3: 4 TTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCA R RF: GTCTGTAAAATGGGCATGAACGTATTTTATTCTGAATACCCAAGTCATCTTTTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCA RR: CAGACATTTTACCCGTACTTGCATAAAATAAGACTTATGGGTTCAGTAGAAAACCTTTAGAGGAAGTTGGACTTCTGGATATTAGTTCGGT F2: 3 GGACTT 2 Unidirectional alignment (log-probability: -32.3) CTGTAAAATGGGCATGAACGTATTTgATTCTGAATACCCA-------TTcaggTTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCA CTGTAAAATGGGCATGAACGTATTTTATTCTGAATACCCAAGTCATCTT----TTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCA Template switch alignment (log-probability: -22) CTGTAAAATGGGCATGAACGTATTTgATTCTGAATACCCA|TTCAGG|TTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCA CTGTAAAATGGGCATGAACGTATTTTATTCTGAATACCCA|TTCAGG|TTGGAAATCTCCTTCAACCTGAAGACCTATAATCAAGCCA ========= Event 306 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGGAGCAGAGTGAATATGAGCAATGACAGATACAGTTCTCCTTTGGACTTGTTTGTATTAT ↓ 1 3 4 2 Chimp: TTGGAGCAGAGTGAATATGAGAACT-GTATCTGCAGTTCTCATTTGGACTTGTTTGTACTAT ↑ 1 3 4 2 Gorilla: TTGGAGCAGAGTGAATATGAGCAATGACAGATACAGTTCTCCTTTGGACTTGTTTGTATTAT Human: TTGGAGCAGAGTGAATATGAGCAATGACAGATACAGTTCTCCTTTGGACTTGTTTGTATTAT Cluster: [ ] Orangutan: TTGGAGCAGAGTGAATATGAGCAATGACAGATACAGTTCTCCTTTGGACTTGTTTGTATTAT Human > Chimp ------------- chr11:15133689-15133699 Template switch process: F1: L AGCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG 1 F3: 4 CAGTTCTCATTTGGACTTGTTTGTACTATTTTTCTATCTGACTGGCCTG R RF: AGCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAGCAATGACAGATACAGTTCTCCTTTGGACTTGTTTGTATTATTTTTCTATCTGACTGGCCTG RR: TCGTTTCCGTATCTTGACCGAACCTCGTCTCACTTATACTCGTTACTGTCTATGTCAAGAGGAAACCTGAACAAACATAATAAAAAGATAGACTGACCGGAC F2: 3 GTCTATGTCAA 2 Unidirectional alignment (log-probability: -48.1) GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG-----------AactgtatctgCAGTTCTCaTTTGGACTTGTTTGTAcTATTTTTCTATCTG GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAGCAATGACAGATA----------CAGTTCTCCTTTGGACTTGTTTGTATTATTTTTCTATCTG Template switch alignment (log-probability: -28.8) GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG|AACTGTATCTG|CAGTTCTCaTTTGGACTTGTTTGTAcTATTTTTCTATCTG GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG|AACTGTATCTG|CAGTTCTCCTTTGGACTTGTTTGTATTATTTTTCTATCTG Gorilla > Chimp --------------- chr11:15133689-15133699 Template switch process: F1: L AGCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG 1 F3: 4 CAGTTCTCATTTGGACTTGTTTGTACTATTTTTCTATCTGACTGGCCTG R RF: AGCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAGCAATGACAGATACAGTTCTCCTTTGGACTTGTTTGTATTATTTTTCTATCTGACTGGCCTG RR: TCGTTTCCGTATCTTGACCGAACCTCGTCTCACTTATACTCGTTACTGTCTATGTCAAGAGGAAACCTGAACAAACATAATAAAAAGATAGACTGACCGGAC F2: 3 GTCTATGTCAA 2 Unidirectional alignment (log-probability: -46.7) GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG-----------AactgtatctgCAGTTCTCaTTTGGACTTGTTTGTAcTATTTTTCTATCTG GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAGCAATGACAGATA----------CAGTTCTCCTTTGGACTTGTTTGTATTATTTTTCTATCTG Template switch alignment (log-probability: -28.4) GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG|AACTGTATCTG|CAGTTCTCaTTTGGACTTGTTTGTAcTATTTTTCTATCTG GCAAAGGCATAGAACTGGCTTGGAGCAGAGTGAATATGAG|AACTGTATCTG|CAGTTCTCCTTTGGACTTGTTTGTATTATTTTTCTATCTG ========= Event 307 ========= Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: ATGAGGGTCTAAGGCATCCGGAGCTTTGGTCTGGGCTTTCTAACGCGACCAAG Chimp: ATGAGGGTCGAAGGCATCCGGACCAAAGCTCCAGGCTTTCTAACCCGACCAAG Gorilla: ATGAGGATCTAAGGCATCCGGACCAAAGCTCCGGGCTTTCTAACCCGACCAAG ↑ 3 1 2 4 Human: ATGAGGGTCTAAGGCATCCGGAGCTTTGGTCTGGGCTTTCTAACGCGACCAAG Cluster: [ ] Orangutan: ATGAGGGTCTAAGGCATCCGGACCAAAGCTCCGGGCTTTCTAACCCGACCAAG Human > Gorilla --------------- chr11:19919961-19919970 Template switch process: F1: L GCTGGTGCCTAGTGTAACAATGAGGATCTAAGGCATCCGGA 1 F3: 4 GGGCTTTCTAACCCGACCAAGCTCCTGAAGCCAAAGGGAA R RF: GCTGGTGCCTAGTGTAACAATGAGGGTCTAAGGCATCCGGAGCTTTGGTCTGGGCTTTCTAACGCGACCAAGCTCCTGAAGCCAAAGGGAA RR: CGACCACGGATCACATTGTTACTCCCAGATTCCGTAGGCCTCGAAACCAGACCCGAAAGATTGCGCTGGTTCGAGGACTTCGGTTTCCCTT F2: 3 CCTCGAAACC 2 Unidirectional alignment (log-probability: -44.7) CTGGTGCCTAGTGTAACAATGAGGaTCTAAGGCATCCGGaccaaAGC-----TCcGGGCTTTCTAACcCGACCAAGCTCCTGAAGCCAAAGGGAA CTGGTGCCTAGTGTAACAATGAGGGTCTAAGGCATCCGG-----AGCTTTGGTCTGGGCTTTCTAACGCGACCAAGCTCCTGAAGCCAAAGGGAA Template switch alignment (log-probability: -28) CTGGTGCCTAGTGTAACAATGAGGaTCTAAGGCATCCGGA|CCAAAGCTCC|GGGCTTTCTAACcCGACCAAGCTCCTGAAGCCAAAGGGAA CTGGTGCCTAGTGTAACAATGAGGGTCTAAGGCATCCGGA|CCAAAGCTCC|GGGCTTTCTAACGCGACCAAGCTCCTGAAGCCAAAGGGAA ========= Event 308 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCATTACAGGTGCTCAAAAAGTAC------TTGAATAATAATTataaaaaccata-gcattctctattgagcttttggtataccaagccttatgctttagatacgaaacttcacttaattctcacaattctgtaaggttggtgctattctccttatttcatagttcaagaaagcagggacagcaaggtt ↓ 1 4 3 2 Chimp: TCCATTACAGGTGCTCAAAAA--GC---TTGATGAATAATAATTataaaaaccata-gcattctctattgagcttttggtataccaagccttatgctttagatacgaaacttcacttaattctcacaattctataaggttggtgctattctccttatttcatagttcaagaaagcagggacagcaaggtt Gorilla: TCCATTACAGGTGCTCAAAAAGTAC------TTGAATAATAATTataaaaaccata-gcattctctattgagcttttggtataccaagccttatgctttagataggaaacttcacttaattctcacaattctataaggttggtgctattctccttatttcatagttcaagaaagcagggacagcaaggtt Human: TCCATTACAGGTGCTCAAAAAGTAC------TTGAATAATAATTataaaaaccata-gcattctctattgagcttttggtataccaagccttatgctttagatacgaaacttcacttaattctcacaattctgtaaggttggtgctattctccttatttcatagttcaagaaagcagggacagcaaggtt Cluster: [ ] Orangutan: TCCATTATAGGTGCTTAAAAAGTCCTTC---ATGAATAATAATTATAGAAACCATAGCCATTCTAtattgagcttttggtataccaagccctatgctttagatacaaagcttcacttaattctcacaattctataaggttggtgctattctccttatttcatagttcaagaaagcagggacagcaaagtt Human > Chimp ------------- chr11:20911801-20911805 Template switch process: F1: L CTGACATGGTTATTTGTGCATCCATTACAGGTGCTCAAAAAG 1 F3: 4 TGAATAATAATTATAAAAACCATAGCATTCTCTATTGAGC R RF: CTGACATGGTTATTTGTGCATCCATTACAGGTGCTCAAAAAGTACTTGAATAATAATTATAAAAACCATAGCATTCTCTATTGAGCTTTTGGTATACCAAGCCTTATGCTTTAGATACGAAACTTCACTTAATTCTCACAATTCTGTAAGGTTGGTGCTATTCTCCTTATTTCATAGTTCAAG RR: GACTGTACCAATAAACACGTAGGTAATGTCCACGAGTTTTTCATGAACTTATTATTAATATTTTTGGTATCGTAAGAGATAACTCGAAAACCATATGGTTCGGAATACGAAATCTATGCTTTGAAGTGAATTAAGAGTGTTAAGACATTCCAACCACGATAAGAGGAATAAAGTATCAAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -25.6) GACATGGTTATTTGTGCATCCATTACAGGTGCTCAAAAAG--CTtgaTGAATAATAATTATAAAAACCATAGCATTCTCTATTGAGC GACATGGTTATTTGTGCATCCATTACAGGTGCTCAAAAAGTACT---TGAATAATAATTATAAAAACCATAGCATTCTCTATTGAGC Template switch alignment (log-probability: -15.9) GACATGGTTATTTGTGCATCCATTACAGGTGCTCAAAAAG|CTTGA|TGAATAATAATTATAAAAACCATAGCATTCTCTATTGAGC GACATGGTTATTTGTGCATCCATTACAGGTGCTCAAAAAG|CTTGA|TGAATAATAATTATAAAAACCATAGCATTCTCTATTGAGC ========= Event 309 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Chimp: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↓ 1 3 4 2 ↑ 13 24 Gorilla: ATAGTCTATTCGTTATATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↓ 13 24 Human: ATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Cluster: [ ] Orangutan: ATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Gorilla > Human --------------- chr1:127883212-127883252 Template switch process: F1: L TATACATGATATATTTACTTCCCCA 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC RR: ATATGCACTATATAAATGAAGGGGTCAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTAACCCCTTCATTTATATAGTGCAAG F2: 3 CAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTA 2 Unidirectional alignment (log-probability: -50.6) TATACaTGATATATTTACTTCCCCAaTTGTGGTGTAAGCATttttagagg---------ATGCTTACACCACAAcTGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCAT---------CCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -25.7) TATACaTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC Gorilla > Chimp --------------- chr1:100864544-100864584 Template switch process: F1: L TATACATGATATATTTACTTCCCCA 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC RR: ATATGCACTATATAAATGAAGGGGTCAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTAACCCCTTCATTTATATAGTGCAAG F2: 3 CAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTA 2 Unidirectional alignment (log-probability: -50.6) TATACaTGATATATTTACTTCCCCAaTTGTGGTGTAAGCATttttagagg---------ATGCTTACACCACAAcTGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCAT---------CCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -25.7) TATACaTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC Chimp > Gorilla --------------- chr1:100158312-100158372 Template switch process: F1: L TATAC 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC RR: ATATGTACTATATAAATGAAGGGGTTAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTGCAAG F2: 3 TAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTG 2 Unidirectional alignment (log-probability: -50.6) TATACgTGATATATTTACTTCCCCAgTTGTGGTGTAAGCATcctctaaaa---------ATGCTTACACCACAAtTGGGGAAGTAAATATATCACGTTC TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCAT---------TTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -22.2) TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC ========= Event 310 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: agtgatccatctgccttggcctcccaaagttctggattgcaggtatgagccgtcgtacctgcccCATGTGTTCTTTTTTATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Chimp: agtgatccatctgccttggcctcccaaagttctggattacaggtatgagccgtcgtacctgcccCATGTGTTCTTTTTTATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Gorilla: agtgatccatctgccttggcctcccaaagttctggattacaggtatgagccctcgtacctgcccCATGTGTTCTTTTTTATAGTCTATTCGTTATATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↑ 4 1 3 2 Human: agtgatccatctgccttggcctcccaaagttctggattgcaggtatgagccgtcgtacctgcccCATGTGTTCTTTTTTATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Cluster: [ ] Orangutan: agtgatccatctgccttggcctcccaaagttctggattacaggtatgagccatcgtacctgtccCATGTGTTCTTTTTTATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Human > Gorilla --------------- chr1:100158312-100158349 Template switch process: F1: L CCCTCGTACCTGCCCCATGTGTTCTTTTTTATAGTCTATTCGTTATATAC 1 F3: 4 TCT R RF: CCGTCGTACCTGCCCCATGTGTTCTTTTTTATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCT RR: GGCAGCATGGACGGGGTACACAAGAAAAAATATCAGATAAGTAATATATGTACTATATAAATGAAGGGGTTAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTGCAAGGATAAGA F2: 3 CCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTG 2 Unidirectional alignment (log-probability: -45.4) TGCCCCATGTGTTCTTTTTTATAGTCTATTCgTTATATACgTGATATATTTACTTCCCCAgTTGTGGTGTAAGCATccTct TGCCCCATGTGTTCTTTTTTATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTA Template switch alignment (log-probability: -30.9) TGCCCCATGTGTTCTTTTTTATAGTCTATTCgTTATATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCC|TCT TGCCCCATGTGTTCTTTTTTATAGTCTATTCATTATATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCC|TCT ========= Event 311 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CTCTCGAAGGAGTGAAATAGTTTAAAAACTTTATGCTATACTATTTATACTATTTGTTTTTGCAAATAA ↓ 13 24 ↑ 13 24 Chimp: CTCTCGAAGGAGTGAAATAGTATAAATAGTATAGCATAAAGTTTTTAAACTATTTGTTTTTGCAAATAA Gorilla: CTCTCGAAGGAGTGAAATACTATAAATAGTACAGCGTAAAGTTTTTAAACTATTTGTTTTTGCAAATAA Human: CTCTCGAAGGAGTGAAATAGTTTAAAAACTTTATGCTATACTATTTATACTATTTGTTTTTGCAAATAA Cluster: [ ] Orangutan: CTCTCGAAGGAGTGAAATAGTATAAATAGTATAGCATAAAGTTTTTAAACTATTTGT-TTTGCAAATAA Chimp > Human ------------- chr11:114574722-114574748 Template switch process: F1: L CTTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGT 1 F3: 4 ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC R RF: CTTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGTATAAATAGTATAGCATAAAGTTTTTAAACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC RR: GAAAGTGGTGTTCAATCAAAGAGAGCTTCCTCACTTTATCATATTTATCATATCGTATTTCAAAAATTTGATAAACAAAAACGTTTATTAAATTTCACACCGACTTTG F2: 3 TATTTATCATATCGTATTTCAAAAATT 2 Unidirectional alignment (log-probability: -55.4) TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAG-----------------------TTTAAaaactttatgctatactatttatACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGTATAAATAGTATAGCATAAAGTTTTTAA-----------------------ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC Template switch alignment (log-probability: -18.6) TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGT|TTAAAAACTTTATGCTATACTATTTAT|ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGT|TTAAAAACTTTATGCTATACTATTTAT|ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC Human > Chimp ------------- chr11:115366677-115366703 Template switch process: F1: L CTTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGT 1 F3: 4 ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC R RF: CTTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGTTTAAAAACTTTATGCTATACTATTTATACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC RR: GAAAGTGGTGTTCAATCAAAGAGAGCTTCCTCACTTTATCAAATTTTTGAAATACGATATGATAAATATGATAAACAAAAACGTTTATTAAATTTCACACCGACTTTG F2: 3 AATTTTTGAAATACGATATGATAAATA 2 Unidirectional alignment (log-probability: -55.4) TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGtataaatagtatagcataaagttTTTAA-----------------------ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAG-----------------------TTTAAAAACTTTATGCTATACTATTTATACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC Template switch alignment (log-probability: -18.6) TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGT|ATAAATAGTATAGCATAAAGTTTTTAA|ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC TTTCACCACAAGTTAGTTTCTCTCGAAGGAGTGAAATAGT|ATAAATAGTATAGCATAAAGTTTTTAA|ACTATTTGTTTTTGCAAATAATTTAAAGTGTGGCTGAAAC ========= Event 312 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: agtgccacctagatctgtaaataaaacTAGGAGACTTCCCTAGTTTTATTTATAGATTTGTGAAAGCAAAT Chimp: attgccacctagatctataaataaaacTAGGGAAGTCTCCTAGTTTTATTTATAGATTTGTGAAAGCAAAT ↑ 3 1 2 4 Gorilla: attgccacctagatctgtaaataaaacTAGGAGACTTCCCTGGTTTTATGTATAGATTTGTGAAAGCAAAT Human: agtgccacctagatctgtaaataaaacTAGGAGACTTCCCTAGTTTTATTTATAGATTTGTGAAAGCAAAT Cluster: [ ] Orangutan: attgccacctagatctataaataa-aGTAGGAGACTCCCCTAGT-TTATTTATAGATTAGTGAAAGCAAAT Gorilla > Chimp --------------- chr11:114978808-114978826 Template switch process: F1: L ACACTGTGCAATTGCCACCTAGATCTATAAATAAAACTAGG 1 F3: 4 TATAGATTTGTGAAAGCAAATATTATTTATTTGTGAAAGC R RF: ACACTGTGCAATTGCCACCTAGATCTGTAAATAAAACTAGGAGACTTCCCTGGTTTTATGTATAGATTTGTGAAAGCAAATATTATTTATTTGTGAAAGC RR: TGTGACACGTTAACGGTGGATCTAGACATTTATTTTGATCCTCTGAAGGGACCAAAATACATATCTAAACACTTTCGTTTATAATAAATAAACACTTTCG F2: 3 TTATTTTGATCCTCTGAAG 2 Unidirectional alignment (log-probability: -45.6) CACTGTGCAATTGCCACCTAGATCTaTAAATAAAACTAGGgaAgTctCCTaGTTTTATtTATAGATTTGTGAAAGCAAATATTATTTATTTGTGAAAGC CACTGTGCAATTGCCACCTAGATCTGTAAATAAAACTAGGAGACTTCCCTGGTTTTATGTATAGATTTGTGAAAGCAAATATTATTTATTTGTGAAAGC Template switch alignment (log-probability: -23.7) CACTGTGCAATTGCCACCTAGATCTaTAAATAAAACTAGG|GAAGTCTCCTAGTTTTATT|TATAGATTTGTGAAAGCAAATATTATTTATTTGTGAAAGC CACTGTGCAATTGCCACCTAGATCTGTAAATAAAACTAGG|GAAGTCTCCTAGTTTTATT|TATAGATTTGTGAAAGCAAATATTATTTATTTGTGAAAGC ========= Event 313 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTTAGTGAATTAGGAAGAAACTCTAAGTAATAACTTAGAGAAGGGAAGTTTAGTATTTAA ↑ 1 3 4 2 Chimp: TGTTAGTGAATTAGGAAGAAA------ACTATTACTTAGAGAAGGGAAGTTTAGTATTTAA Gorilla: TGTTAGTGAATTAGGAAGAAA------ACTATTACTTAGAGAAGGGAAGTTTAGTATTTAA ↓ 1 3 4 2 Human: TGTTAGTGAATTAGGAAGAAACTCTAAGTAATAACTTAGAGAAGGGAAGTTTAGTATTTAA Cluster: [ ] Orangutan: Chimp > Human ------------- chr1:118555952-118555963 Template switch process: F1: L ACAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA 1 F3: 4 ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT R RF: ACAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAAACTATTACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT RR: TGTCTGGACACATTACTCTAACAATCACTTAATCCTTCTTTTGATAATGAATCTCTTCCCTTCAAATCATAAATTCGAAATTATTAA F2: 3 ATAATGAATCTC 2 Unidirectional alignment (log-probability: -37.2) CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAActctaagtaatA-----ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA-----------ACTATTACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT Template switch alignment (log-probability: -16.8) CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA|CTCTAAGTAATA|ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA|CTCTAAGTAATA|ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT Gorilla > Human --------------- chr1:118555952-118555963 Template switch process: F1: L ACAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA 1 F3: 4 ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTTAATAATT R RF: ACAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAAACTATTACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTAAATAATT RR: TGTCTGGACACATTACTCTAACAATCACTTAATCCTTCTTTTGATAATGAATCTCTTCCCTTCAAATCATAAATTCGAATTTATTAA F2: 3 ATAATGAATCTC 2 Unidirectional alignment (log-probability: -41.9) CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAG-AAACTctaagtaATaACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTtAATAATT CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAAACT-------ATTACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTAAATAATT Template switch alignment (log-probability: -22.8) CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA|CTCTAAGTAATA|ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTtAATAATT CAGACCTGTGTAATGAGATTGTTAGTGAATTAGGAAGAAA|CTCTAAGTAATA|ACTTAGAGAAGGGAAGTTTAGTATTTAAGCTTAAATAATT ========= Event 314 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCCCTGTTGGGACTTTTATTCAAAGG------------------ATCATTTAGTCGTAATCAAGATTAATTA ↓ 3 4 1 2 Chimp: GCCGTGTTGGGACTTTTATTCAAAGGATCTAAATGATCCTTTGAATCATTTAGTTGTAATCAAGATTAATTA ↑ 3 4 1 2 Gorilla: GCCCTGTTGGGACTTTTATTCAAAGG------------------ATCATTTAGTTGTAATCAAGATTAATTA Human: GCCCTGTTGGGACTTTTATTCAAAGG------------------ATCATTTAGTCGTAATCAAGATTAATTA Cluster: [ ] Orangutan: GCCCTGTTGGGACTTTGATTCAAAGG------------------ATCATTTGGTTGTAATCAAGATTAATTA Human > Chimp ------------- chr1:109848390-109848404 Template switch process: F1: L CTTTAAGCAAGGTAGGCCGTGTTGGGACTTTTATTCAAAGGATC 1 F3: 4 ATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT R RF: CTTTAAGCAAGGTAGGCCCTGTTGGGACTTTTATTCAAAGGATCATTTAGTCGTAATCAAGATTAATTATTTGCATCCTAT RR: GAAATTCGTTCCATCCGGGACAACCCTGAAAATAAGTTTCCTAGTAAATCAGCATTAGTTCTAATTAATAAACGTAGGATA F2: 3 AGTTTCCTAGTAAAT 2 Unidirectional alignment (log-probability: -48.8) AAGCAAGGTAGGCCgTGTTGGGACTTTTATTCAAAGGatctaaatgatcctttgaATCATTTAGTtGTAATCAAGATTAATTATTTGCATCCTAT AAGCAAGGTAGGCCCTGTTGGGACTTTTATTCAAAGG------------------ATCATTTAGTCGTAATCAAGATTAATTATTTGCATCCTAT Template switch alignment (log-probability: -29.2) AAGCAAGGTAGGCCgTGTTGGGACTTTTATTCAAAGGATC|TAAATGATCCTTTGA|ATCATTTAGTtGTAATCAAGATTAATTATTTGCATCCTAT AAGCAAGGTAGGCCCTGTTGGGACTTTTATTCAAAGGATC|TAAATGATCCTTTGA|ATCATTTAGTCGTAATCAAGATTAATTATTTGCATCCTAT Gorilla > Chimp --------------- chr1:109848390-109848404 Template switch process: F1: L CTTTAAGCAAGGTAGGCCGTGTTGGGACTTTTATTCAAAGGATC 1 F3: 4 ATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT R RF: CTTTAAGCAAGGTAGGCCCTGTTGGGACTTTTATTCAAAGGATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT RR: GAAATTCGTTCCATCCGGGACAACCCTGAAAATAAGTTTCCTAGTAAATCAACATTAGTTCTAATTAATAAACGTAGGATA F2: 3 AGTTTCCTAGTAAAT 2 Unidirectional alignment (log-probability: -42.3) AAGCAAGGTAGGCCgTGTTGGGACTTTTATTCAAAGGatctaaatgatcctttgaATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT AAGCAAGGTAGGCCCTGTTGGGACTTTTATTCAAAGG------------------ATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT Template switch alignment (log-probability: -23.2) AAGCAAGGTAGGCCgTGTTGGGACTTTTATTCAAAGGATC|TAAATGATCCTTTGA|ATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT AAGCAAGGTAGGCCCTGTTGGGACTTTTATTCAAAGGATC|TAAATGATCCTTTGA|ATCATTTAGTTGTAATCAAGATTAATTATTTGCATCCTAT ========= Event 315 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TAATCATTGCTAGAAAATTTCCATATAGCATTCTATATGCTATATGGAAGAGACAAAAATATCAACATG Chimp: TAATCATTGCTGGAAAATTTCCATATAGCATTCTT----TTAC-AGGTAGAGACAAAAATATCAACATG ↓ 3 2 1 4 Gorilla: TAATCATTGCTGGAAAATTTCCATATAGCATTCTATATGCTATATGGAAGAGACAAAAATATCAACATG Human: TAATCATTGCTAGAAAATTTCCATATAGCATTCTATATGCTATATGGAAGAGACAAAAATATCAACATG Cluster: [ ] Orangutan: TAATCATTGCTGGAAAATTTCCATATAGCATTCTATATGCTATATGGAAGAGACAAAAATATCAACATG Chimp > Gorilla --------------- chr1:106912734-106912745 Template switch process: F1: L CCTTTCTTAATCATTGCTGGAAAATTTCCATATAGCATTCTAT 1 F3: 4 AGAGACAAAAATATCAACATGAAAAAGTAACATCAAATAG R RF: CCTTTCTTAATCATTGCTGGAAAATTTCCATATAGCATTCTTTTACAGGTAGAGACAAAAATATCAACATGAAAGAGTAACATCAAATAG RR: GGAAAGAATTAGTAACGACCTTTTAAAGGTATATCGTAAGAAAATGTCCATCTCTGTTTTTATAGTTGTACTTTCTCATTGTAGTTTATC F2: 3 AGGTATATCGTA 2 Unidirectional alignment (log-probability: -46.4) TTCTTAATCATTGCTGGAAAATTTCCATATAGCATTCT-----AtatgctatatGGaAGAGACAAAAATATCAACATGAAAaAGTAACATCAAATAG TTCTTAATCATTGCTGGAAAATTTCCATATAGCATTCTTTTACA----------GGTAGAGACAAAAATATCAACATGAAAGAGTAACATCAAATAG Template switch alignment (log-probability: -28.3) TTCTTAATCATTGCTGGAAAATTTCCATATAGCATTCTaT|ATGCTATATGGA|AGAGACAAAAATATCAACATGAAAaAGTAACATCAAATAG TTCTTAATCATTGCTGGAAAATTTCCATATAGCATTCTTT|ATGCTATATGGA|AGAGACAAAAATATCAACATGAAAGAGTAACATCAAATAG ========= Event 316 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATTCAATGTTTCCAAAGAT-------------------------------------------AAAAGAATTATCTTTTGCTCTTTGG------------ Chimp: AAATTCAATGTTTCCAAAGAT----------------------AAACTTTCTCTTCCAAAAGAGAAAAGAATTATCTTTTGCTCTTTGG------------ ↓ 4 3 1 2 Gorilla: AAATTCAATGTTTCCAAAGAT--AAAAGAATTATCCAAAAGAT---------------------AAAAGAATTATCTTTTGCTCTTTGG------------ Human: AAATTCAATGTTTCCAAAGAT-------------------------------------------AAAAGAATTATCTTTTGCTCTTTGG------------ Cluster: [ ] Orangutan: AAATTCAATGTTTCCA-----AT-----------------------------------------AAAAGAATTATCTTTTGCTCTTAGGTTAATTTCCCAA Chimp > Gorilla --------------- chr1:116442395-116442402 Template switch process: F1: L TGGCAAATTTTTAAGTGTTAAAATTCAATGTTTCCAAAGAT---------------------AAAAGAATTATC 1 F3: 4 AAAAGAATTATCTTTTGCTCTTTGGTTATTTCCAAGACTG R RF: TGGCAAATTTTTAAATGTTAAAATTCAATGTTTCCAAAGATAAACTTTCTCTTCCAAAAGAGAAAAGAATTATCTTTTGCTCTTTGGTTATTTCCAAGACTG RR: ACCGTTTAAAAATTTACAATTTTAAGTTACAAAGGTTTCTATTTGAAAGAGAAGGTTTTCTCTTTTCTTAATAGAAAACGAGAAACCAATAAAGGTTCTGAC F2: 3 TAGAAAAC 2 Unidirectional alignment (log-probability: -42.3) AgTGTTAAAATTCAATGTTTCCAAAGATAAA--------agaattaTCCAAAAGAtAAAAGAATTATCTTTTGCTCTTTGGTTATTTCCAAGACTG AATGTTAAAATTCAATGTTTCCAAAGATAAACTTTCTCT-------TCCAAAAGAGAAAAGAATTATCTTTTGCTCTTTGGTTATTTCCAAGACTG Template switch alignment (log-probability: -33.4) AgTGTTAAAATTCAATGTTTCCAAAGAT---------------------AAAAGAATTATC|CAAAAGAT|AAAAGAATTATCTTTTGCTCTTTGGTTATTTCCAAGACTG AATGTTAAAATTCAATGTTTCCAAAGATAAACTTTCTCTTCCAAAAGAGAAAAGAATTATC|CAAAAGAT|AAAAGAATTATCTTTTGCTCTTTGGTTATTTCCAAGACTG ========= Event 317 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAG---GGTTGATTTCTCATT-CTTTAACA ↑ 3 2 1 4 Chimp: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACT-------------------------------------------------------------------------------------------------------------------------------------------------------TTGTTTGACAGAGGCTCTGATTTCTCATT-CTTTAACA Gorilla: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACT-------------------------------------------------------------------------------------------------------------------------------------------------------TTGTTTGACAGAGGCTCTGATTTCTCATT-CTTTAACA ↓ 3 2 1 4 Human: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAG---GGTTGATTTCTCATT-CTTTAACA Cluster: [ ] Orangutan: CTACCTGTCTGTAACTCCAACCCTGCCCCAACATAAGGTCCTCTGCTTAATTTTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATGTTACTTCTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACCCTGCCCCAACATAAAGGTCCTCTGCATACTTGTTTGACAGAGACTCTGATGTCTCATTCGTTTAACA Chimp > Human ------------- chr1:120255197-120255202 Template switch process: F1: L TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG 1 F3: 4 TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA R RF: TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACTTTGTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATATTACTTCTCAAAAGCAA RR: AAAAGATGGACAGACATTGAGGTTGGGACGGGGTTGTACTCCAGGAGACACATGAAACAAACTGTCTCCGAGACTAAAGAGTAAGAAATTGTTATAATGAAGAGTTTTCGTT F2: 3 TGGGAC 2 Unidirectional alignment (log-probability: -35.8) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAggcagGGT-----------------------------TGATTTCTCATTCTTTAACAATgTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGA-----GGTCCTCTGTGTACTTTGTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATATTACTTCTCAAAAGCAA Template switch alignment (log-probability: -22) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATgTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATATTACTTCTCAAAAGCAA Gorilla > Human --------------- chr1:120255197-120255202 Template switch process: F1: L TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG 1 F3: 4 TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA R RF: TTTTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACTTTGTTTGACAGAGGCTCTGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA RR: AAAAGATGGACAGACATTGAGGTTGGGACGGGGTTGTACTCCAGGAGACACATGAAACAAACTGTCTCCGAGACTAAAGAGTAAGAAATTGTTACAATGAAGAGTTTTCGTT F2: 3 TGGGAC 2 Unidirectional alignment (log-probability: -29.3) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG-----------------------------CagggtTGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGGTCCTCTGTGTACTTTGTTTGACAGAGGCTC-----TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA Template switch alignment (log-probability: -16.5) TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA TTCTACCTGTCTGTAACTCCAACCCTGCCCCAACATGAGG|CAGGGT|TGATTTCTCATTCTTTAACAATGTTACTTCTCAAAAGCAA ========= Event 318 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTCACTTAGAGGCTATAATGTTC--------TTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA Chimp: CTTTCACTTAGAGGCTATAATGTTC--------TTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA ↓ 1 4 3 2 Gorilla: CCTTCACTTAGAGGCTATAATATCA----------------GAAGAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA ↑ 1 4 3 2 Human: CTTTCACTTAGAGGCTATAATGTTC--------TTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA Cluster: [ ] Orangutan: CTTTCACTTAGAGGCTATAATGTTCTTCTTCTC--------CCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA Human > Gorilla --------------- chr11:112377387-112377394 Template switch process: F1: L ACAGTGCTGAAAGAGCCCCTCCTTCACTTAGAGGCTATAAT 1 F3: 4 AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA R RF: TCAGTGCTGAAAGAGCCCCTCTTTCACTTAGAGGCTATAATGTTCTTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA RR: AGTCACGACTTTCTCGGGGAGAAAGTGAATCTCCGATATTACAAGAAGAAGAGGGGGTTTATTGTAAAAGAAGACTATCGGTTAAAAGTGTTTGTTT F2: 3 GAAGACTA 2 Unidirectional alignment (log-probability: -42.5) CAGTGCTGAAAGAGCCCCTCcTTCACTTAGAGGCTATAATatcagaaG---------------AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA CAGTGCTGAAAGAGCCCCTCTTTCACTTAGAGGCTATAAT-------GTTCTTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA Template switch alignment (log-probability: -27.8) CAGTGCTGAAAGAGCCCCTCcTTCACTTAGAGGCTATAAT|ATCAGAAG|AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA CAGTGCTGAAAGAGCCCCTCTTTCACTTAGAGGCTATAAT|ATCAGAAG|AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA Chimp > Gorilla --------------- chr11:112377387-112377394 Template switch process: F1: L ACAGTGCTGAAAGAGCCCCTCCTTCACTTAGAGGCTATAAT 1 F3: 4 AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA R RF: CCAGTGCTGAAAGAGCCCCTCTTTCACTTAGAGGCTATAATGTTCTTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA RR: GGTCACGACTTTCTCGGGGAGAAAGTGAATCTCCGATATTACAAGAAGAAGAGGGGGTTTATTGTAAAAGAAGACTATCGGTTAAAAGTGTTTGTTT F2: 3 GAAGACTA 2 Unidirectional alignment (log-probability: -42.5) CAGTGCTGAAAGAGCCCCTCcTTCACTTAGAGGCTATAATatcagaaG---------------AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA CAGTGCTGAAAGAGCCCCTCTTTCACTTAGAGGCTATAAT-------GTTCTTCTTCTCCCCCAAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA Template switch alignment (log-probability: -27.8) CAGTGCTGAAAGAGCCCCTCcTTCACTTAGAGGCTATAAT|ATCAGAAG|AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA CAGTGCTGAAAGAGCCCCTCTTTCACTTAGAGGCTATAAT|ATCAGAAG|AAATAACATTTTCTTCTGATAGCCAATTTTCACAAACAAA ========= Event 319 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: gcaaacggggagttgcgccgctcacccaaagttacTAGGTTCCAGCTGTGCCCGATGCACGGATGGTGTCCCTATCCTTCTCAGAAAGCAGGTGGGGCAGAGGTCATCCTGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCACTGA-GCCTCACTTTTCCCTTTCTTAGG Chimp: gcaaacggggagttgcgctgctcacccaaagttactcggttCCAGCTGTGCCCGAGGCACGGATGGTGTCCCTATCCTTCTCAGAAAGCAGGTGGGGCAGAGGTCATCCTGGCCCAACCCAGGCGCCAGGATCAAGGCCTTTCACCCACTGT-CCCTCACTTTTCCCTTTCTTAGG Gorilla: GCAAACGGGGAGTTGCACCGCTCACCCAAAGTTACTCGGTTCCAGCTGTGCCCGATGCATGGATGGTGTCCCTATCCTTCTCAGAAAGCAGATGGGGCAGAGGTCATCCTGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCACCGTCCCCTCACTTTTCCCTTTCTTAGG ↓ 3 2 1 4 Human: gcaaacggggagttgcgccgctcacccaaagttacTAGGTTCCAGCTGTGCCCGATGCACGGATGGTGTCCCTATCCTTCTCAGAAAGCAGGTGGGGCAGAGGTCATCCTGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCACTGA-GCCTCACTTTTCCCTTTCTTAGG Cluster: [ ] Orangutan: gcaaacggggagttgtgccgctcacccaaagttactcggttCCAGCTGTGCCCGATGCACGGATGGTGTCCCTGTCCTTCTCAGAAAGCAGGTGGGACAGAGGTCATCCTGGCCCAACCCAGGGGCCGAGCTCAAGGTCTTTCACCCACTGT-CCCTCACTTTTCCCTTTCTTAGG Gorilla > Human --------------- chr11:133950591-133950595 Template switch process: F1: L CTGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCAC 1 F3: 4 CTCACTTTTCCCTTTCTTAGGGCCTGAGCCAGAGGTCGG R RF: GCTCACCCAAAGTTACTCGGTTCCAGCTGTGCCCGATGCATGGATGGTGTCCCTATCCTTCTCAGAAAGCAGATGGGGCAGAGGTCATCCTGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCACCGTCCCCTCACTTTTCCCTTTCTTAGGGCCTGAGCCAGAGGTCGG RR: CGAGTGGGTTTCAATGAGCCAAGGTCGACACGGGCTACGTACCTACCACAGGGATAGGAAGAGTCTTTCGTCTACCCCGTCTCCAGTAGGACCGGGTTGGGTCCGCGGCCCTAGTTCCGGAAAGTGGGTGGCAGGGGAGTGAAAAGGGAAAGAATCCCGGACTCGGTCTCCAGCC F2: 3 CGAGT 2 Unidirectional alignment (log-probability: -26.6) TGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCA-----CtgagCCTCACTTTTCCCTTTCTTAGGGCCTGAGCCAGAGGTCGG TGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCACCGTCC----CCTCACTTTTCCCTTTCTTAGGGCCTGAGCCAGAGGTCGG Template switch alignment (log-probability: -16.3) TGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCAC|TGAGC|CTCACTTTTCCCTTTCTTAGGGCCTGAGCCAGAGGTCGG TGGCCCAACCCAGGCGCCGGGATCAAGGCCTTTCACCCAC|TGAGC|CTCACTTTTCCCTTTCTTAGGGCCTGAGCCAGAGGTCGG ========= Event 320 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTG--------------GGCAGGTTTTTCAGGGCTAATGAGCTGGGGCCAAGGG Chimp: AAGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTG--------------GGCAGGTTTTTCAGGGCTAATGAGCTGGGGCCAAGGG ↑ 3 2 4 1 Gorilla: AAGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTG----------------------------GGCTAATGAGCTGGGGCCAAGGG ↓ 3 2 4 1 Human: AAGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTG--------------GGCAGGTTTTTCAGGGCTAATGAGCTGGGGCCAAGGG Cluster: [ ] Orangutan: AAGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGCAGGTTTTTCAG--------------GGCTAATGAGCTGGGGCCAAGGG Gorilla > Human --------------- chr1:237319131-237319140 Template switch process: F1: L AGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGC 1 F3: 4 GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGAG R RF: AGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGAG RR: TCTCCCTCTATAAAATCGACTTTTTGGAGGGGGACCTAAACCCGATTACTCGACCCCGGTTCCCTCAAAGGTCCCTCCCTC F2: 3 ACTTTTTGGA 2 Unidirectional alignment (log-probability: -31) GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTgggcaggtttttcaGGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTT--------------GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA Template switch alignment (log-probability: -17.1) GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGC|AGGTTTTTCA|GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGC|AGGTTTTTCA|GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA Gorilla > Chimp --------------- chr1:217462374-217462383 Template switch process: F1: L AGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGC 1 F3: 4 GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGAG R RF: AGAGGGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGAG RR: TCTCCCTCTATAAAATCGACTTTTTGGAGGGGGACCTAAACCCGATTACTCGACCCCGGTTCCCTCAAAGGTCCCTCCCTC F2: 3 ACTTTTTGGA 2 Unidirectional alignment (log-probability: -31) GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTgggcaggtttttcaGGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTT--------------GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA Template switch alignment (log-probability: -17.1) GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGC|AGGTTTTTCA|GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA GGAGATATTTTAGCTGAAAAACCTCCCCCTGGATTTGGGC|AGGTTTTTCA|GGGCTAATGAGCTGGGGCCAAGGGAGTTTCCAGGGAGGGA ========= Event 321 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTCCCACAGACTCCCAGGGATCCC----TCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCTTAGGTCCAGGAACAATTGGAAAGTCA ↓ 1 4 3 2 Chimp: GTTCCCACAGACTCCCAGGGAGACC--TCTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCTTAGGTCCAGGAACAATTGGAAAGTCA Gorilla: GTTCCCACAGACTCCCAGGGAGCCCTC--TCTCTGTTCCGATGCAGATTTATCCAACTGGAACCAGCTTAGGTCCAGGAACAATTGGAAATTCA Human: GTTCCCACAGACTCCCAGGGATCCC----TCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCTTAGGTCCAGGAACAATTGGAAAGTCA Cluster: [ ] Orangutan: GTTCCCACAGACTCCCAGGGAGCCCTC--TCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCTTAGGTCCAGGAACAATTGGAAAGTCA Human > Chimp ------------- chr1:108993311-108993315 Template switch process: F1: L TTATCTTGCCATTCCCCCAAGTTCCCACAGACTCCCAGGGA 1 F3: 4 CTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCTT R RF: TTATCTTGCCATTCCCCCAAGTTCCCACAGACTCCCAGGGATCCCTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCTTAGGTC RR: AATAGAACGGTAAGGGGGTTCAAGGGTGTCTGAGGGTCCCTAGGGAGAGACAAGACTACGTCTAAATAGGTTGACCTTGGTCGAATCCAG F2: 3 TCCAG 2 Unidirectional alignment (log-probability: -25.8) TATCTTGCCATTCCCCCAAGTTCCCACAGACTCCCAGGgaGAcCtCTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCT TATCTTGCCATTCCCCCAAGTTCCCACAGACTCCCAGG--GATCCCTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCT Template switch alignment (log-probability: -15.9) TATCTTGCCATTCCCCCAAGTTCCCACAGACTCCCAGGGA|GACCT|CTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCT TATCTTGCCATTCCCCCAAGTTCCCACAGACTCCCAGGGA|GACCT|CTCTCTGTTCTGATGCAGATTTATCCAACTGGAACCAGCT ========= Event 322 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTTTTATGTCCCACTATTAAAGTAGTTCTACCTCTGA--ATTCTGGTAGCTGCTTTCAATCCATATTCCTA Chimp: CTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGAGAGAACTGCTTTATGCTTTCAATCCATATTCCTA ↑ 3 2 1 4 Gorilla: CTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGA--ATTCTGGTAGTTGCTTTCAATCCATATTCCTA Human: CTCTTTTATGTCCCACTATTAAAGTAGTTCTACCTCTGA--ATTCTGGTAGCTGCTTTCAATCCATATTCCTA Cluster: [ ] Orangutan: ATCTTTTATGCCCCACTATTAAAGTAGTTCTCCCTCTGA--ATTCTGGTAGCTGCTTTCTATCCATATTCCTA Gorilla > Chimp --------------- chr11:112040128-112040140 Template switch process: F1: L GTCTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGA 1 F3: 4 TGCTTTCAATCCATATTCCTACCCCGGGATTACTGCCCTT R RF: GTCTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGAATTCTGGTAGTTGCTTTCAATCCATATTCCTACCCTGGGATTACTGCCCTT RR: CAGAGAAAATACAGGGTGATAATTTCATCAAGAGGGAGACTTAAGACCATCAACGAAAGTTAGGTATAAGGATGGGACCCTAATGACGGGAA F2: 3 ATTTCGTCAAGAG 2 Unidirectional alignment (log-probability: -43.9) TCTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGAgagaactgctttA----------TGCTTTCAATCCATATTCCTACCCcGGGATTACTGCCCTT TCTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGA------------ATTCTGGTAGTTGCTTTCAATCCATATTCCTACCCTGGGATTACTGCCCTT Template switch alignment (log-probability: -28.4) TCTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGA|GAGAACTgCTTTA|TGCTTTCAATCCATATTCCTACCCcGGGATTACTGCCCTT TCTCTTTTATGTCCCACTATTAAAGTAGTTCTCCCTCTGA|GAGAACTACTTTA|TGCTTTCAATCCATATTCCTACCCTGGGATTACTGCCCTT ========= Event 323 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGCTTGAACTCTTTAAAGTCATTCATTTTCACAATGACAT-ATTTAAAGTTATTACTAATTTTTC------TGACTCTTTAGtattacgtat Chimp: AGGCTTGAACTCTTTAAAGTCATTCATTTTCACAATGACAT-ATTTAAAGT---TACTAATTTTTC----TTTGCCTCTTTAGtattatgtat Gorilla: ---CTTTAACTCTTTAA-ATATGTCATTGTGAAAATGAATGACTTTAAAGTTATTACTAATTTTTCTTTA--AGACTCTTTAGtattacgtat ↓ 3 1 2 4 Human: AGGCTTGAACTCTTTAAAGTCATTCATTTTCACAATGACAT-ATTTAAAGTTATTACTAATTTTTC------TGACTCTTTAGtattacgtat Cluster: [ ] Orangutan: ---CTTGAACTCTTTAAAGTCATTCATTTTCACAATGACAT-ATTTAAAGTTCTTACTAATTTTTCTTTA--AGACTCTTTAGTATTACAtat Gorilla > Human --------------- chr11:23948234-23948247 Template switch process: F1: L ATT 1 F3: 4 TTTAAAGTTATTACTAATTTTTCT----GACTCTTTAGTATTACGTATTGAATGCCTGCTATGTGCAT R RF: TATGTCATTGTGAAAATGAATGACTTTAAAGTTATTACTAATTTTTCTTTAAGACTCTTTAGTATTACGTATTGAATGCCTGCTATGTGCAT RR: ATACAGTAACACTTTTACTTACTGAAATTTCAATAATGATTAAAAAGAAATTCTGAGAAATCATAATGCATAACTTACGGACGATACACGTA F2: 3 ATACAGTAACACTT 2 Unidirectional alignment (log-probability: -48.9) attttcacaatgacatA-----------------TTTAAAGTTATTACTAATTTTTCT----GACTCTTTAGTATTAC ----------------ATTGTGAAAATGAATGACTTTAAAGTTATTACTAATTTTTCTTTAAGACTCTTTAGTATTAC Template switch alignment (log-probability: -27.1) ATT|TTCACAATGACATA|TTTAAAGTTATTACTAATTTTTCT----GACTCTTTAGTATTAC ATT|TTCACAATGACATA|TTTAAAGTTATTACTAATTTTTCTTTAAGACTCTTTAGTATTAC ========= Event 324 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: gggattacaggcgtgaacagccg-cgcccggccCAGGGTTAGCTTTTCTATGGCAGCAAGAGTGCACCTTTCTTGGT Chimp: gggattacaggcgtgaacAGGCTAACCCCGGCCCAGGGTTAGCTTTTCTATGGCAGCAAGAGTGCACCTTTCTTGGT ↑ 1 4 3 2 Gorilla: gggattacaggcgtgaacagccg-cgcccggccCAGGGTTAGCTTTTCTATGGCATTAAGAGTGCACCTTTCTTGGT Human: gggattacaggcgtgaacagccg-cgcccggccCAGGGTTAGCTTTTCTATGGCAGCAAGAGTGCACCTTTCTTGGT Cluster: [] Orangutan: gggattacagacgtgaacagccg-cgcccggccCAGGGTTAGCTTTTCTATGGCAGCAAGAGTGCACCTTTCTTGGT Gorilla > Chimp --------------- chr11:119289274-119289280 Template switch process: F1: L GAACAG 1 F3: 4 CCGGCCCAGGGTTAGCTTTTCTATGGCAGCAAGAGTGCACCTTTCTTGGTGGGAAATGAGGACACGGTTT R RF: GAACAGCCGCGCCCGGCCCAGGGTTAGCTTTTCTATGGCATTAAGAGTGCACCTTTCTTGGTGGGAAATGAGGACACGGTTT RR: CTTGTCGGCGCGGGCCGGGTCCCAATCGAAAAGATACCGTAATTCTCACGTGGAAAGAACCACCCTTTACTCCTGTGCCAAA F2: 3 CCAATCG 2 Unidirectional alignment (log-probability: -39) GAACAG----GctaacCCCGGCCCAGGGTTAGCTTTTCTATGGCAgcAAGAGTGCAC GAACAGCCGCG-----CCCGGCCCAGGGTTAGCTTTTCTATGGCATTAAGAGTGCAC Template switch alignment (log-probability: -27.5) GAACAG|GCTAACC|CCGGCCCAGGGTTAGCTTTTCTATGGCAgcAAGAGTGCAC GAACAG|GCTAACC|CCGGCCCAGGGTTAGCTTTTCTATGGCATTAAGAGTGCAC ========= Event 325 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GTAAGTCACAAAATTACATTGATCTTAGTTTCATTATGTGAACTTGTTCACATGGTTGTAGAATTTGCTTCCAAATCTAAAGTCttataatattaaaaaattgaataaattaCAAATTCCCCCAATAAAGCCCTacacatatttattttatatgatcacacatatttattttatataatcaTCTGTTTCTTAGAAA Chimp: ATAAGTCACAAAATTACATTGATCTTAGTTTCATTATGTGAACTTGTTCACATGGTTGTAGAATTTGCTTCCAAATCTAAAGTCTTATAATATTAAAAAATTGAATAAATTACAAATTCCCCCAATAAAGCCCTacacatatttattttatataatcacacatatttattttatataatcaTCTGTTTCTTAGAAA Gorilla: GTAAGTCACAAAATTACACTGATCTTAGTTTGATTATGTGAACTTGTTCACATGGTTGTAGAATTTGCTTCCAAATCGAAAGTCTTATAATATTAAAAAATTGAATAAATTACAAATTCCCCCCATATAGCCCTACACATATTTA-----------------------TTTTATATAATCATCTGTTTCTTAGAAA ↓ 3 2 4 1 Human: GTAAGTCACAAAATTACATTGATCTTAGTTTCATTATGTGAACTTGTTCACATGGTTGTAGAATTTGCTTCCAAATCTAAAGTCttataatattaaaaaattgaataaattaCAAATTCCCCCAATAAAGCCCTacacatatttattttatatgatcacacatatttattttatataatcaTCTGTTTCTTAGAAA Cluster: [ ] Orangutan: GTAAGTCACAAAATTACACTGATCTTAGAGTCATTATGTGAACTTGTTCACATGGTTGTAGAATTTGCTTCCAAATCTAAAGTCTTATAATGTTA-AAAATTGAATAAATTACAAATTCCCCCAATAAAGCCCTACAAATATTTA-----------------------TTTTATATAATCATCTGTTTCTTAGAAA Gorilla > Human --------------- chr11:24824693-24824697 Template switch process: F1: L TCTTATAATATTAAAAAATTGAATAAATTACAAATTCCCCCAATAAAGCCCTACACATATTTATTTTATAT 1 F3: 4 CACATATTTA R RF: TGATCTTAGTTTGATTATGTGAACTTGTTCACATGGTTGTAGAATTTGCTTCCAAATCGAAAGTCTTATAATATTAAAAAATTGAATAAATTACAAATTCCCCCCATATAGCCCTACACATATTTATTTTATAT RR: ACTAGAATCAAACTAATACACTTGAACAAGTGTACCAACATCTTAAACGAAGGTTTAGCTTTCAGAATATTATAATTTTTTAACTTATTTAATGTTTAAGGGGGGTATATCGGGATGTGTATAAATAAAATATA F2: 3 ACTAG 2 Unidirectional alignment (log-probability: -51.7) AAATTCCCCCaATAaAGCCCTACACATATTTAttttatatgatcacacatattta AAATTCCCCCCATATAGCCCTACACATATTTA----------------------- Template switch alignment (log-probability: -27.4) AAATTCCCCCaATAaAGCCCTACACATATTTATTTTATAT|GATCA|CACATATTTA AAATTCCCCCCATATAGCCCTACACATATTTATTTTATAT|GATCA|CACATATTTA ========= Event 326 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAACCCAGTGGCTCTGAGCTCAGCACGCGATGCACCCAGGAATGTGGCCTTACG Chimp: GGAACCCAGTGGCTCTGAGCTCAGCACGCAATGCACCCAGGAATGTGGCCTTACG Gorilla: GGAACCCAGTGGCTCTGAGCTAAGCATGCAATGCACCCAGGAATGTGGCCTTACG ↑ 1 43 2 Human: GGAACCCAGTGGCTCTGAGCTCAGCACGCGATGCACCCAGGAATGTGGCCTTACG Cluster: [ ] Orangutan: GGAACCCAGTGGCTCTGATCTCAGCACGCAATGCACCCAGGAATGTGGCCACAAG Human > Gorilla --------------- chr1:913959-913962 Template switch process: F1: L TATCATGTGTCACTGACCCAGGAACCCAGTGGCTCTGAGCTAAGCA 1 F3: 4 ATGCACCCAGGAATGTGGCCTTACGTTGTTACTGTGCCCG R RF: TATCATGTGTCATTGACCCAGGAACCCAGTGGCTCTGAGCTCAGCACGCGATGCACCCAGGAATGTGGCCTTACGTTGTTACTGTGCCCA RR: ATAGTACACAGTAACTGGGTCCTTGGGTCACCGAGACTCGAGTCGTGCGCTACGTGGGTCCTTACACCGGAATGCAACAATGACACGGGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -40.1) GTGTCAcTGACCCAGGAACCCAGTGGCTCTGAGCTaAGCAtGCaATGCACCCAGGAATGTGGCCTTACGTTGTTACTgtgcccg GTGTCATTGACCCAGGAACCCAGTGGCTCTGAGCTCAGCACGCGATGCACCCAGGAATGTGGCCTTACGTTGTTACT------- Template switch alignment (log-probability: -32.9) GTGTCAcTGACCCAGGAACCCAGTGGCTCTGAGCTaAGCA|TGCA|ATGCACCCAGGAATGTGGCCTTACGTTGTTACTGTGCCCg GTGTCATTGACCCAGGAACCCAGTGGCTCTGAGCTCAGCA|TGCA|ATGCACCCAGGAATGTGGCCTTACGTTGTTACTGTGCCCA ========= Event 327 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CAATGACAAATATTTATAATACGATTAAGGTCATAAAAGGTTGTCAC------------------- Chimp: CAATGACAAATATTTATAATACGATTAAGGTCATAAAAGGTTGTCAC------------------- ↓ 1 4 3 2 Gorilla: CAATGACAAATATTTATAATATGACTAAGGTCATAAAAGGTTGTCACATACATGTGGCATAATAGT Human: CAATGACAAATATTTATAATACGATTAAGGTCATAAAAGGTTGTCAC------------------- Cluster: [ ] Orangutan: CAATGACAAATATTTATAATACGATTAAGGTCATAAAAGGTTGTCACATACATGTGGCGTACTGGT Chimp > Gorilla --------------- chr11:26857584-26857587 Template switch process: F1: L CTCTGCAATAGATTAAGTGACAATGACAAATATTTATAATA 1 F3: 4 TAAGGTCATAAAAGGTTGTCACATACATGTGGCATAATAG R RF: CTCTGCAATAGATTAAGTGACAATGACAAATATTTATAATACGATTAAGGTCATAAAAGGTTGTCACATACATGTGGCATAATAG RR: GAGACGTTATCTAATTCACTGTTACTGTTTATAAATATTATGCTAATTCCAGTATTTTCCAACAGTGTATGTACACCGTATTATC F2: 3 CAGT 2 Unidirectional alignment (log-probability: -44.6) TCTGCAATAGATTAAGTGACAATGACAAATATTTATAATAtGAcTAAGGTCATAAAAGGTTGTCACatacatgtggcataatag TCTGCAATAGATTAAGTGACAATGACAAATATTTATAATACGATTAAGGTCATAAAAGGTTGTCAC------------------ Template switch alignment (log-probability: -16.2) TCTGCAATAGATTAAGTGACAATGACAAATATTTATAATA|TGAC|TAAGGTCATAAAAGGTTGTCACATACATGTGGCATAATAG TCTGCAATAGATTAAGTGACAATGACAAATATTTATAATA|TGAC|TAAGGTCATAAAAGGTTGTCACATACATGTGGCATAATAG ========= Event 328 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGACTCACCACCTATTGAGAA-------TAACCTTGCAATGTGACTTAGATGTCATGAAATAAAGTTTAGAA Chimp: TGACTCACCACCTATTGAGAA-------TAACCTTGCAATGCGACTTAGATGTCATGAAATAAAGTTTAGAA ↓ 1 34 2 Gorilla: TGACTCACCGCCTATTGAGAA--------------TCTAAGTCACTTAGATATCATGAAATAAAGTTTAGAA ↑ 1 34 2 Human: TGACTCACCACCTATTGAGAA-------TAACCTTGCAATGTGACTTAGATGTCATGAAATAAAGTTTAGAA Cluster: [ ] Orangutan: TGACTCACCGCCTATTGAGAATAACCTT-------GCAATGTGACTTAGATGTCATGAAATAAAGTTTAGAA Human > Gorilla --------------- chr11:105931291-105931297 Template switch process: F1: L GGTTGTTTGCCACCTCCCTTTGACTCACCGCCTATTGAGAAT 1 F3: 4 ACTTAGATATCATGAAATAAAGTTTAGAAAGTTATTTGTTTAAAACACT R RF: GGTTGTTTGCCACCTCCCTTTGACTCACCACCTATTGAGAATAACCTTGCAATGTGACTTAGATGTCATGAAATAAAGTTTAGAAAGTTATTTGTTTAAAACACT RR: CCAACAAACGGTGGAGGGAAACTGAGTGGTGGATAACTCTTATTGGAACGTTACACTGAATCTACAGTACTTTATTTCAAATCTTTCAATAAACAAATTTTGTGA F2: 3 CTGAATC 2 Unidirectional alignment (log-probability: -39.1) TTGTTTGCCACCTCCCTTTGACTCACCgCCTATTGAGAAT-------CtAaGTcACTTAGATaTCATGAAATAAAGTTTAGAAAGTTATTTGTT TTGTTTGCCACCTCCCTTTGACTCACCACCTATTGAGAATAACCTTGCAATGTGACTTAGATGTCATGAAATAAAGTTTAGAAAGTTATTTGTT Template switch alignment (log-probability: -27.9) TTGTTTGCCACCTCCCTTTGACTCACCgCCTATTGAGAAT|CTAAGTC|ACTTAGATaTCATGAAATAAAGTTTAGAAAGTTATTTGTT TTGTTTGCCACCTCCCTTTGACTCACCACCTATTGAGAAT|CTAAGTC|ACTTAGATGTCATGAAATAAAGTTTAGAAAGTTATTTGTT Chimp > Gorilla --------------- chr11:105931291-105931297 Template switch process: F1: L GGTTGTTTGCCACCTCCCTTTGACTCACCGCCTATTGAGAAT 1 F3: 4 ACTTAGATATCATGAAATAAAGTTTAGAAAGTTATTTGTTTAAAACACT R RF: GGTTGTTTGCCACCTCCCTTTGACTCACCACCTATTGAGAATAACCTTGCAATGCGACTTAGATGTCATGAAATAAAGTTTAGAAAGTTATTTGTTTAAAACACT RR: CCAACAAACGGTGGAGGGAAACTGAGTGGTGGATAACTCTTATTGGAACGTTACGCTGAATCTACAGTACTTTATTTCAAATCTTTCAATAAACAAATTTTGTGA F2: 3 CTGAATC 2 Unidirectional alignment (log-probability: -42.6) TTGTTTGCCACCTCCCTTTGACTCACCgCCTATTGAGAAT--------------ctaagtcACTTAGATaTCATGAAATAAAGTTTAGAAAGTTATTTGTT TTGTTTGCCACCTCCCTTTGACTCACCACCTATTGAGAATAACCTTGCAATGCG-------ACTTAGATGTCATGAAATAAAGTTTAGAAAGTTATTTGTT Template switch alignment (log-probability: -27.9) TTGTTTGCCACCTCCCTTTGACTCACCgCCTATTGAGAAT|CTAAGTC|ACTTAGATaTCATGAAATAAAGTTTAGAAAGTTATTTGTT TTGTTTGCCACCTCCCTTTGACTCACCACCTATTGAGAAT|CTAAGTC|ACTTAGATGTCATGAAATAAAGTTTAGAAAGTTATTTGTT ========= Event 329 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATATAGGCACATATAACACTTTTGTGAATTTTGT ↑ 3 2 1 4 Chimp: TTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCAT---AGTAT-CTTAACACTTTTGTGAATTTTGT Gorilla: TTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCAT---AGTAT-CTTAACACTTTTGTGAATTTTGT ↓ 3 2 1 4 Human: TTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATATAGGCACATATAACACTTTTGTGAATTTTGT Cluster: [ ] Orangutan: TTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCAT---AGTAT-CTTAACAC--TTGTGAATTTTAT Chimp > Human ------------- chr11:132096484-132096493 Template switch process: F1: L TAGCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA 1 F3: 4 TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG R RF: TAGCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATAGTATCTTAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG RR: ATCGAAGTCTTACAGACGTCAATAAACACGGATATACAGTATCATAGAATTGTGAAAACACTTAAAACAACACATTCGAAATTTAGGC F2: 3 ATACACGGAT 2 Unidirectional alignment (log-probability: -34.4) GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA-----TaggcacataTAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATAGTATCT---------TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG Template switch alignment (log-probability: -22.5) GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA|TAGGCACAtA|TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA|TAGGCACAAA|TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG Gorilla > Human --------------- chr11:132096484-132096493 Template switch process: F1: L TAGCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA 1 F3: 4 TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG R RF: TAGCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATAGTATCTTAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG RR: ATCGAAGTCTTACAGACGTCAATAAACACGGATATACAGTATCATAGAATTGTGAAAACACTTAAAACAACACATTCGAAATTTAGGC F2: 3 ATACACGGAT 2 Unidirectional alignment (log-probability: -33.9) GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA-----TaggcacataTAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATAGTATCT---------TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG Template switch alignment (log-probability: -22.5) GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA|TAGGCACAtA|TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG GCTTCAGAATGTCTGCAGTTATTTGTGCCTATATGTCATA|TAGGCACAAA|TAACACTTTTGTGAATTTTGTTGTGTAAGCTTTAAATCCG ========= Event 330 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTGTCCCGTTTGCTGCTCCCATG-----TTCTCTGCAAAGCTACCATACTTTCCCTAATAA------------TAATAAT----AATTACCCTCTTTACATACAATGTGTTTTTGCCATTTTAAAAGAACATTCATGTGCATTATCCTGATT Chimp: ATTGTCCCATTTGCTGCTCCCGTG-----TTCTCTGCAAAGCTACCATACTTTCCCTAATAA-------------------TAATAATTACCCTCTTTACATACAATGTGTTTTTGCCATTTTAAAAGAACATTCATGTGCATTATCCTGATT ↓ 1 4 3 2 Gorilla: ATTGTCCCGTTTGCTGCTCCCATGTTCTGTTCTCTGCAAAGCTACCATACTTTCCCTAATAA----TAATAATT-----------AATTACCCTCTTTACATACAATGTGTTTTTGCCATTTTAAAAGAACATTCATGTGCATTATCCTGATT Human: ATTGTCCCGTTTGCTGCTCCCATG-----TTCTCTGCAAAGCTACCATACTTTCCCTAATAA------------TAATAAT----AATTACCCTCTTTACATACAATGTGTTTTTGCCATTTTAAAAGAACATTCATGTGCATTATCCTGATT Cluster: [ ] Orangutan: GTTGTCCCATTTGCTGCTCCCATG-----TTTTCTGCAAAGCTACCATCCTTTCCCTAATAATAAT-------------------AATTACCCTCTTTATATACAATGTGTTTTTGCCATTTTTAAAGAACATTCATGTGCATTATCCTGATT Chimp > Gorilla --------------- chr11:105739356-105739362 Template switch process: F1: L CACAAACTCCAATAAGCCTCATTGTCCCGTTTGCTGCTCCC 1 F3: 4 GTTCTCTGCAAAGCTACCATACTTTCCCTAATAATAATAAT R RF: CACAAACTCCAATAAGCCTCATTGTCCCATTTGCTGCTCCCGTGTTCTCTGCAAAGCTACCATACTTTCCCTAATAATAATAATTACCCTCTTTACATACAATGTGTTTTTGCCATTTTAAAAGAACAT RR: GTGTTTGAGGTTATTCGGAGTAACAGGGTAAACGACGAGGGCACAAGAGACGTTTCGATGGTATGAAAGGGATTATTATTATTAATGGGAGAAATGTATGTTACACAAAAACGGTAAAATTTTCTTGTA F2: 3 TCTTGTA 2 Unidirectional alignment (log-probability: -45.9) ACAAACTCCAATAAGCCTCATTGTCCCgTTTGCTGCTCCCatgttcTGTTCTCTGCAAAGCTACCATACTTTCCCTAATAAtaataa ACAAACTCCAATAAGCCTCATTGTCCCATTTGCTGCTCCCG-----TGTTCTCTGCAAAGCTACCATACTTTCCCTAATAA------ Template switch alignment (log-probability: -22.2) ACAAACTCCAATAAGCCTCATTGTCCCgTTTGCTGCTCCC|ATGTTCT|GTTCTCTGCAAAGCTACCATACTTTCCCTAATAATAATAA ACAAACTCCAATAAGCCTCATTGTCCCATTTGCTGCTCCC|ATGTTCT|GTTCTCTGCAAAGCTACCATACTTTCCCTAATAATAATAA ========= Event 331 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTCTTGCCTTCTTTCTGGTGGTCTGCCTCACAAATTTCAGCTGTTTAGCCTCCCAAACTG ↓ 1 4 3 2 Chimp: TCTCTTGCCTTCTTTCTGGTG-GCTG--AAACAAATTTCAGCTGTTTAGCCTCCCAAACTG Gorilla: TCTCTTGCCTTCTCTCTGGTGGTCTGCCTCACAGATTTCAGCTGTTTAGCCTCCCAAACTG Human: TCTCTTGCCTTCTTTCTGGTGGTCTGCCTCACAAATTTCAGCTGTTTAGCCTCCCAAACTG Cluster: [ ] Orangutan: tctcttgccttctctctggtggtctgcctcacaaatttcagctgcttagcctcccaaactg Human > Chimp ------------- chr11:105390924-105390928 Template switch process: F1: L AATCATGTTTTCTGCTATGTTCTCTTGCCTTCTTTCTGGTGG 1 F3: 4 ACAAATTTCAGCTGTTTAGCCTCCCAAACTGTGATCTCCA R RF: AATCATGTTTTCTGCTTTGTTCTCTTGCCTTCTTTCTGGTGGTCTGCCTCACAAATTTCAGCTGTTTAGCCTCCCAAACTGTGATCTCCA RR: TTAGTACAAAAGACGAAACAAGAGAACGGAAGAAAGACCACCAGACGGAGTGTTTAAAGTCGACAAATCGGAGGGTTTGACACTAGAGGT F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -33.3) TCATGTTTTCTGCTaTGTTCTCTTGCCTTCTTTCTGGTGG-------CtgaaACAAATTTCAGCTGTTTAGCCTCCCAAACTGTGATCTCCA TCATGTTTTCTGCTTTGTTCTCTTGCCTTCTTTCTGGTGGTCTGCCTC----ACAAATTTCAGCTGTTTAGCCTCCCAAACTGTGATCTCCA Template switch alignment (log-probability: -21.9) TCATGTTTTCTGCTaTGTTCTCTTGCCTTCTTTCTGGTGG|CTGAA|ACAAATTTCAGCTGTTTAGCCTCCCAAACTGTGATCTCCA TCATGTTTTCTGCTTTGTTCTCTTGCCTTCTTTCTGGTGG|CTGAA|ACAAATTTCAGCTGTTTAGCCTCCCAAACTGTGATCTCCA ========= Event 332 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAATTTTGTGATGATGATGAAGTACCAC----TTGGGGAAGCCCAAGAGTTAAGA ↓ 3 1 2 4 Chimp: GAATTTTGTGATGATGATGAAGTGGTAC--TTTTTGGGAAGCCCAAGAGTTAAGA Gorilla: GAATTTTGTAATGATGATGAAGTGGTGCTT--TTTGGGAAGCCCAAGAGTTAAGA Human: GAATTTTGTGATGATGATGAAGTACCAC----TTGGGGAAGCCCAAGAGTTAAGA Cluster: [ ] Orangutan: GAATTTTGTAATGATGATGAAGTGGTACTT--TTTGGGAAGCCCAAGAGTTAAGA Human > Chimp ------------- chr11:106543230-106543236 Template switch process: F1: L AAAAATGCATTTAATCTAGAATTTTGTGATGATGATGAAGT 1 F3: 4 TTTGGGAAGCCCAAGAGTTAAGATGGTAGGGTTCACAAGAAGT R RF: AAAAATGCATTTAATCTAGAATTTTGTGATGATGATGAAGTACCACTTGGGGAAGCCCAAGAGTTAAGATGGTAGGGTTCACAAGAAGT RR: TTTTTACGTAAATTAGATCTTAAAACACTACTACTACTTCATGGTGAACCCCTTCGGGTTCTCAATTCTACCATCCCAAGTGTTCTTCA F2: 3 TTCATGG 2 Unidirectional alignment (log-probability: -34.4) AAAATGCATTTAATCTAGAATTTTGTGATGATGATGAAG-------TGgtactttttGGGAAGCCCAAGAGTTAAGATGGTAGGGTTCACAAGA AAAATGCATTTAATCTAGAATTTTGTGATGATGATGAAGTACCACTTG---------GGGAAGCCCAAGAGTTAAGATGGTAGGGTTCACAAGA Template switch alignment (log-probability: -22.2) AAAATGCATTTAATCTAGAATTTTGTGATGATGATGAAGT|GGTACTT|TTtGGGAAGCCCAAGAGTTAAGATGGTAGGGTTCACAAGA AAAATGCATTTAATCTAGAATTTTGTGATGATGATGAAGT|GGTACTT|TTGGGGAAGCCCAAGAGTTAAGATGGTAGGGTTCACAAGA ========= Event 333 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAGAGAACAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCTGCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAG ↓ 3 2 1 4 Chimp: TTAGAGAACAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCTCCTGTA-------AGGAGGCTCTCGGTTTCCAGCAG ↑ 3 2 1 4 Gorilla: TTAGAGAACAGAGCCTAGCCTTACAGGAGGGAACTAAGCCCTAGTCCCTGCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAG Human: TTAGAGAACAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCTGCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAG Cluster: [ ] Orangutan: TTAGAGAACAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCTGCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAG Human > Chimp ------------- chr11:31921080-31921087 Template switch process: F1: L CAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCT 1 F3: 4 GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG R RF: CAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCTGCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG RR: GTCTCGGATCGGAATGTCCTCCCTTGACTCGGGATCAGGGACGACCATAAGTCCAACTCCGAGAGCCAAAGGTCGTCTTTAGATTTGATAACCATC F2: 3 GAATGTCC 2 Unidirectional alignment (log-probability: -31.9) AGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCTcctgtaaG--------------GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG AGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCT-------GCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG Template switch alignment (log-probability: -16.3) AGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCT|CCTGTAAG|GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG AGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCT|CCTGTAAG|GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG Gorilla > Chimp --------------- chr11:31921080-31921087 Template switch process: F1: L CAGAGCCTAGCCTTACAGGAGGGAACTGAGCCCTAGTCCCT 1 F3: 4 GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG R RF: CAGAGCCTAGCCTTACAGGAGGGAACTAAGCCCTAGTCCCTGCTGGTATTCAGGTTGAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG RR: GTCTCGGATCGGAATGTCCTCCCTTGATTCGGGATCAGGGACGACCATAAGTCCAACTCCGAGAGCCAAAGGTCGTCTTTAGATTTGATAACCATC F2: 3 GAATGTCC 2 Unidirectional alignment (log-probability: -36.6) AGAGCCTAGCCTTACAGGAGGGAACTgAGCCCTAGTCCCTcCTGtaaG----------GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG AGAGCCTAGCCTTACAGGAGGGAACTAAGCCCTAGTCCCTGCTG---GTATTCAGGTTGAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG Template switch alignment (log-probability: -22.3) AGAGCCTAGCCTTACAGGAGGGAACTgAGCCCTAGTCCCT|CCTGTAAG|GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG AGAGCCTAGCCTTACAGGAGGGAACTAAGCCCTAGTCCCT|CCTGTAAG|GAGGCTCTCGGTTTCCAGCAGAAATCTAAACTATTGGTAG ========= Event 334 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGACAAGCACAATTAACCCAAGTCATT----ACTCTCACATTCCTCCTGGGTTTT Chimp: AGACAAGCACAATTAACCCAAGTCATT----ACTCTCACATTCCTCCTGGGTTTT ↓ 3 1 2 4 Gorilla: AGACAAGCACAATTAACCCAAGTCGTAATGACTTCTCACATTCCTCCTGGGTTTT ↑ 3 1 2 4 Human: AGACAAGCACAATTAACCCAAGTCATT----ACTCTCACATTCCTCCTGGGTTTT Cluster: [ ] Orangutan: AGACAAGCACAGTTAACCCAAGTCATT----ACTCTCACATTCCTCCTGGGTTTT Human > Gorilla --------------- chr11:104845247-104845256 Template switch process: F1: L AATTTGAACTCTTCAGAAGACAAGCACAATTAACCCAAGTC 1 F3: 4 CTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG R RF: AATTTGAACTCTTCGGAAGACAAGCACAATTAACCCAAGTCATTACTCTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG RR: TTAAACTTGAGAAGCCTTCTGTTCGTGTTAATTGGGTTCAGTAATGAGAGTGTAAGGAGGACCCAAAAACGACCCACGTTTTCTTC F2: 3 TTCAGTAATG 2 Unidirectional alignment (log-probability: -37.5) ATTTGAACTCTTCaGAAGACAAGCACAATTAACCCAAGTCgtaATgACtTCTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG ATTTGAACTCTTCGGAAGACAAGCACAATTAACCCAAGTC---ATTAC-TCTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG Template switch alignment (log-probability: -22.5) ATTTGAACTCTTCaGAAGACAAGCACAATTAACCCAAGTC|GTAATGACTT|CTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG ATTTGAACTCTTCGGAAGACAAGCACAATTAACCCAAGTC|GTAATGACTT|CTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG Chimp > Gorilla --------------- chr11:104845247-104845256 Template switch process: F1: L AATTTGAACTCTTCAGAAGACAAGCACAATTAACCCAAGTC 1 F3: 4 CTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG R RF: AATTTGAACTCTTCGGAAGACAAGCACAATTAACCCAAGTCATTACTCTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG RR: TTAAACTTGAGAAGCCTTCTGTTCGTGTTAATTGGGTTCAGTAATGAGAGTGTAAGGAGGACCCAAAAACGACCCACGTTTTCTTC F2: 3 TTCAGTAATG 2 Unidirectional alignment (log-probability: -37.5) ATTTGAACTCTTCaGAAGACAAGCACAATTAACCCAAGTCgtaATgACtTCTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG ATTTGAACTCTTCGGAAGACAAGCACAATTAACCCAAGTC---ATTAC-TCTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG Template switch alignment (log-probability: -22.5) ATTTGAACTCTTCaGAAGACAAGCACAATTAACCCAAGTC|GTAATGACTT|CTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG ATTTGAACTCTTCGGAAGACAAGCACAATTAACCCAAGTC|GTAATGACTT|CTCACATTCCTCCTGGGTTTTTGCTGGGTGCAAAAGAAG ========= Event 335 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAAGAGGCCTGACACTTATCCTTGCAATGGCAAGGATATCTCACTCCTTCCTCCCAA ↑ 3 1 4 Chimp: CTAAGAGGCCTGACACTTATCCTTGCCA--------TTATCTCACTCCTTCCTCCCAA Gorilla: CTAAGAGGCCTGACACTTATCCTTGCCA--------TTATCTCACTCCTTCCTCCCAA ↓ 3 1 4 Human: CTAAGAGGCCTGACACTTATCCTTGCAATGGCAAGGATATCTCACTCCTTCCTCCCAA Cluster: [ ] Orangutan: CTAAGAGGCCTGACACTTATCCCTGCCA--------TCATCTCACTCCTTCCTCCCAA Chimp > Human ------------- chr11:103038458-103038468 Template switch process: F1: L AGAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGC 1 F3: 4 TATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT R RF: AGAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGCCATTATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT RR: TCTTTAAGGTGACTTGATTCTCCGGACTGTGAATAGGAACGGTAATAGAGTGAGGAAGGAGGGTTCGGAGAAGAATCGTGCCGA F2: 3 AGGAACGGTAA 2 Unidirectional alignment (log-probability: -28.4) GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGCaATggcaaggaTATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGCCAT--------TATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT Template switch alignment (log-probability: -16.6) GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGC|AATGGCAAGGA|TATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGC|AATGGCAAGGA|TATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT Gorilla > Human --------------- chr11:103038458-103038468 Template switch process: F1: L AGAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGC 1 F3: 4 TATCTCACTCCTTCCTCCCAAGCCTCTTCTTAGCACGGCT R RF: AGAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGCCATTATCTCACTCCTTCCTCCCAAGCCTCTTCTTGGGACGGCT RR: TCTTTAAGGTGACTTGATTCTCCGGACTGTGAATAGGAACGGTAATAGAGTGAGGAAGGAGGGTTCGGAGAAGAACCCTGCCGA F2: 3 AGGAACGGTAA 2 Unidirectional alignment (log-probability: -39) GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGCaATggcaaggaTATCTCACTCCTTCCTCCCAAGCCTCTTCTTaGcACGGCT GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGCCAT--------TATCTCACTCCTTCCTCCCAAGCCTCTTCTTGGGACGGCT Template switch alignment (log-probability: -28.2) GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGC|AATGGCAAGGA|TATCTCACTCCTTCCTCCCAAGCCTCTTCTTaGcACGGCT GAAATTCCACTGAACTAAGAGGCCTGACACTTATCCTTGC|AATGGCAAGGA|TATCTCACTCCTTCCTCCCAAGCCTCTTCTTGGGACGGCT ========= Event 336 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TGGCAAAGAGTTCAATGATTT---------CTCAGG-CCCTGAGGTAGGCATGTCTCAAATCAC Chimp: TGGCAAAGAGTTCAATGATTT---------CTCAGG-CCCTGAGGTAGACATGTCTCAAATCAC ↑ 1 43 2 Gorilla: TGGCAAAGAGTTCAATGATTTGGGGCTCCATACAGGCCCCTGAGGTAGGCATGTCTCAAATCAC Human: TGGCAAAGAGTTCAATGATTT---------CTCAGG-CCCTGAGGTAGGCATGTCTCAAATCAC Cluster: [ ] Orangutan: TGGCAAACAGTTCAATGATTTGGGGCTCCATACAGGCCCCTGAGGTAGGCATGTCTCAAACCAC Gorilla > Chimp --------------- chr11:103345164-103345169 Template switch process: F1: L ATGGCAGTGAACCATTTAAGTGGCAAAGAGTTCAATGATTT 1 F3: 4 CCCTGAGGTAGACATGTCTCAAATCACACTGCCTGGGCCC R RF: ATGGCAGTGAACCATTTAAGTGGCAAAGAGTTCAATGATTTGGGGCTCCATACAGGCCCCTGAGGTAGGCATGTCTCAAATCACACTGCCTGGGCCC RR: TACCGTCACTTGGTAAATTCACCGTTTCTCAAGTTACTAAACCCCGAGGTATGTCCGGGGACTCCATCCGTACAGAGTTTAGTGTGACGGACCCGGG F2: 3 GGACTC 2 Unidirectional alignment (log-probability: -32.6) TGGCAGTGAACCATTTAAGTGGCAAAGAGTTCAATGATTTctcaGG--------------CCCTGAGGTAGaCATGTCTCAAATCACACTGCCTGGGCCC TGGCAGTGAACCATTTAAGTGGCAAAGAGTTCAATGATTT----GGGGCTCCATACAGGCCCCTGAGGTAGGCATGTCTCAAATCACACTGCCTGGGCCC Template switch alignment (log-probability: -22) TGGCAGTGAACCATTTAAGTGGCAAAGAGTTCAATGATTT|CTCAGG|CCCTGAGGTAGaCATGTCTCAAATCACACTGCCTGGGCCC TGGCAGTGAACCATTTAAGTGGCAAAGAGTTCAATGATTT|CTCAGG|CCCTGAGGTAGGCATGTCTCAAATCACACTGCCTGGGCCC ========= Event 337 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAATTGCCCAGGAATGGCAACCA---CATTGTCTGATTCAGACATGGCCATGATTT ↓ 1 3 4 2 Chimp: TCAATTGCCCAGGAATGGCAATCAGACAATGGTCTGATTCAGACATGGCCATGATTT ↑ 1 3 4 2 Gorilla: TCAATTGCCCAGGAATGGCAACCA---CATTGTCTGATTCAGACATGGCCATGATTT Human: TCAATTGCCCAGGAATGGCAACCA---CATTGTCTGATTCAGACATGGCCATGATTT Cluster: [ ] Orangutan: TCAATTGCCCAGGAATGGCAACCA---CATTGTCTGATTCAGACATGGCCATGATTT Human > Chimp ------------- chr11:103335485-103335494 Template switch process: F1: L GTACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAA 1 F3: 4 GTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTAA R RF: GTACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAACCACATTGTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTTA RR: CATGACCAAGAGTTAGGTGTAGTTAACGGGTCCTTACCGTTGGTGTAACAGACTAAGTCTGTACCGGTACTAAAGATCGAAGTAAAAT F2: 3 GTAACAGACT 2 Unidirectional alignment (log-probability: -39.3) TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAAtCAgacaATgGTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTaA TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAACCA---CATTGTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTTA Template switch alignment (log-probability: -22.5) TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAA|TCAGACAATG|GTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTaA TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAA|TCAGACAATG|GTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTTA Gorilla > Chimp --------------- chr11:103335485-103335494 Template switch process: F1: L GTACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAA 1 F3: 4 GTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTAA R RF: GTACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAACCACATTGTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTTA RR: CATGACCAAGAGTTAGGTGTAGTTAACGGGTCCTTACCGTTGGTGTAACAGACTAAGTCTGTACCGGTACTAAAGATCGAAGTAAAAT F2: 3 GTAACAGACT 2 Unidirectional alignment (log-probability: -37.4) TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAAtCAgacaATgGTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTaA TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAACCAC---ATTGTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTTA Template switch alignment (log-probability: -22.5) TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAA|TCAGACAATG|GTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTaA TACTGGTTCTCAATCCACATCAATTGCCCAGGAATGGCAA|TCAGACAATG|GTCTGATTCAGACATGGCCATGATTTCTAGCTTCATTTTA ========= Event 338 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTAGAAGCATATCAGACCAGATTCCATACATTTTGGACACATCTAAG---------GAATCTATTTAATGTCTAATCTACATATT Chimp: GTAGAAGCATATCAGACCAGATTCCATACATTTTGGACACATCTAAG---------GAATCTATTTAATGTCTAATCTACATATT ↑ 3 2 1 4 Gorilla: GTAGAAGCATATCAGACCAGATTCCATACATTTTGGACACATCTAATGTCTAGATGTAGACTATCTAATGTCTAATCTACATATT ↓ 3 2 1 4 Human: GTAGAAGCATATCAGACCAGATTCCATACATTTTGGACACATCTAAG---------GAATCTATTTAATGTCTAATCTACATATT Cluster: [ ] Orangutan: GTAGAAGCATATCAGACCAGATTCCATACATTTTGGACACATCTAAG---------GAATCTATTTAACGTCTAATCTATATATT Gorilla > Human --------------- chr11:46110754-46110759 Template switch process: F1: L AGCATATCAGACCAGATTCCATACATTTTGGACACATCTAA 1 F3: 4 TATTTAATGTCTAATCTACATATTAACAATTTTTTTTTTTTTTT R RF: AGCATATCAGACCAGATTCCATACATTTTGGACACATCTAATGTCTAGATGTAGACTATCTAATGTCTAATCTACATATTAACAATTTTTTTTTTTTTTT RR: TCGTATAGTCTGGTCTAAGGTATGTAAAACCTGTGTAGATTACAGATCTACATCTGATAGATTACAGATTAGATGTATAATTGTTAAAAAAAAAAAAAAA F2: 3 CTAAGG 2 Unidirectional alignment (log-probability: -32.6) GCATATCAGACCAGATTCCATACATTTTGGACACATCTaaggAAT-------------CTATtTAATGTCTAATCTACATATTAACAATTTTTTTTTTT GCATATCAGACCAGATTCCATACATTTTGGACACATCT----AATGTCTAGATGTAGACTATCTAATGTCTAATCTACATATTAACAATTTTTTTTTTT Template switch alignment (log-probability: -22.1) GCATATCAGACCAGATTCCATACATTTTGGACACATCTAA|GGAATC|TATtTAATGTCTAATCTACATATTAACAATTTTTTTTTTT GCATATCAGACCAGATTCCATACATTTTGGACACATCTAA|GGAATC|TATCTAATGTCTAATCTACATATTAACAATTTTTTTTTTT Gorilla > Chimp --------------- chr11:46306560-46306565 Template switch process: F1: L AGCATATCAGACCAGATTCCATACATTTTGGACACATCTAA 1 F3: 4 TATTTAATGTCTAATCTACATATTAACAATTTTTTTTTTTTTTT R RF: AGCATATCAGACCAGATTCCATACATTTTGGACACATCTAATGTCTAGATGTAGACTATCTAATGTCTAATCTACATATTAACAATTTTTTTTTTTTTTT RR: TCGTATAGTCTGGTCTAAGGTATGTAAAACCTGTGTAGATTACAGATCTACATCTGATAGATTACAGATTAGATGTATAATTGTTAAAAAAAAAAAAAAA F2: 3 CTAAGG 2 Unidirectional alignment (log-probability: -42.2) GCATATCAGACCAGATTCCATACATTTTGGACACATCTaaggAAT-------------CTATtTAATGTCTAATCTACATATTAACAATTTTTTTTTTT GCATATCAGACCAGATTCCATACATTTTGGACACATCT----AATGTCTAGATGTAGACTATCTAATGTCTAATCTACATATTAACAATTTTTTTTTTT Template switch alignment (log-probability: -22.1) GCATATCAGACCAGATTCCATACATTTTGGACACATCTAA|GGAATC|TATtTAATGTCTAATCTACATATTAACAATTTTTTTTTTT GCATATCAGACCAGATTCCATACATTTTGGACACATCTAA|GGAATC|TATCTAATGTCTAATCTACATATTAACAATTTTTTTTTTT ========= Event 339 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Chimp: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↓ 1 3 4 2 ↑ 13 24 Gorilla: ATAGTCTATTCGTTATATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↓ 13 24 ↑ 1 3 4 2 Human: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Cluster: [ ] Orangutan: ATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Gorilla > Human --------------- chr1:105095769-105095809 Template switch process: F1: L TATACATGATATATTTACTTCCCCA 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC RR: ATATGCACTATATAAATGAAGGGGTCAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTAACCCCTTCATTTATATAGTGCAAG F2: 3 CAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTA 2 Unidirectional alignment (log-probability: -50.6) TATACaTGATATATTTACTTCCCCAaTTGTGGTGTAAGCATttttagagg---------ATGCTTACACCACAAcTGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCAT---------CCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -25.7) TATACaTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC Human > Gorilla --------------- chr1:100158312-100158372 Template switch process: F1: L TATAC 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC RR: ATATGTACTATATAAATGAAGGGGTTAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTGCAAG F2: 3 TAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTG 2 Unidirectional alignment (log-probability: -50.6) TATACgTGATATATTTACTTCCCCAgTTGTGGTGTAAGCATcctctaaaa---------ATGCTTACACCACAAtTGGGGAAGTAAATATATCACGTTC TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCAT---------TTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -22.2) TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC Gorilla > Chimp --------------- chr1:100864544-100864584 Template switch process: F1: L TATACATGATATATTTACTTCCCCA 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC RR: ATATGCACTATATAAATGAAGGGGTCAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTAACCCCTTCATTTATATAGTGCAAG F2: 3 CAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTA 2 Unidirectional alignment (log-probability: -50.6) TATACaTGATATATTTACTTCCCCAaTTGTGGTGTAAGCATttttagagg---------ATGCTTACACCACAAcTGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCAT---------CCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -25.7) TATACaTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC Chimp > Gorilla --------------- chr1:100158312-100158372 Template switch process: F1: L TATAC 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC RR: ATATGTACTATATAAATGAAGGGGTTAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTGCAAG F2: 3 TAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTG 2 Unidirectional alignment (log-probability: -50.6) TATACgTGATATATTTACTTCCCCAgTTGTGGTGTAAGCATcctctaaaa---------ATGCTTACACCACAAtTGGGGAAGTAAATATATCACGTTC TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCAT---------TTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -22.2) TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC ========= Event 340 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCCACAATAACCCTAGTGTCTCATACTATGATAT------------------------------------------------------------AAAAGTATTCCAATGAAGAAAAACATA Chimp: CTCCACAATAACCCtagtgtctcatactatgatat------------------------------aaaagtatatagtatatcatactatgatataaaagtattccaatgaagaaaaacata Gorilla: CTCCACAATAACCCTAGTGTCTCATACTATGATATAAAAGTACATAGTATATCATACTATGATAT------------------------------AAAAGTATTCCAATGAAGAAAAACATA ↑ 4 3 2 1 Human: CTCCACAATAACCCTAGTGTCTCATACTATGATAT------------------------------------------------------------AAAAGTATTCCAATGAAGAAAAACATA Cluster: [ ] Orangutan: CTCCACAATAACCCTAATGTCTCATACTATGATAT------------------------------------------------------------AAAAGTATTCCAATGAAGAAAAACATA Human > Gorilla --------------- chr11:98697472-98697478 Template switch process: F1: L ATCTCCCTCCACAATAACCCTAGTGTCTCATACTATGATATAAAAGTA 1 F3: 4 TATCATACTATGATATAAAAGTATTCCAATGAAGAAAAACATATATCCTCCCGTAA R RF: ATCTCCCTCCACAATAACCCTAGTGTCTCATACTATGATATAAAAGTATTCCAATGAAGAAAAACATATATCCTCCCATAA RR: TAGAGGGAGGTGTTATTGGGATCACAGAGTATGATACTATATTTTCATAAGGTTACTTCTTTTTGTATATAGGAGGGTATT F2: 3 ATGATAC 2 Unidirectional alignment (log-probability: -59.5) CCACAATAACCCTAGTGTCTCATACTATGATataaaagtacatagtatatcatactatgatATAAAAGTATTCCAATGAAGAAAAAC CCACAATAACCCTAGTGTCTCATACTATGAT------------------------------ATAAAAGTATTCCAATGAAGAAAAAC Template switch alignment (log-probability: -28.2) CCACAATAACCCTAGTGTCTCATACTATGATATAAAAGTA|CATAGTA|TaTCATACTATGATATAAAAGTATTCCAATGAAGAAAAAC CCACAATAACCCTAGTGTCTCATACTATGATATAAAAGTA|CATAGTA|TCTCATACTATGATATAAAAGTATTCCAATGAAGAAAAAC ========= Event 341 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TATGGAGGATAAAATTTACTGCTACTTTCACCATCTCTTTGTAAATAGAACAACATTGACAGAGAGGCATG-----------------------------------------------------------------------------AATAGGTCATCTGGTCCAACTTCCTGCCT ↓ 3 4 2 1 Chimp: TATGGAGGATAAAATTTACTGCTACTTTCACCATCTCTTTGTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCAATGTTGTTCTATTTACAAAGAGATGGTGAAAGTAGCAGTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCATCTGGTCCAACTTCCTGCCT Gorilla: Human: TATGGAGGATAAAATTTACTGCTACTTTCACCATCTCTTTGTAAATAGAACAACATTGACAGAGAGGCATG-----------------------------------------------------------------------------AATAGGTCATCTGGTCCAACTTCCTGCCT Cluster: [ ] Orangutan: TATGGAGGATACTATTTACTGCTACTTTCACCATCTCTTTGTAAATAGAACAACATTGACAGAGAGGCATG-----------------------------------------------------------------------------AATAGGTCATCTGGTCCAACTTCCTGCCT Human > Chimp ------------- chr11:46397866-46397902 Template switch process: F1: L CCATCTCTTTGTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA 1 F3: 4 GTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCATCTGGTCCAACTTCCTGCCTCAAATAAATGC R RF: TGCTACTTTCACCATCTCTTTGTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCATCTGGTCCAACTTCCTGCCTCAAATAAATGC RR: ACGATGAAAGTGGTAGAGAAACATTTATCTTGTTGTAACTGTCTCTCCGTACTTATCCAGTAGACCAGGTTGAAGGACGGAGTTTATTTACG F2: 3 ACGATGAAAGTGGTAGAGAAACATTTATCTTGTTGTA 2 Unidirectional alignment (log-probability: -122) gtaaatagaacaacattgacagagaggcatgaataggtcaatgttgttctatttacaaagagatggtgaaagtagcaGTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA -----------------------------------------------------------------------------GTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA Template switch alignment (log-probability: -20.5) GTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA|ATGTTGTTCTATTTACAAAGAGATGGTGAAAGTAGCA|GTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA GTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA|ATGTTGTTCTATTTACAAAGAGATGGTGAAAGTAGCA|GTAAATAGAACAACATTGACAGAGAGGCATGAATAGGTCA ========= Event 342 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT Chimp: AAGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT Gorilla: AGGCACATGGTCTTTTCTCTACCTGGTA-CATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT ↑ 1 4 3 2 Human: AGGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT Cluster: [ ] Orangutan: AGGCACATGGCCTTTTCTCTAGTTCTTTCTGTGTCTGATGTACCAGGTGACAGCCTCCTGCCCATAT Human > Gorilla --------------- chr11:88261317-88261324 Template switch process: F1: L GCTTGGCCTGGGGCTGGTGGAGGCACATGGTCTTTTCTCTA 1 F3: 4 ATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGATAAT R RF: GCTTGGCCTGGGGCTGGTGGAGGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGATAAT RR: CGAACCGGACCCCGACCACCTCCGTGTACCGGAAAAGAGATCAAGAAAGATACAGACTACATGGTCCACTGTCGGAGGACGGGTCTATTA F2: 3 CATGGTCC 2 Unidirectional alignment (log-probability: -37.7) CTTGGCCTGGGGCTGGTGGAGGCACATGGtCTTTTCTCTAcctgGTaC-----ATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGATAAT CTTGGCCTGGGGCTGGTGGAGGCACATGGCCTTTTCTCTA----GTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGATAAT Template switch alignment (log-probability: -22.3) CTTGGCCTGGGGCTGGTGGAGGCACATGGtCTTTTCTCTA|CCTGGTAC|ATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGATAAT CTTGGCCTGGGGCTGGTGGAGGCACATGGCCTTTTCTCTA|CCTGGTAC|ATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGATAAT ========= Event 343 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTTGGCCTGGGGCTGGTGGAGGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT Chimp: GCTTGGCCTGGGGCTGGTGGAAGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT ↓ 1 4 3 2 Gorilla: GCTTGGCCTGGGGCTGGTGGAGGCACATGGTCTTTTCTCTACCTGGTA-CATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT Human: GCTTGGCCTGGGGCTGGTGGAGGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGACAGCCTCCTGCCCAGAT Cluster: [ ] Orangutan: GCTTGGCCTGGGGCTGGTGGAGGCACATGGCCTTTTCTCTAGTTCTTTCTGTGTCTGATGTACCAGGTGACAGCCTCCTGCCCATAT Chimp > Gorilla --------------- chr11:88261317-88261324 Template switch process: F1: L CCCAGCCAGAATGGGCAAGAGCTTGGCCTGGGGCTGGTGGAGGCACATGGTCTTTTCTCTA 1 F3: 4 ATGTCTGATGTACCAGGTGAC R RF: CCCAGCCAGAATGGGCAAGAGCTTGGCCTGGGGCTGGTGGAAGCACATGGCCTTTTCTCTAGTTCTTTCTATGTCTGATGTACCAGGTGAC RR: GGGTCGGTCTTACCCGTTCTCGAACCGGACCCCGACCACCTTCGTGTACCGGAAAAGAGATCAAGAAAGATACAGACTACATGGTCCACTG F2: 3 CATGGTCC 2 Unidirectional alignment (log-probability: -43.3) CTTGGCCTGGGGCTGGTGGAgGCACATGGtCTTTTCTCTAcctgGTaC-----ATGTCTGATGTACCAGGTGAC CTTGGCCTGGGGCTGGTGGAAGCACATGGCCTTTTCTCTA----GTTCTTTCTATGTCTGATGTACCAGGTGAC Template switch alignment (log-probability: -27.8) CTTGGCCTGGGGCTGGTGGAgGCACATGGtCTTTTCTCTA|CCTGGTAC|ATGTCTGATGTACCAGGTGAC CTTGGCCTGGGGCTGGTGGAAGCACATGGCCTTTTCTCTA|CCTGGTAC|ATGTCTGATGTACCAGGTGAC ========= Event 344 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGTCTCCTGAATTCATCCTTGATTTTGATAAAGTGACTTGATTTATCAGTGGAATTTCGCAGACGTGGCATTTTGCACGGCTAGGATTGATCTTTAAGGTGGCTCAGCGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATT----------------------------------------------------------------------------------GTCAATGATCCATATGGAGAGGAGAT ↑ 3 2 1 4 Chimp: CTGTCTCCTGAATTCATCCTTGACTTTGATAAAGTGACTTGATTTATCAATGGAATTTCGCAGACGTGGCATTTTGCACGGCTAGGATTGATCTTTAAGGTGGCTCAGCGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATT-----------------------------------------ATGTAAGACATCCAGATTTTCTACAAGAGACTCTGGGAAGAATCAGTGATCCATATGGAGAGGAGAT Gorilla: CTGTCTCCTGAATTCATCCTTGACTTTGCTAAAGTGACTTGATTTATCAATGGAATTTCGCAGACGTGGCATTTTGCACGGCTAGGATTGATCTTTAAGGTGGCTCAGCGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATTGTGTAAGACATCCAGATTTTCTACAAGAGACTCTGGGAAGA-----------------------------------------ATCAATGATCCATATGGAGAGGAGAT Human: CTGTCTCCTGAATTCATCCTTGATTTTGATAAAGTGACTTGATTTATCAGTGGAATTTCGCAGACGTGGCATTTTGCACGGCTAGGATTGATCTTTAAGGTGGCTCAGCGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATT----------------------------------------------------------------------------------GTCAATGATCCATATGGAGAGGAGAT Cluster: [ ] Orangutan: ctgtctcctgaattcatccttgACTTTGATAAGGTGACTTGACTTATCAATGGAATTTGACAGACGTGGCATTTTGCAGGGCTAGGATTGATCTTTAAGGTGGCTCAGTGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATTGTGTAAGACATCCAGATATTCTACAAGAGACTCTGGAAAGA-----------------------------------------ATCAATAATCCACATGGAGAGGAGAT Chimp > Human ------------- chr11:94573971-94573975 Template switch process: F1: L GCGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATT 1 F3: 4 TGATCCATATGGAGAGGAGATGCTCTGGTGTTACATGGGT R RF: TTGACTTTGATAAAGTGACTTGATTTATCAATGGAATTTCGCAGACGTGGCATTTTGCACGGCTAGGATTGATCTTTAAGGTGGCTCAGCGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATTATGTAAGACATCCAGATTTTCTACAAGAGACTCTGGGAAGAATCAGTGATCCATATGGAGAGGAGATGCTCTGGTGTTACATGTGT RR: AACTGAAACTATTTCACTGAACTAAATAGTTACCTTAAAGCGTCTGCACCGTAAAACGTGCCGATCCTAACTAGAAATTCCACCGAGTCGCCGAAAGTGAAAACACGAAAAGCCTTTGGGACTCTATAATACATTCTGTAGGTCTAAAAGATGTTCTCTGAGACCCTTCTTAGTCACTAGGTATACCTCTCCTCTACGAGACCACAATGTACACA F2: 3 AACTG 2 Unidirectional alignment (log-probability: -31) CGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATTg-----------------------------------------TCAaTGATCCATATGGAGAGGAGATGCTCTGGTGTTACATGgGT CGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATTATGTAAGACATCCAGATTTTCTACAAGAGACTCTGGGAAGAATCAGTGATCCATATGGAGAGGAGATGCTCTGGTGTTACATGTGT Template switch alignment (log-probability: -21.9) CGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATT|GTCAA|TGATCCATATGGAGAGGAGATGCTCTGGTGTTACATGgGT CGGCTTTCACTTTTGTGCTTTTCGGAAACCCTGAGATATT|GTCAA|TGATCCATATGGAGAGGAGATGCTCTGGTGTTACATGTGT ========= Event 345 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAGATACAGTGCCTTAGAGT-----GCATGCCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGACTGCATGTGGATGATCTTCAGCGTAAGGCATGCTTCTGATTGCTGCTTTCCTA Chimp: GAAGATACAGTGCCTTAGAGT-----ACATGCCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGATTGCATGTGGATGATCTTCAGCGTAAGGCATGCTTCTGATTGCTGCTTTCCTA ↑ 1 4 3 2 Gorilla: GAAGATACAGTGCCTTAGAGTTAAAGTCTTGTCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGATTGCATGTGGATGATCTTCAGCGTAAGGCATGCTTCTGATTGCTGCTTTCCTA ↓ 1 4 3 2 Human: GAAGATACAGTGCCTTAGAGT-----GCATGCCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGACTGCATGTGGATGATCTTCAGCGTAAGGCATGCTTCTGATTGCTGCTTTCCTA Cluster: [ ] Orangutan: GAAGATACAGTGCCTTAGAGTTAAAGTCTTGTCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGATTGCATATGGATGATCTTCAGCATAAGGCATGCTTCTGATTGCTGCTTTCCTA Gorilla > Human --------------- chr11:44112591-44112596 Template switch process: F1: L TAATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT 1 F3: 4 CAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA R RF: TAATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGTTAAAGTCTTGTCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGATTGCATGTGGATGATCTTCAGCGTAAGGCATGC RR: ATTACCTCTGGAACCGTCTTCTTCTATGTCACGGAATCTCAATTTCAGAACAGTCATCGTCCCGACCGTACTCCGGTCAAACTGATTAACGTCAGCACCGAGAAAAACTCTACTGTTTGTCTAACGTACACCTACTAGAAGTCGCATTCCGTACG F2: 3 CGTACG 2 Unidirectional alignment (log-probability: -27.8) AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT-----gCaTGcCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGTTAAAGTCTTGTCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA Template switch alignment (log-probability: -16.5) AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT|GCATGC|CAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT|GCATGC|CAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA Gorilla > Chimp --------------- chr11:44305530-44305535 Template switch process: F1: L TAATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT 1 F3: 4 CAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA R RF: TAATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGTTAAAGTCTTGTCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCAGTCGTGGCTCTTTTTGAGATGACAAACAGATTGCATGT RR: ATTACCTCTGGAACCGTCTTCTTCTATGTCACGGAATCTCAATTTCAGAACAGTCATCGTCCCGACCGTACTCCGGTCAAACTGATTAACGTCAGCACCGAGAAAAACTCTACTGTTTGTCTAACGTACA F2: 3 CGTACA 2 Unidirectional alignment (log-probability: -27.8) AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT-----aCaTGcCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGTTAAAGTCTTGTCAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA Template switch alignment (log-probability: -16.5) AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT|ACATGC|CAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA AATGGAGACCTTGGCAGAAGAAGATACAGTGCCTTAGAGT|ACATGC|CAGTAGCAGGGCTGGCATGAGGCCAGTTTGACTAATTGCA ========= Event 346 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: GTAACTAAATGCTTTATCCATGTTAGCTCAATG-ACTAGAACA--TAGTTAATATTTAATCTGGAGGACAAAGT Chimp: Gorilla: GTAACTAAATGCTTTATCCATATTAAC--TATGTTCTA-GTCATTGAGCTAACATTTAATCTGGAGGACAAAGT ↓ 13 24 ↑ 13 24 Human: GTAACTAAATGCTTTATCCATGTTAGCTCAATG-ACTAGAACA--TAGTTAATATTTAATCTGGAGGACAAAGT Cluster: [ ] Orangutan: GTAACTAAATGCTTTATCCATATTAAC--TATGTTCTA-GTCATTGAGCTAACATTTAATCTAGAGGACAAAGT Gorilla > Human --------------- chr11:130539546-130539574 Template switch process: F1: L TGTCAGTAATCCTGTCAATAGTAACTAAATGCTTTATCCAT 1 F3: 4 ATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT R RF: TGTCAGTAATCCTGTCAGTAGTAACTAAATGCTTTATCCATATTAACTATGTTCTAGTCATTGAGCTAACATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT RR: ACAGTCATTAGGACAGTCATCATTGATTTACGAAATAGGTATAATTGATACAAGATCAGTAACTCGATTGTAAATTAGACCTCCTGTTTCAGTCACAGAGATATTTGATA F2: 3 TAATTGATACAAGATCAGTAACTCGATTG 2 Unidirectional alignment (log-probability: -65.6) GTCAGTAATCCTGTCAaTAGTAACTAAATGCTTTATCCATgTT-------------------AGCtcaatgactagaacatagtTAAtATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT GTCAGTAATCCTGTCAGTAGTAACTAAATGCTTTATCCATATTAACTATGTTCTAGTCATTGAGC-------------------TAACATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT Template switch alignment (log-probability: -24.9) GTCAGTAATCCTGTCAaTAGTAACTAAATGCTTTATCCAT|GTTAGCTCAATGACTAGAACATAGTTAAT|ATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT GTCAGTAATCCTGTCAGTAGTAACTAAATGCTTTATCCAT|GTTAGCTCAATGACTAGAACATAGTTAAT|ATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT Human > Gorilla --------------- chr11:130977653-130977681 Template switch process: F1: L TGTCAGTAATCCTGTCAGTAGTAACTAAATGCTTTATCCAT 1 F3: 4 ATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT R RF: TGTCAGTAATCCTGTCAATAGTAACTAAATGCTTTATCCATGTTAGCTCAATGACTAGAACATAGTTAATATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT RR: ACAGTCATTAGGACAGTTATCATTGATTTACGAAATAGGTACAATCGAGTTACTGATCTTGTATCAATTATAAATTAGACCTCCTGTTTCAGTCACAGAGATATTTGATA F2: 3 CAATCGAGTTACTGATCTTGTATCAATTA 2 Unidirectional alignment (log-probability: -65.6) GTCAGTAATCCTGTCAgTAGTAACTAAATGCTTTATCCATaTTaactatgttctagtcattgAGC-------------------TAAcATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT GTCAGTAATCCTGTCAATAGTAACTAAATGCTTTATCCATGTT-------------------AGCTCAATGACTAGAACATAGTTAATATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT Template switch alignment (log-probability: -24.9) GTCAGTAATCCTGTCAgTAGTAACTAAATGCTTTATCCAT|ATTAACTATGTTCTAGTCATTGAGCTAAC|ATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT GTCAGTAATCCTGTCAATAGTAACTAAATGCTTTATCCAT|ATTAACTATGTTCTAGTCATTGAGCTAAC|ATTTAATCTGGAGGACAAAGTCAGTGTCTCTATAAACTAT ========= Event 347 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GAATTATTAAGCAAATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA--TGACCTTTCATACTGTGGCAATCAA ↑ 3 2 1 4 Chimp: GAATTATTAAACAAATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTAAACATACTTTCATACTGTGGCAATCAA Gorilla: GAATTATTAAGCAAATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA--TGACCTTTCATACTGTGGCAATCAA Human: GAATTATTAAGCAAATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA--TGACCTTTCATACTGTGGCAATCAA Cluster: [ ] Orangutan: GAATTATTAAGCAAATTAGGTCATATCTAATATTTCCCCATGTTTAGTTAAGTA--TGACATTTCATACTGTGGCAATCAA Chimp > Human ------------- chr11:43081701-43081704 Template switch process: F1: L AATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA 1 F3: 4 CTTTCATACTGTGGCAATCAAAAGATACAATGGATATATA R RF: AATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTAAACATACTTTCATACTGTGGCAATCAAAAGATACAATGGGTATATA RR: TTAATCCAGTATAGATTATAAAGGGGTACAAATCGATTCATTTGTATGAAAGTATGACACCGTTAGTTTTCTATGTTACCCATATAT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -33.2) ATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTAtgac------CTTTCATACTGTGGCAATCAAAAGATACAATGGaTATATA ATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA----AACATACTTTCATACTGTGGCAATCAAAAGATACAATGGGTATATA Template switch alignment (log-probability: -21.8) ATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA|TGAC|CTTTCATACTGTGGCAATCAAAAGATACAATGGaTATATA ATTAGGTCATATCTAATATTTCCCCATGTTTAGCTAAGTA|TGAC|CTTTCATACTGTGGCAATCAAAAGATACAATGGGTATATA ========= Event 348 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAATTCTAAGATAGTTCTCAGACTGTGATCATAAATCTTAGTTCAGGCAGTGTAAAAATATCACTTCAAAAATTATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGAC----TGTGATATTATAATGTTAACCAG Chimp: AGAATTCTAAGATAGTTCTCAGATTGTGATCATAAATCTTAGTTCAGGCAGTGTAAAAATATCGCTTCAAAAATTATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGAC------TGATATTATAATATTAACCAG ↓ 3 2 4 Gorilla: AGAATTCTAAGATAGTTCTCAGATTGTGATCATAAATCTTAGTTCAGGCAATGTAAAAATATCGCTTCAAAAATTATTTTTAAAAATCCTAAAGATTATTTTCTCAGAATGACTATCTGTGATATTATAATATTAACCAG Human: AGAATTCTAAGATAGTTCTCAGACTGTGATCATAAATCTTAGTTCAGGCAGTGTAAAAATATCACTTCAAAAATTATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGAC----TGTGATATTATAATGTTAACCAG Cluster: [ ] Orangutan: AGAATTCTAAGATAGTTATCAGATTGTGATCATAAATCTTAGTTCAGGCAATGTAAAAATATCGCTTCA-AAATGATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGACTATCTGTGATATTATAATATTAACCAG Chimp > Gorilla --------------- chr11:43486500-43486504 Template switch process: F1: L TTCAAAAATTATTTTTAAAAATCCTAAAGATTATTTTCTCAGAATGACT 1 F3: 4 TGATATTATAATATTAACCAGAATAAGCTAATATAAAAAA R RF: CAGATTGTGATCATAAATCTTAGTTCAGGCAGTGTAAAAATATCGCTTCAAAAATTATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGACTGATATTATAATATTAACCAGAATAAGCCAATATAAAAAT RR: GTCTAACACTAGTATTTAGAATCAAGTCCGTCACATTTTTATAGCGAAGTTTTTAATAAAAATTTTTAGGATTTCTAATAAAAGAGTTTTACTGACTATAATATTATAATTGGTCTTATTCGGTTATATTTTTA F2: 3 GTCTA 2 Unidirectional alignment (log-probability: -38.8) TATTTTTAAAAATCCTAAAGATTATTTTCTCAgAATGACtatctgTGATATTATAATATTAACCAGAATAAGCtAATATAAAAAa TATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGAC------TGATATTATAATATTAACCAGAATAAGCCAATATAAAAA- Template switch alignment (log-probability: -33.1) TATTTTTAAAAATCCTAAAGATTATTTTCTCAgAATGACT|ATCTG|TGATATTATAATATTAACCAGAATAAGCtAATATAAAAAa TATTTTTAAAAATCCTAAAGATTATTTTCTCAAAATGACT|ATCTG|TGATATTATAATATTAACCAGAATAAGCCAATATAAAAAT ========= Event 349 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: caattgcacttcaatctgggtgacagagcaagaccctgtctccaaaaaaaaaaaaaaaa-aaaaa--aaaaaaaGTCA-----GAGAGGAGAAACCTACCTTGCA Chimp: caattgcacttcaatctgggtgacagagcaagaccctgtctccaaaaaaaaaaaaaaaa------aaaaaaaaaGTCAGAGAGGAGAGGAGAAACCTACCTTGCA ↓ 3 2 1 4 Gorilla: caattgcacttcaatctgggtgacagagcaagaccctgtctccaaaaaaaaaaaaaaaa--------aaaaaaaGTCA-----CAGAGGAGAAACCTACCTTGCA Human: caattgcacttcaatctgggtgacagagcaagaccctgtctccaaaaaaaaaaaaaaaa-aaaaa--aaaaaaaGTCA-----GAGAGGAGAAACCTACCTTGCA Cluster: [ ] Orangutan: caattgcacttcaatctgggtgacagagcaagaccctgtttccaaaaaaaaaaaaaaaaa-------aaaaaaaGTCA-----GAGAGGAGAAACCTACCTTGCA Chimp > Gorilla --------------- chr11:3708284-3708288 Template switch process: F1: L GACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAAA 1 F3: 4 AGAGGAGAAACCTACCTTGCAAATTAGGGAAAGCGAAGAT R RF: GTGACAGAGCAAGACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAAAAAGTCAGAGAGGAGAGGAGAAACCTACCTTGCAAATTAGGGAAAGCGAAGAT RR: CACTGTCTCGTTCTGGGACAGAGGTTTTTTTTTTTTTTTTTTTTTTTTTCAGTCTCTCCTCTCCTCTTTGGATGGAACGTTTAATCCCTTTCGCTTCTA F2: 3 CACTG 2 Unidirectional alignment (log-probability: -26.5) GACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAA--AAGTCAc-----AGAGGAGAAACCTACCTTGCAAATTAGGGAAAGCGAAGAT GACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAAAAAGTCAGAGAGGAGAGGAGAAACCTACCTTGCAAATTAGGGAAAGCGAAGAT Template switch alignment (log-probability: -16.2) GACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAAA|GTCAC|AGAGGAGAAACCTACCTTGCAAATTAGGGAAAGCGAAGAT GACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAAA|GTCAC|AGAGGAGAAACCTACCTTGCAAATTAGGGAAAGCGAAGAT ========= Event 350 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTGTGTAGGAATTCATGGCTATGTTCTGGCTCAGCAGCTAGTGTTGTTATGAATGTATGACCATCTACTTTAGGGATGAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTG------ACTTACTGCTTACTGCTGACAAACTGAG Chimp: TATGTGTAGGAAGTCATGGCTATGTTCTGGCTTAGCAGCTAGTGTTGTTATGAATGTATGACCATCTACTTTAGGGATGAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTG---AGAACAT-AGGCTTACTGCTGACAAGCTGAT Gorilla: TTTGTGTAGGAATTCATGGCTGTGTTCTGGCTCAGCAGCTAGTGTTGTTTTGAATGTATGACCATCTACTTTAGGGATGAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGAGA---ACAT-AGGCTTACTGCTGACAAACTGAG ↑ 3 2 1 4 Human: TTTGTGTAGGAATTCATGGCTATGTTCTGGCTCAGCAGCTAGTGTTGTTATGAATGTATGACCATCTACTTTAGGGATGAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTG------ACTTACTGCTTACTGCTGACAAACTGAG Cluster: [ ] Orangutan: TTTGTGTAGGAATTCATGGCTATGTTCTGGCTCAGCAGCTAGTGTTGTTATGAATGTATCACCATCTACTTTAGGGATGAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGAGA---ACAT-AGGCTTAGTGCTGACAAATTGAG Human > Gorilla --------------- chr11:96449700-96449707 Template switch process: F1: L GAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGA 1 F3: 4 GCTTACTGCTGACAAACTGAGACCTCTGAAATATTAAAAC R RF: CTATGTTCTGGCTCAGCAGCTAGTGTTGTTATGAATGTATGACCATCTACTTTAGGGATGAAATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGACTTACTGCTTACTGCTGACAAACTGAGACCTCTGAAATATTAAAAC RR: GATACAAGACCGAGTCGTCGATCACAACAATACTTACATACTGGTAGATGAAATCCCTACTTTACACTCATCACTATTCATTAATTCATAAACGGTACACTGAATGACGAATGACGACTGTTTGACTCTGGAGACTTTATAATTTTG F2: 3 GATACAAG 2 Unidirectional alignment (log-probability: -32.5) AATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGA------gaacatagGCTTACTGCTGACAAACTGAGACCTCTGAAATATTAAAAC AATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGACTTACT--------GCTTACTGCTGACAAACTGAGACCTCTGAAATATTAAAAC Template switch alignment (log-probability: -16.8) AATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGA|GAACATAG|GCTTACTGCTGACAAACTGAGACCTCTGAAATATTAAAAC AATGTGAGTAGTGATAAGTAATTAAGTATTTGCCATGTGA|GAACATAG|GCTTACTGCTGACAAACTGAGACCTCTGAAATATTAAAAC ========= Event 351 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATGGGTGCCTCAAGAGGATTT---GTCCCTGG------GCTACAGCCCTGGGCAGCTTGGTCCC Chimp: TAATGGGTGCCTCAAGAGGATTT---GTCCCTGG------GCTACAGCCCTGGGCAGCTTGGTCCC ↓ 3 1 24 Gorilla: TAATGGGTGCCTCAAGAGGATTGACAAATCCTGG------------GCCCTGGGCAGCTTGGTCCC ↑ 3 1 24 Human: TAATGGGTGCCTCAAGAGGATTT---GTCCCTGG------GCTACAGCCCTGGGCAGCTTGGTCCC Cluster: [ ] Orangutan: TAATGGGTGCCTCAAGAGGATTT---GTCCCTCGGCTACA------GCCCTGGGCAGCTTGGTCCC Human > Gorilla --------------- chr11:46701194-46701200 Template switch process: F1: L ATCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT 1 F3: 4 CCTGG------GCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCATCTGGA R RF: ATCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATTTGTCCCTGGGCTACAGCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCATCTGGA RR: TAGTCATGGTCTAAAGATGATTACCCACGGAGTTCTCCTAAACAGGGACCCGATGTCGGGACCCGTCGAACCAGGGACTCCAGGACCAGTAGACCT F2: 3 TAAACAG 2 Unidirectional alignment (log-probability: -38.3) TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT-----------gACAaatcctggGCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATTTGTCCCTGGGCTACA--------GCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT Template switch alignment (log-probability: -26.8) TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT|GACAAAT|CCTGG------GCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT|GACAAAT|CCTGGGCTACAGCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT Chimp > Gorilla --------------- chr11:46701194-46701200 Template switch process: F1: L ATCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT 1 F3: 4 CCTGG------GCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCATCTGGA R RF: ATCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATTTGTCCCTGGGCTACAGCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCATCTGGA RR: TAGTCATGGTCTAAAGATGATTACCCACGGAGTTCTCCTAAACAGGGACCCGATGTCGGGACCCGTCGAACCAGGGACTCCAGGACCAGTAGACCT F2: 3 TAAACAG 2 Unidirectional alignment (log-probability: -38.3) TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT-----------gACAaatcctggGCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATTTGTCCCTGGGCTACA--------GCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT Template switch alignment (log-probability: -26.8) TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT|GACAAAT|CCTGG------GCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT TCAGTACCAGATTTCTACTAATGGGTGCCTCAAGAGGATT|GACAAAT|CCTGGGCTACAGCCCTGGGCAGCTTGGTCCCTGAGGTCCTGGTCAT ========= Event 352 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTCACAAGGCAGCCGGAAGCACTCCCGGG---TAATCTCGTCTGGAGATGACTGC Chimp: TTTCACAAGGCAGCCGGAAGCACTCCCGGG---TAATCTCGTCTGGAGATGACTGC ↓ 3 2 1 4 Gorilla: TTTCACAAGGCAGCCGGAAGCACTCCCGGGAGTGCATCTCGTCTGGAGATGACTGC ↑ 3 2 1 4 Human: TTTCACAAGGCAGCCGGAAGCACTCCCGGG---TAATCTCGTCTGGAGATGACTGC Cluster: [ ] Orangutan: TTTCACAAGGCAGCCAGAAGCACTCCCGGC---CAATCTCGTCTGGAGATGACTGC Human > Gorilla --------------- chr11:89559896-89559900 Template switch process: F1: L TGGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG 1 F3: 4 ATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC R RF: TGGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGGTAATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC RR: ACCTTCCGGCAAAAGTGTTCCGTCGGCCTTCGTGAGGGCCCATTAGAGCAGACCTCTACTGACGTAAAGTAATATTAAATTCG F2: 3 CGTGA 2 Unidirectional alignment (log-probability: -26.3) GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGGagtgcATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG---TAATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC Template switch alignment (log-probability: -16.4) GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG|AGTGC|ATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG|AGTGC|ATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC Chimp > Gorilla --------------- chr11:89559896-89559900 Template switch process: F1: L TGGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG 1 F3: 4 ATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC R RF: TGGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGGTAATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC RR: ACCTTCCGGCAAAAGTGTTCCGTCGGCCTTCGTGAGGGCCCATTAGAGCAGACCTCTACTGACGTAAAGTAATATTAAATTCG F2: 3 CGTGA 2 Unidirectional alignment (log-probability: -26.3) GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGGagtgcATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG---TAATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC Template switch alignment (log-probability: -16.4) GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG|AGTGC|ATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC GGAAGGCCGTTTTCACAAGGCAGCCGGAAGCACTCCCGGG|AGTGC|ATCTCGTCTGGAGATGACTGCATTTCATTATAATTTAAGC ========= Event 353 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AACGGCACAGAGCTCAGTGCTCAGTCTTCTAAAAAACTAATAAAATATTAAGTCTCACAATGATAAGCATGGTCT Chimp: AACAGCACAGAGCTCAGTGCTAAGTCTT---CAGACTTAATAAAATATTAAGTCTCACAATGATAAGCATGGTCT ↑ 1 4 3 2 Gorilla: AACAGCACAGAGCTCAGTGCTCAGTCTTCTAAAAAACTAATAAAATATTAAGTCTCACAATGATAAGCATGGTCT Human: AACGGCACAGAGCTCAGTGCTCAGTCTTCTAAAAAACTAATAAAATATTAAGTCTCACAATGATAAGCATGGTCT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr11:96649219-96649223 Template switch process: F1: L CCTAGATTGAAAGGACTAAGAACAGCACAGAGCTCAGTGCTAAGTCTTC 1 F3: 4 TAATAAAATATTAAGTCTCACAATGATAAGCATGGTCTAT R RF: CCTAGATTGAAAGGACTAAGAACAGCACAGAGCTCAGTGCTCAGTCTTCTAAAAAACTAATAAAATATTAAGTCTCACAATGATAAGCATGGTCTAT RR: GGATCTAACTTTCCTGATTCTTGTCGTGTCTCGAGTCACGAGTCAGAAGATTTTTTGATTATTTTATAATTCAGAGTGTTACTATTCGTACCAGATA F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -32.4) AAAGGACTAAGAACAGCACAGAGCTCAGTGCTaAGTCTTcagaCT-------TAATAAAATATTAAGTCTCACAATGATAAGCATGGTCTAT AAAGGACTAAGAACAGCACAGAGCTCAGTGCTCAGTCTT----CTAAAAAACTAATAAAATATTAAGTCTCACAATGATAAGCATGGTCTAT Template switch alignment (log-probability: -22.1) AAAGGACTAAGAACAGCACAGAGCTCAGTGCTaAGTCTTC|AGACT|TAATAAAATATTAAGTCTCACAATGATAAGCATGGTCTAT AAAGGACTAAGAACAGCACAGAGCTCAGTGCTCAGTCTTC|AGACT|TAATAAAATATTAAGTCTCACAATGATAAGCATGGTCTAT ========= Event 354 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: tgttggacagtgcagGCCTGT-ATGATCACAAATCATACGGTTACTACACCATTCAT Chimp: tgttggacagtgcagGCCTGT-ATAATCACAAATCATACGGTTACTACACCATTCAT Gorilla: tgttggacagtgcagGCCTGTCCTGCGCTGTAATCATACGGTTACTACACCATTCAT ↓ 1 3 4 2 Human: tgttggacagtgcagGCCTGT-ATGATCACAAATCATACGGTTACTACACCATTCAT Cluster: [ ] Orangutan: tgttggacagtgcagGCCTGT-ATGATCACAAATCATACAGTTACTACACCATTCAT Gorilla > Human --------------- chr11:98469880-98469888 Template switch process: F1: L CATGTTGCTAGTAGCTACTGTGTTGGACAGTGCAGGCCTGT 1 F3: 4 AATCATACGGTTACTACACCATTCATGAAATTTGTAATGC R RF: CATGTTGCTAGTAGCTACTGTGTTGGACAGTGCAGGCCTGTCCTGCGCTGTAATCATACGGTTACTACACCATTCATGAAATCTGTAATGC RR: GTACAACGATCATCGATGACACAACCTGTCACGTCCGGACAGGACGCGACATTAGTATGCCAATGATGTGGTAAGTACTTTAGACATTACG F2: 3 ACACTAGTA 2 Unidirectional alignment (log-probability: -39.6) ATGTTGCTAGTAGCTACTGTGTTGGACAGTGCAGGCC----------TGTatgatcacaAATCATACGGTTACTACACCATTCATGAAATtTGTAATGC ATGTTGCTAGTAGCTACTGTGTTGGACAGTGCAGGCCTGTCCTGCGCTGT---------AATCATACGGTTACTACACCATTCATGAAATCTGTAATGC Template switch alignment (log-probability: -27.9) ATGTTGCTAGTAGCTACTGTGTTGGACAGTGCAGGCCTGT|ATGATcACA|AATCATACGGTTACTACACCATTCATGAAATtTGTAATGC ATGTTGCTAGTAGCTACTGTGTTGGACAGTGCAGGCCTGT|ATGATTACA|AATCATACGGTTACTACACCATTCATGAAATCTGTAATGC ========= Event 355 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCTCTCAGAAGCAGTCAGAGCGGTTGGG----------ATGTGAACAGAAAGGCTCACAACCTCTCTGACTGCTTCTGAGAGCA Chimp: AGCTCTCAGAAGCAGTCAGAGAGGTTGTG-----AGCCTTTCTGTTCACA-----ACCCAACCGCTCTGACTGCTTCTGAGAGCA Gorilla: AGCTCTCAGAAGCAGTCAGAGAGGTTGTGAGCCT-----TTCTGTTCACA-----ACCCAACCGCTCTGACTGCTTCTGAGAGCA ↑ 13 24 Human: AGCTCTCAGAAGCAGTCAGAGCGGTTGGG----------ATGTGAACAGAAAGGCTCACAACCTCTCTGACTGCTTCTGAGAGCA Cluster: [ ] Orangutan: AGCTCTCAGAAGCAGTCAGAGAGATTGTGAGCCT-----TTCTGTTCACA-----ACCCAACCGCTCTGACTACTTCTAAGAGCA Human > Gorilla --------------- chr11:98114665-98114697 Template switch process: F1: L CTTCTACCCTTTCACAGGTCAGCTCTCAGAAGCAGTCAGAG 1 F3: 4 CTCTGACTGCTTCTGAGAGCACACATCTGGACTGACAGGT R RF: CTTCTACCCTTTCACAGGTCAGCTCTCAGAAGCAGTCAGAGCGGTTGGGATGTGAACAGAAAGGCTCACAACCTCTCTGACTGCTTCTGAGAGCACACATCTGGACTGACAGGT RR: GAAGATGGGAAAGTGTCCAGTCGAGAGTCTTCGTCAGTCTCGCCAACCCTACACTTGTCTTTCCGAGTGTTGGAGAGACTGACGAAGACTCTCGTGTGTAGACCTGACTGTCCA F2: 3 GCCAACCCAACACTTGTCTTTCCGAGTGTTGGA 2 Unidirectional alignment (log-probability: -63.1) TTCTACCCTTTCACAGGTCAGCTCTCAGAAGCAGTCAGAGaGGTTG---------------------tgagcctttctgttcacaaccCAACCgCTCTGACTGCTTCTGAGAGCACACATCTGGACTGACAGGT TTCTACCCTTTCACAGGTCAGCTCTCAGAAGCAGTCAGAGCGGTTGGGATGTGAACAGAAAGGCTCA---------------------CAACCTCTCTGACTGCTTCTGAGAGCACACATCTGGACTGACAGGT Template switch alignment (log-probability: -25.4) TTCTACCCTTTCACAGGTCAGCTCTCAGAAGCAGTCAGAG|AGGTTGTGAGCCTTTCTGTTCACAaCCCAACCG|CTCTGACTGCTTCTGAGAGCACACATCTGGACTGACAGGT TTCTACCCTTTCACAGGTCAGCTCTCAGAAGCAGTCAGAG|AGGTTGTGAGCCTTTCTGTTCACATCCCAACCG|CTCTGACTGCTTCTGAGAGCACACATCTGGACTGACAGGT ========= Event 356 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAGGGCCCTGA-TGTTTACAGGGAATTGAAAG--------ACTACTGGAGGCAATAACCTGAGTGGTTGAGGCACGTGCAC Chimp: CCAGGGCCCTGA-TGTTTACAGGGAATTGAAAGCAATTCCCTGTACTGGAGGCAATAACCCGAGTGGTTGAGGCAAGTGCAC ↑ 3 2 1 4 Gorilla: CCAGGGCCCTGATTATTTACAGGGAATTGAAAG--------ACTACTGGAGGCAATAACCTTAGTGGTTGAGGCAAGTGCAC Human: CCAGGGCCCTGA-TGTTTACAGGGAATTGAAAG--------ACTACTGGAGGCAATAACCTGAGTGGTTGAGGCACGTGCAC Cluster: [] Orangutan: CCAGGGCCCTGA-TGTTTACAGGGAACTGAAAG--------ACTACTGGAGGCAATAACCTGAGTGGTTGAGGCAAGTGCAC Gorilla > Chimp --------------- chr11:98968655-98968664 Template switch process: F1: L CAGGGAATTGAAAG 1 F3: 4 TACTGGAGGCAATAACCCGAGTGGTTGAGGCAAGTGCACTGTCAAGGGTAGAAATAAAA R RF: CAGGGAATTGAAAGACTACTGGAGGCAATAACCTTAGTGGTTGAGGCAAGTGCACTGTCAAGGGTAGAAATAAAA RR: GTCCCTTAACTTTCTGATGACCTCCGTTATTGGAATCACCAACTCCGTTCACGTGACAGTTCCCATCTTTATTTT F2: 3 GTCCCTTAAC 2 Unidirectional alignment (log-probability: -44.4) CAGGGAATTGAAAGcaattccctgTACTGGAGGCAATAACCcgAGTGGTTGAGGCAAGTGCACT CAGGGAATTGAAAG--------ACTACTGGAGGCAATAACCTTAGTGGTTGAGGCAAGTGCACT Template switch alignment (log-probability: -27.8) CAGGGAATTGAAAG|CAATTCCCTG|TACTGGAGGCAATAACCcgAGTGGTTGAGGCAAGTGCACT CAGGGAATTGAAAG|CAATTCCCTG|TACTGGAGGCAATAACCTTAGTGGTTGAGGCAAGTGCACT ========= Event 357 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GCATCCCTATTATTGATGGAGTGGACCAGGGA------GAGACTGGGAATTAGATGTAACCACTTAGC Chimp: GCATCCCTATTATTGATGGAGTGGACCAGGGA------GAGACTGGGAATTAGATGTAACCACTTAGC ↓ 3 1 2 4 ↑ 31 2 4 Gorilla: GCATCCCTATTATTGATGGAGTGGACCCAGTCTCTCCCTGGTCCACTAATTAGATGTAACCACTTAGC ↓ 31 2 4 ↑ 3 1 2 4 Human: GCATCCCTATTATTGATGGAGTGGACCAGGGA------GAGACTGGGAATTAGATGTAACCACTTAGC Cluster: [ ] Orangutan: GCGTCCCTATTGTTGATGGAGTGGACCAGGGA------GAGACTGGGAATTAGATGTAACCACTTAGC Gorilla > Human --------------- chr11:44256210-44256223 Template switch process: F1: L AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC 1 F3: 4 AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT R RF: AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCCAGTCTCTCCCTGGTCCACTAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT RR: TCTCGACCCAAAACCGTAGGGATAATAACTACCTCACCTGGGTCAGAGAGGGACCAGGTGATTAATCTACATTGGTGAATCGTCATCGGACCCATCTTTCA F2: 3 GGGTCAGAGAGGGA 2 Unidirectional alignment (log-probability: -41.8) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC--------------------agggagagactgggAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCCAGTCTCTCCCTGGTCCACT--------------AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Template switch alignment (log-probability: -17.5) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|AGGGAGAGACTGGG|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|AGGGAGAGACTGGG|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Human > Gorilla --------------- chr11:44559057-44559076 Template switch process: F1: L AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC 1 F3: 4 AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT R RF: AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCAGGGAGAGACTGGGAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT RR: TCTCGACCCAAAACCGTAGGGATAATAACTACCTCACCTGGTCCCTCTCTGACCCTTAATCTACATTGGTGAATCGTCATCGGACCCATCTTTCA F2: 3 TCACCTGGTCCCTCTCTGAC 2 Unidirectional alignment (log-probability: -50.1) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCcagtctctccctggtccact--------------AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC--------------------AGGGAGAGACTGGGAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Template switch alignment (log-probability: -18.3) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|CAGTCTCTCCCTGGTCCACT|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|CAGTCTCTCCCTGGTCCACT|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Gorilla > Chimp --------------- chr11:44448485-44448498 Template switch process: F1: L AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC 1 F3: 4 AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT R RF: AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCCAGTCTCTCCCTGGTCCACTAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT RR: TCTCGACCCAAAACCGTAGGGATAATAACTACCTCACCTGGGTCAGAGAGGGACCAGGTGATTAATCTACATTGGTGAATCGTCATCGGACCCATCTTTCA F2: 3 GGGTCAGAGAGGGA 2 Unidirectional alignment (log-probability: -41.8) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC--------------------agggagagactgggAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCCAGTCTCTCCCTGGTCCACT--------------AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Template switch alignment (log-probability: -17.5) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|AGGGAGAGACTGGG|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|AGGGAGAGACTGGG|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Chimp > Gorilla --------------- chr11:44559057-44559076 Template switch process: F1: L AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC 1 F3: 4 AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT R RF: AGAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCAGGGAGAGACTGGGAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT RR: TCTCGACCCAAAACCGTAGGGATAATAACTACCTCACCTGGTCCCTCTCTGACCCTTAATCTACATTGGTGAATCGTCATCGGACCCATCTTTCA F2: 3 TCACCTGGTCCCTCTCTGAC 2 Unidirectional alignment (log-probability: -50.1) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACCcagtctctccctggtccact--------------AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC--------------------AGGGAGAGACTGGGAATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT Template switch alignment (log-probability: -18.3) GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|CAGTCTCTCCCTGGTCCACT|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT GAGCTGGGTTTTGGCATCCCTATTATTGATGGAGTGGACC|CAGTCTCTCCCTGGTCCACT|AATTAGATGTAACCACTTAGCAGTAGCCTGGGTAGAAAGT ========= Event 358 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCTTTGGACTCCGTGTGTCC--------------TTGAGGTTGCCCCAGTCTGGCCTACCGTTCCTGCCCTGC ↓ 1 43 2 Chimp: CCCTTTGGACTCCGTGTGTCC---------------------AGACTCAGTCTGGCCTACCGTTCCTGCCCCGC ↑ 1 43 2 Gorilla: CCCTTTGGACTCCGTGTGTCC-------TTGAGGT-------TGCCCCAGTCTAGCCTACCGTTCCTGCCCCGC Human: CCCTTTGGACTCCGTGTGTCC--------------TTGAGGTTGCCCCAGTCTGGCCTACCGTTCCTGCCCTGC Cluster: [ ] Orangutan: CTCTTTGGACTCCGTGTGTCCTTGAAGT--------------TGCCCCAGTCTAGCCTACCTTTCCTGCACCGC Human > Chimp ------------- chr11:47498949-47498953 Template switch process: F1: L AGGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCC 1 F3: 4 CAGTCTGGCCTACCGTTCCTGCCCCGCACAAAGCTTCAGT R RF: AGGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCCTTGAGGTTGCCCCAGTCTGGCCTACCGTTCCTGCCCTGCACAAAGCTTCAGT RR: TCCTGTGTCATACATTTGTTGGGAAACCTGAGGCACACAGGAACTCCAACGGGGTCAGACCGGATGGCAAGGACGGGACGTGTTTCGAAGTCA F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -33.5) GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCcagaCT-----------CAGTCTGGCCTACCGTTCCTGCCCcGCACAAAGCTTCAGT GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTC----CTTGAGGTTGCCCCAGTCTGGCCTACCGTTCCTGCCCTGCACAAAGCTTCAGT Template switch alignment (log-probability: -21.9) GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCC|AGACT|CAGTCTGGCCTACCGTTCCTGCCCcGCACAAAGCTTCAGT GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCC|AGACT|CAGTCTGGCCTACCGTTCCTGCCCTGCACAAAGCTTCAGT Gorilla > Chimp --------------- chr11:47498949-47498953 Template switch process: F1: L AGGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCC 1 F3: 4 CAGTCTGGCCTACCGTTCCTGCCCCGCACAAAGCTTCAGTAGCCCTC R RF: AGGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCCTTGAGGTTGCCCCAGTCTAGCCTACCGTTCCTGCCCCGCACAAAGCTTTAGTAGCCCTC RR: TCCTGTGTCATACATTTGTTGGGAAACCTGAGGCACACAGGAACTCCAACGGGGTCAGATCGGATGGCAAGGACGGGGCGTGTTTCGAAATCATCGGGAG F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -38.1) GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCcagaCT-----------CAGTCTgGCCTACCGTTCCTGCCCCGCACAAAGCTTcAGT GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTC----CTTGAGGTTGCCCCAGTCTAGCCTACCGTTCCTGCCCCGCACAAAGCTTTAGT Template switch alignment (log-probability: -27.6) GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCC|AGACT|CAGTCTgGCCTACCGTTCCTGCCCCGCACAAAGCTTcAGT GGACACAGTATGTAAACAACCCTTTGGACTCCGTGTGTCC|AGACT|CAGTCTAGCCTACCGTTCCTGCCCCGCACAAAGCTTTAGT ========= Event 359 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATGAGTCATCATCATGCCCCTGATGGAGACTCC-----------AGGTCCCTCCATTCGCAGTTGGTGAATTTGGCCGTTTG Chimp: CGTGAGTCATCGTCATGCCCCTGATGGAGACTCT-----------AGGTCCCTCCATTCGCAGTTGGTGAATTTGGCCCTTTG ↓ 3 2 1 4 Gorilla: CATGAGTCATCGTCATGCCCCTGATGGAGACTCC----------------------ATCAGGGTTGGTGAATTTGGCCCTTTG Human: CATGAGTCATCATCATGCCCCTGATGGAGACTCC-----------AGGTCCCTCCATTCGCAGTTGGTGAATTTGGCCGTTTG Cluster: [ ] Orangutan: CATGAGTCATCGTCATGCCCCTGATGGAGACTCTAGGTTCCTCCA-----------TTCGCAGTTGGTGAATTTGGCCCTTTG Chimp > Gorilla --------------- chr11:33695133-33695139 Template switch process: F1: L CTTCCCCTCATGAGTCATCGTCATGCCCCTGATGGAGACTC 1 F3: 4 GTTGGTGAATTTGGCCCTTTGTCCTATTGGATGTTGCTTT R RF: CTTCCCCACGTGAGTCATCGTCATGCCCCTGATGGAGACTCTAGGTCCCTCCATTCGCAGTTGGTGAATTTGGCCCTTTGTCCTATTGGATGTTGCTTT RR: GAAGGGGTGCACTCAGTAGCAGTACGGGGACTACCTCTGAGATCCAGGGAGGTAAGCGTCAACCACTTAAACCGGGAAACAGGATAACCTACAACGAAA F2: 3 GGACTAC 2 Unidirectional alignment (log-probability: -39.7) TTCCCCtCaTGAGTCATCGTCATGCCCCTGATGGAGACTC----------------CAtcaggGTTGGTGAATTTGGCCCTTTGTCCTATTGGATGTTGCTTT TTCCCCACGTGAGTCATCGTCATGCCCCTGATGGAGACTCTAGGTCCCTCCATTCGCA-----GTTGGTGAATTTGGCCCTTTGTCCTATTGGATGTTGCTTT Template switch alignment (log-probability: -27.7) TTCCCCtCaTGAGTCATCGTCATGCCCCTGATGGAGACTC|CATCAGG|GTTGGTGAATTTGGCCCTTTGTCCTATTGGATGTTGCTTT TTCCCCACGTGAGTCATCGTCATGCCCCTGATGGAGACTC|CATCAGG|GTTGGTGAATTTGGCCCTTTGTCCTATTGGATGTTGCTTT ========= Event 360 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ggttgttatgagaattaaacgaaataaactgcatagtacatagtaaatgttcataaatgttagctattaCCACCATTGTAGTGGAAAGAGGATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTTTTATTGCAAGTCTGAGTAGGTGGGTATTA ↑ 3 2 1 4 Chimp: ggttgttatgagaattaaatgaaataacctgcatagtacatagtaaatgttcataaatgttagctattaCCACCATTGTAGTGGAGAGAGGATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTT----GGGTAGTCTGAGTAGGTGGGTATTA Gorilla: ggttgttatgagaattaaacgaaataaactgcatagtacatagtaaatgttcataaatgttagctattaCCACCATTGTAGTGGAAAGAGGATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTTTTATTGCAAGTCTGAGTAGGTGGGTATTA Human: ggttgttatgagaattaaacgaaataaactgcatagtacatagtaaatgttcataaatgttagctattaCCACCATTGTAGTGGAAAGAGGATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTTTTATTGCAAGTCTGAGTAGGTGGGTATTA Cluster: [ ] Orangutan: ggttgttatgagaattaaatgacataacctgcatagtacatagtaaatgttcataaatgctagctattaCCACCATTGTAGTGGAGAGAGGATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTATAGGTTTATTGCAAGTCTGAGTAGGTGGGTATTA Chimp > Human ------------- chr11:34006945-34006952 Template switch process: F1: L GATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTT 1 F3: 4 AGTCTGAGTAGGTGGGTATTAATTAGGACATTCTGATGAC R RF: TGAAATAACCTGCATAGTACATAGTAAATGTTCATAAATGTTAGCTATTACCACCATTGTAGTGGAGAGAGGATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTTGGGTAGTCTGAGTAGGTGGGTATTAATTAGGACATTCTGATGAC RR: ACTTTATTGGACGTATCATGTATCATTTACAAGTATTTACAATCGATAATGGTGGTAACATCACCTCTCTCCTAGTTAATACCTCCACGGACCGAAACCCCGTCGACATCAACCCATCAGACTCATCCACCCATAATTAATCCTGTAAGACTACTG F2: 3 ACGTTATT 2 Unidirectional alignment (log-probability: -31.4) ATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTT---TtattgcaAGTCTGAGTAGGTGGGTATTAATTAGGACATTCTGATGAC ATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTTGGGT-------AGTCTGAGTAGGTGGGTATTAATTAGGACATTCTGATGAC Template switch alignment (log-probability: -22.3) ATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTT|TTATTgCA|AGTCTGAGTAGGTGGGTATTAATTAGGACATTCTGATGAC ATCAATTATGGAGGTGCCTGGCTTTGGGGCAGCTGTAGTT|TTATTTCA|AGTCTGAGTAGGTGGGTATTAATTAGGACATTCTGATGAC ========= Event 361 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: gagacacaaATTTTCCATAATG----ACCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCC ↓ 1 4 3 2 Chimp: gagacacaaattttcCATAATTAAGTCACCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCC ↑ 1 4 3 2 Gorilla: gagacacaaattttcCATAATG----ACCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCC Human: gagacacaaATTTTCCATAATG----ACCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCC Cluster: [ ] Orangutan: gagacacaaATTTTCCATAATG----ACCCCCATGAAGGTGATTTAAGAGTGAAATATTTAAATCC Human > Chimp ------------- chr11:94391758-94391764 Template switch process: F1: L TTCAACATATGAATTTTAGGGAGACACAAATTTTCCATAAT 1 F3: 4 CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC R RF: TTCAACATATGAATTTTAGGGAGACACAAATTTTCCATAATGACCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC RR: AAGTTGTATACTTAAAATCCCTCTGTGTTTAAAAGGTATTACTGGGGGTACTTCCACTGAATTCTCACTTTATAAATTTAGGGG F2: 3 ACTGAAT 2 Unidirectional alignment (log-probability: -28.7) TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAATtAagtcaCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAATGA----CCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC Template switch alignment (log-probability: -16.2) TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAAT|TAAGTCA|CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAAT|TAAGTCA|CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC Gorilla > Chimp --------------- chr11:94391758-94391764 Template switch process: F1: L TTCAACATATGAATTTTAGGGAGACACAAATTTTCCATAAT 1 F3: 4 CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC R RF: TTCAACATATGAATTTTAGGGAGACACAAATTTTCCATAATGACCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC RR: AAGTTGTATACTTAAAATCCCTCTGTGTTTAAAAGGTATTACTGGGGGTACTTCCACTGAATTCTCACTTTATAAATTTAGGGG F2: 3 ACTGAAT 2 Unidirectional alignment (log-probability: -27.7) TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAATtAagtcaCCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAATGAC----CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC Template switch alignment (log-probability: -16.6) TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAAT|TAAGTCA|CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC TCAACATATGAATTTTAGGGAGACACAAATTTTCCATAAT|TAAGTCA|CCCCATGAAGGTGACTTAAGAGTGAAATATTTAAATCCCC ========= Event 362 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TCACCTTAAACTTGACAGACTCTGAGAATGGGCTGGCCACATGCTGTGCGCAACCCTTAGTGCTCTTCTGTGACTAATATTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTC----TCTCAGAG-GGTTGAAGTTAACTTCTTTATTTC Chimp: Gorilla: TCACCTTAAACTTGACAGACTCTGAGAACGGGCTGGCCACGTGCTGTGCACAACCCTTAGTGCTCTTCTGTGACTAATATTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTCTCTCTCTCAGAGGGGTCGAAGTTAACTTCTTTATTTC ↑ 3 2 1 4 Human: TCACCTTAAACTTGACAGACTCTGAGAATGGGCTGGCCACATGCTGTGCGCAACCCTTAGTGCTCTTCTGTGACTAATATTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTC----TCTCAGAG-GGTTGAAGTTAACTTCTTTATTTC Cluster: [ ] Orangutan: Human > Gorilla --------------- chr11:132005750-132005757 Template switch process: F1: L TAATATTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTCTCTC 1 F3: 4 GGGTCGAAGTTAACTTCTTTATTTCTGAGGTAGGGAAGAAAATGA R RF: CTCTGAGAATGGGCTGGCCACATGCTGTGCGCAACCCTTAGTGCTCTTCTGTGACTAATATTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTCTCTCAGAGGGTTGAAGTTAACTTCTTTATTTCTGAGGTAGGGAAGAAAATGA RR: GAGACTCTTACCCGACCGGTGTACGACACGCGTTGGGAATCACGAGAAGACACTGATTATAAACCTATTAACTAACAACCTTCGAGTCCTTCGGAGAGAGTCTCCCAACTTCAATTGAAGAAATAAAGACTCCATCCCTTCTTTTACT F2: 3 GAGACTCT 2 Unidirectional alignment (log-probability: -33.5) TTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCtctcTCTCTCAGAgGGGTcGAAGTTAACTTCTTTATTTCTGAGGTAGGGAAGAA TTTGGATAATTGATTGTTGGAAGCTCAGGAAGCC----TCTCTCAGA-GGGTTGAAGTTAACTTCTTTATTTCTGAGGTAGGGAAGAA Template switch alignment (log-probability: -22.5) TTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTCTCTC|TCTCAGAG|GGGTcGAAGTTAACTTCTTTATTTCTGAGGTAGGGAAGAA TTTGGATAATTGATTGTTGGAAGCTCAGGAAGCCTCTCTC|TCTCAGAG|GGGTTGAAGTTAACTTCTTTATTTCTGAGGTAGGGAAGAA ========= Event 363 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAGCTCCCATCTTTCAGATG----------GCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTTTGCTTTTCAATCTGATCAGGGTTACCAAATTCAAATTCAAAATATCAGTTCCAAATTTGATTCACTTCA ↓ 4 1 3 2 Chimp: TTAGCTCCCATCTTTCAGATGGCCAACTGAGGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTTTGCTTTTCAATCTGATCAGGGTTACCAAATTCAAATTCAAAATATCAGTTCCAAATTTGATTCACTTCA Gorilla: TTAGCTCCCATCTTTCAGATG----------GCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTTTGCTTTTCAATCTGATCAGGGTTACCAAATTCAAATTCAAAATATCAGTTCCAAATTTGATTCACTTCA Human: TTAGCTCCCATCTTTCAGATG----------GCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTTTGCTTTTCAATCTGATCAGGGTTACCAAATTCAAATTCAAAATATCAGTTCCAAATTTGATTCACTTCA Cluster: [ ] Orangutan: Human > Chimp ------------- chr1:12552873-12552877 Template switch process: F1: L GTGCATTGACTAAGTAAGCCTTAGCTCCCATCTTTCAGATGGCCA 1 F3: 4 GGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTTT R RF: GTGCATTGACTAAGTAAGCCTTAGCTCCCATCTTTCAGATGGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTTTGCTTTTCAATCTGATCAGGGTTACCAAATTCAAATTCAAAATATCAGT RR: CACGTAACTGATTCATTCGGAATCGAGGGTAGAAAGTCTACCGGTGTGACTCCGGACCACGCTACTTCCGGTCTGTTGAAACGAAAAGTTAGACTAGTCCCAATGGTTTAAGTTTAAGTTTTATAGTCA F2: 3 AGTCA 2 Unidirectional alignment (log-probability: -25.3) TTGACTAAGTAAGCCTTAGCTCCCATCTTTCAGATggccaactgaGGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTT TTGACTAAGTAAGCCTTAGCTCCCATCTTTCAGAT----------GGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTT Template switch alignment (log-probability: -16) TTGACTAAGTAAGCCTTAGCTCCCATCTTTCAGATGGCCA|ACTGA|GGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTT TTGACTAAGTAAGCCTTAGCTCCCATCTTTCAGATGGCCA|ACTGA|GGCCACACTGAGGCCTGGTGCGATGAAGGCCAGACAACTT ========= Event 364 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTCTCCATGTTACTTGAGTAACATAAGAGCTTCTTATGGCTCTTATGTTCTGCAGGACGGATGAACTA Chimp: ACTCTCCATGTTACTTGAGTAACATAAGAGCTTCTTATGGCTCTTATGTTCTGCAGGACGGATGAACTA ↑ 1 4 3 2 Gorilla: ACTCTCCATGTTACTTGAGTAT-----CTGCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA ↓ 1 4 3 2 Human: ACTCTCCATGTTACTTGAGTAACATAAGAGCTTCTTATGGCTCTTATGTTCTGCAGGACGGATGAACTA Cluster: [ ] Orangutan: ACTCTCCATGTTACTTGAGTAT-----CTGCTTCTTATGGCTCTTGTGTTCTGCAGGACGGATGAGCTA Gorilla > Human --------------- chr11:48088708-48088715 Template switch process: F1: L TCCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTA 1 F3: 4 GCTTCTTATGGCTCTTATGTTCTGCAGGACGGATGAACTA R RF: TCCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTATCTGCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA RR: AGGACTCCAGAAAGGTACAATGAGAGGTACAATGAACTCATAGACGAAGAATACCGAGAATACAAGACGTCCTGCCCACTCGAT F2: 3 AGAATACA 2 Unidirectional alignment (log-probability: -40.2) CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTAaCataagaGCTTCTTATGGCTCTTATGTTCTGCAGGACGGaTGAaCTA CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTATCT-----GCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA Template switch alignment (log-probability: -27.8) CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTA|ACATAAGA|GCTTCTTATGGCTCTTATGTTCTGCAGGACGGaTGAaCTA CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTA|ACATAAGA|GCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA Gorilla > Chimp --------------- chr11:48382098-48382105 Template switch process: F1: L TCCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTA 1 F3: 4 GCTTCTTATGGCTCTTATGTTCTGCAGGACGGATGAACTA R RF: TCCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTATCTGCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA RR: AGGACTCCAGAAAGGTACAATGAGAGGTACAATGAACTCATAGACGAAGAATACCGAGAATACAAGACGTCCTGCCCACTCGAT F2: 3 AGAATACA 2 Unidirectional alignment (log-probability: -40.2) CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTAaCataagaGCTTCTTATGGCTCTTATGTTCTGCAGGACGGaTGAaCTA CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTATCT-----GCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA Template switch alignment (log-probability: -27.8) CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTA|ACATAAGA|GCTTCTTATGGCTCTTATGTTCTGCAGGACGGaTGAaCTA CCTGAGGTCTTTCCATGTTACTCTCCATGTTACTTGAGTA|ACATAAGA|GCTTCTTATGGCTCTTATGTTCTGCAGGACGGGTGAGCTA ========= Event 365 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCACCCTGAGCACATCAATTAATTTGGTGAAAGAGCTTACACTTTAAGTGTAAGCTTAACATCTCACTGAAATAGTTCA Chimp: CTCACCCTGAGCACATCAATTTATTTGGTGAAAGAGCTTACACTT------------CAACATCTCACTGAAATAGCTCA Gorilla: CTCACCCTGAGCACATCAATTTGTTTGGTGAAAGAGCTTACACTT------------TAACATCTCACTGAAATAGCTCA ↓ 3 2 4 1 Human: CTCACCCTGAGCACATCAATTAATTTGGTGAAAGAGCTTACACTTTAAGTGTAAGCTTAACATCTCACTGAAATAGTTCA Cluster: [] Orangutan: CTCACCCTGAGCACATCAATTTATTTGGTGAAAGAGCTTACACTT------------TAACATCTCACTGAAATAGCTCA Gorilla > Human --------------- chr1:148155532-148155539 Template switch process: F1: L TGGTTTACCCCTTTATTTCACTCACCCTGAGCACATCAATTAATTTGGTGAAAGAGCTTACACTTTAA 1 F3: 4 TTAACAT R RF: TGGTTTACCCCTTTATTTCACTCACCCTGAGCACATCAATTTGTTTGGTGAAAGAGCTTACACTTTAACAT RR: ACCAAATGGGGAAATAAAGTGAGTGGGACTCGTGTAGTTAAACAAACCACTTTCTCGAATGTGAAATTGTA F2: 3 CGAATGTG 2 Unidirectional alignment (log-probability: -39) GAGCACATCAATTaaTTTGGTGAAAGAGCTTACACTttaagtgtaagcTTAACAT GAGCACATCAATTTGTTTGGTGAAAGAGCTTACACT------------TTAACAT Template switch alignment (log-probability: -27.6) GAGCACATCAATTaaTTTGGTGAAAGAGCTTACACTTTAA|GTGTAAGC|TTAACAT GAGCACATCAATTTGTTTGGTGAAAGAGCTTACACTTTAA|GTGTAAGC|TTAACAT ========= Event 366 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCATGCCTGAGTTCTCCAAGCACTGTGGAGTCCACTGACAGGTTACATGATGGCTTCCAACCTTTCTCAAATAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGT-GGC-AGTGCCTCCCGGGAGAGAGGGATGTG Chimp: TCATGCCTGAGTTCTCCAAGCACTGTGGAGTCCACTGACAGGTTACATGATGGCTTCCAACCTTTCTCAAATAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGGGC-AGTGCCTCCCGGGAGAGAGGGATGTG Gorilla: TCATGCCTGAGTTCTCCAAGCACTGTGGAGTCCACTCACAGGTTACATGATGGCTTCCAACCTTTCTCAAATAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGGGCAGGTGACTCCCGGGAGAGAGGGATGTG ↓ 3 2 1 4 Human: TCATGCCTGAGTTCTCCAAGCACTGTGGAGTCCACTGACAGGTTACATGATGGCTTCCAACCTTTCTCAAATAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGT-GGC-AGTGCCTCCCGGGAGAGAGGGATGTG Cluster: [ ] Orangutan: TCATGCCTGAGTTCTCCAAGCACTGTGGAGTCCACTGACAGGTTACATGATGGCTTCCAACCTTTCTCAAATAACCCGCTGAGACCCTTCTTCCAGCCCCACAGAATGTGGGCAGGTGCCTCCCCGGAGAGAGGGATGTG Gorilla > Human --------------- chr1:233994908-233994913 Template switch process: F1: L AAATAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGG 1 F3: 4 CTCCCGGGAGAGAGGGATGTGGGTCCCTCCAGGGAAACCA R RF: GCACTGTGGAGTCCACTCACAGGTTACATGATGGCTTCCAACCTTTCTCAAATAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGGGCAGGTGACTCCCGGGAGAGAGGGATGTGGGTCCCTCCAGGGAAACCA RR: CGTGACACCTCAGGTGAGTGTCCAATGTACTACCGAAGGTTGGAAAGAGTTTATTGGGCGACTCTGGGAAGAAGGTCGGGGTATCTTACACCCGTCCACTGAGGGCCCTCTCTCCCTACACCCAGGGAGGTCCCTTTGGT F2: 3 CGTGAC 2 Unidirectional alignment (log-probability: -26.4) TAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGG-CA-GTGcCTCCCGGGAGAGAGGGATGTGGGTCCCTCCAGGGAAACCA TAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGGGCAGGTGACTCCCGGGAGAGAGGGATGTGGGTCCCTCCAGGGAAACCA Template switch alignment (log-probability: -16.5) TAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGG|CAGTGC|CTCCCGGGAGAGAGGGATGTGGGTCCCTCCAGGGAAACCA TAACCCGCTGAGACCCTTCTTCCAGCCCCATAGAATGTGG|CAGTGC|CTCCCGGGAGAGAGGGATGTGGGTCCCTCCAGGGAAACCA ========= Event 367 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTCTTTTAAAATTAATGAAA----AA-GGGGGATTA-Atattgacagtcagc-------tatatgccaggacacaagg Chimp: AGTCTTTTAAAATTAATGAAA------AGGGGGATTA-Atattgacagtcagc-------tatatgccaggacacaagg ↑ 3 12 4 Gorilla: AGTCTTTTAAAATTAATGAAA-------AGGGGatta-atattgactatatgctatatgctatatgccaggacacaagg Human: AGTCTTTTAAAATTAATGAAA----AA-GGGGGATTA-Atattgacagtcagc-------tatatgccaggacacaagg Cluster: [ ] Orangutan: ACTCTTTTAAAATTAATGAAAAATT---GGGGGATTAAttattgacagtcagc-------tatatgccaggacacaagg Gorilla > Chimp --------------- chr11:89043896-89043900 Template switch process: F1: L GGGGACTAAGGACAAATGTTAGTCTTTTAAAATTAATGAAAAGGGGGATTAATATTGAC 1 F3: 4 GCTATATGCCAG R RF: GGGGACTAAGGACAAATGTTAGTCTTTTAAAATTAATGAAAAGGGG-ATTAATATTGACTATATGCTATATGCTATATGCCAG RR: CCCCTGATTCCTGTTTACAATCAGAAAATTTTAATTACTTTTCCCC-TAATTATAACTGATATACGATATACGATATACGGTC F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -39.5) TAGTCTTTTAAAATTAATGAAAAGGgGGATTAATATTGACagtca------------GCTATATGCCAG TAGTCTTTTAAAATTAATGAAAAGG-GGATTAATATTGAC-----TATATGCTATATGCTATATGCCAG Template switch alignment (log-probability: -27.3) TAGTCTTTTAAAATTAATGAAAAGGGGgATTAATATTGAC|AGTCA|GCTATATGCCAG TAGTCTTTTAAAATTAATGAAAAGGGG-ATTAATATTGAC|AGTCA|GCTATATGCCAG ========= Event 368 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Chimp: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↓ 1 3 4 2 ↑ 13 24 Gorilla: ATAGTCTATTCGTTATATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA ↓ 13 24 ↑ 1 3 4 2 Human: ATAGTCTATTCGTTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Cluster: [ ] Orangutan: ATAGTCTATTCATTATATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTCCTATTCTATTTGTATA Gorilla > Human --------------- chr1:99187857-99187897 Template switch process: F1: L TATACATGATATATTTACTTCCCCA 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC RR: ATATGCACTATATAAATGAAGGGGTCAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTAACCCCTTCATTTATATAGTGCAAG F2: 3 CAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTA 2 Unidirectional alignment (log-probability: -50.6) TATACaTGATATATTTACTTCCCCAaTTGTGGTGTAAGCATttttagagg---------ATGCTTACACCACAAcTGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCAT---------CCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -25.7) TATACaTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC Human > Gorilla --------------- chr1:100158312-100158372 Template switch process: F1: L TATAC 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC RR: ATATGTACTATATAAATGAAGGGGTTAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTGCAAG F2: 3 TAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTG 2 Unidirectional alignment (log-probability: -50.6) TATACgTGATATATTTACTTCCCCAgTTGTGGTGTAAGCATcctctaaaa---------ATGCTTACACCACAAtTGGGGAAGTAAATATATCACGTTC TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCAT---------TTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -22.2) TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC Gorilla > Chimp --------------- chr1:100864544-100864584 Template switch process: F1: L TATACATGATATATTTACTTCCCCA 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC RR: ATATGCACTATATAAATGAAGGGGTCAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTAACCCCTTCATTTATATAGTGCAAG F2: 3 CAACACCACATTCGTAGGAGATTTTTACGAATGTGGTGTTA 2 Unidirectional alignment (log-probability: -50.6) TATACaTGATATATTTACTTCCCCAaTTGTGGTGTAAGCATttttagagg---------ATGCTTACACCACAAcTGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCAGTTGTGGTGTAAGCAT---------CCTCTAAAAATGCTTACACCACAATTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -25.7) TATACaTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC TATACGTGATATATTTACTTCCCCA|ATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAAC|TGGGGAAGTAAATATATCACGTTC Chimp > Gorilla --------------- chr1:100158312-100158372 Template switch process: F1: L TATAC 1 F3: 4 TGGGGAAGTAAATATATCACGTTC R RF: TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCATTTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC RR: ATATGTACTATATAAATGAAGGGGTTAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTGCAAG F2: 3 TAACACCACATTCGTAAAAATCTCCTACGAATGTGGTGTTGACCCCTTCATTTATATAGTG 2 Unidirectional alignment (log-probability: -50.6) TATACgTGATATATTTACTTCCCCAgTTGTGGTGTAAGCATcctctaaaa---------ATGCTTACACCACAAtTGGGGAAGTAAATATATCACGTTC TATACATGATATATTTACTTCCCCAATTGTGGTGTAAGCAT---------TTTTAGAGGATGCTTACACCACAACTGGGGAAGTAAATATATCACGTTC Template switch alignment (log-probability: -22.2) TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC TATAC|GTGATATATTTACTTCCCCAGTTGTGGTGTAAGCATCCTCTAAAAATGCTTACACCACAAT|TGGGGAAGTAAATATATCACGTTC ========= Event 369 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATACCATTCTCTAAAGAGACTAGACCACAGGG----AACTTTAGCACCCCATCCTCCAA ↓ 3 2 1 4 Chimp: GATACCATTCTCTAAAGAGACTAGACCACAGGGTCTAGTCTTTAGCACCCCATCCTCAAA ↑ 3 2 1 4 Gorilla: GATACCATTCTCTAAAGAGACTAGACCACAGGG----AACTTTAGCACCCCATCCTCCAA Human: GATACCATTCTCTAAAGAGACTAGACCACAGGG----AACTTTAGCACCCCATCCTCCAA Cluster: [ ] Orangutan: GATACCATTCTCTAAAGAGACTAGACCACAGGG----AAATTTAGCACCCCATCCTCCAA Human > Chimp ------------- chr1:97796417-97796422 Template switch process: F1: L GCTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG 1 F3: 4 CTTTAGCACCCCATCCTCAAACATTGCAGGACCCAGTTGG R RF: GCTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGGAACTTTAGCACCCCATCCTCCAACATTGCAGGACCCAGTTGG RR: CGAAACGTCTATGGTAAGAGATTTCTCTGATCTGGTGTCCCTTGAAATCGTGGGGTAGGAGGTTGTAACGTCCTGGGTCAACC F2: 3 TGATCT 2 Unidirectional alignment (log-probability: -34.7) CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGGtctagtCTTTAGCACCCCATCCTCaAACATTGCAGGACCCAGTTGG CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG----AACTTTAGCACCCCATCCTCCAACATTGCAGGACCCAGTTGG Template switch alignment (log-probability: -22) CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG|TCTAGT|CTTTAGCACCCCATCCTCaAACATTGCAGGACCCAGTTGG CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG|TCTAGT|CTTTAGCACCCCATCCTCCAACATTGCAGGACCCAGTTGG Gorilla > Chimp --------------- chr1:97796417-97796422 Template switch process: F1: L GCTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG 1 F3: 4 CTTTAGCACCCCATCCTCAAACATTGCAGGACCCAGTTGG R RF: GCTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGGAACTTTAGCACCCCATCCTCCAACATTGCAGGACCCAGTTGG RR: CGAAACGTCTATGGTAAGAGATTTCTCTGATCTGGTGTCCCTTGAAATCGTGGGGTAGGAGGTTGTAACGTCCTGGGTCAACC F2: 3 TGATCT 2 Unidirectional alignment (log-probability: -33.2) CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGGtctagtCTTTAGCACCCCATCCTCaAACATTGCAGGACCCAGTTGG CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG----AACTTTAGCACCCCATCCTCCAACATTGCAGGACCCAGTTGG Template switch alignment (log-probability: -22) CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG|TCTAGT|CTTTAGCACCCCATCCTCaAACATTGCAGGACCCAGTTGG CTTTGCAGATACCATTCTCTAAAGAGACTAGACCACAGGG|TCTAGT|CTTTAGCACCCCATCCTCCAACATTGCAGGACCCAGTTGG ========= Event 370 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAAATTAGGTAATAAAATAAGAATTAG-TACTCCCTGAGATGTTTCTTTAGCCCTTGTAATATTTATAAACAAATGTATGGGATACTGAAGTACTAATTTTAAACCTTATTAGACA Chimp: AAAAATTAGGTAATAAAATAAGAATTAG-TACTCCCTGAGATGTTTCTTTAGCCCTTGTAATATTTATAAACAAATGTATGGGATACTAAAGTACTAATTTTAAACCTTATTAGACA ↑ 1 4 3 2 Gorilla: AAAAATTAGGTAATAAAATAAAAATGATTTTATCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAACAAATGTATGGGATACTAAAGTACTAATTTTAAACCTTATTAGACA ↓ 1 4 3 2 Human: AAAAATTAGGTAATAAAATAAGAATTAG-TACTCCCTGAGATGTTTCTTTAGCCCTTGTAATATTTATAAACAAATGTATGGGATACTGAAGTACTAATTTTAAACCTTATTAGACA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr11:129966790-129966795 Template switch process: F1: L TCCTGGAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAGAAT 1 F3: 4 TCCCTGAGATGTTTCTTTAGCCCTTGTAATATTTATAAAC R RF: TCCTGGAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAAAATGATTTTATCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAACAAATGTATGGGATACTAAAGTACTA RR: AGGACCTTAAAAGGGACTTCTTTTTAATCCATTATTTTATTTTTACTAAAATAGGGACTCTATAAAGAAATCGGGAACATTATAAATATTTGTTTACATACCCTATGATTTCATGAT F2: 3 CATGAT 2 Unidirectional alignment (log-probability: -37.8) GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAgAA-----TTAgtacTCCCTGAGATgTTTCTTTAGCCCTTGTAATATTTATAAAC GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAAAATGATTTTA----TCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAAC Template switch alignment (log-probability: -27.6) GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAgAAT|TAGTAC|TCCCTGAGATgTTTCTTTAGCCCTTGTAATATTTATAAAC GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAAAAT|TAGTAC|TCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAAC Gorilla > Chimp --------------- chr11:130861678-130861683 Template switch process: F1: L TCCTGGAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAGAAT 1 F3: 4 TCCCTGAGATGTTTCTTTAGCCCTTGTAATATTTATAAAC R RF: TCCTGGAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAAAATGATTTTATCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAACAAATGTATGGGATACTAAAGTACTA RR: AGGACCTTAAAAGGGACTTCTTTTTAATCCATTATTTTATTTTTACTAAAATAGGGACTCTATAAAGAAATCGGGAACATTATAAATATTTGTTTACATACCCTATGATTTCATGAT F2: 3 CATGAT 2 Unidirectional alignment (log-probability: -37.8) GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAgAA-----TTAgtacTCCCTGAGATgTTTCTTTAGCCCTTGTAATATTTATAAAC GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAAAATGATTTTA----TCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAAC Template switch alignment (log-probability: -27.6) GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAgAAT|TAGTAC|TCCCTGAGATgTTTCTTTAGCCCTTGTAATATTTATAAAC GAATTTTCCCTGAAGAAAAATTAGGTAATAAAATAAAAAT|TAGTAC|TCCCTGAGATATTTCTTTAGCCCTTGTAATATTTATAAAC ========= Event 371 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGTCTGTGGCAGTGGGACCTACGGCGCCTGTGGTGGCTCAGGCAGCAG Chimp: GGGTCTGTGGCAGTGGGACCTACGGCGCCTGTGGTGGCTCAGACAGCAG ↓ 13 24 Gorilla: GGGTCTGTGGCAGTGGGACCTGCGACGTCTGTGGTGGCTCAGACAGCAG Human: GGGTCTGTGGCAGTGGGACCTACGGCGCCTGTGGTGGCTCAGGCAGCAG Cluster: [ ] Orangutan: GGGTCTGTGGCAGTGGGACCTGCGATGCCTGTGGTGGCTCAGACAGCAG Chimp > Gorilla --------------- chr1:131867684-131867690 Template switch process: F1: L CTGCAGCAGCCAGAGCTCTGGGGTCTGTGGCAGTGGGACCT 1 F3: 4 CTGTGGTGGCTCAGACAGCAGCCACCACCCCCAGAACTGC R RF: CTGCAGCAGCCAGAGCTCTGGGGTCTGTGGCAGTGGGACCTACGGCGCCTGTGGTGGCTCAGACAGCAGCCACCACCCCCAGAACTGC RR: GACGTCGTCGGTCTCGAGACCCCAGACACCGTCACCCTGGATGCCGCGGACACCACCGAGTCTGTCGTCGGTGGTGGGGGTCTTGACG F2: 3 TGCAGCG 2 Unidirectional alignment (log-probability: -44.5) TGCAGCAGCCAGAGCTCTGGGGTCTGTGGCAGTGGGACCTgCGaCGtCTGTGGTGGCTCAGACAGCAGCCACCacccccagaactgc TGCAGCAGCCAGAGCTCTGGGGTCTGTGGCAGTGGGACCTACGGCGCCTGTGGTGGCTCAGACAGCAGCCACC-------------- Template switch alignment (log-probability: -22.1) TGCAGCAGCCAGAGCTCTGGGGTCTGTGGCAGTGGGACCT|GCGaCGT|CTGTGGTGGCTCAGACAGCAGCCACCACCCCCAGAACTGC TGCAGCAGCCAGAGCTCTGGGGTCTGTGGCAGTGGGACCT|GCGCCGT|CTGTGGTGGCTCAGACAGCAGCCACCACCCCCAGAACTGC ========= Event 372 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GTAC-TTGCCGTCCTCAGCCTGCAGGACAGGGCCCTAGGTCGCCAGGGGCCCGGAGCTCAAGGCGCCGGC---TGCACTGTTCACCTCCACCcccattccaatattttaaaagattctccttt Chimp: GTACTGTGCCGTCCTCAGCCTGCAGGACA-GGCCCTAGGTCGCCAGGGGCCCGGAGCTCAAGGCGCCGGCCTGCCCACTGTTCACCTCCACCCCCATTCCA--ATTTTAAAAGATTCTCCTTT ↓ 3 2 1 4 Gorilla: GTAC-TTGCTGTCCTCAGCCTGCAGGACAGGGCCCTAGGTCGCCAGGGGCCCGGAGCTCAAGGCGCCGGC---TGCAGTGTTCACCTCCACCCCCATTCCAATATTTTAAAAGATTCTCCTTT Human: GTAC-TTGCCGTCCTCAGCCTGCAGGACAGGGCCCTAGGTCGCCAGGGGCCCGGAGCTCAAGGCGCCGGC---TGCACTGTTCACCTCCACCcccattccaatattttaaaagattctccttt Cluster: [] Orangutan: GTAC-TTCCCGTCCGCAGCCTGCAGGACAGGGCCCTAGGTCGCCTTGGGCCCGGAGCTCAAGGCACCGGC---TGCACTGTTCACCTCCA-Ccccattccaatattttaaaagattctccttt Chimp > Gorilla --------------- chr1:133493713-133493717 Template switch process: F1: L AGGCGCCGGC 1 F3: 4 TGTTCACCTCCACCCCCATTCCAATATTTTAAAAGATTCTCCTTTTCTGGTATTGTTAAAAGTT R RF: CTGCAGGACAGGCCCTAGGTCGCCAGGGGCCCGGAGCTCAAGGCGCCGGCCTGCCCACTGTTCACCTCCACCCCCATTCCAATTTTAAAAGATTCTCCTTTTCTGGTATTGTTAAAAGTT RR: GACGTCCTGTCCGGGATCCAGCGGTCCCCGGGCCTCGAGTTCCGCGGCCGGACGGGTGACAAGTGGAGGTGGGGGTAAGGTTAAAATTTTCTAAGAGGAAAAGACCATAACAATTTTCAA F2: 3 GACGT 2 Unidirectional alignment (log-probability: -45.7) AGGCGCCGGC-TG--CAgTGTTCACCTCCACCCCCATTCCAatATTTTAAAAGATTCT AGGCGCCGGCCTGCCCACTGTTCACCTCCACCCCCATTCCA--ATTTTAAAAGATTCT Template switch alignment (log-probability: -28.8) AGGCGCCGGC|TGCAG|TGTTCACCTCCACCCCCATTCCAatATTTTAAAAGATTCT AGGCGCCGGC|TGCAG|TGTTCACCTCCACCCCCATTCCA--ATTTTAAAAGATTCT ========= Event 373 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTGGCAGAATTGCCTTTGTATAACTTTCTTTCAGTAAAGAAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAGA Chimp: CTTGGCAGAATTGCCTTTGTATAACTTTCTTTCAGTAAAGAAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAGG ↑ 4 3 1 2 Gorilla: CTTGGCAGAATTGCCTTTGTA-------TTT---------TAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAGA Human: CTTGGCAGAATTGCCTTTGTATAACTTTCTTTCAGTAAAGAAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAGA Cluster: [ ] Orangutan: CTTGGCAGAATTGCCTTTGTA-------TTT---------TAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAGA Gorilla > Chimp --------------- chr1:129447602-129447610 Template switch process: F1: L AGCCATAGAAAAAAAGGGAACTTGGCAGAATTGCCTTTG----------TATAACTTTCTTT 1 F3: 4 AAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAG R RF: AGCCATAGAAAAAAAGGGAACTTGGCAGAATTGCCTTTGTATTTTAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAG RR: TCGGTATCTTTTTTTCCCTTGAACCGTCTTAACGGAAACATAAAATTCAATATCGAAAGAAATGACTTTATTATCGAAATTTCTC F2: 3 AGAAATGAC 2 Unidirectional alignment (log-probability: -43.7) AAAGGGAACTTGGCAGAATTGCCTTTGTATaactttcTTTcagtaaagaAAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAG AAAGGGAACTTGGCAGAATTGCCTTTGTAT-------TTT---------AAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAG Template switch alignment (log-probability: -32.9) AAAGGGAACTTGGCAGAATTGCCTTTG----------TATAaCTTTCTTT|CAGTAAAGA|AAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAG AAAGGGAACTTGGCAGAATTGCCTTTGTATTTTAAGTTATAGCTTTCTTT|CAGTAAAGA|AAGTTATAGCTTTCTTTACTGAAATAATAGCTTTAAAGAG ========= Event 374 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: ATATATTACAAGAAAGAGTGAAAAAT-CATATGGATTTTTCAATCTTCAAACTGAATATTTG ↑ 3 1 2 4 Chimp: ATATATTACAAGAAAGAGTGAAAAATCCATA-TGATTTTTTAATCTTCAAACTGAATATTTG Gorilla: Human: ATATATTACAAGAAAGAGTGAAAAAT-CATATGGATTTTTCAATCTTCAAACTGAATATTTG Cluster: [ ] Orangutan: Chimp > Human ------------- chr1:98733140-98733152 Template switch process: F1: L TTTGCTCTTGTTGGAATATATTACAAGAAAGAGTGAAAAATC 1 F3: 4 AATCTTCAAACTGAATATTTGAATTTCAAGGATGAAGAAG R RF: TTTGCTCTTGTTGGAATATATTACAAGAAAGAGTGAAAAATCCATATGATTTTTTAATCTTCAAACTGAATATTTGAATTTCAAGGATGAAGAAG RR: AAACGAGAACAACCTTATATAATGTTCTTTCTCACTTTTTAGGTATACTAAAAAATTAGAAGTTTGACTTATAAACTTAAAGTTCCTACTTCTTC F2: 3 CTTTTTAGGTATA 2 Unidirectional alignment (log-probability: -28.7) TGCTCTTGTTGGAATATATTACAAGAAAGAGTGAAAAAT-CATATgGATTTTTcAATCTTCAAACTGAATATTTGAATTTCAAGGATGAAGAAG TGCTCTTGTTGGAATATATTACAAGAAAGAGTGAAAAATCCATAT-GATTTTTTAATCTTCAAACTGAATATTTGAATTTCAAGGATGAAGAAG Template switch alignment (log-probability: -16.9) TGCTCTTGTTGGAATATATTACAAGAAAGAGTGAAAAATC|ATATGGATTTTTC|AATCTTCAAACTGAATATTTGAATTTCAAGGATGAAGAAG TGCTCTTGTTGGAATATATTACAAGAAAGAGTGAAAAATC|ATATGGATTTTTC|AATCTTCAAACTGAATATTTGAATTTCAAGGATGAAGAAG ========= Event 375 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ---aaaGATTATAATACTACTACAGTGTTTTCCTATAGGTTTTATTTTTAATAAAGAATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAGTTATTACTGTCATAATTTCTAGCAGAGTAAGTAGAGAAAAGGAGTATAGTTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAACCTCAATCaaattgtaattagggaaataaaaaaactgtaattaggggaatgg Chimp: ---aaaGATTATAATACTACTACAGTGTTTTCCTATAGGTTTTATTTTTAATAAAGAATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAGTTATTACTGTCATAATTTCTAGCAGAGTAAGTAGAGAAAAGGAGTATAGTTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAACCTCAGTCAAATTGTAATTAGGGAAATaaaaaaaCTGCAAT-TGGGGAATGG ↓ 3 2 4 1 Gorilla: ---aaTGATTATAATACTACTACAGTGTTTTCCTATAGGTTTTATTTTTAATAAAGAATTATAAGTTATCggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagattgagaccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaattagccgggcgtggtagtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtgaacccgggaggtggagcttgcagtgagccgagatcgcgccactgcactccagcctgggcgacaaagcaagactccgtctcaaaaaaaaaaaaaaaaaaaaagaaTTATAAGTTATTATTGTCATAATTTCTAGCAGAGTAAGTAGAGAAAAGGAGTATAGCTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAGCCTCAATCAAATTGTAATTAGGGAAATAAAAACACTGTAGTTAGGGGAATGG Human: ---aaaGATTATAATACTACTACAGTGTTTTCCTATAGGTTTTATTTTTAATAAAGAATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAGTTATTACTGTCATAATTTCTAGCAGAGTAAGTAGAGAAAAGGAGTATAGTTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAACCTCAATCaaattgtaattagggaaataaaaaaactgtaattaggggaatgg Cluster: [ ] Orangutan: aGGAATGATTATAATACTACTACAGTGTTT-TCTATAGGTTTTATTTTTAATAAAGAATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAGTTATTACTGTCATAATTTCTAGCAGAGTAAGTAGAGAAAAGGAGTATAGTTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAACCTCAATCAAATTGTAATTAGGGAAATAAAA-AACCGGAATTAGGGGAATGG Chimp > Gorilla --------------- chr1:95693557-95693564 Template switch process: F1: L AGCTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAGCCTCAATCAAATTGTAATTAGGGAAATAAAAA 1 F3: 4 TTAGGG R RF: CTACAGTGTTTTCCTATAGGTTTTATTTTTAATAAAGAATTATAAGTTATTACTGTCATAATTTCTAGCAGAGTAAGTAGAGAAAAGGAGTATAGTTGGAACTTGGGATCTACTAACTTCAATGCTTATTTGCAACCTCAGTCAAATTGTAATTAGGGAAATAAAAA RR: GATGTCACAAAAGGATATCCAAAATAAAAATTATTTCTTAATATTCAATAATGACAGTATTAAAGATCGTCTCATTCATCTCTTTTCCTCATATCAACCTTGAACCCTAGATGATTGAAGTTACGAATAAACGTTGGAGTCAGTTTAACATTAATCCCTTTATTTTT F2: 3 GATGTCAC 2 Unidirectional alignment (log-probability: -45.5) ATTTGCAgCCTCAaTCAAATTGTAATTAGGGAAATAAAAAcACTGtAgTTaGGG ATTTGCAACCTCAGTCAAATTGTAATTAGGGAAATAAAAAAACTGCAATT-GGG Template switch alignment (log-probability: -33.3) ATTTGCAgCCTCAaTCAAATTGTAATTAGGGAAATAAAAA|CACTGTAG|TTAGGG ATTTGCAACCTCAGTCAAATTGTAATTAGGGAAATAAAAA|CACTGTAG|TTAGGG ========= Event 376 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCACGCTTCATCCTATTTTGACCCAGTTGCGGAGCCCATGTTCCAGTTGACCTACCCAACA Chimp: CCACGCTTCATCCTATTTTGACCCAGTTGTGGAGCCCATGTTCTAGTTGACCTACACAACA ↓ 1 4 3 2 Gorilla: CCACGCTTCATCCTATTTTGAAC------ATGAGCCCATGTTCTAGTTGACCTACACAACA Human: CCACGCTTCATCCTATTTTGACCCAGTTGCGGAGCCCATGTTCCAGTTGACCTACCCAACA Cluster: [ ] Orangutan: CCACGCTTCATCCTATTTTGACCTAGTTGTGGAGCCCATGTTCTAGTTGACCTACACAACA Chimp > Gorilla --------------- chr1:135377820-135377824 Template switch process: F1: L GAAGGCACAAAATTCAGTTTCCACGCTTCATCCTATTTTGA 1 F3: 4 AGCCCATGTTCTAGTTGACCTACACAACAAATTCTCCAC R RF: GAAGGCACAAAACTCAGTTTCCACGCTTCATCCTATTTTGACCCAGTTGTGGAGCCCATGTTCTAGTTGACCTACACAACAAATTCTCCAC RR: CTTCCGTGTTTTGAGTCAAAGGTGCGAAGTAGGATAAAACTGGGTCAACACCTCGGGTACAAGATCAACTGGATGTGTTGTTTAAGAGGTG F2: 3 GTACA 2 Unidirectional alignment (log-probability: -32.4) AAGGCACAAAAtTCAGTTTCCACGCTTCATCCTATTTTGA----------acatGAGCCCATGTTCTAGTTGACCTACACAACAAATTCTCCAC AAGGCACAAAACTCAGTTTCCACGCTTCATCCTATTTTGACCCAGTTGTG----GAGCCCATGTTCTAGTTGACCTACACAACAAATTCTCCAC Template switch alignment (log-probability: -21.8) AAGGCACAAAAtTCAGTTTCCACGCTTCATCCTATTTTGA|ACATG|AGCCCATGTTCTAGTTGACCTACACAACAAATTCTCCAC AAGGCACAAAACTCAGTTTCCACGCTTCATCCTATTTTGA|ACATG|AGCCCATGTTCTAGTTGACCTACACAACAAATTCTCCAC ========= Event 377 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CACAGCGCCCACTCACCCCCA----ACAGTGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCC-CCCGCCTGAGGCCTGGAGATCCCAGGGCTGCTGCCCACTGGCCTGAGTCACCCATGCCAG Chimp: CACAGCGCCCACTCACCCCCA----ACAGTGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCC-CCCGCCTGAGGCCTGGAGATCCCAGGGCTGCTGCCCACTGGCCTGAGTCACCCATGCCAG ↑ 1 4 3 2 Gorilla: CACAGCGCCCACTCACCCCCAAACAAAGGGGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCC-CCCGCCTGAGGCCTGGAGATCCCCGGGCTGCTGCCCACTGGCCTGAGTCACCCATGCCAG ↓ 1 4 3 2 Human: CACAGCGCCCACTCACCCCCA----ACAGTGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCC-CCCGCCTGAGGCCTGGAGATCCCAGGGCTGCTGCCCACTGGCCTGAGTCACCCATGCCAG Cluster: [ ] Orangutan: CACAGCGCCCACTCACCCCCA----ACACTGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCCCCCCGCCTGAGGCCTGGAGATCCCAGGGCTGCTGCCCACTGGCCTGAGTCACCCATGCCAG Gorilla > Human --------------- chr1:93826605-93826608 Template switch process: F1: L CCCCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAA 1 F3: 4 GTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG R RF: CCCCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAAACAAAGGGGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCCCCCGCCTGAGGCCTGGAGATCCCCGGGCTGCTGCCCACTG RR: GGGGGTCCTGGGGTCCTCCCGTGTCGCGGGTGAGTGGGGGTTTGTTTCCCCAGGAGGTTTGTTTCCCTCGACCGTCCAGTCTTACTCCCCGGACGGGAGGTCGTACTCCCTCCGACCGCGGGAAGAGTCGTACGACGGGGGCGGACTCCGGACCTCTAGGGGCCCGACGACGGGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -26.4) CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCC-AACA---GtGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAAACAAAGGGGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG Template switch alignment (log-probability: -16.3) CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAA|CAGT|GTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAA|CAGT|GTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG Gorilla > Chimp --------------- chr1:95355877-95355880 Template switch process: F1: L CCCCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAA 1 F3: 4 GTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG R RF: CCCCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAAACAAAGGGGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGGCCTGCCCTCCAGCATGAGGGAGGCTGGCGCCCTTCTCAGCATGCTGCCCCCGCCTGAGGCCTGGAGATCCCCGGGCTGCTGCCCACTG RR: GGGGGTCCTGGGGTCCTCCCGTGTCGCGGGTGAGTGGGGGTTTGTTTCCCCAGGAGGTTTGTTTCCCTCGACCGTCCAGTCTTACTCCCCGGACGGGAGGTCGTACTCCCTCCGACCGCGGGAAGAGTCGTACGACGGGGGCGGACTCCGGACCTCTAGGGGCCCGACGACGGGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -26.4) CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCC-AACA---GtGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAAACAAAGGGGTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG Template switch alignment (log-probability: -16.3) CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAA|CAGT|GTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG CCCAGGACCCCAGGAGGGCACAGCGCCCACTCACCCCCAA|CAGT|GTCCTCCAAACAAAGGGAGCTGGCAGGTCAGAATGAGGGG ========= Event 378 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAAATCCAGAATTGGATGCCAAAGAA-------------------------------------------------------------------------GCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACCAAGGTTATGTTCTACATCATTTCAGACT ↓ 4 3 1 2 Chimp: AGAAATCCAGAATTGGATGCCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACATAACCTTGGTATAAAGAGTCCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACCAAGGTTATGTTCTACATCATTTCAGACT ↑ 4 3 1 2 Gorilla: AGAAATCCAGAATTGGATGCCAAAAAA-------------------------------------------------------------------------GCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACCAAGGTTATGTTCTACATCATTTCAGACT Human: AGAAATCCAGAATTGGATGCCAAAGAA-------------------------------------------------------------------------GCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACCAAGGTTATGTTCTACATCATTTCAGACT Cluster: [ ] Orangutan: AGAAATCCAGAATTGGATGCCAAAAAA-------------------------------------------------------------------------ACAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACCAAGGT--TGTTCTACATCATTTCAGACT Human > Chimp ------------- chr1:14679145-14679164 Template switch process: F1: L GACCATATTCCATGAGAAATCCAGAATTGGATGCCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATAC 1 F3: 4 CCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTT R RF: GACCATATTCCATGAGAAATCCAGAATTGGATGCCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACTATACCAAGGTTAT RR: CTGGTATAAGGTACTCTTTAGGTCTTAACCTACGGTTTCTTCGTTAGAGATTAATATGTACTGGAGGAAGGTCCCTGAGAAATATGATATGGTTCCAATA F2: 3 TGAGAAATATGGTTCCAATA 2 Unidirectional alignment (log-probability: -113) CTCTAATTATACATGACCTCCTTCCAGGGACTCTTtatacataaccttggtataaagagtccaaagaagcaatctctaattatacatgacctccttccag CTCTAATTATACATGACCTCCTTCCAGGGACTCTT----------------------------------------------------------------- Template switch alignment (log-probability: -18.7) CTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATAC|ATAACCTTGGTATAAAGAGT|CCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAG CTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATAC|ATAACCTTGGTATAAAGAGT|CCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAG Gorilla > Chimp --------------- chr1:14679145-14679164 Template switch process: F1: L TTAGACCATATTCCATGAGAAATCCAGAATTGGATGCCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATAC 1 F3: 4 CCAAAGAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTT R RF: TTAGACCATATTCCATGAGAAATCCAGAATTGGATGCCAAAAAAGCAATCTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATACTATACCAAGGTTAT RR: AATCTGGTATAAGGTACTCTTTAGGTCTTAACCTACGGTTTTTTCGTTAGAGATTAATATGTACTGGAGGAAGGTCCCTGAGAAATATGATATGGTTCCAATA F2: 3 TGAGAAATATGGTTCCAATA 2 Unidirectional alignment (log-probability: -118) CTCTAATTATACATGACCTCCTTCCAGGGACTCTTtatacataaccttggtataaagagtccaaagaagcaatctctaattatacatgacctccttccag CTCTAATTATACATGACCTCCTTCCAGGGACTCTT----------------------------------------------------------------- Template switch alignment (log-probability: -30.6) CTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATAC|ATAACCTTGGTATAAAGAGT|CCAAAgAAGCAATCTCTAATTATACATGACCTCCTTCCAG CTCTAATTATACATGACCTCCTTCCAGGGACTCTTTATAC|ATAACCTTGGTATAAAGAGT|CCAAAAAAGCAATCTCTAATTATACATGACCTCCTTCCAG ========= Event 379 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGGAGACAGCAACTCAGAAACGTCCCTATGCACA------GCTGTGGAAGCTCTGAGGACACCCCGGGACTTTT Chimp: AGGGAGACAGGAACTCAGAAACGTCCCTATGCACA------GCTGTGGAAGCTCTGAGGACACCCCGGGACTTTT ↓ 3 2 1 4 Gorilla: AGGGAGACAGGAACTCAGAAACGTCCCTATGCACA------------GGACGTTTGAGGACACCCCGGGACTTTT ↑ 3 2 1 4 Human: AGGGAGACAGCAACTCAGAAACGTCCCTATGCACA------GCTGTGGAAGCTCTGAGGACACCCCGGGACTTTT Cluster: [ ] Orangutan: AGGGAGACGGGAACTCAGAAACGTCCCTATGCACAGCTGTG------GAAGCTCTGAGGACACCCCGGGACTTTT Human > Gorilla --------------- chr1:92983200-92983205 Template switch process: F1: L AGCGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAG 1 F3: 4 TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT R RF: AGCGGTAGGGAGACAGCAACTCAGAAACGTCCCTATGCACAGCTGTGGAAGCTCTGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT RR: TCGCCATCCCTCTGTCGTTGAGTCTTTGCAGGGATACGTGTCGACACCTTCGAGACTCCTGTGGGGCCCTGAAAAATGGGTCGGGACAGGGAAA F2: 3 TTGCAG 2 Unidirectional alignment (log-probability: -35.4) CGGTAGGGAGACAGgAACTCAGAAACGTCCCTATGCACAG------------gacgttTGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT CGGTAGGGAGACAGCAACTCAGAAACGTCCCTATGCACAGCTGTGGAAGCTC------TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT Template switch alignment (log-probability: -22) CGGTAGGGAGACAGgAACTCAGAAACGTCCCTATGCACAG|GACGTT|TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT CGGTAGGGAGACAGCAACTCAGAAACGTCCCTATGCACAG|GACGTT|TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT Chimp > Gorilla --------------- chr1:92983200-92983205 Template switch process: F1: L AGCGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAG 1 F3: 4 TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT R RF: AGCGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAGCTGTGGAAGCTCTGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT RR: TCGCCATCCCTCTGTCCTTGAGTCTTTGCAGGGATACGTGTCGACACCTTCGAGACTCCTGTGGGGCCCTGAAAAATGGGTCGGGACAGGGAAA F2: 3 TTGCAG 2 Unidirectional alignment (log-probability: -29.9) CGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAG------------gacgttTGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT CGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAGCTGTGGAAGCTC------TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT Template switch alignment (log-probability: -16.5) CGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAG|GACGTT|TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT CGGTAGGGAGACAGGAACTCAGAAACGTCCCTATGCACAG|GACGTT|TGAGGACACCCCGGGACTTTTTACCCAGCCCTGTCCCTTT ========= Event 380 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGGTGGGAGAAGAGTGTCTAGTTCCT-GTA--CCCTCTCCACCCACAAGTCTATGGA ↓ 3 1 2 4 Chimp: TTGGTGGGAGAAGAGTGTCTAGTTCCTGGTACAGGAACTCCACCCACAAGTCTCTGGA ↑ 3 1 2 4 Gorilla: TTGGTGGGAGAAGAGTGTCTACTTCCT-GTA--CCCTCTCCACCCACAAGTCTATGGA Human: TTGGTGGGAGAAGAGTGTCTAGTTCCT-GTA--CCCTCTCCACCCACAAGTCTATGGA Cluster: [ ] Orangutan: TTGGTGGGAGAAGAGTGTCTAGTTCCT-GTA--CCCTCTCCACCCACAAGTCTATGGA Human > Chimp ------------- chr11:77473219-77473227 Template switch process: F1: L TCTTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTG 1 F3: 4 CTCCACCCACAAGTCTCTGGAAGCTGAGGCAAGGATAACC R RF: TCTTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTGTACCCTCTCCACCCACAAGTCTATGGAAGCTGAGGCAAGGATAACC RR: AGAACCTCTTATCTAACCACCCTCTTCTCACAGATCAAGGACATGGGAGAGGTGGGTGTTCAGATACCTTCGACTCCGTTCCTATTGG F2: 3 AAGGACATG 2 Unidirectional alignment (log-probability: -40.4) TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTGgtacaggaa------CTCCACCCACAAGTCTcTGGAAGCTGAGGCAAGGATAACC TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTG---------TACCCTCTCCACCCACAAGTCTATGGAAGCTGAGGCAAGGATAACC Template switch alignment (log-probability: -22.4) TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTG|GTACAGGAA|CTCCACCCACAAGTCTcTGGAAGCTGAGGCAAGGATAACC TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTG|GTACAGGAA|CTCCACCCACAAGTCTATGGAAGCTGAGGCAAGGATAACC Gorilla > Chimp --------------- chr11:77473219-77473227 Template switch process: F1: L TCTCTTTCTTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAGTTCCTG 1 F3: 4 CTCCACCCACAAGTCTCTGGAAGCTGAGGCAAGGATAACC R RF: TCTCTTTCTTGGAGAATAGATTGGTGGGAGAAGAGTGTCTACTTCCTGTACCCTCTCCACCCACAAGTCTATGGAAGCTGAGGCAAGGATAACC RR: AGAGAAAGAACCTCTTATCTAACCACCCTCTTCTCACAGATGAAGGACATGGGAGAGGTGGGTGTTCAGATACCTTCGACTCCGTTCCTATTGG F2: 3 AAGGACATG 2 Unidirectional alignment (log-probability: -45) TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAgTTCCTG------gtacaggaaCTCCACCCACAAGTCTcTGGAAGCTGAGGCAAGGATAACC TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTACTTCCTGTACCCT---------CTCCACCCACAAGTCTATGGAAGCTGAGGCAAGGATAACC Template switch alignment (log-probability: -28.1) TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTAgTTCCTG|GTACAGGAA|CTCCACCCACAAGTCTcTGGAAGCTGAGGCAAGGATAACC TTGGAGAATAGATTGGTGGGAGAAGAGTGTCTACTTCCTG|GTACAGGAA|CTCCACCCACAAGTCTATGGAAGCTGAGGCAAGGATAACC ========= Event 381 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGCCTACCAGCTAATGCTAGC------TATGTGAAGACCTTTCACATACCCAATAATG ↓ 3 1 24 Chimp: AGCCTACCAGCTAATGCTAGC---TCATAGCTGAAGACCTTTCACATACCCAATAATG Gorilla: AGCCTACCAGCTAATGCTAGCTCA---TAGCTGAAGA-CTTTCACATACCCAATAATG ↑ 3 1 24 Human: AGCCTACCAGCTAATGCTAGC------TATGTGAAGACCTTTCACATACCCAATAATG Cluster: [ ] Orangutan: AGCCTACCAGCTAATGCTAGCTCA---TAGCTGAAGACCATTCACATACCCAATAATG Human > Chimp ------------- chr1:137231010-137231015 Template switch process: F1: L CAGTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCT 1 F3: 4 TGAAGACCTTTCACATACCCAATAATGATCATTTAAATAT R RF: CAGTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCTATGTGAAGACCTTTCACATACCCAATAATGATCATTTAAATAT RR: GTCACTTAAGTCTATAGAATTCGGATGGTCGATTACGATCGATACACTTCTGGAAAGTGTATGGGTTATTACTAGTAAATTTATA F2: 3 CGATAC 2 Unidirectional alignment (log-probability: -27.3) GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCtcaTAgcTGAAGACCTTTCACATACCCAATAATGATCATTTAAATAT GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGC---TATGTGAAGACCTTTCACATACCCAATAATGATCATTTAAATAT Template switch alignment (log-probability: -16) GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCT|CATAGC|TGAAGACCTTTCACATACCCAATAATGATCATTTAAATAT GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCT|CATAGC|TGAAGACCTTTCACATACCCAATAATGATCATTTAAATAT Human > Gorilla --------------- chr1:138202331-138202336 Template switch process: F1: L CAGTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCT 1 F3: 4 TGAAGA-CTTTCACATACCCAATAATGATCATTTAAATATCTTAAAT R RF: CAGTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCTATGTGAAGACCTTTCACATACCCAATAATGATCATTTAAATATCTTAAAT RR: GTCACTTAAGTCTATAGAATTCGGATGGTCGATTACGATCGATACACTTCTGGAAAGTGTATGGGTTATTACTAGTAAATTTATAGAATTTA F2: 3 CGATAC 2 Unidirectional alignment (log-probability: -36.2) GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCtcaTAgcTGAAGA-CTTTCACATACCCAATAATGATCATTTAAATATC GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGC---TATGTGAAGACCTTTCACATACCCAATAATGATCATTTAAATATC Template switch alignment (log-probability: -26.5) GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCT|CATAGC|TGAAGA-CTTTCACATACCCAATAATGATCATTTAAATATC GTGAATTCAGATATCTTAAGCCTACCAGCTAATGCTAGCT|CATAGC|TGAAGACCTTTCACATACCCAATAATGATCATTTAAATATC ========= Event 382 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCAGTGAAAAAGCCGCTTCTCTTCTTTTTCTGTGGAATGTTCATAGACAAAGCCCtt---tttt ↓ 1 4 3 2 Chimp: TTCAGTGAAAAAGCCGCTTCTATGAACATTCTGTGGAATGTTCATAGACAAAGCCCtt-----tt ↑ 1 4 3 2 Gorilla: TTCAGTGAAAAAGCCGCTTCTCTTCTTTTTCTGTGGAATGTTCATAGACAAAGCCCtt-----tt Human: TTCAGTGAAAAAGCCGCTTCTCTTCTTTTTCTGTGGAATGTTCATAGACAAAGCCCtt---tttt Cluster: [ ] Orangutan: TTCAGTGAAAAAGCTGCTTCTCTTCTTTTTCTGTGGAATGTTCGTAGACAAAGCCCttttt--tt Human > Chimp ------------- chr11:76809156-76809162 Template switch process: F1: L GTCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT 1 F3: 4 TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCA R RF: GTCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCTCTTCTTTTTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTT RR: CAGTAACAGATTGTGTTTCTAAGTCACTTTTTCGGCGAAGAGAAGAAAAAGACACCTTACAAGTATCTGTTTCGGGAAAAAAAA F2: 3 ACAAGTA 2 Unidirectional alignment (log-probability: -41.9) TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCTatgaaca-------TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTT--CA TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT-------CTTCTTTTTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTTTCA Template switch alignment (log-probability: -26.2) TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT|ATGAACA|TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTtca TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT|ATGAACA|TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTT--T Gorilla > Chimp --------------- chr11:76809156-76809162 Template switch process: F1: L GTCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT 1 F3: 4 TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCAAT R RF: GTCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCTCTTCTTTTTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCAAT RR: CAGTAACAGATTGTGTTTCTAAGTCACTTTTTCGGCGAAGAGAAGAAAAAGACACCTTACAAGTATCTGTTTCGGGAAAAAAAAGTTA F2: 3 ACAAGTA 2 Unidirectional alignment (log-probability: -31.1) TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTC-------TatgaacaTTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCAAT TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCTCTTCTTT-------TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCAAT Template switch alignment (log-probability: -16.6) TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT|ATGAACA|TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCAAT TCATTGTCTAACACAAAGATTCAGTGAAAAAGCCGCTTCT|ATGAACA|TTCTGTGGAATGTTCATAGACAAAGCCCTTTTTTTTCAAT ========= Event 383 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTTAGTATCAGTAACCATGATGCTTAGCATTAAGTAGTAAAACATCTCCACTAGTCCATGTGCTGTATGTAGTTACTGTTGTCATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAA--------------------GAATTTACAATTCAGCTGAGTGT Chimp: TGTTAGTATCAGTAACCATGATGCTTAGCATTAAGTAGTAAAACATCTCCACTAGTCCATGTGCTGTATGTAGTTACTGTTGTCATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAA----------GAAGCATCAGGAATTTATAATTCAGCTGAGTGT Gorilla: TGTTAGTATCAGTAACCATGATGCTTAGCATTAAGTAGTAAAACAACTCCACTAGTCCATGTGCTGTATGTAGTTAGTGTTGTCATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAAGAAGCATCAG----------GAATTTACAATTCAGCTGAGTGT ↑ 3 2 4 1 Human: TGTTAGTATCAGTAACCATGATGCTTAGCATTAAGTAGTAAAACATCTCCACTAGTCCATGTGCTGTATGTAGTTACTGTTGTCATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAA--------------------GAATTTACAATTCAGCTGAGTGT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr11:76720232-76720236 Template switch process: F1: L TTGTCATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAAGAA 1 F3: 4 AGGAATTTACAATTCAGCTGAGTGTGAGATAACACAATAATA R RF: GATGCTTAGCATTAAGTAGTAAAACATCTCCACTAGTCCATGTGCTGTATGTAGTTACTGTTGTCATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAAGAATTTACAATTCAGCTGAGTGTGAGATAACACAATAATA RR: CTACGAATCGTAATTCATCATTTTGTAGAGGTGATCAGGTACACGACATACATCAATGACAACAGTAGAATTCCCGTGAACCACTACCACGTTGAATTTTTCTTAAATGTTAAGTCGACTCACACTCTATTGTGTTATTAT F2: 3 CTACG 2 Unidirectional alignment (log-probability: -50.5) CATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAAgaagcatcagGAATTTACAATTCAGCTGAGTGTGAGAtaacacaataa CATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAA----------GAATTTACAATTCAGCTGAGTGTGAGA----------- Template switch alignment (log-probability: -22) CATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAAGAA|GCATC|AgGAATTTACAATTCAGCTGAGTGTGAGATAACACAATAA CATCTTAAGGGCACTTGGTGATGGTGCAACTTAAAAAGAA|GCATC|AAGAATTTACAATTCAGCTGAGTGTGAGATAACACAATAA ========= Event 384 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTCTGCTTTGTACTTTGGAGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCATAT---GCTCTCTGCAAGATTCATTTCATCCCTAACC ↑ 3 2 1 4 Chimp: ATTCTGCTTTGTACTTTGGAGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCACAAATGAATCTCTGCAGGATTCATTTCATCCCTAACC Gorilla: ATTCTGCTTTGTACTTTGGAGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCACAT---GCTCTCTGCAAGATTCATTTCATCCCTAACC Human: ATTCTGCTTTGTACTTTGGAGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCATAT---GCTCTCTGCAAGATTCATTTCATCCCTAACC Cluster: [ ] Orangutan: Chimp > Human ------------- chr11:78231072-78231077 Template switch process: F1: L GAGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCA 1 F3: 4 CTCTGCAAGATTCATTTCATCCCTAACCTTGTCTGGCAGTGTGTGTAT R RF: GAGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCACAAATGAATCTCTGCAGGATTCATTTCATCCCTAACCTTGTCTGGCAGTGTGTGTAT RR: CTCGTATTGTCTTTAAAGATTCCACACTCAAACCTCTCCGTGTTTACTTAGAGACGTCCTAAGTAAAGTAGGGATTGGAACAGACCGTCACACACATA F2: 3 TCGTAT 2 Unidirectional alignment (log-probability: -33.3) AGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCAtatgC-------TCTCTGCAaGATTCATTTCATCCCTAACCTTGTCTGGCAGT AGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCA----CAAATGAATCTCTGCAGGATTCATTTCATCCCTAACCTTGTCTGGCAGT Template switch alignment (log-probability: -22.2) AGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCA|TATGCT|CTCTGCAaGATTCATTTCATCCCTAACCTTGTCTGGCAGT AGCATAACAGAAATTTCTAAGGTGTGAGTTTGGAGAGGCA|TATGCT|CTCTGCAGGATTCATTTCATCCCTAACCTTGTCTGGCAGT ========= Event 385 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTATCCTGATCATGCTCTGATCAGTATATAGGTAGGACCTATATACTGACCAATATTTCCTGGGATTAA ↑ 1 4 3 2 Chimp: TTTATCCTGATCATGCTCTGA------AAATGGTGGGACCTATATACTGACCAATATTTCCTGGGATTAA Gorilla: TTTATCCTGATCATGCTCTGA------AAATGGTGGGACCTATATACTGACCAATATTTCCTGGGATTAA ↓ 1 4 3 2 Human: TTTATCCTGATCATGCTCTGATCAGTATATAGGTAGGACCTATATACTGACCAATATTTCCTGGGATTAA Cluster: [ ] Orangutan: Chimp > Human ------------- chr11:129120035-129120044 Template switch process: F1: L ATGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTGA 1 F3: 4 GGTAGGACCTATATACTGACCAATATTTCCTGGGATTAAGTAAC R RF: ATGTTTTACACTTTTCAATTTTTATCCTGATCATGCTCTGAAAATGGTGGGACCTATATACTGACCAATATTTCCTGGGATTAAGTAAC RR: TACAAAATGTGAAAAGTTAAAAATAGGACTAGTACGAGACTTTTACCACCCTGGATATATGACTGGTTATAAAGGACCCTAATTCATTG F2: 3 ATATATGACT 2 Unidirectional alignment (log-probability: -46.2) TGTTTTACACTTTgCAATTTTTATCCTGATCATGCTCTGAtcagtatataggtA-------GGACCTATATACTGACCAATATTTCCTGGGATTAAG TGTTTTACACTTTTCAATTTTTATCCTGATCATGCTCTGA-------------AAATGGTGGGACCTATATACTGACCAATATTTCCTGGGATTAAG Template switch alignment (log-probability: -28.6) TGTTTTACACTTTgCAATTTTTATCCTGATCATGCTCTGA|TCAGTATATA|GGTaGGACCTATATACTGACCAATATTTCCTGGGATTAAG TGTTTTACACTTTTCAATTTTTATCCTGATCATGCTCTGA|TCAGTATATA|GGTGGGACCTATATACTGACCAATATTTCCTGGGATTAAG Gorilla > Human --------------- chr11:129120035-129120044 Template switch process: F1: L ATGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTGA 1 F3: 4 GGTAGGACCTATATACTGACCAATATTTCCTGGGATTAAGTAAC R RF: ATGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTGAAAATGGTGGGACCTATATACTGACCAATATTTCCTGGGATTAAGTAAC RR: TACAAAATGTGAAACGTTAAAAATAGGACTAGTACGAGACTTTTACCACCCTGGATATATGACTGGTTATAAAGGACCCTAATTCATTG F2: 3 ATATATGACT 2 Unidirectional alignment (log-probability: -39.3) TGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTG---ATcagtatataGGTaGGACCTATATACTGACCAATATTTCCTGGGATTAAG TGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTGAAAAT---------GGTGGGACCTATATACTGACCAATATTTCCTGGGATTAAG Template switch alignment (log-probability: -22.6) TGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTGA|TCAGTATATA|GGTaGGACCTATATACTGACCAATATTTCCTGGGATTAAG TGTTTTACACTTTGCAATTTTTATCCTGATCATGCTCTGA|TCAGTATATA|GGTGGGACCTATATACTGACCAATATTTCCTGGGATTAAG ========= Event 386 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAACAA-----TGTGTCCTGGTCCTGGATTTGG ↓ 3 2 1 4 Chimp: TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAAGAGCTTTCAGTGTCCTGGTCCTGGATTTGG Gorilla: TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAACAA-----TGTGTCCTGGTCCTGGATTTGG Human: TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAACAA-----TGTGTCCTGGTCCTGGATTTGG Cluster: [ ] Orangutan: Human > Chimp ------------- chr11:130000919-130000927 Template switch process: F1: L ATGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAA 1 F3: 4 GTGTCCTGGTCCTGGATTTGGGTCTGTACTCTTTACCTAG R RF: ATGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAACAATGTGTCCTGGTCCTGGATTTGGGTCTGTACTCTTTACCTAG RR: TACAGTTACTGTCCCTTCAAAATTTCGAGAGTGACTTTCTTGTTACACAGGACCAGGACCTAAACCCAGACATGAGAAATGGATC F2: 3 ACTTTCGAG 2 Unidirectional alignment (log-probability: -31.3) TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAAgagctttCA--GTGTCCTGGTCCTGGATTTGGGTCTGTACTCTTTACCTAG TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAA-------CAATGTGTCCTGGTCCTGGATTTGGGTCTGTACTCTTTACCTAG Template switch alignment (log-probability: -22.4) TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAA|GAGCTTTcA|GTGTCCTGGTCCTGGATTTGGGTCTGTACTCTTTACCTAG TGTCAATGACAGGGAAGTTTTAAAGCTCTCACTGAAAGAA|GAGCTTTAA|GTGTCCTGGTCCTGGATTTGGGTCTGTACTCTTTACCTAG ========= Event 387 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGATAAAATTTTAGGATGGTGTACTA---------GTCTTGTCTCTCTTAAAAATTATA Chimp: AGATAAAATTTTAGGATGGTGTACTA---------GTCTTGTCTCTCTTAAAAATTATA ↓ 3 1 42 Gorilla: AGATAAAATTTTAGGATGGTGTACTAAGACTAGTACACTTGTCTCTCTTAAAAATTATA ↑ 3 1 42 Human: AGATAAAATTTTAGGATGGTGTACTA---------GTCTTGTCTCTCTTAAAAATTATA Cluster: [ ] Orangutan: AGATAAAATTTTAGGATGGTGTACTA---------ACCTTGTCTCTCTTAAAAATTATA Human > Gorilla --------------- chr11:76381789-76381799 Template switch process: F1: L TCACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTA 1 F3: 4 CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA R RF: TCACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTAGTCTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA RR: AGTGATAGTTTTCTGTCTATTTTAAAATCCTACCACATGATCAGAACAGAGAGAATTTTTAATATACCAGGAATATATTTCGT F2: 3 ACATGATCAGA 2 Unidirectional alignment (log-probability: -33.6) CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACtaagacTAGTacaCTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTAC------TAGT---CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA Template switch alignment (log-probability: -17.1) CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTA|AGACTAGTACA|CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTA|AGACTAGTACA|CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA Chimp > Gorilla --------------- chr11:76381789-76381799 Template switch process: F1: L TCACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTA 1 F3: 4 CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA R RF: TCACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTAGTCTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA RR: AGTGATAGTTTTCTGTCTATTTTAAAATCCTACCACATGATCAGAACAGAGAGAATTTTTAATATACCAGGAATATATTTCGT F2: 3 ACATGATCAGA 2 Unidirectional alignment (log-probability: -33.6) CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACtaagacTAGTacaCTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTAC------TAGT---CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA Template switch alignment (log-probability: -17.1) CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTA|AGACTAGTACA|CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA CACTATCAAAAGACAGATAAAATTTTAGGATGGTGTACTA|AGACTAGTACA|CTTGTCTCTCTTAAAAATTATATGGTCCTTATATAAAGCA ========= Event 388 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATTTCATCTTCTATTGTTTT----GTACACAAACTCTGAAAAGCTTATTTGAATCTCTAT Chimp: AAATTTCATCTTCTATTGTTTT----GTACACAAACTCTGAGAAGCTTATTTGAATCTCTAT ↓ 1 4 3 2 Gorilla: AAATTTCATCTTCTATTGTTTCAGAGTTTCACGAACTCTGAAAAGCTTATTTGAATCTCTAT ↑ 1 4 3 2 Human: AAATTTCATCTTCTATTGTTTT----GTACACAAACTCTGAAAAGCTTATTTGAATCTCTAT Cluster: [ ] Orangutan: AAATTTCATCTTCTATTGTTTT----GTACACAAACTCTGAAAAGCTTATTTGAATCTCTAG Human > Gorilla --------------- chr1:138840920-138840927 Template switch process: F1: L TATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT 1 F3: 4 CACGAACTCTGAAAAGCTTATTTGAATCTCTATAACCATGATTG R RF: TATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTTTGTACACAAACTCTGAAAAGCTTATTTGAATCTCTATAACCATGATTG RR: ATACTCGTTACCAATGGTGGTTTAAAGTAGAAGATAACAAAACATGTGTTTGAGACTTTTCGAATAAACTTAGAGATATTGGTACTAAC F2: 3 TTTGAGAC 2 Unidirectional alignment (log-probability: -35.3) ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT------CAgagtttcacgAACTCTGAAAAGCTTATTTGAATCTCTATAACCATG ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTTTGTACACA----------AACTCTGAAAAGCTTATTTGAATCTCTATAACCATG Template switch alignment (log-probability: -22.4) ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT|CAGAGTTT|CACgAACTCTGAAAAGCTTATTTGAATCTCTATAACCATG ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT|CAGAGTTT|CACAAACTCTGAAAAGCTTATTTGAATCTCTATAACCATG Chimp > Gorilla --------------- chr1:138840920-138840927 Template switch process: F1: L TATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT 1 F3: 4 CACGAACTCTGAAAAGCTTATTTGAATCTCTATAACCATGATTGTCCACGTTA R RF: TATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTTTGTACACAAACTCTGAGAAGCTTATTTGAATCTCTATAACCATGATTGTCCACGTTA RR: ATACTCGTTACCAATGGTGGTTTAAAGTAGAAGATAACAAAACATGTGTTTGAGACTCTTCGAATAAACTTAGAGATATTGGTACTAACAGGTGCAAT F2: 3 TTTGAGAC 2 Unidirectional alignment (log-probability: -41) ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT------CAgagtttcacgAACTCTGAaAAGCTTATTTGAATCTCTATAACCATG ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTTTGTACACA----------AACTCTGAGAAGCTTATTTGAATCTCTATAACCATG Template switch alignment (log-probability: -28.1) ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT|CAGAGTTT|CACgAACTCTGAaAAGCTTATTTGAATCTCTATAACCATG ATGAGCAATGGTTACCACCAAATTTCATCTTCTATTGTTT|CAGAGTTT|CACAAACTCTGAGAAGCTTATTTGAATCTCTATAACCATG ========= Event 389 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGGGGCTCCAGAGATACAAAGG------------GTA-----------ACTCTGGGTTACCCTTTAACTGCTCCTAACTTG Chimp: TGGGGCTCCAGAGATACAAAGG------------GTA-----------ACTCCGGGTTACCCTTTAACTGCTCCTAACTTG ↑ 1 4 3 2 Gorilla: TGGGGCTCCAGAGATACAAAGTAAGGCCCTGTTAGTCACCTCTTTCTTGGTCCAGGTTACCCTTTAACTGCTCCTAACTTG ↓ 1 4 3 2 Human: TGGGGCTCCAGAGATACAAAGG------------GTA-----------ACTCTGGGTTACCCTTTAACTGCTCCTAACTTG Cluster: [ ] Orangutan: TGGGGCTCCAGAGATACAAAGTAAGGCCTTGTTAGTCACCTCTTTCTTGGTCTGTGTTACCCTTTAACTGCTCCTAACTTG Gorilla > Human --------------- chr1:160354802-160354807 Template switch process: F1: L AAAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAG 1 F3: 4 TCTGGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGGATAA R RF: AAAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAGTAAGGCCCTGTTAGTCACCTCTTTCTTGGTCCAGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGGATAA RR: TTTCACGGAGGATATCGACTACCCCGAGGTCTCTATGTTTCATTCCGGGACAATCAGTGGAGAAAGAACCAGGTCCAATGGGAAATTGACGAGGATTGAACTCCGGAACCTATT F2: 3 CAATGG 2 Unidirectional alignment (log-probability: -36.7) AAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAG---------------------------------ggtaactctgGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG AAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAGTAAGGCCCTGTTAGTCACCTCTTTCTTGGTCCA----------GGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG Template switch alignment (log-probability: -27.6) AAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAG|GGTAAC|TCtgGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG AAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAG|GGTAAC|TCCAGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG Gorilla > Chimp --------------- chr1:138498493-138498498 Template switch process: F1: L AAAGTGCCTCCTATAGCCGATGGGGCTCCAGAGATACAAAG 1 F3: 4 TCCGGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGGATAA R RF: AAAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAGTAAGGCCCTGTTAGTCACCTCTTTCTTGGTCCAGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGGATAA RR: TTTCACGGAGGATATCGACTACCCCGAGGTCTCTATGTTTCATTCCGGGACAATCAGTGGAGAAAGAACCAGGTCCAATGGGAAATTGACGAGGATTGAACTCCGGAACCTATT F2: 3 CAATGG 2 Unidirectional alignment (log-probability: -38.9) AAGTGCCTCCTATAGCcGATGGGGCTCCAGAGATACAAAG---------------------------GGtaacTCCgGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG AAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAGTAAGGCCCTGTTAGTCACCTCTTTCTTGG----TCCAGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG Template switch alignment (log-probability: -27.6) AAGTGCCTCCTATAGCcGATGGGGCTCCAGAGATACAAAG|GGTAAC|TCCgGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG AAGTGCCTCCTATAGCTGATGGGGCTCCAGAGATACAAAG|GGTAAC|TCCAGGTTACCCTTTAACTGCTCCTAACTTGAGGCCTTGG ========= Event 390 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAACTGA-GCCCAAAAGTTG---TGCCTGTAAAATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAGACATTCAGATTCCCTGGCCAGGAGAAACAGTAAGTAAATAAGAGCGTATCTGCTAAGGTGGCCACCACCATTCCTTTGTCCTAAAGCTCTGtaggagaagtccttgggtggtc Chimp: AAAAGTGAGTCCCAAAAGTTG---TGCCTGTAAAATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAGACATTCAGATTCCCTGGCCAGGAGAAACAGTAAGTAAATAAGAGCGTATCTGCTAAGGTGGCCACCACCATTCCTTTGTCCTAAAGCCCTGTAGGAGAAGTCCTTGGATGGTC ↓ 1 4 3 2 Gorilla: AAAAGTGAGTCCCAAAAGTTG------TTACAGAATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAGACATTCAGATTCCCTGGCCAGGAGAAACAGTAAGTAAATAAGAGCGTATCTGCTAAGGTGGCCACCACCATTCCTTTGTCCTAAAGCCCTGTAGGAGAAGTCCTTGGATGGTC Human: AAAACTGA-GCCCAAAAGTTG---TGCCTGTAAAATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAGACATTCAGATTCCCTGGCCAGGAGAAACAGTAAGTAAATAAGAGCGTATCTGCTAAGGTGGCCACCACCATTCCTTTGTCCTAAAGCTCTGtaggagaagtccttgggtggtc Cluster: [ ] Orangutan: AAAAGTGATTCCCAAAAGTTGTGC---CTGTAAAATTATTATAGAAATTGCCCCAGACTTCCAGAAATTGTAGACATTCAGATTCCCTGGGCAGGAGAAACAGTAAGTAAATAAGAGCGTATCTGTTAAGGTGGCCACCACCATTCCTTTGTCCTAAAGCCCTGTAGGAGAAGTCCTTGGCTGATC Chimp > Gorilla --------------- chr1:139474553-139474557 Template switch process: F1: L CTGGCATGGCAATATGTACAAAAAGTGAGTCCCAAAAGTTGT 1 F3: 4 AATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAG R RF: CTGGCATGGCAATATGTACAAAAAGTGAGTCCCAAAAGTTGTGCCTGTAAAATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAGACATTCAGATTCCCTGGCCAGGAGAAACAGTAAGTAAATAAGAGCGTATCTGCTAAGGTGGCCACCACCATTCCTTTGTCCTAAAGCCCTGTA RR: GACCGTACCGTTATACATGTTTTTCACTCAGGGTTTTCAACACGGACATTTTAATAATGTCTTTAACGGGGCCTGAAGGTCTTTAACATCTGTAAGTCTAAGGGACCGGTCCTCTTTGTCATTCATTTATTCTCGCATAGACGATTCCACCGGTGGTGGTAAGGAAACAGGATTTCGGGACAT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -26.8) GGCATGGCAATATGTACAAAAAGTGAGTCCCAAAAGTTGTtacaG-------AATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAG GGCATGGCAATATGTACAAAAAGTGAGTCCCAAAAGTTGT----GCCTGTAAAATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAG Template switch alignment (log-probability: -16.4) GGCATGGCAATATGTACAAAAAGTGAGTCCCAAAAGTTGT|TACAG|AATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAG GGCATGGCAATATGTACAAAAAGTGAGTCCCAAAAGTTGT|TACAG|AATTATTACAGAAATTGCCCCGGACTTCCAGAAATTGTAG ========= Event 391 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TAGGCAGTTAGACCCCAGGCCA------------------------------------------------------------------------------------------CGGTGATAGGGTGCTGATACCATGC ↑ 1 3 2 4 Chimp: TAGGCAGTTAGACCCCAGGCCC---------------------------------------------CTTGTACCGTGGCCCCAGGACATTGGAGGAAATAGGTGTTTAAGGCCATGATAGGGTGCTGATACCATGC Gorilla: TAGGCAGTTAAACCCCAGGCCCCTTGTACCGTGGCCCCAGGACATTGGAGGAAATAGGTGTTTGAGG---------------------------------------------CCATGATAGGGTGCTGATACCATGC ↓ 1 3 2 4 Human: TAGGCAGTTAGACCCCAGGCCA------------------------------------------------------------------------------------------CGGTGATAGGGTGCTGATACCATGC Cluster: [ ] Orangutan: TAGGCAGTTAAACCCCAGGCCCCTTGTACCGTGGCCCCAGGACATTGGAAGAAATAGGTGTTTGAGG---------------------------------------------CCATGACAGGGTGCTGATACCATGC Chimp > Human ------------- chr11:73068534-73068538 Template switch process: F1: L AAGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCCAGGCC 1 F3: 4 GATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG R RF: AAGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCCAGGCCCCTTGTACCGTGGCCCCAGGACATTGGAGGAAATAGGTGTTTAAGGCCATGATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG RR: TTCAGGGTCTTCTCCTTCGGATCCGTCAATCTGGGGTCCGGGGAACATGGCACCGGGGTCCTGTAACCTCCTTTATCCACAAATTCCGGTACTATCCCACGACTATGGTACGTCCCGTCCCGAGAACCAC F2: 3 TGGCA 2 Unidirectional alignment (log-probability: -27.9) AGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCC------------------------------------------------AGGCCAcggTGATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG AGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCCAGGCCCCTTGTACCGTGGCCCCAGGACATTGGAGGAAATAGGTGTTTAAGGCCA---TGATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG Template switch alignment (log-probability: -15.9) AGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCCAGGCC|ACGGT|GATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG AGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCCAGGCC|ACGGT|GATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG Gorilla > Human --------------- chr11:73068534-73068538 Template switch process: F1: L AAGTCCCAGAAGAGGAAGCCTAGGCAGTTAGACCCCAGGCC 1 F3: 4 GATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG R RF: AAGTCCCGGAAGAGGAAGCCTAGGCAGTTAAACCCCAGGCCCCTTGTACCGTGGCCCCAGGACATTGGAGGAAATAGGTGTTTGAGGCCATGATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG RR: TTCAGGGCCTTCTCCTTCGGATCCGTCAATTTGGGGTCCGGGGAACATGGCACCGGGGTCCTGTAACCTCCTTTATCCACAAACTCCGGTACTATCCCACGACTATGGTACGTCCCGTCCCGAGAACCAC F2: 3 TGGCA 2 Unidirectional alignment (log-probability: -38.5) AGTCCCaGAAGAGGAAGCCTAGGCAGTTAgACCCC------------------------------------------------AGGCCAcggTGATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG AGTCCCGGAAGAGGAAGCCTAGGCAGTTAAACCCCAGGCCCCTTGTACCGTGGCCCCAGGACATTGGAGGAAATAGGTGTTTGAGGCCA---TGATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG Template switch alignment (log-probability: -27.4) AGTCCCaGAAGAGGAAGCCTAGGCAGTTAgACCCCAGGCC|ACGGT|GATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG AGTCCCGGAAGAGGAAGCCTAGGCAGTTAAACCCCAGGCC|ACGGT|GATAGGGTGCTGATACCATGCAGGGCAGGGCTCTTGGTG ========= Event 392 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: ATTGGGATTTTGGAGAGCTTTCCCTAGCAAAGCAGGGAATGCTgcagtgtgatgttatg ↓ 4 31 2 Chimp: ATTGGGATTTTGGAGAGCTTTCCCT-GCTTTGCT-AGTTTGCTgcagtgtgatgttatg Gorilla: ATTGGGATTTTGGAGAGCTTTCCCT-GCTTTGCA-AGTTTGCTgcagtgtgatgttatg Human: ATTGGGATTTTGGAGAGCTTTCCCTAGCAAAGCAGGGAATGCTgcagtgtgatgttatg Cluster: [ ] Orangutan: ATTGGGATTTTGGAGAACTTTCCCT-GCTTTGCT-AGTTTGCTgcagtgtgattttatg Human > Chimp ------------- chr1:146763861-146763870 Template switch process: F1: L GTTGTTAAATATGCTAATTGGGATTTTGGAGAGCTTTCCCT 1 F3: 4 TT------------------TGCTGCAGTGTGATGTTATGGAATGACCATCATTAGACTT R RF: GTTGTTAAATATGCTAATTGGGATTTTGGAGAGCTTTCCCTAGCAAAGCAGGGAATGCTGCAGTGTGATGTTATGGAATGACCATCATTAGACTT RR: CAACAATTTATACGATTAACCCTAAAACCTCTCGAAAGGGATCGTTTCGTCCCTTACGACGTCACACTACAATACCTTACTGGTAGTAATCTGAA F2: 3 GATCGTTTCG 2 Unidirectional alignment (log-probability: -39.1) TTGTTAAATATGCTAATTGGGATTTTGGAGAGCTTTCCCT--------------gctttgctagttTGCTGCAGTGTGATGTTATGGAATGACCATCATTAGAC TTGTTAAATATGCTAATTGGGATTTTGGAGAGCTTTCCCTAGCAAAGCAGGGAA------------TGCTGCAGTGTGATGTTATGGAATGACCATCATTAGAC Template switch alignment (log-probability: -27.7) TTGTTAAATATGCTAATTGGGATTTTGGAGAGCTTTCCCT|GCTTTGCTAG|TT------------------TGCTGCAGTGTGATGTTATGGAATGACCATCATTAGAC TTGTTAAATATGCTAATTGGGATTTTGGAGAGCTTTCCCT|GCTTTGCTAG|TTCCCTAGCAAAGCAGGGAATGCTGCAGTGTGATGTTATGGAATGACCATCATTAGAC ========= Event 393 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAACACGAAACCCTTGATCTGTTAGTCACTGACTAACAAGTCAAGTGACTTGACTGCAATCGAA ↑ 3 4 21 Chimp: CAACACGAAACCCTTGATCTGTTAG---------------TCAAGTGACTTGGCTGCAATCGAA Gorilla: CAACACGAAACCCTTGATCTGTTAG---------------TCAAGTGACTTGACTGCAATCGAA Human: CAACACGAAACCCTTGATCTGTTAGTCACTGACTAACAAGTCAAGTGACTTGACTGCAATCGAA Cluster: [ ] Orangutan: CAACACGAAACCCTTGATCTGTTAG---------------TCAAGTGACTTGACTGCAATCGAA Chimp > Human ------------- chr1:83887576-83887584 Template switch process: F1: L ATGGCATTGCCTGCAGCAACACGAAACCCTTGATCTGTTAGTCAC 1 F3: 4 AGTCAAGTGACTTGACTGCAATCGAACTCACCGGATGGGCCT R RF: ATGGCATTGCCTGCAGCAACACGAAACCCTTGATCTGTTAGTCAAGTGACTTGGCTGCAATCGAACTCACCGGATGGGCCT RR: TACCGTAACGGACGTCGTTGTGCTTTGGGAACTAGACAATCAGTTCACTGAACCGACGTTAGCTTGAGTGGCCTACCCGGA F2: 3 ACAATCAGT 2 Unidirectional alignment (log-probability: -38.5) ATTGCCTGCAGCAACACGAAACCCTTGATCTGTTAGTcactgactaacaagtCAAGTGACTTGaCTGCAATCGAACTCACCGGATGGGC ATTGCCTGCAGCAACACGAAACCCTTGATCTGTTAGT---------------CAAGTGACTTGGCTGCAATCGAACTCACCGGATGGGC Template switch alignment (log-probability: -28.5) ATTGCCTGCAGCAACACGAAACCCTTGATCTGTTAGTCAc|TGACTAACA|AGTCAAGTGACTTGaCTGCAATCGAACTCACCGGATGGGC ATTGCCTGCAGCAACACGAAACCCTTGATCTGTTAGTCAA|TGACTAACA|AGTCAAGTGACTTGGCTGCAATCGAACTCACCGGATGGGC ========= Event 394 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCAGTACATGGTGCAT-ATAACGA-GCTGTTACAGCTCGTTATTATGATTCACGGGACAC Chimp: CCCAGTACATGGTGCAT-ATAGGGACTCAATAACAGCTTGTTATTATGATTCACGGGACAC Gorilla: CCCAGTACATGGTGCAT-ATAGGGACTCAATAACAGCTCGTTATTATGATTCACGGGACAC ↓ 1 34 2 Human: CCCAGTACATGGTGCAT-ATAACGA-GCTGTTACAGCTCGTTATTATGATTCACGGGACAC Cluster: [ ] Orangutan: cccagtacatggtgcatagtagggactcaataacagctcgttattatGATTCATGGGACAC Gorilla > Human --------------- chr1:83949319-83949328 Template switch process: F1: L GATAACTTATGAAGCACCGAACCCAGTACATGGTGCATATA 1 F3: 4 ACAGCTCGTTATTATGATTCACGGGACACGCTGCCAAAGT R RF: GATAACTTATGAAACACCGAACCCAGTACATGGTGCATATAGGGACTCAATAACAGCTCGTTATTATGATTCACGGGACACACTGCCAAAGT RR: CTATTGAATACTTTGTGGCTTGGGTCATGTACCACGTATATCCCTGAGTTATTGTCGAGCAATAATACTAAGTGCCCTGTGTGACGGTTTCA F2: 3 TTGTCGAGCA 2 Unidirectional alignment (log-probability: -45.1) ATAACTTATGAAgCACCGAACCCAGTACATGGTGCATATA----------AcgagctgttACAGCTCGTTATTATGATTCACGGGACACgCTGCCAAAGT ATAACTTATGAAACACCGAACCCAGTACATGGTGCATATAGGGACTCAATA---------ACAGCTCGTTATTATGATTCACGGGACACACTGCCAAAGT Template switch alignment (log-probability: -28) ATAACTTATGAAgCACCGAACCCAGTACATGGTGCATATA|ACGAGCTGTT|ACAGCTCGTTATTATGATTCACGGGACACgCTGCCAAAGT ATAACTTATGAAACACCGAACCCAGTACATGGTGCATATA|ACGAGCTGTT|ACAGCTCGTTATTATGATTCACGGGACACACTGCCAAAGT ========= Event 395 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGAGAGTGAGGGTGAGCTC----AGACTTCTAGGTGAAAATAGCCCTCTTAGTTCTATTA Chimp: AAAGAGAGTGAGGGTGAGCTC----AGACTTCTAGGTGA-AATAGCCCTCTTAGTTCTATTA ↓ 1 3 2 4 Gorilla: AAAGAGAGTGAGGGTGAGCTC--------ACCTAGAAGA-ACTAGCCCTCTTAGTTCTATTA ↑ 1 3 2 4 Human: AAAGAGAGTGAGGGTGAGCTC----AGACTTCTAGGTGAAAATAGCCCTCTTAGTTCTATTA Cluster: [ ] Orangutan: AAAGAGGGTGAGGGTGAGCTCAGAC----TTCTTGGTGA-AATAGCCCTCTTAGTTCTATTA Human > Gorilla --------------- chr11:73527393-73527400 Template switch process: F1: L CCTAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCA 1 F3: 4 AACTAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGAAAG R RF: CCTAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCAGACTTCTAGGTGAAAATAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGAAAG RR: GGATCCTAGACGGAGGTAACTTTCTCTCACTCCCACTCGAGTCTGAAGATCCACTTTTATCGGGAGAATCAAGATAATTACCCCCTCCACTCCCTTTC F2: 3 GAAGATCC 2 Unidirectional alignment (log-probability: -36.9) TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCacctagaAG------------AAcTAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGA TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTC-------AGACTTCTAGGTGAAAATAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGA Template switch alignment (log-probability: -22.4) TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCA|CCTAGAAG|AAcTAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGA TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCA|CCTAGAAG|AAATAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGA Chimp > Gorilla --------------- chr11:73527393-73527399 Template switch process: F1: L CCTAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCA 1 F3: 4 GAACTAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGAAAG R RF: CCTAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCAGACTTCTAGGTGAAATAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGGAAAG RR: GGATCCTAGACGGAGGTAACTTTCTCTCACTCCCACTCGAGTCTGAAGATCCACTTTATCGGGAGAATCAAGATAATTACCCCCTCCACTCCCTTTC F2: 3 AAGATCC 2 Unidirectional alignment (log-probability: -33.3) TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCAc----CTAGaaGAAcTAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGG TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCAGACTTCTAGGTGAAATAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGG Template switch alignment (log-probability: -22.3) TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCA|CCTAGAA|GAAcTAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGG TAGGATCTGCCTCCATTGAAAGAGAGTGAGGGTGAGCTCA|CCTAGAA|GAAATAGCCCTCTTAGTTCTATTAATGGGGGAGGTGAGGG ========= Event 396 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAGCGCGACTCAGAGAGGCC----------TTGACACCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACACCTCCACAGTCTCCCCGGAGGAAAGGCCGCACATAGAATTTCAGTCAGGTCTTCTCTCTTTTCTTGC ↑ 1 4 3 2 Chimp: AAAGCGCGACTCAGAGAGGCCTCTGGCTCTCTCAAAGCCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACACCTCCACAGTCTCCCTGGAGGAAAGGCCGCTCATAGAATTTCTGTCAGGTCTTCTCTCTTTTCTTGC Gorilla: AAAGTGCGACTCAGGGAGGCC----------TCGACACCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACACCTCCACAGTCTCCCCAGAGGAAAGGCCGCTCACAGATTTTCAGTCAGGTCTTCTCTCTTTTCTTGC Human: AAAGCGCGACTCAGAGAGGCC----------TTGACACCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACACCTCCACAGTCTCCCCGGAGGAAAGGCCGCACATAGAATTTCAGTCAGGTCTTCTCTCTTTTCTTGC Cluster: [ ] Orangutan: AAGGCGCGACTCAGAGAGGCC----------TCGACACCGAGGGCTGCGATGGTGCTTGTGCTGCCTGAGGGGACACCTCCACAGCCTCCCCGGAGGAAAGGCCGCTCATAGAATTTCAGTTAGGTCTTCTCTCTCTTCTTGC Chimp > Human ------------- chr1:81439824-81439828 Template switch process: F1: L GAAACGAGGTACGGTAAGGCAAAGCGCGACTCAGAGAGGCCT 1 F3: 4 CCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACAC R RF: GAAACGAGGTACGGTAAGGCAAAGCGCGACTCAGAGAGGCCTCTGGCTCTCTCAAAGCCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACACCTCCACAGTCTCCCTGGAGGAAAGGCCGCTCATAGAATTTCTGTCA RR: CTTTGCTCCATGCCATTCCGTTTCGCGCTGAGTCTCTCCGGAGACCGAGAGAGTTTCGGCTCCCGACGCTACCACGAAAACGACGGACTCCCCTGTGGAGGTGTCAGAGGGACCTCCTTTCCGGCGAGTATCTTAAAGACAGT F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -29.1) AACGAGGTACGGTAAGGCAAAGCGCGACTCAGAGAGGCCTtgaca---------------CCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACAC AACGAGGTACGGTAAGGCAAAGCGCGACTCAGAGAGGCCT-----CTGGCTCTCTCAAAGCCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACAC Template switch alignment (log-probability: -15.9) AACGAGGTACGGTAAGGCAAAGCGCGACTCAGAGAGGCCT|TGACA|CCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACAC AACGAGGTACGGTAAGGCAAAGCGCGACTCAGAGAGGCCT|TGACA|CCGAGGGCTGCGATGGTGCTTTTGCTGCCTGAGGGGACAC ========= Event 397 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTCTTCTTTCATAACAATCTTGTTACAAATTCAGGC----AATTTTGTCCTTCCAAAAATCT ↓ 3 2 1 4 Chimp: GCTCTTCTTTCATAACAATCTTGTTACAAATTCTGTAACAAGATTTTGTCCTTCCAAAAATCT ↑ 3 2 1 4 Gorilla: GCTCTTCTTTCATAACAATCTTGTTACAAATTCAGGC----AATTTTGTCCTTCCAAAAATCT Human: GCTCTTCTTTCATAACAATCTTGTTACAAATTCAGGC----AATTTTGTCCTTCCAAAAATCT Cluster: [ ] Orangutan: GTTCTTCTTTCATAACAATCTTGTTACAAATTGAGGC----AATTTTGTCCTTCCA-AAATCT Human > Chimp ------------- chr1:82923183-82923191 Template switch process: F1: L CAGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC 1 F3: 4 ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG R RF: CAGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTCAGGCAATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG RR: GTCTTGTACGAGAAGAAAGTATTGTTAGAACAATGTTTAAGTCCGTTAAAACAGGAAGGTTTTTAGACAAAATTTTGGAAGAAGAC F2: 3 GAACAATGT 2 Unidirectional alignment (log-probability: -31.4) AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTCtgtaacaAG---ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC-------AGGCAATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG Template switch alignment (log-probability: -16.4) AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC|TGTAACAAG|ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC|TGTAACAAG|ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG Gorilla > Chimp --------------- chr1:82923183-82923191 Template switch process: F1: L CAGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC 1 F3: 4 ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG R RF: CAGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTCAGGCAATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG RR: GTCTTGTACGAGAAGAAAGTATTGTTAGAACAATGTTTAAGTCCGTTAAAACAGGAAGGTTTTTAGACAAAATTTTGGAAGAAGAC F2: 3 GAACAATGT 2 Unidirectional alignment (log-probability: -30.9) AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTCtgtaacaAG---ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC-------AGGCAATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG Template switch alignment (log-probability: -16.9) AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC|TGTAACAAG|ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG AGAACATGCTCTTCTTTCATAACAATCTTGTTACAAATTC|TGTAACAAG|ATTTTGTCCTTCCAAAAATCTGTTTTAAAACCTTCTTCTG ========= Event 398 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCTTTCCGTCATGGTCCCATGAGAATTCAGAC Chimp: TACTCTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCTTTCCGTCATGGTCCCATGAGAATTCAGAC Gorilla: TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCA-------TTGGTCCCATGAGAATTCAGAC ↓ 3 2 1 4 Human: TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCTTTCCGTCATGGTCCCATGAGAATTCAGAC Cluster: [ ] Orangutan: TACTGTCCCCTCCCAGGGCTGATGGAAAGCATTCCAGGGCA-------TTGGTCCCATAAGAATTCAGAC Gorilla > Human --------------- chr1:81289833-81289841 Template switch process: F1: L TTACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGC 1 F3: 4 TGGTCCCATGAGAATTCAGACCTGTGTGTGGGGAGTGGCA R RF: TTACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCATTGGTCCCATGAGAATTCAGACCTGTGTGTGGGGAGTGGCA RR: AATGACAGGGGAGGGTCCCGACTGCCTTTCGTAAGGTCCCGTAACCAGGGTACTCTTAAGTCTGGACACACACCCCTCACCGT F2: 3 ACTGCCTTT 2 Unidirectional alignment (log-probability: -26.5) TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCtTtccgtcaTGGTCCCATGAGAATTCAGACCTGTGTGTGGGGAGTGGCA TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGCAT-------TGGTCCCATGAGAATTCAGACCTGTGTGTGGGGAGTGGCA Template switch alignment (log-probability: -16.9) TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGC|TTTCCGTCA|TGGTCCCATGAGAATTCAGACCTGTGTGTGGGGAGTGGCA TACTGTCCCCTCCCAGGGCTGACGGAAAGCATTCCAGGGC|TTTCCGTCA|TGGTCCCATGAGAATTCAGACCTGTGTGTGGGGAGTGGCA ========= Event 399 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAGACCAGTCAAGCTCTAGGGAC------ATCATGTATGCAACTTTTGAAATTTATTACCTC Chimp: GGAAGACCAGTCAAGCTCTAGGGAC------ATCATGTATGCAACTTTTGAAATTTATTACCTC ↓ 1 43 2 Gorilla: GGAAGACCAGTCAAGCTCTAGTTGCATACAAGTCATGTATGCAACTTTTGAAATTTATTACCTC ↑ 1 43 2 Human: GGAAGACCAGTCAAGCTCTAGGGAC------ATCATGTATGCAACTTTTGAAATTTATTACCTC Cluster: [ ] Orangutan: GGAAGACCAGTCAAACTCTAGGGAC------ATCATGTATGCAACTTTTGAAATTTATTACCTC Human > Gorilla --------------- chr1:82373436-82373446 Template switch process: F1: L TTTACGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAG 1 F3: 4 TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA R RF: TTTATGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAGGGACATCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA RR: AAATACTAAGTAACAAAGCACCTTCTGGTCAGTTCGAGATCCCTGTAGTACATACGTTGAAAACTTTAAATAATGGAGAGGTCTTT F2: 3 GAACATACGTT 2 Unidirectional alignment (log-probability: -40.7) TTAcGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAGttgcatacaaG----TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA TTATGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAG----------GGACATCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA Template switch alignment (log-probability: -28.2) TTAcGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAG|TTGCATACAaG|TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA TTATGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAG|TTGCATACATG|TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA Chimp > Gorilla --------------- chr1:82373436-82373446 Template switch process: F1: L TTTACGATTCATTGTTTCGTGGAAGACCAGTCAAGCTCTAG 1 F3: 4 TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA R RF: TTTACGATTCATTGTTTCATGGAAGACCAGTCAAGCTCTAGGGACATCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA RR: AAATGCTAAGTAACAAAGTACCTTCTGGTCAGTTCGAGATCCCTGTAGTACATACGTTGAAAACTTTAAATAATGGAGAGGTCTTT F2: 3 GAACATACGTT 2 Unidirectional alignment (log-probability: -40.7) TTACGATTCATTGTTTCgTGGAAGACCAGTCAAGCTCTAGttgcatacaaG----TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA TTACGATTCATTGTTTCATGGAAGACCAGTCAAGCTCTAG----------GGACATCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA Template switch alignment (log-probability: -28.2) TTACGATTCATTGTTTCgTGGAAGACCAGTCAAGCTCTAG|TTGCATACAaG|TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA TTACGATTCATTGTTTCATGGAAGACCAGTCAAGCTCTAG|TTGCATACATG|TCATGTATGCAACTTTTGAAATTTATTACCTCTCCAGAAA ========= Event 400 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 56 Detected in comparisons: 56 Multiple sequence alignment: Human: tggatgcagagcacataccgtagaagaaagacatcgggcttccatcaacgtgaaaatgttctg Chimp: TGGATGCAGAGCACATACCGTAGAAGAAAGACATCGGGCTTCCATCAACGTGAAAATGTTCTG ↓ 1 3 4 2 ↑ 13 24 Gorilla: TGGATGCAGAGCACATACCGTGGAAGCCCGACGTCTTTCTTCCATCAACGTGAAAATGTTCTG Human: tggatgcagagcacataccgtagaagaaagacatcgggcttccatcaacgtgaaaatgttctg Cluster: [ ] Orangutan: tggatgcagagcacataccatagaagaa--acattgggcttccatcaaagtgaaaatgttctg Gorilla > Chimp --------------- chr11:68479336-68479347 Template switch process: F1: L GGGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTAGAAG 1 F3: 4 CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC R RF: GGGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTGGAAGCCCGACGTCTTTCTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC RR: CCCTACCCGCTTCCGACGAAACCTACGTCTCGTGTATGGCACCTTCGGGCTGCAGAAAGAAGGTAGTTGCACTTTTACAAGACGAGAACTTTTACCTG F2: 3 GGGCTACAGAAA 2 Unidirectional alignment (log-probability: -43) GGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTagaagaaagacatcgGG---------------CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC GGCGAAGGCTGCTTTGGATGCAGAGCACATACCGT---------------GGAAGCCCGACGTCTTTCTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC Template switch alignment (log-probability: -28.4) GGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTaGAAG|AAAGACaTCGGG|CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC GGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTGGAAG|AAAGACGTCGGG|CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC Chimp > Gorilla --------------- chr11:67905274-67905290 Template switch process: F1: L GGGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGT 1 F3: 4 CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC R RF: GGGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTAGAAGAAAGACATCGGGCTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC RR: CCCTACCCGCTTCCGACGAAACCTACGTCTCGTGTATGGCATCTTCTTTCTGTAGCCCGAAGGTAGTTGCACTTTTACAAGACGAGAACTTTTACCTG F2: 3 TTTCTGCAGCCCGAAGG 2 Unidirectional alignment (log-probability: -43) GGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGT---------------GGaagcccgacgtctttCTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC GGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGTAGAAGAAAGACATCGGG---------------CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC Template switch alignment (log-probability: -23.4) GGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGT|GGAAGCCCGAcGTCTTT|CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC GGATGGGCGAAGGCTGCTTTGGATGCAGAGCACATACCGT|GGAAGCCCGATGTCTTT|CTTCCATCAACGTGAAAATGTTCTGCTCTTGAAAATGGAC ========= Event 401 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCAAGAGGTGAAATACAGAAAGCCTTTTTTTCTTGATCTTT-----------------------TCCCGAGATTCAAATCTCCGATTCCCATTTGGGGGCAAGTTTTTTTCTTCACCTTCAATATGAGAATTCAGCGAACTTGAAAGAAAAATCATCTGTG Chimp: CTCAAGAGGTGAAATACAGAACCCCtttttttCTTGATCTTT-----------------------TCCCGAGACTCAAATCTCCGATTCCCATTTGGGGGCAAGtttttttCTTCACCTTCAATATGAGAATTCAGCGAACTTGAAAGAAAAATCATCTGTG ↓ 4 1 3 2 Gorilla: CTCAAGAGGTGAAATACAGAAAGCCtttttttcttgatcttttcccagttcttttcttgatcttttcCTGAGATTCAAATCTCCGATTCCCATTTGGAGGCAAGtttttttCTCCACCTTCAATATGAAAATTCAGCGAACTTGAAAGAAAAATCATCTGTG Human: CTCAAGAGGTGAAATACAGAAAGCCTTTTTTTCTTGATCTTT-----------------------TCCCGAGATTCAAATCTCCGATTCCCATTTGGGGGCAAGTTTTTTTCTTCACCTTCAATATGAGAATTCAGCGAACTTGAAAGAAAAATCATCTGTG Cluster: [] Orangutan: Chimp > Gorilla --------------- chr11:62913262-62913266 Template switch process: F1: L TCAGTCTGGGGGGGAACATTCTCAAGAGGTGAAATACAGAAAGCCTTTTTTTCTTGATCTTTTCCC 1 F3: 4 TTTTCTTGATCT R RF: TCAGTCTGGGGGGGAACATTCTCAAGAGGTGAAATACAGAACCCCTTTTTTTCTTGATCTTTTCCCTTTCCCGAGACTCAAATCTCCGATTCCCATTTGGGGGCAAGTTTTTTTCTTCACCTTCAATATGAGAATTCAGCGAACT RR: AGTCAGACCCCCCCTTGTAAGAGTTCTCCACTTTATGTCTTGGGGAAAAAAAGAACTAGAAAAGGGAAAGGGCTCTGAGTTTAGAGGCTAAGGGTAAACCCCCGTTCAAAAAAAGAAGTGGAAGTTATACTCTTAAGTCGCTTGA F2: 3 CTTGA 2 Unidirectional alignment (log-probability: -48.8) AGGTGAAATACAGAAagCCTTTTTTTCTTGATCTTTtcccagttcttttcttgatct AGGTGAAATACAGAACCCCTTTTTTTCTTGATCTTT--------------------- Template switch alignment (log-probability: -27.3) AGGTGAAATACAGAAagCCTTTTTTTCTTGATCTTTTCCC|AGTTC|TTTTCTTGATCT AGGTGAAATACAGAACCCCTTTTTTTCTTGATCTTTTCCC|AGTTC|TTTTCTTGATCT ========= Event 402 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATCCTCTGGCCTCCCACAGGGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACAGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGAGGGCCCCCATGCCGGGGTCCCAGGCAGAGGTGCTGGA ↑ 3 2 4 1 Chimp: AACCTCTGGCCTCCCACAGGGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACA---------------GGGGTCCCAGGCAGAGGTGCTGGA ↓ 3 2 4 1 Gorilla: ATCCTCTGGCCTCCCACAGGGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGAGGGCCCCCATGCCGGGGTCCCAGGCAGAGGTGCTGGA Human: ATCCTCTGGCCTCCCACAGGGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACAGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGAGGGCCCCCATGCCGGGGTCCCAGGCAGAGGTGCTGGA Cluster: [ ] Orangutan: ATCCTCTGTCCTCCCACAGGGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACAGCCCTTTGAGTTACCTCGGGAGATTGTCAACAGAGGGCCCCCATGCCGGGGTCCCAGGCAGAGGTGCTGGA Chimp > Human ------------- chr11:64843249-64843259 Template switch process: F1: L TGAGTCACAGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGAGG 1 F3: 4 GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG R RF: GGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG RR: CCGTACCCCCGAGGCCCGTCCTCGTCCCTGTTCATCTCTGTTCGTCCTCTCCTTACTCAGTGCCGGGAAACTCAATGGAACCCTCTAACAGTTGTCCCCAGGGTCCGTCTCCACGACCTCCGTCAGTCCCTCCTC F2: 3 CCGTACCCCCG 2 Unidirectional alignment (log-probability: -38.5) CACaGCCCTTTGAGTTACCTTGGGAGATTGTCAACAgagggcccccatgccGGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG CACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACA---------------GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG Template switch alignment (log-probability: -28.7) CACaGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGaGG|GCCCCCATGCC|GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG CACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGGGG|GCCCCCATGCC|GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG Chimp > Gorilla --------------- chr11:64023718-64023728 Template switch process: F1: L TGAGTCACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGAGG 1 F3: 4 GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG R RF: GGCATGGGGGCTCCGGGCAGGAGCAGGGACAAGTAGAGACAAGCAGGAGAGGAATGAGTCACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG RR: CCGTACCCCCGAGGCCCGTCCTCGTCCCTGTTCATCTCTGTTCGTCCTCTCCTTACTCAGTGCCGGGAAACTCAATGGAACCCTCTAACAGTTGTCCCCAGGGTCCGTCTCCACGACCTCCGTCAGTCCCTCCTC F2: 3 CCGTACCCCCG 2 Unidirectional alignment (log-probability: -32.5) CACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAgagggcccccatgccGGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG CACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACA---------------GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG Template switch alignment (log-probability: -22.7) CACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGaGG|GCCCCCATGCC|GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG CACGGCCCTTTGAGTTACCTTGGGAGATTGTCAACAGGGG|GCCCCCATGCC|GGGGTCCCAGGCAGAGGTGCTGGAGGCAGTCAGGGAGGAG ========= Event 403 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTGTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGACCCAAGCTCCCGGCACTCCTTCGCCCACAGCCTTCATGCCAAGGCACCCTTCTCAGCTCCGCCGCAGTAGGAGCAC ↓ 4 1 3 2 Chimp: TGGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGCT------GAGAAGGCCTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGACCCAAGCTCCCGGCACTCCTTCACCCACAGCCTTCATGCCAAGGCACCCTTCTCAGCTCCGCCGCAGTAGGAGCAC Gorilla: CGGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGCT------GAGAAGGCCTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGACCCAAGCTCCCGGCACTCCTTCGCCCACAGCCTTCATGCCAAGGCACCCTTCTCAGCTCCGCCGCAGTAGGAGCAC ↑ 1 4 3 2 Human: TGGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTGTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGACCCAAGCTCCCGGCACTCCTTCGCCCACAGCCTTCATGCCAAGGCACCCTTCTCAGCTCCGCCGCAGTAGGAGCAC Cluster: [ ] Orangutan: CGGGAGAGAAACAGAGGGTGGCCTGTGTGTGTCTCAGGAGGGCT------GAGAAGGCCTCCACAGTAATGACCCAACAGGGGCAAAGATCTGTCTGACCCAAGCTCCTGGCACTCCTTCGCCCACAGCCTTCATGCCAAGGCACCCTTCTCAGCTCCGCCGCAGTAGGAGCAC Human > Chimp ------------- chr11:64904692-64904698 Template switch process: F1: L GGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGG 1 F3: 4 GGCC------------------------------------TCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGAC R RF: GGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTGTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGACCCAAGCTCCCGGCACTCCTTCGCCCACAGCCTTCATGCCAAGGCACCCTTCTCAG RR: CCCTCTCTTTGTCTCCCACCGGAGACACACAGAGTCCTCCCTGTGTGTAATGACACACAGGTGTCATTACTGGGTTGTCCCCGTTTCCAGACAGACTGGGTTCGAGGGCCGTGAGGAAGCGGGTGTCGGAAGTACGGTTCCGTGGGAAGAGTC F2: 3 AAGAGTC 2 Unidirectional alignment (log-probability: -37.8) GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGG-----------------GctgagaaggccTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTC GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTG-----------TCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTC Template switch alignment (log-probability: -28.3) GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGG|CTGAGAA|GGCC------------------------------------TCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTC GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGG|CTGAGAA|GGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTGTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTC Human > Gorilla --------------- chr11:64050846-64050853 Template switch process: F1: L GGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGG 1 F3: 4 GCCTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGAC R RF: GGGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTGTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCTGACCCAAGCTCCCGGCACTCCTTCGCCCACAGCCTTCATGCCAAGGCACCCTTCTCAG RR: CCCTCTCTTTGTCTCCCACCGGAGACACACAGAGTCCTCCCTGTGTGTAATGACACACAGGTGTCATTACTGGGTTGTCCCCGTTTCCAGACAGACTGGGTTCGAGGGCCGTGAGGAAGCGGGTGTCGGAAGTACGGTTCCGTGGGAAGAGTC F2: 3 GAAGAGTC 2 Unidirectional alignment (log-probability: -37.3) GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGG-----------------GctgagaaggccTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCT GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGGACACACATTACTGTGTG-----------TCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCT Template switch alignment (log-probability: -27.9) GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGG|CTGAGAAG|GccTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCT GGAGAGAAACAGAGGGTGGCCTCTGTGTGTCTCAGGAGGG|CTGAGAAG|GTGTCCACAGTAATGACCCAACAGGGGCAAAGGTCTGTCT ========= Event 404 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTCTCAGCCCACACTCACTGATGAGTCATCATCCAGCCCTCACCATCCCTA ↑ 3 1 4 2 Chimp: CCTCTCAGCCCACACTCACTGA------CTCATCCAGCCCTCACCATCCCTA Gorilla: CCTCTCAGCCCACACTCACTGA------CTCATCCAGCCCTCACCATCCCTA Human: CCTCTCAGCCCACACTCACTGATGAGTCATCATCCAGCCCTCACCATCCCTA Cluster: [ ] Orangutan: Chimp > Human ------------- chr11:62472548-62472554 Template switch process: F1: L CCAAATCTCCTCCTTCCCGCCTCTCAGCCCACACTCACTGA 1 F3: 4 TCATCCAGCCCTCACCATCCCTATGAAGTCAACCCTCAAA R RF: CCAAACCTCCTCCTTCCCGCCTCTCAGCCCACACTCACTGACTCATCCAGCCCTCACCATCCCTATGAAGTCAACCCTCAAA RR: GGTTTGGAGGAGGAAGGGCGGAGAGTCGGGTGTGAGTGACTGAGTAGGTCGGGAGTGGTAGGGATACTTCAGTTGGGAGTTT F2: 3 ACTGAGT 2 Unidirectional alignment (log-probability: -31.5) CAAAtCTCCTCCTTCCCGCCTCTCAGCCCACACTCACTGAtgagtcaTCATCCAGCCCTCACCATCCCTATGAAGTCAACCCTCAAA CAAACCTCCTCCTTCCCGCCTCTCAGCCCACACTCACTGA------CTCATCCAGCCCTCACCATCCCTATGAAGTCAACCCTCAAA Template switch alignment (log-probability: -22.1) CAAAtCTCCTCCTTCCCGCCTCTCAGCCCACACTCACTGA|TGAGTCA|TCATCCAGCCCTCACCATCCCTATGAAGTCAACCCTCAAA CAAACCTCCTCCTTCCCGCCTCTCAGCCCACACTCACTGA|TGAGTCA|TCATCCAGCCCTCACCATCCCTATGAAGTCAACCCTCAAA ========= Event 405 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ttattgaCCACTTCTTTCATGTTATTTGTCTGCACCTCTCCGGTCAT-----GATTTCCAA-----ATCTTCTTCTGGATTTATCGGA Chimp: ttattgaCCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCAT-----GATTTCCAA-----ATCTTCTTCTGGATTTATCGGA ↓ 3 2 1 4 Gorilla: TTATTGACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCAG----------ACAAATAACTTCTTCTTCTGGATTTATCAGA Human: ttattgaCCACTTCTTTCATGTTATTTGTCTGCACCTCTCCGGTCAT-----GATTTCCAA-----ATCTTCTTCTGGATTTATCGGA Cluster: [ ] Orangutan: TTATTGACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCAGGTCATGATTT-----CCAA-----ATCTTCTTCTGGATTTATCAGA Chimp > Gorilla --------------- chr1:83906235-83906245 Template switch process: F1: L GACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCA 1 F3: 4 TCTTCTTCTGGATTTATCAGACCTGTTGGTGTTGAACATA R RF: GACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCATGATTTCCAAATCTTCTTCTGGATTTATCGGACCTGTTGGTGTTGAACATA RR: CTGGTGAAGAAAGTTCAATAAACAGACGTGGAGAGGCCAGTACTAAAGGTTTAGAAGAAGACCTAAATAGCCTGGACAACCACAACTTGTAT F2: 3 TCAATAAACAG 2 Unidirectional alignment (log-probability: -41) ACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCAgacaaataacT----------TCTTCTTCTGGATTTATCaGACCTGTTGGTGTTGAACATA ACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCA----------TGATTTCCAAATCTTCTTCTGGATTTATCGGACCTGTTGGTGTTGAACATA Template switch alignment (log-probability: -22.6) ACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCA|GACAAATAACT|TCTTCTTCTGGATTTATCaGACCTGTTGGTGTTGAACATA ACCACTTCTTTCAAGTTATTTGTCTGCACCTCTCCGGTCA|GACAAATAACT|TCTTCTTCTGGATTTATCGGACCTGTTGGTGTTGAACATA ========= Event 406 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AACTGGAGGAGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGG---------------------------------------------------------ACTGACCTGGTTTGCCTTGAAGATCGCGAGGA ↓ 4 3 1 2 Chimp: AACTGGAGGAGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTAACCAGGTCAGTCCTGCCACCATGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTGGTTTGCCTTGAAGATCACAAGGA ↑ 4 3 1 2 Gorilla: AACTGGAGGAGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGG---------------------------------------------------------ACTGACCTGGTTTGCCTTGAAGATCGCGAGGA Human: AACTGGAGGAGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGG---------------------------------------------------------ACTGACCTGGTTTGCCTTGAAGATCGCGAGGA Cluster: [ ] Orangutan: AACTGGAGGAGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGG---------------------------------------------------------AATGACCTGGTTTGCCTTGAAGATCGCGAGGA Human > Chimp ------------- chr1:88020799-88020821 Template switch process: F1: L AGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACT 1 F3: 4 GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTGGTTTGCCTTGAAGATCACAAGGAGTTAAGAG R RF: AGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTGGTTTGCCTTGAAGATCGCGAGGAGTTAAGAG RR: TCTTTCTCCTCTTCGACTCGTTCTCCAAAGTACCACCGTCCTGACTGGACCAAACGGAACTTCTAGCGCTCCTCAATTCTC F2: 3 TACCACCGTCCTGACTGGACCAA 2 Unidirectional alignment (log-probability: -105) AGAGGAgaagctgagcaagaggtttcatggtggcaggactaaccaggtcagtcctgccaccatGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG AGAGGA---------------------------------------------------------GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG Template switch alignment (log-probability: -30.7) AGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACT|AACCAGGTCAGTCCTGCCACCAT|GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG AGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACT|AACCAGGTCAGTCCTGCCACCAT|GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG Gorilla > Chimp --------------- chr1:88020799-88020821 Template switch process: F1: L AGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACT 1 F3: 4 GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTGGTTTGCCTTGAAGATCACAAGGAGTTAAGAG R RF: AGAAAGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTGGTTTGCCTTGAAGATCGCGAGGAGTTAACAG RR: TCTTTCTCCTCTTCGACTCGTTCTCCAAAGTACCACCGTCCTGACTGGACCAAACGGAACTTCTAGCGCTCCTCAATTGTC F2: 3 TACCACCGTCCTGACTGGACCAA 2 Unidirectional alignment (log-probability: -109) AGAGGAgaagctgagcaagaggtttcatggtggcaggactaaccaggtcagtcctgccaccatGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG AGAGGA---------------------------------------------------------GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG Template switch alignment (log-probability: -36) AGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACT|AACCAGGTCAGTCCTGCCACCAT|GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG AGAGGAGAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACT|AACCAGGTCAGTCCTGCCACCAT|GAAGCTGAGCAAGAGGTTTCATGGTGGCAGGACTGACCTG ========= Event 407 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTACGCGCGGGGCCAAGGAGTCGCTGGCCGCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCGCGACTCACGGCCTGGGTGAGCAGCCAGGCCTGGCG Chimp: GCTACGCGCGGGGCCAAGGAGTCGCTGGCCGCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCGCGAC-----TCCTGGGTGAGCAGCCAGGCCTGGCG ↑ 3 2 1 4 Gorilla: GCTACGCGCGGGGCCAAGGAGTCGCTGGCCGCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCAAGGCTCACGGCCTGAGTGAGCAGCCAGGCCTGGCG Human: GCTACGCGCGGGGCCAAGGAGTCGCTGGCCGCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCGCGACTCACGGCCTGGGTGAGCAGCCAGGCCTGGCG Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr11:63964621-63964626 Template switch process: F1: L CGCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGC 1 F3: 4 CCTGGGTGAGCAGCCAGGCCTGGCGCCGCCGTTGCCATAGTTACA R RF: AGTCGCTGGCCGCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCAAGGCTCACGGCCTGAGTGAGCAGCCAGGCCTGGCGCCGCCGTTGCCATAGTTACA RR: TCAGCGACCGGCGTCCCCTCCACGACGGTTGGTGGGCCGGGGGTCGCCGCGTTCCGAGTGCCGGACTCACTCGTCGGTCCGGACCGCGGCGGCAACGGTATCAATGT F2: 3 TCAGCG 2 Unidirectional alignment (log-probability: -33.4) GCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCgcGaCT-----CCTGgGTGAGCAGCCAGGCCTGGCGCCGCCGTTGCCATAG GCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGCAAGGCTCACGGCCTGAGTGAGCAGCCAGGCCTGGCGCCGCCGTTGCCATAG Template switch alignment (log-probability: -22.1) GCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGC|GCGACT|CCTGgGTGAGCAGCCAGGCCTGGCGCCGCCGTTGCCATAG GCAGGGGAGGTGCTGCCAACCACCCGGCCCCCAGCGGCGC|GCGACT|CCTGAGTGAGCAGCCAGGCCTGGCGCCGCCGTTGCCATAG ========= Event 408 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: gcatcctcttctatctggatGAACAACCTACCAGGAGACCTG------------TGTTGCAATTGTTGCAACTGCCTGTGTTGCAA------------TTGCCATCCATGCTGGAGGGCTA Chimp: gcatcctcttctatctggatGAACAACCTACCAGGAGACCTG------------TGTTGCAATTGTTGCAACTGCCTGTGTTGCAA------------TTGCCATCCATGCTGGAGGGCTA ↑ 4 3 2 1 Gorilla: gcatcctcttctatctggatGAACAACCTACCAGGAGACCTG------------------------------------TGTTGCAA------------TTGCCATCCATGCTGGAGGGCTA ↓ 4 3 2 1 Human: gcatcctcttctatctggatGAACAACCTACCAGGAGACCTG------------TGTTGCAATTGTTGCAACTGCCTGTGTTGCAA------------TTGCCATCCATGCTGGAGGGCTA Cluster: [ ] Orangutan: acatcctcttctATGTGGATGAACAACCTACCAGGAGACCCGGGTGACTGCCTG------------------------TGTTGCAATTGTCTGCCCCGTTGCCATCCATGCTGGAGGGCTA Gorilla > Human --------------- chr11:69507134-69507140 Template switch process: F1: L CATCCTCTTCTATCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTG 1 F3: 4 TG-----------------CCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAGACTCAC R RF: CATCCTCTTCTATCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAGACTCAC RR: GTAGGAGAAGATAGACCTACTTGTTGGATGGTCCTCTGGACACAACGTTAACGGTAGGTACGACCTCCCGATCTCTGAGTG F2: 3 CAACGTT 2 Unidirectional alignment (log-probability: -45.4) TCTGGATGAACAACCTACCAGGAGACCtgtgttgcaattgttgcaactgccTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG TCTGGATGAACAACCTACCAGGAGACC------------------------TGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG Template switch alignment (log-probability: -27.6) TCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTG|TTGCAAC|TG-----------------CCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG TCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTG|TTGCAAC|TGAACAACCTACCAGGAGACCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG Gorilla > Chimp --------------- chr11:70111727-70111733 Template switch process: F1: L CATCCTCTTCTATCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTG 1 F3: 4 TG-----------------CCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAGACTCAC R RF: CATCCTCTTCTATCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAGACTCAC RR: GTAGGAGAAGATAGACCTACTTGTTGGATGGTCCTCTGGACACAACGTTAACGGTAGGTACGACCTCCCGATCTCTGAGTG F2: 3 CAACGTT 2 Unidirectional alignment (log-probability: -45.4) TCTGGATGAACAACCTACCAGGAGACCtgtgttgcaattgttgcaactgccTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG TCTGGATGAACAACCTACCAGGAGACC------------------------TGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG Template switch alignment (log-probability: -27.6) TCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTG|TTGCAAC|TG-----------------CCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG TCTGGATGAACAACCTACCAGGAGACCTGTGTTGCAATTG|TTGCAAC|TGAACAACCTACCAGGAGACCTGTGTTGCAATTGCCATCCATGCTGGAGGGCTAGAG ========= Event 409 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTCCTGGACAGCTGAAGGT--TTGCA-----GCAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGGGGCAGTGCTGGGACTCCAGCTGGAAAGCCCGTGTCCTGGACTC Chimp: CATTCCTGGACAGCTGAAGGT--TTGCA-----GCAGCCTGACAGAGCTGCCCCTTGGTTGACAGGCAGGATGGGGCAGTGCTGGGACTCCAGCTGGAAAGCCCGTGTCCTGGACTC Gorilla: CATTCCTGGACAGCTGAAGGT----CCAGCTGGACAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGGGGCAGTGCTGGGACTCCAGCTCGAAAGCCTGTGTCCTGGACTC ↑ 1 4 3 2 Human: CATTCCTGGACAGCTGAAGGT--TTGCA-----GCAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGGGGCAGTGCTGGGACTCCAGCTGGAAAGCCCGTGTCCTGGACTC Cluster: [ ] Orangutan: CATTCCTGGACAGCTGAAGGTTT--GCA-----GCAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGGGGCAGTGCTGGGACCCCAGCTAGAAAGCCCGTGTCCTGGACTC Human > Gorilla --------------- chr11:70443206-70443214 Template switch process: F1: L TTTCCTTCAAATGCACAGGTCATTCCTGGACAGCTGAAGGT 1 F3: 4 CAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGG R RF: TTTCCTTCAAATGCAGGGGTCATTCCTGGACAGCTGAAGGTTTGCAGCAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGGGGCAGTGCTGGGACTCCAGCTGG RR: AAAGGAAGTTTACGTCCCCAGTAAGGACCTGTCGACTTCCAAACGTCGTCGGACCGTCTCGACGGGGAACCAACTGTCCGTCCTACCCCGTCACGACCCTGAGGTCGACC F2: 3 AGGTCGACC 2 Unidirectional alignment (log-probability: -44.5) TTCCTTCAAATGCAcaGGTCATTCCTGGACAGCTGAAGG--TcCAGctggaCAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGG TTCCTTCAAATGCAGGGGTCATTCCTGGACAGCTGAAGGTTTGCAG-----CAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGG Template switch alignment (log-probability: -27.9) TTCCTTCAAATGCAcaGGTCATTCCTGGACAGCTGAAGGT|CCAGCTGGA|CAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGG TTCCTTCAAATGCAGGGGTCATTCCTGGACAGCTGAAGGT|CCAGCTGGA|CAGCCTGGCAGAGCTGCCCCTTGGTTGACAGGCAGGATGG ========= Event 410 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCTTATCTCATTATAGAAT-TCCATGCTTAAGGCTCTCCAACCACTTACATGCAAAGTGGAACGAACAGCTTTA ↓ 1 4 3 2 Chimp: TGCCTTATCTCATTATAGAATTTGCAT--GTAAG------AAACCACTTACATGCAAAGTGGAACGAACAGCTTTA Gorilla: TGCCTTATCTCATTTTAGAAT-TCCATGCTTAAGGCTCTCCAACCACTTACATGCAAAGTGGAATGAACAGCTTTA Human: TGCCTTATCTCATTATAGAAT-TCCATGCTTAAGGCTCTCCAACCACTTACATGCAAAGTGGAACGAACAGCTTTA Cluster: [ ] Orangutan: TGCCTTATCTCATTATAGAAT-TCCATGCTTAAGGCTCTCCAACCACTTACATGCAAAGTGGAACGAACAGCTTTA Human > Chimp ------------- chr1:140125606-140125615 Template switch process: F1: L ACTTCAGCCCTTCACCCACATGCCTTATCTCATTATAGAATT 1 F3: 4 AAACCACTTACATGCAAAGTGGAACGAACAGCTTTAACCAA R RF: ACTTCAGCCCTTCACCCACATGCCTTATCTCATTATAGAATTCCATGCTTAAGGCTCTCCAACCACTTACATGCAAAGTGGAACGAACAGCTTTAACCAA RR: TGAAGTCGGGAAGTGGGTGTACGGAATAGAGTAATATCTTAAGGTACGAATTCCGAGAGGTTGGTGAATGTACGTTTCACCTTGCTTGTCGAAATTGGTT F2: 3 GAATGTACGT 2 Unidirectional alignment (log-probability: -37.9) TTCAGCCCTTCACCCACATGCCTTATCTCATTATAGAATT------------------tgcatgtaagaAACCACTTACATGCAAAGTGGAACGAACAGCTTTAACCA TTCAGCCCTTCACCCACATGCCTTATCTCATTATAGAATTCCATGCTTAAGGCTCTCC-----------AACCACTTACATGCAAAGTGGAACGAACAGCTTTAACCA Template switch alignment (log-probability: -22.6) TTCAGCCCTTCACCCACATGCCTTATCTCATTATAGAATT|TGCATGTAAG|aAACCACTTACATGCAAAGTGGAACGAACAGCTTTAACCA TTCAGCCCTTCACCCACATGCCTTATCTCATTATAGAATT|TGCATGTAAG|CAACCACTTACATGCAAAGTGGAACGAACAGCTTTAACCA ========= Event 411 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GTATTCCCAAGTGAAATTGGGAATTCTGATTCCCAAGGAATCAGAATCCCATCCATATTTGTGGTAT Chimp: Gorilla: GTATTCCCAAGTGAAATTGGGG---CCTATACCCAAGGAATCAGAATCCCATCCATATTTGTGGTAT ↓ 1 4 3 2 Human: GTATTCCCAAGTGAAATTGGGAATTCTGATTCCCAAGGAATCAGAATCCCATCCATATTTGTGGTAT Cluster: [ ] Orangutan: GTATTCCCAAGTGAAATTGGGG---CCTACACCCAAGGAGTCAGAATCCCATCCATATTTGTGGTAT Gorilla > Human --------------- chr1:16384515-16384523 Template switch process: F1: L TACCTGTGAATTCTTTGACTGTATTCCCAAGTGAAATTGGGA 1 F3: 4 CCCAAGGAATCAGAATCCCATCCATATTTGTGGTATGGGA R RF: TACCTGTGAATTCTTTGACTGTATTCCCAAGTGAAATTGGGGCCTATACCCAAGGAATCAGAATCCCATCCATATTTGTGGTATGAGA RR: ATGGACACTTAAGAAACTGACATAAGGGTTCACTTTAACCCCGGATATGGGTTCCTTAGTCTTAGGGTAGGTATAAACACCATACTCT F2: 3 TTAGTCTTA 2 Unidirectional alignment (log-probability: -39.4) CCTGTGAATTCTTTGACTGTATTCCCAAGTGAAATTGGG------AattctgattCCCAAGGAATCAGAATCCCATCCATATTTGTGGTATGgGA CCTGTGAATTCTTTGACTGTATTCCCAAGTGAAATTGGGGCCTATA---------CCCAAGGAATCAGAATCCCATCCATATTTGTGGTATGAGA Template switch alignment (log-probability: -27.9) CCTGTGAATTCTTTGACTGTATTCCCAAGTGAAATTGGGa|ATTCTGATT|CCCAAGGAATCAGAATCCCATCCATATTTGTGGTATGgGA CCTGTGAATTCTTTGACTGTATTCCCAAGTGAAATTGGGG|ATTCTGATT|CCCAAGGAATCAGAATCCCATCCATATTTGTGGTATGAGA ========= Event 412 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACACTTAGAAATATTAAGCAG-------------------AGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGG Chimp: AACACTTAGAAATATTAAGCAG-------------------AGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGG ↓ 4 31 2 Gorilla: AACACTTAGAAATATTAAGCAAGTTTCACATTAAGTGAACTTACTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGG ↑ 4 31 2 Human: AACACTTAGAAATATTAAGCAG-------------------AGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGG Cluster: [ ] Orangutan: AACACTTAGAAATATTAAGCAG-------------------AGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGG Human > Gorilla --------------- chr1:87167027-87167034 Template switch process: F1: L TCAAATGGTGGTGTGGCAGTAACACTTAGAAATATTAAGC--AAGTTTCACATTAAGT 1 F3: 4 TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC R RF: TCAAATGGTGGTGTGGCAGTAACACTTAGAAATATTAAGCAGAGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC RR: AGTTTACCACCACACCGTCATTGTGAATCTTTATAATTCGTCTCCAAAGTGTAATTCATTCAAGTTTTTGGAGTTCAATTTACCG F2: 3 CATTCAAG 2 Unidirectional alignment (log-probability: -53.9) CAGTAACACTTAGAAATATTAAGCAagtttcacattaagtgaacttac----TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC CAGTAACACTTAGAAATATTAAGCA-----------------------GAGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC Template switch alignment (log-probability: -32.5) CAGTAACACTTAGAAATATTAAGC--AaGTTTCACATTAAGT|GAACTTAC|TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC CAGTAACACTTAGAAATATTAAGCAGAGGTTTCACATTAAGT|GAACTTAC|TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC Chimp > Gorilla --------------- chr1:87167027-87167034 Template switch process: F1: L TCAAATGGTGGTGTGGCAGTAACACTTAGAAATATTAAGC--AAGTTTCACATTAAGT 1 F3: 4 TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC R RF: TCAAATGGTGGTGTGGCAGTAACACTTAGAAATATTAAGCAGAGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC RR: AGTTTACCACCACACCGTCATTGTGAATCTTTATAATTCGTCTCCAAAGTGTAATTCATTCAAGTTTTTGGAGTTCAATTTACCG F2: 3 CATTCAAG 2 Unidirectional alignment (log-probability: -53.9) CAGTAACACTTAGAAATATTAAGCAagtttcacattaagtgaacttac----TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC CAGTAACACTTAGAAATATTAAGCA-----------------------GAGGTTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC Template switch alignment (log-probability: -32.5) CAGTAACACTTAGAAATATTAAGC--AaGTTTCACATTAAGT|GAACTTAC|TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC CAGTAACACTTAGAAATATTAAGCAGAGGTTTCACATTAAGT|GAACTTAC|TTTCACATTAAGTAAGTTCAAAAACCTCAAGTTAAATGGC ========= Event 413 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAACATTTTCTGAGAATTTGGACATTGTCATGAGGACACCAGCATAGGGAGA Chimp: TAACATTTTCTGAGAATTTGG--ATGACAATGAGGACACCAACACAGGGAGA Gorilla: TAACATTTTCTGAGAATTTGG--ATGACAATGAGGACACCAGCACAGGGAGA ↓ 1 3 4 2 Human: TAACATTTTCTGAGAATTTGGACATTGTCATGAGGACACCAGCATAGGGAGA Cluster: [ ] Orangutan: TAACATTTTCTGAGAATTTGG--ATGACAATGAGGACAACAGCACAGGGAGA Gorilla > Human --------------- chr1:163613193-163613199 Template switch process: F1: L GAGCCAAGAGCCAACAGAAATAACATTTTCTGAGAATTTGGA 1 F3: 4 ATGAGGACACCAGCATAGGGAGAGTGGGCTTCATGATGCA R RF: GAGCCAAGAGCCAACAGAAATAACATTTTCTGAGAATTTGGATGACAATGAGGACACCAGCACAGGGAGAGTGGGCTTCATGATGCA RR: CTCGGTTCTCGGTTGTCTTTATTGTAAAAGACTCTTAAACCTACTGTTACTCCTGTGGTCGTGTCCCTCTCACCCGAAGTACTACGT F2: 3 CTGTTAC 2 Unidirectional alignment (log-probability: -33.5) GCCAAGAGCCAACAGAAATAACATTTTCTGAGAATTTG---GACAttgtcATGAGGACACCAGCAtAGGGAGAGTGGGCTTCATGATGCA GCCAAGAGCCAACAGAAATAACATTTTCTGAGAATTTGGATGACA-----ATGAGGACACCAGCACAGGGAGAGTGGGCTTCATGATGCA Template switch alignment (log-probability: -22.2) GCCAAGAGCCAACAGAAATAACATTTTCTGAGAATTTGGA|CATTGTC|ATGAGGACACCAGCAtAGGGAGAGTGGGCTTCATGATGCA GCCAAGAGCCAACAGAAATAACATTTTCTGAGAATTTGGA|CATTGTC|ATGAGGACACCAGCACAGGGAGAGTGGGCTTCATGATGCA ========= Event 414 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCTTATTCCTTTGAGATAA---------------CGTCTATTAAGTGCTTAGCTGCTTTTGGACCTATGGTGAGTATTAAACAAGGA Chimp: ATTCTTATTCCTTTGAGATAA---------------CGTTTATTAAGTGCTTAGCTTCTTTTGGACCTATGGTGAGTATTAAACAAGGA ↓ 1 4 3 2 Gorilla: ATTCTTATTCCTTTGAGATAA------------------------------TAGG-TCCTTTGGACCTATGGTGAGTATTAAAAAAGGA ↑ 1 4 3 2 Human: ATTCTTATTCCTTTGAGATAA---------------CGTCTATTAAGTGCTTAGCTGCTTTTGGACCTATGGTGAGTATTAAACAAGGA Cluster: [ ] Orangutan: ATTCTTATTCTTTTGAGATAATGTCTATTAAGTGCT---------------TAGCTGCTTTTGGACCTATGGTGAGTATTAAACAAGGA Human > Gorilla --------------- chr1:142543097-142543103 Template switch process: F1: L ACAGATGTGGAATGAGCATTATTCTTATTCCTTTGAGATAA 1 F3: 4 TTTGGACCTATGGTGAGTATTAAAAAAGGAGTACTTGACA R RF: ACAGATGTGGAACGAGCATTATTCTTATTCCTTTGAGATAACGTCTATTAAGTGCTTAGCTGCTTTTGGACCTATGGTGAGTATTAAACAAGGAGTACTTGACA RR: TGTCTACACCTTGCTCGTAATAAGAATAAGGAAACTCTATTGCAGATAATTCACGAATCGACGAAAACCTGGATACCACTCATAATTTGTTCCTCATGAACTGT F2: 3 CCTGGAT 2 Unidirectional alignment (log-probability: -41.4) CAGATGTGGAAtGAGCATTATTCTTATTCCTTTGAGATAA----------------------TaggtccTTTGGACCTATGGTGAGTATTAAAaAAGGAGTACTTGACA CAGATGTGGAACGAGCATTATTCTTATTCCTTTGAGATAACGTCTATTAAGTGCTTAGCTGCT------TTTGGACCTATGGTGAGTATTAAACAAGGAGTACTTGACA Template switch alignment (log-probability: -27.7) CAGATGTGGAAtGAGCATTATTCTTATTCCTTTGAGATAA|TAGGTCC|TTTGGACCTATGGTGAGTATTAAAaAAGGAGTACTTGACA CAGATGTGGAACGAGCATTATTCTTATTCCTTTGAGATAA|TAGGTCC|TTTGGACCTATGGTGAGTATTAAACAAGGAGTACTTGACA Chimp > Gorilla --------------- chr1:142543097-142543103 Template switch process: F1: L ACAGATGTGGAATGAGCATTATTCTTATTCCTTTGAGATAA 1 F3: 4 TTTGGACCTATGGTGAGTATTAAAAAAGGAGTACTTGACA R RF: ACAGATGTGGAACGAGCATTATTCTTATTCCTTTGAGATAACGTTTATTAAGTGCTTAGCTTCTTTTGGACCTATGGTGAGTATTAAACAAGGAGTACTTGACA RR: TGTCTACACCTTGCTCGTAATAAGAATAAGGAAACTCTATTGCAAATAATTCACGAATCGAAGAAAACCTGGATACCACTCATAATTTGTTCCTCATGAACTGT F2: 3 CCTGGAT 2 Unidirectional alignment (log-probability: -41.4) CAGATGTGGAAtGAGCATTATTCTTATTCCTTTGAGATAA----------------------TaggtccTTTGGACCTATGGTGAGTATTAAAaAAGGAGTACTTGACA CAGATGTGGAACGAGCATTATTCTTATTCCTTTGAGATAACGTTTATTAAGTGCTTAGCTTCT------TTTGGACCTATGGTGAGTATTAAACAAGGAGTACTTGACA Template switch alignment (log-probability: -27.7) CAGATGTGGAAtGAGCATTATTCTTATTCCTTTGAGATAA|TAGGTCC|TTTGGACCTATGGTGAGTATTAAAaAAGGAGTACTTGACA CAGATGTGGAACGAGCATTATTCTTATTCCTTTGAGATAA|TAGGTCC|TTTGGACCTATGGTGAGTATTAAACAAGGAGTACTTGACA ========= Event 415 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATATCTCAAGTGTATCTGATGCTTAGGAATCAAATCAGTGAAGGATTTTCAGAGTATGCATCTATTTAagcataggatagca-- Chimp: AAATATCTCAAGTGTATCTGATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTGTCTATCTATTTAagcataggatggca-- ↓ 3 2 1 4 Gorilla: ACATATCTCAAGTGTATCTGATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTATGCAT-CATTTAagcataggatagcata Human: AAATATCTCAAGTGTATCTGATGCTTAGGAATCAAATCAGTGAAGGATTTTCAGAGTATGCATCTATTTAagcataggatagca-- Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-- Chimp > Gorilla --------------- chr11:75623302-75623306 Template switch process: F1: L TCTGATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTAT 1 F3: 4 ATTTAAGCATAGGATAGCATAGCATAGAATAGGATAGCAT R RF: TCTGATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTGTCTATCTATTTAAGCATAGGATGGCATAGCATAGAATAGGATAGCAT RR: AGACTACGAATCCTTAGTTTAGTCACTTCCTAATACTCTCACAGATAGATAAATTCGTATCCTACCGTATCGTATCTTATCCTATCGTA F2: 3 CTACG 2 Unidirectional alignment (log-probability: -69.7) GATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTaTgcATC-ATTTAAGCATAGGATaGCAtagcatagaataggatagcat GATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTGTCTATCTATTTAAGCATAGGATGGCA--------------------- Template switch alignment (log-probability: -27.4) GATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTaT|GCATC|ATTTAAGCATAGGATaGCATAGCATAGAATAGGATAGCAT GATGCTTAGGAATCAAATCAGTGAAGGATTATGAGAGTGT|GCATC|ATTTAAGCATAGGATGGCATAGCATAGAATAGGATAGCAT ========= Event 416 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACATCCCTGGATGGAGGGCAC----TGGGCAGAGACTCAGCAAACCATGGTTCTGCCGTGCggagacaccgg Chimp: CACATCCCTGGATGGAGGGCAC----TGGGCAGAGACTCAGCAAACCATGGTTCTGCCGTGCggagacaccgg ↓ 1 4 3 2 Gorilla: CACATCCCTGGATGGAGGGCAA--------ACCATGCTCAGCAAACCATGGTTCTGCCGTGCggagacaccgg ↑ 1 4 3 2 Human: CACATCCCTGGATGGAGGGCAC----TGGGCAGAGACTCAGCAAACCATGGTTCTGCCGTGCggagacaccgg Cluster: [ ] Orangutan: CACATGCCTGGATGGAGGGCACTGGG----CAGAGACGCAGCAAACCATGGTTCTGCCGTGCAGAGACACCAG Human > Gorilla --------------- chr11:68217308-68217314 Template switch process: F1: L TTTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA 1 F3: 4 CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC R RF: TTTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCACTGGGCAGAGACTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC RR: AAATCAGAAGTTAGACATCTGTGTAGGGACCTACCTCCCGTGACCCGTCTCTGAGTCGTTTGGTACCAAGACGGCACGCCTCTGTGGCCTCG F2: 3 GTACCAA 2 Unidirectional alignment (log-probability: -29.8) TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA----------AaccatgCTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCACTGGGCAGAGA------CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC Template switch alignment (log-probability: -16.6) TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA|AACCATG|CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA|AACCATG|CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC Chimp > Gorilla --------------- chr11:68217308-68217314 Template switch process: F1: L TTTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA 1 F3: 4 CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC R RF: TTTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCACTGGGCAGAGACTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC RR: AAATCAGAAGTTAGACATCTGTGTAGGGACCTACCTCCCGTGACCCGTCTCTGAGTCGTTTGGTACCAAGACGGCACGCCTCTGTGGCCTCG F2: 3 GTACCAA 2 Unidirectional alignment (log-probability: -29.8) TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA----------AaccatgCTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCACTGGGCAGAGA------CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC Template switch alignment (log-probability: -16.6) TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA|AACCATG|CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC TTAGTCTTCAATCTGTAGACACATCCCTGGATGGAGGGCA|AACCATG|CTCAGCAAACCATGGTTCTGCCGTGCGGAGACACCGGAGC ========= Event 417 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGAATGAAACTAGCATTAGATAACCCTTCTGATTACATGCATCCTGACCGGCTCCTCCTCGGCCTCCCCTCTGTGCTCTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATT--------------------ATCTCTGCCACATCGGATGCAGG ↓ 3 2 4 1 Chimp: TAGAATGAAACTAGCATTAGATAACCCTTCTGATTACATGCATCCTGACCGGCTCCTCCTCGGCCTCCCCTCTGTGCTCTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATT----------ATCGGTTATCATCTCTGCCACATCGGATGCGGG Gorilla: TAGAATGAAACTAGCATTAGATAACCCTTCTGATTACATGCATCCTGACCGGCTCCTCCTCGGCCTCCCCTCTGTGCTCTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATTATCGGTTATC----------ATCTCTGCCACATCGGATGCGGG Human: TAGAATGAAACTAGCATTAGATAACCCTTCTGATTACATGCATCCTGACCGGCTCCTCCTCGGCCTCCCCTCTGTGCTCTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATT--------------------ATCTCTGCCACATCGGATGCAGG Cluster: [ ] Orangutan: TAGAATGAAACTAGCATTAGATAACCCTTCTGATTACATGCATCCTGACCGGCTCCTCCTCAGCCTCCCCTCTGTGCTCTCGCTCTCCAGTGTCTGCAGGCCGCAGGTTTTCATTATCGGTTATC----------ATCTCTGCCACATCGGATGCGGG Human > Chimp ------------- chr1:142894024-142894030 Template switch process: F1: L TGCTCTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATTATC 1 F3: 4 ATCTCTGCCACATCGGATGCGGGATGGGGGTGGGAGAGGG R RF: GATAACCCTTCTGATTACATGCATCCTGACCGGCTCCTCCTCGGCCTCCCCTCTGTGCTCTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATTATCTCTGCCACATCGGATGCAGGATGGGGGTGGGAGAGGG RR: CTATTGGGAAGACTAATGTACGTAGGACTGGCCGAGGAGGAGCCGGAGGGGAGACACGAGAGCGAGAGGTCACAGACCTCCGGCGTCTAAAAGTAATAGAGACGGTGTAGCCTACGTCCTACCCCCACCCTCTCCC F2: 3 CTATTGG 2 Unidirectional alignment (log-probability: -31.3) CTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATTatcggttatcATCTCTGCCACATCGGATGCgGGATGGGGGTGGGAGAGGG CTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATT----------ATCTCTGCCACATCGGATGCAGGATGGGGGTGGGAGAGGG Template switch alignment (log-probability: -22.2) CTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATTATC|GGTTATC|ATCTCTGCCACATCGGATGCgGGATGGGGGTGGGAGAGGG CTCGCTCTCCAGTGTCTGGAGGCCGCAGATTTTCATTATC|GGTTATC|ATCTCTGCCACATCGGATGCAGGATGGGGGTGGGAGAGGG ========= Event 418 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GCAGAAAGATTGAGAAACTCACGGTAAACA------------------GCCCTGAGCTACTTACCCTGAGTGACCCACTGCACGTAGGCCCTAGTTGTTCTCAGCCTCGGGCTTTGGGGAACTTTGGCCCCTGGATCTTTCTCTATCGGGTTTTGGTGCTTATCTTTTCTGGGCAGTTTATGCAACAGGCACCCGTTAACAGAT ↓ 4 1 3 2 Chimp: GCAGAAAGATTGAGAAACTCAGGGTAAACAGCCCTGTGCATGTAAACAGCCCTGGGCTACTTACCCTGAGTGACCCACTGCACGTAGGCCCTAGTTGTTCTCAGCCTCGGGCTTTGGGGAACTTTGGCCCCTGGATCTTTCTCTATCGGGTTTTGGTGCTTATCTTTTCTGGGCAGTTTATGCAACAGGCACCCGTTAACAGAT Gorilla: Human: GCAGAAAGATTGAGAAACTCACGGTAAACA------------------GCCCTGAGCTACTTACCCTGAGTGACCCACTGCACGTAGGCCCTAGTTGTTCTCAGCCTCGGGCTTTGGGGAACTTTGGCCCCTGGATCTTTCTCTATCGGGTTTTGGTGCTTATCTTTTCTGGGCAGTTTATGCAACAGGCACCCGTTAACAGAT Cluster: [ ] Orangutan: Human > Chimp ------------- chr11:74643724-74643726 Template switch process: F1: L CGTGACAAGGGACACGGTCTGCAGAAAGATTGAGAAACTCAGGGTAAACAGCCCTGTGC 1 F3: 4 TAAACAGCCCTGGGCTACTTACCCTGAGTGACCCACTGCACGTAGGCCCTAGT R RF: CATGCGTGACAAGGGACACGGTCTGCAGAAAGATTGAGAAACTCACGGTAAACAGCCCTGAGCTACTTACCCTGAGTGACCCACTGCACGTAGGCCCTAGT RR: GTACGCACTGTTCCCTGTGCCAGACGTCTTTCTAACTCTTTGAGTGCCATTTGTCGGGACTCGATGAATGGGACTCACTGGGTGACGTGCATCCGGGATCA F2: 3 GTA 2 Unidirectional alignment (log-probability: -48.9) TGCAGAAAGATTGAGAAACTCAgGGTAAACAGCCCTGtgcatgtaaacagccctggGCTACTTACCCTGAGTGACCCACTGCA TGCAGAAAGATTGAGAAACTCACGGTAAACAGCCCTGA------------------GCTACTTACCCTGAGTGACCCACTGCA Template switch alignment (log-probability: -34.2) TGCAGAAAGATTGAGAAACTCAgGGTAAACAGCCCTGtGC|ATG|TAAACAGCCCTGgGCTACTTACCCTGAGTGACCCACTGCA TGCAGAAAGATTGAGAAACTCACGGTAAACAGCCCTGAGC|ATG|TAAACAGCCCTGAGCTACTTACCCTGAGTGACCCACTGCA ========= Event 419 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCCCCCGGGTGGGGTCCCAGG---CACAGGGCATGAGCCCTGTGGGGCACCAGGGAGTTGTCTG Chimp: CCCCCCGGGTGGGGTCCCAGG---CACAGGGTATGAGCCCTGTGGGGCACCAGGGAGTTGTCTG ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: CCCCCCAGGTGGGGTCCCAGG------TGGGCTCATGCCCTGTGGGGCACCAGGGAGTTGTCTG ↓ 1 3 4 2 ↑ 1 3 4 2 Human: CCCCCCGGGTGGGGTCCCAGG---CACAGGGCATGAGCCCTGTGGGGCACCAGGGAGTTGTCTG Cluster: [ ] Orangutan: TCCCCTCGGTGGGGTCCCAGGCAC---AGGGCATGAGCCCTGTGGGGCACCAGGGAGTTGTCTG Gorilla > Human --------------- chr11:65622058-65622069 Template switch process: F1: L CACTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGG 1 F3: 4 GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC R RF: CACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGGTGGGCTCATGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC RR: GTGAGAATAAAGAGAGACATGGGGGGTCCACCCCAGGGTCCACCCGAGTACGGGACACCCCGTGGTCCCTCAACAGACGACTCGCCGAAG F2: 3 AGTACGGGACAC 2 Unidirectional alignment (log-probability: -43.9) ACTCTTATTTCTCTCTGTACCCCCCgGGTGGGGTCCCAGGcacagggcatga---------GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC ACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGG------------TGGGCTCATGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Template switch alignment (log-probability: -22.8) ACTCTTATTTCTCTCTGTACCCCCCgGGTGGGGTCCCAGG|CACAGGGCATGA|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC ACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGG|CACAGGGCATGA|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Human > Gorilla --------------- chr11:66470168-66470175 Template switch process: F1: L CACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGGT 1 F3: 4 GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC R RF: CACTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGGCACAGGGCATGAGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC RR: GTGAGAATAAAGAGAGACATGGGGGGCCCACCCCAGGGTCCGTGTCCCGTACTCGGGACACCCCGTGGTCCCTCAACAGACGACTCGCCGAAG F2: 3 TACTCGGG 2 Unidirectional alignment (log-probability: -39.7) CTCTTATTTCTCTCTGTACCCCCCaGGTGGGGTCCCAGG------------tgggctcatGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC CTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGGCACAGGGCATGA---------GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Template switch alignment (log-probability: -27.8) CTCTTATTTCTCTCTGTACCCCCCaGGTGGGGTCCCAGGt|GGGCTCAT|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC CTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGGC|GGGCTCAT|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Gorilla > Chimp --------------- chr11:66403303-66403314 Template switch process: F1: L CACTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGG 1 F3: 4 GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC R RF: CACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGGTGGGCTCATGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC RR: GTGAGAATAAAGAGAGACATGGGGGGTCCACCCCAGGGTCCACCCGAGTACGGGACACCCCGTGGTCCCTCAACAGACGACTCGCCGAAG F2: 3 AGTATGGGACAC 2 Unidirectional alignment (log-probability: -43.9) ACTCTTATTTCTCTCTGTACCCCCCgGGTGGGGTCCCAGGcacagggtatga---------GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC ACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGG------------TGGGCTCATGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Template switch alignment (log-probability: -28.3) ACTCTTATTTCTCTCTGTACCCCCCgGGTGGGGTCCCAGG|CACAGGGtATGA|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC ACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGG|CACAGGGCATGA|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Chimp > Gorilla --------------- chr11:66470168-66470175 Template switch process: F1: L CACTCTTATTTCTCTCTGTACCCCCCAGGTGGGGTCCCAGGT 1 F3: 4 GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC R RF: CACTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGGCACAGGGTATGAGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC RR: GTGAGAATAAAGAGAGACATGGGGGGCCCACCCCAGGGTCCGTGTCCCATACTCGGGACACCCCGTGGTCCCTCAACAGACGACTCGCCGAAG F2: 3 TACTCGGG 2 Unidirectional alignment (log-probability: -39.7) CTCTTATTTCTCTCTGTACCCCCCaGGTGGGGTCCCAGG------------tgggctcatGCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC CTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGGCACAGGGTATGA---------GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC Template switch alignment (log-probability: -27.8) CTCTTATTTCTCTCTGTACCCCCCaGGTGGGGTCCCAGGt|GGGCTCAT|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC CTCTTATTTCTCTCTGTACCCCCCGGGTGGGGTCCCAGGC|GGGCTCAT|GCCCTGTGGGGCACCAGGGAGTTGTCTGCTGAGCGGCTTC ========= Event 420 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCCTTGGCATTGAAAAATGCCAAGGAGGG-TCCTCAGGCA---ACACAGGG Chimp: AAACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTC------------------CAGTTAGGATCCCTCAGGCA---ACACAGGG Gorilla: AAACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTC------------------CAATTAGGATCCCTCAGGCA---ACACAGGG ↓ 4 3 2 1 Human: AAACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCCTTGGCATTGAAAAATGCCAAGGAGGG-TCCTCAGGCA---ACACAGGG Cluster: [ ] Orangutan: AAACTTCTAATATGTACTCTGAAAAATGCCAAGGAGGGTC------------------CAGTTAGGATCCCTCAGGCAACAACACAGGG Gorilla > Human --------------- chr1:79842262-79842268 Template switch process: F1: L CAAACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCC 1 F3: 4 TGAAAAATGCCAAGGAGGGT------------CCTCAGGCAACACAGGGCCATAAGGGGTGGCCCAAGAGCT R RF: CAAACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCCAATTAGGATCCCTCAGGCAACACAGGGCCATAAGGGGTGGCCCAAGAGCT RR: GTTTGAAGATTGTGCATGAGACTTTTTACGGTTCCTCCCAGGTTAATCCTAGGGAGTCCGTTGTGTCCCGGTATTCCCCACCGGGTTCTCGA F2: 3 TACGGTT 2 Unidirectional alignment (log-probability: -60) AACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCCttggcattgaaaaatgccaaggagggt----------CCTCAGGCAACACAGGGCCA AACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCC---------------------------AATTAGGATCCCTCAGGCAACACAGGGCCA Template switch alignment (log-probability: -27.5) AACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCC|TTGGCAT|TGAAAAATGCCAAGGAGGGT------------CCTCAGGCAACACAGGGCCA AACTTCTAACACGTACTCTGAAAAATGCCAAGGAGGGTCC|TTGGCAT|TGAAAAATGCCAAGGAGGGTCCAATTAGGATCCCTCAGGCAACACAGGGCCA ========= Event 421 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GCGTGGGAGGGGCACCTGACCGC---------------------------CAGATGGGCGGTCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGC Chimp: -------------------------------------------------------------------------------------------------- Gorilla: GCGTGGGAGGGGCACCTGACCGCTCATCTGGCATCCACCTGAGCCGCACC----------------------------CTTGGAGGGGCCTTTGGTGC ↓ 3 1 2 4 Human: GCGTGGGAGGGGCACCTGACCGC---------------------------CAGATGGGCGGTCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGC Cluster: [ ] Orangutan: GCCTGGGAGGGGCACCTGACCGCCCATCTGGCGTCCACCTGAGCCGCACC----------------------------CTTGGAAGGGCCTTTGGTGC Gorilla > Human --------------- chr11:728131-728141 Template switch process: F1: L GGCCACACTCAGCACCCTGCGTGGGAGGGGCACCTGACCGC 1 F3: 4 TCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGCCCTCTGCCGGCCGCTCCATG R RF: GGCCACACTCAGCACCCTGCGTGGGAGGGGCACCTGACCGCTCATCTGGCATCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGCCCTCTGCCGGCCGCTCCATG RR: CCGGTGTGAGTCGTGGGACGCACCCTCCCCGTGGACTGGCGAGTAGACCGTAGGTGGACTCGGCGTGGGAACCTCCCCGGAAACCACGGGAGACGGCCGGCGAGGTAC F2: 3 GGCGGGTAGAC 2 Unidirectional alignment (log-probability: -34.2) GCCACACTCAGCACCCTGCGTGGGAGGGGCACCTGACCGC--------CAgatgggcggTCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGCCCT GCCACACTCAGCACCCTGCGTGGGAGGGGCACCTGACCGCTCATCTGGCA---------TCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGCCCT Template switch alignment (log-probability: -23.1) GCCACACTCAGCACCCTGCGTGGGAGGGGCACCTGACCGC|CAGATGgGCGG|TCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGCCCT GCCACACTCAGCACCCTGCGTGGGAGGGGCACCTGACCGC|CAGATGAGCGG|TCCACCTGAGCCGCACCCTTGGAGGGGCCTTTGGTGCCCT ========= Event 422 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGGGGA--AGGGCCAGAGTGG--------------------------GCCACTGTTAGGTGGGCAGCAGATGGCAATGTG ↓ 4 1 3 2 Chimp: GGGGGA--AGGGCCAGAGTGG-------------GCACCTAACAGTGGCCACTGTTAGGTGGGCAGCAGATGGCAGTGTG Gorilla: GGGGGA--AGGGCCAGAGTGGGCACCTAACAGTG-------------GCCACTGTTAGGTGGGCAGCAGATGGCAGTGTG ↑ 4 1 3 2 Human: GGGGGA--AGGGCCAGAGTGG--------------------------GCCACTGTTAGGTGGGCAGCAGATGGCAATGTG Cluster: [ ] Orangutan: GGGGGAACCGGCCCAGAGTGGGCAGCTAACAGTG-------------GCCACTGTTAGGTGGGCAGCAGATGGCAGTGTG Human > Chimp ------------- chr11:65945585-65945594 Template switch process: F1: L GGCTCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGC 1 F3: 4 GGCCACTGTTAGGTGGGCAGCAGATGGCAGTGTGCACACTG R RF: GGCTCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGCCACTGTTAGGTGGGCAGCAGATGGCAATGTGCACACTG RR: CCGAGGTGTATCATCCCCTACTCCCCCTTCCCGGTCTCACCCGGTGACAATCCACCCGTCGTCTACCGTTACACGTGTGAC F2: 3 TGACAATCCA 2 Unidirectional alignment (log-probability: -35.6) TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGggcacctaacagtGGCCACTGTTAGGTGGGCAGCAGATGGCAgTGTGCACACT TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTG-------------GGCCACTGTTAGGTGGGCAGCAGATGGCAATGTGCACACT Template switch alignment (log-probability: -22.6) TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGC|ACCTAACAGT|GGCCACTGTTAGGTGGGCAGCAGATGGCAgTGTGCACACT TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGC|ACCTAACAGT|GGCCACTGTTAGGTGGGCAGCAGATGGCAATGTGCACACT Human > Gorilla --------------- chr11:66029397-66029406 Template switch process: F1: L GGCTCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGC 1 F3: 4 GGCCACTGTTAGGTGGGCAGCAGATGGCAGTGTGCACACTG R RF: GGCTCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGCCACTGTTAGGTGGGCAGCAGATGGCAATGTGCACACTG RR: CCGAGGTGTATCATCCCCTACTCCCCCTTCCCGGTCTCACCCGGTGACAATCCACCCGTCGTCTACCGTTACACGTGTGAC F2: 3 TGACAATCCA 2 Unidirectional alignment (log-probability: -35.1) TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGggcacctaacagtGGCCACTGTTAGGTGGGCAGCAGATGGCAgTGTGCACACT TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTG-------------GGCCACTGTTAGGTGGGCAGCAGATGGCAATGTGCACACT Template switch alignment (log-probability: -22.6) TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGC|ACCTAACAGT|GGCCACTGTTAGGTGGGCAGCAGATGGCAgTGTGCACACT TCCACATAGTAGGGGATGAGGGGGAAGGGCCAGAGTGGGC|ACCTAACAGT|GGCCACTGTTAGGTGGGCAGCAGATGGCAATGTGCACACT ========= Event 423 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TCTCTTCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTTTCCTTGTG-AATTTCCAAATAGGCAC ↓ 3 2 1 4 Chimp: TCTCTTCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAAT-TTCTGAGTG-AATTTCCAAATAGGCAC Gorilla: TCTCTTCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAAT-TTCCGAGTG-AATTTCCAAATAGGCAC Human: TCTCTTCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTTTCCTTGTG-AATTTCCAAATAGGCAC Cluster: [ ] Orangutan: TCTCATCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAAT-TTCCGAGTGAAATTTCCAAGTAGGCAC Human > Chimp ------------- chr1:147795199-147795202 Template switch process: F1: L CTTCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTT 1 F3: 4 GTGAATTTCCAAATAGGCACACTTTTCCCAGTGTGACCAC R RF: CTTCTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTTTCCTTGTGAATTTCCAAATAGGCACACTTTTCCCAGTGTGACCAC RR: GAAGAGTCAAAGACAAAGTCAATGATCGAATGTCCCGTTTAAAAGGAACACTTAAAGGTTTATCCGTGTGAAAAGGGTCACACTGGTG F2: 3 AGTC 2 Unidirectional alignment (log-probability: -27.2) CTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTTctga-----GTGAATTTCCAAATAGGCACACTTTTCCCAGTGTGACCAC CTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTT----TCCTTGTGAATTTCCAAATAGGCACACTTTTCCCAGTGTGACCAC Template switch alignment (log-probability: -15.8) CTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTT|CTGA|GTGAATTTCCAAATAGGCACACTTTTCCCAGTGTGACCAC CTCAGTTTCTGTTTCAGTTACTAGCTTACAGGGCAAATTT|CTGA|GTGAATTTCCAAATAGGCACACTTTTCCCAGTGTGACCAC ========= Event 424 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGCAATATAGGAAAGCCAGTAAACAGAACTGTCCTTGTCAACAAGTCACACACTGCCTAA Chimp: CTGCAATATAGGAAAGCCAGTAAACAGAACTGTCCTTGTCAACAAGTCACACACTGCCTAA ↓ 1 4 3 2 Gorilla: CTGCAATATAGGAAAGCCAGTTGAC-AAGTTGTCCTTGTCAACAAGTCACACACTGCCTAA ↑ 1 4 3 2 Human: CTGCAATATAGGAAAGCCAGTAAACAGAACTGTCCTTGTCAACAAGTCACACACTGCCTAA Cluster: [ ] Orangutan: CTGCAATATAGGAAAGCCAGTAAACAGAACTGTCCTTGTCAACAAGTCACACACTGCCTAA Human > Gorilla --------------- chr1:148540847-148540853 Template switch process: F1: L ACTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT 1 F3: 4 TTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTAT R RF: ACTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGTAAACAGAACTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTAT RR: TGAAGGAAAACGTACAGGTGGACGTTATATCCTTTCGGTCATTTGTCTTGACAGGAACAGTTGTTCAGTGTGTGACGGATTTAAGTAATA F2: 3 GAACAGT 2 Unidirectional alignment (log-probability: -32.6) CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT---------tgacaagtTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGTAAACAGAAC--------TGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA Template switch alignment (log-probability: -22.2) CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT|TGACAAG|tTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT|TGACAAG|CTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA Chimp > Gorilla --------------- chr1:148540847-148540853 Template switch process: F1: L ACTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT 1 F3: 4 TTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTAT R RF: ACTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGTAAACAGAACTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTAT RR: TGAAGGAAAACGTACAGGTGGACGTTATATCCTTTCGGTCATTTGTCTTGACAGGAACAGTTGTTCAGTGTGTGACGGATTTAAGTAATA F2: 3 GAACAGT 2 Unidirectional alignment (log-probability: -32.6) CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT---------tgacaagtTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGTAAACAGAAC--------TGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA Template switch alignment (log-probability: -22.2) CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT|TGACAAG|tTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA CTTCCTTTTGCATGTCCACCTGCAATATAGGAAAGCCAGT|TGACAAG|CTGTCCTTGTCAACAAGTCACACACTGCCTAAATTCATTA ========= Event 425 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCCAACTGTCTAAGTTGCAGC--------------CCCATGAACCTGTGGATCCCGATGACCAAACCCAGGAATCCCCAA Chimp: ACCCAACTGTCTAAGTTGCAGC--------------CCCATGAACCTGTGGATCCTGATGACCAAACCCAGGAATCCCCAA Gorilla: ACCCAACTGTCTAAGTTGCAGT----------------------------CATCGGGATGGCCAAACCCAGGAATCCCCAA ↑ 1 3 4 2 Human: ACCCAACTGTCTAAGTTGCAGC--------------CCCATGAACCTGTGGATCCCGATGACCAAACCCAGGAATCCCCAA Cluster: [ ] Orangutan: ACCCAACTGTCTAAGTTGCAGCCCTAAGAACCTGTG--------------GATCCCAATGACCAAGCCCAGGAATC-CCAG Human > Gorilla --------------- chr11:66364173-66364179 Template switch process: F1: L GATCAGGAGGGGTCTGGGAAACCCAACTGTCTAAGTTGCAG 1 F3: 4 GATGGCCAAACCCAGGAATCCCCAAGAGCATTGCTTTTGTAAGTA R RF: GATCAGGAGGGGTCTGGGAAACCCAACTGTCTAAGTTGCAGCCCCATGAACCTGTGGATCCCGATGACCAAACCCAGGAATCCCCAAGAGCATTGCTTTTGTAAGTA RR: CTAGTCCTCCCCAGACCCTTTGGGTTGACAGATTCAACGTCGGGGTACTTGGACACCTAGGGCTACTGGTTTGGGTCCTTAGGGGTTCTCGTAACGAAAACATTCAT F2: 3 GGCTACT 2 Unidirectional alignment (log-probability: -33.8) ATCAGGAGGGGTCTGGGAAACCCAACTGTCTAAGTTGCAGtC--------------ATCggGATGgCCAAACCCAGGAATCCCCAAGAGCATTGCTTTTGT ATCAGGAGGGGTCTGGGAAACCCAACTGTCTAAGTTGCAGCCCCATGAACCTGTGGATCCCGATGACCAAACCCAGGAATCCCCAAGAGCATTGCTTTTGT Template switch alignment (log-probability: -22.3) ATCAGGAGGGGTCTGGGAAACCCAACTGTCTAAGTTGCAG|TCATCGG|GATGgCCAAACCCAGGAATCCCCAAGAGCATTGCTTTTGT ATCAGGAGGGGTCTGGGAAACCCAACTGTCTAAGTTGCAG|TCATCGG|GATGACCAAACCCAGGAATCCCCAAGAGCATTGCTTTTGT ========= Event 426 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA--------------TGAC----CTCAGTCATTCGTCCCGCCCCAT ↑ 3 2 1 4 Chimp: CCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA-------CACGTATTGAA--CAGCCAGTCATTCGTCCTGCCCCAT Gorilla: CCCAACTTGTGTGGCCCTGAGGTCATTCGACAAACACGTAT-------TGAACA--TCCAGTCATTCGTCCCGCCCCAT ↓ 3 2 1 4 Human: CCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA--------------TGAC----CTCAGTCATTCGTCCCGCCCCAT Cluster: [ ] Orangutan: CCCAACTCGTGTGGCCCTGAGGTCATTCGACAAACATGTAT-------TGAACA--TCCAGTCATTCGTCCCGCCCCAT Chimp > Human ------------- chr11:64488408-64488413 Template switch process: F1: L TCTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA 1 F3: 4 CAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG R RF: TCTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAACACGTATTGAACAGCCAGTCATTCGTCCTGCCCCATCGCCTGCAGCTGCAAACGG RR: AGAGGTCGGGTTGAACACACCGGGACTCCAGTAAGCTGTTTGTGCATAACTTGTCGGTCAGTAAGCAGGACGGGGTAGCGGACGTCGACGTTTGCC F2: 3 TCCAGT 2 Unidirectional alignment (log-probability: -36.5) CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAAtgacct---------------CAGTCATTCGTCCcGCCCCATCGCCTGCAGCTGCAAACGG CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA------CACGTATTGAACAGCCAGTCATTCGTCCTGCCCCATCGCCTGCAGCTGCAAACGG Template switch alignment (log-probability: -22) CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA|TGACCT|CAGTCATTCGTCCcGCCCCATCGCCTGCAGCTGCAAACGG CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA|TGACCT|CAGTCATTCGTCCTGCCCCATCGCCTGCAGCTGCAAACGG Gorilla > Human --------------- chr11:64488408-64488413 Template switch process: F1: L TCTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA 1 F3: 4 CAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG R RF: TCTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAACACGTATTGAACATCCAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG RR: AGAGGTCGGGTTGAACACACCGGGACTCCAGTAAGCTGTTTGTGCATAACTTGTAGGTCAGTAAGCAGGGCGGGGTAGCGGACGTCGACGTTTGCC F2: 3 TCCAGT 2 Unidirectional alignment (log-probability: -30) CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA---------------tgacctCAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAACACGTATTGAACATC------CAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG Template switch alignment (log-probability: -16.5) CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA|TGACCT|CAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG CTCCAGCCCAACTTGTGTGGCCCTGAGGTCATTCGACAAA|TGACCT|CAGTCATTCGTCCCGCCCCATCGCCTGCAGCTGCAAACGG ========= Event 427 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAAGATGGGTCCAGATgtgtggtggcacaaggctgta ↑ 3 2 4 1 Chimp: ATTCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAA----------GATgtgtggtggcacaaggctgta Gorilla: ATTCCCAAATGTCAGTCAGTGGACCAGTTGCATTAGAAGATGGGTCCAGATgtgtggtggcacaaggctgta Human: ATTCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAAGATGGGTCCAGATgtgtggtggcacaaggctgta Cluster: [ ] Orangutan: Chimp > Human ------------- chr1:77766618-77766623 Template switch process: F1: L GCAATTCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAAGATG 1 F3: 4 GATGTGTGGTGGCACAAGGCTGTAATCCCAGCTAAATCGC R RF: GCAATTCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAAGATGTGTGGTGGCACAAGGCTGTAATCCCAGCTAAATCGT RR: CGTTAAGGGTTTACGGTCAGTCACCTGGTCAACGTAATCTTCTACACACCACCGTGTTCCGACATTAGGGTCGATTTAGCA F2: 3 ACCTGG 2 Unidirectional alignment (log-probability: -31.3) TCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAagatgggtccAGATGTGTGGTGGCACAAGGCTGTAATCCCAGCTAAATCGc TCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGA----------AGATGTGTGGTGGCACAAGGCTGTAATCCCAGCTAAATCGT Template switch alignment (log-probability: -22.1) TCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAAGATG|GGTCCA|GATGTGTGGTGGCACAAGGCTGTAATCCCAGCTAAATCGc TCCCAAATGCCAGTCAGTGGACCAGTTGCATTAGAAGATG|GGTCCA|GATGTGTGGTGGCACAAGGCTGTAATCCCAGCTAAATCGT ========= Event 428 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: CCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTACACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTT ↓ 3 1 2 4 ↑ 13 24 Chimp: CCACTTAATAATCTACCCAGCAGTATACTTACCTGTGTACATGGAAGACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTT ↓ 13 24 ↑ 3 1 2 4 Gorilla: CCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTACACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTT Human: CCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTACACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTT Cluster: [ ] Orangutan: CCACTTAATAATCTACCCAGCAGTATACTTACTTGTCTTCCATGTACACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTT Chimp > Human ------------- chr1:171248874-171248884 Template switch process: F1: L TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT 1 F3: 4 ACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTTGA R RF: TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGTGTACATGGAAGACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTTGA RR: AAGTTGGTGAATTATTAGATGGGTCGTCATATGAATGGACACATGTACCTTCTGTCCATTCATATGACGACCCATCTAATAATTCACCAACT F2: 3 CATGTACCTTC 2 Unidirectional alignment (log-probability: -37.6) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGtcttccaTGTAC-------ACAGGTAAGTATACTGtTGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTG-------TGTACATGGAAGACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTTGA Template switch alignment (log-probability: -22.6) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|CTTCCATGTAC|ACAGGTAAGTATACTGtTGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|CTTCCATGTAC|ACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTTGA Human > Chimp ------------- chr1:149555553-149555580 Template switch process: F1: L TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT 1 F3: 4 TGGGTAGATTATTAAGTGGTTGA R RF: TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTACACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTTGA RR: AAGTTGGTGAATTATTAGATGGGTCGTCATATGAATGGACAGAAGGTACATGTGTCCATTCATATGACAACCCATCTAATAATTCACCAACT F2: 3 CGTCATATGAATGGACAGAAGGTACATG 2 Unidirectional alignment (log-probability: -37.6) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTG-------TGTACatggaagACAGGTAAGTATACTGcTGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTAC-------ACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTTGA Template switch alignment (log-probability: -18.4) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|GTACATGGAAGACAGGTAAGTATACTGC|TGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|GTACATGGAAGACAGGTAAGTATACTGC|TGGGTAGATTATTAAGTGGTTGA Gorilla > Chimp --------------- chr1:149555553-149555580 Template switch process: F1: L TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT 1 F3: 4 TGGGTAGATTATTAAGTGGTTGA R RF: TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTACACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTTGA RR: AAGTTGGTGAATTATTAGATGGGTCGTCATATGAATGGACAGAAGGTACATGTGTCCATTCATATGACAACCCATCTAATAATTCACCAACT F2: 3 CGTCATATGAATGGACAGAAGGTACATG 2 Unidirectional alignment (log-probability: -36.6) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTG-------TGTACatggaagACAGGTAAGTATACTGcTGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGTCTTCCATGTAC-------ACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTTGA Template switch alignment (log-probability: -18.9) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|GTACATGGAAGACAGGTAAGTATACTGC|TGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|GTACATGGAAGACAGGTAAGTATACTGC|TGGGTAGATTATTAAGTGGTTGA Chimp > Gorilla --------------- chr1:150254854-150254864 Template switch process: F1: L TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT 1 F3: 4 ACAGGTAAGTATACTGTTGGGTAGATTATTAAGTGGTTGA R RF: TTCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGTGTACATGGAAGACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTTGA RR: AAGTTGGTGAATTATTAGATGGGTCGTCATATGAATGGACACATGTACCTTCTGTCCATTCATATGACGACCCATCTAATAATTCACCAACT F2: 3 CATGTACCTTC 2 Unidirectional alignment (log-probability: -36.6) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGtcttccaTGTAC-------ACAGGTAAGTATACTGtTGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTG-------TGTACATGGAAGACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTTGA Template switch alignment (log-probability: -22.6) TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|CTTCCATGTAC|ACAGGTAAGTATACTGtTGGGTAGATTATTAAGTGGTTGA TCAACCACTTAATAATCTACCCAGCAGTATACTTACCTGT|CTTCCATGTAC|ACAGGTAAGTATACTGCTGGGTAGATTATTAAGTGGTTGA ========= Event 429 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGGATGGTGTGCAGAGGCCAGAGATTGA-TGGTCTCTGGTCCCCGTGGGCCTTCCTGGT-- Chimp: GGGGATGGTGTGCAGAGACCAGAGATTCATCAATCTCT--GCCCCGTGGGCCTTCCTGGT-- ↑ 3 1 2 4 Gorilla: GGGGATGGTGTGCAGAGACCAGAGATTGA-TGGTCTCTGGTCCCCGTGGGCCTTCCTGGT-- Human: GGGGATGGTGTGCAGAGGCCAGAGATTGA-TGGTCTCTGGTCCCCGTGGGCCTTCCTGGT-- Cluster: [ ] Orangutan: GGGGATGGTGTGCAGAGAACAGAGATTGA-TGGTCTCTGGTCCCCGTGGGCCTTCCTGGTGG Gorilla > Chimp --------------- chr11:71273191-71273202 Template switch process: F1: L GGCTGCCCACTGGCGGGGATGGTGTGCAGAGACCAGAGATT 1 F3: 4 CCCCGTGGGCCTTCCTGGTGGGAGAAGGCGTCCCAGAAAG R RF: GGCTGCCCACTGGCGGGGATGGTGTGCAGAGACCAGAGATTGATGGTCTCTGGTCCCCGTGGGCCTTCCTGGTGGGAGAAGGCGTCCCAGAAAG RR: CCGACGGGTGACCGCCCCTACCACACGTCTCTGGTCTCTAACTACCAGAGACCAGGGGCACCCGGAAGGACCACCCTCTTCCGCAGGGTCTTTC F2: 3 GTCTCTAACTAC 2 Unidirectional alignment (log-probability: -37.1) GCTGCCCACTGGCGGGGATGGTGTGCAGAGACCAGAGATtcatcaatctcTG------------CCCCGTGGGCCTTCCTGGTGGGAGAAGGCGTCCCAGAAAG GCTGCCCACTGGCGGGGATGGTGTGCAGAGACCAGAGAT-----------TGATGGTCTCTGGTCCCCGTGGGCCTTCCTGGTGGGAGAAGGCGTCCCAGAAAG Template switch alignment (log-probability: -17.3) GCTGCCCACTGGCGGGGATGGTGTGCAGAGACCAGAGATT|CATCAATCTCTG|CCCCGTGGGCCTTCCTGGTGGGAGAAGGCGTCCCAGAAAG GCTGCCCACTGGCGGGGATGGTGTGCAGAGACCAGAGATT|CATCAATCTCTG|CCCCGTGGGCCTTCCTGGTGGGAGAAGGCGTCCCAGAAAG ========= Event 430 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGGTGGAAGACAAACTTTTCTAGTCACTGTCGTGT Chimp: GCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGGTGG------ACCTTTTCTAGTCACTGTCGTGT Gorilla: GCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGATGG------ACCTTTTCTAGTCACTGTCGTGT ↓ 3 2 1 4 Human: GCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGGTGGAAGACAAACTTTTCTAGTCACTGTCGTGT Cluster: [ ] Orangutan: GCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGGTGG------ACCTTTTCTAGTCACTGTTGTGT Gorilla > Human --------------- chr1:171911854-171911865 Template switch process: F1: L TTGCTGTTGCTTCTTCTCACTGGCTGGTTTGTCTTCCACAG 1 F3: 4 CTTTTCTAGTCACTGTCGTGTCAAAGAAAAGTCTGAGATT R RF: TTGCTGTTGCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGATGGACCTTTTCTAGTCACTGTCGTGTCAAAGAAAAGTCTGAGATT RR: AACGACAACGAAGAAGAGTGACCGACCAAACAGAAGGTGTCTACCTGGAAAAGATCAGTGACAGCACAGTTTCTTTTCAGACTCTAA F2: 3 AAACAGAAGGTG 2 Unidirectional alignment (log-probability: -30.6) TGCTGTTGCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGgTGGaagacaAaCTTTTCTAGTCACTGTCGTGTCAAAGAAAAGTCTGAGATT TGCTGTTGCTTCTTCTCACTGGCTGGTTTGTCTTCCACAGATGG------ACCTTTTCTAGTCACTGTCGTGTCAAAGAAAAGTCTGAGATT Template switch alignment (log-probability: -17.3) TGCTGTTGCTTCTTCTCACTGGCTGGTTTGTCTTCCACAG|GTGGAAGACAAA|CTTTTCTAGTCACTGTCGTGTCAAAGAAAAGTCTGAGATT TGCTGTTGCTTCTTCTCACTGGCTGGTTTGTCTTCCACAG|GTGGAAGACAAA|CTTTTCTAGTCACTGTCGTGTCAAAGAAAAGTCTGAGATT ========= Event 431 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAGGAACTCTTGAAAATATCTCAGCAACATGCATCTAATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCGCTGCA----------------------------------------------------------------------------------------------------------AATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGCTGAGTTGT ↓ 3 4 2 1 Chimp: TAAGGAACTCTTGAAAATATCTCAGCAACATGCATCTAATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCACTGCAAATTATCTGCTTCCTTTAAGAAACTGGGAAGCAGATAATTTGCAGTGAAATTAAACATAGGTTCAATTACATATGTCAGTATGAATTAGATGCATGTTGCTGAGAAAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGCTGAGTTGT ↑ 3 4 2 1 Gorilla: TAAGGAACTCTTGAAAATATCTCAGCAACATGCATCTAATTCATACTGACACATGTAATTGAACCTATGTTTAATTTCGCTGCA----------------------------------------------------------------------------------------------------------AATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGCTGAGTTGT Human: TAAGGAACTCTTGAAAATATCTCAGCAACATGCATCTAATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCGCTGCA----------------------------------------------------------------------------------------------------------AATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGCTGAGTTGT Cluster: [ ] Orangutan: TAAGGAACTCTTGAAAATATCTCAGCAACATGCATCTAATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCCCTGCA----------------------------------------------------------------------------------------------------------AATTATCTGCTTCCTTTAAGAAACTGGGTTAGTAAAATGCTGAGTTGT Human > Chimp ------------- chr1:77972511-77972587 Template switch process: F1: L AATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCACTGCAAATTATCTGCTTCCTTTAAGAAACTGGG 1 F3: 4 AAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGC R RF: TCTCAGCAACATGCATCTAATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCGCTGCAAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGC RR: AGAGTCGTTGTACGTAGATTAAGTATGACTGTATACATTAACTTGGATACAAATTAAAGCGACGTTTAATAGACGAAGGAAATTCTTTGACCCAACCATTTTACG F2: 3 AGAGTCGTTGTACGTAGATTAAGTATGACTGTATACATTAACTTGGATACAAATTAAAGTGACGTTTAATAGACGAA 2 Unidirectional alignment (log-probability: -169) AATTTCaCTGCAAATTATCTGCTTCCTTTAAGAAACTGggaagcagataatttgcagtgaaattaaacataggttcaattacatatgtcagtatgaattagatgcatgttgctgagaaaattatctgcttcctttaagaaactgGGTTGGTAAAATG AATTTCGCTGCAAATTATCTGCTTCCTTTAAGAAACTG----------------------------------------------------------------------------------------------------------GGTTGGTAAAATG Template switch alignment (log-probability: -37.1) AATTTCaCTGCAAATTATCTGCTTCCTTTAAGAAACTGGG|AAGCAGATAATTTGCAGtGAAATTAAACATAGGTTCAATTACATATGTCAGTATGAATTAGATGCATGTTGCTGAGA|AAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATG AATTTCGCTGCAAATTATCTGCTTCCTTTAAGAAACTGGG|AAGCAGATAATTTGCAGCGAAATTAAACATAGGTTCAATTACATATGTCAGTATGAATTAGATGCATGTTGCTGAGA|AAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATG Gorilla > Chimp --------------- chr1:77972511-77972587 Template switch process: F1: L AATTCATACTGACATATGTAATTGAACCTATGTTTAATTTCACTGCAAATTATCTGCTTCCTTTAAGAAACTGGG 1 F3: 4 AAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGC R RF: TCTCAGCAACATGCATCTAATTCATACTGACACATGTAATTGAACCTATGTTTAATTTCGCTGCAAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATGC RR: AGAGTCGTTGTACGTAGATTAAGTATGACTGTGTACATTAACTTGGATACAAATTAAAGCGACGTTTAATAGACGAAGGAAATTCTTTGACCCAACCATTTTACG F2: 3 AGAGTCGTTGTACGTAGATTAAGTATGACTGTATACATTAACTTGGATACAAATTAAAGTGACGTTTAATAGACGAA 2 Unidirectional alignment (log-probability: -174) AATTTCaCTGCAAATTATCTGCTTCCTTTAAGAAACTgggaagcagataatttgcagtgaaattaaacataggttcaattacatatgtcagtatgaattagatgcatgttgctgagaaaattatctgcttcctttaagaaactGGGTTGGTAAAATG AATTTCGCTGCAAATTATCTGCTTCCTTTAAGAAACT----------------------------------------------------------------------------------------------------------GGGTTGGTAAAATG Template switch alignment (log-probability: -48.2) AATTTCaCTGCAAATTATCTGCTTCCTTTAAGAAACTGGG|AAGCAGATAATTTGCAGtGAAATTAAACATAGGTTCAATTACATaTGTCAGTATGAATTAGATGCATGTTGCTGAGA|AAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATG AATTTCGCTGCAAATTATCTGCTTCCTTTAAGAAACTGGG|AAGCAGATAATTTGCAGCGAAATTAAACATAGGTTCAATTACATGTGTCAGTATGAATTAGATGCATGTTGCTGAGA|AAATTATCTGCTTCCTTTAAGAAACTGGGTTGGTAAAATG ========= Event 432 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTATTCTAAGTTTATAACTGATGCTTAGATATAAAGTGATATTTATACTCAATATCAACAATAGTGATATTGAATATAAATTctgagttctaacctaaagtcaga Chimp: tctgactttaggttagaactc-----------------agAATTTATACTCAATATCACTATTGTTGATATTGAGTATAAATATCACTTTATATCTAAGCATCAGT ↑ 1 3 4 2 Gorilla: TTTATTCTAAGTTTATAACTGATGCTTAGATATAAAGTGATATTTATACTCAATATCAACAATAGTGATATTGAGTACAAATTctgagttctaacctaaagtcaga Human: TTTATTCTAAGTTTATAACTGATGCTTAGATATAAAGTGATATTTATACTCAATATCAACAATAGTGATATTGAATATAAATTctgagttctaacctaaagtcaga Cluster: [ ] Orangutan: TTTATTCTAAGTTTATAACTGATGCTTAGATATAAAGTGA-----TTAATCAAAGTCAACAATAGTGATATTGAGTATAAATTctgagttctaacctaaagtcaga Gorilla > Chimp --------------- chr11:71842655-71842718 Template switch process: F1: L ACT 1 F3: 4 TCAG R RF: ACTGATGCTTAGATATAAAGTGATATTTATACTCAATATCAACAATAGTGATATTGAGTACAAATTCTGAGTTCTAACCTAAAGTCAGATATTTTTTGGTTGAGCGATCTTTGGTAAACTACTTTCTCTCTCTGGGTCAAAATTTCTTTCCTTCTGTAATCTCAG RR: TGACTACGAATCTATATTTCACTATAAATATGAGTTATAGTTGTTATCACTATAACTCATGTTTAAGACTCAAGATTGGATTTCAGTCTATAAAAAACCAACTCGCTAGAAACCATTTGATGAAAGAGAGAGACCCAGTTTTAAAGAAAGGAAGACATTAGAGTC F2: 3 ACGAATCTATATTTCACTATAAATATGAGTTATAGTTGTTATCACTATAACTCATATTTAAGAC 2 Unidirectional alignment (log-probability: -104) ACTcaGA-------------------ATTTATACTCAATATCActAtTgtTGATATTGAGTAtaaatatcactttatatctaagCA----------------------TCAG ACT--GATGCTTAGATATAAAGTGATATTTATACTCAATATCAACAATAGTGATATTGAGTA----------------------CAAATTCTGAGTTCTAACCTAAAGTCAG Template switch alignment (log-probability: -27.6) ACT|CAGAATTTaTACTCAATATCACTATTGTTGATATTGAGTATAAATATCACTTTATATCTAAGCA|TCAG ACT|CAGAATTTGTACTCAATATCACTATTGTTGATATTGAGTATAAATATCACTTTATATCTAAGCA|TCAG ========= Event 433 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gtcaatttagggtgatgggtgtacagtattt-----------------acaatattctccgtattAAGTGTCAC Chimp: GTCAATTTAGGGTGATGGGTGTACAGTATTT-----------------ACAATATTCTCCGTATTAAGTGTCAC ↓ 3 2 4 1 Gorilla: gtcaatttagggtgatgggtGTACAGTATTTACAATACTGTACAATTTACAATATTCTCCGTATTAAGTGTCAC Human: gtcaatttagggtgatgggtgtacagtattt-----------------acaatattctccgtattAAGTGTCAC Cluster: [ ] Orangutan: GTCAATTTAGGGTGATGGGTATACAGTATTT-----------------ACAATATTCTCCATATTAAGTGTCAC Chimp > Gorilla --------------- chr11:70964306-70964312 Template switch process: F1: L AATGCCAGTAGTCAATTTAGGGTGATGGGTGTACAGTATTTACAATA 1 F3: 4 ATTTACAATATTCTCCGTATTAAGTGTCACAAAATAAAAATGAT R RF: AATGCCAGTAGTCAATTTAGGGTGATGGGTGTACAGTATTTACAATATTCTCCGTATTAAGTGTCACAAAATAAAAATGAT RR: TTACGGTCATCAGTTAAATCCCACTACCCACATGTCATAAATGTTATAAGAGGCATAATTCACAGTGTTTTATTTTTACTA F2: 3 ACATGTC 2 Unidirectional alignment (log-probability: -35.3) GTAGTCAATTTAGGGTGATGGGTGTACAGTatttacaatactgtacaATTTACAATATTCTCCGTATTAAGTGTCACAAAATAAAAA GTAGTCAATTTAGGGTGATGGGTGTACAGT-----------------ATTTACAATATTCTCCGTATTAAGTGTCACAAAATAAAAA Template switch alignment (log-probability: -16.9) GTAGTCAATTTAGGGTGATGGGTGTACAGTATTTACAATA|CTGTACA|ATTTACAATATTCTCCGTATTAAGTGTCACAAAATAAAAA GTAGTCAATTTAGGGTGATGGGTGTACAGTATTTACAATA|CTGTACA|ATTTACAATATTCTCCGTATTAAGTGTCACAAAATAAAAA ========= Event 434 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGA------------GCAATATATGAGC-------ATCCTACTCATTCCCATAGGTTTCTAACATT Chimp: CATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGA------------GCAATA-------TATGAGCATCCTACTCATTCCCATAGGTTTCTAACATT ↑ 3 2 1 4 Gorilla: CATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGA------GGTACTGCAATT--------------TTCCTACTCACTCCCATAGGTTTCTAACATT ↓ 3 2 1 4 Human: CATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGA------------GCAATATATGAGC-------ATCCTACTCATTCCCATAGGTTTCTAACATT Cluster: [ ] Orangutan: CATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAGGAACC------ACAATT--------------TTCCCAGTCATTCCCATAGGTTTCTAACATT Gorilla > Human --------------- chr1:231657537-231657546 Template switch process: F1: L CCATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAG 1 F3: 4 GCA----TCCTACTCATTCCCATAGGTTTCTAACATTTTGACCAGCTTGATTCTGAT R RF: CCATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAGGTACTGCAATTTTCCTACTCACTCCCATAGGTTTCTAACATTTTGACCAGCTTGATTCTGAT RR: GGTATTTCTGGAGTCTCCAAAGTATATAACGTAGTTTACCTCCATGACGTTAAAAGGATGAGTGAGGGTATCCAAAGATTGTAAAACTGGTCGAACTAAGACTA F2: 3 AGTATATAAC 2 Unidirectional alignment (log-probability: -42.3) ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGA------GCAATaTatgagcaTCCTACTCAtTCCCATAGGTTTCTAACATTTTGACCA ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAGGTACTGCAATTT-------TCCTACTCACTCCCATAGGTTTCTAACATTTTGACCA Template switch alignment (log-probability: -32.8) ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAG|CAATATATGA|GCA----TCCTACTCAtTCCCATAGGTTTCTAACATTTTGACCA ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAG|CAATATATGA|GCAATTTTCCTACTCACTCCCATAGGTTTCTAACATTTTGACCA Gorilla > Chimp --------------- chr1:212335802-212335811 Template switch process: F1: L CCATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAG 1 F3: 4 GCA----TCCTACTCATTCCCATAGGTTTCTAACATTTTGACCAGCTTGATTCTGAT R RF: CCATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAGGTACTGCAATTTTCCTACTCACTCCCATAGGTTTCTAACATTTTGACCAGCTTGATTCTGAT RR: GGTATTTCTGGAGTCTCCAAAGTATATAACGTAGTTTACCTCCATGACGTTAAAAGGATGAGTGAGGGTATCCAAAGATTGTAAAACTGGTCGAACTAAGACTA F2: 3 AGTATATAAC 2 Unidirectional alignment (log-probability: -42.3) ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGA------GCAATaTatgagcaTCCTACTCAtTCCCATAGGTTTCTAACATTTTGACCA ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAGGTACTGCAATTT-------TCCTACTCACTCCCATAGGTTTCTAACATTTTGACCA Template switch alignment (log-probability: -32.8) ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAG|CAATATATGA|GCA----TCCTACTCAtTCCCATAGGTTTCTAACATTTTGACCA ATAAAGACCTCAGAGGTTTCATATATTGCATCAAATGGAG|CAATATATGA|GCAATTTTCCTACTCACTCCCATAGGTTTCTAACATTTTGACCA ========= Event 435 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTTTCCAAGAAAAGACTGAATAGGCTC------------------------TACCAATTCTTTCAAGATTGGCTCTACCAATCTTGAAAGACTGCCATTCAATGATATTGA Chimp: CTTTTCCAAGAAAAGACTGAACAGGCTC------------------------TACCAATTCTTTCAAGATTGGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTGA ↑ 4 3 1 2 Gorilla: CTTTTCCAAGAAAAGACTGAACAGGCTC------------------------------------------------TACCAATCTTGAAAGACTGCCATTCAATGATACTGA ↓ 4 3 1 2 Human: CTTTTCCAAGAAAAGACTGAATAGGCTC------------------------TACCAATTCTTTCAAGATTGGCTCTACCAATCTTGAAAGACTGCCATTCAATGATATTGA Cluster: [ ] Orangutan: CTTTTCCAAGAAAAGACTGAACAGACTCTATGAATTCTTTCAAGATTGGCTC------------------------TACCAATCTTGAAAGACTGCCATTCAATGATACTGA Gorilla > Human --------------- chr11:72870459-72870470 Template switch process: F1: L CCTATATAACTGTGCTTCTACTTTTCCAAGAAAAGACTGAATAGGCTCTACCAAT 1 F3: 4 GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATATTGAGTTA R RF: CCTATATAACTGTGCTTCTACTTTTCCAAGAAAAGACTGAACAGGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTGAGTTA RR: GGATATATTGACACGAAGATGAAAAGGTTCTTTTCTGACTTGTCCGAGATGGTTAGAACTTTCTGACGGTAAGTTACTATGACTCAAT F2: 3 TTAGAACTTTCT 2 Unidirectional alignment (log-probability: -56.5) TTCTACTTTTCCAAGAAAAGACTGAAtAggctctaccaattctttcaagattGGCTCTACCAATCTTGAAAGACTGCCATTCAATGATAtTG TTCTACTTTTCCAAGAAAAGACTGAACA------------------------GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTG Template switch alignment (log-probability: -28.7) TTCTACTTTTCCAAGAAAAGACTGAAtAGGCTCTACCAAT|TCTTTCAAGATT|GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATAtTG TTCTACTTTTCCAAGAAAAGACTGAACAGGCTCTACCAAT|TCTTTCAAGATT|GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTG Gorilla > Chimp --------------- chr11:72803687-72803698 Template switch process: F1: L AACTGTGCTTCTACTTTTCCAAGAAAAGACTGAACAGGCTCTACCAAT 1 F3: 4 GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTGAGTTA R RF: AACTGTGCTTCTACTTTTCCAAGAAAAGACTGAACAGGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTGAGTTA RR: TTGACACGAAGATGAAAAGGTTCTTTTCTGACTTGTCCGAGATGGTTAGAACTTTCTGACGGTAAGTTACTATGACTCAAT F2: 3 TTAGAACTTTCT 2 Unidirectional alignment (log-probability: -45.4) TTCTACTTTTCCAAGAAAAGACTGAACAGGCtctaccaattctttcaagattggcTCTACCAATCTTGAAAGACTGCCATTCAATGATACTG TTCTACTTTTCCAAGAAAAGACTGAACAGGC------------------------TCTACCAATCTTGAAAGACTGCCATTCAATGATACTG Template switch alignment (log-probability: -17.5) TTCTACTTTTCCAAGAAAAGACTGAACAGGCTCTACCAAT|TCTTTCAAGATT|GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTG TTCTACTTTTCCAAGAAAAGACTGAACAGGCTCTACCAAT|TCTTTCAAGATT|GGCTCTACCAATCTTGAAAGACTGCCATTCAATGATACTG ========= Event 436 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CATGTATGTTGATGTATGGATCACTAAT-----TTGAGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAAAA ↑ 1 4 3 2 Chimp: CATGTATGTTGATGTATGGAT--GTGTT-----ATAAGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAAAA Gorilla: CATGTATGTTGATGTATGGAT--GTGTT----------ATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAAAA ↓ 1 4 3 2 Human: CATGTATGTTGATGTATGGATCACTAAT-----TTGAGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAAAA Cluster: [ ] Orangutan: catgtatgttgatgtatggat--gtatTATAAT-----ATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAAAA Chimp > Human ------------- chr1:172902540-172902549 Template switch process: F1: L CTTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT 1 F3: 4 AGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATAT R RF: CTTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGATGTGTTATAAGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATAT RR: GAACCAATACAAGTAATTACGTACATACAACTACATACCTACACAATATTCTATTCATATAGAGTTTAATCACTTACGCTTTCACTATA F2: 3 GTTTAATCAC 2 Unidirectional alignment (log-probability: -34.4) TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAtcactaattTG-------AGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATAT TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGA---------TGTGTTATAAGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATAT Template switch alignment (log-probability: -16.5) TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT|CACTAATTTG|AGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATAT TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT|CACTAATTTG|AGATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATAT Gorilla > Human --------------- chr1:172902540-172902551 Template switch process: F1: L CTTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT 1 F3: 4 ATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAA R RF: CTTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGATGTGTTATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAA RR: GAACCAATACAAGTAATTACGTACATACAACTACATACCTACACAATATTCATATAGAGTTTAATCACTTACGCTTTCACTATATT F2: 3 GAGTTTAATCAC 2 Unidirectional alignment (log-probability: -36.7) TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGATcactaatttgaG----ATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAA TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT-----------GTGTTATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAA Template switch alignment (log-probability: -17.3) TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT|CACTAATTTGAG|ATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAA TTGGTTATGTTCATTAATGCATGTATGTTGATGTATGGAT|CACTAATTTGAG|ATAAGTATATCTCAAATTAGTGAATGCGAAAGTGATATAA ========= Event 437 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGGTGCCACCAAGTAGCCTACATGCCTTCAT----------ATTTCCCCTGAGCAACTGGAAAGTGGCTGTTGCCCCATCATATGGGT Chimp: CTGGTGCCACCAAGTAGCCTACATGCCTTCAT----------ATTTCCCCGGAGCAACTGGAAAGTGGCTGTTGCCCCATCATATGGGT ↓ 3 2 1 4 Gorilla: CTGGTGCCACCAAGTAGCCTACATGCCTTCAT--------------------GGCATGTAGAAAGTGGTTGTTGCCCCATCATATGGGT ↑ 3 2 1 4 Human: CTGGTGCCACCAAGTAGCCTACATGCCTTCAT----------ATTTCCCCTGAGCAACTGGAAAGTGGCTGTTGCCCCATCATATGGGT Cluster: [ ] Orangutan: ctggtgccaccaagtagcccacatgccttcatacttcccctg----------agcaactggaaagtggctgttgccccATCATATGGGT Human > Gorilla --------------- chr1:76297837-76297844 Template switch process: F1: L TCAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCAT 1 F3: 4 GAAAGTGGTTGTTGCCCCATCATATGGGTGGGATCTAATTGGGCAAATG R RF: TCAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCATATTTCCCCTGAGCAACTGGAAAGTGGCTGTTGCCCCATCATATGGGTGGGATCTAATTGGGCAAATG RR: AGTCTACATGACCACGGTGGTTCATCGGATGTACGGAAGTATAAAGGGGACTCGTTGACCTTTCACCGACAACGGGGTAGTATACCCACCCTAGATTAACCCGTTTAC F2: 3 ATGTACGG 2 Unidirectional alignment (log-probability: -37.2) CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCA-----------------TGgcatgtaGAAAGTGGtTGTTGCCCCATCATATGGGTGGGATCTAATT CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCATATTTCCCCTGAGCAACTG-------GAAAGTGGCTGTTGCCCCATCATATGGGTGGGATCTAATT Template switch alignment (log-probability: -22.5) CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCAT|GGCATGTA|GAAAGTGGtTGTTGCCCCATCATATGGGTGGGATCTAATT CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCAT|GGCATGTA|GAAAGTGGCTGTTGCCCCATCATATGGGTGGGATCTAATT Chimp > Gorilla --------------- chr1:76297837-76297844 Template switch process: F1: L TCAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCAT 1 F3: 4 GAAAGTGGTTGTTGCCCCATCATATGGGTGGGATCTAATTGGGCAAATG R RF: TCAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCATATTTCCCCGGAGCAACTGGAAAGTGGCTGTTGCCCCATCATATGGGTGGGATCTAATTGGGCAAATG RR: AGTCTACATGACCACGGTGGTTCATCGGATGTACGGAAGTATAAAGGGGCCTCGTTGACCTTTCACCGACAACGGGGTAGTATACCCACCCTAGATTAACCCGTTTAC F2: 3 ATGTACGG 2 Unidirectional alignment (log-probability: -37.2) CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCA-----------------TGgcatgtaGAAAGTGGtTGTTGCCCCATCATATGGGTGGGATCTAATT CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCATATTTCCCCGGAGCAACTG-------GAAAGTGGCTGTTGCCCCATCATATGGGTGGGATCTAATT Template switch alignment (log-probability: -22.5) CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCAT|GGCATGTA|GAAAGTGGtTGTTGCCCCATCATATGGGTGGGATCTAATT CAGATGTACTGGTGCCACCAAGTAGCCTACATGCCTTCAT|GGCATGTA|GAAAGTGGCTGTTGCCCCATCATATGGGTGGGATCTAATT ========= Event 438 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GACTACCAGCAGTCTCTTCTG----------------------------------GCACTCCTGAGCGCGGCCACCAGAGGGAGTGCC Chimp: GACTACCAGCAGTCTCTTCTGGTGGTCTTCCACCAGAAGAGCGCGGTGGACTTCCGCGCTCGGGAGTGCGGCCACCAGAGGGAGTGCC ↓ 1 3 4 Gorilla: GACTACCAGCAGTCTCTTCTG----------------------------------GCACTCCCGAGCGCGGCCACCAGAGGGAGTGCC Human: GACTACCAGCAGTCTCTTCTG----------------------------------GCACTCCTGAGCGCGGCCACCAGAGGGAGTGCC Cluster: [ ] Orangutan: AACTACCAGCAGTCTCTTCTG----------------------------------GCACTCCCGAGCGCGGCCACCAGAGGGAGCGCC Chimp > Gorilla --------------- chr11:73048859-73048869 Template switch process: F1: L GCTCTGACCTTCCTGCCGAGGACTACCAGCAGTCTCTTCTGG 1 F3: 4 GCGGCCACCAGAGGGAGTGCCTCCCTTTCCTGAGACAGCC R RF: GCTCTGACCTTCCTGCCGAGGACTACCAGCAGTCTCTTCTGGTGGTCTTCCACCAGAAGAGCGCGGTGGACTTCCGCGCTCGGGAGTGCGGCCACCAGAGGGAGTGCCTCCCTTTCCTGAGACAGCC RR: CGAGACTGGAAGGACGGCTCCTGATGGTCGTCAGAGAAGACCACCAGAAGGTGGTCTTCTCGCGCCACCTGAAGGCGCGAGCCCTCACGCCGGTGGTCTCCCTCACGGAGGGAAAGGACTCTGTCGG F2: 3 CGAGCCCTCAC 2 Unidirectional alignment (log-probability: -34.9) TCTGACCTTCCTGCCGAGGACTACCAGCAGTCTCTTCTG----------------------------------GCaCTCccGAGcGCGGCCACCAGAGGGAGTGCCTCCCTTTCCTGAGACAGCC TCTGACCTTCCTGCCGAGGACTACCAGCAGTCTCTTCTGGTGGTCTTCCACCAGAAGAGCGCGGTGGACTTCCGCGCTCGGGAGTGCGGCCACCAGAGGGAGTGCCTCCCTTTCCTGAGACAGCC Template switch alignment (log-probability: -17.2) TCTGACCTTCCTGCCGAGGACTACCAGCAGTCTCTTCTGG|CACTCCCGAGC|GCGGCCACCAGAGGGAGTGCCTCCCTTTCCTGAGACAGCC TCTGACCTTCCTGCCGAGGACTACCAGCAGTCTCTTCTGG|CACTCCCGAGC|GCGGCCACCAGAGGGAGTGCCTCCCTTTCCTGAGACAGCC ========= Event 439 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT---ACTTTGTGGGTACAACCAGTGTTGACCAAT Chimp: TTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT---ACTTTGTGGGTACAACCAGTGTTGACCAAT ↓ 3 2 1 4 Gorilla: TTGAACTTGCCTCTCCCTCTCCAGAGGCCCAGCT------C-TGGAGTACAACCAGTGTTGACCAAT ↑ 3 2 1 4 Human: TTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT---ACTTTGTGGGTACAACCAGTGTTGACCAAT Cluster: [ ] Orangutan: TTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCTACT---TTGTGGGTACAACCAGTGTTGACCAAT Human > Gorilla --------------- chr11:62480703-62480707 Template switch process: F1: L TGAGGGTTTGAACTTGCCTCTCCCTCTCCAGAGGCCCAGCT 1 F3: 4 GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT R RF: TGAGGGTTTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCTACTTTGTGGGTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT RR: ACTCCCAAACTTGGACGGAGAGGGAGAGGTCTCCGGGTCGATGAAACACCCATGTTGGTCACAACTGGTTAGTCCCCCAGTGTACGTTTA F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -32.3) GAGGGTTTGAACtTGCCTCTCCCTCTCCAGAGGCCCAGCTctggA--------GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT GAGGGTTTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT----ACTTTGTGGGTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT Template switch alignment (log-probability: -21.9) GAGGGTTTGAACtTGCCTCTCCCTCTCCAGAGGCCCAGCT|CTGGA|GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT GAGGGTTTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT|CTGGA|GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT Chimp > Gorilla --------------- chr11:62480703-62480707 Template switch process: F1: L TGAGGGTTTGAACTTGCCTCTCCCTCTCCAGAGGCCCAGCT 1 F3: 4 GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT R RF: TGAGGGTTTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCTACTTTGTGGGTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT RR: ACTCCCAAACTTGGACGGAGAGGGAGAGGTCTCCGGGTCGATGAAACACCCATGTTGGTCACAACTGGTTAGTCCCCCAGTGTACGTTTA F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -32.3) GAGGGTTTGAACtTGCCTCTCCCTCTCCAGAGGCCCAGCTctggA--------GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT GAGGGTTTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT----ACTTTGTGGGTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT Template switch alignment (log-probability: -21.9) GAGGGTTTGAACtTGCCTCTCCCTCTCCAGAGGCCCAGCT|CTGGA|GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT GAGGGTTTGAACCTGCCTCTCCCTCTCCAGAGGCCCAGCT|CTGGA|GTACAACCAGTGTTGACCAATCAGGGGGTCACATGCAAAT ========= Event 440 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: gtacaatgggcgtaataGAAATGTGT-ATTACTGAGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCTTTCA ↓ 1 4 3 2 Chimp: gtacaatgggcgtaataGAAACGCCTAGGCACTGTGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCTTTCA Gorilla: gtacaatgcgcgtaataGAAATGTGT-ATTACTGAGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCTTTCA Human: gtacaatgggcgtaataGAAATGTGT-ATTACTGAGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCTTTCA Cluster: [ ] Orangutan: gtacaatgggtgtaataggaatgtgT-Attattgagtatttaaaattgcctaggcactgtgctatgtgctttca Human > Chimp ------------- chr11:60530429-60530435 Template switch process: F1: L TGGGCCTCCATTTCTCATCTGTACAATGGGCGTAATAGAAACG 1 F3: 4 ACTGTGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCTTTCAT R RF: TGGGCCTCCATTTCTCATCTGTACAATGGGCGTAATAGAAATGTGTATTACTGAGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCTTTCAT RR: ACCCGGAGGTAAAGAGTAGACATGTTACCCGCATTATCTTTACACATAATGACTCATAAATTTTAACGGATCCGTGACACGATACACGAAAGTA F2: 3 CGGATCC 2 Unidirectional alignment (log-probability: -37.5) GCCTCCATTTCTCATCTGTACAATGGGCGTAATAGAAAcgcctaggcacTGTGTATT----------TAAAATTGCCTAGGCACTGTGCTATGTGCT GCCTCCATTTCTCATCTGTACAATGGGCGTAATAGAAA-----------TGTGTATTACTGAGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCT Template switch alignment (log-probability: -28.3) GCCTCCATTTCTCATCTGTACAATGGGCGTAATAGAAAcG|CCTAGGC|ACTGtGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCT GCCTCCATTTCTCATCTGTACAATGGGCGTAATAGAAATG|CCTAGGC|ACTGAGTATTTAAAATTGCCTAGGCACTGTGCTATGTGCT ========= Event 441 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGACGAGGGCCACAAAGATCT---TGGCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCAC Chimp: GGATGAGGGCCACAAAGATCT---TGGACCAAAAGGcagtgctcagcatgggttgggtccac ↓ 1 4 3 2 Gorilla: GGACGAGGGCCACAAAGATCTGCACTGCCCAAAAGGcagtgctcagcatgggttgggtccac ↑ 1 4 3 2 Human: GGACGAGGGCCACAAAGATCT---TGGCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCAC Cluster: [ ] Orangutan: GGACGAGGGCCACAAAGATCT---TGGCCCAAAAGGCAGTGCTCAGCACGGGTTGGGTCCAC Human > Gorilla --------------- chr11:60932889-60932893 Template switch process: F1: L AGGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCT 1 F3: 4 GCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCG R RF: AGGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCTTGGCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCG RR: TCCCGGTCGTCCGTAAGAATCCTGCTCCCGGTGTTTCTAGAACCGGGTTTTCCGTCACGAGTCGTACCCAACCCAGGTGTCGC F2: 3 TCACG 2 Unidirectional alignment (log-probability: -26.3) GGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCTgcactGCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCG GGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCT---TGGCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCG Template switch alignment (log-probability: -16.4) GGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCT|GCACT|GCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCG GGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCT|GCACT|GCCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCG Chimp > Gorilla --------------- chr11:60932889-60932895 Template switch process: F1: L AGGGCCAGCAGGCATTCTTAGGACGAGGGCCACAAAGATCT 1 F3: 4 CCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCGGG R RF: AGGGCCAGCAGGCATTCTTAGGATGAGGGCCACAAAGATCTTGGACCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCAGG RR: TCCCGGTCGTCCGTAAGAATCCTACTCCCGGTGTTTCTAGAACCTGGTTTTCCGTCACGAGTCGTACCCAACCCAGGTGTCGTCC F2: 3 CGTCACG 2 Unidirectional alignment (log-probability: -41.9) GGGCCAGCAGGCATTCTTAGGAcGAGGGCCACAAAGATCT----gcactgcCCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCgGG GGGCCAGCAGGCATTCTTAGGATGAGGGCCACAAAGATCTTGGA-------CCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCAGG Template switch alignment (log-probability: -27.7) GGGCCAGCAGGCATTCTTAGGAcGAGGGCCACAAAGATCT|GCACTGC|CCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCgGG GGGCCAGCAGGCATTCTTAGGATGAGGGCCACAAAGATCT|GCACTGC|CCAAAAGGCAGTGCTCAGCATGGGTTGGGTCCACAGCAGG ========= Event 442 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCCCAATTATTTTTCCACTCCTGG--GTTCCAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTTCCAG Chimp: AGCCAAATTATTTTTCCACTCAAGGGTATTCAAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTTCCAG ↑ 1 4 3 2 Gorilla: AGCCCAATTATTTTTCCACTCCTGG--GTTCCAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTTCCAG Human: AGCCCAATTATTTTTCCACTCCTGG--GTTCCAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTTCCAG Cluster: [ ] Orangutan: AGCCCAATTATTTTTCTGCTCCTGG--GTTCCAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTTCCAG Gorilla > Chimp --------------- chr1:152543100-152543110 Template switch process: F1: L GAAGACTTCCATATGCAAGAAGCCAAATTATTTTTCCACTC 1 F3: 4 AGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTT R RF: GAAGACTTTCATATGCAAGAAGCCCAATTATTTTTCCACTCCTGGGTTCCAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTT RR: CTTCTGAAAGTATACGTTCTTCGGGTTAATAAAAAGGTGAGGACCCAAGGTCTTCCGATAAGAACTTATGGGAACTTGGGGAGGACCCAA F2: 3 ACTTATGGGAA 2 Unidirectional alignment (log-probability: -41.5) AAGACTTcCATATGCAAGAAGCCaAATTATTTTTCCACTCaaGGGtaTTCaAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTT AAGACTTTCATATGCAAGAAGCCCAATTATTTTTCCACTCCTGGG--TTCCAGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTT Template switch alignment (log-probability: -28.2) AAGACTTcCATATGCAAGAAGCCaAATTATTTTTCCACTC|AAGGGTATTCA|AGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTT AAGACTTTCATATGCAAGAAGCCCAATTATTTTTCCACTC|AAGGGTATTCA|AGAAGGCTATTCTTGAATACCCTTGAACCCCTCCTGGGTT ========= Event 443 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AACAATGCTGTCTCTCTCAACAATGCTGTCTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAGCATTTTAATCTgccatacagtata Chimp: AACAATGCTGTCTCTCTCAACAATGCTGTCTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAGCATTTTAATCTgccatacagtata ↑ 1 4 3 2 Gorilla: AACAATGCTGTCTCTCTCAACTTT---ACATCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAGCATTTTAATCTgccatacagtata ↓ 1 4 3 2 Human: AACAATGCTGTCTCTCTCAACAATGCTGTCTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAGCATTTTAATCTgccatacagtata Cluster: [ ] Orangutan: AACAATGCTGTCTCTCTCCACTTT---ACATCCCTTTTTTCTAACGCAAGGTATATATTATTTACCACAGCAT-TTAATCTGCCATACGGTATA Gorilla > Human --------------- chr11:74832763-74832770 Template switch process: F1: L ACAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAAC 1 F3: 4 CTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAG R RF: ACAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAACTTTACATCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAGCATT RR: TGTTAACTATATAAACTTCATTGTTACGACAGAGAGAGTTGAAATGTAGGGAAAAAAGATTGGGTTCCATATATAATAAATGGTGTCGTAA F2: 3 TGTCGTAA 2 Unidirectional alignment (log-probability: -32.4) CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCA-----ACAatgctgtcTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAACTTTACA--------TCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA Template switch alignment (log-probability: -22.3) CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAAC|AATGCTGT|cTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAAC|AATGCTGT|ATCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA Gorilla > Chimp --------------- chr11:74833081-74833088 Template switch process: F1: L ACAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAAC 1 F3: 4 CTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAG R RF: ACAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAACTTTACATCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACAGCATT RR: TGTTAACTATATAAACTTCATTGTTACGACAGAGAGAGTTGAAATGTAGGGAAAAAAGATTGGGTTCCATATATAATAAATGGTGTCGTAA F2: 3 TGTCGTAA 2 Unidirectional alignment (log-probability: -32.4) CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCA-----ACAatgctgtcTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAACTTTACA--------TCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA Template switch alignment (log-probability: -22.3) CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAAC|AATGCTGT|cTCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA CAATTGATATATTTGAAGTAACAATGCTGTCTCTCTCAAC|AATGCTGT|ATCCCTTTTTTCTAACCCAAGGTATATATTATTTACCACA ========= Event 444 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAACTAACAATTAGGATCAGATGCCTTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAG--GTCTGCCAAAAGGTATGTATGGTAAAAGTTAAAGCCGTG ↑ 1 4 3 2 Chimp: TAACTAACAATTAGGATCA-GTCCACTAGTGATAAGGCATCTGGTGAGGATGGGGCAG--AGGTCTGCCAGAAGGTATGTGTGGTAAAAGTTAAAGCCGTG Gorilla: TAACTAACAATTAGGATCA-GTCCGCTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAG--GTCTGCCAAAAGGTATGTATGGTAAAAGTTAAAGCCGTG Human: TAACTAACAATTAGGATCAGATGCCTTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAG--GTCTGCCAAAAGGTATGTATGGTAAAAGTTAAAGCCGTG Cluster: [ ] Orangutan: TAACTAACAATTAGGATCA-ATCCACTAGTGATAAGGCATCTGGTGAGGATGGGACAGAG--GTCTGCCAAAAGGTATGTATGGTAAAAGTTAAAGCTGTG Chimp > Human ------------- chr11:7540927-7540932 Template switch process: F1: L CAG 1 F3: 4 TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGCCAAAAGGTATGTATGGTAAAAGTTAAAGCCGTGACCAAGTAGGTTGAGTCCAT R RF: CAGTCCACTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGCCAGAAGGTATGTGTGGTAAAAGTTAAAGCCGTGACCAAGTAGGTTGAGTCCAT RR: GTCAGGTGATCACTATTCCGTAGACCACTCCTACCCCGTCTCCAGACGGTCTTCCATACACACCATTTTCAATTTCGGCACTGGTTCATCCAACTCAGGTA F2: 3 TCCGTA 2 Unidirectional alignment (log-probability: -39.3) CagatgcctTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC C--------TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC Template switch alignment (log-probability: -28.3) CAG|ATGCCT|TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC CAG|ATGCCT|TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC ========= Event 445 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCTGGGCCTTTTACTTCAAAG------GGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCC ↓ 1 4 3 2 Chimp: ACCTGGGCCTTTTACTTCAAAATAAGTCTTCAAAGAGACTTATTTTTCCTTTCATGCCTTTCC ↑ 1 4 3 2 Gorilla: ACCTGGGCCTTTTACTTCAAAG------GGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCC Human: ACCTGGGCCTTTTACTTCAAAG------GGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCC Cluster: [ ] Orangutan: GCCTGGGCCTTTTACTTCAAAG------GGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCC Human > Chimp ------------- chr11:7394724-7394731 Template switch process: F1: L GAAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA 1 F3: 4 TCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCCC R RF: GAAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAAGGGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCCC RR: CTTTCTCTGAAGGGACGTTCTGGACCCGGAAAATGAAGTTTCCCGTTTCTCTGAATAAAAAGGAAAGTACGGAAAGGTACCGGG F2: 3 TCTGAATA 2 Unidirectional alignment (log-probability: -34.2) AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAAataagtctt---CAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA---------GGGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC Template switch alignment (log-probability: -22.3) AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA|ATAAGTCT|tCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA|ATAAGTCT|GCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC Gorilla > Chimp --------------- chr11:7394724-7394731 Template switch process: F1: L GAAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA 1 F3: 4 TCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCCC R RF: GAAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAAGGGCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCCC RR: CTTTCTCTGAAGGGACGTTCTGGACCCGGAAAATGAAGTTTCCCGTTTCTCTGAATAAAAAGGAAAGTACGGAAAGGTACCGGG F2: 3 TCTGAATA 2 Unidirectional alignment (log-probability: -33.7) AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA---ataagtcttCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAAGGG---------CAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC Template switch alignment (log-probability: -22.3) AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA|ATAAGTCT|tCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC AAAGAGACTTCCCTGCAAGACCTGGGCCTTTTACTTCAAA|ATAAGTCT|GCAAAGAGACTTATTTTTCCTTTCATGCCTTTCCATGGCC ========= Event 446 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTAACTAACAATTAGGATCAGATGCCTTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAG Chimp: ATTAACTAACAATTAGGATCA-GTCCACTAGTGATAAGGCATCTGGTGAGGATGGGGCAG-- Gorilla: ATTAACTAACAATTAGGATCA-GTCCGCTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAG ↓ 1 4 3 2 Human: ATTAACTAACAATTAGGATCAGATGCCTTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAG Cluster: [ ] Orangutan: ATTAACTAACAATTAGGATCA-ATCCACTAGTGATAAGGCATCTGGTGAGGATGGGACAGAG Gorilla > Human --------------- chr11:7540927-7540932 Template switch process: F1: L GAAAGCAGTGCAGACAGCCAATTAACTAACAATTAGGATCAG 1 F3: 4 TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC R RF: GAAAGCAGTGCAGACAGCCAATTAACTAACAATTAGGATCAGTCCGCTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC RR: CTTTCGTCACGTCTGTCGGTTAATTGATTGTTAATCCTAGTCAGGCGATCACTATTCCGTAGACCACTCCTACCCCGTCTCCAGACG F2: 3 TCCGTA 2 Unidirectional alignment (log-probability: -28.1) AAGCAGTGCAGACAGCCAATTAACTAACAATTAGGATCAGatgccT----TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC AAGCAGTGCAGACAGCCAATTAACTAACAATTAGGATCAG-----TCCGCTAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC Template switch alignment (log-probability: -16.5) AAGCAGTGCAGACAGCCAATTAACTAACAATTAGGATCAG|ATGCCT|TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC AAGCAGTGCAGACAGCCAATTAACTAACAATTAGGATCAG|ATGCCT|TAGTGATAAGGCATCTGGTGAGGATGGGGCAGAGGTCTGC ========= Event 447 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTCTGTGGCTAAGGAGAGAGAATTGCTAACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGA Chimp: TCTCTGCGGCTAAGGAGAGAGAATTGCTAACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGA ↑ 1 4 3 2 Gorilla: TCTCTGTGGCTAAGGAGAGAGGG--TCTCACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGA ↓ 1 4 3 2 Human: TCTCTGTGGCTAAGGAGAGAGAATTGCTAACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGA Cluster: [ ] Orangutan: TCTCTGTGGCTAAGGAGAGAGGG--TCTCACAAGCAGTTAGCAATTCCCAGAGTAGGACCTGGAGA Gorilla > Human --------------- chr1:72458096-72458103 Template switch process: F1: L GGTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAG 1 F3: 4 ACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA R RF: GGTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAGGGTCTCACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA RR: CCACAGATACGACCCTACTTAGAGACACCGATTCCTCTCTCCCAGAGTGTTCGTCAATCGTTAAGGGTCTCACCCTGGACCTCTCCT F2: 3 ATCGTTAA 2 Unidirectional alignment (log-probability: -30.4) GTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAGaaTtgCTaACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA GTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAGGGT--CTCACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA Template switch alignment (log-probability: -16.7) GTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAG|AATTGCTA|ACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA GTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAG|AATTGCTA|ACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA Gorilla > Chimp --------------- chr1:73566798-73566805 Template switch process: F1: L GGTGTCTATGCTGGGATGAATCTCTGCGGCTAAGGAGAGAG 1 F3: 4 ACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA R RF: GGTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAGGGTCTCACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA RR: CCACAGATACGACCCTACTTAGAGACACCGATTCCTCTCTCCCAGAGTGTTCGTCAATCGTTAAGGGTCTCACCCTGGACCTCTCCT F2: 3 ATCGTTAA 2 Unidirectional alignment (log-probability: -35.9) GTGTCTATGCTGGGATGAATCTCTGcGGCTAAGGAGAGAGaaTtgCTaACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA GTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAGGGT--CTCACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA Template switch alignment (log-probability: -22.3) GTGTCTATGCTGGGATGAATCTCTGcGGCTAAGGAGAGAG|AATTGCTA|ACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA GTGTCTATGCTGGGATGAATCTCTGTGGCTAAGGAGAGAG|AATTGCTA|ACAAGCAGTTAGCAATTCCCAGAGTGGGACCTGGAGAGGA ========= Event 448 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGTCCCTTCTGCTGTTCTAGGGAGCCC------CATGCAAGGCTCACAGTGTGGTggttttgcagttggg Chimp: TTGTCCCTTCTGCTGTCCTAGAGAGCCC------CATGCAAGGCTCACAGTGTGGTggttttgcagttggg ↓ 1 4 3 2 Gorilla: TTGTCCCTTCTGCTGTCCTAGGGAGCCACTGTGAGCTGCAAGGCTCACAGTGTGGTggttttgcagttggg ↑ 1 4 3 2 Human: TTGTCCCTTCTGCTGTTCTAGGGAGCCC------CATGCAAGGCTCACAGTGTGGTggttttgcagttggg Cluster: [ ] Orangutan: TTGTCCCTTCTGCTGTCCCAGGGAGCCC------CATGCAAGGCTCACAGTGTGGTggttttgcagttggg Human > Gorilla --------------- chr11:76638286-76638294 Template switch process: F1: L AGGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGGGAGCC 1 F3: 4 TGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT R RF: AGGAGGGGACCATGTTGTCCCTTCTGCTGTTCTAGGGAGCCCCATGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT RR: TCCTCCCCTGGTACAACAGGGAAGACGACAAGATCCCTCGGGGTACGTTCCGAGTGTCACACCACCAAAACGTCAACCCCTGGA F2: 3 CGAGTGTCA 2 Unidirectional alignment (log-probability: -36.1) GGAGGGGACCATGTTGTCCCTTCTGCTGTcCTAGGGAGCCaCtgtgagcTGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT GGAGGGGACCATGTTGTCCCTTCTGCTGTTCTAGGGAGCCCC------ATGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT Template switch alignment (log-probability: -22.4) GGAGGGGACCATGTTGTCCCTTCTGCTGTcCTAGGGAGCC|ACTGTGAGC|TGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT GGAGGGGACCATGTTGTCCCTTCTGCTGTTCTAGGGAGCC|ACTGTGAGC|TGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT Chimp > Gorilla --------------- chr11:76638286-76638294 Template switch process: F1: L CAGGACAGGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGGGAGCC 1 F3: 4 TGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT R RF: CAGGACAGGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGAGAGCCCCATGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT RR: GTCCTGTCCTCCCCTGGTACAACAGGGAAGACGACAGGATCTCTCGGGGTACGTTCCGAGTGTCACACCACCAAAACGTCAACCCCTGGA F2: 3 CGAGTGTCA 2 Unidirectional alignment (log-probability: -36.2) GGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGgGAGCCaCtgtgagcTGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT GGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGAGAGCCCC------ATGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT Template switch alignment (log-probability: -22.5) GGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGgGAGCC|ACTGTGAGC|TGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT GGAGGGGACCATGTTGTCCCTTCTGCTGTCCTAGAGAGCC|ACTGTGAGC|TGCAAGGCTCACAGTGTGGTGGTTTTGCAGTTGGGGACCT ========= Event 449 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGGTGCCCGAGTTCAGAATTCTCTGAGCAT Chimp: CTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGGTGCCCAAGTTCAGAATTCTCTGAGCAT ↓ 3 2 1 4 Gorilla: CTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGG-CCTAGAGTTCAGAATTCTCTGAGCAT Human: CTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGGTGCCCGAGTTCAGAATTCTCTGAGCAT Cluster: [ ] Orangutan: CTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGGTGCCTGAGTTCAGAATTCTCTGAGCAT Chimp > Gorilla --------------- chr1:72729254-72729258 Template switch process: F1: L AGCCCTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGG 1 F3: 4 AGTTCAGAATTCTCTGAGCATTCCAGATCTCCCAAAGGGT R RF: AGCCCTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGGTGCCCAAGTTCAGAATTCTCTGAGCATTCCAGATATCCCAAAGGGT RR: TCGGGAGACACCCTAAGGTACTAGATCCGGTAGATCACTCCACGGGTTCAAGTCTTAAGAGACTCGTAAGGTCTATAGGGTTTCCCA F2: 3 GATCC 2 Unidirectional alignment (log-probability: -33.3) GCCCTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAG--GCCtAgAGTTCAGAATTCTCTGAGCATTCCAGATcTCCCAAAGGGT GCCCTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGGTGCCCA-AGTTCAGAATTCTCTGAGCATTCCAGATATCCCAAAGGGT Template switch alignment (log-probability: -21.9) GCCCTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGG|CCTAG|AGTTCAGAATTCTCTGAGCATTCCAGATcTCCCAAAGGGT GCCCTCTGTGGGATTCCATGATCTAGGCCATCTAGTGAGG|CCTAG|AGTTCAGAATTCTCTGAGCATTCCAGATATCCCAAAGGGT ========= Event 450 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AACAAAAATAAAGAACATGGA----AAATGTTGCAAAACTAAAGTATTTCTCTAGATCATTCAA ↓ 1 4 3 2 Chimp: AACAAAAATAAAGAACATGGAACTTTAGTTTTGCAAAACTAAAGTATTTCTCTAGATCATTCAA Gorilla: AACAAAAATAAAGAATGTGGA----AAATGTTGCAAAACTAAAGTATTTCTCTAGATCGTTCAA Human: AACAAAAATAAAGAACATGGA----AAATGTTGCAAAACTAAAGTATTTCTCTAGATCATTCAA Cluster: [ ] Orangutan: AACAAAAATAAAGAACATGGA----AAATGTTGCAAAACTAAAGTATTTCTCTAGATCATTCAA Human > Chimp ------------- chr11:128095937-128095944 Template switch process: F1: L TGGAATGCTGGATCTGTGAAAACAAAAATAAAGAACATGGAA 1 F3: 4 TTGCAAAACTAAAGTATTTCTCTAGATCATTCAAATTAAT R RF: TGGAATGCTGGATCTGTGAAAACAAAAATAAAGAACATGGAAAATGTTGCAAAACTAAAGTATTTCTCTAGATCATTCAAATTAAT RR: ACCTTACGACCTAGACACTTTTGTTTTTATTTCTTGTACCTTTTACAACGTTTTGATTTCATAAAGAGATCTAGTAAGTTTAATTA F2: 3 TTGATTTC 2 Unidirectional alignment (log-probability: -28.7) GAATGCTGGATCTGTGAAAACAAAAATAAAGAACATGGAActttAgTtTTGCAAAACTAAAGTATTTCTCTAGATCATTCAAATTAAT GAATGCTGGATCTGTGAAAACAAAAATAAAGAACATGGAA----AATGTTGCAAAACTAAAGTATTTCTCTAGATCATTCAAATTAAT Template switch alignment (log-probability: -16.3) GAATGCTGGATCTGTGAAAACAAAAATAAAGAACATGGAA|CTTTAGTT|TTGCAAAACTAAAGTATTTCTCTAGATCATTCAAATTAAT GAATGCTGGATCTGTGAAAACAAAAATAAAGAACATGGAA|CTTTAGTT|TTGCAAAACTAAAGTATTTCTCTAGATCATTCAAATTAAT ========= Event 451 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTCCCCTCCTAGCTTGACTTTAGTGGTTTCCAATG--------------------TAGAAGTTAACAAAGTATGCCCCATTCCTGTG Chimp: GTCCCCTCCTAGCTTGACTTTGttaacttctacattggaaacttaacttctacattggaaacCACTAAAGTATGCCCCATTCCTGTG Gorilla: GTCCCCTCCTAGCTTGACTTTGTTAACTTCTACAT--------------------TGGAAACCACTAAAGTATGCCCCATTCCTATG ↓ 13 24 ↑ 13 24 Human: GTCCCCTCCTAGCTTGACTTTAGTGGTTTCCAATG--------------------TAGAAGTTAACAAAGTATGCCCCATTCCTGTG Cluster: [ ] Orangutan: GTCCCCTCCTAGCTTGACTTTGGTAACTTCTACAT--------------------TGGAAACCACTAAAGTATGCCCCATTCCTATG Gorilla > Human --------------- chr11:56870613-56870637 Template switch process: F1: L GTGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT 1 F3: 4 AAAGTATGCCCCATTCCTGTGACAAAAGCACAACCATTCT R RF: GTGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTTGTTAACTTCTACATTGGAAACCACTAAAGTATGCCCCATTCCTATGACAAAAGCACAACCATTCT RR: CACCCGTCATGGATAGGGGTCAGGGGAGGATCGAACTGAAACAATTGAAGATGTAACCTTTGGTGATTTCATACGGGGTAAGGATACTGTTTTCGTGTTGGTAAGA F2: 3 CAATTGAAGATGTAACCTTTGGTGA 2 Unidirectional alignment (log-probability: -54.5) TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTTagtggtttccaatgtagaaGTTAAC-------------------AAAGTATGCCCCATTCCTgTGACAAAAGCACAACCATTCT TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT-------------------GTTAACTTCTACATTGGAAACCACTAAAGTATGCCCCATTCCTATGACAAAAGCACAACCATTCT Template switch alignment (log-probability: -24.4) TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT|AGTGGTTTCCAATGTAGAAGTTAAC|AAAGTATGCCCCATTCCTgTGACAAAAGCACAACCATTCT TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT|AGTGGTTTCCAATGTAGAAGTTAAC|AAAGTATGCCCCATTCCTATGACAAAAGCACAACCATTCT Human > Gorilla --------------- chr11:57990536-57990560 Template switch process: F1: L GTGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT 1 F3: 4 AAAGTATGCCCCATTCCTATGACAAAAGCACAACCATTCT R RF: GTGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTTAGTGGTTTCCAATGTAGAAGTTAACAAAGTATGCCCCATTCCTGTGACAAAAGCACAACCATTCT RR: CACCCGTCATGGATAGGGGTCAGGGGAGGATCGAACTGAAATCACCAAAGGTTACATCTTCAATTGTTTCATACGGGGTAAGGACACTGTTTTCGTGTTGGTAAGA F2: 3 TCACCAAAGGTTACATCTTCAATTG 2 Unidirectional alignment (log-probability: -54.5) TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT-------------------GTTAACttctacattggaaaccactAAAGTATGCCCCATTCCTaTGACAAAAGCACAACCATTCT TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTTAGTGGTTTCCAATGTAGAAGTTAAC-------------------AAAGTATGCCCCATTCCTGTGACAAAAGCACAACCATTCT Template switch alignment (log-probability: -24.4) TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT|GTTAACTTCTACATTGGAAACCACT|AAAGTATGCCCCATTCCTaTGACAAAAGCACAACCATTCT TGGGCAGTACCTATCCCCAGTCCCCTCCTAGCTTGACTTT|GTTAACTTCTACATTGGAAACCACT|AAAGTATGCCCCATTCCTGTGACAAAAGCACAACCATTCT ========= Event 452 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGGGAGGGAAAAGATTGACCTGACC-TGA----TGTTCCTGTTAACTCAGCAGCTCC Chimp: TAGGGAGGGAAAAGATTGACCTGACC-TGA----TGTTCCTGTTAACTCAGCAGCTCC ↓ 3 1 2 4 Gorilla: TAGGGAGGGAAAAGATTGACCTGACCATCAGGTCAGGTCCTGTTAACTCAGCAGCTCC Human: TAGGGAGGGAAAAGATTGACCTGACC-TGA----TGTTCCTGTTAACTCAGCAGCTCC Cluster: [ ] Orangutan: TAGGGAGGGAAAAGATTGACCTGACC-TGT----TGTTCCTGTTAACTCGGCAGCTCC Chimp > Gorilla --------------- chr11:57796580-57796590 Template switch process: F1: L GGGAATCTCCAGCAGTAGGGAGGGAAAAGATTGACCTGACC 1 F3: 4 TCCTGTTAACTCAGCAGCTCCCTTTTGAGACCTTTGCAGT R RF: GGGAATCTCTAGCAGTAGGGAGGGAAAAGATTGACCTGACCTGATGTTCCTGTTAACTCAGCAGCTCCCTTTTGAGACCTTTGCAGT RR: CCCTTAGAGATCGTCATCCCTCCCTTTTCTAACTGGACTGGACTACAAGGACAATTGAGTCGTCGAGGGAAAACTCTGGAAACGTCA F2: 3 GGACTGGACTA 2 Unidirectional alignment (log-probability: -41.9) GGAATCTCcAGCAGTAGGGAGGGAAAAGATTGACCTGACC--ATcaggtcaGgTCCTGTTAACTCAGCAGCTCCCTTTTGAGACCTTTGCAGT GGAATCTCTAGCAGTAGGGAGGGAAAAGATTGACCTGACCTGAT-------GTTCCTGTTAACTCAGCAGCTCCCTTTTGAGACCTTTGCAGT Template switch alignment (log-probability: -22.6) GGAATCTCcAGCAGTAGGGAGGGAAAAGATTGACCTGACC|ATCAGGTCAGG|TCCTGTTAACTCAGCAGCTCCCTTTTGAGACCTTTGCAGT GGAATCTCTAGCAGTAGGGAGGGAAAAGATTGACCTGACC|ATCAGGTCAGG|TCCTGTTAACTCAGCAGCTCCCTTTTGAGACCTTTGCAGT ========= Event 453 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTGTAACTACGTTGGACAGA----------AAGTTGTATATCCTGCCTTTTTAAAATTTAAA Chimp: CATTGTAACTACGTTGGACAGA----------AAGTTGTATATCCTGCCTTTTTAAAATTTAAA ↓ 1 43 2 Gorilla: CATTGTAACTACGTTGGACAGGATATACAACTACGTTGTATATCCTGCCTTTTTAAAATTTAAA ↑ 1 43 2 Human: CATTGTAACTACGTTGGACAGA----------AAGTTGTATATCCTGCCTTTTTAAAATTTAAA Cluster: [ ] Orangutan: CATTGTAACTACGTTGGACAGA----------AAGTTGCATATCCTGCCTTTTTAAA----AAA Human > Gorilla --------------- chr1:158240352-158240362 Template switch process: F1: L CCTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG 1 F3: 4 ACGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTATT R RF: CCTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAGAAAGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTATT RR: GGAAAGGGGTCCGAGAAACAGTAACATTGATGCAACCTGTCTTTCAACATATAGGACGGAAAAATTTTAAATTTGTCCGGATAA F2: 3 TCAACATATAG 2 Unidirectional alignment (log-probability: -36.3) CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAGgatatacaactAcGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG----------AAAGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA Template switch alignment (log-probability: -22.7) CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG|GATATACAACT|AcGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG|GATATACAACT|AAGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA Chimp > Gorilla --------------- chr1:158240352-158240362 Template switch process: F1: L CCTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG 1 F3: 4 ACGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTATT R RF: CCTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAGAAAGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTATT RR: GGAAAGGGGTCCGAGAAACAGTAACATTGATGCAACCTGTCTTTCAACATATAGGACGGAAAAATTTTAAATTTGTCCGGATAA F2: 3 TCAACATATAG 2 Unidirectional alignment (log-probability: -36.3) CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAGgatatacaactAcGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG----------AAAGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA Template switch alignment (log-probability: -22.7) CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG|GATATACAACT|AcGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA CTTTCCCCAGGCTCTTTGTCATTGTAACTACGTTGGACAG|GATATACAACT|AAGTTGTATATCCTGCCTTTTTAAAATTTAAACAGGCCTA ========= Event 454 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CTACCGTTTGCCACACACTGCCCCATGTCCCTCACTGCTCCCGTCCTTCCTAGAAGTGAGGTGCTGATACATATAAAAATTATGGATCCCATTTTATGGGACATGAGCTGAAACAGGAGGTTTC Chimp: CTACCGTTTGCCACACACTGC-------CCCTCACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACATATAAAAATTGTGGATCCCATTTTATGGGACATGAGCTGAAACAGGAGGTTAC ↓ 1 4 3 2 Gorilla: CTACCGTTTGCCACACACTGCCCCATGTCCCACACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACATATAAAAATTATGGATCCCATTTTATGGGACATGAGCTGAAACAGGAGGTTTC Human: CTACCGTTTGCCACACACTGCCCCATGTCCCTCACTGCTCCCGTCCTTCCTAGAAGTGAGGTGCTGATACATATAAAAATTATGGATCCCATTTTATGGGACATGAGCTGAAACAGGAGGTTTC Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------------------- Chimp > Gorilla --------------- chr11:67387115-67387122 Template switch process: F1: L TAGAGGGGTAAGGGCCCCTGCTACCGTTTGCCACACACTGCCCC 1 F3: 4 CACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACAT R RF: TAGAGGGACAAGGGCCCCTGCTACCGTTTGCCACACACTGCCCCTCACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACATATAAAAATTGTGGATCCCATTTTATGGGACAT RR: ATCTCCCTGTTCCCGGGGACGATGGCAAACGGTGTGTGACGGGGAGTGACGAGGGCAGGAAGGACCTTCACTCCACGACTATGTATATTTTTAACACCTAGGGTAAAATACCCTGTA F2: 3 ACCCTGTA 2 Unidirectional alignment (log-probability: -37.6) GGGgtAAGGGCCCCTGCTACCGTTTGCCACACACTGCcccatgtCCCaCACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACAT GGGACAAGGGCCCCTGCTACCGTTTGCCACACACTGC-------CCCTCACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACAT Template switch alignment (log-probability: -27.9) GGGgtAAGGGCCCCTGCTACCGTTTGCCACACACTGCCCC|ATGTCCCA|CACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACAT GGGACAAGGGCCCCTGCTACCGTTTGCCACACACTGCCCC|ATGTCCCA|CACTGCTCCCGTCCTTCCTGGAAGTGAGGTGCTGATACAT ========= Event 455 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATCAAGATGGTGTCTGGTGAGCTAT-----TCCATGGCAGTCTTTGCTTGCA ↓ 3 1 24 Chimp: ATATCAAGATGGTGTCTGGTGAGCAATAGCTCACCATGGCAGTCTTTGCTTGCA ↑ 3 1 24 Gorilla: ATATCAAGATGGTGTCTGGTGAGCTAT-----TCCATGGCAGTCTTTGCTTGCA Human: ATATCAAGATGGTGTCTGGTGAGCTAT-----TCCATGGCAGTCTTTGCTTGCA Cluster: [ ] Orangutan: ATATCAAGATGGTGTCTGGTGAGCCAT-----TCCATGGCAGTCTTTGCTTGCA Human > Chimp ------------- chr11:56370035-56370043 Template switch process: F1: L TTTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGC 1 F3: 4 CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG R RF: TTTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGCTATTCCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG RR: AAACTGTACAATTGAATTATAGTTCTACCACAGACCACTCGATAAGGTACCGTCAGAAACGAACGTTGGAGGAATACGGTGACTC F2: 3 ACTCGATAA 2 Unidirectional alignment (log-probability: -30.1) TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGCaATagctcaCCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGCTAT-----TCCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG Template switch alignment (log-probability: -16.4) TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGC|AATAGCTCA|CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGC|AATAGCTCA|CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG Gorilla > Chimp --------------- chr11:56370035-56370043 Template switch process: F1: L TTTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGC 1 F3: 4 CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG R RF: TTTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGCTATTCCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG RR: AAACTGTACAATTGAATTATAGTTCTACCACAGACCACTCGATAAGGTACCGTCAGAAACGAACGTTGGAGGAATACGGTGACTC F2: 3 ACTCGATAA 2 Unidirectional alignment (log-probability: -29.2) TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGCaATagctcaCCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGCTATT-----CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG Template switch alignment (log-probability: -16.9) TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGC|AATAGCTCA|CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG TTGACATGTTAACTTAATATCAAGATGGTGTCTGGTGAGC|AATAGCTCA|CCATGGCAGTCTTTGCTTGCAACCTCCTTATGCCACTGAG ========= Event 456 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCTCTTGAGCATTTTCCAGCAC-----TCAGCTTTGGGTTACAGAACAGCTGTGTCTCTTTTACCATAAAGCTCGTGTGCCTTGTCTCTTACAGTGTCATACAACCCTCAAAGATGAGCACAGGATCCACACAAAAACA Chimp: CTCTCTTGAGCACTTTCCAGCAACTTTTAAAACTCTGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTCGTGTGCCTTGTCTCTTACAGTGTCATACAACCCTCAAAGATGAGCACAGGATCCACACAAAAACA ↓ 1 4 3 2 Gorilla: CTCTCTTGAGCACTTTCCAGCGC-----TCAGCTTTGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTCGTGTGCCTTGTCTCTTACAGTGTCATACAACCCTCAAAGATGAGCACAGGATCCACACAAAAACA Human: CTCTCTTGAGCATTTTCCAGCAC-----TCAGCTTTGGGTTACAGAACAGCTGTGTCTCTTTTACCATAAAGCTCGTGTGCCTTGTCTCTTACAGTGTCATACAACCCTCAAAGATGAGCACAGGATCCACACAAAAACA Cluster: [ ] Orangutan: CTCTCTTGAGCACATTCCAGCAC-----TCAGCTTTGGGTTACAGAACAGCTGTGTCTCCTTTAGTATAAACCTCATGTGCCTTGTCTCTTACAGTGTCATACAACCCTCAAAGATGAGCACAGGATCCACACAAAAACA Chimp > Gorilla --------------- chr11:56506928-56506936 Template switch process: F1: L TGGAACACTGTCACTCAGCCCTCTCTTGAGCACTTTCCAGC 1 F3: 4 TGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTC R RF: TGGAACACTGTCACTCAGCCCTCTCTTGAGCACTTTCCAGCAACTTTTAAAACTCTGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTCGTGTGCCTTGTCTCTTACAGTGTCATACAACCCTCAAAGATGAGC RR: ACCTTGTGACAGTGAGTCGGGAGAGAACTCGTGAAAGGTCGTTGAAAATTTTGAGACCCAATGTCTTGTCGACACAGAGAAAATGATATTTCGAGCACACGGAACAGAGAATGTCACAGTATGTTGGGAGTTTCTACTCG F2: 3 TTCGACTCG 2 Unidirectional alignment (log-probability: -32.4) GGAACACTGTCACTCAGCCCTCTCTTGAGCACTTTCCAGcgctCAgCTT---------TGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTC GGAACACTGTCACTCAGCCCTCTCTTGAGCACTTTCCAG----CAACTTTTAAAACTCTGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTC Template switch alignment (log-probability: -22.4) GGAACACTGTCACTCAGCCCTCTCTTGAGCACTTTCCAGC|GCTCAgCTT|TGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTC GGAACACTGTCACTCAGCCCTCTCTTGAGCACTTTCCAGC|GCTCATCTT|TGGGTTACAGAACAGCTGTGTCTCTTTTACTATAAAGCTC ========= Event 457 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GAACATGGACCAGTAAGTCCATGTTCAAAAGTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGA Chimp: GAACATGGACCAGTAAGTCCAT--------CTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAAA Gorilla: GAACATGGACCAGTAAGTCCAC--------CTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGA ↓ 1 4 3 2 Human: GAACATGGACCAGTAAGTCCATGTTCAAAAGTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGA Cluster: [ ] Orangutan: GAACATGGACCAGTAAGTCCAT--------CTCTAAGGTTTTGAAAAGTTGCTGCTGCTACTATAGA Gorilla > Human --------------- chr1:179530646-179530655 Template switch process: F1: L GTGGATAGCCCAGGTAAGGAGAACATGGACCAGTAAGTCCA 1 F3: 4 TCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGATCAC R RF: GTGGATAGCCCAGGTAAAGAGAACATGGACCAGTAAGTCCACCTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGATCAC RR: CACCTATCGGGTCCATTTCTCTTGTACCTGGTCATTCAGGTGGAGATTCGAAAACTTTTCAACGACGACGATGATGTCTAGTG F2: 3 GAAAACTTGT 2 Unidirectional alignment (log-probability: -39) TGGATAGCCCAGGTAAgGAGAACATGGACCAGTAAGTCCatgttcaaAagTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGATCAC TGGATAGCCCAGGTAAAGAGAACATGGACCAGTAAGTCC--------ACCTCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGATCAC Template switch alignment (log-probability: -28) TGGATAGCCCAGGTAAgGAGAACATGGACCAGTAAGTCCA|TgTTCAAAAG|TCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGATCAC TGGATAGCCCAGGTAAAGAGAACATGGACCAGTAAGTCCA|TTTTCAAAAG|TCTAAGCTTTTGAAAAGTTGCTGCTGCTACTACAGATCAC ========= Event 458 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGTCGGCAGTAACACTGCCGACTGGGTCTAAGGACCCAGGCACGAGAGGCCCCTATGCTGG Chimp: AGTGTTGGCAGTAACactgcc--------ct-tagacccaggcacgagaggcccctatgctgg Gorilla: AGTGTTGGCAGTAACACTGCC--------CT-TAGACCCAGGCACGAGAGGCCCCTATGCTGG ↓ 13 4 2 Human: AGTGTCGGCAGTAACACTGCCGACTGGGTCTAAGGACCCAGGCACGAGAGGCCCCTATGCTGG Cluster: [ ] Orangutan: AGTGTCAGCAGTAACACTGCC--------CT-TAGACCCAGGCACGAGAGGCCCCTATGCTGG Gorilla > Human --------------- chr1:179791228-179791240 Template switch process: F1: L ACCTAACGTTATGAGACTTCAGTGTCGGCAGTAACACTGCC 1 F3: 4 GACCCAGGCACGAGAGGCCCCTATGCTGGCCCTCCTCAGG R RF: ACCTAACGTTATGAGACTTCAGTGTTGGCAGTAACACTGCCCTTAGACCCAGGCACGAGAGGCCCCTATGCTGGCCCTCCTCAGG RR: TGGATTGCAATACTCTGAAGTCACAACCGTCATTGTGACGGGAATCTGGGTCCGTGCTCTCCGGGGATACGACCGGGAGGAGTCC F2: 3 GAATCTGGGTCAG 2 Unidirectional alignment (log-probability: -44.7) CCTAACGTTATGAGACTTCAGTGTcGGCAGTAACACTGCCgactgggtCTaAgGACCCAGGCACGAGAGGCCCCTATGCTGGCCCTCCTCAGG CCTAACGTTATGAGACTTCAGTGTTGGCAGTAACACTGCC--------CTTA-GACCCAGGCACGAGAGGCCCCTATGCTGGCCCTCCTCAGG Template switch alignment (log-probability: -28.4) CCTAACGTTATGAGACTTCAGTGTcGGCAGTAACACTGCC|GaCTGGGTCTAAG|GACCCAGGCACGAGAGGCCCCTATGCTGGCCCTCCTCAGG CCTAACGTTATGAGACTTCAGTGTTGGCAGTAACACTGCC|GCCTGGGTCTAAG|GACCCAGGCACGAGAGGCCCCTATGCTGGCCCTCCTCAGG ========= Event 459 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ggccacTTTCTTCCAATTAAGAACAGACACACATGTGGTAGCTGGAAATCCAGAATTGTCGTGAATAAAGACTCTTACTTGTAGATCCAAGAGATATTTATAACCCCATTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAGCCAGCACTTCCTTCTCTCTGTCACTCAAG Chimp: ggccacTTTCTTCCAATTAAGAACAGACACACATGTGGTAGCTGGAAATCCAGAATTGTCGTGAATAAAGACTCTTACTTGTAGATCCAAGAGATATTTATAACCCCATTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAGCCAGCACCTCCTTCTCTCTGTCACTCAAG ↓ 3 2 1 4 Gorilla: ggccacTTTCTTCCAATTAAGAACAGACACACATGTGGTAGCTGGAAATCCAGAATTGTCGTGAATAAAGACTCTTACTTGTAGATCCAAGAGATATTTATAACCCCATTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAGTATGTTCTTCCTTCTCTCTGTCACTCAAG Human: ggccacTTTCTTCCAATTAAGAACAGACACACATGTGGTAGCTGGAAATCCAGAATTGTCGTGAATAAAGACTCTTACTTGTAGATCCAAGAGATATTTATAACCCCATTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAGCCAGCACTTCCTTCTCTCTGTCACTCAAG Cluster: [ ] Orangutan: ggccacTTTCTTCCAATTAAGAACAGACACACATGTGGTAGCTGGAAATCCAGAATTGTCGTGAATAAAGACTCTTACTTGTAGATCCAAGAAATATTTATAACCCCATTAGACTCTGGACTTCAGAAAGTGCTGGCCTGGTAAACAGTATGTTCTTCCTTCTCTCTAGCACTCAAT Chimp > Gorilla --------------- chr1:158941726-158941733 Template switch process: F1: L ATTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAG 1 F3: 4 TCCTTCTCTCTGTCACTCAAGGGTTTAACTCCTACACAAA R RF: AGAACAGACACACATGTGGTAGCTGGAAATCCAGAATTGTCGTGAATAAAGACTCTTACTTGTAGATCCAAGAGATATTTATAACCCCATTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAGCCAGCACCTCCTTCTCTCTGTCACTCAAGGGTTTAACTCCTACACAAA RR: TCTTGTCTGTGTGTACACCATCGACCTTTAGGTCTTAACAGCACTTATTTCTGAGAATGAACATCTAGGTTCTCTATAAATATTGGGGTAATCTGAGATCTGAAGTCTTTCACGACCGGACCATTTGTCGGTCGTGGAGGAAGAGAGACAGTGAGTTCCCAAATTGAGGATGTGTTT F2: 3 TCTTGTAT 2 Unidirectional alignment (log-probability: -32.5) TTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAG--------tatgttctTCCTTCTCTCTGTCACTCAAGGGTTTAACTCCTACACAAA TTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAGCCAGCACC--------TCCTTCTCTCTGTCACTCAAGGGTTTAACTCCTACACAAA Template switch alignment (log-probability: -22.3) TTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAG|TaTGTTCT|TCCTTCTCTCTGTCACTCAAGGGTTTAACTCCTACACAAA TTAGACTCTAGACTTCAGAAAGTGCTGGCCTGGTAAACAG|TCTGTTCT|TCCTTCTCTCTGTCACTCAAGGGTTTAACTCCTACACAAA ========= Event 460 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATGTACTTAATGATGTTTATTTGTACAAATGAATAT-TTAT-TCATTTGCTTATGTACTTATTCAAG Chimp: TTATGTACTTAATGATGTTTATTTGTACAAATGAATAT-TTAT-TCATTTGCTTATGTACTTATTCAAG ↓ 3 2 1 4 Gorilla: TTATGTACTTAATGATGTTTATTTGTACAAATGAATATTGTACAAATATTGCTTATGTACTTATTCAAG ↑ 3 2 1 4 Human: TTATGTACTTAATGATGTTTATTTGTACAAATGAATAT-TTAT-TCATTTGCTTATGTACTTATTCAAG Cluster: [ ] Orangutan: TTATGTGCTTAATGATGTTTATTTGTACAAATGAGTGT-TTAT-TCATTTGCTTATGTACTTATTCAAG Human > Gorilla --------------- chr11:79542002-79542010 Template switch process: F1: L TATTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT 1 F3: 4 TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT R RF: CATTTATGTACTTAATGATGTTTATTTGTACAAATGAATATTTATTCATTTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT RR: GTAAATACATGAATTACTACAAATAAACATGTTTACTTATAAATAAGTAAACGAATACATGAATAAGTTCTACAAATATGACTTGTGAA F2: 3 ATAAACATG 2 Unidirectional alignment (log-probability: -36.5) TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATTgtacaaaTA-----TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT-------TATTCATTTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT Template switch alignment (log-probability: -22.4) TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT|GTACAAATA|TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT|GTACAAATA|TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT Chimp > Gorilla --------------- chr11:79542002-79542010 Template switch process: F1: L TATTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT 1 F3: 4 TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT R RF: CATTTATGTACTTAATGATGTTTATTTGTACAAATGAATATTTATTCATTTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT RR: GTAAATACATGAATTACTACAAATAAACATGTTTACTTATAAATAAGTAAACGAATACATGAATAAGTTCTACAAATATGACTTGTGAA F2: 3 ATAAACATG 2 Unidirectional alignment (log-probability: -36.5) TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATTgtacaaaTA-----TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT-------TATTCATTTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT Template switch alignment (log-probability: -22.4) TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT|GTACAAATA|TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT TTTATGTACTTAATGATGTTTATTTGTACAAATGAATATT|GTACAAATA|TTGCTTATGTACTTATTCAAGATGTTTATACTGAACACTT ========= Event 461 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAGCAACTTTGCTCCTGTCCGGTCAAG---GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAGCTTCTTTTCTGGCCATGGCAACCTTTCAATGGTTCCTTGACTTTGTTCTGATTTCTGGTGCT Chimp: CCAGCAACTTTGCTGCTGTCCGTTCCAG---GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAGCTTCTTTTCTGGCCATGGCAACCTTTCAATGGTTCCTTGACTTTGTTCTGATTTCTGGTGCT ↓ 1 4 3 2 Gorilla: CCAGCAACTTTGCTGCTGTCCAGTCAAGGCAGCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAGCTTCTTTTCTGGCCATGGCAACCTTTCAATGGTTCCTTGACTTTGTTCTGATTTCTGGTGCT Human: CCAGCAACTTTGCTCCTGTCCGGTCAAG---GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAGCTTCTTTTCTGGCCATGGCAACCTTTCAATGGTTCCTTGACTTTGTTCTGATTTCTGGTGCT Cluster: [ ] Orangutan: CCAGCAATTTTGCTGCTGTCCGGTCAAGGCAGCTGTAGCTAAGAGAGGTGCCATTCTCAGAAGAAGCTGAGCTTCTTTTCTGGCCATGGCAACCTTTCAATGGTTCCTTGACTTTGTTCTGATTTCTGGTGCT Chimp > Gorilla --------------- chr1:17952311-17952320 Template switch process: F1: L AAGACCTCTTGGAGTGAGGACCAGCAACTTTGCTGCTGTCC 1 F3: 4 GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAG R RF: AAGACCTCTTGGAATGAGGACCAGCAACTTTGCTGCTGTCCGTTCCAGGCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAGCTTCTTTTCTGGCCATGGCAACCTTTCAATGGTTCCTTGACT RR: TTCTGGAGAACCTTACTCCTGGTCGTTGAAACGACGACAGGCAAGGTCCGACATCGATTCTTTCCACGGTAAGAGTCTTCTTCGACTCGAAGAAAAGACCGGTACCGTTGGAAAGTTACCAAGGAACTGA F2: 3 ACGGAACTGA 2 Unidirectional alignment (log-probability: -37.4) AGACCTCTTGGAgTGAGGACCAGCAACTTTGCTGCTGTCCagTCaAGgcaGCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAG AGACCTCTTGGAATGAGGACCAGCAACTTTGCTGCTGTCCGTTCCAG---GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAG Template switch alignment (log-probability: -28) AGACCTCTTGGAgTGAGGACCAGCAACTTTGCTGCTGTCC|AGTCAAGGcA|GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAG AGACCTCTTGGAATGAGGACCAGCAACTTTGCTGCTGTCC|AGTCAAGGAA|GCTGTAGCTAAGAAAGGTGCCATTCTCAGAAGAAGCTGAG ========= Event 462 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGCTTCTTGAAATATTTTTC------C--CTAGATCTAGAACTCTAGCTGGTACACCTTCTAATC Chimp: TTGCTTCTTGAAATATTTTTC------C--CTAGATCTAGAACTCTAGCTGGTACACCTTCTAATC ↓ 1 4 3 2 Gorilla: TTGCTTCTTGAAATATTTTTCAAGAGTTCTAGAGATCTAGAACTCTAGCTGGTACACCTTCTAATC ↑ 1 4 3 2 Human: TTGCTTCTTGAAATATTTTTC------C--CTAGATCTAGAACTCTAGCTGGTACACCTTCTAATC Cluster: [ ] Orangutan: ------------------------------------------------------------------ Human > Gorilla --------------- chr11:54974113-54974122 Template switch process: F1: L TTGGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTCA 1 F3: 4 AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA R RF: TTGGAGGCTTGCTAACACTATTGCTTCTTGAAATATTTTTCCCTAGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA RR: AACCTCCGAACGATTGTGATAACGAAGAACTTTATAAAAAGGGATCTAGATCTTGAGATCGACCATGTGGAAGATTAGGTATTT F2: 3 GATCTTGAGA 2 Unidirectional alignment (log-probability: -42.1) GGAGGtTTGCTAACACTATTGCTTCTTGAAATATTTTTCaagagttctag---AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA GGAGGCTTGCTAACACTATTGCTTCTTGAAATATTTTTC-----------CCTAGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA Template switch alignment (log-probability: -28.1) GGAGGtTTGCTAACACTATTGCTTCTTGAAATATTTTTCa|AGAGTTCTAG|AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA GGAGGCTTGCTAACACTATTGCTTCTTGAAATATTTTTCC|AGAGTTCTAG|AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA Chimp > Gorilla --------------- chr11:54974113-54974122 Template switch process: F1: L TTGGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTCA 1 F3: 4 AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA R RF: TTGGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTCCCTAGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA RR: AACCTCCAAACGATTGTGATAACGAAGAACTTTATAAAAAGGGATCTAGATCTTGAGATCGACCATGTGGAAGATTAGGTATTT F2: 3 GATCTTGAGA 2 Unidirectional alignment (log-probability: -36.6) GGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTC---aagagttctagAGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA GGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTCCCT-----------AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA Template switch alignment (log-probability: -22.5) GGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTCa|AGAGTTCTAG|AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA GGAGGTTTGCTAACACTATTGCTTCTTGAAATATTTTTCC|AGAGTTCTAG|AGATCTAGAACTCTAGCTGGTACACCTTCTAATCCATAAA ========= Event 463 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAAAAATCATCCGAAAAACA------AATTAGTAAAGTCATGAAACTATTCATCTTTAGA ↓ 13 4 2 Chimp: aaaaaaaTTATCCGAAAAACATGACTTTACTAATTAAGTCATGAAACTATTCATCTTTAGA ↑ 13 4 2 Gorilla: aaaaaaaTCATCCGAAAAACA------AATTAGTAAAGTCATGAAACTATTCATCTTTAGA Human: AAAAAAATCATCCGAAAAACA------AATTAGTAAAGTCATGAAACTATTCATCTTTAGA Cluster: [ ] Orangutan: AAAAAAATCATTCGAAAAACA------AATTAGTAAAGTCATGAAACTATTCATCTTTAGA Human > Chimp ------------- chr1:69236480-69236493 Template switch process: F1: L GAAGTTGTGGACAAGCCAGGAAAAAAATTATCCGAAAAACA 1 F3: 4 AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA R RF: GAAGTTGTGGACAAGCCAGGAAAAAAATCATCCGAAAAACAAATTAGTAAAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA RR: CTTCAACACCTGTTCGGTCCTTTTTTTAGTAGGCTTTTTGTTTAATCATTTCAGTACTTTGATAAGTAGAAATCTGATTAAGTGTGATT F2: 3 TTAATCATTTCAGT 2 Unidirectional alignment (log-probability: -41.7) AAGTTGTGGACAAGCCAGGAAAAAAATtATCCGAAAAACAtgactttactAATT----AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA AAGTTGTGGACAAGCCAGGAAAAAAATCATCCGAAAAACA----------AATTAGTAAAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA Template switch alignment (log-probability: -23) AAGTTGTGGACAAGCCAGGAAAAAAATtATCCGAAAAACA|TGACTTTACTAATT|AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA AAGTTGTGGACAAGCCAGGAAAAAAATCATCCGAAAAACA|TGACTTTACTAATT|AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA Gorilla > Chimp --------------- chr1:69236480-69236493 Template switch process: F1: L GAAGTTGTGGACAAGCCAGGAAAAAAATTATCCGAAAAACA 1 F3: 4 AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA R RF: GAAGTTGTGGACAAGCCAGGAAAAAAATCATCCGAAAAACAAATTAGTAAAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA RR: CTTCAACACCTGTTCGGTCCTTTTTTTAGTAGGCTTTTTGTTTAATCATTTCAGTACTTTGATAAGTAGAAATCTGATTAAGTGTGATT F2: 3 TTAATCATTTCAGT 2 Unidirectional alignment (log-probability: -40.8) AAGTTGTGGACAAGCCAGGAAAAAAATtATCCGAAAAACAtgactttactAATT----AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA AAGTTGTGGACAAGCCAGGAAAAAAATCATCCGAAAAACA----------AATTAGTAAAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA Template switch alignment (log-probability: -23) AAGTTGTGGACAAGCCAGGAAAAAAATtATCCGAAAAACA|TGACTTTACTAATT|AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA AAGTTGTGGACAAGCCAGGAAAAAAATCATCCGAAAAACA|TGACTTTACTAATT|AAGTCATGAAACTATTCATCTTTAGACTAATTCACACTAA ========= Event 464 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGGGTCCAGGCTGGAGGGGC-CCAATGTAGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGCG---GCATTCTTGGAGGTCCAAGAGGGGCAGCGCCACCTTGGGCCAGGCTCCTCTCCAGCA ↑ 1 4 3 2 Chimp: GGGGGTCCAGGCTGGAGGGGCCACAGGGCAGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCAT---GCGGCATTCTTGGAGGTCCAAGAGGGGCAGCGCCACCTTGGGCCAGGCTCCTCTCCAGCA Gorilla: GGGGGTCCAGGCTGGAGGGGCCACAGGGCAGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGTG---GCATTCTTGGAGGTCCAAGAGGGGCAGCCCCACCTTGGGCCAGGCTCCTCTCCAGCA Human: GGGGGTCCAGGCTGGAGGGGC-CCAATGTAGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGCG---GCATTCTTGGAGGTCCAAGAGGGGCAGCGCCACCTTGGGCCAGGCTCCTCTCCAGCA Cluster: [ ] Orangutan: GGGGGTCGAGGCTGGAGGGGCCACAGGGCAGGTGTAGAGGGACTACAGCTCTGAGGGGCTGCTCCATGCA---GCATTCTTGGAGGTCCAAGAGGGGCAGCCCCACCTTGGGCCAGGCTCCTCTCCAGCA Chimp > Human ------------- chr1:180199823-180199828 Template switch process: F1: L AGCCAGGAAGTGGGAGGGGTGGGGGTCCAGGCTGGAGGGGCC 1 F3: 4 AGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGC R RF: AGCCAGGAAGTGGGAGGGGTGGGGGTCCAGGCTGGAGGGGCCACAGGGCAGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGCGGCATTCTTGGAGGTCCAAGAGGGGCAGCGCCACCTTG RR: TCGGTCCTTCACCCTCCCCACCCCCAGGTCCGACCTCCCCGGTGTCCCGTCCACATCTCCCTGATGTCGGGACTCCCCGACGAGGTACGCCGTAAGAACCTCCAGGTTCTCCCCGTCGCGGTGGAAC F2: 3 TGTAAC 2 Unidirectional alignment (log-probability: -38.7) CCAGGAAGTGGGAGGGGTGGGGGTCCAGGCTGGAGGGGCC------CaatgtAGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATgc CCAGGAAGTGGGAGGGGTGGGGGTCCAGGCTGGAGGGGCCACAGGGC-----AGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCAT-- Template switch alignment (log-probability: -22) CCAGGAAGTGGGAGGGGTGGGGGTCCAGGCTGGAGGGGCC|CAAtGT|AGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGC CCAGGAAGTGGGAGGGGTGGGGGTCCAGGCTGGAGGGGCC|CAAGGT|AGGTGTAGAGGGACTACAGCCCTGAGGGGCTGCTCCATGC ========= Event 465 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGGATTTTGTTAAAATAAGAGTCTCAATGTGGAGATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCTG--------------ATTTCTGGAGTCAAACCATCAT ↓ 3 2 1 4 Chimp: TTGGATTTTGTTAAAATAAGCGTCTCAATGTGGAGATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCAT-------AGAGACTCTTTCTGGAGTCAAACCATCAT Gorilla: TTGGATTTTGTTAAAATAAGAGTCTCAGTGTGGAGATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCGTAGAGACT-------CTTTCTGGAGTCAAACCATCAT Human: TTGGATTTTGTTAAAATAAGAGTCTCAATGTGGAGATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCTG--------------ATTTCTGGAGTCAAACCATCAT Cluster: [ ] Orangutan: TTGGATTTTGTTAAAATAAGAGTCTCAGTGTGGAGATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCGTAGAGACC-------CTTTCTGGAGTCAAACCATCAT Human > Chimp ------------- chr1:68216985-68216994 Template switch process: F1: L GATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCC 1 F3: 4 TTTCTGGAGTCAAACCATCATTCCCTGTCTGGCCACTTGC R RF: GAGTCTCAATGTGGAGATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCTGATTTCTGGAGTCAAACCATCATTCCCTGTCTGGCCACTTGC RR: CTCAGAGTTACACCTCTATAAAATTTCTCTTCAATAGGTTTGGACTTGGACTAAGGACTAAAGACCTCAGTTTGGTAGTAAGGGACAGACCGGTGAACG F2: 3 CTCAGAGATA 2 Unidirectional alignment (log-probability: -33) ATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCatAgagactcTTTCTGGAGTCAAACCATCATTCCCTGTCTGGCCACTTGC ATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCCTGA-------TTTCTGGAGTCAAACCATCATTCCCTGTCTGGCCACTTGC Template switch alignment (log-probability: -22.5) ATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCC|ATaGAGACTC|TTTCTGGAGTCAAACCATCATTCCCTGTCTGGCCACTTGC ATATTTTAAAGAGAAGTTATCCAAACCTGAACCTGATTCC|ATTGAGACTC|TTTCTGGAGTCAAACCATCATTCCCTGTCTGGCCACTTGC ========= Event 466 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTCTAGCAAGGGTTTGTAATGTTAAACACTTCATGTGTTTAACTATTTGTTTTGTTATTATGG Chimp: TTTCTAGCAAGGGTTTGTAAT-CAAGGTACTTCATGTGTTTCACTATTTGTTTTGTTATTATGG Gorilla: TTTCTAGCAAGGGTTTGTAAT-CAAGATACTTCATGTGTTTAACTATTTGTTTTGTTATTATGG ↓ 1 4 3 2 Human: TTTCTAGCAAGGGTTTGTAATGTTAAACACTTCATGTGTTTAACTATTTGTTTTGTTATTATGG Cluster: [ ] Orangutan: TTTCCAGCAAGGGTTTGTAAT-CAAGGTACTTCATGTGTTTAAGTATT-----TGTTATTATGG Gorilla > Human --------------- chr1:63011075-63011081 Template switch process: F1: L TAAGACACCAGCTCTAACCTTTTCTAGCAAGGGTTTGTAAT 1 F3: 4 ACTTCATGTGTTTAACTATTTGTTTTGTTATTATGGAAAA R RF: TAAGACACCAGCTGTAACCTTTTCTAGCAAGGGTTTGTAATCAAGATACTTCATGTGTTTAACTATTTGTTTTGTTATTATGGAAAA RR: ATTCTGTGGTCGACATTGGAAAAGATCGTTCCCAAACATTAGTTCTATGAAGTACACAAATTGATAAACAAAACAATAATACCTTTT F2: 3 CAAATTG 2 Unidirectional alignment (log-probability: -35) AAGACACCAGCTcTAACCTTTTCTAGCAAGGGTTTGTAATgttaaaC-----ACTTCATGTGTTTAACTATTTGTTTTGTTATTATGGAAAA AAGACACCAGCTGTAACCTTTTCTAGCAAGGGTTTGTAAT------CAAGATACTTCATGTGTTTAACTATTTGTTTTGTTATTATGGAAAA Template switch alignment (log-probability: -22.1) AAGACACCAGCTcTAACCTTTTCTAGCAAGGGTTTGTAAT|GTTAAAC|ACTTCATGTGTTTAACTATTTGTTTTGTTATTATGGAAAA AAGACACCAGCTGTAACCTTTTCTAGCAAGGGTTTGTAAT|GTTAAAC|ACTTCATGTGTTTAACTATTTGTTTTGTTATTATGGAAAA ========= Event 467 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAGTGGAAATTGGTGAATGATCCTCTAAAAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTAAGGA-------------TCTGACAGCT-cggaggttgcaa Chimp: GAAGTGGAAATTGGTGAATGATCCTCTAAAAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTAAGGA-------------TCTGACAGCTCAagaggttgcaa Gorilla: GAAGTGGAAATTGGTGAATGATCCTCTAAAAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTATGTGTATGTACATACCTCCTGACAGCT-cggaggttgcaa ↓ 3 2 1 4 Human: GAAGTGGAAATTGGTGAATGATCCTCTAAAAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTAAGGA-------------TCTGACAGCT-cggaggttgcaa Cluster: [ ] Orangutan: GAACTGGAAATTCGTAAATGATCCTCTAAAAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTAGGGA-------------TCTGACAGCT-TGgaggttgcaa Gorilla > Human --------------- chr1:184689072-184689077 Template switch process: F1: L AAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTA 1 F3: 4 TGACAGCTCGGAGGTTGCAAACTGGAGACCACTGCTGTC R RF: GATCCTCTAAAAACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTATGTGTATGTACATACCTCCTGACAGCTCGGAGGTTGCAAACTGGAGACCATTGCTGTC RR: CTAGGAGATTTTTGCTTACCCCAGAAGGAACATGTATGTGTACACCTCCATACACATACATGTATGGAGGACTGTCGAGCCTCCAACGTTTGACCTCTGGTAACGACAG F2: 3 CTAGGA 2 Unidirectional alignment (log-probability: -32.8) AACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTaaggAT-----------------CTGACAGCTCGGAGGTTGCAAACTGGAGACCAcTGCTGTC AACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGT----ATGTGTATGTACATACCTCCTGACAGCTCGGAGGTTGCAAACTGGAGACCATTGCTGTC Template switch alignment (log-probability: -22) AACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTA|AGGATC|TGACAGCTCGGAGGTTGCAAACTGGAGACCAcTGCTGTC AACGAATGGGGTCTTCCTTGTACATACACATGTGGAGGTA|AGGATC|TGACAGCTCGGAGGTTGCAAACTGGAGACCATTGCTGTC ========= Event 468 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCCAGAATTCCTGGCAAATACAG--CCACTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTTTTAGATTCC Chimp: CTTCCAGAATTCCTGGCAAATACAG--CCACTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTTTTAGATTCC ↓ 1 4 3 2 Gorilla: CTTCCAGAATTCCTGGCAAATGATT----CCTGAATCATTTATTTTTCGTTGATGAATCTGGATGTAGTTTTAGATTCC ↑ 1 4 3 2 Human: CTTCCAGAATTCCTGGCAAATACAG--CCACTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTTTTAGATTCC Cluster: [ ] Orangutan: CTTCCAGAATTCCTGGCAAATACAGCC--ACTGAATCATGTATTTTTCATTGATGAATCTGGATGTAGTTTTAGATTCC Human > Gorilla --------------- chr1:166298818-166298822 Template switch process: F1: L CACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAAT 1 F3: 4 CTGAATCATTTATTTTTCGTTGATGAATCTGGATGTAGTT R RF: CACGCAAGTTGCCACTCTCCCTTCCAGAATTCCTGGCAAATACAGCCACTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTT RR: GTGCGTTCAACGGTGAGAGGGAAGGTCTTAAGGACCGTTTATGTCGGTGACTTAGTAAATAAAAAGTAACTACTTAGACCTACATCAA F2: 3 CTTAG 2 Unidirectional alignment (log-probability: -39.2) ACGCAAGTTGCCACTtTCCCTTCCAGAATTCCTGGCAAAT-------gattcCTGAATCATTTATTTTTCgTTGATGAATCTGGATGTAGTT ACGCAAGTTGCCACTCTCCCTTCCAGAATTCCTGGCAAATACAGCCA-----CTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTT Template switch alignment (log-probability: -27.4) ACGCAAGTTGCCACTtTCCCTTCCAGAATTCCTGGCAAAT|GATTC|CTGAATCATTTATTTTTCgTTGATGAATCTGGATGTAGTT ACGCAAGTTGCCACTCTCCCTTCCAGAATTCCTGGCAAAT|GATTC|CTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTT Chimp > Gorilla --------------- chr1:166298818-166298822 Template switch process: F1: L CACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAAT 1 F3: 4 CTGAATCATTTATTTTTCGTTGATGAATCTGGATGTAGTT R RF: CACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAATACAGCCACTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTT RR: GTGCGTTCAACGGTGAAAGGGAAGGTCTTAAGGACCGTTTATGTCGGTGACTTAGTAAATAAAAAGTAACTACTTAGACCTACATCAA F2: 3 CTTAG 2 Unidirectional alignment (log-probability: -33.7) ACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAAT-------gattcCTGAATCATTTATTTTTCgTTGATGAATCTGGATGTAGTT ACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAATACAGCCA-----CTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTT Template switch alignment (log-probability: -21.9) ACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAAT|GATTC|CTGAATCATTTATTTTTCgTTGATGAATCTGGATGTAGTT ACGCAAGTTGCCACTTTCCCTTCCAGAATTCCTGGCAAAT|GATTC|CTGAATCATTTATTTTTCATTGATGAATCTGGATGTAGTT ========= Event 469 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: aaaaaaaaaaaaaaaGGTTGACTCTCTTCTGAGAGGTAA-CTCTCAGAAGAGAGTCAACT-GTATTATTTGATAATTTTATCATGCTAGTCTTAA Chimp: -------------------GACTCTCTTCTGAGAGGTAA-CTCTCAGAAGAGAGTCAACT-GTATTATCTGATAATTTTATCATGCTAGTCTTAA ↑ 3 2 4 1 Gorilla: -------------------GACTCTCTTCTGAGAGGTAA-------------------CT-GTATTATTTGATAGTTTTATCATGCTAGTCTTAA Human: aaaaaaaaaaaaaaaGGTTGACTCTCTTCTGAGAGGTAA-CTCTCAGAAGAGAGTCAACT-GTATTATTTGATAATTTTATCATGCTAGTCTTAA Cluster: [ ] Orangutan: -------------------GACTCTCTTCTGAGAGGTAAC------------------CTGTTATTATTTGATAATTTTATCATGCTAGTCTTAA Gorilla > Chimp --------------- chr11:50966188-50966201 Template switch process: F1: L TTTTGACTTGAATAAAAGGTTGACTCTCTTCTGAGAGGTAACT 1 F3: 4 AACTGTATTATCTGATAATTTTATCATGCTAGTCTTAAGATGAGGGAGTGGTGTGGGT R RF: TTTTGACTTGAATAAAAGGTTGACTCTCTTCTGAGAGGTAACTGTATTATTTGATAGTTTTATCATGCTAGTCTTAAGATGAGGGAGTGGTGTGGGT RR: AAAACTGAACTTATTTTCCAACTGAGAGAAGACTCTCCATTGACATAATAAACTATCAAAATAGTACGATCAGAATTCTACTCCCTCACCACACCCA F2: 3 CTGAGAGAAGACTC 2 Unidirectional alignment (log-probability: -48) TGACTTGAATAAAAGGTTGACTCTCTTCTGAGAGGTaactctcagaagagagtcAACTGTATTATcTGATAaTTTTATCATGCTAGTCTTAAGA TGACTTGAATAAAAGGTTGACTCTCTTCTGAGAGGT------------------AACTGTATTATTTGATAGTTTTATCATGCTAGTCTTAAGA Template switch alignment (log-probability: -29) TGACTTGAATAAAAGGTTGACTCTCTTCTGAGAGGTAACT|CTCAGAAGAGAGTC|AACTGTATTATcTGATAaTTTTATCATGCTAGTCTTAAGA TGACTTGAATAAAAGGTTGACTCTCTTCTGAGAGGTAACT|CTCAGAAGAGAGTC|AACTGTATTATTTGATAGTTTTATCATGCTAGTCTTAAGA ========= Event 470 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAAATAAGCTGACAAGCTCTGTGAATCTATATTCACAGATTGCTATGATGTGTTTTTTT Chimp: CAAAATAAGCTGACAAGCTCTGTGAATCTATAG---TGTATTGTTATGATGTGttttttt Gorilla: CAAAATAAGCTGACAAGCTCTGTGAATCTATAG---TGTATTGCTATGATGTGttttttt ↓ 3 2 1 4 Human: CAAAATAAGCTGACAAGCTCTGTGAATCTATATTCACAGATTGCTATGATGTGTTTTTTT Cluster: [ ] Orangutan: CAAAATAAGCTGACAAGCTCTGTGAATCTATAG---TGTATTGCTATGATGTGGTTTTTT Gorilla > Human --------------- chr11:82201691-82201697 Template switch process: F1: L TGGGCATTTCAAAATAAGCTGACAAGCTCTGTGAATCTATA 1 F3: 4 ATTGCTATGATGTGTTTTTTTCTTTACGAGATGGTTTAAA R RF: TGGGCATTTCAAAATAAGCTGACAAGCTCTGTGAATCTATAGTGTATTGCTATGATGTGTTTTTTTCTTTACGAGATGGTTTAAA RR: ACCCGTAAAGTTTTATTCGACTGTTCGAGACACTTAGATATCACATAACGATACTACACAAAAAAAGAAATGCTCTACCAAATTT F2: 3 GACACTT 2 Unidirectional alignment (log-probability: -29.4) GGGCATTTCAAAATAAGCTGACAAGCTCTGTGAATCTATA---TtcacagATTGCTATGATGTGTTTTTTTCTTTACGAGATGGTTTAAA GGGCATTTCAAAATAAGCTGACAAGCTCTGTGAATCTATAGTGT------ATTGCTATGATGTGTTTTTTTCTTTACGAGATGGTTTAAA Template switch alignment (log-probability: -16.6) GGGCATTTCAAAATAAGCTGACAAGCTCTGTGAATCTATA|TTCACAG|ATTGCTATGATGTGTTTTTTTCTTTACGAGATGGTTTAAA GGGCATTTCAAAATAAGCTGACAAGCTCTGTGAATCTATA|TTCACAG|ATTGCTATGATGTGTTTTTTTCTTTACGAGATGGTTTAAA ========= Event 471 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGCCTTGGCCCTGCTGTTCATGTCTGAAA----CAG--------ACATGTGTGGGCCCCACTTCCTTGC Chimp: TGCATTGGCCCTGCTGTTCATGTCTGAAA----CAG--------ACATGTGTGGGCCCCACTTCCTTGC ↑ 3 2 1 4 Gorilla: TGCCTTGGCCCTGCTGTTCATGTCTGAAA--GGTAG----ACTACCCAGTGTGGGCCCCACTTCCTTGC ↓ 3 2 1 4 Human: TGCCTTGGCCCTGCTGTTCATGTCTGAAA----CAG--------ACATGTGTGGGCCCCACTTCCTTGC Cluster: [ ] Orangutan: TGCCTTGGCCCTGCTGTTCATGTCTGAAAGG--TAGACTA----CCCAGTGTGGGCCCCACTTCCTTGC Gorilla > Human --------------- chr11:126429531-126429537 Template switch process: F1: L TGGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAA 1 F3: 4 GTGTGGGCCCCACTTCCTTGCTGCCTCACTAAGTCTTAGG R RF: TGGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAAGGTAGACTACCCAGTGTGGGCCCCACTTCCTTGCTGCCTCACTGAGTCCTAGG RR: ACCACAGGCACAACGGAACCGGGACGACAAGTACAGACTTTCCATCTGATGGGTCACACCCGGGGTGAAGGAACGACGGAGTGACTCAGGATCC F2: 3 TACAGAC 2 Unidirectional alignment (log-probability: -39.4) GGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAA-----------CAgacatGTGTGGGCCCCACTTCCTTGCTGCCTCACTaAGTCtTAGG GGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAAGGTAGACTACCCA-----GTGTGGGCCCCACTTCCTTGCTGCCTCACTGAGTCCTAGG Template switch alignment (log-probability: -27.7) GGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAA|CAGACAT|GTGTGGGCCCCACTTCCTTGCTGCCTCACTaAGTCtTAGG GGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAA|CAGACAT|GTGTGGGCCCCACTTCCTTGCTGCCTCACTGAGTCCTAGG Gorilla > Chimp --------------- chr11:127247189-127247195 Template switch process: F1: L TGGTGTCCGTGTTGCATTGGCCCTGCTGTTCATGTCTGAAA 1 F3: 4 GTGTGGGCCCCACTTCCTTGCTGCCTCACTAAGTCCTAGG R RF: TGGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAAGGTAGACTACCCAGTGTGGGCCCCACTTCCTTGCTGCCTCACTGAGTCCTAGG RR: ACCACAGGCACAACGGAACCGGGACGACAAGTACAGACTTTCCATCTGATGGGTCACACCCGGGGTGAAGGAACGACGGAGTGACTCAGGATCC F2: 3 TACAGAC 2 Unidirectional alignment (log-probability: -39.4) GGTGTCCGTGTTGCaTTGGCCCTGCTGTTCATGTCTGAAA-----------CAgacatGTGTGGGCCCCACTTCCTTGCTGCCTCACTaAGTCCTAGG GGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAAGGTAGACTACCCA-----GTGTGGGCCCCACTTCCTTGCTGCCTCACTGAGTCCTAGG Template switch alignment (log-probability: -27.7) GGTGTCCGTGTTGCaTTGGCCCTGCTGTTCATGTCTGAAA|CAGACAT|GTGTGGGCCCCACTTCCTTGCTGCCTCACTaAGTCCTAGG GGTGTCCGTGTTGCCTTGGCCCTGCTGTTCATGTCTGAAA|CAGACAT|GTGTGGGCCCCACTTCCTTGCTGCCTCACTGAGTCCTAGG ========= Event 472 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTGTGACATTTAAAAGTCAA--------------------TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATTTATATTTCATATTGCTGTGGAATTGCTTTCATTTCTGTCTCACTTAGGTCTCTGTATGGTAAAGATT ↓ 41 3 2 Chimp: GCTGTGACATTTAAAAGTCAA----------TGCTAAGTGATGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATTTATATTTCATATTGCTGTGGAATTGCTTTCATTTCTGTCTCACTTAGGTCTCTGTATGGTAAAGATT Gorilla: GCTGTGACATTTAAAAGTCAATGCTAAGTGA----------TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATTTATATTTCATATTGCTGTGGAATTGCTTTCATTTCTGTCTCACTTAGGTCTCTGTATGGTAAAGATT Human: GCTGTGACATTTAAAAGTCAA--------------------TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATTTATATTTCATATTGCTGTGGAATTGCTTTCATTTCTGTCTCACTTAGGTCTCTGTATGGTAAAGATT Cluster: [ ] Orangutan: GCTGTGGCATTTAAAAGTCAATGCTAAGTGA----------TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATTTATGTTTCATATTGCTGTGGAATTGCTTTCAATTCTGTCTCACTTAGGTCTCTGTATGGTAAAGATT Human > Chimp ------------- chr11:50779059-50779066 Template switch process: F1: L TAAAAGAGAACCACCCAGAGGCTGTGACATTTAAAAGTCAATG 1 F3: 4 TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATT R RF: TAAAAGAGAACCACCCAGAGGCTGTGACATTTAAAAGTCAATGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATTTATATTTCATATTGCTGTGGAATTGCTTTCATTTCTGTCTCACTTAG RR: ATTTTCTCTTGGTGGGTCTCCGACACTGTAAATTTTCAGTTACAACAAAATTTCTTCGTAAGTCCCCTACAACGGTTGTAAATATAAAGTATAACGACACCTTAACGAAAGTAAAGACAGAGTGAATC F2: 3 AGTGAATC 2 Unidirectional alignment (log-probability: -25.3) AAGAGAACCACCCAGAGGCTGTGACATTTAAAAGTCAatgctaagtgATGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATT AAGAGAACCACCCAGAGGCTGTGACATTTAAAAGTCA----------ATGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATT Template switch alignment (log-probability: -16.3) AAGAGAACCACCCAGAGGCTGTGACATTTAAAAGTCAATG|CTAAGTGA|TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATT AAGAGAACCACCCAGAGGCTGTGACATTTAAAAGTCAATG|CTAAGTGA|TGTTGTTTTAAAGAAGCATTCAGGGGATGTTGCCAACATT ========= Event 473 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTAC-----TCCAAAGAA------TTGTGCCTTGTGTTTGCAGCATC Chimp: TCCTTCC-CCCCTTCTAGAATTCTTTGGATTGTAC-----TCCAAAGAG------TTGTGCCTTGTGTTTGCAGCATC Gorilla: TCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTACTTGTTCCCCACTACTTTGCTCTCTGCCTTGTGTTTGCAGCATC ↓ 3 2 1 4 Human: TCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTAC-----TCCAAAGAA------TTGTGCCTTGTGTTTGCAGCATC Cluster: [ ] Orangutan: TCCTTCCCTTCCTTCTAGAATTCTTTGGATTGTACTTGTTCCCCACTACTTTGCTCTCTGCCTTGTGTTTGCAGCATC Gorilla > Human --------------- chr1:183144461-183144469 Template switch process: F1: L AATACCTCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTACT 1 F3: 4 TGTGCCTTGTGTTTGCAGCATCTCCATTCTCTAAAATTAATA R RF: AATACCTCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTACTTGTTCCCCACTACTTTGCTCTCTGCCTTGTGTTTGCAGCATCTCCATTCTCTAAAATTAATA RR: TTATGGAGGAAGGGAGGGAAGATCTTAAGAAACCTAACATGAACAAGGGGTGATGAAACGAGAGACGGAACACAAACGTCGTAGAGGTAAGAGATTTTAATTAT F2: 3 TAAGAAACC 2 Unidirectional alignment (log-probability: -34.6) TACCTCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTACtccaaagaaTTG--------------------TGCCTTGTGTTTGCAGCATCTCCATTCTCTAAAATTAA TACCTCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTAC---------TTGTTCCCCACTACTTTGCTCTCTGCCTTGTGTTTGCAGCATCTCCATTCTCTAAAATTAA Template switch alignment (log-probability: -22.5) TACCTCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTACT|CCAAAGAAT|TgTGCCTTGTGTTTGCAGCATCTCCATTCTCTAAAATTAA TACCTCCTTCCCTCCCTTCTAGAATTCTTTGGATTGTACT|CCAAAGAAT|TCTGCCTTGTGTTTGCAGCATCTCCATTCTCTAAAATTAA ========= Event 474 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGATATCTGTAGTTAATAACAGCAATGAT---------AGTAACACATAAAAACCatggagtgttaactg Chimp: GCAATATCTGTAGTTAATAACAGCAATGAT---------AGTAACAGATAAAAACCatggagtgttaactg Gorilla: GCGATATCTGTAGTTAATAACAGCAATGCTATCATTGCTGTTAACACATA-AAACCATGGAGTGTTAACTG ↑ 3 1 24 Human: GTGATATCTGTAGTTAATAACAGCAATGAT---------AGTAACACATAAAAACCatggagtgttaactg Cluster: [ ] Orangutan: GCGATATCTGTAGTTAATAACAGCAATGAT---------AGTAACATGTAAAAACCATGGAGTGTTAACTG Human > Gorilla --------------- chr1:163379221-163379233 Template switch process: F1: L ATCACTGATGGCAGCGATATCTGTAGTTAATAACAGCAATG 1 F3: 4 TAACACAT-AAAACCATGGAGTGTTAACTGTATGCTAGGCACAGTGCTTT R RF: ATCACTGATGGCAGTGATATCTGTAGTTAATAACAGCAATGATAGTAACACATAAAAACCATGGAGTGTTAACTGTATGCTAGGCACAGTGCTTT RR: TAGTGACTACCGTCACTATAGACATCAATTATTGTCGTTACTATCATTGTGTATTTTTGGTACCTCACAATTGACATACGATCCGTGTCACGAAA F2: 3 TGTCGTTACTATC 2 Unidirectional alignment (log-probability: -50.4) TCACTGATGGCAGcGATATCTGTAGTTAATAACAGCAATGcTAtcattgctgtTAACACAT-AAAACCATGGAGTGTTAACTGTATGCTAGGCA TCACTGATGGCAGTGATATCTGTAGTTAATAACAGCAATGATA---------GTAACACATAAAAACCATGGAGTGTTAACTGTATGCTAGGCA Template switch alignment (log-probability: -32.9) TCACTGATGGCAGcGATATCTGTAGTTAATAACAGCAATG|CTATCATTGCTGT|TAACACAT-AAAACCATGGAGTGTTAACTGTATGCTAGGCA TCACTGATGGCAGTGATATCTGTAGTTAATAACAGCAATG|CTATCATTGCTGT|TAACACATAAAAACCATGGAGTGTTAACTGTATGCTAGGCA ========= Event 475 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CATGGTGCTTTAGAACAATAG-AGTCTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACGTATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACTGTCATTTGGTATTCGAAGTT ↑ 1 4 3 2 Chimp: CATGGTGCTTTAGAACAATAGCTATGTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACCTATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACTGTCATTTGGTATTCGAAGTT ↓ 1 4 3 2 Gorilla: CATGGTGCTTTAGAACAATAG-AGTCTTCCTGGCTATACAAGTTGTGAAAGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACGTATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACTGTCATTTGGTATTCGAAGTT Human: CATGGTGCTTTAGAACAATAG-AGTCTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACGTATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACTGTCATTTGGTATTCGAAGTT Cluster: [ ] Orangutan: CATGGTGCTTTAGAACAATAG-AGTCTTCCTGGCTACACAAGTTGTAAAGGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACATATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACTGTCATTTGGTATTCGAAGTT Chimp > Human ------------- chr1:64475907-64475910 Template switch process: F1: L GCTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG 1 F3: 4 TTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC R RF: GCTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAGCTATGTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACCTATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACT RR: CGATTGTAGACGTTTTATGTGTACCACGAAATCTTGTTATCGATACAAGGACCGATATGTTCAACACTTCCCTACCAATTCACCAGAGTAACGGTTCGTCTTACATTCGTGTTGGATAACTTATAGTGGTTTAGAACGAGACTGTTAGATTCCAATAGAAAAATTTCTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -25.7) CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAGagtC----TTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG---CTATGTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC Template switch alignment (log-probability: -15.8) CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG|AGTC|TTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG|AGTC|TTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC Chimp > Gorilla --------------- chr1:65169494-65169497 Template switch process: F1: L GCTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG 1 F3: 4 TTCCTGGCTATACAAGTTGTGAAAGGATGGTTAAGTGGTC R RF: GCTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAGCTATGTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTCTCATTGCCAAGCAGAATGTAAGCACAACCTATTGAATATCACCAAATCTTGCTCTGACAATCTAAGGTTATCTTTTTAAAGACT RR: CGATTGTAGACGTTTTATGTGTACCACGAAATCTTGTTATCGATACAAGGACCGATATGTTCAACACTTCCCTACCAATTCACCAGAGTAACGGTTCGTCTTACATTCGTGTTGGATAACTTATAGTGGTTTAGAACGAGACTGTTAGATTCCAATAGAAAAATTTCTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -30.7) CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAGagtC----TTCCTGGCTATACAAGTTGTGAAaGGATGGTTAAGTGGTC CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG---CTATGTTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC Template switch alignment (log-probability: -21.7) CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG|AGTC|TTCCTGGCTATACAAGTTGTGAAaGGATGGTTAAGTGGTC CTAACATCTGCAAAATACACATGGTGCTTTAGAACAATAG|AGTC|TTCCTGGCTATACAAGTTGTGAAGGGATGGTTAAGTGGTC ========= Event 476 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAAT---CTTACTTTTTCGCCCACATTTCCCCT ↓ 3 2 1 4 Chimp: AATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAAGACAAATAATTTTTCGCCCACATTTCCCCT Gorilla: AATCACAGTATAAGTCAAATTATTCGTCTACTCATAGAAT---CTTACTTTTTCTCCCACACTTCCCCT Human: AATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAAT---CTTACTTTTTCGCCCACATTTCCCCT Cluster: [ ] Orangutan: AATCACAGTATAAGTCAAATTATTTGTCTACTCGTAGAAT---CTTACTTTTTCGCGCACATTTCCCCT Human > Chimp ------------- chr1:165476123-165476131 Template switch process: F1: L ACAATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAA 1 F3: 4 TTTTTCGCCCACATTTCCCCTTCTCATACTTAGAAAAAAG R RF: ACAATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAATCTTACTTTTTCGCCCACATTTCCCCTTCTCATACTTAGAAAAAAA RR: TGTTAGTGTCATATTCAGTTTAATAAACAGATGAGTATCTTAGAATGAAAAAGCGGGTGTAAAGGGGAAGAGTATGAATCTTTTTTT F2: 3 AATAAACAG 2 Unidirectional alignment (log-probability: -40.4) CAATCACAGTATAAGTCAAATTATTTGTCTACTCATAGaagacaaatAAT------TTTTCGCCCACATTTCCCCTTCTCATACTTAGAAAAAAg CAATCACAGTATAAGTCAAATTATTTGTCTACTCATAG---------AATCTTACTTTTTCGCCCACATTTCCCCTTCTCATACTTAGAAAAAAA Template switch alignment (log-probability: -22.4) CAATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAA|GACAAATAA|TTTTTCGCCCACATTTCCCCTTCTCATACTTAGAAAAAAg CAATCACAGTATAAGTCAAATTATTTGTCTACTCATAGAA|GACAAATAA|TTTTTCGCCCACATTTCCCCTTCTCATACTTAGAAAAAAA ========= Event 477 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTTCTTTGGTTTGTGCATTTTTAAAAT---------GCCTGTGCAAGGACTAAGAACCTG-----------CTATTCATATTCCCAGGAAA ↓ 4 1 3 2 Chimp: ttttCTTTGGTTTGTGCATTTTTAAAATGTTCTTAGTCCTTTTAAAAGGA-----------CTAAGAACCTGCTATTCATATTCCCAGGAAA Gorilla: TCTTCTTTGGTTTGTGCATTTTTAAAAT---------GCCTGTGCAAGGACTAAGAACCTG-----------CTATTCATATTCCCAGGAAA Human: TTTTCTTTGGTTTGTGCATTTTTAAAAT---------GCCTGTGCAAGGACTAAGAACCTG-----------CTATTCATATTCCCAGGAAA Cluster: [ ] Orangutan: TCTTCTTTGGTTTGTGCATTTTAAAAAT---------GCCTGTGCAAGGACTAGGAACATG-----------CTATTCATATTCCCAGGAAA Human > Chimp ------------- chr1:160673138-160673147 Template switch process: F1: L GAAAAAGCAATTTTTTTCTTTGGTTTGTGCATTTTTAAAATG 1 F3: 4 TTTTAA-----------AAGGACTAAGAACCTGCTATTCATATTCCCAGGAAAAGATAACTGTATCAATTACT R RF: GAAAAAGCAATTTTTTTCTTTGGTTTGTGCATTTTTAAAATGCCTGTGCAAGGACTAAGAACCTGCTATTCATATTCCCAGGAAAAGATAACTGTATCAATTACT RR: CTTTTTCGTTAAAAAAAGAAACCAAACACGTAAAAATTTTACGGACACGTTCCTGATTCTTGGACGATAAGTATAAGGGTCCTTTTCTATTGACATAGTTAATGA F2: 3 CCTGATTCTT 2 Unidirectional alignment (log-probability: -44.6) AAAAGCAATTTTTTTCTTTGGTTTGTGCATTTTTAAAATG-------ttcttagtccttttaaAAGGACTAAGAACCTGCTATTCATATTCCCAGGA AAAAGCAATTTTTTTCTTTGGTTTGTGCATTTTTAAAATGCCTGTGC----------------AAGGACTAAGAACCTGCTATTCATATTCCCAGGA Template switch alignment (log-probability: -27.7) AAAAGCAATTTTTTTCTTTGGTTTGTGCATTTTTAAAATG|TTCTTAGTCC|TTTTAA-----------AAGGACTAAGAACCTGCTATTCATATTCCCAGGA AAAAGCAATTTTTTTCTTTGGTTTGTGCATTTTTAAAATG|TTCTTAGTCC|TTTTAAAATGCCTGTGCAAGGACTAAGAACCTGCTATTCATATTCCCAGGA ========= Event 478 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tGGTAATCCCGGAGCCAGCACAGGAATAGTTGA----TGGAAgaagaaaggaaggaaggg ↓ 3 1 2 4 Chimp: tgGTAATCCCGGAGCCAGCACAGGAATAACTATTCCTGTGAAGAAGAAAGGAAGGAAGGG ↑ 3 1 2 4 Gorilla: tGGTAATCCGGGAGCCAGCACAGGAATAGTTGA----TGGAAGAAGAAAGGAAGGAAGGG Human: tGGTAATCCCGGAGCCAGCACAGGAATAGTTGA----TGGAAgaagaaaggaaggaaggg Cluster: [ ] Orangutan: TGGTAACCCCGGAGCCAGCACAAGGATAGTTGA----TGGAAGAAGAAAGGAAGTAAGGG Human > Chimp ------------- chr1:17384651-17384661 Template switch process: F1: L GACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATA 1 F3: 4 GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA R RF: GACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATAGTTGATGGAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA RR: CTGTCGGACACAGACCATTAGGGCCTCGGTCGTGTCCTTATCAACTACCTTCTTCTTTCCTTCCTTCCCTCACTCCCTCCTTCCACAT F2: 3 TGTCCTTATCA 2 Unidirectional alignment (log-probability: -34.4) ACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATAactattcctGT-----GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA ACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATA---------GTTGATGGAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA Template switch alignment (log-probability: -16.6) ACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATA|ACTATTCCTGT|GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA ACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATA|ACTATTCCTGT|GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA Gorilla > Chimp --------------- chr1:17384651-17384661 Template switch process: F1: L GACAGCCTGTGTCTGGTAATCCCGGAGCCAGCACAGGAATA 1 F3: 4 GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGGTGTA R RF: GACAGCCTGTGTCTGGTAATCCGGGAGCCAGCACAGGAATAGTTGATGGAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGCTGTA RR: CTGTCGGACACAGACCATTAGGCCCTCGGTCGTGTCCTTATCAACTACCTTCTTCTTTCCTTCCTTCCCTCACTCCCTCCTTCGACAT F2: 3 TGTCCTTATCA 2 Unidirectional alignment (log-probability: -44.9) ACAGCCTGTGTCTGGTAATCCcGGAGCCAGCACAGGAATAactattcctGT-----GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGgTGTA ACAGCCTGTGTCTGGTAATCCGGGAGCCAGCACAGGAATA---------GTTGATGGAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGCTGTA Template switch alignment (log-probability: -28.2) ACAGCCTGTGTCTGGTAATCCcGGAGCCAGCACAGGAATA|ACTATTCCTGT|GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGgTGTA ACAGCCTGTGTCTGGTAATCCGGGAGCCAGCACAGGAATA|ACTATTCCTGT|GAAGAAGAAAGGAAGGAAGGGAGTGAGGGAGGAAGCTGTA ========= Event 479 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGTAGCATGATCAACAACCAACTGAGATGAATCTCTCAGTT-GGTTAACCCTGAGCTAGTATCC Chimp: CTGTAGCATGATCAACAACCAACTGGGATGAATCTCTAGTATGTGTTAACCCTGAGCTAGTATCC Gorilla: CTGTAGCATGATCAACAACCAACTGAGATGAATCTCTAGTATGTGTTAACCCTGAGCTAGTATCC ↓ 3 2 1 4 Human: CTGTAGCATGATCAACAACCAACTGAGATGAATCTCTCAGTT-GGTTAACCCTGAGCTAGTATCC Cluster: [ ] Orangutan: CTGTAGCATGATCAACAACCAACTGAGATGAATCTCTAGTATGTGTTAACCCTGAGCTAGTATCC Gorilla > Human --------------- chr11:52590045-52590050 Template switch process: F1: L TGCCCTGTAGCATGATCAACAACCAACTGAGATGAATCTCT 1 F3: 4 GTTAACCCTGAGCTAGTATCCTCTGCAGAATCAGGCTTAC R RF: TGCCCTGTAGCATGATCAACAACCAACTGAGATGAATCTCTAGTATGTGTTAACCCTGAGCTAGTATCCTCTGCAGAATCAGGCTCAC RR: ACGGGACATCGTACTAGTTGTTGGTTGACTCTACTTAGAGATCATACACAATTGGGACTCGATCATAGGAGACGTCTTAGTCCGAGTG F2: 3 GTTGAC 2 Unidirectional alignment (log-probability: -35.1) GCCCTGTAGCATGATCAACAACCAACTGAGATGAATCTC-------TcagttgGTTAACCCTGAGCTAGTATCCTCTGCAGAATCAGGCTtAC GCCCTGTAGCATGATCAACAACCAACTGAGATGAATCTCTAGTATGT------GTTAACCCTGAGCTAGTATCCTCTGCAGAATCAGGCTCAC Template switch alignment (log-probability: -22) GCCCTGTAGCATGATCAACAACCAACTGAGATGAATCTCT|CAGTTG|GTTAACCCTGAGCTAGTATCCTCTGCAGAATCAGGCTtAC GCCCTGTAGCATGATCAACAACCAACTGAGATGAATCTCT|CAGTTG|GTTAACCCTGAGCTAGTATCCTCTGCAGAATCAGGCTCAC ========= Event 480 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAATATAAAACCCATGGCACA---------------------TAGTCCTTGCCTATGGAAACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACTACATTGACACAAAAATTTTTTAAAACTATTTCCATAATTTCTGGTGCTTACCttt-tt-ttcccataggttattggggtacaggtggta Chimp: GGAATATAAAACCCATGGCACA---------------------TAGTCCTTGCCTGTGGAAACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACTACATTGACACAAAAAtttttttAAACTATTTCCATAATTTCTGGTGCTTACCttt-tttttcccataggttattggggtacaagtggta Gorilla: GGAATATAAAACCCATGGCACA------------------------------------------TAGTCCATGGAAATATAACCTGTTTTCTGCATATACTACATTGACACAAAAATTTTTTAAAACTATTTCCATAATTTCTGGTGCTTATCttt-tttttcccataggttattggggtacaggtggta ↓ 4 1 3 2 Human: GGAATATAAAACCCATGGCACA---------------------TAGTCCTTGCCTATGGAAACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACTACATTGACACAAAAATTTTTTAAAACTATTTCCATAATTTCTGGTGCTTACCttt-tt-ttcccataggttattggggtacaggtggta Cluster: [ ] Orangutan: GGAATATAAAACCCATGGCACATAGTCCTTGCCTGTGGAAACA---------------------TAGTCCATGGAAATATAACCTGTTTTCTGCATATAGTACATTGACACAAAAATTTTTTAAAACTATTTCCATAATTTCTGGTGTTTATCtttttttttcccataggttattgtggtacaggtggta Gorilla > Human --------------- chr11:82917054-82917062 Template switch process: F1: L CTTGTGACTGGACCCTTTTGGAATATAAAACCCATGGCACATAGTCCTTG 1 F3: 4 ACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACTACA R RF: CTTGTGACTGGACCCTTTTGGAATATAAAACCCATGGCACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACTACATTGACACAAAAATTTTTTAAAACTATTTCCATAATTTCTGGTGCTTATCTTTTTTTTCCCATAGG RR: GAACACTGACCTGGGAAAACCTTATATTTTGGGTACCGTGTATCAGGTACCTTTATATTGGACAAAAGACGTATATGATGTAACTGTGTTTTTAAAAAATTTTGATAAAGGTATTAAAGACCACGAATAGAAAAAAAAGGGTATCC F2: 3 AAGGTATCC 2 Unidirectional alignment (log-probability: -41.1) GACCCTTTTGGAATATAAAACCCATGGCAcatagtccttgcctatggaaaCATAGTCCATGGAAATATAACCTGTTTTCTGCATATACT GACCCTTTTGGAATATAAAACCCATGGCA---------------------CATAGTCCATGGAAATATAACCTGTTTTCTGCATATACT Template switch alignment (log-probability: -28.2) GACCCTTTTGGAATATAAAACCCATGGCACATAGTCCtTG|CCTATGGaA|ACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACT GACCCTTTTGGAATATAAAACCCATGGCACATAGTCCATG|CCTATGGGA|ACATAGTCCATGGAAATATAACCTGTTTTCTGCATATACT ========= Event 481 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTATTTTCAATTAGGAAGAATGGCAACTGCCACT-----------TAAATGCCATTTAAAATGCTAGAT-TTTCCCTAAC Chimp: TTATTTTCAATTAGGAAGAATGGCAACTGCCACT-----------TAAATGCCATTTAAAATGCTAGAT-TTTCCCTAAC ↑ 3 2 4 1 Gorilla: TTGTTTTCAATTAGGAAGAATGGCAACTGCCACT----------------------TAAAATGCTAGAT-TTTCCCTAAC Human: TTATTTTCAATTAGGAAGAATGGCAACTGCCACT-----------TAAATGCCATTTAAAATGCTAGAT-TTTCCCTAAC Cluster: [ ] Orangutan: TTATTTTTAATTAGGAAGAATGGCAACTGCCACTTAAATGCCATT-----------TAAAATGCTAGATTTTTCCCTAAC Gorilla > Chimp --------------- chr11:82776139-82776144 Template switch process: F1: L ACATAGATTATTTTCAATTAGGAAGAATGGCAACTGCCACTTAAA 1 F3: 4 TTAAAATGCTAGATTTTCCCTAACTGATAAAATGCCAGCAA R RF: ACATAGATTGTTTTCAATTAGGAAGAATGGCAACTGCCACTTAAAATGCTAGATTTTCCCTAACTGATAAAATGCCAGCAA RR: TGTATCTAACAAAAGTTAATCCTTCTTACCGTTGACGGTGAATTTTACGATCTAAAAGGGATTGACTATTTTACGGTCGTT F2: 3 TACCGT 2 Unidirectional alignment (log-probability: -32.2) GATTaTTTTCAATTAGGAAGAATGGCAACTGCCACttaaatgccatTTAAAATGCTAGATTTTCCCTAACTGATAAAATGCCAGCA GATTGTTTTCAATTAGGAAGAATGGCAACTGCCAC-----------TTAAAATGCTAGATTTTCCCTAACTGATAAAATGCCAGCA Template switch alignment (log-probability: -22.1) GATTaTTTTCAATTAGGAAGAATGGCAACTGCCACTTAAA|TGCCAT|TTAAAATGCTAGATTTTCCCTAACTGATAAAATGCCAGCA GATTGTTTTCAATTAGGAAGAATGGCAACTGCCACTTAAA|TGCCAT|TTAAAATGCTAGATTTTCCCTAACTGATAAAATGCCAGCA ========= Event 482 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TGACCCTGCTCTTGTGGAGAA---------------AGAAGGCCAATCCAGTTTCTGGATTGGGCTTTTGATGATGGTTCATCACCA Chimp: TGACCCTGCTCTTGTGGAGAA---------------AGAAGGCCAATCCAGTTTCTGGATTGGCCTTTTGATGATGGTTCATCACCA ↑ 3 4 2 Gorilla: TGACCCTGCTCTTGTGGAGAA--------------------------------ACTGGATTGGCCTTTTGATGATGGTTCATCATCA Human: TGACCCTGCTCTTGTGGAGAA---------------AGAAGGCCAATCCAGTTTCTGGATTGGGCTTTTGATGATGGTTCATCACCA Cluster: [ ] Orangutan: TGACCCTGCTCTTGTGGAGAAAGAAGGCATCCAGTT-----------------TCTGGATTGGCCTTTTGATGATGCTTCATCACCA Gorilla > Chimp --------------- chr11:86612238-86612253 Template switch process: F1: L AGAGTATGTGAAGCAACTGATGACCCTGCTCTTGTGGAGAAAG 1 F3: 4 CTGGATTGGCCTTTTGATGATGGTTCATCACCATCCAACC R RF: AGAGTATGTGAAGCAACTGATGACCCTGCTCTTGTGGAGAAACTGGATTGGCCTTTTGATGATGGTTCATCATCATCCAACC RR: TCTCATACACTTCGTTGACTACTGGGACGAGAACACCTCTTTGACCTAACCGGAAAACTACTACCAAGTAGTAGTAGGTTGG F2: 3 TTTGACCTAACCGGAA 2 Unidirectional alignment (log-probability: -40.9) GTATGTGAAGCAACTGATGACCCTGCTCTTGTGGAGAAAgaaggccaatccagtttCTGGATTGGCCTTTTGATGATGGTTCATCAcCATCCAACC GTATGTGAAGCAACTGATGACCCTGCTCTTGTGGAGAAA-----------------CTGGATTGGCCTTTTGATGATGGTTCATCATCATCCAACC Template switch alignment (log-probability: -28.9) GTATGTGAAGCAACTGATGACCCTGCTCTTGTGGAGAAAg|AAGGCCAATCCAGTTT|CTGGATTGGCCTTTTGATGATGGTTCATCAcCATCCAACC GTATGTGAAGCAACTGATGACCCTGCTCTTGTGGAGAAAC|AAGGCCAATCCAGTTT|CTGGATTGGCCTTTTGATGATGGTTCATCATCATCCAACC ========= Event 483 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATTCAGTCTTTGATTTGAAAACCATTAGAGGCTCTATGAGAGCCTCTAATTCCGAtttttttaaatta ↑ 1 3 4 2 Chimp: AATTCAGTCTTTGATTTGAAAACCA-TGGTTCTTCTCATAGAGCCTCTAATTCCGAttttttaaaatta Gorilla: AATTCAGTCTTTGATTTGAAAGCCA-TGGTTCTTCTCATAGAGCCTCTAATTCCGAtttttttaaatta ↓ 1 3 4 2 Human: AATTCAGTCTTTGATTTGAAAACCATTAGAGGCTCTATGAGAGCCTCTAATTCCGAtttttttaaatta Cluster: [ ] Orangutan: AATTCAGTCTTTGATTTGAAAACCA-TGGTTCTTCTCATAGAGCCTCTAATTCACAttttt-taaatta Chimp > Human ------------- chr11:87946364-87946376 Template switch process: F1: L GTATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCAT 1 F3: 4 AGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT R RF: GTATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCATGGTTCTTCTCATAGAGCCTCTAATTCCGATTTTTTAAAATTATACTTTAAGT RR: CATACTCTTGTAAACCTTAAGTCAGAAACTAAACTTTTGGTACCAAGAAGAGTATCTCGGAGATTAAGGCTAAAAAATTTTAATATGAAATTCA F2: 3 GTATCTCGGAGAT 2 Unidirectional alignment (log-probability: -45) ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCAT-----------TAgaggctctatgaGAGCCTCTAATTCCGATTTTTTtAAATTATACTTTAAGT ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCATGGTTCTTCTCATA------------GAGCCTCTAATTCCGATTTTTTAAAATTATACTTTAAGT Template switch alignment (log-probability: -22.9) ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCAT|TAGAGGCTCTATG|AGAGCCTCTAATTCCGATTTTTTtAAATTATACTTTAAGT ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCAT|TAGAGGCTCTATG|AGAGCCTCTAATTCCGATTTTTTAAAATTATACTTTAAGT Gorilla > Human --------------- chr11:87946364-87946376 Template switch process: F1: L TGATGTATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAACCAT 1 F3: 4 AGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT R RF: TGATGTATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAGCCATGGTTCTTCTCATAGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT RR: ACTACATACTCTTGTAAACCTTAAGTCAGAAACTAAACTTTCGGTACCAAGAAGAGTATCTCGGAGATTAAGGCTAAAAAAATTTAATATGAAATTCA F2: 3 GTATCTCGGAGAT 2 Unidirectional alignment (log-probability: -44) ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAaCCAT-----------TagaggctctatgAGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAGCCATGGTTCTTCTCAT------------AGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT Template switch alignment (log-probability: -23) ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAaCCAT|TAGAGGCTCTATG|AGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT ATGAGAACATTTGGAATTCAGTCTTTGATTTGAAAGCCAT|TAGAGGCTCTATG|AGAGCCTCTAATTCCGATTTTTTTAAATTATACTTTAAGT ========= Event 484 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TATAGTTCTATTAAGATTGGAGCCTTTCAAACAAGAGCTCAATTAGAA ↓ 31 2 4 Chimp: TATAGTTCTATTAAGATTGGAAGGCTCCAAACAAGAGCTCAATTAGAA Gorilla: TATAGTTCTATTAAGATTGGAAGGCTCCAAACAAGAGCTCAGTTAGAA ↑ 31 2 4 Human: TATAGTTCTATTAAGATTGGAGCCTTTCAAACAAGAGCTCAATTAGAA Cluster: [ ] Orangutan: TATAGTTCTATTAAGATTGGATGGCTCCAAACAAGAGCTCAATTAGAA Human > Chimp ------------- chr11:88509778-88509783 Template switch process: F1: L GATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA 1 F3: 4 CAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA R RF: GATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGAGCCTTTCAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA RR: CTACCAGTAAAAAAAATCGAATATCAAGATAATTCTAACCTCGGAAAGTTTGTTCTCGAGTTAATCTTTCGGGATTCTAAACGAAGT F2: 3 CTCGGA 2 Unidirectional alignment (log-probability: -30.1) ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGAaggctc------CAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA------GCCTTTCAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA Template switch alignment (log-probability: -16) ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA|AGGCTC|CAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA|AGGCTC|CAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA Human > Gorilla --------------- chr11:87876660-87876665 Template switch process: F1: L GATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA 1 F3: 4 CAAACAAGAGCTCAGTTAGAAAGCCCTAAGATTTGCTTCA R RF: GATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGAGCCTTTCAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA RR: CTACCAGTAAAAAAAATCGAATATCAAGATAATTCTAACCTCGGAAAGTTTGTTCTCGAGTTAATCTTTCGGGATTCTAAACGAAGT F2: 3 CTCGGA 2 Unidirectional alignment (log-probability: -34.3) ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGAaggcTcCAAACAAGAGCTCAgTTAGAAAGCCCTAAGATTTGCTTCA ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGAGCCTTTCAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA Template switch alignment (log-probability: -22) ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA|AGGCTC|CAAACAAGAGCTCAgTTAGAAAGCCCTAAGATTTGCTTCA ATGGTCATTTTTTTTAGCTTATAGTTCTATTAAGATTGGA|AGGCTC|CAAACAAGAGCTCAATTAGAAAGCCCTAAGATTTGCTTCA ========= Event 485 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAGTACTTGAGTAACTACATGCAGTTAGGAAAATGTTTTATATCCAGTCCTTTTTGCTTTCTAAAAGAGGGCTAAATG-ACAATATAGATAACCTCAAGTGAATCGCGAGTTGTTTTAAATAATAATCCAA-AGTTTTGGATTCTGTTTAAGC-TCTCTGC-ATTTTTTCAGATTCTGTGAAAG ↑ 3 2 1 4 Chimp: TAGTACTTGAGTAACTACATGCAGTTAGGAAAATGTTTTATATCCAGTCCTTTTTGCTTTCTAAAAGAGGGCTAAATG-ACAATATAGATAACCTCAAGTGAATCGGGAGTTGTTTTAAATAATAATCCAA-AGTTTTGGATTCTGTTTAAGC-T--CTGAACTTTTTTCAGATTCTGTGAAAG Gorilla: TAGTACTTGAGTAACTACATGCAGTTAGGAAAATGTTTTATATCCAGTCCTTTTTGCTTTCTAAAAGAGGGCTGAATG-ACAATATAGATAACCTCAAGTGAATTGCGAGTTGTTTTAAATAATAATCCAA-AGTTTTGGATTCTGTTTAAGC-TCTCTGCACTTTTTTCAGATTCTGTGAAAG Human: TAGTACTTGAGTAACTACATGCAGTTAGGAAAATGTTTTATATCCAGTCCTTTTTGCTTTCTAAAAGAGGGCTAAATG-ACAATATAGATAACCTCAAGTGAATCGCGAGTTGTTTTAAATAATAATCCAA-AGTTTTGGATTCTGTTTAAGC-TCTCTGC-ATTTTTTCAGATTCTGTGAAAG Cluster: [ ] Orangutan: TAGTACTTGAGTAACTACATACAGTTAGGAAAATGTTTTATATCCAGTCCTTTTTGCTTTCTAAACGAGGTCTAAATGAACAATATAGATAACCTCAAGTGAATCGGGAGTTGTTTTAAATAATAATCCAAAGGTTTTGGATTCTGTTTAAGCTTCCCTGCACTTTTTACAGATTCTGTGAAAG Chimp > Human ------------- chr1:61351443-61351447 Template switch process: F1: L GTTTTAAATAATAATCCAAAGTTTTGGATTCTGTTTAAGCTCT 1 F3: 4 TTTTTTCAGATTCTGTGAAAGTAGTTTCCTTATGAGATTT R RF: TGCAGTTAGGAAAATGTTTTATATCCAGTCCTTTTTGCTTTCTAAAAGAGGGCTAAATGACAATATAGATAACCTCAAGTGAATCGGGAGTTGTTTTAAATAATAATCCAAAGTTTTGGATTCTGTTTAAGCTCTGAACTTTTTTCAGATTCTGTGAAAGTAGTTTCCTTATGAGATTT RR: ACGTCAATCCTTTTACAAAATATAGGTCAGGAAAAACGAAAGATTTTCTCCCGATTTACTGTTATATCTATTGGAGTTCACTTAGCCCTCAACAAAATTTATTATTAGGTTTCAAAACCTAAGACAAATTCGAGACTTGAAAAAAGTCTAAGACACTTTCATCAAAGGAATACTCTAAA F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -27.1) TTAAATAATAATCCAAAGTTTTGGATTCTGTTTAAGCTCT---CtgcaTTTTTTCAGATTCTGTGAAAGTAGTTTCCTTATGAGATTT TTAAATAATAATCCAAAGTTTTGGATTCTGTTTAAGCTCTGAAC----TTTTTTCAGATTCTGTGAAAGTAGTTTCCTTATGAGATTT Template switch alignment (log-probability: -15.9) TTAAATAATAATCCAAAGTTTTGGATTCTGTTTAAGCTCT|CTGCA|TTTTTTCAGATTCTGTGAAAGTAGTTTCCTTATGAGATTT TTAAATAATAATCCAAAGTTTTGGATTCTGTTTAAGCTCT|CTGCA|TTTTTTCAGATTCTGTGAAAGTAGTTTCCTTATGAGATTT ========= Event 486 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATCACAGGTTTTATAGCCAATTA--------------------------------------------------------------------------------------------TATATTTTTTAAATGTAAACACTAATG-----------GAGACTTCTGTTTGGTAGCAGACATTTCTAATAAATTCAGAAATTTCCTCCATGTCATTCCTAAGC ↓ 4 3 1 2 Chimp: ATATCACAGATTTTATAGCCAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTGAAATTTCTGAATTTATTAGAAATGTCTGCTACCAAACAGAAGTCTCAATTATATATTTTTTAAATGTAAACACTAATG-----------GAGACTTCTGTTTGGTAGCAGACATTTCTAATAaattcagaaatttcctccatatcattcctaagc ↑ 4 3 1 2 Gorilla: ATATCACAGGTTTTATAGCCAATTA--------------------------------------------------------------------------------------------TATATTTTTTAAATGTAAACACTAATG-----------GAGACTTCTGTTTGGTAGCAGACATTTCTAATAaattcagaaatttcctccatgtcattcctaagc Human: ATATCACAGGTTTTATAGCCAATTA--------------------------------------------------------------------------------------------TATATTTTTTAAATGTAAACACTAATG-----------GAGACTTCTGTTTGGTAGCAGACATTTCTAATAAATTCAGAAATTTCCTCCATGTCATTCCTAAGC Cluster: [ ] Orangutan: ATATCACAGGTTTTATAGCCAATTA--------------------------------------------------------------------------------------------TACATTTTTTAAATGT-----------AAACACTAATAGAGACTTTTGTTTGGTAGCAGACATTTCTAATAaattcagaaatttccgccatgtcattcctaagc Human > Chimp ------------- chr1:62076826-62076870 Template switch process: F1: L CCTCCTGGACCTTGAGATATCACAGATTTTATAGCCAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTG 1 F3: 4 CAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTT R RF: CCTCCTGGACCTTGAGATATCACAGGTTTTATAGCCAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTGGGTAGCAGACATTTCTAATAAATTCAGAAATTT RR: GGAGGACCTGGAACTCTATAGTGTCCAAAATATCGGTTAATATATAAAAAATTTACATTTGTGATTACCTCTGAAGACAAACCCATCGTCTGTAAAGATTATTTAAGTCTTTAAA F2: 3 TCTGAAGACAAACCATCGTCTGTAAAGATTATTTAAGTCTTTAAA 2 Unidirectional alignment (log-probability: -146) ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTgaaatttctgaatttattagaaatgtctgctaccaaacagaagtctcaattatatattttttaaatgtaaacactaatggagactt ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTT-------------------------------------------------------------------------------------- Template switch alignment (log-probability: -27.5) ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTG|AAATTTCTGAATTTATTAGAAATGTCTGCTACCAAACAGAAGTCT|CAATTATATATTTTTTAAATGTAAACACTAATGGAGACTT ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTG|AAATTTCTGAATTTATTAGAAATGTCTGCTACCAAACAGAAGTCT|CAATTATATATTTTTTAAATGTAAACACTAATGGAGACTT Gorilla > Chimp --------------- chr1:62076826-62076870 Template switch process: F1: L CCTCCTGGACCTTGAGATATCACAGATTTTATAGCCAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTG 1 F3: 4 CAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTT R RF: CCTCCTGGACCTTGAGATATCACAGGTTTTATAGCCAATTATATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTGGGTAGCAGACATTTCTAATAAATTCAGAAATTT RR: GGAGGACCTGGAACTCTATAGTGTCCAAAATATCGGTTAATATATAAAAAATTTACATTTGTGATTACCTCTGAAGACAAACCCATCGTCTGTAAAGATTATTTAAGTCTTTAAA F2: 3 TCTGAAGACAAACCATCGTCTGTAAAGATTATTTAAGTCTTTAAA 2 Unidirectional alignment (log-probability: -146) ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTgaaatttctgaatttattagaaatgtctgctaccaaacagaagtctcaattatatattttttaaatgtaaacactaatggagactt ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTT-------------------------------------------------------------------------------------- Template switch alignment (log-probability: -27.9) ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTG|AAATTTCTGAATTTATTAGAAATGTCTGCTACCAAACAGAAGTCT|CAATTATATATTTTTTAAATGTAAACACTAATGGAGACTT ATATTTTTTAAATGTAAACACTAATGGAGACTTCTGTTTG|AAATTTCTGAATTTATTAGAAATGTCTGCTACCAAACAGAAGTCT|CAATTATATATTTTTTAAATGTAAACACTAATGGAGACTT ========= Event 487 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAGTCTGTGCATTCACTTTGCTAAGGATTAATC----CTGTTTTTCAAAATTAGCATATACATATATATG--------G Chimp: TTAGTCTGTGCATTCACTTTGCTAAGGATTAATC--CTCTGTTTTTCAAAACTAGtatatatatatatatG----GTTAG ↓ 3 2 1 4 Gorilla: TTAGTCTGTGCATCCACTTTGCTAAGGATTAATCCT--CTGTTTTTCAAAATTAGCatatat--atatatGGTTA----G Human: TTAGTCTGTGCATTCACTTTGCTAAGGATTAATC----CTGTTTTTCAAAATTAGCATATACATATATATG--------G Cluster: [ ] Orangutan: TTAGTCTGTGCATCCACTTTTCTAAGGATTAATCCT--CTGTTTTTCAAAATTAGCATATA----TATATGGTTA----G Chimp > Gorilla --------------- chr1:61738915-61738920 Template switch process: F1: L CTCGTCTTTAGTCTGTGCATCCACTTTGCTAAGGATTAATCCTCTGTTTTTCAAAA 1 F3: 4 TATATATATATGGTTA R RF: CTCATCTTTAGTCTGTGCATTCACTTTGCTAAGGATTAATCCTCTGTTTTTCAAAACTAGTATATATATATATATGGTTA RR: GAGTAGAAATCAGACACGTAAGTGAAACGATTCCTAATTAGGAGACAAAAAGTTTTGATCATATATATATATATACCAAT F2: 3 ACGATT 2 Unidirectional alignment (log-probability: -41.2) GCATcCACTTTGCTAAGGATTAATCCTCTGTTTTTCAAAAtTAG--cATATATATATATGGTTa GCATTCACTTTGCTAAGGATTAATCCTCTGTTTTTCAAAACTAGTATATATATATATATGGTT- Template switch alignment (log-probability: -27.3) GCATcCACTTTGCTAAGGATTAATCCTCTGTTTTTCAAAA|TTAGCA|TATATATATATGGTTA GCATTCACTTTGCTAAGGATTAATCCTCTGTTTTTCAAAA|TTAGCA|TATATATATATGGTTA ========= Event 488 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCACTTATAATTTGAAGAATACTTGTACTGCAGTA------GTATCCAATATTGCCAGTAAttttct Chimp: TTTCCCTTATAATTTGAAGAATACTTGTACAGCAATAGTACAAGTATTCAATATTGCCAGTAAttttct ↑ 3 2 1 4 Gorilla: TTTCACTTATAATTTGAAGAATACTTGTACTGCAATA------GTATCCAATATTGCCAGTAAttttct Human: TTTCACTTATAATTTGAAGAATACTTGTACTGCAGTA------GTATCCAATATTGCCAGTAAttttct Cluster: [ ] Orangutan: tttcacttataatttgaagaatacttgtactgcaata------gtatccaatattgccagtaattttct Gorilla > Chimp --------------- chr1:61156819-61156826 Template switch process: F1: L AAATAGCTTCATTTCCCTTATAATTTGAAGAATACTTGTACAGCAATAGTA 1 F3: 4 CAATATTGCCAGTAATTTTCTTTTCTCTTTTTTTTTT R RF: AAATAGCTTCATTTCACTTATAATTTGAAGAATACTTGTACTGCAATAGTATCCAATATTGCCAGTAATTTTCTTTTCTCTTTTTTTTTT RR: TTTATCGAAGTAAAGTGAATATTAAACTTCTTATGAACATGACGTTATCATAGGTTATAACGGTCATTAAAAGAAAAGAGAAAAAAAAAA F2: 3 TTATGAAC 2 Unidirectional alignment (log-probability: -43.1) TTTCcCTTATAATTTGAAGAATACTTGTACaGCAATagtacaAGTATtCAATATTGCCAGTAATTTTCTTTTCTCTTTTTTTTTT--- TTTCACTTATAATTTGAAGAATACTTGTACTGCAAT------AGTATCCAATATTGCCAGTAATTTTCTTTTCTCTTTTTTTTTTTTT Template switch alignment (log-probability: -28) TTTCcCTTATAATTTGAAGAATACTTGTACaGCAATAGTA|CAAGTATT|CAATATTGCCAGTAATTTTCTTTTCTCTTTTTTTTTT TTTCACTTATAATTTGAAGAATACTTGTACTGCAATAGTA|CAAGTATT|CAATATTGCCAGTAATTTTCTTTTCTCTTTTTTTTTT ========= Event 489 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: cataatttttcttaaacgtgcagtttccaagagactttccaagatgttaagtcaggacatactgTACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCCTTATAAACTGCTTCTAGGGAATCTATTTAGGCAGG ↑ 3 2 4 1 Chimp: cataattttgcttaaaggtgcagtttctaagagactttccaagatgttaagtcaggacatactgTACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATT---------------TCTAGGGAATCTATTTAGGCAGG ↓ 3 2 4 1 Gorilla: cataattttgcttaaaggtgcagtttccaagagactttccaagatgttaagtcaggacatactgTACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCTTTATAAACTGCTTCTAGGGAATCTATTTAGGCAGG Human: cataatttttcttaaacgtgcagtttccaagagactttccaagatgttaagtcaggacatactgTACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCCTTATAAACTGCTTCTAGGGAATCTATTTAGGCAGG Cluster: [ ] Orangutan: cataattttgcttaaaggtgaagtatccaagagactttcaaagatgttatgtgaggacatactCTACATCAAACTCATATCCTCTTCCAGAGTTCGTGTGGAATTTCTTTATAAACTGCTTCTAGAGAATCTATTTAGGCAGG Chimp > Human ------------- chr11:48230108-48230119 Template switch process: F1: L TACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTC 1 F3: 4 TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCCG R RF: GCAGTTTCTAAGAGACTTTCCAAGATGTTAAGTCAGGACATACTGTACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCCA RR: CGTCAAAGATTCTCTGAAAGGTTCTACAATTCAGTCCTGTATGACATGTAGTTTAAGTGTAGGAAAAGGTGTCAAGTACACCTTAAAGATCCCTTAGATAAATCCGTCCAATACACATCTCTAGGT F2: 3 CGTCAAATATTC 2 Unidirectional alignment (log-probability: -38.5) ATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTccttataaactgcttCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC ATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTT---------------CTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC Template switch alignment (log-probability: -28.8) ATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTC|CTTAtAAACTGC|TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC ATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTC|CTTAGAAACTGC|TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC Chimp > Gorilla --------------- chr11:48835297-48835307 Template switch process: F1: L TACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCT 1 F3: 4 TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCCA R RF: GCAGTTTCTAAGAGACTTTCCAAGATGTTAAGTCAGGACATACTGTACATCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCCA RR: CGTCAAAGATTCTCTGAAAGGTTCTACAATTCAGTCCTGTATGACATGTAGTTTAAGTGTAGGAAAAGGTGTCAAGTACACCTTAAAGATCCCTTAGATAAATCCGTCCAATACACATCTCTAGGT F2: 3 CGTCAAATATT 2 Unidirectional alignment (log-probability: -32.5) TCAAATTCACATCCTTTTCCACAGTTCATGTGGAATttctttataaactgcTTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC TCAAATTCACATCCTTTTCCACAGTTCATGTGGAAT---------------TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC Template switch alignment (log-probability: -22.7) TCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCT|TTAtAAACTGC|TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC TCAAATTCACATCCTTTTCCACAGTTCATGTGGAATTTCT|TTAGAAACTGC|TTCTAGGGAATCTATTTAGGCAGGTTATGTGTAGAGATCC ========= Event 490 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTCTTTAAAAATTAATGAAA-----AGGGGATTA-Atattgacagtcagc-------tatatgccaggacacaagg Chimp: AGTCTTTTAAAATTAATGAAA----AGGGGGATTA-Atattgacagtcagc-------tatatgccaggacacaagg ↑ 3 12 4 Gorilla: AGTCTTTTAAAATTAATGAAA-----AGGGGatta-atattgactatatgctatatgctatatgccaggacacaagg Human: AGTCTTTAAAAATTAATGAAA-----AGGGGATTA-Atattgacagtcagc-------tatatgccaggacacaagg Cluster: [ ] Orangutan: ACTCTTTTAAAATTAATGAAAAATT-GGGGGATTAAttattgacagtcagc-------tatatgccaggacacaagg Gorilla > Chimp --------------- chr11:89043896-89043900 Template switch process: F1: L GGGGACTAAGGACAAATGTTAGTCTTTTAAAATTAATGAAAAGGGGGATTAATATTGAC 1 F3: 4 GCTATATGCCAG R RF: GGGGACTAAGGACAAATGTTAGTCTTTTAAAATTAATGAAAAGGGG-ATTAATATTGACTATATGCTATATGCTATATGCCAG RR: CCCCTGATTCCTGTTTACAATCAGAAAATTTTAATTACTTTTCCCC-TAATTATAACTGATATACGATATACGATATACGGTC F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -39.5) TAGTCTTTTAAAATTAATGAAAAGGgGGATTAATATTGACagtca------------GCTATATGCCAG TAGTCTTTTAAAATTAATGAAAAGG-GGATTAATATTGAC-----TATATGCTATATGCTATATGCCAG Template switch alignment (log-probability: -27.3) TAGTCTTTTAAAATTAATGAAAAGGGGgATTAATATTGAC|AGTCA|GCTATATGCCAG TAGTCTTTTAAAATTAATGAAAAGGGG-ATTAATATTGAC|AGTCA|GCTATATGCCAG ========= Event 491 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: cattttagccacaaagagtACTGATGAGAGTACCTCTCATCAGTCAGATA--GGTACAatgttga ↑ 3 2 4 Chimp: cattttagccacaaagagtACTGATGAGAGT------------ACAGATA--GGTACAatgttga ↓ 3 2 4 Gorilla: cattttagccacaaagagtACTGATGAGAGTACCTCTCATCAGTCAGATA--GGTACAatgttga Human: cattttagccacaaagagtACTGATGAGAGTACCTCTCATCAGTCAGATA--GGTACAatgttga Cluster: [ ] Orangutan: cattttagccacaaagagtac------------ctctcatcagtcagataggggtacagtgttga Chimp > Human ------------- chr1:189222256-189222266 Template switch process: F1: L TAGAGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAC 1 F3: 4 CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT R RF: TAGAGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTACAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT RR: ATCTCGCAAAGTAAAATCGGTGTTTCTCATGACTACTCTCATGTCTATCCATGTTACAACTGTGAAAATTCCCACTTATACA F2: 3 TGACTACTCTC 2 Unidirectional alignment (log-probability: -28.2) AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAcctctcatcagtCAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTA------------CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT Template switch alignment (log-probability: -16.7) AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAC|CTCTCATCAGT|CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAC|CTCTCATCAGT|CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT Chimp > Gorilla --------------- chr1:168605443-168605453 Template switch process: F1: L TAGAGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAC 1 F3: 4 CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT R RF: TAGAGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTACAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT RR: ATCTCGCAAAGTAAAATCGGTGTTTCTCATGACTACTCTCATGTCTATCCATGTTACAACTGTGAAAATTCCCACTTATACA F2: 3 TGACTACTCTC 2 Unidirectional alignment (log-probability: -28.2) AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAcctctcatcagtCAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTA------------CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT Template switch alignment (log-probability: -17.2) AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAC|CTCTCATCAGT|CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT AGCGTTTCATTTTAGCCACAAAGAGTACTGATGAGAGTAC|CTCTCATCAGT|CAGATAGGTACAATGTTGACACTTTTAAGGGTGAATATGT ========= Event 492 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CACCACCATCATCGTTATTAT------------CGTAGGCTTCTCTGAGCCTACGAtttttttct-------------------------ttttttt Chimp: CACCACCATCATCGTTATTAT------------CGTAGGCTTCTCTGAGCCTACGAtttttttct------------ttttttcttttttttttttt ↓ 3 2 4 Gorilla: CACCACCATCATCGTTATTAT------------------------GAAGCCTACGAtttttttct---ttttttttt-------------ttttttt Human: CACCACCATCATCGTTATTAT------------CGTAGGCTTCTCTGAGCCTACGAtttttttct-------------------------ttttttt Cluster: [ ] Orangutan: CACCACCATCATCGTTATTATCGCAGGCTTCTC------------TGAGCCTACAGtttttttctttt----------------------ttttttt Chimp > Gorilla --------------- chr11:134518110-134518120 Template switch process: F1: L CCTAGTACTTAACGTGGCATCACCACCATCATCGTTATTAT 1 F3: 4 TTTTTTTCTTTTTTTTTT R RF: CCTAGTACTTAACGTGGCATCACCACCATCATCGTTATTATCGTAGGCTTCTCTGAGCCTACGATTTTTTTCTTTTTTTCTTTTTTTTTT RR: GGATCATGAATTGCACCGTAGTGGTGGTAGTAGCAATAATAGCATCCGAAGAGACTCGGATGCTAAAAAAAGAAAAAAAGAAAAAAAAAA F2: 3 AGCATCCGAAG 2 Unidirectional alignment (log-probability: -32.3) CTAGTACTTAACGTGGCATCACCACCATCATCGTTATTAT------------gaAGCCTACGATTTTTTTCTTTT----TTTTTT CTAGTACTTAACGTGGCATCACCACCATCATCGTTATTATCGTAGGCTTCTCTGAGCCTACGATTTTTTTCTTTTTTTCTTTTTT Template switch alignment (log-probability: -16.5) CTAGTACTTAACGTGGCATCACCACCATCATCGTTATTAT|GAAGCCTACGA|TTTTTTTCTTTTTTTTTT CTAGTACTTAACGTGGCATCACCACCATCATCGTTATTAT|GAAGCCTACGA|TTTTTTTCTTTTTTTTTT ========= Event 493 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAACATGTAAGATTCCACGAGTCT--------TTCTTCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACTTGGGACAAATAAGTGGTCTTAggtcaggcatggtggctcacgcctataatcccagcactttgggaggcca ↓ 1 4 3 2 Chimp: CAACATGTAAGATTCCACGAGATT--ATAGGCATGATCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACTTGGGACAAATAAGTGGTCTTAggtcaggcacggtggctcacgcctataatcccagcactttgggaggcca ↑ 1 4 3 2 Gorilla: CAACATGTAAGATTCCACGAGAGTCT------TTCTTCTCCTACCCTATGTTCTCCCGTCACGTGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACTTGGGACAAATAAGTGGTCTTAggtcaggcacggtagctcacgcctataatcccagcactttgggaggcca Human: CAACATGTAAGATTCCACGAGTCT--------TTCTTCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACTTGGGACAAATAAGTGGTCTTAggtcaggcatggtggctcacgcctataatcccagcactttgggaggcca Cluster: [ ] Orangutan: CAACATGTAAGATTCCACAAGAGTCT------TCCTTCTCCTACCCTATGTTCTCCTGTCACATGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACCTGGGACAAATAAGTGGTCTTAggccaggcatggtggctcacgcctataatcccagcactttgggaggcca Human > Chimp ------------- chr1:18361429-18361441 Template switch process: F1: L CCTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAG 1 F3: 4 TCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTT R RF: CCTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGTCTTTCTTCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACTTGGGACAAATAAGTGGTCTTAGGTCAGGCATGGTGGCTCACGCCTATAAT RR: GGACCCGGGAGTTTGTCGAGGTTGTACATTCTAAGGTGCTCAGAAAGAAGAGGATGGGATACAAGAGGGCAGTGTACATACCACACAAGACGAAGACCCTAGAGTGGTTCCTCATCGTCGTTCTGAACCCTGTTTATTCACCAGAATCCAGTCCGTACCACCGAGTGCGGATATTA F2: 3 AGTACGGATATTA 2 Unidirectional alignment (log-probability: -40.2) CTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAG-------attataggcatgaTCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTT CTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGTCTTTCT-------------TCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTT Template switch alignment (log-probability: -22.9) CTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAG|ATTATAGGCaTGA|TCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTT CTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAG|ATTATAGGCGTGA|TCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTT Gorilla > Chimp --------------- chr1:18361430-18361441 Template switch process: F1: L CTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGA 1 F3: 4 TCTCCTACCCTATGTTCTCCCGTCACATGTATGGTGTGTT R RF: CTGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGAGTCTTTCTTCTCCTACCCTATGTTCTCCCGTCACGTGTATGGTGTGTTCTGCTTCTGGGATCTCACCAAGGAGTAGCAGCAAGACTTGGGACAAATAAGTGGTCTTAGGTCAGGCACGGTAGCTCACGCCTATAA RR: GACCCGGGAGTTTGTCGAGGTTGTACATTCTAAGGTGCTCTCAGAAAGAAGAGGATGGGATACAAGAGGGCAGTGCACATACCACACAAGACGAAGACCCTAGAGTGGTTCCTCATCGTCGTTCTGAACCCTGTTTATTCACCAGAATCCAGTCCGTGCCATCGAGTGCGGATATT F2: 3 AGTACGGATATT 2 Unidirectional alignment (log-probability: -42.3) TGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGA-------TtataggcatgaTCTCCTACCCTATGTTCTCCCGTCACaTGTATGGTGTGTT TGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGAGTCTTTCT-----------TCTCCTACCCTATGTTCTCCCGTCACGTGTATGGTGTGTT Template switch alignment (log-probability: -28.3) TGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGA|TTATAGGCaTGA|TCTCCTACCCTATGTTCTCCCGTCACaTGTATGGTGTGTT TGGGCCCTCAAACAGCTCCAACATGTAAGATTCCACGAGA|TTATAGGCGTGA|TCTCCTACCCTATGTTCTCCCGTCACGTGTATGGTGTGTT ========= Event 494 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGTGACTTGCCTACCAAAAAGATTGGTGAACCATGTTTTCTAAATTTTGTTTTTG ↓ 1 3 4 2 Chimp: AGGTGACTTGCCTACCAAAAACATGGTTC--ACATGTTTTCTAAATTTTGTTTTTG ↑ 1 3 4 2 Gorilla: AGGTGACTTGCCTACCAAAAAGATTGGTGAACCATGTTTTCTAAATTTTGTTTTTG Human: AGGTGACTTGCCTACCAAAAAGATTGGTGAACCATGTTTTCTAAATTTTGTTTTTG Cluster: [ ] Orangutan: AGGTGACTTGCCTACCAAAAAGATTGGTGAACCATGTTTTCTAAATTTTGTTTTTG Human > Chimp ------------- chr1:59006703-59006711 Template switch process: F1: L GGTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAA 1 F3: 4 CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG R RF: GGTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAAGATTGGTGAACCATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG RR: CCACCTGAGTCCTGAGGTAATCCACTGAACGGATGGTTTTTCTAACCACTTGGTACAAAAGATTTAAAACAAAAACTCTCGTTTCCGCATAC F2: 3 ACTTGGTAC 2 Unidirectional alignment (log-probability: -33.2) GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAA----------AACatggttcaCATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAAGATTGGTGAAC--------CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG Template switch alignment (log-probability: -16.4) GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAA|CATGGTTCA|CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAA|CATGGTTCA|CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG Gorilla > Chimp --------------- chr1:59006703-59006711 Template switch process: F1: L GGTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAA 1 F3: 4 CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG R RF: GGTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAAGATTGGTGAACCATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG RR: CCACCTGAGTCCTGAGGTAATCCACTGAACGGATGGTTTTTCTAACCACTTGGTACAAAAGATTTAAAACAAAAACTCTCGTTTCCGCATAC F2: 3 ACTTGGTAC 2 Unidirectional alignment (log-probability: -32.7) GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAA----------AACatggttcaCATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAAGATTGGTGAAC--------CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG Template switch alignment (log-probability: -16.9) GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAA|CATGGTTCA|CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG GTGGACTCAGGACTCCATTAGGTGACTTGCCTACCAAAAA|CATGGTTCA|CATGTTTTCTAAATTTTGTTTTTGAGAGCAAAGGCGTATG ========= Event 495 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTCTACTTCTGCAAAATGTATACCTTCCAAAGAAGG--TATACCTGACCTTGGGGTCAGGTTAAGT Chimp: TATTCTACTTCTGCAAAATGTATACCTTCCAAAGAAGG--TATACCTGACCTTGGGGTCAGGTTAAGT ↑ 3 2 1 4 Gorilla: TATTCTACTTCTGCAAAATGTATACCTTCCAAAGAATGTTTATGTCTCACCTTGGGGTCAGGTTAAGT ↓ 3 2 1 4 Human: TATTCTACTTCTGCAAAATGTATACCTTCCAAAGAAGG--TATACCTGACCTTGGGGTCAGGTTAAGT Cluster: [ ] Orangutan: TATTCTACTTCTGCAAAATGTATACCTTCCAAAGAATGTTTATGTCTCACCTTGGGGTCAGGTTAAGT Gorilla > Human --------------- chr1:191599664-191599670 Template switch process: F1: L CATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA 1 F3: 4 CTGACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGTGTT R RF: CATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAATGTTTATGTCTCACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGTGTT RR: GTAATATAAGATGAAGACGTTTTACATATGGAAGGTTTCTTACAAATACAGAGTGGAACCCCAGTCCAATTCACCGAGATGAACACTACACAA F2: 3 CATATGG 2 Unidirectional alignment (log-probability: -32.7) ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAAggtataccTG----------ACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA--------TGTTTATGTCTCACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT Template switch alignment (log-probability: -22.2) ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA|GGTATAC|CTgACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA|GGTATAC|CTCACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT Gorilla > Chimp --------------- chr1:170283354-170283360 Template switch process: F1: L CATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA 1 F3: 4 CTGACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGTGTT R RF: CATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAATGTTTATGTCTCACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGTGTT RR: GTAATATAAGATGAAGACGTTTTACATATGGAAGGTTTCTTACAAATACAGAGTGGAACCCCAGTCCAATTCACCGAGATGAACACTACACAA F2: 3 CATATGG 2 Unidirectional alignment (log-probability: -32.7) ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAAggtataccTG----------ACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA--------TGTTTATGTCTCACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT Template switch alignment (log-probability: -22.2) ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA|GGTATAC|CTgACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT ATTATATTCTACTTCTGCAAAATGTATACCTTCCAAAGAA|GGTATAC|CTCACCTTGGGGTCAGGTTAAGTGGCTCTACTTGTGATGT ========= Event 496 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: AATACCTAAAGGACAGAACACTCTGAGGTGTTCTGTGACAAAGTTAAC ↓ 13 24 ↑ 13 24 Chimp: AATACCTAAAGGACAGAACACCTCAGAGTGTTCTGTGACAAAGTTAAC Gorilla: AATACCTAAAGGACAGAACACCTCAGAGTGTTCTGTGACAAAGTTAAC ↓ 13 24 ↑ 13 24 Human: AATACCTAAAGGACAGAACACTCTGAGGTGTTCTGTGACAAAGTTAAC Cluster: [ ] Orangutan: AATACCTAAAGGACAGAACACCTCAGAGTGTTCTGTGACAAAGTTAAC Chimp > Human ------------- chr11:42855362-42855367 Template switch process: F1: L AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC 1 F3: 4 GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG R RF: AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACCTCAGAGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG RR: TCGTTGTCTAGATTTACTACTTATGGATTTCCTGTCTTGTGGAGTCTCACAAGACACTGTTTCAATTGGAACTCTAAGTATTGATTC F2: 3 GAGTCT 2 Unidirectional alignment (log-probability: -34.6) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACtCTgAG-GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTgAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC-CTCAGAGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG Template switch alignment (log-probability: -22) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|TCTGAG|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTgAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|TCTGAG|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG Human > Chimp ------------- chr11:43462636-43462641 Template switch process: F1: L AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC 1 F3: 4 GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG R RF: AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACTCTGAGGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG RR: TCGTTGTCTAGATTTACTACTTATGGATTTCCTGTCTTGTGAGACTCCACAAGACACTGTTTCAATTGGAACTCTAAGTATTGACTC F2: 3 AGACTC 2 Unidirectional alignment (log-probability: -34.6) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAcCTCaGA-GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTaAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACA-CTCTGAGGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG Template switch alignment (log-probability: -22) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|CTCAGA|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTaAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|CTCAGA|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG Gorilla > Human --------------- chr11:42855362-42855367 Template switch process: F1: L AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC 1 F3: 4 GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG R RF: AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACCTCAGAGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG RR: TCGTTGTCTAGATTTACTACTTATGGATTTCCTGTCTTGTGGAGTCTCACAAGACACTGTTTCAATTGGAACTCTAAGTATTGATTC F2: 3 GAGTCT 2 Unidirectional alignment (log-probability: -33.2) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACA-CTCtGAgGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTgAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACCTCAGA-GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG Template switch alignment (log-probability: -22) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|TCTGAG|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTgAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|TCTGAG|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG Human > Gorilla --------------- chr11:43545578-43545583 Template switch process: F1: L AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC 1 F3: 4 GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTAAG R RF: AGCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACTCTGAGGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG RR: TCGTTGTCTAGATTTACTACTTATGGATTTCCTGTCTTGTGAGACTCCACAAGACACTGTTTCAATTGGAACTCTAAGTATTGACTC F2: 3 AGACTC 2 Unidirectional alignment (log-probability: -33.2) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC-CTcAGaGTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTaAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACACTCTGAG-GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG Template switch alignment (log-probability: -22) GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|CTCAGA|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTaAG GCAACAGATCTAAATGATGAATACCTAAAGGACAGAACAC|CTCAGA|GTGTTCTGTGACAAAGTTAACCTTGAGATTCATAACTGAG ========= Event 497 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCACAGAGGAATGTGTGTATGTGTGTGCGTGcacacacacac---------------------------acataattataaaattttggcattcaca--cacacacataattataaa----------aca--cacacacacataattataaaaTTTTGGCATTCAAAAACCTCCATCCATAGAA-AAAATTACATTTGCTTTATTCATATT Chimp: TCACAGAGGAATGTGTGTATGTGT----GTGcacacacacac---------------------------acataattataaaattttggcattcaca--cacacacataattataaa----------aca----cacacacattattataaaaTTTTGGCATTCAAAAACCTCCATCCATAGAA-AAAATTACATTTGCTTTATTCATATT ↓ 3 2 4 Gorilla: TCACAGAGGAATGTGTGTATGTGTGTGCATGcacacacatac------------------------------------------------------a--cacccacataattataaaattttggcattca----cacacacataagtataaaattttggcattcaAAAACCTCCATCCATAGaaaaaaaTTACATTAGCTTTATTCATATA Human: TCACAGAGGAATGTGTGTATGTGTGTGCGTGcacacacacac---------------------------acataattataaaattttggcattcaca--cacacacataattataaa----------aca--cacacacacataattataaaaTTTTGGCATTCAAAAACCTCCATCCATAGAA-AAAATTACATTTGCTTTATTCATATT Cluster: [ ] Orangutan: TCACAGAGGAATCTGTGTATGTGTGTGCGTGcacacacacacacaTAATTATAAAATTTTGGCATTcac---------------------------acacacacacataattataaa----------acaca--cacacacataattataaaaTTTTGGCATTCGAAAACCTCCATCCATAGAAAAAAATTACATTTGCTTTATTCATATT Chimp > Gorilla --------------- chr1:171748042-171748051 Template switch process: F1: L TAAAACACCAAAAATATTCACAGAGGAATGTGTGTATGTGTGTGCA 1 F3: 4 TAC R RF: TAAAACACCAAAAATATTCACAGAGGAATGTGTGTATGTGTGTGCACACACACACACATAATTATAAAATTTTGGCATTCACACACACACATAATTATAAAACACACACACATTATTATAAAATTTTGGCATTCAAAAACCTCCATCCATAGAAAAAATTAC RR: ATTTTGTGGTTTTTATAAGTGTCTCCTTACACACATACACACACGTGTGTGTGTGTGTATTAATATTTTAAAACCGTAAGTGTGTGTGTGTATTAATATTTTGTGTGTGTGTAATAATATTTTAAAACCGTAAGTTTTTGGAGGTAGGTATCTTTTTTAATG F2: 3 ACACACACGT 2 Unidirectional alignment (log-probability: -27) ACCAAAAATATTCACAGAGGAATGTGTGTATGTGTGTGCAtgCACACACAtAC------------------------- ACCAAAAATATTCACAGAGGAATGTGTGTATGTGTGTGCA--CACACACACACATAATTATAAAATTTTGGCATTCAC Template switch alignment (log-probability: -16.1) ACCAAAAATATTCACAGAGGAATGTGTGTATGTGTGTGCA|TGCACACACA|TAC ACCAAAAATATTCACAGAGGAATGTGTGTATGTGTGTGCA|TGCACACACA|TAC ========= Event 498 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATGTCTCTGATGAAGTGGAAGATCCAACATAGACTCATT ↑ 3 2 1 4 Chimp: GATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTC---------TGATGAAGTAAAAGATCCAACATAGACTCATT Gorilla: GATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTC---------TGATGAAGTAAAAGATCCAACATAGACTCATT ↓ 3 2 1 4 Human: GATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATGTCTCTGATGAAGTGGAAGATCCAACATAGACTCATT Cluster: [ ] Orangutan: GATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTC---------TGATGAAGTAAAAGATCAAACATAGACTCATT Chimp > Human ------------- chr11:42308644-42308658 Template switch process: F1: L ATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATG 1 F3: 4 AAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG R RF: ATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATGAAGTAAAAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG RR: TACGTCGGTGACCTAGAAGGTGAAGTAGTCTCTGTCCCGAGACTACTTCATTTTCTAGGTTGTATCTGAGTAAAGAGTGTCGTTGTACACTC F2: 3 GGTGAAGTAGTCTCT 2 Unidirectional alignment (log-probability: -35.9) CCACTGGATCTTCCACTTCATCAGAGACAGGGctctgatgtCTCTGATGAAGTggAAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG CCACTGGATCTTCCACTTCATCAGAGACAGGG---------CTCTGATGAAGTAAAAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG Template switch alignment (log-probability: -17.2) CCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATG|TCTCTGATGAAGTGG|AAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG CCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATG|TCTCTGATGAAGTGG|AAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG Gorilla > Human --------------- chr11:42308644-42308658 Template switch process: F1: L ATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATG 1 F3: 4 AAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG R RF: ATGCAGCCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATGAAGTAAAAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG RR: TACGTCGGTGACCTAGAAGGTGAAGTAGTCTCTGTCCCGAGACTACTTCATTTTCTAGGTTGTATCTGAGTAAAGAGTGTCGTTGTACACTC F2: 3 GGTGAAGTAGTCTCT 2 Unidirectional alignment (log-probability: -35) CCACTGGATCTTCCACTTCATCAGAGACAGGGCtctgatgtcTCTGATGAAGTggAAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG CCACTGGATCTTCCACTTCATCAGAGACAGGGC---------TCTGATGAAGTAAAAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG Template switch alignment (log-probability: -17.8) CCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATG|TCTCTGATGAAGTGG|AAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG CCACTGGATCTTCCACTTCATCAGAGACAGGGCTCTGATG|TCTCTGATGAAGTGG|AAGATCCAACATAGACTCATTTCTCACAGCAACATGTGAG ========= Event 499 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATCAATACAGGTACAATTTATCCTAGGAGATGACTGTTGAGTCAAGCTCAACTCAATTCTGaaaaaaa---aaaaaaaaaaaaaaaaaaaaaaGCCCAATATCTTtaatgattacttttatgtgtcaacttgactagacaatggatgcccaagtatttggccactaggtgtttctgtgaggatgtttt ↑ 1 4 3 2 Chimp: ATCAATACAGGTACAATTTATGCTAAGAGATGGCTGTTGAGTCAAGCTCAACTCAATTCTGaaaaaaa-------------------aaaaaaGCCCAATATCTTtaatgattacttttatgtgtcaacttgactagacaatggatgcccaagtatttggccactaggtgtttctgtgaggatgtttt Gorilla: ATCAATACAAGTACAATTTATGCTAGGAAATGCATGTTGAGTCAAGCTCAACTCAATTCTGaaaaaaa-------------------aaaaaaGCCCAATATCTTtaatgattagttttatgtgtcaacttgactagacaatggacgcccaagtatttggccactaggtgtttctgtgaggatgtttt Human: ATCAATACAGGTACAATTTATCCTAGGAGATGACTGTTGAGTCAAGCTCAACTCAATTCTGaaaaaaa---aaaaaaaaaaaaaaaaaaaaaaGCCCAATATCTTtaatgattacttttatgtgtcaacttgactagacaatggatgcccaagtatttggccactaggtgtttctgtgaggatgtttt Cluster: [ ] Orangutan: ATCAATACAGGTACAATTTATGCTAGGAGATGCATGTTGAGTCAAGCTCAACTCAATTCTGaaaaaaaaaa----------------aaaaaaGCCCAATATCTTtaatgattagttttatgtgtcaacttgactagacaatggatgcccaagtatttggccactaggtgtttctgtgaggatgtttt Chimp > Human ------------- chr1:193109483-193109487 Template switch process: F1: L TGGAGCACCTTAGAACAATTATCAATACAGGTACAATTTAT 1 F3: 4 GAGATGACTGTTGAGTCAAGCTCAACTCAATTCTGAAAAAAAAAAAA R RF: TGGAGCACCTTAGAATAATTATCAATACAGGTACAATTTATGCTAAGAGATGGCTGTTGAGTCAAGCTCAACTCAATTCTGAAAAAAAAAAAAAGCCCAATATCTTTAATGATTACTTTTATGTGTCAACTTGACTAGACAATGGATGCCCAAGTATTTGGCCACTAGG RR: ACCTCGTGGAATCTTATTAATAGTTATGTCCATGTTAAATACGATTCTCTACCGACAACTCAGTTCGAGTTGAGTTAAGACTTTTTTTTTTTTTCGGGTTATAGAAATTACTAATGAAAATACACAGTTGAACTGATCTGTTACCTACGGGTTCATAAACCGGTGATCC F2: 3 GATCC 2 Unidirectional alignment (log-probability: -39.1) GGAGCACCTTAGAAcAATTATCAATACAGGTACAATTTATcCTAgGAGATGaCTGTTGAGTCAAGCTCAACTCAATTCTGAAAAA GGAGCACCTTAGAATAATTATCAATACAGGTACAATTTATGCTAAGAGATGGCTGTTGAGTCAAGCTCAACTCAATTCTGAAAAA Template switch alignment (log-probability: -28) GGAGCACCTTAGAAcAATTATCAATACAGGTACAATTTAT|CCTAG|GAGATGaCTGTTGAGTCAAGCTCAACTCAATTCTGAAAAA GGAGCACCTTAGAATAATTATCAATACAGGTACAATTTAT|CCTAG|GAGATGGCTGTTGAGTCAAGCTCAACTCAATTCTGAAAAA ========= Event 500 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAATCC-AAGCATTATAGACATGC-TTGGATTTTTGCTAATTGCAGTTCT Chimp: GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAATCC-AAGCATTATAGACATGC-TTGGATTTTTGCTAATTGCAGTTCT ↑ 4 1 3 2 Gorilla: GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAAAGGAGAGC--AATACACATGC-TTGGATTTTTGCTAATTGCAGTTCT ↓ 4 1 3 2 Human: GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAATCC-AAGCATTATAGACATGC-TTGGATTTTTGCTAATTGCAGTTCT Cluster: [ ] Orangutan: GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAAAGGAGAGC--GATACACATGCTTTGGATTTTTGCTAATTGCAGTTCT Gorilla > Human --------------- chr1:193194643-193194648 Template switch process: F1: L TGTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA 1 F3: 4 CATTATAG--------------------------ACATGCTTGGATTTTTGCTAATTGCAGTTCTGTGATAAAA R RF: TGTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAAAGGAGAGCAATACACATGCTTGGATTTTTGCTAATTGCAGTTCTGTGATAAAA RR: ACACGGGATTCTATACTCTAGTAATATCTGAAACTATAATTTCCTCTCGTTATGTGTACGAACCTAAAAACGATTAACGTCAAGACACTATTTT F2: 3 GAACCT 2 Unidirectional alignment (log-probability: -38.5) GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAAtccaagcattatAG-----------ACATGCTTGGATTTTTGCTAATTGCAGTTCTG GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA------------AGGAGAGCAATACACATGCTTGGATTTTTGCTAATTGCAGTTCTG Template switch alignment (log-probability: -27.8) GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA|TCCAAG|CATTATAG--------------------------ACATGCTTGGATTTTTGCTAATTGCAGTTCTG GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA|TCCAAG|CATTATAGACTTTGATATTAAAGGAGAGCAATACACATGCTTGGATTTTTGCTAATTGCAGTTCTG Gorilla > Chimp --------------- chr1:171922605-171922610 Template switch process: F1: L TGTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA 1 F3: 4 CATTATAG--------------------------ACATGCTTGGATTTTTGCTAATTGCAGTTCTGTGATAAAA R RF: TGTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAAAGGAGAGCAATACACATGCTTGGATTTTTGCTAATTGCAGTTCTGTGATAAAA RR: ACACGGGATTCTATACTCTAGTAATATCTGAAACTATAATTTCCTCTCGTTATGTGTACGAACCTAAAAACGATTAACGTCAAGACACTATTTT F2: 3 GAACCT 2 Unidirectional alignment (log-probability: -38.5) GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAAtccaagcattatAG-----------ACATGCTTGGATTTTTGCTAATTGCAGTTCTG GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA------------AGGAGAGCAATACACATGCTTGGATTTTTGCTAATTGCAGTTCTG Template switch alignment (log-probability: -27.8) GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA|TCCAAG|CATTATAG--------------------------ACATGCTTGGATTTTTGCTAATTGCAGTTCTG GTGCCCTAAGATATGAGATCATTATAGACTTTGATATTAA|TCCAAG|CATTATAGACTTTGATATTAAAGGAGAGCAATACACATGCTTGGATTTTTGCTAATTGCAGTTCTG ========= Event 501 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTATG-AATTATTTAGGTAGT-TC Chimp: TTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTATG-AATTATTTAGGTAGT-TC ↓ 3 2 1 4 Gorilla: TTGAAAGAACTTTAACTCACGTCACAAAAAATCTATTGTGACGTG-AATTATTTAGGTAGT-TC ↑ 3 2 1 4 Human: TTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTATG-AATTATTTAGGTAGT-TC Cluster: [ ] Orangutan: TTGAAAGAACTTTAACTCATGTCACAAAAAATCTATTACAGTATGAAATTATTTAGGTAGTTGC Human > Gorilla --------------- chr1:172441451-172441455 Template switch process: F1: L TATTTGAAAGAACTTTAACTCACGTCACAAAAAATCTATTG 1 F3: 4 TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC R RF: TATTTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTATGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC RR: ATAAACTTTCTTGACATTGAGTGCAGTGTTTTTTAGATAACGTCATACTTAATAAATCCATCAAGAGTTGAAATTTTTAGAAATCG F2: 3 GCAGT 2 Unidirectional alignment (log-probability: -33.6) ATTTGAAAGAACTtTAACTCACGTCACAAAAAATCTATTG-----tgacgTGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC ATTTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTA-----TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC Template switch alignment (log-probability: -21.9) ATTTGAAAGAACTtTAACTCACGTCACAAAAAATCTATTG|TGACG|TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC ATTTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTG|TGACG|TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC Chimp > Gorilla --------------- chr1:172441451-172441455 Template switch process: F1: L TATTTGAAAGAACTTTAACTCACGTCACAAAAAATCTATTG 1 F3: 4 TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC R RF: TATTTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTATGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC RR: ATAAACTTTCTTGACATTGAGTGCAGTGTTTTTTAGATAACGTCATACTTAATAAATCCATCAAGAGTTGAAATTTTTAGAAATCG F2: 3 GCAGT 2 Unidirectional alignment (log-probability: -33.6) ATTTGAAAGAACTtTAACTCACGTCACAAAAAATCTATTG-----tgacgTGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC ATTTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTGCAGTA-----TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC Template switch alignment (log-probability: -21.9) ATTTGAAAGAACTtTAACTCACGTCACAAAAAATCTATTG|TGACG|TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC ATTTGAAAGAACTGTAACTCACGTCACAAAAAATCTATTG|TGACG|TGAATTATTTAGGTAGTTCTCAACTTTAAAAATCTTTAGC ========= Event 502 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTA Chimp: GCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTA ↓ 1 3 4 2 Gorilla: GCAGGAAACGAAAGGGGAACTT---CCAATATAGATTGGAAGCAGCTGCAGTTATATCTA ↑ 1 3 4 2 Human: GCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr11:41623568-41623577 Template switch process: F1: L ACCCAGCCGCTGACTCAGTTGCAGGAAACGAAAGGGGAACT 1 F3: 4 ATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT R RF: ACCCAGCCGCTGACTCAGTTGCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT RR: TGGGTCGGCGACTGAGTCAACGTCCTTTACTTTCCCCTTGAGGTTCGTTTGATATAACCTTCGTCGACGTCAATATAGATAGGAAACTGAGTGA F2: 3 GATATAACCT 2 Unidirectional alignment (log-probability: -38.8) CCCAGCCGCTGACTCAGTTGCAGGAAAcGAAAGGGGAACTtC---CAAtaTAgATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT CCCAGCCGCTGACTCAGTTGCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT Template switch alignment (log-probability: -22.5) CCCAGCCGCTGACTCAGTTGCAGGAAAcGAAAGGGGAACT|TCCAATATAG|ATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT CCCAGCCGCTGACTCAGTTGCAGGAAATGAAAGGGGAACT|TCCAATATAG|ATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT Chimp > Gorilla --------------- chr11:41623568-41623577 Template switch process: F1: L ACCCAGCCGCTGACTCAGTTGCAGGAAACGAAAGGGGAACT 1 F3: 4 ATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT R RF: ACCCAGCTGCTGACTCAGTTGCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT RR: TGGGTCGACGACTGAGTCAACGTCCTTTACTTTCCCCTTGAGGTTCGTTTGATATAACCTTCGTCGACGTCAATATAGATAGGAAACTGAGTGA F2: 3 GATATAACCT 2 Unidirectional alignment (log-probability: -44.3) CCCAGCcGCTGACTCAGTTGCAGGAAAcGAAAGGGGAACTtC---CAAtaTAgATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT CCCAGCTGCTGACTCAGTTGCAGGAAATGAAAGGGGAACTCCAAGCAAACTATATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT Template switch alignment (log-probability: -28) CCCAGCcGCTGACTCAGTTGCAGGAAAcGAAAGGGGAACT|TCCAATATAG|ATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT CCCAGCTGCTGACTCAGTTGCAGGAAATGAAAGGGGAACT|TCCAATATAG|ATTGGAAGCAGCTGCAGTTATATCTATCCTTTGACTCACT ========= Event 503 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGACCCAGCAGGACCTGATCCTGGCAGGACTCCCCAGGCCTCT-GCTCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATG ↓ 3 1 2 4 Chimp: CTGACCCAGCAGGACCTGATCCTGGGAGTCCTGC-CAG-------GATCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATG ↑ 3 1 2 4 Gorilla: CTGACCCAGCAGGACCTGATCCTGGCAGGACTCCCCAGGCCTCT-GCTCTTTAGGTTGCAGTTTTTCCACCCTGCCTGTGTG Human: CTGACCCAGCAGGACCTGATCCTGGCAGGACTCCCCAGGCCTCT-GCTCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATG Cluster: [ ] Orangutan: CTGACCTAGCAGGGCCTGATCCTGGCAGGACTCCCCAGGCCTCTGGGCCTTTAGGTTGCAGCTTTTCCACCCTGCCTGTGTG Human > Chimp ------------- chr11:95034344-95034357 Template switch process: F1: L GGTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG 1 F3: 4 TCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTAC R RF: GGTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGGCAGGACTCCCCAGGCCTCTGCTCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTAC RR: CCATAGGTCGTCCTTTGACTGGGTCGTCCTGGACTAGGACCGTCCTGAGGGGTCCGGAGACGAGAAATTCAACGTCGAAAAGGTGGGACGGACATACCCATG F2: 3 AGGACCGTCCTGAG 2 Unidirectional alignment (log-probability: -34.9) GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGGgagtcctgcCAGGA----------------TCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTAC GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG---------CAGGACTCCCCAGGCCTCTGCTCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTAC Template switch alignment (log-probability: -17) GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG|GAGTCCTGCCAGGA|TCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTAC GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG|GAGTCCTGCCAGGA|TCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTAC Gorilla > Chimp --------------- chr11:95034344-95034357 Template switch process: F1: L GGTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG 1 F3: 4 TCTTTAAGTTGCAGCTTTTCCACCCTGCCTGTATGGGTACCTGCCCCTCCCCAAG R RF: GGTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGGCAGGACTCCCCAGGCCTCTGCTCTTTAGGTTGCAGTTTTTCCACCCTGCCTGTGTGGGTACCTGCCCCTCCCCAAG RR: CCATAGGTCGTCCTTTGACTGGGTCGTCCTGGACTAGGACCGTCCTGAGGGGTCCGGAGACGAGAAATCCAACGTCAAAAAGGTGGGACGGACACACCCATGGACGGGGAGGGGTTC F2: 3 AGGACCGTCCTGAG 2 Unidirectional alignment (log-probability: -51.2) GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGGgagtcctgcCAGGA----------------TCTTTAaGTTGCAGcTTTTCCACCCTGCCTGTaTGGGTAC GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG---------CAGGACTCCCCAGGCCTCTGCTCTTTAGGTTGCAGTTTTTCCACCCTGCCTGTGTGGGTAC Template switch alignment (log-probability: -34.4) GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG|GAGTCCTGCCAGGA|TCTTTAaGTTGCAGcTTTTCCACCCTGCCTGTaTGGGTAC GTATCCAGCAGGAAACTGACCCAGCAGGACCTGATCCTGG|GAGTCCTGCCAGGA|TCTTTAGGTTGCAGTTTTTCCACCCTGCCTGTGTGGGTAC ========= Event 504 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TACCCCTTCCCAAATACCTCAGTATGTTGGGTGGGACACACAATATGTGCAGACTAAATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAG--ATAACTTTTTTTACAATGGAGAAGTAAGC Chimp: taccccttcccaaatacctcagtatgttgggtgggacacacaatatgtgcagactaaatattgattgagttgTATAGAAAAATTCCCATCTTTAAG--ATAACtttttttACAATGGAGAAGTAAGC Gorilla: taccccttcccaaatacctcagtatgttgggtgggacacacaatatgtgaagactaaatattgattgagttgTATAGAAAAATTCCCATCTTTAAG----AACT-GTTTTACAATGGAGAAGTAAGC ↑ 3 2 1 4 Human: TACCCCTTCCCAAATACCTCAGTATGTTGGGTGGGACACACAATATGTGCAGACTAAATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAG--ATAACTTTTTTTACAATGGAGAAGTAAGC Cluster: [ ] Orangutan: TACCCCTTCCCAAATACCTCAGTATGTTGGGTGGGACACACAATATGTGCAGACTAAATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAGGT--AACT-TTTTTACAATGGAGAAGTAAGC Human > Gorilla --------------- chr11:46882706-46882709 Template switch process: F1: L AAATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAGA 1 F3: 4 TTTTACAATGGAGAAGTAAGCTGGAGCCTTATCAGACCAA R RF: AAATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAGATAACTTTTTTTACAATGGAGAAGTAAGCTGGAGCTTTATCAGACCAATCTCTAGAAATATCCCCTAGTTGTAATGTTACTGTCATTTCTTTGATACTAGAAATAATAGGAGTCCTGTCATAAACATGTTTTGCTTTTTGAACACAGT RR: TTTATAACTAACTCAACATATCTTTTTAAGGGTAGAAATTCTATTGAAAAAAATGTTACCTCTTCATTCGACCTCGAAATAGTCTGGTTAGAGATCTTTATAGGGGATCAACATTACAATGACAGTAAAGAAACTATGATCTTTATTATCCTCAGGACAGTATTTGTACAAAACGAAAAACTTGTGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -31.9) ATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAG--AAC-TgTTTTACAATGGAGAAGTAAGCTGGAGCcTTATCAGACCAA ATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAGATAACTTTTTTTACAATGGAGAAGTAAGCTGGAGCTTTATCAGACCAA Template switch alignment (log-probability: -21.8) ATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAGA|ACTG|TTTTACAATGGAGAAGTAAGCTGGAGCcTTATCAGACCAA ATATTGATTGAGTTGTATAGAAAAATTCCCATCTTTAAGA|ACTG|TTTTACAATGGAGAAGTAAGCTGGAGCTTTATCAGACCAA ========= Event 505 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTTTTGTGTATGTGGCTGTCCT----------------------------------------AAATGCATAATGTATGGAACATATTTAATTAAATCCAGGATGGCTAACTATGCACATGTTTGTAATTCTCATG ↓ 4 1 3 2 Chimp: TTTTTTGTGTATGTGGCTGTCCT------------------------AAATGCATGCATTCCTAAATGCATAATGTATGGAACGTATTTAATTAAATCCAGGATGGCTAACTATGCACATGTTTGTAATTCTCACG Gorilla: TTTTCTGTGTATGTGGCTGTCCT--------AAATGCATGCGTTCCT----------------AAATGCATACTGTATGGAACATATTTAATTAAATCCAGGATGGCTAACTATGCACATGTTTGTAATTCTCACG Human: TTTTTTGTGTATGTGGCTGTCCT----------------------------------------AAATGCATAATGTATGGAACATATTTAATTAAATCCAGGATGGCTAACTATGCACATGTTTGTAATTCTCATG Cluster: [ ] Orangutan: TTTTTTGTGTATGTG--------GCATTCCT--------------------------------AAATGCATAATGTATGGAACATATTTAATTAAATCCAGGATGGCTAACTATGCACATGTTTGTAATTCTCACA Human > Chimp ------------- chr1:54301328-54301331 Template switch process: F1: L TTTTTATTATATGAAACATTTTTTGTGTATGTGGCTGTCCTAAATGCAT 1 F3: 4 TCCTAAATGCATAATGTATGGAACGTATTTAATTAAATCCAGGA R RF: TTTTTATTATATGAAACATTTTTTGTGTATGTGGCTGTCCTAAATGCATAATGTATGGAACATATTTAATTAAATCCAGGATGGCTAACTATGC RR: AAAAATAATATACTTTGTAAAAAACACATACACCGACAGGATTTACGTATTACATACCTTGTATAAATTAATTTAGGTCCTACCGATTGATACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -39.9) TATGAAACATTTTTTGTGTATGTGGCTGTCCTAAATGCAtgcattcctaaatgcaTAATGTATGGAACgTATTTAATTAAATCC TATGAAACATTTTTTGTGTATGTGGCTGTCCTAAATGCA----------------TAATGTATGGAACATATTTAATTAAATCC Template switch alignment (log-probability: -22) TATGAAACATTTTTTGTGTATGTGGCTGTCCTAAATGCAT|GCAT|TCCTAAATGCATAATGTATGGAACgTATTTAATTAAATCC TATGAAACATTTTTTGTGTATGTGGCTGTCCTAAATGCAT|GCAT|TCCTAAATGCATAATGTATGGAACATATTTAATTAAATCC ========= Event 506 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCAATGAAATATAACATTTAAGTAAGAC--------ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATGAATGAATATATGCATTATAAAATTGACAGTCTTATAGGCAATAATGGTTGGCTA Chimp: AGCAATGAAATATAACATTTAAGTAAGAC----ACTTACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATGGATGAATATATGCATTATAAAATTGACAGTCTTATAGGCAATAATGGTTGGCTA Gorilla: AGCAATGAAATATAACATTTA----AGACACTT----ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATGGATGAATATATGCATTATAAAATTGACAGTCTTATAGGCAATAATGGTTGGCTA ↓ 1 4 3 2 Human: AGCAATGAAATATAACATTTAAGTAAGAC--------ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATGAATGAATATATGCATTATAAAATTGACAGTCTTATAGGCAATAATGGTTGGCTA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr1:53660330-53660335 Template switch process: F1: L GCAAATTTTAAAGAGAAATTAGCAATGAAATATAACATTTAAG 1 F3: 4 ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATG R RF: GCAAATTTTAAAGAGAAATTAGCAATGAAATATAACATTTAAGACACTTACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATGGATGAATATATGCATTATAAAATTGACAGTCTTA RR: CGTTTAAAATTTCTCTTTAATCGTTACTTTATATTGTAAATTCTGTGAATGTTAGAATATAAACACTCTTATTTATTACTTATTTCTACCTACTTATATACGTAATATTTTAACTGTCAGAAT F2: 3 CAGAAT 2 Unidirectional alignment (log-probability: -26.6) AATTTTAAAGAGAAATTAGCAATGAAATATAACATTtaagTAAGAC----ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATG AATTTTAAAGAGAAATTAGCAATGAAATATAACATT----TAAGACACTTACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATG Template switch alignment (log-probability: -16.5) AATTTTAAAGAGAAATTAGCAATGAAATATAACATTTAAG|TAAGAC|ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATG AATTTTAAAGAGAAATTAGCAATGAAATATAACATTTAAG|TAAGAC|ACAATCTTATATTTGTGAGAATAAATAATGAATAAAGATG ========= Event 507 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAACAAAAAACATTATGTTAAGAACATTTTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTAAAAAAAGTTCTTATTAACAAAATTGTATCTTAGA Chimp: AGAACAAAAAACATTATGTTAAGAACAtttttttCTATTAGTGCTTTCTTTTAATTGTTTTTTAA-AAAGCTC---TTAACAAAATTGTATCTTAGA ↓ 3 2 1 4 Gorilla: AGAACAAAAAACATTATGTTAAGAACAtttttttCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAAAGTTCTTATTAACAAAATTGTATCTTAGA Human: AGAACAAAAAACATTATGTTAAGAACATTTTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTAAAAAAAGTTCTTATTAACAAAATTGTATCTTAGA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr1:174882362-174882368 Template switch process: F1: L ACATTTTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAAA 1 F3: 4 TTAACAAAATTGTATCTTAGAAATGTTGCAATTAAATGTA R RF: TAAGAACATTTTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAAGCTCTTAACAAAATTGTATCTTAGAAATGTTGCAATGAAATGTA RR: ATTCTTGTAAAAAAAGATAATCACGAAAGAAAATTAACAAAAAATTTTTCGAGAATTGTTTTAACATAGAATCTTTACAACGTTACTTTACAT F2: 3 ATTCTTG 2 Unidirectional alignment (log-probability: -37.5) TTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAAaGtTCttaTTAACAAAATTGTATCTTAGAAATGTTGCAATtAAATGTA TTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAA-GCTC---TTAACAAAATTGTATCTTAGAAATGTTGCAATGAAATGTA Template switch alignment (log-probability: -27.8) TTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAAa|GTTCTTA|TTAACAAAATTGTATCTTAGAAATGTTGCAATtAAATGTA TTTTTCTATTAGTGCTTTCTTTTAATTGTTTTTTAAAAAG|GTTCTTA|TTAACAAAATTGTATCTTAGAAATGTTGCAATGAAATGTA ========= Event 508 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGTGGTATCCTTAGGGAACCATGAGGC-CCCATAGTGGATATAGAATAAGCTgtg ↓ 3 2 1 4 Chimp: AGTGGTATCCTTAGGGAACCATGAGGCCCCCATGGTGGATATAGAATAAGCTgtg Gorilla: AGTGGTATCCTTAGGGAACCATGAGGCCCCCATGGTGGATATAGAATAAGCTgtg ↑ 3 2 1 4 Human: AGTGGTATCCTTAGGGAACCATGAGGC-CCCATAGTGGATATAGAATAAGCTgtg Cluster: [ ] Orangutan: AGTGGTATCCTTAGGGAACCATGAGGCCCCCATAGTGGATATAGAATAAGCTgtg Human > Chimp ------------- chr1:18726499-18726502 Template switch process: F1: L AGAAGCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC 1 F3: 4 GTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA R RF: AGAAGCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCCATAGTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA RR: TCTTCGACGGTAAATCACCATAGGAATCCCTTGGTACTCCGGGGTATCACCTATATCTTATTCGACACCCCTATCAATGATCCATGT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -28.5) GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGcCCCCATgGTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTAca GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGG-CCCCATAGTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTA-- Template switch alignment (log-probability: -15.8) GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC|CATG|GTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC|CATG|GTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA Human > Gorilla --------------- chr1:19614580-19614583 Template switch process: F1: L AGAAGCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC 1 F3: 4 GTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA R RF: AGAAGCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCCATAGTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA RR: TCTTCGACGGTAAATCACCATAGGAATCCCTTGGTACTCCGGGGTATCACCTATATCTTATTCGACACCCCTATCAATGATCCATGT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -27.5) GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCCcATgGTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTAca GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC-ATAGTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTA-- Template switch alignment (log-probability: -16.3) GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC|CATG|GTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA GCTGCCATTTAGTGGTATCCTTAGGGAACCATGAGGCCCC|CATG|GTGGATATAGAATAAGCTGTGGGGATAGTTACTAGGTACA ========= Event 509 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCAGAATAATTTTCCTTATGC-TTCAATGT------CTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATTTAAGATTTATCCATCTAGAAATCTAACTTAGATTTGCATTGGCCTCTCAGGACTACTCTTG ↑ 1 4 3 2 Chimp: TCAGAATAATTTTCCTTATGCTTTCACTGT---CTTCTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATTTAAGATTTATCCATCTAGAAATCTAACTTAGATGTGCATTGGCCTCTCAGGACTACTCTCG Gorilla: TCAGAATAATTTTCCTTATGCTTTCAATGTCTT---CTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATTTAAGATTTATCCATCTAGAAATCTAACTTAGATTTGCATTGGCCTCTCAGGACTACTCTTG Human: TCAGAATAATTTTCCTTATGC-TTCAATGT------CTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATTTAAGATTTATCCATCTAGAAATCTAACTTAGATTTGCATTGGCCTCTCAGGACTACTCTTG Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------------------------------- Chimp > Human ------------- chr1:53410909-53410913 Template switch process: F1: L AATCTAAGTCTTCATCTTACTCAGAATAATTTTCCTTATGCTT 1 F3: 4 TCTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATTT R RF: AATTTAAGTCTTCATCGTACTCAGAATAATTTTCCTTATGCTTTCACTGTCTTCTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATTTAAGATTTATCCATCTAGAAATCTAACTTAGATGTGCATTG RR: TTAAATTCAGAAGTAGCATGAGTCTTATTAAAAGGAATACGAAAGTGACAGAAGAAAAGGTGACAAAAGAAGACAAAGTCAGCGTTATATAAATTCTAAATAGGTAGATCTTTAGATTGAATCTACACGTAAC F2: 3 GTAAC 2 Unidirectional alignment (log-probability: -39.4) cTAAGTCTTCATCtTACTCAGAATAATTTTCCTTATGC-TTCAaTGTCTT---TTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATT TTAAGTCTTCATCGTACTCAGAATAATTTTCCTTATGCTTTCACTGTCTTCTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATT Template switch alignment (log-probability: -27.9) cTAAGTCTTCATCtTACTCAGAATAATTTTCCTTATGCTT|CAATG|TCTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATT TTAAGTCTTCATCGTACTCAGAATAATTTTCCTTATGCTT|CAATG|TCTTTTCCACTGTTTTCTTCTGTTTCAGTCGCAATATATT ========= Event 510 ========= Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTATCAttt--------tttttCCTGCCCAGACAATTCTGGGCAGGAACTTTGGCCAATCCAAAGGTGGCTCTGGGCCC Chimp: TTATCAttt--------tttttCCTGCCCAGA-----------------ATTGG-----CCAAAGGTGGCTCTGGGCCC Gorilla: TTATCAttt------tttttttCCTGCCCAGA-----------------ATTGG-----CCAAAGGTGGCTCTGGGCCC ↑ 1 3 2 4 Human: TTATCAttt--------tttttCCTGCCCAGACAATTCTGGGCAGGAACTTTGGCCAATCCAAAGGTGGCTCTGGGCCC Cluster: [ ] Orangutan: TTGTCAttttttttt--tttttCCTGCCCAGA-----------------ATTGG-----CCAAAGGTGGCTCTGGGCCC Human > Gorilla --------------- chr11:39978998-39979013 Template switch process: F1: L AAATGGGTACTCCCATTATCATTTTTTTT 1 F3: 4 GCCAAAGGTGGCTCTGGGCCCCAGCCCCTCTTAAGGGCAAC R RF: AAATGGGTACTCCCATTATCATTTTTTTTCCTGCCCAGACAATTCTGGGCAGGAACTTTGGCCAATCCAAAGGTGGCTCTGGGCCCCAGCCCCTCTTAAGGGCAAC RR: TTTACCCATGAGGGTAATAGTAAAAAAAAGGACGGGTCTGTTAAGACCCGTCCTTGAAACCGGTTAGGTTTCCACCGAGACCCGGGGTCGGGGAGAATTCCCGTTG F2: 3 GTTAAGACCCGTCCTT 2 Unidirectional alignment (log-probability: -38.8) AAATGGGTACTCCCATTATCATTTTTTTTttCCTGCCCAG-------------------------AATtggCCAAAGGTGGCTCTGGGCCCCAGCCCCTCTTAAGGGCAA AAATGGGTACTCCCATTATCATTTTTTTT--CCTGCCCAGACAATTCTGGGCAGGAACTTTGGCCAAT---CCAAAGGTGGCTCTGGGCCCCAGCCCCTCTTAAGGGCAA Template switch alignment (log-probability: -23) AAATGGGTACTCCCATTATCATTTTTTTT|TTCCTGCCCAGAATTG|gCCAAAGGTGGCTCTGGGCCCCAGCCCCTCTTAAGGGCAA AAATGGGTACTCCCATTATCATTTTTTTT|TTCCTGCCCAGAATTG|TCCAAAGGTGGCTCTGGGCCCCAGCCCCTCTTAAGGGCAA ========= Event 511 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CATGTCTAATAAAAGATCATTGAA------------ACACTGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAATTACTC Chimp: CATGTCTAATAAAAGATCATTAAA------AACAACACCCTGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAATTACTC Gorilla: CATGTCTAATAAAAGATCATTAAAAACAAC------ACCCGGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAATTACTC ↓ 1 4 3 2 Human: CATGTCTAATAAAAGATCATTGAA------------ACACTGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAATTACTC Cluster: [ ] Orangutan: CATGTCTAATAAAAGATCATTGAAAACAAC------ACCCTGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAATTACTC Gorilla > Human --------------- chr1:194338729-194338737 Template switch process: F1: L TTTCAACAATGCTTGAGAAACATGTCTAATAAAAGATCATT 1 F3: 4 CTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAAT R RF: TTCCAACAATGCTTGAGAAACATGTCTAATAAAAGATCATTAAAAACAACACCCGGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAAT RR: AAGGTTGTTACGAACTCTTTGTACAGATTATTTTCTAGTAATTTTTGTTGTGGGCCGAAAAGTACGACTCCGTCACAAAGGTTTTTCCCTCTTTA F2: 3 GTCACAAAG 2 Unidirectional alignment (log-probability: -33.4) TtCAACAATGCTTGAGAAACATGTCTAATAAAAGATCATTgAA------ACaCtGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAAT TCCAACAATGCTTGAGAAACATGTCTAATAAAAGATCATTAAAAACAACACCCGGCTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAAT Template switch alignment (log-probability: -22.4) TtCAACAATGCTTGAGAAACATGTCTAATAAAAGATCATT|GAAACACTG|CTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAAT TCCAACAATGCTTGAGAAACATGTCTAATAAAAGATCATT|GAAACACTG|CTTTTCATGCTGAGGCAGTGTTTCCAAAAAGGGAGAAAT ========= Event 512 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ------------------GGGCTA----GAC-TGGGTGGGACTGCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGA ↓ 1 3 4 2 ↑ 1 3 4 2 Chimp: ------------------GGGCTA--GGGACTGCAGTCCCA-CCCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGA ↓ 13 24 ↑ 3 1 2 4 Gorilla: ------------------GGGCTAGG--GAC-TGGGTGGGACTGCAGTCCCTAGCTCATGCCACTGCTTTTAGGGGA Human: ------------------GGGCTA----GAC-TGGGTGGGACTGCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNN--NNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCCTTTTAGGGGA Chimp > Human ------------- chr11:40778799-40778812 Template switch process: F1: L TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAG 1 F3: 4 CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG R RF: TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTGCAGTCCCACCCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG RR: AGGAAGGAGTCCGGGAGGGGATTTTCGTCACCGTACCCGATCCCTGACGTCAGGGTGGGTCAGGGATCGGGTACGGTGACGAAAATCCCCTCCCGGAC F2: 3 GTCAGGGTGGGTCA 2 Unidirectional alignment (log-probability: -33.2) CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAgactgggtGGGACTGCAGTCC----------CTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTA--------GGGACTGCAGTCCCACCCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG Template switch alignment (log-probability: -17) CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAG|ACTGGGTGGGACTG|CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAG|ACTGGGTGGGACTG|CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG Human > Chimp ------------- chr11:41373301-41373316 Template switch process: F1: L TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAG 1 F3: 4 CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG R RF: TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGACTGGGTGGGACTGCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG RR: AGGAAGGAGTCCGGGAGGGGATTTTCGTCACCGTACCCGATCTGACCCACCCTGACGTCAGGGATCGGGTACGGTGACGAAAATCCCCTCCCGGAC F2: 3 CCACCCTGACGTCAGG 2 Unidirectional alignment (log-probability: -36) CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTA--------GGGACTGCAGTCccacccagtcCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGACTGGGTGGGACTGCAGTC----------CCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG Template switch alignment (log-probability: -17.3) CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAG|GGACTGCAGTCCCACC|CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG CTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAG|GGACTGCAGTCCCACC|CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG Gorilla > Chimp --------------- chr11:41373307-41373328 Template switch process: F1: L TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG 1 F3: 4 CATGCCACTGCTTTTAGGGGAGGGCCTG R RF: TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTGGGTGGGACTGCAGTCCCTAGCTCATGCCACTGCTTTTAGGGGAGGGCCTG RR: AGGAAGGAGTCCGGGAGGGGATTTTCGTCACCGTACCCGATCCCTGACCCACCCTGACGTCAGGGATCGAGTACGGTGACGAAAATCCCCTCCCGGAC F2: 3 CCGATCCCTGACCCACCCTGAC 2 Unidirectional alignment (log-probability: -41.1) CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGG----------GACTGcagtcccaccCAGTCCCTAGCcCATGCCACTGCTTTTAGGGGAGGGCCTG CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTGGGTGGGACTG----------CAGTCCCTAGCTCATGCCACTGCTTTTAGGGGAGGGCCTG Template switch alignment (log-probability: -18.4) CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG|CAGTCCCACCCAGTCCCTAGCC|CATGCCACTGCTTTTAGGGGAGGGCCTG CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG|CAGTCCCACCCAGTCCCTAGCC|CATGCCACTGCTTTTAGGGGAGGGCCTG Chimp > Gorilla --------------- chr11:41450795-41450804 Template switch process: F1: L TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG 1 F3: 4 CAGTCCCTAGCTCATGCCACTGCTTTTAGGGGAGGGCCTG R RF: TCCTTCCTCAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTGCAGTCCCACCCAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG RR: AGGAAGGAGTCCGGGAGGGGATTTTCGTCACCGTACCCGATCCCTGACGTCAGGGTGGGTCAGGGATCGGGTACGGTGACGAAAATCCCCTCCCGGAC F2: 3 GTCAGGGTGG 2 Unidirectional alignment (log-probability: -41.1) CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG----------ggtgggactgCAGTCCCTAGCtCATGCCACTGCTTTTAGGGGAGGGCCTG CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTGCAGTCCCACC----------CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG Template switch alignment (log-probability: -22.7) CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG|GGTGGGACTG|CAGTCCCTAGCtCATGCCACTGCTTTTAGGGGAGGGCCTG CAGGCCCTCCCCTAAAAGCAGTGGCATGGGCTAGGGACTG|GGTGGGACTG|CAGTCCCTAGCCCATGCCACTGCTTTTAGGGGAGGGCCTG ========= Event 513 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAATACTTCATTCTTGAGGTCTTCTCAGATAGTATGCTATCTGAGAAGCACACACTATCTCCTGGCA Chimp: TAATACTTCATTCTTGAGGTCTTCTCAGATAGTATGCTATCTGAGAAGCACACACTATCTCCTGGCA Gorilla: TAATACTTCATTCTTGAGGTC-------GTAGCATACTATCTGAGAAGCACACACTATCTCCTGGCA ↓ 1 3 4 2 Human: TAATACTTCATTCTTGAGGTCTTCTCAGATAGTATGCTATCTGAGAAGCACACACTATCTCCTGGCA Cluster: [ ] Orangutan: TAACACTTCATTCTTGAGGTC-------GTGGCATACTATCTGAGGAGCACACATTATCTCCTGGCA Gorilla > Human --------------- chr11:40777887-40777901 Template switch process: F1: L CCCCATCCCCAGTTCAGTTCTAATACTTCATTCTTGAGGTC 1 F3: 4 CTATCTGAGAAGCACACACTATCTCCTGGCAAACAAGGTT R RF: CCCCATCCCCAGTTCAGTTCTAATACTTCATTCTTGAGGTCGTAGCATACTATCTGAGAAGCACACACTATCTCCTGGCAAACAAGGTT RR: GGGGTAGGGGTCAAGTCAAGATTATGAAGTAAGAACTCCAGCATCGTATGATAGACTCTTCGTGTGTGATAGAGGACCGTTTGTTCCAA F2: 3 GTATGATAGACTCTT 2 Unidirectional alignment (log-probability: -37.6) CCCATCCCCAGTTCAGTTCTAATACTTCATTCTTGAGGTCttctcagaTAGtATgCTATCTGAGAAGCACACACTATCTCCTGGCAAACAAGGTT CCCATCCCCAGTTCAGTTCTAATACTTCATTCTTGAGGTC-------GTAGCATACTATCTGAGAAGCACACACTATCTCCTGGCAAACAAGGTT Template switch alignment (log-probability: -17.6) CCCATCCCCAGTTCAGTTCTAATACTTCATTCTTGAGGTC|TTCTCAGATAGTATG|CTATCTGAGAAGCACACACTATCTCCTGGCAAACAAGGTT CCCATCCCCAGTTCAGTTCTAATACTTCATTCTTGAGGTC|TTCTCAGATAGTATG|CTATCTGAGAAGCACACACTATCTCCTGGCAAACAAGGTT ========= Event 514 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCTTATTATGTAATTAACACACACCattgattgattg--------attgattgattgagacagggtcttgttctgtcccccaggctggagtgcagtggtgcaatctcagctcactgcaacctccacctcccaggttcaagagattctcctgcctcagc Chimp: ATTCTTATTATGTAATTAACACACACCattgattgattgattgattgattgattgattgagacagggtcttgttctgtcccccaggctggagtgcagtggtgcaatctcagctcactgcaacctccacctcccaggttcaagcgattctcctgcctcagc ↓ 1 4 3 2 Gorilla: AATCTTATTATGTAATTAACATGAACCattgattgattg--------attgattgattgagacaggatcttgttctgtcccccaggctggagtgcagtggtgcgatctcatctcactgcaacctccacctcccaggttcaagcgattctcctgcctcagc Human: ATTCTTATTATGTAATTAACACACACCattgattgattg--------attgattgattgagacagggtcttgttctgtcccccaggctggagtgcagtggtgcaatctcagctcactgcaacctccacctcccaggttcaagagattctcctgcctcagc Cluster: [ ] Orangutan: ATTCTTATTATGTAATTAACACGCACCattgattgat------------tgattgattgagacagggtcttgttctgtcccccaggctggagtgcagtggtgcaatctcagctcactgcaacctccacctcccgggttcaagcgattctgctgcctcagc Chimp > Gorilla --------------- chr11:125929592-125929597 Template switch process: F1: L GGATTACAGGCGTGAGCATTAATCTTATTATGTAATTAACA 1 F3: 4 ATTGATTGATTGATTGATTGATTGAGACA R RF: GGATTACAGGCGTGAGCATTATTCTTATTATGTAATTAACACACACCATTGATTGATTGATTGATTGATTGATTGATTGAGACAGGGTCTTGTTCTGTCCCCCAGGCTGGAGTGCAGTGGTGCAATCTCAGCTCACTGCAACCTCCACCTCCCAGGTTCA RR: CCTAATGTCCGCACTCGTAATAAGAATAATACATTAATTGTGTGTGGTAACTAACTAACTAACTAACTAACTAACTAACTCTGTCCCAGAACAAGACAGGGGGTCCGACCTCACGTCACCACGTTAGAGTCGAGTGACGTTGGAGGTGGAGGGTCCAAGT F2: 3 CCAAGT 2 Unidirectional alignment (log-probability: -32.4) GATTACAGGCGTGAGCATTAaTCTTATTATGTAATTAACA------------TGaaccATTGATTGATTGATTGATTGATTGAGACA GATTACAGGCGTGAGCATTATTCTTATTATGTAATTAACACACACCATTGATTG----ATTGATTGATTGATTGATTGATTGAGACA Template switch alignment (log-probability: -21.7) GATTACAGGCGTGAGCATTAaTCTTATTATGTAATTAACA|TGAACC|ATTGATTGATTGATTGATTGATTGAGACA GATTACAGGCGTGAGCATTATTCTTATTATGTAATTAACA|TGAACC|ATTGATTGATTGATTGATTGATTGAGACA ========= Event 515 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACACCCTGGGATGACTCTGTTCAATGGTCCCCGAG----------------TTTGAACATATTAAAAGTTTGCTAGTAA ↑ 3 2 1 4 Chimp: AACACCCTGGGATGGCTCTGTTCAATGGTCCCCGAG--------TGTTTTCATTTTTCCATATTAAAAGTTTGCTAGTAA Gorilla: AACACCCTGGGATGGCTCTGTTCAATGGTCCCCGAGTGTTTTCA--------TTTTTCCATGTTAAAAGTTTGCTAGTAA Human: AACACCCTGGGATGACTCTGTTCAATGGTCCCCGAG----------------TTTGAACATATTAAAAGTTTGCTAGTAA Cluster: [ ] Orangutan: AACACCCTGGGATGGCTCTGTTCAGTGGTCCCCCAGTGTTTTCA--------TTTTTCCTTATTAAAAGTTTGCTAGTAA Chimp > Human ------------- chr1:198359561-198359566 Template switch process: F1: L TGCCAAACACCCTGGGATGACTCTGTTCAATGGTCCCCGAGT 1 F3: 4 ATATTAAAAGTTTGCTAGTAATATTTAACATGTTTGTCT R RF: TGCCAAACACCCTGGGATGGCTCTGTTCAATGGTCCCCGAGTGTTTTCATTTTTCCATATTAAAAGTTTGCTAGTAATATTTAACATGTTTGTCT RR: ACGGTTTGTGGGACCCTACCGAGACAAGTTACCAGGGGCTCACAAAAGTAAAAAGGTATAATTTTCAAACGATCATTATAAATTGTACAAACAGA F2: 3 CAAGTT 2 Unidirectional alignment (log-probability: -35) CCAAACACCCTGGGATGaCTCTGTTCAATGGTCCCCGAGT-------------ttgaaCATATTAAAAGTTTGCTAGTAATATTTAACATGTTTGTCT CCAAACACCCTGGGATGGCTCTGTTCAATGGTCCCCGAGTGTTTTCATTTTTC-----CATATTAAAAGTTTGCTAGTAATATTTAACATGTTTGTCT Template switch alignment (log-probability: -22) CCAAACACCCTGGGATGaCTCTGTTCAATGGTCCCCGAGT|TTGAAC|ATATTAAAAGTTTGCTAGTAATATTTAACATGTTTGTCT CCAAACACCCTGGGATGGCTCTGTTCAATGGTCCCCGAGT|TTGAAC|ATATTAAAAGTTTGCTAGTAATATTTAACATGTTTGTCT ========= Event 516 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GATGAAAATCAAAATTATGACATGTTTTTTCACACAAATGCAATTAACATAATTTATATTTTTACTTATAAAATAGGTTACTGTAGTTATACTATAGTTACTTTATAGGTAACTACACATATATGTATTTAAAGCTTTTTGCATATA----------------TGTGAAAAGAAAAGGAAATAAGTGTATTT Chimp: GATGAAAATCAAAATTATGACATGTTTTTTCACACAAATGCAATTAACATAATTTATATTTTTACTTATAAAATAGGTTACTGTAGTTATACTATAGTTACTTTATAGGTAACTACACATATATGTACTTAAAGCTTTTTGCATATA--------TGTAAACATGTGAAAAGAAAAGGAAATAAGTGTATTT Gorilla: GATGAAAATCAAAATTATGACATGTTTTTTCACACAAATGCAATTAACATAATTTATATTTTTACTTATAAAATAGGTTACCGTAGTTATACTATAGTTACTTTATAGGTAACTACACATATATGTACTTAAAGCTTTTTGCATATATGTAAACA--------TGTG-----AAAAGGAAATAAGTGTATTT ↑ 3 2 1 4 Human: GATGAAAATCAAAATTATGACATGTTTTTTCACACAAATGCAATTAACATAATTTATATTTTTACTTATAAAATAGGTTACTGTAGTTATACTATAGTTACTTTATAGGTAACTACACATATATGTATTTAAAGCTTTTTGCATATA----------------TGTGAAAAGAAAAGGAAATAAGTGTATTT Cluster: [ ] Orangutan: GATGAAAATCAAAATTATGACATGTTTTTTCACACAAATGCAATTAATATAATTTATATTTTTACATATAAAATAGGTTATTGTAGTTATACTATAGTTACTTTATAGGTAACTATGCATATATGTACTTAAAGCTTTTTACATATATGTAAACA--------TGTG-----AAAAGGAAATGAGTGTATTT Human > Gorilla --------------- chr1:51752088-51752095 Template switch process: F1: L AGGTAACTACACATATATGTACTTAAAGCTTTTTGCATATATGT 1 F3: 4 GAAAAGGAAATAAGTGTATTTGTAAATATTTTTGCAGTAGT R RF: ACATGTTTTTTCACACAAATGCAATTAACATAATTTATATTTTTACTTATAAAATAGGTTACTGTAGTTATACTATAGTTACTTTATAGGTAACTACACATATATGTATTTAAAGCTTTTTGCATATATGTGAAAAGAAAAGGAAATAAGTGTATTTGTAAATATTTTTGCAGTAGT RR: TGTACAAAAAAGTGTGTTTACGTTAATTGTATTAAATATAAAAATGAATATTTTATCCAATGACATCAATATGATATCAATGAAATATCCATTGATGTGTATATACATAAATTTCGAAAAACGTATATACACTTTTCTTTTCCTTTATTCACATAAACATTTATAAAAACGTCATCA F2: 3 TGTACAAA 2 Unidirectional alignment (log-probability: -42.9) AACTACACATATATGTAcTTAAAGCTTTTTGCATATATGTaAAcAtgtGAAAAGGAAATAAGTGTATTTGTAAATATTTTTGCAGTag AACTACACATATATGTATTTAAAGCTTTTTGCATATATGTGAAAA---GAAAAGGAAATAAGTGTATTTGTAAATATTTTTGCAGT-- Template switch alignment (log-probability: -22.4) AACTACACATATATGTAcTTAAAGCTTTTTGCATATATGT|AAACATGT|GAAAAGGAAATAAGTGTATTTGTAAATATTTTTGCAGTAG AACTACACATATATGTATTTAAAGCTTTTTGCATATATGT|AAACATGT|GAAAAGGAAATAAGTGTATTTGTAAATATTTTTGCAGTAG ========= Event 517 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAATATTTATTTTACTATCTATGAGCT---A-----CTATAAATTAACTACACTTTTCC Chimp: GTAATATTTCTTTTACTATCTATGAGCT---A-----CTATAAATTAACTACACTTTTCC ↓ 3 1 24 Gorilla: GTAATATTTCTTTTACTATCTATGAGCAGTAGCTCATAGATAAATTAACTACACTTTTCC ↑ 3 1 24 Human: GTAATATTTATTTTACTATCTATGAGCT---A-----CTATAAATTAACTACACTTTTCC Cluster: [ ] Orangutan: GTAATATTTCTTTTACTATCTATGAGCT---A-----CTATAAGTTAACTACACTTTTCC Human > Gorilla --------------- chr11:37261992-37262003 Template switch process: F1: L ATTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGC 1 F3: 4 ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT R RF: ATTATTTGTTTAAAGTAATATTTATTTTACTATCTATGAGCTACTATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT RR: TAATAAACAAATTTCATTATAAATAAAATGATAGATACTCGATGATATTTAATTGATGTGAAAAGGTTTTTACATAAAACATAAA F2: 3 GATACTCGATGA 2 Unidirectional alignment (log-probability: -43.6) TTATTTGTTTAAAGTAATATTTcTTTTACTATCTATGAGCagtagctcatag----ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT TTATTTGTTTAAAGTAATATTTATTTTACTATCTATGAGC------------TACTATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT Template switch alignment (log-probability: -22.8) TTATTTGTTTAAAGTAATATTTcTTTTACTATCTATGAGC|AGTAGCTCATAG|ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT TTATTTGTTTAAAGTAATATTTATTTTACTATCTATGAGC|AGTAGCTCATAG|ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT Chimp > Gorilla --------------- chr11:37261992-37262003 Template switch process: F1: L ATTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGC 1 F3: 4 ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT R RF: ATTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGCTACTATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT RR: TAATAAACAAATTTCATTATAAAGAAAATGATAGATACTCGATGATATTTAATTGATGTGAAAAGGTTTTTACATAAAACATAAA F2: 3 GATACTCGATGA 2 Unidirectional alignment (log-probability: -38.1) TTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGC----agtagctcatagATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT TTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGCTACT------------ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT Template switch alignment (log-probability: -17.3) TTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGC|AGTAGCTCATAG|ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT TTATTTGTTTAAAGTAATATTTCTTTTACTATCTATGAGC|AGTAGCTCATAG|ATAAATTAACTACACTTTTCCAAAAATGTATTTTGTATTT ========= Event 518 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCTGTGGAAACTAGTATGTTCTCTGAAAAGAGCACTTTTCAGGTTCTTCTCTTTTTGAAAAG ↑ 3 4 2 Chimp: TCTGTGGAAACTAGTATGTTC---------TGCTCTTTTCAGGTTCTTCTCTTTTTGAAAAG ↓ 3 4 2 Gorilla: TCTGTGGAAACTAGTATGTTCTCTGAAAAGAGCACTTTTCAGGTTCTTCTCTTTTTGAAAAG Human: TCTGTGGAAACTAGTATGTTCTCTGAAAAGAGCACTTTTCAGGTTCTTCTCTTTTTGAAAAG Cluster: [ ] Orangutan: TCTGTGGAAACTAGTAGGTTC---------TGCTCTTTTCAGGTTCTTCTCTTTTTGAAAAG Chimp > Human ------------- chr11:99516442-99516453 Template switch process: F1: L CATATAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT 1 F3: 4 CTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA R RF: CATGTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCTGCTCTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA RR: GTACATCTGATCTTAATCAGAGACACCTTTGATCATACAAGACGAGAAAAGTCCAAGAAGAGAAAAACTTTTCACTCAACCAGTT F2: 3 ACGAGAAAAGTC 2 Unidirectional alignment (log-probability: -35.9) TaTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCTctgaaaagaGCaCTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA TGTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT---------GCTCTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA Template switch alignment (log-probability: -22.8) TaTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT|CTGAAAAGAGCA|CTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA TGTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT|CTGAAAAGAGCA|CTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA Chimp > Gorilla --------------- chr11:99133756-99133767 Template switch process: F1: L CATATAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT 1 F3: 4 CTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA R RF: CATGTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCTGCTCTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA RR: GTACATCTGATCTTAATCAGAGACACCTTTGATCATACAAGACGAGAAAAGTCCAAGAAGAGAAAAACTTTTCACTCAACCAGTT F2: 3 ACGAGAAAAGTC 2 Unidirectional alignment (log-probability: -34.9) TaTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCTctgaaaagaGCaCTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA TGTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT---------GCTCTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA Template switch alignment (log-probability: -22.8) TaTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT|CTGAAAAGAGCA|CTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA TGTAGACTAGAATTAGTCTCTGTGGAAACTAGTATGTTCT|CTGAAAAGAGCA|CTTTTCAGGTTCTTCTCTTTTTGAAAAGTGAGTTGGTCAA ========= Event 519 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: actccgttt------tttttAAAAGCTATTTTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATTACACATGACATCTGATCCATTGGTATTGCTTTTTGTTAGTAACTCTTCATAA Chimp: actccgtttt---ttttttttAAAGCTATTTTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATTACACATGACATCTGATCCATTGGTATTGCTTTTTGTTAGTAACTCTTCATAA ↓ 1 4 3 2 Gorilla: actccgtttt--t--ttttttAAAGCAA--TTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATTACACATGACATCTGATCCATTGGTATTGCTTTTTGTTAGTAACTCTTCATAA Human: actccgttt------tttttAAAAGCTATTTTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATTACACATGACATCTGATCCATTGGTATTGCTTTTTGTTAGTAACTCTTCATAA Cluster: [ ] Orangutan: actccttttttt---tttAAAAAAGCTA--TTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATTACACATGACATCTGATCCATTGGTATTGCTTTTTGTTAGTAACTCTTCATAA Chimp > Gorilla --------------- chr1:207992108-207992115 Template switch process: F1: L TTTCACTCCCTTTTTTCACTCCGTTTTTTTTTTT 1 F3: 4 TTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATT R RF: TTTCACTCCCTTTTTTCACTCCGTTTTTTTTTTTTAAAGCTATTTTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATTACACATGACATCTGATCCATTGGTATTGCTTT RR: AAAGTGAGGGAAAAAAGTGAGGCAAAAAAAAAAAATTTCGATAAAAACAAGTATTTGAGACATCTTAACATCCGTCTTCTTTAATGTGTACTGTAGACTAGGTAACCATAACGAAA F2: 3 TAACGAAA 2 Unidirectional alignment (log-probability: -26.3) TTTCACTCCCTTTTTTCACTCCGTTTTTTTTTT-TAAAGCaA--TTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATT TTTCACTCCCTTTTTTCACTCCGTTTTTTTTTTTTAAAGCTATTTTTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATT Template switch alignment (log-probability: -16.5) TTTCACTCCCTTTTTTCACTCCGTTTTTTTTTTT|AAAGCAAT|TTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATT TTTCACTCCCTTTTTTCACTCCGTTTTTTTTTTT|AAAGCAAT|TTGTTCATAAACTCTGTAGAATTGTAGGCAGAAGAAATT ========= Event 520 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTAATAAGATTTTCAGTTGAAT------TGAGGTCAGGACCTCAATTCATACTAATGGCATGCCA Chimp: TTAATAAGATTTTCAGTTGAAT------TGAGGTCAGGACCTCAATTCATACTAATGGCATGCCA ↑ 1 4 3 2 Gorilla: TTAATAAGATTTTCAGTTGAAG------------ACGGACCTCAATTCATACTCATGGCATGCCA ↓ 1 4 3 2 Human: TTAATAAGATTTTCAGTTGAAT------TGAGGTCAGGACCTCAATTCATACTAATGGCATGCCA Cluster: [ ] Orangutan: TTAATAAGATTTTCAGTTGAATTGAGGT------CAGGACCTCAATTCATACTAATGGCATGCCA Gorilla > Human --------------- chr12:101332424-101332431 Template switch process: F1: L TACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA 1 F3: 4 AGGACCTCAATTCATACTAATGGCATGCCACTGGAGCCATT R RF: TACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAAGACGGACCTCAATTCATACTCATGGCATGCCACTGGAGCCATT RR: ATGTAAGTTATTTAAACGGAAATTATTCTAAAAGTCAACTTCTGCCTGGAGTTAAGTATGAGTACCGTACGGTGACCTCGGTAA F2: 3 CTGGAGTT 2 Unidirectional alignment (log-probability: -39.2) ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA---ttgaggtcaGGACCTCAATTCATACTaATGGCATGCCACTGGAGCCAT ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAAGAC---------GGACCTCAATTCATACTCATGGCATGCCACTGGAGCCAT Template switch alignment (log-probability: -27.8) ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA|TTGAGGTC|aGGACCTCAATTCATACTaATGGCATGCCACTGGAGCCAT ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA|TTGAGGTC|CGGACCTCAATTCATACTCATGGCATGCCACTGGAGCCAT Gorilla > Chimp --------------- chr12:104167612-104167619 Template switch process: F1: L TACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA 1 F3: 4 AGGACCTCAATTCATACTAATGGCATGCCACTGGAGCCATT R RF: TACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAAGACGGACCTCAATTCATACTCATGGCATGCCACTGGAGCCATT RR: ATGTAAGTTATTTAAACGGAAATTATTCTAAAAGTCAACTTCTGCCTGGAGTTAAGTATGAGTACCGTACGGTGACCTCGGTAA F2: 3 CTGGAGTT 2 Unidirectional alignment (log-probability: -39.2) ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA---ttgaggtcaGGACCTCAATTCATACTaATGGCATGCCACTGGAGCCAT ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAAGAC---------GGACCTCAATTCATACTCATGGCATGCCACTGGAGCCAT Template switch alignment (log-probability: -27.8) ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA|TTGAGGTC|aGGACCTCAATTCATACTaATGGCATGCCACTGGAGCCAT ACATTCAATAAATTTGCCTTTAATAAGATTTTCAGTTGAA|TTGAGGTC|CGGACCTCAATTCATACTCATGGCATGCCACTGGAGCCAT ========= Event 521 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACTTAGTTTCTAGTCCTCCTTTAAAA----ATTACTTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAA Chimp: CACTTAGTTTCTAGTCCTCCTTCAAAA----ATTACTTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAA ↓ 1 4 3 2 Gorilla: CACTTAGTTTCTAGTCCTCCTCTTGGG--------ATTCTTCAGAATCCCAAGAAATAAAAGAGATTTGCTAA ↑ 1 4 3 2 Human: CACTTAGTTTCTAGTCCTCCTTTAAAA----ATTACTTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAA Cluster: [ ] Orangutan: CACTTAGTTTCTAGTCCTCCTTTAAAAGTTA----CTTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCT-G Human > Gorilla --------------- chr1:41477853-41477859 Template switch process: F1: L TAAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT 1 F3: 4 TTCTTCAGAATCCCAAGAAATAAAAGAGATTTGCTAAAGATCCAACTA R RF: TAAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCTTTAAAAATTACTTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAAAGATTCAACTA RR: ATTTTTCCGGTTAAGGGTTAGTGAATCAAAGATCAGGAGGAAATTTTTAATGAAGAAGTTTTAGGGTTCTTTATTTTCTCTAAACGATTTCTAAGTTGAT F2: 3 AGGGTTC 2 Unidirectional alignment (log-probability: -40.9) AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT----------CttgggaTTCTTCAgAATCCCAAGAAATAAAAGAGATTTGCTAAAGA AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCTTTAAAAATTAC------TTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAAAGA Template switch alignment (log-probability: -27.9) AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT|CTTGGGA|TTCTTCAgAATCCCAAGAAATAAAAGAGATTTGCTAAAGA AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT|CTTGGGA|TTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAAAGA Chimp > Gorilla --------------- chr1:41477853-41477859 Template switch process: F1: L TAAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT 1 F3: 4 TTCTTCAGAATCCCAAGAAATAAAAGAGATTTGCTAAAGATCCAACTA R RF: TAAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCTTCAAAAATTACTTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAAAGATCCAACTA RR: ATTTTTCCGGTTAAGGGTTAGTGAATCAAAGATCAGGAGGAAGTTTTTAATGAAGAAGTTTTAGGGTTCTTTATTTTCTCTAAACGATTTCTAGGTTGAT F2: 3 AGGGTTC 2 Unidirectional alignment (log-probability: -35.4) AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT----------CttgggaTTCTTCAgAATCCCAAGAAATAAAAGAGATTTGCTAAAGA AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCTTCAAAAATTAC------TTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAAAGA Template switch alignment (log-probability: -22.3) AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT|CTTGGGA|TTCTTCAgAATCCCAAGAAATAAAAGAGATTTGCTAAAGA AAAAAGGCCAATTCCCAATCACTTAGTTTCTAGTCCTCCT|CTTGGGA|TTCTTCAAAATCCCAAGAAATAAAAGAGATTTGCTAAAGA ========= Event 522 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCAGTGTCACCTGTGCTCACTCATCTGTTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTT Chimp: GCAGTGTCACCTGTGCTCACTCATCTGTTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTT ↓ 1 4 3 2 Gorilla: GCAGTGTCACCTGTGCTCACT-GTGACTGTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTT ↑ 1 4 3 2 Human: GCAGTGTCACCTGTGCTCACTCATCTGTTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTT Cluster: [ ] Orangutan: -------------------------------------------------NNNNNNNNNNNN-NNN Human > Gorilla --------------- chr12:29691836-29691840 Template switch process: F1: L CAGGTGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCACT 1 F3: 4 TGTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCTGC R RF: CAGATGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCACTCATCTGTTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCTGC RR: GTCTACAAGGACTCAGGTACCGTCACAGTGGACACGAGTGAGTAGACAAACAACCGACATCAGTGGTCTCTCAGAGAAGACCAAAGACG F2: 3 CAGTG 2 Unidirectional alignment (log-probability: -36.6) AGgTGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCAC--------TgtgactgTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT AGATGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCACTCATCTGTT-------TGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT Template switch alignment (log-probability: -27.4) AGgTGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCACT|GTGAC|TgTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT AGATGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCACT|GTGAC|TTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT Chimp > Gorilla --------------- chr12:29691836-29691840 Template switch process: F1: L CAGGTGTTCCTGAGTCCATGGCAGTGTCACCTGTGCTCACT 1 F3: 4 TGTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCTGC R RF: CAGGTGTTCCTGGGTCCATGGCAGTGTCACCTGTGCTCACTCATCTGTTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCTGC RR: GTCCACAAGGACCCAGGTACCGTCACAGTGGACACGAGTGAGTAGACAAACAACCGACATCAGTGGTCTCTCAGAGAAGACCAAAGACG F2: 3 CAGTG 2 Unidirectional alignment (log-probability: -36.6) AGGTGTTCCTGaGTCCATGGCAGTGTCACCTGTGCTCAC--------TgtgactgTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT AGGTGTTCCTGGGTCCATGGCAGTGTCACCTGTGCTCACTCATCTGTT-------TGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT Template switch alignment (log-probability: -27.4) AGGTGTTCCTGaGTCCATGGCAGTGTCACCTGTGCTCACT|GTGAC|TgTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT AGGTGTTCCTGGGTCCATGGCAGTGTCACCTGTGCTCACT|GTGAC|TTTGTTGGCTGTAGTCACCAGAGAGTCTCTTCTGGTTTCT ========= Event 523 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTTGCCTTT-TCAGTCACT-----------AAGTGCACCAAaataaatta-------------------gaatttcctgaatcaattagaatttccttagaatcaattCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTCTGTGGATCCTAAGGCTCAGAGGATTCTCGCCGCAGCGTTGTTCGGC Chimp: TTTTTGCCTTT-TCAGTCACT------AAGATAAGTGCACCAAaataaatta-------------------gaatttcctgaatcaattagaatttccttagaatcaattCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTCTGTGGATCCTAAGGCTCAGAGGATTCTCGCCGCAGCGTTGTTCGGC ↑ 4 1 3 2 Gorilla: TTTTTGCCTTT-TCAGTCACTAAGAT------AAGTGCACCAAAATAAATTA--------------------------------------GAATTTCCTTAGAATCAATTCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTTTGTGGATCCTAAGGCTCAGAGGATTCTCGCCGCAGCGTTGTTCGGC ↓ 4 1 3 2 Human: TTTTTGCCTTT-TCAGTCACT-----------AAGTGCACCAAaataaatta-------------------gaatttcctgaatcaattagaatttccttagaatcaattCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTCTGTGGATCCTAAGGCTCAGAGGATTCTCGCCGCAGCGTTGTTCGGC Cluster: [ ] Orangutan: CTTTTGCCTTTTCCAGTCACTAAGATA-----AAGTGCACCAAAATAAATTAGAATTTCCTGAATTAATTA-------------------GAATTTCCTTAGAATCAATTCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTCTGTGGATCGCAAGGCTCAGAGGATTCTCGCCGCAGCGTTGTTCGGC Gorilla > Human --------------- chr1:46027729-46027733 Template switch process: F1: L GATAAGCTGAACTAATTAAGCTTTTTGCCTTTTCAGTCAC-----TAAGTGCACCAAAATAAATTAGAATTTCCT 1 F3: 4 AATTAG R RF: GATAAGCTGAACTAATTAAGCTTTTTGCCTTTTCAGTCACTAAGATAAGTGCACCAAAATAAATTAGAATTTCCTAATTTCCTTAGAATCAATTCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTTTGTGGATCCTAAGGCTCAGAGGATTC RR: CTATTCGACTTGATTAATTCGAAAAACGGAAAAGTCAGTGATTCTATTCACGTGGTTTTATTTAATCTTAAAGGATTAAAGGAATCTTAGTTAAGTCACCACTACTGTCCCGGGTAATACTACGTCTCATATATGACTCCAAACACCTAGGATTCCGAGTCTCCTAAG F2: 3 CTAAG 2 Unidirectional alignment (log-probability: -44.9) TTTCAGTCACTAA-----GTGCACCAAAATAAATTAGaatttcctgaatcaattag TTTCAGTCACTAAGATAAGTGCACCAAAATAAATTAG------------------- Template switch alignment (log-probability: -26.2) TTTCAGTCAC-----TAAGTGCACCAAAATAAATTAGAATTTCCT|GAATC|AATTAG TTTCAGTCACTAAGATAAGTGCACCAAAATAAATTAGAATTTCCT|GAATC|AATTAG Gorilla > Chimp --------------- chr1:46772779-46772783 Template switch process: F1: L GATAAGCTGAACTAATTACGCTTTTTGCCTTTTCAGTCACTAAGATAAGTGCACCAAAATAAATTAGAATTTCCT 1 F3: 4 AATTAG R RF: GATAAGCTGAACTAATTAAGCTTTTTGCCTTTTCAGTCACTAAGATAAGTGCACCAAAATAAATTAGAATTTCCTAATTTCCTTAGAATCAATTCAGTGGTGATGACAGGGCCCATTATGATGCAGAGTATATACTGAGGTTTGTGGATCCTAAGGCTCAGAGGATTC RR: CTATTCGACTTGATTAATTCGAAAAACGGAAAAGTCAGTGATTCTATTCACGTGGTTTTATTTAATCTTAAAGGATTAAAGGAATCTTAGTTAAGTCACCACTACTGTCCCGGGTAATACTACGTCTCATATATGACTCCAAACACCTAGGATTCCGAGTCTCCTAAG F2: 3 CTAAG 2 Unidirectional alignment (log-probability: -40.5) GTCACTAAGATAAGTGCACCAAAATAAATTAGaatttcctgaatcaattag GTCACTAAGATAAGTGCACCAAAATAAATTAG------------------- Template switch alignment (log-probability: -21.9) GTCACTAAGATAAGTGCACCAAAATAAATTAGAATTTCCT|GAATC|AATTAG GTCACTAAGATAAGTGCACCAAAATAAATTAGAATTTCCT|GAATC|AATTAG ========= Event 524 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAAGACATAACTGTGGAACTATAAAGTTATTTACATGGAAAATAATTTAA Chimp: AGAAGACATAACTGTGGAACTATAAAGTTATTTACATGGAAAATAATTTAA ↓ 3 1 2 4 Gorilla: AGAAGACATAACTGTGGAACTACTTTATAGTTTACATGGAAAATAATTTAA ↑ 3 1 2 4 Human: AGAAGACATAACTGTGGAACTATAAAGTTATTTACATGGAAAATAATTTAA Cluster: [ ] Orangutan: AGAAGACATAACTGTGGAACTATAAAGTTATTTACATGGAAAATAATTTAA Human > Gorilla --------------- chr12:31635099-31635106 Template switch process: F1: L TTTTAAAAAATCATTCATAAGAAGACATAACTGTGGAACTA 1 F3: 4 TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA R RF: TTTTTAAAAATCATTCATAAGAAGACATAACTGTGGAACTATAAAGTTATTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA RR: AAAAATTTTTAGTAAGTATTCTTCTGTATTGACACCTTGATATTTCAATAAATGTACCTTTTATTAAATTTCCTGTCTTGGTTTGTTTT F2: 3 GATATTTC 2 Unidirectional alignment (log-probability: -36.2) TTTaAAAAATCATTCATAAGAAGACATAACTGTGGAACTActtTAtAG---TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA TTTTAAAAATCATTCATAAGAAGACATAACTGTGGAACTA---TAAAGTTATTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA Template switch alignment (log-probability: -22.3) TTTaAAAAATCATTCATAAGAAGACATAACTGTGGAACTA|CTTTATAG|TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA TTTTAAAAATCATTCATAAGAAGACATAACTGTGGAACTA|CTTTATAG|TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA Chimp > Gorilla --------------- chr12:31635099-31635106 Template switch process: F1: L TTTTAAAAAATCATTCATAAGAAGACATAACTGTGGAACTA 1 F3: 4 TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA R RF: TTTTAAAAAATCATGCATAAGAAGACATAACTGTGGAACTATAAAGTTATTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA RR: AAAATTTTTTAGTACGTATTCTTCTGTATTGACACCTTGATATTTCAATAAATGTACCTTTTATTAAATTTCCTGTCTTGGTTTGTTTT F2: 3 GATATTTC 2 Unidirectional alignment (log-probability: -36.2) TTTAAAAAATCATtCATAAGAAGACATAACTGTGGAACTActtTAtAG---TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA TTTAAAAAATCATGCATAAGAAGACATAACTGTGGAACTA---TAAAGTTATTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA Template switch alignment (log-probability: -22.3) TTTAAAAAATCATtCATAAGAAGACATAACTGTGGAACTA|CTTTATAG|TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA TTTAAAAAATCATGCATAAGAAGACATAACTGTGGAACTA|CTTTATAG|TTTACATGGAAAATAATTTAAAGGACAGAACCAAACAAAA ========= Event 525 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATCTCTAGGATTAAGAGTAATCCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTCCTTGGGGGATAGAACTGGCAGCGGCCTCTTCAAGGA Chimp: CATCTCTAGGATTAAGAGTAATTCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTCCTTGGGGGATAGAACTGGCAGCGGCCTCTTCAAGGA ↓ 1 4 3 2 Gorilla: CATCGCTAGGATTAAGAGTAA--------TAGTT---CTGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTCCTTGGGGGATAGAACTGGCAGCGGCCTCTTCAAGGA ↑ 1 4 3 2 Human: CATCTCTAGGATTAAGAGTAATCCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTCCTTGGGGGATAGAACTGGCAGCGGCCTCTTCAAGGA Cluster: [ ] Orangutan: CATCTCTGGGATAAAGAGTAA--------TAGTT---CTGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTTCTTGGAGGATAGAACTGGCAGCGGCCTCCTCAAGGA Human > Gorilla --------------- chr1:43111362-43111366 Template switch process: F1: L TGGACACCCCCTCAGGAAACCATCGCTAGGATTAAGAGTAAT 1 F3: 4 TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA R RF: TGGACACCCCCTCAGGAAACCATCTCTAGGATTAAGAGTAATCCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTCCTTGGGGGATAGAACT RR: ACCTGTGGGGGAGTCCTTTGGTAGAGATCCTAATTCTCATTAGGTGTGTTTGAAGGTTACGGTGTGTAACCTTCAACGACCTTTCCAGACCCTTTTGTTCTCCTTCCTACCCAGGAACCCCCTATCTTGA F2: 3 CTTGA 2 Unidirectional alignment (log-probability: -32.3) GACACCCCCTCAGGAAACCATCgCTAGGATTAAGAGTAAT--------AgTTC---TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA GACACCCCCTCAGGAAACCATCTCTAGGATTAAGAGTAATCCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA Template switch alignment (log-probability: -21.9) GACACCCCCTCAGGAAACCATCgCTAGGATTAAGAGTAAT|AGTTC|TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA GACACCCCCTCAGGAAACCATCTCTAGGATTAAGAGTAAT|AGTTC|TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA Chimp > Gorilla --------------- chr1:43111362-43111366 Template switch process: F1: L TGGACACCCCCTCAGGAAACCATCGCTAGGATTAAGAGTAAT 1 F3: 4 TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA R RF: TGGACACCCCCTCAGGAAACCATCTCTAGGATTAAGAGTAATTCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACAAGAGGAAGGATGGGTCCTTGGGGGATAGAACT RR: ACCTGTGGGGGAGTCCTTTGGTAGAGATCCTAATTCTCATTAAGTGTGTTTGAAGGTTACGGTGTGTAACCTTCAACGACCTTTCCAGACCCTTTTGTTCTCCTTCCTACCCAGGAACCCCCTATCTTGA F2: 3 CTTGA 2 Unidirectional alignment (log-probability: -31.2) GACACCCCCTCAGGAAACCATCgCTAGGATTAAGAGTAAtagTTC--------------TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA GACACCCCCTCAGGAAACCATCTCTAGGATTAAGAGTAA---TTCACACAAACTTCCAATGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA Template switch alignment (log-probability: -21.9) GACACCCCCTCAGGAAACCATCgCTAGGATTAAGAGTAAT|AGTTC|TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA GACACCCCCTCAGGAAACCATCTCTAGGATTAAGAGTAAT|AGTTC|TGCCACACATTGGAAGTTGCTGGAAAGGTCTGGGAAAACA ========= Event 526 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAATATCAACACCGCTAGGCCCCCAGGGCAAGCTGTGTCTGCCACAGCTTGAGACCCCTAAT----------- Chimp: CCAATATCAACACCGCTAGGC-CCCACCTCAAGCTGTGGCAGACACAGCTTGAGACCCCTAAT----------- ↑ 3 4 1 2 Gorilla: CCAATATCAACACCGCTAGGCCCCCAGGGCAAGCTGTGTCTGCCACAGCTTGAGACCCCTAAT----------- Human: CAAATATCAACACCGCTAGGCCCCCAGGGCAAGCTGTGTCTGCCACAGCTTGAGACCCCTAAT----------- Cluster: [ ] Orangutan: ccaatatcaacacagctaggc-cccagggcaagctgtgtctgccaaagcttgAGACCCCTAAAGGGGTCTCATG Gorilla > Chimp --------------- chr1:180138705-180138720 Template switch process: F1: L CCCAGGTGCCAGAACCAGGACCAATATCAACACCGCTAGGCC--------------------CCAC 1 F3: 4 CACAGCTTGAGACCCCTAATGTCCATGATGGAAGGGTGCA R RF: CCCAGGTGCCAGAACCAGGACCAATATCAACACCGCTAGGCCCCCAGGGCAAGCTGTGTCTGCCACAGCTTGAGACCCCTAATGTCCATGATGGAAGGGTGCA RR: GGGTCCACGGTCTTGGTCCTGGTTATAGTTGTGGCGATCCGGGGGTCCCGTTCGACACAGACGGTGTCGAACTCTGGGGATTACAGGTACTACCTTCCCACGT F2: 3 AGACGGTGTCGAACTC 2 Unidirectional alignment (log-probability: -43.4) TGCCAGAACCAGGACCAATATCAACACCGCTAGGCCCC-----acctCAAGCTGTGgCaGaCACAGCTTGAGACCCCTAATGTCCATGATGGAAGGGTGCA TGCCAGAACCAGGACCAATATCAACACCGCTAGGCCCCCAGGG----CAAGCTGTGTCTGCCACAGCTTGAGACCCCTAATGTCCATGATGGAAGGGTGCA Template switch alignment (log-probability: -28.7) TGCCAGAACCAGGACCAATATCAACACCGCTAGGCC--------------------CCAC|CTCAAGCTGTGGCAGA|CACAGCTTGAGACCCCTAATGTCCATGATGGAAGGGTGCA TGCCAGAACCAGGACCAATATCAACACCGCTAGGCCCCCAGGGCAAGCTGTGTCTGCCAC|CTCAAGCTGTGGCAGA|CACAGCTTGAGACCCCTAATGTCCATGATGGAAGGGTGCA ========= Event 527 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTCAAGCTGCTGGACACTGCAGGTCAGGTTCACCCGCCTGACCACTGCAAATCTCTTAGCTCAT ↑ 1 4 3 2 Chimp: GTCAAGCTGCTGGACACTGCA-ATTATGTTCACCTGCCTGACCCCTGCAAATCTCTTAGCTCAT Gorilla: GTCAAGCTGCTGGACACTACA-ATTATGTTCACCCACCTGACCACTGCAAATCTCTTAGCTCAT Human: GTCAAGCTGCTGGACACTGCAGGTCAGGTTCACCCGCCTGACCACTGCAAATCTCTTAGCTCAT Cluster: [ ] Orangutan: GTCAAGCTGCTGGACGCTGCA-ATTATGTTCACCCGCCTGACCACTGCAAGTCTCTTAGTTCAT Chimp > Human ------------- chr1:208110893-208110898 Template switch process: F1: L GAACATCTTTCTGCTTCCTAGTCAAGCTGCTGGACACTGCA 1 F3: 4 GTTCACCCGCCTGACCACTGCAAATCTCTTAGCTCATTTTACTCCCCTCTGTTTTCT R RF: GAACATCTTTCTGCTTCCTAGTCAAGCTGCTGGACACTGCAATTATGTTCACCTGCCTGACCCCTGCAAATCTCTTAGCTCATTTTACTCCCCTCTGTTTTCT RR: CTTGTAGAAAGACGAAGGATCAGTTCGACGACCTGTGACGTTAATACAAGTGGACGGACTGGGGACGTTTAGAGAATCGAGTAAAATGAGGGGAGACAAAAGA F2: 3 GACTGG 2 Unidirectional alignment (log-probability: -42.1) AACATCTTTCTGCTTCCTAGTCAAGCTGCTGGACACTGCAggtcag-----GTTCACCcGCCTGACCaCTGCAAATCTCTTAGCTCATTTT AACATCTTTCTGCTTCCTAGTCAAGCTGCTGGACACTGCA------ATTATGTTCACCTGCCTGACCCCTGCAAATCTCTTAGCTCATTTT Template switch alignment (log-probability: -28.3) AACATCTTTCTGCTTCCTAGTCAAGCTGCTGGACACTGCA|GGTCAG|GTTCACCcGCCTGACCaCTGCAAATCTCTTAGCTCATTTT AACATCTTTCTGCTTCCTAGTCAAGCTGCTGGACACTGCA|GGTCAG|GTTCACCTGCCTGACCCCTGCAAATCTCTTAGCTCATTTT ========= Event 528 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTCTACCTCCTGGTCCCACTCA--GAGGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGT ↓ 1 4 3 2 Chimp: CTCTCTACCTCCTGGTCCCACCCATCCAGTGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGT ↑ 1 4 3 2 Gorilla: CTCTCTACCTCCTGGTCCCACTCA--GACGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGT Human: CTCTCTACCTCCTGGTCCCACTCA--GAGGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGT Cluster: [ ] Orangutan: CTCTCTACCTCCTGGTCCCACTCA--GAGGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGT Human > Chimp ------------- chr1:183935578-183935583 Template switch process: F1: L AGCTCACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACCCA 1 F3: 4 GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG R RF: AGCTCACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACTCAGAGGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG RR: TCGAGTGAATCGGAGGCTCAGAGAGATGGAGGACCAGGGTGAGTCTCCCCGGCCTACTCGGTGACCTCTAGCTCACGTCGTTTTCCAC F2: 3 TGACCT 2 Unidirectional alignment (log-probability: -31.8) CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACcCAtccAGtGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACTCA--GAGGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG Template switch alignment (log-probability: -22.1) CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACcCA|TCCAGT|GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACTCA|TCCAGT|GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG Gorilla > Chimp --------------- chr1:183935578-183935583 Template switch process: F1: L AGCTCACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACCCA 1 F3: 4 GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG R RF: AGCTCACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACTCAGACGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG RR: TCGAGTGAATCGGAGGCTCAGAGAGATGGAGGACCAGGGTGAGTCTGCCCGGCCTACTCGGTGACCTCTAGCTCACGTCGTTTTCCAC F2: 3 TGACCT 2 Unidirectional alignment (log-probability: -32.5) CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACccatccagT------GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCAC--------TCAGACGGGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG Template switch alignment (log-probability: -22.1) CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACcCA|TCCAGT|GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG CACTTAGCCTCCGAGTCTCTCTACCTCCTGGTCCCACTCA|TCCAGT|GGCCGGATGAGCCACTGGAGATCGAGTGCAGCAAAAGGTG ========= Event 529 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTCTATTTCGTGGGGAAGAT-----------CATTCTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGGTTTAGTCGTGTGCAAATGATTGCAGGCGGCTTGGGAAATGTCCCTGCTCTTCTCTTTGTAAAGCCATGGCATCTTTTCTTCGGATTGATCAGCTAATGGTGGAGTTAAAATT Chimp: TATTCTATTTCGTGGGGAAGATCATTCTGAGATCATTCTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGGTTTAGTCGTGTGCAAATGATTGCAGGCGGCTTGGGAAGTGTCCCTGC-----TCTTTGTAAAGCCATGGCATCTTTTCTTCAGATTGATCAGCCAATGGTGGAGTTAAAATT ↑ 4 1 3 2 Gorilla: TATTCTATTTCGTGGGGAAGAT-----------CATTTTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGGTTTAGTCGTGTGCAAATGATTGCAGGCGGCTTGGGAAATGTCCCTGCTCTTCTCTTTGTAAAGCCATGGCATCTTTTCTTCAGATTGATCAGCTAATGGTGGAGTTAAAATT Human: TATTCTATTTCGTGGGGAAGAT-----------CATTCTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGGTTTAGTCGTGTGCAAATGATTGCAGGCGGCTTGGGAAATGTCCCTGCTCTTCTCTTTGTAAAGCCATGGCATCTTTTCTTCGGATTGATCAGCTAATGGTGGAGTTAAAATT Cluster: [ ] Orangutan: TATTCTA-TTCGTG-GGAAGAT-----------CATTCTGAGTTTGTGTGGGTCTAAATTCTTTCCCGGGTTTAGTCGTGTGCAAATGATTGCAGGCGGCTTGGGAAATGTCCCTGCTCTTCTCTTTGTTAAGCCATGGCATCTTTTCTTCGGATTGATCAGTTAATGGTGGAGTTAAAATT Gorilla > Chimp --------------- chr1:184991230-184991233 Template switch process: F1: L TTTTTTCAGAAAGGTGTTTTATTCTATTTCGTGGGGAAGATCATT 1 F3: 4 GATCATTCTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGGTTTAGTCG R RF: TTTTTTCAGAAAGGTGTTTTATTCTATTTCGTGGGGAAGATCATTTTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGGTTTAGTCGTGTGCAAATGATTGCAGGCGGCTTGGGAAATGTCCCTGCTCTTCTCTTTGTAAAGCCATGGCATCTTTTCTTCAGATTGATCAG RR: AAAAAAGTCTTTCCACAAAATAAGATAAAGCACCCCTTCTAGTAAAACTCAAACACACCCAGATTCAAGAAAGGGCCCAAATCAGCACACGTTTACTAACGTCCGCCGAACCCTTTACAGGGACGAGAAGAGAAACATTTCGGTACCGTAGAAAAGAAGTCTAACTAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -32.3) TCAGAAAGGTGTTTTATTCTATTTCGTGGGGAAGatcattctgagATCATTcTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGG TCAGAAAGGTGTTTTATTCTATTTCGTGGGGAAG-----------ATCATTTTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGG Template switch alignment (log-probability: -22) TCAGAAAGGTGTTTTATTCTATTTCGTGGGGAAGATCATT|CTGA|GATCATTcTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGG TCAGAAAGGTGTTTTATTCTATTTCGTGGGGAAGATCATT|CTGA|GATCATTTTGAGTTTGTGTGGGTCTAAGTTCTTTCCCGGG ========= Event 530 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CGATTTTGCATTGTCCTTTGAGCCACGAAGA-----TAACACGGGTGACTGAGACTGCGCATG Chimp: CGATTTTGCATTGTCCTTTGAGCCATGAAGA-----TAACACGGGTGACTGAGACTGCGCATG ↓ 3 1 2 4 Gorilla: CGATTTTGCATTGTCCTTTGAGCCATCTTCATGGCTCAACAC-GGTGACTGAGACTGCGCATG Human: CGATTTTGCATTGTCCTTTGAGCCACGAAGA-----TAACACGGGTGACTGAGACTGCGCATG Cluster: [ ] Orangutan: CGATTTTGCATTGTCCTTTGAGTCATGAAGA-----TAACACGGGTGACTGAGACTGCGCATG Chimp > Gorilla --------------- chr1:49106694-49106704 Template switch process: F1: L ATGAGCTCTGATCGGCGATTTTGCATTGTCCTTTGAGCCAT 1 F3: 4 AACAC-GGTGACTGAGACTGCGCATGAGTCAACGCCCAGCTTACCT R RF: ATGAGCTCTGATCAGCGATTTTGCATTGTCCTTTGAGCCATGAAGATAACACGGGTGACTGAGACTGCGCATGAGTCAACGCCCAGCTTACCT RR: TACTCGAGACTAGTCGCTAAAACGTAACAGGAAACTCGGTACTTCTATTGTGCCCACTGACTCTGACGCGTACTCAGTTGCGGGTCGAATGGA F2: 3 CTCGGTACTTC 2 Unidirectional alignment (log-probability: -49.8) TGAGCTCTGATCgGCGATTTTGCATTGTCCTTTGAGCCATcttcatggctcaacac------------GGTGACTGAGACTGCGCATGAGTCAACGCCCAGCT TGAGCTCTGATCAGCGATTTTGCATTGTCCTTTGAGCCAT----------------GAAGATAACACGGGTGACTGAGACTGCGCATGAGTCAACGCCCAGCT Template switch alignment (log-probability: -32.6) TGAGCTCTGATCgGCGATTTTGCATTGTCCTTTGAGCCAT|CTTCATGGCTC|AACAC-GGTGACTGAGACTGCGCATGAGTCAACGCCCAGCT TGAGCTCTGATCAGCGATTTTGCATTGTCCTTTGAGCCAT|CTTCATGGCTC|AACACGGGTGACTGAGACTGCGCATGAGTCAACGCCCAGCT ========= Event 531 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTATTGATTTACCCTTGCACT----------------------TTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACTGAAAGTA Chimp: CTATTGATTTACCCTTGCACT----------------------TTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACTGAAAGTA ↓ 41 3 2 Gorilla: CTATTGATTTACCCTTGCACTTCGAAGAGTCTTTGTTTTGTTTTTGaaaaacaaaacaaaaaCTCTTCGAAGTCATATAACTGAAAGTA ↑ 41 3 2 Human: CTATTGATTTACCCTTGCACT----------------------TTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACTGAAAGTA Cluster: [ ] Orangutan: CTATTGATTTACCCTTGCAGT----------------------TTGAAAAACAAAACAAAGACTCTTCGAAGTCATGTAACTGAAAGTA Human > Gorilla --------------- chr1:185597244-185597263 Template switch process: F1: L GGCTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTT 1 F3: 4 TTTGAAAAACAAAACAAAAACTCTTCGAAGTCATATAACTG R RF: GGCTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTTTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACTG RR: CCGAGTTCTGGGATACTTAAGATAACTAAATGGGAACGTGAAACTTTTTGTTTTGTTTCTGAGAAGCTTCAGTATATTGAC F2: 3 TTGTTTTGTTTCTGAGAAGC 2 Unidirectional alignment (log-probability: -48) CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACttcgaagagtctttgttttgttTTTGAAAAACAAAACAAAaACTCTTCGAAGTCATATAACT CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCAC----------------------TTTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACT Template switch alignment (log-probability: -23.8) CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTT|CGAAGAGTCTTTGTTTTGTT|TTTGAAAAACAAAACAAAaACTCTTCGAAGTCATATAACT CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTT|CGAAGAGTCTTTGTTTTGTT|TTTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACT Chimp > Gorilla --------------- chr1:185597244-185597263 Template switch process: F1: L GGCTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTT 1 F3: 4 TTTGAAAAACAAAACAAAAACTCTTCGAAGTCATATAACTG R RF: AGCTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTTTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACTG RR: TCGAGTTCTGGGATACTTAAGATAACTAAATGGGAACGTGAAACTTTTTGTTTTGTTTCTGAGAAGCTTCAGTATATTGAC F2: 3 TTGTTTTGTTTCTGAGAAGC 2 Unidirectional alignment (log-probability: -53.6) CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACttcgaagagtctttgttttgttTTTGAAAAACAAAACAAAaACTCTTCGAAGTCATATAACT CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCAC----------------------TTTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACT Template switch alignment (log-probability: -29.4) CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTT|CGAAGAGTCTTTGTTTTGTT|TTTGAAAAACAAAACAAAaACTCTTCGAAGTCATATAACT CTCAAGACCCTATGAATTCTATTGATTTACCCTTGCACTT|CGAAGAGTCTTTGTTTTGTT|TTTGAAAAACAAAACAAAGACTCTTCGAAGTCATATAACT ========= Event 532 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCCACCCAACTCAGTTATGTCAGGTGTAGAGAGGACAGGCAGAGAGAATATTGACCTG-----------------------AAGGTACTTAGAAGGTATTTAGAA Chimp: TCCCACCCAACTCAGTTATGTCAGGTGTAGAGATTACAGGCAGAGAGAATATTGACCTG-----------------------AAGGTACTTAG-----------AA ↓ 4 3 1 2 Gorilla: TCCCACCCAACTCAGTTATGTCAGGTGTAGAGAGGACAGGCAGAGAGAATATTGACCTGAACCTTCAGGTCAGGTACCTTAGAAGGTACTTAG-----------AA Human: TCCCACCCAACTCAGTTATGTCAGGTGTAGAGAGGACAGGCAGAGAGAATATTGACCTG-----------------------AAGGTACTTAGAAGGTATTTAGAA Cluster: [] Orangutan: TCCCACCCAACTCAGTTATGTCAGGTGTAGAGAGGACAGGCAGAGAGAATATTGACCTG-----------------------AAGGTACTTAG-----------AA Chimp > Gorilla --------------- chr1:39351484-39351490 Template switch process: F1: L AGGATGTTTCCCACCCAACTCAGTTATGTCAGGTGTAGAGAGGACAGGCAGAGAGAATATTGACCTGAA 1 F3: 4 GTCAGGT R RF: AGGATGTTTCCCACCCAACTCAGTTATGTCAGGTGTAGAGATTACAGGCAGAGAGAATATTGACCTGAAGTAGAGATTACAGGCAGAGAGAATATTGACCTGAAGG RR: TCCTACAAAGGGTGGGTTGAGTCAATACAGTCCACATCTCTAATGTCCGTCTCTCTTATAACTGGACTTCATCTCTAATGTCCGTCTCTCTTATAACTGGACTTCC F2: 3 GACTTCC 2 Unidirectional alignment (log-probability: -41.7) CAGGTGTAGAGAggACAGGCAGAGAGAATATTGACCTGaaccttcaggtcaggt CAGGTGTAGAGATTACAGGCAGAGAGAATATTGACCTG---------------- Template switch alignment (log-probability: -27.5) CAGGTGTAGAGAggACAGGCAGAGAGAATATTGACCTGAA|CCTTCAG|GTCAGGT CAGGTGTAGAGATTACAGGCAGAGAGAATATTGACCTGAA|CCTTCAG|GTCAGGT ========= Event 533 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CACAAAACATCTTATCTTAATCACAAGGTAACAACATTTCTCTGAACCCCAAAGTATGGCAAGGTTTCACAAGAATCTGAGA Chimp: CACAAAACATCTTATCTTAAT---------------TTTG---CCATCCCAAAGTATGGCAAAGTTTCACAAGAATCTGAGA ↑ 1 4 3 2 Gorilla: CACAAAACATCTTATCTTAATTACAAGGTAACAACATTTCTCTGAACCCCAAAGTATGGCAAGATTTCACAAGAATCTGAGA Human: CACAAAACATCTTATCTTAATCACAAGGTAACAACATTTCTCTGAACCCCAAAGTATGGCAAGGTTTCACAAGAATCTGAGA Cluster: [ ] Orangutan: CGCAAAACATCTTATCTTAATTACAAGGTTACAACATTTGTCTGAACCCCAAAGTATGGCAAGGTTTCACAAGAATCTGAGA Gorilla > Chimp --------------- chr12:31499385-31499391 Template switch process: F1: L TCCCAATTCTAGTATCTTCACACAAAACATCTTATCTTAATT 1 F3: 4 CCCAAAGTATGGCAAAGTTTCACAAGAATCTGAGACTTTC R RF: TCCCAATTCTAGTATCTTCACACAAAACATCTTATCTTAATTACAAGGTAACAACATTTCTCTGAACCCCAAAGTATGGCAAGATTTCACAAGAATCTGAGACTTTC RR: AGGGTTAAGATCATAGAAGTGTGTTTTGTAGAATAGAATTAATGTTCCATTGTTGTAAAGAGACTTGGGGTTTCATACCGTTCTAAAGTGTTCTTAGACTCTGAAAG F2: 3 TACCGTT 2 Unidirectional alignment (log-probability: -43) CCAATTCTAGTATCTTCACACAAAACATCTTATCTTAATT-------------------------ttgccatCCCAAAGTATGGCAAagTTTCACAAGAATCTGAGACTTTC CCAATTCTAGTATCTTCACACAAAACATCTTATCTTAATTACAAGGTAACAACATTTCTCTGAAC-------CCCAAAGTATGGCAAGATTTCACAAGAATCTGAGACTTTC Template switch alignment (log-probability: -27.7) CCAATTCTAGTATCTTCACACAAAACATCTTATCTTAATT|TTGCCAT|CCCAAAGTATGGCAAagTTTCACAAGAATCTGAGACTTTC CCAATTCTAGTATCTTCACACAAAACATCTTATCTTAATT|TTGCCAT|CCCAAAGTATGGCAAGATTTCACAAGAATCTGAGACTTTC ========= Event 534 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: cactagaaaaggtcttAAAATTAGCAAAGCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACAC--TGTGCTAATATTCTTAAGGGGCAGAAATTA Chimp: cactagaaaaggtcttAAAATTAGCAAAGCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACAC--TGTGCTA--ATTCTTAAGGGGCAGAAATTA Gorilla: cactagaaaaggtcttAAAATTAGCAAAGCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACAC----TGCTA--ATTCTTAAGGGGCAGAAATTA ↓ 3 2 1 4 Human: cactagaaaaggtcttAAAATTAGCAAAGCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACAC--TGTGCTAATATTCTTAAGGGGCAGAAATTA Cluster: [ ] Orangutan: CACTAGAAAAGGTCTTAAAATGAGCAAAGCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACACTG--TGTTA--ATTCTTAAGGGGCAGAAATTA Gorilla > Human --------------- chr1:41629501-41629507 Template switch process: F1: L GCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACACTG 1 F3: 4 ATTCTTAAGGGGCAGAAATTAATTTATCATTGAGTACTCA R RF: ATTAGCAAAGCACTCATATATTGAAAGGTGGGTTTGCTACAAATACACACTGCTAATTCTTAAGGGGCAGAAATTAATTTATCATTGAGTACTCA RR: TAATCGTTTCGTGAGTATATAACTTTCCACCCAAACGATGTTTATGTGTGACGATTAAGAATTCCCCGTCTTTAATTAAATAGTAACTCATGAGT F2: 3 TAATCGT 2 Unidirectional alignment (log-probability: -26.5) CTCATATATTGAAAGGTGGGTTTGCTACAAATACACACtgTGCTAatATTCTTAAGGGGCAGAAATTAATTTATCATTGAGTACTCA CTCATATATTGAAAGGTGGGTTTGCTACAAATACACAC--TGCTA--ATTCTTAAGGGGCAGAAATTAATTTATCATTGAGTACTCA Template switch alignment (log-probability: -16.7) CTCATATATTGAAAGGTGGGTTTGCTACAAATACACACTG|TGCTAAT|ATTCTTAAGGGGCAGAAATTAATTTATCATTGAGTACTCA CTCATATATTGAAAGGTGGGTTTGCTACAAATACACACTG|TGCTAAT|ATTCTTAAGGGGCAGAAATTAATTTATCATTGAGTACTCA ========= Event 535 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTTTGTGATTGATCAAGGAATGAAGACTGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAGCCA--------------GTCCTTGAACAATCACATAATT ↓ 3 1 2 4 ↑ 3 1 2 4 Chimp: TTCTGTGATTGATCAAGGAATGAAGACTGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTACACA-------GTCTTCATTCCTTGAACAATCACATAATT Gorilla: TTCTGTGATTGATCAAGGAATGAAGACTGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATACAGTCTTCA-------TTCCTTGAACAATCACAGAATT Human: TTTTGTGATTGATCAAGGAATGAAGACTGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAGCCA--------------GTCCTTGAACAATCACATAATT Cluster: [ ] Orangutan: TTCTGTGATTGNNNNNNNNNNT---ACCATGTAGAGCAGAAGGCATTTTTCAAATAAACATCCAGTATCAGGATTCCAAGACATTCAGGATGCACAGGTATCCTTAGATGCTGTCTAGAGCGTCCCTCATGGGCACATGATCAGACTTTTCTAATGGCTCATTCTGATCCATTGAGAAGCACAGGAGACCACTGACAAATCAAGttttttttAGGGTCATCTCATATCACATAGTTCACATAGTATGTACTTCAGTTGGCCTTTTTGAAGATTAGAGAGTATGTTCTGTTCCGAGTGGTCATTTCTATCTTTCCCCTTCTAACAGgaaagggagtctcgctgatcacccaggctggagggcagtgtcacaatcatggctcactgcaagatatgcctcccaggttcacgtcattctgttcttcagcctccc-------TTCCTTGATCAATCACAGAATT Chimp > Human ------------- chr1:196324822-196324830 Template switch process: F1: L GTTTTCAGATTATTTTGTGATTGATCAAGGAATGAAGACTG 1 F3: 4 TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT R RF: GTTTTCAGATTATTCTGTGATTGATCAAGGAATGAAGACTGGCTACACAGTCTTCATTCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT RR: CAAAAGTCTAATAAGACACTAACTAGTTCCTTACTTCTGACCGATGTGTCAGAAGTAAGGAACTTGTTAGTGTATTAACTAAAATATTAGGATTATA F2: 3 GACCGATGT 2 Unidirectional alignment (log-probability: -39.4) TTTTCAGATTATTtTGTGATTGATCAAGGAATGAAGACTG---------------TgtagccagTCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT TTTTCAGATTATTCTGTGATTGATCAAGGAATGAAGACTGGCTACACAGTCTTCAT--------TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT Template switch alignment (log-probability: -22.4) TTTTCAGATTATTtTGTGATTGATCAAGGAATGAAGACTG|TGTAGCCAG|TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT TTTTCAGATTATTCTGTGATTGATCAAGGAATGAAGACTG|TGTAGCCAG|TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT Human > Chimp ------------- chr1:175129531-175129546 Template switch process: F1: L GTTTTCAGATTATTCTGTGATTGATCAAGGAATGAAGACTG 1 F3: 4 TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT R RF: GTTTTCAGATTATTTTGTGATTGATCAAGGAATGAAGACTGTGTAGCCAGTCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT RR: CAAAAGTCTAATAAAACACTAACTAGTTCCTTACTTCTGACACATCGGTCAGGAACTTGTTAGTGTATTAACTAAAATATTAGGATTATA F2: 3 TACTTCTGACACATCG 2 Unidirectional alignment (log-probability: -49.1) TTTTCAGATTATTcTGTGATTGATCAAGGAATGAAGACTG--------GctacacagtcttcatTCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT TTTTCAGATTATTTTGTGATTGATCAAGGAATGAAGACTGTGTAGCCAG---------------TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT Template switch alignment (log-probability: -23.3) TTTTCAGATTATTcTGTGATTGATCAAGGAATGAAGACTG|GCTACACAGTCTTCAT|TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT TTTTCAGATTATTTTGTGATTGATCAAGGAATGAAGACTG|GCTACACAGTCTTCAT|TCCTTGAACAATCACATAATTGATTTTATAATCCTAATAT ========= Event 536 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGAGCCA------GAGCCAGTGGCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGTACCACCGGGCATCACTGCATCCACCGAC Chimp: TCTGAGCCA------GAGCCAGTGGCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGTGCCACTGGGCATCACTGCATCCACCGAC ↑ 3 2 1 4 Gorilla: TCTGAGCCA------GAGCCAGTGGCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGCACTACCAGGCATCACTGCATCCACCGAC Human: TCTGAGCCA------GAGCCAGTGGCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGTACCACCGGGCATCACTGCATCCACCGAC Cluster: [ ] Orangutan: TCTGAGCCAGAGCCAGAGCCAGTGGCAAGGGCTTGGGGAGAAGGTGGAGTGTGAGACCACAGAGCACCACCAGGCATCACGGCATCCACCGAC Gorilla > Chimp --------------- chr1:45462840-45462847 Template switch process: F1: L GGCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAG 1 F3: 4 GGCATCACTGCATCCACCGACAAGGGCTGCCTCCTCCTCT R RF: CAGTGGCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGCACTACCAGGCATCACTGCATCCACCGACAAGGGCTGCCTCCTCCTCT RR: GTCACCGTTCCCGAACCCCTCCTCCACCTTACACTCTGGTGTCTCGTGATGGTCCGTAGTGACGTAGGTGGCTGTTCCCGACGGAGGAGGAGA F2: 3 GTCACCGT 2 Unidirectional alignment (log-probability: -28.9) GCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGtgCcACtgGGCATCACTGCATCCACCGACAAGGGCTGCCTCCTCCTCT GCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAGCACTACCAGGCATCACTGCATCCACCGACAAGGGCTGCCTCCTCCTCT Template switch alignment (log-probability: -16.7) GCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAG|TGCCACTG|GGCATCACTGCATCCACCGACAAGGGCTGCCTCCTCCTCT GCAAGGGCTTGGGGAGGAGGTGGAATGTGAGACCACAGAG|TGCCACTG|GGCATCACTGCATCCACCGACAAGGGCTGCCTCCTCCTCT ========= Event 537 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTCCCTTCCCTCCCTCTTCTCG------GGGATACACCTCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCATCACATTTTATTTTTATAAA Chimp: GTTCCCTTCCCTCCCTCTTCTCG------GGGATACACCTCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCATCACATTTTATTTTTATAAA ↓ 1 4 3 2 Gorilla: GTTCCCTTCCCTCCCTCTTCTTG-------------CCAGCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCATCACATTTTATTTTTATAAA ↑ 1 4 3 2 Human: GTTCCCTTCCCTCCCTCTTCTCG------GGGATACACCTCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCATCACATTTTATTTTTATAAA Cluster: [ ] Orangutan: GTTCCCTTCCCTCCCTCTTCTCGGGACAC-------ACCTCCCCCTGGCAGGCTGGCCTTCGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCATCACATTTTATTTTTATAAA Human > Gorilla --------------- chr12:27554821-27554826 Template switch process: F1: L CGACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT 1 F3: 4 CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC R RF: CGACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCTCGGGGATACACCTCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCA RR: GCTGAGAAAGAGACGAAGGACAAGGGAAGGGAGGGAGAAGAGCCCCTATGTGGAGGGGGACCGTCCGACCGGAACCACCATAGGTCACTTCGTGCGCAAGTTGGGTGTCGGGTCAATAGAGACCCTAAACCAAATGTTCGGGACCGT F2: 3 GACCGT 2 Unidirectional alignment (log-probability: -28.4) GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT------------TgccagCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCTCGGGGATACACCT-----CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC Template switch alignment (log-probability: -16.5) GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT|TGCCAG|CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT|TGCCAG|CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC Chimp > Gorilla --------------- chr12:27554821-27554826 Template switch process: F1: L CGACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT 1 F3: 4 CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC R RF: CGACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCTCGGGGATACACCTCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCACGCGTTCAACCCACAGCCCAGTTATCTCTGGGATTTGGTTTACAAGCCCTGGCA RR: GCTGAGAAAGAGACGAAGGACAAGGGAAGGGAGGGAGAAGAGCCCCTATGTGGAGGGGGACCGTCCGACCGGAACCACCATAGGTCACTTCGTGCGCAAGTTGGGTGTCGGGTCAATAGAGACCCTAAACCAAATGTTCGGGACCGT F2: 3 GACCGT 2 Unidirectional alignment (log-probability: -28.4) GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT------------TgccagCCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCTCGGGGATACACCT-----CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC Template switch alignment (log-probability: -16.5) GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT|TGCCAG|CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC GACTCTTTCTCTGCTTCCTGTTCCCTTCCCTCCCTCTTCT|TGCCAG|CCCCCTGGCAGGCTGGCCTTGGTGGTATCCAGTGAAGCAC ========= Event 538 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATAATTAAGTCCATGCTGT--GAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAA ↓ 1 4 3 2 Chimp: ATATAATTAAGTCCATGCTGTAGAATCTTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAA ↑ 1 4 3 2 Gorilla: ATATAATTAAGTCCATGCTGT--GAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGGAA Human: ATATAATTAAGTCCATGCTGT--GAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAA Cluster: [ ] Orangutan: ATATAATTAAGTCCATGCCGT--GAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAA Human > Chimp ------------- chr12:27474219-27474225 Template switch process: F1: L CAGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT 1 F3: 4 TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC R RF: CAGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGTGAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC RR: GTCAGGATTTATCTTAATCCTATATTAATTCAGGTACGACACTCCCAGACCTCCTTCTAAGATTGAACCTCCCACTCCCTTTGTAG F2: 3 TCTAAGA 2 Unidirectional alignment (log-probability: -31.5) AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGtagaatcT-----TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTG-------TGAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC Template switch alignment (log-probability: -16.2) AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT|AGAATCT|TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT|AGAATCT|TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC Gorilla > Chimp --------------- chr12:27474219-27474225 Template switch process: F1: L CAGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT 1 F3: 4 TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGAAACATC R RF: CAGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGTGAGGGTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGGAACATC RR: GTCAGGATTTATCTTAATCCTATATTAATTCAGGTACGACACTCCCAGACCTCCTTCTAAGATTGAACCTCCCACTCCCCTTGTAG F2: 3 TCTAAGA 2 Unidirectional alignment (log-probability: -36.5) AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT-----agaatctTCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGaAACATC AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGTGAGGG-------TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGGAACATC Template switch alignment (log-probability: -22.1) AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT|AGAATCT|TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGaAACATC AGTCCTAAATAGAATTAGGATATAATTAAGTCCATGCTGT|AGAATCT|TCTGGAGGAAGATTCTAACTTGGAGGGTGAGGGGAACATC ========= Event 539 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GAAAACTGGGGTGTGTAAAAGTCTCCAGGGCCTCTGTCCACAGCAGGAAAAGCTCAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCGTAACTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGC----CTGTTTCATGTGCGGGCTCCTGCTTCTGATCTTATGGCAGTTGCCTAATTGCCAATGACTGTTTCTGTGGACACGAGGGTCTGCT Chimp: GAAAACTGGGGTGTGTAAAAGTCTCCAGGGCCTCTGTCCACAGCAGGAAAAGCTCAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCGTAACTCAAGAGATAGAAGGCAGTGATCTTCCTGCACTGT--CTCTGTTTCATGTGCGGGCTCCTGCTTCTGATCTTATGGCAATTGCCTAATTGCCAATGACTGTTTATGTGGACACGAGAGTCTGCT Gorilla: GAAAACTGGGGTGTGTAAAAGTCTCCAAGGCCTCTGTCCACAGCAGGAAAAGCTCAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCAGACTTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCT--CTGTTTCATGTGCGGGCTCCTGCTTCTGATCTTATGGCAGTTGCCTAATTGCCAATGACTGTTACTGTGGACATGAGGGTCTGCT ↓ 1 4 3 2 ↑ 3 2 1 4 Human: GAAAACTGGGGTGTGTAAAAGTCTCCAGGGCCTCTGTCCACAGCAGGAAAAGCTCAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCGTAACTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGC----CTGTTTCATGTGCGGGCTCCTGCTTCTGATCTTATGGCAGTTGCCTAATTGCCAATGACTGTTTCTGTGGACACGAGGGTCTGCT Cluster: [ ] Orangutan: GAAAACTGGGGTGTGTAAAAGTCTCCAGGGCCTCTGTCCACAGCAGGAAAAGCTCACAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCATAACTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCT--CTGTTTCATGTGCGGGCTCCTGCTTCTGATCTTATGGCAGTTGCCTAATTGCCAATGACTGTTTCTGTGGACACGAGGGTCTGCT Gorilla > Human --------------- chr12:26755394-26755398 Template switch process: F1: L CAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCC 1 F3: 4 TCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTG R RF: CAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCAGACTTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTCTGTTTCATGTGCGGGCTCCTGCTTCTGATCTTATGGCAGTTGCCTAATTGCCAATGACTGTTAC RR: GTCTCGTCTAACCTGTGTCCCCCTCCGTTGGAGTCGGCGGGTCTGAAGTTCTCTATCTTCCGTCACTAGAAGGACGTGGCGGAGACAAAGTACACGCCCGAGGACGAAGACTAGAATACCGTCAACGGATTAACGGTTACTGACAATG F2: 3 CAATG 2 Unidirectional alignment (log-probability: -33.1) AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCgtAacTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGC--CTG AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCAGACTTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTCTG Template switch alignment (log-probability: -21.8) AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCC|GTAAC|TCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTg AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCC|GTAAC|TCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTC Human > Gorilla --------------- chr12:27030356-27030360 Template switch process: F1: L CAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCC 1 F3: 4 TCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCT-----------------CTG R RF: AGTCTCCAGGGCCTCTGTCCACAGCAGGAAAAGCTCAGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCGTAACTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTGTTTCATGTGCGGGCTCCTG RR: TCAGAGGTCCCGGAGACAGGTGTCGTCCTTTTCGAGTCTCGTCTAACCTGTGTCCCCCTCCGTTGGAGTCGGCGGGCATTGAGTTCTCTATCTTCCGTCACTAGAAGGACGTGGCGGACAAAGTACACGCCCGAGGAC F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -35.9) AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCagActTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCctCTG AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCCGTAACTCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGC--CTG Template switch alignment (log-probability: -27) AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCC|AGACT|TCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCT-----------------CTG AGAGCAGATTGGACACAGGGGGAGGCAACCTCAGCCGCCC|AGACT|TCAAGAGATAGAAGGCAGTGATCTTCCTGCACCGCCTGTTTCATGTGCGGGCTCCTG ========= Event 540 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGAGCGCGTCCCCAGGGTGGGCGGCTGCCACCGCCCG--GAGAGTCCTTGAGGGATGCC Chimp: AGGAGCGCGTCCCCAGGGTGGGCGGCTGCCACCGCCCG--GAGAGTCCTTGAGGGATGCC ↑ 3 1 2 4 Gorilla: AGGAGCGCGTCCCCAGGGTGGGCGGTGGCAGCCTCAAG--GAGAGTCCTTGAGGGATGCC Human: AGGAGCGCGTCCCCAGGGTGGGCGGCTGCCACCGCCCG--GAGAGTCCTTGAGGGATGCC Cluster: [ ] Orangutan: AGGAGCGCGTCCCCAGGGTGGGCGGCTGCCACCGCCCGGAGAGAGTCCTTGAGGGATGCC Gorilla > Chimp --------------- chr12:27631517-27631528 Template switch process: F1: L CGTTCCGGTGGCAGCAAGGAGCGCGTCCCCAGGGTGGGCGG 1 F3: 4 GGAGAGTCCTTGAGGGATGCCACGGGGGCACGGGTGGTCT R RF: CGTTCCTGTGGCAGCAAGGAGCGCGTCCCCAGGGTGGGCGGTGGCAGCCTCAAGGAGAGTCCTTGAGGGATGCCACGGGGGCACGGGTGGTCT RR: GCAAGGACACCGTCGTTCCTCGCGCAGGGGTCCCACCCGCCACCGTCGGAGTTCCTCTCAGGAACTCCCTACGGTGCCCCCGTGCCCACCAGA F2: 3 CCCGCCACCGTC 2 Unidirectional alignment (log-probability: -44) GTTCCgGTGGCAGCAAGGAGCGCGTCCCCAGGGTGGGCGG------------ctgccaccgcccGGAGAGTCCTTGAGGGATGCCACGGGGGCACGGGTGGTCT GTTCCTGTGGCAGCAAGGAGCGCGTCCCCAGGGTGGGCGGTGGCAGCCTCAA------------GGAGAGTCCTTGAGGGATGCCACGGGGGCACGGGTGGTCT Template switch alignment (log-probability: -22.8) GTTCCgGTGGCAGCAAGGAGCGCGTCCCCAGGGTGGGCGG|CTGCCACCGCCC|GGAGAGTCCTTGAGGGATGCCACGGGGGCACGGGTGGTCT GTTCCTGTGGCAGCAAGGAGCGCGTCCCCAGGGTGGGCGG|CTGCCACCGCCC|GGAGAGTCCTTGAGGGATGCCACGGGGGCACGGGTGGTCT ========= Event 541 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCCATGCTCTTTACAGTCTTATAGCAGCAGGTGGTAACTCTTG--------CAAATCt--------------ttt ↓ 13 24 Chimp: GTCCATGCTCTTTACAGTCTTT----TGCAAGAGTTACCACCTG----CTGCTATATCt--------------ttt Gorilla: GTCCATGCTCTTTACGGTCTTT----TGCAAGAGTTACCACCTGCTGC----TATATCt----------------- Human: GTCCATGCTCTTTACAGTCTTATAGCAGCAGGTGGTAACTCTTG--------CAAATCt--------------ttt Cluster: [ ] Orangutan: GTCCATGTTCTTTACAGTCTTT----TGCAAGAGTTACCACCTGCTGC----TATATCttttctgttttgttt--- Human > Chimp ------------- chr12:33517002-33517027 Template switch process: F1: L CATACCCCCATTCAGTTTTAGTCCATGCTCTTTACAGTCTT 1 F3: 4 ATC-TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTC R RF: CATACCCCCATTCAGTTTTAGTCCATGCTCTTTACAGTCTTATAGCAGCAGGTGGTAACTCTTGCAAATCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTC RR: GTATGGGGGTAAGTCAAAATCAGGTACGAGAAATGTCAGAATATCGTCGTCCACCATTGAGAACGTTTAGAAAAAAAAAAAAAAAAAAAAAACTCTGCCTCAG F2: 3 TATCGTCGTCCACCATTGAGAACGTT 2 Unidirectional alignment (log-probability: -61.2) ATACCCCCATTCAGTTTTAGTCCATGCTCTTTACAGTCTT--------------------TTGCAAgagttaccacctgctgctatATC-TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTC ATACCCCCATTCAGTTTTAGTCCATGCTCTTTACAGTCTTATAGCAGCAGGTGGTAACTCTTGCAA--------------------ATCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTC Template switch alignment (log-probability: -28.7) ATACCCCCATTCAGTTTTAGTCCATGCTCTTTACAGTCTT|TTGCAAGAGTTACCACCTGCTGCTAT|ATC-TTTTTTTTTTTTTTTTTTTTTGAGACGGAGTC ATACCCCCATTCAGTTTTAGTCCATGCTCTTTACAGTCTT|TTGCAAGAGTTACCACCTGCTGCTAT|ATCTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTC ========= Event 542 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATGGGGCCAATGAAGTCCTTTT------------------------------------GACT----GATAGATATCTTCTTGCTCAAGGCAATTTTTAAGCGAGGCTCATGGTAAACAATGCTGATTTATAAAACCACTGTACAATGTATTGTCTGATGTATA Chimp: TTATGGGGCCAATGAAGTCCTTTT------------------GACTAATAGGCACCTTTTGACT----GATAGATAGCTTCTTGCTCAAGGCAATTTTTAAGCGAGGCTCATGGTAAACAATGCTGATTTATAAAACCACTGTACAATGTATTGTCTGATGTTTA Gorilla: TTATGGGGCCAATGAAGTCCTTTTGACTAATAGGTACCTTTT------------------GACT--------GATAGCTTCTTGCTCAAGGCAATTTTTAAGCGAGGCTCATGGTAAACAATGCTGATTTATAAAATCACTGTACAATGTATTGTCTGATGTATA ↑ 4 1 3 2 Human: TTATGGGGCCAATGAAGTCCTTTT------------------------------------GACT----GATAGATATCTTCTTGCTCAAGGCAATTTTTAAGCGAGGCTCATGGTAAACAATGCTGATTTATAAAACCACTGTACAATGTATTGTCTGATGTATA Cluster: [ ] Orangutan: TTATGGGGCCAATGAAGTCCTTTTGACTAATAGGCACCTTTT------------------GACTGATA----GATAGCTTCTTGCTCAAGGCAGTTTTTAAGTGAGGCTCATGGTAAACAATGCCGATTTATAAAACCACTGTACAATGTATTGTCTGATGTATA Human > Gorilla --------------- chr12:105289424-105289427 Template switch process: F1: L GTTTTAATAGTTAGCAATTATGGGGCCAATGAAGTCCTTTTGACTAATAG 1 F3: 4 CTTTTGACTGATAG----CTTCTTGCTCAAGGCAATTTTTAAGCGAGGCTCATGGTAA R RF: GTTTTAATAGTTAGCAATTATGGGGCCAATGAAGTCCTTTTGACTGATAGATATCTTCTTGCTCAAGGCAATTTTTAAGCGAGGCTCATGGTAAACAATGCTGATTTATAAAACCACTGTAC RR: CAAAATTATCAATCGTTAATACCCCGGTTACTTCAGGAAAACTGACTATCTATAGAAGAACGAGTTCCGTTAAAAATTCGCTCCGAGTACCATTTGTTACGACTAAATATTTTGGTGACATG F2: 3 CATG 2 Unidirectional alignment (log-probability: -42.2) TTAGCAATTATGGGGCCAATGAAGTCCTTTTGACTaATAggtaccttttgactGATAgCTTCTTGCTCAAGGCAATTTTTAAGC TTAGCAATTATGGGGCCAATGAAGTCCTTTTGACTGATA--------------GATATCTTCTTGCTCAAGGCAATTTTTAAGC Template switch alignment (log-probability: -32.3) TTAGCAATTATGGGGCCAATGAAGTCCTTTTGACTaATAG|GTAC|CTTTTGACTGATAG----CTTCTTGCTCAAGGCAATTTTTAAGC TTAGCAATTATGGGGCCAATGAAGTCCTTTTGACTGATAG|GTAC|CTTTTGACTGATAGATATCTTCTTGCTCAAGGCAATTTTTAAGC ========= Event 543 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGTGTCTGTTTCCTGCAGCGATCCTATCTAAATCTCTGCTCAAAATTCATATGGGCTAAGTACAAGGCACTATGGTAAATGCAGTAATACAGGTAGTAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATATCGTGCCTTATTCAATATACCATT Chimp: CAGTGTCTGTTTCCTGCAGCGATCCTATCTAAATCTCTGCTCAAAATTCATATGGGCTAAGTACAAGGCATTATGGTAAATGCAGTAATACAGGTAGTAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATATCATGCCTTATTCAATATACCATT Gorilla: CAGTGTCTGTTTCCTGCAGCGATCCTATCTAAATCTCTGCTCAAAATTCATATGGGCTAAGTACAAGGCACTATGGTAAATGCAGTAATACAGGTAGCAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATGTCATGCCTTATTCAATATACCATT ↓ 3 2 1 4 Human: CAGTGTCTGTTTCCTGCAGCGATCCTATCTAAATCTCTGCTCAAAATTCATATGGGCTAAGTACAAGGCACTATGGTAAATGCAGTAATACAGGTAGTAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATATCGTGCCTTATTCAATATACCATT Cluster: [ ] Orangutan: CAGTATCTGTTTCCTGCAGCGATCCTATCTAAATCTCTGCTCAAAATTCATATGGACTAAGTACAAGGCACTATGATAAATGCAGTAATACAGGTAGTAGTGATTTAAAACTGTGTAGCATTTTATAGCGATATATCATGCCTTATTCAATATACCATT Gorilla > Human --------------- chr12:30225028-30225031 Template switch process: F1: L GTAGTAGTGATTTAAAACTGTGTAGCATTTTATAGCAATAT 1 F3: 4 TGCCTTATTCAATATACCATTTGATACACACACACACACA R RF: CGATCCTATCTAAATCTCTGCTCAAAATTCATATGGGCTAAGTACAAGGCACTATGGTAAATGCAGTAATACAGGTAGCAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATGTCATGCCTTATTCAATATACCATTTGATACACACACACACACA RR: GCTAGGATAGATTTAGAGACGAGTTTTAAGTATACCCGATTCATGTTCCGTGATACCATTTACGTCATTATGTCCATCGTCACTAAATTTTGACACATCGTAAAATATCGTTATACAGTACGGAATAAGTTATATGGTAAACTATGTGTGTGTGTGTGT F2: 3 GCTA 2 Unidirectional alignment (log-probability: -33) TAGtAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATaTCgTGCCTTATTCAATATACCATTTGATACACACACAcacaca TAGCAGTGATTTAAAACTGTGTAGCATTTTATAGCAATATGTCATGCCTTATTCAATATACCATTTGATACACACACA------ Template switch alignment (log-probability: -21.7) TAGtAGTGATTTAAAACTGTGTAGCATTTTATAGCAATAT|ATCG|TGCCTTATTCAATATACCATTTGATACACACACACACACA TAGCAGTGATTTAAAACTGTGTAGCATTTTATAGCAATAT|ATCG|TGCCTTATTCAATATACCATTTGATACACACACACACACA ========= Event 544 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATCTCACTTTTTATCATCAT--------------ACTGGCA--------------------------------------TAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCAAT ↑ 1 4 3 2 Chimp: AATCTCACTTTTTATCATCAT-------CTCAGTGCCTGGTA-------------------TTGGTGCCCTTAGGTCTGTGAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCAAT Gorilla: AATCTCACTTTTTATCATCATCTCAGTG-------CCTGGTATTGGTGCCCTTAGGTCTGT-------------------GAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCAAT ↓ 1 4 3 2 Human: AATCTCACTTTTTATCATCAT--------------ACTGGCA--------------------------------------TAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCAAT Cluster: [ ] Orangutan: AATCTCACTTTTTATCATCATCTCAATG-------CCTGGTATTGGTCCCCTTAGGTCTGT-------------------GAGCAGCATTGCATTATGCCAGTAAATGAATACTTAAATCAAT Chimp > Human ------------- chr12:24622457-24622464 Template switch process: F1: L CTGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT 1 F3: 4 AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA R RF: CTGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCATCTCAGTGCCTGGTATTGGTGCCCTTAGGTCTGTGAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA RR: GACTCAAAGAAGTAATCTTTTTAGAGTGAAAAATAGTAGTAGAGTCACGGACCATAACCACGGGAATCCAGACACTTGTCGTAACGCAATACGGTCATTTACTTATGAATTTAGT F2: 3 TACGGTCA 2 Unidirectional alignment (log-probability: -34.4) TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATcatactggCAT----------------------------------AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCAT--------CATCTCAGTGCCTGGTATTGGTGCCCTTAGGTCTGTGAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA Template switch alignment (log-probability: -16.3) TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT|ACTGGCAT|AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT|ACTGGCAT|AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA Gorilla > Human --------------- chr12:24622457-24622464 Template switch process: F1: L CTGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT 1 F3: 4 AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA R RF: CTGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCATCTCAGTGCCTGGTATTGGTGCCCTTAGGTCTGTGAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA RR: GACTCAAAGAAGTAATCTTTTTAGAGTGAAAAATAGTAGTAGAGTCACGGACCATAACCACGGGAATCCAGACACTTGTCGTAACGCAATACGGTCATTTACTTATGAATTTAGT F2: 3 TACGGTCA 2 Unidirectional alignment (log-probability: -33.1) TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT-------aCTGGcAT-------------------AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCATCTCAGTGCCTGGTATTGGTGCCCTTAGGTCTGTGAACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA Template switch alignment (log-probability: -16.7) TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT|ACTGGCAT|AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA TGAGTTTCTTCATTAGAAAAATCTCACTTTTTATCATCAT|ACTGGCAT|AACAGCATTGCGTTATGCCAGTAAATGAATACTTAAATCA ========= Event 545 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GATTTAAACTGGAGCCTTTCTACTGCCT-CAGGGCCATGGTATAATTGCAATTTTAGT Chimp: GATTTAAACTGGAGCCTTTCTACTGCCT-CAGGGCCATGGTATAATTGCAattttagt ↓ 3 2 1 4 Gorilla: GATTTAAACTGGAGCCTTTCTACTGCCTCCAGTAGCAAGGTATAATTGCAattttagt ↑ 3 2 1 4 Human: GATTTAAACTGGAGCCTTTCTACTGCCT-CAGGGCCATGGTATAATTGCAATTTTAGT Cluster: [ ] Orangutan: GATTTAAACCGGAGCCTTTCTACTGCCT-CAGGGCCATGGTATAATTGCAattttagt Human > Gorilla --------------- chr12:109693327-109693332 Template switch process: F1: L TGGCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC 1 F3: 4 CAAGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTTT R RF: TAGCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTCAGGGCCATGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTTT RR: ATCGGTTTCGGTCCTAAATTTGACCTCGGAAAGATGACGGAGTCCCGGTACCATATTAACGTTAAAATCATTAAAAACGATGTAAAAA F2: 3 GATGAC 2 Unidirectional alignment (log-probability: -44.5) GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTCcagtAG---CAaGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC----AGGGCCATGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT Template switch alignment (log-probability: -27.6) GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC|CAGTAG|CAaGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC|CAGTAG|CATGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT Chimp > Gorilla --------------- chr12:109693327-109693332 Template switch process: F1: L TGGCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC 1 F3: 4 CAAGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTTT R RF: TAGCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTCAGGGCCATGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTTT RR: ATCGGTTTCGGTCCTAAATTTGACCTCGGAAAGATGACGGAGTCCCGGTACCATATTAACGTTAAAATCATTAAAAACGATGTAAAAA F2: 3 GATGAC 2 Unidirectional alignment (log-probability: -44.5) GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTCcagtAG---CAaGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC----AGGGCCATGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT Template switch alignment (log-probability: -27.6) GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC|CAGTAG|CAaGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT GCCAAAGCCAGGATTTAAACTGGAGCCTTTCTACTGCCTC|CAGTAG|CATGGTATAATTGCAATTTTAGTAATTTTTGCTACATTTT ========= Event 546 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGGCATCCTTTGTGAGGTCAAGAGCTTCA--------------------------------------------------------------------------------------ACTACTTGGAGAGTTCTGGAAAGAGCtacagtttagtggttaggagctctggcattagattacttgggtccaacttcaggatctgccacttactattatgt Chimp: TGGGCATCCTTTGTGAGGTCAAgagcttca---------------------------------------------------actacttggagcttcaacaagctccaagagcttcaactacttggagAGTTCTGGAAAGAGCtacagtttagtggttaggagctctggcattagattacttgggtccaactttaggatctgccacttactattatgt Gorilla: TGGGCATCCTTTGTGAGGTCAAGAGCTTCA----------------ACTACTTGGAGCTTCAGGAAGCTCCAAGAGCTTCA-----------------------------------ACTACCTGGAGAGTTCTGGAAAGAGCtacagtttagtggttaggagctctggcattagattacttgggtccaacttcaggatctgccacttactattatgt ↑ 4 3 2 1 Human: TGGGCATCCTTTGTGAGGTCAAGAGCTTCA--------------------------------------------------------------------------------------ACTACTTGGAGAGTTCTGGAAAGAGCtacagtttagtggttaggagctctggcattagattacttgggtccaacttcaggatctgccacttactattatgt Cluster: [ ] Orangutan: TGGGCATCCTTTGTGAGGTCAAgagcttcaactacttggagcttca----------------------------------------------------------------------actacttggagAATTCTGGAAAGAGCtacagtttagtgattaggagctctggcattagactacttgggtccaacttcaggatctgccacttactattatgt Human > Gorilla --------------- chr1:42564391-42564395 Template switch process: F1: L GGCTGCATTTGTGGGCATCCTTTGTGAGGTCAAGAGCTTCAACTACTTGGAG--------------------------------------------------------------CTTCAGGA 1 F3: 4 CAAGAGCTTCAACTACCTGGAGAGTTCTGGAAAGAGCTACAGTTTAGTGGTTAGGAG R RF: GGCTGCATTTGTGGGCATCCTTTGTGAGGTCAAGAGCTTCAACTACTTGGAGAGTTCTGGAAAGAGCTACAGTTTAGTGGTTAGGAGCTCTGGCATTAGATTACTTGGGTCCAACTTCAGGACT RR: CCGACGTAAACACCCGTAGGAAACACTCCAGTTCTCGAAGTTGATGAACCTCTCAAGACCTTTCTCGATGTCAAATCACCAATCCTCGAGACCGTAATCTAATGAACCCAGGTTGAAGTCCTGA F2: 3 CTCGA 2 Unidirectional alignment (log-probability: -61.3) TTTGTGAGGTCAAGAGCTTCAACTACTtggagcttcaggaagctccaagagcttcaactaccTGGAGAGTTCTGGAAAGAGCTAC TTTGTGAGGTCAAGAGCTTCAACTACT-----------------------------------TGGAGAGTTCTGGAAAGAGCTAC Template switch alignment (log-probability: -35.7) TTTGTGAGGTCAAGAGCTTCAACTACTTGGAG--------------------------------------------------------------CTTCAGGA|AGCTC|CAAGAGCTTCAACTACcTGGAGAGTTCTGGAAAGAGCTAC TTTGTGAGGTCAAGAGCTTCAACTACTTGGAGAGTTCTGGAAAGAGCTACAGTTTAGTGGTTAGGAGCTCTGGCATTAGATTACTTGGGTCCAACTTCAGGA|AGCTC|CAAGAGCTTCAACTACTTGGAGAGTTCTGGAAAGAGCTAC ========= Event 547 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AATTCAACACAGCCCTGCCTCGGCAGTCCGAGTCCTGGAAGGGACCTTGGGGAC-----TGCTGACTGCAGGTTCCTTGGCTACAG Chimp: AATTCAACACAGCCCTGCCTCGGCAGTCCGAGTCCTGGAAGGGACCTTGGGGAC-----TGCCGACTGCAGGTTCCTCGGCTACAG ↑ 3 2 1 4 Gorilla: AATTCAACACAGCCCTGCCTCGGCAGTCTGAGTCCTGGAAGGGACCTTGGGGTC----------CCTGCAGGTTCCTCGGCTACAG Human: AATTCAACACAGCCCTGCCTCGGCAGTCCGAGTCCTGGAAGGGACCTTGGGGAC-----TGCTGACTGCAGGTTCCTTGGCTACAG Cluster: [ ] Orangutan: AATTCAACACAGCCCTGCCTTGGCAGTCCGAGTCCTGGAAGGGACCTTGGGGACTGCTG-----ACTGCAGGTTCCTCGGCTACAG Gorilla > Chimp --------------- chr12:113712788-113712795 Template switch process: F1: L GCCCTGCCTCGGCAGTCCGAGTCCTGGAAGGGACCTTGGGG 1 F3: 4 CTGCAGGTTCCTCGGCTACAGGGACGGCTGCTGTGCTTAC R RF: GCCCTGCCTCGGCAGTCTGAGTCCTGGAAGGGACCTTGGGGTCCCTGCAGGTTCCTCGGCTACAGGGACGGCTGCTGTGCTTAC RR: CGGGACGGAGCCGTCAGACTCAGGACCTTCCCTGGAACCCCAGGGACGTCCAAGGAGCCGATGTCCCTGCCGACGACACGAATG F2: 3 AGCCGTCA 2 Unidirectional alignment (log-probability: -34.7) CCCTGCCTCGGCAGTCcGAGTCCTGGAAGGGACCTTGGGGaCtgccgaCTGCAGGTTCCTCGGCTACAGGGACGGCTGCTGTGCTTAC CCCTGCCTCGGCAGTCTGAGTCCTGGAAGGGACCTTGGGGTC-----CCTGCAGGTTCCTCGGCTACAGGGACGGCTGCTGTGCTTAC Template switch alignment (log-probability: -22.3) CCCTGCCTCGGCAGTCcGAGTCCTGGAAGGGACCTTGGGG|ACTGCCGA|CTGCAGGTTCCTCGGCTACAGGGACGGCTGCTGTGCTTAC CCCTGCCTCGGCAGTCTGAGTCCTGGAAGGGACCTTGGGG|ACTGCCGA|CTGCAGGTTCCTCGGCTACAGGGACGGCTGCTGTGCTTAC ========= Event 548 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATAATTTTTGGTCTAAGACTTTCCTTCTGGAAA------GAAGAAACTACCAAAAGTGGTT Chimp: AATAATTTTTGGTCTAAGACTTTCCTTCTGGAAA------GAAGAAACTACCAAAAGTGGTT ↑ 3 1 2 4 Gorilla: AATAATTTTTGGTCTAAGACTTTC----CAGAAGGACTCCTAAGAAACTACCAAAAGTGGTT ↓ 3 1 2 4 Human: AATAATTTTTGGTCTAAGACTTTCCTTCTGGAAA------GAAGAAACTACCAAAAGTGGTT Cluster: [ ] Orangutan: AATAATTTTTGGTCTAAGACTTTC----CAGAAGGACTCCTAAGAAACTACCAACAGTGGTT Gorilla > Human --------------- chr12:111079209-111079218 Template switch process: F1: L ACGTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC 1 F3: 4 AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT R RF: ACGTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCCAGAAGGACTCCTAAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT RR: TGCATGTTCGTCCAATCTTATTAAAAACCAGATTCTGAAAGGTCTTCCTGAGGATTCTTTGATGGTTTTCACCAACGGGGACCTTTCCCTAAGA F2: 3 GAAAGGTCTT 2 Unidirectional alignment (log-probability: -32.7) GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCCttctggaaAG----------AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC--------AGAAGGACTCCTAAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT Template switch alignment (log-probability: -17) GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC|TTCTGGAAAG|AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC|TTCTGGAAAG|AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT Gorilla > Chimp --------------- chr12:114124087-114124096 Template switch process: F1: L ACGTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC 1 F3: 4 AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT R RF: ACGTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCCAGAAGGACTCCTAAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT RR: TGCATGTTCGTCCAATCTTATTAAAAACCAGATTCTGAAAGGTCTTCCTGAGGATTCTTTGATGGTTTTCACCAACGGGGACCTTTCCCTAAGA F2: 3 GAAAGGTCTT 2 Unidirectional alignment (log-probability: -32.7) GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCCttctggaaAG----------AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC--------AGAAGGACTCCTAAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT Template switch alignment (log-probability: -17) GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC|TTCTGGAAAG|AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT GTACAAGCAGGTTAGAATAATTTTTGGTCTAAGACTTTCC|TTCTGGAAAG|AAGAAACTACCAAAAGTGGTTGCCCCTGGAAAGGGATTCT ========= Event 549 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGTCTTTCTGACTCTAGGACTGAGG Chimp: CCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGTCTTTCTGACTCTAGGACTGAGG ↓ 3 2 1 4 Gorilla: CCTCAAAGCACTGCTTCCCTGCCACCCTCTGCTGTGGGTG-GCACCTTCTGACTCTAGGACTGAGG ↑ 3 2 1 4 Human: CCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGTCTTTCTGACTCTAGGACTGAGG Cluster: [ ] Orangutan: CCTCAAAGTGCTGCTTCCCTGCCACCCTCTGCTGTGGTC--TGTCTTTCTGACTCTAGGACTGAGG Human > Gorilla --------------- chr12:111179679-111179684 Template switch process: F1: L CCCTCCTCAAAGCACTGCTTCCCTGCCACCCTCTGCTGTGG 1 F3: 4 CCTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTGTT R RF: CCCTCCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGTCTTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTGTT RR: GGGAGGAGTTTCGCGACGAAGGGACGGTGGGAGACGACACCAGATACAGAAAGACTGAGATCCTGACTCCCCGACCCCGACACAAAACAA F2: 3 ACGGTG 2 Unidirectional alignment (log-probability: -37.7) CCTCCTCAAAGCaCTGCTTCCCTGCCACCCTCTGCTGTGG-----GTggcaCcTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG CCTCCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGT----CTTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG Template switch alignment (log-probability: -27.6) CCTCCTCAAAGCaCTGCTTCCCTGCCACCCTCTGCTGTGG|GTGGCA|CcTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG CCTCCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGG|GTGGCA|CTTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG Chimp > Gorilla --------------- chr12:111179679-111179684 Template switch process: F1: L CCCTCCTCAAAGCACTGCTTCCCTGCCACCCTCTGCTGTGG 1 F3: 4 CCTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTGTT R RF: CCCTCCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGTCTTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTGTT RR: GGGAGGAGTTTCGCGACGAAGGGACGGTGGGAGACGACACCAGATACAGAAAGACTGAGATCCTGACTCCCCGACCCCGACACAAAACAA F2: 3 ACGGTG 2 Unidirectional alignment (log-probability: -37.7) CCTCCTCAAAGCaCTGCTTCCCTGCCACCCTCTGCTGTGG-----GTggcaCcTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG CCTCCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGGTCTATGT----CTTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG Template switch alignment (log-probability: -27.6) CCTCCTCAAAGCaCTGCTTCCCTGCCACCCTCTGCTGTGG|GTGGCA|CcTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG CCTCCTCAAAGCGCTGCTTCCCTGCCACCCTCTGCTGTGG|GTGGCA|CTTTCTGACTCTAGGACTGAGGGGCTGGGGCTGTGTTTTG ========= Event 550 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCCTCCTCTGCAGCACCCTTGGGATACCTGTAGGAGCCAGGGTAGTCCTGGGCCAGGACTAGCCCAGGGAGGCCTTTCTGA ↑ 4 3 1 2 Chimp: CCCTCCTCTGCAGCACCCTTGGGATACCTATAGGAGC----------------CAGGACTAGCCCAGGGAGGCCTTTCTGA ↓ 4 3 1 2 Gorilla: CCCTCCTCTGCAGCACCCTTGAGATACCTGTAGGAGCCAGGGTAGTCCTGGGCCAGGACTAGCCCAGGGAGGCCTTTCTGA Human: CCCTCCTCTGCAGCACCCTTGGGATACCTGTAGGAGCCAGGGTAGTCCTGGGCCAGGACTAGCCCAGGGAGGCCTTTCTGA Cluster: [ ] Orangutan: TCCTCCCCTGAAGCACCCTTAGGATACCTGTAGGAGCCAGGATAGTCCTGGGCCAGGACTAGCCCAGGGAGGCCTTTCTGA Chimp > Human ------------- chr12:113177546-113177554 Template switch process: F1: L CCCTAATTTTAGCCCTCCTCTGCAGCACCCTTGGGATACCTGTAGGAGCCAGGG 1 F3: 4 GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAACT R RF: CCCTAATTTTAGCCCTCCTCTGCAGCACCCTTGGGATACCTATAGGAGCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAACT RR: GGGATTAAAATCGGGAGGAGACGTCGTGGGAACCCTATGGATATCCTCGGTCCTGATCGGGTCCCTCCGGAAAGACTGTTAGTGTTTGA F2: 3 GGTCCTGAT 2 Unidirectional alignment (log-probability: -40) CTCCTCTGCAGCACCCTTGGGATACCTgTAGGAGCCAGggtagtcctgggccagGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA CTCCTCTGCAGCACCCTTGGGATACCTATAGGAGCCAG----------------GACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA Template switch alignment (log-probability: -28.7) CTCCTCTGCAGCACCCTTGGGATACCTgTAGGAGCCAGGg|TAGTCCTGG|GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA CTCCTCTGCAGCACCCTTGGGATACCTATAGGAGCCAGGA|TAGTCCTGG|GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA Chimp > Gorilla --------------- chr12:113126923-113126931 Template switch process: F1: L GCACAAATCCCTAATTTTAGCCCTCCTCTGCAGCACCCTTGAGATACCTGTAGGAGCCAGGG 1 F3: 4 GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAACT R RF: GCACAAATCCCTAATTTTAGCCCTCCTCTGCAGCACCCTTGGGATACCTATAGGAGCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAACT RR: CGTGTTTAGGGATTAAAATCGGGAGGAGACGTCGTGGGAACCCTATGGATATCCTCGGTCCTGATCGGGTCCCTCCGGAAAGACTGTTAGTGTTTGA F2: 3 GGTCCTGAT 2 Unidirectional alignment (log-probability: -45.2) CTCCTCTGCAGCACCCTTGaGATACCTgTAGGAgccagggtagtcctggGCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA CTCCTCTGCAGCACCCTTGGGATACCTATAGGA----------------GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA Template switch alignment (log-probability: -34) CTCCTCTGCAGCACCCTTGaGATACCTgTAGGAGCCAGGg|TAGTCCTGG|GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA CTCCTCTGCAGCACCCTTGGGATACCTATAGGAGCCAGGA|TAGTCCTGG|GCCAGGACTAGCCCAGGGAGGCCTTTCTGACAATCACAAA ========= Event 551 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: GTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCCTT------GCCTAACTCCTTGGCAAAGAAA ↓ 3 1 2 4 ↑ 3 1 2 4 Chimp: GTTACAGATGCAACATGTGTTCATGCAAGGGGCAGGTCTGCAGGTTGCATGAACCTAACTCCTTGGCAAAGAAA ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: GTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCTTT------GCCTAACTCCTTGGCAAAGAAA Human: GTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCCTT------GCCTAACTCCTTGGCAAAGAAA Cluster: [ ] Orangutan: GTTACAGATGCAACATGTGTTCATGCGACCTGCAGACCTGTCCCTT------GCCTAACTCCTTGGCAAAGAAA Chimp > Human ------------- chr12:118100941-118100959 Template switch process: F1: L GATGAACTTCAGAGTTACAGATGCAACATGTGTTCATGCAA 1 F3: 4 CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG R RF: GATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAAGGGGCAGGTCTGCAGGTTGCATGAACCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG RR: CTACTTGAAATCTCAATGTCTACGTTGTACACAAGTACGTTCCCCGTCCAGACGTCCAACGTACTTGGATTGAGGAACCGTTTCTTTATTTCCTTGTCACCGAACC F2: 3 GTTCCCCGTCCAGACGTCC 2 Unidirectional alignment (log-probability: -54.2) ATGAACTTcAGAGTTACAGATGCAACATGTGTTCATGCAAcctgcagacctgccccttG------------------------CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA------------------GGGGCAGGTCTGCAGGTTGCATGAACCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Template switch alignment (log-probability: -23.6) ATGAACTTcAGAGTTACAGATGCAACATGTGTTCATGCAA|CCTGCAGACCTGCCCCTTG|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA|CCTGCAGACCTGCCCCTTG|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Human > Chimp ------------- chr12:121257406-121257430 Template switch process: F1: L GATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA 1 F3: 4 CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG R RF: GATGAACTTCAGAGTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCCTTGCCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG RR: CTACTTGAAGTCTCAATGTCTACGTTGTACACAAGTACGTTGGACGTCTGGACGGGGAACGGATTGAGGAACCGTTTCTTTATTTCCTTGTCACCGAACC F2: 3 AAGTACGTTGGACGTCTGGACGGGG 2 Unidirectional alignment (log-probability: -62.6) ATGAACTTtAGAGTTACAGATGCAACATGTGTTCATGCAA------------------GgggcaggtctgcaggttgcatgaaCCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ATGAACTTCAGAGTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCCTTG------------------------CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Template switch alignment (log-probability: -24.4) ATGAACTTtAGAGTTACAGATGCAACATGTGTTCATGCAA|GGGGCAGGTCTGCAGGTTGCATGAA|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ATGAACTTCAGAGTTACAGATGCAACATGTGTTCATGCAA|GGGGCAGGTCTGCAGGTTGCATGAA|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Gorilla > Chimp --------------- chr12:121257407-121257430 Template switch process: F1: L GATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAAG 1 F3: 4 CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG R RF: GATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCTTTGCCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG RR: CTACTTGAAATCTCAATGTCTACGTTGTACACAAGTACGTTGGACGTCTGGACGGGAAACGGATTGAGGAACCGTTTCTTTATTTCCTTGTCACCGAACC F2: 3 AAGTACGTTGGACGTCTGGACGGG 2 Unidirectional alignment (log-probability: -56.1) TGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA------------------GgggcaggtctgcaggttgcatgaaCCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG TGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAACCTGCAGACCTGCCCTTTG------------------------CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Template switch alignment (log-probability: -24.3) TGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAAg|GGGCAGGTCTGCAGGTTGCATGAA|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG TGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAAC|GGGCAGGTCTGCAGGTTGCATGAA|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Chimp > Gorilla --------------- chr12:118121246-118121264 Template switch process: F1: L GATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA 1 F3: 4 CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG R RF: GATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAAGGGGCAGGTCTGCAGGTTGCATGAACCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG RR: CTACTTGAAATCTCAATGTCTACGTTGTACACAAGTACGTTCCCCGTCCAGACGTCCAACGTACTTGGATTGAGGAACCGTTTCTTTATTTCCTTGTCACCGAACC F2: 3 GTTTCCCGTCCAGACGTCC 2 Unidirectional alignment (log-probability: -47.7) ATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAAcctgcagacctgccctttG------------------------CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA------------------GGGGCAGGTCTGCAGGTTGCATGAACCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG Template switch alignment (log-probability: -23.7) ATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA|CCTGCAGACCTGCCCtTTG|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ATGAACTTTAGAGTTACAGATGCAACATGTGTTCATGCAA|CCTGCAGACCTGCCCCTTG|CCTAACTCCTTGGCAAAGAAATAAAGGAACAGTGGCTTGG ========= Event 552 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACTATAAGGTAATTAACTTCTTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTG Chimp: ACTATAAGGTAATTAACTTCTTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTG ↓ 13 24 ↑ 13 24 Gorilla: ACTATAAGGTAATTAACTTCTCTCAGTTCAGATTTTCATATTTAAGAAGATACCTTCCTGAACTG ↓ 13 24 ↑ 13 24 Human: ACTATAAGGTAATTAACTTCTTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTG Cluster: [ ] Orangutan: ACTATAAGATAATTAACTTCTTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTG Gorilla > Human --------------- chr1:36597533-36597555 Template switch process: F1: L ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT 1 F3: 4 AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT R RF: ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCTCTCAGTTCAGATTTTCATATTTAAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT RR: TGAAAGTGTAACATTACAAATGATATTCCATTAATTGAAGAGAGTCAAGTCTAAAAGTATAAATTCTTCTATGGAAGGACTTGACTTAGTGTAAGTTGATTGTA F2: 3 GAGTCAAGTCTAAAAGTATAAAT 2 Unidirectional alignment (log-probability: -51.9) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTC---------------------TTAaatatgaaaatctgaactgagAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCTCTCAGTTCAGATTTTCATATTTA---------------------AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Template switch alignment (log-probability: -18.7) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|TAAATATGAAAATCTGAACTGAG|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|TAAATATGAAAATCTGAACTGAG|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Human > Gorilla --------------- chr1:36759338-36759360 Template switch process: F1: L ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT 1 F3: 4 AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT R RF: ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCTTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT RR: TGAAAGTGTAACATTACAAATGATATTCCATTAATTGAAGAATTTATACTTTTAGACTTGACTCTCTTCTATGGAAGGACTTGACTTAGTGTAAGTTGATTGTA F2: 3 ATTTATACTTTTAGACTTGACTC 2 Unidirectional alignment (log-probability: -51.9) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCtctcagttcagattttcatatTTA---------------------AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTC---------------------TTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Template switch alignment (log-probability: -18.7) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|CTCAGTTCAGATTTTCATATTTA|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|CTCAGTTCAGATTTTCATATTTA|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Gorilla > Chimp --------------- chr1:37262675-37262697 Template switch process: F1: L ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT 1 F3: 4 AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT R RF: ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCTCTCAGTTCAGATTTTCATATTTAAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT RR: TGAAAGTGTAACATTACAAATGATATTCCATTAATTGAAGAGAGTCAAGTCTAAAAGTATAAATTCTTCTATGGAAGGACTTGACTTAGTGTAAGTTGATTGTA F2: 3 GAGTCAAGTCTAAAAGTATAAAT 2 Unidirectional alignment (log-probability: -51.9) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTC---------------------TTAaatatgaaaatctgaactgagAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCTCTCAGTTCAGATTTTCATATTTA---------------------AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Template switch alignment (log-probability: -18.7) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|TAAATATGAAAATCTGAACTGAG|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|TAAATATGAAAATCTGAACTGAG|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Chimp > Gorilla --------------- chr1:36759338-36759360 Template switch process: F1: L ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT 1 F3: 4 AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT R RF: ACTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCTTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT RR: TGAAAGTGTAACATTACAAATGATATTCCATTAATTGAAGAATTTATACTTTTAGACTTGACTCTCTTCTATGGAAGGACTTGACTTAGTGTAAGTTGATTGTA F2: 3 ATTTATACTTTTAGACTTGACTC 2 Unidirectional alignment (log-probability: -51.9) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCtctcagttcagattttcatatTTA---------------------AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTC---------------------TTAAATATGAAAATCTGAACTGAGAGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT Template switch alignment (log-probability: -18.7) CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|CTCAGTTCAGATTTTCATATTTA|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT CTTTCACATTGTAATGTTTACTATAAGGTAATTAACTTCT|CTCAGTTCAGATTTTCATATTTA|AGAAGATACCTTCCTGAACTGAATCACATTCAACTAACAT ========= Event 553 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TACCTGCTAAAATAGAGTGGTAACAGAGTCAGAGGAGAAGAACAC----TATCAAGTTACAAGTGGAATAAG Chimp: TACCTGCTAAAATAGAGTGGTAACAGAGTCAGAGGAGAAGAATAC----TATCAACTTACAAGTGGAATAAG Gorilla: TACCTGCTAAAATAGAGTGGTAACAGAGGCTTCTCCTCT-GACTCTGTAACTCAAGTTACAAGTGGAATAAG ↑ 3 1 2 4 Human: TACCTGCTAAAATAGAGTGGTAACAGAGTCAGAGGAGAAGAACAC----TATCAAGTTACAAGTGGAATAAG Cluster: [ ] Orangutan: TACCTGCTAAAATGGAGTGGTAACAGAGTCAGAGCAGAAGAATAC----GATCAAGTTACAAGTGGAATAAG Human > Gorilla --------------- chr12:5322284-5322303 Template switch process: F1: L GTGTGTACTTTAATACCTGCTAAAATAGAGTGGTAACAGAGGC 1 F3: 4 TCAAGTTACAAGTGGAATAAGAGCCACAGGATATTTCCCT R RF: GTGTGTACTTTAATACCTGCTAAAATAGAGTGGTAACAGAGTCAGAGGAGAAGAACACTATCAAGTTACAAGTGGAATAAGAGCCACAGGATATTTCCCT RR: CACACATGAAATTATGGACGATTTTATCTCACCATTGTCTCAGTCTCCTCTTCTTGTGATAGTTCAATGTTCACCTTATTCTCGGTGTCCTATAAAGGGA F2: 3 CAATGTCTCAGTCTCCTCTT 2 Unidirectional alignment (log-probability: -53.2) TGTACTTTAATACCTGCTAAAATAGAGTGGTAACAGAG-------------------gcttctcctctgactctgtaacTCAAGTTACAAGTGGAATAAGAGCCACAGGATATTTCCCT TGTACTTTAATACCTGCTAAAATAGAGTGGTAACAGAGTCAGAGGAGAAGAACACTA----------------------TCAAGTTACAAGTGGAATAAGAGCCACAGGATATTTCCCT Template switch alignment (log-probability: -29.4) TGTACTTTAATACCTGCTAAAATAGAGTGGTAACAGAGgC|TTCTCCTCTGACTCTGTaAC|TCAAGTTACAAGTGGAATAAGAGCCACAGGATATTTCCCT TGTACTTTAATACCTGCTAAAATAGAGTGGTAACAGAGTC|TTCTCCTCTGACTCTGTTAC|TCAAGTTACAAGTGGAATAAGAGCCACAGGATATTTCCCT ========= Event 554 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGGGCGGTGGCCTCTCCCCCAGGAATCCTCATTCCTGGGGCATCAAGGCCCACGGACTTA ↑ 3 1 42 Chimp: TGGGGCGGTGGCCTCTCCCCCAGGAA----------TGAGGCATCAAGGCCCACGGACTTA Gorilla: TGGGGCGGTGGCCTCTCCCCCAGGAA----------TGAGGCATCAAGGCCCACGGACTTA ↓ 3 1 42 Human: TGGGGCGGTGGCCTCTCCCCCAGGAATCCTCATTCCTGGGGCATCAAGGCCCACGGACTTA Cluster: [ ] Orangutan: CAGGGTGCTGGCCTCTCCCCCAGGAA----------TGAGGCAGCAAGGCCCACGGACTTA Chimp > Human ------------- chr12:9340952-9340963 Template switch process: F1: L CCAGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAT 1 F3: 4 GGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA R RF: CCAGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAATGAGGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA RR: GGTCTCTTTACCCACACCCCGCCACCGGAGAGGGGGTCCTTACTCCGTAGTTCCGGGTGCCTGAATCTGGTGGGACCCGGGGGT F2: 3 GGTCCTTACTCC 2 Unidirectional alignment (log-probability: -31.3) AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAtcctcattccTGgGGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAA----------TGAGGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA Template switch alignment (log-probability: -16.8) AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAT|CCTCATTCCTGG|GGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAT|CCTCATTCCTGG|GGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA Gorilla > Human --------------- chr12:9340952-9340963 Template switch process: F1: L CCAGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAT 1 F3: 4 GGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA R RF: CCAGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAATGAGGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA RR: GGTCTCTTTACCCACACCCCGCCACCGGAGAGGGGGTCCTTACTCCGTAGTTCCGGGTGCCTGAATCTGGTGGGACCCGGGGGT F2: 3 GGTCCTTACTCC 2 Unidirectional alignment (log-probability: -30.8) AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAtcctcattccTGgGGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAA----------TGAGGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA Template switch alignment (log-probability: -17.3) AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAT|CCTCATTCCTGG|GGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA AGAGAAATGGGTGTGGGGCGGTGGCCTCTCCCCCAGGAAT|CCTCATTCCTGG|GGCATCAAGGCCCACGGACTTAGACCACCCTGGGCCCCCA ========= Event 555 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCCAACCAGCACAGCACTGAGC-TATA---AAGAACTAAGTCAATAGATAAATGAATGAA Chimp: CTCCAACCAGCACAGCACTGAGC-TATA---AAGAACTAAGTCAATAGATAAATGAATGAA ↓ 3 1 2 4 Gorilla: CTCCAACCAGCACAGCACTGAGCTTATAGCTCAGAACTAATTCAATAGATAAATGAATGAA ↑ 3 1 2 4 Human: CTCCAACCAGCACAGCACTGAGC-TATA---AAGAACTAAGTCAATAGATAAATGAATGAA Cluster: [ ] Orangutan: CTCCAAGCAGCACAGCGCTGAGC-TATA---AAGAACTAAGTTAATAGATAAATGAATGAA Human > Gorilla --------------- chr12:9581241-9581248 Template switch process: F1: L CCTTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCT 1 F3: 4 AGAACTAATTCAATAGATAAATGAATGAATAGCATGAATTTGCATGGGA R RF: CCTTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCTATAAAGAACTAAGTCAATAGATAAATGAATGAATAGCATGAATTTGCATGGGA RR: GGAAAAGACCTGGGGTGTGAGGTTGGTCGTGTCGTGACTCGATATTTCTTGATTCAGTTATCTATTTACTTACTTATCGTACTTAAACGTACCCT F2: 3 CTCGATAT 2 Unidirectional alignment (log-probability: -37.6) TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCtTATAgctcAGAACTAAtTCAATAGATAAATGAATGAATAGCATGAATT TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGC-TATAA---AGAACTAAGTCAATAGATAAATGAATGAATAGCATGAATT Template switch alignment (log-probability: -22.5) TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCT|TATAGCTC|AGAACTAAtTCAATAGATAAATGAATGAATAGCATGAATT TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCT|TATAGCTC|AGAACTAAGTCAATAGATAAATGAATGAATAGCATGAATT Chimp > Gorilla --------------- chr12:9581241-9581248 Template switch process: F1: L CCTTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCT 1 F3: 4 AGAACTAATTCAATAGATAAATGAATGAATAGCATGAATTTGCATGGGA R RF: CCTTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCTATAAAGAACTAAGTCAATAGATAAATGAATGAATAGCATGAATTTGCATGGGA RR: GGAAAAGACCTGGGGTGTGAGGTTGGTCGTGTCGTGACTCGATATTTCTTGATTCAGTTATCTATTTACTTACTTATCGTACTTAAACGTACCCT F2: 3 CTCGATAT 2 Unidirectional alignment (log-probability: -37.6) TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCtTATAgctcAGAACTAAtTCAATAGATAAATGAATGAATAGCATGAATT TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGC-TATAA---AGAACTAAGTCAATAGATAAATGAATGAATAGCATGAATT Template switch alignment (log-probability: -22.5) TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCT|TATAGCTC|AGAACTAAtTCAATAGATAAATGAATGAATAGCATGAATT TTTTCTGGACCCCACACTCCAACCAGCACAGCACTGAGCT|TATAGCTC|AGAACTAAGTCAATAGATAAATGAATGAATAGCATGAATT ========= Event 556 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAAAGACTGAAGATAAAGAGTCAATCCATTGACAAAAGTGTCAAGCACACTCAATTT ↓ 3 2 1 4 Chimp: CTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAACCT---------------C-----AG-----TGTGTGTCAAGCACACTCAATTT Gorilla: CTGTCCTGTAAAAATGGGGCATTGAGGTTAGaaaaaaaGACTGAAGATAAAGAGTCAATCCATTGACAAAAGTGTCAAGCACACTCAATTT Human: CTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAAAGACTGAAGATAAAGAGTCAATCCATTGACAAAAGTGTCAAGCACACTCAATTT Cluster: [ ] Orangutan: CTGTCCTATAAAAATGGGGCATTGAGGTTAGAAAAAAAGACTGAAGATAAAGAGTCAATCCATTGACTAAAGTATCAAGCACACTCAGTTT Human > Chimp ------------- chr12:121361554-121361561 Template switch process: F1: L TTCACTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAA 1 F3: 4 TGTGTCAAGCACACTCAATTTTGCAGTGTCAAGTTGCTTTT R RF: TTCACTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAAAGACTGAAGATAAAGAGTCAATCCATTGACAAAAGTGTCAAGCACACTCAATTTTGCAGTGTCAAGTTGCTTTT RR: AAGTGACAGGACATTTTTACCCCGTGACTCCAATCTTTTTTTCTGACTTCTATTTCTCAGTTAGGTAACTGTTTTCACAGTTCGTGTGAGTTAAAACGTCACAGTTCAACGAAAA F2: 3 GTGACTCC 2 Unidirectional alignment (log-probability: -35.8) TCACTGTCCTGTAAAAATGGGGCACTGAGGTTAGAA----------------------------------AAAAcctcagtgtGTGTCAAGCACACTCAATTTTGCAGTGTCAAGTTGCTTT TCACTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAAAGACTGAAGATAAAGAGTCAATCCATTGACAAAA---------GTGTCAAGCACACTCAATTTTGCAGTGTCAAGTTGCTTT Template switch alignment (log-probability: -22.3) TCACTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAA|CCTCAGTG|tGTGTCAAGCACACTCAATTTTGCAGTGTCAAGTTGCTTT TCACTGTCCTGTAAAAATGGGGCACTGAGGTTAGAAAAAA|CCTCAGTG|AGTGTCAAGCACACTCAATTTTGCAGTGTCAAGTTGCTTT ========= Event 557 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCAGTGTATTTGACTTTAAAGCAGTAGAGATACTGCTGAATAATCACATTAAAGA Chimp: CCAGTGTATTTGACTTTAAAGCAGTAGAGATACTGCTGAATAATCACATTAAAGA ↑ 1 3 4 2 Gorilla: CCAGTGTATTTGACTTTAAAG---TCTCTCTACTGCTGAATAATCACATTAAAGA ↓ 1 3 4 2 Human: CCAGTGTATTTGACTTTAAAGCAGTAGAGATACTGCTGAATAATCACATTAAAGA Cluster: [ ] Orangutan: CCAGTGTATTTGACTTTAAAG---TCTCTCTACTGCTAAATAATCACATTAAAGA Gorilla > Human --------------- chr12:118413162-118413170 Template switch process: F1: L TAACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG 1 F3: 4 TACTGCTGAATAATCACATTAAAGAAATTGAGATGAAACA R RF: TAACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAGTCTCTCTACTGCTGAATAATCACATTAAAGAAATGGAGATGAAACA RR: ATTGAAAAATTTAAAAATTCGGTCACATAAACTGAAATTTCAGAGAGATGACGACTTATTAGTGTAATTTCTTTACCTCTACTTTGT F2: 3 AGAGATGAC 2 Unidirectional alignment (log-probability: -37.9) AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG-----CagtagagaTACTGCTGAATAATCACATTAAAGAAATtGAGATGAAACA AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAGTCTCTC--------TACTGCTGAATAATCACATTAAAGAAATGGAGATGAAACA Template switch alignment (log-probability: -22.4) AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG|CAGTAGAGA|TACTGCTGAATAATCACATTAAAGAAATtGAGATGAAACA AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG|CAGTAGAGA|TACTGCTGAATAATCACATTAAAGAAATGGAGATGAAACA Gorilla > Chimp --------------- chr12:121586027-121586035 Template switch process: F1: L TAACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG 1 F3: 4 TACTGCTGAATAATCACATTAAAGAAATTGAGATGAAACA R RF: TAACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAGTCTCTCTACTGCTGAATAATCACATTAAAGAAATGGAGATGAAACA RR: ATTGAAAAATTTAAAAATTCGGTCACATAAACTGAAATTTCAGAGAGATGACGACTTATTAGTGTAATTTCTTTACCTCTACTTTGT F2: 3 AGAGATGAC 2 Unidirectional alignment (log-probability: -37.9) AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG-----CagtagagaTACTGCTGAATAATCACATTAAAGAAATtGAGATGAAACA AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAGTCTCTC--------TACTGCTGAATAATCACATTAAAGAAATGGAGATGAAACA Template switch alignment (log-probability: -22.4) AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG|CAGTAGAGA|TACTGCTGAATAATCACATTAAAGAAATtGAGATGAAACA AACTTTTTAAATTTTTAAGCCAGTGTATTTGACTTTAAAG|CAGTAGAGA|TACTGCTGAATAATCACATTAAAGAAATGGAGATGAAACA ========= Event 558 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGT-----------------------AAGAAAAACATGATACTGAAA Chimp: ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGT-----------------------AAGAAAAACATGATACTGAAA ↓ 4 3 2 1 Gorilla: ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTATTCTAATAGTTTTATAAACTATTAGAAAAACATGATACTGAAA ↑ 4 3 2 1 Human: ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGT-----------------------AAGAAAAACATGATACTGAAA Cluster: [ ] Orangutan: ATAATATCTTAAATCTAGTTTTCACAAACTATTATTAGAAT-----------------------AAGAAAAACATGATACTGAAA Human > Gorilla --------------- chr12:118191757-118191765 Template switch process: F1: L ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA 1 F3: 4 TTTTATAAACTATT---------AGAAAAACATGATACTGAAATGGCTTTTCTGTTACAAGTT R RF: ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTAAGAAAAACATGATACTGAAATGGCTTTTCTGTTACAAGTT RR: TATTATAGAATTTAGATCAAAAATATTTGATAATCTTCTCATTCTTTTTGTACTATGACTTTACCGAAAAGACAATGTTCAA F2: 3 GATAATCTT 2 Unidirectional alignment (log-probability: -44) AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTAttctaatagttttataaactattAGAAAAACATGATACTGAAATGGCTT AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA-----------------------AGAAAAACATGATACTGAAATGGCTT Template switch alignment (log-probability: -27.4) AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA|TTCTAATAG|TTTTATAAACTATT---------AGAAAAACATGATACTGAAATGGCTT AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA|TTCTAATAG|TTTTATAAACTATTAGAAGAGTAAGAAAAACATGATACTGAAATGGCTT Chimp > Gorilla --------------- chr12:118191757-118191765 Template switch process: F1: L ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA 1 F3: 4 TTTTATAAACTATT---------AGAAAAACATGATACTGAAATGGCTTTTCTGTTACAAGTT R RF: ATAATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTAAGAAAAACATGATACTGAAATGGCTTTTCTGTTACAAGTT RR: TATTATAGAATTTAGATCAAAAATATTTGATAATCTTCTCATTCTTTTTGTACTATGACTTTACCGAAAAGACAATGTTCAA F2: 3 GATAATCTT 2 Unidirectional alignment (log-probability: -44) AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTAttctaatagttttataaactattAGAAAAACATGATACTGAAATGGCTT AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA-----------------------AGAAAAACATGATACTGAAATGGCTT Template switch alignment (log-probability: -27.4) AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA|TTCTAATAG|TTTTATAAACTATT---------AGAAAAACATGATACTGAAATGGCTT AATATCTTAAATCTAGTTTTTATAAACTATTAGAAGAGTA|TTCTAATAG|TTTTATAAACTATTAGAAGAGTAAGAAAAACATGATACTGAAATGGCTT ========= Event 559 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: actcagttcacacatacagatgttgacaATTAAACAATGTTTCA--AGGCAGT-ACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGC ↓ 3 2 1 4 ↑ 1 4 3 2 Chimp: ACTCAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAATTGTCAACATCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGC ↓ 1 4 3 2 ↑ 3 2 1 4 Gorilla: ACTCAGTGCACACATACAGATGTTGACAATTAAACAATGTTTCA--AGGCAGT-ACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGC Human: actcagttcacacatacagatgttgacaATTAAACAATGTTTCA--AGGCAGT-ACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGC Cluster: [ ] Orangutan: Chimp > Human ------------- chr12:121768563-121768568 Template switch process: F1: L CAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA 1 F3: 4 ACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA R RF: CAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAATTGTCAACATCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA RR: GTCAAGTGTGTATGTCTACAACTGTTAATTTGTTACAAAGTTAACAGTTGTAGAATATTATTTTGACGGGTCTTCTCCCGTGACCACCGTTT F2: 3 TGACGG 2 Unidirectional alignment (log-probability: -31.7) GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAaggcagtA----------CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA GTTCACACATACAGATGTTGACAATTAAACAATGTTTCA-------ATTGTCAACATCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA Template switch alignment (log-probability: -22.1) GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA|GGCAGT|aCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA|GGCAGT|TCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA Human > Chimp ------------- chr12:125117715-125117724 Template switch process: F1: L CAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA 1 F3: 4 CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA R RF: CAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAAGGCAGTACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA RR: GTCAAGTGTGTATGTCTACAACTGTTAATTTGTTACAAAGTTCCGTCATGAATATTATTTTGACGGGTCTTCTCCCGTGACCACCGTTT F2: 3 TACAACTGTT 2 Unidirectional alignment (log-probability: -35.9) GTTCACACATACAGATGTTGACAATTAAACAATGTTTCA-------AttgtcaacatCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAAGGCAGTA----------CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA Template switch alignment (log-probability: -16.5) GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA|TTGTCAACAT|CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA|TTGTCAACAT|CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA Gorilla > Chimp --------------- chr12:125117715-125117724 Template switch process: F1: L CAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA 1 F3: 4 CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA R RF: CAGTGCACACATACAGATGTTGACAATTAAACAATGTTTCAAGGCAGTACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA RR: GTCACGTGTGTATGTCTACAACTGTTAATTTGTTACAAAGTTCCGTCATGAATATTATTTTGACGGGTCTTCTCCCGTGACCACCGTTT F2: 3 TACAACTGTT 2 Unidirectional alignment (log-probability: -40.9) GTtCACACATACAGATGTTGACAATTAAACAATGTTTCA-------AttgtcaacatCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA GTGCACACATACAGATGTTGACAATTAAACAATGTTTCAAGGCAGTA----------CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA Template switch alignment (log-probability: -22.5) GTtCACACATACAGATGTTGACAATTAAACAATGTTTCAA|TTGTCAACAT|CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA GTGCACACATACAGATGTTGACAATTAAACAATGTTTCAA|TTGTCAACAT|CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA Chimp > Gorilla --------------- chr12:122107596-122107601 Template switch process: F1: L CAGTGCACACATACAGATGTTGACAATTAAACAATGTTTCAA 1 F3: 4 ACTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA R RF: CAGTTCACACATACAGATGTTGACAATTAAACAATGTTTCAATTGTCAACATCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAAA RR: GTCAAGTGTGTATGTCTACAACTGTTAATTTGTTACAAAGTTAACAGTTGTAGAATATTATTTTGACGGGTCTTCTCCCGTGACCACCGTTT F2: 3 TGACGG 2 Unidirectional alignment (log-probability: -36.7) GTgCACACATACAGATGTTGACAATTAAACAATGTTTCAA----------ggcagtaCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAATTGTCAACAT-------CTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA Template switch alignment (log-probability: -27.6) GTgCACACATACAGATGTTGACAATTAAACAATGTTTCAA|GGCAGT|aCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA GTTCACACATACAGATGTTGACAATTAAACAATGTTTCAA|GGCAGT|TCTTATAATAAAACTGCCCAGAAGAGGGCACTGGTGGCAA ========= Event 560 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGGTGTGATTGGAGCTACTGCCATGCATTGCATGGCACCCCACTGTGCAGTGTCTGTACCAAT Chimp: AAGGTGTGATTGGAGCTTCTGCCATGCATT-----GGTCCCCACTGTGCAGTGTCTGGACCAAT Gorilla: AAGGTGTGATTGGAGCTACTGCCATGCATT-----GGTCCCCATTGTGCAGTGTCTGTACCAAT ↓ 3 2 1 4 Human: AAGGTGTGATTGGAGCTACTGCCATGCATTGCATGGCACCCCACTGTGCAGTGTCTGTACCAAT Cluster: [ ] Orangutan: AAGGTGTGATTGGAGCTACTGCCATGCATT-----GGTCCCCACTGTGCAGCGTCTGTACCAAT Gorilla > Human --------------- chr12:7111984-7111990 Template switch process: F1: L TCCCCTCTGGGAAGGTGTGATTGGAGCTACTGCCATGCATTG 1 F3: 4 CCCCACTGTGCAGTGTCTGTACCAATGATCTAATTCGTTCCTCACA R RF: TCCCCTCTGGGAAGGTGTGATTGGAGCTACTGCCATGCATTGGTCCCCATTGTGCAGTGTCTGTACCAATGACCTAATTCGTTCCTCACA RR: AGGGGAGACCCTTCCACACTAACCTCGATGACGGTACGTAACCAGGGGTAACACGTCACAGACATGGTTACTGGATTAAGCAAGGAGTGT F2: 3 ACGGTAC 2 Unidirectional alignment (log-probability: -40.3) CCCTCTGGGAAGGTGTGATTGGAGCTACTGCCATGCATTgcatgGcaCCCCAcTGTGCAGTGTCTGTACCAATGAtCTAATTCGTTC CCCTCTGGGAAGGTGTGATTGGAGCTACTGCCATGCATT-----GGTCCCCATTGTGCAGTGTCTGTACCAATGACCTAATTCGTTC Template switch alignment (log-probability: -27.8) CCCTCTGGGAAGGTGTGATTGGAGCTACTGCCATGCATTG|CATGGCA|CCCCAcTGTGCAGTGTCTGTACCAATGAtCTAATTCGTTC CCCTCTGGGAAGGTGTGATTGGAGCTACTGCCATGCATTG|CATGGCA|CCCCATTGTGCAGTGTCTGTACCAATGACCTAATTCGTTC ========= Event 561 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAAAAGTGTTCTTTTCCTAACCGGGTCCTCACCCGGTTAGGATCTGGGGTGTCTGGCTTTG ↑ 3 1 4 2 Chimp: CAAAAAGTGTTCTTTTCCTAACCGG-----------GTGAGGATCTGGGGTGTCTGGCTTTG Gorilla: CAAAAAGTGTTCTTTTCCTAACCGG-----------GTGAGGATCTGGGGTGTCTGGCTTTG ↓ 3 1 4 2 Human: CAAAAAGTGTTCTTTTCCTAACCGGGTCCTCACCCGGTTAGGATCTGGGGTGTCTGGCTTTG Cluster: [ ] Orangutan: CAAAAAGTGTTCTTTTCCTAACCGG-----------GTGAGGATCTGGGGTGTCTGGCTTTG Chimp > Human ------------- chr12:117023728-117023739 Template switch process: F1: L AGTCAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGT 1 F3: 4 AGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC R RF: AGTCAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGTGAGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC RR: TCAGTTCACTTTATGGGTTTTTCACAAGAAAAGGATTGGCCCACTCCTAGACCCCACAGACCGAAACATCGAGAACGGAAATTG F2: 3 TTGGCCCACTCC 2 Unidirectional alignment (log-probability: -32.8) CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGggtcctcacccGGTtAGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCG-----------GGTGAGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC Template switch alignment (log-probability: -16.8) CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGT|CCTCACCCGGTT|AGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGT|CCTCACCCGGTT|AGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC Gorilla > Human --------------- chr12:117023728-117023739 Template switch process: F1: L AGTCAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGT 1 F3: 4 AGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC R RF: AGTCAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGTGAGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC RR: TCAGTTCACTTTATGGGTTTTTCACAAGAAAAGGATTGGCCCACTCCTAGACCCCACAGACCGAAACATCGAGAACGGAAATTG F2: 3 TTGGCCCACTCC 2 Unidirectional alignment (log-probability: -32.3) CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGggtcctcacccGGTtAGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCG-----------GGTGAGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC Template switch alignment (log-probability: -17.3) CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGT|CCTCACCCGGTT|AGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC CAAGTGAAATACCCAAAAAGTGTTCTTTTCCTAACCGGGT|CCTCACCCGGTT|AGGATCTGGGGTGTCTGGCTTTGTAGCTCTTGCCTTTAAC ========= Event 562 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGCCCACACTTCAGCTCAGCTAGG--GCTTCCCAGCTTGTCTTACTACCACTAATT Chimp: TGCCCACACTTCAGCTCAGCTAGG--GCTTCCCAGCTTGTCTTACTACCACTAATT ↑ 3 1 2 4 Gorilla: TGCCCACACTTCAGCTCAGCTGGGAAGC------TCTTGTCTTACTACCACTAAAT ↓ 3 1 2 4 Human: TGCCCACACTTCAGCTCAGCTAGG--GCTTCCCAGCTTGTCTTACTACCACTAATT Cluster: [ ] Orangutan: TGCCCACACCTCAGCTCAGCTGGGAAGC------TCTTGTCTTACTACCACTAATT Gorilla > Human --------------- chr1:212501052-212501060 Template switch process: F1: L CCTTGAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTAGG 1 F3: 4 CTTGTCTTACTACCACTAATTAGTCACTTTCATTGCATAC R RF: CCTTGAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTGGGAAGCTCTTGTCTTACTACCACTAAATAGTCACTTTCATTGCATAC RR: GGAACTTAACAAAGAGTCACACGGGTGTGAAGTCGAGTCGACCCTTCGAGAACAGAATGATGGTGATTTATCAGTGAAAGTAACGTATG F2: 3 GACCCTTCG 2 Unidirectional alignment (log-probability: -40.5) GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTaGG--GCTtcccagCTTGTCTTACTACCACTAAtTAGTCACTTTCATTGCATAC GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTGGGAAGCT------CTTGTCTTACTACCACTAAATAGTCACTTTCATTGCATAC Template switch alignment (log-probability: -28) GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTaGG|GCTTCCCAG|CTTGTCTTACTACCACTAAtTAGTCACTTTCATTGCATAC GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTGGG|GCTTCCCAG|CTTGTCTTACTACCACTAAATAGTCACTTTCATTGCATAC Gorilla > Chimp --------------- chr1:191454054-191454062 Template switch process: F1: L CTTTGAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTAGG 1 F3: 4 CTTGTCTTACTACCACTAATTAGTCACTTTCATTGCATAC R RF: CCTTGAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTGGGAAGCTCTTGTCTTACTACCACTAAATAGTCACTTTCATTGCATAC RR: GGAACTTAACAAAGAGTCACACGGGTGTGAAGTCGAGTCGACCCTTCGAGAACAGAATGATGGTGATTTATCAGTGAAAGTAACGTATG F2: 3 GACCCTTCG 2 Unidirectional alignment (log-probability: -46) GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTaGG--GCTtcccagCTTGTCTTACTACCACTAAtTAGTCACTTTCATTGCATAC GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTGGGAAGCT------CTTGTCTTACTACCACTAAATAGTCACTTTCATTGCATAC Template switch alignment (log-probability: -33.5) GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTaGG|GCTTCCCAG|CTTGTCTTACTACCACTAAtTAGTCACTTTCATTGCATAC GAATTGTTTCTCAGTGTGCCCACACTTCAGCTCAGCTGGG|GCTTCCCAG|CTTGTCTTACTACCACTAAATAGTCACTTTCATTGCATAC ========= Event 563 ========= Phylogenetic placement: unresolved Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: CAGGACCCAGCTAGATTCTGGAACTAGATCGGGAAGAAGGCAAGTGGCTCTACACTGGAGTGCAGGAGAGGTGGGATGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCGGTTCAATTTGCAATAGAAGCAAACtg ↓ 3 2 1 4 Chimp: CAGGACCCAGTTAGATTCTGGAACTAGATCGAGAAGAAGGCAAGTGGCTCTACACTGGAGTGCAGGAGACGTGGGATGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCAGTTCCATTTGCAATAGAAGCAAACtg Gorilla: CAGGACCCGGTTAGATTCTGGAACTAGATCGGGAAGAAGGCAAGTGGCTCTACACTGGAGTGCAGGAGAGGTGGGATGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCAGTTCAATTTGCAATAGAAGCAAACtg Human: CAGGACCCAGCTAGATTCTGGAACTAGATCGGGAAGAAGGCAAGTGGCTCTACACTGGAGTGCAGGAGAGGTGGGATGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCGGTTCAATTTGCAATAGAAGCAAACtg Cluster: [ ] Orangutan: CAGGACCCAGTTAGATTCTGGAACTAAATCAGGAAGGAGGCAAGTGGCTCTACACTGGAGTGCAGGAGAGGTGGGATGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTTCCGGTTCAATTTGCAATAGAAGAAAACTC Human > Chimp ------------- chr12:5926410-5926415 Template switch process: F1: L TGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCC 1 F3: 4 ATTTGCAATAGAAGCAAACTGTGTGTGTGTGTGTGTGTGT R RF: GGAACTAGATCGGGAAGAAGGCAAGTGGCTCTACACTGGAGTGCAGGAGAGGTGGGATGAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCGGTTCAATTTGCAATAGAAGCAAACTGTGTGTGTGTGTGTGTGTGT RR: CCTTGATCTAGCCCTTCTTCCGTTCACCGAGATGTGACCTCACGTCCTCTCCACCCTACTCTGGGAACCCCTATTGTTTCTCGAAGTTTATTGGACGGCCAAGTTAAACGTTATCTTCGTTTGACACACACACACACACACACA F2: 3 CCTTGA 2 Unidirectional alignment (log-probability: -25.7) GAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCaGTTCcATTTGCAATAGAAGCAAACTGTGTGTGTGTGTGTGTgtgt GAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCCGGTTCAATTTGCAATAGAAGCAAACTGTGTGTGTGTGTGTGT---- Template switch alignment (log-probability: -16) GAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCC|AGTTCC|ATTTGCAATAGAAGCAAACTGTGTGTGTGTGTGTGTGTGT GAGACCCTTGGGGATAACAAAGAGCTTCAAATAACCTGCC|AGTTCC|ATTTGCAATAGAAGCAAACTGTGTGTGTGTGTGTGTGTGT ========= Event 564 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CGGCTTTGCTCACCCACCAACAGCTA-------GGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGAGACA ↓ 1 4 3 2 Chimp: CGGCTTTGCTCACCCACCAACTTCCAGCTCTTCTGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGAGACA ↑ 1 4 3 2 Gorilla: CGGCTTTGCTCACCCACCAACAGCTA-------GGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGAGACA Human: CGGCTTTGCTCACCCACCAACAGCTA-------GGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGAGACA Cluster: [ ] Orangutan: TGGCTTTGCTCACCCACCAACAGCTA-------GGAGCTGGAAGGCTCAGAAGAGCTGGGGCGGGCGT-GGAGAGACA Human > Chimp ------------- chr12:10839557-10839566 Template switch process: F1: L CTCTTCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACTTC 1 F3: 4 GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA R RF: CTCTTCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACAGCTAGGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA RR: GAGAAGGGGGTCGAAAACCAGCCGAAACGAGTGGGTGGTTGTCGATCCTCGACCTTCCGAGTCTTCTCGACCCCACCCGTACCCTCT F2: 3 TCTTCTCGAC 2 Unidirectional alignment (log-probability: -39) TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACttCcAGctcttctGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACAGCTAG-------GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA Template switch alignment (log-probability: -28.6) TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACttC|CAGCTCTTCT|GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACAGC|CAGCTCTTCT|GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA Gorilla > Chimp --------------- chr12:10839557-10839566 Template switch process: F1: L CTCTTCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACTTC 1 F3: 4 GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA R RF: CTCTTCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACAGCTAGGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA RR: GAGAAGGGGGTCGAAAACCAGCCGAAACGAGTGGGTGGTTGTCGATCCTCGACCTTCCGAGTCTTCTCGACCCCACCCGTACCCTCT F2: 3 TCTTCTCGAC 2 Unidirectional alignment (log-probability: -37.6) TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACttCcAGctcttctGAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACAGCTAG-------GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA Template switch alignment (log-probability: -28.1) TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACttC|CAGCTCTTCT|GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA TCCCCCAGCTTTTGGTCGGCTTTGCTCACCCACCAACAGC|CAGCTCTTCT|GAGCTGGAAGGCTCAGAAGAGCTGGGGTGGGCATGGGAGA ========= Event 565 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTGCTATAACTATGGAGTAAAACTTTGGGC---TCTCAAGAGGATTTCAAATCTC ↓ 3 1 2 4 Chimp: CTCTGCTATAACTATGGAGTAAAACTCATAGTTTTACTCAAGAGGATTTCAAATCTC ↑ 3 1 2 4 Gorilla: CTCTGCTATAACTATGGAGTAAAACTTTGGGC---TCTCAAGAGGATTTCAAATCTC Human: CTCTGCTATAACTATGGAGTAAAACTTTGGGC---TCTCAAGAGGATTTCAAATCTC Cluster: [ ] Orangutan: CTCTGCTATAACTATGGAGTAAAACTTTGGGC---TCTCAAGAGGATTTCAAATCTC Human > Chimp ------------- chr1:191692667-191692676 Template switch process: F1: L TATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACT 1 F3: 4 CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT R RF: TATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACTTTGGGCTCTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT RR: ATAAAGATAAAATTTGAGACGATATTGATACCTCATTTTGAAACCCGAGAGTTCTCCTAAAGTTTAGAGTCGACAGACGGACCCCTGA F2: 3 ATTTTGATAC 2 Unidirectional alignment (log-probability: -35.9) ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAA-------CTcatagttttaCTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACTTTGGGCT----------CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT Template switch alignment (log-probability: -22.5) ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACT|CAtAGTTTTA|CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACT|CAAAGTTTTA|CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT Gorilla > Chimp --------------- chr1:191692667-191692676 Template switch process: F1: L TATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACT 1 F3: 4 CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT R RF: TATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACTTTGGGCTCTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT RR: ATAAAGATAAAATTTGAGACGATATTGATACCTCATTTTGAAACCCGAGAGTTCTCCTAAAGTTTAGAGTCGACAGACGGACCCCTGA F2: 3 ATTTTGATAC 2 Unidirectional alignment (log-probability: -35.4) ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAA-------CTcatagttttaCTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACTTTGGGCT----------CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT Template switch alignment (log-probability: -22.5) ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACT|CAtAGTTTTA|CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT ATTTCTATTTTAAACTCTGCTATAACTATGGAGTAAAACT|CAAAGTTTTA|CTCAAGAGGATTTCAAATCTCAGCTGTCTGCCTGGGGACT ========= Event 566 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTCTATCTGATGCACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGAT----------------------TCTCAGGTAAAGAAAAAAATAAG ↓ 3 2 4 1 Chimp: tttctatctgACGCACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGAT-----------TCTGCATTTGTTCTCAGGTAAAGaaaaaaaTAAG Gorilla: TTTCTATCTGACGCACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCTGCATTTGT-----------TCTCAGGTAAAGaaaaaaaTAAG ↑ 3 2 4 1 Human: TTTCTATCTGATGCACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGAT----------------------TCTCAGGTAAAGAAAAAAATAAG Cluster: [ ] Orangutan: TTGCTATCTGACGCACAAACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCTACATTTGT-----------TCTCAGGTAAAGAAAAAAATAAG Human > Chimp ------------- chr12:5275678-5275684 Template switch process: F1: L CACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCT 1 F3: 4 TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGAT R RF: CACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGAT RR: GTGTGTGTTTACGGTAAAAACTTACACATCCCTTCGAGCTAAGAGTCCATTTCTTTTTTTATTCTACAGAGTTATTTTCTA F2: 3 GTTTACG 2 Unidirectional alignment (log-probability: -26.7) CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGAttctgcatttgTTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGA-----------TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA Template switch alignment (log-probability: -16.2) CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCT|GCATTTG|TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCT|GCATTTG|TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA Human > Gorilla --------------- chr12:4986886-4986892 Template switch process: F1: L CACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCT 1 F3: 4 TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGAT R RF: CACACACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGAT RR: GTGTGTGTTTACGGTAAAAACTTACACATCCCTTCGAGCTAAGAGTCCATTTCTTTTTTTATTCTACAGAGTTATTTTCTA F2: 3 GTTTACG 2 Unidirectional alignment (log-probability: -26.7) CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGAttctgcatttgTTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGA-----------TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA Template switch alignment (log-probability: -16.7) CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCT|GCATTTG|TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA CACAAATGCCATTTTTGAATGTGTAGGGAAGCTCGATTCT|GCATTTG|TTCTCAGGTAAAGAAAAAAATAAGATGTCTCAATAAAAGA ========= Event 567 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGAAATGAAAACCTGCAATGCATTTTTAGCTaaaa----aaaa----aaaaTGCACCAATAGAGGCAAAGAGGA Chimp: TCAGAAATGAAAACCTGCAATTCC-ATTTAGCCaaaa----aaaaaaaaaaaaTGCACCAATAGAGGCAAAGAGGA ↓ 1 4 3 2 Gorilla: TCAGAAATGAAAACCTGCAATGCATTTTTAGCCaaaa-------a----aaaaTGCACCAATAGAGGCAAAGAGGA Human: TCAGAAATGAAAACCTGCAATGCATTTTTAGCTaaaa----aaaa----aaaaTGCACCAATAGAGGCAAAGAGGA Cluster: [ ] Orangutan: TCAGAAATGAAAACCTGCAATTCATTTTTAGCCaaaaaaaa---a----aaaaTGCACCAATAGAGGCAAAGAGGA Chimp > Gorilla --------------- chr12:126413392-126413397 Template switch process: F1: L AAGGGACATACAAAGGAATATCAGAAATGAAAACCTGCAAT 1 F3: 4 TTAGCC-------AAAAAAAAATGCACCAATAGAGGCAA R RF: AAGGGACATACAAAGGAATATCAGAAATGAAAACCTGCAATTCCATTTAGCCAAAAAAAAAAAAAAAATGCACCAATAGAGGCAA RR: TTCCCTGTATGTTTCCTTATAGTCTTTACTTTTGGACGTTAAGGTAAATCGGTTTTTTTTTTTTTTTTACGTGGTTATCTCCGTT F2: 3 TTTACG 2 Unidirectional alignment (log-probability: -36.5) AGGGACATACAAAGGAATATCAGAAATGAAAACCTGCAatgcATT---TTTAGCC-------AAAAAAAAATGCACCAATAGAGGCAA AGGGACATACAAAGGAATATCAGAAATGAAAACCTGCA----ATTCCATTTAGCCAAAAAAAAAAAAAAAATGCACCAATAGAGGCAA Template switch alignment (log-probability: -26.4) AGGGACATACAAAGGAATATCAGAAATGAAAACCTGCAAT|GCATTT|TTAGCC-------AAAAAAAAATGCACCAATAGAGGCAA AGGGACATACAAAGGAATATCAGAAATGAAAACCTGCAAT|GCATTT|TTAGCCAAAAAAAAAAAAAAAATGCACCAATAGAGGCAA ========= Event 568 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC---------GGGTGTCTCTCTCCATCAGATT ↓ 3 2 1 4 Chimp: CATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGACTGACATAAATGGTGTCTCTCTCCATCAGATT ↑ 3 2 1 4 Gorilla: CATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC---------GAGTGTCTCTCTCCATCAGATT Human: CATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC---------GGGTGTCTCTCTCCATCAGATT Cluster: [ ] Orangutan: CATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC---------CGGTGTCTTTCTCCATCAGATT Human > Chimp ------------- chr12:120357461-120357470 Template switch process: F1: L CCCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC 1 F3: 4 GGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT R RF: CCCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGACGGGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT RR: GGGTAAAGAGTTTGGGGTCTTTAAATACAGTCAAGGTTCTGCCCACAGAGAGAGGTAGTCTAATATTGGAAACCGACCCGCA F2: 3 TAAATACAGT 2 Unidirectional alignment (log-probability: -29.9) CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGACtgacataaatGGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC---------GGGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT Template switch alignment (log-probability: -16.5) CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC|TGACATAAAT|GGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC|TGACATAAAT|GGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT Gorilla > Chimp --------------- chr12:120357461-120357470 Template switch process: F1: L CCCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC 1 F3: 4 GGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGTG R RF: CCCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGACGAGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGTG RR: GGGTAAAGAGTTTGGGGTCTTTAAATACAGTCAAGGTTCTGCTCACAGAGAGAGGTAGTCTAATATTGGAAACCGACCCGCAC F2: 3 TAAATACAGT 2 Unidirectional alignment (log-probability: -33.6) CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGACtGAcataaatgGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC-GA--------GTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT Template switch alignment (log-probability: -22.5) CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC|TGACATAAAT|gGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT CCATTTCTCAAACCCCAGAAATTTATGTCAGTTCCAAGAC|TGACATAAAT|AGTGTCTCTCTCCATCAGATTATAACCTTTGGCTGGGCGT ========= Event 569 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATGGAGATGCAGTCTAGAAA----------GAGCATTTGCAAATATTATGGCTTACAT----- Chimp: TATGGAGATGCAGTCTAGAAA----------GAGCATTTGCAAATATTATGGCTTACAT----- ↓ 1 43 2 Gorilla: TATGGAGATGCAGTCTAGAAATTTGCAAATGCAGCATTTGCAAATATTATGGTTTACAT----- ↑ 1 43 2 Human: TATGGAGATGCAGTCTAGAAA----------GAGCATTTGCAAATATTATGGCTTACAT----- Cluster: [ ] Orangutan: TATGGAGATGCAGTCTAGAAA----------GAGCA-TTGCAAATANNNNNNNNNNTATATAGC Human > Gorilla --------------- chr12:7444958-7444968 Template switch process: F1: L AAAAATATACTTTGCAAAACTATGGAGATGCAGTCTAGAAA 1 F3: 4 AGCATTTGCAAATATTATGGTTTACATGCATATGGAATAA R RF: AAAAATGTACTTTGCAAAACTATGGAGATGCAGTCTAGAAAGAGCATTTGCAAATATTATGGCTTACATGCATATGGAATAA RR: TTTTTACATGAAACGTTTTGATACCTCTACGTCAGATCTTTCTCGTAAACGTTTATAATACCGAATGTACGTATACCTTATT F2: 3 CGTAAACGTTT 2 Unidirectional alignment (log-probability: -41.8) AAAATaTACTTTGCAAAACTATGGAGATGCAGTCTAGAAAtttgcaaatgcAGCATTTGCAAATATTATGGtTTACATGCATATGGAATAA AAAATGTACTTTGCAAAACTATGGAGATGCAGTCTAGAAA----------GAGCATTTGCAAATATTATGGCTTACATGCATATGGAATAA Template switch alignment (log-probability: -28.2) AAAATaTACTTTGCAAAACTATGGAGATGCAGTCTAGAAA|TTTGCAAATGC|AGCATTTGCAAATATTATGGtTTACATGCATATGGAATAA AAAATGTACTTTGCAAAACTATGGAGATGCAGTCTAGAAA|TTTGCAAATGC|AGCATTTGCAAATATTATGGCTTACATGCATATGGAATAA Chimp > Gorilla --------------- chr12:7444958-7444968 Template switch process: F1: L AAAAATATACTTTGCAAAACTATGGAGATGCAGTCTAGAAA 1 F3: 4 AGCATTTGCAAATATTATGGTTTACATGCATATGGAATAA R RF: AAAAATGTACTTTGCAAAACTATGGAGATGCAGTCTAGAAAGAGCATTTGCAAATATTATGGCTTACATGCATATGGAATAA RR: TTTTTACATGAAACGTTTTGATACCTCTACGTCAGATCTTTCTCGTAAACGTTTATAATACCGAATGTACGTATACCTTATT F2: 3 CGTAAACGTTT 2 Unidirectional alignment (log-probability: -41.8) AAAATaTACTTTGCAAAACTATGGAGATGCAGTCTAGAAAtttgcaaatgcAGCATTTGCAAATATTATGGtTTACATGCATATGGAATAA AAAATGTACTTTGCAAAACTATGGAGATGCAGTCTAGAAA----------GAGCATTTGCAAATATTATGGCTTACATGCATATGGAATAA Template switch alignment (log-probability: -28.2) AAAATaTACTTTGCAAAACTATGGAGATGCAGTCTAGAAA|TTTGCAAATGC|AGCATTTGCAAATATTATGGtTTACATGCATATGGAATAA AAAATGTACTTTGCAAAACTATGGAGATGCAGTCTAGAAA|TTTGCAAATGC|AGCATTTGCAAATATTATGGCTTACATGCATATGGAATAA ========= Event 570 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCACCTGCAGGGAGGCAGCTGGAGGC------------ATGACGGCTCAGCACTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG-------------CCCTCATGCCTCCCGGTAACCAGGTGTCGTCA Chimp: CCACCTGCAGGGAGGCAGCTGGAGGC------------ATGACGGCTCAGCACTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG-------------CCCTCATGCCTCCCGGTAGCCAGGTGTCGTCA ↑ 1 4 3 2 Gorilla: CCACCTGCAGGGAGGCAGCTGCAGGC------------------------AGCTCCAGGTGCCTGGAGGCATTCCCGTATGCgctgagccctcatgctgagccctcatgcCTCCCGGTAGCCAGGTGTCGTCA ↓ 1 4 3 2 Human: CCACCTGCAGGGAGGCAGCTGGAGGC------------ATGACGGCTCAGCACTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG-------------CCCTCATGCCTCCCGGTAACCAGGTGTCGTCA Cluster: [ ] Orangutan: CCACCTGCAGGGAGGCAGCTGGAGGCATGACGGCTCAG------------CACTCCAGGTGCCTGGAGGCATTCCCGTATGTGCCGAG-------------CCCTCATGCTTCCCGGTAGCCAGGTGTCGTCA Gorilla > Human --------------- chr12:10169619-10169637 Template switch process: F1: L CTCACATTGATGACCTCATCCCACCTGCAGGGAGGCAGCTG 1 F3: 4 CTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG R RF: CTCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTGCAGGCAGCTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAGCCCTCATGCTGAGCCCTCATGCCTC RR: GAGTGCAACTACTGGAGTAGGGTGGACGTCCCTCCGTCGACGTCCGTCGAGGTCCACGGACCTCCGTAAGGGCATACGCGACTCGGGAGTACGACTCGGGAGTACGGAG F2: 3 ACGACTCGGCAGTACGGAG 2 Unidirectional alignment (log-probability: -51.7) TCACaTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTGgAGGCAtgacggctcagcaCTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG---- TCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTGCAGGCA------------GCTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAGCCCT Template switch alignment (log-probability: -29.1) TCACaTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTG|GAGGCATGAcGGCTCAGCA|CTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG TCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTG|GAGGCATGAGGGCTCAGCA|CTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG Gorilla > Chimp --------------- chr12:10618008-10618026 Template switch process: F1: L CTCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTG 1 F3: 4 CTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG R RF: CTCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTGCAGGCAGCTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAGCCCTCATGCTGAGCCCTCATGCCTC RR: GAGTGCAACTACTGGAGTAGGGTGGACGTCCCTCCGTCGACGTCCGTCGAGGTCCACGGACCTCCGTAAGGGCATACGCGACTCGGGAGTACGACTCGGGAGTACGGAG F2: 3 ACGACTCGGCAGTACGGAG 2 Unidirectional alignment (log-probability: -46.2) TCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTGgAGGCAtgacggctcagcaCTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG---- TCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTGCAGGCA------------GCTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAGCCCT Template switch alignment (log-probability: -23.6) TCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTG|GAGGCATGAcGGCTCAGCA|CTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG TCACGTTGATGACCTCATCCCACCTGCAGGGAGGCAGCTG|GAGGCATGAGGGCTCAGCA|CTCCAGGTGCCTGGAGGCATTCCCGTATGCGCTGAG ========= Event 571 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTTCATCATTTGGGGATGGTTATACAAAAACTCTGtttt-------tt-----ttGTAAGGATGGGAAGGGCATT Chimp: TTTTCATCATTTGGGGATGGTTATACAAAAACAGAGTTTT-------TGTATAACTGTAAGGATGGGAAGGGCATT ↑ 3 1 2 4 Gorilla: TTTTCATCATTTGGGGATGGTTATACAAAAACTCTGTTTT---------------TGTAAGGATGGGAAGGGCATT Human: TTTTCATCATTTGGGGATGGTTATACAAAAACTCTGtttt-------tt-----ttGTAAGGATGGGAAGGGCATT Cluster: [ ] Orangutan: TTTTCATCATTTGGGGATGGTC-------AACAGAGTTTTTGTATAA---------CTAAGGATGGGAAGGGCATT Gorilla > Chimp --------------- chr12:18890492-18890507 Template switch process: F1: L ACCATATCTTTTTCATCATTTGGGGATGGTTATACAAAAAC 1 F3: 4 TGTAAGGATGGGAAGGGCATTATCTCTACTACCTTTAACA R RF: ACCATATCTTTTTCATCATTTGGGGATGGTTATACAAAAACTCTGTTTTTGTAAGGATGGGAAGGGCATTATCTCTACTAGCTTTAACA RR: TGGTATAGAAAAAGTAGTAAACCCCTACCAATATGTTTTTGAGACAAAAACATTCCTACCCTTCCCGTAATAGAGATGATCGAAATTGT F2: 3 CAATATGTTTTTGAGA 2 Unidirectional alignment (log-probability: -44.6) CCATATCTTTTTCATCATTTGGGGATGGTTATACAAAAACagaGTTTTtgtataacTGTAAGGATGGGAAGGGCATTATCTCTACTAcCTTTAACA CCATATCTTTTTCATCATTTGGGGATGGTTATACAAAAACTCTGTTTT--------TGTAAGGATGGGAAGGGCATTATCTCTACTAGCTTTAACA Template switch alignment (log-probability: -23.3) CCATATCTTTTTCATCATTTGGGGATGGTTATACAAAAAC|AGAGTTTTTGTATAAC|TGTAAGGATGGGAAGGGCATTATCTCTACTAcCTTTAACA CCATATCTTTTTCATCATTTGGGGATGGTTATACAAAAAC|AGAGTTTTTGTATAAC|TGTAAGGATGGGAAGGGCATTATCTCTACTAGCTTTAACA ========= Event 572 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGATGTTGTTCCTGCAGGGGAC--------------TATGTTTTAGACTATAAAACATtttgtattttgcacagactgaaa ↓ 3 1 4 2 ↑ 1 3 4 2 Chimp: AGATGTTGTTCCTGCAGGGGAT-------TAGACAAAATGTTTTATAGTCTAAAACATTTTGTATTTTGCACAGACTGAAA Gorilla: AGATGTTGTTCCTGCAGGGGATTAGACAA-------AATGTTTTACAGTCTAAAACATTTTGTATTTTGCAGAGACTGAAA Human: AGATGTTGTTCCTGCAGGGGAC--------------TATGTTTTAGACTATAAAACATtttgtattttgcacagactgaaa Cluster: [ ] Orangutan: AGATGTTGTTCCTGCAGGGGATTAGACAA-------AATGTTTTATAGTCTAAAACATTTTGTATTTTGTACAGACTG--a Chimp > Human ------------- chr12:11947124-11947135 Template switch process: F1: L AAGATTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGACTA 1 F3: 4 TAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC R RF: AAGATTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGATTAGACAAAATGTTTTATAGTCTAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC RR: TTCTAAATGGACGGAACCTATCTACAACAAGGACGTCCCCTAATCTGTTTTACAAAATATCAGATTTTGTAAAACATAAAACGTGTCTGACTTTTGAAAAAAG F2: 3 ATCAGATTTTGT 2 Unidirectional alignment (log-probability: -35.4) TTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGAcT-------ATGTTTTAgAcTaTAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC TTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGATTAGACAAAATGTTTTATAGTCTAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC Template switch alignment (log-probability: -22.8) TTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGAcTA|TGTTTTAGACTA|TAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC TTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGATTA|TGTTTTAGACTA|TAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC Human > Chimp ------------- chr12:12542728-12542743 Template switch process: F1: L AAGATTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGA-------TTAGAC 1 F3: 4 TAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC R RF: AAGATTTACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGACTATGTTTTAGACTATAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC RR: TTCTAAATGGACGGAACCTATCTACAACAAGGACGTCCCCTGATACAAAATCTGATATTTTGTAAAACATAAAACGTGTCTGACTTTTGAAAAAAG F2: 3 CTGATATTTTGTAAAA 2 Unidirectional alignment (log-probability: -45.1) ACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGAtTagacaaaATGTTTTAtAgTcTAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC ACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGACT-------ATGTTTTAGACTATAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC Template switch alignment (log-probability: -27.9) ACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGA-------TTAGAC|AAAATGTTTTATAGTC|TAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC ACCTGCCTTGGATAGATGTTGTTCCTGCAGGGGACTATGTTTTAGAC|AAAATGTTTTATAGTC|TAAAACATTTTGTATTTTGCACAGACTGAAAACTTTTTTC ========= Event 573 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: cataatgagatcatgcagtgtttat-----------------------cttgagttgaactttttttt-tCCATCAAGCCAATTGTTTTAGCGTCTTTATGTATTTTAGAAACAAATGAGAATTGTAATGT--------CAAGGCCTTCAGCATTGACTAGT Chimp: cataatgagatcgtgcagtgtttat-----------------------cttGAGTTGAACtttttttt-tCCATCAAGCCAATTGTTTTAGCGTCTTTATGTATTTTAGAAGCAAATGAGAATTGTAATGG----ATAAACAGGCCTTCAGCATTGACTAGT Gorilla: cataatgagattatgcagtgtttatcttgagttgaacgcagtgtttatcttgagttgaactttttttttCCCATCAAGCCAATTGTTTTAGCGTCTTTATGTATTTTAGAAGAAAATGAGAATTGTAATGGATAA----ACAGGCCTTCAGCATTGACTAGT ↑ 3 2 1 4 Human: cataatgagatcatgcagtgtttat-----------------------cttgagttgaactttttttt-tCCATCAAGCCAATTGTTTTAGCGTCTTTATGTATTTTAGAAACAAATGAGAATTGTAATGT--------CAAGGCCTTCAGCATTGACTAGT Cluster: [ ] Orangutan: cataatgagatcatgcagtgt----------------------------ttgAGTTGAACtttt-ttt-tCCATCAAGCCAACTGTTTTAGTGTCTTTATGTATTTTAGAAGCAAATGAGAATTGTAATGGATAA----ACAGGCCTTCAGCATTGACTAGT Human > Gorilla --------------- chr12:11997596-11997602 Template switch process: F1: L AGCGTCTTTATGTATTTTAGAAGAAAATGAGAATTGTAATG 1 F3: 4 AGGCCTTCAGCATTGACTAGTTTGGAGCTAACTCTTAGAA R RF: GTTTATCTTGAGTTGAACTTTTTTTTTCCATCAAGCCAATTGTTTTAGCGTCTTTATGTATTTTAGAAACAAATGAGAATTGTAATGTCAAGGCCTTCAGCATTGACTAGTTTGGAGCTAACTCTTAGAA RR: CAAATAGAACTCAACTTGAAAAAAAAAGGTAGTTCGGTTAACAAAATCGCAGAAATACATAAAATCTTTGTTTACTCTTAACATTACAGTTCCGGAAGTCGTAACTGATCAAACCTCGATTGAGAATCTT F2: 3 CAAATAG 2 Unidirectional alignment (log-probability: -41.9) GCGTCTTTATGTATTTTAGAAgaAAATGAGAATTGTAATGgataaac---AGGCCTTCAGCATTGACTAGTTTGGAGCTAACTCTTAGAA GCGTCTTTATGTATTTTAGAAACAAATGAGAATTGTAATG-------TCAAGGCCTTCAGCATTGACTAGTTTGGAGCTAACTCTTAGAA Template switch alignment (log-probability: -27.7) GCGTCTTTATGTATTTTAGAAgaAAATGAGAATTGTAATG|GATAAAC|AGGCCTTCAGCATTGACTAGTTTGGAGCTAACTCTTAGAA GCGTCTTTATGTATTTTAGAAACAAATGAGAATTGTAATG|GATAAAC|AGGCCTTCAGCATTGACTAGTTTGGAGCTAACTCTTAGAA ========= Event 574 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTCCCATTTGTGGTGACATACCACAATAAGCCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT ↑ 4 1 3 2 Chimp: TTTCCCATTTGTGGTGACATA----------CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAat Gorilla: TTTCCCATTTGTGGTGACATA----------CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT Human: TTTCCCATTTGTGGTGACATACCACAATAAGCCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT Cluster: [ ] Orangutan: TTTCCCATTTGTGGTGACATA----------CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT Chimp > Human ------------- chr12:13432643-13432649 Template switch process: F1: L TGCATTTTGATGGTTAAAAATTTCCCATTTGTGGTGACATACCA 1 F3: 4 CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT R RF: TGCATTTTGATGGTTAAAAATTTCCCATTTGTGGTGACATACCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT RR: ACGTAAAACTACCAATTTTTAAAGGGTAAACACCACTGTATGGTCACTTACACCGAATAACAAAAGACCAGATATCTTTTA F2: 3 GAATAAC 2 Unidirectional alignment (log-probability: -25.3) TTTTGATGGTTAAAAATTTCCCATTTGTGGTGACATAccacaataagCCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT TTTTGATGGTTAAAAATTTCCCATTTGTGGTGACATA----------CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT Template switch alignment (log-probability: -16.2) TTTTGATGGTTAAAAATTTCCCATTTGTGGTGACATACCA|CAATAAG|CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT TTTTGATGGTTAAAAATTTCCCATTTGTGGTGACATACCA|CAATAAG|CCAGTGAATGTGGCTTATTGTTTTCTGGTCTATAGAAAAT ========= Event 575 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TCAAGATTCTAAATATTCAGAGACT------------TACGTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACAAAAAAGGTAATTCTGAATTTTAATTACTTTGAA ↑ 1 4 3 2 Chimp: TCAAGATTCTAAATATTCAGAATCTAAATGTAATTTAAATGTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACAAAAAAGGTAATTCTGAATTTTAATTACTTTGAA Gorilla: TCAAGATTCTAAATATTCAGAGACT------------TATGTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACAAAAAAGGTAATTCTGAATTTTAATTACTTTGAA Human: TCAAGATTCTAAATATTCAGAGACT------------TACGTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACAAAAAAGGTAATTCTGAATTTTAATTACTTTGAA Cluster: [ ] Orangutan: TCAAGATTCTAAATATTCACAGAAT------------TATGTACATTTCAAAAGTAATCAAATCAGACACTTCTGAAACAAAAAAGGTAATTCTGAATTTTAATTACTTTTAA Chimp > Human ------------- chr12:127415121-127415127 Template switch process: F1: L AAAAGGAGGGAAAGTGGGAGTCAAGATTCTAAATATTCAGA 1 F3: 4 GTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACA R RF: AAAAGGAGGGAAAGTGGGAGTCAAGATTCTAAATATTCAGAATCTAAATGTAATTTAAATGTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACAAAAAAGGTAATTC RR: TTTTCCTCCCTTTCACCCTCAGTTCTAAGATTTATAAGTCTTAGATTTACATTAAATTTACATGTAATTTTTTCATTAGTTTAGTCTGTGAAGACTTTGTTTTTTCCATTAAG F2: 3 CATTCAG 2 Unidirectional alignment (log-probability: -32.2) AAAGGAGGGAAAGTGGGAGTCAAGATTCTAAATATTCAGAgacttac-------------------GTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACA AAAGGAGGGAAAGTGGGAGTCAAGATTCTAAATATTCAGA-------ATCTAAATGTAATTTAAATGTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACA Template switch alignment (log-probability: -22.1) AAAGGAGGGAAAGTGGGAGTCAAGATTCTAAATATTCAGA|GAcTTAC|GTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACA AAAGGAGGGAAAGTGGGAGTCAAGATTCTAAATATTCAGA|GAATTAC|GTACATTAAAAAAGTAATCAAATCAGACACTTCTGAAACA ========= Event 576 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCTGCACAGATAATAAGAAAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATT----------------------------------------------------------------------------------------------------------------GAGCCTTCAGAGAT----------ATTGgtgtatgtgtgtgtgtatgtgtgcctgtgtgtaacactta ↓ 4 3 1 2 Chimp: CCCTGCACAGATAATAAGAAAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATT-------------GAGCCTACATACACACACACATACACCAATATCTCTGAAGGCTAAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCTTCAGAGAT----------ATTGgtgtatgtgtgtgtgtatgtgtgcctgtgtgtAACACTTA ↑ 4 3 1 2 Gorilla: CCCTGCACAGATAATAAGAAAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGTATAGTTAAGCAGCTGGAATT----------------------------------------------------------------------------------------------------------------GAGCCTTCAGAGAT----------ATTGgtgtatgtgtgtgtgtatgtgtgcctgtgtgtAACACTTA Human: CCCTGCACAGATAATAAGAAAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATT----------------------------------------------------------------------------------------------------------------GAGCCTTCAGAGAT----------ATTGgtgtatgtgtgtgtgtatgtgtgcctgtgtgtaacactta Cluster: [ ] Orangutan: CCCTGCACAGATAGTAAGAAAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGGTGTAAACAC---------------------------------------------------------------------------------------------------CAGCCTTCAGAGATACCGTCTGTTCTTGgtgtatgtgtgtgtgtatgtgtgcctgtgtgtAACACTTA Human > Chimp ------------- chr12:14505603-14505639 Template switch process: F1: L AGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCT 1 F3: 4 AAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCTTCAGAGATATTGGTGTATGTGTGTGTGTATGTGT R RF: AGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCTTCAGAGATATTGGTGTATGTGTGTGTGTATGTGT RR: TCACCTGTCTCAGGACTACCGTATCAATTCGTCGACCTTAACTCGGAAGTCTCTATAACCACATACACACACACATACACA F2: 3 TCGGAAGTCTCTATAACCACATACACACACACATACA 2 Unidirectional alignment (log-probability: -147) agagtcctgatggcatagttaagcagctggaattgagcctacatacacacacacatacaccaatatctctgaaggctaaatctcacctgcagAGTGGACAGAGTCCTGATGGCATAG --------------------------------------------------------------------------------------------AGTGGACAGAGTCCTGATGGCATAG Template switch alignment (log-probability: -20.8) AGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCT|ACATACACACACACATACACCAATATCTCTGAAGGCT|AAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAG AGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCT|ACATACACACACACATACACCAATATCTCTGAAGGCT|AAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAG Gorilla > Chimp --------------- chr12:14505603-14505639 Template switch process: F1: L AGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCT 1 F3: 4 AAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGCATAGTTAAGCAGCTGGAATTGAGCCTTCAGAGATATTGGTGTATGTGTGTGTGTATGTGT R RF: AGTGGACAGAGTCCTGATGGTATAGTTAAGCAGCTGGAATTGAGCCTTCAGAGATATTGGTGTATGTGTGTGTGTATGTGT RR: TCACCTGTCTCAGGACTACCATATCAATTCGTCGACCTTAACTCGGAAGTCTCTATAACCACATACACACACACATACACA F2: 3 TCGGAAGTCTCTATAACCACATACACACACACATACA 2 Unidirectional alignment (log-probability: -153) agagtcctgatggcatagttaagcagctggaattgagcctacatacacacacacatacaccaatatctctgaaggctaaatctcacctgcagAGTGGACAGAGTCCTGATGGcATAG --------------------------------------------------------------------------------------------AGTGGACAGAGTCCTGATGGTATAG Template switch alignment (log-probability: -32.8) AGAGTCCTGATGGcATAGTTAAGCAGCTGGAATTGAGCCT|ACATACACACACACATACACCAATATCTCTGAAGGCT|AAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGcATAG AGAGTCCTGATGGTATAGTTAAGCAGCTGGAATTGAGCCT|ACATACACACACACATACACCAATATCTCTGAAGGCT|AAATCTCACCTGCAGAGTGGACAGAGTCCTGATGGTATAG ========= Event 577 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTTGTAATAATCTTTTTCTTTGC-ATAACTGCAAAGGAGACAGAAAGTTTTGAGGT ↑ 3 1 2 4 Chimp: TCTTGTAATAATCTTTTTCTTTGCAGTTAGTACAATGGAGACAGAAAGTTTTGAGGT Gorilla: TCTTGTAATAATCTTTTTCTTTGCAGTTAGTACAATGGAGACAGAAAGTTTTGAGGT ↓ 3 1 2 4 Human: TCTTGTAATAATCTTTTTCTTTGC-ATAACTGCAAAGGAGACAGAAAGTTTTGAGGT Cluster: [ ] Orangutan: TCTTGTAATAATCTTTTTCTTTGCAGTTAGTACAATGGAGACAGAAAGTTTTGAGGT Chimp > Human ------------- chr1:36963233-36963242 Template switch process: F1: L TCAGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA 1 F3: 4 GGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT R RF: TCAGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCAGTTAGTACAATGGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT RR: AGTCGGACTCTTAATCAAGAACATTATTAGAAAAAGAAACGTCAATCATGTTACCTCTGTCTTTCAAAACTCCATAAGACAGAGACTGTCTTA F2: 3 AAACGTCAAT 2 Unidirectional alignment (log-probability: -33.2) AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA-----TAactgCAAaGGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCAGTTAGTA----CAATGGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT Template switch alignment (log-probability: -16.5) AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA|TAACTGCAAA|GGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA|TAACTGCAAA|GGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT Gorilla > Human --------------- chr1:36963233-36963242 Template switch process: F1: L TCAGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA 1 F3: 4 GGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT R RF: TCAGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCAGTTAGTACAATGGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT RR: AGTCGGACTCTTAATCAAGAACATTATTAGAAAAAGAAACGTCAATCATGTTACCTCTGTCTTTCAAAACTCCATAAGACAGAGACTGTCTTA F2: 3 AAACGTCAAT 2 Unidirectional alignment (log-probability: -32.3) AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA-----TAactgCAAaGGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCAGTTAGTA----CAATGGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT Template switch alignment (log-probability: -17) AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA|TAACTGCAAA|GGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT AGCCTGAGAATTAGTTCTTGTAATAATCTTTTTCTTTGCA|TAACTGCAAA|GGAGACAGAAAGTTTTGAGGTATTCTGTCTCTGACAGAAT ========= Event 578 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGAGCTTACACTCCAAACCTCTAAAC----TGTATTGGCTCagtataaaaatatggac Chimp: CAGAGCTTACACTCCAAACCTCTAAAC----TGTATTGGCTCagtataaaaatatggac ↓ 3 12 4 Gorilla: CAGAGCTTACACTCCAAACCTCTAAACTCAGTATAGAGGCTCagtataaaaatatggac ↑ 3 12 4 Human: CAGAGCTTACACTCCAAACCTCTAAAC----TGTATTGGCTCagtataaaaatatggac Cluster: [ ] Orangutan: CAGAGCTTACACTCCAAACCTCTAAAC----TGTATTGGCTCAGTATAAAAATATGGAC Human > Gorilla --------------- chr1:37061200-37061209 Template switch process: F1: L TGGCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT 1 F3: 4 GCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT R RF: TGGCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACTGTATTGGCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT RR: ACCGTCATACTTAGGTCTCGAATGTGAGGTTTGGAGATTTGACATAACCGAGTCATATTTTTATACCTGGTCTAGGTATACTTCAAA F2: 3 GAGATATGAC 2 Unidirectional alignment (log-probability: -32) GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACTcaGTATagaGGCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT--GTATT--GGCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT Template switch alignment (log-probability: -22.5) GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT|CAGTaTAGAG|GCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT|CAGTTTAGAG|GCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT Chimp > Gorilla --------------- chr1:37061200-37061209 Template switch process: F1: L TGGCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT 1 F3: 4 GCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT R RF: TGGCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACTGTATTGGCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT RR: ACCGTCATACTTAGGTCTCGAATGTGAGGTTTGGAGATTTGACATAACCGAGTCATATTTTTATACCTGGTCTAGGTATACTTCAAA F2: 3 GAGATATGAC 2 Unidirectional alignment (log-probability: -32) GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACTcaGTATagaGGCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT--GTATT--GGCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT Template switch alignment (log-probability: -22.5) GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT|CAGTaTAGAG|GCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT GCAGTATGAATCCAGAGCTTACACTCCAAACCTCTAAACT|CAGTTTAGAG|GCTCAGTATAAAAATATGGACCAGATCCATATGAAGTTT ========= Event 579 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: aagaaaaagaaaaagaaaTTTGGGCTAGCAGTGGAAGAGGGTAACTTTGAGGCAATGTCCAttt-----ttttttAAAAACAGTGACTGTCTAGAAACATATTCCTCCTGCCCTTATCTTTCTTTTTCTTTCTGCCCCCGACTTTACAAGGTTCCAGTGATGGGAATTTC Chimp: aaga-aaagaaaaagaaaTTT-GGCTAGT-ATGGAAGAGGGTAACTTTGAGGCAATGTCCt---tttttttttttttAA-ACGTGACTGTCTAGAAACATATTCCTCCTGCCCTTATCTTTCTTTTTCTTTCTGCCCTTGACTTTACAAGGTTCCAGTGATGGGAATTTC ↑ 1 4 3 2 Gorilla: aaga-aaagaaaaagaaaTTTGGGCTAGCAGTGGAAGAGGGTAACTTTGAGGCAATGTCCAttt-----ttttttAAAAACAGTGACTGTCTAGAAACATATTCCTCCTGCCCTTATCTTTCTTTTTCTTTCTGCCCCTGACTTTACAAGGTTCCAGTGATGGGAATTTC Human: aagaaaaagaaaaagaaaTTTGGGCTAGCAGTGGAAGAGGGTAACTTTGAGGCAATGTCCAttt-----ttttttAAAAACAGTGACTGTCTAGAAACATATTCCTCCTGCCCTTATCTTTCTTTTTCTTTCTGCCCCCGACTTTACAAGGTTCCAGTGATGGGAATTTC Cluster: [ ] Orangutan: --------aaaaaagaaaTTTGGGCTACCAGTGGAAGAGGGTAACTGTGAGTCAGTGTCCAT--------TTTTTAAAAACAGTGACTGTCTAGAAACATATTCCTCCTGCCCTTATCTTTCTTTTTCTTTCTGCCCCCAACTTTTCATGGTTCCAGTGATGGGAATTTC Gorilla > Chimp --------------- chr1:37659697-37659702 Template switch process: F1: L AAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAGAAATTTGG 1 F3: 4 TGGAAGAGGGTAACTTTGAGGCAATGTCCTTTTTTTT R RF: AAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAGAAATTTGGGCTAGCAGTGGAAGAGGGTAACTTTGAGGCAATGTCCATTTTTTTTTAAAAACAGTGACTGTCTAGAAACATATTCCTCCTGCCCTTATCTTTCTTTTTCTTTCTGCCCCTGACTTTACAAG RR: TTTTTTTTTTTTTTTTTTCTTTTCTTTTCTTTTTCTTTAAACCCGATCGTCACCTTCTCCCATTGAAACTCCGTTACAGGTAAAAAAAAATTTTTGTCACTGACAGATCTTTGTATAAGGAGGACGGGAATAGAAAGAAAAAGAAAGACGGGGACTGAAATGTTC F2: 3 ATGATC 2 Unidirectional alignment (log-probability: -41.4) AAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAGAAATTTGG-CTAGtA-TGGAAGAGGGTAACTTTGAGGCAATGTCCtTTTTTtt AAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAGAAATTTGGGCTAGCAGTGGAAGAGGGTAACTTTGAGGCAATGTCCATTTTT-- Template switch alignment (log-probability: -27.5) AAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAGAAATTTGG|CTaGTA|TGGAAGAGGGTAACTTTGAGGCAATGTCCtTTTTTTT AAAAAAAAAAAAAAAGAAAAGAAAAGAAAAAGAAATTTGG|CTTGTA|TGGAAGAGGGTAACTTTGAGGCAATGTCCATTTTTTT ========= Event 580 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ggaagcttacagggttgtcact----------tacctaaggtctcaTTCTTGGGATAG----ACAAACACTTTCACTTTCTTCATT Chimp: ggaagcttagagggttgtcaaa-----tgagacacctaaggtctcaTTCTTGGGATAG----ACAAACACTTTCACTTTCTTCATT Gorilla: ggaagcttagagggttgtcaaatgaga-----cacctaaggtctcaTTCTTGGGATAG--------ACACTTTCACTTTCTTCATT ↑ 1 4 3 2 Human: ggaagcttacagggttgtcact----------tacctaaggtctcaTTCTTGGGATAG----ACAAACACTTTCACTTTCTTCATT Cluster: [ ] Orangutan: ggaagcttagagggttgtcact----------tacctaaggtctcaTTCTTGGGATAGACAA----ACACTTTCACTTTCTTCATT Human > Gorilla --------------- chr12:19142744-19142751 Template switch process: F1: L GGTTGTCA 1 F3: 4 ACCTAAGGTCTCATTCTTGGGATAG----ACACTTTCACTTTCTTCATTCACCATACTAGATACATTTT R RF: GGTTGTCACTTACCTAAGGTCTCATTCTTGGGATAGACAAACACTTTCACTTTCTTCATTCACCATACTAGATACATTTT RR: CCAACAGTGAATGGATTCCAGAGTAAGAACCCTATCTGTTTGTGAAAGTGAAAGAAGTAAGTGGTATGATCTATGTAAAA F2: 3 CAGAGTAA 2 Unidirectional alignment (log-probability: -39) GGTTGTCAaaTgagacACCTAAGGTCTCATTCTTGGGATAG----ACACTTTCACTTTCT GGTTGTCACTT-----ACCTAAGGTCTCATTCTTGGGATAGACAAACACTTTCACTTTCT Template switch alignment (log-probability: -26.5) GGTTGTCA|AATGAGAC|ACCTAAGGTCTCATTCTTGGGATAG----ACACTTTCACTTTCT GGTTGTCA|AATGAGAC|ACCTAAGGTCTCATTCTTGGGATAGACAAACACTTTCACTTTCT ========= Event 581 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CGATGGCCTTCCCACAGAGGGTGAGGAGAGGGCTAGCGAATGGGTGAGTGCAGTTGAC------CTCTGTTCTGATGGGCAGATGGCAGGGGCGGGTTCAGGAGGTGGAGGCCAGAGGAGGATTGCGTGTCTTGGGGGAAGCCAGTGGTCTTGCAGAAATGGTCAGAACATGTTTCTGGTCTGCT Chimp: CGATGGCCTTCCCACAGAGGGGGAGGAGAGGGCTAGCGAATGGGTGAGTGCAGTCGGC---CTTCTCTGTTCTGATGGGCAGATGGCAGGGGCGGGTTCAGGAGGTGGAGGCCAGAGGAGGATTGCGTGTCTTGGGGGAAGCCAGTGGTCTTGCAGAAATGGTCAGAACATGTTTCTGGTCTGCT Gorilla: CGATGGCCTTCCCACAGAGGGGGAGGAAAGGGCTAGCGAATGGGTGAGTGCAGTCAGCCTT---CTCTGTTCTGATGGGCAGATGGCAGGGACGGGTTCAGGAGGTGGAGGCCGGAGGAGGATTGCGTGTCTTGGGGGAAGCCAGTGGTCTTGCAGAAATGGTCAGAACATGTTTCTGGTCTGCT ↓ 1 4 3 2 Human: CGATGGCCTTCCCACAGAGGGTGAGGAGAGGGCTAGCGAATGGGTGAGTGCAGTTGAC------CTCTGTTCTGATGGGCAGATGGCAGGGGCGGGTTCAGGAGGTGGAGGCCAGAGGAGGATTGCGTGTCTTGGGGGAAGCCAGTGGTCTTGCAGAAATGGTCAGAACATGTTTCTGGTCTGCT Cluster: [ ] Orangutan: CAATGGCCTTCCCACAGAGGGGGAGGAGAGGGCTAGCGAATGAGTGAGTGCAGTCGGCCTT---CTCTGTTCTGATGGGCAGATGGCAGGGGCGCGTTCAGGAGGTGGAGGCCGGAGGAGGATTGCGTGTCTTGGGGGAAGCCAGTGGTCTTGCAGAAATGGTCAGAACATGTTTCTGGTCTGCT Gorilla > Human --------------- chr12:122122047-122122050 Template switch process: F1: L CCTGTGCTGGCGACCCTAGGCGATGGCCTTCCCACAGAGGGTGAGGAGAGGGCTAGCGAATGGGTGAGTGCAGT 1 F3: 4 CTCTGTT R RF: CCTGTGCTGGCGACCCTAGGCGATGGCCTTCCCACAGAGGGGGAGGAAAGGGCTAGCGAATGGGTGAGTGCAGTCAGCCTTCTCTGTTCTGATGGGCAGATGGCAGGGACGGGTTCAGGAGGTGGAGGCCGGAGGAGGATTGCGTGTCTTGGGGGAAGCCAGTGGTCTTGCAGAAATGGTCA RR: GGACACGACCGCTGGGATCCGCTACCGGAAGGGTGTCTCCCCCTCCTTTCCCGATCGCTTACCCACTCACGTCAGTCGGAAGAGACAAGACTACCCGTCTACCGTCCCTGCCCAAGTCCTCCACCTCCGGCCTCCTCCTAACGCACAGAACCCCCTTCGGTCACCAGAACGTCTTTACCAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -36.3) CAGAGGGtGAGGAgAGGGCTAGCGAATGGGTGAGTGCAG------TTgacCTCTGTT CAGAGGGGGAGGAAAGGGCTAGCGAATGGGTGAGTGCAGTCAGCCTT---CTCTGTT Template switch alignment (log-probability: -27.3) CAGAGGGtGAGGAgAGGGCTAGCGAATGGGTGAGTGCAGT|TGAC|CTCTGTT CAGAGGGGGAGGAAAGGGCTAGCGAATGGGTGAGTGCAGT|TGAC|CTCTGTT ========= Event 582 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTTCCTGGTGCTTGGTGATGGCTCTTAAGAGGCTGTTGAGGGATGGTTTGGCCCTCAAAAG--AGAGGCTGGTGGGAGCTCCCA-------------------------------------------------------------------------TGCTGGGGAAGATTCATTCATTCATTGGGAGCTCCCATGCTGGGAGatccatccatccatccatccat Chimp: AGTTCCTGGTGCTTGGTGATGGCTCTTAAGAGGCTGTTGAGGGATGGTTTGGCCCTCAAAAG--AGAGGCTGGTGGGAGCTCCCA--------------------------------------------------------------------------------------------------------------TGCTGGGAGatccatccatccatccatccat ↑ 3 2 1 4 Gorilla: AGTTCCTGGTGCTTGGTGATGGCTCTTAAGAGGCTGTTGAGGGATGGTTTGGCCCTCAAAAG--AGAGGCTGGTGGGAGCTCCCA------------------------------------TGCTGGGGGAGATTCATTCATTCATTGGGAGCTCCCA-------------------------------------TGCTGGGAGatccatccatccatcc------ Human: AGTTCCTGGTGCTTGGTGATGGCTCTTAAGAGGCTGTTGAGGGATGGTTTGGCCCTCAAAAG--AGAGGCTGGTGGGAGCTCCCA-------------------------------------------------------------------------TGCTGGGGAAGATTCATTCATTCATTGGGAGCTCCCATGCTGGGAGatccatccatccatccatccat Cluster: [ ] Orangutan: AGTTCCTGGTGCTTGGTGATGGCTCTTAAGAGGCTGTGGAGGGATGGTTTGGCCCTCAAAAGAGAGAGGCTGGTGGGAGCTCCCATGCTGGGGGAGATTCATTCATCATTTGGAGCTCCCA--------------------------------------------------------------------------TGCTGGGAGatccatccatccatccatccat Gorilla > Chimp --------------- chr12:9189626-9189632 Template switch process: F1: L GATGGTTTGGCCCTCAAAAGAGAGGCTGGTGGGAGCTCCCATGCTGGG 1 F3: 4 TCCATCCATCCATCCATCCATCCATC R RF: TGGCTCTTAAGAGGCTGTTGAGGGATGGTTTGGCCCTCAAAAGAGAGGCTGGTGGGAGCTCCCATGCTGGGGGAGATTCATTCATTCATTGGGAGCTCCCATGCTGGGAGATCCATCCATCCATCCATCCATCCATC RR: ACCGAGAATTCTCCGACAACTCCCTACCAAACCGGGAGTTTTCTCTCCGACCACCCTCGAGGGTACGACCCCCTCTAAGTAAGTAAGTAACCCTCGAGGGTACGACCCTCTAGGTAGGTAGGTAGGTAGGTAGGTAG F2: 3 ACCTAGA 2 Unidirectional alignment (log-probability: -40.9) GGCCCTCAAAAGAGAGGCTGGTGGGAGCTCCCATGCTG-------------------------------------GGAGATCCATCCATCCATCCatccatccatccatc GGCCCTCAAAAGAGAGGCTGGTGGGAGCTCCCATGCTGGGGGAGATTCATTCATTCATTGGGAGCTCCCATGCTGGGAGATCCATCCATCCATCC--------------- Template switch alignment (log-probability: -22) GGCCCTCAAAAGAGAGGCTGGTGGGAGCTCCCATGCTGGG|AGAtCCA|TCCATCCATCCATCCATCCATCCATC GGCCCTCAAAAGAGAGGCTGGTGGGAGCTCCCATGCTGGG|AGAGCCA|TCCATCCATCCATCCATCCATCCATC ========= Event 583 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATCCAGAAGAGTCATTATCCAAGG ↓ 3 1 2 4 Chimp: ATAATCAATTTCTCTCCTGTGTAG-------------TCACACAGAAGAGTCATTATCCAAGG ↑ 3 1 2 4 Gorilla: ATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATCCAGAAGAGTCATTATCCAAGG Human: ATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATCCAGAAGAGTCATTATCCAAGG Cluster: [ ] Orangutan: ATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATACAGAAGAGTCATTATCCAAGG Human > Chimp ------------- chr12:7911308-7911314 Template switch process: F1: L TATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT 1 F3: 4 CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT R RF: TATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATCCAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT RR: ATATAAAGGTCATTTAAACTATTAGTTAAAGAGAGGACACACTGATAAGAGACAATTATAGGTCTTCTCAGTAATAGGTTCCGACCTGACGTGACCAACAA F2: 3 ACACTGA 2 Unidirectional alignment (log-probability: -32.2) ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGTagtcaca--------------------CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT-------GACTATTCTCTGTTAATATCCAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT Template switch alignment (log-probability: -16.2) ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT|AGTCACA|CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT|AGTCACA|CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT Gorilla > Chimp --------------- chr12:7911308-7911314 Template switch process: F1: L TATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT 1 F3: 4 CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT R RF: TATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATCCAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT RR: ATATAAAGGTCATTTAAACTATTAGTTAAAGAGAGGACACACTGATAAGAGACAATTATAGGTCTTCTCAGTAATAGGTTCCGACCTGACGTGACCAACAA F2: 3 ACACTGA 2 Unidirectional alignment (log-probability: -31.7) ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT--------------------agtcacaCAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGTGACTATTCTCTGTTAATATC-------CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT Template switch alignment (log-probability: -16.6) ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT|AGTCACA|CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT ATATTTCCAGTAAATTTGATAATCAATTTCTCTCCTGTGT|AGTCACA|CAGAAGAGTCATTATCCAAGGCTGGACTGCACTGGTTGTT ========= Event 584 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGGATATCTTTCTAGTAAAGATGATCAGTTTCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGACTT Chimp: AGGGATATCTTTCTAGTAAAGATGATCAGTTTCTAAGCATAAAACTGATCAttttttttCTTTAGAGGACTT ↑ 1 4 3 2 Gorilla: AGGGATATCTTTCTAGTAAAGG---------CCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT ↓ 1 4 3 2 Human: AGGGATATCTTTCTAGTAAAGATGATCAGTTTCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGACTT Cluster: [ ] Orangutan: AGGGATATCTTTCTAGTAAAGG---------CCTAAGCATTAAACTGATCATCTTTTTTCTTTAGAGGAGTT Gorilla > Human --------------- chr1:213276292-213276302 Template switch process: F1: L CATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG 1 F3: 4 CTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGACTT R RF: CATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAGGCCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT RR: GTATAAATAGCCTAAGTGAATCCCTATAGAAAGATCATTTCCGGATTCGTATTTTGACTAGTAGAAAAAAGAAATCTCCTCAA F2: 3 TTTGACTAGTA 2 Unidirectional alignment (log-probability: -40.4) ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAGatgatcagtttCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAcTT ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG---------GCCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT Template switch alignment (log-probability: -22.6) ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG|ATGATCAGTTT|CTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAcTT ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG|ATGATCAGTTT|CTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT Gorilla > Chimp --------------- chr1:192250302-192250312 Template switch process: F1: L CATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG 1 F3: 4 CTAAGCATAAAACTGATCATTTTTTTTCTTTAGAGGACTT R RF: CATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAGGCCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT RR: GTATAAATAGCCTAAGTGAATCCCTATAGAAAGATCATTTCCGGATTCGTATTTTGACTAGTAGAAAAAAGAAATCTCCTCAA F2: 3 TTTGACTAGTA 2 Unidirectional alignment (log-probability: -45.9) ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAGatgatcagtttCTAAGCATAAAACTGATCATtTTTTTTCTTTAGAGGAcTT ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG---------GCCTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT Template switch alignment (log-probability: -28.2) ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG|ATGATCAGTTT|CTAAGCATAAAACTGATCATtTTTTTTCTTTAGAGGAcTT ATATTTATCGGATTCACTTAGGGATATCTTTCTAGTAAAG|ATGATCAGTTT|CTAAGCATAAAACTGATCATCTTTTTTCTTTAGAGGAGTT ========= Event 585 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: CCCCTGAAAACAATGCGTGCCAATGTACCGTACGTACACAAATGCCGTTTGAATCACGTCTAGACAAATCTCCATCAATTAGTAGAATGAAATGCAATTGCATATT-CCAAGGGCTTCCCTTGGATCTTTGGGAGTGCATTACAT Chimp: CCCCTGAAAACAATGCGTGCCAATGTACTGTACGTACACAAATGCCGTTTGAATCACCTCTAGACAAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATTTCATTGGGGGCTTCCCTTGGATCTTTGGGAGTGCATTACAT ↓ 1 4 3 2 ↑ 3 2 1 4 Gorilla: CCCCTGAAAACAATGCGTGCCAATGTACCGTATGTACACAAATGCTGTTTGAATCACGTCTAGACAAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATATT-CCAAGGGCTTCCCTTGGATCTTTGGGAGTGCATTACAT Human: CCCCTGAAAACAATGCGTGCCAATGTACCGTACGTACACAAATGCCGTTTGAATCACGTCTAGACAAATCTCCATCAATTAGTAGAATGAAATGCAATTGCATATT-CCAAGGGCTTCCCTTGGATCTTTGGGAGTGCATTACAT Cluster: [ ] Orangutan: CCCCTGAAAACAATGCGTGGCAATGTACC----GTACACAAATGCCATTTGAATCACATCTATACAAATCTCCGTCAATTGGTAGAATGAAATGCAATTGCATATT-CCAAAGGCTTCCCTCGGATCTTTGGGAGTGCATTACAT Gorilla > Chimp --------------- chr12:132893757-132893762 Template switch process: F1: L GACAAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATTT 1 F3: 4 GGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC R RF: CCAATGTACCGTATGTACACAAATGCTGTTTGAATCACGTCTAGACAAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATATTCCAAGGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC RR: GGTTACATGGCATACATGTGTTTACGACAAACTTAGTGCAGATCTGTTTAGAGGTAGTTAACCATCTTACTTTACGTTAACGTATAAGGTTCCCGAAGGGAACCTAGAAACCCTCACGTAATGTAGGAATG F2: 3 GGTTAC 2 Unidirectional alignment (log-probability: -32.5) AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCAT-------ttcattggGGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATATTCCAA--------GGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC Template switch alignment (log-probability: -22.1) AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATtT|CATTGG|GGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATAT|CATTGG|GGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC Chimp > Gorilla --------------- chr12:129467098-129467103 Template switch process: F1: L GACAAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATAT 1 F3: 4 GGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC R RF: GACAAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATTTCATTGGGGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC RR: CTGTTTAGAGGTAGTTAACCATCTTACTTTACGTTAACGTAAAGTAACCCCCGAAGGGAACCTAGAAACCCTCACGTAATGTAGGAATG F2: 3 GAACCT 2 Unidirectional alignment (log-probability: -31.1) AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCAT--------attccaaGGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATTTCATTGG-------GGGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC Template switch alignment (log-probability: -22) AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATaT|TCCAAG|GGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC AAATCTCCATCAATTGGTAGAATGAAATGCAATTGCATTT|TCCAAG|GGCTTCCCTTGGATCTTTGGGAGTGCATTACATCCTTAC ========= Event 586 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTCCCAGGCCCCTGCCTGGAGC----------------------------------------TCAAAACCCAGAGCCCATTGTTAGACATGGAGATCCA ↓ 4 1 3 2 Chimp: TTCTCCCAGGCCCCTGCCTGGAGC--------------------TCAAAATGGGCTCAGAGAGCTCAAAACCCAGAGCCCATTGTTAGACATGGAGATCCA Gorilla: TTCTCCCAGGCCCCTGCCTGGAGCTCAAGATGGGCTCAGAGAGC--------------------TCAAAACCCAGAGCCCATTGTTAGACATGGAGATCCA Human: TTCTCCCAGGCCCCTGCCTGGAGC----------------------------------------TCAAAACCCAGAGCCCATTGTTAGACATGGAGATCCA Cluster: [ ] Orangutan: Human > Chimp ------------- chr1:20404480-20404488 Template switch process: F1: L AAGCCTCTTCTTCTTCCTTCTCCCAGGCCCCTGCCTGGAGCTCAAAA 1 F3: 4 AGAGCTCAAAACCCAGAGCCCATTGTTAGACATGGAGATCCACAC R RF: AAGCCTCTTCTTCTTCCTTCTCCCAGGCCCCTGCCTGGAGCTCAAAACCCAGAGCCCATTGTTAGACATGGAGATCCACAC RR: TTCGGAGAAGAAGAAGGAAGAGGGTCCGGGGACGGACCTCGAGTTTTGGGTCTCGGGTAACAATCTGTACCTCTAGGTGTG F2: 3 GACTCGGGT 2 Unidirectional alignment (log-probability: -39.7) TTCTTCTTCCTTCTCCCAGGCCCCTGCCTGGAGCTCAAAatgggctcagagagctcaaaACCCAGAGCCCATTGTTAGACATGGAGATC TTCTTCTTCCTTCTCCCAGGCCCCTGCCTGGAGCTCAAA--------------------ACCCAGAGCCCATTGTTAGACATGGAGATC Template switch alignment (log-probability: -28.6) TTCTTCTTCCTTCTCCCAGGCCCCTGCCTGGAGCTCAAAA|TGGGCTCaG|aGAGCTCAAAACCCAGAGCCCATTGTTAGACATGGAGATC TTCTTCTTCCTTCTCCCAGGCCCCTGCCTGGAGCTCAAAA|TGGGCTCTG|GGAGCTCAAAACCCAGAGCCCATTGTTAGACATGGAGATC ========= Event 587 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACTTTTAAAGTGTTGTTTATAAAACTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACA-------------------------------------------------------------------------------TGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAGTTTATGATGAAATGTATCCC Chimp: CACTTTTAAAGTGTTGTTTATAAAACTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACA-------------------------------------------------------------------------------TGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAGTTTATGATGAAATGTATCCC ↓ 4 1 3 2 Gorilla: CACTTTTAAAGTGTTGTTTATAAAACTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACA-----------TGAGTTCTTCATGATAAAGCTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAGTTTATGATGAAATGTATCCC ↑ 4 1 3 2 Human: CACTTTTAAAGTGTTGTTTATAAAACTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACA-------------------------------------------------------------------------------TGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAGTTTATGATGAAATGTATCCC Cluster: [ ] Orangutan: CACTTTTAAAGT---GTTTATAAAACTGTGTATAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACGTGAGTTCTTCA--------------------------------------------------------------------TGATTTTTAATGGATGTGCTCCATAATGTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAGTTTATGATGAAATGTATCCC Human > Gorilla --------------- chr12:278992-278998 Template switch process: F1: L AAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTT 1 F3: 4 ATAAAGCTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACAT R RF: AAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAG RR: TTTCAAGGACTTAGAAATCTCAACTGAGTTCTAACCACTGTACTCAAAATTACCTACACGAGGTATTGGACCAGAGGTGTAGCCCTACACAGAAAAGAGGTACCTC F2: 3 GTACTTC 2 Unidirectional alignment (log-probability: -103) ctgaatctttagagttgactcaagattggtgacatgagttcttcatgataaagctgtgtttAAAGTTCCTGAATCTTTAGAGTTGAC -------------------------------------------------------------AAAGTTCCTGAATCTTTAGAGTTGAC Template switch alignment (log-probability: -29) CTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTT|CTtCATG|ATAAAgCTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGAC CTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTT|CTCCATG|ATAAAACTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGAC Chimp > Gorilla --------------- chr12:278992-278998 Template switch process: F1: L AAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTT 1 F3: 4 ATAAAGCTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACAT R RF: AAAGTTCCTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTTTTAATGGATGTGCTCCATAACCTGGTCTCCACATCGGGATGTGTCTTTTCTCCATGGAG RR: TTTCAAGGACTTAGAAATCTCAACTGAGTTCTAACCACTGTACTCAAAATTACCTACACGAGGTATTGGACCAGAGGTGTAGCCCTACACAGAAAAGAGGTACCTC F2: 3 GTACTTC 2 Unidirectional alignment (log-probability: -103) ctgaatctttagagttgactcaagattggtgacatgagttcttcatgataaagctgtgtttAAAGTTCCTGAATCTTTAGAGTTGAC -------------------------------------------------------------AAAGTTCCTGAATCTTTAGAGTTGAC Template switch alignment (log-probability: -29) CTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTT|CTtCATG|ATAAAgCTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGAC CTGAATCTTTAGAGTTGACTCAAGATTGGTGACATGAGTT|CTCCATG|ATAAAACTGTGTTTAAAGTTCCTGAATCTTTAGAGTTGAC ========= Event 588 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCAGAATACCATACCTCATTTACAGTGGTTTTTGATTAGTGGCCTCCAAAGAACATATGTTTTCATTA ↓ 3 1 2 4 Chimp: ACCAGAATACCATACCTCATTTACCACT-------GTAAATGGCCTCCGAAGAACATATGTTTTCATTA Gorilla: ACCAGAATACCATACCTCATTCACGGTGGTTTTTGATTAGTGGCCTCGGAAGAACATATGTTTTCATTA Human: ACCAGAATACCATACCTCATTTACAGTGGTTTTTGATTAGTGGCCTCCAAAGAACATATGTTTTCATTA Cluster: [ ] Orangutan: ACCAGAATACCGTACCTCATTCACAGTGGTTTTTGATTAGTGGCCTCGGAAGAACATATGTTTTCATTA Human > Chimp ------------- chr12:1505420-1505428 Template switch process: F1: L AATTGAATATCTAGCAGACCAGAATACCATACCTCATTTAC 1 F3: 4 TGGCCTCCGAAGAACATATGTTTTCATTATGTGAAAATTAAGGAAATTG R RF: AATTGAATATCTAGCAGACCAGAATACCATACCTCATTTACAGTGGTTTTTGATTAGTGGCCTCCAAAGAACATATGTTTTCATTATGTGAAAATTAAGGAAATTG RR: TTAACTTATAGATCGTCTGGTCTTATGGTATGGAGTAAATGTCACCAAAAACTAATCACCGGAGGTTTCTTGTATACAAAAGTAATACACTTTTAATTCCTTTAAC F2: 3 AAATGTCAC 2 Unidirectional alignment (log-probability: -39.5) ATTGAATATCTAGCAGACCAGAATACCATACCTCATTTACcactgtaaA---------------TGGCCTCCgAAGAACATATGTTTTCATTATGTGAAAATTA ATTGAATATCTAGCAGACCAGAATACCATACCTCATTTAC--------AGTGGTTTTTGATTAGTGGCCTCCAAAGAACATATGTTTTCATTATGTGAAAATTA Template switch alignment (log-probability: -22.6) ATTGAATATCTAGCAGACCAGAATACCATACCTCATTTAC|CACTGTAAA|TGGCCTCCgAAGAACATATGTTTTCATTATGTGAAAATTA ATTGAATATCTAGCAGACCAGAATACCATACCTCATTTAC|CACTGTAAA|TGGCCTCCAAAGAACATATGTTTTCATTATGTGAAAATTA ========= Event 589 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTTTTGGTATATGTGGACACAAAT-----GCACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTT Chimp: GTTTTGGTATATGTGGACACAAAT-----GCACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTT ↑ 1 4 3 2 Gorilla: GTTTTGGTATATGTGGACACAGCTTACGGTGACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTT ↓ 1 4 3 2 Human: GTTTTGGTATATGTGGACACAAAT-----GCACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTT Cluster: [ ] Orangutan: GTCTTGGTATATGTGGACACAGCTTACGGTGACTTGTACTAAAATGCATTTATCTCCATTCTCCTCTCTT Gorilla > Human --------------- chr1:213778390-213778394 Template switch process: F1: L AGGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA 1 F3: 4 ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC R RF: AGGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACAGCTTACGGTGACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC RR: TCCTAAATGACGTTCCGGTCCAAAACCATATACACCTGTGTCGAATGCCACTGAACATGATTTTACGTAAATAGAGGAAAGAGGAGAGAAG F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -25.4) GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACAaatGC--------ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA---GCTTACGGTGACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC Template switch alignment (log-probability: -16.4) GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA|AATGC|ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA|AATGC|ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC Gorilla > Chimp --------------- chr1:192756927-192756931 Template switch process: F1: L AGGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA 1 F3: 4 ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC R RF: AGGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACAGCTTACGGTGACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC RR: TCCTAAATGACGTTCCGGTCCAAAACCATATACACCTGTGTCGAATGCCACTGAACATGATTTTACGTAAATAGAGGAAAGAGGAGAGAAG F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -25.4) GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACAaatGC--------ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA---GCTTACGGTGACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC Template switch alignment (log-probability: -16.4) GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA|AATGC|ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC GGATTTACTGCAAGGCCAGGTTTTGGTATATGTGGACACA|AATGC|ACTTGTACTAAAATGCATTTATCTCCTTTCTCCTCTCTTC ========= Event 590 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGACAAGACAGGAACACAAGACTTGGGGAAATC--------------TTTCCCCAAGTCTAGTTCATCTGGGTCACCTGCCA Chimp: AGGACAAGACAGGAACACAAGACTTGGGGAAATC--------------TTTCCCCAAGTCTAGTTCATCTGGGTCACCTGCCA ↑ 3 1 4 Gorilla: AGGACAAGACAGGAACACAAGACTTGGGGAAAGA----------------------------TTTCATCTGGGTCACCTGCCA ↓ 3 1 4 Human: AGGACAAGACAGGAACACAAGACTTGGGGAAATC--------------TTTCCCCAAGTCTAGTTCATCTGGGTCACCTGCCA Cluster: [ ] Orangutan: tggacaagaCAGGAACACAAGA--------CAGATTTCCCCAAGTCTA--------------GTTCATCTGGGTCACCTGCCA Gorilla > Human --------------- chr1:214491799-214491813 Template switch process: F1: L GGAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA 1 F3: 4 AGTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGCTT R RF: GGAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAAGATTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGCTT RR: CCTCTGATTTCCTGTTCTGTCCTTGTGTTCTGAACCCCTTTCTAAAGTAGACCCAGTGGACGGTCTCGTTTGCAGGTGGACGAA F2: 3 TCTGAACCCCTTTCT 2 Unidirectional alignment (log-probability: -42.1) GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAAtctttccccaagtctAgTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA--------------GATTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC Template switch alignment (log-probability: -23.2) GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA|TCTTTCCCCAAGTCT|AgTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA|TCTTTCCCCAAGTCT|ATTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC Gorilla > Chimp --------------- chr1:193477928-193477942 Template switch process: F1: L GGAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA 1 F3: 4 AGTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGCTT R RF: GGAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAAGATTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGCTT RR: CCTCTGATTTCCTGTTCTGTCCTTGTGTTCTGAACCCCTTTCTAAAGTAGACCCAGTGGACGGTCTCGTTTGCAGGTGGACGAA F2: 3 TCTGAACCCCTTTCT 2 Unidirectional alignment (log-probability: -42.1) GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAAtctttccccaagtctAgTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA--------------GATTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC Template switch alignment (log-probability: -23.2) GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA|TCTTTCCCCAAGTCT|AgTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC GAGACTAAAGGACAAGACAGGAACACAAGACTTGGGGAAA|TCTTTCCCCAAGTCT|ATTTCATCTGGGTCACCTGCCAGAGCAAACGTCCACCTGC ========= Event 591 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 56 Detected in comparisons: 56 Multiple sequence alignment: Human: acagtcccattgggggattgggttctaccccaaattcacatgtggtgaatttggggtagaacacaatccagtccacaacaagga Chimp: acaGTCCCATTGGGGGATTGGGTTCTACCCCAAATTCACATGTGGTGAATTTGGGTTAGAACACAATCCAGTCCACAAcaagga ↓ 13 24 ↑ 13 24 Gorilla: acaGTCCCATTGGGGGATTGTGTTCTAACCCAAATTCACCTCATGTGAATTTGGGGTAGAACCCAATCCAGTCCACAAcaagga Human: acagtcccattgggggattgggttctaccccaaattcacatgtggtgaatttggggtagaacacaatccagtccacaacaagga Cluster: [ ] Orangutan: acagtcccattgggggattgggttctaccccaaattcacatgtggtgaatttgggttagaacacaatccagtccacaacaagga Gorilla > Chimp --------------- chr12:122295218-122295260 Template switch process: F1: L AAACAAACAAACAAACAAACAAACAAAACAAA-AACAGTCCCATTGGGGGATTG 1 F3: 4 CAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCATCTCAGAGACCAGAACCAAGGGCTGCCTGGTGAGCTAATCAAAGAACTCCCTTCTCAGGC R RF: AAACAAACAAACAAACAAACAAACAAAACAAAAAACAGTCCCATTGGGGGATTGTGTTCTAACCCAAATTCACCTCATGTGAATTTGGGGTAGAACCCAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCATCTCAGAGAGCAGAACCAAGGGCTGCCTGGTGAGCTAATCAAAGAACTCCCTTCTCAGGC RR: TTTGTTTGTTTGTTTGTTTGTTTGTTTTGTTTTTTGTCAGGGTAACCCCCTAACACAAGATTGGGTTTAAGTGGAGTACACTTAAACCCCATCTTGGGTTAGGTCAGGTGTTGTTCCTATCATTAACTTTTTCGAGTAGAGTCTCTCGTCTTGGTTCCCGACGGACCACTCGATTAGTTTCTTGAGGGAAGAGTCCG F2: 3 ACAAGATTGGGTTTAAGTGGTGTACACTTAAACCCCATCTTGG 2 Unidirectional alignment (log-probability: -62.2) AACAAACAAACAAAACAAAA-ACAGTCCCATTGGGGGATTGgGTTCTAcCCCAAATTCACaTgtgGTGAATTTGGGtTAGAACaCAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA AACAAACAAACAAAACAAAAAACAGTCCCATTGGGGGATTGTGTTCTAACCCAAATTCACCTCATGTGAATTTGGGGTAGAACCCAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA Template switch alignment (log-probability: -43.5) AACAAACAAACAAAACAAA-AACAGTCCCATTGGGGGATTG|GGTTCTACCCCAAATTCACATGtGGTGAATTTGGGTTAGAACA|CAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA AACAAACAAACAAAACAAAAAACAGTCCCATTGGGGGATTG|GGTTCTACCCCAAATTCACATGAGGTGAATTTGGGTTAGAACA|CAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA Chimp > Gorilla --------------- chr12:119287763-119287805 Template switch process: F1: L AAACAAACAAACAAACAAACAAACAAAACAAAAAACAGTCCCATTGGGGGATTG 1 F3: 4 CAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCATCTCAGAGAGCAGAACCAAGGGCTGCCTGGTGAGCTAATCAAAGAACTCCCTTCTCAGGC R RF: AAACAAACAAACAAACAAACAAACAAAACAAAAA-CAGTCCCATTGGGGGATTGGGTTCTACCCCAAATTCACATGTGGTGAATTTGGGTTAGAACACAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCATCTCAGAGACCAGAACCAAGGGCTGCCTGGTGAGCTAATCAAAGAACTCCCTTCTCAGGC RR: TTTGTTTGTTTGTTTGTTTGTTTGTTTTGTTTTT-GTCAGGGTAACCCCCTAACCCAAGATGGGGTTTAAGTGTACACCACTTAAACCCAATCTTGTGTTAGGTCAGGTGTTGTTCCTATCATTAACTTTTTCGAGTAGAGTCTCTGGTCTTGGTTCCCGACGGACCACTCGATTAGTTTCTTGAGGGAAGAGTCCG F2: 3 CCAAGATGGGGTTTAAGTGTACTCCACTTAAACCCAATCTTGT 2 Unidirectional alignment (log-probability: -63.6) ACAAACAAACAAAACAAAAAaCAGTCCCATTGGGGGATTGtGTTCTAaCCCAAATTCACcTcatGTGAATTTGGGgTAGAACcCAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA ACAAACAAACAAAACAAAAA-CAGTCCCATTGGGGGATTGGGTTCTACCCCAAATTCACATGTGGTGAATTTGGGTTAGAACACAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA Template switch alignment (log-probability: -44.9) ACAAACAAACAAAACAAAAAaCAGTCCCATTGGGGGATTG|TGTTCTAACCCAAATTCACCtCATGTGAATTTGGGGTAGAACC|CAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA ACAAACAAACAAAACAAAAA-CAGTCCCATTGGGGGATTG|TGTTCTAACCCAAATTCACCACATGTGAATTTGGGGTAGAACC|CAATCCAGTCCACAACAAGGATAGTAATTGAAAAAGCTCA ========= Event 592 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tttatattttctctctttcttGAGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATAT----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT ↓ 3 2 1 4 Chimp: tttatattttctctttttcttgaGATATCCTTTAGGATATACCTAGGGTATATCTTGAGATATAGATATCTCA--AGGTAGAAGGCAGCTGGTGTGT Gorilla: tttatattttctctttttcttgaGATATCCTTTAGGATATAGCTAAGGTATATCTTGAGATAT----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Human: tttatattttctctctttcttGAGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATAT----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Cluster: [ ] Orangutan: tttatattttctctttttcttgaGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATAC----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Human > Chimp ------------- chr1:194054980-194054989 Template switch process: F1: L AGATATCCTTTAGGATATACCTAGGGTATATCTTGAGATATA 1 F3: 4 GGTAGAAGGCAGCTGGTGTGTTCAGTGATGTAGGTTGTCA R RF: TTGAGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATATACCTTAGGTGGTAGAAGGCAGCTGGTGTGTTCAGTGATGTAGGTTGTCA RR: AACTCTATAGGAAATCCTATATGGATTCCATATAGAACTCTATATGGAATCCACCATCTTCCGTCGACCACACAAGTCACTACATCCAACAGT F2: 3 AACTCTATAG 2 Unidirectional alignment (log-probability: -41.9) ATATCCTTTAGGATATACCTAgGGTATATCTTGAGATATA--------gatatctcaaGGTAGAAGGCAGCTGGTGTGTTCAGTGATGTAGGTTGTCA ATATCCTTTAGGATATACCTAAGGTATATCTTGAGATATACCTTAGGT----------GGTAGAAGGCAGCTGGTGTGTTCAGTGATGTAGGTTGTCA Template switch alignment (log-probability: -22.5) ATATCCTTTAGGATATACCTAgGGTATATCTTGAGATATA|GATATCTCAA|GGTAGAAGGCAGCTGGTGTGTTCAGTGATGTAGGTTGTCA ATATCCTTTAGGATATACCTAAGGTATATCTTGAGATATA|GATATCTCAA|GGTAGAAGGCAGCTGGTGTGTTCAGTGATGTAGGTTGTCA ========= Event 593 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: tttatattttctctctttcttGAGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATAT----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Chimp: tttatattttctctttttcttgaGATATCCTTTAGGATATACCTAGGGTATATCTTGAGATATAGATATCTCA--AGGTAGAAGGCAGCTGGTGTGT ↑ 3 2 1 4 Gorilla: tttatattttctctttttcttgaGATATCCTTTAGGATATAGCTAAGGTATATCTTGAGATAT----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Human: tttatattttctctctttcttGAGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATAT----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Cluster: [ ] Orangutan: tttatattttctctttttcttgaGATATCCTTTAGGATATACCTAAGGTATATCTTGAGATAC----ACCTTAGGTGGTAGAAGGCAGCTGGTGTGT Gorilla > Chimp --------------- chr1:194054980-194054989 Template switch process: F1: L TTTATATTTTCTCTTTTTCTTGAGATATCCTTTAGGATATACCTAGGGTATATCTTGAGATATA 1 F3: 4 GGTAGAAGGC R RF: TTTATATTTTCTCTTTTTCTTGAGATATCCTTTAGGATATAGCTAAGGTATATCTTGAGATATACCTTAGGTGGTAGAAGGC RR: AAATATAAAAGAGAAAAAGAACTCTATAGGAAATCCTATATCGATTCCATATAGAACTCTATATGGAATCCACCATCTTCCG F2: 3 AACTCTATAG 2 Unidirectional alignment (log-probability: -46.4) ATATCCTTTAGGATATAcCTAgGGTATATCTTGAGATATagatatctcaA--------GGTAGAAGGC ATATCCTTTAGGATATAGCTAAGGTATATCTTGAGATAT----------ACCTTAGGTGGTAGAAGGC Template switch alignment (log-probability: -27.9) ATATCCTTTAGGATATAcCTAgGGTATATCTTGAGATATA|GATATCTCAA|GGTAGAAGGC ATATCCTTTAGGATATAGCTAAGGTATATCTTGAGATATA|GATATCTCAA|GGTAGAAGGC ========= Event 594 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTATCCCAGAGAAGCAGAGGTTTATGCCATCTGGCATAAACCTCGCTGGATGACCTCCTT ↑ 1 4 3 2 Chimp: AGTATCCCAGAGAAGCAGAGGAAT-----ATCTGGCATAAACCTCGCTGGATGACCTCCTT Gorilla: AATATCCCAGAGAAGCAGAGGAAT-----ATCTGGCATAAACCTCACTGGATGACCTCCTT ↓ 1 4 3 2 Human: AGTATCCCAGAGAAGCAGAGGTTTATGCCATCTGGCATAAACCTCGCTGGATGACCTCCTT Cluster: [ ] Orangutan: AGTATCCCAGAGAAGCAGAGGAAT-----ATCTGGCATAATCCTCACTGGATGACCTCCTT Chimp > Human ------------- chr12:15131655-15131662 Template switch process: F1: L AAAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGG 1 F3: 4 ATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT R RF: AAAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGGAATATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT RR: TTTCACTGAGTCTCACTGATTCATAGGGTCTCTTCGTCTCCTTATAGACCGTATTTGGAGCGACCTACTGGAGGAATATGTCTA F2: 3 CCGTATTT 2 Unidirectional alignment (log-probability: -30.1) AAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGGttTatgccATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT AAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGGAAT-----ATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT Template switch alignment (log-probability: -16.3) AAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGG|TTTATGCC|ATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT AAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGG|TTTATGCC|ATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT Gorilla > Human --------------- chr12:15131655-15131662 Template switch process: F1: L AAAGTGACTCAGAGTGACTAAGTATCCCAGAGAAGCAGAGG 1 F3: 4 ATCTGGCATAAACCTCGCTGGATGACCTCCTTATACAGAT R RF: AAAGTGACTCAGAGTGACTAAATATCCCAGAGAAGCAGAGGAATATCTGGCATAAACCTCACTGGATGACCTCCTTATACAGAT RR: TTTCACTGAGTCTCACTGATTTATAGGGTCTCTTCGTCTCCTTATAGACCGTATTTGGAGTGACCTACTGGAGGAATATGTCTA F2: 3 CCGTATTT 2 Unidirectional alignment (log-probability: -40.2) AAGTGACTCAGAGTGACTAAgTATCCCAGAGAAGCAGAGGttTatgccATCTGGCATAAACCTCgCTGGATGACCTCCTTATACAGAT AAGTGACTCAGAGTGACTAAATATCCCAGAGAAGCAGAGGAAT-----ATCTGGCATAAACCTCACTGGATGACCTCCTTATACAGAT Template switch alignment (log-probability: -27.8) AAGTGACTCAGAGTGACTAAgTATCCCAGAGAAGCAGAGG|TTTATGCC|ATCTGGCATAAACCTCgCTGGATGACCTCCTTATACAGAT AAGTGACTCAGAGTGACTAAATATCCCAGAGAAGCAGAGG|TTTATGCC|ATCTGGCATAAACCTCACTGGATGACCTCCTTATACAGAT ========= Event 595 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTCTGAGTGCTGAGAAGACA--TCCGAGTTTCAGCCCAGTCAGCGTT Chimp: TTATCTGAGTGCTGAGAAGACA--TCCGAGTTTCAGCCCAGTCAGCGTT ↓ 1 3 42 Gorilla: TTCTCTGAGTGCTGAGAAGACTCGGATGAGTTTCAGCCCAGTCAGCGTT ↑ 1 3 42 Human: TTCTCTGAGTGCTGAGAAGACA--TCCGAGTTTCAGCCCAGTCAGCGTT Cluster: [ ] Orangutan: TTCTCTGAGTGCTGAGAAGACA--TCTGAGTTTGAGCCCAGTCAGAGTT Human > Gorilla --------------- chr12:15131810-15131815 Template switch process: F1: L CCAACATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGAC 1 F3: 4 GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT R RF: CCAAGATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGACATCCGAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT RR: GGTTCTACACTTAATGTCTCAAGAGACTCACGACTCTTCTGTAGGCTCAAAGTCGGGTCAGTCGCAAGTCTTTAGAAACACTTCA F2: 3 TAGGCT 2 Unidirectional alignment (log-probability: -32) CAAcATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGACtcggAT--GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT CAAGATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGAC----ATCCGAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT Template switch alignment (log-probability: -22) CAAcATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGAC|TCGGAT|GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT CAAGATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGAC|TCGGAT|GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT Chimp > Gorilla --------------- chr12:15131810-15131815 Template switch process: F1: L CCAACATGTGAATTACAGAGTTCTCTGAGTGCTGAGAAGAC 1 F3: 4 GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT R RF: CCAAGATGTGAATTACAGAGTTATCTGAGTGCTGAGAAGACATCCGAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT RR: GGTTCTACACTTAATGTCTCAATAGACTCACGACTCTTCTGTAGGCTCAAAGTCGGGTCAGTCGCAAGTCTTTAGAAACACTTCA F2: 3 TAGGCT 2 Unidirectional alignment (log-probability: -37.5) CAAcATGTGAATTACAGAGTTcTCTGAGTGCTGAGAAGACtcggAT--GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT CAAGATGTGAATTACAGAGTTATCTGAGTGCTGAGAAGAC----ATCCGAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT Template switch alignment (log-probability: -27.5) CAAcATGTGAATTACAGAGTTcTCTGAGTGCTGAGAAGAC|TCGGAT|GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT CAAGATGTGAATTACAGAGTTATCTGAGTGCTGAGAAGAC|TCGGAT|GAGTTTCAGCCCAGTCAGCGTTCAGAAATCTTTGTGAAGT ========= Event 596 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AAAGGGAAGAAAGTATTTCAGGTCATACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGACCTTGACATTTTGAAGGCCCACTGATCAGCTGTCCTAGCTGGGCCCCCTTGAATTTTTCTCAAACCTGTCTCT ↑ 1 4 3 2 Chimp: AAAGGGAAGAAAGTATTTCAG--AGTACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGACCTTGACATTTTGAAGGCCCACTGATCAGCTGTCCTAGCTGGGCCCCCTTGACTTTTTCTCAAACCTGTCTCT Gorilla: AAAGGGAGGAAAGTATTTCAGGTCATACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGACCTTGACATTTTGAAGGCCCACTGATCAGCTGTCCTAGCTGGGCCCCCTTGAATTTTTCTCAAACCTGTCTCT Human: AAAGGGAAGAAAGTATTTCAGGTCATACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGACCTTGACATTTTGAAGGCCCACTGATCAGCTGTCCTAGCTGGGCCCCCTTGAATTTTTCTCAAACCTGTCTCT Cluster: [ ] Orangutan: AAAGGGAAGAAAGTATTTCAGGTCATACCTAAAGCACTTCTCCTAATGGTGACTGAAATTCAGCCCTTGACATTTTGAAGGCCCACTGATCAGCTGTCCTAGCTGGGCCCCCTTGAATTTTTCTAAAACCTGTCTCT Chimp > Human ------------- chr12:14960319-14960322 Template switch process: F1: L GCTGGCTGGGAAGTCCTCTAAAAGGGAAGAAAGTATTTCAG 1 F3: 4 TACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGAC R RF: GCTGGCTGGGAAGTCCTCTAAAAGGGAAGAAAGTATTTCAGAGTACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGACCTTGACATTTTGAAGGCCCACTGATCAGCTGTCCTAGCTGGGCCCCCTTGAC RR: CGACCGACCCTTCAGGAGATTTTCCCTTCTTTCATAAAGTCTCATGGATTTCGTGAAGAGGATTACCACCGACTTTAAGTCTGGAACTGTAAAACTTCCGGGTGACTAGTCGACAGGATCGACCCGGGGGAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -25.5) CTGGCTGGGAAGTCCTCTAAAAGGGAAGAAAGTATTTCAGgtcA-TACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGAC CTGGCTGGGAAGTCCTCTAAAAGGGAAGAAAGTATTTCAG---AGTACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGAC Template switch alignment (log-probability: -15.8) CTGGCTGGGAAGTCCTCTAAAAGGGAAGAAAGTATTTCAG|GTCA|TACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGAC CTGGCTGGGAAGTCCTCTAAAAGGGAAGAAAGTATTTCAG|GTCA|TACCTAAAGCACTTCTCCTAATGGTGGCTGAAATTCAGAC ========= Event 597 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAGTCTGAGAGGTGGAGAGCTTTTGGCTGGGAATGGCTGGGATTTTTCTTTTCCTCCCCTATCGATTATTTCCTCCAC----------CCTTCTTAAGAA--------AAGCTTCAATTTTTAAATAAGATAGC Chimp: AGAAGTCTGAGAGGTGGAGAGCTTTTGGCTGGGAATGGCTGGGATTTTTCTTTTCCTCCTCTATCGATTATTTCCTCCAC-----CCTTTCCTTCTTAAGAA--------AAGCTTCAATTTTTAAACAAGATAGC Gorilla: AGAAGTCTGAGAGGTGGAGAGCTTTTGGCTGGGAATGGCTGGGATTTTTCTTTTCCTCCCCTATCGATTATTTCCTCCAC----------CCTTCTTAAGAAGGGTGATTAAAAATCAATTTTTAAATAAGATAGC ↓ 3 2 1 4 Human: AGAAGTCTGAGAGGTGGAGAGCTTTTGGCTGGGAATGGCTGGGATTTTTCTTTTCCTCCCCTATCGATTATTTCCTCCAC----------CCTTCTTAAGAA--------AAGCTTCAATTTTTAAATAAGATAGC Cluster: [ ] Orangutan: AGAAGTCTGAGAGGTGGAGAGCTCTTGGCTGGGAATGGCTGGGATTTTTCTTTTCCTCCCCTATCGATTATTTCCTCCACCCTTT-----CCTTCGTAAGAA--------AAGCTTCAATTTTTAAATAAGATAGC Gorilla > Human --------------- chr12:14890192-14890196 Template switch process: F1: L TTTCCTCCCCTATCGATTATTTCCTCCACCCTTCTTAAGAA 1 F3: 4 TCAATTTTTAAATAAGATAGCAAATATCAAATAAAAATTA R RF: AGCTTTTGGCTGGGAATGGCTGGGATTTTTCTTTTCCTCCCCTATCGATTATTTCCTCCACCCTTCTTAAGAAGGGTGATTAAAAATCAATTTTTAAATAAGATAGCAAATATCAAATAAAAATTA RR: TCGAAAACCGACCCTTACCGACCCTAAAAAGAAAAGGAGGGGATAGCTAATAAAGGAGGTGGGAAGAATTCTTCCCACTAATTTTTAGTTAAAAATTTATTCTATCGTTTATAGTTTATTTTTAAT F2: 3 TCGAA 2 Unidirectional alignment (log-probability: -25.5) TTCCTCCCCTATCGATTATTTCCTCCACCCTTCTTAAG-----------AAAAgctTCAATTTTTAAATAAGATAGCAAATATCAAATAAAAATTA TTCCTCCCCTATCGATTATTTCCTCCACCCTTCTTAAGAAGGGTGATTAAAAA---TCAATTTTTAAATAAGATAGCAAATATCAAATAAAAATTA Template switch alignment (log-probability: -16.4) TTCCTCCCCTATCGATTATTTCCTCCACCCTTCTTAAGAA|AAGCT|TCAATTTTTAAATAAGATAGCAAATATCAAATAAAAATTA TTCCTCCCCTATCGATTATTTCCTCCACCCTTCTTAAGAA|AAGCT|TCAATTTTTAAATAAGATAGCAAATATCAAATAAAAATTA ========= Event 598 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGTGTCCAGGGAGACCCAGATGCAGCCCCACTCATGGCTACAAGCCCTGCCTGCC ↓ 3 2 1 4 Chimp: GTGTGTCCAGGGAGACCCAGATGCAGCCCTGCATCTGGCTACAAGCCCTGCCTGCC ↑ 3 2 1 4 Gorilla: GTGTGTCCAGGGAGACCCAGATGCAGCCCCACTCATGGCTACAAGCCCTGCCTGCC Human: GTGTGTCCAGGGAGACCCAGATGCAGCCCCACTCATGGCTACAAGCCCTGCCTGCC Cluster: [ ] Orangutan: GTGTGTCCAGGGAGACCCAGATGCAGCCCCACTCATGGCTACAAGCCCTGCCTGCC Human > Chimp ------------- chr1:20723263-20723268 Template switch process: F1: L AGAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC 1 F3: 4 TGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA R RF: AGAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCCCACTCATGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA RR: TCTCCGCCCGTCCACACAGGTCCCTCTGGGTCTACGTCGGGGTGAGTACCGATGTTCGGGACGGACGGGGCCGTCCCAGTGTATTGT F2: 3 CTACGT 2 Unidirectional alignment (log-probability: -28.6) GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCCtgcatC-----TGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC-----CACTCATGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA Template switch alignment (log-probability: -16) GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC|TGCATC|TGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC|TGCATC|TGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA Gorilla > Chimp --------------- chr1:20723263-20723268 Template switch process: F1: L AGAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC 1 F3: 4 TGGCTACAAGCCCTGCCTGCCCCGGCAGGGTCACATAACA R RF: AGAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCCCACTCATGGCTACAAGCCCTGCCTGCCCCAGCAGGGTCACATAACA RR: TCTCCGCCCGTCCACACAGGTCCCTCTGGGTCTACGTCGGGGTGAGTACCGATGTTCGGGACGGACGGGGTCGTCCCAGTGTATTGT F2: 3 CTACGT 2 Unidirectional alignment (log-probability: -33.6) GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCCtgcatC-----TGGCTACAAGCCCTGCCTGCCCCgGCAGGGTCACATAACA GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC-----CACTCATGGCTACAAGCCCTGCCTGCCCCAGCAGGGTCACATAACA Template switch alignment (log-probability: -22) GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC|TGCATC|TGGCTACAAGCCCTGCCTGCCCCgGCAGGGTCACATAACA GAGGCGGGCAGGTGTGTCCAGGGAGACCCAGATGCAGCCC|TGCATC|TGGCTACAAGCCCTGCCTGCCCCAGCAGGGTCACATAACA ========= Event 599 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAATGTATCCATGCTCACAGTTATCTTCAGT-------AAGGCTAgacatacacacgcaca Chimp: AGGAATGTATCCATGCTCACAGTTATCTTCAGT-------AAGGCTAGacatacacacgcaca ↓ 3 2 1 4 Gorilla: AGGAATGTATCCATGCTCACAGTTATCTTCAGTGATAACTGAAGCTAGacatacacacgcaca ↑ 3 2 1 4 Human: AGGAATGTATCCATGCTCACAGTTATCTTCAGT-------AAGGCTAgacatacacacgcaca Cluster: [ ] Orangutan: AGGAATGTATCCATGCTCACAATTATCTTCAGT-------AAGACTAGACATACACACGCTCA Human > Gorilla --------------- chr12:15543225-15543232 Template switch process: F1: L TAAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGT 1 F3: 4 AAGCTAGACATACACACGCACACACACATAAATAACAAACAA R RF: TAAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGTAAGGCTAGACATACACACGCACACACACATAAATAACAAACAA RR: ATTTTAGATCCTTACATAGGTACGAGTGTCAATAGAAGTCATTCCGATCTGTATGTGTGCGTGTGTGTGTATTTATTGTTTGTT F2: 3 GTCAATAG 2 Unidirectional alignment (log-probability: -32) AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGtgataacTgAaGCTAGACATACACACGCACACACACATAAATAACAAAC AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAG-------TAAGGCTAGACATACACACGCACACACACATAAATAACAAAC Template switch alignment (log-probability: -22.3) AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGT|GATAACTG|AaGCTAGACATACACACGCACACACACATAAATAACAAAC AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGT|GATAACTG|AGGCTAGACATACACACGCACACACACATAAATAACAAAC Chimp > Gorilla --------------- chr12:15543225-15543232 Template switch process: F1: L TAAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGT 1 F3: 4 AAGCTAGACATACACACGCACACACACATAAATAACAAACAA R RF: TAAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGTAAGGCTAGACATACACACGCACACACACATAAATAACAAACAA RR: ATTTTAGATCCTTACATAGGTACGAGTGTCAATAGAAGTCATTCCGATCTGTATGTGTGCGTGTGTGTGTATTTATTGTTTGTT F2: 3 GTCAATAG 2 Unidirectional alignment (log-probability: -32) AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGtgataacTgAaGCTAGACATACACACGCACACACACATAAATAACAAAC AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAG-------TAAGGCTAGACATACACACGCACACACACATAAATAACAAAC Template switch alignment (log-probability: -22.3) AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGT|GATAACTG|AaGCTAGACATACACACGCACACACACATAAATAACAAAC AAAATCTAGGAATGTATCCATGCTCACAGTTATCTTCAGT|GATAACTG|AGGCTAGACATACACACGCACACACACATAAATAACAAAC ========= Event 600 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: CCCAAAATTGGCACATCCAAATAAG-TAGTTTACTTCAAAGGAAATAAACAGTGCTTGTGGGCTAAAACG Chimp: CCCAAAATTGGCACATCCAAAGAAATAAGTTTATTTCTTTTGAAATAAACAGTGCTTGTGGGCTAAAACG ↓ 1 3 4 2 ↑ 3 4 1 2 Gorilla: CCCAAAATTGGCACATCCAAATAAG-TAGTTTATTTCAAAAGAAATAAACAGTGCTTGTGGGCTAAAACG Human: CCCAAAATTGGCACATCCAAATAAG-TAGTTTACTTCAAAGGAAATAAACAGTGCTTGTGGGCTAAAACG Cluster: [ ] Orangutan: CCCAAAATTGGCACATCCAAATAAG-TAGTTTATTTCTAAAGAAATAAACAGTGCTTGTGGGCTAAAACA Gorilla > Chimp --------------- chr1:194960929-194960941 Template switch process: F1: L ACATAATTTATTACTCTGGACCCAAAATTGGCACATCC-------------------AAAGAAATAA 1 F3: 4 GAAATAAACAGTGCTTGTGGGCTAAA R RF: ACATAATTTATTACTCTGGACCCAAAATTGGCACATCCAAATAAGTAGTTTATTTCAAAAGAAATAAACAGTGCTTGTGGGCTAAA RR: TGTATTAAATAATGAGACCTGGGTTTTAACCGTGTAGGTTTATTCATCAAATAAAGTTTTCTTTATTTGTCACGAACACCCGATTT F2: 3 TTTTCTTTATTTG 2 Unidirectional alignment (log-probability: -45.5) TATTACTCTGGACCCAAAATTGGCACATCCAAAgAAaTaAGTTTATTTCttttGAAATAAACAGTGCTTGTGGGCTAAA TATTACTCTGGACCCAAAATTGGCACATCCAAATAAGT-AGTTTATTTCAAAAGAAATAAACAGTGCTTGTGGGCTAAA Template switch alignment (log-probability: -27.9) TATTACTCTGGACCCAAAATTGGCACATCC-------------------AAAGAAATAA|GTTTATTTCTTTT|GAAATAAACAGTGCTTGTGGGCTAAA TATTACTCTGGACCCAAAATTGGCACATCCAAATAAGTAGTTTATTTCAAAAGAAATAA|GTTTATTTCTTTT|GAAATAAACAGTGCTTGTGGGCTAAA Chimp > Gorilla --------------- chr1:195738835-195738847 Template switch process: F1: L ACATAATTTATTACTCTGGACCCAAAATTGGCACATCCAAATAAGTA 1 F3: 4 GAAATAAACAGTGCTTGTGGGCTAAA R RF: ACATAATTTATTACTCTGGACCCAAAATTGGCACATCCAAAGAAATAAGTTTATTTCTTTTGAAATAAACAGTGCTTGTGGGCTAAA RR: TGTATTAAATAATGAGACCTGGGTTTTAACCGTGTAGGTTTCTTTATTCAAATAAAGAAAACTTTATTTGTCACGAACACCCGATTT F2: 3 AAAACTTTATTTG 2 Unidirectional alignment (log-probability: -44.1) TTATTACTCTGGACCCAAAATTGGCACATCCAAAtAAgT-AGTTTATTTCaaaaGAAATAAACAGTGCTTGTGGGCTAAA TTATTACTCTGGACCCAAAATTGGCACATCCAAAGAAATAAGTTTATTTCTTTTGAAATAAACAGTGCTTGTGGGCTAAA Template switch alignment (log-probability: -28.2) TTATTACTCTGGACCCAAAATTGGCACATCCAAAtAAgTA|GTTTATTTCAAAA|GAAATAAACAGTGCTTGTGGGCTAAA TTATTACTCTGGACCCAAAATTGGCACATCCAAAGAAATA|GTTTATTTCAAAA|GAAATAAACAGTGCTTGTGGGCTAAA ========= Event 601 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCTCTCTGTATACTTGCTCAAGATCAGGCTCAAATGCAAATG------------GAGCCTGATCTTGAGCAAGTATACAGAGAGGAGCCA Chimp: CCTCTCTGTATACTTGCTCAAGATCAGGCTCCAATGCAAATG------------GAGCCTGATCTTGAGCAAGTATACAGAGAGGAGCCA ↑ 3 2 4 1 Gorilla: CCTCTCTGTATACTTGCTCAAGATCAGGCTCCAATGCAAATG------------------------GAGCAAGTATACAGAGAGGAGCCA ↓ 3 2 4 1 Human: CCTCTCTGTATACTTGCTCAAGATCAGGCTCAAATGCAAATG------------GAGCCTGATCTTGAGCAAGTATACAGAGAGGAGCCA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------------NNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr12:116995381-116995388 Template switch process: F1: L CTCTCTGTATACTTGCTCAAGATCAGGCTCAAATGCAAATGGAGC 1 F3: 4 GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA R RF: CTCTCTGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGGAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA RR: GAGAGACATATGAACGAGTTCTAGTCCGAGGTTACGTTTACCTCGTTCATATGTCTCTCCTCGGTTTGTTAGGTCTACCCT F2: 3 TTCTAGTC 2 Unidirectional alignment (log-probability: -33.7) TGTATACTTGCTCAAGATCAGGCTCaAATGCAAATGgagcctgatcttGAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA TGTATACTTGCTCAAGATCAGGCTCCAATGCAAATG------------GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA Template switch alignment (log-probability: -22.4) TGTATACTTGCTCAAGATCAGGCTCaAATGCAAATGGAGC|CTGATCTT|GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA TGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGGAGC|CTGATCTT|GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA Gorilla > Chimp --------------- chr12:120255858-120255865 Template switch process: F1: L CTCTCTGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGGAGC 1 F3: 4 GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA R RF: CTCTCTGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGGAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA RR: GAGAGACATATGAACGAGTTCTAGTCCGAGGTTACGTTTACCTCGTTCATATGTCTCTCCTCGGTTTGTTAGGTCTACCCT F2: 3 TTCTAGTC 2 Unidirectional alignment (log-probability: -28.1) TGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGgagcctgatcttGAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA TGTATACTTGCTCAAGATCAGGCTCCAATGCAAATG------------GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA Template switch alignment (log-probability: -16.8) TGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGGAGC|CTGATCTT|GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA TGTATACTTGCTCAAGATCAGGCTCCAATGCAAATGGAGC|CTGATCTT|GAGCAAGTATACAGAGAGGAGCCAAACAATCCAGATGGGA ========= Event 602 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGACTTTGAATGTAATTCATTTGCTACAAAGTG---------GGTTTTCACCCC--CTGCTCTTCTC-TTTCACTCACA Chimp: TTGACTTTGAATGTAATTCATTTGCTACAAAGTG---------GGTTTTCACCCC--CTGCTCTTCTC-TTTCACTCACA ↓ 3 2 1 4 Gorilla: TTGACTTTGAATGTAATTCATTTGCTACAAAGTA-----------------GCAA--ATGCTCTTCTC-TTTCACTCACA ↑ 3 2 1 4 Human: TTGACTTTGAATGTAATTCATTTGCTACAAAGTG---------GGTTTTCACCCC--CTGCTCTTCTC-TTTCACTCACA Cluster: [ ] Orangutan: TTGACTTTGAATGTAATTCATTTGCTACAAAGTGGGGTTTTCA--------CCCCCCTGGCTCTTCTCTTTTCACTCACA Human > Gorilla --------------- chr12:116310317-116310323 Template switch process: F1: L GTTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT 1 F3: 4 GCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG R RF: GTTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGTGGGTTTTCACCCCCTGCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG RR: CAATTTTTAACTGAAACTTACATTAAGTAAACGATGTTTCACCCAAAAGTGGGGGACGAGAAGAGAAAGTGAGTGTAGGTGTAAAAGCAAAGATC F2: 3 TAAACGA 2 Unidirectional alignment (log-probability: -30) TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT--------------agcaaaTGCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGTGGGTTTTCACCCCC------TGCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG Template switch alignment (log-probability: -16.6) TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT|AGCAAAT|GCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT|AGCAAAT|GCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG Chimp > Gorilla --------------- chr12:116310317-116310323 Template switch process: F1: L GTTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT 1 F3: 4 GCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG R RF: GTTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGTGGGTTTTCACCCCCTGCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG RR: CAATTTTTAACTGAAACTTACATTAAGTAAACGATGTTTCACCCAAAAGTGGGGGACGAGAAGAGAAAGTGAGTGTAGGTGTAAAAGCAAAGATC F2: 3 TAAACGA 2 Unidirectional alignment (log-probability: -30) TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT--------------agcaaaTGCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGTGGGTTTTCACCCCC------TGCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG Template switch alignment (log-probability: -16.6) TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT|AGCAAAT|GCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG TTAAAAATTGACTTTGAATGTAATTCATTTGCTACAAAGT|AGCAAAT|GCTCTTCTCTTTCACTCACATCCACATTTTCGTTTCTAG ========= Event 603 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGTTTAATTTCTTCTTGAAACGTATAAAATTCTAAAGACTG------------------------------------GCTGACTTTAGCTTGTCAGGAGGAAGAGCTAGTAGAGTTTGCAA-GGAGAAGAAATACGTGcagggctggaactagggt Chimp: CTGTTTAATTTCTTCTTGAAAC--ATAAAATTCTAAAGACTG------------------GCTGGCTGTCTACAAATGGCTGACTTTAGCTTGTCAGGAGGAAGAGCTAGTAGAGTTTGCAA-GGAGAAGAAATACGTGcagggctggaactagggt Gorilla: CTGTTTAATTTCTTCTTGAAATATCTAAAATTCTAAAGACTGGCTGGCTGTCTACAAATG------------------GCTGACTTTAGCTTGTCAGGAGGAAGAGCTAGTAGAGTTTGCAAGACAGAAGAAATACGTGcagggctggaactagggt ↓ 1 4 3 2 Human: CTGTTTAATTTCTTCTTGAAACGTATAAAATTCTAAAGACTG------------------------------------GCTGACTTTAGCTTGTCAGGAGGAAGAGCTAGTAGAGTTTGCAA-GGAGAAGAAATACGTGcagggctggaactagggt Cluster: [ ] Orangutan: ctgtttaatttcttcttgaaacatctaaaattctaaagactggctggctgtctacAAATG------------------GCTGACTTTAGCTTGTCAGGAGGAAGAGCTAGTAGAGTTTCCAAGAGAGAAGAAATGCATGcagggctggaactagggt Gorilla > Human --------------- chr1:217685045-217685048 Template switch process: F1: L ACGTGAATCATAGGGGACTGCTGTTTAATTTCTTCTTGAAA 1 F3: 4 TAAAATTCTAAAGACTGGCTGA R RF: ACGTGAATCATAGGGGACTGCTGTTTAATTTCTTCTTGAAATATCTAAAATTCTAAAGACTGGCTGGCTGTCTACAAATGGCTGACTTTAGCTTGTCAGGAGGAAGAGCTAGTAGAGTTTGCAAGACAGAAGAAATACG RR: TGCACTTAGTATCCCCTGACGACAAATTAAAGAAGAACTTTATAGATTTTAAGATTTCTGACCGACCGACAGATGTTTACCGACTGAAATCGAACAGTCCTCCTTCTCGATCATCTCAAACGTTCTGTCTTCTTTATGC F2: 3 ATGC 2 Unidirectional alignment (log-probability: -28.2) CGTGAATCATAGGGGACTGCTGTTTAATTTCTTCTTGAAAcgTaTAAAATTCTAAAGAC------------------TGGCTGA CGTGAATCATAGGGGACTGCTGTTTAATTTCTTCTTGAAATATCTAAAATTCTAAAGACTGGCTGGCTGTCTACAAATGGCTGA Template switch alignment (log-probability: -21.3) CGTGAATCATAGGGGACTGCTGTTTAATTTCTTCTTGAAA|CGTA|TAAAATTCTAAAGACTGGCTGa CGTGAATCATAGGGGACTGCTGTTTAATTTCTTCTTGAAA|CGTA|TAAAATTCTAAAGACTGGCTGG ========= Event 604 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCAGTAGGTCCAGTCGAGAAACTAGCC----------TGGGATTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGTCCACATATGCACAAACACACACCTCACTGTGGGTACCTCATATCTAGTTCCTAATCTAAATTCTCCCAGGGATTCCTCTGTGATCCTGACTTCCCAGCTTCAGGCTGCGATTGCCTT Chimp: TTCAGTAGGTCCAGTCGAGAACCTAGCC-----TCTCCTCTCCTTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGTCCACATATGCACAAACACACACCTCACTGTGGGTACCTCATATCTAGTTCCTAATCTAAATTCTCCCAGGGATTCCTCTGTGATCCTGACTTCCCAGCTTCAGGCTGCGATTGCCTT Gorilla: TTCAGTAGGTCCAGTCGAGAACCTAGCGTCTCC-----TCTCCTTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGTCCACATATGCACAAACACACACCTCACTGTGGGTACCTCATATCTAGTTCCTAATCTAAATTCTCCCAGGGATTCCTCTGTGATCCTGACTTCCCAGCTTCAGGCTGCGATTGCCTT ↓ 1 4 3 2 Human: TTCAGTAGGTCCAGTCGAGAAACTAGCC----------TGGGATTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGTCCACATATGCACAAACACACACCTCACTGTGGGTACCTCATATCTAGTTCCTAATCTAAATTCTCCCAGGGATTCCTCTGTGATCCTGACTTCCCAGCTTCAGGCTGCGATTGCCTT Cluster: [ ] Orangutan: TTCAGTAGGTCCAGTTGAGAACCTAGCCTCTCC-----TCTCCTTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATTTCCACATATGCACAAACACACACCTCACTGTGGGTACCTCGTATGTAGTTCCTAATCTAAATTCT-CCAGGGATTCCTCTGTGATCCTGACTTTCCAGCTTCAGGCTGTGATTGCCTT Gorilla > Human --------------- chr1:217011620-217011625 Template switch process: F1: L AAAAAAACTTCACTCCTCGTTTCAGTAGGTCCAGTCGAGAAACTAGC 1 F3: 4 TTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGT R RF: AAAAAAACTTCACTCCTCGTTTCAGTAGGTCCAGTCGAGAACCTAGCGTCTCCTCTCCTTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGTCCACATATGCACAAACACACACCTCACTGTGGGTACCTCATATCTAGTTCCTAATCTAAATTCTCCCAGGGATTCCTCTGTGATCCTGACTTCCCAG RR: TTTTTTTGAAGTGAGGAGCAAAGTCATCCAGGTCAGCTCTTGGATCGCAGAGGAGAGGAACGAAACCCTAACCAAAACAGAACCTCTTCTGTATTACAGGTGTATACGTGTTTGTGTGTGGAGTGACACCCATGGAGTATAGATCAAGGATTAGATTTAAGAGGGTCCCTAAGGAGACACTAGGACTGAAGGGTC F2: 3 AGGGTC 2 Unidirectional alignment (log-probability: -33.9) CTTCACTCCTCGTTTCAGTAGGTCCAGTCGAGAAaCTAG----------CCtgggaTTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGT CTTCACTCCTCGTTTCAGTAGGTCCAGTCGAGAACCTAGCGTCTCCTCTCC-----TTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGT Template switch alignment (log-probability: -22.2) CTTCACTCCTCGTTTCAGTAGGTCCAGTCGAGAAaCTAGC|CTGGGA|TTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGT CTTCACTCCTCGTTTCAGTAGGTCCAGTCGAGAACCTAGC|CTGGGA|TTGCTTTGGGATTGGTTTTGTCTTGGAGAAGACATAATGT ========= Event 605 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTACTAGAGGGGGTTGCGTATTC-----ATCTTTGGATACTTTTtgtagttgagagaacaatggaag Chimp: GTACTAGAGGGGGTTGCGTATTC-----ATCTTTGGATACTTTTTGtagttgagagaacaatggaag ↓ 1 4 3 2 Gorilla: GTACTAGAGGGGGTTGCGTATACAAAAAGTATTTGGATACTTTTtgtaattgagagaacaatggaag ↑ 1 4 3 2 Human: GTACTAGAGGGGGTTGCGTATTC-----ATCTTTGGATACTTTTtgtagttgagagaacaatggaag Cluster: [ ] Orangutan: GTACTAGAGGGGGTTGCATATTC-----ATCTTTGGATACTTTTtgtagttgagagaacaatggaag Human > Gorilla --------------- chr1:197260313-197260322 Template switch process: F1: L TTGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTAT 1 F3: 4 TTTGGATACTTTTTGTAATTGAGAGAACAATGGAAGAAAG R RF: TTGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTATTCATCTTTGGATACTTTTTGTAGTTGAGAGAACAATGGAAGAAAG RR: AACAAAACAAAAAGTTGGTCCATGATCTCCCCCAACGCATAAGTAGAAACCTATGAAAAACATCAACTCTCTTGTTACCTTCTTTC F2: 3 ATGAAAAACA 2 Unidirectional alignment (log-probability: -34.7) TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTATaCAaaaagTaTTTGGATACTTTTTGTAaTTGAGAGAACAATGGAAGAAAG TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTATTCA-----TCTTTGGATACTTTTTGTAGTTGAGAGAACAATGGAAGAAAG Template switch alignment (log-probability: -22.5) TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTAT|ACAAAAAGTA|TTTGGATACTTTTTGTAaTTGAGAGAACAATGGAAGAAAG TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTAT|ACAAAAAGTA|TTTGGATACTTTTTGTAGTTGAGAGAACAATGGAAGAAAG Chimp > Gorilla --------------- chr1:197260313-197260322 Template switch process: F1: L TTGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTAT 1 F3: 4 TTTGGATACTTTTTGTAATTGAGAGAACAATGGAAGAAAG R RF: TTGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTATTCATCTTTGGATACTTTTTGTAGTTGAGAGAACAATGGAAGAAAG RR: AACAAAACAAAAAGTTGGTCCATGATCTCCCCCAACGCATAAGTAGAAACCTATGAAAAACATCAACTCTCTTGTTACCTTCTTTC F2: 3 ATGAAAAACA 2 Unidirectional alignment (log-probability: -34.7) TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTATaCAaaaagTaTTTGGATACTTTTTGTAaTTGAGAGAACAATGGAAGAAAG TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTATTCA-----TCTTTGGATACTTTTTGTAGTTGAGAGAACAATGGAAGAAAG Template switch alignment (log-probability: -22.5) TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTAT|ACAAAAAGTA|TTTGGATACTTTTTGTAaTTGAGAGAACAATGGAAGAAAG TGTTTTGTTTTTCAACCAGGTACTAGAGGGGGTTGCGTAT|ACAAAAAGTA|TTTGGATACTTTTTGTAGTTGAGAGAACAATGGAAGAAAG ========= Event 606 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATGTGGCATTGCTTGTTGTCGTAATTTCCTGTGCCTGAGACCTAACTTTGTCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTGGTACTGTGGTCTACGAGGTGGATGCTTCTCTTTGG ↓ 3 2 1 4 Chimp: CATGTGGCATTGCTTGTTGTTGTAATTTCCTGTGCCTGAGACCTAACTTTGTCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGT-GTA-CGAGGTCTACAAGGTGGATGCTTGTCTTTGG ↑ 3 2 1 4 Gorilla: CATGTGGCATTGCTTGTTGTCGTAATTTCCTGTGCCTGAGACCTAACTTCATCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGAAGTGGTACTGTGGTCTACGAGGTGGATGCTTGTCTTTGG Human: CATGTGGCATTGCTTGTTGTCGTAATTTCCTGTGCCTGAGACCTAACTTTGTCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTGGTACTGTGGTCTACGAGGTGGATGCTTCTCTTTGG Cluster: [ ] Orangutan: CATGTGACATTGCTTGTTGTCATAATTTCCTGTGCCTGAGACCTAACTTTGTCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAAGGGCTGTGGGAGTGGTACTGTGGTCTAGGAAGTGGATGCTTGTCTTTGG Human > Chimp ------------- chr12:18733166-18733170 Template switch process: F1: L AAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTG 1 F3: 4 GGTCTACAAGGTGGATGCTTGTCTTTGGAAAGAAACAGTAATTAGAGT R RF: TCGTAATTTCCTGTGCCTGAGACCTAACTTTGTCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTGGTACTGTGGTCTACGAGGTGGATGCTTCTCTTTGGAAAGAAACAGTAATTAGAGT RR: AGCATTAAAGGACACGGACTCTGGATTGAAACAGTCGTTAAACCGGTTTTAATTCGGAACCCAGAGTTGAACTTTGTGTAGAACGCAGTTTCCAGGTGTCCCCGACACCCTCACCATGACACCAGATGCTCCACCTACGAAGAGAAACCTTTCTTTGTCATTAATCTCA F2: 3 AGCAT 2 Unidirectional alignment (log-probability: -39.3) ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAG------TGTacgaGGTCTACaAGGTGGATGCTTgTCTTTGGAAAGAAACAGTA ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTGGTACTGT----GGTCTACGAGGTGGATGCTTCTCTTTGGAAAGAAACAGTA Template switch alignment (log-probability: -28.1) ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTG|TACGA|GGTCTACaAGGTGGATGCTTgTCTTTGGAAAGAAACAGTA ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTG|TACGA|GGTCTACGAGGTGGATGCTTCTCTTTGGAAAGAAACAGTA Gorilla > Chimp --------------- chr12:18733166-18733170 Template switch process: F1: L CTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGGAGTG 1 F3: 4 GGTCTACAAGGTGGATGCTTGTCTTTGGAAAGAAACAGTAATTAGAGT R RF: TCGTAATTTCCTGTGCCTGAGACCTAACTTCATCAGCAATTTGGCCAAAATTAAGCCTTGGGTCTCAACTTGAAACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGAAGTGGTACTGTGGTCTACGAGGTGGATGCTTGTCTTTGGAAAGAAACAGTAATTAGAGT RR: AGCATTAAAGGACACGGACTCTGGATTGAAGTAGTCGTTAAACCGGTTTTAATTCGGAACCCAGAGTTGAACTTTGTGTAGAACGCAGTTTCCAGGTGTCCCCGACACCTTCACCATGACACCAGATGCTCCACCTACGAACAGAAACCTTTCTTTGTCATTAATCTCA F2: 3 AGCAT 2 Unidirectional alignment (log-probability: -37.5) ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGgAGT-GTAC-GaGGTCTACaAGGTGGATGCTTGTCTTTGGAAAGAAACAGTA ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGAAGTGGTACTGTGGTCTACGAGGTGGATGCTTGTCTTTGGAAAGAAACAGTA Template switch alignment (log-probability: -27.7) ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGgAGTG|TACGA|GGTCTACaAGGTGGATGCTTGTCTTTGGAAAGAAACAGTA ACACATCTTGCGTCAAAGGTCCACAGGGGCTGTGGAAGTG|TACGA|GGTCTACGAGGTGGATGCTTGTCTTTGGAAAGAAACAGTA ========= Event 607 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCTGTGTTATAGGTTTGCAATGCACCAAG--GGCTT-ATGAAAGCTGGTATCATTGAT ↓ 3 1 2 4 Chimp: GTCTGTGTTATAGGTTTGCAATGCACCTTGGTGCATT-ATGAAAGCTGGTATCATTGAT ↑ 3 1 2 4 Gorilla: GTCTGTGTTATAGGTTTGCAATGCACCAAG--GGCTTATTGAAAGCTGGTATCATTGAT Human: GTCTGTGTTATAGGTTTGCAATGCACCAAG--GGCTT-ATGAAAGCTGGTATCATTGAT Cluster: [ ] Orangutan: GTCTGTGTTATAGGTTTGCAATGCACCAAG--GGCTT-ATGAAAGCTGGTATCATTGAT Human > Chimp ------------- chr1:29897826-29897833 Template switch process: F1: L TTGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC 1 F3: 4 TTATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGC R RF: TTGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACCAAGGGCTTATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGC RR: AACAATCAATTGTTCAGACACAATATCCAAACGTTACGTGGTTCCCGAATACTTTCGACCATAGTAACTAAACGTCTTACGGTTCCG F2: 3 ACGTGGTT 2 Unidirectional alignment (log-probability: -31.5) TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACcttggtgCA-----TTATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGC TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCAC-------CAAGGGCTTATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGC Template switch alignment (log-probability: -16.3) TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC|TTGGTGCA|TTATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGC TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC|TTGGTGCA|TTATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGC Gorilla > Chimp --------------- chr1:29897826-29897835 Template switch process: F1: L TTGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC 1 F3: 4 ATGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGCTTG R RF: TTGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACCAAGGGCTTATTGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGCTTG RR: AACAATCAATTGTTCAGACACAATATCCAAACGTTACGTGGTTCCCGAATAACTTTCGACCATAGTAACTAAACGTCTTACGGTTCCGAAC F2: 3 TTACGTGGTT 2 Unidirectional alignment (log-probability: -35.5) TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC---------TtggtgcattaTGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGCTT TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACCAAGGGCTTAT----------TGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGCTT Template switch alignment (log-probability: -22.5) TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC|TTGGTGCATT|aTGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGCTT TGTTAGTTAACAAGTCTGTGTTATAGGTTTGCAATGCACC|TTGGTGCATT|TTGAAAGCTGGTATCATTGATTTGCAGAATGCCAAGGCTT ========= Event 608 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCTATTTTAACTTCTTTCAAAGTTAATGGATCATTCTGT---TCTTAGAGTT--TGGCTGCAGT Chimp: ATTCTATTTTAACTTCTTTCAAAGTTAATGGATCATTCTGT---TCTTAGAGTT--TGGCTGCAGT ↓ 3 1 2 4 Gorilla: ATTCTATTTTAACTTCTTTCAGAGTTAGTGGATCAGAATGATCCACTTAGAGTT--TGGCTGCAGT ↑ 3 1 2 4 Human: ATTCTATTTTAACTTCTTTCAAAGTTAATGGATCATTCTGT---TCTTAGAGTT--TGGCTGCAGT Cluster: [ ] Orangutan: ATTCTGTTTTAACTTCCTTCAAAATTAATGGGTCATTCTGT---TCTTAGAGTTTCAGGCTGCTGT Human > Gorilla --------------- chr12:19192205-19192214 Template switch process: F1: L TTTTCTTTCATCTTTTAAAAATTCTATTTTAACTTCTTTCAGAGTTAGTGGATCA 1 F3: 4 CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC R RF: TTTTCTTTCATCTTTTAAAAATTCTATTTTAACTTCTTTCAAAGTTAATGGATCATTCTGTTCTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC RR: AAAAGAAAGTAGAAAATTTTTAAGATAAAATTGAAGAAAGTTTCAATTACCTAGTAAGACAAGAATCTCAAACCGACGTCAGAAACAATGGACTCCTTATAG F2: 3 ACCTAGTAAG 2 Unidirectional alignment (log-probability: -46.6) TAAAAATTCTATTTTAACTTCTTTCAgAGTTAgTGGATcagaatgatcCA-------CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC TAAAAATTCTATTTTAACTTCTTTCAAAGTTAATGGAT----------CATTCTGTTCTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC Template switch alignment (log-probability: -28.4) TAAAAATTCTATTTTAACTTCTTTCAgAGTTAgTGGATCA|GAATGATCCA|CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC TAAAAATTCTATTTTAACTTCTTTCAAAGTTAATGGATCA|GAATGATCCA|CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC Chimp > Gorilla --------------- chr12:19192205-19192214 Template switch process: F1: L TTTTCTTTCATCTTTTAAAAATTCTATTTTAACTTCTTTCAGAGTTAGTGGATCA 1 F3: 4 CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC R RF: TTTTCTTTCATCTTTTAAAAATTCTATTTTAACTTCTTTCAAAGTTAATGGATCATTCTGTTCTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC RR: AAAAGAAAGTAGAAAATTTTTAAGATAAAATTGAAGAAAGTTTCAATTACCTAGTAAGACAAGAATCTCAAACCGACGTCAGAAACAATGGACTCCTTATAG F2: 3 ACCTAGTAAG 2 Unidirectional alignment (log-probability: -46.6) TAAAAATTCTATTTTAACTTCTTTCAgAGTTAgTGGATcagaatgatcCA-------CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC TAAAAATTCTATTTTAACTTCTTTCAAAGTTAATGGAT----------CATTCTGTTCTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC Template switch alignment (log-probability: -28.4) TAAAAATTCTATTTTAACTTCTTTCAgAGTTAgTGGATCA|GAATGATCCA|CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC TAAAAATTCTATTTTAACTTCTTTCAAAGTTAATGGATCA|GAATGATCCA|CTTAGAGTTTGGCTGCAGTCTTTGTTACCTGAGGAATATC ========= Event 609 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: tgagttagcacctaatattgtttactataGGAAGTTAAAATAAAATTAGAGACCATATATAGCAGGTACCATAACATTGACTAAAACACCATAAGTGCTTCATAAACAGGAGGTATGGTTTATGTGATAATAATAAATGTAATGTTATCA-----------------------ATGAATAGTAAACATGAAATGTAATGAGCTTGTGAGCATCAATGTAT Chimp: tgagtgagcacctaatattgtttactataGGAAGTTAAAATAAAATTAGAGACCATATATAGCAGGTACCATAACATTGACTAAAACACCATAAGTGCTTCATAAACAGGAGGTATGGTTTATGTGATAATAATAAATGTAATGTTATCA-----------------------ATGAATAGTAAACATGAAACGTAATGAGCTTGTGAGCATCAATGTAT Gorilla: tgagtgagcacctaatattgtttactataGGAAGTTAAAATAAAATTAGAGACCATATATAGCAGGTACCATAACATTGACTAAAACACCATAAGTGCTTCATAAACAGGAGGTATGGTTTATGTGATAATAATAAATGTAATGTTATCA----------------------------------------------ATGAGCTTGTGAGCATCAATGTAT ↓ 3 2 4 1 Human: tgagttagcacctaatattgtttactataGGAAGTTAAAATAAAATTAGAGACCATATATAGCAGGTACCATAACATTGACTAAAACACCATAAGTGCTTCATAAACAGGAGGTATGGTTTATGTGATAATAATAAATGTAATGTTATCA-----------------------ATGAATAGTAAACATGAAATGTAATGAGCTTGTGAGCATCAATGTAT Cluster: [ ] Orangutan: tgagtgagcacctaatattgtttactataGGAAGTTAAAATAAAATTAGAGACCACATATAGCAGGTACCATAACAT----TAAAACACCATAAGTGCTTCATAAACAGGAGGTATGGTTTATGTGATAAAAATAAATGTAATGTTATCAATGAATAGTAAACATGAAACGTA-----------------------ATGAGCTTGTGAGCATCTGTGTGT Gorilla > Human --------------- chr1:219407500-219407508 Template switch process: F1: L GAGGTATGGTTTATGTGATAATAATAAATGTAATGTTATCAATGA 1 F3: 4 ATGAAATGT----AATGAGCTTGTGAGCATCAATGTATGTTACTGTAAGTATTT R RF: GTTTACTATAGGAAGTTAAAATAAAATTAGAGACCATATATAGCAGGTACCATAACATTGACTAAAACACCATAAGTGCTTCATAAACAGGAGGTATGGTTTATGTGATAATAATAAATGTAATGTTATCAATGAGCTTGTGAGCATCAATGTATGTTACTGTAAGTATTT RR: CAAATGATATCCTTCAATTTTATTTTAATCTCTGGTATATATCGTCCATGGTATTGTAACTGATTTTGTGGTATTCACGAAGTATTTGTCCTCCATACCAAATACACTATTATTATTTACATTACAATAGTTACTCGAACACTCGTAGTTACATACAATGACATTCATAAA F2: 3 CAAATGATA 2 Unidirectional alignment (log-probability: -44) ATGGTTTATGTGATAATAATAAATGTAATGTTATCaatgaatagtaaacatgaaatgtAATGAGCTTGTGAGCATCAATGTATGTTACT ATGGTTTATGTGATAATAATAAATGTAATGTTATC-----------------------AATGAGCTTGTGAGCATCAATGTATGTTACT Template switch alignment (log-probability: -32.7) ATGGTTTATGTGATAATAATAAATGTAATGTTATCAATGA|ATAGTAAAC|ATGaAATGT----AATGAGCTTGTGAGCATCAATGTATGTTACT ATGGTTTATGTGATAATAATAAATGTAATGTTATCAATGA|ATAGTAAAC|ATGTAATGTTATCAATGAGCTTGTGAGCATCAATGTATGTTACT ========= Event 610 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAGCTAAGTCAAACTTGTTTTGTGATGTGAACTTAAGTTCATATCACATCTCATTTTCTTTCATATT Chimp: TAAGTTAAGTCAAACTTGTTT------------TCAAGTTCATATCACATCTCATTTTCTTTCATATA Gorilla: TAAGCTAAGTCAAACTTGTTT------------TCAAGTTCATATCACATCTCATTTTCTTTCATATT ↓ 1 4 2 Human: TAAGCTAAGTCAAACTTGTTTTGTGATGTGAACTTAAGTTCATATCACATCTCATTTTCTTTCATATT Cluster: [ ] Orangutan: TAAGCTAAGTCAAACTTGTTT------------TCAAGTTCATATCACATGTCATTTTCTTTCATATT Gorilla > Human --------------- chr12:19227915-19227927 Template switch process: F1: L TCAAAATCTAAACAGTAATATAAGCTAAGTCAAACTTGTTTT 1 F3: 4 AAGTTCATATCACATCTCATTTTCTTTCATATTCATTTCT R RF: TCAAAATCTAAACAGTAATATAAGCTAAGTCAAACTTGTTTTCAAGTTCATATCACATCTCATTTTCTTTCATATTCATTTCT RR: AGTTTTAGATTTGTCATTATATTCGATTCAGTTTGAACAAAAGTTCAAGTATAGTGTAGAGTAAAAGAAAGTATAAGTAAAGA F2: 3 TTCAAGTGTAGTG 2 Unidirectional alignment (log-probability: -33.7) AAAATCTAAACAGTAATATAAGCTAAGTCAAACTTGTTTtgtgatgtgaacTtAAGTTCATATCACATCTCATTTTCTTTCATATTCATTTCT AAAATCTAAACAGTAATATAAGCTAAGTCAAACTTGTTT------------TCAAGTTCATATCACATCTCATTTTCTTTCATATTCATTTCT Template switch alignment (log-probability: -22.9) AAAATCTAAACAGTAATATAAGCTAAGTCAAACTTGTTTT|GTGATgTGAACTT|AAGTTCATATCACATCTCATTTTCTTTCATATTCATTTCT AAAATCTAAACAGTAATATAAGCTAAGTCAAACTTGTTTT|GTGATATGAACTT|AAGTTCATATCACATCTCATTTTCTTTCATATTCATTTCT ========= Event 611 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTATAACTTTATTACAATCAAATAAAGTCAGTTAACTTTATTTGATTTAACTCCCTATGAGAACT ↑ 3 2 1 4 Chimp: ATTATAACTTTATTACAATCAAATAAAGTCAGTTA---------CATTTAACTCCCTATAAGAACT Gorilla: ATTATAACTTTATTAGAATCAAATAAAGTGAGTCA---------CATTTAACTCCCTATGAGAACT Human: ATTATAACTTTATTACAATCAAATAAAGTCAGTTAACTTTATTTGATTTAACTCCCTATGAGAACT Cluster: [ ] Orangutan: ATTATAACTTTATTACAATTAAATAAAGTGAGTTA---------CATTTAACTCCCTATGAGAACT Chimp > Human ------------- chr12:113279986-113279995 Template switch process: F1: L TATTGTATTATAACTTTATTACAATCAAATAAAGTCAGTTA 1 F3: 4 ATTTAACTCCCTATGAGAACTAAGTTCATATCACTTCCAA R RF: TATTGTATTATAACTTTATTACAATCAAATAAAGTCAGTTACATTTAACTCCCTATAAGAACTAAGTTCATATCACTTCCAA RR: ATAACATAATATTGAAATAATGTTAGTTTATTTCAGTCAATGTAAATTGAGGGATATTCTTGATTCAAGTATAGTGAAGGTT F2: 3 GTTTATTTCA 2 Unidirectional alignment (log-probability: -35.9) ATTGTATTATAACTTTATTACAATCAAATAAAGTCAGTTAactttatttgATTTAACTCCCTATgAGAACTAAGTTCATATCACTTCCAA ATTGTATTATAACTTTATTACAATCAAATAAAGTCAGTTA---------CATTTAACTCCCTATAAGAACTAAGTTCATATCACTTCCAA Template switch alignment (log-probability: -22.5) ATTGTATTATAACTTTATTACAATCAAATAAAGTCAGTTA|ACTTTATTTG|ATTTAACTCCCTATgAGAACTAAGTTCATATCACTTCCAA ATTGTATTATAACTTTATTACAATCAAATAAAGTCAGTTA|ACTTTATTTG|ATTTAACTCCCTATAAGAACTAAGTTCATATCACTTCCAA ========= Event 612 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATGAGCTTACTGGTGTCAAAAGACACTTGCAGAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGAAGAACCAGTCTGTTATCAAGGGATACCACTGGTGATTTCATGGTGTTGCATGTATTTCATGTCACTGGTGAAAATAATTTT ↓ 1 4 3 2 Chimp: CATGAGCTTACTGGTGTCAAA----CATGGCAAAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGAAGAACTAGTCTGCTATCAAGGGATACCACTGGTGATTTCATGGTGTTGCATGTATTTCGTGTCACTGGTGAAAATAATTTT Gorilla: CATGAGCTTAATGGTGTCAAAGGACACTTGCAAAACAAATCTGGCTGCCATGTTTGTGCCTCACATGGAAGAACTAGTCTGCTATCAAGGGATACCACTGGTGATTTCATGGTGTTGCATGTATTTCATGTCACTGGTGAAAACAATTTT Human: CATGAGCTTACTGGTGTCAAAAGACACTTGCAGAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGAAGAACCAGTCTGTTATCAAGGGATACCACTGGTGATTTCATGGTGTTGCATGTATTTCATGTCACTGGTGAAAATAATTTT Cluster: [ ] Orangutan: CATGAGCTTGCTGGTGTCAAAGGACAATTGCAAAACTAATCTGGCTGCCATGTTTGTGCCTCACATGGAAGAACTAGTCTGCTATCAAGGGATACCACTGGTGATTTCATGGTGTTGCA-TTATTTCATGTCATTGGTGAAAACAATTTT Human > Chimp ------------- chr12:116380964-116380967 Template switch process: F1: L AACAACAAACCATTTCTGGTCATGAGCTTACTGGTGTCAAA 1 F3: 4 GCAAAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGAAGAA R RF: AACAACAAACCATTCCTGGTCATGAGCTTACTGGTGTCAAAAGACACTTGCAGAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGAAGAACCAGTCTGTTATCAAGGGATACCACTGGTGATTTCATGGTGTTGCATGTATTTCATG RR: TTGTTGTTTGGTAAGGACCAGTACTCGAATGACCACAGTTTTCTGTGAACGTCTTGTTTAGACCGGCGGTACAAACACGGAGTGTACCTTCTTGGTCAGACAATAGTTCCCTATGGTGACCACTAAAGTACCACAACGTACATAAAGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -37.8) ACAACAAACCATTtCTGGTCATGAGCTTACTGGTGTCAAacatggcAA-----------AACAAATCTGGCCGCCATGTTTGTGCCTCACATGGA ACAACAAACCATTCCTGGTCATGAGCTTACTGGTGTCAA-------AAGACACTTGCAGAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGA Template switch alignment (log-probability: -27.8) ACAACAAACCATTtCTGGTCATGAGCTTACTGGTGTCAAA|CATG|GCAaAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGA ACAACAAACCATTCCTGGTCATGAGCTTACTGGTGTCAAA|CATG|GCAGAACAAATCTGGCCGCCATGTTTGTGCCTCACATGGA ========= Event 613 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: TATGGATGACATATAAAATAT---TCTTCAGGAATTATTGAATCACATTCTAAAGGCTGAAAAAGGTATAGGGTTTTCT-GATTACCTGCAACAGAGGGTATAAAATATGTGTCCAATGGATT Chimp: Gorilla: TATGGATGACATATAAAATATTCT---TCAGGAATTATTGAATCACATTCTAAA-GCAGAAAACCCTATACCTTTTTCAGCCTTATCTGTAACAGAGGGTATAAGGTATGTGTCCAATGGATT ↓ 1 3 2 4 Human: TATGGATGACATATAAAATAT---TCTTCAGGAATTATTGAATCACATTCTAAAGGCTGAAAAAGGTATAGGGTTTTCT-GATTACCTGCAACAGAGGGTATAAAATATGTGTCCAATGGATT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr1:308407-308413 Template switch process: F1: L ----GTTGGAGAACTTTATTTATGGATGACATATAAAATATTCTTCAGGAATTATTGAATCACATTCTAAAG 1 F3: 4 AAGGT R RF: GCTAGTTGGAGAACTTTATTTATGGATGACATATAAAATATTCTTCAGGAATTATTGAATCACATTCTAAAGCAGAAAACCCTATACCTTTTTCAGCCTTATCTGTAACAGAGGGTATAAGGT RR: CGATCAACCTCTTGAAATAAATACCTACTGTATATTTTATAAGAAGTCCTTAATAACTTAGTGTAAGATTTCGTCTTTTGGGATATGGAAAAAGTCGGAATAGACATTGTCTCCCATATTCCA F2: 3 AAAGTCG 2 Unidirectional alignment (log-probability: -39) ATAAAATATTCTTCAGGAATTATTGAATCACATTCTAAAgGCtGAAAAaggT ATAAAATATTCTTCAGGAATTATTGAATCACATTCTAAA-GCAGAAAACCCT Template switch alignment (log-probability: -26.4) ATAAAATATTCTTCAGGAATTATTGAATCACATTCTAAAG|GCTGAAA|AAGGT ATAAAATATTCTTCAGGAATTATTGAATCACATTCTAAAG|GCTGAAA|AAGGT ========= Event 614 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: GTCTG---TTATTTTTTCCTTAGGTTGGGCTTGTATTAACAA--TTTTCCCAACTGATACAGcagcacttct Chimp: Gorilla: GTCTGTTA---TTTTTTCCTTGGGAA--AATTGTTAATACAAGCCCAACCTAACTGATACAGCAGCACTTCT ↑ 13 24 Human: GTCTG---TTATTTTTTCCTTAGGTTGGGCTTGTATTAACAA--TTTTCCCAACTGATACAGcagcacttct Cluster: [ ] Orangutan: Human > Gorilla --------------- chr1:302312-302339 Template switch process: F1: L AATCAATACATTGTTCACAGGTCTGTTATTTTTTCCTT 1 F3: 4 AACTGATACAGCAGCACTTCTCAAACGCTTTCATGACATA R RF: AATCAATACACTGTTCACAGGTCTGTTATTTTTTCCTTAGGTTGGGCTTGTATTAACAATTTTCCCAACTGATACAGCAGCACTTCTCAAATGCTTTCATGACATA RR: TTAGTTATGTGACAAGTGTCCAGACAATAAAAAAGGAATCCAACCCGAACATAATTGTTAAAAGGGTTGACTATGTCGTCGTGAAGAGTTTACGAAAGTACTGTAT F2: 3 TCCAACCCGAACATAATTGTTAAAAGGG 2 Unidirectional alignment (log-probability: -72.9) AATCAATACAtTGTTCACAGGTCTGTTATTTTTTCCTTgggaaaattgttaatacaagcccaA------------------------CCtAACTGATACAGCAGCACTTCTCAAAcGCTTTCATGACATA AATCAATACACTGTTCACAGGTCTGTTATTTTTTCCTT------------------------AGGTTGGGCTTGTATTAACAATTTTCCCAACTGATACAGCAGCACTTCTCAAATGCTTTCATGACATA Template switch alignment (log-probability: -30.3) AATCAATACAtTGTTCACAGGTCTGTTATTTTTTCCTT|GGGAAAATTGTTAATACAAGCCCAACCT|AACTGATACAGCAGCACTTCTCAAAcGCTTTCATGACATA AATCAATACACTGTTCACAGGTCTGTTATTTTTTCCTT|GGGAAAATTGTTAATACAAGCCCAACCT|AACTGATACAGCAGCACTTCTCAAATGCTTTCATGACATA ========= Event 615 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCTAAAACATCTGTTAAAATA-GAGTAGGTTCTTGGAAGAACGAAATCCTATTAACTTATTACAAAAGTTA ↓ 13 24 ↑ 13 24 Chimp: CCTAAAACATCTGTTAAAATAGGATTTCGTTCTTCCAAGAACCTAC-TCTATTAACTTATTACAAAAGTTA Gorilla: CCTAAAACATCTGTTAAAATAGGATTTCGTTCTTCCAAGAACCAAC-TCCATTAACTTATTACAAAAGTTA ↓ 31 2 4 ↑ 13 24 Human: CCTAAAACATCTGTTAAAATA-GAGTAGGTTCTTGGAAGAACGAAATCCTATTAACTTATTACAAAAGTTA Cluster: [ ] Orangutan: CCTAAAACATCTGTTAAAATAGGATTTCGTTCTTCCAAGAACCAAC-TCTATTAACTTACTACAAAAGTTA Chimp > Human ------------- chr1:226892909-226892933 Template switch process: F1: L AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG 1 F3: 4 CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA R RF: AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGGATTTCGTTCTTCCAAGAACCTACTCTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA RR: TTAATCCTGTGTTCAATCCTGGATTTTGTAGACAATTTTATCCTAAAGCAAGAAGGTTCTTGGATGAGATAATTGAATAATGTTTTCAATAGATTCATTCTATAGAT F2: 3 CTAAAGCAAGAAGGTTCTTGGATGA 2 Unidirectional alignment (log-probability: -58.4) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG-------------------------agtaggttcttggaagaacgaaatcCTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGGATTTCGTTCTTCCAAGAACCTACT-------------------------CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA Template switch alignment (log-probability: -18.4) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|AGTAGGTTCTTGGAAGAACGAAATC|CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|AGTAGGTTCTTGGAAGAACGAAATC|CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA Human > Chimp ------------- chr1:207403104-207403128 Template switch process: F1: L AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG 1 F3: 4 CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA R RF: AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGAGTAGGTTCTTGGAAGAACGAAATCCTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA RR: TTAATCCTGTGTTCAATCCTGGATTTTGTAGACAATTTTATCTCATCCAAGAACCTTCTTGCTTTAGGATAATTGAATAATGTTTTCAATAGATTCATTCTATAGAT F2: 3 TCATCCAAGAACCTTCTTGCTTTAG 2 Unidirectional alignment (log-probability: -58.4) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG-------------------------gatttcgttcttccaagaacctactCTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGAGTAGGTTCTTGGAAGAACGAAATC-------------------------CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA Template switch alignment (log-probability: -18.4) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|GATTTCGTTCTTCCAAGAACCTACT|CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|GATTTCGTTCTTCCAAGAACCTACT|CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA Gorilla > Human --------------- chr1:226892909-226892935 Template switch process: F1: L AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG 1 F3: 4 ATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA R RF: AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGGATTTCGTTCTTCCAAGAACCAACTCCATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA RR: TTAATCCTGTGTTCAATCCTGGATTTTGTAGACAATTTTATCCTAAAGCAAGAAGGTTCTTGGTTGAGGTAATTGAATAATGTTTTCAATAGATTCATTCTATAGATTT F2: 3 TCCTAAAGCAAGAAGGTTCTTGGATGA 2 Unidirectional alignment (log-probability: -60.2) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGagtaG-----GTTCTTggAAGAACgAAaTCCtATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG----GATTTCGTTCTTCCAAGAACCAACTCC-ATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA Template switch alignment (log-probability: -24.7) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|AGTaGGTTCTTGGAAGAACGAAATCCT|ATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|AGTTGGTTCTTGGAAGAACGAAATCCT|ATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA Human > Gorilla --------------- chr1:206867076-206867100 Template switch process: F1: L AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG 1 F3: 4 CCATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA R RF: AATTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGAGTAGGTTCTTGGAAGAACGAAATCCTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTAAA RR: TTAATCCTGTGTTCAATCCTGGATTTTGTAGACAATTTTATCTCATCCAAGAACCTTCTTGCTTTAGGATAATTGAATAATGTTTTCAATAGATTCATTCTATAGATTT F2: 3 TCAACCAAGAACCTTCTTGCTTTAG 2 Unidirectional alignment (log-probability: -60.2) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG----GatttcGTTCTTccAAGAACcAAcTCC-ATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAGAGTAG-----GTTCTTGGAAGAACGAAATCCTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA Template switch alignment (log-probability: -30) TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|GATTTCGTTCTTCCAAGAACCaACT|CcATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA TTAGGACACAAGTTAGGACCTAAAACATCTGTTAAAATAG|GATTTCGTTCTTCCAAGAACCTACT|CTATTAACTTATTACAAAAGTTATCTAAGTAAGATATCTA ========= Event 616 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GATTAGGGAGGGTTGTAATCTCT-TTAGGCTCTCTGATTCTTGA--TAGATGTGTTTGTCTCTTTTGGCTGAACTTTAGGAATTTAATTAGTTGGATTCAGCATGCCTGGGATATAGGTTATTTTATAAACTTTTAGCTGTGCTGTGACAGCTGTCTAAAGATGCCACAATGCAAAATCCA ↑ 1 4 3 2 Chimp: GATTAGGGAGGGTTGTAATCTGTTTTCAGCTCTCTGATTCTTGA--TAGATGTGTTTGTCTCTTTTGGCTGAACTTTAGGAATTTAGTTAGTTGGATTCAGCATGCCTGGGATATGGGTTATTTTATAAACTTTTAGCTGTGCTGTGACAGCTGTCTAAAGATGCCACAATGCAAAATCCG Gorilla: GATTAGGGAGGGTTGTAATCTCTTTTCGGCTCTCTGATTCTTGA--TAGATGTGTTTGTCTCTTTTGGCTGAACTTTAGGAATTTAATTAGTTGGATTCAGCATGCCTGGGATATAGGTTATTTTATAAAGTTTTAGCTGTGCTGTGACAGCTGTCTAAAGATGCCACAATGCAAAATCCG Human: GATTAGGGAGGGTTGTAATCTCT-TTAGGCTCTCTGATTCTTGA--TAGATGTGTTTGTCTCTTTTGGCTGAACTTTAGGAATTTAATTAGTTGGATTCAGCATGCCTGGGATATAGGTTATTTTATAAACTTTTAGCTGTGCTGTGACAGCTGTCTAAAGATGCCACAATGCAAAATCCA Cluster: [ ] Orangutan: GATTAGGGAGGGTTGTAATCTCTTTTCGGTTCTCTGATTCTTTATCAAGATGTGTTTGTCTCTTTTGGCCGAACTTTAGGAATTTAATTAGTTGGATTCAGCATGCCTGGGATGTAGGTTATTTTATCAACTTTTAGCTGTGCTGTGACTGCTGTCTAAAGATGCCACAATGCAAAATCCG Chimp > Human ------------- chr12:112650551-112650556 Template switch process: F1: L TAAAGCAGAAGGGCCCATCTGATTAGGGAGGGTTGTAATCT 1 F3: 4 GCTCTCTGATTCTTGATAGATGTGTTTGTCTCTTTTGGCT R RF: TAAAGCAGAAGGGCCCATCTGATTAGGGAGGGTTGTAATCTGTTTTCAGCTCTCTGATTCTTGATAGATGTGTTTGTCTCTTTTGGCTGAACTTTAGGAATTTAGTTAGTTGGATTCAGCATGCCTGGGATATGGGTTATTTTATAAACTTTTAGCTGTGCTGTGACAGCTGTCTAAAG RR: ATTTCGTCTTCCCGGGTAGACTAATCCCTCCCAACATTAGACAAAAGTCGAGAGACTAAGAACTATCTACACAAACAGAGAAAACCGACTTGAAATCCTTAAATCAATCAACCTAAGTCGTACGGACCCTATACCCAATAAAATATTTGAAAATCGACACGACACTGTCGACAGATTTC F2: 3 GATTTC 2 Unidirectional alignment (log-probability: -28.6) AAAGCAGAAGGGCCCATCTGATTAGGGAGGGTTGTAATCTctttaG------GCTCTCTGATTCTTGATAGATGTGTTTGTCTCTTTTGGCT AAAGCAGAAGGGCCCATCTGATTAGGGAGGGTTGTAATCT-----GTTTTCAGCTCTCTGATTCTTGATAGATGTGTTTGTCTCTTTTGGCT Template switch alignment (log-probability: -16) AAAGCAGAAGGGCCCATCTGATTAGGGAGGGTTGTAATCT|CTTTAG|GCTCTCTGATTCTTGATAGATGTGTTTGTCTCTTTTGGCT AAAGCAGAAGGGCCCATCTGATTAGGGAGGGTTGTAATCT|CTTTAG|GCTCTCTGATTCTTGATAGATGTGTTTGTCTCTTTTGGCT ========= Event 617 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGATGGCCTAAAGGACACCATTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCA ↓ 1 4 3 2 Chimp: CAGATGGCCTAAAGGACACCA----GAACTACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCA ↑ 1 4 3 2 Gorilla: CAGATGGCCTAAAGGACACCATTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCA Human: CAGATGGCCTAAAGGACACCATTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCA Cluster: [ ] Orangutan: CAGATGGCCTAAAGGACACCATTTCTAATAACCAGAAAGGTAGTTCTTCGCTTCCAAATATCTCCA Human > Chimp ------------- chr12:115709702-115709706 Template switch process: F1: L ACCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA 1 F3: 4 ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT R RF: ACCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCATTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT RR: TGGAAGTATCGGTCCACCTTGTCTACCGGATTTCCTGTGGTAAAGATTATTGGTCTTTCCATCAAGAAGGGAAGGTTTATAGAGGTTAGA F2: 3 TCAAG 2 Unidirectional alignment (log-probability: -27.3) CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCAgaacT--------ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA----TTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT Template switch alignment (log-probability: -15.9) CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA|GAACT|ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA|GAACT|ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT Gorilla > Chimp --------------- chr12:115709702-115709706 Template switch process: F1: L ACCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA 1 F3: 4 ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT R RF: ACCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCATTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT RR: TGGAAGTATCGGTCCACCTTGTCTACCGGATTTCCTGTGGTAAAGATTATTGGTCTTTCCATCAAGAAGGGAAGGTTTATAGAGGTTAGA F2: 3 TCAAG 2 Unidirectional alignment (log-probability: -26.8) CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCAgaacT--------ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA----TTTCTAATAACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT Template switch alignment (log-probability: -16.4) CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA|GAACT|ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT CCTTCATAGCCAGGTGGAACAGATGGCCTAAAGGACACCA|GAACT|ACCAGAAAGGTAGTTCTTCCCTTCCAAATATCTCCAATCT ========= Event 618 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAAACCAGTCCTGGATAGTACTAATTATTAAA-----------------------------CATTAACATATGCAGGCACTGAAAAATGGTTTGTATATATCATCACATTTAAATGTGA Chimp: AATAAACCAGTCCTGGATAGTACTAATTATTAAA-----------------------------CATTAACATATGCAGGCACTGAAAAATGGTTTGAATATATCATCACATTTAAATGTGA ↓ 3 2 1 4 Gorilla: AATAAACCAGTCCTGGATAGTACTAATTATTAAA----------------------------------------------------------TTAGT-ACTATCATCACATTTAAATGTGA ↑ 3 2 1 4 Human: AATAAACCAGTCCTGGATAGTACTAATTATTAAA-----------------------------CATTAACATATGCAGGCACTGAAAAATGGTTTGTATATATCATCACATTTAAATGTGA Cluster: [ ] Orangutan: AATAAACCAGTCCTGGATAGTACTAATTATTAAACATTAACATATGCAGGCACTGAAAAATGG-----------------------------TTTGTATTTATCATCACATTTAAATGTGA Human > Gorilla --------------- chr1:27748716-27748722 Template switch process: F1: L ATCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAA 1 F3: 4 TATCATCACATTTAAATGTGAGAGATTCTACTTTTTCCAC R RF: ATCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAACATTAACATATGCAGGCACTGAAAAATGGTTTGTATATATCATCACATTTAAATGTGAGAGATCCTACTTTTTCCAC RR: TAGGGTATTATTTGGTCAGGACCTATCATGATTAATAATTTGTAATTGTATACGTCCGTGACTTTTTACCAAACATATATAGTAGTGTAAATTTACACTCTCTAGGATGAAAAAGGTG F2: 3 CATGATT 2 Unidirectional alignment (log-probability: -36.6) TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAattagtAC------------------------------------TATCATCACATTTAAATGTGAGAGATtCTACTTTTTCCAC TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAA------ACATTAACATATGCAGGCACTGAAAAATGGTTTGTATATATCATCACATTTAAATGTGAGAGATCCTACTTTTTCCAC Template switch alignment (log-probability: -22.1) TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAA|TTAGTAC|TATCATCACATTTAAATGTGAGAGATtCTACTTTTTCCAC TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAA|TTAGTAC|TATCATCACATTTAAATGTGAGAGATCCTACTTTTTCCAC Chimp > Gorilla --------------- chr1:27748716-27748722 Template switch process: F1: L ATCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAA 1 F3: 4 TATCATCACATTTAAATGTGAGAGATTCTACTTTTTCCAC R RF: ATCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAACATTAACATATGCAGGCACTGAAAAATGGTTTGAATATATCATCACATTTAAATGTGAGAGATCCTACTTTTTTCAC RR: TAGGGTATTATTTGGTCAGGACCTATCATGATTAATAATTTGTAATTGTATACGTCCGTGACTTTTTACCAAACTTATATAGTAGTGTAAATTTACACTCTCTAGGATGAAAAAAGTG F2: 3 CATGATT 2 Unidirectional alignment (log-probability: -42.1) TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAattagtAC------------------------------------TATCATCACATTTAAATGTGAGAGATtCTACTTTTTcCAC TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAA------ACATTAACATATGCAGGCACTGAAAAATGGTTTGAATATATCATCACATTTAAATGTGAGAGATCCTACTTTTTTCAC Template switch alignment (log-probability: -27.7) TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAA|TTAGTAC|TATCATCACATTTAAATGTGAGAGATtCTACTTTTTcCAC TCCCATAATAAACCAGTCCTGGATAGTACTAATTATTAAA|TTAGTAC|TATCATCACATTTAAATGTGAGAGATCCTACTTTTTTCAC ========= Event 619 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GATTAAGTAAAATATATAATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAG-----------------------------------------------------------------------------------------------------------------------TCTAACATTAAGAAATAATGTTAGACTTAGGCCACAAGTCTTGGTCATCaa Chimp: GATTAAGTAAAATATATAATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAG-----------------------------------------------------------------------------------------------------------------------TCTAACATTAAGAAATAATGTTAGACTTAAGCCACAAGTCTTGGTCATCaa Gorilla: GATTAAGTAAAATATATAATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAG-----------------------------------------------------------------------------------------------------------------------TCTAACATTATTTCTTAATGTTAGACTTAAGCCACAAGTCTTGGTCATCaa ↑ 3 1 2 4 Human: GATTAAGTAAAATATATAATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAG-----------------------------------------------------------------------------------------------------------------------TCTAACATTAAGAAATAATGTTAGACTTAGGCCACAAGTCTTGGTCATCaa Cluster: [ ] Orangutan: CATTAAGTAAAGTATATAATTATAGTTTATTAAATTGCTTTACTTTAAGGACTTACATGTTTTCTAGAAGTCCATATTTCACCAATCTCTGAAGACTGCATCACCCTTAGGCTCTTCTGAGAATAATAAAAATAAGAACATGAGAAGAACGTGCACTATTTAGGAGAATAGAAGGTGAGAAGAAAATCTGGGATGACAATGTGGATGATCTAAGTTTTTCAATGTAGAACCCTCAACAGCAGAGAGAAGTGTATCCCCATAAGACTGTATGGGCACAGACTCTTCAGTATTGAAATAAATTCTCATTTATTGTTTGACAGATATACATTTTTAATTTACTTCATACTATGCCCAAATTTAAAAATGGAAATAAATTTATATTATA---TAACAGCTAATTTACATGGCATGTTTCCCCTAAATACATCATTTTAAGGCATTCCTTATTTTACTTACATCCTGGCCCATCAAGCATTCTGTGACTTATGAATATCATGATTTGAAAAAAATAGCATTAAGAAATAATGTTAGACTTAAGCCACAAGTCTTGGTCATCaa Human > Gorilla --------------- chr12:115373402-115373421 Template switch process: F1: L TTTATTAGATTAAGTAAAATATATAATTAAGTCTAACATTA 1 F3: 4 GCCACAAGTCTTGGTCATCAAGACA R RF: TTTATTAGATTAAGTAAAATATATAATTAAGTCTAACATTAAGAAATAATGTTAGACTTAGGCCACAAGTCTTGGTCATCAAGACA RR: AAATAATCTAATTCATTTTATATATTAATTCAGATTGTAATTCTTTATTACAATCTGAATCCGGTGTTCAGAACCAGTAGTTCTGT F2: 3 AATTCAGATTGTAATTCTTT 2 Unidirectional alignment (log-probability: -33.6) TTATTAGATTAAGTAAAATATATAATTAAGTCTAACATT-----AtttctTAATGTTAGACTTAaGCCACAAGTCTTGGTCATCAAGACA TTATTAGATTAAGTAAAATATATAATTAAGTCTAACATTAAGAAA-----TAATGTTAGACTTAGGCCACAAGTCTTGGTCATCAAGACA Template switch alignment (log-probability: -17.9) TTATTAGATTAAGTAAAATATATAATTAAGTCTAACATTA|TTTCTTAATGTTAGACTTAA|GCCACAAGTCTTGGTCATCAAGACA TTATTAGATTAAGTAAAATATATAATTAAGTCTAACATTA|TTTCTTAATGTTAGACTTAA|GCCACAAGTCTTGGTCATCAAGACA ========= Event 620 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ctttagTGCTCCCTTAAGCACGAATCAAACATGAAGTCTTCATAATGATAATTCTggccatgcacagtggc------------------------------------------------------------------------------------------------------------------------- Chimp: ctttagTGCTCCCTTAGGCACTAATCAAACATGAAGTCTTCATAATGATAATTCTggccgtgcacagtggc------------------------------------------------------------------------------------------------------------------------- Gorilla: ctctagTGCTCCCTTAAGCACTAATCA------AAGTCTTCATAATGATAATTCTggccatgcacagtggctcacacctgtaatcccagcactttgAAATAGATAGATTTTGATAATAGCAAAGAAAGGGCATAACCCAAAGACCTCGCTAGAGCAAGTCACCATTCCCATGGATGCTTTATTCATCTTCTT ↓ 41 3 2 Human: ctttagTGCTCCCTTAAGCACGAATCAAACATGAAGTCTTCATAATGATAATTCTggccatgcacagtggc------------------------------------------------------------------------------------------------------------------------- Cluster: [ ] Orangutan: ctttagTGCTCCCTTAAGCACTAATCAAACATGAAGTCTTAATAATGATAATTCTggccgtgcacagtggc------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr1:218186144-218186147 Template switch process: F1: L GACCCCAGCCCCTCCTTAACCTTTAGTGCTCCCTTAAGCACGAATCAAA 1 F3: 4 AAGTCTTCATAATGATAATTCTGGCCATGCACAGTGGC R RF: GACCCCAGCCCCTCCTTAACCTCTAGTGCTCCCTTAAGCACTAATCAAAGTCTTCATAATGATAATTCTGGCCATGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGAAATAGATAGATTTTGATAATAGCAAAGAAAGGGCATAACCCAAAGACCTCGCTAGAGCAAGTCACCATTCCCATG RR: CTGGGGTCGGGGAGGAATTGGAGATCACGAGGGAATTCGTGATTAGTTTCAGAAGTATTACTATTAAGACCGGTACGTGTCACCGAGTGTGGACATTAGGGTCGTGAAACTTTATCTATCTAAAACTATTATCGTTTCTTTCCCGTATTGGGTTTCTGGAGCGATCTCGTTCAGTGGTAAGGGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -37.5) CCCTCCTTAACCTtTAGTGCTCCCTTAAGCACgAATCAaacatgAAGTCTTCATAATGATAATTCTGGCCATGCACAGTGGC-- CCCTCCTTAACCTCTAGTGCTCCCTTAAGCACTAATCA------AAGTCTTCATAATGATAATTCTGGCCATGCACAGTGGCTC Template switch alignment (log-probability: -27.4) CCCTCCTTAACCTtTAGTGCTCCCTTAAGCACgAATCAAA|CATG|AAGTCTTCATAATGATAATTCTGGCCATGCACAGTGGC CCCTCCTTAACCTCTAGTGCTCCCTTAAGCACTAATCAAA|CATG|AAGTCTTCATAATGATAATTCTGGCCATGCACAGTGGC ========= Event 621 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCTGTGGAGGTGAAAGACACAGA----CTAGAGTCCCAAGGATGGAATCTAAGCTCC ↓ 3 1 2 4 Chimp: ACCTGTGGAGGTGAAAGACACAGACTCTCTAGTCTTTCAAGGATGGAATCTAAGCTCC ↑ 3 1 2 4 Gorilla: ACCTGTGGAGGTGAAAGACACAGA----CTAGAGTCCCAAGGATGGAATCTAAGCTCC Human: ACCTGTGGAGGTGAAAGACACAGA----CTAGAGTCCCAAGGATGGAATCTAAGCTCC Cluster: [ ] Orangutan: ACCTGTGGAGGTGAAAGACACAGA----CTAGAGTCCCAAGGATGGAATCTAAGCTCC Human > Chimp ------------- chr1:200379085-200379095 Template switch process: F1: L TATGATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT 1 F3: 4 CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG R RF: TATGATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACTAGAGTCCCAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG RR: ATACTAACTTCCTCCGGTGGACACCTCCACTTTCTGTGTCTGATCTCAGGGTTCCTACCTTAGATTCGAGGTCCATGTGTCAACCGGATC F2: 3 TTTCTGATCTC 2 Unidirectional alignment (log-probability: -35.8) GATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT------CtctagtctttCAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG GATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACTAGAGTCC----------CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG Template switch alignment (log-probability: -22.7) GATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT|CTCTAGTCTtT|CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG GATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT|CTCTAGTCTGT|CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG Gorilla > Chimp --------------- chr1:200379085-200379095 Template switch process: F1: L TATGATTGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT 1 F3: 4 CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG R RF: TATGATAGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACTAGAGTCCCAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG RR: ATACTATCTTCCTCCGGTGGACACCTCCACTTTCTGTGTCTGATCTCAGGGTTCCTACCTTAGATTCGAGGTCCATGTGTCAACCGGATC F2: 3 TTTCTGATCTC 2 Unidirectional alignment (log-probability: -40.9) GATtGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT------CtctagtctttCAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG GATAGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACTAGAGTCC----------CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG Template switch alignment (log-probability: -28.2) GATtGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT|CTCTAGTCTtT|CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG GATAGAAGGAGGCCACCTGTGGAGGTGAAAGACACAGACT|CTCTAGTCTGT|CAAGGATGGAATCTAAGCTCCAGGTACACAGTTGGCCTAG ========= Event 622 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCTGGATAATTTCTCAACCA---ACAATGTACATTATTAGAATGAAAACTGtttta Chimp: TTCTGGATAATttctcaacca---acaatgtaca---ttagaatgaaaactgtt--- Gorilla: TTCTGGATAATTTCTCAACCAACAACAATGTACA---TTAGAATGAAAACTGTT--- ↓ 1 3 4 Human: TTCTGGATAATTTCTCAACCA---ACAATGTACATTATTAGAATGAAAACTGtttta Cluster: [ ] Orangutan: TTCTGGGTAATttctcaacca---acaatataca---ttagaatg--aactgtt--- Gorilla > Human --------------- chr1:33333665-33333672 Template switch process: F1: L TTAAGAAAGTAAGTAGGATGTTCTGGATAATTTCTCAACCAACAA 1 F3: 4 ATTAGAATGAAAACTGTTTTATTTTTTT R RF: TTAAGAAAGTAAGTAGGATGTTCTGGATAATTTCTCAACCAACAACAATGTACATTAGAATGAAAACTGTTATTTTTTT RR: AATTCTTTCATTCATCCTACAAGACCTATTAAAGAGTTGGTTGTTGTTACATGTAATCTTACTTTTGACAATAAAAAAA F2: 3 TTACATGT 2 Unidirectional alignment (log-probability: -44.6) AAAGTAAGTAGGATGTTCTGGATAATTTCTCAACCAAC---AATGTACattATTAGAATGAAAACTGTTttatTTTTTT AAAGTAAGTAGGATGTTCTGGATAATTTCTCAACCAACAACAATGTAC---ATTAGAATGAAAACTGTT---ATTTTTT Template switch alignment (log-probability: -29.1) AAAGTAAGTAGGATGTTCTGGATAATTTCTCAACCAACAA|TGTACATT|ATTAGAATGAAAACTGttTTATTTTTTT AAAGTAAGTAGGATGTTCTGGATAATTTCTCAACCAACAA|TGTACATT|ATTAGAATGAAAACTG--TTATTTTTTT ========= Event 623 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGTTGAACAGAAGCTAGAG------CTAAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC ↓ 1 4 3 2 Chimp: GGAGTTGAACAGAAGCTAGAGTGTCTAGTGAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC ↑ 1 4 3 2 Gorilla: GGAGTTGAACAGAAGCTAGAG------CTAAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC Human: GGAGTTGAACAGAAGCTAGAG------CTAAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC Cluster: [ ] Orangutan: AGAGTTGAACAGAAGCTAGAG------CTAAGTGCTAAACTCACTAGACATCTGTCAGCATCCGTCCATC Human > Chimp ------------- chr1:201158131-201158139 Template switch process: F1: L TCTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAG 1 F3: 4 AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC R RF: TCTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAGCTAAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC RR: AGAATAGAGGACCCGTGACACCTCAACTTGTCTTCGATCTCGATTCACGATTTGAGTGATCTGTAGACGGTCGTAGGCAGGTAG F2: 3 GTGATCTGT 2 Unidirectional alignment (log-probability: -29.8) CTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAGtgtCTAgtgAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC CTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAG---CTA---AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC Template switch alignment (log-probability: -16.4) CTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAG|TGTCTAGTG|AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC CTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAG|TGTCTAGTG|AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC Gorilla > Chimp --------------- chr1:201158131-201158139 Template switch process: F1: L TCTTATCTCCTGGGCACTGTGGAGTTGAACAGAAGCTAGAG 1 F3: 4 AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC R RF: TCTTATCTCCCGGGCACTGTGGAGTTGAACAGAAGCTAGAGCTAAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC RR: AGAATAGAGGGCCCGTGACACCTCAACTTGTCTTCGATCTCGATTCACGATTTGAGTGATCTGTAGACGGTCGTAGGCAGGTAG F2: 3 GTGATCTGT 2 Unidirectional alignment (log-probability: -34.8) CTTATCTCCtGGGCACTGTGGAGTTGAACAGAAGCTAGAGtgtCTAgtgAGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC CTTATCTCCCGGGCACTGTGGAGTTGAACAGAAGCTAGAG---CTA---AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC Template switch alignment (log-probability: -22.4) CTTATCTCCtGGGCACTGTGGAGTTGAACAGAAGCTAGAG|TGTCTAGTG|AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC CTTATCTCCCGGGCACTGTGGAGTTGAACAGAAGCTAGAG|TGTCTAGTG|AGTGCTAAACTCACTAGACATCTGCCAGCATCCGTCCATC ========= Event 624 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: tctaaccaaaatgggatcagg-----tgatcccatatgaatactattgtaatgtgtatg Chimp: TCTAACCAAAAAGGGATCAGATCAGATGGGATCATA-CAATACTATTGTAATGTGTATG ↓ 13 2 4 Gorilla: TCTAACCAAAATGGGATCAGA-----TGATCCCATATGAATACTATTGTAATGTGTATG Human: tctaaccaaaatgggatcagg-----tgatcccatatgaatactattgtaatgtgtatg Cluster: [ ] Orangutan: tctaaccaaaatgggatcaga-----tgatcccatatgaatactattgtaatgtgtatg Chimp > Gorilla --------------- chr12:70652031-70652041 Template switch process: F1: L CCATCCTAAATGGCTTGTTTTCTAACCAAAATGGGATCAGAT 1 F3: 4 AATACTATTGTAATGTGTATGTTTATTTAACAAGATATTA R RF: CCATCCTAAATGGCTTGTTTTCTAACCAAAAAGGGATCAGATCAGATGGGATCATACAATACTATTGTAATGTGTATGTTTATTTAACAAGATATTA RR: GGTAGGATTTACCGAACAAAAGATTGGTTTTTCCCTAGTCTAGTCTACCCTAGTATGTTATGATAACATTACACATACAAATAAATTGTTCTATAAT F2: 3 GTATACCCTAG 2 Unidirectional alignment (log-probability: -39.4) ATCCTAAATGGCTTGTTTTCTAACCAAAAtGGGATCAGATgatccCAtATG---------AATACTATTGTAATGTGTATGTTTATTTAACAAGATATTA ATCCTAAATGGCTTGTTTTCTAACCAAAAAGGGATCAGAT-----CAGATGGGATCATACAATACTATTGTAATGTGTATGTTTATTTAACAAGATATTA Template switch alignment (log-probability: -28.2) ATCCTAAATGGCTTGTTTTCTAACCAAAAtGGGATCAGAT|GATCCCATaTG|AATACTATTGTAATGTGTATGTTTATTTAACAAGATATTA ATCCTAAATGGCTTGTTTTCTAACCAAAAAGGGATCAGAT|GATCCCATCTG|AATACTATTGTAATGTGTATGTTTATTTAACAAGATATTA ========= Event 625 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGG-----CTTTGAGGGATGCCCAGAGTGCCCCCCACC ↓ 3 1 2 4 Chimp: TCCCCTTTCTGCCCCAGTACACTTGAC-------CCTCTGGTCAAGTGTTTGAGGGTTGCCCAGAGTGccccccacc ↑ 3 1 2 4 Gorilla: TCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGG-----CTTTGAGGGATGCCCAGAGTGccccccacc Human: TCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGG-----CTTTGAGGGATGCCCAGAGTGCCCCCCACC Cluster: [ ] Orangutan: TCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGG-----CTTTGAGGGATGCCCAGAGTGCCCCCCACC Human > Chimp ------------- chr1:26056708-26056720 Template switch process: F1: L GCTTCAGCCGTTTCTCCCCTTTCTGCCCCAGTACACTTGACC 1 F3: 4 TTTGAGGGTTGCCCAGAGTGCCCCCCACCCCCAGGCTTCAAGGAAGAGA R RF: GCTTCAGCTGTTTCTCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGGCTTTGAGGGATGCCCAGAGTGCCCCCCACCCCCAGGCTTCAAGGAAGAGA RR: CGAAGTCGACAAAGAGGGGAAAGACGGGGTCATGTGAACTGGTCTCTGGACGACCCGAAACTCCCTACGGGTCTCACGGGGGGTGGGGGTCCGAAGTTCCTTCTCT F2: 3 GTGAACTGGTCTC 2 Unidirectional alignment (log-probability: -51.2) TTCAGCcGTTTCTCCCCTTTCTGCCCCAGTACACTTGACC--------------CTctggtcaagtgtTTGAGGGtTGCCCAGAGTGCCCCCCACCCCCAGGCTTCA TTCAGCTGTTTCTCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGGCT------------TTGAGGGATGCCCAGAGTGCCCCCCACCCCCAGGCTTCA Template switch alignment (log-probability: -29.1) TTCAGCcGTTTCTCCCCTTTCTGCCCCAGTACACTTGACC|CTCTGGTCAAGTG|TTTGAGGGtTGCCCAGAGTGCCCCCCACCCCCAGGCTTCA TTCAGCTGTTTCTCCCCTTTCTGCCCCAGTACACTTGACC|CTCTGGTCAAGTG|TTTGAGGGATGCCCAGAGTGCCCCCCACCCCCAGGCTTCA Gorilla > Chimp --------------- chr1:26056708-26056720 Template switch process: F1: L GCTTCAGCCGTTTCTCCCCTTTCTGCCCCAGTACACTTGACC 1 F3: 4 TTTGAGGGTTGCCCAGAGTGCCCCCCACCCCCAGGCTTCAAGGAAGAGA R RF: GCTTCAGCCATTTCTCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGGCTTTGAGGGATGCCCAGAGTGCCCCCCACCCCCAGGCTTCAAGGAAGAGA RR: CGAAGTCGGTAAAGAGGGGAAAGACGGGGTCATGTGAACTGGTCTCTGGACGACCCGAAACTCCCTACGGGTCTCACGGGGGGTGGGGGTCCGAAGTTCCTTCTCT F2: 3 GTGAACTGGTCTC 2 Unidirectional alignment (log-probability: -49.8) TTCAGCCgTTTCTCCCCTTTCTGCCCCAGTACACTTGACC--------------CtctggtcaagtgTTTGAGGGtTGCCCAGAGTGCCCCCCACCCCCAGGCTTCA TTCAGCCATTTCTCCCCTTTCTGCCCCAGTACACTTGACCAGAGACCTGCTGGGC------------TTTGAGGGATGCCCAGAGTGCCCCCCACCCCCAGGCTTCA Template switch alignment (log-probability: -28.7) TTCAGCCgTTTCTCCCCTTTCTGCCCCAGTACACTTGACC|CTCTGGTCAAGTG|TTTGAGGGtTGCCCAGAGTGCCCCCCACCCCCAGGCTTCA TTCAGCCATTTCTCCCCTTTCTGCCCCAGTACACTTGACC|CTCTGGTCAAGTG|TTTGAGGGATGCCCAGAGTGCCCCCCACCCCCAGGCTTCA ========= Event 626 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTCAACAAAAGTGTATAATT--------CTCTTTATTCTTGCAGGAGTTTCCCCTTGTTCAAattaaataaatatttattg Chimp: TGTCAGCAAAAGTGTATAATT--------CTCTTTATTCTTGCAGGAGTTTCCCCTTGTtcaaattaaataaatatttattg ↓ 1 4 3 2 Gorilla: TGTCAGCAAAAGTGTATAATT----------------TGAACAAGGAGTTTCCCCTTGTtcaaattaaataaatatttattg ↑ 1 4 3 2 Human: TGTCAACAAAAGTGTATAATT--------CTCTTTATTCTTGCAGGAGTTTCCCCTTGTTCAAattaaataaatatttattg Cluster: [ ] Orangutan: TGTCGGCAAAAATGTATAATTCTCTTTAT--------TCTTGCAGGAATTTCCCCTTGTTCAAattaaataaatatttattg Human > Gorilla --------------- chr1:26002331-26002336 Template switch process: F1: L AGAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATT 1 F3: 4 AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA R RF: AGAATATATTCTCCTTAAAATGTCAACAAAAGTGTATAATTCTCTTTATTCTTGCAGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA RR: TCTTATATAAGAGGAATTTTACAGTTGTTTTCACATATTAAGAGAAATAAGAACGTCCTCAAAGGGGAACAAGTTTAATTTATTTATAAATAACT F2: 3 ACAAGT 2 Unidirectional alignment (log-probability: -35.5) GAATATATTCTCCTTAAAATGTCAgCAAAAGTGTATAATT--------------tgaacaAGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA GAATATATTCTCCTTAAAATGTCAACAAAAGTGTATAATTCTCTTTATTCTTGC------AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA Template switch alignment (log-probability: -22) GAATATATTCTCCTTAAAATGTCAgCAAAAGTGTATAATT|TGAACA|AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA GAATATATTCTCCTTAAAATGTCAACAAAAGTGTATAATT|TGAACA|AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA Chimp > Gorilla --------------- chr1:26002331-26002336 Template switch process: F1: L AGAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATT 1 F3: 4 AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA R RF: AGAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATTCTCTTTATTCTTGCAGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA RR: TCTTATATAAGAGGAATTTTACAGTCGTTTTCACATATTAAGAGAAATAAGAACGTCCTCAAAGGGGAACAAGTTTAATTTATTTATAAATAACT F2: 3 ACAAGT 2 Unidirectional alignment (log-probability: -30) GAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATT--------------tgaacaAGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA GAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATTCTCTTTATTCTTGC------AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA Template switch alignment (log-probability: -16.5) GAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATT|TGAACA|AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA GAATATATTCTCCTTAAAATGTCAGCAAAAGTGTATAATT|TGAACA|AGGAGTTTCCCCTTGTTCAAATTAAATAAATATTTATTGA ========= Event 627 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTATTCTGCCTTCTCCAGTTTTTGCTTTATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACCAAGCCACCCTGTAAAGCTGTTAACCCAATCTTCTCTC ↑ 1 4 3 2 Chimp: TTATTCTGCCTTCTCCAGTTTCT-ATGAATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACCAAGCCACCCTGTAAAGCTGTTAACCCAATCTTCTCTC Gorilla: TTATTCTGCCTTCTCCAGTTTCT-ATGAATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACCAAGCCACCCTGTAAAGCTGTTAACCCAGTCTTCTCTC Human: TTATTCTGCCTTCTCCAGTTTTTGCTTTATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACCAAGCCACCCTGTAAAGCTGTTAACCCAATCTTCTCTC Cluster: [ ] Orangutan: TTATTCTGGCTTCTCCAGTTTCT-ATGAATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACCAAGCCACCCTGTAAAGCTGTTAACCCAATCTTCTGTC Chimp > Human ------------- chr12:109637649-109637654 Template switch process: F1: L ACAACATTCAAGTTTTTGCTTTATTCTGCCTTCTCCAGTTTTT 1 F3: 4 TTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACC R RF: ACAACATTCAAGTTTTTGCTTTATTCTGCCTTCTCCAGTTTCTATGAATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACCAAGCCACCCTGTAAAGC RR: TGTTGTAAGTTCAAAAACGAAATAAGACGGAAGAGGTCAAAGATACTTAAGACGAAAAACCCATTCGTCCCTTCTGGTGATTCTTGGTTCGGTGGGACATTTCG F2: 3 ATTTCG 2 Unidirectional alignment (log-probability: -31.5) ACATTCAAGTTTTTGCTTTATTCTGCCTTCTCCAGtttttgcTTT------ATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACC ACATTCAAGTTTTTGCTTTATTCTGCCTTCTCCAG-------TTTCTATGAATTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACC Template switch alignment (log-probability: -22) ACATTCAAGTTTTTGCTTTATTCTGCCTTCTCCAGTTTtT|GCTTTA|TTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACC ACATTCAAGTTTTTGCTTTATTCTGCCTTCTCCAGTTTCT|GCTTTA|TTCTGCTTTTTGGGTAAGCAGGGAAGACCACTAAGAACC ========= Event 628 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGTTTAAGGTTTTGCACAGT---------TTCTTCCAAGACAATTCAGAATCATATCCCTTCATCAGAGTTTTC Chimp: CTGTTTAAGGTTTTGCACAGT---------TTCTTCCAAGACAATTCCGAATCATATCCCTTCATCAGAGTTTTC Gorilla: CTGTTTAAGGTTTTGCACAGT------------------TATGATTCTGAATCATATCCCTTCATCAGAGTTTTC ↑ 1 34 2 Human: CTGTTTAAGGTTTTGCACAGT---------TTCTTCCAAGACAATTCAGAATCATATCCCTTCATCAGAGTTTTC Cluster: [ ] Orangutan: CTGTTTAAGGTTGTGCACAGTTTCTTCCGA---------GACAATTCAGAATCATATCCCTTCATCAGAGTTTTC Human > Gorilla --------------- chr12:61637171-61637178 Template switch process: F1: L GTCTTTAAGTCCCCTTTTCCCTGTTTAAGGTTTTGCACAGTT 1 F3: 4 GAATCATATCCCTTCATCAGAGTTTTCATTTGGCCCCAGG R RF: GTCTTTAAGTCCACTTTTCCCTGTTTAAGGTTTTGCACAGTTTCTTCCAAGACAATTCAGAATCATATCCCTTCATCAGAGTTTTCATTTGGCCCCAGG RR: CAGAAATTCAGGTGAAAAGGGACAAATTCCAAAACGTGTCAAAGAAGGTTCTGTTAAGTCTTAGTATAGGGAAGTAGTCTCAAAAGTAAACCGGGGTCC F2: 3 TCTTAGTA 2 Unidirectional alignment (log-probability: -33.6) CTTTAAGTCCcCTTTTCCCTGTTTAAGGTTTTGCACAGTT---------AtgATTCtGAATCATATCCCTTCATCAGAGTTTTCATTTGGCCCCAGG CTTTAAGTCCACTTTTCCCTGTTTAAGGTTTTGCACAGTTTCTTCCAAGACAATTCAGAATCATATCCCTTCATCAGAGTTTTCATTTGGCCCCAGG Template switch alignment (log-probability: -22.3) CTTTAAGTCCcCTTTTCCCTGTTTAAGGTTTTGCACAGTT|ATGATTCT|GAATCATATCCCTTCATCAGAGTTTTCATTTGGCCCCAGG CTTTAAGTCCACTTTTCCCTGTTTAAGGTTTTGCACAGTT|ATGATTCT|GAATCATATCCCTTCATCAGAGTTTTCATTTGGCCCCAGG ========= Event 629 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGATCAAAACATCCTACCCTCTTTGGCTATTGCcaaatcttatcaaaggcctacta ↑ 13 4 2 Chimp: agatcaaaacatcctACCCTC-----TAATAGCcaaatcttatcaaaggcctacta Gorilla: agatcaaaacatcctACCCTC-----TAATAGCcaaatcttatcaaaggcctacta ↓ 13 4 2 Human: AGATCAAAACATCCTACCCTCTTTGGCTATTGCcaaatcttatcaaaggcctacta Cluster: [ ] Orangutan: AGATCAAAACATCCTACCCTC-----TAATAGCCAAATCttatcaaaggcctacta Chimp > Human ------------- chr1:223410069-223410077 Template switch process: F1: L CATATCAGATCAAAGCTACAAGATCAAAACATCCTACCCTCT 1 F3: 4 GCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG R RF: CATATCAGATCAAAGCTACGAGATCAAAACATCCTACCCTCTAATAGCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG RR: GTATAGTCTAGTTTCGATGCTCTAGTTTTGTAGGATGGGAGATTATCGGTTTAGAATAGTTTCCGGATGATATACGGTCCGTGAAC F2: 3 TTATCGGTT 2 Unidirectional alignment (log-probability: -36.1) TATCAGATCAAAGCTACaAGATCAAAACATCCTACCCTCTttggctATtGCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG TATCAGATCAAAGCTACGAGATCAAAACATCCTACCCTCT-----AATAGCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG Template switch alignment (log-probability: -22.4) TATCAGATCAAAGCTACaAGATCAAAACATCCTACCCTCT|TTGGCTATT|GCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG TATCAGATCAAAGCTACGAGATCAAAACATCCTACCCTCT|TTGGCTATT|GCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG Gorilla > Human --------------- chr1:223410069-223410077 Template switch process: F1: L CATATCAGATCAAAGCTACAAGATCAAAACATCCTACCCTCT 1 F3: 4 GCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG R RF: CATATCAGATCAAAGCTACGAGATCAAAACATCCTACCCTCTAATAGCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG RR: GTATAGTCTAGTTTCGATGCTCTAGTTTTGTAGGATGGGAGATTATCGGTTTAGAATAGTTTCCGGATGATATACGGTCCGTGAAC F2: 3 TTATCGGTT 2 Unidirectional alignment (log-probability: -34.7) TATCAGATCAAAGCTACaAGATCAAAACATCCTACCCTCTttggctATtGCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG TATCAGATCAAAGCTACGAGATCAAAACATCCTACCCTCTA-----ATAGCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG Template switch alignment (log-probability: -22.4) TATCAGATCAAAGCTACaAGATCAAAACATCCTACCCTCT|TTGGCTATT|GCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG TATCAGATCAAAGCTACGAGATCAAAACATCCTACCCTCT|TTGGCTATT|GCCAAATCTTATCAAAGGCCTACTATATGCCAGGCACTTG ========= Event 630 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTGGGCCCTGGGCAGCGCCTGGACCTGAGGTGGAATGGGCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGTCCAAAGTGGGCCCATTCCTGTCGCCGTTGCACGCAAC ↑ 4 1 3 2 Chimp: TTGGGCCCTGGGCAGCGCCTGCAC---------------CAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGTCCAAAGTGGGCCCATTCCTGTCGCCGTTGCACGCAAC ↓ 4 1 3 2 Gorilla: TTGGGCCCTGGGCAGCGCCTGGACCTGAGGTGGAATGGGCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGTCCAAAGTGGGCCCATTCCTGTCTCCATTGCACGCAAC Human: TTGGGCCCTGGGCAGCGCCTGGACCTGAGGTGGAATGGGCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGTCCAAAGTGGGCCCATTCCTGTCGCCGTTGCACGCAAC Cluster: [ ] Orangutan: TTGGGCCCTGGGCAGCGCCTGGACCTGAGGTGGAATGGGCAGAGGTGCAGGAAGGGGAGGCATGCCTGGCCCTGCTGGTCCAAAGTGGGCCCATTCCTGTCTCCGTTGCACGCAAC Chimp > Human ------------- chr1:25919368-25919375 Template switch process: F1: L TCCAGCTGCTCCCTGGTCTGTTGGGCCCTGGGCAGCGCCTGGACCTGAGGTG 1 F3: 4 AGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT R RF: TCCAGCTGCTCCCTGGTCTGTTGGGCCCTGGGCAGCGCCTGCACCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGTCCAAAGTGGGCCCATTC RR: AGGTCGACGAGGGACCAGACAACCCGGGACCCGTCGCGGACGTGGTCTCCACGTCCTTCCCCTTCGTGCGGATCGGGACGACCAGGTTTCACCCGGGTAAG F2: 3 CGGGTAAG 2 Unidirectional alignment (log-probability: -38.5) CTGGTCTGTTGGGCCCTGGGCAGCGCCTGgACctgaggtggaatgggCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT CTGGTCTGTTGGGCCCTGGGCAGCGCCTGCAC---------------CAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT Template switch alignment (log-probability: -28.5) CTGGTCTGTTGGGCCCTGGGCAGCGCCTGgACCtGAGGTG|GAATGGGC|AGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT CTGGTCTGTTGGGCCCTGGGCAGCGCCTGCACCAGAGGTG|GAATGGGC|AGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT Chimp > Gorilla --------------- chr1:25758377-25758384 Template switch process: F1: L TCCAGCTGCTCCCTGGTCTGTTGGGCCCTGGGCAGCGCCTGGACCTGAGGTG 1 F3: 4 AGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT R RF: TCCAGCTGCTCCCTGGTCTGTTGGGCCCTGGGCAGCGCCTGCACCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGTCCAAAGTGGGCCCATTC RR: AGGTCGACGAGGGACCAGACAACCCGGGACCCGTCGCGGACGTGGTCTCCACGTCCTTCCCCTTCGTGCGGATCGGGACGACCAGGTTTCACCCGGGTAAG F2: 3 CGGGTAAG 2 Unidirectional alignment (log-probability: -38) CTGGTCTGTTGGGCCCTGGGCAGCGCCTGgACctgaggtggaatgggCAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT CTGGTCTGTTGGGCCCTGGGCAGCGCCTGCAC---------------CAGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT Template switch alignment (log-probability: -28) CTGGTCTGTTGGGCCCTGGGCAGCGCCTGgACCtGAGGTG|GAATGGGC|AGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT CTGGTCTGTTGGGCCCTGGGCAGCGCCTGCACCAGAGGTG|GAATGGGC|AGAGGTGCAGGAAGGGGAAGCACGCCTAGCCCTGCTGGT ========= Event 631 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: tgatatacg-ggggtggAGGGTTAGTTCTAGGACTA--------------------------------------------------------------------CCCCTGTAGTCCTAGAACTAACCCTCCACCGATATGGACTGATTTTATGTATTGAAGTTATT Chimp: tgatatatg-ggggtggAGGGTTAGTTCTAGGACTA--------------------------------------------------------------------------------------------------------------CTTTATGTATTGAAGTTATT Gorilla: tgatatacg-ggggtggAGGCTTAGTTCTAGGACTA-------------------------CCAGGGGTAGTCCTAGAACTAACCCTCCACAGATATGGACTGA------------------------------------------TTTTATGTATTGAAGTTATT ↓ 1 3 4 2 Human: tgatatacg-ggggtggAGGGTTAGTTCTAGGACTA--------------------------------------------------------------------CCCCTGTAGTCCTAGAACTAACCCTCCACCGATATGGACTGATTTTATGTATTGAAGTTATT Cluster: [ ] Orangutan: tgatatgcagtggggggaggggtagtcctagaa---ctaaccctccacagatacggaCTGA-------------------------------------------------------------------------------------NNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr1:22433636-22433656 Template switch process: F1: L GGATTTTGATATACGGGGGTGGAGG 1 F3: 4 GTAGTCCTAGAACTAACCCTCCACCGATATGGACTGATTTTATGTATTGAAGTTATTTCCCTATAAAGATGCTTAGA R RF: GGATTTTGATATACGGGGGTGGAGGCTTAGTTCTAGGACTACCAGGGGTAGTCCTAGAACTAACCCTCCACAGATATGGACTGATTTTATGTATTGAAGTTATTTCCCTATAAAGATGCTTAGA RR: CCTAAAACTATATGCCCCCACCTCCGAATCAAGATCCTGATGGTCCCCATCAGGATCTTGATTGGGAGGTGTCTATACCTGACTAAAATACATAACTTCAATAAAGGGATATTTCTACGAATCT F2: 3 TCCCCATCAGGATCTTGATTG 2 Unidirectional alignment (log-probability: -36.7) GGATTTTGATATACGGGGGTGGAGGgTTAGTTCTAGGACTACC----cctGTAGTCCTAGAACTAACCCTCCACcGATATGGACTGATTT GGATTTTGATATACGGGGGTGGAGGCTTAGTTCTAGGACTACCAGGG---GTAGTCCTAGAACTAACCCTCCACAGATATGGACTGATTT Template switch alignment (log-probability: -24.4) GGATTTTGATATACGGGGGTGGAGG|GTTAGTTCTAGGACTACCCCT|GTAGTCCTAGAACTAACCCTCCACcGATATGGACTGATTT GGATTTTGATATACGGGGGTGGAGG|GTTAGTTCTAGGACTACCCCT|GTAGTCCTAGAACTAACCCTCCACAGATATGGACTGATTT ========= Event 632 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTGTAAGGAGCAGGAGCTGACCTGT-------CAGGGG--AAGGGGCATGAAGAGAGAAGCCA Chimp: CTTTGTAAGGAGCAGGAGCTGACCTGT-------CAGGGG--AAGGGGCATGAAGAGAGAAGCCA ↓ 3 1 4 Gorilla: CTTTGTAAGGAGCAGGAGCTGACCTGTCCCCTGACAGGTCATGAAGGGCATGAAGAGAGAAGCCA Human: CTTTGTAAGGAGCAGGAGCTGACCTGT-------CAGGGG--AAGGGGCATGAAGAGAGAAGCCA Cluster: [ ] Orangutan: CTTTGTAAGGAGCAGGAGCTGACCTGT-------CAGGGG--AAGCGGCATGAAGAGAGAAGCCA Chimp > Gorilla --------------- chr1:22583046-22583058 Template switch process: F1: L CTCTCCCCTGCAGACTTTGTAAGGAGCAGGAGCTGACCTGTC 1 F3: 4 TGAA-GGGCATGAAGAGAGAAGCCATGACTCGTCCCCTGGTTGGG R RF: CTCTCCCCTGCAGACTTTGTAAGGAGCAGGAGCTGACCTGTCAGGGGAAGGGGCATGAAGAGAGAAGCCATGACTCGTCCCCTGGTTGGG RR: GAGAGGGGACGTCTGAAACATTCCTCGTCCTCGACTGGACAGTCCCCTTCCCCGTACTTCTCTCTTCGGTACTGAGCAGGGGACCAACCC F2: 3 ACTGGACAGTCCC 2 Unidirectional alignment (log-probability: -44) CTCCCCTGCAGACTTTGTAAGGAGCAGGAGCTGACCTGTCccctgacaggtcatgaA-------GGGCATGAAGAGAGAAGCCATGACTCGTCCCCTGGT CTCCCCTGCAGACTTTGTAAGGAGCAGGAGCTGACCTGTC----------------AGGGGAAGGGGCATGAAGAGAGAAGCCATGACTCGTCCCCTGGT Template switch alignment (log-probability: -32.8) CTCCCCTGCAGACTTTGTAAGGAGCAGGAGCTGACCTGTC|CCCTGACAGGTCA|tGAA-GGGCATGAAGAGAGAAGCCATGACTCGTCCCCTGGT CTCCCCTGCAGACTTTGTAAGGAGCAGGAGCTGACCTGTC|CCCTGACAGGTCA|GGAAGGGGCATGAAGAGAGAAGCCATGACTCGTCCCCTGGT ========= Event 633 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TCACGGGCTTTCTTTCTCCCAAGAACTGGCCCAAAGGCCAGTTCTTTTCCCAGGGGACCCAAAAC ↑ 1 3 4 2 Chimp: TCACGGGCTTTCTTTCTCCCAT---T-------TGGGCCAGTTCTTTTCCCAGGGGACCCAAAAC Gorilla: TCACAGGCTTTCTTTCTCCCAAGAACTGGTCCAAAGGCCAGTTCT-TTCCCAGGGGACCCAAAAC Human: TCACGGGCTTTCTTTCTCCCAAGAACTGGCCCAAAGGCCAGTTCTTTTCCCAGGGGACCCAAAAC Cluster: [ ] Orangutan: Chimp > Human ------------- chr12:2414897-2414910 Template switch process: F1: L GTTGGACAGGGGTGCTGGGATCACGGGCTTTCTTTCTCCCA 1 F3: 4 GGCCAGTTCTTTTCCCAGGGGACCCAAAACAGGGCTTACC R RF: GTTGGACAGGGGTGCTGGGATCACGGGCTTTCTTTCTCCCATTTGGGCCAGTTCTTTTCCCAGGGGACCCAAAACAGGGCTTGCC RR: CAACCTGTCCCCACGACCCTAGTGCCCGAAAGAAAGAGGGTAAACCCGGTCAAGAAAAGGGTCCCCTGGGTTTTGTCCCGAACGG F2: 3 AAACCCGGTCAAGA 2 Unidirectional alignment (log-probability: -47.5) TTGGACAGGGGTGCTGGGATCACGGGCTTTCTTTCTCCCA----agaactggcccaaaGGCCAGTTCTTTTCCCAGGGGACCCAAAACAGGGCTTaCC TTGGACAGGGGTGCTGGGATCACGGGCTTTCTTTCTCCCATTTG--------------GGCCAGTTCTTTTCCCAGGGGACCCAAAACAGGGCTTGCC Template switch alignment (log-probability: -23) TTGGACAGGGGTGCTGGGATCACGGGCTTTCTTTCTCCCA|AGAACTGGCCCAAA|GGCCAGTTCTTTTCCCAGGGGACCCAAAACAGGGCTTaCC TTGGACAGGGGTGCTGGGATCACGGGCTTTCTTTCTCCCA|AGAACTGGCCCAAA|GGCCAGTTCTTTTCCCAGGGGACCCAAAACAGGGCTTGCC ========= Event 634 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGAAGGATGAAGGCAGAAATGTCAGATTTCCTGATGTTACTACAGGCTATGTGGAGG------------------------------TGAAAATGCATCCTGAGGGCTGCAAA ↓ 3 2 4 1 Chimp: AGGAAGGATGAAGGCAGAAATGTCAGATTTCCTGATGTTACTACAGGCTATGTGGAGG---------------TGAAAAGACATGCGGTGAAAATGCATCCCGAGGGCTGCAAA Gorilla: AGAAAGGATGAAGGCAGAAATGTCAGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAAAGACGTGCAG---------------TGAAAATGCATCCCGAGGGCTGCAAA Human: AGGAAGGATGAAGGCAGAAATGTCAGATTTCCTGATGTTACTACAGGCTATGTGGAGG------------------------------TGAAAATGCATCCTGAGGGCTGCAAA Cluster: [ ] Orangutan: TGGAAAGATGAAGGCAGAAATGTCAGATTTCCTGATGTTACTACAGGATATGTGGAGGTGAAAAGGCGTGTGG---------------TGAAAATGCATCCTAAGGGCTGCAAA Human > Chimp ------------- chr1:203188092-203188096 Template switch process: F1: L AAATGTCAGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAAA 1 F3: 4 GCGGTGAAAATGCATCCCGAGGGCTGCAAAATGTGGCACTTGTA R RF: AAATGTCAGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAAATGCATCCTGAGGGCTGCAAAATGTGGCACTTGTA RR: TTTACAGTCTAAAGGACTACAATGATGTCCGATACACCTCCACTTTTACGTAGGACTCCCGACGTTTTACACCGTGAACAT F2: 3 TACAG 2 Unidirectional alignment (log-probability: -38.5) AGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAAagacatgcggtgaaaATGCATCCcGAGGGCTGCAAAATGTGGCACT AGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAA---------------ATGCATCCTGAGGGCTGCAAAATGTGGCACT Template switch alignment (log-probability: -28.1) AGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAAA|GACAT|GcGGTGAAAATGCATCCcGAGGGCTGCAAAATGTGGCACT AGATTTCCTGATGTTACTACAGGCTATGTGGAGGTGAAAA|GACAT|GAGGTGAAAATGCATCCTGAGGGCTGCAAAATGTGGCACT ========= Event 635 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT-----TTGGCTGTGTAGGTGTGAGTTTCAG Chimp: AAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT-----TTGGCTGTGTAGGTGTGAGTTTCAG ↓ 3 2 1 4 Gorilla: AAAATCCAAACCATATTTTTCTTATGTGATGTCCAATCACATAAGATTGTGTAGGTGTGAGTTTCAG ↑ 3 2 1 4 Human: AAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT-----TTGGCTGTGTAGGTGTGAGTTTCAG Cluster: [ ] Orangutan: AAAATCCAAACCATATTTTTCTTATGGGATGTCCAAT-----TTGGCTGTGTAGGTGTGAGTTTCAG Human > Gorilla --------------- chr12:60653871-60653879 Template switch process: F1: L AAGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT 1 F3: 4 TTGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTAC R RF: AAGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAATTTGGCTGTGTAGGTGTGAGTTTCAGATAAGACGAAATGCATTTAC RR: TTCTTTTTAGGTTTGGTATAAAAAGAATACACTACAGGTTAAACCGACACATCCACACTCAAAGTCTATTCTGCTTTACGTAAATG F2: 3 AGAATACAC 2 Unidirectional alignment (log-probability: -39.3) AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT----CacataagatTGTGTAGGTGTGAGTTTCAGATAAGAtGAAATGCATTTA AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAATTTGGC---------TGTGTAGGTGTGAGTTTCAGATAAGACGAAATGCATTTA Template switch alignment (log-probability: -27.9) AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT|CACATAAGA|tTGTGTAGGTGTGAGTTTCAGATAAGAtGAAATGCATTTA AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT|CACATAAGA|CTGTGTAGGTGTGAGTTTCAGATAAGACGAAATGCATTTA Chimp > Gorilla --------------- chr12:60653871-60653879 Template switch process: F1: L AAGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT 1 F3: 4 TTGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTAC R RF: AAGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAATTTGGCTGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTAC RR: TTCTTTTTAGGTTTGGTATAAAAAGAATACACTACAGGTTAAACCGACACATCCACACTCAAAGTCTATTCTACTTTACGTAAATG F2: 3 AGAATACAC 2 Unidirectional alignment (log-probability: -33.8) AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT----CacataagatTGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTA AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAATTTGGC---------TGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTA Template switch alignment (log-probability: -22.4) AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT|CACATAAGA|tTGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTA AGAAAAATCCAAACCATATTTTTCTTATGTGATGTCCAAT|CACATAAGA|CTGTGTAGGTGTGAGTTTCAGATAAGATGAAATGCATTTA ========= Event 636 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTCATGGGATCGACATAAAC----------------------TGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG Chimp: TCTCATGGGATCGACATAAACCTGTAGGATAACGTCCTACGTTAGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG ↑ 4 3 2 1 Gorilla: TCTCATGGGATCGACATAAAC----------------------TGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG Human: TCTCATGGGATCGACATAAAC----------------------TGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG Cluster: [ ] Orangutan: TCTCATGGGATCGACGTAAAC----------------------TGCCTGTAGGATAACGTCCAAACCCCTCAATCTGGGGTTGG Gorilla > Chimp --------------- chr1:203587236-203587240 Template switch process: F1: L ATTGAAGACTAATCTTGAGGTCTCATGGGATCGACATAAA---CCTGTAGGATAACGTCCTA 1 F3: 4 GCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG R RF: ATTGAAGACTAATCTTGAGGTCTCATGGGATCGACATAAACTGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG RR: TAACTTCTGATTAGAACTCCAGAGTACCCTAGCTGTATTTGACGGACATCCTATTGCAGGTTTGGCGAGTTAAACCCCAACC F2: 3 ATTGC 2 Unidirectional alignment (log-probability: -48) GTCTCATGGGATCGACATAAACctgtaggataacgtcctacgttaGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG GTCTCATGGGATCGACATAAAC----------------------TGCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG Template switch alignment (log-probability: -32.2) GTCTCATGGGATCGACATAAA---CCTGTAGGATAACGTCCtA|CGTTA|GCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG GTCTCATGGGATCGACATAAACTGCCTGTAGGATAACGTCCAA|CGTTA|GCCTGTAGGATAACGTCCAAACCGCTCAATTTGGGGTTGG ========= Event 637 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: cacctttggatgtccaatgcatggcacagtctccagcacactgtgagagagctcaatGTGTGAGAAACTGATGAGTCAAGTTTCCTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGTCAATTGTCTGATGACAATTGACAGTGACTCAAACAGGCAGAAG ↓ 3 2 1 4 ↑ 1 4 3 2 Chimp: cacctttggatgtccaatgcatggcacagtctccagcacactgtgagAGAGCTGAATGTGTGAGAAACTGATGAGTCAAGTTTCCTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACA--CTGTGCT-----ATGGATGACAATTGACAGTGACTCAAACAGGCAGAAG Gorilla: CACCTTTGGATGTCCAATGCATGGCACAGTCTCCGGCACACTGTGAGAGAGCTGAATGTGTGAGAAACTGATGAGTCAAGTTTCCTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGCT-----ATGGATGACAATTGACAGTGACTCAAACAGGCAGAAG ↓ 1 4 3 2 Human: cacctttggatgtccaatgcatggcacagtctccagcacactgtgagagagctcaatGTGTGAGAAACTGATGAGTCAAGTTTCCTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGTCAATTGTCTGATGACAATTGACAGTGACTCAAACAGGCAGAAG Cluster: [ ] Orangutan: cacctttggatgtccaatgcatggcacagtctctagcacactgtgagAGAGCTGAATGTGTGAGAAACTGATGAGTCAAGTTTCCTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGCT-----ATGGATGACAATTGACAGTGACTCAAACAGGCAGAAG Chimp > Human ------------- chr12:24901190-24901200 Template switch process: F1: L CTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTG 1 F3: 4 TGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC R RF: CTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTGTGCTATGGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC RR: GAAGGGAGAGACTTGGCGGTCCTACACTCTAGTAATCCTGTGACACGATACCTACTGTTAACTGTCACTGAGTTTGTCCGTCTTCTCGTCG F2: 3 CTGTTAACTGT 2 Unidirectional alignment (log-probability: -41.7) TCTCTGAACCGCCAGGATGTGAGATCATTAGGACACT---CTgTGtcaattgtctGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG TCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTGTGCTATG----------GATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG Template switch alignment (log-probability: -28.7) TCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTcTG|TGTCAATTGTC|tGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG TCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTGTG|TGTCAATTGTC|GGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG Human > Chimp ------------- chr12:71181936-71181943 Template switch process: F1: L CTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACT 1 F3: 4 GATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC R RF: CATGGCACAGTCTCCAGCACACTGTGAGAGAGCTCAATGTGTGAGAAACTGATGAGTCAAGTTTCCTTCCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGTCAATTGTCTGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC RR: GTACCGTGTCAGAGGTCGTGTGACACTCTCTCGAGTTACACACTCTTTGACTACTCAGTTCAAAGGAAGGGAGAGACTTGGCGGTCCTACACTCTAGTAATCCTGTGAGACACAGTTAACAGACTACTGTTAACTGTCACTGAGTTTGTCCGTCTTCTCGTCG F2: 3 GTATCGTG 2 Unidirectional alignment (log-probability: -32) CCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACTgtgCTaTG----------GATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC CCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACT---CTGTGTCAATTGTCTGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC Template switch alignment (log-probability: -22.3) CCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACT|GTGCtATG|GATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC CCCTCTCTGAACCGCCAGGATGTGAGATCATTAGGACACT|GTGCCATG|GATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC Gorilla > Human --------------- chr12:24901192-24901200 Template switch process: F1: L CTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTG 1 F3: 4 TGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC R RF: CTCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGCTATGGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAGC RR: GAGACTTGGCGGTCCTACACTCTAGTAATCCTGTGAGACACGATACCTACTGTTAACTGTCACTGAGTTTGTCCGTCTTCTCGTCG F2: 3 CTGTTAACT 2 Unidirectional alignment (log-probability: -32.3) TCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTGtcaattgtCT---GATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG TCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTG--------CTATGGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG Template switch alignment (log-probability: -22.4) TCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTG|TCAATTGTC|tGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG TCTGAACCGCCAGGATGTGAGATCATTAGGACACTCTGTG|TCAATTGTC|GGATGACAATTGACAGTGACTCAAACAGGCAGAAGAGCAG ========= Event 638 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTACCTCAGTGGTTCAAGTTCAAAGTTTGTCAACAAGTTATTTGAATAAAGGGCAATAAAAATAGAGAGGTTTAAAAAAATAAGATGAGTATTTTTTCTTAATTTATAAACCCACAAGAGATAAAAATGGAAATCAAAGCTCTTGGCAA----------------------------------------TATTCAAAATATTTGAATATTTAAAAGAAGAACT Chimp: TTTTACCTCAGTGGTTCAAGTTCAAAGTTTGTCAACAAGTTATTTGAATAAACAGCAACAAAAATAGAGAGGTTTaaaaaaaTAAGATGAGTATTTTTTCTTAATTTATAAACCCACAAGAGATAAAAATGGAAATCAAAACTCTTGGCAA--------------------TTTTCAAAATATTTTGAACATATTCAAAATATTTGAATATTTAAAAGAAGAACT Gorilla: TTTTACCTCAGTGGTTCAAGTTCAAAGTTTGTCAACAAGTTATTTGAATAAAGGGCAACAAAAATAGAGAGGTTTaaaaaaaTAAGATGAGTATTTTTTCTTAATTTATAAACCCACAAGAGATAAAAATGGAAATCAAAGCTCTTGGCATTTTTCAAAATATTTTGAACA--------------------TATTCAAAATATTTGAATATTTAAAAGAAGAACT ↑ 3 2 4 1 Human: TTTTACCTCAGTGGTTCAAGTTCAAAGTTTGTCAACAAGTTATTTGAATAAAGGGCAATAAAAATAGAGAGGTTTAAAAAAATAAGATGAGTATTTTTTCTTAATTTATAAACCCACAAGAGATAAAAATGGAAATCAAAGCTCTTGGCAA----------------------------------------TATTCAAAATATTTGAATATTTAAAAGAAGAACT Cluster: [ ] Orangutan: TTTTACCTCAATGGTTCAAGTTCAAAGTTTGTCAACAAGTTATTTGAAAAAAGGGCAACAAAAGTAGAGAGGTTTAAAAAAATAAGATGAGTAttttt-tttAATTTATAAACCCACAAGAGATAAAAATGGAAATCAAAGCTCTTGGCAATTTTCAAAATGTTTTGAACA--------------------TATTCAAAATATTTGAATATTTAAAAGAAGAACT Human > Gorilla --------------- chr12:73283989-73283993 Template switch process: F1: L AAACCCACAAGAGATAAAAATGGAAATCAAAGCTCTTGGCATTTTTCAAAATATTT 1 F3: 4 ATATTCAAAATATTTGAATATTTAAAAGAAGAACTCATGCT R RF: GTTCAAAGTTTGTCAACAAGTTATTTGAATAAAGGGCAATAAAAATAGAGAGGTTTAAAAAAATAAGATGAGTATTTTTTCTTAATTTATAAACCCACAAGAGATAAAAATGGAAATCAAAGCTCTTGGCAATATTCAAAATATTTGAATATTTAAAAGAAGAACTCATGCT RR: CAAGTTTCAAACAGTTGTTCAATAAACTTATTTCCCGTTATTTTTATCTCTCCAAATTTTTTTATTCTACTCATAAAAAAGAATTAAATATTTGGGTGTTCTCTATTTTTACCTTTAGTTTCGAGAACCGTTATAAGTTTTATAAACTTATAAATTTTCTTCTTGAGTACGA F2: 3 CAAGT 2 Unidirectional alignment (log-probability: -39.7) AAAATGGAAATCAAAGCTCTTGGCAtttttcaaaatattttgaacATATTCAAAATATTTGAATATTTAAAAGAAGAACTCATGC AAAATGGAAATCAAAGCTCTTGGCA--------------------ATATTCAAAATATTTGAATATTTAAAAGAAGAACTCATGC Template switch alignment (log-probability: -27.8) AAAATGGAAATCAAAGCTCTTGGCAtTtTTCAAAATATTT|TGAAC|ATATTCAAAATATTTGAATATTTAAAAGAAGAACTCATGC AAAATGGAAATCAAAGCTCTTGGCAATATTCAAAATATTT|TGAAC|ATATTCAAAATATTTGAATATTTAAAAGAAGAACTCATGC ========= Event 639 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: aagtgagtggcaggagccaccatgcctggccTGGAGAAAGTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATCATGGCTGAAAAGAAAAGGACACTGA Chimp: aagtgagtggcaggagccaccatgcctggccTGGAGAAAGTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATTATGTCTGAAAAGAAAAGGACACTGA ↓ 3 2 1 4 Gorilla: aagtgagtggcatgagccaccatgcctgcccTGGAGAAAGTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATCATGGCTGAAAAGAAAAGGACACTGA Human: aagtgagtggcaggagccaccatgcctggccTGGAGAAAGTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATCATGGCTGAAAAGAAAAGGACACTGA Cluster: [ ] Orangutan: aagtgagtggcatgagccaccatgcctggccTGGATAAAGTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATCATGGCTGAAAACAAAAGGACACTGA Chimp > Gorilla --------------- chr12:73251393-73251397 Template switch process: F1: L GTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCAT 1 F3: 4 CTGAAAAGAAAAGGACACTGAAAAAATCACTGGAATTGAT R RF: CCATGCCTGGCCTGGAGAAAGTATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATTATGTCTGAAAAGAAAAGGACACTGAAGAAATCACTGGAATTGAT RR: GGTACGGACCGGACCTCTTTCATAGAATTTGTTCGATTACTCTCCAGTATCTCTGTTGGTAATACAGACTTTTCTTTTCCTGTGACTTCTTTAGTGACCTTAACTA F2: 3 GGTAC 2 Unidirectional alignment (log-probability: -35.9) TATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATcATGgCTGAAAAGAAAAGGACACTGAAaAAATCACTGgaattgat TATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCATTATGTCTGAAAAGAAAAGGACACTGAAGAAATCACTG-------- Template switch alignment (log-probability: -21.9) TATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCAT|CATGG|CTGAAAAGAAAAGGACACTGAAaAAATCACTGGAATTGAT TATCTTAAACAAGCTAATGAGAGGTCATAGAGACAACCAT|CATGG|CTGAAAAGAAAAGGACACTGAAGAAATCACTGGAATTGAT ========= Event 640 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGAAGACCTTTCGTACTTACCAGTGCAT-------CAAAACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT Chimp: AAGAAGACCTTTCATACTTACCAGTGCAT-------CAAAACCAAAAGCATGAACGAAAA-AAGATTGGATTCAAATAT Gorilla: AAGAAGACCTTTCGTACTTACCAGTGCGAAAGCACTGGTAACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT ↑ 3 2 4 1 Human: AAGAAGACCTTTCGTACTTACCAGTGCAT-------CAAAACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr12:59867216-59867223 Template switch process: F1: L TTATTATCTTTACTAAGAAGACCTTTCGTACTTACCAGTG---------------------CGAAA 1 F3: 4 AACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT R RF: TTATTATCTTTACTAAGAAGACCTTTCGTACTTACCAGTGCATCAAAACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT RR: AATAATAGAAATGATTCTTCTGGAAAGCATGAATGGTCACGTAGTTTTGGTTTTCGTACTTGCTTTTTCTCTAACCTAAGTTTATA F2: 3 TGGTCACG 2 Unidirectional alignment (log-probability: -38.1) ATCTTTACTAAGAAGACCTTTCGTACTTACCAGTGC-----gaaagcactggtAACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT ATCTTTACTAAGAAGACCTTTCGTACTTACCAGTGCATCAA------------AACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT Template switch alignment (log-probability: -27.7) ATCTTTACTAAGAAGACCTTTCGTACTTACCAGTG---------------------CGAAA|GCACTGGT|AACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT ATCTTTACTAAGAAGACCTTTCGTACTTACCAGTGCATCAAAACCAAAAGCATGAACGAAA|GCACTGGT|AACCAAAAGCATGAACGAAAAAGAGATTGGATTCAAATAT ========= Event 641 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TTTAGCATGTCTTTTCTAGCAAGAGGTACATTTACCTATTGCTCAATTCTAAAATGCCTGAG ↑ 3 2 1 4 Chimp: TTTAGCATGTCTTTTCTAGCAATAGGTACATTTAC-AAGTTCTCAATTCTAAAATGCCTGAG Gorilla: -------------------------------------------------------------- Human: TTTAGCATGTCTTTTCTAGCAAGAGGTACATTTACCTATTGCTCAATTCTAAAATGCCTGAG Cluster: [ ] Orangutan: -------------------------------------------------------------- Chimp > Human ------------- chr1:225278779-225278784 Template switch process: F1: L CTTTTCTTTAGCATGTCTTTTCTAGCAAGAGGTACATTTAC 1 F3: 4 CTCAATTCTAAAATGCCTGAGAATGTATTCAGAGCAGTTT R RF: CTTTTCTTTAGCATGTCTTTTCTAGCAATAGGTACATTTACAAGTTCTCAATTCTAAAATGCCTGAGAATGTATTCAGAGCAGTTT RR: GAAAAGAAATCGTACAGAAAAGATCGTTATCCATGTAAATGTTCAAGAGTTAAGATTTTACGGACTCTTACATAAGTCTCGTCAAA F2: 3 GTTATC 2 Unidirectional alignment (log-probability: -36) TTTTCTTTAGCATGTCTTTTCTAGCAAgAGGTACATTTAC-----CtattgcTCAATTCTAAAATGCCTGAGAATGTATTCAGAGCAGTTT TTTTCTTTAGCATGTCTTTTCTAGCAATAGGTACATTTACAAGTTC------TCAATTCTAAAATGCCTGAGAATGTATTCAGAGCAGTTT Template switch alignment (log-probability: -22) TTTTCTTTAGCATGTCTTTTCTAGCAAgAGGTACATTTAC|CTATTG|CTCAATTCTAAAATGCCTGAGAATGTATTCAGAGCAGTTT TTTTCTTTAGCATGTCTTTTCTAGCAATAGGTACATTTAC|CTATTG|CTCAATTCTAAAATGCCTGAGAATGTATTCAGAGCAGTTT ========= Event 642 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TGTGCAGTACTCACCCCCTCCGTCTG---CTCCCTCCAAGG--TGTGGGGGTGGGCAGTGCTCAGGGC--CTCCTCGGA---GCCAAAGGACAGCATGGTCGGCA Chimp: TGTGCAGTACTCACCCCCTCCGTCTG---CTCCCTCCAAGG--TGTGGGGGTGGGCAGTGCTCAGGGC--CTCCTCGGA---GCCAAAGGACAGCATGGTCGGCA ↓ 13 24 ↑ 13 24 Gorilla: TGTGCAGTACTCACCCCCTCCATCTG------GCTCCGAGG----AGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAGCAAAGGACAGCATGGTCGGCA ↓ 13 24 ↑ 13 24 Human: TGTGCAGTACTCACCCCCTCCGTCTG---CTCCCTCCAAGG--TGTGGGGGTGGGCAGTGCTCAGGGC--CTCCTCGGA---GCCAAAGGACAGCATGGTCGGCA Cluster: [ ] Orangutan: TGTGCAGTACTCACCTGCTCCGTCTGCTC---CCTCCAAGGTG--TAGGGGTGGGCAGTGCTCAGGAC--CTCCTCGGA---GCCAAAGGACAGCATGGTTGGCA Gorilla > Human --------------- chr1:23110214-23110261 Template switch process: F1: L CTGCACCTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCGTCTG 1 F3: 4 CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG R RF: CTGCACCTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTGGCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAGCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG RR: GACGTGGAGGTCCGTCCGAGACACGTCATGAGTGGGGGAGGTAGACCGAGGCTCCTCCGGGACTCGTGACGGGTGGGGGTGTGGAACCTCCCTCGTTTCCTGTCGTACCAGCCGTGTCTCCTTCCCCATGGACC F2: 3 CGAGGCTCCTCCGGGACTCGTGACGGGTGGGGGTGTGGAACCTCCCTC 2 Unidirectional alignment (log-probability: -94.7) CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCgTCTGctccctccaaggtgtgggggtgggcagtgctcagggcctcctcggaGC----------------------------------------------CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTG----------------------------------------------GCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAGCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Template switch alignment (log-probability: -27.4) CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCgTCTG|CTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGC|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTG|CTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGC|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Human > Gorilla --------------- chr1:23350160-23350207 Template switch process: F1: L CTGCACCTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTG 1 F3: 4 CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG R RF: CTGCACCTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCGTCTGCTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGCCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG RR: GACGTGGAGGTCCGTCCGAGACACGTCATGAGTGGGGGAGGCAGACGAGGGAGGTTCCACACCCCCACCCGTCACGAGTCCCGGAGGAGCCTCGGTTTCCTGTCGTACCAGCCGTGTCTCCTTCCCCATGGACC F2: 3 GAGGGAGGTTCCACACCCCCACCCGTCACGAGTCCCGGAGGAGCCTCG 2 Unidirectional alignment (log-probability: -94.7) CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCaTCTG----------------------------------------------GCtccgaggaggccctgagcactgcccacccccacaccttggagggagCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCGTCTGCTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGC----------------------------------------------CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Template switch alignment (log-probability: -27.4) CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCaTCTG|GCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAG|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCGTCTG|GCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAG|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Gorilla > Chimp --------------- chr1:23723774-23723821 Template switch process: F1: L CTGCACCTCCAGGCAGGATCTGTGCAGTACTCACCCCCTCCGTCTG 1 F3: 4 CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG R RF: CTGCACCTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTGGCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAGCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG RR: GACGTGGAGGTCCGTCCGAGACACGTCATGAGTGGGGGAGGTAGACCGAGGCTCCTCCGGGACTCGTGACGGGTGGGGGTGTGGAACCTCCCTCGTTTCCTGTCGTACCAGCCGTGTCTCCTTCCCCATGGACC F2: 3 CGAGGCTCCTCCGGGACTCGTGACGGGTGGGGGTGTGGAACCTCCCTC 2 Unidirectional alignment (log-probability: -100) CTCCAGGCAGGaTCTGTGCAGTACTCACCCCCTCCgTCTGctccctccaaggtgtgggggtgggcagtgctcagggcctcctcggaGC----------------------------------------------CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTG----------------------------------------------GCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAGCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Template switch alignment (log-probability: -33) CTCCAGGCAGGaTCTGTGCAGTACTCACCCCCTCCgTCTG|CTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGC|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTG|CTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGC|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Chimp > Gorilla --------------- chr1:23350160-23350207 Template switch process: F1: L CTGCACCTCCAGGCAGGCTCTGTGCAGTACTCACCCCCTCCATCTG 1 F3: 4 CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG R RF: CTGCACCTCCAGGCAGGATCTGTGCAGTACTCACCCCCTCCGTCTGCTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGCCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG RR: GACGTGGAGGTCCGTCCTAGACACGTCATGAGTGGGGGAGGCAGACGAGGGAGGTTCCACACCCCCACCCGTCACGAGTCCCGGAGGAGCCTCGGTTTCCTGTCGTACCAGCCGTGTCTCCTTCCCCATGGACC F2: 3 GAGGGAGGTTCCACACCCCCACCCGTCACGAGTCCCGGAGGAGCCTCG 2 Unidirectional alignment (log-probability: -100) CTCCAGGCAGGcTCTGTGCAGTACTCACCCCCTCCaTCTG----------------------------------------------GCtccgaggaggccctgagcactgcccacccccacaccttggagggagCAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGATCTGTGCAGTACTCACCCCCTCCGTCTGCTCCCTCCAAGGTGTGGGGGTGGGCAGTGCTCAGGGCCTCCTCGGAGC----------------------------------------------CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG Template switch alignment (log-probability: -33) CTCCAGGCAGGcTCTGTGCAGTACTCACCCCCTCCaTCTG|GCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAG|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG CTCCAGGCAGGATCTGTGCAGTACTCACCCCCTCCGTCTG|GCTCCGAGGAGGCCCTGAGCACTGCCCACCCCCACACCTTGGAGGGAG|CAAAGGACAGCATGGTCGGCACAGAGGAAGGGGTACCTGG ========= Event 643 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 125 Detected in comparisons: 1256 Multiple sequence alignment: Human: TATGTATAATATTAATAGTGACTTAGAATATTTA----------------------------------------------------AGTAAATATA-CTAAATATTCTAAGTAACTATTAGAATTCCCAGTATA ↓ 3 1 2 4 ↑ 13 24 Chimp: TATGTATAATATTAATAGTGACTTAGAATATTT-----------------------------------------------------AGTATATTTACTTAAATATTCTAAGTCACTATTAGAATTCCCAGTATA ↑ 3 1 2 4 Gorilla: TATGTATAATATTAATAGTGACTTACAATATTTA----------------------------------------------------AGTAAATATA-CTAAATTTTCTAAGTAACTATTAGAATTCCCAGTGTA Human: TATGTATAATATTAATAGTGACTTAGAATATTTA----------------------------------------------------AGTAAATATA-CTAAATATTCTAAGTAACTATTAGAATTCCCAGTATA Cluster: [ ] Orangutan: TATGTATAATATTAATAGTTACTTAGAATATTTAAGTAaatatactaaatttacttagaatatactaaatttatttagaatatctaaGTAAATATA-CTAAATATTCTAAGTAACTGTTAGAATTCTCAGTATA Chimp > Human ------------- chr12:107563625-107563635 Template switch process: F1: L TACAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA 1 F3: 4 TAAATATTCTAAGTAACTATTAGAATTCCCAGTATAAGAA R RF: TACAATCTTATGTATAATATTAATAGTGACTTAGAATATTTAGTATATTTACTTAAATATTCTAAGTCACTATTAGAATTCCCAGTATAAGAA RR: ATGTTAGAATACATATTATAATTATCACTGAATCTTATAAATCATATAAATGAATTTATAAGATTCAGTGATAATCTTAAGGGTCATATTCTT F2: 3 CATATAAATGA 2 Unidirectional alignment (log-probability: -40.7) CAATCTTATGTATAATATTAATAGTGACTTAGAATATTTaAGTAaATaTACT-AAATATTCTAAGTaACTATTAGAATTCCCAGTATAAGAA CAATCTTATGTATAATATTAATAGTGACTTAGAATATTT-AGTATATTTACTTAAATATTCTAAGTCACTATTAGAATTCCCAGTATAAGAA Template switch alignment (log-probability: -22.7) CAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA|AGTAAATATAC|TAAATATTCTAAGTaACTATTAGAATTCCCAGTATAAGAA CAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA|AGTAAATATAC|TAAATATTCTAAGTCACTATTAGAATTCCCAGTATAAGAA Human > Chimp ------------- chr12:65154999-65155024 Template switch process: F1: L TACAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA 1 F3: 4 ACTATTAGAATTCCCAGTATAAGAA R RF: TACAATCTTATGTATAATATTAATAGTGACTTAGAATATTTAAGTAAATATACTAAATATTCTAAGTAACTATTAGAATTCCCAGTATAAGAA RR: ATGTTAGAATACATATTATAATTATCACTGAATCTTATAAATTCATTTATATGATTTATAAGATTCATTGATAATCTTAAGGGTCATATTCTT F2: 3 CTGAATCTTATAAATTCATTTATATG 2 Unidirectional alignment (log-probability: -40.7) CAATCTTATGTATAATATTAATAGTGACTTAGAATATTT-AGTAtATtTACtTAAATATTCTAAGTcACTATTAGAATTCCCAGTATAAGAA CAATCTTATGTATAATATTAATAGTGACTTAGAATATTTAAGTAAATATAC-TAAATATTCTAAGTAACTATTAGAATTCCCAGTATAAGAA Template switch alignment (log-probability: -18.2) CAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA|GTATATTTACTTAAATATTCTAAGTC|ACTATTAGAATTCCCAGTATAAGAA CAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA|GTATATTTACTTAAATATTCTAAGTC|ACTATTAGAATTCCCAGTATAAGAA Gorilla > Chimp --------------- chr12:65154999-65155015 Template switch process: F1: L TGTTATTTTACAATCTTATGTATAATATTAATAGTGACTTAGAATATTTA 1 F3: 4 TTCTAAGTCACTATTAGAATTCCCAGTATAAGAATCAAGAGTAGAGATT R RF: TGTTATTTTACAATCTTATGTATAATATTAATAGTGACTTACAATATTTAAGTAAATATACTAAATTTTCTAAGTAACTATTAGAATTCCCAGTGTAAGAATCAAGAGTAGAGATT RR: ACAATAAAATGTTAGAATACATATTATAATTATCACTGAATGTTATAAATTCATTTATATGATTTAAAAGATTCATTGATAATCTTAAGGGTCACATTCTTAGTTCTCATCTCTAA F2: 3 ATAAATTCATTTATATG 2 Unidirectional alignment (log-probability: -55.7) CAATCTTATGTATAATATTAATAGTGACTTAgAATATTT-AGTAtATtTACtTAAATaTTCTAAGTcACTATTAGAATTCCCAGTaTAAGAATCAAGA CAATCTTATGTATAATATTAATAGTGACTTACAATATTTAAGTAAATATAC-TAAATTTTCTAAGTAACTATTAGAATTCCCAGTGTAAGAATCAAGA Template switch alignment (log-probability: -34.9) CAATCTTATGTATAATATTAATAGTGACTTAgAATATTTA|GTATATTTACTTAAATA|TTCTAAGTcACTATTAGAATTCCCAGTaTAAGAATCAAGA CAATCTTATGTATAATATTAATAGTGACTTACAATATTTA|GTATATTTACTTAAATA|TTCTAAGTAACTATTAGAATTCCCAGTGTAAGAATCAAGA ========= Event 644 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTTCAGAGCTCGTTCTGTTCTTTATTATTA------CTCAAGAGGGATCATTTTTACCATCTGG Chimp: CTTTCAGAGCTCGTTCTGTTCTTTATTATTA------CTCAAGTGGGATCATTTTTACCATCTGG Gorilla: CTTTCAGAGCTCGTTCTGTTCTTGAGTAACA------------CGGGATCATTTTTACCATCTGG ↓ 3 12 4 Human: CTTTCAGAGCTCGTTCTGTTCTTTATTATTA------CTCAAGAGGGATCATTTTTACCATCTGG Cluster: [ ] Orangutan: CTTTCAGAGCTCATTCTGTTCTTTATTATTACTCAAG------TGGAATCATTTTTACCATTTGG Gorilla > Human --------------- chr12:107649938-107649947 Template switch process: F1: L AGAATACCCATTTCCTGGCTTTCAGAGCTCGTTCTGTTCTTTATTA 1 F3: 4 GGGATCATTTTTACCATCTGGTACTAATGAGTTGTGGTAG R RF: AGAATACCCATTTCCTGGCTTTCAGAGCTCGTTCTGTTCTTGAGTAACACGGGATCATTTTTACCATCTGGTACTAATGAGTTGTGGTAG RR: TCTTATGGGTAAAGGACCGAAAGTCTCGAGCAAGACAAGAACTCATTGTGCCCTAGTAAAAATGGTAGACCATGATTACTCAACACCATC F2: 3 AGAACTCATT 2 Unidirectional alignment (log-probability: -39.7) CCCATTTCCTGGCTTTCAGAGCTCGTTCTGTTCTTtattattactcaaGA-------GGGATCATTTTTACCATCTGGTACTAATGAGTTGTGGTAG CCCATTTCCTGGCTTTCAGAGCTCGTTCTGTTCTT-------------GAGTAACACGGGATCATTTTTACCATCTGGTACTAATGAGTTGTGGTAG Template switch alignment (log-probability: -28.2) CCCATTTCCTGGCTTTCAGAGCTCGTTCTGTTCTTtAtTA|TTACTCAAGA|GGGATCATTTTTACCATCTGGTACTAATGAGTTGTGGTAG CCCATTTCCTGGCTTTCAGAGCTCGTTCTGTTCTTGAGTA|TTACTCAAGA|GGGATCATTTTTACCATCTGGTACTAATGAGTTGTGGTAG ========= Event 645 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TACAGGAGAGACTTCTCTTTT----------CTCCTGGCCAATGGCCAGGAGAGGTTTCTTCAAGGGGGTCC Chimp: TACAGGAGAGACTTCTCTTTT----------CTCCTGGCCAATGGCCAGGAGAGGTTTCTTCAAGGGGGTCC ↑ 134 2 Gorilla: TACAGGAGAGACTTCTCTTTT--------------------TTGGCCAGGAGAGGTTTCTTCAAGGGGGTCC ↓ 134 2 Human: TACAGGAGAGACTTCTCTTTT----------CTCCTGGCCAATGGCCAGGAGAGGTTTCTTCAAGGGGGTCC Cluster: [ ] Orangutan: TACAGGAGAGCCTTCTCTTTTCTCCTGGCCA----------ATGGCCAGGAGAGGTTTCTTCAAGGGGGTCC Gorilla > Human --------------- chr12:130578422-130578432 Template switch process: F1: L TTTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT 1 F3: 4 TGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG R RF: TTTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTTTTGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG RR: AAAACGAAGAGAACACTGAGATGTCCTCTCTGAAGAGAAAAAACCGGTCCTCTCCAAAGAAGTTCCCCCAGGGACTTTGGAC F2: 3 AACCGGTCCTC 2 Unidirectional alignment (log-probability: -30.8) TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTTctcctggccaaTGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT----------TTGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG Template switch alignment (log-probability: -17.1) TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT|CTCCTGGCCAA|TGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT|CTCCTGGCCAA|TGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG Gorilla > Chimp --------------- chr12:134308975-134308985 Template switch process: F1: L TTTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT 1 F3: 4 TGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG R RF: TTTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTTTTGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG RR: AAAACGAAGAGAACACTGAGATGTCCTCTCTGAAGAGAAAAAACCGGTCCTCTCCAAAGAAGTTCCCCCAGGGACTTTGGAC F2: 3 AACCGGTCCTC 2 Unidirectional alignment (log-probability: -30.8) TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTTctcctggccaaTGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT----------TTGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG Template switch alignment (log-probability: -17.1) TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT|CTCCTGGCCAA|TGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG TTTGCTTCTCTTGTGACTCTACAGGAGAGACTTCTCTTTT|CTCCTGGCCAA|TGGCCAGGAGAGGTTTCTTCAAGGGGGTCCCTGAAACCTG ========= Event 646 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: caggcaccttaagaggtaagcaagctttgtccttgagacttcctgagtgaccttgaagactgcatccctacttaa Chimp: CAGGCACCTTAAGAGGTAAGCAAGCTTTGTCCTTGAGACTTCCTGATCACTCAGGAAGACTGCATCCCTACTTAA ↑ 3 1 2 4 Gorilla: CAGGCACCTTAAGAGGTAAGCGAGCTTTGCCCTTGAGACTTCCTGAGTGACCTTGAAGACTGCATCCCTACTTAA Human: caggcaccttaagaggtaagcaagctttgtccttgagacttcctgagtgaccttgaagactgcatccctacttaa Cluster: [ ] Orangutan: CAGGCACCTTAAGAGGTAAGCGAGCTTTGCCCTTGAGCATTCCTGAGTGACCTTGAAGACTGCATCCCTACTTAA Gorilla > Chimp --------------- chr12:73204409-73204416 Template switch process: F1: L CTCTCCAAACCCAGCAAAGGCAGGCACCTTAAGAGGTAAGCAAGCTTTGTCCTTGAGACTTCCTGA 1 F3: 4 GAAGACTGCATCCCTA R RF: CTCTCCAAACCCAGCAAAGGCAGGCACCTTAAGAGGTAAGCGAGCTTTGCCCTTGAGACTTCCTGAGTGACCTTGAAGACTGCATCCCTA RR: GAGAGGTTTGGGTCGTTTCCGTCCGTGGAATTCTCCATTCGCTCGAAACGGGAACTCTGAAGGACTCACTGGAACTTCTGACGTAGGGAT F2: 3 GACTCACT 2 Unidirectional alignment (log-probability: -42.1) CCTTAAGAGGTAAGCaAGCTTTGtCCTTGAGACTTCCTGatcactcAG-------GAAGACTGCATCCCTA CCTTAAGAGGTAAGCGAGCTTTGCCCTTGAGACTTCCTG-------AGTGACCTTGAAGACTGCATCCCTA Template switch alignment (log-probability: -27.8) CCTTAAGAGGTAAGCaAGCTTTGtCCTTGAGACTTCCTGA|TCACTCAG|GAAGACTGCATCCCTA CCTTAAGAGGTAAGCGAGCTTTGCCCTTGAGACTTCCTGA|TCACTCAG|GAAGACTGCATCCCTA ========= Event 647 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCACATCTGTCATCTCCTTGACAGTGTTCCAGGCTGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTGCTCACATCTGGC ↓ 1 4 3 2 Chimp: GCACATCTGTCATCTCCTTGATGA--------CACGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTGCTCACATCTGGC ↑ 1 4 3 2 Gorilla: GCACATCTGTCATCTCCTTGACAGTGTTCCAGGCTGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTGCTCACATCTGGC Human: GCACATCTGTCATCTCCTTGACAGTGTTCCAGGCTGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTGCTCACATCTGGC Cluster: [ ] Orangutan: GCACATCTGTCATCTCCTTGACAGTGTTCCAGGCTGAGAATAAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCCGCTCACATCTGGC Human > Chimp ------------- chr1:205858156-205858161 Template switch process: F1: L AAGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA 1 F3: 4 GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG R RF: AAGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGACAGTGTTCCAGGCTGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG RR: TTCGACTGGGTTCCTCCTTCCGTGTAGACAGTAGAGGAACTGTCACAAGGTCCGACTCGTGCTCGAGGACCTTCGCCGACACACAGTTCCGAGAC F2: 3 CACAGT 2 Unidirectional alignment (log-probability: -29) AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGatgacAC-------------GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTG-----ACAGTGTTCCAGGCTGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG Template switch alignment (log-probability: -16) AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA|TGACAC|GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA|TGACAC|GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG Gorilla > Chimp --------------- chr1:205858156-205858161 Template switch process: F1: L AAGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA 1 F3: 4 GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG R RF: AAGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGACAGTGTTCCAGGCTGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG RR: TTCGACTGGGTTCCTCCTTCCGTGTAGACAGTAGAGGAACTGTCACAAGGTCCGACTCGTGCTCGAGGACCTTCGCCGACACACAGTTCCGAGAC F2: 3 CACAGT 2 Unidirectional alignment (log-probability: -28.5) AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA-------------TgacacGAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGACAGTGTTCCAGGCT-----GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG Template switch alignment (log-probability: -16.5) AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA|TGACAC|GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG AGCTGACCCAAGGAGGAAGGCACATCTGTCATCTCCTTGA|TGACAC|GAGCACGAGCTCCTGGAAGCGGCTGTGTGTCAAGGCTCTG ========= Event 648 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACACAGTGTTTGCATTACAAAAAC-----CTGTTCTTTACTTCCTAGTCTTGTTTCAGTCTTAATATCAGAAGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGA--------------TGGCTAGCTTGTTTGGGATTCA ↓ 3 2 41 Chimp: ACACAGTGTTTGCATTACAAAAAC-----CTGTTCTATACTTCCTAGTCTTGTTTCAGTCTTAATATCAGAAGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGATGAGAACAGGTTTTTGGCTAGCTTGTTTGGGATTCA Gorilla: ACACAGTGTTTGCATTACAAAAAC----------CTTTACTTCCTAGTCTTGTTTCAGTCTTAATATCAGAAGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGA--------------TGGCTAGCTTGTTTGGGATTCA Human: ACACAGTGTTTGCATTACAAAAAC-----CTGTTCTTTACTTCCTAGTCTTGTTTCAGTCTTAATATCAGAAGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGA--------------TGGCTAGCTTGTTTGGGATTCA Cluster: [ ] Orangutan: ACACAGTGTTTGCATTACAGAAACCTGTT-----CTTTACTTCCTAGTCTTGTTTCAGTCTTAATATCAGAAGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGG--------------TGGCTAGCTTGTTTGGGATTCA Human > Chimp ------------- chr12:72544966-72544977 Template switch process: F1: L AGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGATG 1 F3: 4 TGGCTAGCTTGTTTGGGATTCATCTAAACTGCTGGCAATA R RF: AAAACCTGTTCTTTACTTCCTAGTCTTGTTTCAGTCTTAATATCAGAAGTTCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGATGGCTAGCTTGTTTGGGATTCATCTAAACTGCTGGCAATA RR: TTTTGGACAAGAAATGAAGGATCAGAACAAAGTCAGAATTATAGTCTTCAAGAACTCAAGTTTTATTCGTGTTGTACAGTAGGTCCCTACCGATCGAACAAACCCTAAGTAGATTTGACGACCGTTAT F2: 3 TTTTGGACAAGA 2 Unidirectional alignment (log-probability: -31.1) TCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGAtgagaacaggttttTGGCTAGCTTGTTTGGGATTCATCTAAACTGCTGGCAATA TCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGA--------------TGGCTAGCTTGTTTGGGATTCATCTAAACTGCTGGCAATA Template switch alignment (log-probability: -16.8) TCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGATG|AGAACAGGTTTT|TGGCTAGCTTGTTTGGGATTCATCTAAACTGCTGGCAATA TCTTGAGTTCAAAATAAGCACAACATGTCATCCAGGGATG|AGAACAGGTTTT|TGGCTAGCTTGTTTGGGATTCATCTAAACTGCTGGCAATA ========= Event 649 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGACTTACACATATTTATTAAAACAGGTGAAATCTGAAAATGAGAGTGGAA--------GAAAG----ACAGACAGAAACACTGTCACTGCACTATCACAGGAAGGTGAATGAAACTGAGGGAAGGAAGGGATGCTCA Chimp: GTGACTTACACATATTTATTA-AACAGTTGAAATTTGAAAATGAGAGTGGAA----GAGAGAAAG----ACAGACAGAAACACTGTCACTGCACTATCACAGGAAGGTGAATGAAACTGAGGGAAGGAAGGGATGCTCA ↑ 1 4 3 2 Gorilla: GTGACTTACACATATTTATTAAAACAGGTGAAATTTGAAAATGAGAGTGGAAGAGA----GAAAG--------ACAGAAACACTGTCACTGCACTATCACAGGGAGGTGAATGAAACTGAGGGAAGGAAGGGATGCTCA Human: GTGACTTACACATATTTATTAAAACAGGTGAAATCTGAAAATGAGAGTGGAA--------GAAAG----ACAGACAGAAACACTGTCACTGCACTATCACAGGAAGGTGAATGAAACTGAGGGAAGGAAGGGATGCTCA Cluster: [ ] Orangutan: GTGACTTACACATATTTATTAAAACAGGTGAAATTTGAAAATGAGAGTGGAAGAGA----GAAAGACAG----ACAGAAACACTGTCACTGCACTTTCACAGGAAGGTGAATGAAACTGAGGGAAGGAAGGGATGCTCA Gorilla > Chimp --------------- chr12:73007228-73007231 Template switch process: F1: L GTAGTTAGTAGATAAAAATAGTGACTTACACATATTTATTAAA 1 F3: 4 TGAAATTTGAAAATGAGAGTGGAAGAGAGAAAGACA R RF: GTAGTTAGTAGATAAAAATAGTGACTTACACATATTTATTAAAACAGGTGAAATTTGAAAATGAGAGTGGAAGAGAGAAAGACAGAAACACTGTCACTGCACTATCACAGGGAGGTGAATGAAACTG RR: CATCAATCATCTATTTTTATCACTGAATGTGTATAAATAATTTTGTCCACTTTAAACTTTTACTCTCACCTTCTCTCTTTCTGTCTTTGTGACAGTGACGTGATAGTGTCCCTCCACTTACTTTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -27.5) GTTAGTAGATAAAAATAGTGACTTACACATATTTATTAAA-CAGtTGAAATTTGAAAATGAGAGTGGAAGAGAGAAAGaca GTTAGTAGATAAAAATAGTGACTTACACATATTTATTAAAACAGGTGAAATTTGAAAATGAGAGTGGAAGAGAGAAAG--- Template switch alignment (log-probability: -16.2) GTTAGTAGATAAAAATAGTGACTTACACATATTTATTAAA|CAGT|TGAAATTTGAAAATGAGAGTGGAAGAGAGAAAGACA GTTAGTAGATAAAAATAGTGACTTACACATATTTATTAAA|CAGT|TGAAATTTGAAAATGAGAGTGGAAGAGAGAAAGACA ========= Event 650 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTCTTCAGAATGAGAAGAAGGTGACT-------AAAGATGTTTGACTAAATCAGTCATGGAGGACCT ↓ 3 1 2 4 Chimp: AGTCTTCAGAATGAGAAGAAGGTGACTCTTTAGTCACCTTGTTTGACTAAATCAGTCATGGAGGACCT ↑ 3 1 2 4 Gorilla: AGTCTTCAGAATGAGAAGAAGGTGACT-------AAAGATGTTTGACCAAATCAGTCATGGAGGACCA Human: AGTCTTCAGAATGAGAAGAAGGTGACT-------AAAGATGTTTGACTAAATCAGTCATGGAGGACCT Cluster: [ ] Orangutan: AGTCTTCAGAATGAGAAGAAGGTGACT-------AAAGATGTTTGACTAAATCAGTCATGGAGGACCT Human > Chimp ------------- chr1:21837821-21837832 Template switch process: F1: L TTTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT 1 F3: 4 TGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCA R RF: TTTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACTAAAGATGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCA RR: AAAATTAATACACTTCAGAAGTCTTACTCTTCTTCCACTGATTTCTACAAACTGATTTAGTCAGTACCTCCTGGACCTAAGAGGGT F2: 3 TCCACTGATTTC 2 Unidirectional alignment (log-probability: -38.6) TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT-----ctttagtcacctTGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCA TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACTAAAGA------------TGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCA Template switch alignment (log-probability: -16.8) TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT|CTTTAGTCACCT|TGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCA TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT|CTTTAGTCACCT|TGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCA Gorilla > Chimp --------------- chr1:21837821-21837832 Template switch process: F1: L TTTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT 1 F3: 4 TGTTTGACTAAATCAGTCATGGAGGACCTGGATTCTCCCAGACCTCCCT R RF: TTTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACTAAAGATGTTTGACCAAATCAGTCATGGAGGACCAGGATTCTCCCAGACCTCCCT RR: AAAATTAATACACTTCAGAAGTCTTACTCTTCTTCCACTGATTTCTACAAACTGGTTTAGTCAGTACCTCCTGGTCCTAAGAGGGTCTGGAGGGA F2: 3 TCCACTGATTTC 2 Unidirectional alignment (log-probability: -49.3) TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT-----ctttagtcacctTGTTTGACtAAATCAGTCATGGAGGACCtGGATTCTCCCA TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACTAAAGA------------TGTTTGACCAAATCAGTCATGGAGGACCAGGATTCTCCCA Template switch alignment (log-probability: -28.5) TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT|CTTTAGTCACCT|TGTTTGACtAAATCAGTCATGGAGGACCtGGATTCTCCCA TTTAATTATGTGAAGTCTTCAGAATGAGAAGAAGGTGACT|CTTTAGTCACCT|TGTTTGACCAAATCAGTCATGGAGGACCAGGATTCTCCCA ========= Event 651 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACCCCCCATGAGGCTCATGCCAGGCAGAGTGGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCC----CGTCCTCCCAGACAACCCTGTGTGGAGCCACGATTGGGACCCGGCGCCATCTGGAGCCCAGCACTCAC Chimp: AACCCCCCATGAGGCTCATGCTAGGCAGAGTAGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCC----CGTCCTCCCAGACAACCTTGTGTGGAGCCACGATTGGGACCCGGCGCCATCTGGAGCCCAGCACTCAC ↓ 1 3 2 4 Gorilla: AACCCCCCATGAGGCTCATGCTAGGCA-------------------------------------------CCAGGTCCCAATCGTGGCTCCACACAGGGTTGTCTGGGAGGA----CGGG--ACGGTGTCATCTGGAGCCCAGCACTCAC ↑ 1 3 2 4 Human: AACCCCCCATGAGGCTCATGCCAGGCAGAGTGGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCC----CGTCCTCCCAGACAACCCTGTGTGGAGCCACGATTGGGACCCGGCGCCATCTGGAGCCCAGCACTCAC Cluster: [ ] Orangutan: Human > Gorilla --------------- chr1:20971203-20971255 Template switch process: F1: L AGCTTCCAGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCA 1 F3: 4 CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG R RF: CGCTTCCAGGCACAGGGACCAACCCCCCATGAGGCTCATGCCAGGCAGAGTGGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCCCGTCCTCCCAGACAACCCTGTGTGGAGCCACGATTGGGACCCGGCGCCATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG RR: GCGAAGGTCCGTGTCCCTGGTTGGGGGGTACTCCGAGTACGGTCCGTCTCACCCCATGTTCCGGGCCTTCGACGGTCACGACCGGTCTCTGTGGCAGGGCAGGAGGGTCTGTTGGGACACACCTCGGTGCTAACCCTGGGCCGCGGTAGACCTCGGGTCGTGAGTGTGCCACCCGAGGAGACCCC F2: 3 TGTGGCAGGGCAGGAGGGTCTGTTGGGACACACCTCGGTGCTAACCCTGGACC 2 Unidirectional alignment (log-probability: -111) AGGCACAGGGACCAACCCCCCATGAGGCTCATGCtAGGCA-------------------------------------------------------------------------------------------------CcaggtcccaatcgtggctccacacagggttgtctgggaggacgggacggtgtCATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG AGGCACAGGGACCAACCCCCCATGAGGCTCATGCCAGGCAGAGTGGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCCCGTCCTCCCAGACAACCCTGTGTGGAGCCACGATTGGGACCCGGCGC----------------------------------------------------CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG Template switch alignment (log-probability: -39.1) AGGCACAGGGACCAACCCCCCATGAGGCTCATGCtAGGCA|CCaGGTCCCAATCGTGGCTCCACACAGGGTTGTCTGGGAGGACGGGACGGTGT|CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG AGGCACAGGGACCAACCCCCCATGAGGCTCATGCCAGGCA|CCGGGTCCCAATCGTGGCTCCACACAGGGTTGTCTGGGAGGACGGGACGGTGT|CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG Chimp > Gorilla --------------- chr1:20971203-20971255 Template switch process: F1: L CAGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCA 1 F3: 4 CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG R RF: CAGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCAGAGTAGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCCCGTCCTCCCAGACAACCTTGTGTGGAGCCACGATTGGGACCCGGCGCCATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG RR: GTCCGTGTCCCTGGTTGGGGGGTACTCCGAGTACGATCCGTCTCATCCCATGTTCCGGGCCTTCGACGGTCACGACCGGTCTCTGTGGCAGGGCAGGAGGGTCTGTTGGAACACACCTCGGTGCTAACCCTGGGCCGCGGTAGACCTCGGGTCGTGAGTGTGCCACCCGAGGAGACCCC F2: 3 TGTGGCAGGGCAGGAGGGTCTGTTGGGACACACCTCGGTGCTAACCCTGGACC 2 Unidirectional alignment (log-probability: -100) AGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCA-------------------------------------------------------------------------------------------------CcaggtcccaatcgtggctccacacagggttgtctgggaggacgggacggtgtCATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG AGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCAGAGTAGGGTACAAGGCCCGGAAGCTGCCAGTGCTGGCCAGAGACACCGTCCCGTCCTCCCAGACAACCTTGTGTGGAGCCACGATTGGGACCCGGCGC----------------------------------------------------CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG Template switch alignment (log-probability: -33.5) AGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCA|CCaGGTCCCAATCGTGGCTCCACACAgGGTTGTCTGGGAGGACGGGACGGTGT|CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG AGGCACAGGGACCAACCCCCCATGAGGCTCATGCTAGGCA|CCGGGTCCCAATCGTGGCTCCACACAAGGTTGTCTGGGAGGACGGGACGGTGT|CATCTGGAGCCCAGCACTCACACGGTGGGCTCCTCTGGGG ========= Event 652 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCCCTCA----GTTGGACCCCACTAGGCCCCAAC Chimp: GCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCCCTCA----GTTGGACCCCACTAGGCCCCAAC ↑ 3 2 1 4 Gorilla: GCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCAGCCAAGGGCCTGGACCCCACTAGGCCCCAAC ↓ 3 2 1 4 Human: GCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCCCTCA----GTTGGACCCCACTAGGCCCCAAC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr1:20677825-20677831 Template switch process: F1: L TCCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC 1 F3: 4 TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCGCCA R RF: TCCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCAGCCAAGGGCCTGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCACCA RR: AGGGTCCGGGTCCGAGGCTGTTCCGTGACTCCCAGAACCCGTCGGTTCCCGGACCTGGGGTGATCCGGGGTTGTCGGGTACAGACGGGTGGT F2: 3 TGACTCC 2 Unidirectional alignment (log-probability: -33.8) CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC---------CCtcagtTGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCgCCA CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCAGCCAAGGGCC-----TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCACCA Template switch alignment (log-probability: -22.1) CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC|CCTCAGT|TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCgCCA CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC|CCTCAGT|TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCACCA Gorilla > Chimp --------------- chr1:21250743-21250749 Template switch process: F1: L TCCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC 1 F3: 4 TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCGCCA R RF: TCCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCAGCCAAGGGCCTGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCACCA RR: AGGGTCCGGGTCCGAGGCTGTTCCGTGACTCCCAGAACCCGTCGGTTCCCGGACCTGGGGTGATCCGGGGTTGTCGGGTACAGACGGGTGGT F2: 3 TGACTCC 2 Unidirectional alignment (log-probability: -33.8) CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC---------CCtcagtTGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCgCCA CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGCAGCCAAGGGCC-----TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCACCA Template switch alignment (log-probability: -22.1) CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC|CCTCAGT|TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCgCCA CCCAGGCCCAGGCTCCGACAAGGCACTGAGGGTCTTGGGC|CCTCAGT|TGGACCCCACTAGGCCCCAACAGCCCATGTCTGCCCACCA ========= Event 653 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AATCAGCTGTGTGGGGCCACTTGATCACAAGAGAAGTATGTGAGAATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC----------ATCAAAGACATATAATGCGAATGGAAG Chimp: AATCAGCTGTGTGGGGCCACTTGATCACAAGAGAAGTATGTGAGAATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGCTATCCTATCTTTGATAGACATATAATGCGAATGGAAG ↓ 3 2 1 4 Gorilla: AATCAGCTGTGTGGGGCCACTTGATCACAAGAGAAGTATGTGAGAATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC----------ATCAAGGACATATAATGCAAATGGAAG Human: AATCAGCTGTGTGGGGCCACTTGATCACAAGAGAAGTATGTGAGAATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC----------ATCAAAGACATATAATGCGAATGGAAG Cluster: [ ] Orangutan: AATCAGCTGTGTGGGGCCACTTGATCACAAGAGAAGTATGTAAGAATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC----------ATCAAAGACATATAATGCGAATGGAAG Chimp > Gorilla --------------- chr12:77360873-77360878 Template switch process: F1: L AATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC 1 F3: 4 GACATATAATGCAAATGGAAGGATGATGGCCAGAAGTTGT R RF: CTTGATCACAAGAGAAGTATGTGAGAATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGCTATCCTATCTTTGATAGACATATAATGCGAATGGAAGGATGATGGCCAGAAGTTGT RR: GAACTAGTGTTCTCTTCATACACTCTTACTTTTACTACTGAACTTTCCTTAAGGTTTTAGGAAACGATAGGATAGAAACTATCTGTATATTACGCTTACCTTCCTACTACCGGTCTTCAACA F2: 3 GAACTA 2 Unidirectional alignment (log-probability: -34.1) ATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC---------------AtcaagGACATATAATGCaAATGGAAGGATGATGGCCAGAAGTTGT ATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGCTATCCTATCTTTGATA-----GACATATAATGCGAATGGAAGGATGATGGCCAGAAGTTGT Template switch alignment (log-probability: -22) ATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC|ATCAAG|GACATATAATGCaAATGGAAGGATGATGGCCAGAAGTTGT ATGAAAATGATGACTTGAAAGGAATTCCAAAATCCTTTGC|ATCAAG|GACATATAATGCGAATGGAAGGATGATGGCCAGAAGTTGT ========= Event 654 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCTGCAGCCTAGTTTCTCTCAGTGTG----CCTTACAG---CCAAAGCCAAAGACTGAGGCCGAC Chimp: GCCTGCAGCCTAGTTTCTCTCAGTGTG----CCTTACAG---CCAAAGCCAAAGACTGAGGCCAAC ↓ 1 3 2 4 Gorilla: GCCTGCAGCCTAGTTTCTCTCGGTCTG--------TAAG------CAGCCAAAGACTGAGGCCAAC Human: GCCTGCAGCCTAGTTTCTCTCAGTGTG----CCTTACAG---CCAAAGCCAAAGACTGAGGCCGAC Cluster: [ ] Orangutan: GCCTGCAGCCTAGTTTCTCTCAGTGTGTCTT----ACAGCCA---AAGCCAAAGACTGAGGCCAAC Chimp > Gorilla --------------- chr1:208658694-208658700 Template switch process: F1: L GTTTAAGGCAGAGAAGAGCGGCCTGCAGCCTAGTTTCTCTCGGT 1 F3: 4 CAGCCAAAGACTGAGGCCAACTCCCAGGACAGGGCCGCTAC R RF: GTTTAAGGCAGAGAAGAGCGGCCTGCAGCCTAGTTTCTCTCAGTGTGCCTTACAGCCAAAGCCAAAGACTGAGGCCAACTCCCAGGACAGGGCCGCTAC RR: CAAATTCCGTCTCTTCTCGCCGGACGTCGGATCAAAGAGAGTCACACGGAATGTCGGTTTCGGTTTCTGACTCCGGTTGAGGGTCCTGTCCCGGCGATG F2: 3 GAATGTC 2 Unidirectional alignment (log-probability: -37.4) AAGGCAGAGAAGAGCGGCCTGCAGCCTAGTTTCTCTC------------------ggtctgtaagcAGCCAAAGACTGAGGCCAACTCCCAGGACAGGGCCGCTA AAGGCAGAGAAGAGCGGCCTGCAGCCTAGTTTCTCTCAGTGTGCCTTACAGCCAA-----------AGCCAAAGACTGAGGCCAACTCCCAGGACAGGGCCGCTA Template switch alignment (log-probability: -27.8) AAGGCAGAGAAGAGCGGCCTGCAGCCTAGTTTCTCTCgGT|CTGTAAG|cAGCCAAAGACTGAGGCCAACTCCCAGGACAGGGCCGCTA AAGGCAGAGAAGAGCGGCCTGCAGCCTAGTTTCTCTCAGT|CTGTAAG|AAGCCAAAGACTGAGGCCAACTCCCAGGACAGGGCCGCTA ========= Event 655 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAAAAAGGATCACTATAGACTGGCCTCCCTACCAATAAGTTTTGTTGGAAATTAACCTTTCCCTATACTAAGCCTGGGCCAGttttttt-----tgtttttCAAAT Chimp: ACAAAAAGGATCACTATAGACTGGCCTCCCTACCAATAAGTTTTGTTGGAAATTAACCTTTCCCTATACTAAGCCTGGGCCAGtttttt---ttttttttttCAAAT ↓ 3 2 1 4 Gorilla: ACAAAAAGGATCACTATAGACTGGCCTCCCTACTAATAAGTTTTGTTGGAAATTAAGCTTTCCCTATACTAAGCC-AGGCCAGttttttt-----tttttttCAAAT Human: ACAAAAAGGATCACTATAGACTGGCCTCCCTACCAATAAGTTTTGTTGGAAATTAACCTTTCCCTATACTAAGCCTGGGCCAGttttttt-----tgtttttCAAAT Cluster: [] Orangutan: ACAAAAAGGATCACTATAGACTGGCCTCCCTACCAATAAGTTCTGTTGGAAATTAACCTTTCCCTATACTAAGCCTAGGCCAGttttttttt---tttttttCAAAT Chimp > Gorilla --------------- chr12:78017610-78017617 Template switch process: F1: L AATAAGTTTTGTTGGAAATTAAGCTTTCCCTATACTAAGCC 1 F3: 4 TTTTTTTTTTTTTCAAATGCAGGTATAATT R RF: ACTGGCCTCCCTACCAATAAGTTTTGTTGGAAATTAACCTTTCCCTATACTAAGCCTGGGCCAGTTTTTTTTTTTTTTTTCAAATGCAGGTATAATT RR: TGACCGGAGGGATGGTTATTCAAAACAACCTTTAATTGGAAAGGGATATGATTCGGACCCGGTCAAAAAAAAAAAAAAAAGTTTACGTCCATATTAA F2: 3 TGACCGGA 2 Unidirectional alignment (log-probability: -31.8) ATAAGTTTTGTTGGAAATTAAgCTTTCCCTATACTAAGCCa-GGCCAG--TTTTTTTTTTTTTTCAAATGCAGGTATAATT ATAAGTTTTGTTGGAAATTAACCTTTCCCTATACTAAGCCTGGGCCAGTTTTTTTTTTTTTTTTCAAATGCAGGTATAATT Template switch alignment (log-probability: -22) ATAAGTTTTGTTGGAAATTAAgCTTTCCCTATACTAAGCC|AGGCCAGT|TTTTTTTTTTTTTCAAATGCAGGTATAATT ATAAGTTTTGTTGGAAATTAACCTTTCCCTATACTAAGCC|AGGCCAGT|TTTTTTTTTTTTTCAAATGCAGGTATAATT ========= Event 656 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: tt---t---ttttttttGGAC------AC----AGTTGTAGGACTTCTGGTAGGAAATCCTGCT Chimp: tt----tttttttttttGGAC------AC----AGTTGTAGGACTTCCGGTAGGAAGTCCTGCT Gorilla: ttttt----ttttttttGGACAGTCCTACAACTGTTTGTAGGACTTCTGGTAGGAAATCCTGCT ↑ 3 4 2 Human: tt---t---ttttttttGGAC------AC----AGTTGTAGGACTTCTGGTAGGAAATCCTGCT Cluster: [ ] Orangutan: ---------ttttttttGGAC------AC----AGTTGTAGGACTTCCGGTAGGAAATCCTGCT Human > Gorilla --------------- chr12:78327127-78327139 Template switch process: F1: L AATGAGTACAATGGCAGCATTTTTTTTTTTTTTTTTGGACA 1 F3: 4 TTGTAGGACTTCTGGTAGGAAATCCTGCTTCATTCTGAAT R RF: AATGAGTACAATGGCAGCATTTTTTTTTTTTTT--TGGACACAGTTGTAGGACTTCTGGTAGGAAATCCTGCTTCATTCTGAAT RR: TTACTCATGTTACCGTCGTAAAAAAAAAAAAAA--ACCTGTGTCAACATCCTGAAGACCATCCTTTAGGACGAAGTAAGACTTA F2: 3 TGTCAACATCCTG 2 Unidirectional alignment (log-probability: -49.7) ATGAGTACAATGGCAGCATTTTTTTTTTTTTTtttggacagtcctacaactgT--------TTGTAGGACTTCTGGTAGGAAATCCTGCTTCATTCTGAAT ATGAGTACAATGGCAGCATTTTTTTTTTTTTT--------------------TGGACACAGTTGTAGGACTTCTGGTAGGAAATCCTGCTTCATTCTGAAT Template switch alignment (log-probability: -30) ATGAGTACAATGGCAGCATTTTTTTTTTTTTTttTGGACA|GTCCTACAACTGT|TTGTAGGACTTCTGGTAGGAAATCCTGCTTCATTCTGAAT ATGAGTACAATGGCAGCATTTTTTTTTTTTTT--TGGACA|GTCCTACAACTGT|TTGTAGGACTTCTGGTAGGAAATCCTGCTTCATTCTGAAT ========= Event 657 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TACGCCGGCCCAAACAGCTGAATCACTGTTTAGTGCTGTCATATCTGCA Chimp: TACGCCGGCCCAAACAGCTGAGCCACTGTTTAGTGCTGTCATATCTGCA ↓ 1 3 4 Gorilla: TACGCCGGCCCTAACAGCTGAACAGTGGTTTAGTGCTGTCATATCTGCA ↑ 1 3 4 Human: TACGCCGGCCCAAACAGCTGAATCACTGTTTAGTGCTGTCATATCTGCA Cluster: [ ] Orangutan: cactccggcccAAACAGCTGAACCACTGTTCAGTGCTGTCATATCTGCA Human > Gorilla --------------- chr1:210593813-210593817 Template switch process: F1: L CTCAGTATGGACGTGTGGATACGCCGGCCCTAACAGCTGAA 1 F3: 4 GTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG R RF: CTCAGTATGGACGTGTGGATACGCCGGCCCAAACAGCTGAATCACTGTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG RR: GAGTCATACCTGCACACCTATGCGGCCGGGTTTGTCGACTTAGTGACAAATCACGACAGTATAGACGTGAATTAAGGTGGGTAACC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -33.2) TCAGTATGGACGTGTGGATACGCCGGCCCtAACAGCTGAA-CAgTgGTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG TCAGTATGGACGTGTGGATACGCCGGCCCAAACAGCTGAATCACT-GTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG Template switch alignment (log-probability: -21.9) TCAGTATGGACGTGTGGATACGCCGGCCCtAACAGCTGAA|CAGTG|GTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG TCAGTATGGACGTGTGGATACGCCGGCCCAAACAGCTGAA|CAGTG|GTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG Chimp > Gorilla --------------- chr1:210593812-210593818 Template switch process: F1: L CCTCAGTATGGACGTGTGGATACGCCGGCCCTAACAGCTGA 1 F3: 4 TTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG R RF: CCTCAGTATGGACGTGTGGATACGCCGGCCCAAACAGCTGAGCCACTGTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG RR: GGAGTCATACCTGCACACCTATGCGGCCGGGTTTGTCGACTCGGTGACAAATCACGACAGTATAGACGTGAATTAAGGTGGGTAACC F2: 3 GGTGACA 2 Unidirectional alignment (log-probability: -33.6) CTCAGTATGGACGTGTGGATACGCCGGCCCtAACAGCTGAacagtG-----GTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG CTCAGTATGGACGTGTGGATACGCCGGCCCAAACAGCTGA-----GCCACTGTTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG Template switch alignment (log-probability: -22.1) CTCAGTATGGACGTGTGGATACGCCGGCCCtAACAGCTGA|ACAGTGG|TTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG CTCAGTATGGACGTGTGGATACGCCGGCCCAAACAGCTGA|ACAGTGG|TTTAGTGCTGTCATATCTGCACTTAATTCCACCCATTGG ========= Event 658 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCAGGGACTGCCCACTGAAAA------TATAGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGGTCTTTGTCTGTAAAATGAGGAAGATGAACTAGAGCACATCTCTGGCTCCCTCTGCCTGGGCAGTGACTCTCACCTCCCTGGACTGCAAGGCGACAGGACAGCACC Chimp: GCAGGGACTGTCCACTGAAAATTAGTCCAGGGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGGTCTTTGTCAGTAAAATGAGGAAGATGAACTAGAGCACATCTCTGGCTCCCTCTGCCTGGGCAGTGACTCTCACCTCCCTGGACTGCAAGGCGACCGGGCAGCACC ↑ 1 4 3 2 Gorilla: GCAGGGACTGTCCACTGAAAA------TATAGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGGTCTTTGCCAGTAAAATGAGGAAGATGAACTAGAGCACATCTCTGGCTCCCTCTGCCTGGGCAGTGACTCTCACCTCCCTGGACTAAAAGGCGACAGGACAGCGCC Human: GCAGGGACTGCCCACTGAAAA------TATAGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGGTCTTTGTCTGTAAAATGAGGAAGATGAACTAGAGCACATCTCTGGCTCCCTCTGCCTGGGCAGTGACTCTCACCTCCCTGGACTGCAAGGCGACAGGACAGCACC Cluster: [ ] Orangutan: GCAGGGACTGCCCACTGAAAA------TATAGACTAATGCAGAGGTGGCTGAGGGGACAAGGATACcagggtctttgtcagtaaaatgaggaagatgaactagagcacatctctggctccctCTGCCTGGGCAGTGACTCTCGCATCCCTGGACTGCAAGGCGACAGGACAGCACG Gorilla > Chimp --------------- chr1:210106945-210106953 Template switch process: F1: L ATGATGGAAGCCATTGGCCTGCAGGGACTGTCCACTGAAAAT 1 F3: 4 GACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGG R RF: ATGATGGAAGCCATTGGCCTGCAGGGACTGTCCACTGAAAATATAGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGGTCTTTGCCAGTAAAATGAGGAAGATGAACTAGAGCACATCTCTGGCTCCCTCTGCCTGGGCAGTGACTCTCACCTCCCTGGACTA RR: TACTACCTTCGGTAACCGGACGTCCCTGACAGGTGACTTTTATATCTGATTACGTCTCCACCGACTCCCCTGTCCCTATGGTCCCAGAAACGGTCATTTTACTCCTTCTACTTGATCTCGTGTAGAGACCGAGGGAGACGGACCCGTCACTGAGAGTGGAGGGACCTGAT F2: 3 GGACCTGAT 2 Unidirectional alignment (log-probability: -30.6) GATGGAAGCCATTGGCCTGCAGGGACTGTCCACTGAAAATtagtccAggGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGG GATGGAAGCCATTGGCCTGCAGGGACTGTCCACTGAAAAT------ATAGACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGG Template switch alignment (log-probability: -16.9) GATGGAAGCCATTGGCCTGCAGGGACTGTCCACTGAAAAT|TAGTCCAGG|GACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGG GATGGAAGCCATTGGCCTGCAGGGACTGTCCACTGAAAAT|TAGTCCAGG|GACTAATGCAGAGGTGGCTGAGGGGACAGGGATACCAGGG ========= Event 659 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGG------------------------------------------------------------TCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAAAAG ↓ 3 4 2 1 Chimp: ATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCAAAGACCACTAAGTAAAATAATATTCTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAAAAG Gorilla: ATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGG------------------------------------------------------------TCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAAAAG Human: ATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGG------------------------------------------------------------TCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAAAAG Cluster: [ ] Orangutan: ATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGG------------------------------------------------------------TCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAAAAG Human > Chimp ------------- chr12:60041576-60041601 Template switch process: F1: L AATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGC 1 F3: 4 TTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAA R RF: AATAAAGAGGGACACTCAAAGAATATTATTTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAGATATTTTGGAA RR: TTATTTCTCCCTGTGAGTTTCTTATAATAAAATGAATCACCAGAAACGTAAACATTAAGAAACGGAGTTCTATAAAACCTT F2: 3 CTTATAATAAAATGAATCACCAGAAA 2 Unidirectional alignment (log-probability: -97.2) ATTATTttacttagtggtctttgcatttgtaattctttgcaaagaccactaagtaaaataatattcTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAG ATTATT------------------------------------------------------------TTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAG Template switch alignment (log-probability: -19.1) ATTATTTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGC|AAAGACCACTAAGTAAAATAATATTC|TTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAG ATTATTTTACTTAGTGGTCTTTGCATTTGTAATTCTTTGC|AAAGACCACTAAGTAAAATAATATTC|TTACTTAGTGGTCTTTGCATTTGTAATTCTTTGCCTCAAG ========= Event 660 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATCATATAGCTCAGTAGCCACATAGCATATGCAGCATATGCTATGTCTAAATATGCTGCTACCAA Chimp: AATCATATAGCTCAGTAGCCATATAGC---------ATATGCTATGTCTAAATATGCTGCTACCAA Gorilla: AATCATATAGCTCAGTAGCCATGTAGC---------ATATGCTATGTCTAAATATGCTGCTACCAA ↓ 1 43 2 Human: AATCATATAGCTCAGTAGCCACATAGCATATGCAGCATATGCTATGTCTAAATATGCTGCTACCAA Cluster: [ ] Orangutan: AATCATGTAGCTCAGTAGCCATATAGC---------ATATGCTATGTCTAAATATGCTGCTACCAA Gorilla > Human --------------- chr12:102787079-102787090 Template switch process: F1: L ACTACAGTCCTTTGAGCTATAATCATATAGCTCAGTAGCCA 1 F3: 4 AGCATATGCTATGTCTAAATATGCTGCTACCAACTGTGGAATA R RF: ACTATAGTCCTTTGAGCTATAATCATATAGCTCAGTAGCCATGTAGCATATGCTATGTCTAAATATGCTGCTACCAACTGTGGAATA RR: TGATATCAGGAAACTCGATATTAGTATATCGAGTCATCGGTACATCGTATACGATACAGATTTATACGACGATGGTTGACACCTTAT F2: 3 CGTATACGATAC 2 Unidirectional alignment (log-probability: -34.9) CTAcAGTCCTTTGAGCTATAATCATATAGCTCAGTAGCCacatagcatATGcAGCATATGCTATGTCTAAATATGCTGCTACCAACTGTGGA CTATAGTCCTTTGAGCTATAATCATATAGCTCAGTAGCC---------ATGTAGCATATGCTATGTCTAAATATGCTGCTACCAACTGTGGA Template switch alignment (log-probability: -22.8) CTAcAGTCCTTTGAGCTATAATCATATAGCTCAGTAGCCA|CATAGCATATGC|AGCATATGCTATGTCTAAATATGCTGCTACCAACTGTGGA CTATAGTCCTTTGAGCTATAATCATATAGCTCAGTAGCCA|CATAGCATATGC|AGCATATGCTATGTCTAAATATGCTGCTACCAACTGTGGA ========= Event 661 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GAATAATTGTTTTCAGTCTTAACTGTTTGATGAATGAATTAAAC-TCTATTACATGCTTTCTAGTTGA Chimp: GAATAATTGTTTTCAGTCTTAACTGTTTGATGAATGAATTAAAC-TCTATTACATGCTTTCTAGTTGA ↓ 13 24 ↑ 13 24 Gorilla: GAATAATTGTTTTCAGTCTTA-GAGTTTAATTCATTCATCAAACAGTTATTACATGCTTTCTAGTTGA ↑ 13 24 Human: GAATAATTGTTTTCAGTCTTAACTGTTTGATGAATGAATTAAAC-TCTATTACATGCTTTCTAGTTGA Cluster: [ ] Orangutan: GAATAATTGTTTTCAGTCTTAACTGTTTGATGAATGAATTAAAC-TCTATTACATGCTTTCTAGTTGA Human > Gorilla --------------- chr12:54329613-54329637 Template switch process: F1: L TTTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA 1 F3: 4 TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA R RF: TTTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTAACTGTTTGATGAATGAATTAAACTCTATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA RR: AAATCCAGACTAACCTCCTTCTTATTAACAAAAGTCAGAATTGACAAACTACTTACTTAATTTGAGATAATGTACGAAAGATCAACTTAAACAGCACTCTTCTCCT F2: 3 TGACAAACTACTTACTTAATTTGAG 2 Unidirectional alignment (log-probability: -56) TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTagagtttaattcattcatcaAACaGT--------------------TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTT--------------------AACTGTTTGATGAATGAATTAAACTCTATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA Template switch alignment (log-probability: -18.9) TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA|GAGTTTAATTCATTCATCAAACAGT|TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA|GAGTTTAATTCATTCATCAAACAGT|TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA Gorilla > Chimp --------------- chr12:60045905-60045929 Template switch process: F1: L TTTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA 1 F3: 4 TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA R RF: TTTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTAGAGTTTAATTCATTCATCAAACAGTTATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA RR: AAATCCAGACTAACCTCCTTCTTATTAACAAAAGTCAGAATCTCAAATTAAGTAAGTAGTTTGTCAATAATGTACGAAAGATCAACTTAAACAGCACTCTTCTCCT F2: 3 CTCAAATTAAGTAAGTAGTTTGTCA 2 Unidirectional alignment (log-probability: -56) TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTT--------------------AACtGTttgatgaatgaattaaactcTATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTAGAGTTTAATTCATTCATCAAACAGT--------------------TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA Template switch alignment (log-probability: -18.9) TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA|ACTGTTTGATGAATGAATTAAACTC|TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA|ACTGTTTGATGAATGAATTAAACTC|TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA Chimp > Gorilla --------------- chr12:54329613-54329637 Template switch process: F1: L TTTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA 1 F3: 4 TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA R RF: TTTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTAACTGTTTGATGAATGAATTAAACTCTATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA RR: AAATCCAGACTAACCTCCTTCTTATTAACAAAAGTCAGAATTGACAAACTACTTACTTAATTTGAGATAATGTACGAAAGATCAACTTAAACAGCACTCTTCTCCT F2: 3 TGACAAACTACTTACTTAATTTGAG 2 Unidirectional alignment (log-probability: -56) TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTagagtttaattcattcatcaAACaGT--------------------TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTT--------------------AACTGTTTGATGAATGAATTAAACTCTATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA Template switch alignment (log-probability: -18.9) TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA|GAGTTTAATTCATTCATCAAACAGT|TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA TTAGGTCTGATTGGAGGAAGAATAATTGTTTTCAGTCTTA|GAGTTTAATTCATTCATCAAACAGT|TATTACATGCTTTCTAGTTGAATTTGTCGTGAGAAGAGGA ========= Event 662 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCACaaaaa-aaaaTTTTTATTTCGATTTTTAA----ATCGAAATAAATACAGGCTCATTATTTGAAAACATAG ↑ 3 2 1 4 Chimp: CCACaaaaa-aaaaTTTTTATTTCGATTTTTAA--AAGTGTACACAAATACAGGCTCATTATTTGAAAACATAG Gorilla: CCACaaaaa-aaaaTTTTTATTTCGATTTTTAAAA--GTGTACACAAATACAGTCTCATTATTTGAAAACATAG ↓ 3 2 1 4 Human: CCACaaaaa-aaaaTTTTTATTTCGATTTTTAA----ATCGAAATAAATACAGGCTCATTATTTGAAAACATAG Cluster: [ ] Orangutan: CCATaaaaaaaaaaaaTTTATTTCGATTTTTAAAA--GTGTACAGAAATACAGGCTCATTATTTGAAAACATAG Chimp > Human ------------- chr12:100419367-100419373 Template switch process: F1: L TCTTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA 1 F3: 4 AAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGA R RF: TCTTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAAAGTGTACACAAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGA RR: AGAAACAGGGGTGTTTTTTTTTAAAAATAAAGCTAAAAATTTTCACATGTGTTTATGTCCGAGTAATAAACTTTTGTATCTTTTACCGTCT F2: 3 TAAAGCT 2 Unidirectional alignment (log-probability: -31.7) TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAAtcgaaat---------AAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGA TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA-------AGTGTACACAAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGA Template switch alignment (log-probability: -16.2) TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA|TCGAAAT|AAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGA TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA|TCGAAAT|AAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGA Gorilla > Human --------------- chr12:100419367-100419373 Template switch process: F1: L TCTTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA 1 F3: 4 AAATACAGGCTCATTATTTGAAAACATAGAAAATGGCAGATCCTATTTA R RF: TCTTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAAAGTGTACACAAATACAGTCTCATTATTTGAAAACATAGAAAATGGCAGATCCTATTTA RR: AGAAACAGGGGTGTTTTTTTTTAAAAATAAAGCTAAAAATTTTCACATGTGTTTATGTCAGAGTAATAAACTTTTGTATCTTTTACCGTCTAGGATAAAT F2: 3 TAAAGCT 2 Unidirectional alignment (log-probability: -36.8) TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA---------tcgaaatAAATACAGgCTCATTATTTGAAAACATAGAAAATGGCAGA TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAAAGTGTACAC-------AAATACAGTCTCATTATTTGAAAACATAGAAAATGGCAGA Template switch alignment (log-probability: -22.4) TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA|TCGAAAT|AAATACAGgCTCATTATTTGAAAACATAGAAAATGGCAGA TTTGTCCCCACAAAAAAAAATTTTTATTTCGATTTTTAAA|TCGAAAT|AAATACAGTCTCATTATTTGAAAACATAGAAAATGGCAGA ========= Event 663 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAAAATTCTCA----GACAAATTTACAGAAA---------CAGAGTGAGTCCATGTAAGAAAC Chimp: TGAAAATTCTCA--GAGACAAATTTACAGAAACCTGTAAATTTGAGTGAGTCCATGTAAGAAAC ↑ 3 2 1 4 Gorilla: TGAAAATTCTCAGA--GACAAATTTACAGAAA---------CAGAGTGAGTCCATGTAAGAAAC Human: TGAAAATTCTCA----GACAAATTTACAGAAA---------CAGAGTGAGTCCATGTAAGAAAC Cluster: [ ] Orangutan: TGAAAATTCTCAGA--GACAAATTTACAGAAA---------CAGAGTGAGTCCATGTAAGAAAC Gorilla > Chimp --------------- chr12:58628530-58628539 Template switch process: F1: L GCACTGCCTTGAAAATTCTCAGAGACAAATTTACAGAAAC 1 F3: 4 GAGTGAGTCCATGTAAGAAACCTGACCTTATACACAGGGA R RF: GCACTGCCTTGAAAATTCTCAGAGACAAATTTACAGAAACAGAGTGAGTCCATGTAAGAAACCTGACCTTATACACAGGGA RR: CGTGACGGAACTTTTAAGAGTCTCTGTTTAAATGTCTTTGTCTCACTCAGGTACATTCTTTGGACTGGAATATGTGTCCCT F2: 3 TTTAAATGTC 2 Unidirectional alignment (log-probability: -29.3) GCACTGCCTTGAAAATTCTCAGAGACAAATTTACAGAAACctgtaaatttGAGTGAGTCCATGTAAGAAACCTGACCTTATACACAGGGA GCACTGCCTTGAAAATTCTCAGAGACAAATTTACAGAAAC---------AGAGTGAGTCCATGTAAGAAACCTGACCTTATACACAGGGA Template switch alignment (log-probability: -17) GCACTGCCTTGAAAATTCTCAGAGACAAATTTACAGAAAC|CTGTAAATTT|GAGTGAGTCCATGTAAGAAACCTGACCTTATACACAGGGA GCACTGCCTTGAAAATTCTCAGAGACAAATTTACAGAAAC|CTGTAAATTT|GAGTGAGTCCATGTAAGAAACCTGACCTTATACACAGGGA ========= Event 664 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tgaagctttctcttgtaaacactgaaactttCCA-------CATTTATGCTTTATGCTCTTTAA ↓ 3 2 1 4 Chimp: tgaagctttctcttgtaaacactgaaactttCCAGTTTCAGTGTTTATGCTTTATGCTCTTTAA ↑ 3 2 1 4 Gorilla: tgaagctttctcttgtaaacactgaaactttCCA-------CATTTATGCTTTATGCTCTTTAA Human: tgaagctttctcttgtaaacactgaaactttCCA-------CATTTATGCTTTATGCTCTTTAA Cluster: [ ] Orangutan: tgaagctttctcttgtaaacactgaaactttCCA-------CATTTATGCTTTATGCTTTTTAA Human > Chimp ------------- chr1:212124929-212124937 Template switch process: F1: L ATATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA 1 F3: 4 TTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG R RF: ATATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCACATTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG RR: TATATTGACTTCGAAAGAGAACATTTGTGACTTTGAAAGGTGTAAATACGAAATACGAGAAATTTTGTTTTATATTATTATGC F2: 3 GTGACTTTG 2 Unidirectional alignment (log-probability: -31.2) TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCAgtttCAgtgTTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA----CA---TTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG Template switch alignment (log-probability: -16.4) TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA|GTTTCAGTG|TTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA|GTTTCAGTG|TTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG Gorilla > Chimp --------------- chr1:212124929-212124937 Template switch process: F1: L ATATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA 1 F3: 4 TTTATGCTTTATGCTCTTTAAAACAAAATATAATAATACG R RF: ATATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCACATTTATGCTTTATGCTCTTTAAAACAAAATATAATA RR: TATATTGACTTCGAAAGAGAACATTTGTGACTTTGAAAGGTGTAAATACGAAATACGAGAAATTTTGTTTTATATTAT F2: 3 GTGACTTTG 2 Unidirectional alignment (log-probability: -44.7) TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCAgtttCAgtgTTTATGCTTTATGCTCTTTAAAACAAAATataATAATACG TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA----CA---TTTATGCTTTATGCTCTTTAAAACAAAAT---ATAATACG Template switch alignment (log-probability: -30.7) TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA|GTTTCAGTG|TTTATGCTTTATGCTCTTTAAAACAAAATATAATaatacg TATAACTGAAGCTTTCTCTTGTAAACACTGAAACTTTCCA|GTTTCAGTG|TTTATGCTTTATGCTCTTTAAAACAAAATATAAT-----A ========= Event 665 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGTGGGCTAACAGGACAGGAAACAGGAACATGGGTTAAAAACCCATGTTTGAATTGGAATATTCCAAGA ↑ 1 3 4 2 Chimp: TGTGGGCTAACAGGACAGGAA------ACATGGGTTTTTAACCCATGTTTGAATTGGAATATTCCAAGA Gorilla: TGTGGGCTAACAGGACAGGAAACAGGAACATGGATTAAAAACCCATGTTTGAATTGGAATATTCCAAGA Human: TGTGGGCTAACAGGACAGGAAACAGGAACATGGGTTAAAAACCCATGTTTGAATTGGAATATTCCAAGA Cluster: [ ] Orangutan: TGTGGGCTAACAGGACAGGAAACGGGAACATGGGTTAAAAACCCATGTTTGAATTGGAATATTCCAAGA Chimp > Human ------------- chr1:14761574-14761586 Template switch process: F1: L CTCAGCATAACTGGGTGCAGTGTGGGCTAACAGGACAGGAAACAGG 1 F3: 4 AACCCATGTTTGAATTGGAATATTCCAAGACCAGGATGTG R RF: CTCAGCATAACTGGGTGCAGTGTGGGCTAACAGGACAGGAAACATGGGTTTTTAACCCATGTTTGAATTGGAATATTCCAAGACCAGGATGTG RR: GAGTCGTATTGACCCACGTCACACCCGATTGTCCTGTCCTTTGTACCCAAAAATTGGGTACAAACTTAACCTTATAAGGTTCTGGTCCTACAC F2: 3 AAATTGGGTACAA 2 Unidirectional alignment (log-probability: -37.6) ATAACTGGGTGCAGTGTGGGCTAACAGGACAGGAaacaggAACATGGGTTaaaAACCCATGTTTGAATTGGAATATTCCAAGACCAGGATGTG ATAACTGGGTGCAGTGTGGGCTAACAGGACAGGA------AACATGGGTTTTTAACCCATGTTTGAATTGGAATATTCCAAGACCAGGATGTG Template switch alignment (log-probability: -23) ATAACTGGGTGCAGTGTGGGCTAACAGGACAGGAAACAgG|AACATGGGTTAAA|AACCCATGTTTGAATTGGAATATTCCAAGACCAGGATGTG ATAACTGGGTGCAGTGTGGGCTAACAGGACAGGAAACATG|AACATGGGTTAAA|AACCCATGTTTGAATTGGAATATTCCAAGACCAGGATGTG ========= Event 666 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGTAAATGGGCCTCTGGCTAGGGGCTATTATAGCCCCTAGGCTATTATCTCATGATCTTCCAAGTACC Chimp: TAGTAAATGGGCCTCTGGCTAGGGGCTATTATAGCCCCTAGGCTATTATCTCATGATCTTCCAAGTACC ↑ 3 4 2 1 Gorilla: TAGTAAATGGGCCTCTGGCTAGGGGC-----------------TATTATCTCATGATCTTCCAAGTACC ↓ 3 4 2 1 Human: TAGTAAATGGGCCTCTGGCTAGGGGCTATTATAGCCCCTAGGCTATTATCTCATGATCTTCCAAGTACC Cluster: [ ] Orangutan: --------------------------------------------------------------------- Gorilla > Human --------------- chr1:14599984-14599991 Template switch process: F1: L TTATACCAGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTAT 1 F3: 4 GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGGTAGTG R RF: TTATACCAGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATAGTG RR: AATATGGTCACCCCAATCATTTACCCGGAGACCGATCCCCGATAATAGAGTACTAGAAGGTTCATGGTCTCTACCTATCAC F2: 3 ATCCCCGA 2 Unidirectional alignment (log-probability: -40.8) AGTGGGGTTAGTAAATGGGCCTCTGGCTAGGggctattatagcccctaGGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGgTA AGTGGGGTTAGTAAATGGGCCTCTGGCTAGG-----------------GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATA Template switch alignment (log-probability: -22.5) AGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTAT|AGCCCCTA|GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGgTA AGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTAT|AGCCCCTA|GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATA Gorilla > Chimp --------------- chr1:15159217-15159224 Template switch process: F1: L TTATACCAGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTAT 1 F3: 4 GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATAGTG R RF: TTATACCAGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATAGTG RR: AATATGGTCACCCCAATCATTTACCCGGAGACCGATCCCCGATAATAGAGTACTAGAAGGTTCATGGTCTCTACCTATCAC F2: 3 ATCCCCGA 2 Unidirectional alignment (log-probability: -35.3) AGTGGGGTTAGTAAATGGGCCTCTGGCTAGGggctattatagcccctaGGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATA AGTGGGGTTAGTAAATGGGCCTCTGGCTAGG-----------------GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATA Template switch alignment (log-probability: -17) AGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTAT|AGCCCCTA|GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATA AGTGGGGTTAGTAAATGGGCCTCTGGCTAGGGGCTATTAT|AGCCCCTA|GGCTATTATCTCATGATCTTCCAAGTACCAGAGATGGATA ========= Event 667 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTCCAATACAGACATACTGCTGGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACC-----------------------------------------TTGCATTTGTGAGGTGTTCA Chimp: TTTTCCAATACAGATATATTGCTGGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACC-----------------------------------------T------------------- Gorilla: TTTTCCAATACAGATATATTGCTGGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACCATCCAGCAATCGGTGTGTTCATCAAAGACTGTATGTGAACCTTGCATTTGTGAGGTGTTCA ↑ 3 2 4 1 Human: TTTTCCAATACAGACATACTGCTGGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACC-----------------------------------------TTGCATTTGTGAGGTGTTCA Cluster: [ ] Orangutan: TTTTCCAATACAGATACATTGCTGGATGCAATAGATGTGTTCATCAAAGACTGTATGTGAACC-----------------------------------------TTGCATTTGTGAGGTGTTC- Human > Gorilla --------------- chr1:13523641-13523648 Template switch process: F1: L TGGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACC 1 F3: 4 ATCGGTGTGTTCATCAAAGACTGTATGTGAACCTTGCATTTGTGAGGTGTTCATTGACTGCATGTGTGATAAG R RF: TGCTGGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACCTTGCATTTGTGAGGTGTTCATTGACTGCATGTGTGATAAG RR: ACGACCTACGCTAGCTACACAAGTAGCTTCTGACGTACACTTGGAACGTAAACACTCCACAAGTAACTGACGTACACACTATTC F2: 3 ACGACCTA 2 Unidirectional alignment (log-probability: -69.8) GGATGCGATCGATGTGTTCATCGAAGACTGCatgtgaaccatccagcaatcggtgtgttcatcaaagactgtATGTGAACCTTGCATT GGATGCGATCGATGTGTTCATCGAAGACTGC-----------------------------------------ATGTGAACCTTGCATT Template switch alignment (log-probability: -34.1) GGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACC|ATCCAGCA|ATCGgTGTGTTCATCaAAGACTGtATGTGAACCTTGCATT GGATGCGATCGATGTGTTCATCGAAGACTGCATGTGAACC|ATCCAGCA|ATCGATGTGTTCATCGAAGACTGCATGTGAACCTTGCATT ========= Event 668 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCAGCGCACTGTGCTTTCCTTGTTGTGCGCTGGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCCATCCCTCCATGGCCTCCCTCTCAGGCCCTCCATGTGCGTCCACTCTCCAGCCCATGTCTGCCACCCACAGCCGAGGCCCCTGGACCTGGCCCCCAGCGGGGGCTG ↓ 1 4 3 2 Chimp: ACCAGCGCACTGTGCTTTCCT---TGTGTCCAGGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCCATCCCTCCATGGCCTCCCTTTCAGGCCGTCCATGTGTGTCCACCCTCCAGCCCATGTCTGCCACCCACAGCCGAGGCCCCTGGACCTGGCCCCCAGCGGGGGCTG Gorilla: ACCAGCACACCGTGCTTTCCTTGTTGTGTCCAGGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCCATCCCTCCATGGCCTCCCTCTCAGGCCCTCCATGTGTGTCCACCCTCCGGCGCATGTCTGCTACCCACAGCCGAGGCCCCTGGACCTGGCCCCCAGCAGGGGCTG Human: ACCAGCGCACTGTGCTTTCCTTGTTGTGCGCTGGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCCATCCCTCCATGGCCTCCCTCTCAGGCCCTCCATGTGCGTCCACTCTCCAGCCCATGTCTGCCACCCACAGCCGAGGCCCCTGGACCTGGCCCCCAGCGGGGGCTG Cluster: [ ] Orangutan: ACCAGCACGCTGTGCTTTCCTTGTTGTGTCCAGGAGATATAATCAGCGGGTGGGTGACCCTCTGGGGGTTCCATGCCTCCATGGTCTCGCTCTCAGGGCGTCTCCGTGTCTCCACCCTTGAGCCCAAGCCTGCCACCCACAGCCTAGACCCGTGGACCAGGGCCCCCTGGAGGCCTG Human > Chimp ------------- chr1:214668499-214668503 Template switch process: F1: L GCTTCCTGTGGGAAGGTCCCACCAGCGCACTGTGCTTTCCTTGT 1 F3: 4 GGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCC R RF: GCTTCCTGTGGGAAGGTCCCACCAGCGCACTGTGCTTTCCTTGTTGTGCGCTGGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCCATCCCTCCATGGCCTCCCTCTCAGGCCCTCCATGTGCGTCCACTCTCCAGCCCATGTCTGCCACCCACAGCCGAGGCCCCTGGAC RR: CGAAGGACACCCTTCCAGGGTGGTCGCGTGACACGAAAGGAACAACACGCGACCTCTATTTTATTCGCCCACCCACTGGGAGACCCCCAAGGTAGGGAGGTACCGGAGGGAGAGTCCGGGAGGTACACGCAGGTGAGAGGTCGGGTACAGACGGTGGGTGTCGGCTCCGGGGACCTG F2: 3 ACCTG 2 Unidirectional alignment (log-probability: -28.8) CCTGTGGGAAGGTCCCACCAGCGCACTGTGCTTTCCTTGTgtcca--------GGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCC CCTGTGGGAAGGTCCCACCAGCGCACTGTGCTTTCCTTGT-----TGTGCGCTGGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCC Template switch alignment (log-probability: -16) CCTGTGGGAAGGTCCCACCAGCGCACTGTGCTTTCCTTGT|GTCCA|GGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCC CCTGTGGGAAGGTCCCACCAGCGCACTGTGCTTTCCTTGT|GTCCA|GGAGATAAAATAAGCGGGTGGGTGACCCTCTGGGGGTTCC ========= Event 669 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATAGTTGTGAACCTGACAACGTGACCTTGTCCTCCTcaatgggacatcaggggaaatctg Chimp: TATAGTTGTGAACCTGACAACGTGACCTTGT----CACGTTGGGACACCAGGGGAAATCTG ↑ 3 2 1 4 Gorilla: TATAGTTGTGAACCTGACAACGTGACCTTGTCCTCCTCAATGGGACACCAGGGGAAATCTG Human: TATAGTTGTGAACCTGACAACGTGACCTTGTCCTCCTcaatgggacatcaggggaaatctg Cluster: [ ] Orangutan: TATAGTCGTGAACCTGACAatgtgaccttgtcctcctcaatgggacactaggggaaatctg Gorilla > Chimp --------------- chr1:214669914-214669917 Template switch process: F1: L GGGCATTTGGTATAGTTGTGAACCTGACAACGTGACCTTGTC 1 F3: 4 TGGGACACCAGGGGAAATCTGCAGGGACTCATAGGGAGGG R RF: GGGCATTTGGTATAGTTGTGAACCTGACAACGTGACCTTGTCCTCCTCAATGGGACACCAGGGGAAATCTGCAGGGACTCATAGGGAGGG RR: CCCGTAAACCATATCAACACTTGGACTGTTGCACTGGAACAGGAGGAGTTACCCTGTGGTCCCCTTTAGACGTCCCTGAGTATCCCTCCC F2: 3 TGCA 2 Unidirectional alignment (log-probability: -25.3) GCATTTGGTATAGTTGTGAACCTGACAACGTGACCTTGTC-------AcgtTGGGACACCAGGGGAAATCTGCAGGGACTCATAGGGAGGG GCATTTGGTATAGTTGTGAACCTGACAACGTGACCTTGTCCTCCTCAA---TGGGACACCAGGGGAAATCTGCAGGGACTCATAGGGAGGG Template switch alignment (log-probability: -16.3) GCATTTGGTATAGTTGTGAACCTGACAACGTGACCTTGTC|ACGT|TGGGACACCAGGGGAAATCTGCAGGGACTCATAGGGAGGG GCATTTGGTATAGTTGTGAACCTGACAACGTGACCTTGTC|ACGT|TGGGACACCAGGGGAAATCTGCAGGGACTCATAGGGAGGG ========= Event 670 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CGTAGAAAGCAGCAGATGAAAAA--------TATCGATGCCCCTTTGGCATGTAAA ↓ 3 1 4 2 Chimp: CGTAGAAAGCAGCAGATGAAAAATCGATATTTTTCGATGCCCCTTTGGCATGTAAA Gorilla: CGTAGAAAGCAGCAGATGAAAAA--------TATCAATGCCCCGTTGGCATGTAAA Human: CGTAGAAAGCAGCAGATGAAAAA--------TATCGATGCCCCTTTGGCATGTAAA Cluster: [ ] Orangutan: TGTAGAAAGCAGCAGATGAAAAA--------TATCGATGCCCCATTGGCATGTAAA Human > Chimp ------------- chr1:13973359-13973367 Template switch process: F1: L TATAAGCCTTGTCCTACACGTAGAAAGCAGCAGATGAAAAAT 1 F3: 4 TCGATGCCCCTTTGGCATGTAAATTTCGGCTAATTCAGCC R RF: TATAAGCCTTGTCCTACACGTAGAAAGCAGCAGATGAAAAATATCGATGCCCCTTTGGCATGTAAATTTCGGCTAATTCAGCC RR: ATATTCGGAACAGGATGTGCATCTTTCGTCGTCTACTTTTTATAGCTACGGGGAAACCGTACATTTAAAGCCGATTAAGTCGG F2: 3 TTTTATAGC 2 Unidirectional alignment (log-probability: -28.4) TAAGCCTTGTCCTACACGTAGAAAGCAGCAGATGAAAAATcgatattttTCGATGCCCCTTTGGCATGTAAATTTCGGCTAATTCAGCC TAAGCCTTGTCCTACACGTAGAAAGCAGCAGATGAAAAAT--------ATCGATGCCCCTTTGGCATGTAAATTTCGGCTAATTCAGCC Template switch alignment (log-probability: -16.4) TAAGCCTTGTCCTACACGTAGAAAGCAGCAGATGAAAAAT|CGATATTTT|TCGATGCCCCTTTGGCATGTAAATTTCGGCTAATTCAGCC TAAGCCTTGTCCTACACGTAGAAAGCAGCAGATGAAAAAT|CGATATTTT|TCGATGCCCCTTTGGCATGTAAATTTCGGCTAATTCAGCC ========= Event 671 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCTTAAAATTTGACTCTAATATTTTATTCTTATCCATTTATTCTTATCACACCTACATTTACAGAAATTCTCATACCTCATTATTCTCctaagaggttggcttcatctctccccccatcaaaaatgctgtagaggtgactcaacattgggatttattactggc ↓ 1 4 3 2 Chimp: ATTCTTAAAATTTGACTCTAA--TTTGACT------------------CCACACCTACATTTACAGAAATTCTCATACCTCATTATTCTCCTAAGAGGTTGGCTTCACCTCTCCCCCCATCAAAAAtgctgtagaggtgactcaacattgagatttattactggc Gorilla: ATTCTTAAAATTTGACTCTAATATTTTATTCTTATCCATTTATTCTTATCACACCTACATTTACAGAAATTCTCATACCTCATTATTCTCCTAAGAGGTTGGCTTCACCTCTCCCCCCATCAAAAAtgctgtagaggtgactcaacattgggatttattactggc Human: ATTCTTAAAATTTGACTCTAATATTTTATTCTTATCCATTTATTCTTATCACACCTACATTTACAGAAATTCTCATACCTCATTATTCTCctaagaggttggcttcatctctccccccatcaaaaatgctgtagaggtgactcaacattgggatttattactggc Cluster: [ ] Orangutan: --TCTTAAAATTTGACTCTAATATTTTATTCTTATCCATTTATTCTTATCACACCTACATTTACAGAAATTCTCATACCTCATTATTCTCCTAAGAGGTTGGCTTCACCCCTCCTCCCATCAAAAATGCTGTAGATGCgactcaacattgggatttattactggc Human > Chimp ------------- chr1:217822791-217822797 Template switch process: F1: L CAAATAATACACTATTTAAAATTCTTAAAATTTGACTCTAAT 1 F3: 4 CACACCTACATTTACAGAAATTCTCATACCTCATTATTCT R RF: CAAATAATACACTATTTAAAATTCTTAAAATTTGACTCTAATATTTTATTCTTATCCATTTATTCTTATCACACCTACATTTACAGAAATTCTCATACCTCATTATTCTCCTAAGAGGTTGGCTTCATCTCTCCCCCCATCAAAAATGCTGTAGAGGTGACTCAA RR: GTTTATTATGTGATAAATTTTAAGAATTTTAAACTGAGATTATAAAATAAGAATAGGTAAATAAGAATAGTGTGGATGTAAATGTCTTTAAGAGTATGGAGTAATAAGAGGATTCTCCAACCGAAGTAGAGAGGGGGGTAGTTTTTACGACATCTCCACTGAGTT F2: 3 CTCAGTT 2 Unidirectional alignment (log-probability: -31.1) AATAATACACTATTTAAAATTCTTAAAATTTGACTCTAAT--------------------------TtgactcCACACCTACATTTACAGAAATTCTCATACCTCATTATTCT AATAATACACTATTTAAAATTCTTAAAATTTGACTCTAATATTTTATTCTTATCCATTTATTCTTAT------CACACCTACATTTACAGAAATTCTCATACCTCATTATTCT Template switch alignment (log-probability: -22.2) AATAATACACTATTTAAAATTCTTAAAATTTGACTCTAAT|TTGAcTC|CACACCTACATTTACAGAAATTCTCATACCTCATTATTCT AATAATACACTATTTAAAATTCTTAAAATTTGACTCTAAT|TTGAGTC|CACACCTACATTTACAGAAATTCTCATACCTCATTATTCT ========= Event 672 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTCAGGGCCGTAATTTCTCAGTCTTGTGGGAAGCTTTGCAGGTGGGGAG-AC--------------TGTGTGAGCCCCCTTGAATGTAGCTAGGATC Chimp: TTTCAGGGCCGTAATTTCTCAGTCTTGTGGGAAGCTTTGCAGGTGGGGAG-AC--------------TGTGTGAGCCCCCTTGAATGTAGCTAGGATC ↑ 3 2 1 4 Gorilla: TTTCAGGGCCGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGATGTCTCCCCACCTCCTTGAATGTGAGCCTCCTTGAATGTAGCTAGGATC ↓ 3 2 1 4 Human: TTTCAGGGCCGTAATTTCTCAGTCTTGTGGGAAGCTTTGCAGGTGGGGAG-AC--------------TGTGTGAGCCCCCTTGAATGTAGCTAGGATC Cluster: [ ] Orangutan: TTTCAGGGCCGTGATTTCTCAGTCTTGTGGGAAGCTTTGCAGGTGGGGAG-AC--------------TGTGTGAGCCCCCTTGAATGTAGCTAGGATC Gorilla > Human --------------- chr12:30202145-30202149 Template switch process: F1: L CCGTAATTTCTCAGTCTTGTGGGAAGCTTTGCAGGTGGGGA 1 F3: 4 TGTGAGCCCCCTTGAATGTAGCTAGGATCTGCCAACGCTGGGTGGATTA R RF: CCGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGATGTCTCCCCACCTCCTTGAATGTGAGCCTCCTTGAATGTAGCTAGGATCTGCCAACGCTGGGTGGATTG RR: GGCATTAAAGAGTCAGAACACCCTTGGAAACGTCCACCCCTACAGAGGGGTGGAGGAACTTACACTCGGAGGAACTTACATCGATCCTAGACGGTTGCGACCCACCTAAC F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -42.6) CGTAATTTCTCAGTCTTGTGGGAAgCTTTGCAGGTGGGGAgacTG------------------TGTGAGCCcCCTTGAATGTAGCTAGGATCTGCCAACGCTG CGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGA---TGTCTCCCCACCTCCTTGAATGTGAGCCTCCTTGAATGTAGCTAGGATCTGCCAACGCTG Template switch alignment (log-probability: -33.1) CGTAATTTCTCAGTCTTGTGGGAAgCTTTGCAGGTGGGGA|GACTG|TGTGAGCCcCCTTGAATGTAGCTAGGATCTGCCAACGCTG CGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGA|GACTG|TGTGAGCCTCCTTGAATGTAGCTAGGATCTGCCAACGCTG Gorilla > Chimp --------------- chr12:76621251-76621255 Template switch process: F1: L CCGTAATTTCTCAGTCTTGTGGGAAGCTTTGCAGGTGGGGA 1 F3: 4 TGTGAGCCCCCTTGAATGTAGCTAGGATCTGCCAACGCTGGGTGGATTA R RF: CCGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGATGTCTCCCCACCTCCTTGAATGTGAGCCTCCTTGAATGTAGCTAGGATCTGCCAACGCTGGGTGGATTG RR: GGCATTAAAGAGTCAGAACACCCTTGGAAACGTCCACCCCTACAGAGGGGTGGAGGAACTTACACTCGGAGGAACTTACATCGATCCTAGACGGTTGCGACCCACCTAAC F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -42.6) CGTAATTTCTCAGTCTTGTGGGAAgCTTTGCAGGTGGGGAgacTG------------------TGTGAGCCcCCTTGAATGTAGCTAGGATCTGCCAACGCTG CGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGA---TGTCTCCCCACCTCCTTGAATGTGAGCCTCCTTGAATGTAGCTAGGATCTGCCAACGCTG Template switch alignment (log-probability: -33.1) CGTAATTTCTCAGTCTTGTGGGAAgCTTTGCAGGTGGGGA|GACTG|TGTGAGCCcCCTTGAATGTAGCTAGGATCTGCCAACGCTG CGTAATTTCTCAGTCTTGTGGGAACCTTTGCAGGTGGGGA|GACTG|TGTGAGCCTCCTTGAATGTAGCTAGGATCTGCCAACGCTG ========= Event 673 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CATAATACACGTTTGCAGAGAAGCCTCCAGCTGTGGCAGCGCGTCACTCCAGGAAGCACAGGCTGGAGGAAGGGGGAAGTTTCCCGAGCACCACTGACAGTACTCCCGGTTCCGAGGCTGGATTTCTATAGCAACGGAC Chimp: CATAATACACGTTTGCAGAAAAGCCTCCAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGAGGAAGGGGGAAGTTTCCCGAGCACCACTGACAGTACTCCCGGTTCCGAGGCTGGATTTCTATAGCAACGGAC ↑ 1 4 3 2 Gorilla: CATAATACATGTTTGCAGAAACATGCGCAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGAGGAAGGGGGAAGTTTCCCGAGCACCACTTACAGTACTCCCGGTTCCGAGGCTGGATTTCTATAGCAACGGAC Human: CATAATACACGTTTGCAGAGAAGCCTCCAGCTGTGGCAGCGCGTCACTCCAGGAAGCACAGGCTGGAGGAAGGGGGAAGTTTCCCGAGCACCACTGACAGTACTCCCGGTTCCGAGGCTGGATTTCTATAGCAACGGAC Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr1:19446063-19446068 Template switch process: F1: L GGGAGGGGAGAAGATAAAACCATAATACACGTTTGCAGAAA 1 F3: 4 CAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGA R RF: GGGAGGGGAGAAGATAAAACCATAATACATGTTTGCAGAAACATGCGCAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGAGGAAGGGGGAAGTTTCCCGAGCACCACTTACAGTACTCCCGGTTCCGAGGCT RR: CCCTCCCCTCTTCTATTTTGGTATTATGTACAAACGTCTTTGTACGCGTCGACACCGTCGCGTAGTGAGGTCCTTCGTGTCCGACCTCCTTCCCCCTTCAAAGGGCTCGTGGTGAATGTCATGAGGGCCAAGGCTCCGA F2: 3 CTCCGA 2 Unidirectional alignment (log-probability: -33.6) GGAGGGGAGAAGATAAAACCATAATACAcGTTTGCAGAAAagcctC-----CAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGA GGAGGGGAGAAGATAAAACCATAATACATGTTTGCAGAAA-----CATGCGCAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGA Template switch alignment (log-probability: -22) GGAGGGGAGAAGATAAAACCATAATACAcGTTTGCAGAAA|AGCCTC|CAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGA GGAGGGGAGAAGATAAAACCATAATACATGTTTGCAGAAA|AGCCTC|CAGCTGTGGCAGCGCATCACTCCAGGAAGCACAGGCTGGA ========= Event 674 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: --------------------------------------------------------------------------------------------------------AAATAAATGTT----TA--TAAC--AGTCTTCTTAAT--ATTCCTAAAAGTTTGTTTTCTAAACAAACTTTTCAGT----TTCGATATGATAAT---------------------------------------------------------------GTTCCATGTGAAAATGAGTTCAGTTTTGATATGATAATGTTCCATGTGAAAATATTTATAGAAGG------------------------------------------------------------------------------------------------------CAGAATGGCTTTGTTTTTATTAGATTTATCCCTACTCAGCACCACAGAGTTTAGCTTTCCACTGATTTGATGAATGAAAGTACTTGGGTGCCACAACAAAAAG----------CATTATAAAAAATTCTAGACATGTATA--TTCCATTTTC----------------------------------------------------------------------------------------------------------GAATAAGAAATGGGATTAAGGaaaa--aaaaaaCTTTATAGTGTTGCATGTTCTGGCCAGATGTGCTTCCTGAAGCAACATAGCAACATATCCAATGCAATGATGCCAttttttttttt------------------tt---------------------------------------------------------------- Chimp: --------------------------------------------------------------------------------------------------------AAATAAATGTT----TA--TGAC--AGTCTTCTTAAT--ATTCCTAAAAGTTTGTTTTCTAAACAAACTTTTCAGT----TTCGATATGATAAT---------------------------------------------------------------GTTCCATGTGAAAATGAGTTCAGTTTCGATATGATAATGTTCCATGTGAAAATATTTATAGAAGG------------------------------------------------------------------------------------------------------CAGAATGGCTTTGTTTTTATTAGATTTATCCCTACTCAGCACCACAGAGTTTAGCTTTCCACTGATTTGATGAATGAAAGTACTTGGGTACCACAACAAAAAG----------CATTATAA-ATATTCTAGACATGTATA--TTCCATTTTC----------------------------------------------------------------------------------------------------------GAATAAGAAATTGGATTAAGGaaa-aaaaaaaaCTTTATAGTGTTGCATGTTCTGGCCAGATGTGCTTCCTGAAGCAACATAGCAACATATCCAATGCAATGATGCCAttttttttt--------------------tt---------------------------------------------------------------- ↑ 1 3 2 4 Gorilla: TTTGTTGTGGCACCCAAGTACTTTCATTCATCAAATCAGTGGAAAGCTAAACTCTGTGGTGCTGAGTAGGGATAAATCTAATAAAAACAAAGCCATTCTGCCTTCTATAAATATTTTCACATGGAACATTATCATATCAAA----ACTGAAAAGTTTGTTTAGAAAACAAACTTTTAGGA--------ATATTAAGAA------------------------------------------------------------------------------------------------------------------------------GA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--------------------TGTCATAAACATTTATTTGGTTAAAGTTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATTCTCATTTTT------------------GTACGTTTAAAATGCATACTTGggccgggcatagtgggtcatgcctgtaatcccagcactttggga Human: --------------------------------------------------------------------------------------------------------AAATAAATGTT----TA--TAAC--AGTCTTCTTAAT--ATTCCTAAAAGTTTGTTTTCTAAACAAACTTTTCAGT----TTCGATATGATAAT---------------------------------------------------------------GTTCCATGTGAAAATGAGTTCAGTTTTGATATGATAATGTTCCATGTGAAAATATTTATAGAAGG------------------------------------------------------------------------------------------------------CAGAATGGCTTTGTTTTTATTAGATTTATCCCTACTCAGCACCACAGAGTTTAGCTTTCCACTGATTTGATGAATGAAAGTACTTGGGTGCCACAACAAAAAG----------CATTATAAAAAATTCTAGACATGTATA--TTCCATTTTC----------------------------------------------------------------------------------------------------------GAATAAGAAATGGGATTAAGGaaaa--aaaaaaCTTTATAGTGTTGCATGTTCTGGCCAGATGTGCTTCCTGAAGCAACATAGCAACATATCCAATGCAATGATGCCAttttttttttt------------------tt---------------------------------------------------------------- Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------------------AAATAAATGTT----TA--TGAC--AGTCTTCTTAATAT--TCCTAAAAGTTTGTTTTCTAAACAGACTTTTCGGTTTCA----ATATGATAATGTTCCATGTGAAAATGAGTTCAGTTTCGATATGATAATGTTCCATGTGAAAATATTTATAGAA---------------------------------------------------------------GGCAGAATGGCTTTGTTTTTATTAGACTTATCCCTACTCAGCACCACAGGGTTTAGCTTTCCACTGATTTGATGAATGAAAGTACTTGGGTGCCACAACAAAAA------------------------------------------------------------------------------------------------------GCATTATAAAA----------AATCCTAGACACGTATA--TTCCGTTTTCGAATAAGAAATTGGATTAAGGaaaaaaaaaaaaCTTTATAGTGTTGCATGTTCTGGCCAGATGTGCTTCCTGAAGTAACACAGCAACATATCCAAGGCAATGATGC----------------------------------------------------------------------------------------------------------Cattttttatttattttttatttatttatttat---------------------------------------------------------------- Gorilla > Chimp --------------- chr12:85705928-85706000 Template switch process: F1: L TA 1 F3: 4 TGTG R RF: TACTTTCATTCATCAAATCAGTGGAAAGCTAAACTCTGTGGTGCTGAGTAGGGATAAATCTAATAAAAACAAAGCCATTCTGCCTTCTATAAATATTTTCACATGGAACATTATCATATCAAAACTGAAAAGTTTGTTTAGAAAACAAACTTTTAGGAATATTAAGAAGACTGTCA RR: ATGAAAGTAAGTAGTTTAGTCACCTTTCGATTTGAGACACCACGACTCATCCCTATTTAGATTATTTTTGTTTCGGTAAGACGGAAGATATTTATAAAAGTGTACCTTGTAATAGTATAGTTTTGACTTTTCAAACAAATCTTTTGTTTGAAAATCCTTATAATTCTTCTGACAGT F2: 3 ACCTTGTAATAGTATAGCTTTGACTTTTCAAACAAATCTTTTGTTTGAAAATCCTTATAATTCTTCTGACAGT 2 Unidirectional alignment (log-probability: -124) tatgacagtcttcttaatattcctAAAAGTTTGTTTtctAAACAAACTTTT--------------cagtttcgatatgataatgttccatgtg ------------------------AAAAGTTTGTTTAGAAAACAAACTTTTAGGAATATTAAGAA---------------------------- Template switch alignment (log-probability: -28.7) TA|TGACAGTCTTCTTAATATTCCTAAAAGTTTGTTTTCTAAACAAACTTTTCAGTTTcGATATGATAATGTTCCA|TGTG TA|TGACAGTCTTCTTAATATTCCTAAAAGTTTGTTTTCTAAACAAACTTTTCAGTTTTGATATGATAATGTTCCA|TGTG ========= Event 675 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAAAACTCAGATGTAATATGAACTCTAGGTCTACTATTCATACATATTCTCAAACAGTTCAAAACAATACAGATAAAAATATGTTCAATTCTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTAAAAGAATCCTCCTTCTTCCTGTTGTTTG Chimp: TCAAAACTCAGATGTAATATGAACTCTAGGTCTACCATTCATACATATTCTCAAACAGTTCAAAACAATACAGATAAAAATATGTTCAATTCTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTGT---TCACCTCCTTCTTCCTGCTGTTTG ↑ 3 2 1 4 Gorilla: TCAAAACTCAGATGTAATATGAACTCTAGGTCTACCATTCATACATATTCTCAAACAGTTCAAAACAATACAGATAAAAATATGTTCAATTCTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTAAAAGAATCCTCCTTCTTCCTGCTGTTTG Human: TCAAAACTCAGATGTAATATGAACTCTAGGTCTACTATTCATACATATTCTCAAACAGTTCAAAACAATACAGATAAAAATATGTTCAATTCTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTAAAAGAATCCTCCTTCTTCCTGTTGTTTG Cluster: [ ] Orangutan: TCAAAACTCAGATGTAATATGAACTCTAGGTCTACCATTCATACATATTCTCAAACAGTTCAAAACAATACAGATAAAAATATGTTCAATTCTTTTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTAAAAGAATCCTCCTTCTTTCTGCTGTTTG Gorilla > Chimp --------------- chr1:10585643-10585647 Template switch process: F1: L TCTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTT 1 F3: 4 CCTCCTTCTTCCTGCTGTTTGTTGAGGTAAAATGTCAGCA R RF: TGAACTCTAGGTCTACCATTCATACATATTCTCAAACAGTTCAAAACAATACAGATAAAAATATGTTCAATTCTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTAAAAGAATCCTCCTTCTTCCTGCTGTTTGTTGAGGTAAAATGTCAGCA RR: ACTTGAGATCCAGATGGTAAGTATGTATAAGAGTTTGTCAAGTTTTGTTATGTCTATTTTTATACAAGTTAAGATAAAATTTTACTTTGTATGTAAGTACACTTCTCACAAATTTTCTTAGGAGGAAGAAGGACGACAAACAACTCCATTTTACAGTCGT F2: 3 ACTTG 2 Unidirectional alignment (log-probability: -26.8) CTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTTgttcA-------CCTCCTTCTTCCTGCTGTTTGTTGAGGTAAAATGTCAGCA CTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTT----AAAAGAATCCTCCTTCTTCCTGCTGTTTGTTGAGGTAAAATGTCAGCA Template switch alignment (log-probability: -16.4) CTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTT|GTTCA|CCTCCTTCTTCCTGCTGTTTGTTGAGGTAAAATGTCAGCA CTATTTTAAAATGAAACATACATTCATGTGAAGAGTGTTT|GTTCA|CCTCCTTCTTCCTGCTGTTTGTTGAGGTAAAATGTCAGCA ========= Event 676 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGTGGGAGTGAATGCTAAAGAGGAGACCTGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACA------------------CAGGCAAAAGGGGCCCCACAGCCTGGGTCCCCAGGTGAAAGAGCAGGAAACGGGAATGTCTCCCGGGTCTTGACATGTGGTTG Chimp: GGGTGGGAGTGAATGCTAAAGAGGAGACTGGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACA------------------CAGGCAAAAGGGGCCCCACAGCCTGGGTCCCCAGGTGAAAGAACAGGAAACGGGAATGTCT-CCGGGTCTTGACATGTGGTTG Gorilla: GGGTGGGAGTGAATGCTAAAG-AGAGACTGGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACA------------------------------------CAGCCTGGGTCCCCAGGTGAAAGAACAGGAAACGGGAATGTCT-CCGGGTCTTGACATGTGGTTG ↓ 1 4 3 2 Human: GGGTGGGAGTGAATGCTAAAGAGGAGACCTGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACA------------------CAGGCAAAAGGGGCCCCACAGCCTGGGTCCCCAGGTGAAAGAGCAGGAAACGGGAATGTCTCCCGGGTCTTGACATGTGGTTG Cluster: [ ] Orangutan: GGGTGGGAGTGAATGCTAAAGAGGAGACTGGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACACAGGCAAAAGGGGCCCCA------------------CAGCCTGGGTCCCCAGGTGAAAGAGCAGGAAACGGGAATGTCT-CCGGGTCTTGACATGTGGTTG Gorilla > Human --------------- chr12:4141108-4141114 Template switch process: F1: L GAGCTCAGGGGCCTGTGGGTGGGTGGGAGTGAATGCTAAAGAG 1 F3: 4 GGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACACAG R RF: GGGCTCAGGGGCCTGTGGGTGGGTGGGAGTGAATGCTAAAGAGAGACTGGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACACAGCCTGGGTCCCCAGGTGAAAGAACAGGAAACGGGAATGTCTC RR: CCCGAGTCCCCGGACACCCACCCACCCTCACTTACGATTTCTCTCTGACCCTCCGGGTCCCTTTTCCAGTACTGGGTGATTTATGTGTCGGACCCAGGGGTCCACTTTCTTGTCCTTTGCCCTTACAGAG F2: 3 TCCAGAG 2 Unidirectional alignment (log-probability: -40) CTCAGGGGCCTGTGGGTGGGTGGGAGTGAATGCTAAAGAgGAGACctGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACAcag CTCAGGGGCCTGTGGGTGGGTGGGAGTGAATGCTAAAGA-GAGACTGGGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACA--- Template switch alignment (log-probability: -27.7) CTCAGGGGCCTGTGGGTGGGTGGGAGTGAATGCTAAAGAG|GAGACcT|GGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACACAG CTCAGGGGCCTGTGGGTGGGTGGGAGTGAATGCTAAAGAG|GAGACAT|GGAGGCCCAGGGAAAAGGTCATGACCCACTAAATACACAG ========= Event 677 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTGGAGATAGGATTGTGTCTTAGAATAAAGGAGGGTTTCTTC-----TAAGACACGTCT-T-TAAATATTACCCAAAACAATG ↑ 3 2 1 4 Chimp: GGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGTGCGGTA-----CAAAACACGTCT-T-GAAATATTACCCAAAACAATG Gorilla: GGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGTGCGGTA-----CAAAACACGTCT-T-GAAATATTACCCAAAACAATG ↓ 3 2 1 4 Human: GGTGGAGATAGGATTGTGTCTTAGAATAAAGGAGGGTTTCTTC-----TAAGACACGTCT-T-TAAATATTACCCAAAACAATG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr1:239651351-239651360 Template switch process: F1: L TGTAGGTGGAGATAGGATTGTGTCTTAGAATAAAGGAGGGT 1 F3: 4 ACACGTCTTTAAATATTACCCAAAACAATGTTGTTTCTGCTTCAAAATGT R RF: TGTAGGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGTGCGGTACAAAACACGTCTTGAAATATTACCCAAAACAATGTTGTTTCTGCTTCAAAATGT RR: ACATCCACCTCTATCCTAACACAGAATCTTCTTTCCTCCCACGCCATGTTTTGTGCAGAACTTTATAATGGGTTTTGTTACAACAAAGACGAAGTTTTACA F2: 3 GAATCTTCTT 2 Unidirectional alignment (log-probability: -46.6) GTAGGTGGAGATAGGATTGTGTCTTAGAAtAAAGGAGGGTttcttctaaG---------ACACGTCTTtAAATATTACCCAAAACAATGTTGTTTCTGC GTAGGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGT---------GCGGTACAAAACACGTCTTGAAATATTACCCAAAACAATGTTGTTTCTGC Template switch alignment (log-probability: -28.7) GTAGGTGGAGATAGGATTGTGTCTTAGAAtAAAGGAGGGT|TTCTTCTAAG|ACACGTCTTtAAATATTACCCAAAACAATGTTGTTTCTGC GTAGGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGT|TTCTTCTAAG|ACACGTCTTGAAATATTACCCAAAACAATGTTGTTTCTGC Gorilla > Human --------------- chr1:239651351-239651360 Template switch process: F1: L TGTAGGTGGAGATAGGATTGTGTCTTAGAATAAAGGAGGGT 1 F3: 4 ACACGTCTTTAAATATTACCCAAAACAATGTTGTTTCTGCTTCAAAATGT R RF: TGTAGGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGTGCGGTACAAAACACGTCTTGAAATATTACCCAAAACAATGTTGTTTCTGCTTCAAAATGT RR: ACATCCACCTCTATCCTAACACAGAATCTTCTTTCCTCCCACGCCATGTTTTGTGCAGAACTTTATAATGGGTTTTGTTACAACAAAGACGAAGTTTTACA F2: 3 GAATCTTCTT 2 Unidirectional alignment (log-probability: -45.2) GTAGGTGGAGATAGGATTGTGTCTTAGAAtAAAGGAGGGTttcttctaaG---------ACACGTCTTtAAATATTACCCAAAACAATGTTGTTTCTGC GTAGGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGT---------GCGGTACAAAACACGTCTTGAAATATTACCCAAAACAATGTTGTTTCTGC Template switch alignment (log-probability: -28.3) GTAGGTGGAGATAGGATTGTGTCTTAGAAtAAAGGAGGGT|TTCTTCTAAG|ACACGTCTTtAAATATTACCCAAAACAATGTTGTTTCTGC GTAGGTGGAGATAGGATTGTGTCTTAGAAGAAAGGAGGGT|TTCTTCTAAG|ACACGTCTTGAAATATTACCCAAAACAATGTTGTTTCTGC ========= Event 678 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGACCCCCAAAAAAGCCGGG------------GGGATCTGTGAAAAACAGATCCAAGTGTATTTGATATTTGG Chimp: CAGACCCCCAAAAAAGCCGGG------GGTTGGGGGAC---CGAAAAATAGATCCAAGTGTATTTGATATTTGG Gorilla: CAGACCCCCAAAAAAGCCGGGGGTTGG------GGGAC---CGAAAAACAGATCCAAGTGTATTTGATATTTGG ↓ 1 4 3 2 Human: CAGACCCCCAAAAAAGCCGGG------------GGGATCTGTGAAAAACAGATCCAAGTGTATTTGATATTTGG Cluster: [ ] Orangutan: CAGACCCCCAAAAAAGCCGGGGGTTGG------GGGAC---CGAAAAACAGATCCAAGTGTATTTGATATTTGG Gorilla > Human --------------- chr12:93654825-93654831 Template switch process: F1: L TCTGAGACCTTTTGTGAAATCAGACCCCCAAAAAAGCCGGGGG 1 F3: 4 GAAAAACAGATCCAAGTGTATTTGATATTTGGCATTCTCC R RF: TCTGAGACCTTATGTGAAATCAGACCCCCAAAAAAGCCGGGGGTTGGGGGACCGAAAAACAGATCCAAGTGTATTTGATATTTGGCATTCTCC RR: AGACTCTGGAATACACTTTAGTCTGGGGGTTTTTTCGGCCCCCAACCCCCTGGCTTTTTGTCTAGGTTCACATAAACTATAAACCGTAAGAGG F2: 3 TGTCTAG 2 Unidirectional alignment (log-probability: -35.3) GAGACCTTtTGTGAAATCAGACCCCCAAAAAAGCCGGGGggatctGT---------GAAAAACAGATCCAAGTGTATTTGATATTTGGCATTCTCC GAGACCTTATGTGAAATCAGACCCCCAAAAAAGCCGGGG------GTTGGGGGACCGAAAAACAGATCCAAGTGTATTTGATATTTGGCATTCTCC Template switch alignment (log-probability: -22.2) GAGACCTTtTGTGAAATCAGACCCCCAAAAAAGCCGGGGG|GATCTGT|GAAAAACAGATCCAAGTGTATTTGATATTTGGCATTCTCC GAGACCTTATGTGAAATCAGACCCCCAAAAAAGCCGGGGG|GATCTGT|GAAAAACAGATCCAAGTGTATTTGATATTTGGCATTCTCC ========= Event 679 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: tgtctggccTCATTTCTGGAA-------GTCTTTAACAAGCCAGCATTCCATAGCTGGCTTGTTAAAGACTGTATGGGATGGTGAATTTT Chimp: tgtctggccTCATTTCTGGAA-------GTCTTTAACAAGCCAGCATTCCATAGCTGGATTGTTAAAGACTGTATGGGATGGTGAATTTT ↑ 1 4 3 2 Gorilla: tgtctggccTCATTTCTGGAA--------------TGAGGCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGATGGTGAATTTT ↓ 1 4 3 2 Human: tgtctggccTCATTTCTGGAA-------GTCTTTAACAAGCCAGCATTCCATAGCTGGCTTGTTAAAGACTGTATGGGATGGTGAATTTT Cluster: [ ] Orangutan: tgtctggccTCATTTCTGGAAGTCTTTA-------ACAAGCCAGCATTCCATAGCTGGATTGTTAAAGACTGTATGGGATGGTGAATTTT Gorilla > Human --------------- chr1:236613940-236613950 Template switch process: F1: L ATTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAA 1 F3: 4 GCCAGCATTCCATAGCTGGCTTGTTAAAGACTGTATGGGA R RF: ATTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAATGAGGCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGA RR: TAATGTCCGCACTCGGTGGCACAGACCGGAGTAAAGACCTTACTCCGGTCGTAAGGTATCGACCTAACAATTTCTGATATACCCT F2: 3 AACAATTTCTG 2 Unidirectional alignment (log-probability: -46.2) TTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGA---AGtctttaacaaGCCAGCATTCCATAGCTGGcTTGTTAAAGACTgTATGGGA TTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAATGAG----------GCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGA Template switch alignment (log-probability: -28.2) TTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAA|GTCTTTAACAA|GCCAGCATTCCATAGCTGGcTTGTTAAAGACTgTATGGGA TTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAA|GTCTTTAACAA|GCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGA Gorilla > Chimp --------------- chr1:215726959-215726969 Template switch process: F1: L ATTACAGGCGTGAGCCACCATGTCTGGCCTCATTTCTGGAA 1 F3: 4 GCCAGCATTCCATAGCTGGATTGTTAAAGACTGTATGGGA R RF: ATTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAATGAGGCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGA RR: TAATGTCCGCACTCGGTGGCACAGACCGGAGTAAAGACCTTACTCCGGTCGTAAGGTATCGACCTAACAATTTCTGATATACCCT F2: 3 AACAATTTCTG 2 Unidirectional alignment (log-probability: -46.2) TTACAGGCGTGAGCCACCaTGTCTGGCCTCATTTCTGGA---AGtctttaacaaGCCAGCATTCCATAGCTGGATTGTTAAAGACTgTATGGGA TTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAATGAG----------GCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGA Template switch alignment (log-probability: -28.2) TTACAGGCGTGAGCCACCaTGTCTGGCCTCATTTCTGGAA|GTCTTTAACAA|GCCAGCATTCCATAGCTGGATTGTTAAAGACTgTATGGGA TTACAGGCGTGAGCCACCGTGTCTGGCCTCATTTCTGGAA|GTCTTTAACAA|GCCAGCATTCCATAGCTGGATTGTTAAAGACTATATGGGA ========= Event 680 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCAATCTGGACTCAGCTGCAGCCAGTGGGCTCTTACCCTTTGCAGATCTC ↑ 13 4 2 Chimp: TCCAATCTGGACTCAGCTGCACA--C-TGGCTcttaccctttgcagatctc Gorilla: TCCAATCTGGACTCAGCTGCACA--C-TGGCTCTTACcctttgcagatctc ↓ 13 4 2 Human: TCCAATCTGGACTCAGCTGCAGCCAGTGGGCTCTTACCCTTTGCAGATCTC Cluster: [ ] Orangutan: TCCAATCTGGACTCAGCTGCACA--C-TGGCTcttaccctttgcagatctc Chimp > Human ------------- chr12:129514483-129514489 Template switch process: F1: L GAGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA 1 F3: 4 GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA R RF: GAGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCACACTGGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA RR: CTCCAGACCCGACCTTCGAAAGGTTAGACCTGAGTCGACGTGTGACCGAGAATGGGAAACGTCTAGAGTCAAGGGAATCGACTTT F2: 3 GTGACCG 2 Unidirectional alignment (log-probability: -31.4) AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCAgccagtg----GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA-------CACTGGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA Template switch alignment (log-probability: -16.2) AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA|GCCAGTG|GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA|GCCAGTG|GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA Gorilla > Human --------------- chr12:129514483-129514489 Template switch process: F1: L GAGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA 1 F3: 4 GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA R RF: GAGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCACACTGGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA RR: CTCCAGACCCGACCTTCGAAAGGTTAGACCTGAGTCGACGTGTGACCGAGAATGGGAAACGTCTAGAGTCAAGGGAATCGACTTT F2: 3 GTGACCG 2 Unidirectional alignment (log-probability: -30.5) AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCAgcCAgTgGGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA--CACT-GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA Template switch alignment (log-probability: -16.6) AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA|GCCAGTG|GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA AGGTCTGGGCTGGAAGCTTTCCAATCTGGACTCAGCTGCA|GCCAGTG|GGCTCTTACCCTTTGCAGATCTCAGTTCCCTTAGCTGAAA ========= Event 681 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGACGCGGGATGGGCTTCGTAGGCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGG-------------AGAAACCCAATTCTTGCCAGCACGT Chimp: TGACGCGGGATGGGCTTCGTAGGCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGG-------------AGAAGCCCAATTCTTGCCAGCACGT Gorilla: TGACGCGGGATGGGCTTCGTAGGCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGGAGAAGCCTAGGGGAGAAGCCCAATTCTTGCCAGCACGT ↑ 3 2 4 1 Human: TGACGCGGGATGGGCTTCGTAGGCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGG-------------AGAAACCCAATTCTTGCCAGCACGT Cluster: [ ] Orangutan: TGACGCGGGATGGGCTTCGTAGGCTGGTTGGGG-GTATTACAGCTTCCCAGGAAGAGGAGAAGCCTAGGGAAGAAGCCCAATTCTTGCCAGCACGT Human > Gorilla --------------- chr1:7451811-7451815 Template switch process: F1: L CGTAGGCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGGAGAA 1 F3: 4 GGGGAGAAGCCCAATTCTTGCCAGCACGTGGTGGGCGCAGGCGCTCATA R RF: CGTAGGCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGGAGAAACCCAATTCTTGCCAGCACGTGGTGGGCGCAGGCGCTCATA RR: GCATCCGACCAACACCCAATAATGTCGAAGGGTCCTTCCCCTCTTTGGGTTAAGAACGGTCGTGCACCACCCGCGTCCGCGAGTAT F2: 3 ATCCG 2 Unidirectional alignment (log-probability: -35.2) GCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGggagaagcctaggGGAGAAgCCCAATTCTTGCCAGCACGTGGTGGGCGCAG GCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGG-------------GGAGAAACCCAATTCTTGCCAGCACGTGGTGGGCGCAG Template switch alignment (log-probability: -22.2) GCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGGAGAA|GCCTA|GGGGAGAAgCCCAATTCTTGCCAGCACGTGGTGGGCGCAG GCTGGTTGTGGGTTATTACAGCTTCCCAGGAAGGGGAGAA|GCCTA|GGGGAGAAACCCAATTCTTGCCAGCACGTGGTGGGCGCAG ========= Event 682 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGAAAATTATGTGGACATTAACATTTTATGAATATTTACTTGAAAAAAACATTGGGTTGTAATAGCTCtaaatttatttttaataatatataaCTGTGAATATCCGTCAGAGCATATGACTTACCAGAG ↓ 1 4 3 2 Chimp: GGAAAATTATGTGGACATTAAAATTTTATG-TGACTTACTTGaaaaaaaCATTGGGTTGTAATAGCTCTAAATTTATTTTTAATAATATATAACTGTGAATATCCATCAAAGCATATGACTTACCAGAG Gorilla: GGAAAATTATGTGGACATTAAAATTTTATG-TGACTTACTTGaaaaaaaCATTGGGTTGTAATAGCTCTAAATTTATTTTTAATAATATATAACTGTGAATATCCATCAGAGCATATGACTTACCAGAG ↑ 1 4 3 2 Human: GGAAAATTATGTGGACATTAACATTTTATGAATATTTACTTGAAAAAAACATTGGGTTGTAATAGCTCtaaatttatttttaataatatataaCTGTGAATATCCGTCAGAGCATATGACTTACCAGAG Cluster: [ ] Orangutan: GGAAAATTATGTGGACATTAAAATTTTATG-TGACTTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTTCT-TTTAATAATATATAACTGTGAATATCCATCAAAGCATATGACTTACCAGAG Human > Chimp ------------- chr12:48982555-48982558 Template switch process: F1: L GGAGAAATTAGTTTCCTTTGGGAAAATTATGTGGACATTAAAATTTTATG 1 F3: 4 TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT R RF: AGAGAAATTAGTTTCCTTTGGGAAAATTATGTGGACATTAACATTTTATGAATATTTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTTATTTTTAATAATATATAACTGTGAATATCCGTCA RR: TCTCTTTAATCAAAGGAAACCCTTTTAATACACCTGTAATTGTAAAATACTTATAAATGAACTTTTTTTGTAACCCAACATTATCGAGATTTAAATAAAAATTATTATATATTGACACTTATAGGCAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -37.7) GTTTCCTTTGGGAAAATTATGTGGACATTAAaATTTTATG----TgacTTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT GTTTCCTTTGGGAAAATTATGTGGACATTAACATTTTATGAATAT---TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT Template switch alignment (log-probability: -27.9) GTTTCCTTTGGGAAAATTATGTGGACATTAAaATTTTATG|TGAC|TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT GTTTCCTTTGGGAAAATTATGTGGACATTAACATTTTATG|TGAC|TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT Human > Gorilla --------------- chr12:45263235-45263238 Template switch process: F1: L AGAGAAATTAGTTTCCTTTGGGAAAATTATGTGGACATTAAAATTTTATG 1 F3: 4 TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT R RF: AGAGAAATTAGTTTCCTTTGGGAAAATTATGTGGACATTAACATTTTATGAATATTTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTTATTTTTAATAATATATAACTGTGAATATCCGTCA RR: TCTCTTTAATCAAAGGAAACCCTTTTAATACACCTGTAATTGTAAAATACTTATAAATGAACTTTTTTTGTAACCCAACATTATCGAGATTTAAATAAAAATTATTATATATTGACACTTATAGGCAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -30.8) GTTTCCTTTGGGAAAATTATGTGGACATTAAaATTTTATG----TgacTTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT GTTTCCTTTGGGAAAATTATGTGGACATTAACATTTTATGAATAT---TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT Template switch alignment (log-probability: -22) GTTTCCTTTGGGAAAATTATGTGGACATTAAaATTTTATG|TGAC|TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT GTTTCCTTTGGGAAAATTATGTGGACATTAACATTTTATG|TGAC|TTACTTGAAAAAAACATTGGGTTGTAATAGCTCTAAATTT ========= Event 683 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT-------C---TCATGATTGTTCTAATTGAAATGTAA ↓ 3 2 1 4 Chimp: GTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAATTGTTTTTCTGACAATAATTGTTCTAATTGAAATGTAA ↑ 3 2 1 4 Gorilla: GTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT-------C---TCATGATTGTTCTAATTGAAATGTAA Human: GTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT-------C---TCATGATTGTTCTAATTGAAATGTAA Cluster: [ ] Orangutan: GTAAAGATT----CTCACTTATTATCAGAAAAACAAT-------C---TCATGATTGTTCTAATTGAAATGTAA Human > Chimp ------------- chr12:48703677-48703692 Template switch process: F1: L TCTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT 1 F3: 4 ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG R RF: TCTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAATCTCATGATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG RR: AGATCATTTCTAAGAGAGAGTGAATAACAGTCTTTTTGTTAGAGTACTAACAAGATTAACTTTACATTTCGGTTTGAAAAGTCACTC F2: 3 ATAACAGTCTTTTTGT 2 Unidirectional alignment (log-probability: -41.5) CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT----TGtttttctgacaataATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAATCTCATG--------------ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG Template switch alignment (log-probability: -17.3) CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT|TGTTTTTCTGACAATA|ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT|TGTTTTTCTGACAATA|ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG Gorilla > Chimp --------------- chr12:48703677-48703692 Template switch process: F1: L TCTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT 1 F3: 4 ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG R RF: TCTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAATCTCATGATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG RR: AGATCATTTCTAAGAGAGAGTGAATAACAGTCTTTTTGTTAGAGTACTAACAAGATTAACTTTACATTTCGGTTTGAAAAGTCACTC F2: 3 ATAACAGTCTTTTTGT 2 Unidirectional alignment (log-probability: -41) CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT----TGtttttctgacaataATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAATCTCATG--------------ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG Template switch alignment (log-probability: -17.8) CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT|TGTTTTTCTGACAATA|ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG CTAGTAAAGATTCTCTCTCACTTATTGTCAGAAAAACAAT|TGTTTTTCTGACAATA|ATTGTTCTAATTGAAATGTAAAGCCAAACTTTTCAGTGAG ========= Event 684 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAGAGTGATATGTTTTCTTTTCTTTATGAAGTGAGAGAGAAGTAGACAAGCCAGAGAAGTAAACAAAGGCCATCTAAGCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT Chimp: TTAGAGTGATATGTTTTCTTTCCT-----------------------------------------TAAGGACACTTAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT ↑ 1 4 3 2 Gorilla: TTAGAGTGGTATGTTTTCTTTTCTTTATGAAGTGAGAGAGAAGTAGACAAGCCAGAGAAGTAAACAAAGGCCATCTAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT Human: TTAGAGTGATATGTTTTCTTTTCTTTATGAAGTGAGAGAGAAGTAGACAAGCCAGAGAAGTAAACAAAGGCCATCTAAGCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT Cluster: [ ] Orangutan: TTAGAGTGATATGTTTTCTTTTCTTTATGAAGGGAGAGAGAAGTAGACAAGCCAGAGAAGTAAACAAAGGCCATTTAACCTAAACAGACGTCCTTAATCCACGTCTGAATTCAGT Gorilla > Chimp --------------- chr1:220739962-220739970 Template switch process: F1: L ACAAACTGCCTTACTTCATGTTAGAGTGATATGTTTTCTTTCCTT 1 F3: 4 TAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT R RF: ACAAACTGCCTTACTTCATGTTAGAGTGGTATGTTTTCTTTTCTTTATGAAGTGAGAGAGAAGTAGACAAGCCAGAGAAGTAAACAAAGGCCATCTAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT RR: TGTTTGACGGAATGAAGTACAATCTCACCATACAAAAGAAAAGAAATACTTCACTCTCTCTTCATCTGTTCGGTCTCTTCATTTGTTTCCGGTAGATTGGATTTGTTCACAGGAATTAGGTGTAGACTTAAGTCA F2: 3 TCACAGGAA 2 Unidirectional alignment (log-probability: -40.8) CTGCCTTACTTCATGTTAGAGTGaTATGTTTTCTTTcCTT-----------------------------------------AAGGaCActTAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT CTGCCTTACTTCATGTTAGAGTGGTATGTTTTCTTTTCTTTATGAAGTGAGAGAGAAGTAGACAAGCCAGAGAAGTAAACAAAGGCCATCTAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT Template switch alignment (log-probability: -28) CTGCCTTACTTCATGTTAGAGTGaTATGTTTTCTTTcCTT|AAGGACACT|TAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT CTGCCTTACTTCATGTTAGAGTGGTATGTTTTCTTTTCTT|AAGGACACT|TAACCTAAACAAGTGTCCTTAATCCACATCTGAATTCAGT ========= Event 685 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGCAAACAGAAAGAGGAGTGCATATTTCAACACTGCAGAGTAGGAAACAAACACCAACAAGAGAGTCACCCTTGATGTGAAATGTTATGCAAAGTTCAAAGAGGCTGCACAC ↑ 3 2 1 4 Chimp: CAGCAAACAGAAAGAGGAGTGCATATTTCAACACTGCAGAGTAGGAAACAAACACCAACAAGAGAGTCACCCTCGATGTGAAAT---GTGTGAAGTTCAAAGAGGCTGCACAC Gorilla: CAGCAAACAGAAAGAGGAGTGCATATTTCAACACTGCAGAGTAGGAAACAAACACCAACAAGAGAGTCACCCTCGATGTGAAATGTTGTGCAAAGTTCAAAGAGGCTGCACAC Human: CAGCAAACAGAAAGAGGAGTGCATATTTCAACACTGCAGAGTAGGAAACAAACACCAACAAGAGAGTCACCCTTGATGTGAAATGTTATGCAAAGTTCAAAGAGGCTGCACAC Cluster: [ ] Orangutan: CAGCAAACAGAAAGAGGAGTGCATATTTCAACACTGCAGAGTAGGAACCAAACACCAACAAGAGAGTCACCCTCGATGTGAAATGTTGTGCCAAGTTCAAAGAGGCTGCACAC Chimp > Human ------------- chr1:241296375-241296380 Template switch process: F1: L GGAAACAAACACCAACAAGAGAGTCACCCTTGATGTGAAATGT 1 F3: 4 AAGTTCAAAGAGGCTGCACACTGACAAGTCGCTACTGGAA R RF: TGCATATTTCAACACTGCAGAGTAGGAAACAAACACCAACAAGAGAGTCACCCTCGATGTGAAATGTGTGAAGTTCAAAGAGGCTGCACACTGACAAGTCGCTACTGGAA RR: ACGTATAAAGTTGTGACGTCTCATCCTTTGTTTGTGGTTGTTCTCTCAGTGGGAGCTACACTTTACACACTTCAAGTTTCTCCGACGTGTGACTGTTCAGCGATGACCTT F2: 3 ACGTAT 2 Unidirectional alignment (log-probability: -33.3) AACAAACACCAACAAGAGAGTCACCCTtGATGTGAAATGttaTGcaAAGTTCAAAGAGGCTGCACACTGACAAGTCGCTACTGGAA AACAAACACCAACAAGAGAGTCACCCTCGATGTGAAATG---TGTGAAGTTCAAAGAGGCTGCACACTGACAAGTCGCTACTGGAA Template switch alignment (log-probability: -22.1) AACAAACACCAACAAGAGAGTCACCCTtGATGTGAAATGT|TATGCA|AAGTTCAAAGAGGCTGCACACTGACAAGTCGCTACTGGAA AACAAACACCAACAAGAGAGTCACCCTCGATGTGAAATGT|TATGCA|AAGTTCAAAGAGGCTGCACACTGACAAGTCGCTACTGGAA ========= Event 686 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GTATCCAGAATTTGTGTATTGCTTGCTACCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCTC ↑ 1 4 3 2 Chimp: GTATCCAGAATTTGTGTATTG----CCCCCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCTC Gorilla: Human: GTATCCAGAATTTGTGTATTGCTTGCTACCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCTC Cluster: [ ] Orangutan: Chimp > Human ------------- chr1:4101264-4101269 Template switch process: F1: L CA-TAAGAAACCAGCAGAGGGTATCCAGAATTTGTGTATTGC 1 F3: 4 CCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCT R RF: CATTAAGAAACCAGCAGAGGGTATCCAGAATTTGTGTATTGCCCCCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCT RR: GTAATTCTTTGGTCGTCTCCCATAGGTCTTAAACACATAACGGGGGATTCTAATCCCCGATCGTTGGACAGGTAAAGACGAGGA F2: 3 ATCGTT 2 Unidirectional alignment (log-probability: -38.9) A-TAAGAAACCAGCAGAGGGTATCCAGAATTTGTGTAttgcTTGCtaCCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCT ATTAAGAAACCAGCAGAGGGTATCCAGAATTTGTGTA----TTGCCCCCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCT Template switch alignment (log-probability: -26.3) A-TAAGAAACCAGCAGAGGGTATCCAGAATTTGTGTATTGC|TTGCTA|CCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCT ATTAAGAAACCAGCAGAGGGTATCCAGAATTTGTGTATTGC|TTGCTA|CCTAAGATTAGGGGCTAGCAACCTGTCCATTTCTGCTCCT ========= Event 687 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AATTCTCATTGTCTTATTCATCGGGGTG----CCAG-CTTTGAAGCATGCCTCAGGGTG ↓ 3 1 24 Chimp: AATTCTCATTGTCTTATTCATCGGGGTG--CGCTGGCATTTGAAGCATGCCTCAGGGTG Gorilla: AATTCTCATTGTCTTATTCATTGGGGTGCG--CTGGCATTTGAAGCATGCCTCAGGGTG ↑ 3 1 24 Human: AATTCTCATTGTCTTATTCATCGGGGTG----CCAG-CTTTGAAGCATGCCTCAGGGTG Cluster: [ ] Orangutan: Human > Chimp ------------- chr1:221317268-221317274 Template switch process: F1: L CAGAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGC 1 F3: 4 TTTGAAGCATGCCTCAGGGTGCTTTCTGTCAAGCATGGCA R RF: CAGAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGCCAGCTTTGAAGCATGCCTCAGGGTGCTTTCTGCCAAGCATGGCA RR: GTCTTCCAACAAATTAAGAGTAACAGAATAAGTAGCCCCACGGTCGAAACTTCGTACGGAGTCCCACGAAAGACGGTTCGTACCGT F2: 3 ACGGTCG 2 Unidirectional alignment (log-probability: -34.4) GAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGCgctggCA--TTTGAAGCATGCCTCAGGGTGCTTTCTGtCAAGCATGGCA GAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGC-----CAGCTTTGAAGCATGCCTCAGGGTGCTTTCTGCCAAGCATGGCA Template switch alignment (log-probability: -22.2) GAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGC|GCTGGCA|TTTGAAGCATGCCTCAGGGTGCTTTCTGtCAAGCATGGCA GAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGC|GCTGGCA|TTTGAAGCATGCCTCAGGGTGCTTTCTGCCAAGCATGGCA Human > Gorilla --------------- chr1:221972928-221972934 Template switch process: F1: L TAAGGGCCAGAAGGTTGTTTAATTCTCATTGTCTTATTCATTGGGGTGC 1 F3: 4 TTTGAAGCATGCCTCAGGGTGCTTTCTGTCAAGCATGGCA R RF: TAAGGGCCAGAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGCCAGCTTTGAAGCATGCCTCAGGGTGCTTTCTGCCAAGCATGGCA RR: ATTCCCGGTCTTCCAACAAATTAAGAGTAACAGAATAAGTAGCCCCACGGTCGAAACTTCGTACGGAGTCCCACGAAAGACGGTTCGTACCGT F2: 3 ACGGTCG 2 Unidirectional alignment (log-probability: -39.1) GAAGGTTGTTTAATTCTCATTGTCTTATTCATtGGGGTGC--GCtggcaTTTGAAGCATGCCTCAGGGTGCTTTCTGtCAAGCATGGCA GAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGCCAGC-----TTTGAAGCATGCCTCAGGGTGCTTTCTGCCAAGCATGGCA Template switch alignment (log-probability: -27.9) GAAGGTTGTTTAATTCTCATTGTCTTATTCATtGGGGTGC|GCTGGCA|TTTGAAGCATGCCTCAGGGTGCTTTCTGtCAAGCATGGCA GAAGGTTGTTTAATTCTCATTGTCTTATTCATCGGGGTGC|GCTGGCA|TTTGAAGCATGCCTCAGGGTGCTTTCTGCCAAGCATGGCA ========= Event 688 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGATGCTACTTAATTAAATAT--TTTCATTTTGA--------------------CAAGAAACAGTAATTCTTTTGAAAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC Chimp: AGATGCTACTTAATTAAATAT--TTTCATTTTGA--------------------CAAGAAACAGTAATTCTTTTGAAAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC ↓ 1 4 3 2 Gorilla: AGATGCTACTTAATTAAATAT----TGATGCTGA----------------------------------------AAGAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC ↑ 1 4 3 2 Human: AGATGCTACTTAATTAAATAT--TTTCATTTTGA--------------------CAAGAAACAGTAATTCTTTTGAAAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC Cluster: [ ] Orangutan: AGATGCTACTTAATTAAATATTT--TCATTTTGACAAGAAACAGTAATTCTTTT--------------------GAAAACTATGCTAAATTGGCATCTTAATAATTTCATGTTGAGC Human > Gorilla --------------- chr12:87287755-87287759 Template switch process: F1: L AAGAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT 1 F3: 4 TGAAAGAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC R RF: AAGAAGGGAATTAATAACACAGATGCTACTTAATTAAATATTTTCATTTTGACAAGAAACAGTAATTCTTTTGAAAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC RR: TTCTTCCCTTAATTATTGTGTCTACGATGAATTAATTTATAAAAGTAAAACTGTTCTTTGTCATTAAGAAAACTTTTGATACGATTTAACCGTAGAATTATTAGAGTACAACTCG F2: 3 CGTAG 2 Unidirectional alignment (log-probability: -38.1) GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT---------------------------------gatgctgaaagAACTATGCTAAATTGGCATCTTAATAATCTCATG GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATTTTCATTTTGACAAGAAACAGTAATTCTTTTGAA-----------AACTATGCTAAATTGGCATCTTAATAATCTCATG Template switch alignment (log-probability: -29.1) GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT|GATGC|TGAAagAACTATGCTAAATTGGCATCTTAATAATCTCATG GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT|GATGC|TGAA--AACTATGCTAAATTGGCATCTTAATAATCTCATG Chimp > Gorilla --------------- chr12:87287755-87287759 Template switch process: F1: L AAGAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT 1 F3: 4 TGAAAGAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC R RF: AAGAAGGGAATTAATAACACAGATGCTACTTAATTAAATATTTTCATTTTGACAAGAAACAGTAATTCTTTTGAAAACTATGCTAAATTGGCATCTTAATAATCTCATGTTGAGC RR: TTCTTCCCTTAATTATTGTGTCTACGATGAATTAATTTATAAAAGTAAAACTGTTCTTTGTCATTAAGAAAACTTTTGATACGATTTAACCGTAGAATTATTAGAGTACAACTCG F2: 3 CGTAG 2 Unidirectional alignment (log-probability: -38.1) GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT---------------------------------gatgctgaaagAACTATGCTAAATTGGCATCTTAATAATCTCATG GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATTTTCATTTTGACAAGAAACAGTAATTCTTTTGAA-----------AACTATGCTAAATTGGCATCTTAATAATCTCATG Template switch alignment (log-probability: -29.1) GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT|GATGC|TGAAagAACTATGCTAAATTGGCATCTTAATAATCTCATG GAAGGGAATTAATAACACAGATGCTACTTAATTAAATATT|GATGC|TGAA--AACTATGCTAAATTGGCATCTTAATAATCTCATG ========= Event 689 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGATGGTGTTTTGGATATGA---------ACCATTAACAGGCTTTGaaaaaataaaaaaaaGGTCAAA Chimp: AAGATGGTGTTTTGGATATGA---------ACCATTAACAGGCTTTGaaaaaataaaaaaaaGGTCAAA ↓ 41 3 2 Gorilla: AAGATGGTGTTTTGGATATGAACATTCAAAGCCATTAACAGGCTTTGaaaaaataaaaaaaaGGTCAAA Human: AAGATGGTGTTTTGGATATGA---------ACCATTAACAGGCTTTGaaaaaataaaaaaaaGGTCAAA Cluster: [ ] Orangutan: AAGATGGTGTTTTGGATATGA---------ACCATTAACAGGCTTTGaaaaaata-aaaaaaGGTCAAA Chimp > Gorilla --------------- chr12:87848943-87848949 Template switch process: F1: L AGAAGTTGATAATGCTGAATAAGATGGTGTTTTGGATATGAACA 1 F3: 4 CCATTAACAGGCTTTGAAAAAATAAAAAAAAGGTCAAACC R RF: AGAAGTTGATAATGCTGAATAAGATGGTGTTTTGGATATGAACCATTAACAGGCTTTGAAAAAATAAAAAAAAGGTCAAACC RR: TCTTCAACTATTACGACTTATTCTACCACAAAACCTATACTTGGTAATTGTCCGAAACTTTTTTATTTTTTTTCCAGTTTGG F2: 3 GAAACTT 2 Unidirectional alignment (log-probability: -32) GTTGATAATGCTGAATAAGATGGTGTTTTGGATATGAAcattcaaagCCATTAACAGGCTTTGAAAAAATAAAAAAAAGGTCAAACc GTTGATAATGCTGAATAAGATGGTGTTTTGGATATGAA---------CCATTAACAGGCTTTGAAAAAATAAAAAAAAGGTCAAAC- Template switch alignment (log-probability: -22.2) GTTGATAATGCTGAATAAGATGGTGTTTTGGATATGAACa|TTCAAAG|CCATTAACAGGCTTTGAAAAAATAAAAAAAAGGTCAAACC GTTGATAATGCTGAATAAGATGGTGTTTTGGATATGAACC|TTCAAAG|CCATTAACAGGCTTTGAAAAAATAAAAAAAAGGTCAAACC ========= Event 690 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCTGATGGGTTATTTGGATTTGATTCAGGCTCTGAATCAAGCTGATTCAAGGTGTGAGTAACA ↑ 3 24 1 Chimp: TCTGATGGGTTATTTGGATTTGATTCAG------------GCTGATTCAAGGTGTGAGTAACA ↓ 3 24 1 Gorilla: TCTGATGGGTTATTTGGATTTGATTCAGGCTCTGAATCAAGCTGATTCAAGGTGTGAGTAACA Human: TCTGATGGGTTATTTGGATTTGATTCAGGCTCTGAATCAAGCTGATTCAAGGTGTGAGTAACA Cluster: [ ] Orangutan: TCTGATGGGTTATTTGAATTTGATTCAGGCTCTGAATCAAGCTGATTCAAGGTGTGAGTGACA Chimp > Human ------------- chr1:242755658-242755666 Template switch process: F1: L TGCATCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT 1 F3: 4 GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT R RF: CACATCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT RR: GTGTAGAGTCGGAAGACTACCCAATAAACCTAAACTAAGTCCGACTAAGTTCCACACTCATTGTACTGAAACGTAAAACGA F2: 3 AACTAAGTC 2 Unidirectional alignment (log-probability: -40.2) TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCTctgaatcaagctGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT------------GATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT Template switch alignment (log-probability: -28.4) TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT|CTGAATCAA|GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT|CTGAATCAA|GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT Chimp > Gorilla --------------- chr1:222661475-222661483 Template switch process: F1: L TGCATCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT 1 F3: 4 GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT R RF: CACATCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT RR: GTGTAGAGTCGGAAGACTACCCAATAAACCTAAACTAAGTCCGACTAAGTTCCACACTCATTGTACTGAAACGTAAAACGA F2: 3 AACTAAGTC 2 Unidirectional alignment (log-probability: -39.2) TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGgctctgaatcaaGCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAG------------GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT Template switch alignment (log-probability: -28) TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT|CTGAATCAA|GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT TCTCAGCCTTCTGATGGGTTATTTGGATTTGATTCAGGCT|CTGAATCAA|GCTGATTCAAGGTGTGAGTAACATGACTTTGCATTTTGCT ========= Event 691 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCAGTCCCTTGGCCAAACACTCAGCAATGTTACCATTGCTGACATTCTCAGGATGGAGGAGG ↑ 1 4 3 2 Chimp: GCCAGTCCCTTGGCCAAACACCCAG--TTGTTACCATTGCTGACATTCTCAGGATGGAGGAGG Gorilla: GCCAGTCCCTTGGCCAAACACCCAG--TTGTTACCATTGCTGACATTCTCAGGATGGAGGAGG Human: GCCAGTCCCTTGGCCAAACACTCAGCAATGTTACCATTGCTGACATTCTCAGGATGGAGGAGG Cluster: [ ] Orangutan: GCCAGTCCCTTGGCCAAACACCCAG--TTGTTACCATTGCTGACATTCTCAGGATGGAGGAGG Chimp > Human ------------- chr12:90353131-90353138 Template switch process: F1: L CAAGATTCAAGTAAAGATAGGCCAGTCCCTTGGCCAAACAC 1 F3: 4 GTTACCATTGCTGACATTCTCAGGATGGAGGAGGTAGGC R RF: CAAGATTCAAGTAAAGATAGGCCAGTCCCTTGGCCAAACACCCAGTTGTTACCATTGCTGACATTCTCAGGATGGAGGAGGTAGGC RR: GTTCTAAGTTCATTTCTATCCGGTCAGGGAACCGGTTTGTGGGTCAACAATGGTAACGACTGTAAGAGTCCTACCTCCTCCATCCG F2: 3 TAACGACT 2 Unidirectional alignment (log-probability: -25.8) AAGATTCAAGTAAAGATAGGCCAGTCCCTTGGCCAAACACtCAGcaaTGTTACCATTGCTGACATTCTCAGGATGGAGGAGGTAGGC AAGATTCAAGTAAAGATAGGCCAGTCCCTTGGCCAAACACCCAG--TTGTTACCATTGCTGACATTCTCAGGATGGAGGAGGTAGGC Template switch alignment (log-probability: -16.3) AAGATTCAAGTAAAGATAGGCCAGTCCCTTGGCCAAACAC|TCAGCAAT|GTTACCATTGCTGACATTCTCAGGATGGAGGAGGTAGGC AAGATTCAAGTAAAGATAGGCCAGTCCCTTGGCCAAACAC|TCAGCAAT|GTTACCATTGCTGACATTCTCAGGATGGAGGAGGTAGGC ========= Event 692 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGACAACATAAATATATTCA----------TGTTTTACAGTTCTTTCAACAAATAGCATCA Chimp: TAGACAACATAAATATATGCAACTGTAAAACAGTTTTACAGTTCTTTCAAAAAATAGCATCA ↑ 134 2 Gorilla: TAGACAACATAAATATATGCA----------TGTTTTACAGTTCTTTCAACAAATAGCATCA Human: TAGACAACATAAATATATTCA----------TGTTTTACAGTTCTTTCAACAAATAGCATCA Cluster: [ ] Orangutan: TAGGCAACATAAATATATGAA----------TGTTTTACAGTTCTTTCAACAAATAGCATCA Gorilla > Chimp --------------- chr12:47122342-47122352 Template switch process: F1: L ATCTCACTTCAGGCCACTTTTAGACAACATAAATATATGCA 1 F3: 4 GTTTTACAGTTCTTTCAAAAAATAGCATCAAATTCCTTTA R RF: ATCTCACTTCAGGCCACCTTTAGACAACATAAATATATGCATGTTTTACAGTTCTTTCAACAAATAGCATCAAATTCCTTTA RR: TAGAGTGAAGTCCGGTGGAAATCTGTTGTATTTATATACGTACAAAATGTCAAGAAAGTTGTTTATCGTAGTTTAAGGAAAT F2: 3 ACAAAATGTCA 2 Unidirectional alignment (log-probability: -41.8) TCTCACTTCAGGCCACtTTTAGACAACATAAATATATGCAactgtaaaacaGTTTTACAGTTCTTTCAAaAAATAGCATCAAATTCCTTTA TCTCACTTCAGGCCACCTTTAGACAACATAAATATATGCA----------TGTTTTACAGTTCTTTCAACAAATAGCATCAAATTCCTTTA Template switch alignment (log-probability: -28.2) TCTCACTTCAGGCCACtTTTAGACAACATAAATATATGCA|ACTGTAAAACA|GTTTTACAGTTCTTTCAAaAAATAGCATCAAATTCCTTTA TCTCACTTCAGGCCACCTTTAGACAACATAAATATATGCA|ACTGTAAAACA|GTTTTACAGTTCTTTCAACAAATAGCATCAAATTCCTTTA ========= Event 693 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAG-----AAGTAAATTACTCAGATGTACACAGGATATTTAACCATTCATTACAT------------------------------AACATGGTAAAATCTGAAAAATAATTATG ↓ 3 2 4 1 Chimp: CAG-----AAGTAAATTACTCAGATGTACACAGGATATCTAACCATTCATTACAT---------------AACATGCTACTGAATAACATGGTAAAATCTGAAAAATAATTATG Gorilla: CAG----------AATTACTCAGATGTACACAGGATATCTAACCATTCATTACATAACATGCTACTGAAT---------------AACATGGTAAAATCTGAAAAATAATTCTG Human: CAG-----AAGTAAATTACTCAGATGTACACAGGATATTTAACCATTCATTACAT------------------------------AACATGGTAAAATCTGAAAAATAATTATG Cluster: [ ] Orangutan: CAGAAGTA-----AATTACTCAGATGTACACAGGATATTTAACCATTCATTACATAACATGCTACTGAAT---------------AACATGGTAAAATCTGAAAAATAATTAT- Human > Chimp ------------- chr1:222936488-222936491 Template switch process: F1: L ATTACTCAGATGTACACAGGATATCTAACCATTCATTACATAACATGCTA 1 F3: 4 ATAACATGGTAAAATCTGAAAAATAATTATGAGATTTTTTTT R RF: ATTACTCAGATGTACACAGGATATTTAACCATTCATTACATAACATGGTAAAATCTGAAAAATAATTATGAGATTTTTTTT RR: TAATGAGTCTACATGTGTCCTATAAATTGGTAAGTAATGTATTGTACCATTTTAGACTTTTTATTAATACTCTAAAAAAAA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -51.4) TGTACACAGGATATcTAACCATTCATTACATAACatgctactgaataacATGGTAAAATCTGAAAAATAATTATGAGATTTTtt TGTACACAGGATATTTAACCATTCATTACATAAC---------------ATGGTAAAATCTGAAAAATAATTATGAGATTTT-- Template switch alignment (log-probability: -28) TGTACACAGGATATcTAACCATTCATTACATAACATGcTA|CTGA|ATAACATGGTAAAATCTGAAAAATAATTATGAGATTTTTT TGTACACAGGATATTTAACCATTCATTACATAACATGGTA|CTGA|ATAACATGGTAAAATCTGAAAAATAATTATGAGATTTTTT ========= Event 694 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTACTATGCAGCAAGCTAGT------ATGATTTAAGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCTTGCCTTCAAACTCTGCTTAGTGGGAGCGGGAATCATATATGCCATTCTGCACAGCACAAAGCATAGCACATTATCTGGTACATGG Chimp: CCTACTATGCGGCAAGCTAGT---ATTATGCTTTAAGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCTTGCCTTCAAACTCTGCTTAGTGGGAGCAGGAATCATATATGCCATTCTGCACAGCACAAAGCATAGCACATTATCTGGTACATGG Gorilla: CCTACTATGCGGCAAGCTAGTATT---ATGCTTTGAGGATATCACAAGCCTCAAAAAGTTTGATCCCTTCTTGCCTTCAAACTCTGCTTAGTGGGAGCAGGAATCATATATGCCATTCTGCACAGCACAAAGCATAGCACGTTATCTGGTACATGG ↑ 1 4 3 2 Human: CCTACTATGCAGCAAGCTAGT------ATGATTTAAGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCTTGCCTTCAAACTCTGCTTAGTGGGAGCGGGAATCATATATGCCATTCTGCACAGCACAAAGCATAGCACATTATCTGGTACATGG Cluster: [ ] Orangutan: CCTACTATGCGGCAAGCTAGTATT---ATGCTTTGAGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCGTGCCTGCAAACTCTgcttagtgggagcaggaatcgtatatgccattctgcacagcacaaagcatagcacattgtctggtacatgg Human > Gorilla --------------- chr1:223967856-223967864 Template switch process: F1: L TTTGACAACATTTTAAAGCACCTACTATGCGGCAAGCTAGTAT 1 F3: 4 AGGATATCACAAGCCTCAAAAAGTTTGATCCCTTCTTGCC R RF: TTTGACAACATTTTAAAGCACCTACTATGCAGCAAGCTAGTATGATTTAAGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCTTGCCTTCAAACTCTGCTTAGTGGGAGCGGGAATCATATATGCCATTCTGCACAGCACAAAGCATA RR: AAACTGTTGTAAAATTTCGTGGATGATACGTCGTTCGATCATACTAAATTCCTATAGTGTTCCGAGTTTTTCAAACTAGGGAAGAACGGAAGTTTGAGACGAATCACCCTCGCCCTTAGTATATACGGTAAGACGTGTCGTGTTTCGTAT F2: 3 GTTTCGTAT 2 Unidirectional alignment (log-probability: -37.4) GACAACATTTTAAAGCACCTACTATGCgGCAAGCTAGtatTATGcTTTgAGGATATCACAAGcCTCAAAAAGTTTGATCCCTTCTTGCC GACAACATTTTAAAGCACCTACTATGCAGCAAGCTAG---TATGATTTAAGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCTTGCC Template switch alignment (log-probability: -28) GACAACATTTTAAAGCACCTACTATGCgGCAAGCTAGTAT|TATGCTTTG|AGGATATCACAAGcCTCAAAAAGTTTGATCCCTTCTTGCC GACAACATTTTAAAGCACCTACTATGCAGCAAGCTAGTAT|TATGCTTTG|AGGATATCACAAGGCTCAAAAAGTTTGATCCCTTCTTGCC ========= Event 695 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCA-GTGCACAGCACAGGAATCCTTTATTTAA Chimp: TCCAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCA-GGGCACAGCACAGGAATCCTTTATTGAA ↓ 3 2 1 4 Gorilla: TCCAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAGCTGCA-CGCACAGGAATCCTTTATTTAA Human: TCCAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCA-GTGCACAGCACAGGAATCCTTTATTTAA Cluster: [ ] Orangutan: TCCAAGAGTTTTACACAGTGTGCAGATTTAGTTACACATCAGCTGCACAGCACAGGAATCCTTTATTTAA Chimp > Gorilla --------------- chr1:224192831-224192836 Template switch process: F1: L TCCAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAG 1 F3: 4 GCACAGGAATCCTTTATTTAAGAAATATCAGGAACTAATT R RF: TCCAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAGGGCACAGCACAGGAATCCTTTATTGAAGAAATATCAGGAACTAATT RR: AGGTTCTCAAAATGTGCCACACGTCTAACTCAATGTGTAGTCCCGTGTCGTGTCCTTAGGAAATAACTTCTTTATAGTCCTTGATTAA F2: 3 CACGTC 2 Unidirectional alignment (log-probability: -33.2) CAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAGctGCAC-GCACAGGAATCCTTTATTtAAGAAATATCAGGAACTAATT CAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAGG-GCACAGCACAGGAATCCTTTATTGAAGAAATATCAGGAACTAATT Template switch alignment (log-probability: -22) CAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAG|CTGCAC|GCACAGGAATCCTTTATTtAAGAAATATCAGGAACTAATT CAAGAGTTTTACACGGTGTGCAGATTGAGTTACACATCAG|CTGCAC|GCACAGGAATCCTTTATTGAAGAAATATCAGGAACTAATT ========= Event 696 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCAACAAGTATTAGATTTAGCCCAAGTCTTGGAAAGTCTTCCAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCCTGCCCTTCCCCATCTCCTATTCCCTGATCCCTCCACTGCTTTGTGACCCAAGCATGCAGGCCTTGTGTGGCTGTCAGCGCCCAGGTCCTCCTATTCA Chimp: TCCAACAAGTATTAGATTTAGCTG------------------AAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCCTGCCCTTCCCCATCTCCTATTCCCTGATCCCTCCACTGCTTTGTGACCCAAGCATGCAGGCCTTGTGTTGCTGTCAGCGCCCAGGTCCTCCTATTCA ↑ 1 4 3 2 Gorilla: TCCAACAAGTATTAGATTTAGTCCAAGTCTTGGAAAATCTTCCAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCCTGCCCTTCCCCATCTCCTATTCCCTGATCCCTCCACTGCTTTGTGACCCAAGCATGCAGGCCTTGTGTTGCTGTCAGCGCCCAGGTCCTCCTGTTCA Human: TCCAACAAGTATTAGATTTAGCCCAAGTCTTGGAAAGTCTTCCAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCCTGCCCTTCCCCATCTCCTATTCCCTGATCCCTCCACTGCTTTGTGACCCAAGCATGCAGGCCTTGTGTGGCTGTCAGCGCCCAGGTCCTCCTATTCA Cluster: [ ] Orangutan: TCCAACAAGTGTTAGATTTAGCCCAAGTCTTGGAAAATCTTCCAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCCTGCCCTTC-GCGTCCCCTATTCCCTGATCCCTCCACTGCTTTGTGAACCAAGCATGCAGGCCTTGTGTTGCTGTCAGCGCCCAGGTCCTCCTACTCA Gorilla > Chimp --------------- chr1:224668142-224668145 Template switch process: F1: L AAGCACTTGACTACTTTGAGTCCAACAAGTATTAGATTTAG 1 F3: 4 AAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCC R RF: AAGCACTTGACTACTTTGAGTCCAACAAGTATTAGATTTAGTCCAAGTCTTGGAAAATCTTCCAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCCTGCCCTTCCCCATCTCCTATTCCCTGATCCCTCCACTGCTTTGTGACCCAAGCATGCAGGCCTTGTGTTGCTGTCAG RR: TTCGTGAACTGATGAAACTCAGGTTGTTCATAATCTAAATCAGGTTCAGAACCTTTTAGAAGGTTTCTTCTATTTTAAAGAGAAACCAACGTAAGACTTAGGGACGGGAAGGGGTAGAGGATAAGGGACTAGGGAGGTGACGAAACACTGGGTTCGTACGTCCGGAACACAACGACAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -26) AGCACTTGACTACTTTGAGTCCAACAAGTATTAGATTTAG---------------------CtgaAAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCC AGCACTTGACTACTTTGAGTCCAACAAGTATTAGATTTAGTCCAAGTCTTGGAAAATCTTCC---AAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCC Template switch alignment (log-probability: -16.2) AGCACTTGACTACTTTGAGTCCAACAAGTATTAGATTTAG|CTGA|AAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCC AGCACTTGACTACTTTGAGTCCAACAAGTATTAGATTTAG|CTGA|AAAGAAGATAAAATTTCTCTTTGGTTGCATTCTGAATCCC ========= Event 697 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAAGATAACTTAGGACTCCCCCCACCT----------------------------------ACTACTACACACCTGGCAATTTATAAGTATCTGATGAC Chimp: AATAAGATAACTTAGGACTCCCCCCACCT----------------------------------ACCACTACACACCTGGCAATTTATAAGTATCTGATGAC ↓ 4 1 3 2 Gorilla: AATAAGATAACTTAGGACTCCCCCCACCT-----------------ACTGCCACCCCCCATCTACTACTACACACCTGGCAATTTATAAGTATCTGATGAC Human: AATAAGATAACTTAGGACTCCCCCCACCT----------------------------------ACTACTACACACCTGGCAATTTATAAGTATCTGATGAC Cluster: [ ] Orangutan: AATAAGATAACTTATGACTCCCCCCACCTACTGCCACCCCCCACCT-----------------ACTACTACACACCTGGCAATTTCTAAGTATCTGATGAC Chimp > Gorilla --------------- chr12:128894236-128894240 Template switch process: F1: L TCCCCATGTAAAAATAAGATAACTTAGGACTCCCCCCACCTAC 1 F3: 4 CCCCCCATCTACTACTACACACCTGGCAATTTATAAGTATCTGATGACAGACT R RF: TCCCCATGTAAAAATAAGATAACTTAGGACTCCCCCCACCTACCACTACACACCTGGCAATTTATAAGTATCTGATGACAGACT RR: AGGGGTACATTTTTATTCTATTGAATCCTGAGGGGGGTGGATGGTGATGTGTGGACCGTTAAATATTCATAGACTACTGTCTGA F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -40.9) CCATGTAAAAATAAGATAACTTAGGACTCCCCCCACctactgccaccccccatCTACtACTACACACCTGGCAATTTATAAGTAT CCATGTAAAAATAAGATAACTTAGGACTCCCCCCAC-----------------CTACCACTACACACCTGGCAATTTATAAGTAT Template switch alignment (log-probability: -27.8) CCATGTAAAAATAAGATAACTTAGGACTCCCCCCACCTAC|TGCCA|CCCCCCAtCTACtACTACACACCTGGCAATTTATAAGTAT CCATGTAAAAATAAGATAACTTAGGACTCCCCCCACCTAC|TGCCA|CCCCCCACCTACCACTACACACCTGGCAATTTATAAGTAT ========= Event 698 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTCTTCCAGGCAGCCTCCAG---TGCCCCTTCCGGGATCCTGGCTGGATCAGGCTGACTGTC Chimp: GTTCTTCCAGGCAGCCTCCAG---TGCCCCTTCCGGGATCCTGGCTGCATCAGGCTGACTGTC ↓ 1 4 3 2 Gorilla: GTTCTTCCAGGCAGCCTCCAGCAGGATCCCTTCCGGGATCCTGGCTGGATCAGGCTGACTTTC ↑ 1 4 3 2 Human: GTTCTTCCAGGCAGCCTCCAG---TGCCCCTTCCGGGATCCTGGCTGGATCAGGCTGACTGTC Cluster: [ ] Orangutan: GTTCTTCCAGGCAGCCTCCAG---TCCCCCTTCTGGGATCCTGGCTGGATCAGGCTGACATTC Human > Gorilla --------------- chr12:92425596-92425601 Template switch process: F1: L TTAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAG 1 F3: 4 CCCTTCCGGGATCCTGGCTGGATCAGGCTGACTTTCCTTG R RF: TTAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAGTGCCCCTTCCGGGATCCTGGCTGGATCAGGCTGACTGTCCTTG RR: AATTAGGTGGGAACCCCGTTCAAGAAGGTCCGTCGGAGGTCACGGGGAAGGCCCTAGGACCGACCTAGTCCGACTGACAGGAAC F2: 3 TAGGAC 2 Unidirectional alignment (log-probability: -33.5) TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCA--GCaggatCCCTTCCGGGATCCTGGCTGGATCAGGCTGACTtTCCTTG TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAGTGC-----CCCTTCCGGGATCCTGGCTGGATCAGGCTGACTGTCCTTG Template switch alignment (log-probability: -22) TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAG|CAGGAT|CCCTTCCGGGATCCTGGCTGGATCAGGCTGACTtTCCTTG TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAG|CAGGAT|CCCTTCCGGGATCCTGGCTGGATCAGGCTGACTGTCCTTG Chimp > Gorilla --------------- chr12:92425596-92425601 Template switch process: F1: L TTAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAG 1 F3: 4 CCCTTCCGGGATCCTGGCTGGATCAGGCTGACTTTCCTTG R RF: TTAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAGTGCCCCTTCCGGGATCCTGGCTGCATCAGGCTGACTGTCCTTG RR: AATTAGGTGGGAACCCCGTTCAAGAAGGTCCGTCGGAGGTCACGGGGAAGGCCCTAGGACCGACGTAGTCCGACTGACAGGAAC F2: 3 TAGGAC 2 Unidirectional alignment (log-probability: -39) TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCA--GCaggatCCCTTCCGGGATCCTGGCTGgATCAGGCTGACTtTCCTTG TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAGTGC-----CCCTTCCGGGATCCTGGCTGCATCAGGCTGACTGTCCTTG Template switch alignment (log-probability: -27.5) TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAG|CAGGAT|CCCTTCCGGGATCCTGGCTGgATCAGGCTGACTtTCCTTG TAATCCACCCTTGGGGCAAGTTCTTCCAGGCAGCCTCCAG|CAGGAT|CCCTTCCGGGATCCTGGCTGCATCAGGCTGACTGTCCTTG ========= Event 699 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATTATTGGAGGATAAACTT-------TGGCTATATGAGT---CTAGTTTTAAAGGACTAAAA--AAAGGAAAGGGCCTCC Chimp: TGATTATTGGATGATAAACTT-------TCGCTATATGAGT---CTAGTTTTAAAGGACTaaaa--aaaGGAAAGGGCCTCC ↓ 1 4 3 2 Gorilla: TGATTATTGGAGGATAAACTT--------------TTTAGT------CCTTTAAAGGACTaaaa--aaaGGAAAGGGCCTCC ↑ 1 4 3 2 Human: TGATTATTGGAGGATAAACTT-------TGGCTATATGAGT---CTAGTTTTAAAGGACTAAAA--AAAGGAAAGGGCCTCC Cluster: [ ] Orangutan: TGATTATTGGAGGATAAACTTTGGCTAT-------ATGAGTCTA---GTTTTAAATGACTAAAAAAGAAGGAAAGGGCCTCC Human > Gorilla --------------- chr12:93362566-93362572 Template switch process: F1: L CTTCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTT 1 F3: 4 TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA R RF: CTTCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTTGGCTATATGAGTCTAGTTTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA RR: GAAGACGGTCACATTTGTCTACTAATAACCTCCTATTTGAAACCGATATACTCAGATCAAAATTTCCTGATTTTTTTCCTTTCCCGGAGGGATTTGATT F2: 3 CCTGATT 2 Unidirectional alignment (log-probability: -29.7) TCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTTt------------TAGTccTTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA TCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTTGGCTATATGAGTCTAGT--TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA Template switch alignment (log-probability: -16.6) TCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTT|TTAGTCC|TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA TCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTT|TTAGTCC|TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA Chimp > Gorilla --------------- chr12:93362566-93362572 Template switch process: F1: L CTTCTGCCAGTGTAAACAGATGATTATTGGAGGATAAACTTT 1 F3: 4 TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA R RF: CTTCTGCCAGTGTAAACAGATGATTATTGGATGATAAACTTTCGCTATATGAGTCTAGTTTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA RR: GAAGACGGTCACATTTGTCTACTAATAACCTACTATTTGAAAGCGATATACTCAGATCAAAATTTCCTGATTTTTTTCCTTTCCCGGAGGGATTTGATT F2: 3 CCTGATT 2 Unidirectional alignment (log-probability: -35.2) TCTGCCAGTGTAAACAGATGATTATTGGAgGATAAACTT------------TtTAGTccTTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA TCTGCCAGTGTAAACAGATGATTATTGGATGATAAACTTTCGCTATATGAGTCTAGT--TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA Template switch alignment (log-probability: -22.2) TCTGCCAGTGTAAACAGATGATTATTGGAgGATAAACTTT|TTAGTCC|TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA TCTGCCAGTGTAAACAGATGATTATTGGATGATAAACTTT|TTAGTCC|TTTAAAGGACTAAAAAAAGGAAAGGGCCTCCCTAAACTAA ========= Event 700 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA----GTAAATGGGGCAATCGTTAAAGAGT Chimp: CCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA----GTAAATGGGGCAATCGTTAAAGAGC Gorilla: CCTTATAACCATTTCCTCTCTATAGATGGTAGAGTAATCTATAGATGGGGCAATCTTTAAAGAGT ↑ 3 2 1 4 Human: CCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA----GTAAATGGGGCAATCGTTAAAGAGT Cluster: [ ] Orangutan: CCTTATAACCATTTCCTCTCTATAGATGGTAGGGTA----GTAAATGGGGCAATCTTTAAAGAGT Human > Gorilla --------------- chr12:91736683-91736690 Template switch process: F1: L ACAGCCCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA 1 F3: 4 ATGGGGCAATCTTTAAAGAGTTTCAGCTTTTATTCTCCCC R RF: ACAGCCCTTATAACCATTTCCTCTCTATAGATGGTAGAGTAGTAAATGGGGCAATCGTTAAAGAGTTTCAGCTTTTATTCTCCCC RR: TGTCGGGAATATTGGTAAAGGAGAGATATCTACCATCTCATCATTTACCCCGTTAGCAATTTCTCAAAGTCGAAAATAAGAGGGG F2: 3 GATATCTA 2 Unidirectional alignment (log-probability: -33.3) CAGCCCTTATAACCATTTCCTCTCTATAGATGGTAGAGTAatctaTAgATGGGGCAATCtTTAAAGAGTTTCAGCTTTTATTCTCCCC CAGCCCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA----GTAAATGGGGCAATCGTTAAAGAGTTTCAGCTTTTATTCTCCCC Template switch alignment (log-probability: -22.3) CAGCCCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA|ATCTATAG|ATGGGGCAATCtTTAAAGAGTTTCAGCTTTTATTCTCCCC CAGCCCTTATAACCATTTCCTCTCTATAGATGGTAGAGTA|ATCTATAG|ATGGGGCAATCGTTAAAGAGTTTCAGCTTTTATTCTCCCC ========= Event 701 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: tctgtttatgaatATTGGTAAGTATACATA------------CCGAGCTTAA-----GGCAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGG ↑ 1 3 4 2 Chimp: tctgtttatgaatATTGGTAAATATTCATAATTTTTATGAATATGAGCTTAACTTGCCTTAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGG ↓ 1 3 4 2 Gorilla: tctgtttatgaatATTGGTAAGTATACATA------------CTGAGCTTAA-----GGCAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGG Human: tctgtttatgaatATTGGTAAGTATACATA------------CCGAGCTTAA-----GGCAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGG Cluster: [ ] Orangutan: tctgtttatgaatATTGGTAAGTATACATA------------CTGAGCTTAA-----GGCAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTCT Chimp > Human ------------- chr12:86381017-86381038 Template switch process: F1: L GTAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAA 1 F3: 4 AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGT R RF: GTAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAAATATTCATAATTTTTATGAATATGAGCTTAACTTGCCTTAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGT RR: CATTGGGAACTAAAGGAAAAAGACAAATACTTATAACCATTTATAAGTATTAAAAATACTTATACTCGAATTGAACGGAATTCGAGTCATACATATGAAGTACTTCAGTCTTCAACCA F2: 3 CGGAATTCGAGCCATACATATG 2 Unidirectional alignment (log-probability: -60.7) TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAAgTATaCATA------------------------------ccgagcttaaggcAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGT-- TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAAATATTCATAATTTTTATGAATATGAGCTTAACTTGCCTT-------------AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGTAA Template switch alignment (log-probability: -24) TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAA|GTATACATACcGAGCTTAAGGC|AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGT TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAA|GTATACATACTGAGCTTAAGGC|AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGT Chimp > Gorilla --------------- chr12:39318137-39318158 Template switch process: F1: L GTAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAA 1 F3: 4 AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGTGA R RF: GTAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAAATATTCATAATTTTTATGAATATGAGCTTAACTTGCCTTAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGTAA RR: CATTGGGAACTAAAGGAAAAAGACAAATACTTATAACCATTTATAAGTATTAAAAATACTTATACTCGAATTGAACGGAATTCGAGTCATACATATGAAGTACTTCAGTCTTCAACCATT F2: 3 CGGAATTCGAGTCATACATATG 2 Unidirectional alignment (log-probability: -60.6) TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAAgTATaCATA------------cTGAGCTTAAggC-------AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGTga TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAAATATTCATAATTTTTATGAATATGAGCTTAA--CTTGCCTTAAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGT-- Template switch alignment (log-probability: -24.1) TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAA|GTATACATACTGAGCTTAAGGC|AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGTgA TAACCCTTGATTTCCTTTTTCTGTTTATGAATATTGGTAA|GTATACATACTGAGCTTAAGGC|AAGCTCAGTATGTATACTTCATGAAGTCAGAAGTTGGTAA ========= Event 702 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCTAAATACAACTTTCTTAGGATAATCCTTCTGATTATCCTAAGACACAGGCAGCTCTGAC Chimp: CCTAAATACAACTTTCTTAGGATAATCCTTCTGATTATCCTAAGACACAGGCAGCTCTGAA ↑ 3 1 2 4 Gorilla: CCTAAATACAACTTTCTTAGGATAATCAGAAGGATTATCGTAAGACACAGGCAGCTCTGAC ↓ 3 1 2 4 Human: CCTAAATACAACTTTCTTAGGATAATCCTTCTGATTATCCTAAGACACAGGCAGCTCTGAC Cluster: [ ] Orangutan: CCTAAATACAACTTTCTTAGGATAATCCTTCTGATTATCTTAAGACATAGGCAGCTCTGAC Gorilla > Human --------------- chr12:86310511-86310523 Template switch process: F1: L CTGAGGAATCCTGCCCTAAATACAACTTTCTTAGGATAATC 1 F3: 4 TAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG R RF: CTGAGGAATTCTGCCCTAAATACAACTTTCTTAGGATAATCAGAAGGATTATCGTAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG RR: GACTCCTTAAGACGGGATTTATGTTGAAAGAATCCTATTAGTCTTCCTAATAGCATTCTGTGTCCGTCGAGACTGTTCTGTTCTCGGATCCGTC F2: 3 CCTATTAGTCTTC 2 Unidirectional alignment (log-probability: -39.2) TGAGGAATcCTGCCCTAAATACAACTTTCTTAGGATAATC-----cttctGATTATCcTAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG TGAGGAATTCTGCCCTAAATACAACTTTCTTAGGATAATCAGAAG-----GATTATCGTAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG Template switch alignment (log-probability: -22.9) TGAGGAATcCTGCCCTAAATACAACTTTCTTAGGATAATC|CTTCTGATTATCC|TAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG TGAGGAATTCTGCCCTAAATACAACTTTCTTAGGATAATC|CTTCTGATTATCC|TAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG Gorilla > Chimp --------------- chr12:43004542-43004554 Template switch process: F1: L CTGAGGAATCCTGCCCTAAATACAACTTTCTTAGGATAATC 1 F3: 4 TAAGACACAGGCAGCTCTGAAAAGACAAGAGCCTAGGCAG R RF: CTGAGGAATTCTGCCCTAAATACAACTTTCTTAGGATAATCAGAAGGATTATCGTAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG RR: GACTCCTTAAGACGGGATTTATGTTGAAAGAATCCTATTAGTCTTCCTAATAGCATTCTGTGTCCGTCGAGACTGTTCTGTTCTCGGATCCGTC F2: 3 CCTATTAGTCTTC 2 Unidirectional alignment (log-probability: -44.7) TGAGGAATcCTGCCCTAAATACAACTTTCTTAGGATAATC-----cttctGATTATCcTAAGACACAGGCAGCTCTGAaAAGACAAGAGCCTAGGCAG TGAGGAATTCTGCCCTAAATACAACTTTCTTAGGATAATCAGAAG-----GATTATCGTAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG Template switch alignment (log-probability: -28.4) TGAGGAATcCTGCCCTAAATACAACTTTCTTAGGATAATC|CTTCTGATTATCC|TAAGACACAGGCAGCTCTGAaAAGACAAGAGCCTAGGCAG TGAGGAATTCTGCCCTAAATACAACTTTCTTAGGATAATC|CTTCTGATTATCC|TAAGACACAGGCAGCTCTGACAAGACAAGAGCCTAGGCAG ========= Event 703 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAGATAGGTTATTGTACCTT------CC----------------------TG--AGAGAGCAAACAAAATGACTGCTTA Chimp: CCAGATAGGTTATTGTACCTT---CAACC-----------TGTCTCTCAGGAGAGAGAGAGCAAACAAAATGACTGCTTA Gorilla: CCAGATAGGTTATTGTACCTTCAA---CCTGTCTCTCAGG-----------AG--AGAGAGCAAACAAAATGACTGCTTA ↑ 3 4 2 Human: CCAGATAGGTTATTGTACCTT------CC----------------------TG--AGAGAGCAAACAAAATGACTGCTTA Cluster: [ ] Orangutan: ccagataggttattgtaccttcaa---cctgtctCTCAGG-----------AG--AGAGAGCAAACAAAATGACTGCTTA Human > Gorilla --------------- chr12:4759940-4759949 Template switch process: F1: L TCTCTGAGGATCTTTAAGTACCAGATAGGTTATTGTACCTTCAACCTG 1 F3: 4 GAGAGAGCAAACAAAATGACTGCTTAAACCTTCTTTTTTA R RF: TCTCTGAGGATCTTTAAGTACCAGATAGGTTATTGTACCTT---CCTGAGAGAGCAAACAAAATGACTGCTTAAACCTTCTTTTTTA RR: AGAGACTCCTAGAAATTCATGGTCTATCCAATAACATGGAA---GGACTCTCTCGTTTGTTTTACTGACGAATTTGGAAGAAAAAAT F2: 3 AGGACTCTCT 2 Unidirectional alignment (log-probability: -40.8) GATCTTTAAGTACCAGATAGGTTATTGTACCTTCaacctgtctCTcaggaGAGAGAGCAAACAAAATGACTGCTTAAACCTTCTTTTTTA GATCTTTAAGTACCAGATAGGTTATTGTACCTTC---------CT-----GAGAGAGCAAACAAAATGACTGCTTAAACCTTCTTTTTTA Template switch alignment (log-probability: -31.2) GATCTTTAAGTACCAGATAGGTTATTGTACCTTcaaCCTG|TCTCTCAGGA|GAGAGAGCAAACAAAATGACTGCTTAAACCTTCTTTTTTA GATCTTTAAGTACCAGATAGGTTATTGTACCTT---CCTG|TCTCTCAGGA|GAGAGAGCAAACAAAATGACTGCTTAAACCTTCTTTTTTA ========= Event 704 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: GGTCCCTTAGTCTTAAAATACTGATTCTTGAGATGCTTCCTTCTAATTTGGGAGAAAACTGTGTTAATTATCAACTCATGTGAAATTAAAGTCTGCAGCCACCCCCC------------- Chimp: Gorilla: GGTCCCTTAGTCTTAAAATACTGATTCTTGAGATGCTTCCTTCTAATTTGGGAGAAAACTGTGTTAATTATCAACT--CGTGAAATTAAAGTCTTCAGTCACCCCCCAACCTGCTCtttc ↑ 3 2 1 4 Human: GGTCCCTTAGTCTTAAAATACTGATTCTTGAGATGCTTCCTTCTAATTTGGGAGAAAACTGTGTTAATTATCAACTCATGTGAAATTAAAGTCTGCAGCCACCCCCC------------- Cluster: [ ] Orangutan: Human > Gorilla --------------- chr1:1338745-1338749 Template switch process: F1: L CTTCCTTCTAATTTGGGAGAAAACTGTGTTAATTATCAACTC--GTGAAATTAAAGTCT 1 F3: 4 CACCCCCCAACCTGCTCTTT R RF: ACTGATTCTTGAGATGCTTCCTTCTAATTTGGGAGAAAACTGTGTTAATTATCAACTCATGTGAAATTAAAGTCTGCAGCCACCCCCCAACCTGCTCTTT RR: TGACTAAGAACTCTACGAAGGAAGATTAAACCCTCTTTTGACACAATTAATAGTTGAGTACACTTTAATTTCAGACGTCGGTGGGGGGTTGGACGAGAAA F2: 3 TGACT 2 Unidirectional alignment (log-probability: -45.9) AGAAAACTGTGTTAATTATCAACTC--GTGAAATTAAAGTCTtCAGtCACCCCCCaacctgctcttt AGAAAACTGTGTTAATTATCAACTCATGTGAAATTAAAGTCTGCAGCCACCCCCC------------ Template switch alignment (log-probability: -26.1) AGAAAACTGTGTTAATTATCAACTC--GTGAAATTAAAGTCT|TCAGT|CACCCCCCAACCTGCTCTTT AGAAAACTGTGTTAATTATCAACTCATGTGAAATTAAAGTCT|TCAGT|CACCCCCCAACCTGCTCTTT ========= Event 705 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GCCAAGTGCAGTTGACTGTCTGGGTTTACAAAATAAA-------CCCAGAAGCAGCCTGACGTCTCCGCTCGT Chimp: GCCAAGTGCAGTTGACTGTCTGGGTTTACAAAATAAA-------CCCAGAAGCAGCCTGACGTCTCCGCTCGC ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: GCCAAGTGCAGTTGACTGTCTGGGTTTATTTTGTAAA--------------CCAGCCTGACGTCTCCGCTCGC ↑ 3 1 2 4 Human: GCCAAGTGCAGTTGACTGTCTGGGTTTACAAAATAAA-------CCCAGAAGCAGCCTGACGTCTCCGCTCGT Cluster: [ ] Orangutan: GCCAAGTGCAGTTGACTGTCTGGGTTTACAAAATAAACCCAGAA-------GCAGCCTGACGTCTCCGCTCGC Human > Gorilla --------------- chr12:94333787-94333796 Template switch process: F1: L CCACCCAGGCCGAGGAATCCCCGGACCTCTTAGAGCTTTGCTTTGGGGCAAGGGCCAAGGAGGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA 1 F3: 4 CAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCGGGGAGGGAAGTCGGGAACGTTTCCTCTCCACAGGGATCTCTGCTGGGAGGAAGTAACCGG R RF: CCACCCAGGCCAAGGAATCCCCGGACCTCTTAGAGCTTTGCTTTGGGGCAAGGGCCAAGGAGGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTACAAAATAAACCCAGAAGCAGCCTGACGTCTCCGCTCGTTTCTAGGGAGGAGGTCGCGGGGAGGGAAGTCGGGAACGTTTCCTCTCCACAGGGATATCTGCTGGGAGGAAGTAACCGG RR: GGTGGGTCCGGTTCCTTAGGGGCCTGGAGAATCTCGAAACGAAACCCCGTTCCCGGTTCCTCCGAAACGGACGCGGTTCACGTCAACTGACAGACCCAAATGTTTTATTTGGGTCTTCGTCGGACTGCAGAGGCGAGCAAAGATCCCTCCTCCAGCGCCCCTCCCTTCAGCCCTTGCAAAGGAGAGGTGTCCCTATAGACGACCCTCCTTCATTGGCC F2: 3 CAAATGTTTT 2 Unidirectional alignment (log-probability: -58.2) GGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTattttgtaaAC----------------CAGCCTGACGTCTCCGCTCGcTTCTgGGGAGGAGGTCGCG GGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTT---------ACAAAATAAACCCAGAAGCAGCCTGACGTCTCCGCTCGTTTCTAGGGAGGAGGTCGCG Template switch alignment (log-probability: -41.6) GGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA|TTTTGTAAAC|CAGCCTGACGTCTCCGCTCGcTTCTgGGGAGGAGGTCGCG GGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA|TTTTGTAAAC|CAGCCTGACGTCTCCGCTCGTTTCTAGGGAGGAGGTCGCG Gorilla > Chimp --------------- chr12:94274723-94274736 Template switch process: F1: L CCACCCAGGCCAAGGAATCCCCGGACCTCTTAGAGCTTTGCTTTGGGGCAAGGGCCAAGGAAGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA 1 F3: 4 AAGCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCGTGGAGGGAAGTCGGGAACGTTTCCTCTCCACAGGGATCTCTGCTGGGAGGAAGTAACCGG R RF: CCACCCAGGCCGAGGAATCCCCGGACCTCTTAGAGCTTTGCTTTGGGGCAAGGGCCAAGGAGGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTATTTTGTAAACCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCGGGGAGGGAAGTCGGGAACGTTTCCTCTCCACAGGGATCTCTGCTGGGAGGAAGTAACCGG RR: GGTGGGTCCGGCTCCTTAGGGGCCTGGAGAATCTCGAAACGAAACCCCGTTCCCGGTTCCTCCGAAACGGACGCGGTTCACGTCAACTGACAGACCCAAATAAAACATTTGGTCGGACTGCAGAGGCGAGCGAAGACCCCTCCTCCAGCGCCCCTCCCTTCAGCCCTTGCAAAGGAGAGGTGTCCCTAGAGACGACCCTCCTTCATTGGCC F2: 3 GACCCAAATAAAAC 2 Unidirectional alignment (log-probability: -62.4) aGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTT---------ACaaaataaacccagaagCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTC GGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTATTTTGTAAAC----------------CAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTC Template switch alignment (log-probability: -42.2) aGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA|CAAAATAAACCCAG|AAgCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTC GGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA|CAAAATAAACCCAG|AACCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTC Chimp > Gorilla --------------- chr12:94333787-94333796 Template switch process: F1: L CCACCCAGGCCGAGGAATCCCCGGACCTCTTAGAGCTTTGCTTTGGGGCAAGGGCCAAGGAGGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA 1 F3: 4 CAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCGGGGAGGGAAGTCGGGAACGTTTCCTCTCCACAGGGATCTCTGCTGGGAGGAAGTAACCGG R RF: CCACCCAGGCCAAGGAATCCCCGGACCTCTTAGAGCTTTGCTTTGGGGCAAGGGCCAAGGAAGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTACAAAATAAACCCAGAAGCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCGTGGAGGGAAGTCGGGAACGTTTCCTCTCCACAGGGATCTCTGCTGGGAGGAAGTAACCGG RR: GGTGGGTCCGGTTCCTTAGGGGCCTGGAGAATCTCGAAACGAAACCCCGTTCCCGGTTCCTTCGAAACGGACGCGGTTCACGTCAACTGACAGACCCAAATGTTTTATTTGGGTCTTCGTCGGACTGCAGAGGCGAGCGAAGACCCCTCCTCCAGCGCACCTCCCTTCAGCCCTTGCAAAGGAGAGGTGTCCCTAGAGACGACCCTCCTTCATTGGCC F2: 3 CAAATGTTTT 2 Unidirectional alignment (log-probability: -52.7) gGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTattttgtaaAC----------------CAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCG AGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTT---------ACAAAATAAACCCAGAAGCAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCG Template switch alignment (log-probability: -36.1) gGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA|TTTTGTAAAC|CAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCG AGCTTTGCCTGCGCCAAGTGCAGTTGACTGTCTGGGTTTA|TTTTGTAAAC|CAGCCTGACGTCTCCGCTCGCTTCTGGGGAGGAGGTCGCG ========= Event 706 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTCGATGCTCGCGTGTGATGCTTTCCAC----AGA---ACTTCTTCTGGCTCTTCAGCCAG ↓ 3 2 4 Chimp: CCTCGATGCTCGCGTGTGATGCTTTCCACATCTGGAAAGCATTCTTCTGGCTCTTCAGCCAG ↑ 3 2 4 Gorilla: CCTCGATGCTCGCGTGCGATGCTTTCCAC----AGA---ACTTCTTCTGGCTCTTCAGCCAG Human: CCTCGATGCTCGCGTGTGATGCTTTCCAC----AGA---ACTTCTTCTGGCTCTTCAGCCAG Cluster: [ ] Orangutan: -------------------------------------------------------------- Human > Chimp ------------- chr1:1908637-1908647 Template switch process: F1: L CCTCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACA 1 F3: 4 TTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC R RF: CCTCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACAGAACTTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC RR: GGAGGTCCGGGTGGAGCTACGAGCGCACACTACGAAAGGTGTCTTGAAGAAGACCGAGAAGTCGGTCTACCTCCCTCATCTCAACG F2: 3 ACGAAAGGTCT 2 Unidirectional alignment (log-probability: -37.2) TCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACA----TctggaaagcatTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC TCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACAGAACT-----------TCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC Template switch alignment (log-probability: -22.7) TCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACA|TcTGGAAAGCA|TTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC TCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACA|TGTGGAAAGCA|TTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC Gorilla > Chimp --------------- chr1:1908637-1908647 Template switch process: F1: L CCTCCAGGCCCACCTCGATGCTCGCGTGTGATGCTTTCCACA 1 F3: 4 TTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC R RF: CCTCCAGGCCCACCTCGATGCTCGCGTGCGATGCTTTCCACAGAACTTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC RR: GGAGGTCCGGGTGGAGCTACGAGCGCACGCTACGAAAGGTGTCTTGAAGAAGACCGAGAAGTCGGTCTACCTCCCTCATCTCAACG F2: 3 ACGAAAGGTCT 2 Unidirectional alignment (log-probability: -41.8) TCCAGGCCCACCTCGATGCTCGCGTGtGATGCTTTCCACAtctgGAAagcaTTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC TCCAGGCCCACCTCGATGCTCGCGTGCGATGCTTTCCACA----GAA---CTTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC Template switch alignment (log-probability: -28.2) TCCAGGCCCACCTCGATGCTCGCGTGtGATGCTTTCCACA|TcTGGAAAGCA|TTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC TCCAGGCCCACCTCGATGCTCGCGTGCGATGCTTTCCACA|TGTGGAAAGCA|TTCTTCTGGCTCTTCAGCCAGATGGAGGGAGTAGAGTTGC ========= Event 707 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CTGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCACTCAGAATGAAAAAGTATAACCATTTAGAAAGTCTAAGAATTTTC ↑ 3 4 1 Chimp: CTGTAGAGAAGAGAATTCAATTCTGAAAAA-----------------------GTATAACCATTTAGAAAGTCTAAGAATTTTC Gorilla: CTGTAGAGAAGAGAATTCAATTCtgaaaaagtataaccactcagaatgaaaaagtataaccatttagaaAGTCTAAGAATTTTC Human: CTGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCACTCAGAATGAAAAAGTATAACCATTTAGAAAGTCTAAGAATTTTC Cluster: [ ] Orangutan: CTGTAGAGAAGAGAATTCAATTCtgaaaaagtataaccatttagaatgaaaaagtataaccatttagaaAGTCTAAGAATTTTC Chimp > Human ------------- chr1:870131-870136 Template switch process: F1: L TTTGCCTCCACCTGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCACT 1 F3: 4 GAAAAAGTATAACCATTTAGAAAGTCTAAGAATTTTCAAATCTTAG R RF: TTTGCCTCCACCTGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCATTTAGAAAGTCTAAGAATTTTCAAATCTTAG RR: AAACGGAGGTGGACATCTCTTCTCTTAAGTTAAGACTTTTTCATATTGGTAAATCTTTCAGATTCTTAAAAGTTTAGAATC F2: 3 TAAGAC 2 Unidirectional alignment (log-probability: -44) TGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCActcagaatgaaaaagtataaccaTTTAGAAAGTCTAAGAATTTTCAAA TGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCA-----------------------TTTAGAAAGTCTAAGAATTTTCAAA Template switch alignment (log-probability: -22.3) TGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCAcT|CAGAAT|GAAAAAGTATAACCATTTAGAAAGTCTAAGAATTTTCAAA TGTAGAGAAGAGAATTCAATTCTGAAAAAGTATAACCATT|CAGAAT|GAAAAAGTATAACCATTTAGAAAGTCTAAGAATTTTCAAA ========= Event 708 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: TCACATGAAGTGTCACTTCTA---------GAAAATGGCTTTTCTTCCACAACTAAAGTAAAATCACTTGGGG Chimp: Gorilla: TCACATGAAGTGTCACTTCTAGTTGTGGAAGAAAAGCCATTT---------TCTAAAGTAAAATCACTTGGGG ↓ 13 24 ↑ 13 24 Human: TCACATGAAGTGTCACTTCTA---------GAAAATGGCTTTTCTTCCACAACTAAAGTAAAATCACTTGGGG Cluster: [ ] Orangutan: TCACATCAAGTGTCACTCCTAGTTGTGGAAGAAAAGCCATTT---------TCTAAAGTAAAATCACTTGGGG Gorilla > Human --------------- chr1:248654677-248654697 Template switch process: F1: L TTTCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG 1 F3: 4 CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG R RF: TTTCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAGTTGTGGAAGAAAAGCCATTTTCTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG RR: AAAGGAGGGGTCGTCATAAAAGTGTACTTCACAGTGAAGATCAACACCTTCTTTTCGGTAAAAGATTTCATTTTAGTGAACCCCTTAGAAATCTTGCTATCTC F2: 3 AACACCTTCTTTTCGGTAAAA 2 Unidirectional alignment (log-probability: -51.9) TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG---------------------aaaatggcttttcttccacaaCTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAGTTGTGGAAGAAAAGCCATTTT---------------------CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG Template switch alignment (log-probability: -18.4) TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG|AAAATGGCTTTTCTTCCACAA|CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG|AAAATGGCTTTTCTTCCACAA|CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG Human > Gorilla --------------- chr1:228612630-228612650 Template switch process: F1: L TTTCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG 1 F3: 4 CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG R RF: TTTCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAGAAAATGGCTTTTCTTCCACAACTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG RR: AAAGGAGGGGTCGTCATAAAAGTGTACTTCACAGTGAAGATCTTTTACCGAAAAGAAGGTGTTGATTTCATTTTAGTGAACCCCTTAGAAATCTTGCTATCTC F2: 3 TTTTACCGAAAAGAAGGTGTT 2 Unidirectional alignment (log-probability: -51.9) TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG---------------------ttgtggaagaaaagccattttCTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAGAAAATGGCTTTTCTTCCACAA---------------------CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG Template switch alignment (log-probability: -18.4) TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG|TTGTGGAAGAAAAGCCATTTT|CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG TCCTCCCCAGCAGTATTTTCACATGAAGTGTCACTTCTAG|TTGTGGAAGAAAAGCCATTTT|CTAAAGTAAAATCACTTGGGGAATCTTTAGAACGATAGAG ========= Event 709 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: TCCATGAATGAAAACAGTTACC------ATTTA----AATAAATAGGCAGATAAAGGGGGGTGGTAACTAAGGCAGTATGTAA Chimp: Gorilla: TCCATGAATGAAAACAGTTACTACCCCCCTTTATCTG----CCTATTTATTTAA------ATGGTAACTAAGGCAGTATGTAA ↓ 1 3 42 Human: TCCATGAATGAAAACAGTTACC------ATTTA----AATAAATAGGCAGATAAAGGGGGGTGGTAACTAAGGCAGTATGTAA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr1:248447044-248447073 Template switch process: F1: L GAGGGAAAGTAGACTACTTTTCCATGAATGAAAACAGTTAC 1 F3: 4 TGGTAACTAAGGCAGTATGTAATTAGAACTGGAGATAAG R RF: GAGGGAAAGTAGATTACTTTTCCATGAATGAAAACAGTTACTACCCCCCTTTATCTGCCTATTTATTTAAATGGTAACTAAGGCAGTATGTAATTAGAACTGGAGATAAA RR: CTCCCTTTCATCTAATGAAAAGGTACTTACTTTTGTCAATGATGGGGGGAAATAGACGGATAAATAAATTTACCATTGATTCCGTCATACATTAATCTTGACCTCTATTT F2: 3 GGGGGGAAATAGACGGATAAATAAATTTAC 2 Unidirectional alignment (log-probability: -74.3) AGGGAAAGTAGAcTACTTTTCCATGAATGAAAACAGTTAC----------------------cATTTAAAtaaataggcagataaaggggggTGGTAACTAAGGCAGTATGTAATTAGAACTGGAGAT-AAG AGGGAAAGTAGATTACTTTTCCATGAATGAAAACAGTTACTACCCCCCTTTATCTGCCTATTTATTTAAA----------------------TGGTAACTAAGGCAGTATGTAATTAGAACTGGAGATAAAG Template switch alignment (log-probability: -30.6) AGGGAAAGTAGAcTACTTTTCCATGAATGAAAACAGTTAC|CATTTAAATAAATAGGCAGATAAAGGGGGG|TGGTAACTAAGGCAGTATGTAATTAGAACTGGAGATAAg AGGGAAAGTAGATTACTTTTCCATGAATGAAAACAGTTAC|CATTTAAATAAATAGGCAGATAAAGGGGGG|TGGTAACTAAGGCAGTATGTAATTAGAACTGGAGATAAA ========= Event 710 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGTACAGGCTTAATTTCTTAAAAAGTCAGTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTGGGATCAAATTAAACTTCATTCCCTTGATTTTGTGAATTTGGAGTAGCCTGTAATACAAACTCGGTAGAGAATAGCACCCATAACCCTGACTAACTTTCAACTGCCCTTATAAGGTCT ↑ 1 4 3 2 Chimp: TGTACAGGCTTAATTTCTTAA---GC--CTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTGGGATCAAATTAAACTTCATTCCCTTGATTTTGTGAATTTGGAGTAGCCTGTAATACAAACTCGGTAGAGAATAGCACCCATAACCCTGACTAACTTTCAACTGCCCTTATAAGGTCT Gorilla: TGTACAGGCTTAATTTCTTAAAAAGTCAGTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTGGGATCAAATTAAACTTCATTCCCTTGATTTTGTGAATTTGGAGTAGCCTGTAATACAAACTCGGTAGAGAATAGCACCCATAACCCTGAGTAACTTTCAACTGCCCTTATAAGGTCT Human: TGTACAGGCTTAATTTCTTAAAAAGTCAGTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTGGGATCAAATTAAACTTCATTCCCTTGATTTTGTGAATTTGGAGTAGCCTGTAATACAAACTCGGTAGAGAATAGCACCCATAACCCTGACTAACTTTCAACTGCCCTTATAAGGTCT Cluster: [ ] Orangutan: TGTACAGGCTTAATTTCTTAAAAAGTCAGTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTGGGATCAAATTAAACTTAATTCCCTTGATTTTGTGAATTTTGAGTAGCCTGTAATACAAACTCGGTAGAGAATAGTACCCACAACCCTGACTAACTTTCAACTGCCGTTATAAGGTCT Chimp > Human ------------- chr12:83270612-83270619 Template switch process: F1: L AATCTTTATAACTAAGAAGATGTACAGGCTTAATTTCTTAA 1 F3: 4 TGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTG R RF: AATCTTTATAACTAAGAAGATGTACAGGCTTAATTTCTTAAGCCTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTGGGATCAAATTAAACTTCATTCCCTTGATTTTGTGAATTTGGAGTAGCCTGTAATACAAACTCGGTAGAGAATAGCACCCATAACCCTGACTAACTTT RR: TTAGAAATATTGATTCTTCTACATGTCCGAATTAAAGAATTCGGACAACCCATTATGAGAACAAACATCTTTGGTCGTGTCAACCCTAGTTTAATTTGAAGTAAGGGAACTAAAACACTTAAACCTCATCGGACATTATGTTTGAGCCATCTCTTATCGTGGGTATTGGGACTGATTGAAA F2: 3 GACTGAAA 2 Unidirectional alignment (log-probability: -31.3) ATCTTTATAACTAAGAAGATGTACAGGCTTAATTTCTTAaaaagtcAG--TGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTG ATCTTTATAACTAAGAAGATGTACAGGCTTAATTTCTTA-------AGCCTGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTG Template switch alignment (log-probability: -22.3) ATCTTTATAACTAAGAAGATGTACAGGCTTAATTTCTTAA|AAAGTcAG|TGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTG ATCTTTATAACTAAGAAGATGTACAGGCTTAATTTCTTAA|AAAGTTAG|TGTTGGGTAATACTCTTGTTTGTAGAAACCAGCACAGTTG ========= Event 711 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGTGAGAGGCCCTCAGCCAG-CTACAGGTATGGGAGATTTGGAGGAGAATGGTTCCCTTGGAGTACTCAGTAAGATGCAGCAGAGAGCAT Chimp: CTGTGAGAGGCCCTCAGCCAGCCTGCAGGTATGGGAGATTTGGAGGTGAATGGTTCCCTTGGAGTACTCAGTAAGATGCAGCAGAGAGCAT Gorilla: CTGTGAGAGGCCCTCAGCCAGCCTGAGGGTATGGGAGATTTGGAGGTGAATGGTTCCCTTGGAGTACTCAGTAAGATGCAGCAGAGAGCAT ↑ 1 4 3 2 Human: CTGTGAGAGGCCCTCAGCCAG-CTACAGGTATGGGAGATTTGGAGGAGAATGGTTCCCTTGGAGTACTCAGTAAGATGCAGCAGAGAGCAT Cluster: [ ] Orangutan: CTGTGAGAGGCCCTCAGCCAGCCTGAGGGTATGGGAGATTTGGAGGTGAATGGCTCCCTTGGAGTACTCAGTAAGATGTAGCAGAGAGCAT Human > Gorilla --------------- chr12:5245591-5245595 Template switch process: F1: L ATGGTAGCTCCTGCCCATGCCTGTGAGAGGCCCTCAGCCAGC 1 F3: 4 GGTATGGGAGATTTGGAGGTGAATGGTTCCCTTGGAGTAC R RF: ATGGTAGCTCCTGCCCATGCCTGTGAGAGGCCCTCAGCCAGCTACAGGTATGGGAGATTTGGAGGAGAATGGTTCCCTTGGAGTACTCAG RR: TACCATCGAGGACGGGTACGGACACTCTCCGGGAGTCGGTCGATGTCCATACCCTCTAAACCTCCTCTTACCAAGGGAACCTCATGAGTC F2: 3 GAGTC 2 Unidirectional alignment (log-probability: -33.6) GGTAGCTCCTGCCCATGCCTGTGAGAGGCCCTCAGCCAGC----ctgagGGTATGGGAGATTTGGAGGtGAATGGTTCCCTTGGAGTAC GGTAGCTCCTGCCCATGCCTGTGAGAGGCCCTCAGCCAGCTACA-----GGTATGGGAGATTTGGAGGAGAATGGTTCCCTTGGAGTAC Template switch alignment (log-probability: -21.9) GGTAGCTCCTGCCCATGCCTGTGAGAGGCCCTCAGCCAGC|CTGAG|GGTATGGGAGATTTGGAGGtGAATGGTTCCCTTGGAGTAC GGTAGCTCCTGCCCATGCCTGTGAGAGGCCCTCAGCCAGC|CTGAG|GGTATGGGAGATTTGGAGGAGAATGGTTCCCTTGGAGTAC ========= Event 712 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CTGGGCCCCACCCTGGCACACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGT-CACACATTGGCTCTGACTGGAGGA ↓ 3 2 1 4 Chimp: CTGGGCCCCACCCTGGCACACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCAGTGTGACTAAGCAGGAGCAGGTACATTGGCTCTGACTGGAGGA Gorilla: CTGGGCCCCACCCTGGCACACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGCAGGTACATTGGCTCTGACTGGAGAA ↑ 3 2 1 4 Human: CTGGGCCCCACCCTGGCACACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGT-CACACATTGGCTCTGACTGGAGGA Cluster: [ ] Orangutan: CTGGGCCCCACCCTGGCACACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGCAGGTACATTGGCTCTGACTGGAGGA Human > Chimp ------------- chr12:99558370-99558374 Template switch process: F1: L GAGTTCTGTCCCCTGCCTGTGGCAGTGTGACTAAGCAGGAG 1 F3: 4 ACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT R RF: ACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGTCACACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT RR: TGGACTCCCCGTGACCCCGTCACTCACTCAAGACAGGGGACGGACACCGACACACTGATTCGTCCTCAGTGTGTAACCGAGACTGACCTCCTCTCGTTTGTTCCAGAGACA F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -33) AGTTCTGTCCCCTGCCTGTGGCaGTGTGACTAAGCAGGAgcagGT---ACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT AGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGA----GTCACACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT Template switch alignment (log-probability: -21.9) AGTTCTGTCCCCTGCCTGTGGCaGTGTGACTAAGCAGGAG|CAGGT|ACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT AGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAG|CAGGT|ACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT Human > Gorilla --------------- chr12:99562276-99562280 Template switch process: F1: L GAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAG 1 F3: 4 ACATTGGCTCTGACTGGAGAAGAGCAAACAAGGTCTCTGT R RF: ACCTGAGGGGCACTGGGGCAGTGAGTGAGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGTCACACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT RR: TGGACTCCCCGTGACCCCGTCACTCACTCAAGACAGGGGACGGACACCGACACACTGATTCGTCCTCAGTGTGTAACCGAGACTGACCTCCTCTCGTTTGTTCCAGAGACA F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -32.1) AGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAG---CaggtACATTGGCTCTGACTGGAGaAGAGCAAACAAGGTCTCTGT AGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAGTCAC----ACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT Template switch alignment (log-probability: -21.9) AGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAG|CAGGT|ACATTGGCTCTGACTGGAGaAGAGCAAACAAGGTCTCTGT AGTTCTGTCCCCTGCCTGTGGCTGTGTGACTAAGCAGGAG|CAGGT|ACATTGGCTCTGACTGGAGGAGAGCAAACAAGGTCTCTGT ========= Event 713 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GATAAAGTCCACTTTTAACTT-----TTACCTACggattatacaataatccataggtaatttggatcatacaataatccataggtaatttggatcTCCTTGACAG Chimp: GATAAAGTCCACTTTTAACTT-----TCACCTATGGAT----------------------------TATACAATAATCCATAGGTAATCTGGATCTCCTTGACAG ↑ 1 3 4 2 Gorilla: GATAAAGTCCACTTTTAACTT----------TATGGAT----------------------------TATTGTATAATCCATAGGTAATCTGGATCTCCTTGACAG Human: GATAAAGTCCACTTTTAACTT-----TTACCTACggattatacaataatccataggtaatttggatcatacaataatccataggtaatttggatcTCCTTGACAG Cluster: [ ] Orangutan: GATAAAGTCCACTTTTAACTTTTACC-----TATGGAT----------------------------TATACAATAATCCATAGGTAATTTGGATCTCCTTGACAG Gorilla > Chimp --------------- chr12:39188307-39188322 Template switch process: F1: L TTCCAGATGAAAAAACACTAGATAAAGTCCACTTTTAACTTTC 1 F3: 4 ATAATCCATAGGTAATCTGGATCTCCT R RF: TTCCAGATGAAAAAACACTAGATAAAGTCCACTTTTAACTTTATGGATTATTGTATAATCCATAGGTAATCTGGATCTCCT RR: AAGGTCTACTTTTTTGTGATCTATTTCAGGTGAAAATTGAAATACCTAATAACATATTAGGTATCCATTAGACCTAGAGGA F2: 3 ACATATTAGGTATCCA 2 Unidirectional alignment (log-probability: -34.6) CAGATGAAAAAACACTAGATAAAGTCCACTTTTAACTTtcaccTATGGATTATacaATAATCCATAGGTAATCTGGATCTCCT CAGATGAAAAAACACTAGATAAAGTCCACTTTTAACTT-----TATGGATTATTGTATAATCCATAGGTAATCTGGATCTCCT Template switch alignment (log-probability: -23) CAGATGAAAAAACACTAGATAAAGTCCACTTTTAACTTTc|ACCTATGGATTATACA|ATAATCCATAGGTAATCTGGATCTCCT CAGATGAAAAAACACTAGATAAAGTCCACTTTTAACTTTA|ACCTATGGATTATACA|ATAATCCATAGGTAATCTGGATCTCCT ========= Event 714 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGTAGGAGTTCAGTGTGGTT-----CTGCATTAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTTGGTGTGAATGCAGTTTTTTTCTGAATGCATTAG Chimp: CTGTAGGAGCTCAGTGTGGTT----------GCAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTTGGTGTGAATGCAGTT-TTTTCTGAATGCATTAG Gorilla: CTGTAGGAGCTCAGTGTGGTT----------GCAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTTGGTGTGAATGCAGTT-TTTTCTGAATGCATTAG ↓ 1 4 3 2 Human: CTGTAGGAGTTCAGTGTGGTT-----CTGCATTAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTTGGTGTGAATGCAGTTTTTTTCTGAATGCATTAG Cluster: [ ] Orangutan: CTGTAGGAGCTCAGTGTGGTTCTGCA-----TTAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTTGGTGTGAATGCAGTT-TGTTCTAAATGCATTAG Gorilla > Human --------------- chr12:79107647-79107653 Template switch process: F1: L GAAGGATGTAGGAGGAAAAGCTGTAGGAGTTCAGTGTGGTT 1 F3: 4 AAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTT R RF: GAAGGATGTAGGAGGAAAAGCTGTAGGAGCTCAGTGTGGTTGCAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTTGGTGTGAATGCAG RR: CTTCCTACATCCTCCTTTTCGACATCCTCGAGTCACACCAACGTTCCTCCCGAAACGTACGGATAAACTCCTTAGTCATGAAACCACACTTACGTC F2: 3 TTACGTC 2 Unidirectional alignment (log-probability: -33.4) AAGGATGTAGGAGGAAAAGCTGTAGGAGtTCAGTGTGGTtcTGCattAAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTT AAGGATGTAGGAGGAAAAGCTGTAGGAGCTCAGTGTGGT--TGC---AAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTT Template switch alignment (log-probability: -22.1) AAGGATGTAGGAGGAAAAGCTGTAGGAGtTCAGTGTGGTT|CTGCATT|AAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTT AAGGATGTAGGAGGAAAAGCTGTAGGAGCTCAGTGTGGTT|CTGCATT|AAGGAGGGCTTTGCATGCCTATTTGAGGAATCAGTACTTT ========= Event 715 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAAGAAGGAAGGTTTTGAGC---------TGGTGACTCTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCTG Chimp: AAAAGAAGGAAGGTTTTGAGC---------TGGTGACTCTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCT- ↑ 4 1 3 2 Gorilla: AAAAGAAGGAAGGTTTTGAGC------------------TGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCTG Human: AAAAGAAGGAAGGTTTTGAGC---------TGGTGACTCTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCTG Cluster: [ ] Orangutan: AAAAGAAGAAAGGTTTCGAGCTGGTGGTTC---------TGAAGCAGCAAAGTGACCTGTCAGGATACCTTCTCTG Gorilla > Chimp --------------- chr12:101442377-101442382 Template switch process: F1: L CCCTCAACATTTGAGTTCTTAAAAGAAGGAAGGTTTTGAGCTG 1 F3: 4 CTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCT R RF: CCCTCAACATTTGAGTTCTTAAAAGAAGGAAGGTTTTGAGCTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCT RR: GGGAGTTGTAAACTCAAGAATTTTCTTCCTTCCAAAACTCGACTTCGTCGTTTCAGTGGACAGTCCTACGGAAGAGA F2: 3 TCAGTG 2 Unidirectional alignment (log-probability: -30.7) TCAACATTTGAGTTCTTAAAAGAAGGAAGGTTTTGAGctggtgactCTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCT---- TCAACATTTGAGTTCTTAAAAGAAGGAAGGTTTTGAG---------CTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCTGTTT Template switch alignment (log-probability: -16.5) TCAACATTTGAGTTCTTAAAAGAAGGAAGGTTTTGAGCTG|GTGACT|CTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCT TCAACATTTGAGTTCTTAAAAGAAGGAAGGTTTTGAGCTG|GTGACT|CTGAAGCAGCAAAGTCACCTGTCAGGATGCCTTCTCT ========= Event 716 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: cagccccagaagaaccatacagctgagcccagtcaacccagagaatcacaagagatataaacagttgttttagggcactaaatgttgggatgatatgcagtaaaagataacAAAACACTGACTGCTACAGGCCAGGGAAGCAAGAGGCAGCTGGAGGAGTCAGCAAAGGTGGATTAT ↑ 3 2 4 1 Chimp: cagccccagaagaaccatacagctgagcccagtcaacccagagaatcacaagagatataaacagttgttttagggcactaaatgttgggatgatatgCAGTAAAAGATAACAAAACACTGACTGCTACAGGCCAGGGAAGCAAG----------AGGAGTCAGCAAAGGTGGATTAT Gorilla: cagccccagaagaaccatacagctgagcccagtcaacccagagaatcacaagagatataaacagttgttttagggcactaaatgttgggatgatatgcagtaaaagataacaaaacaCTGACTGCTACAGGCCAGGGAAGCAAGAGGCAGCTGGAGGAGTCAGGAAAGGTGGCTTAT Human: cagccccagaagaaccatacagctgagcccagtcaacccagagaatcacaagagatataaacagttgttttagggcactaaatgttgggatgatatgcagtaaaagataacAAAACACTGACTGCTACAGGCCAGGGAAGCAAGAGGCAGCTGGAGGAGTCAGCAAAGGTGGATTAT Cluster: [ ] Orangutan: cagccccagaagaaccatacagctgagcccagtcaacccagagaatcacaagagatataaacagttgttttagggcactaaatgttgggatgatatgcagtaaaagataacAAAACACTGACTGCTACAGGCCAAGGAAGCAAGAGGCAGCTGGAGGAGTCAGCAGAGGTGGATTAT Chimp > Human ------------- chr1:25599254-25599259 Template switch process: F1: L AAGATAACAAAACACTGACTGCTACAGGCCAGGGAAGCAAGAGG 1 F3: 4 GAGGAGTCAGCAAAGGTGGATTATTAGCCGGGCCATGGTTA R RF: CAGCTGAGCCCAGTCAACCCAGAGAATCACAAGAGATATAAACAGTTGTTTTAGGGCACTAAATGTTGGGATGATATGCAGTAAAAGATAACAAAACACTGACTGCTACAGGCCAGGGAAGCAAGAGGAGTCAGCAAAGGTGGATTATTAGCCAGGCCATGGTTA RR: GTCGACTCGGGTCAGTTGGGTCTCTTAGTGTTCTCTATATTTGTCAACAAAATCCCGTGATTTACAACCCTACTATACGTCATTTTCTATTGTTTTGTGACTGACGATGTCCGGTCCCTTCGTTCTCCTCAGTCGTTTCCACCTAATAATCGGTCCGGTACCAAT F2: 3 GTCGAC 2 Unidirectional alignment (log-probability: -31.3) TAACAAAACACTGACTGCTACAGGCCAGGGAAGCAAgaggcagctgGAGGAGTCAGCAAAGGTGGATTATTAGCCgGGCCATGGTT TAACAAAACACTGACTGCTACAGGCCAGGGAAGCAA----------GAGGAGTCAGCAAAGGTGGATTATTAGCCAGGCCATGGTT Template switch alignment (log-probability: -22.1) TAACAAAACACTGACTGCTACAGGCCAGGGAAGCAAGAGG|CAGCTG|GAGGAGTCAGCAAAGGTGGATTATTAGCCgGGCCATGGTT TAACAAAACACTGACTGCTACAGGCCAGGGAAGCAAGAGG|CAGCTG|GAGGAGTCAGCAAAGGTGGATTATTAGCCAGGCCATGGTT ========= Event 717 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTATCAGGGAATTTTTTCATTCTAAAGAATGAATTCTTTAGAATTTGTTAAAACttttt-- ↑ 1 4 3 2 Chimp: GGTATCAGGGAATTTTTTCAT----TACAATGAATTCTTTAGAATTTGTTAAAACtttt--- Gorilla: GGTATCAGGGAATTTTTTCAT----TACAATGAATTCTTTAGAATTTGTTAAAACttctttt ↓ 1 4 3 2 Human: GGTATCAGGGAATTTTTTCATTCTAAAGAATGAATTCTTTAGAATTTGTTAAAACttttt-- Cluster: [ ] Orangutan: GGTATCAGGGAATTTTTTCAT----TACAATGAATTCTTTAGAATTTGTTAAAACttctttt Chimp > Human ------------- chr12:58279508-58279513 Template switch process: F1: L TATTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATT 1 F3: 4 AATGAATTCTTTAGAATTTGTTAAAACTTTTTTTTTT R RF: TATTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATTACAATGAATTCTTTAGAATTTGTTAAAACTTTTTTTTTT RR: ATAAAGATGAAATTATTGTACCATAGTCCCTTAAAAAAGTAATGTTACTTAAGAAATCTTAAACAATTTTGAAAAAAAAAA F2: 3 GAAATC 2 Unidirectional alignment (log-probability: -34.2) TTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATTctaaAgAATGAATTCTTTAGAATTTGTTAAAACTTTTTTTttt TTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATT----ACAATGAATTCTTTAGAATTTGTTAAAACTTTTTTT--- Template switch alignment (log-probability: -16) TTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATT|CTAAAG|AATGAATTCTTTAGAATTTGTTAAAACTTTTTTTTTT TTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATT|CTAAAG|AATGAATTCTTTAGAATTTGTTAAAACTTTTTTTTTT Gorilla > Human --------------- chr12:58279508-58279513 Template switch process: F1: L TATTTCTACTTTAATAACATGGTATCAGGGAATTTTTTCATT 1 F3: 4 AATGAATTCTTTAGAATTTGTTAAAACTTTTTT R RF: TATTTCTACTTTAATAACACGGTATCAGGGAATTTTTTCATTACAATGAATTCTTTAGAATTTGTTAAAACTTCTTT RR: ATAAAGATGAAATTATTGTGCCATAGTCCCTTAAAAAAGTAATGTTACTTAAGAAATCTTAAACAATTTTGAAGAAA F2: 3 GAAATC 2 Unidirectional alignment (log-probability: -37.7) TTTCTACTTTAATAACAtGGTATCAGGGAATTTTTTCATTctaaAgAATGAATTCTTTAGAATTTGTTAAAAC-------TTTTTT TTTCTACTTTAATAACACGGTATCAGGGAATTTTTTCATT----ACAATGAATTCTTTAGAATTTGTTAAAACTTCTTTTTTTTTT Template switch alignment (log-probability: -27.4) TTTCTACTTTAATAACAtGGTATCAGGGAATTTTTTCATT|CTAAAG|AATGAATTCTTTAGAATTTGTTAAAACTTtTTT TTTCTACTTTAATAACACGGTATCAGGGAATTTTTTCATT|CTAAAG|AATGAATTCTTTAGAATTTGTTAAAACTTCTTT ========= Event 718 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 124 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTAATAAGGGTTTGGGTTGTTATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAACAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAATAGTACCATATA ↓ 1 3 2 4 ↑ 1 3 4 2 Chimp: TTAATAAGGGTTTGGGTTGTTG--------------------------------TTACTAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAATAGTACCATATA Gorilla: TTAATAAGGGTTTGGGTTGTTG--------------------------------TTACTAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAATAGTACCATATA ↑ 1 3 2 4 Human: TTAATAAGGGTTTGGGTTGTTATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAACAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAATAGTACCATATA Cluster: [ ] Orangutan: TTAATAAGGGTTTGGGTTGTTG--------------------------------TTACTAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAATAGTACCATAT- Chimp > Human ------------- chr1:26238061-26238098 Template switch process: F1: L TCTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT 1 F3: 4 AAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA R RF: TCTGTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTGTTACTAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA RR: AGACAACATCTACGTCACTTAATTATTCCCAAACCCAACAACAATGATTCTCTTATGATATCTCCAGTGATTTCATGTAATCTCTTT F2: 3 CAATGATTCTCTTATGATATCTCCAGTGATTTCATGTA 2 Unidirectional alignment (log-probability: -79.2) CTaTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTaTgTACTttagtgacctctatagtattctcttagtaacAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA CTGTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTGT-TACT-------------------------------AAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA Template switch alignment (log-probability: -25.9) CTaTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT|ATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAAC|AAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA CTGTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT|ATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAAC|AAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA Human > Chimp ------------- chr1:25327965-25327971 Template switch process: F1: L TCTGTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT 1 F3: 4 AGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA R RF: TCTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAACAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA RR: AGATAACATCTACGTCACTTAATTATTCCCAAACCCAACAATACATGAAATCACTGGAGATATCATAAGAGAATCATTGTTCTCTTATGATATCTCCAGTGATTTCATGTAATCTCTTT F2: 3 ATCATTG 2 Unidirectional alignment (log-probability: -34.8) CTgTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTgT-TACT-------------------------------AAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA CTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAACAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA Template switch alignment (log-probability: -22.1) CTgTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT|GTTACTA|AGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA CTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT|GTTACTA|AGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA Human > Gorilla --------------- chr1:26339692-26339698 Template switch process: F1: L TCTGTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT 1 F3: 4 AGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA R RF: TCTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAACAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA RR: AGATAACATCTACGTCACTTAATTATTCCCAAACCCAACAATACATGAAATCACTGGAGATATCATAAGAGAATCATTGTTCTCTTATGATATCTCCAGTGATTTCATGTAATCTCTTT F2: 3 ATCATTG 2 Unidirectional alignment (log-probability: -33.4) CTgTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTgT-TACT-------------------------------AAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA CTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTTATGTACTTTAGTGACCTCTATAGTATTCTCTTAGTAACAAGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA Template switch alignment (log-probability: -22.1) CTgTTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT|GTTACTA|AGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA CTATTGTAGATGCAGTGAATTAATAAGGGTTTGGGTTGTT|GTTACTA|AGAGAATACTATAGAGGTCACTAAAGTACATTAGAGAAA ========= Event 719 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTAGGGTCCTGGCCATGTGTTTAGTGTGCTAAACTTTCTCCTTTGTTCTCAGGC Chimp: CTAGGGTCCTGGCCATGTGTTTAGTGTGCTAAACTTTCTCCTTTGTTCTCAGGC ↑ 3 1 2 4 Gorilla: CTAGGGTCCTGGCCATGTGTTTAGCACAG-CCCCTTTCTCCTTTGTTCTCAGGC ↓ 3 1 2 4 Human: CTAGGGTCCTGGCCATGTGTTTAGTGTGCTAAACTTTCTCCTTTGTTCTCAGGC Cluster: [ ] Orangutan: CTAGGGCCCTGGCCATGTGTTTAGCACAG-CCCCTTTCTCCTTTGTTCTCAGGC Gorilla > Human --------------- chr1:26277989-26277997 Template switch process: F1: L CCAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG 1 F3: 4 CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC R RF: CCAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAGCACAGCCCCTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC RR: GGTCGACGGAACACAGGGATCCCAGGACCGGTACACAAATCGTGTCGGGGAAAGAGGAAACAAGAGTCCGGAAGGTCCATCAGGGGAAG F2: 3 AAATCGTGT 2 Unidirectional alignment (log-probability: -34) CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG--------tgtgctaaaCTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAGCACAGCCC---------CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC Template switch alignment (log-probability: -16.9) CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG|TGTGCTAAA|CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG|TGTGCTAAA|CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC Gorilla > Chimp --------------- chr1:25368405-25368413 Template switch process: F1: L CCAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG 1 F3: 4 CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC R RF: CCAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAGCACAGCCCCTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC RR: GGTCGACGGAACACAGGGATCCCAGGACCGGTACACAAATCGTGTCGGGGAAAGAGGAAACAAGAGTCCGGAAGGTCCATCAGGGGAAG F2: 3 AAATCGTGT 2 Unidirectional alignment (log-probability: -34) CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG--------tgtgctaaaCTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAGCACAGCCC---------CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC Template switch alignment (log-probability: -16.9) CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG|TGTGCTAAA|CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC CAGCTGCCTTGTGTCCCTAGGGTCCTGGCCATGTGTTTAG|TGTGCTAAA|CTTTCTCCTTTGTTCTCAGGCCTTCCAGGTAGTCCCCTTC ========= Event 720 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: attAGTCTTCCCAGCAATGGTTC-------GGCAGCAACAGTTGGTTGATGGTATTTtctttccccactcccagaatga Chimp: ATTAGTCTTCCCAGCAATGGTTC-------GGCAGCAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGAATGA ↓ 4 3 1 2 Gorilla: ATTAGTCTTCCCAGCAATGGTATTGAAAATACCATCAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGAATGA ↑ 4 3 1 2 Human: attAGTCTTCCCAGCAATGGTTC-------GGCAGCAACAGTTGGTTGATGGTATTTtctttccccactcccagaatga Cluster: [ ] Orangutan: ATTAGTCTTCCCAGCAATGGTTC-------GGCAGCAGCAGTTGGTTGATGGTATTTTCTTTCCACACTCCCAGAATGA Human > Gorilla --------------- chr12:26928485-26928495 Template switch process: F1: L CTTCTTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATG-------------------------GTATT 1 F3: 4 CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA R RF: CTTCTTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGTTCGGCAGCAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA RR: GAAGAAAGAACAGATAAGGGTAATCAGAAGGGTCGTTACCAAGCCGTCGTTGTCAACCAACTACCATAAAAGAAAGGGGTGAGGGTCT F2: 3 TACCATAAAAG 2 Unidirectional alignment (log-probability: -39.6) TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGTattgaaaataccaT------CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGT-------------TCGGCAGCAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA Template switch alignment (log-probability: -28.2) TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATG-------------------------GTATT|GAAAATACCAT|CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGTTCGGCAGCAACAGTTGGTTGATGGTATT|GAAAATACCAT|CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA Chimp > Gorilla --------------- chr12:26928485-26928495 Template switch process: F1: L CTTCTTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATG-------------------------GTATT 1 F3: 4 CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA R RF: CTTCTTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGTTCGGCAGCAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA RR: GAAGAAAGAACAGATAAGGGTAATCAGAAGGGTCGTTACCAAGCCGTCGTTGTCAACCAACTACCATAAAAGAAAGGGGTGAGGGTCT F2: 3 TACCATAAAAG 2 Unidirectional alignment (log-probability: -39.6) TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGTattgaaaataccaT------CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGT-------------TCGGCAGCAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA Template switch alignment (log-probability: -28.2) TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATG-------------------------GTATT|GAAAATACCAT|CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA TTTCTTGTCTATTCCCATTAGTCTTCCCAGCAATGGTTCGGCAGCAACAGTTGGTTGATGGTATT|GAAAATACCAT|CAACAGTTGGTTGATGGTATTTTCTTTCCCCACTCCCAGA ========= Event 721 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: atggcttctttccttaaacctcatgaatcaacatttactagcttcTAGTTTATTTGCATACTAgaagctagtaaatgttgattcatgacgtttaaggaaagaa------- ↓ 3 1 2 4 ↑ 13 24 Chimp: atggcttctttccttaaacctcatgaatcaacatttactagcttcTAGTATGCAAATAAACTAgaagctagtaaatgttgattcatgaggtttaaggaaagaa------- ↓ 13 24 ↑ 13 24 Gorilla: atggcttctttccttaaacctcatgaatcaacatttactagcttcTAGTTTATTTGCATACTAgaagctagtaaatgttgattcatgaggtttaaggaaagaa------- Human: atggcttctttccttaaacctcatgaatcaacatttactagcttcTAGTTTATTTGCATACTAgaagctagtaaatgttgattcatgacgtttaaggaaagaa------- Cluster: [ ] Orangutan: atggcttctttccttaaacctcatgaatcaacatttactagcttcTAGTTTATTTGTGTACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr12:73508132-73508141 Template switch process: F1: L TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT 1 F3: 4 ACTAGAAGCTAGTAAATGTTGATTCATGACGTTTAAGGAA R RF: TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTATGCAAATAAACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA RR: AAAGGAATTTGGAGTACTTAGTTGTAAATGATCGAAGATCATACGTTTATTTGATCTTCGATCATTTACAACTAAGTACTCCAAATTCCTT F2: 3 TACGTTTATT 2 Unidirectional alignment (log-probability: -39.1) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTttatttgcAT--------ACTAGAAGCTAGTAAATGTTGATTCATGAcGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT--------ATGCAAATAAACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA Template switch alignment (log-probability: -22.5) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|TTATTTGCAT|ACTAGAAGCTAGTAAATGTTGATTCATGAcGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|TTATTTGCAT|ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA Human > Chimp ------------- chr12:29986343-29986382 Template switch process: F1: L TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT 1 F3: 4 GTTTAAGGAA R RF: TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTTTATTTGCATACTAGAAGCTAGTAAATGTTGATTCATGACGTTTAAGGAA RR: AAAGGAATTTGGAGTACTTAGTTGTAAATGATCGAAGATCAAATAAACGTATGATCTTCGATCATTTACAACTAAGTACTGCAAATTCCTT F2: 3 GAGTACTTAGTTGTAAATGATCGAAGATCAAATAAACGTA 2 Unidirectional alignment (log-probability: -39.1) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT--------ATgcaaataaACTAGAAGCTAGTAAATGTTGATTCATGAgGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTTTATTTGCAT--------ACTAGAAGCTAGTAAATGTTGATTCATGACGTTTAAGGAA Template switch alignment (log-probability: -19.6) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|ATGCAAATAAACTAGAAGCTAGTAAATGTTGATTCATGAG|GTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|ATGCAAATAAACTAGAAGCTAGTAAATGTTGATTCATGAG|GTTTAAGGAA Gorilla > Chimp --------------- chr12:29986343-29986352 Template switch process: F1: L TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT 1 F3: 4 ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA R RF: TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTTTATTTGCATACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA RR: AAAGGAATTTGGAGTACTTAGTTGTAAATGATCGAAGATCAAATAAACGTATGATCTTCGATCATTTACAACTAAGTACTCCAAATTCCTT F2: 3 AATAAACGTA 2 Unidirectional alignment (log-probability: -32.6) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT--------ATgcaaataaACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTTTATTTGCAT--------ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA Template switch alignment (log-probability: -17) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|ATGCAAATAA|ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|ATGCAAATAA|ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA Chimp > Gorilla --------------- chr12:26284852-26284861 Template switch process: F1: L TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT 1 F3: 4 ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA R RF: TTTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTATGCAAATAAACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA RR: AAAGGAATTTGGAGTACTTAGTTGTAAATGATCGAAGATCATACGTTTATTTGATCTTCGATCATTTACAACTAAGTACTCCAAATTCCTT F2: 3 TACGTTTATT 2 Unidirectional alignment (log-probability: -32.6) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGTttatttgcAT--------ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT--------ATGCAAATAAACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA Template switch alignment (log-probability: -17) TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|TTATTTGCAT|ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA TTCCTTAAACCTCATGAATCAACATTTACTAGCTTCTAGT|TTATTTGCAT|ACTAGAAGCTAGTAAATGTTGATTCATGAGGTTTAAGGAA ========= Event 722 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGACATGGCACAGCAGCTGCGTGTATACCAGGAGCTGATGAATGTCAAGCTGGCCCTG---GACATCAAGACTGCCACCTACAAGAAGC ↓ 3 2 1 4 Chimp: AGGACATGGCACAGCAGCTGCGTGTATACCAGGAGCTGATGAATGTCAAGGTGGCCCTGGTATACACGCAGACTGCCACCTACAAGAAGC Gorilla: AGGACATGGCACAGCAGTTGCGTGTATACCAGGAGCTGATGAATATCAAGCTGGCCCTG---GACATCAAGACTGCCACATACAAGAAGC Human: AGGACATGGCACAGCAGCTGCGTGTATACCAGGAGCTGATGAATGTCAAGCTGGCCCTG---GACATCAAGACTGCCACCTACAAGAAGC Cluster: [ ] Orangutan: AGGACATGGCACAGCAGCTGCGTGTATACCAGGAGCTGATGAATGTCAAGCTGGCCCTG---GACATCAAAACTGCCACCTACAAGAAGC Human > Chimp ------------- chr12:109327493-109327501 Template switch process: F1: L CACAGCAGCTGCGTGTATACCAGGAGCTGATGAATGTCAAGGTGGCCCTGG 1 F3: 4 AGACTGCCACCTACAAGAAGCTGCTGGAGGGTGAAGAGAG R RF: CACAGCAGCTGCGTGTATACCAGGAGCTGATGAATGTCAAGCTGGCCCTGGACATCAAGACTGCCACCTACAAGAAGCTGCTGGAGGGTGAAGAGAG RR: GTGTCGTCGACGCACATATGGTCCTCGACTACTTACAGTTCGACCGGGACCTGTAGTTCTGACGGTGGATGTTCTTCGACGACCTCCCACTTCTCTC F2: 3 CGCACATAT 2 Unidirectional alignment (log-probability: -39.3) CGTGTATACCAGGAGCTGATGAATGTCAAGgTGGCCCTGGtatACAcgcAGACTGCCACCTACAAGAAGCTGCTGGAGGGTGAAGAGAG CGTGTATACCAGGAGCTGATGAATGTCAAGCTGGCCCTGG---ACATCAAGACTGCCACCTACAAGAAGCTGCTGGAGGGTGAAGAGAG Template switch alignment (log-probability: -22.6) CGTGTATACCAGGAGCTGATGAATGTCAAGgTGGCCCTGG|TATACACGC|AGACTGCCACCTACAAGAAGCTGCTGGAGGGTGAAGAGAG CGTGTATACCAGGAGCTGATGAATGTCAAGCTGGCCCTGG|TATACACGC|AGACTGCCACCTACAAGAAGCTGCTGGAGGGTGAAGAGAG ========= Event 723 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: gtctcgggtatgtctttatcagcagcatgaaaatggactaatacaGTAC----------------------------------------------------------------------------------ATAATTGTACATGTGTGTATGTGGTACATCCCCCACCTCATAGAAAATACCTGTAGTAACTCCATGGGAAAACTAACCTTAAAATATGA Chimp: gtctcaggtatgtctttatcagcagcatgaaaatggactaatacaGTAC----------------------------------------------------------------------------------ATAATTGTACATGTGTGTATGTGGTACATCCCCCACCTCATAGAAAATACCTGTAGTAACTCCATGGGAAAACTAACCTTAAAAGATGA ↓ 4 1 3 2 Gorilla: gtctcgggtatgtctttatcagcagcatgaaaatggactaatacaGTACTCCCATGGAGTTACTACAGGTATTTTCTATGAGGTGGGGGATGTACCACATACACACATGTACAGCAGCATGAAAATGGACTAATACAGTACATATGTGTATGTGGTACATCCCCCACCTCATTGAAAATACCTGTAGTAACTCCATGGGAAAACTAACCTTAAAAGATGA ↑ 4 1 3 2 Human: gtctcgggtatgtctttatcagcagcatgaaaatggactaatacaGTAC----------------------------------------------------------------------------------ATAATTGTACATGTGTGTATGTGGTACATCCCCCACCTCATAGAAAATACCTGTAGTAACTCCATGGGAAAACTAACCTTAAAATATGA Cluster: [ ] Orangutan: gtctcgggtatgtctttatcagcagcatgaaaacggactaatacaGTAC----------------------------------------------------------------------------------GTAATTGTACATGTGTGTATGTGGTACATCCCCCATCTCATGGAAAATACCTGTAGTAACTCCATGGGAAAACTAACCTTAAAAGATGA Human > Gorilla --------------- chr12:109215810-109215871 Template switch process: F1: L TATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC 1 F3: 4 CAGCAGCATGAAAATGGACTAATACAGTACATA----------TGTGTATGTGGTACATCCCCCACCTCATTGAAAATACCTG R RF: TATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTACATAATTGTACATGTGTGTATGTGGTACATCCCCCACCTCATAGAAAATACCTGTAGTAACTCCATGGGA RR: ATACAGAAATAGTCGTCGTACTTTTACCTGATTATGTCATGTATTAACATGTACACACATACACCATGTAGGGGGTGGAGTATCTTTTATGGACATCATTGAGGTACCCT F2: 3 ATGTACACACATACACCATGTAGGGGGTGGAGTATCTTTTATGGACATCATTGAGGTACCCT 2 Unidirectional alignment (log-probability: -157) ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC-----TcccatggagttactacaggtattttctatgaggtgggggatgtaccacatacacacatgtacagcagcatgaaaatggactaatacaGTACATaTGTGTAT ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTACATAATT---------------------------------------------------------------------------------------GTACATGTGTGTAT Template switch alignment (log-probability: -40) ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC|TCCCATGGAGTTACTACAGGTATTTTCTATGAGGTGGGGGATGTACCACATACACACATGTA|CAGCAGCATGAAAATGGACTAATACAGTACATA----------TGTGTAT ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC|TCCCATGGAGTTACTACAGGTATTTTCTATGAGGTGGGGGATGTACCACATACACACATGTA|CAGCAGCATGAAAATGGACTAATACAGTACATAATTGTACATGTGTGTAT Chimp > Gorilla --------------- chr12:109215810-109215871 Template switch process: F1: L TATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC 1 F3: 4 CAGCAGCATGAAAATGGACTAATACAGTACATA----------TGTGTATGTGGTACATCCCCCACCTCATTGAAAATACCTG R RF: TATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTACATAATTGTACATGTGTGTATGTGGTACATCCCCCACCTCATAGAAAATACCTGTAGTAACTCCATGGGA RR: ATACAGAAATAGTCGTCGTACTTTTACCTGATTATGTCATGTATTAACATGTACACACATACACCATGTAGGGGGTGGAGTATCTTTTATGGACATCATTGAGGTACCCT F2: 3 ATGTACACACATACACCATGTAGGGGGTGGAGTATCTTTTATGGACATCATTGAGGTACCCT 2 Unidirectional alignment (log-probability: -157) ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC-----TcccatggagttactacaggtattttctatgaggtgggggatgtaccacatacacacatgtacagcagcatgaaaatggactaatacaGTACATaTGTGTAT ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTACATAATT---------------------------------------------------------------------------------------GTACATGTGTGTAT Template switch alignment (log-probability: -40) ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC|TCCCATGGAGTTACTACAGGTATTTTCTATGAGGTGGGGGATGTACCACATACACACATGTA|CAGCAGCATGAAAATGGACTAATACAGTACATA----------TGTGTAT ATGTCTTTATCAGCAGCATGAAAATGGACTAATACAGTAC|TCCCATGGAGTTACTACAGGTATTTTCTATGAGGTGGGGGATGTACCACATACACACATGTA|CAGCAGCATGAAAATGGACTAATACAGTACATAATTGTACATGTGTGTAT ========= Event 724 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTACTCTCAATTAAGTCTTCAAGTAGTGCATTTTATTAAATAAGTCTCTCTCTAGTGTTTCCAATGTATTTTTTATAAATTTCTTCCCATTCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAAC--------------ATTCTATTTTATACATCTTGATGATATGTATAAAATGAGATG Chimp: AGTACTCTCAATTAAGTCTTCAAGTAGTGCATTTTATTAAATAAGTCTCTCTCTAGTGTTTCCAATGTATTTTTTATAAATTTCTCCCCATTCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAAC--------------ATTCTATTTTATACATCTT---GATATGTATAAAATGAGATG ↓ 3 2 1 4 Gorilla: AGTAGTCTCAATTAAGTCTTCAAGTAGTGCATTTTATTAAATAAGTCTCTCTCTAGTGTTTCCAATGTATTTTTTATAAATTTCTCCCCATTCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAAC----------------------------ATCTTGATGATATGTATAAAATGAGATG Human: AGTACTCTCAATTAAGTCTTCAAGTAGTGCATTTTATTAAATAAGTCTCTCTCTAGTGTTTCCAATGTATTTTTTATAAATTTCTTCCCATTCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAAC--------------ATTCTATTTTATACATCTTGATGATATGTATAAAATGAGATG Cluster: [ ] Orangutan: AGTACTCTCAATTCAGTCTTCAAGTAATGCATTTTATTAAATAAGTCTCTCTCTAGTGTTTCCAATGTATTTTTTATAAATTTCTCCCCATTCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAACATTCTATTTTATAC--------------ATCTTGATGATATGTATAAAATGAGGTG Chimp > Gorilla --------------- chr12:25586301-25586305 Template switch process: F1: L TCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAACAT 1 F3: 4 TGATATGTATAAAATGAGATGTTTAAAATTAACTATAAATT R RF: TCAAGTAGTGCATTTTATTAAATAAGTCTCTCTCTAGTGTTTCCAATGTATTTTTTATAAATTTCTCCCCATTCATCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAACATTCTATTTTATACATCTTGATATGTATAAAATGAGATGTTTAAAATTAACTATAAATT RR: AGTTCATCACGTAAAATAATTTATTCAGAGAGAGATCACAAAGGTTACATAAAAAATATTTAAAGAGGGGTAAGTAGTTTCGAGATTTGAGACGGAGAAAGGATGTTTTCTTGTAAGATAAAATATGTAGAACTATACATATTTTACTCTACAAATTTTAATTGATATTTAA F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -25.7) TCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAA--------------CATCTtgaTGATATGTATAAAATGAGATGTTTAAAATTAACTATAAAT TCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAACATTCTATTTTATACATCT---TGATATGTATAAAATGAGATGTTTAAAATTAACTATAAAT Template switch alignment (log-probability: -16.4) TCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAACAT|CTTGA|TGATATGTATAAAATGAGATGTTTAAAATTAACTATAAAT TCAAAGCTCTAAACTCTGCCTCTTTCCTACAAAAGAACAT|CTTGA|TGATATGTATAAAATGAGATGTTTAAAATTAACTATAAAT ========= Event 725 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAATTTAAGAGATCAATTCAGAAAATAACCCATGGGTTATTTTCTATCCTGGGGTAGACTTTTTAA ↑ 3 2 1 4 Chimp: GAATTTAAGAGATCAATTCAGAAAATAACCCATA----------AATCCTGGGGTAGACTTTTTAA Gorilla: GAATTTAAGAGATCAATTCAGAAAATAACCCATG----------AATCCTGGGGTAGACTTTTTAA ↓ 3 2 1 4 Human: GAATTTAAGAGATCAATTCAGAAAATAACCCATGGGTTATTTTCTATCCTGGGGTAGACTTTTTAA Cluster: [ ] Orangutan: GAATTTAAGAGATCAATTCAGAAAATAACCCATC----------AATCCTGGGATAGACTTTTTAA Chimp > Human ------------- chr12:72665406-72665417 Template switch process: F1: L CATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCAT 1 F3: 4 ATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA R RF: CATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATAAATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA RR: GTAATCATCTTAAATTCTCTAGTTAAGTCTTTTATTGGGTATTTAGGACCCCATCTGAAAAATTTCTAATATTTTTTCTTTCT F2: 3 TCTTTTATTGGG 2 Unidirectional alignment (log-probability: -37.3) ATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCAtgggttatttTctATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA ATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCA----------TAAATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA Template switch alignment (log-probability: -16.8) ATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCAT|GGGTTATTTTCT|ATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA ATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCAT|GGGTTATTTTCT|ATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA Gorilla > Human --------------- chr12:72665407-72665417 Template switch process: F1: L ATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATG 1 F3: 4 ATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA R RF: ATTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATGAATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA RR: TAATCATCTTAAATTCTCTAGTTAAGTCTTTTATTGGGTACTTAGGACCCCATCTGAAAAATTTCTAATATTTTTTCTTTCT F2: 3 TCTTTTATTGG 2 Unidirectional alignment (log-probability: -30.8) TTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATGggttattttctATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA TTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATG----------AATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA Template switch alignment (log-probability: -17.1) TTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATG|GGTTATTTTCT|ATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA TTAGTAGAATTTAAGAGATCAATTCAGAAAATAACCCATG|GGTTATTTTCT|ATCCTGGGGTAGACTTTTTAAAGATTATAAAAAAGAAAGA ========= Event 726 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: tgcttgttatACATAAGTATAAAAAAA-----------GGTTAtgaatacctttttatatacttatatatttatata Chimp: tgcttgttatacataagtatataaaaa-----------ggttatgaatacctttttatatacttatatatttatata Gorilla: tgcttgttatACATAAGTATATAAAAAGGTCTTCATAAGGTTAtgaatacctttttatatacttatatatttatata ↑ 1 4 3 2 Human: tgcttgttatACATAAGTATAAAAAAA-----------GGTTAtgaatacctttttatatacttatatatttatata Cluster: [ ] Orangutan: tgcttgttatACATAAGTATATAAAAA-----------GGttatgaatatctttttatatacttatatatttatata Human > Gorilla --------------- chr12:25147269-25147283 Template switch process: F1: L ATTGGTTCACAACTCACCAATGCTTGTTATACATAAGTATA 1 F3: 4 AAGGTTATGAATACCTTTTTATATACTTATATATTTATATAA R RF: ATTGGTTCACAACTCACCAATGCTTGTTATACATAAGTATAAAAAAAGGTTATGAATACCTTTTTATATACTTATATATTTATATAA RR: TAACCAAGTGTTGAGTGGTTACGAACAATATGTATTCATATTTTTTTCCAATACTTATGGAAAAATATATGAATATATAAATATATT F2: 3 TACTTCTGGAAAAAT 2 Unidirectional alignment (log-probability: -32.3) TTGGTTCACAACTCACCAATGCTTGTTATACATAAGTATAtAAAaaggtcttcatAAGGTTATGAATACCTTTTTATATACTTATATATTTATAT TTGGTTCACAACTCACCAATGCTTGTTATACATAAGTATAAAAA-----------AAGGTTATGAATACCTTTTTATATACTTATATATTTATAT Template switch alignment (log-probability: -23.2) TTGGTTCACAACTCACCAATGCTTGTTATACATAAGTATA|TAAAAAGGTcTTCAT|AAGGTTATGAATACCTTTTTATATACTTATATATTTATAT TTGGTTCACAACTCACCAATGCTTGTTATACATAAGTATA|TAAAAAGGTATTCAT|AAGGTTATGAATACCTTTTTATATACTTATATATTTATAT ========= Event 727 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: tatagacataagccatcatgcctagcTAAT----AAATATTTCTTggccgggcacggtggct Chimp: tatagacataagccatcatgcctagcTAAT----AAATATTTCTTggccgggcacggtggct Gorilla: tatagacataagccatcatgcctagcTAATGCTAGGCTAGTGCTTggccgggcacggtggct ↑ 3 2 1 4 Human: tatagacataagccatcatgcctagcTAAT----AAATATTTCTTggccgggcacggtggct Cluster: [ ] Orangutan: -------------------------------------------------------------- Human > Gorilla --------------- chr12:103589209-103589215 Template switch process: F1: L AGTGCTGGAATTATAGACATAAGCCATCATGCCTAGCTAAT 1 F3: 4 TAGTGCTTGGCCGGGCACGGTGGCTCATGCCTGTAATCCCAGCAT R RF: AGTGCTGGAATTATAGACATAAGCCATCATGCCTAGCTAATAAATATTTCTTGGCCGGGCACGGTGGCTCATGCCTGTAATCCCAGCAT RR: TCACGACCTTAATATCTGTATTCGGTAGTACGGATCGATTATTTATAAAGAACCGGCCCGTGCCACCGAGTACGGACATTAGGGTCGTA F2: 3 CGGATCG 2 Unidirectional alignment (log-probability: -38.3) GTGCTGGAATTATAGACATAAGCCATCATGCCTAGCTAA--------TgctaggctagtgCTTGGCCGGGCACGGTGGCTCATGCCTGTAATCCC GTGCTGGAATTATAGACATAAGCCATCATGCCTAGCTAATAAATATTT------------CTTGGCCGGGCACGGTGGCTCATGCCTGTAATCCC Template switch alignment (log-probability: -27.8) GTGCTGGAATTATAGACATAAGCCATCATGCCTAGCTAAT|GCTAGGC|TAgTgCTTGGCCGGGCACGGTGGCTCATGCCTGTAATCCC GTGCTGGAATTATAGACATAAGCCATCATGCCTAGCTAAT|GCTAGGC|TATTTCTTGGCCGGGCACGGTGGCTCATGCCTGTAATCCC ========= Event 728 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGCAATCAGATGGATGGCCGGTGCTCCTTATTCAT ↓ 3 2 1 4 Chimp: AGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGC-TTAGGAAACTTGGCCGGTGCTCCTTATTCAT ↑ 3 2 1 4 Gorilla: AGAGAGACGTCATCATTGCAGTTTCCAAAGTACTTGCAATCAGATGGATGGCCGGTGCTCCTTATTCAT Human: AGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGCAATCAGATGGATGGCCGGTGCTCCTTATTCAT Cluster: [ ] Orangutan: AGAAAGATGTCATCATTGCTGTTTCCTAAGTACTTGCAATCAGATGGATGGCCGGTGCTCCTTATTCAT Human > Chimp ------------- chr12:110620739-110620748 Template switch process: F1: L AACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGC 1 F3: 4 TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA R RF: AACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGCAATCAGATGGATGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA RR: TTGTTCTCTCTGCAGTAGTAACGTCAAAGGATTCATGAACGTTAGTCTACCTACCGGCCACGAGGAATAAGTACAGATGTAACTTCTGCGAT F2: 3 TCAAAGGATT 2 Unidirectional alignment (log-probability: -36.1) ACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGC-----------ttaggaaactTGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA ACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGCAATCAGATGGA----------TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA Template switch alignment (log-probability: -16.5) ACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGC|TTAGGAAACT|TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA ACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGC|TTAGGAAACT|TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA Gorilla > Chimp --------------- chr12:110620739-110620748 Template switch process: F1: L AACAAGAGAGACGTCATCATTGCAGTTTCCTAAGTACTTGC 1 F3: 4 TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA R RF: AACAAGAGAGACGTCATCATTGCAGTTTCCAAAGTACTTGCAATCAGATGGATGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA RR: TTGTTCTCTCTGCAGTAGTAACGTCAAAGGTTTCATGAACGTTAGTCTACCTACCGGCCACGAGGAATAAGTACAGATGTAACTTCTGCGAT F2: 3 TCAAAGGATT 2 Unidirectional alignment (log-probability: -41.1) ACAAGAGAGACGTCATCATTGCAGTTTCCtAAGTACTTGC-----------ttaggaaactTGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA ACAAGAGAGACGTCATCATTGCAGTTTCCAAAGTACTTGCAATCAGATGGA----------TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA Template switch alignment (log-probability: -28) ACAAGAGAGACGTCATCATTGCAGTTTCCtAAGTACTTGC|TTaGGAAACT|TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA ACAAGAGAGACGTCATCATTGCAGTTTCCAAAGTACTTGC|TTTGGAAACT|TGGCCGGTGCTCCTTATTCATGTCTACATTGAAGACGCTA ========= Event 729 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGAGTATGTCTTCCCTTGATTGTT---CACTTCACTACCGCTCAGCCTG---------------------------------ACTAAACAACGTATTGGATTTAGCCAATGAG Chimp: TTGAGTATGTCTTCCCTTGATTGTT---TA-----------GTCAGGCTG----------------------AGCGGTAGTGAAGTGAACAATGTACTGGATTTAGCCAATGAG Gorilla: TTGAGTATGTCTTCCCTTGATTGTT---TA-----------GTCAGGCTG-----------AGCGGTAGTGA-----------AATGAACAATGTATTGGATTTAGCCAATGAG ↑ 3 1 2 4 Human: TTGAGTATGTCTTCCCTTGATTGTT---CACTTCACTACCGCTCAGCCTG---------------------------------ACTAAACAACGTATTGGATTTAGCCAATGAG Cluster: [ ] Orangutan: TTGAGTATGTCTGACCTTGATTGTTTTAGA-----------GTCAGGCTGAGTGGTAGGGA----------------------AATGAACAATGTACTGGAGTTAGCCAATGAG Human > Gorilla --------------- chr12:110456936-110456967 Template switch process: F1: L AGGCAAGCAATACCTCTTGAGTATGTCTTCCCTTGATTGTT 1 F3: 4 GTATTGGATTTAGCCAATGAGTATAGTTGACTATTTTTGC R RF: AGGCAAGCAATACCTCTTGAGTATGTCTTCCCTTGATTGTTCACTTCACTACCGCTCAGCCTGACTAAACAACGTATTGGATTTAGCCAATGAGTATAGTTAACTATTTTTGC RR: TCCGTTCGTTATGGAGAACTCATACAGAAGGGAACTAACAAGTGAAGTGATGGCGAGTCGGACTGATTTGTTGCATAACCTAAATCGGTTACTCATATCAATTGATAAAAACG F2: 3 TAACAAGTAAAGTGATGGCGAGTCGGACTGAT 2 Unidirectional alignment (log-probability: -67.5) GGCAAGCAATACCTCTTGAGTATGTCTTCCCTTGATTGTT------------------------TAgtcaggctgagcggtagtgaaatgAACAAtGTATTGGATTTAGCCAATGAGTATAGTTgACTATTTTTGC GGCAAGCAATACCTCTTGAGTATGTCTTCCCTTGATTGTTCACTTCACTACCGCTCAGCCTGACTA------------------------AACAACGTATTGGATTTAGCCAATGAGTATAGTTAACTATTTTTGC Template switch alignment (log-probability: -30.8) GGCAAGCAATACCTCTTGAGTATGTCTTCCCTTGATTGTT|TAGTCAGGCTGAGCGGTAGTGAAaTGAACAAT|GTATTGGATTTAGCCAATGAGTATAGTTgACTATTTTTGC GGCAAGCAATACCTCTTGAGTATGTCTTCCCTTGATTGTT|TAGTCAGGCTGAGCGGTAGTGAAGTGAACAAT|GTATTGGATTTAGCCAATGAGTATAGTTAACTATTTTTGC ========= Event 730 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTT----CTGTTTGTCATAGTA-------ATACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATTTTTC Chimp: CTCTT----CTGTTTGTCATAACAAACATGTTCACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATTTTTC ↑ 1 4 3 2 Gorilla: CTCTT----CTGTTTGTCATAGTA-------ATACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATTTTTC Human: CTCTT----CTGTTTGTCATAGTA-------ATACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATTTTTC Cluster: [ ] Orangutan: CTCTTCTCTTTGTTTGTCATAGTA-------ATACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATTTTTC Gorilla > Chimp --------------- chr12:25147390-25147400 Template switch process: F1: L ATGACTGAGTCCTCTGAAACCTCTCTCTTCTGTTTGTCATA 1 F3: 4 CACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATT R RF: ATGACTGAGTCCTCTGAAACCTCTCTCTTCTGTTTGTCATAGTAATACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTATT RR: TACTGACTCAGGAGACTTTGGAGAGAGAAGACAAACAGTATCATTATGAAACCCACTTGTTGTACAACCAATTCAAAGAGACATAA F2: 3 TTGTACAAACA 2 Unidirectional alignment (log-probability: -37.6) TGACTGAGTCCTCTGAAACCTCTCTCTTCTGTTTGTCATAacAAacatgttcACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTAT TGACTGAGTCCTCTGAAACCTCTCTCTTCTGTTTGTCATAGTAA-------TACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTAT Template switch alignment (log-probability: -28.2) TGACTGAGTCCTCTGAAACCTCTCTCTTCTGTTTGTCATA|ACaAACATGTT|cACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTAT TGACTGAGTCCTCTGAAACCTCTCTCTTCTGTTTGTCATA|ACCAACATGTT|TACTTTGGGTGAACAACATGTTGGTTAAGTTTCTCTGTAT ========= Event 731 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGGACTGTTAAATGTCTGTTGCAGTCAAGTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAG ↑ 1 4 3 2 Chimp: GTGGACTGTTAAATGTCTGTTC------CCTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAG Gorilla: GTGGACTGTTAAATGTCTGTTC------CCTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAG Human: GTGGACTGTTAAATGTCTGTTGCAGTCAAGTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAG Cluster: [ ] Orangutan: GTGGACTGTTAAGTGTTTGTTC------CCTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAG Chimp > Human ------------- chr12:65653276-65653283 Template switch process: F1: L TCAGAAATTGCTGCTGTTAAGTGGACTGTTAAATGTCTGTTGC 1 F3: 4 TGCAGACAACTTGACTAAACTGACTTTAGATAGAAGTAT R RF: TCAGAAATTGCTGCTGTTAAGTGGACTGTTAAATGTCTGTTCCCTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAGTAT RR: AGTCTTTAACGACGACAATTCACCTGACAATTTACAGACAAGGGAACGTCTGTTGAACTGATTTGACTGAAATCTATCTTCATA F2: 3 TGAACTGA 2 Unidirectional alignment (log-probability: -31.6) GAAATTGCTGCTGTTAAGTGGACTGTTAAATGTCTGTTgCagtcaagTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAGTAT GAAATTGCTGCTGTTAAGTGGACTGTTAAATGTCTGTTCC------CTTGCAGACAACTTGACTAAACTGACTTTAGATAGAAGTAT Template switch alignment (log-probability: -22.3) GAAATTGCTGCTGTTAAGTGGACTGTTAAATGTCTGTTgC|AGTCAAGT|TGCAGACAACTTGACTAAACTGACTTTAGATAGAAGTAT GAAATTGCTGCTGTTAAGTGGACTGTTAAATGTCTGTTCC|AGTCAAGT|TGCAGACAACTTGACTAAACTGACTTTAGATAGAAGTAT ========= Event 732 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ctggtgctgaaTGTGAGTACT----AGTACT-------GTTTACTAAGGGAATACttttaaatgtttgtttttttaatgtgttgttgttttCTTTAAAATCAAGACCAGTTGTTACAAAGAAGTAACATGTTTTAATGTCATTGTCGTTTAAAAAATATTTTTACTTCTTAAAGTAGACTAGCCAAAAGGTCCCGAACTTGG Chimp: ctggtgctgaaTGTGAGTACT----AGTACTGTTTACTGTTTACTAAGGGAATACttttaaatgtttgtttttttaatgtgttgtttttttctttAAAATCAAGACCAGTTGTTACAAAGAGGTAACATGTTT-TATGTCATTGTCGTTTAAAAAATATTTTTACTTCTTAAAGTAGACTAGCCAAAAGGTCCCGAACTTGG ↓ 1 4 3 2 Gorilla: ctggtgctgaaTGTGAGTACTAGCTAGTACT-------GTTTACTAAAGGAATACttttaaatgtttgtttttttaatgtgttgtttttttctttAAAATCAAGACCAGTTGTTACAAAGAGGTAACATGTTT-TATGTCATTGTCGTTTAAAAAATATTTTTACTTCTTAAAGTAGACTAGCCAAAAGGTCCCGAACTTGG Human: ctggtgctgaaTGTGAGTACT----AGTACT-------GTTTACTAAGGGAATACttttaaatgtttgtttttttaatgtgttgttgttttCTTTAAAATCAAGACCAGTTGTTACAAAGAAGTAACATGTTTTAATGTCATTGTCGTTTAAAAAATATTTTTACTTCTTAAAGTAGACTAGCCAAAAGGTCCCGAACTTGG Cluster: [ ] Orangutan: ctggtgctgaaT--------------GTACT-------GTTTACTAAAGGAATAct-ttaaatgtttgttcttttaatgtgttgtttttttCTTTAAAATCAAGACCAGTTGTTACAAAGAGGTAACATGTTT-TATGTCATTGTCGTTTAAAAAATATTTTTACTTCTTAAAGTAGACTAGCCATAAGGTCCCGAACTTGG Chimp > Gorilla --------------- chr12:64225902-64225905 Template switch process: F1: L ATTGGAGTAAAGATGAGAGACTGGTGCTGAATGTGAGTACTAG 1 F3: 4 TACTGTTTACTAAAGGAATACTTTTAAATGTTTGTTTTTTTAATGTGTTGTTTT R RF: ATTGGAGTAAAGATGAGAGACTGGTGCTGAATGTGAGTACTAGTACTGTTTACTGTTTACTAAGGGAATACTTTTAAATGTTTGTTTTTTTAATGTGTTGTTTTTTTCTTTAAAATCAAGACCAGTTGTTACAAAGAGGTAACATGTTTTATGTCATTGTCGTTTAAAAAATATTTTTACTTCTTAAAGTAGACTAG RR: TAACCTCATTTCTACTCTCTGACCACGACTTACACTCATGATCATGACAAATGACAAATGATTCCCTTATGAAAATTTACAAACAAAAAAATTACACAACAAAAAAAGAAATTTTAGTTCTGGTCAACAATGTTTCTCCATTGTACAAAATACAGTAACAGCAAATTTTTTATAAAAATGAAGAATTTCATCTGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -32.5) GGAGTAAAGATGAGAGACTGGTGCTGAATGTGAGTACTAG-------ctagTACTGTTTACTAAaGGAATACTTTTAAATGTTTGTTTTTT GGAGTAAAGATGAGAGACTGGTGCTGAATGTGAGTACTAGTACTGTT----TACTGTTTACTAAGGGAATACTTTTAAATGTTTGTTTTTT Template switch alignment (log-probability: -22.1) GGAGTAAAGATGAGAGACTGGTGCTGAATGTGAGTACTAG|CTAG|TACTGTTTACTAAaGGAATACTTTTAAATGTTTGTTTTTT GGAGTAAAGATGAGAGACTGGTGCTGAATGTGAGTACTAG|CTAG|TACTGTTTACTAAGGGAATACTTTTAAATGTTTGTTTTTT ========= Event 733 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCCAATTTATGAAACACAAGTTATCC ↓ 31 2 4 Chimp: ACTTCATTTTGGAAGACTACGAATTTCAAT-----------------CCGTTTATGAAACACAAGTTATCC ↑ 31 2 4 Gorilla: ACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCTAATTTATGAAACACAAGTTATCC Human: ACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCCAATTTATGAAACACAAGTTATCC Cluster: [ ] Orangutan: ACTTCATTTTGGAAGACTATGGATTGAAATTTTTTAATAAAAATTTCTAATTTATGAAACACAAGTTATCC Human > Chimp ------------- chr12:114642131-114642142 Template switch process: F1: L AAGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG 1 F3: 4 TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG R RF: AAGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCCAATTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG RR: TTCCCCTTGGAGTACAAACTTGAAGTAAAACCTTCTGATGCCTAACTTTAAAAAATTATTTTTAAAGGTTAAATACTTTGTGTTCAATAGGTTTATTACGGAGGTAGGTC F2: 3 GCCTAACTTTAA 2 Unidirectional alignment (log-probability: -36.9) AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG---------------------------AATTTcaatccgtttATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCCAATTT----------ATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG Template switch alignment (log-probability: -16.8) AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG|AATTTCAATCCG|TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG|AATTTCAATCCG|TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG Gorilla > Chimp --------------- chr12:114642131-114642142 Template switch process: F1: L AAGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG 1 F3: 4 TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG R RF: AAGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCTAATTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG RR: TTCCCCTTGGAGTACAAACTTGAAGTAAAACCTTCTGATGCCTAACTTTAAAAAATTATTTTTAAAGATTAAATACTTTGTGTTCAATAGGTTTATTACGGAGGTAGGTC F2: 3 GCCTAACTTTAA 2 Unidirectional alignment (log-probability: -36.4) AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG---------------------------AAtttcaatccgTTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACGGATTGAAATTTTTTAATAAAAATTTCTAA----------TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG Template switch alignment (log-probability: -17.3) AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG|AATTTCAATCCG|TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG AGGGGAACCTCATGTTTGAACTTCATTTTGGAAGACTACG|AATTTCAATCCG|TTTATGAAACACAAGTTATCCAAATAATGCCTCCATCCAG ========= Event 734 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGCCTGGAAGCTGGTAAAGCTTAAAAGATACAGACTGGACCCGAGGCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGC------------TCACTTGAGTGTGCCATGAATGT Chimp: GGGCCTGGAAGCTGGTAAAGCTTAAAAGATACAGACTGGACCCGAGGCACTGAGTTGGTTTAATACTGTGAGCTGAAATGTGGGTGC------------TCACTTGAGTGTGCCATGAATAT ↓ 3 2 4 1 Gorilla: GGGCCTGGAAGCTGGTAAAGCTTAAAAGATACAGACTGGACCCGAGGCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCATTTTAAGCCTCACTTGAGTGTGCCATGAATAT ↑ 3 2 4 1 Human: GGGCCTGGAAGCTGGTAAAGCTTAAAAGATACAGACTGGACCCGAGGCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGC------------TCACTTGAGTGTGCCATGAATGT Cluster: [ ] Orangutan: GGGCCTGGAAGCTGGGAAAGCTTAAAAGATACAGACTGGACCTG-AGCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCATTTTAAGGATCACTTGAGTGTACCAT-CATAT Human > Gorilla --------------- chr12:67027076-67027083 Template switch process: F1: L GCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCA 1 F3: 4 CTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAAG R RF: GCTTAAAAGATACAGACTGGACCCGAGGCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCACTTGAGTGTGCCATGAATGTGAAAATGCATTTCCAAG RR: CGAATTTTCTATGTCTGACCTGGGCTCCGTGACTCAACCAAATTATGACACTCGACGTTACACCCACGAGTGAACTCACACGGTACTTACACTTTTACGTAAAGGTTC F2: 3 CGAATTTT 2 Unidirectional alignment (log-probability: -33.7) TGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGctcattttaagcCTCACTTGAGTGTGCCATGAATaTGAAAATGCATTTCCAA TGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTG------------CTCACTTGAGTGTGCCATGAATGTGAAAATGCATTTCCAA Template switch alignment (log-probability: -22.4) TGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCA|TTTTAAGC|CTCACTTGAGTGTGCCATGAATaTGAAAATGCATTTCCAA TGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCA|TTTTAAGC|CTCACTTGAGTGTGCCATGAATGTGAAAATGCATTTCCAA Chimp > Gorilla --------------- chr12:67027076-67027083 Template switch process: F1: L GCACTGAGTTGGTTTAATACTGTGAGCTGCAATGTGGGTGCTCA 1 F3: 4 CTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAAG R RF: GCTTAAAAGATACAGACTGGACCCGAGGCACTGAGTTGGTTTAATACTGTGAGCTGAAATGTGGGTGCTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAAG RR: CGAATTTTCTATGTCTGACCTGGGCTCCGTGACTCAACCAAATTATGACACTCGACTTTACACCCACGAGTGAACTCACACGGTACTTATACTTTTACGTAAAGGTTC F2: 3 CGAATTTT 2 Unidirectional alignment (log-probability: -33.7) TGAGTTGGTTTAATACTGTGAGCTGcAATGTGGGTGctcattttaagcCTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAA TGAGTTGGTTTAATACTGTGAGCTGAAATGTGGGTG------------CTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAA Template switch alignment (log-probability: -22.4) TGAGTTGGTTTAATACTGTGAGCTGcAATGTGGGTGCTCA|TTTTAAGC|CTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAA TGAGTTGGTTTAATACTGTGAGCTGAAATGTGGGTGCTCA|TTTTAAGC|CTCACTTGAGTGTGCCATGAATATGAAAATGCATTTCCAA ========= Event 735 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAAACCATGTACCCACAGTCAACAATTTCAACTCTGAACTTCAAATGCAACAATTTCAACTCTGAACTTCAATTT-------TATATATAAAATCAGCATGCCAGGTGTTGGCTTACACT ↑ 4 1 3 2 Chimp: CAAAACCATGTACCCACAGTC----------------------------AACAATTTCAACTCTGAACTTCAATTT-------TATATATAAAATCAGCATGCCAGGTGTTGGCTTACACT Gorilla: -------------------------------------------------------------------ATTCAATTT--------------TAAATCAGCATGCCAGGTGTTGGCTTACACT Human: CAAAACCATGTACCCACAGTCAACAATTTCAACTCTGAACTTCAAATGCAACAATTTCAACTCTGAACTTCAATTT-------TATATATAAAATCAGCATGCCAGGTGTTGGCTTACACT Cluster: [ ] Orangutan: -------------------------------------------------------------------CTTCAATTTTATATAT-------AAAATCAGCATGCCAGGTGTTGGCTTACACT Chimp > Human ------------- chr12:63713988-63713991 Template switch process: F1: L ATAGCCAAAATGAACATTTCCAAAACCATGTACCCACAGTCAACAATTTCAACTCTGAACTTCAA 1 F3: 4 AACAATTTCAACTCTGAACTTCAATTTTATATATAAAATC R RF: ATAGCCAAAATGAACATTTCCAAAACCATGTACCCACAGTCAACAATTTCAACTCTGAACTTCAATTTTATATATAAAATCAGCAT RR: TATCGGTTTTACTTGTAAAGGTTTTGGTACATGGGTGTCAGTTGTTAAAGTTGAGACTTGAAGTTAAAATATATATTTTAGTCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -51.2) CCATGTACCCACAGTCAACAATTTCAACTCTGAACTTcaaatgcaacaatttcaactctgaacttCAATTTTATATATAAAATC CCATGTACCCACAGTCAACAATTTCAACTCTGAACTT----------------------------CAATTTTATATATAAAATC Template switch alignment (log-probability: -16.2) CCATGTACCCACAGTCAACAATTTCAACTCTGAACTTCAA|ATGC|AACAATTTCAACTCTGAACTTCAATTTTATATATAAAATC CCATGTACCCACAGTCAACAATTTCAACTCTGAACTTCAA|ATGC|AACAATTTCAACTCTGAACTTCAATTTTATATATAAAATC ========= Event 736 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATCAGTTCAAGTCATCCTTAAATT----TTTAAAGTTCAATTGTAATACCTTATTAAAATAGA ↓ 1 4 3 2 Chimp: TATCAGTTCAAGTCATCCTTACAATTGAACTTAAAGTTCAATTGTAATACCTTATTAAAATAGA ↑ 1 4 3 2 Gorilla: TATCAGTTCAAGTCATCCTTAAATT----TTTAAAGTTCAATTGTAATACCTTATTAAAATAGA Human: TATCAGTTCAAGTCATCCTTAAATT----TTTAAAGTTCAATTGTAATACCTTATTAAAATAGA Cluster: [ ] Orangutan: TATCAGTTCAAGTCATCCTTAAATT----TTTAAAGTTCAATTGTAATACCTTATTAAAATAGA Human > Chimp ------------- chr12:65314757-65314765 Template switch process: F1: L CTTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTA 1 F3: 4 TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC R RF: CTTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTAAATTTTTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC RR: GAATGTAAATATTGTTTTTAATAGTCAAGTTCAGTAGGAATTTAAAAATTTCAAGTTAACATTATGGAATAATTTTATCTAGAAAG F2: 3 CAAGTTAAC 2 Unidirectional alignment (log-probability: -28.7) TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTAcAaTTgaacTTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTAAATTT----TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC Template switch alignment (log-probability: -16.4) TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTA|CAATTGAAC|TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTA|CAATTGAAC|TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC Gorilla > Chimp --------------- chr12:65314757-65314765 Template switch process: F1: L CTTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTA 1 F3: 4 TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC R RF: CTTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTAAATTTTTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC RR: GAATGTAAATATTGTTTTTAATAGTCAAGTTCAGTAGGAATTTAAAAATTTCAAGTTAACATTATGGAATAATTTTATCTAGAAAG F2: 3 CAAGTTAAC 2 Unidirectional alignment (log-probability: -27.7) TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTAcAaTTgaacTTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTAAATTT----TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC Template switch alignment (log-probability: -16.9) TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTA|CAATTGAAC|TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC TTACATTTATAACAAAAATTATCAGTTCAAGTCATCCTTA|CAATTGAAC|TTAAAGTTCAATTGTAATACCTTATTAAAATAGATCTTTC ========= Event 737 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA----TGATCTTCCCAGAATTATTTTTTACCAT ↑ 3 2 1 4 Chimp: AATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA--CTTGG-TAACCCAGAATTATTCTTTACCAT Gorilla: AATAGGGAAATGCTTTGGGAAGATCATAGAGGGGTTACT--CGG-TAACCCAGAATTATTTTTTACCAT ↓ 3 2 1 4 Human: AATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA----TGATCTTCCCAGAATTATTTTTTACCAT Cluster: [ ] Orangutan: AATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTACT--CAG-TAACCCAGAATTGTTTTTTACCAT Chimp > Human ------------- chr12:63838240-63838246 Template switch process: F1: L GGCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA 1 F3: 4 CCCAGAATTATTTTTTACCATTCTTAAAGGTAGGCACCAG R RF: GGCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTACTTGGTAACCCAGAATTATTCTTTACCATTCTTAAAGGTAGGCACCAG RR: CCGTTTATCCCTTTACGAAACCCTTCTAGTATTTCCCCAATGAACCATTGGGTCTTAATAAGAAATGGTAAGAATTTCCATCCGTGGTC F2: 3 TTCTAGT 2 Unidirectional alignment (log-probability: -33.2) GCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTAtgatCTT-----CCCAGAATTATTtTTTACCATTCTTAAAGGTAGGCACCAG GCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA----CTTGGTAACCCAGAATTATTCTTTACCATTCTTAAAGGTAGGCACCAG Template switch alignment (log-probability: -22.1) GCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA|TGATCTT|CCCAGAATTATTtTTTACCATTCTTAAAGGTAGGCACCAG GCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA|TGATCTT|CCCAGAATTATTCTTTACCATTCTTAAAGGTAGGCACCAG Gorilla > Human --------------- chr12:63838240-63838246 Template switch process: F1: L TCATGAAGTGGCAAATAGGGAAATGCTTTGGGAAGATCATAAAGGGGTTA 1 F3: 4 CCCAGAATTATTTTTTACCATTCTTAAAGGTAGGCACCAG R RF: TCATGAAGTGGCAAATAGGGAAATGCTTTGGGAAGATCATAGAGGGGTTACTCGGTAACCCAGAATTATTTTTTACCATTCTTCAAGGTAGGCACCAG RR: AGTACTTCACCGTTTATCCCTTTACGAAACCCTTCTAGTATCTCCCCAATGAGCCATTGGGTCTTAATAAAAAATGGTAAGAAGTTCCATCCGTGGTC F2: 3 TTCTAGT 2 Unidirectional alignment (log-probability: -42.3) GCAAATAGGGAAATGCTTTGGGAAGATCATAaAGGGGTT--------AtgatcttCCCAGAATTATTTTTTACCATTCTTaAAGGTAGGCACCAG GCAAATAGGGAAATGCTTTGGGAAGATCATAGAGGGGTTACTCGGTAA-------CCCAGAATTATTTTTTACCATTCTTCAAGGTAGGCACCAG Template switch alignment (log-probability: -27.9) GCAAATAGGGAAATGCTTTGGGAAGATCATAaAGGGGTTA|TGATCTT|CCCAGAATTATTTTTTACCATTCTTaAAGGTAGGCACCAG GCAAATAGGGAAATGCTTTGGGAAGATCATAGAGGGGTTA|TGATCTT|CCCAGAATTATTTTTTACCATTCTTCAAGGTAGGCACCAG ========= Event 738 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 156 Detected in comparisons: 1256 Multiple sequence alignment: Human: ATGGAAGATTGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCC-------------------AGTTTAAGA---AAGATCTCTGTG ↑ 13 2 4 Chimp: ATGGAAGATTGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCACTGGATGCTCTCTTAAGATCTCTTAAGA---AAGATCTCTGTG ↓ 13 2 4 ↑ 4 3 1 2 Gorilla: ATGGAAGATTGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCC-------------------AGTTTAAGA---AAGATCTCTGTG Human: ATGGAAGATTGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCC-------------------AGTTTAAGA---AAGATCTCTGTG Cluster: [ ] Orangutan: ATGGAAGATTGCCTTCCTTTCTTAAGATCTCTAAAAGAGTACTGAGCATCC-------------------AGTTTAAGAAAGAAGATCTCTGTG Chimp > Human ------------- chr12:60587108-60587111 Template switch process: F1: L TGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC 1 F3: 4 TTAAGAAAGATCTCTGTGATAAGAAGCCCACCGCAGTTTT R RF: TGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCACTGGATGCTCTCTTAAGATCTCTTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT RR: ACGGAAGGAAGGAATTCTAGAGATTTTCTCATGACTCGTAGTGACCTACGAGAGAATTCTAGAGAATTCTTTCTAGAGACACTATTCTTCGGGTGTCGTCAAAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -32.6) GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC----------------------CagtTTAAGAAAGATCTCTGTGATAAGAAGCCCACcGCAGTTTT GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCACTGGATGCTCTCTTAAGATCTC---TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT Template switch alignment (log-probability: -21.8) GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC|CAGT|TTAAGAAAGATCTCTGTGATAAGAAGCCCACcGCAGTTTT GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC|CAGT|TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT Gorilla > Chimp --------------- chr12:62298931-62298941 Template switch process: F1: L TGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC 1 F3: 4 TCTTAAGATCTC-----------------------TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT R RF: TGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCCAGTTTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT RR: ACGGAAGGAAGGAATTCTAGAGATTTTCTCATGACTCGTAGGTCAAATTCTTTCTAGAGACACTATTCTTCGGGTGTCGTCAAAA F2: 3 CTCGTAGGTCA 2 Unidirectional alignment (log-probability: -52.4) GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCactggatgctctcttaagatctC---TTAAGAAAGATCTCTGTGATAAGAAGCC GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC----------------------CAGTTTAAGAAAGATCTCTGTGATAAGAAGCC Template switch alignment (log-probability: -33.9) GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC|ACTGGATGCTC|tCTTAAGATCTC-----------------------TTAAGAAAGATCTCTGTGATAAGAAGCC GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC|ACTGGATGCTC|CCTTAAGATCTCTAAAAGAGTACTGAGCATCCAGTTTAAGAAAGATCTCTGTGATAAGAAGCC Chimp > Gorilla --------------- chr12:61581537-61581540 Template switch process: F1: L TGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC 1 F3: 4 TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT R RF: TGCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCACTGGATGCTCTCTTAAGATCTCTTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT RR: ACGGAAGGAAGGAATTCTAGAGATTTTCTCATGACTCGTAGTGACCTACGAGAGAATTCTAGAGAATTCTTTCTAGAGACACTATTCTTCGGGTGTCGTCAAAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -26.1) GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC----------------------CagtTTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATCACTGGATGCTCTCTTAAGATCTC---TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT Template switch alignment (log-probability: -16.2) GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC|CAGT|TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT GCCTTCCTTCCTTAAGATCTCTAAAAGAGTACTGAGCATC|CAGT|TTAAGAAAGATCTCTGTGATAAGAAGCCCACAGCAGTTTT ========= Event 739 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAATATAAGCACACATCACT-----------TAAGCATAGACACTAAAGAAGGTTCAATTTGGAGT ↓ 41 3 2 Chimp: AAAATATAAGCACACATCACTTATAGTGTCTATAAGCATAGACACTAAAGAAGGTTCCATTTGGAGT Gorilla: AAAATATAAGCACACATCACT-----------TAAGCATAGACACTAAAGAAGGTTCCATTTGGAGT Human: AAAATATAAGCACACATCACT-----------TAAGCATAGACACTAAAGAAGGTTCAATTTGGAGT Cluster: [ ] Orangutan: AAAATATAAGCACACATCACT-----------TAAGCATAGACACTAAAGAAGATTCCATTTGGAGT Human > Chimp ------------- chr12:62192971-62192979 Template switch process: F1: L TTCAGGTAAATGAGGTCCTAAAAATATAAGCACACATCACTTA 1 F3: 4 TAAGCATAGACACTAAAGAAGGTTCCATTTGGAGTCTTTT R RF: TTCAGGTAAATGAGGTCCTAAAAATATAAGCACACATCACTTAAGCATAGACACTAAAGAAGGTTCAATTTGGAGTCTTTT RR: AAGTCCATTTACTCCAGGATTTTTATATTCGTGTGTAGTGAATTCGTATCTGTGATTTCTTCCAAGTTAAACCTCAGAAAA F2: 3 ATCTGTGAT 2 Unidirectional alignment (log-probability: -32.7) AGGTAAATGAGGTCCTAAAAATATAAGCACACATCACTtatagtgtctaTAAGCATAGACACTAAAGAAGGTTCcATTTGGAGTCTTTT AGGTAAATGAGGTCCTAAAAATATAAGCACACATCACT-----------TAAGCATAGACACTAAAGAAGGTTCAATTTGGAGTCTTTT Template switch alignment (log-probability: -22.4) AGGTAAATGAGGTCCTAAAAATATAAGCACACATCACTTA|TAGTGTCTA|TAAGCATAGACACTAAAGAAGGTTCcATTTGGAGTCTTTT AGGTAAATGAGGTCCTAAAAATATAAGCACACATCACTTA|TAGTGTCTA|TAAGCATAGACACTAAAGAAGGTTCAATTTGGAGTCTTTT ========= Event 740 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATCACATATAGTTCAACAATAT----------------TGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGATACA--AGAAGAAAATTCTGGAATCT----------TAATAAGAGTCATTGTTGTTATTATTTAATATACAATGCTAACAATAATAATTTTCTCA Chimp: TGATCACATATAATTCAACAATAT----------------TGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGAAA--CAAGAAGAAAATTCTGGAATCT-----TAATTTAATAAGAGTCATTGTTGTTATTATTTAATATACAATGCTAACAATAATAATTTTCTCA ↓ 4 1 3 2 Gorilla: TGATCACATATAGTTCAACAATATTGAAAGAGCATAAAATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGATACA--AGAAGAAAATTCTAGAATCTTAATT-----TAATAAGAGTCATTGTTGTTATTATTTAATATACAATGCTAACAATAATAATTTTCTCA ↑ 4 1 3 2 Human: TGATCACATATAGTTCAACAATAT----------------TGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGATACA--AGAAGAAAATTCTGGAATCT----------TAATAAGAGTCATTGTTGTTATTATTTAATATACAATGCTAACAATAATAATTTTCTCA Cluster: [ ] Orangutan: TGATCACATATAGTTCAACATTATTGAAAGAGTATAAAATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGATACA--AGAAGAAAATTCTGGAACCTTAATT-----TAATAACAGTCATTGTTATTATTATTTAATATACAATGCTAACAGTAATAATTTTCTCA Human > Gorilla --------------- chr12:61666665-61666668 Template switch process: F1: L TTTATATTTTGTTAAAATGATCACATATAGTTCAACAATATTGAAAGA 1 F3: 4 AAAATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTG R RF: TTTATATTTTGTTAAAATGATCACATATAGTTCAACAATATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGATACAAGAAGAAAATTCTGGAATCTTAATAAGAGTCATTGTTGTTATTATTTAATATACAATGC RR: AAATATAAAACAATTTTACTAGTGTATATCAAGTTGTTATAACTTTCTTAATCTTTAAAGAGAAGTCATTCTCTTGGTGACTATGTTCTTCTTTTAAGACCTTAGAATTATTCTCAGTAACAACAATAATAAATTATATGTTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -33.9) TTGTTAAAATGATCACATATAGTTCAACAATattgaaagagcataaaATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC TTGTTAAAATGATCACATATAGTTCAACAAT----------------ATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC Template switch alignment (log-probability: -22) TTGTTAAAATGATCACATATAGTTCAACAATATTGAAAGA|GCAT|AAaATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC TTGTTAAAATGATCACATATAGTTCAACAATATTGAAAGA|GCAT|AATATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC Chimp > Gorilla --------------- chr12:61666665-61666668 Template switch process: F1: L TTTATATTTTGTTAAAATGATCACATATAGTTCAACAATATTGAAAGA 1 F3: 4 AAAATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTG R RF: TTTATATTTTGTTAAAATGATCACATATAATTCAACAATATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAACCACTGAAACAAGAAGAAAATTCTGGAATCTTAATTTAATAAGAGTCATTGTTGTTATTATTTAATATACAATGC RR: AAATATAAAACAATTTTACTAGTGTATATTAAGTTGTTATAACTTTCTTAATCTTTAAAGAGAAGTCATTCTCTTGGTGACTTTGTTCTTCTTTTAAGACCTTAGAATTAAATTATTCTCAGTAACAACAATAATAAATTATATGTTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -39.4) TTGTTAAAATGATCACATATAgTTCAACAATattgaaagagcataaaATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC TTGTTAAAATGATCACATATAATTCAACAAT----------------ATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC Template switch alignment (log-probability: -27.6) TTGTTAAAATGATCACATATAgTTCAACAATATTGAAAGA|GCAT|AAaATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC TTGTTAAAATGATCACATATAATTCAACAATATTGAAAGA|GCAT|AATATTGAAAGAATTAGAAATTTCTCTTCAGTAAGAGAAC ========= Event 741 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGCTTCATATTTAAACATTA------TTGTACAAAATATAATTTTACCTAAACTT ↓ 13 42 Chimp: TTGCTTCATATTTAAACATTA---TTTTTGTAC-AAATATAATTTTACCTAAACTT Gorilla: TTGCTTCATATTTAAACATTATTA---TTGTACAAAATATAATTTTACCTAAACTT Human: TTGCTTCATATTTAAACATTA------TTGTACAAAATATAATTTTACCTAAACTT Cluster: [ ] Orangutan: TTGCTTCATATTTAAACATTATTT---TTGTACAAATTA-TATTTTACCTAAACTT Human > Chimp ------------- chr12:61564520-61564526 Template switch process: F1: L TTCATATATTATATTTTAGTTTGCTTCATATTTAAACATTATT 1 F3: 4 AAATATAATTTTACCTAAACTTATGTCTTTCTCTTTATTC R RF: TTTATATATTATATTTTAGTTTGCTTCATATTTAAACATTATTGTACAAAATATAATTTTACCTAAACTTATGTCTTTCTCTTTATTC RR: AAATATATAATATAAAATCAAACGAAGTATAAATTTGTAATAACATGTTTTATATTAAAATGGATTTGAATACAGAAAGAGAAATAAG F2: 3 CATGTTT 2 Unidirectional alignment (log-probability: -31.5) ATATATTATATTTTAGTTTGCTTCATATTTAAACATTAtttTTGTAC-AAATATAATTTTACCTAAACTTATGTCTTTCTCTTTATTC ATATATTATATTTTAGTTTGCTTCATATTTAAACATTA---TTGTACAAAATATAATTTTACCTAAACTTATGTCTTTCTCTTTATTC Template switch alignment (log-probability: -22.2) ATATATTATATTTTAGTTTGCTTCATATTTAAACATTATT|TTTGTAC|AAATATAATTTTACCTAAACTTATGTCTTTCTCTTTATTC ATATATTATATTTTAGTTTGCTTCATATTTAAACATTATT|TTTGTAC|AAATATAATTTTACCTAAACTTATGTCTTTCTCTTTATTC ========= Event 742 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: tatgagcatctcgatctagttata----gaagtcagaagtttatgatggactgatt Chimp: TATGAGCATCTCGATCTAGTTCTGACTTCTAGTCAGAAGTTTATGATGGACTGATT ↑ 1 3 4 2 Gorilla: TATGAGCATCTCGATCTAGTTATA----GGAGTCAGAAGTTTATGATGGACTGATT Human: tatgagcatctcgatctagttata----gaagtcagaagtttatgatggactgatt Cluster: [ ] Orangutan: tatgagcatctcgatctagttata----gaagtcagaagtttatgatggactgatt Gorilla > Chimp --------------- chr12:61594808-61594816 Template switch process: F1: L TAATAGACTCTTATTGGTCATATGAGCATCTCGATCTAGTT 1 F3: 4 AGTCAGAAGTTTATGATGGACTGATTCCAAGATACATTGT R RF: TAATAGACTCTTATTGGTCATATGAGCATCTCGATCTAGTTATAGGAGTCAGAAGTTTATGATGGACTGATTCCAAGATACATTGT RR: ATTATCTGAGAATAACCAGTATACTCGTAGAGCTAGATCAATATCCTCAGTCTTCAAATACTACCTGACTAAGGTTCTATGTAACA F2: 3 TCTTCAGTC 2 Unidirectional alignment (log-probability: -33.8) AATAGACTCTTATTGGTCATATGAGCATCTCGATCTAGTT-----ctgacttctAGTCAGAAGTTTATGATGGACTGATTCCAAGATACATTGT AATAGACTCTTATTGGTCATATGAGCATCTCGATCTAGTTATAGG---------AGTCAGAAGTTTATGATGGACTGATTCCAAGATACATTGT Template switch alignment (log-probability: -22.4) AATAGACTCTTATTGGTCATATGAGCATCTCGATCTAGTT|CTGACTtCT|AGTCAGAAGTTTATGATGGACTGATTCCAAGATACATTGT AATAGACTCTTATTGGTCATATGAGCATCTCGATCTAGTT|CTGACTCCT|AGTCAGAAGTTTATGATGGACTGATTCCAAGATACATTGT ========= Event 743 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CTCTTTGGGTTTTGAAAAAGCTGATGGTTTAAACAAATTTACTTATTATTTTTTGGCTTTAGTTTTAGGATATCTTGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTATCAAGCTTGAATGGCTATTCTCAGAATAGCTTTATAT ↓ 3 2 1 4 Chimp: CTCTTTGGGTTTTGAAAAAGCTGATTGTTTAAACAAATTTACTTATTATTTTTTGGCTTTAGTTTTAGGATATCTTTCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTAATCAG----------CATTCTCAGAATAGCTTTATAT Gorilla: CTCTTTGGGTTTTGAAAAAGCTGATGGTTTAAACAAATTTACTTATGATTTTTTGGCTTTAGTTTTAGGATATCTTGCATGGCAAATTTATTGTGTTGCTTTGATATAGCTATTAATCAG----------CATTCTCAGAATAGCTTTATAT ↑ 3 2 1 4 Human: CTCTTTGGGTTTTGAAAAAGCTGATGGTTTAAACAAATTTACTTATTATTTTTTGGCTTTAGTTTTAGGATATCTTGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTATCAAGCTTGAATGGCTATTCTCAGAATAGCTTTATAT Cluster: [ ] Orangutan: CTCTTTGGGTTTTGAAAAAGCTGATGGTTTAAAGAAATTTACTTATTATTTTTTGGCTTTAATTTTAGGATATCTTGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTAATCAG----------CATTCTCAGAATAGCTTTATAT Human > Chimp ------------- chr12:74192787-74192792 Template switch process: F1: L TTTCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTA 1 F3: 4 ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA R RF: GCTGATGGTTTAAACAAATTTACTTATTATTTTTTGGCTTTAGTTTTAGGATATCTTGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTATCAAGCTTGAATGGCTATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA RR: CGACTACCAAATTTGTTTAAATGAATAATAAAAAACCGAAATCAAAATCCTATAGAACGTACCGTTTAAATAACACAACGGAACTATATCGATAATAGTTCGAACTTACCGATAAGAGTCTTATCGAAATATAAATAATGTTCGTTAAACAT F2: 3 CGACTA 2 Unidirectional alignment (log-probability: -35.5) TtCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTAatcAGC----------ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA TGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTATCAAGCTTGAATGGCTATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA Template switch alignment (log-probability: -22) TtCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTA|ATCAGC|ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA TGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTA|ATCAGC|ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA Human > Gorilla --------------- chr12:71209450-71209455 Template switch process: F1: L TTGCATGGCAAATTTATTGTGTTGCTTTGATATAGCTATTA 1 F3: 4 ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA R RF: GCTGATGGTTTAAACAAATTTACTTATTATTTTTTGGCTTTAGTTTTAGGATATCTTGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTATCAAGCTTGAATGGCTATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA RR: CGACTACCAAATTTGTTTAAATGAATAATAAAAAACCGAAATCAAAATCCTATAGAACGTACCGTTTAAATAACACAACGGAACTATATCGATAATAGTTCGAACTTACCGATAAGAGTCTTATCGAAATATAAATAATGTTCGTTAAACAT F2: 3 CGACTA 2 Unidirectional alignment (log-probability: -33.6) TGCATGGCAAATTTATTGTGTTGCtTTGATATAGCTATTAatcAGC----------ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA TGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTATCAAGCTTGAATGGCTATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA Template switch alignment (log-probability: -22) TGCATGGCAAATTTATTGTGTTGCtTTGATATAGCTATTA|ATCAGC|ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA TGCATGGCAAATTTATTGTGTTGCCTTGATATAGCTATTA|ATCAGC|ATTCTCAGAATAGCTTTATATTTATTACAAGCAATTTGTA ========= Event 744 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATAATAAACATCAAAATAATCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTACTTTGTAAGAGTGTTCCTAAGAAAAAATAATTCTACCTATCCCAAATTGTCTTtgtgtgtgtgtgtgCAT-----GTTTTTTTGATGAACAATTTT Chimp: AAATAATAAACATCAAAATAATCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCTGTGAAATACTTTGTAATAGTGTTCCTGAGAAAAAATAGTTCTACCTATCCCAAATTGTCTTTGCGTGTGTGTGTGCATGGtttttttttttGATGAACAATTTT ↓ 1 4 3 2 Gorilla: AAATAATAAACATCAAAATAACATGCACACGCTTCAAATCCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTACTTTGTAATAGTGTTCTTAAGAAAAAATAATTCTACCTATCCCAAATTGTCTTtgtgtgtgtgtgtgCAT-----GtttttttGATGAACAATTTT ↑ 1 4 3 2 Human: AAATAATAAACATCAAAATAATCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTACTTTGTAAGAGTGTTCCTAAGAAAAAATAATTCTACCTATCCCAAATTGTCTTtgtgtgtgtgtgtgCAT-----GTTTTTTTGATGAACAATTTT Cluster: [ ] Orangutan: AAATAATAAACATCAAAATAATCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTACTTTGTAACATTGTTCCTAAGAAAAAATAATTCTGCCTATCCCAAATTGTCTTtgtgtgtgtgtgtgCCT-----GTTTTTTTGATGAACAATTTT Human > Gorilla --------------- chr12:59711947-59711955 Template switch process: F1: L CAAATAAATGATAAATGTTGAAATAATAAACATCAAAATAA 1 F3: 4 GCTTCAAATCCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTAC R RF: CAAATAAATGATAACTGTTGAAATAATAAACATCAAAATAATCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTACTTTGTAAGAGTGTTCCTAAGAAAAAATAATTCTACCTATCCCAAATTGTCTTTGTGTGTGTGTGTGCATG RR: GTTTATTTACTATTGACAACTTTATTATTTGTAGTTTTATTAGTGATATTCGAAGTTTTGGTAAAAAATGTTAAAATCAGACACTATAGACACTTGATGAAACATTCTCACAAGGATTCTTTTTTATTAAGATGGATAGGGTTTAACAGAAACACACACACACACGTAC F2: 3 CACACGTAC 2 Unidirectional alignment (log-probability: -44.8) AAATAAATGATAAaTGTTGAAATAATAAACATCAAAATAAcatgcaCAC-----GCTTCAAAtCCATTTTTTACAATTTTAGTCTGTGATATCT AAATAAATGATAACTGTTGAAATAATAAACATCAAAATAAT-----CACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCT Template switch alignment (log-probability: -28.1) AAATAAATGATAAaTGTTGAAATAATAAACATCAAAATAA|CATGCACAC|GCTTCAAAtCCATTTTTTACAATTTTAGTCTGTGATATCT AAATAAATGATAACTGTTGAAATAATAAACATCAAAATAA|CATGCACAC|GCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCT Chimp > Gorilla --------------- chr12:59711947-59711955 Template switch process: F1: L CAAATAAATGATAAATGTTGAAATAATAAACATCAAAATAA 1 F3: 4 GCTTCAAATCCATTTTTTACAATTTTAGTCTGTGATATCTGTGAACTAC R RF: CAAATAAATGATAAATGTTGAAATAATAAACATCAAAATAATCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCTGTGAAATACTTTGTAATAGTGTTCCTGAGAAAAAATAGTTCTACCTATCCCAAATTGTCTTTGCGTGTGTGTGTGCATG RR: GTTTATTTACTATTTACAACTTTATTATTTGTAGTTTTATTAGTGATATTCGAAGTTTTGGTAAAAAATGTTAAAATCAGACACTATAGACACTTTATGAAACATTATCACAAGGACTCTTTTTTATCAAGATGGATAGGGTTTAACAGAAACGCACACACACACGTAC F2: 3 CACACGTAC 2 Unidirectional alignment (log-probability: -44.8) AAATAAATGATAAATGTTGAAATAATAAACATCAAAATAAcatgcaCAC-----GCTTCAAAtCCATTTTTTACAATTTTAGTCTGTGATATCT AAATAAATGATAAATGTTGAAATAATAAACATCAAAATAA-----TCACTATAAGCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCT Template switch alignment (log-probability: -28.1) AAATAAATGATAAATGTTGAAATAATAAACATCAAAATAA|CATGCACAC|GCTTCAAAtCCATTTTTTACAATTTTAGTCTGTGATATCT AAATAAATGATAAATGTTGAAATAATAAACATCAAAATAA|CATGCACAC|GCTTCAAAACCATTTTTTACAATTTTAGTCTGTGATATCT ========= Event 745 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TAATCTTCCTTCACACATGGA-CCGTA----------------AACGGTTCCCAGTTGTCTGAGAGCC ↑ 1 3 4 2 Chimp: TAATCTTCCTTCACACATGGATTCATA--------ATGTGATTTACGGTTCCCAGTTGTCTGAGAGCC Gorilla: TAATCTTCCTTCACACATGGATTCATAATGTGATT--------TACGGTTCCCAGTTGTCTGAGAGCC ↓ 1 3 4 2 Human: TAATCTTCCTTCACACATGGA-CCGTA----------------AACGGTTCCCAGTTGTCTGAGAGCC Cluster: [ ] Orangutan: TAATCTTCCTTCACACATGGATTCATAATGTGATT--------TACGGTTCCCAGTTGTCTGAGAGCC Chimp > Human ------------- chr12:56921782-56921787 Template switch process: F1: L GAATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA 1 F3: 4 ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG R RF: GAATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGATTCATAATGTGATTTACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG RR: CTTACAATAAATGGACTTTAATTAGAAGGAAGTGTGTACCTAAGTATTACACTAAATGCCAAGGGTCAACAGACTCTCGGAGTACTCCCAAAGATC F2: 3 AATGCC 2 Unidirectional alignment (log-probability: -30.5) AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGaccgtaA---------------ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGG------ATTCATAATGTGATTTACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG Template switch alignment (log-probability: -16) AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA|CCGTAA|ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA|CCGTAA|ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG Gorilla > Human --------------- chr12:56921782-56921787 Template switch process: F1: L GAATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA 1 F3: 4 ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG R RF: GAATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGATTCATAATGTGATTTACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG RR: CTTACAATAAATGGACTTTAATTAGAAGGAAGTGTGTACCTAAGTATTACACTAAATGCCAAGGGTCAACAGACTCTCGGAGTACTCCCAAAGATC F2: 3 AATGCC 2 Unidirectional alignment (log-probability: -30) AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA---------------ccgtaaACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGATTCATAATGTGATTT------ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG Template switch alignment (log-probability: -16.5) AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA|CCGTAA|ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG AATGTTATTTACCTGAAATTAATCTTCCTTCACACATGGA|CCGTAA|ACGGTTCCCAGTTGTCTGAGAGCCTCATGAGGGTTTCTAG ========= Event 746 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTCCAGCGGCTCAGTCTCTGAAATACCCGTAAGTGGGTATTTCAATACATGAGGACCCTTGTATTGTT Chimp: CTTCCAGCGGCTCAGTCTCTGAAATATCCGTAAGTGGGTATTTCAATACATGAGGACCCTTGTATTGTT ↑ 3 1 4 2 Gorilla: CTTCCAGCGGCTCAGTCTCTGAAATACCCA--------------CTTACATGAGGACCCTTGTATTGTT ↓ 3 1 4 2 Human: CTTCCAGCGGCTCAGTCTCTGAAATACCCGTAAGTGGGTATTTCAATACATGAGGACCCTTGTATTGTT Cluster: [ ] Orangutan: CTTCCAGCGGCTCAGTCTCTGAAATATCCA--------------CTTACATGAGGACCCTTGTATTGTC Gorilla > Human --------------- chr12:55879395-55879410 Template switch process: F1: L CACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCC 1 F3: 4 ATACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGTA R RF: CACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCCACTTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGTA RR: GTGACGGTTCCCGAAGGTCGCCGAGTCAGAGACTTTATGGGTGAATGTACTCCTGGGAACATAACAACTGTAGACGTCCTCCAT F2: 3 ACTTTATGGGTGAATG 2 Unidirectional alignment (log-probability: -43.7) ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCCgtaagtgggtatttcaA--TACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCC----------------ACTTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT Template switch alignment (log-probability: -23.3) ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCC|GTAAGTGGGTATTTCA|aTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCC|GTAAGTGGGTATTTCA|TTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT Gorilla > Chimp --------------- chr12:57419929-57419944 Template switch process: F1: L AAACACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATATCC 1 F3: 4 ATACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGTA R RF: AAACACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCCACTTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGTA RR: TTTGTGACGGTTCCCGAAGGTCGCCGAGTCAGAGACTTTATGGGTGAATGTACTCCTGGGAACATAACAACTGTAGACGTCCTCCAT F2: 3 ACTTTATGGGTGAATG 2 Unidirectional alignment (log-probability: -48.2) ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATA-----TccgtaagtgggtatttcaaTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCCACT-------------------TACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT Template switch alignment (log-probability: -28.9) ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATAtCC|GTAAGTGGGTATTTCA|aTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT ACTGCCAAGGGCTTCCAGCGGCTCAGTCTCTGAAATACCC|GTAAGTGGGTATTTCA|TTACATGAGGACCCTTGTATTGTTGACATCTGCAGGAGGT ========= Event 747 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTCAACAAGTATTTGGTTATTTCTTTTTTCTATTTAGGTTAAT ↑ 3 42 1 Chimp: AGAAAAAAGAAATAACCAAATACTTGTTGGTTATT--------------------TCTTTTTTCTATTTAGGTTAAT ↓ 3 42 1 Gorilla: AGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTCAACAAGTATTTGGTTATTTCTTTTTTCTATTTAGGTTAAT Human: AGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTCAACAAGTATTTGGTTATTTCTTTTTTCTATTTAGGTTAAT Cluster: [ ] Orangutan: AGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTCAACAAGTATTTGGTTATTTCTTTTTTCTATTTAGGTTAAT Chimp > Human ------------- chr12:53851357-53851365 Template switch process: F1: L CTAAATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTC 1 F3: 4 TTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGGTGCTTAGGC R RF: CTAAATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGGTGCTTAGGC RR: GATTTATCTTTTTTCTTTATTGGTTTATGAACAACCAATAAAGAAAAAAGATAAATCCAATTATCTAGGTCCACGAATCCG F2: 3 TATGAACAA 2 Unidirectional alignment (log-probability: -39.7) AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTcaacaagtatttggttatttCTTTTTTCTATTTAGGTTAATAGATCCAGG AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTT--------------------CTTTTTTCTATTTAGGTTAATAGATCCAGG Template switch alignment (log-probability: -16.6) AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTC|AACAAGTAT|TTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGG AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTC|AACAAGTAT|TTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGG Chimp > Gorilla --------------- chr12:54691830-54691838 Template switch process: F1: L CTAAATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTC 1 F3: 4 TTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGGTGCTTAGGC R RF: CTAAATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGGTGCTTAGGC RR: GATTTATCTTTTTTCTTTATTGGTTTATGAACAACCAATAAAGAAAAAAGATAAATCCAATTATCTAGGTCCACGAATCCG F2: 3 TATGAACAA 2 Unidirectional alignment (log-probability: -39.6) AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTAtttcaacaagtatttggttaTTTCTTTTTTCTATTTAGGTTAATAGATCCAGG AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTA--------------------TTTCTTTTTTCTATTTAGGTTAATAGATCCAGG Template switch alignment (log-probability: -17.1) AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTC|AACAAGTAT|TTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGG AATAGAAAAAAGAAATAACCAAATACTTGTTGGTTATTTC|AACAAGTAT|TTGGTTATTTCTTTTTTCTATTTAGGTTAATAGATCCAGG ========= Event 748 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGACTAACATGAATCAGATTGTTTCTGTCTTCGGTAAGTTTACATT-----------TAGTCAGAGTATAGAAATAATGTGAACAAGCACAGA ↓ 3 1 2 4 Chimp: AGGACTAACATGAATCAGATTGAC-----------TAAATGTAAACTTACCGAAGACAGAAACAAAGTATAGATATAATGTGAACAAGCACAGA Gorilla: aggactaacatgaatcagattgtttctgtcttcggtaagtttacatt-----------tagtcagattatagatataatgtgaacaagcaCAGA Human: AGGACTAACATGAATCAGATTGTTTCTGTCTTCGGTAAGTTTACATT-----------TAGTCAGAGTATAGAAATAATGTGAACAAGCACAGA Cluster: [ ] Orangutan: AGGACTAACATGAATCAGATTGTTTTTGTCTTTGGTAAG-----------------------------TTAGATATAATGTGAACAAGCACAGA Human > Chimp ------------- chr12:55186674-55186705 Template switch process: F1: L AACTATAGATGCCCAAGGCAGGACTAACATGAATCAGATTG 1 F3: 4 AGTATAGATATAATGTGAACAAGCACAGAGTAAGAAGAGATTATTTCCC R RF: AACTATAGATGCCCAAGGCAGGACTAACATGAATCAGATTGTTTCTGTCTTCGGTAAGTTTACATTTAGTCAGAGTATAGAAATAATGTGAACAAGCACAGAGTAAGAAGAGATTATTTCCC RR: TTGATATCTACGGGTTCCGTCCTGATTGTACTTAGTCTAACAAAGACAGAAGCCATTCAAATGTAAATCAGTCTCATATCTTTATTACACTTGTTCGTGTCTCATTCTTCTCTAATAAAGGG F2: 3 AACAAAGACAGAAGCCATTCAAATGTAAATCA 2 Unidirectional alignment (log-probability: -74.8) ACTATAGATGCCCAAGGCAGGACTAACATGAATCAGATTGactaaatgtaaacttaccgaagacagaaacaa--------------------------------AGTATAGAtATAATGTGAACAAGCACAGAGTAAGAAGAGA ACTATAGATGCCCAAGGCAGGACTAACATGAATCAGATTG--------------------------------TTTCTGTCTTCGGTAAGTTTACATTTAGTCAGAGTATAGAAATAATGTGAACAAGCACAGAGTAAGAAGAGA Template switch alignment (log-probability: -25.4) ACTATAGATGCCCAAGGCAGGACTAACATGAATCAGATTG|ACTAAATGTAAACTTACCGAAGACAGAAACAA|AGTATAGAtATAATGTGAACAAGCACAGAGTAAGAAGAGA ACTATAGATGCCCAAGGCAGGACTAACATGAATCAGATTG|ACTAAATGTAAACTTACCGAAGACAGAAACAA|AGTATAGAAATAATGTGAACAAGCACAGAGTAAGAAGAGA ========= Event 749 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: agaactataAATTTTATAACTGTTATG------TTTATAAGATATATCTATGCTATTTTATGTAGCAGTACATTTACTTCTATTGttataaaaatatt-ttttaaagaaaatttCTAACTATTCTTTCACTGAAAGAACATGGAATCATCtg ↓ 1 4 3 2 Chimp: agaactataAATTTTATAACT--CAGT------GTTATAAGATATATCTATGCTATTGTATGTAGCAGTACATTTACTTCTATTGTTATAAAAATATT-TTTTAAAGAAAATTTCTAACTATTCTTTCACTGAAAGAACATGGAATCATCTG Gorilla: agaactataAATTTTATAACT--CAGTGTTATGTTTATAAGATATATCTATGCTATTGTATGTAGCAGTACATTTACTTCTATTGTTATAAAAATATT-TTTTAAAGAAAATTTCTAACTATTCTTTCACTGAAAGAACATGGAATCATCtg Human: agaactataAATTTTATAACTGTTATG------TTTATAAGATATATCTATGCTATTTTATGTAGCAGTACATTTACTTCTATTGttataaaaatatt-ttttaaagaaaatttCTAACTATTCTTTCACTGAAAGAACATGGAATCATCtg Cluster: [ ] Orangutan: agaactataaattttataact--cag--ttatgtttATAAGATATATCTATGCTATTGTACGTAGCAGTACATTTACTTCTATTGTTATAAAAATATTTTTTTAAAGAAAATTTCTAACTGTCCTTTCACTGAAAGAACATGGAATCATCtg Human > Chimp ------------- chr12:54950154-54950158 Template switch process: F1: L TTTTTGAAGAGCATATGACTAGAACTATAAATTTTATAACT 1 F3: 4 TTATAAGATATATCTATGCTATTGTATGTAGCAGTACATT R RF: TTTTTGAAGAGCATATGACTAGAACTATAAATTTTATAACTGTTATGTTTATAAGATATATCTATGCTATTTTATGTAGCAGTACATTTACTTCTATTGTTATAAAAATATTTTTTAAAGAAAATTTCTAACTATTCTTTCACTG RR: AAAAACTTCTCGTATACTGATCTTGATATTTAAAATATTGACAATACAAATATTCTATATAGATACGATAAAATACATCGTCATGTAAATGAAGATAACAATATTTTTATAAAAAATTTCTTTTAAAGATTGATAAGAAAGTGAC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -33.2) TTTTGAAGAGCATATGACTAGAACTATAAATTTTATAACtcagTG------TTATAAGATATATCTATGCTATTgTATGTAGCAGTACATT TTTTGAAGAGCATATGACTAGAACTATAAATTTTATAAC----TGTTATGTTTATAAGATATATCTATGCTATTTTATGTAGCAGTACATT Template switch alignment (log-probability: -21.9) TTTTGAAGAGCATATGACTAGAACTATAAATTTTATAACT|CAGTG|TTATAAGATATATCTATGCTATTgTATGTAGCAGTACATT TTTTGAAGAGCATATGACTAGAACTATAAATTTTATAACT|CAGTG|TTATAAGATATATCTATGCTATTTTATGTAGCAGTACATT ========= Event 750 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAACATTGTCATTTAATACTCACACCTGAC-------TTTGTACTTTTTATATTTTTTAATACCAAAACT Chimp: TAAACATTGTCGTTTAATACTCACACCTGac-------tttgtactttttatattttttaataccaaaact Gorilla: TAAACATTGTCATTTAATACTCACACCTGACAAAGTCAGGTGTGAGTTTGGTATTTTTTAATACCAAAACT ↑ 3 1 2 4 Human: TAAACATTGTCATTTAATACTCACACCTGAC-------TTTGTACTTTTTATATTTTTTAATACCAAAACT Cluster: [ ] Orangutan: TAAACATTGTCGTTTAATACTCAGACCTGAC-------TTTACACTTTTTATATTTTTTAATACCAAAACT Human > Gorilla --------------- chr12:54040964-54040978 Template switch process: F1: L TCATTCAGATTAAACATTGTCATTTAATACTCACACCTGAC 1 F3: 4 TTTGGTATTTTTTAATACCAAAACTTAATCTTATATTTTTCACTT R RF: TCATTCAGATTAAACATTGTCATTTAATACTCACACCTGACTTTGTACTTTTTATATTTTTTAATACCAAAACTTAATCTTATATTTTTCACTT RR: AGTAAGTCTAATTTGTAACAGTAAATTATGAGTGTGGACTGAAACATGAAAAATATAAAAAATTATGGTTTTGAATTAGAATATAAAAAGTGAA F2: 3 GAGTGTGGACTGAAA 2 Unidirectional alignment (log-probability: -48.2) CATTCAGATTAAACATTGTCATTTAATACTCACACCTGACaaagtcaggtgtgagTTTG--------gTATTTTTTAATACCAAAACTTAATCTTATATTTTT CATTCAGATTAAACATTGTCATTTAATACTCACACCTGAC---------------TTTGTACTTTTTATATTTTTTAATACCAAAACTTAATCTTATATTTTT Template switch alignment (log-probability: -28.8) CATTCAGATTAAACATTGTCATTTAATACTCACACCTGAC|AAAGTCAGGTGTGAG|TTTggTATTTTTTAATACCAAAACTTAATCTTATATTTTT CATTCAGATTAAACATTGTCATTTAATACTCACACCTGAC|AAAGTCAGGTGTGAG|TTTTATATTTTTTAATACCAAAACTTAATCTTATATTTTT ========= Event 751 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ccaccatgctcgtccTGAATATTCTTTGTGTTTTTTTCTGA-------CAGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGGAAATTTCTCTAAATGTAAATCCTGGAAAGCTTGCAGAGATTTAA ↓ 3 2 1 4 ↑ 1 4 3 2 Chimp: ccaccatgctcgtccTGAATATTCTTTGTGtttttttCTGAACACAAAGAATAGTAGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGGAAATTTCTCTAAATGTAAATCCTGGAAAGCTTGCAGAGATTTAA ↓ 1 4 3 2 ↑ 3 2 1 4 Gorilla: ccaccatgctcgtccTGAATATTCTTTGTGtttttttCTGA-------CAGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGGAAATTTCTCTAAATGTAAATCCTGGAAAGCTGGCAGAGATTTAA Human: ccaccatgctcgtccTGAATATTCTTTGTGTTTTTTTCTGA-------CAGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGGAAATTTCTCTAAATGTAAATCCTGGAAAGCTTGCAGAGATTTAA Cluster: [ ] Orangutan: ccaccatgctcgtccTGAATATTCTTTGTGTTTTTTTCTGA-------CGGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTGTTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGAAAATTTCTCTAAATGTAAATCCTGGAAGGCTTGCAGAGATTTAA Chimp > Human ------------- chr12:1017323-1017330 Template switch process: F1: L CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA 1 F3: 4 GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG R RF: CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGAACACAAAGAATAGTAGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGGAAATTTCTCTAAATGTAAATCCTGGAAAGCTTG RR: GGTGGTACGAGCAGGACTTATAAGAAACACAAAAAAAGACTTGTGTTTCTTATCATCACTACACTTATCATCACTTAACTATCACTTTGACATAACAATTATTTGTGTATTAAATTCTATTCGGTCTAAAGACCATTATAAGAAGAGTCTTAATCTAAAATCCTTTAAAGAGATTTACATTTAGGACCTTTCGAAC F2: 3 TTTCGGAC 2 Unidirectional alignment (log-probability: -33.4) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGAcaggcttt---------------GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA--------ACACAAAGAATAGTAGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG Template switch alignment (log-probability: -22.3) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|CAgGCTTT|GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|CAAGCTTT|GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG Human > Chimp ------------- chr12:1068160-1068171 Template switch process: F1: L CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA 1 F3: 4 GTAGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG R RF: CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGACAGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG RR: GGTGGTACGAGCAGGACTTATAAGAAACACAAAAAAAGACTGTCCGAAACACTACACTTATCATCACTTAACTATCACTTTGACATAAC F2: 3 ATAAGAAACACA 2 Unidirectional alignment (log-probability: -43.1) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA--------acacaaagaatagtaGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGACAGGCTTT---------------GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA Template switch alignment (log-probability: -28.8) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|ACACAAAGAATA|gTaGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|ACACAAAGAATA|TTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA Gorilla > Chimp --------------- chr12:1068160-1068171 Template switch process: F1: L CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA 1 F3: 4 GTAGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG R RF: CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGACAGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG RR: GGTGGTACGAGCAGGACTTATAAGAAACACAAAAAAAGACTGTCCGAAACACTACACTTATCATCACTTAACTATCACTTTGACATAAC F2: 3 ATAAGAAACACA 2 Unidirectional alignment (log-probability: -42.6) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGaacacaaagaatagtA--------GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTG---------------ACAGGCTTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA Template switch alignment (log-probability: -28.4) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|ACACAAAGAATA|gTaGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|ACACAAAGAATA|TTTGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTA Chimp > Gorilla --------------- chr12:949870-949877 Template switch process: F1: L CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA 1 F3: 4 GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG R RF: CCACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGAACACAAAGAATAGTAGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTGTTAATAAACACATAATTTAAGATAAGCCAGATTTCTGGTAATATTCTTCTCAGAATTAGATTTTAGGAAATTTCTCTAAATGTAAATCCTGGAAAGCTTG RR: GGTGGTACGAGCAGGACTTATAAGAAACACAAAAAAAGACTTGTGTTTCTTATCATCACTACACTTATCATCACTTAACTATCACTTTGACATAACAATTATTTGTGTATTAAATTCTATTCGGTCTAAAGACCATTATAAGAAGAGTCTTAATCTAAAATCCTTTAAAGAGATTTACATTTAGGACCTTTCGAAC F2: 3 TTTCGGAC 2 Unidirectional alignment (log-probability: -32.9) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTG---------------AcaggctttGTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGAACACAAAGAATAGTA--------GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG Template switch alignment (log-probability: -22.3) CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|CAgGCTTT|GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG CACCATGCTCGTCCTGAATATTCTTTGTGTTTTTTTCTGA|CAAGCTTT|GTGATGTGAATAGTAGTGAATTGATAGTGAAACTGTATTG ========= Event 752 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTGTTTTAAATAGTGGGTGGTCT------------TTTCAG---TGAT----CTGTTCTGAAAAGACCACCCACTATTCACCC-C Chimp: ttgttttAAATAGTGGGTGGTCT------------TTTCAG---TGAT----CTGTTCTGAAAAGAGCACCCACTGTTCACCC-- Gorilla: TTGTTTTAAATAGTGGGTGGTGT------------TTTCAGAACAGAT-------CACTGAAAAGACCACCCACTATTCACCC-C ↓ 1 3 4 2 ↑ 13 24 Human: TTGTTTTAAATAGTGGGTGGTCT------------TTTCAG---TGAT----CTGTTCTGAAAAGACCACCCACTATTCACCC-C Cluster: [ ] Orangutan: --ATGTACAAcagtgggggacgttccccaccctgtgtccag---tgatctca---ttgttcaaatcccagctatgatgaaacctg Gorilla > Human --------------- chr12:54873026-54873042 Template switch process: F1: L GAAAGCTTTTGTTTGTTTGTTTGTTTTAAATAGTGGGTGGT 1 F3: 4 CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA R RF: GAAAGCTTTTATTTGTTTGTTTGTTTTAAATAGTGGGTGGTGTTTTCAGAACAGATCACTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA RR: CTTTCGAAAATAAACAAACAAACAAAATTTATCACCCACCACAAAAGTCTTGTCTAGTGACTTTTCTGGTGGGTGATAAGTGGGGTTCATCATCCGAT F2: 3 TTGTCTAGTGACTTTTC 2 Unidirectional alignment (log-probability: -45.2) AAAGCTTTTgTTTGTTTGTTTGTTTTAAATAGTGGGTGGTcTTTTCAGtgatctgtt---------CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA AAAGCTTTTATTTGTTTGTTTGTTTTAAATAGTGGGTGGTGTTTTCAG---------AACAGATCACTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA Template switch alignment (log-probability: -23.4) AAAGCTTTTgTTTGTTTGTTTGTTTTAAATAGTGGGTGGT|CTTTTCAGTGATCTGTT|CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA AAAGCTTTTATTTGTTTGTTTGTTTTAAATAGTGGGTGGT|CTTTTCAGTGATCTGTT|CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA Human > Gorilla --------------- chr12:55722301-55722309 Template switch process: F1: L GAAAGCTTTTATTTGTTTGTTTGTTTTAAATAGTGGGTGGTGTTTTCAG 1 F3: 4 CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA R RF: GAAAGCTTTTGTTTGTTTGTTTGTTTTAAATAGTGGGTGGTCTTTTCAGTGATCTGTTCTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA RR: CTTTCGAAAACAAACAAACAAACAAAATTTATCACCCACCAGAAAAGTCACTAGACAAGACTTTTCTGGTGGGTGATAAGTGGGGTTCATCATCCGAT F2: 3 ACTAGACAA 2 Unidirectional alignment (log-probability: -45.2) TaTTTGTTTGTTTGTTTTAAATAGTGGGTGGTgTTTTCAGaacagatca---------CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA TGTTTGTTTGTTTGTTTTAAATAGTGGGTGGTCTTTTCAG---------TGATCTGTTCTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA Template switch alignment (log-probability: -28.1) TaTTTGTTTGTTTGTTTTAAATAGTGGGTGGTgTTTTCAG|AACAGATCA|CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA TGTTTGTTTGTTTGTTTTAAATAGTGGGTGGTCTTTTCAG|AACAGATCA|CTGAAAAGACCACCCACTATTCACCCCAAGTAGTAGGCTA ========= Event 753 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTATTATATGGTGAACAGGTCCCATGTCAACCATGGGAAAAACAAGGTAGTTTGGGA ↑ 3 1 4 2 Chimp: CTTATTATATGGTGAACAGGT--------TGACATGGGAAAAACAAGGTAGTTTGGGA Gorilla: CTTATTACATGGTGAACAGGT--------TGACATGGGAAAAACAAGGTAGTTTGGGA ↓ 3 1 4 2 Human: CTTATTATATGGTGAACAGGTCCCATGTCAACCATGGGAAAAACAAGGTAGTTTGGGA Cluster: [ ] Orangutan: CTTATTATATGGTGAACAGGC--------TGACATGGGAAAAGCAAGGTAGTTTGGGA Chimp > Human ------------- chr12:80874135-80874145 Template switch process: F1: L TTAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGT 1 F3: 4 CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT R RF: TTAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGTTGACATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT RR: AATTATTTCGGATCCTCAGTGAATAATATACCACTTGTCCAACTGTACCCTTTTTGTTCCATCAAACCCTATTGTTCTAATGTA F2: 3 CAACTGTACCC 2 Unidirectional alignment (log-probability: -37.1) TAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGT---cccatgtcaacCATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT TAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGTTGA-----------CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT Template switch alignment (log-probability: -16.6) TAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGT|CCCATGTCAAC|CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT TAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGT|CCCATGTCAAC|CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT Gorilla > Human --------------- chr12:80874135-80874145 Template switch process: F1: L TTAATAAAGCCTAGGAGTCACTTATTATATGGTGAACAGGT 1 F3: 4 CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT R RF: TTAATAAAGCCTAGGAGTCACTTATTACATGGTGAACAGGTTGACATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT RR: AATTATTTCGGATCCTCAGTGAATAATGTACCACTTGTCCAACTGTACCCTTTTTGTTCCATCAAACCCTATTGTTCTAATGTA F2: 3 CAACTGTACCC 2 Unidirectional alignment (log-probability: -42.1) TAATAAAGCCTAGGAGTCACTTATTAtATGGTGAACAGGTcccatgtcaac---CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT TAATAAAGCCTAGGAGTCACTTATTACATGGTGAACAGGT-----------TGACATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT Template switch alignment (log-probability: -22.6) TAATAAAGCCTAGGAGTCACTTATTAtATGGTGAACAGGT|CCCATGTCAAC|CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT TAATAAAGCCTAGGAGTCACTTATTACATGGTGAACAGGT|CCCATGTCAAC|CATGGGAAAAACAAGGTAGTTTGGGATAACAAGATTACAT ========= Event 754 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTACCCTAACAGTGTTGCATG---GAAACCTATCATACAAAATATAAAATTATAGAGTCAGATACTTCC Chimp: TTACCCTAACAGTGTTGCATG---GAAACCTATCATACAAAATATACAATTATAGAGTCAGATACTTCC Gorilla: TTACCCTAACAGTGTTGCATGTTTTATATTTCGCATACAAAATATAAAATTATAGAGTCAGATACttcc ↑ 1 4 3 2 Human: TTACCCTAACAGTGTTGCATG---GAAACCTATCATACAAAATATAAAATTATAGAGTCAGATACTTCC Cluster: [ ] Orangutan: TTACCCTAACAGTGTTGCATG---GAAACCTATCATACAAAATATAAAATTATAGAGTCAGATACTTCC Human > Gorilla --------------- chr12:80178336-80178347 Template switch process: F1: L ATTGGGTAACTGAACATGACTTACCCTAACAGTGTTGCATG 1 F3: 4 CATACAAAATATAAAATTATAGAGTCAGATACTTCCAAGA R RF: ACTGGGTAACTGAACATGACTTACCCTAACAGTGTTGCATGGAAACCTATCATACAAAATATAAAATTATAGAGTCAGATACTTCCAAGA RR: TGACCCATTGACTTGTACTGAATGGGATTGTCACAACGTACCTTTGGATAGTATGTTTTATATTTTAATATCTCAGTCTATGAAGGTTCT F2: 3 GCTTTATATTTT 2 Unidirectional alignment (log-probability: -42.4) tTGGGTAACTGAACATGACTTACCCTAACAGTGTTGCATG--------TtttatatttcgCATACAAAATATAAAATTATAGAGTCAGATACTTCCAAGA CTGGGTAACTGAACATGACTTACCCTAACAGTGTTGCATGGAAACCTAT-----------CATACAAAATATAAAATTATAGAGTCAGATACTTCCAAGA Template switch alignment (log-probability: -28.3) tTGGGTAACTGAACATGACTTACCCTAACAGTGTTGCATG|TTTTATATTTcG|CATACAAAATATAAAATTATAGAGTCAGATACTTCCAAGA CTGGGTAACTGAACATGACTTACCCTAACAGTGTTGCATG|TTTTATATTTTG|CATACAAAATATAAAATTATAGAGTCAGATACTTCCAAGA ========= Event 755 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGACTGCATTGCTAGAATCAGCTTA-----AGGTAAAAtttgtttgtttgtttcatttaagagacaagagtctagcttggttgctgaagcttgagtacagtggagagctcctagttcactgtagcctcgaacttcttggcttaagccatccttccaccagaggctc Chimp: AAGACTGCATTGCTAGAATCAGCTTA-----AGGTAAAATTTGtttgtttgtttcatt--tgagacaagagtctagcttggttgctgaagcttgagtacagtggagagctcctagttcactgtaacctcgaacttcttggcttaagccatcctcccaccagaggctc Gorilla: AAGACTGCATTGCTAGAATCAATCCACAAATCAATAAAAtttgtttgtttgtttcatttaagagacaagagtctagcttggttgctgaagcttgagtacagtggagagctcctagttcactgcagcctcgaacttcttggcttaagccatcctcccaccagaggctc ↓ 1 4 3 2 Human: AAGACTGCATTGCTAGAATCAGCTTA-----AGGTAAAAtttgtttgtttgtttcatttaagagacaagagtctagcttggttgctgaagcttgagtacagtggagagctcctagttcactgtagcctcgaacttcttggcttaagccatccttccaccagaggctc Cluster: [ ] Orangutan: AAGACTGCATTGCTAGAATCAGCTTA-----AGGTAAAAtttgt----ttgtttcatttaagagacaagagtcttgcttggttgctgaagcttgagtacagtggagagctcctagttcactgcagcgtcgaacttcttggcttaagccatcctcccactggaggctc Gorilla > Human --------------- chr1:28371095-28371101 Template switch process: F1: L TGTGTATGTCCTCCTGTTGGAAGACTGCATTGCTAGAATCA 1 F3: 4 GTAAAATTTGTTTGTTTGTTTCATTTAAGAGACAAGAGTCT R RF: TGTGTATGTCCTCCTGTTGGAAGACTGCATTGCTAGAATCAATCCACAAATCAATAAAATTTGTTTGTTTGTTTCATTTAAGAGACAAGAGTCTAGCTTGGTTGCTGAAGCTTGAGTACAGTGGAGAGCTCCTAGTTCACTGCAGCCTCGAACTTCTTGGCTTAAGC RR: ACACATACAGGAGGACAACCTTCTGACGTAACGATCTTAGTTAGGTGTTTAGTTATTTTAAACAAACAAACAAAGTAAATTCTCTGTTCTCAGATCGAACCAACGACTTCGAACTCATGTCACCTCTCGAGGATCAAGTGACGTCGGAGCTTGAAGAACCGAATTCG F2: 3 GAATTCG 2 Unidirectional alignment (log-probability: -32.8) GTGTATGTCCTCCTGTTGGAAGACTGCATTGCTAGAATC-------------AgcttaaggTAAAATTTGTTTGTTTGTTTCATTTAAGAGACAAGAGTC GTGTATGTCCTCCTGTTGGAAGACTGCATTGCTAGAATCAATCCACAAATCAA--------TAAAATTTGTTTGTTTGTTTCATTTAAGAGACAAGAGTC Template switch alignment (log-probability: -22.2) GTGTATGTCCTCCTGTTGGAAGACTGCATTGCTAGAATCA|GCTTAAG|gTAAAATTTGTTTGTTTGTTTCATTTAAGAGACAAGAGTC GTGTATGTCCTCCTGTTGGAAGACTGCATTGCTAGAATCA|GCTTAAG|ATAAAATTTGTTTGTTTGTTTCATTTAAGAGACAAGAGTC ========= Event 756 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ttctagcagtctatagcactgtaTATT----------------------CATGGTCTTGTATCATAGACATCATTAC ↓ 4 3 2 1 Chimp: ttctagcagtctatagcactgtaTATTCATGGTCTCATGAATGTATATTCATGGTCTTGTATCATAGACATCATTAC Gorilla: ttctagcagtctatagcacagtaTATT----------------------CATGGTCTTGTATCATAGACATCATTAC Human: ttctagcagtctatagcactgtaTATT----------------------CATGGTCTTGTATCATAGACATCATTAC Cluster: [ ] Orangutan: ttctagcagtctatagcactgtaTATT----------------------CATGGTCTTGTATCATAGACATCATTAC Human > Chimp ------------- chr12:52232248-52232253 Template switch process: F1: L ATAAGAGAATTAAGTTCTAGCAGTCTATAGCACTGTATATTCATGGTCT 1 F3: 4 TGTATATTCATGGTCTTGTATCATAGACATCATTACTGAGTGTTAAAG R RF: ATAAGAGAATTAAGTTCTAGCAGTCTATAGCACTGTATATTCATGGTCTTGTATCATAGACATCATTACTGAGTGTTAAAG RR: TATTCTCTTAATTCAAGATCGTCAGATATCGTGACATATAAGTACCAGAACATAGTATCTGTAGTAATGACTCACAATTTC F2: 3 AAGTAC 2 Unidirectional alignment (log-probability: -42.6) TTAAGTTCTAGCAGTCTATAGCACTGTATATTCATGGtctcatgaatgtatattcatggTCTTGTATCATAGACATCATTACTGAG TTAAGTTCTAGCAGTCTATAGCACTGTATATTCATGG----------------------TCTTGTATCATAGACATCATTACTGAG Template switch alignment (log-probability: -16.3) TTAAGTTCTAGCAGTCTATAGCACTGTATATTCATGGTCT|CATGAA|TGTATATTCATGGTCTTGTATCATAGACATCATTACTGAG TTAAGTTCTAGCAGTCTATAGCACTGTATATTCATGGTCT|CATGAA|TGTATATTCATGGTCTTGTATCATAGACATCATTACTGAG ========= Event 757 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTCATCTCTTATTACTGCTGtttaataattcctttattaaacagctttagcatttattttccata Chimp: TATTCATCTCTTATTATTGCTGTTTAATAATTCCTTTTTTAAACAGCTTTAGCATTTATTTTCCATA ↑ 3 2 1 4 Gorilla: TATTCATCTCTTATTATTGCTGTTTAATAATTCCTTATAT---ATGCTTTAGCATTTATTTTCCATA Human: TATTCATCTCTTATTACTGCTGtttaataattcctttattaaacagctttagcatttattttccata Cluster: [ ] Orangutan: TATTCGTCTCTTATTATTGCTGTTTAATAATTCCTTGTAT---ATGCTTTAGTATTTATTTTTCATA Gorilla > Chimp --------------- chr12:52555198-52555205 Template switch process: F1: L CAGGCTATTCATCTCTTATTATTGCTGTTTAATAATTCCTTTT 1 F3: 4 CTTTAGCATTTATTTTCCATATGATCTTTAATACGATTT R RF: CAGGCTATTCATCTCTTATTATTGCTGTTTAATAATTCCTTATATATGCTTTAGCATTTATTTTCCATATGATCTTTAATATGATTT RR: GTCCGATAAGTAGAGAATAATAACGACAAATTATTAAGGAATATATACGAAATCGTAAATAAAAGGTATACTAGAAATTATACTAAA F2: 3 GACAAATT 2 Unidirectional alignment (log-probability: -37.4) GCTATTCATCTCTTATTATTGCTGTTTAATAATTCCTTtTtTAaacaGCTTTAGCATTTATTTTCCATATGATCTTTAATAcGATTT GCTATTCATCTCTTATTATTGCTGTTTAATAATTCCTTATATAT---GCTTTAGCATTTATTTTCCATATGATCTTTAATATGATTT Template switch alignment (log-probability: -27.8) GCTATTCATCTCTTATTATTGCTGTTTAATAATTCCTTtT|TTAAACAG|CTTTAGCATTTATTTTCCATATGATCTTTAATAcGATTT GCTATTCATCTCTTATTATTGCTGTTTAATAATTCCTTAT|TTAAACAG|CTTTAGCATTTATTTTCCATATGATCTTTAATATGATTT ========= Event 758 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAAGGAATGCTTAAACCACTGAG----------------GTGATGAGGAGTAAACAAAATAAATACAGACTCCAG ↓ 4 1 3 2 Chimp: AGAAGGAATGCTTAAACCACTGAGGTGGTTTACTCCTGAGGTGAGGAGGAGTAAACAAAATAAATACGGACTCCAG Gorilla: AGAAGGAATGCTTAAACCACTGAG----------------GTGATGAGGAGTAAACAAAATAAATACAGACTCCAG Human: AGAAGGAATGCTTAAACCACTGAG----------------GTGATGAGGAGTAAACAAAATAAATACAGACTCCAG Cluster: [ ] Orangutan: Human > Chimp ------------- chr12:52324133-52324140 Template switch process: F1: L ATAATAATGTCATTTATAGAAGGAATGCTTAAACCACTGAGGTG 1 F3: 4 CTGAGGTGAGGAGGAGTAAACAAAATAAATACGGACTCCAGAAGGCATGA R RF: ATAATAATGTCATTTATAGAAGGAATGCTTAAACCACTGAGGTGATGAGGAGTAAACAAAATAAATACAGACTCCAGAAGGCATGA RR: TATTATTACAGTAAATATCTTCCTTACGAATTTGGTGACTCCACTACTCCTCATTTGTTTTATTTATGTCTGAGGTCTTCCGTACT F2: 3 CTCATTTG 2 Unidirectional alignment (log-probability: -46) TAATGTCATTTATAGAAGGAATGCTTAAACCACTGAGGTGgtttactcctgaggtgAgGAGGAGTAAACAAAATAAATACgGACTCCA TAATGTCATTTATAGAAGGAATGCTTAAACCACTGAGGTG----------------ATGAGGAGTAAACAAAATAAATACAGACTCCA Template switch alignment (log-probability: -28.5) TAATGTCATTTATAGAAGGAATGCTTAAACCACTGAGGTG|GTTTACTC|CTGAGGTGAgGAGGAGTAAACAAAATAAATACgGACTCCA TAATGTCATTTATAGAAGGAATGCTTAAACCACTGAGGTG|GTTTACTC|CTGAGGTGATGAGGAGTAAACAAAATAAATACAGACTCCA ========= Event 759 ========= Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TAGGGATACCCAGTGAGAAGAAGCACACAACTATTTGTTGTTTCAGAAGAATGTTAATAGT Chimp: TAGGGATACCCAGTGAGAAGAAGCACACAAATA---GATATTTCAGAAGAATGTTGATAGT Gorilla: TAGGGATACCCAGTGAGAAGACGCACACAAACA---GATATTTCAGAAGAATGTTAATAGT ↑ 1 3 2 4 Human: TAGGGATACCCAGTGAGAAGAAGCACACAACTATTTGTTGTTTCAGAAGAATGTTAATAGT Cluster: [ ] Orangutan: TAGGGATACCCAGTGAGAAGAAGCACACAAATA---TATATTTCAGAAGAATGTTAATAGT Human > Gorilla --------------- chr12:50979092-50979098 Template switch process: F1: L GAAGAGAGTAAGAGGCCAGTTAGGGATACCCAGTGAGAAGACGCACACAA 1 F3: 4 TTTCAGAAGAATGTTAATAGTTTCCATTTCTCCCTTCCCC R RF: GAAGAGAGTAAGAGGCCAGTTAGGGATACCCAGTGAGAAGAAGCACACAACTATTTGTTGTTTCAGAAGAATGTTAATAGTTTCCATTTCTCCCTTCCCC RR: CTTCTCTCATTCTCCGGTCAATCCCTATGGGTCACTCTTCTTCGTGTGTTGATAAACAACAAAGTCTTCTTACAATTATCAAAGGTAAAGAGGGAAGGGG F2: 3 ATAGACA 2 Unidirectional alignment (log-probability: -36.9) AGAGGCCAGTTAGGGATACCCAGTGAGAAGAcGCACACAA----------acagataTTTCAGAAGAATGTTAATAGTTTCCATTTCTCCCTTCCCC AGAGGCCAGTTAGGGATACCCAGTGAGAAGAAGCACACAACTATTTGTTG-------TTTCAGAAGAATGTTAATAGTTTCCATTTCTCCCTTCCCC Template switch alignment (log-probability: -27.9) AGAGGCCAGTTAGGGATACCCAGTGAGAAGAcGCACACAA|ACAgATA|TTTCAGAAGAATGTTAATAGTTTCCATTTCTCCCTTCCCC AGAGGCCAGTTAGGGATACCCAGTGAGAAGAAGCACACAA|ACAAATA|TTTCAGAAGAATGTTAATAGTTTCCATTTCTCCCTTCCCC ========= Event 760 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGTTTATATTTAGGATCAGACATATGATTAT---ACAGTCACAATAATTAATGATA ↓ 3 1 2 4 Chimp: GGTTTATATTTAGGATCAGACATATAATCATATGTCAGTCACAATAATTAATGATA ↑ 3 1 2 4 Gorilla: GGTTTATATTTAGGATCAGACATATGATTAT---ACAGTCACAATAATTAATGATA Human: GGTTTATATTTAGGATCAGACATATGATTAT---ACAGTCACAATAATTAATGATA Cluster: [ ] Orangutan: GGTTTATATTTAGGATCAGACATATGATTAT---ACAGTCACAATAATTAATGATA Human > Chimp ------------- chr12:86265183-86265192 Template switch process: F1: L TGGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATAT 1 F3: 4 CAGTCACAATAATTAATGATAGTTTACTTATTTTAAGAAC R RF: TGGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATATGATTATACAGTCACAATAATTAATGATAGTTCACTTATTTTAAGAAC RR: ACCAAACCCTTCTCAACCAAATATAAATCCTAGTCTGTATACTAATATGTCAGTGTTATTAATTACTATCAAGTGAATAAAATTCTTG F2: 3 TGTATACTAA 2 Unidirectional alignment (log-probability: -33.3) GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATATaATcATAtgtCAGTCACAATAATTAATGATAGTTtACTTATTTTAAGAAC GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATATGATTATA---CAGTCACAATAATTAATGATAGTTCACTTATTTTAAGAAC Template switch alignment (log-probability: -22.5) GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATAT|AATCATATGT|CAGTCACAATAATTAATGATAGTTtACTTATTTTAAGAAC GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATAT|AATCATATGT|CAGTCACAATAATTAATGATAGTTCACTTATTTTAAGAAC Gorilla > Chimp --------------- chr12:86265183-86265192 Template switch process: F1: L TGGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATAT 1 F3: 4 CAGTCACAATAATTAATGATAGTTTACTTATTTTAAGAAC R RF: TGGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATATGATTATACAGTCACAATAATTAATGATAGTTCACTTATTTTAAGAAC RR: ACCAAACCCTTCTCAACCAAATATAAATCCTAGTCTGTATACTAATATGTCAGTGTTATTAATTACTATCAAGTGAATAAAATTCTTG F2: 3 TGTATACTAA 2 Unidirectional alignment (log-probability: -31.9) GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATATaATcATAtgtCAGTCACAATAATTAATGATAGTTtACTTATTTTAAGAAC GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATATGATTATA---CAGTCACAATAATTAATGATAGTTCACTTATTTTAAGAAC Template switch alignment (log-probability: -22.5) GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATAT|AATCATATGT|CAGTCACAATAATTAATGATAGTTtACTTATTTTAAGAAC GGTTTGGGAAGAGTTGGTTTATATTTAGGATCAGACATAT|AATCATATGT|CAGTCACAATAATTAATGATAGTTCACTTATTTTAAGAAC ========= Event 761 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGTATGAATGAGGTGAAAGA--ATGTGCATTCCTAGCTAAATGCCAAATTCC Chimp: AAGTATGAATGAGGTGTAAGA--ATGTGCATTCCTAGCTAAATGCCAAATTCC Gorilla: AAGTATGAATGAGGTGAAAGA----ATGCATCCCTAGCTAAATGCCAAATTCC ↓ 3 1 2 4 Human: AAGTATGAATGAGGTGAAAGA--ATGTGCATTCCTAGCTAAATGCCAAATTCC Cluster: [ ] Orangutan: AAGTGTGAATGAGGTGAAAGAAC--GTGCATTCCTAGCTAAATGCCAAATTCC Gorilla > Human --------------- chr1:220447229-220447234 Template switch process: F1: L AGTCACTTCTGTGGTTCTTAAAGTATGAATGAGGTGAAAGAATG 1 F3: 4 CCTAGCTAAATGCCAAATTCCAAAGCCTTTAGTACAAAAA R RF: AGTCACTTATGTGGTTCTTAAAGTATGAATGAGGTGAAAGAATGCATCCCTAGCTAAATGCCAAATTCCAAAGCCTTTAGTACAAAAC RR: TCAGTGAATACACCAAGAATTTCATACTTACTCCACTTTCTTACGTAGGGATCGATTTACGGTTTAAGGTTTCGGAAATCATGTTTTG F2: 3 TTACGT 2 Unidirectional alignment (log-probability: -33.1) ACTTcTGTGGTTCTTAAAGTATGAATGAGGTGAAAGAAtgTGCATtCCTAGCTAAATGCCAAATTCCAAAGCCTTTAGTACAAAAa ACTTATGTGGTTCTTAAAGTATGAATGAGGTGAAAGAA--TGCATCCCTAGCTAAATGCCAAATTCCAAAGCCTTTAGTACAAAA- Template switch alignment (log-probability: -27.6) ACTTcTGTGGTTCTTAAAGTATGAATGAGGTGAAAGAATG|TGCATT|CCTAGCTAAATGCCAAATTCCAAAGCCTTTAGTACAAAAa ACTTATGTGGTTCTTAAAGTATGAATGAGGTGAAAGAATG|TGCATT|CCTAGCTAAATGCCAAATTCCAAAGCCTTTAGTACAAAAC ========= Event 762 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAGTCATTCAACTGCACTGACATACAGCATACATACAGCATACT-----GACAAAGAACCCCCAGTATCATCCTT Chimp: GGAGTCATTCAACTGCACTGCT---------ATATACAGCATACT-----GACGAAGAACCCCCAGTATCATCCTT ↓ 3 2 1 4 Gorilla: GGAGTCATTCAACTGCACTGCT---------ATATACAGCATACTGTATATAGCATGAACCCCCAGTATCATCCTT Human: GGAGTCATTCAACTGCACTGACATACAGCATACATACAGCATACT-----GACAAAGAACCCCCAGTATCATCCTT Cluster: [ ] Orangutan: GGAGTCATTCAACTGCACTGCT---------ATATACAGCATACT-----GACAAAGAACCCCCTGTATCATCCTT Chimp > Gorilla --------------- chr12:48074321-48074328 Template switch process: F1: L CAGAAGGAGTCATTCAACTGCACTGCTATATACAGCATACTG 1 F3: 4 ATGAACCCCCAGTATCATCCTTTTCCCACTTCTCATTCCCCC R RF: CAGAAGGAGTCATTCAACTGCACTGCTATATACAGCATACTGACGAAGAACCCCCAGTATCATCCTTTTCCCACTTCTCATTCCCCC RR: GTCTTCCTCAGTAAGTTGACGTGACGATATATGTCGTATGACTGCTTCTTGGGGGTCATAGTAGGAAAAGGGTGAAGAGTAAGGGGG F2: 3 CGATATAT 2 Unidirectional alignment (log-probability: -34.7) GAAGGAGTCATTCAACTGCACTGCTATATACAGCATACTGtatatAgcAtGAACCCCCAGTATCATCCTTTTCCCACTTCTCATTCCC GAAGGAGTCATTCAACTGCACTGCTATATACAGCATACTG-----ACGAAGAACCCCCAGTATCATCCTTTTCCCACTTCTCATTCCC Template switch alignment (log-probability: -22.3) GAAGGAGTCATTCAACTGCACTGCTATATACAGCATACTG|TATATAGC|AtGAACCCCCAGTATCATCCTTTTCCCACTTCTCATTCCC GAAGGAGTCATTCAACTGCACTGCTATATACAGCATACTG|TATATAGC|AAGAACCCCCAGTATCATCCTTTTCCCACTTCTCATTCCC ========= Event 763 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: gaaaaatCTATAACTTGAAGCCC-----------TGTAAAGCAAAGATTTACCAAACTTTAGATT ↓ 3 4 2 Chimp: gaaaaaTCTATAACTTGAAGCTTTGCTTTACAGGGGTAAAGCAAAGACTTACCAAACTTTAGATT ↑ 3 4 2 Gorilla: gaaaaaTCTATAACTTGAAGCCC-----------TGTAAAGCAAAGATTTACCAAACTTTAGATT Human: gaaaaatCTATAACTTGAAGCCC-----------TGTAAAGCAAAGATTTACCAAACTTTAGATT Cluster: [ ] Orangutan: gaaaaaTCTATAACTGTAAGCCC-----------TGTAAAGCAAAGTTTTACCAAACTTTAGATT Human > Chimp ------------- chr12:48651950-48651963 Template switch process: F1: L GGGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGC 1 F3: 4 GTAAAGCAAAGACTTACCAAACTTTAGATTTTATACCCCC R RF: GGGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGCCCTGTAAAGCAAAGATTTACCAAACTTTAGATTTTATACCCCC RR: CCCTTCTCTTTTCCTTTTTTCTTTTTAGATATTGAACTTCGGGACATTTCGTTTCTAAATGGTTTGAAATCTAAAATATGGGGG F2: 3 GGGACATTTCGTTT 2 Unidirectional alignment (log-probability: -44.7) GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGCttTgctttacagggGTAAAGCAAAGAcTTACCAAACTTTAGATTTTATACCCCC GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGCCCT-----------GTAAAGCAAAGATTTACCAAACTTTAGATTTTATACCCCC Template switch alignment (log-probability: -23) GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGC|TTTGCTTTACAGGG|GTAAAGCAAAGAcTTACCAAACTTTAGATTTTATACCCCC GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGC|TTTGCTTTACAGGG|GTAAAGCAAAGATTTACCAAACTTTAGATTTTATACCCCC Gorilla > Chimp --------------- chr12:48651950-48651963 Template switch process: F1: L GGGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGC 1 F3: 4 GTAAAGCAAAGACTTACCAAACTTTAGATTTTATACCCCC R RF: GGGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGCCCTGTAAAGCAAAGATTTACCAAACTTTAGATTTTATACCCCC RR: CCCTTCTCTTTTCCTTTTTTCTTTTTAGATATTGAACTTCGGGACATTTCGTTTCTAAATGGTTTGAAATCTAAAATATGGGGG F2: 3 GGGACATTTCGTTT 2 Unidirectional alignment (log-probability: -43.3) GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGCttTgctttacagggGTAAAGCAAAGAcTTACCAAACTTTAGATTTTATACCCCC GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGCCCT-----------GTAAAGCAAAGATTTACCAAACTTTAGATTTTATACCCCC Template switch alignment (log-probability: -23) GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGC|TTTGCTTTACAGGG|GTAAAGCAAAGAcTTACCAAACTTTAGATTTTATACCCCC GGAAGAGAAAAGGAAAAAAGAAAAATCTATAACTTGAAGC|TTTGCTTTACAGGG|GTAAAGCAAAGATTTACCAAACTTTAGATTTTATACCCCC ========= Event 764 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTATTACCAGAAACAATTTTCTTGATG-----TTC-----TACTAAAGCTTTCTCAAATTTT ↓ 3 1 24 Chimp: TATTATTACCAGAAACAATTTTCTTGATGAGAACATCAAGAAAGCTAAAGCTTTCTCAAATTTT ↑ 3 1 24 Gorilla: TATTATTACCAGAAACAATTTTCTTGATG-----TTC-----TACTAAAGCTTTCTCAAATTTT Human: TATTATTACCAGAAACAATTTTCTTGATG-----TTC-----TACTAAAGCTTTCTCAAATTTT Cluster: [ ] Orangutan: TATTATTACCAGAAACAATTTCCTTGACG-----TTC-----TACTAAAGGGTTCTCAAATTTT Human > Chimp ------------- chr12:48571159-48571172 Template switch process: F1: L AGCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG 1 F3: 4 GCTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTGT R RF: AGCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATGTTCTACTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTGT RR: TCGTGGTATCACATAATAATGGTCTTTGTTAAAAGAACTACAAGATGATTTCGAAAGAGTTTAAAATTAATTTCTCTACCGAAACA F2: 3 AAAGAACTACAAGA 2 Unidirectional alignment (log-probability: -41.5) GCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG----AgaacatcaagaaagCTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG GCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATGTTCTA--------------CTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG Template switch alignment (log-probability: -23) GCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG|AGAACATCAAGAAA|gCTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG GCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG|AGAACATCAAGAAA|ACTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG Gorilla > Chimp --------------- chr12:48571159-48571172 Template switch process: F1: L AGCACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG 1 F3: 4 GCTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTGT R RF: AGTACCATAGTGTATTATTACCAGAAACAATTTTCTTGATGTTCTACTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTGT RR: TCATGGTATCACATAATAATGGTCTTTGTTAAAAGAACTACAAGATGATTTCGAAAGAGTTTAAAATTAATTTCTCTACCGAAACA F2: 3 AAAGAACTACAAGA 2 Unidirectional alignment (log-probability: -46.5) GcACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG----AgaacatcaagaaagCTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG GTACCATAGTGTATTATTACCAGAAACAATTTTCTTGATGTTCTA--------------CTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG Template switch alignment (log-probability: -28.6) GcACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG|AGAACATCAAGAAA|gCTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG GTACCATAGTGTATTATTACCAGAAACAATTTTCTTGATG|AGAACATCAAGAAA|ACTAAAGCTTTCTCAAATTTTAATTAAAGAGATGGCTTTG ========= Event 765 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 345 Detected in comparisons: 3456 Multiple sequence alignment: Human: GGCAAAAGCCCTTGTTAGGATATGCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATATGCTAACAAGGGCTTTTGCTCG Chimp: GGCAAAAGCCCTTGTTAGGATATGCCATGCAGTCCAATATGCATCTATTCCAATATGTGCATATTGGACTGCATGGTATATGCTAACAAGGGCTTTTGCTCC ↑ 3 1 2 4 Gorilla: GGCAAAAGCCCTTGTTAGGATATACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGCATACGCTAACAAGGGCTTTTGCTCG ↓ 3 1 2 4 ↑ 13 24 Human: GGCAAAAGCCCTTGTTAGGATATGCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATATGCTAACAAGGGCTTTTGCTCG Cluster: [ ] Orangutan: GGTAAAAGCCCTTGTTAGCATATGCCATGCAGTCCAATATGCACGTATTCCAATATGTGCATATTGGACAGGATGGTATATGCTAACAAGGGCTTTTGCTCG Gorilla > Human --------------- chr12:47064072-47064129 Template switch process: F1: L CAAAAGCCCTTGTTAGGATAT 1 F3: 4 GCTAACAAGGGCTTTT R RF: CAAAAGCCCTTGTTAGGATATACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGCATACGCTAACAAGGGCTTTT RR: GTTTTCGGGAACAATCCTATATGGTACGTCAGGTTATACGTGTATAACCTTATATACGTATAACCTGACGTACCGTATGCGATTGTTCCCGAAAA F2: 3 TATATGGTACGTCAGGTTATACGTGTATAACCTTATATACGTATAACCTGACGTACCG 2 Unidirectional alignment (log-probability: -40) CAAAAGCCCTTGTTAGGATATgCCATGCAGTCCAATATGCAtATATTccAATATgTGCATATTGGACTGCATGGtATAtGCTAACAAGGGCTTTT CAAAAGCCCTTGTTAGGATATACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGCATACGCTAACAAGGGCTTTT Template switch alignment (log-probability: -22.1) CAAAAGCCCTTGTTAGGATAT|GCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATAT|GCTAACAAGGGCTTTT CAAAAGCCCTTGTTAGGATAT|GCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATAT|GCTAACAAGGGCTTTT Human > Gorilla --------------- chr12:47733583-47733636 Template switch process: F1: L CAAAAGCCCTTGTTAGGATAT 1 F3: 4 ATACGCTAACAAGGGCTTTT R RF: CAAAAGCCCTTGTTAGGATATGCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATATGCTAACAAGGGCTTTT RR: GTTTTCGGGAACAATCCTATACGGTACGTCAGGTTATACGTATATAAGGTTATACACGTATAACCTGACGTACCATATACGATTGTTCCCGAAAA F2: 3 CGGTACGTCAGGTTATACGTATATAAGGTTATACACGTATAACCTGACGTACCA 2 Unidirectional alignment (log-probability: -40) CAAAAGCCCTTGTTAGGATATaCCATGCAGTCCAATATGCAcATATTggAATATaTGCATATTGGACTGCATGGcATAcGCTAACAAGGGCTTTT CAAAAGCCCTTGTTAGGATATGCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATATGCTAACAAGGGCTTTT Template switch alignment (log-probability: -27.2) CAAAAGCCCTTGTTAGGATAT|ACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGC|ATAcGCTAACAAGGGCTTTT CAAAAGCCCTTGTTAGGATAT|ACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGC|ATATGCTAACAAGGGCTTTT Gorilla > Chimp --------------- chr12:48389195-48389252 Template switch process: F1: L CAAAAGCCCTTGTTAGGATAT 1 F3: 4 GCTAACAAGGGCTTTT R RF: CAAAAGCCCTTGTTAGGATATACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGCATACGCTAACAAGGGCTTTT RR: GTTTTCGGGAACAATCCTATATGGTACGTCAGGTTATACGTGTATAACCTTATATACGTATAACCTGACGTACCGTATGCGATTGTTCCCGAAAA F2: 3 TATATGGTACGTCAGGTTATACGTGTATAACCTTATCTACGTATAACCTGACGTACCG 2 Unidirectional alignment (log-probability: -45.5) CAAAAGCCCTTGTTAGGATATgCCATGCAGTCCAATATGCAtcTATTccAATATgTGCATATTGGACTGCATGGtATAtGCTAACAAGGGCTTTT CAAAAGCCCTTGTTAGGATATACCATGCAGTCCAATATGCACATATTGGAATATATGCATATTGGACTGCATGGCATACGCTAACAAGGGCTTTT Template switch alignment (log-probability: -27.6) CAAAAGCCCTTGTTAGGATAT|GCCATGCAGTCCAATATGCATcTATTCCAATATGTGCATATTGGACTGCATGGTATAT|GCTAACAAGGGCTTTT CAAAAGCCCTTGTTAGGATAT|GCCATGCAGTCCAATATGCATATATTCCAATATGTGCATATTGGACTGCATGGTATAT|GCTAACAAGGGCTTTT ========= Event 766 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAAACAGCTCTTGAGTCAAG---GAGCTACGTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCACTGGTATCTAAAATGCTGTAGGAGATGAT Chimp: taaaacagctcttaagtcaag---gagctacgttgtcatatgtgaaaaagaGCTGTTAGCTAAGAAAGCACTGGTAGCTAAAATGCTGTAGGAGATGAT Gorilla: CAAAACAGCTCTTGAGTCAAG------GCAAGTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCACTGGTAGCTAAAATGCTGTAGGAGATGAT ↓ 1 4 3 2 Human: TAAAACAGCTCTTGAGTCAAG---GAGCTACGTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCACTGGTATCTAAAATGCTGTAGGAGATGAT Cluster: [ ] Orangutan: caaaacagctcttgagtcaaggag---ttacgctgtcatatgtgaaaaagaGCTGTTAGCTAAGAAAGCACTGGTAGCTAAAACGCTGTAGGAGATGAT Gorilla > Human --------------- chr12:87625160-87625165 Template switch process: F1: L TGCAAGAAACATGTTAGAAGTAAAACAGCTCTTGAGTCAAGG 1 F3: 4 GTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCAC R RF: TGCAAGAAACATGTTAGAAGCAAAACAGCTCTTGAGTCAAGGCAAGTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCACTGGTAGCT RR: ACGTTCTTTGTACAATCTTCGTTTTGTCGAGAACTCAGTTCCGTTCAACAGTATACACTTTTTCTCGACAATCGATTCTTTCGTGACCATCGA F2: 3 CATCGA 2 Unidirectional alignment (log-probability: -31.8) CAAGAAACATGTTAGAAGtAAAACAGCTCTTGAGTCAAGGagctAcGTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCAC CAAGAAACATGTTAGAAGCAAAACAGCTCTTGAGTCAAGGC---AAGTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCAC Template switch alignment (log-probability: -22) CAAGAAACATGTTAGAAGtAAAACAGCTCTTGAGTCAAGG|AGCTAC|GTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCAC CAAGAAACATGTTAGAAGCAAAACAGCTCTTGAGTCAAGG|AGCTAC|GTTGTCATATGTGAAAAAGAGCTGTTAGCTAAGAAAGCAC ========= Event 767 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGTTAAACTATAGTGATGATGCTGTGCCCAGCATCTTTTACTGCTTCTGATTTTA ↑ 3 1 2 4 Chimp: ATGTTAAACTATAGTGATGATGCTGGGC----AAACTTTTACTGCTTCTAATTTTA Gorilla: ATGTTAAACTATAGTGATGATGCTGGGC----AAACTTTTACTGCTTCTGATTTTA ↓ 3 1 2 4 Human: ATGTTAAACTATAGTGATGATGCTGTGCCCAGCATCTTTTACTGCTTCTGATTTTA Cluster: [ ] Orangutan: -------------------------------------------------------- Chimp > Human ------------- chr12:45385377-45385386 Template switch process: F1: L TAAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTG 1 F3: 4 CTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC R RF: TAAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTGGGCAAACTTTTACTGCTTCTAATTTTAATGAGAATTTCTCTAGTGC RR: ATTCTGTGAGTCACTTTACAATTTGATATCACTACTACGACCCGTTTGAAAATGACGAAGATTAAAATTACTCTTAAAGAGATCACG F2: 3 TACGACCCGT 2 Unidirectional alignment (log-probability: -40.7) AAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTGtGCccagcAtCTTTTACTGCTTCTgATTTTAATGAGAATTTCTCTAGTGC AAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTGGGC----AAACTTTTACTGCTTCTAATTTTAATGAGAATTTCTCTAGTGC Template switch alignment (log-probability: -22.5) AAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTG|TGCCCAGCAT|CTTTTACTGCTTCTgATTTTAATGAGAATTTCTCTAGTGC AAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTG|TGCCCAGCAT|CTTTTACTGCTTCTAATTTTAATGAGAATTTCTCTAGTGC Gorilla > Human --------------- chr12:45385377-45385386 Template switch process: F1: L TAAGACACTCAGTGAAATGTTAAACTATAGTGATGATGCTG 1 F3: 4 CTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC R RF: TAAGACACTCAGTGGAATGTTAAACTATAGTGATGATGCTGGGCAAACTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC RR: ATTCTGTGAGTCACCTTACAATTTGATATCACTACTACGACCCGTTTGAAAATGACGAAGACTAAAATTACTCTTAAAGAGATCACG F2: 3 TACGACCCGT 2 Unidirectional alignment (log-probability: -38.8) AAGACACTCAGTGaAATGTTAAACTATAGTGATGATGCTGtGCccagcAtCTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC AAGACACTCAGTGGAATGTTAAACTATAGTGATGATGCTGGGC----AAACTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC Template switch alignment (log-probability: -22.5) AAGACACTCAGTGaAATGTTAAACTATAGTGATGATGCTG|TGCCCAGCAT|CTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC AAGACACTCAGTGGAATGTTAAACTATAGTGATGATGCTG|TGCCCAGCAT|CTTTTACTGCTTCTGATTTTAATGAGAATTTCTCTAGTGC ========= Event 768 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGGGAGAGGATATTAGGACATCACCTAATATCAGTATTCACCACATAATTTAtttctcaattataaaatgaggatggattaaacaattgat----ttttttttctagcccttatactctgtggttttCTTTCAGAGAGcagagattatcaaccattttcagcaactctctgg Chimp: TAAGGGAGAGGATATTAGGACG----TTGACAACAGTATTCACCACATAATTCATTTCTCAATTATAAAATGAGGATGGATTAAACGATTGAt---tttttttttCTAGCCCTTATACTCTGTGGTTTTCTTTCAGAGAGcagagattatcaaccattttcagcaactctctag Gorilla: TAAGGGAGAGGATATTAGGACG----TTGACAACAGTATTCACCACATAATTTATTTCTCAATTATAAAATGAGGATGGATTAAACGATTGAtttt-ttttttttATAGCTCTTATACTCTGTGGTTTTCTTTCAGAGAGcagagattatcaaccattttcagcaactctctgg ↑ 1 4 3 2 Human: TAAGGGAGAGGATATTAGGACATCACCTAATATCAGTATTCACCACATAATTTAtttctcaattataaaatgaggatggattaaacaattgat----ttttttttctagcccttatactctgtggttttCTTTCAGAGAGcagagattatcaaccattttcagcaactctctgg Cluster: [ ] Orangutan: TAAGGGAGAGGATATTAGGACG----TTGACAACAGTATTCACCACATAATTTATTTTTCAATTATAAAATGAGGATGGATTAAATGACTGAtttt-ttttttttCTAGCTCTAATAGTCTGTAGTTTTCTTTCAGAGAGCAGAGATTATCA-ACATTTTCAGCAACTCTCTGG Human > Gorilla --------------- chr12:46020007-46020014 Template switch process: F1: L AACTACACTGCTATTTCTCATAAGGGAGAGGATATTAGGAC 1 F3: 4 CAGTATTCACCACATAATTTATTTCTCAATTATAAAATGA R RF: AACTACACTGCTATTTCTCATAAGGGAGAGGATATTAGGACATCACCTAATATCAGTATTCACCACATAATTTATTTCTCAATTATAAAATGAGGATGGATTAAACAATTGATTTTTTTTTCTAGCCCTTATACTCTGTGGTTTTCTTTCAGAGAGCAGAGATTATCAAC RR: TTGATGTGACGATAAAGAGTATTCCCTCTCCTATAATCCTGTAGTGGATTATAGTCATAAGTGGTGTATTAAATAAAGAGTTAATATTTTACTCCTACCTAATTTGTTAACTAAAAAAAAAGATCGGGAATATGAGACACCAAAAGAAAGTCTCTCGTCTCTAATAGTTG F2: 3 AACAGTTG 2 Unidirectional alignment (log-probability: -31.3) ACTACACTGCTATTTCTCATAAGGGAGAGGATATTAGGACgttgacaA-----------CAGTATTCACCACATAATTTATTTCTCAATTATAAAATGA ACTACACTGCTATTTCTCATAAGGGAGAGGATATTAGGAC-------ATCACCTAATATCAGTATTCACCACATAATTTATTTCTCAATTATAAAATGA Template switch alignment (log-probability: -22.3) ACTACACTGCTATTTCTCATAAGGGAGAGGATATTAGGAC|GTTGAcAA|CAGTATTCACCACATAATTTATTTCTCAATTATAAAATGA ACTACACTGCTATTTCTCATAAGGGAGAGGATATTAGGAC|GTTGATAA|CAGTATTCACCACATAATTTATTTCTCAATTATAAAATGA ========= Event 769 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTAAAAATAACTAGAATATTGAGCTATCAAGATAGCTCAAGTGTGTTTTAATAATTCATCA Chimp: TCTAAAAATAACTAGAATATTGAGCTATCAAGATAGCTCAAGTGTGTTTTAATAATTCATCA ↑ 3 1 2 4 Gorilla: TCTAAAAATAACTAGAATATTGAGCTATCTTGGG-----TGGTGTGTTTTAATAATTCATCA ↓ 3 1 2 4 Human: TCTAAAAATAACTAGAATATTGAGCTATCAAGATAGCTCAAGTGTGTTTTAATAATTCATCA Cluster: [ ] Orangutan: TCTAAAAATAACTAGAATATTGAGCTATCTTGGG-----TGGTGTGTTTTAATAATTCATCA Gorilla > Human --------------- chr12:124329504-124329515 Template switch process: F1: L ACTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC 1 F3: 4 GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT R RF: ACTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATCTTGGGTGGTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT RR: TGATTGTCCGTAAGATTTTTATTGATCTTATAACTCGATAGAACCCACCACACAAAATTATTAAGTAGTAGTCGTTATTCCTACCAGA F2: 3 AACTCGATAGAA 2 Unidirectional alignment (log-probability: -38.2) CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC-------aagatagctcaaGTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATCTTGGGTG------------GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT Template switch alignment (log-probability: -17.3) CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC|AAGATAGCTCAA|GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC|AAGATAGCTCAA|GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT Gorilla > Chimp --------------- chr12:127838083-127838094 Template switch process: F1: L ACTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC 1 F3: 4 GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT R RF: ACTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATCTTGGGTGGTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT RR: TGATTGTCCGTAAGATTTTTATTGATCTTATAACTCGATAGAACCCACCACACAAAATTATTAAGTAGTAGTCGTTATTCCTACCAGA F2: 3 AACTCGATAGAA 2 Unidirectional alignment (log-probability: -38.2) CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC-------aagatagctcaaGTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATCTTGGGTG------------GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT Template switch alignment (log-probability: -17.3) CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC|AAGATAGCTCAA|GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT CTAACAGGCATTCTAAAAATAACTAGAATATTGAGCTATC|AAGATAGCTCAA|GTGTGTTTTAATAATTCATCATCAGCAATAAGGATGGTCT ========= Event 770 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGCTAGAGACAGGAGATAGG-----------AGGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCA Chimp: AGGCTAGAGACAGGAGATAGG-----------AGGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCA ↓ 14 3 2 Gorilla: AGGCTAGAGACAGGAGATAGGATAAGAACCAATAGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCA ↑ 14 3 2 Human: AGGCTAGAGACAGGAGATAGG-----------AGGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCA Cluster: [ ] Orangutan: AGGCTAGAGACAGGAGATAGG-----------AGGTTGCTATTGGTCCTTCCATTTTTCACAGTGCATCA Human > Gorilla --------------- chr12:88723607-88723617 Template switch process: F1: L TGGTAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAT 1 F3: 4 GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA R RF: TGGTAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAGGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA RR: ACCATTTTTGTGTTATGTTTTCCGATCTCTGTCCTCTATCCTCCGATGATAACCAAGAAGGTAAAAAGTGTCACGTAGTCTAT F2: 3 ATAACCAAGAA 2 Unidirectional alignment (log-probability: -32.2) TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAtaagaaccaataGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAG-----------GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA Template switch alignment (log-probability: -22.7) TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAt|AAGAACCAATA|GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAG|AAGAACCAATA|GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA Chimp > Gorilla --------------- chr12:88723607-88723617 Template switch process: F1: L TGGTAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAT 1 F3: 4 GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA R RF: TGGTAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAGGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA RR: ACCATTTTTGTGTTATGTTTTCCGATCTCTGTCCTCTATCCTCCGATGATAACCAAGAAGGTAAAAAGTGTCACGTAGTCTAT F2: 3 ATAACCAAGAA 2 Unidirectional alignment (log-probability: -32.2) TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAtaagaaccaataGCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAG-----------GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA Template switch alignment (log-probability: -22.7) TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAt|AAGAACCAATA|GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA TAAAAACACAATACAAAAGGCTAGAGACAGGAGATAGGAG|AAGAACCAATA|GCTACTATTGGTTCTTCCATTTTTCACAGTGCATCAGATA ========= Event 771 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAAGCAGGGCT----AGACCAAGAAGAGCCTCTAGAGCTCTTTTTTTGC Chimp: TTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAAGCAGGGCT----AGACCAAGAAGAGCCTCTAGAGCTCtttttttGC ↓ 3 2 1 4 Gorilla: TTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAATTTGGGGCC--------AAAGAAGAGTCTCTAGAGCTCtttttttGC ↑ 3 2 1 4 Human: TTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAAGCAGGGCT----AGACCAAGAAGAGCCTCTAGAGCTCTTTTTTTGC Cluster: [ ] Orangutan: ----------TTACAGCTTTGGCCCCAAACTCAAAAGCAGGGCTAGAC----CAAGAAGAGCCTCTAGAGCTCTTTTTTTCC Human > Gorilla --------------- chr12:44396511-44396520 Template switch process: F1: L CCTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA 1 F3: 4 AAGAAGAGTCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCTTGGGTATTG R RF: CCTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAAGCAGGGCTAGACCAAGAAGAGCCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCTTGGGTATTG RR: GGACTTAATCTCACTTAATCTCGAAACCGGGGTTTGAGTTTTCGTCCCGATCTGGTTCTTCTCGGAGATCTCGAGAAAAAAACGGGAACAAAGGAACCCATAAC F2: 3 ACCGGGGTTT 2 Unidirectional alignment (log-probability: -39.9) CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAtttggggccA-------------AAGAAGAGtCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA---------AGCAGGGCTAGACCAAGAAGAGCCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT Template switch alignment (log-probability: -22.7) CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA|TTTGGGGCCA|AAGAAGAGtCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA|TTTGGGGCCA|AAGAAGAGCCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT Chimp > Gorilla --------------- chr12:44396511-44396520 Template switch process: F1: L CCTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA 1 F3: 4 AAGAAGAGTCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCTTGGGTATTG R RF: CCTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAAGCAGGGCTAGACCAAGAAGAGCCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCTTGGGTATTG RR: GGACTTAATCTCACTTAATCTCGAAACCGGGGTTTGAGTTTTCGTCCCGATCTGGTTCTTCTCGGAGATCTCGAGAAAAAAACGGGAACAAAGGAACCCATAAC F2: 3 ACCGGGGTTT 2 Unidirectional alignment (log-probability: -39.9) CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAAtttggggccA-------------AAGAAGAGtCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA---------AGCAGGGCTAGACCAAGAAGAGCCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT Template switch alignment (log-probability: -22.7) CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA|TTTGGGGCCA|AAGAAGAGtCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT CTGAATTAGAGTGAATTAGAGCTTTGGCCCCAAACTCAAA|TTTGGGGCCA|AAGAAGAGCCTCTAGAGCTCTTTTTTTGCCCTTGTTTCCT ========= Event 772 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: tttttAAGTACAGAATTTCTGTACT-TAAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGTAACCATGGTGGATAAGCTACTGTGCTTATAAAAAGATCATTT ↓ 1 4 3 2 Chimp: tttttAAGTACAGAATTTCTGCAGTAGAAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGTAACCATGGTGGATAAGCTACTGTTCTTATAAAAAGATCATTT Gorilla: ------------------------------------------------------------------------------------------------------------- Human: tttttAAGTACAGAATTTCTGTACT-TAAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGTAACCATGGTGGATAAGCTACTGTGCTTATAAAAAGATCATTT Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------------------- Human > Chimp ------------- chr12:44806585-44806590 Template switch process: F1: L AAAACAAGAA-TTTTTTTTTTTTAAGTACAGAATTTCTG 1 F3: 4 AAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGT R RF: AAAACAAGAATTTTTTTTTTTTTAAGTACAGAATTTCTGTACTTAAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGTAACCATGGTGGATAAGCTACTG RR: TTTTGTTCTTAAAAAAAAAAAAATTCATGTCTTAAAGACATGAATTTGATGTCCTCCAGACCTTTAACATGGTCTCGACAGACATTGGTACCACCTATTCGATGAC F2: 3 GATGAC 2 Unidirectional alignment (log-probability: -40.3) AAAACAAGAA-TTTTTTTTTTTTAAGTACAGAATTTCTG-----cagtagAAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGT AAAACAAGAATTTTTTTTTTTTTAAGTACAGAATTTCTGTACTT------AAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGT Template switch alignment (log-probability: -26.2) AAAACAAGAA-TTTTTTTTTTTTAAGTACAGAATTTCTG|CAGTAG|AAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGT AAAACAAGAATTTTTTTTTTTTTAAGTACAGAATTTCTG|CAGTAG|AAACTACAGGAGGTCTGGAAATTGTACCAGAGCTGTCTGT ========= Event 773 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GACAGATGAAAAATACAAATGCATA------GGATTAAAAGGAAAGTGCCCAAAAA Chimp: GACAGATGAAAAATACAAATGCATA------GGATTAAAAGGAAAGTGCCCAAAAA ↓ 3 1 24 Gorilla: GACAGATGAAAAATACAAATGCATAATCCTATGCATAAAAGGAAAGTGCCCAAAAA ↑ 3 1 24 Human: GACAGATGAAAAATACAAATGCATA------GGATTAAAAGGAAAGTGCCCAAAAA Cluster: [ ] Orangutan: GACAGATGAAAAATACAAATGCATA------GGATTAAAAGGAAAGTGCCCAAAAA Human > Gorilla --------------- chr12:89710206-89710215 Template switch process: F1: L CAACTGATAGTACTTTGACAGATGAAAAATACAAATGCATA 1 F3: 4 TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA R RF: CAACTGATAGTACTTTGACAGATGAAAAATACAAATGCATAGGATTAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA RR: GTTGACTATCATGAAACTGTCTACTTTTTATGTTTACGTATCCTAATTTTCCTTTCACGGGTTTTTATATATTGATCCTAAATAT F2: 3 ACGTATCCTA 2 Unidirectional alignment (log-probability: -32.3) AACTGATAGTACTTTGACAGATGAAAAATACAAATGCATA--ATcctatgcaTAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA AACTGATAGTACTTTGACAGATGAAAAATACAAATGCATAGGAT--------TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA Template switch alignment (log-probability: -17) AACTGATAGTACTTTGACAGATGAAAAATACAAATGCATA|ATCCTATGCA|TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA AACTGATAGTACTTTGACAGATGAAAAATACAAATGCATA|ATCCTATGCA|TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA Chimp > Gorilla --------------- chr12:89710206-89710215 Template switch process: F1: L CAACTGATAGTACTTTGACAGATGAAAAATACAAATGCATA 1 F3: 4 TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA R RF: CAACTGATAGAACTTTGACAGATGAAAAATACAAATGCATAGGATTAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA RR: GTTGACTATCTTGAAACTGTCTACTTTTTATGTTTACGTATCCTAATTTTCCTTTCACGGGTTTTTATATATTGATCCTAAATAT F2: 3 ACGTATCCTA 2 Unidirectional alignment (log-probability: -37.8) AACTGATAGtACTTTGACAGATGAAAAATACAAATGCATA--ATcctatgcaTAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA AACTGATAGAACTTTGACAGATGAAAAATACAAATGCATAGGAT--------TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA Template switch alignment (log-probability: -22.5) AACTGATAGtACTTTGACAGATGAAAAATACAAATGCATA|ATCCTATGCA|TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA AACTGATAGAACTTTGACAGATGAAAAATACAAATGCATA|ATCCTATGCA|TAAAAGGAAAGTGCCCAAAAATATATAACTAGGATTTATA ========= Event 774 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATACTCATGTATTTGAAGTACAAAA--TGC--AATACTACTCCAAGGTTCCAGCC Chimp: ATACTCATGTATTTGAAGTACCAAA--TGC--AATACTACTCCAAGGTTCCAGCC ↓ 3 1 24 Gorilla: ATACTCATGTATTTGAAGTACAAAATTTGCATTTTACTACTCCAAGTTTCCAGCC ↑ 3 1 24 Human: ATACTCATGTATTTGAAGTACAAAA--TGC--AATACTACTCCAAGGTTCCAGCC Cluster: [ ] Orangutan: ATACTCATGTATTTGAAGTACCAAA--TGC--AATACTACTCCAAGGTTCCAGCC Human > Gorilla --------------- chr12:89956744-89956751 Template switch process: F1: L CTTAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAAT 1 F3: 4 TACTACTCCAAGTTTCCAGCCCCTTCCTGCTTCAAGCCCT R RF: CTTAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAATGCAATACTACTCCAAGGTTCCAGCCCCTTCCTGCTTCAAGCCCT RR: GAATTCTTGATTTTATTATGAGTACATAAACTTCATGTTTTACGTTATGATGAGGTTCCAAGGTCGGGGAAGGACGAAGTTCGGGA F2: 3 TTTACGTT 2 Unidirectional alignment (log-probability: -37.5) TAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAAttTGCAtttTACTACTCCAAGtTTCCAGCCCCTTCCTGCTTCAAGCCCT TAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAA--TGCAA--TACTACTCCAAGGTTCCAGCCCCTTCCTGCTTCAAGCCCT Template switch alignment (log-probability: -22.3) TAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAAT|TTGCATTT|TACTACTCCAAGtTTCCAGCCCCTTCCTGCTTCAAGCCCT TAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAAT|TTGCATTT|TACTACTCCAAGGTTCCAGCCCCTTCCTGCTTCAAGCCCT Chimp > Gorilla --------------- chr12:89956744-89956751 Template switch process: F1: L CTAGCTTAAGAACTAAAATAATACTCATGTATTTGAAGTACAAAAT 1 F3: 4 TACTACTCCAAGTTTCCAGCCCCTTCCTGCTTCAAGCCCT R RF: CTAGCTTAAGAACTAAAATAATACTCATGTATTTGAAGTACCAAATGCAATACTACTCCAAGGTTCCAGCCCCTTCCTGCTTCAAGCCCT RR: GATCGAATTCTTGATTTTATTATGAGTACATAAACTTCATGGTTTACGTTATGATGAGGTTCCAAGGTCGGGGAAGGACGAAGTTCGGGA F2: 3 TTTACGTT 2 Unidirectional alignment (log-probability: -42.3) TAAGAACTAAAATAATACTCATGTATTTGAAGTA-------CAAaatttgcatttTACTACTCCAAGtTTCCAGCCCCTTCCTGCTTCAAGCCCT TAAGAACTAAAATAATACTCATGTATTTGAAGTACCAAATGCAA-----------TACTACTCCAAGGTTCCAGCCCCTTCCTGCTTCAAGCCCT Template switch alignment (log-probability: -27.9) TAAGAACTAAAATAATACTCATGTATTTGAAGTACaAAAT|TTGCATTT|TACTACTCCAAGtTTCCAGCCCCTTCCTGCTTCAAGCCCT TAAGAACTAAAATAATACTCATGTATTTGAAGTACCAAAT|TTGCATTT|TACTACTCCAAGGTTCCAGCCCCTTCCTGCTTCAAGCCCT ========= Event 775 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCCAGTTTAATCTTTACCAGGTCACATGCAATTGTATCAATACACAGTAATGATCTCTCAGCACA ↓ 3 2 1 4 Chimp: ACCAGTTTAATCTTTACCAGGTCACATGCAATTGTAT-GTGACCCAGTAATGATCTCTCAGCACA Gorilla: ACCAGTTTAATCTTTACCAGGTCACATGCAATTGTATCAATACCCAGTAATGATCTCTCAGCACA Human: GCCAGTTTAATCTTTACCAGGTCACATGCAATTGTATCAATACACAGTAATGATCTCTCAGCACA Cluster: [ ] Orangutan: ACCAGTTTAATCTTTACCAGGTCACATGCAATTGTATCAATACCCAGTAATGATCTCTCAGCACA Human > Chimp ------------- chr12:93446455-93446460 Template switch process: F1: L AACTACCAGTTTAATCTTTACCAGGTCACATGCAATTGTAT 1 F3: 4 CAGTAATGATCTCTCAGCACACTAATTTTATTTACATTCT R RF: AACTGCCAGTTTAATCTTTACCAGGTCACATGCAATTGTATCAATACACAGTAATGATCTCTCAGCACACTAATTTTATTTACATTCT RR: TTGACGGTCAAATTAGAAATGGTCCAGTGTACGTTAACATAGTTATGTGTCATTACTAGAGAGTCGTGTGATTAAAATAAATGTAAGA F2: 3 CCAGTG 2 Unidirectional alignment (log-probability: -34.6) ACTaCCAGTTTAATCTTTACCAGGTCACATGCAATTGTATgtgacC------CAGTAATGATCTCTCAGCACACTAATTTTATTTACATTCT ACTGCCAGTTTAATCTTTACCAGGTCACATGCAATTGTAT-----CAATACACAGTAATGATCTCTCAGCACACTAATTTTATTTACATTCT Template switch alignment (log-probability: -22) ACTaCCAGTTTAATCTTTACCAGGTCACATGCAATTGTAT|GTGACC|CAGTAATGATCTCTCAGCACACTAATTTTATTTACATTCT ACTGCCAGTTTAATCTTTACCAGGTCACATGCAATTGTAT|GTGACC|CAGTAATGATCTCTCAGCACACTAATTTTATTTACATTCT ========= Event 776 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AACTTTATCTTCCTTAGAATAAAACCTCTGGAGGTTCAGCACTGTTTCCACCTCC Chimp: AACTTTATCTTCCTTAGAATAAAACCTCTGGAGGTTCAGCACTGTTTCCACCTCC ↑ 1 3 4 2 Gorilla: AACTTTATCTTCCTTAGAATA-AATCTCCAGAGGTTCAGCACTGTTTCCATCTCC ↓ 1 3 4 2 Human: AACTTTATCTTCCTTAGAATAAAACCTCTGGAGGTTCAGCACTGTTTCCACCTCC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr12:42601396-42601403 Template switch process: F1: L GGTCTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAA 1 F3: 4 AGGTTCAGCACTGTTTCCACCTCCTTCTCTTGCCGTTGA R RF: GGTCTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAATCTCCAGAGGTTCAGCACTGTTTCCATCTCCTTCTCTTGCCGTTGA RR: CCAGAGGGAAAGGGGGGATATTGAAATAGAAGGAATCTTATTTAGAGGTCTCCAAGTCGTGACAAAGGTAGAGGAAGAGAACGGCAACT F2: 3 GGTCTCCA 2 Unidirectional alignment (log-probability: -34.5) CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAAacCTCtgGAGGTTCAGCACTGTTTCCAcCTCCTTCTCTTGCCGTTGA CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAAT-CTCCAGAGGTTCAGCACTGTTTCCATCTCCTTCTCTTGCCGTTGA Template switch alignment (log-probability: -22.3) CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAA|ACCTCTGG|AGGTTCAGCACTGTTTCCAcCTCCTTCTCTTGCCGTTGA CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAA|ACCTCTGG|AGGTTCAGCACTGTTTCCATCTCCTTCTCTTGCCGTTGA Gorilla > Chimp --------------- chr12:43846187-43846194 Template switch process: F1: L GGTCTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAA 1 F3: 4 AGGTTCAGCACTGTTTCCACCTCCTTCTCTTGCCGTTGA R RF: GGTCTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAATCTCCAGAGGTTCAGCACTGTTTCCATCTCCTTCTCTTGCCGTTGA RR: CCAGAGGGAAAGGGGGGATATTGAAATAGAAGGAATCTTATTTAGAGGTCTCCAAGTCGTGACAAAGGTAGAGGAAGAGAACGGCAACT F2: 3 GGTCTCCA 2 Unidirectional alignment (log-probability: -34.5) CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAAacCTCtgGAGGTTCAGCACTGTTTCCAcCTCCTTCTCTTGCCGTTGA CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAAT-CTCCAGAGGTTCAGCACTGTTTCCATCTCCTTCTCTTGCCGTTGA Template switch alignment (log-probability: -22.3) CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAA|ACCTCTGG|AGGTTCAGCACTGTTTCCAcCTCCTTCTCTTGCCGTTGA CTCCCTTTCCCCCCTATAACTTTATCTTCCTTAGAATAAA|ACCTCTGG|AGGTTCAGCACTGTTTCCATCTCCTTCTCTTGCCGTTGA ========= Event 777 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATAAAACTCTGAGCCTTAT------------TATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA Chimp: AAGTAAAACTCTGAGCCTTAT------------TATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA ↓ 1 3 4 2 Gorilla: AAATAAAACTCTGAGCCTTATTTTTGTTCCGTGTATAAAATATGATTATTTTATACACGGAACAAAAATGTATTATGTATTATTTA ↑ 1 3 4 2 Human: AAATAAAACTCTGAGCCTTAT------------TATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr12:43256915-43256938 Template switch process: F1: L CGGTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTATT 1 F3: 4 TATTTTATACACGGAACAAAAATGTATTATGTATTATTTA R RF: TGGTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTATTATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA RR: ACCACAAAAGAATAGTTTGGTTTATTTTGAGACTCGGAATAATATTTTATTAGTATAAAATATGTGCCTTGTTTTTACATAATACATAATAAAT F2: 3 TAGTATAAAATATGTGCCTTGTTT 2 Unidirectional alignment (log-probability: -55.9) GTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTATttttgttccgtgTATAAAATAtgatTATTTTATACACGGAACAAAAATGTATTATGTATTATTTA GTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTAT------------TATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA Template switch alignment (log-probability: -24.3) GTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTATT|TTTGTTCCGTGTATAAAATATGAT|TATTTTATACACGGAACAAAAATGTATTATGTATTATTTA GTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTATT|TTTGTTCCGTGTATAAAATATGAT|TATTTTATACACGGAACAAAAATGTATTATGTATTATTTA Chimp > Gorilla --------------- chr12:43256915-43256938 Template switch process: F1: L CGGTGTTTTCTTATCAAACCAAATAAAACTCTGAGCCTTATT 1 F3: 4 TATTTTATACACGGAACAAAAATGTATTATGTATTATTTA R RF: CGGTGTTTTCTTATCAAACCAAGTAAAACTCTGAGCCTTATTATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA RR: GCCACAAAAGAATAGTTTGGTTCATTTTGAGACTCGGAATAATATTTTATTAGTATAAAATATGTGCCTTGTTTTTACATAATACATAATAAAT F2: 3 TAGTATAAAATATGTGCCTTGTTT 2 Unidirectional alignment (log-probability: -55.9) GTGTTTTCTTATCAAACCAAaTAAAACTCTGAGCCTTATttttgttccgtgTATAAAATAtgatTATTTTATACACGGAACAAAAATGTATTATGTATTATTTA GTGTTTTCTTATCAAACCAAGTAAAACTCTGAGCCTTAT------------TATAAAATAATCATATTTTATACACGGAACAAAAATGTATTATGTATTATTTA Template switch alignment (log-probability: -24.3) GTGTTTTCTTATCAAACCAAaTAAAACTCTGAGCCTTATT|TTTGTTCCGTGTATAAAATATGAT|TATTTTATACACGGAACAAAAATGTATTATGTATTATTTA GTGTTTTCTTATCAAACCAAGTAAAACTCTGAGCCTTATT|TTTGTTCCGTGTATAAAATATGAT|TATTTTATACACGGAACAAAAATGTATTATGTATTATTTA ========= Event 778 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTATAATTTTGCCTTTGTGGTGCAGATAGATTATAC--------------------CTGCACCAAGAGAAAGGTCACTGAAGAT ↑ 3 2 1 4 Chimp: GTTATAATTTTGCCTTTGTGGTGCAGATAGATTATAC----------CCAAGTGTCTATTTATAAAGAGAAAGGTCACTGAAGAT Gorilla: GTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACCCAAGTGTCT----------ATTTATAAAGAGAAAGGTCACTGAAGAT ↓ 3 2 1 4 Human: GTTATAATTTTGCCTTTGTGGTGCAGATAGATTATAC--------------------CTGCACCAAGAGAAAGGTCACTGAAGAT Cluster: [ ] Orangutan: GTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACCCAAGTGTCT----------ATTTATACAGAGAAAGGTCACTGAAGAT Chimp > Human ------------- chr12:91221613-91221618 Template switch process: F1: L GTTGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACC 1 F3: 4 AAGAGAAAGGTCACTGAAGATGCAGAGTGCATTCACTGGA R RF: GTTGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACCCAAGTGTCTATTTATAAAGAGAAAGGTCACTGAAGATGCAGAGTGCGTTCACTGGA RR: CAACCAATATTAAAACGGAAACACCACGTCTATCTAATATGGGTTCACAGATAAATATTTCTCTTTCCAGTGACTTCTACGTCTCACGCAAGTGACCT F2: 3 CCACGT 2 Unidirectional alignment (log-probability: -35.1) TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACctgcaCC---------------AAGAGAAAGGTCACTGAAGATGCAGAGTGCaTTCACTGGA TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATAC-----CCAAGTGTCTATTTATAAAGAGAAAGGTCACTGAAGATGCAGAGTGCGTTCACTGGA Template switch alignment (log-probability: -22) TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACC|TGCACC|AAGAGAAAGGTCACTGAAGATGCAGAGTGCaTTCACTGGA TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACC|TGCACC|AAGAGAAAGGTCACTGAAGATGCAGAGTGCGTTCACTGGA Gorilla > Human --------------- chr12:91221613-91221618 Template switch process: F1: L GTTGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACC 1 F3: 4 AAGAGAAAGGTCACTGAAGATGCAGAGTGCATTCACTGGA R RF: GTTGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACCCAAGTGTCTATTTATAAAGAGAAAGGTCACTGAAGATGCAGAGTGCGTTCACTGGA RR: CAACCAATATTAAAACGGAAACACCACGTCTATCTAATATGGGTTCACAGATAAATATTTCTCTTTCCAGTGACTTCTACGTCTCACGCAAGTGACCT F2: 3 CCACGT 2 Unidirectional alignment (log-probability: -34.1) TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACctgcaCC---------------AAGAGAAAGGTCACTGAAGATGCAGAGTGCaTTCACTGGA TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATAC-----CCAAGTGTCTATTTATAAAGAGAAAGGTCACTGAAGATGCAGAGTGCGTTCACTGGA Template switch alignment (log-probability: -22) TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACC|TGCACC|AAGAGAAAGGTCACTGAAGATGCAGAGTGCaTTCACTGGA TGGTTATAATTTTGCCTTTGTGGTGCAGATAGATTATACC|TGCACC|AAGAGAAAGGTCACTGAAGATGCAGAGTGCGTTCACTGGA ========= Event 779 ========= Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TTTGGTCAAAAATCTCAATATGGTATTATCTCTTGGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCCCCATATATTGGGGGAAAAAAATAATACACTTTTTTGGGGGGTAAGTT Chimp: TTTGGTCAAAAATCTCAATAT-----------GCGGCATTGATTTTTCAAAATGACAGaaaaaaaTTAAATT-CCCATATATTGGCGGA-AAAAATAATACACTTTTTTGGGGGGTAAGTT ↓ 1 4 3 2 Gorilla: TTTGGTCAAAAATCTCAATATGGTATTATCTCTTGGCATTGATTTTTCAAAATGACAGaaaaaaaTTAAATTCCCCATATATTGGGGGaaaaaaaTAATACACTTTTTTGGGGGGTAAGTT Human: TTTGGTCAAAAATCTCAATATGGTATTATCTCTTGGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCCCCATATATTGGGGGAAAAAAATAATACACTTTTTTGGGGGGTAAGTT Cluster: [ ] Orangutan: TTTGGTCAAAAATCTCAATGTGGTATTATCTCTTGGCATTGATTTTTCAAAATGACATAAAAAAATTAAATTCCCCATGTATTGGGGGAAA----AAATACACTTTTTTG-GGGGTAAGTT Chimp > Gorilla --------------- chr1:29291456-29291467 Template switch process: F1: L GGCAATTTACGCTGTTAACATTTGGTCAAAAATCTCAATATG 1 F3: 4 GGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCC R RF: GGCAATTTACGCTGTTAACATTTGGTCAAAAATCTCAATATGCGGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCCCATATATTGGCGGAAAAAATAATAC RR: CCGTTAAATGCGACAATTGTAAACCAGTTTTTAGAGTTATACGCCGTAACTAAAAAGTTTTACTGTCTTTTTTTAATTTAAGGGTATATAACCGCCTTTTTTATTATG F2: 3 TTCTCTATTATG 2 Unidirectional alignment (log-probability: -40.4) CAATTTACGCTGTTAACATTTGGTCAAAAATCTCAATATGgtattatctcttGGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCc CAATTTACGCTGTTAACATTTGGTCAAAAATCTCAATATGC-----------GGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTC- Template switch alignment (log-probability: -28.3) CAATTTACGCTGTTAACATTTGGTCAAAAATCTCAATATG|GTATTATcTcTT|GGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCC CAATTTACGCTGTTAACATTTGGTCAAAAATCTCAATATG|GTATTATTTTTT|GGCATTGATTTTTCAAAATGACAGAAAAAAATTAAATTCC ========= Event 780 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGATGGGAACATTCTAGAGAGAGAATACACATATAGGACT-----TGATAAAAGTCCTATATGTGTA---TTCTTTTTTTGCAATTAAAAGTTTTAT ↑ 3 1 2 4 Chimp: TGATGGGAACATTCTAGAGAGAGAATACACATATAGGACTTTTATCAATAAA----------------------ACTTTTGCAATTAAAAGTTTTAT Gorilla: TGATGGGAACATTCTAGAGAGAGAATACACATATAGGACT-----TGATAAAAGTCCTATATATGTA------tttttttGCAATTAAAAATTTTAT Human: TGATGGGAACATTCTAGAGAGAGAATACACATATAGGACT-----TGATAAAAGTCCTATATGTGTA---TTCTTTTTTTGCAATTAAAAGTTTTAT Cluster: [ ] Orangutan: TGATGGGAACATTCTAGAAAGAGAATGCACATATAGGACT-----TGATAAAAGTCCTATATGTGTATTC---TTTTTTTGCAATTAAAAGTTTTAT Chimp > Human ------------- chr12:88590759-88590785 Template switch process: F1: L GTGATGGGAACATTCTAGAGAGAGAATACACATATAGGACTT 1 F3: 4 TTTTGCAATTAAAAGTTTTATTAACATAAATATTTGCGAC R RF: GTGATGGGAACATTCTAGAGAGAGAATACACATATAGGACTTTTATCAATAAAACTTTTGCAATTAAAAGTTTTATTAACATAAATATTTGCGAC RR: CACTACCCTTGTAAGATCTCTCTCTTATGTGTATATCCTGAAAATAGTTATTTTGAAAACGTTAATTTTCAAAATAATTGTATTTATAAACGCTG F2: 3 TTTCTTATGTGTATATCCTGAAAATAG 2 Unidirectional alignment (log-probability: -57.7) GATGGGAACATTCTAGAGAGAGAATACACATATAGGACTTgataaaagtcctatatgtgtattctTT-----------TTTTGCAATTAAAAGTTTTATTAACATAAATATTTGCGAC GATGGGAACATTCTAGAGAGAGAATACACATATAGGACTT-------------------------TTATCAATAAAACTTTTGCAATTAAAAGTTTTATTAACATAAATATTTGCGAC Template switch alignment (log-probability: -24.6) GATGGGAACATTCTAGAGAGAGAATACACATATAGGACTT|GATAAAAGTCCTATATGTGTATTCTtT|TTTTGCAATTAAAAGTTTTATTAACATAAATATTTGCGAC GATGGGAACATTCTAGAGAGAGAATACACATATAGGACTT|GATAAAAGTCCTATATGTGTATTCTCT|TTTTGCAATTAAAAGTTTTATTAACATAAATATTTGCGAC ========= Event 781 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTAGACAACACAGAAGGCAGAGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGT-----------------------------------------------------TTGACTCAAAACATATGCCTCCCCT ↓ 3 4 2 1 Chimp: ACTAGACAACACAGAAGGCAGAGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACACTGGCTCCTCTCCTCTGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAAAACATATGCCTCCCCT ↑ 3 4 2 1 Gorilla: ACTAGACAACACAGAAGGCAGAGGAGAGGAGCCAGTGTTACAGAGCCATGTGCTGT-----------------------------------------------------TTGACTCAAAACATATGCCTCCCCT Human: ACTAGACAACACAGAAGGCAGAGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGT-----------------------------------------------------TTGACTCAAAACATATGCCTCCCCT Cluster: [ ] Orangutan: ACTAGACAACACAGAAGGCAGAGGAGAGGAGCCAGTGTTATGGAGCCATGTGCTGT-----------------------------------------------------TTGACTCAAAAGATATGCCTCCCCT Human > Chimp ------------- chr12:94361356-94361372 Template switch process: F1: L AGGCAGAGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGAC 1 F3: 4 GAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAAAACATATGCCTCCCCTCACCTCTAACCAGGC R RF: AGGCAGAGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAAAACATATGCCTCCCCTCACCTCTAACCAGGC RR: TCCGTCTCCTCTCCTCGGTCACAATGCCTCGGTACACGACAAACTGAGTTTTGTATACGGAGGGGAGTGGAGATTGGTCCG F2: 3 TCTCCTCTCCTCGGTCA 2 Unidirectional alignment (log-probability: -87.1) AGGAgaggagccagtgttacggagccatgtgctgtttgacactggctcctctcctctGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAA AGGA-----------------------------------------------------GAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAA Template switch alignment (log-probability: -18) AGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGAC|ACTGGCTCCTCTCCTCT|GAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAA AGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGAC|ACTGGCTCCTCTCCTCT|GAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAA Gorilla > Chimp --------------- chr12:94361356-94361372 Template switch process: F1: L AGGCAGAGGAGAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGAC 1 F3: 4 GAGGAGCCAGTGTTACGGAGCCATGTGCTGTTTGACTCAAAACATATGCCTCCCCTCACCTCTAACCAGGC R RF: AGGCAGAGGAGAGGAGCCAGTGTTACAGAGCCATGTGCTGTTTGACTCAAAACATATGCCTCCCCTCACCTCTAACCAGGC RR: TCCGTCTCCTCTCCTCGGTCACAATGTCTCGGTACACGACAAACTGAGTTTTGTATACGGAGGGGAGTGGAGATTGGTCCG F2: 3 TCTCCTCTCCTCGGTCA 2 Unidirectional alignment (log-probability: -92.6) AGGAgaggagccagtgttacggagccatgtgctgtttgacactggctcctctcctctGAGGAGCCAGTGTTACgGAGCCATGTGCTGTTTGACTCAA AGGA-----------------------------------------------------GAGGAGCCAGTGTTACAGAGCCATGTGCTGTTTGACTCAA Template switch alignment (log-probability: -29.8) AGGAGAGGAGCCAGTGTTACgGAGCCATGTGCTGTTTGAC|ACTGGCTCCTCTCCTCT|GAGGAGCCAGTGTTACgGAGCCATGTGCTGTTTGACTCAA AGGAGAGGAGCCAGTGTTACAGAGCCATGTGCTGTTTGAC|ACTGGCTCCTCTCCTCT|GAGGAGCCAGTGTTACAGAGCCATGTGCTGTTTGACTCAA ========= Event 782 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 346 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATT-TCTGATTATTTCAATGAACTCTCAGGAGA Chimp: TCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATT-TCTGATTGTTTCAATGAACTCTCAGGAGA ↓ 13 24 Gorilla: TCCTGAGAGTTCATTGAAACAATCA-GAAATACAAATTTTGTATTTGCTGATTGTTTCAATGAACTCTCAGGAGA ↓ 13 24 ↑ 3 1 2 4 Human: TCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATT-TCTGATTATTTCAATGAACTCTCAGGAGA Cluster: [ ] Orangutan: --------------------------------------------------------------------------- Gorilla > Human --------------- chr12:91607760-91607779 Template switch process: F1: L AAAACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG 1 F3: 4 CTGATTATTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA R RF: AAAACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAGAAATACAAATTTTGTATTTGCTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA RR: TTTTGAGATCCCAAAGAGGACTCTCAAGTAACTTTGTTAGTCTTTATGTTTAAAACATAAACGACTAACAAAGTTACTTGAGAGTCCTCTTTGGGATAAACATATATAT F2: 3 TTTATGTTTAAAACATAAAC 2 Unidirectional alignment (log-probability: -33.5) AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAGcAAATACAAAaTTTGTATTT-CTGATTaTTTCAATGAACTCTCAGGAGAAACCCTATTTGT AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG-AAATACAAATTTTGTATTTGCTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT Template switch alignment (log-probability: -24) AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG|CAAATACAAAATTTGTATTT|CTGATTaTTTCAATGAACTCTCAGGAGAAACCCTATTTGT AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG|CAAATACAAAATTTGTATTT|CTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT Human > Gorilla --------------- chr12:91182608-91182634 Template switch process: F1: L AAAACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG 1 F3: 4 TTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA R RF: AAAACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATTTCTGATTATTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA RR: TTTTGAGATCCCAAAGAGGACTCTCAAGTAACTTTGTTAGTCGTTTATGTTTTAAACATAAAGACTAATAAAGTTACTTGAGAGTCCTCTTTGGGATAAACATATATAT F2: 3 GTTAGTCGTTTATGTTTTAAACATAAA 2 Unidirectional alignment (log-probability: -33.5) AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG-AAATACAAAtTTTGTATTTgCTGATTgTTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATTT-CTGATTATTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA Template switch alignment (log-probability: -19.2) AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG|AAATACAAATTTTGTATTTGCTGATTG|TTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG|AAATACAAATTTTGTATTTGCTGATTG|TTTCAATGAACTCTCAGGAGAAACCCTATTTGTATATATA Chimp > Gorilla --------------- chr12:91182608-91182627 Template switch process: F1: L AAAACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG 1 F3: 4 CTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT R RF: AAAACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATTTCTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT RR: TTTTGAGATCCCAAAGAGGACTCTCAAGTAACTTTGTTAGTCGTTTATGTTTTAAACATAAAGACTAACAAAGTTACTTGAGAGTCCTCTTTGGGATAAACA F2: 3 GTTTATGTTTTAAACATAAA 2 Unidirectional alignment (log-probability: -27.9) AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG-AAATACAAAtTTTGTATTTgCTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAGCAAATACAAAATTTGTATTT-CTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT Template switch alignment (log-probability: -18.3) AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG|AAATACAAATTTTGTATTTG|CTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT AACTCTAGGGTTTCTCCTGAGAGTTCATTGAAACAATCAG|AAATACAAATTTTGTATTTG|CTGATTGTTTCAATGAACTCTCAGGAGAAACCCTATTTGT ========= Event 783 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTATCAGAAAATCTGGTCAACAGATCACCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATGGGTGATCTTTTTAGCTTCTCAGAACTCA ↑ 1 4 3 2 Chimp: GTATCAGAAAATCTGGTCAACTGTGGGCCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATAGGTGATCTTTTTAGCTTCTCAGAACTCA Gorilla: GTATCAGAAAATCTGGTCAACTGTGGGCCACAGTGGTGGTGATGGGGTAGAGAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATGGGTGATCTTTTTAGCTTCTCAGAACTCA ↓ 1 4 3 2 Human: GTATCAGAAAATCTGGTCAACAGATCACCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATGGGTGATCTTTTTAGCTTCTCAGAACTCA Cluster: [ ] Orangutan: GTATCAGAAAATCTGGTCAACTGTGGGCCACAGTGGTAGTGATGGGGTAGAGAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATGGGTGGTCTTTTTAGCGTCTCAGAACTCA Chimp > Human ------------- chr12:40297422-40297427 Template switch process: F1: L TAATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC 1 F3: 4 CCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGG R RF: TAATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAACTGTGGGCCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATAGGTGATCT RR: ATTAGTGGAACCTTCACCGTCATAGTCTTTTAGACCAGTTGACACCCGGTGTCACCACCACTACCCCATCTGTCAACCATCGAACCCATTCCTATAAACGTCAAAACTTATCCACTAGA F2: 3 ACTAGA 2 Unidirectional alignment (log-probability: -30.1) AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAACagatca------CCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGG AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC------TGTGGGCCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGG Template switch alignment (log-probability: -16) AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC|AGATCA|CCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGG AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC|AGATCA|CCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGG Gorilla > Human --------------- chr12:40297422-40297427 Template switch process: F1: L TAATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC 1 F3: 4 CCACAGTGGTGGTGATGGGGTAGACAGTTGGTAGCTTGGG R RF: TAATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAACTGTGGGCCACAGTGGTGGTGATGGGGTAGAGAGTTGGTAGCTTGGGTAAGGATATTTGCAGTTTTGAATGGGTGATCT RR: ATTAGTGGAACCTTCACCGTCATAGTCTTTTAGACCAGTTGACACCCGGTGTCACCACCACTACCCCATCTCTCAACCATCGAACCCATTCCTATAAACGTCAAAACTTACCCACTAGA F2: 3 ACTAGA 2 Unidirectional alignment (log-probability: -34.3) AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAACaGatcaCCACAGTGGTGGTGATGGGGTAGAcAGTTGGTAGCTTGGG AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAACTGTGGGCCACAGTGGTGGTGATGGGGTAGAGAGTTGGTAGCTTGGG Template switch alignment (log-probability: -22) AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC|AGATCA|CCACAGTGGTGGTGATGGGGTAGAcAGTTGGTAGCTTGGG AATCACCTTGGAAGTGGCAGTATCAGAAAATCTGGTCAAC|AGATCA|CCACAGTGGTGGTGATGGGGTAGAGAGTTGGTAGCTTGGG ========= Event 784 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGGTGCATTATTTATGTTCTTCCCCATATAAACTCATTGTTTATATGAGTTTATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAAGTCTTTTGTGCccaacctggccaacacagtgaaaccccatctctactaaaaatacaaaaattagcccagtatggtggtatgtgcctgtagtcccagctacccaggaggctgag ↓ 1 4 3 2 Chimp: CAGGTGCATTATTTATGTTCT-------------------------TGGTCTAATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAAGTCTTTTGTGCccaacctggccaacacagtgaaaccccatctctactaaaaatacaaaaattagcccagtatggtgatatgtgcctgtagtcccagctacccaggaggctgag Gorilla: CAGGTGCATTATTTATGTTCT-------------------------TGGTCTAATTCCTTCCCCATATAAACTCATTGTTACGTTGATAAGAAGTCTtttgtgaccaacctggccaacacagtgaaaccccatctctactaaaaatacaaaaattagcccagtatggtgatatgtgcctgtagtcccagctacccaggaggctgag Human: CAGGTGCATTATTTATGTTCTTCCCCATATAAACTCATTGTTTATATGAGTTTATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAAGTCTTTTGTGCccaacctggccaacacagtgaaaccccatctctactaaaaatacaaaaattagcccagtatggtggtatgtgcctgtagtcccagctacccaggaggctgag Cluster: [ ] Orangutan: CAGGTGCATTATTTATGTTCT-------------------------TGTTCTAATTCCTTCCCCATATAAGCTCATTGTTATGTTAATAAGAAGTCTTTTGCACccagcctggccaacatagtgaaaccccatctctattaaaaatacaaaaattagcccagtgtggtggtacgcacctgtagtcccagctacccattaggctgag Human > Chimp ------------- chr12:38724642-38724647 Template switch process: F1: L TCTTAGCGGCACTGATGAAACAGGTGCATTATTTATGTTCTT 1 F3: 4 ATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAA R RF: TCTTAGCGGCACTGATGAAACAGGTGCATTATTTATGTTCTTCCCCATATAAACTCATTGTTTATATGAGTTTATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAAGTCTTTTGTGCCCAACCTGGCCAACACAGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCCAGTATGGTGGTATGTGCCTGTAGTCC RR: AGAATCGCCGTGACTACTTTGTCCACGTAATAAATACAAGAAGGGGTATATTTGAGTAACAAATATACTCAAATAAGGAAGGGGTATATTTGAGTAACAATGTAATTATTCTTCAGAAAACACGGGTTGGACCGGTTGTGTCACTTTGGGGTAGAGATGATTTTTATGTTTTTAATCGGGTCATACCACCATACACGGACATCAGG F2: 3 ATCTGG 2 Unidirectional alignment (log-probability: -31.4) TTAGCGGCACTGATGAAACAGGTGCATTATTTATGTTCTTggtcta-------------------------------ATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAA TTAGCGGCACTGATGAAACAGGTGCATTATTTATGTTCTT------CCCCATATAAACTCATTGTTTATATGAGTTTATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAA Template switch alignment (log-probability: -22) TTAGCGGCACTGATGAAACAGGTGCATTATTTATGTTCTT|GGtCTA|ATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAA TTAGCGGCACTGATGAAACAGGTGCATTATTTATGTTCTT|GGACTA|ATTCCTTCCCCATATAAACTCATTGTTACATTAATAAGAA ========= Event 785 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCTCCCAGGAGGACAGTTACTGCCAAAAGAATGTAGTATTAAAGTTTGCAAAAGCGGATAAAATGTAAAGGTAATAGCTCTGGC---------------CATTCATACTCAGTTCTAGATGTCAAACTTAG-AAGTTTCTAAAGATAA Chimp: TTCTCCCAGGAGGACAGTTACTGCCAAAAGAATGTAGTATTAAAGTTTGCAAAAGTGGATAAAATGTAAAGGTAATAGCTCTGGC---------------CATTCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTAAAGATAA ↓ 3 2 4 1 Gorilla: TCCTCCCCGGAGGACAGTTACTGCCAAAAGAATGTAGTATTAAAGTTTGCAAAAGTGGATAAAATGTAAAGGTAATAGCTCTGTTCTAGATGTCAAACTCAGTTCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTAAAGATAA Human: TCCTCCCAGGAGGACAGTTACTGCCAAAAGAATGTAGTATTAAAGTTTGCAAAAGCGGATAAAATGTAAAGGTAATAGCTCTGGC---------------CATTCATACTCAGTTCTAGATGTCAAACTTAG-AAGTTTCTAAAGATAA Cluster: [ ] Orangutan: TCCTCCCAGGAGGACAGTTACTGCCAAAAGAATATAGTATTAAAGTTTGCAAAAGTGGATAAAATGTAAAGGTAATAGCTCTGGC---------------CATTCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTAAAGATAA Chimp > Gorilla --------------- chr12:37830731-37830734 Template switch process: F1: L AAGTTTGCAAAAGTGGATAAAATGTAAAGGTAATAGCTCT---------------GTTCTAGATGTCAAACT 1 F3: 4 TCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTA R RF: ACTGCCAAAAGAATGTAGTATTAAAGTTTGCAAAAGTGGATAAAATGTAAAGGTAATAGCTCTGGCCATTCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTA RR: TGACGGTTTTCTTACATCATAATTTCAAACGTTTTCACCTATTTTACATTTCCATTATCGAGACCGGTAAGTATGAGTCAAGATCTACAGTTTGAATCTTTCAAAGAT F2: 3 TGAC 2 Unidirectional alignment (log-probability: -46.7) TAAAATGTAAAGGTAATAGCTCTGttctagatgtcaaactcaG---TTCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTA TAAAATGTAAAGGTAATAGCTCTG------------------GCCATTCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTA Template switch alignment (log-probability: -27.1) TAAAATGTAAAGGTAATAGCTCT---------------GTTCTAGATGTCAAACT|CAGT|TCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTA TAAAATGTAAAGGTAATAGCTCTGGCCATTCATACTCAGTTCTAGATGTCAAACT|CAGT|TCATACTCAGTTCTAGATGTCAAACTTAGAAAGTTTCTA ========= Event 786 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CCCGATCTCAGCTGCGTTGGGCGCGCAGGGGTGGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATCAGACCTGCCTGACCAGTGCACGCCCAACCCCTGCGATAGGAAGGGGACCCAAG ↑ 1 4 3 2 Chimp: CCCGATCTCAGCTGCGTTGGG--CACGGGGTGGGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATCAGACCTGCCTGACCAGTGCACGCCCAACCCCTGCGATAGGAAGGGGACCCAAG Gorilla: Human: CCCGATCTCAGCTGCGTTGGGCGCGCAGGGGTGGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATCAGACCTGCCTGACCAGTGCACGCCCAACCCCTGCGATAGGAAGGGGACCCAAG Cluster: [ ] Orangutan: Chimp > Human ------------- chr13:524430-524436 Template switch process: F1: L ACCCGAGACCCCACAGCCGCCCCGATCTCAGCTGCGTTGGGCGCG 1 F3: 4 GGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATC R RF: ACCCGAGACCCCACAGCCGCCCCGATCTCAGCTGCGTTGGGCACGGGGTGGGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATCAGACCTGCCTGACCAGTGCACGCCCAACCCCTG RR: TGGGCTCTGGGGTGTCGGCGGGGCTAGAGTCGACGCAACCCGTGCCCCACCCCCGTCGACTTGTACTAAAAGGTGAAACACAGGGGTTAGTCTGGACGGACTGGTCACGTGCGGGTTGGGGAC F2: 3 TGGGGAC 2 Unidirectional alignment (log-probability: -31.6) AGACCCCACAGCCGCCCCGATCTCAGCTGCGTTGGGCgCgcaGGGGT-GGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATC AGACCCCACAGCCGCCCCGATCTCAGCTGCGTTGGGCAC---GGGGTGGGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATC Template switch alignment (log-probability: -22.2) AGACCCCACAGCCGCCCCGATCTCAGCTGCGTTGGGCgCG|CAGGGGT|GGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATC AGACCCCACAGCCGCCCCGATCTCAGCTGCGTTGGGCACG|CAGGGGT|GGGGCAGCTGAACATGATTTTCCACTTTGTGTCCCCAATC ========= Event 787 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tttttttttGATGATACAACCTA-------GGTTTGTTCAAGGTGTCCATCAACT ↓ 3 1 42 Chimp: tttttttttGATGATACAACCTAGAAACCTAGGTTGTTCAAGGTGTCCATCAACT ↑ 3 1 42 Gorilla: tttttttttGATGATACAACCTA-------GGTTTGTTCAAGGTGTCCATCAACT Human: tttttttttGATGATACAACCTA-------GGTTTGTTCAAGGTGTCCATCAACT Cluster: [ ] Orangutan: tttttctttgatgatacaaccta-------ggtttgttcaaggtgtcCATCAACT Human > Chimp ------------- chr12:99065372-99065380 Template switch process: F1: L TCCAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG 1 F3: 4 TTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA R RF: TCCAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAGGTTTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA RR: AGGTTATGAGTAAAGGGAAAAAAAAAACTACTATGTTGGATCCAAACAAGTTCCACAGGTAGTTGAGACTATCTACTTAGTACT F2: 3 GGATCCAAA 2 Unidirectional alignment (log-probability: -27) CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAGaaacctaGgTTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG-------GTTTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA Template switch alignment (log-probability: -16.4) CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG|AAACCTAGG|TTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG|AAACCTAGG|TTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA Gorilla > Chimp --------------- chr12:99065372-99065380 Template switch process: F1: L TCCAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG 1 F3: 4 TTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA R RF: TCCAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAGGTTTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA RR: AGGTTATGAGTAAAGGGAAAAAAAAAACTACTATGTTGGATCCAAACAAGTTCCACAGGTAGTTGAGACTATCTACTTAGTACT F2: 3 GGATCCAAA 2 Unidirectional alignment (log-probability: -26.5) CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAGaaacctaGgTTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG-------GTTTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA Template switch alignment (log-probability: -16.9) CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG|AAACCTAGG|TTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA CAATACTCATTTCCCTTTTTTTTTTGATGATACAACCTAG|AAACCTAGG|TTGTTCAAGGTGTCCATCAACTCTGATAGATGAATCATGA ========= Event 788 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCCGGGTTGTAGCCAATTTGCTTAATATAAGTGCTA---TCGTTTTTTGCAATTTCCTCTTCT Chimp: GTCCAGGTTGTAGCCAATTTGCTTAATGTAAGTGCTG---TTGTTTTTTGCAATTTCCTCTTCT ↓ 3 2 1 4 Gorilla: GTCCAAGTTGTAGCCAATTTGCTTAATGTAAGTGCATTAAGCACTTTTTGCAATTTCCTCTTCT Human: GTCCGGGTTGTAGCCAATTTGCTTAATATAAGTGCTA---TCGTTTTTTGCAATTTCCTCTTCT Cluster: [ ] Orangutan: GTCCAGGTTGTAGCCAATTTGCTTAATATAAGTGCTG---TCGTTTTTCGCAATTTCCTCTTCT Chimp > Gorilla --------------- chr12:96629226-96629233 Template switch process: F1: L TACTGTGTCCAAGTTGTAGCCAATTTGCTTAATGTAAGTGC 1 F3: 4 CTTTTTGCAATTTCCTCTTCTGGCCATAGGGTGGCTCAGTG R RF: TACTGTGTCCAGGTTGTAGCCAATTTGCTTAATGTAAGTGCTGTTGTTTTTTGCAATTTCCTCTTCTGGCCATAGGGTGGCTCAGTG RR: ATGACACAGGTCCAACATCGGTTAAACGAATTACATTCACGACAACAAAAAACGTTAAAGGAGAAGACCGGTATCCCACCGAGTCAC F2: 3 ACGAATTA 2 Unidirectional alignment (log-probability: -39.4) ACTGTGTCCAaGTTGTAGCCAATTTGCTTAATGTAAGTGC------attaagcacTTTTTGCAATTTCCTCTTCTGGCCATAGGGTGGCTCAGT ACTGTGTCCAGGTTGTAGCCAATTTGCTTAATGTAAGTGCTGTTGT---------TTTTTGCAATTTCCTCTTCTGGCCATAGGGTGGCTCAGT Template switch alignment (log-probability: -27.8) ACTGTGTCCAaGTTGTAGCCAATTTGCTTAATGTAAGTGC|ATTAAGCA|cTTTTTGCAATTTCCTCTTCTGGCCATAGGGTGGCTCAGT ACTGTGTCCAGGTTGTAGCCAATTTGCTTAATGTAAGTGC|ATTAAGCA|TTTTTTGCAATTTCCTCTTCTGGCCATAGGGTGGCTCAGT ========= Event 789 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTATAAACTAAGCCATGGGAT-----------GCTACTGCTATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGTACCTAACTgtatagtatggtaggacaaagatgagctttggaatcaagcaaaccttagcactgatacatggctcttttacttatttgcagtcacagacaaggaacttaac Chimp: TTATAAACTAAGCCATGGGAT-----------GCTACTGCAATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGTACCTAACTgtatagtatggtaggacaaagatgagctttggaatcaagcaaaccttagcactgatacatggctcttttacttatttgcagtcacaggcaaggaacttaac ↑ 4 1 3 2 Gorilla: TTATAAACTAAGCCATGGGAT----------------------GCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGTACCTAACTgtatagtatggtaggacaaagatgagctttggaatcaagcaaaccttagcactaatacatggctcttttacttatttgcagtcacaggcaaggaacttaac Human: TTATAAACTAAGCCATGGGAT-----------GCTACTGCTATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGTACCTAACTgtatagtatggtaggacaaagatgagctttggaatcaagcaaaccttagcactgatacatggctcttttacttatttgcagtcacagacaaggaacttaac Cluster: [ ] Orangutan: TTATAAACTAAGCCATGGGATGCTACTGCTAT-----------GCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGTACTTAACTgtatagtatggtaggacaaagatgagctttggaatcaagcaaaccttagcactgatacacggctcttttacttatttgcagtcacaggcaaggaacttaac Gorilla > Chimp --------------- chr12:100089539-100089543 Template switch process: F1: L TATGTTCCTTGGCTAATATTTTATAAACTAAGCCATGGGATGCTA 1 F3: 4 ATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGT R RF: TATGTTCCTTGGCTAATATTTTATAAACTAAGCCATGGGATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAGGTACCTAACTGTATAGTATGGTAGGACAAAGATGAGCTTTGGAATCAAGCAAACCTTAGCACTAATACATGGCTCTTTTACTTATTTGCAG RR: ATACAAGGAACCGATTATAAAATATTTGATTCGGTACCCTACGATTATTTAAATCTTTATAAATAACTTATGGAAATTCCATGGATTGACATATCATACCATCCTGTTTCTACTCGAAACCTTAGTTCGTTTGGAATCGTGATTATGTACCGAGAAAATGAATAAACGTC F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -26.7) TCCTTGGCTAATATTTTATAAACTAAGCCATGGGatgctactgcaATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAG TCCTTGGCTAATATTTTATAAACTAAGCCATGGG-----------ATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAG Template switch alignment (log-probability: -16.5) TCCTTGGCTAATATTTTATAAACTAAGCCATGGGATGCTA|CTGCA|ATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAG TCCTTGGCTAATATTTTATAAACTAAGCCATGGGATGCTA|CTGCA|ATGCTAATAAATTTAGAAATATTTATTGAATACCTTTAAG ========= Event 790 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCCATAATTGGGACAACTGCCTATTGTGGAATAGGCAAGTTTGCCAAGTTTCCTCGATC ↑ 3 1 24 Chimp: ATTCCATAATTGGGACAACTGCCTATT---------CCACATTTGCCAAGTTTCCTCGATC Gorilla: ATTCCATAATTGGGACAACTGCCTATT---------CCACATTTGCCAAGTTTCCTCGATC Human: ATTCCATAATTGGGACAACTGCCTATTGTGGAATAGGCAAGTTTGCCAAGTTTCCTCGATC Cluster: [ ] Orangutan: ATTCCATAATTGGGACAACTGCCTATT---------CCACATTTGCCAAGTTTCCTCGATC Chimp > Human ------------- chr12:98701896-98701907 Template switch process: F1: L TTTTTTCTTTTACTATTCCATAATTGGGACAACTGCCTATT 1 F3: 4 AGTTTGCCAAGTTTCCTCGATCACTGTCAGCCACTAATTTTT R RF: TTTTTTCTTTTACTATTCCATAATTGGGACAACTGCCTATTCCACATTTGCCAAGTTTCCTCGATCACTGTCAGCCACTAATTTTT RR: AAAAAAGAAAATGATAAGGTATTAACCCTGTTGACGGATAAGGTGTAAACGGTTCAAAGGAGCTAGTGACAGTCGGTGATTAAAAA F2: 3 ACGGATAAGGTG 2 Unidirectional alignment (log-probability: -41.5) TTTTTCTTTTACTATTCCATAATTGGGACAACTGCCTATT-----gtggaataggcaagTTTGCCAAGTTTCCTCGATCACTGTCAGCCACTAATTT TTTTTCTTTTACTATTCCATAATTGGGACAACTGCCTATTCCACA--------------TTTGCCAAGTTTCCTCGATCACTGTCAGCCACTAATTT Template switch alignment (log-probability: -28.4) TTTTTCTTTTACTATTCCATAATTGGGACAACTGCCTATT|GTGGAATAGGCA|AgTTTGCCAAGTTTCCTCGATCACTGTCAGCCACTAATTT TTTTTCTTTTACTATTCCATAATTGGGACAACTGCCTATT|GTGGAATAGGCA|A-TTTGCCAAGTTTCCTCGATCACTGTCAGCCACTAATTT ========= Event 791 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACCACGATGCTGTTGTCTTTGTCAAGAAAGG----------AATGCTTTTTCAGTAAAATGCAACCCCACTGA Chimp: CACCACGACGCTGTTGTCTTTGTCAAGAAAGG----------AATGCTTTTTCAGTAAAATGCAACCCCACTGA ↓ 3 2 1 4 Gorilla: CACCACGACGCTGTTGTCTTTGTCAAGTGACA--------------------AAGTAAAATGCAACCCCACTGA ↑ 3 2 1 4 Human: CACCACGATGCTGTTGTCTTTGTCAAGAAAGG----------AATGCTTTTTCAGTAAAATGCAACCCCACTGA Cluster: [ ] Orangutan: CACCAGGACGCTGTTGTCTTTGTCAAGAAAGGAATGCTTTTT----------CAGTAAAATGCAACCCCGCTGA Human > Gorilla --------------- chr12:98512898-98512903 Template switch process: F1: L GCTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAG 1 F3: 4 AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC R RF: GCTTTCTACTTCAGCACCACGATGCTGTTGTCTTTGTCAAGAAAGGAATGCTTTTTCAGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC RR: CGAAAGATGAAGTCGTGGTGCTACGACAACAGAAACAGTTCTTTCCTTACGAAAAAGTCATTTTACGTTGGGGTGACTGGTGCGAACTGTAGTGTCG F2: 3 AACAGT 2 Unidirectional alignment (log-probability: -32.6) CTTTCTACTTCAGCACCACGAcGCTGTTGTCTTTGTCAAGtgacAA--------------AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC CTTTCTACTTCAGCACCACGATGCTGTTGTCTTTGTCAAG----AAAGGAATGCTTTTTCAGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC Template switch alignment (log-probability: -22) CTTTCTACTTCAGCACCACGAcGCTGTTGTCTTTGTCAAG|TGACAA|AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC CTTTCTACTTCAGCACCACGATGCTGTTGTCTTTGTCAAG|TGACAA|AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC Chimp > Gorilla --------------- chr12:98512898-98512903 Template switch process: F1: L GCTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAG 1 F3: 4 AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC R RF: GCTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAGAAAGGAATGCTTTTTCAGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC RR: CGAAAGATGAAGTCGTGGTGCTGCGACAACAGAAACAGTTCTTTCCTTACGAAAAAGTCATTTTACGTTGGGGTGACTGGTGCGAACTGTAGTGTCG F2: 3 AACAGT 2 Unidirectional alignment (log-probability: -27.1) CTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAGtgacAA--------------AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC CTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAG----AAAGGAATGCTTTTTCAGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC Template switch alignment (log-probability: -16.5) CTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAG|TGACAA|AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC CTTTCTACTTCAGCACCACGACGCTGTTGTCTTTGTCAAG|TGACAA|AGTAAAATGCAACCCCACTGACCACGCTTGACATCACAGC ========= Event 792 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTCTTTGTCTGAATAAAATCATGTTGACAGGTACTACATCCTAG---------------------------TACCTGTCAACa---tgatgacagtatatgttgacagt Chimp: ctctttgtctgaataaaatcatgttgacaggtacTACATCCTAG---------------------------TACCTGTCAACa---tgatgacagtatatgttgacagt ↑ 3 2 1 4 Gorilla: ctctttatctgaataaaatcatgttgacaggtacTACATCCTAGTACCCGTCTTCTGTGTCACTCACCTAGTACCTGTCAACA------TGACAGTATATGTTGATAGT ↓ 3 2 1 4 Human: CTCTTTGTCTGAATAAAATCATGTTGACAGGTACTACATCCTAG---------------------------TACCTGTCAACa---tgatgacagtatatgttgacagt Cluster: [ ] Orangutan: CTCTTTGTCTGAATAAAATCATGTTGACAGGTACTACATCCTAG---------------------------TACCTGTCAACATGA---TGACAGTATATGTTGATAGT Gorilla > Human --------------- chr12:97864565-97864574 Template switch process: F1: L TTTGTCTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACC 1 F3: 4 ATGACAGTATATGTTGACAGTATATG R RF: TTTATCTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACCCGTCTTCTGTGTCACTCACCTAGTACCTGTCAACATGACAGTATATGTTGATAGTATATG RR: AAATAGACTTATTTTAGTACAACTGTCCATGATGTAGGATCATGGGCAGAAGACACAGTGAGTGGATCATGGACAGTTGTACTGTCATATACAACTATCATATAC F2: 3 GTACAACTGT 2 Unidirectional alignment (log-probability: -37.3) CTGAATAAAATCATGTTGACAGGTACTACAT---------------------------CCTAGTACCTGTCAACatgATGACAGTATATGTTGAcAGTATATG CTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACCCGTCTTCTGTGTCACTCACCTAGTACCTGTCAAC---ATGACAGTATATGTTGATAGTATATG Template switch alignment (log-probability: -27.8) CTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACC|TGTCAACATG|ATGACAGTATATGTTGAcAGTATATG CTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACC|TGTCAACATG|ATGACAGTATATGTTGATAGTATATG Gorilla > Chimp --------------- chr12:100640208-100640217 Template switch process: F1: L TTTGTCTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACC 1 F3: 4 ATGACAGTATATGTTGACAGTATATG R RF: TTTATCTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACCCGTCTTCTGTGTCACTCACCTAGTACCTGTCAACATGACAGTATATGTTGATAGTATATG RR: AAATAGACTTATTTTAGTACAACTGTCCATGATGTAGGATCATGGGCAGAAGACACAGTGAGTGGATCATGGACAGTTGTACTGTCATATACAACTATCATATAC F2: 3 GTACAACTGT 2 Unidirectional alignment (log-probability: -37.3) CTGAATAAAATCATGTTGACAGGTACTACAT---------------------------CCTAGTACCTGTCAACatgATGACAGTATATGTTGAcAGTATATG CTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACCCGTCTTCTGTGTCACTCACCTAGTACCTGTCAAC---ATGACAGTATATGTTGATAGTATATG Template switch alignment (log-probability: -27.8) CTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACC|TGTCAACATG|ATGACAGTATATGTTGAcAGTATATG CTGAATAAAATCATGTTGACAGGTACTACATCCTAGTACC|TGTCAACATG|ATGACAGTATATGTTGATAGTATATG ========= Event 793 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTCAGAAAGGACAATGGGCATTACTTAAATGTCCCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTGATTTT Chimp: GTTTCAGAAAGGACAATGGGCTT---TCACCTGTTTCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTGATTTT ↑ 1 4 3 2 Gorilla: GTTTCAGAAAGGACAATGGGCATTACTTAAATGTCCCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTGATTTT Human: GTTTCAGAAAGGACAATGGGCATTACTTAAATGTCCCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTGATTTT Cluster: [ ] Orangutan: GTTTCAGAAACGACAATGGGCATTACTTAAATGTCCCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTGATTTT Gorilla > Chimp --------------- chr12:102026630-102026639 Template switch process: F1: L CAACCTGAATAAGATAGCAGGTTTCAGAAAGGACAATGGGCTTT 1 F3: 4 AGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTG R RF: CAACCTGAATAAGATAGCAGGTTTCAGAAAGGACAATGGGCATTACTTAAATGTCCCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTG RR: GTTGGACTTATTCTATCGTCCAAAGTCTTTCCTGTTACCCGTAATGAATTTACAGGGTCAAACAAGTGGGACTTTGTCTACGTCTCTATAATTCAC F2: 3 CTTTGTCCAC 2 Unidirectional alignment (log-probability: -38.3) CTGAATAAGATAGCAGGTTTCAGAAAGGACAATGGGCtTT-----------CacctgtttCAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTG CTGAATAAGATAGCAGGTTTCAGAAAGGACAATGGGCATTACTTAAATGTCC--------CAGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTG Template switch alignment (log-probability: -28.1) CTGAATAAGATAGCAGGTTTCAGAAAGGACAATGGGCtTT|CAcCTGTTTC|AGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTG CTGAATAAGATAGCAGGTTTCAGAAAGGACAATGGGCATT|CATCTGTTTC|AGTTTGTTCACCCTGAAACAGATGCAGAGATATTAAGTG ========= Event 794 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AATAATAATTTAGAAATGGCAGCTGTAAAA----TCTATGATAGATTTAAAGGCATTTTGTTC ↓ 1 3 4 2 Chimp: AATAATAATTTAGAAATGGCATATCATAGATTTTACTATGATAGATTTAAAGGCATTTTGTTC ↑ 1 3 4 2 Gorilla: AATAATAATTTAGAAATGGCAGCTGTAAAA----TCTATGATAGATTTAAAGGCATTTTGTTC Human: AATAATAATTTAGAAATGGCAGCTGTAAAA----TCTATGATAGATTTAAAGGCATTTTGTTC Cluster: [ ] Orangutan: GATAATAATTTAGAAATGGCAGCTGTAAAA----TCTATGATAGATTTAAAGGCATTTTGTTC Human > Chimp ------------- chr12:101331484-101331497 Template switch process: F1: L TGGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCA 1 F3: 4 CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC R RF: TGGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCAGCTGTAAAATCTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC RR: ACCTTCGTACACCTATGGATTTATTATTAAATCTTTACCGTCGACATTTTAGATACTATCTAAATTTCCGTAAAACAAGAGATTTTGAATG F2: 3 ATTTTAGATACTAT 2 Unidirectional alignment (log-probability: -40.3) GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGC---------ATatcatagattttaCTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCAGCTGTAAAAT-------------CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC Template switch alignment (log-probability: -17) GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCA|TATCATAGATTTTA|CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCA|TATCATAGATTTTA|CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC Gorilla > Chimp --------------- chr12:101331484-101331497 Template switch process: F1: L TGGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCA 1 F3: 4 CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAC R RF: TGGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCAGCTGTAAAATCTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAT RR: ACCTTCGTACACCTATGGATTTATTATTAAATCTTTACCGTCGACATTTTAGATACTATCTAAATTTCCGTAAAACAAGAGATTTTGAATA F2: 3 ATTTTAGATACTAT 2 Unidirectional alignment (log-probability: -45.3) GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGC---------ATatcatagattttaCTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAc GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCAGCTGTAAAAT-------------CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAT Template switch alignment (log-probability: -23) GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCA|TATCATAGATTTTA|CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAc GGAAGCATGTGGATACCTAAATAATAATTTAGAAATGGCA|TATCATAGATTTTA|CTATGATAGATTTAAAGGCATTTTGTTCTCTAAAACTTAT ========= Event 795 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTT---TTCTGTGGGTGAAGAACTCGGGAG-------------------------------------------------TATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCACTTCTGAGCTGAAAGGATGCT--CTTTGTGCT Chimp: CTT---TTCTGTGGGTGAAGAACTCGGGAG-------------------------------------------------TATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCACTTCTGAGCTGAAAGGATGCT--CTTTGTGCT ↓ 4 1 3 2 Gorilla: CTT---TTCTGTGGGTGAAGAACTCGGGAG-------------------------TATCTGAGTTCAGGTACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCACTTCTGAGCTGAAAGGATGCT----CTGTGCT ↑ 4 1 3 2 Human: CTT---TTCTGTGGGTGAAGAACTCGGGAG-------------------------------------------------TATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCACTTCTGAGCTGAAAGGATGCT--CTTTGTGCT Cluster: [ ] Orangutan: CTTTTTATCTGTGAGTGAAGAACTCGggagtatcgagtgttcaggtactgaggag------------------------tatcagactcttctggttctgagTCTCATGAAGCTTTTCACTTCTGAGCTGAAAGGATGCTCT--TTGTGCT Human > Gorilla --------------- chr12:98337047-98337050 Template switch process: F1: L TGGTGTATGATAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTA---------------TCTGAGT 1 F3: 4 GTACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCA R RF: TGGTGTATGATAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCACTTCTGAGCTGA RR: ACCACATACTATTCGAAAAGACACCCACTTCTTGAGCCCTCATAGTCTGAGAAGACCAAGACTCAGAGTACTTCGAAAAGTGAAGACTCGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -45.4) TAAGCTTTTCTGTGGGTGAAGAACTCGGGagtatctgagttcaggtactcgggAGTATCAGACTCTTCTGGTTCTGAGTCTCAT TAAGCTTTTCTGTGGGTGAAGAACTCGGG------------------------AGTATCAGACTCTTCTGGTTCTGAGTCTCAT Template switch alignment (log-probability: -32.7) TAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTA---------------TCTGAGT|TCAG|GtACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCAT TAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTATCAGACTCTTCTGGTTCTGAGT|TCAG|GAACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCAT Chimp > Gorilla --------------- chr12:98337047-98337050 Template switch process: F1: L TGGTGTATGATAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTA---------------TCTGAGT 1 F3: 4 GTACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCA R RF: TGGTGTATGATAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCATGAAGCTTTTCACTTCTGAGCTGA RR: ACCACATACTATTCGAAAAGACACCCACTTCTTGAGCCCTCATAGTCTGAGAAGACCAAGACTCAGAGTACTTCGAAAAGTGAAGACTCGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -45.4) TAAGCTTTTCTGTGGGTGAAGAACTCGGGagtatctgagttcaggtactcgggAGTATCAGACTCTTCTGGTTCTGAGTCTCAT TAAGCTTTTCTGTGGGTGAAGAACTCGGG------------------------AGTATCAGACTCTTCTGGTTCTGAGTCTCAT Template switch alignment (log-probability: -32.7) TAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTA---------------TCTGAGT|TCAG|GtACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCAT TAAGCTTTTCTGTGGGTGAAGAACTCGGGAGTATCAGACTCTTCTGGTTCTGAGT|TCAG|GAACTCGGGAGTATCAGACTCTTCTGGTTCTGAGTCTCAT ========= Event 796 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCGATCTTCTTCAGGCTATGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGACATGCTA------------ACTCTCAG-----AAGGGTAACATGGCATCAGTCTGAA ↓ 3 2 1 4 Chimp: TGCCGATCTTCTTCAGGCTATGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGATATGCATAGGTATGATTGGGTTCATAGAAACATAGGGTAACATGGCATCAGTCTGAA ↑ 3 2 1 4 Gorilla: TGCCAATCTTCTTCAGGCTCTGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGACATGCTA------------ACTAGCAG-----AAGTATAACAtggcatcagtctgaa Human: TGCCGATCTTCTTCAGGCTATGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGACATGCTA------------ACTCTCAG-----AAGGGTAACATGGCATCAGTCTGAA Cluster: [ ] Orangutan: TGCCAATCTTCTTCAGGCTCTGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATATCTACTATGACATGCTA------------ACTAGCAG-----AAGGGTAACAtggcatcagtctgaa Human > Chimp ------------- chr12:34932380-34932412 Template switch process: F1: L CCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGA 1 F3: 4 AGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCT R RF: ATGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGACATGCTAACTCTCAGAAGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCT RR: TACAAAGATACTTGGGTTAGTATGGATACGTATAGAAAACGTATGGACGATACTGTACGATTGAGAGTCTTCCCATTGTACCGTAGTCAGACTTTAAACTTAGGAAAAGA F2: 3 TACAAAGATACTTGGGTTAGTATGGATACGTAT 2 Unidirectional alignment (log-probability: -65) CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGatatgcataggtatgattgggttcatagaaACAT-------------AGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCT CCAATCATACCTATGCATATCTTTTGCATACCTGCTATG------------------------------ACATGCTAACTCTCAGAAGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCT Template switch alignment (log-probability: -19.3) CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGA|TATGCATAGGTATGATTGGGTTCATAGAAACAT|AGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCT CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGA|TATGCATAGGTATGATTGGGTTCATAGAAACAT|AGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCT Gorilla > Chimp --------------- chr12:34932380-34932411 Template switch process: F1: L CCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGA 1 F3: 4 TAGGGTAACATGGCATCAGTCTGAAATTTGAATCCTTTTCTGCCA R RF: TGTTTCTATGAACCCAATCATACCTATGCATATCTTTTGCATACCTGCTATGACATGCTAACTAGCAGAAGTATAACATGGCATCAGTCTGAAATTTGAATCCTTTTCTGCCA RR: ACAAAGATACTTGGGTTAGTATGGATACGTATAGAAAACGTATGGACGATACTGTACGATTGATCGTCTTCATATTGTACCGTAGTCAGACTTTAAACTTAGGAAAAGACGGT F2: 3 ACAAAGATACTTGGGTTAGTATGGATACGTAT 2 Unidirectional alignment (log-probability: -71.5) CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGAtATGC--------------AtaggtatgattgggttcatagaaacatagggTAACATGGCATCAGTCTGAAATTTGAATCCTTTTC CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGACATGCTAACTAGCAGAAGTA-------------------------------TAACATGGCATCAGTCTGAAATTTGAATCCTTTTC Template switch alignment (log-probability: -33.9) CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGA|TATGCATAGGTATGATTGGGTTCATAGAAACA|TAgggTAACATGGCATCAGTCTGAAATTTGAATCCTTTTC CCAATCATACCTATGCATATCTTTTGCATACCTGCTATGA|TATGCATAGGTATGATTGGGTTCATAGAAACA|TA---TAACATGGCATCAGTCTGAAATTTGAATCCTTTTC ========= Event 797 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGTT--TACTAAGAAGGCTAGTCATCATGAA Chimp: aaacaccaaagtaaatGAGATCTGAGGCCTCTAAGTT--TACTAAGAAGGCTAGTCATCATGAA Gorilla: AAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGTCAGATCTGAGAAGGCTAGTCATCATGAA ↑ 3 2 1 4 Human: AAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGTT--TACTAAGAAGGCTAGTCATCATGAA Cluster: [ ] Orangutan: AAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGTT--GACTAAGAACGCTAGTCATCATGAA Human > Gorilla --------------- chr12:99753750-99753754 Template switch process: F1: L ATACAAAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGT 1 F3: 4 CTGAGAAGGCTAGTCATCATGAAGCCATTTTTGGACACCAGGG R RF: ATACAAAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGTTTACTAAGAAGGCTAGTCATCATGAAGCCATTTTTGGACACCAGGG RR: TATGTTTTGTGGTTTCCTTTACTCTAGACTCCAGAGATTCAAATGATTCTTCCGATCAGTAGTACTTCGGTAAAAACCTGTGGTCCC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -32.1) TACAAAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGTcagaT--CTgAGAAGGCTAGTCATCATGAAGCCATTTTTGGACACCA TACAAAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGT----TTACTAAGAAGGCTAGTCATCATGAAGCCATTTTTGGACACCA Template switch alignment (log-probability: -22) TACAAAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGT|CAGAT|CTgAGAAGGCTAGTCATCATGAAGCCATTTTTGGACACCA TACAAAACACCAAAGGAAATGAGATCTGAGGTCTCTAAGT|CAGAT|CTAAGAAGGCTAGTCATCATGAAGCCATTTTTGGACACCA ========= Event 798 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CATCCCAGCTGCCACTTGGCTGGGGAAATGTCAACATTATATTAAATCACAGACACAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGTTCCCAAGCCCCCAGTAGGGAGGGACCACCTTTGCC ↑ 3 2 4 1 Chimp: CATCCCAGCTGCCACTTGGCTGGGGAAATGTCAACATTATATTAAATCACAGACACAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCC---------------CCCAGTAGGGAGGGACCATCTTTGCC ↓ 3 2 4 1 Gorilla: CATCCCAGCTGCCACTTGGCTGGGGAAATGTCAACATTATATTAAATCACAGACACAGACAGGAGAACACTTGTCACCCACCTCCTGTCTGTCCCCCCAGTTCCCAAGCCCCCAGTAGGGAGGGACCATCTTTGCC Human: CATCCCAGCTGCCACTTGGCTGGGGAAATGTCAACATTATATTAAATCACAGACACAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGTTCCCAAGCCCCCAGTAGGGAGGGACCACCTTTGCC Cluster: [ ] Orangutan: CGTCCCAGGTGCCACTTGGCTGGGGAAATGTCAACATTATATTAAATCACAGACGCAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGTTCCCAAGCCGCCAGTGGGGAGGGACTATCTTTGCC Chimp > Human ------------- chr1:218653262-218653268 Template switch process: F1: L ACAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGT 1 F3: 4 CCCCCAGTAGGGAGGGACCACCTTTGCCTGTCTCACTGTGCT R RF: CTGGGGAAATGTCAACATTATATTAAATCACAGACACAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTGCT RR: GACCCCTTTACAGTTGTAATATAATTTAGTGTCTGTGTCTGTCCTCTTGTGAACAGTGGGTGGAGAACAGACAGGGGGGTCATCCCTCCCTGGTAGAAACGGACAGAGTGACACGA F2: 3 GAACCCT 2 Unidirectional alignment (log-probability: -38.5) GGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGttcccaagcccccagTAGGGAGGGACCAcCTTTGCCTGTCTCACTGTG GGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAG---------------TAGGGAGGGACCATCTTTGCCTGTCTCACTGTG Template switch alignment (log-probability: -28.3) GGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGT|TCCCaAG|CCCCCAGTAGGGAGGGACCAcCTTTGCCTGTCTCACTGTG GGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGT|TCCCCAG|CCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTG Chimp > Gorilla --------------- chr1:198471436-198471442 Template switch process: F1: L ACAGACAGGAGAACACTTGTCACCCACCTCCTGTCTGTCCCCCCAGT 1 F3: 4 CCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTGCT R RF: CTGGGGAAATGTCAACATTATATTAAATCACAGACACAGACAGGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTGCT RR: GACCCCTTTACAGTTGTAATATAATTTAGTGTCTGTGTCTGTCCTCTTGTGAACAGTGGGTGGAGAACAGACAGGGGGGTCATCCCTCCCTGGTAGAAACGGACAGAGTGACACGA F2: 3 GAACCCT 2 Unidirectional alignment (log-probability: -38) GGAGAACACTTGTCACCCACCTCcTGTCTGTCcccccagttcccaagCCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTG GGAGAACACTTGTCACCCACCTCTTGTCTGTC---------------CCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTG Template switch alignment (log-probability: -27.9) GGAGAACACTTGTCACCCACCTCcTGTCTGTCCCCCCAGT|TCCCaAG|CCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTG GGAGAACACTTGTCACCCACCTCTTGTCTGTCCCCCCAGT|TCCCCAG|CCCCCAGTAGGGAGGGACCATCTTTGCCTGTCTCACTGTG ========= Event 799 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: GCCAAATATAATCTCTTAATT-AGTGAGATTTGAGAATGACTCTTATCTATATAATATCCTGGCT Chimp: GCCAAATATAATCTCTCAATT-AGTGAGATTTGAGAATGACTCTTATCTATATAATATCCTGGCT ↓ 13 24 ↑ 13 24 Gorilla: GCCAAATATAATCTCTCAATTAAGAGTCATTCTCGAATCTCA-CTATCTATATAATATCCTGGCT Human: GCCAAATATAATCTCTTAATT-AGTGAGATTTGAGAATGACTCTTATCTATATAATATCCTGGCT Cluster: [ ] Orangutan: GCCAAATATAATCTCTCAATT-AGTGAGATTTAAGAATGACTCTCATCTATATAATATCCTGGCT Gorilla > Chimp --------------- chr13:86313762-86313782 Template switch process: F1: L ATATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA 1 F3: 4 TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT R RF: ATATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTAAGAGTCATTCTCGAATCTCACTATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT RR: TATAATAAAACATTATGAAACGGTTTATATTAGAGAGTTAATTCTCAGTAAGAGCTTAGAGTGATAGATATATTATAGGACCGAAAAAGTCATATGAATGGTA F2: 3 TCTCAGTAAGAGTTTAGAGTG 2 Unidirectional alignment (log-probability: -51.9) ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA---------------------gtgagatttgagaatgactctTATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTAAGAGTCATTCTCGAATCTCAC---------------------TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT Template switch alignment (log-probability: -23.9) ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA|GTGAGATTtGAGAATGACTCT|TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA|GTGAGATTCGAGAATGACTCT|TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT Chimp > Gorilla --------------- chr13:83493927-83493947 Template switch process: F1: L ATATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA 1 F3: 4 TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT R RF: ATATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTAGTGAGATTTGAGAATGACTCTTATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT RR: TATAATAAAACATTATGAAACGGTTTATATTAGAGAGTTAATCACTCTAAACTCTTACTGAGAATAGATATATTATAGGACCGAAAAAGTCATATGAATGGTA F2: 3 CACTCTAAGCTCTTACTGAGA 2 Unidirectional alignment (log-probability: -51.9) ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA---------------------agagtcattctcgaatctcacTATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTAGTGAGATTTGAGAATGACTCT---------------------TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT Template switch alignment (log-probability: -23.9) ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA|AGAGTCATTCTCgAATCTCAC|TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT ATTATTTTGTAATACTTTGCCAAATATAATCTCTCAATTA|AGAGTCATTCTCAAATCTCAC|TATCTATATAATATCCTGGCTTTTTCAGTATACTTACCAT ========= Event 800 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTGATCTAGCCAAGAGGCTGTGGGCTAAGT ↑ 3 2 1 4 Chimp: TCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTAAAG--TCCAAGAGGCTGTGGGCTAAGT Gorilla: CCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTAAAG--TCCAAGAGGCTGTGGGCTAAGT ↓ 3 2 1 4 Human: CCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTGATCTAGCCAAGAGGCTGTGGGCTAAGT Cluster: [ ] Orangutan: CCAATGGGTGACATTGCACCTAGATCACTGGTATGTAAAG--TCCAAGAGGCTGTGGGCTAAGT Chimp > Human ------------- chr13:102457242-102457248 Template switch process: F1: L CATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGT 1 F3: 4 CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC R RF: CATTATCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTAAAGTCCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC RR: GTAATAGTTACCCACCGCAACTTGGATCTAGTGACCATACATTTCAGGTTCTCCGACACCCGATTCAAACGTGTGGACTCTGTCCG F2: 3 GATCTAG 2 Unidirectional alignment (log-probability: -37.4) ATTAcCAATGGGTGGCGTTGAACCTAGATCACTGGTAT-----GTgatctagCCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC ATTATCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTAAAGT-------CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC Template switch alignment (log-probability: -22.1) ATTAcCAATGGGTGGCGTTGAACCTAGATCACTGGTATGT|GATCTAG|CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC ATTATCAATGGGTGGCGTTGAACCTAGATCACTGGTATGT|GATCTAG|CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC Gorilla > Human --------------- chr13:102457242-102457248 Template switch process: F1: L CATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGT 1 F3: 4 CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC R RF: CATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTAAAGTCCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC RR: GTAATGGTTACCCACCGCAACTTGGATCTAGTGACCATACATTTCAGGTTCTCCGACACCCGATTCAAACGTGTGGACTCTGTCCG F2: 3 GATCTAG 2 Unidirectional alignment (log-probability: -30.4) ATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTgAtcTagCCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC ATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGTAAAGT--CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC Template switch alignment (log-probability: -16.6) ATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGT|GATCTAG|CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC ATTACCAATGGGTGGCGTTGAACCTAGATCACTGGTATGT|GATCTAG|CCAAGAGGCTGTGGGCTAAGTTTGCACACCTGAGACAGGC ========= Event 801 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTGGGTCTGGAGTCCCTGGAGTCTCTG-AAGACTCTGGGCTGAGCCTGTCCCCCT Chimp: CTGGGTCTGGAGTCCCTGGAGTCTCTG-AAGACTCTGGGCTGAGCCTGTCCCCCT ↑ 3 2 1 4 Gorilla: CTGGGTCTGGAGTCCCTGGAGTCTCTGACAGGGACTGGGCTGAGCCTGTCCCCCT ↓ 3 2 1 4 Human: CTGGGTCTGGAGTCCCTGGAGTCTCTG-AAGACTCTGGGCTGAGCCTGTCCCCCT Cluster: [ ] Orangutan: CTGGGTCTGGAGTCCCTGGAGTCTCTG-AAGACTCTGGTCTGAGCCTGTCCCCCT Gorilla > Human --------------- chr1:218065424-218065428 Template switch process: F1: L GGACGGCAGATAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA 1 F3: 4 CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA R RF: GGAAGGCAGACAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGACAGGGACTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA RR: CCTTCCGTCTGTCGGACCCAGACCTCAGGGACCTCAGAGACTGTCCCTGACCCGACTCGGACAGGGGGAGGTGACCGGGGTGGACTGT F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -37.7) AcGGCAGAtAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA-----AgactCTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA AAGGCAGACAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGACAGGGA----CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA Template switch alignment (log-probability: -27.4) AcGGCAGAtAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA|AGACT|CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA AAGGCAGACAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA|AGACT|CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA Gorilla > Chimp --------------- chr1:198470566-198470570 Template switch process: F1: L GGACGGCAGATAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA 1 F3: 4 CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA R RF: GGAAGGCAGACAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGACAGGGACTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA RR: CCTTCCGTCTGTCGGACCCAGACCTCAGGGACCTCAGAGACTGTCCCTGACCCGACTCGGACAGGGGGAGGTGACCGGGGTGGACTGT F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -37.7) AcGGCAGAtAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA-----AgactCTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA AAGGCAGACAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGACAGGGA----CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA Template switch alignment (log-probability: -27.4) AcGGCAGAtAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA|AGACT|CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA AAGGCAGACAGCCTGGGTCTGGAGTCCCTGGAGTCTCTGA|AGACT|CTGGGCTGAGCCTGTCCCCCTCCACTGGCCCCACCTGACA ========= Event 802 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGATTGCAAAAGCTATTCAT----TGTCTA---TTATAAACAACTAATTTTTAAGGTAATT Chimp: TTGATTGCGAAAGCTATTCAT----TGTCTA---TTATAAACAACTAATTTTTAAGGTAATT ↑ 1 34 2 Gorilla: TTGATTGCGAAAGCTATTCATTAGTTGTTTATAATAATAAACAACTAATTTTTAAGGTAATT ↓ 1 34 2 Human: TTGATTGCAAAAGCTATTCAT----TGTCTA---TTATAAACAACTAATTTTTAAGGTAATT Cluster: [ ] Orangutan: TTGATTGCGAAAGCTATTCAT----TGTCTA---TTATAAACAATTAATTTTTAAGATAATT Gorilla > Human --------------- chr13:100116342-100116348 Template switch process: F1: L GTAGGAAAATACTGCAACAATTGATTGCAAAAGCTATTCATT 1 F3: 4 ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG R RF: GTAGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATTAGTTGTTTATAATAATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG RR: CATCCTTTTATGACGTTGTTAACTAACGCTTTCGATAAGTAATCAACAAATATTATTATTTGTTGATTAAAAATTCCATTAATACGTTCCTTTTTC F2: 3 TTATCTG 2 Unidirectional alignment (log-probability: -36.9) AGGAAAATACTGCAACAATTGATTGCaAAAGCTATTCATT--------------gtctattATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG AGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATTAGTTGTTTATAATA-------ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG Template switch alignment (log-probability: -27.7) AGGAAAATACTGCAACAATTGATTGCaAAAGCTATTCATT|GTcTATT|ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG AGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATT|GTTTATT|ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG Gorilla > Chimp --------------- chr13:85847931-85847937 Template switch process: F1: L GTAGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATT 1 F3: 4 ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG R RF: GTAGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATTAGTTGTTTATAATAATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG RR: CATCCTTTTATGACGTTGTTAACTAACGCTTTCGATAAGTAATCAACAAATATTATTATTTGTTGATTAAAAATTCCATTAATACGTTCCTTTTTC F2: 3 TTATCTG 2 Unidirectional alignment (log-probability: -31.4) AGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATT--------------gtctattATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG AGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATTAGTTGTTTATAATA-------ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG Template switch alignment (log-probability: -22.2) AGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATT|GTcTATT|ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG AGGAAAATACTGCAACAATTGATTGCGAAAGCTATTCATT|GTTTATT|ATAAACAACTAATTTTTAAGGTAATTATGCAAGGAAAAAG ========= Event 803 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATTTTGCTCAATTTTTCTCG--TATCAATCCTAAATGTCCATTCCATTAAGTCAAGCTCCCTGAGT Chimp: AATTTTGCTCAATTTTTCTCG--TATCAATCCTAAATGTCCGTTCCGCTAAGTCAAGCTCCCTGAGT ↓ 3 1 2 4 Gorilla: AATTTTGCTCAATTTTTCTCGTATATTGATACGAAATGTCCGTTCCGTTAAGTCAAGCTCCCTGAGT ↑ 3 1 2 4 Human: AATTTTGCTCAATTTTTCTCG--TATCAATCCTAAATGTCCATTCCATTAAGTCAAGCTCCCTGAGT Cluster: [ ] Orangutan: AATTTTGCTCAATTTTTCTCG--TATCAATCCTAAATGTCCGTTCCGTTAAGTCAAGCTCCCTGAGT Human > Gorilla --------------- chr13:85145841-85145849 Template switch process: F1: L GTTCAATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTAT 1 F3: 4 AAATGTCCGTTCCGTTAAGTCAAGCTCCCTGAGTTTGCTTAAATTTCCCTTTCA R RF: GTTCAATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTATCAATCCTAAATGTCCATTCCATTAAGTCAAGCTCCCTGAGTTTGCTTAAATTTCCCTTTCA RR: CAAGTTAAACTGTACGTATATTAAAACGAGTTAAAAAGAGCATAGTTAGGATTTACAGGTAAGGTAATTCAGTTCGAGGGACTCAAACGAATTTAAAGGGAAAGT F2: 3 GCATAGTTA 2 Unidirectional alignment (log-probability: -45.2) AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTA-------TattgatacgAAATGTCCgTTCCgTTAAGTCAAGCTCCCTGAGTTTGCTT AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTATCAATCCT---------AAATGTCCATTCCATTAAGTCAAGCTCCCTGAGTTTGCTT Template switch alignment (log-probability: -28.3) AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTAT|ATTGATACG|AAATGTCCgTTCCgTTAAGTCAAGCTCCCTGAGTTTGCTT AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTAT|ATTGATACG|AAATGTCCATTCCATTAAGTCAAGCTCCCTGAGTTTGCTT Chimp > Gorilla --------------- chr13:85145841-85145849 Template switch process: F1: L GTTCAATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTAT 1 F3: 4 AAATGTCCGTTCCGTTAAGTCAAGCTCCCTGAGTTTGCTT R RF: GTTCAATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTATCAATCCTAAATGTCCGTTCCGCTAAGTCAAGCTCCCTGAGTTTGCTT RR: CAAGTTAAACTGTACGTATATTAAAACGAGTTAAAAAGAGCATAGTTAGGATTTACAGGCAAGGCGATTCAGTTCGAGGGACTCAAACGAA F2: 3 GCATAGTTA 2 Unidirectional alignment (log-probability: -39.5) AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTA-------TattgatacgAAATGTCCGTTCCGtTAAGTCAAGCTCCCTGAGTTTGCTT AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTATCAATCCT---------AAATGTCCGTTCCGCTAAGTCAAGCTCCCTGAGTTTGCTT Template switch alignment (log-probability: -22.5) AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTAT|ATTGATACG|AAATGTCCGTTCCGtTAAGTCAAGCTCCCTGAGTTTGCTT AATTTGACATGCATATAATTTTGCTCAATTTTTCTCGTAT|ATTGATACG|AAATGTCCGTTCCGCTAAGTCAAGCTCCCTGAGTTTGCTT ========= Event 804 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCATATTCAGTGCACATAAAGCAAAGGT-----ATTGTCCAGTGTTAGTACCTATGAATCA Chimp: TTCATATTCAGTGCACAT-AAGCAAAGGT-----ATTGTCCAGTGTTAGTACCTATGAATCA ↓ 3 1 2 4 Gorilla: TTCATATTCAGTGCACAT-AAGCAAAGGAATACCTTTGCTTAGTGTTAGTACCCATGAATCA Human: TTCATATTCAGTGCACATAAAGCAAAGGT-----ATTGTCCAGTGTTAGTACCTATGAATCA Cluster: [ ] Orangutan: TTCATATTCACTACACAT-AAGCAAAGGT-----ATTGTCCAGTGTTAGTACCTATGAATCA Chimp > Gorilla --------------- chr13:12926328-12926340 Template switch process: F1: L TGTTAAAAATATGTTTCATATTCAGTGCACATAAGCAAAGG 1 F3: 4 AGTGTTAGTACCCATGAATCATCAATAAAAACAGTTGCTT R RF: TGTTAAAAATATGTTTCATATTCAGTGCACATAAGCAAAGGTATTGTCCAGTGTTAGTACCTATGAATCATCAATAAAAACAGTTGCTT RR: ACAATTTTTATACAAAGTATAAGTCACGTGTATTCGTTTCCATAACAGGTCACAATCATGGATACTTAGTAGTTATTTTTGTCAACGAA F2: 3 TTCGTTTCCATAA 2 Unidirectional alignment (log-probability: -43.8) GTTAAAAATATGTTTCATATTCAGTGCACATAAGCAAAGGaatacctttgctT-------AGTGTTAGTACCcATGAATCATCAATAAAAACAGTTGCTT GTTAAAAATATGTTTCATATTCAGTGCACATAAGCAAAGG------------TATTGTCCAGTGTTAGTACCTATGAATCATCAATAAAAACAGTTGCTT Template switch alignment (log-probability: -22.9) GTTAAAAATATGTTTCATATTCAGTGCACATAAGCAAAGG|AATACCTTTGCTT|AGTGTTAGTACCcATGAATCATCAATAAAAACAGTTGCTT GTTAAAAATATGTTTCATATTCAGTGCACATAAGCAAAGG|AATACCTTTGCTT|AGTGTTAGTACCTATGAATCATCAATAAAAACAGTTGCTT ========= Event 805 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCCATTAAAATGAAATTCTTTTCGAATGTTCGTTAAATTCTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAATATTCTATGCTACATATTTA ↑ 1 4 3 2 Chimp: TCCCATTAAAATGAAATTCTTG----CTGTTCGTTAAATTCTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAATATTCTATGCTACATATTTA Gorilla: TCCCATTAAAATGAAATTCTTG----CCGTTCGTTAAATTCTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAATGTTCTATGCTACATATTTA Human: TCCCATTAAAATGAAATTCTTTTCGAATGTTCGTTAAATTCTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAATATTCTATGCTACATATTTA Cluster: [ ] Orangutan: TCCCATTAAAATGAAATTCTTG----CCATTCGTTAAATTCGTTTCGAATATTATTATGCTACATATTTACATTTTACTACATGGCTATCCTCTGGAAAAGAAATATGGTATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTCTTTCTTTTGAAAGGGTCCTTTCTCGTGTGAGAGGTCAGATGTGCCAGTAATTAGAAATGTGTAGCCCTTACCTAATATCTGCAAGGAGAACATCCCATTAAAATGAAATTCTGCCATTCGTTAAATTCTTTCGAATATTTTATGCTACATATTTA Chimp > Human ------------- chr13:103656119-103656124 Template switch process: F1: L CAATATTTGCAAAGAGAACATCCCATTAAAATGAAATTCTT 1 F3: 4 TGTTCGTTAAATTCTTTTCGAATATTCTATGCTACATATT R RF: CAATATTTGCAAAGAGAACATCCCATTAAAATGAAATTCTTGCTGTTCGTTAAATTCTTTTCGAATATTCTATGCTACATATT RR: GTTATAAACGTTTCTCTTGTAGGGTAATTTTACTTTAAGAACGACAAGCAATTTAAGAAAAGCTTATAAGATACGATGTATAA F2: 3 AAGCTT 2 Unidirectional alignment (log-probability: -28.7) AATATTTGCAAAGAGAACATCCCATTAAAATGAAATTCTTttcgaaTGTTCGTTAAATTCTTTTCGAATATTCTATGCTACATATT AATATTTGCAAAGAGAACATCCCATTAAAATGAAATTCTT----GCTGTTCGTTAAATTCTTTTCGAATATTCTATGCTACATATT Template switch alignment (log-probability: -16) AATATTTGCAAAGAGAACATCCCATTAAAATGAAATTCTT|TTCGAA|TGTTCGTTAAATTCTTTTCGAATATTCTATGCTACATATT AATATTTGCAAAGAGAACATCCCATTAAAATGAAATTCTT|TTCGAA|TGTTCGTTAAATTCTTTTCGAATATTCTATGCTACATATT ========= Event 806 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGATTATGTACTTAATCTGTTTTCCATTGGGAAAACAATGGACGGATTCTGAA ↑ 1 3 4 2 Chimp: AGATTATGTACTTAATCTGTTCATCAAT-GGAAAACAATGGACGGATTCTGAA Gorilla: AGATTATGTACTTAATCTGTTCATCAGT-GGAAAACAATGGACGGATTCTGAA Human: AGATTATGTACTTAATCTGTTTTCCATTGGGAAAACAATGGACGGATTCTGAA Cluster: [ ] Orangutan: AGATTATGTATTTAATCTGTTCATCAAC-AGAAAACAATGGACGGATTCTGAA Chimp > Human ------------- chr13:9783540-9783547 Template switch process: F1: L ATCTGAAAGGTCGGAGGATGAGATTATGTACTTAATCTGTT 1 F3: 4 GGAAAACAATGGACGGATTCTGAAGAAATAGCACCTTTAT R RF: ATTTGAAAGGTCGGAGGATGAGATTATGTACTTAATCTGTTCATCAATGGAAAACAATGGACGGATTCTGAAGAAATAGCACCTTTAT RR: TAAACTTTCCAGCCTCCTACTCTAATACATGAATTAGACAAGTAGTTACCTTTTGTTACCTGCCTAAGACTTCTTTATCGTGGAAATA F2: 3 GTTACCTT 2 Unidirectional alignment (log-probability: -37.5) TcTGAAAGGTCGGAGGATGAGATTATGTACTTAATCTGTT------TtccattgGGAAAACAATGGACGGATTCTGAAGAAATAGCACCTTTAT TTTGAAAGGTCGGAGGATGAGATTATGTACTTAATCTGTTCATCAAT-------GGAAAACAATGGACGGATTCTGAAGAAATAGCACCTTTAT Template switch alignment (log-probability: -22.3) TcTGAAAGGTCGGAGGATGAGATTATGTACTTAATCTGTT|TTCCATTG|GGAAAACAATGGACGGATTCTGAAGAAATAGCACCTTTAT TTTGAAAGGTCGGAGGATGAGATTATGTACTTAATCTGTT|TTCCATTG|GGAAAACAATGGACGGATTCTGAAGAAATAGCACCTTTAT ========= Event 807 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCTTTGATAGGAAATGAAAGAACATTCTCTTTTCTTAAAAACATCATGGAGTCATCTACTCTTATGTAACCTTTTTAATTGAAAAATTTAGAAC ↓ 3 1 2 4 Chimp: GTCTTTGATAGGAAATGAAAGAAAATGTTCT-------------------------------------------TTTAATTGAAAAATTTAGAAC Gorilla: GTCTTTGATAGGAAATGAAAGAACATTCTCTTTTCTTAAAAACATCATGGAGTCATCTACTCTTATGTAATGTTTTTAACTGAAAAATTTAGAAC Human: GTCTTTGATAGGAAATGAAAGAACATTCTCTTTTCTTAAAAACATCATGGAGTCATCTACTCTTATGTAACCTTTTTAATTGAAAAATTTAGAAC Cluster: [ ] Orangutan: GTCTTTGATAGGAAATGAAAGAACATTCTCTTTTCTTAAAAACATCATGGAGTCATCTACTTTTATGTAATGTTTTTAGTTGAAAAATTTAGAAC Human > Chimp ------------- chr13:10502418-10502425 Template switch process: F1: L AGAGACAAAAAGATGATTGTCTTTGATAGGAAATGAAAGAA 1 F3: 4 TTTAATTGAAAAATTTAGAACAAAATTTAGATCTATTTTG R RF: AGAGACAAAAAGATGATTGTCTTTGATAGGAAATGAAAGAACATTCTCTTTTCTTAAAAACATCATGGAGTCATCTACTCTTATGTAACCTTTTTAATTGAAAAATTTAGAACAAAATTTAGATCTATTTTG RR: TCTCTGTTTTTCTACTAACAGAAACTATCCTTTACTTTCTTGTAAGAGAAAAGAATTTTTGTAGTACCTCAGTAGATGAGAATACATTGGAAAAATTAACTTTTTAAATCTTGTTTTAAATCTAGATAAAAC F2: 3 TCTTGTAA 2 Unidirectional alignment (log-probability: -31.2) GAGACAAAAAGATGATTGTCTTTGATAGGAAATGAAAGAAaATgtTC-------------------------------------------TTTTAATTGAAAAATTTAGAACAAAATTTAGATCTATTTTG GAGACAAAAAGATGATTGTCTTTGATAGGAAATGAAAGAACATTCTCTTTTCTTAAAAACATCATGGAGTCATCTACTCTTATGTAACCTTTTTAATTGAAAAATTTAGAACAAAATTTAGATCTATTTTG Template switch alignment (log-probability: -16.3) GAGACAAAAAGATGATTGTCTTTGATAGGAAATGAAAGAA|AATGTTCT|TTTAATTGAAAAATTTAGAACAAAATTTAGATCTATTTTG GAGACAAAAAGATGATTGTCTTTGATAGGAAATGAAAGAA|AATGTTCT|TTTAATTGAAAAATTTAGAACAAAATTTAGATCTATTTTG ========= Event 808 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGAGGATGAAGTGAAAAGTTTCAG-----------TGATCTGAAAGTGATGATCTGAGTTTATAGTCtga Chimp: agaGGATGAAGTGGAAAGTTTCAG-----------TGATCTGAAAGTGATGATCTGAGTTTATAGTCtga ↑ 3 4 2 1 Gorilla: aCAGGATGAAGTGGAAAGTTTCAG----------------------TGATGATCTGAGTTTATAGTCtga ↓ 3 4 2 1 Human: AGAGGATGAAGTGAAAAGTTTCAG-----------TGATCTGAAAGTGATGATCTGAGTTTATAGTCtga Cluster: [ ] Orangutan: AGAGGATGAAATGGAAAGTTTCAGTGATCTGAAAG-----------TGATGATCTGAGTTTATAGTCtga Gorilla > Human --------------- chr13:102946718-102946722 Template switch process: F1: L TGAATGGCAGAAAAGGAAGAGGATGAAGTGAAAAGTTTCAGTGAT 1 F3: 4 AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGTGT R RF: TGAATGGCAGAAAAGGAACAGGATGAAGTGGAAAGTTTCAGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGTGT RR: ACTTACCGTCTTTTCCTTGTCCTACTTCACCTTTCAAAGTCACTACTAGACTCAAATATCAGACTATACCAAACCGACACA F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -37.7) GGCAGAAAAGGAAgAGGATGAAGTGaAAAGTTTCagtgatctgaaAGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT GGCAGAAAAGGAACAGGATGAAGTGGAAAGTTTC-----------AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT Template switch alignment (log-probability: -27.5) GGCAGAAAAGGAAgAGGATGAAGTGaAAAGTTTCAGTGAT|CTGAA|AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT GGCAGAAAAGGAACAGGATGAAGTGGAAAGTTTCAGTGAT|CTGAA|AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT Gorilla > Chimp --------------- chr13:88710121-88710125 Template switch process: F1: L TGAATGGCAGAAAAGGAAGAGGATGAAGTGGAAAGTTTCAGTGAT 1 F3: 4 AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGTGT R RF: TGAATGGCAGAAAAGGAACAGGATGAAGTGGAAAGTTTCAGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGTGT RR: ACTTACCGTCTTTTCCTTGTCCTACTTCACCTTTCAAAGTCACTACTAGACTCAAATATCAGACTATACCAAACCGACACA F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -32.2) GGCAGAAAAGGAAgAGGATGAAGTGGAAAGTTTCagtgatctgaaAGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT GGCAGAAAAGGAACAGGATGAAGTGGAAAGTTTC-----------AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT Template switch alignment (log-probability: -22) GGCAGAAAAGGAAgAGGATGAAGTGGAAAGTTTCAGTGAT|CTGAA|AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT GGCAGAAAAGGAACAGGATGAAGTGGAAAGTTTCAGTGAT|CTGAA|AGTGATGATCTGAGTTTATAGTCTGATATGGTTTGGCTGT ========= Event 809 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTA-TTCCAttt-ttttttCAATT------GATG-GAAAATATGC-AATAT ↓ 13 42 Chimp: TATTA-TTCCAttt--tttttCAATT---GATGATG-GAAAATATGC-AATAT Gorilla: TATTA-TTCCAttt--tttttCAATTGAT---GATG-GAAAATATGC-AATGT Human: TATTA-TTCCAttt-ttttttCAATT------GATG-GAAAATATGC-AATAT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNN-NNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr13:7301262-7301268 Template switch process: F1: L AAATTTCCTTATATACCTATTATTCCATTTTTTTT 1 F3: 4 TGATGGAAAATATGCAATATATTATTACACGGAGCAGCAGT R RF: CAATTTCCTTATATACCTATTATTCCATTTTTTTTTCAATTGATGGAAAATATGCAATATATTATTACACGGAGCAGCAGT RR: GTTAAAGGAATATATGGATAATAAGGTAAAAAAAAAGTTAACTACCTTTTATACGTTATATAATAATGTGCCTCGTCGTCA F2: 3 AGTTAAC 2 Unidirectional alignment (log-probability: -31.5) aAATTTCCTTATATACCTATTATTCCA-TTTTTTTTCAATtgaTGATGGAAAATATGCAATATATTATTACACGGAGCAGCAG CAATTTCCTTATATACCTATTATTCCATTTTTTTTTCAAT---TGATGGAAAATATGCAATATATTATTACACGGAGCAGCAG Template switch alignment (log-probability: -22) aAATTTCCTTATATACCTATTATTCCATTTTTTTT|CAATTGA|TGATGGAAAATATGCAATATATTATTACACGGAGCAGCAG CAATTTCCTTATATACCTATTATTCCATTTTTTTT|CAATTGA|TGATGGAAAATATGCAATATATTATTACACGGAGCAGCAG ========= Event 810 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCCTCTTATTTTCTGCAGACCCGTGTAATT----ACGGGTAACTTCCAATGTTTCCAC ↑ 1 3 4 2 Chimp: CCCCTCTTATTTTCTGCAGACTGATGTAATT--ACACGGGTAACTTCCAATGTTTCCAC Gorilla: CCCCTCTTATTTTCTGCAGACTGATGTAATTAC--ACGGGTAACTTCCAATGTTTCCAC ↓ 1 3 4 2 Human: CCCCTCTTATTTTCTGCAGACCCGTGTAATT----ACGGGTAACTTCCAATGTTTCCAC Cluster: [ ] Orangutan: CCCCCATTATTTTCTGCAGACTGATGTAATTAC--ACGGGTAACTTCCAATGTTTCCAC Chimp > Human ------------- chr13:6127957-6127966 Template switch process: F1: L TACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGAC 1 F3: 4 ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG R RF: TACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGACTGATGTAATTACACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG RR: ATGCTGGACGTGTTAATAACGGGGAGAATAAAAGACGTCTGACTACATTAATGTGCCCATTGAAGGTTACAAAGGTGAAATTAATAACGAAAC F2: 3 TTAATGTGCC 2 Unidirectional alignment (log-probability: -29.1) ACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGACccgTGTAATT--ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG ACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGACTGATGTAATTACACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG Template switch alignment (log-probability: -16.5) ACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGAC|CCGTGTAATT|ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG ACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGAC|CCGTGTAATT|ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG Gorilla > Human --------------- chr13:6127957-6127966 Template switch process: F1: L TACGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGAC 1 F3: 4 ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG R RF: TATGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGACTGATGTAATTACACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG RR: ATACTGGACGTGTTAATAACGGGGAGAATAAAAGACGTCTGACTACATTAATGTGCCCATTGAAGGTTACAAAGGTGAAATTAATAACGAAAC F2: 3 TTAATGTGCC 2 Unidirectional alignment (log-probability: -33.2) AcGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGACccgTGTAATT--ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG ATGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGACTGATGTAATTACACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG Template switch alignment (log-probability: -22.5) AcGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGAC|CCGTGTAATT|ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG ATGACCTGCACAATTATTGCCCCTCTTATTTTCTGCAGAC|CCGTGTAATT|ACGGGTAACTTCCAATGTTTCCACTTTAATTATTGCTTTG ========= Event 811 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTTGTTTAAATATCAGCCCATGAGGATATC--------ATGGCTGTCAATGTCAATCTCTTCTgagacagaaaaagagagagaaagagatgcagaga------------ga----gagagagagagagaATTAGAATGGAAAATATCAGTCAAATCCCCTGACCCCTGATCCAGCAATACATGAAGCCACTGGCATTCAGATT ↑ 1 4 3 2 Chimp: TGTTGTTTTAATATCAGCCCATGAGGATATA----GCCATTTGCTGTCAATGTCAATCTCTTCTgagacagaaaaagagagagaaagagatgcagaga--------------gaaagagagagagagagaaTTAGAATGGAAAATATCAGTCAAATCCCCTGACCCCTGATCCAGCAATACATGAAGCCACTGGCATTCAGATT Gorilla: TGTTGTTTTAATATCAGCCCATGAGGATATAGCCA----TTTGCTGTCAAGGTCAATCTCTTCTgagacagaaaaagagagagaaagagatgcagagagagagagagaga------gagagagagagagaATTAGAATGGAAAATATCAGTCAAATCCCCTGACCCCTGATCCAGCAATACGTGAAGCCACTGGCATTCAGACT ↓ 3 2 1 4 Human: TGTTGTTTAAATATCAGCCCATGAGGATATC--------ATGGCTGTCAATGTCAATCTCTTCTgagacagaaaaagagagagaaagagatgcagaga------------ga----gagagagagagagaATTAGAATGGAAAATATCAGTCAAATCCCCTGACCCCTGATCCAGCAATACATGAAGCCACTGGCATTCAGATT Cluster: [ ] Orangutan: TGTTGTTTTAATATCAGCCCATGAGGATATAGCCA----TTTGCTGTCAAGATCAATCTCTTCTgagacagaaaaagagagagaaagagatgcagaga----------------------gagagagagaattagaatggaaaatatcagtcaaatcccctgactcctgatccagcaatacatgaagcca-cggcattcagact Chimp > Human ------------- chr13:5715351-5715354 Template switch process: F1: L AATGCCCTCTCTGTTGTTTAAATATCAGCCCATGAGGATAT 1 F3: 4 GCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGA R RF: AATGCCCTCTCTGTTGTTTTAATATCAGCCCATGAGGATATAGCCATTTGCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGAGAAAGAGATGCAGAGAGAAAGAGAGAGAGAGAGAATTAGAATGGAAAATATCAGTCAAATCCCCTGACCCCTGATCCAGCAATACATG RR: TTACGGGAGAGACAACAAAATTATAGTCGGGTACTCCTATATCGGTAAACGACAGTTACAGTTAGAGAAGACTCTGTCTTTTTCTCTCTCTTTCTCTACGTCTCTCTTTCTCTCTCTCTCTCTTAATCTTACCTTTTATAGTCAGTTTAGGGGACTGGGGACTAGGTCGTTATGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -33.3) ATGCCCTCTCTGTTGTTTaAATATCAGCCCATGAGGATA--------TcatgGCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGA ATGCCCTCTCTGTTGTTTTAATATCAGCCCATGAGGATATAGCCATTT----GCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGA Template switch alignment (log-probability: -21.8) ATGCCCTCTCTGTTGTTTaAATATCAGCCCATGAGGATAT|CATG|GCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGA ATGCCCTCTCTGTTGTTTTAATATCAGCCCATGAGGATAT|CATG|GCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGA Gorilla > Human --------------- chr13:5715351-5715354 Template switch process: F1: L AATGCCCTCTCTGTTGTTTAAATATCAGCCCATGAGGATAT 1 F3: 4 GCTGTCAATGTCAATCTCTTCTGAGACAGAAAAAGAGAGAGAAAGAGAT R RF: AATGCCCTCTCTGTTGTTTTAATATCAGCCCATGAGGATATAGCCATTTGCTGTCAAGGTCAATCTCTTCTGAGACAGAAAAAGAGAGAGAAAGAGAT RR: TTACGGGAGAGACAACAAAATTATAGTCGGGTACTCCTATATCGGTAAACGACAGTTCCAGTTAGAGAAGACTCTGTCTTTTTCTCTCTCTTTCTCTA F2: 3 GTAC 2 Unidirectional alignment (log-probability: -37.6) ATGCCCTCTCTGTTGTTTaAATATCAGCCCATGAGGATAT---CA-TgGCTGTCAAtGTCAATCTCTTCTGAGACAGAAAAAGAGAGA ATGCCCTCTCTGTTGTTTTAATATCAGCCCATGAGGATATAGCCATTTGCTGTCAAGGTCAATCTCTTCTGAGACAGAAAAAGAGAGA Template switch alignment (log-probability: -27.5) ATGCCCTCTCTGTTGTTTaAATATCAGCCCATGAGGATAT|CATG|GCTGTCAAtGTCAATCTCTTCTGAGACAGAAAAAGAGAGA ATGCCCTCTCTGTTGTTTTAATATCAGCCCATGAGGATAT|CATG|GCTGTCAAGGTCAATCTCTTCTGAGACAGAAAAAGAGAGA ========= Event 812 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AAAGACAGCCTGAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAATGATAC----------------------------------------------------ACAGTGAAGTCACAGATTATAA ↑ 3 2 1 4 Chimp: AAAGACAGCCTGAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAA-TATAA--------------------------ACTCAACAGACCTGAATTCTCAAGCATCAGTGAAGTCACAGATTATAA Gorilla: Human: AAAGACAGCCTGAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAATGATAC----------------------------------------------------ACAGTGAAGTCACAGATTATAA Cluster: [ ] Orangutan: aaagacagcctgagccaagtgtatcattcccaatcatttcattgttagaa-tacaaactcaacagacctgaattctcaagca--------------------------tcagtgaagtcacaggttataa Chimp > Human ------------- chr13:3391591-3391596 Template switch process: F1: L CTGAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAAT 1 F3: 4 CAGTGAAGTCACAGATTATAATATCCATGCATTCATTTTA R RF: CTGAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAATATAAACTCAACAGACCTGAATTCTCAAGCATCAGTGAAGTCACAGATTATAATATCCATGCGTTCATTTTA RR: GACTCGGTTCACATAGTAAGGGTTAGTAAAGTAACAATCTTATATTTGAGTTGTCTGGACTTAAGAGTTCGTAGTCACTTCAGTGTCTAATATTATAGGTACGCAAGTAAAAT F2: 3 ACATAG 2 Unidirectional alignment (log-probability: -35.9) GAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAATgatacA------------------------------CAGTGAAGTCACAGATTATAATATCCATGCaTTCATTTTA GAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAAT-----ATAAACTCAACAGACCTGAATTCTCAAGCATCAGTGAAGTCACAGATTATAATATCCATGCGTTCATTTTA Template switch alignment (log-probability: -22) GAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAAT|GATACA|CAGTGAAGTCACAGATTATAATATCCATGCaTTCATTTTA GAGCCAAGTGTATCATTCCCAATCATTTCATTGTTAGAAT|GATACA|CAGTGAAGTCACAGATTATAATATCCATGCGTTCATTTTA ========= Event 813 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gcttccctggaTGGGGACAAAACAC------------------------------------------ACTTCCTTCCGCTTGTCACCATCCCTGGCTCCTTCAACTCGGTCCGTCTCCATGACGTGTTCCTCTGCTTCTCTTCCTCC Chimp: GCTTCCCTGGATGGGGACAAATCAC------------------------------------------ACTTCCTTCTGCTTGTCACCATCCCTGGCTCCTTCCACTCGGTCCGTCTCCATGACGTGTTCCTCTGCTTCTCTTTCTCC ↓ 1 4 3 2 Gorilla: GCTTCCCTGGATGGGGACAAAACAC------------------------------------------------------------------------------------GTCGTCTCCATGACGTGTTCCTCTGCTTCTCTTCCTCC Human: gcttccctggaTGGGGACAAAACAC------------------------------------------ACTTCCTTCCGCTTGTCACCATCCCTGGCTCCTTCAACTCGGTCCGTCTCCATGACGTGTTCCTCTGCTTCTCTTCCTCC Cluster: [ ] Orangutan: GCTTCCCTGGATGGGGACAAAACACACTTCCTTCTGCTTGTCGCCATCCCTGGCTCCTTCCACTCGG------------------------------------------CCCGTCTCCATGACGTGTTCCTCTGCTTCTCTTCCTCC Chimp > Gorilla --------------- chr13:93903515-93903521 Template switch process: F1: L GTAAGTCTCATGAAACAAAAGCTTCCCTGGATGGGGACAAA 1 F3: 4 GTCTCCATGACGTGTTCCTCTGCTTCTCTTCCTCCGAAT R RF: GTAAGTCTCATGAAACAAAAGCTTCCCTGGATGGGGACAAATCACACTTCCTTCTGCTTGTCACCATCCCTGGCTCCTTCCACTCGGTCCGTCTCCATGACGTGTTCCTCTGCTTCTCTTTCTCCAAAT RR: CATTCAGAGTACTTTGTTTTCGAAGGGACCTACCCCTGTTTAGTGTGAAGGAAGACGAACAGTGGTAGGGACCGAGGAAGGTGAGCCAGGCAGAGGTACTGCACAAGGAGACGAAGAGAAAGAGGTTTA F2: 3 CTGCACA 2 Unidirectional alignment (log-probability: -39.4) TAAGTCTCATGAAACAAAAGCTTCCCTGGATGGGGACAAAaCAC-----------------------------------------GT-CGTCTCCATGACGTGTTCCTCTGCTTCTCTTcCTCCgAAT TAAGTCTCATGAAACAAAAGCTTCCCTGGATGGGGACAAATCACACTTCCTTCTGCTTGTCACCATCCCTGGCTCCTTCCACTCGGTCCGTCTCCATGACGTGTTCCTCTGCTTCTCTTTCTCCAAAT Template switch alignment (log-probability: -27.6) TAAGTCTCATGAAACAAAAGCTTCCCTGGATGGGGACAAA|ACACGTC|GTCTCCATGACGTGTTCCTCTGCTTCTCTTcCTCCgAAT TAAGTCTCATGAAACAAAAGCTTCCCTGGATGGGGACAAA|ACACGTC|GTCTCCATGACGTGTTCCTCTGCTTCTCTTTCTCCAAAT ========= Event 814 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tttgaacATGGAGGATAGGACA--GTCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACTTCTGAGTCACAGGTCTTCTCCTGGTAGC ↓ 1 4 3 2 Chimp: tttgaacATGGAGGATAGGACGACTTCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACTTCTGAGTCACAGGTCTTCTCCTGGTAGC Gorilla: tttgaacATGGAGGATAGGACA--GTCACATGACATTCGCACGAGTAGAGAGAGGAACATTGACTTCTGAGTCACAGGTCTTCTCCTGGTAGC Human: tttgaacATGGAGGATAGGACA--GTCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACTTCTGAGTCACAGGTCTTCTCCTGGTAGC Cluster: [ ] Orangutan: TTTGAACATGGAGGATAGGACA--GTCACACGACATTCGCACGAGTGG--AGAGGAATGTTGACTTCTGAGTTACAGGTCTTCTCCTGGTAGC Human > Chimp ------------- chr13:96226619-96226622 Template switch process: F1: L CCTGGTTAGACTGGTCAGCATTTGAACATGGAGGATAGGAC 1 F3: 4 TCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACT R RF: CCTGGTTAGGCTGGTCAGCATTTGAACATGGAGGATAGGACAGTCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACTTCTGAGTC RR: GGACCAATCCGACCAGTCGTAAACTTGTACCTCCTATCCTGTCAGTGTACTGTAAGCGTGTTCATCTCTCTCCTTGCAACTGAAGACTCAG F2: 3 TCAG 2 Unidirectional alignment (log-probability: -31.5) CTGGTTAGaCTGGTCAGCATTTGAACATGGAGGATAGGAC-GactTCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACT CTGGTTAGGCTGGTCAGCATTTGAACATGGAGGATAGGACAG---TCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACT Template switch alignment (log-probability: -21.8) CTGGTTAGaCTGGTCAGCATTTGAACATGGAGGATAGGAC|GACT|TCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACT CTGGTTAGGCTGGTCAGCATTTGAACATGGAGGATAGGAC|GACT|TCACATGACATTCGCACAAGTAGAGAGAGGAACGTTGACT ========= Event 815 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTATAACAAATACGGGTTAAGCTGCATTTTTTAAAAGGAATTAAATAGGCCTCAGCTTCCTTATATGCAAAACATAAAATTTCTCTTCATCATAACATTTTTAAATAGGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGTGCTCTGAAAATTCAAGTCATTTTTT Chimp: CCTATAACAAATACGGGTTAAGCTGCATTTTTTAAAAGGAATTAAATAGGCCTCAGCTTCCTTATATGCAAAACATAAAATTTCTCTTCATCATAACATTTTTAAATAGGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGAGCTCTGAAAATTCAAGTCATTTTTT Gorilla: CCTATAACAAATACGGGTTAAGCTGCATTTTTAAAAAGGAATTAAATAGGCCTCAGCTTCCTTATATGCAAAACATAAAATTTCTCTTCATCATAACATTTTTAAATAGGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGAGCTTTGAAAATTCAAGTCATTTTTT ↑ 3 2 1 4 Human: CCTATAACAAATACGGGTTAAGCTGCATTTTTTAAAAGGAATTAAATAGGCCTCAGCTTCCTTATATGCAAAACATAAAATTTCTCTTCATCATAACATTTTTAAATAGGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGTGCTCTGAAAATTCAAGTCATTTTTT Cluster: [ ] Orangutan: TCTATAACAAATACGGGTTAAGCTGCATTTTTAAAAAGGAATTAAATAGGCCTCAGCTTCCTTATATGCAAAACATAAAATTTCTCTTCTTCACAACATTTTTAAATAGGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGAGCTTGGAAAATTCAAGTTATTTTTT Human > Gorilla --------------- chr13:2892986-2892990 Template switch process: F1: L GGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAG 1 F3: 4 TGAAAATTCAAGTCATTTTTTATTTTGTCAATTTTGTATA R RF: AAGCTGCATTTTTTAAAAGGAATTAAATAGGCCTCAGCTTCCTTATATGCAAAACATAAAATTTCTCTTCATCATAACATTTTTAAATAGGAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGTGCTCTGAAAATTCAAGTCATTTTTTATTTTGTCAATTTTGTATA RR: TTCGACGTAAAAAATTTTCCTTAATTTATCCGGAGTCGAAGGAATATACGTTTTGTATTTTAAAGAGAAGTAGTATTGTAAAAATTTATCCTCTAGACTTACAGAAAGTCGAGATGTCTAGATTAGAATCACGAGACTTTTAAGTTCAGTAAAAAATAAAACAGTTAAAACATAT F2: 3 TTCGA 2 Unidirectional alignment (log-probability: -29) GAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGaGCTtTGAAAATTCAAGTCATTTTTTATTTTGTCAATTttgtata GAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAGTGCTCTGAAAATTCAAGTCATTTTTTATTTTGTCAATT------- Template switch alignment (log-probability: -16.4) GAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAG|AGCTT|TGAAAATTCAAGTCATTTTTTATTTTGTCAATTTTGTATA GAGATCTGAATGTCTTTCAGCTCTACAGATCTAATCTTAG|AGCTT|TGAAAATTCAAGTCATTTTTTATTTTGTCAATTTTGTATA ========= Event 816 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGCAAAAAATGGCTTCATTTTTTCTAGACTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGTC ↑ 1 4 3 2 Chimp: GGGCAAAAAATGGCTTCATTT------ACCTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGTC Gorilla: GGGCAAAAAATGGCTTCATTT------ACCTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGTC Human: GGGCAAAAAATGGCTTCATTTTTTCTAGACTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGTC Cluster: [ ] Orangutan: GGGCAAAAAATGGCTCCATTT------ACCTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGTC Chimp > Human ------------- chr13:2733163-2733169 Template switch process: F1: L ATATCTGCCAAGGCATTAATGGGCAAAAAATGGCTTCATTTT 1 F3: 4 CTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGT R RF: ATATCTGCCAAGGCATTAATGGGCAAAAAATGGCTTCATTTACCTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGT RR: TATAGACGGTTCCGTAATTACCCGTTTTTTACCGAAGTAAATGGAGTAAGGACTTACAGATCTTAATTTCTTTTTCCCTTACA F2: 3 AGATCTT 2 Unidirectional alignment (log-probability: -31.3) ATCTGCCAAGGCATTAATGGGCAAAAAATGGCTTCATTTtttctagA-CTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGT ATCTGCCAAGGCATTAATGGGCAAAAAATGGCTTCATTT-------ACCTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGT Template switch alignment (log-probability: -22.2) ATCTGCCAAGGCATTAATGGGCAAAAAATGGCTTCATTTt|TTCTAGA|CTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGT ATCTGCCAAGGCATTAATGGGCAAAAAATGGCTTCATTTA|TTCTAGA|CTCATTCCTGAATGTCTAGAATTAAAGAAAAAGGGAATGT ========= Event 817 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AACCAGACAAAAGGAGGAACACAAATGGG---------AAATGATATGAAAACAGATGGAAA ↓ 3 1 24 Chimp: AACCAGACAAAAGGAGGAACACAAATGGTTTCCCATTTGTGGGATATGAAAACAGATGGAAA Gorilla: AACCAGACAAAAGGAGGAACACAAACGGG---------AAATGATATGAAAACAGATGGAAA Human: AACCAGACAAAAGGAGGAACACAAATGGG---------AAATGATATGAAAACAGATGGAAA Cluster: [ ] Orangutan: AACCAGACAAAAGGAGGAACACAAATGGG---------AAATGATATGAAAACAGATGGAAA Human > Chimp ------------- chr13:93411286-93411298 Template switch process: F1: L AAAGGATTCAGAAAACCAGACAAAAGGAGGAACACAAATGG 1 F3: 4 GGATATGAAAACAGATGGAAAGGTAGTGGGTTTTTTCCACA R RF: AAAGGATTCAGAAAACCAGACAAAAGGAGGAACACAAATGGGAAATGATATGAAAACAGATGGAAAGGTAGTGGGTTTTTTCCACA RR: TTTCCTAAGTCTTTTGGTCTGTTTTCCTCCTTGTGTTTACCCTTTACTATACTTTTGTCTACCTTTCCATCACCCAAAAAAGGTGT F2: 3 GTGTTTACCCTTT 2 Unidirectional alignment (log-probability: -40) AAGGATTCAGAAAACCAGACAAAAGGAGGAACACAAATGG----TttcccatttgtggGATATGAAAACAGATGGAAAGGTAGTGGGTTTTTTCCAC AAGGATTCAGAAAACCAGACAAAAGGAGGAACACAAATGGGAAAT-------------GATATGAAAACAGATGGAAAGGTAGTGGGTTTTTTCCAC Template switch alignment (log-probability: -22.9) AAGGATTCAGAAAACCAGACAAAAGGAGGAACACAAATGG|TTTCCCATTTGTG|gGATATGAAAACAGATGGAAAGGTAGTGGGTTTTTTCCAC AAGGATTCAGAAAACCAGACAAAAGGAGGAACACAAATGG|TTTCCCATTTGTG|TGATATGAAAACAGATGGAAAGGTAGTGGGTTTTTTCCAC ========= Event 818 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCACAACAACCTCAGCCCAGGCAATCATTCTGGC-ATTTAATTCATACTCATTATAT---ATTGCCTTGATGCTTTCCATAAATGAA Chimp: CCACAACAACCTCAGCCCAGGCAATCATTCTGGCAATGTAATTCATACTCATTATAT---ATTGCCTTGATGCTTTCCATAAATGAA Gorilla: CCACAACAACCTCAGCCCAGGCAATCATTCTGGC-ATTTAATTCATACTCATTATATGATGATGCTTTGATGCTTTCCATAAATGAA ↓ 3 2 1 4 Human: CCACAACAACCTCAGCCCAGGCAATCATTCTGGC-ATTTAATTCATACTCATTATAT---ATTGCCTTGATGCTTTCCATAAATGAA Cluster: [ ] Orangutan: CCACAACAACCTCAGCCCAGGTAGTCATTCTGGC-ATTTAATTCATACTCATTATAT---ATTGCCTTGATGTTTTCCATAAATGAA Gorilla > Human --------------- chr13:107578586-107578591 Template switch process: F1: L CCCAGGCAATCATTCTGGCATTTAATTCATACTCATTATAT 1 F3: 4 TTGATGCTTTCCATAAATGAAAATCTTATATATTACCTAT R RF: CCCAGGCAATCATTCTGGCATTTAATTCATACTCATTATATGATGATGCTTTGATGCTTTCCATAAATGAAAATCTTATGTATTACCTAT RR: GGGTCCGTTAGTAAGACCGTAAATTAAGTATGAGTAATATACTACTACGAAACTACGAAAGGTATTTACTTTTAGAATACATAATGGATA F2: 3 CCGTTA 2 Unidirectional alignment (log-probability: -31.9) CCAGGCAATCATTCTGGCATTTAATTCATACTCATTATAT-AT--TGCcTTGATGCTTTCCATAAATGAAAATCTTATaTATTACCTAT CCAGGCAATCATTCTGGCATTTAATTCATACTCATTATATGATGATGCTTTGATGCTTTCCATAAATGAAAATCTTATGTATTACCTAT Template switch alignment (log-probability: -22) CCAGGCAATCATTCTGGCATTTAATTCATACTCATTATAT|ATTGCC|TTGATGCTTTCCATAAATGAAAATCTTATaTATTACCTAT CCAGGCAATCATTCTGGCATTTAATTCATACTCATTATAT|ATTGCC|TTGATGCTTTCCATAAATGAAAATCTTATGTATTACCTAT ========= Event 819 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAACATGTTCTTTACTTCTTTTACCATGGTGTTAACAGTAGCCATCTCTTTC Chimp: AAACATGTTCTTTACTTCTTTCACCATGGTATTAACCGTAGCCATCTCTTTC ↑ 13 24 Gorilla: AAACATGTTCTTTACTTCTTTTACCATGGTGTTAACCGTAGCCATCTCTTTC Human: AAACATGTTCTTTACTTCTTTTACCATGGTGTTAACAGTAGCCATCTCTTTC Cluster: [ ] Orangutan: AAACATGTTCTTTACTTCTTTTATCATGGTGTTAACCGTAGCCATCTCTTTC Gorilla > Chimp --------------- chr13:98296659-98296668 Template switch process: F1: L TTTACTACAGATGTTAAAGGAAACATGTTCTTTACTTCTTT 1 F3: 4 TTAACCGTAGCCATCTCTTTCTTCATAGGCCCACAGCACG R RF: TTTACTATAGATGTTAAAGGAAACATGTTCTTTACTTCTTTTACCATGGTGTTAACCGTAGCCATCTCTTTCTTCATAGACCCACAGCACG RR: AAATGATATCTACAATTTCCTTTGTACAAGAAATGAAGAAAATGGTACCACAATTGGCATCGGTAGAGAAAGAAGTATCTGGGTGTCGTGC F2: 3 ATGGTACCAC 2 Unidirectional alignment (log-probability: -41.7) TTACTAcAGATGTTAAAGGAAACATGTTCTTTACTTCTTTcACCATGGTaTTAACCGTAGCCATCTCTTTCTTCATAGgcccacagcacg TTACTATAGATGTTAAAGGAAACATGTTCTTTACTTCTTTTACCATGGTGTTAACCGTAGCCATCTCTTTCTTCATAG------------ Template switch alignment (log-probability: -28) TTACTAcAGATGTTAAAGGAAACATGTTCTTTACTTCTTT|CACCATGGTA|TTAACCGTAGCCATCTCTTTCTTCATAGgCCCACAGCACG TTACTATAGATGTTAAAGGAAACATGTTCTTTACTTCTTT|CACCATGGTA|TTAACCGTAGCCATCTCTTTCTTCATAGACCCACAGCACG ========= Event 820 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTT--------------------AATTGACTGGAACAGGTCAGACATGATGAGATGGTTGAGGATGT Chimp: AGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTT--------------------AATTGACTGGGGCAGGTCAGACCTGATGAGATGGTTGAGGATGT ↓ 3 2 1 4 Gorilla: AGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGTCCTAGTT----------------------------------------CCATGATGAGATGGTTGAGGATGT ↑ 3 2 1 4 Human: AGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTT--------------------AATTGACTGGAACAGGTCAGACATGATGAGATGGTTGAGGATGT Cluster: [ ] Orangutan: AGTTGTGTGGAGCATAGCTTGGAACTAGGACAGTCACGACCAGTTAATTGACTGGAACAGGTCAg--------------------acatgatgagatggttgaggatgt Human > Gorilla --------------- chr13:8040113-8040121 Template switch process: F1: L ACACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG 1 F3: 4 CATGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAG R RF: ACACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTTAATTGACTGGAACAGGTCAGACATGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAG RR: TGTGTCAGCACACCTCATATCGAACCTTGATCCTGTCAGTCCTGGTCAATTAACTGACCTTGTCCAGTCTGTACTACTCTACCAACTCCTACAAACTTCTGTAAAACTTC F2: 3 CTTGATCCT 2 Unidirectional alignment (log-probability: -34.1) CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGtcCtAGTT--------------------cCATGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAG CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTTAATTGACTGGAACAGGTCAGACATGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAG Template switch alignment (log-probability: -16.9) CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG|TCCTAGTTC|CATGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAG CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG|TCCTAGTTC|CATGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAG Chimp > Gorilla --------------- chr13:8040113-8040123 Template switch process: F1: L ACACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG 1 F3: 4 TGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAGGT R RF: ACACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTTAATTGACTGGGGCAGGTCAGACCTGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAGGT RR: TGTGTCAGCACACCTCATATCGAACCTTGATCCTGTCAGTCCTGGTCAATTAACTGACCCCGTCCAGTCTGGACTACTCTACCAACTCCTACAAACTTCTGTAAAACTTCCA F2: 3 ACCTTGATCCT 2 Unidirectional alignment (log-probability: -38) CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG-------------------------------tcctagttccaTGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAGGT CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAGGACCAGTTAATTGACTGGGGCAGGTCAGACC-----------TGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAGGT Template switch alignment (log-probability: -17.1) CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG|TCCTAGTTCCA|TGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAGGT CACAGTCGTGTGGAGTATAGCTTGGAACTAGGACAGTCAG|TCCTAGTTCCA|TGATGAGATGGTTGAGGATGTTTGAAGACATTTTGAAGGT ========= Event 821 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGCTTTATTGATAACTCAGC------AATTGTTTAACTGAATTATTAAATTAATGAA ↓ 3 1 2 4 Chimp: TTGCTTTATTGATAACTCAGCAAAAACAATT-----GCTGAATTATTAAATTAATGAA ↑ 3 1 2 4 Gorilla: TTGCTTTATTGATAACTCAGC------AATTGTTTAACTGAATTATTAAATTAATGAA Human: TTGCTTTATTGATAACTCAGC------AATTGTTTAACTGAATTATTAAATTAATGAA Cluster: [ ] Orangutan: TTGCTTTATTGATAACTCAGC------AATTGTTTAACTGAATTATTAAGTTAATGAA Human > Chimp ------------- chr13:7921766-7921774 Template switch process: F1: L TGTTATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAA 1 F3: 4 CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG R RF: TGTTATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAATTGTTTAACTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG RR: ACAATACATAATTATTCGTCAACGAAATAACTATTGAGTCGTTAACAAATTGACTTAATAATTTAATTACTTTAATAAAGGATATTCTTCC F2: 3 GTTAACAAA 2 Unidirectional alignment (log-probability: -30.1) TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGcaaaaaCAATTG-----CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAG------CAATTGTTTAACTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG Template switch alignment (log-probability: -16.4) TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAA|AAACAATTG|CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAA|AAACAATTG|CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG Gorilla > Chimp --------------- chr13:7921766-7921774 Template switch process: F1: L TGTTATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAA 1 F3: 4 CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG R RF: TGTTATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAATTGTTTAACTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG RR: ACAATACATAATTATTCGTCAACGAAATAACTATTGAGTCGTTAACAAATTGACTTAATAATTTAATTACTTTAATAAAGGATATTCTTCC F2: 3 GTTAACAAA 2 Unidirectional alignment (log-probability: -29.6) TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGcaaaaaCAATTG-----CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAG------CAATTGTTTAACTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG Template switch alignment (log-probability: -16.9) TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAA|AAACAATTG|CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG TATGTATTAATAAGCAGTTGCTTTATTGATAACTCAGCAA|AAACAATTG|CTGAATTATTAAATTAATGAAATTATTTCCTATAAGAAGG ========= Event 822 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGTCGGCGGGGGTCCTGGGC-----------------CTGATGCTGTGGGGGGGCAGGTGGGCCAGGGA Chimp: AGGTCGGCGGGGGTCCTGGGC-----------------CTGATGCTGTgggggggCAGGTGGGCCAGGGA Gorilla: AGGTCGGCGGGGGTCCTGGGCTGCAGcccccccACAGCATCAGGCTGTTGGGGGGCAGGTGGGCCAGGGA ↓ 1 3 2 4 Human: AGGTCGGCGGGGGTCCTGGGC-----------------CTGATGCTGTGGGGGGGCAGGTGGGCCAGGGA Cluster: [ ] Orangutan: AGGTCGGCGGGGGTCCTGGGC--------------------------------TGCAGCCCACCCACAGC Gorilla > Human --------------- chr13:1281941-1281951 Template switch process: F1: L GCCCTGCAGGGAGAGCGCAGAGGTCGGCGGGGGTCCTGGGC 1 F3: 4 GGGGGGCAGGTGGGCCAGGGATGCCGGCTCATCTGTGGGC R RF: GCCCTGCAGGGAGAGCGCAGAGGTCGGCGGGGGTCCTGGGCTGCAGCCCCCCCACAGCATCAGGCTGTTGGGGGGCAGGTGGGCCAGGGATGCCGGCTCATCTGTGGGC RR: CGGGACGTCCCTCTCGCGTCTCCAGCCGCCCCCAGGACCCGACGTCGGGGGGGTGTCGTAGTCCGACAACCCCCCGTCCACCCGGTCCCTACGGCCGAGTAGACACCCG F2: 3 GTGTCGTAGTC 2 Unidirectional alignment (log-probability: -33.1) CCCTGCAGGGAGAGCGCAGAGGTCGGCGGGGGTCCTGGGCctgaT---------------------GCTGTgGGGGGGCAGGTGGGCCAGGGATGCCGGCTCATCTGTGGGC CCCTGCAGGGAGAGCGCAGAGGTCGGCGGGGGTCCTGGGC----TGCAGCCCCCCCACAGCATCAGGCTGTTGGGGGGCAGGTGGGCCAGGGATGCCGGCTCATCTGTGGGC Template switch alignment (log-probability: -17.1) CCCTGCAGGGAGAGCGCAGAGGTCGGCGGGGGTCCTGGGC|CTGATGCTGTG|GGGGGGCAGGTGGGCCAGGGATGCCGGCTCATCTGTGGGC CCCTGCAGGGAGAGCGCAGAGGTCGGCGGGGGTCCTGGGC|CTGATGCTGTG|GGGGGGCAGGTGGGCCAGGGATGCCGGCTCATCTGTGGGC ========= Event 823 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TCTCTTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAGGGTTGTCTCTAAATTTATTTATTTATTTAGAGAcaggttggagtgcagtggctcaatca ↑ 4 3 2 1 Chimp: TCTCTTTTTTATTAAAGTCTTAT------------------------------------TTATTTATTTAGAGAcaggttggagtgcagtggctcaatca Gorilla: TCTCttttttattaaagtcttatttatttatttagagacagggttgtctctaaatttatttatttatttaGAGAcaggttggagtgcagtggctcaatca Human: TCTCTTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAGGGTTGTCTCTAAATTTATTTATTTATTTAGAGAcaggttggagtgcagtggctcaatca Cluster: [ ] Orangutan: Chimp > Human ------------- chr13:94783307-94783317 Template switch process: F1: L TAGAACTACCCTATTAATTCTCTTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAGGGT 1 F3: 4 TTATTTATTTATTTAGAGACAGGTTGGAGTGCAGTGGCTCAATC R RF: TAGAACTACCCTATTAATTCTCTTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAGGTTGGAGTGCAGTGGCTCAATC RR: ATCTTGATGGGATAATTAAGAGAAAAAATAATTTCAGAATAAATAAATAAATCTCTGTCCAACCTCACGTCACCGAGTTAG F2: 3 TAAATCTCTGT 2 Unidirectional alignment (log-probability: -62.7) TTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAgggttgtctctaaatttatttatttatttagagacaGGTTGGAGTGCAGTGGCTC TTTTTTATTAAAGTCTTATTTATTTATTTAGAGACA------------------------------------GGTTGGAGTGCAGTGGCTC Template switch alignment (log-probability: -23.1) TTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAGGgT|TGTCTCTAAAT|TTATTTATTTATTTAGAGACAGGTTGGAGTGCAGTGGCTC TTTTTTATTAAAGTCTTATTTATTTATTTAGAGACAGGTT|TGTCTCTAAAT|TTATTTATTTATTTAGAGACAGGTTGGAGTGCAGTGGCTC ========= Event 824 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCCTGCAGCGAGCATGAGCACTAAGTCTCTCGCGAGGAGAAGCTCGACACTTTATAGTCGGCCAGGGGCTGGGCGGGGCGTCTCCTGGCGCAGGCGCACTTCCGTGCGTGGTGAGCGAGCCGGAGCGCGCCTGCGTGTTGCGACTTCGGGAAAAGGCGGGTGCTGACG Chimp: CCCCTGCAGCGAGCATGAGCACTAAG----TCGCGAGGAGAAGCTCGACACTTTATAGTCGGCCAGGGGCTGGGCGGGGCGTCTCCTGGCGCAGGCGCACTTCCGTGCGTGGTGTGCGAGCCGGGGCGCGCCTGCGTGTTGCGACTTCGGGAAAAGGCGGGTGCTGGAG ↑ 1 4 3 2 Gorilla: CCCCTGCAGCGAGCATGAGCAAGAAGTCTCTCACGAGCAGAAGCTCGACACTTTATAGTCCGCCAGGGGCTGGGCGGGGCGTCTCCTGGCGCAGGCGCACTTCCGTGCGTGGTGTGCGAGCGGGAGTGCGCCTGCGTGTTGCGACTTAGGGAAAAGGCGGGTGCTGACG Human: CCCCTGCAGCGAGCATGAGCACTAAGTCTCTCGCGAGGAGAAGCTCGACACTTTATAGTCGGCCAGGGGCTGGGCGGGGCGTCTCCTGGCGCAGGCGCACTTCCGTGCGTGGTGAGCGAGCCGGAGCGCGCCTGCGTGTTGCGACTTCGGGAAAAGGCGGGTGCTGACG Cluster: [ ] Orangutan: CCCCTGCAGCGAGCATGAGCACAAAGTCTCTCGCGAGGAGAAGCTCGACACTTTATAGTCGGCCACTGGCTGGGCGGGGCGTCTCCTGGCGCAAGCGCACTTCCGTGCGTGGCGTACGAGCCGGAGCGCTCCTACGTGTTGCGACTTCGGGAAAAGGCGGGTGCTGACG Gorilla > Chimp --------------- chr13:94715629-94715636 Template switch process: F1: L ACGCTCGCCCTGACCTCCGACCCCTGCAGCGAGCATGAGCA 1 F3: 4 CGAGGAGAAGCTCGACACTTTATAGTCGGCCAGGGGCTGGGCGGG R RF: ACGCTCGCCCTGACCTCCGACCCCTGCAGCGAGCATGAGCAAGAAGTCTCTCACGAGCAGAAGCTCGACACTTTATAGTCCGCCAGGGGCTGGGCGGGGCGTCTCCTGGCGCAGGCGCACTTCCGTGCGTGGTGTGCGAGCGGGAGTGCGCCTGCGTGTTGCGACTTAG RR: TGCGAGCGGGACTGGAGGCTGGGGACGTCGCTCGTACTCGTTCTTCAGAGAGTGCTCGTCTTCGAGCTGTGAAATATCAGGCGGTCCCCGACCCGCCCCGCAGAGGACCGCGTCCGCGTGAAGGCACGCACCACACGCTCGCCCTCACGCGGACGCACAACGCTGAATC F2: 3 GCTGAATC 2 Unidirectional alignment (log-probability: -38.9) CGCTCGCCCTGACCTCCGACCCCTGCAGCGAGCATGAGCActAAG----TCgCGAGgAGAAGCTCGACACTTTATAGTCgGCCAGGGGCTGG CGCTCGCCCTGACCTCCGACCCCTGCAGCGAGCATGAGCAAGAAGTCTCTCACGAGCAGAAGCTCGACACTTTATAGTCCGCCAGGGGCTGG Template switch alignment (log-probability: -27.9) CGCTCGCCCTGACCTCCGACCCCTGCAGCGAGCATGAGCA|CTAAGTCG|CGAGgAGAAGCTCGACACTTTATAGTCgGCCAGGGGCTGG CGCTCGCCCTGACCTCCGACCCCTGCAGCGAGCATGAGCA|CTAAGTCG|CGAGCAGAAGCTCGACACTTTATAGTCCGCCAGGGGCTGG ========= Event 825 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAAGCTTTCTGTCACTTCAATAATG---CCAGGATGCTGGGGAGCAGCCGGAGTAGTCT Chimp: AGAAGCTTTCTGTCACTTCAATAATG---CCAGGATGCTGGGGAGCAGCCGGAGTAGTCT ↓ 1 3 4 2 Gorilla: AGAAGCTTTCTGTCACTTCAAAATCAGCATCCTGATGCTGGGGAGCAGCCGGAGTAGTCT ↑ 1 3 4 2 Human: AGAAGCTTTCTGTCACTTCAATAATG---CCAGGATGCTGGGGAGCAGCCGGAGTAGTCT Cluster: [ ] Orangutan: AGAAG----CTGTCACTTCAATAATG---CCAGGATGCTGGGGAGCAGACAGAGTAGTCT Human > Gorilla --------------- chr13:91873397-91873405 Template switch process: F1: L AACAGCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAA-AAT 1 F3: 4 GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG R RF: AACAGCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAATAATGCCAGGATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG RR: TTGTCGAGAGTCTACGTCGGTCTTCGAAAGACAGTGAAGTTATTACGGTCCTACGACCCCTCGTCGGCCTCATCAGACCCTCTGTCCTCC F2: 3 TCCTACGAC 2 Unidirectional alignment (log-probability: -36.9) GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAAaatcagcatccT--------GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAA-----------TAATGCCAGGATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG Template switch alignment (log-probability: -26.7) GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAA-AAT|CAGCATCCT|GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAATAAT|CAGCATCCT|GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG Chimp > Gorilla --------------- chr13:91873397-91873405 Template switch process: F1: L AACAGCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAA-AAT 1 F3: 4 GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG R RF: AACAGCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAATAATGCCAGGATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG RR: TTGTCGAGAGTCTACGTCGGTCTTCGAAAGACAGTGAAGTTATTACGGTCCTACGACCCCTCGTCGGCCTCATCAGACCCTCTGTCCTCC F2: 3 TCCTACGAC 2 Unidirectional alignment (log-probability: -36.9) GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAAaatcagcatccT--------GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAA-----------TAATGCCAGGATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG Template switch alignment (log-probability: -26.7) GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAA-AAT|CAGCATCCT|GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG GCTCTCAGATGCAGCCAGAAGCTTTCTGTCACTTCAATAAT|CAGCATCCT|GATGCTGGGGAGCAGCCGGAGTAGTCTGGGAGACAGGAGG ========= Event 826 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGGaaaaaaataaaaaTGCTGAGACTCC------AAGTCCAAGTTCTCAGCTAATTCtttttttttt---ttttt Chimp: AAAGGaaaaaaataaaaaTGCTGAGACTCC------AAGTCCAAGTTCTCAGCTAAttctttttttttt---tt--- ↓ 3 2 1 4 Gorilla: AAAGGaaaaaaataaaaaTGCTGAGACTCC------------AAGTTCTCAGCtttttttttttttttt-------- Human: AAAGGaaaaaaataaaaaTGCTGAGACTCC------AAGTCCAAGTTCTCAGCTAATTCtttttttttt---ttttt Cluster: [ ] Orangutan: AAAGGAAAAAAATTAAAATGCGGAGACTCCAAGTCC------AAGTTCTCAGCTAAttcttttttttttttt----- Chimp > Gorilla --------------- chrCABD030160293:57-67 Template switch process: F1: L TTGTTAACCAGAAAGGAAAAAAATAAAAATGCTGAGACTCCAAGT 1 F3: 4 TTTTTTTTTTTTTTTTTTTT R RF: TTGTTAACCAGAAAGGAAAAAAATAAAAATGCTGAGACTCCAAGTCCAAGTTCTCAGCTAATTCTTTTTTTTTTTTTTTTTTTT RR: AACAATTGGTCTTTCCTTTTTTTATTTTTACGACTCTGAGGTTCAGGTTCAAGAGTCGATTAAGAAAAAAAAAAAAAAAAAAAA F2: 3 TTTTCGACTCT 2 Unidirectional alignment (log-probability: -35.8) AACCAGAAAGGAAAAAAATAAAAATGCTGAGACTCCAA------GTTCTCAGCTttTTtTTTTTTTTTTTTTTTTTt AACCAGAAAGGAAAAAAATAAAAATGCTGAGACTCCAAGTCCAAGTTCTCAGCTAATTCTTTTTTTTTTTTTTTTT- Template switch alignment (log-probability: -22.2) AACCAGAAAGGAAAAAAATAAAAATGCTGAGACTCCAAGT|TCTCAGCtTTT|TTTTTTTTTTTTTTTTTTTT AACCAGAAAGGAAAAAAATAAAAATGCTGAGACTCCAAGT|TCTCAGCATTT|TTTTTTTTTTTTTTTTTTTT ========= Event 827 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGCCCATTGCCATAGCCTGGGCTATGATCCCAATCATTATTCTCACCCAGATGGTAA ↑ 3 4 2 Chimp: TGCCCATTGCCATAGCCTGGGTTGGG------ATCATTATTCTCACCCAGATGGTAA Gorilla: TGCCCATTGCCATAGCCTGGGTTGGG------ATCATTATTCTCACCCAGATGGTAA ↓ 3 4 2 Human: TGCCCATTGCCATAGCCTGGGCTATGATCCCAATCATTATTCTCACCCAGATGGTAA Cluster: [ ] Orangutan: TGCCCATTGCCATAGCCTGGGTTGGG------ATCATTATTCTCACCCAGATGGTAA Chimp > Human ------------- chr13:90503474-90503482 Template switch process: F1: L AACTCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGCT 1 F3: 4 ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC R RF: AACTCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGTTGGGATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC RR: TTGAGAACACAGAAGAGGACACGGGTAACGGTATCGGACCCAACCCTAGTAATAAGAGTGGGTCTACCATTGACCCTAACGGATTG F2: 3 ACCCTAGTA 2 Unidirectional alignment (log-probability: -37.2) TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCC-----TGGGctatgatcccaATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGTTGGG-----------ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC Template switch alignment (log-probability: -22.4) TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGcT|ATGATCCCA|ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGTT|ATGATCCCA|ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC Gorilla > Human --------------- chr13:90503474-90503482 Template switch process: F1: L AACTCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGCT 1 F3: 4 ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC R RF: AACTCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGTTGGGATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC RR: TTGAGAACACAGAAGAGGACACGGGTAACGGTATCGGACCCAACCCTAGTAATAAGAGTGGGTCTACCATTGACCCTAACGGATTG F2: 3 ACCCTAGTA 2 Unidirectional alignment (log-probability: -36.1) TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGcTatGatcccaATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGTTGGG------ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC Template switch alignment (log-probability: -22.4) TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGcT|ATGATCCCA|ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC TCTTGTGTCTTCTCCTGTGCCCATTGCCATAGCCTGGGTT|ATGATCCCA|ATCATTATTCTCACCCAGATGGTAACTGGGATTGCCTAAC ========= Event 828 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: aagcgattctccttcctcagcctc---AGAAATTTG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAGGTCTCAGTCTCAAATTTCTGAGGCTCacactcctatgcaaggaag Chimp: aagcgattctccttcctcagcctc---AGAAATTTG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGactgagacctgtctcaaatttctgaggttcacactcctatgcaaggaag Gorilla: aagcgattctccttcctcagcctc---AGAAATTTG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACTGAGACCTGTCTCAAATTTCTGAGGTTCCCactcctatgcaaggaag ↓ 3 1 2 4 ↑ 13 24 Human: aagcgattctccttcctcagcctc---AGAAATTTG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAGGTCTCAGTCTCAAATTTCTGAGGCTCacactcctatgcaaggaag Cluster: [ ] Orangutan: aagcgattctccttcctcagcctcccgagtaactggaattacaggcgcatgccaccacacacagctaatttgtagttttagtagagccagagttaacatcatgttgcccaggctggtctcaaactcctgacctcaagtgatccacccgccttggcctcccaaagtgctgggattacaggcatgagccaccatgcccagcctggattcttcttttgtggttctttttttttccccccctttcttcccctctattttctcttcacaggactcaagacttcgaaacctgctaaacatgagctttcaagacctacccatctaggaataaaccatcttagccgtgagagatcagatgaaacctgagaccagggatgcattttattgtaaaatgctttctccagaagactttttaaagaaaaggtggaaaTGTGAAAGGAAAATACCTTGGGCTCTTtcaagctgggaaccgctcagggcaaatcggctttccattctattcaagtcatccctttgctcacagagatagacgcatattctgattgccttctttgaaaagacttatcagaaactctaaagaatgcaccatatctgtctcttacctatatgtgatctggaagcccccggggagggttggggtgggcagccttgctttgagctgtctccgcctttctggagagaacaaattgtacttcttacacattgatggatggctgatgtctccctaaaacgtataaaaccaagctgtgccccgaccaccttgggcaaatgtcatcaggacttcctgaggctatgtcatgggcacagcctcaaccttggcaaaataaactttctaaattaactgagacctgtctcaaatttctgaggttcacactcctatgcaaggaag Gorilla > Human --------------- chr13:90881075-90881100 Template switch process: F1: L GTTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC 1 F3: 4 TCACACTCCTATGCAAGGAAGG R RF: GTTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGACTGAGACCTGTCTCAAATTTCTGAGGTTCCCACTCCTATGCAAGGAAGG RR: CAAGTTCGCTAAGAGGAAGGAGTCGGAGTCTTTAAACTCTGACTCTGGACAGAGTTTAAAGACTCCAAGGGTGAGGATACGTTCCTTCC F2: 3 CGGAGTCTTTAAACTCTGACTCTGGA 2 Unidirectional alignment (log-probability: -43.6) TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC--------aggtctcaGTCTCAAATTTCTGAGGcTCaCACTCCTATGCAAGGAAGG TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGACTGAGACCT--------GTCTCAAATTTCTGAGGTTCCCACTCCTATGCAAGGAAGG Template switch alignment (log-probability: -24.1) TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC|AGGTCTCAGTCTCAAATTTCTGAGGC|TCaCACTCCTATGCAAGGAAGG TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC|AGGTCTCAGTCTCAAATTTCTGAGGC|TCCCACTCCTATGCAAGGAAGG Human > Gorilla --------------- chr13:92083247-92083254 Template switch process: F1: L GTTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC 1 F3: 4 GTCTCAAATTTCTGAGGTTCCCACTCCTATGCAAGGAAGG R RF: GTTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGACAGGTCTCAGTCTCAAATTTCTGAGGCTCACACTCCTATGCAAGGAAGG RR: CAAGTTCGCTAAGAGGAAGGAGTCGGAGTCTTTAAACTCTGTCCAGAGTCAGAGTTTAAAGACTCCGAGTGTGAGGATACGTTCCTTCC F2: 3 TCCAGAGT 2 Unidirectional alignment (log-probability: -43.6) TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC--------tgagacctGTCTCAAATTTCTGAGGtTCcCACTCCTATGCAAGGAAGG TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGACAGGTCTCA--------GTCTCAAATTTCTGAGGCTCACACTCCTATGCAAGGAAGG Template switch alignment (log-probability: -27.8) TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC|TGAGACCT|GTCTCAAATTTCTGAGGtTCcCACTCCTATGCAAGGAAGG TTCAAGCGATTCTCCTTCCTCAGCCTCAGAAATTTGAGAC|TGAGACCT|GTCTCAAATTTCTGAGGCTCACACTCCTATGCAAGGAAGG ========= Event 829 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGTTGACTTCAT----ATCAGACTTTAAATCAACCAAGAAGGTAGTC------TAGCATTTCTAATGACATTATC Chimp: AGTTGACTTCAT----ATCAGACTTTAAATCAACCAAGAAGGTAGTC------TAGCATTTCTAATGACATTATC ↑ 3 2 1 4 Gorilla: AGTTGACTTCATATCTATCAGACTTTAAATCAACCAAGAAGGTTGATTAGCATTAGCATTTCTAATGACATTATC Human: AGTTGACTTCAT----ATCAGACTTTAAATCAACCAAGAAGGTAGTC------TAGCATTTCTAATGACATTATC Cluster: [ ] Orangutan: AGTTGACTTCAT----ATCAGACTTTCAATCAACCAAGAAGGTAGTC------TAGCATTTCTAATGACATTATC Gorilla > Chimp --------------- chr13:92327640-92327644 Template switch process: F1: L TTGACTTCA----TATCAGACTTTAAATCAACCAAGAAGGT 1 F3: 4 AGCATTTCTAATGACATTATCTCTGGATAGCCTGCTGAA R RF: TTGACTTCATATCTATCAGACTTTAAATCAACCAAGAAGGTTGATTAGCATTAGCATTTCTAATGACATTATCTCTGGATAGCCTGCTGAA RR: AACTGAAGTATAGATAGTCTGAAATTTAGTTGGTTCTTCCAACTAATCGTAATCGTAAAGATTACTGTAATAGAGACCTATCGGACGACTT F2: 3 TCTGA 2 Unidirectional alignment (log-probability: -36.8) TTGACTTCAT----ATCAGACTTTAAATCAACCAAGAAGG----------TagtcTAGCATTTCTAATGACATTATCTCTGGATAGCCTGCTGAA TTGACTTCATATCTATCAGACTTTAAATCAACCAAGAAGGTTGATTAGCAT----TAGCATTTCTAATGACATTATCTCTGGATAGCCTGCTGAA Template switch alignment (log-probability: -26.2) TTGACTTCA----TATCAGACTTTAAATCAACCAAGAAGGT|AGTCT|AGCATTTCTAATGACATTATCTCTGGATAGCCTGCTGAA TTGACTTCATATCTATCAGACTTTAAATCAACCAAGAAGGT|AGTCT|AGCATTTCTAATGACATTATCTCTGGATAGCCTGCTGAA ========= Event 830 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATGTGCCATTGACGTTAGAAAACTTGATGAAATGGAACAGAGGAGCTTCATGCTTTCTACGTTTCTGAACA---ACAAGTCGTACATCTGGGAA Chimp: CATGTGCCATTGACGTTAGAAAACTTGATGAAATGGAACAGAGGAG-----------CTACGTTTCTGA---ACAACAAGTCGTACATCTGGGAA ↓ 3 2 41 Gorilla: CATGTGCCATTGACGTTAGAAAA--CGATGAAATGGAACAGAGGAGCTTCATGCTTTCTACGTTTCTGAACA---ACAAGTCGTACATCTGGGAA Human: CATGTGCCATTGACGTTAGAAAACTTGATGAAATGGAACAGAGGAGCTTCATGCTTTCTACGTTTCTGAACA---ACAAGTCGTACATCTGGGAA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr13:4424285-4424293 Template switch process: F1: L TGAAATGGAACAGAGGAGCT 1 F3: 4 CTACGTTTCTGAACAACAAGTCGTACATCTGGGAAATAACTTTTTTTTTTTTTTT R RF: AAAACTTGATGAAATGGAACAGAGGAGCTACGTTTCTGAACAACAAGTCGTACATCTGGGAAATAACTTTTTTTTTTTTTTT RR: TTTTGAACTACTTTACCTTGTCTCCTCGATGCAAAGACTTGTTGTTCAGCATGTAGACCCTTTATTGAAAAAAAAAAAAAAA F2: 3 TTTCGTACT 2 Unidirectional alignment (log-probability: -47.6) TGAAATGGAACAGAGGAGCTtcatgctttctACGTTTCTGAACAACAAGTCGTACATCTGGGAAATAAC TGAAATGGAACAGAGGAGCT-----------ACGTTTCTGAACAACAAGTCGTACATCTGGGAAATAAC Template switch alignment (log-probability: -27.8) TGAAATGGAACAGAGGAGCT|TCAtGcTTT|CTACGTTTCTGAACAACAAGTCGTACATCTGGGAAATAAC TGAAATGGAACAGAGGAGCT|TCAAGTTTT|CTACGTTTCTGAACAACAAGTCGTACATCTGGGAAATAAC ========= Event 831 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTTGCTTTCTAAAGTAAACAGGGT---GGCC---AGGTCTGGTTCTATTTAACCCCACTT Chimp: CCTTTGCTTTCTAAAGTAAACAGGGT---GGCC---AGGTCTGGTTCTATTTAACCCCACTT Gorilla: CCTTTGCTTTCTAAAGTAAACAGGGTGCTGGCCACCCTGTGGGGTTCTATTTAACCCCACTT ↑ 3 1 4 Human: CCTTTGCTTTCTAAAGTAAACAGGGT---GGCC---AGGTCTGGTTCTATTTAACCCCACTT Cluster: [ ] Orangutan: CCTTTGCTTTCTAAAGTAAACAGGGT---GGCC---AGGTCTGGTTCTATTTAACCCCACTT Human > Gorilla --------------- chr13:89618576-89618588 Template switch process: F1: L TGTTTCTAGGTTGTTCCTTTGCTTTCTAAAGTAAACAGGGTG 1 F3: 4 GG---GGTTCTATTTAACCCCACTTGTCCCTTTCCCTTCACATTG R RF: TGTTTCTAGGTTGTTCCTTTGCTTTCTAAAGTAAACAGGGTGGCCAGGTCTGGTTCTATTTAACCCCACTTGTCCCTTTCCCTTCACATTG RR: ACAAAGATCCAACAAGGAAACGAAAGATTTCATTTGTCCCACCGGTCCAGACCAAGATAAATTGGGGTGAACAGGGAAAGGGAAGTGTAAC F2: 3 TGTCCCACCGGTC 2 Unidirectional alignment (log-probability: -39.7) TTTCTAGGTTGTTCCTTTGCTTTCTAAAGTAAACAGGGTG-------CTggccaccctgtggGGTTCTATTTAACCCCACTTGTCCCTTTCCCTTCACAT TTTCTAGGTTGTTCCTTTGCTTTCTAAAGTAAACAGGGTGGCCAGGTCT-------------GGTTCTATTTAACCCCACTTGTCCCTTTCCCTTCACAT Template switch alignment (log-probability: -27.4) TTTCTAGGTTGTTCCTTTGCTTTCTAAAGTAAACAGGGTG|CTGGCCACCCTGT|GG---GGTTCTATTTAACCCCACTTGTCCCTTTCCCTTCACAT TTTCTAGGTTGTTCCTTTGCTTTCTAAAGTAAACAGGGTG|CTGGCCACCCTGT|GGTCTGGTTCTATTTAACCCCACTTGTCCCTTTCCCTTCACAT ========= Event 832 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAACAAAAAATCTTTTACTATCAG---------GCCCTTTATGTTGGACAAGTTTAGCTCTTCTAAAT Chimp: AGGAACAAAAAATCTTTTACTGTCAG---------GCCCTTTATGTTGGGCAAGTTTAGCTCTTCTAAAT ↓ 3 1 4 2 Gorilla: AGGAACAAAAAATCTTTTACTATCAGGCATAAAGGGCCTGTTATGTTGGACAAGTTTAGCTCTTCTAAAT ↑ 3 1 4 2 Human: AGGAACAAAAAATCTTTTACTATCAG---------GCCCTTTATGTTGGACAAGTTTAGCTCTTCTAAAT Cluster: [ ] Orangutan: AGGAACAAAAAATCTTTTACTATCAG---------GCCCTTTATGTTGGACAAGTTTAACTCTTCTAAAT Human > Gorilla --------------- chr13:7273984-7273995 Template switch process: F1: L AGTACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGC 1 F3: 4 TTATGTTGGACAAGTTTAGCTCTTCTAAATGTCAGAATTT R RF: AGTACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGCCCTTTATGTTGGACAAGTTTAGCTCTTCTAAATATCAGAATTT RR: TCATGTGTCATTCTTTCCTTGTTTTTTAGAAAATGATAGTCCGGGAAATACAACCTGTTCAAATCGAGAAGATTTATAGTCTTAAA F2: 3 GTCCGGGAAATA 2 Unidirectional alignment (log-probability: -39.2) ACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGCataaagggCCTgTTATGTTGGACAAGTTTAGCTCTTCTAAATgTCAGAATTT ACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGC--------CCT-TTATGTTGGACAAGTTTAGCTCTTCTAAATATCAGAATTT Template switch alignment (log-probability: -22.8) ACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGC|ATAAAGGGCCTG|TTATGTTGGACAAGTTTAGCTCTTCTAAATgTCAGAATTT ACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGC|ATAAAGGGCCTG|TTATGTTGGACAAGTTTAGCTCTTCTAAATATCAGAATTT Chimp > Gorilla --------------- chr13:7273984-7273995 Template switch process: F1: L GTAATAGTACACAGTAAGAAAGGAACAAAAAATCTTTTACTATCAGGC 1 F3: 4 TTATGTTGGACAAGTTTAGCTCTTCTAAATGTCAGAATTTGTGAAAGACT R RF: GTAATAGTACACAGTAAGAAAGGAACAAAAAATCTTTTACTGTCAGGCCCTTTATGTTGGGCAAGTTTAGCTCTTCTAAATGTCAGAATTTGTGAAAGACT RR: CATTATCATGTGTCATTCTTTCCTTGTTTTTTAGAAAATGACAGTCCGGGAAATACAACCCGTTCAAATCGAGAAGATTTACAGTCTTAAACACTTTCTGA F2: 3 GTCCGGGAAATA 2 Unidirectional alignment (log-probability: -44.9) ACACAGTAAGAAAGGAACAAAAAATCTTTTACTaTCAGGCataaagggCCTgTTATGTTGGaCAAGTTTAGCTCTTCTAAATGTCAGAATTT ACACAGTAAGAAAGGAACAAAAAATCTTTTACTGTCAGGC--------CCT-TTATGTTGGGCAAGTTTAGCTCTTCTAAATGTCAGAATTT Template switch alignment (log-probability: -28.7) ACACAGTAAGAAAGGAACAAAAAATCTTTTACTaTCAGGC|ATAAAGGGCCTG|TTATGTTGGaCAAGTTTAGCTCTTCTAAATGTCAGAATTT ACACAGTAAGAAAGGAACAAAAAATCTTTTACTGTCAGGC|ATAAAGGGCCTG|TTATGTTGGGCAAGTTTAGCTCTTCTAAATGTCAGAATTT ========= Event 833 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CGTCACCTACACACATGCAAA-----------GAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA ↓ 4 1 3 2 Chimp: CGTCACCTACACACATGCAAAGAACGCATTCAGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA Gorilla: CGTCACCTACACACATGCAAA-----------GAAACATCTTCTGAATGAGGATGCTAAGTCATGTTCACA Human: CGTCACCTACACACATGCAAA-----------GAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA Cluster: [ ] Orangutan: CGTCACCTACACACATGCAAA-----------GAAACATCTTCTAAATGCGGATGCAAAGTCATGTTCACA Human > Chimp ------------- chr13:89093295-89093301 Template switch process: F1: L GAAGATACACTTCAAACCACCGTCACCTACACACATGCAAAGAA 1 F3: 4 AGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACAG R RF: GAAGATACACTTCAAACCACCGTCACCTACACACATGCAAAGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACAG RR: CTTCTATGTGAAGTTTGGTGGCAGTGGATGTGTGTACGTTTCTTTGTAGAAGACTTACGCCTACGATTCAGTACAAGTGTC F2: 3 CTTACGC 2 Unidirectional alignment (log-probability: -26.7) ATACACTTCAAACCACCGTCACCTACACACATGCAAagaacgcattcAGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA ATACACTTCAAACCACCGTCACCTACACACATGCAA-----------AGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA Template switch alignment (log-probability: -16.2) ATACACTTCAAACCACCGTCACCTACACACATGCAAAGAA|CGCATTC|AGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA ATACACTTCAAACCACCGTCACCTACACACATGCAAAGAA|CGCATTC|AGAAACATCTTCTGAATGCGGATGCTAAGTCATGTTCACA ========= Event 834 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGCTGAAAAGGATAGTCATACAG---TCAATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAAGCCACAGGATAAAGCCTGAATCCTTAATGGCAAGTTTGGTGTGGCATGTGACTCTGAGCCTGTTGCCGGCATT ↑ 1 4 3 2 Chimp: TGCTGAAAAGGATAGTCATACTTTTCATAATTGTGAAGAAAATTAAGGTCCTCGGGTTaaaaaaaCAAGCCACAGGATAAAGCCTGAATCCTTAATGGCAAGTTTGGTGTGGCATGTGACTCTGAGCCTGTTGCCAGCATT Gorilla: TGCTGAAAAGGATAGTCATACAG---CCAATTGTGAAGAAAATTAAGGTCCTCGGGTTaaaaaaaCAAGCCACAGGATAAAGCCTGAATCCTTAGTGGCAAGTTTGGTGTGGCATGTGATTCTGAGCCTGTTGCCGGCATT Human: TGCTGAAAAGGATAGTCATACAG---TCAATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAAGCCACAGGATAAAGCCTGAATCCTTAATGGCAAGTTTGGTGTGGCATGTGACTCTGAGCCTGTTGCCGGCATT Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------------------------------------------------------- Chimp > Human ------------- chr13:25503713-25503716 Template switch process: F1: L TTAGGTGCCATA-ACTCTGATGCTGAAAAGGATAGTCATAC 1 F3: 4 AATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAA R RF: TTAGGTGCCATACACTCTGATGCTGAAAAGGATAGTCATACTTTTCATAATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAAGCCACAGGATAAAGCCTGAATCCTTAATGGCAAGTTTGGTGTGGCATGTGACT RR: AATCCACGGTATGTGAGACTACGACTTTTCCTATCAGTATGAAAAGTATTAACACTTCTTTTAATTCCAGGAGCCCAATTTTTTTGTTCGGTGTCCTATTTCGGACTTAGGAATTACCGTTCAAACCACACCGTACACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -37.5) TTAGGTGCCATA-ACTCTGATGCTGAAAAGGATAGTCATAC-------agtcAATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAA TTAGGTGCCATACACTCTGATGCTGAAAAGGATAGTCATACTTTTCAT----AATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAA Template switch alignment (log-probability: -26) TTAGGTGCCATA-ACTCTGATGCTGAAAAGGATAGTCATAC|AGTC|AATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAA TTAGGTGCCATACACTCTGATGCTGAAAAGGATAGTCATAC|AGTC|AATTGTGAAGAAAATTAAGGTCCTCGGGTTAAAAAAACAA ========= Event 835 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tttttttGGTCTAAATTGCATATTCGAAATATTAATTATTTAGGAGCTTTGGCAGCCTACAGTTTTCCAACTGAAGCATCATGTTACAAAGGAACTGTAGGTGACTACTTACTCCAGTTCCTCAAATATTGTTGCTTACTATTTTAGCACTTTGTTACATTTT Chimp: tt-ttttGGTCTAAATTGCATATTCGAAATATTAATTATTTAGGAGCTTTGGCAGCCTACAGTTTTCCAACTGAAGCATCATGTTACAAAGGAACTGTAGGTGACTACTTACTCCAGTTCCTCAAATATTGTTACTTACTA-TTTAGCACTTTGTTACAtttt ↓ 3 2 1 4 Gorilla: tt-ttttGGTCTAAATTGCATATTCGAAATATTAATTATTTAGGAGCTTTGGCAGCCTACAGTTTTCCAACTGAAGCATCATGTTACAAATGAACTGTAGGTGACTACTTACTCCAATTCCTCAAATATTGTTACCGAATATTTTAGCACTTTGTTACAtttt Human: tttttttGGTCTAAATTGCATATTCGAAATATTAATTATTTAGGAGCTTTGGCAGCCTACAGTTTTCCAACTGAAGCATCATGTTACAAAGGAACTGTAGGTGACTACTTACTCCAGTTCCTCAAATATTGTTGCTTACTATTTTAGCACTTTGTTACATTTT Cluster: [ ] Orangutan: tt-ttttggtctaaattgcatattcaaaatattaattattTAGGAGCTTTGGCAGCCTACAGTTTTTCAACTGAAGCATCATGTTACAAATGAACTGTAGGTGACTACTTACTCCAGTTCCTCAAATATTTTTACTTAATATTTTAGCACTTTGTTACATTTT Chimp > Gorilla --------------- chr13:87029449-87029455 Template switch process: F1: L CTGTAGGTGACTACTTACTCCAATTCCTCAAATATTGTTAC 1 F3: 4 TTTAGCACTTTGTTACATTTTTTTAATTTCCCTGTTGGAC R RF: ATATTCGAAATATTAATTATTTAGGAGCTTTGGCAGCCTACAGTTTTCCAACTGAAGCATCATGTTACAAAGGAACTGTAGGTGACTACTTACTCCAGTTCCTCAAATATTGTTACTTACTATTTAGCACTTTGTTACATTTTTTTAATTTCCCTGTTGGAC RR: TATAAGCTTTATAATTAATAAATCCTCGAAACCGTCGGATGTCAAAAGGTTGACTTCGTAGTACAATGTTTCCTTGACATCCACTGATGAATGAGGTCAAGGAGTTTATAACAATGAATGATAAATCGTGAAACAATGTAAAAAAATTAAAGGGACAACCTG F2: 3 TATAAGC 2 Unidirectional alignment (log-probability: -34.5) TGTAGGTGACTACTTACTCCAaTTCCTCAAATATTGTTACcgAaTAtTTTAGCACTTTGTTACATTTTTTTAATTTCCCTGTTGGAC TGTAGGTGACTACTTACTCCAGTTCCTCAAATATTGTTACTTACTA-TTTAGCACTTTGTTACATTTTTTTAATTTCCCTGTTGGAC Template switch alignment (log-probability: -22.1) TGTAGGTGACTACTTACTCCAaTTCCTCAAATATTGTTAC|CGAATAT|TTTAGCACTTTGTTACATTTTTTTAATTTCCCTGTTGGAC TGTAGGTGACTACTTACTCCAGTTCCTCAAATATTGTTAC|CGAATAT|TTTAGCACTTTGTTACATTTTTTTAATTTCCCTGTTGGAC ========= Event 836 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCTCTCAGCCTGGCCCAGGTCTCA-----GGGCCTGTTCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCACCCTGGGCAGACTGGGCATGCTGACCTCACTCTGGAGCTCCTCT ↑ 1 4 3 2 Chimp: CCTCTCAGCCTGGCCCAGGTCCTGGAGCCTGGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCACCCTGGGCAGACTGGGCATGCTGACCTCACTCTGGAGCTCCTCT ↓ 1 4 3 2 Gorilla: CCTCTCAGCCTGGCCCAGGTCTCA-----GGGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCATCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCACCCTGGGCAGACTGGGCATGCTGACCTCACTCTGGAGCTCCTCT Human: CCTCTCAGCCTGGCCCAGGTCTCA-----GGGCCTGTTCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCACCCTGGGCAGACTGGGCATGCTGACCTCACTCTGGAGCTCCTCT Cluster: [ ] Orangutan: CCTCTCAGCCTGGCCCAGGTCTCA-----GAGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCGCCCTGGGCAGACTGGGCATGCTGACCTCACTCTGGAGCTCCTCT Chimp > Human ------------- chr13:85601070-85601073 Template switch process: F1: L AGAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTC 1 F3: 4 GGCCTGTTCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTT R RF: AGAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTCCTGGAGCCTGGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCACCCTGGGCAGACTGGGCATGCTGA RR: TCTCCTGGAGAGGGCAGAGGGGAGAGTCGGACCGGGTCCAGGACCTCGGACCGGACAGGACCTCGGCGTAGACCTGAACAAGGGGCAGTCCTGAACAACGGTCCGAGAGTCCGACGACGGGTCGGACAACTTTGGAGACGGGTGGGACCCGTCTGACCCGTACGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -31.9) GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGT--------CTcagGGCCTGTtCTGGAGCCGCATCTGGACTTGTTCCCCGTCAG GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTCCTGGAGCCT---GGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAG Template switch alignment (log-probability: -21.9) GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTC|TCAG|GGCCTGTtCTGGAGCCGCATCTGGACTTGTTCCCCGTCAG GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTC|TCAG|GGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAG Chimp > Gorilla --------------- chr13:86756265-86756268 Template switch process: F1: L AGAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTC 1 F3: 4 GGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCATCAG R RF: AGAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTCCTGGAGCCTGGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAGGACTTGTTGCCAGGCTCTCAGGCTGCTGCCCAGCCTGTTGAAACCTCTGCCCACCCTGGGCAGACTGGGCATGCTGA RR: TCTCCTGGAGAGGGCAGAGGGGAGAGTCGGACCGGGTCCAGGACCTCGGACCGGACAGGACCTCGGCGTAGACCTGAACAAGGGGCAGTCCTGAACAACGGTCCGAGAGTCCGACGACGGGTCGGACAACTTTGGAGACGGGTGGGACCCGTCTGACCCGTACGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -30.9) GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGT--------CTcagGGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCaTCAG GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTCCTGGAGCCT---GGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAG Template switch alignment (log-probability: -21.7) GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTC|TCAG|GGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCaTCAG GAGGACCTCTCCCGTCTCCCCTCTCAGCCTGGCCCAGGTC|TCAG|GGCCTGTCCTGGAGCCGCATCTGGACTTGTTCCCCGTCAG ========= Event 837 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCCTTCTTTAGATTGCCTGAAAGCTGACC------AAGAACGGTTAAGTTAGAGACATCTA Chimp: TCCCTTCTTTAGATTGCCTGAAAGCTGACC------AAGAACGGTTAAGTTAGAGACATCTA ↓ 3 1 2 4 Gorilla: TCCCTTCTTTAGATTGCCTGAAAGCTGGTTAGCTTTCAGAATGGTTAAGTTAGAGACATCTA ↑ 3 1 2 4 Human: TCCCTTCTTTAGATTGCCTGAAAGCTGACC------AAGAACGGTTAAGTTAGAGACATCTA Cluster: [ ] Orangutan: TCTCTTCTTTAGATTGCCTGAAAGCTGACC------AAGAATGGTTAAGTTAGAGACCTCTA Human > Gorilla --------------- chr13:87979258-87979267 Template switch process: F1: L AATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG 1 F3: 4 AGAATGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAAAAGAT R RF: AATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTGACCAAGAACGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAAAAGAT RR: TTAAGTTGTTCTTGAGGGAAGAAATCTAACGGACTTTCGACTGGTTCTTGCCAATTCAATCTCTGTAGATAAGGGGTCTGAGATTTTCTA F2: 3 CTTTCGATTG 2 Unidirectional alignment (log-probability: -40.8) ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG----gttagctttcAGAAtGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTGACCA----------AGAACGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA Template switch alignment (log-probability: -28.2) ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG|GTtAGCTTTC|AGAAtGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG|GTCAGCTTTC|AGAACGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA Chimp > Gorilla --------------- chr13:87979258-87979267 Template switch process: F1: L AATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG 1 F3: 4 AGAATGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAAAAGAT R RF: AATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTGACCAAGAACGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAAAAGAT RR: TTAAGTTGTTCTTGAGGGAAGAAATCTAACGGACTTTCGACTGGTTCTTGCCAATTCAATCTCTGTAGATAAGGGGTCTGAGATTTTCTA F2: 3 CTTTCGATTG 2 Unidirectional alignment (log-probability: -40.8) ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG----gttagctttcAGAAtGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTGACCA----------AGAACGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA Template switch alignment (log-probability: -28.2) ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG|GTtAGCTTTC|AGAAtGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA ATTCAACAAGAACTCCCTTCTTTAGATTGCCTGAAAGCTG|GTCAGCTTTC|AGAACGGTTAAGTTAGAGACATCTATTCCCCAGACTCTAA ========= Event 838 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGCTTCCTCTCTAAGCGCTTGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGG----------GTGTCATAAGATGACACCCTTCTA ↓ 3 2 1 4 Chimp: TGCTCCCTCTCTAAGCGCTTGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGG-----CGCCTCCATCATAAGATGACACCCTTCTA Gorilla: TGCTCCCTCTCTAAGCGCTTGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACATGCAGGCGCCT-----CCATCATAAGATGACACCCTTCTA ↑ 3 2 1 4 Human: TGCTTCCTCTCTAAGCGCTTGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGG----------GTGTCATAAGATGACACCCTTCTA Cluster: [ ] Orangutan: TGCTCCCTCTCTAAGCGCTTGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCC------GGGGCCACAGGCTTTCTCTGCCCAGAGGACGTGCAGGCACCT-----CCATCATAAGATGACACCCTTCTA Human > Chimp ------------- chr1:196487144-196487150 Template switch process: F1: L GGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGC 1 F3: 4 TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG R RF: TGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGGTGTCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG RR: ACCTCCGAAATTACGAATCAGGAGTTGGGGATTGGGAGGGGTGTCACGAAGGAGGTGATCAGGAGAAATGTATCAGGTTTAGGGGGCCCCGGCCCCGGCGTCCGAAAGAGACGGGTCTCCTGCACGTCCCACAGTATTCTACTGTGGGAAGATAAGGATTTGACTAATTCCC F2: 3 ACCTCCG 2 Unidirectional alignment (log-probability: -32.8) CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGcgcctcca---TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGG--------GTGTCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG Template switch alignment (log-probability: -22.2) CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGc|GCCTCCA|TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGG|GCCTCCA|TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG Human > Gorilla --------------- chr1:195976505-195976511 Template switch process: F1: L CCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACATGCAGGC 1 F3: 4 TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG R RF: TGGAGGCTTTAATGCTTAGTCCTCAACCCCTAACCCTCCCCACAGTGCTTCCTCCACTAGTCCTCTTTACATAGTCCAAATCCCCCGGGGCCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGGTGTCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG RR: ACCTCCGAAATTACGAATCAGGAGTTGGGGATTGGGAGGGGTGTCACGAAGGAGGTGATCAGGAGAAATGTATCAGGTTTAGGGGGCCCCGGCCCCGGCGTCCGAAAGAGACGGGTCTCCTGCACGTCCCACAGTATTCTACTGTGGGAAGATAAGGATTTGACTAATTCCC F2: 3 ACCTCCG 2 Unidirectional alignment (log-probability: -37.9) CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACaTGCAG---GcgcctccaTCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGGTG--------TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG Template switch alignment (log-probability: -27.9) CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACaTGCAGGc|GCCTCCA|TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG CCGGGGCCGCAGGCTTTCTCTGCCCAGAGGACGTGCAGGG|GCCTCCA|TCATAAGATGACACCCTTCTATTCCTAAACTGATTAAGGG ========= Event 839 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TGTGCCTCCCCATCACCTTCA-----------TCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCGGGACTTGGGTTTCTGTCCTAATATCCTGCTCATCCGTGTGAATGTCCCAGGGCCCTTCCTTGCCATCCTCAGTGGCCTTCACATGACTGTAGC Chimp: Gorilla: TGTGCCTCCCCATCACCTTCATCTTCACTGCATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCAGGACTTGGGTTTCTGTCCTAATATCCTGCTCATCCGTGTGAATGTCCCAGGGCCCTTCCTTGCCATCCTCAGTGGCCTTCACATGACTGTAGC ↑ 4 1 3 2 Human: TGTGCCTCCCCATCACCTTCA-----------TCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCGGGACTTGGGTTTCTGTCCTAATATCCTGCTCATCCGTGTGAATGTCCCAGGGCCCTTCCTTGCCATCCTCAGTGGCCTTCACATGACTGTAGC Cluster: [ ] Orangutan: TGTGCCTCCCCATCACCTTCATCTTCACTGCATCTTCTGTCTTCCCTGTCATCTCCCTTCATCCATCCGGGACTTGGGTTTCTGTCCTAATGTCCTGCTTATCCGTGTGAATGTCCCAGGGTCCTTCCTTGCCATCCTCAGTGGCCTTCACATGACTGTAGC Human > Gorilla --------------- chr1:33080883-33080886 Template switch process: F1: L GCTGCCTGGCTCTACTCTGCTGTGCCTCCCCATCACCTTCATCTTC 1 F3: 4 CATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCAGGA R RF: GCTGCCTGGCTCTACTCTGCTGTGCCTCCCCATCACCTTCATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCGGGACTTGGGTTTCTGTCCTAATATCCTGCTCATCCGTGTGAATGTCCCAGGGCCCTTCCTTGCCATCCTCAGT RR: CGACGGACCGAGATGAGACGACACGGAGGGGTAGTGGAAGTAGAAGATAGAAGGGACAGTGGAGGGAAGTAGGTAGGCCCTGAACCCAAAGACAGGATTATAGGACGAGTAGGCACACTTACAGGGTCCCGGGAAGGAACGGTAGGAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -32.2) TGGCTCTACTCTGCTGTGCCTCCCCATCACCTTcatcttcactgCATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCaG TGGCTCTACTCTGCTGTGCCTCCCCATCACCTT-----------CATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCGG Template switch alignment (log-probability: -21.9) TGGCTCTACTCTGCTGTGCCTCCCCATCACCTTCATCTTC|ACTG|CATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCaG TGGCTCTACTCTGCTGTGCCTCCCCATCACCTTCATCTTC|ACTG|CATCTTCTATCTTCCCTGTCACCTCCCTTCATCCATCCGG ========= Event 840 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGAGGGGAGATTAATTTCTTACATT--------TATCTTACTCTTCTGCCTTAGCCTGCTCT----------------------------------------------------------------------------------TTGAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATGCTTAAAATAAAAG Chimp: AGGAGAGGAGATAAATTTCTTACATT----TATTTATCTTACTCTTCTGCCTTAGCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGTGTACTTCTCTATTACATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATGCTTAAAATAAAAG ↑ 4 3 1 2 Gorilla: AGGAGGGGAGATTAATTTCTTACATTTATT----TATCTTACTCTTCTGCCTTAGCCTGCTCT----------------------------------------------------------------------------------TTGAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATGCTTAAAATAAAAG Human: AGGAGGGGAGATTAATTTCTTACATT--------TATCTTACTCTTCTGCCTTAGCCTGCTCT----------------------------------------------------------------------------------TTGAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATGCTTAAAATAAAAG Cluster: [ ] Orangutan: AGGAGGGGAGATTAATTTCTTACATTTATT----TATCTTACTCTTCTGCCTTAGCCTGCTCT----------------------------------------------------------------------------------TCAAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATGCTTAAAATAAAAG Gorilla > Chimp --------------- chr13:90468960-90468970 Template switch process: F1: L CATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGT 1 F3: 4 TTACATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATG R RF: CATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGTACTCTCATG RR: GTAAATAAATAGAATGAGAAGACGGAATCGGACGAGAAACTCGGATTTTTGTTAATATTATCTCTTCATGAGAGTAC F2: 3 ATCTCTTCATG 2 Unidirectional alignment (log-probability: -123) gcctgctctttgagcctaaaaacaattataatagagaagtgtacttctctattaCATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCT ------------------------------------------------------CATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCT Template switch alignment (log-probability: -18.6) GCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGT|GTACTTCTCTA|TTACATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCT GCCTGCTCTTTGAGCCTAAAAACAATTATAATAGAGAAGT|GTACTTCTCTA|TTACATTTATTTATCTTACTCTTCTGCCTTAGCCTGCTCT ========= Event 841 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTTTACATATGTATTCTCTC--TCTCTGTcacacacac----------acacacacacacacacacacac--------------------acacacacacaAGAAAGGTTAACAGTTGAGGTTGATTTATTGCCC Chimp: TGTTTACATATGTATTCTCTC--TCTCTGTcacacacac--------------------------------acacacacacaaacacacacacacacacacacGAAAGGTTAACAGTTGAGGTTGATTTATTGCCC ↑ 1 4 3 2 Gorilla: TGTTTACATATGTATTCTCTC----TCTGTcacacacacaca----cac------------------------------------------acacacacacaTGAAAGGTTAACAGCTGAGGTTGATTTATTGCCC ↓ 1 4 3 2 Human: TGTTTACATATGTATTCTCTC--TCTCTGTcacacacac----------acacacacacacacacacacac--------------------acacacacacaAGAAAGGTTAACAGTTGAGGTTGATTTATTGCCC Cluster: [ ] Orangutan: TGTTTACATATGTATTCTCTCTC--TCTGTcacacacacacacacacac------------------------------------------acacacacacacGAAAGGTTAACAGTTGAGGTTGATTTATTGCCC Gorilla > Human --------------- chr1:33414166-33414166 Template switch process: F1: L AAATAAGTGCCCATGCATCATGTTTACATATGTATT 1 F3: 4 TCTCTCTCTGTCACACACACACACACACACACACACACAC R RF: AAATAAGTGCCCATGCATCATGTTTACATATGTATTCTCTCTCTGTCACACACACACACACACACACACACATGAAAGGTTAACAGCTGAGGTTGATTTATTGCCCCAAATAACCTGCCCCAGGATAGATTATTGTAATTAGCCTCACTTATTTTCAGTG RR: TTTATTCACGGGTACGTAGTACAAATGTATACATAAGAGAGAGACAGTGTGTGTGTGTGTGTGTGTGTGTGTACTTTCCAATTGTCGACTCCAACTAAATAACGGGGTTTATTGGACGGGGTCCTATCTAATAACATTAATCGGAGTGAATAAAAGTCAC F2: 3 C 2 Unidirectional alignment (log-probability: -39.1) AAATAAGTGCCCATGCATCATGTTTACATATGTATTCTCTCTCTcTgtcacacacacacacaCACACACACACACAC AAATAAGTGCCCATGCATCATGTTTACATATGTATTCTCTCTCTGT----------------CACACACACACACAC Template switch alignment (log-probability: -26.7) AAATAAGTGCCCATGCATCATGTTTACATATGTATT|C|TCTCTCTCTGTCACACACACACACACACACACACACacac AAATAAGTGCCCATGCATCATGTTTACATATGTATT|C|TCTCTCTCTGTCACACACACACACACACACACACAC---A Gorilla > Chimp --------------- chr1:32749219-32749219 Template switch process: F1: L AAATAAGTGCCCATGCATCATGTTTACATATGTATTCTCTCTCTCTGTCACACACACACACACACACA 1 F3: 4 ACACACAC R RF: AAATAAGTGCCCATGCATCATGTTTACATATGTATTCTCTCTC--TGTCACACACACACACACACACACACACATGAAAGGTTAACAGCTGAGGTTGATTTATTGCCCCAAATAACCTGCCCCAGGATAGATTATTGTAATTAGCCTCACTTATTTTCAGTGT RR: TTTATTCACGGGTACGTAGTACAAATGTATACATAAGAGAGAG--ACAGTGTGTGTGTGTGTGTGTGTGTGTGTACTTTCCAATTGTCGACTCCAACTAAATAACGGGGTTTATTGGACGGGGTCCTATCTAATAACATTAATCGGAGTGAATAAAAGTCACA F2: 3 A 2 Unidirectional alignment (log-probability: -40.4) TATGTATTCTCTCTCTctGTCACACACACACACACacacaaacacacac TATGTATTCTCTCTCT--GTCACACACACACACAC-------------- Template switch alignment (log-probability: -28.3) TATGTATTCTCTCTCtcTGTCACACACACACACACACACA|A|ACACACAC TATGTATTCTCTCTC--TGTCACACACACACACACACACA|A|ACACACAC ========= Event 842 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACGGAATCTGGTCCCATGCAG--CTAAGACTGCCCCTGGCCCTTTCTCA ↓ 13 42 Chimp: ACGGAATCTGGTCCCATGCAGTCTTAGGACTGCCCCTGGCCCTTTCTCA Gorilla: GTGGAATCTGGTCCCATGCAG--CTAAGACTGCCCCTGGCCCTTTCTCA Human: ACGGAATCTGGTCCCATGCAG--CTAAGACTGCCCCTGGCCCTTTCTCA Cluster: [ ] Orangutan: ATGGAATCTGGTCCCATGCAG--CTAAGACTGCCCCTGGCCTTTTCTCA Human > Chimp ------------- chr13:15818279-15818284 Template switch process: F1: L AGAGGAGCTCCTCAAACCCCACGGAATCTGGTCCCATGCAG 1 F3: 4 GACTGCCCCTGGCCCTTTCTCAGGGTCCTGCCCAAAAGCC R RF: AGAGGAGCTCCTCAAACCCCACGGAATCTGGTCCCATGCAGCTAAGACTGCCCCTGGCCCTTTCTCAGGGTCCTGCCCAAAAGCC RR: TCTCCTCGAGGAGTTTGGGGTGCCTTAGACCAGGGTACGTCGATTCTGACGGGGACCGGGAAAGAGTCCCAGGACGGGTTTTCGG F2: 3 GATTCT 2 Unidirectional alignment (log-probability: -25.8) GAGGAGCTCCTCAAACCCCACGGAATCTGGTCCCATGCAGtctTAgGACTGCCCCTGGCCCTTTCTCAGGGTCCTGCCCAAAAGCC GAGGAGCTCCTCAAACCCCACGGAATCTGGTCCCATGCAG--CTAAGACTGCCCCTGGCCCTTTCTCAGGGTCCTGCCCAAAAGCC Template switch alignment (log-probability: -16) GAGGAGCTCCTCAAACCCCACGGAATCTGGTCCCATGCAG|TCTTAG|GACTGCCCCTGGCCCTTTCTCAGGGTCCTGCCCAAAAGCC GAGGAGCTCCTCAAACCCCACGGAATCTGGTCCCATGCAG|TCTTAG|GACTGCCCCTGGCCCTTTCTCAGGGTCCTGCCCAAAAGCC ========= Event 843 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GCAAGCTTGAATACATTTCAGAAGCTCTTCTAACTTAGAGAAGCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATAGA ↑ 4 1 3 2 Chimp: GCAAGCTTGAATACATTTCAGAA-------------------GCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATAGA Gorilla: Human: GCAAGCTTGAATACATTTCAGAAGCTCTTCTAACTTAGAGAAGCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATAGA Cluster: [ ] Orangutan: GCAAGCTTGAATACATTTCAGAAGCCCTTCTAACTTAGAGAAGCTCTCCCACTTCTTAGTAAAAAGTGCCATAGGACAGA Chimp > Human ------------- chr13:31481231-31481236 Template switch process: F1: L TTTTAAGAAGAAATCAAAGCAAGCTTGAATACATTTCAGAAGCTCTTCTA 1 F3: 4 AGAAGCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATAGAGC R RF: TTTTAAGAAGAAATCAAAGCAAGCTTGAATACATTTCAGAAGCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATAGAGC RR: AAAATTCTTCTTTAGTTTCGTTCGAACTTATGTAAAGTCTTCGAGAAGGTGAAGAATCATTTATCACGGTATCCTATCTCG F2: 3 GATTCA 2 Unidirectional alignment (log-probability: -38.2) AAATCAAAGCAAGCTTGAATACATTTCAGAAGCTCTtctaacttagagaagctctTCCACTTCTTAGTAAATAGTGCCATAGGATA AAATCAAAGCAAGCTTGAATACATTTCAGAAGCTCT-------------------TCCACTTCTTAGTAAATAGTGCCATAGGATA Template switch alignment (log-probability: -28.3) AAATCAAAGCAAGCTTGAATACATTTCAGAAGCTCTTCtA|ACTtAG|AGAAGCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATA AAATCAAAGCAAGCTTGAATACATTTCAGAAGCTCTTCCA|ACTAAG|AGAAGCTCTTCCACTTCTTAGTAAATAGTGCCATAGGATA ========= Event 844 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTTTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCATTTAAAC ↓ 1 3 4 2 Chimp: TTTTTAAACCTCAGTCATTATC-AGAATTCTGCATTATCAATGCAGAATTCTCAGTCATTATCATTTAAAC Gorilla: tttttaaacctcagtcattatc-AGAATTCTGCATTATCAATGCAGAATTCTCAGTCATTATCATTTAAAC Human: TTTTTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCATTTAAAC Cluster: [ ] Orangutan: Human > Chimp ------------- chr13:16307354-16307368 Template switch process: F1: L TTCCTGGATTCATGTGGTGTTTTTTAAACCTCAGTCATTATCA 1 F3: 4 AATGCAGAATTCTCAGTCATTATCAT R RF: TTCCTGGATTCATGTGGTGTTTTTTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCAT RR: AAGGACCTAAGTACACCACAAAAAATTTGGAGTCAGTAATAATAGTTAAGACGTAACTATTACGTCTTAAGAGTCAGTAATAGTA F2: 3 CTATTACGTCTTAAG 2 Unidirectional alignment (log-probability: -40.5) CTGGATTCATGTGGTGTTTTTTAAACCTCAGTCATTatcagaattctgcATTATCAAT--------------GCAGAATTCTCAGTCATTATCAT CTGGATTCATGTGGTGTTTTTTAAACCTCAGTCATT-------------ATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCAT Template switch alignment (log-probability: -22.9) CTGGATTCATGTGGTGTTTTTTAAACCTCAGTCATTATcA|GAATTCTGCATTATC|AATGCAGAATTCTCAGTCATTATCAT CTGGATTCATGTGGTGTTTTTTAAACCTCAGTCATTATTA|GAATTCTGCATTATC|AATGCAGAATTCTCAGTCATTATCAT ========= Event 845 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAACATTGATTTTATATAATTTGAGGCATCTGAAATGCATAGACACATCCCACTTAAGGA Chimp: AAAACATTGACTTTATATAATTTCAGGCATCTGAAATGCATAGACACATCCCACTTAAGGA ↑ 3 2 4 1 Gorilla: AAAACATTGATTTTATATAATTTCAGG-----------CATAGACACATCCCACTTAAGGA ↓ 3 2 4 1 Human: AAAACATTGATTTTATATAATTTGAGGCATCTGAAATGCATAGACACATCCCACTTAAGGA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr13:31697149-31697155 Template switch process: F1: L AATACTTGGACAACCTTCAAAACATTGATTTTATATAATTTGAGGCAT 1 F3: 4 GCATAGACACATCCCACTTAAGGATCTATCTACGTTGCACC R RF: AATACTTGGACAACCTTCAAAACATTGATTTTATATAATTTCAGGCATAGACACATCCCACTTAAGGATCTATCTACGTTGCACC RR: TTATGAACCTGTTGGAAGTTTTGTAACTAAAATATATTAAAGTCCGTATCTGTGTAGGGTGAATTCCTAGATAGATGCAACGTGG F2: 3 TAAAGTC 2 Unidirectional alignment (log-probability: -32.3) GACAACCTTCAAAACATTGATTTTATATAATTTgAGgcatctgaaatGCATAGACACATCCCACTTAAGGATCTATCTACGTTGCAC GACAACCTTCAAAACATTGATTTTATATAATTTCAG-----------GCATAGACACATCCCACTTAAGGATCTATCTACGTTGCAC Template switch alignment (log-probability: -22.3) GACAACCTTCAAAACATTGATTTTATATAATTTgAGGCAT|CTGAAAT|GCATAGACACATCCCACTTAAGGATCTATCTACGTTGCAC GACAACCTTCAAAACATTGATTTTATATAATTTCAGGCAT|CTGAAAT|GCATAGACACATCCCACTTAAGGATCTATCTACGTTGCAC Gorilla > Chimp --------------- chr13:16439864-16439870 Template switch process: F1: L CTTGGACAACCTTCAAAACATTGACTTTATATAATTTCAGGCAT 1 F3: 4 GCATAGACACATCCCACTTAAGGATCTATCTACATTGCACC R RF: CTTGGACAACCTTCAAAACATTGATTTTATATAATTTCAGGCATAGACACATCCCACTTAAGGATCTATCTACGTTGCACC RR: GAACCTGTTGGAAGTTTTGTAACTAAAATATATTAAAGTCCGTATCTGTGTAGGGTGAATTCCTAGATAGATGCAACGTGG F2: 3 TAAAGTC 2 Unidirectional alignment (log-probability: -37.7) GACAACCTTCAAAACATTGAcTTTATATAATTTCAGgcatctgaaatGCATAGACACATCCCACTTAAGGATCTATCTACaTTGCAC GACAACCTTCAAAACATTGATTTTATATAATTTCAG-----------GCATAGACACATCCCACTTAAGGATCTATCTACGTTGCAC Template switch alignment (log-probability: -27.8) GACAACCTTCAAAACATTGAcTTTATATAATTTCAGGCAT|CTGAAAT|GCATAGACACATCCCACTTAAGGATCTATCTACaTTGCAC GACAACCTTCAAAACATTGATTTTATATAATTTCAGGCAT|CTGAAAT|GCATAGACACATCCCACTTAAGGATCTATCTACGTTGCAC ========= Event 846 ========= Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCATTTAAAC Chimp: TTAAACCTCAGTCATTATC-AGAATTCTGCATTATCAATGCAGAATTCTCAGTCATTATCATTTAAAC Gorilla: ttaaacctcagtcattatc-AGAATTCTGCATTATCAATGCAGAATTCTCAGTCATTATCATTTAAAC ↑ 1 3 4 2 Human: TTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCATTTAAAC Cluster: [ ] Orangutan: Human > Gorilla --------------- chr13:13202409-13202423 Template switch process: F1: L GGTGTTTTTTAAACCTCAGTCATTATCA 1 F3: 4 AATGCAGAATTCTCAGTCATTATCATTTAAACCAGAAGTA R RF: GGTGTTTTTTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCATTTAAACCAGAAGTA RR: CCACAAAAAATTTGGAGTCAGTAATAATAGTTAAGACGTAACTATTACGTCTTAAGAGTCAGTAATAGTAAATTTGGTCTTCAT F2: 3 CTATTACGTCTTAAG 2 Unidirectional alignment (log-probability: -38.6) GGTGTTTTTTAAACCTCAGTCATTATcA-gAATTCTGCATTatcAATGCAGAATTCTCAGTCATTATCATTTAAACCAGAAGTA GGTGTTTTTTAAACCTCAGTCATTATTATCAATTCTGCATTGATAATGCAGAATTCTCAGTCATTATCATTTAAACCAGAAGTA Template switch alignment (log-probability: -22.8) GGTGTTTTTTAAACCTCAGTCATTATcA|GAATTCTGCATTATC|AATGCAGAATTCTCAGTCATTATCATTTAAACCAGAAGTA GGTGTTTTTTAAACCTCAGTCATTATTA|GAATTCTGCATTATC|AATGCAGAATTCTCAGTCATTATCATTTAAACCAGAAGTA ========= Event 847 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGAGGTTCACAAAACTTCTGGTCCCCTGGACCAAGCCAGATCTGACCTTGGTCT ↑ 3 1 24 Chimp: GTGAGGTTCACAAAACTTCTGGTCC--A----GGAGCCAGATCTGACCTTGGTCT Gorilla: GTGAGGTTCACAAAACTTCTGGTCC--A----GGAGCCAGATCTGACCTTGGTCT ↓ 3 1 24 Human: GTGAGGTTCACAAAACTTCTGGTCCCCTGGACCAAGCCAGATCTGACCTTGGTCT Cluster: [ ] Orangutan: GTGAGGTTCACGAAACTTCTGGTCC--A----GGAGCCAGATCTGACCTTGGTCT Chimp > Human ------------- chr13:82562562-82562570 Template switch process: F1: L ATCTTTAGTCAATAGAGTGAGGTTCACAAAACTTCTGGTCC 1 F3: 4 AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA R RF: ATCTTTAGTCAATCGAGTGAGGTTCACAAAACTTCTGGTCCAGGAGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA RR: TAGAAATCAGTTAGCTCACTCCAAGTGTTTTGAAGACCAGGTCCTCGGTCTAGACTGGAACCAGAATTGAGGTAGGTCAAGAGT F2: 3 ACCAGGTCC 2 Unidirectional alignment (log-probability: -38.7) TCTTTAGTCAATaGAGTGAGGTTCACAAAACTTCTGGTcccctggaCCA--AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA TCTTTAGTCAATCGAGTGAGGTTCACAAAACTTCTGGT--------CCAGGAGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA Template switch alignment (log-probability: -22.4) TCTTTAGTCAATaGAGTGAGGTTCACAAAACTTCTGGTCC|CCTGGACCA|AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA TCTTTAGTCAATCGAGTGAGGTTCACAAAACTTCTGGTCC|CCTGGACCA|AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA Gorilla > Human --------------- chr13:82562562-82562570 Template switch process: F1: L ATCTTTAGTCAATAGAGTGAGGTTCACAAAACTTCTGGTCC 1 F3: 4 AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA R RF: ATCTTTAGTCAGTAGAGTGAGGTTCACAAAACTTCTGGTCCAGGAGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA RR: TAGAAATCAGTCATCTCACTCCAAGTGTTTTGAAGACCAGGTCCTCGGTCTAGACTGGAACCAGAATTGAGGTAGGTCAAGAGT F2: 3 ACCAGGTCC 2 Unidirectional alignment (log-probability: -37.8) TCTTTAGTCAaTAGAGTGAGGTTCACAAAACTTCTGGTcccctggaCCA--AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA TCTTTAGTCAGTAGAGTGAGGTTCACAAAACTTCTGGT--------CCAGGAGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA Template switch alignment (log-probability: -22.4) TCTTTAGTCAaTAGAGTGAGGTTCACAAAACTTCTGGTCC|CCTGGACCA|AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA TCTTTAGTCAGTAGAGTGAGGTTCACAAAACTTCTGGTCC|CCTGGACCA|AGCCAGATCTGACCTTGGTCTTAACTCCATCCAGTTCTCA ========= Event 848 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AAGGCTGAAACTGAAACTCTACAGAAGCGTTCTGTAAACGCTTTCTCCAACCCACCGTTGC ↑ 3 41 2 Chimp: AAGGCTGAAACTGAAACTCTACAG------------AACGCTTTCTCCAACCCACCGTTGC Gorilla: Human: AAGGCTGAAACTGAAACTCTACAGAAGCGTTCTGTAAACGCTTTCTCCAACCCACCGTTGC Cluster: [ ] Orangutan: AAGGCTGAAACTGAAACTCTACAG------------AACGCTTTCTCCAACACACCATTGC Chimp > Human ------------- chr13:80566599-80566608 Template switch process: F1: L GCAAATAGCTGGAAGTAAAGGCTGAAACTGAAACTCTACAGAA 1 F3: 4 AACGCTTTCTCCAACCCACCGTTGCTCCCTTTTTCTTACC R RF: GCAAATAGCTGGAAGTAAAGGCTGAAACTGAAACTCTACAGAACGCTTTCTCCAACCCACCGTTGCTCCCTTTTTCTTACC RR: CGTTTATCGACCTTCATTTCCGACTTTGACTTTGAGATGTCTTGCGAAAGAGGTTGGGTGGCAACGAGGGAAAAAGAATGG F2: 3 ATGTCTTGCG 2 Unidirectional alignment (log-probability: -28.2) AATAGCTGGAAGTAAAGGCTGAAACTGAAACTCTACAGaagcgttctgtaAACGCTTTCTCCAACCCACCGTTGCTCCCTTTTTCTTACC AATAGCTGGAAGTAAAGGCTGAAACTGAAACTCTACAG------------AACGCTTTCTCCAACCCACCGTTGCTCCCTTTTTCTTACC Template switch alignment (log-probability: -16.6) AATAGCTGGAAGTAAAGGCTGAAACTGAAACTCTACAGAA|GCGTTCTGTA|AACGCTTTCTCCAACCCACCGTTGCTCCCTTTTTCTTACC AATAGCTGGAAGTAAAGGCTGAAACTGAAACTCTACAGAA|GCGTTCTGTA|AACGCTTTCTCCAACCCACCGTTGCTCCCTTTTTCTTACC ========= Event 849 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAAAAGAAACCAAAACCTACTTCTAAAAGTAGAAGTAGGGCCTCTAAGGCCCTATTTCCTGCCTTCCAG ↓ 1 3 24 Chimp: aaaaaGAAACCAAAACCTACTCTTA---------------------GAGCCCTATTTCCTGCCTTCCAG Gorilla: aaaaaGAAACCAAAACCTACTCTTA---------------------GAGCCCTATTTCCTGCCTTCCAG ↑ 1 3 24 Human: AAAAAGAAACCAAAACCTACTTCTAAAAGTAGAAGTAGGGCCTCTAAGGCCCTATTTCCTGCCTTCCAG Cluster: [ ] Orangutan: AAAAAGAAACCAAAACCTACTCTTA---------------------GAGCCCTATTTCCTGCCTTCCAG Human > Chimp ------------- chr13:82868822-82868827 Template switch process: F1: L TTTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACT 1 F3: 4 GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA R RF: TTTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACTTCTAAAAGTAGAAGTAGGGCCTCTAAGGCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA RR: AAAAAATTTATGGAGAAATTTTTTTCTTTGGTTTTGGATGAAGATTTTCATCTTCATCCCGGAGATTCCGGGATAAAGGACGGAAGGTCCAACCGAGTTAATAACACT F2: 3 AGATTC 2 Unidirectional alignment (log-probability: -29.7) TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTA----------------------CTCTtAGaGCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACTTCTAAAAGTAGAAGTAGGGCCTCTAAG-GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA Template switch alignment (log-probability: -16) TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACT|CTTAGA|GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACT|CTTAGA|GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA Human > Gorilla --------------- chr13:82639774-82639779 Template switch process: F1: L GTTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACT 1 F3: 4 GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA R RF: TTTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACTTCTAAAAGTAGAAGTAGGGCCTCTAAGGCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA RR: AAAAAATTTATGGAGAAATTTTTTTCTTTGGTTTTGGATGAAGATTTTCATCTTCATCCCGGAGATTCCGGGATAAAGGACGGAAGGTCCAACCGAGTTAATAACACT F2: 3 AGATTC 2 Unidirectional alignment (log-probability: -34.1) TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACTctTAgA---------------------GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACTTCTAAAAGTAGAAGTAGGGCCTCTAAGGCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA Template switch alignment (log-probability: -22) TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACT|CTTAGA|GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA TTTTTAAATACCTCTTTAAAAAAAGAAACCAAAACCTACT|CTTAGA|GCCCTATTTCCTGCCTTCCAGGTTGGCTCAATTATTGTGA ========= Event 850 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGTTCTAGTGGGATCAGGAACA----------------ATAATAATACAGAACAATAATAAAaataactgcagttactacttattgagcatcttatatatttttggcattgttacagatgcatatattgcccctaataatcacaacagccctacaggcaggaattacactcatggtatagctgtagatatggaaagctcagagtc Chimp: AAGTTCTAGTGGGATCAGGAACA----------------ATAATAATACAGAACAATAATAAAaataactgcagttactacttattgagcatcttatatatttttggcattgttacagatgcatatattgcccctaataatcacaacagccctacaggcaggaattacactcatggtatagctgtagatatggaaagctcagagtc ↑ 4 1 3 2 Gorilla: AAGTTCTAGTGGGATCAGGAACA--------------------------------ATAATAAAaataatcgcagttactacttattgagcatcttatatatttttggcattgttacagatgcatacattgcccctaataatcacaacagccctacaggcaggaattacactcatggtatagctgtagatatggaaagctcagagtc ↓ 4 1 3 2 Human: AAGTTCTAGTGGGATCAGGAACA----------------ATAATAATACAGAACAATAATAAAaataactgcagttactacttattgagcatcttatatatttttggcattgttacagatgcatatattgcccctaataatcacaacagccctacaggcaggaattacactcatggtatagctgtagatatggaaagctcagagtc Cluster: [ ] Orangutan: AAGTTCTAGTGGGATCAGGAACAATAATAATACAGAACA----------------ATAATAAAaataactgcagttactacttattgagcgtcttatatatttttggcattgttacagatgcatatattgcccctaacaatcataacagccctacaggcaggaattacactcattgtatagctgcagatatggaaagcttagagtc Gorilla > Human --------------- chr13:80486172-80486176 Template switch process: F1: L ACGTCCCTTGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAA 1 F3: 4 AACAATAATAAAAATAACTGCAGTTACTACTTATTGAGCATCTT R RF: ACGTCCCTTGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAAAAATAATCGCAGTTACTACTTATTGAGCATCTTATATATTTTTGGCATTGTTACAGATGCATACATTGCCCCTAATAATCACAACAGCCCTACAGGCAGGAATTACACTCATGGTATAGCTGTA RR: TGCAGGGAACTATAGTTTTTCAAGATCACCCTAGTCCTTGTTATTATTTTTATTAGCGTCAATGATGAATAACTCGTAGAATATATAAAAACCGTAACAATGTCTACGTATGTAACGGGGATTATTAGTGTTGTCGGGATGTCCGTCCTTAATGTGAGTACCATATCGACAT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -44.9) TGATATCAAAAAGTTCTAGTGGGATCAGGAAcaataataatacagaaCAATAATAAAAATAActGCAGTTACTACTTATTGAGCA TGATATCAAAAAGTTCTAGTGGGATCAGGAA----------------CAATAATAAAAATAATCGCAGTTACTACTTATTGAGCA Template switch alignment (log-probability: -27.7) TGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAA|TACAG|AACAATAATAAAAATAActGCAGTTACTACTTATTGAGCA TGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAA|TACAG|AACAATAATAAAAATAATCGCAGTTACTACTTATTGAGCA Gorilla > Chimp --------------- chr13:81820458-81820462 Template switch process: F1: L ACGTCCCTTGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAA 1 F3: 4 AACAATAATAAAAATAACTGCAGTTACTACTTATTGAGCATCTT R RF: ACGTCCCTTGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAAAAATAATCGCAGTTACTACTTATTGAGCATCTTATATATTTTTGGCATTGTTACAGATGCATACATTGCCCCTAATAATCACAACAGCCCTACAGGCAGGAATTACACTCATGGTATAGCTGTA RR: TGCAGGGAACTATAGTTTTTCAAGATCACCCTAGTCCTTGTTATTATTTTTATTAGCGTCAATGATGAATAACTCGTAGAATATATAAAAACCGTAACAATGTCTACGTATGTAACGGGGATTATTAGTGTTGTCGGGATGTCCGTCCTTAATGTGAGTACCATATCGACAT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -44.9) TGATATCAAAAAGTTCTAGTGGGATCAGGAAcaataataatacagaaCAATAATAAAAATAActGCAGTTACTACTTATTGAGCA TGATATCAAAAAGTTCTAGTGGGATCAGGAA----------------CAATAATAAAAATAATCGCAGTTACTACTTATTGAGCA Template switch alignment (log-probability: -27.7) TGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAA|TACAG|AACAATAATAAAAATAActGCAGTTACTACTTATTGAGCA TGATATCAAAAAGTTCTAGTGGGATCAGGAACAATAATAA|TACAG|AACAATAATAAAAATAATCGCAGTTACTACTTATTGAGCA ========= Event 851 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTCTTTAAAGGGTGAGGTCTCTT-----TATTGATAATCAACATTTTACAAAATAAAATGAACATATTTTTC Chimp: TCTCTTTAAAGGGTGAGGTCTCTT-----TATTGATAATCAACATTTTACAAAATAAAATGAACATATTTTTC ↓ 1 4 3 2 Gorilla: TCTCTTTAAAGGGTGAGGTCTTTTGTAAAACGTGATAATCAACGTTTTACAAAATAAAATGAACATATTTTTC ↑ 1 4 3 2 Human: TCTCTTTAAAGGGTGAGGTCTCTT-----TATTGATAATCAACATTTTACAAAATAAAATGAACATATTTTTC Cluster: [ ] Orangutan: TCTCTTTAAAGGGTGAGGTCTCTT-----TATTGATAATCAACATTTTACAAAATAAAATGAACATATTTTTC Human > Gorilla --------------- chr13:81625401-81625411 Template switch process: F1: L CATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT 1 F3: 4 TGATAATCAACGTTTTACAAAATAAAATGAACATATTTTT R RF: CATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCTCTTTATTGATAATCAACATTTTACAAAATAAAATGAACATATTTTT RR: GTACGAAATAAACTTAAAATAGAGAAATTTCCCACTCCAGAGAAATAACTATTAGTTGTAAAATGTTTTATTTTACTTGTATAAAAA F2: 3 GCAAAATGTTT 2 Unidirectional alignment (log-probability: -40.4) ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT-TTTgTaaaacgTGATAATCAACgTTTTACAAAATAAAATGAACATATTTTT ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCTCTTTAT------TGATAATCAACATTTTACAAAATAAAATGAACATATTTTT Template switch alignment (log-probability: -28.2) ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT|TTTGTAAAAcG|TGATAATCAACgTTTTACAAAATAAAATGAACATATTTTT ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT|TTTGTAAAATG|TGATAATCAACATTTTACAAAATAAAATGAACATATTTTT Chimp > Gorilla --------------- chr13:81625401-81625411 Template switch process: F1: L CATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT 1 F3: 4 TGATAATCAACGTTTTACAAAATAAAATGAACATATTTTT R RF: CATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCTCTTTATTGATAATCAACATTTTACAAAATAAAATGAACATATTTTT RR: GTACGAAATAAACTTAAAATAGAGAAATTTCCCACTCCAGAGAAATAACTATTAGTTGTAAAATGTTTTATTTTACTTGTATAAAAA F2: 3 GCAAAATGTTT 2 Unidirectional alignment (log-probability: -40.4) ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT-TTTgTaaaacgTGATAATCAACgTTTTACAAAATAAAATGAACATATTTTT ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCTCTTTAT------TGATAATCAACATTTTACAAAATAAAATGAACATATTTTT Template switch alignment (log-probability: -28.2) ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT|TTTGTAAAAcG|TGATAATCAACgTTTTACAAAATAAAATGAACATATTTTT ATGCTTTATTTGAATTTTATCTCTTTAAAGGGTGAGGTCT|TTTGTAAAATG|TGATAATCAACATTTTACAAAATAAAATGAACATATTTTT ========= Event 852 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tGTGTTTCTGGTCTTCTCAGAGTACGGCTT-TAAGAATCAATCTGggctggacgtggtggc ↓ 1 4 3 2 Chimp: TGTGTTTCTGGTCTTCTCAGATTGATT-CT-TAAGAATCAATCTGggctggacgtggtggc ↑ 1 4 3 2 Gorilla: TGTGTTTCTGGTCTTCTCAGAGTACGGCTT-TAAGAATCAATCTGggctggacgtggtggc Human: tGTGTTTCTGGTCTTCTCAGAGTACGGCTT-TAAGAATCAATCTGggctggacgtggtggc Cluster: [ ] Orangutan: TGTGTTTCTGGTCTTCTCAGAGTACGGCTTTAAAGAATCAATCTGggctggacgtggtggc Human > Chimp ------------- chr13:83460563-83460569 Template switch process: F1: L TTATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA 1 F3: 4 TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG R RF: TTATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGAGTACGGCTTTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG RR: AATAAAAGTAATTTTATTTAACACAAAGACCAGAAGAGTCTCATGCCGAAATTCTTAGTTAGACCCGACCTGCACCACCGAGTACGGAC F2: 3 CTTAGTT 2 Unidirectional alignment (log-probability: -30.1) TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA-------TtgattcTTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGAGTACGGCT------TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG Template switch alignment (log-probability: -16.2) TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA|TTGATTC|TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA|TTGATTC|TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG Gorilla > Chimp --------------- chr13:83460563-83460569 Template switch process: F1: L TTATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA 1 F3: 4 TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG R RF: TTATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGAGTACGGCTTTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG RR: AATAAAAGTAATTTTATTTAACACAAAGACCAGAAGAGTCTCATGCCGAAATTCTTAGTTAGACCCGACCTGCACCACCGAGTACGGAC F2: 3 CTTAGTT 2 Unidirectional alignment (log-probability: -29.6) TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA-------TtgattcTTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGAGTACGGCT------TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG Template switch alignment (log-probability: -16.6) TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA|TTGATTC|TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG TATTTTCATTAAAATAAATTGTGTTTCTGGTCTTCTCAGA|TTGATTC|TTAAGAATCAATCTGGGCTGGACGTGGTGGCTCATGCCTG ========= Event 853 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGTGCCTAGAGGTTACATATGTTACTTTCTTCTCA---------------GAAAGTAACATTCTggcccagagtggtggctc Chimp: TGGTGCCTAGAGGCTACATATGTTACTTTCTTCTCA---------------GAAAGTAACACTCTggcccagagtggtggctc ↓ 3 12 4 Gorilla: TGGTGCCTAGAGGCTACATATGTTACTTTCTTCTGAGAAACTTTCTGAGAAGAAAGTAACATTCTggcccagagtggtggctc ↑ 3 4 12 Human: TGGTGCCTAGAGGTTACATATGTTACTTTCTTCTCA---------------GAAAGTAACATTCTggcccagagtggtggctc Cluster: [ ] Orangutan: TGGTGCCTAGAGGCTACGTATGTTACTTTCTTCTCA---------------GAAAGTAACATTCTggcccggagtggtggctc Human > Gorilla --------------- chr13:83305227-83305236 Template switch process: F1: L AGAAGCCTGGTGCCTAGAGGCTACATATGTTACTTTCTTCTGAGAAA 1 F3: 4 AGAAAGTAACATTCTGGCCCAGAGTGGTGGCTCACACCTGT R RF: AGAAGCCTGGTGCCTAGAGGTTACATATGTTACTTTCTTCTCAGAAAGTAACATTCTGGCCCAGAGTGGTGGCTCACACCTGT RR: TCTTCGGACCACGGATCTCCAATGTATACAATGAAAGAAGAGTCTTTCATTGTAAGACCGGGTCTCACCACCGAGTGTGGACA F2: 3 AGAGTCTTTC 2 Unidirectional alignment (log-probability: -43.5) TGGTGCCTAGAGGcTACATATGTTACTTTCTTCTgagaaactttctgagaAGAAAGTAACATTCTGGCCCAGAGTGGTGGCTCACACCTG TGGTGCCTAGAGGTTACATATGTTACTTTCTTCT---------------CAGAAAGTAACATTCTGGCCCAGAGTGGTGGCTCACACCTG Template switch alignment (log-probability: -28.2) TGGTGCCTAGAGGcTACATATGTTACTTTCTTCTgAGAAA|CTTTCTGAGA|AGAAAGTAACATTCTGGCCCAGAGTGGTGGCTCACACCTG TGGTGCCTAGAGGTTACATATGTTACTTTCTTCTCAGAAA|CTTTCTGAGA|AGAAAGTAACATTCTGGCCCAGAGTGGTGGCTCACACCTG Chimp > Gorilla --------------- chr13:83305227-83305248 Template switch process: F1: L AGAAGCCTGGTGCCTAGAGGCTACATATGTTACTTTCTTCTGAGAAA 1 F3: 4 TCTGGCCCAGAGTGGTGGCTCACACCTGT R RF: AGAAGCCTGGTGCCTAGAGGCTACATATGTTACTTTCTTCTCAGAAAGTAACACTCTGGCCCAGAGTGGTGGCTCACACCTGT RR: TCTTCGGACCACGGATCTCCGATGTATACAATGAAAGAAGAGTCTTTCATTGTGAGACCGGGTCTCACCACCGAGTGTGGACA F2: 3 TACAATGAAAGAAGAGTCTTTC 2 Unidirectional alignment (log-probability: -43.5) TGGTGCCTAGAGGCTACATATGTTACTTTCTTCTgagaaactttctgagaAGAAAGTAACAtTCTGGCCCAGAGTGGTGGCTCACACCTGT TGGTGCCTAGAGGCTACATATGTTACTTTCTTCT---------------CAGAAAGTAACACTCTGGCCCAGAGTGGTGGCTCACACCTGT Template switch alignment (log-probability: -23.9) TGGTGCCTAGAGGCTACATATGTTACTTTCTTCTgAGAAA|CTTTCTGAGAAGAAAGTAACAT|TCTGGCCCAGAGTGGTGGCTCACACCTGT TGGTGCCTAGAGGCTACATATGTTACTTTCTTCTCAGAAA|CTTTCTGAGAAGAAAGTAACAT|TCTGGCCCAGAGTGGTGGCTCACACCTGT ========= Event 854 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAACAAAGCATTAGGTTAACTTCTGTACATGGAA-------TGAACCCTTAGTACACCTTCTTAAA ↓ 3 2 1 4 Chimp: AAAACAAAGCATTAGGTTAACTTCTGTACATGGAAGTACAGAAGTAACCTTAGTACACCTTCTTAAA Gorilla: AAAACAAAGCTCTAGGTTAACTTCTGTACATGGAA-------TGAACTCTTAGTACACCTTCTTAAA Human: AAAACAAAGCATTAGGTTAACTTCTGTACATGGAA-------TGAACCCTTAGTACACCTTCTTAAA Cluster: [ ] Orangutan: AAAACAAAGTTCTAGGTTAACTTCTGTACATGGAA-------TGAACCCTTAGTACACATTCTTAAA Human > Chimp ------------- chr13:19628287-19628296 Template switch process: F1: L CTTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA 1 F3: 4 AACCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGTAT R RF: CTTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAATGAACCCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGTAT RR: GAATAGTTTTGTTTCGTAATCCAATTGAAGACATGTACCTTACTTGGGAATCATGTGGAAGAATTTGGAAGAGTAAATCTAACATA F2: 3 TGAAGACATG 2 Unidirectional alignment (log-probability: -38.6) TTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA-----gtacagaagtaaCCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGT TTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAATGAAC------------CCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGT Template switch alignment (log-probability: -22.6) TTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA|GTACAGAAGT|AaCCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGT TTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA|GTACAGAAGT|ACCCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGT ========= Event 855 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTCCTTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA-------TGAACCCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGTA Chimp: ATTTCCTTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAAGTACAGAAGTAACCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGTA ↑ 3 2 1 4 Gorilla: ATTTCCTTATCAAAACAAAGCTCTAGGTTAACTTCTGTACATGGAA-------TGAACTCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGTA Human: ATTTCCTTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA-------TGAACCCTTAGTACACCTTCTTAAACCTTCTCATTTAGATTGTA Cluster: [] Orangutan: ATTTCCTTATCAAAACAAAGTTCTAGGTTAACTTCTGTACATGGAA-------TGAACCCTTAGTACACATTCTTAAACCTTCTCATTTAGATTGTA Gorilla > Chimp --------------- chr13:19628287-19628296 Template switch process: F1: L AAGCATAATATTAGAGTTTCATTTCCTTATCAAAACAAAGCATTAGGTTAACTTCTGTACATGGAA 1 F3: 4 AACCTTA R RF: AAGCATAATATTAGAGTTTCATTTCCTTATCAAAACAAAGCTCTAGGTTAACTTCTGTACATGGAATGAACTCTTAGTACACCTTCTTAAACCTTC RR: TTCGTATTATAATCTCAAAGTAAAGGAATAGTTTTGTTTCGAGATCCAATTGAAGACATGTACCTTACTTGAGAATCATGTGGAAGAATTTGGAAG F2: 3 TGAAGACATG 2 Unidirectional alignment (log-probability: -50.5) TTATCAAAACAAAGCatTAGGTTAACTTCTGTACATGGAAgtacagaagtaac------CTTA TTATCAAAACAAAGCTCTAGGTTAACTTCTGTACATGGAA-------------TGAACTCTTA Template switch alignment (log-probability: -33.3) TTATCAAAACAAAGCatTAGGTTAACTTCTGTACATGGAA|GTACAGAAGT|AACCTTa TTATCAAAACAAAGCTCTAGGTTAACTTCTGTACATGGAA|GTACAGAAGT|AACCTTC ========= Event 856 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTAAAAACTTCTGTAAA-TTCTGAAACAGCGGGTCTGTGTTTCAGAATTTTGTGTTTGCCTCATGTTT ↑ 3 2 1 4 Chimp: GTTAAAAACTTCTGTAAA-TTCTGAAACAGCGCGTCTG-----TAACCTTTTGTGTTTGCCTCATGTTT Gorilla: GTTAAAAACTTCTGTAAA-TTCTGAAACAGTGGGTCTG-----TAACCTTTTGTGTTTGCCTCATGTTT ↓ 3 2 1 4 Human: GTTAAAAACTTCTGTAAA-TTCTGAAACAGCGGGTCTGTGTTTCAGAATTTTGTGTTTGCCTCATGTTT Cluster: [ ] Orangutan: GTTAAAAACTTCTATAAATTTCTGAAACAGCGGATCTG-----TAAGCTTTTGTGTTTGCCTCATGTAT Chimp > Human ------------- chr13:79520038-79520046 Template switch process: F1: L GTCCTTCAGTGTTAAAAACTTCTGTAAATTCTGAAACAGCGGGTCTGT 1 F3: 4 TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA R RF: GTCCTTCAGTGTTAAAAACTTCTGTAAATTCTGAAACAGCGCGTCTGTAACCTTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA RR: CAGGAAGTCACAATTTTTGAAGACATTTAAGACTTTGTCGCGCAGACATTGGAAAACACAAACGGAGTACAAAAACCAATGACTTGAAAAAT F2: 3 AAGACTTTG 2 Unidirectional alignment (log-probability: -37.4) GTGTTAAAAACTTCTGTAAATTCTGAAACAGCGgGTCTGTgtttcagAA--TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA GTGTTAAAAACTTCTGTAAATTCTGAAACAGCGCGTCTGT-------AACCTTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA Template switch alignment (log-probability: -22.5) GTGTTAAAAACTTCTGTAAATTCTGAAACAGCGgGTCTGT|GTTTCAGAA|TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA GTGTTAAAAACTTCTGTAAATTCTGAAACAGCGCGTCTGT|GTTTCAGAA|TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA Gorilla > Human --------------- chr13:79520038-79520046 Template switch process: F1: L GAGTCCTTCAGTGTTAAAAACTTCTGTAAATTCTGAAACAGCGGGTCTGT 1 F3: 4 TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA R RF: GAGTCCTTCAGTGTTAAAAACTTCTGTAAATTCTGAAACAGTGGGTCTGTAACCTTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA RR: CTCAGGAAGTCACAATTTTTGAAGACATTTAAGACTTTGTCACCCAGACATTGGAAAACACAAACGGAGTACAAAAACCAATGACTTGAAAAAT F2: 3 AAGACTTTG 2 Unidirectional alignment (log-probability: -36.5) GTGTTAAAAACTTCTGTAAATTCTGAAACAGcGGGTCTGTgtttcagAA--TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA GTGTTAAAAACTTCTGTAAATTCTGAAACAGTGGGTCTGT-------AACCTTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA Template switch alignment (log-probability: -22.6) GTGTTAAAAACTTCTGTAAATTCTGAAACAGcGGGTCTGT|GTTTCAGAA|TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA GTGTTAAAAACTTCTGTAAATTCTGAAACAGTGGGTCTGT|GTTTCAGAA|TTTTGTGTTTGCCTCATGTTTTTGGTTACTGAACTTTTTA ========= Event 857 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACACTATCTGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTCCCCAAGCTGT Chimp: ACACT--ATGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTCCCCAAGCTGT ↑ 3 1 2 4 Gorilla: ACACTATCTGCCTTAGGATGTGCTGGGCAATAGGCCCAGCATGCTGGCATGTCCCCAAGCTGT ↓ 3 1 2 4 Human: ACACTATCTGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTCCCCAAGCTGT Cluster: [ ] Orangutan: ACACTATCTGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTCCCCAATCTGT Gorilla > Human --------------- chr1:33973204-33973217 Template switch process: F1: L TCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGC 1 F3: 4 GCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA R RF: TCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCAATAGGCCCAGCATGCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA RR: AGGAGGGGACGGGTGTGATAGACGGAATCCTACACGACCCGTTATCCGGGTCGTACGACCGTACAGGGGTTCGACACAACTGTCGTCCTTCTTGT F2: 3 CACGACCCGTTATC 2 Unidirectional alignment (log-probability: -33.7) CCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGC-----ctattGCCCAGCAcGCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA CCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCAATAG-----GCCCAGCATGCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA Template switch alignment (log-probability: -17.5) CCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGC|CTATTGCCCAGCAC|GCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA CCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGC|CTATTGCCCAGCAC|GCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA Gorilla > Chimp --------------- chr1:33307934-33307947 Template switch process: F1: L TCCTCCCCTGCCCACACTA--TGCCTTAGGATGTGCTGGGC 1 F3: 4 GCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA R RF: TCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCAATAGGCCCAGCATGCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA RR: AGGAGGGGACGGGTGTGATAGACGGAATCCTACACGACCCGTTATCCGGGTCGTACGACCGTACAGGGGTTCGACACAACTGTCGTCCTTCTTGT F2: 3 CACGACCCGTTATC 2 Unidirectional alignment (log-probability: -43.5) TCCTCCCCTGCCCACACTA--TGCCTTAGGATGTGCTGGGC-----ctattGCCCAGCAcGCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA TCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCAATAG-----GCCCAGCATGCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA Template switch alignment (log-probability: -27.3) TCCTCCCCTGCCCACACTA--TGCCTTAGGATGTGCTGGGC|CTATTGCCCAGCAC|GCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA TCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGC|CTATTGCCCAGCAC|GCTGGCATGTCCCCAAGCTGTGTTGACAGCAGGAAGAACA ========= Event 858 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGATCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTC Chimp: GGATCCTCCCCTGCCCACACT--ATGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTC ↓ 4 1 2 Gorilla: GGATCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCAATAGGCCCAGCATGCTGGCATGTC Human: GGATCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTC Cluster: [ ] Orangutan: GGATCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGCATGTC Chimp > Gorilla --------------- chr1:34247788-34247792 Template switch process: F1: L GCCAGAATCCAGCCCTGCTAGGATCCTCCCCTGCCCACACTATCTGCCTTAGGATGTGCTGGGC 1 F3: 4 GCCCAGCATGCTGGC R RF: GCCAGAATCCAGCCCTGCTAGGATCCTCCCCTGCCCACACTA--TGCCTTAGGATGTGCTGGGCCTATTGCCCAGCACGCTGGC RR: CGGTCTTAGGTCGGGACGATCCTAGGAGGGGACGGGTGTGAT--ACGGAATCCTACACGACCCGGATAACGGGTCGTGCGACCG F2: 3 GATAA 2 Unidirectional alignment (log-probability: -46.1) CCTCCCCTGCCCACACTAtcTGCCTTAGGATGTGCTGGGCaatag-----GCCCAGCAtGCTGGC CCTCCCCTGCCCACACTA--TGCCTTAGGATGTGCTGGGC-----CTATTGCCCAGCACGCTGGC Template switch alignment (log-probability: -34.4) CCTCCCCTGCCCACACTAtcTGCCTTAGGATGTGCTGGGC|AATAG|GCCCAGCAtGCTGGC CCTCCCCTGCCCACACTA--TGCCTTAGGATGTGCTGGGC|AATAG|GCCCAGCACGCTGGC ========= Event 859 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCAGCTGCTCCCAGAAGAAC-----GGG---CGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGCCCA Chimp: CCCAGCTGCTCCCAGAAGAAC-----GGG---CGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGCCCA ↓ 1 4 3 2 Gorilla: CCCAGCTGCTCCCAGAAGAACATAGGTGGCATAGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGCCCA ↑ 1 4 3 2 Human: CCCAGCTGCTCCCAGAAGAAC-----GGG---CGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGCCCA Cluster: [ ] Orangutan: CCCAGCTGCTCCCAGAAGAAC-----GGG---CGGGTTGGTCCCTATGCCACCCGTGGAGAGCTACTGGCCGCCCA Human > Gorilla --------------- chr13:78527477-78527488 Template switch process: F1: L ACTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC 1 F3: 4 GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC R RF: ACTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAACGGGCGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC RR: TGAAGCGTTGAACTTAACCAGGGTCGACGAGGGTCTTCTTGCCCGCCCAACCAGGGATACGGTGGGGACCTCTCGATGAGCGGCG F2: 3 ATACGGTGGATA 2 Unidirectional alignment (log-probability: -37.7) CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAACataggtGGCataGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC-----GGGC---GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC Template switch alignment (log-probability: -28.3) CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC|AtaGGTGGCATA|GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC|AGGGGTGGCATA|GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC Chimp > Gorilla --------------- chr13:78527477-78527488 Template switch process: F1: L ACTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC 1 F3: 4 GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC R RF: ACTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAACGGGCGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC RR: TGAAGCGTTGAACTTAACCAGGGTCGACGAGGGTCTTCTTGCCCGCCCAACCAGGGATACGGTGGGGACCTCTCGATGAGCGGCG F2: 3 ATACGGTGGATA 2 Unidirectional alignment (log-probability: -37.7) CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAACataggtGGCataGGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC-----GGGC---GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC Template switch alignment (log-probability: -28.3) CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC|AtaGGTGGCATA|GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC CTTCGCAACTTGAATTGGTCCCAGCTGCTCCCAGAAGAAC|AGGGGTGGCATA|GGGTTGGTCCCTATGCCACCCCTGGAGAGCTACTCGCCGC ========= Event 860 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTTTCTTTAATAAAAGTGT--GTGTGTATGTacatacacaca-------------- Chimp: GTTTTTCTTTAATAAAAGTGT--GTGTGTATGTacatacacaca-------------- ↓ 3 1 24 Gorilla: GTTTTTCTTTAATAAAAGTGT----GTGTATGTacatacacaca--------cacaca ↑ 3 1 24 Human: GTTTTTCTTTAATAAAAGTGT--GTGTGTATGTacatacacaca-------------- Cluster: [ ] Orangutan: --TTTTCTCTAATAAAAGTGTGT--GTGTATGTacatacacacacatacaca------ Human > Gorilla --------------- chr13:77990470-77990483 Template switch process: F1: L ATATTCACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGT 1 F3: 4 ACACACACACACACATATATAC R RF: ATATTCACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGTGTATGTACATACACACACACACACATATATAC RR: TATAAGTGGTTCACTAAAAACAAAAAGAAATTATTTTCACACACACATACATGTATGTGTGTGTGTGTGTATATATG F2: 3 CACACATACATGTA 2 Unidirectional alignment (log-probability: -29.3) CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGT--GTATGTACATacacacACACACACACACACATATATAC CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGTGTATGTACAT------ACACACACACACACATATATAC Template switch alignment (log-probability: -17.2) CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGT|ATGTACATACACAC|ACACACACACACACATATATAC CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGT|ATGTACATACACAC|ACACACACACACACATATATAC Chimp > Gorilla --------------- chr13:77990470-77990483 Template switch process: F1: L ATATTCACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGT 1 F3: 4 ACACACACACACACATATATAC R RF: ATATTCACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGTGTATGTACATACACACACACACACGTATACAC RR: TATAAGTGGTTCACTAAAAACAAAAAGAAATTATTTTCACACACACATACATGTATGTGTGTGTGTGTGCATATGTG F2: 3 CACACATACATGTA 2 Unidirectional alignment (log-probability: -40.3) CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGT--GTATGTACATacacacACACACACACACACaTATAtAC CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGTGTATGTACAT------ACACACACACACACGTATACAC Template switch alignment (log-probability: -28.2) CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGT|ATGTACATACACAC|ACACACACACACACaTATAtAC CACCAAGTGATTTTTGTTTTTCTTTAATAAAAGTGTGTGT|ATGTACATACACAC|ACACACACACACACGTATACAC ========= Event 861 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTACTCGACAGGATTTTGATTAGCCAT ↓ 3 2 1 4 Chimp: ATATTTTAAGAATATACGTGACGGTAAACGCAGATT--AC---------------------CGTCGACAGGATTTTGATTAGCCAT ↑ 3 2 1 4 Gorilla: ATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTACTTGACAGGATTTTGATTAGCCAT Human: ATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTACTCGACAGGATTTTGATTAGCCAT Cluster: [ ] Orangutan: ATATTTTAAGAATATACATGATGGTAAACGCAGACTCTCTCCACATTTTAGACTGGATATTACTCGACAGGATTTTGATTAGCCAT Human > Chimp ------------- chr13:80255398-80255403 Template switch process: F1: L ATAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGA 1 F3: 4 TCGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAA R RF: ATAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTACTCGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAA RR: TATTTGGTATAAAATTCTTATATGCACTGCCATTTGCGTCTGAGAGAGGTGTAAAATCTGCCCTATAATGAGCTGTCCTAAAACTAATCGGTACTTCAATTCTAAAAATT F2: 3 GCCATT 2 Unidirectional alignment (log-probability: -25.3) TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAG-------------------------ATTACcgTCGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAA TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTAC--TCGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAA Template switch alignment (log-probability: -16) TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGA|TTACCG|TCGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAA TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGA|TTACCG|TCGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAA Gorilla > Chimp --------------- chr13:80255398-80255405 Template switch process: F1: L ATAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGA 1 F3: 4 GACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAATT R RF: ATAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTACTTGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAATT RR: TATTTGGTATAAAATTCTTATATGCACTGCCATTTGCGTCTGAGAGAGGTGTAAAATCTGCCCTATAATGAACTGTCCTAAAACTAATCGGTACTTCAATTCTAAAAATTAA F2: 3 CTGCCATT 2 Unidirectional alignment (log-probability: -30.4) TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAG-------------------------ATTACcgTcGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAATT TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGACTCTCTCCACATTTTAGACGGGATATTAC--TTGACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAATT Template switch alignment (log-probability: -16.7) TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGA|TTACCGTC|GACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAATT TAAACCATATTTTAAGAATATACGTGACGGTAAACGCAGA|TTACCGTC|GACAGGATTTTGATTAGCCATGAAGTTAAGATTTTTAATT ========= Event 862 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTTAATCTCCTCTACACAGAAATTCTGGAGTCACCTCTGATACAAACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTAATAAACAGTTAGTGGCTATAAGGAAAAATCTTCCTCAGAATTTCATATTCAGATCAGATCTATTGACA Chimp: TCTTAATCTCCTCTACACAGAAATTCTGGAGTCACCTCTGATACAAACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTACTAAACATTTAGTGGCTATAAGGAAAAATCTTC-------------CTTCAGATCAGATCTATTGACA ↓ 3 2 4 1 Gorilla: TCTTAATCTCCTCTACACAGAAATTCTGGAGTCACCTCTGATACAAACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTAATAAACATATAGTGGCTATAAGGAAAAATCTTCCTCAGAATTTCGTATTCAGATCAGATCTATTGACA Human: TCTTAATCTCCTCTACACAGAAATTCTGGAGTCACCTCTGATACAAACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTAATAAACAGTTAGTGGCTATAAGGAAAAATCTTCCTCAGAATTTCATATTCAGATCAGATCTATTGACA Cluster: [ ] Orangutan: TCTTAATCTCCTCTACATAGAAATTCTGGAGTCACCTCTGATACAAACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTAATAAACATTTAGTGGCTATAAGGAAAAATCTTCCTTAGAATTTCATATTCAGATCAGATCTattgaca Chimp > Gorilla --------------- chr13:79902195-79902203 Template switch process: F1: L ACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTAATAAACATATAGTGGCTATAAGGAAAAATCTTCCT 1 F3: 4 GTATT R RF: GAAATTCTGGAGTCACCTCTGATACAAACCCATTTCAAATGTTTTCAAAAGTATGTTGAGAATAATTACTAAACATTTAGTGGCTATAAGGAAAAATCTTCCTTCAGATCAGATCTATT RR: CTTTAAGACCTCAGTGGAGACTATGTTTGGGTAAAGTTTACAAAAGTTTTCATACAACTCTTATTAATGATTTGTAAATCACCGATATTCCTTTTTAGAAGGAAGTCTAGTCTAGATAA F2: 3 CTTTAAGAC 2 Unidirectional alignment (log-probability: -40.6) AATTAaTAAACATaTAGTGGCTATAAGGAAAAATCTTCCtcagaatttcgtaTT AATTACTAAACATTTAGTGGCTATAAGGAAAAATCTTCC-------------TT Template switch alignment (log-probability: -33.4) AATTAaTAAACATaTAGTGGCTATAAGGAAAAATCTTCCT|CAGAATTTC|gTATT AATTACTAAACATTTAGTGGCTATAAGGAAAAATCTTCCT|CAGAATTTC|CTATT ========= Event 863 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTATGTATGTATTTATATATGCCATTATGATAATGGCATATATCTTCTAAACAATATGTT Chimp: TTTATGTATGTATTTATATATGCCATTATCATAATTTAAAATATCTTCTAAACATTATGTT Gorilla: TTTATGTATGTATTTATATATGCCATTATCATAATTTAAAATATCTTCTAAACAATATGTT ↓ 3 12 4 Human: TTTATGTATGTATTTATATATGCCATTATGATAATGGCATATATCTTCTAAACAATATGTT Cluster: [ ] Orangutan: TTTATGTATGTATTTATATATGCCATTATTATAATTTAAAATATCTTCTAAACAATATGTT Gorilla > Human --------------- chr13:76434262-76434272 Template switch process: F1: L TTGCTGTCTATATTTATGTATGTATTTATATATGCCATTAT 1 F3: 4 ATATCTTCTAAACAATATGTTTTATTTGCCTTTAAATATA R RF: TTGCTGTCTATATTTATGTATGTATTTATATATGCCATTATCATAATTTAAAATATCTTCTAAACAATATGTTTTATTTGCCTTTAAATATA RR: AACGACAGATATAAATACATACATAAATATATACGGTAATAGTATTAAATTTTATAGAAGATTTGTTATACAAAATAAACGGAAATTTATAT F2: 3 TACGGTAATAG 2 Unidirectional alignment (log-probability: -28.9) TGCTGTCTATATTTATGTATGTATTTATATATGCCATTATgATAATggcAtATATCTTCTAAACAATATGTTTTATTTGCCTTTAAATATA TGCTGTCTATATTTATGTATGTATTTATATATGCCATTATCATAATTTAAAATATCTTCTAAACAATATGTTTTATTTGCCTTTAAATATA Template switch alignment (log-probability: -17.1) TGCTGTCTATATTTATGTATGTATTTATATATGCCATTAT|GATAATGGCAT|ATATCTTCTAAACAATATGTTTTATTTGCCTTTAAATATA TGCTGTCTATATTTATGTATGTATTTATATATGCCATTAT|GATAATGGCAT|ATATCTTCTAAACAATATGTTTTATTTGCCTTTAAATATA ========= Event 864 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTTATTATGCTAACACATTACCAGTTCTTAAACCTAATAGACACACAGGGCAAATACACACAGAGCTTTTCTTTAAAAACTAATTAGACATCTCAGAAAAC Chimp: GCTGATTATGCTAACACATTACCAGTTCTTAAACCTAATAGACACACAGGGCAAAT--------------------------------ACATCTCAGAAAAC ↑ 4 1 3 2 Gorilla: GCTTATTATGCTAACACATTA------------CCTAATAGACACACAGGGCAAATACACACAGAGCTTTTCTTTAAAAACTAATTAGACATCTCAGAAAAC Human: GCTTATTATGCTAACACATTACCAGTTCTTAAACCTAATAGACACACAGGGCAAATACACACAGAGCTTTTCTTTAAAAACTAATTAGACATCTCAGAAAAC Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------------ Gorilla > Chimp --------------- chr13:77029815-77029823 Template switch process: F1: L TCTGGCAATTAATTAAAGCTGCTGATTATGCTAACACATTACC 1 F3: 4 ACCTAATAGACACACAGGGCAAAT R RF: TCTGGCAATTAATTAAAGCTGCTTATTATGCTAACACATTACCTAATAGACACACAGGGCAAATACACACAGAGCTTTTCTTTAAAAACT RR: AGACCGTTAATTAATTTCGACGAATAATACGATTGTGTAATGGATTATCTGTGTGTCCCGTTTATGTGTGTCTCGAAAAGAAATTTTTGA F2: 3 AATTCTTGA 2 Unidirectional alignment (log-probability: -41) GGCAATTAATTAAAGCTGCTgATTATGCTAACACATTaccagttcttaaACCTAATAGACACACAGGGCAAAT----------------- GGCAATTAATTAAAGCTGCTTATTATGCTAACACATT------------ACCTAATAGACACACAGGGCAAATACACACAGAGCTTTTCT Template switch alignment (log-probability: -27.5) GGCAATTAATTAAAGCTGCTgATTATGCTAACACATTACC|AGTTcTTAA|ACCTAATAGACACACAGGGCAAAT GGCAATTAATTAAAGCTGCTTATTATGCTAACACATTACC|AGTTTTTAA|ACCTAATAGACACACAGGGCAAAT ========= Event 865 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGAGAAACTGGAGAAAAAGC-A---CATCATTCCTGCACATCCTAAGGAATT-------------------------------------------ATCGTGGGTCATGTGTCTTTGCTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGTGTTTTT Chimp: AAAGAGAAACTGGAGAAAAAGC-A---CATCATTCCTGCACATCCTAAGGAATT-------------------------------------------ATCATGGGTCATGTATCTTTGTTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGGGTTTTT ↓ 1 3 2 4 Gorilla: AAAGAGAAACTGGAGAAAAAGACCCATGATAATTCCTTAGGATGTGCAGGAATG--------------------------------------------------------------------------------------ATGAGGCTTTATCAGTGTTTTT ↑ 1 3 2 4 Human: AAAGAGAAACTGGAGAAAAAGC-A---CATCATTCCTGCACATCCTAAGGAATT-------------------------------------------ATCGTGGGTCATGTGTCTTTGCTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGTGTTTTT Cluster: [ ] Orangutan: AAAGAGGAACTGGAGAAAAAGC-A---CATCATTCCTGCACATCCTAAGGAATCATCGTGGGTCATGTGTCTTTGTTCATATGTAAATAATCCATAG-------------------------------------------TTGAGGCTTTATCGGTGTTTTT Human > Gorilla --------------- chr13:79243157-79243190 Template switch process: F1: L ATTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG 1 F3: 4 TGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG R RF: ATTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAGCACATCATTCCTGCACATCCTAAGGAATTATCGTGGGTCATGTGTCTTTGCTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG RR: TAACTAGTCTTATACATTTGTTTCTCTTTGACCTCTTTTTCGTGTAGTAAGGACGTGTAGGATTCCTTAATAGCACCCAGTACACAGAAACGAGTATACATTTATTAGGTATCAACTCCGAAATAGTCACAAAAATCTTGAACTTACTATTTTC F2: 3 AGTAAGGACGTGTAGGATTCCTTAATAGTACCCA 2 Unidirectional alignment (log-probability: -73.2) TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAGacccatgataattccttaggatgtgcaggaatga-------------------------------------------------------------------------TGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG----------------------------------CACATCATTCCTGCACATCCTAAGGAATTATCGTGGGTCATGTGTCTTTGCTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG Template switch alignment (log-probability: -25.6) TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG|ACCCAtGATAATTCCTTAGGATGTGCAGGAATGA|TGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG|ACCCACGATAATTCCTTAGGATGTGCAGGAATGA|TGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG Chimp > Gorilla --------------- chr13:79243157-79243190 Template switch process: F1: L ATTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG 1 F3: 4 TGAGGCTTTATCAGTGTTTTTAGAACTTGAATGATAAAAG R RF: ATTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAGCACATCATTCCTGCACATCCTAAGGAATTATCATGGGTCATGTATCTTTGTTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGGGTTTTTAGAACTTGAATGATAAAAG RR: TAACTAGTCTTATACATTTGTTTCTCTTTGACCTCTTTTTCGTGTAGTAAGGACGTGTAGGATTCCTTAATAGTACCCAGTACATAGAAACAAGTATACATTTATTAGGTATCAACTCCGAAATAGTCCCAAAAATCTTGAACTTACTATTTTC F2: 3 AGTAAGGACGTGTAGGATTCCTTAATAGTACCCA 2 Unidirectional alignment (log-probability: -78.8) TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAGacccatgataattccttaggatgtgcaggaatga-------------------------------------------------------------------------TGAGGCTTTATCAGtGTTTTTAGAACTTGAATGATAAAAG TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG----------------------------------CACATCATTCCTGCACATCCTAAGGAATTATCATGGGTCATGTATCTTTGTTCATATGTAAATAATCCATAGTTGAGGCTTTATCAGGGTTTTTAGAACTTGAATGATAAAAG Template switch alignment (log-probability: -25.6) TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG|ACCCATGATAATTCCTTAGGATGTGCAGGAATGA|TGAGGCTTTATCAGtGTTTTTAGAACTTGAATGATAAAAG TTGATCAGAATATGTAAACAAAGAGAAACTGGAGAAAAAG|ACCCATGATAATTCCTTAGGATGTGCAGGAATGA|TGAGGCTTTATCAGGGTTTTTAGAACTTGAATGATAAAAG ========= Event 866 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTCACGAGT-TAATTTGGGG---TGGGGTGACTTACGGTAATGTAATTGTGAATTTT Chimp: ACTCACGAGTTGAATTTGGGG---AGGGGTGACTTACGGTAATGTAATTGTGAATTTT ↓ 1 3 4 Gorilla: ACTCAAGAGTTGAATTTGGGG------AGTAAGTCACTGTAATGTAATTGTGAATTTT Human: ACTCACGAGT-TAATTTGGGG---TGGGGTGACTTACGGTAATGTAATTGTGAATTTT Cluster: [ ] Orangutan: ACTCACAAGTTGAATTTGGGGAGG---GGTGACTTACTGTAATGTAATTGTGAATTTT Chimp > Gorilla --------------- chr13:74105645-74105650 Template switch process: F1: L ATTATGTTTTGTTATTCTCTACTCAAGAGTTGAATTTGGGGAG 1 F3: 4 ACTGTAATGTAATTGTGAATTTTATGTGTCCACATGACTCACC R RF: ATTATGTTTTGTTATTCTCTACTCACGAGTTGAATTTGGGGAGGGGTGACTTACGGTAATGTAATTGTGAATTTTATGTGTCCACATGACTCACC RR: TAATACAAAACAATAAGAGATGAGTGCTCAACTTAAACCCCTCCCCACTGAATGCCATTACATTAACACTTAAAATACACAGGTGTACTGAGTGG F2: 3 CTGAAT 2 Unidirectional alignment (log-probability: -38.8) ATGTTTTGTTATTCTCTACTCAaGAGTTGAATTTGGGGA---GTaAgTcACtGTAATGTAATTGTGAATTTTATGTGTCCACATGACTC ATGTTTTGTTATTCTCTACTCACGAGTTGAATTTGGGGAGGGGTGACTTACGGTAATGTAATTGTGAATTTTATGTGTCCACATGACTC Template switch alignment (log-probability: -27.6) ATGTTTTGTTATTCTCTACTCAaGAGTTGAATTTGGGGAG|TAAGTC|ACtGTAATGTAATTGTGAATTTTATGTGTCCACATGACTC ATGTTTTGTTATTCTCTACTCACGAGTTGAATTTGGGGAG|TAAGTC|ACGGTAATGTAATTGTGAATTTTATGTGTCCACATGACTC ========= Event 867 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAGCAGCAGTG-TATTTTCCTAAGCACTGCTTAGGAACCCCAGAACTCCCAACCTA ↑ 3 2 1 4 Chimp: TTAGCAGCAGTG-TATTTTCCTAAGCAC------ACAACCCCAGAACTCCCAAccta Gorilla: TTAGCAGCAGTG-TATTTTCCTAAGCAC------ACAACCCCAGAACTCCCAACCTA ↓ 3 2 1 4 Human: CTAGCAGCAGTG-TATTTTCCTAAGCACTGCTTAGGAACCCCAGAACTCCCAACCTA Cluster: [ ] Orangutan: TTAGCAGCAGTGTCATTTTCCTAAGCAC------ACAACCCCAGAACTCCCAACCTA Chimp > Human ------------- chr13:72255956-72255963 Template switch process: F1: L TATGACCTCACCTGCTAGCAGCAGTGTATTTTCCTAAGCAC 1 F3: 4 AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC R RF: TATGACCTCACCTGTTAGCAGCAGTGTATTTTCCTAAGCACACAACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC RR: ATACTGGAGTGGACAATCGTCGTCACATAAAAGGATTCGTGTGTTGGGGTCTTGAGGGTTGGATAGAAAATAAAAGGGAGTGG F2: 3 GGATTCGT 2 Unidirectional alignment (log-probability: -37.5) ATGACCTCACCTGcTAGCAGCAGTGTATTTTCCTAAGCACtgcttaggAACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC ATGACCTCACCTGTTAGCAGCAGTGTATTTTCCTAAGCACAC------AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC Template switch alignment (log-probability: -22.3) ATGACCTCACCTGcTAGCAGCAGTGTATTTTCCTAAGCAC|TGCTTAGG|AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC ATGACCTCACCTGTTAGCAGCAGTGTATTTTCCTAAGCAC|TGCTTAGG|AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC Gorilla > Human --------------- chr13:72255956-72255963 Template switch process: F1: L TATGACCTCACCTGCTAGCAGCAGTGTATTTTCCTAAGCAC 1 F3: 4 AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCACC R RF: TATGACCTCACCTGTTAGCAGCAGTGTATTTTCCTAAGCACACAACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCATC RR: ATACTGGAGTGGACAATCGTCGTCACATAAAAGGATTCGTGTGTTGGGGTCTTGAGGGTTGGATAGAAAATAAAAGGGAGTAG F2: 3 GGATTCGT 2 Unidirectional alignment (log-probability: -41.6) ATGACCTCACCTGcTAGCAGCAGTGTATTTTCCTAAGCACtgcttaggAACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCAcC ATGACCTCACCTGTTAGCAGCAGTGTATTTTCCTAAGCAC------ACAACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCATC Template switch alignment (log-probability: -27.8) ATGACCTCACCTGcTAGCAGCAGTGTATTTTCCTAAGCAC|TGCTTAGG|AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCAcC ATGACCTCACCTGTTAGCAGCAGTGTATTTTCCTAAGCAC|TGCTTAGG|AACCCCAGAACTCCCAACCTATCTTTTATTTTCCCTCATC ========= Event 868 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGAGCCTGATGATTTTGTTAT---AA----TATTCATGAAACATAGTAAAATGGAAAAA Chimp: CCTGAGCCTGATGATTTTGTTAT---AA----TATTCATGAAACATAGTAAAATGGAAAAA ↓ 1 3 4 2 Gorilla: CCTGAGCCTGATGATTTTGTTTCATGAATATTAATTCATGAAACATAGTAAAATGGAAAAA ↑ 1 3 4 2 Human: CCTGAGCCTGATGATTTTGTTAT---AA----TATTCATGAAACATAGTAAAATGGAAAAA Cluster: [ ] Orangutan: CTTGATCCTGATTATTTTGTTAT---AA----TTTTCATGGAAAATAGTAAAATGGAAAAA Human > Gorilla --------------- chr13:23829350-23829361 Template switch process: F1: L CTTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT 1 F3: 4 ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG R RF: CGTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTTATAATATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG RR: GCATACAATGTACCGGTTCTGGACTCGGACTACTAAAACAATATTATAAGTACTTTGTATCATTTTACCTTTTTTAGGTGTCTGTC F2: 3 ATTATAAGTACT 2 Unidirectional alignment (log-probability: -41.8) tTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTTtcatgaATAtTaATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG GTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT------ATAAT-ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG Template switch alignment (log-probability: -22.8) tTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT|TCATGAATATTA|ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG GTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT|TCATGAATATTA|ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG Chimp > Gorilla --------------- chr13:23829350-23829361 Template switch process: F1: L CTTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT 1 F3: 4 ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG R RF: CGTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTTATAATATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG RR: GCATACAATGTACCGGTTCTGGACTCGGACTACTAAAACAATATTATAAGTACTTTGTATCATTTTACCTTTTTTAGGTGTCTGTC F2: 3 ATTATAAGTACT 2 Unidirectional alignment (log-probability: -41.8) tTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTTtcatgaATAtTaATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG GTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT------ATAAT-ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG Template switch alignment (log-probability: -22.8) tTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT|TCATGAATATTA|ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG GTATGTTACATGGCCAAGACCTGAGCCTGATGATTTTGTT|TCATGAATATTA|ATTCATGAAACATAGTAAAATGGAAAAAATCCACAGACAG ========= Event 869 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: T-TTTTCATGGTGAAAAATTG----------------------------------TCTTACAGATCTGTTGAAACTTTCCTATTCCTTGa ↑ 1 3 2 4 Chimp: T-TTTTCATGGTGAAAAATTG-----------------TCTTACAATTTTTCTTGTCTTACAGATCTGCTGAAACTTTCCTATTCCTTGa Gorilla: ttttttCATGGTGAAAAATTGTCTTACAATTTTTCTTG-----------------TCTTACAGATCTGTTGAAACTTTCCTATTCCTTGa Human: T-TTTTCATGGTGAAAAATTG----------------------------------TCTTACAGATCTGTTGAAACTTTCCTATTCCTTGa Cluster: [ ] Orangutan: T-TTTTCATGGTGAAAAATTG----------------------------------TCTTACAGATCTGATGAAACTTTCTTATTCCTTGa Chimp > Human ------------- chr13:69854593-69854599 Template switch process: F1: L TATCTTTCTTAGCTTTTATGTTTTTTCATGGTGAAAAATTGTCTTACA 1 F3: 4 TGAAACTTTCCTATTCCTTGAAAAA R RF: TATCTTTCTTAGCTTTTATGTTTTTTCATGGTGAAAAATTGTCTTACAATTTTTCTTGTCTTACAGATCTGCTGAAACTTTCCTATTCCTTGAAAAA RR: ATAGAAAGAATCGAAAATACAAAAAAGTACCACTTTTTAACAGAATGTTAAAAAGAACAGAATGTCTAGACGACTTTGAAAGGATAAGGAACTTTTT F2: 3 TGTCTAG 2 Unidirectional alignment (log-probability: -25) TTAGCTTTTATGTTTTTTCATGGTGAAAAATTGTC-----------------TTACAGATCTGtTGAAACTTTCCTATTCCTTGAAAAA- TTAGCTTTTATGTTTTTTCATGGTGAAAAATTGTCTTACAATTTTTCTTGTCTTACAGATCTGCTGAAACTTTCCTATTCCTTGAAAAAA Template switch alignment (log-probability: -16) TTAGCTTTTATGTTTTTTCATGGTGAAAAATTGTCTTACA|GATCTGT|TGAAACTTTCCTATTCCTTGAAAAA TTAGCTTTTATGTTTTTTCATGGTGAAAAATTGTCTTACA|GATCTGT|TGAAACTTTCCTATTCCTTGAAAAA ========= Event 870 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGAAAGTCATTTCCTGAGTA---ATTGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGG ↓ 1 4 3 2 Chimp: CTGAAAGTCATTTCCTGAGTAGCATTGGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGG Gorilla: CTGAAAGTCATTTCCTGAGTA---ATTGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGG Human: CTGAAAGTCATTTCCTGAGTA---ATTGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGG Cluster: [ ] Orangutan: CTGAAAGTCATTTACCGAGTA---ATTGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGG Human > Chimp ------------- chr13:69950067-69950072 Template switch process: F1: L AAATATTCATAAGAAGGATTCTGAAAGTCATTTCCTGAGTA 1 F3: 4 GCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGGA R RF: AAATATTCATAAGAAGGATTCTGAAAGTCATTTCCTGAGTAATTGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGGA RR: TTTATAAGTATTCTTCCTAAGACTTTCAGTAAAGGACTCATTAACGGTCAGTTCACGGTTACGATTCGAACTCTCCTACACCCT F2: 3 GTTACG 2 Unidirectional alignment (log-probability: -25.5) AATATTCATAAGAAGGATTCTGAAAGTCATTTCCTGAGTAgcATTgGCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGGA AATATTCATAAGAAGGATTCTGAAAGTCATTTCCTGAGTA--ATT-GCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGGA Template switch alignment (log-probability: -16) AATATTCATAAGAAGGATTCTGAAAGTCATTTCCTGAGTA|GCATTG|GCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGGA AATATTCATAAGAAGGATTCTGAAAGTCATTTCCTGAGTA|GCATTG|GCCAGTCAAGTGCCAATGCTAAGCTTGAGAGGATGTGGGA ========= Event 871 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTTAATCTACCCACTTCTCTTCTTCCT----CCTGGC-----------AGAGATCAGCTGCAACACTGCCACTGGGTG ↑ 31 2 4 Chimp: TTTAATCTACCCACTTCTCTTTCTCCTGATCTCTGCCAGGAGGTGGGGAGAGC---TCTGCAACACTGCCACTGGGTG ↓ 31 2 4 Gorilla: TTTAATCTACCCACTTCTCTTCTTCCT----CCTGGC-----------AGAGATCAGCTGCAACACTGCCACTGGGTG Human: TTTAATCTACCCACTTCTCTTCTTCCT----CCTGGC-----------AGAGATCAGCTGCAACACTGCCACTGGGTG Cluster: [ ] Orangutan: Chimp > Human ------------- chr13:47832623-47832637 Template switch process: F1: L CAGACAACAGTGTGAATTAATTTAATCTACCCACTTCTCTTCTTCCT 1 F3: 4 CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG R RF: CAGACAACAGTGTGAATTAATTTAATCTACCCACTTCTCTTTCTCCTGATCTCTGCCAGGAGGTGGGGAGAGCTCTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG RR: GTCTGTTGTCACACTTAATTAAATTAGATGGGTGAAGAGAAAGAGGACTAGAGACGGTCCTCCACCCCTCTCGAGACGTTGTGACGGTGACCCACCCCTCTCTCTCCGTCTTGC F2: 3 GACTAGAGACGGTCC 2 Unidirectional alignment (log-probability: -50.1) CAGTGTGAATTAATTTAATCTACCCACTTCTCTT-------------------------------CTtcctcctggcagagatcagCTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG CAGTGTGAATTAATTTAATCTACCCACTTCTCTTTCTCCTGATCTCTGCCAGGAGGTGGGGAGAGCT-------------------CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG Template switch alignment (log-probability: -29.2) CAGTGTGAATTAATTTAATCTACCCACTTCTCTTctTCCT|CCTGGCAGAGATCAG|CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG CAGTGTGAATTAATTTAATCTACCCACTTCTCTTTCTCCT|CCTGGCAGAGATCAG|CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG Chimp > Gorilla --------------- chr13:29733034-29733048 Template switch process: F1: L CAGACAACAGTGTGAATTAATTTAATCTACCCACTTCTCTTCTTCCT 1 F3: 4 CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG R RF: CAGACAACAGTGTGAATTAATTTAATCTACCCACTTCTCTTTCTCCTGATCTCTGCCAGGAGGTGGGGAGAGCTCTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG RR: GTCTGTTGTCACACTTAATTAAATTAGATGGGTGAAGAGAAAGAGGACTAGAGACGGTCCTCCACCCCTCTCGAGACGTTGTGACGGTGACCCACCCCTCTCTCTCCGTCTTGC F2: 3 GACTAGAGACGGTCC 2 Unidirectional alignment (log-probability: -49.6) CAGTGTGAATTAATTTAATCTACCCACTTCTCTT-------------------------------CTtcctcctggcagagatcagCTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG CAGTGTGAATTAATTTAATCTACCCACTTCTCTTTCTCCTGATCTCTGCCAGGAGGTGGGGAGAGCT-------------------CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG Template switch alignment (log-probability: -28.8) CAGTGTGAATTAATTTAATCTACCCACTTCTCTTctTCCT|CCTGGCAGAGATCAG|CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG CAGTGTGAATTAATTTAATCTACCCACTTCTCTTTCTCCT|CCTGGCAGAGATCAG|CTGCAACACTGCCACTGGGTGGGGAGAGAGAGGCAGAACG ========= Event 872 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCTACCCCAGCACATACACAAGAGAATT--------CATAATGAATTCTCTTG------TGGAAGAGATCCCTGACAAAG ↑ 3 12 4 Chimp: CCCTACCCCAGCACATACACAAGAGAATT----CATTCATTATGAATTCTCTTG---TCATGGAAGAGATCCCTGACAAAG Gorilla: CCCTATCCCAGCACATACACAAGAGAATTCATT----CATTATGAATTCTCTTGTCA---TGGAAGAGATCCCTGACAAAG ↓ 3 1 2 4 Human: CCCTACCCCAGCACATACACAAGAGAATT--------CATAATGAATTCTCTTG------TGGAAGAGATCCCTGACAAAG Cluster: [ ] Orangutan: CCCTACCCCAGCACATACACAAGAGAATTCATA----ATGAATGAATTCTCTTGTCA---TGGAAGAGATCCCTGACAAAG Chimp > Human ------------- chr13:66411628-66411641 Template switch process: F1: L TGGATTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCAT 1 F3: 4 TGGAAGAGATCCCTGACAAAGGCA R RF: TGGATTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCATTCATTATGAATTCTCTTGTCATGGAAGAGATCCCTGACAAAGGCA RR: ACCTAAAATTGAGGGATGGGGTCGTGTATGTGTTCTCTTAAGTAAGTAATACTTAAGAGAACAGTACCTTCTCTAGGGACTGTTTCCGT F2: 3 GTTCTCTTAAGTAA 2 Unidirectional alignment (log-probability: -27.5) TTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCATa----ATGAATTCTCTTG---TGGAAGAGATCCCTGACAAAGGCA TTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCATTCATTATGAATTCTCTTGTCATGGAAGAGATCCCTGACAAAGGCA Template switch alignment (log-probability: -16.8) TTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCAT|AATGAATTCTCTTG|TGGAAGAGATCCCTGACAAAGGCA TTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCAT|AATGAATTCTCTTG|TGGAAGAGATCCCTGACAAAGGCA Gorilla > Human --------------- chr13:66411628-66411641 Template switch process: F1: L TGGATTTTAACTCCCTACCCCAGCACATACACAAGAGAATTCAT 1 F3: 4 TGGAAGAGATCCCTGACAAAGGCA R RF: TGGATTTTAACTCCCTATCCCAGCACATACACAAGAGAATTCATTCATTATGAATTCTCTTGTCATGGAAGAGATCCCTGACAAAGGCA RR: ACCTAAAATTGAGGGATAGGGTCGTGTATGTGTTCTCTTAAGTAAGTAATACTTAAGAGAACAGTACCTTCTCTAGGGACTGTTTCCGT F2: 3 GTTCTCTTAAGTAA 2 Unidirectional alignment (log-probability: -32) TTTTAACTCCCTAcCCCAGCACATACACAAGAGA----ATTCATaATGAATTCTCTTG---TGGAAGAGATCCCTGACAAAGGCA TTTTAACTCCCTATCCCAGCACATACACAAGAGAATTCATTCATTATGAATTCTCTTGTCATGGAAGAGATCCCTGACAAAGGCA Template switch alignment (log-probability: -22.7) TTTTAACTCCCTAcCCCAGCACATACACAAGAGAATTCAT|AATGAATTCTCTTG|TGGAAGAGATCCCTGACAAAGGCA TTTTAACTCCCTATCCCAGCACATACACAAGAGAATTCAT|AATGAATTCTCTTG|TGGAAGAGATCCCTGACAAAGGCA ========= Event 873 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAGTTTGGTTATACACTCGATTCTTCA-------------------------------------------------------------------------------------------------------------TATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAGGAATAATAAAGTGCAATTTGGTCTCTAAttttgtggcagatgtatttc ↓ 4 3 1 2 Chimp: GAAGTTTGGTTATACACTCGATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTTAAATTAGAGACCAAATTGCACTTTATTATTCCTTTGAGTGTGTGATACCTGTATAACTATGATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAGGAATAATAAAGTGCAATTTGGTCTCTAAttttgtggcagatgtatttc ↑ 4 3 1 2 Gorilla: GAAGTTTGGTTATACACTCGATTCTTCA-------------------------------------------------------------------------------------------------------------TATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAGGAATAGTAAAGTGCAATTTGGTCTCTAAttttgtggcagatgtatttc Human: GAAGTTTGGTTATACACTCGATTCTTCA-------------------------------------------------------------------------------------------------------------TATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAGGAATAATAAAGTGCAATTTGGTCTCTAAttttgtggcagatgtatttc Cluster: [ ] Orangutan: GAAGTATGGTTGTACCCTTGATTCTTCA-------------------------------------------------------------------------------------------------------------TATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAGGAATAATAAGGTGCAATTTGGTCTCTAATTTTGTGGCAGATTTATTTC Human > Chimp ------------- chr13:66947046-66947102 Template switch process: F1: L TCTGTAATTAAGTGAAGTTTGGTTATACACTCGATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTTAAA 1 F3: 4 GATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTC R RF: TCTGTAATTAAGTGAAGTTTGGTTATACACTCGATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAAAAGGAATAATAAAGTGCAATTTGGTCTCTAA RR: AGACATTAATTCACTTCAAACCAATATGTGAGCTAAGAAGTATAACGACCTCTTCGTATCAATATGTCCATAGTGTGTGAGTTTTTTCCTTATTATTTCACGTTAAACCAGAGATT F2: 3 TATCAATATGTCCATAGTGTGTGAGTTTCCTTATTATTTCACGTTAAACCAGAGATT 2 Unidirectional alignment (log-probability: -168) TGCTGGAGAAGCATAGTTATACAGGTATCACACACttaaattagagaccaaattgcactttattattcctttgagtgtgtgatacctgtataactatgattcttcatattgctggagaagcatagttatacaggtat TGCTGGAGAAGCATAGTTATACAGGTATCACACAC------------------------------------------------------------------------------------------------------ Template switch alignment (log-probability: -29) TGCTGGAGAAGCATAGTTATACAGGTATCACACACTtAAA|TTAGAGACCAAATTGCACTTTATTATTCCTTTGAGTGTGTGATACCTGTATAACTAT|GATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTAT TGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAA|TTAGAGACCAAATTGCACTTTATTATTCCTTTGAGTGTGTGATACCTGTATAACTAT|GATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTAT Gorilla > Chimp --------------- chr13:66947046-66947102 Template switch process: F1: L TCTGTAATTAAGTGAAGTTTGGTTATACACTCGATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTTAAA 1 F3: 4 GATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTC R RF: TCTGTAATTAAGTGAAGTTTGGTTATACACTCGATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAAAAAGGAATAGTAAAGTGCAATTTGGTCTCTAA RR: AGACATTAATTCACTTCAAACCAATATGTGAGCTAAGAAGTATAACGACCTCTTCGTATCAATATGTCCATAGTGTGTGAGTTTTTTCCTTATCATTTCACGTTAAACCAGAGATT F2: 3 TATCAATATGTCCATAGTGTGTGAGTTTCCTTATTATTTCACGTTAAACCAGAGATT 2 Unidirectional alignment (log-probability: -168) TGCTGGAGAAGCATAGTTATACAGGTATCACACACttaaattagagaccaaattgcactttattattcctttgagtgtgtgatacctgtataactatgattcttcatattgctggagaagcatagttatacaggtat TGCTGGAGAAGCATAGTTATACAGGTATCACACAC------------------------------------------------------------------------------------------------------ Template switch alignment (log-probability: -35) TGCTGGAGAAGCATAGTTATACAGGTATCACACACTtAAA|TTAGAGACCAAATTGCACTTTAtTATTCCTTTGAGTGTGTGATACCTGTATAACTAT|GATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTAT TGCTGGAGAAGCATAGTTATACAGGTATCACACACTCAAA|TTAGAGACCAAATTGCACTTTACTATTCCTTTGAGTGTGTGATACCTGTATAACTAT|GATTCTTCATATTGCTGGAGAAGCATAGTTATACAGGTAT ========= Event 874 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATGGCATCAACTCTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAA-GCATCAAGAGGAGTTTACTTTTTATACCTTATGTGAATGTGAGAGTTTATGTCATCAGCTCATCCTTGG Chimp: ATGGCATCAACTCTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAA-GCATCAAGAGGAGTTTACTTTTTATACCTTATGGGAATGTGAGAGTTTATGTCATCAGCTCATCCTTGG ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: ATGGCATCAACTCTCACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGAT-GCTTGCTAGAAAGACATCAAGAGGAGTTTACTTTTTATACCTTATGTGAGTGTGAGAGTTTATGTCATCAGCTCATCCTTGG ↓ 3 1 2 4 ↑ 1 3 4 2 Human: ATGGCATCAACTCTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAA-GCATCAAGAGGAGTTTACTTTTTATACCTTATGTGAATGTGAGAGTTTATGTCATCAGCTCATCCTTGG Cluster: [ ] Orangutan: ATGGCATCAACTCTCACATTCACATAAGGTATAAAAAGTAAACTCCTCTTAATGTCTTTCTAGCAA-GCATCAAGAGGAGTTTACTTTTTATACCTTATGTGAATGTGAGAGTTTATGTCatcagctcatccttgg Gorilla > Human --------------- chr13:48684419-48684466 Template switch process: F1: L CTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATG 1 F3: 4 ATGTG R RF: CTCACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATGCTTGCTAGAAAGACATCAAGAGGAGTTTACTTTTTATACCTTATGTG RR: GAGTGTAAGTGTATTCCATATTTTTCATTTGAGGAGAACTACGAACGATCTTTCTGTAGTTCTCCTCAAATGAAAAATATGGAATACAC F2: 3 AGTGTATTCCATATTTTTCATTTGAGGAGAACTACGAACGATCTTTCT 2 Unidirectional alignment (log-probability: -44.4) CACATTCcCATAAGGTATAAAAAGTAAACTCCTCTTGATGtCTTtCTAGcAAG-CATCAAGAGGAGTTTACTTTTTATACCTTATGTGAaTGTG CACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATG-CTTGCTAGAAAGACATCAAGAGGAGTTTACTTTTTATACCTTATGTGAGTGTG Template switch alignment (log-probability: -26.5) CACATTCcCATAAGGTATAAAAAGTAAACTCCTCTTGATG|TCTTTCTAGCAAGCATCAAGAGGAGTTTACTTTTTATACCTTATGTGA|ATGTG CACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATG|TCTTTCTAGCAAGCATCAAGAGGAGTTTACTTTTTATACCTTATGTGA|ATGTG Human > Gorilla --------------- chr13:30554525-30554570 Template switch process: F1: L CTCACATTC 1 F3: 4 CATCAAGAGGAGTTTACTTTTTATACCTTATGTGAGTGTG R RF: CTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAAGCATCAAGAGGAGTTTACTTTTTATACCTTATGTGAATGTG RR: GAGTGTAAGGGTATTCCATATTTTTCATTTGAGGAGAACTACAGAAAGATCGTTCGTAGTTCTCCTCAAATGAAAAATATGGAATACACTTACAC F2: 3 AGAAAGATCGTTCGTAGTTCTCCTCAAATGAAAAATATGGAATACA 2 Unidirectional alignment (log-probability: -44.4) CTCACATTCaCATAAGGTATAAAAAGTAAACTCCTCTTGATG-CTTgCTAGaAAGaCATCAAGAGGAGTTTACTTTTTATACCTTATGTGAgTGTG CTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAAG-CATCAAGAGGAGTTTACTTTTTATACCTTATGTGAATGTG Template switch alignment (log-probability: -26.3) CTCACATTC|ACATAAGGTATAAAAAGTAAACTCCTCTTGATGCTTGCTAGAAAGA|CATCAAGAGGAGTTTACTTTTTATACCTTATGTGAgTGTG CTCACATTC|ACATAAGGTATAAAAAGTAAACTCCTCTTGATGCTTGCTAGAAAGA|CATCAAGAGGAGTTTACTTTTTATACCTTATGTGAATGTG Gorilla > Chimp --------------- chr13:33684095-33684142 Template switch process: F1: L CTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATG 1 F3: 4 ATGTG R RF: CTCACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATGCTTGCTAGAAAGACATCAAGAGGAGTTTACTTTTTATACCTTATGTG RR: GAGTGTAAGTGTATTCCATATTTTTCATTTGAGGAGAACTACGAACGATCTTTCTGTAGTTCTCCTCAAATGAAAAATATGGAATACAC F2: 3 AGGGTATTCCATATTTTTCATTTGAGGAGAACTACGAACGATCTTTCT 2 Unidirectional alignment (log-probability: -49.9) CACATTCcCATAAGGTATAAAAAGTAAACTCCTCTTGATGtCTTtCTAGcAAG-CATCAAGAGGAGTTTACTTTTTATACCTTATGgGAaTGTG CACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATG-CTTGCTAGAAAGACATCAAGAGGAGTTTACTTTTTATACCTTATGTGAGTGTG Template switch alignment (log-probability: -32.1) CACATTCcCATAAGGTATAAAAAGTAAACTCCTCTTGATG|TCTTTCTAGCAAGCATCAAGAGGAGTTTACTTTTTATACCTTATGgGA|ATGTG CACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATG|TCTTTCTAGCAAGCATCAAGAGGAGTTTACTTTTTATACCTTATGTGA|ATGTG Chimp > Gorilla --------------- chr13:30554558-30554570 Template switch process: F1: L CTCACATTCACATAAGGTATAAAAAGTAAACTCCTCTTGATG 1 F3: 4 CATCAAGAGGAGTTTACTTTTTATACCTTATGTGAGTGTG R RF: CTCACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAAGCATCAAGAGGAGTTTACTTTTTATACCTTATGGGAATGTG RR: GAGTGTAAGGGTATTCCATATTTTTCATTTGAGGAGAACTACAGAAAGATCGTTCGTAGTTCTCCTCAAATGAAAAATATGGAATACCCTTACAC F2: 3 AGAAAGATCGTTC 2 Unidirectional alignment (log-probability: -49.9) CACATTCaCATAAGGTATAAAAAGTAAACTCCTCTTGATG-CTTgCTAGaAAGaCATCAAGAGGAGTTTACTTTTTATACCTTATGtGAgTGTG CACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATGTCTTTCTAGCAAG-CATCAAGAGGAGTTTACTTTTTATACCTTATGGGAATGTG Template switch alignment (log-probability: -34) CACATTCaCATAAGGTATAAAAAGTAAACTCCTCTTGATG|CTTGCTAGAAAGA|CATCAAGAGGAGTTTACTTTTTATACCTTATGtGAgTGTG CACATTCCCATAAGGTATAAAAAGTAAACTCCTCTTGATG|CTTGCTAGAAAGA|CATCAAGAGGAGTTTACTTTTTATACCTTATGGGAATGTG ========= Event 875 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CACAGAAAACAATGAAAATTAGGCACGAGATGCCT-AAATTTCCATTCTCACAGCTG ↓ 3 1 2 4 ↑ 3 1 2 4 Chimp: CACAGAAAACAATGAAAATTAGGCATCTCGTGCCTAAAATTTCCATTCTCACAGCTG Gorilla: cacagaaaacaatgaaaattaggcatctcgtgcctaaaattTCCATTCTCACAGCTG Human: CACAGAAAACAATGAAAATTAGGCACGAGATGCCT-AAATTTCCATTCTCACAGCTG Cluster: [ ] Orangutan: CACAGAAAACAATGAAAATTAGGCATCTCGTGCCTAAAATTTCCATTCTCACAGCTG Chimp > Human ------------- chr13:63780186-63780195 Template switch process: F1: L CTGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA 1 F3: 4 AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC R RF: CTGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCATCTCGTGCCTAAAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC RR: GACGTTACGTTTTGTCGTGTCTTTTGTTACTTTTAATCCGTAGAGCACGGATTTTAAAGGTAAGAGTGTCGACTGTATTAGTAATAGGTAGG F2: 3 TCCGTAGAGC 2 Unidirectional alignment (log-probability: -34.6) TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCAcgagatgccT----------AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA---------TCTCGTGCCTAAAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC Template switch alignment (log-probability: -16.5) TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA|CGAGATGCCT|AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA|CGAGATGCCT|AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC Human > Chimp ------------- chr13:64821658-64821668 Template switch process: F1: L CTGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA 1 F3: 4 AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC R RF: CTGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCACGAGATGCCTAAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC RR: GACGTTACGTTTTGTCGTGTCTTTTGTTACTTTTAATCCGTGCTCTACGGATTTAAAGGTAAGAGTGTCGACTGTATTAGTAATAGGTAGG F2: 3 ATCCGTGCTCT 2 Unidirectional alignment (log-probability: -36) TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA---------TctcgtgcctaAAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCACGAGATGCCT----------AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC Template switch alignment (log-probability: -16.6) TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA|TCTCGTGCCTA|AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC TGCAATGCAAAACAGCACAGAAAACAATGAAAATTAGGCA|TCTCGTGCCTA|AAATTTCCATTCTCACAGCTGACATAATCATTATCCATCC ========= Event 876 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGAAGCAATTTAGCAAAGTTGGCTGCC---------TAAGCAGCCAAGGGTCCTGTGGTGCCTGTTAA Chimp: TGAAGCAATTTAGCAAAGTTGGCTGCC---------TAAGCAGCCAAGGGTCCTGTGGTGCCTGTTAA ↑ 3 1 42 Gorilla: TGAAGCAATTTAGCAAAGTTGGCTGCT------------------TAGGGTCCTGTGCTGCCTGTTAA ↓ 3 1 42 Human: TGAAGCAATTTAGCAAAGTTGGCTGCC---------TAAGCAGCCAAGGGTCCTGTGGTGCCTGTTAA Cluster: [ ] Orangutan: TGAAGCAATTTAGCAAAGTTGGCTGCCTAAGCAGCC---------AAGGGTCCTGTGGTGCCTGTTAA Gorilla > Human --------------- chr13:63849304-63849314 Template switch process: F1: L ACATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGC 1 F3: 4 AGGGTCCTGTGGTGCCTGTTAAAATCCAGCAAAAGCAGGG R RF: ACATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGCTTAGGGTCCTGTGCTGCCTGTTAAAATCCAGCAAAAGCAGGG RR: TGTAGTACCTTTGGTACTTCGTTAAATCGTTTCAACCGACGAATCCCAGGACACGACGGACAATTTTAGGTCGTTTTCGTCCC F2: 3 ACCGACGAATC 2 Unidirectional alignment (log-probability: -34.9) CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGCcTaagcagccaAGGGTCCTGTGgTGCCTGTTAAAATCCAGCAAAAGCAGGG CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGCTT---------AGGGTCCTGTGCTGCCTGTTAAAATCCAGCAAAAGCAGGG Template switch alignment (log-probability: -22.6) CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGC|CTAAGCAGCCA|AGGGTCCTGTGgTGCCTGTTAAAATCCAGCAAAAGCAGGG CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGC|CTAAGCAGCCA|AGGGTCCTGTGCTGCCTGTTAAAATCCAGCAAAAGCAGGG Gorilla > Chimp --------------- chr13:64897418-64897428 Template switch process: F1: L ACATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGC 1 F3: 4 AGGGTCCTGTGGTGCCTGTTAAAATCCAGCAAAAGCAGGG R RF: ACATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGCTTAGGGTCCTGTGCTGCCTGTTAAAATCCAGCAAAAGCAGGG RR: TGTAGTACCTTTGGTACTTCGTTAAATCGTTTCAACCGACGAATCCCAGGACACGACGGACAATTTTAGGTCGTTTTCGTCCC F2: 3 ACCGACGAATC 2 Unidirectional alignment (log-probability: -34.9) CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGCcTaagcagccaAGGGTCCTGTGgTGCCTGTTAAAATCCAGCAAAAGCAGGG CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGCTT---------AGGGTCCTGTGCTGCCTGTTAAAATCCAGCAAAAGCAGGG Template switch alignment (log-probability: -22.6) CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGC|CTAAGCAGCCA|AGGGTCCTGTGgTGCCTGTTAAAATCCAGCAAAAGCAGGG CATCATGGAAACCATGAAGCAATTTAGCAAAGTTGGCTGC|CTAAGCAGCCA|AGGGTCCTGTGCTGCCTGTTAAAATCCAGCAAAAGCAGGG ========= Event 877 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: acacacacacTCCCAAACTAATAAAATACTTAAACTTAAACAACTAACTCAGCAGAA--------------------------------------------------------------------------------------TTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTACTAAAATGCAGCTC ↓ 3 4 2 1 Chimp: acatacacacTCCCAAACTAATAAAATACTTAAACTTAAACAACTAACTCAGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTCATGATGATAAATTCTGCTGAGTTAGTTGTTTAAGTTTAAGTATTTTATTAGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTACTAAAATGCAGCTC ↑ 3 4 2 1 Gorilla: acacacacacTCCCAAACTAATAAAACACTTAAACTTAAACAACTAACTCAGCAGAA--------------------------------------------------------------------------------------TTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTACTAAAATGCAGCTC Human: acacacacacTCCCAAACTAATAAAATACTTAAACTTAAACAACTAACTCAGCAGAA--------------------------------------------------------------------------------------TTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTACTAAAATGCAGCTC Cluster: [ ] Orangutan: acacacacacTCCCAAACTAATAAAACACTT------AAACAACTAACTCAGCAGAA--------------------------------------------------------------------------------------TTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTACTAAAATGCAGCTC Human > Chimp ------------- chr13:64452053-64452101 Template switch process: F1: L ACTAATAAAATACTTAAACTTAAACAACTAACTCAGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTC 1 F3: 4 AGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTAC R RF: ACTAATAAAATACTTAAACTTAAACAACTAACTCAGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTAC RR: TGATTATTTTATGAATTTGAATTTGTTGATTGAGTCGTCTTAAATAGTAGTAATTAAGATTTCGTAAACCTAAGAGTCATG F2: 3 TTATTTTATGAATTTGAATTTGTTGATTGAGTCGTCTTAAATAGTAGTA 2 Unidirectional alignment (log-probability: -135) AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTcatgatgataaattctgctgagttagttgtttaagtttaagtattttattagaatttatcatcattaattctaaagcatttggattCTCA AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATT--------------------------------------------------------------------------------------CTCA Template switch alignment (log-probability: -21.9) AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTC|ATGATGATAAATTCTGCTGAGTTAGTTGTTTAAGTTTAAGTATTTTATT|AGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCA AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTC|ATGATGATAAATTCTGCTGAGTTAGTTGTTTAAGTTTAAGTATTTTATT|AGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCA Gorilla > Chimp --------------- chr13:64452053-64452101 Template switch process: F1: L ACTAATAAAATACTTAAACTTAAACAACTAACTCAGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTC 1 F3: 4 AGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTAC R RF: ACTAATAAAACACTTAAACTTAAACAACTAACTCAGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCAGTAC RR: TGATTATTTTGTGAATTTGAATTTGTTGATTGAGTCGTCTTAAATAGTAGTAATTAAGATTTCGTAAACCTAAGAGTCATG F2: 3 TTATTTTATGAATTTGAATTTGTTGATTGAGTCGTCTTAAATAGTAGTA 2 Unidirectional alignment (log-probability: -140) AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTcatgatgataaattctgctgagttagttgtttaagtttaagtattttattagaatttatcatcattaattctaaagcatttggattCTCA AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATT--------------------------------------------------------------------------------------CTCA Template switch alignment (log-probability: -33.7) AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTC|ATGATGATAAATTCTGCTGAGTTAGTTGTTTAAGTTTAAGTaTTTTATT|AGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCA AGCAGAATTTATCATCATTAATTCTAAAGCATTTGGATTC|ATGATGATAAATTCTGCTGAGTTAGTTGTTTAAGTTTAAGTGTTTTATT|AGAATTTATCATCATTAATTCTAAAGCATTTGGATTCTCA ========= Event 878 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCAAATGCAAGCAAAGAAAGTGAGTACTTTCATCTCTATGCTATTAATG ↑ 3 1 2 4 Chimp: CTCAAATGCAAGCAAAGAAAGTACTCA-CTTCATCTCTATGCTATTCATG Gorilla: CTCAAATGCAAGCAGAGAAAGTATTCA-CTTCATCTCTATGCTATTAATG Human: CTCAAATGCAAGCAAAGAAAGTGAGTACTTTCATCTCTATGCTATTAATG Cluster: [ ] Orangutan: CTCAAACGCAAGCAGAGAAGGTATTCA-CTTCATCTCTATGCTATTAATG Chimp > Human ------------- chr13:51919873-51919879 Template switch process: F1: L TGCTTTTCTGACTCCCCCACTCAAATGCAAGCAAAGAAAGT 1 F3: 4 TTCATCTCTATGCTATTAATGCATCATGCCTAGCTCATAG R RF: TGCTTTTCTGACTCCCCCACTCAAATGCAAGCAAAGAAAGTACTCACTTCATCTCTATGCTATTCATGCATCATGCCTAGCTCATAG RR: ACGAAAAGACTGAGGGGGTGAGTTTACGTTCGTTTCTTTCATGAGTGAAGTAGAGATACGATAAGTACGTAGTACGGATCGAGTATC F2: 3 TCATGAG 2 Unidirectional alignment (log-probability: -33.1) GCTTTTCTGACTCCCCCACTCAAATGCAAGCAAAGAAagtgAGTACT---TTCATCTCTATGCTATTaATGCATCATGCCTAGCTCATAG GCTTTTCTGACTCCCCCACTCAAATGCAAGCAAAGAA----AGTACTCACTTCATCTCTATGCTATTCATGCATCATGCCTAGCTCATAG Template switch alignment (log-probability: -22.1) GCTTTTCTGACTCCCCCACTCAAATGCAAGCAAAGAAAGT|GAGTACT|TTCATCTCTATGCTATTaATGCATCATGCCTAGCTCATAG GCTTTTCTGACTCCCCCACTCAAATGCAAGCAAAGAAAGT|GAGTACT|TTCATCTCTATGCTATTCATGCATCATGCCTAGCTCATAG ========= Event 879 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGTTAAGATGAGTGGTCGCTATA---TAAAGGCAAATGAAAAACGTGTCCTTTACCTT ↓ 1 3 4 2 Chimp: AAGTTAAGATGAGTGGTCGCTCATTTGCCTTTGCAAATGAAAAACGTGTCCTTTACCTT ↑ 1 3 4 2 Gorilla: AAGTTAAGATGAGTGGTCGCTATA---TAAAGGCAAATGAAAAACGTGTCCTTTACCTT Human: AAGTTAAGATGAGTGGTCGCTATA---TAAAGGCAAATGAAAAACGTGTCCTTTACCTT Cluster: [ ] Orangutan: AAGTTAAGATGAGTGGTCGCTATA---TAAAGGCAAATGAAAAACATGTCCTTTACCTT Human > Chimp ------------- chr13:36936825-36936835 Template switch process: F1: L AAGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT 1 F3: 4 GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC R RF: AAGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCTATATAAAGGCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC RR: TTCTAAACCTTATCCCCAACTTCAATTCTACTCACCAGCGATATATTTCCGTTTACTTTTTGCACAGGAAATGGAAGAGTGTGTGTGGG F2: 3 TTTCCGTTTAC 2 Unidirectional alignment (log-probability: -37.4) AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT--------catttgcctttGCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCTATATAAAG-----------GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC Template switch alignment (log-probability: -16.6) AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT|CATTTGCCTTT|GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT|CATTTGCCTTT|GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC Gorilla > Chimp --------------- chr13:36936825-36936835 Template switch process: F1: L AAGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT 1 F3: 4 GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCC R RF: AAGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCTATATAAAGGCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCT RR: TTCTAAACCTTATCCCCAACTTCAATTCTACTCACCAGCGATATATTTCCGTTTACTTTTTGCACAGGAAATGGAAGAGTGTGTGTGGA F2: 3 TTTCCGTTTAC 2 Unidirectional alignment (log-probability: -42.4) AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT--------catttgcctttGCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCc AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCTATATAAAG-----------GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCT Template switch alignment (log-probability: -22.6) AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT|CATTTGCCTTT|GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCc AGATTTGGAATAGGGGTTGAAGTTAAGATGAGTGGTCGCT|CATTTGCCTTT|GCAAATGAAAAACGTGTCCTTTACCTTCTCACACACACCT ========= Event 880 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGTTACAGCTATTGCTTTTACCCCACTTTCCCC----------ACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTT Chimp: TAGTTACAGCTATTGCTTTTATCCCACTTTCCCC----------ACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTT ↓ 1 4 3 2 Gorilla: TAGTTACAGCTATTGCTTTTACCCCACTTAGCCC--------------------TAATAAGGGCTAATAAACAGAAGTTTCTGTT ↑ 1 4 3 2 Human: TAGTTACAGCTATTGCTTTTACCCCACTTTCCCC----------ACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTT Cluster: [ ] Orangutan: GAGTTACAGCTATTGCTTTTACCCCACTTTCCCCGCAAAAACAA----------AAATAAGGGCTAATAAACAGAAGGTTCTGTT Human > Gorilla --------------- chr13:33602156-33602161 Template switch process: F1: L TAGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTT 1 F3: 4 AATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT R RF: TAGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTTTCCCCACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT RR: ATCTTTTATTAAATCAATGTCGATAACGAAAATGGGGTGAAAGGGGTGTTTTTGTTTTTATTCCCGATTATTTGTCTTCAAAGACAAAGATACCGAA F2: 3 TCCCGA 2 Unidirectional alignment (log-probability: -28) AGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTTagCCC----------tAATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT AGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTTTCCCCACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT Template switch alignment (log-probability: -16.5) AGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTT|AGCCCT|AATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT AGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTT|AGCCCT|AATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT Chimp > Gorilla --------------- chr13:33602156-33602161 Template switch process: F1: L GAAAATTTTAGAAAATAATTTAGTTACAGCTATTGCTTTTACCCCACTT 1 F3: 4 AATAAGGGCTAATAAACAGAAGTTTCTGTTTCTATGGCTT R RF: GAAAATTTTAGAAAATAATTTAGTTACAGCTATTGCTTTTATCCCACTTTCCCCACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTTTCTCTGGCTT RR: CTTTTAAAATCTTTTATTAAATCAATGTCGATAACGAAAATAGGGTGAAAGGGGTGTTTTTGTTTTTATTCCCGATTATTTGTCTTCAAAGACAAAGAGACCGAA F2: 3 TCCCGA 2 Unidirectional alignment (log-probability: -39.2) AGAAAATAATTTAGTTACAGCTATTGCTTTTAcCCCACTTagCCC----------tAATAAGGGCTAATAAACAGAAGTTTCTGTTTCTaTGGCTT AGAAAATAATTTAGTTACAGCTATTGCTTTTATCCCACTTTCCCCACAAAAACAAAAATAAGGGCTAATAAACAGAAGTTTCTGTTTCTCTGGCTT Template switch alignment (log-probability: -27.7) AGAAAATAATTTAGTTACAGCTATTGCTTTTAcCCCACTT|AGCCCT|AATAAGGGCTAATAAACAGAAGTTTCTGTTTCTaTGGCTT AGAAAATAATTTAGTTACAGCTATTGCTTTTATCCCACTT|AGCCCT|AATAAGGGCTAATAAACAGAAGTTTCTGTTTCTCTGGCTT ========= Event 881 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTACTAAGTGGTAACCATAGTTCATTAAAGGCATGGAGAAACTTCAGGATATCGTTTTAAAAGACAAAACAACTTTCTAGTCAGTGACAGGTGAGGTAGGTGTAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAGTGAACATGAATTATGAATGACAGGGTAAACAAGATCAAACCCTT Chimp: TTACTAAGTGGTAACCATAGTTCATTAAAGGCATGGAGAAACTTCAGGATATCGTTTTAAAAGACAAAACAACTTTCTAGTCAGTGACAGGTGAGGTAGGTGTAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAGTAAACATGAATTATGAATGACAGGGTACACAAGATCAAACCCTT Gorilla: TTACTAAGTGGTAACCATAGTTCATTAAAGGCATGGAGAAACTTCAGGATATCGTTTTAAAAGACAAAACAACTTTCTAGTCAGTGACAGGTGAAGTAGGTGTAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCA------------------------GGTAAACAAGATCAAACCCTT ↓ 3 2 4 1 Human: TTACTAAGTGGTAACCATAGTTCATTAAAGGCATGGAGAAACTTCAGGATATCGTTTTAAAAGACAAAACAACTTTCTAGTCAGTGACAGGTGAGGTAGGTGTAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAGTGAACATGAATTATGAATGACAGGGTAAACAAGATCAAACCCTT Cluster: [ ] Orangutan: TTACTGAGTGGTAACCATAGTTCATTAAAGGCATGGAGAAACTTCAGGATATCGTTTTAAAAGACAAAACAACTTTCTAGTCAGTGACAGGTGAGGTAGGTGTAGATTCCTTGGTGTCAAAAAGAATTATGAATGACAGCA------------------------GGTAAACAAGATCAAACCCTT Gorilla > Human --------------- chr13:61660359-61660363 Template switch process: F1: L TGTAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAG 1 F3: 4 ATGAATTATGAATGACAG--GGTAAACAAGATCAAACCCTTTACAGATTACACCTTCCTG R RF: GTTCATTAAAGGCATGGAGAAACTTCAGGATATCGTTTTAAAAGACAAAACAACTTTCTAGTCAGTGACAGGTGAAGTAGGTGTAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAGGTAAACAAGATCAAACCCTTTACAGATTACACCTTCCTG RR: CAAGTAATTTCCGTACCTCTTTGAAGTCCTATAGCAAAATTTTCTGTTTTGTTGAAAGATCAGTCACTGTCCACTTCATCCACATCTAAGGAACCACAGTTTTCCTTAATACTTACTGTCGTCCATTTGTTCTAGTTTGGGAAATGTCTAATGTGGAAGGAC F2: 3 CAAGT 2 Unidirectional alignment (log-probability: -45.4) TAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAgtgaacatgaattatgaatgacagGGTAAACAAGATCAAACCCTTT TAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCA------------------------GGTAAACAAGATCAAACCCTTT Template switch alignment (log-probability: -32.2) TAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAG|TGAAC|AtGAATTATGAATGACAG--GGTAAACAAGATCAAACCCTTT TAGATTCCTTGGTGTCAAAAGGAATTATGAATGACAGCAG|TGAAC|AGGAATTATGAATGACAGCAGGTAAACAAGATCAAACCCTTT ========= Event 882 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGAATAAAATGAGAATATCTCTTAATT------------TATTAGTGACTTCAGTGAGTTGTATAATGGCCCTG ↓ 134 2 Chimp: CAGAATAAAATGAGAATATCTCTTAATTTTCTGAAGTCACTAATAGTGACTTCAGTGAGTTGTATAATGGCCCTG ↑ 134 2 Gorilla: CAGAATAAAATGAGAATATCTGTTAATT------------TATTAGTGACTTCAGTGAGTTGTATAATGGCCCTG Human: CAGAATAAAATGAGAATATCTCTTAATT------------TATTAGTGACTTCAGTGAGTTGTATAATGGCCCTG Cluster: [ ] Orangutan: cagaaTAAAATGAGAATATCTTTTAATT------------TATTAGTGACTTCAGTGAGTTGTATAATGGCCCTG Human > Chimp ------------- chr13:61813396-61813408 Template switch process: F1: L ATTCTTTTATAATCAGAATAAAATGAGAATATCTCTTAATTTT 1 F3: 4 TAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT R RF: ATTCTTTTATAATCAGAATAAAATGAGAATATCTCTTAATTTATTAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT RR: TAAGAAAATATTAGTCTTATTTTACTCTTATAGAGAATTAAATAATCACTGAAGTCACTCAACATATTACCGGGACTTTTCTAA F2: 3 AATCACTGAAGTC 2 Unidirectional alignment (log-probability: -34.2) CTTTTATAATCAGAATAAAATGAGAATATCTCTTAATTttctgaagtcacTAaTAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT CTTTTATAATCAGAATAAAATGAGAATATCTCTTAATT------------TATTAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT Template switch alignment (log-probability: -22.9) CTTTTATAATCAGAATAAAATGAGAATATCTCTTAATTTt|CTGAAGTCACTAA|TAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT CTTTTATAATCAGAATAAAATGAGAATATCTCTTAATTTA|CTGAAGTCACTAA|TAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT Gorilla > Chimp --------------- chr13:61813396-61813408 Template switch process: F1: L ATAGGTGATTCTTTTATAATCAGAATAAAATGAGAATATCTCTTAATTTT 1 F3: 4 TAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT R RF: ATAGGCGATTCTTTTATAATCAGAATAAAATGAGAATATCTGTTAATTTATTAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT RR: TATCCGCTAAGAAAATATTAGTCTTATTTTACTCTTATAGACAATTAAATAATCACTGAAGTCACTCAACATATTACCGGGACTTTTCTAA F2: 3 AATCACTGAAGTC 2 Unidirectional alignment (log-probability: -44.8) CTTTTATAATCAGAATAAAATGAGAATATCTcTTAATTttctgaagtcacTAaTAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT CTTTTATAATCAGAATAAAATGAGAATATCTGTTAATT------------TATTAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT Template switch alignment (log-probability: -34.2) CTTTTATAATCAGAATAAAATGAGAATATCTcTTAATTTt|CTGAAGTCACTAA|TAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT CTTTTATAATCAGAATAAAATGAGAATATCTGTTAATTTA|CTGAAGTCACTAA|TAGTGACTTCAGTGAGTTGTATAATGGCCCTGAAAAGATT ========= Event 883 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATCTCACATTCGTTTGACATGGTCACTAAC--------ATGTTTTgtggtggtggtggtggtggtggtggtggtggtggtgatggtTTTCATTAAGAAGATTAAAAACTATGGCAAAGGCTGATTGTACTGGTACATAACACAAGTGCAATTGTATAAAAGTGACCATTCAATGAAGACTAAAGCA Chimp: ATCTCACATTCGTTTGACATGGTCACTAGC--------ATGTTTTgtggtggtggtg---------gtggtggtggtggtgATAGTTTTCATTAAGAAGAGTAAAAACTATGGCAAAGGCTGATTGTACTGGTACATAACACAAGGGCAATTGTATAAAAGTGACCATTCGATGAAGACTAAAGCA Gorilla: ATCTCACATTCGTTTGACATTGTCACTAACATGTTAACATGTTTTgtggtggtggtg---------gtggtggtggtggtgatggtTTTCATTAAGAAGAGTAAAAACTATGGCAAAGGCTGATTGTAGTGGTACATAACACAAGTGCAATTGTATGAAAGTGACCATTCAATGAAGACTAAAGCA ↓ 1 4 3 2 Human: ATCTCACATTCGTTTGACATGGTCACTAAC--------ATGTTTTgtggtggtggtggtggtggtggtggtggtggtggtgatggtTTTCATTAAGAAGATTAAAAACTATGGCAAAGGCTGATTGTACTGGTACATAACACAAGTGCAATTGTATAAAAGTGACCATTCAATGAAGACTAAAGCA Cluster: [ ] Orangutan: ATCTCACATTCGTTTGACATTGTCACTAAC--------ATGTTTTgtggtggtgg---------------tggtggtggtgatggtTTTCATTAAGCAGAGTAAAAACTATGGCAAAGGCTGATTGTACTGGTACATAACACAAGTGCAATTATATAAAAGTGACCATTCAATGAAGACTAAAGCA Gorilla > Human --------------- chr13:60543992-60543996 Template switch process: F1: L TTCATAATTTGATCTCACATTCGTTTGACATGGTCACTAACATGTT 1 F3: 4 GTGGTGGTGGTGGTGGTGGTGGTGGTGGTG R RF: TTCATAATTTGATCTCACATTCGTTTGACATTGTCACTAACATGTTAACATGTTTTGTGGTGGTGGTGGTGGTGGTGGTGGTGATGGTTTTCATTAAGAAGAGTAAAAACTATGGCAAAGGCTGATTGTAGTGGTACATAACACAA RR: AAGTATTAAACTAGAGTGTAAGCAAACTGTAACAGTGATTGTACAATTGTACAAAACACCACCACCACCACCACCACCACCACTACCAAAAGTAATTCTTCTCATTTTTGATACCGTTTCCGACTAACATCACCATGTATTGTGTT F2: 3 GTGTT 2 Unidirectional alignment (log-probability: -36.4) ATTTGATCTCACATTCGTTTGACATgGTCAC--------TAACATGTTTTGTGGTGGTGGTGGTGGTGGTGGTGgtggtggtg ATTTGATCTCACATTCGTTTGACATTGTCACTAACATGTTAACATGTTTTGTGGTGGTGGTGGTGGTGGTGGTG--------- Template switch alignment (log-probability: -27.3) ATTTGATCTCACATTCGTTTGACATgGTCACTAACATGTT|TTGTG|GTGGTGGTGGTGGTGGTGGTGGTGGTGgTG ATTTGATCTCACATTCGTTTGACATTGTCACTAACATGTT|TTGTG|GTGGTGGTGGTGGTGGTGGTGGTGGTGATG ========= Event 884 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: TATATGCaaatttaagaataattcattatatatttgtttattaaaatttGACTCAAAT Chimp: TATATGCAAATTTAAGAATAATTCATTATATATTTGTTTATTAAAATTGGACTCAAAT ↓ 13 24 ↑ 13 24 Gorilla: TATATGCAAATTTAAGAATAAACAAATATATAATGAATTATTAAAATTTAACTCAAAT Human: TATATGCaaatttaagaataattcattatatatttgtttattaaaatttGACTCAAAT Cluster: [ ] Orangutan: TATATGCAAATTTAAGAATAAACATATATATAATGAATTATTAAAATTTGACT----- Gorilla > Chimp --------------- chr13:61615083-61615098 Template switch process: F1: L CTAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA 1 F3: 4 TTATTAAAATTGGACTCAAATCAAGATATGTATAATAGTA R RF: CTAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAAACAAATATATAATGAATTATTAAAATTTAACTCAAATCAAGATATGTATAATAGTA RR: GATCCATTTATAAGTCACTTATATACGTTTAAATTCTTATTTGTTTATATATTACTTAATAATTTTAAATTGAGTTTAGTTCTATACATATTATCAT F2: 3 TGTTTATATATTACTT 2 Unidirectional alignment (log-probability: -55.5) TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATA----------------AttcattatatatttgtTTATTAAAATTggACTCAAATCAAGATATGTATAATAGTA TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAAACAAATATATAATGAA----------------TTATTAAAATTTAACTCAAATCAAGATATGTATAATAGTA Template switch alignment (log-probability: -28.8) TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA|TTCATTATATATTTGT|TTATTAAAATTggACTCAAATCAAGATATGTATAATAGTA TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA|TTCATTATATATTTGT|TTATTAAAATTTAACTCAAATCAAGATATGTATAATAGTA Chimp > Gorilla --------------- chr13:61406325-61406340 Template switch process: F1: L CTAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA 1 F3: 4 TTATTAAAATTTAACTCAAATCAAGATATGTATAATAGTA R RF: CTAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAATTCATTATATATTTGTTTATTAAAATTGGACTCAAATCAAGATATGTATAATAGTA RR: GATCCATTTATAAGTCACTTATATACGTTTAAATTCTTATTAAGTAATATATAAACAAATAATTTTAACCTGAGTTTAGTTCTATACATATTATCAT F2: 3 AAGTAATATATAAACA 2 Unidirectional alignment (log-probability: -55.5) TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA----------------acaaatatataatgaaTTATTAAAATTtaACTCAAATCAAGATATGTATAATAGTA TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAATTCATTATATATTTGT----------------TTATTAAAATTGGACTCAAATCAAGATATGTATAATAGTA Template switch alignment (log-probability: -28.8) TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA|ACAAATATATAATGAA|TTATTAAAATTtaACTCAAATCAAGATATGTATAATAGTA TAGGTAAATATTCAGTGAATATATGCAAATTTAAGAATAA|ACAAATATATAATGAA|TTATTAAAATTGGACTCAAATCAAGATATGTATAATAGTA ========= Event 885 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATAA-ATAAACCCAACAGACC----TCAGTCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGTTTTTTCTGCCTCCTAATAGTCCTTAAAATGAACTGAGGGACTCACATAAAATGCCCT Chimp: A-----ATAAACCCAACAGACT--GAGTATTCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGTTTTTTCTGCCTCCTAATAGTCCTTAAAATGAACTGAGGGACTCACATAAAATGCCCT Gorilla: AATAA-ATAAACCCAACAGACTGA--GTATTCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGTTTTTTCTGCCTCCTAATAGTCCTTAAAATGAACTGAGGGACTCACACAAAATGCCCT ↓ 1 4 3 2 Human: AATAA-ATAAACCCAACAGACC----TCAGTCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGTTTTTTCTGCCTCCTAATAGTCCTTAAAATGAACTGAGGGACTCACATAAAATGCCCT Cluster: [ ] Orangutan: AATAAATTAAACCCAACAGACTGA--GTATTAACCAAAAGGATGACCATTTCTGTCAATTGGCAGATTGCT-TTTCTGCCTCCTAATAGTCCTTAAAATGAACTGAAGGACACACATAAAGTGCCCT Gorilla > Human --------------- chr1:35554206-35554210 Template switch process: F1: L CTCTGGTTCCAAAACAAAACAAATAAATAAACCCAACAGAC 1 F3: 4 TCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGT R RF: CTCTGGTTCCAAAACAAAACAAATAAATAAACCCAACAGACTGAGTATTCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGTTTTTTCTGCCTCCTAATAGTCCTTAAAATGAACTGAG RR: GAGACCAAGGTTTTGTTTTGTTTATTTATTTGGGTTGTCTGACTCATAAGTGGTTTTCCTACTGGTAAAGACAGTTAATCGTCTAACAAAAAAGACGGAGGATTATCAGGAATTTTACTTGACTC F2: 3 GACTC 2 Unidirectional alignment (log-probability: -27.8) TCTGGTTCCAAAACAAAACAAATAAATAAACCCAACAGAcCTcAG---TCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGT TCTGGTTCCAAAACAAAACAAATAAATAAACCCAACAGA-CTGAGTATTCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGT Template switch alignment (log-probability: -16.4) TCTGGTTCCAAAACAAAACAAATAAATAAACCCAACAGAC|CTCAG|TCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGT TCTGGTTCCAAAACAAAACAAATAAATAAACCCAACAGAC|CTCAG|TCACCAAAAGGATGACCATTTCTGTCAATTAGCAGATTGT ========= Event 886 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ttgCCTACATTTTAATGAACCAGTTTATGTAAGATTCAT---------T-------ATATACTCAGTGGTAGTAAATGTC Chimp: ttgccTACATTTTAATGAACCAGTTTATGTAAGATTCAT---------T-------ATATACTCAGTGGTAGTAAATGTC ↓ 3 4 2 1 Gorilla: ttgccTACATTTGAATGAACCAGTTTATGTAAGATTCATAAACTGGTTTATGTAAGATTCACTCAGTGGTAGTAAATGTC ↑ 3 4 2 1 Human: ttgCCTACATTTTAATGAACCAGTTTATGTAAGATTCAT---------T-------ATATACTCAGTGGTAGTAAATGTC Cluster: [ ] Orangutan: TT-GCTACATTTTAATGAACCAGTTTATGTAAGATTCGT---------T-------ATATACTCAGTGGTAGTAAATGTC Human > Gorilla --------------- chr1:35926736-35926742 Template switch process: F1: L AATTGCCTACATTTGAATGAACCAGTTTATGTAAGATTCAT 1 F3: 4 TTTATGTAAGATTC-------ACTCAGTGGTAGTAAATGTCCTCCCAACCAAACCACCACA R RF: AATTGCCTACATTTTAATGAACCAGTTTATGTAAGATTCATTATATACTCAGTGGTAGTAAATGTCCTCCCAACCAAACCACCACA RR: TTAACGGATGTAAAATTACTTGGTCAAATACATTCTAAGTAATATATGAGTCACCATCATTTACAGGAGGGTTGGTTTGGTGGTGT F2: 3 GGTCAAA 2 Unidirectional alignment (log-probability: -54.7) ATTGCCTACATTTgAATGAACCAGTTTATGTAAGATTCAtaaactggtTTATgTaagattcACTCAGTGGTAGTAAATGTCCTCCCA ATTGCCTACATTTTAATGAACCAGTTTATGTAAGATTCA---------TTATAT-------ACTCAGTGGTAGTAAATGTCCTCCCA Template switch alignment (log-probability: -32.6) ATTGCCTACATTTgAATGAACCAGTTTATGTAAGATTCAT|AAACTGG|TTTATGTAAGATTC-------ACTCAGTGGTAGTAAATGTCCTCCCA ATTGCCTACATTTTAATGAACCAGTTTATGTAAGATTCAT|AAACTGG|TTTATGTAAGATTCATTATATACTCAGTGGTAGTAAATGTCCTCCCA Chimp > Gorilla --------------- chr1:35926736-35926742 Template switch process: F1: L AATTGCCTACATTTGAATGAACCAGTTTATGTAAGATTCAT 1 F3: 4 TTTATGTAAGATTC-------ACTCAGTGGTAGTAAATGTCCTCCCAACCAAACCACCACA R RF: AATTGCCTACATTTTAATGAACCAGTTTATGTAAGATTCATTATATACTCAGTGGTAGTAAATGTCCTCCCAACCAAACCACCACA RR: TTAACGGATGTAAAATTACTTGGTCAAATACATTCTAAGTAATATATGAGTCACCATCATTTACAGGAGGGTTGGTTTGGTGGTGT F2: 3 GGTCAAA 2 Unidirectional alignment (log-probability: -54.7) ATTGCCTACATTTgAATGAACCAGTTTATGTAAGATTCAtaaactggtTTATgTaagattcACTCAGTGGTAGTAAATGTCCTCCCA ATTGCCTACATTTTAATGAACCAGTTTATGTAAGATTCA---------TTATAT-------ACTCAGTGGTAGTAAATGTCCTCCCA Template switch alignment (log-probability: -32.6) ATTGCCTACATTTgAATGAACCAGTTTATGTAAGATTCAT|AAACTGG|TTTATGTAAGATTC-------ACTCAGTGGTAGTAAATGTCCTCCCA ATTGCCTACATTTTAATGAACCAGTTTATGTAAGATTCAT|AAACTGG|TTTATGTAAGATTCATTATATACTCAGTGGTAGTAAATGTCCTCCCA ========= Event 887 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTAAGGAGAGAAGTGGTTATC------TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTC Chimp: TGTAAGGAGAGAAGTGGTTATCTATAGATGTGCTTCATCTATAGTCTGTAAAAGCTAAGAAT-T ↑ 1 4 3 2 Gorilla: TGTAAGGAGAGAAGTGGTTATT------TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTC Human: TGTAAGGAGAGAAGTGGTTATC------TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTC Cluster: [ ] Orangutan: TGGAAGGGGAGAAGTGGTTATC------TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTC Gorilla > Chimp --------------- chr1:34929132-34929138 Template switch process: F1: L ACTGACAGTGAAGAATGGAATGTAAGGAGAGAAGTGGTTAT 1 F3: 4 TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTCAAA R RF: ACCGACAGTGAAGAATGGAATGTAAGGAGAGAAGTGGTTATTTGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTCCAA RR: TGGCTGTCACTTCTTACCTTACATTCCTCTCTTCACCAATAAACACGAAGTAGATATCAGACATTTTCGATTCTTAAGGTT F2: 3 AGATATC 2 Unidirectional alignment (log-probability: -40.3) CtGACAGTGAAGAATGGAATGTAAGGAGAGAAGTGGTTATctatagaTGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATT-CAAA CCGACAGTGAAGAATGGAATGTAAGGAGAGAAGTGGTTATT------TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTCCAAA Template switch alignment (log-probability: -27.6) CtGACAGTGAAGAATGGAATGTAAGGAGAGAAGTGGTTAT|CTATAGA|TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTCaAA CCGACAGTGAAGAATGGAATGTAAGGAGAGAAGTGGTTAT|CTATAGA|TGTGCTTCATCTATAGTCTGTAAAAGCTAAGAATTCCAA ========= Event 888 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAGATGCTAGGCATCTGCTT-------------------------TTTAGGGTTGCCTAAAAGGCAACCCTTTCTCAGTGATAAATTAACTCCTAAG Chimp: ATAGATGCTAGGCATCTGCTT--------------------------------------------------TTTCTCGGTGATAAATTAACTCCTAAG Gorilla: ATAGATGCTAGGCATCTGCTTTTTAGGGTTGC---------------------------------------CTTTTAGGTGATAAATTAACTCCTAAG ↓ 3 4 2 Human: ATAGATGCTAGGCATCTGCTT-------------------------TTTAGGGTTGCCTAAAAGGCAACCCTTTCTCAGTGATAAATTAACTCCTAAG Cluster: [ ] Orangutan: ATAGATGCTAAGCACCTGCCTTTTAGGGTTGCCTTTTAGGCAACCC-------------------------TTTCTCGGTGATAAACTAACTCCTAAG Gorilla > Human --------------- chr13:58036132-58036144 Template switch process: F1: L TTTATATCTGCAACATAGGCATAGATGCTAGGCATCTGCTTTTTAGGGTTGCCT 1 F3: 4 TTCTCAGTGATAAATTAACTCCTAAGAGTCTGGAGCAGAGATTCCA R RF: TTTATATCTGCAACATAGGCATAGATGCTAGGCATCTGCTTTTTAGGGTTGCCTTTTAGGTGATAAATTAACTCCTAAGAGTCTGGAGCAGAGATTCCA RR: AAATATAGACGTTGTATCCGTATCTACGATCCGTAGACGAAAAATCCCAACGGAAAATCCACTATTTAATTGAGGATTCTCAGACCTCGTCTCTAAGGT F2: 3 TCCCAACGGAAAA 2 Unidirectional alignment (log-probability: -47.8) ATAGGCATAGATGCTAGGCATCTGCTTTTTAGGGTTGCCtaaaaggcaaccctTTcTcaGTGATAAATTAACTCCTAAGAGTCTGGAGCAGAG ATAGGCATAGATGCTAGGCATCTGCTTTTTAGGGTTGCC--------------TTTTAGGTGATAAATTAACTCCTAAGAGTCTGGAGCAGAG Template switch alignment (log-probability: -34.4) ATAGGCATAGATGCTAGGCATCTGCTTTTTAGGGTTGCCT|AAAAGGCAACCCT|TTcTcaGTGATAAATTAACTCCTAAGAGTCTGGAGCAGAG ATAGGCATAGATGCTAGGCATCTGCTTTTTAGGGTTGCCT|AAAAGGCAACCCT|TTTTAGGTGATAAATTAACTCCTAAGAGTCTGGAGCAGAG ========= Event 889 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAATTTCTTTAAACTGATTCATGATAGTACTAGAAATGCACTGATAGGCTTCAGTAATATAATTATAAATATCCATTTATTCATAGATGAATATGATTTTGTCTAAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTGCACAAACTTTAGTATTTGTATATGAA ↓ 3 2 1 4 Chimp: CAAATTTCTGTAAACTGATTCATGATGGTACTAGAAATGCACTGATAGGCTTCAGTAATATAATTATAAATATCCATTTATTCATAGATGAATATGATTTTGTCTAAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTTCATGAACTTTAGTATTTGTATATGAA Gorilla: CAAATTTCTGTAAACTGATTCATGATGGTTCTAGAAATGCAGTGATAGGCTTCAGTAATATAATTATAAATATCCATTTATTCATAGATGAATATGATTTTGTCTAAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTTCACAAACTTTAGTATTTGTACATGAA Human: CAAATTTCTTTAAACTGATTCATGATAGTACTAGAAATGCACTGATAGGCTTCAGTAATATAATTATAAATATCCATTTATTCATAGATGAATATGATTTTGTCTAAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTGCACAAACTTTAGTATTTGTATATGAA Cluster: [ ] Orangutan: CAAATTTCTGTAAACTGATTCATGATGGTACTCGAAATGCACTGATAGGCTTCAGTAATATAATTATAAATATCCATTTATTCATAGATGAATATGATTTTGTCTAAATTTTCATGTGCTGGAAAGAAACCACGTAATTAAAATTTCACGAACTTGAGTATTTGTATATGAA Human > Chimp ------------- chr13:58799247-58799252 Template switch process: F1: L TAAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATT 1 F3: 4 ACTTTAGTATTTGTATATGAAACCCACATCTAGTGACAA R RF: TCATGATAGTACTAGAAATGCACTGATAGGCTTCAGTAATATAATTATAAATATCCATTTATTCATAGATGAATATGATTTTGTCTAAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTGCACAAACTTTAGTATTTGTATATGAAACCCACATCTAGTGACAA RR: AGTACTATCATGATCTTTACGTGACTATCCGAAGTCATTATATTAATATTTATAGGTAAATAAGTATCTACTTATACTAAAACAGATTTAAAAGGACACGACTTTTCTTTGGTGTATTCATTTTAACGTGTTTGAAATCATAAACATATACTTTGGGTGTAGATCACTGTT F2: 3 AGTACT 2 Unidirectional alignment (log-probability: -30.2) AAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTtCAtgAACTTTAGTATTTGTATATGAAACCCACATCTAGTGAcaa AAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATTGCACAAACTTTAGTATTTGTATATGAAACCCACATCTAGTGA--- Template switch alignment (log-probability: -16) AAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATT|TCATGA|ACTTTAGTATTTGTATATGAAACCCACATCTAGTGACAA AAATTTTCCTGTGCTGAAAAGAAACCACATAAGTAAAATT|TCATGA|ACTTTAGTATTTGTATATGAAACCCACATCTAGTGACAA ========= Event 890 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GACTGGTACTCTTTTCTGCTG-------------GCTTAGTTCCTAGGCAAATGACTCCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTAGGAACTAAGCCAGCAGAAAAGAGTACCA Chimp: GACTGGTACTCTTTTCTGCTG-------------GCTTAGTTCCTAGGCAAATGACTCCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTAGGAACTAAGCCAGCAGAAAAGAGTACCA ↑ 4 1 3 2 Gorilla: GACTGGTACTCTTTTCTGCTG--------------------------GCAAATGACTCCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTAGGAACTAAGCCAGCAGAAAAGAGTACCA ↓ 4 1 3 2 Human: GACTGGTACTCTTTTCTGCTG-------------GCTTAGTTCCTAGGCAAATGACTCCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTAGGAACTAAGCCAGCAGAAAAGAGTACCA Cluster: [ ] Orangutan: GACTGCTGCTCTTTTCTGCTGGCTTAGTTCCTAG-------------GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAGAAAAGAGTACCA Gorilla > Human --------------- chr1:213046264-213046273 Template switch process: F1: L AAGGGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGC 1 F3: 4 GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAAA R RF: AAGGGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAAA RR: TTCCCAGAAATCTTCTTAGACTGACCATGAGAAAAGACGACCGTTTACTGAGGTAACGGATCCTTGATTCGGTCGTCTTTT F2: 3 ATCCTTGATT 2 Unidirectional alignment (log-probability: -29.6) GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTggcttagttcctaGGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCT-------------GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA Template switch alignment (log-probability: -17.1) GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGC|TTAGTTCCTA|GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGC|TTAGTTCCTA|GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA Gorilla > Chimp --------------- chr1:193345158-193345167 Template switch process: F1: L AAGGGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGC 1 F3: 4 GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAAA R RF: AAGGGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAAA RR: TTCCCAGAAATCTTCTTAGACTGACCATGAGAAAAGACGACCGTTTACTGAGGTAACGGATCCTTGATTCGGTCGTCTTTT F2: 3 ATCCTTGATT 2 Unidirectional alignment (log-probability: -29.6) GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTggcttagttcctaGGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCT-------------GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA Template switch alignment (log-probability: -17.1) GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGC|TTAGTTCCTA|GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA GGTCTTTAGAAGAATCTGACTGGTACTCTTTTCTGCTGGC|TTAGTTCCTA|GGCAAATGACTCCATTGCCTAGGAACTAAGCCAGCAGAAA ========= Event 891 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: --------------------AACATGGCATTTCACATTAGAAAggaaaagaatgactatagtaaata------------------------------ttgttgggacaactggttatccgtttggaaaaaattatatgttccagtcattctttatatcatatacagaataaatt Chimp: --------------------AACATGGCATTTCACATTAGAAAGGAAAAGAATGACTATAGTAAATA------------------------------TTGTTGGGACAACTGGTTATCCGTTTGGAAAAAATTATATGTTCCAGTCATTCTTTATATCATATACAGAATAAATT ↓ 1 43 2 Gorilla: ---------------------------------------------TAAAGAATGACTGGAACATATCATTTTTTCCAAACGGATAACCAGTTGTCCCAAGTTGGGACAACTGGTTATCCGTTTGGAAAAAATGATATGTTCCAGTCATTCTTTATATCATATACAGAATAAATT Human: --------------------AACATGGCATTTCACATTAGAAAggaaaagaatgactatagtaaata------------------------------ttgttgggacaactggttatccgtttggaaaaaattatatgttccagtcattctttatatcatatacagaataaatt Cluster: [ ] Orangutan: ggcgtttcacattagaaagg-------------------------aaaagaatgactacagtaaata------------------------------tt-------------gttatccatttggaaaaaatgatatgttccaatcattctttatatcatatacaaaataaatt Chimp > Gorilla --------------- chr1:192813609-192813662 Template switch process: F1: L GATA 1 F3: 4 GTTGGGACAACTGGTTATCCGTTTGGAAAAAATGATATGT R RF: GATAAACATGGCATTTCACATTAGAAAGGAAAAGAATGACTATAGTAAATATTGTTGGGACAACTGGTTATCCGTTTGGAAAAAATTATATGTTCCAGTCATTCTTTA RR: CTATTTGTACCGTAAAGTGTAATCTTTCCTTTTCTTACTGATATCATTTATAACAACCCTGTTGACCAATAGGCAAACCTTTTTTAATATACAAGGTCAGTAAGAAAT F2: 3 AACCCTGTTGACCAATAGGCAAACCTTTTTTACTATACAAGGTCAGTAAGAAAT 2 Unidirectional alignment (log-probability: -102) GATA-------------------------tAAAGAATGACTggaacatatcattttttccaaacggataaccagttgtcccaA-----------GTTGGGACAACTGGTTATCCGTTTGGAAAAAATgATATGT GATAAACATGGCATTTCACATTAGAAAGGAAAAGAATGACT-----------------------------------------ATAGTAAATATTGTTGGGACAACTGGTTATCCGTTTGGAAAAAATTATATGT Template switch alignment (log-probability: -32.7) GATA|TAAAGAATGACTGGAACATATcATTTTTTCCAAACGGATAACCAGTTGTCCCAA|GTTGGGACAACTGGTTATCCGTTTGGAAAAAATgATATGT GATA|TAAAGAATGACTGGAACATATAATTTTTTCCAAACGGATAACCAGTTGTCCCAA|GTTGGGACAACTGGTTATCCGTTTGGAAAAAATTATATGT ========= Event 892 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GCAGTTTATTATAGCTGAGCAATCACTGAATTGAAAACAAAACATTTTCAATTCAGTGATTGCTTTT-CATAAACATTAAGGACATGAC Chimp: GCAGTTTATTATAGCTGAGCAATCACTGAATTGAAAACAAAACATTTTCAATTCAGTGATTGCTTTT-CATAAACATTAAGGACATGAC ↑ 3 2 1 4 Gorilla: GCAGTTTATTGTAGCTGAGCAATCACTGAATTGAAAACAAAACAGG------------TTTCCTTTTCAATAAACATTAAGGACATGAC Human: GCAGTTTATTATAGCTGAGCAATCACTGAATTGAAAACAAAACATTTTCAATTCAGTGATTGCTTTT-CATAAACATTAAGGACATGAC Cluster: [ ] Orangutan: GCAGTTTATTATAGCTGAGCAATCACTGAATTGAAAACAAAACAGG------------TTTCCTTTTCAATAAACATTAAGGACATGAC Gorilla > Chimp --------------- chr13:43862218-43862235 Template switch process: F1: L GTTTATTATAGCTGAGCAATCACTGAATTGAAAACAAAACA 1 F3: 4 CTTTTC-ATAAACATTAAGGACATGACCTGGAGATAAGAAGATAAGA R RF: GTTTATTGTAGCTGAGCAATCACTGAATTGAAAACAAAACAGGTTTCCTTTTCAATAAACATTAAGGACATGACCTGGAGATAAGAAGATAAGA RR: CAAATAACATCGACTCGTTAGTGACTTAACTTTTGTTTTGTCCAAAGGAAAAGTTATTTGTAATTCCTGTACTGGACCTCTATTCTTCTATTCT F2: 3 GTTAGTGACTTAACTTTT 2 Unidirectional alignment (log-probability: -52.5) TTTATTaTAGCTGAGCAATCACTGAATTGAAAACAAAACA-------TTTTCAattcagtgattgcttttcATAAACATTAAGGACATGACCTGGAGATAAGAAG TTTATTGTAGCTGAGCAATCACTGAATTGAAAACAAAACAGGTTTCCTTTTCA------------------ATAAACATTAAGGACATGACCTGGAGATAAGAAG Template switch alignment (log-probability: -33.5) TTTATTaTAGCTGAGCAATCACTGAATTGAAAACAAAACA|TTTTCAATTCAGTGATTG|CTTTTC-ATAAACATTAAGGACATGACCTGGAGATAAGAAG TTTATTGTAGCTGAGCAATCACTGAATTGAAAACAAAACA|TTTTCAATTCAGTGATTG|CTTTTCAATAAACATTAAGGACATGACCTGGAGATAAGAAG ========= Event 893 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAATGGGTTCTGCTGCTGCAGTTCATCTCCAGCAATAACACAG----------------------------------------AACAATGGTGCGCCGCAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAACTGGCAGTGATCGGATAATCGGCTCT Chimp: AGAATGGGTTCTGCTGCTGCAGTTCATCTCCAGCAATAACACAG----------------------------------------AACAATGGCGTGCCACAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAACTGGCAGCGATCAGATAATCGGCTTT ↑ 4 1 3 2 Gorilla: AGAATGGGTTCTGCTGCCGCAGTTCATCTCTAGCAATAACACAG--------------------------------------------------------------------------------AACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAACTGGCAGTGATCGGATAATCGGCTCT Human: AGAATGGGTTCTGCTGCTGCAGTTCATCTCCAGCAATAACACAG----------------------------------------AACAATGGTGCGCCGCAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAACTGGCAGTGATCGGATAATCGGCTCT Cluster: [ ] Orangutan: AGAATGGGTTCTTCTGCTGCAGTTCATCTCCAGCAATAACACAGAACAATGGTGCACCGCAGTTCATCTCCAGCAATAACACAG----------------------------------------AACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAACTGGCACTGATTGGATAATCGGCTCT Gorilla > Chimp --------------- chr13:43449696-43449700 Template switch process: F1: L ATGGGTTCTGCTGCTGCAGTTCATCTCCAGCAATAACACAGAACAATGGCG 1 F3: 4 CAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAA R RF: ATGGGTTCTGCTGCCGCAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTACAAGCAATGCTAACTCTGGAACAGAACTGGCA RR: TACCCAAGACGACGGCGTCAAGTAGAGATCGTTATTGTGTCTTGTTACCGCTCATGTTCGTTACGATTGAGACCTTGTCTTGACCGT F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -73.9) tgctgcagttcatctccagcaataacacagaacaatggcgTGCCaCAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTAC ----------------------------------------TGCCGCAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTAC Template switch alignment (log-probability: -28.2) TGCtGCAGTTCATCTCcAGCAATAACACAGAACAATGGCG|TGCCA|CAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTAC TGCCGCAGTTCATCTCTAGCAATAACACAGAACAATGGCG|TGCCA|CAGTTCATCTCTAGCAATAACACAGAACAATGGCGAGTAC ========= Event 894 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ttCTTCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATG ↓ 13 24 ↑ 13 24 Chimp: t-tttCCAGTGTCAGTTTAGGATCATGAAACAAGTTTCAGGACAATACACTCTTAAAGATTATG ↓ 13 24 ↑ 13 24 Gorilla: t-tttCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATG Human: ttCTTCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATG Cluster: [ ] Orangutan: t-tttCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATG Chimp > Human ------------- chr13:60898806-60898827 Template switch process: F1: L GATGAGAATTTGAATTTTTTTTCTTCCAGTGTCAGTTTAGG 1 F3: 4 AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGA R RF: GATGAGAATTTGAATTTTTTTT-TTCCAGTGTCAGTTTAGGATCATGAAACAAGTTTCAGGACAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT RR: CTACTCTTAAACTTAAAAAAAA-AAGGTCACAGTCAAATCCTAGTACTTTGTTCAAAGTCCTGTTATGTGAGAATTTCTAATACGGATAAGTCTTGTACATCA F2: 3 TAGTACTTTGTTCAAAGTCCTG 2 Unidirectional alignment (log-probability: -54.5) ATGAGAATTTGAATTTTTTTTcTTCCAGTGTCAGTTTAGGgTCcTGAAACttGTTTCAtGAtAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGa ATGAGAATTTGAATTTTTTTT-TTCCAGTGTCAGTTTAGGATCATGAAACAAGTTTCAGGACAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT Template switch alignment (log-probability: -35.6) ATGAGAATTTGAATTTTTTTTcTTCCAGTGTCAGTTTAGG|GTCCTGAAACTTGTTTCATGAT|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGa ATGAGAATTTGAATTTTTTTT-TTCCAGTGTCAGTTTAGG|GTCCTGAAACTTGTTTCATGAT|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT Human > Chimp ------------- chr13:45976407-45976428 Template switch process: F1: L GATGAGAATTTGAATTTTTTTT-TTCCAGTGTCAGTTTAGG 1 F3: 4 AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT R RF: GATGAGAATTTGAATTTTTTTTCTTCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGA RR: CTACTCTTAAACTTAAAAAAAAGAAGGTCACAGTCAAATCCCAGGACTTTGAACAAAGTACTATTATGTGAGAATTTCTAATACGGATAAGTCTTGTACATCT F2: 3 CAGGACTTTGAACAAAGTACTA 2 Unidirectional alignment (log-probability: -53.1) GATGAGAATTTGAATTTTTTTT-TTCCAGTGTCAGTTTAGGaTCaTGAAACaaGTTTCAgGAcAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGt GATGAGAATTTGAATTTTTTTTCTTCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGA Template switch alignment (log-probability: -34.2) GATGAGAATTTGAATTTTTTTT-TTCCAGTGTCAGTTTAGG|ATCATGAAACAAGTTTCAGGAC|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGt GATGAGAATTTGAATTTTTTTTCTTCCAGTGTCAGTTTAGG|ATCATGAAACAAGTTTCAGGAC|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGA Gorilla > Chimp --------------- chr13:45976407-45976428 Template switch process: F1: L TGATGAGAATTTGAATTTTTTTTTTCCAGTGTCAGTTTAGG 1 F3: 4 AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT R RF: TGATGAGAATTTGA--TTTTTTTTTCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT RR: ACTACTCTTAAACT--AAAAAAAAAGGTCACAGTCAAATCCCAGGACTTTGAACAAAGTACTATTATGTGAGAATTTCTAATACGGATAAGTCTTGTACATCA F2: 3 CAGGACTTTGAACAAAGTACTA 2 Unidirectional alignment (log-probability: -47.2) GATGAGAATTTGAatTTTTTTTTTCCAGTGTCAGTTTAGGaTCaTGAAACaaGTTTCAgGAcAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT GATGAGAATTTGA--TTTTTTTTTCCAGTGTCAGTTTAGGGTCCTGAAACTTGTTTCATGATAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT Template switch alignment (log-probability: -31.1) GATGAGAATTTGAatTTTTTTTTTCCAGTGTCAGTTTAGG|ATCATGAAACAAGTTTCAGGAC|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT GATGAGAATTTGA--TTTTTTTTTCCAGTGTCAGTTTAGG|ATCATGAAACAAGTTTCAGGAC|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT Chimp > Gorilla --------------- chr13:42996156-42996177 Template switch process: F1: L TGATGAGAATTTGA--TTTTTTTTTCCAGTGTCAGTTTAGG 1 F3: 4 AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT R RF: TGATGAGAATTTGAATTTTTTTTTTCCAGTGTCAGTTTAGGATCATGAAACAAGTTTCAGGACAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT RR: ACTACTCTTAAACTTAAAAAAAAAAGGTCACAGTCAAATCCTAGTACTTTGTTCAAAGTCCTGTTATGTGAGAATTTCTAATACGGATAAGTCTTGTACATCA F2: 3 TAGTACTTTGTTCAAAGTCCTG 2 Unidirectional alignment (log-probability: -44.4) TGATGAGAATTTGA--TTTTTTTTTCCAGTGTCAGTTTAGGgTCcTGAAACttGTTTCAtGAtAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT TGATGAGAATTTGAATTTTTTTTTTCCAGTGTCAGTTTAGGATCATGAAACAAGTTTCAGGACAATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT Template switch alignment (log-probability: -28.3) TGATGAGAATTTGA--TTTTTTTTTCCAGTGTCAGTTTAGG|GTCCTGAAACTTGTTTCATGAT|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT TGATGAGAATTTGAATTTTTTTTTTCCAGTGTCAGTTTAGG|GTCCTGAAACTTGTTTCATGAT|AATACACTCTTAAAGATTATGCCTATTCAGAACATGTAGT ========= Event 895 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTAGAATGTGGCTAAACCAGCGTGTGCTGTTGG---ATTATTGTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGAT Chimp: GGTAGAATGTGGCTAAACCAGAGTGTGCTGATGG---ATTATTGTGGTCTGCAGTGCATAagaggttaagacaaccgat Gorilla: GGTAGAATGTGGCTAAACCAGTGTGTGCTGATGC------ACTGTGGTCTGCAGTGCATAagaggttaagacaaccgat ↑ 1 4 3 2 Human: GGTAGAATGTGGCTAAACCAGCGTGTGCTGTTGG---ATTATTGTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGAT Cluster: [ ] Orangutan: GGTAGAATGTGGCTAAACCAGCATGTGCTGATGGATT---ATTGTGGTctgtggtgcataagaggttaagacaaccgat Human > Gorilla --------------- chr13:55928595-55928601 Template switch process: F1: L ACTGTTGGCTATTAAGAACAGGTAGAATGTGGCTAAACCAGTGTGTGCTG 1 F3: 4 GTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGATTTG R RF: ACTGTTGGCTATTAAGAACAGGTAGAATGTGGCTAAACCAGCGTGTGCTGTTGGATTATTGTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGATTTG RR: TGACAACCGATAATTCTTGTCCATCTTACACCGATTTGGTCGCACACGACAACCTAATAACACCAGACGTCACGTATTCTCCAATTCTGTTGGCTAAAC F2: 3 TCACGTA 2 Unidirectional alignment (log-probability: -32.4) ATTAAGAACAGGTAGAATGTGGCTAAACCAGtGTGTGCTG-------ATgcacTGTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGATTTG ATTAAGAACAGGTAGAATGTGGCTAAACCAGCGTGTGCTGTTGGATTAT----TGTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGATTTG Template switch alignment (log-probability: -22.3) ATTAAGAACAGGTAGAATGTGGCTAAACCAGtGTGTGCTG|ATGCACT|GTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGATTTG ATTAAGAACAGGTAGAATGTGGCTAAACCAGCGTGTGCTG|ATGCACT|GTGGTCTGCAGTGCATAAGAGGTTAAGACAACCGATTTG ========= Event 896 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAAAATATAGCAAAGGCTTTAAAGACTTAACAAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGT---- Chimp: GTAAAATATAGCAAAGGCTTTAAAGACTTAACAAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGT---T ↓ 1 4 3 2 Gorilla: gtaaaatATAGCAAAGGCTTTCAAGACTT---AAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTAT- Human: GTAAAATATAGCAAAGGCTTTAAAGACTTAACAAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGT---- Cluster: [ ] Orangutan: GTAAAATATAGCAAAGGCTTTAAACAC-----TAACAAGTTTTAAGTCTTGGTAAATTCCCTACAGTTAT- Chimp > Gorilla --------------- chr13:44311582-44311590 Template switch process: F1: L AAGGAACCATAAAATGACTAGTAAAATATAGCAAAGGCTTT 1 F3: 4 AACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTAT R RF: AAGGAACCATAAAATGACTAGTAAAATATAGCAAAGGCTTTAAAGACTTAACAAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTAT RR: TTCCTTGGTATTTTACTGATCATTTTATATCGTTTCCGAAATTTCTGAATTGTTTGTTCAAAATTCAGAACCATTTGGGGGATGTCAATA F2: 3 ATTCAGAAC 2 Unidirectional alignment (log-probability: -24.8) AGGAACCATAAAATGACTAGTAAAATATAGCAAAGGCTTTcAAGACTT---AAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTAt AGGAACCATAAAATGACTAGTAAAATATAGCAAAGGCTTTAAAGACTTAACAAACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTA- Template switch alignment (log-probability: -16.8) AGGAACCATAAAATGACTAGTAAAATATAGCAAAGGCTTT|CAAGACTTA|AACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTAT AGGAACCATAAAATGACTAGTAAAATATAGCAAAGGCTTT|CAAGACTTA|AACAAGTTTTAAGTCTTGGTAAACCCCCTACAGTTAT ========= Event 897 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATTAGGAATTGAATGAGTACCTCTACGCTTAAAATATTTAAGCATAGAGGTAt--tttttttATTAATTAACATAC ↓ 3 1 2 4 Chimp: ATATTAGGAATTGAATGAGTACCTCTATGCTTAAATATTTTAAGCATAGAGGTAt---ttttttATTAATTAACATAC ↑ 3 1 2 4 Gorilla: ATATTAGGAATTGAATGAGTACCTCTATGCTTAAAATATTTAAGCATAGAGGTAttt-ttttttATTAATTAACATAC Human: ATATTAGGAATTGAATGAGTACCTCTACGCTTAAAATATTTAAGCATAGAGGTAt--tttttttATTAATTAACATAC Cluster: [ ] Orangutan: ATATTAGGAATTGAATGACTACCTCTATGCTTAAAATATTTAAGCATAGAGGT-T---TTTTTAATTAATTAACATAC Human > Chimp ------------- chr13:51116131-51116157 Template switch process: F1: L GGTAGACTTCTTTCATATTAGGAATTGAATGAGTACCTCTA 1 F3: 4 TTTTTTTATTAATTAACATACTT R RF: GGTAGACTTCTTTCATATTAGGAATTGAATGAGTACCTCTACGCTTAAAATATTTAAGCATAGAGGTATTTTTTTTATTAATTAACATACTT RR: CCATCTGAAGAAAGTATAATCCTTAACTTACTCATGGAGATGCGAATTTTATAAATTCGTATCTCCATAAAAAAAATAATTAATTGTATGAA F2: 3 ATGGAGATACGAATTTTATAAATTCGT 2 Unidirectional alignment (log-probability: -35) GTAGACTTCTTTCATATTAGGAATTGAATGAGTACCTCTAtGCTTAAAtatTTTAAGCATAGAGGTATTTTTTT-ATTAATTAACATACTT GTAGACTTCTTTCATATTAGGAATTGAATGAGTACCTCTACGCTTAAAATATTTAAGCATAGAGGTATTTTTTTTATTAATTAACATACTT Template switch alignment (log-probability: -24.3) GTAGACTTCTTTCATATTAGGAATTGAATGAGTACCTCTA|TGCTTAAATATTTTAAGCaTAGAGGTA|TTTTTTTATTAATTAACATACTT GTAGACTTCTTTCATATTAGGAATTGAATGAGTACCTCTA|TGCTTAAATATTTTAAGCGTAGAGGTA|TTTTTTTATTAATTAACATACTT Gorilla > Chimp --------------- chr13:51116139-51116157 Template switch process: F1: L TCTTTCATATTAGGAATTGAATGAGTACCTCTATGCTTAAA 1 F3: 4 TTTTTTTATTAATTAACATACT R RF: TTTTTCATATTAGGAATTGAATGAGTACCTCTATGCTTAAAATATTTAAGCATAGAGGTATTTTTTTTTATTAATTAACATACT RR: AAAAAGTATAATCCTTAACTTACTCATGGAGATACGAATTTTATAAATTCGTATCTCCATAAAAAAAAATAATTAATTGTATGA F2: 3 ATGGAGATACGAATTTTAT 2 Unidirectional alignment (log-probability: -33.1) cTTTCATATTAGGAATTGAATGAGTACCTCTATGCTTAAAtatTTTAAGCATAGAGGTA--TTTTTTTATTAATTAACATACT TTTTCATATTAGGAATTGAATGAGTACCTCTATGCTTAAAATATTTAAGCATAGAGGTATTTTTTTTTATTAATTAACATACT Template switch alignment (log-probability: -23.2) cTTTCATATTAGGAATTGAATGAGTACCTCTATGCTTAAA|TATTTTAAGCATAGAGGTA|TTTTTTTATTAATTAACATACT TTTTCATATTAGGAATTGAATGAGTACCTCTATGCTTAAA|TATTTTAAGCATAGAGGTA|TTTTTTTATTAATTAACATACT ========= Event 898 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: cattaatgaattttatgatat---gCCTCAAAATTT---GTATATGTTTTACAAAGTATAGG Chimp: CATTAATGAATTTTATGATAT---GCCTCAAAATTT---GTATATGTTTTAGAAAGTATAGG ↓ 13 24 ↑ 13 24 Gorilla: CATTAATGAATTTTATGATAT------ACAAATTTTGAGGCATATGTTTTAGAAAGTATAGG Human: cattaatgaattttatgatat---gCCTCAAAATTT---GTATATGTTTTACAAAGTATAGG Cluster: [ ] Orangutan: cattaatgaattttatgataCATC---TCAAAATTT---GTATATGTTTTAGAAAGTATAGG Gorilla > Chimp --------------- chr13:50687189-50687202 Template switch process: F1: L GTATTGAATTGTACACATGACATTAATGAATTTTATGATAT 1 F3: 4 ATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT R RF: GTATTGAATTGTACACATGACATTAATGAATTTTATGATATACAAATTTTGAGGCATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT RR: CATAACTTAACATGTGTACTGTAATTACTTAAAATACTATATGTTTAAAACTCCGTATACAAAATCTTTCATATCCCATACAGATCAAATAAAAA F2: 3 TGTTTAAAACTCCG 2 Unidirectional alignment (log-probability: -37.8) TATTGAATTGTACACATGACATTAATGAATTTTATGATATgCctcaAAATTT----GtATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT TATTGAATTGTACACATGACATTAATGAATTTTATGATATAC----AAATTTTGAGGCATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT Template switch alignment (log-probability: -17.5) TATTGAATTGTACACATGACATTAATGAATTTTATGATAT|GCCTCAAAATTTGT|ATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT TATTGAATTGTACACATGACATTAATGAATTTTATGATAT|GCCTCAAAATTTGT|ATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT Chimp > Gorilla --------------- chr13:50340957-50340970 Template switch process: F1: L GTATTGAATTGTACACATGACATTAATGAATTTTATGATAT 1 F3: 4 ATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT R RF: GTATTGAATTGTACACATGACATTAATGAATTTTATGATATGCCTCAAAATTTGTATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT RR: CATAACTTAACATGTGTACTGTAATTACTTAAAATACTATACGGAGTTTTAAACATATACAAAATCTTTCATATCCCATACAGATCAAATAAAAA F2: 3 CGGAGTTTTAAACA 2 Unidirectional alignment (log-probability: -37.8) TATTGAATTGTACACATGACATTAATGAATTTTATGATATaC----AAATTTtgagGcATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT TATTGAATTGTACACATGACATTAATGAATTTTATGATATGCCTCAAAATTT----GTATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT Template switch alignment (log-probability: -17.5) TATTGAATTGTACACATGACATTAATGAATTTTATGATAT|ACAAATTTTGAGGC|ATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT TATTGAATTGTACACATGACATTAATGAATTTTATGATAT|ACAAATTTTGAGGC|ATATGTTTTAGAAAGTATAGGGTATGTCTAGTTTATTTTT ========= Event 899 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: ATC-ATATTATTTGTTATT-TCTGAT--AGTCTACATTCTTACATTGTAG----atttattt-atttattattat-tttGC Chimp: ATC-ATATTATTTGTTATT-TCTGAT-AAATCTACAATGTAAGAATGTAG----A-CTATTT-ATTTATTATTAT-TTTGC ↓ 1 3 2 4 ↑ 3 4 2 Gorilla: ATC-ATATTATTTGTTATT-TATGAT--AGTCTACATTCTTACATCGTAG--------ATTT-ATTTATTATTAT-TTTGC Human: ATC-ATATTATTTGTTATT-TCTGAT--AGTCTACATTCTTACATTGTAG----atttattt-atttattattat-tttGC Cluster: [ ] Orangutan: ATCAATATTATTTGTTATTTACTGATA-AATCTACAATGTAAGAATGTAGACta----ttttattttattattatttttGC Gorilla > Chimp --------------- chr13:49739515-49739539 Template switch process: F1: L GTAATCTCTTTATCTCACATTTATCATATTATTTGTTATTTCTGATA 1 F3: 4 ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT R RF: GTAATCTCTTTATCTCACATTTATCATATTATTTGTTATTTATGATAGTCTACATTCTTACATCGTAGATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT RR: CATTAGAGAAATAGAGTGTAAATAGTATAATAAACAATAAATACTATCAGATGTAAGAATGTAGCATCTAAATAAATAATAATAAAACGATATGTTAGAAATTATAGA F2: 3 TCAGATGTAAGAATGTAACATCTAA 2 Unidirectional alignment (log-probability: -62.9) CTTTATCTCACATTTATCATATTATTTGTTATTTcTGAtaaatctacaatgtaagaatgTAGaCT-----------------ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT CTTTATCTCACATTTATCATATTATTTGTTATTTATGA---------------------TAGTCTACATTCTTACATCGTAGATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT Template switch alignment (log-probability: -30.1) CTTTATCTCACATTTATCATATTATTTGTTATTTcTGATA|AATCTACaATGTAAGAATGTAGACT|ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT CTTTATCTCACATTTATCATATTATTTGTTATTTATGATA|AATCTACGATGTAAGAATGTAGACT|ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT Chimp > Gorilla --------------- chr13:46787622-46787642 Template switch process: F1: L GTAATCTCTTTATCTCACATTTATCATATTATTTGTTATTTATGATA 1 F3: 4 ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT R RF: GTAATCTCTTTATCTCACATTTATCATATTATTTGTTATTTCTGATAAATCTACAATGTAAGAATGTAGACTATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT RR: CATTAGAGAAATAGAGTGTAAATAGTATAATAAACAATAAAGACTATTTAGATGTTACATTCTTACATCTGATAAATAAATAATAATAAAACGATATGTTAGAAATTATAGA F2: 3 GATGCTACATTCTTACATCTG 2 Unidirectional alignment (log-probability: -57.3) CTTTATCTCACATTTATCATATTATTTGTTATTTaTGA---------------------TAGtCTacattcttacatcgtagATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT CTTTATCTCACATTTATCATATTATTTGTTATTTCTGATAAATCTACAATGTAAGAATGTAGACT-----------------ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT Template switch alignment (log-probability: -29.6) CTTTATCTCACATTTATCATATTATTTGTTATTTaTGATA|GTCTACATTCTTACATcGTAG|ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT CTTTATCTCACATTTATCATATTATTTGTTATTTCTGATA|GTCTACATTCTTACATTGTAG|ATTTATTTATTATTATTTTGCTATACAATCTTTAATATCT ========= Event 900 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: taccatgtacgcacagcactga--------------cacacagatgctgacacacatatatccacagtaccgacacCTCCTAACACTGTTCCATACATAAACACACGCTCACTGGGCCTCATACTGCAAACACACCCAGTACCCACCAGCATCCACACCCAAGAGACGCATGT Chimp: TACCATGTACGCACAGCACTGA--------------CACACAGATGCTGACACACATATATCCACAGTACCAACACCTCCTAACACTGTTCCATACATAAACACACGCTCACTGGGCCTCATACTGCAAACACACCCAGTACCCACCAGCATCCACACCCAAGAGATACATGT ↑ 4 1 3 2 Gorilla: TACCATGTACGCACAGCACTGA----------------------------CACACATATATCCACAGTACCGACACCTCCTAACACTGTTCCATACATAAACACACGCTCACTGGGCCTCATACTGTAAACACACCCAGTACCCACCAGCATCCACACCCAAGAGACACATGT Human: taccatgtacgcacagcactga--------------cacacagatgctgacacacatatatccacagtaccgacacCTCCTAACACTGTTCCATACATAAACACACGCTCACTGGGCCTCATACTGCAAACACACCCAGTACCCACCAGCATCCACACCCAAGAGACGCATGT Cluster: [ ] Orangutan: TACCATGTACGCACAGCACTGACACACAGACGCTGA--------------CACACATACATCCACAGTACCGACACCTCCTAACGCTCTTCCATACATAAACACACGCTCACTGGGCCTCATACTGCAAACACACCCAGTACCCACCAGCATCCACACCCAAGAGACACATGT Gorilla > Chimp --------------- chr1:35916479-35916483 Template switch process: F1: L ACGCATATACAGATGCTGATACCATGTACGCACAGCACTGACACACA 1 F3: 4 TGACACACATATATCCACAGTACCAACACCTCCTAACACTGTT R RF: ACGCATATACAGATGCTGATACCATGTACGCACAGCACTGACACACATATATCCACAGTACCGACACCTCCTAACACTGTTCCATACATAAACACACGCTCACTGGGCCTCATACTGTAAACACACCCAGTACCCACCAGCATC RR: TGCGTATATGTCTACGACTATGGTACATGCGTGTCGTGACTGTGTGTATATAGGTGTCATGGCTGTGGAGGATTGTGACAAGGTATGTATTTGTGTGCGAGTGACCCGGAGTATGACATTTGTGTGGGTCATGGGTGGTCGTAG F2: 3 CGTAG 2 Unidirectional alignment (log-probability: -36.5) TACAGATGCTGATACCATGTACGCACAGCACTgacacacagatgctGACACACATATATCCACAGTACCaACACCTCCTAACACT TACAGATGCTGATACCATGTACGCACAGCACT--------------GACACACATATATCCACAGTACCGACACCTCCTAACACT Template switch alignment (log-probability: -22.1) TACAGATGCTGATACCATGTACGCACAGCACTGACACACA|GATGC|TGACACACATATATCCACAGTACCaACACCTCCTAACACT TACAGATGCTGATACCATGTACGCACAGCACTGACACACA|GATGC|TGACACACATATATCCACAGTACCGACACCTCCTAACACT ========= Event 901 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGTCATAGGAACCATGAATG-----------------GCTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCC Chimp: TAGTCATAGGAACCATGAATG-----------------ACTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCC ↓ 134 2 Gorilla: TAGTCATAGGAACCATGAATGAAGTCGTACTCTGAAGTCGTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCC Human: TAGTCATAGGAACCATGAATG-----------------GCTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCC Cluster: [ ] Orangutan: TAGTCATAGGAACCATGAATG-----------------ACTACTTCAGAATATGACTAGAGAATAAAGTATATTTCC Chimp > Gorilla --------------- chr13:48903379-48903396 Template switch process: F1: L AGAGAACTTGAACCCTAGAGTAGTCATAGGAACCATGAATGA 1 F3: 4 TACTTCAGAGTACGACTAGAGAATAAAGTATATTTCCTAG R RF: AGATAACTTGAACCCTAGAGTAGTCATAGGAACCATGAATGACTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCCTAG RR: TCTATTGAACTTGGGATCTCATCAGTATCCTTGGTACTTACTGATGAAGTCTCATGCTGATCTCTTATTTCATATAAAGGATC F2: 3 GCTGAAGTCTCATGCTGA 2 Unidirectional alignment (log-probability: -46.4) AgAACTTGAACCCTAGAGTAGTCATAGGAACCATGAATGAagtcgtactctgaagtcgTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCCTAG ATAACTTGAACCCTAGAGTAGTCATAGGAACCATGAATGA-----------------CTACTTCAGAGTACGACTAGAGAATAAAGTATATTTCCTAG Template switch alignment (log-probability: -29.1) AgAACTTGAACCCTAGAGTAGTCATAGGAACCATGAATGA|AGTCGTACTCTGAAGTcG|TACTTCAGAGTACGACTAGAGAATAAAGTATATTTCCTAG ATAACTTGAACCCTAGAGTAGTCATAGGAACCATGAATGA|AGTCGTACTCTGAAGTAG|TACTTCAGAGTACGACTAGAGAATAAAGTATATTTCCTAG ========= Event 902 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ACAACGTTTAAAGATGTCCATATAATATTATGGACATATAATATTACGTCCATATTATGGAATATTATATGG ↑ 4 1 3 2 Chimp: ACAACGTTTAAAGATGTCCATATAAT----------------ATTACGTCCATATTATGGAATATTATGTGG Gorilla: ACAACGTTTAAAGATGTTcatataatattatggacatataatattacatccatattatggaatattatatgg Human: ACAACGTTTAAAGATGTCCATATAATATTATGGACATATAATATTACGTCCATATTATGGAATATTATATGG Cluster: [ ] Orangutan: ACAACATTTAAAGATGTCCATATAATATTATGGACATATAACATTATGTCCATATTATGGAATATTATATAG Chimp > Human ------------- chr13:47876725-47876729 Template switch process: F1: L CATACAAGTCATTTTACAACGTTTAAAGATGTCCATATAATATTA 1 F3: 4 ATATAATATTACGTCCATATTATGGAATATTATATGGACATTGACAA R RF: CATACAAGTCATTTTACAACGTTTAAAGATGTCCATATAATATTACGTCCATATTATGGAATATTATGTGGACATTGACAA RR: GTATGTTCAGTAAAATGTTGCAAATTTCTACAGGTATATTATAATGCAGGTATAATACCTTATAATACACCTGTAACTGTT F2: 3 CAGGT 2 Unidirectional alignment (log-probability: -39.9) AAGTCATTTTACAACGTTTAAAGATGTCCATATAATATTatggacatataatattACGTCCATATTATGGAATATTATaTGGACA AAGTCATTTTACAACGTTTAAAGATGTCCATATAATATT----------------ACGTCCATATTATGGAATATTATGTGGACA Template switch alignment (log-probability: -22.1) AAGTCATTTTACAACGTTTAAAGATGTCCATATAATATTA|TGGAC|ATATAATATTACGTCCATATTATGGAATATTATaTGGACA AAGTCATTTTACAACGTTTAAAGATGTCCATATAATATTA|TGGAC|ATATAATATTACGTCCATATTATGGAATATTATGTGGACA ========= Event 903 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATCTAGATGAAGCTTGTTATTG----T-TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATATGTTCAATTTTCAAAGGTGGACTTTCTATCTCACAACAAACTTAAATATTATTGTGATTAATTAAAGAATACTAGGTTCCTTCTTGACAATGCTGGCTATGGAAAACATCTC ↓ 1 4 3 2 Chimp: AATCTAGATGAAGCTTGTTATCA--TTG-TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATATGTTCAATTTTCAAAGGTGGACTTTCTACCTCTCAACAAACTTAAATATTATTGTGATTAATTAAAGAATACTAGATGCCTTCTTGACAATGCTGGCTATGGAAAACACCTC Gorilla: GATCTAGATGAAGCTTGTTATCATT--GTTTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATATGTTCAATTTTCAAAGGTGGACTTTCTACCTCTCAACAAACTTAAATATTATTGTGATTAATTAAAGAATACTAGGTGCCTTCTTGACAATGCTGGCTATGGAAAACATCTC Human: AATCTAGATGAAGCTTGTTATTG----T-TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATATGTTCAATTTTCAAAGGTGGACTTTCTATCTCACAACAAACTTAAATATTATTGTGATTAATTAAAGAATACTAGGTTCCTTCTTGACAATGCTGGCTATGGAAAACATCTC Cluster: [ ] Orangutan: AATCTAAATGAAGCTTGTTATCATT--GTTTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATATGCTCAATTTTCAAAGGTGGACTTTCTACCTCTCAACAAACTTAAATCTTATTGTGATTAATTAAAGAATACTAGGTGCCTTCTTGACAATGCTGGCTATGGAAAACATCTC Human > Chimp ------------- chr13:49063188-49063192 Template switch process: F1: L AGGAAATTATAATTTCTCAAAATCTAGATGAAGCTTGTTAT 1 F3: 4 TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATAT R RF: AGGAAATTATAATTTCTCAAAATCTAGATGAAGCTTGTTATTGTTTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATATGTTCAATTTTCAAAGGTGGACTTTCTATCTCACAACAAACTTAAATATTATTGTGATTAATTAAAGAATACTAGGTTCCTTCTTGACAATG RR: TCCTTTAATATTAAAGAGTTTTAGATCTACTTCGAACAATAACAAAAAAGAAAAGTACTATCTACACAAAGTATCAACGGTATACAAGTTAAAAGTTTCCACCTGAAAGATAGAGTGTTGTTTGAATTTATAATAACACTAATTAATTTCTTATGATCCAAGGAAGAACTGTTAC F2: 3 GTTAC 2 Unidirectional alignment (log-probability: -25.5) GGAAATTATAATTTCTCAAAATCTAGATGAAGCTTGTTatcATTG-TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATAT GGAAATTATAATTTCTCAAAATCTAGATGAAGCTTGTT---ATTGTTTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATAT Template switch alignment (log-probability: -15.9) GGAAATTATAATTTCTCAAAATCTAGATGAAGCTTGTTAT|CATTG|TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATAT GGAAATTATAATTTCTCAAAATCTAGATGAAGCTTGTTAT|CATTG|TTTTTCTTTTCATGATAGATGTGTTTCATAGTTGCCATAT ========= Event 904 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGTA------------------------CCTGTCTATggccaggtgcagtggct ↑ 3 2 1 4 Chimp: GCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGTG------------GCATAAAGAAATACTGACTATggccaggtgcagtggct Gorilla: GCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGTGGCATAAAGAAAT------------ACTGACTATggccaggtgcagtggct Human: GCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGTA------------------------CCTGTCTATggccaggtgcagtggct Cluster: [ ] Orangutan: GCTATAGTTCATCTATGAAACAGGCACCCTAAGACTGTGGCATAAAGAAAT------------ACTGACTATggctgggtgcggtggct Chimp > Human ------------- chr13:67041540-67041545 Template switch process: F1: L ATTGCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGT 1 F3: 4 CTATGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCA R RF: ATTGCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGTGGCATAAAGAAATACTGACTATGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCA RR: TAACGATATCAAGTAGATACTTTGTCCATGGGATTCTGACACCGTATTTCTTTATGACTGATACCGGTCCACGTCACCGAGTGCGGACATTAGGGTCGT F2: 3 TGTCCA 2 Unidirectional alignment (log-probability: -29.2) TTGCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGT-----------------AcctgtCTATGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCA TTGCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGTGGCATAAAGAAATACTGA-----CTATGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCA Template switch alignment (log-probability: -16) TTGCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGT|ACCTGT|CTATGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCA TTGCTATAGTTCATCTATGAAACAGGTACCCTAAGACTGT|ACCTGT|CTATGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAGCA ========= Event 905 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGGTAATAAATTCAATCGTATG----------------GCATAATTGCCATATGGCATAATAGATTTTGTTTGTTTATCTGT Chimp: TGGTAATAAATTCAATCGTATG----------------GCATAATTGCCATATGGCATAATGGATTTTGTTTGTTTATCTGT ↑ 4 2 1 Gorilla: TGGTAATAAATTCAATCGTATG--------------------------------GCATAATGGATTTTGTTTGTTTATCGGT ↓ 4 2 1 Human: TGGTAATAAATTCAATCGTATG----------------GCATAATTGCCATATGGCATAATAGATTTTGTTTGTTTATCTGT Cluster: [ ] Orangutan: TGGTAATAAATTCAATCGTATGGCATAATTGCCATATG----------------GCATAATGGATTTTGTTTGTTTATCTGT Gorilla > Human --------------- chr13:67118505-67118510 Template switch process: F1: L ATAAGCCAACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAAT 1 F3: 4 ATGGCATAATAGATTTTGTTTGTTTATCTGTGCTTCATTAAAGTGAGCTCC R RF: ATAAGCCAACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAATGGATTTTGTTTGTTTATCGGTGCTTCATTAAAGTGAGCTCC RR: TATTCGGTTGTCAAAATAAACCATTATTTAAGTTAGCATACCGTATTACCTAAAACAAACAAATAGCCACGAAGTAATTTCACTCGAGG F2: 3 TACCGT 2 Unidirectional alignment (log-probability: -45) ACAGTTTTATTTGGTAATAAATTCAATCGTAtggcataattgccataTGGCATAATaGATTTTGTTTGTTTATCtGTGCTTCATTA ACAGTTTTATTTGGTAATAAATTCAATCGTA----------------TGGCATAATGGATTTTGTTTGTTTATCGGTGCTTCATTA Template switch alignment (log-probability: -28) ACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAAT|TGCCAT|ATGGCATAATaGATTTTGTTTGTTTATCtGTGCTTCATTA ACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAAT|TGCCAT|ATGGCATAATGGATTTTGTTTGTTTATCGGTGCTTCATTA Gorilla > Chimp --------------- chr13:52218255-52218260 Template switch process: F1: L ATAAGCCAACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAAT 1 F3: 4 ATGGCATAATGGATTTTGTTTGTTTATCTGTGCTTCATTAAAG R RF: ATAAGCCAACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAATGGATTTTGTTTGTTTATCGGTGCTTCATTAAAG RR: TATTCGGTTGTCAAAATAAACCATTATTTAAGTTAGCATACCGTATTACCTAAAACAAACAAATAGCCACGAAGTAATTTC F2: 3 TACCGT 2 Unidirectional alignment (log-probability: -39.4) ACAGTTTTATTTGGTAATAAATTCAATCGTAtggcataattgccataTGGCATAATGGATTTTGTTTGTTTATCtGTGCTTCATTA ACAGTTTTATTTGGTAATAAATTCAATCGTA----------------TGGCATAATGGATTTTGTTTGTTTATCGGTGCTTCATTA Template switch alignment (log-probability: -22.3) ACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAAT|TGCCAT|ATGGCATAATGGATTTTGTTTGTTTATCtGTGCTTCATTA ACAGTTTTATTTGGTAATAAATTCAATCGTATGGCATAAT|TGCCAT|ATGGCATAATGGATTTTGTTTGTTTATCGGTGCTTCATTA ========= Event 906 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: gagggatgaatTCAGTGCCTGACTGGAGTCCCTTGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGATGTTTTGGCATAGG ↑ 1 4 3 2 Chimp: gagggatgaatTCAGTGCCTGGC----------TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGATGTTTTGGTATAGG Gorilla: gagggatcaattcagtGCCTGGC----------TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCGGATGTTTTGGTATAGG ↓ 1 4 3 2 Human: gagggatgaatTCAGTGCCTGACTGGAGTCCCTTGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGATGTTTTGGCATAGG Cluster: [ ] Orangutan: gagggatcaattcagtGCCTGGC----------TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGATGTTTCGGTATAGG Chimp > Human ------------- chr1:212098910-212098921 Template switch process: F1: L CTCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTG 1 F3: 4 TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT R RF: CTCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTGGCTGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT RR: GAGGTGGAGTGTCAATAACACTCCCTACTTAAGTCACGGACCGACATCAAGGAAGTGGGGATCTTCCCTGAGGTCAGGGTCTA F2: 3 TCCCTGAGGTCA 2 Unidirectional alignment (log-probability: -31.3) TCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTGaCtggagtccctTGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT TCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTGGC----------TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT Template switch alignment (log-probability: -16.8) TCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTG|ACTGGAGTCCCT|TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT TCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTG|ACTGGAGTCCCT|TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT Gorilla > Human --------------- chr1:212098910-212098921 Template switch process: F1: L CTCCACCTCACAGTTATTGTGAGGGATGAATTCAGTGCCTG 1 F3: 4 TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCAGAT R RF: CTCCACCTCACAGTTATTGTGAGGGATCAATTCAGTGCCTGGCTGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCGGAT RR: GAGGTGGAGTGTCAATAACACTCCCTAGTTAAGTCACGGACCGACATCAAGGAAGTGGGGATCTTCCCTGAGGTCAGGGCCTA F2: 3 TCCCTGAGGTCA 2 Unidirectional alignment (log-probability: -41.8) TCCACCTCACAGTTATTGTGAGGGATgAATTCAGTGCCTGaCtggagtccctTGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCaGAT TCCACCTCACAGTTATTGTGAGGGATCAATTCAGTGCCTGGC----------TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCGGAT Template switch alignment (log-probability: -28.3) TCCACCTCACAGTTATTGTGAGGGATgAATTCAGTGCCTG|ACTGGAGTCCCT|TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCaGAT TCCACCTCACAGTTATTGTGAGGGATCAATTCAGTGCCTG|ACTGGAGTCCCT|TGTAGTTCCTTCACCCCTAGAAGGGACTCCAGTCCCGGAT ========= Event 907 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCAGACATTTCTAGTACTGT----------------GCTATATACAGTTGTACAACATAGcatttctattctgc ↓ 1 4 3 2 Chimp: TTCAGACATTTCTAGTACTGT--------TGTACAACAGTATATACAGTTGTACAACATAGCATTTCTATTCTGC Gorilla: TTCAGACATTCCTAGTACTGTTGTACAAC--------AGTATATACAGTTGTACAGCATAGCATTTCTATTCTGC Human: TTCAGACATTTCTAGTACTGT----------------GCTATATACAGTTGTACAACATAGcatttctattctgc Cluster: [ ] Orangutan: TTCAGACATTTCTAGTACTGT----------------GCTATATACAGTTGTACAACATAGCATTTCTATTCTGC Human > Chimp ------------- chr13:52758616-52758626 Template switch process: F1: L AATTTTAATATTCCAAAGAATTCAGACATTTCTAGTACTGT 1 F3: 4 ATATACAGTTGTACAACATAGCATTTCTATTCTGCTTAA R RF: AATTTTAATATTCCAAAGAATTCAGACATTTCTAGTACTGTGCTATATACAGTTGTACAACATAGCATTTCTATTCTGCTTAA RR: TTAAAATTATAAGGTTTCTTAAGTCTGTAAAGATCATGACACGATATATGTCAACATGTTGTATCGTAAAGATAAGACGAATT F2: 3 TGACAACATGT 2 Unidirectional alignment (log-probability: -34.1) ATTTTAATATTCCAAAGAATTCAGACATTTCTAGTACTGTtgtacaacaG-TATATACAGTTGTACAACATAGCATTTCTATTCTGCTTAA ATTTTAATATTCCAAAGAATTCAGACATTTCTAGTACTGT---------GCTATATACAGTTGTACAACATAGCATTTCTATTCTGCTTAA Template switch alignment (log-probability: -22.6) ATTTTAATATTCCAAAGAATTCAGACATTTCTAGTACTGT|TGTACAACaGT|ATATACAGTTGTACAACATAGCATTTCTATTCTGCTTAA ATTTTAATATTCCAAAGAATTCAGACATTTCTAGTACTGT|TGTACAACTGT|ATATACAGTTGTACAACATAGCATTTCTATTCTGCTTAA ========= Event 908 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCGGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGGA----------------CTGCTCCTGGGGGCGCGTTTCTCCGG ↑ 3 2 1 4 Chimp: GAGGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGCA--------GCCGTGCGGGGCTTCTGGGGGCGCGTTTCTCCGG Gorilla: GCGGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGCAGCCTTGCG--------GGGCTTCTGGGGGCGCGTTTCTCCGG ↓ 3 2 1 4 Human: GCGGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGGA----------------CTGCTCCTGGGGGCGCGTTTCTCCGG Cluster: [ ] Orangutan: Chimp > Human ------------- chr1:3698935-3698939 Template switch process: F1: L GGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG 1 F3: 4 CTCCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGTTCC R RF: GGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGCAGCCGTGCGGGGCTTCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGTTCC RR: CCACCGGGACCCGGAGCGTCAGGACGTCTGTGTGCAGACCCGTCGGCACGCCCCGAAGACCCCCGCGCAAAGAGGCCACACTCCACACCTTTCAAGG F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -32) GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGgactgctC---------------CTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG-------CAGCCGTGCGGGGCTTCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT Template switch alignment (log-probability: -22) GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG|GACTG|CTcCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG|GACTG|CTTCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT Gorilla > Human --------------- chr1:3698935-3698939 Template switch process: F1: L GGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG 1 F3: 4 CTCCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGTTCC R RF: GGTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGCAGCCTTGCGGGGCTTCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGTTCC RR: CCACCGGGACCCGGAGCGTCAGGACGTCTGTGTGCAGACCCGTCGGAACGCCCCGAAGACCCCCGCGCAAAGAGGCCACACTCCACACCTTTCAAGG F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -31.1) GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTG-----------GGGactGCTcCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGGCAGCCTTGCGGG---GCTTCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT Template switch alignment (log-probability: -22) GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG|GACTG|CTcCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT GTGGCCCTGGGCCTCGCAGTCCTGCAGACACACGTCTGGG|GACTG|CTTCTGGGGGCGCGTTTCTCCGGTGTGAGGTGTGGAAAGT ========= Event 909 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: agagtatgGCATTATCTCATATAAA--------------TTACTTTGAAAAGTTAATGAGATTTTCTATTTATACCATTTATTTCCT ↓ 13 24 ↑ 13 24 Chimp: agagtatgGCATTATCTCATAGAAA-------ATCTCATTAACTTTTCAAAGT-------AATTTATATTTATACCATTTATTTCCT Gorilla: agagtatgGCATTATCTCATAGAAAATCTCAT-------TAACTTTTCAAAGT-------AATTTATATTTATACCATTTATTTCCT ↓ 13 24 ↑ 13 24 Human: agagtatgGCATTATCTCATATAAA--------------TTACTTTGAAAAGTTAATGAGATTTTCTATTTATACCATTTATTTCCT Cluster: [ ] Orangutan: aGACTATGGCATTATCTCATAGAAAATCTCAT-------TAACTTTTCAAAGT-------AATTTATATTTATCCCATTTATTTCCT Chimp > Human ------------- chr13:68844065-68844095 Template switch process: F1: L GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATA 1 F3: 4 TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT R RF: GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATAGAAAATCTCATTAACTTTTCAAAGTAATTTATATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT RR: CATACATATACATATACATATCTCATACCGTAATAGAGTATCTTTTAGAGTAATTGAAAAGTTTCATTAAATATAAATATGGTAAATAAAGGAAATTATCTCCGGTATATCA F2: 3 CTTTTAGAGTAATTGAAAAGTTTCATTAAAT 2 Unidirectional alignment (log-probability: -62.9) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATAtAAA------------------------TTActttgaaaagttaatgagattttcTATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATAGAAAATCTCATTAACTTTTCAAAGTAATTTA------------------------TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT Template switch alignment (log-probability: -19.1) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|TAAATTACTTTGAAAAGTTAATGAGATTTTC|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|TAAATTACTTTGAAAAGTTAATGAGATTTTC|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT Human > Chimp ------------- chr13:54017788-54017818 Template switch process: F1: L GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATA 1 F3: 4 TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT R RF: GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATATAAATTACTTTGAAAAGTTAATGAGATTTTCTATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT RR: CATACATATACATATACATATCTCATACCGTAATAGAGTATATTTAATGAAACTTTTCAATTACTCTAAAAGATAAATATGGTAAATAAAGGAAATTATCTCCGGTATATCA F2: 3 ATTTAATGAAACTTTTCAATTACTCTAAAAG 2 Unidirectional alignment (log-probability: -62.9) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATAgAAAatctcattaacttttcaaagtaatTTA------------------------TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATATAAA------------------------TTACTTTGAAAAGTTAATGAGATTTTCTATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT Template switch alignment (log-probability: -19.1) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|GAAAATCTCATTAACTTTTCAAAGTAATTTA|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|GAAAATCTCATTAACTTTTCAAAGTAATTTA|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT Gorilla > Human --------------- chr13:68844065-68844095 Template switch process: F1: L GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATA 1 F3: 4 TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT R RF: GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATAGAAAATCTCATTAACTTTTCAAAGTAATTTATATTTATACCATTTATTTCCTTTAATAGAGGCCATATGGT RR: CATACATATACATATACATATCTCATACCGTAATAGAGTATCTTTTAGAGTAATTGAAAAGTTTCATTAAATATAAATATGGTAAATAAAGGAAATTATCTCCGGTATACCA F2: 3 CTTTTAGAGTAATTGAAAAGTTTCATTAAAT 2 Unidirectional alignment (log-probability: -67.5) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA------------------------TAAattactttgaaaagttaatgagatTTTcTATTTATACCATTTATTTCCTTTAATAGAGGCCATATaGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATAGAAAATCTCATTAACTTTTCAAAGTAA------------------------TTTATATTTATACCATTTATTTCCTTTAATAGAGGCCATATGGT Template switch alignment (log-probability: -25.2) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|TAAATTACTTTGAAAAGTTAATGAGATTTTC|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATaGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|TAAATTACTTTGAAAAGTTAATGAGATTTTC|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATGGT Human > Gorilla --------------- chr13:51136327-51136357 Template switch process: F1: L GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATA 1 F3: 4 TATTTATACCATTTATTTCCTTTAATAGAGGCCATATGGT R RF: GTATGTATATGTATATGTATAGAGTATGGCATTATCTCATATAAATTACTTTGAAAAGTTAATGAGATTTTCTATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT RR: CATACATATACATATACATATCTCATACCGTAATAGAGTATATTTAATGAAACTTTTCAATTACTCTAAAAGATAAATATGGTAAATAAAGGAAATTATCTCCGGTATATCA F2: 3 ATTTAATGAAACTTTTCAATTACTCTAAAAG 2 Unidirectional alignment (log-probability: -67.5) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATAgaaaatctcattaacttttcaaagTAA------------------------TTTaTATTTATACCATTTATTTCCTTTAATAGAGGCCATATgGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA------------------------TAAATTACTTTGAAAAGTTAATGAGATTTTCTATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT Template switch alignment (log-probability: -25.2) TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|GAAAATCTCATTAACTTTTCAAAGTAATTTA|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATgGT TATGTATATGTATATGTATAGAGTATGGCATTATCTCATA|GAAAATCTCATTAACTTTTCAAAGTAATTTA|TATTTATACCATTTATTTCCTTTAATAGAGGCCATATAGT ========= Event 910 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ctattattTTAGTCTTTTTCATATGTTGAATGTAA------------TCAGTAATATCAATATTTGGCTT Chimp: ctattattTTAGTCTTTTTCATATGTTGAATGTAA------------TCAGTAATATCAATATTTGGCTT ↓ 3 2 4 1 Gorilla: CTATTATTTTAGTCTTTTTCATATGTTGAATGTAATCAACATATGAATCAGTAATATCAATATTTGGCTT Human: ctattattTTAGTCTTTTTCATATGTTGAATGTAA------------TCAGTAATATCAATATTTGGCTT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------------NNNNNNNNNNNNNNNNNNNNNNN Chimp > Gorilla --------------- chr13:50954968-50954974 Template switch process: F1: L TTTTTACTATTATTTTAGTCTTTTTCATATGTTGAATGTAATCA 1 F3: 4 AATCAGTAATATCAATATTTGGCTTACATGATGCTTTAACTA R RF: TTTTTACTATTATTTTAGTCTTTTTCATATGTTGAATGTAATCAGTAATATCAATATTTGGCTTACATGATGCTTTAACTA RR: AAAAATGATAATAAAATCAGAAAAAGTATACAACTTACATTAGTCATTATAGTTATAAACCGAATGTACTACGAAATTGAT F2: 3 GTATACA 2 Unidirectional alignment (log-probability: -28.1) TACTATTATTTTAGTCTTTTTCATATGTTGAATGTaatcaacatatgAATCAGTAATATCAATATTTGGCTTACATGATGCTTTAAC TACTATTATTTTAGTCTTTTTCATATGTTGAATGT------------AATCAGTAATATCAATATTTGGCTTACATGATGCTTTAAC Template switch alignment (log-probability: -16.7) TACTATTATTTTAGTCTTTTTCATATGTTGAATGTAATCA|ACATATG|AATCAGTAATATCAATATTTGGCTTACATGATGCTTTAAC TACTATTATTTTAGTCTTTTTCATATGTTGAATGTAATCA|ACATATG|AATCAGTAATATCAATATTTGGCTTACATGATGCTTTAAC ========= Event 911 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAATTGCTAAATTCTGTTCTTCAGAATTTTAGAATTCTTTCA-------------------GAATTCTGTTCTTCCAATTTTAGATTT Chimp: caattgctaaattctgttcttca-------------------GAATTTTAGAATTCTTACAGAATTCTGTTCTTCCAATTTTATATTT Gorilla: CAATTGCTAAATTCTGTTCTTCA--------------------------------------GAATTCTGTTCTTCCAATTTTAGATTT ↓ 4 3 2 Human: CAATTGCTAAATTCTGTTCTTCAGAATTTTAGAATTCTTTCA-------------------GAATTCTGTTCTTCCAATTTTAGATTT Cluster: [ ] Orangutan: CAGTTGCTAAATTTTGTTCTTCA--------------------------------------GAATTCTGTTCTTCCAATTTTAGATTT Gorilla > Human --------------- chr13:67301645-67301652 Template switch process: F1: L TTCAAAAAGACTTTTCTTCAATTGCTAAATTCTGTTCTTCAGAATTTT 1 F3: 4 TTCAGAATTCTGTTCTTCCAATTTTAGATTTTCCAAACGTACAA R RF: TTCAAAAAGACTTTTCTTCAATTGCTAAATTCTGTTCTTCAGAATTCTGTTCTTCCAATTTTAGATTTTCCAAACGTACAA RR: AAGTTTTTCTGAAAAGAAGTTAACGATTTAAGACAAGAAGTCTTAAGACAAGAAGGTTAAAATCTAAAAGGTTTGCATGTT F2: 3 TCTTAAGA 2 Unidirectional alignment (log-probability: -38.2) GACTTTTCTTCAATTGCTAAATTCTGTTCTTcagaattttagaattctttCAGAATTCTGTTCTTCCAATTTTAGATTTTCCAAACGT GACTTTTCTTCAATTGCTAAATTCTGTTCTT-------------------CAGAATTCTGTTCTTCCAATTTTAGATTTTCCAAACGT Template switch alignment (log-probability: -22.5) GACTTTTCTTCAATTGCTAAATTCTGTTCTTCAGAATTtT|AGAATTCT|TTCAGAATTCTGTTCTTCCAATTTTAGATTTTCCAAACGT GACTTTTCTTCAATTGCTAAATTCTGTTCTTCAGAATTCT|AGAATTCT|TTCAGAATTCTGTTCTTCCAATTTTAGATTTTCCAAACGT ========= Event 912 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGACTCCCTCTAGCGGGAACACTCGCTGCCGGCACTGGGTGCTCTGTGGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCGAGGGCTCTCAAGGCCGGTCCTGCAGGGTCCGAGGTGGGTGGGGAAggtgggcaggttgagggtgggcagggttgagCTCACAATTCTGGCTGTGCCC Chimp: CTGGCTCCCTCTAGCGGGAACACTCGCTGCCGGCACTGGGTGCTCTGTGGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCGAGGGCTCTCAAGGCCGGTCCTGCAGGGTCCAAGGTGGGTGGGGAAggtgggcaggttgagggtgggcagggttgagCTCACAATTCTGGCTGTGCCC Gorilla: CTGACTCCCTCTAGCGGGAACGCTCACTGCCGGCACTGGGTGCTCTGTGGTGACCGAGGGCTCACAAGGCCGGTCCTGCCTGGTCCGAGGAGGGTGGCGAACCTTCGCAAGTCGACTTTGTACCATGTATTAGCACCCAATTTTTGTTTTTCCCTGCATACATGGTTCCTGTCtctatttttgcccttacttctacttttgcccttatttctCTTGTGTnnnnnnnnnnCTGCCGGCACTGGGTGCTCTGTGGTGACCGAGGGCTCACAAGGCCGGTCCTGCAGGGTCCGAGGTGGGTGGGGAAggtgggcaggttgagggtgggcagggttgagCTCACAATTCTGGCTGTGCCC ↑ 1 4 3 2 Human: CTGACTCCCTCTAGCGGGAACACTCGCTGCCGGCACTGGGTGCTCTGTGGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCGAGGGCTCTCAAGGCCGGTCCTGCAGGGTCCGAGGTGGGTGGGGAAggtgggcaggttgagggtgggcagggttgagCTCACAATTCTGGCTGTGCCC Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggatgggtagatgggtagatggatggatNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr1:3437183-3437187 Template switch process: F1: L AGCCTCGCAGCTTTGAGCCTCTGACTCCCTCTAGCGGGAAC 1 F3: 4 CTGCCGGCACTGGGTGCTCTGTGGTGACCGAGGGCTCACA R RF: AGCCTCACAGCTTTGAGCCTCTGACTCCCTCTAGCGGGAACACTCGCTGCCGGCACTGGGTGCTCTGTGGTGACCGAGGGCTCTCAAGGCCGGTCCTGCAGGGTCCGAGGTGGGTGGGGAAGGTGGGCAGGTTGAGGGTGGGCAGGGTTGAGC RR: TCGGAGTGTCGAAACTCGGAGACTGAGGGAGATCGCCCTTGTGAGCGACGGCCGTGACCCACGAGACACCACTGGCTCCCGAGAGTTCCGGCCAGGACGTCCCAGGCTCCACCCACCCCTTCCACCCGTCCAACTCCCACCCGTCCCAACTCG F2: 3 ACTCG 2 Unidirectional alignment (log-probability: -44.4) GCCTCgCAGCTTTGAGCCTCTGACTCCCTCTAGCGGGAACgCTCaCTGCCGGCACTGGGTGCTCTGTGGTGaccgagggctcaca GCCTCACAGCTTTGAGCCTCTGACTCCCTCTAGCGGGAACACTCGCTGCCGGCACTGGGTGCTCTGTGGTG-------------- Template switch alignment (log-probability: -27.4) GCCTCgCAGCTTTGAGCCTCTGACTCCCTCTAGCGGGAAC|GCTCA|CTGCCGGCACTGGGTGCTCTGTGGTGACCGAGGGCTCaCA GCCTCACAGCTTTGAGCCTCTGACTCCCTCTAGCGGGAAC|GCTCA|CTGCCGGCACTGGGTGCTCTGTGGTGACCGAGGGCTCTCA ========= Event 913 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGTTCTTTTCTTGCCAACAC--AGTGGTTGAGAGCCGGTATGTGCTATCTGTCTCGGTTT Chimp: GTGTTCTTTTCTTGCCAACAC--AGTTGTTGAGAGCCGGTATGTGCTATCTGTCTCGGGTT ↓ 1 4 3 2 Gorilla: GTGTTCTTTTCTTGCCAACACATACCGGTTGAGAGCCGGTATGTGCTATCTGTCTTGGGTT Human: CTGTTCTTTTCTTGCCAACAC--AGTGGTTGAGAGCCGGTATGTGCTATCTGTCTCGGTTT Cluster: [ ] Orangutan: GTGTTCTTTTCTTGCCAACAC--AGTGGTTGAGAGCCGGTATGTGCTATCTGTCTCGGGTT Chimp > Gorilla --------------- chr13:43004446-43004450 Template switch process: F1: L CAGGGTGCCGAATGAACCTAGTGTTCTTTTCTTGCCAACACA 1 F3: 4 GTTGAGAGCCGGTATGTGCTATCTGTCTTGGGTTTATAGT R RF: CAGGGTGCCGAATGAACCTAGTGTTCTTTTCTTGCCAACACAGTTGTTGAGAGCCGGTATGTGCTATCTGTCTCGGGTTTATAGT RR: GTCCCACGGCTTACTTGGATCACAAGAAAAGAACGGTTGTGTCAACAACTCTCGGCCATACACGATAGACAGAGCCCAAATATCA F2: 3 GCCAT 2 Unidirectional alignment (log-probability: -32) GGGTGCCGAATGAACCTAGTGTTCTTTTCTTGCCAACACA--TaccgGTTGAGAGCCGGTATGTGCTATCTGTCTtGGGTTTATAGT GGGTGCCGAATGAACCTAGTGTTCTTTTCTTGCCAACACAGTT----GTTGAGAGCCGGTATGTGCTATCTGTCTCGGGTTTATAGT Template switch alignment (log-probability: -21.9) GGGTGCCGAATGAACCTAGTGTTCTTTTCTTGCCAACACA|TACCG|GTTGAGAGCCGGTATGTGCTATCTGTCTtGGGTTTATAGT GGGTGCCGAATGAACCTAGTGTTCTTTTCTTGCCAACACA|TACCG|GTTGAGAGCCGGTATGTGCTATCTGTCTCGGGTTTATAGT ========= Event 914 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGTTCTATAAATTAAGTTT-------------CTGTATGATACCTGATAATAACATGGAAATATAGACAG ↓ 14 3 2 Chimp: TCTGTTCTATAAATTAAGTTTATTTATCAGGTATCAGCATGATACCTGATAATAACATGGAAATATAGACAG ↑ 14 3 2 Gorilla: TATGTTCTATAAATTAAGTTT-------------CTGCATGATACCTGATAATAACATGGAAATATAGACAG Human: TCTGTTCTATAAATTAAGTTT-------------CTGTATGATACCTGATAATAACATGGAAATATAGACAG Cluster: [ ] Orangutan: TCTGTTCTATAAATTAAGTTT-------------CTGCATGATACCTGGTAATAACATGGAAATATAGACAG Human > Chimp ------------- chr13:57558846-57558858 Template switch process: F1: L AATAATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTAT 1 F3: 4 GCATGATACCTGATAATAACATGGAAATATAGACAGAGATAG R RF: AATAATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTCTGTATGATACCTGATAATAACATGGAAATATAGACAGAGATAG RR: TTATTATAAATTTTATTGTTAGACAAGATATTTAATTCAAAGACATACTATGGACTATTATTGTACCTTTATATCTGTCTCTATC F2: 3 ACTATGGACTATT 2 Unidirectional alignment (log-probability: -41.6) AATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTaTtTatcaggtatcagcATGATACCTGATAATAACATGGAAATATAGACAGAGAT AATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTCTGT-------------ATGATACCTGATAATAACATGGAAATATAGACAGAGAT Template switch alignment (log-probability: -29) AATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTaT|TTATCAGGTATCA|GcATGATACCTGATAATAACATGGAAATATAGACAGAGAT AATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTCT|TTATCAGGTATCA|GTATGATACCTGATAATAACATGGAAATATAGACAGAGAT Gorilla > Chimp --------------- chr13:57558846-57558858 Template switch process: F1: L AATAATATTTAAAATAACAATCTGTTCTATAAATTAAGTTTAT 1 F3: 4 GCATGATACCTGATAATAACATGGAAATATAGACAGAGAT R RF: AATAATATTTAAAATAACAATATGTTCTATAAATTAAGTTTCTGCATGATACCTGATAATAACATGGAAATATAGACAGAGAT RR: TTATTATAAATTTTATTGTTATACAAGATATTTAATTCAAAGACGTACTATGGACTATTATTGTACCTTTATATCTGTCTCTA F2: 3 ACTATGGACTATT 2 Unidirectional alignment (log-probability: -40.6) AATATTTAAAATAACAATcTGTTCTATAAATTAAGTTtatttatcaggtaTCaGCATGATACCTGATAATAACATGGAAATATAGACAGAGAT AATATTTAAAATAACAATATGTTCTATAAATTAAGTT-------------TCTGCATGATACCTGATAATAACATGGAAATATAGACAGAGAT Template switch alignment (log-probability: -28.5) AATATTTAAAATAACAATcTGTTCTATAAATTAAGTTTaT|TTATCAGGTATCA|GCATGATACCTGATAATAACATGGAAATATAGACAGAGAT AATATTTAAAATAACAATATGTTCTATAAATTAAGTTTCT|TTATCAGGTATCA|GCATGATACCTGATAATAACATGGAAATATAGACAGAGAT ========= Event 915 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 345 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACTGAAGCTGAAACAAGGGAAGTTTCTGGGGGACACTTCCGAGAAAGATGCAGTGTGGACCATCT Chimp: ACTGAAGCTGAAACAAGGGAAGTTTCTGGGGGACACTTCCCAGAAAGATGCAGTGTGGACCATCT ↑ 3 1 4 2 Gorilla: ACTGAAGCTGAAACAAGGGAAGTGT-----------CCCCCAGAAAGATGCAGTGTGGACCATCT ↓ 3 1 4 2 ↑ 1 3 2 4 Human: ACTGAAGCTGAAACAAGGGAAGTTTCTGGGGGACACTTCCGAGAAAGATGCAGTGTGGACCATCT Cluster: [ ] Orangutan: ACTGAAGCTGAAACAAGGGAAGTGT-----------CCCCCAGAAAGATGCAGTGTGGAATGTCT Gorilla > Human --------------- chr13:75235533-75235547 Template switch process: F1: L CTGAACCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT 1 F3: 4 CCGAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG R RF: CTGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTGTCCCCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG RR: GACTCGGTCTTCCAGTTCTGACTTCGACTTTGTTCCCTTCACAGGGGGTCTTTCTACGTCACACCTGGTAGATGACCCATGGTCTCAC F2: 3 TTCACAGGGGGTCTT 2 Unidirectional alignment (log-probability: -48.9) TGAaCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTtTCtgggggacacttCCgAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA TGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTGTC-----------CCCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA Template switch alignment (log-probability: -28.7) TGAaCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT|TTCTGGGGGACACTT|CCgAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA TGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT|TTCTGGGGGACACTT|CCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA Human > Gorilla --------------- chr13:57641968-57641975 Template switch process: F1: L CTGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT 1 F3: 4 GAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG R RF: CTGAACCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTTTCTGGGGGACACTTCCGAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG RR: GACTTGGTCTTCCAGTTCTGACTTCGACTTTGTTCCCTTCAAAGACCCCCTGTGAAGGCTCTTTCTACGTCACACCTGGTAGATGACCCATGGTCTCAC F2: 3 ACCCCCTG 2 Unidirectional alignment (log-probability: -33.6) TGAgCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTgTC-----------cCCcAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG TGAACCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTTTCTGGGGGACACTTCCGAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG Template switch alignment (log-probability: -22.2) TGAgCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT|GTCCCCCA|GAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG TGAACCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT|GTCCCCCA|GAAAGATGCAGTGTGGACCATCTACTGGGTACCAGAGTG Gorilla > Chimp --------------- chr13:60575528-60575542 Template switch process: F1: L CTGAACCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT 1 F3: 4 CCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA R RF: CTGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTGTCCCCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA RR: GACTCGGTCTTCCAGTTCTGACTTCGACTTTGTTCCCTTCACAGGGGGTCTTTCTACGTCACACCTGGTAGATGACCCATGGTCT F2: 3 TTCACAGGGGGTCTT 2 Unidirectional alignment (log-probability: -43.3) TGAaCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTtTCtgggggacacttCCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA TGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGTGTC-----------CCCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA Template switch alignment (log-probability: -23.2) TGAaCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT|TTCTGGGGGACACTT|CCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA TGAGCCAGAAGGTCAAGACTGAAGCTGAAACAAGGGAAGT|TTCTGGGGGACACTT|CCCAGAAAGATGCAGTGTGGACCATCTACTGGGTACCAGA ========= Event 916 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAAAGGAGGTGCTTAGAGTCCG---GGCTGGCT-----CAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGG Chimp: GTAAAGGAGGTGCTTAGAGTCCG---GGCTGGCT-----CAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGG ↓ 3 2 4 Gorilla: GTAAAGGAGGTGCTTAGAGTCTG------TGAGT----------CAGCCCGGCAGCTGTGCTAGTGCTTGG ↑ 3 2 4 Human: GTAAAGGAGGTGCTTAGAGTCCG---GGCTGGCT-----CAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGG Cluster: [ ] Orangutan: GTAAAGGAGGTGCTTAGAGTCCGGGC---TGGCTCAGGC-----CGGCCGGGCAGCTGTGCTAGCGCTTGG Human > Gorilla --------------- chr1:3485069-3485079 Template switch process: F1: L GTCGAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCTG 1 F3: 4 GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG R RF: GTCGAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCCGGGCTGGCTCAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG RR: CAGCTTTGTCTCCGGTCTCCCATTTCCTCCACGAATCTCAGGCCCGACCGAGTCCGGCCGGCCCGTCGACACGATCACGAACCTCAAGGACGAGTCAGGGGC F2: 3 CCCGACTGAGT 2 Unidirectional alignment (log-probability: -38.9) GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTctgtgagtcagcCC--------------------GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGT------------CCGGGCTGGCTCAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG Template switch alignment (log-probability: -28.2) GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCtG|TGAGtCAGCCC|GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCCG|TGAGCCAGCCC|GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG Chimp > Gorilla --------------- chr1:3485069-3485079 Template switch process: F1: L GTCGAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCTG 1 F3: 4 GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG R RF: GTCGAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCCGGGCTGGCTCAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG RR: CAGCTTTGTCTCCGGTCTCCCATTTCCTCCACGAATCTCAGGCCCGACCGAGTCCGGCCGGCCCGTCGACACGATCACGAACCTCAAGGACGAGTCAGGGGC F2: 3 CCCGACTGAGT 2 Unidirectional alignment (log-probability: -38.9) GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTctgtgagtcagcCC--------------------GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGT------------CCGGGCTGGCTCAGGCCGGCCGGGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG Template switch alignment (log-probability: -28.2) GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCtG|TGAGtCAGCCC|GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG GAAACAGAGGCCAGAGGGTAAAGGAGGTGCTTAGAGTCCG|TGAGCCAGCCC|GGCAGCTGTGCTAGTGCTTGGAGTTCCTGCTCAGTCCCCG ========= Event 917 ========= Phylogenetic placement: unresolved Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: TTTGTTAAAAATTGTAGTGTTACAAAGCAATTCTTATGCTAGCTGCAGCA------------------------------------------------------------------------------------------------------------------------------------------------GCTAGCATAAGAATTGCTTTGTAA------TACAATTTTTAACAAAGATTT Chimp: TTTGTTAAAAATTGTAGTGTTACAAAGCAATTCTTATGCTAGCTGCTGCA------------------------------------------------------------------------GCTAAAATCATTTTAAAGGGTTGCTTGTGAAGGAATTGTACTGTGAGTCTTCCAATGATTTTAGCTGCAGCAGCTAGCGTAAGAATTGCTTTGTAA---TACTACAGTTTTTAACAAAGATTT Gorilla: TTTGTTAAAAATTGTAGTGTTACAAAGCAATTCTTATGCTAGCTGCTGCAGCTAAAATCATTTTAAAGGGTTGCATGTGAAGGAATTGTACTGTGAGTCTTCCAATGATTTTAGCTGCAGCA------------------------------------------------------------------------GCTAGTGTAAGAATTGCTTTGTAATAC---TACAATTTTTAACAAAGATTT ↓ 3 12 4 Human: TTTGTTAAAAATTGTAGTGTTACAAAGCAATTCTTATGCTAGCTGCAGCA------------------------------------------------------------------------------------------------------------------------------------------------GCTAGCATAAGAATTGCTTTGTAA------TACAATTTTTAACAAAGATTT Cluster: [ ] Orangutan: TTTGTTAAAAATTGTGGTGTTACAAAGCAATTCTTATGCTAGCTGCTGCAGCTAAAATCATTTTAAAGGGTTGCATGTGAAGGAATTGTACTGTGAGTCTTCCAATGATTTTAGCTGCAGCA------------------------------------------------------------------------GCTAGCGTAAGAATTGCTTTGTAATAC---TACAATTTTTAACAAAGGTTT Gorilla > Human --------------- chr13:75640171-75640198 Template switch process: F1: L C 1 F3: 4 TACAATTTTTAACAAAGATTTACCATAGTGATTACAGGTGTGAGCCACCGCACCTGGCCTGGGCTCTGCTATTTAAATCCTGTAGGTCTCAGTTTTTTCC R RF: TTACAAAGCAATTCTTATGCTAGCTGCTGCAGCTAAAATCATTTTAAAGGGTTGCATGTGAAGGAATTGTACTGTGAGTCTTCCAATGATTTTAGCTGCAGCAGCTAGTGTAAGAATTGCTTTGTAATACTACAATTTTTAACAAAGATTTACCATAGTGATTACAGGTGTGAGCCACCGCACCTGGCCTGGACTCTGCTATTTAAATCCTGTAGGTCTCAGTTTTTTCC RR: AATGTTTCGTTAAGAATACGATCGACGACGTCGATTTTAGTAAAATTTCCCAACGTACACTTCCTTAACATGACACTCAGAAGGTTACTAAAATCGACGTCGTCGATCACATTCTTAACGAAACATTATGATGTTAAAAATTGTTTCTAAATGGTATCACTAATGTCCACACTCGGTGGCGTGGACCGGACCTGAGACGATAAATTTAGGACATCCAGAGTCAAAAAAGG F2: 3 AATGTTTCGTTAAGAATACGATCGACGA 2 Unidirectional alignment (log-probability: -36.4) CAGCAGCTAGcaTAAGAATTGCTTTGTAA---TACAATTTTTAACAAAGATTTACCATAGTGATTACAGGTG CAGCAGCTAGTGTAAGAATTGCTTTGTAATACTACAATTTTTAACAAAGATTTACCATAGTGATTACAGGTG Template switch alignment (log-probability: -25.3) C|AGCAGCTAGCATAAGAATTGCTTTGTAA|TACAATTTTTAACAAAGATTTACCATAGTGATTACAGGTG C|AGCAGCTAGCATAAGAATTGCTTTGTAA|TACAATTTTTAACAAAGATTTACCATAGTGATTACAGGTG ========= Event 918 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATTATGTTACTGGCATAGCATGACC---------AAAGGAATGACTTTCCATAGTTCC ↓ 3 1 42 Chimp: CATTATGTTACTGGCATAGCATGACCCTTTGGTCATGAGGAATGACTTTCCGTAGTTCC ↑ 3 1 42 Gorilla: CATTATATTACTGGCATAGCATGACC---------AAAGGAATGACTTTCCATAGTTCC Human: CATTATGTTACTGGCATAGCATGACC---------AAAGGAATGACTTTCCATAGTTCC Cluster: [ ] Orangutan: CATTATGTTACTGGCACAGCATGACC---------AAAGGAATGACTTTCCATAGTTCC Human > Chimp ------------- chr13:62216710-62216720 Template switch process: F1: L GCTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACC 1 F3: 4 AGGAATGACTTTCCGTAGTTCCTCATTATATCTGGAGGTG R RF: GCTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACCAAAGGAATGACTTTCCATAGTTCCTCATTATATCTGGAGGTG RR: CGATTATACAAACTCGTAATACAATGACCGTATCGTACTGGTTTCCTTACTGAAAGGTATCAAGGAGTAATATAGACCTCCAC F2: 3 GTACTGGTTTC 2 Unidirectional alignment (log-probability: -41.9) CTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACCctttggtcatgAGGAATGACTTTCCgTAGTTCCTCATTATATCTGGAGGTG CTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACC---------AAAGGAATGACTTTCCATAGTTCCTCATTATATCTGGAGGTG Template switch alignment (log-probability: -22.6) CTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACC|CTTTGGTCATG|AGGAATGACTTTCCgTAGTTCCTCATTATATCTGGAGGTG CTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACC|CTTTGGTCATG|AGGAATGACTTTCCATAGTTCCTCATTATATCTGGAGGTG Gorilla > Chimp --------------- chr13:62216710-62216720 Template switch process: F1: L GCTAATATGTTTGAGCATTATGTTACTGGCATAGCATGACC 1 F3: 4 AGGAATGACTTTCCGTAGTTCCTCATTATATCTGGAGGTG R RF: GCTAATATGTTTGAGCATTATATTACTGGCATAGCATGACCAAAGGAATGACTTTCCATAGTTCCTCATTATATCTGGAGGTG RR: CGATTATACAAACTCGTAATATAATGACCGTATCGTACTGGTTTCCTTACTGAAAGGTATCAAGGAGTAATATAGACCTCCAC F2: 3 GTACTGGTTTC 2 Unidirectional alignment (log-probability: -45.9) CTAATATGTTTGAGCATTATgTTACTGGCATAGCATGACCctttggtcatgAGGAATGACTTTCCgTAGTTCCTCATTATATCTGGAGGTG CTAATATGTTTGAGCATTATATTACTGGCATAGCATGACC---------AAAGGAATGACTTTCCATAGTTCCTCATTATATCTGGAGGTG Template switch alignment (log-probability: -28.2) CTAATATGTTTGAGCATTATgTTACTGGCATAGCATGACC|CTTTGGTCATG|AGGAATGACTTTCCgTAGTTCCTCATTATATCTGGAGGTG CTAATATGTTTGAGCATTATATTACTGGCATAGCATGACC|CTTTGGTCATG|AGGAATGACTTTCCATAGTTCCTCATTATATCTGGAGGTG ========= Event 919 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTTGGAGGGAGTGTACAGTGTTACAGCCACTGTAACACTGCAGGagtcaagtgatatc ↑ 3 2 1 4 Chimp: CCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATG-CCTGCAGGagtcaagtgatgtc Gorilla: CCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATG-CCTGCAGGagtcaagtgatgtc ↓ 3 2 1 4 Human: CCTTGGAGGGAGTGTACAGTGTTACAGCCACTGTAACACTGCAGGagtcaagtgatatc Cluster: [ ] Orangutan: CCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATG-CCTGCAGGagtcaagtgatgtc Chimp > Human ------------- chr13:35869946-35869953 Template switch process: F1: L CGACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA 1 F3: 4 CTGCAGGAGTCAAGTGATATCCATGAATGAAGCAGGTGGG R RF: CGACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATGCCTGCAGGAGTCAAGTGATGTCCATGAATGAAGCAGGTGGG RR: GCTGTATGGAAGGAACCTCCCTCACATGTCACAATGTCGGTCACTACGGACGTCCTCAGTTCACTACAGGTACTTACTTCGTCCACCC F2: 3 ACAATGTC 2 Unidirectional alignment (log-probability: -37.5) GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA------CtgtaacaCTGCAGGAGTCAAGTGATaTCCATGAATGAAGCAGGTGGG GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATGC-------CTGCAGGAGTCAAGTGATGTCCATGAATGAAGCAGGTGGG Template switch alignment (log-probability: -22.3) GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA|CTGTAACA|CTGCAGGAGTCAAGTGATaTCCATGAATGAAGCAGGTGGG GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA|CTGTAACA|CTGCAGGAGTCAAGTGATGTCCATGAATGAAGCAGGTGGG Gorilla > Human --------------- chr13:35869946-35869953 Template switch process: F1: L CGACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA 1 F3: 4 CTGCAGGAGTCAAGTGATATCCATGAATGAAGCAGGTGGG R RF: CGACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATGCCTGCAGGAGTCAAGTGATGTCCATGAATGAAGCAGGTGGG RR: GCTGTATGGAAGGAACCTCCCTCACATGTCACAATGTCGGTCACTACGGACGTCCTCAGTTCACTACAGGTACTTACTTCGTCCACCC F2: 3 ACAATGTC 2 Unidirectional alignment (log-probability: -36.5) GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA------CtgtaacaCTGCAGGAGTCAAGTGATaTCCATGAATGAAGCAGGTGGG GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCAGTGATGC-------CTGCAGGAGTCAAGTGATGTCCATGAATGAAGCAGGTGGG Template switch alignment (log-probability: -22.3) GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA|CTGTAACA|CTGCAGGAGTCAAGTGATaTCCATGAATGAAGCAGGTGGG GACATACCTTCCTTGGAGGGAGTGTACAGTGTTACAGCCA|CTGTAACA|CTGCAGGAGTCAAGTGATGTCCATGAATGAAGCAGGTGGG ========= Event 920 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAGGGTTGAAGGTTAACTAACA------------------GAATTGATTATTCAAATCATGATGTAC ↓ 43 2 1 Chimp: TGAGGGTTGAAGGTTAACTAACAGAATTGAATCCTGTAACAGAATTGATTATTCAAATCATGATGTAC ↑ 43 2 1 Gorilla: TGAGGGTTGAAGGTTAACTAACA------------------GAATTGATTATTCAAATCATGATGTAC Human: TGAGGGTTGAAGGTTAACTAACA------------------GAATTGATTATTCAAATCATGATGTAC Cluster: [ ] Orangutan: TGAGGGTTGAAGGTT----AACA------------------GAATTGATTATTCAAATCATGATGTAC Human > Chimp ------------- chr13:36226480-36226486 Template switch process: F1: L TGCCTATTGGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGA 1 F3: 4 AACAGAATTGATTATTCAAATCATGATGTACTCCTTCAATCACC R RF: TGCCTATTGGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGATTATTCAAATCATGATGTACTCCTTCAATCACC RR: ACGGATAACCCCATGACGACTCCCAACTTCCAATTGATTGTCTTAACTAATAAGTTTAGTACTACATGAGGAAGTTAGTGG F2: 3 TGTCCTA 2 Unidirectional alignment (log-probability: -36.8) GGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTgaatcctgtaacagaattGATTATTCAAATCATGATGTACTCCTTCAAT GGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATT------------------GATTATTCAAATCATGATGTACTCCTTCAAT Template switch alignment (log-probability: -22.4) GGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGA|ATcCTGT|AACAGAATTGATTATTCAAATCATGATGTACTCCTTCAAT GGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGA|ATTCTGT|AACAGAATTGATTATTCAAATCATGATGTACTCCTTCAAT Gorilla > Chimp --------------- chr13:36226480-36226486 Template switch process: F1: L TGCCTATTGGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGA 1 F3: 4 AACAGAATTGATTATTCAAATCATGATGTACTCCTTCAATCACC R RF: TGCCTATTGGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGATTATTCAAATCATGATGTACTCCTTCAATCACC RR: ACGGATAACCCCATGACGACTCCCAACTTCCAATTGATTGTCTTAACTAATAAGTTTAGTACTACATGAGGAAGTTAGTGG F2: 3 TGTCCTA 2 Unidirectional alignment (log-probability: -36.8) GGGGTACTGCTGAGGGTTGAAGGTTAACTAAcagaattgaatcctgtaaCAGAATTGATTATTCAAATCATGATGTACTCCTTCAAT GGGGTACTGCTGAGGGTTGAAGGTTAACTAA------------------CAGAATTGATTATTCAAATCATGATGTACTCCTTCAAT Template switch alignment (log-probability: -22.4) GGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGA|ATcCTGT|AACAGAATTGATTATTCAAATCATGATGTACTCCTTCAAT GGGGTACTGCTGAGGGTTGAAGGTTAACTAACAGAATTGA|ATTCTGT|AACAGAATTGATTATTCAAATCATGATGTACTCCTTCAAT ========= Event 921 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAATGTATGAAATGCTTAAACACAGTGC--ACacttctacttattctttaacatctagttccaatgtcacctctgcagtgaagactgccctttttctcctg ↓ 1 4 3 2 Chimp: GAATGTATGAAATGCTTAAACTCACTGCACACacttctacttattctttaacatctagtttcaatgtcacctctgcagtgaagactgccctttttctcctg Gorilla: GAATGTATGAAATGCTTAAACACGCTGC--ACacttctacttattctttaacatctagttccaatgtcacctctgcagtgaagactgccctttttctcctg Human: GAATGTATGAAATGCTTAAACACAGTGC--ACacttctacttattctttaacatctagttccaatgtcacctctgcagtgaagactgccctttttctcctg Cluster: [ ] Orangutan: GAATGTATGAAATGCTTAAACACACTGT--ACacttctacttattctttaacatctagttccaatgtcacctctgtagtgaagagtgccctttttctcctg Human > Chimp ------------- chr13:35477351-35477358 Template switch process: F1: L CAAGAGATGGAAAAATATGAGAATGTATGAAATGCTTAAAC 1 F3: 4 CACACTTCTACTTATTCTTTAACATCTAGTTTCAATGTCAC R RF: CAAGAGATGGAAAAATATGAGAATGTATGAAATGCTTAAACACAGTGCACACTTCTACTTATTCTTTAACATCTAGTTCCAATGTCACCTCTGCAGTGA RR: GTTCTCTACCTTTTTATACTCTTACATACTTTACGAATTTGTGTCACGTGTGAAGATGAATAAGAAATTGTAGATCAAGGTTACAGTGGAGACGTCACT F2: 3 ACGTCACT 2 Unidirectional alignment (log-probability: -31.8) AAGAGATGGAAAAATATGAGAATGTATGAAATGCTTAAACtCAcTGcaCACACTTCTACTTATTCTTTAACATCTAGTTtCAATGTCA AAGAGATGGAAAAATATGAGAATGTATGAAATGCTTAAACACAGTG--CACACTTCTACTTATTCTTTAACATCTAGTTCCAATGTCA Template switch alignment (log-probability: -22.3) AAGAGATGGAAAAATATGAGAATGTATGAAATGCTTAAAC|TCACTGCA|CACACTTCTACTTATTCTTTAACATCTAGTTtCAATGTCA AAGAGATGGAAAAATATGAGAATGTATGAAATGCTTAAAC|TCACTGCA|CACACTTCTACTTATTCTTTAACATCTAGTTCCAATGTCA ========= Event 922 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTCATATTACCATTCACAAAT---------------------------------------------------GCCCATGTAAGTCTGTTATTTTAGACTTGA ↓ 3 4 1 2 Chimp: TTTCATATTACCATTCACAAAT-------------------------------GCCCATTTACATGGGCATTTGCCCATGTAAGTCTATTATTTTAGACTTGA Gorilla: TTTCATATTACCATTCACAAAT-----------GCCCATTTACATGGGCATTT--------------------GCCCATGTAAGTCTATTATTTTAGACTTGA ↑ 3 4 1 2 Human: TTTCATATTACCATTCACAAAT---------------------------------------------------GCCCATGTAAGTCTGTTATTTTAGACTTGA Cluster: [ ] Orangutan: TTTCATATTACCATTCATTT--AACTTTTAAAT----------------------------------------GCCCATGTAAGTCTATTATTTTAGACTTGA Human > Chimp ------------- chr13:67657685-67657697 Template switch process: F1: L TTCTACAGTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAT 1 F3: 4 TGCCCATGTAAGTCTATTATTTTAGACTTGACACTGAGAAA R RF: TTCTACAGTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCATGTAAGTCTGTTATTTTAGACTTGACAGTGAGAAA RR: AAGATGTCAAAAGTTTTACAAAGTATAATGGTAAGTGTTTACGGGTACATTCAGACAATAAAATCTGAACTGTCACTCTTT F2: 3 TTACGGGTACATT 2 Unidirectional alignment (log-probability: -51.7) GTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAtttacatgggcatttgcccaTGTAAGTCTaTTATTTTAGACTTGACAcTGAGAA GTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCA--------------------TGTAAGTCTGTTATTTTAGACTTGACAGTGAGAA Template switch alignment (log-probability: -29) GTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAT|TTACATGGGCATT|TGCCCATGTAAGTCTaTTATTTTAGACTTGACAcTGAGAA GTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAT|TTACATGGGCATT|TGCCCATGTAAGTCTGTTATTTTAGACTTGACAGTGAGAA Human > Gorilla --------------- chr13:64827292-64827304 Template switch process: F1: L TTCTACAGTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAT 1 F3: 4 TGCCCATGTAAGTCTATTATTTTAGACTTGACAGTGAGAAA R RF: TTCTACAGTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCATGTAAGTCTGTTATTTTAGACTTGACAGTGAGAAA RR: AAGATGTCAAAAGTTTTACAAAGTATAATGGTAAGTGTTTACGGGTACATTCAGACAATAAAATCTGAACTGTCACTCTTT F2: 3 TTACGGGTACATT 2 Unidirectional alignment (log-probability: -45.2) GTTTTCAAAATGTTTCATATTACCATTCACAAAtgcccatttacatgggcattTGCCCATGTAAGTCTaTTATTTTAGACTTGACAGTGAGAA GTTTTCAAAATGTTTCATATTACCATTCACAAA--------------------TGCCCATGTAAGTCTGTTATTTTAGACTTGACAGTGAGAA Template switch alignment (log-probability: -23.1) GTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAT|TTACATGGGCATT|TGCCCATGTAAGTCTaTTATTTTAGACTTGACAGTGAGAA GTTTTCAAAATGTTTCATATTACCATTCACAAATGCCCAT|TTACATGGGCATT|TGCCCATGTAAGTCTGTTATTTTAGACTTGACAGTGAGAA ========= Event 923 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATCTCTATTTTGAATTTCCATTTGTCCCAAAG--CA--ATAATCCAACTATTTCAGGATTC Chimp: AAATCTCTATTTTGAATTTCCATTTGTCCCATGGACAAATGGAATCCAACTATTTCAGCATTC ↑ 3 2 1 4 Gorilla: AAATCTCTATTTTGAATTTCCATTTGTCCCAAAG--CA--ATAATCCAACTATTTCAGGATTC Human: AAATCTCTATTTTGAATTTCCATTTGTCCCAAAG--CA--ATAATCCAACTATTTCAGGATTC Cluster: [ ] Orangutan: AAATCTCTATTTTGAATTTCCATTTGTCCCAAAG--CA--ATAATCCAACTATTTCAGGATTC Gorilla > Chimp --------------- chr13:67223798-67223807 Template switch process: F1: L CTTTCTTCTTAAATCTCTATTTTGAATTTCCATTTGTCCCAT 1 F3: 4 AATCCAACTATTTCAGCATTCATCACTTATTGCACTGATT R RF: CTTTCTTCTTAAATCTCTATTTTGAATTTCCATTTGTCCCAAAGCAATAATCCAACTATTTCAGGATTCATCACTTATTGCACTGATT RR: GAAAGAAGAATTTAGAGATAAAACTTAAAGGTAAACAGGGTTTCGTTATTAGGTTGATAAAGTCCTAAGTAGTGAATAACGTGACTAA F2: 3 GGTAAACAGG 2 Unidirectional alignment (log-probability: -40.8) TTCTTCTTAAATCTCTATTTTGAATTTCCATTTGTCCC------ATggacaaatggAATCCAACTATTTCAGcATTCATCACTTATTGCACTGATT TTCTTCTTAAATCTCTATTTTGAATTTCCATTTGTCCCAAAGCAAT----------AATCCAACTATTTCAGGATTCATCACTTATTGCACTGATT Template switch alignment (log-probability: -28.1) TTCTTCTTAAATCTCTATTTTGAATTTCCATTTGTCCCAt|GGACAAATGG|AATCCAACTATTTCAGcATTCATCACTTATTGCACTGATT TTCTTCTTAAATCTCTATTTTGAATTTCCATTTGTCCCAA|GGACAAATGG|AATCCAACTATTTCAGGATTCATCACTTATTGCACTGATT ========= Event 924 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAAGGAGTAAGCATATTTTATACTATA---------CAGAGCATGCCATTTTGGTGGTAG Chimp: CAAGGAGTAAGCATATTTTATACTATA---------CAGAGCATGCCATTTTGGTGGTAG ↓ 3 1 4 Gorilla: CAACGAGTAAGCATATTTTATACTATATCTGTATAGTATAGCATGCCATTTTGGTGGTAG ↑ 3 1 4 Human: CAAGGAGTAAGCATATTTTATACTATA---------CAGAGCATGCCATTTTGGTGGTAG Cluster: [ ] Orangutan: CAAGGGGGAAGAATATTTTATACTATA---------CAGAGCATGCCTTTTTGGTGGTAG Human > Gorilla --------------- chr13:33218159-33218170 Template switch process: F1: L TACTACTTTGGGAGCAACGAGTAAGCATATTTTATACTATA 1 F3: 4 AGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT R RF: TACTACTTTGGGAGCAAGGAGTAAGCATATTTTATACTATACAGAGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT RR: ATGATGAAACCCTCGTTCCTCATTCGTATAAAATATGATATGTCTCGTACGGTAAAACCACCATCGTACCAATATTTTTAATTA F2: 3 TATGATATGTCT 2 Unidirectional alignment (log-probability: -40.4) ACTACTTTGGGAGCAAcGAGTAAGCATATTTTATACTATAtctgtatagtAtAGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT ACTACTTTGGGAGCAAGGAGTAAGCATATTTTATACTATA---------CAGAGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT Template switch alignment (log-probability: -22.8) ACTACTTTGGGAGCAAcGAGTAAGCATATTTTATACTATA|TCTGTATAGTAT|AGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT ACTACTTTGGGAGCAAGGAGTAAGCATATTTTATACTATA|TCTGTATAGTAT|AGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT Chimp > Gorilla --------------- chr13:33218159-33218170 Template switch process: F1: L TACTACTTTGGGAGCAACGAGTAAGCATATTTTATACTATA 1 F3: 4 AGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT R RF: TACTACTTTGGGAGCAAGGAGTAAGCATATTTTATACTATACAGAGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT RR: ATGATGAAACCCTCGTTCCTCATTCGTATAAAATATGATATGTCTCGTACGGTAAAACCACCATCGTACCAATATTTTTAATTA F2: 3 TATGATATGTCT 2 Unidirectional alignment (log-probability: -40.4) ACTACTTTGGGAGCAAcGAGTAAGCATATTTTATACTATAtctgtatagtAtAGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT ACTACTTTGGGAGCAAGGAGTAAGCATATTTTATACTATA---------CAGAGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT Template switch alignment (log-probability: -22.8) ACTACTTTGGGAGCAAcGAGTAAGCATATTTTATACTATA|TCTGTATAGTAT|AGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT ACTACTTTGGGAGCAAGGAGTAAGCATATTTTATACTATA|TCTGTATAGTAT|AGCATGCCATTTTGGTGGTAGCATGGTTATAAAAATTAAT ========= Event 925 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTTCCATTTCCTATATTTCATACCAGAGCCTCTTCTAGGACATAGATTGGCCTATGTCCTGAAATCAAAACAAAGGGTATATGAAAATGTACAACAGACACTGTGAGGTACACAGAAAAGGATTATCCAATGATAGAAAGAAACATGAAAGAAAGGCATGAGGCTT Chimp: TTTTCCATTTCCTATATTTCATACAAGAGCCTCTTCTAGGACATAGATTGGCAT------------AAGGGCAAAGGGTATATGAAAATGTACAACAGACACTGTGAGGTACACAGAAAAGGATTATTCAATGATAGAAAGAAACATGAAAGAAAGGCATGAGGCTT Gorilla: TTTTCCATTTCCTATATTTCACACAAGAGCCTCTTCTAGGACATAGATTGGCTT------------AAGGGCAAAGGGTATATGAAAATGTACAACAGACACTGTGAGGTACACAGAAAAGGATTATCCAATGATAGAAAGAAACATGAAAGAGAGGCATGAGGCTT ↓ 3 2 1 4 Human: TTTTCCATTTCCTATATTTCATACCAGAGCCTCTTCTAGGACATAGATTGGCCTATGTCCTGAAATCAAAACAAAGGGTATATGAAAATGTACAACAGACACTGTGAGGTACACAGAAAAGGATTATCCAATGATAGAAAGAAACATGAAAGAAAGGCATGAGGCTT Cluster: [ ] Orangutan: TTTTCCATTTCCTATATTTCATACAAGAGCCTCTTCTAGGACATAGATTGGCAT------------AAGGGCAAAGGGTATATGAAAATGTACAACAGACACTGTGAGGTACACAGAAAAGGATTATCCAATGATAGAAAGAAACATGAAAGAAAGGCATAAGGCTT Gorilla > Human --------------- chr13:33254168-33254175 Template switch process: F1: L ATAAATATGATTTTAACTGCTTTTCCATTTCCTATATTTCATACCAGAGCCTCTTCTAGGACATAGATTGGC 1 F3: 4 TGAAA R RF: ACAAATATGATTTTAACTGCTTTTCCATTTCCTATATTTCACACAAGAGCCTCTTCTAGGACATAGATTGGCTTAAGGGCAAAGGGTATATGAAAATGTACAACAGACACTGTGAGGTACACAGAAAAGGATTATCCAATGATAGAAAGAAACATGAAA RR: TGTTTATACTAAAATTGACGAAAAGGTAAAGGATATAAAGTGTGTTCTCGGAGAAGATCCTGTATCTAACCGAATTCCCGTTTCCCATATACTTTTACATGTTGTCTGTGACACTCCATGTGTCTTTTCCTAATAGGTTACTATCTTTCTTTGTACTTT F2: 3 CCTGTATC 2 Unidirectional alignment (log-probability: -45.7) TATATTTCAtACcAGAGCCTCTTCTAGGACATAGATTGGCcTatgtcctgaaa TATATTTCACACAAGAGCCTCTTCTAGGACATAGATTGGCTT----------- Template switch alignment (log-probability: -33.2) TATATTTCAtACcAGAGCCTCTTCTAGGACATAGATTGGC|CTATGTCC|TGAAA TATATTTCACACAAGAGCCTCTTCTAGGACATAGATTGGC|CTATGTCC|TGAAA ========= Event 926 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATTTTCGCTCTGGGAATGTAATACTTGAAAATA-----------TACCTGTTTTGTTTTGTTTGTT Chimp: TTATTTTCGCTCTGGAAATGTAATACTTGAAAATA-----------TACCtgttttgttttgtttgtt ↓ 3 2 14 Gorilla: TTATTTTCGCTCTGGAAATGTAATACTTGAAAATATTCAAGTATTACACCtgttttgttttgtttgtt ↑ 3 2 14 Human: TTATTTTCGCTCTGGGAATGTAATACTTGAAAATA-----------TACCTGTTTTGTTTTGTTTGTT Cluster: [ ] Orangutan: TTATTTTCGGTCTGGAAATGTAATACTTGAAAATA-----------TACCtgttttgttttgtttgtt Human > Gorilla --------------- chr13:31720871-31720881 Template switch process: F1: L CGTGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATAT 1 F3: 4 ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC R RF: TGTGTTTTATTTTCGCTCTGGGAATGTAATACTTGAAAATATACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC RR: ACACAAAATAAAAGCGAGACCCTTACATTATGAACTTTTATATGGACAAAACAAAACAAACAAATAAAAGGTTGTAACCAAG F2: 3 CATTATGAACT 2 Unidirectional alignment (log-probability: -37.8) TGTTTTATTTTCGCTCTGGaAATGTAATACTTGAAAATATtcaagtattacACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC TGTTTTATTTTCGCTCTGGGAATGTAATACTTGAAAATAT-----------ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC Template switch alignment (log-probability: -28.2) TGTTTTATTTTCGCTCTGGaAATGTAATACTTGAAAATAT|TCAAGTATTAC|ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC TGTTTTATTTTCGCTCTGGGAATGTAATACTTGAAAATAT|TCAAGTATTAC|ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC Chimp > Gorilla --------------- chr13:31720871-31720881 Template switch process: F1: L CGTGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATAT 1 F3: 4 ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC R RF: TGTGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATATACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC RR: ACACAAAATAAAAGCGAGACCTTTACATTATGAACTTTTATATGGACAAAACAAAACAAACAAATAAAAGGTTGTAACCAAG F2: 3 CATTATGAACT 2 Unidirectional alignment (log-probability: -32.2) TGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATATtcaagtattacACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC TGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATAT-----------ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC Template switch alignment (log-probability: -22.7) TGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATAT|TCAAGTATTAC|ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC TGTTTTATTTTCGCTCTGGAAATGTAATACTTGAAAATAT|TCAAGTATTAC|ACCTGTTTTGTTTTGTTTGTTTATTTTCCAACATTGGTTC ========= Event 927 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGAGAGGAAATATCTTTTCTCTAGTTTTCAAAGAGGCAGCTTATAGGCTTACAATACCTTTGGTCATT ↓ 1 4 3 2 Chimp: GTGAGAGGAAATATCTTTTCT----GCCTATAAGAGACAGCTTATAGGCTTACAATACCTTTGGTCATT Gorilla: GTGAGAGGAAATATCTTTTCTCTAGTTTTCAAAGAGGCAGCTTATAGGCTTACAATACCTTTGGTCATT Human: GTGAGAGGAAATATCTTTTCTCTAGTTTTCAAAGAGGCAGCTTATAGGCTTACAATACCTTTGGTCATT Cluster: [ ] Orangutan: GTGAGAGGAAATATCTTTTCTCTAGTTCTCAAAGAGGCAGCTTATAGGCTTACAATACCCTTGGTCATT Human > Chimp ------------- chr13:34374875-34374880 Template switch process: F1: L TATCTGAAAATGTGTGCACAGTGAGAGGAAATATCTTTTCT 1 F3: 4 AAGAGACAGCTTATAGGCTTACAATACCTTTGGTCATTTTATTCAC R RF: TATCTGAAAATGTGTGCACAGTGAGAGGAAATATCTTTTCTCTAGTTTTCAAAGAGGCAGCTTATAGGCTTACAATACCTTTGGTCATTTTATTCAC RR: ATAGACTTTTACACACGTGTCACTCTCCTTTATAGAAAAGAGATCAAAAGTTTCTCCGTCGAATATCCGAATGTTATGGAAACCAGTAAAATAAGTG F2: 3 TATCCG 2 Unidirectional alignment (log-probability: -36.3) ATCTGAAAATGTGTGCACAGTGAGAGGAAATATCTTTTCtgcctaT----------AAGAGaCAGCTTATAGGCTTACAATACCTTTGGTCATTTT ATCTGAAAATGTGTGCACAGTGAGAGGAAATATCTTTTC------TCTAGTTTTCAAAGAGGCAGCTTATAGGCTTACAATACCTTTGGTCATTTT Template switch alignment (log-probability: -22.1) ATCTGAAAATGTGTGCACAGTGAGAGGAAATATCTTTTCT|GCCTAT|AAGAGaCAGCTTATAGGCTTACAATACCTTTGGTCATTTT ATCTGAAAATGTGTGCACAGTGAGAGGAAATATCTTTTCT|GCCTAT|AAGAGGCAGCTTATAGGCTTACAATACCTTTGGTCATTTT ========= Event 928 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGATATAAAATCACCAAACAAAATGAAAAGATgtttt----gtttgtttttgttttAATAGAAAA Chimp: CTGATGTAAAATCCCCAAACAAAATGAAAAGACATTTT----GTTTGTTTTTGTTCTAATAGAAAA ↑ 3 2 1 4 Gorilla: CTGATATAAAATCACCAAACAAAATGAAAAGATGTTTT--------GTTTTTGTTCTAATAGAAAA Human: CTGATATAAAATCACCAAACAAAATGAAAAGATgtttt----gtttgtttttgttttAATAGAAAA Cluster: [ ] Orangutan: CTGATATAAAACCACCAAACAAAATGAAAAGACgttttgttt----gtttttgttttAATAGAAAA Gorilla > Chimp --------------- chr13:34455261-34455267 Template switch process: F1: L GTAAATGAACTGATGTAAAATCCCCAAACAAAATGAAAAGA 1 F3: 4 TTTGTTTTTGTTCTAATAGAAAACTAGATGCCCAGGAGACCAA R RF: GTAAATGAACTGATATAAAATCACCAAACAAAATGAAAAGATGTTTTGTTTTTGTTCTAATAGAAAACTAGATGCCCAGGAGACCAA RR: CATTTACTTGACTATATTTTAGTGGTTTGTTTTACTTTTCTACAAAACAAAAACAAGATTATCTTTTGATCTACGGGTCCTCTGGTT F2: 3 GTTTTAC 2 Unidirectional alignment (log-probability: -38.8) TAAATGAACTGATgTAAAATCcCCAAACAAAATGAAAAGAcattTtgTTTGTTTTTGTTCTAATAGAAAACTAGATGCCCAGGAGAC TAAATGAACTGATATAAAATCACCAAACAAAATGAAAAGA----TGTTTTGTTTTTGTTCTAATAGAAAACTAGATGCCCAGGAGAC Template switch alignment (log-probability: -27.7) TAAATGAACTGATgTAAAATCcCCAAACAAAATGAAAAGA|CATTTTG|TTTGTTTTTGTTCTAATAGAAAACTAGATGCCCAGGAGAC TAAATGAACTGATATAAAATCACCAAACAAAATGAAAAGA|CATTTTG|TTTGTTTTTGTTCTAATAGAAAACTAGATGCCCAGGAGAC ========= Event 929 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAATCTATTTTCCCCACCACTTTTCTGTTAC ↓ 3 2 1 4 Chimp: CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAACAAGTTCTTCCCCACCACTTTTCTGTTAC ↑ 3 2 1 4 Gorilla: CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAATCTATTTCCCCCACCACTTTTCTGTTAC Human: CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAATCTATTTTCCCCACCACTTTTCTGTTAC Cluster: [ ] Orangutan: CAGTACCTAAATTGTCATAGAACTTGTTCACGATAGTCAAATCTATTTTCCCCACCACTCTTCTGTTAC Human > Chimp ------------- chr13:68819438-68819444 Template switch process: F1: L TCAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA 1 F3: 4 TTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG R RF: TCAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAATCTATTTTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG RR: AGTCATGGATTTAACAGTATCTTGAACAAATGCTATCAGTTTAGATAAAAGGGGTGGTGAAAAGACAATGTGGTATGTCACCATAAAC F2: 3 CTTGAAC 2 Unidirectional alignment (log-probability: -31.6) CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAcaagttc-------TTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA-------ATCTATTTTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG Template switch alignment (log-probability: -16.2) CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA|CAAGTTC|TTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA|CAAGTTC|TTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG Gorilla > Chimp --------------- chr13:68819438-68819444 Template switch process: F1: L TCAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA 1 F3: 4 TTCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTGGA R RF: TCAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAATCTATTTCCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTGGA RR: AGTCATGGATTTAACAGTATCTTGAACAAATGCTATCAGTTTAGATAAAGGGGGTGGTGAAAAGACAATGTGGTATGTCACCATAAACCT F2: 3 CTTGAAC 2 Unidirectional alignment (log-probability: -32.6) CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA--------CaagttcttCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAAATCTATTTC--------CCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG Template switch alignment (log-probability: -22.2) CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA|CAAGTTC|TtCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG CAGTACCTAAATTGTCATAGAACTTGTTTACGATAGTCAA|CAAGTTC|TCCCCCACCACTTTTCTGTTACACCATACAGTGGTATTTG ========= Event 930 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ttttacatgcttttatagttcagtttaataagatcaaattaacaagattttaataagtgtagtaagcttgctgtttgacctcctcttgtttctttgatttacctatatgcatataattttccacttacatttttttacctctgtcc-----------ttccttctgagatcattttccttAC Chimp: TTTTACATGCTTTTATAGTTCAGTTTAATAAGATCAAATTAACAAGATTTTAATAAGTGTAGTAAGCTTGCTGTTTGACCTCCTCTTGTTTCTTTGATTTACCTATATGCATATAATTTTCCGCTTACAtttttttACCTCTGTCCTTCCTCTGACCTTCCTTCTGAGATCATTTTCCTTAC ↑ 3 2 4 1 Gorilla: TTTTACATGCTTTTATAGTTCAGTTTAATAAGATAAAATTAACAAGATTTTAATAAGTGTAGTAAGCTTGCTGTTTGACCTCCTCTTGTTTCTTTGATTTACCTATATGCATATAATTTTCTGCTTACAtttttttACCTCTGTCC-----------TTCCTTCTGAGATCATTTTCCTTAC Human: ttttacatgcttttatagttcagtttaataagatcaaattaacaagattttaataagtgtagtaagcttgctgtttgacctcctcttgtttctttgatttacctatatgcatataattttccacttacatttttttacctctgtcc-----------ttccttctgagatcattttccttAC Cluster: [ ] Orangutan: ttttacatgcttttatagttcagtttaataagataaaattaacaagattttaataagtatagtaagcttgctgtttgacctcctcttgtttctttgatttacctatatgcatataattttctgcttacatttttttacctctgtcc-----------ttccttctgagatcgttttccttAC Gorilla > Chimp --------------- chr13:69361063-69361066 Template switch process: F1: L TATGCATATAATTTTCCGCTTACATTTTTTTACCTCTGTCCTTCCT 1 F3: 4 CCTTCCTTCTGAGATCATTTTCCTTACACATGTGATCTCAAT R RF: TCAGTTTAATAAGATAAAATTAACAAGATTTTAATAAGTGTAGTAAGCTTGCTGTTTGACCTCCTCTTGTTTCTTTGATTTACCTATATGCATATAATTTTCTGCTTACATTTTTTTACCTCTGTCCTTCCTTCTGAGATCATTTTCCTTACACATGTGATCTCAAT RR: AGTCAAATTATTCTATTTTAATTGTTCTAAAATTATTCACATCATTCGAACGACAAACTGGAGGAGAACAAAGAAACTAAATGGATATACGTATATTAAAAGACGAATGTAAAAAAATGGAGACAGGAAGGAAGACTCTAGTAAAAGGAATGTGTACACTAGAGTTA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -32.2) TATAATTTTCcGCTTACATTTTTTTACCTCTGTccttcctctgaCCTTCCTTCTGAGATCATTTTCCTTACACATGTGATCTCA TATAATTTTCTGCTTACATTTTTTTACCTCTGT-----------CCTTCCTTCTGAGATCATTTTCCTTACACATGTGATCTCA Template switch alignment (log-probability: -21.9) TATAATTTTCcGCTTACATTTTTTTACCTCTGTCCTTCCT|CTGA|CCTTCCTTCTGAGATCATTTTCCTTACACATGTGATCTCA TATAATTTTCTGCTTACATTTTTTTACCTCTGTCCTTCCT|CTGA|CCTTCCTTCTGAGATCATTTTCCTTACACATGTGATCTCA ========= Event 931 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTGGTTATAAATCTATTGAGCAACTGAAA---AAACAAAAACCACACAATAGTACACAATAT Chimp: ACTGGTTATAAATCTATTGAGCAACTGaaa---aaacaaaaaaCACACAATAGTACACAATAT Gorilla: ACTGGTTATAAATCTATTGAGCAACTTTCAGTTGCTCAAAAAACACACAATAGTACACAATAT ↑ 3 1 2 4 Human: ACTGGTTATAAATCTATTGAGCAACTGAAA---AAACAAAAACCACACAATAGTACACAATAT Cluster: [ ] Orangutan: GCTGGTTATAAATCTATTGAGCAAGTGaaa---aaacaaaaaaCACACAATAGTACACAATAT Human > Gorilla --------------- chr13:29908138-29908147 Template switch process: F1: L TCTTAATTCCAAAAAACTGGTTATAAATCTATTGAGCAACT 1 F3: 4 CAAAAAACACACAATAGTACACAATATCGTCATTTCTATAAATTTCT R RF: TCTTAATTCCAAAAAACTGGTTATAAATCTATTGAGCAACTGAAAAAACAAAAACCACACAATAGTACACAATATCATCATTTCTATAAATTTCT RR: AGAATTAAGGTTTTTTGACCAATATTTAGATAACTCGTTGACTTTTTTGTTTTTGGTGTGTTATCATGTGTTATAGTAGTAAAGATATTTAAAGA F2: 3 TCGTTGACTT 2 Unidirectional alignment (log-probability: -46.5) CTTAATTCCAAAAAACTGGTTATAAATCTATTGAGCAACT-------ttcagttgctCAAAAAaCACACAATAGTACACAATATCgTCATTTCTATA CTTAATTCCAAAAAACTGGTTATAAATCTATTGAGCAACTGAAAAAA----------CAAAAACCACACAATAGTACACAATATCATCATTTCTATA Template switch alignment (log-probability: -28.2) CTTAATTCCAAAAAACTGGTTATAAATCTATTGAGCAACT|TTCAGTTGCT|CAAAAAaCACACAATAGTACACAATATCgTCATTTCTATA CTTAATTCCAAAAAACTGGTTATAAATCTATTGAGCAACT|TTCAGTTGCT|CAAAAACCACACAATAGTACACAATATCATCATTTCTATA ========= Event 932 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTTACTTATTGTTAGGGTATTCCAAAGAACTTTGGAAAATTGGCGATGATATGTTT Chimp: ACTTACTTATTGTTAGTGTATC------TTCTTTGGAAAATTGGCGATGATATGTTT Gorilla: ATTTACTTATTGTTAGGGTATC------TTCTTTGGAAAATTGGCGATGATATGTTT ↓ 1 3 4 2 Human: ACTTACTTATTGTTAGGGTATTCCAAAGAACTTTGGAAAATTGGCGATGATATGTTT Cluster: [ ] Orangutan: ACTTACTTATTGTCAGGATATC------TTCTTTGGAAAATTGGCGATGATATGTTT Gorilla > Human --------------- chr13:29673230-29673238 Template switch process: F1: L AAACAGACAGTACTCTTTGGACTTACTTATTGTTAGGGTAT 1 F3: 4 CTTTGGAAAATTGGCGATGATATGTTTGTTTGTTGTATAA R RF: AAACAGACAGTACTCTTTGGATTTACTTATTGTTAGGGTATCTTCTTTGGAAAATTGGCGATGATATGTTTGTTTGTTGTATAA RR: TTTGTCTGTCATGAGAAACCTAAATGAATAACAATCCCATAGAAGAAACCTTTTAACCGCTACTATACAAACAAACAACATATT F2: 3 AAGAAACCT 2 Unidirectional alignment (log-probability: -37.8) AACAGACAGTACTCTTTGGAcTTACTTATTGTTAGGGTA--TTccaaagaaCTTTGGAAAATTGGCGATGATATGTTTGTTTGTTGTATAA AACAGACAGTACTCTTTGGATTTACTTATTGTTAGGGTATCTT--------CTTTGGAAAATTGGCGATGATATGTTTGTTTGTTGTATAA Template switch alignment (log-probability: -22.4) AACAGACAGTACTCTTTGGAcTTACTTATTGTTAGGGTAT|TCCAAAGAA|CTTTGGAAAATTGGCGATGATATGTTTGTTTGTTGTATAA AACAGACAGTACTCTTTGGATTTACTTATTGTTAGGGTAT|TCCAAAGAA|CTTTGGAAAATTGGCGATGATATGTTTGTTTGTTGTATAA ========= Event 933 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAATGATAGTAAAATATGTAGGAAGATCATGTGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATCTATAGACCCA ↑ 1 4 3 2 Chimp: CAATGATAGTAAAATATGTAGCAAGAGTGCATGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATCTGTAGACTCA Gorilla: CAATGATAGTAAAATATGTAGCAAGAGCGCATGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATCTGTAGACTCA Human: CAATGATAGTAAAATATGTAGGAAGATCATGTGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATCTATAGACCCA Cluster: [ ] Orangutan: CAATGATAGTAAAATATGTAGGAAGATCACATGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATCTATAGACTCA Chimp > Human ------------- chr13:85377791-85377795 Template switch process: F1: L TGGAATTAAATTCCTTGAGTCAATGATAGTAAAATATGTAGGAAGA 1 F3: 4 TGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATC R RF: TGGAATTAAATTCCTTGAGTCAATGATAGTAAAATATGTAGCAAGAGTGCATGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATC RR: ACCTTAATTTAAGGAACTCAGTTACTATCATTTTATACATCGTTCTCACGTACAGATTGATAAGAAACACTTTATTGTACTGTAACTCTAG F2: 3 GTACT 2 Unidirectional alignment (log-probability: -33.1) TAAATTCCTTGAGTCAATGATAGTAAAATATGTAGgAAGAtcatGTG----TCTAACTATTCTTTGTGAAATAACATGACATTGAGATC TAAATTCCTTGAGTCAATGATAGTAAAATATGTAGCAAGA----GTGCATGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATC Template switch alignment (log-probability: -22) TAAATTCCTTGAGTCAATGATAGTAAAATATGTAGgAAGA|TCATG|TGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATC TAAATTCCTTGAGTCAATGATAGTAAAATATGTAGCAAGA|TCATG|TGTCTAACTATTCTTTGTGAAATAACATGACATTGAGATC ========= Event 934 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: atggcgaattatctcccaGTA------------------------------------------------------CACCGAGGGTGCATAGATAAACAAAAAAGGAGCT Chimp: atggcgaattatctcccaGTA---------------------------CATAAATGCAGAGAAAAAGAAAACCTGCACCCTCAGTGTGTAGATAAACAAAAAAGGAGCT Gorilla: atggcaaattatctcccaGTACATAAATGCAGAGAAAAAGAAAACCTG---------------------------CACCCTCGGTGTGTAGATAAACAAAAAAGGAGCT ↓ 1 3 2 4 Human: atggcgaattatctcccaGTA------------------------------------------------------CACCGAGGGTGCATAGATAAACAAAAAAGGAGCT Cluster: [ ] Orangutan: atggagaattatctcccaGTATATAAATGCAGAGCAAAAGAAAACCTG---------------------------CACCCTCGGTGTGTAGATAAACACAAAAGGAGCT Gorilla > Human --------------- chr13:26318510-26318520 Template switch process: F1: L TGTAGAAAGGGAGGGTACACATGGCGAATTATCTCCCAGTACA 1 F3: 4 TAGATAAACAAAAAAGGAGCTTTCCAATGTATTTTTTTAA R RF: TGTAGAAAGGGAGGGTACACATGGCAAATTATCTCCCAGTACATAAATGCAGAGAAAAAGAAAACCTGCACCCTCGGTGTGTAGATAAACAAAAAAGGAGCTTTCCAATGTATTTTTTT RR: ACATCTTTCCCTCCCATGTGTACCGTTTAATAGAGGGTCATGTATTTACGTCTCTTTTTCTTTTGGACGTGGGAGCCACACATCTATTTGTTTTTTCCTCGAAAGGTTACATAAAAAAA F2: 3 ACGTGGGAGCC 2 Unidirectional alignment (log-probability: -55) AGAAAGGGAGGGTACACATGGCgAATTATCTCCCAGTACA--------------------------------------ccgagggtgcaTAGATAAACAAAAAAGGAGCTTTCCAATGTATTTTTTTaa AGAAAGGGAGGGTACACATGGCAAATTATCTCCCAGTACATAAATGCAGAGAAAAAGAAAACCTGCACCCTCGGTGTG-----------TAGATAAACAAAAAAGGAGCTTTCCAATGTATTTTTTTTT Template switch alignment (log-probability: -32.3) AGAAAGGGAGGGTACACATGGCgAATTATCTCCCAGTACA|CCGAGGGTGCA|TAGATAAACAAAAAAGGAGCTTTCCAATGTATTTTTTtaa AGAAAGGGAGGGTACACATGGCAAATTATCTCCCAGTACA|CCGAGGGTGCA|TAGATAAACAAAAAAGGAGCTTTCCAATGTATTTTTT--T ========= Event 935 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CAATGAAAGTAATTTTTGTAT-TTTTCTCGTGTATCGAAAATAT---------------AGTGCTATAATTACAAAGCAC Chimp: caaagaaagaaaTCTTTGTAT-TTTTCTCGCATATCGAAAATAT---------------AGTGCTATAATTACAAAGCAC ↓ 3 2 4 1 Gorilla: CAAAGAAAGAAATCTTTGTAT-TTTTCTCGCATATCGAAAATATGCGAGAAAAATATAATGTGCTATAATTACAAAGCAC Human: CAATGAAAGTAATTTTTGTAT-TTTTCTCGTGTATCGAAAATAT---------------AGTGCTATAATTACAAAGCAC Cluster: [ ] Orangutan: CAAAGAAAGAAATCTTTATATTTTTTCTCACATATCGAAAATAT---------------AGTGCTATAATTACAAAGCAC Chimp > Gorilla --------------- chr13:24860599-24860609 Template switch process: F1: L AAGAAAGAAATCTTTGTATTTTTCTCGCATATCGAAAATAT 1 F3: 4 ATAATGTGCTATAATTACAAAGCACAACATTAAGATGTAAACTAT R RF: AAGAAAGAAATCTTTGTATTTTTCTCGCATATCGAAAATATAGTGCTATAATTACAAAGCACAACATTAAGATGTAAACTAT RR: TTCTTTCTTTAGAAACATAAAAAGAGCGTATAGCTTTTATATCACGATATTAATGTTTCGTGTTGTAATTCTACATTTGATA F2: 3 TAAAAAGAGCG 2 Unidirectional alignment (log-probability: -38) AGAAAGAAATCTTTGTATTTTTCTCGCATATCGAAAATATgcgagaaaaatataatGTGCTATAATTACAAAGCACAACATTAAGATGTAA AGAAAGAAATCTTTGTATTTTTCTCGCATATCGAAAATAT---------------AGTGCTATAATTACAAAGCACAACATTAAGATGTAA Template switch alignment (log-probability: -28.3) AGAAAGAAATCTTTGTATTTTTCTCGCATATCGAAAATAT|GCGAGAAAAAT|ATAatGTGCTATAATTACAAAGCACAACATTAAGATGTAA AGAAAGAAATCTTTGTATTTTTCTCGCATATCGAAAATAT|GCGAGAAAAAT|ATATAGTGCTATAATTACAAAGCACAACATTAAGATGTAA ========= Event 936 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTGGCAAAATGGTAGGTCTA-TCAGTTGGTGACTGTTCTAAACCATTAAGTTATC--AACTAATTAGTCATAGCAATTATCACACCATTTAATGTAGCATTAATT Chimp: TTTGGCAAAATGGTAGGTTTA-TCAGTTGGTGACTGTTCTAAACCATTAAGTTATC--AACTAATTAGTCATAGCAATTATCACACCATTTAATGTAGCATTAATT ↓ 1 3 2 4 Gorilla: TTTGGCAAAATGGTAGGTTTATCCAGTTGGTGACTGTTCTAAACCATTAAGCTATGACCATTAATTAGTCATAGCTATTATCACACCATTTAATGCAGCATTAATT Human: TTTGGCAAAATGGTAGGTCTA-TCAGTTGGTGACTGTTCTAAACCATTAAGTTATC--AACTAATTAGTCATAGCAATTATCACACCATTTAATGTAGCATTAATT Cluster: [] Orangutan: TTTGGCAAAATGGTATGTTTATCCAGTTGGTGACTGTTCTAAACCATTAAGTTACC--AACTAATTAGTCATAGCAATTATCATACCATTTAATGTAGCATTAATT Chimp > Gorilla --------------- chr13:73450995-73451000 Template switch process: F1: L GGCATCACAAAATGGCAAAATTTGGCAAAATGGTAGGTTTATCCAGTTGGTGACTGTTCTAAACCATTAAG 1 F3: 4 CCATTA R RF: GGCATCACAAAATGGCAAAATTTGGCAAAATGGTAGGTTTAT-CAGTTGGTGACTGTTCTAAACCATTAAGAGTTATCAACTAATTAGTCATAG RR: CCGTAGTGTTTTACCGTTTTAAACCGTTTTACCATCCAAATA-GTCAACCACTGACAAGATTTGGTAATTCTCAATAGTTGATTAATCAGTATC F2: 3 AGTATC 2 Unidirectional alignment (log-probability: -41.5) GGTAGGTTTATcCAGTTGGTGACTGTTCTAAACCATTAAGcTATgaCcAtTA GGTAGGTTTAT-CAGTTGGTGACTGTTCTAAACCATTAAGTTAT--CAACTA Template switch alignment (log-probability: -27.5) GGTAGGTTTATcCAGTTGGTGACTGTTCTAAACCATTAAG|CTATGA|CCATTA GGTAGGTTTAT-CAGTTGGTGACTGTTCTAAACCATTAAG|CTATGA|CCATTA ========= Event 937 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GACAGTAATAAGTATATGAGA------AGAAAC--TGTAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATATGTCTACCTGGTTGAAATCATAATAGAGATTCCACCTAGTATACTGAATTATATCTCT-AAGGGACTACTGCAAAAGATAAGGACAGTTTCTGTCAGAGCAGACAGTCATTTGATGCGATCTTTTCTCTTCTTCCAAAATAACTGCCAAAGGAAAAGTGAAGGGAGCTCACTTCTGGCACTAGCTGATGGTGATATTATCCATGAGAGCTAATCCTGCCAGAAATTTGCTCTGATCCCAATATTCACAGCTATATA----------------------------CTCCTCTGTATCTAATCAAAAGAATTTCCCTTATCAACTCCTTTCTTAGGCACAATGTTTACTGTTCTTTCCAACGTTAAGCATTGAATGTCTCTTTACTACCTTGATGCTCTATCAGATATCATTGCAATTTCTATAATATAATCTCCAACTTCTCACTGTTCACTACCCCTTGATTACATAAACATGTTCAAGTATCTCCTGTCTTAAATGTTACTGTAGAACACAGAAAACCTTCCTTGACTTCATGCTCCCCATCATATAATATTCATCCATTTGttcttttattcaacaaactttgttttgcaaacctattgtggtccaggtattgttccacagtatggaattatagacatatagaacaataaacatgcaaaTATTGCAAGAAAGTGGAAGGTAATTAACAGCAATAAGAAAAATATGATAAATGTTGACAGAAAGGCCAATTAGGTCGTCAGTGAATGAGAATTAATGCTAACAAATTTGTGCTTTCATAACCTGAGGTCAGAGTGCTCCTGGCACTCACTAACTCCATAGATAGTGTCATGACCCCCAACTCcaaaaggaattttgacatatttgaaaaacagaaataagtccagtgtgggtgaaagatgtgtgtaatggggtacatgagaaaagtcagacaggagagcaggagccagatcacacaggaccttgtaaggtaggaccttaaagggtagggaatgttgcttttattttaagtaaaaatgggaagacatagaaggattttaaagaagaaatgcagatgacctaatcagaccttttagccatgacttaggatgttttagggggatggataccaaggaaagaatagaaacaggaaaaccaattagaagacttcagaggttttaggagactagagataatatttatattatttttattattaaagtaagtatagacaagtgaaagatttgaaatgtgttttaggtttaaaattatcaagatatcttgaagagcttggtattaaatataa------------------------------------------------------------------------------------------------------------------------ ↑ 1 4 3 2 Chimp: GACAGTAATAAGTATATGAGA---AGAAGAA--ACTCTAGCATAAATATAATGGCAGAAAGTTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATGTTTCTAATATGTCTACCTGGTTGAAATCATAATAGAGATTCCACCTAGTATACTGAATTATATCTCTAAGGGACTACTGCAAAAGATAAGGACAGTTTCTGTCAGAGCAGACAGTC Gorilla: GACAGTAATAAGTATATGAGAAGA---AGAAAC--TGTAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATATGTCTACCTGGTTGAAATCATAATAGAGATTCCACCTAGTATACTGAATTATATCTCT-AAGGGACTACTGCAAAAGATAAGGACAGTTTCTGTCAGAGCAGACAGTCATTTGATGCGATCTTTTCTCTTCTTCCaaaaaaaCTGCCAAAGGAAAAGTGAAGGGAGCTCACTTCTGGCACTAGCTGATGGTGATATTACCCATGAGAGCTAATCCTGCCAGAAATTTGCTCTGATCCCAATATTCACAGCTATATA------CTCCTCTGTATTTAAACTTTTC-----------------------------CTTATCAACCCCTTTCTTAGGCACAATGTTTACTGTTCTTTCCAGTGTTAAGCATTGAATGTCTCTTTACTACCTTGATGCTCTATCAGGTATCATTGCAATTTCTATAATATAATCTCCAACTTCTCACTGTTCACTACCCCTTGATTACATAAACATGTTCAAGTATCTCCTGTCTTAAATGTTACTGCAGAACACAGAAAACCTTCCTTGACTTCATGCTCCCCATTATATAATATTCATTCATTTGTTCTTTTATTCAATAAACTTTGTTTTGCAAACCTATTGTGGTCCAGGTATTGTTCCACAGTATGGAATTATAGACATATAGAACAATAAACATGCAAATATTGCAAGAAAGTGGAAGGTAATTAACAGCATTAAGAAAAATATGATAAATGTTGACAGAAAGGCCAATTGGGTCGTCAGTGAATGAGAATTAATGCTAACAAATTTGTGCTGTCATAACCTGAGGTCAGAGTGCTCCTGGCACTCACTAACTCCATAGATAGTGTCATGACCTCCAACTCCAAAaggagttttgacatatttgaaaaacagaaataagtccagtgtgggtgaaagatgtgtgtaatggggtacatgagaaaagtcagacaggagagcaggagccagatcacacaggaccttgtaaggtaggaccttaaagggtagggaatgttgcttttattttaagtaaaaatgggaagacatagaaggattttaaagaggaaatgcagatgacctaatcagaccttttagccatgacttaggatgttttagggggatggataccaaggaaagaatagaaacaggaaaaccaattagaagacttcagaggttttaggagactagagataatatttatattatttttattattaaagtaagtatagacaagtgaaagatttgaaatgtgttttaggtttaaaattatcaagacatcttgaagagctaggtattaaatataa------------------------------------------------------------------------------------------------------------------------ Human: GACAGTAATAAGTATATGAGA------AGAAAC--TGTAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATATGTCTACCTGGTTGAAATCATAATAGAGATTCCACCTAGTATACTGAATTATATCTCT-AAGGGACTACTGCAAAAGATAAGGACAGTTTCTGTCAGAGCAGACAGTCATTTGATGCGATCTTTTCTCTTCTTCCAAAATAACTGCCAAAGGAAAAGTGAAGGGAGCTCACTTCTGGCACTAGCTGATGGTGATATTATCCATGAGAGCTAATCCTGCCAGAAATTTGCTCTGATCCCAATATTCACAGCTATATA----------------------------CTCCTCTGTATCTAATCAAAAGAATTTCCCTTATCAACTCCTTTCTTAGGCACAATGTTTACTGTTCTTTCCAACGTTAAGCATTGAATGTCTCTTTACTACCTTGATGCTCTATCAGATATCATTGCAATTTCTATAATATAATCTCCAACTTCTCACTGTTCACTACCCCTTGATTACATAAACATGTTCAAGTATCTCCTGTCTTAAATGTTACTGTAGAACACAGAAAACCTTCCTTGACTTCATGCTCCCCATCATATAATATTCATCCATTTGttcttttattcaacaaactttgttttgcaaacctattgtggtccaggtattgttccacagtatggaattatagacatatagaacaataaacatgcaaaTATTGCAAGAAAGTGGAAGGTAATTAACAGCAATAAGAAAAATATGATAAATGTTGACAGAAAGGCCAATTAGGTCGTCAGTGAATGAGAATTAATGCTAACAAATTTGTGCTTTCATAACCTGAGGTCAGAGTGCTCCTGGCACTCACTAACTCCATAGATAGTGTCATGACCCCCAACTCcaaaaggaattttgacatatttgaaaaacagaaataagtccagtgtgggtgaaagatgtgtgtaatggggtacatgagaaaagtcagacaggagagcaggagccagatcacacaggaccttgtaaggtaggaccttaaagggtagggaatgttgcttttattttaagtaaaaatgggaagacatagaaggattttaaagaagaaatgcagatgacctaatcagaccttttagccatgacttaggatgttttagggggatggataccaaggaaagaatagaaacaggaaaaccaattagaagacttcagaggttttaggagactagagataatatttatattatttttattattaaagtaagtatagacaagtgaaagatttgaaatgtgttttaggtttaaaattatcaagatatcttgaagagcttggtattaaatataa------------------------------------------------------------------------------------------------------------------------ Cluster: [ ] Orangutan: GACAGTAATAAGTATATGAGAAGA---AGAAAC--TGTAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATATGTCTACCTGGTTGAAATAATAATAGAGATTCCATCTAGTATACTTAATTATATCTCTAAAGGGACTACTGCAAAAGATAAGGACAGTTTCTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCTTC---------------------------------------------------CTTATCAATCCCTTTCTTAGGCACCATGTTTACTGTTCTTTCCAGTGTTAAGCATTGAATGTCTCTTTACTACCTTGATGCTCTATCAGGTATTATTGCAATTTCTATAATAGAATCTCCAACTTCTCACTGTTCACTACCCCTTGATTACATAAACATGTTCAAGTATCTCCTGTCTTAAATGTTACTGCAGAACACAGAAAACCTTCCTTGACTTCATGCTCCCCATTATATAATATTCATTCATTTGttcttttattcaacaaactttgttttgcaaacctactgtggtccaggtattgttccaCAGTATGGAATTATAGACATATAGAAAAATAAACATGCAAATATTGGAAGAAAATGGAACGTAATTAACAGCAATAAGAAAAATATGATAAATGTTGATAGAAAGGCCAATTGGGTCGTCAGTGAATAAGAATTAATGCTAAAAAATTTGTGCTGTCATAACCTGGGGTCAGAGTGCTCCTGGTACTCACTAGCTCCATAGATAGTGTCATGACCTCCAACTTCAAAaggagttttgacatatttgaaaaacagaaataaatccagtgtgggtgaaagatgtgtgtaatggggtacatcagaaaagtcagacaggagagcaggagccagatcgcacaggaccttgtaagataggaccttatagggtatggaatgttgcttttattttaagtataaatgggaagacatagaaggattttaaagaggaaatgcagatgacccaattagaccttttagctatgacttaggatgttttagggggatggataccaagggaagaatagaaacaggaaaaccaattagaagacttcagagattttaggagactagagacaatatttatattatttttattattaaagtaagtatagacaagtgaaagatttgaaatgtgttttgggtttaaaattatcaagacatcttgaagagctaggtattaaatataa------------------------------------------------------------------------------------------------------------------------ Chimp > Human ------------- chr13:92525540-92525543 Template switch process: F1: L GCTTAGAAGATACTTTGGGTGACAGTAATAAGTATATGAGAAGAA 1 F3: 4 TAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATA R RF: GCTTAGAAGATACTTTGGATGACAGTAATAAGTATATGAGAAGAAGAAACTCTAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATATGTCTACCTGGTTGAAATCATAATAGAGATTCCACCTAGTATACTGAATTATATCTCTAAGGGACTACTGCAAAAGATAAGGACAGT RR: CGAATCTTCTATGAAACCTACTGTCATTATTCATATACTCTTCTTCTTTGAGATCGTATTTATATTACCGTCTTTCAATTTACAAAGATTATACAGATGGACCAACTTTAGTATTATCTCTAAGGTGGATCATATGACTTAATATAGAGATTCCCTGATGACGTTTTCTATTCCTGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -48.9) GAAGATACTTTGGgTGACAGTAATAAGTATATG---AGAAGAAACTgTAGCATAAATATAATGGCAGAAAGTTAaatgtttctaata GAAGATACTTTGGATGACAGTAATAAGTATATGAGAAGAAGAAACTCTAGCATAAATATAATGGCAGAAAGTTA------------- Template switch alignment (log-probability: -21.8) GAAGATACTTTGGgTGACAGTAATAAGTATATGAGAAGAA|ACTG|TAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATA GAAGATACTTTGGATGACAGTAATAAGTATATGAGAAGAA|ACTG|TAGCATAAATATAATGGCAGAAAGTTAAATGTTTCTAATA ========= Event 938 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAAAATAAACCAAAAAATCTCCAGCGTTGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGAATAATGTGGCAACGTATATGAAGAAAACATTTTTAGACAAAGCTATTCAGTGCTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTATGTAGCTTCCTAGCTGCATG Chimp: TTAAAATAAACCAAAAAATCTCCAGCGTTGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGAATAATGTGGCAATGTATATGAAGAAAACAATTTTAGACAAAGCTATTCAGTGCTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTATGTAGCTTCCTAGCTGCATG ↓ 1 4 3 2 Gorilla: TTAAAATAAACCAAAAAATCT-TAGC-ATGCTCATATCTGTTAATCAATATGAAAAGCTCTATCATGAATAATGTGGCAACCTACATGAAGAAAACACTTTCAGACAAAGCTATTCAGTAGTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTATGTGGCTTCCTTGCTGCATG ↑ 1 4 3 2 Human: TTAAAATAAACCAAAAAATCTCCAGCGTTGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGAATAATGTGGCAACGTATATGAAGAAAACATTTTTAGACAAAGCTATTCAGTGCTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTATGTAGCTTCCTAGCTGCATG Cluster: [ ] Orangutan: TTAAAATAAACCAAAAAATCTCCAGCGTTGCTCATATCTGTTCATCAATATGAAAAGCTCCATTATGAATAATGTGGCAACATATATGAAGAAAACAATTTTAGACAAAGCTATTCAGTGCTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTATGTAGCTTCCTAGCTGCATG Human > Gorilla --------------- chr13:75376517-75376521 Template switch process: F1: L TAACAATATATTGATATAGATTAAAATAAACCAAAAAATCT 1 F3: 4 TGCTCATATCTGTTAATCAATATGAAAAGCTCTATCATGA R RF: TAACAATATATCGATATAGATTAAAATAAACCAAAAAATCTCCAGCGTTGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGAATAATGTGGCAACGTATATGAAGAAAACATTTTTAGACAAAGCTATTCAGTGCTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTA RR: ATTGTTATATAGCTATATCTAATTTTATTTGGTTTTTTAGAGGTCGCAACGAGTATAGACAAGTAGTTATACTTTTCGAGATAGTACTTATTACACCGTTGCATATACTTCTTTTGTAAAAATCTGTTTCGATAAGTCACGAAAAGAGAAGAAGAAAGTTGTGTATTTATTTTCGTTAACGAT F2: 3 ACGAT 2 Unidirectional alignment (log-probability: -37.7) AACAATATATtGATATAGATTAAAATAAACCAAAAAATCT------TagcaTGCTCATATCTGTTaATCAATATGAAAAGCTCTATCATGA AACAATATATCGATATAGATTAAAATAAACCAAAAAATCTCCAGCGT----TGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGA Template switch alignment (log-probability: -27.4) AACAATATATtGATATAGATTAAAATAAACCAAAAAATCT|TAGCA|TGCTCATATCTGTTaATCAATATGAAAAGCTCTATCATGA AACAATATATCGATATAGATTAAAATAAACCAAAAAATCT|TAGCA|TGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGA Chimp > Gorilla --------------- chr13:75376517-75376521 Template switch process: F1: L TAACAATATATTGATATAGATTAAAATAAACCAAAAAATCT 1 F3: 4 TGCTCATATCTGTTAATCAATATGAAAAGCTCTATCATGA R RF: TAACAATATATCGATATAGATTAAAATAAACCAAAAAATCTCCAGCGTTGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGAATAATGTGGCAATGTATATGAAGAAAACAATTTTAGACAAAGCTATTCAGTGCTTTTCTCTTCTTCTTTCAACACATAAATAAAAGCAATTGCTA RR: ATTGTTATATAGCTATATCTAATTTTATTTGGTTTTTTAGAGGTCGCAACGAGTATAGACAAGTAGTTATACTTTTCGAGATAGTACTTATTACACCGTTACATATACTTCTTTTGTTAAAATCTGTTTCGATAAGTCACGAAAAGAGAAGAAGAAAGTTGTGTATTTATTTTCGTTAACGAT F2: 3 ACGAT 2 Unidirectional alignment (log-probability: -37.7) AACAATATATtGATATAGATTAAAATAAACCAAAAAATCT------TagcaTGCTCATATCTGTTaATCAATATGAAAAGCTCTATCATGA AACAATATATCGATATAGATTAAAATAAACCAAAAAATCTCCAGCGT----TGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGA Template switch alignment (log-probability: -27.4) AACAATATATtGATATAGATTAAAATAAACCAAAAAATCT|TAGCA|TGCTCATATCTGTTaATCAATATGAAAAGCTCTATCATGA AACAATATATCGATATAGATTAAAATAAACCAAAAAATCT|TAGCA|TGCTCATATCTGTTCATCAATATGAAAAGCTCTATCATGA ========= Event 939 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCCTAATCATATCTCTTTTACTGGTTTCATAACTTCATAGATAATAATACTTGCCT ↓ 3 2 1 4 Chimp: ATCTTAATCATATCTCTTTTACTGGTTTCATCAGTACATAGATAATAATACTTGCCT Gorilla: ATCCTAATCATATCTCTTTTACTGGTTTCATAAGTTCATAGATAATAATAGTTGCCT Human: ATCCTAATCATATCTCTTTTACTGGTTTCATAACTTCATAGATAATAATACTTGCCT Cluster: [ ] Orangutan: ATCCTAATCATTTATCTTTTACTGGTTTCATAAGTTCATAGATAATAATACTTGCCT Human > Chimp ------------- chr13:78042435-78042439 Template switch process: F1: L AAACAAAGCAATCTTAATCATATCTCTTTTACTGGTTTCAT 1 F3: 4 CATAGATAATAATACTTGCCTATGACCAATGTACTTT R RF: AAACAAAGCAATCCTAATCATATCTCTTTTACTGGTTTCATAACTTCATAGATAATAATACTTGCCTATGACCAATGTACTTT RR: TTTGTTTCGTTAGGATTAGTATAGAGAAAATGACCAAAGTATTGAAGTATCTATTATTATGAACGGATACTGGTTACATGAAA F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -32.1) AACAAAGCAATCtTAATCATATCTCTTTTACTGGTTTCATcAgTaCATAGATAATAATACTTGCCTATGACCAATGTACTTT--- AACAAAGCAATCCTAATCATATCTCTTTTACTGGTTTCATAACTTCATAGATAATAATACTTGCCTATGACCAATGTACTTTGAA Template switch alignment (log-probability: -21.8) AACAAAGCAATCtTAATCATATCTCTTTTACTGGTTTCAT|CAGTA|CATAGATAATAATACTTGCCTATGACCAATGTACTTT AACAAAGCAATCCTAATCATATCTCTTTTACTGGTTTCAT|CAGTA|CATAGATAATAATACTTGCCTATGACCAATGTACTTT ========= Event 940 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGATGAGAAAAATACAGTTGAAGAACTTCAAAGTTCT---TCAGTAGATTTAAAAGTAATTCTT Chimp: AGAATGAGAAAAATACAGTTGAAGAACTTCAAAGTTCT---TCAGTAGATTTAAAAGTAATTCTT ↑ 3 2 1 4 Gorilla: AGAATGAGAGAAATACAGTTGAAGAACTTCAAAAGTAGACGGTGGTAGATTTAAAAGTAATTCTT Human: AGGATGAGAAAAATACAGTTGAAGAACTTCAAAGTTCT---TCAGTAGATTTAAAAGTAATTCTT Cluster: [ ] Orangutan: AGAATGAGAAAAATACAGTTGAAGAACTTCAAAAGTAGAAGGTGGTAGATTTAAAAGTAATTTTT Gorilla > Chimp --------------- chr13:22300827-22300834 Template switch process: F1: L TCCTTTCAAGAATGAGAAAAATACAGTTGAAGAACTTCAAA 1 F3: 4 GTAGATTTAAAAGTAATTCTTGGCCAGGCGCGGTGGCTCA R RF: TCCTTTCAAGAATGAGAGAAATACAGTTGAAGAACTTCAAAAGTAGACGGTGGTAGATTTAAAAGTAATTCTTGGCCAGGTGCGGTGGCTCA RR: AGGAAAGTTCTTACTCTCTTTATGTCAACTTCTTGAAGTTTTCATCTGCCACCATCTAAATTTTCATTAAGAACCGGTCCACGCCACCGAGT F2: 3 ACTTCTTG 2 Unidirectional alignment (log-probability: -42.3) CCTTTCAAGAATGAGAaAAATACAGTTGAAGAACTTCAAA----------GttcttcaGTAGATTTAAAAGTAATTCTTGGCCAGGcGCGGTGGCTCA CCTTTCAAGAATGAGAGAAATACAGTTGAAGAACTTCAAAAGTAGACGGTG-------GTAGATTTAAAAGTAATTCTTGGCCAGGTGCGGTGGCTCA Template switch alignment (log-probability: -27.8) CCTTTCAAGAATGAGAaAAATACAGTTGAAGAACTTCAAA|GTTCTTCA|GTAGATTTAAAAGTAATTCTTGGCCAGGcGCGGTGGCTCA CCTTTCAAGAATGAGAGAAATACAGTTGAAGAACTTCAAA|GTTCTTCA|GTAGATTTAAAAGTAATTCTTGGCCAGGTGCGGTGGCTCA ========= Event 941 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAA-------GTTGATGATGGAGTTTTACTTA Chimp: ATGaaaaaaaTAATTGAAAACTAGTTTGGGAGAAAAAACTAGTTTGATGATGGAGTTTTACTTA ↑ 3 2 1 4 Gorilla: ATGaaaaaaaTAATTGAAAACTAGTTTGGGAGAAA-------GTTGATGATGGAGTTTTATTTA Human: ATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAA-------GTTGATGATGGAGTTTTACTTA Cluster: [ ] Orangutan: ATGAAAAAAATGACTGAAAACTAGTTTGGGAGAAA-------GTTGATGATGGAGTTTTTCTTA Gorilla > Chimp --------------- chr13:79064316-79064323 Template switch process: F1: L TATGCAATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAA 1 F3: 4 TTGATGATGGAGTTTTACTTATAATTCAATTTGAGGACAG R RF: TATGCAATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAAGTTGATGATGGAGTTTTATTTATACTTCAATTTGAGGACAG RR: ATACGTTACTTTTTTTATTAACTTTTGATCAAACCCTCTTTCAACTACTACCTCAAAATAAATATGAAGTTAAACTCCTGTC F2: 3 TGATCAAA 2 Unidirectional alignment (log-probability: -37.5) ATGCAATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAAaaactagtTTGATGATGGAGTTTTAcTTATAaTTCAATTTGAGGACAG ATGCAATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAA-------GTTGATGATGGAGTTTTATTTATACTTCAATTTGAGGACAG Template switch alignment (log-probability: -27.8) ATGCAATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAA|AAACTAGT|TTGATGATGGAGTTTTAcTTATAaTTCAATTTGAGGACAG ATGCAATGAAAAAAATAATTGAAAACTAGTTTGGGAGAAA|AAACTAGT|TTGATGATGGAGTTTTATTTATACTTCAATTTGAGGACAG ========= Event 942 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTAAG----ACAATTTTATATTTCTGCAAATGACTTATGCAGAAATATAATTAGGGaatgcacatttag Chimp: TTTTAAG--ACACAATTTTATATTTCTGCAAATGACTTATGCAGAAATATAATTAGGGaatgcacatttag ↑ 3 2 1 4 Gorilla: TTTTAAGAC--ACAATTTTATATTTCTGCAAATGACTTATGT---CTTACAATTAGGGaatgcacatttag ↓ 3 2 1 4 Human: TTTTAAG----ACAATTTTATATTTCTGCAAATGACTTATGCAGAAATATAATTAGGGaatgcacatttag Cluster: [ ] Orangutan: --TTAAGAC--ACAATTTTATATTTCTGAAAATGACTTACGT---CTTACAATTAGGGaatgcacatttag Gorilla > Human --------------- chr13:94577777-94577785 Template switch process: F1: L TGTTTTAAG--ACAATTTTATATTTCTGCAAATGACTTATG 1 F3: 4 AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA R RF: TGTTTTAAGACACAATTTTATATTTCTGCAAATGACTTATGTCTTACAATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA RR: ACAAAATTCTGTGTTAAAATATAAAGACGTTTACTGAATACAGAATGTTAATCCCTTACGTGTAAATCACTTAATAAAAAAGGACTT F2: 3 TATAAAGAC 2 Unidirectional alignment (log-probability: -42.2) TGTTTTAAGA--CAATTTTATATTTCTGCAAATGACTTATGcagaaataT-----AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA TGTTTTAAGACACAATTTTATATTTCTGCAAATGACTTATG--------TCTTACAATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA Template switch alignment (log-probability: -26.7) TGTTTTAAG--ACAATTTTATATTTCTGCAAATGACTTATG|CAGAAATAT|AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA TGTTTTAAGACACAATTTTATATTTCTGCAAATGACTTATG|CAGAAATAT|AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA Gorilla > Chimp --------------- chr13:80236050-80236058 Template switch process: F1: L TTTTAAGACACAATTTTATATTTCTGCAAATGACTTATG 1 F3: 4 AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA R RF: TTTTAAGACACAATTTTATATTTCTGCAAATGACTTATGTCTTACAATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA RR: AAAATTCTGTGTTAAAATATAAAGACGTTTACTGAATACAGAATGTTAATCCCTTACGTGTAAATCACTTAATAAAAAAGGACTT F2: 3 TATAAAGAC 2 Unidirectional alignment (log-probability: -32.4) TTTTAAGACACAATTTTATATTTCTGCAAATGACTTATG-----CagaaatatAATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA TTTTAAGACACAATTTTATATTTCTGCAAATGACTTATGTCTTAC--------AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA Template switch alignment (log-probability: -16.8) TTTTAAGACACAATTTTATATTTCTGCAAATGACTTATG|CAGAAATAT|AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA TTTTAAGACACAATTTTATATTTCTGCAAATGACTTATG|CAGAAATAT|AATTAGGGAATGCACATTTAGTGAATTATTTTTTCCTGAA ========= Event 943 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGTTCTTATTTACTCTGATA-CTATTGAG--------TCCAATAGCATGAGAAATGCCCACTTC ↑ 1 3 4 2 Chimp: AGGTTCTTATTTACTCTGATACATATTAAA----TGGACTCAATAGCATGAGAAATGCCCACTTC Gorilla: AGGTTCTTATTTACTCTGATACATATTAAATGGA----CTCAATAGCATGAGAAATGCCCACTTC Human: AGGTTCTTATTTACTCTGATA-CTATTGAG--------TCCAATAGCATGAGAAATGCCCACTTC Cluster: [ ] Orangutan: AGGTTCTTACTTACTCTGATACATATTAAATGGA----CTCAATAGCATGAGAAATGCCCACTTC Chimp > Human ------------- chr13:93736872-93736880 Template switch process: F1: L ATTCACAAAATACACTGTTAAGGTTCTTATTTACTCTGATAC 1 F3: 4 CAATAGCATGAGAAATGCCCACTTCTGTTAGCTAAACTGA R RF: ATTCACAAAATACACTGTTAAGGTTCTTATTTACTCTGATACATATTAAATGGACTCAATAGCATGAGAAATGCCCACTTCTGTTAGCTAAACTGA RR: TAAGTGTTTTATGTGACAATTCCAAGAATAAATGAGACTATGTATAATTTACCTGAGTTATCGTACTCTTTACGGGTGAAGACAATCGATTTGACT F2: 3 CTGAGTTAT 2 Unidirectional alignment (log-probability: -33.3) TCACAAAATACACTGTTAAGGTTCTTATTTACTCTGAT-------------ACTattgagtcCAATAGCATGAGAAATGCCCACTTCTGTTAGCTAAACTGA TCACAAAATACACTGTTAAGGTTCTTATTTACTCTGATACATATTAAATGGACT--------CAATAGCATGAGAAATGCCCACTTCTGTTAGCTAAACTGA Template switch alignment (log-probability: -16.4) TCACAAAATACACTGTTAAGGTTCTTATTTACTCTGATAC|TATTGAGTC|CAATAGCATGAGAAATGCCCACTTCTGTTAGCTAAACTGA TCACAAAATACACTGTTAAGGTTCTTATTTACTCTGATAC|TATTGAGTC|CAATAGCATGAGAAATGCCCACTTCTGTTAGCTAAACTGA ========= Event 944 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCTG-AAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAAGAGACTGCAATTTAAGAAGCGATCTCTCAAATTTCTTCTTGCTG Chimp: TCTG-AAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAAGAGACTGCAATTTAAGAAGCGAACTCTCAAATTTCTTCTTGCTG ↓ 3 1 2 4 ↑ 13 24 Gorilla: TCTG-AAGAAATTTGAGAGATCGCTTCTTAAATTGCAGTCTCTTGTCTGCTACGTTGTCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAAGTGACTGCAGATTAAGAAGCGATCTCTCAAATTTCTTCTTGCTG ↓ 13 24 ↑ 13 24 Human: TCTG-AAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAAGAGACTGCAATTTAAGAAGCGATCTCTCAAATTTCTTCTTGCTG Cluster: [ ] Orangutan: CCTGAAAGAAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNgggggggggAGAGAAGGATGATTGAGAAAAGGAGTAGTAGACAAGGCGTTAAAAAGGGTGTAGAAGGAAAAAGGTGACGAGGAAAGGCATTGTTATGGAAttttttttttttttATTCTTCAGGAGAAAAAAGAACCAAAAGGACTGCCAAACAAAGGCGATTTTTAAAGCGATCTCTCAAATTTCTTCTTGCTG Gorilla > Human --------------- chr13:93976584-93976630 Template switch process: F1: L TACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA 1 F3: 4 TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG R RF: TACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAATTGCAGTCTCTTGTCTGCTACGTTGTCCCAGACAAGTGACTGCAGATTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG RR: ATGTTGACGCCAGACTTCTTTAAACTCTCTAGCGAAGAATTTAACGTCAGAGAACAGACGATGCAACAGGGTCTGTTCACTGACGTCTAATTCTTCGCTAGAGAGTTTAAAGAAGAACGACACTGATC F2: 3 TAACGTCAGAGAACAGACGATGCAACAGGGTCTGTTCACTGACGTCT 2 Unidirectional alignment (log-probability: -75.4) ACAgCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAtcTGCAGTCaCTTGTCTGggaCaACGTaG---CAGACAAGaGACTGCAatTTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG ACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAATTGCAGTCTCTTGTCTG---CTACGTTGTCCCAGACAAGTGACTGCAGATTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG Template switch alignment (log-probability: -27.2) ACAgCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|TCTGCAGTCACTTGTCTGGGACAACGTAGCAGACAAGAGACTGCAAT|TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG ACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|TCTGCAGTCACTTGTCTGGGACAACGTAGCAGACAAGAGACTGCAAT|TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG Human > Gorilla --------------- chr13:76799236-76799282 Template switch process: F1: L TACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA 1 F3: 4 TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG R RF: TACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAGCAGACAAGAGACTGCAATTTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG RR: ATGTCGACGCCAGACTTCTTTAAACTCTCTAGCGAAGAATTAGACGTCAGTGAACAGACCCTGTTGCATCGTCTGTTCTCTGACGTTAAATTCTTCGCTAGAGAGTTTAAAGAAGAACGACACTGATC F2: 3 AGACGTCAGTGAACAGACCCTGTTGCATCGTCTGTTCTCTGACGTTA 2 Unidirectional alignment (log-probability: -75.4) ACAaCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAatTGCAGTCtCTTGTCTG---CtACGTtGtccCAGACAAGtGACTGCAgaTTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG ACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAG---CAGACAAGAGACTGCAATTTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG Template switch alignment (log-probability: -27.2) ACAaCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|ATTGCAGTCTCTTGTCTGCTACGTTGTCCCAGACAAGTGACTGCAGA|TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG ACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|ATTGCAGTCTCTTGTCTGCTACGTTGTCCCAGACAAGTGACTGCAGA|TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG Gorilla > Chimp --------------- chr13:79624542-79624588 Template switch process: F1: L TACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA 1 F3: 4 TTAAGAAGCGAACTCTCAAATTTCTTCTTGCTGTGACTAG R RF: TACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAATTGCAGTCTCTTGTCTGCTACGTTGTCCCAGACAAGTGACTGCAGATTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG RR: ATGTTGACGCCAGACTTCTTTAAACTCTCTAGCGAAGAATTTAACGTCAGAGAACAGACGATGCAACAGGGTCTGTTCACTGACGTCTAATTCTTCGCTAGAGAGTTTAAAGAAGAACGACACTGATC F2: 3 TAACGTCAGAGAACAGACGATGCAACAGGGTCTGTTCACTGACGTCT 2 Unidirectional alignment (log-probability: -80.9) ACAgCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAtcTGCAGTCaCTTGTCTGggaCaACGTaG---CAGACAAGaGACTGCAatTTAAGAAGCGAaCTCTCAAATTTCTTCTTGCTGTGACTAG ACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAATTGCAGTCTCTTGTCTG---CTACGTTGTCCCAGACAAGTGACTGCAGATTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG Template switch alignment (log-probability: -32.7) ACAgCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|TCTGCAGTCACTTGTCTGGGACAACGTAGCAGACAAGAGACTGCAAT|TTAAGAAGCGAaCTCTCAAATTTCTTCTTGCTGTGACTAG ACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|TCTGCAGTCACTTGTCTGGGACAACGTAGCAGACAAGAGACTGCAAT|TTAAGAAGCGATCTCTCAAATTTCTTCTTGCTGTGACTAG Chimp > Gorilla --------------- chr13:76799236-76799294 Template switch process: F1: L TACAACTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA 1 F3: 4 CTCTCAAATTTCTTCTTGCTGTGACTAG R RF: TACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAGCAGACAAGAGACTGCAATTTAAGAAGCGAACTCTCAAATTTCTTCTTGCTGTGACTAG RR: ATGTCGACGCCAGACTTCTTTAAACTCTCTAGCGAAGAATTAGACGTCAGTGAACAGACCCTGTTGCATCGTCTGTTCTCTGACGTTAAATTCTTCGCTTGAGAGTTTAAAGAAGAACGACACTGATC F2: 3 TAGCGAAGAATTAGACGTCAGTGAACAGACCCTGTTGCATCGTCTGTTCTCTGACGTTA 2 Unidirectional alignment (log-probability: -80.9) ACAaCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAAatTGCAGTCtCTTGTCTG---CtACGTtGtccCAGACAAGtGACTGCAgaTTAAGAAGCGAtCTCTCAAATTTCTTCTTGCTGTGACTAG ACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAATCTGCAGTCACTTGTCTGGGACAACGTAG---CAGACAAGAGACTGCAATTTAAGAAGCGAACTCTCAAATTTCTTCTTGCTGTGACTAG Template switch alignment (log-probability: -28.4) ACAaCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|ATTGCAGTCTCTTGTCTGCTACGTTGTCCCAGACAAGTGACTGCAGATTAAGAAGCGAT|CTCTCAAATTTCTTCTTGCTGTGACTAG ACAGCTGCGGTCTGAAGAAATTTGAGAGATCGCTTCTTAA|ATTGCAGTCTCTTGTCTGCTACGTTGTCCCAGACAAGTGACTGCAGATTAAGAAGCGAT|CTCTCAAATTTCTTCTTGCTGTGACTAG ========= Event 945 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTGGTAATAATAGCATACTTT--------------------------------ATTTCTTACTTTATAAAAGGATAATTTATTGGAAGAAATGGATAGTttctcatctaacacttgagaaaaaca--gtggttcagtgacctccagagtagcagatatga Chimp: CGTTGGTAATAATAACATACTTT----------------ATTTCTGAGTCACTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGAAATGGATAGTttctcatctaacacttgagaaaaaca--gtggttcagtgacctccagagtagcagatatga Gorilla: CATTGGTAATAATAGCATACTTTATTTCTGAGTCACTTT----------------ATTTCTTACTTTATAAAAGGATAATTTATTGGAAGAAATGGATAGTttctcatctaacacttgagaaaaacagtgtggttcagtgacctccagagtagcagatatga ↑ 4 1 3 2 Human: CATTGGTAATAATAGCATACTTT--------------------------------ATTTCTTACTTTATAAAAGGATAATTTATTGGAAGAAATGGATAGTttctcatctaacacttgagaaaaaca--gtggttcagtgacctccagagtagcagatatga Cluster: [ ] Orangutan: CATTGGTAATAATAGCATACTTTATTTCTGAGTCACTTT----------------ATTTCTCACTTTATAAAAGGATAATTTATTGGAAGAAATGGATAGTTTCTCATCTAACACTTGAGAAAAACA--GTGGTTCATTGACCTCCAGAGTAGCAGATATGA Human > Gorilla --------------- chr13:18416493-18416496 Template switch process: F1: L TTGCATTCCAGTTTCCGTCATTGGTAATAATAGCATACTTTATTTCTGA 1 F3: 4 CTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGAAATG R RF: TTGCATTCCAGTTTCCATCATTGGTAATAATAGCATACTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGAAATGGATAGTTTCTCATCTAACACTTGAGAAAAACAGTGGTTCAGTGAC RR: AACGTAAGGTCAAAGGTAGTAACCATTATTATCGTATGAAATAAAGAATGAAATATTTTCCTATTAAATAACCTTCTTTACCTATCAAAGAGTAGATTGTGAACTCTTTTTGTCACCAAGTCACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -39.4) AGTTTCCgTCATTGGTAATAATAGCATactttatttctgagtcACTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGA AGTTTCCATCATTGGTAATAATAGCAT----------------ACTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGA Template switch alignment (log-probability: -27.6) AGTTTCCgTCATTGGTAATAATAGCATACTTTATTTCTgA|GTCA|CTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGA AGTTTCCATCATTGGTAATAATAGCATACTTTATTTCTTA|GTCA|CTTTATTTCTTACTTTATAAAAGGATAATTTATTGGAAGA ========= Event 946 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTCCCTGTCCCTCTCACAGATCGAAGGAGGATGAACCTCCTTTGATCTGTCATTAGCCTGTCCCTAT Chimp: GTCCCTGTCCCTCTCACAGATCGAAGGAGGATGAACCTCCTTCGATCTGTCATTAGCCTGTCCCTAT ↑ 3 1 2 4 Gorilla: GTCCCTATCCCTCTCACAGATCGAAGGAGGTTCATCCTC-------CTGTCATTAGCCTGTCCCTAT ↓ 3 1 2 4 Human: GTCCCTGTCCCTCTCACAGATCGAAGGAGGATGAACCTCCTTTGATCTGTCATTAGCCTGTCCCTAT Cluster: [ ] Orangutan: GTCCCTATCCCTCTCACA------------------------------------------------- Gorilla > Human --------------- chr13:98361773-98361788 Template switch process: F1: L GTCATTAGCCTGTCCCTGTCCCTCTCACAGATCGAAGGAGG 1 F3: 4 CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT R RF: GTCATTAGCCTGTCCCTATCCCTCTCACAGATCGAAGGAGGTTCATCCTCCTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT RR: CAGTAATCGGACAGGGATAGGGAGAGTGTCTAGCTTCCTCCAAGTAGGAGGACAGTAATCGGACAGGGATAGGGATAGGGAATCCTACAA F2: 3 TAGTTTCCTCCAAGTA 2 Unidirectional alignment (log-probability: -43.2) TCATTAGCCTGTCCCTgTCCCTCTCACAGATCGAAGGAGGaTgAaCCTCctttgatCTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT TCATTAGCCTGTCCCTATCCCTCTCACAGATCGAAGGAGGTTCATCCTC-------CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT Template switch alignment (log-probability: -28.8) TCATTAGCCTGTCCCTgTCCCTCTCACAGATCGAAGGAGG|ATGAACCTCCTTtGAT|CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT TCATTAGCCTGTCCCTATCCCTCTCACAGATCGAAGGAGG|ATGAACCTCCTTCGAT|CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT Gorilla > Chimp --------------- chr13:84041776-84041791 Template switch process: F1: L GTCATTAGCCTGTCCCTGTCCCTCTCACAGATCGAAGGAGG 1 F3: 4 CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT R RF: GTCATTAGCCTGTCCCTATCCCTCTCACAGATCGAAGGAGGTTCATCCTCCTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT RR: CAGTAATCGGACAGGGATAGGGAGAGTGTCTAGCTTCCTCCAAGTAGGAGGACAGTAATCGGACAGGGATAGGGATAGGGAATCCTACAA F2: 3 TAGCTTCCTCCAAGTA 2 Unidirectional alignment (log-probability: -43.2) TCATTAGCCTGTCCCTgTCCCTCTCACAGATCGAAGGAGGaTgAaCCTCcttcgatCTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT TCATTAGCCTGTCCCTATCCCTCTCACAGATCGAAGGAGGTTCATCCTC-------CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT Template switch alignment (log-probability: -23.3) TCATTAGCCTGTCCCTgTCCCTCTCACAGATCGAAGGAGG|ATGAACCTCCTTCGAT|CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT TCATTAGCCTGTCCCTATCCCTCTCACAGATCGAAGGAGG|ATGAACCTCCTTCGAT|CTGTCATTAGCCTGTCCCTATCCCTATCCCTTAGGATGTT ========= Event 947 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCACAGGTTTTGCATCTGCC----ATCCCTGGGCATTGCACAGCCCTGGGG Chimp: GTCACAGGTTTTGCATCCGCC----ATCCCTGGGCATTGCACAGCCCTGGGG ↓ 3 4 2 Gorilla: GTCACAGGTTTTGCATCCGCCCAGGGATGTTGGGCATTGCACAGCCCTGGGG Human: GTCACAGGTTTTGCATCTGCC----ATCCCTGGGCATTGCACAGCCCTGGGG Cluster: [ ] Orangutan: ATCACAGGTTTCGCATCCGCC----ATTCCTGGGCATTGCACAGCCCTGGGG Chimp > Gorilla --------------- chr13:82281019-82281026 Template switch process: F1: L CCTCCCTCCGGAGAACAAGCGTCACAGGTTTTGCATCCGCC 1 F3: 4 TTGGGCATTGCACAGCCCTGGGGAGGCCAGGAGCCCATAGG R RF: CCTCCCTCCGGAGAACAAGCGTCACAGGTTTTGCATCCGCCATCCCTGGGCATTGCACAGCCCTGGGGAGGCCAGGAGCCCATAGG RR: GGAGGGAGGCCTCTTGTTCGCAGTGTCCAAAACGTAGGCGGTAGGGACCCGTAACGTGTCGGGACCCCTCCGGTCCTCGGGTATCC F2: 3 GTAGGGAC 2 Unidirectional alignment (log-probability: -32.3) CTCCCTCCGGAGAACAAGCGTCACAGGTTTTGCATCCG----CCCagggatgtTGGGCATTGCACAGCCCTGGGGAGGCCAGGAGCCCATAG CTCCCTCCGGAGAACAAGCGTCACAGGTTTTGCATCCGCCATCCC--------TGGGCATTGCACAGCCCTGGGGAGGCCAGGAGCCCATAG Template switch alignment (log-probability: -22.3) CTCCCTCCGGAGAACAAGCGTCACAGGTTTTGCATCCGCC|CAGGGATG|tTGGGCATTGCACAGCCCTGGGGAGGCCAGGAGCCCATAG CTCCCTCCGGAGAACAAGCGTCACAGGTTTTGCATCCGCC|CAGGGATG|CTGGGCATTGCACAGCCCTGGGGAGGCCAGGAGCCCATAG ========= Event 948 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGGAAAAATAATCATTTTACAGGT---------GGAGTGACAGAGACACTGGAGTTAA Chimp: TAGGAAAAATAACCATTTTACAGGT---------GGAGTGACAGAGACACTGGAGTTAA Gorilla: TAGGAAAAATAATCATTTTACAGGTGCTCCACCTGTAGAGACAGAGACACTGGAGTTAA ↑ 3 1 42 Human: TAGGAAAAATAATCATTTTACAGGT---------GGAGTGACAGAGACACTGGAGTTAA Cluster: [ ] Orangutan: taggaaaaataatcattttacaggt---------ggagtgacAGAGACACTGGAGTTAA Human > Gorilla --------------- chr1:39971937-39971946 Template switch process: F1: L TGGGCCATTTCACATTTAGGAAAAATAATCATTTTACAGGTG 1 F3: 4 AGAGACAGAGACACTGGAGTTAAGAATCACTCCAGTAAGTCCA R RF: TGGGCCATTTCACATTTAGGAAAAATAATCATTTTACAGGTGGAGTGACAGAGACACTGGAGTTAAGAATCACTCCAGTAAGTCCA RR: ACCCGGTAAAGTGTAAATCCTTTTTATTAGTAAAATGTCCACCTCACTGTCTCTGTGACCTCAATTCTTAGTGAGGTCATTCAGGT F2: 3 TGTCCACCTC 2 Unidirectional alignment (log-probability: -34.9) GGCCATTTCACATTTAGGAAAAATAATCATTTTACAGGtgctccaccTGtAGaGACAGAGACACTGGAGTTAAGAATCACTCCAGTAAGT GGCCATTTCACATTTAGGAAAAATAATCATTTTACAGG---------TGGAGTGACAGAGACACTGGAGTTAAGAATCACTCCAGTAAGT Template switch alignment (log-probability: -22.6) GGCCATTTCACATTTAGGAAAAATAATCATTTTACAGGTG|CTCCACCTGT|AGaGACAGAGACACTGGAGTTAAGAATCACTCCAGTAAGT GGCCATTTCACATTTAGGAAAAATAATCATTTTACAGGTG|CTCCACCTGT|AGTGACAGAGACACTGGAGTTAAGAATCACTCCAGTAAGT ========= Event 949 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: aaaCTCATGAAGTCTACCCCTAAGATTTATATGCTTAACTGTTAAGCTCTGCTGCCTCTTGT------TCAGAAAGAACACTAGTGATAATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATTCCT---AGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATT Chimp: aaaCTCATGAAGTCTACCCCTAAGATTTATATGCTTAACTGTTAAGCTCTGCTGCCTCTTGT------TCAGAAAGAACACTAGTGATAATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATTCTT---AGGTGGGGCCTAGGaaaaaaaTAGCTGGATGTATT ↑ 3 2 1 4 Gorilla: aaactCATGAAGTCTACCCCTAAGATTTATATGCTTAACTGTTAAGCTCTGCTGCCTCTTGT------TCAGAAAGAACACTAGTGATAATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATCCACAGATGGTGGGGCCTAGGaaaaaaaTAGCTGGATGTATT ↓ 1 4 3 2 Human: aaaCTCATGAAGTCTACCCCTAAGATTTATATGCTTAACTGTTAAGCTCTGCTGCCTCTTGT------TCAGAAAGAACACTAGTGATAATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATTCCT---AGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATT Cluster: [ ] Orangutan: aaaCTCATGAAGTCTACCCCTAAGATTTATATGCTTAACTGTTAAGCTCTGCTGCCTCTTCTTTGGAACCAGAAAGAACACTAGTGATAACATAGCCAAGGTTATCCATTCACAGATGAAGACTATCTATCCACAGATGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATT Gorilla > Human --------------- chr14:6785309-6785314 Template switch process: F1: L ATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT 1 F3: 4 GTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA R RF: ATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATCCACAGATGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA RR: TATATGGGTTCCAATAGGTAAGTGTCTACTTCTGATAGATAGGTGTCTACCACCCCGGATCCTTTTTTTATCGACCTACATAAGGCTTT F2: 3 GATCCT 2 Unidirectional alignment (log-probability: -26.8) TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT-------TcctaGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATCCACAGAT----GGTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA Template switch alignment (log-probability: -16.5) TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT|TCCTAG|GTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT|TCCTAG|GTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA Gorilla > Chimp --------------- chr14:6485856-6485861 Template switch process: F1: L ATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT 1 F3: 4 GTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA R RF: CTAAGATTTATATGCTTAACTGTTAAGCTCTGCTGCCTCTTGTTCAGAAAGAACACTAGTGATAATATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATCCACAGATGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA RR: GATTCTAAATATACGAATTGACAATTCGAGACGACGGAGAACAAGTCTTTCTTGTGATCACTATTATATGGGTTCCAATAGGTAAGTGTCTACTTCTGATAGATAGGTGTCTACCACCCCGGATCCTTTTTTTATCGACCTACATAAGGCTTT F2: 3 GATTCT 2 Unidirectional alignment (log-probability: -26.8) TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT-------TcttaGGTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTATCCACAGAT----GGTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA Template switch alignment (log-probability: -16.5) TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT|TCTTAG|GTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA TATACCCAAGGTTATCCATTCACAGATGAAGACTATCTAT|TCTTAG|GTGGGGCCTAGGAAAAAAATAGCTGGATGTATTCCGAAA ========= Event 950 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ----agtggtagggctgagcccagtgtccagacctctagaaggtacatgccaattttctctccactacctgacgctgccttctgATTTTTAAACATACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTCACTGGGAGCTTCAGGGAAACAGACCAT ↑ 3 2 1 4 Chimp: ----agtggtagggctgagcccagtgtccagacctccagaaggtacatgccaattttctctcctctacctgacgctgccttctgATTTTTAAACATACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTC----TAAGCTTCAGGGAAACAGACCAT Gorilla: ----agtggtagggctgagcccagtgtccagacctccagaaggtacatgccaattttctctccactacctgacgctgccttctgATTTTTAAACATACCTTATTCCAAATTTTCTTAGAATTAGCAACCATGCTTCACTGGGAGCTTCAGGGAAACAGACCAT Human: ----agtggtagggctgagcccagtgtccagacctctagaaggtacatgccaattttctctccactacctgacgctgccttctgATTTTTAAACATACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTCACTGGGAGCTTCAGGGAAACAGACCAT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTTGATTT---TACATA-ATTATTCCAAATT--TTTAGAATTAGCAACT-GGCTTCACT-GGAG-CTCAGGGAAACAGACCAT Chimp > Human ------------- chr14:100743027-100743032 Template switch process: F1: L TACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTC 1 F3: 4 AGCTTCAGGGAAACAGACCATCTCAGGCCGCATCACTTCC R RF: CCCAGTGTCCAGACCTCCAGAAGGTACATGCCAATTTTCTCTCCTCTACCTGACGCTGCCTTCTGATTTTTAAACATACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTCTAAGCTTCAGGGAAACAGACCATCTCAGGCCGCATCACTTCC RR: GGGTCACAGGTCTGGAGGTCTTCCATGTACGGTTAAAAGAGAGGAGATGGACTGCGACGGAAGACTAAAAATTTGTATGGAATAAGGTTTAAAAGAATCTTAATCGTTGGCACGAAGATTCGAAGTCCCTTTGTCTGGTAGAGTCCGGCGTAGTGAAGG F2: 3 GGGTCA 2 Unidirectional alignment (log-probability: -28.4) ACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTC-ActgggAGCTTCAGGGAAACAGACCATCTCAGGCCGCATCACTTCC ACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTCTA-----AGCTTCAGGGAAACAGACCATCTCAGGCCGCATCACTTCC Template switch alignment (log-probability: -16) ACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTC|ACTGGG|AGCTTCAGGGAAACAGACCATCTCAGGCCGCATCACTTCC ACCTTATTCCAAATTTTCTTAGAATTAGCAACCGTGCTTC|ACTGGG|AGCTTCAGGGAAACAGACCATCTCAGGCCGCATCACTTCC ========= Event 951 ========= Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TATCACATTGATATGAAGCATCTATGCAAAAAGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAATTTGGTCT ↓ 1 4 3 2 Chimp: TATCACATTGATATGAAGCATTTATAC--TGAGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAATTTGGTCT Gorilla: TATCACATTGATATGAAGCATTTATAC--TGAGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAATTTGGTCT Human: TATCACATTGATATGAAGCATCTATGCAAAAAGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAATTTGGTCT Cluster: [ ] Orangutan: TATCACATTGATATGAAGCATTTATAC--TGAGTAATGCATCTATGGAAAAGCTCAGTTGATGAAAGAAATTTGGTCT Human > Chimp ------------- chr14:86219224-86219228 Template switch process: F1: L AGAAGTCTGCCCATGTTCAATATCACATTGATATGAAGCATTTAT 1 F3: 4 GTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAAT R RF: AGAAGTCTGCCCATGTTCAATATCACATTGATATGAAGCATCTATGCAAAAAGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAAT RR: TCTTCAGACGGGTACAAGTTATAGTGTAACTATACTTCGTAGATACGTTTTTCATTACGTAGATACGTTTTCGAGTCAACTACTTTCTTTA F2: 3 AGTCA 2 Unidirectional alignment (log-probability: -31.7) TCTGCCCATGTTCAATATCACATTGATATGAAGCATtTAtacTG-----AGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAAT TCTGCCCATGTTCAATATCACATTGATATGAAGCATCTA---TGCAAAAAGTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAAT Template switch alignment (log-probability: -22) TCTGCCCATGTTCAATATCACATTGATATGAAGCATtTAT|ACTGA|GTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAAT TCTGCCCATGTTCAATATCACATTGATATGAAGCATCTAT|ACTGA|GTAATGCATCTATGCAAAAGCTCAGTTGATGAAAGAAAT ========= Event 952 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGCAGCATATCTCCCCCAGCAG---------------AGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGCCCGCCAAGGAAGGCACTCCAGCCCCTGACCAAAGCAGGGGAGACCTCAGGCAAATGCCACCCTGTTCCAG Chimp: CCTGCAGCACATCTCCCCCAGCAG---------------AGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGCCCGCCAAGGAAGGCACTCCAGCCCCTGACCAAAGCAGGAGAGACCTCAGGCAAATGCCACCCTGTACCAG ↓ 4 1 3 2 Gorilla: CCTGCAGCACATCTCCCCCAGGGGACCTAGTGTCCCTGAGGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGCCCGCCAAGGAAGGCACTCCAGCCCCTGACCAAAGCAGGAGAGACCTCAGGCAAATGCCACCCTGTTCCAG Human: CCTGCAGCATATCTCCCCCAGCAG---------------AGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGCCCGCCAAGGAAGGCACTCCAGCCCCTGACCAAAGCAGGGGAGACCTCAGGCAAATGCCACCCTGTTCCAG Cluster: [ ] Orangutan: CCTGCAGCATGTCTCCCCCAGCAG---------------AGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGCCCGCCAAGGAAGGCACTCTAGCCCCTGACCAAGGCAGGAGAGACCTCAGGAAAATGCCACCCTGTTCCAG Chimp > Gorilla --------------- chr14:85192239-85192244 Template switch process: F1: L TCATGTGACTGCACCAACAGCCTGCAGCACATCTCCCCCA-----------GGGGACCTAGTGTC 1 F3: 4 GCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGC R RF: TCATGTGACTGCACCAACAGCCTGCAGCACATCTCCCCCAGCAGAGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGCCCGCCAAGGAAGGCACTCCAGCCCCTGACCAAAGCAGGAGAGACCTCAGG RR: AGTACACTGACGTGGTTGTCGGACGTCGTGTAGAGGGGGTCGTCTCGGGAACTCCTGGATCACAGAGATTCAGGGTTTCAGTCCGGGCGGTTCCTTCCGTGAGGTCGGGGACTGGTTTCGTCCTCTCTGGAGTCC F2: 3 GAGTCC 2 Unidirectional alignment (log-probability: -43.5) CAACAGCCTGCAGCACATCTCCCCCAGggGAcctagtgtccctgagGCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGC CAACAGCCTGCAGCACATCTCCCCCAGCAGA---------------GCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGC Template switch alignment (log-probability: -32.6) CAACAGCCTGCAGCACATCTCCCCCA-----------GgGGACCTAGTGTC|CCTGAG|GCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGC CAACAGCCTGCAGCACATCTCCCCCAGCAGAGCCCTTGAGGACCTAGTGTC|CCTGAG|GCCCTTGAGGACCTAGTGTCTCTAAGTCCCAAAGTCAGGC ========= Event 953 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CGGTGGAGATAACACACGTGCACATGCATGTATGTGCACTCAGACACGTGGGTAGGCCCACACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGCATGCGTGTGCGTGGGCAGCATGCTGCAGCCT Chimp: CGGTGGAGGTAACACACGTGCACATGCATGTATGTGCACTCAGACACGTGGGTAGGCCCACACATGCATCTGTGCATCATGGGCAGCACGctgtgtgtgcatgcgtgtgcgtgggcagcatgctgcagcct Gorilla: CGGTGGAGATAACACACGTGCACATGCATGTATGTGCACTCAGACACGTGGGTAGGCCCACACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGCTCACGTGCATGTGGGCAGCATGCTGCAGCCT ↓ 3 2 1 4 Human: CGGTGGAGATAACACACGTGCACATGCATGTATGTGCACTCAGACACGTGGGTAGGCCCACACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGCATGCGTGTGCGTGGGCAGCATGCTGCAGCCT Cluster: [ ] Orangutan: CGGTGGAGATAACACACGTGCACATGCATGTATGTGCACTCAGACACGTGGGCAGGCCCACACATGCATCTGTGCATCATGGGTGGCATGCTGTGTGTGCACACGTGTGTGTGAGCAGCATGCTGCAGCCT Gorilla > Human --------------- chr14:102514135-102514144 Template switch process: F1: L ACACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGC 1 F3: 4 GTGGGCAGCATGCTGCAGCCTGCATTTGTGTGTCCTGTGT R RF: GCACATGCATGTATGTGCACTCAGACACGTGGGTAGGCCCACACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGCTCACGTGCATGTGGGCAGCATGCTGCAGCCTGCATTTGTGTGTCCTGTGT RR: CGTGTACGTACATACACGTGAGTCTGTGCACCCATCCGGGTGTGTACGTAGACACGTAGTACCCGCCGTGCGACACACACGAGTGCACGTACACCCGTCGTACGACGTCGGACGTAAACACACAGGACACA F2: 3 CGTGTGCGTA 2 Unidirectional alignment (log-probability: -32.6) CACATGCATCTGTGCATCATGGGCGGCACGCTGTGTG--------TGCATgcgtgtgcGTGGGCAGCATGCTGCAGCCTGCATTTGTGTGTCCTGTGT CACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGCTCACGTGCAT--------GTGGGCAGCATGCTGCAGCCTGCATTTGTGTGTCCTGTGT Template switch alignment (log-probability: -22.5) CACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGC|ATGCgTGTGC|GTGGGCAGCATGCTGCAGCCTGCATTTGTGTGTCCTGTGT CACATGCATCTGTGCATCATGGGCGGCACGCTGTGTGTGC|ATGCATGTGC|GTGGGCAGCATGCTGCAGCCTGCATTTGTGTGTCCTGTGT ========= Event 954 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGGAGGGGGCTGGACGCTTC---------------------CAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCGTCCGGGCGCAGAGGGGCCAAGGCTGGC-------------TG ↓ 4 1 3 2 Chimp: CAGGAGGGGGCTGGACGCTTCCAGGGACCCTGGCCCCACTGCCAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCGTCCGGGCGCAGAGGGGCCAAGGCTGGC----TCTCGCGGCGG Gorilla: ------------------------------------------------------------------------------------------------------------nnnn---------GG Human: CAGGAGGGGGCTGGACGCTTC---------------------CAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCGTCCGGGCGCAGAGGGGCCAAGGCTGGC-------------TG Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------------GG Human > Chimp ------------- chr14:88434001-88434014 Template switch process: F1: L GCCTGTCGCCGCGGCGGGGACAGGAGGGGGCTGGACGCTTCCAGGGA 1 F3: 4 CCAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCGT R RF: GCCTGTCGCCGCGGCGGGGACAGGAGGGGGCTGGACGCTTCCAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCGTCCGGGCGCAGAGGGGCCAAGG RR: CGGACAGCGGCGCCGCCCCTGTCCTCCCCCGACCTGCGAAGGTCCCTTTGACTCCGGGACCGCGCGGGTCGCAGGCGCGCAGGCCCGCGTCTCCCCGGTTCC F2: 3 GTCACCCCGGTCCC 2 Unidirectional alignment (log-probability: -41.1) GCCGCGGCGGGGACAGGAGGGGGCTGGACGCTTCCAGGGaccctggccccactgccagggAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCG GCCGCGGCGGGGACAGGAGGGGGCTGGACGCTTCCAGGG---------------------AAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCG Template switch alignment (log-probability: -29.1) GCCGCGGCGGGGACAGGAGGGGGCTGGACGCTTCCAGGGA|CCcTGGCCCCaCTG|CCAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCG GCCGCGGCGGGGACAGGAGGGGGCTGGACGCTTCCAGGGA|CCTTGGCCCCTCTG|CCAGGGAAACTGAGGCCCTGGCGCGCCCAGCGTCCGCGCG ========= Event 955 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGC-TGAGCGTCTGAAGAGG------------------------------TCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGCCAGGTTTGGGTGGTCTGAGTACCTGGTGCGGGGCCACTGAAGGAGGGGGCTGGTTGCTGCTGACCTGTGAGG-GGGAGAGGGTGAAA ↓ 4 1 3 2 Chimp: TTGC-TGAGCGTCTGAAGAGG---------------TCATGGCCCAGGTGGTCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGCCAGGTTTGGGTGGTCTGAGTACCTGGTGCGGGGCCACTGAAGGAGGGGGCTGGTTGCTGCTGACCTGTGAGG-GGGAGAGGGTGAAA Gorilla: ttgcttgagcgtctgaagaggtcatggcccaggtgg---------------tcatggccacCACGGGCTGGCTTTGGTGAAACTGTGGCCAGGTTTGGGTGGTCTGAGTACCTGGTGTGGGGCCACTGAAGGAGGGGGCTGGTTGCTGCTGACCTGTGAGGGGGGAAAGGGTGAAA Human: TTGC-TGAGCGTCTGAAGAGG------------------------------TCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGCCAGGTTTGGGTGGTCTGAGTACCTGGTGCGGGGCCACTGAAGGAGGGGGCTGGTTGCTGCTGACCTGTGAGG-GGGAGAGGGTGAAA Cluster: [ ] Orangutan: TTGC-TGAGCGTCTGAAGAGGTCATGGCCCAGGTGG---------------TCATGGCCACCATGGGCTGGCTTTGGTGGCACTGTGGCCAGGTTCGGGTTGTCTGAGCACCTGGTGTGGGGCCACTGAAGGAGGGGGCTGGTTGCTGCTGACCTGTGAGG-GGGAGAGGGTGAAA Human > Chimp ------------- chr14:2941476-2941480 Template switch process: F1: L GAAGGGCATCAGGCCCCTGCCTTGCTGAGCGTCTGAAGAGGTCATGGCC 1 F3: 4 GGTCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGCCA R RF: GAAGGGCATCAGGCCCCTGCCTTGCTGAGCGTCTGAAGAGGTCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGCCAGGTTTGGGTGGTCTGAGTACCTGGTGCGGGGCCACTGAAGGAGGGGGCTGGTTGCTGCTGACCTG RR: CTTCCCGTAGTCCGGGGACGGAACGACTCGCAGACTTCTCCAGTACCGGTGGTGCCCGACCGAAACCACCGTGACACCGGTCCAAACCCACCAGACTCATGGACCACGCCCCGGTGACTTCCTCCCCCGACCAACGACGACTGGAC F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -32.5) CAGGCCCCTGCCTTGCTGAGCGTCTGAAGAGGTCATGgcccaggtggtcatgGCCACCACGGGCTGGCTTTGGTGGCACTGTGGC CAGGCCCCTGCCTTGCTGAGCGTCTGAAGAGGTCATG---------------GCCACCACGGGCTGGCTTTGGTGGCACTGTGGC Template switch alignment (log-probability: -16.1) CAGGCCCCTGCCTTGCTGAGCGTCTGAAGAGGTCATGGCC|CAGGT|GGTCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGC CAGGCCCCTGCCTTGCTGAGCGTCTGAAGAGGTCATGGCC|CAGGT|GGTCATGGCCACCACGGGCTGGCTTTGGTGGCACTGTGGC ========= Event 956 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG--------------------CTTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTGTCCTGGC-TTATCTCTGCTGTACCTGTGAAATATTCCACACA Chimp: AATCATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG--------------------CTTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTGTCCTGGC-TCATCTCTGCTGTACCTGTGAAATATTCCACACA ↓ 4 1 3 2 Gorilla: AATCATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG-TAAAGCACATTTCGTGTGCTTTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTGTCCTGGC-TTATCTCTGCTGTACCTGTGAAATATTCCACACA Human: AATCATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG--------------------CTTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTGTCCTGGC-TTATCTCTGCTGTACCTGTGAAATATTCCACACA Cluster: [ ] Orangutan: AATCATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATGT-------------------GTTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTGTCCTGGCTTCATCTCTGCTGTACCTGTGAAATATTCCACACA Chimp > Gorilla --------------- chr14:3196512-3196518 Template switch process: F1: L CATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG 1 F3: 4 CATTTCGTGTGCT-------------TTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTG R RF: CATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATGCTTACAGATGTTTGCTCTTTCTTTGTTCCATGAGAACGCTGTCCTGGCTCATCTCTGCTGTA RR: GTAGTAACCGTGATCAGTAAAGCACACGAAACTTCTTCTACGAATGTCTACAAACGAGAAAGAAACAAGGTACTCTTGCGACAGGACCGAGTAGAGACGACAT F2: 3 ACGAAAT 2 Unidirectional alignment (log-probability: -43.7) ATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATGtaaagcacatttcgtgtgctTTACAGATGTTTGCTCTTTCTTTGTTC ATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG-------------------CTTACAGATGTTTGCTCTTTCTTTGTTC Template switch alignment (log-probability: -32.9) ATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG|TAaAGCA|CATTTCGTGTGCT-------------TTACAGATGTTTGCTCTTTCTTTGTTC ATCATTGGCACTAGTCATTTCGTGTGCTTTGAAGAAGATG|TACAGCA|CATTTCGTGTGCTTTGAAGAAGATGCTTACAGATGTTTGCTCTTTCTTTGTTC ========= Event 957 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: acatttactatatgctggactttgtgctgatcactttccatgtataacaactttcaagcctgccagaaatcctgttttttaaagtatctttcttatttttacaaatTAATATACATACACTTTaaaaaaaaaaGTCAACCAATAGAGGAAATAAAAAATAGCCCCCTAATGACCCACACTTTA-----AACAGCAGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACATAC------------------------------ATATCCTT-TCAAACCCTT-TC--------------------------------------------------------------------------------------------------TACACCACAAAACACTTTCCTTCCTTTTTCACAATGAGGCCACATGAAGTAGAATGTTAGTTTTCCAGCTAACAATATGTTTTGTCAGCTGAAAAACA-TTCT----ACCTCATCCtttttttt--ttttttttttt----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttttttgagatgcagtcttgctctgtcgccagactggagtgcagtggcgcgatctcggctcattgcgacctccacctcccaggttcaagcaattctcctgcctcagcctcccgagtagctgggactacaggtgcgtgcaaccacgcccagctaatttctgtatttttagtagagacgggatttcaccgtgttagccaggatggtctcaatctcctgaccttgtgatctgcccgcctcggcctcccaaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgctgggattacaggtgtgagccacagcatccagccCTCATTCTCTTTTTT--------------------------------AAGGCTATTTCTCTATATGATCACATCATAAT--------------------------------TTATTTAGAGACAGGCATTATTAggcagggtgctgtggctcacacctgtaatcccagcactttggga ↑ 1 4 3 2 Chimp: acatttactatatgctggactttgtgctgatcactttccatgtataacaactttcaagcctgccagaaatcctgttttttaaagtatctttcttatttttacaaatTAATATACATAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCAGCCCTCATTCTCTTTTTT----------------------------------------------------------------AAGGCTATTTCTCTATATGATCACATCATAATTTATTTAGAGACAGGCATTATTAggctgggtgctgtggctcacacctgtaatcccagcactttggga Gorilla: acatttactatatgctggactttgtgctgatcactttccatgtataacaactttcaagcctgccagaaatcctgttttttaaagtatctttcttatttttacaaatTAATATACATACGCTTTaaaaaaaaaaGTCAACCAATAGAGGAAATAAAAAATAGCCCCCTAATGACCCACACTACAGTCTAAAAATGAAATAAGACATGAGCAAAAATCACTATGATGaaaaaaaaaaGTATGCCCTGGGTAATGTTCTGTAGACTCTTTGCATTCGTGGATTTAATATTCATAATTTCAACAATTCAAAAGTTCCTGCAGTGGCCCATGGCAGTATAGAACTTGAGGAGATGATTGAATCCCCTGTAGGGTAAGACTAGTACATGCAATGAATTGCAGCATTGGTAAATGAACTAAGTTGCCTTCCCAATACCTCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCGAGGTGTCCTTATTGCTTCCTAT------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCGannnnnnnnnnnnnnnnnnnnn-------------nnnnnnnnnnnnnnnn----------------------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnggga Human: acatttactatatgctggactttgtgctgatcactttccatgtataacaactttcaagcctgccagaaatcctgttttttaaagtatctttcttatttttacaaatTAATATACATACACTTTaaaaaaaaaaGTCAACCAATAGAGGAAATAAAAAATAGCCCCCTAATGACCCACACTTTA-----AACAGCAGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACATAC------------------------------ATATCCTT-TCAAACCCTT-TC--------------------------------------------------------------------------------------------------TACACCACAAAACACTTTCCTTCCTTTTTCACAATGAGGCCACATGAAGTAGAATGTTAGTTTTCCAGCTAACAATATGTTTTGTCAGCTGAAAAACA-TTCT----ACCTCATCCtttttttt--ttttttttttt----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttttttgagatgcagtcttgctctgtcgccagactggagtgcagtggcgcgatctcggctcattgcgacctccacctcccaggttcaagcaattctcctgcctcagcctcccgagtagctgggactacaggtgcgtgcaaccacgcccagctaatttctgtatttttagtagagacgggatttcaccgtgttagccaggatggtctcaatctcctgaccttgtgatctgcccgcctcggcctcccaaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgctgggattacaggtgtgagccacagcatccagccCTCATTCTCTTTTTT--------------------------------AAGGCTATTTCTCTATATGATCACATCATAAT--------------------------------TTATTTAGAGACAGGCATTATTAggcagggtgctgtggctcacacctgtaatcccagcactttggga Cluster: [ ] Orangutan: acatttactatatgctagactttgtgctgatcactttccatgtataacaactttcaagcctgccagaaatcctgtTTTTTAAAGTATCTTTCTTATTTTTACAAATTAATATACATACACTTTaaaaaaaaaaGTCAACCAATACAGGAAATAAAACATAGCCCCCTAATGACCAACACTTTA-----AACAGCAGGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACATAC------------------------------ATATCCTT-TCAAACCCCT-TCTACACCACAAAACACTTTCCTTCCTTTTTCACAATGAGGCCACATGAAGTAGAATGTTAGTTTTCCAGCTAACAATATGTTTTGTCAGCTGAAAAATA---------------------------------------------------------------------------------------------------TTCT----ATCTCAttct-------tt----------tttttttgagatgcagtctcgctgtcgccaggactggagtgcagtggcccgatctcggctcattgcgacctccacctcccaggttaaagcattctcctgcctcagcctcccgagtagttgggactacaNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----------------------------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr14:103824320-103824335 Template switch process: F1: L AC 1 F3: 4 ATCCAGCCCTCATTCTCTTTTTTAAGGCTATTTCTCTATATGATCACATCATAATTTATTTAGAGACAGGCATTATTAGGCAGGGTGCTGTGGCT R RF: ACTTTGTGCTGATCACTTTCCATGTATAACAACTTTCAAGCCTGCCAGAAATCCTGTTTTTTAAAGTATCTTTCTTATTTTTACAAATTAATATACATATACCCAGCCCTCATTCTCTTTTTTAAGGCTATTTCTCTATATGATCACATCATAATTTATTTAGAGACAGGCATTATTAGGCTGGGTGCTGTGGCTCACACCT RR: TGAAACACGACTAGTGAAAGGTACATATTGTTGAAAGTTCGGACGGTCTTTAGGACAAAAAATTTCATAGAAAGAATAAAAATGTTTAATTATATGTATATGGGTCGGGAGTAAGAGAAAAAATTCCGATAAAGAGATATACTAGTGTAGTATTAAATAAATCTCTGTCCGTAATAATCCGACCCACGACACCGAGTGTGGA F2: 3 CGACACCGAGTGTGGA 2 Unidirectional alignment (log-probability: -42.9) ACaggtgtgagccacagcatCCAGCCCTCATTCTCTTTTTTAAGGCTATTTCTCTATA AC------------------CCAGCCCTCATTCTCTTTTTTAAGGCTATTTCTCTATA Template switch alignment (log-probability: -29.5) AC|AGGTGTGAGCCACAGC|AtCCAGCCCTCATTCTCTTTTTTAAGGCTATTTCTCTATA AC|AGGTGTGAGCCACAGC|ACCCAGCCCTCATTCTCTTTTTTAAGGCTATTTCTCTATA ========= Event 958 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: AGGGAAGTCAGGTGTAGACTGAAGCTCTTAAGACTCTTAAGAGCTTCTACGGTCCAGGGTGTCAcc Chimp: Gorilla: ggggAAGTCAGGTGTAGACTG----------TGCTCTTAAGAGCTTCTACGGTCCAGGGTGTCAcc ↓ 1 43 2 Human: AGGGAAGTCAGGTGTAGACTGAAGCTCTTAAGACTCTTAAGAGCTTCTACGGTCCAGGGTGTCAcc Cluster: [ ] Orangutan: Gorilla > Human --------------- chr14:104194522-104194533 Template switch process: F1: L TGTCAGGGCTGTGTTGAGGGAGGGAAGTCAGGTGTAGACTG 1 F3: 4 CTCTTAAGAGCTTCTACGGTCCAGGGTGTCACCTACGGTC R RF: TGTCAGGGCTGTGTTGAGGGGGGGAAGTCAGGTGTAGACTGTGCTCTTAAGAGCTTCTACGGTCCAGGGTGTCACCTACGGTC RR: ACAGTCCCGACACAACTCCCCCCCTTCAGTCCACATCTGACACGAGAATTCTCGAAGATGCCAGGTCCCACAGTGGATGCCAG F2: 3 AGAATTCTCGAA 2 Unidirectional alignment (log-probability: -41.8) GTCAGGGCTGTGTTGAGGGaGGGAAGTCAGGTGTAGACTGaagctcttaagaCTCTTAAGAGCTTCTACGGTCCAGGGTGTCACCTACGGTC GTCAGGGCTGTGTTGAGGGGGGGAAGTCAGGTGTAGACTG----------TGCTCTTAAGAGCTTCTACGGTCCAGGGTGTCACCTACGGTC Template switch alignment (log-probability: -22.8) GTCAGGGCTGTGTTGAGGGaGGGAAGTCAGGTGTAGACTG|AAGCTCTTAAGA|CTCTTAAGAGCTTCTACGGTCCAGGGTGTCACCTACGGTC GTCAGGGCTGTGTTGAGGGGGGGAAGTCAGGTGTAGACTG|AAGCTCTTAAGA|CTCTTAAGAGCTTCTACGGTCCAGGGTGTCACCTACGGTC ========= Event 959 ========= Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCAAACAGAGCCAGGATAGGTGTTGCGAGGGTTGCTGGAGCCCAGGTGTGGGGCCCAGGCACAGTCACACCAGCCCCTCTCGCTCCCCAGGATGCAGCACCCAATGGGGCAGTGAGACCCCTGAGA Chimp: GCCAAACAGAGCCAGGATAGGTGTTGCGGGGGTTGCTGGAGCCCAGGTGTGGGGCCCAGGCACAGTCACACCAGCCCCTCTCGCTCCCCAGGATGCAGCACCCGATGGGGCAGTGAGACCCCTGAGA Gorilla: GCCAAACAGAGCCAGGATAGGCATT-GGGGGGTTGCTGGGGCCCAGGTGTGGGGCCCAGGCACAGTCACACCAGCCCTTCTCGCTCCCCAGGATGCAGCACCCGATGGGGCAGTGAGACCCCTGAGA ↑ 1 4 3 2 Human: GCCAAACAGAGCCAGGATAGGTGTTGCGAGGGTTGCTGGAGCCCAGGTGTGGGGCCCAGGCACAGTCACACCAGCCCCTCTCGCTCCCCAGGATGCAGCACCCAATGGGGCAGTGAGACCCCTGAGA Cluster: [ ] Orangutan: GCCAAACAGAGCCAGGATAGGTGTTGGGGGGGTTGCTGGGGCCCAGGTGTGGGGCCCAGGCACAGTCACACCAGCCCCTCCTGCTCCCCAGGATGCAGCACACGATGGGGCAGTGAGACCCCTGAGA Human > Gorilla --------------- chr14:2597695-2597701 Template switch process: F1: L TGGCCCACCACCCTTAGGTTGCCAAACAGAGCCAGGATAGG 1 F3: 4 GGGTTGCTGGGGCCCAGGTGTGGGGCCCAGGCACAGTCAC R RF: TGGCCCACCACCCTTAGGTTGCCAAACAGAGCCAGGATAGGTGTTGCGAGGGTTGCTGGAGCCCAGGTGTGGGGCCCAGGCACAGTCACACCAGCCCCTCTCGCTCCCCAGGATGCAGCACCCAATG RR: ACCGGGTGGTGGGAATCCAACGGTTTGTCTCGGTCCTATCCACAACGCTCCCAACGACCTCGGGTCCACACCCCGGGTCCGTGTCAGTGTGGTCGGGGAGAGCGAGGGGTCCTACGTCGTGGGTTAC F2: 3 GGGTTAC 2 Unidirectional alignment (log-probability: -33.1) GGCCCACCACCCTTAGGTTGCCAAACAGAGCCAGGATAGGcaTTG-GgGGGTTGCTGGgGCCCAGGTGTGGGGCCCAGGCACAGTCAC GGCCCACCACCCTTAGGTTGCCAAACAGAGCCAGGATAGGTGTTGCGAGGGTTGCTGGAGCCCAGGTGTGGGGCCCAGGCACAGTCAC Template switch alignment (log-probability: -22.1) GGCCCACCACCCTTAGGTTGCCAAACAGAGCCAGGATAGG|CATTGGG|GGGTTGCTGGgGCCCAGGTGTGGGGCCCAGGCACAGTCAC GGCCCACCACCCTTAGGTTGCCAAACAGAGCCAGGATAGG|CATTGGG|GGGTTGCTGGAGCCCAGGTGTGGGGCCCAGGCACAGTCAC ========= Event 960 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCACACCGTGCTGAGAGGCCTGGCGTCCACCTGCAGCCCAAGGCAGCTCCAAAAGA Chimp: TGCACACCATGCTGAGGGGCCCTGC--ACACCTGCAGCCCAAGGCAGCTCCAAAGGA ↑ 1 4 3 2 Gorilla: TGCACACCATGCTGAGGGGCCTGGCGTCCACCTGCAGCCCGAGGCAGCTCCAAAGGA Human: TGCACACCGTGCTGAGAGGCCTGGCGTCCACCTGCAGCCCAAGGCAGCTCCAAAAGA Cluster: [ ] Orangutan: TGCACACCATGCTGAGGGGCCTGGCGTCCACCTGCAGCCTGAGGCAGTCCCAAAGGA Gorilla > Chimp --------------- chr14:90099486-90099490 Template switch process: F1: L CAGCAGCCTCCGGACTGCCCTGCACACCATGCTGAGGGGCC 1 F3: 4 CACCTGCAGCCCAAGGCAGCTCCAAAGGAAGGTCCTGGTG R RF: CAGCAGCCTCTGGACTGCCCTGCACACCATGCTGAGGGGCCTGGCGTCCACCTGCAGCCCGAGGCAGCTCCAAAGGAAGGTCCTGGTG RR: GTCGTCGGAGACCTGACGGGACGTGTGGTACGACTCCCCGGACCGCAGGTGGACGTCGGGCTCCGTCGAGGTTTCCTTCCAGGACCAC F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -37.7) AGCAGCCTCcGGACTGCCCTGCACACCATGCTGAGGGGCC------CtgcaCACCTGCAGCCCaAGGCAGCTCCAAAGGAAGGTCCTGGTG AGCAGCCTCTGGACTGCCCTGCACACCATGCTGAGGGGCCTGGCGTC----CACCTGCAGCCCGAGGCAGCTCCAAAGGAAGGTCCTGGTG Template switch alignment (log-probability: -27.4) AGCAGCCTCcGGACTGCCCTGCACACCATGCTGAGGGGCC|CTGCA|CACCTGCAGCCCaAGGCAGCTCCAAAGGAAGGTCCTGGTG AGCAGCCTCTGGACTGCCCTGCACACCATGCTGAGGGGCC|CTGCA|CACCTGCAGCCCGAGGCAGCTCCAAAGGAAGGTCCTGGTG ========= Event 961 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CGAAGAATGGGATGGAGGGCAGAGTGCTGGACCAACAC----TCTGCCTTGAACTTGAGTAGAGCTC Chimp: CGAAGAGTGGGATGGAGGGCAGAGTGTTGGTCCAGCTG--TTATCACCTTGAACTTGAGTAGAGCTC Gorilla: CGAAGAATGGGATGGAGGGCAGAGTGTTGGTCCAGCTGTT--ATCACCTTGAACTTGAGTAGAGCTC ↓ 3 1 2 4 Human: CGAAGAATGGGATGGAGGGCAGAGTGCTGGACCAACAC----TCTGCCTTGAACTTGAGTAGAGCTC Cluster: [ ] Orangutan: CGAAGAATGGGATGGAGGGCAGAGTGTTGGTCCGGCTGTT--ATCACCTTGAACTTGAGTAGAGCTC Gorilla > Human --------------- chr1:207246316-207246331 Template switch process: F1: L CCCCTGGCTGATGCACGAAGAATGGGATGGAGGGCAGAGTG 1 F3: 4 CCTTGAACTTGAGTAGAGCTCTCTTCGGGCATTAGGGTTG R RF: CCCCTGGCTGATGCACGAAGAATGGGATGGAGGGCAGAGTGTTGGTCCAGCTGTTATCACCTTGAACTTGAGTAGAGCTCTCTTCGGGCATTAGGGTTG RR: GGGGACCGACTACGTGCTTCTTACCCTACCTCCCGTCTCACAACCAGGTCGACAATAGTGGAACTTGAACTCATCTCGAGAGAAGCCCGTAATCCCAAC F2: 3 GTCTCACAACCAGGTC 2 Unidirectional alignment (log-probability: -42.3) CCCTGGCTGATGCACGAAGAATGGGATGGAGGGCAGAGTGcTGGaCCAacactctG---------CCTTGAACTTGAGTAGAGCTCTCTTCGGGCATTAGGGTTG CCCTGGCTGATGCACGAAGAATGGGATGGAGGGCAGAGTGTTGGTCCA-------GCTGTTATCACCTTGAACTTGAGTAGAGCTCTCTTCGGGCATTAGGGTTG Template switch alignment (log-probability: -17.8) CCCTGGCTGATGCACGAAGAATGGGATGGAGGGCAGAGTG|CTGGACCAACACTCTG|CCTTGAACTTGAGTAGAGCTCTCTTCGGGCATTAGGGTTG CCCTGGCTGATGCACGAAGAATGGGATGGAGGGCAGAGTG|CTGGACCAACACTCTG|CCTTGAACTTGAGTAGAGCTCTCTTCGGGCATTAGGGTTG ========= Event 962 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AAATGGGCTGGAGTCTTTCCAGTCTTCTA------AGAGCAAGCTAAAGGCAGACTT ↓ 3 1 2 4 Chimp: AAATGGGCTGGAGTCTTTCCAGTCTTTAGAAGACTGGAGCAAGCTAAAGGCAGACTT Gorilla: --------------------------------------------------------- Human: AAATGGGCTGGAGTCTTTCCAGTCTTCTA------AGAGCAAGCTAAAGGCAGACTT Cluster: [ ] Orangutan: --------------------------------------------------------- Human > Chimp ------------- chr14:88198613-88198622 Template switch process: F1: L ATGGAAAATTTACTAAAATGGGCTGGAGTCTTTCCAGTCTT 1 F3: 4 GAGCAAGCTAAAGGCAGACTTAAATCTTATAGCTTCCAAA R RF: ATGGAAAATTTACTAAAATGGGCTGGAGTCTTTCCAGTCTTCTAAGAGCAAGCTAAAGGCAGACTTAAATCTTACAGCTTCCAAA RR: TACCTTTTAAATGATTTTACCCGACCTCAGAAAGGTCAGAAGATTCTCGTTCGATTTCCGTCTGAATTTAGAATGTCGAAGGTTT F2: 3 GTCAGAAGAT 2 Unidirectional alignment (log-probability: -41.7) TGGAAAATTTACTAAAATGGGCTGGAGTCTTTCCAGTCTT----tagaagactgGAGCAAGCTAAAGGCAGACTTAAATCTTAtAGCTTCCAAA TGGAAAATTTACTAAAATGGGCTGGAGTCTTTCCAGTCTTCTAA----------GAGCAAGCTAAAGGCAGACTTAAATCTTACAGCTTCCAAA Template switch alignment (log-probability: -22.5) TGGAAAATTTACTAAAATGGGCTGGAGTCTTTCCAGTCTT|TAGAAGACTG|GAGCAAGCTAAAGGCAGACTTAAATCTTAtAGCTTCCAAA TGGAAAATTTACTAAAATGGGCTGGAGTCTTTCCAGTCTT|TAGAAGACTG|GAGCAAGCTAAAGGCAGACTTAAATCTTACAGCTTCCAAA ========= Event 963 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGGGCGCTGGGGCCTGAGATCATCAGGCC--C-------TAGCCTGATGACTCAGGAGTCTAGCCCTCC Chimp: TAGGGCGCTGGGGCCTGAGATCATCAGGCC--C-------TAGCCTGATGACCCAGGAGTCTAGCCCTCC ↑ 1 3 4 2 Gorilla: TAGGGCGCTGGGGCCTGAGATGCCTGGACCACCTGTGGTAGGGCCTGATGACCCAGGAGTCTAGCCCTCC ↓ 1 3 4 2 Human: TAGGGCGCTGGGGCCTGAGATCATCAGGCC--C-------TAGCCTGATGACTCAGGAGTCTAGCCCTCC Cluster: [ ] Orangutan: TAGGGTGCTGGGACCTGAGATCCCTGGACCACCTGTGGTAGGGCCTGATGACCCAGGAGTCTAGCCCTCC Gorilla > Human --------------- chr14:20988914-20988925 Template switch process: F1: L CCACAGAAGGAAAGTCCAATTAGGGCGCTGGGGCCTGAGAT 1 F3: 4 GCCTGATGACTCAGGAGTCTAGCCCTCCAGATGAACTGGC R RF: CCACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGATGCCTGGACCACCTGTGGTAGGGCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC RR: GGTGTCTTCCCTTCAGGTTAATCCCGCGACCCCGGACTCTACGGACCTGGTGGACACCATCCCGGACTACTGGGTCCTCAGATCGGGAGGTCTACTTGACCG F2: 3 ATCCCGGACTAC 2 Unidirectional alignment (log-probability: -50) CACAGAAGGaAAGTCCAATTAGGGCGCTGGGGCCTGAGAT---------------------catcaggccctaGCCTGATGACtCAGGAGTCTAGCCCTCCAGATGAACTGGC CACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGATGCCTGGACCACCTGTGGTAGG------------GCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC Template switch alignment (log-probability: -28.3) CACAGAAGGaAAGTCCAATTAGGGCGCTGGGGCCTGAGAT|CATCAGGCCCTA|GCCTGATGACtCAGGAGTCTAGCCCTCCAGATGAACTGGC CACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGAT|CATCAGGCCCTA|GCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC Gorilla > Chimp --------------- chr14:4690519-4690530 Template switch process: F1: L CCACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGAT 1 F3: 4 GCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC R RF: CCACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGATGCCTGGACCACCTGTGGTAGGGCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC RR: GGTGTCTTCCCTTCAGGTTAATCCCGCGACCCCGGACTCTACGGACCTGGTGGACACCATCCCGGACTACTGGGTCCTCAGATCGGGAGGTCTACTTGACCG F2: 3 ATCCCGGACTAC 2 Unidirectional alignment (log-probability: -39) CACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGAT---------------------catcaggccctaGCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC CACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGATGCCTGGACCACCTGTGGTAGG------------GCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC Template switch alignment (log-probability: -17.3) CACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGAT|CATCAGGCCCTA|GCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC CACAGAAGGGAAGTCCAATTAGGGCGCTGGGGCCTGAGAT|CATCAGGCCCTA|GCCTGATGACCCAGGAGTCTAGCCCTCCAGATGAACTGGC ========= Event 964 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTGTGGGCAGGACACAACCATTTAGGCAACGTTTTTACATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTG------TAGTAGAGTTGTCCTAGCTCTACTA ↓ 3 2 1 4 Chimp: GCTGTGGGCAGGACATAACCATTTAGGCAACGTTTTTACATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTG---CCAAATGAGAGTTGTCCTAGCTCTACTA Gorilla: GCTGTGGGCAGGACACAACCATTTAGGCAACGTTTTTACATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCATGATTGCCA---AATGAGAGTTGTCCTAGCTCTACTA Human: GCTGTGGGCAGGACACAACCATTTAGGCAACGTTTTTACATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTG------TAGTAGAGTTGTCCTAGCTCTACTA Cluster: [ ] Orangutan: GCTGTGGGCAGGACACAACCATTTAGGAAACGTT-TTACATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTTCCA---AATGAGAGTTGTCCTAGCTCTACTA Human > Chimp ------------- chr14:4933693-4933699 Template switch process: F1: L CATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTG 1 F3: 4 AGAGTTGTCCTAGCTCTACTACACAAAATGGTACAATGAA R RF: CATTTAGGCAACGTTTTTACATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTGTAGTAGAGTTGTCCTAGCTCTACTACACAAAATGGTACAATGAA RR: GTAAATCCGTTGCAAAAATGTAACACTTCACAGTAAGGGTCGAGGGGGATGAGTGCTAACATCATCTCAACAGGATCGAGATGATGTGTTTTACCATGTTACTT F2: 3 GTAAACC 2 Unidirectional alignment (log-probability: -31.4) ATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATtgccaaaTG----AGAGTTGTCCTAGCTCTACTACACAAAATGGTACAATGAA ATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGAT-------TGTAGTAGAGTTGTCCTAGCTCTACTACACAAAATGGTACAATGAA Template switch alignment (log-probability: -22.1) ATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTG|CcAAATG|AGAGTTGTCCTAGCTCTACTACACAAAATGGTACAATGAA ATTGTGAAGTGTCATTCCCAGCTCCCCCTACTCACGATTG|CTAAATG|AGAGTTGTCCTAGCTCTACTACACAAAATGGTACAATGAA ========= Event 965 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: GAGTAGTGTCAGCAAGGTGTGTC-TGAATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCTCTGTTGAGTGGAACCTCATCTCCCCTTGTTTTGTGTTTTCAAGCTCAGAAATATTCATTAGTGTAACAA ↓ 1 3 42 ↑ 1 4 3 2 Chimp: GAGTAGTGTCAGCAAGGTGTGATTCAGATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACTCTGTTGAGTGGAACCTCGTCTCCCCTTGTTTTGTGTTTTCAAAGTCAGAAATATTCATTAGTGTAACAA Gorilla: GAGTAGTGTCAGCAAGGTGTGTC-TGAATCAGGTTTTCTGGGTTGTGTAATTGATGTGTATATACCTCTGTTGAGTGGAACCTCATCTCCCCTTGTTTTGTGTTTTCAAGCTCAGAAATATTCATTAGTGTAACAA Human: GAGTAGTGTCAGCAAGGTGTGTC-TGAATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCTCTGTTGAGTGGAACCTCATCTCCCCTTGTTTTGTGTTTTCAAGCTCAGAAATATTCATTAGTGTAACAA Cluster: [ ] Orangutan: GAGTAGGGTCAGCAAGGTGTGTC-TGAATCAGATTTTCTGGGTCATGTAATTGATGTGTATATACCTCTCTTGAGTGGAACCTCATCTTCCCTTGTTTTGTGTTTTCAAGCACAGAAATATTCATTAGTGTAACAA Chimp > Human ------------- chr14:84703478-84703482 Template switch process: F1: L TGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG 1 F3: 4 ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCT R RF: TGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGATTCAGATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACTCTGTTGAGTGGAACCTCGTCTCCCCTTGTTTTGTGTTTTCAAAGTCAGA RR: ACTTTTACTGGAAGGGATACCTCATCACAGTCGTTCCACACTAAGTCTAGTCCAAAAGACCCAGTACATTAACTACACATATATTGAGACAACTCACCTTGGAGCAGAGGGGAACAAAACACAAAAGTTTCAGTCT F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -33.1) GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGtgtcTGA-----ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAcCT GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTG----TGATTCAGATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACT Template switch alignment (log-probability: -21.9) GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|TCTGA|ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAcCT GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|TCTGA|ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACT Human > Chimp ------------- chr14:85882140-85882145 Template switch process: F1: L TGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG 1 F3: 4 ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACT R RF: TGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGTCTGAATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCT RR: ACTTTTACTGGAAGGGATACCTCATCACAGTCGTTCCACACAGACTTAGTCCAAAAGACCCAGTACATTAACTACACATATATGGA F2: 3 GACTTA 2 Unidirectional alignment (log-probability: -34.5) GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTG----TGAttcagATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAaCT GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGTCTGA-----ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCT Template switch alignment (log-probability: -22) GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|ATTCAG|ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAaCT GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|ATTCAG|ATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCT ========= Event 966 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGCCTGAGTTAACCAGACAGT-TAACTGACTGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTTTCAGAGAGGTAAAGTG Chimp: TGCCTGAGTTAACCAGACAGTTCCACCCACGGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTTTCAGAGAGATAAAGTG Gorilla: TGCCTGAGTTAACCAGACAGTTCCACCCACGGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTTTCAGAGAGATAAAGTG ↓ 1 4 3 2 Human: TGCCTGAGTTAACCAGACAGT-TAACTGACTGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTTTCAGAGAGGTAAAGTG Cluster: [ ] Orangutan: TGCCTGAGTTAACCAGACAGTTCCACCCACAGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTTTCAGAGAGATAAAGTG Gorilla > Human --------------- chr14:84560131-84560135 Template switch process: F1: L AAAAGTGGGGTTAAATGCTCTGCCTGAGTTAACCAGACAGTT 1 F3: 4 ACTGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTT R RF: AAAAGTGGGGTTAAATGCTCTGCCTGAGTTAACCAGACAGTTCCACCCACGGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTCTTT RR: TTTTCACCCCAATTTACGAGACGGACTCAATTGGTCTGTCAAGGTGGGTGCCCTGGAGTCAATGGTCTGACCCCTAACTCTTGTCAAGAAA F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -32.6) AAGTGGGGTTAAATGCTCTGCCTGAGTTAACCAGACAGTT---------aactgactGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTC AAGTGGGGTTAAATGCTCTGCCTGAGTTAACCAGACAGTTCCACCCACG--------GGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTC Template switch alignment (log-probability: -22) AAGTGGGGTTAAATGCTCTGCCTGAGTTAACCAGACAGTT|AACTG|ACtGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTC AAGTGGGGTTAAATGCTCTGCCTGAGTTAACCAGACAGTT|AACTG|ACGGGACCTCAGTTACCAGACTGGGGATTGAGAACAGTTC ========= Event 967 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: GTGTGGTAGATGTGGACAAGTGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGTC-TGAATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCTCTGTTGAGTGGAACCTCATCTCCCCTTGTTTTGTGTTTTCAAGCTCAGAAATATTCATTAGTGTAACAA Chimp: GTGTGGTAGATGTGGACAAGTGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGATTCAGATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACTCTGTTGAGTGGAACCTCGTCTCCCCTTGTTTTGTGTTTTCAAAGTCAGAAATATTCATTAGTGTAACAA ↓ 1 4 3 2 ↑ 1 3 2 4 Gorilla: GTGTGGTAGATGTGGACAAGTAAAAATGACATTCCCTATGGAGTAGTGTCAGCAAGGTGTGTC-TGAATCAGGTTTTCTGGGTTGTGTAATTGATGTGTATATACCTCTGTTGAGTGGAACCTCATCTCCCCTTGTTTTGTGTTTTCAAGCTCAGAAATATTCATTAGTGTAACAA Human: GTGTGGTAGATGTGGACAAGTGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGTC-TGAATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATACCTCTGTTGAGTGGAACCTCATCTCCCCTTGTTTTGTGTTTTCAAGCTCAGAAATATTCATTAGTGTAACAA Cluster: [ ] Orangutan: GTGTGGTAGATGTGCACAAGTAAAAATGACATTCCTTATGGAGTAGGGTCAGCAAGGTGTGTC-TGAATCAGATTTTCTGGGTCATGTAATTGATGTGTATATACCTCTCTTGAGTGGAACCTCATCTTCCCTTGTTTTGTGTTTTCAAGCACAGAAATATTCATTAGTGTAACAA Gorilla > Chimp --------------- chr14:85882140-85882145 Template switch process: F1: L CAGGGAGAGTGAAAATGGAGGTGTGGTAGATGTGGACAAGTGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG 1 F3: 4 ATCA R RF: CAGGGAGAGTGAAAATGGAGGTGTGGTAGATGTGGACAAGTAAAAATGACATTCCCTATGGAGTAGTGTCAGCAAGGTGTGTCTGAATCA RR: GTCCCTCTCACTTTTACCTCCACACCATCTACACCTGTTCATTTTTACTGTAAGGGATACCTCATCACAGTCGTTCCACACAGACTTAGT F2: 3 GACTTA 2 Unidirectional alignment (log-probability: -39.1) gAAAATGACcTTCCCTATGGAGTAGTGTCAGCAAGGTG----TGAttcagATCA AAAAATGACATTCCCTATGGAGTAGTGTCAGCAAGGTGTGTCTGA-----ATCA Template switch alignment (log-probability: -27.6) gAAAATGACcTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|ATTCAG|ATCA AAAAATGACATTCCCTATGGAGTAGTGTCAGCAAGGTGTG|ATTCAG|ATCA Chimp > Gorilla --------------- chr14:23023513-23023517 Template switch process: F1: L CAGGGAGAGTGAAAATGGAGGTGTGGTAGATGTGGACAAGTAAAAATGACATTCCCTATGGAGTAGTGTCAGCAAGGTGTG 1 F3: 4 ATCA R RF: CAGGGAGAGTGAAAATGGAGGTGTGGTAGATGTGGACAAGTGAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTGATTCAGATCAGGTTTTCTGGGTCATGTAATTGATGTGTATATAACTCTGTTGAGTGGAACCTCGTCTCCCCTTGTTTTGTGTTTTCAAAGTCAGA RR: GTCCCTCTCACTTTTACCTCCACACCATCTACACCTGTTCACTTTTACTGGAAGGGATACCTCATCACAGTCGTTCCACACTAAGTCTAGTCCAAAAGACCCAGTACATTAACTACACATATATTGAGACAACTCACCTTGGAGCAGAGGGGAACAAAACACAAAAGTTTCAGTCT F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -37.7) aAAAATGACaTTCCCTATGGAGTAGTGTCAGCAAGGTGtgtcTGA-----ATCA GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTG----TGATTCAGATCA Template switch alignment (log-probability: -27.5) aAAAATGACaTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|TCTGA|ATCA GAAAATGACCTTCCCTATGGAGTAGTGTCAGCAAGGTGTG|TCTGA|ATCA ========= Event 968 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GACTTAAATACACACAATTAAAC----TGTATTCCTTTTCCAGGGACCTGaaaaccctttactaacactgttctcattcatcttcagaagacccataaaggtagccatggttactgttactaaatgtacagatataaaatgcaggcacacagaatcagtgacctggctatgtcataata Chimp: GACTTAAATACACACAATTAAAC----TGTATTCCTTTTCCAGGGACCTGaaaaccctttactaacactgttctcattcatcttcagaagacccataaaggtagccatggttactgttactaaatgtacagatataaaatgcaggcacacagaatcagtgacctggctatgtcataata ↑ 1 4 3 2 Gorilla: GACTTAAATACACACAATTAATTATTAATTATTCCTTTTCCAGGGACCTGaaaaccctttactaacactgttctcattcatcttcagaagacccgtaaaggtagccatgattactgctactaaatgtacagatataaaatgcaggcacacagaatcagtgacctggctatgtcataata ↓ 1 4 3 2 Human: GACTTAAATACACACAATTAAAC----TGTATTCCTTTTCCAGGGACCTGaaaaccctttactaacactgttctcattcatcttcagaagacccataaaggtagccatggttactgttactaaatgtacagatataaaatgcaggcacacagaatcagtgacctggctatgtcataata Cluster: [ ] Orangutan: GACTTAAATACACACAATTAAAC----TGTATTCCTTTTCCAGGGACCTGaaaaccctttactaacactgttctcattcatcttcagaagacccttaaaggtagccatggttactgttactaaatgtacagatataaaatgcaggcacacagaatcagtgacctggctatgtcataata Gorilla > Human --------------- chr14:23093658-23093661 Template switch process: F1: L ACCTCTAAATTAAACGCAATGACTTAAATACACACAATTAA 1 F3: 4 TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT R RF: ACCTCTTAATTAAACGCAATGACTTAAATACACACAATTAATTATTAATTATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACTGTTCTCATTCATCTTCAGAAGACCCGTAAAGGTAGCCATGATTACTGCTACTAAATGTACAGATATAAAATGCAGGCACACAGAATCAGT RR: TGGAGAATTAATTTGCGTTACTGAATTTATGTGTGTTAATTAATAATTAATAAGGAAAAGGTCCCTGGACTTTTGGGAAATGATTGTGACAAGAGTAAGTAGAAGTCTTCTGGGCATTTCCATCGGTACTAATGACGATGATTTACATGTCTATATTTTACGTCCGTGTGTCTTAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -32.3) CCTCTaAATTAAACGCAATGACTTAAATACACACAATTAA--------actgTATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT CCTCTTAATTAAACGCAATGACTTAAATACACACAATTAATTATTAAT----TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT Template switch alignment (log-probability: -21.7) CCTCTaAATTAAACGCAATGACTTAAATACACACAATTAA|ACTG|TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT CCTCTTAATTAAACGCAATGACTTAAATACACACAATTAA|ACTG|TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT Gorilla > Chimp --------------- chr14:6835269-6835272 Template switch process: F1: L ACCTCTTAATTAAACGCAATGACTTAAATACACACAATTAA 1 F3: 4 TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT R RF: ACCTCTTAATTAAACGCAATGACTTAAATACACACAATTAATTATTAATTATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACTGTTCTCATTCATCTTCAGAAGACCCGTAAAGGTAGCCATGATTACTGCTACTAAATGTACAGATATAAAATGCAGGCACACAGAATCAGT RR: TGGAGAATTAATTTGCGTTACTGAATTTATGTGTGTTAATTAATAATTAATAAGGAAAAGGTCCCTGGACTTTTGGGAAATGATTGTGACAAGAGTAAGTAGAAGTCTTCTGGGCATTTCCATCGGTACTAATGACGATGATTTACATGTCTATATTTTACGTCCGTGTGTCTTAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -26.8) CCTCTTAATTAAACGCAATGACTTAAATACACACAATTAA--------actgTATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT CCTCTTAATTAAACGCAATGACTTAAATACACACAATTAATTATTAAT----TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT Template switch alignment (log-probability: -16.2) CCTCTTAATTAAACGCAATGACTTAAATACACACAATTAA|ACTG|TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT CCTCTTAATTAAACGCAATGACTTAAATACACACAATTAA|ACTG|TATTCCTTTTCCAGGGACCTGAAAACCCTTTACTAACACT ========= Event 969 ========= Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTTTCCCACCCTGTTGTTTACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTCCTGGTATGGTTAGTGTGTGCTTTCAGG ↑ 3 2 1 4 Chimp: ATTTTCCCACCCTGTTGTTTACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTT----AGTGGTTAGTGTGTGCTTTCAGG ↓ 3 2 1 4 Gorilla: ATTTTCCCACCCTGTTGTTTACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTCCTGGTATGGTTAGTGTGTGCTTTCAGG Human: ATTTTCCCACCCTGTTGTTTACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTCCTGGTATGGTTAGTGTGTGCTTTCAGG Cluster: [ ] Orangutan: ATTTTCCCACCCTGTTGTTTACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTCCTGGTATGGTTAGTGTGTGCTTTCAGG Chimp > Human ------------- chr14:82057196-82057202 Template switch process: F1: L GAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT 1 F3: 4 TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC R RF: TACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTTAGTGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC RR: ATGGTCCCGGACCTTATCCATGACTCTTTGGGACAGTTGTCGACTAGGTCCGAATCACCAATCACACACGAAAGTCCTCTGGTGGTTGTGGTCGTG F2: 3 ATGGTCC 2 Unidirectional alignment (log-probability: -28.4) AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTcctggTA-TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT-----TAGTGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC Template switch alignment (log-probability: -16.2) AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT|CCTGGTA|TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT|CCTGGTA|TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC Chimp > Gorilla --------------- chr14:20404596-20404602 Template switch process: F1: L GAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT 1 F3: 4 TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC R RF: TACCAGGGCCTGGAATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTTAGTGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC RR: ATGGTCCCGGACCTTATCCATGACTCTTTGGGACAGTTGTCGACTAGGTCCGAATCACCAATCACACACGAAAGTCCTCTGGTGGTTGTGGTCGTG F2: 3 ATGGTCC 2 Unidirectional alignment (log-probability: -27.9) AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCTcctggTA-TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT-----TAGTGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC Template switch alignment (log-probability: -16.6) AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT|CCTGGTA|TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC AATAGGTACTGAGAAACCCTGTCAACAGCTGATCCAGGCT|CCTGGTA|TGGTTAGTGTGTGCTTTCAGGAGACCACCAACACCAGCAC ========= Event 970 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCTGCTTGAGCTAGTTTCATACTTTCACCAAGTATGAATAGGTCTTTCCCTGGGGAA Chimp: GCTGCTTGAGCTAGTTTCATACTTTCACCAAGTATGAATAGGTCTTTCCCTGGGGAA ↑ 3 1 4 2 Gorilla: GCTGCTTGAGCTGGTTTCATACTT--------GGTGAATAGGTCTTTCCCTGGGGAA ↓ 3 1 4 2 Human: GCTGCTTGAGCTAGTTTCATACTTTCACCAAGTATGAATAGGTCTTTCCCTGGGGAA Cluster: [ ] Orangutan: GCTGGTTGAACTAGTTTCATACTT--------GGTGAATAGGTCTTTCCCTGGGGAA Gorilla > Human --------------- chr14:82039833-82039842 Template switch process: F1: L TTTCTTAAACTGGGAGAGCTGCTTGAGCTAGTTTCATACTT 1 F3: 4 TGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC R RF: TTTCTTAAACTGGGAGAGCTGCTTGAGCTGGTTTCATACTTGGTGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC RR: AAAGAATTTGACCCTCTCGACGAACTCGACCAAAGTATGAACCACTTATCCAGAAAGGGACCCCTTGTAGTAAAGGACGACGG F2: 3 ATGAACCACT 2 Unidirectional alignment (log-probability: -39) TTCTTAAACTGGGAGAGCTGCTTGAGCTaGTTTCATACTTtcaccaagtaTGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC TTCTTAAACTGGGAGAGCTGCTTGAGCTGGTTTCATACTT--------GGTGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC Template switch alignment (log-probability: -22.5) TTCTTAAACTGGGAGAGCTGCTTGAGCTaGTTTCATACTT|TCACCAAGTA|TGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC TTCTTAAACTGGGAGAGCTGCTTGAGCTGGTTTCATACTT|TCACCAAGTA|TGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC Gorilla > Chimp --------------- chr14:83269339-83269348 Template switch process: F1: L TTTCTTAAACTGGGAGAGCTGCTTGAGCTAGTTTCATACTT 1 F3: 4 TGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC R RF: TTTCTTAAACTGGGAGAGCTGCTTGAGCTGGTTTCATACTTGGTGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC RR: AAAGAATTTGACCCTCTCGACGAACTCGACCAAAGTATGAACCACTTATCCAGAAAGGGACCCCTTGTAGTAAAGGACGACGG F2: 3 ATGAACCACT 2 Unidirectional alignment (log-probability: -39) TTCTTAAACTGGGAGAGCTGCTTGAGCTaGTTTCATACTTtcaccaagtaTGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC TTCTTAAACTGGGAGAGCTGCTTGAGCTGGTTTCATACTT--------GGTGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC Template switch alignment (log-probability: -22.5) TTCTTAAACTGGGAGAGCTGCTTGAGCTaGTTTCATACTT|TCACCAAGTA|TGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC TTCTTAAACTGGGAGAGCTGCTTGAGCTGGTTTCATACTT|TCACCAAGTA|TGAATAGGTCTTTCCCTGGGGAACATCATTTCCTGCTGCC ========= Event 971 ========= Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTCTTTTTATCTCTCTAAATTTTATAGTCATTCAG--------------TCATATGTGATATTTTATACATTTAACCATA----TGTATCATATTCT ↓ 13 24 ↑ 13 24 Chimp: GTCTTTTTATCTCTCTAAATT--------------TTATAGTCATTCAGTCATATGGTTAAATGTATAAAATATCACATA----TGTATCATATTCT Gorilla: GTCTTTTTATCTCTCTAAATTTTATAGTCATTCAG--------------TCATATGGTTAAATGTATAAAATATCGCATA----TGTATCATATTCT ↓ 3 2 4 ↑ 1 3 4 Human: GTCTTTTTATCTCTCTAAATTTTATAGTCATTCAG--------------TCATATGTGATATTTTATACATTTAACCATA----TGTATCATATTCT Cluster: [ ] Orangutan: gtgtttttatctctctaaattttatagtcattcag--------------tcatatggttaaatgtataaaatatcacatatgctggtatcatattcc Chimp > Human ------------- chr14:25872262-25872281 Template switch process: F1: L ATATTATATATTAAGTTTCTGTCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG 1 F3: 4 CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC R RF: ATATTATATATTAAGTTTCTGTCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGGTTAAATGTATAAAATATCACATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC RR: TATAATATATAATTCAAAGACAGAAAAATAGAGAGATTTAAAATATCAGTAAGTCAGTATACCAATTTACATATTTTATAGTGTATACATAGTATAAGATATGACCTCGTACACACAATTGG F2: 3 CAATTTACATATTTTATAGT 2 Unidirectional alignment (log-probability: -51.1) CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG--------------------tgatattttatacatttaacCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGGTTAAATGTATAAAATATCA--------------------CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC Template switch alignment (log-probability: -18.1) CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG|TGATATTTTATACATTTAAC|CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG|TGATATTTTATACATTTAAC|CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC Human > Chimp ------------- chr14:9554933-9554952 Template switch process: F1: L ATATTATATATTAAGTTTCTGTCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG 1 F3: 4 CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC R RF: ATATTATATATTAAGTTTCTGTCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGTGATATTTTATACATTTAACCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC RR: TATAATATATAATTCAAAGACAGAAAAATAGAGAGATTTAAAATATCAGTAAGTCAGTATACACTATAAAATATGTAAATTGGTATACATAGTATAAGATATGACCTCGTACACACAATTGG F2: 3 ACTATAAAATATGTAAATTG 2 Unidirectional alignment (log-probability: -51.1) CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG--------------------gttaaatgtataaaatatcaCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGTGATATTTTATACATTTAAC--------------------CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC Template switch alignment (log-probability: -18.1) CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG|GTTAAATGTATAAAATATCA|CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG|GTTAAATGTATAAAATATCA|CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC Gorilla > Human --------------- chr14:25872263-25872281 Template switch process: F1: L TCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGT 1 F3: 4 CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC R RF: TCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGGTTAAATGTATAAAATATCGCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC RR: AGAAAAATAGAGAGATTTAAAATATCAGTAAGTCAGTATACCAATTTACATATTTTATAGCGTATACATAGTATAAGATATGACCTCGTACACACAATTGG F2: 3 CAATTTACATATTTTATAG 2 Unidirectional alignment (log-probability: -50.4) TTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATAT--------------------GtgatattttatacatttaacCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC TTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGGTTAAATGTATAAAATATCG--------------------CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC Template switch alignment (log-probability: -23.7) TTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGt|GATATTTTATACATTTAAC|CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC TTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGG|GATATTTTATACATTTAAC|CATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC Human > Gorilla --------------- chr14:71481766-71481784 Template switch process: F1: L TCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG 1 F3: 4 GCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC R RF: TCTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGTGATATTTTATACATTTAACCATATGTATCATATTCTATACTGGAGCATGTGTGTTAACC RR: AGAAAAATAGAGAGATTTAAAATATCAGTAAGTCAGTATACACTATAAAATATGTAAATTGGTATACATAGTATAAGATATGACCTCGTACACACAATTGG F2: 3 CTATAAAATATGTAAATTG 2 Unidirectional alignment (log-probability: -50.4) CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG--------------------gttaaatgtataaaatatcgCATATGTATCATATTCTATACTGGAGCATGTGTGTTAAC CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATGTGATATTTTATACATTTAAC--------------------CATATGTATCATATTCTATACTGGAGCATGTGTGTTAAC Template switch alignment (log-probability: -23.7) CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG|GTTAAATGTATAAAATATC|gCATATGTATCATATTCTATACTGGAGCATGTGTGTTAAC CTTTTTATCTCTCTAAATTTTATAGTCATTCAGTCATATG|GTTAAATGTATAAAATATC|CCATATGTATCATATTCTATACTGGAGCATGTGTGTTAAC ========= Event 972 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GACTGATGATACTTGAATTATGAGTATGTTATTTTGGATTTATAATTAATACAATTTTTAATCAGTTC ↓ 1 3 42 Chimp: GACTGATGATACTTGAATTATAAATCCAAAATGACATACTTATAATTGATACAATTTTTAATCAGTTC ↑ 1 3 42 Gorilla: GACTGACGATACTTGAATTATGAGTATGTCATTTTGGATTTATAATTGATACAATTTTTAATCAGTTC Human: GACTGATGATACTTGAATTATGAGTATGTTATTTTGGATTTATAATTAATACAATTTTTAATCAGTTC Cluster: [ ] Orangutan: CACTGATGATACTTGAATTACGAGTATGTCACTTTGGATTTATAATTGATACAATTTTTAATCAGTTC Human > Chimp ------------- chr14:82528114-82528131 Template switch process: F1: L GTGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATTAT 1 F3: 4 TTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTATTTGTTTGT R RF: GTGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATTATGAGTATGTTATTTTGGATTTATAATTAATACAATTTTTAATCAGTTCTCCATGACGTATTTGTTTGT RR: CACCAGACCATTAAATCTTTCTGACTACTATGAACTTAATACTCATACAATAAAACCTAAATATTAATTATGTTAAAAATTAGTCAAGAGGTACTGCATAAACAAACA F2: 3 CATACAGTAAAACCTAAA 2 Unidirectional alignment (log-probability: -54) TGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATT------------------ATaaatccaaaatgacatacTTATAATTgATACAATTTTTAATCAGTTCTCCATGACGTA TGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATTATGAGTATGTTATTTTGGAT------------------TTATAATTAATACAATTTTTAATCAGTTCTCCATGACGTA Template switch alignment (log-probability: -29.7) TGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATTAT|AAATCCAAAATgACATAC|TTATAATTgATACAATTTTTAATCAGTTCTCCATGACGTA TGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATTAT|AAATCCAAAATAACATAC|TTATAATTAATACAATTTTTAATCAGTTCTCCATGACGTA Gorilla > Chimp --------------- chr14:82528114-82528131 Template switch process: F1: L GTGGTCTGGTAATTTAGAAAGACTGATGATACTTGAATTAT 1 F3: 4 TTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTA R RF: GTGGTCTAGTAATTTAGAAAGACTGACGATACTTGAATTATGAGTATGTCATTTTGGATTTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTA RR: CACCAGATCATTAAATCTTTCTGACTGCTATGAACTTAATACTCATACAGTAAAACCTAAATATTAACTATGTTAAAAATTAGTCAAGAGGTACTGCAT F2: 3 CATACAGTAAAACCTAAA 2 Unidirectional alignment (log-probability: -58.1) TGGTCTgGTAATTTAGAAAGACTGAtGATACTTGAATTATaA--------------ATccaaaatgacatacTTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTA TGGTCTAGTAATTTAGAAAGACTGACGATACTTGAATTATGAGTATGTCATTTTGGAT--------------TTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTA Template switch alignment (log-probability: -29.1) TGGTCTgGTAATTTAGAAAGACTGAtGATACTTGAATTAT|AAATCCAAAATGACATAC|TTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTA TGGTCTAGTAATTTAGAAAGACTGACGATACTTGAATTAT|AAATCCAAAATGACATAC|TTATAATTGATACAATTTTTAATCAGTTCTCCATGACGTA ========= Event 973 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTAATACACCTTAGGAACAAGTGCTGT-----TAGTAACAGAGTTTGGGGTTGATACATTCAAC Chimp: GTTAATACACCTTAGGAACAAGTGCTGT-----TAGTAACAGAGTTTAGGGTTGATACATTCAAC ↓ 1 4 3 2 Gorilla: GTTAATACACCTTAGGAACAAACTCTGTTAAGTTAGTAACAGAGTTTGGGGTTGATACATTCAAC ↑ 1 4 3 2 Human: GTTAATACACCTTAGGAACAAGTGCTGT-----TAGTAACAGAGTTTGGGGTTGATACATTCAAC Cluster: [ ] Orangutan: GTTAATACACCTTAGGAACAAGTGCTGT-----TAGGAACAGAGTTTGGGGTTGATACATTCAAC Human > Gorilla --------------- chr14:19606203-19606211 Template switch process: F1: L GAGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA 1 F3: 4 AGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAATGC R RF: GAGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAAGTGCTGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAATGC RR: CTCTTCCGATGATGTCGACTCAATTATGTGGAATCCTTGTTCACGACAATCATTGTCTCAAACCCCAACTATGTAAGTTGATGTTACG F2: 3 ATTGTCTCA 2 Unidirectional alignment (log-probability: -34.7) AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAAactctGTtaaGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAA AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA-----GTGCTGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAA Template switch alignment (log-probability: -22.5) AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA|ACTCTGTTA|aGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAA AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA|ACTCTGTTA|TGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAA Chimp > Gorilla --------------- chr14:19606203-19606211 Template switch process: F1: L GAGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA 1 F3: 4 AGTTAGTAACAGAGTTTGGGGTTGATACATTCAACTACAATGC R RF: GAGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAAGTGCTGTTAGTAACAGAGTTTAGGGTTGATACATTCAACTACAATGC RR: CTCTTCCGATGATGTCGACTCAATTATGTGGAATCCTTGTTCACGACAATCATTGTCTCAAATCCCAACTATGTAAGTTGATGTTACG F2: 3 ATTGTCTCA 2 Unidirectional alignment (log-probability: -40.2) AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAAactctGTtaaGTTAGTAACAGAGTTTgGGGTTGATACATTCAACTACAA AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA-----GTGCTGTTAGTAACAGAGTTTAGGGTTGATACATTCAACTACAA Template switch alignment (log-probability: -28) AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA|ACTCTGTTA|aGTTAGTAACAGAGTTTgGGGTTGATACATTCAACTACAA AGAAGGCTACTACAGCTGAGTTAATACACCTTAGGAACAA|ACTCTGTTA|TGTTAGTAACAGAGTTTAGGGTTGATACATTCAACTACAA ========= Event 974 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAACTCAATTCGTATGGCAGAT----------TTTTTCTTAACTAAAGCAACTTATTCATGTCTCTACAGACTCACATGCAGACATACAGTA Chimp: TAATTCAATTCGTATGGCAGAT----------TTTTTCTTAACTAAAGCAACTTATTCATGTCCCTACAGACTCACATGCAGACATACAGTA ↓ 1 4 3 2 Gorilla: TAACTCAATTCGTATGGCAGAG-------------------TCTGTAGGGACTTATTCATGTCCCTACAGACTCACATGCAGACATACAGTA ↑ 1 4 3 2 Human: TAACTCAATTCGTATGGCAGAT----------TTTTTCTTAACTAAAGCAACTTATTCATGTCTCTACAGACTCACATGCAGACATACAGTA Cluster: [ ] Orangutan: TAACTCAATTCGTATGGCAGATTTCTTTCTTA---------ACTAAAGCAACTTATTCATATCCCCACAGACTCACAGGCAGACATACAGTA Human > Gorilla --------------- chr14:18106824-18106833 Template switch process: F1: L GGGAATCAAAATCATACATCTAACTCAATTCGTATGGCAGA 1 F3: 4 ACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG R RF: GGGAATCAAAATCATACATCTAACTCAATTCGTATGGCAGATTTTTTCTTAACTAAAGCAACTTATTCATGTCTCTACAGACTCACATGCAGACATACAG RR: CCCTTAGTTTTAGTATGTAGATTGAGTTAAGCATACCGTCTAAAAAAGAATTGATTTCGTTGAATAAGTACAGAGATGTCTGAGTGTACGTCTGTATGTC F2: 3 GGGATGTCTG 2 Unidirectional alignment (log-probability: -41.5) GGAATCAAAATCATACATCTAACTCAATTCGTATGGCAG-------------------AgtctgtagggACTTATTCATGTCcCTACAGACTCACATGCAGACATACAG GGAATCAAAATCATACATCTAACTCAATTCGTATGGCAGATTTTTTCTTAACTAAAGCA----------ACTTATTCATGTCTCTACAGACTCACATGCAGACATACAG Template switch alignment (log-probability: -28) GGAATCAAAATCATACATCTAACTCAATTCGTATGGCAGA|GTCTGTAGgG|ACTTATTCATGTCcCTACAGACTCACATGCAGACATACAG GGAATCAAAATCATACATCTAACTCAATTCGTATGGCAGA|GTCTGTAGAG|ACTTATTCATGTCTCTACAGACTCACATGCAGACATACAG Chimp > Gorilla --------------- chr14:18106824-18106833 Template switch process: F1: L GGGAATCAAAATCATACATCTAACTCAATTCGTATGGCAGA 1 F3: 4 ACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG R RF: GGGAATCAAAATCATACATCTAATTCAATTCGTATGGCAGATTTTTTCTTAACTAAAGCAACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG RR: CCCTTAGTTTTAGTATGTAGATTAAGTTAAGCATACCGTCTAAAAAAGAATTGATTTCGTTGAATAAGTACAGGGATGTCTGAGTGTACGTCTGTATGTC F2: 3 GGGATGTCTG 2 Unidirectional alignment (log-probability: -41.5) GGAATCAAAATCATACATCTAAcTCAATTCGTATGGCAG-------------------AgtctgtagggACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG GGAATCAAAATCATACATCTAATTCAATTCGTATGGCAGATTTTTTCTTAACTAAAGCA----------ACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG Template switch alignment (log-probability: -22.5) GGAATCAAAATCATACATCTAAcTCAATTCGTATGGCAGA|GTCTGTAGGG|ACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG GGAATCAAAATCATACATCTAATTCAATTCGTATGGCAGA|GTCTGTAGGG|ACTTATTCATGTCCCTACAGACTCACATGCAGACATACAG ========= Event 975 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGGCAAGATTAGAAATATTATATAAACTTCTCAGTTTATATACAGTAAGACATTTAAAAA ↑ 3 1 2 4 Chimp: TGGGCAAGATTAGAAATATTATATAAACTGAG----AAACATACAGTAAGACATTTAAAAA Gorilla: TGGGCAAGATTAGAAATATTACATAAACTGAG----AAACATACAGTAAGACATTTAAAAA ↓ 3 1 2 4 Human: TGGGCAAGATTAGAAATATTATATAAACTTCTCAGTTTATATACAGTAAGACATTTAAAAA Cluster: [ ] Orangutan: tgggcAACATTAGAAATACTACATAAAGTGAG----AAACATACAGTAAGACATTTAAAAA Chimp > Human ------------- chr14:78179684-78179694 Template switch process: F1: L TTCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACT 1 F3: 4 ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT R RF: TTCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACTGAGAAACATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT RR: AAGAAAGGAGAAACCCGTTCTAATCTTTATAATATATTTGACTCTTTGTATGTCATTCTGTAAATTTTTTATAATGTGAGACATCCTA F2: 3 TATTTGACTCT 2 Unidirectional alignment (log-probability: -37.3) TCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACT-------tctcagtttatATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT TCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACTGAGAAAC-----------ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT Template switch alignment (log-probability: -16.6) TCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACT|TCTCAGTTTAT|ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT TCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACT|TCTCAGTTTAT|ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT Gorilla > Human --------------- chr14:78179684-78179694 Template switch process: F1: L GTGTCCTCTTCTTTCCTCTTTGGGCAAGATTAGAAATATTATATAAACT 1 F3: 4 ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT R RF: GTGTCCTCTTCTTTCCTCTTTGGGCAAGATTAGAAATATTACATAAACTGAGAAACATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT RR: CACAGGAGAAGAAAGGAGAAACCCGTTCTAATCTTTATAATGTATTTGACTCTTTGTATGTCATTCTGTAAATTTTTTATAATGTGAGACATCCTA F2: 3 TATTTGACTCT 2 Unidirectional alignment (log-probability: -42.4) TCTTTCCTCTTTGGGCAAGATTAGAAATATTAtATAAACttctcagtttaT-------ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT TCTTTCCTCTTTGGGCAAGATTAGAAATATTACATAAAC-----------TGAGAAACATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT Template switch alignment (log-probability: -22.8) TCTTTCCTCTTTGGGCAAGATTAGAAATATTAtATAAACT|TCTCAGTTTAT|ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT TCTTTCCTCTTTGGGCAAGATTAGAAATATTACATAAACT|TCTCAGTTTAT|ATACAGTAAGACATTTAAAAAATATTACACTCTGTAGGAT ========= Event 976 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTGAACACTTTTATTAACCAG---------------------AGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCAC Chimp: GCTGAACACTTTTATTAACCAG---------------------AGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCAC ↓ 4 3 12 Gorilla: GCTGAACACTTTTATTAACCAAATAAGTACCAAATTGGTACTTATTTATATAAGTACCAATAAAATGCCAAGTGGAAGCAC ↑ 4 3 12 Human: GCTGAACACTTTTATTAACCAG---------------------AGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCAC Cluster: [ ] Orangutan: GCTGAACACTTTTATTAACCAG---------------------AATTATGTAAGTACCAATAAAATGCCGAGTGGAAGCAC Human > Gorilla --------------- chr14:16409429-16409440 Template switch process: F1: L AGGATATACATCAAGACTTAGCTGAACACTTTTATTAACCAA------ATAAGTACCAA 1 F3: 4 TTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT R RF: AGGATATACATCAAGACTTAGCTGAACACTTTTATTAACCAGAGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT RR: TCCTATATGTAGTTCTGAATCGACTTGTGAAAATAATTGGTCTCAATATATTCATGGTTATTTTACGGTTCACCTTCGTGTTAA F2: 3 TATTCATGGTTA 2 Unidirectional alignment (log-probability: -52.2) AGACTTAGCTGAACACTTTTATTAACCAaataagtaccaaattggtacttAtTTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT AGACTTAGCTGAACACTTTTATTAACCA---------------------GAGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT Template switch alignment (log-probability: -33.1) AGACTTAGCTGAACACTTTTATTAACCAa------ATAAGTACCAA|ATTGGTACTTAT|TTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT AGACTTAGCTGAACACTTTTATTAACCAGAGTTATATAAGTACCAA|ATTGGTACTTAT|TTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT Chimp > Gorilla --------------- chr14:16409429-16409440 Template switch process: F1: L AGGATATACATCAAGACTTAGCTGAACACTTTTATTAACCAA------ATAAGTACCAA 1 F3: 4 TTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT R RF: AGGATATACATCAAGACTTAGCTGAACACTTTTATTAACCAGAGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT RR: TCCTATATGTAGTTCTGAATCGACTTGTGAAAATAATTGGTCTCAATATATTCATGGTTATTTTACGGTTCACCTTCGTGTTAA F2: 3 TATTCATGGTTA 2 Unidirectional alignment (log-probability: -52.2) AGACTTAGCTGAACACTTTTATTAACCAaataagtaccaaattggtacttAtTTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT AGACTTAGCTGAACACTTTTATTAACCA---------------------GAGTTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT Template switch alignment (log-probability: -33.1) AGACTTAGCTGAACACTTTTATTAACCAa------ATAAGTACCAA|ATTGGTACTTAT|TTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT AGACTTAGCTGAACACTTTTATTAACCAGAGTTATATAAGTACCAA|ATTGGTACTTAT|TTATATAAGTACCAATAAAATGCCAAGTGGAAGCACAATT ========= Event 977 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCACCAACTTTGGTATTGGCTAT----------------AGCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAATTAAAGAAAAGTggccaggcctgg ↓ 1 3 4 2 Chimp: CCACCAACTTTGGTATTGGCTTT--------AATTGAAGTGCTC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAATTAAAGAAAAGTggccaggcctgg Gorilla: CCAGCCACTT-------TTCTTTAATTGAAG--------TGCTATAGCCAATACCAAATTTGGTGGCCTCCCATCCAACTTACAATTTACAGAATAGCACCTATACATTTAGTCTGCTGACTCTAAACGTCTCCCAGTAATCAAACTGTGTGTGAAATTCATAGTATGGGGCACACTnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Human: CCACCAACTTTGGTATTGGCTAT----------------AGCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAATTAAAGAAAAGTggccaggcctgg Cluster: [ ] Orangutan: Human > Chimp ------------- chr14:80436231-80436244 Template switch process: F1: L ATTGTAAGTTGGATGGGAGGCCACCAACTTTGGTATTGGCT 1 F3: 4 CTTCAATTAAAGAAAAGTGGCCAGGCCTGGTGGCTCATGC R RF: ATTGTAAGTTGGATGGGAGGCCACCAACTTTGGTATTGGCTATAGCACTTCAATTAAAGAAAAGTGGCCAGGCCTGGTGGCTCATGC RR: TAACATTCAACCTACCCTCCGGTGGTTGAAACCATAACCGATATCGTGAAGTTAATTTCTTTTCACCGGTCCGGACCACCGAGTACG F2: 3 TCGTGAAGTTAATT 2 Unidirectional alignment (log-probability: -34.5) TTGTAAGTTGGATGGGAGGCCACCAACTTTGGTATTGGCTtTAattgaagtGCtCTTCAATTAAAGAAAAGTGGCCAGGCCTGGTGGCTCATGC TTGTAAGTTGGATGGGAGGCCACCAACTTTGGTATTGGCTATA--------GCACTTCAATTAAAGAAAAGTGGCCAGGCCTGGTGGCTCATGC Template switch alignment (log-probability: -17) TTGTAAGTTGGATGGGAGGCCACCAACTTTGGTATTGGCT|TTAATTGAAGTGCT|CTTCAATTAAAGAAAAGTGGCCAGGCCTGGTGGCTCATGC TTGTAAGTTGGATGGGAGGCCACCAACTTTGGTATTGGCT|TTAATTGAAGTGCT|CTTCAATTAAAGAAAAGTGGCCAGGCCTGGTGGCTCATGC ========= Event 978 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGATTGCTAAATACCCTGTATTTGTGTGTGCatatatatatatatatatatatacacacacatatatataaataGGGAGAG ↓ 1 3 4 2 Chimp: TTGATTGCTAAATACCCTGTA--TGTGTGTGCatatatatatatatatacaca----tatatatatataAAAATAGGGAGAG Gorilla: TTGATTGCTAAATACCCTGTA--TGTGTGTGCTtatatatatatatata----------tatacatataAAAATAGGGAGAG Human: TTGATTGCTAAATACCCTGTATTTGTGTGTGCatatatatatatatatatatatacacacacatatatataaataGGGAGAG Cluster: [] Orangutan: TTGATTGCTAAATACCCTGTA--TGTGTGTGCTTATATATA--------------------------TATAAATAGGGAGAG Human > Chimp ------------- chr14:79227716-79227740 Template switch process: F1: L TTATGTGGCCTAAGATACATTTGATTGCTAAATACCCTGTAT 1 F3: 4 CACATATATA R RF: TTATGTGGCCTAAGATACATTTGATTGCTAAATACCCTGTATTTGTGTGTGCATATATATATATATATATATATACACACACATATATA RR: AATACACCGGATTCTATGTAAACTAACGATTTATGGGACATAAACACACACGTATATATATATATATATATATATGTGTGTGTATATAT F2: 3 ATATATATATATATATACGTGTGTG 2 Unidirectional alignment (log-probability: -34.5) ATGTGGCCTAAGATACATTTGATTGCTAAATACCCTGTA--TGTGTGTGCATATATATATATATATacacATATATA-------- ATGTGGCCTAAGATACATTTGATTGCTAAATACCCTGTATTTGTGTGTGCATATATATATATATAT----ATATATACACACACA Template switch alignment (log-probability: -23.8) ATGTGGCCTAAGATACATTTGATTGCTAAATACCCTGTAT|GTGTGTGcATATATATATATATATA|CACATATATA ATGTGGCCTAAGATACATTTGATTGCTAAATACCCTGTAT|GTGTGTGTATATATATATATATATA|CACATATATA ========= Event 979 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTTAGTGCATCACAATCTGATAATTTT---------GCCTTTAGTGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGTGATGCAAC Chimp: CTTTAGTGCGTCACAGTCTGATAATTTT---------GCCTTTAGTGCACTGAAGACACTAAAGGCAAAATTATCAGATTACAATGGTGCAAC Gorilla: CTTTAGTGCATCACAATCTGACAATTTT------------------GCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGTGATGCAAC ↓ 1 4 3 2 Human: CTTTAGTGCATCACAATCTGATAATTTT---------GCCTTTAGTGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGTGATGCAAC Cluster: [ ] Orangutan: CTTTAGTGCATCACAATCTGATCATTTTGCCTTTAGT---------GCACTGAAGGCACTAAAGGCAAAATCATCAGATTACGATGATGCAGC Gorilla > Human --------------- chr14:77454982-77454996 Template switch process: F1: L ATGCAAAGCATAGGAAATGCCTTTAGTGCATCACAATCTGA 1 F3: 4 TGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGTG R RF: ATGCGAAGCATAGGAAATGCCTTTAGTGCATCACAATCTGACAATTTTGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGTG RR: TACGCTTCGTATCCTTTACGGAAATCACGTAGTGTTAGACTGTTAAAACGTGACTTCCTTGATTTCCGTTTTAATAGTCTAATACCAC F2: 3 GATTTCCGTTTTAAT 2 Unidirectional alignment (log-probability: -35) TGCaAAGCATAGGAAATGCCTTTAGTGCATCACAATCTGAtAATTTtgcctttagTGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGT TGCGAAGCATAGGAAATGCCTTTAGTGCATCACAATCTGACAATTT---------TGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGT Template switch alignment (log-probability: -23.2) TGCaAAGCATAGGAAATGCCTTTAGTGCATCACAATCTGA|TAATTTTGCCTTTAG|TGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGT TGCGAAGCATAGGAAATGCCTTTAGTGCATCACAATCTGA|TAATTTTGCCTTTAG|TGCACTGAAGGAACTAAAGGCAAAATTATCAGATTATGGT ========= Event 980 ========= Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTAAACGTGGATCTTCTTTAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCCATTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAG----------------------------TTTTCAAGTAGTATCTGGCCCTAAAAAGTTTTCAAGTAGTTATCAAATTTcagtggaccc Chimp: ACTAAACGTGGATCTTCTTTAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCTGTTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAG----------------------------TTTTCAAGTAGTATCTGGCCCTAAAAAATTTTCAAGTAGTTATCAAATTTcagtggaccc ↑ 3 2 4 1 Gorilla: ACTAAACGTGGATCTTCTTTAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCCATTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAG--------------------------------------------------------TTTTCAAGTAGTTATCAAATTTcagtggaccc ↓ 3 2 4 1 Human: ACTAAACGTGGATCTTCTTTAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCCATTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAG----------------------------TTTTCAAGTAGTATCTGGCCCTAAAAAGTTTTCAAGTAGTTATCAAATTTcagtggaccc Cluster: [ ] Orangutan: ACTAAATGTGGATCTTCTTTAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCCATTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGTATCTGGCCCTAAAATG----------------------------TTTTCAAGTAGTTATCAAATTTcagtggaccc Gorilla > Human --------------- chr14:76939594-76939604 Template switch process: F1: L ACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGT 1 F3: 4 AAAAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTGAACAA R RF: TAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCCATTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTGAACAA RR: ATCTCAGTCTACCTTCACATCACGAATTTTCCGGTAAATTTTACCAGAATTGATCAATTCCGACGATCTTATATTTCGGGGTTTTCTTTTCAAAAGTTCATCAATAGTTTAAAGTCACCTGGGAACTTGTT F2: 3 ATCCCGGTCTA 2 Unidirectional alignment (log-probability: -51.1) GCTAGAATATAAAGCCCCAAAAGAAAagttttcaagtagtatctggccctaaaaAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG GCTAGAATATAAAGCCCCAAAAGAAA----------------------------AGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG Template switch alignment (log-probability: -28.6) GCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGT|ATCTGgCcCTA|AAAAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG GCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGT|ATCTGACTCTA|AAAAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG Gorilla > Chimp --------------- chr14:78118821-78118831 Template switch process: F1: L ACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGT 1 F3: 4 AAAAATTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTGAACAA R RF: TAGAGTCAGATGGAAGTGTAGTGCTTAAAAGGCCATTTAAAATGGTCTTAACTAGTTAAGGCTGCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTGAACAA RR: ATCTCAGTCTACCTTCACATCACGAATTTTCCGGTAAATTTTACCAGAATTGATCAATTCCGACGATCTTATATTTCGGGGTTTTCTTTTCAAAAGTTCATCAATAGTTTAAAGTCACCTGGGAACTTGTT F2: 3 ATCCCGGTCTA 2 Unidirectional alignment (log-probability: -51.1) GCTAGAATATAAAGCCCCAAAAGAAAAGttttcaagtagtatctggccctaaaaaaTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG GCTAGAATATAAAGCCCCAAAAGAAAAG----------------------------TTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG Template switch alignment (log-probability: -34.1) GCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGT|ATCTGgCcCTA|AAAAaTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG GCTAGAATATAAAGCCCCAAAAGAAAAGTTTTCAAGTAGT|ATCTGACTCTA|AAAAGTTTTCAAGTAGTTATCAAATTTCAGTGGACCCTTG ========= Event 981 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CAGAAACTTTAACTTAGCACT----TTTA----ACTTAGCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTAAGAAGTCAGTATTCTTGCCAT Chimp: CAGAAACTTTAACTTAGCACT----TTTA----ACTTAGCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTAAGAAGTCAGTATTCTTGCCAT ↑ 1 4 3 2 Gorilla: CAGAAACTTTAACTTAGCACTTGATTTTAGAAGCCTTTCCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTAAGAAGTCAGTATTCTTGCCAT Human: CAGAAACTTTAACTTAGCACT----TTTA----ACTTAGCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTAAGAAGTCAGTATTCTTGCCAT Cluster: [ ] Orangutan: CAGAAACTTTAACTTAGCACTTGATTTTAGAAGCCTTTCCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTAAGAAGTCAGCATTCTTGCCAT Gorilla > Chimp --------------- chr14:14679589-14679597 Template switch process: F1: L AGTGAACAAGTTGGAAGACACAGAAACTTTAACTTAGCACTT 1 F3: 4 CATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTA R RF: AGTGAACAAGTTGGAAGACACAGAAACTTTAACTTAGCACTTGATTTTAGAAGCCTTTCCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTA RR: TCACTTGTTCAACCTTCTGTGTCTTTGAAATTGAATCGTGAACTAAAATCTTCGGAAAGGTAAATTTTCAGTTTAGAACTTACCCAGAAATGTTTCAAT F2: 3 GATTCAATT 2 Unidirectional alignment (log-probability: -33) TGAACAAGTTGGAAGACACAGAAACTTTAACTTAGCACTTttaacttaG----------------CATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTA TGAACAAGTTGGAAGACACAGAAACTTTAACTTAGCACTT--------GATTTTAGAAGCCTTTCCATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTA Template switch alignment (log-probability: -22.4) TGAACAAGTTGGAAGACACAGAAACTTTAACTTAGCACTT|TTAACTTaG|CATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTA TGAACAAGTTGGAAGACACAGAAACTTTAACTTAGCACTT|TTAACTTTG|CATTTAAAAGTCAAATCTTGAATGGGTCTTTACAAAGTTA ========= Event 982 ========= Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TTGGAGATGCAGTCATAGCTCCCAAC--TTGCAGTGCATCAGATAACCCACACAGAACAGAAAC ↓ 1 4 3 2 Chimp: TTGGAGATGCAGTCATAGCTC-CATCTGATGCAGTGCATCAGATAACCCACACAGAACAGAAAC Gorilla: ---------------------------------------------------------------- Human: TTGGAGATGCAGTCATAGCTCCCAAC--TTGCAGTGCATCAGATAACCCACACAGAACAGAAAC Cluster: [ ] Orangutan: ---------------------------------------------------------------- Human > Chimp ------------- chr1:42573725-42573730 Template switch process: F1: L CACAAATGCCCAGAGTGTGGTTGGAGATGCAGTCATAGCTCC 1 F3: 4 TGCAGTGCATCAGATAACCCACACAGAACAGAAACTGTAT R RF: CACAAATGCCCAGAGTGTGGTTGGAGATGCAGTCATAGCTCCCAACTTGCAGTGCATCAGATAACCCACACAGAACAGAAACTGTAT RR: GTGTTTACGGGTCTCACACCAACCTCTACGTCAGTATCGAGGGTTGAACGTCACGTAGTCTATTGGGTGTGTCTTGTCTTTGACATA F2: 3 AGTCTA 2 Unidirectional alignment (log-probability: -30) CAAATGCCCAGAGTGTGGTTGGAGATGCAGTCATAGCTCCatctga-----TGCAGTGCATCAGATAACCCACACAGAACAGAAACTGTAT CAAATGCCCAGAGTGTGGTTGGAGATGCAGTCATAGCTCC------CAACTTGCAGTGCATCAGATAACCCACACAGAACAGAAACTGTAT Template switch alignment (log-probability: -16) CAAATGCCCAGAGTGTGGTTGGAGATGCAGTCATAGCTCC|ATCTGA|TGCAGTGCATCAGATAACCCACACAGAACAGAAACTGTAT CAAATGCCCAGAGTGTGGTTGGAGATGCAGTCATAGCTCC|ATCTGA|TGCAGTGCATCAGATAACCCACACAGAACAGAAACTGTAT ========= Event 983 ========= Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: tatataaataaaGGTATTTCATGCCATTTACTTTTGCATGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAAAAGTTATGAGATTTTAGTCAATATTC ↑ 4 1 3 2 Chimp: TATATAAATAAAGGTATTTCAT-----------------GCCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAAAAGTTATGAGATTTTAGTCAATATTC Gorilla: TATATAAATAAAGGTATTTCATGCCATTTACTTTTGCATGTCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAAAAGTTATGAGATTTTAGTCAATATTC Human: tatataaataaaGGTATTTCATGCCATTTACTTTTGCATGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAAAAGTTATGAGATTTTAGTCAATATTC Cluster: [ ] Orangutan: TATATAAATAAAGGTATTTCATGCCATTTATTTTTGCGTGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAAAAGTTATGAGATTTTAGTCAATATTC Chimp > Human ------------- chr14:73399413-73399421 Template switch process: F1: L CCCCTGCCAAAAATATAAATATATAAATAAAGGTATTTCATGCCAT 1 F3: 4 CATGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAA R RF: CCCCTGCCAAAAATATAAATATATAAATAAAGGTATTTCATGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGCCAAAAGTTA RR: GGGGACGGTTTTTATATTTATATATTTATTTCCATAAAGTACGGTATGAAGACTTGTATACAAAGTACCGAGCAAACGGTTTTCAAT F2: 3 GTTTTCATT 2 Unidirectional alignment (log-probability: -35.4) CCAAAAATATAAATATATAAATAAAGGTATTTCATGCCATttacttttgcatgccatACTTCTGAACATATGTTTCATGGCTCGTTTGC CCAAAAATATAAATATATAAATAAAGGTATTTCATGCCAT-----------------ACTTCTGAACATATGTTTCATGGCTCGTTTGC Template switch alignment (log-probability: -22.5) CCAAAAATATAAATATATAAATAAAGGTATTTCATGCCAT|TtACTTTTG|CATGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGC CCAAAAATATAAATATATAAATAAAGGTATTTCATGCCAT|TAACTTTTG|CATGCCATACTTCTGAACATATGTTTCATGGCTCGTTTGC ========= Event 984 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCAGGCTGGTTGCTCCCTAGTTTTGC----CGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTT ↓ 1 4 3 2 Chimp: GCAGGCTGGTTGCTCCCTAGTATTATCCCTAGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTT ↑ 1 4 3 2 Gorilla: GCAGGCTGGTTGCTCCCTAGTTTTGC----CGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTT Human: GCAGGCTGGTTGCTCCCTAGTTTTGC----CGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTT Cluster: [ ] Orangutan: GCAGACTGGTCGCTCCCTAGTTTTGC----TGTATTTCCTAGAGGTAATAACCCCTGTTTGGGATATTT Human > Chimp ------------- chr14:74843282-74843292 Template switch process: F1: L TCTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGT 1 F3: 4 TATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC R RF: TCTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGTTTTGCCGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC RR: AGAGCTTCTAAGATATATGACGTCCGACCAACGAGGGATCAAAACGGCATAAAGGATCCCCATTATTGGGGACAAACCCTATAAAGG F2: 3 GATCCCTATTA 2 Unidirectional alignment (log-probability: -34.7) CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGTaTTatCcctaGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGTTTTGCC----GTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC Template switch alignment (log-probability: -22.6) CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGT|ATTAtCCCTAG|TATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGT|ATTACCCCTAG|TATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC Gorilla > Chimp --------------- chr14:74843282-74843292 Template switch process: F1: L TCTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGT 1 F3: 4 TATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC R RF: TCTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGTTTTGCCGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC RR: AGAGCTTCTAAGATATATGACGTCCGACCAACGAGGGATCAAAACGGCATAAAGGATCCCCATTATTGGGGACAAACCCTATAAAGG F2: 3 GATCCCTATTA 2 Unidirectional alignment (log-probability: -33.3) CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGTaTTatCcctaGTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGTTTTGCC----GTATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC Template switch alignment (log-probability: -22.6) CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGT|ATTAtCCCTAG|TATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC CTCGAAGATTCTATATACTGCAGGCTGGTTGCTCCCTAGT|ATTACCCCTAG|TATTTCCTAGGGGTAATAACCCCTGTTTGGGATATTTCC ========= Event 985 ========= Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AAATGTGCAAAGATAACAGGCCCA---AGAT--------TTACAGTGCTTGTAAATCCATGAAAGTGAAATGAACCTA Chimp: AAATGTGCAAAGATAACAGGC-CA---AGAT--------TTACAGTGCTTGTAAATCTATGAAAGTGAAGTGAACCTA Gorilla: AAATGTGCAAAGATAACAGGC-CCATGTGACTTATTCTCTTCAAGTGCTTGTAAATCTATGAAAGTGAAGTGAACCTA ↓ 1 4 3 2 Human: AAATGTGCAAAGATAACAGGCCCA---AGAT--------TTACAGTGCTTGTAAATCCATGAAAGTGAAATGAACCTA Cluster: [ ] Orangutan: TAATGTGCAAAGATAACAGGC-CCATGTGACCTATTCTCTTCAAGTGCTTGTAAATCTATGAAAGTGAAATGAACCTA Gorilla > Human --------------- chr14:73592020-73592027 Template switch process: F1: L AGATGAAAATGGGCACAAGAAAATGTGCAAAGATAACAGGCCCA 1 F3: 4 AGTGCTTGTAAATCCATGAAAGTGAAATGAACCTAAAGAA R RF: AGATGAAAATGGGCACAAGAAAATGTGCAAAGATAACAGGCCCATGTGACTTATTCTCTTCAAGTGCTTGTAAATCTATGAAAGTGAAGTGAACCTAAAGAA RR: TCTACTTTTACCCGTGTTCTTTTACACGTTTCTATTGTCCGGGTACACTGAATAAGAGAAGTTCACGAACATTTAGATACTTTCACTTCACTTGGATTTCTT F2: 3 CATTTAGA 2 Unidirectional alignment (log-probability: -42.7) GAAAATGGGCACAAGAAAATGTGCAAAGATAACAGGCCCA-----------------AgatttacAGTGCTTGTAAATCcATGAAAGTGAAaTGAACCTAAAGAA GAAAATGGGCACAAGAAAATGTGCAAAGATAACAGGCCCATGTGACTTATTCTCTTCA-------AGTGCTTGTAAATCTATGAAAGTGAAGTGAACCTAAAGAA Template switch alignment (log-probability: -27.9) GAAAATGGGCACAAGAAAATGTGCAAAGATAACAGGCCCA|AGATTTAC|AGTGCTTGTAAATCcATGAAAGTGAAaTGAACCTAAAGAA GAAAATGGGCACAAGAAAATGTGCAAAGATAACAGGCCCA|AGATTTAC|AGTGCTTGTAAATCTATGAAAGTGAAGTGAACCTAAAGAA ========= Event 986 ========= Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GAAAGGTAAAGGAAAAGGACA--------------------------CTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTCCCTATCATTAGAAAGAAAAATGTATAATGAAAACTGACAATAAAGACATGAAGGGCTAATTTTCAATTTCAATTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTTTGAATGATGCGTCTTTGGAATTTTATGAGG ↓ 4 1 3 2 Chimp: GAAAGGTAAAGGAAAAGGACA-------------CTCAGTTGCATCACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTCCCTATCATTAGAAAGAAAAATATATAATGAAAACTGACAATAAAGACACGAAGGGCTAATTTTCAACTTCAATTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTTTGAATGATGCCTCTTTGGAATTTTATGAGG Gorilla: GAAAGGTAAAGGAAAAGGACACTCAGTTGCATCA-------------CTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTCCCTATCATTAGAAAGAAAAATAAATAATGAAAACTGACAATAAAGACATGAAGGGCTAATTTTCAATTTCAGTTTGTCTTTTTGAATGATGCCTCTTTGGAATTTTATGAGGGGTAAATGATATTTGAAATGAAGTCTTTTAAATAAGTTATCTTTTGGGTAGTTATTTTGCACACCTTTAAAATGCATTTTACTTATTTGTGGTGGGTGGAGTGGAAAGATGAATTCTGGAGAAGTTGAGAGGAAAACAATTTCAGGAGGTAATGGATGAACTTGGTCTGGAAGATTAATCAGGGCAGTTGTAAGAGAGTGCCAAATGCATAACCAGAGTAGAACTAAATATCTGATTGTAATTAAAACTTTAGGTTTCTAATGGCTGCATGAAAGATATTTTAATAAACGTGAAATGCACTTTCTAAATGGCACGCTAACTTTTAATGACTTGGGTGTTTTGTTTGATTAGTAACCTGGACTGTTAAATTAAAGCCAACTGCAAGTGCATGATAAAATATTGATGGTTTCAGGCAAATGAATTGGGAGAGTTATGCTTGACAGATTTTTTGTATCATTAAGGATTTTAACTGGTGGAAAATATATATTGCTGGTGCTTAAAGATAGTTAAAGAGGATCTTCCTGTTTGTATGACCTCGTTTCAATTTTACAGTAATAATAAGGGAGAAATCTGAATTATTCACAGATGATTGGTCAAGAGAGGTCACTTAATTAAAAAAGTGTTATTTTAATTACACCTGTTTCACATTCCTGGAATAGGAAATTAAATATTTTGCGGCATTTGATTATTTCTGTTTCACAGAATACCTGGACTTTTGCTGATTCTTGTGAAGACCTTACATTGTCATGTGTGAGGCTTGTACTGCTTGTTTTAAAGCAGGGAGTTTTGCTTTAAGAATCAGAATTTAAGAAATAGTTTTTTATGGTCAATTTTAGAAATAGTGCAAGAAGAAAAAACATAATTTTATGGGCATATGTACACAGGCATGTGTAATATATATAGTATCGTATGTGAAAGATAATTTCTAGAAGGAAATAAGAGGCATGGTTACTTCTAGGCAGCAAAGCTGTGGAGTCAAAACAAAGGGAAGTTTTATTTCTTTGTTTTTGTGAAATGACAATGTGTTTTGCAGTGAGAATGTCTTAATTTTATGAAAAAGTTTCCCTTTGAAACCAAAATTTATCTTTTAACAACTTAACTGTCCCTTTTCATGTGTCTCTCCTTGTAACAGAACATTTTCTTGATTTTGCCAGATGATATGGTTATTTTTAGGAGGTTTTATCACTGCATCCTTCCTTCCTTCTGTCCCCACAACCATTCATCGATCCTCAAATATTTAGTGTTTCTTGTCTCTTAATGCTTTTTATAGCCTACATAAAAGTAACTTTTGGAGaaannnnnnnnnnaaTAAAGACATGAAGGGCTAATTTTCAATTTCAGTTTGTCTTTTTGAATGATGCCTCTTTGGAATTTTATGAGG ↑ 4 1 3 2 Human: GAAAGGTAAAGGAAAAGGACA--------------------------CTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTCCCTATCATTAGAAAGAAAAATGTATAATGAAAACTGACAATAAAGACATGAAGGGCTAATTTTCAATTTCAATTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTTTGAATGATGCGTCTTTGGAATTTTATGAGG Cluster: [ ] Orangutan: GAAAGGTAAAGAAAA-AGACACTCCGTTGCATCA-------------CTCAGTTAGAAAACTGTAAGAAAATGCTTGTCGAACTTTCCCTATCATTAGAAAGAAAAATAAATAATGAAAACTGACAATAAAGGCACGAAGGGCTAATTTTCAATTTCAATTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTCTGAATGATGCCTCTTTGGAATTTTATGAGG Human > Chimp ------------- chr14:73784089-73784092 Template switch process: F1: L AAGAGAAGTAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTT 1 F3: 4 CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTC R RF: AAGAGAAGTAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTCCCTATCATTAGAAAGAAAAATGTATAATGAAAACTGACAATAAAGACATGAAGGGCTAATTTTCAATTTCAATTTGTCTTTTTGAATGATGC RR: TTCTCTTCATCCTTTTTAACCTTTCCATTTCCTTTTCCTGTGAGTCAATCTTTTGACATTCTTTTACGAACAACTTTAAAGGGATAGTAATCTTTCTTTTTACATATTACTTTTGACTGTTATTTCTGTACTTCCCGATTAAAAGTTAAAGTTAAACAGAAAAACTTACTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -29.6) TAGGAAAAATTGGAAAGGTAAAGGAAAAGGAcactcagttgcatCACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT TAGGAAAAATTGGAAAGGTAAAGGAAAAGGA-------------CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT Template switch alignment (log-probability: -16) TAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTT|GCAT|CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT TAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTT|GCAT|CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT Human > Gorilla --------------- chr14:10949345-10949348 Template switch process: F1: L AAGAGAAGTAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTT 1 F3: 4 CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTC R RF: AAGAGAAGTAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATTTCCCTATCATTAGAAAGAAAAATGTATAATGAAAACTGACAATAAAGACATGAAGGGCTAATTTTCAATTTCAATTTGTCTTTTTGAATGATGC RR: TTCTCTTCATCCTTTTTAACCTTTCCATTTCCTTTTCCTGTGAGTCAATCTTTTGACATTCTTTTACGAACAACTTTAAAGGGATAGTAATCTTTCTTTTTACATATTACTTTTGACTGTTATTTCTGTACTTCCCGATTAAAAGTTAAAGTTAAACAGAAAAACTTACTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -29.6) TAGGAAAAATTGGAAAGGTAAAGGAAAAGGAcactcagttgcatCACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT TAGGAAAAATTGGAAAGGTAAAGGAAAAGGA-------------CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT Template switch alignment (log-probability: -16.5) TAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTT|GCAT|CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT TAGGAAAAATTGGAAAGGTAAAGGAAAAGGACACTCAGTT|GCAT|CACTCAGTTAGAAAACTGTAAGAAAATGCTTGTTGAAATT ========= Event 987 ========= Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAACCGAACCCCAGTGTGCTGAAGGCATTTTGCCTTCACCTGCACCCGTTACATATC ↑ 1 3 4 2 Chimp: ATAACCGAACCCCAGTGTGCTTCAGGCAAAATGCCTTCACCTGCACCCATTACATATC Gorilla: ATAACTGAACCCCAGTGTGCTTCAGGCAAAATGCCTTCACCTGCAACCATTACATATC Human: ATAACCGAACCCCAGTGTGCTGAAGGCATTTTGCCTTCACCTGCACCCGTTACATATC Cluster: [ ] Orangutan: ---------------------------------------------------------- Chimp > Human ------------- chr14:75810021-75810030 Template switch process: F1: L GTCTACACTTGGCACAAACCATAACCGAACCCCAGTGTGCT 1 F3: 4 TGCCTTCACCTGCACCCGTTACATATCTAATTTTTGCTTT R RF: GTCTACACTTGGCACAAACCATAACCGAACCCCAGTGTGCTTCAGGCAAAATGCCTTCACCTGCACCCATTACATATCTAATTTTTGCTTT RR: CAGATGTGAACCGTGTTTGGTATTGGCTTGGGGTCACACGAAGTCCGTTTTACGGAAGTGGACGTGGGTAATGTATAGATTAAAAACGAAA F2: 3 TTTACGGAAG 2 Unidirectional alignment (log-probability: -36.7) TCTACACTTGGCACAAACCATAACCGAACCCCAGTGTGCTgaAGGCAtttTGCCTTCACCTGCACCCgTTACATATCTAATTTTTGCTTT TCTACACTTGGCACAAACCATAACCGAACCCCAGTGTGCTTCAGGCAAAATGCCTTCACCTGCACCCATTACATATCTAATTTTTGCTTT Template switch alignment (log-probability: -22.5) TCTACACTTGGCACAAACCATAACCGAACCCCAGTGTGCT|GAAGGCATTT|TGCCTTCACCTGCACCCgTTACATATCTAATTTTTGCTTT TCTACACTTGGCACAAACCATAACCGAACCCCAGTGTGCT|GAAGGCATTT|TGCCTTCACCTGCACCCATTACATATCTAATTTTTGCTTT ========= Event 988 ========= Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: caacaagagcgaaactctgtctcaaaaaataaaaaaataaataaataataaaaaataaaaaaagaaaGCAGAGGGAAGAAGAAAAGAGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAAAC--AAATAAGAGGGttt----------------ttt-------ttttttctgagacggagtctcg Chimp: caacaagagcgaaactctgtctcaaaaaataaaaaaataaataaataataaaaaataaaaaaagaaaGCAGAGGGAAGAAGAAAAGAGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAA--ACAAATAAGAGGGttt-------------------tttttttttttttctgagatggagtctcg ↑ 3 2 4 1 Gorilla: caacaagaacgaaactctgtctcaaaaaataaaaaaataaataaataataaaaaataaaaaaagaaaGCAGAGGGAAGAAGAAAAGAGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAAAC--AAATAAGAGGGttt-------------ttt----------ttnnnnnnnnnnnnnnnnnnnn Human: caacaagagcgaaactctgtctcaaaaaataaaaaaataaataaataataaaaaataaaaaaagaaaGCAGAGGGAAGAAGAAAAGAGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAAAC--AAATAAGAGGGttt----------------ttt-------ttttttctgagacggagtctcg Cluster: [ ] Orangutan: caacaagagcgaaactctgtctcaaaaaataaataaataaataaataataaaaaataaaaaaagaaaGCAGAGGGAAGAAGAAAAGAGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAAAC--AAATAAGAGGGtttttttttttttttt-------------ttttttctgagacagagtctcg Gorilla > Chimp --------------- chr14:77140775-77140781 Template switch process: F1: L AGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAAACAAATAAGAGGGTTTTTTTT 1 F3: 4 TCTGAGATGGA R RF: AAAAAAAGAAAGCAGAGGGAAGAAGAAAAGAGGGGGCAAGTCAGATAGCAAAAGCTCATAATTGGGAGAAAACAAATAAGAGGGTTTTTTTTTCTCAAAAAATAAAAAAATAAATAAATAATAAAAAATAAAAAAA RR: TTTTTTTCTTTCGTCTCCCTTCTTCTTTTCTCCCCCGTTCAGTCTATCGTTTTCGAGTATTAACCCTCTTTTGTTTATTCTCCCAAAAAAAAAGAGTTTTTTATTTTTTTATTTATTTATTATTTTTTATTTTTTT F2: 3 TTTTTTT 2 Unidirectional alignment (log-probability: -44) AGCTCATAATTGGGAGAAAACAAATAAGAGGGTTTTTTTT--------------ttttttttctgagatgga AGCTCATAATTGGGAGAAAACAAATAAGAGGGTTTTTTTTNNNNNNNNNNNNNN------------------ Template switch alignment (log-probability: -33.1) AGCTCATAATTGGGAGAAAACAAATAAGAGGGTTTTTTTT|TTTTTTT|TCTgagatgga AGCTCATAATTGGGAGAAAACAAATAAGAGGGTTTTTTTT|TTTTTTT|TCT-------G ========= Event 989 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAGAAAAATAGGATGATTACAAATGG-------AAAAATTAAGAACAAAATCACTTC Chimp: ACAGAAAAATAGGATGATTACAAATGG-------AAAAATTAAGAACAAAATCACTTC ↓ 3 1 24 Gorilla: ACAGAAAAATAGGGTGATTACAAATGTTTCCATTTGTAATTAAGAACAAAATCACTTC ↑ 3 1 24 Human: ACAGAAAAATAGGATGATTACAAATGG-------AAAAATTAAGAACAAAATCACTTC Cluster: [ ] Orangutan: ACAGAAAAATAGGATGATTACAAATGG-------AAAAATTAAGAACAAAATCACTTC Human > Gorilla --------------- chr14:13187156-13187166 Template switch process: F1: L GGGCAGAAGGGAAAAACAGAAAAATAGGGTGATTACAAATG 1 F3: 4 AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA R RF: GGGCAGAAGGGAAAAACAGAAAAATAGGATGATTACAAATGGAAAAATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA RR: CCCGTCTTCCCTTTTTGTCTTTTTATCCTACTAATGTTTACCTTTTTAATTCTTGTTTTAGTGAAGTATAGACCCAAAGACATTT F2: 3 TGTTTACCTTT 2 Unidirectional alignment (log-probability: -42.2) GGCAGAAGGGAAAAACAGAAAAATAGGgTGATTACAAATGtttccatttgt----AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA GGCAGAAGGGAAAAACAGAAAAATAGGATGATTACAAATG-----------GAAAAATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA Template switch alignment (log-probability: -22.6) GGCAGAAGGGAAAAACAGAAAAATAGGgTGATTACAAATG|TTTCCATTTGT|AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA GGCAGAAGGGAAAAACAGAAAAATAGGATGATTACAAATG|TTTCCATTTGT|AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA Chimp > Gorilla --------------- chr14:13187156-13187166 Template switch process: F1: L GGGCAGAAGGGAAAAACAGAAAAATAGGGTGATTACAAATG 1 F3: 4 AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA R RF: GGGCAGAAGGGAAAAACAGAAAAATAGGATGATTACAAATGGAAAAATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA RR: CCCGTCTTCCCTTTTTGTCTTTTTATCCTACTAATGTTTACCTTTTTAATTCTTGTTTTAGTGAAGTATAGACCCAAAGACATTT F2: 3 TGTTTACCTTT 2 Unidirectional alignment (log-probability: -42.2) GGCAGAAGGGAAAAACAGAAAAATAGGgTGATTACAAATGtttccatttgt----AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA GGCAGAAGGGAAAAACAGAAAAATAGGATGATTACAAATG-----------GAAAAATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA Template switch alignment (log-probability: -22.6) GGCAGAAGGGAAAAACAGAAAAATAGGgTGATTACAAATG|TTTCCATTTGT|AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA GGCAGAAGGGAAAAACAGAAAAATAGGATGATTACAAATG|TTTCCATTTGT|AATTAAGAACAAAATCACTTCATATCTGGGTTTCTGTAAA ========= Event 990 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AACTTTAATTACTTCTTGGTTTCTCATAAGGTTTCCCTTATGAGAAAGtttttttttaaaaagta ↑ 1 4 3 2 Chimp: AACTTTAATTACTTCTTGGTTCTTGT----TTTTCCCTTATGAGAAAGtttttttta-aaaagta Gorilla: AACTTTAATTACTTCTTGGTTCTTGT----TTTTCCCTTATGAGAAAGtttttttta-aaaagta ↓ 1 4 3 2 Human: AACTTTAATTACTTCTTGGTTTCTCATAAGGTTTCCCTTATGAGAAAGtttttttttaaaaagta Cluster: [ ] Orangutan: AACTTTAATTACTTCTTGGTTCTTGT----TTTTCCCTTATGAgaaagttttttaaaaaaaagta Chimp > Human ------------- chr14:75416453-75416462 Template switch process: F1: L CATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTT 1 F3: 4 TTTCCCTTATGAGAAAGTTTTTTTTTAAAAAGTAAAGCGG R RF: CATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTTCTTGTTTTTCCCTTATGAGAAAGTTTTTTTTAAAAAGTAAAGCGG RR: GTAGATGTACGGAAGAACACTTGAAATTAATGAAGAACCAAGAACAAAAAGGGAATACTCTTTCAAAAAAAATTTTTCATTTCGCC F2: 3 GGAATACTCT 2 Unidirectional alignment (log-probability: -46) ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGT-----TTctcataaggTTTCCCTTATGAGAAAGtTTTTTTTTAAAAAGTAAAGCGG ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTTCTTGTT---------TTTCCCTTATGAGAAAG-TTTTTTTTAAAAAGTAAAGCGG Template switch alignment (log-probability: -28.2) ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTT|TCTCATAAGG|TTTCCCTTATGAGAAAGtTTTTTTTTAAAAAGTAAAGCGG ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTT|TCTCATAAGG|TTTCCCTTATGAGAAAG-TTTTTTTTAAAAAGTAAAGCGG Gorilla > Human --------------- chr14:75416453-75416462 Template switch process: F1: L CATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTT 1 F3: 4 TTTCCCTTATGAGAAAGTTTTTTTTTAAAAAGTAAAGCGG R RF: CATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTTCTTGTTTTTCCCTTATGAGAAAGTTTTTTTTAAAAAGTAAAGCGG RR: GTAGATGTACGGAAGAACACTTGAAATTAATGAAGAACCAAGAACAAAAAGGGAATACTCTTTCAAAAAAAATTTTTCATTTCGCC F2: 3 GGAATACTCT 2 Unidirectional alignment (log-probability: -45) ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGT-----TTctcataaggTTTCCCTTATGAGAAAGtTTTTTTTTAAAAAGTAAAGCGG ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTTCTTGTT---------TTTCCCTTATGAGAAAG-TTTTTTTTAAAAAGTAAAGCGG Template switch alignment (log-probability: -28.2) ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTT|TCTCATAAGG|TTTCCCTTATGAGAAAGtTTTTTTTTAAAAAGTAAAGCGG ATCTACATGCCTTCTTGTGAACTTTAATTACTTCTTGGTT|TCTCATAAGG|TTTCCCTTATGAGAAAG-TTTTTTTTAAAAAGTAAAGCGG ========= Event 991 ========= Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: caaaactcatctataatacaatacccagaaacaacAGGAGTTGTGCAAACAACAGTAGTTGTTTCTGGGTATCGTATTAAATTCTAACCttttt Chimp: caaaaCTCATCTATAATACAATACCCAGAAACAACAGGAGTTGTGCAAACAACAGTAGTTGTTTCTGGGTATCGTATTAAATTCTAACCttttt ↓ 3 1 2 4 ↑ 13 24 Gorilla: caaaaCTCATCTATAATACAATACCCAGAAACAACTACTGTTGTTTGCACAACTCCTGTTGTTTCTGGGTATTGTATTAAATTCTAACCttttt Human: caaaactcatctataatacaatacccagaaacaacAGGAGTTGTGCAAACAACAGTAGTTGTTTCTGGGTATCGTATTAAATTCTAACCttttt Cluster: [ ] Orangutan: caaaactcatctataatacaatacccagaaacaacAGGAGTTGTGCAAACAACAGTAGTTGTTTCTGGGTATCGTATTAAATTCTAACCttttt Gorilla > Chimp --------------- chr1:42894850-42894871 Template switch process: F1: L AAAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC 1 F3: 4 GTTGTTTCTGGGTATCGTATTAAATTCTAACCTTTTTTTT R RF: AAAAAACAAAACTCATCTATAATACAATACCCAGAAACAACTACTGTTGTTTGCACAACTCCTGTTGTTTCTGGGTATTGTATTAAATTCTAACCTTTTTTTT RR: TTTTTTGTTTTGAGTAGATATTATGTTATGGGTCTTTGTTGATGACAACAAACGTGTTGAGGACAACAAAGACCCATAACATAATTTAAGATTGGAAAAAAAA F2: 3 ATGACAACAAACGTGTTGAGGA 2 Unidirectional alignment (log-probability: -56) AAAAACAAAACTCATCTATAATACAATACCCAGAAACAACaggagttgtgcaaacaacagTA--------------------GTTGTTTCTGGGTATcGTATTAAATTCTAACCTTTTTTTT AAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC--------------------TACTGTTGTTTGCACAACTCCTGTTGTTTCTGGGTATTGTATTAAATTCTAACCTTTTTTTT Template switch alignment (log-probability: -24.1) AAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC|AGGAGTTGTGCAAACAACAGTA|GTTGTTTCTGGGTATcGTATTAAATTCTAACCTTTTTTTT AAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC|AGGAGTTGTGCAAACAACAGTA|GTTGTTTCTGGGTATTGTATTAAATTCTAACCTTTTTTTT Chimp > Gorilla --------------- chr1:43912046-43912083 Template switch process: F1: L AAAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC 1 F3: 4 GTATTAAATTCTAACCTTTTTTTT R RF: AAAAAACAAAACTCATCTATAATACAATACCCAGAAACAACAGGAGTTGTGCAAACAACAGTAGTTGTTTCTGGGTATCGTATTAAATTCTAACCTTTTTTTT RR: TTTTTTGTTTTGAGTAGATATTATGTTATGGGTCTTTGTTGTCCTCAACACGTTTGTTGTCATCAACAAAGACCCATAGCATAATTTAAGATTGGAAAAAAAA F2: 3 TTATGGGTCTTTGTTGTCCTCAACACGTTTGTTGTCAT 2 Unidirectional alignment (log-probability: -56) AAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC--------------------TActgttgtttgcacaactcctGTTGTTTCTGGGTATtGTATTAAATTCTAACCTTTTTTTT AAAAACAAAACTCATCTATAATACAATACCCAGAAACAACAGGAGTTGTGCAAACAACAGTA--------------------GTTGTTTCTGGGTATCGTATTAAATTCTAACCTTTTTTTT Template switch alignment (log-probability: -20.2) AAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC|TACTGTTGTTTGCACAACTCCTGTTGTTTCTGGGTATT|GTATTAAATTCTAACCTTTTTTTT AAAAACAAAACTCATCTATAATACAATACCCAGAAACAAC|TACTGTTGTTTGCACAACTCCTGTTGTTTCTGGGTATT|GTATTAAATTCTAACCTTTTTTTT ========= Event 992 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGAAATATCTTTCTATTTTC-----------AGTGACACCTGTTTATGTCTATGGCTTTCACATCTTGCACA Chimp: TGGAAATATCTTTCTATTTTC-----------AGTGACACCTGTTTATATCTATGGCTTTCACATCTTGCACA ↓ 1 4 3 2 Gorilla: TGGAAATATCTTTCTATTTTCATAGATATAAACATGACACCTGTTTATATCTATGGCTTTCACATCTTGCACA Human: TGGAAATATCTTTCTATTTTC-----------AGTGACACCTGTTTATGTCTATGGCTTTCACATCTTGCACA Cluster: [ ] Orangutan: CGGAAATATCTTTCTATTTTC-----------AGTGACATCTGTTTATATCTATGGCTTTCACATCTTGCACA Chimp > Gorilla --------------- chr14:79703795-79703806 Template switch process: F1: L AAGTTTATATACTGTTTACATGGAAATATCTTTCTATTTTCA 1 F3: 4 TGACACCTGTTTATATCTATGGCTTTCACATCTTGCACAT R RF: AAGTTTATATACTGTTTACATGGAAATATCTTTCTATTTTCAGTGACACCTGTTTATATCTATGGCTTTCACATCTTGCACAT RR: TTCAAATATATGACAAATGTACCTTTATAGAAAGATAAAAGTCACTGTGGACAAATATAGATACCGAAAGTGTAGAACGTGTA F2: 3 ACAAATATAGAT 2 Unidirectional alignment (log-probability: -32.2) GTTTATATACTGTTTACATGGAAATATCTTTCTATTTTCAtagatataaacaTGACACCTGTTTATATCTATGGCTTTCACATCTTGCACAT GTTTATATACTGTTTACATGGAAATATCTTTCTATTTTCAG-----------TGACACCTGTTTATATCTATGGCTTTCACATCTTGCACAT Template switch alignment (log-probability: -17.3) GTTTATATACTGTTTACATGGAAATATCTTTCTATTTTCA|TAGATATAAACA|TGACACCTGTTTATATCTATGGCTTTCACATCTTGCACAT GTTTATATACTGTTTACATGGAAATATCTTTCTATTTTCA|TAGATATAAACA|TGACACCTGTTTATATCTATGGCTTTCACATCTTGCACAT ========= Event 993 ========= Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTACTGCTCAGCAACATGTTCAATT-------------------------------------GAGGTGTTTACAACAAAGGATACAGAGAATC ↓ 3 4 1 2 Chimp: CTACTGCTCAGCAACATGTTCAATT------------GAGGTGTTGTAAACACCTCAATGAAGAGGTGTTTACAACAAAGGATACAGAGAATC ↑ 3 4 1 2 Gorilla: CTACTGCTCAGCAACATGTTCAATT-------------------------------------GAGGTGTTTACAACAAAGGATACAGAGAATC Human: CTACTGCTCAGCAACATGTTCAATT-------------------------------------GAGGTGTTTACAACAAAGGATACAGAGAATC Cluster: [ ] Orangutan: CTACTGCTCAGCAACATGTTCAATTCTACTCAATGAA-------------------------GAGGTGTTTACAACAAAGGATACAGAGAATC Human > Chimp ------------- chr14:18923724-18923740 Template switch process: F1: L TATAAAAGCTCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTT 1 F3: 4 GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG R RF: TATAAAAGCTCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG RR: ATATTTTCGAGACATCGATGACGAGTCGTTGTACAAGTTAACTCCACAAATGTTGTTTCCTATGTCTCTTAGAGGACATTC F2: 3 AAGTAACTCCACAAATG 2 Unidirectional alignment (log-probability: -46.9) TCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTgttgtaaacacctcaatgaagaggtGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG TCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGT-------------------------GTTTACAACAAAGGATACAGAGAATCTCCTGTAAG Template switch alignment (log-probability: -29.5) TCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTT|GTAAACACCTCAATgaA|GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG TCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTT|GTAAACACCTCAATTGA|GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG Gorilla > Chimp --------------- chr14:18923724-18923740 Template switch process: F1: L TATAAAAGCTCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTT 1 F3: 4 GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG R RF: TATAAAAGCTCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG RR: ATATTTTCGAGACATCGATGACGAGTCGTTGTACAAGTTAACTCCACAAATGTTGTTTCCTATGTCTCTTAGAGGACATTC F2: 3 AAGTAACTCCACAAATG 2 Unidirectional alignment (log-probability: -46.8) TCTGTAGCTACTGCTCAGCAACATGTTCAATTgaggtgttgtaaacacctcaatgaaGAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG TCTGTAGCTACTGCTCAGCAACATGTTCAATT-------------------------GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG Template switch alignment (log-probability: -29.1) TCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTT|GTAAACACCTCAATgaA|GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG TCTGTAGCTACTGCTCAGCAACATGTTCAATTGAGGTGTT|GTAAACACCTCAATTGA|GAGGTGTTTACAACAAAGGATACAGAGAATCTCCTGTAAG ========= Event 994 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAGAGACTCAATAGGTGCC-----CTGAGGCCTGGGCCGCCAGGCAAAGCTGC Chimp: AGGAGAGACTCAATAGGTGCC-----CTGAGGCCTGGGCCGCCAGGCAAAGCTGC ↓ 3 1 42 Gorilla: AGGAGAGACTCAATAGGTGCCCAGGCCTCAGGGCTGGGCCGCCAGGCAAAGCTGC ↑ 3 1 42 Human: AGGAGAGACTCAATAGGTGCC-----CTGAGGCCTGGGCCGCCAGGCAAAGCTGC Cluster: [ ] Orangutan: AGGAGAGACTCAATAGGGGCC-----CTGAGGCCTGGGCCGCCAGGCAAAGCTGC Human > Gorilla --------------- chr1:184697528-184697538 Template switch process: F1: L AACTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCC 1 F3: 4 CTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG R RF: AACTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCCTGAGGCCTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG RR: TTGACTGTAGTTTCATAGCTTCCTCTCTGAGTTATCCACGGGACTCCGGACCCGGCGGTCCGTTTCGACGTGGTGTAGAATCGTGGAC F2: 3 GGGACTCCGGA 2 Unidirectional alignment (log-probability: -29.2) CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCccaggCCTcAGGgCTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGC-----CCTGAGGCCTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG Template switch alignment (log-probability: -17.2) CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCC|AGGCCTCAGGG|CTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCC|AGGCCTCAGGG|CTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG Chimp > Gorilla --------------- chr1:184697528-184697538 Template switch process: F1: L AACTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCC 1 F3: 4 CTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG R RF: AACTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCCTGAGGCCTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG RR: TTGACTGTAGTTTCATAGCTTCCTCTCTGAGTTATCCACGGGACTCCGGACCCGGCGGTCCGTTTCGACGTGGTGTAGAATCGTGGAC F2: 3 GGGACTCCGGA 2 Unidirectional alignment (log-probability: -29.2) CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCccaggCCTcAGGgCTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGC-----CCTGAGGCCTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG Template switch alignment (log-probability: -17.2) CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCC|AGGCCTCAGGG|CTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG CTGACATCAAAGTATCGAAGGAGAGACTCAATAGGTGCCC|AGGCCTCAGGG|CTGGGCCGCCAGGCAAAGCTGCACCACATCTTAGCACCTG ========= Event 995 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTCTATTATCCATCTATAAAAATCACTGGTATAAATACT-------ACCGCCCTGGGGCAACAACAGCAA Chimp: ACTTATATTATCCATCTATAAAAATCATTGGTATAAATACT-------ACCGCCCTGGGGCAACAACAGCAA ↓ 3 2 1 4 Gorilla: ACTTATATTATCCATCTATAGAAATCATTGGTATAAATACCAATGATTGTTGCCCTGGGGCAACAACAGCAA Human: ACTTCTATTATCCATCTATAAAAATCACTGGTATAAATACT-------ACCGCCCTGGGGCAACAACAGCAA Cluster: [ ] Orangutan: ACTTATATTATCCATCTATAAAAATCATTGGTATAAATCCT-------ACCGCCCTGGGGCAACAACAGCAA Chimp > Gorilla --------------- chr14:8774273-8774283 Template switch process: F1: L AACTTATATTATCCATCTATAGAAATCATTGGTATAAATAC 1 F3: 4 GCCCTGGGGCAACAACAGCAACAAACAAATGAAAACTGTT R RF: AACTTATATTATCCATCTATAAAAATCATTGGTATAAATACTACCGCCCTGGGGCAACAACAGCAACAAACAAATGAAAACTGTT RR: TTGAATATAATAGGTAGATATTTTTAGTAACCATATTTATGATGGCGGGACCCCGTTGTTGTCGTTGTTTGTTTACTTTTGACAA F2: 3 TTGTTAGTAAC 2 Unidirectional alignment (log-probability: -40.7) ACTTATATTATCCATCTATAgAAATCATTGGTATAAATACcaatgattgtT---GCCCTGGGGCAACAACAGCAACAAACAAATGAAAACTGTT ACTTATATTATCCATCTATAAAAATCATTGGTATAAATAC----------TACCGCCCTGGGGCAACAACAGCAACAAACAAATGAAAACTGTT Template switch alignment (log-probability: -28.2) ACTTATATTATCCATCTATAgAAATCATTGGTATAAATAC|CAATGATTgTT|GCCCTGGGGCAACAACAGCAACAAACAAATGAAAACTGTT ACTTATATTATCCATCTATAAAAATCATTGGTATAAATAC|CAATGATTTTT|GCCCTGGGGCAACAACAGCAACAAACAAATGAAAACTGTT ========= Event 996 ========= Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAAATTTATTCGTTTGTTATCAAAAG---CTTTACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCA Chimp: TGAAATTTATTCGTTTGTTATCAAAAG---CTTTACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCA ↓ 1 4 3 2 Gorilla: TGAAATTTATTCGTTTGTTATTTTGAA------CACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCA ↑ 1 4 3 2 Human: TGAAATTTATTCGTTTGTTATCAAAAG---CTTTACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCA Cluster: [ ] Orangutan: TGAAATTTATTCGTTTGTTATCAAAAGCTT---TACTTAGATTGTGTTCAAAATGTTGTTATAAAAGATCCA Human > Gorilla --------------- chr14:82620317-82620323 Template switch process: F1: L CCTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT 1 F3: 4 ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG R RF: CCTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTATCAAAAGCTTTACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG RR: GGAACTCTCCAGTTGACACTACTTTAAATAAGCAAACAATAGTTTTCGAAATGAATCTACCACAAGTTTTACAACAATATTTTCTACGTTC F2: 3 CAAGTTT 2 Unidirectional alignment (log-probability: -26.8) CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT-------TTTgaacACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTATCAAAAGCTTT----ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG Template switch alignment (log-probability: -16.6) CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT|TTTGAAC|ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT|TTTGAAC|ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG Chimp > Gorilla --------------- chr14:82620317-82620323 Template switch process: F1: L CCTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT 1 F3: 4 ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG R RF: CCTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTATCAAAAGCTTTACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG RR: GGAACTCTCCAGTTGACACTACTTTAAATAAGCAAACAATAGTTTTCGAAATGAATCTACCACAAGTTTTACAACAATATTTTCTACGTTC F2: 3 CAAGTTT 2 Unidirectional alignment (log-probability: -26.8) CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT-------TTTgaacACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTATCAAAAGCTTT----ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG Template switch alignment (log-probability: -16.6) CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT|TTTGAAC|ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG CTTGAGAGGTCAACTGTGATGAAATTTATTCGTTTGTTAT|TTTGAAC|ACTTAGATGGTGTTCAAAATGTTGTTATAAAAGATGCAAG ========= Event 997 ========= Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gttttgagttaatggagaAATTAGTAATTTCCATA--------TATGATCAAGGACTGGAACACACAAAAAT Chimp: GTTTTGAGTTAATGGAGAAATTAGTAATTTCCATA--------TATGATCAAGGACTGGAATACACAAAAAT ↓ 4 1 3 2 Gorilla: gttttgagttaatggagaAATTAGTAATTTCTTGATCATTAGTAATGATCAAGGACTGGAATACACAAAAAT Human: gttttgagttaatggagaAATTAGTAATTTCCATA--------TATGATCAAGGACTGGAACACACAAAAAT Cluster: [ ] Orangutan: gttttgagttaatggagaAATTAGTAATTTCCATA--------TATGATCAAGGACTGGAATACACAAAAAT Chimp > Gorilla --------------- chr14:84449222-84449227 Template switch process: F1: L CAAGATCAAAGTTTTGAGTTAATGGAGAAATTAGTAATTTC 1 F3: 4 ATTAGTA----------ATGATCAAGGACTGGAATACACAAAAATGATATCAGATGC R RF: CAAGATCAAAGTTTTGAGTTAATGGAGAAATTAGTAATTTCCATATATGATCAAGGACTGGAATACACAAAAATGATATCAGATGC RR: GTTCTAGTTTCAAAACTCAATTACCTCTTTAATCATTAAAGGTATATACTAGTTCCTGACCTTATGTGTTTTTACTATAGTCTACG F2: 3 CTAGTT 2 Unidirectional alignment (log-probability: -38.1) AAGATCAAAGTTTTGAGTTAATGGAGAAATTAGTAATTTC----TtgatcattagtaATGATCAAGGACTGGAATACACAAAAATGATAT AAGATCAAAGTTTTGAGTTAATGGAGAAATTAGTAATTTCCATAT------------ATGATCAAGGACTGGAATACACAAAAATGATAT Template switch alignment (log-probability: -26.9) AAGATCAAAGTTTTGAGTTAATGGAGAAATTAGTAATTTC|TTGATC|ATTAGTA----------ATGATCAAGGACTGGAATACACAAAAATGATAT AAGATCAAAGTTTTGAGTTAATGGAGAAATTAGTAATTTC|TTGATC|ATTAGTAATTTCCATATATGATCAAGGACTGGAATACACAAAAATGATAT ========= Event 998 ========= Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCACCATCACTGAACGTGTATAGCACTTTCCCA------GGCTCTGGTCCTATATCAGGCAC ↓ 3 2 1 4 Chimp: ATCACCATCACTGAACGTGTATAGCACTTTCCCAGTGCTATACTCTGGTCCTATATCAGGCAC Gorilla: ATCACCATCACTGAACGTGTATAGCACTTTCCCA------GGCTCTGGTCCTATATCAGGCTC Human: ATCACCATCACTGAACGTGTATAGCACTTTCCCA------GGCTCTGGTCCTATATCAGGCAC Cluster: [ ] Orangutan: ATCACCATCACTGAACGTGTATAGCACTTTCCCA------GGCTCTGGTCCTATATCAGGCAC Human > Chimp ------------- chr14:68929201-68929207 Template switch process: F1: L CTGCATCATCACCATCACTGAACGTGTATAGCACTTTCCCAG 1 F3: 4 CTCTGGTCCTATATCAGGCACGTGTTGCAAAGAGAATGTT R RF: CTGCATCATCACCATCACTGAACGTGTATAGCACTTTCCCAGGCTCTGGTCCTATATCAGGCACGTGTTGCAAAGAGAATGTT RR: GACGTAGTAGTGGTAGTGACTTGCACATATCGTGAAAGGGTCCGAGACCAGGATATAGTCCGTGCACAACGTTTCTCTTACAA F2: 3 ATATCGT 2 Unidirectional alignment (log-probability: -25.6) GCATCATCACCATCACTGAACGTGTATAGCACTTTCCCAGtgctataCTCTGGTCCTATATCAGGCACGTGTTGCAAAGAGAATGTT GCATCATCACCATCACTGAACGTGTATAGCACTTTCCCAG------GCTCTGGTCCTATATCAGGCACGTGTTGCAAAGAGAATGTT Template switch alignment (log-probability: -16.2) GCATCATCACCATCACTGAACGTGTATAGCACTTTCCCAG|TGCTATA|CTCTGGTCCTATATCAGGCACGTGTTGCAAAGAGAATGTT GCATCATCACCATCACTGAACGTGTATAGCACTTTCCCAG|TGCTATA|CTCTGGTCCTATATCAGGCACGTGTTGCAAAGAGAATGTT ========= Event 999 ========= Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTTCTTCACAAGATAATAGAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGACTGGGTGAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGTCATTTGTTCAGTTAACCTAA ↑ 4 1 3 2 Chimp: AGTTCTTCACAAGATAATAGAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATC----------------------------------------------------------------------------------------------CATTGGTTGGGAGGTGGGACTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGTCATTTCTTCAGCTAACCTAA Gorilla: AGTTCTTCACAAGATAATAGAATATTACATAATGAAAAAACTTAATGTGATGTCCAATTAAGAATTTGTATGAATC----------------------------------------------------------------------------------------------CATTGGTTGGGAGGAGGGACTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGTCATTTGTTCAGTTAACCTAA ↓ 4 1 3 2 Human: AGTTCTTCACAAGATAATAGAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGACTGGGTGAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGTCATTTGTTCAGTTAACCTAA Cluster: [ ] Orangutan: AGTTCTTCACAAGATAATAGAATATTATATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATC----------------------------------------------------------------------------------------------CATTGGTTGGGAGGAGGGGCTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGTCATTTGTTCAGTTAACCTAA Chimp > Human ------------- chr14:66985130-66985136 Template switch process: F1: L AAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGG 1 F3: 4 GAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGGGTAGTATTG R RF: AAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGTGGGACTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGT RR: TTTTTAAATTACACTACAGGTTAATTCTTAAACATACTTAGGTAACCAACCCTCCACCCTGACCCACTTCCCCATCATAACTACTCTTCTTTACGATGATTATCTCTTCTATTCATTTAGGTCCGACTACTAAGATTATTAGTTTTTCAATTCTTCTCAAGTTTGGATCA F2: 3 TGGGTCA 2 Unidirectional alignment (log-probability: -146) tgtatgaatccattggttgggaggagggactgggtgaaggactgggtgaatattacataatgaAAAAATTTAATGTGATGTCCAATT ---------------------------------------------------------------AAAAATTTAATGTGATGTCCAATT Template switch alignment (log-probability: -35.6) TGTATGAATCCATTGGTTGGGAGGaGGGACTGGGTGAAGG|ACTgGGT|GAATATTACATAATGAAAAAATTTAATGTGATGTCCAATT TGTATGAATCCATTGGTTGGGAGGTGGGACTGGGTGAAGG|ACTAGGT|GAATATTACATAATGAAAAAATTTAATGTGATGTCCAATT Gorilla > Human --------------- chr14:66985130-66985136 Template switch process: F1: L AAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGG 1 F3: 4 GAATATTACATAATGAAAAAATTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGGGTAGTATTG R RF: AAAAACTTAATGTGATGTCCAATTAAGAATTTGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGGGGTAGTATTGATGAGAAGAAATGCTACTAATAGAGAAGATAAGTAAATCCAGGCTGATGATTCTAATAATCAAAAAGTTAAGAAGAGTTCAAACCTAGT RR: TTTTTGAATTACACTACAGGTTAATTCTTAAACATACTTAGGTAACCAACCCTCCTCCCTGACCCACTTCCCCATCATAACTACTCTTCTTTACGATGATTATCTCTTCTATTCATTTAGGTCCGACTACTAAGATTATTAGTTTTTCAATTCTTCTCAAGTTTGGATCA F2: 3 TGGGTCA 2 Unidirectional alignment (log-probability: -146) tgtatgaatccattggttgggaggagggactgggtgaaggactgggtgaatattacataatgaAAAAAtTTAATGTGATGTCCAATT ---------------------------------------------------------------AAAAACTTAATGTGATGTCCAATT Template switch alignment (log-probability: -35.1) TGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGG|ACTgGGT|GAATATTACATAATGAAAAAAtTTAATGTGATGTCCAATT TGTATGAATCCATTGGTTGGGAGGAGGGACTGGGTGAAGG|ACTAGGT|GAATATTACATAATGAAAAAACTTAATGTGATGTCCAATT ========== Event 1000 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCTCCTGGGATGCTAAGGAAGTAGCCACTCTT----ATGGGAGAGTTACTATTTGAATTGA ↓ 3 2 1 4 Chimp: AGCTCTTGGGATGCTAAGGAAGTAGCCACTCTTAGCTACTTGAGAGTTACTATTTGAATTGA ↑ 3 2 1 4 Gorilla: AGCTCCTGGGATGCTAAGGAAGTAGCCACTCTT----ATGGGAGAGTTACTATTAGAATTGA Human: AGCTCCTGGGATGCTAAGGAAGTAGCCACTCTT----ATGGGAGAGTTACTATTTGAATTGA Cluster: [ ] Orangutan: AGCTCCTGGGCTGCGAAGAAAGTAGCCACTCTT----ATGGGATAGTTACTATTTGAATTGA Human > Chimp ------------- chr14:22112658-22112664 Template switch process: F1: L CAGTTCTAAGCTCTTGGGATGCTAAGGAAGTAGCCACTCTTA 1 F3: 4 GAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC R RF: CAGTTCTAAGCTCCTGGGATGCTAAGGAAGTAGCCACTCTTATGGGAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC RR: GTCAAGATTCGAGGACCCTACGATTCCTTCATCGGTGAGAATACCCTCTCAATGATAAACTTAACTCTCCACATAATCTAGGGTG F2: 3 TTCATCG 2 Unidirectional alignment (log-probability: -35.9) GTTCTAAGCTCtTGGGATGCTAAGGAAGTAGCCACTCTTA--GctacttGAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC GTTCTAAGCTCCTGGGATGCTAAGGAAGTAGCCACTCTTATGG------GAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC Template switch alignment (log-probability: -22.2) GTTCTAAGCTCtTGGGATGCTAAGGAAGTAGCCACTCTTA|GCTACTT|GAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC GTTCTAAGCTCCTGGGATGCTAAGGAAGTAGCCACTCTTA|GCTACTT|GAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC Gorilla > Chimp --------------- chr14:22112658-22112664 Template switch process: F1: L CAGTTCTAAGCTCTTGGGATGCTAAGGAAGTAGCCACTCTTA 1 F3: 4 GAGAGTTACTATTTGAATTGAGAGGTGTATTAGATCCCAC R RF: CAGTTCTAAGCTCCTGGGATGCTAAGGAAGTAGCCACTCTTATGGGAGAGTTACTATTAGAATTGAGAGGTGTATTAGATCCCAC RR: GTCAAGATTCGAGGACCCTACGATTCCTTCATCGGTGAGAATACCCTCTCAATGATAATCTTAACTCTCCACATAATCTAGGGTG F2: 3 TTCATCG 2 Unidirectional alignment (log-probability: -40.4) GTTCTAAGCTCtTGGGATGCTAAGGAAGTAGCCACTCTTA--GctacttGAGAGTTACTATTtGAATTGAGAGGTGTATTAGATCCCAC GTTCTAAGCTCCTGGGATGCTAAGGAAGTAGCCACTCTTATGG------GAGAGTTACTATTAGAATTGAGAGGTGTATTAGATCCCAC Template switch alignment (log-probability: -27.7) GTTCTAAGCTCtTGGGATGCTAAGGAAGTAGCCACTCTTA|GCTACTT|GAGAGTTACTATTtGAATTGAGAGGTGTATTAGATCCCAC GTTCTAAGCTCCTGGGATGCTAAGGAAGTAGCCACTCTTA|GCTACTT|GAGAGTTACTATTAGAATTGAGAGGTGTATTAGATCCCAC ========== Event 1001 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGACTAATACATAATTCACT---------AGAGAATGCCATTCAATTA-----------GCTAGAACAATGGTTCATGATGTAATTTTTCTCA Chimp: TAGACTAATACATAATTCACT---------AGAGAATGCCATTCAATTA-----------GCTAGAACAATGGTTCATGATGTAATTTTTCTCA ↓ 1 3 2 4 Gorilla: TAGACTAATACATAATTCACT------------------AATTGAATTG----------------------CATTCATGATGTAATTTTTCTCA ↑ 1 3 2 4 Human: TAGACTAATACATAATTCACT---------AGAGAATGCCATTCAATTA-----------GCTAGAACAATGGTTCATGATGTAATTTTTCTCA Cluster: [ ] Orangutan: TAGACTAATACATAATTGGCTAGAGAATGC---------CGTTCAATTAGCTAGAACAAT-----------GGTTCATGATGTAATTTGTCTCA Human > Gorilla --------------- chr14:4699813-4699823 Template switch process: F1: L TCATTTCACTGCCAATGTGATAGACTAATACATAATTCACTA 1 F3: 4 TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT R RF: TCATTTCACTGTCAATGTGATAGACTAATACATAATTCACTAGAGAATGCCATTCAATTAGCTAGAACAATGGTTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT RR: AGTAAAGTGACAGTTACACTATCTGATTATGTATTAAGTGATCTCTTACGGTAAGTTAATCGATCTTGTTACCAAGTACTACATTAAAAAGAGTAACAACTTATGAAATTTAA F2: 3 ACGTTAAGTTA 2 Unidirectional alignment (log-probability: -43.2) ATTTCACTGcCAATGTGATAGACTAATACATAATTCACT---------------------------AATtGaattgcaTTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT ATTTCACTGTCAATGTGATAGACTAATACATAATTCACTAGAGAATGCCATTCAATTAGCTAGAACAATGG-------TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT Template switch alignment (log-probability: -28.2) ATTTCACTGcCAATGTGATAGACTAATACATAATTCACTA|ATTGAATtGCA|TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT ATTTCACTGTCAATGTGATAGACTAATACATAATTCACTA|ATTGAATGGCA|TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT Chimp > Gorilla --------------- chr14:4699813-4699823 Template switch process: F1: L TCATTTCACTGCCAATGTGATAGACTAATACATAATTCACTA 1 F3: 4 TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT R RF: TCATTTCACTGTCAATGTGATAGACTAATACATAATTCACTAGAGAATGCCATTCAATTAGCTAGAACAATGGTTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT RR: AGTAAAGTGACAGTTACACTATCTGATTATGTATTAAGTGATCTCTTACGGTAAGTTAATCGATCTTGTTACCAAGTACTACATTAAAAAGAGTAACAACTTATGAAATTTAA F2: 3 ACGTTAAGTTA 2 Unidirectional alignment (log-probability: -43.2) ATTTCACTGcCAATGTGATAGACTAATACATAATTCACT---------------------------AATtGaattgcaTTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT ATTTCACTGTCAATGTGATAGACTAATACATAATTCACTAGAGAATGCCATTCAATTAGCTAGAACAATGG-------TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT Template switch alignment (log-probability: -28.2) ATTTCACTGcCAATGTGATAGACTAATACATAATTCACTA|ATTGAATtGCA|TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT ATTTCACTGTCAATGTGATAGACTAATACATAATTCACTA|ATTGAATGGCA|TTCATGATGTAATTTTTCTCATTGTTGAATACTTTAAATT ========== Event 1002 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTGGTACAAATTAGGTTATAA----------------------GACCAGTATAGTTGAAATGTATAGAGAA-AAAGAGGCTGTAGCAAGAAAATTTTGAAAAGGAAGAGAGAGAAAGGTAATGAGGTCAATATCATTTGTATTTGACTCCATGCATTAAGAAGTCACTGAAATATTTAAAGCAAGGTGAG ↓ 4 1 3 2 Chimp: GTTTGGTACAAATTAGGTTATAA-----------GATCAGTATAAGACCAGTATAGTTGAAATGTATAGAGAA-AAAGAGGCTGTAGCAAGAAAATTTTGAAAAGGAAGAAAGAGAAAGGTAATGAGGTCAATATCATTTGTATTTGACTCCATGCATTAAGAAGTCACTGAAAGATTTAAAGCAAGGTGAG Gorilla: GTTTGGTACAAATTAGGTTATAAGAGCAGTATAA-----------GACCAGTATAGTTgaaatgtatagagaaaaaagaggctgtaggaagaaaattttgaaaaggaagaaaaagaaagaTAATGAGGTCAATATCATTTGTATTTGACTCCATGCATTAAGAAGTCACTGAAAGATTTAAAGCAAGGTGAG Human: GTTTGGTACAAATTAGGTTATAA----------------------GACCAGTATAGTTGAAATGTATAGAGAA-AAAGAGGCTGTAGCAAGAAAATTTTGAAAAGGAAGAGAGAGAAAGGTAATGAGGTCAATATCATTTGTATTTGACTCCATGCATTAAGAAGTCACTGAAATATTTAAAGCAAGGTGAG Cluster: [ ] Orangutan: GTTTGGTACAAATTAGGTtataagaccagtataa-----------gaccagtataTTTGAAATGTATAGAGAA-AAAGAGGCTGTAGCAAGAAAATTTTGAAAAGGAAGAAAGAGAAAGGTAATGAGGTCAATATCATTTGTATTTGACTCCATGCATTAAGAAGTCACAGAAAGATTTAAAGCAAGGTGAG Human > Chimp ------------- chr14:66915086-66915090 Template switch process: F1: L GTATAGGTACAGAAACGAGTTTGGTACAAATTAGGTTATAAGA 1 F3: 4 ATAAGACCAGTATAGTTGAAATGTATAGAGAAAAAGAGGCTGTA R RF: GTATAGGTACAGAAACGAGTTTGGTACAAATTAGGTTATAAGACCAGTATAGTTGAAATGTATAGAGAAAAAGAGGCTGTAGCAAGAAAATTTTGAAAAGGAAGAGAGAGAAAGGTAATGAGGTCAATATCATTTGTATTTGACTCCATGCATTAAGAAGTCACTGA RR: CATATCCATGTCTTTGCTCAAACCATGTTTAATCCAATATTCTGGTCATATCAACTTTACATATCTCTTTTTCTCCGACATCGTTCTTTTAAAACTTTTCCTTCTCTCTCTTTCCATTACTCCAGTTATAGTAAACATAAACTGAGGTACGTAATTCTTCAGTGACT F2: 3 TGACT 2 Unidirectional alignment (log-probability: -26.7) TAGGTACAGAAACGAGTTTGGTACAAATTAGGTtataagatcagTATAAGACCAGTATAGTTGAAATGTATAGAGAAAAAGAGGC TAGGTACAGAAACGAGTTTGGTACAAATTAGGT-----------TATAAGACCAGTATAGTTGAAATGTATAGAGAAAAAGAGGC Template switch alignment (log-probability: -16) TAGGTACAGAAACGAGTTTGGTACAAATTAGGTTATAAGA|TCAGT|ATAAGACCAGTATAGTTGAAATGTATAGAGAAAAAGAGGC TAGGTACAGAAACGAGTTTGGTACAAATTAGGTTATAAGA|TCAGT|ATAAGACCAGTATAGTTGAAATGTATAGAGAAAAAGAGGC ========== Event 1003 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GATTGTGACTATATACTTGGGTCAGTTTATGTATTGATTCACATTCACTTATTTTGACCAATAtttctttcttttctt-- Chimp: GATTGTGACTATATACTTGGGTCAGTTTATGTATTGATTCACATTCACTTATTTTGACCAATAtttctttcttttctt-- ↑ 3 2 1 4 Gorilla: GATTGTGATTATATACTTGGGTCAGTTTATGTATTGATTCACATTCACTTATTTCG-ACAATAtttctttcttttctttc Human: GATTGTGACTATATACTTGGGTCAGTTTATGTATTGATTCACATTCACTTATTTTGACCAATAtttctttcttttctt-- Cluster: [ ] Orangutan: GATCATGACTATATACTTAGGTCAGTTTATGTATTGATTCACAGTCACTTATTTTGGCCAATAtttctttctt------- Gorilla > Chimp --------------- chr14:66879313-66879315 Template switch process: F1: L TACTTGGGTCAGTTTATGTATTGATTCACATTCACTTATTTTGACCAATATTTCTTTCTTTTCTTT 1 F3: 4 TTTTTTTTTTTTTT R RF: TACTTGGGTCAGTTTATGTATTGATTCACATTCACTTATTTCGA-CAATATTTCTTTCTTTTCTTTCTTTTTTTTTTTTTTCTGAGACAGA RR: ATGAACCCAGTCAAATACATAACTAAGTGTAAGTGAATAAAGCT-GTTATAAAGAAAGAAAAGAAAGAAAAAAAAAAAAAAGACTCTGTCT F2: 3 TCT 2 Unidirectional alignment (log-probability: -38.8) CACATTCACTTATTTtGAcCAATATTTCTTTCTTTTCTtttcTTtTTTTTTTTTTTT CACATTCACTTATTTCGA-CAATATTTCTTTCTTTTCT----TTCTTTTTTTTTTTT Template switch alignment (log-probability: -32.8) CACATTCACTTATTTtGAcCAATATTTCTTTCTTTTCTTT|TCT|TTTTTTTTTTTTTT CACATTCACTTATTTCGA-CAATATTTCTTTCTTTTCTTT|TCT|TTTTTTTTTTTTTT ========== Event 1004 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: GATCAATGCATATTGAAGATAGACT-TACTGAACATATTGAGGAAAGAATATTT-CTGTGTTTAAATGAA Chimp: GATCAATGCATATTGAAGATATTCTTTCCTCAATATGTTCAG-TAAGTCTATTTCTTGTGTTTAAATGAA ↓ 13 24 ↑ 13 24 Gorilla: GATCAATGCATATTGAAGATAGACT-TACTGAACATATTGAGGAAAGAATATTTCTTGTGTTTAAATGAA Human: GATCAATGCATATTGAAGATAGACT-TACTGAACATATTGAGGAAAGAATATTT-CTGTGTTTAAATGAA Cluster: [ ] Orangutan: GATCAATGCATATTGAAGATAGACT-TACTGAACATATTGAGGAAAGAATATTTCTTGTGTTTAAATGAA Gorilla > Chimp --------------- chr14:25626592-25626618 Template switch process: F1: L GCTTAGAGCAGGCTTGGATGGATCAATGCATATTGAAGATA 1 F3: 4 TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT R RF: GCTTAGAGTAGGCTTGGATGGATCAATGCATATTGAAGATAGACTTACTGAACATATTGAGGAAAGAATATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT RR: CGAATCTCATCCGAACCTACCTAGTTACGTATAACTTCTATCTGAATGACTTGTATAACTCCTTTCTTATAAAGAACACAAATTTACTTTCGATACTTTCGATTAAAA F2: 3 CTGAATGACTTGTATAACTCCTTTCTT 2 Unidirectional alignment (log-probability: -66.3) CTTAGAGcAGGCTTGGATGGATCAATGCATATTGAAGAT---------------------------AttctttcctcaatatgttcagtaagtcTATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT CTTAGAGTAGGCTTGGATGGATCAATGCATATTGAAGATAGACTTACTGAACATATTGAGGAAAGAA---------------------------TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT Template switch alignment (log-probability: -24.7) CTTAGAGcAGGCTTGGATGGATCAATGCATATTGAAGATA|TTCTTTCCTCAATATGTTCAGTAAGTC|TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT CTTAGAGTAGGCTTGGATGGATCAATGCATATTGAAGATA|TTCTTTCCTCAATATGTTCAGTAAGTC|TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT Chimp > Gorilla --------------- chr14:87371771-87371797 Template switch process: F1: L GCTTAGAGTAGGCTTGGATGGATCAATGCATATTGAAGATA 1 F3: 4 TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT R RF: GCTTAGAGCAGGCTTGGATGGATCAATGCATATTGAAGATATTCTTTCCTCAATATGTTCAGTAAGTCTATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT RR: CGAATCTCGTCCGAACCTACCTAGTTACGTATAACTTCTATAAGAAAGGAGTTATACAAGTCATTCAGATAAAGAACACAAATTTACTTTCGATACTTTCGATTAAAA F2: 3 AAGAAAGGAGTTATACAAGTCATTCAG 2 Unidirectional alignment (log-probability: -66.3) CTTAGAGtAGGCTTGGATGGATCAATGCATATTGAAGATA---------------------------gacttactgaacatattgaggaaagaaTATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT CTTAGAGCAGGCTTGGATGGATCAATGCATATTGAAGATATTCTTTCCTCAATATGTTCAGTAAGTC---------------------------TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT Template switch alignment (log-probability: -24.7) CTTAGAGtAGGCTTGGATGGATCAATGCATATTGAAGATA|GACTTACTGAACATATTGAGGAAAGAA|TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT CTTAGAGCAGGCTTGGATGGATCAATGCATATTGAAGATA|GACTTACTGAACATATTGAGGAAAGAA|TATTTCTTGTGTTTAAATGAAAGCTATGAAAGCTAATTTT ========== Event 1005 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTGTATGCTTAGTAATGGACACAGTTCTAATTCCATAAGAGACATTTCAGGATGTCTCTTAACTTGCCCTTT Chimp: AGTGTATGCTTAGTAATGGAC-----------------------ATCCTGAAATGTCTCTTAAATTGCCCTTT ↑ 1 3 24 Gorilla: AGTGTATGCTTAGTAATGGACATAGTTCTAATTCCATAGGAGACATTTCAGGATGTCTCTTAACTTGCCCTTT Human: AGTGTATGCTTAGTAATGGACACAGTTCTAATTCCATAAGAGACATTTCAGGATGTCTCTTAACTTGCCCTTT Cluster: [ ] Orangutan: ------------------------------------------------------------------------- Gorilla > Chimp --------------- chr14:66779917-66779922 Template switch process: F1: L ATAAGTATACTTGTAAGGTCAGTGTATGCTTAGTAATGGACAT 1 F3: 4 ATGTCTCTTAAATTGCCCTTTAAACTTTTGAGCTCTTTTT R RF: ATAAGTATACTTGTAAGGTCAGTGTATGCTTAGTAATGGACATAGTTCTAATTCCATAGGAGACATTTCAGGATGTCTCTTAACTTGCCCTTTAAACTTGTGAGCTCTTTTT RR: TATTCATATGAACATTCCAGTCACATACGAATCATTACCTGTATCAAGATTAAGGTATCCTCTGTAAAGTCCTACAGAGAATTGAACGGGAAATTTGAACACTCGAGAAAAA F2: 3 AAGTCC 2 Unidirectional alignment (log-probability: -40.3) AGTATACTTGTAAGGTCAGTGTATGCTTAGTAATGGACATcctgaA----------------------------ATGTCTCTTAAaTTGCCCTTTAAACTTtTGAGCTCTTTTT AGTATACTTGTAAGGTCAGTGTATGCTTAGTAATGGACAT-----AGTTCTAATTCCATAGGAGACATTTCAGGATGTCTCTTAACTTGCCCTTTAAACTTGTGAGCTCTTTTT Template switch alignment (log-probability: -27.6) AGTATACTTGTAAGGTCAGTGTATGCTTAGTAATGGACAT|CCTGAA|ATGTCTCTTAAaTTGCCCTTTAAACTTtTGAGCTCTTTTT AGTATACTTGTAAGGTCAGTGTATGCTTAGTAATGGACAT|CCTGAA|ATGTCTCTTAACTTGCCCTTTAAACTTGTGAGCTCTTTTT ========== Event 1006 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: TTATTTTCAATTGTCCTTTTA-----------------CAATATGCAGCCATTTCTTTTGACACCAGGGTAAACAGAAGTGAG Chimp: TTATCTTCAATTGTCCTTTTAATTGTAAAAAGAAATGGCTGCATATTGCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAG ↓ 1 3 4 ↑ 3 1 4 2 Gorilla: TTATCTTCAATTGTCCTTTTA-----------------CAATATGCAGCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAG Human: TTATTTTCAATTGTCCTTTTA-----------------CAATATGCAGCCATTTCTTTTGACACCAGGGTAAACAGAAGTGAG Cluster: [ ] Orangutan: ----------------------------------------------------------------------------------- Gorilla > Chimp --------------- chr14:26597822-26597845 Template switch process: F1: L ACATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTT--AAT 1 F3: 4 GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC R RF: ACATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTACAATATGCAGCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC RR: TGTAATACTTCATTCTTTGAAATAGAAGTTAACAGGAAAATGTTATACGTCGGTAAAGAAAACTGTGGTCCCATTTGTCTTCATTCTGCG F2: 3 TTATACGTCGGTAAAGAAAAATGT 2 Unidirectional alignment (log-probability: -57) TTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTA--------AttgtaaaaagaaatggctgcatattGCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC TTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTACAATATGCA-------------------------GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC Template switch alignment (log-probability: -34.2) TTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTT--AAT|TGTaAAAAGAAATGGCTGCATATT|GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC TTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTACAAT|TGTCAAAAGAAATGGCTGCATATT|GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC Chimp > Gorilla --------------- chr14:88330377-88330385 Template switch process: F1: L ACATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTA 1 F3: 4 GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC R RF: ACATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTAATTGTAAAAAGAAATGGCTGCATATTGCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC RR: TGTAATACTTCATTCTTTGAAATAGAAGTTAACAGGAAAATTAACATTTTTCTTTACCGACGTATAACGGTAAAGAAAACTGTGGTCCCATTTGTCTTCATTCTGCG F2: 3 ACGTATAAC 2 Unidirectional alignment (log-probability: -33.4) CATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTAcaatatgcA-------------------------GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC CATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTA--------ATTGTAAAAAGAAATGGCTGCATATTGCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC Template switch alignment (log-probability: -16.9) CATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTA|CAATATGCA|GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC CATTATGAAGTAAGAAACTTTATCTTCAATTGTCCTTTTA|CAATATGCA|GCCATTTCTTTTGACACCAGGGTAAACAGAAGTAAGACGC ========== Event 1007 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: atggcataatgttattaatacagtgtatcagcttatattttctgaaCTATTCAAGACTAGAAAATTTCCAGA-------ATACTGTATTTTTACAAAAGAGAAATGTT Chimp: atggcataatgttattaatacagtgtATCAGCTTATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGA-------ATACTGTATTTTTACAAAAGAGAAATGTT ↑ 3 2 41 Gorilla: ATGGCATAATGTTATTAATACAGTGTATCAGCTTATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGA--------------ATTTTTACAAAAGAGAAATGTT ↓ 3 2 41 Human: atggcataatgttattaatacagtgtatcagcttatattttctgaaCTATTCAAGACTAGAAAATTTCCAGA-------ATACTGTATTTTTACAAAAGAGAAATGTT Cluster: [ ] Orangutan: atggcataatgttattaatatagtgtatcagcttatattttctgaactattcaagactagaaattttccagaagactat-------atttttacaaaggagaaatgtt Gorilla > Human --------------- chr14:64050978-64050982 Template switch process: F1: L GTGTATCAGCTTATATTTTCTGAACTATTCAAGACTAGAAAATTTCCAGAAT 1 F3: 4 ATTTTTACAAAAGAGAAATGTTAACAATTCTTT R RF: ACAGTGTATCAGCTTATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAATTTTTACAAAAGAGAAATGTTAACAATTCTTT RR: TGTCACATAGTCGAATATAAAAGACTTGATAAGTTCTGATCTTTAAAAGGTCTTAAAAATGTTTTCTCTTTACAATTGTTAAGAAA F2: 3 TGTCA 2 Unidirectional alignment (log-probability: -33.6) ATATTTTCTGAACTATTCAAGACTAGAAAaTTTCCAGAatactgtATTTTTACAAAAGAGAAATGTTAACAATTCTTT------- ATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGA-------ATTTTTACAAAAGAGAAATGTTAACAATTCTTTTCTTTCT Template switch alignment (log-probability: -22) ATATTTTCTGAACTATTCAAGACTAGAAAaTTTCCAGAAT|ACTGT|ATTTTTACAAAAGAGAAATGTTAACAATTCTTT ATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAAT|ACTGT|ATTTTTACAAAAGAGAAATGTTAACAATTCTTT Gorilla > Chimp --------------- chr14:65040274-65040278 Template switch process: F1: L CTTATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAAT 1 F3: 4 ATTTTTACAAAAGAGAAATGTTAACAATTCTTT R RF: ACAGTGTATCAGCTTATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAATTTTTACAAAAGAGAAATGTTAACAATTCTTT RR: TGTCACATAGTCGAATATAAAAGACTTGATAAGTTCTGATCTTTAAAAGGTCTTAAAAATGTTTTCTCTTTACAATTGTTAAGAAA F2: 3 TGTCA 2 Unidirectional alignment (log-probability: -28) ATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAatactgtATTTTTACAAAAGAGAAATGTTAACAATTCTTT------- ATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGA-------ATTTTTACAAAAGAGAAATGTTAACAATTCTTTTCTTTCT Template switch alignment (log-probability: -16.2) ATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAAT|ACTGT|ATTTTTACAAAAGAGAAATGTTAACAATTCTTT ATATTTTCTGAACTATTCAAGACTAGAAATTTTCCAGAAT|ACTGT|ATTTTTACAAAAGAGAAATGTTAACAATTCTTT ========== Event 1008 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: ---------------------------TTAGAAACTTCATTGAAGAAAACTAAAACCAATAGGTCTCAAGCCACTATGTGTGGGAATGAACACTTCCTTTTGCTTCATATGTAGGCATTGTGTATCTCTTCTGGATTATACTTTCTATCTGTGTATCTATGCTTTGACTCTTAGTAGTTTTTCATGTTATAAAATTGATTTGCATTGGGAAAACACATTTTTAAAAAGGAGTAAAGAG-----------CAGAAACaagatcaataaactcaaccagaatatatctctgtgtataccatctggcatgaatctttcttaaaacatggtatttattaccactacgcatatttgtggttttatttaggtaaagttgtcttttttatatctttaatagatgtatgttttctttaactgttagtgttttcaataaggcactctgtgcatattctggatttcctttgtttgacactcatatgcagaacatatttgtttccttgtatgactttcaccagattgttctccatggcattggattcatgttcagtggtatcttttccagttcatgatgtttttaatgcatatctcatttttgtaatggttcaattgttttctttccttagctttattatcattcatcttcttttgttttctcaGATGcaatagaggaaaataactaagagcacagattttggagccatacagcttgggatacaatcccttctgtgctgggtaaccttgatcaagttacttaatctttcataaactttgctgtaatgttaaaaaaatgggaataatgataccatttaccttattgggttgctgtgaggaatgcatgagcacttggttgagtacctgacTGGAGCGGGATGAAGCATTTAGTAACTGAGTGCTCAAGCAGTCCAATCAAAAAATAAAGGAGACTA----TT-------AATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCtttcctttttgattt---tt----a----------------------------- Chimp: TCATAGCTAATTAATTTTCTTAGGCAAAGAGTAGGCT------------------------------------------------------------------------------------------------CATT---------------------------------------------------------------------TAAAACACTCCTTTTTaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagcaaaaaacccacctcttatata----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aaaatcaaaaaggaaaGGAGACTA--TTTTAAACAGAGATAATAGCCATTGCTATT-------ATTAAAATAGTCTCCTTTCTTTTTTGATTGGACTT--CT-TGAACACTCAGTTACTAAGTGCTTCATCC ↓ 1 4 3 2 ↑ 1 4 3 2 Gorilla: ---------------------------TTAGAAACTTCATTGAAGAAAACTAAAACCAATAGGTCTCAAGCCACTATGTGTGGGAATGAACACTTCCTTTTGCTTCATATGTAGGCATTGTGTATCTCTTCTGGATTATACTTTGTATCTGTGTATCTATGCTTTGATTCTTAGTAGATTTTCATGTTATAAAATTGATTTGCATTGGGAAAACACATTTTTAAAAAGGAGTAAAGAG-----------CAGAAACaagatcaataaactcaaccagaatatatctctgtgtataccatccggcatgaatctttcttaaaacatggtatttgttaccactatgcatatttgtggttttatttaggtaaagttgtcttttttatatctttaatagacgtatgttttctttaactgttagtgttttcaataaggcactctgtgcatattctggatttcctttgtttgacactcatatGCAGAACATATTTGTTTCCTTGTATGACTTTCACCAGATTGTTCTCCACGGCACTGGATTCATGTTCAGTGGTATCTTTTCCAGTTCATGATGTTTTTAATGCGTATCTCATTTTTGTAATGGTTCAATTGTTTTCTTTCCTTAGCTTTATTATCATTCATCTTCTTTTGTTTTCTCAGATGcagtagaggaaaataactaagagcacagattttggagccatacagcttgggatacaatcccttccgtgctgggtaaccttgatcaagttacttaatctttcataaactttgctgtaatgtta-aaaaatgggaataatgataccatttaccttattgggttgctgtgaggattgcatgagcacttggttgagtacctgactggagtgggatgaagcacttagtaactgAGTGTTCAAGAAGTCCAATCAAAAAAGAAAGGAGACTATT--TT-------AATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCtttcctttttgattt---tt----a----------------------------- Human: ---------------------------TTAGAAACTTCATTGAAGAAAACTAAAACCAATAGGTCTCAAGCCACTATGTGTGGGAATGAACACTTCCTTTTGCTTCATATGTAGGCATTGTGTATCTCTTCTGGATTATACTTTCTATCTGTGTATCTATGCTTTGACTCTTAGTAGTTTTTCATGTTATAAAATTGATTTGCATTGGGAAAACACATTTTTAAAAAGGAGTAAAGAG-----------CAGAAACaagatcaataaactcaaccagaatatatctctgtgtataccatctggcatgaatctttcttaaaacatggtatttattaccactacgcatatttgtggttttatttaggtaaagttgtcttttttatatctttaatagatgtatgttttctttaactgttagtgttttcaataaggcactctgtgcatattctggatttcctttgtttgacactcatatgcagaacatatttgtttccttgtatgactttcaccagattgttctccatggcattggattcatgttcagtggtatcttttccagttcatgatgtttttaatgcatatctcatttttgtaatggttcaattgttttctttccttagctttattatcattcatcttcttttgttttctcaGATGcaatagaggaaaataactaagagcacagattttggagccatacagcttgggatacaatcccttctgtgctgggtaaccttgatcaagttacttaatctttcataaactttgctgtaatgttaaaaaaatgggaataatgataccatttaccttattgggttgctgtgaggaatgcatgagcacttggttgagtacctgacTGGAGCGGGATGAAGCATTTAGTAACTGAGTGCTCAAGCAGTCCAATCAAAAAATAAAGGAGACTA----TT-------AATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCtttcctttttgattt---tt----a----------------------------- Cluster: [ ] Orangutan: ---------------------------TTAGAAACTTCACTGAAGAAAACTAAATCCAATAGGTCTCAAGCCACTATGTGTGGAAATGAACACTTCCTTTTGCTTCGTATGTAAGCATTGTGTATCTCTTCTGGAttatactttgtatctgtgtatttatgctttgattctgagtaGTTTTTCATGTTATAAAATTGATTTGCATTGGGAAAACACATTTTTAAAAAGAAGTAAAGAG-----------CAAAAACAAGATCAATAaactcaaccaaaatatatctctgtgtataccatccggcatgaatctttcttaaaacatgatatttattaccactatgcatatttgtggttgtatttaggtaaaattgtcttttttatatctttaatagatgtatgttttctttaactgttagtgttttcaataacgcactctgtgcatattctggatttcc-ttGTTTGACACTCATATGCAGAACATATTTGTTTCCTTGCATGACTTTCACCAGATTGTTCTCCATGGCATTGGATTCATGTTCAGGGGTATCTTTTCCAGTTCATGATATTTTTAATGTGTATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NN-------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNN-------------------------------- Gorilla > Chimp --------------- chr14:27699225-27699311 Template switch process: F1: L AAA 1 F3: 4 TTGA R RF: AAATGGGAATAATGATACCATTTACCTTATTGGGTTGCTGTGAGGATTGCATGAGCACTTGGTTGAGTACCTGACTGGAGTGGGATGAAGCACTTAGTAACTGAGTGTTCAAGAAGTCCAATCAAAAAAGAAAGGAGACTATTTTAATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCTTTCCTTTTTGA RR: TTTACCCTTATTACTATGGTAAATGGAATAACCCAACGACACTCCTAACGTACTCGTGAACCAACTCATGGACTGACCTCACCCTACTTCGTGAATCATTGACTCACAAGTTCTTCAGGTTAGTTTTTTCTTTCCTCTGATAAAATTATTATCGTTACCGATAATAGAGACAAATTTTATCAGAGGAAAGGAAAAACT F2: 3 CTTCAGGTTAGTTTTTTCTTTCCTCTGATAAAATTATTATCGTTACCGATAATAGAGACAAATTTTATCAGAGGAAAGGAAAAACTA 2 Unidirectional alignment (log-probability: -93.4) AA----AATCAAAAAgGAAAGGAGACTATTTTAaacagagATAATAGCcATtGCTATTA-------TTAAAATAGTCTCCTTTCtTTTTTGATTggacttcTTgA AAGTCCAATCAAAAAAGAAAGGAGACTATTTTA-------ATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCTTTCCTTTTTGATT-------TTTA Template switch alignment (log-probability: -25) AAA|ATCAAAAAGGAAAGGAGACTATTTTAAACAGAGATAATAGCCATTGCTATTATTAAAATAGTCTCCTTTCTTTTTTGATTGGACTTC|TTGA AAA|ATCAAAAAGGAAAGGAGACTATTTTAAACAGAGATAATAGCCATTGCTATTATTAAAATAGTCTCCTTTCTTTTTTGATTGGACTTC|TTGA Chimp > Gorilla --------------- chr14:89424732-89424827 Template switch process: F1: L CT 1 F3: 4 TTTTTA R RF: CTTAGGCAAAGAGTAGGCTCATTTAAAACACTCCTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCAAAAAACCCACCTCTTATATAAAAATCAAAAAGGAAAGGAGACTATTTTAAACAGAGATAATAGCCATTGCTATTATTAAAATAGTCTCCTTTCTTTTTTGATTGGACTTCTTGAACACTC RR: GAATCCGTTTCTCATCCGAGTAAATTTTGTGAGGAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGTTTTTTGGGTGGAGAATATATTTTTAGTTTTTCCTTTCCTCTGATAAAATTTGTCTCTATTATCGGTAACGATAATAATTTTATCAGAGGAAAGAAAAAACTAACCTGAAGAACTTGTGAG F2: 3 AGTTTTTCCTTTCCTCTGATAAAATTTGTCTCTATTATCGGTAACGATAATAATTTTATCAGAGGAAAGAAAAAACTAACCTGAAGAACTTGTGAG 2 Unidirectional alignment (log-probability: -107) ctgagtgttcaagAAgtccAATCAAAAAaGAAAGGAGACTATTTTA-------ATAATAGCaATgGCTATTAtctctgtTTAAAATAGTCTCCTTTCcTTTTTGATT-------TTtA -------------AA----AATCAAAAAGGAAAGGAGACTATTTTAAACAGAGATAATAGCCATTGCTATTA-------TTAAAATAGTCTCCTTTCTTTTTTGATTGGACTTCTTGA Template switch alignment (log-probability: -26.2) CT|GAGTGTTCAAGAAGTCCAATCAAAAAAGAAAGGAGACTATTTTAATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCTTTCCTTTTTGA|TTTTTA CT|GAGTGTTCAAGAAGTCCAATCAAAAAAGAAAGGAGACTATTTTAATAATAGCAATGGCTATTATCTCTGTTTAAAATAGTCTCCTTTCCTTTTTGA|TTTTTA ========== Event 1009 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAAGAGGTGAACAACAGACT------GTCCTGGCTTGTGAATAACAAGATATGAGCCAAATACCTT Chimp: TCAAGAGGTGAACAACAGACTTGTTATTCACTGGCTTGTGAATAACAAGATATGAGCCAAATACCTT ↑ 1 4 3 2 Gorilla: CCAAGAGGTGAACAACAGACT------GTCCTGGCTTGTGAATAACAAGATATGAGCCAAATACCTT Human: CCAAGAGGTGAACAACAGACT------GTCCTGGCTTGTGAATAACAAGATATGAGCCAAATACCTT Cluster: [ ] Orangutan: CCAAGAGGTGAACAACAGACT------GTCCTGGCTTGTGAATAACAAGACATGAGCCAAATACCTT Gorilla > Chimp --------------- chr14:28049496-28049504 Template switch process: F1: L TCCCCAAAATAGAGTACATGTCAAGAGGTGAACAACAGACT 1 F3: 4 CTGGCTTGTGAATAACAAGATATGAGCCAAATACCTTATT R RF: TCCCCAAAATAGAGTACATGCCAAGAGGTGAACAACAGACTGTCCTGGCTTGTGAATAACAAGATATGAGCCAAATACCTTATT RR: AGGGGTTTTATCTCATGTACGGTTCTCCACTTGTTGTCTGACAGGACCGAACACTTATTGTTCTATACTCGGTTTATGGAATAA F2: 3 ACTTATTGT 2 Unidirectional alignment (log-probability: -39.2) CCCCAAAATAGAGTACATGtCAAGAGGTGAACAACAGACTtgttattca---CTGGCTTGTGAATAACAAGATATGAGCCAAATACCTTATT CCCCAAAATAGAGTACATGCCAAGAGGTGAACAACAGACT---------GTCCTGGCTTGTGAATAACAAGATATGAGCCAAATACCTTATT Template switch alignment (log-probability: -22.4) CCCCAAAATAGAGTACATGtCAAGAGGTGAACAACAGACT|TGTTATTCA|CTGGCTTGTGAATAACAAGATATGAGCCAAATACCTTATT CCCCAAAATAGAGTACATGCCAAGAGGTGAACAACAGACT|TGTTATTCA|CTGGCTTGTGAATAACAAGATATGAGCCAAATACCTTATT ========== Event 1010 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATAATGAGAAGGAAATGATTCT---------CATAAAAAGGAAAGAAGTGATCATTTGTAAG Chimp: TATAATGAGAAGGAAATGATTCT---------CATAAAAAGGAAAGAAGTGATCATTTGTAAG ↓ 13 4 2 Gorilla: TATAATGAGAAGGAAATGATTTCCTTTTTATGAGTAAAAAGGAAAGAAGTGATCATTTGTAAG ↑ 13 4 2 Human: TATAATGAGAAGGAAATGATTCT---------CATAAAAAGGAAAGAAGTGATCATTTGTAAG Cluster: [ ] Orangutan: TATAATGAGAAGGAAATGATTCT---------CATAAAAAGGAAAGAAGTGATCATTTGTAAG Human > Gorilla --------------- chr14:61033901-61033913 Template switch process: F1: L TCACATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT 1 F3: 4 TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA R RF: TCAGATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATTCTCATAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA RR: AGTCTAACATATTCGACAAAATATTACTCTTCCTTTACTAAGAGTATTTTTCCTTTCTTCACTAGTAAACATTCGAACTTTACTT F2: 3 GAGTATTTTTCCT 2 Unidirectional alignment (log-probability: -45) CAcATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATTtcctttttatgag----TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA CAGATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT-------------CTCATAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA Template switch alignment (log-probability: -22.9) CAcATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT|TCCTTTTTATGAG|TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA CAGATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT|TCCTTTTTATGAG|TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA Chimp > Gorilla --------------- chr14:61033901-61033913 Template switch process: F1: L TCACATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT 1 F3: 4 TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA R RF: TCAGATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATTCTCATAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA RR: AGTCTAACATATTCGACAAAATATTACTCTTCCTTTACTAAGAGTATTTTTCCTTTCTTCACTAGTAAACATTCGAACTTTACTT F2: 3 GAGTATTTTTCCT 2 Unidirectional alignment (log-probability: -45) CAcATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATTtcctttttatgag----TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA CAGATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT-------------CTCATAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA Template switch alignment (log-probability: -22.9) CAcATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT|TCCTTTTTATGAG|TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA CAGATTGTATAAGCTGTTTTATAATGAGAAGGAAATGATT|TCCTTTTTATGAG|TAAAAAGGAAAGAAGTGATCATTTGTAAGCTTGAAATGAA ========== Event 1011 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGAATCAATGCTTTTATCTAAAAGAACT----CCTTTGATGGGAGCACAGTTTATATACCAT ↓ 4 3 21 Chimp: AAGAATCAATGCTTTTATCTAAAAGAACTCAGTTCTTTTAAAAGAGCACAGTTTATATACCAT ↑ 4 3 21 Gorilla: AAGAATCAATGCTTTTATCTAAAAGAACT----CCTTTGATGGGAGCACAGTTTATATACCAT Human: AAGAATCAATGCTTTTATCTAAAAGAACT----CCTTTGATGGGAGCACAGTTTATATACCAT Cluster: [ ] Orangutan: AAGAATCAATGCTTTTATCTAAAAGAACT----CCTTTGATGGGAGCACAGTTTATATACCAT Human > Chimp ------------- chr14:60851425-60851432 Template switch process: F1: L AGCTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC 1 F3: 4 TAAAA---------------GAGCACAGTTTATATACCATTAAACTTAGACAAAAGATGG R RF: AGCTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTCCTTTGATGGGAGCACAGTTTATATACCATTAAACTTAGACAAAAGATGG RR: TCGAGTCTAGGTTTCTTAGTTACGAAAATAGATTTTCTTGAGGAAACTACCCTCGTGTCAAATATATGGTAATTTGAATCTGTTTTCTACC F2: 3 TTTCTTGA 2 Unidirectional alignment (log-probability: -40.3) CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC---------agttcttttaaaaGAGCACAGTTTATATACCATTAAACTTAGACAAAA CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTCCTTTGATGG-------------GAGCACAGTTTATATACCATTAAACTTAGACAAAA Template switch alignment (log-probability: -27.4) CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC|AGTTCTTT|TAAAA---------------GAGCACAGTTTATATACCATTAAACTTAGACAAAA CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC|AGTTCTTT|TAAAAGAACTCCTTTGATGGGAGCACAGTTTATATACCATTAAACTTAGACAAAA Gorilla > Chimp --------------- chr14:60851425-60851432 Template switch process: F1: L AGCTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC 1 F3: 4 TAAAA---------------GAGCACAGTTTATATACCATTAAACTTAGACAAAAGATGG R RF: AGCTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTCCTTTGATGGGAGCACAGTTTATATACCATTAAACTTAGACAAAAGATGG RR: TCGAGTCTAGGTTTCTTAGTTACGAAAATAGATTTTCTTGAGGAAACTACCCTCGTGTCAAATATATGGTAATTTGAATCTGTTTTCTACC F2: 3 TTTCTTGA 2 Unidirectional alignment (log-probability: -38.9) CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTCagttCTTTtAaaaGAGCACAGTTTATATACCATTAAACTTAGACAAAA CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC----CTTTGATGGGAGCACAGTTTATATACCATTAAACTTAGACAAAA Template switch alignment (log-probability: -27.4) CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC|AGTTCTTT|TAAAA---------------GAGCACAGTTTATATACCATTAAACTTAGACAAAA CTCAGATCCAAAGAATCAATGCTTTTATCTAAAAGAACTC|AGTTCTTT|TAAAAGAACTCCTTTGATGGGAGCACAGTTTATATACCATTAAACTTAGACAAAA ========== Event 1012 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTACTATATAGATGACTGAGAGTTTCTGT---------GATAGAGGGGTATGTTCAAGCAG ↓ 3 12 4 Chimp: tTACTATATAGATGACTGAGAGTTTCTGTCTCAGAAACTCTAGAGGGGTATGTTCAAGCAG ↑ 3 12 4 Gorilla: TTACTATATAGATGACTGAGAGTTTCTGT---------GATAGAGGGGTATGTTCAAGCAG Human: TTACTATATAGATGACTGAGAGTTTCTGT---------GATAGAGGGGTATGTTCAAGCAG Cluster: [ ] Orangutan: TTACTATATAGATGACTGAGAGTTTCTGT---------GATAGAGGGGTATGTTCAAGCAA Human > Chimp ------------- chr14:31654030-31654040 Template switch process: F1: L ATCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT 1 F3: 4 TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA R RF: ATCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGTGATAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA RR: TAGTTTTGGAAGAATGATATATCTACTGACTCTCAAAGACACTATCTCCCCATACAAGTTCGTCAATACTCTGTGAAAGTAAT F2: 3 CTCAAAGACTC 2 Unidirectional alignment (log-probability: -34.1) TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGTctcaGAaactcTAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT----GA-----TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA Template switch alignment (log-probability: -22.6) TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT|CtCAGAAACTC|TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT|CACAGAAACTC|TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA Gorilla > Chimp --------------- chr14:31654030-31654040 Template switch process: F1: L ATCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT 1 F3: 4 TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA R RF: ATCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGTGATAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA RR: TAGTTTTGGAAGAATGATATATCTACTGACTCTCAAAGACACTATCTCCCCATACAAGTTCGTCAATACTCTGTGAAAGTAAT F2: 3 CTCAAAGACTC 2 Unidirectional alignment (log-probability: -33.6) TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGTctcaGAaactcTAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT----GA-----TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA Template switch alignment (log-probability: -22.6) TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT|CtCAGAAACTC|TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA TCAAAACCTTCTTACTATATAGATGACTGAGAGTTTCTGT|CACAGAAACTC|TAGAGGGGTATGTTCAAGCAGTTATGAGACACTTTCATTA ========== Event 1013 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAAGTGCCCACTCTAGGCAAGG----GCAT-AAGGCATATAGTGACATATAGTGATCTCTGCCCCATA Chimp: GAAAGTGCCCACTCTAGGCAAAG----GCATATAGGCATATAGTGACATATAGTGATCTCTGCCCCATA ↓ 1 4 3 2 Gorilla: GAAAGTGCCCACTCTAGGCAAAT--------GTCACTATATAGTGACATATAGTGATCTCTGCCTCATA ↑ 1 4 3 2 Human: GAAAGTGCCCACTCTAGGCAAGG----GCAT-AAGGCATATAGTGACATATAGTGATCTCTGCCCCATA Cluster: [ ] Orangutan: GGCAGTGCCCACTCTAGGAAAAGGCAT----ATAGGCATATAGTGACATATAGTGATCTCTGCCCCATA Human > Gorilla --------------- chr14:30876622-30876629 Template switch process: F1: L TACCTGGAATGAGTCACCGGGAAAGTGCCCACTCTAGGCAA 1 F3: 4 ATATAGTGACATATAGTGATCTCTGCCTCATAACTCAATG R RF: TACCTGGAATGAGTCACTGGGAAAGTGCCCACTCTAGGCAAGGGCATAAGGCATATAGTGACATATAGTGATCTCTGCCCCATAACTCAATG RR: ATGGACCTTACTCAGTGACCCTTTCACGGGTGAGATCCGTTCCCGTATTCCGTATATCACTGTATATCACTAGAGACGGGGTATTGAGTTAC F2: 3 TCACTGTA 2 Unidirectional alignment (log-probability: -43.7) ACCTGGAATGAGTCACcGGGAAAGTGCCCACTCTAGGCAA-----------atgtcactATATAGTGACATATAGTGATCTCTGCCtCATAACTCAATG ACCTGGAATGAGTCACTGGGAAAGTGCCCACTCTAGGCAAGGGCATAAGGC--------ATATAGTGACATATAGTGATCTCTGCCCCATAACTCAATG Template switch alignment (log-probability: -27.8) ACCTGGAATGAGTCACcGGGAAAGTGCCCACTCTAGGCAA|ATGTCACT|ATATAGTGACATATAGTGATCTCTGCCtCATAACTCAATG ACCTGGAATGAGTCACTGGGAAAGTGCCCACTCTAGGCAA|ATGTCACT|ATATAGTGACATATAGTGATCTCTGCCCCATAACTCAATG Chimp > Gorilla --------------- chr14:30876623-30876630 Template switch process: F1: L ACCTGGAATGAGTCACCGGGAAAGTGCCCACTCTAGGCAAA 1 F3: 4 TATAGTGACATATAGTGATCTCTGCCTCATAACTCAATG R RF: ACCTGGAATGAGTCACTGGGAAAGTGCCCACTCTAGGCAAAGGCATATAGGCATATAGTGACATATAGTGATCTCTGCCCCATAACTCAATG RR: TGGACCTTACTCAGTGACCCTTTCACGGGTGAGATCCGTTTCCGTATATCCGTATATCACTGTATATCACTAGAGACGGGGTATTGAGTTAC F2: 3 ATCACTGT 2 Unidirectional alignment (log-probability: -42.3) CCTGGAATGAGTCACcGGGAAAGTGCCCACTCTAGGCAAA-----------tgtcactATATAGTGACATATAGTGATCTCTGCCtCATAACTCAATG CCTGGAATGAGTCACTGGGAAAGTGCCCACTCTAGGCAAAGGCATATAGGC-------ATATAGTGACATATAGTGATCTCTGCCCCATAACTCAATG Template switch alignment (log-probability: -27.8) CCTGGAATGAGTCACcGGGAAAGTGCCCACTCTAGGCAAA|TGTCACTA|TATAGTGACATATAGTGATCTCTGCCtCATAACTCAATG CCTGGAATGAGTCACTGGGAAAGTGCCCACTCTAGGCAAA|TGTCACTA|TATAGTGACATATAGTGATCTCTGCCCCATAACTCAATG ========== Event 1014 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 346 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTGCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGCCCAGAGCA----CAGTC Chimp: AAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTTCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGCCCAGAGCA----CAGTC ↓ 3 1 2 4 Gorilla: AAATGTCTTCAGGGGGTGACTTCAATTCAAGCTTTGAATT------GCCCAGAGCCCAATTCAATTTGAACTGAATTCAAAGCTGCCCagagcacaaacagtc ↓ 3 1 2 4 ↑ 1 4 3 2 Human: AAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTGCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGCCCAGAGCA----CAGTC Cluster: [ ] Orangutan: AAATGTCTCCAGGGAGTGACTTCAATTCAAAGCCTG--------------------------------------------CGCTTCCCAGAGCACAAACAGTC Gorilla > Human --------------- chr1:4962281-4962294 Template switch process: F1: L ATATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA 1 F3: 4 CTGCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGC R RF: ATATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAGCTTTGAATTGCCCAGAGCCCAATTCAATTTGAACTGAATTCAAAGCTGC RR: TATATAAGTACTTTACAGAAGTCCCCCACTGAAGTTAAGTTCGAAACTTAACGGGTCTCGGGTTAAGTTAAACTTGACTTAAGTTTCGACG F2: 3 GAAGTTAAGTTCGA 2 Unidirectional alignment (log-probability: -41.7) TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAagcTTGAATtgaagcTGCCCAGAGCCCAATTCAATTTGAAtTGAATTCAAAGCT TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAGCTTTGAAT------TGCCCAGAGCCCAATTCAATTTGAACTGAATTCAAAGCT Template switch alignment (log-probability: -28.6) TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA|AGCTTGAATTGAAG|cTGCCCAGAGCCCAATTCAATTTGAAtTGAATTCAAAGCT TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA|AGCTTGAATTGAAG|TTGCCCAGAGCCCAATTCAATTTGAACTGAATTCAAAGCT Human > Gorilla --------------- chr1:4656512-4656520 Template switch process: F1: L ATATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA 1 F3: 4 TGCCCAGAGCCCAATTCAATTTGAACTGAATTCAAAGCTGC R RF: ATATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTGCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGC RR: TATATAAGTACTTTACAGAAGTCCCCCACTGAAGTTAAGTTTCGAACTTAACTTCGACGGGTCTCGGGTTAAGTTAAACTTAACTTAAGTTTCGACG F2: 3 TAAGTTTCG 2 Unidirectional alignment (log-probability: -33.4) TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAgctTTGAAT------TGCCCAGAGCCCAATTCAATTTGAAcTGAATTCAAAGCTG TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTGCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTG Template switch alignment (log-probability: -22.4) TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA|GCTTTGAAT|TGCCCAGAGCCCAATTCAATTTGAAcTGAATTCAAAGCTG TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA|GCTTTGAAT|TGCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTG Chimp > Gorilla --------------- chr1:4656512-4656522 Template switch process: F1: L ATATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA 1 F3: 4 CCCAGAGCCCAATTCAATTTGAACTGAATTCAAAGCTGCC R RF: ATATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTTCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGCC RR: TATATAAGTACTTTACAGAAGTCCCCCACTGAAGTTAAGTTTCGAACTTAACTTCGAAGGGTCTCGGGTTAAGTTAAACTTAACTTAAGTTTCGACGG F2: 3 GTTAAGTTTCG 2 Unidirectional alignment (log-probability: -33.4) TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAgctTTGAATTG------CCCAGAGCCCAATTCAATTTGAAcTGAATTCAAAGCTGCC TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAAAGCTTGAATTGAAGCTTCCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGCC Template switch alignment (log-probability: -22.6) TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA|GCTTTGAATTG|CCCAGAGCCCAATTCAATTTGAAcTGAATTCAAAGCTGCC TATATTCATGAAATGTCTTCAGGGGGTGACTTCAATTCAA|GCTTTGAATTG|CCCAGAGCCCAATTCAATTTGAATTGAATTCAAAGCTGCC ========== Event 1015 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAATGGTGCCAAACTTTGAAATCCTAGTAAAAGTTTACTAGGATTTACCACTTTTGATTAATGGCTCCATCAT Chimp: ATAATGGTGCCAAACTTTGAAATCCTAGTAAAAGTTTACTAGGATTTACCACTCTTGATTAATGGCTCCATCAT ↑ 3 1 2 4 Gorilla: ATAATGGTGCCAAACTTTGAAATCCTAGTAAA-----------CTTGTCCACTTTTGATTAATGGCTCCATCAT ↓ 3 1 2 4 Human: ATAATGGTGCCAAACTTTGAAATCCTAGTAAAAGTTTACTAGGATTTACCACTTTTGATTAATGGCTCCATCAT Cluster: [ ] Orangutan: ATAATGGTGCCAAACTTTGAAATCCTGGTAAA-----------CTTGTCCACTTTTGATTA-TTGCTCCATCAT Gorilla > Human --------------- chr14:58394823-58394837 Template switch process: F1: L GAACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA 1 F3: 4 ACCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGAG R RF: GAACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAACTTGTCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGAG RR: CTTGTTTAATATTACCACGGTTTGAAACTTTAGGATCATTTGAACAGGTGAAAACTAATTACCGAGGTAGTAGGTGACGGTCACTC F2: 3 TTTAGGATCATTTGA 2 Unidirectional alignment (log-probability: -43.3) AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAAagtttactaggaTTtaCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGA AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA-----------CTTGTCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGA Template switch alignment (log-probability: -23.2) AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA|AGTTTACTAGGATTT|aCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGA AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA|AGTTTACTAGGATTT|TCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGA Gorilla > Chimp --------------- chr14:59256002-59256016 Template switch process: F1: L GAACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA 1 F3: 4 ACCACTCTTGATTAATGGCTCCATCATCCACTGCCAGTGAGGATTCT R RF: GAACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAACTTGTCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGAGGATTCT RR: CTTGTTTAATATTACCACGGTTTGAAACTTTAGGATCATTTGAACAGGTGAAAACTAATTACCGAGGTAGTAGGTGACGGTCACTCCTAAGA F2: 3 TTTAGGATCATTTGA 2 Unidirectional alignment (log-probability: -48.9) AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAAagtttactaggaTTtaCCACTcTTGATTAATGGCTCCATCATCCACTGCCAGTGA AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA-----------CTTGTCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGA Template switch alignment (log-probability: -28.8) AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA|AGTTTACTAGGATTT|aCCACTcTTGATTAATGGCTCCATCATCCACTGCCAGTGA AACAAATTATAATGGTGCCAAACTTTGAAATCCTAGTAAA|AGTTTACTAGGATTT|TCCACTTTTGATTAATGGCTCCATCATCCACTGCCAGTGA ========== Event 1016 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: GAAAAACCTCTGGCTTGAAATTACGTAA------TTCTCTTAGC------AGTTAAGTTATGTAGCTAGTATTTGAAATT Chimp: GAAAAACCTCTGGCTTGAAATTACATAA------TTCTCTTAGC------TGTTAAGTTATGTAGCTAGTATATGAAGTT Gorilla: GAAAAACCTCTGGCTTGAAATAACTTAA------------CAGCTAAGAGAATTACGTAATGTAGCTAGTATTTGAAGTT ↓ 13 24 ↑ 13 24 Human: GAAAAACCTCTGGCTTGAAATTACGTAA------TTCTCTTAGC------AGTTAAGTTATGTAGCTAGTATTTGAAATT Cluster: [ ] Orangutan: GAAAAGAGTTTGGCTTGAAATTGAGTAATTCTCT------TAGC------TGTTAAGTTACATAGCTAGTATTTGAAGTT Gorilla > Human --------------- chr14:48378395-48378420 Template switch process: F1: L CCAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAAT 1 F3: 4 ATGTAGCTAGTATTTGAAATTATGTCTATTTTACTTCTGA R RF: CCAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAATAACTTAACAGCTAAGAGAATTACGTAATGTAGCTAGTATTTGAAGTTATGTCTATTTTACTTCTGA RR: GGTTCCAAAAAAAGGATTAACTTTTTGGAGACCGAACTTTATTGAATTGTCGATTCTCTTAATGCATTACATCGATCATAAACTTCAATACAGATAAAATGAAGACT F2: 3 TTGAATTGACGATTCTCTTAATGCAT 2 Unidirectional alignment (log-probability: -56) CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAA--------------------TTACGTAattctcttagcagttaagttATGTAGCTAGTATTTGAAaTTATGTCTATTTTACTTCTGA CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAATAACTTAACAGCTAAGAGAATTACGTA--------------------ATGTAGCTAGTATTTGAAGTTATGTCTATTTTACTTCTGA Template switch alignment (log-probability: -30.1) CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAAT|TACGTAATTCTCTTAGCaGTTAAGTT|ATGTAGCTAGTATTTGAAaTTATGTCTATTTTACTTCTGA CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAAT|TACGTAATTCTCTTAGCTGTTAAGTT|ATGTAGCTAGTATTTGAAGTTATGTCTATTTTACTTCTGA Human > Gorilla --------------- chr14:31653934-31653959 Template switch process: F1: L CCAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAAT 1 F3: 4 ATGTAGCTAGTATTTGAAGTTATGTCTATTTTACTTCTGA R RF: CCAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAATTACGTAATTCTCTTAGCAGTTAAGTTATGTAGCTAGTATTTGAAATTATGTCTATTTTACTTCTGA RR: GGTTCCAAAAAAAGGATTAACTTTTTGGAGACCGAACTTTAATGCATTAAGAGAATCGTCAATTCAATACATCGATCATAAACTTTAATACAGATAAAATGAAGACT F2: 3 ATGCATTAAGAGAATCGACAATTCAA 2 Unidirectional alignment (log-probability: -56) CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAataacttaacagctaagagaATTACGTA--------------------ATGTAGCTAGTATTTGAAgTTATGTCTATTTTACTTCTGA CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAA--------------------ATTACGTAATTCTCTTAGCAGTTAAGTTATGTAGCTAGTATTTGAAATTATGTCTATTTTACTTCTGA Template switch alignment (log-probability: -30.1) CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAAT|AACTTAACaGCTAAGAGAATTACGTA|ATGTAGCTAGTATTTGAAgTTATGTCTATTTTACTTCTGA CAAGGTTTTTTTCCTAATTGAAAAACCTCTGGCTTGAAAT|AACTTAACTGCTAAGAGAATTACGTA|ATGTAGCTAGTATTTGAAATTATGTCTATTTTACTTCTGA ========== Event 1017 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGAT---AATTGCCATGAAAGAAAACATAAAAGTA Chimp: AACGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGAT---AATTGCCATGAAAGAAAACATAAAAGTA ↑ 3 2 1 4 Gorilla: AAAGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGAT------AGAAATGAAAGAAAACATAAAAGTA ↓ 3 2 1 4 Human: AAAGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGAT---AATTGCCATGAAAGAAAACATAAAAGTA Cluster: [ ] Orangutan: AAAGAAGAAAACATTATCAGGCAAATATTTAGATAAAATTGATAAT---TGCCATGAAAGAAAACATAAAAGTA Gorilla > Human --------------- chr14:48620219-48620224 Template switch process: F1: L AGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA 1 F3: 4 ATGAAAGAAAACATAAAAGTATTTGATTTAGAGTAGGGAT R RF: AGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATAGAAATGAAAGAAAACATAAAAGTATTTGATTTACAGTAGGGAT RR: TCTTCTTTTGTAATAGTCCGTTAATAAATCTATTTTGACTATCTTTACTTTCTTTTGTATTTTCATAAACTAAATGTCATCCCTA F2: 3 CCGTTA 2 Unidirectional alignment (log-probability: -31.8) AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATAattGccATGAAAGAAAACATAAAAGTATTTGATTTAgAGTAGGGAT AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA---GAAATGAAAGAAAACATAAAAGTATTTGATTTACAGTAGGGAT Template switch alignment (log-probability: -22) AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA|ATTGCC|ATGAAAGAAAACATAAAAGTATTTGATTTAgAGTAGGGAT AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA|ATTGCC|ATGAAAGAAAACATAAAAGTATTTGATTTACAGTAGGGAT Gorilla > Chimp --------------- chr14:32679961-32679966 Template switch process: F1: L CGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA 1 F3: 4 ATGAAAGAAAACATAAAAGTATTTGATTTAGAGTAGGGAT R RF: AGAAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATAGAAATGAAAGAAAACATAAAAGTATTTGATTTACAGTAGGGAT RR: TCTTCTTTTGTAATAGTCCGTTAATAAATCTATTTTGACTATCTTTACTTTCTTTTGTATTTTCATAAACTAAATGTCATCCCTA F2: 3 CCGTTA 2 Unidirectional alignment (log-probability: -37.3) AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATAattGccATGAAAGAAAACATAAAAGTATTTGATTTAgAGTAGGGAT AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA---GAAATGAAAGAAAACATAAAAGTATTTGATTTACAGTAGGGAT Template switch alignment (log-probability: -27.5) AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA|ATTGCC|ATGAAAGAAAACATAAAAGTATTTGATTTAgAGTAGGGAT AAGAAAACATTATCAGGCAATTATTTAGATAAAACTGATA|ATTGCC|ATGAAAGAAAACATAAAAGTATTTGATTTACAGTAGGGAT ========== Event 1018 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TAGCTTAATTAAATTAGGCAGCAGCAGCTTTAGAAGCTGCTGCTGTCAGTTGGAACAG ↑ 1 3 4 2 Chimp: TAGCTTAATTAAATTAGGCAG---CAGCTTCTAAAGCTGCTGCTGTCAGTTGGAACAG Gorilla: TAGCTTAATTAAATTAGGCAG---CAGCTTCTAAAGCTGCTGCTGTCAGTTGGAACAG ↓ 1 3 4 2 Human: TAGCTTAATTAAATTAGGCAGCAGCAGCTTTAGAAGCTGCTGCTGTCAGTTGGAACAG Cluster: [ ] Orangutan: Chimp > Human ------------- chr14:48690869-48690876 Template switch process: F1: L ATTTTTTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC 1 F3: 4 AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA R RF: ATTTTTTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGCTTCTAAAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA RR: TAAAAAAAGATGAAAAAATAATCGAATTAATTTAATCCGTCGTCGAAGATTTCGACGACGACAGTCAACCTTGTCCGTGACGTCTTTTAT F2: 3 GATTTCGA 2 Unidirectional alignment (log-probability: -31.5) TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC----AgctttagAAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGCTTCTA-------AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA Template switch alignment (log-probability: -16.4) TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC|AGCTTTAG|AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC|AGCTTTAG|AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA Gorilla > Human --------------- chr14:48690869-48690876 Template switch process: F1: L ATTTTTTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC 1 F3: 4 AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA R RF: ATTTTTTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGCTTCTAAAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA RR: TAAAAAAAGATGAAAAAATAATCGAATTAATTTAATCCGTCGTCGAAGATTTCGACGACGACAGTCAACCTTGTCCGTGACGTCTTTTAT F2: 3 GATTTCGA 2 Unidirectional alignment (log-probability: -31) TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC----AgctttagAAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGCTTCTA-------AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA Template switch alignment (log-probability: -16.8) TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC|AGCTTTAG|AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA TTTCTACTTTTTTATTAGCTTAATTAAATTAGGCAGCAGC|AGCTTTAG|AAGCTGCTGCTGTCAGTTGGAACAGGCACTGCAGAAAATA ========== Event 1019 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTAACTCTCTGGGGCCTCGTT-TGTGATTCTTTAGAAACCCAGACTACCTTCACACC-ACAGTGCCGTGTAT Chimp: ACTAGCTCTCTGGGGCCTCGTCAAGGTAGTCTTTAGAAACCCAGACTACCTTGACACC-ACAGTGCCGTGTAT ↑ 1 4 3 2 Gorilla: ACTAGCTCTCTGGGGCCTCGTT-TGTGATTCTTTAGAAACCCAGACTACCTTGACACCACCAGTGCCGTGTAT Human: ACTAACTCTCTGGGGCCTCGTT-TGTGATTCTTTAGAAACCCAGACTACCTTCACACC-ACAGTGCCGTGTAT Cluster: [ ] Orangutan: ACTAGCTCTCTGGGGCCTTGTT-TGTGATTCTTTAGAAACCCAGACCACCTTGACACC-ATAGTGCCATGTAT Gorilla > Chimp --------------- chr14:33254394-33254401 Template switch process: F1: L GTCAGCAAACAAACTGTGTCACTAGCTCTCTGGGGCCTCGT 1 F3: 4 TCTTTAGAAACCCAGACTACCTTGACACCA-CAGTGCCGT R RF: GTCAGCAAACAAACTGTGTCACTAGCTCTCTGGGGCCTCGTTTGTGATTCTTTAGAAACCCAGACTACCTTGACACCACCAGTGCCGT RR: CAGTCGTTTGTTTGACACAGTGATCGAGAGACCCCGGAGCAAACACTAAGAAATCTTTGGGTCTGATGGAACTGTGGTGGTCACGGCA F2: 3 GATGGAAC 2 Unidirectional alignment (log-probability: -42.3) TCAGCAAACAAACTGTGTCACTAGCTCTCTGGGGCCTCG-------TcaaggtagTCTTTAGAAACCCAGACTACCTTGACACCA-CAGTGCCGT TCAGCAAACAAACTGTGTCACTAGCTCTCTGGGGCCTCGTTTGTGAT--------TCTTTAGAAACCCAGACTACCTTGACACCACCAGTGCCGT Template switch alignment (log-probability: -26.5) TCAGCAAACAAACTGTGTCACTAGCTCTCTGGGGCCTCGT|CAAGGTAG|TCTTTAGAAACCCAGACTACCTTGACACCA-CAGTGCCGT TCAGCAAACAAACTGTGTCACTAGCTCTCTGGGGCCTCGT|CAAGGTAG|TCTTTAGAAACCCAGACTACCTTGACACCACCAGTGCCGT ========== Event 1020 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TTAAGCACTATGTAGCCAGGATAATACCTCAATCATAGTAATACCCCAGTTACTATAATTGAGGTATTATCCTGGCTACATAGTGCTTAAGt ↑ 3 1 2 4 Chimp: TTAAGCACTATGTAGCCAGGATAATACCTCAATTATAGTAATTGGGGTATTACTATGATTGAGGTATTTCACTGGCTACATAGTGCTTAAGT Gorilla: -------------------------------------------------------------------------------------------- Human: TTAAGCACTATGTAGCCAGGATAATACCTCAATCATAGTAATACCCCAGTTACTATAATTGAGGTATTATCCTGGCTACATAGTGCTTAAGt Cluster: [ ] Orangutan: Chimp > Human ------------- chr14:57626602-57626639 Template switch process: F1: L CCTTTAATTTAAGCACTATGTAGCCAGGATAATACCTCAAT 1 F3: 4 CTGGCTACATAGTGCTTAAGTTAAAA R RF: TCTTTAATTTAAGCACTATGTAGCCAGGATAATACCTCAATTATAGTAATTGGGGTATTACTATGATTGAGGTATTTCACTGGCTACATAGTGCTTAAGTTAAAA RR: AGAAATTAAATTCGTGATACATCGGTCCTATTATGGAGTTAATATCATTAACCCCATAATGATACTAACTCCATAAAGTGACCGATGTATCACGAATTCAATTTT F2: 3 CTATTATGGAGTTAATATCATTGACCCCATAATGATAC 2 Unidirectional alignment (log-probability: -66.2) CTTTAATTTAAGCACTATGTAGCCAGGATAATACCTCAATcATAGTAA------TAccccagTTACTATaATTGAGGTATTatcCTGGCTACATAGTGCTTAAGTTAAAA CTTTAATTTAAGCACTATGTAGCCAGGATAATACCTCAATTATAGTAATTGGGGTA------TTACTATGATTGAGGTATTTCACTGGCTACATAGTGCTTAAGTTAAAA Template switch alignment (log-probability: -31.7) CTTTAATTTAAGCACTATGTAGCCAGGATAATACCTCAAT|CATAGTAATACCCCAgTTACTATAATTGAGGTATTATC|CTGGCTACATAGTGCTTAAGTTAAAA CTTTAATTTAAGCACTATGTAGCCAGGATAATACCTCAAT|CATAGTAATACCCCAATTACTATAATTGAGGTATTATC|CTGGCTACATAGTGCTTAAGTTAAAA ========== Event 1021 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCTTTCTACCTAAGTGTATGTCCTTTAGAGGACAGAGAAAAGCTGAGAataa ↑ 1 3 4 2 Chimp: AGCTTTCTACCGAAGTGTATGGC--CTAAAGGACAGAGAAAAGCTGAGAataa Gorilla: AGCTTTCTACCAAAGTGTATGGC--CTAAAGGACAGAGAAAAGCTGAGAataa Human: AGCTTTCTACCTAAGTGTATGTCCTTTAGAGGACAGAGAAAAGCTGAGAataa Cluster: [ ] Orangutan: AGCTTTCTACTGAAGTGTATACC--CTAAAGGACAGAGAAAAGCTGAGAataa Chimp > Human ------------- chr14:57392642-57392649 Template switch process: F1: L TAGTGAAGTCAGTGTTTCTCAGCTTTCTACCTAAGTGTATG 1 F3: 4 AGGACAGAGAAAAGCTGAGAATAAGCATGAAATTTCTTTC R RF: TAGTGAAGTCAGTGTTTCTCAGCTTTCTACCGAAGTGTATGGCCTAAAGGACAGAGAAAAGCTGAGAATAAGCATGAAATTTCTTTC RR: ATCACTTCAGTCACAAAGAGTCGAAAGATGGCTTCACATACCGGATTTCCTGTCTCTTTTCGACTCTTATTCGTACTTTAAAGAAAG F2: 3 GATTTCCT 2 Unidirectional alignment (log-probability: -31.8) AGTGAAGTCAGTGTTTCTCAGCTTTCTACCtAAGTGTATGtCCttTAgAGGACAGAGAAAAGCTGAGAATAAGCATGAAATTTCTTTC AGTGAAGTCAGTGTTTCTCAGCTTTCTACCGAAGTGTATGGCC--TAAAGGACAGAGAAAAGCTGAGAATAAGCATGAAATTTCTTTC Template switch alignment (log-probability: -22.3) AGTGAAGTCAGTGTTTCTCAGCTTTCTACCtAAGTGTATG|TCCTTTAG|AGGACAGAGAAAAGCTGAGAATAAGCATGAAATTTCTTTC AGTGAAGTCAGTGTTTCTCAGCTTTCTACCGAAGTGTATG|TCCTTTAG|AGGACAGAGAAAAGCTGAGAATAAGCATGAAATTTCTTTC ========== Event 1022 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CACTGCTATAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAA-----------TACAGCTGAAATACAA----------AAATACAGC Chimp: CACTGCTATAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAA-----------TACAGCTGAAATACAA----------AAATACAGC ↑ 3 2 4 1 Gorilla: CACTGCTATAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAA----------------------TACAA----------AAATACAGC Human: CACTGCTATAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAA-----------TACAGCTGAAATACAA----------AAATACAGC Cluster: [ ] Orangutan: CACTGCTGTAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAATAAAGCTGAAA-----------TACAAAATAAGTGATGAATACAGC Gorilla > Chimp --------------- chr14:33955202-33955206 Template switch process: F1: L CTATAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAATACA 1 F3: 4 AATACAAAAATACAGCTACAATCATCACTTTACCTCACCTTA R RF: CTATAGAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAATACAAAAATACAGCTACAATCATCACTTTACCTCACCTTA RR: GATATCTTATACTCAGTCGTCCCGGAAGGTCGATCGACCTTATGTTTTTATGTCGATGTTAGTAGTGAAATGGAGTGGAAT F2: 3 AGTCG 2 Unidirectional alignment (log-probability: -26.7) GAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGaatacagctgaAATACAAAAATACAGCTACAATCATCACTTTACCTCACCT GAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGG-----------AATACAAAAATACAGCTACAATCATCACTTTACCTCACCT Template switch alignment (log-probability: -16.5) GAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAATACA|GCTGA|AATACAAAAATACAGCTACAATCATCACTTTACCTCACCT GAATATGAGTCAGCAGGGCCTTCCAGCTAGCTGGAATACA|GCTGA|AATACAAAAATACAGCTACAATCATCACTTTACCTCACCT ========== Event 1023 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTTTGTCTTGGCTGGTGTCAAAATG-----------GACTCTTTAAAAACTGTCCTCAGGAAGATTCCCCATCCAACTCTGAACAGCCTGGACTGATCTTTTTCTGATTTTTAGGGGTCTTGTGAACAAGAGTCAGGTGGGCGGGCAGCTCTTG Chimp: CTTTTGTCTTGGCTGGTGTCAAAATGGACTCAAAATGGACTCTTTAAAAACTGGCCTCAGGAAGATTCCCCATCCAACTCTGAACAGCCTGGACTGATCTTTTTCTGATTTTTAGGGGTCTTGTGAACAAGAGTCAGGTGGGCGGGCAGCTCTTG ↑ 4 1 3 2 Gorilla: CTTTTGTCTTGGCTGGTGTCAAAATG-----------AACTCTTTAAAAACTGGCCTCAGGAAGATTCCCCATCCAACTCTGAACAGCCTGGACTGATCTTTTTCTGATTTTTAGGGGTCTTGTGAACAAGAGTCAGGTGGGCGGGCAGCTCTTG Human: CTTTTGTCTTGGCTGGTGTCAAAATG-----------GACTCTTTAAAAACTGTCCTCAGGAAGATTCCCCATCCAACTCTGAACAGCCTGGACTGATCTTTTTCTGATTTTTAGGGGTCTTGTGAACAAGAGTCAGGTGGGCGGGCAGCTCTTG Cluster: [ ] Orangutan: CTTTTGTCTTGGCTGGTGTCAAAACG-----------GACTCTTTAAAAACTGGCCTCAGGAAGATTCCCCATCCAACTCTGAACAGCCTGGACTGAGCTTTTTCTGATTTTTAGGGGTCTTGTGAACAAGAGTCAGGTGGGCAGGCAGCTCTTG Gorilla > Chimp --------------- chr14:57805517-57805520 Template switch process: F1: L GACTCTGGGTCCTGGCTTTTGTCTTGGCTGGTGTCAAAATG 1 F3: 4 CAAAATGGACTCTTTAAAAACTGGCCTCAGGAAGATTCCCCATCCAAC R RF: GACTCTGGGTCCTGGCTTTTGTCTTGGCTGGTGTCAAAATGAACTCTTTAAAAACTGGCCTCAGGAAGATTCCCCATCCAACTCTGAACAGCCTGGACTGATCTTTTTCTGATTTTTAGGGGTCTTGTGAACAAGAGTC RR: CTGAGACCCAGGACCGAAAACAGAACCGACCACAGTTTTACTTGAGAAATTTTTGACCGGAGTCCTTCTAAGGGGTAGGTTGAGACTTGTCGGACCTGACTAGAAAAAGACTAAAAATCCCCAGAACACTTGTTCTCAG F2: 3 TCAG 2 Unidirectional alignment (log-probability: -32.2) ACTCTGGGTCCTGGCTTTTGTCTTGGCTGGTGTCAAAAtggactcaaaaTGgACTCTTTAAAAACTGGCCTCAGGAAGATTCCC ACTCTGGGTCCTGGCTTTTGTCTTGGCTGGTGTCAAAA-----------TGAACTCTTTAAAAACTGGCCTCAGGAAGATTCCC Template switch alignment (log-probability: -21.9) ACTCTGGGTCCTGGCTTTTGTCTTGGCTGGTGTCAAAATG|GACT|CAAAATGgACTCTTTAAAAACTGGCCTCAGGAAGATTCCC ACTCTGGGTCCTGGCTTTTGTCTTGGCTGGTGTCAAAATG|GACT|CAAAATGAACTCTTTAAAAACTGGCCTCAGGAAGATTCCC ========== Event 1024 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATCTACCTAGTAGCCTGTGGGATAACCTTAACTCTTAGAACTTTCTTCAAAGGATGGTGGTGAGAATGGGGTATACTGCCAGGCCCTGGCCTA-CGGGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGAG-----CTATCCCTGTAAACACAGGAGACATGGT Chimp: AATCTACCTAGTAGCCTGTGGGATAACCTTAACTCTTAGAACTTTCTTCAAAGGATGGTGGTGAGAATGGGGTATACTGCCAGGCCCTGGCCTA-CGGGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGAG-----CTATCCCTGTAAACACAGGAGACATGGT ↑ 3 2 1 4 Gorilla: AATCTACCTAGTAGCCTGTGGGATAACCTTAACTCTTAGAACTTTCTTCAAAGGATGGTGGTGAGAATGGGGTATACTGCCAGGCCCTGGCCTA-CGGGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGACATGGTGTAAACATGTAAACACAGGAGACATGGT ↓ 3 2 1 4 Human: AATCTACCTAGTAGCCTGTGGGATAACCTTAACTCTTAGAACTTTCTTCAAAGGATGGTGGTGAGAATGGGGTATACTGCCAGGCCCTGGCCTA-CGGGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGAG-----CTATCCCTGTAAACACAGGAGACATGGT Cluster: [ ] Orangutan: AATCTACCTAGTAGCCTGTGGGATAACCTTAACTCTTAGAACTTTCTCCTATGTATGTTGGTAAGAGTGGGGTATACTGGCGGGGCGTGACATAAAAAGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGAG-----CTATCCCTGTAAACACAGGAGACATGGT Gorilla > Human --------------- chr14:56800789-56800796 Template switch process: F1: L TACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA 1 F3: 4 TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC R RF: GGGATAACCTTAACTCTTAGAACTTTCTTCAAAGGATGGTGGTGAGAATGGGGTATACTGCCAGGCCCTGGCCTACGGGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGACATGGTGTAAACATGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC RR: CCCTATTGGAATTGAGAATCTTGAAAGAAGTTTCCTACCACCACTCTTACCCCATATGACGGTCCGGGACCGGATGCCCTCAAACATCCCGGATGAAAACCTCCGTTAGGTTGGGACTACCGACATGGATACTGTACCACATTTGTACATTTGTGTCCTCTGTACCACAGATATAACAAATTCCTG F2: 3 CCCTATCG 2 Unidirectional alignment (log-probability: -31.3) ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGAgctatccC------------TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA-------CATGGTGTAAACATGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC Template switch alignment (log-probability: -22.3) ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA|GcTATCCC|TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA|GTTATCCC|TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC Gorilla > Chimp --------------- chr14:57600734-57600741 Template switch process: F1: L TACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA 1 F3: 4 TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC R RF: GGGATAACCTTAACTCTTAGAACTTTCTTCAAAGGATGGTGGTGAGAATGGGGTATACTGCCAGGCCCTGGCCTACGGGAGTTTGTAGGGCCTACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGACATGGTGTAAACATGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC RR: CCCTATTGGAATTGAGAATCTTGAAAGAAGTTTCCTACCACCACTCTTACCCCATATGACGGTCCGGGACCGGATGCCCTCAAACATCCCGGATGAAAACCTCCGTTAGGTTGGGACTACCGACATGGATACTGTACCACATTTGTACATTTGTGTCCTCTGTACCACAGATATAACAAATTCCTG F2: 3 CCCTATCG 2 Unidirectional alignment (log-probability: -31.3) ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGAgctatccC------------TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA-------CATGGTGTAAACATGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC Template switch alignment (log-probability: -22.3) ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA|GcTATCCC|TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC ACTTTTGGAGGCAATCCAACCCTGATGGCTGTACCTATGA|GTTATCCC|TGTAAACACAGGAGACATGGTGTCTATATTGTTTAAGGAC ========== Event 1025 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GGTTTCTAGAGTCCGGTAGGTAATCTAGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTAAAATTTGATAGCTGTACAAATATATATAATTTAGATCAATTTTCTTACATTTCTGAAAGGGTTTGAGGTTCTTTCTAAATTTCTTGATAAATTTCATGTGGTGGATTTGTTTCCAACT Chimp: GGTTTCTAGAGTCCCGTAGGT-ACATGGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTAAAATTTGATAGCTGTACAAATATATATAATTTAGCTCAATTTTCTTACATTTCTGAAAGGGTTTGAGGTTCTTTCTAAATTTCTTGATAAATTTCATGTGGTGGATTTGTTTCCAACT Gorilla: GGTTTCTAGAGTCCGGTAGGT-ACATGGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTAAAATTTGATAGCTGTACAAATATATATAATTTAGCTCAATTTTCTTACATTTCTGAAAGGGTTTGAGGTTCTTTCTAAATTTCTTGATAAATTTCATGTGGTTGATTTGTTTCCAACT ↑ 1 4 3 2 Human: GGTTTCTAGAGTCCGGTAGGTAATCTAGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTAAAATTTGATAGCTGTACAAATATATATAATTTAGATCAATTTTCTTACATTTCTGAAAGGGTTTGAGGTTCTTTCTAAATTTCTTGATAAATTTCATGTGGTGGATTTGTTTCCAACT Cluster: [ ] Orangutan: GGTTTCTACAGTCCCGTAGGT-ACGTGGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTAAAATTTGATAGCTGTACAAATATATATAATTTAGCCCAATTTTCTTACATTTCTGAAAGGATTTGAGGTTCTTCCTAAATTTCTTGATAAATTTCATGTGGTGGATTTGTTTCCAACT Human > Gorilla --------------- chr14:56843489-56843492 Template switch process: F1: L CAGGCAGCAGAATCACCATTGGTTTCTAGAGTCCGGTAGGTA 1 F3: 4 GACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTA R RF: CAGGCAGCAGAATCACCACTGGTTTCTAGAGTCCGGTAGGTAATCTAGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTAAAATTTGATAGCTGTACAAATATATATAATTTAGATCAATTTTCTTACATTTCTGAAAGGGTTTGAGGTTCTTTCTAAATTTCTTGATAAATTTCATG RR: GTCCGTCGTCTTAGTGGTGACCAAAGATCTCAGGCCATCCATTAGATCTGAAACCATTAGTTTCTGTACAACTTTAAAAATCATAATTTTAAACTATCGACATGTTTATATATATTAAATCTAGTTAAAAGAATGTAAAGACTTTCCCAAACTCCAAGAAAGATTTAAAGAACTATTTAAAGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -32.2) GGCAGCAGAATCACCAtTGGTTTCTAGAGTCCGGTAGG-----TAcatgGACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTA GGCAGCAGAATCACCACTGGTTTCTAGAGTCCGGTAGGTAATCTA----GACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTA Template switch alignment (log-probability: -21.8) GGCAGCAGAATCACCAtTGGTTTCTAGAGTCCGGTAGGTA|CATG|GACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTA GGCAGCAGAATCACCACTGGTTTCTAGAGTCCGGTAGGTA|CATG|GACTTTGGTAATCAAAGACATGTTGAAATTTTTAGTATTA ========== Event 1026 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCTAAATGTCTATACTCCAAAGC----------------AAAATTCTTAG----GAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAACAGCCT----------CCAGGTACCTCCAGGAGCACCGACCTCTCCGTGGGCAGGTAACACAGCACTGCTCCTCTGAGTCCTAACAGGAACACCTGCCCCATCAAG Chimp: ACCTAAAAGTCTGTACTCCAAAGC----------------AAAATTCTTAGAAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAACAGCCT----------CCAGGTACCTCCAGGAGCACCGACCTCTCCATGGGCAGGTAACACAGCACTGCTCCTCTGAGTCCTAACAGGAACACCTGCCCCATCAAG ↑ 4 1 3 2 Gorilla: ACCTAAAAGTCTATACTCCAAAGC--------------------------------AAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAACAGCCT--------------------CCAGGAGCACCGACCTCTCCATGGGCAGGTAACACAGCACTGCTCCTCTGAGTCCTAACAGGAACACCTGCCCCATCAAG Human: ACCTAAATGTCTATACTCCAAAGC----------------AAAATTCTTAG----GAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAACAGCCT----------CCAGGTACCTCCAGGAGCACCGACCTCTCCGTGGGCAGGTAACACAGCACTGCTCCTCTGAGTCCTAACAGGAACACCTGCCCCATCAAG Cluster: [ ] Orangutan: ACCTAAAAGTCTATACTCCAAAGCAAAGTTCTTAGAAAGC----------------AAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAGCAGCCTCCAGGTACCT----------CCAGGAGCACCGACCTCTCCATGGGCAGGTAACACAGCACTGCTCCTCTGCATCCTAACAGGAACACCTGCCCCATCAAG Gorilla > Chimp --------------- chr14:56963146-56963151 Template switch process: F1: L CAGAAGCCAAGGGCAACACCTAAAAGTCTGTACTCCAAAGCAAAAT 1 F3: 4 AAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAAC R RF: CAGAAGCCAAGGGCAACACCTAAAAGTCTATACTCCAAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAGGAAACAGCCTCCAGGAGCACCGACCTCTCCATGGGCAGGTAACACAGCACTGCTCCTCTGAGTCCTAACA RR: GTCTTCGGTTCCCGTTGTGGATTTTCAGATATGAGGTTTCGTTTTAGTTCGTTTAGTTGTCTTCTCCTTCCACATCCTTTGTCGGAGGTCCTCGTGGCTGGAGAGGTACCCGTCCATTGTGTCGTGACGAGGAGACTCAGGATTGT F2: 3 GATTCT 2 Unidirectional alignment (log-probability: -39.4) CCAAGGGCAACACCTAAAAGTCTgTACTCCaaagcaaaattcttagAAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAG CCAAGGGCAACACCTAAAAGTCTATACTCC----------------AAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAG Template switch alignment (log-probability: -27.8) CCAAGGGCAACACCTAAAAGTCTgTACTCCAAAGCAAAAT|TcTTAG|AAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAG CCAAGGGCAACACCTAAAAGTCTATACTCCAAAGCAAAAT|TGTTAG|AAAGCAAAATCAAGCAAATCAACAGAAGAGGAAGGTGTAG ========== Event 1027 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACATTCAT--TCAGGTTCCTATACTCCTTACCA ↓ 3 2 1 4 Chimp: ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACATCCATGTGGAGGTTCCTATACTCCTTACCA Gorilla: Human: ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACATTCAT--TCAGGTTCCTATACTCCTTACCA Cluster: [ ] Orangutan: ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACATTCAT--TCAGGTTCCTATACTCCTTACCA Human > Chimp ------------- chr14:36099740-36099747 Template switch process: F1: L CACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACAT 1 F3: 4 AGGTTCCTATACTCCTTACCAGGCTGGACCCTGCGTAGAT R RF: CACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACATTCATTCAGGTTCCTATACTCCTTACCAGGTTGGACCCTGCGTAGAT RR: GTGAGGTACCGGAGGAGAGGGGTGTACCTACGGAACGTGTAAGTAAGTCCAAGGATATGAGGAATGGTCCAACCTGGGACGCATCTA F2: 3 GGTGTACC 2 Unidirectional alignment (log-probability: -37.5) ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACA-----TCcatgtggAGGTTCCTATACTCCTTACCAGGcTGGACCCTGCGTAGAT ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACATTCATTC-------AGGTTCCTATACTCCTTACCAGGTTGGACCCTGCGTAGAT Template switch alignment (log-probability: -22.3) ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACAT|CCATGTGG|AGGTTCCTATACTCCTTACCAGGcTGGACCCTGCGTAGAT ACTCCATGGCCTCCTCTCCCCACATGGATGCCTTGCACAT|CCATGTGG|AGGTTCCTATACTCCTTACCAGGTTGGACCCTGCGTAGAT ========== Event 1028 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATATAAAGTCCACAAATCTTAAAT--ATATTTAAGAAT--ACCTATATAACAAACATCCAGATAGAAA Chimp: ATATAAAGTCCACAAATCTTAAAT--ATATTTAAGAAC--ACCTATATAACAAACATCCAGATAGAAA ↓ 13 24 ↑ 13 24 Gorilla: ATATAAAGTCCACAAATCTTATATAGGTATTCTTAAAT----ATATTTAACAAACATCCCGATAGAAA ↓ 13 24 ↑ 13 24 Human: ATATAAAGTCCACAAATCTTAAAT--ATATTTAAGAAT--ACCTATATAACAAACATCCAGATAGAAA Cluster: [ ] Orangutan: ATATAAAGTCCACAAATCTTAAAT--ATATTTAAGAATAT--CTGTATAACAAACATCCAGATAGAAA Gorilla > Human --------------- chr14:52902526-52902547 Template switch process: F1: L ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA 1 F3: 4 TAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG R RF: ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTATATAGGTATTCTTAAATATATTTAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG RR: TAAGACAACTTCATATTGAATATATTTCAGGTGTTTAGAATATATCCATAAGAATTTATATAAATTGTTTGTAGGGCTATCTTTATATTTTGTGACTTTTGAC F2: 3 ATATCCATAAGAATTTATATAA 2 Unidirectional alignment (log-probability: -47.1) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTT--------------AAATATATTtaagaatacctataTAACAAACATCCaGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTATATAGGTATTCTTAAATATATT--------------TAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG Template switch alignment (log-probability: -24.1) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|AATATATTTAAGAATACCTATA|TAACAAACATCCaGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|AATATATTTAAGAATACCTATA|TAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG Human > Gorilla --------------- chr14:36114068-36114089 Template switch process: F1: L ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA 1 F3: 4 TAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG R RF: ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTAAATATATTTAAGAATACCTATATAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG RR: TAAGACAACTTCATATTGAATATATTTCAGGTGTTTAGAATTTATATAAATTCTTATGGATATATTGTTTGTAGGTCTATCTTTATATTTTGTGACTTTTGAC F2: 3 TTATATAAATTCTTATGGATAT 2 Unidirectional alignment (log-probability: -47.1) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTtatataggtattctTAAATATATT--------------TAACAAACATCCcGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCT--------------TAAATATATTTAAGAATACCTATATAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG Template switch alignment (log-probability: -24.1) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|TATAGGTATTCTTAAATATATT|TAACAAACATCCcGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|TATAGGTATTCTTAAATATATT|TAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG Gorilla > Chimp --------------- chr14:37080561-37080582 Template switch process: F1: L ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA 1 F3: 4 TAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG R RF: ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTATATAGGTATTCTTAAATATATTTAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG RR: TAAGACAACTTCATATTGAATATATTTCAGGTGTTTAGAATATATCCATAAGAATTTATATAAATTGTTTGTAGGGCTATCTTTATATTTTGTGACTTTTGAC F2: 3 ATATCCACAAGAATTTATATAA 2 Unidirectional alignment (log-probability: -47.1) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTT--------------AAATATATTtaagaacacctataTAACAAACATCCaGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTATATAGGTATTCTTAAATATATT--------------TAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG Template switch alignment (log-probability: -29.6) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|AATATATTTAAGAAcACCTATA|TAACAAACATCCaGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|AATATATTTAAGAATACCTATA|TAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG Chimp > Gorilla --------------- chr14:36114068-36114089 Template switch process: F1: L ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA 1 F3: 4 TAACAAACATCCCGATAGAAATATAAAACACTGAAAACTG R RF: ATTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTAAATATATTTAAGAACACCTATATAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG RR: TAAGACAACTTCATATTGAATATATTTCAGGTGTTTAGAATTTATATAAATTCTTGTGGATATATTGTTTGTAGGTCTATCTTTATATTTTGTGACTTTTGAC F2: 3 TTATATAAATTCTTATGGATAT 2 Unidirectional alignment (log-probability: -47.1) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTtatataggtattctTAAATATATT--------------TAACAAACATCCcGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCT--------------TAAATATATTTAAGAACACCTATATAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG Template switch alignment (log-probability: -29.6) TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|TATAGGTaTTCTTAAATATATT|TAACAAACATCCcGATAGAAATATAAAACACTGAAAACTG TTCTGTTGAAGTATAACTTATATAAAGTCCACAAATCTTA|TATAGGTGTTCTTAAATATATT|TAACAAACATCCAGATAGAAATATAAAACACTGAAAACTG ========== Event 1029 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAATCTCCTCAACAAGTTATATGCTTTCATTGCA-----------TCTTAGCTTTTGTTTGAAATGCTCA Chimp: GGAATCTCCTCAACAAGTTATATGCTTTCATTGCATATATATGCTTTCATTGCTTTTGTTTGAAATGCTCA ↑ 4 2 1 Gorilla: GGAATCTCCTCAACAAGTTATATGCTTTCATTACA-----------TCTTAGCTTTTGTTTGAAATGCTCA Human: GGAATCTCCTCAACAAGTTATATGCTTTCATTGCA-----------TCTTAGCTTTTGTTTGAAATGCTCA Cluster: [ ] Orangutan: GGAATCTCCTCAACAAGTTATATGCTTTCATTGCA-----------TCTTAGCTTTTGTTTGAAATGCTCA Gorilla > Chimp --------------- chr14:55301673-55301678 Template switch process: F1: L GACTATTCAGGAATCTCCTCAACAAGTTATATGCTTTCATT 1 F3: 4 ATATGCTTTCATT--------GCTTTTGTTTGAAATGCTCATTTGTCCTATCTTATTGGAG R RF: GACTATTCAGGAATCTCCTCAACAAGTTATATGCTTTCATTACATCTTAGCTTTTGTTTGAAATGCTCATTTGTCCTATCTTATTGGAG RR: CTGATAAGTCCTTAGAGGAGTTGTTCAATATACGAAAGTAATGTAGAATCGAAAACAAACTTTACGAGTAAACAGGATAGAATAACCTC F2: 3 TATACG 2 Unidirectional alignment (log-probability: -43.4) ACTATTCAGGAATCTCCTCAACAAGTTATATGCTTTCATTgCAtatatatgcttTCaTtGCTTTTGTTTGAAATGCTCATTTGTCC ACTATTCAGGAATCTCCTCAACAAGTTATATGCTTTCATTACA-----------TCTTAGCTTTTGTTTGAAATGCTCATTTGTCC Template switch alignment (log-probability: -27) ACTATTCAGGAATCTCCTCAACAAGTTATATGCTTTCATT|GCATAT|ATATGCTTTCATT--------GCTTTTGTTTGAAATGCTCATTTGTCC ACTATTCAGGAATCTCCTCAACAAGTTATATGCTTTCATT|GCATAT|ATATGCTTTCATTACATCTTAGCTTTTGTTTGAAATGCTCATTTGTCC ========== Event 1030 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATCAATGTGTTAGAGAACTTA-----ACTAAGATTTTTAAAG---ATAACTATGTAAATATATCAATACTAAC--TCTCT ↓ 13 24 ↑ 13 24 Chimp: ATCAATGTGTTAGAGAACTTA-----GT---TATCTTTAAAAATCTTAGTTATGTAAATGTATCAATACTAAC--TCTCT Gorilla: ATCAATGTGTTAGAGAACTAA----------GATTTTTAAAG---ATAACTATGTAAATATATCAATACTAAC----TCT Human: ATCAATGTGTTAGAGAACTTA-----ACTAAGATTTTTAAAG---ATAACTATGTAAATATATCAATACTAAC--TCTCT Cluster: [ ] Orangutan: ATCAATGTGTTAGAGAACTTAACTAA-----GATTTTTAAAG---ATAACTATGTAAATGTATCAATACTAACTC--TCT Chimp > Human ------------- chr14:54355966-54355986 Template switch process: F1: L TGTTTAAAAATTTGGTGTGTATCAATGTGTTAGAGAACTTA 1 F3: 4 TATGTAAATATATCAATACTAACTCTCTAAATAAAGGAAACTGTACACTT R RF: TGTTTAAAAATTTGGTGTCTATCAATGTGTTAGAGAACTTAGTTATCTTTAAAAATCTTAGTTATGTAAATGTATCAATACTAACTCTCTAAATAAAGGAAACTGTACACTT RR: ACAAATTTTTAAACCACAGATAGTTACACAATCTCTTGAATCAATAGAAATTTTTAGAATCAATACATTTACATAGTTATGATTGAGAGATTTATTTCCTTTGACATGTGAA F2: 3 CAATAGAAATTTTTAGAATCA 2 Unidirectional alignment (log-probability: -64.5) GTTTAAAAATTTGGTGTgTATCAATGTGTTAGAGAACTTA---------------------actaagatttttaaagataacTATGTAAATaTATCAATACTAACTCTCTAAATAAAGGAAA GTTTAAAAATTTGGTGTCTATCAATGTGTTAGAGAACTTAGTTATCTTTAAAAATCTTAGT---------------------TATGTAAATGTATCAATACTAACTCTCTAAATAAAGGAAA Template switch alignment (log-probability: -30) GTTTAAAAATTTGGTGTgTATCAATGTGTTAGAGAACTTA|ACTAAGATTTTTAAAGATAAC|TATGTAAATaTATCAATACTAACTCTCTAAATAAAGGAAA GTTTAAAAATTTGGTGTCTATCAATGTGTTAGAGAACTTA|ACTAAGATTTTTAAAGATAAC|TATGTAAATGTATCAATACTAACTCTCTAAATAAAGGAAA Human > Chimp ------------- chr14:38538661-38538681 Template switch process: F1: L TGTTTAAAAATTTGGTGTCTATCAATGTGTTAGAGAACTTA 1 F3: 4 TATGTAAATGTATCAATACTAACTCTCTAAATAAAGGAAACTGTACACTT R RF: TGTTTAAAAATTTGGTGTGTATCAATGTGTTAGAGAACTTAACTAAGATTTTTAAAGATAACTATGTAAATATATCAATACTAACTCTCTAAATAAAGGAAACTGTACACTT RR: ACAAATTTTTAAACCACACATAGTTACACAATCTCTTGAATTGATTCTAAAAATTTCTATTGATACATTTATATAGTTATGATTGAGAGATTTATTTCCTTTGACATGTGAA F2: 3 TGATTCTAAAAATTTCTATTG 2 Unidirectional alignment (log-probability: -64.5) GTTTAAAAATTTGGTGTcTATCAATGTGTTAGAGAACTTA---------------------gttatctttaaaaatcttagtTATGTAAATgTATCAATACTAACTCTCTAAATAAAGGAAA GTTTAAAAATTTGGTGTGTATCAATGTGTTAGAGAACTTAACTAAGATTTTTAAAGATAAC---------------------TATGTAAATATATCAATACTAACTCTCTAAATAAAGGAAA Template switch alignment (log-probability: -30) GTTTAAAAATTTGGTGTcTATCAATGTGTTAGAGAACTTA|GTTATCTTTAAAAATCTTAGT|TATGTAAATgTATCAATACTAACTCTCTAAATAAAGGAAA GTTTAAAAATTTGGTGTGTATCAATGTGTTAGAGAACTTA|GTTATCTTTAAAAATCTTAGT|TATGTAAATATATCAATACTAACTCTCTAAATAAAGGAAA ========== Event 1031 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTCTCTCTAGTCTTCCCCATATGTAC-----TTCACAGTGGTTTGTAGTAAACACATTTA Chimp: CCTTCTCTCTAGTCTTCCCCATATGTAC-----TTCACAGTGGTTTGTAGTAAACACATTTA ↓ 3 1 2 4 Gorilla: CCTTCTCTCTAGTCTTCCCCATATGTACTGAAGTACATATGGGTTTGTAGTAAACACATTTA ↑ 3 1 2 4 Human: CCTTCTCTCTAGTCTTCCCCATATGTAC-----TTCACAGTGGTTTGTAGTAAACACATTTA Cluster: [ ] Orangutan: CCTTCTCTCTAGTCTTCCCCATATGTAC-----TTCACAGTGGTTTGTAGTAAACACATTTA Human > Gorilla --------------- chr14:37446999-37447010 Template switch process: F1: L TCTTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACT 1 F3: 4 GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC R RF: TCTTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACTTCACAGTGGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC RR: AGAAAATTTAAAGGGAAGAGAGATCAGAAGGGGTATACATGAAGTGTCACCAAACATCATTTGTGTAAATCATAAAACAAAGATAAAAG F2: 3 GTATACATGAAG 2 Unidirectional alignment (log-probability: -38.3) TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTAC-------TgaagtacatatgGGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACTTCACAGT------------GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC Template switch alignment (log-probability: -17.3) TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACT|GAAGTACATATG|GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACT|GAAGTACATATG|GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC Chimp > Gorilla --------------- chr14:37446999-37447010 Template switch process: F1: L TCTTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACT 1 F3: 4 GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC R RF: TCTTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACTTCACAGTGGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC RR: AGAAAATTTAAAGGGAAGAGAGATCAGAAGGGGTATACATGAAGTGTCACCAAACATCATTTGTGTAAATCATAAAACAAAGATAAAAG F2: 3 GTATACATGAAG 2 Unidirectional alignment (log-probability: -38.3) TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTAC-------TgaagtacatatgGGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACTTCACAGT------------GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC Template switch alignment (log-probability: -17.3) TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACT|GAAGTACATATG|GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC TTTTAAATTTCCCTTCTCTCTAGTCTTCCCCATATGTACT|GAAGTACATATG|GGTTTGTAGTAAACACATTTAGTATTTTGTTTCTATTTTC ========== Event 1032 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTGTAAGCCCTAGAATTCCCTTCACCATTTGTGAAGGTGGGTTCCTGACTTTGGGGCTA ↑ 3 1 42 Chimp: TGTGTAAGCCCTAGAATTCCCTTCAC---------AAATGGGTTCCTGACTTTGGGGCTA Gorilla: TGTGTAAGCCCTAGAATTCCCTTCAC---------AAATGGGTTCCTGACTTTGGGGCTA ↓ 3 1 42 Human: TGTGTAAGCCCTAGAATTCCCTTCACCATTTGTGAAGGTGGGTTCCTGACTTTGGGGCTA Cluster: [ ] Orangutan: Chimp > Human ------------- chr1:45520306-45520317 Template switch process: F1: L CAAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC 1 F3: 4 TGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC R RF: CAAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCACAAATGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC RR: GTTTAGAAATCCATAACACATTCGGGATCTTAAGGGAAGTGTTTACCCAAGGACTGAAACCCCGATTATAGGGTCCCGCTTTTG F2: 3 GGAAGTGTTTAC 2 Unidirectional alignment (log-probability: -35.9) AAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCACcatttgtgaAggTGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC AAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC---------AAATGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC Template switch alignment (log-probability: -16.8) AAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC|CATTTGTGAAGG|TGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC AAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC|CATTTGTGAAGG|TGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC Gorilla > Human --------------- chr1:45520306-45520317 Template switch process: F1: L CAAATCTTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC 1 F3: 4 TGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC R RF: CAAATCTT-AGGTATTGTGTAAGCCCTAGAATTCCCTTCACAAATGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC RR: GTTTAGAA-TCCATAACACATTCGGGATCTTAAGGGAAGTGTTTACCCAAGGACTGAAACCCCGATTATAGGGTCCCGCTTTTG F2: 3 GGAAGTGTTTAC 2 Unidirectional alignment (log-probability: -46.1) AAATCtTTAGGTATTGTGTAAGCCCTAGAATTCCCTTCACcatttgtgaAggTGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC AAATC-TTAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC---------AAATGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC Template switch alignment (log-probability: -28.4) AAATCTTtAGGTATTGTGTAAGCCCTAGAATTCCCTTCAC|CATTTGTGAAGG|TGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC AAATCTT-AGGTATTGTGTAAGCCCTAGAATTCCCTTCAC|CATTTGTGAAGG|TGGGTTCCTGACTTTGGGGCTAATATCCCAGGGCGAAAAC ========== Event 1033 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GTTTTTTCTTAAAAAATTGTT------------A-CTGAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGTTCCTTAAAGATAAGCTCTCT ↑ 1 4 3 2 Chimp: GTTTTTTCTTAAAAAATTGTTTTAAGCTCAAAAGCTCAAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGTTCCTTAAAGATAAGCTCTCT ↓ 1 4 3 2 Gorilla: GTTTTTTCTTAAAAAATTGTT------------A-CTGAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGTTCCTTAAAGATAAGCTCTCT Human: GTTTTTTCTTAAAAAATTGTT------------A-CTGAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGTTCCTTAAAGATAAGCTCTCT Cluster: [ ] Orangutan: GTTTTTTCTTAAAAAATTGTT------------A-CTGAAAAAGCTATTGGCAACTCAAGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGTTCCTTAAAGATAAGCTCTCT Chimp > Human ------------- chr14:51607981-51607984 Template switch process: F1: L TGATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT 1 F3: 4 AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG R RF: TGATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTTTTAAGCTCAAAAGCTCAAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGT RR: ACTATAACTGATTAAGGAGACAAAAAAGAATTTTTTAACAAAATTCGAGTTTTCGAGTTTTTTCGAAAACCGTTGAGTCCCAATTATAGACAAAACTCAATATTTTTTATTAGAGTAAGAAATACGACTTATTTCGTCATTAACTCGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -26.3) GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT----------------ActgAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTTTTAAGCTCAAAAGCTCA---AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG Template switch alignment (log-probability: -15.8) GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT|ACTG|AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT|ACTG|AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG Chimp > Gorilla --------------- chr14:52273291-52273294 Template switch process: F1: L TGATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT 1 F3: 4 AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG R RF: TGATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTTTTAAGCTCAAAAGCTCAAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAGTTATAAAAAATAATCTCATTCTTTATGCTGAATAAAGCAGTAATTGAGCAGT RR: ACTATAACTGATTAAGGAGACAAAAAAGAATTTTTTAACAAAATTCGAGTTTTCGAGTTTTTTCGAAAACCGTTGAGTCCCAATTATAGACAAAACTCAATATTTTTTATTAGAGTAAGAAATACGACTTATTTCGTCATTAACTCGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -25.8) GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT----------------ActgAAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTTTTAAGCTCAAAAGCTCA---AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG Template switch alignment (log-probability: -16.2) GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT|ACTG|AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG GATATTGACTAATTCCTCTGTTTTTTCTTAAAAAATTGTT|ACTG|AAAAAGCTTTTGGCAACTCAGGGTTAATATCTGTTTTGAG ========== Event 1034 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: taggcaggcagtgcttgtggtcagCCTTCAGTCTG-GGTCCC------------TGTGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTGTCTGACCT Chimp: TAGGCAGGCAGTGCTTGTGGTCAGCCCTCAGTCTGGAGTCCC------------TGTGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTGTCTGACCT Gorilla: TAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGGAGTCCCTTCAGCCTTCAGTCTGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTGTCTGACCT ↑ 4 1 3 2 Human: taggcaggcagtgcttgtggtcagCCTTCAGTCTG-GGTCCC------------TGTGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTGTCTGACCT Cluster: [ ] Orangutan: TAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGGAGTCCC------------TGTGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTGTCTGACCT Human > Gorilla --------------- chr14:39515322-39515327 Template switch process: F1: L AAGTGCTAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGG 1 F3: 4 TTCAGCCTTCAGTC----------TGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTG R RF: AAGTGCTAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGGGTCCCTGTGGTCGGTAAGTTGAGGGGGATGGGACTCAGCTATTTCTG RR: TTCACGATCCGTCCGTCACGAACACCAGTCGGAAGTCAGACCCAGGGACACCAGCCATTCAACTCCCCCTACCCTGAGTCGATAAAGAC F2: 3 CCCTGA 2 Unidirectional alignment (log-probability: -44.9) GTGCTAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGGaGTCCCttcagccttcagTcTGGTCGGTAAGTTGAGGGGGATGGGA GTGCTAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGG-GTCCC------------TGTGGTCGGTAAGTTGAGGGGGATGGGA Template switch alignment (log-probability: -32.6) GTGCTAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGG|AGTCCC|tTCAGCCTTCAGTC----------TGGTCGGTAAGTTGAGGGGGATGGGA GTGCTAGGCAGGCAGTGCTTGTGGTCAGCCTTCAGTCTGG|AGTCCC|GTCAGCCTTCAGTCTGGGTCCCTGTGGTCGGTAAGTTGAGGGGGATGGGA ========== Event 1035 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTACTCTTTGCCGGTGTTTC------CATTACAGGAGAAGAGGGATGTGGAAGACC Chimp: TTTACTCTTTGCCGGTGTTTC------CATTACAGGAGAAGAGGGATGTGGAAGACC ↓ 13 4 2 Gorilla: TTTACTGTTTGCCGGTGTTTCTCCTGTAATGACAGGAGAAGAGGGATGTGGAAGACC Human: TTTACTCTTTGCCGGTGTTTC------CATTACAGGAGAAGAGGGATGTGGAAGACC Cluster: [ ] Orangutan: TTTACTCTTTGCCAGTGTTTC------CATTACAGGAGAAGAGGGATATGGAAGACC Chimp > Gorilla --------------- chr14:39448935-39448944 Template switch process: F1: L ACTATTTCTTTATTACTGACTTTACTGTTTGCCGGTGTTTC 1 F3: 4 ACAGGAGAAGAGGGATGTGGAAGACCCAGTTTGGAAGGGG R RF: ACTATTTCTTTATTACTGACTTTACTCTTTGCCGGTGTTTCCATTACAGGAGAAGAGGGATGTGGAAGACCCAGTTTGGAAGGGG RR: TGATAAAGAAATAATGACTGAAATGAGAAACGGCCACAAAGGTAATGTCCTCTTCTCCCTACACCTTCTGGGTCAAACCTTCCCC F2: 3 GTAATGTCCT 2 Unidirectional alignment (log-probability: -36.1) CTATTTCTTTATTACTGACTTTACTgTTTGCCGGTGTTTCtcctgtaATgACAGGAGAAGAGGGATGTGGAAGACCCAGTTTGGAAGGGG CTATTTCTTTATTACTGACTTTACTCTTTGCCGGTGTTTCC------ATTACAGGAGAAGAGGGATGTGGAAGACCCAGTTTGGAAGGGG Template switch alignment (log-probability: -22.5) CTATTTCTTTATTACTGACTTTACTgTTTGCCGGTGTTTC|TCCTGTAATG|ACAGGAGAAGAGGGATGTGGAAGACCCAGTTTGGAAGGGG CTATTTCTTTATTACTGACTTTACTCTTTGCCGGTGTTTC|TCCTGTAATG|ACAGGAGAAGAGGGATGTGGAAGACCCAGTTTGGAAGGGG ========== Event 1036 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGTACTTCCCTGAAAATGAATCCTCCCTTGC---------------------------------------------------------------------------------------------------------------------------------------------------------TGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTGTCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCCATAGTGACAGGTGAACCCTTAGACTGCAGCACAATGGTAGGAAGGAGATACTCTT Chimp: TCTGTACTTCCCTGAAAATGAATCCTCCCTTGCTGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTATCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCGACAGTGACAGATGAACCCTTAGACTACAGCACAATTCAGCAGACCTCCCTTGTTGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTATCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCCATAGTGGCAGGTGAACCCTTAGACTGCAGCACAATGGTAGGAAGGAGATACTCTT ↑ 4 3 2 1 Gorilla: TCTGTACTTCCCTGAAAATGAATCCTCCCTTGC---------------------------------------------------------------------------------------------------------------------------------------------------------TGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTATCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCCATAGTGACAGGTGAACCCTTAGACTGCAGCACAATGGTAGGAAGGAGATACTCTT Human: TCTGTACTTCCCTGAAAATGAATCCTCCCTTGC---------------------------------------------------------------------------------------------------------------------------------------------------------TGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTGTCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCCATAGTGACAGGTGAACCCTTAGACTGCAGCACAATGGTAGGAAGGAGATACTCTT Cluster: [ ] Orangutan: TCTGTACTTCCCTGAAAATGAATCCTCTCTTGC---------------------------------------------------------------------------------------------------------------------------------------------------------TGAGTGCAGTTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAGATTTTTTATCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGTCCATAGTGATAGGTGAACCCTTAGACTGCAGCACAATGCTAGGAAGGAGATACTCTT Gorilla > Chimp --------------- chr14:41751568-41751573 Template switch process: F1: L CCCCTCCCTCTGTACTTCCCTGAAAATGAATCCTCCCTTGCTGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTATCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCGACAGTGACAGATGAACCCTTAGACTACAGCACAAT 1 F3: 4 GA--CCTCCCTTGTTGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTT R RF: CCCCTCCCTCTGTACTTCCCTGAAAATGAATCCTCCCTTGCTGAATGCAGCTTATCAAGATATAAGTGAATCAGTAGCCTTGAGTCTTGGAAATTTTTTATCTCTTCTGTTTGTTCCCAAAGACCATCACTTACAAAGCCCATAGTGACAGGTGAACCCTTAGACTGCAGCACAAT RR: GGGGAGGGAGACATGAAGGGACTTTTACTTAGGAGGGAACGACTTACGTCGAATAGTTCTATATTCACTTAGTCATCGGAACTCAGAACCTTTAAAAAATAGAGAAGACAAACAAGGGTTTCTGGTAGTGAATGTTTCGGGTATCACTGTCCACTTGGGAATCTGACGTCGTGTTA F2: 3 ACGACT 2 Unidirectional alignment (log-probability: -228) agccgacagtgacagatgaacccttagactacagcacaattcagcagacctcccttgttgaatgcagcttatcaagatataagtga -------------------------------------------------------------------------------------- Template switch alignment (log-probability: -57) AGCCgAcAGTGACAGaTGAACCCTTAGACTaCAGCACAAT|TCAGCA|GA--CCTCCCTTGtTGAATGCAGCTTATCAAGATATAAGTGA AGCCCATAGTGACAGGTGAACCCTTAGACTGCAGCACAAT|TCAGCA|GAATCCTCCCTTGCTGAATGCAGCTTATCAAGATATAAGTGA ========== Event 1037 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGTCATTGCACACACACACG----CACGC--------ATGCGTGCACATATGTATTTTTTTCTCC ↓ 1 3 4 2 Chimp: GAGTCATTGCACACACACACG--CGCACGC----ATGCGTGCGTGCACATACGTAtttttttCTCC Gorilla: GAGTCATTGcacacacacacacG--CGCGCATGC----ATGCGTGCACATATGTAtttttttCTCC Human: GAGTCATTGCACACACACACG----CACGC--------ATGCGTGCACATATGTATTTTTTTCTCC Cluster: [ ] Orangutan: GAGTCATTGCACACACACATGCA--CGCGTGTGC----ATATGTGCACATATGTAT-TTTTTCTCC Human > Chimp ------------- chr14:44566422-44566432 Template switch process: F1: L TATACTGTTCGGGGGAGGGGGAGTCATTGCACACACACACGC 1 F3: 4 TGCGTGCACATACGTATTTTTTTCTCCCTGAAAGTAACAT R RF: TATACTGTTCGGGGGAGGGGGAGTCATTGCACACACACACGCACGCATGCGTGCACATATGTATTTTTTTCTCCCTGAAAGTAACAT RR: ATATGACAAGCCCCCTCCCCCTCAGTAACGTGTGTGTGTGCGTGCGTACGCACGTGTATACATAAAAAAAGAGGGACTTTCATTGTA F2: 3 GCGTACGCACG 2 Unidirectional alignment (log-probability: -35.8) TACTGTTCGGGGGAGGGGGAGTCATTGCACACACACAcgCGCACGCAtgcgTGCGTGCACATAcGTATTTTTTTCTCCCTGAAAGTAACAT TACTGTTCGGGGGAGGGGGAGTCATTGCACACACACA--CGCACGCA----TGCGTGCACATATGTATTTTTTTCTCCCTGAAAGTAACAT Template switch alignment (log-probability: -22.7) TACTGTTCGGGGGAGGGGGAGTCATTGCACACACACACGC|GCACGCATGCG|TGCGTGCACATAcGTATTTTTTTCTCCCTGAAAGTAACAT TACTGTTCGGGGGAGGGGGAGTCATTGCACACACACACGC|GCACGCATGCG|TGCGTGCACATATGTATTTTTTTCTCCCTGAAAGTAACAT ========== Event 1038 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAGCTAGCATTTGCATACAGACCTTTACTATAATTCTACTTCGGGGAAAGGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC------CACTGCACTAAATAAGGTATGTC ↓ 3 2 1 4 Chimp: AAGCTAGCATTTGCATAGAGACCTTTACTATAATTCTACTTCGGGGAAAGGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC---AGGTCCTGCACTAAATAAGGTATGTC Gorilla: AAGCTAGCATTTGCATAGAGACCTTTACTATAATTCTACTTCGGGGAAAGGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGCAGG---TCCTGCACTAAATAAGGTATATC ↑ 3 2 1 4 Human: AAGCTAGCATTTGCATACAGACCTTTACTATAATTCTACTTCGGGGAAAGGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC------CACTGCACTAAATAAGGTATGTC Cluster: [ ] Orangutan: AAGCTAGCACCTTCCTAGAGACCTTTACTATAATTCTACTTTGGGGAAAGGAAGGGCAAATTCAACTAATA--CTGATTTCCATTAATGCAGG---TCCTGCACTAAGTAAGGTATGTC Human > Chimp ------------- chr14:46888082-46888086 Template switch process: F1: L GGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC 1 F3: 4 CTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC R RF: GACCTTTACTATAATTCTACTTCGGGGAAAGGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGCCACTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC RR: CTGGAAATGATATTAAGATGAAGCCCCTTTCCTTCCCGTTTAAGTTGATTATGAGACTAAAGGTAATTACGGTGACGTGATTTATTCCATACAGAAATGAAGGTGGTACTAAG F2: 3 CTGGA 2 Unidirectional alignment (log-probability: -26.9) GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGCaggtC-CTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC----CACTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC Template switch alignment (log-probability: -15.9) GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC|AGGTC|CTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC|AGGTC|CTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC Human > Gorilla --------------- chr14:46905056-46905060 Template switch process: F1: L GGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC 1 F3: 4 CTGCACTAAATAAGGTATATCTTTACTTCCACCATGATTC R RF: GACCTTTACTATAATTCTACTTCGGGGAAAGGAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGCCACTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC RR: CTGGAAATGATATTAAGATGAAGCCCCTTTCCTTCCCGTTTAAGTTGATTATGAGACTAAAGGTAATTACGGTGACGTGATTTATTCCATACAGAAATGAAGGTGGTACTAAG F2: 3 CTGGA 2 Unidirectional alignment (log-probability: -31.8) GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGCaggtcCTGCACTAAATAAGGTATaTCTTTACTTCCACCATGATTC GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC---CACTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC Template switch alignment (log-probability: -21.9) GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC|AGGTC|CTGCACTAAATAAGGTATaTCTTTACTTCCACCATGATTC GAAGGGCAAATTCAACTAATACTCTGATTTCCATTAATGC|AGGTC|CTGCACTAAATAAGGTATGTCTTTACTTCCACCATGATTC ========== Event 1039 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGACTGCAGATCCCCTTCTGC---------CACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTTCTTT Chimp: TGACTGCAGATCCCCTTCTGC---------CACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTCCTTT ↓ 1 4 3 2 Gorilla: TGACTGCAGATCCCCTTCTGC------------------AATGACACACTAAGTCATTGGCAGGCAGGGGAGTCCTTT ↑ 1 4 3 2 Human: TGACTGCAGATCCCCTTCTGC---------CACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTTCTTT Cluster: [ ] Orangutan: TGACTGCAGATCCCCTTCTGCCACAGTTAC---------CATGTGACACTAAGTCATTGGCAGGCAGAGGAGTCCTTT Human > Gorilla --------------- chr14:48264498-48264503 Template switch process: F1: L TGTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC 1 F3: 4 ACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC R RF: TGTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGCCACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTTCTTTTGAATTC RR: ACATAGAAATTTCTCGGATCACTGACGTCTAGGGGAAGACGGTGTCAATAGTACACTGTGATTCAGTAACCGTCCGTCCCCTCAAGAAAACTTAAG F2: 3 CAGTAA 2 Unidirectional alignment (log-probability: -33.5) GTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC---------aATGacACACTAAGTCATTGGCAGGCAGGGGAGTcCTTTTGAATTC GTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGCCACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTTCTTTTGAATTC Template switch alignment (log-probability: -22) GTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC|AATGAC|ACACTAAGTCATTGGCAGGCAGGGGAGTcCTTTTGAATTC GTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC|AATGAC|ACACTAAGTCATTGGCAGGCAGGGGAGTTCTTTTGAATTC Chimp > Gorilla --------------- chr14:48264498-48264503 Template switch process: F1: L TGTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC 1 F3: 4 ACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC R RF: TATATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGCCACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC RR: ATATAGAAATTTCTCGGATCACTGACGTCTAGGGGAAGACGGTGTCAATAGTACACTGTGATTCAGTAACCGTCCGTCCCCTCAGGAAAACTTAAG F2: 3 CAGTAA 2 Unidirectional alignment (log-probability: -33.5) gTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC---------aATGacACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC ATATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGCCACAGTTATCATGTGACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC Template switch alignment (log-probability: -22) gTATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC|AATGAC|ACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC ATATCTTTAAAGAGCCTAGTGACTGCAGATCCCCTTCTGC|AATGAC|ACACTAAGTCATTGGCAGGCAGGGGAGTCCTTTTGAATTC ========== Event 1040 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTACCCAGTTTTTAAATGAAGCTGTGGTTCCCATTTAATGGCTATGCCTGAA Chimp: TCTACCCAGTTTTTAAATGAAGCTGTGGTTCCCATTTAATGGCTATGCCTGAA ↓ 3 1 2 4 Gorilla: TCTACCCAGTTTTTAAATGAAGCCACAGCT-TCATTTAATGGCTATGCCTGAA ↑ 3 1 2 4 Human: TCTACCCAGTTTTTAAATGAAGCTGTGGTTCCCATTTAATGGCTATGCCTGAA Cluster: [ ] Orangutan: TCTACCCAGTTTTTAAATGAAGCTGTGGTTCCCATTTAATGGCTATGCCTGAA Human > Gorilla --------------- chr14:45327568-45327575 Template switch process: F1: L AAGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGC 1 F3: 4 CATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA R RF: AAGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGCTGTGGTTCCCATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA RR: TTCTAACCTGTGGGGACGAGATGGGTCAAAAATTTACTTCGACACCAAGGGTAAATTACCGATACGGACTTCTATGTACCTTGTTATTTT F2: 3 TTCGACAC 2 Unidirectional alignment (log-probability: -31.1) AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAG--------CCacagcttCATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGCTGTGGTTCC-------CATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA Template switch alignment (log-probability: -16.7) AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGC|CACAGCTT|CATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGC|CACAGCTT|CATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA Chimp > Gorilla --------------- chr14:45327568-45327575 Template switch process: F1: L AAGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGC 1 F3: 4 CATTTAATGGCTATGCCTGAAGATACATGGAACAATAAAA R RF: AAGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGCTGTGGTTCCCATTTAATGGCTATGCCTGAAGACACATGGAACAATAAAA RR: TTCTAACCTGTGGGGACGAGATGGGTCAAAAATTTACTTCGACACCAAGGGTAAATTACCGATACGGACTTCTGTGTACCTTGTTATTTT F2: 3 TTCGACAC 2 Unidirectional alignment (log-probability: -36.6) AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAG--------CCacagcttCATTTAATGGCTATGCCTGAAGAtACATGGAACAATAAAA AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGCTGTGGTTCC-------CATTTAATGGCTATGCCTGAAGACACATGGAACAATAAAA Template switch alignment (log-probability: -22.3) AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGC|CACAGCTT|CATTTAATGGCTATGCCTGAAGAtACATGGAACAATAAAA AGATTGGACACCCCTGCTCTACCCAGTTTTTAAATGAAGC|CACAGCTT|CATTTAATGGCTATGCCTGAAGACACATGGAACAATAAAA ========== Event 1041 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA--CTTAA---------TCTTTAAAATTCACATCCTTCA Chimp: TAGATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA--CTTAA---------TCTTTAAAATTCACATCCTTCA ↓ 3 2 1 4 Gorilla: TAGATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGATAGTGGATCACCAAAGGATTTAAAATTCACATCCTTCA ↑ 3 2 1 4 Human: TAGATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA--CTTAA---------TCTTTAAAATTCACATCCTTCA Cluster: [ ] Orangutan: TAGATAAGAATATTGCAACCCTATGGTGATCCACTATCCTGGA--CTTAA---------TCTTTAAAATTCACATCCTTCA Human > Gorilla --------------- chr14:47894866-47894882 Template switch process: F1: L GATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA 1 F3: 4 ATTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTTA R RF: GATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGACTTAATCTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTTA RR: CTATTCTTATAACGTTGGGAAACCACTAGGTGATAGGACCTGAATTAGAAATTTTAAGTGTAGGAAGTCTCTTTCCTTAAGTAAAAAT F2: 3 GGAAACCACTAGGTGAT 2 Unidirectional alignment (log-probability: -46.9) ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGgatagtggatcaccaaagGA-------TTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTG------------------GACTTAATCTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT Template switch alignment (log-probability: -23.4) ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA|TAGTGGATCACCAAAGG|aTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA|TAGTGGATCACCAAAGG|CTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT Chimp > Gorilla --------------- chr14:47894866-47894882 Template switch process: F1: L GATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA 1 F3: 4 ATTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTTA R RF: GATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGACTTAATCTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTTA RR: CTATTCTTATAACGTTGGGAAACCACTAGGTGATAGGACCTGAATTAGAAATTTTAAGTGTAGGAAGTCTCTTTCCTTAAGTAAAAAT F2: 3 GGAAACCACTAGGTGAT 2 Unidirectional alignment (log-probability: -46.9) ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGgatagtggatcaccaaagGA-------TTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTG------------------GACTTAATCTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT Template switch alignment (log-probability: -23.4) ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA|TAGTGGATCACCAAAGG|aTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT ATAAGAATATTGCAACCCTTTGGTGATCCACTATCCTGGA|TAGTGGATCACCAAAGG|CTTTAAAATTCACATCCTTCAGAGAAAGGAATTCATTTTT ========== Event 1042 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATACTTATTTGAATATTTATG-------ACTGGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGGAATTTACAAGAAATTCTCCAAAATACTCAGTTATCACTGAGGACTAATGTG Chimp: ATACTTATTTGAATATTTATG-------ACTGGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGGAATTTACAAGAAATTCTCCAAAATACTCAGTTATCACTGAGGACTAATGTG ↑ 1 4 3 2 Gorilla: ATACTTATTTGAATATTTATGTTAATTTTTTAGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGGAATTTACAAGAAATTCTCCAAAATACTCAGTTATCACTGAGGACTAATGTG ↓ 1 4 3 2 Human: ATACTTATTTGAATATTTATG-------ACTGGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGGAATTTACAAGAAATTCTCCAAAATACTCAGTTATCACTGAGGACTAATGTG Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr14:43273231-43273234 Template switch process: F1: L TGCCCAGCCATCATT---TTATACTTATTTGAATATTTATG 1 F3: 4 GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG R RF: TGCCCAGCCATCATTTTATTATACTTATTTGAATATTTATGTTAATTTTTTAGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGGAATTTACAAGAAATTCTCCAAAATACTCAGT RR: ACGGGTCGGTAGTAAAATAATATGAATAAACTTATAAATACAATTAAAAAATCAATCGATTTTTTGATAAGTTACTTCGAAAGTAGGTGTCCTTAAATGTTCTTTAAGAGGTTTTATGAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -35.3) TGCCCAGCCATCATTTTAT---ACTTATTTGAATATTTATG----------ActgGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG TGCCCAGCCATCATTTTATTATACTTATTTGAATATTTATGTTAATTTTTTA---GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG Template switch alignment (log-probability: -26) TGCCCAGCCATCATT---TTATACTTATTTGAATATTTATG|ACTG|GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG TGCCCAGCCATCATTTTATTATACTTATTTGAATATTTATG|ACTG|GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG Gorilla > Chimp --------------- chr14:43858225-43858228 Template switch process: F1: L TGCCCAGCCATCATT---TTATACTTATTTGAATATTTATG 1 F3: 4 GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG R RF: TGCCCAGCCATCATTTTATTATACTTATTTGAATATTTATGTTAATTTTTTAGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGGAATTTACAAGAAATTCTCCAAAATACTCAGT RR: ACGGGTCGGTAGTAAAATAATATGAATAAACTTATAAATACAATTAAAAAATCAATCGATTTTTTGATAAGTTACTTCGAAAGTAGGTGTCCTTAAATGTTCTTTAAGAGGTTTTATGAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -35.3) TGCCCAGCCATCATTTTAT---ACTTATTTGAATATTTATG----------ActgGTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG TGCCCAGCCATCATTTTATTATACTTATTTGAATATTTATGTTAATTTTTTA---GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG Template switch alignment (log-probability: -26) TGCCCAGCCATCATT---TTATACTTATTTGAATATTTATG|ACTG|GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG TGCCCAGCCATCATTTTATTATACTTATTTGAATATTTATG|ACTG|GTTAGCTAAAAAACTATTCAATGAAGCTTTCATCCACAGG ========== Event 1043 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GCACAAGCGGATATTTTAGAGGTA---CAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTATACCTGAGCAAGTGAAATTAAGA ↑ 1 4 3 2 Chimp: GCACAAGCGGATATTTTAGAGTAATATTAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTGTACCTGAGCAAGTGAAATTAAGA ↓ 1 4 3 2 Gorilla: GCACAAGCGGATATTTTAGAGGTA---CAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTATATCTGAGCAAGTGAAATTAAGA Human: GCACAAGCGGATATTTTAGAGGTA---CAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTATACCTGAGCAAGTGAAATTAAGA Cluster: [ ] Orangutan: GCACAAGCGGATATTTTAGAGGTA---CAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTATACCTGAGCAAGTGAAATTAAGA Chimp > Human ------------- chr14:42706223-42706226 Template switch process: F1: L TTTTACAGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG 1 F3: 4 AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG R RF: TTTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAGTAATATTAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTGTAC RR: AAAATGGCAAGAGTTTCAAACGTGTTCGCCTATAAAATCTCATTATAATCACATTATATTCTCGAAGACTTTTACAGGTGAATTCAACAAAACATG F2: 3 CATG 2 Unidirectional alignment (log-probability: -33.2) TTTACaGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG-------gtacAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG TTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAGTAATATT----AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG Template switch alignment (log-probability: -21.8) TTTACaGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG|GTAC|AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG TTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG|GTAC|AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG Chimp > Gorilla --------------- chr14:43291574-43291577 Template switch process: F1: L TTTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG 1 F3: 4 AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG R RF: TTTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAGTAATATTAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTGTTTTGTAC RR: AAAATGGCAAGAGTTTCAAACGTGTTCGCCTATAAAATCTCATTATAATCACATTATATTCTCGAAGACTTTTACAGGTGAATTCAACAAAACATG F2: 3 CATG 2 Unidirectional alignment (log-probability: -26.7) TTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG-------gtacAGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG TTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAGTAATATT----AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG Template switch alignment (log-probability: -16.2) TTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG|GTAC|AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG TTTACCGTTCTCAAAGTTTGCACAAGCGGATATTTTAGAG|GTAC|AGTGTAATATAAGAGCTTCTGAAAATGTCCACTTAAGTTG ========== Event 1044 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ACAGAGATTGGATGGCTGGGT---------------------------GACTACTTTGGTGCATTTCCAGAGC ↑ 13 2 4 Chimp: ATAGAGATTGGATGGCTGGGTAGTCATCCAAACTTGATGCACAAAGTAGTTAACTTTGGTGCATTTCCAGAGC Gorilla: ACAGAAATTGGATGGCTGGGT---------------------------GACTACTTTGGTGCATTTCCAGAGC Human: ACAGAGATTGGATGGCTGGGT---------------------------GACTACTTTGGTGCATTTCCAGAGC Cluster: [ ] Orangutan: ACAGAGATTGGATGGCTGGGT---------------------------GACTGCTTTGGTGCATTTCCAGAGC Chimp > Human ------------- chr14:63961402-63961405 Template switch process: F1: L CTTGCAGCAAGGCTGAGTAAACAGAGATTGGATGGCTGGGT 1 F3: 4 ACTTTGGTGCATTTCCAGAGCCTGTGAACCAAATGGCAGA R RF: CTTGCAGCAAGGCTGAGTAAATAGAGATTGGATGGCTGGGTAGTCATCCAAACTTGATGCACAAAGTAGTTAACTTTGGTGCATTTCCAGAGCCTGTGAACCAAATGGCAGA RR: GAACGTCGTTCCGACTCATTTATCTCTAACCTACCGACCCATCAGTAGGTTTGAACTACGTGTTTCATCAATTGAAACCACGTAAAGGTCTCGGACACTTGGTTTACCGTCT F2: 3 TCAG 2 Unidirectional alignment (log-probability: -34.5) TTGCAGCAAGGCTGAGTAAAcAGAGATTGGATGGCTGGGtgacTA-------------------------------CTTTGGTGCATTTCCAGAGCCTGTGAACCAAATGGCAGA TTGCAGCAAGGCTGAGTAAATAGAGATTGGATGGCTGGG----TAGTCATCCAAACTTGATGCACAAAGTAGTTAACTTTGGTGCATTTCCAGAGCCTGTGAACCAAATGGCAGA Template switch alignment (log-probability: -21.8) TTGCAGCAAGGCTGAGTAAAcAGAGATTGGATGGCTGGGT|GACT|ACTTTGGTGCATTTCCAGAGCCTGTGAACCAAATGGCAGA TTGCAGCAAGGCTGAGTAAATAGAGATTGGATGGCTGGGT|GACT|ACTTTGGTGCATTTCCAGAGCCTGTGAACCAAATGGCAGA ========== Event 1045 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTAGTACCGTATGACCTTGAAG--ATTAGCTCCTTCCTGTTTACACTGAATT ↓ 1 34 2 Chimp: TCCTAGTACCATATGACCTTGGAGCTAATAGCTCCTTCCTGTTTACACTGAATT Gorilla: TCCTAGTACCATATGACCTTGAAG--ATTAGCTCCTTCCTGTTTACACTGAATT Human: TCCTAGTACCGTATGACCTTGAAG--ATTAGCTCCTTCCTGTTTACACTGAATT Cluster: [ ] Orangutan: TCCTAGTACCGTATGACCTTGAAG--ATTAGCTCCTTCCTGTTTACACTGAATT Human > Chimp ------------- chr14:48547423-48547429 Template switch process: F1: L CCACTGACAAGGAGGGACTTTCCTAGTACCATATGACCTTG 1 F3: 4 TAGCTCCTTCCTGTTTACACTGAATTGCTCTCACTATCAG R RF: CCACTGACAAGGAGGGACTTTCCTAGTACCGTATGACCTTGAAGATTAGCTCCTTCCTGTTTACACTGAATTGCTCTCACTATCAG RR: GGTGACTGTTCCTCCCTGAAAGGATCATGGCATACTGGAACTTCTAATCGAGGAAGGACAAATGTGACTTAACGAGAGTGATAGTC F2: 3 AATCGAG 2 Unidirectional alignment (log-probability: -31.8) CACTGACAAGGAGGGACTTTCCTAGTACCaTATGACCTTGgAGctAaTAGCTCCTTCCTGTTTACACTGAATTGCTCTCACTATCAG CACTGACAAGGAGGGACTTTCCTAGTACCGTATGACCTTGAAG--ATTAGCTCCTTCCTGTTTACACTGAATTGCTCTCACTATCAG Template switch alignment (log-probability: -22.1) CACTGACAAGGAGGGACTTTCCTAGTACCaTATGACCTTG|GAGCTAA|TAGCTCCTTCCTGTTTACACTGAATTGCTCTCACTATCAG CACTGACAAGGAGGGACTTTCCTAGTACCGTATGACCTTG|GAGCTAA|TAGCTCCTTCCTGTTTACACTGAATTGCTCTCACTATCAG ========== Event 1046 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTCAGTGTGTAGTAAAATCT----------TCGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAA Chimp: CTTCAGTGTGTAGTAAAATCTTATACACGTGTAGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAA ↑ 1 4 3 2 Gorilla: CTTCAGTGTGTAGTAAAATCT----------TCGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAA Human: CTTCAGTGTGTAGTAAAATCT----------TCGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAA Cluster: [ ] Orangutan: CTTCAGTGTGTAGTAAAATCT----------TTGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAG Gorilla > Chimp --------------- chr14:48496772-48496782 Template switch process: F1: L TATGTACCATCACATCCTAACTTCAGTGTGTAGTAAAATCTT 1 F3: 4 GAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAAC R RF: TATGTACCATCACATCCTAACTTCAGTGTGTAGTAAAATCTTCGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAAC RR: ATACATGGTAGTGTAGGATTGAAGTCACACATCATTTTAGAAGCTTTTCAGATGTGCACATATAAGAGTGTCCGAGATCGTTG F2: 3 ATGTGCACATA 2 Unidirectional alignment (log-probability: -30.8) TGTACCATCACATCCTAACTTCAGTGTGTAGTAAAATCTtatacacgtgTaGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAAC TGTACCATCACATCCTAACTTCAGTGTGTAGTAAAATCT----------TCGAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAAC Template switch alignment (log-probability: -17.2) TGTACCATCACATCCTAACTTCAGTGTGTAGTAAAATCTT|ATACACGTGTA|GAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAAC TGTACCATCACATCCTAACTTCAGTGTGTAGTAAAATCTT|ATACACGTGTA|GAAAAGTCTACACGTGTATATTCTCACAGGCTCTAGCAAC ========== Event 1047 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: gaagggagagattAATTCTCCCACCAGAATTAATCTCTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCTTGGAATCCAGAAAGACT ↑ 4 3 2 Chimp: gaagggagagattAATTCTCC---------------CTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCTTGGAATCCAGAAAGACT Gorilla: gaagggagagattAATTCTCCCACCAGAGTTAATATCTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCTTGGAATCCAGAAAGACT Human: gaagggagagattAATTCTCCCACCAGAATTAATCTCTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCTTGGAATCCAGAAAGACT Cluster: [ ] Orangutan: gaagggagagattAATTCT-CCACCAGTGTTAATCTCTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCTTGGAATCCAGAAAGACT Chimp > Human ------------- chr14:64922806-64922819 Template switch process: F1: L GAGAGATTCCTCAATATATAGAAGGGAGAGATTAATTCTCCC 1 F3: 4 CTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCT R RF: GAGAGATTCCTCAATATATAGAAGGGAGAGATTAATTCTCCCTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCT RR: CTCTCTAAGGAGTTATATATCTTCCCTCTCTAATTAAGAGGGAAGGAGTTATGTATCTTCCCTCTCTAATTAAGACCACGA F2: 3 TCTAATTAAGACCA 2 Unidirectional alignment (log-probability: -32.5) GAGATTCCTCAATATATAGAAGGGAGAGATTAATTCTCCCaccagaattaatctcTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCT GAGATTCCTCAATATATAGAAGGGAGAGATTAATTCTCCC---------------TTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCT Template switch alignment (log-probability: -17) GAGATTCCTCAATATATAGAAGGGAGAGATTAATTCTCCC|ACCAGAATTAATCT|CTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCT GAGATTCCTCAATATATAGAAGGGAGAGATTAATTCTCCC|ACCAGAATTAATCT|CTTCCTCAATACATAGAAGGGAGAGATTAATTCTGGTGCT ========== Event 1048 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGGGGAGGGCAATAGGGGATAGTGCTGTTCTCCC ↓ 3 2 1 4 Chimp: TCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG------ACTTGAGGGGATAGTGCTGTTCTCCC ↑ 3 2 1 4 Gorilla: TCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGGGGAGGGCAATAGGGGATAGTGCTGTTCTCCC Human: TCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGGGGAGGGCAATAGGGGATAGTGCTGTTCTCCC Cluster: [ ] Orangutan: TCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGGGGAGGGCAATAGAGGATAGTGCTGTTCTCCC Human > Chimp ------------- chr14:49278942-49278946 Template switch process: F1: L GAGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG 1 F3: 4 AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC R RF: GAGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGGGGAGGGCAATAGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC RR: CTCATCGAGTCAAGTCTTTACGATAAGTTCAAATCCCTTTCCCCTCCCGTTATCCCCTATCACGACAAGAGGGGACTCTTTTCCACCTGTAG F2: 3 GTTCA 2 Unidirectional alignment (log-probability: -27.4) AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGacttG----------AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG----GGGAGGGCAATAGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC Template switch alignment (log-probability: -15.9) AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG|ACTTG|AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG|ACTTG|AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC Gorilla > Chimp --------------- chr14:49278942-49278946 Template switch process: F1: L GAGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG 1 F3: 4 AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC R RF: GAGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGGGGAGGGCAATAGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC RR: CTCATCGAGTCAAGTCTTTACGATAAGTTCAAATCCCTTTCCCCTCCCGTTATCCCCTATCACGACAAGAGGGGACTCTTTTCCACCTGTAG F2: 3 GTTCA 2 Unidirectional alignment (log-probability: -26.9) AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAGacttG----------AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG----GGGAGGGCAATAGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC Template switch alignment (log-probability: -16.4) AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG|ACTTG|AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC AGTAGCTCAGTTCAGAAATGCTATTCAAGTTTAGGGAAAG|ACTTG|AGGGGATAGTGCTGTTCTCCCCTGAGAAAAGGTGGACATC ========== Event 1049 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAGTAGTAAACTTAAACACCATATTTTACTATATCTCAACAGATAGAATATAAGACCAATT-TTTTTATTGGTAAAAAGTTCCCATACTTTTTACCAATAAAAAAATTGGTCTTATATTCTATCTGTTGAGATACAGTAAAATATGGTAAAGTCATGAGGTTTTTGGTGT Chimp: AGAAGTAGTAAACTTAAACACCATATTTTACTATATCTCAACAGATAGAATGTAAGACCAAtt-tttttATTGGTAAAAAGTTCCCATACT----------------------------------------------------------AAGAGTCATGAGGTTTTTGGTGT Gorilla: AGAAGTAGTAAACTTAAACACCATATTTTACTATATCTCAACAGATAGAATATAAGACCAAtt-tttttATTGGTAAAAAGTTCCCATACT----------------------------------------------------------AAGAGTCATGAGGTTTTTGGTGT ↓ 3 2 1 4 Human: AGAAGTAGTAAACTTAAACACCATATTTTACTATATCTCAACAGATAGAATATAAGACCAATT-TTTTTATTGGTAAAAAGTTCCCATACTTTTTACCAATAAAAAAATTGGTCTTATATTCTATCTGTTGAGATACAGTAAAATATGGTAAAGTCATGAGGTTTTTGGTGT Cluster: [ ] Orangutan: AGAAGTAGTAAACTT--ACACCATATTTTACTATATCTCAACAGATAGAATTTAAGACCAAttttttttACTGGTAAAAAGTTCCCATACT----------------------------------------------------------AAGAGTCATGGGGTTTTTGGTGT Gorilla > Human --------------- chr14:41512754-41512812 Template switch process: F1: L ATATAAGACCAATTTTTTTATTGGTAAAAAGTTCCCATACT 1 F3: 4 AAAGTCATGAGGTTTTTGGTGTTGTTACATCAAATTCTGGGG R RF: ACCATATTTTACTATATCTCAACAGATAGAATATAAGACCAATTTTTTTATTGGTAAAAAGTTCCCATACTAAGAGTCATGAGGTTTTTGGTGTTGTTACATCAAATTCTGGGG RR: TGGTATAAAATGATATAGAGTTGTCTATCTTATATTCTGGTTAAAAAAATAACCATTTTTCAAGGGTATGATTCTCAGTACTCCAAAAACCACAACAATGTAGTTTAAGACCCC F2: 3 TGGTATAAAATGACATAGAGTTGTCTATCTTATATTCTGGTTAAAAAAATAACCATTTT 2 Unidirectional alignment (log-probability: -105) TATAAGACCAATTTTTTTATTGGTAAAAAGTTCCCATACTttttaccaataaaaaaattggtcttatattctatctgttgagatacagtaaaatatggtAaAGTCATGAGGTTTTTGGTGTTGTTACATCAAATTCTGG TATAAGACCAATTTTTTTATTGGTAAAAAGTTCCCATACT----------------------------------------------------------AAGAGTCATGAGGTTTTTGGTGTTGTTACATCAAATTCTGG Template switch alignment (log-probability: -34.3) TATAAGACCAATTTTTTTATTGGTAAAAAGTTCCCATACT|TTTTACCAATAAAAAAATTGGTCTTATATTCTATCTGTTGAGATAcAGTAAAATATGGT|AaAGTCATGAGGTTTTTGGTGTTGTTACATCAAATTCTGG TATAAGACCAATTTTTTTATTGGTAAAAAGTTCCCATACT|TTTTACCAATAAAAAAATTGGTCTTATATTCTATCTGTTGAGATATAGTAAAATATGGT|AGAGTCATGAGGTTTTTGGTGTTGTTACATCAAATTCTGG ========== Event 1050 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCCTGTCCACCAAGGATAGATGGGCTGACTGTGGTTGGGTCAG-TCGAGATTTAACAGACAACTTA ↓ 13 24 ↑ 13 24 Chimp: CCCTGTCCACCAAGGATAGAT-GACTGACCCAACCACAGTCAGCCCGAGATTTAACAGACAACTTA Gorilla: CCCTGTCCACCAAGGATAGAT-GACTGACCCAACCACAGTCAGCCCGAGATTTAACAGACAACTTA ↓ 13 24 ↑ 13 24 Human: CCCTGTCCACCAAGGATAGATGGGCTGACTGTGGTTGGGTCAG-TCGAGATTTAACAGACAACTTA Cluster: [ ] Orangutan: CCCTGTCCACCCAGGACAGAT-GACTGACCCAACCACAGTCAGCCCGAGATGTAACAGACAACTTA Chimp > Human ------------- chr14:66057779-66057800 Template switch process: F1: L CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG 1 F3: 4 CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG R RF: CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGACTGACCCAACCACAGTCAGCCCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG RR: GACGTGGAAACAAGAACCTCGGGACAGGTGGTTCCTATCTACTGACTGGGTTGGTGTCAGTCGGGCTCTAAATTGTCTGTTGAATAAAATTTACTCCTTTCCTC F2: 3 TGACTGGGTTGGTGTCAGTCGG 2 Unidirectional alignment (log-probability: -53.9) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG----------------------ggctgactgtggttgggtcagtCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGACTGACCCAACCACAGTCAGCC----------------------CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Template switch alignment (log-probability: -18) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|GGCTGACTGTGGTTGGGTCAGT|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|GGCTGACTGTGGTTGGGTCAGT|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Human > Chimp ------------- chr14:50424431-50424452 Template switch process: F1: L CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG 1 F3: 4 CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG R RF: CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGGGCTGACTGTGGTTGGGTCAGTCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG RR: GACGTGGAAACAAGAACCTCGGGACAGGTGGTTCCTATCTACCCGACTGACACCAACCCAGTCAGCTCTAAATTGTCTGTTGAATAAAATTTACTCCTTTCCTC F2: 3 CCGACTGACACCAACCCAGTCA 2 Unidirectional alignment (log-probability: -53.9) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG----------------------actgacccaaccacagtcagccCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGGGCTGACTGTGGTTGGGTCAGT----------------------CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Template switch alignment (log-probability: -18) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|ACTGACCCAACCACAGTCAGCC|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|ACTGACCCAACCACAGTCAGCC|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Gorilla > Human --------------- chr14:66057779-66057800 Template switch process: F1: L CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG 1 F3: 4 CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG R RF: CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGACTGACCCAACCACAGTCAGCCCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG RR: GACGTGGAAACAAGAACCTCGGGACAGGTGGTTCCTATCTACTGACTGGGTTGGTGTCAGTCGGGCTCTAAATTGTCTGTTGAATAAAATTTACTCCTTTCCTC F2: 3 TGACTGGGTTGGTGTCAGTCGG 2 Unidirectional alignment (log-probability: -53.4) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG----------------------ggctgactgtggttgggtcagtCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGACTGACCCAACCACAGTCAGCC----------------------CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Template switch alignment (log-probability: -18.6) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|GGCTGACTGTGGTTGGGTCAGT|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|GGCTGACTGTGGTTGGGTCAGT|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Human > Gorilla --------------- chr14:49470041-49470062 Template switch process: F1: L CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG 1 F3: 4 CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG R RF: CTGCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGGGCTGACTGTGGTTGGGTCAGTCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG RR: GACGTGGAAACAAGAACCTCGGGACAGGTGGTTCCTATCTACCCGACTGACACCAACCCAGTCAGCTCTAAATTGTCTGTTGAATAAAATTTACTCCTTTCCTC F2: 3 CCGACTGACACCAACCCAGTCA 2 Unidirectional alignment (log-probability: -53.4) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG----------------------actgacccaaccacagtcagccCGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATGGGCTGACTGTGGTTGGGTCAGT----------------------CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG Template switch alignment (log-probability: -18.6) GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|ACTGACCCAACCACAGTCAGCC|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG GCACCTTTGTTCTTGGAGCCCTGTCCACCAAGGATAGATG|ACTGACCCAACCACAGTCAGCC|CGAGATTTAACAGACAACTTATTTTAAATGAGGAAAGGAG ========== Event 1051 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGCTCACACAGGTGGGTCTGC----------AGAGAGCAGCTAG----------------------------------------CGGCCTCAGATGGTCTCACAC ↑ 1 3 2 4 Chimp: CTGCTCACACAGGTGGGTCTGT-----GAGGCTGA-GGCCGCTAG--------------------CTGCTCTCTGCAGACCATGCCGGCCTCAGATGGTCTCACAC Gorilla: CTGCTCACACAGGTGGGTCTGTGAGGC-----TGA-GGCCGCTAGCTGCTCTCTGCAGACCATGC--------------------CGGCCTCAGATGGTCTCACAC ↓ 1 3 2 4 Human: CTGCTCACACAGGTGGGTCTGC----------AGAGAGCAGCTAG----------------------------------------CGGCCTCAGATGGTCTCACAC Cluster: [ ] Orangutan: CTGCGCACACAGGTGGGTCTGTGAGGC-----TGA-GG-CGCTAGCTGCTCTCTGCAGACCATGC--------------------CGGCCTCAGATGGTCTCACAC Chimp > Human ------------- chr14:63312909-63312922 Template switch process: F1: L AGGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTG 1 F3: 4 CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC R RF: AGGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTGTGAGGCTGAGGCCGCTAGCTGCTCTCTGCAGACCATGCCGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC RR: TCCTTCATATTGACGTACACGACGAGTGTGTCCACCCAGACACTCCGACTCCGGCGATCGACGAGAGACGTCTGGTACGGCCGGAGTCTACCAGAGTGTGAGGCACCACCGTCACCTCG F2: 3 GATCGACGAGAGAC 2 Unidirectional alignment (log-probability: -41.7) GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTC-------------------------------------TGCagagagcagctagCGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTGTGAGGCTGAGGCCGCTAGCTGCTCTCTGCAGACCATGC-------------CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC Template switch alignment (log-probability: -17) GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTG|CAGAGAGCAGCTAG|CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTG|CAGAGAGCAGCTAG|CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC Gorilla > Human --------------- chr14:63312909-63312922 Template switch process: F1: L AGGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTG 1 F3: 4 CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC R RF: AGGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTGTGAGGCTGAGGCCGCTAGCTGCTCTCTGCAGACCATGCCGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC RR: TCCTTCATATTGACGTACACGACGAGTGTGTCCACCCAGACACTCCGACTCCGGCGATCGACGAGAGACGTCTGGTACGGCCGGAGTCTACCAGAGTGTGAGGCACCACCGTCACCTCG F2: 3 GATCGACGAGAGAC 2 Unidirectional alignment (log-probability: -41.2) GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCT-------------------------------------GCagagagcagctagCGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTGTGAGGCTGAGGCCGCTAGCTGCTCTCTGCAGACCATGC-------------CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC Template switch alignment (log-probability: -17.5) GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTG|CAGAGAGCAGCTAG|CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC GGAAGTATAACTGCATGTGCTGCTCACACAGGTGGGTCTG|CAGAGAGCAGCTAG|CGGCCTCAGATGGTCTCACACTCCGTGGTGGCAGTGGAGC ========== Event 1052 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATTATTTTATCTATTCCTGGTTGAGGTTGATTATGATATTCTGG Chimp: ATGAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATTATTTTAT----CCCTGGTTGAGGTTGATTATGATATTCTGG Gorilla: ATGAGAATTAACTAAGGGGACCAGGAATAGATAAAACTA--------------------TGAGGTTGATTATGATATTCTGG ↓ 3 2 4 1 Human: ATGAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATTATTTTATCTATTCCTGGTTGAGGTTGATTATGATATTCTGG Cluster: [ ] Orangutan: --GAGAATTAACTAAGGGGACCAGGAATATATAAAACTA--------------------TGCTGTTGATTGTGATATTCTGG Gorilla > Human --------------- chr14:43664059-43664075 Template switch process: F1: L AGATGAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATTA 1 F3: 4 TGAGGTTGATTATGATATTCTGGCATATTACAGTTATTTA R RF: AGATGAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATGAGGTTGATTATGATATTCTGGCATATTACAGTTATTTA RR: TCTACTCTTAATTGATTCCCCTGGTCCTTATCTATTTTGATACTCCAACTAATACTATAAGACCGTATAATGTCAATAAAT F2: 3 TGGTCCTTATCTATTTT 2 Unidirectional alignment (log-probability: -39.6) GAGAATTAACTAAGGGGACCAGGAATAGATAAAACTAttattttatctattcctggtTGAGGTTGATTATGATATTCTGGCATATTACAGTTATTTA GAGAATTAACTAAGGGGACCAGGAATAGATAAAACTA--------------------TGAGGTTGATTATGATATTCTGGCATATTACAGTTATTTA Template switch alignment (log-probability: -23.5) GAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATtA|TTTTATCTATTCCTGGT|TGAGGTTGATTATGATATTCTGGCATATTACAGTTATTTA GAGAATTAACTAAGGGGACCAGGAATAGATAAAACTATGA|TTTTATCTATTCCTGGT|TGAGGTTGATTATGATATTCTGGCATATTACAGTTATTTA ========== Event 1053 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCATATCACCTGCTTTACAGGATTTTTCACCAGAAAAATCTTCTTATTTTAGTTTAACTT Chimp: GCCATATCACCTGCTTTACAGGATTTTTCACCAGAAAAATCTTCTTATTTTAGTTTAACTT ↑ 1 4 3 2 Gorilla: GCCATATCACCTGCTTTACAG-------AGCCAGAAAAATCTTTTTATTTTAGTTTAACTT ↓ 1 4 3 2 Human: GCCATATCACCTGCTTTACAGGATTTTTCACCAGAAAAATCTTCTTATTTTAGTTTAACTT Cluster: [ ] Orangutan: GCCATATCATCTGCTTTAAAG-------AGCCAGAAAAATCTTTTTATTTTAGTTTAACTT Gorilla > Human --------------- chr14:62690487-62690494 Template switch process: F1: L AAACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG 1 F3: 4 ACCAGAAAAATCTTCTTATTTTAGTTTAACTTAAAAAACAA R RF: AAACAGAATATTATTGTATAGCCATATCACCTGCTTTACAGAGCCAGAAAAATCTTTTTATTTTAGTTTAACTTAAAAAACAC RR: TTTGTCTTATAATAACATATCGGTATAGTGGACGAAATGTCTCGGTCTTTTTAGAAAAATAAAATCAAATTGAATTTTTTGTG F2: 3 CTTTTTAG 2 Unidirectional alignment (log-probability: -43.1) AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAGgatttttcaCCAGAAAAATCTTcTTATTTTAGTTTAACTTAAAAAACA AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG-------AGCCAGAAAAATCTTTTTATTTTAGTTTAACTTAAAAAACA Template switch alignment (log-probability: -33.3) AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG|GATTTTTC|aCCAGAAAAATCTTcTTATTTTAGTTTAACTTAAAAAACA AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG|GATTTTTC|GCCAGAAAAATCTTTTTATTTTAGTTTAACTTAAAAAACA Gorilla > Chimp --------------- chr14:47012815-47012822 Template switch process: F1: L AAACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG 1 F3: 4 ACCAGAAAAATCTTCTTATTTTAGTTTAACTTAAAAAACAA R RF: AAACAGAATATTATTGTATAGCCATATCACCTGCTTTACAGAGCCAGAAAAATCTTTTTATTTTAGTTTAACTTAAAAAACAC RR: TTTGTCTTATAATAACATATCGGTATAGTGGACGAAATGTCTCGGTCTTTTTAGAAAAATAAAATCAAATTGAATTTTTTGTG F2: 3 CTTTTTAG 2 Unidirectional alignment (log-probability: -43.1) AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAGgatttttcaCCAGAAAAATCTTcTTATTTTAGTTTAACTTAAAAAACA AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG-------AGCCAGAAAAATCTTTTTATTTTAGTTTAACTTAAAAAACA Template switch alignment (log-probability: -33.3) AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG|GATTTTTC|aCCAGAAAAATCTTcTTATTTTAGTTTAACTTAAAAAACA AACAGAATATTATTGTATAGCCATATCACCTGCTTTACAG|GATTTTTC|GCCAGAAAAATCTTTTTATTTTAGTTTAACTTAAAAAACA ========== Event 1054 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGA Chimp: TAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGA ↓ 1 3 4 Gorilla: TAAGGCAGGAATGGTACAAGTACATCAGTCAGGTTAAGTTGATAGTGGA ↑ 1 3 4 Human: TAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGA Cluster: [ ] Orangutan: TAAGGTAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGA Human > Gorilla --------------- chr14:40551679-40551685 Template switch process: F1: L CAATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGT 1 F3: 4 TCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT R RF: CAATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT RR: GTTACTGATCCTTTTTCTTCATTCCGTCCTTACCATGTTCACGACTACAGTCCAATTCAACTATCACCTCGATTATGAACAAAGTTA F2: 3 GACTACA 2 Unidirectional alignment (log-probability: -28.8) AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGTaCatcaGTCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT Template switch alignment (log-probability: -16.6) AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGT|ACATCAG|TCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGT|ACATCAG|TCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT Chimp > Gorilla --------------- chr14:40551679-40551685 Template switch process: F1: L CAATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGT 1 F3: 4 TCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT R RF: CAATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT RR: GTTACTGATCCTTTTTCTTCATTCCGTCCTTACCATGTTCACGACTACAGTCCAATTCAACTATCACCTCGATTATGAACAAAGTTA F2: 3 GACTACA 2 Unidirectional alignment (log-probability: -28.8) AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGTaCatcaGTCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGTGCTGATGTCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT Template switch alignment (log-probability: -16.6) AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGT|ACATCAG|TCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT AATGACTAGGAAAAAGAAGTAAGGCAGGAATGGTACAAGT|ACATCAG|TCAGGTTAAGTTGATAGTGGAGCTAATACTTGTTTCAAT ========== Event 1055 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCAGATCATGGTTCGTCTTCCT------------------------GTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG Chimp: TTCAGATCATGGTTCGTCTTCCT------------------------GTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG ↓ 4 3 2 1 Gorilla: TTCAGATCATGGTTCGTCTTCCTGTTACTCGGAACTGAGTAACTCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG ↑ 4 3 2 1 Human: TTCAGATCATGGTTCGTCTTCCT------------------------GTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------- Human > Gorilla --------------- chr1:47415653-47415659 Template switch process: F1: L CCGTGACACCTTCCCAGGTTCAGATCATGGTTCGTCTTCCTGTTACTC-------GGAACT 1 F3: 4 TCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG R RF: CCGTGACACCTTCCCAGGTTCAGATCATGGTTCGTCTTCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG RR: GGCACTGTGGAAGGGTCCAAGTCTAGTACCAAGCAGAAGGACAATGAGGTCCCACCCTTGGTGGAATCGGGGACGAGAGTC F2: 3 CAATGAG 2 Unidirectional alignment (log-probability: -45.4) CAGGTTCAGATCATGGTTCGTCTTCctgttactcggaactgagtaactcCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC CAGGTTCAGATCATGGTTCGTCTTC------------------------CTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC Template switch alignment (log-probability: -32.6) CAGGTTCAGATCATGGTTCGTCTTCCTGTTACTC-------GGAACt|GAGTAAC|TCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC CAGGTTCAGATCATGGTTCGTCTTCCTGTTACTCCAGGGTGGGAACC|GAGTAAC|TCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC Chimp > Gorilla --------------- chr1:47415653-47415659 Template switch process: F1: L CCGTGACACCTTCCCAGGTTCAGATCATGGTTCGTCTTCCTGTTACTC-------GGAACT 1 F3: 4 TCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG R RF: CCGTGACACCTTCCCAGGTTCAGATCATGGTTCGTCTTCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTCTCAG RR: GGCACTGTGGAAGGGTCCAAGTCTAGTACCAAGCAGAAGGACAATGAGGTCCCACCCTTGGTGGAATCGGGGACGAGAGTC F2: 3 CAATGAG 2 Unidirectional alignment (log-probability: -45.4) CAGGTTCAGATCATGGTTCGTCTTCctgttactcggaactgagtaactcCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC CAGGTTCAGATCATGGTTCGTCTTC------------------------CTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC Template switch alignment (log-probability: -32.6) CAGGTTCAGATCATGGTTCGTCTTCCTGTTACTC-------GGAACt|GAGTAAC|TCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC CAGGTTCAGATCATGGTTCGTCTTCCTGTTACTCCAGGGTGGGAACC|GAGTAAC|TCCTGTTACTCCAGGGTGGGAACCACCTTAGCCCCTGCTC ========== Event 1056 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAATGATTTGTCTAAGCAAGGA-AACGGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGCTTCTCACAGGATAGCTACACATTTTCAGAGAACTGAAATATCCAGCCAAGGACTAA Chimp: GAAATGATTTGTCTAAGCAAGGA-AACGGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGCTTCTCACAGGATAGCTACACATTTTCAGAGAACTGAAATATCCAGCCAAGGACTAA ↓ 1 4 3 2 Gorilla: GAAATGATTTGTCTAAGCAAGTCAGTTGGTAGGACTGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGCTTCTCACAGGATAGCTACACATTTTCAGAGAACTGAAATATCCAGCCAAGGACTAA ↑ 1 4 3 2 Human: GAAATGATTTGTCTAAGCAAGGA-AACGGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGCTTCTCACAGGATAGCTACACATTTTCAGAGAACTGAAATATCCAGCCAAGGACTAA Cluster: [ ] Orangutan: GAAATGATTTGTCTAAGCAAGTCAGTTGGTAGGACTGTTGCCTTCAACTATACTATACTGTTTCCAGGATGTTTGCTTATCACAGGATAGCTACACATTTTCAGAGAACTGAAATATCCAGCCAAGGACTAA Human > Gorilla --------------- chr14:39571421-39571426 Template switch process: F1: L ATACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG 1 F3: 4 GGTAGGACTGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGC R RF: ATACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAGGAAACGGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGCTTCTCACAGGATAGCTACACATTTTCAGAGAACTGA RR: TATGACTCTTTTCTTCTCTACTTTACTAAACAGATTCGTTCCTTTGCCATCCTGGCAAAGGAAGTTGATATGATATGACAAAGGTTCTACAAACGAAGAGTGTCCTATCGATGTGTAAAAGTCTCTTGACT F2: 3 TTGACT 2 Unidirectional alignment (log-probability: -35.2) TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG-----tcagttGGTAGGACtGTTTCCTTCAACTATACTATACTGTTTCCAA TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAGGAAAC------GGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAA Template switch alignment (log-probability: -22.2) TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG|TCAGTT|GGTAGGACtGTTTCCTTCAACTATACTATACTGTTTCCAA TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG|TCAGTT|GGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAA Chimp > Gorilla --------------- chr14:39571421-39571426 Template switch process: F1: L ATACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG 1 F3: 4 GGTAGGACTGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGC R RF: ATACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAGGAAACGGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAAGATGTTTGCTTCTCACAGGATAGCTACACATTTTCAGAGAACTGA RR: TATGACTCTTTTCTTCTCTACTTTACTAAACAGATTCGTTCCTTTGCCATCCTGGCAAAGGAAGTTGATATGATATGACAAAGGTTCTACAAACGAAGAGTGTCCTATCGATGTGTAAAAGTCTCTTGACT F2: 3 TTGACT 2 Unidirectional alignment (log-probability: -35.2) TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG-----tcagttGGTAGGACtGTTTCCTTCAACTATACTATACTGTTTCCAA TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAGGAAAC------GGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAA Template switch alignment (log-probability: -22.2) TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG|TCAGTT|GGTAGGACtGTTTCCTTCAACTATACTATACTGTTTCCAA TACTGAGAAAAGAAGAGATGAAATGATTTGTCTAAGCAAG|TCAGTT|GGTAGGACCGTTTCCTTCAACTATACTATACTGTTTCCAA ========== Event 1057 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTGGTTGGCCACAGGTGCAATTT------GCAGACATCATCTGCAAATAAAAGCTTTCTTACAAAATTC Chimp: TCTGGTTGGCCACAGGTGCAATTT------GCAGACATCATCTGCAAATGAAAGCTTTCTTACAAAATTC ↑ 1 3 4 2 Gorilla: TCTGGTTGGCCACAGGTGCAACCAGGTGCAACAGATGATGTCTGCAAATAAAAGCTTTCTTACAAAATTC ↓ 1 3 4 2 Human: TCTGGTTGGCCACAGGTGCAATTT------GCAGACATCATCTGCAAATAAAAGCTTTCTTACAAAATTC Cluster: [ ] Orangutan: TCTGGTTGGCCACAGGTGCAATTT------GCAGACATCATCTGCAAATAAAAGCTTTCTTACAAAATTC Gorilla > Human --------------- chr14:68989551-68989563 Template switch process: F1: L AGTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA 1 F3: 4 TCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA R RF: AGTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAACCAGGTGCAACAGATGATGTCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA RR: TCAACAGCCAGGAGGGGTAAAGACCAACCGGTGTCCACGTTGGTCCACGTTGTCTACTACAGACGTTTATTTTCGAAAGAATGTTTTAAGAAAGGGAATT F2: 3 ACTACAGACGTTT 2 Unidirectional alignment (log-probability: -40.3) GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA-------------------tttgcagacatcaTCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAACCAGGTGCAACAGATGATG-------------TCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA Template switch alignment (log-probability: -17.4) GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA|TTTGCAGACATCA|TCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA|TTTGCAGACATCA|TCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA Gorilla > Chimp --------------- chr14:53386231-53386243 Template switch process: F1: L AGTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA 1 F3: 4 TCTGCAAATGAAAGCTTTCTTACAAAATTCTTTCCCTTAAGGTACATGTA R RF: AGTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAACCAGGTGCAACAGATGATGTCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAAGGTACATGTA RR: TCAACAGCCAGGAGGGGTAAAGACCAACCGGTGTCCACGTTGGTCCACGTTGTCTACTACAGACGTTTATTTTCGAAAGAATGTTTTAAGAAAGGGAATTCCATGTACAT F2: 3 ACTACAGACGTTT 2 Unidirectional alignment (log-probability: -46) GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA-------------------tttgcagacatcaTCTGCAAATgAAAGCTTTCTTACAAAATTCTTTCCCTTAA GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAACCAGGTGCAACAGATGATG-------------TCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA Template switch alignment (log-probability: -23.1) GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA|TTTGCAGACATCA|TCTGCAAATgAAAGCTTTCTTACAAAATTCTTTCCCTTAA GTTGTCGGTCCTCCCCATTTCTGGTTGGCCACAGGTGCAA|TTTGCAGACATCA|TCTGCAAATAAAAGCTTTCTTACAAAATTCTTTCCCTTAA ========== Event 1058 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAAATGTACAATTATATAAAATAGCCCAGGAATTACAGCCAAAAAACATTAATAATTATTGGCAACTCT--------------------ATATTACTTTGTTTGCATCCTT ↓ 3 2 4 1 Chimp: CCAAATGTACAATTATATAAAATAGCCCAGGAATTACAGCCAAAAAACATTAATAATTATTGGCAACTCT----------ATGCTATTTTATATTACTTTGTTTGCATCCTT Gorilla: CCAAATGTACAATTATATAAAATAGCCCAGGAATTACAGCCAAAAAACATTAATAATTATTGGCAACTCTATGTTATTTT----------ATATTACTTTGTTTGCATCCTT Human: CCAAATGTACAATTATATAAAATAGCCCAGGAATTACAGCCAAAAAACATTAATAATTATTGGCAACTCT--------------------ATATTACTTTGTTTGCATCCTT Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------- Human > Chimp ------------- chr14:55929462-55929468 Template switch process: F1: L GGAATTACAGCCAAAAAACATTAATAATTATTGGCAACTCTAT 1 F3: 4 TATATTACTTTGTTTGCATCCTTATAGTGTTGGCCTATTAT R RF: AAATAGCCCAGGAATTACAGCCAAAAAACATTAATAATTATTGGCAACTCTATATTACTTTGTTTGCATCCTTATAGTGTTGGCTTATTAT RR: TTTATCGGGTCCTTAATGTCGGTTTTTTGTAATTATTAATAACCGTTGAGATATAATGAAACAAACGTAGGAATATCACAACCGAATAATA F2: 3 TTTATCG 2 Unidirectional alignment (log-probability: -31.3) ATTACAGCCAAAAAACATTAATAATTATTGGCAACTCtatgctatttTATATTACTTTGTTTGCATCCTTATAGTGTTGGCcTATTA ATTACAGCCAAAAAACATTAATAATTATTGGCAACTC----------TATATTACTTTGTTTGCATCCTTATAGTGTTGGCTTATTA Template switch alignment (log-probability: -22.2) ATTACAGCCAAAAAACATTAATAATTATTGGCAACTCTAT|GCTATTT|TATATTACTTTGTTTGCATCCTTATAGTGTTGGCcTATTA ATTACAGCCAAAAAACATTAATAATTATTGGCAACTCTAT|GCTATTT|TATATTACTTTGTTTGCATCCTTATAGTGTTGGCTTATTA ========== Event 1059 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAGCAGTTAAAACATGCTATGTACTAGATTC-----ATGCAAAGGATTTCATACCACTTGACA Chimp: TGAGCAGTTAAAACATGCTATGTACTAGATTC-----ATGCAAAGGATTTCATACCACTTGACA ↓ 3 1 2 4 Gorilla: TGAGCAGTTAAAACATGCTATGTACTAGATGAATCTAGTACATAGGATTTCATACCACTTGACA ↑ 3 1 2 4 Human: TGAGCAGTTAAAACATGCTATGTACTAGATTC-----ATGCAAAGGATTTCATACCACTTGACA Cluster: [ ] Orangutan: TGAGCAGTTAAAACATGCTATGTACTAGATTC-----ATGCAAAGGATTTCATACCACTGGACA Human > Gorilla --------------- chr14:55315577-55315589 Template switch process: F1: L AGAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT 1 F3: 4 AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT R RF: AGAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGATTCATGCAAAGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT RR: TCTTTTATGAGACTCGTCAATTTTGTACGATACATGATCTAAGTACGTTTCCTAAAGTATGGTGAACTGTCCATCTTTCAATTCGGGTA F2: 3 TACATGATCTAAG 2 Unidirectional alignment (log-probability: -38.3) GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGATgaatctagtacaT-------AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT------------TCATGCAAAGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT Template switch alignment (log-probability: -17.4) GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT|GAATCTAGTACAT|AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT|GAATCTAGTACAT|AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT Chimp > Gorilla --------------- chr14:55315577-55315589 Template switch process: F1: L AGAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT 1 F3: 4 AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT R RF: AGAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGATTCATGCAAAGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT RR: TCTTTTATGAGACTCGTCAATTTTGTACGATACATGATCTAAGTACGTTTCCTAAAGTATGGTGAACTGTCCATCTTTCAATTCGGGTA F2: 3 TACATGATCTAAG 2 Unidirectional alignment (log-probability: -38.3) GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGATgaatctagtacaT-------AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT------------TCATGCAAAGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT Template switch alignment (log-probability: -17.4) GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT|GAATCTAGTACAT|AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT GAAAATACTCTGAGCAGTTAAAACATGCTATGTACTAGAT|GAATCTAGTACAT|AGGATTTCATACCACTTGACAGGTAGAAAGTTAAGCCCAT ========== Event 1060 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGTGATTAGCAGTTCCTCAGGGTTCCTTTGGGAACCCTGAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCTCTGCTGGACTA Chimp: AGGTGATTAGCAGTTCCTCAGGGTTCCTTTGGGAACCCTGAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCTCTGCTGGACTA ↑ 4 1 3 2 Gorilla: AGGTGATTAGCAGTTCCTCAGGG---------------------TTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCTCTGCTGGACTA ↓ 4 1 3 2 Human: AGGTGATTAGCAGTTCCTCAGGGTTCCTTTGGGAACCCTGAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCTCTGCTGGACTA Cluster: [ ] Orangutan: AGGTGATTAGCAG------------------------------------------TTCATTTGGGGTCCAGGGTTTGTGAGGCTCTGCTGGACTA Gorilla > Human --------------- chr14:70317749-70317755 Template switch process: F1: L AGAGCCCAGCTCAGACACAGGTGATTAGCAGTTCCTCAGGGTTC-----------CTTTGGG 1 F3: 4 AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCT R RF: AGAGCCCAGCTCAGACAAAGGTGATTAGCAGTTCCTCAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCT RR: TCTCGGGTCGAGTCTGTTTCCACTAATCGTCAAGGAGTCCCAAGGACTCGTCAAGGAAACCCCAGGTCCCAAACACTCCGA F2: 3 GTCCCAA 2 Unidirectional alignment (log-probability: -46.6) CAGACAcAGGTGATTAGCAGTTCCTCagggttcctttgggaaccctgAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA CAGACAAAGGTGATTAGCAGTTCCTC---------------------AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA Template switch alignment (log-probability: -32.8) CAGACAcAGGTGATTAGCAGTTCCTCAGGGTTC-----------CTTTGGG|AACCCTG|AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA CAGACAAAGGTGATTAGCAGTTCCTCAGGGTTCCTGAGCAGTTCCTTTGGG|AACCCTG|AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA Gorilla > Chimp --------------- chr14:54794666-54794672 Template switch process: F1: L AGAGCCCAGCTCAGACACAGGTGATTAGCAGTTCCTCAGGGTTC-----------CTTTGGG 1 F3: 4 AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCT R RF: AGAGCCCAGCTCAGACAAAGGTGATTAGCAGTTCCTCAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGAGGCT RR: TCTCGGGTCGAGTCTGTTTCCACTAATCGTCAAGGAGTCCCAAGGACTCGTCAAGGAAACCCCAGGTCCCAAACACTCCGA F2: 3 GTCCCAA 2 Unidirectional alignment (log-probability: -46.6) CAGACAcAGGTGATTAGCAGTTCCTCagggttcctttgggaaccctgAGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA CAGACAAAGGTGATTAGCAGTTCCTC---------------------AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA Template switch alignment (log-probability: -32.8) CAGACAcAGGTGATTAGCAGTTCCTCAGGGTTC-----------CTTTGGG|AACCCTG|AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA CAGACAAAGGTGATTAGCAGTTCCTCAGGGTTCCTGAGCAGTTCCTTTGGG|AACCCTG|AGGGTTCCTGAGCAGTTCCTTTGGGGTCCAGGGTTTGTGA ========== Event 1061 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: tcaatataagacttgttgaatATA------T--------TCAACCTCTATTTTTGAAAATAGAGGTTGAATATATAttcaaactc--tttttct ↑ 1 3 4 2 Chimp: tcaatataagacttgtagaaaatagaattgttgaaaatagaaACCTCTATTTTCAAAAATAGAGGTTGAATATATAttcaaactc--tttttct Gorilla: tcaatataagacttgttgaatATA------T--------TCAACCTCTGTTTTTGAAAATAGAGGTTGAATATATAttcaaactc--tttttct Human: tcaatataagacttgttgaatATA------T--------TCAACCTCTATTTTTGAAAATAGAGGTTGAATATATAttcaaactc--tttttct Cluster: [] Orangutan: tcaatataaggcttgttgaatATA------T--------TCAAACTCTATTTTTGAAAATAG-AGTTGAATATACAttcaaactctgtttttct Chimp > Human ------------- chr14:73391028-73391048 Template switch process: F1: L TTGTTGAA 1 F3: 4 AAAATAGAGGTTGAATATATATTCAAACTCTTTTTCTGCT R RF: TTGTAGAAAATAGAATTGTTGAAAATAGAAACCTCTATTTTCAAAAATAGAGGTTGAATATATATTCAAACTCTTTTTCTGCT RR: AACATCTTTTATCTTAACAACTTTTATCTTTGGAGATAAAAGTTTTTATCTCCAACTTATATATAAGTTTGAGAAAAAGACGA F2: 3 GTTTTTATCTCCAACTTATAT 2 Unidirectional alignment (log-probability: -47.3) TTGTTGAAtATAttcAACCTCTATTTTtgAAAATAGAGGTTGAATATATATTCAAACTCTTTTTCTGCT TTGTTGAAAATA-GAAACCTCTATTTTCAAAAATAGAGGTTGAATATATATTCAAACTCTTTTTCTGCT Template switch alignment (log-probability: -23.2) TTGTtGAA|TATATTCAACCTCTATTTTTG|AAAATAGAGGTTGAATATATATTCAAACTCTTTTTCTGCT TTGTAGAA|TATATTCAACCTCTATTTTTG|AAAATAGAGGTTGAATATATATTCAAACTCTTTTTCTGCT ========== Event 1062 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: GGAGCCAACCAGGCCATGCATCTAAGCGATCCAAGCCTCAGGATCAGGAAT ↓ 13 2 4 ↑ 3 1 24 Chimp: GGAGCCAACCTGGCCATGCAT---CGCTTACCAAGCCTCAGGATCAGGAAT Gorilla: GGAGCCAACCTGGCCATGCAT---CACTTACCAAGCCTCAGGATCAGGAAT Human: GGAGCCAACCAGGCCATGCATCTAAGCGATCCAAGCCTCAGGATCAGGAAT Cluster: [ ] Orangutan: GGAGCCAACCTGGCCATGCAT---TGCTTACCAAGCCTCAGGATCAGGAAT Chimp > Human ------------- chr14:73775531-73775538 Template switch process: F1: L GCCCCTGCTCCCTCCCTCGGGGAGCCAACCAGGCCATGCATC 1 F3: 4 CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC R RF: GCCCCTGCTCCCTCCCTCGGGGAGCCAACCTGGCCATGCATCGCTTACCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC RR: CGGGGACGAGGGAGGGAGCCCCTCGGTTGGACCGGTACGTAGCGAATGGTTCGGAGTCCTAGTCCTTAGCGAAGGTCAGGTCTCGGG F2: 3 TAGCGAAT 2 Unidirectional alignment (log-probability: -35.9) CCCTGCTCCCTCCCTCGGGGAGCCAACCaGGCCATGCATC---TAagcgatCCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC CCCTGCTCCCTCCCTCGGGGAGCCAACCTGGCCATGCATCGCTTA------CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC Template switch alignment (log-probability: -22.3) CCCTGCTCCCTCCCTCGGGGAGCCAACCaGGCCATGCATC|TAAGCGAT|CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC CCCTGCTCCCTCCCTCGGGGAGCCAACCTGGCCATGCATC|TAAGCGAT|CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC Human > Chimp ------------- chr14:58294621-58294625 Template switch process: F1: L GCCCCTGCTCCCTCCCTCGGGGAGCCAACCTGGCCATGCATC 1 F3: 4 CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC R RF: GCCCCTGCTCCCTCCCTCGGGGAGCCAACCAGGCCATGCATCTAAGCGATCCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC RR: CGGGGACGAGGGAGGGAGCCCCTCGGTTGGTCCGGTACGTAGATTCGCTAGGTTCGGAGTCCTAGTCCTTAGCGAAGGTCAGGTCTCGGG F2: 3 ATTCG 2 Unidirectional alignment (log-probability: -31.8) CCCTGCTCCCTCCCTCGGGGAGCCAACCtGGCCATGCATCgctTA------CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC CCCTGCTCCCTCCCTCGGGGAGCCAACCAGGCCATGCATC---TAAGCGATCCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC Template switch alignment (log-probability: -21.9) CCCTGCTCCCTCCCTCGGGGAGCCAACCtGGCCATGCATC|GCTTA|CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC CCCTGCTCCCTCCCTCGGGGAGCCAACCAGGCCATGCATC|GCTTA|CCAAGCCTCAGGATCAGGAATCGCTTCCAGTCCAGAGCCC ========== Event 1063 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGGTTTCAGAAATTTagtatatctgtcttttataagtatatctgtcttttataagtatatctATATCTTTACTTAAACAGAGAAATTTAAG Chimp: TAGGTTTCAGAAATTTAGTATATCTGTCTTTTATAAG-------------------TATATCTATATCTTTACTTAAACAGAGAAATTTAAG ↓ 3 2 1 4 Gorilla: TAGGTTTCAGAAATTTAGTGTATCTGTCTTTTACAGA-------------------TA------------TACTTAAACAGAGAAATTTAAG Human: TAGGTTTCAGAAATTTagtatatctgtcttttataagtatatctgtcttttataagtatatctATATCTTTACTTAAACAGAGAAATTTAAG Cluster: [ ] Orangutan: TAGGTTTCAGAAATTTAGTATATCTGTCTTTTACAGA-------------------TA------------TACTTAAACAGAGAAATTCAAG Chimp > Gorilla --------------- chr14:58311066-58311072 Template switch process: F1: L GAGAAATTTAGGTTTCAGAAATTTAGTGTATCTGTCTTTTA 1 F3: 4 ACTTAAACAGAGAAATTTAAGTTTCATGAAAAAGATAAC R RF: GAGAAATTTAGGTTTCAGAAATTTAGTATATCTGTCTTTTATAAGTATATCTATATCTTTACTTAAACAGAGAAATTTAAGTTTCATGAAAAAGATAAC RR: CTCTTTAAATCCAAAGTCTTTAAATCATATAGACAGAAAATATTCATATAGATATAGAAATGAATTTGTCTCTTTAAATTCAAAGTACTTTTTCTATTG F2: 3 TATAGAC 2 Unidirectional alignment (log-probability: -32.7) AGAAATTTAGGTTTCAGAAATTTAGTgTATCTGTCTTTTacagATA----------------TACTTAAACAGAGAAATTTAAGTTTCATGAAAAAGATAAC AGAAATTTAGGTTTCAGAAATTTAGTATATCTGTCTTTT----ATAAGTATATCTATATCTTTACTTAAACAGAGAAATTTAAGTTTCATGAAAAAGATAAC Template switch alignment (log-probability: -22.1) AGAAATTTAGGTTTCAGAAATTTAGTgTATCTGTCTTTTA|CAGATAT|ACTTAAACAGAGAAATTTAAGTTTCATGAAAAAGATAAC AGAAATTTAGGTTTCAGAAATTTAGTATATCTGTCTTTTA|CAGATAT|ACTTAAACAGAGAAATTTAAGTTTCATGAAAAAGATAAC ========== Event 1064 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ttgcagtgagccaagatcgccactgcactccagcctgggtgacacagcgagactccatctcaaaagaaa-aaaaaaatagctaacgattccccccaggtctAATACCTGGTAGATCATTCCATAGTTCACAGCCATGCAGTGGTTGATGCAGACCACCAGGGCT ↑ 3 2 1 4 Chimp: ttgcagtgagccaagatcgccactgcactccagcctgggcgacacagctacactccgtctcaaaagaaa--aaaaaatagctaacgattccccccaggtctAATACCTGGTAGATCATTCCATAGTTCACAGCCA-----TCATTGATGCAGACCACCAGGGCT Gorilla: ttgcagtgagccaagatcgccactgcactccagcctgggtgacacagctacactccgtctcaaaagaaa--aaaaaatagctaacaattccccccaggtctAATACCTGGTAGATCATTCCATAGTTCACAGCCA-----TCATTGATGCAGACCACCAGGGCT ↓ 3 2 1 4 Human: ttgcagtgagccaagatcgccactgcactccagcctgggtgacacagcgagactccatctcaaaagaaa-aaaaaaatagctaacgattccccccaggtctAATACCTGGTAGATCATTCCATAGTTCACAGCCATGCAGTGGTTGATGCAGACCACCAGGGCT Cluster: [ ] Orangutan: ttgcagtgagccgagatcaccactgtactccagcctgggtgacacagcgcgactctgtctcaaaagaaaa-aaaaaatagctaacaattccccccaggtctAATACCTGGTAGATCATTCCATAGTTCACAGCCA-----TCATTGATGCAGACCACCAGGACT Chimp > Human ------------- chr14:32170790-32170796 Template switch process: F1: L CAGGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT 1 F3: 4 TTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG R RF: CCACTGCACTCCAGCCTGGGCGACACAGCTACACTCCGTCTCAAAAGAAAAAAAAATAGCTAACGATTCCCCCCAGGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCATCATTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG RR: GGTGACGTGAGGTCGGACCCGCTGTGTCGATGTGAGGCAGAGTTTTCTTTTTTTTTATCGATTGCTAAGGGGGGTCCAGATTATGGACCATCTAGTAAGGTATCAAGTGTCGGTAGTAACTACGTCTGGTGGTCCCGAAGACTGAGGTAACACAGAC F2: 3 GGTGACG 2 Unidirectional alignment (log-probability: -28.4) GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCATgCAgtggTTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT-CA----TTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG Template switch alignment (log-probability: -16.2) GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT|GCAGTGG|TTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT|GCAGTGG|TTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG Gorilla > Human --------------- chr14:32170790-32170796 Template switch process: F1: L CAGGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT 1 F3: 4 TTGATGCAGACCACCAGGGCTTCTGACTCCATTGTGTCTG R RF: CCACTGCACTCCAGCCTGGGTGACACAGCTACACTCCGTCTCAAAAGAAAAAAAAATAGCTAACAATTCCCCCCAGGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCATCATTGATGCAGACCACCAGGGCTTCTGACTCCACTGTGTCTG RR: GGTGACGTGAGGTCGGACCCACTGTGTCGATGTGAGGCAGAGTTTTCTTTTTTTTTATCGATTGTTAAGGGGGGTCCAGATTATGGACCATCTAGTAAGGTATCAAGTGTCGGTAGTAACTACGTCTGGTGGTCCCGAAGACTGAGGTGACACAGAC F2: 3 GGTGACG 2 Unidirectional alignment (log-probability: -33.4) GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCATgCAgtggTTGATGCAGACCACCAGGGCTTCTGACTCCAtTGTGTCTG GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT-CA----TTGATGCAGACCACCAGGGCTTCTGACTCCACTGTGTCTG Template switch alignment (log-probability: -22.2) GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT|GCAGTGG|TTGATGCAGACCACCAGGGCTTCTGACTCCAtTGTGTCTG GGTCTAATACCTGGTAGATCATTCCATAGTTCACAGCCAT|GCAGTGG|TTGATGCAGACCACCAGGGCTTCTGACTCCACTGTGTCTG ========== Event 1065 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTC-CACTGAGGCTCCACTCTCGGCTGCAATAACAGGGC ↓ 1 4 3 2 Chimp: GCTGGCCGGCCCCATCCCCAC---------AGTGGAGCCGAGGCTCCACTCTCGGCTGCAATAACAGGGC ↑ 1 4 3 2 Gorilla: GCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTC-CACTGAGGCTCCACTCTCGGCTGCAATAACAGGGC Human: GCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTC-CACTGAGGCTCCACTCTCGGCTGCAATAACAGGGC Cluster: [ ] Orangutan: GCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTC-CACTGAGGCTCCACTCTCGGCTGCAATAACAGGGC Human > Chimp ------------- chr14:32443005-32443013 Template switch process: F1: L CTGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC 1 F3: 4 GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT R RF: CTGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTCCACTGAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT RR: GACGGGGTCCAGGTAAATCCCGACCGGCCGGGGTAGGGGTGAGGAAGGCGACAGGTGACTCCGAGGTGAGAGCCGACGTTATTGTCCCGAAACCCATA F2: 3 CCGAGGTGA 2 Unidirectional alignment (log-probability: -34.9) TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAcagtggagcC-----------------GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCA---------CTCCTTCCGCTGTCCACTGAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT Template switch alignment (log-probability: -16.4) TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC|AGTGGAGCC|GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC|AGTGGAGCC|GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT Gorilla > Chimp --------------- chr14:32443005-32443013 Template switch process: F1: L CTGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC 1 F3: 4 GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT R RF: CTGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTCCACTGAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT RR: GACGGGGTCCAGGTAAATCCCGACCGGCCGGGGTAGGGGTGAGGAAGGCGACAGGTGACTCCGAGGTGAGAGCCGACGTTATTGTCCCGAAACCCATA F2: 3 CCGAGGTGA 2 Unidirectional alignment (log-probability: -34.4) TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC-----------------agtggagccGAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCACTCCTTCCGCTGTCCACT---------GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT Template switch alignment (log-probability: -16.9) TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC|AGTGGAGCC|GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT TGCCCCAGGTCCATTTAGGGCTGGCCGGCCCCATCCCCAC|AGTGGAGCC|GAGGCTCCACTCTCGGCTGCAATAACAGGGCTTTGGGTAT ========== Event 1066 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATATACTTGCTCAGTTTCAGAGAAGGAGTCCCTTCTCGACCATAAATATAAACCCAGG ↑ 3 1 2 4 Chimp: ATACACTTGCTCAGTTTCAGAGAAGGGACTCCTTCTTGACCATAAATATAAACCCAGG Gorilla: ATACACTTCCTCATTTTCAGAGAAGGGACTCCTTCTTGACCATAAATATAAACCCAGG Human: ATATACTTGCTCAGTTTCAGAGAAGGAGTCCCTTCTCGACCATAAATATAAACCCAGG Cluster: [ ] Orangutan: ATACACTTGCTCAATTTCAGAGAAGGGACTCCTTCTTGACCATAAATATAAACCCAGG Chimp > Human ------------- chr14:28707154-28707164 Template switch process: F1: L TAAGACCTGTGGAGTATATACTTGCTCAGTTTCAGAGAAGG 1 F3: 4 GACCATAAATATAAACCCAGGAGCCTCCTAGAATAGAAGC R RF: TAAGACCTGTGGAGTATACACTTGCTCAGTTTCAGAGAAGGGACTCCTTCTTGACCATAAATATAAACCCAGGAGCCTCCTAGAATAGAAGC RR: ATTCTGGACACCTCATATGTGAACGAGTCAAAGTCTCTTCCCTGAGGAAGAACTGGTATTTATATTTGGGTCCTCGGAGGATCTTATCTTCG F2: 3 CTCTTCCCTGA 2 Unidirectional alignment (log-probability: -36.8) AAGACCTGTGGAGTATAtACTTGCTCAGTTTCAGAGAAGGagtcCCTTCTcGACCATAAATATAAACCCAGGAGCCTCCTAGAATAGAAGC AAGACCTGTGGAGTATACACTTGCTCAGTTTCAGAGAAGGGACTCCTTCTTGACCATAAATATAAACCCAGGAGCCTCCTAGAATAGAAGC Template switch alignment (log-probability: -22.6) AAGACCTGTGGAGTATAtACTTGCTCAGTTTCAGAGAAGG|AGTCCCTTCTC|GACCATAAATATAAACCCAGGAGCCTCCTAGAATAGAAGC AAGACCTGTGGAGTATACACTTGCTCAGTTTCAGAGAAGG|AGTCCCTTCTC|GACCATAAATATAAACCCAGGAGCCTCCTAGAATAGAAGC ========== Event 1067 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTATCCCTCTATTATCCTCCCGTCTCTCTTTAAGGAGACAGTCAGATACTGAAAATGGGACTT--TTTT Chimp: CTATCCCTCTATTATCCTCCCATCTCTCTTTAAGGAGACAGTCAGATACTGAAAATGGGACttt-tttt ↓ 1 4 3 2 Gorilla: CTATCCCTCTATTATCCTCCCGTATCTGTTTAAGGAGACAGTCAGATACTGAAAATGGGACtttttttt Human: CTATCCCTCTATTATCCTCCCGTCTCTCTTTAAGGAGACAGTCAGATACTGAAAATGGGACTT--TTTT Cluster: [ ] Orangutan: CTATCCCTCTATTATCCTCCCATCTCTCTTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTTTT Chimp > Gorilla --------------- chr14:28911347-28911353 Template switch process: F1: L TTCTGTCTGCCCGCATCTATCTATCCCTCTATTATCCTCCC 1 F3: 4 TTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTTT R RF: TTCTGTCTGCCCGCATCTATCTATCCCTCTATTATCCTCCCATCTCTCTTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTTT RR: AAGACAGACGGGCGTAGATAGATAGGGAGATAATAGGAGGGTAGAGAGAAATTCCTCTGTCAGTCTATGACTTTTACCCTGAAAAAAA F2: 3 GTCTATG 2 Unidirectional alignment (log-probability: -26) TCTGTCTGCCCGCATCTATCTATCCCTCTATTATCCTCCCgTaTCTgTTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTTt TCTGTCTGCCCGCATCTATCTATCCCTCTATTATCCTCCCATCTCTCTTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTT- Template switch alignment (log-probability: -16.6) TCTGTCTGCCCGCATCTATCTATCCCTCTATTATCCTCCC|GTATCTG|TTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTTT TCTGTCTGCCCGCATCTATCTATCCCTCTATTATCCTCCC|GTATCTG|TTTAAGGAGACAGTCAGATACTGAAAATGGGACTTTTTTT ========== Event 1068 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCCTTCATGGTTTATTTGAAAA-------TCTGATACAAGTTATGGAAAAAACAATTGAG ↓ 1 3 4 2 Chimp: TTCCTTCATGGTTTATTTGAACTTGTATCAGATGATACAAGTTATGGAAAAAACAATTGAG ↑ 1 3 4 2 Gorilla: TTCCTTCATGGTTTATTTGAAAA-------TCTGATACAAGTTATGGAAAAAACAATTGAG Human: TTCCTTCATGGTTTATTTGAAAA-------TCTGATACAAGTTATGGAAAAAACAATTGAG Cluster: [ ] Orangutan: TTCTTTCATGGTTTATTTGAAAA-------TCTGATATAAGTTATGGAAAAAACAACTGAG Human > Chimp ------------- chr14:64911293-64911303 Template switch process: F1: L TTTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA 1 F3: 4 TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC R RF: TTTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAAAATCTGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC RR: AAAGTTTCCCTACTTACACAAAGGAAGTACCAAATAAACTTTTAGACTATGTTCAATACCTTTTTTGTTAACTCGATTTTTTTAG F2: 3 AGACTATGTTC 2 Unidirectional alignment (log-probability: -35.7) TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA---CttgtatcagaTGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAAAATC----------TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC Template switch alignment (log-probability: -16.6) TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA|CTTGTATCAGA|TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA|CTTGTATCAGA|TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC Gorilla > Chimp --------------- chr14:64911293-64911303 Template switch process: F1: L TTTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA 1 F3: 4 TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC R RF: TTTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAAAATCTGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC RR: AAAGTTTCCCTACTTACACAAAGGAAGTACCAAATAAACTTTTAGACTATGTTCAATACCTTTTTTGTTAACTCGATTTTTTTAG F2: 3 AGACTATGTTC 2 Unidirectional alignment (log-probability: -35.2) TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA---CttgtatcagaTGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAAAATC----------TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC Template switch alignment (log-probability: -17.1) TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA|CTTGTATCAGA|TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC TTCAAAGGGATGAATGTGTTTCCTTCATGGTTTATTTGAA|CTTGTATCAGA|TGATACAAGTTATGGAAAAAACAATTGAGCTAAAAAAATC ========== Event 1069 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTCTTGTTTCCCCAGGAGGTGGAAACA------TACATACTGCAGTGCCTTTCAACATCTGAAAATCAGCTGGT Chimp: TTCTCTTGTTTCCCCAGGAGG--------TTGAAAGGCATACTGCAATGCCTTTCAACGTCTGAAAATCAGCTGGT ↑ 1 4 3 2 Gorilla: TTCTCTTGTTTCCCCAGGAGGTGGAAACA------TACATACTGCAATGCCTTTCAAGGTCTGAAAATCAGCTGGT Human: TTCTCTTGTTTCCCCAGGAGGTGGAAACA------TACATACTGCAGTGCCTTTCAACATCTGAAAATCAGCTGGT Cluster: [ ] Orangutan: TTCTCTTGTTTCCCCAGGAGGTGGAAACA------TACATACTGCAACGCCTTTCAAGGTCTGAAAATCAGCTGGT Gorilla > Chimp --------------- chr14:25532434-25532441 Template switch process: F1: L CTTTAGGTTAGGTGTACCTGTTCTCTTGTTTCCCCAGGAGGT 1 F3: 4 ATACTGCAATGCCTTTCAACGTCTGAAAATCAGCTGGTG R RF: CTTTAGGCTAGGTGTACCTGTTCTCTTGTTTCCCCAGGAGGTGGAAACATACATACTGCAATGCCTTTCAAGGTCTGAAAATCAGCTGGTG RR: GAAATCCGATCCACATGGACAAGAGAACAAAGGGGTCCTCCACCTTTGTATGTATGACGTTACGGAAAGTTCCAGACTTTTAGTCGACCAC F2: 3 CGGAAAGT 2 Unidirectional alignment (log-probability: -38.7) TTAGGtTAGGTGTACCTGTTCTCTTGTTTCCCCAGGAGGTtGAA--AggCATACTGCAATGCCTTTCAAcGTCTGAAAATCAGCTGGTG TTAGGCTAGGTGTACCTGTTCTCTTGTTTCCCCAGGAGGTGGAAACATACATACTGCAATGCCTTTCAAGGTCTGAAAATCAGCTGGTG Template switch alignment (log-probability: -27.8) TTAGGtTAGGTGTACCTGTTCTCTTGTTTCCCCAGGAGGT|TGAAAGGC|ATACTGCAATGCCTTTCAAcGTCTGAAAATCAGCTGGTG TTAGGCTAGGTGTACCTGTTCTCTTGTTTCCCCAGGAGGT|TGAAAGGC|ATACTGCAATGCCTTTCAAGGTCTGAAAATCAGCTGGTG ========== Event 1070 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATCAGGCTCAAGCTTTTCTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTATA------GTCATTCTACTCTTAAAGACTGAGAC ↑ 3 2 1 4 Chimp: ATCAGGCTCAAGCTTTTCTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTACTATAACTTTTACTCTACTCTTAAAGACTGAGAC ↓ 3 2 1 4 Gorilla: ATCAGGCTCAAGCTTTTCTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTATA------GTCATTCTACTCTTAAAGACTGAGAC Human: ATCAGGCTCAAGCTTTTCTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTATA------GTCATTCTACTCTTAAAGACTGAGAC Cluster: [ ] Orangutan: ATCAGGCTGAAGCTTTTCTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTATA------GTCATTCTACTCTTAAAGACTGAGAC Chimp > Human ------------- chr14:80739584-80739590 Template switch process: F1: L CTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA 1 F3: 4 TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT R RF: CTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTACTATAACTTTTACTCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT RR: GATACTGATCATCATGTATGTCTTAGTATGAGATTTTCAATGATATTGAAAATGAGATGAGAATTTCTGACTCTGATAAAATCTGTGTTTCAAA F2: 3 TACTGAT 2 Unidirectional alignment (log-probability: -31.9) TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTAtagtcat-------------TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA-------CTATAACTTTTACTCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT Template switch alignment (log-probability: -16.2) TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA|TAGTCAT|TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA|TAGTCAT|TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT Chimp > Gorilla --------------- chr14:64462452-64462458 Template switch process: F1: L CTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA 1 F3: 4 TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT R RF: CTATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTACTATAACTTTTACTCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT RR: GATACTGATCATCATGTATGTCTTAGTATGAGATTTTCAATGATATTGAAAATGAGATGAGAATTTCTGACTCTGATAAAATCTGTGTTTCAAA F2: 3 TACTGAT 2 Unidirectional alignment (log-probability: -31.4) TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA-------------tagtcatTCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTACTATAACTTTTAC-------TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT Template switch alignment (log-probability: -16.6) TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA|TAGTCAT|TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT TATGACTAGTAGTACATACAGAATCATACTCTAAAAGTTA|TAGTCAT|TCTACTCTTAAAGACTGAGACTATTTTAGACACAAAGTTT ========== Event 1071 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAATAACATTGTATTCTTCTTTGATATATATGTGCAAC-------------ATGTTTTTTATTTACACGAACA ↓ 3 2 41 Chimp: GAAATAACATTGTATTCTTCTTTGATATATATGTGCAACATATATATCAAAGATGTTTTTTATTTACACGAACA ↑ 3 2 41 Gorilla: GAAATAACATTGTATTCTTCTTTGATATATATGTGCAAC-------------ATGTTTTTTATTTACATGAACA Human: GAAATAACATTGTATTCTTCTTTGATATATATGTGCAAC-------------ATGTTTTTTATTTACACGAACA Cluster: [ ] Orangutan: GAAATAACATTGTATTCTTCTTTCATATGTATGTGCAAC-------------ATGTTTTTTATTTACACGAACA Human > Chimp ------------- chr14:67135552-67135562 Template switch process: F1: L CAGAAATAACATTGTATTCTTCTTTGATATATATGTGCAACAT 1 F3: 4 ATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA R RF: CAGAAATAACATTGTATTCTTCTTTGATATATATGTGCAACATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA RR: GTCTTTATTGTAACATAAGAAGAAACTATATATACACGTTGTACAAAAAATAAATGTGCTTGTTAATAATGTCAAATGACT F2: 3 GAAACTATATA 2 Unidirectional alignment (log-probability: -29.6) AAATAACATTGTATTCTTCTTTGATATATATGTGCAACatatatatcaaagATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA AAATAACATTGTATTCTTCTTTGATATATATGTGCAAC-------------ATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA Template switch alignment (log-probability: -16.7) AAATAACATTGTATTCTTCTTTGATATATATGTGCAACAT|ATATATCAAAG|ATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA AAATAACATTGTATTCTTCTTTGATATATATGTGCAACAT|ATATATCAAAG|ATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA Gorilla > Chimp --------------- chr14:67135552-67135562 Template switch process: F1: L CAGAAATAACATTGTATTCTTCTTTGATATATATGTGCAACAT 1 F3: 4 ATGTTTTTTATTTACACGAACAATTATTACAGTTTACTGA R RF: CAGAAATAACATTGTATTCTTCTTTGATATATATGTGCAACATGTTTTTTATTTACATGAACAATTATTACAGTTTACTGA RR: GTCTTTATTGTAACATAAGAAGAAACTATATATACACGTTGTACAAAAAATAAATGTACTTGTTAATAATGTCAAATGACT F2: 3 GAAACTATATA 2 Unidirectional alignment (log-probability: -35.1) AAATAACATTGTATTCTTCTTTGATATATATGTGCAACatatatatcaaagATGTTTTTTATTTACAcGAACAATTATTACAGTTTACTGA AAATAACATTGTATTCTTCTTTGATATATATGTGCAAC-------------ATGTTTTTTATTTACATGAACAATTATTACAGTTTACTGA Template switch alignment (log-probability: -22.7) AAATAACATTGTATTCTTCTTTGATATATATGTGCAACAT|ATATATCAAAG|ATGTTTTTTATTTACAcGAACAATTATTACAGTTTACTGA AAATAACATTGTATTCTTCTTTGATATATATGTGCAACAT|ATATATCAAAG|ATGTTTTTTATTTACATGAACAATTATTACAGTTTACTGA ========== Event 1072 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTCTGCCACAGCCCTCGAGTAGTATTGTTACTGAGTAGTCAGTAACAATACACCAGATGATATCATTCAAA Chimp: CTTCTGCCACAGCCCTCGAGT--------------CTACTCAGTAACAATATACCAGATGATATCATTCAAA Gorilla: CTTCTGCCACAGCCCTCGAGT--------------CTACTCAGTAACAATACACCAGATGATATCATTCAAA ↓ 3 4 2 Human: CTTCTGCCACAGCCCTCGAGTAGTATTGTTACTGAGTAGTCAGTAACAATACACCAGATGATATCATTCAAA Cluster: [ ] Orangutan: CTTCTGCCACAGCCCTCAAGT--------------CCACTCAGTAACAATACACCAGACGACATCATTCAAA Gorilla > Human --------------- chr14:84348515-84348531 Template switch process: F1: L GACTCCAGGTTCATTCCACTCTTCTGCCACAGCCCTCGAGTA 1 F3: 4 TCAGTAACAATACACCAGATGATATCATTCAAAAGTTCAG R RF: GACTCCAGGTTCATTCCACTCTTCTGCCACAGCCCTCGAGTCTACTCAGTAACAATACACCAGATGATATCATTCAAAAGTTCAG RR: CTGAGGTCCAAGTAAGGTGAGAAGACGGTGTCGGGAGCTCAGATGAGTCATTGTTATGTGGTCTACTATAGTAAGTTTTCAAGTC F2: 3 GATGAGTCATTGTTATG 2 Unidirectional alignment (log-probability: -42.1) CTCCAGGTTCATTCCACTCTTCTGCCACAGCCCTCGAGTagtattgttactgagTAgTCAGTAACAATACACCAGATGATATCATTCAAAAGTTCAG CTCCAGGTTCATTCCACTCTTCTGCCACAGCCCTCGAGT--------------CTACTCAGTAACAATACACCAGATGATATCATTCAAAAGTTCAG Template switch alignment (log-probability: -23.4) CTCCAGGTTCATTCCACTCTTCTGCCACAGCCCTCGAGTa|GTATTGTTACTGAGTAG|TCAGTAACAATACACCAGATGATATCATTCAAAAGTTCAG CTCCAGGTTCATTCCACTCTTCTGCCACAGCCCTCGAGTC|GTATTGTTACTGAGTAG|TCAGTAACAATACACCAGATGATATCATTCAAAAGTTCAG ========== Event 1073 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 125 Detected in comparisons: 1256 Multiple sequence alignment: Human: AACTAAAAAGTACTTGAGAAACTTCT---TTGAGACTTGCTACCTATGCTCAAAAGC ↓ 1 3 4 2 ↑ 1 3 4 Chimp: AACTAAAAAGTACTTGAGAAAAGTCTCAAAGGAGACTTGCTACCTATGCTCAAAAGC ↑ 1 3 4 2 Gorilla: AACTAAAAAGTACTTGAGAAACTTCT---TTGAGACTTGCTACCTAAGCTCAAAAGC Human: AACTAAAAAGTACTTGAGAAACTTCT---TTGAGACTTGCTACCTATGCTCAAAAGC Cluster: [ ] Orangutan: AACTAAAAAGTACTTGAGAAACTTCT---TTGAGACTTGCTGCCTAAGCTCAAAAGC Chimp > Human ------------- chr14:83961247-83961255 Template switch process: F1: L CTTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA 1 F3: 4 GACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT R RF: CTTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAAAGTCTCAAAGGAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT RR: GAAACTTTGTGGTTTCTGTTTTGATTTTTCATGAACTCTTTTCAGAGTTTCCTCTGAACGATGGATACGAGTTTTCGGTTTCCTTGTTCCA F2: 3 AGTTTCTTC 2 Unidirectional alignment (log-probability: -31.7) TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAActtcttt----------GAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA-------AGTCTCAAAGGAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT Template switch alignment (log-probability: -22.3) TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA|CTtCTTTGA|GACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA|CTCCTTTGA|GACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT Human > Chimp ------------- chr14:68662825-68662834 Template switch process: F1: L CTTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA 1 F3: 4 GAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT R RF: CTTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAACTTCTTTGAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT RR: GAAACTTTGTGGTTTCTGTTTTGATTTTTCATGAACTCTTTGAAGAAACTCTGAACGATGGATACGAGTTTTCGGTTTCCTTGTTCCA F2: 3 GAAACTCTGA 2 Unidirectional alignment (log-probability: -35.9) TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA-------agtctcaaagGAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAACTTCTTT----------GAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT Template switch alignment (log-probability: -16.5) TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA|AGTCTCAAAG|GAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT TTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA|AGTCTCAAAG|GAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT Gorilla > Chimp --------------- chr14:68662825-68662834 Template switch process: F1: L CTTTGAAACACCAAAGACAAAACTAAAAAGTACTTGAGAAA 1 F3: 4 GAGACTTGCTACCTATGCTCAAAAGCCAAAGGAACAAGGT R RF: CTTTGAAGCACCAAAGACAAAACTAAAAAGTACTTGAGAAACTTCTTTGAGACTTGCTACCTAAGCTCAAAAGCCAAAGGAACAAGGT RR: GAAACTTCGTGGTTTCTGTTTTGATTTTTCATGAACTCTTTGAAGAAACTCTGAACGATGGATTCGAGTTTTCGGTTTCCTTGTTCCA F2: 3 GAAACTCTGA 2 Unidirectional alignment (log-probability: -46.4) TTTGAAaCACCAAAGACAAAACTAAAAAGTACTTGAGAAA-------agtctcaaagGAGACTTGCTACCTAtGCTCAAAAGCCAAAGGAACAAGGT TTTGAAGCACCAAAGACAAAACTAAAAAGTACTTGAGAAACTTCTTT----------GAGACTTGCTACCTAAGCTCAAAAGCCAAAGGAACAAGGT Template switch alignment (log-probability: -28) TTTGAAaCACCAAAGACAAAACTAAAAAGTACTTGAGAAA|AGTCTCAAAG|GAGACTTGCTACCTAtGCTCAAAAGCCAAAGGAACAAGGT TTTGAAGCACCAAAGACAAAACTAAAAAGTACTTGAGAAA|AGTCTCAAAG|GAGACTTGCTACCTAAGCTCAAAAGCCAAAGGAACAAGGT ========== Event 1074 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTGGAAACGTGTGGCTTCAAATTGTATACTG-----------ATAGATGTTCCAGCTGAGTGGGAC ↓ 3 1 2 4 Chimp: TGTGGAAACGTGTGGCTTCAAATTGTATACTATCAGTATACAATTTGATGTTCCAGCTGAGTGGGAC ↑ 3 1 2 4 Gorilla: TGTGGAAACTTGTGGCTTCAAATTGTATACTG-----------ATAGATGTTCCAGCTGAGTGGGAC Human: TGTGGAAACGTGTGGCTTCAAATTGTATACTG-----------ATAGATGTTCCAGCTGAGTGGGAC Cluster: [ ] Orangutan: TGTGGAATCATGTGGCTTAAAATTGTATACTG-----------ATAGATGTTACAGCTGAGTGGGAC Human > Chimp ------------- chr14:70338246-70338260 Template switch process: F1: L GAGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATACT 1 F3: 4 GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT R RF: GAGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATACTGATAGATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT RR: CTCACTTAATACACCTTTGCACACCGAAGTTTAACATATGACTATCTACAAGGTCGACTCACCCTGACGACTCTACTATATAAGA F2: 3 TTTAACATATGACTA 2 Unidirectional alignment (log-probability: -41.4) AGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATAC---TAtcagtatacaatttGATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT AGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATACTGATA--------------GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT Template switch alignment (log-probability: -17.1) AGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATACT|ATCAGTATACAATTT|GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT AGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATACT|ATCAGTATACAATTT|GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT Gorilla > Chimp --------------- chr14:70338246-70338260 Template switch process: F1: L GAGTGAATTATGTGGAAACGTGTGGCTTCAAATTGTATACT 1 F3: 4 GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT R RF: GAGTGAATTATGTGGAAACTTGTGGCTTCAAATTGTATACTGATAGATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT RR: CTCACTTAATACACCTTTGAACACCGAAGTTTAACATATGACTATCTACAAGGTCGACTCACCCTGACGACTCTACTATATAAGA F2: 3 TTTAACATATGACTA 2 Unidirectional alignment (log-probability: -46.4) AGTGAATTATGTGGAAACgTGTGGCTTCAAATTGTATAC---TAtcagtatacaatttGATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT AGTGAATTATGTGGAAACTTGTGGCTTCAAATTGTATACTGATA--------------GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT Template switch alignment (log-probability: -23.2) AGTGAATTATGTGGAAACgTGTGGCTTCAAATTGTATACT|ATCAGTATACAATTT|GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT AGTGAATTATGTGGAAACTTGTGGCTTCAAATTGTATACT|ATCAGTATACAATTT|GATGTTCCAGCTGAGTGGGACTGCTGAGATGATATATTCT ========== Event 1075 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAA------------GTAACATTTCAATAGTTTTCTTGTTTT Chimp: CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAG------------GTAACACTTCAATAGTTTTCTTGTTTT ↓ 3 2 4 Gorilla: CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGTTGGGGAACAAATAAAACTTCAATAGTTTTCTTGTTTT ↑ 3 2 4 Human: CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAA------------GTAACATTTCAATAGTTTTCTTGTTTT Cluster: [ ] Orangutan: CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAA------------GTAACACTTCAATAGTTTTCTTGTTTT Human > Gorilla --------------- chr14:69117092-69117102 Template switch process: F1: L TTCCACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGT 1 F3: 4 TAAAACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAAAAACAT R RF: TTCCACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGTAACATTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAAAAACAT RR: AAGGTGATTGACGGGAGTTCTGAAACAAGGGGTTGTATTTTCATTGTAAAGTTATCAAAAGAACAAAACATTTAAGGAAATTTTTGTA F2: 3 AAACAAGGGGT 2 Unidirectional alignment (log-probability: -39.3) CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGttggggaacaaaTAAaAcTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAG------------TAACATTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA Template switch alignment (log-probability: -28.4) CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGT|TGGGGAACAAA|TAAaAcTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGT|TGGGGAACAAA|TAACATTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA Chimp > Gorilla --------------- chr14:69117092-69117102 Template switch process: F1: L CTTCCACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAAGT 1 F3: 4 TAAAACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAAAAAC R RF: CTTCCACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAGGTAACACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAAAAAA RR: GAAGGTGATTGACGGGAGTTCTGAAACAAGGGGTTGTATTTCCATTGTGAAGTTATCAAAAGAACAAAACATTTAAGGAAATTTTTT F2: 3 AAACAAGGGGT 2 Unidirectional alignment (log-probability: -47.4) CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAaGttggggaacaaaTAAaACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAGG------------TAACACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA Template switch alignment (log-probability: -33.9) CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAaGT|TGGGGAACAAA|TAAaACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA CACTAACTGCCCTCAAGACTTTGTTCCCCAACATAAAGGT|TGGGGAACAAA|TAACACTTCAATAGTTTTCTTGTTTTGTAAATTCCTTTAA ========== Event 1076 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGGCTTTAACAAAAATGGTAA----AAAATATAATAAGGCATTCTGATTCATGCAGTCATTATGAAT Chimp: GTGGCTTTAACAAAAATGGTAA----AAAATATAATAAGGCATTCTGATTCATGCAGTCATTATGAAT ↓ 1 4 3 2 Gorilla: GTGGCTTTAACAAAAATGGTAT--------CAGAATAAGGCATTCTGATTCATGCAGTCATTATGAAT ↑ 1 4 3 2 Human: GTGGCTTTAACAAAAATGGTAA----AAAATATAATAAGGCATTCTGATTCATGCAGTCATTATGAAT Cluster: [ ] Orangutan: ATGGCCTTAACAAAAATGGTAAAAAA----TATAATAAGGCATTCTGATTCATGCAGTCATTATGAAT Human > Gorilla --------------- chr14:70080647-70080650 Template switch process: F1: L AGATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTA 1 F3: 4 AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC R RF: AGATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTAAAAAATATAATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC RR: TCTAAAAAATTAGTAACAACCACCGAAATTGTTTTTACCATTTTTTATATTATTCCGTAAGACTAAGTACGTCAGTAATACTTATGTGG F2: 3 GACT 2 Unidirectional alignment (log-probability: -25.3) GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGG-------TATcagAATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTAAAAAATAT---AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC Template switch alignment (log-probability: -16.2) GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTA|TCAG|AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTA|TCAG|AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC Chimp > Gorilla --------------- chr14:70080647-70080650 Template switch process: F1: L AGATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTA 1 F3: 4 AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC R RF: AGATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTAAAAAATATAATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC RR: TCTAAAAAATTAGTAACAACCACCGAAATTGTTTTTACCATTTTTTATATTATTCCGTAAGACTAAGTACGTCAGTAATACTTATGTGG F2: 3 GACT 2 Unidirectional alignment (log-probability: -25.3) GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGG-------TATcagAATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTAAAAAATAT---AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC Template switch alignment (log-probability: -16.2) GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTA|TCAG|AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC GATTTTTTAATCATTGTTGGTGGCTTTAACAAAAATGGTA|TCAG|AATAAGGCATTCTGATTCATGCAGTCATTATGAATACACC ========== Event 1077 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: taactcaaaatttgacagatacagtcacatagcacaatgtg--ggtatgtgataagccagggaga Chimp: TAACTCAAAGTTTGACAGATACAGTCACATAGCACAATCTG--GGTATGTGATAAgccagggaga ↓ 3 1 2 4 Gorilla: TAACTCAAAGTTTGACAGATA--CTCACATTGTGCTATGTGACTGTATGTGATAAgccagggaga Human: taactcaaaatttgacagatacagtcacatagcacaatgtg--ggtatgtgataagccagggaga Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr14:20633973-20633986 Template switch process: F1: L CAAATAGAGAGTTTATCCTATAACTCAAAGTTTGACAGATAC--TCACAT 1 F3: 4 GTATGTGATAAGCCAGGGAGAATTTGAGAATTTTTCTTAG R RF: AAAATAGAGAGTTTATCCTATAACTCAAAGTTTGACAGATACAGTCACATAGCACAATCTGGGTATGTGATAAGCCAGGGAGAATTTGAGAATTTTTCTTAG RR: TTTTATCTCTCAAATAGGATATTGAGTTTCAAACTGTCTATGTCAGTGTATCGTGTTAGACCCATACACTATTCGGTCCCTCTTAAACTCTTAAAAAGAATC F2: 3 TCAGTGTATCGTGT 2 Unidirectional alignment (log-probability: -55.9) GAGTTTATCCTATAACTCAAAGTTTGACAGATAC--------------------tcacattgtgctatgtgactGTATGTGATAAGCCAGGGAGAATTTGAGAATTTTTCTTAG GAGTTTATCCTATAACTCAAAGTTTGACAGATACAGTCACATAGCACAATCTGG--------------------GTATGTGATAAGCCAGGGAGAATTTGAGAATTTTTCTTAG Template switch alignment (log-probability: -33) GAGTTTATCCTATAACTCAAAGTTTGACAGATAC--TCACAT|TGTGCTATGTGACT|GTATGTGATAAGCCAGGGAGAATTTGAGAATTTTTCTTAG GAGTTTATCCTATAACTCAAAGTTTGACAGATACAGTCACAT|TGTGCTATGTGACT|GTATGTGATAAGCCAGGGAGAATTTGAGAATTTTTCTTAG ========== Event 1078 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTAAAATCTGTGGAAGGCTTGGTAACATATACATATTCTTGTATATGTTACCAAAATAAAATTTTGGTAAAATTTTAT ↑ 3 1 4 2 Chimp: TGTAAAATCTGTGGAAGGCTTGGTAACATATACA------AGA----ATAACACATATTAAATTTTGGTAAAATTTTAT Gorilla: TGTAAAATCTGTGGAAGTCTTGGTAACATATACA------AGA----ATAACACATATTAAATTTTGGTAAAATT---- Human: TGTAAAATCTGTGGAAGGCTTGGTAACATATACATATTCTTGTATATGTTACCAAAATAAAATTTTGGTAAAATTTTAT Cluster: [ ] Orangutan: TGTAAAATCTGTGGAAGGCTTGGTAACATATACA------AGA----ATAACACACATTAAATTTTGGTAAAATT---- Chimp > Human ------------- chr14:20333522-20333542 Template switch process: F1: L CAGAAAATGTAAAATCTGTGGAAGGCTTGGTAACATATACA 1 F3: 4 AATA---------AAATTTTGGTAAAATTTTATTTAATCTGTATAGATCCATC R RF: CAGAAAATGTAAAATCTGTGGAAGGCTTGGTAACATATACAAGAATAACACATATTAAATTTTGGTAAAATTTTATTTAATCTGTATAGATCCATC RR: GTCTTTTACATTTTAGACACCTTCCGAACCATTGTATATGTTCTTATTGTGTATAATTTAAAACCATTTTAAAATAAATTAGACATATCTAGGTAG F2: 3 AACCATTGTATATGTTCTTAT 2 Unidirectional alignment (log-probability: -51.9) AGAAAATGTAAAATCTGTGGAAGGCTTGGTAACATAT-----------ACATATTcttgtatatgttaccaaaataAAATTTTGGTAAAATTTTATTTAATCTGTATAGATC AGAAAATGTAAAATCTGTGGAAGGCTTGGTAACATATACAAGAATAACACATATT---------------------AAATTTTGGTAAAATTTTATTTAATCTGTATAGATC Template switch alignment (log-probability: -28.6) AGAAAATGTAAAATCTGTGGAAGGCTTGGTAACATATACA|TATTCTTGTATATGTTACCAA|AATA---------AAATTTTGGTAAAATTTTATTTAATCTGTATAGATC AGAAAATGTAAAATCTGTGGAAGGCTTGGTAACATATACA|TATTCTTGTATATGTTACCAA|AATAACACATATTAAATTTTGGTAAAATTTTATTTAATCTGTATAGATC ========== Event 1079 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAAATAAACACATCACAATAAATTGG--------C---TTTATCAGTGTTATAAGCATGCATA Chimp: TAAAATAAACACTTCACAATAAATTGG--------C---TTTATCAGTGTTATAAGCATGCATA Gorilla: TAAAATAAACACATCACAATAAATTGATAAAGCCAATTTATAATCAGTGTTATAAGCATGCATA ↑ 3 1 4 2 Human: TAAAATAAACACATCACAATAAATTGG--------C---TTTATCAGTGTTATAAGCATGCATA Cluster: [ ] Orangutan: TAAAATAGACACATCACAATAAATCGA--------C---TTTATCAGTGTTATAAGCATGCATA Human > Gorilla --------------- chr14:20536841-20536854 Template switch process: F1: L ATTTACTAATTATGGTAAAATAAACACATCACAATAAATTG 1 F3: 4 TAATCAGTGTTATAAGCATGCATAGTTTCTAAAAGATCACAG R RF: ATTTACTAATTATGGTAAAATAAACACATCACAATAAATTGGCTTTATCAGTGTTATAAGCATGCATAGTTTCTAAAAGATCATAG RR: TAAATGATTAATACCATTTTATTTGTGTAGTGTTATTTAACCGAAATAGTCACAATATTCGTACGTATCAAAGATTTTCTAGTATC F2: 3 ATTTAACCGAAATA 2 Unidirectional alignment (log-probability: -49.4) TTTACTAATTATGGTAAAATAAACACATCACAATAAATTGataaagccaatttata-----ATCAGTGTTATAAGCATGCATAGTTTCTAAAAGATCAc TTTACTAATTATGGTAAAATAAACACATCACAATAAATTG----------------GCTTTATCAGTGTTATAAGCATGCATAGTTTCTAAAAGATCAT Template switch alignment (log-probability: -28.6) TTTACTAATTATGGTAAAATAAACACATCACAATAAATTG|ATAAAGCCAATTTA|TaATCAGTGTTATAAGCATGCATAGTTTCTAAAAGATCAc TTTACTAATTATGGTAAAATAAACACATCACAATAAATTG|ATAAAGCCAATTTA|TTATCAGTGTTATAAGCATGCATAGTTTCTAAAAGATCAT ========== Event 1080 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTCCAAGGGGTCTAACCTGGGATTCAAGTGAGATTTGGAATTGCTTTtgtggtggaacgagctggatctgttgtgagatctgggttgggtctgcttagacttgaagctctgttttgtcattcttagctttggtatcttgagcaagtcacttgacctctctattcttcagttt ↑ 4 1 3 2 Chimp: ATTCCAAGGGGTCTAACCTGG-----------GATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGTTGTgagctctgggttgggtctgcttagacttgaagctctgttttgtcattcttagctttggtatcttgagcaagtcacttgacctctctattcttcagttt ↓ 4 1 3 2 Gorilla: ATTCCAAGGGGTCTAACCTGGGATTCAAGTGAGATTTGGAATTGCTTTTGTGGTGGAACGAGCTGGATCTGTTGTgagctctgggttcggtctgcttggacttgaagctctgttttgtcattcttagctttggtatcttgagcaagtcacttgacctctctattcttcagttt Human: ATTCCAAGGGGTCTAACCTGGGATTCAAGTGAGATTTGGAATTGCTTTtgtggtggaacgagctggatctgttgtgagatctgggttgggtctgcttagacttgaagctctgttttgtcattcttagctttggtatcttgagcaagtcacttgacctctctattcttcagttt Cluster: [ ] Orangutan: AGTCCAAGGGGTCTAACCTGGGATTCAAGTGAGATTTGGAATTGCTTTTGTGGTGGAACGAGCTGGATCTGTTGTgagctctgggttgggtctgcttagacttgaagctctgttttgtcattcttagctttgggatctagagcaagtcacttgacctctctattcttcagttt Chimp > Human ------------- chr14:31467347-31467353 Template switch process: F1: L GCCCTTCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATT 1 F3: 4 GATTTGGAATTGCTTTTGTGGTGGAACGAGCTGGATCTGT R RF: GCCCTTCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGTTGTGAGCTCTGGGTTGGGTCTGCTTAGACTTGAAGCTCTGTTTTGTCATTCTTAGCTTTGGTATCTTGAGCAAGTCACTTG RR: CGGGAAGTCGAACCACTCTCTAAGGTTCCCCAGATTGGACCCTAAACCTTAACGAAAACACCACCTTGTTCGACCTAGACAACACTCGAGACCCAACCCAGACGAATCTGAACTTCGAGACAAAACAGTAAGAATCGAAACCATAGAACTCGTTCAGTGAAC F2: 3 AGTGAAC 2 Unidirectional alignment (log-probability: -32.7) TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGgattcaagtgaGATTTGGAATTGCTTTTGTGGTGGAACgAGCTGGATCTGT TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGG-----------GATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGT Template switch alignment (log-probability: -22.2) TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATT|CAAGTGA|GATTTGGAATTGCTTTTGTGGTGGAACgAGCTGGATCTGT TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATT|CAAGTGA|GATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGT Chimp > Gorilla --------------- chr14:31758024-31758030 Template switch process: F1: L GCCCTTCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATT 1 F3: 4 GATTTGGAATTGCTTTTGTGGTGGAACGAGCTGGATCTGT R RF: GCCCTTCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGTTGTGAGCTCTGGGTTGGGTCTGCTTAGACTTGAAGCTCTGTTTTGTCATTCTTAGCTTTGGTATCTTGAGCAAGTCACTTG RR: CGGGAAGTCGAACCACTCTCTAAGGTTCCCCAGATTGGACCCTAAACCTTAACGAAAACACCACCTTGTTCGACCTAGACAACACTCGAGACCCAACCCAGACGAATCTGAACTTCGAGACAAAACAGTAAGAATCGAAACCATAGAACTCGTTCAGTGAAC F2: 3 AGTGAAC 2 Unidirectional alignment (log-probability: -32.2) TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGgattcaagtgaGATTTGGAATTGCTTTTGTGGTGGAACgAGCTGGATCTGT TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGG-----------GATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGT Template switch alignment (log-probability: -22.2) TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATT|CAAGTGA|GATTTGGAATTGCTTTTGTGGTGGAACgAGCTGGATCTGT TCAGCTTGGTGAGAGATTCCAAGGGGTCTAACCTGGGATT|CAAGTGA|GATTTGGAATTGCTTTTGTGGTGGAACAAGCTGGATCTGT ========== Event 1081 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACTCAAGTAAGAGAAATGGA-----ACACTGGGAGGTGATGGAAAGAATTAG ↑ 1 3 4 Chimp: AACTCAAGTAAGAGAAATGGAATTTCCCAG-TGGAGGTGATGGAAAGAATTAG Gorilla: AACTCAAGTAAGAGAAATGGA-----AAACTGAGAGGTGATGGAAAGAACTAG Human: AACTCAAGTAAGAGAAATGGA-----ACACTGGGAGGTGATGGAAAGAATTAG Cluster: [ ] Orangutan: AACTCAAGTAAGAGAAATGGA-----ACACTGGGAGGTGATGGAAAGAATAAG Chimp > Human ------------- chr14:84361075-84361079 Template switch process: F1: L CATGTAATAGAAGGGAGAGGAACTCAAGTAAGAGAAATGGAA 1 F3: 4 GGAGGTGATGGAAAGAATTAGACGTGGAGTTAAGGTGTCT R RF: CATGTAATAGAAGGGAGAGGAACTCAAGTAAGAGAAATGGAATTTCCCAGTGGAGGTGATGGAAAGAATTAGACGTGGAGTTAAGGTGTCT RR: GTACATTATCTTCCCTCTCCTTGAGTTCATTCTCTTTACCTTAAAGGGTCACCTCCACTACCTTTCTTAATCTGCACCTCAATTCCACAGA F2: 3 GTCAC 2 Unidirectional alignment (log-probability: -28.8) TGTAATAGAAGGGAGAGGAACTCAAGTAAGAGAAATGGAAcactg---------GGAGGTGATGGAAAGAATTAGACGTGGAGTTAAGGTGTCT TGTAATAGAAGGGAGAGGAACTCAAGTAAGAGAAATGGAA-----TTTCCCAGTGGAGGTGATGGAAAGAATTAGACGTGGAGTTAAGGTGTCT Template switch alignment (log-probability: -15.9) TGTAATAGAAGGGAGAGGAACTCAAGTAAGAGAAATGGAA|CACTG|GGAGGTGATGGAAAGAATTAGACGTGGAGTTAAGGTGTCT TGTAATAGAAGGGAGAGGAACTCAAGTAAGAGAAATGGAA|CACTG|GGAGGTGATGGAAAGAATTAGACGTGGAGTTAAGGTGTCT ========== Event 1082 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: gccacgctgcaaagacacagatgcttgagagagcctggcacattggcagagcTGTGCCAGGCTCTCTCAAGCATCTGTGTCATTGTAAAATTAT-------- Chimp: gccaccctgcaaagacacagatgcttgagagagcctggcacattggcagagcCGTGCCAGGCTCTCTCAAGCGTCTGTGTCTTTGTAAAATTAT-------- Gorilla: gccaccctgcaaagacacagatgcttgagagagcctggcacattggcagagcCGTGCCAGGCTCTCTCAAGTGCCTGTGTCTTTGTAAAATTATTTACAAAG ↓ 3 2 1 4 Human: gccacgctgcaaagacacagatgcttgagagagcctggcacattggcagagcTGTGCCAGGCTCTCTCAAGCATCTGTGTCATTGTAAAATTAT-------- Cluster: [ ] Orangutan: tccaccctgcaaagacacagatgcttgagagagcctggcacgttggcagagccg------------------------------------------------ Gorilla > Human --------------- chr14:89064618-89064640 Template switch process: F1: L GAGCCTGGCACATTGGCAGAGC 1 F3: 4 TGTGTCATTGTAAAATTAT R RF: GATGCTTGAGAGAGCCTGGCACATTGGCAGAGCCGTGCCAGGCTCTCTCAAGTGCCTGTGTCTTTGTAAAATTAT RR: CTACGAACTCTCTCGGACCGTGTAACCGTCTCGGCACGGTCCGAGAGAGTTCACGGACACAGAAACATTTTAATA F2: 3 CTACGAACTCTCTCGGACCGTGT 2 Unidirectional alignment (log-probability: -36.7) GAGCCTGGCACATTGGCAGAGCtGTGCCAGGCTCTCTCAAGcatCTGTGTCaTTGTAAAATTAT---------------------------- GAGCCTGGCACATTGGCAGAGCCGTGCCAGGCTCTCTCAAGTGCCTGTGTCTTTGTAAAATTATTTACAAAGAAAGCAACTCTGTGCTTTCT Template switch alignment (log-probability: -23.1) GAGCCTGGCACATTGGCAGAGC|TGTGCCAGGCTCTCTCAAGCATC|TGTGTCaTTGTAAAATTAT GAGCCTGGCACATTGGCAGAGC|TGTGCCAGGCTCTCTCAAGCATC|TGTGTCTTTGTAAAATTAT ========== Event 1083 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTGAAAGGGATGAGATTTCTGAGCCCAAGGGCTCAGAAGGGCTTTCAAGATATCTCT Chimp: CTTGAAAGGGATGAGGTTTCTGAGCCCAAGAA----CAAGGGCTTTCAAGATATCTCT Gorilla: CTTGAAAGGGATGAGGTTTCTGAGCCCAAGAA----CAAGGGCTTTCAAGATATCTCT ↓ 3 2 1 4 Human: CTTGAAAGGGATGAGATTTCTGAGCCCAAGGGCTCAGAAGGGCTTTCAAGATATCTCT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr14:16770705-16770711 Template switch process: F1: L TTTCTGAACACCTTGAAAGGGATGAGATTTCTGAGCCCAAG 1 F3: 4 AAGGGCTTTCAAGATATCTCTAGGAATCCTCAGTCTCTTG R RF: TTTCTGAACACCTTGAAAGGGATGAGGTTTCTGAGCCCAAGAACAAGGGCTTTCAAGATATCTCTAGGAATCCTCAGTCTCTTG RR: AAAGACTTGTGGAACTTTCCCTACTCCAAAGACTCGGGTTCTTGTTCCCGAAAGTTCTATAGAGATCCTTAGGAGTCAGAGAAC F2: 3 GACTCGG 2 Unidirectional alignment (log-probability: -33.2) TTCTGAACACCTTGAAAGGGATGAGaTTTCTGAGCCCAAGggctcAgAAGGGCTTTCAAGATATCTCTAGGAATCCTCAGTCTCTTG TTCTGAACACCTTGAAAGGGATGAGGTTTCTGAGCCCAAGA----ACAAGGGCTTTCAAGATATCTCTAGGAATCCTCAGTCTCTTG Template switch alignment (log-probability: -22.1) TTCTGAACACCTTGAAAGGGATGAGaTTTCTGAGCCCAAG|GGCTCAG|AAGGGCTTTCAAGATATCTCTAGGAATCCTCAGTCTCTTG TTCTGAACACCTTGAAAGGGATGAGGTTTCTGAGCCCAAG|GGCTCAG|AAGGGCTTTCAAGATATCTCTAGGAATCCTCAGTCTCTTG ========== Event 1084 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CAATTTAGAAACTGCTGTTGGACTCCCATCCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGGAAAGCAAAAAGCATGCTGGTCTTCTAAGTGCAGCTTTATTGGCATTTGGCTTCCT ↓ 1 4 3 2 Chimp: CAATTTAGAAACTGCTGTTGGACTAG--CTCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGGAAAGCAAAAAGCACGCTGGTCTTCTAAGTGCAGCTTTATTGGCGTTTGGCTTCCT Gorilla: CAATTTAGAAACTGCTGTTGGGCTAG--CTCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGGAAAGCAAAAAGCATGCTGGTCTTCTAAGTGCAGCTTTATTGGCATTTGGCTTCCT ↑ 1 4 3 2 Human: CAATTTAGAAACTGCTGTTGGACTCCCATCCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGGAAAGCAAAAAGCATGCTGGTCTTCTAAGTGCAGCTTTATTGGCATTTGGCTTCCT Cluster: [ ] Orangutan: CAATTTAGAAACTGCTGTTGGACTAG--CTCCGTGGATGGGAGGTCATTCCCTTCCTTAATGGGATTTGGAAAGCAAAA-ACATGCTGGTCTTCTAAGTGCAGCTTTACTGGCGTTTGGCTTCTT Human > Chimp ------------- chr14:17579131-17579134 Template switch process: F1: L AACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACT 1 F3: 4 CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG R RF: AACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACTCCCATCCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGGAAAGCAAAAAGCATGCTGGTCTTCTAAGTGCAGCT RR: TTGAAAGAAAAGGTCACGTTAAATCTTTGACGACAACCTGAGGGTAGGGCACCTACCCTCCGGTAAGAGAAGGAATTGCCCTAAACCTTTCGTTTTTCGTACGACCAGAAGATTCACGTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -27.2) ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGActagCT------CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGA----CTCCCATCCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG Template switch alignment (log-probability: -15.8) ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACT|AGCT|CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACT|AGCT|CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG Human > Gorilla --------------- chr14:17560387-17560390 Template switch process: F1: L GCAAACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGGCT 1 F3: 4 CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG R RF: GCAAACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACTCCCATCCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGGAAAGCAAAAAGCATGCTGGTCTTCTAAGTGCAGCT RR: CGTTTGAAAGAAAAGGTCACGTTAAATCTTTGACGACAACCTGAGGGTAGGGCACCTACCCTCCGGTAAGAGAAGGAATTGCCCTAAACCTTTCGTTTTTCGTACGACCAGAAGATTCACGTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -31.2) ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGG---------gctagctCCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACTCCCATC-------CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG Template switch alignment (log-probability: -21.8) ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGgCT|AGCT|CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG ACTTTCTTTTCCAGTGCAATTTAGAAACTGCTGTTGGACT|AGCT|CCGTGGATGGGAGGCCATTCTCTTCCTTAACGGGATTTGG ========== Event 1085 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATGTGACATCTCCTAAGAGTGCTGGTGCCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGGCTTTGGGG Chimp: TGATGTGACATCTCCTAAGAGTGCTGGTGCCCCTGACGGGGGCAGGGGAACAGTCTCTAGCCACGGCTTTGGGG Gorilla: TGATGTGACATCTCCTAAGAG-A-CTGTTCCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGACTTTGGGG ↑ 1 4 3 2 Human: TGATGTGACATCTCCTAAGAGTGCTGGTGCCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGGCTTTGGGG Cluster: [ ] Orangutan: TGATGTGACATCTCCTAAGAGTGCTGGTGCCCCTGACGGGGGGAGGGGAACAGTCTCCAGCCATGGCTTTGGGG Human > Gorilla --------------- chr14:74599763-74599768 Template switch process: F1: L GTGGTCATCCTCCTGGGAAATGATGTGACATCTCCTAAGAG 1 F3: 4 CCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGACTT R RF: GTGGTCACCCTCCTGGGAAATGATGTGACATCTCCTAAGAGTGCTGGTGCCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGGCTT RR: CACCAGTGGGAGGACCCTTTACTACACTGTAGAGGATTCTCACGACCACGGGGACTGCCCCCGTCCCCTTGTCAGAGGTCGGTGCCGAA F2: 3 TTGTCA 2 Unidirectional alignment (log-probability: -39.2) TGGTCAtCCTCCTGGGAAATGATGTGACATCTCCTAAGAGactgtT-------CCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGaCTT TGGTCACCCTCCTGGGAAATGATGTGACATCTCCTAAGAG-----TGCTGGTGCCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGGCTT Template switch alignment (log-probability: -27.5) TGGTCAtCCTCCTGGGAAATGATGTGACATCTCCTAAGAG|ACTGTT|CCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGaCTT TGGTCACCCTCCTGGGAAATGATGTGACATCTCCTAAGAG|ACTGTT|CCCCTGACGGGGGCAGGGGAACAGTCTCCAGCCACGGCTT ========== Event 1086 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TCTTTAGATACTGGTAGATATCATTAGTAAAAACTGAATGGTTTTTACTAATAAAGCTGGGCACAGGCCAAGG Chimp: TCTTTAGATGCTGGTAGATAT-----CTAAAAACCATTCAGTTTTTACTGATAAAGCTGGGCACAGGCCAAGG ↓ 1 3 4 2 Gorilla: TCTTTAGATGCTGGTAGATATTATTAGTAAAAACTGAATGGTTTTTACTAATAAAGCTGGGCACAGGCCAAGG Human: TCTTTAGATACTGGTAGATATCATTAGTAAAAACTGAATGGTTTTTACTAATAAAGCTGGGCACAGGCCAAGG Cluster: [ ] Orangutan: TCTTTAGATGCTGGTAGATATCATTAGTAAAAACTGAATG---GTGAGAAATACAGCTGGGCACAGCCCAAGG Chimp > Gorilla --------------- chr14:74749029-74749047 Template switch process: F1: L CTAGAGGATGAAGGTATTTCTCTTTAGATGCTGGTAGATAT 1 F3: 4 GTTTTTACTAATAAAGCTGGGCACAGGCCAAGGCAGACATGAATGACAGG R RF: CTAGAGGATGAAGGTATTTCTCTTTAGATGCTGGTAGATATCTAAAAACCATTCAGTTTTTACTGATAAAGCTGGGCACAGGCCAAGGCAGACATGAATGACAGG RR: GATCTCCTACTTCCATAAAGAGAAATCTACGACCATCTATAGATTTTTGGTAAGTCAAAAATGACTATTTCGACCCGTGTCCGGTTCCGTCTGTACTTACTGTCC F2: 3 GTAAGTCAAAAATGATTAT 2 Unidirectional alignment (log-probability: -54.3) TAGAGGATGAAGGTATTTCTCTTTAGATGCTGGTAGATATtattagtaaaaactgaatg--------------GTTTTTACTaATAAAGCTGGGCACAGGCCAAGGCAGACAT TAGAGGATGAAGGTATTTCTCTTTAGATGCTGGTAGATAT-------------------CTAAAAACCATTCAGTTTTTACTGATAAAGCTGGGCACAGGCCAAGGCAGACAT Template switch alignment (log-probability: -29.4) TAGAGGATGAAGGTATTTCTCTTTAGATGCTGGTAGATAT|TATtAGTAAAAACTGAATG|GTTTTTACTaATAAAGCTGGGCACAGGCCAAGGCAGACAT TAGAGGATGAAGGTATTTCTCTTTAGATGCTGGTAGATAT|TATCAGTAAAAACTGAATG|GTTTTTACTGATAAAGCTGGGCACAGGCCAAGGCAGACAT ========== Event 1087 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAAGAGTGAGGAGCCTCGTA------GAAGTCCCATGAGGGAACTCAAGGG---------------------ACCAGTTCCCAGGAGTGGGGGACCTGTTCCCAGCCTCAGAGATCATGAACCTGCAGAGTGGCTGGGTGCAGTGGCTcacattgggacgctgaggtgggcagatcacctgaagtcaggagaccagcctggccaaca Chimp: ACAAGAGTGAGGAGCCTCGTA---GGAGAGGTCCCATGAGGGAACTCAAGGG---------------------ACCAGTTCCCAGGAGTGGGGGACCTGTTCCCAGCCTCAGAGATCATGAACCTGCAGAGTggctgggtgcggtggctcacattgggaggctgaggtgggcagatcacctgaagtcaggagaccagcctggccaaca ↑ 3 2 1 4 Gorilla: ACAAGAGTGAGGAGCCTCGTAGGA---GAGGTCCCATGAGGGAACTCAAGGG------------------------------------------ACCTGTTCCCAGCCTCAGAGATCATGAACCTGCAGAGTGGCTGGGTGTGGTGGCTcacattggaaggctgaggtgggcagatcacctgaagtcaggagaccagcctggccaaca Human: ACAAGAGTGAGGAGCCTCGTA------GAAGTCCCATGAGGGAACTCAAGGG---------------------ACCAGTTCCCAGGAGTGGGGGACCTGTTCCCAGCCTCAGAGATCATGAACCTGCAGAGTGGCTGGGTGCAGTGGCTcacattgggacgctgaggtgggcagatcacctgaagtcaggagaccagcctggccaaca Cluster: [ ] Orangutan: ACAAGAGTGAGGAGCCACGTAGGA---GACGTCCCATGAGGGAACTCAAGGGACCAGTTCCCAGAAGTGGGGG---------------------ACCTGTTCCCAGCCTCAGAGATCATGAACCTGCAGAGTGGCTGGGTGCAGTGGCTcacattgggaggctgaggtgggaggatcacctgaggtcaggagaccagcctggccaaca Gorilla > Chimp --------------- chr14:76173600-76173606 Template switch process: F1: L GGCACACAAAGTTCAAAGGGACAAGAGTGAGGAGCCTCGTAGGAGAGGTCCCATGAGGGAACTCAAGGGACC 1 F3: 4 AGGAG R RF: GGCACACAAAGTTCAAAGGGACAAGAGTGAGGAGCCTCGTAGGAGAGGTCCCATGAGGGAACTCAAGGGACCTGTTCCCAGCCTCAGAGATCATGAACCTGCAGAGTGGCTGGGTGTGGTGGCTCACATTGGAAGGCTGAGGTGGGCAGATCACCTGAAGTCAGGAG RR: CCGTGTGTTTCAAGTTTCCCTGTTCTCACTCCTCGGAGCATCCTCTCCAGGGTACTCCCTTGAGTTCCCTGGACAAGGGTCGGAGTCTCTAGTACTTGGACGTCTCACCGACCCACACCACCGAGTGTAACCTTCCGACTCCACCCGTCTAGTGGACTTCAGTCCTC F2: 3 CCCTTGA 2 Unidirectional alignment (log-probability: -29.3) AGCCTCGTAGGAGAGGTCCCATGAGGGAACTCAAGGGaccagttcccaggag AGCCTCGTAGGAGAGGTCCCATGAGGGAACTCAAGGG--------------- Template switch alignment (log-probability: -16.5) AGCCTCGTAGGAGAGGTCCCATGAGGGAACTCAAGGGACC|AGTTCCC|AGGAG AGCCTCGTAGGAGAGGTCCCATGAGGGAACTCAAGGGACC|AGTTCCC|AGGAG ========== Event 1088 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATCTTATTTCTTCCTAGTAGGGTTCAGCTTCACTCACCTTGGTTACATGGATGTCATCACCTGAATGCTTTGTATCAACAATTGTTTTAAACATGAAAAGCAGTTGTAGTAA------AATTAAAACCTTGCATTTCATTCCCAGATGTTCTATTAACTTAAGTTGTAGGGATAGCGGG-GGTGC----ACCAAGATTCTAATGGGTTTAATATAATCAAAACACTTGTTCACTGTATGTTTATTGAGTTT-CTC--------------------------------------------------------------------------- Chimp: AATCTTATTTCTTCCTAGTAGTGTTTTGA---------------------------------------------------------------------------TTATACTAA---ACCCATTAGAATCTTG--GTGC-ACCCCCGCTATCCCTACAACTTAAGTTAATAGAACATCTGGGAATGA--AATGCAAGGTTTTAA---TTTTACTACA------ACTGCTTTT-----CATGTTTAAAACAATT-GTG--------------------------------------------------------------------------- Gorilla: AATCTTATTTCTTCCTAGTAGTGTTTTGA---------------------------------------------------------------------------TTATACTAAACC---CATTAGAATCTTG--GTGC-ACCCCCGCTATCCCTACAACTTAAGTTAATAGAACATCTGGGAATGAAG--TGCAAGGttttaa---ttttactaca------attgctttt-----catgtttaaaacaattgTTGATACAAAGCATTCAGGTGATGACATCCATGTAACCAAGGTGAGTGAAGCTGAACCCTGGGAAAGAGTCATAATTG ↓ 1 3 4 2 Human: AATCTTATTTCTTCCTAGTAGGGTTCAGCTTCACTCACCTTGGTTACATGGATGTCATCACCTGAATGCTTTGTATCAACAATTGTTTTAAACATGAAAAGCAGTTGTAGTAA------AATTAAAACCTTGCATTTCATTCCCAGATGTTCTATTAACTTAAGTTGTAGGGATAGCGGG-GGTGC----ACCAAGATTCTAATGGGTTTAATATAATCAAAACACTTGTTCACTGTATGTTTATTGAGTTT-CTC--------------------------------------------------------------------------- Cluster: [ ] Orangutan: AATCTTTTTTCTTCCTAGTAGTGTTTTGA---------------------------------------------------------------------------TTATACTAAACC---CATTAGAATCTTG--GTGC-ACC-CCACTATCCCTACAACTTAAGTTAATAGAACATCTGGGAATGAAA--TGCAAGGTTTTAA---TTTTGCTACA------ACTGCTTTT-----CATGTTTAAAACAATTGTTGATACAAAGCATTCAGGTGATGACATCCATGTAACCAAGGTGAGTGAAGCTGAACCCTGGGAAAGAGTCATAATTG Gorilla > Human --------------- chr14:91551670-91551831 Template switch process: F1: L TAATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAG 1 F3: 4 AGAT R RF: TAATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAGCATCTTGCCTCAGCCTCCCAAAGTGTGATTACAGGCATGAGCCATCACACCCAGCCTACGTAACTAATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAGTGTTTTGATTATACTAAACCCATTAGAATCTTGGTGCACCCCCGCTATCCCTACAACTTAAGTTAATAGAACATCTGGGAATGAAGTGCAAGGTTTTAATTTTACTACAATTGCTTTTCATGTTTAAAACAATTGTTGATACAAAGCATTCAGGTGATGACATCCATGTAACCAAGGTGAGTGAAGCTGAACC RR: ATTATGTGTAATAAATGAACTTAGAATAAAGAAGGATCATCGTAGAACGGAGTCGGAGGGTTTCACACTAATGTCCGTACTCGGTAGTGTGGGTCGGATGCATTGATTATGTGTAATAAATGAACTTAGAATAAAGAAGGATCATCACAAAACTAATATGATTTGGGTAATCTTAGAACCACGTGGGGGCGATAGGGATGTTGAATTCAATTATCTTGTAGACCCTTACTTCACGTTCCAAAATTAAAATGATGTTAACGAAAAGTACAAATTTTGTTAACAACTATGTTTCGTAAGTCCACTACTGTAGGTACATTGGTTCCACTCACTTCGACTTGG F2: 3 ACCACGTGGGGGCGATAGGGATGTTGAATTCAATTATCTTGTAGACCCTTACTTTACGTTCCAAAATTAAAATGATGTTGACGAAAAGTACAAATTTTGTTAACAACTATGTTTCGTAAGTCCACTACTGTAGGTACATTGGTTCCACTCACTTCGACTTGG 2 Unidirectional alignment (log-probability: -256) AATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAG-------------------------------------------------------------------------------------------GGTtcagcttcactcaccttggttacatggatgtcatcacctgaatgctttgtatcaacaattgttttaaacatgaaaagcagttgtagtaaaattaaaaccttgcatttcattcccagatgttctattaacttaagttgtagggatagcgggggtgcaccaagat AATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAGTGTTTTGATTATACTAAACCCATTAGAATCTTGGTGCACCCCCGCTATCCCTACAACTTAAGTTAATAGAACATCTGGGAATGAAGTGCAAGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -46.2) AATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAG|GGTTCAGCTTCACTCACCTTGGTTACATGGATGTCATCACCTGAATGCTTTGTATCAACAATTGTTTTAAACATGAAAAGCAgTTGTAGTAAAATTAAAACCTTGCAtTTCATTCCCAGATGTTCTATTAACTTAAGTTGTAGGGATAGCGGGGGTGCACCA|AGAT AATACACATTATTTACTTGAATCTTATTTCTTCCTAGTAG|GGTTCAGCTTCACTCACCTTGGTTACATGGATGTCATCACCTGAATGCTTTGTATCAACAATTGTTTTAAACATGAAAAGCAATTGTAGTAAAATTAAAACCTTGCACTTCATTCCCAGATGTTCTATTAACTTAAGTTGTAGGGATAGCGGGGGTGCACCA|AGAT ========== Event 1089 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAGGGGATTATATTGGTCAGTAG--AGGTCCAAC---TAC---TGAAGAGAAGAGTGCACGGGGG ↑ 3 1 2 4 Chimp: GAAGGGGATTATATTGGTCAGTAGTTGGACCTCAC------GGGGGAAGAGAAGAGTGCACGGGGG Gorilla: GAAGGGGATTATATTGGTCAGTAGTTGGACCTCAC---------GGAAGAGAAGAGTGCACGGGGG ↓ 3 1 2 4 Human: GAAGGGGATTATATTGGTCAGTAG--AGGTCCAAC---TAC---TGAAGAGAAGAGTGCACGGGGG Cluster: [ ] Orangutan: GAAGGGGATTAAGTTGGTCAGTAGTTGGACCTCTCGGG------GGAAGAGAAGAGCGCACGGGGG Chimp > Human ------------- chr14:92323019-92323031 Template switch process: F1: L AGAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG 1 F3: 4 GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA R RF: AGAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAGTTGGACCTCACGGGGGAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA RR: TCTCTTTTTCCCTCTTCCTTCCCCTAATATAACCAGTCATCAACCTGGAGTGCCCCCTTCTCTTCTCACGTGCCCCCTCACGCGGGATGCCCTGCT F2: 3 TCATCAACCTGGA 2 Unidirectional alignment (log-probability: -39.1) GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAGaggtccaactacT--------------GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG------------TTGGACCTCACGGGGGAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA Template switch alignment (log-probability: -16.9) GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG|AGGTCCAACTACT|GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG|AGGTCCAACTACT|GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA Gorilla > Human --------------- chr14:92323019-92323031 Template switch process: F1: L AGAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG 1 F3: 4 GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA R RF: AGAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAGTTGGACCTCACGGAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA RR: TCTCTTTTTCCCTCTTCCTTCCCCTAATATAACCAGTCATCAACCTGGAGTGCCTTCTCTTCTCACGTGCCCCCTCACGCGGGATGCCCTGCT F2: 3 TCATCAACCTGGA 2 Unidirectional alignment (log-probability: -38.5) GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAGaggtccaactacT-----------GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG------------TTGGACCTCACGGAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA Template switch alignment (log-probability: -17.4) GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG|AGGTCCAACTACT|GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA GAGAAAAAGGGAGAAGGAAGGGGATTATATTGGTCAGTAG|AGGTCCAACTACT|GAAGAGAAGAGTGCACGGGGGAGTGCGCCCTACGGGACGA ========== Event 1090 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCCTCTTCCACAGTCCCCGA--GCCCCAAGCTCATCACCAATACCGAGAATCAC Chimp: TGCGTCTTCCACAGTCCCCGA--GCCCCAAGCTCATCACCAATACTGAGAATCAC Gorilla: TGCCTCTTCCACAGTCCCCGATGAGCTTGGGCTCATCACCAATACTGAGAATCAC ↑ 1 3 4 2 Human: TGCCTCTTCCACAGTCCCCGA--GCCCCAAGCTCATCACCAATACCGAGAATCAC Cluster: [ ] Orangutan: TGCCTCTTCCACAGTCCCTGA--GCTCCAAGCTCATCACCAATACTGAGAATCAC Human > Gorilla --------------- chr14:76330279-76330287 Template switch process: F1: L ACACACTGGGAGGACGTTGCTGCCTCTTCCACAGTCCCCGA 1 F3: 4 GCTCATCACCAATACTGAGAATCACACAATGAAGTCAGAG R RF: ACACACTGGGAGGATGTTGCTGCCTCTTCCACAGTCCCCGAGCCCCAAGCTCATCACCAATACCGAGAATCACACAATGAAGTCAGAG RR: TGTGTGACCCTCCTACAACGACGGAGAAGGTGTCAGGGGCTCGGGGTTCGAGTAGTGGTTATGGCTCTTAGTGTGTTACTTCAGTCTC F2: 3 GGTTCGAGT 2 Unidirectional alignment (log-probability: -43.5) CACACTGGGAGGAcGTTGCTGCCTCTTCCACAGTCCCCGAtgagcttgG------GCTCATCACCAATACtGAGAATCACACAATGAAGTCAGAG CACACTGGGAGGATGTTGCTGCCTCTTCCACAGTCCCCGA--------GCCCCAAGCTCATCACCAATACCGAGAATCACACAATGAAGTCAGAG Template switch alignment (log-probability: -27.9) CACACTGGGAGGAcGTTGCTGCCTCTTCCACAGTCCCCGA|TGAGCTTGG|GCTCATCACCAATACtGAGAATCACACAATGAAGTCAGAG CACACTGGGAGGATGTTGCTGCCTCTTCCACAGTCCCCGA|TGAGCTTGG|GCTCATCACCAATACCGAGAATCACACAATGAAGTCAGAG ========== Event 1091 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAC---ACACACTGGGAGGATGTTGCTGCCTCTTCCACAGTCCCCGA--GCCCCAAGCTCATCACCAATACCGAGAATCAC Chimp: CCAC---ACACACTGGGAGGATGTTGCTGCGTCTTCCACAGTCCCCGA--GCCCCAAGCTCATCACCAATACTGAGAATCAC ↓ 1 3 4 2 Gorilla: CCAC---ACACACTGGGAGGACGTTGCTGCCTCTTCCACAGTCCCCGATGAGCTTGGGCTCATCACCAATACTGAGAATCAC Human: CCAC---ACACACTGGGAGGATGTTGCTGCCTCTTCCACAGTCCCCGA--GCCCCAAGCTCATCACCAATACCGAGAATCAC Cluster: [ ] Orangutan: CCACACCACACACTGGGAGGATGTTGCTGCCTCTTCCACAGTCCCTGA--GCTCCAAGCTCATCACCAATACTGAGAATCAC Chimp > Gorilla --------------- chr14:76330279-76330287 Template switch process: F1: L GAAGTTGGTACCTAATTTGCAGACCACACACACTGGGAGGACGTTGCTGCCTCTTCCACAGTCCCCGA 1 F3: 4 GCTCATCACCAATA R RF: GAAGTTGGTACCTAATTTGCAGACCACACACACTGGGAGGATGTTGCTGCGTCTTCCACAGTCCCCGAGCCCCAAGCTCATCACCAATA RR: CTTCAACCATGGATTAAACGTCTGGTGTGTGTGACCCTCCTACAACGACGCAGAAGGTGTCAGGGGCTCGGGGTTCGAGTAGTGGTTAT F2: 3 GGTTCGAGT 2 Unidirectional alignment (log-probability: -43.5) CACACTGGGAGGAcGTTGCTGCcTCTTCCACAGTCCCCGAtgagcttgG------GCTCATCACCAATA CACACTGGGAGGATGTTGCTGCGTCTTCCACAGTCCCCGA--------GCCCCAAGCTCATCACCAATA Template switch alignment (log-probability: -27.9) CACACTGGGAGGAcGTTGCTGCcTCTTCCACAGTCCCCGA|TGAGCTTGG|GCTCATCACCAATA CACACTGGGAGGATGTTGCTGCGTCTTCCACAGTCCCCGA|TGAGCTTGG|GCTCATCACCAATA ========== Event 1092 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAATTAGGAGAATCACAGACATTTTCTTTAGG---TAGATCTTAAAAGCACACACAG Chimp: TCAAATTAGGAGAATCACAGACATTTTCTTTAGG---TAGATCTTAAAAGCACACACAG ↓ 3 2 1 4 Gorilla: TCAAATTAGGAGAATCACAGACATTTTCTTTAAATGTCAGATCTTAAAAGCACACACAG ↑ 3 2 1 4 Human: TCAAATTAGGAGAATCACAGACATTTTCTTTAGG---TAGATCTTAAAAGCACACACAG Cluster: [ ] Orangutan: TCAAATTAGGAGAACCACAAACATTTTCTTTAGG---TAGATCTTAAAAGCACACACAG Human > Gorilla --------------- chr14:75983899-75983904 Template switch process: F1: L GTTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA 1 F3: 4 AGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA R RF: GTTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTAGGTAGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA RR: CAATAGACAAGTTTAATCCTCTTAGTGTCTGTAAAAGAAATCCATCTAGAATTTTCGTGTGTGTCGGAGTATCCATGAAAAATT F2: 3 CTGTAA 2 Unidirectional alignment (log-probability: -26.3) TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTAaatGtcAGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA---GGTAGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA Template switch alignment (log-probability: -16.5) TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA|AATGTC|AGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA|AATGTC|AGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA Chimp > Gorilla --------------- chr14:75983899-75983904 Template switch process: F1: L GTTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA 1 F3: 4 AGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA R RF: GTTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTAGGTAGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA RR: CAATAGACAAGTTTAATCCTCTTAGTGTCTGTAAAAGAAATCCATCTAGAATTTTCGTGTGTGTCGGAGTATCCATGAAAAATT F2: 3 CTGTAA 2 Unidirectional alignment (log-probability: -26.3) TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTAaatGtcAGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA---GGTAGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA Template switch alignment (log-probability: -16.5) TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA|AATGTC|AGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA TTATCTGTTCAAATTAGGAGAATCACAGACATTTTCTTTA|AATGTC|AGATCTTAAAAGCACACACAGCCTCATAGGTACTTTTTAA ========== Event 1093 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: AGCATGGTAAGTATGTCTGTTGCAGGTCTGGATTATCCACCTTCTTCAAACTCCAGGGCTAAGTCTGGGATTATCTCCAAGAGCCGGCATGCAACCTGAAGTTTAGGTAAACTGTCTCATTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGGGATAATGAGTAGAAACTCATTATCTACTG ↓ 3 2 1 4 Chimp: AGCATGGTAAGTATGTCTGTTGCAGGTTTGGATTATCCACCTTCTTCAAACTCCAGGGCTAAGTCTGGGATTATCTCCAAGAGCCTGCATGCAACCTGAAGTTTAGGTAAACTGTCTCATTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGGTGCA--AAATAGAAACTCATTATCTACTG Gorilla: AGCATGGTAAGTATGTCTGTTGCAGGTCTGGATTATCCACCTTCTTCAAACTCCAGGGCTAAGTCTGGGATTATCTCCAAGAGCCTGCATGCAACCTGAAGTTTAGGTAAACTGTCTCATTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGGTGCA--AAATAGAAACTCATTATCTACTG Human: AGCATGGTAAGTATGTCTGTTGCAGGTCTGGATTATCCACCTTCTTCAAACTCCAGGGCTAAGTCTGGGATTATCTCCAAGAGCCGGCATGCAACCTGAAGTTTAGGTAAACTGTCTCATTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGGGATAATGAGTAGAAACTCATTATCTACTG Cluster: [ ] Orangutan: AGCATGGTAAGTATGTCTGTTGCAGGTTTGGATTATCCACCTTCTTCAAACTCCAGGGCTAAGTCTGGGATGATCTCCAAGAGCCTGCATGCAACCTGAAGTTTAGGTAAACAGTCTCATTCACCTCGCTGTTCCCAGTGTGGGATCCCCAGGGCTTGGTGCA--AAATGGAAACTCACTATCTACTG Human > Chimp ------------- chr14:14859411-14859415 Template switch process: F1: L ATTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGG 1 F3: 4 AATAGAAACTCATTATCTACTGATAGCTGAATTAAATTTAAA R RF: TTGCAGGTCTGGATTATCCACCTTCTTCAAACTCCAGGGCTAAGTCTGGGATTATCTCCAAGAGCCGGCATGCAACCTGAAGTTTAGGTAAACTGTCTCATTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGGGATAATGAGTAGAAACTCATTATCTACTGATAGCTGAATTAAATTTAAA RR: AACGTCCAGACCTAATAGGTGGAAGAAGTTTGAGGTCCCGATTCAGACCCTAATAGAGGTTCTCGGCCGTACGTTGGACTTCAAATCCATTTGACAGAGTAAGTGGAGCGACAAGGGTCACGCTCTAGGGGTCCCGACCCCTATTACTCATCTTTGAGTAATAGATGACTATCGACTTAATTTAAATTT F2: 3 AACGT 2 Unidirectional alignment (log-probability: -31.7) TTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGGtgcaaaa---------TAGAAACTCATTATCTACTGATAGCTGAATTAAATTTA TTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGG-------GATAATGAGTAGAAACTCATTATCTACTGATAGCTGAATTAAATTTA Template switch alignment (log-probability: -21.9) TTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGG|TGCAA|AaTAGAAACTCATTATCTACTGATAGCTGAATTAAATTTA TTCACCTCGCTGTTCCCAGTGCGAGATCCCCAGGGCTGGG|TGCAA|AGTAGAAACTCATTATCTACTGATAGCTGAATTAAATTTA ========== Event 1094 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCAGCCCTCACTGGCGGCTGCTGGACTTT---CTGTAGGACTCAGTCATGCATGGGATGCTG Chimp: CTCAGCCCTCGCTGGCGGCTGCTGGACTTT---CTGTAGGACTCAGTCATGCATGGGATGCTG ↓ 1 3 4 2 Gorilla: CTCAGCCCTCACTGGCGGCTG--AGTCCTACAGAAGTAGGACTCAATCATGCATGGGATGCTG ↑ 1 3 4 2 Human: CTCAGCCCTCACTGGCGGCTGCTGGACTTT---CTGTAGGACTCAGTCATGCATGGGATGCTG Cluster: [ ] Orangutan: --------------------------------------------------------------- Human > Gorilla --------------- chr14:78069819-78069830 Template switch process: F1: L CCCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTG 1 F3: 4 GTAGGACTCAATCATGCATGGGATGCTGCATTCACAGATC R RF: CCCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTGCTGGACTTTCTGTAGGACTCAGTCATGCATGGGATGCTGCATTCACAGATC RR: GGGAAACGACGGTTTTGAACGAGTCGGGAGTGACCGCCGACGACCTGAAAGACATCCTGAGTCAGTACGTACCCTACGACGTAAGTGTCTAG F2: 3 AAGACATCCTGA 2 Unidirectional alignment (log-probability: -44) CCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTG-----------agtcctacagaaGTAGGACTCAaTCATGCATGGGATGCTGCATTCACAGATC CCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTGCTGGACTTTCT------------GTAGGACTCAGTCATGCATGGGATGCTGCATTCACAGATC Template switch alignment (log-probability: -22.8) CCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTG|AGTCCTACAGAA|GTAGGACTCAaTCATGCATGGGATGCTGCATTCACAGATC CCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTG|AGTCCTACAGAA|GTAGGACTCAGTCATGCATGGGATGCTGCATTCACAGATC Chimp > Gorilla --------------- chr14:78069819-78069830 Template switch process: F1: L CCCTTTGCTGCCAAAACTTGCTCAGCCCTCACTGGCGGCTG 1 F3: 4 GTAGGACTCAATCATGCATGGGATGCTGCATTCACAGATC R RF: CCCTTTGCTGCCAAAACTTGCTCAGCCCTCGCTGGCGGCTGCTGGACTTTCTGTAGGACTCAGTCATGCATGGGATGCTGCATTCACAGATC RR: GGGAAACGACGGTTTTGAACGAGTCGGGAGCGACCGCCGACGACCTGAAAGACATCCTGAGTCAGTACGTACCCTACGACGTAAGTGTCTAG F2: 3 AAGACATCCTGA 2 Unidirectional alignment (log-probability: -49.5) CCTTTGCTGCCAAAACTTGCTCAGCCCTCaCTGGCGGCTG-----------agtcctacagaaGTAGGACTCAaTCATGCATGGGATGCTGCATTCACAGATC CCTTTGCTGCCAAAACTTGCTCAGCCCTCGCTGGCGGCTGCTGGACTTTCT------------GTAGGACTCAGTCATGCATGGGATGCTGCATTCACAGATC Template switch alignment (log-probability: -28.3) CCTTTGCTGCCAAAACTTGCTCAGCCCTCaCTGGCGGCTG|AGTCCTACAGAA|GTAGGACTCAaTCATGCATGGGATGCTGCATTCACAGATC CCTTTGCTGCCAAAACTTGCTCAGCCCTCGCTGGCGGCTG|AGTCCTACAGAA|GTAGGACTCAGTCATGCATGGGATGCTGCATTCACAGATC ========== Event 1095 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGGGACTGAATGCCATTTACAGGGGCTGATTTCAGCCCCTGTAATGCAGTTTTCTCAAAAAAGGTAAGTGGG Chimp: AAGGGACTGAATGCCATTTACAGGGGCTG-------------AAATGCAGTTCTCTCAAAAAAGGTACGTGGG Gorilla: AGGGGACTGAATGCCATTTACAGGGGCTG-------------AAATGCAGTTCTCTCAAAAAAGGTAAGTGGG ↓ 3 142 Human: AGGGGACTGAATGCCATTTACAGGGGCTGATTTCAGCCCCTGTAATGCAGTTTTCTCAAAAAAGGTAAGTGGG Cluster: [ ] Orangutan: AGGGGACTGAATGCCATTTACAGGGGCTG-------------AAATGCAGTTCTCTCAAAAAAGGTAAGTGGG Gorilla > Human --------------- chr14:94163544-94163556 Template switch process: F1: L GTACTAATGCCAAGGGGACTGAATGCCATTTACAGGGGCTGA 1 F3: 4 AATGCAGTTTTCTCAAAAAAGGTAAGTGGGGAAGAAATCAAGTAACAGAT R RF: GTACTAATGCCAAGGGGACTGAATGCCATTTACAGGGGCTGAAATGCAGTTCTCTCAAAAAAGGTAAGTGGGGAAGAAATCAAGTAACAGAT RR: CATGATTACGGTTCCCCTGACTTACGGTAAATGTCCCCGACTTTACGTCAAGAGAGTTTTTTCCATTCACCCCTTCTTTAGTTCATTGTCTA F2: 3 TGTCCCCGACTTT 2 Unidirectional alignment (log-probability: -35.3) ACTAATGCCAAGGGGACTGAATGCCATTTACAGGGGCTGAtttcagcccctgtAATGCAGTTtTCTCAAAAAAGGTAAGTGGGGAAGAAATCA ACTAATGCCAAGGGGACTGAATGCCATTTACAGGGGCTGA-------------AATGCAGTTCTCTCAAAAAAGGTAAGTGGGGAAGAAATCA Template switch alignment (log-probability: -23.2) ACTAATGCCAAGGGGACTGAATGCCATTTACAGGGGCTGA|TTTCAGCCCCTGT|AATGCAGTTtTCTCAAAAAAGGTAAGTGGGGAAGAAATCA ACTAATGCCAAGGGGACTGAATGCCATTTACAGGGGCTGA|TTTCAGCCCCTGT|AATGCAGTTCTCTCAAAAAAGGTAAGTGGGGAAGAAATCA ========== Event 1096 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: taccacaggggtgcgcggcctcactTA---CCATCTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG Chimp: TACCACAGGGGTGCGCGGCCTCACTTA---CCGTCTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG ↑ 1 4 3 2 Gorilla: TACCACAGGGGTGCGCGGCCTTACTTGAAAAGCCCTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG Human: taccacaggggtgcgcggcctcactTA---CCATCTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG Cluster: [ ] Orangutan: TACCACAGGAGTGTGTGGCCTCACTTGAAAAGCCCTGTGGTAAGCCCAGAGAGTCATAAGAGGATCTTAAGGAG Gorilla > Chimp --------------- chr14:79833357-79833361 Template switch process: F1: L GCCTTAGAGTCAGTCTATGTTACCACAGGGGTGCGCGGCCTCACTT 1 F3: 4 CTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG R RF: GCCTTAGAGTCAGTCTATGTTACCACAGGGGTGCGCGGCCTTACTTGAAAAGCCCTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG RR: CGGAATCTCAGTCAGATACAATGGTGTCCCCACGCGCCGGAATGAACTTTTCGGGACACCATTCGGGTCTGCCAGTATTCTCCTAGAATTCCTC F2: 3 TGCCA 2 Unidirectional alignment (log-probability: -33.8) GAGTCAGTCTATGTTACCACAGGGGTGCGCGGCCTcACTT--------accgtCTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG GAGTCAGTCTATGTTACCACAGGGGTGCGCGGCCTTACTTGAAAAGCC-----CTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG Template switch alignment (log-probability: -22) GAGTCAGTCTATGTTACCACAGGGGTGCGCGGCCTcACTT|ACCGT|CTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG GAGTCAGTCTATGTTACCACAGGGGTGCGCGGCCTTACTT|ACCGT|CTGTGGTAAGCCCAGACGGTCATAAGAGGATCTTAAGGAG ========== Event 1097 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: ACTGA-TTCCTCTCCAGAGGAAAA-AAGGCAGTTAGTTCTTCAATGCAAGGTGAACCtgaaacaacctttgcaaaaattataacagtgagagaaatttaacagaactgactccatcttgcttctaacatcacaagctaactgtctttgctaatcactatgtgtgggc Chimp: ACTGA-TTCCTCTCCAGAGGA-----------ATTGTTCTTCAATGCAAGGTGAACCtgaaacaacctttgcaaaaattataacagtgagagaaatttaacataactgactccatcttgcttctaacatcacaagctaactgtctttgctaatcactatgtgtgggc ↓ 1 4 3 2 Gorilla: ACTGA-TTCCTCTCCAGAGGAAAA-AAGGCAGTTAGTTCTTCAATGCAAGGTGAACCtgaaacaacctttgca-aaattataacagtgagagaaatttaacataactgactccatcttgcttctaacatcacaagctaactgtctttgctaatcactatgtgtgggc Human: ACTGA-TTCCTCTCCAGAGGAAAA-AAGGCAGTTAGTTCTTCAATGCAAGGTGAACCtgaaacaacctttgcaaaaattataacagtgagagaaatttaacagaactgactccatcttgcttctaacatcacaagctaactgtctttgctaatcactatgtgtgggc Cluster: [ ] Orangutan: ACTGATTTCCTCTCCAGAGGAAAAAAAG----GCAGTTCTTTAATGCAAGGTGAACCtgaaacaacctttgca-aaattataacagtgagagaaatttaacataactgactccatcttgcttctaacatcacaagctaactgtctttgctaatcactatgtgtgggc Chimp > Gorilla --------------- chr1:49914840-49914850 Template switch process: F1: L TGTGGGACAATTAGACCCTCTACTGATTCCTCTCCAGAGGAAA 1 F3: 4 GTTCTTCAATGCAAGGTGAACCTGAAACAACCTTTGCAA R RF: TGTGGGACAATTAGACCCTCTACTGATTCCTCTCCAGAGGAATTGTTCTTCAATGCAAGGTGAACCTGAAACAACCTTTGCAAAAATTATAACAGTGAGAGAAATTTAACATAACTGACTCCATCTTGCTTCTAACATCACAAGCTAACTGTCTTT RR: ACACCCTGTTAATCTGGGAGATGACTAAGGAGAGGTCTCCTTAACAAGAAGTTACGTTCCACTTGGACTTTGTTGGAAACGTTTTTAATATTGTCACTCTCTTTAAATTGTATTGACTGAGGTAGAACGAAGATTGTAGTGTTCGATTGACAGAAA F2: 3 ATTGACGGAAA 2 Unidirectional alignment (log-probability: -37.6) GGGACAATTAGACCCTCTACTGATTCCTCTCCAGAGGAAaaaaggcagtTaGTTCTTCAATGCAAGGTGAACCTGAAACAACCTTTGCAA- GGGACAATTAGACCCTCTACTGATTCCTCTCCAGAGGAA----------TTGTTCTTCAATGCAAGGTGAACCTGAAACAACCTTTGCAAA Template switch alignment (log-probability: -28.2) GGGACAATTAGACCCTCTACTGATTCCTCTCCAGAGGAAa|AAAGgCAGTTA|GTTCTTCAATGCAAGGTGAACCTGAAACAACCTTTGCAA GGGACAATTAGACCCTCTACTGATTCCTCTCCAGAGGAAT|AAAGACAGTTA|GTTCTTCAATGCAAGGTGAACCTGAAACAACCTTTGCAA ========== Event 1098 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AGTGTTGCTCATTTTATTAATCACTAGGGTCTAG--------------TGACTAATTTCTACCAGTCTACATG Chimp: AGTGTTGCTCATTTTATTAGTCACTAGGGTCTAC-------AAAGGCTGAAATAATTTCTACCAGTCTACATG ↓ 3 2 1 4 Gorilla: AGTGTTGCTCATTTTATTAATCACTAGGGTCTAG--------------TGACTAATTTCTACCAGTCTACATG Human: AGTGTTGCTCATTTTATTAATCACTAGGGTCTAG--------------TGACTAATTTCTACCAGTCTACATG Cluster: [ ] Orangutan: AGTGTTGCTCATTTTATTAGTCACTAGGGTCTACAAAGGCT-------GAAATAATTTCTACCAGTCTACATG Chimp > Gorilla --------------- chr14:9255720-9255724 Template switch process: F1: L CATTTTTGAGTGTTGCTCATTTTATTAATCACTAGGGTCTA 1 F3: 4 TAATTTCTACCAGTCTACATGACTTACTAGGTGACTTTGT R RF: CGTTTTTGAGTGTTGCTCATTTTATTAGTCACTAGGGTCTACAAAGGCTGAAATAATTTCTACCAGTCTACATGACTTACTAGGTGACTTTGT RR: GCAAAAACTCACAACGAGTAAAATAATCAGTGATCCCAGATGTTTCCGACTTTATTAAAGATGGTCAGATGTACTGAATGATCCACTGAAACA F2: 3 CAGTG 2 Unidirectional alignment (log-probability: -38) aTTTTTGAGTGTTGCTCATTTTATTAaTCACTAGGGTCTagtgAC-----------TAATTTCTACCAGTCTACATGACTTACTAGGTGACTTTGT GTTTTTGAGTGTTGCTCATTTTATTAGTCACTAGGGTCT----ACAAAGGCTGAAATAATTTCTACCAGTCTACATGACTTACTAGGTGACTTTGT Template switch alignment (log-probability: -27.4) aTTTTTGAGTGTTGCTCATTTTATTAaTCACTAGGGTCTA|GTGAC|TAATTTCTACCAGTCTACATGACTTACTAGGTGACTTTGT GTTTTTGAGTGTTGCTCATTTTATTAGTCACTAGGGTCTA|GTGAC|TAATTTCTACCAGTCTACATGACTTACTAGGTGACTTTGT ========== Event 1099 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAATAGGATGCAGTGGAGTC---AGGACTCAAGGCCCACTAGACAGCCAACTCAAATGCAG ↓ 1 43 2 Chimp: CAAATAGGATGCAGTGGAGTCTAGTGGGCCTAAGGCCCACTAGAGAGCCAACTCAAATGCAG ↑ 1 43 2 Gorilla: CAAATAGGATGCAGTGGAGTC---AGGACTCAAGGCCCACTAGACAGCCAACTCAAATGCAG Human: CAAATAGGATGCAGTGGAGTC---AGGACTCAAGGCCCACTAGACAGCCAACTCAAATGCAG Cluster: [ ] Orangutan: CAAATAGGATGCAGTGGAGTC---AGGACTCAAGGCCCACTAGACAGCCAACTCAAATGCAG Human > Chimp ------------- chr14:10086483-10086492 Template switch process: F1: L TCCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTC 1 F3: 4 AAGGCCCACTAGAGAGCCAACTCAAATGCAGATGAAGAAG R RF: TCCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTCAGGACTCAAGGCCCACTAGACAGCCAACTCAAATGCAGATGAAGAAG RR: AGGTATCGATAGTGTAGTGTGTTTATCCTACGTCACCTCAGTCCTGAGTTCCGGGTGATCTGTCGGTTGAGTTTACGTCTACTTCTTC F2: 3 TCCGGGTGAT 2 Unidirectional alignment (log-probability: -41.9) CCATAGCTATCACATCACACAAATAGGATGCAGTGGAG-------TCtagtgggcctAAGGCCCACTAGAgAGCCAACTCAAATGCAGATGAAGAAG CCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTCAGGACTC----------AAGGCCCACTAGACAGCCAACTCAAATGCAGATGAAGAAG Template switch alignment (log-probability: -22.5) CCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTC|TAGTGGGCCT|AAGGCCCACTAGAgAGCCAACTCAAATGCAGATGAAGAAG CCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTC|TAGTGGGCCT|AAGGCCCACTAGACAGCCAACTCAAATGCAGATGAAGAAG Gorilla > Chimp --------------- chr14:10086483-10086492 Template switch process: F1: L TCCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTC 1 F3: 4 AAGGCCCACTAGAGAGCCAACTCAAATGCAGATGAAGAAG R RF: TCCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTCAGGACTCAAGGCCCACTAGACAGCCAACTCAAATGCAGATGAGGAAG RR: AGGTATCGATAGTGTAGTGTGTTTATCCTACGTCACCTCAGTCCTGAGTTCCGGGTGATCTGTCGGTTGAGTTTACGTCTACTCCTTC F2: 3 TCCGGGTGAT 2 Unidirectional alignment (log-probability: -46.4) CCATAGCTATCACATCACACAAATAGGATGCAGTGGAG-------TCtagtgggcctAAGGCCCACTAGAgAGCCAACTCAAATGCAGATGAaGAAG CCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTCAGGACTC----------AAGGCCCACTAGACAGCCAACTCAAATGCAGATGAGGAAG Template switch alignment (log-probability: -28) CCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTC|TAGTGGGCCT|AAGGCCCACTAGAgAGCCAACTCAAATGCAGATGAaGAAG CCATAGCTATCACATCACACAAATAGGATGCAGTGGAGTC|TAGTGGGCCT|AAGGCCCACTAGACAGCCAACTCAAATGCAGATGAGGAAG ========== Event 1100 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAAGTTCTTTGTTCTAAA-CAC-TGCACTAATCA Chimp: CTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAAGTTCTTTGTTCTAAA-CAC-TGCACTAATCA ↓ 1 3 4 2 Gorilla: CTTCATATAGCACATATGTCA---------TAGAACA-----AAGAACTTTGTTCTTTGTTCTAAA-CAC-TGCACTAATCA ↑ 1 3 4 2 Human: CTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAAGTTCTTTGTTCTAAA-CAC-TGCACTAATCA Cluster: [ ] Orangutan: TTTCATATAGCACCTATGTCA---------------------CAGAACAAAGAACTT-----TAAACCGCTAGCACTAATCA Human > Gorilla --------------- chr14:9958685-9958698 Template switch process: F1: L AGCCTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCATA 1 F3: 4 GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC R RF: AGCCTAGAAGTTTTAAAATGCTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAAGTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC RR: TCGGATCTTCAAAATTTTACGAAGTATATCGTGTATACAGTATACACGATATCTTGTGTCAAATCTTGTTTCAAGAAACAAGATTTGTGACGTGATTAGTCAGGTACACTG F2: 3 TTTCAAGAAACAAG 2 Unidirectional alignment (log-probability: -37.4) CTAaAAGTTTTAAAATGCTTCATATAGCACATATGTCA---------------------TAGAACAAAgaactttGTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC CTAGAAGTTTTAAAATGCTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAA-------GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC Template switch alignment (log-probability: -23.1) CTAaAAGTTTTAAAATGCTTCATATAGCACATATGTCATA|GAACAAAGAACTTT|GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC CTAGAAGTTTTAAAATGCTTCATATAGCACATATGTCATA|GAACAAAGAACTTT|GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC Chimp > Gorilla --------------- chr14:9958685-9958698 Template switch process: F1: L AGCCTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCATA 1 F3: 4 GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC R RF: AGCCTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAAGTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC RR: TCGGATTTTCAAAATTTTACGAAGTATATCGTGTATACAGTATACACGATATCTTGTGTCAAATCTTGTTTCAAGAAACAAGATTTGTGACGTGATTAGTCAGGTACACTG F2: 3 TTTCAAGAAACAAG 2 Unidirectional alignment (log-probability: -31.9) CTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCA---------------------TAGAACAAAgaactttGTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC CTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCATATGTGCTATAGAACACAGTTTAGAACAAA-------GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC Template switch alignment (log-probability: -17.6) CTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCATA|GAACAAAGAACTTT|GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC CTAAAAGTTTTAAAATGCTTCATATAGCACATATGTCATA|GAACAAAGAACTTT|GTTCTTTGTTCTAAACACTGCACTAATCAGTCCATGTGAC ========== Event 1101 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAACTTTTGGGAAGTTTTTTTCTGAT-TCACTTAAAAATAAttttaataaatt Chimp: GGAAACTTTTGGGAAGtttttttCTGAC-TCACTTAAAAATAATTTTAATAAATT Gorilla: GGAAACTTTTGGGAAGTTTTTAAGTGAGTCCACTTAAAAATAATTTTAATAAATT ↑ 1 3 4 2 Human: GGAAACTTTTGGGAAGTTTTTTTCTGAT-TCACTTAAAAATAAttttaataaatt Cluster: [ ] Orangutan: GGAAACTTTTGGGAAGTTTTTTTCTGAC-TCACTTAAAAATAATTTTAATCAATT Human > Gorilla --------------- chr14:81879911-81879919 Template switch process: F1: L AAACGTGTGCTAAAATTTTGGGAAACTTTTGGGAAGTTTTT 1 F3: 4 CACTTAAAAATAATTTTAATAAATTGTAAGTCAAACTAAC R RF: AAATGTGTGCTAAAATTTTGGGAAACTTTTGGGAAGTTTTTTTCTGATTCACTTAAAAATAATTTTAATAAATTGTAAGTCAAACTAAC RR: TTTACACACGATTTTAAAACCCTTTGAAAACCCTTCAAAAAAAGACTAAGTGAATTTTTATTAAAATTATTTAACATTCAGTTTGATTG F2: 3 CTGAGTGAA 2 Unidirectional alignment (log-probability: -39.5) AAcGTGTGCTAAAATTTTGGGAAACTTTTGGGAAGTTT--------TTaagtgagtcCACTTAAAAATAATTTTAATAAATTGTAAGTCAAACTAAC AATGTGTGCTAAAATTTTGGGAAACTTTTGGGAAGTTTTTTTCTGATT---------CACTTAAAAATAATTTTAATAAATTGTAAGTCAAACTAAC Template switch alignment (log-probability: -27.9) AAcGTGTGCTAAAATTTTGGGAAACTTTTGGGAAGTTTTT|AAGTGAgTC|CACTTAAAAATAATTTTAATAAATTGTAAGTCAAACTAAC AATGTGTGCTAAAATTTTGGGAAACTTTTGGGAAGTTTTT|AAGTGAATC|CACTTAAAAATAATTTTAATAAATTGTAAGTCAAACTAAC ========== Event 1102 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAGAAATAGTTTAACATGTCC-----------------ACAGCAACCCGGACAGGCAAACAGGCTG Chimp: TCAAGAAATAGTTTAACATGTCC-----------------ACAGCATCCCTGACAGGCAAACAGGCTG ↓ 4 3 21 Gorilla: TCAAGAAATAGTTTAACATGTCCACAGCGTCATGCTGTCCACAGCAACCCTGACAGGCAAACAGGCTG Human: TCAAGAAATAGTTTAACATGTCC-----------------ACAGCAACCCGGACAGGCAAACAGGCTG Cluster: [ ] Orangutan: TCAAGAAATAGCTTAACATGTCC-----------------ACGGCAACCCTGACAGGCAAACAGGCTG Chimp > Gorilla --------------- chr14:83496513-83496517 Template switch process: F1: L TCTCAGCAAACGTCAAGCTCAAGAAATAGTTTAACATGTCCACAGCGTC 1 F3: 4 GTCCACAGCAACCCTGACAGGCAAACAGGCTGGGATCCTGCCCCGGTCTGC R RF: TCTCAGCAAACGTCAAGCTCAAGAAATAGTTTAACATGTCCACAGCATCCCTGACAGGCAAACAGGCTGGGATTCTGCCCCGGTCTGC RR: AGAGTCGTTTGCAGTTCGAGTTCTTTATCAAATTGTACAGGTGTCGTAGGGACTGTCCGTTTGTCCGACCCTAAGACGGGGCCAGACG F2: 3 TCGTA 2 Unidirectional alignment (log-probability: -46.5) ACGTCAAGCTCAAGAAATAGTTTAACAtgtccacagcgtcatgcTGTCCACAGCAaCCCTGACAGGCAAACAGGCTGGGATcCTG ACGTCAAGCTCAAGAAATAGTTTAACA-----------------TGTCCACAGCATCCCTGACAGGCAAACAGGCTGGGATTCTG Template switch alignment (log-probability: -33.4) ACGTCAAGCTCAAGAAATAGTTTAACATGTCCACAGCgTC|ATGCT|GTCCACAGCAaCCCTGACAGGCAAACAGGCTGGGATcCTG ACGTCAAGCTCAAGAAATAGTTTAACATGTCCACAGCATC|ATGCT|GTCCACAGCATCCCTGACAGGCAAACAGGCTGGGATTCTG ========== Event 1103 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCAGATTTTGTTTCCTTTTTGAAAGGCTGTTGCCTTTCAAACATCTGGAATTAATGCCGCGGC ↑ 3 14 2 Chimp: TCAGATTTTGTTTCCTTTTTGAAAGG------------CAACATCTGGAATTAATGCCGCGGC Gorilla: TCAGATTTTGTTTCCTTTTTGAAAGG------------CAACATCTGGAATTAATGCCGCGGC ↓ 3 14 2 Human: TCAGATTTTGTTTCCTTTTTGAAAGGCTGTTGCCTTTCAAACATCTGGAATTAATGCCGCGGC Cluster: [ ] Orangutan: TCAGATTTTGTTTCCTTTTTGAAAGG------------CAACATCTGGAGTTAATGCCGCGGC Chimp > Human ------------- chr1:50424639-50424650 Template switch process: F1: L AAGAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC 1 F3: 4 AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC R RF: AAGAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGCAACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC RR: TTCTCCATTGTCCAAAGTCTAAAACAAAGGAAAAACTTTCCGTTGTAGACCTTAATTACGGCGCCGGGAGCCCGCTCAGCGG F2: 3 ACTTTCCGTTGT 2 Unidirectional alignment (log-probability: -28.2) GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGCtgttgcctttcaAACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC------------AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC Template switch alignment (log-probability: -16.8) GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC|TGTTGCCTTTCA|AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC|TGTTGCCTTTCA|AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC Gorilla > Human --------------- chr1:50424639-50424650 Template switch process: F1: L AAGAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC 1 F3: 4 AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC R RF: AAGAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGCAACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC RR: TTCTCCATTGTCCAAAGTCTAAAACAAAGGAAAAACTTTCCGTTGTAGACCTTAATTACGGCGCCGGGAGCCCGCTCAGCGG F2: 3 ACTTTCCGTTGT 2 Unidirectional alignment (log-probability: -28.2) GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGCtgttgcctttcaAACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC------------AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC Template switch alignment (log-probability: -17.3) GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC|TGTTGCCTTTCA|AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC GAGGTAACAGGTTTCAGATTTTGTTTCCTTTTTGAAAGGC|TGTTGCCTTTCA|AACATCTGGAATTAATGCCGCGGCCCTCGGGCGAGTCGCC ========== Event 1104 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ----------gtgtgtgtgtgtgtgtgtgtgtgtgtTACTT------GTAAAAACACTTAACatggatatgtttgttatcctgattatgatgggagtatcacaagtatatgcataaatccagactca ↓ 1 4 3 2 Chimp: ----------gt------------gtgtgtgtgtgtTACTT---GTGGTAAAAACACTTAACatggatatgtttgttatcctgattatgatgggagtatcacaagtatatgcataaatccagactca Gorilla: --------------------------gtgtgtgtgtTACTTGTG---GTAAAAACACTTAACatggatatgtttgttatcctgattatgatgggagtatcacaagtatatgcataaatccagactca ↑ 1 4 3 2 Human: ----------gtgtgtgtgtgtgtgtgtgtgtgtgtTACTT------GTAAAAACACTTAACatggatatgtttgttatcctgattatgatgggagtatcacaagtatatgcataaatccagactca Cluster: [ ] Orangutan: gtgtgtgtgt----------------gtgtgtgtgtgtgttgtg---GTAAAAACACTTAACatggatatgtttgttatcctgattatgatgggagtatcacaagtatatgcataaatccagactca Human > Chimp ------------- chr1:50696347-50696354 Template switch process: F1: L TCGTGTGTGTGTGTGTGTGTGTGT 1 F3: 4 GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA R RF: TCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTACTTGTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTATGATGGGAGTATCACAAGTA RR: AGCACACACACACACACACACACACACACACACACAATGAACATTTTTGTGAATTGTACCTATACAAACAATAGGACTAATACTACCCTCATAGTGTTCAT F2: 3 GTGTTCAT 2 Unidirectional alignment (log-probability: -26) TC------------GTGTGTGTGTGTGTGTGTGTGTTACTTgtgGTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA TCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTACTT---GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA Template switch alignment (log-probability: -15.9) TCGTGTGTGTGTGTGTGTGTGTGT|TACTTGTG|GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA TCGTGTGTGTGTGTGTGTGTGTGT|TACTTGTG|GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA Human > Gorilla --------------- chr1:51666374-51666381 Template switch process: F1: L TCGTGTGTGTGTGTGTGTGT 1 F3: 4 GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA R RF: TCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTACTTGTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTATGATGGGAGTATCACAAGTA RR: AGCACACACACACACACACACACACACACACACACAATGAACATTTTTGTGAATTGTACCTATACAAACAATAGGACTAATACTACCCTCATAGTGTTCAT F2: 3 GTGTTCAT 2 Unidirectional alignment (log-probability: -25.5) TCGTGTGTGTGTGTGTGTG----------------TTACTTgtgGTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA TCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTACTT---GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA Template switch alignment (log-probability: -16.2) TCGTGTGTGTGTGTGTGTGT|TACTTGTG|GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA TCGTGTGTGTGTGTGTGTGT|TACTTGTG|GTAAAAACACTTAACATGGATATGTTTGTTATCCTGATTA ========== Event 1105 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAAACCAATGGAGCAAATTCCTACAGAGAATCATCTCTGTAGGAATTTAAGAGCAGGTAGAAAGAT Chimp: GAAAACCAATGGAGCAAATTCCTACAGAGAATCATCTCTGTAGGAATTTAAGAGCAGGTAGAAAGAT ↑ 3 1 42 Gorilla: GAAAACCAATGGAGCAAATTCCTGCAGAGA-------------TGATTTAAGAGCAGGTAGAAAGAT ↓ 3 1 42 Human: GAAAACCAATGGAGCAAATTCCTACAGAGAATCATCTCTGTAGGAATTTAAGAGCAGGTAGAAAGAT Cluster: [ ] Orangutan: GAAAACCAATGGAGCAAATTCCTACAGAGA-------------AGATATAAGAGCAGGTAGAAAGAT Gorilla > Human --------------- chr1:50937004-50937018 Template switch process: F1: L GCCAAAGGAAATGTAGGAGAAAACCAATGGAGCAAATTCCTACAGAGA 1 F3: 4 ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT R RF: GCCAAAGGAAATGTAGGAGAAAACCAATGGAGCAAATTCCTGCAGAGATGATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT RR: CGGTTTCCTTTACATCCTCTTTTGGTTACCTCGTTTAAGGACGTCTCTACTAAATTCTCGTCCATCTTTCTAAGTTCAACTGTTTCAAGA F2: 3 AGGATGTCTCTACTA 2 Unidirectional alignment (log-probability: -45) AAATGTAGGAGAAAACCAATGGAGCAAATTCCTaCAGAGAatcatctcTGtaggaATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT AAATGTAGGAGAAAACCAATGGAGCAAATTCCTGCAGAGA--------TG-----ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT Template switch alignment (log-probability: -28.8) AAATGTAGGAGAAAACCAATGGAGCAAATTCCTaCAGAGA|ATCATCTCTGtAGGA|ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT AAATGTAGGAGAAAACCAATGGAGCAAATTCCTGCAGAGA|ATCATCTCTGCAGGA|ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT Gorilla > Chimp --------------- chr1:50528074-50528088 Template switch process: F1: L GCCAAAGGAAATGTAGGAGAAAACCAATGGAGCAAATTCCTACAGAGA 1 F3: 4 ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT R RF: GCCAAAGGAAATGTAGGAGAAAACCAATGGAGCAAATTCCTGCAGAGATGATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT RR: CGGTTTCCTTTACATCCTCTTTTGGTTACCTCGTTTAAGGACGTCTCTACTAAATTCTCGTCCATCTTTCTAAGTTCAACTGTTTCAAGA F2: 3 AGGATGTCTCTACTA 2 Unidirectional alignment (log-probability: -45) AAATGTAGGAGAAAACCAATGGAGCAAATTCCTaCAGAGAatcatctcTGtaggaATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT AAATGTAGGAGAAAACCAATGGAGCAAATTCCTGCAGAGA--------TG-----ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT Template switch alignment (log-probability: -28.8) AAATGTAGGAGAAAACCAATGGAGCAAATTCCTaCAGAGA|ATCATCTCTGtAGGA|ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT AAATGTAGGAGAAAACCAATGGAGCAAATTCCTGCAGAGA|ATCATCTCTGCAGGA|ATTTAAGAGCAGGTAGAAAGATTCAAGTTGACAAAGTTCT ========== Event 1106 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TACACAATTCAAAACCACCTGCAGAGCCAACTCTCTAGAAGTAAAATTAAAGCTATACTAATTCTGAGTGAATCC--------TGCAAAGGGTCTAACTTAATGAGCT Chimp: TACACAATTCAAAACCACCTGCAGAGCCAACTCTCTAGAAGTAAAATTAAAGCTATACTAATTCTGAGTGAATCC----CTACCAAAAAGGGTCTAACTTAATGAGCT Gorilla: TACACAATTCAAAACCACTTGCAGAGCCAACTCTCTAGAAGTAAAATTAAAGCTATACTAACTCTGAGTGAATCCCTAC----CAATAAGGGTCTAACTTAATGAGCT ↓ 3 2 1 4 Human: TACACAATTCAAAACCACCTGCAGAGCCAACTCTCTAGAAGTAAAATTAAAGCTATACTAATTCTGAGTGAATCC--------TGCAAAGGGTCTAACTTAATGAGCT Cluster: [ ] Orangutan: TACACAATTCAAAACCACCCGCAGAGGCAACTCTCTAGAAGTAAAATTAAAGCTATACTAACTCTGAGTGAATCCCTAC----CGAAAAGGGCCTAACTTAATGAGCT Gorilla > Human --------------- chr1:197257648-197257651 Template switch process: F1: L CTAGAAGTAAAATTAAAGCTATACTAATTCTGAGTGAATCC 1 F3: 4 AAGGGTCTAACTTAATGAGCTAGTTAAAACAACTTTGAGT R RF: TGCAGAGCCAACTCTCTAGAAGTAAAATTAAAGCTATACTAACTCTGAGTGAATCCCTACCAATAAGGGTCTAACTTAATGAGCTGGTTAAAACAACTTTGAGT RR: ACGTCTCGGTTGAGAGATCTTCATTTTAATTTCGATATGATTGAGACTCACTTAGGGATGGTTATTCCCAGATTGAATTACTCGACCAATTTTGTTGAAACTCA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -36.4) TAGAAGTAAAATTAAAGCTATACTAAtTCTGAGTGAATCC-------TgcaAAGGGTCTAACTTAATGAGCTaGTTAAAACAACTTTGAGT TAGAAGTAAAATTAAAGCTATACTAACTCTGAGTGAATCCCTACCAAT---AAGGGTCTAACTTAATGAGCTGGTTAAAACAACTTTGAGT Template switch alignment (log-probability: -27.3) TAGAAGTAAAATTAAAGCTATACTAAtTCTGAGTGAATCC|TGCA|AAGGGTCTAACTTAATGAGCTaGTTAAAACAACTTTGAGT TAGAAGTAAAATTAAAGCTATACTAACTCTGAGTGAATCC|TGCA|AAGGGTCTAACTTAATGAGCTGGTTAAAACAACTTTGAGT ========== Event 1107 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGGACACCTGCAGCTACTCCCCATTTCA-CTTTCTGGGAGGAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATTCCTGACTTGGGCTGACATGCTAAACACGGGTAAGAATTTCCAATACTAGGCTGAGTGGTTCAGGCTGAGGAACTGATCCCCTATCGTGGAGCAATC Chimp: AAGGACAGCTGCAGCTACTCCTCAGTTCA-CCTTCTGGGAggagcagattcctgacttgggctgagatgctaaacatgggtaagaatttccaatactaggctgagcggttcaggctgaggaactgatcccctaccatggagcagattcctgacttgggctgacatgctaaacatgcgtaagaatttccaatactaggctgagcggttcaggctgaggaactgatcccctaccatggagcagattcctgacttgcgctgacatgctaaacatgcgtaagaatttccaagaactctggcgggttcaggcctgaggaactgaatcccgctaccattgaagggcagattctgaccttgcgctgacatgtaaacatgcgtaacgaatttcccaatacttagcggtgagcgttcagctgagaacttgactcccctaccatgcgagcagattccgattgccgctgacatgctaatacatggtaaatgaattctccaataacctaggctgagcgcgttcaggctgaggaactgatcccctatcatgctggctgcgttcctgattgtgctgacatgctaaacatgcgtaagaatttccaatactaggctgagcggttcaggctgaggaactgatcccctaccatggagcagattcctgacttgcgctgacatgctaaacatgggtaagaatttccaatactaggctgagcggttcaggctgaggaactgatcccctatcatggagcagattcctgacttgcactgagatgctaaacatgcgtaagaatttccaataccaggctgagcggttcaggctgaggaactgatcccctaccatggagcaATC ↑ 1 4 3 2 Gorilla: AAGGACACCTGCAGCTACTCCCCATTTCA-CCTTCTGGGAGGAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATTCCTGACTTGGGCTGACATGCTAAACACGGGTAAGAATTTCCAACACTAGGCTGAGCGGTTCAGGCTGAGGAACTGATCCCCTACCATGGAGCAATC Human: AAGGACACCTGCAGCTACTCCCCATTTCA-CTTTCTGGGAGGAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATTCCTGACTTGGGCTGACATGCTAAACACGGGTAAGAATTTCCAATACTAGGCTGAGTGGTTCAGGCTGAGGAACTGATCCCCTATCGTGGAGCAATC Cluster: [ ] Orangutan: AAGGACACCTGCAGCTACTCCTCATTTCACCCTTCTGGGAGGAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGATTCCTGACTCGGTCTGATATGCTAAACATGGGTAAGAATTTCCAATACTAGGCTGAGCGGTTCAGGCTGAGGAACTGATCCCCTATCATGGAGCAATC Gorilla > Chimp --------------- chr15:82466692-82466695 Template switch process: F1: L CTCTAGCAGGTGGTGACAGAAAGGACAGCTGCAGCTACTCC 1 F3: 4 TTCACCTTCTGGGAGGAGCAGATTCCTGACTTGGGCTGAG R RF: CTCCAGCAGGTGGTGACAGAAAGGACACCTGCAGCTACTCCCCATTTCACCTTCTGGGAGGAGCAGATTCCTGACTTGGGCTGACATGCTAAACACGGGTAAGAATTTCCAACACTAGGCTGAGCGGTTCAGGCTGAGGAACTGA RR: GAGGTCGTCCACCACTGTCTTTCCTGTGGACGTCGATGAGGGGTAAAGTGGAAGACCCTCCTCGTCTAAGGACTGAACCCGACTGTACGATTTGTGCCCATTCTTAAAGGTTGTGATCCGACTCGCCAAGTCCGACTCCTTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -59.9) TCtAGCAGGTGGTGACAGAAAGGACAgCTGCAGCTACTCCtCAgTTCACCTTCTGGGAGGAGCagattcctgacttgggctgag TCCAGCAGGTGGTGACAGAAAGGACACCTGCAGCTACTCCCCATTTCACCTTCTGGGAGGAGC--------------------- Template switch alignment (log-probability: -32.8) TCtAGCAGGTGGTGACAGAAAGGACAgCTGCAGCTACTCC|TCAG|TTCACCTTCTGGGAGGAGCAGATTCCTGACTTGGGCTGAg TCCAGCAGGTGGTGACAGAAAGGACACCTGCAGCTACTCC|TCAG|TTCACCTTCTGGGAGGAGCAGATTCCTGACTTGGGCTGAC ========== Event 1108 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATGAGCACTTAGATCATGCTCAC-------AGTTCTGTGAGTCACTGGGACGATTTTGTTCT Chimp: AATGAGCACTTAGATCATGCTCAC-------AGTTCTGTGAGTCACTGGGACAATTTTGTTCT ↑ 3 1 24 Gorilla: AATGAGCACTTAGATCATGCTCAC--------------AGAATCACTGGGACGATTTTGTTCT ↓ 3 1 24 Human: AATGAGCACTTAGATCATGCTCAC-------AGTTCTGTGAGTCACTGGGACGATTTTGTTCT Cluster: [ ] Orangutan: AATGAGCACTTAGATCATGCTCACAGTTCTG-------TGAGTCACTGGGACGATTTTCTTTG Gorilla > Human --------------- chr15:22850211-22850219 Template switch process: F1: L TCTCAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAG 1 F3: 4 TCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT R RF: TCTCAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAGAATCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT RR: AGAGTCACCGTATCTCCTTACTCGTGAATCTAGTACGAGTGTCTTAGTGACCCTGCTAAAACAAGACATGGGAAGTGAGACAACA F2: 3 GAGTGTCTT 2 Unidirectional alignment (log-probability: -26.5) CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAgttctgtGAgTCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACA-------GAATCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT Template switch alignment (log-probability: -16.9) CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAG|TTCTGTGAG|TCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAG|TTCTGTGAG|TCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT Gorilla > Chimp --------------- chr15:79096943-79096951 Template switch process: F1: L TCTCAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAG 1 F3: 4 TCACTGGGACAATTTTGTTCTGTACCCTTCACTCTGTTGT R RF: TCTCAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAGAATCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT RR: AGAGTCACCGTATCTCCTTACTCGTGAATCTAGTACGAGTGTCTTAGTGACCCTGCTAAAACAAGACATGGGAAGTGAGACAACA F2: 3 GAGTGTCTT 2 Unidirectional alignment (log-probability: -32) CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAgttctgtGAgTCACTGGGACaATTTTGTTCTGTACCCTTCACTCTGTTGT CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACA-------GAATCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT Template switch alignment (log-probability: -22.4) CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAG|TTCTGTGAG|TCACTGGGACaATTTTGTTCTGTACCCTTCACTCTGTTGT CAGTGGCATAGAGGAATGAGCACTTAGATCATGCTCACAG|TTCTGTGAG|TCACTGGGACGATTTTGTTCTGTACCCTTCACTCTGTTGT ========== Event 1109 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTGGAGCAGGAGCTTTCTAAA--GACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAG Chimp: AGTGGAGCAGGAGCTTTCTAAA--GACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAG ↓ 1 4 3 2 Gorilla: AGTGGAGCAGGAGCTTTCTAAG----ATACTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAG ↑ 1 4 3 2 Human: GGTGGAGCAGGAGCTTTCTAAA--GACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAG Cluster: [ ] Orangutan: AGTGGAGCAGGAGCTTTCTAAAGA--CTTTTTTAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAG Human > Gorilla --------------- chr15:77723604-77723608 Template switch process: F1: L AGGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAA 1 F3: 4 TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA R RF: AGGGTTACTTGAAAGTTTGTGGTGGAGCAGGAGCTTTCTAAAGACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA RR: TCCCAATGAACTTTCAAACACCACCTCGTCCTCGAAAGATTTCTGAAAATCTTTTTCATCATAGAACTCCTAAAGACAGGATTCGAAT F2: 3 CATAG 2 Unidirectional alignment (log-probability: -33.3) GGGTTACTTGAAAGTTTGTaGTGGAGCAGGAGCTTTCTAAgAtAC---TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA GGGTTACTTGAAAGTTTGTGGTGGAGCAGGAGCTTTCTAA-AGACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA Template switch alignment (log-probability: -21.9) GGGTTACTTGAAAGTTTGTaGTGGAGCAGGAGCTTTCTAA|GATAC|TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA GGGTTACTTGAAAGTTTGTGGTGGAGCAGGAGCTTTCTAA|GATAC|TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA Chimp > Gorilla --------------- chr15:77723604-77723608 Template switch process: F1: L AGGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAA 1 F3: 4 TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA R RF: AGGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAAAGACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA RR: TCCCAATGAACTTTCAAACATCACCTCGTCCTCGAAAGATTTCTGAAAATCTTTTTCATCATAGAACTCCTAAAGACAGGATTCGAAT F2: 3 CATAG 2 Unidirectional alignment (log-probability: -27.8) GGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAAgAtAC---TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA GGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAA-AGACTTTTAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA Template switch alignment (log-probability: -16.4) GGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAA|GATAC|TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA GGGTTACTTGAAAGTTTGTAGTGGAGCAGGAGCTTTCTAA|GATAC|TAGAAAAAGTAGTATCTTGAGGATTTCTGTCCTAAGCTTA ========== Event 1110 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCCTTACCTGAGGTAAGCTTTACTTAGGTTAAGTCT--------------GAATATGGTAACAGTTAGTGAAAATA Chimp: ATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCT--------------GAATATGGTAACAGTTAGTGAAAATA ↓ 4 3 2 1 Gorilla: ATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTGTTACCTAAGTCTTTACTTAGGTAACAGTTAGTGAAAATA Human: ATTCCTTACCTGAGGTAAGCTTTACTTAGGTTAAGTCT--------------GAATATGGTAACAGTTAGTGAAAATA Cluster: [ ] Orangutan: ATTCTGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCT--------------GAATATGGTAACAGTTAGTGAAAATA Chimp > Gorilla --------------- chr1:175821037-175821046 Template switch process: F1: L ATAATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTG 1 F3: 4 CTTTACTTA----------------GGTAACAGTTAGTGAAAATAGAAATGGACCAAAGTCTTTA R RF: ATAATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTGAATATGGTAACAGTTAGTGAAAATAGAAATGGACCAAAGTCTTTA RR: TATTAAGGCATGGACTCCATTCGAAATGAATCCAATTCAGACTTATACCATTGTCAATCACTTTTATCTTTACCTGGTTTCAGAAAT F2: 3 TGAATCCATT 2 Unidirectional alignment (log-probability: -46.7) AATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTGttacctaagtctttacttA----GGTAACAGTTAGTGAAAATAGAAATGGACCA AATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTG------------------AATATGGTAACAGTTAGTGAAAATAGAAATGGACCA Template switch alignment (log-probability: -33.3) AATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTG|TtACCTAAGT|CTTTACTTA----------------GGTAACAGTTAGTGAAAATAGAAATGGACCA AATTCCGTACCTGAGGTAAGCTTTACTTAGGTTAAGTCTG|TAACCTAAGT|CTTTACTTAGGTTAAGTCTGAATATGGTAACAGTTAGTGAAAATAGAAATGGACCA ========== Event 1111 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTTTTCCTGTCTTTCAGTAACAGACTCGAGCTCAAGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATACCTGTTCTTAATCTTTTAGTTTTCTGCCACTTTTCTGAGAATGCTTTCCCAAAGCTTGCTA Chimp: TTTTTTCCTGTCTTTCAGTAACAGACTC-TTCTCAAGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATACCTGTTCTTAATCTTTTAGTTTTCTGCCACTTTTCTGAGAATGCTTTCCCAAAGCTTGCTA Gorilla: TTTTTTCCTGTCTTTCAGTAATAGACTC-TTCTCAGGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATACCTGTTCTTAATCTTTTAGTTTTCTGCCACTTTTCTGAGAATGCTTTCCCAAAGCTTGCTA ↑ 1 4 3 2 Human: TTTTTTCCTGTCTTTCAGTAACAGACTCGAGCTCAAGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATACCTGTTCTTAATCTTTTAGTTTTCTGCCACTTTTCTGAGAATGCTTTCCCAAAGCTTGCTA Cluster: [ ] Orangutan: TTTTTTCCTGTGTTTCAGTAATAGACTC-TTCTCAAGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCGAATACCTGTTCTTAATCTTTTAGTTTTCTGCCACTTTTCTGAGAATGCTTTCCCAAAGCTTGCTA Human > Gorilla --------------- chr15:3916704-3916710 Template switch process: F1: L TGAGTTACTATTCCATCTTCTTTTTTCCTGTCTTTCAGTAATAGACTC 1 F3: 4 GATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATAC R RF: TGAGTTACTATTCCATCTTCTTTTTTCCTGTCTTTCAGTAACAGACTCGAGCTCAAGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATACCTGTTCTTAATCTTTTAGTTTTCTGCCACTTTTCTGAGAA RR: ACTCAATGATAAGGTAGAAGAAAAAAGGACAGAAAGTCATTGTCTGAGCTCGAGTTCTAATCTGTGATCGGATTAGAAACCAAGAGACGGTTTATGGACAAGAATTAGAAAATCAAAAGACGGTGAAAAGACTCTT F2: 3 GACTCTT 2 Unidirectional alignment (log-probability: -33.2) TATTCCATCTTCTTTTTTCCTGTCTTTCAGTAAtAGACTC-ttCTCAgGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATAC TATTCCATCTTCTTTTTTCCTGTCTTTCAGTAACAGACTCGAGCTCAAGATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATAC Template switch alignment (log-probability: -22.3) TATTCCATCTTCTTTTTTCCTGTCTTTCAGTAAtAGACTC|TTCTCAG|GATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATAC TATTCCATCTTCTTTTTTCCTGTCTTTCAGTAACAGACTC|TTCTCAG|GATTAGACACTAGCCTAATCTTTGGTTCTCTGCCAAATAC ========== Event 1112 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGAGGCCATACTGTATTATTGTG-AAATTG-------------CTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCCCCAAGGACTAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGCCCCTAAAGAAATGCAATTTTCAGTATCCTCCCTAAGTTCTCCA Chimp: GGAAGGCCGTACTGTATTATTGTG-AAATTG-------------CTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCACCAAGGACTAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGCCCCTAAAGAAATGCAATTTTCAGTATCCTCCCTAAGTTCTCCA ↓ 1 4 3 2 Gorilla: GGGAGGCCGTACTGTATTATTCTGAAAATTG--------------------------CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCCCCAAGGACTAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGTCCCTAAAGCAATGCAATTTTCAGTATCCTCCCTAAGTTCTCCA ↑ 1 4 3 2 Human: GGGAGGCCATACTGTATTATTGTG-AAATTG-------------CTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCCCCAAGGACTAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGCCCCTAAAGAAATGCAATTTTCAGTATCCTCCCTAAGTTCTCCA Cluster: [ ] Orangutan: GGGAGGCCGTACTGTATTATTGTG-AAATTGCTGGATAGTTAGA-------------CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCACCGAGGACCAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGCCCCTAAAGAAATGCAATTTTCAGTATCCTCCCTAAGTTCTCCA Human > Gorilla --------------- chr15:4142231-4142240 Template switch process: F1: L GAATGGACCATCTTCACTTTGGGAGGCCGTACTGTATTATT 1 F3: 4 CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC R RF: GAATGGACCATCTTCACTTTGGGAGGCCATACTGTATTATTGTGAAATTGCTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCCCCAAGGACTAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGCCCCTAAAGAAATGCAATTTTCAG RR: CTTACCTGGTAGAAGTGAAACCCTCCGGTATGACATAATAACACTTTAACGACCTATCAATCTGACTTCCGGGAGGTACATGAAGAACTATCAAGAGTCTCCGGGAATGGATTGGGGGGTTCCTGATTGACGTCCTGTGTTTCGAGACGTTTTCCGAAACAATACTAATCGGGGATTTCTTTACGTTAAAAGTC F2: 3 GTTAAAAGTC 2 Unidirectional alignment (log-probability: -33.9) AATGGACCATCTTCACTTTGGGAGGCCgTACTGTATTATTcTGaAAATTG-------------CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC AATGGACCATCTTCACTTTGGGAGGCCATACTGTATTATTGTG-AAATTGCTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC Template switch alignment (log-probability: -22.5) AATGGACCATCTTCACTTTGGGAGGCCgTACTGTATTATT|CTGAAAATTG|CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC AATGGACCATCTTCACTTTGGGAGGCCATACTGTATTATT|CTGAAAATTG|CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC Chimp > Gorilla --------------- chr15:4142231-4142240 Template switch process: F1: L GAATGGACCATCTTCACTTTGGGAGGCCGTACTGTATTATT 1 F3: 4 CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC R RF: GAATGGACCATCTTCACTTTGGAAGGCCGTACTGTATTATTGTGAAATTGCTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGCCCTTACCTAACCCACCAAGGACTAACTGCAGGACACAAAGCTCTGCAAAAGGCTTTGTTATGATTAGCCCCTAAAGAAATGCAATTTTCAG RR: CTTACCTGGTAGAAGTGAAACCTTCCGGCATGACATAATAACACTTTAACGACCTATCAATCTGACTTCCGGGAGGTACATGAAGAACTATCAAGAGTCTCCGGGAATGGATTGGGTGGTTCCTGATTGACGTCCTGTGTTTCGAGACGTTTTCCGAAACAATACTAATCGGGGATTTCTTTACGTTAAAAGTC F2: 3 GTTAAAAGTC 2 Unidirectional alignment (log-probability: -33.9) AATGGACCATCTTCACTTTGGgAGGCCGTACTGTATTATTcTGaAAATTG-------------CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC AATGGACCATCTTCACTTTGGAAGGCCGTACTGTATTATTGTG-AAATTGCTGGATAGTTAGACTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC Template switch alignment (log-probability: -22.5) AATGGACCATCTTCACTTTGGgAGGCCGTACTGTATTATT|CTGAAAATTG|CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC AATGGACCATCTTCACTTTGGAAGGCCGTACTGTATTATT|CTGAAAATTG|CTGAAGGCCCTCCATGTACTTCTTGATAGTTCTCAGAGGC ========== Event 1113 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTTGGATGACTTACTGTCGATATATGCTATCCTCCC---------ACAGTCTAGTTACGCGTGGCATC Chimp: CCTTTGGATGACTTACTGTCCATATATGCTATCCTCCC---------ACAGTCTAGTTACACGTGGCATC ↓ 3 2 1 4 Gorilla: CCTTTGGATGACTTACTGTCCATATATGCTATCCTCCTAGCATATATGGAGTCTAGTTACGCATGGCATC Human: CCTTTGGATGACTTACTGTCGATATATGCTATCCTCCC---------ACAGTCTAGTTACGCGTGGCATC Cluster: [ ] Orangutan: CCTTTGGATGACTTACTGTCCATATATGCCATCCTCCC---------ACAGTGTAGTTATGCGTGGCATC Chimp > Gorilla --------------- chr15:4333866-4333877 Template switch process: F1: L AAGCCCTTTGGATGACTTACTGTCCATATATGCTATCCTCC 1 F3: 4 AGTCTAGTTACGCATGGCATCTGCATAGTCAGGCTCAGAC R RF: AAGCCCTTTGGATGACTTACTGTCCATATATGCTATCCTCCCACAGTCTAGTTACACGTGGCATCTGCATAGTCAGGCTCAGAC RR: TTCGGGAAACCTACTGAATGACAGGTATATACGATAGGAGGGTGTCAGATCAATGTGCACCGTAGACGTATCAGTCCGAGTCTG F2: 3 GGTATATACGAT 2 Unidirectional alignment (log-probability: -45.9) AGCCCTTTGGATGACTTACTGTCCATATATGCTATCCTCCtAgcatatatggAGTCTAGTTACgCaTGGCATCTGCATAGTCAGGCTCAGAC AGCCCTTTGGATGACTTACTGTCCATATATGCTATCCTCCCA---------CAGTCTAGTTACACGTGGCATCTGCATAGTCAGGCTCAGAC Template switch alignment (log-probability: -28.3) AGCCCTTTGGATGACTTACTGTCCATATATGCTATCCTCC|TAGCATATATGG|AGTCTAGTTACgCaTGGCATCTGCATAGTCAGGCTCAGAC AGCCCTTTGGATGACTTACTGTCCATATATGCTATCCTCC|TAGCATATATGG|AGTCTAGTTACACGTGGCATCTGCATAGTCAGGCTCAGAC ========== Event 1114 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: aaaccttgcaaattcaaatgcctactGCAAACTTTTAATCATCGAAAATGCTTCAGGAAAAGAAGTAGAGGTAGAATGTATGATACTCagtgtgttttttcagttggattaaaagtatgtttctttcaattggattaaaaTCAGGGTGGAGGGTCACACATAACCTTTGTGCCCTCCCAA ↓ 3 2 1 4 Chimp: AAACCTTGCAAATTCAAATGCCTACTGCAAACTTTTAATCATCGAAAATGCTTCAGGAAAAGAAGTAGAGGTAGAATGTATGATACTCagtgtgttttttcagttggattaaaagtatgtttctttcaattggattaaaaTCAGGATGGAGGGTTAGGCATAACCTTTGTGCCCTCCCAA Gorilla: AAACCTTGCAAATTCAAATGCCTACTGCAAACTTTTAATCATCGAAAATGCTTCAGGAAAAGAAGTAGAGGTAGAATGTATGATACTCAGTGttttttttCAATTGGATTAAAAGTATGTTTCTTTCAGTTGGATTAAAATCAGGGTGGAGGGTTAGGCATAACCTTTGTGCCCTCCCAA Human: aaaccttgcaaattcaaatgcctactGCAAACTTTTAATCATCGAAAATGCTTCAGGAAAAGAAGTAGAGGTAGAATGTATGATACTCagtgtgttttttcagttggattaaaagtatgtttctttcaattggattaaaaTCAGGGTGGAGGGTCACACATAACCTTTGTGCCCTCCCAA Cluster: [ ] Orangutan: aaaccttGCAGATTCAAATGCCTACTGCAAACTTTTAATCATCAAGAATGCTTCAGAAAAAGAAGTAGAGGTAGAACGTTTGATACTCAGTGTGGTTTTTCAGTTGGATTAAAAGTATGTTTCTTTCCATTGGATTAAAATCAGGGTGGAGGGTAAGGCATAACCTTTGTGCCCTCCCAA Human > Chimp ------------- chr15:7261610-7261614 Template switch process: F1: L TGGATTAAAAGTATGTTTCTTTCAATTGGATTAAAATCAGGATGGAGGGT 1 F3: 4 ATAACCTTTGTGCCCTCCCAACAAAAGCAACATAG R RF: GCCTACTGCAAACTTTTAATCATCGAAAATGCTTCAGGAAAAGAAGTAGAGGTAGAATGTATGATACTCAGTGTGTTTTTTCAGTTGGATTAAAAGTATGTTTCTTTCAATTGGATTAAAATCAGGGTGGAGGGTCACACATAACCTTTGTGCCCTCCCAACAAAAGCAACATAG RR: CGGATGACGTTTGAAAATTAGTAGCTTTTACGAAGTCCTTTTCTTCATCTCCATCTTACATACTATGAGTCACACAAAAAAGTCAACCTAATTTTCATACAAAGAAAGTTAACCTAATTTTAGTCCCACCTCCCAGTGTGTATTGGAAACACGGGAGGGTTGTTTTCGTTGTATC F2: 3 CGGAT 2 Unidirectional alignment (log-probability: -32.2) GTATGTTTCTTTCAATTGGATTAAAATCAGGaTGGAGGGTtAggCATAACCTTTGTGCCCTCCCAACAAAAGCAACATAG---- GTATGTTTCTTTCAATTGGATTAAAATCAGGGTGGAGGGTCACACATAACCTTTGTGCCCTCCCAACAAAAGCAACATAGGCTC Template switch alignment (log-probability: -22) GTATGTTTCTTTCAATTGGATTAAAATCAGGaTGGAGGGT|TAGGC|ATAACCTTTGTGCCCTCCCAACAAAAGCAACATAG GTATGTTTCTTTCAATTGGATTAAAATCAGGGTGGAGGGT|TAGGC|ATAACCTTTGTGCCCTCCCAACAAAAGCAACATAG ========== Event 1115 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACAGCCCTCCAAAAGAAAAGGGA--------CTGCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGG Chimp: ACAGCCCTCCAAAAGAAAAGGTG----AAGTTATCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGG Gorilla: ACAGCCCTCCAAAAGAAAAGGTGAAGT----TATCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGG ↓ 1 4 3 2 Human: ACAGCCCTCCAAAAGAAAAGGGA--------CTGCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGG Cluster: [ ] Orangutan: ACAGCCCTCCAAAAGAAAAGGTGATGT----TATCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGG Gorilla > Human --------------- chr15:26490416-26490420 Template switch process: F1: L TCCCATCACTCTGCAATTGCACAGCCCTCCAAAAGAAAAGG 1 F3: 4 CTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGGGCA R RF: TCCCATCACTCTGCAATTGCACAGCCCTCCAAAAGAAAAGGTGAAGTTATCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGGGCA RR: AGGGTAGTGAGACGTTAACGTGTCGGGAGGTTTTCTTTTCCACTTCAATAGAAAGGGTCTTCGTCAGGTAGACCTCGGGTCCGCTCCCGT F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -25.3) CCCATCACTCTGCAATTGCACAGCCCTCCAAAAGAAAAGGgacTG-------CTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGGGCA CCCATCACTCTGCAATTGCACAGCCCTCCAAAAGAAAAGG---TGAAGTTATCTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGGGCA Template switch alignment (log-probability: -16.4) CCCATCACTCTGCAATTGCACAGCCCTCCAAAAGAAAAGG|GACTG|CTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGGGCA CCCATCACTCTGCAATTGCACAGCCCTCCAAAAGAAAAGG|GACTG|CTTTCCCAGAAGCAGTCCATCTGGAGCCCAGGCGAGGGCA ========== Event 1116 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGGAGGCTCTCAGTGCAGAACGCGGGGGGCCTGAAGGCCTCAGATGTAGGCCCTTGAACTTGTGTTATAACATGGACTCTCTTCCTCACTGCCAGAGAGAGGCGGGGGCAGCAGAGACATCATCTGGAAT-GC-ACTCGATGGGGCC-TTCACT-GGCCCCCCACAGTGGGGTGAGGTGACA-CCAGCA Chimp: CAGGAGGCTCTCAGTGCAGAACGTGGAGGGCCTGAAGGCCTCAGATGTAGGCCCTTGAACTTGTGTTATAACATGGACTCTCTTCCTCACTGCCAGAGAGAGGCGGGGGCAGCAGAGACATCATCTGGAAT-GC-ACTCGATGGGGCC-TTCACT-GGCCCCCCACGGTGGGGTGAGGTGACA-CCAGCA ↑ 3 2 1 4 Gorilla: CAGGAGGCTCTCAGTGCAGAACGTGGGGGGCCTGAAGGCCTCAGATGTAGGCCCTTGAACTTGTGTTATAACATGGACTCTCTTCCTCACTGCCAGAGAGAGGCGGGGGCAGCAGAGACATCAGCTGGAAT-GC-ACTCGATGGGGCC-TTCACT------TCTATCTGGGGGTGAGGTGACA-CCAGCA Human: CAGGAGGCTCTCAGTGCAGAACGCGGGGGGCCTGAAGGCCTCAGATGTAGGCCCTTGAACTTGTGTTATAACATGGACTCTCTTCCTCACTGCCAGAGAGAGGCGGGGGCAGCAGAGACATCATCTGGAAT-GC-ACTCGATGGGGCC-TTCACT-GGCCCCCCACAGTGGGGTGAGGTGACA-CCAGCA Cluster: [ ] Orangutan: CAGGAGGCTCTCAGTGCAGAACGTGGGGGTCCTGAAGGCCTCAGATGTGGGCCCTTGAACTTGTGTTATAACATAGACTCCCTTCCTTACTGCCAGAGAGAGGCAGGGGCAGCAGAGACATCATCTGGAATGGCACCTCAATGGGGCCTTTCACTT-----CTATCTGAGGGGTGAGGTGACACCCAGCA Gorilla > Chimp --------------- chr15:74381830-74381842 Template switch process: F1: L GCAGAGACATCATCTGGAATGCACTCGATGGGGCCTTCACT 1 F3: 4 GGGGTGAGGTGACACCAGCATTCAGTGAACAGATTTGAGG R RF: AACGTGGGGGGCCTGAAGGCCTCAGATGTAGGCCCTTGAACTTGTGTTATAACATGGACTCTCTTCCTCACTGCCAGAGAGAGGCGGGGGCAGCAGAGACATCAGCTGGAATGCACTCGATGGGGCCTTCACTTCTATCTGGGGGTGAGGTGACACCAGCATTCAGTGAACAGATTTGAGG RR: TTGCACCCCCCGGACTTCCGGAGTCTACATCCGGGAACTTGAACACAATATTGTACCTGAGAGAAGGAGTGACGGTCTCTCTCCGCCCCCGTCGTCTCTGTAGTCGACCTTACGTGAGCTACCCCGGAAGTGAAGATAGACCCCCACTCCACTGTGGTCGTAAGTCACTTGTCTAAACTCC F2: 3 TGGCACCCCCCGG 2 Unidirectional alignment (log-probability: -43.8) CAGAGACATCAtCTGGAATGCACTCGATGGGGCCTTCACTggccccccacggT-------GGGGTGAGGTGACACCAGCATTCAGTGAACAGATTTGAGG CAGAGACATCAGCTGGAATGCACTCGATGGGGCCTTCACT------------TCTATCTGGGGGTGAGGTGACACCAGCATTCAGTGAACAGATTTGAGG Template switch alignment (log-probability: -28.4) CAGAGACATCAtCTGGAATGCACTCGATGGGGCCTTCACT|GGCCCCCCACGgT|GGGGTGAGGTGACACCAGCATTCAGTGAACAGATTTGAGG CAGAGACATCAGCTGGAATGCACTCGATGGGGCCTTCACT|GGCCCCCCACGTT|GGGGTGAGGTGACACCAGCATTCAGTGAACAGATTTGAGG ========== Event 1117 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGGCAGAGTGTCACTGTCCTCT--------------------TGCTCGTCTCCGCATCCATTGGCAGTGCAGCCCTTACAGACTTGTGGCCGTGCAGACTGGGATGCGTGCCATTC Chimp: TGTGGCAGAGTGTTACTGTCCTCT--------------------TGCTCGTCTCCGCATCCATTGGCAGTGCAGCCCTTACAGACTTGTGGCCATGCAGACTGGGATGCGCGCCATTC ↓ 4 1 3 2 Gorilla: TGTGGCAGAGTGTCACTGTCCTCTTGCTCGTTTCTGCATCCTCTTGCTCGTCTCCGCAACCATTGGCAGTGCAGCCCTTACAGACTTGTGGCCGTGCAGACTGGGATGCGCGCCATTC Human: TGTGGCAGAGTGTCACTGTCCTCT--------------------TGCTCGTCTCCGCATCCATTGGCAGTGCAGCCCTTACAGACTTGTGGCCGTGCAGACTGGGATGCGTGCCATTC Cluster: [ ] Orangutan: TGTGGCAGAGTGTCACTGTCCTCT--------------------TGCTCATCTCTGCAGCCATTGGCAGTGCAGCCCTTACAGACTTGTGGCCGTGCAGACTGGCATGCACGCCATTC Chimp > Gorilla --------------- chr15:74669817-74669821 Template switch process: F1: L CCACCCCTTCTCAGGAGTGTGGCAGAGTGTCACTGTCCTCTTGCTCGTTTC 1 F3: 4 CCTCTTGCTCGTCTCCGCAACCATTGGCAGTGCAGCCCTTACAGA R RF: CCACCCCTTCTCAGGAGTGTGGCAGAGTGTTACTGTCCTCTTGCTCGTCTCCGCATCCATTGGCAGTGCAGCCCTTACAGACTTGTGGCCATGCA RR: GGTGGGGAAGAGTCCTCACACCGTCTCACAATGACAGGAGAACGAGCAGAGGCGTAGGTAACCGTCACGTCGGGAATGTCTGAACACCGGTACGT F2: 3 TACGT 2 Unidirectional alignment (log-probability: -50.7) CAGGAGTGTGGCAGAGTGTcACTGtcctcttgctcgtttctgcaTCCTCTTGCTCGTCTCCGCAaCCATTGGCAGTGCAGCCCTT CAGGAGTGTGGCAGAGTGTTACTG--------------------TCCTCTTGCTCGTCTCCGCATCCATTGGCAGTGCAGCCCTT Template switch alignment (log-probability: -33.3) CAGGAGTGTGGCAGAGTGTcACTGTCCTCTTGCTCGTtTC|TGCAT|CCTCTTGCTCGTCTCCGCAaCCATTGGCAGTGCAGCCCTT CAGGAGTGTGGCAGAGTGTTACTGTCCTCTTGCTCGTCTC|TGCAT|CCTCTTGCTCGTCTCCGCATCCATTGGCAGTGCAGCCCTT ========== Event 1118 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAAACCTCAGGTCGAGGACTTCGCTCCTAACTCAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGC ↓ 1 4 3 2 Chimp: TAAAACCTCAGGTCGAGGACT------TTCAGACAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGC ↑ 1 4 3 2 Gorilla: TAAAACCTCAGGTCGAGGACTTCGCTCCTAACTCAATGATAAGGTCTGAAAATCCAAGCCAGTGTGGGC Human: TAAAACCTCAGGTCGAGGACTTCGCTCCTAACTCAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGC Cluster: [ ] Orangutan: TAAAACCTCAGGTCGAGGACTTCGCTCCTAACTCAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGC Human > Chimp ------------- chr15:10853453-10853457 Template switch process: F1: L AGGCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT 1 F3: 4 CAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC R RF: AGGCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTTCGCTCCTAACTCAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC RR: TCCGGGACTGAAACCTGGTTATTTTGGAGTCCAGCTCCTGAAGCGAGGATTGAGTTACTATTCCAGACTTTTAGGCTCGGTCACACCCGAACG F2: 3 AGACT 2 Unidirectional alignment (log-probability: -27.4) GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT----------TcagaCAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTTCGCTCCTAACT----CAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC Template switch alignment (log-probability: -15.9) GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT|TCAGA|CAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT|TCAGA|CAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC Gorilla > Chimp --------------- chr15:10853453-10853457 Template switch process: F1: L AGGCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT 1 F3: 4 CAATGATAAGGTCTGAAAATCCGAGCCAGTGTGGGCTTGC R RF: AGGCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTTCGCTCCTAACTCAATGATAAGGTCTGAAAATCCAAGCCAGTGTGGGCTTGC RR: TCCGGGACTGAAACCTGGTTATTTTGGAGTCCAGCTCCTGAAGCGAGGATTGAGTTACTATTCCAGACTTTTAGGTTCGGTCACACCCGAACG F2: 3 AGACT 2 Unidirectional alignment (log-probability: -32.4) GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT----------TcagaCAATGATAAGGTCTGAAAATCCgAGCCAGTGTGGGCTTGC GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTTCGCTCCTAACT----CAATGATAAGGTCTGAAAATCCAAGCCAGTGTGGGCTTGC Template switch alignment (log-probability: -21.9) GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT|TCAGA|CAATGATAAGGTCTGAAAATCCgAGCCAGTGTGGGCTTGC GCCCTGACTTTGGACCAATAAAACCTCAGGTCGAGGACTT|TCAGA|CAATGATAAGGTCTGAAAATCCAAGCCAGTGTGGGCTTGC ========== Event 1119 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATGCCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCC-A----CTGTAGTAGAGATGTGTGCACACC ↓ 3 2 1 4 Chimp: CATGCCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCCTGCAACACATAGTAGAGATGTGTGCACACC ↑ 3 2 1 4 Gorilla: CATGCCAGCCGGTCCTCTCTGTGTTGCAGGCATGCGGTGGAGCC-G----CTGTAGTAGAGATGTGTGCACACC Human: CATGCCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCC-A----CTGTAGTAGAGATGTGTGCACACC Cluster: [ ] Orangutan: CATGCCAGCTGGTCCTCTCTGCGTTGCGGGCACGCGGTGGAGCC-G----CTGTAGTAGAGGTATGTGCACACC Human > Chimp ------------- chr15:11554478-11554486 Template switch process: F1: L GCCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCC 1 F3: 4 TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA R RF: GCCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCCACTGTAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA RR: CGGTCGGCCAGGAGAGACACAACGTCCGTGCGCCACCTCGGTGACATCATCTCTACACACGTGTGGCGACCCCACCAATGTAAGT F2: 3 ACACAACGT 2 Unidirectional alignment (log-probability: -31.3) CCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGC--CTGcaacacaTAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA CCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCCACTG-------TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA Template switch alignment (log-probability: -16.4) CCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCC|TGCAACACA|TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA CCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCC|TGCAACACA|TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA Gorilla > Chimp --------------- chr15:11554478-11554486 Template switch process: F1: L GCCAGCCGGTCCTCTCTGTGTTGCAGGCACGCGGTGGAGCC 1 F3: 4 TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA R RF: GCCAGCCGGTCCTCTCTGTGTTGCAGGCATGCGGTGGAGCCGCTGTAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA RR: CGGTCGGCCAGGAGAGACACAACGTCCGTACGCCACCTCGGCGACATCATCTCTACACACGTGTGGCGACCCCACCAATGTAAGT F2: 3 ACACAACGT 2 Unidirectional alignment (log-probability: -36.3) CCAGCCGGTCCTCTCTGTGTTGCAGGCAcGCGGTGGAGC--CTGcaacacaTAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA CCAGCCGGTCCTCTCTGTGTTGCAGGCATGCGGTGGAGCCGCTG-------TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA Template switch alignment (log-probability: -22.4) CCAGCCGGTCCTCTCTGTGTTGCAGGCAcGCGGTGGAGCC|TGCAACACA|TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA CCAGCCGGTCCTCTCTGTGTTGCAGGCATGCGGTGGAGCC|TGCAACACA|TAGTAGAGATGTGTGCACACCGCTGGGGTGGTTACATTCA ========== Event 1120 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACATGATTTCAAATCCAACCCGTTGGATGTACTTCCGTTGAAGTACATCTCCTTCCAAGCTCATATCAT ↑ 4 13 2 Chimp: ACATGATTTCAAATCCAACCC---------------GTTAAAGTACATCTCCTTCCAAGCTCATATCAT Gorilla: ACATGATTTCAAATCCAACCC---------------GTTAAAGTACATCTCCTTCCAAGCTCATATCAT ↓ 4 13 2 Human: ACATGATTTCAAATCCAACCCGTTGGATGTACTTCCGTTGAAGTACATCTCCTTCCAAGCTCATATCAT Cluster: [ ] Orangutan: ACATGATTTCAAATCCAACCC---------------GTTAAAGTACATCTCCTTCCAAGCTCATATCGT Chimp > Human ------------- chr1:5318232-5318240 Template switch process: F1: L TGGAATCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTG 1 F3: 4 CCGTTGAAGTACATCTCCTTCCAAGCTCATATCATTCCTTGAATTC R RF: TGGAATCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTAAAGTACATCTCCTTCCAAGCTCATATCATTCCTTGAATTC RR: ACCTTAGATATTCCGACCACTGTACTAAAGTTTAGGTTGGGCAATTTCATGTAGAGGAAGGTTCGAGTATAGTAAGGAACTTAAG F2: 3 TTCATGTAG 2 Unidirectional alignment (log-probability: -38.5) TCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGttggatgtacttccgTTgAAGTACATCTCCTTCCAAGCTCATATCATTCCTT TCTATAAGGCTGGTGACATGATTTCAAATCCAACCCG---------------TTAAAGTACATCTCCTTCCAAGCTCATATCATTCCTT Template switch alignment (log-probability: -28.6) TCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTg|GATGTACTT|CCGTTgAAGTACATCTCCTTCCAAGCTCATATCATTCCTT TCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTA|GATGTACTT|CCGTTAAAGTACATCTCCTTCCAAGCTCATATCATTCCTT Gorilla > Human --------------- chr1:5318232-5318240 Template switch process: F1: L TGGAATCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTG 1 F3: 4 CCGTTGAAGTACATCTCCTTCCAAGCTCATATCATTCCTTGAATTC R RF: TGGAATCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTAAAGTACATCTCCTTCCAAGCTCATATCATTCCTTGAATTC RR: ACCTTAGATATTCCGACCACTGTACTAAAGTTTAGGTTGGGCAATTTCATGTAGAGGAAGGTTCGAGTATAGTAAGGAACTTAAG F2: 3 TTCATGTAG 2 Unidirectional alignment (log-probability: -38) TCTATAAGGCTGGTGACATGATTTCAAATCCAACccgttggatgtacttCCGTTgAAGTACATCTCCTTCCAAGCTCATATCATTCCTT TCTATAAGGCTGGTGACATGATTTCAAATCCAAC---------------CCGTTAAAGTACATCTCCTTCCAAGCTCATATCATTCCTT Template switch alignment (log-probability: -28.2) TCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTg|GATGTACTT|CCGTTgAAGTACATCTCCTTCCAAGCTCATATCATTCCTT TCTATAAGGCTGGTGACATGATTTCAAATCCAACCCGTTA|GATGTACTT|CCGTTAAAGTACATCTCCTTCCAAGCTCATATCATTCCTT ========== Event 1121 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCTGGGTCTGGGCATCATTCTGACTTCTCCAACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGA-----------ATATGTCAGGAATATTTCTTCAGCTGAAGAAATAA Chimp: CCTGGGTCTGGGCATCGTTCTGACTTCTCCAACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGA-----------ATATGTCAGGAATATTTCTTCAGCTGAAGAAATAA ↑ 3 2 4 1 Gorilla: CCTGGGTCTGGGCATCATTCTGACTTCTCCAACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGA----------------------ATATTTCTTCAGCTGAAGAAATAA ↓ 3 2 4 1 Human: CCTGGGTCTGGGCATCATTCTGACTTCTCCAACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGA-----------ATATGTCAGGAATATTTCTTCAGCTGAAGAAATAA Cluster: [ ] Orangutan: CCTGGGTCTGGGCATCATTCTGACTTCTCCAACCAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGAATATGTCAGGA-----------ATATTTCTTCAGCTGAAGAAATAA Gorilla > Human --------------- chr15:33605721-33605725 Template switch process: F1: L ACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGAATAT 1 F3: 4 GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATGTC R RF: CTGACTTCTCCAACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATGTC RR: GACTGAAGAGGTTGCTCGTGTGTCCCTTGTATATAGAACGTCTTCCCTAACCTTATAAAGAAGTCGACTTCTTTATTTCAAAGACAACTACAG F2: 3 GACTG 2 Unidirectional alignment (log-probability: -26.7) CACACAGGGAACATATATCTTGCAGAAGGGATTGgaatatgtcagGAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG CACACAGGGAACATATATCTTGCAGAAGGGATTG-----------GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG Template switch alignment (log-probability: -16.5) CACACAGGGAACATATATCTTGCAGAAGGGATTGGAATAT|GTCAG|GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG CACACAGGGAACATATATCTTGCAGAAGGGATTGGAATAT|GTCAG|GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG Gorilla > Chimp --------------- chr15:13857041-13857045 Template switch process: F1: L ACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGAATAT 1 F3: 4 GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATGTC R RF: CTGACTTCTCCAACGAGCACACAGGGAACATATATCTTGCAGAAGGGATTGGAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATGTC RR: GACTGAAGAGGTTGCTCGTGTGTCCCTTGTATATAGAACGTCTTCCCTAACCTTATAAAGAAGTCGACTTCTTTATTTCAAAGACAACTACAG F2: 3 GACTG 2 Unidirectional alignment (log-probability: -26.7) CACACAGGGAACATATATCTTGCAGAAGGGATTGgaatatgtcagGAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG CACACAGGGAACATATATCTTGCAGAAGGGATTG-----------GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG Template switch alignment (log-probability: -16.5) CACACAGGGAACATATATCTTGCAGAAGGGATTGGAATAT|GTCAG|GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG CACACAGGGAACATATATCTTGCAGAAGGGATTGGAATAT|GTCAG|GAATATTTCTTCAGCTGAAGAAATAAAGTTTCTGTTGATG ========== Event 1122 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: atttatGTGAAAATGAGTACAATTTCCCATAGATAGGTAAGGAAAGAAAAGattttttatatatat--atttt----------------------tatatatatatatttttatatatgtttatatat-ataaaaatat----atatata-tataAAATCTTTTCTTTCCTTACCTATCTATGGGAAATTGTACTCATTTTCACACAC-A ↑ 1 4 3 2 Chimp: atTTATGTGAAAATGAGTACCATTTCCCAT----AGGTAAGG-----AAAGattttttatatatatatatttt-----------------------------------------ttatataaacatat-ataaaaatat--atatatata-tataaaaTCTTTTCTTTCCTTACCTATCTATGGGAAATTGTACTCATTTTCACACAC-A Gorilla: -------------------------------------------------------------------------ttatatataa------------------------------------aaaatatat-atataaacat----atatata-caaaaaaTCTTTTCTTTCCTTACCTATCTATGGAAAATTGTACTCATTTTCACACAC-A Human: atttatGTGAAAATGAGTACAATTTCCCATAGATAGGTAAGGAAAGAAAAGattttttatatatat--atttt----------------------tatatatatatatttttatatatgtttatatat-ataaaaatat----atatata-tataAAATCTTTTCTTTCCTTACCTATCTATGGGAAATTGTACTCATTTTCACACAC-A Cluster: [ ] Orangutan: -------------------------------------------------------------------------NNNNNNNNNNNNNNNNNNNNNN------------------------NNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr15:33794259-33794305 Template switch process: F1: L TATAAATATATATTTATGTGAAAATGAGTAC 1 F3: 4 TTTTTATATATATATATT R RF: TATAAATATATATTTATGTGAAAATGAGTACCATTTCCCATAGGTAAGGAAAGATTTTTTATATATATATATTTTTTATATAAACATATATAAAAATATATATATATATATAAAATCTTTTCTTTCCTTACCTATCTATGGGAAATT RR: ATATTTATATATAAATACACTTTTACTCATGGTAAAGGGTATCCATTCCTTTCTAAAAAATATATATATATAAAAAATATATTTGTATATATTTTTATATATATATATATATTTTAGAAAAGAAAGGAATGGATAGATACCCTTTAA F2: 3 ATATATATATTTTTTAGAAAAGAAAGGAATGGATAGATACCCTTTAA 2 Unidirectional alignment (log-probability: -73.4) TATAAATATATATTTATGTGAAAATGAGTACaATTTCCCatagATAGGTAAGGAAAGAaaagattttttatatatataTTTTTATATATATATATT-- TATAAATATATATTTATGTGAAAATGAGTACCATTTCCC----ATAGGTAAGGAAAGA-------------------TTTTTTATATATATATATTTT Template switch alignment (log-probability: -26.5) TATAAATATATATTTATGTGAAAATGAGTAC|AATTTCCCATAGATAGGTAAGGAAAGAAAAGATTTTtTATATATATA|TTTTTATATATATATATT TATAAATATATATTTATGTGAAAATGAGTAC|AATTTCCCATAGATAGGTAAGGAAAGAAAAGATTTTATATATATATA|TTTTTATATATATATATT ========== Event 1123 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCATGCTTCCATCCCAACAAA------CTGAACTAGTTACCTCAGAACTGGAAAACTTGAAGGCATTTGC Chimp: TCATGCTTCCATCCCAACAAA-----------CTAGTTACCTCAGACCTGGAAAACTTGAAGGCATTTGC Gorilla: TCAGGCTTCCATCCCAACAAA---CCA-----GTTGTTACCTCAGAACTGGAAAACTTGAAGGCATTTGC ↑ 1 4 3 2 Human: TCATGCTTCCATCCCAACAAA------CTGAACTAGTTACCTCAGAACTGGAAAACTTGAAGGCATTTGC Cluster: [ ] Orangutan: TCATGCTTCCATCCCAACAAACAA--------CTAGTTACCTCAGAACTGGAAAACTTGAAAGCATTTGC Human > Gorilla --------------- chr15:69147013-69147017 Template switch process: F1: L TACTTCTCTAGCCCTTTCCTTCAGGCTTCCATCCCAACAAAC 1 F3: 4 GTTACCTCAGAACTGGAAAACTTGAAGGCATTTGCCTAGA R RF: TACTTCTCTAGCCCTTTCCTTCATGCTTCCATCCCAACAAACTGAACTAGTTACCTCAGAACTGGAAAACTTGAAGGCATTTGCCTAGA RR: ATGAAGAGATCGGGAAAGGAAGTACGAAGGTAGGGTTGTTTGACTTGATCAATGGAGTCTTGACCTTTTGAACTTCCGTAAACGGATCT F2: 3 TTGAC 2 Unidirectional alignment (log-probability: -32.2) CTTCTCTAGCCCTTTCCTTCAgGCTTCCATCCCAACAAACcagtT------GTTACCTCAGAACTGGAAAACTTGAAGGCATTTGCCTAGA CTTCTCTAGCCCTTTCCTTCATGCTTCCATCCCAACAAAC----TGAACTAGTTACCTCAGAACTGGAAAACTTGAAGGCATTTGCCTAGA Template switch alignment (log-probability: -21.9) CTTCTCTAGCCCTTTCCTTCAgGCTTCCATCCCAACAAAC|CAGTT|GTTACCTCAGAACTGGAAAACTTGAAGGCATTTGCCTAGA CTTCTCTAGCCCTTTCCTTCATGCTTCCATCCCAACAAAC|CAGTT|GTTACCTCAGAACTGGAAAACTTGAAGGCATTTGCCTAGA ========== Event 1124 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAATTAAATGATATGTAAAA----CATATGTGGACTATG-----------GATTTTGtctaaaacaataatgtgatataaaaatgtctcagatttattgttagacaaa Chimp: TTAATTAAATGATATGTAAAA----CATATGTGGACTATG-----------GATTTTGtctaaaacaataatgtgatataaaaatatctcagatttattgttagacaaa Gorilla: TTAATTAAATGATATGTAAAA--------CGTGGACTATGGAAGACATTTGGATTTTGtctaaaacaataatgtgatataaaaatatctgagatttattgttagacaaa ↑ 4 1 3 2 Human: TTAATTAAATGATATGTAAAA----CATATGTGGACTATG-----------GATTTTGtctaaaacaataatgtgatataaaaatgtctcagatttattgttagacaaa Cluster: [ ] Orangutan: TTAATTAAATGATATATAAAACATA----TGTGGACTATGGAAGACATTTGAATTTtgtctaaaacaataatgtgatgtaaaaatatctgagatttattgttagacaaa Human > Gorilla --------------- chr15:68730683-68730689 Template switch process: F1: L TGTCTGGGATGCTTAAAGTGTTAATTAAATGATATGTAAAAC----GTGGACTATGGA 1 F3: 4 TGGATTTTGTCTAAAACAATA R RF: TGTCTGGGATGCTTAAAGTGTTAATTAAATGATATGTAAAACATATGTGGACTATGGATTTTGTCTAAAACAATAATGTGATATAAAAATGTCT RR: ACAGACCCTACGAATTTCACAATTAATTTACTATACATTTTGTATACACCTGATACCTAAAACAGATTTTGTTATTACACTATATTTTTACAGA F2: 3 TTACAGA 2 Unidirectional alignment (log-probability: -36.5) AAAGTGTTAATTAAATGATATGTAAAAC----GTGGACTAtggaagacattTGGATTTTGTCTAAAACAATA AAAGTGTTAATTAAATGATATGTAAAACATATGTGGACTA-----------TGGATTTTGTCTAAAACAATA Template switch alignment (log-probability: -26.4) AAAGTGTTAATTAAATGATATGTAAAAC----GTGGACTATGGA|AGACATT|TGGATTTTGTCTAAAACAATA AAAGTGTTAATTAAATGATATGTAAAACATATGTGGACTATGGA|AGACATT|TGGATTTTGTCTAAAACAATA ========== Event 1125 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTTTATGATCTTAAGTTCTATGGTTCCTTTAAGAACCATAGAACTTACACAATCCAAA ↑ 1 3 4 2 Chimp: CCTTTATGATCTTAAGTTCTACGGTTCTTAAAGGAACCATAGAACTTACACAATCCAAA Gorilla: CCTTTATGATCTTAAGTTCTACGGTTCTTAAAGGAACCATAGAACTTACACAATCCAAA ↓ 1 3 4 2 Human: CCTTTATGATCTTAAGTTCTATGGTTCCTTTAAGAACCATAGAACTTACACAATCCAAA Cluster: [ ] Orangutan: CCTTTATGATCTTA---------------CACAGAACCACAGAACTTACACAATCCAAA Chimp > Human ------------- chr15:66139562-66139573 Template switch process: F1: L GTCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTA 1 F3: 4 GAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA R RF: GTCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTACGGTTCTTAAAGGAACCATAGAACTTACACAATCCAAAAGACTTTGGAAGAA RR: CAGTAAAAAAATAAAGGAGAGGAAATACTAGAATTCAAGATGCCAAGAATTTCCTTGGTATCTTGAATGTGTTAGGTTTTCTGAAACCTTCTT F2: 3 AATTTCCTTGGT 2 Unidirectional alignment (log-probability: -36.2) TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTAtGGTTCctTTAA--GAACCATAGAACTTACACAATCCAAAAaACTTTGGAAGAA TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTACGGTTC--TTAAAGGAACCATAGAACTTACACAATCCAAAAGACTTTGGAAGAA Template switch alignment (log-probability: -22.8) TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTA|TGGTTCCTTTAA|GAACCATAGAACTTACACAATCCAAAAaACTTTGGAAGAA TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTA|TGGTTCCTTTAA|GAACCATAGAACTTACACAATCCAAAAGACTTTGGAAGAA Gorilla > Human --------------- chr15:66139562-66139573 Template switch process: F1: L GTCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTA 1 F3: 4 GAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA R RF: GTCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTACGGTTCTTAAAGGAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA RR: CAGTAAAAAAATAAAGGAGAGGAAATACTAGAATTCAAGATGCCAAGAATTTCCTTGGTATCTTGAATGTGTTAGGTTTTTTGAAACCTTCTT F2: 3 AATTTCCTTGGT 2 Unidirectional alignment (log-probability: -28.9) TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTAtGGTTCcTttAaGAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTACGGTTCTTAAAGGAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA Template switch alignment (log-probability: -17.3) TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTA|TGGTTCCTTTAA|GAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA TCATTTTTTTATTTCCTCTCCTTTATGATCTTAAGTTCTA|TGGTTCCTTTAA|GAACCATAGAACTTACACAATCCAAAAAACTTTGGAAGAA ========== Event 1126 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTTAAAGCTAAAGAATCTCAGTGAAAACACAGATGCATCTTGAGTATCCAG ↓ 3 1 2 4 Chimp: TTTTAAAGCTAAAGAATCTCAGTTTTCACTGAGATGCATCTTGAGTATCCAG ↑ 3 1 2 4 Gorilla: TTTTAAAGCTAAAGAATCTCAGTGAAAACACAGATGCATCTTGAGTATCCAG Human: TTTTAAAGCTAAAGAATCTCAGTGAAAACACAGATGCATCTTGAGTATCCAG Cluster: [ ] Orangutan: TCTTAAAGCCAAAGAATCTCAGTGAAAACACAGATGCATCTTGAGTATCCAG Human > Chimp ------------- chr15:66448931-66448938 Template switch process: F1: L TTGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGT 1 F3: 4 AGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA R RF: TTGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGTGAAAACACAGATGCATCTTGAGTATCCAGTGTACTGTCGCTATAGACA RR: AACGTATTCTGTTACACAAAAATTTCGATTTCTTAGAGTCACTTTTGTGTCTACGTAGAACTCATAGGTCACATGACAGCGATATCTGT F2: 3 GTCACTTT 2 Unidirectional alignment (log-probability: -37.6) TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGttttcacTG-------AGATGCATCTTGAGTATCCAGTGTACTGTCGCTtTAGACA TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAG-------TGAAAACACAGATGCATCTTGAGTATCCAGTGTACTGTCGCTATAGACA Template switch alignment (log-probability: -22.3) TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGT|TTTCACTG|AGATGCATCTTGAGTATCCAGTGTACTGTCGCTtTAGACA TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGT|TTTCACTG|AGATGCATCTTGAGTATCCAGTGTACTGTCGCTATAGACA Gorilla > Chimp --------------- chr15:66448931-66448938 Template switch process: F1: L TTGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGT 1 F3: 4 AGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA R RF: TTGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGTGAAAACACAGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA RR: AACGTATTCTGTTACACAAAAATTTCGATTTCTTAGAGTCACTTTTGTGTCTACGTAGAACTCATAGGTCACATGACAGCGAAATCTGT F2: 3 GTCACTTT 2 Unidirectional alignment (log-probability: -31.1) TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGttttcacTG-------AGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAG-------TGAAAACACAGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA Template switch alignment (log-probability: -16.7) TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGT|TTTCACTG|AGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA TGCATAAGACAATGTGTTTTTAAAGCTAAAGAATCTCAGT|TTTCACTG|AGATGCATCTTGAGTATCCAGTGTACTGTCGCTTTAGACA ========== Event 1127 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: CAGATAGCGATTTTATACTTTCT-TCCCATAGTAAACTATGGATGACAAATTCTTGACTCCATCATCA ↓ 13 24 ↑ 13 24 Chimp: CAGATAGCGATTTTATACTTTGTCATCCATAGTTTACTATGG-GAAGAAATTCTTGACTCCATCATCA ↓ 13 24 ↑ 13 24 Gorilla: CAGATAGCGATTTTATACTTTCT-TCCCATAGTAAACTATGGATGACAAATTCTTGACTCCATCATCA Human: CAGATAGCGATTTTATACTTTCT-TCCCATAGTAAACTATGGATGACAAATTCTTGACTCCATCATCA Cluster: [ ] Orangutan: CAGATAGCGATTTTATACTTTCT-TCCCATAGTAAACTATGGATGAAAAATTCTTGACTCCATCATCA Chimp > Human ------------- chr15:37423259-37423283 Template switch process: F1: L CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT 1 F3: 4 AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG R RF: CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTGTCATCCATAGTTTACTATGGGAAGAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG RR: GACTATTACTCCTCTTGTATGTCTATCGCTAAAATATGAAACAGTAGGTATCAAATGATACCCTTCTTTAAGAACTGAGGTAGTAGTGTAAGGTCGGTACTGGTAC F2: 3 CAGTAGGTATCAAATGATACCCTTC 2 Unidirectional alignment (log-probability: -58.4) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT-------------------------cttcccatagtaaactatggatgacAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTGTCATCCATAGTTTACTATGGGAAG-------------------------AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Template switch alignment (log-probability: -18.4) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|CTTCCCATAGTAAACTATGGATGAC|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|CTTCCCATAGTAAACTATGGATGAC|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Human > Chimp ------------- chr15:17800970-17800994 Template switch process: F1: L CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT 1 F3: 4 AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG R RF: CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTCTTCCCATAGTAAACTATGGATGACAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG RR: GACTATTACTCCTCTTGTATGTCTATCGCTAAAATATGAAAGAAGGGTATCATTTGATACCTACTGTTTAAGAACTGAGGTAGTAGTGTAAGGTCGGTACTGGTAC F2: 3 GAAGGGTATCATTTGATACCTACTG 2 Unidirectional alignment (log-probability: -58.4) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT-------------------------gtcatccatagtttactatgggaagAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTCTTCCCATAGTAAACTATGGATGAC-------------------------AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Template switch alignment (log-probability: -18.4) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|GTCATCCATAGTTTACTATGGGAAG|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|GTCATCCATAGTTTACTATGGGAAG|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Gorilla > Chimp --------------- chr15:17800970-17800994 Template switch process: F1: L CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT 1 F3: 4 AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG R RF: CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTCTTCCCATAGTAAACTATGGATGACAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG RR: GACTATTACTCCTCTTGTATGTCTATCGCTAAAATATGAAAGAAGGGTATCATTTGATACCTACTGTTTAAGAACTGAGGTAGTAGTGTAAGGTCGGTACTGGTAC F2: 3 GAAGGGTATCATTTGATACCTACTG 2 Unidirectional alignment (log-probability: -57.8) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT-------------------------gtcatccatagtttactatgggaagAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTCTTCCCATAGTAAACTATGGATGAC-------------------------AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Template switch alignment (log-probability: -18.9) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|GTCATCCATAGTTTACTATGGGAAG|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|GTCATCCATAGTTTACTATGGGAAG|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Chimp > Gorilla --------------- chr15:15320308-15320332 Template switch process: F1: L CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT 1 F3: 4 AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG R RF: CTGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTGTCATCCATAGTTTACTATGGGAAGAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG RR: GACTATTACTCCTCTTGTATGTCTATCGCTAAAATATGAAACAGTAGGTATCAAATGATACCCTTCTTTAAGAACTGAGGTAGTAGTGTAAGGTCGGTACTGGTAC F2: 3 CAGTAGGTATCAAATGATACCCTTC 2 Unidirectional alignment (log-probability: -57.8) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT-------------------------cttcccatagtaaactatggatgacAAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTTGTCATCCATAGTTTACTATGGGAAG-------------------------AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG Template switch alignment (log-probability: -18.9) TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|CTTCCCATAGTAAACTATGGATGAC|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG TGATAATGAGGAGAACATACAGATAGCGATTTTATACTTT|CTTCCCATAGTAAACTATGGATGAC|AAATTCTTGACTCCATCATCACATTCCAGCCATGACCATG ========== Event 1128 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCATTCAGCCAGCAGAGGCTGCATTCTAGGAAT--------------------------GCAGCCTTTTCATTTCCTTACTTTT Chimp: ACCATTCAGCCAGCAGAGGCTGCATTCTAGGAAC-------------AACCCAACCCTCAGAGACCTTTTCATTTCCTTACTTTT Gorilla: ACCATTCAGCCAGCAGAGGCTGCATTCTAGGAACAACCCAACCCTCA-------------GAGACCTTTTCATTTCCTTACTTTT ↓ 3 2 1 4 Human: ACCATTCAGCCAGCAGAGGCTGCATTCTAGGAAT--------------------------GCAGCCTTTTCATTTCCTTACTTTT Cluster: [ ] Orangutan: AGCATTCAGCCAGCAGAGGCTGCATTCTAGGAAGAACCCAACCCTCA-------------GAGACCTTTTCATTTCCTTACTTTT Gorilla > Human --------------- chr15:37376827-37376831 Template switch process: F1: L GATGGGTGACCATTCAGCCAGCAGAGGCTGCATTCTAGGAA 1 F3: 4 CCTTTTCATTTCCTTACTTTTCCCCAAAGGGCTCAGATAA R RF: GATGGGTGACCATTCAGCCAGCAGAGGCTGCATTCTAGGAACAACCCAACCCTCAGAGACCTTTTCATTTCCTTACTTTTCCCCAAAGGGCTCAGATAA RR: CTACCCACTGGTAAGTCGGTCGTCTCCGACGTAAGATCCTTGTTGGGTTGGGAGTCTCTGGAAAAGTAAAGGAATGAAAAGGGGTTTCCCGAGTCTATT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -28.7) ATGGGTGACCATTCAGCCAGCAGAGGCTGCATTCTAGGA------------------AtgcagCCTTTTCATTTCCTTACTTTTCCCCAAAGGGCTCAGATAA ATGGGTGACCATTCAGCCAGCAGAGGCTGCATTCTAGGAACAACCCAACCCTCAGAGA-----CCTTTTCATTTCCTTACTTTTCCCCAAAGGGCTCAGATAA Template switch alignment (log-probability: -16.4) ATGGGTGACCATTCAGCCAGCAGAGGCTGCATTCTAGGAA|TGCAG|CCTTTTCATTTCCTTACTTTTCCCCAAAGGGCTCAGATAA ATGGGTGACCATTCAGCCAGCAGAGGCTGCATTCTAGGAA|TGCAG|CCTTTTCATTTCCTTACTTTTCCCCAAAGGGCTCAGATAA ========== Event 1129 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATACTGAGTGTTTTTCTACACGCA-----CAAGGTCTGTCAAACTGTCAGTGAGAGTTTTTACC ↓ 1 4 3 2 Chimp: AATACTGAGTGTTTTTCTACATGCAGTTTGACAGGTCTGTCAAACTGTCAGTGAGAGTTTTTACC Gorilla: AATACTGAGTGTTTTTCTACATGCA-----CAAGGTCTATCAAACTGTCAGTGAGAGTTTTTAC- Human: AATACTGAGTGTTTTTCTACACGCA-----CAAGGTCTGTCAAACTGTCAGTGAGAGTTTTTACC Cluster: [ ] Orangutan: AATACTGAGTGTTCTTCTACATGCA-----CAAGGTCTGTCAAACTGTCAGTGAGAGTTTTTACC Human > Chimp ------------- chr15:64918613-64918619 Template switch process: F1: L TCTGGTTGGTTTTTAAAGGCAATACTGAGTGTTTTTCTACATGCA 1 F3: 4 AGGTCTGTCAAACTGTCAGTGAGAGTTTTTACCTCTGACT R RF: TCTGGTTGGTTTTTAAAGGCAATACTGAGTGTTTTTCTACACGCACAAGGTCTGTCAAACTGTCAGTGAGAGTTTTTACCTCTGACT RR: AGACCAACCAAAAATTTCCGTTATGACTCACAAAAAGATGTGCGTGTTCCAGACAGTTTGACAGTCACTCTCAAAAATGGAGACTGA F2: 3 CAGTTTG 2 Unidirectional alignment (log-probability: -35.8) TTGGTTTTTAAAGGCAATACTGAGTGTTTTTCTACatgcagtttgAC-----AGGTCTGTCAAACTGTCAGTGAGAGTTTTTACCTCTGACT TTGGTTTTTAAAGGCAATACTGAGTGTTTTTCTAC----------ACGCACAAGGTCTGTCAAACTGTCAGTGAGAGTTTTTACCTCTGACT Template switch alignment (log-probability: -22.2) TTGGTTTTTAAAGGCAATACTGAGTGTTTTTCTACAtGCA|GTTTGAC|AGGTCTGTCAAACTGTCAGTGAGAGTTTTTACCTCTGACT TTGGTTTTTAAAGGCAATACTGAGTGTTTTTCTACACGCA|GTTTGAC|AGGTCTGTCAAACTGTCAGTGAGAGTTTTTACCTCTGACT ========== Event 1130 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTCACTGCCTGCAGGCCCACT-GCAGCAGCACTGACAcagagcctacaggagctcag-gccccctaatgagagttaggcagcagatctaaagggaatgaatacatcgtgctttttttatagctcatttttatttgctttgcatgagaaatctcatgggcatt Chimp: CCTCACTGCCTGCAGGCTCACAGATAGCAGCACTGACACAGAGCCTACAGGAGCTCAGGGCCACCTAATGAGAGTTAGCCAGCAGATCTAAAGGGAATGAATACATCGTGCTTCTTTTATAGCTCATTTTTATTTGCTTTGCATGAGAAATCTCTTGGGCGTT Gorilla: CCTCACTGCCTGCAGGCCCACAGATAGCAGCACTGACAcagagcctacaggagctcagggccacctaatgagagttaggcagcagatctaaagggaatgaatacattgtgcttcttttatagctcatttatatttgctttgcatgagaaatctcatggacgtt ↓ 1 4 3 2 Human: CCTCACTGCCTGCAGGCCCACT-GCAGCAGCACTGACAcagagcctacaggagctcag-gccccctaatgagagttaggcagcagatctaaagggaatgaatacatcgtgctttttttatagctcatttttatttgctttgcatgagaaatctcatgggcatt Cluster: [ ] Orangutan: CCTCGCTG-CTGCA-GCCCACAGATAGCAGCACTGACACAGAG-CTAAAGGAGATCAG-GCC-ACTAATGAGAG-TAGGCAGCAGATCTAAAGGGAATGAATACATCGTGCTTCTTTTATAGCTCAT-TTTATTTGCTTTGCATGAGAAATCTCATGGGCGTT Gorilla > Human --------------- chr15:62278981-62278984 Template switch process: F1: L ATCAAGCCCAGCTGAACTGCCCTCACTGCCTGCAGGCCCAC 1 F3: 4 GCAGCACTGACACAGAGCCTACAGGAGCTCAGGCCCCC R RF: ATCAAGCCCAGCTGAACTGCCCTCACTGCCTGCAGGCCCACAGATAGCAGCACTGACACAGAGCCTACAGGAGCTCAGGGCCACCTAATGAGAGTTAGGCAGCAGATCTAAAGGGAATGAATACATTGTGCTTCTTTTATAGCTCATTTATATTTGCTTTGCA RR: TAGTTCGGGTCGACTTGACGGGAGTGACGGACGTCCGGGTGTCTATCGTCGTGACTGTGTCTCGGATGTCCTCGAGTCCCGGTGGATTACTCTCAATCCGTCGTCTAGATTTCCCTTACTTATGTAACACGAAGAAAATATCGAGTAAATATAAACGAAACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -37.3) TCAAGCCCAGCTGAACTGCCCTCACTGCCTGCAGGCCCACtGc-AGCAGCACTGACACAGAGCCTACAGGAGCTCA-GGCCcCC TCAAGCCCAGCTGAACTGCCCTCACTGCCTGCAGGCCCACAGATAGCAGCACTGACACAGAGCCTACAGGAGCTCAGGGCCACC Template switch alignment (log-probability: -27.2) TCAAGCCCAGCTGAACTGCCCTCACTGCCTGCAGGCCCAC|TGCA|GCAGCACTGACACAGAGCCTACAGGAGCTCAGGcCCcC TCAAGCCCAGCTGAACTGCCCTCACTGCCTGCAGGCCCAC|TGCA|GCAGCACTGACACAGAGCCTACAGGAGCTCAGGGCCAC ========== Event 1131 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCACATAGCTTTGGACACAGACCTACTCCCCTGGGGGCTGAGGGAGGTCACTGGGAGGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGC---------------CAGTGGCCCAGACTTTGAAACAG Chimp: GCCACATAGCTTTGGACTCAGACCTGCTCCCCTGGGGGCTGAGGGAGGTCACTGGGAGGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGC---------------CAGTGGCCCAGACTTTGAAACAG ↓ 3 2 4 1 Gorilla: GCCACATAGCTTTGGACACAGACCTACTCCCCTGGGGGCTGAGGGAGGTCACTGGGAGGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGCCAGGGAGCAGCTCTCCAGTGGCCCAGACTTTGAAACAG Human: GCCACATAGCTTTGGACACAGACCTACTCCCCTGGGGGCTGAGGGAGGTCACTGGGAGGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGC---------------CAGTGGCCCAGACTTTGAAACAG Cluster: [ ] Orangutan: GCCACATAGCTTTGGACACAGACCTACTCCTCTGGGGGCTGAGGGAGGTCACTGGGAGGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGCCAGGGAGCAGCTCTCCAGTGGCCCAGACTTTGAAACAC Chimp > Gorilla --------------- chr15:18077802-18077812 Template switch process: F1: L GGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGCCAG 1 F3: 4 CCAGTGGCCCAGACTTTGAAACAGGCCAGGCAGAGGCCAGG R RF: AGACCTGCTCCCCTGGGGGCTGAGGGAGGTCACTGGGAGGTGATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGCCAGTGGCCCAGACTTTGAAACAGGCCAGGCAGAGGCCAGG RR: TCTGGACGAGGGGACCCCCGACTCCCTCCAGTGACCCTCCACTAGAAAAAGGTGGAGCCTAACTCGTTCTCTTCCGACGGTCACCGGGTCTGAAACTTTGTCCGGTCCGTCTCCGGTCC F2: 3 TCTCGACGAGG 2 Unidirectional alignment (log-probability: -32.5) ATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGccagggagcagctctCCAGTGGCCCAGACTTTGAAACAGGCCAGGCAGAGGCCAG ATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTG---------------CCAGTGGCCCAGACTTTGAAACAGGCCAGGCAGAGGCCAG Template switch alignment (log-probability: -22.7) ATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGCCAG|GGAGCAGcTCT|CCAGTGGCCCAGACTTTGAAACAGGCCAGGCAGAGGCCAG ATCTTTTTCCACCTCGGATTGAGCAAGAGAAGGCTGCCAG|GGAGCAGGTCT|CCAGTGGCCCAGACTTTGAAACAGGCCAGGCAGAGGCCAG ========== Event 1132 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTAAGCCCTGTTAAAGCTACTGT------------TGTATAGACACTTAGGAACTCTTGCT ↓ 3 14 2 Chimp: ATTTAAGCCCTGTTAAAGCTACTGTTTATACAACAGTAGTATAGACACTTAGGAACTCTTGCT ↑ 3 14 2 Gorilla: ATTTAAGCCCTGTTAAAGCTACTGT------------TGTATAGACACTTAGGAACTCTTGCT Human: ATTTAAGCCCTGTTAAAGCTACTGT------------TGTATAGACACTTAGGAACTCTTGCT Cluster: [ ] Orangutan: ATTTAAGCCCTGTTAAAGCTACTGT------------TGTATAGACACTTAGGAACTCTTGCT Human > Chimp ------------- chr15:21197446-21197457 Template switch process: F1: L AAGATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT 1 F3: 4 GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG R RF: AAGATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTTGTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG RR: TTCTATATTGTAAAAGTAAATTCGGGACAATTTCGATGACAACATATCTGTGAATCCTTGAGAACGATTAGATTAATTGTAC F2: 3 ATGACAACATAT 2 Unidirectional alignment (log-probability: -28.2) GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTTtatacaacagtaGTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT------------GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG Template switch alignment (log-probability: -16.8) GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT|TATACAACAGTA|GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT|TATACAACAGTA|GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG Gorilla > Chimp --------------- chr15:21197446-21197457 Template switch process: F1: L AAGATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT 1 F3: 4 GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG R RF: AAGATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTTGTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG RR: TTCTATATTGTAAAAGTAAATTCGGGACAATTTCGATGACAACATATCTGTGAATCCTTGAGAACGATTAGATTAATTGTAC F2: 3 ATGACAACATAT 2 Unidirectional alignment (log-probability: -28.2) GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTTtatacaacagtaGTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT------------GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG Template switch alignment (log-probability: -17.3) GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT|TATACAACAGTA|GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG GATATAACATTTTCATTTAAGCCCTGTTAAAGCTACTGTT|TATACAACAGTA|GTATAGACACTTAGGAACTCTTGCTAATCTAATTAACATG ========== Event 1133 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAGGAAATGTATAGAGTCAGCTAAGATCTTATGTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG ↑ 1 4 3 2 Chimp: GAAGGAAATGTATAGAGTCAGTTAAGAT---GACTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG Gorilla: GAAGGAAATGTATAGAGTCAGTTAAGAT---GACTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG ↓ 1 4 3 2 Human: GAAGGAAATGTATAGAGTCAGCTAAGATCTTATGTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG Cluster: [ ] Orangutan: GAAGGAAATGTATAGAGTCAGTTAAGAT---GACTAAACAAATATTTACATAAGATT-AGCTTTAATAAAAATG Chimp > Human ------------- chr15:42212011-42212016 Template switch process: F1: L GGACAGAAAATCAGCACTCAGAAGGAAATGTATAGAGTCAGCTAAGAT 1 F3: 4 TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG R RF: GGACAGAAAATCAGCACTCAGAAGGAAATGTATAGAGTCAGTTAAGATGACTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG RR: CCTGTCTTTTAGTCGTGAGTCTTCCTTTACATATCTCAGTCAATTCTACTGATTTGTTTATAAATGTATTCTAATCCGAAATTATTTTTAC F2: 3 GTATTC 2 Unidirectional alignment (log-probability: -34.5) AATCAGCACTCAGAAGGAAATGTATAGAGTCAGcTAAGatcttATG--TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG AATCAGCACTCAGAAGGAAATGTATAGAGTCAGTTAAG-----ATGACTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG Template switch alignment (log-probability: -22.2) AATCAGCACTCAGAAGGAAATGTATAGAGTCAGcTAAGAT|CTTATG|TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG AATCAGCACTCAGAAGGAAATGTATAGAGTCAGTTAAGAT|CTTATG|TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG Gorilla > Human --------------- chr15:42212011-42212016 Template switch process: F1: L GGACAGAAAATCAGCACTCAGAAGGAAATGTATAGAGTCAGCTAAGAT 1 F3: 4 TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG R RF: GGACAGAAAATCAGCACTCAGAAGGAAATGTATAGAGTCAGTTAAGATGACTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG RR: CCTGTCTTTTAGTCGTGAGTCTTCCTTTACATATCTCAGTCAATTCTACTGATTTGTTTATAAATGTATTCTAATCCGAAATTATTTTTAC F2: 3 GTATTC 2 Unidirectional alignment (log-probability: -33.6) AATCAGCACTCAGAAGGAAATGTATAGAGTCAGcTAAGAT--CttatgTAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG AATCAGCACTCAGAAGGAAATGTATAGAGTCAGTTAAGATGAC-----TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG Template switch alignment (log-probability: -22.2) AATCAGCACTCAGAAGGAAATGTATAGAGTCAGcTAAGAT|CTTATG|TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG AATCAGCACTCAGAAGGAAATGTATAGAGTCAGTTAAGAT|CTTATG|TAAACAAATATTTACATAAGATTAGGCTTTAATAAAAATG ========== Event 1134 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: accttcaCTTGAACGATTATACCT--CAATTACTTCACAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAAAGGCTAATAAGTGAAAGG Chimp: ACCTTCACTCGGACGATTATACCT--CAATTACTTCACGATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATAGGCTAATAAATGAGAGG Gorilla: ACCTTCACTTGGACGATTATAGCT----CTTACTTCAGAATGGTGAATACAATTGTAaaggaagaaaaactgaag---------taaatgaagtaaataggctaataaatgaaagggagaaacactgcaaggaatatttgctaaaacttggttttaagtgacaaaatctatgcctgtgaaccaagaataaaatgtctattttgcatggaaaaaaacaatcacctggaccctttacaaaacactgccgctctggctgtgttccggaccagatgaggctgcttaggagtggggccaggccgagggagcatgacagctcccaggtgattcccctgtgcagccaggctgagaatcgtggctgtaaatcctgagccctggagggtgccccgggaaaacggatctccactctgtcacccccagctcctggaggcgggatcctggctgnnnnnnnnnngtaaggaagaaaaactgaagtaaatgaagtaaataggctaataaatgaaagggagaaacactgcaaggaatatttgctaaaacttggttttaagtgacaaaatctatgcctgtgaaccaagaataaaatgtctattttgcatggaaaaaaacaatcacctggaccctttacaaaacactgccgctctggctgtgttccggaccagatgaggctgcttaggagtggggccaggccgagggagcatgacagctcccaggtgattcccctgtgcagccaggctgagaatcgtggctgtaaatcctgagccctggagggtgccccgggaaaacggatctccactctgtcacccccagctcccggaggcgggatcctggctggCTGAGCGGGGCCGTGTCCTGGACAGCGAGGACATGGGCCACAGTGCTGAAGCCACACAGGCCCTTCTGCGGCGGCTGGAGGCCACCAAGAGAGACCTGGAAGCGTTCAGCCCACGCATCGAGCGGTTGCAGCAGACAGCAGCACTCCTGGAGAGCAGGAAGAACCCAGAAAGGTGGGCGGGAGCCACACCATCCGGGAAGGAGCAGAGAGAAGCCCCCTACAGAGATGGCAGGAGACTGCTCCAGCCTGGAAGGGAAGGGCTGCAGTCCAGACTGTCGCTCTCTTCCCACAGCCCCAAGGTGCTAGCCCAGCTGCAGGCAGTTCGGGAGGCCCACACAGAGCTGCTGCGGAGGGCAGAGGCCAGGGGGCACGGCCTGCAGGAGCAGCTGCAGCTACACCAGCTGGAGCGAGAGACCCTGCTCCTCGACGCCTGGCTGACCACCAAGGCGGCCACCGCCGAGTCCCAGGACTACGGGCAGGACCTGGAGGGTGTCAAGGTGAGTCACTCCTGAGCAAACCTCACCGGGAGTGGGCAGAGGCTGAGGAAGGCCTGCCTTGGGATGAAAGGGTTGCTGGGGAGTCAGTAGAAAGGAGCCTGGAGAGGGTGTCCTAGGGAGGATCCCGATGGTTCCAGAACCTGGGCTGAGGGATTTCAGAGCCATCAGAGTCTGCTGAGCTCTTCATGAGCTTTGAGAGCTCATGATACCATCnnnnnnnnnnAGCATGACagctcccaggtgattcccctgtgcagccaggctgagaatcGTGGCTGTAAATCCTGAGCCCTGGAGGGTGCCCCGGGAAAACGGATCTCCACTCTGTCACCCCCAGCTCCCGGAGGCGGGATCCTGGCTGGCTGAGCGGGGCCGTGTCCTGGACAGCGAGGACATGGGCCACAGTGCTGAAGCCACACAGGCCCTTCTGCGGCGGCTGGAGGCCACCAAGAGAGACCTGGAAGCGTTCAGCCCACACATCGCATCGAGCGGTTGCAGCAGACAGCAGCACTCCTGGAGAGCAGGAAGAACCCAGAAAGGTGGGCGGGAGCCACACCATCCGGGAAGGAGCAGAGAGAAGCCCTCTACAGAGATGGCAGGAGACTGCTCCAGCCTGGAAAGGAAGGGCTGCAGTCCAGACTGTCGCTCTCTTCCCACAGCCCCAAGGTGCTAGCCCAGCTGCAGGCAGTTCGGGAGGCCCACGCAGAGCTGCTGCGGAGGGCAGAGGCCAGGGAGCACGGCCTGCAGGAGCAGCTGCAGCTACACCAGCTGGAGCGAGAGACCCTGCTCCTCAACGCCTGGCTGACCACCAAGGCGGCCACCGCCGAGTCCCAGGACTACGGGCAGGACCTGGAGGGTGTCAAGGTGAGTCACTCCTGAGCAAACCTCACGGGGAGTGGGCAGAGGCTGAGGAAGGCCTGCCTTGGGATGAAAAGGTTGCTGGGGAGTCAGCAGAAAGGAGCCTGGAGAGGGTGTCCTAGGGAGGATCCCGATGGTTCCAGAACCTGGGCTGAGGGATTTCAGAGCCATCAGAGTCTGCTGAGCTCTTCATGAGCTTTGAGAGCTCATGATACCATCTCGAGTGACCCTGCTGGGCCTCACACCTTTGCAGGTGCTGGAAGAGAAGTTTGATGCCTTCAGAAAGGAAGTGCAGAGCCTGGGCCAGGCCGAAnnnnnnnnnnATGCCCTGGATTCTCTGGGAGTCATGGGGACAGGGAACTCCTTGGGGACAAGTTAGTGGGGTCCCGTGAAACTTCAAGCACAACTGTGGGAGTCCCCCAAGGGTCAGCAACATCCGCATCCTCCTGCCTCCTCCCCCACAGAACCTGGAGAGTGAGATGAGCAGCCACGAGGCTCTGACCCGGGTGGTGCTGGGCACTGGGCACAAGCTGGTGCAGGCTGGGCACTTTGCCGCCCACGAGGTGGCCGCCCGGGTGCAGCAGCTGGAGAAGGCCATGGCCCACCTGCGGGCAGAGGCGGCGTGGAGGTGGCTTCTGCTGCAGCAGGCTCAGGAGGCCCAGCGGTTTCTGACTGAGGTGAGGGGAGTGATGGGCAGGGCACAGCGGGCAGGCCTGGAACACAGGGCGAGTGCGGCCGGGAGGTAACTCCGGGGCTCCTGGCCTGGGCACCTTTCGTCTCCTCCACTCAGTGGTCTCCTGCCCCCAAGGGCTTCCTTCCACATGTTTCCCAGAACACAGCTGCTGGCTGGGTTGGCTTTTGTCTTTTTTCCCTCTAGATcagtggttctcaaccagggctttacatgagaatcacctggAACCTTCACTTGGACGATTATAGCTCTTACTTCAGAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGTAAATGAAGTAAATAGGCTAATAAATGAAAGG ↑ 1 4 3 2 Human: accttcaCTTGAACGATTATACCT--CAATTACTTCACAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAAAGGCTAATAAGTGAAAGG Cluster: [ ] Orangutan: ACCTTCC-CTGGACGATCATACCTCA--ATTACTTCAGAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGTAAATGAAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAATAGGCTAATAAATGAAAGG Human > Gorilla --------------- chr15:60928671-60928679 Template switch process: F1: L TTACATGAGAATCACCTGGAACCTTCACTTGGACGATTATAGCTC 1 F3: 4 AATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGTAA R RF: TTACATGAGAATCACCTGGAACCTTCACTTGAACGATTATACCTCAATTACTTCACAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGTAA RR: AATGTACTCTTAGTGGACCTTGGAAGTGAACTTGCTAATATGGAGTTAATGAAGTGTTACCACTTATGTTAACATTTCCTTCTTTTTGACTTCATT F2: 3 GACTTCATT 2 Unidirectional alignment (log-probability: -38.7) TGAGAATCACCTGGAACCTTCACTTGgACGATTATAgCTC--TTACTTCAgAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGtaa TGAGAATCACCTGGAACCTTCACTTGAACGATTATACCTCAATTACTTCACAATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAG--- Template switch alignment (log-probability: -28) TGAGAATCACCTGGAACCTTCACTTGgACGATTATAgCTC|TTACTTCAG|AATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGTAA TGAGAATCACCTGGAACCTTCACTTGAACGATTATACCTC|TTACTTCAG|AATGGTGAATACAATTGTAAAGGAAGAAAAACTGAAGTAA ========== Event 1135 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC---AGGACTCCTGGCACTGGAGTCAAGAGTGT Chimp: CCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC---AGGACTCCTGGCACTGGAGTCAAGAGTGT ↓ 3 2 1 4 Gorilla: CCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC------TCAGTTGGCACTGGAGTCAAGAGTGT ↑ 3 2 1 4 Human: CCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC---AGGACTCCTGGCACTGGAGTCAAGAGTGT Cluster: [ ] Orangutan: CCTAGGCAGGTCCCTACAAACTGAGCACAAAGGCAGG---ACTCCTGGCACTGGAGTCAAGAGTGT Human > Gorilla --------------- chr15:21372105-21372109 Template switch process: F1: L GGCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC 1 F3: 4 TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA R RF: GGCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGCAGGACTCCTGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA RR: CCGGGAGGGATCCGTCCAGGGATGTTTGACTCGTGTTTCCGTCCTGAGGACCGTGACCTCAGTTCTCACACCCGTGGGACTCGGTTCGT F2: 3 TGACT 2 Unidirectional alignment (log-probability: -28.2) GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGG--------CtcagtTGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGCAGGACTCC-----TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA Template switch alignment (log-probability: -16.4) GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC|TCAGT|TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC|TCAGT|TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA Chimp > Gorilla --------------- chr15:21372105-21372109 Template switch process: F1: L GGCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC 1 F3: 4 TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA R RF: GGCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGCAGGACTCCTGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA RR: CCGGGAGGGATCCGTCCAGGGATGTTTGACTCGTGTTTCCGTCCTGAGGACCGTGACCTCAGTTCTCACACCCGTGGGACTCGGTTCGT F2: 3 TGACT 2 Unidirectional alignment (log-probability: -28.2) GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGG--------CtcagtTGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGCAGGACTCC-----TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA Template switch alignment (log-probability: -16.4) GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC|TCAGT|TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA GCCCTCCCTAGGCAGGTCCCTACAAACTGAGCACAAAGGC|TCAGT|TGGCACTGGAGTCAAGAGTGTGGGCACCCTGAGCCAAGCA ========== Event 1136 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACACATTACTGTCATCCCTATCTGGCATTCTAGCTAATCAGCTCTATTGGG-----------CAACTAATTTTTAAATTAA-----GT------------------------TATGATCAATTGATTAAGTTATAATCAGTACCCCTCATGACATTATAAATCATGTTTTTAATTG Chimp: ACACATTACTGTCATCCCTATCTGGCATTCTAGCTAATCAGCTCTATTGGGCTGattagctataactaattttttaattattattagctataacttaatttttaaattaagttatgatcaattgattaaGTTATAATCAGTACCC-CCATGACATTATAAATCATGTTTTTAATTG ↑ 3 2 1 4 Gorilla: ACACATTACTGTCATCCCTATTTGGTATTCTAGCTAATCAGCTCTATTGGG-----------CAACTAATTTTAAAATTAA-----GT------------------------TATGATCAATTGATTAAGTTATAATCAGTACCCCTCATGACATTATAAATCATGTTTTTAATTG Human: ACACATTACTGTCATCCCTATCTGGCATTCTAGCTAATCAGCTCTATTGGG-----------CAACTAATTTTTAAATTAA-----GT------------------------TATGATCAATTGATTAAGTTATAATCAGTACCCCTCATGACATTATAAATCATGTTTTTAATTG Cluster: [ ] Orangutan: ACACATTATTGTCATCTCTATCTGGTATTCTAGCTAATCAGTTCTATTGGG-----------CAACTAATTTTTAAATTAA-----GT------------------------TATGATCAATTGATTAAGTTATAATCAGTACCCCTCATGACATTATAAATCATGTTTTTAATTG Gorilla > Chimp --------------- chr15:23892164-23892171 Template switch process: F1: L CCACCCTCCTTTGGTGTCTTACACATTACTGTCATCCCTATCTGGCATTCTAGCTAATCAGCTCTATTGGGC 1 F3: 4 TATAAC R RF: CCACCCTCCTTTGGTGTCTTACACATTACTGTCATCCCTATTTGGTATTCTAGCTAATCAGCTCTATTGGGCAACTAATTTTAAAATTAAGTTATGATCAATTGATTAAGTTATAATCAGTACCCCTCATGACATTATAAA RR: GGTGGGAGGAAACCACAGAATGTGTAATGACAGTAGGGATAAACCATAAGATCGATTAGTCGAGATAACCCGTTGATTAAAATTTTAATTCAATACTAGTTAACTAATTCAATATTAGTCATGGGGAGTACTGTAATATTT F2: 3 CGATTAGT 2 Unidirectional alignment (log-probability: -37.7) CATCCCTATcTGGcATTCTAGCTAATCAGCTCTATTGGGCtgattagctatAAC CATCCCTATTTGGTATTCTAGCTAATCAGCTCTATTGGGC-----------AAC Template switch alignment (log-probability: -33.2) CATCCCTATcTGGcATTCTAGCTAATCAGCTCTATTGGGC|TGATTAGC|TATAAc CATCCCTATTTGGTATTCTAGCTAATCAGCTCTATTGGGC|TGATTAGC|TATAAA ========== Event 1137 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: TCTCCTTAAGCATTCCGTTAGATTCTACATTACTTTTCTTCAG------GAAT------GCTACCTGAGGTGTTTTTGCTG ↓ 13 24 ↑ 1 3 24 Chimp: TCTCCTTAAGCATTCCGTTAG------C------ATTCCTGAAGAAAAGTAATGTAGAATCTACCTGAGGTGTTTTTGCTG Gorilla: TCTCCTTAAGCATTCCATTAGATTCTACATTACTTTAATTCAG------GAAT------GCTACCTGAGGTGTTTTTGCTG Human: TCTCCTTAAGCATTCCGTTAGATTCTACATTACTTTTCTTCAG------GAAT------GCTACCTGAGGTGTTTTTGCTG Cluster: [ ] Orangutan: TCTCCTTAAGCATTCCGTTAGAGTCTATGTTACTTTTCCTCAG------GAAT------GCTACCTGAGGTGTTTTTGCTG Chimp > Human ------------- chr15:44450068-44450094 Template switch process: F1: L ATGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG 1 F3: 4 CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT R RF: ATGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAGCATTCCTGAAGAAAAGTAATGTAGAATCTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT RR: TACTTTATTACTAGGAATACAGAGGAATTCGTAAGGCAATCGTAAGGACTTCTTTTCATTACATCTTAGATGGACTCCACAAAAACGACACCAACCTCTCCAACTTAA F2: 3 GTAAGGACTTCTTTTCATTACATCTTA 2 Unidirectional alignment (log-probability: -58.4) TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG-------------------------ATtctacattacttttcttcaggaatgCTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAGCATTCCTGAAGAAAAGTAATGTAGAAT-------------------------CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT Template switch alignment (log-probability: -18.6) TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG|ATTCTACATTACTTTTCTTCAGGAATG|CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG|ATTCTACATTACTTTTCTTCAGGAATG|CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT Human > Chimp ------------- chr15:25052491-25052517 Template switch process: F1: L ATGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG 1 F3: 4 CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT R RF: ATGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAGATTCTACATTACTTTTCTTCAGGAATGCTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT RR: TACTTTATTACTAGGAATACAGAGGAATTCGTAAGGCAATCTAAGATGTAATGAAAAGAAGTCCTTACGATGGACTCCACAAAAACGACACCAACCTCTCCAACTTAA F2: 3 TAAGATGTAATGAAAAGAAGTCCTTAC 2 Unidirectional alignment (log-probability: -58.4) TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAGcattcctgaagaaaagtaatgtagaAT-------------------------CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG-------------------------ATTCTACATTACTTTTCTTCAGGAATGCTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT Template switch alignment (log-probability: -18.6) TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG|CATTCCTGAAGAAAAGTAATGTAGAAT|CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT TGAAATAATGATCCTTATGTCTCCTTAAGCATTCCGTTAG|CATTCCTGAAGAAAAGTAATGTAGAAT|CTACCTGAGGTGTTTTTGCTGTGGTTGGAGAGGTTGAATT ========== Event 1138 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCTGAAACTTGAAGAGATAGAAGTTTCGTTTTATGTCTTCCATCTATCAATCAGTCTCATATG Chimp: CCTGAAACTTGAAGAGGTAGAAGTTTGGTTTTATGTCTTCCATCTATCAATCAGTCTCATATG Gorilla: CCTGAAACTTGAAGAGATAGATGGAAGACATAAAACGAAAATTCTATCAATCAGTCTCATATG ↓ 31 2 4 ↑ 13 24 Human: CCTGAAACTTGAAGAGATAGAAGTTTCGTTTTATGTCTTCCATCTATCAATCAGTCTCATATG Cluster: [ ] Orangutan: CCTGAAACTTGAAGAAATAGAAGTTTGGTTTTATGTCTTCCATCTATCAATCAGTCTCATATG Gorilla > Human --------------- chr15:56007479-56007497 Template switch process: F1: L CATAGAAGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGAAG 1 F3: 4 TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC R RF: CATAGATGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGATGGAAGACATAAAACGAAAATTCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC RR: GTATCTACAGAAGTCTGAAGGGACTTTGAACTTCTCTATCTACCTTCTGTATTTTGCTTTTAAGATAGTTAGTCAGAGTATACGTTCCATGAACCAAAGGGG F2: 3 ACCTTCTGTATTTTGCTTT 2 Unidirectional alignment (log-probability: -57.4) AGAaGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGA---------------------agtttcgttttatgtcttccaTCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC AGATGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGATGGAAGACATAAAACGAAAAT---------------------TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC Template switch alignment (log-probability: -29.2) AGAaGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGAaG|TTTCGTTTTATGTCTTCCA|TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC AGATGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGATG|TTTCGTTTTATGTCTTCCA|TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC Human > Gorilla --------------- chr15:56732802-56732822 Template switch process: F1: L CATAGATGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGA 1 F3: 4 TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC R RF: CATAGAAGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGAAGTTTCGTTTTATGTCTTCCATCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC RR: GTATCTTCAGAAGTCTGAAGGGACTTTGAACTTCTCTATCTTCAAAGCAAAATACAGAAGGTAGATAGTTAGTCAGAGTATACGTTCCATGAACCAAAGGGG F2: 3 TAAAAGCAAAATACAGAAGGT 2 Unidirectional alignment (log-probability: -57.4) ATAGAtGTCTTCAGACTTCCCTGAAACTTGAAGAGATAG---------------------AtggaagacataaaacgaaaatTCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC ATAGAAGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGAAGTTTCGTTTTATGTCTTCCA---------------------TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC Template switch alignment (log-probability: -29.4) ATAGAtGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGA|TGGAAGACATAAAACGAAAaT|TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC ATAGAAGTCTTCAGACTTCCCTGAAACTTGAAGAGATAGA|TGGAAGACATAAAACGAAACT|TCTATCAATCAGTCTCATATGCAAGGTACTTGGTTTCCCC ========== Event 1139 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAATGCTGTAAGTCAGAGAGACTGACTTATGGTATAGAGACCATACAGAGAGACCTTCAATGCTGTAAGTCTGGCTAGAGAAAAATTAA Chimp: TCAATGCTGTAAGTCAGAGAGACTGACTTATGGTATAGAGACCATACAGAGAGACCTTCAATGCTGTAAGTCTGGCTAGAGAAAAAGTAA ↓ 13 2 4 Gorilla: TCAATGCTCTAAGTCAGAGAG------------------------------------------CA--GTGTCTGGCTAGAGAAAAAGTAA Human: TCAATGCTGTAAGTCAGAGAGACTGACTTATGGTATAGAGACCATACAGAGAGACCTTCAATGCTGTAAGTCTGGCTAGAGAAAAATTAA Cluster: [ ] Orangutan: TCAATGCTCTAAGTCAGAGAG------------------------------------------CA--GTGTCTGGCTAGAGAAAAAGTAA Chimp > Gorilla --------------- chr15:56488070-56488073 Template switch process: F1: L TGATAGTTCAATTTTTACCTTCAATGCTCTAAGTCAGAGAG 1 F3: 4 GTCTGGCTAGAGAAAAAGTAACGGTCTTCCAGCCACCATT R RF: TGATAGTTCAATTTTTACCTTCAATGCTGTAAGTCAGAGAGACTGACTTATGGTATAGAGACCATACAGAGAGACCTTCAATGCTGTAAGTCTGGCTAGAGAAAAAGTAACGGTCTTCCAGCCACCATT RR: ACTATCAAGTTAAAAATGGAAGTTACGACATTCAGTCTCTCTGACTGAATACCATATCTCTGGTATGTCTCTCTGGAAGTTACGACATTCAGACCGATCTCTTTTTCATTGCCAGAAGGTCGGTGGTAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -34) GATAGTTCAATTTTTACCTTCAATGCTcTAAGTCAGAGA------------------------------------------GCaGT--GTCTGGCTAGAGAAAAAGTAACGGTCTTCCAGCCACCATT GATAGTTCAATTTTTACCTTCAATGCTGTAAGTCAGAGAGACTGACTTATGGTATAGAGACCATACAGAGAGACCTTCAATGCTGTAAGTCTGGCTAGAGAAAAAGTAACGGTCTTCCAGCCACCATT Template switch alignment (log-probability: -21.7) GATAGTTCAATTTTTACCTTCAATGCTcTAAGTCAGAGAG|CAGT|GTCTGGCTAGAGAAAAAGTAACGGTCTTCCAGCCACCATT GATAGTTCAATTTTTACCTTCAATGCTGTAAGTCAGAGAG|CAGT|GTCTGGCTAGAGAAAAAGTAACGGTCTTCCAGCCACCATT ========== Event 1140 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAGGATCAAGTTTGCTAACTTATAAAGGCATGGGCAAAA----TGCACAAATGTTGAGCAAAACCATTC ↓ 13 24 ↑ 13 24 Chimp: AAGGATCAAGTTTGCTAACTTGTGC----ATTTTGCCCATGCCTTTATAAATGTTGAGCAAAACCATTC ↓ 13 24 ↑ 13 24 Gorilla: AAGGATCAAGTTTGCTAACTTATAAAGGCATGGGCAAAA----TGCACAAATGTTGAGCAAAACCATTC Human: AAGGATCAAGTTTGCTAACTTATAAAGGCATGGGCAAAA----TGCACAAATGTTGAGCAAAACCATTC Cluster: [ ] Orangutan: AAGGATCAACTACGCTAACTTATGAAGGCATGGGCAAAA----TGCACAAATGTTGAGCAAAGCCATTC Chimp > Human ------------- chr15:55610140-55610162 Template switch process: F1: L TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT 1 F3: 4 AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA R RF: TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTTGTGCATTTTGCCCATGCCTTTATAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA RR: ATTCTTTCAATGTATATTTTTTCCTAGTTCAAACGATTGAACACGTAAAACGGGTACGGAAATATTTACAACTCGTTTTGGTAAGTTATTCGTGAACTACTCGT F2: 3 CACGTAAAACGGGTACGGAAATA 2 Unidirectional alignment (log-probability: -52.4) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAAC---------------------TTATAaaggcatgggcaaaatgcacaAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTTGTGCATTTTGCCCATGCCTTTATA---------------------AATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Template switch alignment (log-probability: -18.1) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|ATAAAGGCATGGGCAAAATGCAC|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|ATAAAGGCATGGGCAAAATGCAC|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Human > Chimp ------------- chr15:56280562-56280584 Template switch process: F1: L TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT 1 F3: 4 AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA R RF: TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTTATAAAGGCATGGGCAAAATGCACAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA RR: ATTCTTTCAATGTATATTTTTTCCTAGTTCAAACGATTGAATATTTCCGTACCCGTTTTACGTGTTTACAACTCGTTTTGGTAAGTTATTCGTGAACTACTCGT F2: 3 TATTTCCGTACCCGTTTTACGTG 2 Unidirectional alignment (log-probability: -52.4) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTtgtgcattttgcccatgccttTAT---------------------AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACT---------------------TATAAAGGCATGGGCAAAATGCACAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Template switch alignment (log-probability: -18.1) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|GTGCATTTTGCCCATGCCTTTAT|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|GTGCATTTTGCCCATGCCTTTAT|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Gorilla > Chimp --------------- chr15:56280562-56280584 Template switch process: F1: L TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT 1 F3: 4 AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA R RF: TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTTATAAAGGCATGGGCAAAATGCACAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA RR: ATTCTTTCAATGTATATTTTTTCCTAGTTCAAACGATTGAATATTTCCGTACCCGTTTTACGTGTTTACAACTCGTTTTGGTAAGTTATTCGTGAACTACTCGT F2: 3 TATTTCCGTACCCGTTTTACGTG 2 Unidirectional alignment (log-probability: -51.9) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACttgtgcattttgcccatgcctTTAT---------------------AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAAC---------------------TTATAAAGGCATGGGCAAAATGCACAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Template switch alignment (log-probability: -18.7) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|GTGCATTTTGCCCATGCCTTTAT|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|GTGCATTTTGCCCATGCCTTTAT|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Chimp > Gorilla --------------- chr15:56327961-56327983 Template switch process: F1: L TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT 1 F3: 4 AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA R RF: TAAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTTGTGCATTTTGCCCATGCCTTTATAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA RR: ATTCTTTCAATGTATATTTTTTCCTAGTTCAAACGATTGAACACGTAAAACGGGTACGGAAATATTTACAACTCGTTTTGGTAAGTTATTCGTGAACTACTCGT F2: 3 CACGTAAAACGGGTACGGAAATA 2 Unidirectional alignment (log-probability: -51.9) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACT---------------------TATaaaggcatgggcaaaatgcacAAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTTGTGCATTTTGCCCATGCCTTTAT---------------------AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA Template switch alignment (log-probability: -18.7) AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|ATAAAGGCATGGGCAAAATGCAC|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA AAGAAAGTTACATATAAAAAAGGATCAAGTTTGCTAACTT|ATAAAGGCATGGGCAAAATGCAC|AAATGTTGAGCAAAACCATTCAATAAGCACTTGATGAGCA ========== Event 1141 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: taaatttgtgttagtattttcagcaaa--------------aacagttgacatttggggcataca Chimp: TAAATTTGTGTTAGTATTTTCAGCAAA--------------AACAGTTGACATTTGGGGCATACA ↓ 3 4 2 1 Gorilla: TAAATTTGTGTTAGTATTTTCAGCAAAAACATTTGCTGAAAAACAGTTGACATTTGGGGCATACA Human: taaatttgtgttagtattttcagcaaa--------------aacagttgacatttggggcataca Cluster: [ ] Orangutan: TAAATTTGTATTAGTATTTTCAGCAAA--------------AACAGCTGACATTTGGGGCATACA Chimp > Gorilla --------------- chr15:25437931-25437938 Template switch process: F1: L CTATTCACACAAACTAAATTTGTGTTAGTATTTTCAGCAAAAACA 1 F3: 4 AAAACAGTTGACATTTGGGGCATACATTGAGTAGTAAGCTCT R RF: CTATTCACACATACTAAATTTGTGTTAGTATTTTCAGCAAAAACAGTTGACATTTGGGGCATACATTGAGTAGTAAGCTCT RR: GATAAGTGTGTATGATTTAAACACAATCATAAAAGTCGTTTTTGTCAACTGTAAACCCCGTATGTAACTCATCATTCGAGA F2: 3 AGTCGTTT 2 Unidirectional alignment (log-probability: -36.5) CACACAaACTAAATTTGTGTTAGTATTTTCAGCaaaaacatttgctgAAAAACAGTTGACATTTGGGGCATACATTGAGTAGTAAGCT CACACATACTAAATTTGTGTTAGTATTTTCAGC--------------AAAAACAGTTGACATTTGGGGCATACATTGAGTAGTAAGCT Template switch alignment (log-probability: -22.4) CACACAaACTAAATTTGTGTTAGTATTTTCAGCAAAAACA|TTTGCTGA|AAAACAGTTGACATTTGGGGCATACATTGAGTAGTAAGCT CACACATACTAAATTTGTGTTAGTATTTTCAGCAAAAACA|TTTGCTGA|AAAACAGTTGACATTTGGGGCATACATTGAGTAGTAAGCT ========== Event 1142 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGATGACCTCTTCAAGAAGCATGATTCTGATCATGCCTTTTCTCTCTTCTCCTTCC ↑ 3 1 2 4 Chimp: TGATGACCTCTTCAAGAAGCATGATG-----AGAGCCTTTTCTCTCTTCTCCTTCC Gorilla: TGATGACCTCTTCAAGAAGCATGATTCTCATCATGCcttttctctcttctccttcc Human: TGATGACCTCTTCAAGAAGCATGATTCTGATCATGCCTTTTCTCTCTTCTCCTTCC Cluster: [ ] Orangutan: TGATGACCTCTTCAAGAAGCATGATTCTCATCATGCCTTTTCTCTCTTCTCCTTCC Chimp > Human ------------- chr15:48431045-48431054 Template switch process: F1: L TTGCTCCCTAATCAACTGATGACCTCTTCAAGAAGCATGAT 1 F3: 4 CCTTTTCTCTCTTCTCCTTCCCTTATTTTTTATTTATTT R RF: TTGCTCCCTAATCAACTGATGACCTCTTCAAGAAGCATGATGAGAGCCTTTTCTCTCTTCTCCTTCCCTTATTTTTTATTTATTT RR: AACGAGGGATTAGTTGACTACTGGAGAAGTTCTTCGTACTACTCTCGGAAAAGAGAGAAGAGGAAGGGAATAAAAAATAAATAAA F2: 3 GTACTAGTCT 2 Unidirectional alignment (log-probability: -34.3) TGCTCCCTAATCAACTGATGACCTCTTCAAGAAGCATGattctgatcATG----CCTTTTCTCTCTTCTCCTTCCCTTATTTTTTATTTATTT TGCTCCCTAATCAACTGATGACCTCTTCAAGAAGCATG---------ATGAGAGCCTTTTCTCTCTTCTCCTTCCCTTATTTTTTATTTATTT Template switch alignment (log-probability: -22.5) TGCTCCCTAATCAACTGATGACCTCTTCAAGAAGCATGAT|TCTgATCATG|CCTTTTCTCTCTTCTCCTTCCCTTATTTTTTATTTATTT TGCTCCCTAATCAACTGATGACCTCTTCAAGAAGCATGAT|TCTCATCATG|CCTTTTCTCTCTTCTCCTTCCCTTATTTTTTATTTATTT ========== Event 1143 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGCTTGGCCTTAACTCTGAAGTA-CTGGACAGATGCAGTTAAATACCAGTGTGG-GGGGAATGTATAAACACTTTCTAGTGATGTGCATCCAGAGTTCTACTGTAAGCAC ↓ 1 4 3 2 Chimp: GGCTTGGCCTTAACTCTGAAGGATGCAGACAGATGCAGTTAAATACCAGTGTGG-GGGGAATGTATAAACACTTTGTAGTGATGTGCATCCAGAGTTCTGCTGTAAGCAC Gorilla: GGCTTGGCCTTAACTCTGAAGGATGCAGACAGATGCAGTTAAATACCAGTGTGG-GGGGAATGTATAAACACTTTCTAGTGATGTGCATCCAGAGTTCTGCTGTAAGCAC ↑ 1 4 3 2 Human: GGCTTGGCCTTAACTCTGAAGTA-CTGGACAGATGCAGTTAAATACCAGTGTGG-GGGGAATGTATAAACACTTTCTAGTGATGTGCATCCAGAGTTCTACTGTAAGCAC Cluster: [ ] Orangutan: GGCTTGGCCTTAATTCTGAAGTA-CTGGACAGATGCAGTTAAATACCAGTGTGGGGGGGAATGTATAAACACTTTCTAGTGATGTGCATCCAGAGTTCTGCTGTAAGCAC Human > Chimp ------------- chr15:28958158-28958163 Template switch process: F1: L ACTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG 1 F3: 4 GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA R RF: ACTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAGTACTGGACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAAACACTTTCTAGTGATGTGCATC RR: TGACTTAATCTTTACCTCTACCGAACCGGAATTGAGACTTCATGACCTGTCTACGTCAATTTATGGTCACACCCCCCTTACATATTTGTGAAAGATCACTACACGTAG F2: 3 ACGTAG 2 Unidirectional alignment (log-probability: -28.5) CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG----GatgcaGACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAGTACTG-----GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA Template switch alignment (log-probability: -16) CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG|GATGCA|GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG|GATGCA|GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA Human > Gorilla --------------- chr15:26614627-26614632 Template switch process: F1: L ACTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG 1 F3: 4 GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA R RF: ACTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAGTACTGGACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAAACACTTTCTAGTGATGTGCATC RR: TGACTTAATCTTTACCTCTACCGAACCGGAATTGAGACTTCATGACCTGTCTACGTCAATTTATGGTCACACCCCCCTTACATATTTGTGAAAGATCACTACACGTAG F2: 3 ACGTAG 2 Unidirectional alignment (log-probability: -28) CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG----GatgcaGACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAGTACTG-----GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA Template switch alignment (log-probability: -16.5) CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG|GATGCA|GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA CTGAATTAGAAATGGAGATGGCTTGGCCTTAACTCTGAAG|GATGCA|GACAGATGCAGTTAAATACCAGTGTGGGGGGAATGTATAA ========== Event 1144 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAGTTATCTTGCCCAACTGCAATAGCCATTATTCCCAACCTAGCTATTGCAT ↑ 3 4 2 Chimp: CCAGTTATCTTGCCCAACTGC-ATGG---CTATTCCCAACCTAGCTATTGCAT Gorilla: CCAGTTATCTTGCCCAACTGC-ATGG---CTATTCCCAACCTAGCTATTGCAT Human: CCAGTTATCTTGCCCAACTGCAATAGCCATTATTCCCAACCTAGCTATTGCAT Cluster: [ ] Orangutan: CCAGTTATCTTGCCCAACTGC-ATGG---CTATTCCCTACCTAGCTATTGCAT Chimp > Human ------------- chr15:47841986-47841993 Template switch process: F1: L GGGACTCTGAATAATTAGATCCAGTTATCTTGCCCAACTGCA 1 F3: 4 TATTCCCAACCTAGCTATTGCATAGACAGAGCCTCTGATA R RF: GGGACTCTGAATAATTAGATCCAGTTATCTTGCCCAACTGCATGGCTATTCCCAACCTAGCTATTGCATAGACAGAGCCTCTGATA RR: CCCTGAGACTTATTAATCTAGGTCAATAGAACGGGTTGACGTACCGATAAGGGTTGGATCGATAACGTATCTGTCTCGGAGACTAT F2: 3 TACCGATA 2 Unidirectional alignment (log-probability: -31.4) GACTCTGAATAATTAGATCCAGTTATCTTGCCCAACTGcaatagcCAT---TATTCCCAACCTAGCTATTGCATAGACAGAGCCTCTGATA GACTCTGAATAATTAGATCCAGTTATCTTGCCCAACTG-------CATGGCTATTCCCAACCTAGCTATTGCATAGACAGAGCCTCTGATA Template switch alignment (log-probability: -16.3) GACTCTGAATAATTAGATCCAGTTATCTTGCCCAACTGCA|ATAGCCAT|TATTCCCAACCTAGCTATTGCATAGACAGAGCCTCTGATA GACTCTGAATAATTAGATCCAGTTATCTTGCCCAACTGCA|ATAGCCAT|TATTCCCAACCTAGCTATTGCATAGACAGAGCCTCTGATA ========== Event 1145 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGTCCTCCCACGCGCCTTCATTGCATATAGAGAAGTATGCAATGGAGAATGTGAACCCAGAC Chimp: CTGTCCTCCCACACGCCTTCA---GGTATAGACAAATATGCAACGGAGAATGTGAACCCGGAC Gorilla: CTGTCCTCCCACGCGCCTTCA---GGTATAGAGAAGTATGCAATGGAGAATGTGAACCCAGAC ↓ 1 4 3 2 Human: CTGTCCTCCCACGCGCCTTCATTGCATATAGAGAAGTATGCAATGGAGAATGTGAACCCAGAC Cluster: [ ] Orangutan: CTGTCCTCCCGCACGCCTTCA---GGTATAGAGAAATATGCAAGGGAGAATGTGAACCCAGAC Gorilla > Human --------------- chr15:48010498-48010502 Template switch process: F1: L CAGTGCCCTGCAAAACAACTCTGTCCTCCCACGCGCCTTCA 1 F3: 4 TATAGAGAAGTATGCAATGGAGAATGTGAACCCAGACATT R RF: CAGTGCCCTGCAAAACAACTCTGTCCTCCCACGCGCCTTCAGGTATAGAGAAGTATGCAATGGAGAATGTGAACCCAGACATT RR: GTCACGGGACGTTTTGTTGAGACAGGAGGGTGCGCGGAAGTCCATATCTCTTCATACGTTACCTCTTACACTTGGGTCTGTAA F2: 3 ACGTT 2 Unidirectional alignment (log-probability: -26.3) AGTGCCCTGCAAAACAACTCTGTCCTCCCACGCGCCTTCAttgcaTATAGAGAAGTATGCAATGGAGAATGTGAACCCAGACATT AGTGCCCTGCAAAACAACTCTGTCCTCCCACGCGCCTTCA---GGTATAGAGAAGTATGCAATGGAGAATGTGAACCCAGACATT Template switch alignment (log-probability: -16.4) AGTGCCCTGCAAAACAACTCTGTCCTCCCACGCGCCTTCA|TTGCA|TATAGAGAAGTATGCAATGGAGAATGTGAACCCAGACATT AGTGCCCTGCAAAACAACTCTGTCCTCCCACGCGCCTTCA|TTGCA|TATAGAGAAGTATGCAATGGAGAATGTGAACCCAGACATT ========== Event 1146 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GATGCCTGCTGCACTGGTCCTTTAGAGGTTAGAGTAGTAGGCTGCTTAGGTC Chimp: GATGCCTGCTGCACTGGTCCTTTAGAGGTTAGAGTAGTAGGCTGCTTAGGTC ↓ 3 1 2 4 Gorilla: GATGCCTGCTGCACTGGTCCTTTCTCTAAAGGAGTAGTAGGCTGCTTAGGTC ↑ 3 1 2 4 Human: GATGCCTGCTGCACTGGTCCTTTAGAGGTTAGAGTAGTAGGCTGCTTAGGTC Cluster: [ ] Orangutan: GATGCCTGCTGCACTGATCCTTTAGAGGCTAGAGTAGTAGGCTGCTTAGGTC Human > Gorilla --------------- chr15:26040188-26040195 Template switch process: F1: L TGCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT 1 F3: 4 GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG R RF: TGCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTTAGAGGTTAGAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG RR: ACGCTCGAACGTTCCGACCTACGGACGACGTGACCAGGAAATCTCCAATCTCATCATCCGACGAATCCAGTTGTTACCTTCAAGTCTTC F2: 3 GAAATCTC 2 Unidirectional alignment (log-probability: -29.6) GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTTctctaaAG------GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT------AGAGGTTAGAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG Template switch alignment (log-probability: -16.7) GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT|CTCTAAAG|GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT|CTCTAAAG|GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG Chimp > Gorilla --------------- chr15:26040188-26040195 Template switch process: F1: L TGCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT 1 F3: 4 GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG R RF: TGCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTTAGAGGTTAGAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG RR: ACGCTCGAACGTTCCGACCTACGGACGACGTGACCAGGAAATCTCCAATCTCATCATCCGACGAATCCAGTTGTTACCTTCAAGTCTTC F2: 3 GAAATCTC 2 Unidirectional alignment (log-probability: -29.6) GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTTctctaaAG------GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT------AGAGGTTAGAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG Template switch alignment (log-probability: -16.7) GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT|CTCTAAAG|GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG GCGAGCTTGCAAGGCTGGATGCCTGCTGCACTGGTCCTTT|CTCTAAAG|GAGTAGTAGGCTGCTTAGGTCAACAATGGAAGTTCAGAAG ========== Event 1147 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTTGCGTTTAGCACTGATAAACTTGCACTTTGCTTTTATCAAGTCACTGAACCAT Chimp: TTTGCCTTTAGCACTGATAAAAGCAAAGTGCAAGTTAATCAAGTCACTGAACCAT Gorilla: TTTGCCTTTAGCACTGATAAAAGCAAAGTGCAAGTTTATCAAGTCACTGAACCAT ↓ 13 24 ↑ 13 24 Human: TTTGCGTTTAGCACTGATAAACTTGCACTTTGCTTTTATCAAGTCACTGAACCAT Cluster: [ ] Orangutan: TTTGCCTTTAGCACTGATAAAAGCAAAGTACAAGTTGATCAAGTCACTGAACCAT Gorilla > Human --------------- chr15:55124834-55124846 Template switch process: F1: L GCTATCTCTGCAGGATAATCTTTGCGTTTAGCACTGATAAA 1 F3: 4 TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT R RF: GCTATCTCTGCAGGATAATCTTTGCCTTTAGCACTGATAAAAGCAAAGTGCAAGTTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT RR: CGATAGAGACGTCCTATTAGAAACGGAAATCGTGACTATTTTCGTTTCACGTTCAAATAGTTCAGTGACTTGGTAACAAAGTACTGTAGGACCA F2: 3 TCGTTTCACGTTC 2 Unidirectional alignment (log-probability: -45.5) CTATCTCTGCAGGATAATCTTTGCgTTTAGCACTGATAAA-------------cttgcactttgctTTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT CTATCTCTGCAGGATAATCTTTGCCTTTAGCACTGATAAAAGCAAAGTGCAAG-------------TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT Template switch alignment (log-probability: -22.9) CTATCTCTGCAGGATAATCTTTGCgTTTAGCACTGATAAA|CTTGCACTTTGCT|TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT CTATCTCTGCAGGATAATCTTTGCCTTTAGCACTGATAAA|CTTGCACTTTGCT|TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT Human > Gorilla --------------- chr15:55830987-55830999 Template switch process: F1: L GCTATCTCTGCAGGATAATCTTTGCCTTTAGCACTGATAAA 1 F3: 4 TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT R RF: GCTATCTCTGCAGGATAATCTTTGCGTTTAGCACTGATAAACTTGCACTTTGCTTTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT RR: CGATAGAGACGTCCTATTAGAAACGCAAATCGTGACTATTTGAACGTGAAACGAAAATAGTTCAGTGACTTGGTAACAAAGTACTGTAGGACCA F2: 3 GAACGTGAAACGA 2 Unidirectional alignment (log-probability: -45.5) CTATCTCTGCAGGATAATCTTTGCcTTTAGCACTGATAAA-------------agcaaagtgcaagTTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT CTATCTCTGCAGGATAATCTTTGCGTTTAGCACTGATAAACTTGCACTTTGCT-------------TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT Template switch alignment (log-probability: -22.9) CTATCTCTGCAGGATAATCTTTGCcTTTAGCACTGATAAA|AGCAAAGTGCAAG|TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT CTATCTCTGCAGGATAATCTTTGCGTTTAGCACTGATAAA|AGCAAAGTGCAAG|TTTATCAAGTCACTGAACCATTGTTTCATGACATCCTGGT ========== Event 1148 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: -TTTTCCCTATTAACTCTTTAGTGCAACCTTTTGCACTAAATCATTAGACAGTAAACACT ↑ 3 1 24 Chimp: -ttttCCCTATTAACTCTTTAGTGCA--------AAAGGAATCattagacagtaaacact Gorilla: -ttttCCCTATTAACTCTTTAGTGGA--------AAAGGAATCATTAGACAGTAAACACT ↓ 3 1 24 Human: -TTTTCCCTATTAACTCTTTAGTGCAACCTTTTGCACTAAATCATTAGACAGTAAACACT Cluster: [ ] Orangutan: tttttCCCTATTAACTCTTTAGTGCA--------AAAGGAATCATTAGGCAGTAAACACT Chimp > Human ------------- chr15:50000970-50000981 Template switch process: F1: L CTACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAA 1 F3: 4 AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC R RF: CTACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAAAAGGAATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC RR: GATGAAACAACATAAAAAAAGGGATAATTGAGAAATCACGTTTTCCTTAGTAATCTGTCATTTGTGAAACTGAGTCTCCACAGAAG F2: 3 ATCACGTTTTCC 2 Unidirectional alignment (log-probability: -37.1) ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAAccttttgcactA---AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAA-----------AAGGAATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC Template switch alignment (log-probability: -16.8) ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAA|CCTTTTGCACTA|AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAA|CCTTTTGCACTA|AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC Gorilla > Human --------------- chr15:50000970-50000981 Template switch process: F1: L GGCTACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGCAA 1 F3: 4 AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC R RF: GGCTACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGGAAAAGGAATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC RR: CCGATGAAACAACATAAAAAAAGGGATAATTGAGAAATCACCTTTTCCTTAGTAATCTGTCATTTGTGAAACTGAGTCTCCACAGAAG F2: 3 ATCACGTTTTCC 2 Unidirectional alignment (log-probability: -42.2) ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGcAAccttttgcactA---AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGGAA-----------AAGGAATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC Template switch alignment (log-probability: -28.4) ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGcAA|CCTTTTgCACTA|AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC ACTTTGTTGTATTTTTTTCCCTATTAACTCTTTAGTGGAA|CCTTTTCCACTA|AATCATTAGACAGTAAACACTTTGACTCAGAGGTGTCTTC ========== Event 1149 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGCACAGCTGTTAAATTAAGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAAGAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCAATAGCAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGATGGTCCTCCCACTC-------------CAGCCTCATAATGCACCCTGGGTGGTG ↑ 3 2 1 4 Chimp: CAGCACAGCTGTTAAATTAAGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAAGAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCAATAGCAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTCATAATAATGCACCTGGGTGCATAATGCACCCTGGGTGGTG ↓ 3 2 1 4 Gorilla: CAGCACAGCTGTTAAATTAAGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAAGAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCAATAGCAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTC-------------CAGCCTCATAATGCACCCTGGGTGATG Human: CAGCACAGCTGTTAAATTAAGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAAGAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCAATAGCAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGATGGTCCTCCCACTC-------------CAGCCTCATAATGCACCCTGGGTGGTG Cluster: [ ] Orangutan: CAGCACAGCTGTTAAATTAAGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAACAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCGATAACAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGATGGTCCTCCCACTC-------------TAGCCTCATAATGCACCCTGAGTGGTG Chimp > Human ------------- chr15:48630317-48630322 Template switch process: F1: L ACTATTCCTTCCTCAATTAAATACAGATGGTCCTCCCACTC 1 F3: 4 CATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT R RF: AGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAAGAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCAATAGCAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTCATAATAATGCACCTGGGTGCATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT RR: TCCGACAACCATCGATAAAGAACTTTGGGAAATTTCTCGACAAGGGATCACTTGTCCCGTTTACAGTGGTTATCGTCTAGTCCGTTATCCAATGATAAGGAAGGAGTTAATTTATGTCTGCCAGGAGGGTGAGTATTATTACGTGGACCCACGTATTACGTGGGACCCACCACCCTCTTTGGGGTCCAGAGA F2: 3 TCCGAC 2 Unidirectional alignment (log-probability: -36.7) CTATTCCTTCCTCAATTAAATACAGAtGGTCCTCCCACTC-------------------CagcctcATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT CTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTCATAATAATGCACCTGGGTGC------ATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT Template switch alignment (log-probability: -22) CTATTCCTTCCTCAATTAAATACAGAtGGTCCTCCCACTC|CAGCCT|CATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT CTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTC|CAGCCT|CATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT Chimp > Gorilla --------------- chr15:49283737-49283742 Template switch process: F1: L ACTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTC 1 F3: 4 CATAATGCACCCTGGGTGATGGGAGAAACCCCAGGTCTCT R RF: AGGCTGTTGGTAGCTATTTCTTGAAACCCTTTAAAGAGCTGTTCCCTAGTGAACAGGGCAAATGTCACCAATAGCAGATCAGGCAATAGGTTACTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTCATAATAATGCACCTGGGTGCATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT RR: TCCGACAACCATCGATAAAGAACTTTGGGAAATTTCTCGACAAGGGATCACTTGTCCCGTTTACAGTGGTTATCGTCTAGTCCGTTATCCAATGATAAGGAAGGAGTTAATTTATGTCTGCCAGGAGGGTGAGTATTATTACGTGGACCCACGTATTACGTGGGACCCACCACCCTCTTTGGGGTCCAGAGA F2: 3 TCCGAC 2 Unidirectional alignment (log-probability: -35.7) CTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTC-------------------cagcctCATAATGCACCCTGGGTGaTGGGAGAAACCCCAGGTCTCT CTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTCATAATAATGCACCTGGGTG------CATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT Template switch alignment (log-probability: -22) CTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTC|CAGCCT|CATAATGCACCCTGGGTGaTGGGAGAAACCCCAGGTCTCT CTATTCCTTCCTCAATTAAATACAGACGGTCCTCCCACTC|CAGCCT|CATAATGCACCCTGGGTGGTGGGAGAAACCCCAGGTCTCT ========== Event 1150 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACAGTACCGTGTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCAT----GACCTTCCCGAGTTACACAAAT Chimp: AACAGTACCGTGTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCAT----GACCTTCCCGAGTTCCACAAAT ↓ 3 2 1 4 Gorilla: AACAGTACCGTGTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCACAATGAACCTTCCCGAGTTCCACAAAT ↑ 3 2 1 4 Human: AACAGTACCGTGTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCAT----GACCTTCCCGAGTTACACAAAT Cluster: [ ] Orangutan: AACAGTACCGTGTGACCTCTCATTGTGAAAGCAAGAATGCAATGGGCAGTCAC----GACCTTCCCAAGTTCCACAAAT Human > Gorilla --------------- chr15:49662470-49662475 Template switch process: F1: L GTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCA 1 F3: 4 ACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA R RF: GTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCATGACCTTCCCGAGTTACACAAATTTGCCTTGCAGAGAAAGCA RR: CACTGGAGAGTAACACTTTCGTTCTTACGTTATCCGTCAGTACTGGAAGGGCTCAATGTGTTTAAACGGAACGTCTCTTTCGT F2: 3 AGTAAC 2 Unidirectional alignment (log-probability: -31.9) TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCacaATGaACCTTCCCGAGTTcCACAAATTTGCCTTGCAGAGAAAGCA TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTC---ATG-ACCTTCCCGAGTTACACAAATTTGCCTTGCAGAGAAAGCA Template switch alignment (log-probability: -22) TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCA|CAATGA|ACCTTCCCGAGTTcCACAAATTTGCCTTGCAGAGAAAGCA TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCA|CAATGA|ACCTTCCCGAGTTACACAAATTTGCCTTGCAGAGAAAGCA Chimp > Gorilla --------------- chr15:49662470-49662475 Template switch process: F1: L GTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCA 1 F3: 4 ACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA R RF: GTGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCATGACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA RR: CACTGGAGAGTAACACTTTCGTTCTTACGTTATCCGTCAGTACTGGAAGGGCTCAAGGTGTTTAAACGGAACGTCTCTTTCGT F2: 3 AGTAAC 2 Unidirectional alignment (log-probability: -26.4) TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCacaATGaACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTC---ATG-ACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA Template switch alignment (log-probability: -16.5) TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCA|CAATGA|ACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA TGACCTCTCATTGTGAAAGCAAGAATGCAATAGGCAGTCA|CAATGA|ACCTTCCCGAGTTCCACAAATTTGCCTTGCAGAGAAAGCA ========== Event 1151 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: GGTCtttttttttGTATATAGATAGATAGATACGTATATCTGTAtct--------atctgtctgtctgtctgtct Chimp: GGTCtttttttttGTATATAGATAGATAGATACGTATAT------CT--------ATCTGTCTGTCTGTCTATCT ↓ 3 2 4 1 ↑ 3 1 2 4 Gorilla: GGTCtttttttttGTATATAG----ATAGATACGtatatctgtatctatctatctgtctgtctgtctgtctatct Human: GGTCtttttttttGTATATAGATAGATAGATACGTATATCTGTAtct--------atctgtctgtctgtctgtct Cluster: [ ] Orangutan: --------------------------------------------------------------------------- Gorilla > Chimp --------------- chr15:47180583-47180589 Template switch process: F1: L ATAAAGCAACAACTACTATGGGTCTTTTTTTTTGTATATAGATAGATAG 1 F3: 4 TATCTATCTGTCTGT R RF: ATAAAGCAACAACTACTATGGGTCTTTTTTTTTGTATATAGATAGATACGTATATCTGTATCTATCTATCTGTCTGT RR: TATTTCGTTGTTGATGATACCCAGAAAAAAAAACATATATCTATCTATGCATATAGACATAGATAGATAGACAGACA F2: 3 ATGCATA 2 Unidirectional alignment (log-probability: -32.4) CAACTACTATGGGTCTTTTTTTTTGTATATagatAGATAGATACGTA--------------TATCTaTCTGTCTGT CAACTACTATGGGTCTTTTTTTTTGTATAT----AGATAGATACGTATATCTGTATCTATCTATCTGTCTGTCTGT Template switch alignment (log-probability: -21.7) CAACTACTATGGGTCTTTTTTTTTGTATATAGATAGATAg|ATACGTA|TATCTATCTGTCTGT CAACTACTATGGGTCTTTTTTTTTGTATATAGATAGATAC|ATACGTA|TATCTATCTGTCTGT Chimp > Gorilla --------------- chr15:47326696-47326701 Template switch process: F1: L ATAAAGCAACAACTACTATGGGTCTTTTTTTTTGTAT----ATAGATAGATACGTATATCT 1 F3: 4 ATCTATCTGTCTGTCTGT R RF: ATAAAGCAACAACTACTATGGGTCTTTTTTTTTGTATATAGATAGATAGATACGTATATCTATCTGTCTGTCTGT RR: TATTTCGTTGTTGATGATACCCAGAAAAAAAAACATATATCTATCTATCTATGCATATAGATAGACAGACAGACA F2: 3 TCTATG 2 Unidirectional alignment (log-probability: -46.3) ATGGGTCTTTTTTTTTGTATATAGATAGATA----CGTAtatctgtatctatcTATCTgTCTGTCTGT ATGGGTCTTTTTTTTTGTATATAGATAGATAGATACGTA--------------TATCTATCTGTCTGT Template switch alignment (log-probability: -26.3) ATGGGTCTTTTTTTTTGTAT----ATAGATAGATACGTATATCT|GTATCT|ATCTATCTGTCTGTCTGT ATGGGTCTTTTTTTTTGTATATAGATAGATAGATACGTATATCT|GTATCT|ATCTATCTGTCTGTCTGT ========== Event 1152 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCTTTCTTTTGATTACAGCGCC--CCTCTT----CGCAGTAAGGAGTCTGT----------------TCATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGATGAGGGAATGGGTACAAGAAAGCCC Chimp: TCCTTTCTTTTGATTACAGCGTA--CCTCTT----CGCAGTAAGGAGTCTGT----------------TCATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGATGAGGGAATGGGT-AAAGAAAGCCC ↓ 1 4 3 2 Gorilla: TCCTTTCTTTTGATTACAGCGCC----TCATCTAGGGCAGGTGCAAGCGTGTTAACCCCACCTGAACTGCATTCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGATGAGGGAATGGGTACAAGAAAGCCC Human: TCCTTTCTTTTGATTACAGCGCC--CCTCTT----CGCAGTAAGGAGTCTGT----------------TCATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGATGAGGGAATGGGTACAAGAAAGCCC Cluster: [ ] Orangutan: TCCTTTCTTTTGATTACAGCGCCCC--TCTT----CGCAGTAAGGAGTCTGT----------------TCATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGATGAGGGAATGGGTACAAGAAAGCCC Chimp > Gorilla --------------- chr15:46525724-46525767 Template switch process: F1: L AGATTCAACTGTACTCCTTTTCCTTTCTTTTGATTACAGCG 1 F3: 4 CATTCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGAT R RF: AGATTCAACTGTGCTCCTTTTCCTTTCTTTTGATTACAGCGTACCTCTTCGCAGTAAGGAGTCTGTTCATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCTAGATGAGG RR: TCTAAGTTGACACGAGGAAAAGGAAAGAAAACTAATGTCGCATGGAGAAGCGTCATTCCTCAGACAAGTACGTCAAGTCCACCCCGATTGTGCGAACGTGGACGGGATCTACTCC F2: 3 GTCAAGTCCACCCCAATTGTGCGAACGTGGACGGGATCTACTCC 2 Unidirectional alignment (log-probability: -95.2) GATTCAACTGTaCTCCTTTTCCTTTCTTTTGATTACAGCGcctcatctagggcaggtgcaagcgtgttaaccccacctgaactgcatT-----------------------------CAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCT GATTCAACTGTGCTCCTTTTCCTTTCTTTTGATTACAGCG-----------------------------------------------TACCTCTTCGCAGTAAGGAGTCTGTTCATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCT Template switch alignment (log-probability: -37.9) GATTCAACTGTaCTCCTTTTCCTTTCTTTTGATTACAGCG|CCTCATCTAGGGCAGGTGCAAGCGTGTTAaCCCCACCTGAACTG|CATtCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCT GATTCAACTGTGCTCCTTTTCCTTTCTTTTGATTACAGCG|CCTCATCTAGGGCAGGTGCAAGCGTGTTAGCCCCACCTGAACTG|CATGCAGTTCAGGTGGGGCTAACACGCTTGCACCTGCCCT ========== Event 1153 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: catttcagggcCTTCCTGAATGTGGGTCAGCAGGGTCTTCACAGTGGAGCAAGCCCCTGCTATACACTC Chimp: CATTTCAGGGCCTTCCTGAAT------CTACACTGTCTTCACAGTAGAGCAAGCCCCTGCTATACACTC Gorilla: catttcagggcCTTCCTGAAT------CTACACTGTCTTCACAGTAGAGCAAGCCCCTGCTATACACTC ↑ 1 4 3 2 Human: catttcagggcCTTCCTGAATGTGGGTCAGCAGGGTCTTCACAGTGGAGCAAGCCCCTGCTATACACTC Cluster: [ ] Orangutan: CATTTCAGGGCCTTCTTGAAT------CCACACTATCTTCACAGTAGAGCAAGCCCCTGCTATACACTC Human > Gorilla --------------- chr15:35127212-35127219 Template switch process: F1: L TTGTACATAGATCAGAGGTACATTTCAGGGCCTTCCTGAAT 1 F3: 4 TCTTCACAGTAGAGCAAGCCCCTGCTATACACTCATAGA R RF: TTGTACATAGATCAGAGGTACATTTCAGGGCCTTCCTGAATGTGGGTCAGCAGGGTCTTCACAGTGGAGCAAGCCCCTGCTATACACTCATAGA RR: AACATGTATCTAGTCTCCATGTAAAGTCCCGGAAGGACTTACACCCAGTCGTCCCAGAAGTGTCACCTCGTTCGGGGACGATATGTGAGTATCT F2: 3 GTCACATC 2 Unidirectional alignment (log-probability: -36.9) TGTACATAGATCAGAGGTACATTTCAGGGCCTTCCTGAAT-------------ctacactGTCTTCACAGTaGAGCAAGCCCCTGCTATACACTCATAGA TGTACATAGATCAGAGGTACATTTCAGGGCCTTCCTGAATGTGGGTCAGCAGG-------GTCTTCACAGTGGAGCAAGCCCCTGCTATACACTCATAGA Template switch alignment (log-probability: -27.8) TGTACATAGATCAGAGGTACATTTCAGGGCCTTCCTGAAT|CTaCACTG|TCTTCACAGTaGAGCAAGCCCCTGCTATACACTCATAGA TGTACATAGATCAGAGGTACATTTCAGGGCCTTCCTGAAT|CTCCACTG|TCTTCACAGTGGAGCAAGCCCCTGCTATACACTCATAGA ========== Event 1154 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GACCACCAGTAAAAAGTTTTTGCAAAAGCTCTGGTTCCTTTGAATCATGGCCCTTCTcccccaccaccccacccccaCAGTGGTGGCAACGGCTGCAGTT--------------------------GGGCAGCGGTTTTACCTCCATTTT ↓ 3 2 4 1 Chimp: GACCACCAATAAAAAGTTTTTGCAAAAGCTCTGGTTCCTTTGAATCATGGCCCTTCTcccccaccaccccacccccacAGTGGTGGCAACGGCTGCAGTT---------------GGGCTGCAATTGGGCAGCGGTTTTACCTCCATTTT Gorilla: GACCACCAATAAAAAGTTTTTGCAAAAGCTCTGGTTCCTTTGAATCATGGCCCTTCTcccccaccaccccacccccacAGTGGTGGCAACGGCTGCAGTTGGGCTGAGGGCCACC-----------AGGCAGCGGTTTTACCTCCATTTT Human: GACCACCAGTAAAAAGTTTTTGCAAAAGCTCTGGTTCCTTTGAATCATGGCCCTTCTcccccaccaccccacccccaCAGTGGTGGCAACGGCTGCAGTT--------------------------GGGCAGCGGTTTTACCTCCATTTT Cluster: [ ] Orangutan: GACCACCAATAAAAAGTTTTTGCAAAAGCTCTGATTCCTTTGAATCATGGCCCTCCTcccccaccaccccacccccacAGTGGTGGCAACGGCTGCAGTTGGGCTGGGGGCCACC-----------AGGCAGCGGTTTTACCTCCATTTT Human > Chimp ------------- chr15:38062287-38062291 Template switch process: F1: L CCCACCACCCCACCCCCACAGTGGTGGCAACGGCTGCAGTTGGGC 1 F3: 4 TTGGGCAGCGGTTTTACCTCCATTTTGAGACCAGACGACTGG R RF: TTGCAAAAGCTCTGGTTCCTTTGAATCATGGCCCTTCTCCCCCACCACCCCACCCCCACAGTGGTGGCAACGGCTGCAGTTGGGCAGCGGTTTTACCTCCATTTTGAGACCAGACAACTGG RR: AACGTTTTCGAGACCAAGGAAACTTAGTACCGGGAAGAGGGGGTGGTGGGGTGGGGGTGTCACCACCGTTGCCGACGTCAACCCGTCGCCAAAATGGAGGTAAAACTCTGGTCTGTTGACC F2: 3 AACGT 2 Unidirectional alignment (log-probability: -32.7) CACCCCACCCCCACAGTGGTGGCAACGGCTGCAGttgggctgcaaTTGGGCAGCGGTTTTACCTCCATTTTGAGACCAGACgACT CACCCCACCCCCACAGTGGTGGCAACGGCTGCAG-----------TTGGGCAGCGGTTTTACCTCCATTTTGAGACCAGACAACT Template switch alignment (log-probability: -22) CACCCCACCCCCACAGTGGTGGCAACGGCTGCAGTTGGGC|TGCAA|TTGGGCAGCGGTTTTACCTCCATTTTGAGACCAGACgACT CACCCCACCCCCACAGTGGTGGCAACGGCTGCAGTTGGGC|TGCAA|TTGGGCAGCGGTTTTACCTCCATTTTGAGACCAGACAACT ========== Event 1155 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCTG-TTATCAACTAAACCCCAGAGCTAAATC ↑ 3 2 1 4 Chimp: TTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATC Gorilla: TTGCCTCTGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATC Human: TTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCTG-TTATCAACTAAACCCCAGAGCTAAATC Cluster: [ ] Orangutan: CTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATC Chimp > Human ------------- chr15:58279913-58279920 Template switch process: F1: L GGCAAGATTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGC 1 F3: 4 ACTAAACCCCAGAGCTAAATCGGATAGTCATCCATCATTG R RF: GGCAAGATTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATCGGAGAGTCATCCATCATTG RR: CCGTTCTAACGGGGTCTCCGTTTTCAACTATTGTCGAGACGGAAGACCTCTGATTTGGGGTCTCGATTTAGCCTCTCAGTAGGTAGTAAC F2: 3 ACTATTGT 2 Unidirectional alignment (log-probability: -39.1) GCAAGATTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCtgttatca---------ACTAAACCCCAGAGCTAAATCGGAtAGTCATCCATCATTG GCAAGATTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGC--------CTTCTGGAGACTAAACCCCAGAGCTAAATCGGAGAGTCATCCATCATTG Template switch alignment (log-probability: -22.3) GCAAGATTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGC|TGTTATCA|ACTAAACCCCAGAGCTAAATCGGAtAGTCATCCATCATTG GCAAGATTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGC|TGTTATCA|ACTAAACCCCAGAGCTAAATCGGAGAGTCATCCATCATTG ========== Event 1156 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCTG-TTATCAACTAAACCCCAGAGCTAAATCGGATAGTCATCCATCATTGAGCTA Chimp: TTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATCGGAGAGTCATCCATCATTGAGCTA Gorilla: TTGCCTCTGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATCAGAGAGTCATCCATCATTGAGCTA ↓ 3 2 1 4 Human: TTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCTG-TTATCAACTAAACCCCAGAGCTAAATCGGATAGTCATCCATCATTGAGCTA Cluster: [ ] Orangutan: CTGCCCCAGAGGCAAAAGTTGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATCGGAGAGTCATCCATCATTGAGCTA Gorilla > Human --------------- chr15:58279913-58279920 Template switch process: F1: L AACAGCTCTGC 1 F3: 4 ACTAAACCCCAGAGCTAAATCGGATAGTCATCCATCATTGAGCTAGGACTCTTAAAGGGGGCTGA R RF: TGATAACAGCTCTGCCTTCTGGAGACTAAACCCCAGAGCTAAATCAGAGAGTCATCCATCATTGAGCTAGGACTCTTAAAGGGGGCTGA RR: ACTATTGTCGAGACGGAAGACCTCTGATTTGGGGTCTCGATTTAGTCTCTCAGTAGGTAGTAACTCGATCCTGAGAATTTCCCCCGACT F2: 3 ACTATTGT 2 Unidirectional alignment (log-probability: -43.6) AACAGCTCTGC---------tgttatcaACTAAACCCCAGAGCTAAATCgGAtAGTCATCCATCATTG AACAGCTCTGCCTTCTGGAG--------ACTAAACCCCAGAGCTAAATCAGAGAGTCATCCATCATTG Template switch alignment (log-probability: -27.6) AACAGCTCTGC|TGTTATCA|ACTAAACCCCAGAGCTAAATCgGAtAGTCATCCATCATTG AACAGCTCTGC|TGTTATCA|ACTAAACCCCAGAGCTAAATCAGAGAGTCATCCATCATTG ========== Event 1157 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ctcttggttagaagcaagtcacaggtcccacccacactcaaagggagaggaccatgcaaggtgtgaacaccaagagacaaggatggtgttgtgggggcaccctatgagtctgtccaccacaGCAGGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTTCCAGTGTCATGGGTTTAGATCAGCATTGTTAGGGT ↑ 3 2 4 1 Chimp: ctcttggttagaagcaagtcacaggtcccacccacactcaaagggagaggaccatgcaaggtgtgaacaccaagagacaaggatggtgttgggggggcaccctgtgagtctgtccaccacaGCAGGGACCATGTTTTGATCATCATGTTTCAGCATCAT---------------GGGTTTAGATCAGCATTGTTAGGGT ↓ 3 2 4 1 Gorilla: ctcttggttaggagcaagtcacaggtcccacccacactcaaagggagaggaccatgcaaggtgtgaacaccaagagacaaggatggtgttgggggggcaccctatgagtctgtccaccacaGCAGGGACCATGTTTGGATCATCATGTTTCAGCATCATGGGTTCCAGTGTCATGGGTTTAGATCAGCATTGTTAGGGT Human: ctcttggttagaagcaagtcacaggtcccacccacactcaaagggagaggaccatgcaaggtgtgaacaccaagagacaaggatggtgttgtgggggcaccctatgagtctgtccaccacaGCAGGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTTCCAGTGTCATGGGTTTAGATCAGCATTGTTAGGGT Cluster: [ ] Orangutan: ctcttggttagaagcaagtcacaggtcccacccacactcaaagggagaggaccatgcaaggtgtgaacaccaagagacaaggatggtgttgggggggcaccctatgagtctgtccaccacaGCAGGGACCATGTTTTGATCATCATGTTTCAACATCATGGGTTCCAGTGTCATGGGTTTAGATCAGCATTGTTAGGGT Chimp > Human ------------- chr15:59451100-59451105 Template switch process: F1: L ACAGCAGGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTT 1 F3: 4 TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATTATCA R RF: CACAGGTCCCACCCACACTCAAAGGGAGAGGACCATGCAAGGTGTGAACACCAAGAGACAAGGATGGTGTTGGGGGGGCACCCTGTGAGTCTGTCCACCACAGCAGGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATTATCA RR: GTGTCCAGGGTGGGTGTGAGTTTCCCTCTCCTGGTACGTTCCACACTTGTGGTTCTCTGTTCCTACCACAACCCCCCCGTGGGACACTCAGACAGGTGGTGTCGTCCCTGGTACAAAACTAGTAGTACAAAGTCGTAGTACCCAAATCTAGTCGTAACAATCCCACTAGTCTCTAATAGT F2: 3 GTGACC 2 Unidirectional alignment (log-probability: -32.5) GGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTTccagtgtcatgggttTAGATCAGCATTGTTAGGGTGATCAGAGATT GGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTT---------------TAGATCAGCATTGTTAGGGTGATCAGAGATT Template switch alignment (log-probability: -22.2) GGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTT|CCaGTG|TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATT GGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTT|CCTGTG|TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATT Chimp > Gorilla --------------- chr15:37884330-37884335 Template switch process: F1: L ACAGCAGGGACCATGTTTGGATCATCATGTTTCAGCATCATGGGTT 1 F3: 4 TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATTATCA R RF: CACAGGTCCCACCCACACTCAAAGGGAGAGGACCATGCAAGGTGTGAACACCAAGAGACAAGGATGGTGTTGGGGGGGCACCCTGTGAGTCTGTCCACCACAGCAGGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATTATCA RR: GTGTCCAGGGTGGGTGTGAGTTTCCCTCTCCTGGTACGTTCCACACTTGTGGTTCTCTGTTCCTACCACAACCCCCCCGTGGGACACTCAGACAGGTGGTGTCGTCCCTGGTACAAAACTAGTAGTACAAAGTCGTAGTACCCAAATCTAGTCGTAACAATCCCACTAGTCTCTAATAGT F2: 3 GTGACC 2 Unidirectional alignment (log-probability: -38) GGGACCATGTTTgGATCATCATGTTTCAGCAtcatgggttccagtgTCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATT GGGACCATGTTTTGATCATCATGTTTCAGCA---------------TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATT Template switch alignment (log-probability: -27.7) GGGACCATGTTTgGATCATCATGTTTCAGCATCATGGGTT|CCaGTG|TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATT GGGACCATGTTTTGATCATCATGTTTCAGCATCATGGGTT|CCTGTG|TCATGGGTTTAGATCAGCATTGTTAGGGTGATCAGAGATT ========== Event 1158 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGATTTCCAAAGGATAAACAAG-GGAGCAAAAAGTAGGCTGAAATACTGAAGCGAAGAAGGAAAAGGAGATTGCTCAGAGCTGTACTGGGCTAAGAA Chimp: GGATTTCCAAAAGATAAACAAG-GGAGCAAAAAGTAGGCTGAAATACTGAAGCGAAGAAGGAAAAGGAGATTGCTCAGAGCTGTACTGGGCTAAGAA ↓ 1 4 3 2 Gorilla: GGATTTCCAAAAGATAAACAAT-GAGCAAAAAAGTAGGCTGAAATACTGAAGCAAAGAAGGAAAAGGAGATTGCTCAGAGCTGTACTGGGCTAAGAA Human: GGATTTCCAAAGGATAAACAAG-GGAGCAAAAAGTAGGCTGAAATACTGAAGCGAAGAAGGAAAAGGAGATTGCTCAGAGCTGTACTGGGCTAAGAA Cluster: [ ] Orangutan: GGATTTCCAAAAGATAAACAAGGGGAGCAAAAACTAGCCTGAAATACTGAAGCAAAGAAGGAAAAGGAGATTGCTCAGAGCTGTACTGGGCTAAGAA Chimp > Gorilla --------------- chr15:37370390-37370395 Template switch process: F1: L AAAGTTGACTTTGAGGGAGAGGATTTCCAAAAGATAAACAA 1 F3: 4 AAAAAGTAGGCTGAAATACTGAAGCAAAGAAGGAAAAGGA R RF: AAAGTTGACTTTGGGGGAGAGGATTTCCAAAAGATAAACAAGGGAGCAAAAAGTAGGCTGAAATACTGAAGCGAAGAAGGAAAAGGAGATTGCTCA RR: TTTCAACTGAAACCCCCTCTCCTAAAGGTTTTCTATTTGTTCCCTCGTTTTTCATCCGACTTTATGACTTCGCTTCTTCCTTTTCCTCTAACGAGT F2: 3 ACGAGT 2 Unidirectional alignment (log-probability: -38.7) AAGTTGACTTTGaGGGAGAGGATTTCCAAAAGATAAACAAt-GAGCaAAAAAGTAGGCTGAAATACTGAAGCaAAGAAGGAAAAGGA AAGTTGACTTTGGGGGAGAGGATTTCCAAAAGATAAACAAGGGAGC-AAAAAGTAGGCTGAAATACTGAAGCGAAGAAGGAAAAGGA Template switch alignment (log-probability: -27.5) AAGTTGACTTTGaGGGAGAGGATTTCCAAAAGATAAACAA|TGAGCA|AAAAAGTAGGCTGAAATACTGAAGCaAAGAAGGAAAAGGA AAGTTGACTTTGGGGGAGAGGATTTCCAAAAGATAAACAA|TGAGCA|AAAAAGTAGGCTGAAATACTGAAGCGAAGAAGGAAAAGGA ========== Event 1159 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GGGGTGGCAAATTGACCAGAC-AATGAACTTTCTGGCCCCTCTCCCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATACACGCTTGGTACTGGGAGAGGGGCCAAAAAGTTCATTTTTACAACCTCTATGAAACC ↑ 1 4 3 2 Chimp: GGGGTGGCAAATTGACCAGAC-------GTTTCTGGCCCCTCTCCCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATACACGCTTGGTACTGGGAGAGGGGCCAAAAAGTTCATTTTTACAACCTCTATGAAACC Gorilla: GGGGTGGCAAATTGACCAGAC-AATGAACTTTCTGGCCCCTCTCCCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATACATGCTTGGTACTGGGAGAGGGGCCAGAAAGTTCATTTTTACAACCTCTATGAAACC Human: GGGGTGGCAAATTGACCAGAC-AATGAACTTTCTGGCCCCTCTCCCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATACACGCTTGGTACTGGGAGAGGGGCCAAAAAGTTCATTTTTACAACCTCTATGAAACC Cluster: [ ] Orangutan: GGGGTGGCAAATTGACCAGACATGTAAACTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAGAAAGTTCATTTTTACAACCTCTATGAAACC Chimp > Human ------------- chr15:59328413-59328419 Template switch process: F1: L AAAAGGAACCCACCTTCATTGGGGTGGCAAATTGACCAGAC 1 F3: 4 TTTCTGGCCCCTCTCCCAATACACGCTTGGTACTGGGAGA R RF: AAAAGGAACCCACCTTCGTTGGGGTGGCAAATTGACCAGACGTTTCTGGCCCCTCTCCCAATACACGCTTGGTACTGGGAGAGGGGCCAAAAAGTTCATT RR: TTTTCCTTGGGTGGAAGCAACCCCACCGTTTAACTGGTCTGCAAAGACCGGGGAGAGGGTTATGTGCGAACCATGACCCTCTCCCCGGTTTTTCAAGTAA F2: 3 CAAGTAA 2 Unidirectional alignment (log-probability: -31.5) AAAGGAACCCACCTTCaTTGGGGTGGCAAATTGACCAGACaatgaacTTTCTGGCCCCTCTCCCAATACACGCTTGGTACTGGGAGA AAAGGAACCCACCTTCGTTGGGGTGGCAAATTGACCAGAC------GTTTCTGGCCCCTCTCCCAATACACGCTTGGTACTGGGAGA Template switch alignment (log-probability: -22.1) AAAGGAACCCACCTTCaTTGGGGTGGCAAATTGACCAGAC|AATGAAC|TTTCTGGCCCCTCTCCCAATACACGCTTGGTACTGGGAGA AAAGGAACCCACCTTCGTTGGGGTGGCAAATTGACCAGAC|AATGAAC|TTTCTGGCCCCTCTCCCAATACACGCTTGGTACTGGGAGA ========== Event 1160 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ACAGTCCAGCATAGTGGACTGGGGGCTGGGA--------------------------------------------------------CTCCTAAGATGGGGCAGTAAGGTTGCAA ↓ 4 3 2 1 Chimp: ACAGTCCAGCATAGTGGACTGGGGGCTGGGA----------------------------CTCCTAAGTAGAAGTCTGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA Gorilla: ACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAGTAGAAGTCTGGGGGCTGGGA----------------------------CTCCTAAGATGGGGCAGTAAGGTTGCAA ↑ 4 3 2 1 Human: ACAGTCCAGCATAGTGGACTGGGGGCTGGGA--------------------------------------------------------CTCCTAAGATGGGGCAGTAAGGTTGCAA Cluster: [ ] Orangutan: ACAGTCCAGCATAGTGGACTGGGGGCTGGGACTGCTAAGTAGAAGTCTGGGGGCTGGGA----------------------------CTCCTAAGATGGGGCAGTAAGGTTGTAA Human > Chimp ------------- chr15:40218741-40218748 Template switch process: F1: L TGCTGTAGAGACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG 1 F3: 4 TGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAAATTTGGGGCAGT R RF: TGCTATAGAGACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAAATTTGGGGCAGT RR: ACGATATCTCTGTCAGGTCGTATCACCTGACCCCCGACCCTGAGGATTCTACCCCGTCATTCCAACGTTTAAACCCCGTCA F2: 3 CTGAAGAT 2 Unidirectional alignment (log-probability: -57.2) GACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAGtagaagtctgggggctgggactcctaagATGGGGCAGTAAGGTTGCAA GACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG----------------------------ATGGGGCAGTAAGGTTGCAA Template switch alignment (log-probability: -28.6) GACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG|TAGaAGTC|TGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA GACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG|TAGGAGTC|TGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA Human > Gorilla --------------- chr15:37845316-37845323 Template switch process: F1: L TGCTGTAGAGACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG 1 F3: 4 TGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAAATTTGGGGCAGT R RF: TGCTATAGAGACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAAATTTGGGGCAGT RR: ACGATATCTCTGTCAGGTCGTATCACCTGACCCCCGACCCTGAGGATTCTACCCCGTCATTCCAACGTTTAAACCCCGTCA F2: 3 CTGAAGAT 2 Unidirectional alignment (log-probability: -56.7) GACAGTCCAGCATAGTGGActgggggctgggactcctaagtagaagtCTGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA GACAGTCCAGCATAGTGGA----------------------------CTGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA Template switch alignment (log-probability: -28.3) GACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG|TAGaAGTC|TGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA GACAGTCCAGCATAGTGGACTGGGGGCTGGGACTCCTAAG|TAGGAGTC|TGGGGGCTGGGACTCCTAAGATGGGGCAGTAAGGTTGCAA ========== Event 1161 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATAGTTGCATCAAACAAAATTC-------CTAT-AGAACTTAAGCAAATATCACAGTT Chimp: ACATAGTTGCATCAAACAAAACTC-------CTAT-AGAACTTAAGCAAGTATCACAGTT Gorilla: ACACAGTTGCATCAAACAAAACTCCTGAATCCTATAGGAACTTAAGCAAATATCATAGTT ↓ 1 3 42 Human: ACATAGTTGCATCAAACAAAATTC-------CTAT-AGAACTTAAGCAAATATCACAGTT Cluster: [ ] Orangutan: ACATAGCTGCATCAAACAAAACTCCTGAATCCTATAGGAACTTAAGCAAATATCACAGTT Gorilla > Human --------------- chr15:59271521-59271529 Template switch process: F1: L AGTTCCACCAGGATATCTTTACATAGTTGCATCAAACAAAA 1 F3: 4 AACTTAAGCAAATATCACAGTTCCCTGTTGATAATGAAG R RF: AGTTCCACCAGGATATCTTTACACAGTTGCATCAAACAAAACTCCTGAATCCTATAGGAACTTAAGCAAATATCATAGTTCCCTGTTGATAATGAAG RR: TCAAGGTGGTCCTATAGAAATGTGTCAACGTAGTTTGTTTTGAGGACTTAGGATATCCTTGAATTCGTTTATAGTATCAAGGGACAACTATTACTTC F2: 3 GATATCCTT 2 Unidirectional alignment (log-probability: -37.7) GTTCCACCAGGATATCTTTACAtAGTTGCATCAAACAAA-------AtTCCTATA-GAACTTAAGCAAATATCAcAGTTCCCTGTTGATAATGAAG GTTCCACCAGGATATCTTTACACAGTTGCATCAAACAAAACTCCTGAATCCTATAGGAACTTAAGCAAATATCATAGTTCCCTGTTGATAATGAAG Template switch alignment (log-probability: -27.9) GTTCCACCAGGATATCTTTACAtAGTTGCATCAAACAAAA|TTCCTATAG|AACTTAAGCAAATATCAcAGTTCCCTGTTGATAATGAAG GTTCCACCAGGATATCTTTACACAGTTGCATCAAACAAAA|TTCCTATAG|AACTTAAGCAAATATCATAGTTCCCTGTTGATAATGAAG ========== Event 1162 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAAAGTTTTCTGATCTGAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------TTATCAAATTCTAAAGAAAAAGTCTTTAGAATT---------------------------------TGATAATTTCAGATCAGAAAACTT Chimp: TCAAAGTTTTCTGATCTGAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATCAAATTCTAAAGAAAAAGTCTTTAGAATTTGATAATTTCAGATCAGAAAACTT ↑ 3 1 2 4 Gorilla: TCAAGGTTTTCTGATCTGAAA-------------------------------------------------------------------------------------------------------------------------------TTATCAAATTCTAAAGACTTTTTCTTTAGAATT------------------------------------------------------------------TGTTAATTTCAGATCAGAAAACTT Human: TCAAAGTTTTCTGATCTGAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------TTATCAAATTCTAAAGAAAAAGTCTTTAGAATT---------------------------------TGATAATTTCAGATCAGAAAACTT Cluster: [ ] Orangutan: TCAAAGTTTTCTGATCTGAAATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---------------------------------------------------------------------------------------------------NNNNNNNNNNNNATCAGAAAACTT Gorilla > Chimp --------------- chr15:39806479-39806497 Template switch process: F1: L GTATGACTTAATATCAAATATCAAAGTTTTCTGATCTGAAATTATCAAATTCTAAAGA 1 F3: 4 TAATTTCAGATCAGAAAACTTTGATATTTGAGTCTGAAGA R RF: ATATGACTTACTATCAAATATCAAGGTTTTCTGATCTGAAATTATCAAATTCTAAAGACTTTTTCTTTAGAATTTGTTAATTTCAGATCAGAAAACTTTGATATTTGAGTCTGAAGA RR: TATACTGAATGATAGTTTATAGTTCCAAAAGACTAGACTTTAATAGTTTAAGATTTCTGAAAAAGAAATCTTAAACAATTAAAGTCTAGTCTTTTGAAACTATAAACTCAGACTTCT F2: 3 AGTTTAAGATTTCTGAAAA 2 Unidirectional alignment (log-probability: -50.6) TATCAAaGTTTTCTGATCTGAAATTATCAAATTCTAAAGAaaaag-----TCTTTAGAATTTGaTAATTTCAGATCAGAAAACTTTGATATTTGAGTCTGAAGA TATCAAGGTTTTCTGATCTGAAATTATCAAATTCTAAAGA-----CTTTTTCTTTAGAATTTGTTAATTTCAGATCAGAAAACTTTGATATTTGAGTCTGAAGA Template switch alignment (log-probability: -35.1) TATCAAaGTTTTCTGATCTGAAATTATCAAATTCTAAAGA|AAAAGTCTTTAGAATTTGA|TAATTTCAGATCAGAAAACTTTGATATTTGAGTCTGAAGA TATCAAGGTTTTCTGATCTGAAATTATCAAATTCTAAAGA|AAAAGTCTTTAGAATTTGA|TAATTTCAGATCAGAAAACTTTGATATTTGAGTCTGAAGA ========== Event 1163 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTATTATAATAAATGAACTACGTCCAC--------------------GTGTACAC-ACCCATAACTCTGTGGCATTGTCCTCTC Chimp: ATTATTATAATAAATGAACTAAGTCCAC--------------------GTGTACAC-ACCCATAGCTCTGTGGCATTGTCCTCTC ↑ 1 3 2 4 Gorilla: ATTATTATAATAAATGAACTACGTCCACGTTACATGGATGTGTACTCCATGTACACGTCCCATAGCTCTGTGGCATTGTCCTCTC ↓ 1 3 2 4 Human: ATTATTATAATAAATGAACTACGTCCAC--------------------GTGTACAC-ACCCATAACTCTGTGGCATTGTCCTCTC Cluster: [ ] Orangutan: ATTATTATAATAAATGAACTACGCCCAC--------------------ATATACAC-ACCCATAGCTCTGTGGCATTGTCCTCTT Gorilla > Human --------------- chr15:41619361-41619367 Template switch process: F1: L GCAAAAGGTTACTATTATTATAATAAATGAACTACGTCCACGT 1 F3: 4 CCCATAACTCTGTGGCATTGTCCTCTCTTTGTGGCATGCCTCTGACC R RF: GCAAAAGGTTACTATTATTATAATAAATGAACTACGTCCACGTTACATGGATGTGTACTCCATGTACACGTCCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCCTCTGACC RR: CGTTTTCCAATGATAATAATATTATTTACTTGATGCAGGTGCAATGTACCTACACATGAGGTACATGTGCAGGGTATCGAGACACCGTAACAGGAGAGAAACACCGTACGGAGACTGG F2: 3 ACACATG 2 Unidirectional alignment (log-probability: -33) AAAGGTTACTATTATTATAATAAATGAACTACGTCCACG--------------------TGTACAC-aCCCATAaCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC AAAGGTTACTATTATTATAATAAATGAACTACGTCCACGTTACATGGATGTGTACTCCATGTACACGTCCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC Template switch alignment (log-probability: -22.4) AAAGGTTACTATTATTATAATAAATGAACTACGTCCACGT|GTACACA|CCCATAaCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC AAAGGTTACTATTATTATAATAAATGAACTACGTCCACGT|GTACACA|CCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC Gorilla > Chimp --------------- chr15:42046901-42046907 Template switch process: F1: L GCACCCGGCAAAAGTTTACTATTATTATAATAAATGAACTAAGTCCACGT 1 F3: 4 CCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC R RF: GCGCCCGGCAAAAGGTTACTATTATTATAATAAATGAACTACGTCCACGTTACATGGATGTGTACTCCATGTACACGTCCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC RR: CGCGGGCCGTTTTCCAATGATAATAATATTATTTACTTGATGCAGGTGCAATGTACCTACACATGAGGTACATGTGCAGGGTATCGAGACACCGTAACAGGAGAGAAACACCGTACGG F2: 3 ACACATG 2 Unidirectional alignment (log-probability: -44) AAAGtTTACTATTATTATAATAAATGAACTAaGTCCACG--------------------TGTACAC-aCCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC AAAGGTTACTATTATTATAATAAATGAACTACGTCCACGTTACATGGATGTGTACTCCATGTACACGTCCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC Template switch alignment (log-probability: -33.4) AAAGtTTACTATTATTATAATAAATGAACTAaGTCCACGT|GTACACA|CCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC AAAGGTTACTATTATTATAATAAATGAACTACGTCCACGT|GTACACA|CCCATAGCTCTGTGGCATTGTCCTCTCTTTGTGGCATGCC ========== Event 1164 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGAGATAGGAATTGATTGATTTA-------------------TGTATCTCTGAGGGAGAGTCCCTCAAAACTTCT ↓ 4 3 2 Chimp: TGGAGATAGGAATTGATTGATTTATGTATCCCTCAGAGATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCT ↑ 4 3 2 Gorilla: TGGAGATAGGAATTGATTGATTTA-------------------TGTATCTCTGAGGGAGAGTCCCTCAAAACTTCT Human: TGGAGATAGGAATTGATTGATTTA-------------------TGTATCTCTGAGGGAGAGTCCCTCAAAACTTCT Cluster: [ ] Orangutan: TGGAGATAGGAATTGATTGATTGA-------------------TTTATCTCTGAGGGAGAGCCCCTCAAAACTTCT Human > Chimp ------------- chr15:41154526-41154533 Template switch process: F1: L CTATAGACTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATC 1 F3: 4 ATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAGTATCG R RF: CTATAGACTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAGTATCA RR: GATATCTGAAATAAACCACCTCTATCCTTAACTAACTAAATACATAGAGACTCCCTCTCAGGGAGTTTTGAAGATCATAGT F2: 3 GAGACTCC 2 Unidirectional alignment (log-probability: -44.2) CTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATccctcagagatttatgtatCTCTGAGGGAGAGTCCCTCAAAACTTCTAG CTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTAT-------------------CTCTGAGGGAGAGTCCCTCAAAACTTCTAG Template switch alignment (log-probability: -22.5) CTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATC|CCTCAGAG|ATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAG CTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATC|CCTCAGAG|ATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAG Gorilla > Chimp --------------- chr15:41154526-41154533 Template switch process: F1: L CTATAGACTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATC 1 F3: 4 ATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAGTATCG R RF: CTATAGACTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAGTATCG RR: GATATCTGAAATAAACCACCTCTATCCTTAACTAACTAAATACATAGAGACTCCCTCTCAGGGAGTTTTGAAGATCATAGC F2: 3 GAGACTCC 2 Unidirectional alignment (log-probability: -38.2) CTTTATTTGGTGGAGATAGGAATTGATTGATTtatgtatccctcagagattTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAG CTTTATTTGGTGGAGATAGGAATTGATTGATT-------------------TATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAG Template switch alignment (log-probability: -17) CTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATC|CCTCAGAG|ATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAG CTTTATTTGGTGGAGATAGGAATTGATTGATTTATGTATC|CCTCAGAG|ATTTATGTATCTCTGAGGGAGAGTCCCTCAAAACTTCTAG ========== Event 1165 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTCATTTTGAAAACAATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAA-----------------------------------------------GAGTTTTCTAACACAGCCCAGACATCTACC ↓ 3 4 2 1 Chimp: AGTCATTTTGAAAACAATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTTAACTTTGGCCTCTTTTCAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACACAGCCCAGACATCTACC ↑ 3 4 2 1 Gorilla: AGTCATTTTGAAAACCATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAA-----------------------------------------------GAGTTTTCTGACACAGCCCAGACATCTACC Human: AGTCATTTTGAAAACAATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAA-----------------------------------------------GAGTTTTCTAACACAGCCCAGACATCTACC Cluster: [ ] Orangutan: AGTCATTTTGAAAACAATGAAAAGAGGCCAAAATTAAGTCTAACAAATGCTTAA-----------------------------------------------GAGTTTTCTAACACAGCCCAGACATCTACC Human > Chimp ------------- chr15:41851175-41851190 Template switch process: F1: L ACAATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTT 1 F3: 4 CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACACAGCCCAGACATCTACCTATTCCTGCC R RF: ACAATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACACAGCCCAGACATCTACCTATTCCTGCC RR: TGTTACTTTTCTCCGGTTTCAATTCAGATTGTTTACGAATTCTCAAAAGATTGTGTCGGGTCTGTAGATGGATAAGGACGG F2: 3 TTTTCTCCGGTTTCAA 2 Unidirectional alignment (log-probability: -78.5) AAAAGAGGCcaaagttaagtctaacaaatgcttaagagttaactttggcctcttttCAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACAC AAAAGAGGC-----------------------------------------------CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACAC Template switch alignment (log-probability: -17.8) AAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTT|AACTTTGGCCTCTTTT|CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACAC AAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTT|AACTTTGGCCTCTTTT|CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACAC Gorilla > Chimp --------------- chr15:41851175-41851190 Template switch process: F1: L ACAATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTT 1 F3: 4 CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTAACACAGCCCAGACATCTACCTATTCCTGCCCTGGCTTCAG R RF: ACCATGAAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTGACACAGCCCAGACATCTACCTATTCCTGCCCTGGCTTCAG RR: TGGTACTTTTCTCCGGTTTCAATTCAGATTGTTTACGAATTCTCAAAAGACTGTGTCGGGTCTGTAGATGGATAAGGACGGGACCGAAGTC F2: 3 TTTTCTCCGGTTTCAA 2 Unidirectional alignment (log-probability: -89.6) AAAAGAGGCcaaagttaagtctaacaaatgcttaagagttaactttggcctcttttCAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTaACAC AAAAGAGGC-----------------------------------------------CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTGACAC Template switch alignment (log-probability: -29.7) AAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTT|AACTTTGGCCTCTTTT|CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTaACAC AAAAGAGGCCAAAGTTAAGTCTAACAAATGCTTAAGAGTT|AACTTTGGCCTCTTTT|CAAAGTTAAGTCTAACAAATGCTTAAGAGTTTTCTGACAC ========== Event 1166 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: ATTCTGAAAAGGATCAGCAAT-TTTAAAACATAATTTTAAAACAATTAttttttgaggtgcagtctcgctgtgtcacccaggctggggtgcagtggcaaaatcttggctcacggccacctccacctcctgggctcaggtgattcttccatctcagccacctgagtagctgggagtacaggcatgc Chimp: ATTCTGAAAAGGATCAGCAATACTCAGGACATAATTTTAAAACAATTGttttttgagatgcagtctcgctctgtcacccaggctggggtgcagtggcaaaatctcggctcactgcaacctccacctcctgggctcaggcgattctcccatctcagcctcctgagtagctgggactacaggcatgc Gorilla: ATTCTGAAAAGGATCAGCAATACTCAGGACATAATTTTAAAACAATTAttttttgagatgcagtctcgctctgtcacccaggctggggtgcagtggcaaaatctcagctcactgcaacctccacctcctgggctcaggtgattctcccatctcagcctcctgagtagctgggactacaggcgtgt ↑ 1 4 3 2 Human: ATTCTGAAAAGGATCAGCAAT-TTTAAAACATAATTTTAAAACAATTAttttttgaggtgcagtctcgctgtgtcacccaggctggggtgcagtggcaaaatcttggctcacggccacctccacctcctgggctcaggtgattcttccatctcagccacctgagtagctgggagtacaggcatgc Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNgtgccgtggcaaaatctctgctcactgcaacctctacctcctgggctcaggtgattctctcatcctcccgtcctgatgagctgggactacaggcatgc Human > Gorilla --------------- chr15:39048962-39048968 Template switch process: F1: L CAATGCCTTTTATTACCATCATTCTGAAAAGGATCAGCAAT 1 F3: 4 ACATAATTTTAAAACAATTATTTTTTGAGATGCAGTCTCG R RF: CAATGCCTTTTATTACCATCATTCTGAAAAGGATCAGCAATTTTAAAACATAATTTTAAAACAATTATTTTTTGAGGTGCAGTCTCGCTGTGTCACCCAGGCTGGGGTGCAGTGGCAAAATCTTGGCTCACGGCCACCTCCACCTCCTGGGCTCAGGTGATTCTTCCATCTCAGCCACCTGAGT RR: GTTACGGAAAATAATGGTAGTAAGACTTTTCCTAGTCGTTAAAATTTTGTATTAAAATTTTGTTAATAAAAAACTCCACGTCAGAGCGACACAGTGGGTCCGACCCCACGTCACCGTTTTAGAACCGAGTGCCGGTGGAGGTGGAGGACCCGAGTCCACTAAGAAGGTAGAGTCGGTGGACTCA F2: 3 GGACTCA 2 Unidirectional alignment (log-probability: -35) AATGCCTTTTATTACCATCATTCTGAAAAGGATCAGCAAT-----ActcaggACATAATTTTAAAACAATTATTTTTTGAGaTGCAGTCTCG AATGCCTTTTATTACCATCATTCTGAAAAGGATCAGCAATTTTAAA------ACATAATTTTAAAACAATTATTTTTTGAGGTGCAGTCTCG Template switch alignment (log-probability: -22.1) AATGCCTTTTATTACCATCATTCTGAAAAGGATCAGCAAT|ACTCAGG|ACATAATTTTAAAACAATTATTTTTTGAGaTGCAGTCTCG AATGCCTTTTATTACCATCATTCTGAAAAGGATCAGCAAT|ACTCAGG|ACATAATTTTAAAACAATTATTTTTTGAGGTGCAGTCTCG ========== Event 1167 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCCTAAAAATACAACAAAAATAAACCTTCTTTCCAGTTTAGCCTACATATAAATCAGATTGTCTTC----AGTTACTGGT------TTA------------CTGAATAAATGATTACAAGTAGA Chimp: TTCCTAAAAATACAACAAAAATAAACCTTCTTTCCAGTTTAGCCTACATATAAATCAGATTGTCTTC--AGAGTTACTGGT------TTA------------CTGAATAAATGATTACAAGTAGA ↑ 3 2 1 4 Gorilla: TTCCTAAAAATACAACAAAAATAAACCTTCTTTCCAGTTTAGCCTACATACAAATCAGATTGTCTTCAG--AGTTACTGAATAATGATTACATTATTACAAGTAGAATAAATGATTACAAGTAGA Human: TTCCTAAAAATACAACAAAAATAAACCTTCTTTCCAGTTTAGCCTACATATAAATCAGATTGTCTTC----AGTTACTGGT------TTA------------CTGAATAAATGATTACAAGTAGA Cluster: [ ] Orangutan: TTCCTAGAAATACAACAAAAATAAACCTTCTTTCCAGTTTAGCCTACATACAAATCAGATTGTCTTCAG--AGTTACTGGT------TTA------------CTGAATAAAGGATTACAAGTAGA Gorilla > Chimp --------------- chr1:56044934-56044940 Template switch process: F1: L CTTCTTTCCAGTTTAGCCTACATATAAATCAGATTGTCTTCAGAGTTACTG 1 F3: 4 GAATAAATGATTACAAGTAGATCTGAAAGTATTTATTAAA R RF: AATAAACCTTCTTTCCAGTTTAGCCTACATACAAATCAGATTGTCTTCAGAGTTACTGAATAATGATTACATTATTACAAGTAGAATAAATGATTACAAGTAGATCTGAAAGTATTTATTAAA RR: TTATTTGGAAGAAAGGTCAAATCGGATGTATGTTTAGTCTAACAGAAGTCTCAATGACTTATTACTAATGTAATAATGTTCATCTTATTTACTAATGTTCATCTAGACTTTCATAAATAATTT F2: 3 TCATTTG 2 Unidirectional alignment (log-probability: -37.6) TTTAGCCTACATAtAAATCAGATTGTCTTCAGAGTTACTG-------------------------gtttactGAATAAATGATTACAAGTAGATCTGAAAGTATTTATTAAA TTTAGCCTACATACAAATCAGATTGTCTTCAGAGTTACTGAATAATGATTACATTATTACAAGTA-------GAATAAATGATTACAAGTAGATCTGAAAGTATTTATTAAA Template switch alignment (log-probability: -27.9) TTTAGCCTACATAtAAATCAGATTGTCTTCAGAGTTACTG|GTTTAcT|GAATAAATGATTACAAGTAGATCTGAAAGTATTTATTAAA TTTAGCCTACATACAAATCAGATTGTCTTCAGAGTTACTG|GTTTATT|GAATAAATGATTACAAGTAGATCTGAAAGTATTTATTAAA ========== Event 1168 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATCTTAAAAGAGTCATAAAAGTC------TGCATGTGGAGAGATAGCACATCCTAAGTTATAGGTGGttatagaatt Chimp: TATCTTAAAAGAGTCATAAAAGTC------TGCATGTGGAGAGATAGCACATCCTAAGTTATAGGTGGttatagaatt ↓ 1 4 3 2 Gorilla: TATCTTAAAAGAGTCATAAAACTT------------AGGAGAGATAGCACATCCTAAGTTATAGGTGGttatagaatt ↑ 1 4 3 2 Human: TATCTTAAAAGAGTCATAAAAGTC------TGCATGTGGAGAGATAGCACATCCTAAGTTATAGGTGGttatagaatt Cluster: [ ] Orangutan: TATCTTAAAAGAGTCATAAAAGTCTGCATG------TGGAGAGATAGCACATGCTAAGTTATAGGTGGttatagaatt Human > Gorilla --------------- chr15:40553681-40553685 Template switch process: F1: L CTCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA 1 F3: 4 GAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT R RF: CTCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAAGTCTGCATGTGGAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT RR: GAGATATAAGTTCTTCGATAATAGAATTTTCTCAGTATTTTCAGACGTACACCTCTCTATCGTGTAGGATTCAATATCCACCAATATCTTA F2: 3 GATTC 2 Unidirectional alignment (log-probability: -26.9) TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA----------cttaGGAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAAGTCTGCATGT----GGAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT Template switch alignment (log-probability: -16.3) TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA|CTTAG|GAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA|CTTAG|GAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT Chimp > Gorilla --------------- chr15:40553681-40553685 Template switch process: F1: L CTCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA 1 F3: 4 GAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT R RF: CTCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAAGTCTGCATGTGGAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT RR: GAGATATAAGTTCTTCGATAATAGAATTTTCTCAGTATTTTCAGACGTACACCTCTCTATCGTGTAGGATTCAATATCCACCAATATCTTA F2: 3 GATTC 2 Unidirectional alignment (log-probability: -26.9) TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA----------cttaGGAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAAGTCTGCATGT----GGAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT Template switch alignment (log-probability: -16.3) TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA|CTTAG|GAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT TCTATATTCAAGAAGCTATTATCTTAAAAGAGTCATAAAA|CTTAG|GAGAGATAGCACATCCTAAGTTATAGGTGGTTATAGAAT ========== Event 1169 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: aatggccatgggattcagtta---gagtccaggatactcaattcgtcttttgctgaaatttttggagaagagacacttgctctctccCGAGAAGGTGTGAGGTCTGATAAAGTATAAAAAGTGTTTAAGGGACTATAAGAGCTGTTTTGGAGAG Chimp: AATGGCCATGAGATTCAGTTA---GAGTCCAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAAGAGACACTTGCTCTCTCCCGAGAAGGTGTGAGGTCTGATAAAGTATAAAAAGTGTTTAAGGGACTATAAGAGCTGTTTTGGAGAG ↑ 1 4 3 2 Gorilla: AATGGCCATGAGATTCAGTTAGTTAGATTCAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAAGAGACACTTGCTCTCTCCCAAGAAGGTGTGAGGTCTGATAAAGTATAAAAAGTGTTTAAGGGACTATAAGAGCTGTTTTGGAGAG Human: aatggccatgggattcagtta---gagtccaggatactcaattcgtcttttgctgaaatttttggagaagagacacttgctctctccCGAGAAGGTGTGAGGTCTGATAAAGTATAAAAAGTGTTTAAGGGACTATAAGAGCTGTTTTGGAGAG Cluster: [ ] Orangutan: aatggccatgagattcaGTTA---GAGTCCAGGATACTCAATTCGTCTTTTGTTGAAATTTTTGGAGAGGAGACACTTGCTCTCTCCTGAGAAGGTTAGAGGTCTGATAAAGTATAAAAATTGTTTAAGGGACTATAAGAGCTGTTTTGGAGAG Gorilla > Chimp --------------- chr15:40292109-40292112 Template switch process: F1: L GCTATGATGGTTGGTTCTAGAATGGCCATGAGATTCAGTTAG 1 F3: 4 CAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAA R RF: GCTATGATGGTTGGTTCTAGAATGGCCATGAGATTCAGTTAGTTAGATTCAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAAGAGACACTTGCTCTCTCCCAAGAAGGTGTGAGGTCTGATAAAGTATAAAAAGTGTTTAAGGGACT RR: CGATACTACCAACCAAGATCTTACCGGTACTCTAAGTCAATCAATCTAAGTCCTATGAGTTAAGCAGAAAACGACTTTAAAAACCTCTTCTCTGTGAACGAGAGAGGGTTCTTCCACACTCCAGACTATTTCATATTTTTCACAAATTCCCTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -26.4) TATGATGGTTGGTTCTAGAATGGCCATGAGATTCAGTTAG--AG-TcCAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAA TATGATGGTTGGTTCTAGAATGGCCATGAGATTCAGTTAGTTAGATTCAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAA Template switch alignment (log-probability: -16.3) TATGATGGTTGGTTCTAGAATGGCCATGAGATTCAGTTAG|AGTC|CAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAA TATGATGGTTGGTTCTAGAATGGCCATGAGATTCAGTTAG|AGTC|CAGGATACTCAATTCGTCTTTTGCTGAAATTTTTGGAGAA ========== Event 1170 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GAGCAAGGTCTGGGGATGAGGGGCTGCGACCACTGGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTCTCTAGGTGGGCTCCATCCCTGCCAATGCTGCAGACGACGGACAGTGGTCACAGGGGCTGATTTCTGCTG ↑ 4 1 3 2 Chimp: GAGCAAGGTCTGGGGATGAGGG---------------GCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTCTCTAGGTGGGCTCCATCCCTGCCAATGCTGCAGACGACGGACAGTGGTCACAGGGGCTGATTTCTGCTG ↓ 4 1 3 2 Gorilla: GAGCAAGGTCTGGGGATGAGGGGCTGCGACCACTGGGGCTGCCTGCCCTCAAGGCCAATTTCTCGACTCTACTCTCTAGGTGGGCTCCATCCCTGCCAATGCTGCAGACGACGGACAGTGGTCACAGGGGCTGATTTCTGCTG Human: GAGCAAGGTCTGGGGATGAGGGGCTGCGACCACTGGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTCTCTAGGTGGGCTCCATCCCTGCCAATGCTGCAGACGACGGACAGTGGTCACAGGGGCTGATTTCTGCTG Cluster: [ ] Orangutan: GAGCAAGGTGTGGGGATGAGGGGCTGCGACCACTGGGGCTACCTACCCTTATGGCCAGTTTCTTGACTCTAC--TCTAGGTGGGCTCCATCCCTGCCAATGCTGCCGACGACGGACAGTGGTCACAGGGGCTGATTTCTGCTG Chimp > Human ------------- chr15:62835685-62835691 Template switch process: F1: L GGGTACAAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC 1 F3: 4 GGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTCTCT R RF: GGGTACAAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTCTCTAGGTGGGCTCCATCCCTGCCAATGCTGCAGACGACGGACAGTGGTC RR: CCCATGTTCAGACCAAGGGCTCGTTCCAGACCCCTACTCCCCGACGGACGGGAGTACCGGTTAAAGAGCTGAGATGAGAGATCCACCCGAGGTAGGGACGGTTACGACGTCTGCTGCCTGTCACCAG F2: 3 TCACCAG 2 Unidirectional alignment (log-probability: -32.5) AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGCgaccactggggctgcCTGCCCTCATGGCCAATTTCTCGACTCTACTC AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC---------------CTGCCCTCATGGCCAATTTCTCGACTCTACTC Template switch alignment (log-probability: -16.3) AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC|GACCACT|GGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTC AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC|GACCACT|GGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTC Chimp > Gorilla --------------- chr15:41263965-41263971 Template switch process: F1: L GGGTACAAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC 1 F3: 4 GGGGCTGCCTGCCCTCAAGGCCAATTTCTCGACTCTACTCTCT R RF: GGGTACAAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTCTCTAGGTGGGCTCCATCCCTGCCAATGCTGCAGACGACGGACAGTGGTC RR: CCCATGTTCAGACCAAGGGCTCGTTCCAGACCCCTACTCCCCGACGGACGGGAGTACCGGTTAAAGAGCTGAGATGAGAGATCCACCCGAGGTAGGGACGGTTACGACGTCTGCTGCCTGTCACCAG F2: 3 TCACCAG 2 Unidirectional alignment (log-probability: -38) AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGgggctgcgaccactgGGGCTGCCTGCCCTCAaGGCCAATTTCTCGACTCTACTC AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAG---------------GGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTC Template switch alignment (log-probability: -22.3) AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC|GACCACT|GGGGCTGCCTGCCCTCAaGGCCAATTTCTCGACTCTACTC AAGTCTGGTTCCCGAGCAAGGTCTGGGGATGAGGGGCTGC|GACCACT|GGGGCTGCCTGCCCTCATGGCCAATTTCTCGACTCTACTC ========== Event 1171 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTGGATGAAGTAGAGCACGG---TCCATGAGGACGCAATAGAGCACATGTGTACACATCAGCATCTCAGCACTTTCCATGGACCCTGGCCCTCTCTGTGGCTAGGCATTGGTGGCAGTCCCAAG ↓ 1 4 3 2 Chimp: GTTGGATGAAGTAGAGCACGGCTAGCCACGAGGCCACAATAGAGCACATGTGTACACATCAGCATCTCAGCACTTTCCATGGACCCCGGCCCTCTCTGTGGCTAGGCATTGGTGGCAGCCCCAAG Gorilla: GTTGGATGAAGTAGAGCACAG---TCCATGAGGCCACAATAGAGCACATGTGTACACACCAGCATCTCAGCACTTTCCATGGACCCTGGCCCTCTCTGTGGCTAGGCATTGGTGGCAGCCCCAAG Human: GTTGGATGAAGTAGAGCACGG---TCCATGAGGACGCAATAGAGCACATGTGTACACATCAGCATCTCAGCACTTTCCATGGACCCTGGCCCTCTCTGTGGCTAGGCATTGGTGGCAGTCCCAAG Cluster: [ ] Orangutan: GTTGGATGAAGTAGAGCACGG---TCCATGAGGCCACAATAGAGCACACGTGTACACATCAGCATCTCAGCACTTTTCATGGACCCTGGTCCTCTCTGTGGCTAGGCATTGGTGGCAGCCCCAAG Human > Chimp ------------- chr15:43827778-43827785 Template switch process: F1: L TGAAGGTAATCAGCATGACTGTTGGATGAAGTAGAGCACGG 1 F3: 4 GAGGCCACAATAGAGCACATGTGTACACATCAGCATCTCAGCACTTT R RF: TGAAGGTAATCAGCATGACTGTTGGATGAAGTAGAGCACGGTCCATGAGGACGCAATAGAGCACATGTGTACACATCAGCATCTCAGCACTTTCCATGGACCCTGGCCCTCTCTGTGGCTAG RR: ACTTCCATTAGTCGTACTGACAACCTACTTCATCTCGTGCCAGGTACTCCTGCGTTATCTCGTGTACACATGTGTAGTCGTAGAGTCGTGAAAGGTACCTGGGACCGGGAGAGACACCGATC F2: 3 CACCGATC 2 Unidirectional alignment (log-probability: -39.3) GAAGGTAATCAGCATGACTGTTGGATGAAGTAGAGCACGGctagCCAcGAGGcCaCAATAGAGCACATGTGTACACATCAGCATCTCA GAAGGTAATCAGCATGACTGTTGGATGAAGTAGAGCACGG---TCCATGAGGACGCAATAGAGCACATGTGTACACATCAGCATCTCA Template switch alignment (log-probability: -28.4) GAAGGTAATCAGCATGACTGTTGGATGAAGTAGAGCACGG|CTAGCCAC|GAGGcCaCAATAGAGCACATGTGTACACATCAGCATCTCA GAAGGTAATCAGCATGACTGTTGGATGAAGTAGAGCACGG|CTAGCCAC|GAGGACGCAATAGAGCACATGTGTACACATCAGCATCTCA ========== Event 1172 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CGCCTTGCAGTCGGGCTTCCTGCTGGCTTTCCAGTCAGCTGCTGGCTTTCCAGAGGCTCTTGTGGTCtggtgtggtgaagagcactttgagagggtgagactcagcaggattcaggccctaattctgctgactgaccagctatgcacacccaggg Chimp: CGCCTTGCAGTCAGGCTTCCTG-------------------CTGGCTTTCCAGAGGCTCTTgcggtctggtgtagtgaagagcactttgagagggtgagactcagcaggattcaggccctaattctgctgactgaccagctatgcacacccaggg ↓ 4 1 3 2 Gorilla: CGCCTTGCAGTCGGGCTTCCTGCTGGCTTTCCAGTCAGCTGCTGGCTTTCCAGAGGCTCTTgcggtctggtgtagtgaagagcactttgagagggtgggactcagcaggattcaggccctaattctgctgactgaccagctatgcacacccaggg Human: CGCCTTGCAGTCGGGCTTCCTGCTGGCTTTCCAGTCAGCTGCTGGCTTTCCAGAGGCTCTTGTGGTCtggtgtggtgaagagcactttgagagggtgagactcagcaggattcaggccctaattctgctgactgaccagctatgcacacccaggg Cluster: [ ] Orangutan: CGCCTTGCAGTCAGGCTTCTTGCTGGCTTTCCAGTCAGCTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAATGACGAACACTTTGAGAGGGTGAGACTCAGCAGGATTCAGGCCCTGATTCTGCTGACTGACGAGCTATGCACACCCAGGG Chimp > Gorilla --------------- chr15:38519965-38519968 Template switch process: F1: L AATGAATCCCTGCCTAACTCGCCTTGCAGTCGGGCTTCCTGCTGGCTTTCCAG 1 F3: 4 CTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAGTGAAGA R RF: AATGAATCCCTGCCTAACTCGCCTTGCAGTCAGGCTTCCTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAGTGAAGAGCACTTTGAGAGGGTGAGACTCAGCAGGATTCAGGCCCTAATTCTGCTGACTGA RR: TTACTTAGGGACGGATTGAGCGGAACGTCAGTCCGAAGGACGACCGAAAGGTCTCCGAGAACGCCAGACCACATCACTTCTCGTGAAACTCTCCCACTCTGAGTCGTCCTAAGTCCGGGATTAAGACGACTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -43.7) CTAACTCGCCTTGCAGTCgGGCTTCctgctggctttccagtcagCTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAGTGA CTAACTCGCCTTGCAGTCAGGCTTC-------------------CTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAGTGA Template switch alignment (log-probability: -22.1) CTAACTCGCCTTGCAGTCgGGCTTCCTGCTGGCTTTCCAG|TCAG|CTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAGTGA CTAACTCGCCTTGCAGTCAGGCTTCCTGCTGGCTTTCCAG|TCAG|CTGCTGGCTTTCCAGAGGCTCTTGCGGTCTGGTGTAGTGA ========== Event 1173 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTTCATGGGAAATACAAGGGGGATACAGTGGTATGAACACTATGACGTGCACAT Chimp: GTTCGTGGGAAATACAAGGGGGATACAGTGGTATGAACACTATGGCGTGCACAT ↑ 1 3 4 2 Gorilla: GTTCGTGGGAAATACAAGGGG---GC-ACTGTATGAACACTATGACGTGCACAT ↓ 1 3 4 2 Human: GTTCATGGGAAATACAAGGGGGATACAGTGGTATGAACACTATGACGTGCACAT Cluster: [ ] Orangutan: GTTCGTGGGAAATACAGGGGG----C-ACTGTATGAACACTATGACGTGCACAT Gorilla > Human --------------- chr15:36772837-36772844 Template switch process: F1: L ACAAAATTGTGAATGTGGATGTTCATGGGAAATACAAGGGGG 1 F3: 4 GTATGAACACTATGACGTGCACATATAGAGTAGGAACTCA R RF: ACAAAATTGTGAATGTGGATGTTCGTGGGAAATACAAGGGGGCACTGTATGAACACTATGACGTGCACATATAGAATAGGAACTCA RR: TGTTTTAACACTTACACCTACAAGCACCCTTTATGTTCCCCCGTGACATACTTGTGATACTGCACGTGTATATCTTATCCTTGAGT F2: 3 GTGACATA 2 Unidirectional alignment (log-probability: -43) AAAATTGTGAATGTGGATGTTCaTGGGAAATACAAGGGGGataCAgTgGTATGAACACTATGACGTGCACATATAGAgTAGGAACTCA AAAATTGTGAATGTGGATGTTCGTGGGAAATACAAGGGGG---CACT-GTATGAACACTATGACGTGCACATATAGAATAGGAACTCA Template switch alignment (log-probability: -27.8) AAAATTGTGAATGTGGATGTTCaTGGGAAATACAAGGGGG|ATACAGTG|GTATGAACACTATGACGTGCACATATAGAgTAGGAACTCA AAAATTGTGAATGTGGATGTTCGTGGGAAATACAAGGGGG|ATACAGTG|GTATGAACACTATGACGTGCACATATAGAATAGGAACTCA Gorilla > Chimp --------------- chr15:37152867-37152874 Template switch process: F1: L ACAAAATCGTGAATGTGGATGTTCGTGGGAAATACAAGGGGG 1 F3: 4 GTATGAACACTATGGCGTGCACATATAGAATAGGAACTCA R RF: ACAAAATTGTGAATGTGGATGTTCGTGGGAAATACAAGGGGGCACTGTATGAACACTATGACGTGCACATATAGAATAGGAACTCA RR: TGTTTTAACACTTACACCTACAAGCACCCTTTATGTTCCCCCGTGACATACTTGTGATACTGCACGTGTATATCTTATCCTTGAGT F2: 3 GTGACATA 2 Unidirectional alignment (log-probability: -43) AAAATcGTGAATGTGGATGTTCGTGGGAAATACAAGGGGGataCAgTgGTATGAACACTATGgCGTGCACATATAGAATAGGAACTCA AAAATTGTGAATGTGGATGTTCGTGGGAAATACAAGGGGG---CACT-GTATGAACACTATGACGTGCACATATAGAATAGGAACTCA Template switch alignment (log-probability: -27.8) AAAATcGTGAATGTGGATGTTCGTGGGAAATACAAGGGGG|ATACAGTG|GTATGAACACTATGgCGTGCACATATAGAATAGGAACTCA AAAATTGTGAATGTGGATGTTCGTGGGAAATACAAGGGGG|ATACAGTG|GTATGAACACTATGACGTGCACATATAGAATAGGAACTCA ========== Event 1174 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACAAGTGCTGGGGAGCAAAGAT--GGGATCAGGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAGAAGAGGAGCTTGGGGACAA Chimp: ACAAGTGCTGGGGAGCAAAGAC--GGGATCAGGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAGAAGAGGAGCTTGGGGACAA ↑ 1 4 3 2 Gorilla: ACAAGTGCTGGGGAGCAAAGAC----TCCCATGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAGAAGAGGAGCTTGGGGACAA ↓ 1 4 3 2 Human: ACAAGTGCTGGGGAGCAAAGAT--GGGATCAGGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAGAAGAGGAGCTTGGGGACAA Cluster: [ ] Orangutan: ACAAGTGCTGGGGAGCAAAGACGG--GATCAGGGTCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAGAAGAGGGGCTTGGGGACAA Gorilla > Human --------------- chr15:66162154-66162162 Template switch process: F1: L AGTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGA 1 F3: 4 GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG R RF: AGTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGACTCCCATGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG RR: TCACGGTGGTATACCCTGTTTGTTCACGACCCCTCGTTTCTGAGGGTACCGGTTGGTGGGACTCTTCATTCCAAGTCCGACTCGGGTC F2: 3 GACTAGGGT 2 Unidirectional alignment (log-probability: -32.5) GTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAG------ATgggatcagGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG GTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGACTCCCAT--------GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG Template switch alignment (log-probability: -22.4) GTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGA|TGGGaTCAG|GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG GTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGA|TGGGCTCAG|GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG Gorilla > Chimp --------------- chr15:47029739-47029746 Template switch process: F1: L GTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGAC 1 F3: 4 GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG R RF: GTGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGACTCCCATGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG RR: CACGGTGGTATACCCTGTTTGTTCACGACCCCTCGTTTCTGAGGGTACCGGTTGGTGGGACTCTTCATTCCAAGTCCGACTCGGGTC F2: 3 GACTAGGG 2 Unidirectional alignment (log-probability: -32.1) TGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGACgggaT--CAgGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG TGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGAC----TCCCATGGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG Template switch alignment (log-probability: -22.3) TGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGAC|GGGaTCAG|GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG TGCCACCATATGGGACAAACAAGTGCTGGGGAGCAAAGAC|GGGCTCAG|GGCCAACCACCCTGAGAAGTAAGGTTCAGGCTGAGCCCAG ========== Event 1175 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCTACTCTCTTTCTTGCAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT-GGTC-------CTACAGATGCATCCTTGTCTATCAA Chimp: TCCTACTCTCTTTCTTGCAGTAGGATCAATTCTCATTGCCCCACAGATTAACAGCAGT-GGTC-------CTACAGATGCATCCTTGTCTATCAA ↑ 3 2 1 4 Gorilla: TCCTACTCTCTTTCTTGCAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGTCTATCCTTGTCTATCAAGATGCATCCTTGTCTATCAA ↓ 3 2 1 4 Human: TCCTACTCTCTTTCTTGCAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT-GGTC-------CTACAGATGCATCCTTGTCTATCAA Cluster: [ ] Orangutan: TCCTACTCTCTTTCTTGCAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT-GGTC-------CTACAGATGCATCCTTGTCTATCAA Gorilla > Human --------------- chr15:35586272-35586279 Template switch process: F1: L CAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT 1 F3: 4 AGATGCATCCTTGTCTATCAAAAAAGCAACTTGCTCAGGA R RF: CAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGTCTATCCTTGTCTATCAAGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA RR: GTCATCCTAGTTAAGAATAACGGGGTGTCTAATTGTCGTCAGATAGGAACAGATAGTTCTACGTAGGAACAGATAGTTCTTTCGTTGAACGAGTCCT F2: 3 CATCCTGG 2 Unidirectional alignment (log-probability: -37) AGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGTggtcctaC---------------AGATGCATCCTTGTCTATCAAaAAAGCAACTTGCTCAGGA AGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT-------CTATCCTTGTCTATCAAGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA Template switch alignment (log-probability: -27.8) AGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT|GgTCCTAC|AGATGCATCCTTGTCTATCAAaAAAGCAACTTGCTCAGGA AGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT|GATCCTAC|AGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA Gorilla > Chimp --------------- chr15:35935228-35935235 Template switch process: F1: L CAGTAGGATCAATTCTCATTGCCCCACAGATTAACAGCAGT 1 F3: 4 AGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA R RF: CAGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGTCTATCCTTGTCTATCAAGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA RR: GTCATCCTAGTTAAGAATAACGGGGTGTCTAATTGTCGTCAGATAGGAACAGATAGTTCTACGTAGGAACAGATAGTTCTTTCGTTGAACGAGTCCT F2: 3 CATCCTGG 2 Unidirectional alignment (log-probability: -37) AGTAGGATCAATTCTcATTGCCCCACAGATTAACAGCAGTggtcctaC---------------AGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA AGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT-------CTATCCTTGTCTATCAAGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA Template switch alignment (log-probability: -27.8) AGTAGGATCAATTCTcATTGCCCCACAGATTAACAGCAGT|GgTCCTAC|AGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA AGTAGGATCAATTCTTATTGCCCCACAGATTAACAGCAGT|GATCCTAC|AGATGCATCCTTGTCTATCAAGAAAGCAACTTGCTCAGGA ========== Event 1176 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGGGAGGCCATACCACCAGCATTTG-----CACACCAG--------------CAGCGGCAGAAGAGTCTGTGCCGGTGTGCACCCTACCGGGTAGGGA Chimp: GAAGGGAGGCCATACCACCAGCATTTG-----CACACCAG--------------CAGCGGCAGAAGAGTCTGTGCCGGCGTGCACCCTACCGGGTGGGGA ↓ 1 3 2 4 Gorilla: GAAGGGAGGCCATACCACCAGACTCTT----------CTG----------------------------CCGCTGCTGGTGTGCACCCTACCGGGTGGGGA ↑ 1 3 2 4 Human: GAAGGGAGGCCATACCACCAGCATTTG-----CACACCAG--------------CAGCGGCAGAAGAGTCTGTGCCGGTGTGCACCCTACCGGGTAGGGA Cluster: [ ] Orangutan: GAAGTGAGGCCACGCTACCAGCATTTGCACAC-----CAGCAGTGGCAGAAGAG--------------TCT--------GTGCACCCTAC-CGGTGGGGA Human > Gorilla --------------- chr15:35754704-35754720 Template switch process: F1: L GGATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCAG 1 F3: 4 GGTGTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCC R RF: GGATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCAGCATTTGCACACCAGCAGCGGCAGAAGAGTCTGTGCCGGTGTGCACCCTACCGGGTAGGGAATTCAAGCAGCTCTCC RR: CCTACTCACGGGTATCTCCTCTTCCCTCCGGTATGGTGGTCGTAAACGTGTGGTCGTCGCCGTCTTCTCAGACACGGCCACACGTGGGATGGCCCATCCCTTAAGTTCGTCGAGAGG F2: 3 TCGTCGCCGTCTTCTCA 2 Unidirectional alignment (log-probability: -50.6) GATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCAgactcttctgccGC-------------------------------TGCtGGTGTGCACCCTACCGGGTgGGGAATTCAAGCAGCTCTCC GATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCA------------GCATTTGCACACCAGCAGCGGCAGAAGAGTCTGTGCCGGTGTGCACCCTACCGGGTAGGGAATTCAAGCAGCTCTCC Template switch alignment (log-probability: -23.4) GATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCAG|ACTCTTCTGCCGCTGCT|GGTGTGCACCCTACCGGGTgGGGAATTCAAGCAGCTCTCC GATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCAG|ACTCTTCTGCCGCTGCT|GGTGTGCACCCTACCGGGTAGGGAATTCAAGCAGCTCTCC Chimp > Gorilla --------------- chr15:35754704-35754723 Template switch process: F1: L GGATGAGTGCCCATAGAGGAGAAGGGAGGCCATACCACCAG 1 F3: 4 GTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCCTCC R RF: GGATGAGTGCCCATA---GAGAAGGGAGGCCATACCACCAGCATTTGCACACCAGCAGCGGCAGAAGAGTCTGTGCCGGCGTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCCTCC RR: CCTACTCACGGGTAT---CTCTTCCCTCCGGTATGGTGGTCGTAAACGTGTGGTCGTCGCCGTCTTCTCAGACACGGCCGCACGTGGGATGGCCCACCCCTTAAGTTCGTCGAGAGGAGG F2: 3 TGGTCGTCGCCGTCTTCTCA 2 Unidirectional alignment (log-probability: -64.6) GATGAGTGCCCATAGaggAGAAGGGAGGCCATACCACCAgactcttctgccGC-------------------------------TGCtGGtGTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCCTCC GATGAGTGCCCATAG---AGAAGGGAGGCCATACCACCA------------GCATTTGCACACCAGCAGCGGCAGAAGAGTCTGTGCCGGCGTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCCTCC Template switch alignment (log-probability: -32.3) GATGAGTGCCCATAgagGAGAAGGGAGGCCATACCACCAG|ACTCTTCTGCCGCTGCTGGT|GTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCCTCC GATGAGTGCCCATA---GAGAAGGGAGGCCATACCACCAG|ACTCTTCTGCCGCTGCTGGT|GTGCACCCTACCGGGTGGGGAATTCAAGCAGCTCTCCTCC ========== Event 1177 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGAGGCAACCCCAACATTTCAGCC----------------------------------CCTGGTGGCCAGGGGTCCCTGTTGGGCCCCC ↓ 4 3 2 Chimp: TGAGGCAACCCCAACATTTCAGCC-----------------CCTGTGACCACCCAGCCCCTGGTGGCCAGTGGTCCCTGTTGGGCCCCC Gorilla: TGAGGCAACCCCAACATTTCAGCCCCTGTGACCACCCAGCC-----------------CCTGGTGGCCAGTGGTCCCTGTTGGGCCCCC ↑ 4 3 2 Human: TGAGGCAACCCCAACATTTCAGCC----------------------------------CCTGGTGGCCAGGGGTCCCTGTTGGGCCCCC Cluster: [ ] Orangutan: TGAGGCAACCCCAACATTTCAGCCTCTGTGACCACCCAGCC-----------------CCTGGTGGCCAGTGGTCCCTGTTGGGCCCCC Human > Chimp ------------- chr15:35401246-35401253 Template switch process: F1: L GGAGCCACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTG 1 F3: 4 CAGCCCCTGGTGGCCAGTGGTCCCTGTTGGGCCCCCTCAGGAGGT R RF: GGAGCCACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTGGTGGCCAGGGGTCCCTGTTGGGCCCCCTCAGGAGGT RR: CCTCGGTGACAGTGGAGACTCCGTTGGGGTTGTAAAGTCGGGGACCACCGGTCCCCAGGGACAACCCGGGGGAGTCCTCCA F2: 3 CCACCAGT 2 Unidirectional alignment (log-probability: -41.4) CACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCctgtgaccacccagcccCTGGTGGCCAGtGGTCCCTGTTGGGCCCCCTCAG CACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCC-----------------CTGGTGGCCAGGGGTCCCTGTTGGGCCCCCTCAG Template switch alignment (log-probability: -28.4) CACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTG|TGaCCACC|CAGCCCCTGGTGGCCAGtGGTCCCTGTTGGGCCCCCTCAG CACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTG|TGGCCACC|CAGCCCCTGGTGGCCAGGGGTCCCTGTTGGGCCCCCTCAG Human > Gorilla --------------- chr15:35465868-35465875 Template switch process: F1: L GGAGCCACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTG 1 F3: 4 CAGCCCCTGGTGGCCAGTGGTCCCTGTTGGGCCCCCTCAGGAGGT R RF: GGAGCCACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTGGTGGCCAGGGGTCCCTGTTGGGCCCCCTCAGGAGGT RR: CCTCGGTGACAGTGGAGACTCCGTTGGGGTTGTAAAGTCGGGGACCACCGGTCCCCAGGGACAACCCGGGGGAGTCCTCCA F2: 3 CCACCAGT 2 Unidirectional alignment (log-probability: -40.8) CACTGTCACCTCTGAGGCAACCCCAACATTTcagcccctgtgaccaccCAGCCCCTGGTGGCCAGtGGTCCCTGTTGGGCCCCCTCAG CACTGTCACCTCTGAGGCAACCCCAACATTT-----------------CAGCCCCTGGTGGCCAGGGGTCCCTGTTGGGCCCCCTCAG Template switch alignment (log-probability: -28) CACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTG|TGaCCACC|CAGCCCCTGGTGGCCAGtGGTCCCTGTTGGGCCCCCTCAG CACTGTCACCTCTGAGGCAACCCCAACATTTCAGCCCCTG|TGGCCACC|CAGCCCCTGGTGGCCAGGGGTCCCTGTTGGGCCCCCTCAG ========== Event 1178 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GTGTGTGTTTGGGCTATAAAGCATTTTTAAAGTTTAAGTGTACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAAATGCTGTCTGGGAAGTCTTGGCAGTACACCTATC ↑ 3 2 4 1 Chimp: GTGTGTGTTTGGGCTATAAAGCATTTTTAAAGTTTAAGTGCACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCT--------------GGGAAGTCTTGGCAGTACACCTATC Gorilla: GTGTGTGTTTGGGCTATAAAGCATTTTTAAAGTTTAAGTGTACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAAATGCTGTCTGGGAAGTCTTGGCAGTACACCTATC Human: GTGTGTGTTTGGGCTATAAAGCATTTTTAAAGTTTAAGTGTACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAAATGCTGTCTGGGAAGTCTTGGCAGTACACCTATC Cluster: [ ] Orangutan: GTGTTAGTTTGGGCTATAAAGCATTTTTAAAGTTTAAGTGTACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAAATGCTGTCTGGGAAGTCTTGGCAGTACACCTATC Chimp > Human ------------- chr15:34612688-34612692 Template switch process: F1: L AGTGTACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAA 1 F3: 4 GTCTGGGAAGTCTTGGCAGTACACCTATCCCAAGGATCTAGTAT R RF: AGCATTTTTAAAGTTTAAGTGCACTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAAGTCTTGGCAGTACACCTATCCCAAGGATCTAGTAT RR: TCGTAAAAATTTCAAATTCACGTGAAACAAGGACTAGGACTTTCTAGACCTATAAAGACCCTTCAGAACCGTCATGTGGATAGGGTTCCTAGATCATA F2: 3 TCGTA 2 Unidirectional alignment (log-probability: -37) CTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAaatgctgtctgggaAGTCTTGGCAGTACACCTATCCCAAGGATCTA CTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGA--------------AGTCTTGGCAGTACACCTATCCCAAGGATCTA Template switch alignment (log-probability: -28.1) CTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAA|ATGCT|gTCTGGGAAGTCTTGGCAGTACACCTATCCCAAGGATCTA CTTTGTTCCTGATCCTGAAAGATCTGGATATTTCTGGGAA|ATGCT|TTCTGGGAAGTCTTGGCAGTACACCTATCCCAAGGATCTA ========== Event 1179 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTCTAAGGACAGCTTAGAGGCAGTTGCTGAGGCAGTTCAGAGGGGTGGAGCTGACCTGGAAGGGGTTTGAGGTCAGCGCTGGAGGTAGAAGGCTCAGCAGACATGGTTCTCAGACAGA Chimp: GCTGTAAGGACAGCT---TGGC------------AGTTCAGAGGGGTGGAGCTGACTTGGAAGGGGTTTGGGGTCAGCGCTGGAGGTAGAAGGCTCAGCAGACATGGTTCTCAGACAGA ↓ 4 1 3 2 Gorilla: GCTGTAAGGACAGCT---TGGCAGTTGCTGAGGCAGTTCAGAGGGGTGGAGCTGACCTGGAAGGAGTTTGGGGTCAGCGCTGGAGGTAGAAGGCTCAGCAGACATGGTTCTCAGACAGA Human: GCTCTAAGGACAGCTTAGAGGCAGTTGCTGAGGCAGTTCAGAGGGGTGGAGCTGACCTGGAAGGGGTTTGAGGTCAGCGCTGGAGGTAGAAGGCTCAGCAGACATGGTTCTCAGACAGA Cluster: [ ] Orangutan: GCTGTAAGGACAGCT---TGGCAGTTGCTGAGGCAGTTCAGAGGGGTGGAGCTGACCTGGAAGGGGTTTGCGGTCAGCGCTGGAGGTAGAAGGCTCAGCAGACATGGTTCGCAGACAGA Chimp > Gorilla --------------- chr15:47982292-47982296 Template switch process: F1: L TTAATTTTCACCCATGAGCTCTGCTGTAAGGACAGCTTGGCAGTT 1 F3: 4 GGCAGTTCAGAGGGGTGGAGCTGACCTGGAAGGAGTTTGGGGT R RF: TTAATTTTCACCCATGAGCTCTGCTGTAAGGACAGCTTGGCAGTTCAGAGGGGTGGAGCTGACTTGGAAGGGGTTTGGGGTCAGCGCTGGAGGTAGAAGGCTCAGC RR: AATTAAAAGTGGGTACTCGAGACGACATTCCTGTCGAACCGTCAAGTCTCCCCACCTCGACTGAACCTTCCCCAAACCCCAGTCGCGACCTCCATCTTCCGAGTCG F2: 3 AGTCG 2 Unidirectional alignment (log-probability: -39.2) TTTCACCCATGAGCTCTGCTGTAAGGACAGCTTGgcagttgctgagGCAGTTCAGAGGGGTGGAGCTGACcTGGAAGGaGTTTGG TTTCACCCATGAGCTCTGCTGTAAGGACAGCTTG------------GCAGTTCAGAGGGGTGGAGCTGACTTGGAAGGGGTTTGG Template switch alignment (log-probability: -27.6) TTTCACCCATGAGCTCTGCTGTAAGGACAGCTTGGCAGTT|GCTGA|GGCAGTTCAGAGGGGTGGAGCTGACcTGGAAGGaGTTTGG TTTCACCCATGAGCTCTGCTGTAAGGACAGCTTGGCAGTT|GCTGA|GGCAGTTCAGAGGGGTGGAGCTGACTTGGAAGGGGTTTGG ========== Event 1180 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AATGGAAATTCCACTCTGACAGTGACGGCAGCTGGTGGTACAAAATTGGGCGGTGTC--------------TCCGCCTAGGCAGGAAAAACACCAGCTCCAGGCAGTCAGCCGTTGCCTTACCTGGAGGGCTGATCAACCGTCACAAATGTGTTTAAAATTTCTA ↑ 1 4 3 2 Chimp: AATGGAAATTCCACTCTGACATTGACAGCAGCTGGTGGTACAA--------------AATTGGGCGGTGTCTCCGCCTAGGCAGGAAAAACACCAGCTCCAGGCAGTCAGCCGTTGCCTTACCTGGAGAGCTGATCAACCGTCACAAATGTGTTTAAAATTTCTA Gorilla: AATGGAAATTCCACTCTGACAGTGACAGCAGCTGGTGGTATAAAATTGGGCGGTGTC--------------TCTGCCTAGGCAGGAAAAACACCAGCTCCAGGCAGTCAGCCGTTGCCTTACCTGGAGAGCTGATCAACTGTCACAAATGTGTTTAAAATTTCTA Human: AATGGAAATTCCACTCTGACAGTGACGGCAGCTGGTGGTACAAAATTGGGCGGTGTC--------------TCCGCCTAGGCAGGAAAAACACCAGCTCCAGGCAGTCAGCCGTTGCCTTACCTGGAGGGCTGATCAACCGTCACAAATGTGTTTAAAATTTCTA Cluster: [ ] Orangutan: AATGGAAATTCCACTCTGACAGTGACAGCAGCTGGTGGTACAAAATTGGGCGGTGTC--------------TCTGCCTAGGCAGGAAAAACACCAGCTCCAGGTAGTCAGCCATTGCCTTACCTGGAGGGCTGATCAACCGTCACAAATATGTTTAAAATTTCTA Chimp > Human ------------- chr15:68805262-68805267 Template switch process: F1: L ACTGCTATTTCAGAAACACCAATGGAAATTCCACTCTGACA 1 F3: 4 GCAGCTGGTGGTACAAAATTGGGCGGTGTC R RF: ACTGCTATTTCAGAAACACCAATGGAAATTCCACTCTGACATTGACAGCAGCTGGTGGTACAAAATTGGGCGGTGTCTCCGCCTAGGCAGGAAAAACACCAGCTCCAGGCAGTCAGCCGTTGCCTTACCTGGAGAGCTGATCAACCGTCAC RR: TGACGATAAAGTCTTTGTGGTTACCTTTAAGGTGAGACTGTAACTGTCGTCGACCACCATGTTTTAACCCGCCACAGAGGCGGATCCGTCCTTTTTGTGGTCGAGGTCCGTCAGTCGGCAACGGAATGGACCTCTCGACTAGTTGGCAGTG F2: 3 GCAGTG 2 Unidirectional alignment (log-probability: -25.6) CTGCTATTTCAGAAACACCAATGGAAATTCCACTCTGACAgTGACgGCAGCTGGTGGTACAAAATTGGGCGGtgtc CTGCTATTTCAGAAACACCAATGGAAATTCCACTCTGACATTGACAGCAGCTGGTGGTACAAAATTGGGCGG---- Template switch alignment (log-probability: -15.8) CTGCTATTTCAGAAACACCAATGGAAATTCCACTCTGACA|GTGACG|GCAGCTGGTGGTACAAAATTGGGCGGTGTC CTGCTATTTCAGAAACACCAATGGAAATTCCACTCTGACA|GTGACG|GCAGCTGGTGGTACAAAATTGGGCGGTGTC ========== Event 1181 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTTAAATACTGCCTCCACACCCCCTCTACCCCCcacacacatacacaca----------cacacGTGTGTGTGTTT-CGGGGCTGCTCAGGAGG Chimp: TATTTAAAAACTGCCTCcacaccccctctaccccccacacacatacacaca----------cacacGTGTGTGTGTTTCAGGGGCTGCTCAGGAGG Gorilla: TATTTAAATACTGCCTCCACAACCCCTCTAACCCCcacacacatacacaca--------------------cGTGTTTCAGGGGCTGCTCAGGAGG ↓ 3 14 2 Human: TATTTAAATACTGCCTCCACACCCCCTCTACCCCCcacacacatacacaca----------cacacGTGTGTGTGTTT-CGGGGCTGCTCAGGAGG Cluster: [ ] Orangutan: TATTTAAATACTGCCTCCACACCCCCGCTACCCCCcacacacatacacacacacacGTGTG----------TGTGTTTCAGGGGCTGCTCAGGAGG Gorilla > Human --------------- chr15:68843898-68843907 Template switch process: F1: L AGTTTTGTTCTCCTTCATTGTATTTAAATACTGCCTCCACACCCCCTCTACCCCCCACACACATACACACAC 1 F3: 4 GTGTTTCG R RF: AGTTTTGTTCTCCTTCATTGTATTTAAATACTGCCTCCACAACCCCTCTAACCCCCACACACATACACACACGTGTTTCA RR: TCAAAACAAGAGGAAGTAACATAAATTTATGACGGAGGTGTTGGGGAGATTGGGGGTGTGTGTATGTGTGTGCACAAAGT F2: 3 TGTGTGCACA 2 Unidirectional alignment (log-probability: -46.1) GCCTCCACAcCCCCTCTAcCCCCCACACACATACACACACacacgtgtgtGTGTTTC-G GCCTCCACAACCCCTCTAACCCCCACACACATACACACAC----------GTGTTTCAG Template switch alignment (log-probability: -33.5) GCCTCCACAcCCCCTCTAcCCCCCACACACATACACACAC|ACACGTGTGT|GTGTTTCg GCCTCCACAACCCCTCTAACCCCCACACACATACACACAC|ACACGTGTGT|GTGTTTCA ========== Event 1182 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ---------TTTAATGTCAGTCTCTCTCACCTACTCTTTACACAGTGTG-GACCAGTGGTCTGCTTAAAG-----AGTAGTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACTATGTAAAGAGTAGGTGAGAGA-----------------------------------------------------------GGCTGACATTAAAGAAGTCTTA ↓ 1 3 4 2 Chimp: ---------TTTAATGTCAGCCTCTCTCACCTACTCTTTACATAGTGTG-GACTA-----CTCTTTAAGCAGACCACTGGTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACTATGTAAAGAGTAGGTGAGAGA-----------------------------------------------------------GGCTGACATTAAAGAAGTCTTA Gorilla: ---------TTTAATGTCAGCCTCTCTCACCTACTCTTTACATAGTGTG-GACCAGTGGTCTGCTTAAAG-----AGTAGTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACTATGTAAAGAGTAGGTGAGAGA-----------------------------------------------------------GGCTGACATTAAAGAAGTCTTA Human: ---------TTTAATGTCAGTCTCTCTCACCTACTCTTTACACAGTGTG-GACCAGTGGTCTGCTTAAAG-----AGTAGTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACTATGTAAAGAGTAGGTGAGAGA-----------------------------------------------------------GGCTGACATTAAAGAAGTCTTA Cluster: [ ] Orangutan: ctgcctggaattgatgcctgtcacttttgctcacttttta----g----tgacc-----------------------------aaaacaagccacacgacaatctgtcttcaaggggacagacagtgcaagtctgtcactggtttctgaagacaacaaggtatcaggtgagcagtgctaTATTCTACAGGAAATGAATCATTCATGGCTTGGACTCCTTAATGAGCATAATGAACTTTGAATTATATTAGTAATTGCTATTATAAATAATAATGTGTAATTTCCTTTGTATTTTTTCTAGTACAGCATTCTTTATACCAGAATTATACAAAGACTCTGAAAGTGAGTAAATGTGTAAGCTAATATTTTCTTTTAGGTGGGTGGAAAACCATAatttattcattcaacaggtattaactaagactta Human > Chimp ------------- chr15:31911523-31911575 Template switch process: F1: L TAATGTCAG 1 F3: 4 GTCCACACTATGTAAAGAGTAGGTGAGAGAGGCTGACATT R RF: TAATGTCAGTCTCTCTCACCTACTCTTTACACAGTGTGGACCAGTGGTCTGCTTAAAGAGTAGTCCACACTATGTAAAGAGTAGGTGAGAGAGGCTGACATT RR: ATTACAGTCAGAGAGAGTGGATGAGAAATGTGTCACACCTGGTCACCAGACGAATTTCTCATCAGGTGTGATACATTTCTCATCCACTCTCTCCGACTGTAA F2: 3 GTCACCAGACGAATTTCTCATCAGGTGTGATACATTTCTCATCCACTCTCTCC 2 Unidirectional alignment (log-probability: -61.4) TAATGTCAGcCTCTCTCACCTACTCTTTACAtAGTGTGGAC-------------------TActctttaagcagaccactgGTCCACACTATGTAAAGAGTAGGTGAGAGAGGCTGACATT TAATGTCAGTCTCTCTCACCTACTCTTTACACAGTGTGGACCAGTGGTCTGCTTAAAGAGTA-------------------GTCCACACTATGTAAAGAGTAGGTGAGAGAGGCTGACATT Template switch alignment (log-probability: -21.2) TAATGTCAG|CCTCTCTCACCTACTCTTTACATAGTGTGGACTACTCTTTAAGCAGACCACTG|GTCCACACTATGTAAAGAGTAGGTGAGAGAGGCTGACATT TAATGTCAG|CCTCTCTCACCTACTCTTTACATAGTGTGGACTACTCTTTAAGCAGACCACTG|GTCCACACTATGTAAAGAGTAGGTGAGAGAGGCTGACATT ========== Event 1183 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGCAGCTTGTAGAAGGCCGACCAGGTGTCAGACCCTTGAA-----TGTACTCTTTACACAGATTGACTCT Chimp: GTGCAGCTTGTGGAAGGCCGACCAGGTATCAGACCCTTGAA-----TGTACTCTTTACACAGATTGACTCT Gorilla: GTGCAGCTTGTGGAAGGCCGACCAGGTGTCAGACCCTTGACACCTGGTCAGTCTTTACACAGATTGACTCT ↑ 3 2 1 4 Human: GTGCAGCTTGTAGAAGGCCGACCAGGTGTCAGACCCTTGAA-----TGTACTCTTTACACAGATTGACTCT Cluster: [ ] Orangutan: GTGCAGtttgtggaaggccgactaggtgtcagacccttgaa-----tgtactctttacacagattgactct Human > Gorilla --------------- chr15:31809245-31809253 Template switch process: F1: L CGTGCAGCTTGTGGAAGGCCGACCAGGTGTCAGACCCTTGA 1 F3: 4 AGTCTTTACACAGATTGACTCTGATTCTCACAACTGTCAAGG R RF: CGTGCAGCTTGTAGAAGGCCGACCAGGTGTCAGACCCTTGAATGTACTCTTTACACAGATTGACTCTGATTCTCACAACTGTCAAGG RR: GCACGTCGAACATCTTCCGGCTGGTCCACAGTCTGGGAACTTACATGAGAAATGTGTCTAACTGAGACTAAGAGTGTTGACAGTTCC F2: 3 CTGGTCCAC 2 Unidirectional alignment (log-probability: -40.8) GTGCAGCTTGTgGAAGGCCGACCAGGTGTCAGACCCTTG-----ACacctggtcagTCTTTACACAGATTGACTCTGATTCTCACAACTGTCAA GTGCAGCTTGTAGAAGGCCGACCAGGTGTCAGACCCTTGAATGTAC----------TCTTTACACAGATTGACTCTGATTCTCACAACTGTCAA Template switch alignment (log-probability: -28) GTGCAGCTTGTgGAAGGCCGACCAGGTGTCAGACCCTTGA|CACCTGGTC|AgTCTTTACACAGATTGACTCTGATTCTCACAACTGTCAA GTGCAGCTTGTAGAAGGCCGACCAGGTGTCAGACCCTTGA|CACCTGGTC|ACTCTTTACACAGATTGACTCTGATTCTCACAACTGTCAA ========== Event 1184 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCCAAAGAGGAGGCTCACA--------GTAGTCCTGGACAAGTTTAGGATGCACACAATGAA Chimp: ATTCCAAAGAGGAGGCTCACAACTTGTCCAGAGTCCTGGACAAGTTTAAGATGCACACAATGAA ↑ 1 4 3 2 Gorilla: ATTCCAAAGAGGAGGCTCACA--------ATAGTCCTGGACAAGTTTAGGATGCACACAATGAA Human: ATTCCAAAGAGGAGGCTCACA--------GTAGTCCTGGACAAGTTTAGGATGCACACAATGAA Cluster: [ ] Orangutan: ATTGCAAAGAGGAGGCTCACA--------ATAGTCCTGGACAAGTTTAGGATGCACACAATGAA Gorilla > Chimp --------------- chr15:32123689-32123697 Template switch process: F1: L TTTAGGGGTGTCCTACACTTATTCCAAAGAGGAGGCTCACAA 1 F3: 4 AGTCCTGGACAAGTTTAAGATGCACACAATGAAACATGAA R RF: TTTAGGGGGGTCCTACACTTATTCCAAAGAGGAGGCTCACAATAGTCCTGGACAAGTTTAGGATGCACACAATGAAACATGAA RR: AAATCCCCCCAGGATGTGAATAAGGTTTCTCCTCCGAGTGTTATCAGGACCTGTTCAAATCCTACGTGTGTTACTTTGTACTT F2: 3 GACCTGTTC 2 Unidirectional alignment (log-probability: -39) TAGGGGtGTCCTACACTTATTCCAAAGAGGAGGCTCACAacttgtccAgAGTCCTGGACAAGTTTAaGATGCACACAATGAAACATGAA TAGGGGGGTCCTACACTTATTCCAAAGAGGAGGCTCACA--------ATAGTCCTGGACAAGTTTAGGATGCACACAATGAAACATGAA Template switch alignment (log-probability: -27.9) TAGGGGtGTCCTACACTTATTCCAAAGAGGAGGCTCACAA|CTTGTCCAG|AGTCCTGGACAAGTTTAaGATGCACACAATGAAACATGAA TAGGGGGGTCCTACACTTATTCCAAAGAGGAGGCTCACAA|CTTGTCCAG|AGTCCTGGACAAGTTTAGGATGCACACAATGAAACATGAA ========== Event 1185 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCACAGGCAGTAGAAGGCACC----TGGCTAACACACGGTGCAGATTCTGGGACAGAAACCTTCAACGGCCCCTCAGTGCCTATGCAGTATAGAGTGA Chimp: GCACAGGCAGTAGGAGGCACC----TGGCTAACACACGGTGCAGATTCTGGGACAGAAACCTTCAACGGCCCCTCAGTGCCTATGCAATATAGAGTGA ↓ 1 4 3 2 Gorilla: GCACAGGCAGTAGGAGGCACC--------TACTGCACGATGCAGATTCTGGGACAGAAACCTCCAACGGCCCCTCAGTGCCTATGCAGTATACAGTGA Human: GCACAGGCAGTAGAAGGCACC----TGGCTAACACACGGTGCAGATTCTGGGACAGAAACCTTCAACGGCCCCTCAGTGCCTATGCAGTATAGAGTGA Cluster: [ ] Orangutan: GCACAGGCAGTAGGAGGCACCTGGC----TAACACACGGTGCAGATTCTGGGACAGAAACCTCCAATGGCCCTTAAGTGCCTATGCAGTACAGAGTGA Chimp > Gorilla --------------- chr15:32238574-32238577 Template switch process: F1: L TGGCCATCCCAGCTCCTCATGCACAGGCAGTAGGAGGCACCT 1 F3: 4 CACGATGCAGATTCTGGGACAGAAACCTCCAACGGCCCCTCAGTG R RF: TGGCCATCCCAGCTCCTCATGCACAGGCAGTAGGAGGCACCTGGCTAACACACGGTGCAGATTCTGGGACAGAAACCTTCAACGGCCCCTCAGTG RR: ACCGGTAGGGTCGAGGAGTACGTGTCCGTCATCCTCCGTGGACCGATTGTGTGCCACGTCTAAGACCCTGTCTTTGGAAGTTGCCGGGGAGTCAC F2: 3 GTCA 2 Unidirectional alignment (log-probability: -36.4) GCCATCCCAGCTCCTCATGCACAGGCAGTAGGAGGCACCT-------ActgCACGaTGCAGATTCTGGGACAGAAACCTcCAACGGCCCCT GCCATCCCAGCTCCTCATGCACAGGCAGTAGGAGGCACCTGGCTAACA---CACGGTGCAGATTCTGGGACAGAAACCTTCAACGGCCCCT Template switch alignment (log-probability: -27.4) GCCATCCCAGCTCCTCATGCACAGGCAGTAGGAGGCACCT|ACTG|CACGaTGCAGATTCTGGGACAGAAACCTcCAACGGCCCCT GCCATCCCAGCTCCTCATGCACAGGCAGTAGGAGGCACCT|ACTG|CACGGTGCAGATTCTGGGACAGAAACCTTCAACGGCCCCT ========== Event 1186 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GAACAGAATTGACTCCCAGGCCAC-----CCTCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTTC Chimp: GAACAGAATTGACTCCCAGGCCAC-----CCTCCAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTTC Gorilla: GAACAGAATTGACTCCCAGGCTCCTATAAAGTCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTTC ↑ 1 4 3 2 Human: GAACAGAATTGACTCCCAGGCCAC-----CCTCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTTC Cluster: [ ] Orangutan: GAACAGAATTGACTCCCACGCCAC-----CCTCTAGCTCCTGACTTCATAGGGCTCAACTCAGTTGTGGTTC Human > Gorilla --------------- chr15:31485222-31485230 Template switch process: F1: L TCCTCTGCTTGAGATTCCCAGAACAGAATTGACTCCCAGGCT 1 F3: 4 TCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTT R RF: TCCTCTGCTTGAGATTCCCAGAACAGAATTGACTCCCAGGCCACCCTCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTT RR: AGGAGACGAACTCTAAGGGTCTTGTCTTAACTGAGGGTCCGGTGGGAGATCGAGGACTGAAATATCCCGAGTCGAGTCAACACCAA F2: 3 GAAATATCC 2 Unidirectional alignment (log-probability: -35.3) CTCTGCTTGAGATTCCCAGAACAGAATTGACTCCCAGG-----CtcctataaagTCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTT CTCTGCTTGAGATTCCCAGAACAGAATTGACTCCCAGGCCACCC----------TCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTT Template switch alignment (log-probability: -22.4) CTCTGCTTGAGATTCCCAGAACAGAATTGACTCCCAGGCt|CCTATAAAG|TCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTT CTCTGCTTGAGATTCCCAGAACAGAATTGACTCCCAGGCC|CCTATAAAG|TCTAGCTCCTGACTTTATAGGGCTCAGCTCAGTTGTGGTT ========== Event 1187 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GGATGAAATACAGGTGGTTGAAAACTTAACCACCTATAAA---------------------------------------------------------------ACTTAATTATACTTGGACAGGTATAA ↓ 3 4 2 1 Chimp: GGATGAAATATAGGTGGTTGAAAACTTAACTACCTATAAA--------------------------------ACTTAAGGTTAAGTTTTCAACCACCTATAAAACTTAATTATACTTGGACAGGTATAA Gorilla: --------------------------------------------------------------------------------------------------------------------------------- Human: GGATGAAATACAGGTGGTTGAAAACTTAACCACCTATAAA---------------------------------------------------------------ACTTAATTATACTTGGACAGGTATAA Cluster: [ ] Orangutan: GGATGAAATATAGGTGGTTGAAAACTTAACCACCTATAAAACTTAAGGTTAAGTTTTCAACCCACCTATAAA-------------------------------ACTTAATTATACTTGGACAGGTATAA Human > Chimp ------------- chr15:53539825-53539836 Template switch process: F1: L GGGATGAAATATAGGTGGTTGAAAACTTAACTACCTATAAAACTTAA 1 F3: 4 AACCACCTATAAAACTTAATTATACTTGGACAGGTATAATTAAAGAATCCTGA R RF: GGGATGAAATACAGGTGGTTGAAAACTTAACCACCTATAAAACTTAATTATACTTGGACAGGTATAATTAAAGAATCCTGA RR: CCCTACTTTATGTCCACCAACTTTTGAATTGGTGGATATTTTGAATTAATATGAACCTGTCCATATTAATTTCTTAGGACT F2: 3 CTTTTGAATTGG 2 Unidirectional alignment (log-probability: -61.5) AATAtAGGTGGTTGAAAACTTAactacctataaaacttaaggttaagttttcaACCACCTATAAAACTTAATTATACTTGGACAGGTATAAT AATACAGGTGGTTGAAAACTTA-------------------------------ACCACCTATAAAACTTAATTATACTTGGACAGGTATAAT Template switch alignment (log-probability: -29.1) AATAtAGGTGGTTGAAAACTTAACtACCTATAAAACTTAA|GGTTAAGTTTTC|AACCACCTATAAAACTTAATTATACTTGGACAGGTATAAT AATACAGGTGGTTGAAAACTTAACCACCTATAAAACTTAA|GGTTAAGTTTTC|AACCACCTATAAAACTTAATTATACTTGGACAGGTATAAT ========== Event 1188 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGAAGTCCAAGCACCAAAAC-ACTGGCCAGGTTGGGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATC ↓ 1 4 3 2 Chimp: CAGAAGTCCAAGCACCAAAACATCTGTACA-----GGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATC ↑ 1 4 3 2 Gorilla: CAGAAGTCCAAGCACCAAAAC-ACTGGCCAGGTTGGGTTGCACACCTGTACAGATGCAGGACCAGTGGCCCATC Human: CAGAAGTCCAAGCACCAAAAC-ACTGGCCAGGTTGGGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATC Cluster: [ ] Orangutan: CAGAAGTCCAAGCCCTAAAAC-ACTGGCCAGGTTGGGTTGCACACCTGTACAGACGCAGGGCCACTGGCCCATC Human > Chimp ------------- chr15:30057934-30057941 Template switch process: F1: L GGCTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACA 1 F3: 4 GGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC R RF: GGCTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACACTGGCCAGGTTGGGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC RR: CCGACTGAAAGACTCATCTTGTCTTCAGGTTCGTGGTTTTGTGACCGGTCCAACCCGACGTGTGGACATGTCTACGTCCTGGTCACCGGGTAGG F2: 3 ACATGTCT 2 Unidirectional alignment (log-probability: -33.3) CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAacatctgtACA------------GGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAA--------ACACTGGCCAGGTTGGGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC Template switch alignment (log-probability: -16.3) CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACA|TCTGTACA|GGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACA|TCTGTACA|GGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC Gorilla > Chimp --------------- chr15:30057934-30057941 Template switch process: F1: L GGCTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACA 1 F3: 4 GGCTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCCTCT R RF: GGCTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACACTGGCCAGGTTGGGTTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCCTCT RR: CCGACTGAAAGACTCATCTTGTCTTCAGGTTCGTGGTTTTGTGACCGGTCCAACCCAACGTGTGGACATGTCTACGTCCTGGTCACCGGGTAGGAGA F2: 3 ACATGTCT 2 Unidirectional alignment (log-probability: -35.4) CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACatctgtACaGGC----------TGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAAC------ACTGGCCAGGTTGGGTTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC Template switch alignment (log-probability: -22.4) CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACA|TCTGTACA|GGcTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC CTGACTTTCTGAGTAGAACAGAAGTCCAAGCACCAAAACA|TCTGTACA|GGTTGCACACCTGTACAGATGCAGGACCAGTGGCCCATCC ========== Event 1189 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCCTTCTCCTTCATATTTAGG--------------------TCGTGTTAGCTCCTGGACAGTCCTCCAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACC Chimp: CCTCCTTCTCCTTCATATTTAGG--------------------TTGTGTTAGCTCCTGGACAGTCCTCCAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACC ↓ 1 4 3 2 Gorilla: CCTCCTTCTCCTTCATATTTATA----------------------------------------TCTGACAGTCCCACCTGTCAGATCTCTCGTTCCCCTCCTTACC ↑ 1 4 3 2 Human: CCTCCTTCTCCTTCATATTTAGG--------------------TCGTGTTAGCTCCTGGACAGTCCTCCAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACC Cluster: [ ] Orangutan: CCTCCTTCTCCTTCATACTTAGGTTGTGTTAGCTCCTGGACAG--------------------TCCTCCAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACC Human > Gorilla --------------- chr1:170560845-170560851 Template switch process: F1: L TAACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAT 1 F3: 4 AGTCCCACCTGTCAGATCTCTCGTTCCCCTCCTTACCTC R RF: TAACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAGGTCGTGTTAGCTCCTGGACAGTCCTCCAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACCTC RR: ATTGTACAAAGTTTTGAGAAGGAGGAAGAGGAAGTATAAATCCAGCACAATCGAGGACCTGTCAGGAGGTCAGGGTGGACAGTCTAGAGAGAAAGGGGAGGAATGGAG F2: 3 CAGTCTA 2 Unidirectional alignment (log-probability: -37.6) ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTA---------------------------tatctgaCAGTCCCACCTGTCAGATCTCTCgTTCCCCTCCTTACCTC ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAGGTCGTGTTAGCTCCTGGACAGTCCTC-------CAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACCTC Template switch alignment (log-probability: -27.7) ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAt|ATCTGAC|AGTCCCACCTGTCAGATCTCTCgTTCCCCTCCTTACCTC ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAG|ATCTGAC|AGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACCTC Chimp > Gorilla --------------- chr1:170560845-170560850 Template switch process: F1: L TAACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAT 1 F3: 4 CAGTCCCACCTGTCAGATCTCTCGTTCCCCTCCTTACCTC R RF: TAACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAGGTTGTGTTAGCTCCTGGACAGTCCTCCAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACCTC RR: ATTGTACAAAGTTTTGAGAAGGAGGAAGAGGAAGTATAAATCCAACACAATCGAGGACCTGTCAGGAGGTCAGGGTGGACAGTCTAGAGAGAAAGGGGAGGAATGGAG F2: 3 AGTCTA 2 Unidirectional alignment (log-probability: -37.6) ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTA---------------------------tatctgaCAGTCCCACCTGTCAGATCTCTCgTTCCCCTCCTTACCTC ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAGGTTGTGTTAGCTCCTGGACAGTCCTC-------CAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACCTC Template switch alignment (log-probability: -27.5) ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAt|ATCTGA|CAGTCCCACCTGTCAGATCTCTCgTTCCCCTCCTTACCTC ACATGTTTCAAAACTCTTCCTCCTTCTCCTTCATATTTAG|ATCTGA|CAGTCCCACCTGTCAGATCTCTCTTTCCCCTCCTTACCTC ========== Event 1190 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCACACCCCAACTTGAAGGG---TGAATGAG------TACCCAGGCACTCCCTGCCTGGGTGCACACTGTGGCTCCTTGTCCCCCTC Chimp: CCCACACCCCAACTTGAAGGG---TGAATGAG------TACCCAGGCACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCCTC ↓ 1 4 3 2 Gorilla: CCCACACCCCAACTTGAAGGG------GTGTG------------CACACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCCTC ↑ 1 4 3 2 Human: CCCACACCCCAACTTGAAGGG---TGAATGAG------TACCCAGGCACTCCCTGCCTGGGTGCACACTGTGGCTCCTTGTCCCCCTC Cluster: [ ] Orangutan: CCCACACCCCAACTTGAAGGGTGA---ATGAGTACCCA------GGCACTCCCTGCCTGGGTGCACACTGGGGCTCCCTGTCCCCCTC Human > Gorilla --------------- chr15:53085033-53085039 Template switch process: F1: L CCTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGGG 1 F3: 4 CACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC R RF: CCTGTAAGTCCAGAGGAACCCCCACACCCCAACTTGAAGGGTGAATGAGTACCCAGGCACTCCCTGCCTGGGTGCACACTGTGGCTCCTTGTCCCCC RR: GGACATTCAGGTCTCCTTGGGGGTGTGGGGTTGAACTTCCCACTTACTCATGGGTCCGTGAGGGACGGACCCACGTGTGACACCGAGGAACAGGGGG F2: 3 ACGTGTG 2 Unidirectional alignment (log-probability: -41.1) CTGTAAGTCCAGAGGAgCCCCCACACCCCAACTTGAAGG---------------GGtgtgcaCACTCCCTGCCTGGGTGCACACTGTGGCTCCcTGTCCCCC CTGTAAGTCCAGAGGAACCCCCACACCCCAACTTGAAGGGTGAATGAGTACCCAGG------CACTCCCTGCCTGGGTGCACACTGTGGCTCCTTGTCCCCC Template switch alignment (log-probability: -27.7) CTGTAAGTCCAGAGGAgCCCCCACACCCCAACTTGAAGGG|GTGTGCA|CACTCCCTGCCTGGGTGCACACTGTGGCTCCcTGTCCCCC CTGTAAGTCCAGAGGAACCCCCACACCCCAACTTGAAGGG|GTGTGCA|CACTCCCTGCCTGGGTGCACACTGTGGCTCCTTGTCCCCC Chimp > Gorilla --------------- chr15:53085033-53085039 Template switch process: F1: L CCTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGGG 1 F3: 4 CACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC R RF: CCTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGGGTGAATGAGTACCCAGGCACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC RR: GGACATTCAGGTCTCCTCGGGGGTGTGGGGTTGAACTTCCCACTTACTCATGGGTCCGTGAGGGACGGACCCACGTGTGACACCGAGGGACAGGGGG F2: 3 ACGTGTG 2 Unidirectional alignment (log-probability: -30) CTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGG---------------GGtgtgcaCACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC CTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGGGTGAATGAGTACCCAGG------CACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC Template switch alignment (log-probability: -16.6) CTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGGG|GTGTGCA|CACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC CTGTAAGTCCAGAGGAGCCCCCACACCCCAACTTGAAGGG|GTGTGCA|CACTCCCTGCCTGGGTGCACACTGTGGCTCCCTGTCCCCC ========== Event 1191 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGCCAGGAGCCCTGGGGAGCCAATGGGGCT--------AGAGATGGGTGAGTGACAGCCAC Chimp: GTGCCAGAAGCCCTGGGGAGACAATGGGGCT--------AGAGATGGGTGAGTGACAGCCAC Gorilla: GTGCCAGGAGCCTTGGGGAGCCAATGGGGCTCCCCATTGGCAGATGGGTGAGTGACAGCCAC ↑ 3 2 1 4 Human: GTGCCAGGAGCCCTGGGGAGCCAATGGGGCT--------AGAGATGGGTGAGTGACAGCCAC Cluster: [ ] Orangutan: GTGCCAGAAGCCCTGGGGAGCCAATGGGGCT--------AGAGATGGGTGAGTGACAGCCAC Human > Gorilla --------------- chr15:26982499-26982508 Template switch process: F1: L AGTGCAGAGTGTGCCAGGAGCCTTGGGGAGCCAATGGGGCT 1 F3: 4 AGATGGGTGAGTGACAGCCACATGCTACCCTGCTGAGAGG R RF: AGTGCAGAGTGTGCCAGGAGCCCTGGGGAGCCAATGGGGCTAGAGATGGGTGAGTGACAGCCACATGCTACCCTGCTGAGAGT RR: TCACGTCTCACACGGTCCTCGGGACCCCTCGGTTACCCCGATCTCTACCCACTCACTGTCGGTGTACGATGGGACGACTCTCA F2: 3 CGGTTACCCC 2 Unidirectional alignment (log-probability: -44.5) GTGCAGAGTGTGCCAGGAGCCtTGGGGAGCCAATGGGGCTccccattggcAGATGGGTGAGTGACAGCCACATGCTACCCTGCTGAGAGg GTGCAGAGTGTGCCAGGAGCCCTGGGGAGCCAATGGGGCT--------AGAGATGGGTGAGTGACAGCCACATGCTACCCTGCTGAGAGT Template switch alignment (log-probability: -28) GTGCAGAGTGTGCCAGGAGCCtTGGGGAGCCAATGGGGCT|CCCCATTGGC|AGATGGGTGAGTGACAGCCACATGCTACCCTGCTGAGAGg GTGCAGAGTGTGCCAGGAGCCCTGGGGAGCCAATGGGGCT|CCCCATTGGC|AGATGGGTGAGTGACAGCCACATGCTACCCTGCTGAGAGT ========== Event 1192 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGTGTTTGGAAGCTGCGTGTG--CACAGCAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAGATCGGACCCCAGG Chimp: ATGTGTTTGGAAGCTGCGTGTG--CACAGCAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAGATCGGACCCCAGG ↓ 1 4 3 2 Gorilla: ATGTGTTTGGAAGCTGCGTGTAGCTTCCAAAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAGATCGGACCCCAGG ↑ 1 4 3 2 Human: ATGTGTTTGGAAGCTGCGTGTG--CACAGCAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAGATCGGACCCCAGG Cluster: [ ] Orangutan: ATGTGTTTGGAAGCTGCGTGTG--CACAGCAGACTGGCTGTTGCTACTAACCCTTTGGAAGCTGATGGAGATCGGACCCCAGG Human > Gorilla --------------- chr15:55031070-55031078 Template switch process: F1: L ATAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT 1 F3: 4 AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG R RF: ATAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGTGCACAGCAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG RR: TATCCGCCCCTTCACGTCCCTACACAAACCTTCGACGCACACGTGTCGTCTGGGCGACAACGATGATTGGCAAACCTTCGACTACCTC F2: 3 AACCTTCGA 2 Unidirectional alignment (log-probability: -29.5) TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT----AGCttccaaAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGTGCACAGC------AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG Template switch alignment (log-probability: -16.9) TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT|AGCTTCCAA|AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT|AGCTTCCAA|AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG Chimp > Gorilla --------------- chr15:55031070-55031078 Template switch process: F1: L ATAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT 1 F3: 4 AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG R RF: ATAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGTGCACAGCAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG RR: TATCCGCCCCTTCACGTCCCTACACAAACCTTCGACGCACACGTGTCGTCTGGGCGACAACGATGATTGGCAAACCTTCGACTACCTC F2: 3 AACCTTCGA 2 Unidirectional alignment (log-probability: -29.5) TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT----AGCttccaaAGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGTGCACAGC------AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG Template switch alignment (log-probability: -16.9) TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT|AGCTTCCAA|AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG TAGGCGGGGAAGTGCAGGGATGTGTTTGGAAGCTGCGTGT|AGCTTCCAA|AGACCCGCTGTTGCTACTAACCGTTTGGAAGCTGATGGAG ========== Event 1193 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCGGGCAGGATGCTGTCATGCCACCTTCCCTTCTGCACGTCCTGACCTGGCATCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCA-TTGCCCCCACTCCCTGCCCAG Chimp: CCTCGGGCAGGATGCTGTCATGCCACCTTCCCTTCTGCACGTCCTGACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCA-TTGCCCCCACTCCCTGCCCAG ↓ 3 2 1 4 Gorilla: CCTCGGGCAGGATGCTGTCATGCCACCTTCCCTTCTGCACGTCCTGACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGTCTCC-------TGGGCATTTGCCCCCACTCCCTGCCCAG ↑ 3 2 1 4 Human: CCTCGGGCAGGATGCTGTCATGCCACCTTCCCTTCTGCACGTCCTGACCTGGCATCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCA-TTGCCCCCACTCCCTGCCCAG Cluster: [ ] Orangutan: CCTCGGGCAGGATGCTGCCTTGCCACCTTCTCTTCTGCACATCCTGACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGTCTCC-------TGGGCA-TTGCCCCCACTCCCTGCCCAG Human > Gorilla --------------- chr15:26439235-26439239 Template switch process: F1: L ACGTCCTGACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGTCTCCTG 1 F3: 4 TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT R RF: ATGCCACCTTCCCTTCTGCACGTCCTGACCTGGCATCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCATTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT RR: TACGGTGGAAGGGAAGACGTGCAGGACTGGACCGTAGGATGGATCAATTTCCAGGAGTCCGGAGGACGGGGGACTCGTAACGGGGGTGAGGGACGGGTCTGTGTCGACAGGAACAGGA F2: 3 TACGG 2 Unidirectional alignment (log-probability: -39.1) ACCTGGCAcCCTACCTAGTTAAAGGTCCTCAGGtCT-------CCTGgGCAtTTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT ACCTGGCATCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCA-TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT Template switch alignment (log-probability: -27.6) ACCTGGCAcCCTACCTAGTTAAAGGTCCTCAGGtCTCCTG|GGCAT|TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT ACCTGGCATCCTACCTAGTTAAAGGTCCTCAGGCCTCCTG|GGCAT|TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT Chimp > Gorilla --------------- chr15:26439235-26439239 Template switch process: F1: L ACGTCCTGACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGTCTCCTG 1 F3: 4 TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT R RF: ATGCCACCTTCCCTTCTGCACGTCCTGACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCATTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT RR: TACGGTGGAAGGGAAGACGTGCAGGACTGGACCGTGGGATGGATCAATTTCCAGGAGTCCGGAGGACGGGGGACTCGTAACGGGGGTGAGGGACGGGTCTGTGTCGACAGGAACAGGA F2: 3 TACGG 2 Unidirectional alignment (log-probability: -33.6) ACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGtCT-------CCTGgGCAtTTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT ACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGCCTCCTGCCCCCTGAGCA-TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT Template switch alignment (log-probability: -22.1) ACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGtCTCCTG|GGCAT|TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT ACCTGGCACCCTACCTAGTTAAAGGTCCTCAGGCCTCCTG|GGCAT|TTGCCCCCACTCCCTGCCCAGACACAGCTGTCCTTGTCCT ========== Event 1194 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ---------------AGGAATAAATGCTACCAAGTGCTTCTTTGGGATGAGAGGTCATCTTGACCTGCTGCCCAAGTGCTCGTTTGTGATGATGATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAG----CCTTGTAGCATTTACTGCAGAACAACTCAATCTGCA ↓ 3 2 1 4 Chimp: ---------------AGGAATAAATGCTACCAAGTGCTTCTCTGGGATGAGAGGTCATCTTGACCTGCTGCCCAAGTGCTCGTTTGTGATGATGATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAG--CACTTGGTAGCATTTATTGCAGAACAACTCAATCTGCA Gorilla: ---------------AGGAATAAATGCTACCAAGTGCTTCTTTGGGATGAGAGGTCATCTTGACCTGCTGCCCAAGTGCTCGTTTGTGATGATGATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGCA--CTTGGTAGCATTTATTGCAGAACAACTCAATCTGCA ↑ 3 2 1 4 Human: ---------------AGGAATAAATGCTACCAAGTGCTTCTTTGGGATGAGAGGTCATCTTGACCTGCTGCCCAAGTGCTCGTTTGTGATGATGATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAG----CCTTGTAGCATTTACTGCAGAACAACTCAATCTGCA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCA--CTTGGTAGTATTTATTGCAGAACAACTCGATCTGCA Human > Chimp ------------- chr15:59137754-59137769 Template switch process: F1: L GATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC 1 F3: 4 TGCAGAACAACTCAATCTGCAAGTTGTTT R RF: ATAAATGCTACCAAGTGCTTCTTTGGGATGAGAGGTCATCTTGACCTGCTGCCCAAGTGCTCGTTTGTGATGATGATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGCCTTGTAGCATTTACTGCAGAACAACTCAATCTGCAAGTTGTTC RR: TATTTACGATGGTTCACGAAGAAACCCTACTCTCCAGTAGAACTGGACGACGGGTTCACGAGCAAACACTACTACTACGTGAAACACTAGTTCTACTGGAGAGTAGGGTCTCTTCGGAACATCGTAAATGACGTCTTGTTGAGTTAGACGTTCAACAAG F2: 3 TATTTACGATGGTTCA 2 Unidirectional alignment (log-probability: -36) TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGCaCTTgGTAGCATTTAtTGCAGAACAACTCAATCTGCAAGTTGTTt TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC-CTT-GTAGCATTTACTGCAGAACAACTCAATCTGCAAGTTGTTC Template switch alignment (log-probability: -23.1) TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC|ACTTGGTAGCATTTAT|TGCAGAACAACTCAATCTGCAAGTTGTTt TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC|ACTTGGTAGCATTTAT|TGCAGAACAACTCAATCTGCAAGTTGTTC Human > Gorilla --------------- chr15:56899705-56899720 Template switch process: F1: L GATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC 1 F3: 4 TGCAGAACAACTCAATCTGCAAGTTGTTC R RF: ATAAATGCTACCAAGTGCTTCTTTGGGATGAGAGGTCATCTTGACCTGCTGCCCAAGTGCTCGTTTGTGATGATGATGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGCCTTGTAGCATTTACTGCAGAACAACTCAATCTGCAAGTTGTTC RR: TATTTACGATGGTTCACGAAGAAACCCTACTCTCCAGTAGAACTGGACGACGGGTTCACGAGCAAACACTACTACTACGTGAAACACTAGTTCTACTGGAGAGTAGGGTCTCTTCGGAACATCGTAAATGACGTCTTGTTGAGTTAGACGTTCAACAAG F2: 3 TATTTACGATGGTTCA 2 Unidirectional alignment (log-probability: -29.1) TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGCaCTTgGTAGCATTTAtTGCAGAACAACTCAATCTGCAAGTTGTTC TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC-CTT-GTAGCATTTACTGCAGAACAACTCAATCTGCAAGTTGTTC Template switch alignment (log-probability: -17.5) TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC|ACTTGGTAGCATTTAT|TGCAGAACAACTCAATCTGCAAGTTGTTC TGCACTTTGTGATCAAGATGACCTCTCATCCCAGAGAAGC|ACTTGGTAGCATTTAT|TGCAGAACAACTCAATCTGCAAGTTGTTC ========== Event 1195 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAGAATCCTGGGCAGATGGGGATTCTGCTTCCAAAAAGGAAGCAGCATCACCAcatccattcaacaaac ↑ 1 4 3 2 Chimp: CTAGAATCCTGGGCAGATGGGAGTCTTGAG-TCAAAAAGGAAGCAGCATCACCAcatccattcaacaaac Gorilla: CTAGAATCCTGGGCAGATGGGAGTCTTGAG-TCAAAAAGGAAGCAGCATCCCCAcatccattcaacaaac ↓ 1 4 3 2 Human: CTAGAATCCTGGGCAGATGGGGATTCTGCTTCCAAAAAGGAAGCAGCATCACCAcatccattcaacaaac Cluster: [ ] Orangutan: CTAGAATCCTGGGCAGATGGGAGTCTTGAG-TCAAAAAGGAAGCAGCATCACCAcatccattcaacaaac Chimp > Human ------------- chr15:78003892-78003902 Template switch process: F1: L TTGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG 1 F3: 4 CAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT R RF: TTGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGGAGTCTTGAGTCAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT RR: AACTGTGTTTCCCGGTGTTTGATCTTAGGACCCGTCTACCCTCAGAACTCAGTTTTTCCTTCGTCGTAGTGGTGTAGGTAAGTTGTTTGTA F2: 3 CTTCGTCTTAG 2 Unidirectional alignment (log-probability: -37.5) TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG----------gattctgcttcCAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGGAGTCTTGAGT-----------CAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT Template switch alignment (log-probability: -22.6) TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG|GATtCTGCTTC|CAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG|GATGCTGCTTC|CAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT Gorilla > Human --------------- chr15:78003892-78003902 Template switch process: F1: L TTGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG 1 F3: 4 CAAAAAGGAAGCAGCATCACCACATCCATTCAACAAACAT R RF: TTGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGGAGTCTTGAGTCAAAAAGGAAGCAGCATCCCCACATCCATTCAACAAACAT RR: AACTGTGTTTCCCGGTGTTTGATCTTAGGACCCGTCTACCCTCAGAACTCAGTTTTTCCTTCGTCGTAGGGGTGTAGGTAAGTTGTTTGTA F2: 3 CTTCGTCTTAG 2 Unidirectional alignment (log-probability: -42.1) TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG------GAtTctgcttcCAAAAAGGAAGCAGCATCaCCACATCCATTCAACAAACAT TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGGAGTCTTGAGT-------CAAAAAGGAAGCAGCATCCCCACATCCATTCAACAAACAT Template switch alignment (log-probability: -28.2) TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG|GATtCTGCTTC|CAAAAAGGAAGCAGCATCaCCACATCCATTCAACAAACAT TGACACAAAGGGCCACAAACTAGAATCCTGGGCAGATGGG|GATGCTGCTTC|CAAAAAGGAAGCAGCATCCCCACATCCATTCAACAAACAT ========== Event 1196 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTCAGGCTCACAATGGTGATGTAAAATCTTCATCTCCCAGCGCCATTTCAGTATACTTATAATAAAGAGGCAGCATGTAATT-TATTAATTTCATTATTGCTTCAAAATCA Chimp: ACTCAGGCTCACAATGGGGATGTAAAATCTTCATCTCCCAGCGCCATTTCAGTATACTTATAATAAAGAGGCAGCATGTAATT-TATTAATTTCATTATTGCTTCAAAATCA Gorilla: ACTCAGGCTCACAATGGTGATGTAAAATCTTCATCTCCTGGCGCCATTTCAGTATACTTAAATTAA-TAAATTACATGCTGCCTCTTTATTATCATTATTGCTTCAAAATCA ↓ 4 1 3 2 Human: ACTCAGGCTCACAATGGTGATGTAAAATCTTCATCTCCCAGCGCCATTTCAGTATACTTATAATAAAGAGGCAGCATGTAATT-TATTAATTTCATTATTGCTTCAAAATCA Cluster: [] Orangutan: ACTCAGGCTCACAATGGTGACGTAAAATCATCATCTCCCAGTGCCATTTCAGTATACTT--AATA----AATTACATGCTGCCTCTTTATTATCATTATTGCTTCAAAATCA Gorilla > Human --------------- chr15:23393347-23393361 Template switch process: F1: L TTTACTCAGGCTCACAATGGTGATGTAAAATCTTCATCTCCCAGCGCCATTTCAGTATACTTA 1 F3: 4 ATGTA R RF: TTTACTCAGGCTCACAATGGTGATGTAAAATCTTCATCTCCTGGCGCCATTTCAGTATACTTAAAATCTTCATCTCCTGGCGCCATTTCAGTATACTTAAATTAATAAATTACATGCTGCCTCTTTATTA RR: AAATGAGTCCGAGTGTTACCACTACATTTTAGAAGTAGAGGACCGCGGTAAAGTCATATGAATTTTAGAAGTAGAGGACCGCGGTAAAGTCATATGAATTTAATTATTTAATGTACGACGGAGAAATAAT F2: 3 CGACGGAGAAATAAT 2 Unidirectional alignment (log-probability: -56.7) TGTAAAATCTTCATCTCCcaGCGCCATTTCAGTATACTTAtaataaagaggcagcatgtA------------------ TGTAAAATCTTCATCTCCTGGCGCCATTTCAGTATACTTA-------------------AATTAATAAATTACATGCT Template switch alignment (log-probability: -28.3) TGTAAAATCTTCATCTCCcaGCGCCATTTCAGTATACTTA|TAATAAAGAGGCAGC|ATGTA TGTAAAATCTTCATCTCCTGGCGCCATTTCAGTATACTTA|TAATAAAGAGGCAGC|ATGTA ========== Event 1197 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTCACAAGGCTAAGAAACTTA-ACAGGG--CTGAT--CCGAGGAATGTTTAAGAACCTTCCTGGGCAGG Chimp: TTCACAAGGCTAAGAAACTTA-ACAGGG--CTGAT--CCGAGGAATGTTTAAGAACCTTCCTGGGCAGG ↓ 13 24 ↑ 13 24 Gorilla: TTCACAAGGCTAAGAAACTTAAACATTCCTCGGAT----CAGCCC-TGTTAAGAACCTTCCTGGGCAGG ↑ 13 24 Human: TTCACAAGGCTAAGAAACTTA-ACAGGG--CTGAT--CCGAGGAATGTTTAAGAACCTTCCTGGGCAGG Cluster: [ ] Orangutan: TTCACAAGGCTAAGAAACTTA-ACAGGG--CTGATCT--GAGGAATGTTTAAGAACCTTCCTGGGCAGG Human > Gorilla --------------- chr15:23512897-23512917 Template switch process: F1: L CTTTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA 1 F3: 4 TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA R RF: CTTTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAACAGGGCTGATCCGAGGAATGTTTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA RR: GAAACCTCCTACATTTACGGAAGTGTTCCGATTCTTTGAATTGTCCCGACTAGGCTCCTTACAAATTCTTGGAAGGACCCGTCCCGGTAACAACACCTTCGTT F2: 3 GTCCCGACTAGGCTCCTTACA 2 Unidirectional alignment (log-probability: -51.1) TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAAacattcctcggatCAGccCTG-------------TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA-------------CAGGGCTGATCCGAGGAATGTTTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA Template switch alignment (log-probability: -18.4) TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA|ACATTCCTCGGATCAGCCCTG|TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA|ACATTCCTCGGATCAGCCCTG|TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA Gorilla > Chimp --------------- chr15:23620400-23620420 Template switch process: F1: L CTTTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA 1 F3: 4 TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA R RF: CTTTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAAACATTCCTCGGATCAGCCCTGTTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA RR: GAAACCTCCTACATTTACGGAAGTGTTCCGATTCTTTGAATTTGTAAGGAGCCTAGTCGGGACAATTCTTGGAAGGACCCGTCCCGGTAACAACACCTTCGTT F2: 3 TGTAAGGAGCCTAGTCGGGAC 2 Unidirectional alignment (log-probability: -51.1) TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA-------------CAGggCTGatccgaggaatgtTTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAAACATTCCTCGGATCAGCCCTG-------------TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA Template switch alignment (log-probability: -18.4) TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA|CAGGGCTGATCCGAGGAATGT|TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA|CAGGGCTGATCCGAGGAATGT|TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA Chimp > Gorilla --------------- chr15:23512897-23512917 Template switch process: F1: L CTTTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA 1 F3: 4 TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA R RF: CTTTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAACAGGGCTGATCCGAGGAATGTTTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA RR: GAAACCTCCTACATTTACGGAAGTGTTCCGATTCTTTGAATTGTCCCGACTAGGCTCCTTACAAATTCTTGGAAGGACCCGTCCCGGTAACAACACCTTCGTT F2: 3 GTCCCGACTAGGCTCCTTACA 2 Unidirectional alignment (log-probability: -51.1) TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAAacattcctcggatCAGccCTG-------------TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA-------------CAGGGCTGATCCGAGGAATGTTTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA Template switch alignment (log-probability: -18.4) TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA|ACATTCCTCGGATCAGCCCTG|TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA TTGGAGGATGTAAATGCCTTCACAAGGCTAAGAAACTTAA|ACATTCCTCGGATCAGCCCTG|TTAAGAACCTTCCTGGGCAGGGCCATTGTTGTGGAAGCAA ========== Event 1198 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGCCCATATGTGGGGGACGTCACTGCTC-ACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCACATCTGGGGCCAGCAAAGGACCCCTGT ↑ 4 1 3 2 Chimp: GTCGGCCCTTGGCAGACTTGGGGGGCGTC-----------------------ACTGCTC-ACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCACATCTGGGGCCAGCAAAGGACCCCTGT ↓ 4 1 3 2 Gorilla: GTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGCCCATATGTGGGGGACGTCACTGCTC-ACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCATATCTGGGGCCAGCAAAGGACCCCTGT Human: GTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGCCCATATGTGGGGGACGTCACTGCTC-ACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCACATCTGGGGCCAGCAAAGGACCCCTGT Cluster: [ ] Orangutan: GTCTGCCCTTGGCAGACTTGGGGGACGTC-----------------------ACTGCTCATCCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCACATCTGGGGCCAGCAAAGGGCCCCTGT Chimp > Human ------------- chr15:78263845-78263852 Template switch process: F1: L AGAGAGGGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC 1 F3: 4 GGGGGACGTCACTGCTCACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGG R RF: AGAGAGGGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGCTCACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCACATCTGG RR: TCTCTCCCGTGACAGCCGGGAACCGTCTGAACCCCCCGCAGTGACGAGTGGAACTCCCTGAATTCCCAAGGGTCACCACCCGTAAGCTCTCCTATGACAGGTGTAGACC F2: 3 TGTATACC 2 Unidirectional alignment (log-probability: -44) GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGCccatatgtgggggacgtcactgcTCACCTTGAGGGACTTAAGGGTTCC GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC-----------------------TCACCTTGAGGGACTTAAGGGTTCC Template switch alignment (log-probability: -28.5) GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC|CCAtATGT|GGGGGaCGTCACTGCTCACCTTGAGGGACTTAAGGGTTCC GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC|CCAGATGT|GGGGGGCGTCACTGCTCACCTTGAGGGACTTAAGGGTTCC Chimp > Gorilla --------------- chr15:57038168-57038175 Template switch process: F1: L AGAGAGGGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC 1 F3: 4 GGGGGACGTCACTGCTCACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGG R RF: AGAGAGGGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGCTCACCTTGAGGGACTTAAGGGTTCCCAGTGGTGGGCATTCGAGAGGATACTGTCCACATCTGG RR: TCTCTCCCGTGACAGCCGGGAACCGTCTGAACCCCCCGCAGTGACGAGTGGAACTCCCTGAATTCCCAAGGGTCACCACCCGTAAGCTCTCCTATGACAGGTGTAGACC F2: 3 TGTATACC 2 Unidirectional alignment (log-probability: -44) GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGtcactgcccatatgtgggggacgTCACTGCTCACCTTGAGGGACTTAAGGGTTCC GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCG-----------------------TCACTGCTCACCTTGAGGGACTTAAGGGTTCC Template switch alignment (log-probability: -28.1) GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC|CCAtATGT|GGGGGaCGTCACTGCTCACCTTGAGGGACTTAAGGGTTCC GGCACTGTCGGCCCTTGGCAGACTTGGGGGGCGTCACTGC|CCAGATGT|GGGGGGCGTCACTGCTCACCTTGAGGGACTTAAGGGTTCC ========== Event 1199 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACCCTGAGAGTAGGGAGGCTCCAGCC------------------TGTCCTGGAATCATCTCCAGCCT----------GTCTCACACTCAGCATTCCAGGTCTGCCTGGCGTCCAGCTG ↑ 4 1 3 2 Chimp: AACCCTGAGAGTAGGGAGGCTCCAGCC----------------------------------------T----------GTCTCACACTCAGCATTCCAGGTCTGCCTGGCGTCCAGCTG Gorilla: AACCCTGAGAGTAGGGAGGCTCCAGCCTGTCctggaatcatctcc----------------------a------gcctgtctcacactcagcattccaggtctgcctggcgtccagctg Human: AACCCTGAGAGTAGGGAGGCTCCAGCC------------------TGTCCTGGAATCATCTCCAGCCT----------GTCTCACACTCAGCATTCCAGGTCTGCCTGGCGTCCAGCTG Cluster: [ ] Orangutan: AACCCTGAGAGTAGGGAGGCTCCAGCCTGTCCTGGAatcatctcc----------------------agcctct----gtctcacactcagcattccaggtctgcctgatgtccagctg Chimp > Human ------------- chr15:79003086-79003095 Template switch process: F1: L GAACAGTCAGGAGAAACCCTGAGAGTAGGGAGGCTCCAGCCTGTC 1 F3: 4 CTCCAGCCTGTCTCACACTCAGCATTCCAGGTCTGCCTGGCGTCCAGC R RF: GAACAGTCAGGAGAAACCCTGAGAGTAGGGAGGCTCCAGCCTGTCTCACACTCAGCATTCCAGGTCTGCCTGGCGTCCAGC RR: CTTGTCAGTCCTCTTTGGGACTCTCATCCCTCCGAGGTCGGACAGAGTGTGAGTCGTAAGGTCCAGACGGACCGCAGGTCG F2: 3 TACTAAGGTC 2 Unidirectional alignment (log-probability: -42.6) GTCAGGAGAAACCCTGAGAGTAGGGAGGCTCCAGCCTgtcctggaatcatctccagcctGTCTCACACTCAGCATTCCAGGTCTGCCTGG GTCAGGAGAAACCCTGAGAGTAGGGAGGCTCCAGCCT----------------------GTCTCACACTCAGCATTCCAGGTCTGCCTGG Template switch alignment (log-probability: -28.7) GTCAGGAGAAACCCTGAGAGTAGGGAGGCTCCAGCCTGTC|CTGGAATcaT|CTCCAGCCTGTCTCACACTCAGCATTCCAGGTCTGCCTGG GTCAGGAGAAACCCTGAGAGTAGGGAGGCTCCAGCCTGTC|CTGGAATGCT|CTCCAGCCTGTCTCACACTCAGCATTCCAGGTCTGCCTGG ========== Event 1200 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTTCAATTATAAATCCTCAGTTTTTCAT---------ACTAAGGCTTAAGTTT------------TCGGTTACTGAAATTGAAAATCCATACATAAACA Chimp: TTTTCAATTATAAATCCTCAGTTTTTCAT---------ACTAAGGCTTAAGTTT------------TCGGTTACTGAAATTGAAAATCCATACATAAACA ↓ 3 1 4 2 ↑ 1 3 2 4 Gorilla: TTTTCAATTATAAATCCTCAGTTTTTCAATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAATCTGGTTACTGAAATTGAAAATCCATACATAAACA ↓ 1 3 2 4 ↑ 3 1 4 2 Human: TTTTCAATTATAAATCCTCAGTTTTTCAT---------ACTAAGGCTTAAGTTT------------TCGGTTACTGAAATTGAAAATCCATACATAAACA Cluster: [ ] Orangutan: TTTTCAATTATAAATCCTCAGTTTTTCAT---------ACTAAGGCTTAATTTT------------TTGGTTACTGAAATTGAAAATCCATACATAAACA Gorilla > Human --------------- chr15:22521044-22521062 Template switch process: F1: L CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA 1 F3: 4 GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA R RF: CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCAATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAATCTGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA RR: GTATAAAAAAAGTAAAAGTTAATATTTAGGAGTCAAAAAGTTAAAGTCATTGGCTTTTGAATTCGGAATCATACTTTTAGACCAATGACTTTAACTTTTAGGTATGTATTTGTACTATTAT F2: 3 CTTTTGAATTCGGAATCAT 2 Unidirectional alignment (log-probability: -48.1) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCAtactaaggcttaagtTTTC-----------------------------------GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA--------------ATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAATCTGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Template switch alignment (log-probability: -18.2) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|TACTAAGGCTTAAGTTTTC|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|TACTAAGGCTTAAGTTTTC|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Human > Gorilla --------------- chr15:22645722-22645761 Template switch process: F1: L CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA 1 F3: 4 GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA R RF: CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCATACTAAGGCTTAAGTTTTCGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA RR: GTATAAAAAAAGTAAAAGTTAATATTTAGGAGTCAAAAAGTATGATTCCGAATTCAAAAGCCAATGACTTTAACTTTTAGGTATGTATTTGTACTATTAT F2: 3 TCTAAAAGTATGATTCCGAATTCAAAAGCCAATGACTTTA 2 Unidirectional alignment (log-probability: -77.2) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA--------------aTTTCagtaaccgaaaacttaagccttagtatgaaaatctGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCATACTAAGGCTTAAGTTTTC-----------------------------------GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Template switch alignment (log-probability: -26.3) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|ATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAAtCT|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|ATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAAACT|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Gorilla > Chimp --------------- chr15:22667620-22667638 Template switch process: F1: L CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA 1 F3: 4 GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA R RF: CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCAATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAATCTGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA RR: GTATAAAAAAAGTAAAAGTTAATATTTAGGAGTCAAAAAGTTAAAGTCATTGGCTTTTGAATTCGGAATCATACTTTTAGACCAATGACTTTAACTTTTAGGTATGTATTTGTACTATTAT F2: 3 CTTTTGAATTCGGAATCAT 2 Unidirectional alignment (log-probability: -48.1) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCAtactaaggcttaagtTTTC-----------------------------------GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA--------------ATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAATCTGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Template switch alignment (log-probability: -18.2) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|TACTAAGGCTTAAGTTTTC|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|TACTAAGGCTTAAGTTTTC|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Chimp > Gorilla --------------- chr15:22645722-22645761 Template switch process: F1: L CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA 1 F3: 4 GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA R RF: CATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCATACTAAGGCTTAAGTTTTCGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA RR: GTATAAAAAAAGTAAAAGTTAATATTTAGGAGTCAAAAAGTATGATTCCGAATTCAAAAGCCAATGACTTTAACTTTTAGGTATGTATTTGTACTATTAT F2: 3 TCTAAAAGTATGATTCCGAATTCAAAAGCCAATGACTTTA 2 Unidirectional alignment (log-probability: -77.2) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA--------------aTTTCagtaaccgaaaacttaagccttagtatgaaaatctGGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCATACTAAGGCTTAAGTTTTC-----------------------------------GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA Template switch alignment (log-probability: -26.3) ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|ATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAAtCT|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ATATTTTTTTCATTTTCAATTATAAATCCTCAGTTTTTCA|ATTTCAGTAACCGAAAACTTAAGCCTTAGTATGAAAAACT|GGTTACTGAAATTGAAAATCCATACATAAACATGATAATA ========== Event 1201 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: T----CTGTTTACACAATGGTAAAGCTCCCTTCTGCATTAGGGAGCTTTGCAGATTGGGCTCTAGTCGA ↑ 1 4 3 2 Chimp: T----CTGTTTACACAATGGTGG---ACTCTTCTGCATTAGGGAGCTTTGCAGATTAGGCTCTAGTCGA Gorilla: T--------CTACACAATGGTGG---ACTCTTCTGCATTAGGGAGCTTTGCAGATTGGGCTCTAGTCGA Human: T----CTGTTTACACAATGGTAAAGCTCCCTTCTGCATTAGGGAGCTTTGCAGATTGGGCTCTAGTCGA Cluster: [ ] Orangutan: TCTGT----TTACACAATGGTGG---ACTCTTCTGCATTAGAGAGCTTTGTAGATTGGGCTCTAGTCGA Chimp > Human ------------- chr15:22057571-22057578 Template switch process: F1: L TCTAGGAACCATGGGAAGATAGAATCTGTTTACACAATGGT 1 F3: 4 CTTCTGCATTAGGGAGCTTTGCAGATTGGGCTCTAGTCGA R RF: TCTAGGAACCATGGGAAGATAGAATCTGTTTACACAATGGTGGACTCTTCTGCATTAGGGAGCTTTGCAGATTAGGCTCTAGTCGA RR: AGATCCTTGGTACCCTTCTATCTTAGACAAATGTGTTACCACCTGAGAAGACGTAATCCCTCGAAACGTCTAATCCGAGATCAGCT F2: 3 CCTCGAAA 2 Unidirectional alignment (log-probability: -38.9) CTAGGAACCATGGGAAGATAGAATCTGTTTACACAATGGTaaagctcc-----CTTCTGCATTAGGGAGCTTTGCAGATTgGGCTCTAGTCGA CTAGGAACCATGGGAAGATAGAATCTGTTTACACAATGGT--------GGACTCTTCTGCATTAGGGAGCTTTGCAGATTAGGCTCTAGTCGA Template switch alignment (log-probability: -22.3) CTAGGAACCATGGGAAGATAGAATCTGTTTACACAATGGT|AAAGCTCC|CTTCTGCATTAGGGAGCTTTGCAGATTgGGCTCTAGTCGA CTAGGAACCATGGGAAGATAGAATCTGTTTACACAATGGT|AAAGCTCC|CTTCTGCATTAGGGAGCTTTGCAGATTAGGCTCTAGTCGA ========== Event 1202 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AACATCATGGATTCCATTTTCAGTGCAGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGT ↑ 1 4 3 2 Chimp: AACATCATGGATTCCATTTTCT---AGGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGT Gorilla: AACATCATGGATTCCATTTTCT---AGGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGT ↓ 1 4 3 2 Human: AACATCATGGATTCCATTTTCAGTGCAGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGT Cluster: [ ] Orangutan: AACATCATGGATTCCATTTTCT---AGGCTGTACTCGCTGCATTGGTCATTTGGATGGGCCTGT Chimp > Human ------------- chr15:80740357-80740362 Template switch process: F1: L TACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC 1 F3: 4 GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT R RF: TACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTCTAGGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT RR: ATGCTATCTGAGACTAGTCTTTGTAGTACCTAAGGTAAAAGATCCGACATGAGCGACGTGACCAGTAAACCTACCCGGGCACCA F2: 3 ACGTGA 2 Unidirectional alignment (log-probability: -27) ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC-AGtgcaGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTCTAG----GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT Template switch alignment (log-probability: -16) ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC|AGTGCA|GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC|AGTGCA|GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT Gorilla > Human --------------- chr15:80740357-80740362 Template switch process: F1: L TACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC 1 F3: 4 GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT R RF: TACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTCTAGGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT RR: ATGCTATCTGAGACTAGTCTTTGTAGTACCTAAGGTAAAAGATCCGACATGAGCGACGTGACCAGTAAACCTACCCGGGCACCA F2: 3 ACGTGA 2 Unidirectional alignment (log-probability: -26.5) ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC-AGtgcaGCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTCTAG----GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT Template switch alignment (log-probability: -16.5) ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC|AGTGCA|GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT ACGATAGACTCTGATCAGAAACATCATGGATTCCATTTTC|AGTGCA|GCTGTACTCGCTGCACTGGTCATTTGGATGGGCCCGTGGT ========== Event 1203 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GCCAGAATCCCTCCCAGGGTTTCTTTGCTCAAGAGACACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTGAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAGTTTCTCATCTGAAACCTTGCTCTGCCATGAGCTTACCTGCACGTCACCT ↓ 1 4 3 2 Chimp: GCCAGAATCCCTCCCAGGGTTCA----------TGGCACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTGAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAGTTTCTCATCTGAAACCTTGCTCTGCCATGAGCTTACCTGCACGTCACCT Gorilla: GCCAGAATCCCTCCCAGGGTTCA----------TGGCACCTTCTTTGCTCGAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTGAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAGTTTCTCTTCTGAAACCTTGCTCTGCCATGAGCTTACCTACACGTCACCT ↑ 1 4 3 2 Human: GCCAGAATCCCTCCCAGGGTTTCTTTGCTCAAGAGACACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTGAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAGTTTCTCATCTGAAACCTTGCTCTGCCATGAGCTTACCTGCACGTCACCT Cluster: [ ] Orangutan: GCCAGAATCCCTCCCAGGTTTCA----------TGGCACCCTCTTTGCTCCAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTAAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAATTTCTCATCTGAAACCTTGCCCTGCCATGAGCTTACCTGCATGTCACCT Human > Chimp ------------- chr15:61998393-61998397 Template switch process: F1: L AAACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT 1 F3: 4 CACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC R RF: AAACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTTTCTTTGCTCAAGAGACACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTGAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAGTTTCTCATCTGAAACCTTGCTCTGCCATG RR: TTTGGTATCGTACGTGACTTCGGTCTTAGGGAGGGTCCCAAAGAAACGAGTTCTCTGTGGAAGAAACGAGTTCTCTGTGTCGGAGAGGATCCGAGGGAAGACGTCCCGGACTCGACACTCGAACGAAGGTAAGGAAGGTCATGGACGGGGTCTCAAAGAGTAGACTTTGGAACGAGACGGTAC F2: 3 GGTAC 2 Unidirectional alignment (log-probability: -29.1) AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTTcatgg---------------CACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT-----TCTTTGCTCAAGAGACACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC Template switch alignment (log-probability: -15.9) AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT|CATGG|CACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT|CATGG|CACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC Human > Gorilla --------------- chr15:59680638-59680642 Template switch process: F1: L AAACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT 1 F3: 4 CACCTTCTTTGCTCGAGAGACACAGCCTCTCCTAGGCTCC R RF: AAACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTTTCTTTGCTCAAGAGACACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCCCTTCTGCAGGGCCTGAGCTGTGAGCTTGCTTCCATTCCTTCCAGTACCTGCCCCAGAGTTTCTCATCTGAAACCTTGCTCTGCCATG RR: TTTGGTATCGTACGTGACTTCGGTCTTAGGGAGGGTCCCAAAGAAACGAGTTCTCTGTGGAAGAAACGAGTTCTCTGTGTCGGAGAGGATCCGAGGGAAGACGTCCCGGACTCGACACTCGAACGAAGGTAAGGAAGGTCATGGACGGGGTCTCAAAGAGTAGACTTTGGAACGAGACGGTAC F2: 3 GGTAC 2 Unidirectional alignment (log-probability: -33.5) AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTTcaT----------GgCACCTTCTTTGCTCgAGAGACACAGCCTCTCCTAGGCTCC AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTTTCTTTGCTCAAGAGACACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC Template switch alignment (log-probability: -21.9) AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT|CATGG|CACCTTCTTTGCTCgAGAGACACAGCCTCTCCTAGGCTCC AACCATAGCATGCACTGAAGCCAGAATCCCTCCCAGGGTT|CATGG|CACCTTCTTTGCTCAAGAGACACAGCCTCTCCTAGGCTCC ========== Event 1204 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTAT------------------------------------------------------CTGATCAGAGCAGGCCACCCAATCACAGC ↑ 3 2 1 4 Chimp: AAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTAT---------------------------CCTTTTAGTTGACAGAAAATAAAAAACATGGACACAGCAGGCCACCCAATCACAGC Gorilla: AAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATCCTTTTAGTTGACAGAAAATAAAAAAC---------------------------ATGGACACAGCAGGCCACCCAATCACAGC ↓ 3 2 1 4 Human: AAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTAT------------------------------------------------------CTGATCAGAGCAGGCCACCCAATCACAGC Cluster: [ ] Orangutan: AAGAATTTTAAAGTCTCCTCTGATCAGAATTTGCTATCCTTTTAGTTGACAGAAAATAAAAAAC---------------------------ATGGACACAGCAGGCCACCCAATCACAGC Chimp > Human ------------- chr15:80978858-80978864 Template switch process: F1: L AGTCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC 1 F3: 4 AGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG R RF: AGTCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATCCTTTTAGTTGACAGAAAATAAAAAACATGGACACAGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG RR: TCAGTTCTCAAAATTTCAGAAGAGACTAGTCTTAAACGATAGGAAAATCAACTGTCTTTTATTTTTTGTACCTGTGTCGTCCGGTGGGTTAGTGTCGTCCACGAACCTCCCCTCAC F2: 3 GACTAGT 2 Unidirectional alignment (log-probability: -30.4) TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC---------------------------TGatCAgAGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATCCTTTTAGTTGACAGAAAATAAAAAACATGGACACAGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG Template switch alignment (log-probability: -16.2) TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC|TGATCAG|AGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC|TGATCAG|AGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG Gorilla > Human --------------- chr15:80978858-80978864 Template switch process: F1: L AGTCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC 1 F3: 4 AGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG R RF: AGTCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATCCTTTTAGTTGACAGAAAATAAAAAACATGGACACAGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG RR: TCAGTTCTCAAAATTTCAGAAGAGACTAGTCTTAAACGATAGGAAAATCAACTGTCTTTTATTTTTTGTACCTGTGTCGTCCGGTGGGTTAGTGTCGTCCACGAACCTCCCCTCAC F2: 3 GACTAGT 2 Unidirectional alignment (log-probability: -28.9) TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC---------------------------TGatCAgAGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATCCTTTTAGTTGACAGAAAATAAAAAACATGGACACAGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG Template switch alignment (log-probability: -16.6) TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC|TGATCAG|AGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG TCAAGAGTTTTAAAGTCTTCTCTGATCAGAATTTGCTATC|TGATCAG|AGCAGGCCACCCAATCACAGCAGGTGCTTGGAGGGGAGTG ========== Event 1205 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGCAGCCAGACAACGTCAGA-------------------------CAGGCTCCGATTATAAGTAAGAACTGCCT Chimp: GGGCAGCCAGACAACGTCAGA-------------------------CAGGCTCCGATTATAAGTAAGAACTGCCT ↑ 1 3 2 4 Gorilla: GGGCAGCCAGACAACGTCAGAACAAGAGGCGGCAGAACTGGAGCCTGGAGCTCTGATTATAAGTAAGAACTGCCT ↓ 1 3 2 4 Human: GGGCAGCCAGACAACGTCAGA-------------------------CAGGCTCCGATTATAAGTAAGAACTGCCT Cluster: [ ] Orangutan: GGGCAGCCAGACAACGTCAGAACAAGAGGCGGCAGAACTGGAGCCTGGAGCTCTGATTATAAGTAAGAACTGCCT Gorilla > Human --------------- chr15:81553575-81553582 Template switch process: F1: L GAGTGATCATAGGAGTAAAAGGGCAGCCAGACAACGTCAGA 1 F3: 4 GATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT R RF: GAGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGAACAAGAGGCGGCAGAACTGGAGCCTGGAGCTCTGATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT RR: CTCACTAGTATCCTCACTTTCCCGTCGGTCTGTTGCAGTCTTGTTCTCCGCCGTCTTGACCTCGGACCTCGAGACTAATATTCATTCTTGACGGAAGAGGAGAAAGACTGGGGA F2: 3 CCTCGGAC 2 Unidirectional alignment (log-probability: -33.1) AGTGATCATAGGAGTaAAAGGGCAGCCAGACAACGTCAGA-----------CAG--------------GCTCcGATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT AGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGAACAAGAGGCGGCAGAACTGGAGCCTGGAGCTCTGATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT Template switch alignment (log-probability: -22.3) AGTGATCATAGGAGTaAAAGGGCAGCCAGACAACGTCAGA|CAGGCTCC|GATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT AGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGA|CAGGCTCC|GATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT Gorilla > Chimp --------------- chr15:62683065-62683072 Template switch process: F1: L GAGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGA 1 F3: 4 GATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT R RF: GAGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGAACAAGAGGCGGCAGAACTGGAGCCTGGAGCTCTGATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT RR: CTCACTAGTATCCTCACTTTCCCGTCGGTCTGTTGCAGTCTTGTTCTCCGCCGTCTTGACCTCGGACCTCGAGACTAATATTCATTCTTGACGGAAGAGGAGAAAGACTGGGGA F2: 3 CCTCGGAC 2 Unidirectional alignment (log-probability: -27.5) AGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGA-----------CAG--------------GCTCcGATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT AGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGAACAAGAGGCGGCAGAACTGGAGCCTGGAGCTCTGATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT Template switch alignment (log-probability: -16.7) AGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGA|CAGGCTCC|GATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT AGTGATCATAGGAGTGAAAGGGCAGCCAGACAACGTCAGA|CAGGCTCC|GATTATAAGTAAGAACTGCCTTCTCCTCTTTCTGACCCCT ========== Event 1206 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TGCTGGTGTGTCTGTTGCAGGCCATGGCCACGTCGGCCATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTCttctcctgcctcagcctcctgagtagctggattacaggcatgtgccaccacacctggctaatattttgtatttttagtagagatgtggtttgtccatgttggtcaggc ↑ 4 1 3 2 Chimp: TGCTGGTGTGTCTGTTGCAGGC---------------CATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTCttctcctgcctcagcctcctgagtagctggattacaggcatgtgccaccacacctggctaatattttgtatttttagtagagatgtggtttgtccatgttggtcaggc Gorilla: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: TGCTGGTGTGTCTGTTGCAGGCCATGGCCACGTCGGCCATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTCttctcctgcctcagcctcctgagtagctggattacaggcatgtgccaccacacctggctaatattttgtatttttagtagagatgtggtttgtccatgttggtcaggc Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Chimp > Human ------------- chr15:82972408-82972414 Template switch process: F1: L ACAATAGAATGCAACTTTATGCTGGTGTGTCTGTTGCAGGCCATGG 1 F3: 4 GGCCATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTCTTC R RF: ACAATAGAATGCAACTTTATGCTGGTGTGTCTGTTGCAGGCCATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTCTTCTCCTGCCTCAGCCTCCTGAGTAGCTGGATTACAGGCATGTGCCACCACACCTGGCTAATATTTTGTATTTTTAGTAGAGATGTGG RR: TGTTATCTTACGTTGAAATACGACCACACAGACAACGTCCGGTACCTTTCGTGGGCTCACCTTTATTTATCTTTTAAGAAGAGGACGGAGTCGGAGGACTCATCGACCTAATGTCCGTACACGGTGGTGTGGACCGATTATAAAACATAAAAATCATCTCTACACC F2: 3 CTGCACC 2 Unidirectional alignment (log-probability: -32.5) GAATGCAACTTTATGCTGGTGTGTCTGTTGCAGGCCATGGccacgtcggccatggAAAGCACCCGAGTGGAAATAAATAGAAAATTC GAATGCAACTTTATGCTGGTGTGTCTGTTGCAGGCCATGG---------------AAAGCACCCGAGTGGAAATAAATAGAAAATTC Template switch alignment (log-probability: -22.3) GAATGCAACTTTATGCTGGTGTGTCTGTTGCAGGCCATGG|CCACgTC|GGCCATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTC GAATGCAACTTTATGCTGGTGTGTCTGTTGCAGGCCATGG|CCACATC|GGCCATGGAAAGCACCCGAGTGGAAATAAATAGAAAATTC ========== Event 1207 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAGGTggtcttaaagtgcaggttg--acctttgctgagtccaagctccaacacccccaggtagg Chimp: TAAGGTGGTCTTAAAGTGCAGCTTGGACTCTTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGG ↑ 1 4 3 2 Gorilla: TAAGGTGGTCTTAAAGTGCAGGTTG--ACCTTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGG Human: TAAGGTggtcttaaagtgcaggttg--acctttgctgagtccaagctccaacacccccaggtagg Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr15:18900328-18900336 Template switch process: F1: L TGTTCAGGGAGATGGTGTCATAAGGTGGTCTTAAAGTGCAG 1 F3: 4 TTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGGAGTT R RF: TGTTCAGGGAGATGGTGTCATAAGGTGGTCTTAAAGTGCAGGTTGACCTTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGGAGTT RR: ACAAGTCCCTCTACCACAGTATTCCACCAGAATTTCACGTCCAACTGGAAACGACTCAGGTTCGAGGTTGTGGGGGTCCATCCTCAA F2: 3 CTCAGGTTC 2 Unidirectional alignment (log-probability: -29.1) GTTCAGGGAGATGGTGTCATAAGGTGGTCTTAAAGTGCAGcTTgGACtCTTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGGAGTT GTTCAGGGAGATGGTGTCATAAGGTGGTCTTAAAGTGCAGGTT-GAC-CTTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGGAGTT Template switch alignment (log-probability: -16.8) GTTCAGGGAGATGGTGTCATAAGGTGGTCTTAAAGTGCAG|CTTGGACTC|TTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGGAGTT GTTCAGGGAGATGGTGTCATAAGGTGGTCTTAAAGTGCAG|CTTGGACTC|TTTGCTGAGTCCAAGCTCCAACACCCCCAGGTAGGAGTT ========== Event 1208 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGCCTTCTATGCACCTGGCT--------------------GATGTCTGGTGGGTCTTTAGCAGTGCGCTTAGCAACCAGACACT ↓ 4 1 3 2 Chimp: GTGCCTTCTATGCACCTGGCT----------GATGACTGCTGATGTCTGGTGGGTCCTTAGCAGTGTGCTTAGCAACCAGACACT Gorilla: GTGCCTTCTATGCACCTGGCTGATGACTGCT----------GATGTCTGGTGGGTCCTTAGCAGTGCGCTTAGCAACCAGACACT Human: GTGCCTTCTATGCACCTGGCT--------------------GATGTCTGGTGGGTCTTTAGCAGTGCGCTTAGCAACCAGACACT Cluster: [ ] Orangutan: GTGCCTTCTATGCACCTGGCTGATGACTGCT----------GATGTCTGGTGGGTCCTTAGCAGTGTGCTTAGCAACCAGACACT Human > Chimp ------------- chr15:64622968-64622971 Template switch process: F1: L GAGGGCTGTTCACCTAGGTGGTGCCTTCTATGCACCTGGCTGATG 1 F3: 4 CTGATGTCTGGTGGGTCCTTAGCAGTGTGCTTAGCAACCAGA R RF: GAGGGCTGTTCACCTAGGTGGTGCCTTCTATGCACCTGGCTGATGTCTGGTGGGTCTTTAGCAGTGCGCTTAGCAACCAGA RR: CTCCCGACAAGTGGATCCACCACGGAAGATACGTGGACCGACTACAGACCACCCAGAAATCGTCACGCGAATCGTTGGTCT F2: 3 GTCA 2 Unidirectional alignment (log-probability: -37.3) CTGTTCACCTAGGTGGTGCCTTCTATGCACCTGgctgatgactGCTGATGTCTGGTGGGTCcTTAGCAGTGtGCTTAGCAACCA CTGTTCACCTAGGTGGTGCCTTCTATGCACCTG----------GCTGATGTCTGGTGGGTCTTTAGCAGTGCGCTTAGCAACCA Template switch alignment (log-probability: -27.9) CTGTTCACCTAGGTGGTGCCTTCTATGCACCTGGCTGATG|ACTG|CTGATGTCTGGTGGGTCcTTAGCAGTGtGCTTAGCAACCA CTGTTCACCTAGGTGGTGCCTTCTATGCACCTGGCTGATG|ACTG|CTGATGTCTGGTGGGTCTTTAGCAGTGCGCTTAGCAACCA ========== Event 1209 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATAAATTTTATTCCATTCCAAATGTTACTTAAGTAACATTTGGAAACCACTAAACTTTAG Chimp: AATAAATTTTATTCCATTCCAAATGTTACTTAAGTAACATTTGGAAACCACTAAACTTTAG ↑ 1 4 3 2 Gorilla: AATAAATTTTATTCCATTCCAT-------ATAAGTAACATTTGGAAACCACTAAACTTTAG ↓ 1 4 3 2 Human: AATAAATTTTATTCCATTCCAAATGTTACTTAAGTAACATTTGGAAACCACTAAACTTTAG Cluster: [ ] Orangutan: AATAAATTTGATTCCATTG----------CTAAGTAACATTTGGAAATCACTAAACTTTAG Gorilla > Human --------------- chr15:17004632-17004640 Template switch process: F1: L TTTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCA 1 F3: 4 TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG R RF: TTTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCATATAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG RR: AAACATTTGATCCTCGTCCGTTATTTAAAATAAGGTAAGGTATATTCATTGTAAACCTTTGGTGATTTGAAATCAACTGATTC F2: 3 TCATTGTAA 2 Unidirectional alignment (log-probability: -26.5) TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCAaAtgttactTAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCATA-------TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG Template switch alignment (log-probability: -16.9) TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCA|AATGTTACT|TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCA|AATGTTACT|TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG Gorilla > Chimp --------------- chr15:17551535-17551543 Template switch process: F1: L TTTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCA 1 F3: 4 TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG R RF: TTTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCATATAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG RR: AAACATTTGATCCTCGTCCGTTATTTAAAATAAGGTAAGGTATATTCATTGTAAACCTTTGGTGATTTGAAATCAACTGATTC F2: 3 TCATTGTAA 2 Unidirectional alignment (log-probability: -26.5) TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCAaAtgttactTAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCATA-------TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG Template switch alignment (log-probability: -16.9) TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCA|AATGTTACT|TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG TTGTAAACTAGGAGCAGGCAATAAATTTTATTCCATTCCA|AATGTTACT|TAAGTAACATTTGGAAACCACTAAACTTTAGTTGACTAAG ========== Event 1210 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAATACCCATGTACTTTTTTTCTGAAATAAAATATCCTTAAATGATACAATAACTTATTAGCATAATTTTTTACAAGCAATATTTCTTCCCCAATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAATTCAGAAAT--------TTATGTACAGACACAAATTG ↑ 3 2 1 4 Chimp: TAATACCCATGTACtttttttCTGAAATAAAATATCCTTAAATGATACAATAACTTATTAGCATAATTTTTTACAAGCAATATTTCTTCCCCAATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAAGTTAGAGAT----TTATTTATGTACAGACACAAATTG Gorilla: TAATACCCATGTACtttttttCTGAAATAAAATATCCTTAAATGATACAATAACTTATTAGCATAATTTTTTACAAGCAATATTTCTTCCCCAATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAAGTTAGAAAT--------TTATGTACAGACATAAATTG Human: TAATACCCATGTACTTTTTTTCTGAAATAAAATATCCTTAAATGATACAATAACTTATTAGCATAATTTTTTACAAGCAATATTTCTTCCCCAATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAATTCAGAAAT--------TTATGTACAGACACAAATTG Cluster: [ ] Orangutan: TAATACCCATGTACTTTTTTTCTGAAATAAAATATCCTTAAATGATACAATAACTTATTAGCATAATTTTTTACAAGCAATATTTCTTCTCCAATGTTAAATTCATAGATTCCAGTTATCCCACGACCTTGACGTTAGAAATTTAT----TTATGTACAGACACAAACTG Chimp > Human ------------- chr1:58677334-58677340 Template switch process: F1: L AATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAA 1 F3: 4 ATTTATGTACAGACACAAATTGAATCTTTAAATACAAAGAGC R RF: TTCTGAAATAAAATATCCTTAAATGATACAATAACTTATTAGCATAATTTTTTACAAGCAATATTTCTTCCCCAATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAAGTTAGAGATTTATTTATGTACAGACACAAATTGAATCTTTAAATACAAAGAGC RR: AAGACTTTATTTTATAGGAATTTACTATGTTATTGAATAATCGTATTAAAAAATGTTCGTTATAAAGAAGGGGTTACAATTTAAGTATCTAAGGTCAATAGGGTCCTGGAACTTCAATCTCTAAATAAATACATGTCTGTGTTTAACTTAGAAATTTATGTTTCTCG F2: 3 AAGACTT 2 Unidirectional alignment (log-probability: -28.8) ATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAA---------TTcagaaATTTATGTACAGACACAAATTGAATCTTTAAATACAAAGA ATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAAGTTAGAGATTT-----ATTTATGTACAGACACAAATTGAATCTTTAAATACAAAGA Template switch alignment (log-probability: -16.2) ATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAA|TTCAGAA|ATTTATGTACAGACACAAATTGAATCTTTAAATACAAAGA ATGTTAAATTCATAGATTCCAGTTATCCCAGGACCTTGAA|TTCAGAA|ATTTATGTACAGACACAAATTGAATCTTTAAATACAAAGA ========== Event 1211 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAGAAGTGTTATTACAAAG--------------GATCCGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATATACTCCTAAGGAGAAACTCTTTGTG Chimp: TCAAGAAGTGTTATTACAAAG-------GAGAGTATATCCGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATATACTCCTAAGGAGAAACTCTTTGTG Gorilla: TCAAGAAGTGTTATTACAAAGGAGAGTA-------TATCTGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATATACTCCTAAGGAGAAACTCTTCGTG ↑ 1 4 3 2 Human: TCAAGAAGTGTTATTACAAAG--------------GATCCGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATATACTCCTAAGGAGAAACTCTTTGTG Cluster: [ ] Orangutan: TCAAGAAGTGTTATTACAAAGGAGAGTA-------TATCCGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATATACTCCTAAGGAGAAACTCTTTGTG Human > Gorilla --------------- chr1:59554360-59554369 Template switch process: F1: L CGCTCCCAGTAACCCTTTGTTCAAGAAGTGTTATTACAAAGGA 1 F3: 4 GAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATA R RF: TGCTCCCAGTAACCCTTTGTTCAAGAAGTGTTATTACAAAGGATCCGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATATACTC RR: ACGAGGGTCATTGGGAAACAAGTTCTTCACAATAATGTTTCCTAGGCTTCGATTGTTCGGACAGGTTAGAGAAGGTGAGGATCTATATGAG F2: 3 TCTATATGAG 2 Unidirectional alignment (log-probability: -32.1) TCCCAGTAACCCTTTGTTCAAGAAGTGTTATTACAAAGGagagtatATCtGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATA TCCCAGTAACCCTTTGTTCAAGAAGTGTTATTACAAAGG-------ATCCGAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATA Template switch alignment (log-probability: -22.6) TCCCAGTAACCCTTTGTTCAAGAAGTGTTATTACAAAGGA|GAGTATATCT|GAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATA TCCCAGTAACCCTTTGTTCAAGAAGTGTTATTACAAAGGA|GAGTATATCT|GAAGCTAACAAGCCTGTCCAATCTCTTCCACTCCTAGATA ========== Event 1212 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTTTCTGAGTGAGGGACTCA----------------GGG------GTTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGGACAAGGACAATGTAAATGGTCTCGTGAATATCTCGGCTTTCTCACTGTACtgggttgaataatg Chimp: GCTTTCTGAGTGAGGGACTCA--------CTCAGAATAGG---ACCCGTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGGACAAGGACAATGTAAATGGTCTCGTGAATATCTCGGCTTTCTCACTGTACtgagttgaatagtg Gorilla: GCTTTCTGAGTGAGGGACTCACTCAGAAT--------AGGACC---CTTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGGACAAGGACAATGTAAATGGTCTCGTGAATATCTCGGCTTTCTCACTGTACTGGGTTGAACAGTG ↑ 4 3 2 1 Human: GCTTTCTGAGTGAGGGACTCA----------------GGG------GTTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGGACAAGGACAATGTAAATGGTCTCGTGAATATCTCGGCTTTCTCACTGTACtgggttgaataatg Cluster: [ ] Orangutan: GCTTTTTGAGTGAGGGACTCA----------------GGG------GTTTCCTAAAGGGGTCCTATTCACAGAGCAGCTCTCCATGGACTAGAACACTGTAAATGGTCTCGTGAATGTCTCAGCTTTCTCACTGTACtgggttgaatagtg Human > Gorilla --------------- chr15:16640509-16640519 Template switch process: F1: L AAAATGAAATAACTGACTATGCTTTCTGAGTGAGGGACTCA------------------------------------------------------------------------------------CTCA 1 F3: 4 TTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGG R RF: AAAATGAAATAACTGACTATGCTTTCTGAGTGAGGGACTCAGGGGTTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGGACAAGGACAATGTAAATGGTCTCGTGAATATCTCGGCTTTCTCA RR: TTTTACTTTATTGACTGATACGAAAGACTCACTCCCTGAGTCCCCAAAGGATTTCCCCAGGATAAGTGCCCCGTTGAAAGGTACCTGTTCCTGTTACATTTACCAGAGCACTTATAGAGCCGAAAGAGT F2: 3 CCCAGGATAAG 2 Unidirectional alignment (log-probability: -42.4) GAAATAACTGACTATGCTTTCTGAGTGAGGGACTCActcagaataggaccc----TTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGG GAAATAACTGACTATGCTTTCTGAGTGAGGGACTCA---------------GGGGTTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGG Template switch alignment (log-probability: -31.3) GAAATAACTGACTATGCTTTCTGAGTGAGGGACTCA------------------------------------------------------------------------------------CTCA|GAATAGGACCC|TTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGG GAAATAACTGACTATGCTTTCTGAGTGAGGGACTCAGGGGTTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGGACAAGGACAATGTAAATGGTCTCGTGAATATCTCGGCTTTCTCA|GAATAGGACCC|TTTCCTAAAGGGGTCCTATTCACGGGGCAACTTTCCATGG ========== Event 1213 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: caTAGTATATCTT------TT--------------------CTTTC----CTGACTATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGTGTCACTATCatttt-------ttt Chimp: caTAGTATATCTT------TT----------CTTTCCGTTTCTTTC----TTGACTATTTCTGAGTAGTCACTTAGCTGGAAGAGACTGTTGGGTGTCACTATCAtttttttttttttt Gorilla: cGTAGTATATCTT------TTCTTTCCGTTT----------CTTTC--------TTATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGTGTCACTATCATTTT--------GT ↓ 1 4 3 2 Human: caTAGTATATCTT------TT--------------------CTTTC----CTGACTATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGTGTCACTATCatttt-------ttt Cluster: [ ] Orangutan: caTAGTATATCTTTTCCTTTTCTTTCCATTT----------CTTTCTTGA----CTATTTCTGAATAGTCACTTAGCTGGAAG-----------AGTCACTATCAtttt--------tt Gorilla > Human --------------- chr15:85964993-85964996 Template switch process: F1: L CTTGGGTGACATAATTTGACCCATAACATAGTATATCTTTTCTTTCC 1 F3: 4 TATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGT R RF: CTTGGGTGACATAATTTGACCCATAACGTAGTATATCTTTTCTTTCCGTTTCTTTCTTATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGTGTCA RR: GAACCCACTGTATTAAACTGGGTATTGCATCATATAGAAAAGAAAGGCAAAGAAAGAATAAAGACTTATCAGTGAATCGACCTTCTCTGACAACCCACAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -31) GACATAATTTGACCCATAACaTAGTATATCTTTTCTTTC---------CTgacTATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGT GACATAATTTGACCCATAACGTAGTATATCTTTTCTTTCCGTTTCTTTCT---TATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGT Template switch alignment (log-probability: -21.9) GACATAATTTGACCCATAACaTAGTATATCTTTTCTTTCC|TGAC|TATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGT GACATAATTTGACCCATAACGTAGTATATCTTTTCTTTCC|TGAC|TATTTCTGAATAGTCACTTAGCTGGAAGAGACTGTTGGGT ========== Event 1214 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCTGGAGCACAGTCTCCAA----------GGGGAGAGAAGAGCCCCATG------TGCCCATGGCAGATGAGAGTTCTGAGCAGCCT Chimp: CCTCTGGAGCACAGTCTCCAA----------GGGGAGAGAAGAGCCCCATG------TGCCCATGGCAGATGAGAGTTCTGAACAGCCT Gorilla: CCTCTGGAGCACAGTCTCCAA--------------------GACTGCCATG------------GGGCAGATGAGAGTTCTGAGCAGCCT ↑ 1 3 4 2 Human: CCTCTGGAGCACAGTCTCCAA----------GGGGAGAGAAGAGCCCCATG------TGCCCATGGCAGATGAGAGTTCTGAGCAGCCT Cluster: [ ] Orangutan: CCTCTGGAGCACAGTCTCCAAGGGGAGAGAA----------GAGCCACATGGGCCCA------TAGCAGATGAGAGTTCTGAGCAGCCT Human > Gorilla --------------- chr15:64516281-64516289 Template switch process: F1: L TTTCTTCAGCCTCCGTTCAGCCTCTGGAGCACAGTCTCCAAGA 1 F3: 4 GGCAGATGAGAGTTCTGAGCAGCCTGGTGGGTGGCTATAA R RF: TTTCTTCAGCCTCCGTTCAGCCTCTGGAGCACAGTCTCCAAGGGGAGAGAAGAGCCCCATGTGCCCATGGCAGATGAGAGTTCTGAGCAGCCTGGTGGGTGGCTATAA RR: AAAGAAGTCGGAGGCAAGTCGGAGACCTCGTGTCAGAGGTTCCCCTCTCTTCTCGGGGTACACGGGTACCGTCTACTCTCAAGACTCGTCGGACCACCCACCGATATT F2: 3 GGTACCGTC 2 Unidirectional alignment (log-probability: -33.4) CTTCAGCCTCCGTTCAGCCTCTGGAGCACAGTCTCCAAGactgccatGG------------------------GGCAGATGAGAGTTCTGAGCAGCCTGGTGGGTGGCTATAA CTTCAGCCTCCGTTCAGCCTCTGGAGCACAGTCTCCAAG--------GGGAGAGAAGAGCCCCATGTGCCCATGGCAGATGAGAGTTCTGAGCAGCCTGGTGGGTGGCTATAA Template switch alignment (log-probability: -22.4) CTTCAGCCTCCGTTCAGCCTCTGGAGCACAGTCTCCAAGa|CTGCCATGG|GGCAGATGAGAGTTCTGAGCAGCCTGGTGGGTGGCTATAA CTTCAGCCTCCGTTCAGCCTCTGGAGCACAGTCTCCAAGG|CTGCCATGG|GGCAGATGAGAGTTCTGAGCAGCCTGGTGGGTGGCTATAA ========== Event 1215 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CCATATTTGTAGGTGGTTACAGTGTTGTGAGGAAGGTGTGATTTACAGGAAAATACAAATTTCTTTGCATAAGCTCCTCACTGAGTCAGGCTGGGCAAGAAGATTAACTTCTATGGCAAGTGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAAACTGAGGGAAATCTATAGGGAGGTACGAGCT ↑ 3 2 4 1 Chimp: CCATATTTGTAGGTGGTTACAGTGTTGTGAGGAAGGTGTGATTTACAGGAAAATACAAATTTCTTTGCATAAGCTCCTCACTGAGTCAGGCTGGGCAAGAAGATTAACTTCTATGGCAAGTGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAG-----------GGAAATCTATAGGGAGGTACGAGCT Gorilla: CCATATTTGTAGGTGGTTACAGTGTTGTGAGGAAGGTGTGATTTACAGGAAAATACAAATTTCTTTGCATAAGCTCCTCACTGAGTCAGGCTGGGCAAGAAGATTAACTTCTACGGCAAGTGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAAACTGAGGAAAATCTATAGAGAGGTACAAGCT Human: CCATATTTGTAGGTGGTTACAGTGTTGTGAGGAAGGTGTGATTTACAGGAAAATACAAATTTCTTTGCATAAGCTCCTCACTGAGTCAGGCTGGGCAAGAAGATTAACTTCTATGGCAAGTGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAAACTGAGGGAAATCTATAGGGAGGTACGAGCT Cluster: [ ] Orangutan: CCATATTTGTAGGTGGTTACAGTGTTGTGAGGAAGGTGTGATTTACAGGAAAATACAAATTTCTTTGCATAAGCTCCTCACTGAGTCAGGTTGGGCAAGAAGATTAACTTCTATGGCAAGTGAAAGTTTCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAAACTGAGGGAAATCTATGGAGAGGTACGAGCT Chimp > Human ------------- chr15:15824213-15824216 Template switch process: F1: L GGCAAGTGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAA 1 F3: 4 AGGGAAATCTATAGGGAGGTACGAGCTGTACAAGCTTCAGCA R RF: CAGTGTTGTGAGGAAGGTGTGATTTACAGGAAAATACAAATTTCTTTGCATAAGCTCCTCACTGAGTCAGGCTGGGCAAGAAGATTAACTTCTATGGCAAGTGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAATCTATAGGGAGGTACGAGCTGTACAAGCTTCAGCA RR: GTCACAACACTCCTTCCACACTAAATGTCCTTTTATGTTTAAAGAAACGTATTCGAGGAGTGACTCAGTCCGACCCGTTCTTCTAATTGAAGATACCGTTCACTTTCAAGGATCTCGGACGGAGATCAGAGATCTCCCTTTAGATATCCCTCCATGCTCGACATGTTCGAAGTCGT F2: 3 GTCA 2 Unidirectional alignment (log-probability: -26.7) TGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAgagggaaaactGAGGGAAATCTATAGGGAGGTACGAGCTGTACAAGCTTCAG TGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTA-----------GAGGGAAATCTATAGGGAGGTACGAGCTGTACAAGCTTCAG Template switch alignment (log-probability: -15.9) TGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAA|ACTG|AGGGAAATCTATAGGGAGGTACGAGCTGTACAAGCTTCAG TGAAAGTTCCTAGAGCCTGCCTCTAGTCTCTAGAGGGAAA|ACTG|AGGGAAATCTATAGGGAGGTACGAGCTGTACAAGCTTCAG ========== Event 1216 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCACCAATTATCAGTACTTATGCTATTTAGACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTAAC----AGATACTCTTCTTTTGTGGTGAGTTA ↓ 3 2 1 4 Chimp: CTCACCAATTATCAGTACTTATGCTATTTAAACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTAGC--ATAGATATTCTTCTTTTGTGGTGAGTTA Gorilla: CTCACCAATTATCAGTACTTATGCTATTTAAACATCTTTTTTGGACCTGTTGTTTGTCTTACAGATATCTAACAT--AGATATTCTTCTTTTGTGGTGAGTTA Human: CTCACCAATTATCAGTACTTATGCTATTTAGACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTAAC----AGATACTCTTCTTTTGTGGTGAGTTA Cluster: [ ] Orangutan: CTCACCAATTATCAGTACTTAAGCTATTTAAACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTAACAT--AGATATTCTTCTTTTGTGGTGAGTTA Human > Chimp ------------- chr15:67369416-67369420 Template switch process: F1: L AACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTA 1 F3: 4 GATATTCTTCTTTTGTGGTGAGTTATCAACAAAAGTTGTTTAAAA R RF: TATGCTATTTAGACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTAACAGATACTCTTCTTTTGTGGTGAGTTATCAAGAAAAGTTGTTTAAAT RR: ATACGATAAATCTGTAGAAAAAACCTGGACTACAAACAGAATGTCTATAGATTGTCTATGAGAAGAAAACACCACTCAATAGTTCTTTTCAACAAATTTA F2: 3 ATACG 2 Unidirectional alignment (log-probability: -46.5) ACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTAgcAtAGATAtTCTTCTTTTGTGGTGAGTTATCAAcAAAAGTTGTT ACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTA--ACAGATACTCTTCTTTTGTGGTGAGTTATCAAGAAAAGTTGTT Template switch alignment (log-probability: -40) ACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTA|GCATA|GATAtTCTTCTTTTGTGGTGAGTTATCAAcAAAAGTTGTT ACATCTTTTTTGGACCTGATGTTTGTCTTACAGATATCTA|GCATA|GATACTCTTCTTTTGTGGTGAGTTATCAAGAAAAGTTGTT ========== Event 1217 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCTTTACTGAGAGCTCTTGGCAGAAACCGGGACTCCTCTCGAAGGGTAGGGGTAAGAGGAATTAGAGATATTGATCCAAACCTGAGTTCTACAGGAGATCCTTTCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTCGACGTCACAACGCTTCATTCAGTGT Chimp: CTTCTTTACTGAGAGCTCTTGGCAGAAACCAGGACTCCTCTCGAAGGGTAGGGGTAAGAGGAATTAGAGAGATTGATCCAAACCTGAGTTCTACAGGAGGTCCTTTCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTCGACGTCACAACGCTTCATTCAAT-- Gorilla: CTTCTTTACTGAGAGCTCTTGGCAGAAACCAGGACTCCTCTTGAAGGGTAGGGGTAAGAGGAATTAGAGATATTGATCCAAACCTGAGTTCTACAGGAGATCCTTTCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTTGCCATCACAACGCTTCATTCAAT-- ↑ 3 2 1 4 Human: CTTCTTTACTGAGAGCTCTTGGCAGAAACCGGGACTCCTCTCGAAGGGTAGGGGTAAGAGGAATTAGAGATATTGATCCAAACCTGAGTTCTACAGGAGATCCTTTCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTCGACGTCACAACGCTTCATTCAGTGT Cluster: [ ] Orangutan: CTTCTTTACTGAGAGCTCTTGGCAGAAACCAGGACTCCTCTCGAAGGGTAGGGGTAAGAGGAATTAGAGATATTGATCCAAACCTGAGTTCTACAGGAGATCCTTTCCCATCCATCCTGCCAAACCCCAACGTGACGTTTTCATTTGACGTCACGACGCTTCATTCAAT-- Human > Gorilla --------------- chr15:65582013-65582017 Template switch process: F1: L TTCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATT 1 F3: 4 TCACAACGCTTCATTCAATGTTAC R RF: TGGCAGAAACCGGGACTCCTCTCGAAGGGTAGGGGTAAGAGGAATTAGAGATATTGATCCAAACCTGAGTTCTACAGGAGATCCTTTCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTCGACGTCACAACGCTTCATTCAGTGTGAC RR: ACCGTCTTTGGCCCTGAGGAGAGCTTCCCATCCCCATTCTCCTTAATCTCTATAACTAGGTTTGGACTCAAGATGTCCTCTAGGAAAGGGTAGGTAGGACGGTTTGGGGTTTCACTGCAAAAGTAAGCTGCAGTGTTGCGAAGTAAGTCACACTG F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -36.1) TCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTtGcCaTCACAACGCTTCATTCAaTGTtAC---------------- TCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATTCGACGTCACAACGCTTCATTCAGTGTGACACAGGTTCTGTGTCAC Template switch alignment (log-probability: -27) TCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATT|TGCCA|TCACAACGCTTCATTCAaTGTtAC TCCCATCCATCCTGCCAAACCCCAAAGTGACGTTTTCATT|TGCCA|TCACAACGCTTCATTCAGTGTGAC ========== Event 1218 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCATTAGAAGGGTTAGAAGTCCACC----------------AGAAGCTTGCTGGTGGACTCCCAGAAGCTCTCACATA ↑ 1 4 3 2 Chimp: ATTCATTAGAAGGGTTAGAAGACTCTC--------ATGGTGGCTTATGCTTGCTGGTGGACTCCCAGAAGCTCTCACATA Gorilla: ATTCATTAGAAGGGTTAGAAGACTCTCATGGTGGC--------TTATGCTTGCTGGTCGACTCCCAGAAGCTCTCACATA Human: ATTCATTAGAAGGGTTAGAAGTCCACC----------------AGAAGCTTGCTGGTGGACTCCCAGAAGCTCTCACATA Cluster: [ ] Orangutan: ATTCATTAGAAGGGTTAGAAGACTTTTATGGTGGC--------TTATGCTTGCTGGTGGACTCCCAGAAGCTCTCACATA Chimp > Human ------------- chr15:14358977-14358984 Template switch process: F1: L CCTCTGTTTCTTGAGGTTCTATTCATTAGAAGGGTTAGAAG 1 F3: 4 AAGCTTGCTGGTGGACTCCCAGAAGCTCTCACATACTGAGCT R RF: CCTCTGTTTCTTGAGGTTCTATTCATTAGAAGGGTTAGAAGACTCTCATGGTGGCTTATGCTTGCTGGTGGACTCCCAGAAGCTCTCACATACTGAGCT RR: GGAGACAAAGAACTCCAAGATAAGTAATCTTCCCAATCTTCTGAGAGTACCACCGAATACGAACGACCACCTGAGGGTCTTCGAGAGTGTATGACTCGA F2: 3 GACCACCT 2 Unidirectional alignment (log-probability: -35) CTCTGTTTCTTGAGGTTCTATTCATTAGAAGGGTTAGAAGtccaccagaA-----------------GCTTGCTGGTGGACTCCCAGAAGCTCTCACATACTGAG CTCTGTTTCTTGAGGTTCTATTCATTAGAAGGGTTAGAAG---------ACTCTCATGGTGGCTTATGCTTGCTGGTGGACTCCCAGAAGCTCTCACATACTGAG Template switch alignment (log-probability: -22.3) CTCTGTTTCTTGAGGTTCTATTCATTAGAAGGGTTAGAAG|TCCACCAG|AaGCTTGCTGGTGGACTCCCAGAAGCTCTCACATACTGAG CTCTGTTTCTTGAGGTTCTATTCATTAGAAGGGTTAGAAG|TCCACCAG|ATGCTTGCTGGTGGACTCCCAGAAGCTCTCACATACTGAG ========== Event 1219 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTGGTCATGTTTAGCTGATTGGTGCCATATGGCACCAATGTATTGGGAAGAGTCTGA Chimp: TCCTGGTCATGTTTAGCTGATA--AGCCATATGGCACCAATGTATTGGGAAGAGTCTGA Gorilla: TCCTGGTCATGCTTAGCTGATA--AGCCGTATGGCACCAATGTATTGGGAAGAGTCTGC ↓ 1 4 3 2 Human: TCCTGGTCATGTTTAGCTGATTGGTGCCATATGGCACCAATGTATTGGGAAGAGTCTGA Cluster: [ ] Orangutan: TCCTGGTCATGCTTAGCTGATA--AGCCATATGGCACCGATGTATTGGGAAGAGT-CGA Gorilla > Human --------------- chr15:87534372-87534379 Template switch process: F1: L TCTCATATGGAATTCTCACTTCCTGGTCATGTTTAGCTGAT 1 F3: 4 TATGGCACCAATGTATTGGGAAGAGTCTGAGCAAGCTTTT R RF: TCTCATATGGAATTCTCACTTCCTGGTCATGCTTAGCTGATAAGCCGTATGGCACCAATGTATTGGGAAGAGTCTGCGCAAGCTTTT RR: AGAGTATACCTTAAGAGTGAAGGACCAGTACGAATCGACTATTCGGCATACCGTGGTTACATAACCCTTCTCAGACGCGTTCGAAAA F2: 3 ACCGTGGT 2 Unidirectional alignment (log-probability: -41.4) CTCATATGGAATTCTCACTTCCTGGTCATGtTTAGCTGATtggtGCCaTATGGCACCAATGTATTGGGAAGAGTCTGaGCAAGCTTTT CTCATATGGAATTCTCACTTCCTGGTCATGCTTAGCTGAT--AAGCCGTATGGCACCAATGTATTGGGAAGAGTCTGCGCAAGCTTTT Template switch alignment (log-probability: -27.8) CTCATATGGAATTCTCACTTCCTGGTCATGtTTAGCTGAT|TGGTGCCA|TATGGCACCAATGTATTGGGAAGAGTCTGaGCAAGCTTTT CTCATATGGAATTCTCACTTCCTGGTCATGCTTAGCTGAT|TGGTGCCA|TATGGCACCAATGTATTGGGAAGAGTCTGCGCAAGCTTTT ========== Event 1220 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCTTGGACTGTAGCTCTTTC--AACGTAAGGCTGTCTTGAGGAAAGATAAGTCTTTGCTGG Chimp: GTCTTGGACTGTAGCTCTTTCCTCAAGTAAGGCTGTCTTGAGGAAAGATAAGTCTTTGCTGG ↑ 1 4 3 2 Gorilla: GTCTTGGACTGTAGCTCTTTC--AACTTAAGGTTGTCTTGAGGAAAGATAAGTCTTTGCTGG Human: GTCTTGGACTGTAGCTCTTTC--AACGTAAGGCTGTCTTGAGGAAAGATAAGTCTTTGCTGG Cluster: [ ] Orangutan: GTCTTGGACTGTAACTCTTTC--AACATAAGGCTGTCTTGAGGAAAGATAAGTATTTGCTGG Gorilla > Chimp --------------- chr15:68622382-68622387 Template switch process: F1: L TTAGGGAGTAATTTTCAAGTGTCTTGGACTGTAGCTCTTTC 1 F3: 4 TAAGGCTGTCTTGAGGAAAGATAAGTCTTTGCTGGTTTGTGCTGCT R RF: TTAGGGAGTAATTTTCAAGTGTCTTGGACTGTAGCTCTTTCAACTTAAGGTTGTCTTGAGGAAAGATAAGTCTTTGCTGGTTTGTGCTGCT RR: AATCCCTCATTAAAAGTTCACAGAACCTGACATCGAGAAAGTTGAATTCCAACAGAACTCCTTTCTATTCAGAAACGACCAAACACGACGA F2: 3 GAACTC 2 Unidirectional alignment (log-probability: -32.1) TAGGGAGTAATTTTCAAGTGTCTTGGACTGTAGCTCTTTC--CTcaagTAAGGcTGTCTTGAGGAAAGATAAGTCTTTGCTGGTTTGT TAGGGAGTAATTTTCAAGTGTCTTGGACTGTAGCTCTTTCAACT----TAAGGTTGTCTTGAGGAAAGATAAGTCTTTGCTGGTTTGT Template switch alignment (log-probability: -22.2) TAGGGAGTAATTTTCAAGTGTCTTGGACTGTAGCTCTTTC|CTCAAG|TAAGGcTGTCTTGAGGAAAGATAAGTCTTTGCTGGTTTGT TAGGGAGTAATTTTCAAGTGTCTTGGACTGTAGCTCTTTC|CTCAAG|TAAGGTTGTCTTGAGGAAAGATAAGTCTTTGCTGGTTTGT ========== Event 1221 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: a----------aaa--aaaaaaaaGTTAACTGTTTTGATTGTTTTTTTGTATGTCT Chimp: a-------------aaaaaaaaaaGTTAACtattatgattgtttttttgtttgtct Gorilla: a----aaaaaa-----aaaaaaaaGTTAACTATTGTGATTGtttttttgtttgtct ↓ 31 2 4 Human: a----------aaa--aaaaaaaaGTTAACTGTTTTGATTGTTTTTTTGTATGTCT Cluster: [ ] Orangutan: aaaaa-----------aaaaaaaaGTTAACTATTATGATTGtttttttttttgtct Gorilla > Human --------------- chr15:88640958-88640968 Template switch process: F1: L GGGCAACAGAGCCAGGAAAAAAAAAAAA 1 F3: 4 TGATTGTTTTTTTGTATGTCTGTTTTATTATTATTTTTTT R RF: GGGCAACAGAGCCAGGAAAAAAAAAAAAAAAGTTAACTATTGTGATTGTTTTTTTGTTTGTCTGTTTTATTATTATTTTTTT RR: CCCGTTGTCTCGGTCCTTTTTTTTTTTTTTTCAATTGATAACACTAACAAAAAAACAAACAGACAAAATAATAATAAAAAAA F2: 3 TTTGTCAATTG 2 Unidirectional alignment (log-probability: -38.6) GGGCAACAGAGCCAGGAAAAAAAAAAAA---GTTAACTgTTtTGATTGTTTTTTTGTaTGTCTGTTTTATTATTATTTTttt GGGCAACAGAGCCAGGAAAAAAAAAAAAAAAGTTAACTATTGTGATTGTTTTTTTGTTTGTCTGTTTTATTATTATTTT--- Template switch alignment (log-probability: -27.8) GGGCAACAGAGCCAGGAAAAAAAAAAAA|GTTAACTgTTT|TGATTGTTTTTTTGTaTGTCTGTTTTATTATTATTTTTTT GGGCAACAGAGCCAGGAAAAAAAAAAAA|GTTAACTTTTT|TGATTGTTTTTTTGTTTGTCTGTTTTATTATTATTTTTTT ========== Event 1222 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GAGCCCGAGTTCTTTGTGCTCGCAAAATTGTGTACGCAATTTTGCTTGTCTGAGCCGTTAAGGGG ↑ 1 4 3 2 Chimp: GAGCCCGAGTTCTTTGTGCTC------ATATGTATGCAATTTTGCTTGTCTGAGCCGTTAAGGGG Gorilla: GAGCCCGAGTTCTTTGTGCTT------GTATGTACACAATTTTTCTTGTCTGAGCCGTTAAGGGG Human: GAGCCCGAGTTCTTTGTGCTCGCAAAATTGTGTACGCAATTTTGCTTGTCTGAGCCGTTAAGGGG Cluster: [ ] Orangutan: GAGCCTGAGTTCTCTGTGCTT------ATATGTATGCAATTTTGCTTGTCTGAGCCGTTAAGGGG Chimp > Human ------------- chr15:12776555-12776563 Template switch process: F1: L ACAGGTTCCAATCTATTTAGGAGCCCGAGTTCTTTGTGCTC 1 F3: 4 TGTACGCAATTTTGCTTGTCTGAGCCGTTAAGGGGGCTGCCCCAA R RF: ACAGGTTCCAATCTATTTGGGAGCCCGAGTTCTTTGTGCTCATATGTATGCAATTTTGCTTGTCTGAGCCGTTAAGGGGGCTGCCCCAA RR: TGTCCAAGGTTAGATAAACCCTCGGGCTCAAGAAACACGAGTATACATACGTTAAAACGAACAGACTCGGCAATTCCCCCGACGGGGTT F2: 3 GTTAAAACG 2 Unidirectional alignment (log-probability: -43.6) CAGGTTCCAATCTATTTaGGAGCCCGAGTTCTTTGTGCTCgcaaaatTgTGTAcGCAATTTTGCTTGTCTGAGCCGTTAAGGGGGCTGC CAGGTTCCAATCTATTTGGGAGCCCGAGTTCTTTGTGCTC------ATATGTATGCAATTTTGCTTGTCTGAGCCGTTAAGGGGGCTGC Template switch alignment (log-probability: -28.5) CAGGTTCCAATCTATTTaGGAGCCCGAGTTCTTTGTGCTC|GCAAAATTG|TGTAcGCAATTTTGCTTGTCTGAGCCGTTAAGGGGGCTGC CAGGTTCCAATCTATTTGGGAGCCCGAGTTCTTTGTGCTC|GCAAAATTG|TGTATGCAATTTTGCTTGTCTGAGCCGTTAAGGGGGCTGC ========== Event 1223 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: aggcaggagaatcacctgaacctgagaggcagaggcttcagtgagccgaggccacaccactgcactccggccttggtgacagagactctgcctcgaaagataaaaaTAATAATGAAAGTAATATTGGGATTATACTG------------------------TACATTCTTTCTTACATGTATGGT ↓ 3 2 4 1 Chimp: aggcaggagaatcacctgaacctgagaggcagaggtttcagtgagccgagaccacaccactgcactccggcctgggtgacagagactctgcctcaaaaaataaaaaTAATAATGAAAGTAATGTTGGGATTATACTG------------TACACTCAGGTGTACATTCTTTCTTACATGTATGGT Gorilla: aggcaggagaatcacctgaacctgagaggcagaggtttcagtgagccgagaccacaccactgcactccggcctgggtgacagagactctgcctcaaaaaataaaaataataatgaaaGTAATGTTGGGATTATACTGTACACTCAGGTG------------TACATTCTTTCTTACATGTATGGT ↑ 3 2 4 1 Human: aggcaggagaatcacctgaacctgagaggcagaggcttcagtgagccgaggccacaccactgcactccggccttggtgacagagactctgcctcgaaagataaaaaTAATAATGAAAGTAATATTGGGATTATACTG------------------------TACATTCTTTCTTACATGTATGGT Cluster: [ ] Orangutan: Human > Chimp ------------- chr15:71055458-71055464 Template switch process: F1: L AAAATAAAAATAATAATGAAAGTAATGTTGGGATTATACTGTACA 1 F3: 4 GTACATTCTTTCTTACATGTATGGTGAATATATTTTGACAA R RF: ACCTGAGAGGCAGAGGCTTCAGTGAGCCGAGGCCACACCACTGCACTCCGGCCTTGGTGACAGAGACTCTGCCTCGAAAGATAAAAATAATAATGAAAGTAATATTGGGATTATACTGTACATTCTTTCTTACATGTATGGTGAATATATTTTGACAA RR: TGGACTCTCCGTCTCCGAAGTCACTCGGCTCCGGTGTGGTGACGTGAGGCCGGAACCACTGTCTCTGAGACGGAGCTTTCTATTTTTATTATTACTTTCATTATAACCCTAATATGACATGTAAGAAAGAATGTACATACCACTTATATAAAACTGTT F2: 3 TGGACTC 2 Unidirectional alignment (log-probability: -40.2) AAAAATAATAATGAAAGTAATgTTGGGATTATACTGTACactcaggtgtacATTCTTTCTTACATGTATGGTGAATATATTTTGACA AAAAATAATAATGAAAGTAATATTGGGATTATACTGTAC------------ATTCTTTCTTACATGTATGGTGAATATATTTTGACA Template switch alignment (log-probability: -28.2) AAAAATAATAATGAAAGTAATgTTGGGATTATACTGTACA|CTCAGGT|GTACATTCTTTCTTACATGTATGGTGAATATATTTTGACA AAAAATAATAATGAAAGTAATATTGGGATTATACTGTACA|CTCAGGT|GTACATTCTTTCTTACATGTATGGTGAATATATTTTGACA Human > Gorilla --------------- chr15:68889866-68889872 Template switch process: F1: L AAAATAAAAATAATAATGAAAGTAATGTTGGGATTATACTGTACA 1 F3: 4 GTACATTCTTTCTTACATGTATGGTGAATATATTTTGACAA R RF: ACCTGAGAGGCAGAGGCTTCAGTGAGCCGAGGCCACACCACTGCACTCCGGCCTTGGTGACAGAGACTCTGCCTCGAAAGATAAAAATAATAATGAAAGTAATATTGGGATTATACTGTACATTCTTTCTTACATGTATGGTGAATATATTTTGACAA RR: TGGACTCTCCGTCTCCGAAGTCACTCGGCTCCGGTGTGGTGACGTGAGGCCGGAACCACTGTCTCTGAGACGGAGCTTTCTATTTTTATTATTACTTTCATTATAACCCTAATATGACATGTAAGAAAGAATGTACATACCACTTATATAAAACTGTT F2: 3 TGGACTC 2 Unidirectional alignment (log-probability: -39.2) AAAAATAATAATGAAAGTAATgTTGGGATTATACtgtacactcaggTGTACATTCTTTCTTACATGTATGGTGAATATATTTTGACA AAAAATAATAATGAAAGTAATATTGGGATTATAC------------TGTACATTCTTTCTTACATGTATGGTGAATATATTTTGACA Template switch alignment (log-probability: -27.8) AAAAATAATAATGAAAGTAATgTTGGGATTATACTGTACA|CTCAGGT|GTACATTCTTTCTTACATGTATGGTGAATATATTTTGACA AAAAATAATAATGAAAGTAATATTGGGATTATACTGTACA|CTCAGGT|GTACATTCTTTCTTACATGTATGGTGAATATATTTTGACA ========== Event 1224 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTCTAATAGGAAATCTTGGTAACAGTAT-ATGTTACCATTAAAGGGAAGCCTGG Chimp: GGTCTAATAGGAAATCTTGGT---GCTATACTGTTACCATTAAAGGGAAGCCTGG Gorilla: GGTCTAATAGGAAATCTTGGT---GCTATACTGTTACCATTAAAGGGAAGCCTGG ↓ 1 3 4 2 Human: GGTCTAATAGGAAATCTTGGTAACAGTAT-ATGTTACCATTAAAGGGAAGCCTGG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr15:90758899-90758907 Template switch process: F1: L CTGAGGGAGTGGGAAGGGTAGGTCTAATAGGAAATCTTGGT 1 F3: 4 TGTTACCATTAAAGGGAAGCCTGGATTCCAGGCAGATCAA R RF: CTGAGGGAGTGGGAAGGGTAGGTCTAATAGGAAATCTTGGTGCTATACTGTTACCATTAAAGGGAAGCCTGGATTCCAGGCAGATCAA RR: GACTCCCTCACCCTTCCCATCCAGATTATCCTTTAGAACCACGATATGACAATGGTAATTTCCCTTCGGACCTAAGGTCCGTCTAGTT F2: 3 ATATGACAA 2 Unidirectional alignment (log-probability: -33.9) TGAGGGAGTGGGAAGGGTAGGTCTAATAGGAAATCTTGGT-------aacagtataTGTTACCATTAAAGGGAAGCCTGGATTCCAGGCAGATCAA TGAGGGAGTGGGAAGGGTAGGTCTAATAGGAAATCTTGGTGCTATAC---------TGTTACCATTAAAGGGAAGCCTGGATTCCAGGCAGATCAA Template switch alignment (log-probability: -16.9) TGAGGGAGTGGGAAGGGTAGGTCTAATAGGAAATCTTGGT|AACAGTATA|TGTTACCATTAAAGGGAAGCCTGGATTCCAGGCAGATCAA TGAGGGAGTGGGAAGGGTAGGTCTAATAGGAAATCTTGGT|AACAGTATA|TGTTACCATTAAAGGGAAGCCTGGATTCCAGGCAGATCAA ========== Event 1225 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAATCCACTGGATTTTATATCAGAAACAGAAAAAATATGAAAAGGAATAG Chimp: AAAATCCACTGGATTTTATATCAGAAACAGAAAAAATATGAAAAGGAATAG ↓ 3 1 2 4 Gorilla: AAAATCCACTGGATTTTATATCTTTCTGATAAAAAATATGAAAAGGAATAG ↑ 3 1 2 4 Human: AAAATCCACTGGATTTTATATCAGAAACAGAAAAAATATGAAAAGGAATAG Cluster: [ ] Orangutan: AAAATCCACTGGATTTTATATCAGAAACAGAAGAAATATGAAAAGGAATAG Human > Gorilla --------------- chr15:69862310-69862317 Template switch process: F1: L TTGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC 1 F3: 4 AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA R RF: TTGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATCAGAAACAGAAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA RR: AACGGTATAGATCATGAACTTTTAGGTGACCTAAAATATAGTCTTTGTCTTTTTTATACTTTTCCTTATCACTTTATTTCTCAACTTCT F2: 3 TAGTCTTT 2 Unidirectional alignment (log-probability: -32.5) TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC--------tttctgatAAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATCAGAAACAG--------AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA Template switch alignment (log-probability: -16.7) TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC|TTTCTGAT|AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC|TTTCTGAT|AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA Chimp > Gorilla --------------- chr15:69862310-69862317 Template switch process: F1: L TTGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC 1 F3: 4 AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA R RF: TTGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATCAGAAACAGAAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA RR: AACGGTATAGATCATGAACTTTTAGGTGACCTAAAATATAGTCTTTGTCTTTTTTATACTTTTCCTTATCACTTTATTTCTCAACTTCT F2: 3 TAGTCTTT 2 Unidirectional alignment (log-probability: -32.5) TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC--------tttctgatAAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATCAGAAACAG--------AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA Template switch alignment (log-probability: -16.7) TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC|TTTCTGAT|AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA TGCCATATCTAGTACTTGAAAATCCACTGGATTTTATATC|TTTCTGAT|AAAAAATATGAAAAGGAATAGTGAAATAAAGAGTTGAAGA ========== Event 1226 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: caaggttgagaacAAGTATAGTAGAGCAACACTTATACAGTTTCAGCACTATTTCTGTAATTATCT ↓ 1 4 3 2 Chimp: caaggttgagaacAAGTATAGCTG----AAACTTATACAGTTTCAGCACTATTTCTGTAATTATCT ↑ 1 4 3 2 Gorilla: caagtttgagaacAAGTATAGTAGAGCAGCACTTATACAGTTTCAGCACTATTTCTGTAATTATCT Human: caaggttgagaacAAGTATAGTAGAGCAACACTTATACAGTTTCAGCACTATTTCTGTAATTATCT Cluster: [ ] Orangutan: caaggttgagaaccaGTATAGTAGAGCAACACTTATACAGTTTCAGCACTATTTCTGTAATTATCT Human > Chimp ------------- chr15:72508032-72508036 Template switch process: F1: L AGATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAG 1 F3: 4 ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC R RF: AGATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAGTAGAGCAACACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC RR: TCTACTAAGGTTATACGACGGTTCCAACTCTTGTTCATATCATCTCGTTGTGAATATGTCAAAGTCGTGATAAAGACATTAATAGAGTGG F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -27.3) GATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAG--------CtgaaACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC GATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAGTAGAGCAAC----ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC Template switch alignment (log-probability: -15.9) GATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAG|CTGAA|ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC GATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAG|CTGAA|ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC Gorilla > Chimp --------------- chr15:72508032-72508036 Template switch process: F1: L AGATGATTCCAATATGCTGCCAAGGTTGAGAACAAGTATAG 1 F3: 4 ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC R RF: AGATGATTCCAATATGCTGCCAAGTTTGAGAACAAGTATAGTAGAGCAGCACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC RR: TCTACTAAGGTTATACGACGGTTCAAACTCTTGTTCATATCATCTCGTCGTGAATATGTCAAAGTCGTGATAAAGACATTAATAGAGTGG F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -32.3) GATGATTCCAATATGCTGCCAAGgTTGAGAACAAGTAT--------AGCtgaaACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC GATGATTCCAATATGCTGCCAAGTTTGAGAACAAGTATAGTAGAGCAGC----ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC Template switch alignment (log-probability: -21.9) GATGATTCCAATATGCTGCCAAGgTTGAGAACAAGTATAG|CTGAA|ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC GATGATTCCAATATGCTGCCAAGTTTGAGAACAAGTATAG|CTGAA|ACTTATACAGTTTCAGCACTATTTCTGTAATTATCTCACC ========== Event 1227 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCTGAAGCTCGAAAGGAATCTGGAGCAAGATTGAGAGAGCTTCCCATACCAACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACCCTCAA-GAAAAGAAAAAATAGCACTGAAG ↑ 3 2 1 4 Chimp: ACCTGAAGCTCGAAGGGAATCTGGAGCAAGATTGAGAGAGCTTCCCATACCAACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACCTTTTCGTGAAAGAAAAAATAGCACTGAAG Gorilla: ACCTGAAGCTCGAAGGGAATCTGGAGCAAGATTGAGAGAGCTTCCCATACCAACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACCTTTCAAGAAAAGAAAAAATAGCACTGAAG Human: ACCTGAAGCTCGAAAGGAATCTGGAGCAAGATTGAGAGAGCTTCCCATACCAACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACCCTCAA-GAAAAGAAAAAATAGCACTGAAG Cluster: [ ] Orangutan: ACCTGAAGCTTGAAGGGAATCTGGAGCAAGATTTAGAGAGCTTCCCATACCAACCTCCAGATA-TTTACAGCTGAGAAGGTATCCACTCACCTTTTCTTAAAAGAAAAAATAGCACTCAAG Chimp > Human ------------- chr15:92186398-92186404 Template switch process: F1: L AACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACC 1 F3: 4 AAAGAAAAAATAGCACTGAAGGTCCCTTTCCCATGTCAAA R RF: TCTGGAGCAAGATTGAGAGAGCTTCCCATACCAACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACCTTTTCGTGAAAGAAAAAATAGCACTGAAGGTCCCTTTCCCATGTCAAA RR: AGACCTCGTTCTAACTCTCTCGAAGGGTATGGTTGGAGGTCTATAAAATGTCGACTCTTCCATAGGTGAGTGGAAAAGCACTTTCTTTTTTATCGTGACTTCCAGGGAAAGGGTACAGTTT F2: 3 AGAACTC 2 Unidirectional alignment (log-probability: -31.6) ACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACCctcaaga--------AAAGAAAAAATAGCACTGAAGGTCCCTTTCCCATGTCAAA ACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACC-------TTTTCGTGAAAGAAAAAATAGCACTGAAGGTCCCTTTCCCATGTCAAA Template switch alignment (log-probability: -22.1) ACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACC|CTCaAGA|AAAGAAAAAATAGCACTGAAGGTCCCTTTCCCATGTCAAA ACCTCCAGATATTTTACAGCTGAGAAGGTATCCACTCACC|CTCCAGA|AAAGAAAAAATAGCACTGAAGGTCCCTTTCCCATGTCAAA ========== Event 1228 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTTCAACTGGAGTGAAATGAAAAAAGGCACT Chimp: GGTTGCCATGGCAGTTCCTCCAGTTGGCTCTT----TTTCAGTGAAATGAAAAAAGGCACT Gorilla: GGTTGCCATGGCAGTTCCTCCAGTTGGCTCTT----TTTCAGTGAAATGAAAAAAGGCACT ↓ 3 2 1 4 Human: GGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTTCAACTGGAGTGAAATGAAAAAAGGCACT Cluster: [ ] Orangutan: GGTTGCCATGGCAGTTCCTCCAGTTGGCTCTT----TTTCAGTGAAATGAAAAAAGGCACT Gorilla > Human --------------- chr15:92160377-92160383 Template switch process: F1: L CTATTATGCGGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTT 1 F3: 4 AGTGAAATGAAAAAAGGCACTTGTTAGGGGGCAGGGAAAA R RF: CTATTATGCGGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTTTTCAGTGAAATGAAAAAAGGCACTTGTTAGGGGGCAGGGAAAA RR: GATAATACGCCAACGGTACCGTCAAGGAGGTCAACCGAGAAAAAGTCACTTTACTTTTTTCCGTGAACAATCCCCCGTCCCTTTT F2: 3 GGTCAAC 2 Unidirectional alignment (log-probability: -27.7) ATTATGCGGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTTcaacTggAGTGAAATGAAAAAAGGCACTTGTTAGGGGGCAGGGAAAA ATTATGCGGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTT----TTCAGTGAAATGAAAAAAGGCACTTGTTAGGGGGCAGGGAAAA Template switch alignment (log-probability: -16.6) ATTATGCGGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTT|CAACTGG|AGTGAAATGAAAAAAGGCACTTGTTAGGGGGCAGGGAAAA ATTATGCGGTTGCCATGGCAGTTCCTCCAGTTGGCTCTTT|CAACTGG|AGTGAAATGAAAAAAGGCACTTGTTAGGGGGCAGGGAAAA ========== Event 1229 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: atTAATGAATAGACAGATAGA--CGGATGATAGCAAAGCTACCA--TATCTATTTCCAAGCCAGTCTCC Chimp: atTAATGAATAGACAGATAGA--CGGATGATAGCAAAGCTACTA--TATCTATTTCCAAGCCAGTCTCC ↓ 13 24 ↑ 13 24 Gorilla: atTAATGAATAGACAGATAGA----TATAGTAGCTTTGCTATCATCCGTCTATTTCCAAGCCAGTCTCC ↓ 13 24 ↑ 13 24 Human: atTAATGAATAGACAGATAGA--CGGATGATAGCAAAGCTACCA--TATCTATTTCCAAGCCAGTCTCC Cluster: [ ] Orangutan: atTAATGAATAGACA----GACG--GATGATAGCAAAGCTACTA--TATCTATTTCCAAGCCAGTCTCC Gorilla > Human --------------- chr15:8380798-8380820 Template switch process: F1: L CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA 1 F3: 4 TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA R RF: CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGATATAGTAGCTTTGCTATCATCCGTCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA RR: GTATAAATAATTTCTTGACTTAATTACTTATCTGTCTATCTATATCATCGAAACGATAGTAGGCAGATAAAGGTTCGGTCAGAGGTAGACGGAGACTGTCATTT F2: 3 ATACCATCGAAACGATAGTAGGC 2 Unidirectional alignment (log-probability: -51.9) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA---------------------CGgatgatagcaaagctaccataTCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGATATAGTAGCTTTGCTATCATCCG---------------------TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Template switch alignment (log-probability: -24.2) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|CGGATGATAGCAAAGCTACcATA|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|CGGATGATAGCAAAGCTACTATA|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Human > Gorilla --------------- chr15:8652193-8652215 Template switch process: F1: L CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA 1 F3: 4 TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA R RF: CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGACGGATGATAGCAAAGCTACCATATCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA RR: GTATAAATAATTTCTTGACTTAATTACTTATCTGTCTATCTGCCTACTATCGTTTCGATGGTATAGATAAAGGTTCGGTCAGAGGTAGACGGAGACTGTCATTT F2: 3 GCCTACTATCGTTTCGATGATAT 2 Unidirectional alignment (log-probability: -51.9) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAG---------------------ATAtagtagctttgctatcatccgTCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGACGGATGATAGCAAAGCTACCATA---------------------TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Template switch alignment (log-probability: -24.2) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|TATaGTAGCTTTGCTATCATCCG|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|TATGGTAGCTTTGCTATCATCCG|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Gorilla > Chimp --------------- chr15:8743163-8743185 Template switch process: F1: L CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA 1 F3: 4 TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA R RF: CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGATATAGTAGCTTTGCTATCATCCGTCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA RR: GTATAAATAATTTCTTGACTTAATTACTTATCTGTCTATCTATATCATCGAAACGATAGTAGGCAGATAAAGGTTCGGTCAGAGGTAGACGGAGACTGTCATTT F2: 3 ATATCATCGAAACGATAGTAGGC 2 Unidirectional alignment (log-probability: -49) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGAcggatgatagcaaagctacTATA-------------------TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA-------------------TATAGTAGCTTTGCTATCATCCGTCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Template switch alignment (log-probability: -18.7) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|CGGATGATAGCAAAGCTACTATA|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|CGGATGATAGCAAAGCTACTATA|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Chimp > Gorilla --------------- chr15:8652193-8652215 Template switch process: F1: L CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA 1 F3: 4 TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA R RF: CATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGACGGATGATAGCAAAGCTACTATATCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA RR: GTATAAATAATTTCTTGACTTAATTACTTATCTGTCTATCTGCCTACTATCGTTTCGATGATATAGATAAAGGTTCGGTCAGAGGTAGACGGAGACTGTCATTT F2: 3 GCCTACTATCGTTTCGATGATAT 2 Unidirectional alignment (log-probability: -49) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA-------------------TATAgtagctttgctatcatccgTCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGACGGATGATAGCAAAGCTACTATA-------------------TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA Template switch alignment (log-probability: -18.7) ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|TATAGTAGCTTTGCTATCATCCG|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ATATTTATTAAAGAACTGAATTAATGAATAGACAGATAGA|TATAGTAGCTTTGCTATCATCCG|TCTATTTCCAAGCCAGTCTCCATCTGCCTCTGACAGTAAA ========== Event 1230 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGCATAGTCTCAGTTGTGACCTAACGGACTCAATGACTTTGTTCACTAACACAT Chimp: AGCATAGTCTCAGTTGTGACCTAACGGACTCAATGACTTTGTTCACTAACACAT ↑ 3 2 4 Gorilla: AGCATAGTCTCAGTTGTGACCGTTATGACTCAACGACTTTGTTCACTAACACAT ↓ 3 2 4 Human: AGCATAGTCTCAGTTGTGACCTAACGGACTCAATGACTTTGTTCACTAACACAT Cluster: [ ] Orangutan: AGCATAGTCTCAGTTGTGACTGTTATGACTCAATGACTTTGTTCACTAACACAT Gorilla > Human --------------- chr15:7821548-7821552 Template switch process: F1: L GGCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC 1 F3: 4 GACTCAATGACTTTGTTCACTAACACATTCTGCCTTTCATAGCCTCAT R RF: GGCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACCGTTATGACTCAACGACTTTGTTCACTAACACATTCTGCCTTTCATAGCCTCAT RR: CCGATCCCCTACGAAAACTTTCGTATCAGAGTCAACACTGGCAATACTGAGTTGCTGAAACAAGTGATTGTGTAAGACGGAAAGTATCGGAGTA F2: 3 GCAAT 2 Unidirectional alignment (log-probability: -32.2) GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC----TaacgGACTCAAtGACTTTGTTCACTAACACATTCTGCCTTTCAT GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACCGTTAT----GACTCAACGACTTTGTTCACTAACACATTCTGCCTTTCAT Template switch alignment (log-probability: -22.1) GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC|TAACG|GACTCAAtGACTTTGTTCACTAACACATTCTGCCTTTCAT GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC|TAACG|GACTCAACGACTTTGTTCACTAACACATTCTGCCTTTCAT Gorilla > Chimp --------------- chr15:8196457-8196461 Template switch process: F1: L GGCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC 1 F3: 4 GACTCAATGACTTTGTTCACTAACACATTCTGCCTTTCATAGCCTCAT R RF: GGCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACCGTTATGACTCAACGACTTTGTTCACTAACACATTCTGCCTTTCATAGCCTCAT RR: CCGATCCCCTACGAAAACTTTCGTATCAGAGTCAACACTGGCAATACTGAGTTGCTGAAACAAGTGATTGTGTAAGACGGAAAGTATCGGAGTA F2: 3 GCAAT 2 Unidirectional alignment (log-probability: -32.2) GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC----TaacgGACTCAAtGACTTTGTTCACTAACACATTCTGCCTTTCAT GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACCGTTAT----GACTCAACGACTTTGTTCACTAACACATTCTGCCTTTCAT Template switch alignment (log-probability: -22.1) GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC|TAACG|GACTCAAtGACTTTGTTCACTAACACATTCTGCCTTTCAT GCTAGGGGATGCTTTTGAAAGCATAGTCTCAGTTGTGACC|TAACG|GACTCAACGACTTTGTTCACTAACACATTCTGCCTTTCAT ========== Event 1231 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: --------------------ACATTGTAC--TTTTACTACATTGAT-TTTAAACTT-----TTCTT---TTAAGAAAACTTTTAAGAAAAGTTTAATAATCAATGTAGTAAAAGAGTACAATGTTTAACTTAGCAAATGCTAA Chimp: --------------------ACACTGTACTCTTTTACTACATTGATTATTAAACTT-----TT---CTTTTAAGAAAACTTTTAAGAAAAGTTTAATAATCAATGTAGTAAAAGAGTACAATGTTTAACGTAGCAAATGCTAA ↑ 1 4 3 2 Gorilla: --------------------ATATTGTAC--TCTTACTACATTGATTATTaaactt-------------ttaagaaaacttttaagaaaagtttAATAATCAATGTAGTAAAAGAGTACAATGTTTAACTTAGCAAATGCTAA Human: --------------------ACATTGTAC--TTTTACTACATTGAT-TTTAAACTT-----TTCTT---TTAAGAAAACTTTTAAGAAAAGTTTAATAATCAATGTAGTAAAAGAGTACAATGTTTAACTTAGCAAATGCTAA Cluster: [ ] Orangutan: CCCCCCACTAAAGACACCCCCCCtttttt--ttttATtatatatat-ataatatatatata--------t----TACAGTTAAAAGAAAAGTTTAATAATCAATGTAGTAAAACAGTACAATGTTTAACTTAGCAAATGCTAA Gorilla > Chimp --------------- chr15:8892910-8892946 Template switch process: F1: L TATATTTATATAGCAAATATATATATATTTGCTAAGTTAAA 1 F3: 4 CTTTTAAGAAAACTT R RF: TATATTTATATAGCAAATATATATATATTTGCTAAGTTAAATATTGTACTCTTACTACATTGATTATTAAACTTTTAAGAAAACTTTTAAGAAAAGTTTAATAATCAATGTAGTAAAAGAGTACAATG RR: ATATAAATATATCGTTTATATATATATAAACGATTCAATTTATAACATGAGAATGATGTAACTAATAATTTGAAAATTCTTTTGAAAATTCTTTTCAAATTATTAGTTACATCATTTTCTCATGTTAC F2: 3 TTTTCAAATTATTAGTTACATCATTTTCTCATGTCAC 2 Unidirectional alignment (log-probability: -41.8) ATATTTATATAGCAAATATATATATATTTGCTAAGTTAAAcAcTGTACTCttTTACTACATTGATTATTAAActtttCTTTTAAGAAAACTT ATATTTATATAGCAAATATATATATATTTGCTAAGTTAAATATTGTACTC--TTACTACATTGATTATTAAA-----CTTTTAAGAAAACTT Template switch alignment (log-probability: -25.4) ATATTTATATAGCAAATATATATATATTTGCTAAGTTAAA|CAcTGTACTCTTTTACTACATTGATTATTAAACTTTT|CTTTTAAGAAAACTT ATATTTATATAGCAAATATATATATATTTGCTAAGTTAAA|CATTGTACTCTTTTACTACATTGATTATTAAACTTTT|CTTTTAAGAAAACTT ========== Event 1232 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: AGCCACACAGACCTAAGTTGGCGCATGCATGTGTGTGTGCGCGTGCAGGcacaca----------cac-- Chimp: AGCCACACAGATCTAAGTTGGCGCATGCGTGTGTGTGTGCGCGCACATGcacaca----------cac-- Gorilla: AGCCACACAGACCTAAGTTGGTGCATGCGTGTGTGTGTGCGCGCACATGcacaca----------cac-- ↑ 3 2 1 4 Human: AGCCACACAGACCTAAGTTGGCGCATGCATGTGTGTGTGCGCGTGCAGGcacaca----------cac-- Cluster: [ ] Orangutan: AGCCACACAGACCTAAGTTGGCGCATGCGTGTGTGTGCG--CACGCATGcacacacacacacacacacac Human > Gorilla --------------- chr15:5885231-5885238 Template switch process: F1: L TTCTTGAAGGGTGTGGCTGCAGCCACACAGACCTAAGTTGGTGCATGCGTGTGTGTGTGCGCG 1 F3: 4 CACACACACAAACA R RF: TTCTTGAAGGGTGTGGCTGCAGCCACACAGACCTAAGTTGGCGCATGCATGTGTGTGTGCGCGTGCAGGCACACACACAAACA RR: AAGAACTTCCCACACCGACGTCGGTGTGTCTGGATTCAACCGCGTACGTACACACACACGCGCACGTCCGTGTGTGTGTTTGT F2: 3 ACGTACAC 2 Unidirectional alignment (log-probability: -44.3) CACACAGACCTAAGTTGGtGCATGCgTGTGTGTGTGCGCGcaCAtGCACACAC----ACACAaACA CACACAGACCTAAGTTGGCGCATGCATGTGTGTGTGCGCGTGCAGGCACACACACAAACACACACA Template switch alignment (log-probability: -27.7) CACACAGACCTAAGTTGGtGCATGCgTGTGTGTGTGCGCG|CACATGCA|CACACACACAAACA CACACAGACCTAAGTTGGCGCATGCATGTGTGTGTGCGCG|CACATGCA|CACACACACAAACA ========== Event 1233 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTCATAAAACTTGCCATTTATGCATT------AA------TTGCTTAATTAATCATGTCAT Chimp: CATTCATAAAACTTGCCATTTATGCATT------AA------TTGCTTAATTAAtcatgtcat ↓ 4 2 1 Gorilla: CATTCATAAAACTTGCCATTTATGCATTATGCATAATTATGCATGCTTAATTAAtcatgtcat ↑ 4 2 1 Human: CATTCATAAAACTTGCCATTTATGCATT------AA------TTGCTTAATTAATCATGTCAT Cluster: [ ] Orangutan: CATTCATAAatcttgccatttatgcatt------aa------ttgcttaattaatcatgtcat Human > Gorilla --------------- chr15:74457360-74457366 Template switch process: F1: L TGTGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA 1 F3: 4 TTATGCA-----TGCTTAATTAATCATGTCATACTTGCCCATCTCTGTAGGT R RF: TGTGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTAATTGCTTAATTAATCATGTCATACTTGCCCATCTCTGTAGGT RR: ACACAAAAACGCGGTAAGTATTTTGAACGGTAAATACGTAATTAACGAATTAATTAGTACAGTATGAACGGGTAGAGACATCCA F2: 3 AATACGT 2 Unidirectional alignment (log-probability: -37.9) TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTAtgcataattATgcaTGCTTAATTAATCATGTCATACTTGCCCATCTC TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA---------AT---TGCTTAATTAATCATGTCATACTTGCCCATCTC Template switch alignment (log-probability: -26.8) TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA|TGCATAA|TTATGCA-----TGCTTAATTAATCATGTCATACTTGCCCATCTC TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA|TGCATAA|TTATGCATTAATTGCTTAATTAATCATGTCATACTTGCCCATCTC Chimp > Gorilla --------------- chr15:74457360-74457366 Template switch process: F1: L TGTGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA 1 F3: 4 TTATGCA-----TGCTTAATTAATCATGTCATACTTGCCCATCTCTGTAGGT R RF: TGTGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTAATTGCTTAATTAATCATGTCATACTTGCCCATCTCTGTAGGT RR: ACACAAAAACGCGGTAAGTATTTTGAACGGTAAATACGTAATTAACGAATTAATTAGTACAGTATGAACGGGTAGAGACATCCA F2: 3 AATACGT 2 Unidirectional alignment (log-probability: -37.9) TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTAtgcataattATgcaTGCTTAATTAATCATGTCATACTTGCCCATCTC TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA---------AT---TGCTTAATTAATCATGTCATACTTGCCCATCTC Template switch alignment (log-probability: -26.8) TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA|TGCATAA|TTATGCA-----TGCTTAATTAATCATGTCATACTTGCCCATCTC TGTTTTTGCGCCATTCATAAAACTTGCCATTTATGCATTA|TGCATAA|TTATGCATTAATTGCTTAATTAATCATGTCATACTTGCCCATCTC ========== Event 1234 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTGCATCAAGCCAGAAGACACGAGACCTTTCCAAAGGGCTCATGTCTTCTGGCCTGATGCAC ↓ 1 3 4 2 Chimp: TGTGCATCAAGCCAGAAGACATGAGCCCTTTGGAAAGGTCTCATGTCTTCTGGCTTGATGCAC ↑ 1 3 4 2 Gorilla: TGTGCATCAAGCCAGAAGACATAAGACCTTTCCAAAGAGCTCATGTCTTCTGGCTTGATGCAC Human: TGTGCATCAAGCCAGAAGACACGAGACCTTTCCAAAGGGCTCATGTCTTCTGGCCTGATGCAC Cluster: [ ] Orangutan: ggt---------------ccatgagacctttccaaaggtctcatgTCTT-------------- Human > Chimp ------------- chr1:59553993-59554010 Template switch process: F1: L TGTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACA 1 F3: 4 CTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG R RF: TGTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACACGAGACCTTTCCAAAGGGCTCATGTCTTCTGGCCTGATGCACATTTTTGTGTCCCCTG RR: ACACGTATTTCGGATCGTTTACACGTAGTTCGGTCTTCTGTGCTCTGGAAAGGTTTCCCGAGTACAGAAGACCGGACTACGTGTAAAAACACAGGGGAC F2: 3 TGGAAAGGTTTCCCGAGT 2 Unidirectional alignment (log-probability: -36.8) GTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACAtGAGcCCTTTggAAAGGtCTCATGTCTTCTGGCtTGATGCACATTTTTGTGTCCCCTG GTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACACGAGACCTTTCCAAAGGGCTCATGTCTTCTGGCCTGATGCACATTTTTGTGTCCCCTG Template switch alignment (log-probability: -23.5) GTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACA|TGAGCCCTTTGGAAAGGT|CTCATGTCTTCTGGCtTGATGCACATTTTTGTGTCCCCTG GTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACA|TGAGCCCTTTGGAAAGGT|CTCATGTCTTCTGGCCTGATGCACATTTTTGTGTCCCCTG Gorilla > Chimp --------------- chr1:59553994-59554010 Template switch process: F1: L GTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACAT 1 F3: 4 CTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG R RF: GTGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACATAAGACCTTTCCAAAGAGCTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG RR: CACGTATTTCGGATCGTTTACACGTAGTTCGGTCTTCTGTATTCTGGAAAGGTTTCTCGAGTACAGAAGACCGAACTACGTGTAAAAACACAGGGGAC F2: 3 TGGAAAGGTTTCCCGAG 2 Unidirectional alignment (log-probability: -34.5) TGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACATgAGcCCTTTggAAAGgtCTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG TGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACATAAGACCTTTCCAAAGAGCTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG Template switch alignment (log-probability: -23.4) TGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACAT|GAGCcCTTTGGAAAGGT|CTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG TGCATAAAGCCTAGCAAATGTGCATCAAGCCAGAAGACAT|GAGCTCTTTGGAAAGGT|CTCATGTCTTCTGGCTTGATGCACATTTTTGTGTCCCCTG ========== Event 1235 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGGCTCAGACAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG ↑ 4 3 2 1 Chimp: AGGAAGACAAGTTCCTTTTCAAGC--------------------------TATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG Gorilla: AGGGAGACAAGTTCCTTTTCAAGC--------------------------TATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG ↓ 4 3 2 1 Human: AGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGGCTCAGACAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG Cluster: [ ] Orangutan: AGGAAGACAAG----------TGC--------------------------TATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG Chimp > Human ------------- chr15:5807326-5807331 Template switch process: F1: L CCTTTATGAATATGAAAAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGG 1 F3: 4 CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGGAATGA R RF: CCTTTATGAATATGAAAAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGGAATGA RR: GGAAATACTTATACTTTTCCTTCTGTTCAAGGAAAAGTTCGATAAAAAAGACTCCGTTGTCTTGAAAGGACAAACCTTACT F2: 3 AGACTC 2 Unidirectional alignment (log-probability: -48.3) AAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGggctcagacaagctattttttctgagGCAACAGAACTTTCCTGTTTGG AAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAG--------------------------GCAACAGAACTTTCCTGTTTGG Template switch alignment (log-probability: -22.4) AAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGg|CTCAGA|CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG AAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGC|CTCAGA|CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG Gorilla > Human --------------- chr15:5807326-5807331 Template switch process: F1: L CCTTTATGAATATGAAAAGGAAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGG 1 F3: 4 CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGGAATGA R RF: CCTTTATGAATATGAAAAGGGAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGGAATGA RR: GGAAATACTTATACTTTTCCCTCTGTTCAAGGAAAAGTTCGATAAAAAAGACTCCGTTGTCTTGAAAGGACAAACCTTACT F2: 3 AGACTC 2 Unidirectional alignment (log-probability: -53.8) AAGGaAGACAAGTTCCTTTTcaagctattttttctgagggctcagaCAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG AAGGGAGACAAGTTCCTTTT--------------------------CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG Template switch alignment (log-probability: -28) AAGGaAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGg|CTCAGA|CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG AAGGGAGACAAGTTCCTTTTCAAGCTATTTTTTCTGAGGC|CTCAGA|CAAGCTATTTTTTCTGAGGCAACAGAACTTTCCTGTTTGG ========== Event 1236 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: gAAAGATCAAGCACAAATTGCTTAA----TAAACTGTGGCCATATACATGAT Chimp: gAAAGATCAAGCACAAATTGCTTAA----TAAACTGTGGCCATATACATGAT ↓ 3 1 24 Gorilla: gAAAGATCAAGCACAAATTGCTTTATTAAGCAACTGTGGCCATATACATGAT ↑ 3 1 24 Human: gAAAGATCAAGCACAAATTGCTTAA----TAAACTGTGGCCATATACATGAT Cluster: [ ] Orangutan: gAAAGATCAAGCACAAATTGCTTAA----TAAACTGTGGCCATATACATGAT Human > Gorilla --------------- chr15:75761069-75761076 Template switch process: F1: L AGAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGCTT 1 F3: 4 AACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC R RF: AGAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGCTTAATAAACTGTGGCCATATACATGATTATTCATCTATCTTCCCAC RR: TCTTTGGGGTTTCTTGGACTTTCTAGTTCGTGTTTAACGAATTATTTGACACCGGTATATGTACTAATAAGTAGATAGAAGGGTG F2: 3 CGAATTAT 2 Unidirectional alignment (log-probability: -33.3) GAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGCtttaTTAAgcAACTGTGGCCATATACATGATTATTCATCcATCTTCCCAC GAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGC----TTAATAAACTGTGGCCATATACATGATTATTCATCTATCTTCCCAC Template switch alignment (log-probability: -22.3) GAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGCTT|TATTAAGC|AACTGTGGCCATATACATGATTATTCATCcATCTTCCCAC GAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGCTT|TATTAAGC|AACTGTGGCCATATACATGATTATTCATCTATCTTCCCAC Chimp > Gorilla --------------- chr15:75761069-75761076 Template switch process: F1: L AGAAACCCCAAAGAACCTGAAAGATCAAGCACAAATTGCTT 1 F3: 4 AACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC R RF: AGAAACCCCAAAGCACCTGAAAGATCAAGCACAAATTGCTTAATAAACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC RR: TCTTTGGGGTTTCGTGGACTTTCTAGTTCGTGTTTAACGAATTATTTGACACCGGTATATGTACTAATAAGTAGGTAGAAGGGTG F2: 3 CGAATTAT 2 Unidirectional alignment (log-probability: -33.3) GAAACCCCAAAGaACCTGAAAGATCAAGCACAAATTGCtttaTTAAgcAACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC GAAACCCCAAAGCACCTGAAAGATCAAGCACAAATTGC----TTAATAAACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC Template switch alignment (log-probability: -22.3) GAAACCCCAAAGaACCTGAAAGATCAAGCACAAATTGCTT|TATTAAGC|AACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC GAAACCCCAAAGCACCTGAAAGATCAAGCACAAATTGCTT|TATTAAGC|AACTGTGGCCATATACATGATTATTCATCCATCTTCCCAC ========== Event 1237 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: tgggaaatacagcctcaagct-gactggctatggccACCCTAAGGAGACTGTGGATTAGTAAGAGGGAAAGTTCTAGGTTATTGAGTTCTACTTATATGGAATAAGAGGTGATGGAT-TTTGAGAGAAAACCAGTCTTCTACTCCAGTCTGCCTTGCATAGCCAATCA Chimp: TGGGAAATACAGCCTCAAGCT-GACTGGCTATGGCCACCCTAAGGAGACTGTGGATTAGTAAGAGGGAAAGTTCTAGGTTATTGAGTTCTACTTATATGGAATAAGAGGTGATGGAT-TTTGAGAGAAAACCAGTCTTCTACTCCAGTCTGCCTTGCATAGCCAGTCA ↑ 1 4 3 2 Gorilla: TGGGAAATACAGCCTCAAGCTGTATTTCCTATGGCCACCCTAAGGAGACTGTAGATTAGTAAGAGGGAAAGTTCTAGGTTATTGAGTTCTACTTATATGGAATAAGAGGTGATGGATTTTTGAGAGAAAACCAGTCTTCTACTCCAGTCTGCCTTGCATAGCCAATCA Human: tgggaaatacagcctcaagct-gactggctatggccACCCTAAGGAGACTGTGGATTAGTAAGAGGGAAAGTTCTAGGTTATTGAGTTCTACTTATATGGAATAAGAGGTGATGGAT-TTTGAGAGAAAACCAGTCTTCTACTCCAGTCTGCCTTGCATAGCCAATCA Cluster: [ ] Orangutan: tgggaaatacagcctcaagct-gactggctatggccACCCTAAGGAGACTGTGGATTAGTAAGAGGGAAAGTTCTAGGTTATTGGGTTCTACTTATATGGAATAAGAGGTGATGGAT-TTTGAGAGAAAACCAGTCTTCTACTCCAGTCTGCCTTGCATAGCCAATCA Gorilla > Chimp --------------- chr15:78304111-78304115 Template switch process: F1: L CATTGAGGTGCAATGAATGATGGGAAATACAGCCTCAAGCTG 1 F3: 4 CTATGGCCACCCTAAGGAGACTGTGGATTAGTAAGAGGGA R RF: CATTGAGGTGCAATGAATGATGGGAAATACAGCCTCAAGCTGTATTTCCTATGGCCACCCTAAGGAGACTGTAGATTAGTAAGAGGGAAAGTTCTAGGTTATTGAGTTCTACTTATATGGAATAAGAGGTGATGGATTTTTGAGAGAAAACCAGTCTTCTACTCCAGT RR: GTAACTCCACGTTACTTACTACCCTTTATGTCGGAGTTCGACATAAAGGATACCGGTGGGATTCCTCTGACATCTAATCATTCTCCCTTTCAAGATCCAATAACTCAAGATGAATATACCTTATTCTCCACTACCTAAAAACTCTCTTTTGGTCAGAAGATGAGGTCA F2: 3 GGTCA 2 Unidirectional alignment (log-probability: -33.1) TTGAGGTGCAATGAATGATGGGAAATACAGCCTCAAGCTG-AcTggCTATGGCCACCCTAAGGAGACTGTgGATTAGTAAGAGGGA TTGAGGTGCAATGAATGATGGGAAATACAGCCTCAAGCTGTATTTCCTATGGCCACCCTAAGGAGACTGTAGATTAGTAAGAGGGA Template switch alignment (log-probability: -21.9) TTGAGGTGCAATGAATGATGGGAAATACAGCCTCAAGCTG|ACTGG|CTATGGCCACCCTAAGGAGACTGTgGATTAGTAAGAGGGA TTGAGGTGCAATGAATGATGGGAAATACAGCCTCAAGCTG|ACTGG|CTATGGCCACCCTAAGGAGACTGTAGATTAGTAAGAGGGA ========== Event 1238 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTAAGGACTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGG---------------------------------------TTAGCCAGAAGAGAGCTGATGC ↓ 3 2 4 Chimp: TTAAGGACTCTGCTTTGGAGTACAAATGAGAAACTACATTTTAGG--------------------------TTTCTCATTTGTACTAGCCAGAAGAGAGCTGATGC Gorilla: TTAAGGACTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGG-------------TTTCTCATTTGTA-------------CTAGCCAGAAGAGAGCTGATGC ↑ 3 2 4 Human: TTAAGGACTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGG---------------------------------------TTAGCCAGAAGAGAGCTGATGC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--------------------------NNNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr15:78684197-78684208 Template switch process: F1: L AAGACTTAAGGACTCTGCTTTGGAGTACAAATGAGAAACTACATTTTAGGTT 1 F3: 4 TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG R RF: AAGACTTAAGGACTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTTAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG RR: TTCTGAATTCCTGAGACGAAACCTCATGTTTACTCTTTGATATAAAATCCAATCGGTCTTCTCTCGACTACGGTCAGGAGACCTTAGAAAC F2: 3 CATGTTTACTCT 2 Unidirectional alignment (log-probability: -35.7) CTCTGCTTTGGAGTACAAATGAGAAACTAcATTTTAGGTTtctcatttgtactAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG CTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTT-------------AGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG Template switch alignment (log-probability: -23) CTCTGCTTTGGAGTACAAATGAGAAACTAcATTTTAGGTT|TCTCATTTGTAC|TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG CTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTT|TCTCATTTGTAC|TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG Human > Gorilla --------------- chr15:76671585-76671596 Template switch process: F1: L GGACTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTT 1 F3: 4 TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG R RF: GGACTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTTAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG RR: CCTGAGACGAAACCTCATGTTTACTCTTTGATATAAAATCCAATCGGTCTTCTCTCGACTACGGTCAGGAGACCTTAGAAAC F2: 3 CATGTTTACTCT 2 Unidirectional alignment (log-probability: -29.6) CTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTttctcatttgtacTAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG CTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGT-------------TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG Template switch alignment (log-probability: -17.3) CTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTT|TCTCATTTGTAC|TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG CTCTGCTTTGGAGTACAAATGAGAAACTATATTTTAGGTT|TCTCATTTGTAC|TAGCCAGAAGAGAGCTGATGCCAGTCCTCTGGAATCTTTG ========== Event 1239 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGTAGTGGGGAGGGGAGAGAGGGAGCATGCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT ↓ 1 4 3 2 Chimp: TGGTAGTGGGGAGGGGAGAGACATAG--GCCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT ↑ 1 4 3 2 Gorilla: TGGTAGTGGGGAGGGGAGAGAGGGAGCATGCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT Human: TGGTAGTGGGGAGGGGAGAGAGGGAGCATGCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT Cluster: [ ] Orangutan: TGGTAGTGGGGAGGGGAGAGAGGGAGCATGCTTTTTCCGGGAGGCC--TGTCAGGATGGCGGGTGGACGT Human > Chimp ------------- chr15:4092241-4092247 Template switch process: F1: L AGAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA 1 F3: 4 CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT R RF: AGAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGAGGGAGCATGCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT RR: TCTCGTCCCTAAGGGGGACCACCATCACCCCTCCCCTCTCTCCCTCGTACGAAAAAGGTCCTCCGGATACAGTCCTACCACCCACCTGCA F2: 3 CGGATAC 2 Unidirectional alignment (log-probability: -31.7) GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGAcataggc---------CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA-------GGGAGCATGCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT Template switch alignment (log-probability: -16.2) GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA|CATAGGC|CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA|CATAGGC|CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT Gorilla > Chimp --------------- chr15:4092241-4092247 Template switch process: F1: L AGAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA 1 F3: 4 CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT R RF: AGAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGAGGGAGCATGCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT RR: TCTCGTCCCTAAGGGGGACCACCATCACCCCTCCCCTCTCTCCCTCGTACGAAAAAGGTCCTCCGGATACAGTCCTACCACCCACCTGCA F2: 3 CGGATAC 2 Unidirectional alignment (log-probability: -30.8) GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA-----CATaggcCTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGAGGGAGCATG---CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT Template switch alignment (log-probability: -16.6) GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA|CATAGGC|CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT GAGCAGGGATTCCCCCTGGTGGTAGTGGGGAGGGGAGAGA|CATAGGC|CTTTTTCCAGGAGGCCTATGTCAGGATGGTGGGTGGACGT ========== Event 1240 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAGGAGACTTTTCAAGCAAATGCT-AAAGCATTTGTTTTAGTTAGCCAGCACTA ↑ 3 1 2 4 Chimp: CAAGGAGACTTTTCAAGCAAATGCTTTAAGACAGTGTTTTAGTTAGCCAGCACTA Gorilla: CAAGGAGACTTTTCAAGCAAATGCTTTAAGACAGTGTTTTAGTTAGCCAGCACTA ↓ 3 1 2 4 Human: CAAGGAGACTTTTCAAGCAAATGCT-AAAGCATTTGTTTTAGTTAGCCAGCACTA Cluster: [ ] Orangutan: CAAGGAGACTTTTCAAGCAAATGCTTTAAGACAGTGTTTTAGTTTGCCAGCACTA Chimp > Human ------------- chr1:60175924-60175931 Template switch process: F1: L AATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT 1 F3: 4 TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA R RF: AATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCTTTAAGACAGTGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA RR: TTACTGTCGAGTCCCTGTTCCTCTGAAAAGTTCGTTTACGAAATTCTGTCACAAAATCAATCGGTCGTGATCGGTTACAATTAATTTAAT F2: 3 TTACGAAA 2 Unidirectional alignment (log-probability: -30.1) ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCTaaagcaTT-------TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT------TTAAGACAGTGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA Template switch alignment (log-probability: -16.3) ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT|AAAGCATT|TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT|AAAGCATT|TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA Gorilla > Human --------------- chr1:60175924-60175931 Template switch process: F1: L AATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT 1 F3: 4 TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA R RF: AATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCTTTAAGACAGTGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA RR: TTACTGTCGAGTCCCTGTTCCTCTGAAAAGTTCGTTTACGAAATTCTGTCACAAAATCAATCGGTCGTGATCGGTTACAATTAATTTAAT F2: 3 TTACGAAA 2 Unidirectional alignment (log-probability: -29.6) ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCTaaagcaTT-------TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT------TTAAGACAGTGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA Template switch alignment (log-probability: -16.7) ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT|AAAGCATT|TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA ATGACAGCTCAGGGACAAGGAGACTTTTCAAGCAAATGCT|AAAGCATT|TGTTTTAGTTAGCCAGCACTAGCCAATGTTAATTAAATTA ========== Event 1241 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAAGCTGATTTGCCTGTCCCCATGCGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAG-GGGGGTGACCGCAAAAAGAAAGTGAGATGTGTTGCCGCCACAGCGGAGGGCTTGCCAGAGCCAGCATCAGAGTTGGTGGGTTCCCTG Chimp: AAAGCTGATTTGCCTGTCCCCATGCGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAgggggggTGACTGCAAAAAGAAAGTGAGATGTGTTGCTGCCACAGTGGAGGGCTTGCCAGAGCCAGCATCAGAGTTGGTGGGTTCCCTG ↓ 13 24 ↑ 1 4 3 2 Gorilla: AAAGCTGATTTGCCTGTCCCCGCATGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAG-GGGGGTGACTGCAAAAAGAAAGTGAGACGTGTTGCCGCCACAGTGGAGGGCTTGCCAGAGCCAGCATCAGAGTTGGTGGGTTCCCTG Human: AAAGCTGATTTGCCTGTCCCCATGCGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAG-GGGGGTGACCGCAAAAAGAAAGTGAGATGTGTTGCCGCCACAGCGGAGGGCTTGCCAGAGCCAGCATCAGAGTTGGTGGGTTCCCTG Cluster: [ ] Orangutan: AAAGCTGATTTGCCTGTCCCCATGCGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAG-GGGGGTGACTGCAAAAAGAAGGTGAGATGTGTTGCTGCCACAGTGGAGGGCTTGCCAGAGCCAGCATCAGAGTTGGTGGCTTCCTTG Gorilla > Chimp --------------- chr15:2726334-2726337 Template switch process: F1: L TGGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCC 1 F3: 4 GGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGGG R RF: TGGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCCGCATGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGGGGGGTGACTGCAAAAAGAAAGTGAGACGTGTTGCCGCCACAGTGGAGGGCTTGCCAGAGCCAGCAT RR: ACCTTCCCAGGGGGGTCCGTTTTCGACTAAACGGACAGGGGCGTACCCCGTGTCCCACGAACCTTCACCAACCCGGAAACGTCCCCCCACTGACGTTTTTCTTTCACTCTGCACAACGGCGGTGTCACCTCCCGAACGGTCTCGGTCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -31.4) GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCCatgcGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGGg GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCCGCATGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGG- Template switch alignment (log-probability: -16.2) GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCC|ATGC|GGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGGG GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCC|ATGC|GGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGGG Chimp > Gorilla --------------- chr15:2420088-2420091 Template switch process: F1: L TGGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCC 1 F3: 4 GGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGG R RF: TGGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCCATGCGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGG RR: ACCTTCCCAGGGGGGTCCGTTTTCGACTAAACGGACAGGGGTACGCCCCGTGTCCCACGAACCTTCACCAACCCGGAAACGTCC F2: 3 TACG 2 Unidirectional alignment (log-probability: -30.1) GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCCgcatGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGG- GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCCATGCGGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGGG Template switch alignment (log-probability: -16.2) GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCC|GCAT|GGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGG GGAAGGGTCCCCCCAGGCAAAAGCTGATTTGCCTGTCCCC|GCAT|GGGGCACAGGGTGCTTGGAAGTGGTTGGGCCTTTGCAGG ========== Event 1242 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CGGAGCCGAGCCAGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATGAACAGGAAGGCTTGATCGAT ↓ 3 2 1 4 Chimp: CGGAGCCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTGCTTA------------TGGTTGAACAGGAAGGCTTGATCGAT ↑ 3 2 1 4 Gorilla: CGGAGTCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATTAACAGGAAGGCTTGATCGAT Human: CGGAGCCGAGCCAGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATGAACAGGAAGGCTTGATCGAT Cluster: [ ] Orangutan: GGGAGCCAAGCCGGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATTAACAGGAAGGCTTGATCGAT Human > Chimp ------------- chr15:3560233-3560240 Template switch process: F1: L ACGGAGCCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTG 1 F3: 4 TGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATG R RF: ACGGAGCCGAGCCAGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATA RR: TGCCTCGGCTCGGTCACCTTTGGTATTCGGACAGAGTAGACAGAGATTTGACGAGTGTCCTACTTGTCCTTCCGAACTAGCTATGACTAAAATGTCAGTAT F2: 3 TGGTATTC 2 Unidirectional alignment (log-probability: -44.2) CGGAGCCGAGCCgGTGGAAACCATAAGCCTGTCTCATCTgcttatgGT-------------------TGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATg CGGAGCCGAGCCAGTGGAAACCATAAGCCTGTCTCATCT-------GTCTCTAAACTGCTCACAGGATGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATA Template switch alignment (log-probability: -28.3) CGGAGCCGAGCCgGTGGAAACCATAAGCCTGTCTCATCTG|CTTATGGT|TGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATg CGGAGCCGAGCCAGTGGAAACCATAAGCCTGTCTCATCTG|CTTATGGT|TGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATA Gorilla > Chimp --------------- chr15:3560233-3560240 Template switch process: F1: L ACGGAGCCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTG 1 F3: 4 TGAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATGGG R RF: ACGGAGTCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATTAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATGGG RR: TGCCTCAGCTCGGCCACCTTTGGTATTCGGACAGAGTAGACAGAGATTTGACGAGTGTCCTAATTGTCCTTCCGAACTAGCTATGACTAAAATGTCAGTACCC F2: 3 TGGTATTC 2 Unidirectional alignment (log-probability: -41.7) CGGAGcCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTG----------------------cttatggttgAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATG CGGAGTCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTGTCTCTAAACTGCTCACAGGATT----------AACAGGAAGGCTTGATCGATACTGATTTTACAGTCATG Template switch alignment (log-probability: -27.8) CGGAGcCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTG|CTTATGGT|TgAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATG CGGAGTCGAGCCGGTGGAAACCATAAGCCTGTCTCATCTG|CTTATGGT|TTAACAGGAAGGCTTGATCGATACTGATTTTACAGTCATG ========== Event 1243 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAGGCTGCTCCAGGAGTTGATCTTGAGGGGCAATGTTTACTCTGGATCAAGGCAA----------------CTAACTGGAGACATCTC Chimp: AGAGGCTACTCCAGGAGTTGATCTCAAGGGGCAATGTTTA----------------CTCTGGATCAAGGCAACTAACTGGAGACATCTC ↓ 1 4 3 2 Gorilla: AGAGGCTACTCCAGGAGTTGACCTTGAGGGGCAATGTTTACTCTGGATCGAGGCAA----------------CTAACTGGAGACATCTC Human: AGAGGCTGCTCCAGGAGTTGATCTTGAGGGGCAATGTTTACTCTGGATCAAGGCAA----------------CTAACTGGAGACATCTC Cluster: [ ] Orangutan: GGAGGCTACTCCAGGAGTTTATCTTGAGGGGCAGTGGTTACTCTGGATCAAGGCAA----------------CTAACTGGAGACATCTC Chimp > Gorilla --------------- chr15:2972142-2972147 Template switch process: F1: L AAGACTAAATAAGCAAGACCAGAGGCTACTCCAGGAGTTGA 1 F3: 4 GGGGCAATGTTTACTCTGGATCGAGGCAA R RF: AAGACTAAATAAGCAAGACCAGAGGCTACTCCAGGAGTTGATCTCAAGGGGCAATGTTTACTCTGGATCAAGGCAA RR: TTCTGATTTATTCGTTCTGGTCTCCGATGAGGTCCTCAACTAGAGTTCCCCGTTACAAATGAGACCTAGTTCCGTT F2: 3 AGTTCC 2 Unidirectional alignment (log-probability: -35.9) AGACTAAATAAGCAAGACCAGAGGCTACTCCAGGAGTTGAcCTtgAGGGGCAATGTTTACTCTGGATCgaggcaA AGACTAAATAAGCAAGACCAGAGGCTACTCCAGGAGTTGATCTCAAGGGGCAATGTTTACTCTGGATC------A Template switch alignment (log-probability: -21.7) AGACTAAATAAGCAAGACCAGAGGCTACTCCAGGAGTTGA|CCTTGA|GGGGCAATGTTTACTCTGGATCgAGGCAA AGACTAAATAAGCAAGACCAGAGGCTACTCCAGGAGTTGA|CCTTGA|GGGGCAATGTTTACTCTGGATCAAGGCAA ========== Event 1244 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGTGCCTGTCACCATCCTCAGTACAGC-CCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGC Chimp: CTGTGCCTGTCACCATCCTCAGTACAGC-CCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGC ↓ 1 4 3 2 Gorilla: CTGTGCCTGTCACCATCCTCACCTGAGCCACCCGTGGCTCAGGTGGCCAACTCATGGTGTGGC ↑ 1 4 3 2 Human: CTGTGCCTGTCACCATCCTCAGTACAGC-CCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGC Cluster: [ ] Orangutan: CTGTGCCTGTCACCATCCTCAGTACAGC-CCCCATGGCTCAGGTGGCCAACTCGTGGTGTGGC Human > Gorilla --------------- chr1:62152145-62152153 Template switch process: F1: L TATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA 1 F3: 4 CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG R RF: TATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCAGTACAGCCCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG RR: ATATACACTTTAGGAGGAGGGACACGGACAGTGGTAGGAGTCATGTCGGGGGCACCGAGTCCACCGGTTGAGTACCACACCGAACCCAC F2: 3 ACCGAGTCC 2 Unidirectional alignment (log-probability: -31) ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA------CCtgagccaCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCAGTACAGCC-------CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG Template switch alignment (log-probability: -16.9) ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA|CCTGAGCCA|CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA|CCTGAGCCA|CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG Chimp > Gorilla --------------- chr1:62152145-62152153 Template switch process: F1: L TATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA 1 F3: 4 CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG R RF: TATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCAGTACAGCCCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG RR: ATATACACTTTAGGAGGAGGGACACGGACAGTGGTAGGAGTCATGTCGGGGGCACCGAGTCCACCGGTTGAGTACCACACCGAACCCAC F2: 3 ACCGAGTCC 2 Unidirectional alignment (log-probability: -31) ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA------CCtgagccaCCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCAGTACAGCC-------CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG Template switch alignment (log-probability: -16.9) ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA|CCTGAGCCA|CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG ATATGTGAAATCCTCCTCCCTGTGCCTGTCACCATCCTCA|CCTGAGCCA|CCCGTGGCTCAGGTGGCCAACTCATGGTGTGGCTTGGGTG ========== Event 1245 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCTACCTCCTGGCCCACGCTGGGGATCGACCGATCCCCATCACTCCACTCATCATCAGAG Chimp: GCTACCTCCTGGCCCACGCTGGGGATCGACCGATCCCCATCACTCCACTCATCATCAGAA ↑ 3 1 4 Gorilla: GCTACCTCCTGGCCCACGCTGGGGATCG----------GTCACTCCACTCATCATCAGAG ↓ 3 1 4 Human: GCTACCTCCTGGCCCACGCTGGGGATCGACCGATCCCCATCACTCCACTCATCATCAGAG Cluster: [ ] Orangutan: GCTACCTCCT---------AGGGGATCG----------GTCACTCCACTCATCATCAGAG Gorilla > Human --------------- chr1:6159623-6159633 Template switch process: F1: L GACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG 1 F3: 4 TCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG R RF: GACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCGGTCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG RR: CTGCCGGGACTCTCGATGGAGGACCGGGTGCGACCCCTAGCCAGTGAGGTGAGTAGTAGTCTCCGGTGACGAGTGTCGAGTC F2: 3 ACCCCTAGCCA 2 Unidirectional alignment (log-probability: -30.8) ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCGaccgatccccaTCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG----------GTCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG Template switch alignment (log-probability: -17.1) ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG|ACCGATCCCCA|TCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG|ACCGATCCCCA|TCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG Gorilla > Chimp --------------- chr1:5403744-5403754 Template switch process: F1: L GACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG 1 F3: 4 TCACTCCACTCATCATCAGAAGCCACTGCTCACAGCTCAG R RF: GACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCGGTCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG RR: CTGCCGGGACTCTCGATGGAGGACCGGGTGCGACCCCTAGCCAGTGAGGTGAGTAGTAGTCTCCGGTGACGAGTGTCGAGTC F2: 3 ACCCCTAGCCA 2 Unidirectional alignment (log-probability: -36.3) ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCGaccgatccccaTCACTCCACTCATCATCAGAaGCCACTGCTCACAGCTCAG ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG----------GTCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG Template switch alignment (log-probability: -22.6) ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG|ACCGATCCCCA|TCACTCCACTCATCATCAGAaGCCACTGCTCACAGCTCAG ACGGCCCTGAGAGCTACCTCCTGGCCCACGCTGGGGATCG|ACCGATCCCCA|TCACTCCACTCATCATCAGAGGCCACTGCTCACAGCTCAG ========== Event 1246 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: AAGGATCTTTGCAGACGCGGCCTAGTCAAGGACTAGGCCCAGGTGGGACCGTCCACATG Chimp: Gorilla: AAGGATCTTTGCAGACGCGGCCTAGTCAAGGAC---CTCCAGGTGGGACCGTCCACGTG ↓ 3 2 1 4 Human: AAGGATCTTTGCAGACGCGGCCTAGTCAAGGACTAGGCCCAGGTGGGACCGTCCACATG Cluster: [ ] Orangutan: AAGGATCTTTGCAGATGCGGCCTAGTCAAGGAC---CTCCAGGTGGGACCGTCCGCGTG Gorilla > Human --------------- chr16:89206171-89206175 Template switch process: F1: L CTTGGGAAAAGGATCTTTGCAGACGCGGCCTAGTCAAGGAC 1 F3: 4 CCAGGTGGGACCGTCCACATGGGCCTTCGCTCCCACACTG R RF: CTTGGGAAAAGGATCTTTGCAGACGCGGCCTAGTCAAGGACCTCCAGGTGGGACCGTCCACGTGGGCCTTCGCTCCGACACTG RR: GAACCCTTTTCCTAGAAACGTCTGCGCCGGATCAGTTCCTGGAGGTCCACCCTGGCAGGTGCACCCGGAAGCGAGGCTGTGAC F2: 3 CGGAT 2 Unidirectional alignment (log-probability: -37.3) TTGGGAAAAGGATCTTTGCAGACGCGGCCTAGTCAAGGACtaggcCCAGGTGGGACCGTCCACaTGGGCCTTCGCTCCcACACTG TTGGGAAAAGGATCTTTGCAGACGCGGCCTAGTCAAGGAC---CTCCAGGTGGGACCGTCCACGTGGGCCTTCGCTCCGACACTG Template switch alignment (log-probability: -27.4) TTGGGAAAAGGATCTTTGCAGACGCGGCCTAGTCAAGGAC|TAGGC|CCAGGTGGGACCGTCCACaTGGGCCTTCGCTCCcACACTG TTGGGAAAAGGATCTTTGCAGACGCGGCCTAGTCAAGGAC|TAGGC|CCAGGTGGGACCGTCCACGTGGGCCTTCGCTCCGACACTG ========== Event 1247 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ACATCTCTGATAGCATTTTCAGAGAAGTCACCAGAGACCAGCCCTTGGCAATGACTggtgagtggatggatggataatagatggatgtgtgactcagaggatgaaagatggatg ↑ 4 1 3 2 Chimp: ACATCTCTGATAGCATTTTCA------------GAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGATGGATAATAGATGGATGTGTGACTCAGAGGATGAAAGATGGATG ↓ 4 1 3 2 Gorilla: ACATCTCTGATAGCATTTTCAGAGAAGTCACCAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGATGGATAATAGATGGATGTGTGACTCAGAGGATGAAAGATGGATG Human: ACATCTCTGATAGCATTTTCAGAGAAGTCACCAGAGACCAGCCCTTGGCAATGACTggtgagtggatggatggataatagatggatgtgtgactcagaggatgaaagatggatg Cluster: [ ] Orangutan: ACATCTCTGATAGCATTTTCAGAGAA--GACCAGAGACCAGCCGTTGGCAATGACTGGTGAGTGGATGGATGGATAATAGATGGATGTGTGACTCAGAGGATGAAAGATGGATG Chimp > Human ------------- chr16:11485775-11485780 Template switch process: F1: L TCTTCCCTTTTTCCATCCAGACATCTCTGATAGCATTTTCAGAGA 1 F3: 4 CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGATGG R RF: TCTTCCCTTTTTCAATCCAGACATCTCTGATAGCATTTTCAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGATGGATAATAGATGGATGTGTGACT RR: AGAAGGGAAAAAGTTAGGTCTGTAGAGACTATCGTAAAAGTCTCTGGTCGGGAACCGTTACTGACCACTCACCTACCTACCTATTATCTACCTACACACTGA F2: 3 CACTGA 2 Unidirectional alignment (log-probability: -34.2) CCTTTTTCcATCCAGACATCTCTGATAGCATTTTCAGAgaagtcaccagaGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT CCTTTTTCAATCCAGACATCTCTGATAGCATTTTCAGA------------GACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT Template switch alignment (log-probability: -22.1) CCTTTTTCcATCCAGACATCTCTGATAGCATTTTCAGAGA|AGTCAC|CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT CCTTTTTCAATCCAGACATCTCTGATAGCATTTTCAGAGA|AGTCAC|CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT Chimp > Gorilla --------------- chr16:11785754-11785759 Template switch process: F1: L TCTTCCCTTTTTCCATCCAGACATCTCTGATAGCATTTTCAGAGA 1 F3: 4 CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGATGG R RF: TCTTCCCTTTTTCAATCCAGACATCTCTGATAGCATTTTCAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGATGGATAATAGATGGATGTGTGACT RR: AGAAGGGAAAAAGTTAGGTCTGTAGAGACTATCGTAAAAGTCTCTGGTCGGGAACCGTTACTGACCACTCACCTACCTACCTATTATCTACCTACACACTGA F2: 3 CACTGA 2 Unidirectional alignment (log-probability: -33.7) CCTTTTTCcATCCAGACATCTCTGATAGCATTTTcagagaagtcacCAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT CCTTTTTCAATCCAGACATCTCTGATAGCATTTT------------CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT Template switch alignment (log-probability: -22.2) CCTTTTTCcATCCAGACATCTCTGATAGCATTTTCAGAGA|AGTCAC|CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT CCTTTTTCAATCCAGACATCTCTGATAGCATTTTCAGAGA|AGTCAC|CAGAGACCAGCCCTTGGCAATGACTGGTGAGTGGATGGAT ========== Event 1248 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTTCTCCAGGCTATGtgaatgttgatggcattaata-aatagcttttgaat--gttgaaggtattcaaaa-ataacttttT-aaaaaaaaaTCCTGACACTTGTAGCAAGGACAGGAACATATTTGCT Chimp: GTTTTCTCCAGGCTATGTGAATGTTGATGGCATTAATA-AAT-ATTTTTGAACACCTTC--AACATTCAAAAGCTAACTTTTT--aaaaaaaaTCCTGACACTTGTAGCAAGGACAGGAACATATTTGCT ↓ 1 3 2 4 Gorilla: GTTTTCTCCAGGCTATGTGAACTTTGATGGCATTAATA-AATAGCTTTTGAAT--GTTGAAGGTATTCAAAA-ATAACTTTTT--TaaaaaaaTCCTGACACTTGTAGCAAGGACAGGAACATATTTGCT Human: GTTTTCTCCAGGCTATGtgaatgttgatggcattaata-aatagcttttgaat--gttgaaggtattcaaaa-ataacttttT-aaaaaaaaaTCCTGACACTTGTAGCAAGGACAGGAACATATTTGCT Cluster: [] Orangutan: GTTTTCTCCAGGCTATGTGAATGTTGATGGCATTAATAAAATAACTTCAGAAT--GTTGAAGGTATTCAGAA-ATAACTTTTTT-aaaaaaaaTTCTGACACTTCTAGCAAGGACAGGAACATATCTGCT Chimp > Gorilla --------------- chr16:67513856-67513872 Template switch process: F1: L TATCAGTCAGTGCCAATGTAGTTTTCTCCAGGCTATGTGAACTTTGATGGCATTAATAAATA 1 F3: 4 GT R RF: TATCAGTCAGTGCCAATGTAGTTTTCTCCAGGCTATGTGAATGTTGATGGCATTAATAAATATTTTTGAACACCTTCAACATTCAAAAGCTAACTTTTTAAAAAAAATCCTGACACTTGTAGCAAGGACAGGAACATATTTGCTACTTTGTGCTTTAGCCTGGAAGCCTGT RR: ATAGTCAGTCACGGTTACATCAAAAGAGGTCCGATACACTTACAACTACCGTAATTATTTATAAAAACTTGTGGAAGTTGTAAGTTTTCGATTGAAAAATTTTTTTTAGGACTGTGAACATCGTTCCTGTCCTTGTATAAACGATGAAACACGAAATCGGACCTTCGGACA F2: 3 GAAGTTGTAAGTTTTCG 2 Unidirectional alignment (log-probability: -55.2) TTTCTCCAGGCTATGTGAActTTGATGGCATTAATAAATAgcttttgaatgttgaaggT----------------- TTTCTCCAGGCTATGTGAATGTTGATGGCATTAATAAATA------------------TTTTTGAACACCTTCAAC Template switch alignment (log-probability: -28.5) TTTCTCCAGGCTATGTGAActTTGATGGCATTAATAAATA|GCTTTTGAATGTTGAAG|GT TTTCTCCAGGCTATGTGAATGTTGATGGCATTAATAAATA|GCTTTTGAATGTTGAAG|GT ========== Event 1249 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGAATGAAA-TTACTATGAAGGCTT--CTA-TCTGACACTGTCAAAGGCAAGAG ↓ 3 1 2 4 Chimp: CAGAATGAAA-TTACTATGAAGGCAGAAGCC-TTTGACACTGTCAAAGGCAAGAG ↑ 3 1 2 4 Gorilla: CAGAATGAAA-TTTCTATGAAGGCTT--CTA-TCTGACACTGTCAAAGGCAAGAG Human: CAGAATGAAA-TTACTATGAAGGCTT--CTA-TCTGACACTGTCAAAGGCAAGAG Cluster: [ ] Orangutan: AAGAATGAAATTTACTATGAAGGCTT--CTATCCTGACACTGTCCAAGGCAAGAG Human > Chimp ------------- chr16:14132873-14132881 Template switch process: F1: L CATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGGC 1 F3: 4 TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT R RF: CATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGGCTTCTATCTGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT RR: GTAAGTGCCCATTTTATTGTCTTACTTTAATGATACTTCCGAAGATAGACTGTGACAGTTTCCGTTCTCACTCCCGTATAGGTCGGAA F2: 3 TTCCGAAGA 2 Unidirectional alignment (log-probability: -31.5) ATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGGcagaagcCTT-----TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT ATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGG-------CTTCTATCTGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT Template switch alignment (log-probability: -16.4) ATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGGC|AGAAGCCTT|TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT ATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGGC|AGAAGCCTT|TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT Gorilla > Chimp --------------- chr16:14132873-14132881 Template switch process: F1: L CATTCACGGGTAAAATAACAGAATGAAATTACTATGAAGGC 1 F3: 4 TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT R RF: CATTCATGGGTAAAATAACAGAATGAAATTTCTATGAAGGCTTCTATCTGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT RR: GTAAGTACCCATTTTATTGTCTTACTTTAAAGATACTTCCGAAGATAGACTGTGACAGTTTCCGTTCTCACTCCCGTATAGGTCGGAA F2: 3 TTCCGAAGA 2 Unidirectional alignment (log-probability: -42) ATTCAcGGGTAAAATAACAGAATGAAATTaCTATGAAGGcagaagcCTT-----TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT ATTCATGGGTAAAATAACAGAATGAAATTTCTATGAAGG-------CTTCTATCTGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT Template switch alignment (log-probability: -27.9) ATTCAcGGGTAAAATAACAGAATGAAATTaCTATGAAGGC|AGAAGCCTT|TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT ATTCATGGGTAAAATAACAGAATGAAATTTCTATGAAGGC|AGAAGCCTT|TGACACTGTCAAAGGCAAGAGTGAGGGCATATCCAGCCTT ========== Event 1250 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATATAAGCATCACT--CTGACTTTTGCAGTTATAGTAAG----TGATTATCTCTTATTTTAACTAT Chimp: CATATAAGCATCA--CTCTGACTTTTGCAGTTAT--ATAG----TGATTATCTCTTATTTTAACTAT ↓ 3 2 1 4 Gorilla: CATATAAGCATCACT--CTGACTTTTGCAGTTAT--ATAGTAAGTCATTATCTCTTATTTTAACTAT Human: CATATAAGCATCACT--CTGACTTTTGCAGTTATAGTAAG----TGATTATCTCTTATTTTAACTAT Cluster: [ ] Orangutan: CATATAAGCATCACT--CTGACTTTTGCAGTTAT--ATAGTAAGTGATTATCTCTTATTTTAACTAT Chimp > Gorilla --------------- chr16:14386449-14386453 Template switch process: F1: L TGGCATATAAGCATCACTCTGACTTTTGCAGTTATATAGT 1 F3: 4 ATTATCTCTTATTTTAACTATAATCAAGAAGAAAAT-----------------AAAT R RF: TGGCATATAAGCATCACTCTGACTTTTGCAGTTATATAGTGATTATCTCTTATTTTAACTATAATCAAGAAGAAAATTAACTTTTTTTACTTTGAAAT RR: ACCGTATATTCGTAGTGAGACTGAAAACGTCAATATATCACTAATAGAGAATAAAATTGATATTAGTTCTTCTTTTAATTGAAAAAAATGAAACTTTA F2: 3 CTGAA 2 Unidirectional alignment (log-probability: -36.2) TGGCATATAAGCATCACTCTGACTTTTGCAGTTATATAGtaagTcATTATCTCTTATTTTAACTATAATCAAGAAGAAAATaaaT TGGCATATAAGCATCACTCTGACTTTTGCAGTTATATAG----TGATTATCTCTTATTTTAACTATAATCAAGAAGAAAAT---T Template switch alignment (log-probability: -26.9) TGGCATATAAGCATCACTCTGACTTTTGCAGTTATATAGT|AAGTC|ATTATCTCTTATTTTAACTATAATCAAGAAGAAAAT-----------------AAAT TGGCATATAAGCATCACTCTGACTTTTGCAGTTATATAGT|AAGTC|ATTATCTCTTATTTTAACTATAATCAAGAAGAAAATTAACTTTTTTTACTTTGAAAT ========== Event 1251 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GATTTTATGAGAATCCTCATAAA--------------------------------------TCAGGCAACTTCCCTGATTGCCTATGAAAAACAAAAATT ↑ 1 4 3 2 Chimp: GATTTTATGAGAATCCTCATATG-------------------ACCTGCCAACTTTATCACTACAACCACCTTCCCTGATTGCCTATGAAAAACAAAAATT Gorilla: GATTTTATGAGAATCCTCATATGACCTGCCAACTTTATCACT-------------------ACAACCAACTTCCCTGATTGCCTATGAAAAACAAAAATT ↓ 1 4 3 2 Human: GATTTTATGAGAATCCTCATAAA--------------------------------------TCAGGCAACTTCCCTGATTGCCTATGAAAAACAAAAATT Cluster: [ ] Orangutan: GATTTTATGAGAATCCTCATATGACCTGCCAACTTTATCACT-------------------ACAACCAACTTCCCTGATTGTCTATGAAAAACAAAAATT Chimp > Human ------------- chr1:187361957-187361963 Template switch process: F1: L ACAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA 1 F3: 4 CAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCTTTA R RF: ACAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATATGACCTGCCAACTTTATCACTACAACCACCTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCTTTA RR: TGTCTCTAGAGACAAGTCAACTAAAATACTCTTAGGAGTATACTGGACGGTTGAAATAGTGATGTTGGTGGAAGGGACTAACGGATACTTTTTGTTTTTAATTCAGAAAT F2: 3 GGACTAA 2 Unidirectional alignment (log-probability: -37) CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA-----------------------------aatcaggcaaCTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATATGACCTGCCAACTTTATCACTACAACCAC----------CTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT Template switch alignment (log-probability: -22.2) CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA|AATCAGG|CAaCTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA|AATCAGG|CACCTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT Gorilla > Human --------------- chr1:187361957-187361963 Template switch process: F1: L ACAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA 1 F3: 4 CAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT R RF: ACAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATATGACCTGCCAACTTTATCACTACAACCAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT RR: TGTCTCTAGAGACAAGTCAACTAAAATACTCTTAGGAGTATACTGGACGGTTGAAATAGTGATGTTGGTTGAAGGGACTAACGGATACTTTTTGTTTTTAATTCAGA F2: 3 GGACTAA 2 Unidirectional alignment (log-probability: -32) CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA--------------------------aatcaggCAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATATGACCTGCCAACTTTATCACTACAAC-------CAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT Template switch alignment (log-probability: -16.6) CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA|AATCAGG|CAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT CAGAGATCTCTGTTCAGTTGATTTTATGAGAATCCTCATA|AATCAGG|CAACTTCCCTGATTGCCTATGAAAAACAAAAATTAAGTCT ========== Event 1252 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTACTTATTTaaaaaataaaaaaGCA----------TATAATGCTTTTTTAGTCTTAAATTTAAAAATTG Chimp: TTTACTTATTTaaaaaataaaaaaGCA----------TATAATGCTTTTTTAGTCTTAAATTTAAAAATTG ↑ 3 1 4 Gorilla: TTTACTTATTTaaaaaataaaaaaGCA--------------------TTATAGTCTTAAATTTAAAAATTG ↓ 3 1 4 Human: TTTACTTATTTaaaaaataaaaaaGCA----------TATAATGCTTTTTTAGTCTTAAATTTAAAAATTG Cluster: [ ] Orangutan: TTTACTTATTTaaaaaataaaaaaGCATATAATGCTT----------TTTTAGTCTTGAATTTAAAAATTT Gorilla > Human --------------- chr16:14536007-14536018 Template switch process: F1: L CTTTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAT 1 F3: 4 TAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA R RF: CTTTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCATTATAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA RR: GAAACGACACAAGGAAATGAATAAATTTTTTATTTTTTCGTAATATCAGAATTTAAATTTTTAACATAATGTGTAATAAGTGAT F2: 3 TTTTTCGTAATA 2 Unidirectional alignment (log-probability: -30.8) TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAtataatgcttTTtTAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCA----------TTATAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA Template switch alignment (log-probability: -17.3) TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAT|ATAATGCTTTTT|TAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAT|ATAATGCTTTTT|TAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA Gorilla > Chimp --------------- chr16:14980470-14980481 Template switch process: F1: L CTTTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAT 1 F3: 4 TAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA R RF: CTTTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCATTATAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA RR: GAAACGACACAAGGAAATGAATAAATTTTTTATTTTTTCGTAATATCAGAATTTAAATTTTTAACATAATGTGTAATAAGTGAT F2: 3 TTTTTCGTAATA 2 Unidirectional alignment (log-probability: -30.8) TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAtataatgcttTTtTAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCA----------TTATAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA Template switch alignment (log-probability: -17.3) TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAT|ATAATGCTTTTT|TAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA TTGCTGTGTTCCTTTACTTATTTAAAAAATAAAAAAGCAT|ATAATGCTTTTT|TAGTCTTAAATTTAAAAATTGTATTACACATTATTCACTA ========== Event 1253 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAAGAAAATAGCCCAAGCACAGCTCAAAAAGCTCTA---------------------------------------------------------------AAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACACTGTGAAACATTCT ↓ 4 3 1 2 Chimp: ATAAGAAAATAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGATCCACCCACCCCCTTGTCGCTACATCCCAGTTTTTACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACACTGTGAAACATTCT ↑ 4 3 1 2 Gorilla: ATAAGAAAACAGCCCAAGCACAGCTCAAAAAGCTCTA---------------------------------------------------------------AAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACACTGTGAAACATTCT Human: ATAAGAAAATAGCCCAAGCACAGCTCAAAAAGCTCTA---------------------------------------------------------------AAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACACTGTGAAACATTCT Cluster: [ ] Orangutan: ATAAGAAAATACCCCAAGCACAGCACAAAAAGCTCTA---------------------------------------------------------------AAAACTGGGATGTAGCAACAAGGGGGTGGGTGGTGCACACTGTGAAACATTCT Human > Chimp ------------- chr16:64750057-64750090 Template switch process: F1: L AAACATAAGAAAATAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGAT 1 F3: 4 ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACAC R RF: AAACATAAGAAAATAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACAC RR: TTTGTATTCTTTTATCGGGTTCGTGTCGAGTTTTTCGAGATTTTTGACCCTACATCGCTGTTCCCCCACCCACCACGTGTG F2: 3 TTTTTGACCCTACATCGCTGTTCCCCCACCCACC 2 Unidirectional alignment (log-probability: -101) ATAGCCCAAGCacagctcaaaaagctctaaaaactgggatccacccacccccttgtcgctacatcccagtttttACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG ATAGCCCAAGC---------------------------------------------------------------ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG Template switch alignment (log-probability: -19.9) ATAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGAT|CCACCCACCCCCTTGTCGCTACATCCCAGTTTTT|ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG ATAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGAT|CCACCCACCCCCTTGTCGCTACATCCCAGTTTTT|ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG Gorilla > Chimp --------------- chr16:64750057-64750090 Template switch process: F1: L AAACATAAGAAAATAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGAT 1 F3: 4 ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACAC R RF: AAACATAAGAAAACAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAGGGGGTGGGTGGTGCACAC RR: TTTGTATTCTTTTGTCGGGTTCGTGTCGAGTTTTTCGAGATTTTTGACCCTACATCGCTGTTCCCCCACCCACCACGTGTG F2: 3 TTTTTGACCCTACATCGCTGTTCCCCCACCCACC 2 Unidirectional alignment (log-probability: -107) AtAGCCCAAGCacagctcaaaaagctctaaaaactgggatccacccacccccttgtcgctacatcccagtttttACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG ACAGCCCAAGC---------------------------------------------------------------ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG Template switch alignment (log-probability: -26.2) AtAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGAT|CCACCCACCCCCTTGTCGCTACATCCCAGTTTTT|ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG ACAGCCCAAGCACAGCTCAAAAAGCTCTAAAAACTGGGAT|CCACCCACCCCCTTGTCGCTACATCCCAGTTTTT|ACAGCTCAAAAAGCTCTAAAAACTGGGATGTAGCGACAAG ========== Event 1254 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAGGCTGGACAGGGAGCTGGGCACCT------------------------CCTGCCCCAGTTAGGCC-CCCCAGCGGGGTCTCA Chimp: AGAGGCTGGACAGGGAGCTGGGCACCT------------------------CCTGCCCCAGTTAGGcccccccAGCGGGGTCTCA ↓ 4 31 2 Gorilla: AGAGGCTGGACAGGGAGCTGGGCACCTCCTGCTCCCTAACTGGGGGCACCTCCTGCCCCAGTTAGGcccccccAGCGGGGTCTCA Human: AGAGGCTGGACAGGGAGCTGGGCACCT------------------------CCTGCCCCAGTTAGGCC-CCCCAGCGGGGTCTCA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr16:1841726-1841733 Template switch process: F1: L CGCTCACTGCCCTCAGAGGCTGGACAGGGAGCTGGGCACCTCCTGCTCC 1 F3: 4 GGGCACCTCCTGCCCCAGTTAGGCCCCCCCAGCGGGGTCTCACCTGCC R RF: CGCTCACTGCCCTCAGAGGCTGGACAGGGAGCTGGGCACCTCCTGCCCCAGTTAGGCCCCCCCAGCGGGGTCTCACCTGCC RR: GCGAGTGACGGGAGTCTCCGACCTGTCCCTCGACCCGTGGAGGACGGGGTCAATCCGGGGGGGTCGCCCCAGAGTGGACGG F2: 3 GGTCAATC 2 Unidirectional alignment (log-probability: -45.4) CCCTCAGAGGCTGGACAGGGAGCTGGGCACctcctgctccctaactgggggcacCTCCTGCCCCAGTTAGGCCCCCCCAGCGGGGTCT CCCTCAGAGGCTGGACAGGGAGCTGGGCAC------------------------CTCCTGCCCCAGTTAGGCCCCCCCAGCGGGGTCT Template switch alignment (log-probability: -22.7) CCCTCAGAGGCTGGACAGGGAGCTGGGCACCTCCTGCtCC|CTAACTGG|GGGCACCTCCTGCCCCAGTTAGGCCCCCCCAGCGGGGTCT CCCTCAGAGGCTGGACAGGGAGCTGGGCACCTCCTGCCCC|CTAACTGG|GGGCACCTCCTGCCCCAGTTAGGCCCCCCCAGCGGGGTCT ========== Event 1255 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTCACTTTAAAACTCCTTTTTAATACAGTGT--------------------TCTCCACCTTCCCAACCCCAGATGTTA---------GGCTGACCTCTCAGCCTCTGGCTGTCCTTTCT Chimp: TTTCACTTTAAAACTCCTTTTTAATACAGTGT--------------------TCTCCACCTCTCCAACCCCAGATGTTA---------GGCTGACCTCTCAGCCTCTGGCTGTCCTTTCT ↓ 3 1 2 4 Gorilla: TTTCACTTTAAAACTCCTTTTTAATACAGCCC----------------------------------------TGTATTA------------------AACAGCCTCTGGCTGTCCTTTCT ↑ 3 1 2 4 Human: TTTCACTTTAAAACTCCTTTTTAATACAGTGT--------------------TCTCCACCTTCCCAACCCCAGATGTTA---------GGCTGACCTCTCAGCCTCTGGCTGTCCTTTCT Cluster: [ ] Orangutan: TTTCACTTTAAAACTCCTTTTTAATACAGTGTTCTCCACCTCCCCAACCCCA--------------------GATGTTAGGCTGACCT---------CTCAGCCTCTGGCTGTCCTTTCT Human > Gorilla --------------- chr16:79480336-79480347 Template switch process: F1: L CCCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG 1 F3: 4 CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA R RF: CCCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAGTGTTCTCCACCTTCCCAACCCCAGATGTTAGGCTGACCTCTCAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA RR: GGGGGTGACCGCAAAGTGAAATTTTGAGGAAAAATTATGTCACAAGAGGTGGAAGGGTTGGGGTCTACAATCCGACTGGAGAGTCGGAGACCGACAGGAAAGATCCAGGGAAAGAGACCCGT F2: 3 AAATTATGTCCC 2 Unidirectional alignment (log-probability: -39.6) CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG-------------------------------------CcCTgtattaaaCAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAGTGTTCTCCACCTTCCCAACCCCAGATGTTAGGCTGACCTCT--------CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA Template switch alignment (log-probability: -22.8) CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG|CcCTGTATTAAA|CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG|CACTGTATTAAA|CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA Chimp > Gorilla --------------- chr16:79480336-79480347 Template switch process: F1: L CCCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG 1 F3: 4 CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA R RF: CCCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAGTGTTCTCCACCTCTCCAACCCCAGATGTTAGGCTGACCTCTCAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA RR: GGGGGTGACCGCAAAGTGAAATTTTGAGGAAAAATTATGTCACAAGAGGTGGAGAGGTTGGGGTCTACAATCCGACTGGAGAGTCGGAGACCGACAGGAAAGATCCAGGGAAAGAGACCCGT F2: 3 AAATTATGTCCC 2 Unidirectional alignment (log-probability: -39.6) CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG-------------------------------------CcCTgtattaaaCAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAGTGTTCTCCACCTCTCCAACCCCAGATGTTAGGCTGACCTCT--------CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA Template switch alignment (log-probability: -22.8) CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG|CcCTGTATTAAA|CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA CCCCACTGGCGTTTCACTTTAAAACTCCTTTTTAATACAG|CACTGTATTAAA|CAGCCTCTGGCTGTCCTTTCTAGGTCCCTTTCTCTGGGCA ========== Event 1256 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGGCCACCCTTACTTCCCAGGTGCTGTGCTGGGTGACGAGGGCAAGCGCCACGCTGAGGATGGTACATGGTTCCGGCCCTGACTCAGGAGCACAGAGACAAGCTCTGGTCAGGGCGTACAACGGGGCCTCTTGCAT----------------------------------------CCATCCCTCC--------ACAAGAGCAGGAGGAAGGTTCTGCTGCCTGCTGAGACCAC Chimp: AGGGCCACCCTTACTTCCCAGGTGCTGTGCTGGGTGACGAGGGCAAGCGCCACGCTGAGGATGGTACATGGTTCCGGCCCTGACTCACGAGCACAGAGACAGGCTCTGGTCAGGGCGTACAACAGGGCCTCTCGCAT----------------------------------------CCATCCCTCC--------ACAAGAGCAGGAGGAAGGTCCTGCTGCCTGCTGGGACCAC ↓ 3 2 1 4 Gorilla: AGGGCCACCCTTACTTCCCAGGTGCTGTGCTGGGTGCCGAGGGCAAGCGCCACGCTGAGGATGGTACATGGTTCCGGCCCTGACTCAGGAGCACAGAGACAGGATCTGGTCAGGGCGTACAACAGGGCCTCTCGCAT----------------------------------------CCATCCCTCC----------------AGGCACCTGGTTCTGCTGCCTGCTGGGACCAC Human: AGGGCCACCCTTACTTCCCAGGTGCTGTGCTGGGTGACGAGGGCAAGCGCCACGCTGAGGATGGTACATGGTTCCGGCCCTGACTCAGGAGCACAGAGACAAGCTCTGGTCAGGGCGTACAACGGGGCCTCTTGCAT----------------------------------------CCATCCCTCC--------ACAAGAGCAGGAGGAAGGTTCTGCTGCCTGCTGAGACCAC Cluster: [ ] Orangutan: AGGGCCACCCTTACTTCCCAGGTGCTGTGCTGGGTGCCGAGGGCAAGCGCCACGCTGAGGATGGTACATGGTTCCGGCCCTGACTCAGGAGCACAGAGACAGGCTCTGGTCACGGCATACAACAGGGCCTCTCGCATCCCTGCTGTGACCAGGAGAGGCAAGCCACGGAACCTCCTTCCATCCCTCCACAAGACC--------AGGAGGAAGGTTCCGCTGCCTGCCGGGACCAC Chimp > Gorilla --------------- chr16:79271796-79271801 Template switch process: F1: L TGGTCAGGGCGTACAACAGGGCCTCTCGCATCCATCCCTCCAG 1 F3: 4 GGTTCTGCTGCCTGCTGGGACCACCGCACCCTCAGCAAATCCAG R RF: AGGTGCTGTGCTGGGTGACGAGGGCAAGCGCCACGCTGAGGATGGTACATGGTTCCGGCCCTGACTCACGAGCACAGAGACAGGCTCTGGTCAGGGCGTACAACAGGGCCTCTCGCATCCATCCCTCCACAAGAGCAGGAGGAAGGTCCTGCTGCCTGCTGGGACCACCGCACCCTCAGCAAATCCAG RR: TCCACGACACGACCCACTGCTCCCGTTCGCGGTGCGACTCCTACCATGTACCAAGGCCGGGACTGAGTGCTCGTGTCTCTGTCCGAGACCAGTCCCGCATGTTGTCCCGGAGAGCGTAGGTAGGGAGGTGTTCTCGTCCTCCTTCCAGGACGACGGACGACCCTGGTGGCGTGGGAGTCGTTTAGGTC F2: 3 TCCACG 2 Unidirectional alignment (log-probability: -36.7) TCAGGGCGTACAACAGGGCCTCTCGCATCCATCCCTCC-----------AGGcAcctGGTtCTGCTGCCTGCTGGGACCACCGCACCCTCAGCAAAT TCAGGGCGTACAACAGGGCCTCTCGCATCCATCCCTCCACAAGAGCAGGAGGAA---GGTCCTGCTGCCTGCTGGGACCACCGCACCCTCAGCAAAT Template switch alignment (log-probability: -27.7) TCAGGGCGTACAACAGGGCCTCTCGCATCCATCCCTCCAg|GCACCT|GGTtCTGCTGCCTGCTGGGACCACCGCACCCTCAGCAAAT TCAGGGCGTACAACAGGGCCTCTCGCATCCATCCCTCCAC|GCACCT|GGTCCTGCTGCCTGCTGGGACCACCGCACCCTCAGCAAAT ========== Event 1257 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAAGTCATTTAGATTAGAGAAG--------------------------------AACTCCCTGTAAGTTTAggccagatgcagtagctcacacctgcaattgcagcactttgggaggccgaggc Chimp: TGAAGTCATTTAGATTAGAGAAG----------------AACTCTGCAATTTAAGAACTCCCTGTAAGTTTAggccagatgcagtggctcacacctgcaattgcagcactttgggaggccgaggc Gorilla: TGAAGTCATTTAGATTAGAGAAGAACTCTGCAATTTAAG----------------AACTCCCTGTAAGTTTAggccagatgcagtggctcacacctgcaattgcagcactttgggaggccgaggc ↑ 4 1 3 2 Human: TGAAGTCATTTAGATTAGAGAAG--------------------------------AACTCCCTGTAAGTTTAggccagatgcagtagctcacacctgcaattgcagcactttgggaggccgaggc Cluster: [ ] Orangutan: TGAAGTCATTTAGATTAGAGAAGAACTCTGCAATTTAAG----------------AACTCCCTGTAAGTTTAggccagatgcggtggctcacacctgcaatcacagcactttgggaggccgaggc Human > Gorilla --------------- chr16:20373884-20373890 Template switch process: F1: L AGGAAATGTAAGAGTTACTGAAGTCATTTAGATTAGAGAAGAACTC 1 F3: 4 TAAGAACTCCCTGTAAGTTTAGGCCAGATGCAGTGGCTCACACC R RF: AGGAAATGTAAGAGTTACTGAAGTCATTTAGATTAGAGAAGAACTCCCTGTAAGTTTAGGCCAGATGCAGTAGCTCACACCTGCAATTGCA RR: TCCTTTACATTCTCAATGACTTCAGTAAATCTAATCTCTTCTTGAGGGACATTCAAATCCGGTCTACGTCATCGAGTGTGGACGTTAACGT F2: 3 TTAACGT 2 Unidirectional alignment (log-probability: -39.4) TGTAAGAGTTACTGAAGTCATTTAGATTAGAGAagaactctgcaatttaAGAACTCCCTGTAAGTTTAGGCCAGATGCAGTgGCTCA TGTAAGAGTTACTGAAGTCATTTAGATTAGAGA----------------AGAACTCCCTGTAAGTTTAGGCCAGATGCAGTAGCTCA Template switch alignment (log-probability: -27.9) TGTAAGAGTTACTGAAGTCATTTAGATTAGAGAAGAACTC|TGCAATT|tAAGAACTCCCTGTAAGTTTAGGCCAGATGCAGTgGCTCA TGTAAGAGTTACTGAAGTCATTTAGATTAGAGAAGAACTC|TGCAATT|GAAGAACTCCCTGTAAGTTTAGGCCAGATGCAGTAGCTCA ========== Event 1258 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ctcattcTCATGTTGCAGAATGCAGAGGGTGAC---TCTTACTATGTATATTGTTATGATTATCA Chimp: ctcattcTCATGTTGCAGAATGCAGAGGGTGAC---TCTTACTATGTATATTGTTATGATTATCA ↓ 3 2 1 4 Gorilla: ctcattcTCATGTTGCAGAATGCAGAGGGTGAC------TGCATTGTATATTGTTATGATTATCA Human: ctcattcTCATGTTGCAGAATGCAGAGGGTGAC---TCTTACTATGTATATTGTTATGATTATCA Cluster: [ ] Orangutan: ctcattcTCATGTTGCAGAATGCAGAGGGCAACTCT---TACTATGTATATTGTTATGATTATCA Chimp > Gorilla --------------- chr16:20372945-20372948 Template switch process: F1: L ATTTCAAACTCATTCTCATGTTGCAGAATGCAGAGGGTGACT 1 F3: 4 TGTATATTGTTATGATTATCATTGCTGTGTCTCATTTTAT R RF: ATTTCAAACTCATTCTCATGTTGCAGAATGCAGAGGGTGACTCTTACTATGTATATTGTTATGATTATCATTGCTGTGTCTCATTTTAT RR: TAAAGTTTGAGTAAGAGTACAACGTCTTACGTCTCCCACTGAGAATGATACATATAACAATACTAATAGTAACGACACAGAGTAAAATA F2: 3 TACG 2 Unidirectional alignment (log-probability: -26.8) TTCAAACTCATTCTCATGTTGCAGAATGCAGAGGGTGACT-------gcatTGTATATTGTTATGATTATCATTGCTGTGTCTCATTTTAT TTCAAACTCATTCTCATGTTGCAGAATGCAGAGGGTGACTCTTACTA----TGTATATTGTTATGATTATCATTGCTGTGTCTCATTTTAT Template switch alignment (log-probability: -16.3) TTCAAACTCATTCTCATGTTGCAGAATGCAGAGGGTGACT|GCAT|TGTATATTGTTATGATTATCATTGCTGTGTCTCATTTTAT TTCAAACTCATTCTCATGTTGCAGAATGCAGAGGGTGACT|GCAT|TGTATATTGTTATGATTATCATTGCTGTGTCTCATTTTAT ========== Event 1259 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGGGTAGGCCTTTCTTGGTGCT--------------------------CTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCTTTATGGATGCAAGTTCATCCTTAAGAGAAACTC ↓ 4 1 3 2 Chimp: GGGGTAGGCCTTTCTTGGTGCT-------------CTTTCTTGCAGCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCTTTATGGATGCAAGTTCATCCTTAAGAGAAACTC Gorilla: GGGGTAGGCCTTTCTTGGTGCTCTTTCTTGCAGCT-------------CTTTGATGGATATCGATGTTGGCAAGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCGTTATGGATGCAAGTTCATCCTTAAGAGAAACTC ↑ 4 1 3 2 Human: GGGGTAGGCCTTTCTTGGTGCT--------------------------CTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCTTTATGGATGCAAGTTCATCCTTAAGAGAAACTC Cluster: [ ] Orangutan: GGGGTAGGCCTTTCTTGGTGCTCTTTCTTGCAGCT-------------CTTTGATGGATATCGATGTTGGCAGGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCTTTATGGATGCAAGTTCATCCTTAAGAGAAACTC Human > Chimp ------------- chr1:62261292-62261297 Template switch process: F1: L TGACCAGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTT 1 F3: 4 GCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCACCA R RF: TGACCAGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCTTTATGGATGCAAG RR: ACTGGTCACTAGGGTCTCACCCCATCCGGAAAGAACCACGAGAAACTACCTATAACTACAACCGTTCACGAAGTGAGTGGTCGAGTACGTACACCTAGGGTTCTAAGATCCCTATATCGTTAGGGAAATACCTACGTTC F2: 3 ACGTTC 2 Unidirectional alignment (log-probability: -29.6) AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTgctctttcttgcaGCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCA AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGT-------------GCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCA Template switch alignment (log-probability: -16.2) AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTT|CTTGCA|GCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCA AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTT|CTTGCA|GCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCA Human > Gorilla --------------- chr1:63249414-63249419 Template switch process: F1: L TGACCAGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTT 1 F3: 4 GCTCTTTGATGGATATCGATGTTGGCAAGTGCTTCACTCACCA R RF: TGACCAGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCACCAGCTCATGCATGTGGATCCCAAGATTCTAGGGATATAGCAATCCCTTTATGGATGCAAG RR: ACTGGTCACTAGGGTCTCACCCCATCCGGAAAGAACCACGAGAAACTACCTATAACTACAACCGTTCACGAAGTGAGTGGTCGAGTACGTACACCTAGGGTTCTAAGATCCCTATATCGTTAGGGAAATACCTACGTTC F2: 3 ACGTTC 2 Unidirectional alignment (log-probability: -35.1) AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGctctttcttgcagCTCTTTGATGGATATcGATGTTGGCAAGTGCTTCACTCA AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTG-------------CTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCA Template switch alignment (log-probability: -22.2) AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTT|CTTGCA|GCTCTTTGATGGATATcGATGTTGGCAAGTGCTTCACTCA AGTGATCCCAGAGTGGGGTAGGCCTTTCTTGGTGCTCTTT|CTTGCA|GCTCTTTGATGGATATTGATGTTGGCAAGTGCTTCACTCA ========== Event 1260 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCAAGCTGCATCTCATTTTT-----ACACCAAAAGCAAGATGTTGACCTTGATCAGTTAAGttcaacaagcaag ↓ 1 4 3 2 Chimp: TGCAAGCTGCATCTCATTTTTGACCAAGGTCAAAAGCAAGATGTTGACCTTGatcagttaagttcaacaagcaag Gorilla: TGCAAGCTGCATCTCATTTTT-----GCACCAAAAGCAAGATGTTGACCTTGatcaattaggttcaacaagcaag Human: TGCAAGCTGCATCTCATTTTT-----ACACCAAAAGCAAGATGTTGACCTTGATCAGTTAAGttcaacaagcaag Cluster: [ ] Orangutan: TGCAAGCTGCATCTCATTTTT-----ACACCAAAAGCAAGATGTTCACCTTGATCAGTTAAGttcaacaagcaag Human > Chimp ------------- chr16:58060695-58060703 Template switch process: F1: L ATTCATCTCCCATCTCAGCTTGCAAGCTGCATCTCATTTTT 1 F3: 4 CAAAAGCAAGATGTTGACCTTGATCAGTTAAGTTCAACAA R RF: ATTCATCTCCCATCTCAGCTTGCAAGCTGCATCTCATTTTTACACCAAAAGCAAGATGTTGACCTTGATCAGTTAAGTTCAACAA RR: TAAGTAGAGGGTAGAGTCGAACGTTCGACGTAGAGTAAAAATGTGGTTTTCGTTCTACAACTGGAACTAGTCAATTCAAGTTGTT F2: 3 TGGAACCAG 2 Unidirectional alignment (log-probability: -34.3) TTCATCTCCCATCTCAGCTTGCAAGCTGCATCTCATTTTtgaccaaggT----CAAAAGCAAGATGTTGACCTTGATCAGTTAAGTTCAACAA TTCATCTCCCATCTCAGCTTGCAAGCTGCATCTCATTTT---------TACACCAAAAGCAAGATGTTGACCTTGATCAGTTAAGTTCAACAA Template switch alignment (log-probability: -22.4) TTCATCTCCCATCTCAGCTTGCAAGCTGCATCTCATTTTT|GAcCAAGGT|CAAAAGCAAGATGTTGACCTTGATCAGTTAAGTTCAACAA TTCATCTCCCATCTCAGCTTGCAAGCTGCATCTCATTTTT|GATCAAGGT|CAAAAGCAAGATGTTGACCTTGATCAGTTAAGTTCAACAA ========== Event 1261 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTCTAGTTGTTTTTTGAGATTGAATC--CAGGCTTCAGTCAGATTGCTGCACCCTCCTCAC Chimp: TTTTCTAGTTGTTTTTTGAGATTGAATC--CAGGCTTCAGTCAGATTGCTGCACCCTCCTCAC ↓ 1 34 2 Gorilla: TTTTCTAGTTGTTTTTTGAGACTGAATC----TGACTGAGTCAGATTGCTGCACCCTCCTCAC ↑ 1 34 2 Human: TTTTCTAGTTGTTTTTTGAGATTGAATC--CAGGCTTCAGTCAGATTGCTGCACCCTCCTCAC Cluster: [ ] Orangutan: TTTTCTAGTTGTTTTTTGAGATTGAATCCA--GGCTTCAGTCAGATTGTTGCACCCTCCTCAC Human > Gorilla --------------- chr16:56316511-56316516 Template switch process: F1: L CCTTGGCTTCATCATCTGCATTTTCTAGTTGTTTTTTGAGACTGAATC 1 F3: 4 AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC R RF: CCTTGGCTTCATCATCTGCATTTTCTAGTTGTTTTTTGAGATTGAATCCAGGCTTCAGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC RR: GGAACCGAAGTAGTAGACGTAAAAGATCAACAAAAAACTCTAACTTAGGTCCGAAGTCAGTCTAACGACGTGGGAGGAGTGAAGGTGGAATCGGAG F2: 3 GTCAGT 2 Unidirectional alignment (log-probability: -35.3) TCATCATCTGCATTTTCTAGTTGTTTTTTGAGAcTGAA--------TCtgactgAGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC TCATCATCTGCATTTTCTAGTTGTTTTTTGAGATTGAATCCAGGCTTC------AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC Template switch alignment (log-probability: -22.2) TCATCATCTGCATTTTCTAGTTGTTTTTTGAGAcTGAATC|TGACTG|AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC TCATCATCTGCATTTTCTAGTTGTTTTTTGAGATTGAATC|TGACTG|AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC Chimp > Gorilla --------------- chr16:56316511-56316516 Template switch process: F1: L CCTTGGCTTCATCATCTGCATTTTCTAGTTGTTTTTTGAGACTGAATC 1 F3: 4 AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC R RF: CCTTGGCTTCATCATCTGCATTTTCTAGTTGTTTTTTGAGATTGAATCCAGGCTTCAGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC RR: GGAACCGAAGTAGTAGACGTAAAAGATCAACAAAAAACTCTAACTTAGGTCCGAAGTCAGTCTAACGACGTGGGAGGAGTGAAGGTGGAATCGGAG F2: 3 GTCAGT 2 Unidirectional alignment (log-probability: -35.3) TCATCATCTGCATTTTCTAGTTGTTTTTTGAGAcTGAA--------TCtgactgAGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC TCATCATCTGCATTTTCTAGTTGTTTTTTGAGATTGAATCCAGGCTTC------AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC Template switch alignment (log-probability: -22.2) TCATCATCTGCATTTTCTAGTTGTTTTTTGAGAcTGAATC|TGACTG|AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC TCATCATCTGCATTTTCTAGTTGTTTTTTGAGATTGAATC|TGACTG|AGTCAGATTGCTGCACCCTCCTCACTTCCACCTTAGCCTC ========== Event 1262 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCATTTAGAGGAAAGGCCCTGGTCCTTCATCAGTAGCCCCTAGGCCTGCTAACTGTAGAGACTCTCATTTGGCTCTAGTGAGGCTGCTCTCTGAAGTCAGGGTCCGGAGCTAGCCCCTT-GCCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCC-----------TGGGGGACTGCTGGGGTCACTCTCCCTGCATTCCTT Chimp: CCATTTAGAGGAAAGGCCCTGGTTCTTCATCAGTAGCCCCTAGGCCTGCTAACTGTAGAGACTCTCATTTGGCTCTAGTGGGGCTGCTCTCTGGAGTCAGGGTCCGGAGCTAGCCCCCTGCCCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCC-----------TGGGGGCCAGCTGGGGTCACTCTCCCTGCATTCCTT Gorilla: CCATTTAGAGGAAAGGCCCCAGTCCTTCATCAGTAGCCCCTAGGCCTGCTAACTGTAGAGACTCTCATTTGGCTCTAGTGGGGCTGCTCTCTGGAGTCAGGGTCTGGAGCCAGCCCCCTGCCCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCC----------------------TGGGGTCACTCTCCCTGCATTCCTT ↓ 3 2 4 1 Human: CCATTTAGAGGAAAGGCCCTGGTCCTTCATCAGTAGCCCCTAGGCCTGCTAACTGTAGAGACTCTCATTTGGCTCTAGTGAGGCTGCTCTCTGAAGTCAGGGTCCGGAGCTAGCCCCTT-GCCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCC-----------TGGGGGACTGCTGGGGTCACTCTCCCTGCATTCCTT Cluster: [ ] Orangutan: TCATTTAGAGGAAAGGCCCTAGTCCTTCATCAGTAGCCCCTAGGCCTGCTAACTGTAGAGACTCTTATTTGGCTCTAGTGGGGCTGCTCTCCGGAGTCAGGGTCCGGAGCCAGCCCCCTGCCCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCCTGGGGGCCTGC-----------TGGGGTCACTCTCCCTGCATTCCTC Gorilla > Human --------------- chr1:6290913-6290917 Template switch process: F1: L G-CCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCCTGGGG 1 F3: 4 CTGGGGTCACTCTCCCTGCATTCCTTAGAGTGGCCCCTTCT R RF: CAGTCCTTCATCAGTAGCCCCTAGGCCTGCTAACTGTAGAGACTCTCATTTGGCTCTAGTGGGGCTGCTCTCTGGAGTCAGGGTCTGGAGCCAGCCCCCTGCCCAGCTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCCTGGGGTCACTCTCCCTGCATTCCTTAGAGTGGCCCCTTCT RR: GTCAGGAAGTAGTCATCGGGGATCCGGACGATTGACATCTCTGAGAGTAAACCGAGATCACCCCGACGAGAGACCTCAGTCCCAGACCTCGGTCGGGGGACGGGTCGACATACTGACGAGAAGAGTTTTCACCCCCCGGGGACCCCAGTGAGAGGGACGTAAGGAATCTCACCGGGGAAGA F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -36.5) CTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCctgggggactgCTGGGGTCACTCTCCCTGCATTCCTTAGAGTGGCCCCTTC CTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCC-----------CTGGGGTCACTCTCCCTGCATTCCTTAGAGTGGCCCCTTC Template switch alignment (log-probability: -26.3) CTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCCTGGGG|GACTG|CTGGGGTCACTCTCCCTGCATTCCTTAGAGTGGCCCCTTC CTGTATGACTGCTCTTCTCAAAAGTGGGGGGCCCCTGGGG|GACTG|CTGGGGTCACTCTCCCTGCATTCCTTAGAGTGGCCCCTTC ========== Event 1263 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ggcgttagccactgcgcctagccTCCAGAGTCAtttcttatcactctgtttcttatcactgagtttATTCTGCCTGAGGGCAAGAGAGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCTGGGCCGCCCTAGAATCAGGGCAT--- Chimp: ggcgttagccactgcgcctagccTCCAGAGTCAtttcttatcactctgtttcttatcactgagtttATTCTGCCTGAGGGCAAGAGAGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCCGGGCCGCCCTAGAATCAGGGCAT--- ↓ 3 2 1 4 Gorilla: ggcgttagccactgcgcctagccTCCAGAGTCAtttcttatcactctgtttcttatcactgagtttATTCTGCCTGAGGGCAAGAGAGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCCAGGCTGCCCTAGAATCAGGGCATTTA Human: ggcgttagccactgcgcctagccTCCAGAGTCAtttcttatcactctgtttcttatcactgagtttATTCTGCCTGAGGGCAAGAGAGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCTGGGCCGCCCTAGAATCAGGGCAT--- Cluster: [ ] Orangutan: ggcgtgagccactgcgcccagccTCCAGAGTCATTTCTTATCACTCTGTTTCTTATCGCTGAGTTTATTCTGCCTGAGGGCAAGAGAGTAAAGCCAATTTAAATCGTGCACACCTGAGCTCCTTCCGGGCCGCCCTAGAATCAGGGCATTTA Chimp > Gorilla --------------- chr16:56003444-56003448 Template switch process: F1: L GAGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCC 1 F3: 4 GCCCTAGAATCAGGGCATTTATGGCCTAGGGCACAGGGAC R RF: AGCCTCCAGAGTCATTTCTTATCACTCTGTTTCTTATCACTGAGTTTATTCTGCCTGAGGGCAAGAGAGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCCGGGCCGCCCTAGAATCAGGGCATTTATGGCCTAGGGCACAGGGAC RR: TCGGAGGTCTCAGTAAAGAATAGTGAGACAAAGAATAGTGACTCAAATAAGACGGACTCCCGTTCTCTCATTTCGGTTAAATTTAGCACGTGAAGGCTCGAGGAAGGCCCGGCGGGATCTTAGTCCCGTAAATACCGGATCCCGTGTCCCTG F2: 3 TCGGA 2 Unidirectional alignment (log-probability: -50.3) AGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCCaGGCtGCCCTAGAATCAGGGCATttatggcctagggcacagggac AGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCCGGGCCGCCCTAGAATCAGGGCAT---------------------- Template switch alignment (log-probability: -16.4) AGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCC|AGGCT|GCCCTAGAATCAGGGCATTTATGGCCTAGGGCACAGGGAC AGTAAAGCCAATTTAAATCGTGCACTTCCGAGCTCCTTCC|AGGCT|GCCCTAGAATCAGGGCATTTATGGCCTAGGGCACAGGGAC ========== Event 1264 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAAGGGTCAGAT--GTTTGCCTAGCGT----AGTATTAATATATAAATA-CACTA Chimp: TTAAGGGTCAGAT--GTTTGCCTAGTACACTAGGCATTAATATATAAATA-CACTA ↑ 3 1 2 4 Gorilla: TTAAGGGTCAGAT--GTTTGCCTAGTGT----AGTATTAATATATAAATA-CACTA Human: TTAAGGGTCAGAT--GTTTGCCTAGCGT----AGTATTAATATATAAATA-CACTA Cluster: [ ] Orangutan: TTAAGGGTCAGATGTATTTGCCTAGTGT----AGTATTAATATATAAATACGACTA Gorilla > Chimp --------------- chr1:62635192-62635200 Template switch process: F1: L TTGACCAATAGTTTGTATTAAGGGTCAGATGTTTGCCTAGT 1 F3: 4 ATTAATATATAAATACACTAAGATAGAAATAACCTTAATA R RF: TTTACCAATAGTTTGTATTAAGGGTCAGATGTTTGCCTAGTGTAGTATTAATATATAAATACACTAAGATAGAAATAACCTTAATA RR: AAATGGTTATCAAACATAATTCCCAGTCTACAAACGGATCACATCATAATTATATATTTATGTGATTCTATCTTTATTGGAATTAT F2: 3 CGGATCACA 2 Unidirectional alignment (log-probability: -38.8) TgACCAATAGTTTGTATTAAGGGTCAGATGTTTGCCTAGTacActagGcATTAATATATAAATACACTAAGATAGAAATAACCTTAATA TTACCAATAGTTTGTATTAAGGGTCAGATGTTTGCCTAGTGTA----GTATTAATATATAAATACACTAAGATAGAAATAACCTTAATA Template switch alignment (log-probability: -22.4) TgACCAATAGTTTGTATTAAGGGTCAGATGTTTGCCTAGT|ACACTAGGC|ATTAATATATAAATACACTAAGATAGAAATAACCTTAATA TTACCAATAGTTTGTATTAAGGGTCAGATGTTTGCCTAGT|ACACTAGGC|ATTAATATATAAATACACTAAGATAGAAATAACCTTAATA ========== Event 1265 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTATCAATGATGCAAGCCATCCTGAATTTATATTCAGGATGTTCCCATACTGCTGGACTC ↑ 3 1 2 4 Chimp: TTATCAATGATGCAAGCCATCCTGAATAT-----AAGCCTGTTCCCATACTGCTGGACTC Gorilla: TTATCAATGATGCAAGCCATCCTGTATAT-----AAGCCTGTTCCCATACTGCTGGACTC ↓ 3 1 2 4 Human: TTATCAATGATGCAAGCCATCCTGAATTTATATTCAGGATGTTCCCATACTGCTGGACTC Cluster: [ ] Orangutan: TTATCAATGATGCAAGCCATCATGAATAT-----AAGCCTGTTTCCATACTGCTAGACTC Chimp > Human ------------- chr16:64786598-64786609 Template switch process: F1: L AACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGAAT 1 F3: 4 TGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT R RF: AACTCAAGAAATTCTTATCAATGATGCAAGCCATCCTGAATATAAGCCTGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT RR: TTGAGTTCTTTAAGAATAGTTACTACGTTCGGTAGGACTTATATTCGGACAAGGGTATGACGACCTGAGAGTCTACCCGTGATAAAGA F2: 3 AGGACTTATATT 2 Unidirectional alignment (log-probability: -42.1) ACTCAAGAgATTCTTATCAATGATGCAAGCCATCCTGAATtTAtattcAGgaTGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT ACTCAAGAAATTCTTATCAATGATGCAAGCCATCCTGAATATA-----AGCCTGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT Template switch alignment (log-probability: -22.8) ACTCAAGAgATTCTTATCAATGATGCAAGCCATCCTGAAT|TTATATTCAGGA|TGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT ACTCAAGAAATTCTTATCAATGATGCAAGCCATCCTGAAT|TTATATTCAGGA|TGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT Gorilla > Human --------------- chr16:64786598-64786609 Template switch process: F1: L GTAAACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGAAT 1 F3: 4 TGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT R RF: GTAAACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGTATATAAGCCTGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT RR: CATTTGAGTTCTCTAAGAATAGTTACTACGTTCGGTAGGACATATATTCGGACAAGGGTATGACGACCTGAGAGTCTACCCGTGATAAAGA F2: 3 AGGACTTATATT 2 Unidirectional alignment (log-probability: -40.3) ACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGaATtTAtattcAGgaTGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT ACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGTATATA-----AGCCTGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT Template switch alignment (log-probability: -28.4) ACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGaAT|TTATATtCAGGA|TGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT ACTCAAGAGATTCTTATCAATGATGCAAGCCATCCTGTAT|TTATATACAGGA|TGTTCCCATACTGCTGGACTCTCAGATGGGCACTATTTCT ========== Event 1266 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGTCTGAAAATCCCTGTTATCCAACAG-----CAATCCCAGAAGAGCGATGGCCTCAG Chimp: AAGGTCTGGAAATCCCTGTTATCCAACAG-----CAATCCCAGAAGAGCGATGGCTTCAG ↓ 3 1 2 4 Gorilla: AAGGTCTGGAAATCCCTGTTATCCAACTGCTGTTGGATACCAGAAGAGCGATGGCCTCAG ↑ 3 1 2 4 Human: AAGGTCTGAAAATCCCTGTTATCCAACAG-----CAATCCCAGAAGAGCGATGGCCTCAG Cluster: [ ] Orangutan: AAGGTCTGGAAATCCCTGTCATCCAACAG-----CAATCCCAGAAGAGCGATGGCCTCAG Human > Gorilla --------------- chr16:27064423-27064434 Template switch process: F1: L TAAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAAC 1 F3: 4 CCAGAAGAGCGATGGCCTCAGGTTCATGTAGGGCTTGGAG R RF: TAAGCCTGGATGTGAAGGTCTGAAAATCCCTGTTATCCAACAGCAATCCCAGAAGAGCGATGGCCTCAGGTTCAGGTAGGGCTTGGAG RR: ATTCGGACCTACACTTCCAGACTTTTAGGGACAATAGGTTGTCGTTAGGGTCTTCTCGCTACCGGAGTCCAAGTCCATCCCGAACCTC F2: 3 ATAGGTTGTCGT 2 Unidirectional alignment (log-probability: -45.8) AAGCCTGGATGTGAAGGTCTGgAAATCCCTGTTATCCAACtGCtgttggATaCCAGAAGAGCGATGGCCTCAGGTTCAtGTAGGGCTTGGAG AAGCCTGGATGTGAAGGTCTGAAAATCCCTGTTATCCAACAGC-----AATCCCAGAAGAGCGATGGCCTCAGGTTCAGGTAGGGCTTGGAG Template switch alignment (log-probability: -28.3) AAGCCTGGATGTGAAGGTCTGgAAATCCCTGTTATCCAAC|TGCTGTTGGATA|CCAGAAGAGCGATGGCCTCAGGTTCAtGTAGGGCTTGGAG AAGCCTGGATGTGAAGGTCTGAAAATCCCTGTTATCCAAC|TGCTGTTGGATA|CCAGAAGAGCGATGGCCTCAGGTTCAGGTAGGGCTTGGAG Chimp > Gorilla --------------- chr16:27064423-27064434 Template switch process: F1: L TAAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAAC 1 F3: 4 CCAGAAGAGCGATGGCCTCAGGTTCATGTAGGGCTTGGAG R RF: TAAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAACAGCAATCCCAGAAGAGCGATGGCTTCAGGTTCAGGTAGGGCTTGGAG RR: ATTCGGACCTACACTTCCAGACCTTTAGGGACAATAGGTTGTCGTTAGGGTCTTCTCGCTACCGAAGTCCAAGTCCATCCCGAACCTC F2: 3 ATAGGTTGTCGT 2 Unidirectional alignment (log-probability: -45.8) AAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAACtGCtgttggATaCCAGAAGAGCGATGGCcTCAGGTTCAtGTAGGGCTTGGAG AAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAACAGCA-----ATCCCAGAAGAGCGATGGCTTCAGGTTCAGGTAGGGCTTGGAG Template switch alignment (log-probability: -28.3) AAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAAC|TGCTGTTGGATA|CCAGAAGAGCGATGGCcTCAGGTTCAtGTAGGGCTTGGAG AAGCCTGGATGTGAAGGTCTGGAAATCCCTGTTATCCAAC|TGCTGTTGGATA|CCAGAAGAGCGATGGCTTCAGGTTCAGGTAGGGCTTGGAG ========== Event 1267 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCACTTTCGAGCCCTGGACCCCAGGCCAGCTAATGAGGCTGACTGGATGTCCAGAGCTGGCCAG---------------------------------------------------------------------GCCACTGGGCCCTGAGCCAGAGACAAGGTC ↓ 3 4 2 1 Chimp: CCACTTTCGAGCCCTGGACCCCAGGCCAGCTAGTGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGCATCCAGTCAGCCTCACTAGCTGGCCTGGGGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGCCCTGAGCCAGAGACAAGGTC ↑ 3 4 2 1 Gorilla: CCACTTTCCAGCCCTGGACCCCAGGCCAGCTAGTGAGGCTGACTGGATGTCCAGAGCTGGCCAG---------------------------------------------------------------------GCCACTGGGCCCTGAGCCAGAGACAAGGTC Human: CCACTTTCGAGCCCTGGACCCCAGGCCAGCTAATGAGGCTGACTGGATGTCCAGAGCTGGCCAG---------------------------------------------------------------------GCCACTGGGCCCTGAGCCAGAGACAAGGTC Cluster: [ ] Orangutan: CCACTTTCGAGCCCTGGACCCCAGGCCAGCTAGTGAGGCTGACTGGATGTCCAGAGCTGGCCAG---------------------------------------------------------------------GCCACTGGGCCCTGAGCCAGAGACAAGGTC Human > Chimp ------------- chr16:26987552-26987580 Template switch process: F1: L GGCCAGCTAGTGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC 1 F3: 4 GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGCCCTGAGCCAGAGACAAGGTCACCTGGGCTG R RF: CCCAGGCCAGCTAATGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGCCCTGAGCCAGAGACAAGGTCACCTGGGCTG RR: GGGTCCGGTCGATTACTCCGACTGACCTACAGGTCTCGACCGGTCCGGTGACCCGGGACTCGGTCTCTGTTCCAGTGGACCCGAC F2: 3 GGGTCCGGTCGATCACTCCGACTGACCTA 2 Unidirectional alignment (log-probability: -116) gaggctgactggatgtccagagctggccaggccactgggcatccagtcagcctcactagctggcctgggGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC ---------------------------------------------------------------------GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC Template switch alignment (log-probability: -31.5) GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC|ATCCAGTCAGCCTCAcTAGCTGGCCTGGG|GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC|ATCCAGTCAGCCTCATTAGCTGGCCTGGG|GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC Gorilla > Chimp --------------- chr16:26987552-26987580 Template switch process: F1: L GGCCAGCTAGTGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC 1 F3: 4 GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGCCCTGAGCCAGAGACAAGGTCACCTGGGCTG R RF: CCCAGGCCAGCTAGTGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGCCCTGAGCCAGAGACAAGGTCACCTGGGCTG RR: GGGTCCGGTCGATCACTCCGACTGACCTACAGGTCTCGACCGGTCCGGTGACCCGGGACTCGGTCTCTGTTCCAGTGGACCCGAC F2: 3 GGGTCCGGTCGATCACTCCGACTGACCTA 2 Unidirectional alignment (log-probability: -110) gaggctgactggatgtccagagctggccaggccactgggcatccagtcagcctcactagctggcctgggGAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC ---------------------------------------------------------------------GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC Template switch alignment (log-probability: -20.3) GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC|ATCCAGTCAGCCTCACTAGCTGGCCTGGG|GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC|ATCCAGTCAGCCTCACTAGCTGGCCTGGG|GAGGCTGACTGGATGTCCAGAGCTGGCCAGGCCACTGGGC ========== Event 1268 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: gaggcggagcttgcagtgagctgagatcacactactgcactccagcctgggtgacagaactagactccgtctcagaaaaaaaaaaaaaaaaaaaaaaaaaaaaGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCCCAGTGCTTGTTTTCCTAGCAATAGC Chimp: gaggcggagcttgcagtgagctgagatcacactactgcactccagcctgggtgacagaactagactccgtctcag---------aaaa--aaaaaaaaaaaaagaGTTGACTTCCTCCTCAATGCATGTGGCACACTCCTCAATGCTTGTTTTCCTAGCAATAGC Gorilla: gaggcggagcttgcagtgagctgagatcacactactgcactccagcctgggtgacagaactagactccgtctcagg---------aaa---aaaaaaaaaaaaGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCTCAGCGCTTGTTTTCCTAGCAATATC ↑ 3 2 1 4 Human: gaggcggagcttgcagtgagctgagatcacactactgcactccagcctgggtgacagaactagactccgtctcagaaaaaaaaaaaaaaaaaaaaaaaaaaaaGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCCCAGTGCTTGTTTTCCTAGCAATAGC Cluster: [ ] Orangutan: gaggcagagcttgcagtgagctgagatcacactactgcactccagcctgggtgacagaactagactctgtctcaga---------aa------aaaaaaaaaaGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCTTAGCGCTTGTTTTCCTAGCAATATC Human > Gorilla --------------- chr16:52962505-52962509 Template switch process: F1: L AAAAAGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCC 1 F3: 4 GCTTGTTTTCCTAGCAATATCTAACGGCCTGCGGATGTGG R RF: GCTGAGATCACACTACTGCACTCCAGCCTGGGTGACAGAACTAGACTCCGTCTCAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCCCAGTGCTTGTTTTCCTAGCAATAGCTAACGGCCTGCGGATGTGT RR: CGACTCTAGTGTGATGACGTGAGGTCGGACCCACTGTCTTGATCTGAGGCAGAGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTCACCTGAAGGAGGAGTTACGTACACCGTGTGAGGGGTCACGAACAAAAGGATCGTTATCGATTGCCGGACGCCTACACA F2: 3 CGACT 2 Unidirectional alignment (log-probability: -47.3) AAAAGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCtCAGcGCTTGTTTTCCTAGCAATAtCTAAcggcctgcggatgtgg AAAAGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCCCCAGTGCTTGTTTTCCTAGCAATAGCTAA---------------- Template switch alignment (log-probability: -27.4) AAAAGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCC|TCAGC|GCTTGTTTTCCTAGCAATAtCTAACGGCCTGCGGATGTGg AAAAGAGTGGACTTCCTCCTCAATGCATGTGGCACACTCC|TCAGC|GCTTGTTTTCCTAGCAATAGCTAACGGCCTGCGGATGTGT ========== Event 1269 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAGGGAGGGGTGAGTGACCTGACCCACGATGCAGGGACATTCACACAGTGTCACGCTG ↓ 13 24 ↑ 13 24 Chimp: AAGGGAGGGGTGAGTGACCTGTCCCTGCATCGTGGGTCATTCACACAGTGTCATGCTG Gorilla: AAGGGAGGGGTGAGTGACCTGTCCCTGCATCGTGGGTCATTCACACAGTGTCACGCTG ↓ 13 24 ↑ 13 24 Human: AAGGGAGGGGTGAGTGACCTGACCCACGATGCAGGGACATTCACACAGTGTCACGCTG Cluster: [ ] Orangutan: AAGGGATGGGTGAGTGACCTGTCCCTGCATCGTGGGTCATTCACTCAGTGTCATGCTG Chimp > Human ------------- chr16:29847504-29847519 Template switch process: F1: L CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG 1 F3: 4 CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT R RF: CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGTCCCTGCATCGTGGGTCATTCACACAGTGTCATGCTGCATCAACGTCAGGCACTGT RR: GTAGACCTTTCTAACACCCCTTCCCTCCCCACTCACTGGACAGGGACGTAGCACCCAGTAAGTGTGTCACAGTACGACGTAGTTGCAGTCCGTGACA F2: 3 AGGGACGTAGCACCCA 2 Unidirectional alignment (log-probability: -45.2) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGaCCCacgaTGCA----GGGaCATTCACACAGTGTCAcGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGTCCC----TGCATCGTGGGTCATTCACACAGTGTCATGCTGCATCAACGTCAGGCACTGT Template switch alignment (log-probability: -23.3) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|ACCCACGATGCAGGGA|CATTCACACAGTGTCAcGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|ACCCACGATGCAGGGA|CATTCACACAGTGTCATGCTGCATCAACGTCAGGCACTGT Human > Chimp ------------- chr16:28828088-28828103 Template switch process: F1: L CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG 1 F3: 4 CATTCACACAGTGTCATGCTGCATCAACGTCAGGCACTGT R RF: CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGACCCACGATGCAGGGACATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT RR: GTAGACCTTTCTAACACCCCTTCCCTCCCCACTCACTGGACTGGGTGCTACGTCCCTGTAAGTGTGTCACAGTGCGACGTAGTTGCAGTCCGTGACA F2: 3 TGGGTGCTACGTCCCT 2 Unidirectional alignment (log-probability: -45.2) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGtCCC----TGCAtcgtGGGtCATTCACACAGTGTCAtGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGACCCACGATGCA----GGGACATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT Template switch alignment (log-probability: -23.3) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|TCCCTGCATCGTGGGT|CATTCACACAGTGTCAtGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|TCCCTGCATCGTGGGT|CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT Gorilla > Human --------------- chr16:29847504-29847519 Template switch process: F1: L CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG 1 F3: 4 CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT R RF: CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGTCCCTGCATCGTGGGTCATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT RR: GTAGACCTTTCTAACACCCCTTCCCTCCCCACTCACTGGACAGGGACGTAGCACCCAGTAAGTGTGTCACAGTGCGACGTAGTTGCAGTCCGTGACA F2: 3 AGGGACGTAGCACCCA 2 Unidirectional alignment (log-probability: -37.8) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGaCCCacgaTGCA----GGGaCATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGTCCC----TGCATCGTGGGTCATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT Template switch alignment (log-probability: -17.8) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|ACCCACGATGCAGGGA|CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|ACCCACGATGCAGGGA|CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT Human > Gorilla --------------- chr16:29994377-29994392 Template switch process: F1: L CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG 1 F3: 4 CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT R RF: CATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGACCCACGATGCAGGGACATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT RR: GTAGACCTTTCTAACACCCCTTCCCTCCCCACTCACTGGACTGGGTGCTACGTCCCTGTAAGTGTGTCACAGTGCGACGTAGTTGCAGTCCGTGACA F2: 3 TGGGTGCTACGTCCCT 2 Unidirectional alignment (log-probability: -37.8) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGtCCC----TGCAtcgtGGGtCATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTGACCCACGATGCA----GGGACATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT Template switch alignment (log-probability: -17.8) ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|TCCCTGCATCGTGGGT|CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT ATCTGGAAAGATTGTGGGGAAGGGAGGGGTGAGTGACCTG|TCCCTGCATCGTGGGT|CATTCACACAGTGTCACGCTGCATCAACGTCAGGCACTGT ========== Event 1270 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAGACCAACGAGCCACACGCCCCGTAGCCTCCGGCTTGTCTTTGTGGCCTTCGT ↑ 1 43 2 Chimp: tagaccaacgagccACACGCCTTATTTCCTACGGCTTGTCTTTGTGGCCTTCGT Gorilla: tagaccaacgagccACACACCTTGCTTCCTCCGGCTTGTCTTTGTGGCCTTCGT Human: TAGACCAACGAGCCACACGCCCCGTAGCCTCCGGCTTGTCTTTGTGGCCTTCGT Cluster: [ ] Orangutan: ------------------------------------------------------ Chimp > Human ------------- chr16:3182714-3182719 Template switch process: F1: L CTAAGCGAGAATCATACCCCTAGACCAACGAGCCACACGCC 1 F3: 4 CCTCCGGCTTGTCTTTGTGGCCTTCGTGGAGTCCTCGTGGCCAG R RF: CTAAGCGAGAATCATACCCCTAGACCAACGAGCCACACGCCTTATTTCCTACGGCTTGTCTTTGTGGCCTTCGTGGAGTCCTCGTGGCCAG RR: GATTCGCTCTTAGTATGGGGATCTGGTTGCTCGGTGTGCGGAATAAAGGATGCCGAACAGAAACACCGGAAGCACCTCAGGAGCACCGGTC F2: 3 GATGCC 2 Unidirectional alignment (log-probability: -36) TAAGCGAGAATCATACCCCTAGACCAACGAGCCACACGCC----------CcgtagcctccGGCTTGTCTTTGTGGCCTTCGTGGAGTCCTCGTGG TAAGCGAGAATCATACCCCTAGACCAACGAGCCACACGCCTTATTTCCTAC----------GGCTTGTCTTTGTGGCCTTCGTGGAGTCCTCGTGG Template switch alignment (log-probability: -22.1) TAAGCGAGAATCATACCCCTAGACCAACGAGCCACACGCC|CCGTAG|CCTcCGGCTTGTCTTTGTGGCCTTCGTGGAGTCCTCGTGG TAAGCGAGAATCATACCCCTAGACCAACGAGCCACACGCC|CCGTAG|CCTACGGCTTGTCTTTGTGGCCTTCGTGGAGTCCTCGTGG ========== Event 1271 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGGCCAAAAAATGTCATTAACTTTATGAAAGCTCATATCTTCTATTCATGAAGGTCATATTTTC ↓ 3 2 1 4 Chimp: TAGGCCAAAAAATGTCATTAACTTTATGA-AGGTCATAAAG-TTATTCATGAAGGTCATATTTTC Gorilla: TAGGCCAAAAAATGTCATTAACCTTATGAAAGCTCATATCTTCTATTCATGAAGGTCATATTTTC Human: TAGGCCAAAAAATGTCATTAACTTTATGAAAGCTCATATCTTCTATTCATGAAGGTCATATTTTC Cluster: [ ] Orangutan: taggccaaaaaatgtcattaactttatgaaagctcatatcttctattcatgaaggtcatattttc Human > Chimp ------------- chr16:44968179-44968188 Template switch process: F1: L ATAGTAATGTTTTAGGCCAAAAAATGTCATTAACTTTATGAAGG 1 F3: 4 ATTCATGAAGGTCATATTTTCTAGACTTTGTGAAATGAA R RF: ATAGTAATGTTTTAGGCCAAAAAATGTCATTAACTTTATGAAAGCTCATATCTTCTATTCATGAAGGTCATATTTTCTAGACTTTGTGAAATGAA RR: TATCATTACAAAATCCGGTTTTTTACAGTAATTGAAATACTTTCGAGTATAGAAGATAAGTACTTCCAGTATAAAAGATCTGAAACACTTTACTT F2: 3 TTGAAATACT 2 Unidirectional alignment (log-probability: -37.6) TAATGTTTTAGGCCAAAAAATGTCATTAACTTTATGAA-------------ggtcataaagtTATTCATGAAGGTCATATTTTCTAGACTTTGTGAAATGAA TAATGTTTTAGGCCAAAAAATGTCATTAACTTTATGAAAGCTCATATCTTC-----------TATTCATGAAGGTCATATTTTCTAGACTTTGTGAAATGAA Template switch alignment (log-probability: -22.6) TAATGTTTTAGGCCAAAAAATGTCATTAACTTTATGAAgG|TCATAAAGTT|ATTCATGAAGGTCATATTTTCTAGACTTTGTGAAATGAA TAATGTTTTAGGCCAAAAAATGTCATTAACTTTATGAAAG|TCATAAAGTT|ATTCATGAAGGTCATATTTTCTAGACTTTGTGAAATGAA ========== Event 1272 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGAGTTCACATCTAGCCCCATG--TCTGGCATCTCCACGGGGGCCAGG Chimp: TGTGAGTTCACATCTAGCCCCATG--TCTGGCATCTCCACGGGGGCCAGG ↓ 3 1 2 4 Gorilla: TGTGAGTTCACATCTAGCCCCAGACATGGGGCATCTCCACGGGGGCCAGG ↑ 3 1 2 4 Human: TGTGAGTTCACATCTAGCCCCATG--TCTGGCATCTCCACGGGGGCCAGG Cluster: [ ] Orangutan: TATGAGTTCACATCTAGCCCCATG--TCTGGCCTCTCCACGGGCACCAGG Human > Gorilla --------------- chr16:77650905-77650911 Template switch process: F1: L GTGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCA 1 F3: 4 GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC R RF: GTGCGGGAGCTGCCAGCACTGTGAGTTCACATCTAGCCCCATGTCTGGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC RR: CACGCCCTCGACGGTCGTGACACTCAAGTGTAGATCGGGGTACAGACCGTAGAGGTGCCCCCGGTCCCTTGGGTGACCGTTCTCGG F2: 3 GGTACAG 2 Unidirectional alignment (log-probability: -42) TGCGGGAGCTGCCAGtgCTGTGAGTTCACATCTAGCCCCAgacatgg-----GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC TGCGGGAGCTGCCAGCACTGTGAGTTCACATCTAGCCCCA-------TGTCTGGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC Template switch alignment (log-probability: -27.7) TGCGGGAGCTGCCAGtgCTGTGAGTTCACATCTAGCCCCA|GACATGG|GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC TGCGGGAGCTGCCAGCACTGTGAGTTCACATCTAGCCCCA|GACATGG|GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC Chimp > Gorilla --------------- chr16:77650905-77650911 Template switch process: F1: L GTGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCA 1 F3: 4 GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAGCC R RF: GTGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCATGTCTGGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAACC RR: CACGCCCTCGACGGTCACGACACTCAAGTGTAGATCGGGGTACAGACCGTAGAGGTGCCCCCGGTCCCTTGGGTGACCGTTCTTGG F2: 3 GGTACAG 2 Unidirectional alignment (log-probability: -36.5) TGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCA-----gacatggGGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAgCC TGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCATGTCT-------GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAACC Template switch alignment (log-probability: -22.1) TGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCA|GACATGG|GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAgCC TGCGGGAGCTGCCAGTGCTGTGAGTTCACATCTAGCCCCA|GACATGG|GGCATCTCCACGGGGGCCAGGGAACCCACTGGCAAGAACC ========== Event 1273 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: ttgccagtcggatgaaatctatg---catggttcccccaaaacacgtatccatgcgcgtatctgcaaaactggcac Chimp: TTGCCAGTCGGATGAAATCTATG---CATGGTTCCCCCAAAACACGTATCCATGCACGTATCTGCGAAACTGGCAC ↑ 1 4 3 2 Gorilla: TTGCCAGTCGGATGAAATCTACG------TGTTCCCCCAAAACACGTATCCATGCACGTATCTGCAAAACTGGCAC Human: ttgccagtcggatgaaatctatg---catggttcccccaaaacacgtatccatgcgcgtatctgcaaaactggcac Cluster: [ ] Orangutan: ttgccagtcggaagaaatctatgcat---ggttcccccaaaacacgtatccatgcacacacctgcaaaactggcac Gorilla > Chimp --------------- chr16:77719603-77719609 Template switch process: F1: L TTACTGGTCTCTCGTGCTCTTTGCCAGTCGGATGAAATCTA 1 F3: 4 TTCCCCCAAAACACGTATCCATGCACGTATCTGCGAAAC R RF: TTACTGGTCTCTCGTGCTCTTTGCCAGTCGGATGAAATCTACGTGTTCCCCCAAAACACGTATCCATGCACGTATCTGCAAAAC RR: AATGACCAGAGAGCACGAGAAACGGTCAGCCTACTTTAGATGCACAAGGGGGTTTTGTGCATAGGTACGTGCATAGACGTTTTG F2: 3 GGTACGT 2 Unidirectional alignment (log-probability: -31.8) TACTGGTCTCTCGTGCTCTTTGCCAGTCGGATGAAATCTAtGcatgGTTCCCCCAAAACACGTATCCATGCACGTATCTGCgAAAC TACTGGTCTCTCGTGCTCTTTGCCAGTCGGATGAAATCTACGT---GTTCCCCCAAAACACGTATCCATGCACGTATCTGCAAAAC Template switch alignment (log-probability: -22.1) TACTGGTCTCTCGTGCTCTTTGCCAGTCGGATGAAATCTA|TGCATGG|TTCCCCCAAAACACGTATCCATGCACGTATCTGCgAAAC TACTGGTCTCTCGTGCTCTTTGCCAGTCGGATGAAATCTA|TGCATGG|TTCCCCCAAAACACGTATCCATGCACGTATCTGCAAAAC ========== Event 1274 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AAGGCTTGCTTGGGTACTTAA----GGGTTCTTGACCCCTGGGACTGTAGGGTA ↓ 13 4 2 Chimp: AAGGCTTGCTTGGGTACTTAAGCAAGTACCCTTGACCCCTGGGACTGTAGGGTA Gorilla: Human: AAGGCTTGCTTGGGTACTTAA----GGGTTCTTGACCCCTGGGACTGTAGGGTA Cluster: [ ] Orangutan: AAGGCTTGCTTGGGTACTTAA----GGGTTCTTGACCCCTGGGACTGTAGGGTA Human > Chimp ------------- chr1:64382705-64382712 Template switch process: F1: L TTTTTAGTACCGCACTAGAAAAGGCTTGCTTGGGTACTTAAG 1 F3: 4 CTTGACCCCTGGGACTGTAGGGTAAAGTTGCAATGCTCAG R RF: TTTTTAGTACCGCACTAGAAAAGGCTTGCTTGGGTACTTAAGGGTTCTTGACCCCTGGGACTGTAGGGTAAAGTTGCAATGCTCAG RR: AAAAATCATGGCGTGATCTTTTCCGAACGAACCCATGAATTCCCAAGAACTGGGGACCCTGACATCCCATTTCAACGTTACGAGTC F2: 3 CCATGAAC 2 Unidirectional alignment (log-probability: -32.9) TTTAGTACCGCACTAGAAAAGGCTTGCTTGGGTACTTAAGcaagtacc----CTTGACCCCTGGGACTGTAGGGTAAAGTTGCAATGCTCAG TTTAGTACCGCACTAGAAAAGGCTTGCTTGGGTACTTAAG--------GGTTCTTGACCCCTGGGACTGTAGGGTAAAGTTGCAATGCTCAG Template switch alignment (log-probability: -22.3) TTTAGTACCGCACTAGAAAAGGCTTGCTTGGGTACTTAAG|CAAGtACC|CTTGACCCCTGGGACTGTAGGGTAAAGTTGCAATGCTCAG TTTAGTACCGCACTAGAAAAGGCTTGCTTGGGTACTTAAG|CAAGAACC|CTTGACCCCTGGGACTGTAGGGTAAAGTTGCAATGCTCAG ========== Event 1275 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGACCAGTTTGTGGGATGAAAGCGTAACATTGTTACGCTTTCTCCCTTTCTGTCACACGGGAGA Chimp: TGGACCAGTTTGTGGGATGAAAGCGTGACATTGTG-----AGCTTCCTTTCTGTCACACGGGAGA Gorilla: TGGACCAGTTTGTGGGATGAAAGCGTAACATTGTG-----AGCTTCCTTTCTGTCACACGGGAGA ↓ 3 2 1 4 Human: TGGACCAGTTTGTGGGATGAAAGCGTAACATTGTTACGCTTTCTCCCTTTCTGTCACACGGGAGA Cluster: [ ] Orangutan: TGGACCAGTTTGTGGGATGAAAGCGTAACATCGTG-----AGCTTCCTTTCTGTCACACAGGAGA Gorilla > Human --------------- chr1:64568281-64568288 Template switch process: F1: L CAGCTGTTGGACCAGTTTGTGGGATGAAAGCGTAACATTGT 1 F3: 4 CTCCCTTTCTGTCACACGGGAGAAGCTGATAACAACTTGGCAT R RF: CAGCTGTTGGACCAGTTTGTGGGATGAAAGCGTAACATTGTGAGCTTCCTTTCTGTCACACGGGAGAAGCTGATAACAACTTGGCAT RR: GTCGACAACCTGGTCAAACACCCTACTTTCGCATTGTAACACTCGAAGGAAAGACAGTGTGCCCTCTTCGACTATTGTTGAACCGTA F2: 3 TTTCGCAT 2 Unidirectional alignment (log-probability: -33.4) AGCTGTTGGACCAGTTTGTGGGATGAAAGCGTAACATTGTtAcGCTTtctcCCTTTCTGTCACACGGGAGAAGCTGATAACAACTTGG AGCTGTTGGACCAGTTTGTGGGATGAAAGCGTAACATTGTGA-GCTT----CCTTTCTGTCACACGGGAGAAGCTGATAACAACTTGG Template switch alignment (log-probability: -22.3) AGCTGTTGGACCAGTTTGTGGGATGAAAGCGTAACATTGT|TACGCTTT|CTcCCTTTCTGTCACACGGGAGAAGCTGATAACAACTTGG AGCTGTTGGACCAGTTTGTGGGATGAAAGCGTAACATTGT|TACGCTTT|CTTCCTTTCTGTCACACGGGAGAAGCTGATAACAACTTGG ========== Event 1276 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAAATAAAATACTCAAATCAGCAAAATAGAATTTTGCTACCTGCCATAAATTCAAGG Chimp: TAAAATAAAATA---------------------------------------------- Gorilla: TAAAATAAAATACTCAAATCAA-GGTACAGAATTTTGCTACCTGCCATAAATTCAAGG ↓ 1 4 3 2 Human: TAAAATAAAATACTCAAATCAGCAAAATAGAATTTTGCTACCTGCCATAAATTCAAGG Cluster: [ ] Orangutan: TGAAATAAAATATTCAAATCAA-GGTATAGAATTTTGCTACCTGCCATAAATTCAAGG Gorilla > Human --------------- chr16:46579124-46579130 Template switch process: F1: L GGAAATACATCTAAAGAAGCTAAAATAAAATACTCAAATCA 1 F3: 4 AGAATTTTGCTACCTGCCATAAATTCAAGGTCACACTAAG R RF: GGAAATACATCTAAAGAAGCTAAAATAAAATACTCAAATCAAGGTACAGAATTTTGCTACCTGCCATAAATTCAAGGTCACACTAAG RR: CCTTTATGTAGATTTCTTCGATTTTATTTTATGAGTTTAGTTCCATGTCTTAAAACGATGGACGGTATTTAAGTTCCAGTGTGATTC F2: 3 TAAAACG 2 Unidirectional alignment (log-probability: -31) GAAATACATCTAAAGAAGCTAAAATAAAATACTCAAATCA------gcaaaatAGAATTTTGCTACCTGCCATAAATTCAAGGTCACACTAAG GAAATACATCTAAAGAAGCTAAAATAAAATACTCAAATCAAGGTAC-------AGAATTTTGCTACCTGCCATAAATTCAAGGTCACACTAAG Template switch alignment (log-probability: -16.6) GAAATACATCTAAAGAAGCTAAAATAAAATACTCAAATCA|GCAAAAT|AGAATTTTGCTACCTGCCATAAATTCAAGGTCACACTAAG GAAATACATCTAAAGAAGCTAAAATAAAATACTCAAATCA|GCAAAAT|AGAATTTTGCTACCTGCCATAAATTCAAGGTCACACTAAG ========== Event 1277 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCATTTCTTACTGTGTTGTCACCCACTGTGCCAAGGTCTATGACTGCCACTGTCACtttttt---tt--ttttttttgagtcaaggtctttgttgcccagactgggatacagtggtatgattacggctcactgcagcttcgaactcttaggctca Chimp: GCATTTCTTACTGTGTTGTCATGCACTGTGCCAAGGTCTATGACTGCCACTGTCACtttttt-----ttttttttttgagtcaaggtctttgtcgcccagactgggatacagtggtatgattacggctcactgcagcttcgaactcttaggctca Gorilla: GCATTTCTTACTGTGTTGTCATGCAGTAAGTCAAGGTCTATGACTGCCACTGTCACtttttt--------tttttttgagtcaaggtctttgtcgcccagactgggatacagtggtatgattacggctcactgcagcttcgaactcttaggctca ↑ 1 4 3 2 Human: GCATTTCTTACTGTGTTGTCACCCACTGTGCCAAGGTCTATGACTGCCACTGTCACtttttt---tt--ttttttttgagtcaaggtctttgttgcccagactgggatacagtggtatgattacggctcactgcagcttcgaactcttaggctca Cluster: [ ] Orangutan: GCATTTCTTACTGTGTTGTCATGCACTGTGCCAAGGTCTATGACTGCCACTGTCACttttttttt----ttttttttgagtcaaggtctttgtcgcccagactgggatacagtggtatgattacagctcactgcagcttccaactcttaggctca Human > Gorilla --------------- chr16:44281899-44281906 Template switch process: F1: L TAGCCTTTACTTATTTACTAGCATTTCTTACTGTGTTGTCA 1 F3: 4 GTCAAGGTCTATGACTGCCACTGTCACTTTTTTTTTTTT R RF: TAGCCTTTACTTATTTACTAGCATTTCTTACTGTGTTGTCACCCACTGTGCCAAGGTCTATGACTGCCACTGTCACTTTTTTTTTTTTTTTTGAGTCAAGGTCTTTGTTGCCCAGACTGGGATACAGTGGTATGATTACGGCTCACTGCA RR: ATCGGAAATGAATAAATGATCGTAAAGAATGACACAACAGTGGGTGACACGGTTCCAGATACTGACGGTGACAGTGAAAAAAAAAAAAAAAACTCAGTTCCAGAAACAACGGGTCTGACCCTATGTCACCATACTAATGCCGAGTGACGT F2: 3 AATGACGT 2 Unidirectional alignment (log-probability: -37.9) AGCCTTTACTTATTTACTAGCATTTCTTACTGTGTTGTCA-------TGCagtaagtCAAGGTCTATGACTGCCACTGTCACTTTTTTTTTTTT--- AGCCTTTACTTATTTACTAGCATTTCTTACTGTGTTGTCACCCACTGTGC-------CAAGGTCTATGACTGCCACTGTCACTTTTTTTTTTTTTTT Template switch alignment (log-probability: -27.8) AGCCTTTACTTATTTACTAGCATTTCTTACTGTGTTGTCA|TGCAGTaA|GtCAAGGTCTATGACTGCCACTGTCACTTTTTTTTTTTT AGCCTTTACTTATTTACTAGCATTTCTTACTGTGTTGTCA|TGCAGTGA|GCCAAGGTCTATGACTGCCACTGTCACTTTTTTTTTTTT ========== Event 1278 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ctgcactgtggtcctagcagccattctgaggtgacaggagctgtagccttatgtcacggatgaggaaactgaggcttagccaggggaagtggtctcccacggtGCTGGTCCAGTGCCCA---GATGGCACCCTTCCTGTTGAACTCAGC Chimp: ctgcactgtggtcctagcagccattctgaggtgacaggagctgtagccttatgtcacggatgaggaaactgaggcttagccaggggaagtggtctcccacggtGCTGGTCCAGTGCCCA---GCTGGCACCCTTCCTGTTGAACTCAGC Gorilla: ctgcattgtggtcctagcagccattctgaggtgacaggagctgtagccttatgtcacggatgaggaaactgaggcttagccaggggaagtggtctcccatggtGCTGGTCCAGTGCCCAGGGTCCAGTACCCTTCCTGTTGAACTCAGC ↓ 3 2 1 4 Human: ctgcactgtggtcctagcagccattctgaggtgacaggagctgtagccttatgtcacggatgaggaaactgaggcttagccaggggaagtggtctcccacggtGCTGGTCCAGTGCCCA---GATGGCACCCTTCCTGTTGAACTCAGC Cluster: [ ] Orangutan: ctgcactgtggtcctaccaaccactctgaggtgacagaagctgtagccctatgtcacggatgaggaagctgaggcttagccaggggaagtggtctcccatggtgctggtccagtgccca---gctggcactCTTCCTGTTGAACTCGGC Gorilla > Human --------------- chr1:242460298-242460302 Template switch process: F1: L GCCAGGGGAAGTGGTCTCCCACGGTGCTGGTCCAGTGCCCAG 1 F3: 4 ACCCTTCCTGTTGAACTCAGCCACTCTTCAGGCCTGGGCA R RF: GCCATTCTGAGGTGACAGGAGCTGTAGCCTTATGTCACGGATGAGGAAACTGAGGCTTAGCCAGGGGAAGTGGTCTCCCATGGTGCTGGTCCAGTGCCCAGGGTCCAGTACCCTTCCTGTTGAACTCAGCCACTCTTCAGGCCTGGGCA RR: CGGTAAGACTCCACTGTCCTCGACATCGGAATACAGTGCCTACTCCTTTGACTCCGAATCGGTCCCCTTCACCAGAGGGTACCACGACCAGGTCACGGGTCCCAGGTCATGGGAAGGACAACTTGAGTCGGTGAGAAGTCCGGACCCGT F2: 3 CGGTA 2 Unidirectional alignment (log-probability: -33.8) CAGGGGAAGTGGTCTCCCAcGGTGCTGGTCCAGTGCCCAG--------atggcACCCTTCCTGTTGAACTCAGCCACTCTTCAGGCCTGGGCA CAGGGGAAGTGGTCTCCCATGGTGCTGGTCCAGTGCCCAGGGTCCAGT-----ACCCTTCCTGTTGAACTCAGCCACTCTTCAGGCCTGGGCA Template switch alignment (log-probability: -21.9) CAGGGGAAGTGGTCTCCCAcGGTGCTGGTCCAGTGCCCAG|ATGGC|ACCCTTCCTGTTGAACTCAGCCACTCTTCAGGCCTGGGCA CAGGGGAAGTGGTCTCCCATGGTGCTGGTCCAGTGCCCAG|ATGGC|ACCCTTCCTGTTGAACTCAGCCACTCTTCAGGCCTGGGCA ========== Event 1279 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACACC-----GGCTGGTTAAGGTGCAGGGACAA Chimp: CCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACACC-----AGCTGGTTAAGGTGCAGGGACAA ↓ 3 2 1 4 Gorilla: CCCTTCTAAGGGGAACAAGTGCTCTCAGGTGACACTGAGAACACTGGTTAAGGTGCAGGGACAA ↑ 3 2 1 4 Human: CCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACACC-----GGCTGGTTAAGGTGCAGGGACAA Cluster: [ ] Orangutan: CCCTTCTAAGGGGAACAAGTGTTCTGAGGTGACACC-----AGCTGGTTAAGGTGCAGGGACAA Human > Gorilla --------------- chr1:222680678-222680685 Template switch process: F1: L CTGGGTCCCTTCTAAGGGGAACAAGTGCTCTCAGGTGACAC 1 F3: 4 CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG R RF: CTGGGTCCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACACCGGCTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG RR: GACCCAGGGAAGATTCCCCTTGTTCACAAGAGTCCACTGTGGCCGACCAATTCCACGTCCCTGTTCGGGTCTTCGGAGGGGGTC F2: 3 ACAAGAGT 2 Unidirectional alignment (log-probability: -34.7) TGGGTCCCTTCTAAGGGGAACAAGTGcTCTCAGGTGACACtGagaacaCTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG TGGGTCCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACACCG-----GCTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG Template switch alignment (log-probability: -22.3) TGGGTCCCTTCTAAGGGGAACAAGTGcTCTCAGGTGACAC|TGAGAACA|CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG TGGGTCCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACAC|TGAGAACA|CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG Chimp > Gorilla --------------- chr1:222680678-222680685 Template switch process: F1: L CTGGGTCCCTTCTAAGGGGAACAAGTGCTCTCAGGTGACAC 1 F3: 4 CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG R RF: CTGGGTCCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACACCAGCTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG RR: GACCCAGGGAAGATTCCCCTTGTTCACAAGAGTCCACTGTGGTCGACCAATTCCACGTCCCTGTTCGGGTCTTCGGAGGGGGTC F2: 3 ACAAGAGT 2 Unidirectional alignment (log-probability: -34.9) TGGGTCCCTTCTAAGGGGAACAAGTGcTCTCAGGTGACACtgagaaCA-CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG TGGGTCCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACAC------CAGCTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG Template switch alignment (log-probability: -22.3) TGGGTCCCTTCTAAGGGGAACAAGTGcTCTCAGGTGACAC|TGAGAACA|CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG TGGGTCCCTTCTAAGGGGAACAAGTGTTCTCAGGTGACAC|TGAGAACA|CTGGTTAAGGTGCAGGGACAAGCCCAGAAGCCTCCCCCAG ========== Event 1280 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCAGAACCATCTGGTGATTTGCTCCTTAGACCAAAAATTAGATAATATGTTTCTT Chimp: TCCAGAACCATCTGGTGATTTGCTTCTTAGACCAAAAATTAGATAATGTGTTTCTT ↑ 3 1 2 4 Gorilla: TCCAGAACCATCTGGTGATTTGGTCTAAGGAGCATAAATTAGATAATGTGTTTCTT Human: TCCAGAACCATCTGGTGATTTGCTCCTTAGACCAAAAATTAGATAATATGTTTCTT Cluster: [ ] Orangutan: TCCAGAACCATTTGGTGATTTCCTCCTTAGACCAAAAATTAGATAATGTGTTTCTT Gorilla > Chimp --------------- chr1:222620669-222620681 Template switch process: F1: L ACTACAATAAGTTATTTGTTCCAGAACCATCTGGTGATTTG 1 F3: 4 AAATTAGATAATGTGTTTCTTTATAAAATCATAAAGTCAT R RF: ACTACAATAAGTTATTTGTTCCAGAACCATCTGGTGATTTGGTCTAAGGAGCATAAATTAGATAATGTGTTTCTTTATAAAATCATAAAGTCAT RR: TGATGTTATTCAATAAACAAGGTCTTGGTAGACCACTAAACCAGATTCCTCGTATTTAATCTATTACACAAAGAAATATTTTAGTATTTCAGTA F2: 3 AACCAGATTCTTC 2 Unidirectional alignment (log-probability: -40) CTACAATAAGTTATTTGTTCCAGAACCATCTGGTGATTTG-------------cttcttagaccaaAAATTAGATAATGTGTTTCTTTATAAAATCATAAAGTCAT CTACAATAAGTTATTTGTTCCAGAACCATCTGGTGATTTGGTCTAAGGAGCAT-------------AAATTAGATAATGTGTTTCTTTATAAAATCATAAAGTCAT Template switch alignment (log-probability: -22.9) CTACAATAAGTTATTTGTTCCAGAACCATCTGGTGATTTG|CTtCTTAGACCAA|AAATTAGATAATGTGTTTCTTTATAAAATCATAAAGTCAT CTACAATAAGTTATTTGTTCCAGAACCATCTGGTGATTTG|CTCCTTAGACCAA|AAATTAGATAATGTGTTTCTTTATAAAATCATAAAGTCAT ========== Event 1281 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGCTCTAGTCTTACCATAAGCAGAG----------------CTCTTCTTCTGCTGAGAAACCAATAGA Chimp: CAGCTCTAGTCTTACCATAAGCAGAGCAGAAGAGCTCAGCAGAGCTTCTTCTGCTGAGAAACCAATAGA ↑ 4 3 1 2 Gorilla: CAGCTCTAGTCTTACCATAAGCAGAG----------------CTCTTCTTCTGCTGAGAAACCAATAGA Human: CAGCTCTAGTCTTACCATAAGCAGAG----------------CTCTTCTTCTGCTGAGAAACCAATAGA Cluster: [ ] Orangutan: CAGCTCTAGTCTTACCATAAGCAGAG----------------CTCTTCTTCTGCTGAGAAACCAATAGA Gorilla > Chimp --------------- chr16:38188363-38188372 Template switch process: F1: L ACATCCCTCTGCCTCCAGCTCTAGTCTTACCATAAGCAGAGC 1 F3: 4 AGCAGAG--CTTCTTCTGCTGAGAAACCAATAGACTGGATTTCCTCCTG R RF: ACATCCCTCTGCCTCCAGCTCTAGTCTTACCATAAGCAGAGCTCTTCTTCTGCTGAGAAACCAATAGACTGGATTTCCTCCTG RR: TGTAGGGAGACGGAGGTCGAGATCAGAATGGTATTCGTCTCGAGAAGAAGACGACTCTTTGGTTATCTGACCTAAAGGAGGAC F2: 3 CTCGAGAAGA 2 Unidirectional alignment (log-probability: -39.4) ATCCCTCTGCCTCCAGCTCTAGTCTTACCATAAGCAGAGCagaagagctcagcagagCTTCTTCTGCTGAGAAACCAATAGACTGGATTT ATCCCTCTGCCTCCAGCTCTAGTCTTACCATAAGCAGAGC----------------TCTTCTTCTGCTGAGAAACCAATAGACTGGATTT Template switch alignment (log-probability: -27) ATCCCTCTGCCTCCAGCTCTAGTCTTACCATAAGCAGAGC|AGAAGAGCTC|AGCAGAG--CTTCTTCTGCTGAGAAACCAATAGACTGGATTT ATCCCTCTGCCTCCAGCTCTAGTCTTACCATAAGCAGAGC|AGAAGAGCTC|AGCAGAGCTCTTCTTCTGCTGAGAAACCAATAGACTGGATTT ========== Event 1282 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TAGCCAGGTTCCAAG----------------TAAGACTATTTCACCAGCAAGTGTTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGG--TGAAATAGTCT-TACTTTCTTACTTGGAACCT-GGC-- ↓ 13 24 ↑ 13 24 Chimp: TAGCCAGGTTCCAAG--------TAAGAAAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAGCACTTGCTGG--TGAAATAGTCT---------TACTTGGAACCT-GGC-- Gorilla: TAGCCATGTTCCAAGTAAGAAAG--------TAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAACACTTGCTGG--TGAAATAGTCT---------TACTTGGAACCT-GGC-- ↓ 13 24 ↑ 13 24 Human: TAGCCAGGTTCCAAG----------------TAAGACTATTTCACCAGCAAGTGTTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGG--TGAAATAGTCT-TACTTTCTTACTTGGAACCT-GGC-- Cluster: [ ] Orangutan: ------------------------------------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNAGAACATTTGCAGGATCTGAATAGTTTC--------TATTTTGGTTTTGAGTTA Chimp > Human ------------- chr16:41720984-41721073 Template switch process: F1: L TTCCAAGTAAGA 1 F3: 4 TCTTACTTGGAACC R RF: TTCCAAGTAAGAAAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAGCACTTGCTGGTGAAATAGTCTTACTTGGAACC RR: AAGGTTCATTCTTTCATTCTGATAAAGTGGTCGTTCACAAGAACGACCTTCATCTTCCTTCGGAGGTGAAGGAAAAAGTACCTCGTGAACGACCACTTTATCAGAATGAACCTTGG F2: 3 TTCATTCTGATAAAGTGGTCGTTCACAAGAACGACCTTCATCTTCCTTCGGAGGTGAAGGAAAAAGTACCTTGTGAACGACCACTTTATC 2 Unidirectional alignment (log-probability: -113) TTCC--------AAGTAAGACTATTTCACCAGCAAGTGTTC------------------------------------CATGaaaaaggaagtggaggcttccttctacttccagcaaGAaCACTTGCTGGTGAAATAGtcttacttTCTTACTTGGAACC TTCCAAGTAAGAAAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATG------------------------------------GAGCACTTGCTGGTGAAATAG--------TCTTACTTGGAACC Template switch alignment (log-probability: -31.3) TTCCAAGTAAGA|CTATTTCACCAGCAAGTGtTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTT|TCTTACTTGGAACC TTCCAAGTAAGA|CTATTTCACCAGCAAGTGCTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTT|TCTTACTTGGAACC Human > Chimp ------------- chr16:42425352-42425441 Template switch process: F1: L TTCCAAGTAAGA 1 F3: 4 TCTTACTTGGAACC R RF: TTCCAAGTAAGACTATTTCACCAGCAAGTGTTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTTTCTTACTTGGAACC RR: AAGGTTCATTCTGATAAAGTGGTCGTTCACAAGGTACTTTTTCCTTCACCTCCGAAGGAAGATGAAGGTCGTTCTTGTGAACGACCACTTTATCAGAATGAAAGAATGAACCTTGG F2: 3 GATAAAGTGGTCGTTCACGAGGTACTTTTTCCTTCACCTCCGAAGGAAGATGAAGGTCGTTCTTGTGAACGACCACTTTATCAGAATGAA 2 Unidirectional alignment (log-probability: -113) TTCCaagtaagaAAGTAAGACTATTTCACCAGCAAGTGTTCttgctggaagtagaaggaagcctccacttcctttttCATG------------------------------------GAgCACTTGCTGGTGAAATAG--------TCTTACTTGGAACC TTCC--------AAGTAAGACTATTTCACCAGCAAGTGTTC------------------------------------CATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTTTCTTACTTGGAACC Template switch alignment (log-probability: -31.3) TTCCAAGTAAGA|AAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAgCACTTGCTGGTGAAATAG|TCTTACTTGGAACC TTCCAAGTAAGA|AAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAACACTTGCTGGTGAAATAG|TCTTACTTGGAACC Gorilla > Human --------------- chr16:41720984-41721073 Template switch process: F1: L TTCCAAGTAAGA 1 F3: 4 TCTTACTTGGA R RF: TTCCAAGTAAGAAAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAACACTTGCTGGTGAAATAGTCTTACTTGGA RR: AAGGTTCATTCTTTCATTCTGATAAAGTGGTCGTTCACAAGAACGACCTTCATCTTCCTTCGGAGGTGAAGGAAAAAGTACCTTGTGAACGACCACTTTATCAGAATGAACCT F2: 3 TTCATTCTGATAAAGTGGTCGTTCACAAGAACGACCTTCATCTTCCTTCGGAGGTGAAGGAAAAAGTACCTTGTGAACGACCACTTTATC 2 Unidirectional alignment (log-probability: -105) TTCCAAGTAA--------GACTATTTCACCAGCAAGTGTTC------------------------------------CATGaaaaaggaagtggaggcttccttctacttccagcaaGAACACTTGCTGGTGAAATAGtcttacttTCTTACTTGGA TTCCAAGTAAGAAAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATG------------------------------------GAACACTTGCTGGTGAAATAG--------TCTTACTTGGA Template switch alignment (log-probability: -25.8) TTCCAAGTAAGA|CTATTTCACCAGCAAGTGTTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTT|TCTTACTTGGA TTCCAAGTAAGA|CTATTTCACCAGCAAGTGTTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTT|TCTTACTTGGA Human > Gorilla --------------- chr16:42319828-42319917 Template switch process: F1: L TTCCAAGTAAGA 1 F3: 4 TCTTACTTGGA R RF: TTCCAAGTAAGACTATTTCACCAGCAAGTGTTCCATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTTTCTTACTTGGA RR: AAGGTTCATTCTGATAAAGTGGTCGTTCACAAGGTACTTTTTCCTTCACCTCCGAAGGAAGATGAAGGTCGTTCTTGTGAACGACCACTTTATCAGAATGAAAGAATGAACCT F2: 3 GATAAAGTGGTCGTTCACAAGGTACTTTTTCCTTCACCTCCGAAGGAAGATGAAGGTCGTTCTTGTGAACGACCACTTTATCAGAATGAA 2 Unidirectional alignment (log-probability: -105) TTCCAAGTAAGaaagtaagACTATTTCACCAGCAAGTGTTCttgctggaagtagaaggaagcctccacttcctttttCATG------------------------------------GAACACTTGCTGGTGAAATAG--------TCTTACTTGGA TTCCAAGTAAG--------ACTATTTCACCAGCAAGTGTTC------------------------------------CATGAAAAAGGAAGTGGAGGCTTCCTTCTACTTCCAGCAAGAACACTTGCTGGTGAAATAGTCTTACTTTCTTACTTGGA Template switch alignment (log-probability: -25.8) TTCCAAGTAAGA|AAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAACACTTGCTGGTGAAATAG|TCTTACTTGGA TTCCAAGTAAGA|AAGTAAGACTATTTCACCAGCAAGTGTTCTTGCTGGAAGTAGAAGGAAGCCTCCACTTCCTTTTTCATGGAACACTTGCTGGTGAAATAG|TCTTACTTGGA ========== Event 1283 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CCAGCCCTCAAGGCCCCTGAGGC--TAA----AGCCTCAGATTTCAGATCCCTCAGCT ↑ 3 1 2 4 Chimp: CCAGCCCTCGAGGCCCCTGAGGCTTTAAAATTAGAACCAGATTTCAGATCCCTCAGCT Gorilla: ---------------------------------------------------------- Human: CCAGCCCTCAAGGCCCCTGAGGC--TAA----AGCCTCAGATTTCAGATCCCTCAGCT Cluster: [ ] Orangutan: ---------------------------------------------------------- Chimp > Human ------------- chr16:49470769-49470775 Template switch process: F1: L GGGAGACAGGGGTTTGGACCAGCCCTCAAGGCCCCTGAGGCT 1 F3: 4 CAGATTTCAGATCCCTCAGCTCTGCCCAAATTCTCACCAC R RF: GGGAGACAGGGGTTTGGACCAGCCCTCGAGGCCCCTGAGGCTTTAAAATTAGAACCAGATTTCAGATCCCTCAGCTCTGCCCAAATTCTCACCAC RR: CCCTCTGTCCCCAAACCTGGTCGGGAGCTCCGGGGACTCCGAAATTTTAATCTTGGTCTAAAGTCTAGGGAGTCGAGACGGGTTTAAGAGTGGTG F2: 3 TCCGAAA 2 Unidirectional alignment (log-probability: -36.4) GAGACAGGGGTTTGGACCAGCCCTCaAGGCCCCTGAGGCTaaagccT------------CAGATTTCAGATCCCTCAGCTCTGCCCAAATTCTCACCAC GAGACAGGGGTTTGGACCAGCCCTCGAGGCCCCTGAGGCT------TTAAAATTAGAACCAGATTTCAGATCCCTCAGCTCTGCCCAAATTCTCACCAC Template switch alignment (log-probability: -22.2) GAGACAGGGGTTTGGACCAGCCCTCaAGGCCCCTGAGGCT|AAAGCCT|CAGATTTCAGATCCCTCAGCTCTGCCCAAATTCTCACCAC GAGACAGGGGTTTGGACCAGCCCTCGAGGCCCCTGAGGCT|AAAGCCT|CAGATTTCAGATCCCTCAGCTCTGCCCAAATTCTCACCAC ========== Event 1284 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTGAGGGTACACTCTGAGCCACTGGAACTAGAGTTCCAGCCCAAGCCCAAAGGgc ↑ 1 3 4 2 Chimp: CCTGAGGGTACACTCTGAGCCACTG---GTCTAGTTCCAGCCCAAGCCCAAAGGgc Gorilla: CCTGAGGGTACACTCTGAGCCGCTG---GTCTAGTTCCAGCCCAAACCCAAAGGgc ↓ 1 3 4 2 Human: CCTGAGGGTACACTCTGAGCCACTGGAACTAGAGTTCCAGCCCAAGCCCAAAGGgc Cluster: [ ] Orangutan: CCTGAGGGTACACCCTGAGCCACTG---GTCTAGTTCCAGCCCAAGCCCAAAGGgc Chimp > Human ------------- chr16:39519451-39519456 Template switch process: F1: L GGGCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGG 1 F3: 4 AGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT R RF: GGGCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGGTCTAGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT RR: CCCGTCCTTACCCCGGGGACTCCCATGTGAGACTCGGTGACCAGATCAAGGTCGGGTTCGGGTTTCCCGAACGTCTACCGTCTAA F2: 3 GATCAA 2 Unidirectional alignment (log-probability: -27.3) GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGGaacTagAGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGG---TCTAGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT Template switch alignment (log-probability: -16) GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGG|AACTAG|AGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGG|AACTAG|AGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT Gorilla > Human --------------- chr16:39519451-39519456 Template switch process: F1: L TCAGGGGCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCACTGG 1 F3: 4 AGTTCCAGCCCAAGCCCAAAGGGCTTGCAGATGGCAGATT R RF: TCAGGGGCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCGCTGGTCTAGTTCCAGCCCAAACCCAAAGGGCTTGCAGATGGCAGATT RR: AGTCCCCGTCCTTACCCCGGGGACTCCCATGTGAGACTCGGCGACCAGATCAAGGTCGGGTTTGGGTTTCCCGAACGTCTACCGTCTAA F2: 3 GATCAA 2 Unidirectional alignment (log-probability: -37.4) GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCaCTGGaacTagAGTTCCAGCCCAAgCCCAAAGGGCTTGCAGATGGCAGATT GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCGCTGG---TCTAGTTCCAGCCCAAACCCAAAGGGCTTGCAGATGGCAGATT Template switch alignment (log-probability: -27.6) GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCaCTGG|AACTAG|AGTTCCAGCCCAAgCCCAAAGGGCTTGCAGATGGCAGATT GCAGGAATGGGGCCCCTGAGGGTACACTCTGAGCCGCTGG|AACTAG|AGTTCCAGCCCAAACCCAAAGGGCTTGCAGATGGCAGATT ========== Event 1285 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAATTTTTTTACTGTTGAAT-AGTTGGTGAC--AGTTTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGTGCTT Chimp: TCAAtttttttACTGTTGAAT-AGTTGGCGAC--AGTTTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGTGCTT Gorilla: TCAAtttttttACTGTTGAATAAACTGGCGAC----ATTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGTGCTT ↑ 1 4 3 2 Human: TCAATTTTTTTACTGTTGAAT-AGTTGGTGAC--AGTTTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGTGCTT Cluster: [ ] Orangutan: TCAATTTTTTTACTGTTGAAT-AGTTGGCGACAG--CTTATTTTATTTTAGCCAGTTTTCAGGATTTCGGGGTGCTT Human > Gorilla --------------- chr16:40460533-40460539 Template switch process: F1: L TTTGTTTAATATCTCATAAATCAATTTTTTTACTGTTGAATA 1 F3: 4 GACA--TTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGTGCTT R RF: TTTGTTTAATATCTCATAAATCAATTTTTTTACTGTTGAATAGTTGGTGACAGTTTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGTGCTT RR: AAACAAATTATAGAGTATTTAGTTAAAAAAATGACAACTTATCAACCACTGTCAAATAAAATAAAATCGGTCAAAAGTCCTAAACCCCCACGAA F2: 3 CGGTCAA 2 Unidirectional alignment (log-probability: -37.1) TGTTTAATATCTCATAAATCAATTTTTTTACTGTTGAATA------------aactggcgacaTTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGT TGTTTAATATCTCATAAATCAATTTTTTTACTGTTGAATAGTTGGTGACAGT-----------TTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGT Template switch alignment (log-probability: -26.6) TGTTTAATATCTCATAAATCAATTTTTTTACTGTTGAATA|AACTGGC|GACA--TTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGT TGTTTAATATCTCATAAATCAATTTTTTTACTGTTGAATA|AACTGGC|GACAGTTTATTTTATTTTAGCCAGTTTTCAGGATTTGGGGGT ========== Event 1286 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CATTTCTGATTTTCTAGAAAAGAGTTCA---GATTCCTTATCACAGCATTTAAGGACATCCATGTTCTGACCCtgacctagttgggctgt ↓ 3 1 2 4 ↑ 1 4 3 2 Chimp: CATTTCTGATTTTCTAGAAAAGAGTGAACTCTTTTCCTTATCATAGCATTTAAGGACATCCATGTTCTGACCCtgacctagttgggctgt Gorilla: CATTTCTGATTTTCTAGAAAAGAGTTCA---GATTCCTTATCATAGCATTTACGGACATCCATGATCTAACCCtgacctagttgggctgt Human: CATTTCTGATTTTCTAGAAAAGAGTTCA---GATTCCTTATCACAGCATTTAAGGACATCCATGTTCTGACCCtgacctagttgggctgt Cluster: [ ] Orangutan: CATTTCTGATTTTCTAGAAAAGAGTTCA---GATTCCTTATCATAGCATTTAAGGACATCCATGATCTGACCCtgacctagtttggctgt Chimp > Human ------------- chr1:65499868-65499872 Template switch process: F1: L ACATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT 1 F3: 4 TTCCTTATCACAGCATTTAAGGACATCCATGTTCTGACCC R RF: ACATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGTGAACTCTTTTCCTTATCATAGCATTTAAGGACATCCATGTTCTGACCC RR: TGTAAATTCTGACACGGTAAAGACTAAAAGATCTTTTCTCACTTGAGAAAAGGAATAGTATCGTAAATTCCTGTAGGTACAAGACTGGG F2: 3 AGACT 2 Unidirectional alignment (log-probability: -31.8) CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGTtcaGA------TTCCTTATCAcAGCATTTAAGGACATCCATGTTCTGACCC CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT---GAACTCTTTTCCTTATCATAGCATTTAAGGACATCCATGTTCTGACCC Template switch alignment (log-probability: -21.9) CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT|TCAGA|TTCCTTATCAcAGCATTTAAGGACATCCATGTTCTGACCC CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT|TCAGA|TTCCTTATCATAGCATTTAAGGACATCCATGTTCTGACCC Human > Chimp ------------- chr1:65446872-65446879 Template switch process: F1: L ACATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT 1 F3: 4 TTCCTTATCATAGCATTTAAGGACATCCATGTTCTGACCC R RF: ACATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGTTCAGATTCCTTATCACAGCATTTAAGGACATCCATGTTCTGACCC RR: TGTAAATTCTGACACGGTAAAGACTAAAAGATCTTTTCTCAAGTCTAAGGAATAGTGTCGTAAATTCCTGTAGGTACAAGACTGGG F2: 3 TTCTCAAG 2 Unidirectional alignment (log-probability: -35.9) CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT---GAactcttTTCCTTATCAtAGCATTTAAGGACATCCATGTTCTGACCC CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGTTCAGA------TTCCTTATCACAGCATTTAAGGACATCCATGTTCTGACCC Template switch alignment (log-probability: -22.3) CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT|GAACTCTT|TTCCTTATCAtAGCATTTAAGGACATCCATGTTCTGACCC CATTTAAGACTGTGCCATTTCTGATTTTCTAGAAAAGAGT|GAACTCTT|TTCCTTATCACAGCATTTAAGGACATCCATGTTCTGACCC ========== Event 1287 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TTCTCTTCAAGTTTTGCCAAGTTGTCCCTC-AGCTAAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCTTTCAGGTAGACATTTAGCTTTCCACTGATAGATTTCTCT ↑ 1 4 3 2 Chimp: TTCTCTTCAAGTTTTGCCAAGGTGTCCCTCTTGGAAAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCTTTCAGGTAGACATTTAGCTTTCCACTGATAGATTTCTCT Gorilla: TTCTCTTCAAGTTTTGCCAAGGTGTCCCTC-AGCTAAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCTTTCAGGTAGACATTTAGCTTTCCACTGATAGATTTCTCT Human: TTCTCTTCAAGTTTTGCCAAGTTGTCCCTC-AGCTAAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCTTTCAGGTAGACATTTAGCTTTCCACTGATAGATTTCTCT Cluster: [ ] Orangutan: TTCTCTTcaagttttgccaaggtgtccctc-agctaaatggtcttcttctcccaattcagagaaaagatgaagctttcaggtagacatttagctttccactgatagatttctct Chimp > Human ------------- chr16:34269052-34269055 Template switch process: F1: L CTGGCTATCAGATGAAACAATTCTCTTCAAGTTTTGCCAAGTTGTCCCTC 1 F3: 4 AAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCT R RF: CTGGCTATCAGATGAAACAATTCTCTTCAAGTTTTGCCAAGGTGTCCCTCTTGGAAAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCTTTCAGGTAGACATTTAGCT RR: GACCGATAGTCTACTTTGTTAAGAGAAGTTCAAAACGGTTCCACAGGGAGAACCTTTTACCAGAAGAAGAGGGTTAAGTCTCTTTTCTACTTCGAAAGTCCATCTGTAAATCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -31.7) GATGAAACAATTCTCTTCAAGTTTTGCCAAGtTGTCCCTcagCT----AAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCT GATGAAACAATTCTCTTCAAGTTTTGCCAAGGTGTCCCT---CTTGGAAAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCT Template switch alignment (log-probability: -21.9) GATGAAACAATTCTCTTCAAGTTTTGCCAAGtTGTCCCTC|AGCT|AAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCT GATGAAACAATTCTCTTCAAGTTTTGCCAAGGTGTCCCTC|AGCT|AAATGGTCTTCTTCTCCCAATTCAGAGAAAAGATGAAGCT ========== Event 1288 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAAAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT------AAATAA---AAGAGAGTTTTATCAGCCCAA Chimp: ATAAAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT------AAATAA---AAGACAGTTTTATCAGCCCAA Gorilla: ATAAAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCTTTTATTTAGCAAATTTAGAGAGTTTTATCAGCCCAA ↑ 4 3 1 2 Human: ATAAAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT------AAATAA---AAGAGAGTTTTATCAGCCCAA Cluster: [ ] Orangutan: ATAAAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT------AAATAA---AAGAGAGTTTTATCAGCCCAA Human > Gorilla --------------- chr16:43057536-43057547 Template switch process: F1: L AAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT 1 F3: 4 ATTT----------------------------AGAGAGTTTTATCAGCCCAAATGCAAAACATGACAAAGGT R RF: AAGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCTAAATAAAAGAGAGTTTTATCAGCCCAAATGCAAAACATGACAAAGGT RR: TTCGTAAGACCGACACTAAACCTTTCTTACGACCACAACGATTTATTTTCTCTCAAAATAGTCGGGTTTACGTTTTGTACTGTTTCCA F2: 3 AACGATTTATTT 2 Unidirectional alignment (log-probability: -44) AGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCttttatttagcaaattT-------AGAGAGTTTTATCAGCCCAAATGCAAAACATGACAA AGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGC----------------TAAATAAAAGAGAGTTTTATCAGCCCAAATGCAAAACATGACAA Template switch alignment (log-probability: -28.5) AGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT|TTTATTTAGCAA|ATTT----------------------------AGAGAGTTTTATCAGCCCAAATGCAAAACATGACAA AGCATTCTGGCTGTGATTTGGAAAGAATGCTGGTGTTGCT|TTTATTTAGCAA|ATTTGGAAAGAATGCTGGTGTTGCTAAATAAAAGAGAGTTTTATCAGCCCAAATGCAAAACATGACAA ========== Event 1289 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTG---------------------------------------------------------CTGGTTTCATAACTCTGTTTTGGGA ↓ 3 4 2 1 Chimp: AGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTG-----------------------------CTGGTGCATTTCATTCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGGA Gorilla: AGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTG-CTGGTGCATTTCATTCACCCAGCCATTG----------------------------CTGGTTTCATAACTCTGTTTTGGGA ↑ 34 2 1 Human: AGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTG---------------------------------------------------------CTGGTTTCATAACTCTGTTTTGGGA Cluster: [ ] Orangutan: AGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGC----------------------------------------------------------TCTTTCATAACTCTGTTTTGGGA Human > Chimp ------------- chr16:47351005-47351011 Template switch process: F1: L AGAAGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT 1 F3: 4 ATTCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGGAAACTGCAGCTGCCAA R RF: AGAAGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGGAAACTGCAGCTGCCAA RR: TCTTCGGGACCACGGTTTCAGTGTTTACGTGGGTCGGTAACGACCAAAGTATTGAGACAAAACCCTTTGACGTCGACGGTT F2: 3 CTTTACG 2 Unidirectional alignment (log-probability: -51.2) CCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGTgcatttcattcacccagccattgctggtTTCATAACTCTGTTTTGGG CCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT----------------------------TTCATAACTCTGTTTTGGG Template switch alignment (log-probability: -28.5) CCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT|GCATTTc|ATtCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGG CCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT|GCATTTG|ATGCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGG Human > Gorilla --------------- chr16:47314908-47314913 Template switch process: F1: L AGAAGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT 1 F3: 4 CATTCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGGAAATTGCAGCTGCCAA R RF: AGAAGCCCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGGGAAACTGCAGCTGCCAA RR: TCTTCGGGACCACGGTTTCAGTGTTTACGTGGGTCGGTAACGACCAAAGTATTGAGACAAAACCCTTTGACGTCGACGGTT F2: 3 TTTACG 2 Unidirectional alignment (log-probability: -56.7) CCTGGTGCCAAAGTCACAAATGCACCCAGCCATtgctggtgcatttcattcacccagccatTGCTGGTTTCATAACTCTGTTTTGG CCTGGTGCCAAAGTCACAAATGCACCCAGCCAT----------------------------TGCTGGTTTCATAACTCTGTTTTGG Template switch alignment (log-probability: -33.6) CCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT|GCATTT|cATtCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGG CCTGGTGCCAAAGTCACAAATGCACCCAGCCATTGCTGGT|GCATTT|AATGCACCCAGCCATTGCTGGTTTCATAACTCTGTTTTGG ========== Event 1290 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTATGGGCTGGGTTCTACCCAGGTGCTAGGAACACTCCTTCACAGATGGGTGCTTGGAGGAAGGAAACCCAGCTCTGGTCCATAGAGAGCAAGACGCTGTGCTGCCCTGCCC-ACCTGGCCTCTGCACTCCCCTGCTGGG Chimp: CTTATGGGCTGGGTTCTACCCAGGTGCTAGGAACACTCCTTCACAGATGGGTGCTTGGAGGAAGGAAACCCAGCTCTGGTCCATAGAGAGCAAGACACTGTGCTGCCCTGCCC-ACCTGGCCTCTGCACTCCCCTGCTGGG Gorilla: CTTATGGGCTGGGTTCTACCCAGGTGCTAGGAACACTCCTTCACAGATGGGTGCTTGGAGGAAGGAAACCCAGCTCTGGTCCATAGAGAGCGAGGCGCTGTGCTGCCCTGcccccccccGCCTCTGCACTCCCCTGCTGGG ↓ 3 2 1 4 Human: CTTATGGGCTGGGTTCTACCCAGGTGCTAGGAACACTCCTTCACAGATGGGTGCTTGGAGGAAGGAAACCCAGCTCTGGTCCATAGAGAGCAAGACGCTGTGCTGCCCTGCCC-ACCTGGCCTCTGCACTCCCCTGCTGGG Cluster: [ ] Orangutan: CTTATGGGCTGGGTTCTACCCAGGTGCTAGGAACACTCCTTCACAGATGGGTGCTTGGAGGAAGGGAACCCAGCTCTGGTCCATAGAGAGCAAGATGCTGTGCCGCCCTGCCC-ACCCGGCCTCTGCACTCCCCTGCTGGG Gorilla > Human --------------- chr16:57384664-57384669 Template switch process: F1: L GTGCTTGGAGGAAGGAAACCCAGCTCTGGTCCATAGAGAGCAAGACGCTGTGCTGCCCTGCCC 1 F3: 4 CCTCTGCACTCCCCT R RF: CCAGGTGCTAGGAACACTCCTTCACAGATGGGTGCTTGGAGGAAGGAAACCCAGCTCTGGTCCATAGAGAGCGAGGCGCTGTGCTGCCCTGCCCCCCCCCGCCTCTGCACTCCCCT RR: GGTCCACGATCCTTGTGAGGAAGTGTCTACCCACGAACCTCCTTCCTTTGGGTCGAGACCAGGTATCTCTCGCTCCGCGACACGACGGGACGGGGGGGGGCGGAGACGTGAGGGGA F2: 3 GGTCCA 2 Unidirectional alignment (log-probability: -38.6) CTCTGGTCCATAGAGAGCaAGaCGCTGTGCTGCCCTG-CCCaCCtgGCCTCTGCACTCCCCT CTCTGGTCCATAGAGAGCGAGGCGCTGTGCTGCCCTGCCCCCCCCCGCCTCTGCACTCCCCT Template switch alignment (log-probability: -27.4) CTCTGGTCCATAGAGAGCaAGaCGCTGTGCTGCCCTGCCC|ACCTGG|CCTCTGCACTCCCCT CTCTGGTCCATAGAGAGCGAGGCGCTGTGCTGCCCTGCCC|ACCTGG|CCTCTGCACTCCCCT ========== Event 1291 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTGTATGGAAATTTCCCTGAATAGGT----------ATAATAGGCAATGCATATTATACCttttttttt---tttt--- Chimp: ACTGTATGGAAATTTCCCTGAATAGGT----------ATAATAGGCAATGCATATTATACCttttttttt-------ttt ↑ 1 43 2 Gorilla: ACTGTATGGAAATTTCCCTGAGTAGAT--------------------ATGCATATTATACCtttttttttttt------- Human: ACTGTATGGAAATTTCCCTGAATAGGT----------ATAATAGGCAATGCATATTATACCttttttttt---tttt--- Cluster: [ ] Orangutan: ACTGTATGGAAATTTCCCTGAGTAGGTATAATAGGCA----------ATGCATATTATATCCttt--------------- Gorilla > Chimp --------------- chr16:47887558-47887569 Template switch process: F1: L TAACAATGAAAAAAGCCCTTACTGTATGGAAATTTCCCTGAATAG 1 F3: 4 ATGCATATTATACCTTTTTTTTTTTTTTTTTTTTTTT R RF: TAACAATGAAAAAAGCCCTTACTGTATGGAAATTTCCCTGAGTAGATATGCATATTATACCTTTTTTTTTTTTTTTTTTTTTTG RR: ATTGTTACTTTTTTCGGGAATGACATACCTTTAAAGGGACTCATCTATACGTATAATATGGAAAAAAAAAAAAAAAAAAAAAAC F2: 3 ACGGATAATATG 2 Unidirectional alignment (log-probability: -44.5) ATGAAAAAAGCCCTTACTGTATGGAAATTTCCCTGAaTAGgTataataggcaATGCATATTATACCTTTTTTTTTTTTTTTTTTTTTTt ATGAAAAAAGCCCTTACTGTATGGAAATTTCCCTGAGTAGAT----------ATGCATATTATACCTTTTTTTTTTTTTTTTTTTTTT- Template switch alignment (log-probability: -33.8) ATGAAAAAAGCCCTTACTGTATGGAAATTTCCCTGAaTAG|GTATAATAgGCA|ATGCATATTATACCTTTTTTTTTTTTTTTTTTTTTTt ATGAAAAAAGCCCTTACTGTATGGAAATTTCCCTGAGTAG|GTATAATATGCA|ATGCATATTATACCTTTTTTTTTTTTTTTTTTTTTTG ========== Event 1292 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GGGCTGGGTTATGCCCCTTCCGGGGGGGCAGGCCCGGGAGCGCAGGGCCTGGGTTGCTCGGATGAGGTTTGTGTGGGTGCGGGTGAGGTCAGCTCGCGACCTGGGCTCCCCCGG Chimp: GGGCTGGGTTATGCCCCTTCCGG-CTGGCAGGCCCGGGAGCGCAGGGCCTGGGTTGCTCGGATGAGGTTTGTGTGGGTGCGGGTGAGGTCAGCTCGCGACCTGGGCTCCCCCGG Gorilla: GGGCTGGGTTATGCCCCTTCCAG-CTGGCAGGCCCGGGAGCGCAGGGCCTGAGTTGCTCGGATGAGGTTTGTGTGGGTGCGGGTGAGGTCAGCTCGCGACCTGGGCTCCCCCGG ↑ 1 4 3 2 Human: GGGCTGGGTTATGCCCCTTCCGGGGGGGCAGGCCCGGGAGCGCAGGGCCTGGGTTGCTCGGATGAGGTTTGTGTGGGTGCGGGTGAGGTCAGCTCGCGACCTGGGCTCCCCCGG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr16:48129197-48129201 Template switch process: F1: L AGAAGGTTGGGAGCTGCCAGGGGCTGGGTTATGCCCCTTCC 1 F3: 4 GCAGGCCCGGGAGCGCAGGGCCTGAGTTGCTCGGATGAG R RF: AGAAGGTTGGGAGCTGCCAGGGGCTGGGTTATGCCCCTTCCGGGGGGGCAGGCCCGGGAGCGCAGGGCCTGGGTTGCTCGGATGAGGTTTGTGTGGGTGCGGGTGAGGTCAGCT RR: TCTTCCAACCCTCGACGGTCCCCGACCCAATACGGGGAAGGCCCCCCCGTCCGGGCCCTCGCGTCCCGGACCCAACGAGCCTACTCCAAACACACCCACGCCCACTCCAGTCGA F2: 3 GTCGA 2 Unidirectional alignment (log-probability: -32.2) GAAGGTTGGGAGCTGCCAGGGGCTGGGTTATGCCCCTTCC-----agctGGCAGGCCCGGGAGCGCAGGGCCTGaGTTGCTCGGATGAG GAAGGTTGGGAGCTGCCAGGGGCTGGGTTATGCCCCTTCCGGGGG----GGCAGGCCCGGGAGCGCAGGGCCTGGGTTGCTCGGATGAG Template switch alignment (log-probability: -21.8) GAAGGTTGGGAGCTGCCAGGGGCTGGGTTATGCCCCTTCC|AGCTG|GCAGGCCCGGGAGCGCAGGGCCTGaGTTGCTCGGATGAG GAAGGTTGGGAGCTGCCAGGGGCTGGGTTATGCCCCTTCC|AGCTG|GCAGGCCCGGGAGCGCAGGGCCTGGGTTGCTCGGATGAG ========== Event 1293 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTGGCCCCGCCCACCCTTGAGGCCCTTCCCACTATCGTAACTCATTCCATTCTCTCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCC-------------------------ACAGCCCCTTCCACCACATGGCCTCACCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCA Chimp: TGTGGCCCCGCCCACCCTTGAGGCCCTTCCCACTATCGTAACTCATTCCATTCTCTCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCC-------------------------ACAGCCCCTTCCACCACATGGCCTCACCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCA ↑ 3 2 4 1 Gorilla: TGTGGCCCCGCCCACCCTTGAGGCCCTTCCCACTATCGTAACTCATTCCATTCTCTCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCC------------------------------------------------------ACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCA ↓ 3 2 4 1 Human: TGTGGCCCCGCCCACCCTTGAGGCCCTTCCCACTATCGTAACTCATTCCATTCTCTCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCC-------------------------ACAGCCCCTTCCACCACATGGCCTCACCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCA Cluster: [ ] Orangutan: tgtggccccgcccacccttaaggcccttcccactatcataactcattccgttctctcagctgtggctcctcccaccatgtggcccctc--------ccaccatgtggcccctcctatatcc-----------------------------acagcccctcccatcaccatggctttgggtcctccca Gorilla > Human --------------- chr16:32573277-32573284 Template switch process: F1: L TCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCCACAGCCCCTTCCACCAC 1 F3: 4 ACCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCATTC R RF: GAGGCCCTTCCCACTATCGTAACTCATTCCATTCTCTCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCATTC RR: CTCCGGGAAGGGTGATAGCATTGAGTAAGGTAAGAGAGTCGACACCGAGGAGGGTGGTACACCGGGGAGGATATAGGTGTCGGGGAGGGTGGTGGTACCGAAACCCAGGAGGGTAAG F2: 3 CTCCGGTA 2 Unidirectional alignment (log-probability: -52.6) ACCATGTGGCCCCTCCTATATccacagccccttccaccacatggcctcacCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC ACCATGTGGCCCCTCCTATAT-----------------------------CCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC Template switch alignment (log-probability: -33.8) ACCATGTGGCCCCTCCTATATCCACAGCCCCTtCCACCAC|AtGGCCTC|AcCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC ACCATGTGGCCCCTCCTATATCCACAGCCCCTCCCACCAC|AGGGCCTC|ATCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC Gorilla > Chimp --------------- chr16:33135136-33135143 Template switch process: F1: L TCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCCACAGCCCCTTCCACCAC 1 F3: 4 ACCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCATTC R RF: GAGGCCCTTCCCACTATCGTAACTCATTCCATTCTCTCAGCTGTGGCTCCTCCCACCATGTGGCCCCTCCTATATCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCCATTC RR: CTCCGGGAAGGGTGATAGCATTGAGTAAGGTAAGAGAGTCGACACCGAGGAGGGTGGTACACCGGGGAGGATATAGGTGTCGGGGAGGGTGGTGGTACCGAAACCCAGGAGGGTAAG F2: 3 CTCCGGTA 2 Unidirectional alignment (log-probability: -52.6) ACCATGTGGCCCCTCCTATATccacagccccttccaccacatggcctcacCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC ACCATGTGGCCCCTCCTATAT-----------------------------CCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC Template switch alignment (log-probability: -33.8) ACCATGTGGCCCCTCCTATATCCACAGCCCCTtCCACCAC|AtGGCCTC|AcCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC ACCATGTGGCCCCTCCTATATCCACAGCCCCTCCCACCAC|AGGGCCTC|ATCCACAGCCCCTCCCACCACCATGGCTTTGGGTCCTCCC ========== Event 1294 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGCTTCCCATCTCCACCCCCAATCAGGGTATAATCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCATTTGG ↓ 1 4 3 2 Chimp: AGGCTTCCCATCTCCACCCCCTTA---CTTATAAGCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCATTTGG Gorilla: AGCCTTCCCATCTCCACCCCCAATCAGGGTATAATCTCACATACACTAGCTTATAAGTAAAAATATTTCTCTTCATTTGG Human: AGGCTTCCCATCTCCACCCCCAATCAGGGTATAATCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCATTTGG Cluster: [ ] Orangutan: AGGCTTCCCATCTCCACCCCCAATCAGGGTATAATCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCATTTGG Human > Chimp ------------- chr16:30445207-30445217 Template switch process: F1: L CATGTCTCCTTGGAAGGATGAGGCTTCCCATCTCCACCCCC 1 F3: 4 CTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCA R RF: CATGTCTCCTTGGAAGGATGAGGCTTCCCATCTCCACCCCCAATCAGGGTATAATCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCA RR: GTACAGAGGAACCTTCCTACTCCGAAGGGTAGAGGTGGGGGTTAGTCCCATATTAGAGTGTATGTGATCGAATATTCATTTTTATAAAGGGAAGT F2: 3 GAATATTCATT 2 Unidirectional alignment (log-probability: -34.8) ATGTCTCCTTGGAAGGATGAGGCTTCCCATCTCCACCCCCttact--------TATAAgCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCA ATGTCTCCTTGGAAGGATGAGGCTTCCCATCTCCACCCCC-----AATCAGGGTATAATCTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCA Template switch alignment (log-probability: -16.6) ATGTCTCCTTGGAAGGATGAGGCTTCCCATCTCCACCCCC|TTACTTATAAG|CTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCA ATGTCTCCTTGGAAGGATGAGGCTTCCCATCTCCACCCCC|TTACTTATAAG|CTCACATACACTAGCTTATAAGTAAAAATATTTCCCTTCA ========== Event 1295 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGATAGGTCTATGGGACCAGCATGC-----------------------ATTTGTATAAATCTAGTTGGAGCCCACA ↓ 3 4 1 2 Chimp: GTGATAGGTCTATGGGACCAGCATGCATTTATACAAATGCATTTTATGCATTTGTATAAATCTAGTTGGAGCCCACA ↑ 3 4 1 2 Gorilla: GTGATAGGTCTATGGGACCAGCATGC-----------------------ATTTGTATAAATCTAGTTGGAGCCCACA Human: GTGATAGGTCTATGGGACCAGCATGC-----------------------ATTTGTATAAATCTAGTTGGAGCCCACA Cluster: [ ] Orangutan: GTGATAGGTCTATGGGACCAGCATGC-----------------------ATTTATACAAA---------TGCCCACA Human > Chimp ------------- chr16:51714515-51714529 Template switch process: F1: L ATATCATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTT 1 F3: 4 ATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTGGCTC R RF: ATATCATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTGGCTC RR: TATAGTAGTATCTCTCACTATCCAGATACCCTGGTCGTACGTAAACATATTTAGATCAACCTCGGGTGTATCTTGACCGAG F2: 3 TTTTACGTAAACATA 2 Unidirectional alignment (log-probability: -44) ATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCAtttatacaaatgcattttatgcaTTTGTATAAATCTAGTTGGAGCCCACATAGAACTG ATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCA-----------------------TTTGTATAAATCTAGTTGGAGCCCACATAGAACTG Template switch alignment (log-probability: -29.3) ATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTT|ATACAAATGCATttT|ATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTG ATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTT|ATACAAATGCATGCT|ATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTG Gorilla > Chimp --------------- chr16:51714515-51714529 Template switch process: F1: L ATATCATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTT 1 F3: 4 ATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTGGCTC R RF: ATATCATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTGGCTC RR: TATAGTAGTATCTCTCACTATCCAGATACCCTGGTCGTACGTAAACATATTTAGATCAACCTCGGGTGTATCTTGACCGAG F2: 3 TTTTACGTAAACATA 2 Unidirectional alignment (log-probability: -44) ATCATAGAGAGTGATAGGTCTATGGGACCAGCATgcatttatacaaatgcattttatGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTG ATCATAGAGAGTGATAGGTCTATGGGACCAGCAT-----------------------GCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTG Template switch alignment (log-probability: -28.9) ATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTT|ATACAAATGCATttT|ATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTG ATCATAGAGAGTGATAGGTCTATGGGACCAGCATGCATTT|ATACAAATGCATGCT|ATGCATTTGTATAAATCTAGTTGGAGCCCACATAGAACTG ========== Event 1296 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCTTGCTCTTCATACATGTTTGCTAAGTTGGCACTTAGCAAACATCCCTATGTCATGAACCCT ↑ 3 2 1 4 Chimp: TTCTTGCTCTTCATACATGTTTGCTAAGTTGGTA-TTGTCCTCCATCCCTATGTCATGAACCCT Gorilla: TTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA-TTGTCCTCCATCCCTATGTCATGAACCCT ↓ 3 2 1 4 Human: TTCTTGCTCTTCATACATGTTTGCTAAGTTGGCACTTAGCAAACATCCCTATGTCATGAACCCT Cluster: [ ] Orangutan: TTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA-TTGTCCTCCATCCCTATGTCATGAACCCT Chimp > Human ------------- chr16:61850833-61850841 Template switch process: F1: L AAAAATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA 1 F3: 4 CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA R RF: AAAAATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGTATTGTCCTCCATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA RR: TTTTTATGAAAGAACGAGAAGTATGTACAAACGATTCAACCATAACAGGAGGTAGGGATACAGTACTTGGGATATAATACACATCATAAAT F2: 3 AAACGATTC 2 Unidirectional alignment (log-probability: -36) AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGG---------CacttagcaaaCATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGTATTGTCCTC----------CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA Template switch alignment (log-probability: -22.4) AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGcA|CTTAGCAAA|CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGTA|CTTAGCAAA|CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA Gorilla > Human --------------- chr16:61850833-61850841 Template switch process: F1: L AAATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA 1 F3: 4 CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA R RF: AAATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCATTGTCCTCCATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA RR: TTTATGAAAGAACGAGAAGTATGTACAAACGATTCAACCGTAACAGGAGGTAGGGATACAGTACTTGGGATATAATACACATCATAAAT F2: 3 AAACGATTC 2 Unidirectional alignment (log-probability: -32.5) AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA-------CttagcaaaCATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCATTGTCCTC--------CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA Template switch alignment (log-probability: -16.9) AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA|CTTAGCAAA|CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA AATACTTTCTTGCTCTTCATACATGTTTGCTAAGTTGGCA|CTTAGCAAA|CATCCCTATGTCATGAACCCTATATTATGTGTAGTATTTA ========== Event 1297 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTGAGAGGTCTGTGACTTCAC-----AAAGTCACAGACTTTGTGATAATTAGCTAGATGTTT Chimp: TTTGAGAGGTCTGTGACTTCAC-----AAAGTCACAGACTTTGTGATAATTAGCTAGATGTTT ↑ 1 3 4 2 Gorilla: TTTGAGAGGTCTGTGACTTCAT------------GTGACTTTGTGATAATTAGCTAGATGTTT ↓ 1 3 4 2 Human: TTTGAGAGGTCTGTGACTTCAC-----AAAGTCACAGACTTTGTGATAATTAGCTAGATGTTT Cluster: [ ] Orangutan: TTTGAGAGGTCTGTGACTTCACAGTTC--------------ACTCATAATTAGCTAGATGTTT Gorilla > Human --------------- chr16:62783386-62783395 Template switch process: F1: L GACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA 1 F3: 4 GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA R RF: GACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCATGTGACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA RR: CTGTTGTGGTCACGGTATTAAAACTCTCCAGACACTGAAGTACACTGAAACACTATTAATCGATCTACAAATGAATGTTTACGT F2: 3 ACACTGAAAC 2 Unidirectional alignment (log-probability: -35.2) ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA---caaagtcacaGACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCATGT----------GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA Template switch alignment (log-probability: -17) ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA|CAAAGTCACA|GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA|CAAAGTCACA|GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA Gorilla > Chimp --------------- chr16:53515644-53515653 Template switch process: F1: L GACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA 1 F3: 4 GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA R RF: GACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCATGTGACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA RR: CTGTTGTGGTCACGGTATTAAAACTCTCCAGACACTGAAGTACACTGAAACACTATTAATCGATCTACAAATGAATGTTTACGT F2: 3 ACACTGAAAC 2 Unidirectional alignment (log-probability: -35.2) ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA---caaagtcacaGACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCATGT----------GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA Template switch alignment (log-probability: -17) ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA|CAAAGTCACA|GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA ACAACACCAGTGCCATAATTTTGAGAGGTCTGTGACTTCA|CAAAGTCACA|GACTTTGTGATAATTAGCTAGATGTTTACTTACAAATGCA ========== Event 1298 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AAAGCATATTGTTTGCTTGTTTTGACATCCAGAATAATATCTGTCAAATCCAttttttttttttt-- ↑ 1 4 3 2 Chimp: AAAGCATATTGTTTGCTTGTTCTGCTATCCAGAATAATATCTGTCAAATCCAtttttt-------tt Gorilla: AAAGCATATTGTTTGCTTGTTTTGCCATCCAGAATAATATCTGTCAAATCCtttttttttttttt-- Human: AAAGCATATTGTTTGCTTGTTTTGACATCCAGAATAATATCTGTCAAATCCAttttttttttttt-- Cluster: [ ] Orangutan: AAAGCATATTGTTTGCTTGTTTTGCCATCCAGAATAATATCTGTCAAATCCAttttttt---ttt-- Chimp > Human ------------- chr16:62028031-62028036 Template switch process: F1: L TCCAGATGTCAATCTGTCCAAAAGCATATTGTTTGCTTGTT 1 F3: 4 TCCAGAATAATATCTGTCAAATCCATTTTTTTTTTTTT R RF: TCCAGATGTCAATCTGTCCAAAAGCATATTGTTTGCTTGTTCTGCTATCCAGAATAATATCTGTCAAATCCATTTTTTTTTTTTT RR: AGGTCTACAGTTAGACAGGTTTTCGTATAACAAACGAACAAGACGATAGGTCTTATTATAGACAGTTTAGGTAAAAAAAAAAAAA F2: 3 ACAGTT 2 Unidirectional alignment (log-probability: -34.5) CCAGATGTCAATCTGTCCAAAAGCATATTGTTTGCTTGTTtTGacATCCAGAATAATATCTGTCAAATCCATTTTTTTtttttt CCAGATGTCAATCTGTCCAAAAGCATATTGTTTGCTTGTTCTGCTATCCAGAATAATATCTGTCAAATCCATTTTTTT------ Template switch alignment (log-probability: -16) CCAGATGTCAATCTGTCCAAAAGCATATTGTTTGCTTGTT|TTGACA|TCCAGAATAATATCTGTCAAATCCATTTTTTTTTTTTT CCAGATGTCAATCTGTCCAAAAGCATATTGTTTGCTTGTT|TTGACA|TCCAGAATAATATCTGTCAAATCCATTTTTTTTTTTTT ========== Event 1299 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tcctaatggggctcctgtgTCATGTTTTAACT-GTAATTAGCAAAACAAATTCACATGGTCT-GGGATCAGCTACTCACATGCCTTTTTCTATCTTGAATGTCTTCTACAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAATTTGTTCACTTTTTGTGAACAGATTT Chimp: tcctaatggggctgctgtgTCATGTTTTAACT-GTAATTAGCAAAACAAATTCACATGGTCT-GGGATCAGCTACTCACATGCCTTTTTCTATCTTGAATGTCTTCTACAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAATTTGTTCACTTTTTGTGAACAGATTT ↓ 3 2 1 4 Gorilla: tcctaatggggctgctgtgTCATGTTTTAACT-GTAATTAGCAAAACAAATTCACATGGTCT-GGGATCAGCTACTCACATGCCTTTTTCTATCTTGAATGTCTTCTACAATGTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAA-ACATGATCACTTTTTGTGAACAGATTT ↑ 3 2 1 4 Human: tcctaatggggctcctgtgTCATGTTTTAACT-GTAATTAGCAAAACAAATTCACATGGTCT-GGGATCAGCTACTCACATGCCTTTTTCTATCTTGAATGTCTTCTACAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAATTTGTTCACTTTTTGTGAACAGATTT Cluster: [ ] Orangutan: TCCTAATGGGGCTGCTGTGTCATGATTTAACTGCTAATTAGCAAAACAAATCCACATGGTCTGCGGATCAGGTACTCACATGCCTTTTTCTTTCTTGAATGTCTTCTACAATTTAGTAGCCAAAAGCACAGGAGGCTTTTGAACCAA-ACATCATCACTTTTTGTGAACAGATTT Human > Gorilla --------------- chr16:54330655-54330659 Template switch process: F1: L TACAATGTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA 1 F3: 4 TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA R RF: TCATGTTTTAACTGTAATTAGCAAAACAAATTCACATGGTCTGGGATCAGCTACTCACATGCCTTTTTCTATCTTGAATGTCTTCTACAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAATTTGTTCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA RR: AGTACAAAATTGACATTAATCGTTTTGTTTAAGTGTACCAGACCCTAGTCGATGAGTGTACGGAAAAAGATAGAACTTACAGAAGATGTTAAATCATCGGTTTTCGTCTTCTCCGAAAACTTGATTTTAAACAAGTGAAAAACACTTGTCTAAAATTTATTTAATTAAATGTT F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -32.2) CAATgTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAcatgA-----TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA CAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA----ATTTGTTCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA Template switch alignment (log-probability: -21.9) CAATgTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA|CATGA|TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA CAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA|CATGA|TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA Chimp > Gorilla --------------- chr16:54330655-54330659 Template switch process: F1: L TACAATGTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA 1 F3: 4 TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA R RF: TCATGTTTTAACTGTAATTAGCAAAACAAATTCACATGGTCTGGGATCAGCTACTCACATGCCTTTTTCTATCTTGAATGTCTTCTACAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAATTTGTTCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA RR: AGTACAAAATTGACATTAATCGTTTTGTTTAAGTGTACCAGACCCTAGTCGATGAGTGTACGGAAAAAGATAGAACTTACAGAAGATGTTAAATCATCGGTTTTCGTCTTCTCCGAAAACTTGATTTTAAACAAGTGAAAAACACTTGTCTAAAATTTATTTAATTAAATGTT F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -32.2) CAATgTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAAcatgA-----TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA CAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA----ATTTGTTCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA Template switch alignment (log-probability: -21.9) CAATgTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA|CATGA|TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA CAATTTAGTAGCCAAAAGCAGAAGAGGCTTTTGAACTAAA|CATGA|TCACTTTTTGTGAACAGATTTTAAATAAATTAATTTACAA ========== Event 1300 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGTGATTATAACAAAACAATTTGGCCAT---------GGCACTGTGGCATCATCTCAAT Chimp: TCATGTGATTATAACAAAACAATTTGGCCATGGCCAAATTGGCACTGTGGCATCATCTCAAT ↑ 3 2 1 4 Gorilla: TCATGTGATTATAACAAAACAATTTGGCCAT---------AGCACTGTGGCATCATCTCAAT Human: TCATGTGATTATAACAAAACAATTTGGCCAT---------GGCACTGTGGCATCATCTCAAT Cluster: [ ] Orangutan: TCATGTGATTATAACAAAACAATTTGGCCAT---------GGCACTGTGGCATCACCTCAAT Gorilla > Chimp --------------- chr16:74672788-74672797 Template switch process: F1: L ATTCTCTATATCATGTGATTATAACAAAACAATTTGGCCAT 1 F3: 4 GCACTGTGGCATCATCTCAATACATGCCATCTTATCTCAG R RF: ATTCTCTATATCATGTGATTATAACAAAACAATTTGGCCATAGCACTGTGGCATCATCTCAATACATGCCATCTTATCTCAG RR: TAAGAGATATAGTACACTAATATTGTTTTGTTAAACCGGTATCGTGACACCGTAGTAGAGTTATGTACGGTAGAATAGAGTC F2: 3 GTTAAACCGG 2 Unidirectional alignment (log-probability: -29.4) TTCTCTATATCATGTGATTATAACAAAACAATTTGGCCAtggccaaatTgGCACTGTGGCATCATCTCAATACATGCCATCTTATCTCAG TTCTCTATATCATGTGATTATAACAAAACAATTTGGCCA---------TAGCACTGTGGCATCATCTCAATACATGCCATCTTATCTCAG Template switch alignment (log-probability: -17) TTCTCTATATCATGTGATTATAACAAAACAATTTGGCCAT|GGCCAAATTG|GCACTGTGGCATCATCTCAATACATGCCATCTTATCTCAG TTCTCTATATCATGTGATTATAACAAAACAATTTGGCCAT|GGCCAAATTG|GCACTGTGGCATCATCTCAATACATGCCATCTTATCTCAG ========== Event 1301 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAGTGAGAACTCATACTCGTCTAAAGCTAACGACTTTAG---------------------ACGTTAGCCCAGCCAAATGCTAT ↑ 3 2 1 4 Chimp: AGAGTGAGAGCTCATACTCGTCTAAAGCTAACGAAATTCA-------------AAAATACTGTGTTAGCCCAGCCAAATGCTAT Gorilla: AGAGTGAGAGCTCATACTCAACTAAAGCTAACGAAATTCAAAAATACTGTTCT--------GTGTTAGCCCAGCCAAATGCCAT Human: AGAGTGAGAACTCATACTCGTCTAAAGCTAACGACTTTAG---------------------ACGTTAGCCCAGCCAAATGCTAT Cluster: [ ] Orangutan: AGAGTGAGAGCTCATACTCATCTAAAGCTAATGAAATTCAAAAATCCTGTACT--------GTATTAGCCCAGCCAAATACTAT Chimp > Human ------------- chr1:182266563-182266570 Template switch process: F1: L GTAACACAGAGTGAGAACTCATACTCGTCTAAAGCTAACGA 1 F3: 4 GTTAGCCCAGCCAAATGCTATGGACATCATTTGTTTCTGA R RF: GTAACACAGAGTGAGAGCTCATACTCGTCTAAAGCTAACGAAATTCAAAAATACTGTGTTAGCCCAGCCAAATGCTATGGACATCATTTGTTTCTGA RR: CATTGTGTCTCACTCTCGAGTATGAGCAGATTTCGATTGCTTTAAGTTTTTATGACACAATCGGGTCGGTTTACGATACCTGTAGTAAACAAAGACT F2: 3 CAGATTTC 2 Unidirectional alignment (log-probability: -39.4) TAACACAGAGTGAGAaCTCATACTCGTCTAAAGCTAACGA----------------ctttagacGTTAGCCCAGCCAAATGCTATGGACATCATTTGTTTCTGA TAACACAGAGTGAGAGCTCATACTCGTCTAAAGCTAACGAAATTCAAAAATACTGT--------GTTAGCCCAGCCAAATGCTATGGACATCATTTGTTTCTGA Template switch alignment (log-probability: -22.3) TAACACAGAGTGAGAaCTCATACTCGTCTAAAGCTAACGA|CTTTAGAC|GTTAGCCCAGCCAAATGCTATGGACATCATTTGTTTCTGA TAACACAGAGTGAGAGCTCATACTCGTCTAAAGCTAACGA|CTTTAGAC|GTTAGCCCAGCCAAATGCTATGGACATCATTTGTTTCTGA ========== Event 1302 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTTGTAATTCAATGAAAAATACAGTGAATATCTGAAACCACATGTGCTATTGCTGAGGACAGACAGCCT-GCATACAGAAGTAGCTGCATGAAATTGGTCCAGAATAACAAA ↓ 1 4 3 2 Chimp: ACTTGTAATTCAATGAAAAATTC-------ACGTGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGCCATACAGAAGTAGCTGCATGAAATTGGTCCAGA-TA-AAAA Gorilla: ACTTGTAATTCAATGAAAAATTCAGTAAATATCTGAAACCACATGTGCTATTGCTGAGGACAGACAGCCT-GCATACAGAAGTAGCTGCATGAAATTGGTCCAGAATAACAAA Human: ACTTGTAATTCAATGAAAAATACAGTGAATATCTGAAACCACATGTGCTATTGCTGAGGACAGACAGCCT-GCATACAGAAGTAGCTGCATGAAATTGGTCCAGAATAACAAA Cluster: [ ] Orangutan: ACTTGTAATTCAATGAAAAATTCAGTGAATATCTGAAACCACATGTGCTATTGCTGAGTACAGACAGCCT-GCATACAGAAGTAACTGCATGAAATTGGTCCAGAACAACAAA Human > Chimp ------------- chr1:161818851-161818855 Template switch process: F1: L TTGCAGATGGAAGAGTAACAACTTGTAATTCAATGAAAAAT 1 F3: 4 TGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGCC R RF: TTGCAGATGGAAGAGTAACAACTTGTAATTCAATGAAAAATACAGTGAATATCTGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGCATACAGAAGTAGCTGCATGA RR: AACGTCTACCTTCTCATTGTTGAACATTAAGTTACTTTTTATGTCACTTATAGACTTTGGTGTACACGATAACGACTCCTGTCTGTCGGACGTATGTCTTCATCGACGTACT F2: 3 GCACT 2 Unidirectional alignment (log-probability: -34.6) TGCAGATGGAAGAGTAACAACTTGTAATTCAATGAAAAAT----------TCacgTGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGCc TGCAGATGGAAGAGTAACAACTTGTAATTCAATGAAAAATACAGTGAATATC---TGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGC- Template switch alignment (log-probability: -27.9) TGCAGATGGAAGAGTAACAACTTGTAATTCAATGAAAAAT|TCAcG|TGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGCc TGCAGATGGAAGAGTAACAACTTGTAATTCAATGAAAAAT|TCATG|TGAAACCACATGTGCTATTGCTGAGGACAGACAGCCTGCA ========== Event 1303 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTGCCGAACGACAGGAAAGAAAATAACAACATAT--------------------------------------------------------------------------------------GACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTTGTTTATGCTGCTCACAAGCAAC Chimp: CTTGCCGAACGACAGGAAAGAGAATATTTAAGTCT-------------------------------------------GGACCATTAATCTGAAACAAAACCAGAAGCTATGATTTTCTCCTACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTTGTTTATGCTGCTCACAAGCAAC Gorilla: CTTGCCGAACGACAGGAAAGAGAATATTTAAGTCTGGACCATTAATCTGAAACAAAACCAGAAGCTAGGATTTTCTCC-------------------------------------------CACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTTGTTTATGCTGCTCACAAGCAAC ↓ 1 4 3 2 Human: CTTGCCGAACGACAGGAAAGAAAATAACAACATAT--------------------------------------------------------------------------------------GACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTTGTTTATGCTGCTCACAAGCAAC Cluster: [ ] Orangutan: CTTGCCGAATGACAGGAAAGAGAATATTTAAGTCTGGACCGTTAATCTGAAACAAAACCGGAAGCTATGATTTTCTCC-------------------------------------------CACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTCGTTTATGCTGCTCACAAGCAAC Gorilla > Human --------------- chr1:182217115-182217124 Template switch process: F1: L TGAATGCCCTGGGCAGACACCTTGCCGAACGACAGGAAAGAAAATA 1 F3: 4 ACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTT R RF: TGAATGCCCTGGGCAGACACCTTGCCGAACGACAGGAAAGAGAATATTTAAGTCTGGACCATTAATCTGAAACAAAACCAGAAGCTAGGATTTTCTCCCACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTTGT RR: ACTTACGGGACCCGTCTGTGGAACGGCTTGCTGTCCTTTCTCTTATAAATTCAGACCTGGTAATTAGACTTTGTTTTGGTCTTCGATCCTAAAAGAGGGTGTCCCTACAAGAATCTGTAGTTTGTTTTACAGTATACAACA F2: 3 GTATACAACA 2 Unidirectional alignment (log-probability: -43.3) CCCTGGGCAGACACCTTGCCGAACGACAGGAAAGAaAATA-----------------------------------------------------acaacatatgACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTT CCCTGGGCAGACACCTTGCCGAACGACAGGAAAGAGAATATTTAAGTCTGGACCATTAATCTGAAACAAAACCAGAAGCTAGGATTTTCTCCC----------ACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTT Template switch alignment (log-probability: -22.6) CCCTGGGCAGACACCTTGCCGAACGACAGGAAAGAaAATA|ACAACATATG|ACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTT CCCTGGGCAGACACCTTGCCGAACGACAGGAAAGAGAATA|ACAACATATG|ACAGGGATGTTCTTAGACATCAAACAAAATGTCATATGTT ========== Event 1304 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTAGTGATTGCTAATTTCATTAAGG------CATT--AGCTGATTATAATTCAGTATGT Chimp: TGTAGTGATTGCTAATTTCATTAAGG------CATT--AGCTGATTATAATTCAGTATGT ↓ 3 1 24 Gorilla: TGTAGTGATTGCTAATTTCATTAAGGCTAATGCCTTAATGCTGATTATAATTCAGTATGT ↑ 3 1 24 Human: TGTAGTGATTGCTAATTTCATTAAGG------CATT--AGCTGATTATAATTCAGTATGT Cluster: [ ] Orangutan: TGTAGTGATTGCTAATTTCATTAAGG------CATT--AGCTGATTATAATTCAGTATGT Human > Gorilla --------------- chr1:161521555-161521566 Template switch process: F1: L TGTGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC 1 F3: 4 GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG R RF: TGTGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGCATTAGCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG RR: ACACTTCGTTTCGTTACATCACTAACGATTAAAGTAATTCCGTAATCGACTAATATTAAGTCATACAATTAAATTATAATACCCAC F2: 3 TAATTCCGTAAT 2 Unidirectional alignment (log-probability: -35.2) TGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC--TAatgccttaatGCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG TGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGCATTA----------GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG Template switch alignment (log-probability: -17.3) TGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC|TAATGCCTTAAT|GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG TGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC|TAATGCCTTAAT|GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG Chimp > Gorilla --------------- chr1:161521555-161521566 Template switch process: F1: L TGTGAAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC 1 F3: 4 GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG R RF: TGTGCAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGCATTAGCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG RR: ACACGTCGTTTCGTTACATCACTAACGATTAAAGTAATTCCGTAATCGACTAATATTAAGTCATACAATTAAATTATAATACCCAC F2: 3 TAATTCCGTAAT 2 Unidirectional alignment (log-probability: -40.7) TGaAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGCtaatgccttaAT--GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG TGCAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC----------ATTAGCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG Template switch alignment (log-probability: -22.8) TGaAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC|TAATGCCTTAAT|GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG TGCAGCAAAGCAATGTAGTGATTGCTAATTTCATTAAGGC|TAATGCCTTAAT|GCTGATTATAATTCAGTATGTTAATTTAATATTATGGGTG ========== Event 1305 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCTTTAAAAATACAAACGCTCTGCCAGCTACAAAGGTGTCAAatatatatata--------------------------------------------------------------------------------------------------------------------tatataAGC-------------------------------------------------------------------------------------------------------------- Chimp: ttctttaaaaatacaaacGCTCTTCCAGCTACAAAGGTGTCAAatatatatata--------------------------------------------------------------------------------------------------------tatatatatatatatataAGC-------------------------------------------------------------------------------------------------------------- Gorilla: ttctttaaaaatacaaacGCTTTTCTAGACACAAAGGTGTCAAatatatatata----tgtgtatatatatatgtgtatatatatatatgtgtatatatatgtgtatatatatatgtgtatatatatgtgtatatatatatatgtgtatatatatata------------tatataAGC------------------------------------------------------------------------------------TCGCAGTTACCAGTTCTAAATTTTGA ↓ 1 4 3 2 Human: TTCTTTAAAAATACAAACGCTCTGCCAGCTACAAAGGTGTCAAatatatatata--------------------------------------------------------------------------------------------------------------------tatataAGC-------------------------------------------------------------------------------------------------------------- Cluster: [ ] Orangutan: ttctttaaaaatacaaatgCTTTTCCAGATACAAAGGTGTCAAAAAAatata--tata----------------------------------------------------------------------------------------------------------------tatataAACTCGCAGCTACCAGTTCTAAATTTTATGATTCAGTTATTATTAGAGTATTACAGTATATCTAAAACATATTTTTAAAAACCAGAT-------------------------- Gorilla > Human --------------- chr16:23293212-23293220 Template switch process: F1: L AATAACTAAAATAAAAACTTTTCTTTAAAAATACAAACGCT 1 F3: 4 ACAAAGGTGTCAAATATATATATA R RF: AATAACTAAAATAAAAACTTTTCTTTAAAAATACAAACGCTTTTCTAGACACAAAGGTGTCAAATATATATATATGTGTATATATATATGTGTATATATATATATGTGTATATATATGTGTATATATATATGTGTATATATATGTGTATATATATATATGTGTATATATATATATATATAAGCTCGCAG RR: TTATTGATTTTATTTTTGAAAAGAAATTTTTATGTTTGCGAAAAGATCTGTGTTTCCACAGTTTATATATATATACACATATATATATACACATATATATATATACACATATATATACACATATATATATACACATATATATACACATATATATATATACACATATATATATATATATATTCGAGCGTC F2: 3 TCGACCGTC 2 Unidirectional alignment (log-probability: -36.2) ATAACTAAAATAAAAACTTTTCTTTAAAAATACAAACGCTcTgCcAGctACAAAGGTGTCAAATATATATATA---------------- ATAACTAAAATAAAAACTTTTCTTTAAAAATACAAACGCTTTTCTAGACACAAAGGTGTCAAATATATATATATGTGTATATATATATG Template switch alignment (log-probability: -22) ATAACTAAAATAAAAACTTTTCTTTAAAAATACAAACGCT|CTGCcAGCT|ACAAAGGTGTCAAATATATATATA ATAACTAAAATAAAAACTTTTCTTTAAAAATACAAACGCT|CTGCGAGCT|ACAAAGGTGTCAAATATATATATA ========== Event 1306 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GAATCCTGAACTGATGAAAGCTACCCAAGTGGGTAGCTGTGCGATTTGAGGTCCC ↑ 1 3 4 2 Chimp: GAATCCTGAACTGATGAAAGCCA----CTTGGGTAGCTGTGCGATTTGAGGTCCC Gorilla: GAATCCTGAACTGATGAAAGCCA----CTTGCGTAACTGTGCGATTTGAGGTCCC Human: GAATCCTGAACTGATGAAAGCTACCCAAGTGGGTAGCTGTGCGATTTGAGGTCCC Cluster: [ ] Orangutan: GAATCCTGAACTGATGAAAGCCA----CCTGGGTAGCTGTGCAATTTGAGGTCCC Chimp > Human ------------- chr16:23059762-23059769 Template switch process: F1: L TCATTTCACCCGCAGTCAGGGAATCCTGAACTGATGAAAGC 1 F3: 4 TGGGTAGCTGTGCGATTTGAGGTCCCTTTAGGGCATGTGG R RF: TCATTTCACCCGCAGTCAGGGAATCCTGAACTGATGAAAGCCACTTGGGTAGCTGTGCGATTTGAGGTCCCTTTGGGGCATGTGG RR: AGTAAAGTGGGCGTCAGTCCCTTAGGACTTGACTACTTTCGGTGAACCCATCGACACGCTAAACTCCAGGGAAACCCCGTACACC F2: 3 GAACCCAT 2 Unidirectional alignment (log-probability: -34.7) CATTTCACCCGCAGTCAGGGAATCCTGAACTGATGAAAGctacCCAagTGGGTAGCTGTGCGATTTGAGGTCCCTTTaGGGCATGTGG CATTTCACCCGCAGTCAGGGAATCCTGAACTGATGAAAG----CCACTTGGGTAGCTGTGCGATTTGAGGTCCCTTTGGGGCATGTGG Template switch alignment (log-probability: -22.3) CATTTCACCCGCAGTCAGGGAATCCTGAACTGATGAAAGC|TACCCAAG|TGGGTAGCTGTGCGATTTGAGGTCCCTTTaGGGCATGTGG CATTTCACCCGCAGTCAGGGAATCCTGAACTGATGAAAGC|TACCCAAG|TGGGTAGCTGTGCGATTTGAGGTCCCTTTGGGGCATGTGG ========== Event 1307 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ctcAAGTTCCCCCGAGCTGTC---TCCT-------------CTGGGACTATGCAGCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACACCGCTCTCAGTGAGTGTTCCAAAATGCAATCCAATCCTCTTTCTCTCC Chimp: ctcAAGTTCCCCCGAGCTGTC------T-------------CTGGGACTATGCAGCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACACCGCTCTCAGTGAGTGTTCCAAAATGCAATCCAATCCTCTTTCTCTCC Gorilla: ctcAAGTTCCCCCGAGCTGTC------T--------------------------CCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACACTGCTCTCAGTGAGTGTTCCAAAATGCAATCCAATCCTCTTTCTCTCC ↓ 4 1 3 2 Human: ctcAAGTTCCCCCGAGCTGTC---TCCT-------------CTGGGACTATGCAGCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACACCGCTCTCAGTGAGTGTTCCAAAATGCAATCCAATCCTCTTTCTCTCC Cluster: [ ] Orangutan: ctcAAGCTCCCCCGAGCTGTCTCC---TCTGGGACTATGCA-------------GCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACACCGCTCTCAGTGAGTGTTCCAAAAAGCAATCCAATCCTCTTTCTCTCC Gorilla > Human --------------- chr16:22019389-22019392 Template switch process: F1: L ATATCCAGTGAGTTACCAAACTCAAGTTCCCCCGAGCTGTCTCCTCTGGGACTA 1 F3: 4 GCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACA R RF: ATATCCAGTGAGTTACCAAACTCAAGTTCCCCCGAGCTGTCTCCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCACACTGCTCTCAGTGAGTGTTCCAAAATGCA RR: TATAGGTCACTCAATGGTTTGAGTTCAAGGGGGCTCGACAGAGGAGACCCTGATGTTATAGGGGTTTACGAGAGGAGAGGTGTGACGAGAGTCACTCACAAGGTTTTACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -33.9) ACCAAACTCAAGTTCCCCCGAGCTGTCTCctctgggactatgcagCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCAC ACCAAACTCAAGTTCCCCCGAGCTGTCTC----------------CTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCAC Template switch alignment (log-probability: -22.1) ACCAAACTCAAGTTCCCCCGAGCTGTCTCCTCTGGGACTA|TGCA|gCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCAC ACCAAACTCAAGTTCCCCCGAGCTGTCTCCTCTGGGACTA|TGCA|CCTCTGGGACTACAATATCCCCAAATGCTCTCCTCTCCAC ========== Event 1308 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GACTGACACTTGAGCTACCAGGGAGCCCTAGAGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAG ↑ 4 1 3 2 Chimp: GACTGACACTTGAGCTACCAGG------------GAGCCAAACTAGACCTTGGGTCAGGAAGACAG ↓ 4 1 3 2 Gorilla: GACTGACACTTGAGCTACCAGGGAGCCCTAGAGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAG Human: GACTGACACTTGAGCTACCAGGGAGCCCTAGAGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAG Cluster: [ ] Orangutan: GACTGACACTTGAGCTACCAGGGAGCCCTAGAGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAG Chimp > Human ------------- chr16:22254348-22254351 Template switch process: F1: L GCCGAGGTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCC 1 F3: 4 AGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAATGTC R RF: GCAGAGGTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAATGTC RR: CGTCTCCAGAGTTACAGACCTGACTGTGAACTCGATGGTCCCTCGGTTTGATCTGGAACCCAGTCCTTCTGTCCCTTACAG F2: 3 GATC 2 Unidirectional alignment (log-probability: -34.2) GTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAgccctagagggaGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT GTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGA------------GCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT Template switch alignment (log-probability: -21.9) GTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCC|CTAG|AGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT GTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCC|CTAG|AGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT Chimp > Gorilla --------------- chr16:22204763-22204766 Template switch process: F1: L GCAGAGGTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCC 1 F3: 4 AGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAATGTC R RF: GCAGAGGTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAATGTC RR: CGTCTCCAGAGTTACAGACCTGACTGTGAACTCGATGGTCCCTCGGTTTGATCTGGAACCCAGTCCTTCTGTCCCTTACAG F2: 3 GATC 2 Unidirectional alignment (log-probability: -28.1) GTCTCAATGTCTGGACTGACACTTGAGCTACCAgggagccctagaGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT GTCTCAATGTCTGGACTGACACTTGAGCTACCA------------GGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT Template switch alignment (log-probability: -16.4) GTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCC|CTAG|AGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT GTCTCAATGTCTGGACTGACACTTGAGCTACCAGGGAGCC|CTAG|AGGGAGCCAAACTAGACCTTGGGTCAGGAAGACAGGGAAT ========== Event 1309 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGCACACAGCTTTGTAGACTCATCTTCTGTCCTCAGAAGATGAGTGCTTTGCCTTAGTGCTAGAA ↑ 3 1 2 4 Chimp: CAGCACACAGCTTTGTAGACTCATCTTCT-------GAGGAACCCTGCTTTGCCTTAGTGCTAGAA Gorilla: CAGCACACAGCTTTGTAGACTCATCTTCT-------GAGGAACCCTGCTTTGCCTTAGTGCTAGAA ↓ 3 1 2 4 Human: CAGCACACAGCTTTGTAGACTCATCTTCTGTCCTCAGAAGATGAGTGCTTTGCCTTAGTGCTAGAA Cluster: [ ] Orangutan: CAGCACACAGCTTTGTGGATTCATCTTCT-------GAGGAACCCTGCTTTGCCTTAGTGCTAGAA Chimp > Human ------------- chr16:21665825-21665839 Template switch process: F1: L GCCCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTG 1 F3: 4 TGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT R RF: GCCCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTGAGGAACCCTGCTTTGCCTTAGTGCTAGAAGGACCAGGAATGATAATGT RR: CGGGAAATAACGGTCGTGTGTCGAAACATCTGAGTAGAAGACTCCTTGGGACGAAACGGAATCACGATCTTCCTGGTCCTTACTATTACA F2: 3 GAGTAGAAGACTCCT 2 Unidirectional alignment (log-probability: -46.2) CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCtgtcctcagaagaTGAG------TGCTTTGCCTTAGTGCTAGAAGGACCAGGAAcGATAATGT CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTC-------------TGAGGAACCCTGCTTTGCCTTAGTGCTAGAAGGACCAGGAATGATAATGT Template switch alignment (log-probability: -23.2) CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTG|TCCTCAGAAGATGAG|TGCTTTGCCTTAGTGCTAGAAGGACCAGGAAcGATAATGT CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTG|TCCTCAGAAGATGAG|TGCTTTGCCTTAGTGCTAGAAGGACCAGGAATGATAATGT Gorilla > Human --------------- chr16:21665825-21665839 Template switch process: F1: L GCCCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTG 1 F3: 4 TGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT R RF: GCCCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTGAGGAACCCTGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT RR: CGGGAAATAACGGTCGTGTGTCGAAACATCTGAGTAGAAGACTCCTTGGGACGAAACGGAATCACGATCTTCCTGGTCCTTGCTATTACA F2: 3 GAGTAGAAGACTCCT 2 Unidirectional alignment (log-probability: -39.7) CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCtgtcctcagaagaTGAG------TGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTC-------------TGAGGAACCCTGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT Template switch alignment (log-probability: -17.7) CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTG|TCCTCAGAAGATGAG|TGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT CCTTTATTGCCAGCACACAGCTTTGTAGACTCATCTTCTG|TCCTCAGAAGATGAG|TGCTTTGCCTTAGTGCTAGAAGGACCAGGAACGATAATGT ========== Event 1310 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGATAGCTGCAAGATAGCTGGTCTATCCAACAGG Chimp: AAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAGCTGCAAGATAGCTGGTCTATCCAACAGG ↑ 3 2 1 4 Gorilla: AAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAGT-C--CAATAGCTGGTCTATCCAACAGG ↓ 3 2 1 4 Human: AAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGATAGCTGCAAGATAGCTGGTCTATCCAACAGG Cluster: [ ] Orangutan: AAAGCATGAGCTGTGAAGCCTTGCAGCCGGAAGATAGT-C--CAATAGCTGGTCTATCCAACAGG Gorilla > Human --------------- chr16:68413361-68413367 Template switch process: F1: L ACATGGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGATAG 1 F3: 4 ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA R RF: ACATGGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAGTCCAATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA RR: TGTACCCTTTCGTACTCGACACTTCGGAACGTCGACCTTCTGTCAGGTTATCGACCAGATAGGTTGTCCTCCAGAGGTAGTACTCCTT F2: 3 GAACGTC 2 Unidirectional alignment (log-probability: -35.4) GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAG-------AtagctgcaagATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAGTCCA----------ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA Template switch alignment (log-probability: -22.2) GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGAtAG|CTGCAAG|ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAG|CTGCAAG|ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA Gorilla > Chimp --------------- chr16:59318767-59318773 Template switch process: F1: L TGGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAG 1 F3: 4 ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA R RF: TGGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAGTCCAATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA RR: ACCCTTTCGTACTCGACACTTCGGAACGTCGACCTTCTGTCAGGTTATCGACCAGATAGGTTGTCCTCCAGAGGTAGTACTCCTT F2: 3 GAACGTC 2 Unidirectional alignment (log-probability: -30.5) GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAGcTgCAagATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAG-TCCA--ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA Template switch alignment (log-probability: -16.6) GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAG|CTGCAAG|ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA GGGAAAGCATGAGCTGTGAAGCCTTGCAGCTGGAAGACAG|CTGCAAG|ATAGCTGGTCTATCCAACAGGAGGTCTCCATCATGAGGAA ========== Event 1311 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCTCCACTGCCCTTTCCTCTGGCTCATGTGCTTGCTGACACTGCTCTTCCCGGCAGCAGGGCTGGGAGTCCCAGAGCAGAGA--------------------GGCCTCCTCTGAGTCCCTGCCGTGTCCACAAGCTCATGTCTAAACAGGAGCTAT Chimp: CCCTCCACTGCCCTTTCCTCTGGCTCATGTGCTTGCTGACACTGCTCTTCCCGGCAGCAGGGC--------------------TGGGAGTCCCAGAGCAGAGAGGCCTCCTCTGAGTCCCTGTTGTGTCCACAAGCTCATGTCTAAACAGGAGCTAC ↓ 1 4 3 2 Gorilla: CCCTCCACTGCCCTTTCCTCTAGCTTGTGTGCTTGCTGACATTGCTCTTCCCGGCAGCAGGGCTGGGAGTCCCAGAGCAGAGA--------------------GGCCTCCTCTGAGTCCCTGTTGTGTCCACAAGCTCATGTCTAAACAGGAGCTAC Human: CCCTCCACTGCCCTTTCCTCTGGCTCATGTGCTTGCTGACACTGCTCTTCCCGGCAGCAGGGCTGGGAGTCCCAGAGCAGAGA--------------------GGCCTCCTCTGAGTCCCTGCCGTGTCCACAAGCTCATGTCTAAACAGGAGCTAT Cluster: [ ] Orangutan: CCCTCCACTGCCCTTTCCTCTGGCTCATGTGTTTGCTGACACTGCTCTTCTCAGCAGCAGGGCTGGGAGTCCCAGAGCAGAGA--------------------GGCCTCCTCTGAGTCCCTGTTGTGTCCACAAGCTCATGTCTAAACAGGAGCTAC Chimp > Gorilla --------------- chrCABD030161758:7826-7832 Template switch process: F1: L GCCAGGATGAAGCCTGTCTCCCCTCCACTGCCCTTTCCTCT 1 F3: 4 GTGCTTGCTGACATTGCTCTTCCCGGCAGCAGGGCTGGG R RF: GCTAGGATGAGGCCTGTCTCCCCTCCACTGCCCTTTCCTCTGGCTCATGTGCTTGCTGACACTGCTCTTCCCGGCAGCAGGGCTGGGAGTCCCAGAGCAGAGAGGCCTCCTCTGAGTCCCTGTTGTGTCCACAAGCT RR: CGATCCTACTCCGGACAGAGGGGAGGTGACGGGAAAGGAGACCGAGTACACGAACGACTGTGACGAGAAGGGCCGTCGTCCCGACCCTCAGGGTCTCGTCTCTCCGGAGGAGACTCAGGGACAACACAGGTGTTCGA F2: 3 TGTTCGA 2 Unidirectional alignment (log-probability: -46.8) CcAGGATGAaGCCTGTCTCCCCTCCACTGCCCTTTCCTCTaGCTtgTGTGCTTGCTGACAtTGCTCTTCCCGGCAGCAGGGCtggg CTAGGATGAGGCCTGTCTCCCCTCCACTGCCCTTTCCTCTGGCTCATGTGCTTGCTGACACTGCTCTTCCCGGCAGCAGGGC---- Template switch alignment (log-probability: -33.1) CcAGGATGAaGCCTGTCTCCCCTCCACTGCCCTTTCCTCT|AGCTTGT|GTGCTTGCTGACAtTGCTCTTCCCGGCAGCAGGGCTGGG CTAGGATGAGGCCTGTCTCCCCTCCACTGCCCTTTCCTCT|AGCTTGT|GTGCTTGCTGACACTGCTCTTCCCGGCAGCAGGGCTGGG ========== Event 1312 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AACACAGGCATAGAACCTTCATTGAATTGCCTTCAGGGAAGGCAATTCAGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAAT Chimp: AACACAGGCATAGAACCTTCA--------------------------TAGAGAATTGCCTTCCCTGAGAGGTGGGTCTAGGAAAT Gorilla: AACACAGGCATAGAACCTTCA--------------------------TAGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAAT ↓ 4 3 1 2 Human: AACACAGGCATAGAACCTTCATTGAATTGCCTTCAGGGAAGGCAATTCAGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAAT Cluster: [ ] Orangutan: AACACAGGCATAGAACCTTCA--------------------------TGGAGAATTGCCTT-CCTGAGAGGTGGGTTTAGGAAAT Gorilla > Human --------------- chr16:69134498-69134511 Template switch process: F1: L AAATAAATATGATAAACCGAAACACAGGCATAGAACCTTCAT--TGAATTGCCTTC 1 F3: 4 AGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAATGTG R RF: AAATAAATATGATAAACCGAAACACAGGCATAGAACCTTCATAGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAATGTG RR: TTTATTTATACTATTTGGCTTTGTGTCCGTATCTTGGAAGTATCTCTTAACGGAAGGGACTCTCCACCCAAATCCTTTACAC F2: 3 CTTAACGGAAGGGA 2 Unidirectional alignment (log-probability: -48.3) AACCGAAACACAGGCATAGAACCTTCATtgaattgccttcagggaaggcaattcAGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAATGTG AACCGAAACACAGGCATAGAACCTTCAT--------------------------AGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAATGTG Template switch alignment (log-probability: -33.2) AACCGAAACACAGGCATAGAACCTTCAT--tGAATTGCCTTC|AGGGAAGGCAATTC|AGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAATGTG AACCGAAACACAGGCATAGAACCTTCATAGAGAATTGCCTTC|AGGGAAGGCAATTC|AGAGAATTGCCTTCCCTGAGAGGTGGGTTTAGGAAATGTG ========== Event 1313 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCTGTTTCGTTTTCTCTTCCCTGTCACAAACGAAAGGACAGAGACTGAAGAAGTGTATGTGACATG Chimp: CCTCTGTTTCGTTTTCTCTTCCCTGTCACAAACGAAAGGACAGAGACTGAAGAAGTGTATGTGACATG Gorilla: CCTCTGTTTCGTTTTCTCTTCAGTCT---------CAGGACAGAGACTGAAGAAGTGTGTGTGACAGG ↑ 1 4 3 2 Human: CCTCTGTTTCGTTTTCTCTTCCCTGTCACAAACGAAAGGACAGAGACTGAAGAAGTGTATGTGACATG Cluster: [ ] Orangutan: CCT--CTTTCATTCTCTCTTCTCTGTCACAAACAAAAGGACAGAGACTGAAGAAGTGTATGTGACATG Human > Gorilla --------------- chr16:19285778-19285783 Template switch process: F1: L AAGGAAAAAATTTTATTCTACCTCTGTTTCGTTTTCTCTTC 1 F3: 4 AGGACAGAGACTGAAGAAGTGTGTGTGACAGGATAAAACT R RF: AAGGAAAAAATTTTATTCTACCTCTGTTTCGTTTTCTCTTCCCTGTCACAAACGAAAGGACAGAGACTGAAGAAGTGTATGTGACATGATAAAACT RR: TTCCTTTTTTAAAATAAGATGGAGACAAAGCAAAAGAGAAGGGACAGTGTTTGCTTTCCTGTCTCTGACTTCTTCACATACACTGTACTATTTTGA F2: 3 CTCTGA 2 Unidirectional alignment (log-probability: -39) AGGAAAAAATTTTATTCTACCTCTGTTTCGTTTTCTCTTCagTcTC---------AGGACAGAGACTGAAGAAGTGTgTGTGACAgGATAAAACT AGGAAAAAATTTTATTCTACCTCTGTTTCGTTTTCTCTTCCCTGTCACAAACGAAAGGACAGAGACTGAAGAAGTGTATGTGACATGATAAAACT Template switch alignment (log-probability: -27.5) AGGAAAAAATTTTATTCTACCTCTGTTTCGTTTTCTCTTC|AGTCTC|AGGACAGAGACTGAAGAAGTGTgTGTGACAgGATAAAACT AGGAAAAAATTTTATTCTACCTCTGTTTCGTTTTCTCTTC|AGTCTC|AGGACAGAGACTGAAGAAGTGTATGTGACATGATAAAACT ========== Event 1314 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 14 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATCAGTCTCTATGCTTCACTCTATACTACAGAGTGTAGTACTATCACATATCTACATTTCTG ↑ 3 4 1 2 Chimp: ATCAGTCTCTATGCTTCACTCC---------TCTGTAGTACTATCACATATCTACATTTCTG Gorilla: ATCAGTCTCTATGCTTCACTCC---------TCTGTAGTATTATCACATATCTACATTTCTG ↑ 1 3 2 4 Human: ATCAGTCTCTATGCTTCACTCTATACTACAGAGTGTAGTACTATCACATATCTACATTTCTG Cluster: [ ] Orangutan: ATCAGTCTCTATGTTTCATTCC---------TCTGTAGTATTATCACATATCTACATTTCTG Chimp > Human ------------- chr16:72575992-72576001 Template switch process: F1: L ACCTTACAATGGATTACATTATCAGTCTCTATGCTTCACTC-----TA 1 F3: 4 TGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTG R RF: ACCTTACAATGGATTACATTATCAGTCTCTATGCTTCACTCCTCTGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTG RR: TGGAATGTTACCTAATGTAATAGTCAGAGATACGAAGTGAGGAGACATCATGATAGTGTATAGATGTAAAGACCACAGTACCAC F2: 3 GAGACATCAT 2 Unidirectional alignment (log-probability: -38.5) TTACAATGGATTACATTATCAGTCTCTATGCTTCA---CTCtatactacagagTGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTG TTACAATGGATTACATTATCAGTCTCTATGCTTCACTCCTC------------TGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTG Template switch alignment (log-probability: -27) TTACAATGGATTACATTATCAGTCTCTATGCTTCACTC-----TA|TACTACAGAG|TGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTG TTACAATGGATTACATTATCAGTCTCTATGCTTCACTCCTCTGTA|TACTACAGAG|TGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTG Human > Gorilla --------------- chr16:63688879-63688889 Template switch process: F1: L ACCTTACACTGGATTACATTATCAGTCTCTATGCTTCACTC 1 F3: 4 TATCACATATCTACATTTCTGGTGTCATGGTGGCCAAATG R RF: ACCTTACAATGGATTACATTATCAGTCTCTATGCTTCACTCTATACTACAGAGTGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTGGCCAAATG RR: TGGAATGTTACCTAATGTAATAGTCAGAGATACGAAGTGAGATATGATGTCTCACATCATGATAGTGTATAGATGTAAAGACCACAGTACCACCGGTTTAC F2: 3 TATGATGTCTC 2 Unidirectional alignment (log-probability: -36.7) CCTTACAcTGGATTACATTATCAGTCTCTATGCTTCACTC------------ctcTGTAGTAtTATCACATATCTACATTTCTGGTGTCATGGTGGCCAAATG CCTTACAATGGATTACATTATCAGTCTCTATGCTTCACTCTATACTACAGAG---TGTAGTACTATCACATATCTACATTTCTGGTGTCATGGTGGCCAAATG Template switch alignment (log-probability: -22.6) CCTTACAcTGGATTACATTATCAGTCTCTATGCTTCACTC|CTCTGTAGTAT|TATCACATATCTACATTTCTGGTGTCATGGTGGCCAAATG CCTTACAATGGATTACATTATCAGTCTCTATGCTTCACTC|CTCTGTAGTAT|TATCACATATCTACATTTCTGGTGTCATGGTGGCCAAATG ========== Event 1315 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTGGTGTCTGGGTACAAGATA--------TTACTTATCGATATGATTTATGTATGTGGAGATTAAACTATTTCACACT ↓ 1 3 4 ↑ 13 24 Chimp: GTGGTGTCTGGGTACAAGATA----CATAAATCATATCGATAAG----TAGTATGTGCAGATTAAACTATTTCACACT Gorilla: GTGGTGTCTGGGTACAAGATACATA----AATCATATCTATAAA----TAGTATGTGGAGATTAAACTATTTCACACT Human: GTGGTGTCTGGGTACAAGATA--------TTACTTATCGATATGATTTATGTATGTGGAGATTAAACTATTTCACACT Cluster: [ ] Orangutan: Chimp > Human ------------- chr16:83031469-83031488 Template switch process: F1: L GGCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATAT 1 F3: 4 GTATGTGGAGATTAAACTATTTCACACTCTTAATCAGCCGATTGTCTG R RF: GGCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATACATAAATCATATCGATAAGTAGTATGTGCAGATTAAACTATTTCACACTCTTAATCAGCCGATTGTCTG RR: CCGTCTATTTTTTATATCATCACCACAGACCCATGTTCTATGTATTTAGTATAGCTATTCATCATACACGTCTAATTTGATAAAGTGTGAGAATTAGTCGGCTAACAGAC F2: 3 TATTTAGTATAGCTATTCAT 2 Unidirectional alignment (log-probability: -58.5) CAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGA---------------------TAttacttatcgatatgatttatGTATGTGgAGATTAAACTATTTCACACTCTTAATCAGCCG CAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATACATAAATCATATCGATAAGTA---------------------GTATGTGCAGATTAAACTATTTCACACTCTTAATCAGCCG Template switch alignment (log-probability: -29.9) CAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATAt|TACTTATCGATATGATTTAT|GTATGTGgAGATTAAACTATTTCACACTCTTAATCAGCCG CAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATAC|TACTTATCGATATGATTTAT|GTATGTGCAGATTAAACTATTTCACACTCTTAATCAGCCG Human > Chimp ------------- chr16:73915479-73915499 Template switch process: F1: L GGCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATA 1 F3: 4 GTATGTGCAGATTAAACTATTTCACACTCTTAATCAGCCGATTGTCTG R RF: GGCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATATTACTTATCGATATGATTTATGTATGTGGAGATTAAACTATTTCACACTCTTAATCAGCCGATTGTCTG RR: CCGTCTATTTTTTATATCATCACCACAGACCCATGTTCTATAATGAATAGCTATACTAAATACATACACCTCTAATTTGATAAAGTGTGAGAATTAGTCGGCTAACAGAC F2: 3 ATGAATAGCTATACTAAATAC 2 Unidirectional alignment (log-probability: -58.5) GCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATA---------------------cataaatcatatcgataagtaGTATGTGcAGATTAAACTATTTCACACTCTTAATCAGCCG GCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATATTACTTATCGATATGATTTAT---------------------GTATGTGGAGATTAAACTATTTCACACTCTTAATCAGCCG Template switch alignment (log-probability: -24) GCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATA|CATAAATCATATCGATAAGTA|GTATGTGcAGATTAAACTATTTCACACTCTTAATCAGCCG GCAGATAAAAAATATAGTAGTGGTGTCTGGGTACAAGATA|CATAAATCATATCGATAAGTA|GTATGTGGAGATTAAACTATTTCACACTCTTAATCAGCCG ========== Event 1316 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GACTTCCTCAGCACAACGGCTGTGATTCCTCACAGCCAGCAGCGGTCAGTGGGGGC Chimp: GACTTCCTCAGCACAGTGGCTGTGAG----GAAGCCCAGCAGTGGTCAGTGGGGGC Gorilla: GACTTCCTCAGCACAGCGGCTGTGAG----GAAGCCCAGCAGCGGTCAGTGGGGGC ↓ 3 1 2 4 Human: GACTTCCTCAGCACAACGGCTGTGATTCCTCACAGCCAGCAGCGGTCAGTGGGGGC Cluster: [ ] Orangutan: GACTTCCTCAGCACAGAGGCTGTGAG----GAAGCCCAGCAGCGGTCAGTGGGGGC Gorilla > Human --------------- chr16:74735249-74735258 Template switch process: F1: L GGGATCCCATGGCTGTGACTTCCTCAGCACAACGGCTGTGA 1 F3: 4 CCAGCAGCGGTCAGTGGGGGCAGTGAGGTGGGGCTCTTGG R RF: GGGATCCCATGGCTGTGACTTCCTCAGCACAGCGGCTGTGAGGAAGCCCAGCAGCGGTCAGTGGGGGCAGTGAGGTGGGGCTCTTGG RR: CCCTAGGGTACCGACACTGAAGGAGTCGTGTCGCCGACACTCCTTCGGGTCGTCGCCAGTCACCCCCGTCACTCCACCCCGAGAACC F2: 3 GACACTCCTT 2 Unidirectional alignment (log-probability: -39.4) GGATCCCATGGCTGTGACTTCCTCAGCACAaCGGCTGTGattcctcacAG-----CCAGCAGCGGTCAGTGGGGGCAGTGAGGTGGGGCTCTTGG GGATCCCATGGCTGTGACTTCCTCAGCACAGCGGCTGTG---------AGGAAGCCCAGCAGCGGTCAGTGGGGGCAGTGAGGTGGGGCTCTTGG Template switch alignment (log-probability: -22.5) GGATCCCATGGCTGTGACTTCCTCAGCACAaCGGCTGTGA|TTCCTCACAG|CCAGCAGCGGTCAGTGGGGGCAGTGAGGTGGGGCTCTTGG GGATCCCATGGCTGTGACTTCCTCAGCACAGCGGCTGTGA|TTCCTCACAG|CCAGCAGCGGTCAGTGGGGGCAGTGAGGTGGGGCTCTTGG ========== Event 1317 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGAAGAGGCATCAGACGCAGCTGCCCCCTGCTGTAGGGCACTGGGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGCAGCTGGGTGCAGTGGCTCAGAAGAA Chimp: GGGAAGAGGCATCAGACACAGCTGCCCCCTGCTGTGGGGCACTGGGTTTCCATGCGGAGCCCCTGAGAAAATATAGTACTCAGCAGCCGGGTGCAGTGGCTCAGAAGAA Gorilla: gggaagaggcatcagacgcagctacccccTGCTGTGGGGCACTGGGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTC---AGCCGGGTGCAGTGGCTCAGAAGAA ↓ 3 2 1 4 Human: GGGAAGAGGCATCAGACGCAGCTGCCCCCTGCTGTAGGGCACTGGGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGCAGCTGGGTGCAGTGGCTCAGAAGAA Cluster: [ ] Orangutan: GGGAAGAGGCATCAGAGACAGCTGCCCCCTGCTGTGGGGCACTGGGTTTCCACGTGGAGCCCCTGAGAAAATACAGTACTC---AGCCGGGTGCAGTGGCTCAGAAGAA Gorilla > Human --------------- chr16:15463398-15463401 Template switch process: F1: L ACTGGGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGC 1 F3: 4 GGGTGCAGTGGCTCAGAAGAAGGAGTTCTGGTGTAAAA R RF: AGCTACCCCCTGCTGTGGGGCACTGGGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGCCGGGTGCAGTGGCTCAGAAGAAGGAGTTCTGGTGTAAAA RR: TCGATGGGGGACGACACCCCGTGACCCAAAGGTACGCCTCGGGGACTCTTTTATGTCATGAGTCGGCCCACGTCACCGAGTCTTCTTCCTCAAGACCACATTTT F2: 3 TCGA 2 Unidirectional alignment (log-probability: -27.6) GGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGCagctGGGTGCAGTGGCTCAGAAGAAGGAGTTCTGGTGTAAAA-- GGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGC---CGGGTGCAGTGGCTCAGAAGAAGGAGTTCTGGTGTAAAACA Template switch alignment (log-probability: -16.3) GGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGC|AGCT|GGGTGCAGTGGCTCAGAAGAAGGAGTTCTGGTGTAAAA GGTTTCCATGCGGAGCCCCTGAGAAAATACAGTACTCAGC|AGCT|GGGTGCAGTGGCTCAGAAGAAGGAGTTCTGGTGTAAAA ========== Event 1318 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTGCCTAGACTATCATATATCCGTGCAGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTTCAGAGCATCTCTGCACAGTAGGAAAAAGGAGACAATT ↑ 1 4 3 2 Chimp: TTGCCTGGACTATCATATATCCA---CGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTGCAGAGCATCTCTGCACAGTAGGA-AAAGGAGACAATT ↓ 1 4 3 2 Gorilla: TTGCCTGGACTATCATATATCTGTGCAGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTGCAGAGCATCTCTGCACAGTAGGA-AAAGGAGACAATT Human: TTGCCTAGACTATCATATATCCGTGCAGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTTCAGAGCATCTCTGCACAGTAGGAAAAAGGAGACAATT Cluster: [ ] Orangutan: TTGCCTGGACTATCATATATCCGTGCAGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTGCAGAGCATCTCTGCACAGTAGGA-AAAGGAGACAATT Chimp > Human ------------- chr16:14629125-14629129 Template switch process: F1: L TACATAAGGAAGTAAAGAATTGCCTAGACTATCATATATCC 1 F3: 4 GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT R RF: TACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATCCACGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTGCAGAGCATCTCTGCAC RR: ATGTATTCCTTCATTTCTTAACGGACCTGATAGTATATAGGTGCTTGTACTACGTAGTTTTCCTTGTTCTCGTGTAATATTTAACCCACCTCTTCGTACACCACGTCTCGTAGAGACGTG F2: 3 ACGTG 2 Unidirectional alignment (log-probability: -32.9) ACATAAGGAAGTAAAGAATTGCCTaGACTATCATATATCcgtgCA-GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT ACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATC----CACGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT Template switch alignment (log-probability: -21.9) ACATAAGGAAGTAAAGAATTGCCTaGACTATCATATATCC|GTGCA|GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT ACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATCC|GTGCA|GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT Chimp > Gorilla --------------- chr16:14536669-14536674 Template switch process: F1: L GTACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATC 1 F3: 4 GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT R RF: CTACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATCCACGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAATTGGGTGGAGAAGCATGTGGTGCAGAGCATCTCTGCACA RR: GATGTATTCCTTCATTTCTTAACGGACCTGATAGTATATAGGTGCTTGTACTACGTAGTTTTCCTTGTTCTCGTGTAATATTTAACCCACCTCTTCGTACACCACGTCTCGTAGAGACGTGT F2: 3 ACGTGT 2 Unidirectional alignment (log-probability: -32) TACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATCtgtgCA-GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT TACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATC----CACGAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT Template switch alignment (log-probability: -22) TACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATC|TGTGCA|GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT TACATAAGGAAGTAAAGAATTGCCTGGACTATCATATATC|TGTGCA|GAACATGATGCATCAAAAGGAACAAGAGCACATTATAAAT ========== Event 1319 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTGTTAGTGAAGATCACTCAGAAA-TTATA---------GTATTTACAGTGATTCTCTGC Chimp: GTTGTTAGTGAAGATCACTCAGAAA-TTATA---------GTATTTACAGTGATTCTCTGC ↓ 3 1 4 2 Gorilla: GTTGTTAGTGAAGATCACTCAGAAATCTATAATTTCTGATATATTTACAGTGATTCTCTGC ↑ 3 1 4 2 Human: GTTGTTAGTGAAGATCACTCAGAAA-TTATA---------GTATTTACAGTGATTCTCTGC Cluster: [ ] Orangutan: GTTGTTAGTGAAGATCACTCAGAAA-TTATA---------GTATTTACAGTGATTCTCTGC Human > Gorilla --------------- chr1:160329907-160329918 Template switch process: F1: L TCACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT 1 F3: 4 ATA-TATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTCTCA R RF: TCACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAATTATAGTATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTCTCA RR: AGTGTCCTCGAAGTGACAACAATCACTTCTAGTGAGTCTTTAATATCATAAATGTCACTAAGAGACGGGGAAAATTAACTTAAGAGT F2: 3 GTCTTTAATATC 2 Unidirectional alignment (log-probability: -39.5) ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAATctataatttctgaTA---TATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT-------------TATAGTATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC Template switch alignment (log-probability: -27.1) ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT|CTATAATTTCTG|ATA-TATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT|CTATAATTTCTG|ATAGTATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC Chimp > Gorilla --------------- chr1:160329907-160329918 Template switch process: F1: L TCACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT 1 F3: 4 ATA-TATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTCTCA R RF: TCACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAATTATAGTATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTCTCA RR: AGTGTCCTCGAAGTGACAACAATCACTTCTAGTGAGTCTTTAATATCATAAATGTCACTAAGAGACGGGGAAAATTAACTTAAGAGT F2: 3 GTCTTTAATATC 2 Unidirectional alignment (log-probability: -39.5) ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAATctataatttctgaTA---TATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT-------------TATAGTATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC Template switch alignment (log-probability: -27.1) ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT|CTATAATTTCTG|ATA-TATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC ACAGGAGCTTCACTGTTGTTAGTGAAGATCACTCAGAAAT|CTATAATTTCTG|ATAGTATTTACAGTGATTCTCTGCCCCTTTTAATTGAATTC ========== Event 1320 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTGAAGCCCAAAGGATGAGA---ATAATTAGCTAATTTAATCACTTA--GTATATAGT Chimp: TGTGAAGCTCAAAGGATGAGA---ATAATTAGCTAA-TTAATCACTTA--GTATATAGT Gorilla: TGTGAAGCCCAAAGGATGAGA------ATTAGCTAA-TTAATCACTTA--GTATATAGT ↓ 31 42 Human: TGTGAAGCCCAAAGGATGAGA---ATAATTAGCTAATTTAATCACTTA--GTATATAGT Cluster: [ ] Orangutan: TGTGAAGCCCAAAGGATGAGAATA---ATTAGCTAA-TTAATCACTTAGTGTATATAGT Gorilla > Human --------------- chr16:76802902-76802912 Template switch process: F1: L TGCCCTTTCTGCTTTAAAAGTGTGAAGCCCAAAGGATGAGAAT 1 F3: 4 TTAATCACTTAGTATATAGTAAACTACATATGGGAAACAA R RF: TGCCCTTTCTGCTTTAAAAGTGTGAAGCCCAAAGGATGAGAATTAGCTAATTAATCACTTAGTATATAGTAAACTACATATGGGAAACAA RR: ACGGGAAAGACGAAATTTTCACACTTCGGGTTTCCTACTCTTAATCGATTAATTAGTGAATCATATATCATTTGATGTATACCCTTTGTT F2: 3 TAATCGATTAA 2 Unidirectional alignment (log-probability: -26.5) CCTTTCTGCTTTAAAAGTGTGAAGCCCAAAGGATGAGaatAATTAGCTAAtTTAATCACTTAGTATATAGTAAACTACATATGGGAAACAA CCTTTCTGCTTTAAAAGTGTGAAGCCCAAAGGATGAG---AATTAGCTAA-TTAATCACTTAGTATATAGTAAACTACATATGGGAAACAA Template switch alignment (log-probability: -17.2) CCTTTCTGCTTTAAAAGTGTGAAGCCCAAAGGATGAGAAT|AATTAGCTAAT|TTAATCACTTAGTATATAGTAAACTACATATGGGAAACAA CCTTTCTGCTTTAAAAGTGTGAAGCCCAAAGGATGAGAAT|AATTAGCTAAT|TTAATCACTTAGTATATAGTAAACTACATATGGGAAACAA ========== Event 1321 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTAAGTAAAAACTCATGTTTTCTGGAAAATAAACCAAAAGGGCGTAAAGAATATATAA Chimp: TTAAGTAAAAACTCATGTTTTCTGGAAAATAAACCAAAAGGGCCTAAAGAATATATAA ↓ 13 24 ↑ 13 24 Gorilla: TTAAGTAAAAACTCATGTTTTTTGGTTTATTTTCCAGAAGGGCCTAAAGAATATATAA Human: TTAAGTAAAAACTCATGTTTTCTGGAAAATAAACCAAAAGGGCGTAAAGAATATATAA Cluster: [ ] Orangutan: TTAAGTAAAAACTCACGTTTTCTGGAAAATAAACCAAAAGGGTCTAAAGAATATATAA Gorilla > Chimp --------------- chr16:67829553-67829568 Template switch process: F1: L AAAGAAGGGAAATGAGGAATTTAAGTAAAAACTCATGTTTT 1 F3: 4 AAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT R RF: AAAGAAGGCAAATGAGGAATTTAAGTAAAAACTCATGTTTTTTGGTTTATTTTCCAGAAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT RR: TTTCTTCCGTTTACTCCTTAAATTCATTTTTGAGTACAAAAAACCAAATAAAAGGTCTTCCCGGATTTCTTATATATTTTTCTATTCACTACAATAA F2: 3 AACCAAATAAAAGGTC 2 Unidirectional alignment (log-probability: -49.2) AAGAAGGgAAATGAGGAATTTAAGTAAAAACTCATGTTTTcTGGaaaataaa--------CCAaAAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT AAGAAGGCAAATGAGGAATTTAAGTAAAAACTCATGTTTTTTGG--------TTTATTTTCCAGAAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT Template switch alignment (log-probability: -23.3) AAGAAGGgAAATGAGGAATTTAAGTAAAAACTCATGTTTT|CTGGAAAATAAACCAA|AAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT AAGAAGGCAAATGAGGAATTTAAGTAAAAACTCATGTTTT|CTGGAAAATAAACCAA|AAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT Chimp > Gorilla --------------- chr16:67949394-67949409 Template switch process: F1: L AAAGAAGGCAAATGAGGAATTTAAGTAAAAACTCATGTTTT 1 F3: 4 AAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT R RF: AAAGAAGGGAAATGAGGAATTTAAGTAAAAACTCATGTTTTCTGGAAAATAAACCAAAAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT RR: TTTCTTCCCTTTACTCCTTAAATTCATTTTTGAGTACAAAAGACCTTTTATTTGGTTTTCCCGGATTTCTTATATATTTTTCTATTCACTACAATAA F2: 3 GACCTTTTATTTGGTT 2 Unidirectional alignment (log-probability: -49.2) AAGAAGGcAAATGAGGAATTTAAGTAAAAACTCATGTTTTtTGGtttatttt--------CCAgAAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT AAGAAGGGAAATGAGGAATTTAAGTAAAAACTCATGTTTTCTGG--------AAAATAAACCAAAAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT Template switch alignment (log-probability: -23.3) AAGAAGGcAAATGAGGAATTTAAGTAAAAACTCATGTTTT|TTGGTTTATTTTCCAG|AAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT AAGAAGGGAAATGAGGAATTTAAGTAAAAACTCATGTTTT|TTGGTTTATTTTCCAG|AAGGGCCTAAAGAATATATAAAAAGATAAGTGATGTTATT ========== Event 1322 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CCAATGTATCTGGCATTAACTGTTACC----AGTTAATCAATCCAGTTGGCCAAGTA ↓ 3 2 1 4 Chimp: CCAATGTATCTGGCATTAACTGTTACC--ATAACAGATCAATCCAGTTGGCCAAGTA Gorilla: CCAATGTATCTGGCATTAACTGTTACCAT--AACAGATCAATCCAGTTGGCCAAGTA ↑ 3 2 1 4 Human: CCAATGTATCTGGCATTAACTGTTACC----AGTTAATCAATCCAGTTGGCCAAGTA Cluster: [ ] Orangutan: Human > Chimp ------------- chr1:160893872-160893877 Template switch process: F1: L TAATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA 1 F3: 4 ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT R RF: TAATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCAGTTAATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT RR: ATTATAAATATAAAGGTTACATAGACCGTAATTGACAATGGTCAATTAGTTAGGTCAACCGGTTCATGAAATGTTACCAGATAACA F2: 3 GACAAT 2 Unidirectional alignment (log-probability: -27) ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA--TAacagATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCAGTTA----ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT Template switch alignment (log-probability: -16) ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA|TAACAG|ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA|TAACAG|ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT Human > Gorilla --------------- chr1:160401687-160401692 Template switch process: F1: L TAATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA 1 F3: 4 ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT R RF: TAATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCAGTTAATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT RR: ATTATAAATATAAAGGTTACATAGACCGTAATTGACAATGGTCAATTAGTTAGGTCAACCGGTTCATGAAATGTTACCAGATAACA F2: 3 GACAAT 2 Unidirectional alignment (log-probability: -26.5) ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA--TAacagATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCAGTTA----ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT Template switch alignment (log-probability: -16.5) ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA|TAACAG|ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT ATATTTATATTTCCAATGTATCTGGCATTAACTGTTACCA|TAACAG|ATCAATCCAGTTGGCCAAGTACTTTACAATGGTCTATTGT ========== Event 1323 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTATGTTGTTGTTTCCCTACCCTA---GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTAAGAGACTCTActactacttgctagtattagggttctagaaagttgcttaatcaccctga Chimp: TTTATGTTGCTGTTCCCCTACCCTG---GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTAAGAGACTCTActactacttgctagtattagggttctagaaagttgcttaatcacaatga ↓ 1 4 3 2 Gorilla: TTTATGTTGTTGTTCCCCTACTCTAGAAGAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTAAGAGACTCTActactacttgctagtattagggttctagaaagttgcttaatcacactga Human: TTTATGTTGTTGTTTCCCTACCCTA---GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTAAGAGACTCTActactacttgctagtattagggttctagaaagttgcttaatcaccctga Cluster: [ ] Orangutan: TTTATGTTGTTGTTCCCCTACCCTAGAAGAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTAAGAGACTCTActactacttgctagtattagggttctagaaagttgcttaatcacactgt Chimp > Gorilla --------------- chr16:68576564-68576570 Template switch process: F1: L GAGGAGTTCTGACTTAAGTTTTTATGTTGTTGTTCCCCTAC 1 F3: 4 GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTA R RF: GAGGAGTTCTGACTTAAGTTTTTATGTTGCTGTTCCCCTACCCTGGAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTAAGAGACTCTACTACTACTTGCTAGTATTAGGGTTCTAGA RR: CTCCTCAAGACTGAATTCAAAAATACAACGACAAGGGGATGGGACCTTCTATTTTGATTCACTACAGAAAACAAAGAAAAGTAATTCTCTGAGATGATGATGAACGATCATAATCCCAAGATCT F2: 3 AAGATCT 2 Unidirectional alignment (log-probability: -31.8) AGGAGTTCTGACTTAAGTTTTTATGTTGtTGTTCCCCTACtCTagaaGAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTA AGGAGTTCTGACTTAAGTTTTTATGTTGCTGTTCCCCTACCCTG---GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTA Template switch alignment (log-probability: -22.1) AGGAGTTCTGACTTAAGTTTTTATGTTGtTGTTCCCCTAC|TCTAGAA|GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTA AGGAGTTCTGACTTAAGTTTTTATGTTGCTGTTCCCCTAC|TCTAGAA|GAAGATAAAACTAAGTGATGTCTTTTGTTTCTTTTCATTA ========== Event 1324 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATTCTTCATACCAAACATGTAACACT----AAAAGTAAGTGCAATTCTAAAAGAAATaca Chimp: ATATTCTTCATACCAAACATGTAACACT----AAAAGTAagtgcaattctaaaagaaataca Gorilla: ATATTCTTCATACCAAACATGTAACACTTTTTAGTATGACATGCAATTCTAAAAGAAATACA ↑ 3 1 2 4 Human: ATATTCTTCATACCAAACATGTAACACT----AAAAGTAAGTGCAATTCTAAAAGAAATaca Cluster: [ ] Orangutan: ATGTTCTTCATACCAAACATGTAACACT----AA----AAGTGCAATTCTAAAAGAAATaca Human > Gorilla --------------- chr16:13745425-13745437 Template switch process: F1: L AGTAAGAGAGACAATATTCTTCATACCAAACATGTAACACT 1 F3: 4 TGCAATTCTAAAAGAAATACACGCACACACACAC R RF: AGTAAGAGAGACAATATTCTTCATACCAAACATGTAACACTAAAAGTAAGTGCAATTCTAAAAGAAATACACGCACACACACAC RR: TCATTCTCTCTGTTATAAGAAGTATGGTTTGTACATTGTGATTTTCATTCACGTTAAGATTTTCTTTATGTGCGTGTGTGTGTG F2: 3 ACAGTATGATTTT 2 Unidirectional alignment (log-probability: -45.3) GTAAGAGAGACAATATTCTTCATACCAAACATGTAACACTttttagtatgacA--------TGCAATTCTAAAAGAAATACACGCACACACACAC------ GTAAGAGAGACAATATTCTTCATACCAAACATGTAACACT------------AAAAGTAAGTGCAATTCTAAAAGAAATACACGCACACACACACACACAC Template switch alignment (log-probability: -28.3) GTAAGAGAGACAATATTCTTCATACCAAACATGTAACACT|TTTTAGTaTgACA|TGCAATTCTAAAAGAAATACACGCACACACACAC GTAAGAGAGACAATATTCTTCATACCAAACATGTAACACT|TTTTAGTGTTACA|TGCAATTCTAAAAGAAATACACGCACACACACAC ========== Event 1325 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GAGAAGAAGAAAAAAATTGTTAGAAAATTCAAGCCACAGT----------GA----------AAAACAATGTTTATGtattattt ↓ 13 24 ↑ 13 24 Chimp: GAGAAGAAGaaaaaaaTTGTT-----TT-----TCACTGT-----GGCTTGA-----ATTTTCTAACAATGtttatgtattattt Gorilla: GAGAAGAAGaaaaaaaTTGTT-----TT-----TCACTGTGGCTT-----GAATTTT-----CTAACAATGtttatgtattattt ↓ 13 24 ↑ 13 24 Human: GAGAAGAAGAAAAAAATTGTTAGAAAATTCAAGCCACAGT----------GA----------AAAACAATGTTTATGtattattt Cluster: [ ] Orangutan: GAGAAGAAGAAAAAAATCGTT-----TT-----TCATTATGGCTT-----GAATTTT-----CTAACAATGTTTATGTATTATTT Chimp > Human ------------- chr16:11203241-11203263 Template switch process: F1: L ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT 1 F3: 4 AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT R RF: ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTTTTCACTGTGGCTTGAATTTTCTAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT RR: TATTCTTCTTTTGTAAAGGACTCTTCTTCTTTTTTTAACAAAAAGTGACACCGAACTTAAAAGATTGTTACAAATACATAATAAACATATATAAAAAATAAATA F2: 3 AAAGTGACACCGAACTTAAAAGA 2 Unidirectional alignment (log-probability: -55.4) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGT-----------------------TagaaaattcaagccacagtgaaaAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTTTTCACTGTGGCTTGAATTTTCT-----------------------AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Template switch alignment (log-probability: -18.1) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|AGAAAATTCAAGCCACAGTGAAA|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|AGAAAATTCAAGCCACAGTGAAA|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Human > Chimp ------------- chr16:11393285-11393307 Template switch process: F1: L ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT 1 F3: 4 AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT R RF: ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTAGAAAATTCAAGCCACAGTGAAAAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT RR: TATTCTTCTTTTGTAAAGGACTCTTCTTCTTTTTTTAACAATCTTTTAAGTTCGGTGTCACTTTTTGTTACAAATACATAATAAACATATATAAAAAATAAATA F2: 3 TCTTTTAAGTTCGGTGTCACTTT 2 Unidirectional alignment (log-probability: -55.4) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT-----------------------tttcactgtggcttgaattttctAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTAGAAAATTCAAGCCACAGTGAAA-----------------------AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Template switch alignment (log-probability: -18.1) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|TTTCACTGTGGCTTGAATTTTCT|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|TTTCACTGTGGCTTGAATTTTCT|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Gorilla > Human --------------- chr16:11203241-11203263 Template switch process: F1: L ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT 1 F3: 4 AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT R RF: ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTTTTCACTGTGGCTTGAATTTTCTAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT RR: TATTCTTCTTTTGTAAAGGACTCTTCTTCTTTTTTTAACAAAAAGTGACACCGAACTTAAAAGATTGTTACAAATACATAATAAACATATATAAAAAATAAATA F2: 3 AAAGTGACACCGAACTTAAAAGA 2 Unidirectional alignment (log-probability: -54.9) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGT-----------------------TagaaaattcaagccacagtgaaaAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTTTTCACTGTGGCTTGAATTTTCT-----------------------AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Template switch alignment (log-probability: -18.7) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|AGAAAATTCAAGCCACAGTGAAA|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|AGAAAATTCAAGCCACAGTGAAA|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Human > Gorilla --------------- chr16:11077681-11077703 Template switch process: F1: L ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT 1 F3: 4 AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT R RF: ATAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTAGAAAATTCAAGCCACAGTGAAAAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT RR: TATTCTTCTTTTGTAAAGGACTCTTCTTCTTTTTTTAACAATCTTTTAAGTTCGGTGTCACTTTTTGTTACAAATACATAATAAACATATATAAAAAATAAATA F2: 3 TCTTTTAAGTTCGGTGTCACTTT 2 Unidirectional alignment (log-probability: -54.9) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT-----------------------tttcactgtggcttgaattttctAACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTTAGAAAATTCAAGCCACAGTGAAA-----------------------AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT Template switch alignment (log-probability: -18.7) TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|TTTCACTGTGGCTTGAATTTTCT|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT TAAGAAGAAAACATTTCCTGAGAAGAAGAAAAAAATTGTT|TTTCACTGTGGCTTGAATTTTCT|AACAATGTTTATGTATTATTTGTATATATTTTTTATTTAT ========== Event 1326 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATCAATAATGTATTAAAGTAATACTCAAA-------------AATGGAACAATACTGCACCTTTAAG ↓ 3 1 4 Chimp: TATCAATAATGTATTAAAGTAATACTCAAAACCATTTTTGAGTATTAAAACAATACTGCACCTTTAAG ↑ 3 1 4 Gorilla: TATCAATAATGTATTAAACTAATACTCAAA-------------AATGGAACAATACTGCACCTTTAAG Human: TATCAATAATGTATTAAAGTAATACTCAAA-------------AATGGAACAATACTGCACCTTTAAG Cluster: [ ] Orangutan: TATCAATAATGTATTAAAGTAACACTCAAA-------------AATGGAACAATACTGCACCTTTAAG Human > Chimp ------------- chr16:11845280-11845295 Template switch process: F1: L CTAAATTAACTTATCAATAATGTATTAAAGTAATACTCAAAA 1 F3: 4 AAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGAG R RF: CTAAATTAACTTATCAATAATGTATTAAAGTAATACTCAAAAATGGAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGAG RR: GATTTAATTGAATAGTTATTACATAATTTCATTATGAGTTTTTACCTTGTTATGACGTGGAAATTCTTTTATAATAAAAAGGACTC F2: 3 ATTATGAGTTTTTACC 2 Unidirectional alignment (log-probability: -44.3) AAATTAACTTATCAATAATGTATTAAAGTAATACTCAAAaccatttttgagtattAA---AACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA AAATTAACTTATCAATAATGTATTAAAGTAATACTCAAA----------------AATGGAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA Template switch alignment (log-probability: -23.3) AAATTAACTTATCAATAATGTATTAAAGTAATACTCAAAA|CCATTTTTGAGTATTA|aAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA AAATTAACTTATCAATAATGTATTAAAGTAATACTCAAAA|CCATTTTTGAGTATTA|GAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA Gorilla > Chimp --------------- chr16:11845280-11845295 Template switch process: F1: L CTAAATTAACTTATCAATAATGTATTAAAGTAATACTCAAAA 1 F3: 4 AAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGAG R RF: CTAAATTAACTTATCAATAATGTATTAAACTAATACTCAAAAATGGAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGAG RR: GATTTAATTGAATAGTTATTACATAATTTGATTATGAGTTTTTACCTTGTTATGACGTGGAAATTCTTTTATAATAAAAAGGACTC F2: 3 ATTATGAGTTTTTACC 2 Unidirectional alignment (log-probability: -49.3) AAATTAACTTATCAATAATGTATTAAAgTAATACTCAAAaccatttttgagtattAA---AACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA AAATTAACTTATCAATAATGTATTAAACTAATACTCAAA----------------AATGGAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA Template switch alignment (log-probability: -28.9) AAATTAACTTATCAATAATGTATTAAAgTAATACTCAAAA|CCATTTTTGAGTATTA|aAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA AAATTAACTTATCAATAATGTATTAAACTAATACTCAAAA|CCATTTTTGAGTATTA|GAACAATACTGCACCTTTAAGAAAATATTATTTTTCCTGA ========== Event 1327 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TAGGAACTGCCCCCAGGAAGCTGA------------------------TCTAGCCCCCAGTGTTTGCTTTT ↓ 34 2 1 Chimp: TAGGAACTGCCCCTAGGAAGCTGA------------TCTTCAGCCTGATCTAGCCCCCAGTGTTTGCTTTT Gorilla: TAGGAACTGCCCCCAGGAAGCTGATCTTCAGCCTGA------------TCTAGCCCCCAGTGTTTGCTTTT ↑ 34 2 1 Human: TAGGAACTGCCCCCAGGAAGCTGA------------------------TCTAGCCCCCAGTGTTTGCTTTT Cluster: [ ] Orangutan: TAGGAACTGCCCCCAGGAAGCTGATCTTCAGCCTGA------------TCTAGCCCCCAGTGTTTGCTTTT Human > Chimp ------------- chr16:10785129-10785133 Template switch process: F1: L GACAGACCACCCTTTGGTAGGAACTGCCCCTAGGAAGCTGATCT 1 F3: 4 CTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCTT R RF: GACAGACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCTT RR: CTGTCTGGTGGGAAACCATCCTTGACGGGGGTCCTTCGACTAGATCGGGGGTCACAAACGAAAAAGGAAACAAAAGAA F2: 3 CGACT 2 Unidirectional alignment (log-probability: -41.5) GACCACCCTTTGGTAGGAACTGCCCCtAGGAAGCTGATcttcagcctgatCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT GACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGAT------------CTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT Template switch alignment (log-probability: -22) GACCACCCTTTGGTAGGAACTGCCCCtAGGAAGCTGATCT|TCAGC|CTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT GACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGATCT|TCAGC|CTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT Human > Gorilla --------------- chr16:10458811-10458815 Template switch process: F1: L GACAGACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGATCT 1 F3: 4 CTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCTTCTT R RF: GACAGACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCTTCTT RR: CTGTCTGGTGGGAAACCATCCTTGACGGGGGTCCTTCGACTAGATCGGGGGTCACAAACGAAAAAGGAAACAAAAGAAGAA F2: 3 CGACT 2 Unidirectional alignment (log-probability: -28.1) GACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTgatcttcagcctGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT GACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCT------------GATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT Template switch alignment (log-probability: -16.5) GACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGATCT|TCAGC|CTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT GACCACCCTTTGGTAGGAACTGCCCCCAGGAAGCTGATCT|TCAGC|CTGATCTAGCCCCCAGTGTTTGCTTTTTCCTTTGTTTTCT ========== Event 1328 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTCATGACTGAGCAATCACTGGATATTTTGAAT-------------------------TCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTTTTTCCTCAGTATTGCACAGGTGAACATTTTGTTACTTCAAGATAGTTTTCCTTTGTACTTGGTATGGGCAGGAGCACTTATTTTCTCTATTTCAGCATC Chimp: TTTTCATGACTGAGCAATCACTGGATATTTTGAAT-------------------------TCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTTTTTCCTCAGTATTTCACAGGTGAACATTTTGTTACTTCAAGATAGTTTTCCTTTGTACTTGGTATGGGCAGGAGCACTGATTTTCTCTATTTCAGCATC ↓ 4 1 3 2 Gorilla: TGTTCATGACTGAGCAATCACTGGATATTTTGAAT-----------TCTGCAAACAGTATTCTGCAAATTCTCTTGATGAAGGTTTGCTATATTCTTTTTTCCTCAGTATTGCACAGGTGAACATTTTGTTACTTCAAGATAGTTTTTCTTTGTACTTGGTATGGGCAGGAGCACTGATTTTCTCTATTTCAGCATC ↑ 3 2 4 1 Human: TTTTCATGACTGAGCAATCACTGGATATTTTGAAT-------------------------TCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTTTTTCCTCAGTATTGCACAGGTGAACATTTTGTTACTTCAAGATAGTTTTCCTTTGTACTTGGTATGGGCAGGAGCACTTATTTTCTCTATTTCAGCATC Cluster: [ ] Orangutan: TGTTCATGACTGAGCAATCACTGGATATTCTGAATTCAAACAGTAT--------------TCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTTTTTCCTCAATATTGCACAGGTGAACATTATGTTACTTCAAGATAGTTTTCCTCTGCACTTGGTATGGGCAGGAGCACTGATTTTCTCTATTTCAGCATC Human > Gorilla --------------- chr16:9635900-9635903 Template switch process: F1: L GCAAATTGTTCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAA 1 F3: 4 ATTCTGCAAATTCTCTTGATGAAGGTTTGCTATATTCTTTTT R RF: GCAAATTTTTCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTTTT RR: CGTTTAAAAAGTACTGACTCGTTAGTGACCTATAAAACTTAAGACGTTTAAGAGAACTACTCCCAAACGATATAAGAAAAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -42.1) TCATGACTGAGCAATCACTGGATATTTTGAattctgcaaacagtATTCTGCAAATTCTCTTGATGAaGGTTTGCTATATTCTTT TCATGACTGAGCAATCACTGGATATTTTGA--------------ATTCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTT Template switch alignment (log-probability: -27.5) TCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAA|CAGT|ATTCTGCAAATTCTCTTGATGAaGGTTTGCTATATTCTTT TCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAA|CAGT|ATTCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTT Chimp > Gorilla --------------- chr16:9635900-9635903 Template switch process: F1: L GCAAATTGTTCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAA 1 F3: 4 ATTCTGCAAATTCTCTTGATGAAGGTTTGCTATATTCTTTTT R RF: GCAAATTTTTCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTTTTTCCTCAGTATTTCACAGGTGAACATTTTGTTACTTCAAGATAGTTTTCCTTTGTACTTGGTATGGGCAGGAGCACTG RR: CGTTTAAAAAGTACTGACTCGTTAGTGACCTATAAAACTTAAGACGTTTAAGAGAACTACTCCCAAACGATATAAGAAAAAAGGAGTCATAAAGTGTCCACTTGTAAAACAATGAAGTTCTATCAAAAGGAAACATGAACCATACCCGTCCTCGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -42.1) TCATGACTGAGCAATCACTGGATATTTTGAattctgcaaacagtATTCTGCAAATTCTCTTGATGAaGGTTTGCTATATTCTTT TCATGACTGAGCAATCACTGGATATTTTGA--------------ATTCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTT Template switch alignment (log-probability: -27.5) TCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAA|CAGT|ATTCTGCAAATTCTCTTGATGAaGGTTTGCTATATTCTTT TCATGACTGAGCAATCACTGGATATTTTGAATTCTGCAAA|CAGT|ATTCTGCAAATTCTCTTGATGAGGGTTTGCTATATTCTTT ========== Event 1329 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: agagctgactaaaaatatagt----atgcataattttgtcttattttcataaataaatGGAAAGACACATTAATCGATACCAACATATTAATTACTTAAATAGTAGGAATGAGGATTATTTTGATCATTTTCTTTATGCTAATCTGTATTTTCTAACTT Chimp: AGAGCTGACTAAAAATATAGT----ATGCATAA--TTGTCTTATTTTCATAAATAAATGGAAAGACACATTAATCGATACCAACATATTAATTACTTAAATAGTAGGAATGAGGATTATTTTGATCATTTTCTTTATGCTAATCTGTATTTTCTAACTT ↑ 1 4 3 2 Gorilla: AGAGCTGACTAAAAATATAGT--------ATAATTTTGTCTTATTTTCATACATAAATGGAAAGACACATTAATCGATACCAACGTATCAATTACTTAAATAGTAGGAATGAGGATTATTTTGATCATTTTCTTTATGCTCATCTGTATTTTCTAACTT Human: agagctgactaaaaatatagt----atgcataattttgtcttattttcataaataaatGGAAAGACACATTAATCGATACCAACATATTAATTACTTAAATAGTAGGAATGAGGATTATTTTGATCATTTTCTTTATGCTAATCTGTATTTTCTAACTT Cluster: [ ] Orangutan: agagctgactgaaaatatagtatgt----ataattttgtCTTATTTTCAT----AAATGGAAAGACACATTAATCAATACCAACATA----TTACTTAAATAGTAAGAATGAGGATTATTTTGATCATTTTCTTTATGCTAATCTGTATTTTCTAACTT Gorilla > Chimp --------------- chr1:160449821-160449826 Template switch process: F1: L TCACAATATAGTAATTAAAAAGAGCTGACTAAAAATATAGTAT 1 F3: 4 TTGTCTTATTTTCATAAATAAATGGAAAGACACATTAATC R RF: TCACAATATAGTAATTAAAAAGAGCTGACTAAAAATATAGTATAATTTTGTCTTATTTTCATACATAAATGGAAAGACACATTAATCGATACCAACGTATCAATTACTTAAATAGTAGGAATGAGGATTATTTTGATCATTTTCTTTATGC RR: AGTGTTATATCATTAATTTTTCTCGACTGATTTTTATATCATATTAAAACAGAATAAAAGTATGTATTTACCTTTCTGTGTAATTAGCTATGGTTGCATAGTTAATGAATTTATCATCCTTACTCCTAATAAAACTAGTAAAAGAAATACG F2: 3 AATACG 2 Unidirectional alignment (log-probability: -32.1) CAATATAGTAATTAAAAAGAGCTGACTAAAAATATAGTatgcATAA--TTGTCTTATTTTCATAaATAAATGGAAAGACACATTAATC CAATATAGTAATTAAAAAGAGCTGACTAAAAATATAGT----ATAATTTTGTCTTATTTTCATACATAAATGGAAAGACACATTAATC Template switch alignment (log-probability: -22.1) CAATATAGTAATTAAAAAGAGCTGACTAAAAATATAGTAT|GCATAA|TTGTCTTATTTTCATAaATAAATGGAAAGACACATTAATC CAATATAGTAATTAAAAAGAGCTGACTAAAAATATAGTAT|GCATAA|TTGTCTTATTTTCATACATAAATGGAAAGACACATTAATC ========== Event 1330 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: cagggcagatgtggttcccgTTACATGATGAGTAAC-ACAGGTGATAAATAAACAGTTAACAAGATAA Chimp: cagggcagatgtggttcctgTTACATGATGAGTAAC-ACAGGTGATAAATAAACAGTTAACAAGATAA ↓ 3 2 1 4 Gorilla: cagggcagatgtggttcctgTTACATGATGAGTAACATCATGTAA-CAATAAACAGTTAACAAGATAA Human: cagggcagatgtggttcccgTTACATGATGAGTAAC-ACAGGTGATAAATAAACAGTTAACAAGATAA Cluster: [ ] Orangutan: cggggcagatgtggttcctgTTACATGATGAGTAAC-ACAGGTGA----TAAACAGTTAACAAGATAA Chimp > Gorilla --------------- chr16:73967071-73967079 Template switch process: F1: L TTGAACAGGGCAGATGTGGTTCCTGTTACATGATGAGTAACA 1 F3: 4 AATAAACAGTTAACAAGATAAGAAAAATTGCCAGCGAGTA R RF: TTGAACAGGGCAGATGTGGTTCCTGTTACATGATGAGTAACACAGGTGATAAATAAACAGTTAACAAGATAAGAAAAATTGCCAGCGAGTA RR: AACTTGTCCCGTCTACACCAAGGACAATGTACTACTCATTGTGTCCACTATTTATTTGTCAATTGTTCTATTCTTTTTAACGGTCGCTCAT F2: 3 CAATGTACT 2 Unidirectional alignment (log-probability: -32.6) GAACAGGGCAGATGTGGTTCCTGTTACATGATGAGTAACatcatgtaAC--------AATAAACAGTTAACAAGATAAGAAAAATTGCCAGCGAGTA GAACAGGGCAGATGTGGTTCCTGTTACATGATGAGTAAC--------ACAGGTGATAAATAAACAGTTAACAAGATAAGAAAAATTGCCAGCGAGTA Template switch alignment (log-probability: -16.9) GAACAGGGCAGATGTGGTTCCTGTTACATGATGAGTAACA|TCATGTAAC|AATAAACAGTTAACAAGATAAGAAAAATTGCCAGCGAGTA GAACAGGGCAGATGTGGTTCCTGTTACATGATGAGTAACA|TCATGTAAC|AATAAACAGTTAACAAGATAAGAAAAATTGCCAGCGAGTA ========== Event 1331 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACTGTTTCCATTTATTGTGT-------ATAGTCAAAACACTCTTGAAGTAGCTTTCTC Chimp: CACTGTTTCCATTTATTGTGT-------ATAGTCAAAACACTCTTGAAGTAGCTTTCTC ↓ 13 4 2 Gorilla: CACTGTTTCCATTTATTGTGTGTTTTGACTATTCAAAACACTCTTGAAGTAGCTTTCTC ↑ 13 4 2 Human: CACTGTTTCCATTTATTGTGT-------ATAGTCAAAACACTCTTGAAGTAGCTTTCTC Cluster: [ ] Orangutan: CACAGTTTCCATTTATTGTGC-------ATAGTCAAAACACTCTTGAAGTAGCTTTCTC Human > Gorilla --------------- chr1:69443898-69443908 Template switch process: F1: L TTTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT 1 F3: 4 TCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA R RF: TTTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGTATAGTCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA RR: AAAAGTCAATAAGTCTTATAGTGACAAAGGTAAATAACACATATCAGTTTTGTGAGAACTTCATCGAAAGAGGGTTGTTAGACCT F2: 3 TATCAGTTTTG 2 Unidirectional alignment (log-probability: -32) TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGTgttttgacTAtTCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT-------ATAGTCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA Template switch alignment (log-probability: -17.1) TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT|GTTTTGACTAT|TCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT|GTTTTGACTAT|TCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA Chimp > Gorilla --------------- chr1:69443898-69443908 Template switch process: F1: L TTTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT 1 F3: 4 TCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA R RF: TTTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGTATAGTCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA RR: AAAAGTCAATAAGTCTTATAGTGACAAAGGTAAATAACACATATCAGTTTTGTGAGAACTTCATCGAAAGAGGGTTGTTAGACCT F2: 3 TATCAGTTTTG 2 Unidirectional alignment (log-probability: -32) TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGTgttttgacTAtTCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT-------ATAGTCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA Template switch alignment (log-probability: -17.1) TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT|GTTTTGACTAT|TCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA TTTCAGTTATTCAGAATATCACTGTTTCCATTTATTGTGT|GTTTTGACTAT|TCAAAACACTCTTGAAGTAGCTTTCTCCCAACAATCTGGA ========== Event 1332 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: ccattttgtgcaagtgtatatg----tatgtatacatatacccatgcacataaacacg Chimp: ccattttgtGCAAGTGTATATG----TATGTATACATATACCCATGcacataaacacg ↑ 3 1 2 4 Gorilla: ccattttgtGCAAGTGTATATG--------TATAC-AATACCCATGcacataaacacg Human: ccattttgtgcaagtgtatatg----tatgtatacatatacccatgcacataaacacg Cluster: [ ] Orangutan: ccattttgtgctagtgtatatgtatg----tatacatatacccatgcacataaacaca Gorilla > Chimp --------------- chr1:68616798-68616805 Template switch process: F1: L TCTAAGGCTTAATAGTATTCCATTTTGTGCAAGTGTATATGTAT 1 F3: 4 ATACCCATGCACATAAACACGCACAAGTACACTCACACAC R RF: TCTAAGGCTTAATAGTATTCCATTTTGTGCAAGTGTATATGTATACAATACCCATGCACATAAACACGCACAAGTACACTCACACAC RR: AGATTCCGAATTATCATAAGGTAAAACACGTTCACATATACATATGTTATGGGTACGTGTATTTGTGCGTGTTCATGTGAGTGTGTG F2: 3 TACATATG 2 Unidirectional alignment (log-probability: -27.9) AGGCTTAATAGTATTCCATTTTGTGCAAGTGTATAtgtaTGTATACAtATACCCATGCACATAAACACGCACAAGTACACTCACACAC AGGCTTAATAGTATTCCATTTTGTGCAAGTGTATA----TGTATACA-ATACCCATGCACATAAACACGCACAAGTACACTCACACAC Template switch alignment (log-probability: -16.8) AGGCTTAATAGTATTCCATTTTGTGCAAGTGTATATGTAT|GTATACAT|ATACCCATGCACATAAACACGCACAAGTACACTCACACAC AGGCTTAATAGTATTCCATTTTGTGCAAGTGTATATGTAT|GTATACAT|ATACCCATGCACATAAACACGCACAAGTACACTCACACAC ========== Event 1333 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAGAACCAGTAGGTTCAATGGCT--GTTTCCCTTTTCAGAGAGGAGCCCCAGA Chimp: CAAGAACCAGTAGGTTCAATGGCTAAATAGCCATTTTCAGAGAGGAGCCCCAGA ↑ 3 1 2 4 Gorilla: CAGGAACCAGTAGGTTCAATGGCT--GTTTTCCTTTTCAGAGAGGAGCCCCAGA Human: CAAGAACCAGTAGGTTCAATGGCT--GTTTCCCTTTTCAGAGAGGAGCCCCAGA Cluster: [ ] Orangutan: ----CACCAGTAGGTTCAATGGCT--GTTTCCCTTTTCAGAGAGAAGCCCCAGA Gorilla > Chimp --------------- chr16:5945878-5945886 Template switch process: F1: L GGTGGTCCAGTCATTGTCAAGAACCAGTAGGTTCAATGGCT 1 F3: 4 TTTTCAGAGAGGAGCCCCAGAAGCCTCAATGTAAATGCCT R RF: GGTGGTCCAGTCATTGTCAGGAACCAGTAGGTTCAATGGCTGTTTTCCTTTTCAGAGAGGAGCCCCAGAAGCCTCAATGTAAATGCCT RR: CCACCAGGTCAGTAACAGTCCTTGGTCATCCAAGTTACCGACAAAAGGAAAAGTCTCTCCTCGGGGTCTTCGGAGTTACATTTACGGA F2: 3 ACCGATAAA 2 Unidirectional alignment (log-probability: -39.4) GTGGTCCAGTCATTGTCAaGAACCAGTAGGTTCAATGGCT-------aaatagccaTTTTCAGAGAGGAGCCCCAGAAGCCTCAATGTAAATGCCT GTGGTCCAGTCATTGTCAGGAACCAGTAGGTTCAATGGCTGTTTTCC---------TTTTCAGAGAGGAGCCCCAGAAGCCTCAATGTAAATGCCT Template switch alignment (log-probability: -27.9) GTGGTCCAGTCATTGTCAaGAACCAGTAGGTTCAATGGCT|AAAtAGCCA|TTTTCAGAGAGGAGCCCCAGAAGCCTCAATGTAAATGCCT GTGGTCCAGTCATTGTCAGGAACCAGTAGGTTCAATGGCT|AAACAGCCA|TTTTCAGAGAGGAGCCCCAGAAGCCTCAATGTAAATGCCT ========== Event 1334 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATCAAAATCAAAATGTACCAGGAACTTTAAA-----TTTTATTTAATCCAAATCGGAAGTCTTTTCAGGTGGGG Chimp: TTATCAAAATCAAAATGTACCAGGAACTTTAAA-----TTTTATTTAATCCAAACCGGAACTCTTTTCAGGTGGGG ↓ 3 1 2 4 Gorilla: TTATCAAAATCAAAATATACCAGGAACTAAAGTTCCTGGTTTATTCAATCCAAACAGGAACTCTTTTCAGGTGGGG Human: TTATCAAAATCAAAATGTACCAGGAACTTTAAA-----TTTTATTTAATCCAAATCGGAAGTCTTTTCAGGTGGGG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Gorilla --------------- chr16:5588706-5588716 Template switch process: F1: L AGAAAATTAACCTTTATCAAAATCAAAATATACCAGGAACT 1 F3: 4 TTTATTCAATCCAAACAGGAACTCTTTTCAGGTGGGGTTGGCCTTTTCAAAAATTAA R RF: AGAAAATTAACCTTTATCAAAATCAAAATGTACCAGGAACTTTAAATTTTATTTAATCCAAACCGGAACTCTTTTCAGGTGGGGTTGGCCTTTTCAAAAATTAA RR: TCTTTTAATTGGAAATAGTTTTAGTTTTACATGGTCCTTGAAATTTAAAATAAATTAGGTTTGGCCTTGAGAAAAGTCCACCCCAACCGGAAAAGTTTTTAATT F2: 3 GGTCCTTGAAA 2 Unidirectional alignment (log-probability: -53.2) GAAAATTAACCTTTATCAAAATCAAAATaTACCAGGAAC--TAAAgttcctggTTTATTcAATCCAAACaGGAACTCTTTTCAGGTGGGGTTG GAAAATTAACCTTTATCAAAATCAAAATGTACCAGGAACTTTAAA-------TTTTATTTAATCCAAACCGGAACTCTTTTCAGGTGGGGTTG Template switch alignment (log-probability: -34.1) GAAAATTAACCTTTATCAAAATCAAAATaTACCAGGAACT|AAAGTTCCTGG|TTTATTcAATCCAAACaGGAACTCTTTTCAGGTGGGGTTG GAAAATTAACCTTTATCAAAATCAAAATGTACCAGGAACT|AAAGTTCCTGG|TTTATTTAATCCAAACCGGAACTCTTTTCAGGTGGGGTTG ========== Event 1335 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCAGGCACCTTCATCTCCTGTAACCTATC---TGCTCTCTGTGTACTGTCATTC ↓ 3 2 1 4 Chimp: ACCAGGCACCTTCATCTCCTGTAACCTAGTTACAGCTCTCTGTGTACTGTCATTC ↑ 3 2 1 4 Gorilla: ACCAGGGACCTTCATCTCCTGTAACCTATC---TGCTCTCTGTGTACTGTCATTC Human: ACCAGGCACCTTCATCTCCTGTAACCTATC---TGCTCTCTGTGTACTGTCATTC Cluster: [ ] Orangutan: TCCAGGCACCTTCATCTCCCCTAACCTATC---TGCTCTCTGTGTACTGTCATTC Human > Chimp ------------- chr16:74888676-74888681 Template switch process: F1: L AATATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTA 1 F3: 4 GCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG R RF: AACATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTATCTGCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG RR: TTGTAAAGGTTTGTGGTCCGTGGAAGTAGAGGACATTGGATAGACGAGAGACACATGACAGTAAGTGACTTACGAAAATTCAAC F2: 3 ACATTG 2 Unidirectional alignment (log-probability: -33.2) AtATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTAgttaCaGCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG ACATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTA---TCTGCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG Template switch alignment (log-probability: -22) AtATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTA|GTTACA|GCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG ACATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTA|GTTACA|GCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG Gorilla > Chimp --------------- chr16:74888676-74888681 Template switch process: F1: L AATATTTCCAAACACCAGGCACCTTCATCTCCTGTAACCTA 1 F3: 4 GCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG R RF: AATATTTCCAAACACCAGGGACCTTCATCTCCTGTAACCTATCTGCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG RR: TTATAAAGGTTTGTGGTCCCTGGAAGTAGAGGACATTGGATAGACGAGAGACACATGACAGTAAGTGACTTACGAAAATTCAAC F2: 3 ACATTG 2 Unidirectional alignment (log-probability: -31.8) ATATTTCCAAACACCAGGcACCTTCATCTCCTGTAACCTAgttaCaGCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG ATATTTCCAAACACCAGGGACCTTCATCTCCTGTAACCTAT---CTGCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG Template switch alignment (log-probability: -22) ATATTTCCAAACACCAGGcACCTTCATCTCCTGTAACCTA|GTTACA|GCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG ATATTTCCAAACACCAGGGACCTTCATCTCCTGTAACCTA|GTTACA|GCTCTCTGTGTACTGTCATTCACTGAATGCTTTTAAGTTG ========== Event 1336 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GACCTCCCCCAGCCTCCAGGTGGGGCCCCCACCTGGGTGGGG-CCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTGACCCTCCCACTGGAACATCCAGGTATGTGTTGTCATAGAAACCT ↑ 4 1 3 2 Chimp: GACCTCCCCCAGCCTCCAGGTGG-----------------GG-CCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTGACCCTCCCACTGGAACATCCAGGTATGTGTTGTCATAGAAACCT Gorilla: GACCTCCCCCAGCCTCCAGGTGGGGCCCCCACCTGGGTGGGGCCCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTGACCCTCCCACTGGAACATCCAGGTATGTGTTGTCATAGAAACCT Human: GACCTCCCCCAGCCTCCAGGTGGGGCCCCCACCTGGGTGGGG-CCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTGACCCTCCCACTGGAACATCCAGGTATGTGTTGTCATAGAAACCT Cluster: [ ] Orangutan: GACCGCCCCCAGCCTCCAGGTGG-----------------GG-CCCTCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTGACCCTCCCACTGGAAAATCCAGGTATGTGTTGTCATAGAAACCT Chimp > Human ------------- chr16:81674789-81674794 Template switch process: F1: L AAATAGGAGGAGTGGGAGGACCTCCCCCAGCCTCCAGGTGGGGCCCCC 1 F3: 4 GTGGGGCCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTG R RF: AAATAGGAGGAGTGGGAGGACCTCCCCCAGCCTCCAGGTGGGGCCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCAGGTGACCCTCCCACTGGAACATCCAGGT RR: TTTATCCTCCTCACCCTCCTGGAGGGGGTCGGAGGTCCACCCCGGGGGAGAACTAAAATCGAGACTTGAGAAGGGGTCCACTGGGAGGGTGACCTTGTAGGTCCA F2: 3 GGTCCA 2 Unidirectional alignment (log-probability: -35.4) GGAGTGGGAGGACCTCCCCCAGCCTCCAGGTGGGGCCCccacctgggtggggcccCCTCTTGATTTTAGCTCTGAACTCTTCCCCA GGAGTGGGAGGACCTCCCCCAGCCTCCAGGTGGGGCCC-----------------CCTCTTGATTTTAGCTCTGAACTCTTCCCCA Template switch alignment (log-probability: -16.2) GGAGTGGGAGGACCTCCCCCAGCCTCCAGGTGGGGCCCCC|ACCTGG|GTGGGGCCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCA GGAGTGGGAGGACCTCCCCCAGCCTCCAGGTGGGGCCCCC|ACCTGG|GTGGGGCCCCCTCTTGATTTTAGCTCTGAACTCTTCCCCA ========== Event 1337 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTGCTAACCAAACTAAATTATTAGTT------GCATCATTTCATCTCAACTTCACACAGTTAT Chimp: TTTGCTAACCAAACTAAATTATTAGTT------GCATCATTTCATCTCAACTTCACACAGTTAT ↓ 3 1 2 4 Gorilla: TTTGCTAACCAAACTAAATTATTAGTTGCTGATGCAACTAATAATCTCAACTTCACACAGTTAT ↑ 3 1 2 4 Human: TTTGCTAACCAAACTAAATTATTAGTT------GCATCATTTCATCTCAACTTCACACAGTTAT Cluster: [ ] Orangutan: TTTGCTAACCAAACTAAATTATTAGTT------GCATCATTTCATCTCAACTTCACATAGTTAT Human > Gorilla --------------- chr16:77606636-77606649 Template switch process: F1: L GTGAGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC 1 F3: 4 ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT R RF: GTGAGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGCATCATTTCATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTTCT RR: CACTCACGGATGAGAAACGATTGGTTTGATTTAATAATCAACGTAGTAAAGTAGAGTTGAAGTGTGTCAATAATATAAAAAAGGAAAAAGA F2: 3 ATAATCAACGTAGT 2 Unidirectional alignment (log-probability: -45.2) AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGCtgatgcaactaatA-------ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTcCT AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC-------------ATCATTTCATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTTCT Template switch alignment (log-probability: -23.1) AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC|TGATGCAACTAATA|ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTcCT AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC|TGATGCAACTAATA|ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTTCT Chimp > Gorilla --------------- chr16:77606636-77606649 Template switch process: F1: L GTGAGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC 1 F3: 4 ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT R RF: GTGAGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGCATCATTTCATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT RR: CACTCACGGATGAGAAACGATTGGTTTGATTTAATAATCAACGTAGTAAAGTAGAGTTGAAGTGTGTCAATAATATAAAAAAGGAAAAGGA F2: 3 ATAATCAACGTAGT 2 Unidirectional alignment (log-probability: -39.7) AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGCtgatgcaactaatA-------ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC-------------ATCATTTCATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT Template switch alignment (log-probability: -17.6) AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC|TGATGCAACTAATA|ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT AGTGCCTACTCTTTGCTAACCAAACTAAATTATTAGTTGC|TGATGCAACTAATA|ATCTCAACTTCACACAGTTATTATATTTTTTCCTTTTCCT ========== Event 1338 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACAACTGTATGTCATCATTATTCACTTGTCCCAATTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGACAAATGAACAACGATgaccct Chimp: ACAACTGTATGTCATCATTATTCACTTGTCCCAATTCGCTTTGTTCCCAGTGGAATCCCACAAATATTGGGACAAATGAACAACGATgaccct Gorilla: ACAACTGTATGTCATCATTATTC--------------ACTTTGTTCCCAGTGGAATCCCACAAATATTGGGACAAATGAACAACGATgaccct ↓ 4 1 3 2 Human: ACAACTGTATGTCATCATTATTCACTTGTCCCAATTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGACAAATGAACAACGATgaccct Cluster: [ ] Orangutan: Gorilla > Human --------------- chr16:3565992-3565997 Template switch process: F1: L GGCAGAAGTGTCAGAAAAACAACTGTATGTCATCATTATTCACTT 1 F3: 4 ATTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGACAAAT R RF: GGCAGAAGTGTCAGAAAAACAACTGTATGTCATCATTATTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGACAAAT RR: CCGTCTTCACAGTCTTTTTGTTGACATACAGTAGTAATAAGTGAAACAAGGGTCACCTTAGGGTGTTTATAACCCTGTTTA F2: 3 ACCCTG 2 Unidirectional alignment (log-probability: -31) AAGTGTCAGAAAAACAACTGTATGTCATCATTATtcacttgtcccaatTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGAC AAGTGTCAGAAAAACAACTGTATGTCATCATTAT--------------TCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGAC Template switch alignment (log-probability: -16.7) AAGTGTCAGAAAAACAACTGTATGTCATCATTATTCACTT|GTCCCA|ATTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGAC AAGTGTCAGAAAAACAACTGTATGTCATCATTATTCACTT|GTCCCA|ATTCACTTTGTTCCCAGTGGAATCCCACAAATATTGGGAC ========== Event 1339 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTGGAGCGACCAGCCTGTGG-GGGGTGTGGCGGGCACCGGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCAATCTGCTCCCCGTGGTCCCCCTGGGACGGCGCTTCCAGCTGGGGGGGCTGTTGGCTCCTCAGTGACTTCTGCGGGCACAGGGGGCTCCCAGACAGCCCCTCCAGCTCCACAAGGCCCCAAGCTCCAGGCC-CCCCATGGTTTC Chimp: CCTGGAGCGACCAGCCTGTgggggggTGTGGCAGGCACCAGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCAATCTGCTCCCCGTGGTCCCCCTGGGACGGCGCTTCCAGCCGG-GGGGCTGTTGGCTCCTCAGTGACTTCTGTGGGCACAGGGGGCTCCCAGACAGCCCCTCCAGCTCCACAAGGCCCCAAGCTCCAGAcccccccATGGTTTC Gorilla: CCTGGAGCGACCAGCCTGTGG-GGGGTGTGGCAGGCACCAGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCGATCTGTTCCCCGTGGTCCCCCTGGGACGGCGCTTCCCGCCGG-GTGGCTGTTGGCTCCTCAGTGACTTCTGCGGGCACAGGGGGCTCCCAGACAGCCCCTCCAGCTCCACAAGGCCCCAAGCTCCAGGTC-CCCCATGGTTTC ↓ 4 1 3 2 Human: CCTGGAGCGACCAGCCTGTGG-GGGGTGTGGCGGGCACCGGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCAATCTGCTCCCCGTGGTCCCCCTGGGACGGCGCTTCCAGCTGGGGGGGCTGTTGGCTCCTCAGTGACTTCTGCGGGCACAGGGGGCTCCCAGACAGCCCCTCCAGCTCCACAAGGCCCCAAGCTCCAGGCC-CCCCATGGTTTC Cluster: [ ] Orangutan: CCTGAAGCGACCAGCCTGTGG-GGGGTGTGGCGGGCACCCGTGTGGCCGGCA--CGGTTCTGTGTAACTGGGGCCTGCGATCTGCTCCCTGTGGTCCCCCTGGGACGGCACTTCCAGCCCG-GGGGCTGTTGGCTCCTCAGTGACTTCTGCGGGCCCAGGGGGCTCCCAGACAGCCCCTCCAGCTCCACAAGGCCCCAAGCTCCAGGCC-CCCCATGGTTTC Gorilla > Human --------------- chr16:88820939-88820942 Template switch process: F1: L CCGGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCAATCTGCTCCCCGTGGTCCCCCTGGGACGGCGCTTCC 1 F3: 4 GGGGGG R RF: CCAGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCGATCTGTTCCCCGTGGTCCCCCTGGGACGGCGCTTCCTGTGGCAGGCACCAGTGTGGCCAGCAGCTTGTTCTGTGTAACTGGGGCCTGCGATCTGTTCCCCGTGGTCCCCCTGGGACGGCGCTTCCCGCCGGGTGGCTGTTGGCTCCTCAGTGACTTCTGCGGGCACAGGGGGCTCCCAGACAGCCCCTCCAGCTCCACAAGGCCCCAAGCT RR: GGTCACACCGGTCGTCGAACAAGACACATTGACCCCGGACGCTAGACAAGGGGCACCAGGGGGACCCTGCCGCGAAGGACACCGTCCGTGGTCACACCGGTCGTCGAACAAGACACATTGACCCCGGACGCTAGACAAGGGGCACCAGGGGGACCCTGCCGCGAAGGGCGGCCCACCGACAACCGAGGAGTCACTGAAGACGCCCGTGTCCCCCGAGGGTCTGTCGGGGAGGTCGAGGTGTTCCGGGGTTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -42.5) TGCaATCTGcTCCCCGTGGTCCCCCTGGGACGGCGCTTCCaGCtGGGgGg TGCGATCTGTTCCCCGTGGTCCCCCTGGGACGGCGCTTCCCGCCGGGTG- Template switch alignment (log-probability: -32.9) TGCaATCTGcTCCCCGTGGTCCCCCTGGGACGGCGCTTCC|AGCT|GGGGGG TGCGATCTGTTCCCCGTGGTCCCCCTGGGACGGCGCTTCC|AGCT|GGGGGG ========== Event 1340 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGT---------------------------------------------------------------------------GTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTAGCAGGGCCTTGTTATTGGTGCCACAGGTGAAGGCGCTGGCGTCTCCATGGGGCTGCTCTCCCGGCCCGCACTTGCTGCACTGCCTGCCTGTGGCCTGTGTCTC ↓ 4 1 3 2 Chimp: AGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGT---------------GTGTGCCACGCGGGTGTTCAGACCCAGCATGGGGGGAGCAGTAGTGTGCCCCAGTGCTGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTAGCAGGGCTTTGTTAGTGGTGCCACAGGTGAAGGCGGTGGCGTCTCTATGGGGCTGCTCTCCCGGCCCGCACTTGCTGCACTGCCTGCCTGTGGCCTGTGTCTC ↑ 4 1 3 2 Gorilla: AGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGT---------------------------------------------------------------------------GTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTAGCAGGGCCTTGTTAGTGGTGCCACAGGTGAAGGCGCTGGCGTCTCCATGGGGCTGCTCTCCTGGCCCGCACTTGCTGCACTGCCTGCCTGTGGCCTGTGTCTC Human: AGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGT---------------------------------------------------------------------------GTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTAGCAGGGCCTTGTTATTGGTGCCACAGGTGAAGGCGCTGGCGTCTCCATGGGGCTGCTCTCCCGGCCCGCACTTGCTGCACTGCCTGCCTGTGGCCTGTGTCTC Cluster: [ ] Orangutan: AGGAACCAGAAGCAACTTCAGCGTGCCCCTGTGCTGTGTGTGCCACGCGGGT---------------------------------------------------------------------------GTTCAGACCCAGCATGGAGGGAGCAGCAGGGCCTTGTTAGTGGCGCCACAGGTGAAGGCTCTGGCGTCTCCGTGGGGCTGCTCTCCTGGCCCGCACTTGCTGCACTGCCTGCCTGTGGCCTGTCTCTC Human > Chimp ------------- chr16:1290890-1290894 Template switch process: F1: L AGGGAGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGGGGGA 1 F3: 4 AGTGTGCCCCAGTGCTGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTA R RF: AGGGAGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTAGCAGGGCCTTGTTATTGGTGCCACAGGTGAAGGCGCTGGCGTCTCCATGGGGCTGCTCTCCCGGCCCGCACTTGCTGCACTGC RR: TCCCTCCTTGGTCTTCGTTGAAGTCGCACGGGGTCACGGCACACACGGTGCGCCCACAAGTCTGGGTCGTACCTCCCTGATCGTCCCGGAACAATAACCACGGTGTCCACTTCCGCGACCGCAGAGGTACCCCGACGAGAGGGCCGGGCGTGAACGACGTGACG F2: 3 TGACG 2 Unidirectional alignment (log-probability: -97.2) CgtgtgtgccacgcgggtgttcagacccagcatggggggagcagtagtgtgccccagtgctGTGTGTGCCACGCGGGTGTTCAGA C------------------------------------------------------------GTGTGTGCCACGCGGGTGTTCAGA Template switch alignment (log-probability: -34.9) CGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGgGGGA|GCAGT|AGtGTGCCCCAGTGCtGTGTGTGCCACGCGGGTGTTCAGA CGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGA|GCAGT|AGCGTGCCCCAGTGCCGTGTGTGCCACGCGGGTGTTCAGA Gorilla > Chimp --------------- chr16:1290890-1290894 Template switch process: F1: L AGGGAGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGGGGGA 1 F3: 4 AGTGTGCCCCAGTGCTGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTA R RF: GGGGAGGAACCAGAAGCAACTTCAGCGTGCCCCAGTGCCGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGACTAGCAGGGCCTTGTTAGTGGTGCCACAGGTGAAGGCGCTGGCGTCTCCATGGGGCTGCTCTCCTGGCCCGCACTTGCTGCACTGC RR: CCCCTCCTTGGTCTTCGTTGAAGTCGCACGGGGTCACGGCACACACGGTGCGCCCACAAGTCTGGGTCGTACCTCCCTGATCGTCCCGGAACAATCACCACGGTGTCCACTTCCGCGACCGCAGAGGTACCCCGACGAGAGGACCGGGCGTGAACGACGTGACG F2: 3 TGACG 2 Unidirectional alignment (log-probability: -103) CgtgtgtgccacgcgggtgttcagacccagcatggggggagcagtagtgtgccccagtgctGTGTGTGCCACGCGGGTGTTCAGA C------------------------------------------------------------GTGTGTGCCACGCGGGTGTTCAGA Template switch alignment (log-probability: -39.7) CGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGgGGGA|GCAGT|AGtGTGCCCCAGTGCtGTGTGTGCCACGCGGGTGTTCAGA CGTGTGTGCCACGCGGGTGTTCAGACCCAGCATGGAGGGA|GCAGT|AGCGTGCCCCAGTGCCGTGTGTGCCACGCGGGTGTTCAGA ========== Event 1341 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CGACAGGCAGATGGAGCCCGTGTG--------ATCCTCAGCTGTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCTTTTAGTTTGGATTTTGTTACAGGTGAAGGTGCCTAAAGGTGGGGTG Chimp: GGACAGGCAGATGGAGCCCGTGTG--------ATCCTCAGCTGTGTGATCCACACTCACTTTATCTGAAGCCGCCTCTGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCTTTTAGTTTGGATTTTGTTACAGGTGAAGGTGGCTAAAGGTGGGGTG ↑ 4 1 3 2 Gorilla: GGACAGGCAGATGGAGCCCGTGTG-----------------------ATCCACACTCACTTTATCTGAAGCCGCCTCCGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCTTTTAGTTTGGATTTTGTTACAGCTGAAGGTGCCTAAAGGTGGGGTG ↓ 4 1 3 2 Human: CGACAGGCAGATGGAGCCCGTGTG--------ATCCTCAGCTGTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCTTTTAGTTTGGATTTTGTTACAGGTGAAGGTGCCTAAAGGTGGGGTG Cluster: [ ] Orangutan: ggacaggcAGATGGAGCCTGTGTGATCCTCAG---------------CACCACACTCACTTTATCTGAAGCTGCCTCCGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCCTTTAGTTTGGATTTTGTTACAGCTGAAGGTGCCTGAAGGTGGGGTG Gorilla > Human --------------- chr16:1252423-1252428 Template switch process: F1: L TCCTGTAGCCGTGAGGACGACAGGCAGATGGAGCCCGTGTGATCC 1 F3: 4 GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCACTTCTG R RF: TCCTGTAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCTTTTAGTTTGGATTTTGTTACAGCTGA RR: AGGACATCGGCACTCCTCCTGTCCGTCTACCTCGGGCACACTAGGTGTGAGTGAAATAGACTTCGGCGGAGGCGTGAAGACTCAGTTCTGTAGAAGGAATAACGACACCAACGAAAATCAAACCTAAAACAATGTCGACT F2: 3 TCGACT 2 Unidirectional alignment (log-probability: -38) TAGCCGTGAGGAcGACAGGCAGATGGAGCCCgtgtgatcctcagctGTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCAC TAGCCGTGAGGAGGACAGGCAGATGGAGCCC---------------GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCAC Template switch alignment (log-probability: -22.2) TAGCCGTGAGGAcGACAGGCAGATGGAGCCCGTGTGATCC|TCAGCT|GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCAC TAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGTGATCC|TCAGCT|GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCAC Gorilla > Chimp --------------- chr16:1122611-1122616 Template switch process: F1: L TCCTGTAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGTGATCC 1 F3: 4 GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCTGCACTTCTG R RF: TCCTGTAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCACTTCTGAGTCAAGACATCTTCCTTATTGCTGTGGTTGCTTTTAGTTTGGATTTTGTTACAGCTGA RR: AGGACATCGGCACTCCTCCTGTCCGTCTACCTCGGGCACACTAGGTGTGAGTGAAATAGACTTCGGCGGAGGCGTGAAGACTCAGTTCTGTAGAAGGAATAACGACACCAACGAAAATCAAACCTAAAACAATGTCGACT F2: 3 TCGACT 2 Unidirectional alignment (log-probability: -38) TAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGtgatcctcagctgtgTGATCCACACTCACTTTATCTGAAGCCGCCTCtGCAC TAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTG---------------TGATCCACACTCACTTTATCTGAAGCCGCCTCCGCAC Template switch alignment (log-probability: -22.2) TAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGTGATCC|TCAGCT|GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCtGCAC TAGCCGTGAGGAGGACAGGCAGATGGAGCCCGTGTGATCC|TCAGCT|GTGTGATCCACACTCACTTTATCTGAAGCCGCCTCCGCAC ========== Event 1342 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCCTGCTCCAGCCAGGGAAACTGGAAATAGAG-------TGTCAAGGATCACGCCCAGGTTC ↓ 3 2 1 4 Chimp: TCCCTGCTCCAGCCA-GGAAACTGGAAATAGAGTTTCCAGTTTCAAGGATCACGCCCAGGTTC ↑ 3 2 1 4 Gorilla: TCCCTGCTCCAGCCAGGGAAACTGGAAATAGAG-------TGTCAAGGATCACGCCCAGGTTC Human: TCCCTGCTCCAGCCAGGGAAACTGGAAATAGAG-------TGTCAAGGATCACGCCCAGGTTC Cluster: [ ] Orangutan: TCCCTGTTCCCACCAGGGAAACTAGAAATAGAG-------TGTCAACGATCACATCCAGGTTC Human > Chimp ------------- chr16:1650687-1650694 Template switch process: F1: L TTTTCCGGTCCCTGCTCCAGCCA-GGAAACTGGAAATAGAGT 1 F3: 4 TCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA R RF: TTTTCCGGTCCCTGCTCCAGCCAGGGAAACTGGAAATAGAGTGTCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA RR: AAAAGGCCAGGGACGAGGTCGGTCCCTTTGACCTTTATCTCACAGTTCCTAGTGCGGGTCCAAGATTTTAGGTAGGAAGGGGT F2: 3 TTGACCTT 2 Unidirectional alignment (log-probability: -37.3) TTTCCGGTCCCTGCTCCAGCCA-GGAAACTGGAAATAGAGTtTccagtttCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA TTTCCGGTCCCTGCTCCAGCCAGGGAAACTGGAAATAGAGTGT-------CAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA Template switch alignment (log-probability: -26.5) TTTCCGGTCCCTGCTCCAGCCA-GGAAACTGGAAATAGAGT|TTCCAGTT|TCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA TTTCCGGTCCCTGCTCCAGCCAGGGAAACTGGAAATAGAGT|TTCCAGTT|TCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA Gorilla > Chimp --------------- chr16:1650687-1650694 Template switch process: F1: L TTTTCCGGTCCCTGCTCCAGCCAGG-AAACTGGAAATAGAGT 1 F3: 4 TCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA R RF: TTTTCCGGTCCCTGCTCCAGCCAGGGAAACTGGAAATAGAGTGTCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA RR: AAAAGGCCAGGGACGAGGTCGGTCCCTTTGACCTTTATCTCACAGTTCCTAGTGCGGGTCCAAGATTTTAGGTAGGAAGGGGT F2: 3 TTGACCTT 2 Unidirectional alignment (log-probability: -36.3) TTTCCGGTCCCTGCTCCAGCCAG-GAAACTGGAAATAGagtttccAGTtTCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA TTTCCGGTCCCTGCTCCAGCCAGGGAAACTGGAAATAG-------AGTGTCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA Template switch alignment (log-probability: -26.5) TTTCCGGTCCCTGCTCCAGCCAGG-AAACTGGAAATAGAGT|TTCCAGTT|TCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA TTTCCGGTCCCTGCTCCAGCCAGGGAAACTGGAAATAGAGT|TTCCAGTT|TCAAGGATCACGCCCAGGTTCTAAAATCCATCCTTCCCCA ========== Event 1343 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGGAGAATTTGCCACATCTGG-TC------ACTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGCTAACAAGGAATATATTCATGTTGTACATCGTGATGCAGTacacacacac----- ↑ 1 4 3 2 Chimp: GGGGAGAATTTGCCACATCTGATTC---ACTTCTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGCTAACATGGAATATATTCATGTTGTACATCGTGACGCAGTacacacacac----- Gorilla: GGGGAGAATTTGCCACATCTGATTCACT---TCTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGCTAACAAGGAATATA-TCATGTTGTACATCGTGATGCAGTacacacacac----- Human: GGGGAGAATTTGCCACATCTGG-TC------ACTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGCTAACAAGGAATATATTCATGTTGTACATCGTGATGCAGTacacacacac----- Cluster: [ ] Orangutan: GGGGAGAATTTGCCACATCTGATTCACT---TCTTATTTACACCCCAGTCTGGTGTGCAGAAGTCACTGGGCTAACAAGGAATATATTCATGTTGTACATCATGATGCAGTacacacacacacgca Chimp > Human ------------- chr16:89432154-89432158 Template switch process: F1: L CTTATTCCCCACAGTGCTAAGGGGAGAATTTGCCACATCTG 1 F3: 4 TTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGC R RF: CTTATTCCCCACAGTGCTAAGGGGAGAATTTGCCACATCTGATTCACTTCTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGCTAACATGGAATATATTCATGTTGTACATCGTGAC RR: GAATAAGGGGTGTCACGATTCCCCTCTTAAACGGTGTAGACTAAGTGAAGAATAAATGTGGAGTCAGACCACACGTCTTCAGTGACCCGATTGTACCTTATATAAGTACAACATGTAGCACTG F2: 3 CACTG 2 Unidirectional alignment (log-probability: -25.8) TTATTCCCCACAGTGCTAAGGGGAGAATTTGCCACATCTGgtcA-------CTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGC TTATTCCCCACAGTGCTAAGGGGAGAATTTGCCACATCTG---ATTCACTTCTTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGC Template switch alignment (log-probability: -15.9) TTATTCCCCACAGTGCTAAGGGGAGAATTTGCCACATCTG|GTCAC|TTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGC TTATTCCCCACAGTGCTAAGGGGAGAATTTGCCACATCTG|GTCAC|TTATTTACACCTCAGTCTGGTGTGCAGAAGTCACTGGGC ========== Event 1344 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAAA---GACAATCCCACAAACGCCCCTTTATGCACAG Chimp: TCCTCCATTTTGGCTCAAGCTGGATCCTGAGTA-AA---GACAATCCCACAAACGCCCCTTTATGCACAG Gorilla: TCCTCCATTTTGGCTCAAGCTGGATCCTGAGTA-AA------GATCCAGCAAACGCCCCTTTATGCACAG ↑ 3 2 1 4 Human: TCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAAA---GACAATCCCACAAACGCCCCTTTATGCACAG Cluster: [ ] Orangutan: TCCTCCATTTTGGCTCAAGCTGGATCCTGAGTA-AAGAC---AATCCCACAAATGCCCCTTTATGCACAG Human > Gorilla --------------- chr16:80731836-80731842 Template switch process: F1: L AAGACTCTTCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAA 1 F3: 4 CAAACGCCCCTTTATGCACAGCTTCCCCCACACGCTGTTT R RF: AAGACTCTTCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAAAGACAATCCCACAAACGCCCCTTTATGCACAGCTTCCCCCACACGCTGTTT RR: TTCTGAGAAGGAGGTAAAACCGAGTTCGACCTAGGACTCATTTTCTGTTAGGGTGTTTGCGGGGAAATACGTGTCGAAGGGGGTGTGCGACAAA F2: 3 GACCTAG 2 Unidirectional alignment (log-probability: -27.8) ACTCTTCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAAg----ATCCagCAAACGCCCCTTTATGCACAGCTTCCCCCACACGCTGTTT ACTCTTCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAAAGACAATCCCACAAACGCCCCTTTATGCACAGCTTCCCCCACACGCTGTTT Template switch alignment (log-probability: -16.7) ACTCTTCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAA|GATCCAG|CAAACGCCCCTTTATGCACAGCTTCCCCCACACGCTGTTT ACTCTTCCTCCATTTTGGCTCAAGCTGGATCCTGAGTAAA|GATCCAG|CAAACGCCCCTTTATGCACAGCTTCCCCCACACGCTGTTT ========== Event 1345 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGAGCCGAGACTCTTTGCTCCAGGAGCGCTCCAGGAGTGTGCAGTGTGTGACTGTTT Chimp: TTGAGCCGAGACTCTTTGCTCCAGGAGCGCTCCATGAGTGTGCAGTGTGTGACTGTTT Gorilla: TTGAGCCGAGACTCTTTGCTCCAGGAGCAC-----CGGTGTGCAGTGTGTGACTGTTT ↓ 3 2 4 Human: TTGAGCCGAGACTCTTTGCTCCAGGAGCGCTCCAGGAGTGTGCAGTGTGTGACTGTTT Cluster: [ ] Orangutan: TTGAGCCGAGACTCTTTGCTCCAGGAGCAC-----CGGTGTGCAGTGTGTGACTGTTT Gorilla > Human --------------- chr16:89892476-89892484 Template switch process: F1: L GCGTCAGTGCCTCTTGAGCCGAGACTCTTTGCTCCAGGAGC 1 F3: 4 GTGTGCAGTGTGTGACTGTTTGTTGCCACACTGAGGGCCT R RF: GCGTCAGTGCCTCTTGAGCCGAGACTCTTTGCTCCAGGAGCACCGGTGTGCAGTGTGTGACTGTTTGTTGCCACACTGAGGGCTT RR: CGCAGTCACGGAGAACTCGGCTCTGAGAAACGAGGTCCTCGTGGCCACACGTCACACACTGACAAACAACGGTGTGACTCCCGAA F2: 3 AGGACCTCG 2 Unidirectional alignment (log-probability: -37.8) CGTCAGTGCCTCTTGAGCCGAGACTCTTTGCTCCAGGAG---CGctccaggaGTGTGCAGTGTGTGACTGTTTGTTGCCACACTGAGGGCcT CGTCAGTGCCTCTTGAGCCGAGACTCTTTGCTCCAGGAGCACCG--------GTGTGCAGTGTGTGACTGTTTGTTGCCACACTGAGGGCTT Template switch alignment (log-probability: -27.9) CGTCAGTGCCTCTTGAGCCGAGACTCTTTGCTCCAGGAGC|GCTCCaGGA|GTGTGCAGTGTGTGACTGTTTGTTGCCACACTGAGGGCcT CGTCAGTGCCTCTTGAGCCGAGACTCTTTGCTCCAGGAGC|GCTCCTGGA|GTGTGCAGTGTGTGACTGTTTGTTGCCACACTGAGGGCTT ========== Event 1346 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: GGGATAGGATCACCTTTGCCTCACTGGTAGAGAGCACATAGAGAAAG-CTACTAACTTTTTCTGCTTCTGAA Chimp: GGGATAGGATCACCTTTGCCTCACTGGTAGAGAGCACATAGAGAAAG-CTACTAACTTTTTCTGCCTCTGAA ↓ 13 24 ↑ 13 24 Gorilla: GGGATAGGATCACCTTTGCCTTACTGGTAGTAGCTTTCTCTA-TGTGCTCTCTAACTTTTTCTGCCTCTGAA Human: GGGATAGGATCACCTTTGCCTCACTGGTAGAGAGCACATAGAGAAAG-CTACTAACTTTTTCTGCTTCTGAA Cluster: [ ] Orangutan: GGGAGAGGATCACCTTTGCCTCACTGGTAGAGAGCACATAGAGAAAG-CTTCTAACTTTTTCTGCCTCTGAA Gorilla > Chimp --------------- chr16:10108064-10108083 Template switch process: F1: L TCCCCTTTACCAGACCCCTGGGGATAGGATCACCTTTGCCTCACTGGTAG 1 F3: 4 CTAACTTTTTCTGCCTCTGAATCACTCAGAGTCTGCAA R RF: TCCCCTTTACCAGACCCCTGGGGATAGGATCACCTTTGCCTTACTGGTAGTAGCTTTCTCTATGTGCTCTCTAACTTTTTCTGCCTCTGAATCACCCAGAGTCTGCAA RR: AGGGGAAATGGTCTGGGGACCCCTATCCTAGTGGAAACGGAATGACCATCATCGAAAGAGATACACGAGAGATTGAAAAAGACGGAGACTTAGTGGGTCTCAGACGTT F2: 3 ATCGAAAGAGATACACGAGA 2 Unidirectional alignment (log-probability: -58.6) CAGACCCCTGGGGATAGGATCACCTTTGCCTcACTGGTAGagagcacatagagaaagcTA------------------CTAACTTTTTCTGCCTCTGAATCACtCAGAGTCTGCAA CAGACCCCTGGGGATAGGATCACCTTTGCCTTACTGGTAG------------------TAGCTTTCTCTATGTGCTCTCTAACTTTTTCTGCCTCTGAATCACCCAGAGTCTGCAA Template switch alignment (log-probability: -29.5) CAGACCCCTGGGGATAGGATCACCTTTGCCTcACTGGTAG|AGAGCACATAGAGAAAGCTA|CTAACTTTTTCTGCCTCTGAATCACtCAGAGTCTGCAA CAGACCCCTGGGGATAGGATCACCTTTGCCTTACTGGTAG|AGAGCACATAGAGAAAGCTA|CTAACTTTTTCTGCCTCTGAATCACCCAGAGTCTGCAA Chimp > Gorilla --------------- chr16:10027200-10027219 Template switch process: F1: L TCCCCTTTACCAGACCCCTGGGGATAGGATCACCTTTGCCTTACTGGTAG 1 F3: 4 CTAACTTTTTCTGCCTCTGAATCACCCAGAGTCTGCAA R RF: TCCCCTTTACCAGACCCCTGGGGATAGGATCACCTTTGCCTCACTGGTAGAGAGCACATAGAGAAAGCTACTAACTTTTTCTGCCTCTGAATCACTCAGAGTCTGCAA RR: AGGGGAAATGGTCTGGGGACCCCTATCCTAGTGGAAACGGAGTGACCATCTCTCGTGTATCTCTTTCGATGATTGAAAAAGACGGAGACTTAGTGAGTCTCAGACGTT F2: 3 TCTCGTGTATCTCTTTCGAT 2 Unidirectional alignment (log-probability: -58.6) CAGACCCCTGGGGATAGGATCACCTTTGCCTtACTGGTAG------------------TAgctttctctatgtgctctCTAACTTTTTCTGCCTCTGAATCACcCAGAGTCTGCAA CAGACCCCTGGGGATAGGATCACCTTTGCCTCACTGGTAGAGAGCACATAGAGAAAGCTA------------------CTAACTTTTTCTGCCTCTGAATCACTCAGAGTCTGCAA Template switch alignment (log-probability: -29.5) CAGACCCCTGGGGATAGGATCACCTTTGCCTtACTGGTAG|TAGCTTTCTCTATGTGCTCT|CTAACTTTTTCTGCCTCTGAATCACcCAGAGTCTGCAA CAGACCCCTGGGGATAGGATCACCTTTGCCTCACTGGTAG|TAGCTTTCTCTATGTGCTCT|CTAACTTTTTCTGCCTCTGAATCACTCAGAGTCTGCAA ========== Event 1347 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TACTCAGGCCCCGTCCATGGGCCTGATACACACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGA ↑ 1 4 3 2 Chimp: TACTCAGGCCCCGTCCATGGGA------CTCACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGA Gorilla: TACTCAGGCCCCGTCCATGGGA------CTCACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGA Human: TACTCAGGCCCCGTCCATGGGCCTGATACACACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGA Cluster: [ ] Orangutan: Chimp > Human ------------- chr16:1117126-1117134 Template switch process: F1: L ATAGGAACCCGGAGCGTGACTACTCAGGCCCCGTCCATGGG 1 F3: 4 CACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGAGAAG R RF: ATAGGAACCCGGAGCGTGACTACTCAGGCCCCGTCCATGGGACTCACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGAGAAG RR: TATCCTTGGGCCTCGCACTGATGAGTCCGGGGCAGGTACCCTGAGTGTGACACATAGTCCTGGATCTCGTCTCCGAGACTCTTC F2: 3 ACATAGTCC 2 Unidirectional alignment (log-probability: -25.6) TAGGAACCCGGAGCGTGACTACTCAGGCCCCGTCCATGGGcctgatACaCACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGAGAAG TAGGAACCCGGAGCGTGACTACTCAGGCCCCGTCCATGGG------ACTCACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGAGAAG Template switch alignment (log-probability: -16.4) TAGGAACCCGGAGCGTGACTACTCAGGCCCCGTCCATGGG|CCTGATACA|CACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGAGAAG TAGGAACCCGGAGCGTGACTACTCAGGCCCCGTCCATGGG|CCTGATACA|CACACTGTGTATCAGGACCTAGAGCAGAGGCTCTGAGAAG ========== Event 1348 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTCAAATATTAGTCAATCTAGGTTAAAAT---TACC---TAAAATGTGCTTAAATTAGATGAGTGA Chimp: CATTCAAATATTAGTCAATCTAGGTTAAAAT---TACC---TAAAATGTGCTTAAATTAGATGAGTGA ↓ 3 2 1 4 Gorilla: CATTCAAATATTAGTCAATCTAGGTTAAAAT------C------TAGGTGCTTAAATTAGTTGAGTGA ↑ 3 2 1 4 Human: CATTCAAATATTAGTCAATCTAGGTTAAAAT---TACC---TAAAATGTGCTTAAATTAGATGAGTGA Cluster: [ ] Orangutan: CATTCAAATA---TTCAATCTAGGTTAAAATTAC---CTAA---AATGTGCTTAAATTAGATGAGTGA Human > Gorilla --------------- chr1:70655686-70655689 Template switch process: F1: L AACGGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT 1 F3: 4 GTGCTTAAATTAGTTGAGTGACCCCTTAAAGAAATTAATT R RF: AACAGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAATTACCTAAAATGTGCTTAAATTAGATGAGTGACCCCTTAAAGAAATTAATT RR: TTGTCTCTGAGTAAGTTTATAATCAGTTAGATCCAATTTTAATGGATTTTACACGAATTTAATCTACTCACTGGGGAATTTCTTTAATTAA F2: 3 GATC 2 Unidirectional alignment (log-probability: -37.5) ACgGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT---CT---AgGTGCTTAAATTAGtTGAGTGACCCCTTAAAGAAATTAATT ACAGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAATTACCTAAAATGTGCTTAAATTAGATGAGTGACCCCTTAAAGAAATTAATT Template switch alignment (log-probability: -27.3) ACgGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT|CTAG|GTGCTTAAATTAGtTGAGTGACCCCTTAAAGAAATTAATT ACAGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT|CTAG|GTGCTTAAATTAGATGAGTGACCCCTTAAAGAAATTAATT Chimp > Gorilla --------------- chr1:70655686-70655689 Template switch process: F1: L AACGGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT 1 F3: 4 GTGCTTAAATTAGTTGAGTGACCCCTTAAAGAAATTAATT R RF: AACAGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAATTACCTAAAATGTGCTTAAATTAGATGAGTGACCCCTTAAAGAAATTAATT RR: TTGTCTCTGAGTAAGTTTATAATCAGTTAGATCCAATTTTAATGGATTTTACACGAATTTAATCTACTCACTGGGGAATTTCTTTAATTAA F2: 3 GATC 2 Unidirectional alignment (log-probability: -37.5) ACgGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT---CT---AgGTGCTTAAATTAGtTGAGTGACCCCTTAAAGAAATTAATT ACAGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAATTACCTAAAATGTGCTTAAATTAGATGAGTGACCCCTTAAAGAAATTAATT Template switch alignment (log-probability: -27.3) ACgGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT|CTAG|GTGCTTAAATTAGtTGAGTGACCCCTTAAAGAAATTAATT ACAGAGACTCATTCAAATATTAGTCAATCTAGGTTAAAAT|CTAG|GTGCTTAAATTAGATGAGTGACCCCTTAAAGAAATTAATT ========== Event 1349 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATCGATGTATTTAAGCTTCAGTATTTTGACTTAGAACCCCAGAAATTTCCCGTTATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAA--------------CATAATATACTGAACATTTAGATTCACTGAGAAGACA Chimp: TATCGATGTATTTAAGCTTCAGTATTTTGACTTAGAACCCCAGAAATTTCCCGTTATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAA--------------CATAATATACTGAACATTTAGATTCACTGAGAAGACA ↑ 3 2 4 1 Gorilla: TATCAATGTATTTAAGCTTCAGTATTTTGACTTAGAACCCCAGAAATTTCCCGATATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAA----------------------------CATTTAGATTCACTGAGAAGACA ↓ 3 2 4 1 Human: TATCGATGTATTTAAGCTTCAGTATTTTGACTTAGAACCCCAGAAATTTCCCGTTATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAA--------------CATAATATACTGAACATTTAGATTCACTGAGAAGACA Cluster: [ ] Orangutan: TATCGATGCATTTAAGATTCAGTATTTTGACTTAGAACCCCAGAAATTTCCCGTTATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGGCCATCTGCAACAATTATGAAATGGCTCAACATAATATACTGAA--------------GATTTAGATTCACTGAGAAGACA Gorilla > Human --------------- chr1:70108703-70108711 Template switch process: F1: L GCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACAT 1 F3: 4 AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAAGAA R RF: CAGTATTTTGACTTAGAACCCCAGAAATTTCCCGATATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACATTTAGATTCACTGAGAAGACAAGACATGTGAAAAGGA RR: GTCATAAAACTGAATCTTGGGGTCTTTAAAGGGCTATATATTTATCCACCTTGATGAACTATGACGACTATAAACTGGTAGACGTTGTCAATACTTTACCGAGTTGTAAATCTAAGTGACTCTTCTGTTCTGTACACTTTTCCT F2: 3 GTCATATAA 2 Unidirectional alignment (log-probability: -40.8) ATATTTGACCATCTGCAACAGTTATGAAATGGCTCaacataatatactgAACATTTAGATTCACTGAGAAGACAAGACATGTGAAAA-GA ATATTTGACCATCTGCAACAGTTATGAAATGGCTC--------------AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAAGGA Template switch alignment (log-probability: -28) ATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACAT|AAtATACTG|AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAAGa ATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACAT|AAAATACTG|AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAAGG Gorilla > Chimp --------------- chr1:70164390-70164398 Template switch process: F1: L GCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACAT 1 F3: 4 AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAA R RF: CAGTATTTTGACTTAGAACCCCAGAAATTTCCCGATATATAAATAGGTGGAACTACTTGATACTGCTGATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACATTTAGATTCACTGAGAAGACAAGACATGTGAAAA RR: GTCATAAAACTGAATCTTGGGGTCTTTAAAGGGCTATATATTTATCCACCTTGATGAACTATGACGACTATAAACTGGTAGACGTTGTCAATACTTTACCGAGTTGTAAATCTAAGTGACTCTTCTGTTCTGTACACTTTT F2: 3 GTCATATAA 2 Unidirectional alignment (log-probability: -37.9) ATATTTGACCATCTGCAACAGTTATGAAATGGCTCaacataatatactgAACATTTAGATTCACTGAGAAGACAAGACATGTGAAAA---- ATATTTGACCATCTGCAACAGTTATGAAATGGCTC--------------AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAAGGAA Template switch alignment (log-probability: -22.4) ATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACAT|AAtATACTG|AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAA ATATTTGACCATCTGCAACAGTTATGAAATGGCTCAACAT|AAAATACTG|AACATTTAGATTCACTGAGAAGACAAGACATGTGAAAA ========== Event 1350 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAATTCTCAGTT-----GATAGCC----TGGTGGCTATCCTGCCACAGC-AAAGAGGA- ↑ 3 1 2 4 Chimp: CAAATTCTCAGTT-----GATAGCC--------ACCAGTCCTGCCACAGC-AAAGAGGA- Gorilla: CAAATTCTCAGTT-----GATAGCC--------ACCAGCCCTGCCACAGC-AAAGAGGA- ↓ 3 1 2 4 Human: CAAATTCTCAGTT-----GATAGCC----TGGTGGCTATCCTGCCACAGC-AAAGAGGA- Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr1:178554799-178554807 Template switch process: F1: L TTATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC 1 F3: 4 TCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTAC R RF: TTATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCCACCAGTCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTAC RR: AATATCTTTGTCGTGTCTTTAGTTTAAGAGTCAACTATCGGTGGTCAGGACGGTGTCGTTTCTCCTTGGAAAAAGTCGTGGTGATG F2: 3 ATCGGTGGT 2 Unidirectional alignment (log-probability: -32.9) TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCCtggtggctA----TCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTAC TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC--------ACCAGTCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTAC Template switch alignment (log-probability: -16.4) TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC|TGGTGGCTA|TCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTAC TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC|TGGTGGCTA|TCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTAC Gorilla > Human --------------- chr1:178554799-178554808 Template switch process: F1: L TTATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC 1 F3: 4 CCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTACG R RF: TTATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCCACCAGCCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTACA RR: AATATCTTTGTCGTGTCTTTAGTTTAAGAGTCAACTATCGGTGGTCGGGACGGTGTCGTTTCTCCTTGGAAAAAGTCGTGGTGATGT F2: 3 TATCGGTGGT 2 Unidirectional alignment (log-probability: -40.8) TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGC------CtggtggctatCCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTACg TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCCACCAGC----------CCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTACA Template switch alignment (log-probability: -22.5) TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC|TGGTGGCTAT|CCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTACg TATAGAAACAGCACAGAAATCAAATTCTCAGTTGATAGCC|TGGTGGCTAT|CCTGCCACAGCAAAGAGGAACCTTTTTCAGCACCACTACA ========== Event 1351 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: -TTCGTTCAGATGACACCTGACA----------TGGGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCC ↑ 1 4 3 2 Chimp: -TTCGTTCAGATGACACCTGAGACCCATCTCAGGTGGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCC Gorilla: CTTCATTCAGATGACACCTGAGA----------TGGGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCC Human: -TTCGTTCAGATGACACCTGACA----------TGGGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCC Cluster: [ ] Orangutan: -TTCGTTCAGATGACACCTGACA----------TGGGCCAGAGGACCACTGTGAGCTCTGTCCCTCAGACGCC Chimp > Human ------------- chr1:241548280-241548282 Template switch process: F1: L CCCTGAGCCACTTGCAACCACTTCGTTCAGATGACACCTGACA 1 F3: 4 GCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCCTC R RF: CCCTGAGCCACTTGCAACCACTTCGTTCAGATGACACCTGAGACCCATCTCAGGTGGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCCTCCTGGATGGAGCAGGCGGGACAGAGAGCACCCACGACCAGGCCTCGTGGCCGGTGCCAGGCCTGCTTCCAACCTTTCTCCCACTCAGGGTCTTTGGCCA RR: GGGACTCGGTGAACGTTGGTGAAGCAAGTCTACTGTGGACTCTGGGTAGAGTCCACCGGTCTCCTGGTGGTACTCGAGACAGGGACTCTACGGAGGACCTACCTCGTCCGCCCTGTCTCTCGTGGGTGCTGGTCCGGAGCACCGGCCACGGTCCGGACGAAGGTTGGAAAGAGGGTGAGTCCCAGAAACCGGT F2: 3 GGT 2 Unidirectional alignment (log-probability: -26.1) TGAGCCACTTGCAACCACTTCGTTCAGATGACACCTGAcatG-------------GGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCCTC TGAGCCACTTGCAACCACTTCGTTCAGATGACACCTGA---GACCCATCTCAGGTGGCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCCTC Template switch alignment (log-probability: -21.7) TGAGCCACTTGCAACCACTTCGTTCAGATGACACCTGAcA|TGG|GCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCCTC TGAGCCACTTGCAACCACTTCGTTCAGATGACACCTGAGA|TGG|GCCAGAGGACCACCATGAGCTCTGTCCCTGAGATGCCTC ========== Event 1352 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: tttgtccaagacccttgcCTACTCAgtgggct--------cgtgtccactgggtaagtgggctcgtgtttgctgggtgcctgggGAGA Chimp: tttgtccaagacccttgcCTATGCAGTGGGCT--------CGTGTCCACTGGGTAAGTGGGCTCGTGTTTGCTGGGTGCCTGGAGAGA ↑ 3 4 2 1 Gorilla: tttgtccaagacccttgcCTATGCAGTGGGCT-------------------------------CGTGTTTGCTGGGTGCCTGGGGAGA Human: tttgtccaagacccttgcCTACTCAgtgggct--------cgtgtccactgggtaagtgggctcgtgtttgctgggtgcctgggGAGA Cluster: [ ] Orangutan: tttgtccaagacccttgctTATGCAGTGGGTTCGTGTCCT-----------------------GGTGTTTGTTAGGTGCCTGGGGAGA Gorilla > Chimp --------------- chr1:221695854-221695863 Template switch process: F1: L GCACCCAGCTTTGTCCAAGACCCTTGCCTATGCAGTGGGCTCGTGT 1 F3: 4 AGTGGGCTCGTGTTTGCTGGGTGCCTGGAGAGAGCAGGTTGGTGGACG R RF: GCACCCAGCTTTGTCCAAGACCCTTGCCTATGCAGTGGGCTCGTGTTTGCTGGGTGCCTGGGGAGAGCAGGTTGGTGGACG RR: CGTGGGTCGAAACAGGTTCTGGGAACGGATACGTCACCCGAGCACAAACGACCCACGGACCCCTCTCGTCCAACCACCTGC F2: 3 ATGGGTCACC 2 Unidirectional alignment (log-probability: -49.5) AGCTTTGTCCAAGACCCTTGCCTATGCAGTGGGctcgtgtccactgggtaagtgggCTCGTGTTTGCTGGGTGCCTGGaGAGAGCAGGTT AGCTTTGTCCAAGACCCTTGCCTATGCAGTGGG-----------------------CTCGTGTTTGCTGGGTGCCTGGGGAGAGCAGGTT Template switch alignment (log-probability: -33.9) AGCTTTGTCCAAGACCCTTGCCTATGCAGTGGGCTCGTGT|CCACTGggTA|AGTGGGCTCGTGTTTGCTGGGTGCCTGGaGAGAGCAGGTT AGCTTTGTCCAAGACCCTTGCCTATGCAGTGGGCTCGTGT|CCACTGCATA|AGTGGGCTCGTGTTTGCTGGGTGCCTGGGGAGAGCAGGTT ========== Event 1353 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTCTGCTGGTGGTCTGGCACTCCCC----TCATGTGACAGGCATGTGGCTTTTGGGAGGAAAGA Chimp: TCTCTGCTGGTGGTCTGGCACTCCCC----TCATGTGACAGGCATGTGGCTTTTTGGAGGAAAGA ↓ 1 4 3 2 Gorilla: TCTCTGCTGGTGGTCTGGCACATGCCTGGCACATGTGACAGGCATGTGGCTTTTTGGAGGAAAGA ↑ 1 4 3 2 Human: TCTCTGCTGGTGGTCTGGCACTCCCC----TCATGTGACAGGCATGTGGCTTTTGGGAGGAAAGA Cluster: [ ] Orangutan: TTTCTGCTGGTGGTCTGGCACTCCCC----TCATGTGACAGGCATGTGGCTTTTTGGAGGAAAGA Human > Gorilla --------------- chr17:94830488-94830497 Template switch process: F1: L ACTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCAC 1 F3: 4 CATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT R RF: ACTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCACTCCCCTCATGTGACAGGCATGTGGCTTTTGGGAGGAAAGAATCTTT RR: TGAAGGGTCGTGGGAGGGGGAGAGACGACCACCAGACCGTGAGGGGAGTACACTGTCCGTACACCGAAAACCCTCCTTTCTTAGAAA F2: 3 ACGGTCCGTA 2 Unidirectional alignment (log-probability: -38.8) CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCACatgCCTggcaCATGTGACAGGCATGTGGCTTTTtGGAGGAAAGAATCTTT CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCACTCCCCT----CATGTGACAGGCATGTGGCTTTTGGGAGGAAAGAATCTTT Template switch alignment (log-probability: -28) CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCAC|ATGCCTGgCA|CATGTGACAGGCATGTGGCTTTTtGGAGGAAAGAATCTTT CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCAC|ATGCCTGTCA|CATGTGACAGGCATGTGGCTTTTGGGAGGAAAGAATCTTT Chimp > Gorilla --------------- chr17:94830488-94830497 Template switch process: F1: L ACTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCAC 1 F3: 4 CATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT R RF: ACTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCACTCCCCTCATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT RR: TGAAGGGTCGTGGGAGGGGGAGAGACGACCACCAGACCGTGAGGGGAGTACACTGTCCGTACACCGAAAAACCTCCTTTCTTAGAAA F2: 3 ACGGTCCGTA 2 Unidirectional alignment (log-probability: -33.3) CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCACatgCCTggcaCATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCACTCCCCT----CATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT Template switch alignment (log-probability: -22.5) CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCAC|ATGCCTGgCA|CATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT CTTCCCAGCACCCTCCCCCTCTCTGCTGGTGGTCTGGCAC|ATGCCTGTCA|CATGTGACAGGCATGTGGCTTTTTGGAGGAAAGAATCTTT ========== Event 1354 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGT--TTCAATCATCCCTGACAGTTAAT Chimp: GTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGT--TTCAATCATCCCTGATAGTTAAT ↓ 3 2 1 4 Gorilla: GTTTCAGCCCCACAAGTTGCCTGAGCAGCAGGCTCAGGCAATCATCCCTGTCAGTTAAT ↑ 3 2 1 4 Human: GTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGT--TTCAATCATCCCTGACAGTTAAT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNGGCAGCAGAGT--TTCAATCATCCCTAACAGTTAAT Human > Gorilla --------------- chr17:84126015-84126021 Template switch process: F1: L CACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG 1 F3: 4 CAATCATCCCTGTCAGTTAATAGCATACATGATCATTTTG R RF: CACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGTTTCAATCATCCCTGACAGTTAATAGCATACATGATCATTTTG RR: GTGCTTACCTCAAAGTCGGGGTGTTCAACGGACTCGTCGTCTCAAAGTTAGTAGGGACTGTCAATTATCGTATGTACTAGTAAAAC F2: 3 GGACTCG 2 Unidirectional alignment (log-probability: -36.5) ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG-----gctcaggCAATCATCCCTGtCAGTTAATAGCATACATGATCATTTTG ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGTTT-------CAATCATCCCTGACAGTTAATAGCATACATGATCATTTTG Template switch alignment (log-probability: -22.1) ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG|GCTCAGG|CAATCATCCCTGtCAGTTAATAGCATACATGATCATTTTG ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG|GCTCAGG|CAATCATCCCTGACAGTTAATAGCATACATGATCATTTTG Chimp > Gorilla --------------- chr17:84126015-84126021 Template switch process: F1: L CACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG 1 F3: 4 CAATCATCCCTGTCAGTTAATAGCATACATGATCATTTTG R RF: CACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGTTTCAATCATCCCTGATAGTTAATAGCATACATGATCATTTTG RR: GTGCTTACCTCAAAGTCGGGGTGTTCAACGGACTCGTCGTCTCAAAGTTAGTAGGGACTATCAATTATCGTATGTACTAGTAAAAC F2: 3 GGACTCG 2 Unidirectional alignment (log-probability: -42) ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG-----gctcaggCAATCATCCCTGtcAGTTAATAGCATACATGATCATTTTG ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAGAGTTT-------CAATCATCCCTGATAGTTAATAGCATACATGATCATTTTG Template switch alignment (log-probability: -27.7) ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG|GCTCAGG|CAATCATCCCTGtcAGTTAATAGCATACATGATCATTTTG ACGAATGGAGTTTCAGCCCCACAAGTTGCCTGAGCAGCAG|GCTCAGG|CAATCATCCCTGATAGTTAATAGCATACATGATCATTTTG ========== Event 1355 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTTGTCTAAAATAGTAAAGGCAGGATTGTG-------GTTCATAAGGGGCCTCATCCCA Chimp: GGTTGTCTAAAATAGTAAAGGCAGGATTGTG-------GTTCATAAGGGGCCTCATCCCA ↓ 3 1 2 4 Gorilla: GGTTGTCTAAAATAGTAAAGGCAGGATCACAATCCTGCCTTCATAAGGGGCCTCATCCCA ↑ 3 1 2 4 Human: GGTTGTCTAAAATAGTAAAGGCAGGATTGTG-------GTTCATAAGGGGCCTCATCCCA Cluster: [ ] Orangutan: GGTTGTCTAAAATAGTAAAGGCAGGACTGTA-------GTTCATAAGGGGCCTCATCCCA Human > Gorilla --------------- chr17:82327469-82327480 Template switch process: F1: L GGAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT 1 F3: 4 TTCATAAGGGGCCTCATCCCAGCACACATATCAGATATGT R RF: GGGATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGATTGTGGTTCATAAGGGGCCTCATCCCAGCACACACATCAGATATGT RR: CCCTAGATCAGTAACCAACAGATTTTATCATTTCCGTCCTAACACCAAGTATTCCCCGGAGTAGGGTCGTGTGTGTAGTCTATACA F2: 3 CCGTCCTAACAC 2 Unidirectional alignment (log-probability: -49.2) GaATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGATcacaatcctgcc-----TTCATAAGGGGCCTCATCCCAGCACACAtATCAGATATGT GGATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT------------TGTGGTTCATAAGGGGCCTCATCCCAGCACACACATCAGATATGT Template switch alignment (log-probability: -28.3) GaATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT|CACAATCCTGCC|TTCATAAGGGGCCTCATCCCAGCACACAtATCAGATATGT GGATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT|CACAATCCTGCC|TTCATAAGGGGCCTCATCCCAGCACACACATCAGATATGT Chimp > Gorilla --------------- chr17:82327469-82327480 Template switch process: F1: L GGAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT 1 F3: 4 TTCATAAGGGGCCTCATCCCAGCACACATATCAGATATGT R RF: GGAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGATTGTGGTTCATAAGGGGCCTCATCCCAGCACACACATCAGATATGT RR: CCTTAGATCAGTAACCAACAGATTTTATCATTTCCGTCCTAACACCAAGTATTCCCCGGAGTAGGGTCGTGTGTGTAGTCTATACA F2: 3 CCGTCCTAACAC 2 Unidirectional alignment (log-probability: -43.7) GAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT-----cacaatcctgccTTCATAAGGGGCCTCATCCCAGCACACAtATCAGATATGT GAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGATTGTGG------------TTCATAAGGGGCCTCATCCCAGCACACACATCAGATATGT Template switch alignment (log-probability: -22.8) GAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT|CACAATCCTGCC|TTCATAAGGGGCCTCATCCCAGCACACAtATCAGATATGT GAATCTAGTCATTGGTTGTCTAAAATAGTAAAGGCAGGAT|CACAATCCTGCC|TTCATAAGGGGCCTCATCCCAGCACACACATCAGATATGT ========== Event 1356 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAGGTCCtgtggcagtcaaccatggaggtgttccactgggatccctttttcaagaaagaacttaaccaggtacagtggcttacacctgtaatcccagc ↓ 1 4 3 2 Chimp: TCTTTAAAGAGACTCTCCCTGC------CAC---TGTCCtgtggcagtcaaccatggaggtgttccactgggatccctttttcaagaaagaacttgaccaggtacagtggcttacacctgtaatcccagc ↑ 1 4 3 2 Gorilla: TCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAAGTCCtgtggcagtcaaccatggaggtgttccactgggatccctttttcaagaaagaacttgaccaggtacagtggcttacacctgtaatcccagc Human: TCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAGGTCCtgtggcagtcaaccatggaggtgttccactgggatccctttttcaagaaagaacttaaccaggtacagtggcttacacctgtaatcccagc Cluster: [ ] Orangutan: TCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAGGTCCtgtggcagtcaaccatggagatgttccactgggatctcttcttcaagaaagaacttgaccaggtacagtggcttacacctgtaatcccagc Human > Chimp ------------- chr17:36289851-36289856 Template switch process: F1: L TGGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG 1 F3: 4 TCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC R RF: TGGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAGGTCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATCCCTTTTTCAAGAAAGAACTTAACCAGGTACAGTGG RR: ACCCCTAAAATGGAGAAATGAGAAATTTCTCTGAGAGGGACAGGTTCGTTGACTCCAGGACACCGTCAGTTGGTACCTCCACAAGGTGACCCTAGGGAAAAAGTTCTTTCTTGAATTGGTCCATGTCACC F2: 3 GTCACC 2 Unidirectional alignment (log-probability: -27.6) GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTGccacT-------------GTCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG----TCCAAGCAACTGAGGTCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC Template switch alignment (log-probability: -16) GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG|CCACTG|TCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG|CCACTG|TCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC Gorilla > Chimp --------------- chr17:36289851-36289856 Template switch process: F1: L TGGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG 1 F3: 4 TCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC R RF: TGGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAAGTCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATCCCTTTTTCAAGAAAGAACTTGACCAGGTACAGTGG RR: ACCCCTAAAATGGAGAAATGAGAAATTTCTCTGAGAGGGACAGGTTCGTTGACTTCAGGACACCGTCAGTTGGTACCTCCACAAGGTGACCCTAGGGAAAAAGTTCTTTCTTGAACTGGTCCATGTCACC F2: 3 GTCACC 2 Unidirectional alignment (log-probability: -26.7) GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCT------GCcACT---GTCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTGTCCAAGCAACTGAAGTCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC Template switch alignment (log-probability: -16.5) GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG|CCACTG|TCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC GGGGATTTTACCTCTTTACTCTTTAAAGAGACTCTCCCTG|CCACTG|TCCTGTGGCAGTCAACCATGGAGGTGTTCCACTGGGATC ========== Event 1357 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TACATAGTGATAGGAAGGCTGCATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTGTAGTGTTTTCAAAGTCTCTAGACTATGGGTCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGCATCTAGCGTCATCTGGCGTCATCAGCTC ↓ 3 2 1 4 Chimp: TACATAGTGATAGGAAGGCTGCATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTGCAGTGTTTTCAAAGTCTCTAGACTATGGGTCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGG---CTGCAGTCATCTGGCGTCATCAGCTC Gorilla: TACATAGTGATAGGAAGGCTGCATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTGTAGTGTTTTCAAAGTCTCTAGACTATGGGTCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGG---CTGCAGTCATCTGGCATCATCAGCTC ↑ 3 2 1 4 Human: TACATAGTGATAGGAAGGCTGCATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTGTAGTGTTTTCAAAGTCTCTAGACTATGGGTCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGCATCTAGCGTCATCTGGCGTCATCAGCTC Cluster: [ ] Orangutan: TACATAGTGATATGAAGGCTGTATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTCTAGTGTTTTCAAAGTCTCTAGACTATGCATCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGG---CTGCAGTCATCTGGCATCATCAGCTC Human > Chimp ------------- chr17:29421934-29421937 Template switch process: F1: L AGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGC 1 F3: 4 GTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG R RF: TGCATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTGTAGTGTTTTCAAAGTCTCTAGACTATGGGTCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGCATCTAGCGTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG RR: ACGTAAATTACAGCTCGAGATCAGAAATTTACCTTAGACTTGTGGACATCACAAAAGTTTCAGAGATCTGATACCCAGTCCTCCTTCTTTACTTCCCCTCACCCAGATCTACGAGATCCGTAGATCGCAGTAGACCGCAGTAGTCGAGATTTTACTTCCCGTAGGTC F2: 3 ACGT 2 Unidirectional alignment (log-probability: -25.8) GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGgctGCA------GTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAG---GCATCTAGCGTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG Template switch alignment (log-probability: -15.8) GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGC|TGCA|GTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGC|TGCA|GTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG Human > Gorilla --------------- chr5:55679625-55679628 Template switch process: F1: L AGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGC 1 F3: 4 GTCATCTGGCATCATCAGCTCTAAAATGAAGGGCATCCAG R RF: TGCATTTAATGTCGAGCTCTAGTCTTTAAATGGAATCTGAACACCTGTAGTGTTTTCAAAGTCTCTAGACTATGGGTCAGGAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGCATCTAGCGTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG RR: ACGTAAATTACAGCTCGAGATCAGAAATTTACCTTAGACTTGTGGACATCACAAAAGTTTCAGAGATCTGATACCCAGTCCTCCTTCTTTACTTCCCCTCACCCAGATCTACGAGATCCGTAGATCGCAGTAGACCGCAGTAGTCGAGATTTTACTTCCCGTAGGTC F2: 3 ACGT 2 Unidirectional alignment (log-probability: -30.8) GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGgctGCA------GTCATCTGGCaTCATCAGCTCTAAAATGAAGGGCATCCAG GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAG---GCATCTAGCGTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG Template switch alignment (log-probability: -21.8) GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGC|TGCA|GTCATCTGGCaTCATCAGCTCTAAAATGAAGGGCATCCAG GAGGAAGAAATGAAGGGGAGTGGGTCTAGATGCTCTAGGC|TGCA|GTCATCTGGCGTCATCAGCTCTAAAATGAAGGGCATCCAG ========== Event 1358 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACCAGGCCTAGCTGGGTGGCAGGGCTGGG---CCCAGTC-------------------------CTCTAACTGGTCTGGTGCCGCCTCCTC Chimp: CACCAGGCCTAGCTGGGTGGCAGGGCTGGG---CCCAGTC-------------------------CTCTAACTGGTCTGGTGCCGCCTCCTC ↓ 3 2 1 4 Gorilla: CACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCACCCAGCC---------------------------CTGCCTGGTCTGGTGCCGCCTCCTC ↑ 3 2 1 4 Human: CACCAGGCCTAGCTGGGTGGCAGGGCTGGG---CCCAGTC-------------------------CTCTAACTGGTCTGGTGCCGCCTCCTC Cluster: [ ] Orangutan: CACCAGGCCTAGCTGGGTGGCAGGGctggg---cccagtcctctaactggtctgggcccagtcct--ctaactggtctggTGCCGCCTCCGC Human > Gorilla --------------- chr5:110539502-110539512 Template switch process: F1: L CCACCCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCA 1 F3: 4 CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT R RF: CCACCCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCCAGTCCTCTAACTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT RR: GGTGGGTCTTCGTGGTCCGGATCGACCCACCGTCCCGACCCGGGTCAGGAGATTGACCAGACCACGGCGGAGGAGGAGCGGGTGTGGGGCCCGA F2: 3 CGTCCCGACCC 2 Unidirectional alignment (log-probability: -37) CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCC----------AcccagccctgcCTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCCAGTCCTCTAA-----------CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT Template switch alignment (log-probability: -22.7) CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCa|CCCAGCCCTGC|CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCC|CCCAGCCCTGC|CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT Chimp > Gorilla --------------- chr5:110539502-110539512 Template switch process: F1: L CCACCCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCA 1 F3: 4 CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT R RF: CCACCCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCCAGTCCTCTAACTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT RR: GGTGGGTCTTCGTGGTCCGGATCGACCCACCGTCCCGACCCGGGTCAGGAGATTGACCAGACCACGGCGGAGGAGGAGCGGGTGTGGGGCCCGA F2: 3 CGTCCCGACCC 2 Unidirectional alignment (log-probability: -37) CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCC----------AcccagccctgcCTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCCAGTCCTCTAA-----------CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT Template switch alignment (log-probability: -22.7) CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCa|CCCAGCCCTGC|CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT CCAGAAGCACCAGGCCTAGCTGGGTGGCAGGGCTGGGCCC|CCCAGCCCTGC|CTGGTCTGGTGCCGCCTCCTCCTCGCCCACACCCCGGGCT ========== Event 1359 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGGAAGGTACTTCCAGGCCATCCTTGAAGGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGCAGAAA Chimp: TTGGAAGGTACTTCCAGGCCATGCTTGAAGGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGCAGAAA ↑ 1 4 3 2 Gorilla: TTGGAAGGTACTTCCAGGCCA-------CAGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGCAGAAA Human: TTGGAAGGTACTTCCAGGCCATCCTTGAAGGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGCAGAAA Cluster: [ ] Orangutan: TTGGGTGGTACTTCCAGGCCATCCTTGAAGGAGCTCAG-------------AAAAGCAGCATGGAAAAGCAGAAA Gorilla > Chimp --------------- chr17:2993033-2993041 Template switch process: F1: L GAGGAGGTTGATTCTGGGGCTTGGAAGGTACTTCCAGGCCA 1 F3: 4 GAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGC R RF: GAGGAGGTTGATTCTGGGGTTTGGAAGGTACTTCCAGGCCACAGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGC RR: CTCCTCCAACTAAGACCCCAAACCTTCCATGAAGGTCCGGTGTCTCGAGTCTCACTCAGGAAGTTTGTGGTCGTACCTTTTCG F2: 3 GAAGTTCGT 2 Unidirectional alignment (log-probability: -37.5) AGGAGGTTGATTCTGGGGcTTGGAAGGTACTTCCAGGCCatgcttgAagGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGC AGGAGGTTGATTCTGGGGTTTGGAAGGTACTTCCAGGCC-------ACAGAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGC Template switch alignment (log-probability: -27.9) AGGAGGTTGATTCTGGGGcTTGGAAGGTACTTCCAGGCCA|TGcTTGAAG|GAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGC AGGAGGTTGATTCTGGGGTTTGGAAGGTACTTCCAGGCCA|TGTTTGAAG|GAGCTCAGAGTGAGTCCTTCAAACACCAGCATGGAAAAGC ========== Event 1360 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCA ↓ 3 1 2 4 Chimp: TGGTCCCCTGTCTGAAGGGACCTTC-----AGGTCTGCGGTTCTGCGGAAGTCCA ↑ 3 1 2 4 Gorilla: TGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCA Human: TGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCA Cluster: [ ] Orangutan: TGGTCCCATGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCAGAAGTCCA Human > Chimp ------------- chr17:27920557-27920562 Template switch process: F1: L TCCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCT 1 F3: 4 CTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC R RF: TCCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC RR: AGGGGATAGGGGTGAGATACCAGGGGACAGACTTCCCTGGACTTTATTCCCCGACGCCAAGACGCCTTCAGGTATGAGTGCGCGGTGAAAGG F2: 3 TGGACT 2 Unidirectional alignment (log-probability: -29.2) CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCTtcA-----GGtCTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC Template switch alignment (log-probability: -16) CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCT|TCAGGT|CTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCT|TCAGGT|CTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC Gorilla > Chimp --------------- chr17:27920557-27920562 Template switch process: F1: L TCCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCT 1 F3: 4 CTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC R RF: TCCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC RR: AGGGGATAGGGGTGAGATACCAGGGGACAGACTTCCCTGGACTTTATTCCCCGACGCCAAGACGCCTTCAGGTATGAGTGCGCGGTGAAAGG F2: 3 TGGACT 2 Unidirectional alignment (log-probability: -27.8) CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCTtcA-----GGtCTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCTGAAATAAGGGGCTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC Template switch alignment (log-probability: -16.5) CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCT|TCAGGT|CTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC CCCCTATCCCCACTCTATGGTCCCCTGTCTGAAGGGACCT|TCAGGT|CTGCGGTTCTGCGGAAGTCCATACTCACGCGCCACTTTCC ========== Event 1361 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAGAGTACAACTAAAGAAATTTGGGATGGAAAAGAGTGTAGAAAAACAAACGAGAAATGTATTTTAATT Chimp: TGAGAGTACAACTAAAGAAATTTGTTTTTCTACACTCTTTTCCATCCCAAACGAGAAATGTATTTTAATT ↑ 1 3 4 2 Gorilla: TGAGAGTACAACTAAAGAAATCTGGGATGGAAAAGAGTGTAGAAAAACAAACGAGAAAGGTATTTTAATT Human: TGAGAGTACAACTAAAGAAATTTGGGATGGAAAAGAGTGTAGAAAAACAAACGAGAAATGTATTTTAATT Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr17:79950661-79950686 Template switch process: F1: L TGAAAGCATCTTAACTCCTCTGAGAGTACAACTAAAGAAAT 1 F3: 4 CAAACGAGAAATGTATTTTAATTACCTTATGTTGTATCTC R RF: TGAAAGCATCTTAACTCCTCTGAGAGTACAACTAAAGAAATCTGGGATGGAAAAGAGTGTAGAAAAACAAACGAGAAAGGTATTTTAATTACCTTACGTTGTATCTC RR: ACTTTCGTAGAATTGAGGAGACTCTCATGTTGATTTCTTTAGACCCTACCTTTTCTCACATCTTTTTGTTTGCTCTTTCCATAAAATTAATGGAATGCAACATAGAG F2: 3 CCTACCTTTTCTCACATCTTTTTGTT 2 Unidirectional alignment (log-probability: -68.9) GAAAGCATCTTAACTCCTCTGAGAGTACAACTAAAGAAATttgtttttctacactcttttccatcC-------------------------CAAACGAGAAAtGTATTTTAATTACCTTAtGTTGTATCTC GAAAGCATCTTAACTCCTCTGAGAGTACAACTAAAGAAAT-------------------------CTGGGATGGAAAAGAGTGTAGAAAAACAAACGAGAAAGGTATTTTAATTACCTTACGTTGTATCTC Template switch alignment (log-probability: -30.1) GAAAGCATCTTAACTCCTCTGAGAGTACAACTAAAGAAAT|TTGTTTTTCTACACTCTTTTCCATCC|CAAACGAGAAAtGTATTTTAATTACCTTAtGTTGTATCTC GAAAGCATCTTAACTCCTCTGAGAGTACAACTAAAGAAAT|TTGTTTTTCTACACTCTTTTCCATCC|CAAACGAGAAAGGTATTTTAATTACCTTACGTTGTATCTC ========== Event 1362 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGAGAAGAGCTGACATCATGCATGAGACAAAGGCCACTGTTCATGGGTGGGTGGGGACAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGG--CAGGGAGCCTTGTA-ACCCAGGCC Chimp: CAGAGAAGAGCTGACATCATGCATGAGACAAAGGCCACTGTTCATGGGTGGGTGGGGACAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGG--CAGGGAGCCTTGTA-ACCCAGGCC ↓ 3 2 1 4 Gorilla: CAGAGAAGAGCTGACATCATGCATGAGACAAAGGCCACTGTTCATGGGTGGGTGGGGACAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCTCATGC----TGGAGCCTTGTA-ACCCAGGCC ↑ 3 2 1 4 Human: CAGAGAAGAGCTGACATCATGCATGAGACAAAGGCCACTGTTCATGGGTGGGTGGGGACAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGG--CAGGGAGCCTTGTA-ACCCAGGCC Cluster: [ ] Orangutan: CAGAGAAGAGCTGACATCATGCATGAGACAA-AGCTACTGTTCATGGGTGGGTGGGGACAAGAGTATGAGCATGGGAAGTCTGTGGGTGAGGGTCTGTCACTGGGCA---GGAGCCTTGTAATCCCAGGCC Human > Gorilla --------------- chr5:51558127-51558133 Template switch process: F1: L CAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC 1 F3: 4 GGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG R RF: TGCATGAGACAAAGGCCACTGTTCATGGGTGGGTGGGGACAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGGCAGGGAGCCTTGTAACCCAGGCCCCTGGAACTCAGGCTCAGGG RR: ACGTACTCTGTTTCCGGTGACAAGTACCCACCCACCCCTGTTCTCATACCCGTACCATTCAGACACCCACTCCCAGACAGTGACCCGTCCCTCGGAACATTGGGTCCGGGGACCTTGAGTCCGAGTCCC F2: 3 TCGTACT 2 Unidirectional alignment (log-probability: -36.7) AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC---------tcatgctGGAGCCTTGTAACCCAGGCCCCTGGAACcCAGGCTCAGGG AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGGCAG-------GGAGCCTTGTAACCCAGGCCCCTGGAACTCAGGCTCAGGG Template switch alignment (log-probability: -27.7) AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC|TCATGCt|GGAGCCTTGTAACCCAGGCCCCTGGAACcCAGGCTCAGGG AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC|TCATGCA|GGAGCCTTGTAACCCAGGCCCCTGGAACTCAGGCTCAGGG Chimp > Gorilla --------------- chr5:51558127-51558133 Template switch process: F1: L CAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC 1 F3: 4 GGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG R RF: TGCATGAGACAAAGGCCACTGTTCATGGGTGGGTGGGGACAAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGGCAGGGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG RR: ACGTACTCTGTTTCCGGTGACAAGTACCCACCCACCCCTGTTCTCATACCCGTACCATTCAGACACCCACTCCCAGACAGTGACCCGTCCCTCGGAACATTGGGTCCGGGGACCTTGGGTCCGAGTCCC F2: 3 TCGTACT 2 Unidirectional alignment (log-probability: -31.2) AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC---------tcatgctGGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTCACTGGGCAG-------GGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG Template switch alignment (log-probability: -22.1) AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC|TCATGCt|GGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG AAGAGTATGGGCATGGTAAGTCTGTGGGTGAGGGTCTGTC|TCATGCA|GGAGCCTTGTAACCCAGGCCCCTGGAACCCAGGCTCAGGG ========== Event 1363 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTCATCATCAGGGCCAGGTT-GCCTTTGCTGCCCTCATCAGGCCCTTATACAGCC--------------------AGGGCATTGGTGGTACTCTGGG ↑ 1 3 2 4 Chimp: GTCCATCATCAGGGCCAGGTTGGCCCTGGCT----GTATAAGGGCCTGATGAGGGC----------AGCAAAGGGGTGGGCATTGGTGGTACTCTGGG Gorilla: GTCCATCATCAGGGCCAGGTTGGCCCTGGCT----GTATAAGGGCCTGATGAGGGCAGCAAAGGGG----------TGGGCATTGGTGGTACTCTGGG ↓ 1 3 2 4 Human: GTTCATCATCAGGGCCAGGTT-GCCTTTGCTGCCCTCATCAGGCCCTTATACAGCC--------------------AGGGCATTGGTGGTACTCTGGG Cluster: [ ] Orangutan: gtCCATCATCAGGGCCAGGTTGGCCCTGGCT----GTATAAGGGCCTGATGAGGGCAGCAAAGGGG----------TGGGCATTGGTGGTACTCTGGG Chimp > Human ------------- chr17:33526635-33526668 Template switch process: F1: L CTAAGAATGGGTGCTGGATTGTTCATCATCAGGGCCAGGTTG 1 F3: 4 GGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT R RF: CTAAGAATGGGTGCTGGATTGTCCATCATCAGGGCCAGGTTGGCCCTGGCTGTATAAGGGCCTGATGAGGGCAGCAAAGGGGTGGGCATTGGTGGTACTCTGGGCAGGATATGAGACCCTGCT RR: GATTCTTACCCACGACCTAACAGGTAGTAGTCCCGGTCCAACCGGGACCGACATATTCCCGGACTACTCCCGTCGTTTCCCCACCCGTAACCACCATGAGACCCGTCCTATACTCTGGGACGA F2: 3 ACCGACATATTCCCGGACTACTCCCGTCGTTTCC 2 Unidirectional alignment (log-probability: -84.1) AAGAATGGGTGCTGGATTGTtCATCATCAGGGCCAGGTTGcctttgctgccctcatcaggcccttatacagcca-----------------------------------------GGGCATTGGTGGTACTCTGGGCAGGcTATGAGACCCTGCT AAGAATGGGTGCTGGATTGTCCATCATCAGGGCCAGGTTG----------------------------------GCCCTGGCTGTATAAGGGCCTGATGAGGGCAGCAAAGGGGTGGGCATTGGTGGTACTCTGGGCAGGATATGAGACCCTGCT Template switch alignment (log-probability: -31.5) AAGAATGGGTGCTGGATTGTtCATCATCAGGGCCAGGTTG|CCTTTGCTGCCCTCATCAGGCCCTTATACAGCCA|GGGCATTGGTGGTACTCTGGGCAGGcTATGAGACCCTGCT AAGAATGGGTGCTGGATTGTCCATCATCAGGGCCAGGTTG|CCTTTGCTGCCCTCATCAGGCCCTTATACAGCCA|GGGCATTGGTGGTACTCTGGGCAGGATATGAGACCCTGCT Gorilla > Human --------------- chr17:33526635-33526668 Template switch process: F1: L CTAAGAATGGGTGCTGGATTGTTCATCATCAGGGCCAGGTTG 1 F3: 4 GGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT R RF: CTAAGGATGGGTGCTGGATTGTCCATCATCAGGGCCAGGTTGGCCCTGGCTGTATAAGGGCCTGATGAGGGCAGCAAAGGGGTGGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT RR: GATTCCTACCCACGACCTAACAGGTAGTAGTCCCGGTCCAACCGGGACCGACATATTCCCGGACTACTCCCGTCGTTTCCCCACCCGTAACCACCATGAGACCCGTCCGATACTCTGGGACGA F2: 3 ACCGACATATTCCCGGACTACTCCCGTCGTTTCC 2 Unidirectional alignment (log-probability: -82.3) AAGaATGGGTGCTGGATTGTtCATCATCAGGGCCAGGTTGcctttgctgccctcatcaggcccttatacaGCC-------------------------------------aGGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT AAGGATGGGTGCTGGATTGTCCATCATCAGGGCCAGGTTG------------------------------GCCCTGGCTGTATAAGGGCCTGATGAGGGCAGCAAAGGGGTGGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT Template switch alignment (log-probability: -31.1) AAGaATGGGTGCTGGATTGTtCATCATCAGGGCCAGGTTG|CCTTTGCTGCCCTCATCAGGCCCTTATACAGCCA|GGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT AAGGATGGGTGCTGGATTGTCCATCATCAGGGCCAGGTTG|CCTTTGCTGCCCTCATCAGGCCCTTATACAGCCA|GGGCATTGGTGGTACTCTGGGCAGGCTATGAGACCCTGCT ========== Event 1364 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACAACAGCTAAAGTCTTACCTAGGGATGGTGCATGGGCACCATCCCTAAAAGAGAGAAAGAGATTT Chimp: ACAACAGCTAAAGTCTTACCT-------ATACCCATGCACCATCCCTAAAAGAGAGAAAGAGATTT Gorilla: ACAACAGCTAAAGTCTTACCT-------ATACCCATGCACCATCCCTAAAACAGAGAAAGAGATTT ↓ 1 3 4 2 Human: ACAACAGCTAAAGTCTTACCTAGGGATGGTGCATGGGCACCATCCCTAAAAGAGAGAAAGAGATTT Cluster: [ ] Orangutan: ACAACAGCTAAAGTCTTACCT-------ATACCCATGCACCATCCCTAAAAGAGAGAAAGGGATTT Gorilla > Human --------------- chr1:175459807-175459820 Template switch process: F1: L TGGCTGAAAACCTAACCAGAACAACAGCTAAAGTCTTACCTA 1 F3: 4 GCACCATCCCTAAAAGAGAGAAAGAGATTTATGTGTGGGT R RF: TGGCTGAAAACCTAACCAGAACAACAGCTAAAGTCTTACCTATACCCATGCACCATCCCTAAAACAGAGAAAGAGATTTGTGTGTGGGT RR: ACCGACTTTTGGATTGGTCTTGTTGTCGATTTCAGAATGGATATGGGTACGTGGTAGGGATTTTGTCTCTTTCTCTAAACACACACCCA F2: 3 GGTACGTGGTAGGG 2 Unidirectional alignment (log-probability: -52.2) GCTGAAAACCTAACCAGAACAACAGCTAAAGTCTTACCTA-------gggatggtgcatggGCACCATCCCTAAAAgAGAGAAAGAGATTTaTGTGTGGGT GCTGAAAACCTAACCAGAACAACAGCTAAAGTCTTACCTATACCCAT--------------GCACCATCCCTAAAACAGAGAAAGAGATTTGTGTGTGGGT Template switch alignment (log-probability: -28.6) GCTGAAAACCTAACCAGAACAACAGCTAAAGTCTTACCTA|GGGATGGTGCATGG|GCACCATCCCTAAAAgAGAGAAAGAGATTTaTGTGTGGGT GCTGAAAACCTAACCAGAACAACAGCTAAAGTCTTACCTA|GGGATGGTGCATGG|GCACCATCCCTAAAACAGAGAAAGAGATTTGTGTGTGGGT ========== Event 1365 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: tccttatataTTAATACCCCATT---------------------TACAGATGATCTTGGATCATTTACAGATCCAAGAtcatctgtaaatggggtattaa Chimp: tccttatataTTAATACCCCATT---------------------TACAGATGATCTTGGATCATTTACAGATCCAAGAtcatctgtaaatggggtattaa ↑ 4 31 2 Gorilla: tccttatataTTAATACCCCATT------------------------------------------TACAGATCCAAGAACATCTGTAAATGGGGTATTAA ↓ 4 31 2 Human: tccttatataTTAATACCCCATT---------------------TACAGATGATCTTGGATCATTTACAGATCCAAGAtcatctgtaaatggggtattaa Cluster: [ ] Orangutan: tccttatataTTAATACCCCATTTACAGATGATCTTGGATCATT---------------------TACAGATCCAAGATCATCTGTAAATGGGGTATTAA Gorilla > Human --------------- chr17:33976142-33976151 Template switch process: F1: L ATGAAGCCTTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGAT 1 F3: 4 CATTTACAGATCCAAGATCATCTGTAAATGGGGTATTAATCCCT R RF: ATGAAGCCTTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGATCCAAGAACATCTGTAAATGGGGTATTAATCCCT RR: TACTTCGGAAGGGACCAGAGGAATATATAATTATGGGGTAAATGTCTAGGTTCTTGTAGACATTTACCCCATAATTAGGGA F2: 3 TAGGTTCTAG 2 Unidirectional alignment (log-probability: -46.6) TTCCCTGGTCTCCTTATATATTAATACCCCAtttacagatgatcttggatcaTTTACAGATCCAAGAtCATCTGTAAATGGGGTATTAAT TTCCCTGGTCTCCTTATATATTAATACCCCA---------------------TTTACAGATCCAAGAACATCTGTAAATGGGGTATTAAT Template switch alignment (log-probability: -28.3) TTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGAT|GaTCTTGGAT|CATTTACAGATCCAAGAtCATCTGTAAATGGGGTATTAAT TTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGAT|GTTCTTGGAT|CATTTACAGATCCAAGAACATCTGTAAATGGGGTATTAAT Gorilla > Chimp --------------- chr17:59918488-59918497 Template switch process: F1: L ATGAAGCCTTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGAT 1 F3: 4 CATTTACAGATCCAAGATCATCTGTAAATGGGGTATTAATCCCT R RF: ATGAAGCCTTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGATCCAAGAACATCTGTAAATGGGGTATTAATCCCT RR: TACTTCGGAAGGGACCAGAGGAATATATAATTATGGGGTAAATGTCTAGGTTCTTGTAGACATTTACCCCATAATTAGGGA F2: 3 TAGGTTCTAG 2 Unidirectional alignment (log-probability: -46.6) TTCCCTGGTCTCCTTATATATTAATACCCCAtttacagatgatcttggatcaTTTACAGATCCAAGAtCATCTGTAAATGGGGTATTAAT TTCCCTGGTCTCCTTATATATTAATACCCCA---------------------TTTACAGATCCAAGAACATCTGTAAATGGGGTATTAAT Template switch alignment (log-probability: -28.3) TTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGAT|GaTCTTGGAT|CATTTACAGATCCAAGAtCATCTGTAAATGGGGTATTAAT TTCCCTGGTCTCCTTATATATTAATACCCCATTTACAGAT|GTTCTTGGAT|CATTTACAGATCCAAGAACATCTGTAAATGGGGTATTAAT ========== Event 1366 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCC--ACCCCAATAAAGGAAGTCTTTATTCGACT----TTATTCTGAAGCATCAAATCAT Chimp: cccc--GCCCCAATAAAGGAAGT-------CGAAT--AAAGATTCTGAAGCATCAAATCAT Gorilla: cccc--ACCCCAATAAAGGAAGT-------CGAATAA--AGATTCTGAAGCATCAAATCAT ↓ 3 1 24 Human: CCCC--ACCCCAATAAAGGAAGTCTTTATTCGACT----TTATTCTGAAGCATCAAATCAT Cluster: [ ] Orangutan: CCCCACCCCCCAATAAAGGAAGT-------CGAATAA--AGATTCTGAAGCATCAAATCAT Gorilla > Human --------------- chr17:34798509-34798520 Template switch process: F1: L AAAATAATCTAATCCCACCCCCCCACCCCAATAAAGGAAGTC 1 F3: 4 TATTCTGAAGCATCAAATCATTCTATGATTAGGTGATGGAC R RF: AAAATAATCTAATCCCACCCCCCCACCCCAATAAAGGAAGTCGAATAAAGATTCTGAAGCATCAAATCATTCTATGATTAGGTGATGGAC RR: TTTTATTAGATTAGGGTGGGGGGGTGGGGTTATTTCCTTCAGCTTATTTCTAAGACTTCGTAGTTTAGTAAGATACTAATCCACTACCTG F2: 3 TTCAGCTTATTT 2 Unidirectional alignment (log-probability: -39.7) AATAATCTAATCCCACCCCCCCACCCCAATAAAGGAAGTC--------tttattcgactttATTCTGAAGCATCAAATCATTCTATGATTAGGTGATGGA AATAATCTAATCCCACCCCCCCACCCCAATAAAGGAAGTCGAATAAAG-------------ATTCTGAAGCATCAAATCATTCTATGATTAGGTGATGGA Template switch alignment (log-probability: -22.8) AATAATCTAATCCCACCCCCCCACCCCAATAAAGGAAGTC|TTTATTCGACTT|tATTCTGAAGCATCAAATCATTCTATGATTAGGTGATGGA AATAATCTAATCCCACCCCCCCACCCCAATAAAGGAAGTC|TTTATTCGACTT|GATTCTGAAGCATCAAATCATTCTATGATTAGGTGATGGA ========== Event 1367 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ttgacagacctcaaaCAGGATTGC----------------------------------------------CTTACACAGTTACACTTGGGTGTAAGTGAAGGCCTTACACCCAAACTGGGAGTGG Chimp: ttgacagacctcaaaCAGGATTGC----------------------------------------------CTTACACAGTTACACTTGGGTGTAAGTGAAGGCCTTACACCCAAACTGGGAGTGG Gorilla: ttgacagacctcaaaCAGGATTGC-----------------------CTTACACCCTGTAAGGCAATTGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCTTACACCCAAACTGGGAGTGG ↑ 4 3 2 1 Human: ttgacagacctcaaaCAGGATTGC----------------------------------------------CTTACACAGTTACACTTGGGTGTAAGTGAAGGCCTTACACCCAAACTGGGAGTGG Cluster: [ ] Orangutan: ttgacagacctcaaaCAGGATTGCCTTACACCCTGTAAGGCAATTGC-----------------------CTTACACACTTACACTTGGGTGTAAGTGAAGGCCTTACACCCAAACTGGGAGTGG Human > Gorilla --------------- chr5:116747882-116747889 Template switch process: F1: L CCAAGGTCAAGCTCAGATTGACAGACCTCAAACAGGATTGCCTTACAC-------------------------CCT 1 F3: 4 ATTGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCTTACAC R RF: CCAAGGTCAAGCTCAGATTGACAGACCTCAAACAGGATTGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCTTACAC RR: GGTTCCAGTTCGAGTCTAACTGTCTGGAGTTTGTCCTAACGGAATGTGTCAATGTGAACCCACATTCACTTCCGGAATGTG F2: 3 ACGGAATG 2 Unidirectional alignment (log-probability: -44) CTCAGATTGACAGACCTCAAACAGGATTgccttacaccctgtaaggcaattGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCT CTCAGATTGACAGACCTCAAACAGGATT-----------------------GCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCT Template switch alignment (log-probability: -28.1) CTCAGATTGACAGACCTCAAACAGGATTGCCTTACAC-------------------------CCT|GTAAGGCA|ATTGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCT CTCAGATTGACAGACCTCAAACAGGATTGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCT|GTAAGGCA|ATTGCCTTACACAGTTACACTTGGGTGTAAGTGAAGGCCT ========== Event 1368 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTACATGCTCAGAACTCACA----CAAAGCTCCTACTCGTGCA------------------------------TCTGGTCTACttttattttttat---------------ttttttgagatggagcctcactctcttgcccaggctggagtgcagtggcatgatcttggctcactgcaacctctttctcatgggttca Chimp: TCTACATGCTCAGAACTCACA----CAAAGCTCCTACTCGTGCA------------------------------TCTGGTCTACttttattttttat-------tttttattttttttgagatggagcctcactctgttgcccaggctggagtgcagtggcatgatcttggctcactgcaacctctttctcatgggttca ↓ 1 4 3 2 Gorilla: TCTACATGCTCAGAACTCACACATGCAGAGCTCCTACTCATGCA-----------------------------------------------------ttttatt--------ttttttgagatggagcctcactctgttgcccaggctggagtgcagtggcattatcttggctcactgcaacctctttctcatgggttca Human: TCTACATGCTCAGAACTCACA----CAAAGCTCCTACTCGTGCA------------------------------TCTGGTCTACttttattttttat---------------ttttttgagatggagcctcactctcttgcccaggctggagtgcagtggcatgatcttggctcactgcaacctctttctcatgggttca Cluster: [ ] Orangutan: TCTACATGCTCAGAACTCACA----CAAAGCTCCTACTAGTGCATCTGGTCTACttttttattttttattttta--------------------------------------ttttttgagatggagcctcactctgttgcccaggctggagtgcagtggcatgatcttggctcactgcaacctccttctcatgggttca Chimp > Gorilla --------------- chr5:117015564-117015568 Template switch process: F1: L GACATCTGCCCTCTACTCACTCTACATGCTCAGAACTCACACA 1 F3: 4 AGCTCCTACTCATGCAT R RF: GACATCTGCCCTCTACTCACTCTACATGCTCAGAACTCACACAAAGCTCCTACTCGTGCATCTGGTCTACTTTTATTTTTTATTTTTTATTTTTTTTGAGATGGAGCCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCTTGGCTCACTGCA RR: CTGTAGACGGGAGATGAGTGAGATGTACGAGTCTTGAGTGTGTTTCGAGGATGAGCACGTAGACCAGATGAAAATAAAAAATAAAAAATAAAAAAAACTCTACCTCGGAGTGAGACAACGGGTCCGACCTCACGTCACCGTACTAGAACCGAGTGACGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -35.3) ATCTGCCCTCTACTCACTCTACATGCTCAGAACTCACAcatgCAgAGCTCCTACTCaTGCAT---------------------- ATCTGCCCTCTACTCACTCTACATGCTCAGAACTCACA----CAAAGCTCCTACTCGTGCATCTGGTCTACTTTTATTTTTTAT Template switch alignment (log-probability: -21.3) ATCTGCCCTCTACTCACTCTACATGCTCAGAACTCACACA|TGCAG|AGCTCCTACTCaTGCAT ATCTGCCCTCTACTCACTCTACATGCTCAGAACTCACACA|TGCAG|AGCTCCTACTCGTGCAT ========== Event 1369 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTATGGCTCAATTTTGAATATCT---TCGGTTTTGCTATGTACTGTAATAACTATA------- Chimp: CTATGGCTCAATTTTGAATATCT---TCGGTTTTGCTATGTACTATAATAACTATA------- Gorilla: CTATGGCTCAATTTTGAATATTGTACATAGTTTTGCTATGTACTGTAATAACTATA------- ↑ 1 4 3 2 Human: CTATGGCTCAATTTTGAATATCT---TCGGTTTTGCTATGTACTGTAATAACTATA------- Cluster: [ ] Orangutan: CTACGGCTCAATTTTGAATATCT---tcagttttgctatgtactgtaataactactcagttat Human > Gorilla --------------- chr5:47633440-47633447 Template switch process: F1: L TACCGAGTTGTGCCAAAACACTATGGCTCAATTTTGAATATT 1 F3: 4 TTTTGCTATGTACTGTAATAACTATACACACTCAGTTAT R RF: TACCGAGTTGTGCCAAAACACTATGGCTCAATTTTGAATATCTTCGGTTTTGCTATGTACTGTAATAACTATACACACTCAGTTAT RR: ATGGCTCAACACGGTTTTGTGATACCGAGTTAAAACTTATAGAAGCCAAAACGATACATGACATTATTGATATGTGTGAGTCAATA F2: 3 GATACATG 2 Unidirectional alignment (log-probability: -32.4) CCGAGTTGTGCCAAAACACTATGGCTCAATTTTGAATAT-----tgtacataGTTTTGCTATGTACTGTAATAACTATACACACTCAGTTAT CCGAGTTGTGCCAAAACACTATGGCTCAATTTTGAATATCTTCG--------GTTTTGCTATGTACTGTAATAACTATACACACTCAGTTAT Template switch alignment (log-probability: -22.3) CCGAGTTGTGCCAAAACACTATGGCTCAATTTTGAATATt|GTACATAG|TTTTGCTATGTACTGTAATAACTATACACACTCAGTTAT CCGAGTTGTGCCAAAACACTATGGCTCAATTTTGAATATC|GTACATAG|TTTTGCTATGTACTGTAATAACTATACACACTCAGTTAT ========== Event 1370 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGCACTTAGATCTACTAGTTTCATACACAGGCTGGGGTAGGAGCCTGTGTATGAAACTTCTTAGATGGAAAGCCTTC Chimp: CAGCACTTAAATCTACTAGTTTCATACACAGGCTGGGGTAGGAGCGAC---TTCTCTCTTCTTAGATGGAAAGCCTTC Gorilla: CAGCACTTAGATCTACTAGTTTCATACACAGGCTAGGGTAGGAGCGAC---TTCCCTCTTCTTAGATGGAAAGCCTTC ↓ 3 2 1 4 Human: CAGCACTTAGATCTACTAGTTTCATACACAGGCTGGGGTAGGAGCCTGTGTATGAAACTTCTTAGATGGAAAGCCTTC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr17:47962350-47962361 Template switch process: F1: L ACTTAGATCTACTAGTTTCATACACAGGCTGGGGTAGGAGC 1 F3: 4 CTTCTTAGATGGAAAGCCTTCCAATCAGTTATCACCCTTT R RF: ACTTAGATCTACTAGTTTCATACACAGGCTAGGGTAGGAGCGACTTCCCTCTTCTTAGATGGAAAGCCTTCCAATCAGTTATCACCCTTT RR: TGAATCTAGATGATCAAAGTATGTGTCCGATCCCATCCTCGCTGAAGGGAGAAGAATCTACCTTTCGGAAGGTTAGTCAATAGTGGGAAA F2: 3 AAAGTATGTGTC 2 Unidirectional alignment (log-probability: -40.9) CTTAGATCTACTAGTTTCATACACAGGCTgGGGTAGGAG-------CCTgtgtatgaaaCTTCTTAGATGGAAAGCCTTCCAATCAGTTATCACCCTTT CTTAGATCTACTAGTTTCATACACAGGCTAGGGTAGGAGCGACTTCCCT----------CTTCTTAGATGGAAAGCCTTCCAATCAGTTATCACCCTTT Template switch alignment (log-probability: -22.8) CTTAGATCTACTAGTTTCATACACAGGCTgGGGTAGGAGC|CTGTGTATGAAA|CTTCTTAGATGGAAAGCCTTCCAATCAGTTATCACCCTTT CTTAGATCTACTAGTTTCATACACAGGCTAGGGTAGGAGC|CTGTGTATGAAA|CTTCTTAGATGGAAAGCCTTCCAATCAGTTATCACCCTTT ========== Event 1371 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACCTTGCACTTGGGCTGTGAGTGCACACACAAGTGTGCAGTGCACACATGAGGCACACAGCACAGGCTTT Chimp: ACCTTGCACTTGGGCTGTGAGTGCACACACAAGTGTGCAGTGCACACATGAGGCACACAGCACAGGCTTT ↑ 4 3 1 2 Gorilla: ACCTTGCACTTGGGCTGTGAGTGC-------------------ACACATGAGGCACACAGCACAGGCTTT ↓ 4 3 1 2 Human: ACCTTGCACTTGGGCTGTGAGTGCACACACAAGTGTGCAGTGCACACATGAGGCACACAGCACAGGCTTT Cluster: [ ] Orangutan: ACCTTGCACTTGGGCTGTGAGTGC-------------------ACACGTGAGGCACACAGCACAGGCTTT Gorilla > Human --------------- chr17:46439284-46439292 Template switch process: F1: L GGGCAGTAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACA 1 F3: 4 AGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCATATACA R RF: GGGCAGTAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCATATACA RR: CCCGTCATTCGGTCGGATGGAACGTGAACCCGACACTCACGTGTGTACTCCGTGTGTCGTGTCCGAAAGAAACGTATATGT F2: 3 CGTGTGAAC 2 Unidirectional alignment (log-probability: -38.2) TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTgcacacacaagtgtgcagtGCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGT-------------------GCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT Template switch alignment (log-probability: -22.6) TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACA|CAaGTGTGC|AGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACA|CATGTGTGC|AGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT Gorilla > Chimp --------------- chr17:20648461-20648469 Template switch process: F1: L GGGCAGTAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACA 1 F3: 4 AGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCATATACA R RF: GGGCAGTAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCATATACA RR: CCCGTCATTCGGTCGGATGGAACGTGAACCCGACACTCACGTGTGTACTCCGTGTGTCGTGTCCGAAAGAAACGTATATGT F2: 3 CGTGTGAAC 2 Unidirectional alignment (log-probability: -38.2) TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTgcacacacaagtgtgcagtGCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGT-------------------GCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT Template switch alignment (log-probability: -22.6) TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACA|CAaGTGTGC|AGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT TAAGCCAGCCTACCTTGCACTTGGGCTGTGAGTGCACACA|CATGTGTGC|AGTGCACACATGAGGCACACAGCACAGGCTTTCTTTGCAT ========== Event 1372 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: ATTCAGCTCTAAGAGCTTCAAAAAATCATG--------------GAATTCCATGATTCCAGAGATCAACTGGGCA Chimp: attcagctctaagagcttcaaagaacagct-------gagaccccaattccatgattccagagatcaactgggca Gorilla: ATTCAGCTCTAAGAGCTTCAAGAAACAGCTGAGACCC-------CAATTCCATGATTCCAGAGATCAACTGGGCA ↓ 1 4 3 2 Human: ATTCAGCTCTAAGAGCTTCAAAAAATCATG--------------GAATTCCATGATTCCAGAGATCAACTGGGCA Cluster: [ ] Orangutan: ATTCAGCTCTAAGAGCTTCGAAAAACAGCTGAGACCC-------CAATTCCATGATTCCAGAGATCAACTGGGCA Gorilla > Human --------------- chr17:37716784-37716789 Template switch process: F1: L ATAGAGCCCCTGGCGATTTAATTCAGCTCTAAGAGCTTCAAAAAA 1 F3: 4 AATTCCATGATTCCAGAGATCAACTGGGCACCAGCCTCTA R RF: ATAGAGCCCCTGGCGATTTAATTCAGCTCTAAGAGCTTCAAGAAACAGCTGAGACCCCAATTCCATGATTCCAGAGATCAACTGGGCACCAGCCTCTA RR: TATCTCGGGGACCGCTAAATTAAGTCGAGATTCTCGAAGTTCTTTGTCGACTCTGGGGTTAAGGTACTAAGGTCTCTAGTTGACCCGTGGTCGGAGAT F2: 3 GGTACT 2 Unidirectional alignment (log-probability: -34.4) GCCCCTGGCGATTTAATTCAGCTCTAAGAGCTTCAAaaaatcatgG----------------AATTCCATGATTCCAGAGATCAACTGGGCACCAGCCTCTA GCCCCTGGCGATTTAATTCAGCTCTAAGAGCTTCAA---------GAAACAGCTGAGACCCCAATTCCATGATTCCAGAGATCAACTGGGCACCAGCCTCTA Template switch alignment (log-probability: -22.1) GCCCCTGGCGATTTAATTCAGCTCTAAGAGCTTCAAaAAA|TCATGG|AATTCCATGATTCCAGAGATCAACTGGGCACCAGCCTCTA GCCCCTGGCGATTTAATTCAGCTCTAAGAGCTTCAAGAAA|TCATGG|AATTCCATGATTCCAGAGATCAACTGGGCACCAGCCTCTA ========== Event 1373 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTCTAAGTGGAAGGATGAAGG-TTGTCTTTTTTCTTAAAAGTCACATGGCAGGCGCAGGCTGACAA ↓ 13 24 ↑ 13 24 Chimp: GTCTCAGTGGAAGGATGAAGGTGTGACTTTTAAGAAAAAAGAC-AATGGCAGGCGCAGGCTGACGA Gorilla: GTCTCAGTGGAAGGATGAAGGTGTGACTTTTAAGAAAAAAGAC-AATGGCAGGCGCAGGCTGACGA ↓ 13 24 ↑ 13 24 Human: GTCTAAGTGGAAGGATGAAGG-TTGTCTTTTTTCTTAAAAGTCACATGGCAGGCGCAGGCTGACAA Cluster: [ ] Orangutan: GTCTCAGTGGAAGGATGAAGGTGTGACTTTTAAGAAAAAAGAA-AATGGCAGGCACAGGCTGACGA Chimp > Human ------------- chr17:34071932-34071953 Template switch process: F1: L CTGGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGT 1 F3: 4 ATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA R RF: CTGGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGTGTGACTTTTAAGAAAAAAGACAATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA RR: GACCGATTCTTTTTTTCTTACAGAGTCACCTTCCTACTTCCACACTGAAAATTCTTTTTTCTGTTACCGTCCGCGTCCGACTGCTGTCCACCGCTCTTTGTCGT F2: 3 CACTGAAAATTCTTTTTTCTGT 2 Unidirectional alignment (log-probability: -64.5) GGCTAAGAAAAAAAGAATGTCTaAGTGGAAGGATGAAGGTtgtcttttttcttaaaaGTcAC-----------------ATGGCAGGCGCAGGCTGACaACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGT-----------------GTGACTTTTAAGAAAAAAGACAATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA Template switch alignment (log-probability: -30) GGCTAAGAAAAAAAGAATGTCTaAGTGGAAGGATGAAGGT|TGTCTTTTTTCTTAAAAGTCAC|ATGGCAGGCGCAGGCTGACaACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGT|TGTCTTTTTTCTTAAAAGTCAC|ATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA Human > Chimp ------------- chr17:60019346-60019367 Template switch process: F1: L CTGGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGT 1 F3: 4 ATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA R RF: CTGGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGTTGTCTTTTTTCTTAAAAGTCACATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA RR: GACCGATTCTTTTTTTCTTACAGATTCACCTTCCTACTTCCAACAGAAAAAAGAATTTTCAGTGTACCGTCCGCGTCCGACTGTTGTCCACCGCTCTTTGTCGT F2: 3 ACAGAAAAAAGAATTTTCAGTG 2 Unidirectional alignment (log-probability: -64.5) GGCTAAGAAAAAAAGAATGTCTcAGTGGAAGGATGAAGGT-----------------GTgACttttaagaaaaaagacaATGGCAGGCGCAGGCTGACgACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGTTGTCTTTTTTCTTAAAAGTCAC-----------------ATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA Template switch alignment (log-probability: -30) GGCTAAGAAAAAAAGAATGTCTcAGTGGAAGGATGAAGGT|GTGACTTTTAAGAAAAAAGACA|ATGGCAGGCGCAGGCTGACgACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGT|GTGACTTTTAAGAAAAAAGACA|ATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA Gorilla > Human --------------- chr17:34071932-34071953 Template switch process: F1: L CTGGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGT 1 F3: 4 ATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA R RF: CTGGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGTGTGACTTTTAAGAAAAAAGACAATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA RR: GACCGATTCTTTTTTTCTTACAGAGTCACCTTCCTACTTCCACACTGAAAATTCTTTTTTCTGTTACCGTCCGCGTCCGACTGCTGTCCACCGCTCTTTGTCGT F2: 3 CACTGAAAATTCTTTTTTCTGT 2 Unidirectional alignment (log-probability: -62.6) GGCTAAGAAAAAAAGAATGTCTaAGTGGAAGGATGAAGGTtgtcttttttcttaaaaGTcAC-----------------ATGGCAGGCGCAGGCTGACaACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGT-----------------GTGACTTTTAAGAAAAAAGACAATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA Template switch alignment (log-probability: -29.6) GGCTAAGAAAAAAAGAATGTCTaAGTGGAAGGATGAAGGT|TGTCTTTTTTCTTAAAAGTCAC|ATGGCAGGCGCAGGCTGACaACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGT|TGTCTTTTTTCTTAAAAGTCAC|ATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA Human > Gorilla --------------- chr5:116025278-116025299 Template switch process: F1: L CTGGCTAAGAAAAAAAGAATGTCTCAGTGGAAGGATGAAGGT 1 F3: 4 ATGGCAGGCGCAGGCTGACGACAGGTGGCGAGAAACAGCA R RF: CTGGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGTTGTCTTTTTTCTTAAAAGTCACATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA RR: GACCGATTCTTTTTTTCTTACAGATTCACCTTCCTACTTCCAACAGAAAAAAGAATTTTCAGTGTACCGTCCGCGTCCGACTGTTGTCCACCGCTCTTTGTCGT F2: 3 ACAGAAAAAAGAATTTTCAGTG 2 Unidirectional alignment (log-probability: -62.6) GGCTAAGAAAAAAAGAATGTCTcAGTGGAAGGATGAAGGT-----------------GTgACttttaagaaaaaagacaATGGCAGGCGCAGGCTGACgACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGTTGTCTTTTTTCTTAAAAGTCAC-----------------ATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA Template switch alignment (log-probability: -29.6) GGCTAAGAAAAAAAGAATGTCTcAGTGGAAGGATGAAGGT|GTGACTTTTAAGAAAAAAGACA|ATGGCAGGCGCAGGCTGACgACAGGTGGCGAGAAACAGCA GGCTAAGAAAAAAAGAATGTCTAAGTGGAAGGATGAAGGT|GTGACTTTTAAGAAAAAAGACA|ATGGCAGGCGCAGGCTGACAACAGGTGGCGAGAAACAGCA ========== Event 1374 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGGGGTTCCCCCTGCCCATAAGGAGGTGTGACTTAAGGAGGTGGCCTTGGCGTAGTTTTGCTTCAGAACTCAGGaaa-aaaaaTGTTGGCATTAGTCACTAAGGAGGGAAGTGGCTGG Chimp: ATGGGGTTCCCCCTGCCCATAAGGAGGTGTGACTTAAGGAGGTGGCCTTGGCGTAGTTTTGCTTCAGAACTCAGGaaaaaaaaaTGTTGGCATTAGTCACTAAAGAGGGAAGTGGCTGG ↑ 4 1 3 2 Gorilla: ATGGGGTTCCCCCTGCCCATAA---------------GGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAGGaaaaaaaaaTGTTGGCATTAGTCACTAAAGAGGGAAGTGGCTGG ↓ 4 1 3 2 Human: ATGGGGTTCCCCCTGCCCATAAGGAGGTGTGACTTAAGGAGGTGGCCTTGGCGTAGTTTTGCTTCAGAACTCAGGaaa-aaaaaTGTTGGCATTAGTCACTAAGGAGGGAAGTGGCTGG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr17:37778228-37778232 Template switch process: F1: L TTTGTGGGTACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTG 1 F3: 4 TAAGGAGGTGGCCTTGGCGTAGTTTTGCTTCAGAACTCAGGAA R RF: TTTGTGGGTACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAGGAAAAAAAAATGTTGGCATTAGTCA RR: AAACACCCATGTATTCTTCTACCCCAAGGGGGACGGGTATTCCTCCACCGGAACCACATCAAAACGAAGTCTTGAGTCCTTTTTTTTTACAACCGTAATCAGT F2: 3 TCAGT 2 Unidirectional alignment (log-probability: -38) TACATAAGAAGATGGGGTTCCCCCTGCCCATaaggaggtgtgacttAAGGAGGTGGCCTTGGcGTAGTTTTGCTTCAGAACTCAG TACATAAGAAGATGGGGTTCCCCCTGCCCAT---------------AAGGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAG Template switch alignment (log-probability: -22.1) TACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTG|TGACT|TAAGGAGGTGGCCTTGGcGTAGTTTTGCTTCAGAACTCAG TACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTG|TGACT|TAAGGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAG Gorilla > Chimp --------------- chr17:63500307-63500311 Template switch process: F1: L TTTGTGGGTACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTG 1 F3: 4 TAAGGAGGTGGCCTTGGCGTAGTTTTGCTTCAGAACTCAGGAA R RF: TTTGTGGGTACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAGGAAAAAAAAATGTTGGCATTAGTCA RR: AAACACCCATGTATTCTTCTACCCCAAGGGGGACGGGTATTCCTCCACCGGAACCACATCAAAACGAAGTCTTGAGTCCTTTTTTTTTACAACCGTAATCAGT F2: 3 TCAGT 2 Unidirectional alignment (log-probability: -38) TACATAAGAAGATGGGGTTCCCCCTGCCCATaaggaggtgtgacttAAGGAGGTGGCCTTGGcGTAGTTTTGCTTCAGAACTCAG TACATAAGAAGATGGGGTTCCCCCTGCCCAT---------------AAGGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAG Template switch alignment (log-probability: -22.1) TACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTG|TGACT|TAAGGAGGTGGCCTTGGcGTAGTTTTGCTTCAGAACTCAG TACATAAGAAGATGGGGTTCCCCCTGCCCATAAGGAGGTG|TGACT|TAAGGAGGTGGCCTTGGTGTAGTTTTGCTTCAGAACTCAG ========== Event 1375 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TCACAGGTCCCTTCTCACAAGAGTGCTTGGATAAGGAGTGGACACGCAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAGGCAC--------TCTCTGGGGAAATGTGGACAAATT ↑ 3 2 1 4 Chimp: TCACAGGTCCCTTCTCACAAGAGTGCTTGGATAAGGAGTGGACACGCAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAGTCCATCACCACATTTCTGGGGAAATGTGGACAAATT Gorilla: Human: TCACAGGTCCCTTCTCACAAGAGTGCTTGGATAAGGAGTGGACACGCAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAGGCAC--------TCTCTGGGGAAATGTGGACAAATT Cluster: [ ] Orangutan: TCACAGGTCTCTTCTCACAGGAGTGTTTGGATAAGGAGTGGGCACGCAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAGTCAC--------TCTCTGGGAAAATGTGGACAAATT Chimp > Human ------------- chr17:3840052-3840058 Template switch process: F1: L GCAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAG 1 F3: 4 CTGGGGAAATGTGGACAAATTTCCCACAAAACACCCTGT R RF: AGAGTGCTTGGATAAGGAGTGGACACGCAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAGTCCATCACCACATTTCTGGGGAAATGTGGACAAATTTCCCACAAAACACCCTGT RR: TCTCACGAACCTATTCCTCACCTGTGCGTTCCGTTCCGGTCTTCGTACTCCACTACCGTCCCTTTTCAGGTAGTGGTGTAAAGACCCCTTTACACCTGTTTAAAGGGTGTTTTGTGGGACA F2: 3 TCTCACG 2 Unidirectional alignment (log-probability: -27.5) CAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAGgcacTC------------TCTGGGGAAATGTGGACAAATTTCCCACAAAACACCCTGT CAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAG----TCCATCACCACATTTCTGGGGAAATGTGGACAAATTTCCCACAAAACACCCTGT Template switch alignment (log-probability: -16.1) CAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAG|GCACTCT|CTGGGGAAATGTGGACAAATTTCCCACAAAACACCCTGT CAAGGCAAGGCCAGAAGCATGAGGTGATGGCAGGGAAAAG|GCACTCT|CTGGGGAAATGTGGACAAATTTCCCACAAAACACCCTGT ========== Event 1376 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: gtggctcacgcctgtaagcccagcactttgggaggccgaggcaggtggatcacctgaggtcaggTGGAGAGTGCTGGTGAGGCAGGCTGTGACTGGGC ↑ 3 2 1 4 Chimp: gtggctcacgcctgtaagcccagcactttgggaggccgaggcaggtggatcacctgaggtcaggTGGAG------GCTGAGGCAGGCTGCGACTGGGC Gorilla: gtggctcacgcctgtaagcccagcactttgggaggccgaggcaggtggatcacctgaggtcaggTGGAGGGTGCTGGTGAGGCAGGCTGTGACTGGGC Human: gtggctcacgcctgtaagcccagcactttgggaggccgaggcaggtggatcacctgaggtcaggTGGAGAGTGCTGGTGAGGCAGGCTGTGACTGGGC Cluster: [ ] Orangutan: gtggctcactcctgtaagcccagcactttgggaggccgaggcagatggatcacctgaggtcaggTGGAGGGTGCTGGTGAGGCAGGCTGTGACTGGGC Chimp > Human ------------- chr17:44668307-44668314 Template switch process: F1: L TGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGTGGAG 1 F3: 4 TGAGGCAGGCTGTGACTGGGCCCATGTCAGTGAGCAAGTA R RF: CCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGTGGAGGCTGAGGCAGGCTGCGACTGGGCCCATGTCAGTGAGCAAGTA RR: GGTCGTGAAACCCTCCGGCTCCGTCCACCTAGTGGACTCCAGTCCACCTCCGACTCCGTCCGACGCTGACCCGGGTACAGTCACTCGTTCAT F2: 3 GGTCGTGA 2 Unidirectional alignment (log-probability: -31.6) GGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGTGGAGagtgctGgTGAGGCAGGCTGtGACTGGGCCCATGTCAGTGAGCAAGTA GGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGTGGAG------GCTGAGGCAGGCTGCGACTGGGCCCATGTCAGTGAGCAAGTA Template switch alignment (log-probability: -22.3) GGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGTGGAG|AGTGCTGG|TGAGGCAGGCTGtGACTGGGCCCATGTCAGTGAGCAAGTA GGGAGGCCGAGGCAGGTGGATCACCTGAGGTCAGGTGGAG|AGTGCTGG|TGAGGCAGGCTGCGACTGGGCCCATGTCAGTGAGCAAGTA ========== Event 1377 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ccgccctccACCGCCTGTCATGTTCTCAAGGCAGCTCTGACCACACTGCGATCTGTTGCTGCGTGTGGTTTTCTGGGATGAACGGCTTGCTTCTTTCTCAGGTGTGGCCATGGGGAGAACAAGGACCATGTCTCCAAGAACATGGTGCCATGCCTGGGGCATGC ↑ 3 2 1 4 Chimp: ccgccctccaccgcctgtcatgttctcaaggcagctctgaccacactgcgatCTGTTGCTGCGTGTGGTTTTCTGGGATGAACGGCTTGCTTCTTTCTCAGGTGTGGCCATGGGGAGAACAAGGACCATCTCTCCAGGGT-CTGGTGCCATGCCTGGGGCATGC Gorilla: ccgccctccaccgcctgtcatattctcaaggcagctctgaccaCACTGCGATCTGTTGCTGCGTGTGGTTTTCTGGGATGAACGGCTTGCTTCTTTCTCAGGTGTGGCCATGGGGAGAACAAGGACCATCTCTCCAAGAACACGGTGCCATGCCTGGGACATGC Human: ccgccctccACCGCCTGTCATGTTCTCAAGGCAGCTCTGACCACACTGCGATCTGTTGCTGCGTGTGGTTTTCTGGGATGAACGGCTTGCTTCTTTCTCAGGTGTGGCCATGGGGAGAACAAGGACCATGTCTCCAAGAACATGGTGCCATGCCTGGGGCATGC Cluster: [ ] Orangutan: ccgccctccactgcctgtcatgttctcaaggcacctctgaccacactGTGATCTGTTGCTGCGTGCGGTTTTCTGGGATGAATGGCTTGCTTCCTTCTCAGGTGTGGGCAT-GGGAGAACAAGGACCATCTCTCCAGGGT-CTGGTGTCGTGCCAGAA------ Chimp > Human ------------- chr17:79285197-79285203 Template switch process: F1: L GCTTCTTTCTCAGGTGTGGCCATGGGGAGAACAAGGACCATGTCTCCA 1 F3: 4 GGTGCCATGCCTGGGGCATGCTGGGTCCTTGAAATTTTT R RF: ATGTTCTCAAGGCAGCTCTGACCACACTGCGATCTGTTGCTGCGTGTGGTTTTCTGGGATGAACGGCTTGCTTCTTTCTCAGGTGTGGCCATGGGGAGAACAAGGACCATCTCTCCAGGGTCTGGTGCCATGCCTGGGGCATGCTGGGTCCTTGAAATTTTT RR: TACAAGAGTTCCGTCGAGACTGGTGTGACGCTAGACAACGACGCACACCAAAAGACCCTACTTGCCGAACGAAGAAAGAGTCCACACCGGTACCCCTCTTGTTCCTGGTAGAGAGGTCCCAGACCACGGTACGGACCCCGTACGACCCAGGAACTTTAAAAA F2: 3 TACAAGA 2 Unidirectional alignment (log-probability: -36) CTCAGGTGTGGCCATGGGGAGAACAAGGACCAT---------GTCtccaagaacaTGGTGCCATGCCTGGGGCATGCTGGGTCCTTGAAATTTTT CTCAGGTGTGGCCATGGGGAGAACAAGGACCATCTCTCCAGGGTC----------TGGTGCCATGCCTGGGGCATGCTGGGTCCTTGAAATTTTT Template switch alignment (log-probability: -22.3) CTCAGGTGTGGCCATGGGGAGAACAAGGACCATgTCTCCA|AGAACAT|GGTGCCATGCCTGGGGCATGCTGGGTCCTTGAAATTTTT CTCAGGTGTGGCCATGGGGAGAACAAGGACCATCTCTCCA|AGAACAT|GGTGCCATGCCTGGGGCATGCTGGGTCCTTGAAATTTTT ========== Event 1378 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GATACTGTAAAATGCTGATAGT-AAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAAT Chimp: GATACTGTAAAATGCTGATAGT-AAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAAT ↓ 1 3 24 ↑ 13 24 Gorilla: GATACTGTAAAATGCTGATAGGAGAAAGTGAGAATCCTATTTTTTCTT-TTACTATCTTTAAGATCATCAAAT ↓ 13 24 ↑ 1 3 24 Human: GATACTGTAAAATGCTGATAGT-AAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAAT Cluster: [ ] Orangutan: GATACTGTAAAATGCTGATAGT-AAAAGAAAAAATAGGATTGTCACTTTCTCCTATCTTTAAGATCATCAAAT Gorilla > Human --------------- chr17:39876446-39876475 Template switch process: F1: L ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG 1 F3: 4 CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC R RF: ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGGAGAAAGTGAGAATCCTATTTTTTCTTTTACTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC RR: TATTTACCCCGTGACGTCTTCTATGACATTTTACGACTATCCTCTTTCACTCTTAGGATAAAAAAGAAAATGATAGAAATTCTAGTAGTTTAATATTTCAAACTTTGAGTG F2: 3 CTCTTTCACTCTTAGGATAAAAAAGAAAAT 2 Unidirectional alignment (log-probability: -62.3) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG----------------------------TAaaagaaaaaataggattctcactttctcCTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGGAGAAAGTGAGAATCCTATTTTTTCTTTTA----------------------------CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Template switch alignment (log-probability: -19.5) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|TAAAAGAAAAAATAGGATTCTCACTTTCTC|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|TAAAAGAAAAAATAGGATTCTCACTTTCTC|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Human > Gorilla --------------- chr5:121710671-121710700 Template switch process: F1: L ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG 1 F3: 4 CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC R RF: ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGTAAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC RR: TATTTACCCCGTGACGTCTTCTATGACATTTTACGACTATCATTTTCTTTTTTATCCTAAGAGTGAAAGAGGATAGAAATTCTAGTAGTTTAATATTTCAAACTTTGAGTG F2: 3 ATTTTCTTTTTTATCCTAAGAGTGAAAGAG 2 Unidirectional alignment (log-probability: -62.3) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGgagaaagtgagaatcctattttttctttTA----------------------------CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG----------------------------TAAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Template switch alignment (log-probability: -19.5) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|GAGAAAGTGAGAATCCTATTTTTTCTTTTA|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|GAGAAAGTGAGAATCCTATTTTTTCTTTTA|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Gorilla > Chimp --------------- chr17:65428767-65428796 Template switch process: F1: L ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG 1 F3: 4 CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC R RF: ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGGAGAAAGTGAGAATCCTATTTTTTCTTTTACTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC RR: TATTTACCCCGTGACGTCTTCTATGACATTTTACGACTATCCTCTTTCACTCTTAGGATAAAAAAGAAAATGATAGAAATTCTAGTAGTTTAATATTTCAAACTTTGAGTG F2: 3 CTCTTTCACTCTTAGGATAAAAAAGAAAAT 2 Unidirectional alignment (log-probability: -62.3) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG----------------------------TAaaagaaaaaataggattctcactttctcCTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGGAGAAAGTGAGAATCCTATTTTTTCTTTTA----------------------------CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Template switch alignment (log-probability: -19.5) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|TAAAAGAAAAAATAGGATTCTCACTTTCTC|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|TAAAAGAAAAAATAGGATTCTCACTTTCTC|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Chimp > Gorilla --------------- chr5:121710671-121710700 Template switch process: F1: L ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG 1 F3: 4 CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC R RF: ATAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGTAAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC RR: TATTTACCCCGTGACGTCTTCTATGACATTTTACGACTATCATTTTCTTTTTTATCCTAAGAGTGAAAGAGGATAGAAATTCTAGTAGTTTAATATTTCAAACTTTGAGTG F2: 3 ATTTTCTTTTTTATCCTAAGAGTGAAAGAG 2 Unidirectional alignment (log-probability: -62.3) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAGgagaaagtgagaatcctattttttctttTA----------------------------CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG----------------------------TAAAAGAAAAAATAGGATTCTCACTTTCTCCTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC Template switch alignment (log-probability: -19.5) TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|GAGAAAGTGAGAATCCTATTTTTTCTTTTA|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC TAAATGGGGCACTGCAGAAGATACTGTAAAATGCTGATAG|GAGAAAGTGAGAATCCTATTTTTTCTTTTA|CTATCTTTAAGATCATCAAATTATAAAGTTTGAAACTCAC ========== Event 1379 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGTTTGACATCATTTACCTGGATCTTGTTCTGACAAGATCCATGAGTCAGAAATAGACA Chimp: AGTTTGACATCATTTACCTGGATCTTGTCCTGACAAGATCCATGAGTCAAAAATAGACA Gorilla: AGTTTGACATCATTTACCTGGTACTA----GAACAAGATCCATGAGTCAGAAATAGACA ↓ 1 3 4 2 Human: AGTTTGACATCATTTACCTGGATCTTGTTCTGACAAGATCCATGAGTCAGAAATAGACA Cluster: [ ] Orangutan: AGTTTGACATCATTTACCTGGTACTA----GAACAAGATCCATGAGTCAGAAACAGACA Gorilla > Human --------------- chr17:42342728-42342737 Template switch process: F1: L ATTTTTCAGAGGCAATTGGTAGTTTGACATCATTTACCTGG 1 F3: 4 GACAAGATCCATGAGTCAGAAATAGACACTCAGGACCAGAG R RF: ATTTTTCAGAGGCAATTGGTAGTTTGACATCATTTACCTGGTACTAGAACAAGATCCATGAGTCAGAAATAGACACTCAGGACCAGAG RR: TAAAAAGTCTCCGTTAACCATCAAACTGTAGTAAATGGACCATGATCTTGTTCTAGGTACTCAGTCTTTATCTGTGAGTCCTGGTCTC F2: 3 TCTTGTTCTA 2 Unidirectional alignment (log-probability: -35.3) TTTTTCAGAGGCAATTGGTAGTTTGACATCATTTACCTG------GAtcttgttctgACAAGATCCATGAGTCAGAAATAGACACTCAGGACCAGA TTTTTCAGAGGCAATTGGTAGTTTGACATCATTTACCTGGTACTAGA----------ACAAGATCCATGAGTCAGAAATAGACACTCAGGACCAGA Template switch alignment (log-probability: -22.5) TTTTTCAGAGGCAATTGGTAGTTTGACATCATTTACCTGG|ATCTTGTTCT|gACAAGATCCATGAGTCAGAAATAGACACTCAGGACCAGA TTTTTCAGAGGCAATTGGTAGTTTGACATCATTTACCTGG|ATCTTGTTCT|AACAAGATCCATGAGTCAGAAATAGACACTCAGGACCAGA ========== Event 1380 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGA--------------------------------------------------------------------CAACCATCTGGAAAACATGTAATGG Chimp: AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGA----------------------------------CAACCTCCGAGTGTCATACTTTGTACTCAAATGACAACCATCTGGAAAACATGTAATGG Gorilla: AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGACAACCTCTGAGTGTCATACTTTGTACTCAAATGA----------------------------------CAACCATCTGGAAAACATGTAATGG ↑ 4 3 2 1 Human: AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGA--------------------------------------------------------------------CAACCATCTGGAAAACATGTAATGG Cluster: [ ] Orangutan: AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGACAACCTCCGAGTGTCATACTTTGTATTCAAATGA----------------------------------CAACCATCTGGAAAACATGTAATGG Human > Gorilla --------------- chr5:42841298-42841304 Template switch process: F1: L AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGACAACC 1 F3: 4 GTCATACTTTGTACTCAAATGACAACCATCTGGAAAACATGTAATGGAATATAGATATCTTT R RF: AGAAGTGGGAGGGACAGTAGTCATACTTGGTACTCAGATGACAACCATCTGGAAAACATGTAATGGAATATAGATATCTTT RR: TCTTCACCCTCCCTGTCATCAGTATGAACCATGAGTCTACTGTTGGTAGACCTTTTGTACATTACCTTATATCTATAGAAA F2: 3 TGAGTCT 2 Unidirectional alignment (log-probability: -59.8) GGGAGGGACAGTAGTCATACTTGGTACTCAGATgacaacctctgagtgtcatactttgtactcaaatGACAACCATCTGGAAAACAT GGGAGGGACAGTAGTCATACTTGGTACTCAGAT----------------------------------GACAACCATCTGGAAAACAT Template switch alignment (log-probability: -28.3) GGGAGGGACAGTAGTCATACTTGGTACTCAGATGACAACC|TCTGAGT|GTCATACTTtGTACTCAaATGACAACCATCTGGAAAACAT GGGAGGGACAGTAGTCATACTTGGTACTCAGATGACAACC|TCTGAGT|GTCATACTTGGTACTCAGATGACAACCATCTGGAAAACAT ========== Event 1381 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AGCTGACAGTGCTGTGGGCTGCACTGCCCTCAAGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGGGCACCCCGGGGGAGGGATGGATT ↑ 4 1 3 2 Chimp: AGCTGACAGTGCTGTGGGCTG------GCAGGAGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGGGCACCCCGGGGGAGGGATGGATT Gorilla: Human: AGCTGACAGTGCTGTGGGCTGCACTGCCCTCAAGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGGGCACCCCGGGGGAGGGATGGATT Cluster: [ ] Orangutan: GGCTGACAGTGCTGTGGGCTG------GCAGGAGGCCATAACTGCACCAGAACCCAGCCTGGGGCCTTGAGGGCACCCTGCGGGAGGGATGGATT Chimp > Human ------------- chr17:43861532-43861539 Template switch process: F1: L AATAGCTTGTTGGGAGTCACAGCTGACAGTGCTGTGGGCTG---------CAC 1 F3: 4 AGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGG R RF: AATAGCTTGTTGGGAGTCACAGCTGACAGTGCTGTGGGCTGGCAGGAGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGGGCA RR: TTATCGAACAACCCTCAGTGTCGACTGTCACGACACCCGACCGTCCTCCGGTGTTGACGCGGTCTTGGGTCGGACCCCGGAACTCCCGT F2: 3 ACTCCCGT 2 Unidirectional alignment (log-probability: -37.2) GCTTGTTGGGAGTCACAGCTGACAGTGCTGTGGGCT-----GcactgccctcaAGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGG GCTTGTTGGGAGTCACAGCTGACAGTGCTGTGGGCTGGCAGG-----------AGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGG Template switch alignment (log-probability: -27) GCTTGTTGGGAGTCACAGCTGACAGTGCTGTGGGCTG---------CAC|TGCCCTCA|AGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGG GCTTGTTGGGAGTCACAGCTGACAGTGCTGTGGGCTGGCAGGAGGCCAC|TGCCCTCA|AGGCCACAACTGCGCCAGAACCCAGCCTGGGGCCTTGAGG ========== Event 1382 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TAGGCTCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTG------------------------CCTGCGGCTGGGGCTGGGCGGACAG ↓ 3 2 4 1 Chimp: TAGGCTCTGCCCTCCCTACTCAGCCTGGCTCCCAGGCGTG------------CCTGCCTGAGTGCCTGCGGCTGGGGCTGGGCAGACAG Gorilla: TAGGCTCTGCCCTCCCTACTCAGCCTGGCTCCCAGGCGTGCCTGCCTGAGTG------------CCTGCGGCTGGGGCTGGGCGGACAG ↑ 3 2 4 1 Human: TAGGCTCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTG------------------------CCTGCGGCTGGGGCTGGGCGGACAG Cluster: [ ] Orangutan: TAGGCTCTGCCCTCCCTACTCAGCCTGGCTCCCAGGCGTG------------------------CCTGTGGCTGGGGCCGGGCGGACAG Human > Chimp ------------- chr17:4728059-4728062 Template switch process: F1: L ATAGGCTCTGCCCTCCCTACTCAGCCTGGCTCCCAGGCGTGCCTGC 1 F3: 4 GTGCCTGCGGCTGGGGCTGGGCAGACAGAGGCTGTCTTCACAG R RF: ATAGGCTCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCACAG RR: TATCCGAGACGGGAGAGATGAGTCGGACCGAGGGTCCGCACGGACGCCGACCCCGACCCGCCTGTCTCCGACAGAAGTGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -40.2) TCTGCCCTCcCTACTCAGCCTGGCTCCCAGGCGTGCCtgcctgagtgccTGCGGCTGGGGCTGGGCaGACAGAGGCTGTCTTCA TCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTGCC------------TGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCA Template switch alignment (log-probability: -27.9) TCTGCCCTCcCTACTCAGCCTGGCTCCCAGGCGTGCCTGC|CTGA|GTGCCTGCGGCTGGGGCTGGGCaGACAGAGGCTGTCTTCA TCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTGCCTGC|CTGA|GTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCA Human > Gorilla --------------- chr17:4470691-4470694 Template switch process: F1: L ATAGGCTCTGCCCTCCCTACTCAGCCTGGCTCCCAGGCGTGCCTGC 1 F3: 4 GTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCACAG R RF: ATAGGCTCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCACAG RR: TATCCGAGACGGGAGAGATGAGTCGGACCGAGGGTCCGCACGGACGCCGACCCCGACCCGCCTGTCTCCGACAGAAGTGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -33.7) TCTGCCCTCcCTACTCAGCCTGGCTCCCAGGCgtgcctgcctgaGTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCA TCTGCCCTCTCTACTCAGCCTGGCTCCCAGGC------------GTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCA Template switch alignment (log-probability: -21.9) TCTGCCCTCcCTACTCAGCCTGGCTCCCAGGCGTGCCTGC|CTGA|GTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCA TCTGCCCTCTCTACTCAGCCTGGCTCCCAGGCGTGCCTGC|CTGA|GTGCCTGCGGCTGGGGCTGGGCGGACAGAGGCTGTCTTCA ========== Event 1383 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAACTCACCCTTGCCCCACACCCACCA-AAAATGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGGCATTATAAAACTAGCTACCCAGAAAGGCCAACATCTGTGATGTTATAACTCTAGAACATCTAGATGAAtttttttttGCAACTGAAGTATTAAAAGTGTTATTTTA ↓ 1 4 3 2 Chimp: TAACTCACCCTTGCCCCACACACACCATTCAGTGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGGCACTATAAAACTAGCTATCCAGAAAGGCCAACATCTGTGATGTTATAACTCTAGAACATCTAGATGAAtttttttttGCAACTGAAGTATTAAAAGTGTTATTTTA ↑ 1 4 3 2 Gorilla: TAACTCACCCCTGCCCCACACCCACCA-AAAATGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGGCATTATAAAACTAGCTATCCAGAAAGGCCAACATCTGTGATGTTATAACTCTAGAACATCTAGGTGAATGtttttttGCAACTGAAGTATTAAAAGTGTTATTTTA Human: TAACTCACCCTTGCCCCACACCCACCA-AAAATGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGGCATTATAAAACTAGCTACCCAGAAAGGCCAACATCTGTGATGTTATAACTCTAGAACATCTAGATGAAtttttttttGCAACTGAAGTATTAAAAGTGTTATTTTA Cluster: [ ] Orangutan: TAACTCACCACCGCCCTGCACCCACCA-AAAATGATATAACCCACTGAATTAAGTGAATAGAGTTGTAATGGCATTATAAAACTAGCTATCCAGAAAGGCCAACATCTGTGATGTTATAAATCTAGAACATCTAGATGAAttt-tttttGCAACTGAAGTAATAAAAATGTTATTTTA Human > Chimp ------------- chr17:73724540-73724544 Template switch process: F1: L ATAGGCCTCATTAGTGTCAATAACTCACCCTTGCCCCACACACACCA 1 F3: 4 TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG R RF: ATAGACCTCATTAGTGTCAATAACTCACCCTTGCCCCACACCCACCAAAAATGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGGCATTATAAAACTAGCTACCCAGAAAGGCCAACATCTGTGATGTTATAACTCTAGAACATCTAGATGAATTTTTTTTTGCAACTGAA RR: TATCTGGAGTAATCACAGTTATTGAGTGGGAACGGGGTGTGGGTGGTTTTTACTATACTGGGTGACTTAATCCACTTATCTCAACATTACCGTAATATTTTGATCGATGGGTCTTTCCGGTTGTAGACACTACAATATTGAGATCTTGTAGATCTACTTAAAAAAAAACGTTGACTT F2: 3 GACTT 2 Unidirectional alignment (log-probability: -40.6) TCATTAGTGTCAATAACTCACCCTTGCCCCACACaCACCA----ttcagTGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG TCATTAGTGTCAATAACTCACCCTTGCCCCACACCCACCAAAAA-----TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG Template switch alignment (log-probability: -28) TCATTAGTGTCAATAACTCACCCTTGCCCCACACaCACCA|TTCAG|TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG TCATTAGTGTCAATAACTCACCCTTGCCCCACACCCACCA|TTCAG|TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG Gorilla > Chimp --------------- chr17:73724540-73724544 Template switch process: F1: L ATAGGCCTCATTAGTGTCAATAACTCACCCTTGCCCCACACACACCA 1 F3: 4 TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG R RF: ATAGACCTCATTAGTGTCAATAACTCACCCCTGCCCCACACCCACCAAAAATGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGGCATTATAAAACTAGCTATCCAGAAAGGCCAACATCTGTGATGTTATAACTCTAGAACATCTAGGTGAATGTTTTTTTGCAACTGAA RR: TATCTGGAGTAATCACAGTTATTGAGTGGGGACGGGGTGTGGGTGGTTTTTACTATACTGGGTGACTTAATCCACTTATCTCAACATTACCGTAATATTTTGATCGATAGGTCTTTCCGGTTGTAGACACTACAATATTGAGATCTTGTAGATCCACTTACAAAAAAACGTTGACTT F2: 3 GACTT 2 Unidirectional alignment (log-probability: -44.7) TCATTAGTGTCAATAACTCACCCtTGCCCCACACaCACCAttcag----TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG TCATTAGTGTCAATAACTCACCCCTGCCCCACACCCACCA-----AAAATGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG Template switch alignment (log-probability: -33.1) TCATTAGTGTCAATAACTCACCCtTGCCCCACACaCACCA|TTCAG|TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG TCATTAGTGTCAATAACTCACCCCTGCCCCACACCCACCA|TTCAG|TGATATGACCCACTGAATTAGGTGAATAGAGTTGTAATGG ========== Event 1384 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGACCAGCTGCTCACCATCAGG--CTGCAAGTGTCTACAGTGGAACCAGATGTC Chimp: TGACCAGCTGCTCACCATCAGG--CTGCAAGTGTCTACAGTGGAACCAGATGCC ↓ 1 3 4 2 Gorilla: TGACCAGCTGCTCACCATCAGACACTTGCAGTGTCTACAGTGGAACCAGATGCC ↑ 1 3 4 2 Human: TGACCAGCTGCTCACCATCAGG--CTGCAAGTGTCTACAGTGGAACCAGATGTC Cluster: [ ] Orangutan: TGACCAGCTGCTCACCATCAGG--CTGCGAGTGTCTACAGTGGAAGCAGATGCC Human > Gorilla --------------- chr5:129954155-129954162 Template switch process: F1: L GGGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG 1 F3: 4 AGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG R RF: GGGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAGGCTGCAAGTGTCTACAGTGGAACCAGATGTCCTCTTTGAGGACCAG RR: CCCTACACCTCCTATTTTCCACTGGTCGACGAGTGGTAGTCCGACGTTCACAGATGTCACCTTGGTCTACAGGAGAAACTCCTGGTC F2: 3 CGTTCACA 2 Unidirectional alignment (log-probability: -35) GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAGacacttGC----AGTGTCTACAGTGGAACCAGATGcCCTCTTTGAGGACCAG GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG------GCTGCAAGTGTCTACAGTGGAACCAGATGTCCTCTTTGAGGACCAG Template switch alignment (log-probability: -22.3) GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG|ACACTTGC|AGTGTCTACAGTGGAACCAGATGcCCTCTTTGAGGACCAG GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG|ACACTTGC|AGTGTCTACAGTGGAACCAGATGTCCTCTTTGAGGACCAG Chimp > Gorilla --------------- chr5:129954155-129954162 Template switch process: F1: L GGGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG 1 F3: 4 AGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG R RF: GGGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAGGCTGCAAGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG RR: CCCTACACCTCCTATTTTCCACTGGTCGACGAGTGGTAGTCCGACGTTCACAGATGTCACCTTGGTCTACGGGAGAAACTCCTGGTC F2: 3 CGTTCACA 2 Unidirectional alignment (log-probability: -29.5) GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAGacacttGC----AGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG------GCTGCAAGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG Template switch alignment (log-probability: -16.7) GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG|ACACTTGC|AGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG GGATGTGGAGGATAAAAGGTGACCAGCTGCTCACCATCAG|ACACTTGC|AGTGTCTACAGTGGAACCAGATGCCCTCTTTGAGGACCAG ========== Event 1385 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCGAGAGTGGATCTAAGCCA--CTTAATAGACTGCCTCCTCTCTGACACAGTTTA ↓ 1 3 4 2 Chimp: TGCGAGAGTGGATCTAAGCCACAGTCTATTGACTGTCTCCTCTCTGACACGGTTTA Gorilla: TGCGAGAGTGGATCTAAGCCG--CTTAATAGACTCCCTCCTCTCTGACACGGTTTA Human: TGCGAGAGTGGATCTAAGCCA--CTTAATAGACTGCCTCCTCTCTGACACAGTTTA Cluster: [ ] Orangutan: TGCGAGAATGGATCTAAGCCA--CTC--AAGACTCCCTCCTCTTTGACACAGTTTA Human > Chimp ------------- chr17:78045950-78045957 Template switch process: F1: L TGGTGACATTGACTCTCAGCTGCGAGAGTGGATCTAAGCCAC 1 F3: 4 GACTGTCTCCTCTCTGACACGGTTTAAGGACCCAACAAGTACCCTG R RF: TGGTGACATTGACTCTCAGCTGCGAGAGTGGATCTAAGCCACTTAATAGACTGCCTCCTCTCTGACACAGTTTAAGGACCCAACAAGTACCCTG RR: ACCACTGTAACTGAGAGTCGACGCTCTCACCTAGATTCGGTGAATTATCTGACGGAGGAGAGACTGTGTCAAATTCCTGGGTTGTTCATGGGAC F2: 3 TTATCTGA 2 Unidirectional alignment (log-probability: -42) GTGACATTGACTCTCAGCTGCGAGAGTGGATCTAAGCCACagtctaTT----GACTGtCTCCTCTCTGACACgGTTTAAGGACCCAACAAGT GTGACATTGACTCTCAGCTGCGAGAGTGGATCTAAGCCAC------TTAATAGACTGCCTCCTCTCTGACACAGTTTAAGGACCCAACAAGT Template switch alignment (log-probability: -28.4) GTGACATTGACTCTCAGCTGCGAGAGTGGATCTAAGCCAC|AGTCTATT|GACTGtCTCCTCTCTGACACgGTTTAAGGACCCAACAAGT GTGACATTGACTCTCAGCTGCGAGAGTGGATCTAAGCCAC|AGTCTATT|GACTGCCTCCTCTCTGACACAGTTTAAGGACCCAACAAGT ========== Event 1386 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGGACCATGTCACATGTCTTTGAGAGT----TCTGCAG----------------GAGGCACTGGTGGTGCTGGGCCTCTGTTCAG Chimp: aggaccatgtcacatgtctttgagagt--ttcctgcag--------aactcTCAAAGGCACTGGCGGTGCTGGGCGTCTGTTCAG Gorilla: AGGACCATGTCACATGTCTTTGAGAGTTT--CCTGCAGAACTCTCA--------AAGGCACTGGCGGTGCTGGGCCTCTGTTCAC ↓ 1 3 2 4 ↑ 3 1 4 Human: AGGACCATGTCACATGTCTTTGAGAGT----TCTGCAG----------------GAGGCACTGGTGGTGCTGGGCCTCTGTTCAG Cluster: [ ] Orangutan: AGGACCATGTCACATGTCTTTGAGAGT----TCTGCAG----------------GAGGCACTGGTGGTGCTGGGCCTCTGTTCAG Gorilla > Human --------------- chr17:78184800-78184806 Template switch process: F1: L TGTCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT 1 F3: 4 AGGCACTGGTGGTGCTGGGCCTCTGTTCAGTGGAAACTTGATGGACAAAA R RF: TGTCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTTTCCTGCAGAACTCTCAAAGGCACTGGCGGTGCTGGGCCTCTGTTCACTGGAAACTTGATGGACAAAA RR: ACAGGAACTCCAGGTCCTGGTACAGTGTACAGAAACTCTCAAAGGACGTCTTGAGAGTTTCCGTGACCGCCACGACCCGGAGACAAGTGACCTTTGAACTACCTGTTTT F2: 3 GGACGTC 2 Unidirectional alignment (log-probability: -38) TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT--CTGCAG--------gAGGCACTGGtGGTGCTGGGCCTCTGTTCAgTGGAAACTTG TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTTTCCTGCAGAACTCTCAAAGGCACTGGCGGTGCTGGGCCTCTGTTCACTGGAAACTTG Template switch alignment (log-probability: -27.9) TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT|CTGCAGG|AGGCACTGGtGGTGCTGGGCCTCTGTTCAgTGGAAACTTG TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT|CTGCAGG|AGGCACTGGCGGTGCTGGGCCTCTGTTCACTGGAAACTTG Human > Gorilla --------------- chr17:90874222-90874238 Template switch process: F1: L TGTCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT 1 F3: 4 AGGCACTGGCGGTGCTGGGCCTCTGTTCACTGGAAACTTGATGGACAAAA R RF: TGTCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTTCTGCAGGAGGCACTGGTGGTGCTGGGCCTCTGTTCAGTGGAAACTTGATGGACAAAA RR: ACAGGAACTCCAGGTCCTGGTACAGTGTACAGAAACTCTCAAGACGTCCTCCGTGACCACCACGACCCGGAGACAAGTCACCTTTGAACTACCTGTTTT F2: 3 AACTCTCAAGACGTCCT 2 Unidirectional alignment (log-probability: -51.8) TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTTtcCTGCAGaactctcaaAGGCACTGGcGGTGCTGGGCCTCTGTTCAcTGGAAACTTG TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT--CTGCAG--------GAGGCACTGGTGGTGCTGGGCCTCTGTTCAGTGGAAACTTG Template switch alignment (log-probability: -29.2) TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT|TCCTGCAGAACTCTCAA|AGGCACTGGcGGTGCTGGGCCTCTGTTCAcTGGAAACTTG TCCTTGAGGTCCAGGACCATGTCACATGTCTTTGAGAGTT|TCCTGCAGAACTCTCAA|AGGCACTGGTGGTGCTGGGCCTCTGTTCAGTGGAAACTTG ========== Event 1387 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: tcctcagcctcccaaagtgctgagccactgcgctcggccAGCG-TAAATTTCTTCTAAAGATACATTTT Chimp: tcctcagcctcccaaagtgctgagccactgcgctcagccAGCA-TAAGTTTCTTCTAAAGATACATTTT Gorilla: tcctcagcctcccaaagtgctgagccactgcgctcggccAGCGTTCAGTTTCTTCTAAAGATACATTTT ↑ 3 2 1 4 Human: tcctcagcctcccaaagtgctgagccactgcgctcggccAGCG-TAAATTTCTTCTAAAGATACATTTT Cluster: [ ] Orangutan: ttctcagcttcccaaagtgctgagctactgcgctcggccAGCG-TGAGTTTCTTCTAAAGATACATTTT Human > Gorilla --------------- chr5:132666737-132666740 Template switch process: F1: L CTCAGCCTCCCAAAGTGCTGAGCCACTGCGCTCGGCCAGCGT 1 F3: 4 TTTCTTCTAAAGATACATTTTAGCTATTAAAAAAATC R RF: CTCAGCCTCCCAAAGTGCTGAGCCACTGCGCTCGGCCAGCGTAAATTTCTTCTAAAGATACATTTTAGCTATTAAAAAAATC RR: GAGTCGGAGGGTTTCACGACTCGGTGACGCGAGCCGGTCGCATTTAAAGAAGATTTCTATGTAAAATCGATAATTTTTTTAG F2: 3 GACT 2 Unidirectional alignment (log-probability: -30.3) CAGCCTCCCAAAGTGCTGAGCCACTGCGCTCGGCCAGCGTtcAgTTTCTTCTAAAGATACATTTTAGCTATTAAAAAAATC--- CAGCCTCCCAAAGTGCTGAGCCACTGCGCTCGGCCAGCGTA-AATTTCTTCTAAAGATACATTTTAGCTATTAAAAAAATCTAT Template switch alignment (log-probability: -16.2) CAGCCTCCCAAAGTGCTGAGCCACTGCGCTCGGCCAGCGT|TCAG|TTTCTTCTAAAGATACATTTTAGCTATTAAAAAAATC CAGCCTCCCAAAGTGCTGAGCCACTGCGCTCGGCCAGCGT|TCAG|TTTCTTCTAAAGATACATTTTAGCTATTAAAAAAATC ========== Event 1388 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTACTTACTTTGAAAGGAAAACAGGTT---------ATACCAGGATAAT------TTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTT Chimp: TCTACTTACTTTGAAAGGAAAACAGGTT---------ATACCAGGATAAT------TTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTT ↓ 1 4 3 2 Gorilla: TCTACTTACTTTGAAAGGAAATGATCTG------------------AAAT------------TATCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTT ↑ 1 4 3 2 Human: TCTACTTACTTTGAAAGGAAAACAGGTT---------ATACCAGGATAAT------TTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTT Cluster: [ ] Orangutan: TCTACTTACTTTGAAAGGAAAACAGGTTATACCAGGA---------TAATTTCATC------AGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTT Human > Gorilla --------------- chr5:133219227-133219239 Template switch process: F1: L ACAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA 1 F3: 4 TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT R RF: ACAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAAACAGGTTATACCAGGATAATTTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT RR: TGTTATTACACCAAATGTCAAGATGAATGAAACTTTCCTTTTGTCCAATATGGTCCTATTAAAGTAGTCAGAGTAAAGTCTAGTCTAAACCTCACCAAGACAAAGTCAA F2: 3 ATTAAAGTCTAGT 2 Unidirectional alignment (log-probability: -39.3) CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAAtgatctgaaattA---------------------------TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA------------ACAGGTTATACCAGGATAATTTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT Template switch alignment (log-probability: -22.9) CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA|TGATCTGAAATtA|TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA|TGATCTGAAATGA|TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT Chimp > Gorilla --------------- chr5:133219227-133219239 Template switch process: F1: L ACAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA 1 F3: 4 TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT R RF: ACAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAAACAGGTTATACCAGGATAATTTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT RR: TGTTATTACACCAAATGTCAAGATGAATGAAACTTTCCTTTTGTCCAATATGGTCCTATTAAAGTAGTCAGAGTAAAGTCTAGTCTAAACCTCACCAAGACAAAGTCAA F2: 3 ATTAAAGTCTAGT 2 Unidirectional alignment (log-probability: -39.3) CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAAtgatctgaaattA---------------------------TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA------------ACAGGTTATACCAGGATAATTTCATCAGTCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT Template switch alignment (log-probability: -22.9) CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA|TGATCTGAAATtA|TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT CAATAATGTGGTTTACAGTTCTACTTACTTTGAAAGGAAA|TGATCTGAAATGA|TCTCATTTCAGATCAGATTTGGAGTGGTTCTGTTTCAGTT ========== Event 1389 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: atcacagcctggagatacgtg----acaaacctagggccttgaaaacattacggagctcccaataa Chimp: ATCACAGCCTGGAGATACGTGTTTTCAAGGTCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAA ↑ 1 4 3 2 Gorilla: ATCACAGCCTGGAGATACGTG----ACAAACCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAA Human: atcacagcctggagatacgtg----acaaacctagggccttgaaaacattacggagctcccaataa Cluster: [ ] Orangutan: atcacagcgtggagatacgtg----acaaacctagggccttgaaaacatcacggagctcccaataa Gorilla > Chimp --------------- chr17:51450201-51450209 Template switch process: F1: L GAATATAGCCTCTGCTAGAGATCACAGCCTGGAGATACGTG 1 F3: 4 TCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAAATCAA R RF: GAATATAGCCTCTGCTAGAGATCACAGCCTGGAGATACGTGACAAACCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAAATCAA RR: CTTATATCGGAGACGATCTCTAGTGTCGGACCTCTATGCACTGTTTGGATCCCGGAACTTTTGTAATGCCTCGAGGGTTATTTAGTT F2: 3 GGAACTTTT 2 Unidirectional alignment (log-probability: -35.3) AATATAGCCTCTGCTAGAGATCACAGCCTGGAGATACGTG------ttttcaaggtCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAAATCA AATATAGCCTCTGCTAGAGATCACAGCCTGGAGATACGTGACAAAC----------CTAGGGCCTTGAAAACATTACGGAGCTCCCAATAAATCA Template switch alignment (log-probability: -22.4) AATATAGCCTCTGCTAGAGATCACAGCCTGGAGATACGTG|TTTTCAAGG|tCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAAATCA AATATAGCCTCTGCTAGAGATCACAGCCTGGAGATACGTG|TTTTCAAGG|CCTAGGGCCTTGAAAACATTACGGAGCTCCCAATAAATCA ========== Event 1390 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAAAAATTGGAATATTTCATTCTACTGTAAA----AGTTCATTGGCtctctactaaaaatacaaaaaaaattagccgggcatagtggcgcacgcctgtagtcccagctactcggcaggctgaggcaggagaatggcatgaacccaggaggcggagcttgcag ↓ 3 2 1 4 ↑ 1 4 3 2 Chimp: A-AAAATTGGAATATTTCATTCTACTGTAAAATACAGTAGAATGGCtctctactaaaaatacaaaaaaaattagccgggcatagtggcgcacgtgtgtagtcccagctacttggcaggctgaggcagaagaatggcatgaacccaagaggcggagcttgcag Gorilla: aaaaaaTTGGAATATTTCATTCTACTGTAAA----AGTTCATTGACtctctactaaaaatacaaaaaaaattagccgggcatagtggcacacgcctgtagtcccagctactcggcaggctgaggcaggagaatggcatgaacccaggaggcggagcttgcag Human: AAAAAATTGGAATATTTCATTCTACTGTAAA----AGTTCATTGGCtctctactaaaaatacaaaaaaaattagccgggcatagtggcgcacgcctgtagtcccagctactcggcaggctgaggcaggagaatggcatgaacccaggaggcggagcttgcag Cluster: [ ] Orangutan: ACAAAGTTGGAATATTTCATTCTACTG----------TTTACTGGCtttctactaaaaatacaaa-aaaattagccgggcgtagtggcgcacgcctgtagtcccagctactcgggcggctgaggcgggagaatggcatgaacccgggaggcggagcttgcag Chimp > Human ------------- chr17:30243882-30243887 Template switch process: F1: L AGAAAGTCATAAAAAATTGGAATATTTCATTCTACTGTAAAA 1 F3: 4 TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT R RF: AGAAAGTCAT-AAAAATTGGAATATTTCATTCTACTGTAAAATACAGTAGAATGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCATAGTGGCGCACGTGTGTAGTCCCAGCTACTTGGCAGGCTGAGGCAGAAGAATGGCATGAAC RR: TCTTTCAGTA-TTTTTAACCTTATAAAGTAAGATGACATTTTATGTCATCTTACCGAGAGATGATTTTTATGTTTTTTTTAATCGGCCCGTATCACCGCGTGCACACATCAGGGTCGATGAACCGTCCGACTCCGTCTTCTTACCGTACTTG F2: 3 TACTTG 2 Unidirectional alignment (log-probability: -40.4) AAAGTCATaAAAAATTGGAATATTTCATTCTACTGTAAAagttcAT---------TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT AAAGTCAT-AAAAATTGGAATATTTCATTCTACTGTAAA-----ATACAGTAGAATGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT Template switch alignment (log-probability: -27.7) AAAGTCATaAAAAATTGGAATATTTCATTCTACTGTAAAA|GTTCAT|TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT AAAGTCAT-AAAAATTGGAATATTTCATTCTACTGTAAAA|GTTCAT|TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT Human > Chimp ------------- chr17:30973978-30973987 Template switch process: F1: L AGAAAGTCAT-AAAAATTGGAATATTTCATTCTACTGTAAAA 1 F3: 4 TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT R RF: AGAAAGTCATAAAAAATTGGAATATTTCATTCTACTGTAAAAGTTCATTGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT RR: TCTTTCAGTATTTTTTAACCTTATAAAGTAAGATGACATTTTCAAGTAACCGAGAGATGATTTTTATGTTTTTTTTAATCGGCCCGTA F2: 3 AAGATGACAT 2 Unidirectional alignment (log-probability: -44.6) GAAAGTCAT-AAAAATTGGAATATTTCATTCTACTGTAAA-----ATacagtagaaTGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT GAAAGTCATAAAAAATTGGAATATTTCATTCTACTGTAAAAGTTCAT---------TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT Template switch alignment (log-probability: -26.8) GAAAGTCAT-AAAAATTGGAATATTTCATTCTACTGTAAAA|TACAGTAGAA|TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT GAAAGTCATAAAAAATTGGAATATTTCATTCTACTGTAAAA|TACAGTAGAA|TGGCTCTCTACTAAAAATACAAAAAAAATTAGCCGGGCAT ========== Event 1391 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 156 Detected in comparisons: 1256 Multiple sequence alignment: Human: GAAACAAGCTAGCATTTATATTTTAAATCGCTTACATTCTAGGCCAGTTGACCTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATGATTTAaaatataaa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acataaaata----aatgtgtacaatt------taaaaatatgaaataaaaataacaaaaatgatgaagcaacaggaatctacaataaatgaacaagaaaatttg ↑ 3 2 4 Chimp: ----------atgttttatattttaaatcatttacattCTAGGCCAGTTGACTTATTTTTCTACTAGGTCAACTGGCCTAGAATGTAAGCAATTTAAAATATAAATGCTAGCTTGTTTCCTTGTTGGTTTCATAAGTTTTATTGTAAATGCGATTTTGATTGATTGAAGTCATGGGGATCCCTGTAGCCTAAGTGATGCTCTCATTCCTTTACTTCTTCTAGGAGGTATGGGGGGTGCTACTGAAGAGGGGACATTTTAGGGCCCTTTCAGTGTCCCAGGTTTAGTGAGGGAGGAGGAGTTTTAAATACAGTTCTCCCATTTTGCCACTGATTTGCAGCTTAGTCTTTAGATAGTAGCATGTATTGTATAATTATCTTCAGGATAATGCCACATTTGCATTCATTACTGTTCCTGCTCGTATATTTGCCTTCCAACTCTTTTTGAAAGGAGGGTTGATAATTTCCTTTATTTCCTGCTAGTCATAATATGTAATAAGATTCTGTTTCACACAGGGTTTAATTCCACATTTAAAATGGAAGAAGCTCTACCGTCTTATGATGaaaataaagaataaaaa----------------------------------------------------- ↓ 13 24 ↑ 3 1 2 4 Gorilla: GAAACAAGCTAGCATTTATATTTTAAATTGCTTACATTCTAGGCCAGTTGACTTAGTAGAAAAATAAGTCAACTGGCCTAGaatgtaaatgatttaaaatataaa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acataaaata----aatgtgtacaatt------taaaaatatgaaataaaaataacaaaaatgatgaagcaacaggaatctacaataaatgaacaagaaaatttg Human: GAAACAAGCTAGCATTTATATTTTAAATCGCTTACATTCTAGGCCAGTTGACCTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATGATTTAaaatataaa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acataaaata----aatgtgtacaatt------taaaaatatgaaataaaaataacaaaaatgatgaagcaacaggaatctacaataaatgaacaagaaaatttg Cluster: [ ] Orangutan: gaaacaagctagcatttatattttaaatcacttacattctaggccagttgacttagtagaaaaataagtcaactgacctagaatgtaaatgatttaaaatataaa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acataaaata----aatgtgtacaatt------taaagatatgaaataaaaataacaaaaatgatgaagcgacaggaatctacaataaatgaacaagaaaatttg Chimp > Human ------------- chr17:53578105-53578184 Template switch process: F1: L 1 F3: 4 ATTTAAAATATAAA R RF: CATTTACATTCTAGGCCAGTTGACTTATTTTTCTACTAGGTCAACTGGCCTAGAATGTAAGCAATTTAAAATATAAATGTGC RR: GTAAATGTAAGATCCGGTCAACTGAATAAAAAGATGATCCAGTTGACCGGATCTTACATTCGTTAAATTTTATATTTACACG F2: 3 GTAAATGTAAGATCCGGTCAACTGAATAAAAAGATGATCCAGTTGACCGGATCTTACATTCGCTAAATTTTATATTTACG 2 Unidirectional alignment (log-probability: -92.8) gcaTTTATATTTTAAATCgcTTACATTCTAGGCCAGTTGAC-----------CTAGtagaaaaataaGTCAACTGGCCTAGAATGTAAatgATTTAAAATATAAA-- TGTTTTATATTTTAAATCATTTACATTCTAGGCCAGTTGACTTATTTTTCTACTAG-----------GTCAACTGGCCTAGAATGTAAGCAATTTAAAATATAAATG Template switch alignment (log-probability: -29.8) |GCATTTATATTTTAAATcGCTTACATTCTAGGCCAGTTGACCTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATG|ATTTAAAATATAAA |GCATTTATATTTTAAATTGCTTACATTCTAGGCCAGTTGACCTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATG|ATTTAAAATATAAA Gorilla > Chimp --------------- chr17:52763444-52763515 Template switch process: F1: L TTTATATTTTAAAT 1 F3: 4 ATAAATG R RF: TTTATATTTTAAATTGCTTACATTCTAGGCCAGTTGACTTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATGATTTAAAATATAAAACATAAAATAAATGTGTACAATTTAAAAATATGAAATAAAAATAACAAAAATGATGAAGCAACAGGAATCTACAATAAATG RR: AAATATAAAATTTAACGAATGTAAGATCCGGTCAACTGAATCATCTTTTTATTCAGTTGACCGGATCTTACATTTACTAAATTTTATATTTTGTATTTTATTTACACATGTTAAATTTTTATACTTTATTTTTATTGTTTTTACTACTTCGTTGTCCTTAGATGTTATTTAC F2: 3 TAAAATTTAACGAATGTAAGATCCGGTCAACTGGATCATCTTTTTATTCAGTTGACCGGATCTTACATTTAC 2 Unidirectional alignment (log-probability: -79.7) TTTATATTTTAAATcatTTACATTCTAGGCCAGTTGACTtatttttctacTAG-----------GTCAACTGGCCTAGAATGTAAgcaATTTAAAATATAAAtg TTTATATTTTAAATTGCTTACATTCTAGGCCAGTTGACT-----------TAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATGATTTAAAATATAAA-- Template switch alignment (log-probability: -29) TTTATATTTTAAAT|CATTTACATTCTAGGCCAGTTGACTTATTTTTCTACTAgGTCAACTGGCCTAGAATGTAAGCAATTTAAAAT|ATAAATG TTTATATTTTAAAT|CATTTACATTCTAGGCCAGTTGACTTATTTTTCTACTAAGTCAACTGGCCTAGAATGTAAGCAATTTAAAAT|ATAAATG Chimp > Gorilla --------------- chr5:135461397-135461459 Template switch process: F1: L TTTATATTTTAAAT 1 F3: 4 ATTTAAAATATAAA R RF: TTTATATTTTAAATCATTTACATTCTAGGCCAGTTGACTTATTTTTCTACTAGGTCAACTGGCCTAGAATGTAAGCAATTTAAAATATAAA RR: AAATATAAAATTTAGTAAATGTAAGATCCGGTCAACTGAATAAAAAGATGATCCAGTTGACCGGATCTTACATTCGTTAAATTTTATATTT F2: 3 GTAAATGTAAGATCCGGTCAACTGAATAAAAAGATGATTCAGTTGACCGGATCTTACATTCGT 2 Unidirectional alignment (log-probability: -76.9) TTTATATTTTAAATtgcTTACATTCTAGGCCAGTTGACT-----------TAGtagaaaaataaGTCAACTGGCCTAGAATGTAAatgATTTAAAATATAAA-- TTTATATTTTAAATCATTTACATTCTAGGCCAGTTGACTTATTTTTCTACTAG-----------GTCAACTGGCCTAGAATGTAAGCAATTTAAAATATAAATG Template switch alignment (log-probability: -28) TTTATATTTTAAAT|TGCTTACATTCTAGGCCAGTTGACtTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATG|ATTTAAAATATAAA TTTATATTTTAAAT|TGCTTACATTCTAGGCCAGTTGACCTAGTAGAAAAATAAGTCAACTGGCCTAGAATGTAAATG|ATTTAAAATATAAA ========== Event 1392 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAATCATCAATATGTACATATTTAGCATCTTTGATATGTCTCATGATGAACTGGGAGCTGCaaaaaaaaTGACATAGTTCAGAAGTAAGAGAAAGAGGTGTGAGTGGAAATGAGggggccatgtgatgatgctaagaaggacacctgtgtgggt ↑ 1 4 3 2 Chimp: CCAATCATCAATATGTACATA-TTAGGATCTTTGATATGTCTCATGATGAACTGGGAGCTGCaa-aaaaaTGACATAGTTCAGAAGTAAGAGAAAGAGGTGTGAGTGGAAATGAGggggccatgtgatgatgctaagaaggacacctgtatgggt Gorilla: CCAATCATCAATATGTACATATTTAGCATCTTTGATATGTCTCACAATGAACTGGGAGCTGCaa-aaaaaTGACATAGTTCAGAAGTAAGAGAAAGAGGTGTGAGTGGAAATGAGGGGGCCACGAGATGGTGCTAAGAAGGACAACTGTGTGGGT Human: CCAATCATCAATATGTACATATTTAGCATCTTTGATATGTCTCATGATGAACTGGGAGCTGCaaaaaaaaTGACATAGTTCAGAAGTAAGAGAAAGAGGTGTGAGTGGAAATGAGggggccatgtgatgatgctaagaaggacacctgtgtgggt Cluster: [ ] Orangutan: CCAATCATCAATATGTACATATTTAGCATCTTTGATATATCTCATGATGAACTAGGAGCTGTAA--AAAATGACATAGTTCAGAAGTAAGAGAAAGAGGTGTGAGTGGAAATGAGGGGGCCATGAGATGGTGCTAAGAAGGACACCTGTGTGGGT Chimp > Human ------------- chr17:54489657-54489660 Template switch process: F1: L GATGTGGAGGCATTAGCTATCCAATCATCAATATGTACATATT 1 F3: 4 ATCTTTGATATGTCTCATGATGAACTGGGAGCTGCAAAAA R RF: GATGTGGAGGCATTAGCTATCCAATCATCAATATGTACATATTAGGATCTTTGATATGTCTCATGATGAACTGGGAGCTGCAAAAAAATGACATAGTTCAGAAGTAAGAGAAAGAGGTGTGAGTGGAAATGAGGGGGCCATGTGATGATGCTA RR: CTACACCTCCGTAATCGATAGGTTAGTAGTTATACATGTATAATCCTAGAAACTATACAGAGTACTACTTGACCCTCGACGTTTTTTTACTGTATCAAGTCTTCATTCTCTTTCTCCACACTCACCTTTACTCCCCCGGTACACTACTACGAT F2: 3 CGAT 2 Unidirectional alignment (log-probability: -27) GTGGAGGCATTAGCTATCCAATCATCAATATGTACATAtTTAGcATCTTTGATATGTCTCATGATGAACTGGGAGCTGCAAAAa GTGGAGGCATTAGCTATCCAATCATCAATATGTACATA-TTAGGATCTTTGATATGTCTCATGATGAACTGGGAGCTGCAAAA- Template switch alignment (log-probability: -15.8) GTGGAGGCATTAGCTATCCAATCATCAATATGTACATATT|TAGC|ATCTTTGATATGTCTCATGATGAACTGGGAGCTGCAAAAA GTGGAGGCATTAGCTATCCAATCATCAATATGTACATATT|TAGC|ATCTTTGATATGTCTCATGATGAACTGGGAGCTGCAAAAA ========== Event 1393 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAAGGACCCTTTGAGGAGAGTACAGATGGGATTCCACAGTGGGGTGGGTGGAATGGAAACCTGTACTAGACC--ACCCAGAGGTTCCTTCTAACCCACT ↓ 3 2 1 4 Chimp: AGAAGGACCCTTTGAGGAGAGTACAGATGGGATTCCACAGTGGGGTGGGT-----GGAAACCTGTACTAGACCTGTACTAGAGGTTCCTTCTAACCCACT ↑ 3 2 1 4 Gorilla: AGAAGGACCCTTTGAGGAGAGTACAGATGGGATTCCACAGTGGGGTGGGT-----GGAAACCTGTACTAGACC--ACCCAGAGGTTCCTTCTAACCCACT Human: AGAAGGACCCTTTGAGGAGAGTACAGATGGGATTCCACAGTGGGGTGGGTGGAATGGAAACCTGTACTAGACC--ACCCAGAGGTTCCTTCTAACCCACT Cluster: [ ] Orangutan: agaaggaccctttgaggagagtacagatgggattccacagtggggtgggt-----ggaaacctgtactagata--atccagaggttccttctaacccACT Human > Chimp ------------- chr17:54564796-54564801 Template switch process: F1: L TTCCACAGTGGGGTGGG-----TGGAAACCTGTACTAGACC 1 F3: 4 AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC R RF: AGTACAGATGGGATTCCACAGTGGGGTGGGTGGAATGGAAACCTGTACTAGACCACCCAGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC RR: TCATGTCTACCCTAAGGTGTCACCCCACCCACCTTACCTTTGGACATGATCTGGTGGGTCTCCAAGGAAGATTGGGTGACCAAACCACCCCTTGAGTG F2: 3 TCATGT 2 Unidirectional alignment (log-probability: -40.4) TTCCACAGTGGGGTGGG-----TGGAAACCTGTACTAGA----CCtgtactAGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC TTCCACAGTGGGGTGGGTGGAATGGAAACCTGTACTAGACCACCC------AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC Template switch alignment (log-probability: -26.4) TTCCACAGTGGGGTGGG-----TGGAAACCTGTACTAGACC|TGTACT|AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC TTCCACAGTGGGGTGGGTGGAATGGAAACCTGTACTAGACC|TGTACT|AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC Gorilla > Chimp --------------- chr17:54564796-54564801 Template switch process: F1: L TGGGATTCCACAGTGGGGTGGGTGGAAACCTGTACTAGACC 1 F3: 4 AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC R RF: AGTACAGATGGGATTCCACAGTGGGGTGGGTGGAAACCTGTACTAGACCACCCAGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC RR: TCATGTCTACCCTAAGGTGTCACCCCACCCACCTTTGGACATGATCTGGTGGGTCTCCAAGGAAGATTGGGTGACCAAACCACCCCTTGAGTG F2: 3 TCATGT 2 Unidirectional alignment (log-probability: -29.5) GGGATTCCACAGTGGGGTGGGTGGAAACCTGTACTAGA----CCtgtactAGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC GGGATTCCACAGTGGGGTGGGTGGAAACCTGTACTAGACCACCC------AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC Template switch alignment (log-probability: -16.5) GGGATTCCACAGTGGGGTGGGTGGAAACCTGTACTAGACC|TGTACT|AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC GGGATTCCACAGTGGGGTGGGTGGAAACCTGTACTAGACC|TGTACT|AGAGGTTCCTTCTAACCCACTGGTTTGGTGGGGAACTCAC ========== Event 1394 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CAGCCCCTTCCCCAGATCGAA-GACTAGGGTCTTAGTAAGGAGAGGTAAGGA Chimp: CAGCCCCTTCCCCAGATCGAA-GACTAGGGTCTTAGTAAGGAGAGGTAAGGA Gorilla: CAGCCCCTTCCCCAGATCGAACTACCCTAGTCTTAGTAAGGAGAGGTAAGGA ↓ 1 3 4 2 Human: CAGCCCCTTCCCCAGATCGAA-GACTAGGGTCTTAGTAAGGAGAGGTAAGGA Cluster: [ ] Orangutan: CAGCCCCTTCCCCAGATCGAACTACCCTAGTCTTACTAAGGAGAGGTAAGGA Gorilla > Human --------------- chr17:55263936-55263942 Template switch process: F1: L TTTGTGCCCATTCGTTCTTGCAGCCCCTTCCCCAGATCGAA 1 F3: 4 GTCTTAGTAAGGAGAGGTAAGGAGGGAGGGGAAGAACCTG R RF: TTTGTGCCCATTCGTTCTTGCAGCCCCTTCCCCAGATCGAACTACCCTAGTCTTAGTAAGGAGAGGTAAGGAGGGAGGGGAAGAACCTG RR: AAACACGGGTAAGCAAGAACGTCGGGGAAGGGGTCTAGCTTGATGGGATCAGAATCATTCCTCTCCATTCCTCCCTCCCCTTCTTGGAC F2: 3 GGATCAG 2 Unidirectional alignment (log-probability: -31.1) TTGTGCCCATTCGTTCTTGCAGCCCCTTCCCCAGATCGA--------AgactaggGTCTTAGTAAGGAGAGGTAAGGAGGGAGGGGAAGAACCTG TTGTGCCCATTCGTTCTTGCAGCCCCTTCCCCAGATCGAACTACCCTA-------GTCTTAGTAAGGAGAGGTAAGGAGGGAGGGGAAGAACCTG Template switch alignment (log-probability: -16.6) TTGTGCCCATTCGTTCTTGCAGCCCCTTCCCCAGATCGAA|GACTAGG|GTCTTAGTAAGGAGAGGTAAGGAGGGAGGGGAAGAACCTG TTGTGCCCATTCGTTCTTGCAGCCCCTTCCCCAGATCGAA|GACTAGG|GTCTTAGTAAGGAGAGGTAAGGAGGGAGGGGAAGAACCTG ========== Event 1395 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACAAACTTCTGAACTTAAATGGTCACTCAGTGGCCCTCACTAGTGATCATTTAGCAGTTCATTTTGTCAC Chimp: ACAAACTTCTGAACTTAAATGGTCACTCAGTGGCCCTCACTAGTGATCATTTAGCAGTTCATTTTGTCAC ↑ 3 2 1 4 Gorilla: ACAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGT----TTCCTTTAGCAGTTCATTTTGTCAC ↓ 3 2 1 4 Human: ACAAACTTCTGAACTTAAATGGTCACTCAGTGGCCCTCACTAGTGATCATTTAGCAGTTCATTTTGTCAC Cluster: [ ] Orangutan: ACAGCCTTCTGAACTTAACTCATCACTCAGTGGCCCTCAGT----TTCCTTCAGCAGTTCATTTTGTCAC Gorilla > Human --------------- chr17:82624484-82624491 Template switch process: F1: L TCACAAACTTCTGAACTTAAATGGTCACTCAGTGGCCCTCACT 1 F3: 4 TTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA R RF: TCACAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGTTTCCTTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA RR: AGTGTTTGAAGACTTGAATTTACTAGTGAGTCACCGGGAGTCAAAGGAAATCGTCAAGTAAAACAGTGAACCGAGAAAAACAAAAAT F2: 3 ACTAGTGA 2 Unidirectional alignment (log-probability: -38.8) CAAACTTCTGAACTTAAATGgTCACTCAGTGGCCCTCAcTagtgaTCaTTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA CAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGT----TTCCTTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA Template switch alignment (log-probability: -27.8) CAAACTTCTGAACTTAAATGgTCACTCAGTGGCCCTCAcT|AGTGATCA|TTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA CAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGT|AGTGATCA|TTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA Gorilla > Chimp --------------- chr17:82623077-82623084 Template switch process: F1: L TCACAAACTTCTGAACTTAAATGGTCACTCAGTGGCCCTCACT 1 F3: 4 TTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA R RF: TCACAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGTTTCCTTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA RR: AGTGTTTGAAGACTTGAATTTACTAGTGAGTCACCGGGAGTCAAAGGAAATCGTCAAGTAAAACAGTGAACCGAGAAAAACAAAAAT F2: 3 ACTAGTGA 2 Unidirectional alignment (log-probability: -38.8) CAAACTTCTGAACTTAAATGgTCACTCAGTGGCCCTCAcTagtgaTCaTTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA CAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGT----TTCCTTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA Template switch alignment (log-probability: -27.8) CAAACTTCTGAACTTAAATGgTCACTCAGTGGCCCTCAcT|AGTGATCA|TTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA CAAACTTCTGAACTTAAATGATCACTCAGTGGCCCTCAGT|AGTGATCA|TTTAGCAGTTCATTTTGTCACTTGGCTCTTTTTGTTTTTA ========== Event 1396 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGTTCAGGAGTTTGTGTAAATGTTC---CTGAATATAGATGTTCCCCAGAAC ↓ 1 3 42 Chimp: TTGTTCAGGAATTTGTGTAAA--TTCAGGAAGAATATAGATGTTCCCCAGAAC ↑ 1 3 42 Gorilla: TTGTTCAGGAATTTGTGTAAATGTTC---CTGAATATAGATGTTCCCCAGAAC Human: TTGTTCAGGAGTTTGTGTAAATGTTC---CTGAATATAGATGTTCCCCAGAAC Cluster: [ ] Orangutan: TTGTTCAGGAATTTGTGTAAATGTTC---CTGAATATAGATGTTCCCCAGAAC Human > Chimp ------------- chr17:54693163-54693169 Template switch process: F1: L GTATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAAT 1 F3: 4 GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT R RF: GTATTTGGCCATACATCCTATTGTTCAGGAGTTTGTGTAAATGTTCCTGAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT RR: CATAAACCGGTATGTAGGATAACAAGTCCTCAAACACATTTACAAGGACTTATATCTACAAGGGGTCTTGTCAATCTCTTGAGAACCA F2: 3 AAGGACT 2 Unidirectional alignment (log-probability: -36) ATTTGGCCATACATCCTATTGTTCAGGAaTTTGTGTAAAT-----TcaggaaGAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT ATTTGGCCATACATCCTATTGTTCAGGAGTTTGTGTAAATGTTCCT------GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT Template switch alignment (log-probability: -22.2) ATTTGGCCATACATCCTATTGTTCAGGAaTTTGTGTAAAT|TCAGGAA|GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT ATTTGGCCATACATCCTATTGTTCAGGAGTTTGTGTAAAT|TCAGGAA|GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT Gorilla > Chimp --------------- chr17:54693163-54693169 Template switch process: F1: L GTATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAAT 1 F3: 4 GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT R RF: GTATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAATGTTCCTGAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT RR: CATAAACCGGTATGTAGGATAACAAGTCCTTAAACACATTTACAAGGACTTATATCTACAAGGGGTCTTGTCAATCTCTTGAGAACCA F2: 3 AAGGACT 2 Unidirectional alignment (log-probability: -29.5) ATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAAT-----TcaggaaGAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT ATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAATGTTCCT------GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT Template switch alignment (log-probability: -16.6) ATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAAT|TCAGGAA|GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT ATTTGGCCATACATCCTATTGTTCAGGAATTTGTGTAAAT|TCAGGAA|GAATATAGATGTTCCCCAGAACAGTTAGAGAACTCTTGGT ========== Event 1397 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCC--------------------------------------ATTTCCTTTCCTCAAAGGATAACTTCA Chimp: TAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCC-------------------ATTCCTCTTGGGTAGAAAGATTTCCTTTCCTCAAAGGATAACTTCA Gorilla: TAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCATTCCTCTTGGGTAGAAAG-------------------ATTTCCTTTCCTCAAAGGATAACTTCA ↑ 3 2 4 1 Human: TAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCC--------------------------------------ATTTCCTTTCCTCAAAGGATAACTTCA Cluster: [ ] Orangutan: TAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCATTCCTCTTGGGTAGAAAG-------------------ATTTCCTTTCCTCAAAGGATAACTTCA Human > Gorilla --------------- chr5:137363717-137363729 Template switch process: F1: L TTGGCTAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCA-TTCCT 1 F3: 4 ATTTCCTTTCCTCAAAGGATAACTTCATTCTGAGCAAGTG R RF: TTGGCTAATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCATTTCCTTTCCTCAAAGGATAACTTCATTCTGAGCAAGTG RR: AACCGATTAAGTCTCTGGACGAATGAAAGATGGGTTCACGGTAAAGGAAAGGAGTTTCCTATTGAAGTAAGACTCGTTCAC F2: 3 GAAAGATGGGTTC 2 Unidirectional alignment (log-probability: -38.2) ATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCattcctcttgggtagaaagATTTCCTTTCCTCAAAGGATAACTTCATTCTGAGCAAGTG ATTCAGAGACCTGCTTACTTTCTACCCAAGTGCC-------------------ATTTCCTTTCCTCAAAGGATAACTTCATTCTGAGCAAGTG Template switch alignment (log-probability: -27.3) ATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCA-TTCCT|CTTGGGTAGAAAG|ATTTCCTTTCCTCAAAGGATAACTTCATTCTGAGCAAGTG ATTCAGAGACCTGCTTACTTTCTACCCAAGTGCCATTTCCT|CTTGGGTAGAAAG|ATTTCCTTTCCTCAAAGGATAACTTCATTCTGAGCAAGTG ========== Event 1398 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGAGCTCTTTGCCATGGAGTCAGTGGGGA ↑ 3 2 1 4 Chimp: GTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGGG--TTTTGCCATGGAGTCAGTGGGGA Gorilla: GTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGAGCTCTTTGCCATGGAGTCAGTGGGGA Human: GTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGAGCTCTTTGCCATGGAGTCAGTGGGGA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr17:27689849-27689854 Template switch process: F1: L AATATTGGTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTG 1 F3: 4 TTGCCATGGAGTCAGTGGGGAGCCTTTGAAGACAGGTTC R RF: AATATTGGTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGGGTTTTGCCATGGAGTCAGTGGGGAGCCTTTGAAGACAGGTTC RR: TTATAACCAACCCTCCACCTCTCTCCTCTCGAACGACAAACCCAAAACGGTACCTCAGTCACCCCTCGGAAACTTCTGTCCAAG F2: 3 TCTCGA 2 Unidirectional alignment (log-probability: -25.8) ATATTGGTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGaGctcTTTGCCATGGAGTCAGTGGGGAGCCTTTGAAGACAGGTTC ATATTGGTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTGGG--TTTTGCCATGGAGTCAGTGGGGAGCCTTTGAAGACAGGTTC Template switch alignment (log-probability: -16) ATATTGGTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTG|AGCTCT|TTGCCATGGAGTCAGTGGGGAGCCTTTGAAGACAGGTTC ATATTGGTTGGGAGGTGGAGAGAGGAGAGCTTGCTGTTTG|AGCTCT|TTGCCATGGAGTCAGTGGGGAGCCTTTGAAGACAGGTTC ========== Event 1399 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCCAGACTGGGACCTATCTTTAGGCTGATATC----------TGTGCCCTGTAGAAACTAAGATA Chimp: ACCCAGACTGGGACCTATCTTTAGGCTGATATC----------TGTGCCCTGTAGAAACTAAGATA ↓ 3 1 2 4 Gorilla: ACCCAGACTGGGACCTATCTTTAGGCTGATAGATATCAGCCTAAATGCCCTGTAGAAACTAAGATA ↑ 3 1 2 4 Human: ACCCAGACTGGGACCTATCTTTAGGCTGATATC----------TGTGCCCTGTAGAAACTAAGATA Cluster: [ ] Orangutan: ACCCAGACTGGGACCTATCTTTAGACTGATATC----------TGTGCCTTTTAGAAACTAAGATA Human > Gorilla --------------- chr5:138152522-138152535 Template switch process: F1: L GCTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA 1 F3: 4 TGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT R RF: GCTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATATCTGTGCCCTGTAGAAACTAAGATAAATACTTAAAATACATTAT RR: CGAAAGGTTGTGGGTCTGACCCTGGATAGAAATCCGACTATAGACACGGGACATCTTTGATTCTATTTATGAATTTTATGTAATA F2: 3 AAATCCGACTATAG 2 Unidirectional alignment (log-probability: -45) CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA---GatatcagcctaaaTGCCCTGTAGAAACTAAGATAAATACTTAAAATACAcTAT CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATATCTG-------------TGCCCTGTAGAAACTAAGATAAATACTTAAAATACATTAT Template switch alignment (log-probability: -23) CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA|GATATCAGCCTAAA|TGCCCTGTAGAAACTAAGATAAATACTTAAAATACAcTAT CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA|GATATCAGCCTAAA|TGCCCTGTAGAAACTAAGATAAATACTTAAAATACATTAT Chimp > Gorilla --------------- chr5:138152522-138152535 Template switch process: F1: L GCTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA 1 F3: 4 TGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT R RF: GCTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATATCTGTGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT RR: CGAAAGGTTGTGGGTCTGACCCTGGATAGAAATCCGACTATAGACACGGGACATCTTTGATTCTATTTATGAATTTTATGTGATA F2: 3 AAATCCGACTATAG 2 Unidirectional alignment (log-probability: -39.5) CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA---GatatcagcctaaaTGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATATCTG-------------TGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT Template switch alignment (log-probability: -17.5) CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA|GATATCAGCCTAAA|TGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT CTTTCCAACACCCAGACTGGGACCTATCTTTAGGCTGATA|GATATCAGCCTAAA|TGCCCTGTAGAAACTAAGATAAATACTTAAAATACACTAT ========== Event 1400 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGGGAAGAAGAAGAGTGTGCTGAACAATTCAGAAAAGATAGCTGTCATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACC-----CCCTCTTCAAAGAGGGTTCTTG Chimp: TGGGGAAGAAGAAGAGTGTGCTGAACAATTCAGAAAAGATAGCTGTCATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACC-----CCCTCTTCAAAGAGGGTTCTTG ↓ 3 2 14 Gorilla: TGGGGAAGAAGAAGAGTGTGCTGAACAATTCAGAAAAGATAGCTGTCATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCCTCAGCCCTCTTCAAAGAGGGC----- ↑ 3 2 14 Human: TGGGGAAGAAGAAGAGTGTGCTGAACAATTCAGAAAAGATAGCTGTCATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACC-----CCCTCTTCAAAGAGGGTTCTTG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr1:76634684-76634688 Template switch process: F1: L ATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCC 1 F3: 4 CCTCTTCAAAGAGGGC R RF: GCTGAACAATTCAGAAAAGATAGCTGTCATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCCCCTCTTCAAAGAGGGT RR: CGACTTGTTAAGTCTTTTCTATCGACAGTAATATAAGAAAGACTGTTCCTCATTCTATCTTTGGTGTGGGGGAGAAGTTTCTCCCA F2: 3 CGACT 2 Unidirectional alignment (log-probability: -31.2) TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCctcagCCCTCTTCAAAGAGGGc----------------------- TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACC-----CCCTCTTCAAAGAGGGTTCTTGTGACTATACTTTGAAATT Template switch alignment (log-probability: -21.2) TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCC|TCAGC|CCTCTTCAAAGAGGGc TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCC|TCAGC|CCTCTTCAAAGAGGGT Chimp > Gorilla --------------- chr1:76634684-76634688 Template switch process: F1: L ATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCC 1 F3: 4 CCTCTTCAAAGAGGGC R RF: GCTGAACAATTCAGAAAAGATAGCTGTCATTATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCCCCTCTTCAAAGAGGGT RR: CGACTTGTTAAGTCTTTTCTATCGACAGTAATATAAGAAAGACTGTTCCTCATTCTATCTTTGGTGTGGGGGAGAAGTTTCTCCCA F2: 3 CGACT 2 Unidirectional alignment (log-probability: -31.2) TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCctcagCCCTCTTCAAAGAGGGc----------------------- TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACC-----CCCTCTTCAAAGAGGGTTCTTGTGACTATACTTTGAAATT Template switch alignment (log-probability: -21.2) TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCC|TCAGC|CCTCTTCAAAGAGGGc TATATTCTTTCTGACAAGGAGTAAGATAGAAACCACACCC|TCAGC|CCTCTTCAAAGAGGGT ========== Event 1401 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTACCCCTGACACTCACAGCC--------------------GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCCCTTTGTTGAATGCTTCCAGAAACAATCTGTGCCCCTTGGCAGAAGGGAATGGCTAGAACTCC ↓ 4 1 3 2 Chimp: CTACCCCTGACACTCACAGCC----------GAGCCTGCCAGAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCCCTTTGTTGAATGCTTCCAGAAACAATCTGTGCCCCTTGGCAGAAGGGAATGGCTAGAACTCC Gorilla: CTACCCCTGACACTCACAGCCGAGCCTGCCA----------GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCCCTTTGTTGAATGCTTCCAGAAACAATCTGTGCCCCTTGGCAGAAGGGAATGGCTAGAACTCC Human: CTACCCCTGACACTCACAGCC--------------------GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCCCTTTGTTGAATGCTTCCAGAAACAATCTGTGCCCCTTGGCAGAAGGGAATGGCTAGAACTCC Cluster: [ ] Orangutan: CTACCCCTGACACTCACAGCCGAGCCTGCCA----------GAGCTCAAGGACAGTCTGTCACTGTCATGTGGGGGATGCCCTTTGCTGAATGCTTCCAGAAACAATCTGTGCCCCTTGGCAGAAGGGAATGGCTAGAACTCC Human > Chimp ------------- chr17:26184022-26184027 Template switch process: F1: L GATGCAAGGACACCACCCCTCTACCCCTGACACTCACAGCCGAGC 1 F3: 4 GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCC R RF: GATGCAAGGACACCACCCCTCTACCCCTGACACTCACAGCCGAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCCCTTTGTTGAATGCTTCCAGAAACAATCTGTGCCCCTTGGCAG RR: CTACGTTCCTGTGGTGGGGAGATGGGGACTGTGAGTGTCGGCTCGAGTTCCTGTCAGACAGAGACAGTACACCCCCTACGGGAAACAACTTACGAAGGTCTTTGTTAGACACGGGGAACCGTC F2: 3 ACCGTC 2 Unidirectional alignment (log-probability: -25.3) AAGGACACCACCCCTCTACCCCTGACACTCACAGCCgagcctgccaGAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCC AAGGACACCACCCCTCTACCCCTGACACTCACAGCC----------GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCC Template switch alignment (log-probability: -16.1) AAGGACACCACCCCTCTACCCCTGACACTCACAGCCGAGC|CTGCCA|GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCC AAGGACACCACCCCTCTACCCCTGACACTCACAGCCGAGC|CTGCCA|GAGCTCAAGGACAGTCTGTCTCTGTCATGTGGGGGATGCC ========== Event 1402 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCGAGGAGAGAAATCACATTTAGAGGGTGACACAAAAGGTAAAACGATCTGTCATGGGATTTAGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCTAGACCCAAGTGAACCTAAATCCCATGACAGA Chimp: CCGAGGAGAGAAATCACATTTAGAGGGTGACACAAAAGGTAAAATGATCTGTCATGGGATTTAGG------------------------------------------------------------------------------------------------------------------------------------------------TTCACTTGGGTCTGGAATTATCTAAAATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCTAGACCCAAGTGAACCTAAATCCCATGACAGA ↓ 1 3 4 2 ↑ 13 24 Gorilla: CCGAGGAGAGAAATCACATTTACAGGGTGACACAAAAGGTAAAATGATCTGTCTTGGGATTTAGG--------------------------------------------------------------------TTCACTTGGGTCTGGAATTAACTAAAATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTCATGGGATTTAGG----------------------------------------------------------------------------TTCACTTGGGTCTAGAATTACCTAAAAGGCAATTCCAGACCCAAGTGAACCTAAATCCCATGACAGA ↓ 1 3 4 2 Human: CCGAGGAGAGAAATCACATTTAGAGGGTGACACAAAAGGTAAAACGATCTGTCATGGGATTTAGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCTAGACCCAAGTGAACCTAAATCCCATGACAGA Cluster: [ ] Orangutan: CCGAGGAGAGAAATCACATGTACAGGGTGACACAAAAGGTAAAATGATCTGTCATGGGATTTAGGTTCACTTGTGTCTGGAATTATCTAAAATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTATTTA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr17:58039287-58039321 Template switch process: F1: L T 1 F3: 4 AGACCCAAGTGAACCTAAATCCCATGACAGATCGTTTTAT R RF: TCACATTTACAGGGTGACACAAAAGGTAAAATGATCTGTCTTGGGATTTAGGTTCACTTGGGTCTGGAATTAACTAAAATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCTAGAATTACCTAAAAGGCAATTCCAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT RR: AGTGTAAATGTCCCACTGTGTTTTCCATTTTACTAGACAGAACCCTAAATCCAAGTGAACCCAGACCTTAATTGATTTTAAATCCAAGTGAACCCAGACCTTAACGGAAAATCCAGTACCCTAAATCCAAGTGAACCCAGATCTTAATGGATTTTCCGTTAAGGTCTGGGTTCACTTGGATTTAGGGTACTGTCTAGTAAAATA F2: 3 TCTTAATGGATTTTCCGTTAAGGTCTGGGTTCACT 2 Unidirectional alignment (log-probability: -49.8) ttcacttgggtctggAATTGCCTTTTAGGT-------------------------------------------AATTCtAGACCCAAGTGAACCTAAATCCCATGACAGATCgTTTTAT ---------------AATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCTAGAATTACCTAAAAGGCAATTCCAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT Template switch alignment (log-probability: -24.7) T|TCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCT|AGACCCAAGTGAACCTAAATCCCATGACAGATCgTTTTAT T|TCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCT|AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT Gorilla > Chimp --------------- chr17:57318372-57318394 Template switch process: F1: L ------------------------------------------------------------------------AATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCT 1 F3: 4 AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT R RF: AAATGATCTGTCTTGGGATTTAGGTTCACTTGGGTCTGGAATTAACTAAAATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCTAGAATTACCTAAAAGGCAATTCCAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT RR: TTTACTAGACAGAACCCTAAATCCAAGTGAACCCAGACCTTAATTGATTTTAAATCCAAGTGAACCCAGACCTTAACGGAAAATCCAGTACCCTAAATCCAAGTGAACCCAGATCTTAATGGATTTTCCGTTAAGGTCTGGGTTCACTTGGATTTAGGGTACTGTCTAGTAAAATA F2: 3 TCTTAATGGATTTTCCGTTAAGG 2 Unidirectional alignment (log-probability: -84.3) attgccttttaggtcatgggatttaggTTCACTTGGGTCTgGAATTgCCTtttAGGtAATTCtAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT ---------------------------TTCACTTGGGTCTAGAATTACCTAAAAGGCAATTCCAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT Template switch alignment (log-probability: -32.1) ATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCT|GGAATTGCCTTTTAGGTAATTCT|AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT ATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCT|GGAATTGCCTTTTAGGTAATTCT|AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT Chimp > Gorilla --------------- chr5:139987684-139987718 Template switch process: F1: L T 1 F3: 4 AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT R RF: TCACATTTAGAGGGTGACACAAAAGGTAAAATGATCTGTCATGGGATTTAGGTTCACTTGGGTCTGGAATTATCTAAAATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTCATGGGATTTAGGTTCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCTAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT RR: AGTGTAAATCTCCCACTGTGTTTTCCATTTTACTAGACAGTACCCTAAATCCAAGTGAACCCAGACCTTAATAGATTTTAAATCCAAGTGAACCCAGACCTTAACGGAAAATCCAGTACCCTAAATCCAAGTGAACCCAGACCTTAACGGAAAATCCATTAAGATCTGGGTTCACTTGGATTTAGGGTACTGTCTAGTAAAATA F2: 3 CCTTAACGGAAAATCCATTAAGATCTGGGTTCACT 2 Unidirectional alignment (log-probability: -45.5) TTCACTTGGGTCTaGAATTaCCTaaaAGGcAATTCcAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT TTCACTTGGGTCTGGAATTGCCTTTTAGGTAATTCTAGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT Template switch alignment (log-probability: -19.2) T|TCACTTGGGTCTAGAATTACCTAAAAGGCAATTCC|AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT T|TCACTTGGGTCTAGAATTACCTAAAAGGCAATTCC|AGACCCAAGTGAACCTAAATCCCATGACAGATCATTTTAT ========== Event 1403 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCCACCCTCCAGCGTCCAAAT--------GAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTC Chimp: AGCCACCCTCCAGCGTCCAAAC--------GAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTC ↓ 1 4 3 2 Gorilla: AGCCACCCTCCAGCGTCCAAACAGCTGTGGCAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTC ↑ 1 4 3 2 Human: AGCCACCCTCCAGCGTCCAAAT--------GAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTC Cluster: [ ] Orangutan: AGCCACCCTCCAGTGTCCAAAT--------GAGGCAGCCACAGCTCCCCTGCCAAGGTCTTAGTC Human > Gorilla --------------- chr5:140273173-140273181 Template switch process: F1: L TGGCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAC 1 F3: 4 AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT R RF: TGGCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAATGAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT RR: ACCGGCGAAGGTCGGTGCGATCGGTGGGAGGTCGCAGGTTTACTCCGTCGGTGTCGAGGGGACGGTTCCAGAACCAGAGGTCA F2: 3 CGGTGTCGA 2 Unidirectional alignment (log-probability: -32.2) GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAcagctgTGgcAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAA------TG--AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT Template switch alignment (log-probability: -22.4) GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAc|AGCTGTGGC|AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAT|AGCTGTGGC|AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT Chimp > Gorilla --------------- chr5:140273173-140273181 Template switch process: F1: L GGCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAC 1 F3: 4 AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT R RF: GGCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAACGAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT RR: CCGGCGAAGGTCGGTGCGATCGGTGGGAGGTCGCAGGTTTGCTCCGTCGGTGTCGAGGGGACGGTTCCAGAACCAGAGGTCA F2: 3 CGGTGTCGA 2 Unidirectional alignment (log-probability: -27.9) GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAACagctgtggcAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAC--------GAGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT Template switch alignment (log-probability: -16.9) GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAC|AGCTGTGGC|AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT GCCGCTTCCAGCCACGCTAGCCACCCTCCAGCGTCCAAAC|AGCTGTGGC|AGGCAGCCACAGCTCCCCTGCCAAGGTCTTGGTCTCCAGT ========== Event 1404 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTCACTTTAAAACACATAAGTTCTCAGTGAACGATGTGGCTTAAATGTGCTTTATCCCGATGATAG ↓ 3 2 1 4 Chimp: ATTTCACTTTAAAACACATAAGTTCTCAGTGAACGAG--AACT---TTGTGCTTTATCCCGATGATAG ↑ 3 2 1 4 Gorilla: ATTTCACTTTAAAACACATAAGTTCTCAGTGAACGATGTGGCTTAAATGTGCTTTATCCCGATGATAG Human: ATTTCACTTTAAAACACATAAGTTCTCAGTGAACGATGTGGCTTAAATGTGCTTTATCCCGATGATAG Cluster: [ ] Orangutan: ATTTCACTTTAAAACACATAAGTTCTCAGTGAACGATGTGGCTTAAATGTGCTTTATCCCAATAATAG Human > Chimp ------------- chr17:24351590-24351595 Template switch process: F1: L TGAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA 1 F3: 4 TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA R RF: TGAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGATGTGGCTTAAATGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA RR: ACTTTTAAAGTGAAATTTTGTGTATTCAAGAGTCACTTGCTACACCGAATTTACACGAAATAGGGCTACTATCGATACCTTAATAACTTAGT F2: 3 TTCAAG 2 Unidirectional alignment (log-probability: -28.8) GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGAgaactT----------TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA-----TGTGGCTTAAATGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA Template switch alignment (log-probability: -16) GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA|GAACTT|TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA|GAACTT|TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA Gorilla > Chimp --------------- chr17:24351590-24351595 Template switch process: F1: L TGAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA 1 F3: 4 TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA R RF: TGAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGATGTGGCTTAAATGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA RR: ACTTTTAAAGTGAAATTTTGTGTATTCAAGAGTCACTTGCTACACCGAATTTACACGAAATAGGGCTACTATCGATACCTTAATAACTTAGT F2: 3 TTCAAG 2 Unidirectional alignment (log-probability: -28.3) GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGAgaactT----------TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA-----TGTGGCTTAAATGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA Template switch alignment (log-probability: -16.5) GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA|GAACTT|TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA GAAAATTTCACTTTAAAACACATAAGTTCTCAGTGAACGA|GAACTT|TGTGCTTTATCCCGATGATAGCTATGGAATTATTGAATCA ========== Event 1405 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: atgaaagaGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGG----------AAG-----------ACCTTAACAGGTTaaa--aaaaaaaa Chimp: atgaaagaGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGG----------AAG-----------ACCTTAACAGGTTaaa--a-aaaaaa ↓ 3 1 2 4 Gorilla: atgaaagaGATGTTTAGATTAGAAGCAATGCAGGAATTTGCAGGTCTTCCGCAAATTCCTGCATTGCTTCTAAACAGGTTaaa----aaaaaa ↑ 3 1 2 4 Human: atgaaagaGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGG----------AAG-----------ACCTTAACAGGTTaaa--aaaaaaaa Cluster: [ ] Orangutan: atgaaagaGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGG----------AAG-----------ACCTTAACAGGTTaaaaa--aaaaaa Human > Gorilla --------------- chr5:22147077-22147107 Template switch process: F1: L ATGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC 1 F3: 4 AACAGGTT--AAAAAAAAAAAGTAGGAAAAAACAGGAGGA R RF: ATGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGGAAGACCTTAACAGGTTAAAAAAAAAAAAAGTAGGAAAAAACAGGAGGA RR: TACTTTCTCTACAAATCTAATCTTCGTTACGTCCTTAAACGCCTTCTGGAATTGTCCAATTTTTTTTTTTTTCATCCTTTTTTGTCCTCCT F2: 3 ATCTTCGTTACGTCCTTAAACGCCTTCTGGA 2 Unidirectional alignment (log-probability: -75.5) TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGCaggtcttccgcaaattcctgcattgcttcta----------AACAGGTT--AAAAAAAAAAAGTAGGAAAAAACAGGAGGA TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC-------------------------------GGAAGACCTTAACAGGTTAAAAAAAAAAAAAGTAGGAAAAAACAGGAGGA Template switch alignment (log-probability: -29.5) TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC|AGGTCTTCCGCAAATTCCTGCATTGCTTCTA|AACAGGTT--AAAAAAAAAAAGTAGGAAAAAACAGGAGGA TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC|AGGTCTTCCGCAAATTCCTGCATTGCTTCTA|AACAGGTTAAAAAAAAAAAAAGTAGGAAAAAACAGGAGGA Chimp > Gorilla --------------- chr5:22147077-22147107 Template switch process: F1: L ATGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC 1 F3: 4 AACAGGTT-AAAAAAAAAAAGTAGGAAAAAACAGGAGGAG R RF: ATGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGGAAGACCTTAACAGGTTAAAAAAAAAAAAGTAGGAAAAAACAGGAGGAG RR: TACTTTCTCTACAAATCTAATCTTCGTTACGTCCTTAAACGCCTTCTGGAATTGTCCAATTTTTTTTTTTTCATCCTTTTTTGTCCTCCTC F2: 3 ATCTTCGTTACGTCCTTAAACGCCTTCTGGA 2 Unidirectional alignment (log-probability: -74.2) TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTG-------------CAGGTcttccgcaaattcctgcattgcttctaaacaggTtAAAAAAAAAAAGTAGGAAAAAACAGGAGGAG TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGCGGAAGACCTTAACAGGT---------------------------------TAAAAAAAAAAAAGTAGGAAAAAACAGGAGGAG Template switch alignment (log-probability: -29.4) TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC|AGGTCTTCCGCAAATTCCTGCATTGCTTCTA|AACAGGTT-AAAAAAAAAAAGTAGGAAAAAACAGGAGGAG TGAAAGAGATGTTTAGATTAGAAGCAATGCAGGAATTTGC|AGGTCTTCCGCAAATTCCTGCATTGCTTCTA|AACAGGTTAAAAAAAAAAAAGTAGGAAAAAACAGGAGGAG ========== Event 1406 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: aGCCACTCAGTCACATTCTTTATAAATTCTATGGTTACATGCAATC------------------ACAATGAGAAGCAGTACTTGGTG Chimp: aGCCACTCAGTCACATTCTTTG---------TGATTGCGTGTAACC---------ATAGAATTTATAATGAGAAGCAGTACTTGGTG Gorilla: aGCCACTCAGTCACATTCTTTG---------TGATTGCATGTAACCATAGAATTT---------ATAATGAGAAGCAGTACTTGGTG ↓ 1 3 24 ↑ 13 24 Human: aGCCACTCAGTCACATTCTTTATAAATTCTATGGTTACATGCAATC------------------ACAATGAGAAGCAGTACTTGGTG Cluster: [ ] Orangutan: aGCCACTCAGTCACATTCTTTG---------TGATTGCATGTAACCATATAATTT---------ACAATGAGAAGCAGTACTTGGTG Gorilla > Human --------------- chr17:21590182-21590208 Template switch process: F1: L CAAGACTCTCTCAAAAAAAAAGCCACTCAGTCACATTCTTT 1 F3: 4 AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG R RF: CAAGACTCTCTAAAAAAAAAAGCCACTCAGTCACATTCTTTGTGATTGCATGTAACCATAGAATTTATAATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG RR: GTTCTGAGAGATTTTTTTTTTCGGTGAGTCAGTGTAAGAAACACTAACGTACATTGGTATCTTAAATATTACTCTTCGTCATGAACCACCACCATTATCTTAAATTAC F2: 3 CACTAACGTACATTGGTATCTTAAATA 2 Unidirectional alignment (log-probability: -63.4) AAGACTCTCTcAAAAAAAAAGCCACTCAGTCACATTC-------------------------TTTATaaattctatggttacatgcaatcacAATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG AAGACTCTCTAAAAAAAAAAGCCACTCAGTCACATTCTTTGTGATTGCATGTAACCATAGAATTTAT-------------------------AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG Template switch alignment (log-probability: -24.7) AAGACTCTCTcAAAAAAAAAGCCACTCAGTCACATTCTTT|ATAAATTCTATGGTTACATGCAATCAC|AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG AAGACTCTCTAAAAAAAAAAGCCACTCAGTCACATTCTTT|ATAAATTCTATGGTTACATGCAATCAC|AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG Human > Gorilla --------------- chr5:21647694-21647720 Template switch process: F1: L CAAGACTCTCTAAAAAAAAAAGCCACTCAGTCACATTCTTT 1 F3: 4 AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG R RF: CAAGACTCTCTCAAAAAAAAAGCCACTCAGTCACATTCTTTATAAATTCTATGGTTACATGCAATCACAATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG RR: GTTCTGAGAGAGTTTTTTTTTCGGTGAGTCAGTGTAAGAAATATTTAAGATACCAATGTACGTTAGTGTTACTCTTCGTCATGAACCACCACCATTATCTTAAATTAC F2: 3 TATTTAAGATACCAATGTACGTTAGTG 2 Unidirectional alignment (log-probability: -63.4) AAGACTCTCTaAAAAAAAAAGCCACTCAGTCACATTCtttgtgattgcatgtaaccatagaaTTTAT-------------------------AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG AAGACTCTCTCAAAAAAAAAGCCACTCAGTCACATTC-------------------------TTTATAAATTCTATGGTTACATGCAATCACAATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG Template switch alignment (log-probability: -24.7) AAGACTCTCTaAAAAAAAAAGCCACTCAGTCACATTCTTT|GTGATTGCATGTAACCATAGAATTTAT|AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG AAGACTCTCTCAAAAAAAAAGCCACTCAGTCACATTCTTT|GTGATTGCATGTAACCATAGAATTTAT|AATGAGAAGCAGTACTTGGTGGTGGTAATAGAATTTAATG ========== Event 1407 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTATGCCGTCTTTTGAATT-----CTTCTTTTGGA------AACTTCTGTTTACAAATGTGATTTATAGTGTAG Chimp: ACTTATGCCATCTTTTGAATT-----CTTCTTTTGGA------AACTTCTGTTTACAAATGTGATTTATAGTGTAG ↓ 1 3 2 4 Gorilla: ACTTATGCCATCTTTTGAATT-------------CGA------------AGTTTCCAAATGTGATTTATAGTGTAG ↑ 1 3 2 4 Human: ACTTATGCCGTCTTTTGAATT-----CTTCTTTTGGA------AACTTCTGTTTACAAATGTGATTTATAGTGTAG Cluster: [ ] Orangutan: ACTTATGCCATCTTTTGAATTCTTTT--------GAAAACTTC------TGTTTACAAATGTGATTTATAGTGTAG Human > Gorilla --------------- chr5:21436558-21436565 Template switch process: F1: L ATGTGTTAAATACTAGTGTAACTTATGCCATCTTTTGAATTC 1 F3: 4 CAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC R RF: ATGTGTTAAATACTAGTTTAACTTATGCCGTCTTTTGAATTCTTCTTTTGGAAACTTCTGTTTACAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC RR: TACACAATTTATGATCAAATTGAATACGGCAGAAAACTTAAGAAGAAAACCTTTGAAGACAAATGTTTACACTAAATATCACATCACCCTTACTTATCCATCCG F2: 3 CTTTGAAG 2 Unidirectional alignment (log-probability: -38) GTGTTAAATACTAGTgTAACTTATGCCaTCTTTTGAATTC--------GAA------GTTTcCAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC GTGTTAAATACTAGTTTAACTTATGCCGTCTTTTGAATTCTTCTTTTGGAAACTTCTGTTTACAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC Template switch alignment (log-probability: -27.8) GTGTTAAATACTAGTgTAACTTATGCCaTCTTTTGAATTC|GAAGTTTC|CAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC GTGTTAAATACTAGTTTAACTTATGCCGTCTTTTGAATTC|GAAGTTTC|CAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC Chimp > Gorilla --------------- chr5:21436558-21436565 Template switch process: F1: L ATGTGTTAAATACTAGTGTAACTTATGCCATCTTTTGAATTC 1 F3: 4 CAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC R RF: ATGTGTTAAATACTAGTTTAACTTATGCCATCTTTTGAATTCTTCTTTTGGAAACTTCTGTTTACAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC RR: TACACAATTTATGATCAAATTGAATACGGTAGAAAACTTAAGAAGAAAACCTTTGAAGACAAATGTTTACACTAAATATCACATCACCCTTACTTATCCATCCG F2: 3 CTTTGAAG 2 Unidirectional alignment (log-probability: -32.5) GTGTTAAATACTAGTgTAACTTATGCCATCTTTTGAATTC--------GAA------GTTTcCAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC GTGTTAAATACTAGTTTAACTTATGCCATCTTTTGAATTCTTCTTTTGGAAACTTCTGTTTACAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC Template switch alignment (log-probability: -22.3) GTGTTAAATACTAGTgTAACTTATGCCATCTTTTGAATTC|GAAGTTTC|CAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC GTGTTAAATACTAGTTTAACTTATGCCATCTTTTGAATTC|GAAGTTTC|CAAATGTGATTTATAGTGTAGTGGGAATGAATAGGTAGGC ========== Event 1408 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGACAAGCCGCGGCGGTCTTACAGGGCCCTGGGTGAAGGAACAGGCAAGGGGGATCCCTCGGGCCCCCTCAGGGCCCACAGCTCTGGGCTTAGGGGCAGCTTACGAGAGAGCCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCT---CCTGCGAGTGTGCCTGGGGCTTTGGCG Chimp: AGACAAGCCGCGGCGGTCTTACAGGGCCCTGGGTGAAGGGACAGGCAAGGGGGATCCCTCGGGCCCCCTCAGGGCCCACAGCTCTGGGCTTAGGGGCAGCTTATGAGAGAGCCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCT---CCTGCGAGTGTGCCTGGGGCTTTGGCG ↓ 3 2 1 4 Gorilla: AGACAAGCCGCGGCGGTCTTACAGGACCCTGGGTGAAGGGACAGGCAAGGGGGATCCCTCGGGCCCCCTCAGGGCCCACAGCTCTGGGCTTAGGGGCAGCTTATGAGAGAGCCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCTCCTGTAAGTGTGCCTGGGGCTTTGGCG ↑ 3 2 1 4 Human: AGACAAGCCGCGGCGGTCTTACAGGGCCCTGGGTGAAGGAACAGGCAAGGGGGATCCCTCGGGCCCCCTCAGGGCCCACAGCTCTGGGCTTAGGGGCAGCTTACGAGAGAGCCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCT---CCTGCGAGTGTGCCTGGGGCTTTGGCG Cluster: [ ] Orangutan: AGACAAGCCGTGGCGGTCTTACAGGGCCCTGGGTGAAGGGACAGGCAAGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr17:89265939-89265944 Template switch process: F1: L CCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT 1 F3: 4 AGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC R RF: TACAGGGCCCTGGGTGAAGGAACAGGCAAGGGGGATCCCTCGGGCCCCCTCAGGGCCCACAGCTCTGGGCTTAGGGGCAGCTTACGAGAGAGCCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCTGCGAGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC RR: ATGTCCCGGGACCCACTTCCTTGTCCGTTCCCCCTAGGGAGCCCGGGGGAGTCCCGGGTGTCGAGACCCGAATCCCCGTCGAATGCTCTCTCGGAATCCGAAGACACCTGTCCCTGTCCGACCCTCCCACGGAGGACGCTCACACGGACCCCGAAACCGCAGTTCAAGACTTTACCGGG F2: 3 ATGTCC 2 Unidirectional alignment (log-probability: -26.3) AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCTcctGtaAGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT---GCGAGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC Template switch alignment (log-probability: -16.6) AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT|CCTGTA|AGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT|CCTGTA|AGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC Chimp > Gorilla --------------- chr17:89265939-89265944 Template switch process: F1: L CCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT 1 F3: 4 AGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC R RF: TACAGGGCCCTGGGTGAAGGGACAGGCAAGGGGGATCCCTCGGGCCCCCTCAGGGCCCACAGCTCTGGGCTTAGGGGCAGCTTATGAGAGAGCCTTAGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCTGCGAGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC RR: ATGTCCCGGGACCCACTTCCCTGTCCGTTCCCCCTAGGGAGCCCGGGGGAGTCCCGGGTGTCGAGACCCGAATCCCCGTCGAATACTCTCTCGGAATCCGAAGACACCTGTCCCTGTCCGACCCTCCCACGGAGGACGCTCACACGGACCCCGAAACCGCAGTTCAAGACTTTACCGGG F2: 3 ATGTCC 2 Unidirectional alignment (log-probability: -26.3) AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCTcctGtaAGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT---GCGAGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC Template switch alignment (log-probability: -16.6) AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT|CCTGTA|AGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC AGGCTTCTGTGGACAGGGACAGGCTGGGAGGGTGCCTCCT|CCTGTA|AGTGTGCCTGGGGCTTTGGCGTCAAGTTCTGAAATGGCCC ========== Event 1409 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GGCAGCTGTGGGCTTCCCTGG----------ACTGGTCCAGGCCCC------ATAGG ↑ 1 3 42 Chimp: GGCAGCTGTGGGCTTCCCTGGGTGCCCCCAGCCCAGTCCAGGCCCC------ATAGG Gorilla: Human: GGCAGCTGTGGGCTTCCCTGG----------ACTGGTCCAGGCCCC------ATAGG Cluster: [ ] Orangutan: GGCAGCTGTGGGCCTCCCTGGGTGCCCCCAGCCCAGTCCAGGCCCCATCACCATAGG Chimp > Human ------------- chr17:23226635-23226638 Template switch process: F1: L CTTGGGCTCTGAGGGGGAGTGGCAGCTGTGGGCTTCCCTGG 1 F3: 4 GTCCAGGCCCCATAGGTGGGCACAGCTGGTGGGCAAGCCT R RF: CTTGGGCTCTGAGGGGGAGTGGCAGCTGTGGGCTTCCCTGGGTGCCCCCAGCCCAGTCCAGGCCCCATAGGTGGGCACAGCTGGTGGGCAAGCCT RR: GAACCCGAGACTCCCCCTCACCGTCGACACCCGAAGGGACCCACGGGGGTCGGGTCAGGTCCGGGGTATCCACCCGTGTCGACCACCCGTTCGGA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -26.1) TTGGGCTCTGAGGGGGAGTGGCAGCTGTGGGCTTCCCTGGactG-------------GTCCAGGCCCCATAGGTGGGCACAGCTGGTGGGCAAGCCT TTGGGCTCTGAGGGGGAGTGGCAGCTGTGGGCTTCCCTGG---GTGCCCCCAGCCCAGTCCAGGCCCCATAGGTGGGCACAGCTGGTGGGCAAGCCT Template switch alignment (log-probability: -15.8) TTGGGCTCTGAGGGGGAGTGGCAGCTGTGGGCTTCCCTGG|ACTG|GTCCAGGCCCCATAGGTGGGCACAGCTGGTGGGCAAGCCT TTGGGCTCTGAGGGGGAGTGGCAGCTGTGGGCTTCCCTGG|ACTG|GTCCAGGCCCCATAGGTGGGCACAGCTGGTGGGCAAGCCT ========== Event 1410 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGG------------------------GTGATGCTAATACAGGattagac ↓ 3 2 4 1 Chimp: ATAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGG------------GTCTGCTAATGGGTAATGCTAATACAGGattagac Gorilla: GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGTCTGCTAATGG------------GTAATGCTAATACAGGattagac ↑ 3 2 4 1 Human: GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGG------------------------GTGATGCTAATACAGGattagac Cluster: [ ] Orangutan: GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGTCTACTAATGG------------GTAATGCTAATACAGGattagac Human > Chimp ------------- chr17:62057105-62057112 Template switch process: F1: L GGCATAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGT 1 F3: 4 GGGTAATGCTAATACAGGATTAGACCATTCTCTCATTGCTATAAA R RF: GGCGTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGTGATGCTAATACAGGATTAGACCATTCTCTCATTGCTATAAA RR: CCGCATTTGACCAAAACTACTTTAATCGTCTGGGTGTCCCCCACTACGATTATGTCCTAATCTGGTAAGAGAGTAACGATATTT F2: 3 TAATCGTC 2 Unidirectional alignment (log-probability: -40.2) aTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGTctgctaatgggtaATGCTAATACAGGATTAGACCATTCTCTCATTGCT GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGTG------------ATGCTAATACAGGATTAGACCATTCTCTCATTGCT Template switch alignment (log-probability: -28.4) aTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGT|CTGCTAAT|GGGTaATGCTAATACAGGATTAGACCATTCTCTCATTGCT GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGT|CTGCTAAT|GGGTGATGCTAATACAGGATTAGACCATTCTCTCATTGCT Human > Gorilla --------------- chr5:144647738-144647745 Template switch process: F1: L GGCGTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGT 1 F3: 4 GGGTAATGCTAATACAGGATTAGACCATTCTCTCATTGCTATAAA R RF: GGCGTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGTGATGCTAATACAGGATTAGACCATTCTCTCATTGCTATAAA RR: CCGCATTTGACCAAAACTACTTTAATCGTCTGGGTGTCCCCCACTACGATTATGTCCTAATCTGGTAAGAGAGTAACGATATTT F2: 3 TAATCGTC 2 Unidirectional alignment (log-probability: -33.7) GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGgggtctgctaatGGGTaATGCTAATACAGGATTAGACCATTCTCTCATTGCT GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGG------------GGGTGATGCTAATACAGGATTAGACCATTCTCTCATTGCT Template switch alignment (log-probability: -22.4) GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGT|CTGCTAAT|GGGTaATGCTAATACAGGATTAGACCATTCTCTCATTGCT GTAAACTGGTTTTGATGAAATTAGCAGACCCACAGGGGGT|CTGCTAAT|GGGTGATGCTAATACAGGATTAGACCATTCTCTCATTGCT ========== Event 1411 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTAGTCCAGACCAGTTTTAGATG----------------------GAAAATCTGAGATACACAGTTTTAGTTTtatgtatg Chimp: CCTAGTCCAGACCAGTTTTAGATG----------------------GAAAATCTGAGATACACAGTTTTAGTTTtatgtatg ↓ 4 3 2 Gorilla: CCTAGTCCAGACCAGTTTTAGATGGAAAATCTGTGTATCTCAGATGGAAAATCTGAGATACACAGTTTTAGTTTtatgtatg ↑ 4 3 2 Human: CCTAGTCCAGACCAGTTTTAGATG----------------------GAAAATCTGAGATACACAGTTTTAGTTTtatgtatg Cluster: [ ] Orangutan: CCTAGTCCAGACCAGTTTTAGATG----------------------GAAAATCTGAGATACACAGTTTTAGTTTTATATGTG Human > Gorilla --------------- chr5:19591978-19591985 Template switch process: F1: L TTTTTTGATGATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTG 1 F3: 4 AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTATGTGTG R RF: TTTCTTGATGATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTATGTGTG RR: AAAGAACTACTATCTAGGGATCAGGTCTGGTCAAAATCTACCTTTTAGACTCTATGTGTCAAAATCAAAATACATACACAC F2: 3 CTCTATGT 2 Unidirectional alignment (log-probability: -57.6) ATAGATCCCTAGTCCAGACCAGTTTTagatggaaaatctgtgtatctcAGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT ATAGATCCCTAGTCCAGACCAGTTTT----------------------AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT Template switch alignment (log-probability: -22.6) ATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTG|TGTATCTC|AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT ATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTG|TGTATCTC|AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT Chimp > Gorilla --------------- chr5:19591978-19591985 Template switch process: F1: L TTTTTTGATGATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTG 1 F3: 4 AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTATGTGTG R RF: TTTCTTGATGATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTATGTGTG RR: AAAGAACTACTATCTAGGGATCAGGTCTGGTCAAAATCTACCTTTTAGACTCTATGTGTCAAAATCAAAATACATACACAC F2: 3 CTCTATGT 2 Unidirectional alignment (log-probability: -57.6) ATAGATCCCTAGTCCAGACCAGTTTTagatggaaaatctgtgtatctcAGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT ATAGATCCCTAGTCCAGACCAGTTTT----------------------AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT Template switch alignment (log-probability: -22.6) ATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTG|TGTATCTC|AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT ATAGATCCCTAGTCCAGACCAGTTTTAGATGGAAAATCTG|TGTATCTC|AGATGGAAAATCTGAGATACACAGTTTTAGTTTTATGTAT ========== Event 1412 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: attttttgctacttgtatgcatatg--tgtata----tacacacaaattaaaaattgaaaccat Chimp: ATTTTTTGCTACTTGTATGCATATG--TGTATA----TACACACAAATTAAAAATTGAAACCAT ↑ 3 1 42 Gorilla: ATTTTTTGCTACTTGTATGCACGTG----TATA--------TACAAATTAAAAATTGAAACCAT Human: attttttgctacttgtatgcatatg--tgtata----tacacacaaattaaaaattgaaaccat Cluster: [ ] Orangutan: gttttttactacttgtatgcatatgtg--tatataca----cacaaattaaaaattgaaaccat Gorilla > Chimp --------------- chr17:19921847-19921856 Template switch process: F1: L CAGATATGTAGTTTTGTTCTATTTTTTGCTACTTGTATGCATATGT 1 F3: 4 ACAAATTAAAAATTGAAACCATACTGTACATATTGTCT R RF: CAGATATGTAGTTTTGTTCTATTTTTTGCTACTTGTATGCACGTGTATATACAAATTAAAAATTGAAACCATACTGTACATATTGTCT RR: GTCTATACATCAAAACAAGATAAAAAACGATGAACATACGTGCACATATATGTTTAATTTTTAACTTTGGTATGACATGTATAACAGA F2: 3 CACATATATG 2 Unidirectional alignment (log-probability: -41.7) TGTAGTTTTGTTCTATTTTTTGCTACTTGTATGCatAtGTGTATATacacACAAATTAAAAATTGAAACCATACTGTACATATTGTCT-- TGTAGTTTTGTTCTATTTTTTGCTACTTGTATGC--ACGTGTATAT----ACAAATTAAAAATTGAAACCATACTGTACATATTGTCTTA Template switch alignment (log-probability: -28.1) TGTAGTTTTGTTCTATTTTTTGCTACTTGTATGCAtaTGT|GTATATACAC|ACAAATTAAAAATTGAAACCATACTGTACATATTGTCT TGTAGTTTTGTTCTATTTTTTGCTACTTGTATGCACGTGT|GTATATACAC|ACAAATTAAAAATTGAAACCATACTGTACATATTGTCT ========== Event 1413 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGTTCTCCGAGGCCCACCTCTGATAACCACCCACCTTTCTTCTCTCATGAATCAGAA-ATAATATAGTATTTTTTTGTCCTCA Chimp: AGGTTCTCCGAGGCCCACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCAGAA-ATA--ATAGTAtttttttGTCCTCA ↓ 3 2 1 4 Gorilla: AGGTTCTCCGAGGCCCACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCAATCAGAA--ATAGTAtttttttGTCCTCA Human: AGGTTCTCCGAGGCCCACCTCTGATAACCACCCACCTTTCTTCTCTCATGAATCAGAA-ATAATATAGTATTTTTTTGTCCTCA Cluster: [ ] Orangutan: AGGTTCTCCGAGGCCCACCACTGATAACCACCCACCTTTCTTCTCTAATGAATCAGAA------ATAGTATTTTTTTGTCCTCA Chimp > Gorilla --------------- chr5:18693630-18693635 Template switch process: F1: L CCACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCA 1 F3: 4 AATAGTATTTTTTTGTCCTCAAGTGCTAATT----ATTAT R RF: CCACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCAGAAATAATAGTATTTTTTTGTCCTCAGGTGCTAATTCTTAATTAT RR: GGTGGAGACTATTGGTGGGTGGAAAGAAGAGATTACTTAGTCTTTATTATCATAAAAAAACAGGAGTCCACGATTAAGAATTAATA F2: 3 AGACTA 2 Unidirectional alignment (log-probability: -42) CACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATC---AATcagaAATAGTATTTTTTTGTCCTCAaGTGCTAATT----ATTAT CACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCAGAAAT----AATAGTATTTTTTTGTCCTCAGGTGCTAATTCTTAATTAT Template switch alignment (log-probability: -31.8) CACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCA|ATCAGA|AATAGTATTTTTTTGTCCTCAaGTGCTAATT----ATTAT CACCTCTGATAACCACCCACCTTTCTTCTCTAATGAATCA|ATCAGA|AATAGTATTTTTTTGTCCTCAGGTGCTAATTCTTAATTAT ========== Event 1414 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAGTGTCACAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG Chimp: ACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAGTGTCACAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG ↑ 4 3 2 1 Gorilla: ACACGCCCAGCTATGAATCCAATC------------------------------CAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG ↓ 4 3 2 1 Human: ACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAGTGTCACAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG Cluster: [ ] Orangutan: ACACGCCCAGCTATGAATCCAAA-------------------------------------CTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTC Gorilla > Human --------------- chr17:66862378-66862382 Template switch process: F1: L CTGTGCTTGGGGGCTACACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAG 1 F3: 4 CAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG R RF: CTGTGCTTGGGGGCTACACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG RR: GACACGAACCCCCGATGTGTGCGGGTCGATACTTAGGTTAGGTCGAACACAGTGAATGTTCGACGGAATCTCTCGAGAGAC F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -54) GCCCAGCTATGAATCCAAtccagcttgtgtcacttacaagtgtcacaaTCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT GCCCAGCTATGAATCCAA------------------------------TCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT Template switch alignment (log-probability: -22.5) GCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAG|TGTcA|CAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT GCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAG|TGTAA|CAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT Gorilla > Chimp --------------- chr17:66269320-66269324 Template switch process: F1: L CTGTGCTTGGGGGCTACACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAG 1 F3: 4 CAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG R RF: CTGTGCTTGGGGGCTACACACGCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCTCTCTG RR: GACACGAACCCCCGATGTGTGCGGGTCGATACTTAGGTTAGGTCGAACACAGTGAATGTTCGACGGAATCTCTCGAGAGAC F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -54) GCCCAGCTATGAATCCAAtccagcttgtgtcacttacaagtgtcacaaTCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT GCCCAGCTATGAATCCAA------------------------------TCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT Template switch alignment (log-probability: -22.5) GCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAG|TGTcA|CAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT GCCCAGCTATGAATCCAATCCAGCTTGTGTCACTTACAAG|TGTAA|CAATCCAGCTTGTGTCACTTACAAGCTGCCTTAGAGAGCT ========== Event 1415 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tttagggtgggatgtagtcatatgggtctcaccttgctacaaagagaggctaggaaatgcagtctttattcaaggtggccaggtgcccagccaaacactaagggttctgtgactatggCACTTG----GTGGTGGAGTGGTCGTGAGCCTGG Chimp: tttagggtgggatgtagtcatatgggtctcaccttgctacaaagagaggctaggaaatgcagtctttattcaaggtggccaggtgcccagccaaacactaagggttctgtgactatggCACTTG----GTGGTGGAGTGGTCGTGAGCCTGG ↓ 3 2 1 4 Gorilla: tttagggtgggatgtagtcatatgggtctcactttgctacaaagagaggctatgaaatgcagtctttattcaaggtggccaggtgcccagccaaacactaagggttctgtgactatggCACAGAACCATATGTGGAGTGGTCGTGAGCCTGG ↑ 3 2 1 4 Human: tttagggtgggatgtagtcatatgggtctcaccttgctacaaagagaggctaggaaatgcagtctttattcaaggtggccaggtgcccagccaaacactaagggttctgtgactatggCACTTG----GTGGTGGAGTGGTCGTGAGCCTGG Cluster: [ ] Orangutan: tttagggtgggatgtagtcatatgggtctcaccttgctgcaaagagaggctaggaaatgcagtctttattcaaggtggccatgtgcccagccaaacactaagggttctgtgactatggCACTTG----GTGGTGGAGTGGTCATGAGCCTGG Human > Gorilla --------------- chr5:149084689-149084698 Template switch process: F1: L AGGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC 1 F3: 4 GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT R RF: ATATGGGTCTCACCTTGCTACAAAGAGAGGCTAGGAAATGCAGTCTTTATTCAAGGTGGCCAGGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCACTTGGTGGTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT RR: TATACCCAGAGTGGAACGATGTTTCTCTCCGATCCTTTACGTCAGAAATAAGTTCCACCGGTCCACGGGTCGGTTTGTGATTCCCAAGACACTGATACCGTGAACCACCACCTCACCAGCACTCGGACCGAAATCGACCCTCCGAAGA F2: 3 TATACCAAGA 2 Unidirectional alignment (log-probability: -33.8) GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCACagaaccataT-----GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC---------TTGGTGGTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT Template switch alignment (log-probability: -22.5) GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC|AGAaCCATAT|GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC|AGACCCATAT|GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT Chimp > Gorilla --------------- chr5:149084689-149084698 Template switch process: F1: L AGGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC 1 F3: 4 GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT R RF: ATATGGGTCTCACCTTGCTACAAAGAGAGGCTAGGAAATGCAGTCTTTATTCAAGGTGGCCAGGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCACTTGGTGGTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT RR: TATACCCAGAGTGGAACGATGTTTCTCTCCGATCCTTTACGTCAGAAATAAGTTCCACCGGTCCACGGGTCGGTTTGTGATTCCCAAGACACTGATACCGTGAACCACCACCTCACCAGCACTCGGACCGAAATCGACCCTCCGAAGA F2: 3 TATACCAAGA 2 Unidirectional alignment (log-probability: -33.8) GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCACagaaccataT-----GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC---------TTGGTGGTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT Template switch alignment (log-probability: -22.5) GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC|AGAaCCATAT|GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT GGTGCCCAGCCAAACACTAAGGGTTCTGTGACTATGGCAC|AGACCCATAT|GTGGAGTGGTCGTGAGCCTGGCTTTAGCTGGGAGGCTTCT ========== Event 1416 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGTCAGCACATTTTCTATTTTTA---------------ACCTGCTGCATTCTAACCTGCAAATAGAACTTTCTTCACTAA Chimp: AGGTCAGCACATTTTCTATTTTTA---------------ACCTGCTGCATTCTAACCTGCAAATAGAACTTTCTTCACTAA ↑ 4 3 12 Gorilla: AGGTCAGCACATTTTCTATTTTTA------------------------------ACCTGCAAATAGAACTTTCTTCACTAA ↓ 4 3 12 Human: AGGTCAGCACATTTTCTATTTTTA---------------ACCTGCTGCATTCTAACCTGCAAATAGAACTTTCTTCACTAA Cluster: [ ] Orangutan: AGGCCAGCACATTTTCTATTTTTAACCTGCTGCATTCTA---------------ATCTGCAAATAGAACTTTCTTCACTAA Gorilla > Human --------------- chr17:65869113-65869116 Template switch process: F1: L CAGCCCTTCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGC 1 F3: 4 TTCTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCTGTGCT R RF: CAGCCCTTCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCTGTGCT RR: GTCGGGAAGTCTACGGATCCAGTCGTGTAAAAGATAAAAATTGGACGTTTATCTTGAAAGAAGTGATTATAACAGACACGA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -32.5) TCAGATGCCTAGGTCAGCACATTTTCTATTTTtaacctgctgcattcTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCT TCAGATGCCTAGGTCAGCACATTTTCTATTTT---------------TAACCTGCAAATAGAACTTTCTTCACTAATATTGTCT Template switch alignment (log-probability: -22) TCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGC|TGCA|TTcTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCT TCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGC|TGCA|TTTTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCT Gorilla > Chimp --------------- chr17:65233197-65233200 Template switch process: F1: L CAGCCCTTCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGC 1 F3: 4 TTCTAACCTGCAAATAGAACTTTCTTCACTAACATTGTCTGTGCT R RF: CAGCCCTTCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCTGTGCT RR: GTCGGGAAGTCTACGGATCCAGTCGTGTAAAAGATAAAAATTGGACGTTTATCTTGAAAGAAGTGATTATAACAGACACGA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -38) TCAGATGCCTAGGTCAGCACATTTTCTATTTTtaacctgctgcattcTAACCTGCAAATAGAACTTTCTTCACTAAcATTGTCT TCAGATGCCTAGGTCAGCACATTTTCTATTTT---------------TAACCTGCAAATAGAACTTTCTTCACTAATATTGTCT Template switch alignment (log-probability: -27.5) TCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGC|TGCA|TTcTAACCTGCAAATAGAACTTTCTTCACTAAcATTGTCT TCAGATGCCTAGGTCAGCACATTTTCTATTTTTAACCTGC|TGCA|TTTTAACCTGCAAATAGAACTTTCTTCACTAATATTGTCT ========== Event 1417 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCACCTTTAAAGAGTCTACAAAAGAGGAG--AACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGGAGCACACTGCCTCAACAGTTTCAGTGCACAGTGAAAATCAGAAATATTATAAACAAGAATTGAGACATTCTAAAGTAAGACTAGTGAAATGAATG Chimp: CCCACCTTTAAAGAGTCTACAGAAGAGGAG--AACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGGAGCGCACTGCCTCAACAGTCTCAGTGCACAGTGAAAATCAGAAATATTATAAACAAGAATTGAGACATTCTAAAGTAAGACTAGTGAAATGAATG ↓ 1 4 3 2 Gorilla: CCCACCTTTAAAGAGTCTACAAAAGACTTT----AGTCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGGAGCACACTGCCTCAACAGTTTCAGTGCACAGTGAAAATCAGAAACATTATAAACAAGAATTGAGACATTCTAAAGTAAGACTAGCGAAATGAATG ↑ 1 4 3 2 Human: CCCACCTTTAAAGAGTCTACAAAAGAGGAG--AACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGGAGCACACTGCCTCAACAGTTTCAGTGCACAGTGAAAATCAGAAATATTATAAACAAGAATTGAGACATTCTAAAGTAAGACTAGTGAAATGAATG Cluster: [ ] Orangutan: CCCACCTTTAAAGAGTCTACAAAAGAGGAGAA--CATCTTAAAGTCGGCTAACTTTGAAGAAAGCAACAAGTTTGGAGCACACTGCCTCAACAGTTTCAGTGCACAGTGAAAATCCGAAATATTATAAACAAGAATTGAGACATTCTAAAGTAAGACTAGTAAAATGAATG Human > Gorilla --------------- chr1:221517903-221517908 Template switch process: F1: L CATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAGA 1 F3: 4 TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG R RF: CATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAGAGGAGAACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGGAGCACACTGCCTCAACAGTTTCAGTGCACAGTGAAAATCAGAAATATTATAAACAAGAATTGAGACATTCTAAAG RR: GTATGTCTAAGACGTGGGTGGAAATTTCTCAGATGTTTTCTCCTCTTGTAGAATTTCAGCCGATTGAAACGTCTTTCGTTGTTCAAACCTCGTGTGACGGAGTTGTCAAAGTCACGTGTCACTTTTAGTCTTTATAATATTTGTTCTTAACTCTGTAAGATTTC F2: 3 GATTTC 2 Unidirectional alignment (log-probability: -28.2) ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAGactttAG-------TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAG-----AGGAGAACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG Template switch alignment (log-probability: -16.5) ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAGA|CTTTAG|TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAGA|CTTTAG|TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG Chimp > Gorilla --------------- chr1:221517903-221517908 Template switch process: F1: L ACTCCCATACAGATTCTGCACCCACCTTTAAAGAGTCTACAAAAGA 1 F3: 4 TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG R RF: ACTCCCATACAGATTCTGCACCCACCTTTAAAGAGTCTACAGAAGAGGAGAACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGGAGCGCACTGCCTCAACAGTCTCAGTGCACAGTGAAAATCAGAAATATTATAAACAAGAATTGAGACATTCTAAAG RR: TGAGGGTATGTCTAAGACGTGGGTGGAAATTTCTCAGATGTCTTCTCCTCTTGTAGAATTTCAGCCGATTGAAACGTCTTTCGTTGTTCAAACCTCGCGTGACGGAGTTGTCAGAGTCACGTGTCACTTTTAGTCTTTATAATATTTGTTCTTAACTCTGTAAGATTTC F2: 3 GATTTC 2 Unidirectional alignment (log-probability: -33.8) ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAaAAGactttAG-------TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAGAAG-----AGGAGAACATCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG Template switch alignment (log-probability: -22.1) ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAaAAGA|CTTTAG|TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG ATACAGATTCTGCACCCACCTTTAAAGAGTCTACAGAAGA|CTTTAG|TCTTAAAGTCGGCTAACTTTGCAGAAAGCAACAAGTTTGG ========== Event 1418 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTCACACATTTGCAGTGTGTCT------------------------------TCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGATTGCCTCCTGCGGTCTCCCCTGTCCTTTAGGACAAATGAAAAGTTCA ↓ 4 1 3 2 Chimp: TTTCACACATTTGCAGTGTGTCT---------------TCTGCATGGACGTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGATTGCCTCCTGCGGTCTCCCCTGTCCTTTAGGACAAATGAAAAGTTCA Gorilla: TTTCACACATTTGCAGTGTGTCTTCTGCATGGACGTCT---------------TCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGCTTGCCTCCTGCAGTCTCCCCTGTCCTTTAGGACAAATGAAAAGTTCA ↑ 4 1 3 2 Human: TTTCACACATTTGCAGTGTGTCT------------------------------TCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGATTGCCTCCTGCGGTCTCCCCTGTCCTTTAGGACAAATGAAAAGTTCA Cluster: [ ] Orangutan: TTTCACACATTTGCAGTGTGTCTTCTGCATGGACCTCT---------------TCTGCCACAGGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGCTTGCCTCCTGCCGTCTCCCCTGTCCTTTAGGACAAATGAAAAGTTCA Human > Chimp ------------- chr17:67148756-67148761 Template switch process: F1: L TTCCACAGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGC 1 F3: 4 GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCA R RF: TTCCACAGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGATTGCCTCCTGCGGTCTCCCCTGTCCTT RR: AAGGTGTCGAGTGGAAATAAAGTGTGTAAACGTCACACAGAAGACGGTGTTCGTCCCGTCTCTCCCCGGGAGTGTGTCCGTGCACTAACGGAGGACGCCAGAGGGGACAGGAA F2: 3 CAGGTA 2 Unidirectional alignment (log-probability: -32.5) AGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGCatggacgtcttctgcCACAAGCAGGGCAGAGAGGGGCCCTCACACA AGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGC---------------CACAAGCAGGGCAGAGAGGGGCCCTCACACA Template switch alignment (log-probability: -22.2) AGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGC|AtGGAC|GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACA AGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGC|AAGGAC|GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACA Human > Gorilla --------------- chr5:149916159-149916164 Template switch process: F1: L TTCCACAGCTCACCTTTCTTTCACACATTTGCAGTGTGTCTTCTGC 1 F3: 4 GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCA R RF: TTCCACAGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACAGGCACGTGATTGCCTCCTGCGGTCTCCCCTGTCCTT RR: AAGGTGTCGAGTGGAAATAAAGTGTGTAAACGTCACACAGAAGACGGTGTTCGTCCCGTCTCTCCCCGGGAGTGTGTCCGTGCACTAACGGAGGACGCCAGAGGGGACAGGAA F2: 3 CAGGTA 2 Unidirectional alignment (log-probability: -38) AGCTCACCTTTcTTTCACACATTTGCAGTGTgtcttctgcatggacGTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACA AGCTCACCTTTATTTCACACATTTGCAGTGT---------------GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACA Template switch alignment (log-probability: -27.7) AGCTCACCTTTcTTTCACACATTTGCAGTGTGTCTTCTGC|AtGGAC|GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACA AGCTCACCTTTATTTCACACATTTGCAGTGTGTCTTCTGC|AAGGAC|GTCTTCTGCCACAAGCAGGGCAGAGAGGGGCCCTCACACA ========== Event 1419 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTATACAATTAGATAATCATATACCAAAAGAAatgattcatttcttttggtatatgaatcatttct------tttggtatatgattcatttcAATTAATTCATA Chimp: TATTATACAATTAGATAATCATATACCAAAAGAAATGATTTATT---------------------TCT------TTTGGTATATGATTCATTTCAATTGATTCATA ↑ 3 12 4 Gorilla: TATTATACAATTAGATAATCATATACCAAAAGAAATGAATCATT---------------------TCA------------AATCAATTCATTTCAATTGATTCATA Human: TATTATACAATTAGATAATCATATACCAAAAGAAatgattcatttcttttggtatatgaatcatttct------tttggtatatgattcatttcAATTAATTCATA Cluster: [ ] Orangutan: AATTATACAATTAG------------------AAATGAATCATT---------------------TCTTTTGGT------ATATGATTCATTTCAATTGATTCATA Gorilla > Chimp --------------- chr17:15240034-15240053 Template switch process: F1: L TTCTATTATACAATTAGATAATCATATACCAAAAGAAATGA 1 F3: 4 ATTCATTTCAATTGATTCATAATCATTATGAACCACCTCA R RF: TTCTATTATACAATTAGATAATCATATACCAAAAGAAATGAATCATTTCAAATCAATTCATTTCAATTGATTCATAATCATTATGAACCACCTCG RR: AAGATAATATGTTAATCTATTAGTATATGGTTTTCTTTACTTAGTAAAGTTTAGTTAAGTAAAGTTAACTAAGTATTAGTAATACTTGGTGGAGC F2: 3 GTATATGGTTTTCTTTATTT 2 Unidirectional alignment (log-probability: -54.9) TCTATTATACAATTAGATAATCATATACCAAAAGAAATGAtTtATTTCttttggtatatg------ATTCATTTCAATTGATTCATAATCATTATGAACCACCTCa TCTATTATACAATTAGATAATCATATACCAAAAGAAATGAATCATTTC------------AAATCAATTCATTTCAATTGATTCATAATCATTATGAACCACCTCG Template switch alignment (log-probability: -29.3) TCTATTATACAATTAGATAATCATATACCAAAAGAAATGA|TTtATTTCTTTTGGTATATG|ATTCATTTCAATTGATTCATAATCATTATGAACCACCTCa TCTATTATACAATTAGATAATCATATACCAAAAGAAATGA|TTCATTTCTTTTGGTATATG|ATTCATTTCAATTGATTCATAATCATTATGAACCACCTCG ========== Event 1420 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTTCAATTAAAGGAATATTAGAGGCTAGAAAATTT-------GTAAAAGTTAGGCCAGTTACCTGGAG ↓ 3 2 1 4 Chimp: TATTTCAATTAAAGGAATATTAGAGGCTAGAAAATTAGCCTCTAATAAAAGTTAGGCCAGTTACCTGGAG ↑ 3 2 1 4 Gorilla: TATTTCAATTAAATGAATATTAGAGGCTAGAAAATTT-------GTAAAGGTTAGGCCAGTTACCTGGAG Human: TATTTCAATTAAAGGAATATTAGAGGCTAGAAAATTT-------GTAAAAGTTAGGCCAGTTACCTGGAG Cluster: [ ] Orangutan: TATTTCAATTAAATGAATATTAGAGGCTAGAAAATTT-------GTAAAAGTTAGGCCAGTTACCTGGAG Human > Chimp ------------- chr17:70221823-70221831 Template switch process: F1: L ATGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATT 1 F3: 4 TAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG R RF: ATGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATTTGTAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG RR: TACACATAAAGTTAATTTCCTTATAATCTCCGATCTTTTAAACATTTTCAATCCGGTCAATGGACCTCACACTTGGAGGTGAC F2: 3 AATCTCCGA 2 Unidirectional alignment (log-probability: -27) TGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATTaGcctctaaTAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG TGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATTTG-------TAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG Template switch alignment (log-probability: -16.4) TGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATT|AGCCTCTAA|TAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG TGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATT|AGCCTCTAA|TAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG Gorilla > Chimp --------------- chr17:70221823-70221831 Template switch process: F1: L ATGTGTATTTCAATTAAAGGAATATTAGAGGCTAGAAAATT 1 F3: 4 TAAAAGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTGATTGG R RF: ATGTGTATTTCAATTAAATGAATATTAGAGGCTAGAAAATTTGTAAAGGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTGATTGG RR: TACACATAAAGTTAATTTACTTATAATCTCCGATCTTTTAAACATTTCCAATCCGGTCAATGGACCTCACACTTGGAGGTGACTAACC F2: 3 AATCTCCGA 2 Unidirectional alignment (log-probability: -37.6) TGTGTATTTCAATTAAAgGAATATTAGAGGCTAGAAAATTaGcctctaaTAAAaGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG TGTGTATTTCAATTAAATGAATATTAGAGGCTAGAAAATTTG-------TAAAGGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG Template switch alignment (log-probability: -28) TGTGTATTTCAATTAAAgGAATATTAGAGGCTAGAAAATT|AGCCTCTAA|TAAAaGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG TGTGTATTTCAATTAAATGAATATTAGAGGCTAGAAAATT|AGCCTCTAA|TAAAGGTTAGGCCAGTTACCTGGAGTGTGAACCTCCACTG ========== Event 1421 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTGATCCTTAATTATGCTGCTT--GACTATCAGTAAGCCTTCTTTTT ↓ 3 4 Chimp: ACTGATCCTTAATTATGCTGCGTCAAGCTATCAGTAAGCCTTCTTTTT Gorilla: ACTGATCCTTAATTATGCTGCCT--GACTATCAGTAAGCCTTCTATTT Human: ACTGATCCTTAATTATGCTGCTT--GACTATCAGTAAGCCTTCTTTTT Cluster: [ ] Orangutan: ACTGATCCTTAATTATGCTACTT--GACTATCAGTAAGCCTTCTATTT Human > Chimp ------------- chr1:151077067-151077072 Template switch process: F1: L TTCTCAACGTTGTAAGCTTCACTGATCCTTAATTATGCTGC 1 F3: 4 CTATCAGTAAGCCTTCTTTTTTCCAGACAGGGTAGTTCTC R RF: TTCTCAACGTTGTAAGCTTCACTGATCCTTAATTATGCTGCTTGACTATCAGTAAGCCTTCTTTTTTCCAGACAAGGTAGTTCTC RR: AAGAGTTGCAACATTCGAAGTGACTAGGAATTAATACGACGAACTGATAGTCATTCGGAAGAAAAAAGGTCTGTTCCATCAAGAG F2: 3 GAACTG 2 Unidirectional alignment (log-probability: -31.8) TCTCAACGTTGTAAGCTTCACTGATCCTTAATTATGCTGCgTcAagCTATCAGTAAGCCTTCTTTTTTCCAGACAgGGTAGTTCTC TCTCAACGTTGTAAGCTTCACTGATCCTTAATTATGCTGCTTGA--CTATCAGTAAGCCTTCTTTTTTCCAGACAAGGTAGTTCTC Template switch alignment (log-probability: -22) TCTCAACGTTGTAAGCTTCACTGATCCTTAATTATGCTGC|GTCAAG|CTATCAGTAAGCCTTCTTTTTTCCAGACAgGGTAGTTCTC TCTCAACGTTGTAAGCTTCACTGATCCTTAATTATGCTGC|GTCAAG|CTATCAGTAAGCCTTCTTTTTTCCAGACAAGGTAGTTCTC ========== Event 1422 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGACGGCCAAAGCACGATGAGG------ACCGCTGCCGGCAGCCCGCCCCACCCT Chimp: AGACGCCCAAAGCACGATGAGG------ACCGCTGCCGGCAGCCCGCCCCACCCT Gorilla: AGACGCCCAAAGCACGATGAGCAGCGGTCCTGCTGCCGGCAGCCCGCCCCACCCT ↑ 31 4 2 Human: AGACGGCCAAAGCACGATGAGG------ACCGCTGCCGGCAGCCCGCCCCACCCT Cluster: [ ] Orangutan: AGACGCCCAAAGCACGATGAGG------ACCGCTGCCGGCAGCCCGCCCCACCCT Human > Gorilla --------------- chr1:7457128-7457137 Template switch process: F1: L AAAACCGTGGGAACCCAGAAAGACGCCCAAAGCACGATGAG 1 F3: 4 GCTGCCGGCAGCCCGCCCCACCCTGGGCTCCTCCCCACAC R RF: AAAACCGTGGGAACCCAGAAAGACGGCCAAAGCACGATGAGGACCGCTGCCGGCAGCCCGCCCCACCCTGGGCTCCTCCCCACAC RR: TTTTGGCACCCTTGGGTCTTTCTGCCGGTTTCGTGCTACTCCTGGCGACGGCCGTCGGGCGGGGTGGGACCCGAGGAGGGGTGTG F2: 3 TCCTGGCGAC 2 Unidirectional alignment (log-probability: -36.1) AAACCGTGGGAACCCAGAAAGACGcCCAAAGCACGATGAGcAgcggtcCtGCTGCCGGCAGCCCGCCCCACCCTGGGCTCCTCCCCACAC AAACCGTGGGAACCCAGAAAGACGGCCAAAGCACGATGAGGA------CCGCTGCCGGCAGCCCGCCCCACCCTGGGCTCCTCCCCACAC Template switch alignment (log-probability: -22.5) AAACCGTGGGAACCCAGAAAGACGcCCAAAGCACGATGAG|CAGCGGTCCT|GCTGCCGGCAGCCCGCCCCACCCTGGGCTCCTCCCCACAC AAACCGTGGGAACCCAGAAAGACGGCCAAAGCACGATGAG|CAGCGGTCCT|GCTGCCGGCAGCCCGCCCCACCCTGGGCTCCTCCCCACAC ========== Event 1423 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTATGGTTTATTAACAAGGCA----------GCCTTGTTAATAATCCTAGCCtgccttgtttaataat Chimp: CTATGGTTTATTAACAAGGCA----------GCCTTGTTAATAATCCTAGCCtaccttgtttaataat ↓ 1 3 4 2 Gorilla: CTATGGTTTATTAACAAGGCAAGGATTATTAACAAGGTTAATAATCCTAGCCtaccttgtttaataat ↑ 1 3 4 2 Human: CTATGGTTTATTAACAAGGCA----------GCCTTGTTAATAATCCTAGCCtgccttgtttaataat Cluster: [ ] Orangutan: CTCTGGTTTATTAACAAGGCA----------GCCTTGTTAACAATCCTAGCCTGCCTTGTTTAATGGT Human > Gorilla --------------- chr5:9532355-9532369 Template switch process: F1: L AGTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCA 1 F3: 4 GTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC R RF: AGTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCAGCCTTGTTAATAATCCTAGCCTGCCTTGTTTAATAATCATTCCAC RR: TCACGGGACTGGATTAAACGGATACCAAATAATTGTTCCGTCGGAACAATTATTAGGATCGGACGGAACAAATTATTAGTAAGGTG F2: 3 GAACAATTATTAGGA 2 Unidirectional alignment (log-probability: -46.5) GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCaaggattattaacaAG----GTTAATAATCCTAGCCTaCCTTGTTTAATAATCATTCCAC GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGC--------------AGCCTTGTTAATAATCCTAGCCTGCCTTGTTTAATAATCATTCCAC Template switch alignment (log-probability: -23.2) GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCA|AGGATTATTAACAAG|GTTAATAATCCTAGCCTaCCTTGTTTAATAATCATTCCAC GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCA|AGGATTATTAACAAG|GTTAATAATCCTAGCCTGCCTTGTTTAATAATCATTCCAC Chimp > Gorilla --------------- chr5:9532355-9532369 Template switch process: F1: L AGTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCA 1 F3: 4 GTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC R RF: AGTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCAGCCTTGTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC RR: TCACGGGACTGGATTAAACGGATACCAAATAATTGTTCCGTCGGAACAATTATTAGGATCGGATGGAACAAATTATTAGTAAGGTG F2: 3 GAACAATTATTAGGA 2 Unidirectional alignment (log-probability: -41) GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCaaggattattaacaAG----GTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGC--------------AGCCTTGTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC Template switch alignment (log-probability: -17.6) GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCA|AGGATTATTAACAAG|GTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC GTGCCCTGACCTAATTTGCCTATGGTTTATTAACAAGGCA|AGGATTATTAACAAG|GTTAATAATCCTAGCCTACCTTGTTTAATAATCATTCCAC ========== Event 1424 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGCTCTCAGGGTAGCTCCACTATGAGGCCTCCTCATAGTGTGCCCAGGAGGGACAGAGC ↑ 3 2 1 4 Chimp: TGCTCTCAGGGTAGCTCCACTATGAGACCTCCTGCAGCTGTGCCCAGGAGGGACAGAGC Gorilla: TGCTCTCAGGGTAGCTCCACTATGAGGCCTCCTGCAGCTGTGCCCAGGAGGGACAGAGC ↓ 3 2 1 4 Human: TGCTCTCAGGGTAGCTCCACTATGAGGCCTCCTCATAGTGTGCCCAGGAGGGACAGAGC Cluster: [ ] Orangutan: TGCTCTCAGGGTAGCTCCACTATGAGGCCTCCTGCAGCTGTGCCCAGGAGGGACAGAGC Chimp > Human ------------- chr17:9399303-9399307 Template switch process: F1: L CAAAGGCAGGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCT 1 F3: 4 TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA R RF: CAAAGGCAGGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGACCTCCTGCAGCTGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA RR: GTTTCCGTCCCTCGGACGAGAGTCCCATCGAGGTGATACTCTGGAGGACGTCGACACGGGTCCTCCCTGTCTCGGACCGTAGTCCCGCCCTCT F2: 3 GATAC 2 Unidirectional alignment (log-probability: -33.2) GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGgCCTCCT----CatagTGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGACCTCCTGCAGC----TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA Template switch alignment (log-probability: -22) GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGgCCTCCT|CATAG|TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGACCTCCT|CATAG|TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA Gorilla > Human --------------- chr17:9399303-9399307 Template switch process: F1: L AGGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCT 1 F3: 4 TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA R RF: AGGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCTGCAGCTGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA RR: TCCCTCGGACGAGAGTCCCATCGAGGTGATACTCCGGAGGACGTCGACACGGGTCCTCCCTGTCTCGGACCGTAGTCCCGCCCTCT F2: 3 GATAC 2 Unidirectional alignment (log-probability: -26.6) GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCT----CatagTGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCTGCAGC----TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA Template switch alignment (log-probability: -16.4) GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCT|CATAG|TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA GGGAGCCTGCTCTCAGGGTAGCTCCACTATGAGGCCTCCT|CATAG|TGTGCCCAGGAGGGACAGAGCCTGGCATCAGGGCGGGAGA ========== Event 1425 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTCCCTGTGTGTGGCTGGCATCACCCGGGTCGGAATCACCCAGGTTGCTGATTAC-AAGCACGGCTGCTGCAACCCCGCTTCAGACCCTCTGGCCCGGAGGCGGCCCA ↑ 4 1 3 2 Chimp: GTCCCTGTGTGTGGCTGGCATCA---------------CCCAGGTTGCTGATTAC-AAGCACGGCTGCTGCAACCCCGCTTCAGACCCTCTGGCCCGGAGGAGGCCCA Gorilla: GTCCCTATGTGTGGCTGGCATCACCCGGGTCGGAATCGCCCAGGTTGCTGACTAC-AAGCATGGCTGCTGCAACCCCGCTTCAGACCCTCTGGCCCAGAGGAGGCCCA Human: GTCCCTGTGTGTGGCTGGCATCACCCGGGTCGGAATCACCCAGGTTGCTGATTAC-AAGCACGGCTGCTGCAACCCCGCTTCAGACCCTCTGGCCCGGAGGCGGCCCA Cluster: [ ] Orangutan: GTCCCTGTGTGTGGCTGGGGTCACCTGGGCcggaatcgcccaggttgctgattacaaagcacggctgctgcaaccccgcttcagaccctctggtctggaggaggctca Chimp > Human ------------- chr17:74370088-74370095 Template switch process: F1: L TGTGGACCTCCTAGAGAGGTCCCTGTGTGTGGCTGGCATCACCC 1 F3: 4 ATCACCCAGGTTGCTGATTACAAGCACGGCTGCTGCAACCCCGC R RF: TGTGGACCTCCTAGAGAGGTCCCTGTGTGTGGCTGGCATCACCCAGGTTGCTGATTACAAGCACGGCTGCTGCAACCCCGCTTCAGACCC RR: ACACCTGGAGGATCTCTCCAGGGACACACACCGACCGTAGTGGGTCCAACGACTAATGTTCGTGCCGACGACGTTGGGGCGAAGTCTGGG F2: 3 AGGCTGGG 2 Unidirectional alignment (log-probability: -32.5) GACCTCCTAGAGAGGTCCCTGTGTGTGGCTGGCATCACccgggtcggaatcacCCAGGTTGCTGATTACAAGCACGGCTGCTGCAACC GACCTCCTAGAGAGGTCCCTGTGTGTGGCTGGCATCAC---------------CCAGGTTGCTGATTACAAGCACGGCTGCTGCAACC Template switch alignment (log-probability: -22.4) GACCTCCTAGAGAGGTCCCTGTGTGTGGCTGGCATCACCC|GGGTCgGA|ATCACCCAGGTTGCTGATTACAAGCACGGCTGCTGCAACC GACCTCCTAGAGAGGTCCCTGTGTGTGGCTGGCATCACCC|GGGTCTGA|ATCACCCAGGTTGCTGATTACAAGCACGGCTGCTGCAACC ========== Event 1426 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGGAGGCCCCGGGAGAAGGGTGTGGG-GGCAGCTCTCCGGGCAGGGTCTTTTCTGG Chimp: GAGGAGGCCCCGGGAGAAGGGTGTGGG-GGCAGCTCTCCGGGCAGGGTCTTTTCTGG ↓ 1 3 4 2 Gorilla: GAGGAGGCCCCGGGAGAAGGGAGAGCTGCCCAGCTCTCCGGGCAGGGTCTTTTCTGG ↑ 1 3 4 2 Human: GAGGAGGCCCCGGGAGAAGGGTGTGGG-GGCAGCTCTCCGGGCAGGGTCTTTTCTGG Cluster: [ ] Orangutan: GAGGAGGCCCCGGGAGAAGGGTGTGGG-GGCAGCTCTCCCGGCAGGGTCTTTTCTGG Human > Gorilla --------------- chr5:157030042-157030050 Template switch process: F1: L AGGGAGGCAGCCTGAGGATGGAGGAGGCCCCGGGAGAAGGG 1 F3: 4 CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC R RF: AGGGAGGAAGCCTGAGGGTGGAGGAGGCCCCGGGAGAAGGGTGTGGGGGCAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC RR: TCCCTCCTTCGGACTCCCACCTCCTCCGGGGCCCTCTTCCCACACCCCCGTCGAGAGGCCCGTCCCAGAAAAGACCTTTCGGTCGGTCG F2: 3 CCGTCGAGA 2 Unidirectional alignment (log-probability: -45) GGGAGGcAGCCTGAGGaTGGAGGAGGCCCCGGGAGAAGGGagagctgcc--------CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC GGGAGGAAGCCTGAGGGTGGAGGAGGCCCCGGGAGAAGGG---------TGTGGGGGCAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC Template switch alignment (log-probability: -27.9) GGGAGGcAGCCTGAGGaTGGAGGAGGCCCCGGGAGAAGGG|AGAGCTGCC|CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC GGGAGGAAGCCTGAGGGTGGAGGAGGCCCCGGGAGAAGGG|AGAGCTGCC|CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC Chimp > Gorilla --------------- chr5:157030042-157030050 Template switch process: F1: L AGGGAGGCAGCCTGAGGATGGAGGAGGCCCCGGGAGAAGGG 1 F3: 4 CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC R RF: AGGGAGGCAGCCTGAGGGTGGAGGAGGCCCCGGGAGAAGGGTGTGGGGGCAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC RR: TCCCTCCGTCGGACTCCCACCTCCTCCGGGGCCCTCTTCCCACACCCCCGTCGAGAGGCCCGTCCCAGAAAAGACCTTTCGGTCGGTCG F2: 3 CCGTCGAGA 2 Unidirectional alignment (log-probability: -39.5) GGGAGGCAGCCTGAGGaTGGAGGAGGCCCCGGGAGAA--------GGGagagctgccCAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC GGGAGGCAGCCTGAGGGTGGAGGAGGCCCCGGGAGAAGGGTGTGGGGG---------CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC Template switch alignment (log-probability: -22.4) GGGAGGCAGCCTGAGGaTGGAGGAGGCCCCGGGAGAAGGG|AGAGCTGCC|CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC GGGAGGCAGCCTGAGGGTGGAGGAGGCCCCGGGAGAAGGG|AGAGCTGCC|CAGCTCTCCGGGCAGGGTCTTTTCTGGAAAGCCAGCCAGC ========== Event 1427 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCAACCCTTCGACACTTGGGA----CCCTCAGGTCCCAGCCAGTCTGAGGACCTGAG Chimp: TCCAACCCTTCGACACTTGGGA----CCCTCAGGTCTCAGCCAGTCTGAGGACCTGAG ↓ 3 1 2 4 Gorilla: TCCAACCCTTCGACACTTGGGA--------AGGGTCCCAGCCAGTCTGAGGACCTGAG Human: TCCAACCCTTCGACACTTGGGA----CCCTCAGGTCCCAGCCAGTCTGAGGACCTGAG Cluster: [ ] Orangutan: TCCAACCCTTCGACACTTGGGACCCT----CAGGTCCCAGCCAGTCTGAGGACCTGAG Chimp > Gorilla --------------- chr5:157139558-157139564 Template switch process: F1: L GCAACCCACAGCCCTGGCCTCCAACCCTTCGACACTTGGGA 1 F3: 4 CAGCCAGTCTGAGGACCTGAGGGCCACCCTCTGAATTCAC R RF: GCAACCCACAGCCCTGGCCTCCAACCCTTCGACACTTGGGACCCTCAGGTCTCAGCCAGTCTGAGGACCTGAGGGCCACCCTCTGAATTCAC RR: CGTTGGGTGTCGGGACCGGAGGTTGGGAAGCTGTGAACCCTGGGAGTCCAGAGTCGGTCAGACTCCTGGACTCCCGGTGGGAGACTTAAGTG F2: 3 CCTGGGA 2 Unidirectional alignment (log-probability: -27.7) CAACCCACAGCCCTGGCCTCCAACCCTTCGACACTTGGGA----agGGTCcCAGCCAGTCTGAGGACCTGAGGGCCACCCTCTGAATTCAC CAACCCACAGCCCTGGCCTCCAACCCTTCGACACTTGGGACCCTCAGGTCTCAGCCAGTCTGAGGACCTGAGGGCCACCCTCTGAATTCAC Template switch alignment (log-probability: -16.6) CAACCCACAGCCCTGGCCTCCAACCCTTCGACACTTGGGA|AGGGTCC|CAGCCAGTCTGAGGACCTGAGGGCCACCCTCTGAATTCAC CAACCCACAGCCCTGGCCTCCAACCCTTCGACACTTGGGA|AGGGTCC|CAGCCAGTCTGAGGACCTGAGGGCCACCCTCTGAATTCAC ========== Event 1428 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAAAATCTTGTGCTCACTTCGGCAGCACAAATACTAAAATTGGAACAATACAGAGATTAGCATGGCCCCTGCGCAAGGATGACATGCAAATTTGTGAAGTGTTCCATATTTaaaaaaaaaaatcttgttccataaaaaaaaaaaaTCTTGTCACATGTTGGTTA------------------CAGTTCCCAAAAACACTTCA Chimp: TAAAAATCTTgtgctcacttcggcagcacaaatactaaaattggaacaatacagagattagcatggcccctgcgcaaggatgacatgcaaatttgtgaagtgttccatatttaaaaa---------------------aaaaaaaaTCTTGTCACATGTTGGTTA---------CAGGACATCCAGTTCCCAAAAACACTTCA Gorilla: TAAAAATCTTgtgctcacttcggcagcacaaatactaaaattggaacaatacagagattagcatggcccctgcgcaaggatgacatgcaaatttgtgaagtgttccatatttaaaaa----------------------aaaaaaaTCTTGTCACATGTTGGTTACAGGACATC---------CAGTTCCCAAAAACACTTCA ↓ 1 3 2 4 Human: TAAAAATCTTGTGCTCACTTCGGCAGCACAAATACTAAAATTGGAACAATACAGAGATTAGCATGGCCCCTGCGCAAGGATGACATGCAAATTTGTGAAGTGTTCCATATTTaaaaaaaaaaatcttgttccataaaaaaaaaaaaTCTTGTCACATGTTGGTTA------------------CAGTTCCCAAAAACACTTCA Cluster: [ ] Orangutan: TAAAAATCTTgtgctcacttcggcagcacaaatactaaaattggaacaatacagagattagcatggcccctgcgcaaggatgacatgcaaattcgtgaagtgttccatattttaaaa----------------------aaaaaaaTCTTGTCACATGTTGGTTACGGGACATC---------CAGTTCCCAAAAACACTTCA Gorilla > Human --------------- chr17:76753029-76753034 Template switch process: F1: L CTT 1 F3: 4 TAAAAAAAAAAAATCTTGTCACATGTTGGTTA---------CAGTTCCCAAAAACACTTCATCAGAAAGCACATAGCAGTC R RF: CTTCGGCAGCACAAATACTAAAATTGGAACAATACAGAGATTAGCATGGCCCCTGCGCAAGGATGACATGCAAATTTGTGAAGTGTTCCATATTTAAAAAAAAAAAATCTTGTCACATGTTGGTTACAGGACATCCAGTTCCCAAAAACACTTCATCAGAAAGCACATAGCAGTC RR: GAAGCCGTCGTGTTTATGATTTTAACCTTGTTATGTCTCTAATCGTACCGGGGACGCGTTCCTACTGTACGTTTAAACACTTCACAAGGTATAAATTTTTTTTTTTTAGAACAGTGTACAACCAATGTCCTGTAGGTCAAGGGTTTTTGTGAAGTAGTCTTTCGTGTATCGTCAG F2: 3 ACCTTG 2 Unidirectional alignment (log-probability: -37.1) cttgttccataaaaaAAAAAAATCTTGTCACATGTTGGTTA---------CAGTTCCC ---------------AAAAAAATCTTGTCACATGTTGGTTACAGGACATCCAGTTCCC Template switch alignment (log-probability: -26.5) CTT|GTTCCA|TAAAAAAAAAAAATCTTGTCACATGTTGGTTA---------CAGTTCCC CTT|GTTCCA|TAAAAAAAAAAAATCTTGTCACATGTTGGTTACAGGACATCCAGTTCCC ========== Event 1429 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: cttgctggctggaGGGGGAAGAC--------ACACTGTGGTAATGGCA---AAGTAGCAACACAGAAGGGG Chimp: cttgctggctggagcggGAAGAC--------ACACTGTGGTAATGGCA---AAGTAGCAATACAGAAGGGG Gorilla: cttgctggctggaGGGGGAAGCT-GCCATTACCACTGTGGTAATGGCA---AAGTAGCAACACAGAAGGGG ↑ 1 4 3 2 Human: cttgctggctggaGGGGGAAGAC--------ACACTGTGGTAATGGCA---AAGTAGCAACACAGAAGGGG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNN-------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr5:159445323-159445331 Template switch process: F1: L TTCTTCACCCTTTCCTCCGACTTGCTGGCTGGAGGGGGAAGC 1 F3: 4 CACTGTGGTAATGGCAAAGTAGCAACACAGAAGGGGCCCG R RF: TTCTTCACCCTTTCCTCCGACTTGCTGGCTGGAGGGGGAAGACACACTGTGGTAATGGCAAAGTAGCAACACAGAAGGGGCCCG RR: AAGAAGTGGGAAAGGAGGCTGAACGACCGACCTCCCCCTTCTGTGTGACACCATTACCGTTTCATCGTTGTGTCTTCCCCGGGC F2: 3 CATTACCGT 2 Unidirectional alignment (log-probability: -32.2) CTTCACCCTTTCCTCCGACTTGCTGGCTGGAGGGGGAAGctgccattAC-CACTGTGGTAATGGCAAAGTAGCAACACAGAAGGGGCCCG CTTCACCCTTTCCTCCGACTTGCTGGCTGGAGGGGGAAG--------ACACACTGTGGTAATGGCAAAGTAGCAACACAGAAGGGGCCCG Template switch alignment (log-probability: -22.4) CTTCACCCTTTCCTCCGACTTGCTGGCTGGAGGGGGAAGc|TGCCATTAC|CACTGTGGTAATGGCAAAGTAGCAACACAGAAGGGGCCCG CTTCACCCTTTCCTCCGACTTGCTGGCTGGAGGGGGAAGA|TGCCATTAC|CACTGTGGTAATGGCAAAGTAGCAACACAGAAGGGGCCCG ========== Event 1430 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCACCAAGCAGCCCAGGCCAATTCTGGAGGGCtaatttgtgtccctccagaagcaggtcctgaga--caggg ↑ 1 4 3 2 Chimp: TCCACCAAGCAGCCCAGGCCAGGGGT--GGGGCtaatttgtgtccctccagaagcaggtcctgaga--caggg Gorilla: TCCACCAAGCAGCCCAGGCCAGGGGT--GGGGCtaatttgtgtccctccagaagtaggtcctgaga----cgg Human: TCCACCAAGCAGCCCAGGCCAATTCTGGAGGGCtaatttgtgtccctccagaagcaggtcctgaga--caggg Cluster: [ ] Orangutan: TCCACCAAGCAGCCCAGGCCAGGGGT--GGGGCtaatttgtgtccctccagaagcaggtcctgagaca--ggg Chimp > Human ------------- chr17:77393054-77393061 Template switch process: F1: L CCCAGGAGCCACCTCCCTCCTCCACCAAGCAGCCCAGGCCAA 1 F3: 4 GGCTAATTTGTGTCCCTCCAGAAGCAGGTCCTGAGACAG R RF: CCCAGGAGCCACCTCCCTCCTCCACCAAGCAGCCCAGGCCAGGGGTGGGGCTAATTTGTGTCCCTCCAGAAGCAGGTCCTGAGACAG RR: GGGTCCTCGGTGGAGGGAGGAGGTGGTTCGTCGGGTCCGGTCCCCACCCCGATTAAACACAGGGAGGTCTTCGTCCAGGACTCTGTC F2: 3 GAGGTCTT 2 Unidirectional alignment (log-probability: -32.9) CAGGAGCCACCTCCCTCCTCCACCAAGCAGCCCAGGCCaattctggAGG------GCTAATTTGTGTCCCTCCAGAAGCAGGTCCTGAGACAG CAGGAGCCACCTCCCTCCTCCACCAAGCAGCCCAGGCC--------AGGGGTGGGGCTAATTTGTGTCCCTCCAGAAGCAGGTCCTGAGACAG Template switch alignment (log-probability: -22.3) CAGGAGCCACCTCCCTCCTCCACCAAGCAGCCCAGGCCAa|TTCTGGAG|GGCTAATTTGTGTCCCTCCAGAAGCAGGTCCTGAGACAG CAGGAGCCACCTCCCTCCTCCACCAAGCAGCCCAGGCCAG|TTCTGGAG|GGCTAATTTGTGTCCCTCCAGAAGCAGGTCCTGAGACAG ========== Event 1431 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTGGGCTCTGAGCCTCTTTT--------CAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCTG Chimp: GTTGGGCTCTGAGCCTCTTTT--------CAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCTG ↓ 1 4 3 2 Gorilla: GTTGGGCTCTGAGCCTCTTTTCCATGGTACTGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCTG ↑ 1 4 3 2 Human: GTTGGGCTCTGAGCCTCTTTT--------CAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCTG Cluster: [ ] Orangutan: GTTGGGCTCTGAGCCTCTTTT--------CAGACGTGAGCCTCAGTACTATGCATAAGCTTTCCCATCTCTG Human > Gorilla --------------- chr17:88050916-88050924 Template switch process: F1: L TTGTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTC 1 F3: 4 GACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT R RF: TTGTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTCAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT RR: AACAAGACTAGACGTTACATCAACCCGAGACTCGGAGAAAAGTCTGGACTCGGAGTCATGGTACGTATTCGAAAGGGTAGAGA F2: 3 TCATGGTAC 2 Unidirectional alignment (log-probability: -27.9) GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTccatggtaCtGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTT--------CAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT Template switch alignment (log-probability: -16.9) GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTC|CATGGTACT|GACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTC|CATGGTACT|GACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT Chimp > Gorilla --------------- chr17:88050916-88050924 Template switch process: F1: L TTGTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTC 1 F3: 4 GACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT R RF: TTGTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTCAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT RR: AACAAGACTAGACGTTACATCAACCCGAGACTCGGAGAAAAGTCTGGACTCGGAGTCATGGTACGTATTCGAAAGGGTAGAGA F2: 3 TCATGGTAC 2 Unidirectional alignment (log-probability: -27.9) GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTccatggtaCtGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTT--------CAGACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT Template switch alignment (log-probability: -16.9) GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTC|CATGGTACT|GACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT GTTCTGATCTGCAATGTAGTTGGGCTCTGAGCCTCTTTTC|CATGGTACT|GACCTGAGCCTCAGTACCATGCATAAGCTTTCCCATCTCT ========== Event 1432 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGAATCTAGGAGGAAACTGGCAAATGCCAGAGTGGTCCCGTGGTACAAA Chimp: TGGAATCTAGGAGGAAACTGGCATTT-GAAGAGTGGTCCCGTGGTACAAA Gorilla: TGGAATCTAGGAGGAAACTGGCATTT-GAAGAGTGGTCCCGTGGTACAAA ↓ 3 1 2 4 Human: TGGAATCTAGGAGGAAACTGGCAAATGCCAGAGTGGTCCCGTGGTACAAA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr17:77859443-77859448 Template switch process: F1: L CTTCTGTGTTTTCTGTTTTGGAATCTAGGAGGAAACTGGCA 1 F3: 4 AGAGTGGTCCCGTGGTACAAAGCCCCAGCACCACCACCAC R RF: CTTCTGCGTTTTCTGTTTTGGAATCTAGGAGGAAACTGGCATTTGAAGAGTGGTCCCGTGGTACAAAGCCCCGGCACCACCACCAC RR: GAAGACGCAAAAGACAAAACCTTAGATCCTCCTTTGACCGTAAACTTCTCACCAGGGCACCATGTTTCGGGGCCGTGGTGGTGGTG F2: 3 CCGTAA 2 Unidirectional alignment (log-probability: -39.1) TTCTGtGTTTTCTGTTTTGGAATCTAGGAGGAAACTGGCA----AatgccAGAGTGGTCCCGTGGTACAAAGCCCCaGCACCACCACCAC TTCTGCGTTTTCTGTTTTGGAATCTAGGAGGAAACTGGCATTTGA-----AGAGTGGTCCCGTGGTACAAAGCCCCGGCACCACCACCAC Template switch alignment (log-probability: -27.5) TTCTGtGTTTTCTGTTTTGGAATCTAGGAGGAAACTGGCA|AATGCC|AGAGTGGTCCCGTGGTACAAAGCCCCaGCACCACCACCAC TTCTGCGTTTTCTGTTTTGGAATCTAGGAGGAAACTGGCA|AATGCC|AGAGTGGTCCCGTGGTACAAAGCCCCGGCACCACCACCAC ========== Event 1433 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTGTGGTGGTCTTTCAAGCTTGCTAAAGGATCATTTCaa ↑ 3 2 1 4 Chimp: CCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGT-----GG---TCCACCCTTGCTAAAGGATCATTTCAA Gorilla: CCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGT-----GG---TCCACCCTTGCTAAAGGATCGTTTCAA ↓ 3 2 1 4 Human: CCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTGTGGTGGTCTTTCAAGCTTGCTAAAGGATCATTTCaa Cluster: [ ] Orangutan: Chimp > Human ------------- chr17:5421300-5421314 Template switch process: F1: L TCCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG 1 F3: 4 CTTGCTAAAGGATCATTTCAAAATTTTTTTTAAAAAGTTT R RF: TCCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTGGTCCACCCTTGCTAAAGGATCATTTCAAAATTTTATTTAAAAAGTTT RR: AGGTCGAGAATGGGTGTCTCGAACTTTCTGGTGGTTAATCACCAGGTGGGAACGATTTCCTAGTAAAGTTTTAAAATAAATTTTTCAAA F2: 3 GAACTTTCTGGTGGT 2 Unidirectional alignment (log-probability: -47.6) CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTGtggtggtctttcaaG------CTTGCTAAAGGATCATTTCAAAATTTTtTTTAAAAAGTTT CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG--------------GTCCACCCTTGCTAAAGGATCATTTCAAAATTTTATTTAAAAAGTTT Template switch alignment (log-probability: -23.2) CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG|TGGTGGTCTTTCAAG|CTTGCTAAAGGATCATTTCAAAATTTTtTTTAAAAAGTTT CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG|TGGTGGTCTTTCAAG|CTTGCTAAAGGATCATTTCAAAATTTTATTTAAAAAGTTT Gorilla > Human --------------- chr17:5421300-5421314 Template switch process: F1: L TCCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG 1 F3: 4 CTTGCTAAAGGATCATTTCAAAATTTTTTTTAAAAAGTTT R RF: TCCAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTGGTCCACCCTTGCTAAAGGATCGTTTCAAAATTTTATTTAAAAAGTTT RR: AGGTCGAGAATGGGTGTCTCGAACTTTCTGGTGGTTAATCACCAGGTGGGAACGATTTCCTAGCAAAGTTTTAAAATAAATTTTTCAAA F2: 3 GAACTTTCTGGTGGT 2 Unidirectional alignment (log-probability: -52.1) CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTGtggtggtctttcaaG------CTTGCTAAAGGATCaTTTCAAAATTTTtTTTAAAAAGTTT CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG--------------GTCCACCCTTGCTAAAGGATCGTTTCAAAATTTTATTTAAAAAGTTT Template switch alignment (log-probability: -28.7) CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG|TGGTGGTCTTTCAAG|CTTGCTAAAGGATCaTTTCAAAATTTTtTTTAAAAAGTTT CAGCTCTTACCCACAGAGCTTGAAAGACCACCAATTAGTG|TGGTGGTCTTTCAAG|CTTGCTAAAGGATCGTTTCAAAATTTTATTTAAAAAGTTT ========== Event 1434 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAAAATTCAATACTTTGAGT-----CATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGC ↓ 1 3 4 2 Chimp: TTAAAATTCAATACTTTGAGTCTGGCAATTTGGAAATTGCCAGATCAGGGCAAGCAGGATGC ↑ 1 3 4 2 Gorilla: TTAAAATTCAATACTTTGAGT-----CATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGC Human: TTAAAATTCAATACTTTGAGT-----CATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGC Cluster: [ ] Orangutan: TTAAAATTCAATATGTTGAGT-----CATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGC Human > Chimp ------------- chr17:5513559-5513569 Template switch process: F1: L GTATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTC 1 F3: 4 AAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT R RF: GTATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTCATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT RR: CATAGGATTTTGAGATTAGAAATTTTAAGTTATGAAACTCAGTAAAGGTTTAACGGTCTAGTCCCGTTCGTCCTACGATCCGAATGGA F2: 3 GGTTTAACGGT 2 Unidirectional alignment (log-probability: -30.2) ATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTCtggcaATTTggAAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT ATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTC-----ATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT Template switch alignment (log-probability: -16.7) ATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTC|TGGCAATTTGG|AAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT ATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTC|TGGCAATTTGG|AAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT Gorilla > Chimp --------------- chr17:5513559-5513569 Template switch process: F1: L GTATCCTAAAACTCTAATCTTTAAAATTCAATACTTTGAGTC 1 F3: 4 AAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT R RF: GTATCCTAAAACTGTAATCTTTAAAATTCAATACTTTGAGTCATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT RR: CATAGGATTTTGACATTAGAAATTTTAAGTTATGAAACTCAGTAAAGGTTTAACGGTCTAGTCCCGTTCGTCCTACGATCCGAATGGA F2: 3 GGTTTAACGGT 2 Unidirectional alignment (log-probability: -34.7) ATCCTAAAACTcTAATCTTTAAAATTCAATACTTTGAGTCtggcaATTTggAAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT ATCCTAAAACTGTAATCTTTAAAATTCAATACTTTGAGTC-----ATTTCCAAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT Template switch alignment (log-probability: -22.7) ATCCTAAAACTcTAATCTTTAAAATTCAATACTTTGAGTC|TGGCAATTTGG|AAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT ATCCTAAAACTGTAATCTTTAAAATTCAATACTTTGAGTC|TGGCAATTTGG|AAATTGCCAGATCAGGGCAAGCAGGATGCTAGGCTTACCT ========== Event 1435 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCCTCTGTTCTGTGCATCTAGACAGACGTCCCAGCTGGGGGGCACTGGGCCCCTCC ↓ 1 3 2 4 Chimp: TTTCCTCTGTTCTGTGCATCTG----GACGT----CTTGGGGGGCACTGGGCCCCTCC Gorilla: TTTCCTCTGTTCTGTGCATCTAGACAGACGTCCCAGCTAGGGGGCACTGGGCTCCTCC Human: TTTCCTCTGTTCTGTGCATCTAGACAGACGTCCCAGCTGGGGGGCACTGGGCCCCTCC Cluster: [ ] Orangutan: TTTCCTCTGTTCTGTGCATCTGGACAGACGTCCCAGCTGGGGGGCACTGGGCCCCTCC Human > Chimp ------------- chr17:77856467-77856474 Template switch process: F1: L GAGGCCTGGGCCTTGGAGCCTTTCCTCTGTTCTGTGCATCT 1 F3: 4 TGGGGGGCACTGGGCCCCTCCCCTGTTAACTCTTCAGATG R RF: GAGGCCTGGGCCTTGGAGCCTTTCCTCTGTTCTGTGCATCTAGACAGACGTCCCAGCTGGGGGGCACTGGGCCCCTCCCCTATTAACTCTTCAGATG RR: CTCCGGACCCGGAACCTCGGAAAGGAGACAAGACACGTAGATCTGTCTGCAGGGTCGACCCCCCGTGACCCGGGGAGGGGATAATTGAGAAGTCTAC F2: 3 TCTGCAGG 2 Unidirectional alignment (log-probability: -39.4) AGGCCTGGGCCTTGGAGCCTTTCCTCTGTTCTGTGCAtctggacgTCT----------------TGGGGGGCACTGGGCCCCTCCCCTgTTAACTCTTCAGATG AGGCCTGGGCCTTGGAGCCTTTCCTCTGTTCTGTGCA--------TCTAGACAGACGTCCCAGCTGGGGGGCACTGGGCCCCTCCCCTATTAACTCTTCAGATG Template switch alignment (log-probability: -22.3) AGGCCTGGGCCTTGGAGCCTTTCCTCTGTTCTGTGCATCT|GGACGTCT|TGGGGGGCACTGGGCCCCTCCCCTgTTAACTCTTCAGATG AGGCCTGGGCCTTGGAGCCTTTCCTCTGTTCTGTGCATCT|GGACGTCT|TGGGGGGCACTGGGCCCCTCCCCTATTAACTCTTCAGATG ========== Event 1436 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ATGTCATTCTCTTTTGTGATCACGTTAATTTGGACATGAAAAAGTGACACTAGAAGTT-GGTCCCCACACTGCTGCGGTGGCCTCATGACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGCCGTGAAGATGCCTGGGGCTGCCCCGACAGGAAA ↑ 3 2 1 4 Chimp: ATGTCATTCTCTTTTGTGATCACGTTAATTTGGACATGAAAAAGTGACACTAGAAGTT-GGTCCCCACACTGCTGCGGTGGCCTCATGACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGC---TCAGATGCCGGGGGCTGCCCCGACAGGAAA Gorilla: ATGTCATTCTCTTTTGTGATCACGTTAATTTGGACATGAAAAAGTGACACTAGAAGTTGGGTCCCCACACTGCTGCGGTGGCCTCATGACAGTGCCTGGACAAATCCACGCTTCACCTGAGTCCTGGCCGTGAAGATGCCTGGGGCTGCCCTGACAGGAAA Human: ATGTCATTCTCTTTTGTGATCACGTTAATTTGGACATGAAAAAGTGACACTAGAAGTT-GGTCCCCACACTGCTGCGGTGGCCTCATGACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGCCGTGAAGATGCCTGGGGCTGCCCCGACAGGAAA Cluster: [ ] Orangutan: ATGTCATTCTCTTTCGTGATCACGTTAATTTGGACATGAAAAAGTGGCACAAGAAGTT-GGTCCCCACACTGCTGCGGTGGCCTCATGACAGTGCCTGGAGAAATCCATGCTTCACCTGAGTCCAGGCAGTGAAGATGCCTGGGGCTGCCCCAACAGGAAA Chimp > Human ------------- chr17:79008075-79008079 Template switch process: F1: L GACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGC 1 F3: 4 AGATGCCTGGGGCTGCCCCGACAGGAAACCCTTGCCACGTCCAGAGGG R RF: TCACGTTAATTTGGACATGAAAAAGTGACACTAGAAGTTGGTCCCCACACTGCTGCGGTGGCCTCATGACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGCTCAGATGCCGGGGGCTGCCCCGACAGGAAACCCTTGCCACGTCCAGAGGG RR: AGTGCAATTAAACCTGTACTTTTTCACTGTGATCTTCAACCAGGGGTGTGACGACGCCACCGGAGTACTGTCACGGACCTGTTTAGGTACGAAGTGGACTCAGGACCGAGTCTACGGCCCCCGACGGGGCTGTCCTTTGGGAACGGTGCAGGTCTCCC F2: 3 AGTGC 2 Unidirectional alignment (log-probability: -33) ACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGC-CgtgaAGATGCCtGGGGCTGCCCCGACAGGAAACCCTTGCCACGT ACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGCTC----AGATGCCGGGGGCTGCCCCGACAGGAAACCCTTGCCACGT Template switch alignment (log-probability: -22.1) ACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGC|CGTGA|AGATGCCtGGGGCTGCCCCGACAGGAAACCCTTGCCACGT ACAGTGCCTGGACAAATCCATGCTTCACCTGAGTCCTGGC|CGTGA|AGATGCCGGGGGCTGCCCCGACAGGAAACCCTTGCCACGT ========== Event 1437 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCCACCAGCTTTTGAAAACTCA----------------------------------------------------------------------------------GTGTCTGCCCAGAGAGTATAAAAAACAGTAATAAATAAACGtattgaatatttagtatgttccagatactgtgctaaga Chimp: CTCCACCAGCTTTTGAAAACTCAGTGTTTGCCCAGAGAGTATCAAAAGCAGTAATACATACTAAATATTCAATATGTTTATTTATTACTGCTTTTGATACTCTCAGTGTTTGCCCAGAGAGTATCAAAAGCAGTaataaataaacatattgaatatttagtatgttccagatactgtgctaaga ↑ 4 3 1 2 Gorilla: CTCCACCAGCTTTTGAAAACTCA----------------------------------------------------------------------------------GTGTCTGCCCAGAGAGTATCAAAAGCAGTaataaataaacgtattgaatatttagtatgttccagatactgtgctaaga Human: CTCCACCAGCTTTTGAAAACTCA----------------------------------------------------------------------------------GTGTCTGCCCAGAGAGTATAAAAAACAGTAATAAATAAACGtattgaatatttagtatgttccagatactgtgctaaga Cluster: [ ] Orangutan: CTCCACCAGCTTTTGAAAACTCA----------------------------------------------------------------------------------GTGTCTGCCCAGAGAGTATCAAAAGCAGTAATAAATAAatgtattgaatatttagtatgttccagatactgtgctaaga Gorilla > Chimp --------------- chr1:150298056-150298100 Template switch process: F1: L CATCATATTCAGAAATCTCTCCACCAGCTTTTGAAAACTCAGTGTTTGCCCAGAGAGTATCAAAAGCAGTAATA 1 F3: 4 CTCAGTGTTTGCCCAGAGAGTATCAAAAGCAGTAATAAATAAACATATT R RF: CATCATATTCAGAAATCTCTCCACCAGCTTTTGAAAACTCAGTGTCTGCCCAGAGAGTATCAAAAGCAGTAATAAATAAACGTATTGAATATTTAGTATG RR: GTAGTATAAGTCTTTAGAGAGGTGGTCGAAAACTTTTGAGTCACAGACGGGTCTCTCATAGTTTTCGTCATTATTTATTTGCATAACTTATAAATCATAC F2: 3 TCATAGTTTTCGTCATTATTTATTTGTATAACTTATAAATCATAC 2 Unidirectional alignment (log-probability: -140) AAACTCAGTGTtTGCCCAGAGAGTATCAAAAGCAGTAatacatactaaatattcaatatgtttatttattactgcttttgatactctcagtgtttgcccagagagtatcaaaagcagtaATAAAT AAACTCAGTGTCTGCCCAGAGAGTATCAAAAGCAGTA----------------------------------------------------------------------------------ATAAAT Template switch alignment (log-probability: -44.4) AAACTCAGTGTtTGCCCAGAGAGTATCAAAAGCAGTAATA|CATACTAAATATTCAATAtGTTTATTTATTACTGCTTTTGATACT|CTCAGTGTtTGCCCAGAGAGTATCAAAAGCAGTAATAAAT AAACTCAGTGTCTGCCCAGAGAGTATCAAAAGCAGTAATA|CATACTAAATATTCAATACGTTTATTTATTACTGCTTTTGATACT|CTCAGTGTCTGCCCAGAGAGTATCAAAAGCAGTAATAAAT ========== Event 1438 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTGTTGAGCTGTGACATCATGGCAGGGGTGAGGTCAGGGACAGCTGTGAGCCAGCCAGGGGGCAAGCGTGTAGGTTAGGGGATCAATCATAAAGATTTGGCTCAAGCAGCCGGGAGCCATGGGGGCACCTGAAGGCACTGTTTAAGGAGGTGTGGGTGAACA ↓ 3 2 1 4 Chimp: GCTGTTGAGCTGTGACATCACGGCAGGGGTGAGGTCAGGGACAGCTGTGAGCCAGCCAGGGGGCAAGCGTGTAGGTTAGGGGATCAATCATAAAGATTTGGCTCAAGCAGCCGGGAGCCACGGGGGCACCTGAAGGCGCCATTTAAGGAGGTGTGGGTGAACA Gorilla: GCTGTTGAGCTGTGACATCATGGCAGGGGTGAGGTCAGGGACAGCTGTGAGCCAGCCAGGGGGCAAGCGTGTAGGTTAGGGGATCAATCATAAAGATTTGGCTCAAGCAGCCGGGAGCCATGGGGGCACCTGAAGGCGCTGTTTAAGGAGGTGTGGGTGAACA Human: GCTGTTGAGCTGTGACATCATGGCAGGGGTGAGGTCAGGGACAGCTGTGAGCCAGCCAGGGGGCAAGCGTGTAGGTTAGGGGATCAATCATAAAGATTTGGCTCAAGCAGCCGGGAGCCATGGGGGCACCTGAAGGCACTGTTTAAGGAGGTGTGGGTGAACA Cluster: [ ] Orangutan: GCTGTTGAGCTGTGACATCATGGCAGGGGTGAGGTCAGGGACAGCTGTGAGCCAGTCAGAGGGCAAGCGTGTAGGTTAGGGGATCAATCATAAAGATTTGGCTCAAGCAGCCGGCAGCCACGGGGGCATTTGAAGGTGCTGTTTAAGGAGGTGTGGGTGAACA Human > Chimp ------------- chr17:78517736-78517740 Template switch process: F1: L TTTGGCTCAAGCAGCCGGGAGCCACGGGGGCACCTGAAGGC 1 F3: 4 TTAAGGAGGTGTGGGTGAACAAGGACAG R RF: ATGGCAGGGGTGAGGTCAGGGACAGCTGTGAGCCAGCCAGGGGGCAAGCGTGTAGGTTAGGGGATCAATCATAAAGATTTGGCTCAAGCAGCCGGGAGCCATGGGGGCACCTGAAGGCACTGTTTAAGGAGGTGTGGGTGAACAAGGACAG RR: TACCGTCCCCACTCCAGTCCCTGTCGACACTCGGTCGGTCCCCCGTTCGCACATCCAATCCCCTAGTTAGTATTTCTAAACCGAGTTCGTCGGCCCTCGGTACCCCCGTGGACTTCCGTGACAAATTCCTCCACACCCACTTGTTCCTGTC F2: 3 TACCG 2 Unidirectional alignment (log-probability: -32.4) TTGGCTCAAGCAGCCGGGAGCCAcGGGGGCACCTGAAGGCgCcaTTTAAGGAGGTGTGGGTGAACAAGGACAG----------- TTGGCTCAAGCAGCCGGGAGCCATGGGGGCACCTGAAGGCACTGTTTAAGGAGGTGTGGGTGAACAAGGACAGTGCAATGTACA Template switch alignment (log-probability: -21.6) TTGGCTCAAGCAGCCGGGAGCCAcGGGGGCACCTGAAGGC|GCCAT|TTAAGGAGGTGTGGGTGAACAAGGACAG TTGGCTCAAGCAGCCGGGAGCCATGGGGGCACCTGAAGGC|GCCAT|TTAAGGAGGTGTGGGTGAACAAGGACAG ========== Event 1439 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCAGGTGACACGTGGCTGTCAAGAGTCTGAGGCCCGGCTGGATGGGCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGTCTCAGACTCTTGGTCACAATGGGCACCCAG Chimp: TCAGGTGACACGTGGCTGTCAGG---------------------AGCAGGCAGCCCATCTGTGCCTCCCTATCCAGCCGGGCCTCAGACTCTTGGTCACAATGGGCACCCGG Gorilla: TCAGGTGACACATGGCTGTCAGG---------------------AGCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGCCTCAGACTCTTGGTCACAATGGGCACCCAG ↓ 1 4 3 2 Human: TCAGGTGACACGTGGCTGTCAAGAGTCTGAGGCCCGGCTGGATGGGCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGTCTCAGACTCTTGGTCACAATGGGCACCCAG Cluster: [ ] Orangutan: TCAGGTGACACGTGGCTCTCAGG---------------------AGCAGGCAGCCCATCTGTGCCTCCCCATCCAGCC-GGCCTCAGACTCTTGGTCACAATGGGCACCCAG Gorilla > Human --------------- chr17:78930473-78930496 Template switch process: F1: L TCTGGGAGGTGACACTTCAGTCAGGTGACACGTGGCTGTCA 1 F3: 4 GCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGTCTC R RF: TCTGGGAGGTGACACTTCAGTCAGGTGACACATGGCTGTCAGGAGCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGCCTCAGACTCT RR: AGACCCTCCACTGTGAAGTCAGTCCACTGTGTACCGACAGTCCTCGTCCGTCGGGTAGACACGGAGGGGTAGGTCGGCCCGGAGTCTGAGA F2: 3 GGTAGGTCGGCCCGGAGTCTGAGA 2 Unidirectional alignment (log-probability: -57.7) CTGGGAGGTGACACTTCAGTCAGGTGACACgTGGCTGTCAaGAgtctgaggcccggctggatggGCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGtCTC CTGGGAGGTGACACTTCAGTCAGGTGACACATGGCTGTCAGGA---------------------GCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGCCTC Template switch alignment (log-probability: -29.8) CTGGGAGGTGACACTTCAGTCAGGTGACACgTGGCTGTCA|AGAGTCTGAGGCCCGGCTGGATGG|GCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGtCTC CTGGGAGGTGACACTTCAGTCAGGTGACACATGGCTGTCA|AGAGTCTGAGGCCCGGCTGGATGG|GCAGGCAGCCCATCTGTGCCTCCCCATCCAGCCGGGCCTC ========== Event 1440 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGTCGCACTAAGGCCAGGGTGCTCAGCTGCCGGCTGAGCCCTATCACCTGTCACCCCTT ↑ 1 4 3 2 Chimp: GGGTCGCACTAAGGCCAGGGTCACTGGCTGCCAGCTGAGCCCTATCACCTGTCACCCCTT Gorilla: GGGTCGCACTAAGGCCAGGGTCACTGGCTGCCGGCTGAGCCCTATCACCTGTCACCCCTT Human: GGGTCGCACTAAGGCCAGGGTGCTCAGCTGCCGGCTGAGCCCTATCACCTGTCACCCCTT Cluster: [ ] Orangutan: GACTCGCACTAAGGCCAGGGTCACTGGCTGCCAGCTAAGCCCTATCACCTGTCACCCCTT Chimp > Human ------------- chr17:4154435-4154439 Template switch process: F1: L GTTCCCTGGGGTGGGAGGAAGGGTCGCACTAAGGCCAGGGT 1 F3: 4 GCTGCCGGCTGAGCCCTATCACCTGTCACCCCTTCAGGCTCACCCGA R RF: GTTCCCTGGGGTGGGAGGAAGGGTCGCACTAAGGCCAGGGTCACTGGCTGCCAGCTGAGCCCTATCACCTGTCACCCCTTCAGGCTCACCCGA RR: CAAGGGACCCCACCCTCCTTCCCAGCGTGATTCCGGTCCCAGTGACCGACGGTCGACTCGGGATAGTGGACAGTGGGGAAGTCCGAGTGGGCT F2: 3 ACTCG 2 Unidirectional alignment (log-probability: -31.7) TTCCCTGGGGTGGGAGGAAGGGTCGCACTAAGGCCAGGGtgcTCA---GCTGCCgGCTGAGCCCTATCACCTGTCACCCCTTCAGGCT TTCCCTGGGGTGGGAGGAAGGGTCGCACTAAGGCCAGGG---TCACTGGCTGCCAGCTGAGCCCTATCACCTGTCACCCCTTCAGGCT Template switch alignment (log-probability: -22) TTCCCTGGGGTGGGAGGAAGGGTCGCACTAAGGCCAGGGT|GCTCA|GCTGCCgGCTGAGCCCTATCACCTGTCACCCCTTCAGGCT TTCCCTGGGGTGGGAGGAAGGGTCGCACTAAGGCCAGGGT|GCTCA|GCTGCCAGCTGAGCCCTATCACCTGTCACCCCTTCAGGCT ========== Event 1441 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGCCCCCACCGAGCAAGTGAACA--CCCAGGTGCTC-AGCAGAGGAATTAGCCTGCCTTTCAGGAGATGCTAA---TGAGGCAAGTTGGAAGCGGATGAGGTTCAGCCAGGAAGGAAACTGTTGGCCCCACAGAAGCCCTGGGCACCAGGGGCTGGCACAGAGGCC Chimp: CCTGCCCCCACCGAGCAAGTGAACA--CCCAGATGCTC-AGCAGAGGAATTAGCCTGCCTTTCAGGAGATGC---TAATGAGGCAAGTTGGAAGCGGATGAGGTTCAGCCAGGAAGGAAACTGTTGGCCCCACAGAAGCCCTGGGCACCAGGGGCTGGCACAGAGGCC ↓ 1 4 3 2 Gorilla: CCTGCCCCCACCGAGCAAGTGGTGCTCAGCAGATGCTC-AGCAGAGGAATTAGCCTGCCTTTCAGGAGATGCTAA---TGAGGCTAGTTGGAAGCGGATGAGGTTCAGCCAGGAAGGAAACTGTTGGCCCCACAGAAGCCCTGGGCACCAGGGGCTGGCACAGAGGCC Human: CCTGCCCCCACCGAGCAAGTGAACA--CCCAGGTGCTC-AGCAGAGGAATTAGCCTGCCTTTCAGGAGATGCTAA---TGAGGCAAGTTGGAAGCGGATGAGGTTCAGCCAGGAAGGAAACTGTTGGCCCCACAGAAGCCCTGGGCACCAGGGGCTGGCACAGAGGCC Cluster: [ ] Orangutan: CCTGCCCCCACCGAGCAAGTGAACA--CCCAGGTGCTCAGGCAGAGGAATTAGCCTGCCTTTCAGGAGATGCTAA---TGAGGCAAGTTGGAAGCAGATGAGGTTCAGCCAGGAAGGAAACTGTTGGGCCCACAGAAGCCCTGGGCACCAGGGGCTGGCACAGAGGCC Chimp > Gorilla --------------- chr5:3794402-3794409 Template switch process: F1: L GCCATGCCGGCATGCCTGCCCCTGCCCCCACCGAGCAAGTG 1 F3: 4 CAGATGCTCAGCAGAGGAATTAGCCTGCCTTTCAGGAGAT R RF: GCCATGCCAGCATGCCTGCCCCTGCCCCCACCGAGCAAGTGAACACCCAGATGCTCAGCAGAGGAATTAGCCTGCCTTTCAGGAGATGCTAATGAGGCAAGTTGGAAGCGGATGAGGTTCAGCCAGGAAGGAAACTGTTGGCCCCACAGAAGCCCTGGGCAC RR: CGGTACGGTCGTACGGACGGGGACGGGGGTGGCTCGTTCACTTGTGGGTCTACGAGTCGTCTCCTTAATCGGACGGAAAGTCCTCTACGATTACTCCGTTCAACCTTCGCCTACTCCAAGTCGGTCCTTCCTTTGACAACCGGGGTGTCTTCGGGACCCGTG F2: 3 GACTCGTG 2 Unidirectional alignment (log-probability: -38) CCATGCCgGCATGCCTGCCCCTGCCCCCACCGAGCAAGTG------gtgctcagCAGATGCTCAGCAGAGGAATTAGCCTGCCTTTCAGGAGAT CCATGCCAGCATGCCTGCCCCTGCCCCCACCGAGCAAGTGAACACC--------CAGATGCTCAGCAGAGGAATTAGCCTGCCTTTCAGGAGAT Template switch alignment (log-probability: -27.8) CCATGCCgGCATGCCTGCCCCTGCCCCCACCGAGCAAGTG|GTGCtCAG|CAGATGCTCAGCAGAGGAATTAGCCTGCCTTTCAGGAGAT CCATGCCAGCATGCCTGCCCCTGCCCCCACCGAGCAAGTG|GTGCCCAG|CAGATGCTCAGCAGAGGAATTAGCCTGCCTTTCAGGAGAT ========== Event 1442 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTTTCCCCCTGGGCATTTGG-ATACCACATGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTTCACAGCTGTGGAGTTTCCAGGTGGCTGAACTTGCTGAGGCTGCTGTTTGCTGTGCGCGTGCCATGCCTGAGGCCCTGGGTGCT ↓ 1 4 3 2 Chimp: CCTTTCGCCCTGGGCATTTGGATTGGCACGTGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTTCACAGCTGTGGAGTTTCCAGGTGGCTGAACTTGCTGAGGCTGCTGTTTGCTGTGCGCGTGCCATGCCTGAGGCCCTGGGTGCT Gorilla: CCTTTCCCCCTGGGCATTTGG-ATACCACGTGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTTCACAGCTGTGGAGTTTCCAGGTGGCTGAACTTGCTGAGGCTGCTGTTTGCTGTGCGCGTGCCATGCCTGAGGCCCTGGGTGCT Human: CCTTTCCCCCTGGGCATTTGG-ATACCACATGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTTCACAGCTGTGGAGTTTCCAGGTGGCTGAACTTGCTGAGGCTGCTGTTTGCTGTGCGCGTGCCATGCCTGAGGCCCTGGGTGCT Cluster: [ ] Orangutan: CCTTTCCCC-CGGACGTGTGG-ATACCACGTGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTTCACAGCTGTGGAGTTTCCAGGTGGCTGAACTTGGTGAGGCTGGTGTTTGCTGTGCGCGTGCCATGCCTGAGGCCCTGGGTGCT Human > Chimp ------------- chr17:80598711-80598717 Template switch process: F1: L CCCCACGCCCACAGCACCTCCCTTTCGCCCTGGGCATTTGGAT 1 F3: 4 TGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTT R RF: CCCCACGCCCACAGCACCTCCCTTTCCCCCTGGGCATTTGGATACCACATGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTTCACAGCTGTGGAGTTTCCAGGTGGCTGAACTTGCTGAGGCTGCTGTTTGCTGTGCGCGTGCCA RR: GGGGTGCGGGTGTCGTGGAGGGAAAGGGGGACCCGTAAACCTATGGTGTACCCGTAGAGGGGAAGACGACCGCTTCCGATGTCTTTCAAGTGTCGACACCTCAAAGGTCCACCGACTTGAACGACTCCGACGACAAACGACACGCGCACGGT F2: 3 GCACGGT 2 Unidirectional alignment (log-probability: -36.4) CACGCCCACAGCACCTCCCTTTCgCCCTGGGCATTTGGAtTggCACgTGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTT CACGCCCACAGCACCTCCCTTTCCCCCTGGGCATTTGGA-TACCACATGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTT Template switch alignment (log-probability: -22.2) CACGCCCACAGCACCTCCCTTTCgCCCTGGGCATTTGGAT|TGGCACG|TGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTT CACGCCCACAGCACCTCCCTTTCCCCCTGGGCATTTGGAT|TGGCACG|TGGGCATCTCCCCTTCTGCTGGCGAAGGCTACAGAAAGTT ========== Event 1443 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCGTGG----GCACAAGAGGCCAGGAGGGCAGTGGG Chimp: AGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCATGG----GCACAAGAGGCCAGGAGGGCAGTGGG ↑ 3 2 1 4 Gorilla: AGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCGTGGAGGGCCCTCAGAGGCCAGGAGGGCAGTGGG Human: AGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCGTGG----GCACAAGAGGCCAGGAGGGCAGTGGG Cluster: [ ] Orangutan: AGAGGCCCAGTGCAGGGGCCATGCCCATCAGGGGGCGTGG----GCACAAGAGGCCAGGAGGGCAGTGGA Gorilla > Chimp --------------- chr17:80586311-80586319 Template switch process: F1: L CAGGGAGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGC 1 F3: 4 AGAGGCCAGGAGGGCAGTGGGGCAGGTGGCCCCGCCAGGC R RF: CAGGGAGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCGTGGAGGGCCCTCAGAGGCCAGGAGGGCAGTGGGGCAGGTGGCCCAGCCAGGC RR: GTCCCTCTCCGGGTCACGTCCCCGACACGGGTAGTCTCCCGCACCTCCCGGGAGTCTCCGGTCCTCCCGTCACCCCGTCCACCGGGTCGGTCCG F2: 3 ACACGGGTA 2 Unidirectional alignment (log-probability: -37.9) AGGGAGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCaTGGgcacA--------AGAGGCCAGGAGGGCAGTGGGGCAGGTGGCCCcGCCAGGC AGGGAGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGCGTGG----AGGGCCCTCAGAGGCCAGGAGGGCAGTGGGGCAGGTGGCCCAGCCAGGC Template switch alignment (log-probability: -22.4) AGGGAGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGC|ATGGGCACA|AGAGGCCAGGAGGGCAGTGGGGCAGGTGGCCCcGCCAGGC AGGGAGAGGCCCAGTGCAGGGGCTGTGCCCATCAGAGGGC|ATGGGCACA|AGAGGCCAGGAGGGCAGTGGGGCAGGTGGCCCAGCCAGGC ========== Event 1444 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCTATTCTCACACACCCCAGACCAACTCTAGGTCTCTTCTCTTCAGAACAGGAGCCAA ↑ 3 1 4 2 Chimp: CCCTATTCTCACACACCCCAGAC-----CTAG---AGTTCTCTTCAGAACAGGAGCCAA Gorilla: CCCTATTCTCACACACCCCAGAC-----CTAG---AGTTCTCTTCAGAACAGGAGCCAA ↓ 3 1 4 2 Human: CCCTATTCTCACACACCCCAGACCAACTCTAGGTCTCTTCTCTTCAGAACAGGAGCCAA Cluster: [ ] Orangutan: CCCTATCCTCACAGACCCCAGAC-----CTAG---AGTTCTCTTCAGAACAGGAGCCAA Chimp > Human ------------- chr17:81196406-81196417 Template switch process: F1: L TCAAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC 1 F3: 4 CTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAGC R RF: TCAAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACCTAGAGTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAGC RR: AGTTCGTCGGGACCTCCGGGGATAAGAGTGTGTGGGGTCTGGATCTCAAGAGAAGTCTTGTCCTCGGTTGGCCCCGACGCTGACTCG F2: 3 TCTGGATCTCAA 2 Unidirectional alignment (log-probability: -40.1) AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC-----aactctaggtctcTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACCTAGAG-------------TTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG Template switch alignment (log-probability: -22.8) AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC|AACTCTAGGTCT|cTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC|AACTCTAGGTCT|GTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG Gorilla > Human --------------- chr17:81196406-81196417 Template switch process: F1: L TCAAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC 1 F3: 4 CTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAGC R RF: TCAAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACCTAGAGTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAGC RR: AGTTCGTCGGGACCTCCGGGGATAAGAGTGTGTGGGGTCTGGATCTCAAGAGAAGTCTTGTCCTCGGTTGGCCCCGACGCTGACTCG F2: 3 TCTGGATCTCAA 2 Unidirectional alignment (log-probability: -39.6) AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACcaactctaggtctC-----TTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGAC-------------CTAGAGTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG Template switch alignment (log-probability: -22.8) AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC|AACTCTAGGTCT|cTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG AAGCAGCCCTGGAGGCCCCTATTCTCACACACCCCAGACC|AACTCTAGGTCT|GTTCTCTTCAGAACAGGAGCCAACCGGGGCTGCGACTGAG ========== Event 1445 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AATGCTAACTTCAGGGTAACATTTGCTGAATCCTCT-GAAGCCTTTTAGAGCATGGTGGCACAC Chimp: AATGCTAACTTCAGAGTAACATTTGCTGAATCCTCT-GAAGCCTTTTAGAGCATGGTGGCACAC Gorilla: AATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTGCAAATGTTTTAGAGCATGGTAGCACAC ↑ 3 2 1 4 Human: AATGCTAACTTCAGGGTAACATTTGCTGAATCCTCT-GAAGCCTTTTAGAGCATGGTGGCACAC Cluster: [ ] Orangutan: AATGCTAACTTCAGGGTAACATTTGCTGAATCCTCT-GAAGCCTTATAGAGCGTGGTGGCACAC Human > Gorilla --------------- chr1:149511481-149511486 Template switch process: F1: L TCCTCAATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTG 1 F3: 4 TTTTAGAGCATGGTAGCACACATACTGGGATGTAGCATGA R RF: TCCTCAATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTGAAGCCTTTTAGAGCATGGTGGCACACATACTGGGATGTAGCATGA RR: AGGAGTTACGATTGAAGTCCCATTGTAAACGACTTAGGAGACTTCGGAAAATCTCGTACCACCGTGTGTATGACCCTACATCGTACT F2: 3 GTAAAC 2 Unidirectional alignment (log-probability: -33.6) CTCAATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTG----CaaatgTTTTAGAGCATGGTaGCACACATACTGGGATGTAGCATGA CTCAATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTGAAGCC-----TTTTAGAGCATGGTGGCACACATACTGGGATGTAGCATGA Template switch alignment (log-probability: -22) CTCAATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTG|CAAATG|TTTTAGAGCATGGTaGCACACATACTGGGATGTAGCATGA CTCAATGCTAACTTCAGGGTAACATTTGCTGAATCCTCTG|CAAATG|TTTTAGAGCATGGTGGCACACATACTGGGATGTAGCATGA ========== Event 1446 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TGAGATATATCCTCTTGAAGT-CAAAAGAAAACTGCATACTTAAATAAGAAAAGGAAA ↓ 1 4 3 2 Chimp: TGAGATATATCCTCTTGAAGTATGCAGGAAAACTGCATACTTAAATAAGAAAAGGAAA Gorilla: nnnnnnnnnnnnnnnnnnnnn-nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Human: TGAGATATATCCTCTTGAAGT-CAAAAGAAAACTGCATACTTAAATAAGAAAAGGAAA Cluster: [ ] Orangutan: TTAGATATATCCTCTTGAAGT-CAAAGGAAAACTGCATACTCAAATAAGAAAAGGAAA Human > Chimp ------------- chr1:149774135-149774140 Template switch process: F1: L CTTTAAATTTTGCATTTATTTGAGATATATCCTCTTGAAGT 1 F3: 4 GAAAACTGCATACTTAAATAAGAAAAGGAAAACCCTGATA R RF: CTTTAAATTTTGAATTTATTTGAGATATATCCTCTTGAAGTCAAAAGAAAACTGCATACTTAAATAAGAAAAGGAAAACCCTGATA RR: GAAATTTAAAACTTAAATAAACTCTATATAGGAGAACTTCAGTTTTCTTTTGACGTATGAATTTATTCTTTTCCTTTTGGGACTAT F2: 3 GACGTA 2 Unidirectional alignment (log-probability: -34.5) TTTAAATTTTGcATTTATTTGAGATATATCCTCTTGAAGT----AtgcagGAAAACTGCATACTTAAATAAGAAAAGGAAAACCCTGATA TTTAAATTTTGAATTTATTTGAGATATATCCTCTTGAAGTCAAAA-----GAAAACTGCATACTTAAATAAGAAAAGGAAAACCCTGATA Template switch alignment (log-probability: -22) TTTAAATTTTGcATTTATTTGAGATATATCCTCTTGAAGT|ATGCAG|GAAAACTGCATACTTAAATAAGAAAAGGAAAACCCTGATA TTTAAATTTTGAATTTATTTGAGATATATCCTCTTGAAGT|ATGCAG|GAAAACTGCATACTTAAATAAGAAAAGGAAAACCCTGATA ========== Event 1447 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCCTTGAAAATAACACATCTGA--CTGTGTAGTCACTTCTTCATATGGGAAGA ↑ 1 3 4 2 Chimp: TCCTTGAAAATAACACATCTGG-TTTACACAGTCACTTCTTCATATGGGAAGA ↓ 1 3 4 2 Gorilla: TCCTTGAAAATAACACATCTGA--CTGTGTAGTCACTTCTTCATATGGGAAGA Human: TCCTTGAAAATAACACATCTGA--CTGTGTAGTCACTTCTTCATATGGGAAGA Cluster: [ ] Orangutan: TCCTTGAAAATAACACATCTGGT-TTACACAGTCACTTCTTCATATGGGAAGA Chimp > Human ------------- chr1:170162557-170162563 Template switch process: F1: L GGTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG 1 F3: 4 AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA R RF: GGTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTGGTTTACACAGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA RR: CCAACAAATACGACGATAGTAGGAACTTTTATTGTGTAGACCAAATGTGTCAGTGAAGAAGTATACCCTTCTAGAACCCCCAGGTAACT F2: 3 TGTGTCA 2 Unidirectional alignment (log-probability: -28.7) GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTGactgtGT------AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG-----GTTTACACAGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA Template switch alignment (log-probability: -16.2) GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG|ACTGTGT|AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG|ACTGTGT|AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA Chimp > Gorilla --------------- chr1:149123312-149123318 Template switch process: F1: L GGTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG 1 F3: 4 AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA R RF: GGTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTGGTTTACACAGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA RR: CCAACAAATACGACGATAGTAGGAACTTTTATTGTGTAGACCAAATGTGTCAGTGAAGAAGTATACCCTTCTAGAACCCCCAGGTAACT F2: 3 TGTGTCA 2 Unidirectional alignment (log-probability: -28.2) GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG------ACtgtgtAGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTGGTTTACAC-----AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA Template switch alignment (log-probability: -16.6) GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG|ACTGTGT|AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA GTTGTTTATGCTGCTATCATCCTTGAAAATAACACATCTG|ACTGTGT|AGTCACTTCTTCATATGGGAAGATCTTGGGGGTCCATTGA ========== Event 1448 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GATGTTTTGTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA-AG---------TCCTGTGGTTTCATGTCTTGTC Chimp: gatgttttgtttcagagcctgtgttcACTAGAATTGTCTGTCCACTAGA-AG---------TCCTGTGGTTTCATGTCTTGTC ↓ 4 3 2 1 Gorilla: GATGTTTTGTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGACAGACAATTTGTGTCTGTGGTTTCATGTCTTGTC ↑ 4 3 2 1 Human: GATGTTTTGTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA-AG---------TCCTGTGGTTTCATGTCTTGTC Cluster: [ ] Orangutan: gatgttttgtttcagagcctgtgttcACTAGAATTGTCTGTCCACTAGA-AG---------TCCTGTGGTTTCATGTCTTGTC Human > Gorilla --------------- chr1:148902822-148902830 Template switch process: F1: L GTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA 1 F3: 4 TGTGT-----------------------------CTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGTTCTCC R RF: GTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGAAGTCCTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGTTCTCC RR: CAAAGTCTCGGACACAAGTGATCTTAACAGACAGGTGATCTTCAGGACACCAAAGTACAGAACAGAAAGTAGTCTTTTCAAGAGG F2: 3 TTAACAGAC 2 Unidirectional alignment (log-probability: -39.5) TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA---CagacaatttgtgtCTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGAAGTC-------------CTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT Template switch alignment (log-probability: -28.2) TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA|CAGACAATT|TGTGT-----------------------------CTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA|CAGACAATT|TGTGTTCACTAGAATTGTCTGTCCACTAGAAGTCCTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT Chimp > Gorilla --------------- chr1:148902822-148902830 Template switch process: F1: L GTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA 1 F3: 4 TGTGT-----------------------------CTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGTTCTCC R RF: GTTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGAAGTCCTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGTTCTCC RR: CAAAGTCTCGGACACAAGTGATCTTAACAGACAGGTGATCTTCAGGACACCAAAGTACAGAACAGAAAGTAGTCTTTTCAAGAGG F2: 3 TTAACAGAC 2 Unidirectional alignment (log-probability: -39.5) TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA---CagacaatttgtgtCTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGAAGTC-------------CTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT Template switch alignment (log-probability: -28.2) TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA|CAGACAATT|TGTGT-----------------------------CTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT TTTCAGAGCCTGTGTTCACTAGAATTGTCTGTCCACTAGA|CAGACAATT|TGTGTTCACTAGAATTGTCTGTCCACTAGAAGTCCTGTGGTTTCATGTCTTGTCTTTCATCAGAAAAGT ========== Event 1449 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TACCACCAACATCCCTGCCACTATGCCCAGTGCC--TCTGCTCCATCATCTCGGACATCC ↓ 3 2 1 4 Chimp: TACCACCAACATCCCTGCCACTATGCCCAGTGGCATAGTGCTCCATCATCTTGGACATCC ↑ 3 2 1 4 Gorilla: TACCACCAACATCCCTGCCACTATGCCCAGTGCC--CCTGCTCCATCATCTCGGACATCC Human: TACCACCAACATCCCTGCCACTATGCCCAGTGCC--TCTGCTCCATCATCTCGGACATCC Cluster: [ ] Orangutan: Human > Chimp ------------- chr17:47422749-47422755 Template switch process: F1: L ACCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG 1 F3: 4 GCTCCATCATCTTGGACATCCCCAGCACCACGGTGCCCG R RF: ACCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTGCCTCTGCTCCATCATCTCGGACATCCCCAGCACCACGGTGCCCG RR: TGGTGGGCGATGGTGGTTGTAGGGACGGTGATACGGGTCACGGAGACGAGGTAGTAGAGCCTGTAGGGGTCGTGGTGCCACGGGC F2: 3 TGATACG 2 Unidirectional alignment (log-probability: -36) CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTggcataG----TGCTCCATCATCTtGGACATCCCCAGCACCACGGTGCCCG CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGT------GCCTCTGCTCCATCATCTCGGACATCCCCAGCACCACGGTGCCCG Template switch alignment (log-probability: -22.1) CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG|GCATAGT|GCTCCATCATCTtGGACATCCCCAGCACCACGGTGCCCG CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG|GCATAGT|GCTCCATCATCTCGGACATCCCCAGCACCACGGTGCCCG Gorilla > Chimp --------------- chr17:47422749-47422754 Template switch process: F1: L ACCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG 1 F3: 4 TGCTCCATCATCTTGGACATCCCCAGCACCACGGTGCCCG R RF: ACCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTGCCCCTGCTCCATCATCTCGGACATCCCTAGCACCACGGTGCCCG RR: TGGTGGGCGATGGTGGTTGTAGGGACGGTGATACGGGTCACGGGGACGAGGTAGTAGAGCCTGTAGGGATCGTGGTGCCACGGGC F2: 3 GATACG 2 Unidirectional alignment (log-probability: -40.5) CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG----gcatagTGCTCCATCATCTtGGACATCCCcAGCACCACGGTGCCCG CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTGCCCC------TGCTCCATCATCTCGGACATCCCTAGCACCACGGTGCCCG Template switch alignment (log-probability: -27.5) CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG|GCATAG|TGCTCCATCATCTtGGACATCCCcAGCACCACGGTGCCCG CCACCCGCTACCACCAACATCCCTGCCACTATGCCCAGTG|GCATAG|TGCTCCATCATCTCGGACATCCCTAGCACCACGGTGCCCG ========== Event 1450 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGGCGCCACAGCCTGGCTGAAGGCGCTGGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGG ↓ 1 3 2 4 Chimp: GGAGGCGCCACAGCCTGGCTGGAGGCGCTAATCCA----------------GAGGACCGCGCCGCGAGCGCAGGATCCCGCTGCACCAGTGGG ↑ 1 3 2 4 Gorilla: GGAGGCGCCACAGCCTGGCTGGAGGCGCTGGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGG Human: GGAGGCGCCACAGCCTGGCTGAAGGCGCTGGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGG Cluster: [ ] Orangutan: Human > Chimp ------------- chr17:47653610-47653629 Template switch process: F1: L CCGAGCCAGCCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCT 1 F3: 4 GAGCGCAGGATCCCGCTGCACCAGTGGGCTGGGGGTGCCGCAACAGGA R RF: CCGAGCCAGCCCTACCCACTGGAGGCGCCACAGCCTGGCTGAAGGCGCTGGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGGCTGGGGGTGCCGCAACAGGA RR: GGCTCGGTCGGGATGGGTGACCTCCGCGGTGTCGGACCGACTTCCGCGACCGCGCCGCGCCAGGAGACCTAATCCCGACGCCGCCCTCGCGTGCTAGGGCGACGTGGTCACCCGACCCCCACGGCGTTGTCCT F2: 3 CGCCGCGCCAGGAGACCTAA 2 Unidirectional alignment (log-probability: -62.4) CCCTACCCACTGGAGGCGCCACAGCCTGGCTGgAGGCGCTaatccagaggaccgcGcCGC-------------------------------GAGCGCAgGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG CCCTACCCACTGGAGGCGCCACAGCCTGGCTGAAGGCGCT---------------GGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG Template switch alignment (log-probability: -30) CCCTACCCACTGGAGGCGCCACAGCCTGGCTGgAGGCGCT|AATCCAGAGGACCGCGCCGC|GAGCGCAgGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG CCCTACCCACTGGAGGCGCCACAGCCTGGCTGAAGGCGCT|AATCCAGAGGACCGCGCCGC|GAGCGCACGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG Gorilla > Chimp --------------- chr17:47653610-47653629 Template switch process: F1: L GCCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCT 1 F3: 4 GAGCGCAGGATCCCGCTGCACCAGTGGGCTGGGGGTGCCGCAACAGGA R RF: GCCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCTGGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGGCTGGGGGTGCCGCAACAGGA RR: CGGGATGGGTGACCTCCGCGGTGTCGGACCGACCTCCGCGACCGCGCCGCGCCAGGAGACCTAATCCCGACGCCGCCCTCGCGTGCTAGGGCGACGTGGTCACCCGACCCCCACGGCGTTGTCCT F2: 3 CGCCGCGCCAGGAGACCTAA 2 Unidirectional alignment (log-probability: -55) CCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCTaatccagaggaccgcGcCGC-------------------------------GAGCGCAgGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG CCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCT---------------GGCGCGGCGCGGTCCTCTGGATTAGGGCTGCGGCGGGAGCGCACGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG Template switch alignment (log-probability: -24) CCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCT|AATCCAGAGGACCGCGCCGC|GAGCGCAgGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG CCCTACCCACTGGAGGCGCCACAGCCTGGCTGGAGGCGCT|AATCCAGAGGACCGCGCCGC|GAGCGCACGATCCCGCTGCACCAGTGGGCTGGGGGTGCCG ========== Event 1451 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AAATTTATCAATGAATGCTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACCTTACTGCTCTGTTGGAACATTG----- ↑ 3 2 14 Chimp: AAATTTATCAATGAACGCTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAA-----CTTCTCTGTTGGAACattgtattg ↓ 3 2 14 Gorilla: AAATTTATCAATGAATGCTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACCTTACTGCTCTGTTGGAACATTG----- Human: AAATTTATCAATGAATGCTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACCTTACTGCTCTGTTGGAACATTG----- Cluster: [ ] Orangutan: AAATTTATCAATGAATGCTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACCTTACTGCTCTGTTGGAACATTG----- Chimp > Human ------------- chr1:79565583-79565587 Template switch process: F1: L CTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACCT 1 F3: 4 CTCTGTTGGAACATTG R RF: CTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACTTCTCTGTTGGAACATTG RR: GAGTCATTGAAAACCTTGTAACATAGACAACCTTCATTTTTGAAGAGACAACCTTGTAAC F2: 3 GTCAT 2 Unidirectional alignment (log-probability: -32.4) GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAaccttACTgCTCTGTTGGAACATTG------------------------ GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAA-----ACTTCTCTGTTGGAACATTGTATTGTTAAAAGTAAAAATTAAAT Template switch alignment (log-probability: -21.4) GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACcT|TACTG|CTCTGTTGGAACATTG GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACTT|TACTG|CTCTGTTGGAACATTG Chimp > Gorilla --------------- chr1:80541070-80541074 Template switch process: F1: L CTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACCT 1 F3: 4 CTCTGTTGGAACATTG R RF: CTCAGTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACTTCTCTGTTGGAACATTG RR: GAGTCATTGAAAACCTTGTAACATAGACAACCTTCATTTTTGAAGAGACAACCTTGTAAC F2: 3 GTCAT 2 Unidirectional alignment (log-probability: -31.3) GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAaccttACTgCTCTGTTGGAACATTG------------------------ GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAA-----ACTTCTCTGTTGGAACATTGTATTGTTAAAAGTAAAAATTAAAT Template switch alignment (log-probability: -21.3) GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACcT|TACTG|CTCTGTTGGAACATTG GTAACTTTTGGAACATTGTATCTGTTGGAAGTAAAAACTT|TACTG|CTCTGTTGGAACATTG ========== Event 1452 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGTTCTTTTGTCACCTGGTATGTTGTTAA----------------------------GTCACCTTGTGACTTAACATATTGTTAAGTCATATTGTTCATATTGTGACTTAATGAA Chimp: AGTTCTTTTGTTACCTGGTATGTTGTTAA----------------------------GTCACCTTGTGACTTAACATATTGTTAAGTCATATTGTTCATATTGTGACTTAATGAA Gorilla: AGTTCTTTTGTCACCTGGTATGTTGTTAA--------------------------------------------------------GTCATATTGTTCATATTGTGACTTAATGAA ↓ 4 3 2 1 Human: AGTTCTTTTGTCACCTGGTATGTTGTTAA----------------------------GTCACCTTGTGACTTAACATATTGTTAAGTCATATTGTTCATATTGTGACTTAATGAA Cluster: [ ] Orangutan: GGTTGTTTTGTCACCTGGTATGTTGTTAAGTCACCTTGTGACTTAACATATTGTNNN----------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr1:79534836-79534843 Template switch process: F1: L ATTGCATGAAACAGTTCTTTTGTCACCTGGTATGTTGTTAAGTCACCTTGT 1 F3: 4 ATATTGTTAAGTCATATTGTTCATATTGTGACTTAATGAAGTCAAATCAG R RF: ATTGCATGAAACAGTTCTTTTGTCACCTGGTATGTTGTTAAGTCATATTGTTCATATTGTGACTTAATGAAGTCAAATCAG RR: TAACGTACTTTGTCAAGAAAACAGTGGACCATACAACAATTCAGTATAACAAGTATAACACTGAATTACTTCAGTTTAGTC F2: 3 CAATTCAG 2 Unidirectional alignment (log-probability: -51.1) CAGTTCTTTTGTCACCTGGTATGTTGTTaagtcaccttgtgacttaacatattgttAAGTCATATTGTTCATATTGTGACTTAATGAA CAGTTCTTTTGTCACCTGGTATGTTGTT----------------------------AAGTCATATTGTTCATATTGTGACTTAATGAA Template switch alignment (log-probability: -33.8) CAGTTCTTTTGTCACCTGGTATGTTGTTAAGTCAccTTGT|GACTTAAC|ATaTTGTTAAGTCATATTGTTCATATTGTGACTTAATGAA CAGTTCTTTTGTCACCTGGTATGTTGTTAAGTCATATTGT|GACTTAAC|ATGTTGTTAAGTCATATTGTTCATATTGTGACTTAATGAA ========== Event 1453 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAAC------AAGAAAAAATAATGAAGAGAATACACACA Chimp: TTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAAC------AAGAAAAAATAATGAAGAGAATACACACA ↓ 3 1 2 4 Gorilla: TTTATTTTTAAAGCCACATGGGATGCTTACTTAAGCATC------------CCATAATGAAGAGAATACACACA ↑ 3 1 2 4 Human: TTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAAC------AAGAAAAAATAATGAAGAGAATACACACA Cluster: [ ] Orangutan: TTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAACAAGAAA------AAATAATGAAGAGAATGCACACA Human > Gorilla --------------- chr1:147400573-147400584 Template switch process: F1: L AATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTA 1 F3: 4 ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA R RF: AATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAACAAGAAAAAATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA RR: TTAATTTTTATCAAATAAAAATTTCGGTGTACCCTACGAATTCATTTCTTGTTCTTTTTTATTACTTCTCTTATGTGTGTTGAACTATCTCTTCCCTTT F2: 3 CCCTACGAATTC 2 Unidirectional alignment (log-probability: -38.8) ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTT------------------ActtaagcatcccATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAACAAGAAAAA------------ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA Template switch alignment (log-probability: -17.3) ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTA|CTTAAGCATCCC|ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTA|CTTAAGCATCCC|ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA Chimp > Gorilla --------------- chr1:147400573-147400584 Template switch process: F1: L AATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTA 1 F3: 4 ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA R RF: AATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAACAAGAAAAAATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA RR: TTAATTTTTATCAAATAAAAATTTCGGTGTACCCTACGAATTCATTTCTTGTTCTTTTTTATTACTTCTCTTATGTGTGTTGAACTATCTCTTCCCTTT F2: 3 CCCTACGAATTC 2 Unidirectional alignment (log-probability: -38.8) ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTT------------------ActtaagcatcccATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTAAGTAAAGAACAAGAAAAA------------ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA Template switch alignment (log-probability: -17.3) ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTA|CTTAAGCATCCC|ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA ATTAAAAATAGTTTATTTTTAAAGCCACATGGGATGCTTA|CTTAAGCATCCC|ATAATGAAGAGAATACACACAACTTGATAGAGAAGGGAAA ========== Event 1454 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATTTTCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAG----AGTATCAT-ACAGGCAATTTGGCCTAAGAAA Chimp: ATATTTTCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAG----AGTATCAT-ACAGGCAATTTGGCCTAAGAAA ↓ 3 2 1 4 Gorilla: ATATTTTCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAACCT--------ACATAGCAGGCAATTTGGCCTaaaaaa ↑ 3 2 1 4 Human: ATATTTTCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAG----AGTATCAT-ACAGGCAATTTGGCCTAAGAAA Cluster: [ ] Orangutan: ATATTTTCATACTAGAACTCTATGTAGGCTATCTCTCTGTAAGATAAAAGAGTA----TCAT-ACAGGCAATTTGGCCTAAGAAA Human > Gorilla --------------- chr1:147626979-147626987 Template switch process: F1: L TCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA 1 F3: 4 CAGGCAATTTGGCCTAAAAAACTAAAAATATTGATCCTCT R RF: TCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAGAGTATCATACAGGCAATTTGGCCTAAGAAACTAAAAATATTGATCCTCT RR: AGTATGATCTTGAGATACATCCAATAGAGAGATATTCTATTTTCTCATAGTATGTCCGTTAAACCGGATTCTTTGATTTTTATAACTAGGAGA F2: 3 GATACATCC 2 Unidirectional alignment (log-probability: -39.3) CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA--------CcTAcatagCAGGCAATTTGGCCTAAaAAACTAAAAATATTGATCCTCT CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAGAGTATCATA-----CAGGCAATTTGGCCTAAGAAACTAAAAATATTGATCCTCT Template switch alignment (log-probability: -22.4) CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA|CCTACATAG|CAGGCAATTTGGCCTAAaAAACTAAAAATATTGATCCTCT CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA|CCTACATAG|CAGGCAATTTGGCCTAAGAAACTAAAAATATTGATCCTCT Chimp > Gorilla --------------- chr1:147626979-147626987 Template switch process: F1: L TCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA 1 F3: 4 CAGGCAATTTGGCCTAAAAAACTAAAAATATTGATCCTCT R RF: TCATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAGAGTATCATACAGGCAATTTGGCCTAAGAAACTAAAAATATTGATCCTCT RR: AGTATGATCTTGAGATACATCCAATAGAGAGATATTCTATTTTCTCATAGTATGTCCGTTAAACCGGATTCTTTGATTTTTATAACTAGGAGA F2: 3 GATACATCC 2 Unidirectional alignment (log-probability: -39.3) CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA--------CcTAcatagCAGGCAATTTGGCCTAAaAAACTAAAAATATTGATCCTCT CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAAAAGAGTATCATA-----CAGGCAATTTGGCCTAAGAAACTAAAAATATTGATCCTCT Template switch alignment (log-probability: -22.4) CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA|CCTACATAG|CAGGCAATTTGGCCTAAaAAACTAAAAATATTGATCCTCT CATACTAGAACTCTATGTAGGTTATCTCTCTATAAGATAA|CCTACATAG|CAGGCAATTTGGCCTAAGAAACTAAAAATATTGATCCTCT ========== Event 1455 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGATGGATAGATGTTCCTCTCAAATTTGTTTCCTCCTGAAACAAATT-TTAAAAAATATATAACATAA ↑ 1 4 3 2 Chimp: GGATGGATAGATGTTCCTCTC-------ATTGCTCCTGAAACAAATT-TT-AAAAATATATAACATAA Gorilla: GGATGGATAGATGTTCCTCTC-------GTTGCTCCTGAAACAAATTTTT-AAAAATATATAACATAA ↓ 1 4 3 2 Human: GGATGGATAGATGTTCCTCTCAAATTTGTTTCCTCCTGAAACAAATT-TTAAAAAATATATAACATAA Cluster: [ ] Orangutan: GGATGGATAGATGTTCCTCTC-------ATTGCTCCTGAAACAAATTTTT-AAAAATATATAACATAA Chimp > Human ------------- chr1:167644791-167644800 Template switch process: F1: L TAAGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTCA 1 F3: 4 CTCCTGAAACAAATTTTAAAAAATATATAACATAAGCTAA R RF: TAAGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTCATTGCTCCTGAAACAAATTTTAAAAATATATAACATAAGCTAA RR: ATTCAGAATTCTTTACACAACCTACCTATCTACAAGGAGAGTAACGAGGACTTTGTTTAAAATTTTTATATATTGTATTCGATT F2: 3 CTTTGTTTAA 2 Unidirectional alignment (log-probability: -38.7) AGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTCAaatttgtTTcCTCCTGAAACAAATTTTAAAAaATATATAACATAAGCTAA AGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTCA-------TTGCTCCTGAAACAAATTTTAAAA-ATATATAACATAAGCTAA Template switch alignment (log-probability: -28.2) AGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTCA|AATTTGTTTC|CTCCTGAAACAAATTTTaAAAAATATATAACATAAGCTAA AGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTCA|AATTTGTTTC|CTCCTGAAACAAATTTT-AAAAATATATAACATAAGCTAA Gorilla > Human --------------- chr1:167644790-167644800 Template switch process: F1: L TAAGTCTTAAGAAATGTGTTGGATGGATAGATGTTCCTCTC 1 F3: 4 CTCCTGAAACAAATTTTAAAAAATATATAACATAAGCTA R RF: TAAGTCTTAAGAAATCTGTTGGATGGATAGATGTTCCTCTCGTTGCTCCTGAAACAAATTTTTAAAAATATATAACATAAGCTA RR: ATTCAGAATTCTTTAGACAACCTACCTATCTACAAGGAGAGCAACGAGGACTTTGTTTAAAAATTTTTATATATTGTATTCGAT F2: 3 CTTTGTTTAAA 2 Unidirectional alignment (log-probability: -43.1) AAGTCTTAAGAAATgTGTTGGATGGATAGATGTTCCTCTCaaatttgtTTcCTCCTGAAACAAATTTTaAAAAATATATAACATAAGCTA AAGTCTTAAGAAATCTGTTGGATGGATAGATGTTCCTCTCG-------TTGCTCCTGAAACAAATTTTTAAAAATATATAACATAAGCTA Template switch alignment (log-probability: -28.1) AAGTCTTAAGAAATgTGTTGGATGGATAGATGTTCCTCTC|AAATTTGTTTC|CTCCTGAAACAAATTTTaAAAAATATATAACATAAGCTA AAGTCTTAAGAAATCTGTTGGATGGATAGATGTTCCTCTC|AAATTTGTTTC|CTCCTGAAACAAATTTTTAAAAATATATAACATAAGCTA ========== Event 1456 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCACACTCTTGAAGCACACAGCAGCATCTTCTGAGATGGTTTTCTTCCCCAAA Chimp: ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCACACTCTTGAAGCACACAGCAGCATCTTCTGAGATGGTTTTCTTCCCCAAA ↑ 3 2 4 1 Gorilla: ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACA--------------------CAGCAGTATCTTCTAAGATGGTTTTCTTCCCCAAA Human: ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCACACTCTTGAAGCACACAGCAGCATCTTCTGAGATGGTTTTCTTCCCCAAA Cluster: [ ] Orangutan: ACATGGCATGGCCTGGGCCTTCGAGAGTGTGTACA--------------------TAGCAGCATCTTCTGAGATGGTTTTCTTCCCCAAA Gorilla > Chimp --------------- chr18:71441048-71441057 Template switch process: F1: L ACGAACACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCA 1 F3: 4 GCACACAGCAGCATCTTCTGAGATGGTTTTCTTCCCCAAATAACTTATGAGGACGTAGCC R RF: ACGAACACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCAGTATCTTCTAAGATGGTTTTCTTCCCCAAATAACTTATGAGGACGTAGCC RR: TGCTTGTGTACCGTACCGGAGCCGGAAGTTCTCACACATGTGTCGTCATAGAAGATTCTACCAAAAGAAGGGGTTTATTGAATACTCCTGCATCGG F2: 3 AAGTTCTCAC 2 Unidirectional alignment (log-probability: -50.9) ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTAcacagcacactcttgaagcaCACAGCAGcATCTTCTgAGATGGTTTTCTTCCCCAAA ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTA--------------------CACAGCAGTATCTTCTAAGATGGTTTTCTTCCCCAAA Template switch alignment (log-probability: -34.2) ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCA|CACTCTTGAA|GcACACAGCAGcATCTTCTgAGATGGTTTTCTTCCCCAAA ACATGGCATGGCCTCGGCCTTCAAGAGTGTGTACACAGCA|CACTCTTGAA|GTACACAGCAGTATCTTCTAAGATGGTTTTCTTCCCCAAA ========== Event 1457 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGTAGCTCCAAACCTCACTGACC--------TAAGTGATAGTGGATACTGTTTAT Chimp: ATGTAGCTCCAAACCTCACTGATC--------TAAGTGATAGTGGATACTGTTTAT Gorilla: ATGTAGCTCCAAACCTCACTGACCCTTAGGTCATAGTGATAGTGGATACTGTTTAT ↑ 3 1 4 2 Human: ATGTAGCTCCAAACCTCACTGACC--------TAAGTGATAGTGGATACTGTTTAT Cluster: [ ] Orangutan: ATGTAGCTCCAAACCTCACTGACC--------TAAGTGATAGTGGATACTGTTTAT Human > Gorilla --------------- chr18:3220180-3220188 Template switch process: F1: L GAATCAGGGACTATGAAATGTAGCTCCAAACCTCACTGACC 1 F3: 4 TAGTGATAGTGGATACTGTTTATGTAGAAGGGAAAGCCATG R RF: GAATCAGGGACTATGAAATGTAGCTCCAAACCTCACTGACCTAAGTGATAGTGGATACTGTTTATGTAGAAAGGAAAGCCATG RR: CTTAGTCCCTGATACTTTACATCGAGGTTTGGAGTGACTGGATTCACTATCACCTATGACAAATACATCTTTCCTTTCGGTAC F2: 3 ACTGGATTC 2 Unidirectional alignment (log-probability: -37.7) AATCAGGGACTATGAAATGTAGCTCCAAACCTCACTGACCctTAggtcatAGTGATAGTGGATACTGTTTATGTAGAAgGGAAAGCCAT AATCAGGGACTATGAAATGTAGCTCCAAACCTCACTGACC--TA------AGTGATAGTGGATACTGTTTATGTAGAAAGGAAAGCCAT Template switch alignment (log-probability: -27.9) AATCAGGGACTATGAAATGTAGCTCCAAACCTCACTGACC|CTTAGGTCA|tAGTGATAGTGGATACTGTTTATGTAGAAgGGAAAGCCAT AATCAGGGACTATGAAATGTAGCTCCAAACCTCACTGACC|CTTAGGTCA|AAGTGATAGTGGATACTGTTTATGTAGAAAGGAAAGCCAT ========== Event 1458 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: GCCGTGTTCTGGGAGTCACTGTGATGAGGTGCTGCCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTAACAGGCCCGAGTGGCTAGGAGGTTTGCAGGGAACCAGGTTTCGCTGTGATGAAAGCACCTTGCTGTGGGCTGGGAGGTGGGA Chimp: Gorilla: GCCGTGTTCTGGGAGTCACTGAGACAAGGTGC-TCCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGC-TACAGGCCCGAGTGGCTGGGAGGTTTGCAGGGAACCAGGTTTCGCTGTGATGAAAGCACCTTGCTGTGGGCTGGGAGGTGGGA ↑ 1 4 3 2 Human: GCCGTGTTCTGGGAGTCACTGTGATGAGGTGCTGCCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTAACAGGCCCGAGTGGCTAGGAGGTTTGCAGGGAACCAGGTTTCGCTGTGATGAAAGCACCTTGCTGTGGGCTGGGAGGTGGGA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr18:75426816-75426824 Template switch process: F1: L AGGAAAGATGCCTGTGGATGGCCGTGTTCTGGGAGTCACTGAGA 1 F3: 4 CCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTA R RF: AGGAAAGATGCCTGTGGATGGCCGTGTTCTGGGAGTCACTGTGATGAGGTGCTGCCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTAACAGGCCCGAGTGGCTAGGAGGTTTGCAGGGAACCAGGTTTCGCTGTGATGAAAGCACCTTG RR: TCCTTTCTACGGACACCTACCGGCACAAGACCCTCAGTGACACTACTCCACGACGGACGAAAGCGGGTTGGACTAGACCCCGAGTCTGTCGATTGTCCGGGCTCACCGATCCTCCAAACGTCCCTTGGTCCAAAGCGACACTACTTTCGTGGAAC F2: 3 TCGTGGAAC 2 Unidirectional alignment (log-probability: -34.4) AAGATGCCTGTGGATGGCCGTGTTCTGGGAGTCACTGaGAcaAGGTGCT-CCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTA- AAGATGCCTGTGGATGGCCGTGTTCTGGGAGTCACTGTGATGAGGTGCTGCCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTAA Template switch alignment (log-probability: -22.4) AAGATGCCTGTGGATGGCCGTGTTCTGGGAGTCACTGaGA|CAAGGTGCT|CCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTA AAGATGCCTGTGGATGGCCGTGTTCTGGGAGTCACTGTGA|CAAGGTGCT|CCTGCTTTCGCCCAACCTGATCTGGGGCTCAGACAGCTA ========== Event 1459 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTAGTGTAATATACTCAAGCTGA-------------GCTTCAGAATGCCCAAATACAGATA Chimp: TATTAGTGTAATATACTCAAGCTGA-------------GCTTCAGAATGCACAAATACAGATA ↓ 3 42 1 Gorilla: TATTAGTGTAATATACTCAAGCTGAGCTTCCAGCTTGAGCTTCAGAATGCACAAACACAGATA ↑ 3 42 1 Human: TATTAGTGTAATATACTCAAGCTGA-------------GCTTCAGAATGCCCAAATACAGATA Cluster: [ ] Orangutan: TATTAGTGTAATATACTCAAGCTGA-------------GCTTCAGAATGCACAAATACAGATA Human > Gorilla --------------- chr18:75997491-75997495 Template switch process: F1: L CACCCAAATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTC 1 F3: 4 TGAGCTTCAGAATGCACAAACACAGATAGAGATGCTGAAGAAT R RF: CACCCAAATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTCAGAATGCCCAAATACAGATAGAGATGCTGAAGAAT RR: GTGGGTTTATTATCTTATAATCACATTATATGAGTTCGACTCGAAGTCTTACGGGTTTATGTCTATCTCTACGACTTCTTA F2: 3 TCGAC 2 Unidirectional alignment (log-probability: -40.6) AATAATAGAATATTAGTGTAATATACTCAAGCTgagcttccagcttGAGCTTCAGAATGCaCAAAcACAGATAGAGATGCTGAAG AATAATAGAATATTAGTGTAATATACTCAAGCT-------------GAGCTTCAGAATGCCCAAATACAGATAGAGATGCTGAAG Template switch alignment (log-probability: -27.6) AATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTC|CAGCT|TGAGCTTCAGAATGCaCAAAcACAGATAGAGATGCTGAAG AATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTC|CAGCT|TGAGCTTCAGAATGCCCAAATACAGATAGAGATGCTGAAG Chimp > Gorilla --------------- chr18:75997491-75997495 Template switch process: F1: L CACCCAAATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTC 1 F3: 4 TGAGCTTCAGAATGCACAAACACAGATAGAGATGCTGAAGAAT R RF: CACCCAAATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTCAGAATGCACAAATACAGATAGAGATGCTGAAGAAT RR: GTGGGTTTATTATCTTATAATCACATTATATGAGTTCGACTCGAAGTCTTACGTGTTTATGTCTATCTCTACGACTTCTTA F2: 3 TCGAC 2 Unidirectional alignment (log-probability: -35.1) AATAATAGAATATTAGTGTAATATACTCAAGCTgagcttccagcttGAGCTTCAGAATGCACAAAcACAGATAGAGATGCTGAAG AATAATAGAATATTAGTGTAATATACTCAAGCT-------------GAGCTTCAGAATGCACAAATACAGATAGAGATGCTGAAG Template switch alignment (log-probability: -22.1) AATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTC|CAGCT|TGAGCTTCAGAATGCACAAAcACAGATAGAGATGCTGAAG AATAATAGAATATTAGTGTAATATACTCAAGCTGAGCTTC|CAGCT|TGAGCTTCAGAATGCACAAATACAGATAGAGATGCTGAAG ========== Event 1460 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGTATGCTGAAGATAGTCAGACTTTGTTTTTAAGAATTGAATATTCTGGAAGAGGCTCTTCAGTCCAATCTTTAGTTCTCTCCACAGAGCAAACGAAGTGAAGTGCTGAAGGCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAG-TTAAGGCAGGGTTGCCTTAACTAAA Chimp: GAGTATGCTGAAGATAGTCAGACTTTGTTTTTAAGAATTGAATATTCTGGAAGAGGCTCTTCAGTCCAATCTTTAGTTCTCTCCACAGAGCAAACGAAGTGAAGTGCCGAAGGCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAG-TTAAGGCAGGGTTGCCTTAACTAAA ↓ 3 2 1 4 Gorilla: GAGTATGCTGAAGATAGTCAGACTTTGTTTTTAAGAATTGAATATTCTGGAAGAGGCTCTTCAGTCCAATCTTTAGCGCTCTCCACAGAGCAAACGAAGTGAAGTGCCAAAGGCCTGGAGCCCGAGCTATTCCCACACGGACTCCAGGACAGAGTCTGGCAGGGTTGCCTTAACTAAA ↑ 3 2 1 4 Human: GAGTATGCTGAAGATAGTCAGACTTTGTTTTTAAGAATTGAATATTCTGGAAGAGGCTCTTCAGTCCAATCTTTAGTTCTCTCCACAGAGCAAACGAAGTGAAGTGCTGAAGGCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAG-TTAAGGCAGGGTTGCCTTAACTAAA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr18:2028617-2028621 Template switch process: F1: L GGCCTGGAGCCCGAGCTATTCCCACACGGACTCCAGGACAG 1 F3: 4 GGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT R RF: AGACTTTGTTTTTAAGAATTGAATATTCTGGAAGAGGCTCTTCAGTCCAATCTTTAGTTCTCTCCACAGAGCAAACGAAGTGAAGTGCTGAAGGCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAGTTAAGGCAGGGTTGCCTTAACTAAATCTCTGACAACTGTTTCTT RR: TCTGAAACAAAAATTCTTAACTTATAAGACCTTCTCCGAGAAGTCAGGTTAGAAATCAAGAGAGGTGTCTCGTTTGCTTCACTTCACGACTTCCGGACCTCGGGCTCGACAAGGGTGTGCCTGAGGTCCTGTCAATTCCGTCCCAACGGAATTGATTTAGAGACTGTTGACAAAGAA F2: 3 TCTGA 2 Unidirectional alignment (log-probability: -37.6) GCCTGGAGCCCGAGCTaTTCCCACACGGACTCCAGGACAG---AgtctGGCAGGGTTGCCTTAACTAAATCTCTGAtAACTGTTTCTT GCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAGTTAA----GGCAGGGTTGCCTTAACTAAATCTCTGACAACTGTTTCTT Template switch alignment (log-probability: -27.4) GCCTGGAGCCCGAGCTaTTCCCACACGGACTCCAGGACAG|AGTCT|GGCAGGGTTGCCTTAACTAAATCTCTGAtAACTGTTTCTT GCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAG|AGTCT|GGCAGGGTTGCCTTAACTAAATCTCTGACAACTGTTTCTT Chimp > Gorilla --------------- chr18:2028617-2028621 Template switch process: F1: L GGCCTGGAGCCCGAGCTATTCCCACACGGACTCCAGGACAG 1 F3: 4 GGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT R RF: AGACTTTGTTTTTAAGAATTGAATATTCTGGAAGAGGCTCTTCAGTCCAATCTTTAGTTCTCTCCACAGAGCAAACGAAGTGAAGTGCCGAAGGCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAGTTAAGGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT RR: TCTGAAACAAAAATTCTTAACTTATAAGACCTTCTCCGAGAAGTCAGGTTAGAAATCAAGAGAGGTGTCTCGTTTGCTTCACTTCACGGCTTCCGGACCTCGGGCTCGACAAGGGTGTGCCTGAGGTCCTGTCAATTCCGTCCCAACGGAATTGATTTAGAGACTATTGACAAAGAA F2: 3 TCTGA 2 Unidirectional alignment (log-probability: -32.1) GCCTGGAGCCCGAGCTaTTCCCACACGGACTCCAGGACAG---AgtctGGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT GCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAGTTAA----GGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT Template switch alignment (log-probability: -21.9) GCCTGGAGCCCGAGCTaTTCCCACACGGACTCCAGGACAG|AGTCT|GGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT GCCTGGAGCCCGAGCTGTTCCCACACGGACTCCAGGACAG|AGTCT|GGCAGGGTTGCCTTAACTAAATCTCTGATAACTGTTTCTT ========== Event 1461 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAAGGAGAGTCTTCCCTCAGCCTCCCACCGCATTGGTGGGCGCATTGCCCACCGGCACCCGGGTTCT ↓ 1 3 24 Chimp: AAAGGAGAGTCTTCCCTCAGCCTCCCACC--AAT----------GCGCCCACCGGCACCCGGGTTCT Gorilla: AAAGGAGAGTCTTCCCTCAGCTTCCCACC--AAT----------GCGCCCACCGGCACCCGGGTTCT ↑ 1 3 24 Human: AAAGGAGAGTCTTCCCTCAGCCTCCCACCGCATTGGTGGGCGCATTGCCCACCGGCACCCGGGTTCT Cluster: [ ] Orangutan: AAAGGAGAGTCTTCCCTCAGCCTCCTATC--AAC----------GCGCCCACAGGCACCCGGGTTCT Human > Chimp ------------- chr18:4542238-4542242 Template switch process: F1: L CACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACC 1 F3: 4 GCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG R RF: CACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACCGCATTGGTGGGCGCATTGCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG RR: GTGGACACGGTCTTTCCTCTCAGAAGGGAGTCGGAGGGTGGCGTAACCACCCGCGTAACGGGTGGCCGTGGGCCCAAGAGTCTTGTCTCAGGCGGTCC F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -26.2) ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACCaatGC---------------GCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACC---GCATTGGTGGGCGCATTGCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG Template switch alignment (log-probability: -15.9) ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACC|AATGC|GCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACC|AATGC|GCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG Human > Gorilla --------------- chr18:1424136-1424140 Template switch process: F1: L CCCACAGCCACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCTTCCCACC 1 F3: 4 GCCCACCGGCACCCGGGTTCTCAGAACAGAGTTCGCCAGG R RF: CCCACAGCCACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACCGCATTGGTGGGCGCATTGCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG RR: GGGTGTCGGTGGACACGGTCTTTCCTCTCAGAAGGGAGTCGGAGGGTGGCGTAACCACCCGCGTAACGGGTGGCCGTGGGCCCAAGAGTCTTGTCTCAGGCGGTCC F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -36.9) ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCtTCCCACCaatGC---------------GCCCACCGGCACCCGGGTTCTCAGAACAGAGTtCGCCAGG ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACC---GCATTGGTGGGCGCATTGCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG Template switch alignment (log-probability: -27.6) ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCtTCCCACC|AATGC|GCCCACCGGCACCCGGGTTCTCAGAACAGAGTtCGCCAGG ACCTGTGCCAGAAAGGAGAGTCTTCCCTCAGCCTCCCACC|AATGC|GCCCACCGGCACCCGGGTTCTCAGAACAGAGTCCGCCAGG ========== Event 1462 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGCCTTGCAGTCCAAAGCTCATTACAAGGTTGTATGTTGGAGTGCTTTGCTTTAGGCA------ACTTTCAAGTAAATCAAGAAATGAGCCCTCTC ↓ 1 3 4 2 Chimp: TCTGCCTTGCAGTCCAAAGCT-CTTA----CTTGAAA----------GTTGCCTAAAGCAAAGCACTCCAACAAGTAAATCAAGAAATGAGCCCTCTC Gorilla: TCTGCCTTTCAGTCCAAAGCTCATTataaggttgtatgttggagtgctttgctttaggca------actttcaagtaaatcaagaaatgagccctctc Human: TCTGCCTTGCAGTCCAAAGCTCATTACAAGGTTGTATGTTGGAGTGCTTTGCTTTAGGCA------ACTTTCAAGTAAATCAAGAAATGAGCCCTCTC Cluster: [ ] Orangutan: TCTGCCTTTCAGTCCAAAACTCATTACAAGGTTGTATGTTGGAGTGCTTTGCTTTAGGCA------ACTTTCAAGTAAATCAAGAAATGAGCCCTCTC Human > Chimp ------------- chr1:81718108-81718141 Template switch process: F1: L CTAGAAAAAGCCAACAGATTTCTGCCTTGCAGTCCAAAGCTC 1 F3: 4 CAAGTAAATCAAGAAATGAGCCCTCTCCCATGTTTGCTGC R RF: CTAGAAAAAGCCAACAGATTTCTGCCTTGCAGTCCAAAGCTCATTACAAGGTTGTATGTTGGAGTGCTTTGCTTTAGGCAACTTTCAAGTAAATCAAGAAATGAGCCCTCTCCCATGTTTGCTGC RR: GATCTTTTTCGGTTGTCTAAAGACGGAACGTCAGGTTTCGAGTAATGTTCCAACATACAACCTCACGAAACGAAATCCGTTGAAAGTTCATTTAGTTCTTTACTCGGGAGAGGGTACAAACGACG F2: 3 AACCTCACGAAACGAAATCCGTTGAAAGTTCATT 2 Unidirectional alignment (log-probability: -69.3) AGAAAAAGCCAACAGATTTCTGCCTTGCAGTCCAAAGCTC-----------------------------------------TTacttgaaagttgcctaaagcaaagcactccaaCAAGTAAATCAAGAAATGAGCCCTCTCCCATGTTTGCTGC AGAAAAAGCCAACAGATTTCTGCCTTGCAGTCCAAAGCTCATTACAAGGTTGTATGTTGGAGTGCTTTGCTTTAGGCAACTTT--------------------------------CAAGTAAATCAAGAAATGAGCCCTCTCCCATGTTTGCTGC Template switch alignment (log-probability: -19.5) AGAAAAAGCCAACAGATTTCTGCCTTGCAGTCCAAAGCTC|TTACTTGAAAGTTGCCTAAAGCAAAGCACTCCAA|CAAGTAAATCAAGAAATGAGCCCTCTCCCATGTTTGCTGC AGAAAAAGCCAACAGATTTCTGCCTTGCAGTCCAAAGCTC|TTACTTGAAAGTTGCCTAAAGCAAAGCACTCCAA|CAAGTAAATCAAGAAATGAGCCCTCTCCCATGTTTGCTGC ========== Event 1463 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: catacacacacatatatacacacacatatatatatcctg------cttagtgtgtgtatgtgtgt--gtg----tatatatatatatgt------------atgtgtttgtatatatatatatatatatacacacac----acacatacacacactaagtagcaggattgctggatcatgtggtggc Chimp: catacacac--------------acatatatatatCCTG---CTACTTAgtgtgt------gtgt--g--tgtatatatatatat--at--------------------atacacaaacacatatacacacac----acacacacacacacacacTAAGTagcaggattgctggatcatgtggtagc ↑ 1 4 3 2 Gorilla: catacacacacatatatacacacacatatatatatCCTGCTA---CTTAgtgtgtgtatgtgtgtgtgtg----tgtgtatatatatatatgtgtttgtat--------atacacatatatatatacacacacacac----acacatacacacacTAAGTagcaggattgctggatcatgtggtagc Human: catacacacacatatatacacacacatatatatatcctg------cttagtgtgtgtatgtgtgt--gtg----tatatatatatatgt------------atgtgtttgtatatatatatatatatatacacacac----acacatacacacactaagtagcaggattgctggatcatgtggtggc Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNN------NNNN--N------NNNNN----NN--NN--------------------NNNNNNNNNNNNNNNNNNNNNNACATac----acacacacacacactaagtagcaggattgctggatcatgtggtagc Gorilla > Chimp --------------- chr1:81632779-81632790 Template switch process: F1: L CACATACACACACATATATATA 1 F3: 4 GTGTGTGTGTGTGTATATATATATAT R RF: CACATACACACACATATATACACACACATATATATATCCTGCTACTTAGTGTGTGTATGTGTGTGTGTGTGTGTATATATATATATGTGTTTGTATATACACATATATATATACACACACACACACACATACACACACTAAGTAGCAGGA RR: GTGTATGTGTGTGTATATATGTGTGTGTATATATATAGGACGATGAATCACACACATACACACACACACACACATATATATATATACACAAACATATATGTGTATATATATATGTGTGTGTGTGTGTGTATGTGTGTGATTCATCGTCCT F2: 3 ATTCATCGTCCT 2 Unidirectional alignment (log-probability: -36.9) CACATACACACACATATAT--------------ATATCCTGCTACTTA------------GTGTGTGTGTGTGTATATATatatat CACATACACACACATATATACACACACATATATATATCCTGCTACTTAGTGTGTGTATGTGTGTGTGTGTGTGTATATAT------ Template switch alignment (log-probability: -21.9) CACATACACACACATATATAtA|TCCTGCTACTTA|GTGTGTGTGTGTGTATATATATATAT CACATACACACACATATATACA|TCCTGCTACTTA|GTGTGTGTGTGTGTATATATATATAT ========== Event 1464 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: acaccctatacacagcaaagcactaAGTAGTAGTAGCAGAAGACAGTACCACCGACTTTTCTTGTTCCCACATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTGAGTGCAG-----ATTATTCGGTAAACACTCTTAGGCCTAA ↑ 3 2 1 4 Chimp: acaccctatacacagcaaagcactaAGTAGTAGTAGCAGAAGACAGTACCACCAACTTTTCCTGTTCCCACATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGA----GTGCAGATTAGATTATTCTGTAAACACTCTTAGGCCTAA Gorilla: acaccctatacacaacaaagcactaAGTAGTAGTAGCAGAAGACAGTACCACCGACTTTTCGTGTTCCCACATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGA----GTGCAG-----ATTATTCTGTAAACACTCTTAGGCCTAA Human: acaccctatacacagcaaagcactaAGTAGTAGTAGCAGAAGACAGTACCACCGACTTTTCTTGTTCCCACATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTGAGTGCAG-----ATTATTCGGTAAACACTCTTAGGCCTAA Cluster: [ ] Orangutan: acaccctatacacagcaaagcactaAGTAGTAGTAGCAGAAGACAGTACCACCGACTTTTCCTGTTCCCACGTAAGCATTTCCCTTTAGGGTTCTAAGATGAGGTCATCATTGTTTTTAATCCTG---AAGGGCTACTGA----GTGCAG-----ATTATTCTGTAAACACTCTTAGGCCTAA Chimp > Human ------------- chr18:80159619-80159623 Template switch process: F1: L TGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTG 1 F3: 4 AGATTATTCGGTAAACACTCTTAGGCCTAACCTAGCTAGTCAGTCAAGCA R RF: GCACTAAGTAGTAGTAGCAGAAGACAGTACCACCAACTTTTCCTGTTCCCACATAAGCATTTCCCTTTAGGGCTCTAAGATGAGGTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTGCAGATTAGATTATTCTGTAAACACTCTTAGGCCTAACCTAGCTAGTCAGTCAAGCA RR: CGTGATTCATCATCATCGTCTTCTGTCATGGTGGTTGAAAAGGACAAGGGTGTATTCGTAAAGGGAAATCCCGAGATTCTACTCCAGTAGTAGCAAAAATTAGGACTTCTTCCCGATGACTCACGTCTAATCTAATAAGACATTTGTGAGAATCCGGATTGGATCGATCAGTCAGTTCGT F2: 3 CGTGA 2 Unidirectional alignment (log-probability: -33.3) GTCATCATCGTTTTTAATCCTGAAGAAGGGCTACtgagTGAGTGC-----AGATTATTCgGTAAACACTCTTAGGCCTAACCTAGCTAGT GTCATCATCGTTTTTAATCCTGAAGAAGGGCTAC----TGAGTGCAGATTAGATTATTCTGTAAACACTCTTAGGCCTAACCTAGCTAGT Template switch alignment (log-probability: -22.1) GTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTG|AGTGC|AGATTATTCgGTAAACACTCTTAGGCCTAACCTAGCTAGT GTCATCATCGTTTTTAATCCTGAAGAAGGGCTACTGAGTG|AGTGC|AGATTATTCTGTAAACACTCTTAGGCCTAACCTAGCTAGT ========== Event 1465 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TACACACCAGATGGTTAAAATGGCATAATACAAA--------------------CACATATCGAAAATCAGACCTCAAT Chimp: TACACACCAGATGGTTAAAATGGCATAATACAAA--------------------CACATATCGAAAATCAGACCTCAAT ↓ 3 24 1 Gorilla: TACACACCAGATGGTTAAAATGGCATAATACAAACACATTATGCCATATCGAAACACATATCGAAAATCAGACCTCAAT Human: TACACACCAGATGGTTAAAATGGCATAATACAAA--------------------CACATATCGAAAATCAGACCTCAAT Cluster: [ ] Orangutan: TATACACCAGATGGTTAAAATGGCATAATACAAA--------------------CTCATATCAAAAATCAGACCTCAAT Chimp > Gorilla --------------- chr18:14895966-14895973 Template switch process: F1: L GCATTACTACACACCAGATGGTTAAAATGGCATAATACAAACACAT 1 F3: 4 ATCGAAACACATATCGAAAATCAGACCTCAATAAATAAACCCAATTA R RF: GCATTACTACACACCAGATGGTTAAAATGGCATAATACAAACACATATCGAAAATCAGACCTCAATAAATAAACCCAATTA RR: CGTAATGATGTGTGGTCTACCAATTTTACCGTATTATGTTTGTGTATAGCTTTTAGTCTGGAGTTATTTATTTGGGTTAAT F2: 3 TACCGTAT 2 Unidirectional alignment (log-probability: -39.6) CTACACACCAGATGGTTAAAATGGCATAATACAaacacattatgccatatcgaAACACATATCGAAAATCAGACCTCAATAAATAAAC CTACACACCAGATGGTTAAAATGGCATAATACA--------------------AACACATATCGAAAATCAGACCTCAATAAATAAAC Template switch alignment (log-probability: -28.1) CTACACACCAGATGGTTAAAATGGCATAATACAAACACAT|TATGCCAT|ATcgAAACACATATCGAAAATCAGACCTCAATAAATAAAC CTACACACCAGATGGTTAAAATGGCATAATACAAACACAT|TATGCCAT|ATACAAACACATATCGAAAATCAGACCTCAATAAATAAAC ========== Event 1466 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GATCTGAGGCTCATCTGCAGGCCCA---------CATCCTG--GGTGGGCCAGTCTTTTAGGTGTGTGG Chimp: AATCTGAGGCTCATCTGCAGGCCCA---------CATCCTG--GGTGGGCCAGTCTTTTAGGTGTGTGG ↑ 1 3 4 2 Gorilla: GATCTGAGGCTCATCTGCAGGATGACTGCAGGATGACCCAGGATGTGGGCCAGTCTTTTAGGTGTGTGG ↓ 1 3 4 2 Human: GATCTGAGGCTCATCTGCAGGCCCA---------CATCCTG--GGTGGGCCAGTCTTTTAGGTGTGTGG Cluster: [ ] Orangutan: GATCGGAGGCTCATCTGCAGGCCCA---------CATCCTG--AGTGGGCCAGTCTTTTAGGTATGTGG Gorilla > Human --------------- chr18:78166070-78166081 Template switch process: F1: L TGCTAAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGG 1 F3: 4 GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT R RF: TGCTGAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGGATGACTGCAGGATGACCCAGGATGTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT RR: ACGACTTAGACCGTCGGGATCTAGACTCCGAGTAGACGTCCTACTGACGTCCTACTGGGTCCTACACCCGGTCAGAAAATCCACACACCATCTCCGTTTCTGGA F2: 3 GGTCCTACACCC 2 Unidirectional alignment (log-probability: -44.6) GCTaAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGG-----------------------cccacatcctggGTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT GCTGAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGGATGACTGCAGGATGACCCAGGAT------------GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT Template switch alignment (log-probability: -22.8) GCTaAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGG|CCCACATCCTGG|GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT GCTGAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGG|CCCACATCCTGG|GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT Gorilla > Chimp --------------- chr18:15833338-15833349 Template switch process: F1: L TGCTGAATCTGGCAGCCCTAAATCTGAGGCTCATCTGCAGG 1 F3: 4 GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT R RF: TGCTGAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGGATGACTGCAGGATGACCCAGGATGTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT RR: ACGACTTAGACCGTCGGGATCTAGACTCCGAGTAGACGTCCTACTGACGTCCTACTGGGTCCTACACCCGGTCAGAAAATCCACACACCATCTCCGTTTCTGGA F2: 3 GGTCCTACACCC 2 Unidirectional alignment (log-probability: -44.6) GCTGAATCTGGCAGCCCTAaATCTGAGGCTCATCTGCAGG-----------------------cccacatcctggGTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT GCTGAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGGATGACTGCAGGATGACCCAGGAT------------GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT Template switch alignment (log-probability: -22.8) GCTGAATCTGGCAGCCCTAaATCTGAGGCTCATCTGCAGG|CCCACATCCTGG|GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT GCTGAATCTGGCAGCCCTAGATCTGAGGCTCATCTGCAGG|CCCACATCCTGG|GTGGGCCAGTCTTTTAGGTGTGTGGTAGAGGCAAAGACCT ========== Event 1467 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCTTCTTTGGCCCTTTAGATAGAGGT----------------------ACCTTAACTGTAAACAACTGCAATGAGAGCCT ↓ 4 3 2 1 Chimp: TGCTTCTTTGGCCCTTTAGAT------ACCTTAACTGTACAGTTAAGGTACCTTAACTGTAAACAACTGCAATGAGAGCCT Gorilla: TGCTTCTTTGGCCCTTTAGATAGAGGT----------------------ACCTTAACTGTAAACAACCACAATGAGAGCCT Human: TGCTTCTTTGGCCCTTTAGATAGAGGT----------------------ACCTTAACTGTAAACAACTGCAATGAGAGCCT Cluster: [ ] Orangutan: TGCTTCTTTGGCCCTTTAGATAGAGGT----------------------ACCTTAATTGTAAACAACTGCAATGAGAGCCT Human > Chimp ------------- chr18:59337785-59337791 Template switch process: F1: L TGAGGTGTTAAAATATGAAATGCTTCTTTGGCCCTTTAGAT------ACCTTAACTGTA 1 F3: 4 GGTACCTTAACTGTAAACAACTGCAATGAGAGCCTTCTAGATG R RF: TGAGGTGTTAAAATATGAAATGCTTCTTTGGCCCTTTAGATAGAGGTACCTTAACTGTAAACAACTGCAATGAGAGCCTTCTAGATG RR: ACTCCACAATTTTATACTTTACGAAGAAACCGGGAAATCTATCTCCATGGAATTGACATTTGTTGACGTTACTCTCGGAAGATCTAC F2: 3 AATTGAC 2 Unidirectional alignment (log-probability: -40) TATGAAATGCTTCTTTGGCCCTTTAGATAccttaactgtacagttaAGGTACCTTAACTGTAAACAACTGCAATGAGAGCCTTCTAG TATGAAATGCTTCTTTGGCCCTTTAGATAG----------------AGGTACCTTAACTGTAAACAACTGCAATGAGAGCCTTCTAG Template switch alignment (log-probability: -27) TATGAAATGCTTCTTTGGCCCTTTAGAT------ACCTTAACTGTA|CAGTTAA|GGTACCTTAACTGTAAACAACTGCAATGAGAGCCTTCTAG TATGAAATGCTTCTTTGGCCCTTTAGATAGAGGTACCTTAACTGTA|CAGTTAA|GGTACCTTAACTGTAAACAACTGCAATGAGAGCCTTCTAG ========== Event 1468 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGATGCCCATCCTGGTCTCTCA---GCC--TTAGTCAAGGGTAGCTGAGACAT Chimp: CAGATGCCCATCCTGGTCTCTCAGAAGGCTGAGAGTCAAGGGTAGCTGAGACAT ↑ 3 1 24 Gorilla: CAGATGCCCATCCTGGTCTCTCA---GCC--TTAGTCAAGGGTAGCTGAGACAT Human: CAGATGCCCATCCTGGTCTCTCA---GCC--TTAGTCAAGGGTAGCTGAGACAT Cluster: [ ] Orangutan: CAGATGCCCATCCTGGTCTCTCA---GCC--TTAGTCAAGGGTAGCTGAGACAC Gorilla > Chimp --------------- chr18:58465395-58465403 Template switch process: F1: L CCCCTGGAACCTTCTGGGCAGATGCCCATCCTGGTCTCTCAG 1 F3: 4 AGTCAAGGGTAGCTGAGACATGGTGTCCAAACCTGCAAGC R RF: CCCCCGGAGCCTTCTGGGCAGATGCCCATCCTGGTCTCTCAGCCTTAGTCAAGGGTAGCTGAGACATGGTGTCCAAACCTGCAAGC RR: GGGGGCCTCGGAAGACCCGTCTACGGGTAGGACCAGAGAGTCGGAATCAGTTCCCATCGACTCTGTACCACAGGTTTGGACGTTCG F2: 3 GAGTCGGAA 2 Unidirectional alignment (log-probability: -44.8) CCtGGAaCCTTCTGGGCAGATGCCCATCCTGGTCTCTCagaaggctgAG----AGTCAAGGGTAGCTGAGACATGGTGTCCAAACCTGCAAGC CCCGGAGCCTTCTGGGCAGATGCCCATCCTGGTCTCTC---------AGCCTTAGTCAAGGGTAGCTGAGACATGGTGTCCAAACCTGCAAGC Template switch alignment (log-probability: -27.9) CCtGGAaCCTTCTGGGCAGATGCCCATCCTGGTCTCTCAG|AAGGCTGAG|AGTCAAGGGTAGCTGAGACATGGTGTCCAAACCTGCAAGC CCCGGAGCCTTCTGGGCAGATGCCCATCCTGGTCTCTCAG|AAGGCTGAG|AGTCAAGGGTAGCTGAGACATGGTGTCCAAACCTGCAAGC ========== Event 1469 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCTGTCCACTCGGCACAACTAAAAGGACCAACT ↓ 3 2 1 4 Chimp: TATTCTAGCTGTGACATGGGCTAAGGGGAGGAGCCCTTA---GCCTGTCCACTCGGCACACCTAAAAGGACCAACT ↑ 3 2 1 4 Gorilla: TATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCCGTCCACTCGACACACCTAAAAGGACCAACT Human: TATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCTGTCCACTCGGCACAACTAAAAGGACCAACT Cluster: [ ] Orangutan: TATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCTGTCCACTCAGCACACCTAAAAGGACTAACT Human > Chimp ------------- chr18:57287404-57287411 Template switch process: F1: L GCTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG 1 F3: 4 CTGTCCACTCGGCACACCTAAAAGGACCAACTCAGCATTA R RF: GCTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCTGTCCACTCGGCACAACTAAAAGGACCAACTCAGCATTA RR: CGATAATGATAAGATCGACACTGTACCCGATTCCCCTCCTCTGCCACGGAAAGACAGGTGAGCCGTGTTGATTTTCCTGGTTGAGTCGTAAT F2: 3 CGATTCCC 2 Unidirectional alignment (log-probability: -37.8) CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGA------GCCcTTagcCTGTCCACTCGGCACAcCTAAAAGGACCAACTCAGCATTA CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTT---CTGTCCACTCGGCACAACTAAAAGGACCAACTCAGCATTA Template switch alignment (log-probability: -22.3) CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG|CCCTTAGC|CTGTCCACTCGGCACAcCTAAAAGGACCAACTCAGCATTA CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG|CCCTTAGC|CTGTCCACTCGGCACAACTAAAAGGACCAACTCAGCATTA Gorilla > Chimp --------------- chr18:57287404-57287411 Template switch process: F1: L GCTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG 1 F3: 4 CTGTCCACTCGGCACACCTAAAAGGACCAACTCAGCATTACTTGCAAGACCT R RF: GCTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCCGTCCACTCGACACACCTAAAAGGACCAACTCAGCATTACTTGCAAGACCT RR: CGATAATGATAAGATCGACACTGTACCCGATTCCCCTCCTCTGCCACGGAAAGGCAGGTGAGCTGTGTGGATTTTCCTGGTTGAGTCGTAATGAACGTTCTGGA F2: 3 CGATTCCC 2 Unidirectional alignment (log-probability: -38.4) CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG-----------CCcttagcctGTCCACTCGgCACACCTAAAAGGACCAACTCAGCATTA CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAGACGGTGCCTTTCC--------GTCCACTCGACACACCTAAAAGGACCAACTCAGCATTA Template switch alignment (log-probability: -28.1) CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG|CCCTTAGC|CtGTCCACTCGgCACACCTAAAAGGACCAACTCAGCATTA CTATTACTATTCTAGCTGTGACATGGGCTAAGGGGAGGAG|CCCTTAGC|CCGTCCACTCGACACACCTAAAAGGACCAACTCAGCATTA ========== Event 1470 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AAGCACATTTGCTTTAAATGAGTGACCCCAAGCACATAGAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGAGCTTC ↑ 4 1 3 2 Chimp: AAGCACATTTGCTTTAAATGA-------------------GTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGAGCTTC ↓ 4 1 3 2 Gorilla: AAGCACATTTGCTTTAAATGAGTGACCCCAAGCACATAGAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGAGCTTC Human: AAGCACATTTGCTTTAAATGAGTGACCCCAAGCACATAGAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGAGCTTC Cluster: [ ] Orangutan: AAGCACATTTGCTTTAAATGA----------------------GTGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGAGCTTC Chimp > Human ------------- chr18:57270021-57270033 Template switch process: F1: L CAAAATAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTGA 1 F3: 4 GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGA R RF: CAAAATAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGA RR: GTTTTATTCTAAAATCTTTCTTCGTGTAAACGAAATTTACTCAATACTTTGAGATACACGAACCCCAAACTTATTCGGACT F2: 3 ATACACGAACCCC 2 Unidirectional alignment (log-probability: -38.2) TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGtgaccccaagcacatagagTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAG-------------------TTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT Template switch alignment (log-probability: -23) TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTgA|CCCCAAGCACATA|GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTTA|CCCCAAGCACATA|GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT Chimp > Gorilla --------------- chr18:58291556-58291568 Template switch process: F1: L CAAAATAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTGA 1 F3: 4 GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGA R RF: CAAAATAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCTGA RR: GTTTTATTCTAAAATCTTTCTTCGTGTAAACGAAATTTACTCAATACTTTGAGATACACGAACCCCAAACTTATTCGGACT F2: 3 ATACACGAACCCC 2 Unidirectional alignment (log-probability: -38.2) TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATgagtgaccccaagcacataGAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT TAAGATTTTAGAAAGAAGCACATTTGCTTTAAAT-------------------GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT Template switch alignment (log-probability: -23.1) TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTgA|CCCCAAGCACATA|GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT TAAGATTTTAGAAAGAAGCACATTTGCTTTAAATGAGTTA|CCCCAAGCACATA|GAGTTATGAAACTCTATGTGCTTGGGGTTTGAATAAGCCT ========== Event 1471 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTCTTGGTCTTCACTTTTGGGACCAGACAATTGCTTCATCTTGACCCACTTTGTGATCTGTGTACTCGGCTAATTCCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCAACCCTGGGCCCACCTGGGGAATCTGTCTCTCCC ↓ 3 2 1 4 Chimp: GTTTCTTGGTCTTCACTTTTGGGACCAAACAATTGCTCCATCTTGACCCACTTTGTGATCTGTGTACCCGGCTAATTCCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCGTCC-CAGGCCCACCTGGGGAATCTGTCTCTCCC ↑ 3 2 1 4 Gorilla: GTTTCTTGGTCTTCACTTTTGGGACCAAACAATTGTTTCATCTTGACCCACTTTGTGATCTGTGTACCCGGCTAATTCCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCAACCCTGGGCCCATCTGGGGAATCTGTCTCTCCC Human: GTTTCTTGGTCTTCACTTTTGGGACCAGACAATTGCTTCATCTTGACCCACTTTGTGATCTGTGTACTCGGCTAATTCCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCAACCCTGGGCCCACCTGGGGAATCTGTCTCTCCC Cluster: [ ] Orangutan: GTTTCTTGGTCTTCACTTTTGGAAGCAAACAATTGCTCCATCTTGACCCACTTTGTGATCCGTGTACCCAGCTGATTCCTGAGCACTGATTTC----------------------------C-CGGGCCCACCTGGGGAATCTGTCTTTCCC Human > Chimp ------------- chr18:57882071-57882076 Template switch process: F1: L CCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCC 1 F3: 4 GGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT R RF: TGGGACCAGACAATTGCTTCATCTTGACCCACTTTGTGATCTGTGTACTCGGCTAATTCCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCAACCCTGGGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT RR: ACCCTGGTCTGTTAACGAAGTAGAACTGGGTGAAACACTAGACACATGAGCCGATTAAGGACTCGTGACTAAAGGTTGGGACGACGGAACCGGAACCGGTTGGGACCCGGGTGGACCCCTTAGACAGAGAGGGGACCTCGAAGGGA F2: 3 ACCCTG 2 Unidirectional alignment (log-probability: -28.6) CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGccgtcCCA------GGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGG-----CCAACCCTGGGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT Template switch alignment (log-probability: -16) CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCC|GTCCCA|GGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCC|GTCCCA|GGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT Gorilla > Chimp --------------- chr18:57882071-57882076 Template switch process: F1: L CCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCC 1 F3: 4 GGCCCACCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCTTTCAAGC R RF: TGGGACCAAACAATTGTTTCATCTTGACCCACTTTGTGATCTGTGTACCCGGCTAATTCCTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCAACCCTGGGCCCATCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCTTTCAAGC RR: ACCCTGGTTTGTTAACAAAGTAGAACTGGGTGAAACACTAGACACATGGGCCGATTAAGGACTCGTGACTAAAGGTTGGGACGACGGAACCGGAACCGGTTGGGACCCGGGTAGACCCCTTAGACAGAGAGGGGACCTCGAAGGGAAAGTTCG F2: 3 ACCCTG 2 Unidirectional alignment (log-probability: -33.2) CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCgtCCC-aGGCCCAcCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCCAACCCTGGGCCCATCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT Template switch alignment (log-probability: -22.2) CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCC|GTCCCA|GGCCCAcCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT CTGAGCACTGATTTCCAACCCTGCTGCCTTGGCCTTGGCC|GTCCCA|GGCCCATCTGGGGAATCTGTCTCTCCCCTGGAGCTTCCCT ========== Event 1472 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAATTGGAATGCTGCCACT---------GTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGT Chimp: GGAAATTGGAATGCTGCCACT---------GTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGT ↓ 1 4 3 2 Gorilla: GGAAATTGGAATGCTGCCACTTTCAGGCAATTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGT ↑ 1 4 3 2 Human: GGAAATTGGAATGCTGCCACT---------GTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGT Cluster: [ ] Orangutan: GGAAGTTGGAATGTTGCCACT---------GTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGT Human > Gorilla --------------- chr18:21146657-21146666 Template switch process: F1: L TTGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT 1 F3: 4 TCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTC R RF: TTGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACTGTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTA RR: AACGTTTGGCAACCAAAAACCCTTTAACCTTACGACGGTGACAGACTTAACGGACTTATTTCTTTTCATCCAGGACATTAAT F2: 3 TAACGGACTT 2 Unidirectional alignment (log-probability: -34.9) TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACTttcaggcaatTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTc TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT---------GTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTA Template switch alignment (log-probability: -22.5) TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT|TTCAGGCAAT|TCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTc TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT|TTCAGGCAAT|TCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTA Chimp > Gorilla --------------- chr18:21146657-21146666 Template switch process: F1: L TTGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT 1 F3: 4 TCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTC R RF: TTGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACTGTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTA RR: AACGTTTGGCAACCAAAAACCCTTTAACCTTACGACGGTGACAGACTTAACGGACTTATTTCTTTTCATCCAGGACATTAAT F2: 3 TAACGGACTT 2 Unidirectional alignment (log-probability: -34.9) TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACTttcaggcaatTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTc TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT---------GTCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTA Template switch alignment (log-probability: -22.5) TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT|TTCAGGCAAT|TCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTc TGCAAACCGTTGGTTTTTGGGAAATTGGAATGCTGCCACT|TTCAGGCAAT|TCTGAATTGCCTGAATAAAGAAAAGTAGGTCCTGTAATTA ========== Event 1473 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATAGTGGTAAGTAGGCATTTATCTATCCAGAGATTAACTG---AATGCTAGATAGATACAGCATAGAGAGGTGCTA ↓ 1 3 2 4 ↑ 31 4 2 Chimp: ATAGTGGTAAGTAGGCATTTAG-CATTCA-------GTTA---ATCTCTGGATAGATACAGCATAGAGAGGTGCTA Gorilla: ATAATGGTAAGTAGGCATTTAG-CATTCA-------GTTAATCATCTCTGGATAGATACAGCATAGAGAGGTGCTA Human: ATAGTGGTAAGTAGGCATTTATCTATCCAGAGATTAACTG---AATGCTAGATAGATACAGCATAGAGAGGTGCTA Cluster: [ ] Orangutan: ATAGTGGTAAGTAGGCATTTAG-CATTCA-------GTTA---ATCTCTGGATAGATACAGCATAGAGAGGTGCTA Chimp > Human ------------- chr18:56211405-56211430 Template switch process: F1: L TAACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTA 1 F3: 4 GATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG R RF: TAACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTAGCATTCAGTTAATCTCTGGATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG RR: ATTGGTCAATGGACCGTACGTATCACCATTCATCCGTAAATCGTAAGTCAATTAGAGACCTATCTATGTCGTATCTCTCCACGATGGCATAAGTAAGCC F2: 3 ATCGTAAGTCAATTAGAGACCTATCT 2 Unidirectional alignment (log-probability: -56.5) AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTT------------ATCTatccagagattaactgaatgCTaGATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTAGCATTCAGTTAATCT--------------------CTGGATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG Template switch alignment (log-probability: -18.5) AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTA|TCTATCCAGAGATTAACTGAATGCTA|GATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTA|TCTATCCAGAGATTAACTGAATGCTA|GATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG Human > Chimp ------------- chr18:56982550-56982567 Template switch process: F1: L TAACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTA 1 F3: 4 GATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG R RF: TAACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTATCTATCCAGAGATTAACTGAATGCTAGATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG RR: ATTGGTCAATGGACCGTACGTATCACCATTCATCCGTAAATAGATAGGTCTCTAATTGACTTACGATCTATCTATGTCGTATCTCTCCACGATGGCATAAGTAAGCC F2: 3 GTCTCTAATTGACTTACG 2 Unidirectional alignment (log-probability: -45.5) AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTagcattcagttaATCT--------------------CTgGATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTT------------ATCTATCCAGAGATTAACTGAATGCTAGATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG Template switch alignment (log-probability: -17.5) AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTA|GCATTCAGTTAATCTCTG|GATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG AACCAGTTACCTGGCATGCATAGTGGTAAGTAGGCATTTA|GCATTCAGTTAATCTCTG|GATAGATACAGCATAGAGAGGTGCTACCGTATTCATTCGG ========== Event 1474 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CACTCATTTTCAAACTTCAGTCCACTAAGCAAG-TTTGCATTATGTCAGTTTGTCTCTTTATATCCTCTGCTGTATTTACATCAGCTTTATCTAGGTCCAAGAGCAGTATTACTTAGATTAACAACATTAACAAAT--AA--------------------AGTAAG-TGTTTGCATTATGTTCACCCCTAA ↓ 3 2 4 1 Chimp: CACTCATTTTCAAACTTCAGTCCACTAAGCAAG-TTTGCATTATGTCAGTTTGTCTCTTTATATCCTCTGCTGTATTTACATCAGCTTTATCTAGGTCCAACAGCAGTATTACTTAGATTAACAACATTAACAAAT--AA----------AGTGTGGACAAGTAAG-TGTCTGCATTATGTTCACCCCTAA Gorilla: CACTCATTTTCAAACTTCAGTCCACTAAGCAAG-TTTGCATTATGTCAGTTTGTCTCTTTATATCCTCTGCTGTATTTACATCAGCTTTATCTAGGTCCAACAGCAGTATTACTTAGATTAACAACATTAACAAAT----AGTGTGGACA----------AGGAAG-TGTCTGCATTATGTTCACCCCTAA Human: CACTCATTTTCAAACTTCAGTCCACTAAGCAAG-TTTGCATTATGTCAGTTTGTCTCTTTATATCCTCTGCTGTATTTACATCAGCTTTATCTAGGTCCAAGAGCAGTATTACTTAGATTAACAACATTAACAAAT--AA--------------------AGTAAG-TGTTTGCATTATGTTCACCCCTAA Cluster: [ ] Orangutan: CACTCATTTTCAAACTTCAGTCCACTGAGCAAGTTTTGCATTATGTCAATTTGTCTCTTTATATCCTCTGCTGTATTTACATCAGCTTTATCTAGATCCAAGATCttttttttCCCCCTCCCCAACATTAACGAATAA--AGTGTGGACA----------AGGGAGAGGGCTGCATTATGTTCACCC-CAA Human > Chimp ------------- chr18:54012640-54012645 Template switch process: F1: L CCAACAGCAGTATTACTTAGATTAACAACATTAACAAATAAAGT 1 F3: 4 AAGTAAGTGTCTGCATTATGTTCACCCCTAACATTTAAATTTTCATGCAGA R RF: GTCCACTAAGCAAGTTTGCATTATGTCAGTTTGTCTCTTTATATCCTCTGCTGTATTTACATCAGCTTTATCTAGGTCCAAGAGCAGTATTACTTAGATTAACAACATTAACAAATAAAGTAAGTGTTTGCATTATGTTCACCCCTAACATTTAAATTTTCATGCAGA RR: CAGGTGATTCGTTCAAACGTAATACAGTCAAACAGAGAAATATAGGAGACGACATAAATGTAGTCGAAATAGATCCAGGTTCTCGTCATAATGAATCTAATTGTTGTAATTGTTTATTTCATTCACAAACGTAATACAAGTGGGGATTGTAAATTTAAAAGTACGTCT F2: 3 CAGGTG 2 Unidirectional alignment (log-probability: -37.4) cAGCAGTATTACTTAGATTAACAACATTAACAAATAaagtgtggacAAGTAAGTGTcTGCATTATGTTCACCCCTAACATTTAAAT GAGCAGTATTACTTAGATTAACAACATTAACAAATA----------AAGTAAGTGTTTGCATTATGTTCACCCCTAACATTTAAAT Template switch alignment (log-probability: -28.3) cAGCAGTATTACTTAGATTAACAACATTAACAAATAAAGT|GTGGAC|AAGTAAGTGTcTGCATTATGTTCACCCCTAACATTTAAAT GAGCAGTATTACTTAGATTAACAACATTAACAAATAAAGT|GTGGAC|AAGTAAGTGTTTGCATTATGTTCACCCCTAACATTTAAAT ========== Event 1475 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AATGGCATCTCTTCTCTgaat---ggaccttataatagcactgtcagccaccttgggaagatgc Chimp: AATGGCATCTCTTCTCTGAATGACAGTGCTTATAATAGCACTGTCAGCCACCTTGGGAAGATGC ↑ 1 4 3 2 Gorilla: AATGGCATCTCTTCTCTGAAT---GGACCTTATAATAGCACTGTCAGCCACCTTGGGAAGATGC Human: AATGGCATCTCTTCTCTgaat---ggaccttataatagcactgtcagccaccttgggaagatgc Cluster: [ ] Orangutan: AATGGCATCTCTTCTCTGAAT---GGACCTTATAATAGCCCTGTCAGCCACCTTGGGAAGACAC Gorilla > Chimp --------------- chr18:53806491-53806496 Template switch process: F1: L TAGTAAGGGCCACCAATGAAAATGGCATCTCTTCTCTGAATG 1 F3: 4 CTTATAATAGCACTGTCAGCCACCTTGGGAAGATGCTAAA R RF: TAGTAAGGGCCACCAATGAAAATGGCATCTCTTCTCTGAATGGACCTTATAATAGCACTGTCAGCCACCTTGGGAAGATGCTTAA RR: ATCATTCCCGGTGGTTACTTTTACCGTAGAGAAGAGACTTACCTGGAATATTATCGTGACAGTCGGTGGAACCCTTCTACGAATT F2: 3 GTGACA 2 Unidirectional alignment (log-probability: -31.8) GTAAGGGCCACCAATGAAAATGGCATCTCTTCTCTGAATGacaGtgCTTATAATAGCACTGTCAGCCACCTTGGGAAGATGCTaAA GTAAGGGCCACCAATGAAAATGGCATCTCTTCTCTGAATG---GACCTTATAATAGCACTGTCAGCCACCTTGGGAAGATGCTTAA Template switch alignment (log-probability: -22) GTAAGGGCCACCAATGAAAATGGCATCTCTTCTCTGAATG|ACAGTG|CTTATAATAGCACTGTCAGCCACCTTGGGAAGATGCTaAA GTAAGGGCCACCAATGAAAATGGCATCTCTTCTCTGAATG|ACAGTG|CTTATAATAGCACTGTCAGCCACCTTGGGAAGATGCTTAA ========== Event 1476 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CATTCTCTCCCTCTAACTTGATTC---------------------------------TA---------------------------------GTATCCTAGAAATAACTAGGATACTAGATTCCAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTA Chimp: CATTCTCTCCCTCTAACTTGATTC---------------------------------TA---------------------------------GTATCCTAGAAATAACTAGGATACTAGATTCCAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTA ↑ 4 3 2 1 Gorilla: CATTCTCTCCCTCTAACTTGATTC---------------------------------TA------------------------------------------------------------------GTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTA ↓ 4 3 2 1 Human: CATTCTCTCCCTCTAACTTGATTC---------------------------------TA---------------------------------GTATCCTAGAAATAACTAGGATACTAGATTCCAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTA Cluster: [ ] Orangutan: CATTCTCTCCCTCTGacttgattctagtatcctagaaataactaggatactagattccagtatcctagaaataactaggatactagattcca---------------------------------gtatcctagaaataaAGGCCTTTCCCTTATTTTTA Gorilla > Human --------------- chr18:53492460-53492470 Template switch process: F1: L CCACTGCTATTGGCTCATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAA 1 F3: 4 GATTCCAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTAGTGAA R RF: CCACTGCTATTGGCTCATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTAGTCAA RR: GGTGACGATAACCGAGTAAGAGAGGGAGATTGAACTAAGATCATAGGATCTTTATTTCCGGAGAGGGAATAAAAATCAGTT F2: 3 ATCATAGGATC 2 Unidirectional alignment (log-probability: -63.8) ATTCTCTCCCTCTAACTTGATTCTagtatcctagaaataactaggatactagattccAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT ATTCTCTCCCTCTAACTTGATTCT---------------------------------AGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT Template switch alignment (log-probability: -28.7) ATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAA|CTAGGATACTA|GATTCcAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT ATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAA|CTAGGATACTA|GATTCTAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT Gorilla > Chimp --------------- chr18:54252955-54252965 Template switch process: F1: L CCACTGCTATTGGCTCATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAA 1 F3: 4 GATTCCAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTAGTCAA R RF: CCACTGCTATTGGCTCATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTTTAGTCAA RR: GGTGACGATAACCGAGTAAGAGAGGGAGATTGAACTAAGATCATAGGATCTTTATTTCCGGAGAGGGAATAAAAATCAGTT F2: 3 ATCATAGGATC 2 Unidirectional alignment (log-probability: -58.3) ATTCTCTCCCTCTAACTTGATTCTagtatcctagaaataactaggatactagattccAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT ATTCTCTCCCTCTAACTTGATTCT---------------------------------AGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT Template switch alignment (log-probability: -23.2) ATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAA|CTAGGATACTA|GATTCcAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT ATTCTCTCCCTCTAACTTGATTCTAGTATCCTAGAAATAA|CTAGGATACTA|GATTCTAGTATCCTAGAAATAAAGGCCTCTCCCTTATTTT ========== Event 1477 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: acaaccccctcatATCTTCCTGAGTATAATAAAATA---------------GTTTTGGGGTGGATTTTTACAACAGAGA Chimp: ACAACCCCCTCATATCTTCCTGAGTATAATAAGATA---------------GTTTTGGGGTGGATTTTTACCACAGAGA ↓ 3 2 1 4 Gorilla: acaaccccctcatATCTTCCTGAGTATAATAAGATA-----------------CTCAGGGTGGATTTTTACAACAGAGA ↑ 3 2 1 4 Human: acaaccccctcatATCTTCCTGAGTATAATAAAATA---------------GTTTTGGGGTGGATTTTTACAACAGAGA Cluster: [ ] Orangutan: acaaccccctcatATCTTCCTGAGTATAAGAAGATAATTCCCTCTGGTGAA--ATTGGGGTGGATTTTTACAACAGAAA Human > Gorilla --------------- chr18:54617158-54617162 Template switch process: F1: L TTCCAAAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATA 1 F3: 4 GGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG R RF: TTCCAAAGAACAACCCCCTCATATCTTCCTGAGTATAATAAAATAGTTTTGGGGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG RR: AAGGTTTCTTGTTGGGGGAGTATAGAAGGACTCATATTATTTTATCAAAACCCCACCTAAAAATGTTGTCTCTATATCGGAGGGGGTTTTC F2: 3 GACTC 2 Unidirectional alignment (log-probability: -31.2) AAGAACAACCCCCTCATATCTTCCTGAGTATAATAA---------GatactcaGGGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAAATAGTTTTG-------GGGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG Template switch alignment (log-probability: -22) AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAgATA|CTCAG|GGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAAATA|CTCAG|GGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG Chimp > Gorilla --------------- chr18:54617158-54617162 Template switch process: F1: L AAAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATA 1 F3: 4 GGTGGATTTTTACAACAGAGATATAGCCTCCCCCAAAAG R RF: AAAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATAGTTTTGGGGTGGATTTTTACCACAGAGATATAGCCTCCCCCAAAAG RR: TTTCTTGTTGGGGGAGTATAGAAGGACTCATATTATTCTATCAAAACCCCACCTAAAAATGGTGTCTCTATATCGGAGGGGGTTTTC F2: 3 GACTC 2 Unidirectional alignment (log-probability: -32.2) AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATA------ctcaGGGTGGATTTTTACaACAGAGATATAGCCTCCCCCAAAAG AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATAGTTTTG----GGGTGGATTTTTACCACAGAGATATAGCCTCCCCCAAAAG Template switch alignment (log-probability: -21.8) AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATA|CTCAG|GGTGGATTTTTACaACAGAGATATAGCCTCCCCCAAAAG AAGAACAACCCCCTCATATCTTCCTGAGTATAATAAGATA|CTCAG|GGTGGATTTTTACCACAGAGATATAGCCTCCCCCAAAAG ========== Event 1478 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGATGACAGCCAACCTGTCATGATCAATGGATCATCTGTTTATCTTTTTATTG Chimp: AGGATGACAGCCAACCTGTCATGATCAATGGATCATCTGTTTATCTTTTTATTG ↑ 3 1 4 2 Gorilla: AGGATGACAGCCAACCTGTCA-------TTGATCATCTGTTTATCTTTTTATTG ↓ 3 1 4 2 Human: AGGATGACAGCCAACCTGTCATGATCAATGGATCATCTGTTTATCTTTTTATTG Cluster: [ ] Orangutan: AGGATGACAGCCAACCTATCA-------TTGATCATCCCTTTATCTTTTTATTG Gorilla > Human --------------- chr18:52245267-52245274 Template switch process: F1: L GGGAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCAT 1 F3: 4 GATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG R RF: GGGAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCATTGATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG RR: CCCTTACACCCTCCACAGGGTCCTACTGTCGGTTGGACAGTAACTAGTAGACAAATAGAAAAATAACAATAGATTTGACAAAC F2: 3 GTAACTAG 2 Unidirectional alignment (log-probability: -26.5) GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCatgatcaATgGATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTC-------ATTGATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG Template switch alignment (log-probability: -16.8) GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCAT|GATCAATG|GATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCAT|GATCAATG|GATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG Gorilla > Chimp --------------- chr18:52995296-52995303 Template switch process: F1: L GGGAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCAT 1 F3: 4 GATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG R RF: GGGAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCATTGATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG RR: CCCTTACACCCTCCACAGGGTCCTACTGTCGGTTGGACAGTAACTAGTAGACAAATAGAAAAATAACAATAGATTTGACAAAC F2: 3 GTAACTAG 2 Unidirectional alignment (log-probability: -26.5) GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCatgatcaATgGATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTC-------ATTGATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG Template switch alignment (log-probability: -16.8) GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCAT|GATCAATG|GATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG GAATGTGGGAGGTGTCCCAGGATGACAGCCAACCTGTCAT|GATCAATG|GATCATCTGTTTATCTTTTTATTGTTATCTAAACTGTTTG ========== Event 1479 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TGTTTTCTTCCGGTTAATATCAAGCACAAGTGTCTGAATCATCCTCATGCAGTTATTCTCTCTGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCTGGCGTCTGTCTGTTTTATGTGATTCCAG ↓ 3 2 1 4 Chimp: TGTTTTCTTCCGGTTAATATCAAGCACAAGTGTCTGAATCATCCTCATGCAGTTATTCTCTCTGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTC--TCTTGAGTCTGTTTTATGTGATTCCAG Gorilla: TGTTTTCTTCCGGTTAATATCAAGCATAAGTGTCTGAATCATCCTCATGCAGTTATTCTCTCTGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTC--TCTTGAGTCTGTTTTACGTGATTCCAG Human: TGTTTTCTTCCGGTTAATATCAAGCACAAGTGTCTGAATCATCCTCATGCAGTTATTCTCTCTGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCTGGCGTCTGTCTGTTTTATGTGATTCCAG Cluster: [ ] Orangutan: TGTTTTCTTCCGGTTAATATCAAGCATAAGTGTCTGAATCATCCTCATGCAGTTATTC-TTCCGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTC--TCTTGAGTCTGTTTTATGTGATTCCAG Human > Chimp ------------- chr18:52351638-52351642 Template switch process: F1: L TGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCT 1 F3: 4 GTCTGTTTTATGTGATTCCAGATATCCTACTGACTTTTTT R RF: TCAAGCACAAGTGTCTGAATCATCCTCATGCAGTTATTCTCTCTGAGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCTGGCGTCTGTCTGTTTTATGTGATTCCAGATATCCTACTGACTTTTTT RR: AGTTCGTGTTCACAGACTTAGTAGGAGTACGTCAATAAGAGAGACTCACAGTCTATAATCTCCTAAAATTACGTAGAGAGGAAGACCGCAGACAGACAAAATACACTAAGGTCTATAGGATGACTGAAAAAA F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -25.7) AGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTC-----TCTtgaGTCTGTTTTATGTGATTCCAGATATCCTACTGACTTTTTT AGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCTGGCGTCT---GTCTGTTTTATGTGATTCCAGATATCCTACTGACTTTTTT Template switch alignment (log-probability: -15.9) AGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCT|CTTGA|GTCTGTTTTATGTGATTCCAGATATCCTACTGACTTTTTT AGTGTCAGATATTAGAGGATTTTAATGCATCTCTCCTTCT|CTTGA|GTCTGTTTTATGTGATTCCAGATATCCTACTGACTTTTTT ========== Event 1480 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATTCCAACTCCTGTATTTGGCTTATTCTTTTAGGA---CACGTAATGTACCCATTTAGAAAATT Chimp: AAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGA---CACGTAATGTACCCATTTAGAAAATT ↓ 3 2 1 4 Gorilla: AAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGAATAAGCCAAATGTACCCATTTAGAAAATT ↑ 3 2 1 4 Human: AAATTCCAACTCCTGTATTTGGCTTATTCTTTTAGGA---CACGTAATGTACCCATTTAGAAAATT Cluster: [ ] Orangutan: AAATTCCAACTCTTGTATGTGGCTTATTCTTTTAGGA---CACATAATGTACCCATTTAGAAAATT Human > Gorilla --------------- chr18:52667754-52667761 Template switch process: F1: L GATTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGA 1 F3: 4 AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC R RF: GGTTAAATTCCAACTCCTGTATTTGGCTTATTCTTTTAGGACACGTAATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC RR: CCAATTTAAGGTTGAGGACATAAACCGAATAAGAAAATCCTGTGCATTACATGGGTAAATCTTTTAAGATCTCTTCTTGTTATGAG F2: 3 ACCGAATA 2 Unidirectional alignment (log-probability: -40.5) aTTAAATTCCAACTCtTGTATTTGGCTTATTCTTTTAGGAataagcCA---AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC GTTAAATTCCAACTCCTGTATTTGGCTTATTCTTTTAGGA------CACGTAATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC Template switch alignment (log-probability: -27.8) aTTAAATTCCAACTCtTGTATTTGGCTTATTCTTTTAGGA|ATAAGCCA|AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC GTTAAATTCCAACTCCTGTATTTGGCTTATTCTTTTAGGA|ATAAGCCA|AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC Chimp > Gorilla --------------- chr18:52667754-52667761 Template switch process: F1: L GATTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGA 1 F3: 4 AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC R RF: GGTTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGACACGTAATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC RR: CCAATTTAAGGTTGAGAACATAAACCGAATAAGAAAATCCTGTGCATTACATGGGTAAATCTTTTAAGATCTCTTCTTGTTATGAG F2: 3 ACCGAATA 2 Unidirectional alignment (log-probability: -35) aTTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGAataagcCA---AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC GTTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGA------CACGTAATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC Template switch alignment (log-probability: -22.3) aTTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGA|ATAAGCCA|AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC GTTAAATTCCAACTCTTGTATTTGGCTTATTCTTTTAGGA|ATAAGCCA|AATGTACCCATTTAGAAAATTCTAGAGAAGAACAATACTC ========== Event 1481 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAACAGGAGGGTAGCCCCTCTTACCAATGTAAGAGTAGTACTTTGTTTTTTCAAC Chimp: ATAACAGGAGGGTAGCCCCTCTTACCAATGTAAGAGTAGTACTTTGTTTTTTCAAC ↑ 3 1 24 Gorilla: ATAACAGGAGGTTAGCCCCTCTTA------CATTGGTAGTACTTTGTTTTTTCAAC ↓ 3 1 24 Human: ATAACAGGAGGGTAGCCCCTCTTACCAATGTAAGAGTAGTACTTTGTTTTTTCAAC Cluster: [ ] Orangutan: ATAACAGGAGGTTAGCCCCTCTTA------CGTTGGTAGTACTTTGTTTTTTCAAC Gorilla > Human --------------- chr18:51379067-51379076 Template switch process: F1: L GCATGCTAAATTCCCCCATAACAGGAGGGTAGCCCCTCTTAC 1 F3: 4 GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT R RF: GCATGCTAAATTCCCCCATAACAGGAGGTTAGCCCCTCTTACATTGGTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT RR: CGTACGATTTAAGGGGGTATTGTCCTCCAATCGGGGAGAATGTAACCATCATGAAACAAAAAAGTTGAAATAGTGTGTGGTTATAA F2: 3 AGAATGTAAC 2 Unidirectional alignment (log-probability: -39.3) ATGCTAAATTCCCCCATAACAGGAGGgTAGCCCCTCTTACcaatgtaagA---GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT ATGCTAAATTCCCCCATAACAGGAGGTTAGCCCCTCTTAC---------ATTGGTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT Template switch alignment (log-probability: -22.5) ATGCTAAATTCCCCCATAACAGGAGGgTAGCCCCTCTTAC|CAATGTAAGA|GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT ATGCTAAATTCCCCCATAACAGGAGGTTAGCCCCTCTTAC|CAATGTAAGA|GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT Gorilla > Chimp --------------- chr18:52110953-52110962 Template switch process: F1: L GCATGCTAAATTCCCCCATAACAGGAGGGTAGCCCCTCTTAC 1 F3: 4 GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT R RF: GCATGCTAAATTCCCCCATAACAGGAGGTTAGCCCCTCTTACATTGGTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT RR: CGTACGATTTAAGGGGGTATTGTCCTCCAATCGGGGAGAATGTAACCATCATGAAACAAAAAAGTTGAAATAGTGTGTGGTTATAA F2: 3 AGAATGTAAC 2 Unidirectional alignment (log-probability: -39.3) ATGCTAAATTCCCCCATAACAGGAGGgTAGCCCCTCTTACcaatgtaagA---GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT ATGCTAAATTCCCCCATAACAGGAGGTTAGCCCCTCTTAC---------ATTGGTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT Template switch alignment (log-probability: -22.5) ATGCTAAATTCCCCCATAACAGGAGGgTAGCCCCTCTTAC|CAATGTAAGA|GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT ATGCTAAATTCCCCCATAACAGGAGGTTAGCCCCTCTTAC|CAATGTAAGA|GTAGTACTTTGTTTTTTCAACTTTATCACACACCAATATT ========== Event 1482 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGTATAGGTCAACATATAGGTAGAACTGATATAACCATGCAATCAATC----------------------------------------------------------------CTATTTATCCTCTCCTATTAGTGGAATAATAGTTT ↓ 4 3 1 2 Chimp: TAGTATAGGTCAACATATAGGTAGAACTGATATAACCATGCAATCAATCCTATTTAGGAGAGGATAAATAGGATTGATTGCATGGTAGAACTGATATAACCATGCAATCAATCCTATTTATCCTCTCCTATTAGTGGAATAATAGTTT ↑ 4 3 1 2 Gorilla: TAGTATAGGTCAACATATAGATATAACTGATATAACCATGCAATCAATC----------------------------------------------------------------CTATTTATCCTCTCCTATTAGTGGAATAATAGTTT Human: TAGTATAGGTCAACATATAGGTAGAACTGATATAACCATGCAATCAATC----------------------------------------------------------------CTATTTATCCTCTCCTATTAGTGGAATAATAGTTT Cluster: [ ] Orangutan: TAATATAGGTCAACATATATGTAGAACTGATATAACCATGCAATCAATC----------------------------------------------------------------CTATTTATACTCTCCTATTAGTGGAGTAATAATTT Human > Chimp ------------- chr18:27641968-27641994 Template switch process: F1: L GTCAACATATAGGTAGAACTGATATAACCATGCAATCAATCCTATTTA 1 F3: 4 GGTAGAACTGATATAACCATGCAATCAATCCTATTTATCCTCTCCTATTAGTGGAATAATAGTTTTAAAC R RF: GTCAACATATAGGTAGAACTGATATAACCATGCAATCAATCCTATTTATCCTCTCCTATTAGTGGAATAATAGTTTTAAAC RR: CAGTTGTATATCCATCTTGACTATATTGGTACGTTAGTTAGGATAAATAGGAGAGGATAATCACCTTATTATCAAAATTTG F2: 3 TACGTTAGTTAGGATAAATAGGAGAGG 2 Unidirectional alignment (log-probability: -103) ATAggtagaactgatataaccatgcaatcaatcctatttaggagaggataaataggattgattgcatGGTAGAACTGATATAACCATGCAATCAATCCTATTTATCC ATA----------------------------------------------------------------GGTAGAACTGATATAACCATGCAATCAATCCTATTTATCC Template switch alignment (log-probability: -19.2) ATAGGTAGAACTGATATAACCATGCAATCAATCCTATTTA|GGAGAGGATAAATAGGATTGATTGCAT|GGTAGAACTGATATAACCATGCAATCAATCCTATTTATCC ATAGGTAGAACTGATATAACCATGCAATCAATCCTATTTA|GGAGAGGATAAATAGGATTGATTGCAT|GGTAGAACTGATATAACCATGCAATCAATCCTATTTATCC Gorilla > Chimp --------------- chr18:27641968-27641996 Template switch process: F1: L GTCAACATATAGGTAGAACTGATATAACCATGCAATCAATCCTATTTA 1 F3: 4 TAGAACTGATATAACCATGCAATCAATCCTATTTATCCTCTCCTATTAGTGGAATAATAGTTTTAAAC R RF: GTCAACATATAGATATAACTGATATAACCATGCAATCAATCCTATTTATCCTCTCCTATTAGTGGAATAATAGTTTTAAAC RR: CAGTTGTATATCTATATTGACTATATTGGTACGTTAGTTAGGATAAATAGGAGAGGATAATCACCTTATTATCAAAATTTG F2: 3 GGTACGTTAGTTAGGATAAATAGGAGAGG 2 Unidirectional alignment (log-probability: -113) ATAggtagaactGATATaaccatgcaatcaatcctatttaggagaggataaataggattgattgcatggtagAACTGATATAACCATGCAATCAATCCTATTTATCCTC ATA---------GATAT-------------------------------------------------------AACTGATATAACCATGCAATCAATCCTATTTATCCTC Template switch alignment (log-probability: -36.7) ATAGgTAgAACTGATATAACCATGCAATCAATCCTATTTA|GGAGAGGATAAATAGGATTGATTGCATGG|TAgAACTGATATAACCATGCAATCAATCCTATTTATCCTC ATAGATATAACTGATATAACCATGCAATCAATCCTATTTA|GGAGAGGATAAATAGGATTGATTGCATGG|TATAACTGATATAACCATGCAATCAATCCTATTTATCCTC ========== Event 1483 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: GGAATTAGGAAGCAACTAACCACAA--------------------------------------------------------------------------------ATTGTTATCAAGAATGTACTATTTTCCCCAATGTGAAAAGAAAACATAAAGAGTGAAAAATAATTTATG Chimp: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Gorilla: GGAATTAGGAAGCAACTAACCACAA----------------------------------------ATTGTACTATTTGTGGTACTATTTTCCCCAATGTGAAAAG----------------------------------------AAAACATAGAGAGTGAAAAATAATTTATG ↑ 3 2 4 Human: GGAATTAGGAAGCAACTAACCACAA--------------------------------------------------------------------------------ATTGTTATCAAGAATGTACTATTTTCCCCAATGTGAAAAGAAAACATAAAGAGTGAAAAATAATTTATG Cluster: [ ] Orangutan: GGAATTAGGAAGCAACTAACCACAAATTGTTATCAAGAATGTACTATTTTCCCCAATGTGAAAAG--------------------------------------------------------------------------------AAAACATAAAGAGTGAAAAATAATTTATG Human > Gorilla --------------- chr18:26979403-26979413 Template switch process: F1: L GAGAATATGTTGACAAGGAATTAGGAAGCAACTAACCACAAATTGT 1 F3: 4 TACTATTTTCCCCAATGTGAAAAGAAAACATAGAGAGTGAAAAATAATTTATGATTTCTCATCGATGTCTTCA R RF: GAGAATATGTTGACAAGGAATTAGGAAGCAACTAACCACAAATTGTTATCAAGAATGTACTATTTTCCCCAATGTGAAAAGAAAACATAAAGAGTGAAAAATAATTTATGATTTCTCATCGATGTCTTCA RR: CTCTTATACAACTGTTCCTTAATCCTTCGTTGATTGGTGTTTAACAATAGTTCTTACATGATAAAAGGGGTTACACTTTTCTTTTGTATTTCTCACTTTTTATTAAATACTAAAGAGTAGCTACAGAAGT F2: 3 GGTGTTTATCA 2 Unidirectional alignment (log-probability: -41.6) ATGTTGACAAGGAATTAGGAAGCAACTAACCACAAATTG----------TactatttgtgGTACTATTTTCCCCAATGTGAAAAGAAAACATAgAGAGTGA ATGTTGACAAGGAATTAGGAAGCAACTAACCACAAATTGTTATCAAGAAT----------GTACTATTTTCCCCAATGTGAAAAGAAAACATAAAGAGTGA Template switch alignment (log-probability: -29.1) ATGTTGACAAGGAATTAGGAAGCAACTAACCACAAATTGT|ACtATTTGTGG|TACTATTTTCCCCAATGTGAAAAGAAAACATAgAGAGTGA ATGTTGACAAGGAATTAGGAAGCAACTAACCACAAATTGT|ACAATTTGTGG|TACTATTTTCCCCAATGTGAAAAGAAAACATAAAGAGTGA ========== Event 1484 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCC------------AGAATGGGCAGCAGTTAGATAATAATACT ↓ 3 2 4 1 Chimp: TGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGAGTGCTACTCAGAATGGGCAGCAGTTAGATAATAATATT ↑ 3 2 4 1 Gorilla: CGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCC------------AGAATGGGGAGCAGTTAGATAATAATATT Human: TGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCC------------AGAATGGGCAGCAGTTAGATAATAATACT Cluster: [ ] Orangutan: CGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCC------------AGAATGGGGAGCAGTTAGATAATAATACT Human > Chimp ------------- chr18:50129840-50129847 Template switch process: F1: L ATGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGA 1 F3: 4 CAGAATGGGCAGCAGTTAGATAATAATATTTTACTGCTTTG R RF: ATGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGAATGGGCAGCAGTTAGATAATAATACTTTACTGCTTTG RR: TACGTAAACAAAGTAAAGACTCATCGTGAGGTCCTAAGAGGTCTTACCCGTCGTCAATCTATTATTATGAAATGACGAAAC F2: 3 TCATCGTG 2 Unidirectional alignment (log-probability: -34.2) ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCcagagtgctactCAGAATGGGCAGCAGTTAGATAATAATAtTTTACTGCTTT ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTC------------CAGAATGGGCAGCAGTTAGATAATAATACTTTACTGCTTT Template switch alignment (log-probability: -22.3) ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGA|GTGCTACT|CAGAATGGGCAGCAGTTAGATAATAATAtTTTACTGCTTT ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGA|GTGCTACT|CAGAATGGGCAGCAGTTAGATAATAATACTTTACTGCTTT Gorilla > Chimp --------------- chr18:50129840-50129847 Template switch process: F1: L ATGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGA 1 F3: 4 CAGAATGGGCAGCAGTTAGATAATAATATTTTACTGCTTTGTTTTTGGTT R RF: ACGCATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGAATGGGGAGCAGTTAGATAATAATATTTTACTGCTTTGTTTTTGGTT RR: TGCGTAAACAAAGTAAAGACTCATCGTGAGGTCCTAAGAGGTCTTACCCCTCGTCAATCTATTATTATAAAATGACGAAACAAAAACCAA F2: 3 TCATCGTG 2 Unidirectional alignment (log-probability: -39.3) ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCcagagtgctactCAGAATGGGcAGCAGTTAGATAATAATATTTTACTGCTTT ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTC------------CAGAATGGGGAGCAGTTAGATAATAATATTTTACTGCTTT Template switch alignment (log-probability: -28.1) ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGA|GTGCTACT|CAGAATGGGcAGCAGTTAGATAATAATATTTTACTGCTTT ATTTGTTTCATTTCTGAGTAGCACTCCAGGATTCTCCAGA|GTGCTACT|CAGAATGGGGAGCAGTTAGATAATAATATTTTACTGCTTT ========== Event 1485 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTcattttgttcattctagagccaat-----gaatgggatcttggaacaacggatgaaaa Chimp: GTCATTTTGTTCATTCTAGAGCCAATCCATTCATTGGATTCTTGGAACAACGGATGAAAA ↑ 3 1 2 4 Gorilla: GTCATTTTGTTCATTCTAGAGCCAAT-----GAATGGGATCTTGGAACAATGGATGAAAA Human: GTcattttgttcattctagagccaat-----gaatgggatcttggaacaacggatgaaaa Cluster: [ ] Orangutan: gtcattttgttcattctagagccaat-----gaatgggatcttggaacaacggatgaaaa Gorilla > Chimp --------------- chr18:49113075-49113087 Template switch process: F1: L GTGATCAGGATGTAAGTCATTTTGTTCATTCTAGAGCCAAT 1 F3: 4 TCTTGGAACAACGGATGAAAAGCCAGCAAAGAAAGGTAAA R RF: GTGATCAGGATGTAAGTCATTTTGTTCATTCTAGAGCCAATGAATGGGATCTTGGAACAATGGATGAAAAGCCAGCAAAGAAAGGTAAA RR: CACTAGTCCTACATTCAGTAAAACAAGTAAGATCTCGGTTACTTACCCTAGAACCTTGTTACCTACTTTTCGGTCGTTTCTTTCCATTT F2: 3 TAGGTTACTTACC 2 Unidirectional alignment (log-probability: -44.9) TGATCAGGATGTAAGTCATTTTGTTCATTCTAGAGCCAAtccattcatTGgAT----TCTTGGAACAAcGGATGAAAAGCCAGCAAAGAAAGGTAAA TGATCAGGATGTAAGTCATTTTGTTCATTCTAGAGCCAA---------TGAATGGGATCTTGGAACAATGGATGAAAAGCCAGCAAAGAAAGGTAAA Template switch alignment (log-probability: -28.4) TGATCAGGATGTAAGTCATTTTGTTCATTCTAGAGCCAAT|CCATTCATTGGaT|TCTTGGAACAAcGGATGAAAAGCCAGCAAAGAAAGGTAAA TGATCAGGATGTAAGTCATTTTGTTCATTCTAGAGCCAAT|CCATTCATTGGCT|TCTTGGAACAATGGATGAAAAGCCAGCAAAGAAAGGTAAA ========== Event 1486 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: gaaatatatgacaaacatctt-----------acttaaaagtaaaatattataaacatttacattaaaattataaactgaacagtggtgcctgctaacaatacttcttattccacattattttctgtacctctatatcctaatatttattcatgagaagacaataatatgtttg Chimp: GAAATATATGACAAACATCTT-----------ACTTAAAAGTAAAATATTATAAACATTTACATTAAAATTATAAACTGAACAGTGGTGCCTGCTAACAATACTTCTTATTCCACATTATTTTCTGTACCTCTATATCCTAATATTTATTCATGAGAAGACAATAATATGTTTG ↓ 4 1 3 2 Gorilla: GAAATATATGACAAACATCTTACTTACATGTTACTTAAAAGTAAAATATTATAAACATTTACATTAAAATTATAAACTGAACAGTGGTGCCTGCTAACAATACTTCTTATTCCACATTATTTTCTGTACCTCTATATCCTAATATTTATTCATGAGAAGACAATAATATGTTTG Human: gaaatatatgacaaacatctt-----------acttaaaagtaaaatattataaacatttacattaaaattataaactgaacagtggtgcctgctaacaatacttcttattccacattattttctgtacctctatatcctaatatttattcatgagaagacaataatatgtttg Cluster: [ ] Orangutan: gaaatatataacaaacatctt-----------acttaaaagtaaaatattataaacatttacataaaaattataaactgaacagtggtgcctgctaacgatacttcttattccacattatTTTCTGTACCTCTATATCCTAATATTTATTCATGAGAAGACAATAGTAtgttca Chimp > Gorilla --------------- chr18:48674485-48674488 Template switch process: F1: L TTGACAAAGGATATAATACAGAAATATATGACAAACATCTTACTTA 1 F3: 4 TTACTTAAAAGTAAAATATTATAAACATTTACATTAAAATTA R RF: TTGACAAAGGATATAATACAGAAATATATGACAAACATCTTACTTAAAAGTAAAATATTATAAACATTTACATTAAAATTATAAACTGAACAGTGGTGCCTGCTAACAATACTTCTTATTCCACATTATTTTCTGTACCTCTATATCCTAATATTTATTCATG RR: AACTGTTTCCTATATTATGTCTTTATATACTGTTTGTAGAATGAATTTTCATTTTATAATATTTGTAAATGTAATTTTAATATTTGACTTGTCACCACGGACGATTGTTATGAAGAATAAGGTGTAATAAAAGACATGGAGATATAGGATTATAAATAAGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -26.7) AAGGATATAATACAGAAATATATGACAAACATCttacttacatgTTACTTAAAAGTAAAATATTATAAACATTTACATTAAAAT AAGGATATAATACAGAAATATATGACAAACATC-----------TTACTTAAAAGTAAAATATTATAAACATTTACATTAAAAT Template switch alignment (log-probability: -16.4) AAGGATATAATACAGAAATATATGACAAACATCTTACTTA|CATG|TTACTTAAAAGTAAAATATTATAAACATTTACATTAAAAT AAGGATATAATACAGAAATATATGACAAACATCTTACTTA|CATG|TTACTTAAAAGTAAAATATTATAAACATTTACATTAAAAT ========== Event 1487 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCAGTGGGAATGGAAAATGAATGTTCCCTGAGAAAATCATAATATCTAAAG Chimp: AGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCATTCCCACTGGAAAATGAATGTTCCCTGAGAAAATCATAATATCTAAAG Gorilla: AGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCATTCCCACTGGAAAATGAATGTTCCCTAAGAAAATCATAATATCTAAAG ↓ 3 1 2 4 Human: AGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCAGTGGGAATGGAAAATGAATGTTCCCTGAGAAAATCATAATATCTAAAG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr18:33207522-33207548 Template switch process: F1: L AAAGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCA 1 F3: 4 AGAAAATCATAATATCTAAA R RF: AAAGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCATTCCCACTGGAAAATGAATGTTCCCTAAGAAAATCATAATATCTAAA RR: TTTCACTATTATACTAAAAGAGTCCCTTGTAAGTAAAAGGTAAGGGTGACCTTTTACTTACAAGGGATTCTTTTAGTATTATAGATTT F2: 3 GTCCCTTGTAAGTAAAAGGTAAGGGTG 2 Unidirectional alignment (log-probability: -34.4) AAGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCAgTgggAaTGGAAAATGAATGTTCCCTgAGAAAATCATAATATCTAAA AAGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCATTCCCACTGGAAAATGAATGTTCCCTAAGAAAATCATAATATCTAAA Template switch alignment (log-probability: -18.7) AAGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCA|GTGGGAATGGAAAATGAATGTTCCCTG|AGAAAATCATAATATCTAAA AAGTGATAATATGATTTTCTCAGGGAACATTCATTTTCCA|GTGGGAATGGAAAATGAATGTTCCCTG|AGAAAATCATAATATCTAAA ========== Event 1488 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATCTCCAGAAAAACTGGGATTCCATTTAGTTTACCTTCTGAGGT-AACTAAATGTTTACAAGCATAGAGACGTA ↓ 1 3 4 ↑ 1 3 4 2 Chimp: ATCTCCAGAAAAACTGGGATT---------CTTCCTCAGAAGGTAAACTAAATGTTTACAAGCATAGAGACGTA Gorilla: ATCTCCAGAAAAACTGGGATT---------CTTCCTCAGAAGGTAAACTAAATGTTTACAAGTATAGAGACGTA ↓ 1 3 4 2 Human: ATCTCCAGAAAAACTGGGATTCCATTTAGTTTACCTTCTGAGGT-AACTAAATGTTTACAAGCATAGAGACGTA Cluster: [ ] Orangutan: ATCTCCAGAAAAACTGGGATT---------CTTCCTCAGAAGGTAAACTAAATGTTTACAAGTATAGAGACGTA Chimp > Human ------------- chr18:47452520-47452540 Template switch process: F1: L ATCTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC 1 F3: 4 TAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC R RF: ATCTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTCTTCCTCAGAAGGTAAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC RR: TAGACGATTATTATCAACGTTAGAGGTCTTTTTGACCCTAAGAAGGAGTCTTCCATTTGATTTACAAATGTTCGTATCTCTGCATAAGATAAAATG F2: 3 GGAGTCTTCCATTTGATTTAC 2 Unidirectional alignment (log-probability: -52) CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTCcatttagtttaccttctgaggT-------------AACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTA CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC---------------------TTCCTCAGAAGGTAAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTA Template switch alignment (log-probability: -23.9) CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC|CATTTAGTTTACCTTCTGAGG|tAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTA CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC|CATTTAGTTTACCTTCTGAGG|AAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTA Human > Chimp ------------- chr18:48224558-48224571 Template switch process: F1: L ATCTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC 1 F3: 4 AACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC R RF: ATCTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTCCATTTAGTTTACCTTCTGAGGTAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC RR: TAGACGATTATTATCAACGTTAGAGGTCTTTTTGACCCTAAGGTAAATCAAATGGAAGACTCCATTGATTTACAAATGTTCGTATCTCTGCATAAGATAAAATG F2: 3 ATGGAAGACTCCTT 2 Unidirectional alignment (log-probability: -40.9) CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC---------------------TtcctcagaaggtaAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTCCATTTAGTTTACCTTCTGAGGT-------------AACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC Template switch alignment (log-probability: -23) CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC|TtCCTCAGAAGGTA|AACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC|TACCTCAGAAGGTA|AACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC Gorilla > Human --------------- chr18:47452520-47452540 Template switch process: F1: L ATCTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC 1 F3: 4 TAACTAAATGTTTACAAGCATAGAGACGTATTCTATTTTAC R RF: ATCTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTCTTCCTCAGAAGGTAAACTAAATGTTTACAAGTATAGAGACGTATTCTATTTTAC RR: TAGACGATTATTATCAACGTTAGAGGTCTTTTTGACCCTAAGAAGGAGTCTTCCATTTGATTTACAAATGTTCATATCTCTGCATAAGATAAAATG F2: 3 GGAGTCTTCCATTTGATTTAC 2 Unidirectional alignment (log-probability: -57) CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTCcatttagtttaccttctgaggT-------------AACTAAATGTTTACAAGcATAGAGACGTATTCTATTTTA CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC---------------------TTCCTCAGAAGGTAAACTAAATGTTTACAAGTATAGAGACGTATTCTATTTTA Template switch alignment (log-probability: -29.5) CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC|CATTTAGTTTACCTTCTGAGG|tAACTAAATGTTTACAAGcATAGAGACGTATTCTATTTTA CTGCTAATAATAGTTGCAATCTCCAGAAAAACTGGGATTC|CATTTAGTTTACCTTCTGAGG|AAACTAAATGTTTACAAGTATAGAGACGTATTCTATTTTA ========== Event 1489 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATATTGAAATCCCTCATCCGCTTCTATCTGTTTTCATTTTATCTTTGCCCTTTTTAG Chimp: CATATTGAAATCCCTCATCCGCTTCTATCTGTTTTCGTTTTATATTTGCCCTTTTTAG Gorilla: CATATTGAAATCCCTCATCCGCTTCTAGATAGAAGCGTTTTATCTTTGCCCTTTTTAG ↑ 3 1 2 4 Human: CATATTGAAATCCCTCATCCGCTTCTATCTGTTTTCATTTTATCTTTGCCCTTTTTAG Cluster: [ ] Orangutan: catattgaaatccctcatctgcttctatctgttttcctcttatctttgccctttttag Human > Gorilla --------------- chr18:48395979-48395988 Template switch process: F1: L GCCATTTTCCAAAACATATTGAAATCCCTCATCCGCTTCTA 1 F3: 4 TTTTATCTTTGCCCTTTTTAGTCTATTTTATCCCCTTTCT R RF: GCCGTTTCCCAAAACATATTGAAATCCCTCATCCGCTTCTATCTGTTTTCATTTTATCTTTGCCCTTTTTAGTCTATTTTATCCCCTTTCT RR: CGGCAAAGGGTTTTGTATAACTTTAGGGAGTAGGCGAAGATAGACAAAAGTAAAATAGAAACGGGAAAAATCAGATAAAATAGGGGAAAGA F2: 3 GCGAAGATAG 2 Unidirectional alignment (log-probability: -46.6) CCaTTTtCCAAAACATATTGAAATCCCTCATCCGCTTCTAgatagaagcg----------TTTTATCTTTGCCCTTTTTAGTCTATTTTATCCCCTTTCT CCGTTTCCCAAAACATATTGAAATCCCTCATCCGCTTCTA----------TCTGTTTTCATTTTATCTTTGCCCTTTTTAGTCTATTTTATCCCCTTTCT Template switch alignment (log-probability: -28) CCaTTTtCCAAAACATATTGAAATCCCTCATCCGCTTCTA|GATAGAAGCG|TTTTATCTTTGCCCTTTTTAGTCTATTTTATCCCCTTTCT CCGTTTCCCAAAACATATTGAAATCCCTCATCCGCTTCTA|GATAGAAGCG|TTTTATCTTTGCCCTTTTTAGTCTATTTTATCCCCTTTCT ========== Event 1490 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATGTTCTGACCATTTTTAAGTTAAACTCCCTCATTTTCAGTAGGGGTAGCCCCTGATAACATTCATTTTG Chimp: AAATGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTTAAGTTAAAC-TTCCCCTGATAACATTCATTTTG ↑ 3 2 1 4 Gorilla: AAACGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTTCAGTAGGGGTAGCCCCTGATAACATTCATTTTG Human: AAATGTTCTGACCATTTTTAAGTTAAACTCCCTCATTTTCAGTAGGGGTAGCCCCTGATAACATTCATTTTG Cluster: [ ] Orangutan: AAATGTTCTGACCACTTTTAAGTTAAACTTCCTCGTTTTCAATAGGGGTAGCCCCTGATAACATTCATTTTG Gorilla > Chimp --------------- chr18:47985726-47985736 Template switch process: F1: L TGAAATGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTT 1 F3: 4 CCCCTGATAACATTCATTTTGTATATACAATTAAGTATGA R RF: TGAAACGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTTCAGTAGGGGTAGCCCCTGATAACATTCATTTTGTATATACAATTAAGTATGA RR: ACTTTGCAAGACTGGTAAAAATTCAATTTGAAGGAGTAAAAGTCATCCCCATCGGGGACTATTGTAAGTAAAACATATATGTTAATTCATACT F2: 3 TTCAAATTGAA 2 Unidirectional alignment (log-probability: -42.2) GAAAtGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTTaAGttaaactT--------CCCCTGATAACATTCATTTTGTATATACAATTAAGTATGA GAAACGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTTCAG-------TAGGGGTAGCCCCTGATAACATTCATTTTGTATATACAATTAAGTATGA Template switch alignment (log-probability: -28.2) GAAAtGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTT|AAGTTaAACTT|CCCCTGATAACATTCATTTTGTATATACAATTAAGTATGA GAAACGTTCTGACCATTTTTAAGTTAAACTTCCTCATTTT|AAGTTTAACTT|CCCCTGATAACATTCATTTTGTATATACAATTAAGTATGA ========== Event 1491 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCACACTGAAGCAGGACTCAGTACCTCTTCTCACAACCCAGGAGGAAATCTCTAAAACCAAAATTTTAATTGTAATCATATTTTACAGTCTCATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAATTACCGACAAAATACTTAAAAGTTTTA ↑ 3 2 1 4 Chimp: ACCACACTGAAGCAGGACTCAGTACCTCTTCTCACAACCCAGGAGGAAATCTCTAAAACCAAAATTTTAATTGTAATCATATTTTACAGTCTCATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGA-ATACTAACAAAATACTTAAAAGTTTTA Gorilla: ACCACACTGAAGCAGGACTCAGTACCTCTTCTCACAACCCAGGAGGAAATCTCTAAAACCAAAATTTTAATTGTAATCATATTTTACAGTCTCATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAATTACTAACAAAATACTTAAAAGTTTTA Human: ACCACACTGAAGCAGGACTCAGTACCTCTTCTCACAACCCAGGAGGAAATCTCTAAAACCAAAATTTTAATTGTAATCATATTTTACAGTCTCATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAATTACCGACAAAATACTTAAAAGTTTTA Cluster: [ ] Orangutan: ACCACACTGAAGCAGGACTCAGTACCTCTTCTCAC-ACCCAGGAGGAAATCTCTAAAACCAAAATTTTAATTGTAATCATATTTTACAATCTCATTTGGAATATGGGAACAAGGGGAAGTTACATCACAGAATTACCAACAAAATACTTAAAAGTTTTA Chimp > Human ------------- chr18:46537318-46537322 Template switch process: F1: L CTCATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAAT 1 F3: 4 ACAAAATACTTAAAAGTTTTAACCAGATATGCCTGTTTT R RF: CAGTACCTCTTCTCACAACCCAGGAGGAAATCTCTAAAACCAAAATTTTAATTGTAATCATATTTTACAGTCTCATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAATACTAACAAAATACTTAAAAGTTTTAACCAGATATGCCTGTTTT RR: GTCATGGAGAAGAGTGTTGGGTCCTCCTTTAGAGATTTTGGTTTTAAAATTAACATTAGTATAAAATGTCAGAGTAAACCTTATACCCTTGTTCCCCTTCAATCTAGTGTCTTATGATTGTTTTATGAATTTTCAAAATTGGTCTATACGGACAAAA F2: 3 GCCAT 2 Unidirectional alignment (log-probability: -24.4) ATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAAtTACcgACAAAATACTTAAAAGTTTTAACCAGATATGCCTGTTTT ATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAA-TACTAACAAAATACTTAAAAGTTTTAACCAGATATGCCTGTTTT Template switch alignment (log-probability: -21.9) ATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAAT|TACcG|ACAAAATACTTAAAAGTTTTAACCAGATATGCCTGTTTT ATTTGGAATATGGGAACAAGGGGAAGTTAGATCACAGAAT|TACTG|ACAAAATACTTAAAAGTTTTAACCAGATATGCCTGTTTT ========== Event 1492 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: cagaaaacatatagcacacatta---------tctgaccacaatgtgctaaaacaaaaa Chimp: CAGAAAACATATAGCACACATTA---------TCTGACCACAATGTGCTAAAACAAAAA ↓ 31 4 2 Gorilla: CAGAAAACATATAGCACACATGGTCAGATAATTCTGACCACAATGTGCTAAAACAAAAA Human: cagaaaacatatagcacacatta---------tctgaccacaatgtgctaaaacaaaaa Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr18:66360792-66360802 Template switch process: F1: L ATACTGATAAAATTTAAAAGCAGAAAACATATAGCACACAT 1 F3: 4 TCTGACCACAATGTGCTAAAACAAAAAACTAGTAATGAAA R RF: ATACTGATAAAATTTAAAAGCAGAAAACATATAGCACACATTATCTGACCACAATGTGCTAAAACAAAAAACTAGTAATGAAA RR: TATGACTATTTTAAATTTTCGTCTTTTGTATATCGTGTGTAATAGACTGGTGTTACACGATTTTGTTTTTTGATCATTACTTT F2: 3 TAATAGACTGG 2 Unidirectional alignment (log-probability: -33.6) TACTGATAAAATTTAAAAGCAGAAAACATATAGCACACATggtcagaTAatTCTGACCACAATGTGCTAAAACAAAAAACTAGTAATGAAA TACTGATAAAATTTAAAAGCAGAAAACATATAGCACACAT-------TA--TCTGACCACAATGTGCTAAAACAAAAAACTAGTAATGAAA Template switch alignment (log-probability: -17.1) TACTGATAAAATTTAAAAGCAGAAAACATATAGCACACAT|GGTCAGATAAT|TCTGACCACAATGTGCTAAAACAAAAAACTAGTAATGAAA TACTGATAAAATTTAAAAGCAGAAAACATATAGCACACAT|GGTCAGATAAT|TCTGACCACAATGTGCTAAAACAAAAAACTAGTAATGAAA ========== Event 1493 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAGAAGAAATACATACCACA--------------------CTCATTAGAGTTACTTTATTGGATTTGAAACATAGACAAAT ↑ 1 3 2 4 Chimp: ATAGAAGAAATACATACCACA----------CAAGAAGTAACTCTAATGAGTTAGTTTATTAGATTTGAAACATAGACAAAT Gorilla: ATAGAAGAAATACATACCACACAAGAAGTAA----------CTCTAATGAGTTACTTTATTGGATTTGAAACATAGACAAAT Human: ATAGAAGAAATACATACCACA--------------------CTCATTAGAGTTACTTTATTGGATTTGAAACATAGACAAAT Cluster: [ ] Orangutan: ATAGAAGAAATA-------CACAAGAAGTAA----------CTCTAATGAGTTACTTTATTGGATTTGAAACATAGACAAAT Chimp > Human ------------- chr1:8523663-8523675 Template switch process: F1: L TTTTTCCCAGACAGGATAATATAGAAGAAATACATACCACAC 1 F3: 4 TTTATTGGATTTGAAACATAGACAAATTCGACTCTTAACAACAGAAT R RF: TTTTTCCCAGACAGGATAATATAGAAGAAATACATACCACACAAGAAGTAACTCTAATGAGTTAGTTTATTAGATTTGAAACATAGACAAATTCGACTCTTAACAACAGAAT RR: AAAAAGGGTCTGTCCTATTATATCTTCTTTATGTATGGTGTGTTCTTCATTGAGATTACTCAATCAAATAATCTAAACTTTGTATCTGTTTAAGCTGAGAATTGTTGTCTTA F2: 3 CATTGAGATTACT 2 Unidirectional alignment (log-probability: -41.2) TTTCCCAGACAGGATAATATAGAAGAAATACATACCACACtcattA---------------GAGTTAcTTTATTgGATTTGAAACATAGACAAATTCGACTCTTAACA TTTCCCAGACAGGATAATATAGAAGAAATACATACCACAC-----AAGAAGTAACTCTAATGAGTTAGTTTATTAGATTTGAAACATAGACAAATTCGACTCTTAACA Template switch alignment (log-probability: -23) TTTCCCAGACAGGATAATATAGAAGAAATACATACCACAC|TCATTAGAGTTAC|TTTATTgGATTTGAAACATAGACAAATTCGACTCTTAACA TTTCCCAGACAGGATAATATAGAAGAAATACATACCACAC|TCATTAGAGTTAC|TTTATTAGATTTGAAACATAGACAAATTCGACTCTTAACA ========== Event 1494 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ATTGCGCTATCATCAGTGTTTCACAGGGGCAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCC ↓ 1 4 3 2 Chimp: ATTGCGCTATCATCAGTGTTT----TGACCAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCC Gorilla: -------------------------------------------------------------------- Human: ATTGCGCTATCATCAGTGTTTCACAGGGGCAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCC Cluster: [ ] Orangutan: -------------------------------------------------------------------- Human > Chimp ------------- chr1:7784771-7784774 Template switch process: F1: L ATGGATGAAGGAAGACTATTATTGCGCTATCATCAGTGTTT 1 F3: 4 CAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCCC R RF: ATGGATGAAGGAAGAATATTATTGCGCTATCATCAGTGTTTCACAGGGGCAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCCC RR: TACCTACTTCCTTCTTATAATAACGCGATAGTAGTCACAAAGTGTCCCCGTTCAAGTTTTGAACCAGTTGACCGACAAGACCACACGGG F2: 3 CAGT 2 Unidirectional alignment (log-probability: -31.8) TGGATGAAGGAAGAcTATTATTGCGCTATCATCAGTGTTTtgaC-------CAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCCC TGGATGAAGGAAGAATATTATTGCGCTATCATCAGTGTTT---CACAGGGGCAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCCC Template switch alignment (log-probability: -21.8) TGGATGAAGGAAGAcTATTATTGCGCTATCATCAGTGTTT|TGAC|CAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCCC TGGATGAAGGAAGAATATTATTGCGCTATCATCAGTGTTT|TGAC|CAAGTTCAAAACTTGGTCAACTGGCTGTTCTGGTGTGCCC ========== Event 1495 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCTGGAGGACTTTGAATGTC----TGACTAA-AACTAAAATGTCTTTTAGT--------------------TTTAGTCTTTAAAGCT----------- Chimp: ttctggagGACTTTGAATGTC----TGACTAA-AACTAAAATGTCTTTTAGT--------------------TTTAGTCTTTAAAGCT----------- Gorilla: ttctggagGACTTTGAATGTCCTCCAGACTAAAAAACAGAATgtcttttagttttagtcttttagttttagttttagtctttaaagctaaaagtctttt ↓ 1 4 3 2 Human: TTCTGGAGGACTTTGAATGTC----TGACTAA-AACTAAAATGTCTTTTAGT--------------------TTTAGTCTTTAAAGCT----------- Cluster: [ ] Orangutan: TTCTGGAGGACTTTGAATGTC----TGAC-------------------------------------------ATCAGTCTTTAAAGCT----------- Gorilla > Human --------------- chr18:76470559-76470570 Template switch process: F1: L AAAGATAGATTGGAGCCAGCTTCTGGAGGACTTTGAATGTCT 1 F3: 4 AATGTCTTTTAGTTTTAGTC R RF: AAAGATAGATTGGAGACAGCTTCTGGAGGACTTTGAATGTCCTCCAGACTAAAAAACAGAATGTCTTTTAGTTTTAGTCTTTTAGTTTTAGTTTTAGTC RR: TTTCTATCTAACCTCTGTCGAAGACCTCCTGAAACTTACAGGAGGTCTGATTTTTTGTCTTACAGAAAATCAAAATCAGAAAATCAAAATCAAAATCAG F2: 3 AATCAAAATCAG 2 Unidirectional alignment (log-probability: -52.3) AGATAGATTGGAGcCAGCTTCTGGAGGACTTTGAATGT----CtGACTAAAActAA---AATGTCTTTTAGTTTTAGTC-------------------- AGATAGATTGGAGACAGCTTCTGGAGGACTTTGAATGTCCTCCAGACTAAAA--AACAGAATGTCTTTTAGTTTTAGTCTTTTAGTTTTAGTTTTAGTC Template switch alignment (log-probability: -27.8) AGATAGATTGGAGcCAGCTTCTGGAGGACTTTGAATGTCt|GACTAAAACTAA|AATGTCTTTTAGTTTTAGTC AGATAGATTGGAGACAGCTTCTGGAGGACTTTGAATGTCC|GACTAAAACTAA|AATGTCTTTTAGTTTTAGTC ========== Event 1496 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTAAGAAGCAGAAGAAATC-----CCATCT-------------------TTTCAGAAGCCATTCTGGATT----TAAAAGAATCCAGAATGGCTTCTGAAAAGGATTGAAATTTCTGGTCAATG Chimp: CTCTAAGAAGCAGAAGCAATC-----CCATCT-------------------TTTCAGAAGCCATTCTGGATT----TAAAAGAATCCAGAATGGCTTCTGAAAAGAATTAAAATTTCTGGTCAATG ↑ 3 4 1 2 Gorilla: CTCTAAGAAGCAGAAGCAATC----------T--------------------------------------TT--------TAAATCCAGAATGGCTTCTGAAAAGAATCAAAATTTCTGGTCAATG Human: CTCTAAGAAGCAGAAGAAATC-----CCATCT-------------------TTTCAGAAGCCATTCTGGATT----TAAAAGAATCCAGAATGGCTTCTGAAAAGGATTGAAATTTCTGGTCAATG Cluster: [ ] Orangutan: CTCTAAGAAGCAGAAGCAATCCAATC-----TTTTCAGAAGCCTTTCTGGA-------------------TTTAAA----AGAATCCAGAATGGCTTCTGAAAAGAATTAAAATTTCTGGTCAATG Gorilla > Chimp --------------- chr18:14213124-14213153 Template switch process: F1: L TCATAAGCTGAACCCCTCATCTCTAAGAAGCAGAAGCAATC--------CCA 1 F3: 4 AATCCAGAATGGCTTCTGAAAAGAATTAAAATTTCTGGTC R RF: TCATAAGCTGAACCCCTCATCTCTAAGAAGCAGAAGCAATCTTTTAAATCCAGAATGGCTTCTGAAAAGAATCAAAATTTCTGGTC RR: AGTATTCGACTTGGGGAGTAGAGATTCTTCGTCTTCGTTAGAAAATTTAGGTCTTACCGAAGACTTTTCTTAGTTTTAAAGACCAG F2: 3 GAAAATTTAGGTCTTACCGAAGACTTTTCT 2 Unidirectional alignment (log-probability: -72) AAGCTGAACCCCTCATCTCTAAGAAGCAGAAGCAATCccatcttttcagaagccattctggaTTTaAaagAATCCAGAATGGCTTCTGAAAAGAATtAAAATTTCTGGTC AAGCTGAACCCCTCATCTCTAAGAAGCAGAAGCAATC-------------------------TTTTA---AATCCAGAATGGCTTCTGAAAAGAATCAAAATTTCTGGTC Template switch alignment (log-probability: -35.3) AAGCTGAACCCCTCATCTCTAAGAAGCAGAAGCAATC--------CCA|TCTTTTCAGAAGCCATTCTGGATTTAAAAG|AATCCAGAATGGCTTCTGAAAAGAATtAAAATTTCTGGTC AAGCTGAACCCCTCATCTCTAAGAAGCAGAAGCAATCTTTTAAATCCA|TCTTTTCAGAAGCCATTCTGGATTTAAAAG|AATCCAGAATGGCTTCTGAAAAGAATCAAAATTTCTGGTC ========== Event 1497 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGTTGGGCCTGGGCAGGTAAAGCATGAAACCTAAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGCTAGGTCTCAAGTATAGACCCAGAGTCCTG ↑ 4 1 3 2 Chimp: TGGTTGGGCCTGGGCAGGTAA--------------AGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGCTAGGTTTCAAGTATAGACCCAGAGTCCTG Gorilla: TGGTTGGGCCTGGGCAGGTAA--------------AGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGCTAGGTCTCAAGTATAGACCCAGAGTCCTG Human: TGGTTGGGCCTGGGCAGGTAAAGCATGAAACCTAAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGCTAGGTCTCAAGTATAGACCCAGAGTCCTG Cluster: [ ] Orangutan: TGGTTGGGCCTGGGCAGGTAG--------------AGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGCTAGGTCTCAAGTATAGACCCAGAGTCCTG Chimp > Human ------------- chr18:42963467-42963474 Template switch process: F1: L CAGAATGGCAGAATGGCAGGTGGTTGGGCCTGGGCAGGTAAAGCA 1 F3: 4 AAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGC R RF: CAGAATGGCAGAATGGCAGGTGGTTGGGCCTGGGCAGGTAAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTTGCTAGGTTTCA RR: GTCTTACCGTCTTACCGTCCACCAACCCGGACCCGTCCATTTCGTTCTTTGGGTAGACATTTGTCTCGGGACAGGGGAACGATCCAAAGT F2: 3 TCCAAAGT 2 Unidirectional alignment (log-probability: -31.1) TGGCAGAATGGCAGGTGGTTGGGCCTGGGCAGGtaaagcatgaaaccTAAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTT TGGCAGAATGGCAGGTGGTTGGGCCTGGGCAGG--------------TAAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTT Template switch alignment (log-probability: -16.4) TGGCAGAATGGCAGGTGGTTGGGCCTGGGCAGGTAAAGCA|TGAAACCT|AAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTT TGGCAGAATGGCAGGTGGTTGGGCCTGGGCAGGTAAAGCA|TGAAACCT|AAAGCAAGAAACCCATCTGTAAACAGAGCCCTGTCCCCTT ========== Event 1498 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCACATGGACATTGGCCTGGAT----------ATTATGAACTGCAGCCAAGAGACCAACAGAAAACAAGA Chimp: AGCACATGGACATTGGCCTGGGT----------ATTGTGAACTGCAGCCAAGAGACCAACAGAAAACAAGA ↓ 4 3 2 1 Gorilla: AGCACATGGACATTGGCCTGGACTGCAGCCAACTGCATGAACTGCAGCCAAGAGACCAACAGAAAACAAGA Human: AGCACATGGACATTGGCCTGGAT----------ATTATGAACTGCAGCCAAGAGACCAACAGAAAACAAGA Cluster: [ ] Orangutan: AGCACATGGACATTGGCCTGGAT----------ATTATGAACTGCAGCCAAGAGACCAACAGAAAACAAGA Chimp > Gorilla --------------- chr18:43629275-43629279 Template switch process: F1: L GACACGGCCCCATCACGCTCAGCACATGGACATTGGCCTGG---------ACTGCAGCCAA 1 F3: 4 TGAACTGCAGCCAAGAGACCAACAGAAAACAAGAAAGGTG R RF: GACACGGCCCCATCACGCTCAGCACATGGACATTGGCCTGGGTATTGTGAACTGCAGCCAAGAGACCAACAGAAAACAAGAAAGGTG RR: CTGTGCCGGGGTAGTGCGAGTCGTGTACCTGTAACCGGACCCATAACACTTGACGTCGGTTCTCTGGTTGTCTTTTGTTCTTTCCAC F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -43.6) TCACGCTCAGCACATGGACATTGGCCTGG--AcTGcagccaactgcaTGAACTGCAGCCAAGAGACCAACAGAAAACAAGAAAGGTG TCACGCTCAGCACATGGACATTGGCCTGGGTATTG------------TGAACTGCAGCCAAGAGACCAACAGAAAACAAGAAAGGTG Template switch alignment (log-probability: -26.8) TCACGCTCAGCACATGGACATTGGCCTGG---------ACTGCAGCCAA|CTGCA|TGAACTGCAGCCAAGAGACCAACAGAAAACAAGAAAGGTG TCACGCTCAGCACATGGACATTGGCCTGGGTATTGTGAACTGCAGCCAA|CTGCA|TGAACTGCAGCCAAGAGACCAACAGAAAACAAGAAAGGTG ========== Event 1499 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTTGCATATATACAAATAAT----TTATTAGCTAATGCTAATAAATAAAATTTTCAAATAGGA ↑ 1 3 4 2 Chimp: TTTTGCATATGTACAAATAAT--TGGCATTAGC------TAATAAATAAAATTTTCAAATAGGA Gorilla: TTTTGCATATATACAAATAATTG--GCATTAGC------TAATAAATAAAATTTTCAAATAGGA ↓ 1 3 4 2 Human: TTTTGCATATATACAAATAAT----TTATTAGCTAATGCTAATAAATAAAATTTTCAAATAGGA Cluster: [ ] Orangutan: TTTTGCATATATACAAATAATTG--GCACGAGT------TAATAAATAAAATTTTCAAATAAGA Chimp > Human ------------- chr18:76264679-76264689 Template switch process: F1: L GGAAGTCATTTCCAATCTTGTTTTGCATATATACAAATAATT 1 F3: 4 GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATGTT R RF: GGAAGTCATTTCCAATCTTGTTTTGCATATGTACAAATAATTGGCATTAGCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATGTT RR: CCTTCAGTAAAGGTTAGAACAAAACGTATACATGTTTATTAACCGTAATCGATTATTTATTTTAAAAGTTTATCCTGTTTATGTTCTACAA F2: 3 TAATCGATTAT 2 Unidirectional alignment (log-probability: -40.4) AAGTCATTTCCAATCTTGTTTTGCATATaTACAAATAAT-----TTAttagctaatGCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG AAGTCATTTCCAATCTTGTTTTGCATATGTACAAATAATTGGCATTA---------GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG Template switch alignment (log-probability: -22.7) AAGTCATTTCCAATCTTGTTTTGCATATaTACAAATAATT|TATTAGCTAAT|GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG AAGTCATTTCCAATCTTGTTTTGCATATGTACAAATAATT|TATTAGCTAAT|GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG Gorilla > Human --------------- chr18:76264679-76264689 Template switch process: F1: L GGAAGTCATTTCCAATCTTGTTTTGCATATATACAAATAATT 1 F3: 4 GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATGTT R RF: GAAAGTCATTTCCAATCTTGTTTTGCATATATACAAATAATTGGCATTAGCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATGTT RR: CTTTCAGTAAAGGTTAGAACAAAACGTATATATGTTTATTAACCGTAATCGATTATTTATTTTAAAAGTTTATCCTGTTTATGTTCTACAA F2: 3 TAATCGATTAT 2 Unidirectional alignment (log-probability: -39.4) AAGTCATTTCCAATCTTGTTTTGCATATATACAAATAAT-----TTAttagctaatGCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG AAGTCATTTCCAATCTTGTTTTGCATATATACAAATAATTGGCATTA---------GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG Template switch alignment (log-probability: -22.7) AAGTCATTTCCAATCTTGTTTTGCATATATACAAATAATT|TATTAGCTAAT|GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG AAGTCATTTCCAATCTTGTTTTGCATATATACAAATAATT|TATTAGCTAAT|GCTAATAAATAAAATTTTCAAATAGGACAAATACAAGATG ========== Event 1500 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCACTCTCTTTCTGCTCACT-TCT-------GCAGTCATTTCCATGACTCATTCCCAGTCA Chimp: TCCACTCTCTTTCTGCTCACT-TCT-------GCAGTCATTTCCATGACTCATTCCCCGTCA Gorilla: TCCACTCTCTTTCTGCTCACTGACT--------------GCTCCATGACTCATTCCCAGCCA ↑ 1 3 2 4 Human: TCCACTCTCTTTCTGCTCACT-TCT-------GCAGTCATTTCCATGACTCATTCCCAGTCA Cluster: [ ] Orangutan: TCCACTCTCTTTCTGCTCACT-TCTGCAGTCA-------TTTCCCTGACTCATTCCCAGTCA Human > Gorilla --------------- chr18:38638747-38638752 Template switch process: F1: L AAAACATTTCTAACTGACATTCCACTCTCTTTCTGCTCACT 1 F3: 4 TCCATGACTCATTCCCAGCCAGGGCTGTTGTTTTGTTTCT R RF: AAAACATTTCTAACTGACATTCCACTCTCTTTCTGCTCACTTCTGCAGTCATTTCCATGACTCATTCCCAGTCAGGGCTGTTGTTTTGTTTCT RR: TTTTGTAAAGATTGACTGTAAGGTGAGAGAAAGACGAGTGAAGACGTCAGTAAAGGTACTGAGTAAGGGTCAGTCCCGACAACAAAACAAAGA F2: 3 CGTCAG 2 Unidirectional alignment (log-probability: -33.5) AAACATTTCTAACTGACATTCCACTCTCTTTCTGCTCACTgaCTGC-------TCCATGACTCATTCCCAGcCAGGGCTGTTGTTTTGTTTCT AAACATTTCTAACTGACATTCCACTCTCTTTCTGCTCACT-TCTGCAGTCATTTCCATGACTCATTCCCAGTCAGGGCTGTTGTTTTGTTTCT Template switch alignment (log-probability: -22) AAACATTTCTAACTGACATTCCACTCTCTTTCTGCTCACT|GACTGC|TCCATGACTCATTCCCAGcCAGGGCTGTTGTTTTGTTTCT AAACATTTCTAACTGACATTCCACTCTCTTTCTGCTCACT|GACTGC|TCCATGACTCATTCCCAGTCAGGGCTGTTGTTTTGTTTCT ========== Event 1501 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCACTCTCTTTCTGCTCACT-TCT-------GCAGTCATTTCCATGACTCATTCCCAGTCAGGGCTGTTGTTTTGTTTC Chimp: CCACTCTCTTTCTGCTCACT-TCT-------GCAGTCATTTCCATGACTCATTCCCCGTCAGGGCTGTTGTTTTGTTTC ↓ 1 3 2 4 Gorilla: CCACTCTCTTTCTGCTCACTGACT--------------GCTCCATGACTCATTCCCAGCCAGGGCTGTTGTTTTGTTTC Human: CCACTCTCTTTCTGCTCACT-TCT-------GCAGTCATTTCCATGACTCATTCCCAGTCAGGGCTGTTGTTTTGTTTC Cluster: [ ] Orangutan: CCACTCTCTTTCTGCTCACT-TCTGCAGTCA-------TTTCCCTGACTCATTCCCAGTCAGGGCTGTTGTTTTGTTTC Chimp > Gorilla --------------- chr18:38638747-38638752 Template switch process: F1: L TTTCTGCTCACT 1 F3: 4 TCCATGACTCATTCCCAGCCAGGGCTGTTGTTTTGTTTCTCCCACTTTGACTCTCAGTG R RF: TTTCTGCTCACTTCTGCAGTCATTTCCATGACTCATTCCCCGTCAGGGCTGTTGTTTTGTTTCTCCCACTTTGACTCTCAGTG RR: AAAGACGAGTGAAGACGTCAGTAAAGGTACTGAGTAAGGGGCAGTCCCGACAACAAAACAAAGAGGGTGAAACTGAGAGTCAC F2: 3 CGTCAG 2 Unidirectional alignment (log-probability: -38.9) TTTCTGCTCACTgaCTGC-------TCCATGACTCATTCCCaGcCAGGGCTGTTGTTTTGTTTCT TTTCTGCTCACT-TCTGCAGTCATTTCCATGACTCATTCCCCGTCAGGGCTGTTGTTTTGTTTCT Template switch alignment (log-probability: -27.3) TTTCTGCTCACT|GACTGC|TCCATGACTCATTCCCaGcCAGGGCTGTTGTTTTGTTTCT TTTCTGCTCACT|GACTGC|TCCATGACTCATTCCCCGTCAGGGCTGTTGTTTTGTTTCT ========== Event 1502 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATA--GAAATTATTTTT-TCAGTACTTTAT-AGGTC---CAATTTTGCATATACCAATGTG ↓ 3 2 1 4 Chimp: AAATA--GAAATTATTTTT-TCAGTACTTTAT-AGTACTGAAAATTTTGCATATACCAATGTG ↑ 3 2 1 4 Gorilla: AAATA--GAAATTATTTTT-TCAGTACTTTAT-AGGTC---CAATTTTGCATATGCCAATGTG Human: AAATA--GAAATTATTTTT-TCAGTACTTTAT-AGGTC---CAATTTTGCATATACCAATGTG Cluster: [ ] Orangutan: AAATAATAAATTTATTTTTTCCAAGGCTTTATAAGGTC---CCATTTTNNNNNNNNNNNNNNN Human > Chimp ------------- chr18:38083634-38083640 Template switch process: F1: L TTTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG 1 F3: 4 AATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA R RF: TTTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAGGTCCAATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA RR: AAATATTCCGTTTATCTTTAATAAAAAAGTCATGAAATATCCAGGTTAAAACGTATATGGTTACACGTCTGTACACGTCTGTTTT F2: 3 AAGTCAT 2 Unidirectional alignment (log-probability: -31.4) TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAGtactgaa----AATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG-------GTCCAATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA Template switch alignment (log-probability: -16.2) TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG|TACTGAA|AATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG|TACTGAA|AATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA Gorilla > Chimp --------------- chr18:38083634-38083640 Template switch process: F1: L TTTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG 1 F3: 4 AATTTTGCATATACCAATGTGCAGACATGTGCAGACAAAA R RF: TTTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAGGTCCAATTTTGCATATGCCAATGTGCAGACATGTGCAGACAAAA RR: AAATATTCCGTTTATCTTTAATAAAAAAGTCATGAAATATCCAGGTTAAAACGTATACGGTTACACGTCTGTACACGTCTGTTTT F2: 3 AAGTCAT 2 Unidirectional alignment (log-probability: -36.4) TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG----tactgaaAATTTTGCATATaCCAATGTGCAGACATGTGCAGACAAAA TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAGGTCC-------AATTTTGCATATGCCAATGTGCAGACATGTGCAGACAAAA Template switch alignment (log-probability: -22.1) TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG|TACTGAA|AATTTTGCATATaCCAATGTGCAGACATGTGCAGACAAAA TTATAAGGCAAATAGAAATTATTTTTTCAGTACTTTATAG|TACTGAA|AATTTTGCATATGCCAATGTGCAGACATGTGCAGACAAAA ========== Event 1503 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCAAATAACTTTATGAATTCAAGTTTCTAAAA----------AGGCTGACTGACTTA--------------AAAGTCAGTTAGCCTGCAGCAGGTGGATCCACTATA Chimp: CCCAAATAACTGTAGGAATTCAAGTTTCTACAA----------AGGCTGACTAACTTA--------------AAAGTCAGTTAGCCTGCAGCAGATGGATCCACTATA ↓ 3 2 1 4 Gorilla: CCCAAATAACTGTATGAATTCAAGTTTCTACAA--------------------ACTTG----------------------------AGCAGCAGATGGATCCACTATA Human: CCCAAATAACTTTATGAATTCAAGTTTCTAAAA----------AGGCTGACTGACTTA--------------AAAGTCAGTTAGCCTGCAGCAGGTGGATCCACTATA Cluster: [ ] Orangutan: CCCAAATAACTTTATGAATTCAAGTTTCTACAAAGGCTGGCTA----------ACTTAAAAGTCAGTTAGCC--------------TGCAGCAGGTGGATCCACTATA Chimp > Gorilla --------------- chr18:37585836-37585840 Template switch process: F1: L AGCATTTCCCCAAATAACTGTATGAATTCAAGTTTCTACAAA 1 F3: 4 GCAGCAGATGGATCCACTATATTGCATTATACTGTATAAT R RF: AGCCTTTCCCCAAATAACTGTAGGAATTCAAGTTTCTACAAAGGCTGACTAACTTAAAAGTCAGTTAGCCTGCAGCAGATGGATCCACTATATTGCATTATACTGTATAAT RR: TCGGAAAGGGGTTTATTGACATCCTTAAGTTCAAAGATGTTTCCGACTGATTGAATTTTCAGTCAATCGGACGTCGTCTACCTAGGTGATATAACGTAATATGACATATTA F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -37.4) CaTTTCCCCAAATAACTGTAtGAATTCAAGTTTCTACAAA---------------------------CTtgaGCAGCAGATGGATCCACTATATTGCATTATACTGTATAAT CCTTTCCCCAAATAACTGTAGGAATTCAAGTTTCTACAAAGGCTGACTAACTTAAAAGTCAGTTAGCCT---GCAGCAGATGGATCCACTATATTGCATTATACTGTATAAT Template switch alignment (log-probability: -27.4) CaTTTCCCCAAATAACTGTAtGAATTCAAGTTTCTACAAA|CTTGA|GCAGCAGATGGATCCACTATATTGCATTATACTGTATAAT CCTTTCCCCAAATAACTGTAGGAATTCAAGTTTCTACAAA|CTTGA|GCAGCAGATGGATCCACTATATTGCATTATACTGTATAAT ========== Event 1504 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCTATGCAAATCTTACAGGAGTG-----------GAAACAGTTTAAAGAGAATGTTACTGAGAGGG Chimp: CTCTATGCAAATCTTACAGGAGTG-----------GAAACGGTTTAAAGAGAATGTTACTGAGAGGG ↓ 13 4 2 Gorilla: CTCTATGCAAATCTTACAGGATTAAACCGTTTCCACAAACGGTTTAAAAAGAATGTTACTGAGAGGG Human: CTCTATGCAAATCTTACAGGAGTG-----------GAAACAGTTTAAAGAGAATGTTACTGAGAGGG Cluster: [ ] Orangutan: CTCTATGCAAATCTTACAGGAGTG-----------GAAACGGTTTAAAGAGAATGTTACTGAGAGGG Chimp > Gorilla --------------- chr18:37932994-37933008 Template switch process: F1: L AACTTTTCTCTTAGGGAATGCTCTATGCAAATCTTACAGGA 1 F3: 4 AAACGGTTTAAAAAGAATGTTACTGAGAGGGTGTGATGGT R RF: AACTTTTCTCTTATGGAATGCTCTATGCAAATCTTACAGGAGTGGAAACGGTTTAAAGAGAATGTTACTGAGAGGGTGTGATGGT RR: TTGAAAAGAGAATACCTTACGAGATACGTTTAGAATGTCCTCACCTTTGCCAAATTTCTCTTACAATGACTCTCCCACACTACCA F2: 3 CACCTTTGCCAAATT 2 Unidirectional alignment (log-probability: -53.4) ACTTTTCTCTTAgGGAATGCTCTATGCAAATCTTACAGGAttaaaccgtttccac----AAACGGTTTAAAaAGAATGTTACTGAGAGGGTGTGATGGT ACTTTTCTCTTATGGAATGCTCTATGCAAATCTTACAGGA---------------GTGGAAACGGTTTAAAGAGAATGTTACTGAGAGGGTGTGATGGT Template switch alignment (log-probability: -28.7) ACTTTTCTCTTAgGGAATGCTCTATGCAAATCTTACAGGA|TTAAACCGTTTCCAC|AAACGGTTTAAAaAGAATGTTACTGAGAGGGTGTGATGGT ACTTTTCTCTTATGGAATGCTCTATGCAAATCTTACAGGA|TTAAACCGTTTCCAC|AAACGGTTTAAAGAGAATGTTACTGAGAGGGTGTGATGGT ========== Event 1505 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAACTTACCTTTCTCGTCCCCTCAGGACTTCCAAGTCCTGAGGATGCTGGGCTAACTACTT ↑ 1 4 3 2 Chimp: TAAACTTACCTTTCTCGTCCC----CAGCTTCCAAGTCCTGAGGATGCTGAGCTAACTACTT Gorilla: TAAACTTACCTTTCTCGTCCC----CAGCTTCCAAGTCCTGAGGATGCTGGGCTAACTACTT ↓ 1 4 3 2 Human: TAAACTTACCTTTCTCGTCCCCTCAGGACTTCCAAGTCCTGAGGATGCTGGGCTAACTACTT Cluster: [ ] Orangutan: TAAACTTACCTTTCTCGTCCC----C--ATTCCAAGTCCTGAGGATGCTGGGCTAACTACTT Chimp > Human ------------- chr18:41923436-41923441 Template switch process: F1: L GTCACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCCC 1 F3: 4 CTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG R RF: GTCACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCCCAGCTTCCAAGTCCTGAGGATGCTGAGCTAACTACTTTCCCAG RR: CAGTGTACATTTTAAAATTTATTTGAATGGAAAGAGCAGGGGTCGAAGGTTCAGGACTCCTACGACTCGATTGATGAAAGGGTC F2: 3 AGGACT 2 Unidirectional alignment (log-probability: -32.9) CACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCCctCAGgaCTTCCAAGTCCTGAGGATGCTGgGCTAACTACTTTCCCAG CACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCC--CAG--CTTCCAAGTCCTGAGGATGCTGAGCTAACTACTTTCCCAG Template switch alignment (log-probability: -22) CACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCCC|TCAGGA|CTTCCAAGTCCTGAGGATGCTGgGCTAACTACTTTCCCAG CACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCCC|TCAGGA|CTTCCAAGTCCTGAGGATGCTGAGCTAACTACTTTCCCAG Gorilla > Human --------------- chr18:41923436-41923441 Template switch process: F1: L GTCACATGTAAAATTTTAAATAAACTTACCTTTCTCGTCCCC 1 F3: 4 CTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG R RF: GTCACATGTAATATTTTAAATAAACTTACCTTTCTCGTCCCCAGCTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG RR: CAGTGTACATTATAAAATTTATTTGAATGGAAAGAGCAGGGGTCGAAGGTTCAGGACTCCTACGACCCGATTGATGAAAGGGTC F2: 3 AGGACT 2 Unidirectional alignment (log-probability: -31.9) CACATGTAAaATTTTAAATAAACTTACCTTTCTCGTCCCctCAGgaCTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG CACATGTAATATTTTAAATAAACTTACCTTTCTCGTCCC--CAG--CTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG Template switch alignment (log-probability: -22) CACATGTAAaATTTTAAATAAACTTACCTTTCTCGTCCCC|TCAGGA|CTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG CACATGTAATATTTTAAATAAACTTACCTTTCTCGTCCCC|TCAGGA|CTTCCAAGTCCTGAGGATGCTGGGCTAACTACTTTCCCAG ========== Event 1506 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCAAATGGCTTACAAAACAGTTGAACTTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAA Chimp: AGCAAATGGCTTACAAAACAGTTGAACTTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAA ↓ 1 4 3 2 Gorilla: AGCAAATGGCTTACAAAACAGCTACTAGTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAA ↑ 1 4 3 2 Human: AGCAAATGGCTTACAAAACAGTTGAACTTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAA Cluster: [ ] Orangutan: AGCAATTGGCTTACAAAACAGTTGGACTTTCCCTTTAAACTAATAGCTAAAGAAACGAAAGCCAAA Human > Gorilla --------------- chr18:67213714-67213720 Template switch process: F1: L AGCACTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG 1 F3: 4 TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA R RF: AGCAGTCATGACTCTCTTACAGCAAATGGCTTACAAAACAGTTGAACTTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA RR: TCGTCAGTACTGAGAGAATGTCGTTTACCGAATGTTTTGTCAACTTGAAAGGGAAATTTGATCATCGATTTCTTTGCTTTCGGTTTAT F2: 3 GATCATC 2 Unidirectional alignment (log-probability: -33.6) GCAcTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG-----CTactagTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA GCAGTCATGACTCTCTTACAGCAAATGGCTTACAAAACAGTTGAACT-----TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA Template switch alignment (log-probability: -22.1) GCAcTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG|CTACTAG|TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA GCAGTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG|CTACTAG|TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA Chimp > Gorilla --------------- chr18:67213714-67213720 Template switch process: F1: L AGCACTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG 1 F3: 4 TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA R RF: AGCAGTCATGACTCTCTTACAGCAAATGGCTTACAAAACAGTTGAACTTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA RR: TCGTCAGTACTGAGAGAATGTCGTTTACCGAATGTTTTGTCAACTTGAAAGGGAAATTTGATCATCGATTTCTTTGCTTTCGGTTTAT F2: 3 GATCATC 2 Unidirectional alignment (log-probability: -33.6) GCAcTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG-----CTactagTTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA GCAGTCATGACTCTCTTACAGCAAATGGCTTACAAAACAGTTGAACT-----TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA Template switch alignment (log-probability: -22.1) GCAcTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG|CTACTAG|TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA GCAGTCATGACTCTCTTACAGCAAATGGCTTACAAAACAG|CTACTAG|TTCCCTTTAAACTAGTAGCTAAAGAAACGAAAGCCAAATA ========== Event 1507 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAGCTTCAAGGCCTCAAGTA--ATGCTGCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAACACTGCAGAAAGTACCCACATTGCAGCTAATGAGTGCCTTCCTGCTTGCAGGTGTTTCATAGGCCCAAACCACCAGCATTGTCAGTGATCAGAAAGTGT ↑ 1 4 3 2 Chimp: GAGGCTTCAAGGCCTCAAGTATGTCACTTCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAACACTGCAGAAAGTACCCACATTGCAGCTAATGAGTGCCTTCCTGTTTGCAGGTGTTTCATAGGCCCAAACCACCAGCATTGTCAGTGATCAGAAAGTGT Gorilla: GAAGCTTCAAGGCCTCAAGTA--ATGCTTCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAACACTGCAGAAAGTACCCACATTGCAGCTAATGAGTGCCTCCCTGTTTGCAGGTGTTTCATATGCCCAAACCACCAGCATTGTCAGTGATCAGAAAGAGT Human: GAAGCTTCAAGGCCTCAAGTA--ATGCTGCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAACACTGCAGAAAGTACCCACATTGCAGCTAATGAGTGCCTTCCTGCTTGCAGGTGTTTCATAGGCCCAAACCACCAGCATTGTCAGTGATCAGAAAGTGT Cluster: [ ] Orangutan: GAAGCTTCAAGGCCTCAAGTA--ATTCTTCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAACACTGCAGAAAGTACCCACATTGCAGCTAATGAGTGCCTCCCTGTTTGCAGGTGTTTCATAGGCCCAAACCACCAGCATTGTCAGCGATCAGAAAGTGT Chimp > Human ------------- chr18:37120970-37120975 Template switch process: F1: L CTCCCTGTGGTGATGCTCTGGAAGCTTCAAGGCCTCAAGTA 1 F3: 4 CCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAAC R RF: CTCCCTGTGGTGATGCTCTGGAGGCTTCAAGGCCTCAAGTATGTCACTTCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAACACTGCAGAAAGTACCCACATTGCAGCTAATGAGTGCCTTCCTGTTTGCAGGTGTTTCATAGGCCCAAACCACCAGCAT RR: GAGGGACACCACTACGAGACCTCCGAAGTTCCGGAGTTCATACAGTGAAGGTATTACACTGTCACTCTAAGGAGGACGATACATAGTTGTGACGTCTTTCATGGGTGTAACGTCGATTACTCACGGAAGGACAAACGTCCACAAAGTATCCGGGTTTGGTGGTCGTA F2: 3 GTCGTA 2 Unidirectional alignment (log-probability: -33.2) TCCCTGTGGTGATGCTCTGGAaGCTTCAAGGCCTCAAGTAatgcTG------CCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAAC TCCCTGTGGTGATGCTCTGGAGGCTTCAAGGCCTCAAGTA----TGTCACTTCCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAAC Template switch alignment (log-probability: -22) TCCCTGTGGTGATGCTCTGGAaGCTTCAAGGCCTCAAGTA|ATGCTG|CCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAAC TCCCTGTGGTGATGCTCTGGAGGCTTCAAGGCCTCAAGTA|ATGCTG|CCATAATGTGACAGTGAGATTCCTCCTGCTATGTATCAAC ========== Event 1508 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGTAATTTGTGAAAGTCAGGCCTGTTTCACAGGCCT---GGGGTAATATGACCCATTAAGAACAAGCA Chimp: AAAGTAATTTGTGAAAGTCAGCCTTGTTTCACAGGCTT---GGAGTAATGTGACCCATTAAGAACAAGCG Gorilla: AAAGTAATTTGTGAAAGTCAGGCCTGTGAAATAGGCCT------GTAATGTGACCCATTAAGAACAAGCA ↑ 3 1 2 4 Human: AAAGTAATTTGTGAAAGTCAGGCCTGTTTCACAGGCCT---GGGGTAATATGACCCATTAAGAACAAGCA Cluster: [ ] Orangutan: AAAGTAATTTGTGAAAGTCAGGCCTGTTTCACAGGCCTGGG---TTAATGTGACCCATTGAGAACAAGCA Human > Gorilla --------------- chr18:37928101-37928111 Template switch process: F1: L AATTGAAATAGTAAAAAGTAATTTGTGAAAGTCAGGCCTGT 1 F3: 4 GTAATGTGACCCATTAAGAACAAGCATGTTAATATATTCGCTTGCA R RF: AATTGAAATAGTAAAAAGTAATTTGTGAAAGTCAGGCCTGTTTCACAGGCCTGGGGTAATATGACCCATTAAGAACAAGCATGTTAATATATTCGCTTGCA RR: TTAACTTTATCATTTTTCATTAAACACTTTCAGTCCGGACAAAGTGTCCGGACCCCATTATACTGGGTAATTCTTGTTCGTACAATTATATAAGCGAACGT F2: 3 TCCGGATAAAG 2 Unidirectional alignment (log-probability: -38.9) ATTGAAATAGTAAAAAGTAATTTGTGAAAGTCAGGCCTGTgaaAtAGGCCT---GTAATgTGACCCATTAAGAACAAGCATGTTAATATATTCG ATTGAAATAGTAAAAAGTAATTTGTGAAAGTCAGGCCTGTTTCACAGGCCTGGGGTAATATGACCCATTAAGAACAAGCATGTTAATATATTCG Template switch alignment (log-probability: -28.3) ATTGAAATAGTAAAAAGTAATTTGTGAAAGTCAGGCCTGT|GAAAtAGGCCT|GTAATgTGACCCATTAAGAACAAGCATGTTAATATATTCG ATTGAAATAGTAAAAAGTAATTTGTGAAAGTCAGGCCTGT|GAAACAGGCCT|GTAATATGACCCATTAAGAACAAGCATGTTAATATATTCG ========== Event 1509 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TATCATTGTCTAGAAAGCCTGACAGCCTACATTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATT ↑ 1 4 3 2 Chimp: TATCATTGTCTAGAAAGCCTG--------AGTTGTCCTGTAGGCTGTGCAGTCTGTTGCTTTTATT Gorilla: TATCATTGTCTAGAAAGCCTG--------AGTTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATT ↓ 1 4 3 2 Human: TATCATTGTCTAGAAAGCCTGACAGCCTACATTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATT Cluster: [ ] Orangutan: TATCATTGTCTAGAAAGCCTG--------AGTTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATT Chimp > Human ------------- chr18:36223358-36223366 Template switch process: F1: L AAAGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA 1 F3: 4 TTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTAAAATA R RF: AAAGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGAGTTGTCCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTAAAATA RR: TTTCTGAGTCCCACGTACTCATAGTAACAGATCTTTCGGACTCAACAGGACATCCGACACGTCAGACAACGAAAATAAAAAATTTTAT F2: 3 ACATCCGAC 2 Unidirectional alignment (log-probability: -34.5) AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGAcagcctacaTTGTtCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA--------GTTGTCCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA Template switch alignment (log-probability: -22.5) AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA|CAGCCTACA|TTGTtCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA|CAGCCTACA|TTGTCCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA Gorilla > Human --------------- chr18:36223358-36223366 Template switch process: F1: L AAAGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA 1 F3: 4 TTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA R RF: AAAGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGAGTTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA RR: TTTCTGAGTCCCACGTACTCATAGTAACAGATCTTTCGGACTCAACAAGACATCCGACACGTCAGACAACGAAAATAAAAAAT F2: 3 ACATCCGAC 2 Unidirectional alignment (log-probability: -27.9) AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGAcagcctacaTTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGAG--------TTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA Template switch alignment (log-probability: -16.9) AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA|CAGCCTACA|TTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA AGACTCAGGGTGCATGAGTATCATTGTCTAGAAAGCCTGA|CAGCCTACA|TTGTTCTGTAGGCTGTGCAGTCTGTTGCTTTTATTTTTTA ========== Event 1510 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACATAGCAAGTCATATTAGAAAACTTGAATAGCCCTCACTCTCACAATAACTA-AAATATTAAATGAACTATGTATCGATGACCTGGCAAATGTAAGAAAATGTAAGAAGTCTCAAAAAAATGAAGGTTGCAAATATAGAAAGAGTGAACCACTTG--------------------------------------------------TTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC Chimp: ACATAGCAAGTCATATTAGATAACTTGAATAGCCCTCACTCTCACAATAACTAAAAATATTAAATGAACTATTTATCGATGACCTGGCAAATATAAGAAAATGTAAGAAGTCTCaaaaaaaTGAAGGTTGCAAATATAGAAAGAGTGAACCACTTG--------------------------------------------------TTTTACCTGGTGAAACTGAACTCTGATCTTGGCTC Gorilla: ACATAGCAAGTCATATTAGATAACTTGAATAGCCCTCACTCTCACAATAACTAAAAATATTAAATGAACTATTTATCGATGACCTGGCAAATGTAAGAAAATGTAAGAAGTCTCGAAAAACTGAAGGTTGCAAATATAGAAAGAGTGAACCACTTG-------------------------TTTTACGTGAAACAAGTTTTACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC ↑ 3 2 4 1 Human: ACATAGCAAGTCATATTAGAAAACTTGAATAGCCCTCACTCTCACAATAACTA-AAATATTAAATGAACTATGTATCGATGACCTGGCAAATGTAAGAAAATGTAAGAAGTCTCAAAAAAATGAAGGTTGCAAATATAGAAAGAGTGAACCACTTG--------------------------------------------------TTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC Cluster: [ ] Orangutan: ACATAGCAAGTCATATTAGATAACTTGAATAGCCCTCACTCTCATAATAACTAAAAATATTAAATGAACTATTTATCGATGACCTGGCAAATGTAAGAAAATATAAGAAGTCTCAATAAAATGAAGGTTGCAAATATAGAAAGAGTGAACCACTTGTTTTACTTGAAACAAGTTTTACTTG-------------------------TTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC Human > Gorilla --------------- chr18:36807706-36807713 Template switch process: F1: L AAAAACTGAAGGTTGCAAATATAGAAAGAGTGAACCACTTGTTTTAC---GTGAAA 1 F3: 4 ACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTCTCTGA R RF: AAAACTTGAATAGCCCTCACTCTCACAATAACTAAAATATTAAATGAACTATGTATCGATGACCTGGCAAATGTAAGAAAATGTAAGAAGTCTCAAAAAAATGAAGGTTGCAAATATAGAAAGAGTGAACCACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTCTCTGA RR: TTTTGAACTTATCGGGAGTGAGAGTGTTATTGATTTTATAATTTACTTGATACATAGCTACTGGACCGTTTACATTCTTTTACATTCTTCAGAGTTTTTTTACTTCCAACGTTTATATCTTTCTCACTTGGTGAACAAAATGGACCACTTTAACTTGAGACCAGAACCGAGAGACT F2: 3 TTTTGAAC 2 Unidirectional alignment (log-probability: -52.3) TGCAAATATAGAAAGAGTGAACCacttgttttacgtgaaacaagttttACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC TGCAAATATAGAAAGAGTGAACC-------------------------ACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC Template switch alignment (log-probability: -32.6) TGCAAATATAGAAAGAGTGAACCACTTGTTTTAC---GTGAAA|CAAGTTTT|ACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC TGCAAATATAGAAAGAGTGAACCACTTGTTTTACCTGGTGAAA|CAAGTTTT|ACTTGTTTTACCTGGTGAAATTGAACTCTGGTCTTGGCTC ========== Event 1511 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAATTTGGTCCACTGATATCAGCCAT--TACCAATATTTCCTAGATATTGGTTTAAAAGGAACAC ↓ 1 4 3 2 Chimp: GAATTTGGTCCACTGATATCATCTAGGAAACCAATATTTCCTAGATATTGGTTTAAAAGGAACAC ↑ 1 4 3 2 Gorilla: GAATTTGGTCCACTGATATCAGCCAT--TACCAATATTTCCTAGATACTGGTTTAAAAGGAACAC Human: GAATTTGGTCCACTGATATCAGCCAT--TACCAATATTTCCTAGATATTGGTTTAAAAGGAACAC Cluster: [ ] Orangutan: GAATTTGGCCCACTGATATCAGCCAT--TACCAATATTTCCTAGATATTGGTTTAAAAGGAACAC Human > Chimp ------------- chr18:42554169-42554176 Template switch process: F1: L AAACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA 1 F3: 4 ACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC R RF: AAACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCAGCCATTACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC RR: TTTGAGAAACCGTCCTCAATCTTAAACCAGGTGACTATAGTCGGTAATGGTTATAAAGGATCTATAACCAAATTTTCCTTGTGATAG F2: 3 AAGGATCT 2 Unidirectional alignment (log-probability: -31.5) AACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA-----TctaggaaACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC AACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCAGCCATT-------ACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC Template switch alignment (log-probability: -16.3) AACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA|TCTAGGAA|ACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC AACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA|TCTAGGAA|ACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC Gorilla > Chimp --------------- chr18:42554169-42554176 Template switch process: F1: L AAACTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA 1 F3: 4 ACCAATATTTCCTAGATATTGGTTTAAAAGGAACACTATC R RF: AAATTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCAGCCATTACCAATATTTCCTAGATACTGGTTTAAAAGGAACACTATC RR: TTTAAGAAACCGTCCTCAATCTTAAACCAGGTGACTATAGTCGGTAATGGTTATAAAGGATCTATGACCAAATTTTCCTTGTGATAG F2: 3 AAGGATCT 2 Unidirectional alignment (log-probability: -42) AAcTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA-----TctaggaaACCAATATTTCCTAGATAtTGGTTTAAAAGGAACACTATC AATTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCAGCCATT-------ACCAATATTTCCTAGATACTGGTTTAAAAGGAACACTATC Template switch alignment (log-probability: -27.8) AAcTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA|TCTAGGAA|ACCAATATTTCCTAGATAtTGGTTTAAAAGGAACACTATC AATTCTTTGGCAGGAGTTAGAATTTGGTCCACTGATATCA|TCTAGGAA|ACCAATATTTCCTAGATACTGGTTTAAAAGGAACACTATC ========== Event 1512 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTCTGATTAAGACTTTTAAAATTGCT-------ATTTTGAATAATCTTAGGACAGCAC Chimp: TCTCTGATTAAGACTTTTAAAATTGCT-------ATTTTGAATAATCTTAGGACAGCAC ↑ 3 1 2 4 Gorilla: TCTCTGATTAAGACTTTTAAAATAGCAACATGTTCCCTTGAATAATCTTAGGACAGCAC ↓ 3 1 2 4 Human: TCTCTGATTAAGACTTTTAAAATTGCT-------ATTTTGAATAATCTTAGGACAGCAC Cluster: [ ] Orangutan: TCTCTGATTAAGACTTTTAAAATAGCAACATGTTCCCTTGAATAATCTCAGGACAGCAC Gorilla > Human --------------- chr18:46090179-46090186 Template switch process: F1: L CCAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT 1 F3: 4 TGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG R RF: CCAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAATAGCAACATGTTCCCTTGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG RR: GGTTGATTGTTTGTTGGGAGAGACTAATTCTGAAAATTTTATCGTTGTACAAGGGAACTTATTAGAATCCTGTCGTGTAACTATTCGGATTATAC F2: 3 TTTATCGT 2 Unidirectional alignment (log-probability: -31.4) CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT--------------tgctattTTGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAATAGCAACATGTTCCC-------TTGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG Template switch alignment (log-probability: -16.7) CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT|TGCTATTT|TGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT|TGCTATTT|TGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG Gorilla > Chimp --------------- chr18:43340848-43340855 Template switch process: F1: L CCAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT 1 F3: 4 TGAATAATCTTAGGACAGCACATTGATAAGCCTAATACG R RF: CCAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAATAGCAACATGTTCCCTTGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG RR: GGTTGATTGTTTGTTGGGAGAGACTAATTCTGAAAATTTTATCGTTGTACAAGGGAACTTATTAGAATCCTGTCGTGTAACTATTCGGATTATAC F2: 3 TTTATCGT 2 Unidirectional alignment (log-probability: -36.9) CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT--------------tgctattTTGAATAATCTTAGGACAGCACATTGATAAGCCTAATAcG CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAATAGCAACATGTTCCC-------TTGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG Template switch alignment (log-probability: -22.2) CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT|TGCTATTT|TGAATAATCTTAGGACAGCACATTGATAAGCCTAATAcG CAACTAACAAACAACCCTCTCTGATTAAGACTTTTAAAAT|TGCTATTT|TGAATAATCTTAGGACAGCACATTGATAAGCCTAATATG ========== Event 1513 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCAGAGTTCCTGAGCTGCAGATGAACAGCAGTTCATCTGGGAAGCTTCCTTGGAGT ↑ 1 3 4 2 Chimp: GCCAGAGTTCCTGAGCTGCAG----CCTGCTGTTCATCTGGGAAGCTTCCTTGGAGT Gorilla: GCCAGAGTTCCTGAGCTGCAG----CCTGCTGTTCATCTGGGAAGCTTCCTTGGAGT ↓ 1 3 4 2 Human: GCCAGAGTTCCTGAGCTGCAGATGAACAGCAGTTCATCTGGGAAGCTTCCTTGGAGT Cluster: [ ] Orangutan: GCCAGAGTTCCTGAGCTGCAG----CCTGCTGTTCATCTGGGAAGCTTCCTTGGAGT Chimp > Human ------------- chr18:46435094-46435103 Template switch process: F1: L CAGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG 1 F3: 4 GTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT R RF: CAGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAGCCTGCTGTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT RR: GTCGCCCGTCGGGCCTCTGTCGGTCTCAAGGACTCGACGTCGGACGACAAGTAGACCCTTCGAAGGAACCTCAAACAGTTCTCACCA F2: 3 ACGACAAGTA 2 Unidirectional alignment (log-probability: -34.7) AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAGatgaaCaGCaGTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG----CCTGCTGTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT Template switch alignment (log-probability: -16.5) AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG|ATGAACAGCA|GTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG|ATGAACAGCA|GTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT Gorilla > Human --------------- chr18:46435094-46435103 Template switch process: F1: L CAGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG 1 F3: 4 GTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT R RF: CAGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAGCCTGCTGTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT RR: GTCGCCCGTCGGGCCTCTGTCGGTCTCAAGGACTCGACGTCGGACGACAAGTAGACCCTTCGAAGGAACCTCAAACAGTTCTCACCA F2: 3 ACGACAAGTA 2 Unidirectional alignment (log-probability: -33.3) AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAGatgaaCaGCaGTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG----CCTGCTGTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT Template switch alignment (log-probability: -17) AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG|ATGAACAGCA|GTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT AGCGGGCAGCCCGGAGACAGCCAGAGTTCCTGAGCTGCAG|ATGAACAGCA|GTTCATCTGGGAAGCTTCCTTGGAGTTTGTCAAGAGTGGT ========== Event 1514 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGACGCATAGCTGTTTTGCACAGCTTTTGCAAGT----TGTCAACTTGATGTCAACACAA ↓ 3 2 1 4 Chimp: TGACGCATAGCTGTTTTGCACAGCTTTTGAAAGC--TGTGTCAACTTGATGTCAACACAA Gorilla: TGACGCATAGCTGTTTTGCACAGCTTTTGAAAGCTG--TGTCAACTTGATGTCAACACAA Human: TGACGCATAGCTGTTTTGCACAGCTTTTGCAAGT----TGTCAACTTGATGTCAACACAA Cluster: [ ] Orangutan: TGACGCATAGCTGTTTTGCACAGCTTTTGAAAGCTG--TGTCAACTTGATGTCAACACAA Human > Chimp ------------- chr18:43595797-43595804 Template switch process: F1: L AGGTTCACTGATTGACGCATAGCTGTTTTGCACAGCTTTTG 1 F3: 4 GTCAACTTGATGTCAACACAACATGGAGAAGAGCAGGAA R RF: AGGTTCACTGATTGACGCATAGCTGTTTTGCACAGCTTTTGCAAGTTGTCAACTTGATGTCAACACAACATGGAGAAGAGCAGGAA RR: TCCAAGTGACTAACTGCGTATCGACAAAACGTGTCGAAAACGTTCAACAGTTGAACTACAGTTGTGTTGTACCTCTTCTCGTCCTT F2: 3 TGTCGAAA 2 Unidirectional alignment (log-probability: -25.8) GGTTCACTGATTGACGCATAGCTGTTTTGCACAGCTTTTGaAAGctgTGTCAACTTGATGTCAACACAACATGGAGAAGAGCAGGAA GGTTCACTGATTGACGCATAGCTGTTTTGCACAGCTTTTGCAAG--TTGTCAACTTGATGTCAACACAACATGGAGAAGAGCAGGAA Template switch alignment (log-probability: -16.3) GGTTCACTGATTGACGCATAGCTGTTTTGCACAGCTTTTG|AAAGCTGT|GTCAACTTGATGTCAACACAACATGGAGAAGAGCAGGAA GGTTCACTGATTGACGCATAGCTGTTTTGCACAGCTTTTG|AAAGCTGT|GTCAACTTGATGTCAACACAACATGGAGAAGAGCAGGAA ========== Event 1515 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAGACACAGAGCAGCTTTGCA-----TCCTGTACCAGAGGGATCATTCATGAAGGAGG ↓ 1 4 2 Chimp: TCAGACACAGAGCAGCTTTGCTCTGGTACACGTACCAGAGGGATCATTCATGAAGGAGG ↑ 1 3 4 2 Gorilla: TCAGACACAGAGCAGCTTTGCA-----TCGTGTACCAGAGGGATCATTCATGAAGGAGG Human: TCAGACACAGAGCAGCTTTGCA-----TCCTGTACCAGAGGGATCATTCATGAAGGAGG Cluster: [ ] Orangutan: TCAGACACAGAGCAGCTTTGCA-----TCGTGTACCAGAGGGATCATTCATGAAGGAGG Human > Chimp ------------- chr18:33744813-33744821 Template switch process: F1: L GCTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC 1 F3: 4 CGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA R RF: GCTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGCATCCTGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA RR: CGACTGACACCTAAGACAGAAGTCTGTGTCTCGTCGAAACGTAGGACATGGTCTCCCTAGTAAGTACTTCCTCCCACTGAGTCTTT F2: 3 ACATGGTCT 2 Unidirectional alignment (log-probability: -34.3) CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTG----CTctggtacacGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAA CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGCATCCT---------GTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAA Template switch alignment (log-probability: -22.4) CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC|TCTGGTACA|cGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAA CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC|TCTGGTACA|TGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAA Gorilla > Chimp --------------- chr18:33744813-33744822 Template switch process: F1: L GCTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC 1 F3: 4 GTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA R RF: GCTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGCATCGTGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA RR: CGACTGACACCTAAGACAGAAGTCTGTGTCTCGTCGAAACGTAGCACATGGTCTCCCTAGTAAGTACTTCCTCCCACTGAGTCTTT F2: 3 CACATGGTCT 2 Unidirectional alignment (log-probability: -33.8) CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC----TctggtacacGTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGCATCGT---------GTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA Template switch alignment (log-probability: -17) CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC|TCTGGTACAC|GTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA CTGACTGTGGATTCTGTCTTCAGACACAGAGCAGCTTTGC|TCTGGTACAC|GTACCAGAGGGATCATTCATGAAGGAGGGTGACTCAGAAA ========== Event 1516 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCACCCGAACCCCTTTGTCTGAAC---------------CTCTGTTCAGTGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCGCTGACTgatgcccatcattccacaatca Chimp: TCACCCGAACCCCTTTGTCTGAAC---------------CTCTGTTCAGTGAACCTCTGTCACTCCTACTGACCCCTGAAGcttccccgctgactgatgcccatcattccacaatca ↑ 4 1 3 2 Gorilla: TTACCCGAACCCCTTTGTCTGAAC------------------------------CTCTGTCACTCCTACTGACCCCTGAAGcttccccgctgactgatgcccatcattccacaatca ↓ 4 1 3 2 Human: TCACCCGAACCCCTTTGTCTGAAC---------------CTCTGTTCAGTGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCGCTGACTgatgcccatcattccacaatca Cluster: [ ] Orangutan: TCACCCGAACCCTTTTGTCTGAACCTCTGTTCGGTGAAC---------------CTCTGTCACTACTACTGACCCCTGAAGCTTCCCCGCTGACTGATGCCCATCATTCCACAATCA Gorilla > Human --------------- chr18:48084892-48084895 Template switch process: F1: L GCCAGAGAGGGACTCTGTCACCCGAACCCCTTTGTCTGAACCTCTGT 1 F3: 4 TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCGCTGAC R RF: GCCAGAGAGGGACTCTGTTACCCGAACCCCTTTGTCTGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCGCTGACTGA RR: CGGTCTCTCCCTGAGACAATGGGCTTGGGGAAACAGACTTGGAGACAGTGAGGATGACTGGGGACTTCGAAGGGGCGACTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -38) AGGGACTCTGTcACCCGAACCCCTTTGTCtgaacctctgttcagTGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG AGGGACTCTGTTACCCGAACCCCTTTGTC---------------TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG Template switch alignment (log-probability: -22) AGGGACTCTGTcACCCGAACCCCTTTGTCTGAACCTCTGT|TCAG|TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG AGGGACTCTGTTACCCGAACCCCTTTGTCTGAACCTCTGT|TCAG|TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG Gorilla > Chimp --------------- chr18:45316558-45316561 Template switch process: F1: L GCCAGAGAGGGACTCTGTCACCCGAACCCCTTTGTCTGAACCTCTGT 1 F3: 4 TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCGCTGAC R RF: GCCAGAGAGGGACTCTGTTACCCGAACCCCTTTGTCTGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCGCTGACTGA RR: CGGTCTCTCCCTGAGACAATGGGCTTGGGGAAACAGACTTGGAGACAGTGAGGATGACTGGGGACTTCGAAGGGGCGACTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -38) AGGGACTCTGTcACCCGAACCCCTTTGTCtgaacctctgttcagTGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG AGGGACTCTGTTACCCGAACCCCTTTGTC---------------TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG Template switch alignment (log-probability: -22) AGGGACTCTGTcACCCGAACCCCTTTGTCTGAACCTCTGT|TCAG|TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG AGGGACTCTGTTACCCGAACCCCTTTGTCTGAACCTCTGT|TCAG|TGAACCTCTGTCACTCCTACTGACCCCTGAAGCTTCCCCG ========== Event 1517 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TATGTGAGTCTACCCACAAGCTGACGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAA--------------------------GCAGGAAGAAAAAGCAGGTGCTTTGTTGCTGTCATTTCTGGATTTTAATTAATG ↑ 1 4 3 2 Chimp: TATGTGAGTCTACCCACAAGCCAATGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAA---------------------------------------GCAGGTGCTTTGTTGCTGTCATTTCTGGATTTTAAGTAATG Gorilla: TATGTGACTCTACCCGCAAGCCGATGGGCTGCTGATGTGCCGGGGTGTTGGGAGAAAA-------------GCAGGAAGAACAA-------------GCAGGTGCTTTGTTGCTATCATTTCTGGATTTTAATTAATG Human: TATGTGAGTCTACCCACAAGCTGACGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAA--------------------------GCAGGAAGAAAAAGCAGGTGCTTTGTTGCTGTCATTTCTGGATTTTAATTAATG Cluster: [ ] Orangutan: TATGTGAGTCTACCTGCAAGCCGATGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAAGCAGGAAGAACAA--------------------------GCAGGTGCTTTGTTGCTGTCATTTCTGGATTTTAATTAACG Chimp > Human ------------- chr18:31535037-31535040 Template switch process: F1: L TCAGTGTAGGCTCCAGCTCCTATGTGAGTCTACCCACAAGC 1 F3: 4 GGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAAGCAGGAA R RF: TCAGTGTAGGCTCCAGCTCCTATGTGAGTCTACCCACAAGCCAATGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAAGCAGGTGCTTTGTTGCTGTCA RR: AGTCACATCCGAGGTCGAGGATACACTCAGATGGGTGTTCGGTTACCCGACAACTACACGGCCCCACAACCCTCTTTTCGTCCACGAAACAACGACAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -35.9) CAGTGTAGGCTCCAGCTCCTATGTGAGTCTACCCACAAGCtgAcGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAAgcaggaa CAGTGTAGGCTCCAGCTCCTATGTGAGTCTACCCACAAGCCAATGGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAA------- Template switch alignment (log-probability: -25.9) CAGTGTAGGCTCCAGCTCCTATGTGAGTCTACCCACAAGC|TGAC|GGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAAGCAGgaa CAGTGTAGGCTCCAGCTCCTATGTGAGTCTACCCACAAGC|TGAC|GGGCTGTTGATGTGCCGGGGTGTTGGGAGAAAAGCAG--G ========== Event 1518 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tttttgtttatctttgcttttccatgtttttAAGCTATCTATGATTTT---------------------AAAGAAAGCATCACTTTCATCAGATTA Chimp: tttttgtttatctttgcttttccatgtttttAAGCTATCTATGATTTT---------------------AAAGAAAGCATCACTTTCATCAGATTA ↓ 4 3 2 1 Gorilla: tttttgtttatctttgcttttccatgtttttAAGCTATCTATGATTTTAAAGAAATCATAGATTTCTTTAAAGAAAGCATCACTTTCATCAGATTA ↑ 4 3 2 1 Human: tttttgtttatctttgcttttccatgtttttAAGCTATCTATGATTTT---------------------AAAGAAAGCATCACTTTCATCAGATTA Cluster: [ ] Orangutan: tttttgtttatctttgcttttctatgtttttaagttatctatgatttt---------------------aAAGAAAGCATCACTTTCATCAGATTA Human > Gorilla --------------- chr1:142726815-142726822 Template switch process: F1: L TTATCTTTGCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAA 1 F3: 4 TTC-----------------------TTTAAAGAAAGCATCACTTTCATCAGATTAAACATGCTTTACA R RF: TTATCTTTGCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAAGCATCACTTTCATCAGATTAAACATGCTTTACA RR: AATAGAAACGAAAAGGTACAAAAATTCGATAGATACTAAAATTTCTTTCGTAGTGAAAGTAGTCTAATTTGTACGAAATGT F2: 3 TAGATACT 2 Unidirectional alignment (log-probability: -41.1) GCTTTTCCATGTTTTTAAGCTATCTATGATTttaaagaaatcatagatttctTTAAAGAAAGCATCACTTTCATCAGATTAAACATGC GCTTTTCCATGTTTTTAAGCTATCTATGATT---------------------TTAAAGAAAGCATCACTTTCATCAGATTAAACATGC Template switch alignment (log-probability: -28) GCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAA|TCATAGAT|TTC-----------------------TTTAAAGAAAGCATCACTTTCATCAGATTAAACATGC GCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAA|TCATAGAT|TTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAAGCATCACTTTCATCAGATTAAACATGC Chimp > Gorilla --------------- chr1:142726815-142726822 Template switch process: F1: L TTATCTTTGCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAA 1 F3: 4 TTC-----------------------TTTAAAGAAAGCATCACTTTCATCAGATTAAACATGCTTTACA R RF: TTATCTTTGCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAAGCATCACTTTCATCAGATTAAACATGCTTTACA RR: AATAGAAACGAAAAGGTACAAAAATTCGATAGATACTAAAATTTCTTTCGTAGTGAAAGTAGTCTAATTTGTACGAAATGT F2: 3 TAGATACT 2 Unidirectional alignment (log-probability: -41.1) GCTTTTCCATGTTTTTAAGCTATCTATGATTttaaagaaatcatagatttctTTAAAGAAAGCATCACTTTCATCAGATTAAACATGC GCTTTTCCATGTTTTTAAGCTATCTATGATT---------------------TTAAAGAAAGCATCACTTTCATCAGATTAAACATGC Template switch alignment (log-probability: -28) GCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAA|TCATAGAT|TTC-----------------------TTTAAAGAAAGCATCACTTTCATCAGATTAAACATGC GCTTTTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAA|TCATAGAT|TTCCATGTTTTTAAGCTATCTATGATTTTAAAGAAAGCATCACTTTCATCAGATTAAACATGC ========== Event 1519 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAAATTTTTTATCTATGAATAC----------------TAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTGCAGAAGTAAAATCAGATACAGACGTTGCAG ↓ 1 4 3 2 Chimp: TAAAATTTTTTATCTATGAATGT--------TTACTTCTGAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTGCAGAAGTAAAATCAGATACAGACGTTGCAG Gorilla: TAAAATTTTTTGTCTATGAATGTTTACTTCT--------GAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCCTGCCTGCAGAAGTAAAATCAGATACAGACGTTGCAG Human: TAAAATTTTTTATCTATGAATAC----------------TAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTGCAGAAGTAAAATCAGATACAGACGTTGCAG Cluster: [ ] Orangutan: TAAAATTTTTTATCTATGATTGTTTACTTCT--------GAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTACAGAAGTAAAATCAGATACAGATGTTGCAG Human > Chimp ------------- chr18:31751517-31751526 Template switch process: F1: L TATAAAGGAATTACATGTTTTAAAATTTTTTATCTATGAATG 1 F3: 4 AAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTG R RF: TATAAAGGAATTACATGTTTTAAAATTTTTTATCTATGAATACTAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTGCAGAAGTAAA RR: ATATTTCCTTAATGTACAAAATTTTAAAAAATAGATACTTATGATTCAAAAGAACAGAGGTTGGACACAAGGAAAAGAACGGACGTCTTCATTT F2: 3 GTCTTCATTT 2 Unidirectional alignment (log-probability: -32.7) TAAAGGAATTACATGTTTTAAAATTTTTTATCTATGAAtgttTACTtctgAAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTG TAAAGGAATTACATGTTTTAAAATTTTTTATCTATGAA----TACT----AAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTG Template switch alignment (log-probability: -22.5) TAAAGGAATTACATGTTTTAAAATTTTTTATCTATGAATg|TTTACTTCTG|AAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTG TAAAGGAATTACATGTTTTAAAATTTTTTATCTATGAATA|TTTACTTCTG|AAGTTTTCTTGTCTCCAACCTGTGTTCCTTTTCTTGCCTG ========== Event 1520 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gtgcttgataaggttagctattaCAGTTATGC------CATGCTGCCTATGTGTGGGAGA Chimp: gtgcttgataaggttagctattaCAGTTATGC------CATGCTGCCCATGTGTGGGAGA ↓ 3 1 2 4 Gorilla: gtgcttgataaagttagctattaCAGTCATAACTGTAATATGCTGCCCATGTGTGGGAGA Human: gtgcttgataaggttagctattaCAGTTATGC------CATGCTGCCTATGTGTGGGAGA Cluster: [ ] Orangutan: gtgcttgataaggttaactattaCAGTTATGT------CATGCTGCCCATGTGTGGGAGA Chimp > Gorilla --------------- chr18:31665665-31665676 Template switch process: F1: L TTGGCATGAAGCAAGTGCTTGATAAAGTTAGCTATTACAGT 1 F3: 4 ATGCTGCCCATGTGTGGGAGAGACAGTCTGGAACCACAGG R RF: TTGGCATGAAGCAAGTGCTTGATAAGGTTAGCTATTACAGTTATGCCATGCTGCCCATGTGTGGGAGAGACAGTCTGGGACCACAGG RR: AACCGTACTTCGTTCACGAACTATTCCAATCGATAATGTCAATACGGTACGACGGGTACACACCCTCTCTGTCAGACCCTGGTGTCC F2: 3 TAATGTCAATAC 2 Unidirectional alignment (log-probability: -47.2) TGGCATGAAGCAAGTGCTTGATAAaGTTAGCTATTACAGTcATaaCtgtaatATGCTGCCCATGTGTGGGAGAGACAGTCTGGaACCACAGG TGGCATGAAGCAAGTGCTTGATAAGGTTAGCTATTACAGTTATGCC------ATGCTGCCCATGTGTGGGAGAGACAGTCTGGGACCACAGG Template switch alignment (log-probability: -28.3) TGGCATGAAGCAAGTGCTTGATAAaGTTAGCTATTACAGT|CATAACTGTAAT|ATGCTGCCCATGTGTGGGAGAGACAGTCTGGaACCACAGG TGGCATGAAGCAAGTGCTTGATAAGGTTAGCTATTACAGT|CATAACTGTAAT|ATGCTGCCCATGTGTGGGAGAGACAGTCTGGGACCACAGG ========== Event 1521 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGGGCTAGTGTGGAAAATCAGTGACTCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCATG ↑ 1 4 3 2 Chimp: TTGGGCTAGTGTGGAAAATCA--GGTTCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCATG Gorilla: TTGGGCTAGTGTGGAAAATCA--GGTTCTGGAGGAATGACAGAGTCGCATTTGCTGGTATAGGCATG Human: TTGGGCTAGTGTGGAAAATCAGTGACTCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCATG Cluster: [ ] Orangutan: TTGGGCTAGTGTGGAAAATCA--GGTTCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCATG Chimp > Human ------------- chr18:29769738-29769741 Template switch process: F1: L CAGAGACAGGACTGATGACATTGGGCTAGTGTGGAAAATCAG 1 F3: 4 TCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCAT R RF: CAGAGACAGGACTGATGACATTGGGCTAGTGTGGAAAATCAGGTTCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCAT RR: GTCTCTGTCCTGACTACTGTAACCCGATCACACCTTTTAGTCCAAGACCTCCTTACTGTCTCAGTGTAAACGACCATATCCGTA F2: 3 CAGT 2 Unidirectional alignment (log-probability: -25.5) GAGACAGGACTGATGACATTGGGCTAGTGTGGAAAATCA-GTgacTCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCAT GAGACAGGACTGATGACATTGGGCTAGTGTGGAAAATCAGGT---TCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCAT Template switch alignment (log-probability: -15.8) GAGACAGGACTGATGACATTGGGCTAGTGTGGAAAATCAG|TGAC|TCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCAT GAGACAGGACTGATGACATTGGGCTAGTGTGGAAAATCAG|TGAC|TCTGGAGGAATGACAGAGTCACATTTGCTGGTATAGGCAT ========== Event 1522 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCGGTTCCAGAATAGATGATGTGCACATAA--GGCATTTCAGGGCACATTTTCTG Chimp: GTCGGTTCCAGAATAGATGATATGCACATAA--GGCATTTCAGGGCACATTTTCTG ↓ 3 1 2 4 Gorilla: GTCAGTTCCAGAATAGATGATATGCACCTTATGTGCATTTCAGGGCACATTTTCTG ↑ 3 1 2 4 Human: GTCGGTTCCAGAATAGATGATGTGCACATAA--GGCATTTCAGGGCACATTTTCTG Cluster: [ ] Orangutan: GTCAGTTCCAGAATAGATGATATGCATATAA--GGCATTTCAGGGCACATTTTCTG Human > Gorilla --------------- chr18:9953587-9953594 Template switch process: F1: L CAGTTCTAATCCAACCCCAAGTCAGTTCCAGAATAGATGATATGCAC 1 F3: 4 CATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT R RF: CAGTTCTAATCCAACCCCAAGTCGGTTCCAGAATAGATGATGTGCACATAAGGCATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT RR: GTCAAGATTAGGTTGGGGTTCAGCCAAGGTCTTATCTACTACACGTGTATTCCGTAAAGTCCCGTGTAAAAGACGTGGTCTAATAGAAAGAA F2: 3 GTGTATTC 2 Unidirectional alignment (log-probability: -41.5) AATCCAACCCCAAGTCaGTTCCAGAATAGATGATaTGCACcTtAtgtGCATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT AATCCAACCCCAAGTCGGTTCCAGAATAGATGATGTGCACATAA--GGCATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT Template switch alignment (log-probability: -27.9) AATCCAACCCCAAGTCaGTTCCAGAATAGATGATaTGCAC|CTTATGTG|CATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT AATCCAACCCCAAGTCGGTTCCAGAATAGATGATGTGCAC|CTTATGTG|CATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT Chimp > Gorilla --------------- chr18:9953587-9953594 Template switch process: F1: L TAATCCAACCCCAAGTCAGTTCCAGAATAGATGATATGCAC 1 F3: 4 CATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT R RF: TAATCCAACCCCAAGTCGGTTCCAGAATAGATGATATGCACATAAGGCATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT RR: ATTAGGTTGGGGTTCAGCCAAGGTCTTATCTACTATACGTGTATTCCGTAAAGTCCCGTGTAAAAGACGTGGTCTAATAGAAAGAA F2: 3 GTGTATTC 2 Unidirectional alignment (log-probability: -35.9) AATCCAACCCCAAGTCaGTTCCAGAATAGATGATATGCACcTtAtgtGCATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT AATCCAACCCCAAGTCGGTTCCAGAATAGATGATATGCACATAA--GGCATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT Template switch alignment (log-probability: -22.2) AATCCAACCCCAAGTCaGTTCCAGAATAGATGATATGCAC|CTTATGTG|CATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT AATCCAACCCCAAGTCGGTTCCAGAATAGATGATATGCAC|CTTATGTG|CATTTCAGGGCACATTTTCTGCACCAGATTATCTTTCTT ========== Event 1523 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGCTAGTAC-CCCATAGACTCTTGGCTTGCCAAGAGCCCTTATACAGCAGCTGCCA ↑ 3 1 24 Chimp: GGCTAGTAC-CCCATAGACTCTTGG-------CAAGCCCTTATACAGCAGCTGCCA Gorilla: GGCTAGTAC-CCCATAGACTCTTGG-------CAAGCCCTTATACAGCAGCTGCCA ↓ 3 1 4 Human: GGCTAGTAC-CCCATAGACTCTTGGCTTGCCAAGAGCCCTTATACAGCAGCTGCCA Cluster: [ ] Orangutan: GGCTAGAACCCCCATAGACTCTTGG-------CAAGCCCTTATACAGCAGCTGCCA Chimp > Human ------------- chr18:51456972-51456980 Template switch process: F1: L ATCTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC 1 F3: 4 GCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT R RF: ATCTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGCAAGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT RR: TAGACAGGAAGATCTACCCGATCATGGGGTATCTGAGAACCGTTCGGGAATATGTCGTCGACGGTGACGTATAGGTCGGTGAA F2: 3 AGAACCGTT 2 Unidirectional alignment (log-probability: -27) CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGCttgccaagAGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC-------AAGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT Template switch alignment (log-probability: -16.4) CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC|TTGCCAAGA|GCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC|TTGCCAAGA|GCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT Gorilla > Human --------------- chr18:51456972-51456979 Template switch process: F1: L ATCTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC 1 F3: 4 AGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT R RF: ATCTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGCAAGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT RR: TAGACAGGAAGATCTACCCGATCATGGGGTATCTGAGAACCGTTCGGGAATATGTCGTCGACGGTGACGTATAGGTCGGTGAA F2: 3 GAACCGTT 2 Unidirectional alignment (log-probability: -26.5) CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGCttgccaagAGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGCA-------AGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT Template switch alignment (log-probability: -16.8) CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC|TTGCCAAG|AGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT CTGTCCTTCTAGATGGGCTAGTACCCCATAGACTCTTGGC|TTGCCAAG|AGCCCTTATACAGCAGCTGCCACTGCATATCCAGCCACTT ========== Event 1524 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GCATGTTATTTCCTCTTTAACTGCTTTAATCTCATAAAGCAGTTAATTAGAATTGTTCTGA Chimp: GCCCGTTATTTCCTCTTTAACCCC---CATCTCATAAAGCAGTTAATTAGAATTGTTCTGA Gorilla: GCACGTTATTTCCTCTTTAACCCC---CATCTCATAAAGCAGTTAATTAGAATTGTTCTGA ↓ 1 4 3 2 Human: GCATGTTATTTCCTCTTTAACTGCTTTAATCTCATAAAGCAGTTAATTAGAATTGTTCTGA Cluster: [ ] Orangutan: GCACATTATTTCCTCTTTAACCCC---CATCTCATAAAGCAGTTAATTAGAATTGTTCTGA Gorilla > Human --------------- chr18:52209459-52209465 Template switch process: F1: L GGTAATCCTTTATCTGAAAAGCATGTTATTTCCTCTTTAAC 1 F3: 4 ATCTCATAAAGCAGTTAATTAGAATTGTTCTGAAGACCCA R RF: GGTAATCCTTTATCTGAAAAGCACGTTATTTCCTCTTTAACCCCCATCTCATAAAGCAGTTAATTAGAATTGTTCTGAAGACCCA RR: CCATTAGGAAATAGACTTTTCGTGCAATAAAGGAGAAATTGGGGGTAGAGTATTTCGTCAATTAATCTTAACAAGACTTCTGGGT F2: 3 ATTTCGT 2 Unidirectional alignment (log-probability: -36.4) GTAATCCTTTATCTGAAAAGCAtGTTATTTCCTCTTTAA----CtgctttaATCTCATAAAGCAGTTAATTAGAATTGTTCTGAAGACCCA GTAATCCTTTATCTGAAAAGCACGTTATTTCCTCTTTAACCCCC-------ATCTCATAAAGCAGTTAATTAGAATTGTTCTGAAGACCCA Template switch alignment (log-probability: -22.1) GTAATCCTTTATCTGAAAAGCAtGTTATTTCCTCTTTAAC|TGCTTTA|ATCTCATAAAGCAGTTAATTAGAATTGTTCTGAAGACCCA GTAATCCTTTATCTGAAAAGCACGTTATTTCCTCTTTAAC|TGCTTTA|ATCTCATAAAGCAGTTAATTAGAATTGTTCTGAAGACCCA ========== Event 1525 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTGTAGTTAAACCTGGAATGGTGGTATCA-------TTTGTTGATTTTAGGTAACCATAGT Chimp: GCTGTAGTTAAACCTGGAATGGTGGTATCA-------TTTATTGATTTTAGGTAACCATAGT ↓ 3 1 2 4 Gorilla: GCTGTAGTTAAACCTGGGATGGTGGTATAATGATACCACCATTGATTTTAGGTAACCATAGC ↑ 3 1 2 4 Human: GCTGTAGTTAAACCTGGAATGGTGGTATCA-------TTTGTTGATTTTAGGTAACCATAGT Cluster: [ ] Orangutan: GGTGTAGTTAAACTTGCGATGGTAATATCA-------TTTATTGATTTTAGGTAACCATAGT Human > Gorilla --------------- chr18:50437865-50437877 Template switch process: F1: L ATTATTAAGTAAGGCTGTAGTTAAACCTGGGATGGTGGTAT 1 F3: 4 TTGATTTTAGGTAACCATAGCGTGGCCATTGCATTTACCA R RF: ATTATTAAGTAAGGCTGTAGTTAAACCTGGAATGGTGGTATCATTTGTTGATTTTAGGTAACCATAGTGTGGCCATTGCATTTACCA RR: TAATAATTCATTCCGACATCAATTTGGACCTTACCACCATAGTAAACAACTAAAATCCATTGGTATCACACCGGTAACGTAAATGGT F2: 3 ACCACCATAGTAA 2 Unidirectional alignment (log-probability: -47.7) TTATTAAGTAAGGCTGTAGTTAAACCTGGgATGGTGGTATaatgataccacCA----TTGATTTTAGGTAACCATAGcGTGGCCATTGCATTTACCA TTATTAAGTAAGGCTGTAGTTAAACCTGGAATGGTGGTAT-----------CATTTGTTGATTTTAGGTAACCATAGTGTGGCCATTGCATTTACCA Template switch alignment (log-probability: -28.4) TTATTAAGTAAGGCTGTAGTTAAACCTGGgATGGTGGTAT|AATGATACCACCA|TTGATTTTAGGTAACCATAGcGTGGCCATTGCATTTACCA TTATTAAGTAAGGCTGTAGTTAAACCTGGAATGGTGGTAT|AATGATACCACCA|TTGATTTTAGGTAACCATAGTGTGGCCATTGCATTTACCA Chimp > Gorilla --------------- chr18:50437865-50437876 Template switch process: F1: L ATTATTAAGTAAGGCTGTAGTTAAACCTGGGATGGTGGTAT 1 F3: 4 ATTGATTTTAGGTAACCATAGCGTGGCCATTGCATTTACC R RF: ATTATTAAGTAAGGCTGTAGTTAAACCTGGAATGGTGGTATCATTTATTGATTTTAGGTAACCATAGTGTGGCCATTGCATTTACC RR: TAATAATTCATTCCGACATCAATTTGGACCTTACCACCATAGTAAATAACTAAAATCCATTGGTATCACACCGGTAACGTAAATGG F2: 3 CCACCATAGTAA 2 Unidirectional alignment (log-probability: -47.7) TTATTAAGTAAGGCTGTAGTTAAACCTGGgATGGTGGTATaatgataccacC----ATTGATTTTAGGTAACCATAGcGTGGCCATTGCATTTACC TTATTAAGTAAGGCTGTAGTTAAACCTGGAATGGTGGTAT-----------CATTTATTGATTTTAGGTAACCATAGTGTGGCCATTGCATTTACC Template switch alignment (log-probability: -28.3) TTATTAAGTAAGGCTGTAGTTAAACCTGGgATGGTGGTAT|AATGATACCACC|ATTGATTTTAGGTAACCATAGcGTGGCCATTGCATTTACC TTATTAAGTAAGGCTGTAGTTAAACCTGGAATGGTGGTAT|AATGATACCACC|ATTGATTTTAGGTAACCATAGTGTGGCCATTGCATTTACC ========== Event 1526 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AGGAATTCATCAACCAATAATAACCAGTAAGAA-----------ATAAAACCTAGCTGGTTTTCCTGCCAT ↓ 3 1 2 4 Chimp: AGGAATTCATCAACCAATAATAACCAGTAAGTTATTACTGGTTATTAAAAACTAGCTGGTTTTCCTGCCAT Gorilla: Human: AGGAATTCATCAACCAATAATAACCAGTAAGAA-----------ATAAAACCTAGCTGGTTTTCCTGCCAT Cluster: [ ] Orangutan: AGGAATTCATCAACCAATAATAACCAGTAAGAA-----------ATAAAACCTAGCTGGTTTTCCTGCCAT Human > Chimp ------------- chr1:85923694-85923707 Template switch process: F1: L AAACCTTCACAGGAATTCATCAACCAATAATAACCAGTAAG 1 F3: 4 TAAAAACTAGCTGGTTTTCCTGCCATCATTCAGCACGAACACTAAT R RF: AAACCTTCACAGGAATTCATCAACCAATAATAACCAGTAAGAAATAAAACCTAGCTGGTTTTCCTGCCATCATTCAGCACGAACACTAAT RR: TTTGGAAGTGTCCTTAAGTAGTTGGTTATTATTGGTCATTCTTTATTTTGGATCGACCAAAAGGACGGTAGTAAGTCGTGCTTGTGATTA F2: 3 TATTGGTCATTATT 2 Unidirectional alignment (log-probability: -44.8) AACCTTCACAGGAATTCATCAACCAATAATAACCAGTAAGttAttactggttatTAAAAaCTAGCTGGTTTTCCTGCCATCATTCAGCACGAAC AACCTTCACAGGAATTCATCAACCAATAATAACCAGTAAGAAA-----------TAAAACCTAGCTGGTTTTCCTGCCATCATTCAGCACGAAC Template switch alignment (log-probability: -29.1) AACCTTCACAGGAATTCATCAACCAATAATAACCAGTAAG|TTaTTACTGGTTAT|TAAAAaCTAGCTGGTTTTCCTGCCATCATTCAGCACGAAC AACCTTCACAGGAATTCATCAACCAATAATAACCAGTAAG|TTCTTACTGGTTAT|TAAAACCTAGCTGGTTTTCCTGCCATCATTCAGCACGAAC ========== Event 1527 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAATGAATGAATGGACTGGACTGACTCTGTCA------GTCTCTCCTCCTAGCATGGCACCA ↑ 3 2 1 4 Chimp: CAAATGAATGAATGGACTGGACTGACTCTGTTG---AATTTATCTCCTCCTAGCATGGCACCA Gorilla: CAAATGAATGAATGGACTGGACTGACTCTGTTGAAT---TTATCTCCTCCTAGCATGGCACCA Human: CAAATGAATGAATGGACTGGACTGACTCTGTCA------GTCTCTCCTCCTAGCATGGCACCA Cluster: [ ] Orangutan: CAAATGAATGAATGGACTAGACTGACTCTGTTGAAT---TTATCTCCTCCTAGCATGGCACCA Chimp > Human ------------- chr18:55417575-55417579 Template switch process: F1: L TATTATCTATCAAATGAATGAATGGACTGGACTGACTCTGT 1 F3: 4 TCTCCTCCTAGCATGGCACCAAAAAGGAACTCTGTACATC R RF: TATTATCTATCAAATGAATGAATGGACTGGACTGACTCTGTTGAATTTATCTCCTCCTAGCATGGCACCAAAAAGGAACTCTGTACATC RR: ATAATAGATAGTTTACTTACTTACCTGACCTGACTGAGACAACTTAAATAGAGGAGGATCGTACCGTGGTTTTTCCTTGAGACATGTAG F2: 3 CTGAC 2 Unidirectional alignment (log-probability: -28.7) ATTATCTATCAAATGAATGAATGGACTGGACTGACTCTGTcagtc--------TCTCCTCCTAGCATGGCACCAAAAAGGAACTCTGTACATC ATTATCTATCAAATGAATGAATGGACTGGACTGACTCTGT-----TGAATTTATCTCCTCCTAGCATGGCACCAAAAAGGAACTCTGTACATC Template switch alignment (log-probability: -15.9) ATTATCTATCAAATGAATGAATGGACTGGACTGACTCTGT|CAGTC|TCTCCTCCTAGCATGGCACCAAAAAGGAACTCTGTACATC ATTATCTATCAAATGAATGAATGGACTGGACTGACTCTGT|CAGTC|TCTCCTCCTAGCATGGCACCAAAAAGGAACTCTGTACATC ========== Event 1528 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTTCTGGACTCCTCAAAGTCAGTGACTTTATATTACATTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCCTGACCCCTTATTTCACTGCCAACAA Chimp: tttTTCTGGACTCCTCAAAGTCAGTGACTTTATATTATATTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCCTGACCCCTTATTTCACTGCCAACAA ↑ 3 2 1 4 Gorilla: TTTGTCTGGACTCCTCAAAGTCAGTGACTTTATATTACATTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCTATTTCCCTTATTTCACTGCCAACAA ↓ 3 2 1 4 Human: TTTTTCTGGACTCCTCAAAGTCAGTGACTTTATATTACATTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCCTGACCCCTTATTTCACTGCCAACAA Cluster: [ ] Orangutan: TTTTTCTGGACTCCTCAAAGTCAGTGACTTTATATTACACTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCCTGACCCCTTATTTCACTGCCAACAA Gorilla > Human --------------- chr18:55550400-55550404 Template switch process: F1: L CATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC 1 F3: 4 CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG R RF: GTCAGTGACTTTATATTACATTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCTATTTCCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG RR: CAGTCACTGAAATATAATGTAAATCATATTGTACCCGGGCAAATGGTAGGGTCGTGATAAATAAGATCAAGATAAAGGGAATAAAGTGACGGTTGTTACGCAAGGAGGTTAGGGAC F2: 3 CAGTC 2 Unidirectional alignment (log-probability: -28.1) ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC-----ctgacCCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCTATTT-----CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG Template switch alignment (log-probability: -16.4) ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC|CTGAC|CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC|CTGAC|CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG Gorilla > Chimp --------------- chr18:52911916-52911920 Template switch process: F1: L CATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC 1 F3: 4 CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG R RF: GTCAGTGACTTTATATTACATTTAGTATAACATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCTATTTCCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG RR: CAGTCACTGAAATATAATGTAAATCATATTGTACCCGGGCAAATGGTAGGGTCGTGATAAATAAGATCAAGATAAAGGGAATAAAGTGACGGTTGTTACGCAAGGAGGTTAGGGAC F2: 3 CAGTC 2 Unidirectional alignment (log-probability: -28.1) ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC-----ctgacCCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTCTATTT-----CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG Template switch alignment (log-probability: -16.4) ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC|CTGAC|CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG ATGGGCCCGTTTACCATCCCAGCACTATTTATTCTAGTTC|CTGAC|CCCTTATTTCACTGCCAACAATGCGTTCCTCCAATCCCTG ========== Event 1529 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GCCATGTTTAGCAAGATACATTAAAGCTGAAAATGTGGGTTTGATGTAACAGGACTTGATTACT Chimp: GCCATGTTTAGCAAGATACATCAAACCCACATTTTCAGCTTTAATGTAACAGGACTTGATCACC Gorilla: GCCATGTTTAGCAAGATACATCAAACCCACATTTTCAGCTTTAATGTAACAGGACTTGATTACT ↑ 13 24 Human: GCCATGTTTAGCAAGATACATTAAAGCTGAAAATGTGGGTTTGATGTAACAGGACTTGATTACT Cluster: [ ] Orangutan: GCCATGTTTAGCAAGATACATCAAACCCGCATTTTCAGCTTTAATGTAACAGGACTTGATTACT Human > Gorilla --------------- chr18:52541762-52541783 Template switch process: F1: L TTTTTTGCATTGAGAAGTGGGCCATGTTTAGCAAGATACAT 1 F3: 4 ATGTAACAGGACTTGATTACTCTTTGAGGCCCAAGATTTT R RF: TTTTTTGCATTGAGAAGTGGGCCATGTTTAGCAAGATACATTAAAGCTGAAAATGTGGGTTTGATGTAACAGGACTTGATTACTCTTTGAGGCCCAAGATTTT RR: AAAAAACGTAACTCTTCACCCGGTACAAATCGTTCTATGTAATTTCGACTTTTACACCCAAACTACATTGTCCTGAACTAATGAGAAACTCCGGGTTCTAAAA F2: 3 ATTTCGACTTTTACACCCAAAC 2 Unidirectional alignment (log-probability: -49.7) TTTTTGCATTGAGAAGTGGGCCATGTTTAGCAAGATACATcAAacccacattttcAGC------------TTTaATGTAACAGGACTTGATTACTCTTTGAGGCCCAAGATTTT TTTTTGCATTGAGAAGTGGGCCATGTTTAGCAAGATACATTAA------------AGCTGAAAATGTGGGTTTGATGTAACAGGACTTGATTACTCTTTGAGGCCCAAGATTTT Template switch alignment (log-probability: -18.5) TTTTTGCATTGAGAAGTGGGCCATGTTTAGCAAGATACAT|CAAACCCACATTTTCAGCTTTA|ATGTAACAGGACTTGATTACTCTTTGAGGCCCAAGATTTT TTTTTGCATTGAGAAGTGGGCCATGTTTAGCAAGATACAT|CAAACCCACATTTTCAGCTTTA|ATGTAACAGGACTTGATTACTCTTTGAGGCCCAAGATTTT ========== Event 1530 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGAAGTCACTTATACTTAAAAGTACCAGTAAAAAAGTTGTTTTTATTTAGATGCTGCTAAG ↓ 13 24 ↑ 13 24 Chimp: AGAAGTCACTTATACTTAAAAACAACTTTTTTACTGGTACTTTTATTTAGATGCTGCTAAG Gorilla: AGAAGTCACTTATACTTAAAAACAACTTTTTTACTGGTTCTTTTATTTAGATGCTGCTAAG ↓ 13 24 ↑ 13 24 Human: AGAAGTCACTTATACTTAAAAGTACCAGTAAAAAAGTTGTTTTTATTTAGATGCTGCTAAG Cluster: [ ] Orangutan: AGAAATCACTTATACTTAAAAACAACTTTTTTACTGGTACTTTTATTTAGATGCTGCTAAG Chimp > Human ------------- chr18:56780469-56780487 Template switch process: F1: L TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA 1 F3: 4 TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA R RF: TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAACAACTTTTTTACTGGTACTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA RR: ATTATAAAACTTAAGTGAAGTCTTCAGTGAATATGAATTTTTGTTGAAAAAATGACCATGAAAATAAATCTACGACGATTCAATAGAAAAGTTAATATTT F2: 3 TGTTGAAAAAATGACCATG 2 Unidirectional alignment (log-probability: -43.5) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA---------------GTACcagtaaaaaagttgtTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAACAACTTTTTTACTGGTAC---------------TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Template switch alignment (log-probability: -17.6) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|GTACCAGTAAAAAAGTTGT|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|GTACCAGTAAAAAAGTTGT|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Human > Chimp ------------- chr18:54164340-54164358 Template switch process: F1: L TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA 1 F3: 4 TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA R RF: TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAGTACCAGTAAAAAAGTTGTTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA RR: ATTATAAAACTTAAGTGAAGTCTTCAGTGAATATGAATTTTCATGGTCATTTTTTCAACAAAAATAAATCTACGACGATTCAATAGAAAAGTTAATATTT F2: 3 CATGGTCATTTTTTCAACA 2 Unidirectional alignment (log-probability: -43.5) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAacaacttttttactgGTAC---------------TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA---------------GTACCAGTAAAAAAGTTGTTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Template switch alignment (log-probability: -17.6) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|ACAACTTTTTTACTGGTAC|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|ACAACTTTTTTACTGGTAC|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Gorilla > Human --------------- chr18:56780469-56780487 Template switch process: F1: L TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA 1 F3: 4 TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA R RF: TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAACAACTTTTTTACTGGTTCTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA RR: ATTATAAAACTTAAGTGAAGTCTTCAGTGAATATGAATTTTTGTTGAAAAAATGACCAAGAAAATAAATCTACGACGATTCAATAGAAAAGTTAATATTT F2: 3 TGTTGAAAAAATGACCATG 2 Unidirectional alignment (log-probability: -48.5) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA---------------GTaCcagtaaaaaagttgtTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAACAACTTTTTTACTGGTTC---------------TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Template switch alignment (log-probability: -23.7) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|GtACCAGTAAAAAAGTTGT|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|GAACCAGTAAAAAAGTTGT|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Human > Gorilla --------------- chr18:54087552-54087570 Template switch process: F1: L TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA 1 F3: 4 TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA R RF: TAATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAGTACCAGTAAAAAAGTTGTTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA RR: ATTATAAAACTTAAGTGAAGTCTTCAGTGAATATGAATTTTCATGGTCATTTTTTCAACAAAAATAAATCTACGACGATTCAATAGAAAAGTTAATATTT F2: 3 CTTGGTCATTTTTTCAACA 2 Unidirectional alignment (log-probability: -48.5) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAAacaacttttttactgGTtC---------------TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA---------------GTACCAGTAAAAAAGTTGTTTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA Template switch alignment (log-probability: -23.7) AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|ACAACTTTTTTACTGGTtC|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA AATATTTTGAATTCACTTCAGAAGTCACTTATACTTAAAA|ACAACTTTTTTACTGGTAC|TTTTATTTAGATGCTGCTAAGTTATCTTTTCAATTATAAA ========== Event 1531 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTCATGTTAATCACATGACAC---------TGTAGTCTTGTGAGTTCATGTTATTTATTATTACTCAGATATTGT Chimp: ATTTCATGTTAATCACATGACTCGTAAATAATACGAGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATTAT ↑ 4 3 1 2 Gorilla: ATTTCATGTTAATCACATGACAC---------TGTAGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATTGT Human: ATTTCATGTTAATCACATGACAC---------TGTAGTCTTGTGAGTTCATGTTATTTATTATTACTCAGATATTGT Cluster: [ ] Orangutan: ATTTCATGTTAATCACATGACAC---------TGTAGTCTTGTGAGTTCATATTATTTATTATTACTCAGATATTGT Gorilla > Chimp --------------- chr18:54192552-54192560 Template switch process: F1: L AATTAGTATTTTGTTCTCGCATTTCATGTTAATCACATGAC-----------------TCGTA 1 F3: 4 AGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATT R RF: AATTAGTATTTTGTTCTCGCATTTCATGTTAATCACATGACACTGTAGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATT RR: TTAATCATAAAACAAGAGCGTAAAGTACAATTAGTGTACTGTGACATCAGAACACTCAAGCATAATAAATAATAATGAGTCTATAA F2: 3 GCATAATAA 2 Unidirectional alignment (log-probability: -39.5) TATTTTGTTCTCGCATTTCATGTTAATCACATGAC----TcgtaaataatacgAGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATT TATTTTGTTCTCGCATTTCATGTTAATCACATGACACTGT-------------AGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATT Template switch alignment (log-probability: -27.6) TATTTTGTTCTCGCATTTCATGTTAATCACATGAC-----------------TCGTA|AATAATACG|AGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATT TATTTTGTTCTCGCATTTCATGTTAATCACATGACACTGTAGTCTTGTGAGTTCGTA|AATAATACG|AGTCTTGTGAGTTCGTATTATTTATTATTACTCAGATATT ========== Event 1532 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAGTTAGATTACAAATCACATCTGTTTACCATAAACAGAAACCCAGTTAGACTTCACTATTCCCATCT ↓ 1 4 3 2 Chimp: TGAGTTAGATTACAAATCACA------AACTGTAAACAGAAACCCAGTTAGACTTCACTATTCCCATCT Gorilla: TGAGTTAGATTACAAATCACATCTGTTTACTGTAAACAGAAACCCAGTTAGACTTCACTATTCCCATCT Human: TGAGTTAGATTACAAATCACATCTGTTTACCATAAACAGAAACCCAGTTAGACTTCACTATTCCCATCT Cluster: [ ] Orangutan: TGAGTTAGATTACAAATCACATCTGTTTACTGTAAACAGAAACCCAGTTAGACTTCACCATTCCCATCT Human > Chimp ------------- chr18:65968434-65968438 Template switch process: F1: L GCATTTAATTTCTGGCTAATTGAGTTAGATTACAAATCACA 1 F3: 4 TAAACAGAAACCCAGTTAGACTTCACTATTCCCATCTGAG R RF: GCATTTAATTTCTGGCTAATTGAGTTAGATTACAAATCACATCTGTTTACCATAAACAGAAACCCAGTTAGACTTCACTATTCCCATCTGAG RR: CGTAAATTAAAGACCGATTAACTCAATCTAATGTTTAGTGTAGACAAATGGTATTTGTCTTTGGGTCAATCTGAAGTGATAAGGGTAGACTC F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -27.4) CATTTAATTTCTGGCTAATTGAGTTAGATTACAAATCACA----------AactgTAAACAGAAACCCAGTTAGACTTCACTATTCCCATCTGAG CATTTAATTTCTGGCTAATTGAGTTAGATTACAAATCACATCTGTTTACCA----TAAACAGAAACCCAGTTAGACTTCACTATTCCCATCTGAG Template switch alignment (log-probability: -15.9) CATTTAATTTCTGGCTAATTGAGTTAGATTACAAATCACA|AACTG|TAAACAGAAACCCAGTTAGACTTCACTATTCCCATCTGAG CATTTAATTTCTGGCTAATTGAGTTAGATTACAAATCACA|AACTG|TAAACAGAAACCCAGTTAGACTTCACTATTCCCATCTGAG ========== Event 1533 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TCCACAAGGTTTACTAAATGACTGCCTTTCAAGGCAGTCTGGACTGCCTTGAAAAGGAGAGAAGACTGGCCC ↑ 3 4 1 2 Chimp: TCCACAAGGTTTACTAAATGA------------TAAGTCCAGACTGCCTTGAAAAGGAGAGAAGACTGGCCC Gorilla: ------------------------------------------------------------------------ Human: TCCACAAGGTTTACTAAATGACTGCCTTTCAAGGCAGTCTGGACTGCCTTGAAAAGGAGAGAAGACTGGCCC Cluster: [ ] Orangutan: ------------------------------------------------------------------------ Chimp > Human ------------- chr18:57397524-57397536 Template switch process: F1: L CCAGTGGGGATGAAAAGGTATCCACAAGGTTTACTAAATGA----------CTGCCTT 1 F3: 4 GACTGCCTTGAAAAGGAGAGAAGACTGGCCCAAAGAATGC R RF: CCAGTGGGGATGAAAAGGTATCCACAAGGTTTACTAAATGATAAGTCCAGACTGCCTTGAAAAGGAGAGAAGACTGGCCCAAAGAATGC RR: GGTCACCCCTACTTTTCCATAGGTGTTCCAAATGATTTACTATTCAGGTCTGACGGAACTTTTCCTCTCTTCTGACCGGGTTTCTTACG F2: 3 GTCTGACGGAACT 2 Unidirectional alignment (log-probability: -50.3) GATGAAAAGGTATCCACAAGGTTTACTAAATG--------ActgcctttcaaggcagtctgGACTGCCTTGAAAAGGAGAGAAGACTGGCCCAAAGAATGC GATGAAAAGGTATCCACAAGGTTTACTAAATGATAAGTCCA--------------------GACTGCCTTGAAAAGGAGAGAAGACTGGCCCAAAGAATGC Template switch alignment (log-probability: -27.8) GATGAAAAGGTATCCACAAGGTTTACTAAATGA----------CTGCCTT|TCAAGGCAGTCTG|GACTGCCTTGAAAAGGAGAGAAGACTGGCCCAAAGAATGC GATGAAAAGGTATCCACAAGGTTTACTAAATGATAAGTCCAGACTGCCTT|TCAAGGCAGTCTG|GACTGCCTTGAAAAGGAGAGAAGACTGGCCCAAAGAATGC ========== Event 1534 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAA-AAAGGTGCAAGGATGGAGACAGT--CCTACCTGTCCTGAGCAGGATGGGCCCTGTG Chimp: TTAA-AAAAGTGCAAGGATGGAGACAGT--CCTACCTGTCCTGAGCAGGATGGGCCCTGTG Gorilla: TTAA-AAAGGTGCAAGGATGGGGTCAGGTAGGAACATGTCCTGAGCAGGATGGGCCCTGTG ↑ 1 3 4 2 Human: TTAA-AAAGGTGCAAGGATGGAGACAGT--CCTACCTGTCCTGAGCAGGATGGGCCCTGTG Cluster: [ ] Orangutan: ttaaaaaaagtgcaaggATGGAGACAGT--CCTACCTGTCCTGAGCAGGATGGGCCCTGTG Human > Gorilla --------------- chr18:55721284-55721295 Template switch process: F1: L CACATTAAGCTGGTCTCTCCTTTAAAAAGGTGCAAGGATGG 1 F3: 4 ACATGTCCTGAGCAGGATGGGCCCTGTGCCAAGGGGCCAGGCA R RF: CACATTAAGCTGGTCTCTCCTTTAAAAAGGTGCAAGGATGGAGACAGTCCTACCTGTCCTGAGCAGGATGGGCCCTGTGCCAAGGGGCCAGGCA RR: GTGTAATTCGACCAGAGAGGAAATTTTTCCACGTTCCTACCTCTGTCAGGATGGACAGGACTCGTCCTACCCGGGACACGGTTCCCCGGTCCGT F2: 3 AGGATGGACTGG 2 Unidirectional alignment (log-probability: -41) ACATTAAGCTGGTCTCTCCTTTAAAAAGGTGCAAGGATGGgGtcaggtaggaACA--------TGTCCTGAGCAGGATGGGCCCTGTGCCAAGGGGCCAG ACATTAAGCTGGTCTCTCCTTTAAAAAGGTGCAAGGATGGAG----------ACAGTCCTACCTGTCCTGAGCAGGATGGGCCCTGTGCCAAGGGGCCAG Template switch alignment (log-probability: -28.4) ACATTAAGCTGGTCTCTCCTTTAAAAAGGTGCAAGGATGG|GGtCAGGTAGGA|ACaTGTCCTGAGCAGGATGGGCCCTGTGCCAAGGGGCCAG ACATTAAGCTGGTCTCTCCTTTAAAAAGGTGCAAGGATGG|GGACAGGTAGGA|ACCTGTCCTGAGCAGGATGGGCCCTGTGCCAAGGGGCCAG ========== Event 1535 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAACGGTAGCTGGGTGGTGGGAAGAAT--CCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATAT Chimp: AAACAGTAGCTGGGAGGTGGGTCTTATTAGCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATAT ↑ 1 4 3 2 Gorilla: AAACAGTAGCTGGGAGGTGGGAAGAAT--CCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATAT Human: AAACGGTAGCTGGGTGGTGGGAAGAAT--CCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATAT Cluster: [ ] Orangutan: AAACAGTAGCTGGGAGGTGGGAAGAAT--CCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATAT Gorilla > Chimp --------------- chr18:55430977-55430985 Template switch process: F1: L AAATGAACTGCTTGCTAGAGAAACAGTAGCTGGGAGGTGGG 1 F3: 4 CTACGGTGGCTAATAAGACGTCTCGATCATTTGCATATGC R RF: AAATGAACTGCTTGCTAGAGAAACAGTAGCTGGGAGGTGGGAAGAATCCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATATGC RR: TTTACTTGACGAACGATCTCTTTGTCATCGACCCTCCACCCTTCTTAGGATGCCACCGATTATTCTGCAGAGCTAGTAAACGTATACG F2: 3 GATTATTCT 2 Unidirectional alignment (log-probability: -31) AATGAACTGCTTGCTAGAGAAACAGTAGCTGGGAGGTGGG-----TCttattagCTACGGTGGCTAATAAGACGTCTCGATCATTTGCATATGC AATGAACTGCTTGCTAGAGAAACAGTAGCTGGGAGGTGGGAAGAATC-------CTACGGTGGCTAATAAGACGTCTCGATCATTTGCATATGC Template switch alignment (log-probability: -16.9) AATGAACTGCTTGCTAGAGAAACAGTAGCTGGGAGGTGGG|TCTTATTAG|CTACGGTGGCTAATAAGACGTCTCGATCATTTGCATATGC AATGAACTGCTTGCTAGAGAAACAGTAGCTGGGAGGTGGG|TCTTATTAG|CTACGGTGGCTAATAAGACGTCTCGATCATTTGCATATGC ========== Event 1536 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ACCAGCAGATGCCTGTGGCTGAAGCAGAAGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCGT-GTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACACCACTTGTTTACTTTGTACCTTGTTTACTTTGCCCAAGT ↓ 3 2 1 4 Chimp: ACCAGCAGATGCCTGTGGCTGAAGCAGAAGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCGT-GTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGACCACTGCT----------TCACCTTGTTTACTTTGCCCAAGT Gorilla: ACCAGCAGATGCCTGTGGCTGAAGCAGAAGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCAT-GTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGACCACTGCT----------TCACCTTGTTTACTTTGCCCAAGT ↑ 3 2 1 4 Human: ACCAGCAGATGCCTGTGGCTGAAGCAGAAGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCGT-GTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACACCACTTGTTTACTTTGTACCTTGTTTACTTTGCCCAAGT Cluster: [ ] Orangutan: ACCAGCAGATGCCTGCGGCTGAAGCAGAGGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCGTGTTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGACCATTGCT----------TCACCTTGTTTACTTTGCCCAAGT Human > Chimp ------------- chr18:66292942-66292948 Template switch process: F1: L TCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGACCAC 1 F3: 4 CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA R RF: TGAAGCAGAAGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCGTGTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACACCACTTGTTTACTTTGTACCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA RR: ACTTCGTCTTCTATCTACGTAAGAGTTTCAAAGTCGGACGAGTGTCTAACCGGTGACGTGTAAAGCACATAGATAAATTATAACGGACCTTTAGAGGTTTCCAAAATGGCTTGTGGTGAACAAATGAAACATGGAACAAATGAAACGGGTTCACTGTTCACTCTTTGTCCT F2: 3 ACTTCGT 2 Unidirectional alignment (log-probability: -35.1) TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAcCACtgcttCA---------------CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACAC-----CACTTGTTTACTTTGTACCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA Template switch alignment (log-probability: -22.2) TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAcCAC|TGCTTCA|CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACAC|TGCTTCA|CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA Human > Gorilla --------------- chr18:69077363-69077369 Template switch process: F1: L TCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGACCAC 1 F3: 4 CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAAGA R RF: TGAAGCAGAAGATAGATGCATTCTCAAAGTTTCAGCCTGCTCACAGATTGGCCACTGCACATTTCGTGTATCTATTTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACACCACTTGTTTACTTTGTACCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA RR: ACTTCGTCTTCTATCTACGTAAGAGTTTCAAAGTCGGACGAGTGTCTAACCGGTGACGTGTAAAGCACATAGATAAATTATAACGGACCTTTAGAGGTTTCCAAAATGGCTTGTGGTGAACAAATGAAACATGGAACAAATGAAACGGGTTCACTGTTCACTCTTTGTCCT F2: 3 ACTTCGT 2 Unidirectional alignment (log-probability: -39.1) TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAcCACtgCTT----------cACCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAaGA TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACACCACTTGTTTACTTTGTACCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA Template switch alignment (log-probability: -27.7) TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAcCAC|TGCTTCA|CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAaGA TTAATATTGCCTGGAAATCTCCAAAGGTTTTACCGAACAC|TGCTTCA|CCTTGTTTACTTTGCCCAAGTGACAAGTGAGAAACAGGA ========== Event 1537 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GGAACAGAAGTTACGAAAATAAATTTGGCAAAGTACCTTCGAATAAGTTTGTATTTAAAATCTAACAGAGGAAGAAAGTTGTC Chimp: GGAACAGAAGTTACGAAAATAAATTTGGCAAAGCACCTTCGAATAAGTTTGTATTTAAAATCTAACAGAGGAAGAAAGTTGTC ↓ 13 24 ↑ 13 24 Gorilla: GGAACAGAAGTTACGAAAATAGATTTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATTTAACAGAGGAAGAAAGTTGTC ↓ 13 24 ↑ 13 24 Human: GGAACAGAAGTTACGAAAATAAATTTGGCAAAGTACCTTCGAATAAGTTTGTATTTAAAATCTAACAGAGGAAGAAAGTTGTC Cluster: [ ] Orangutan: GGAACAGAAGTTACGAAAATAAATTTGGCAAAGCACCTTTGAATAAGTTTGTATTTAAAATCTAACAGAGGAAGAAAGTCGTC Gorilla > Human --------------- chr18:58976049-58976089 Template switch process: F1: L GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA 1 F3: 4 TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG R RF: GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAGATTTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATTTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG RR: CTTCCTCGATCATTATAACTCCTTGTCTTCAATGCTTTTATCTAAAATTTATGTTTGAATAAGCTTCCACGAAACGGTTTAAATTGTCTCCTTCTTTCAACAGACAATCCATTACACTGGTC F2: 3 CTAAAATTTATGTTTGAATAAGCTTCCATGAAACGGTTTAA 2 Unidirectional alignment (log-probability: -75) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAaATttggcaaagtaccttcgaataagtttgtaTTTA-----------------------------AAATcTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAGAT-----------------------------TTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATTTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Template switch alignment (log-probability: -26.4) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|AATTTGGCAAAGtACCTTCGAATAAGTTTGTATTTAAAATC|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|AATTTGGCAAAGCACCTTCGAATAAGTTTGTATTTAAAATC|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Human > Gorilla --------------- chr18:56316928-56316968 Template switch process: F1: L GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA 1 F3: 4 TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG R RF: GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAAATTTGGCAAAGTACCTTCGAATAAGTTTGTATTTAAAATCTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG RR: CTTCCTCGATCATTATAACTCCTTGTCTTCAATGCTTTTATTTAAACCGTTTCATGGAAGCTTATTCAAACATAAATTTTAGATTGTCTCCTTCTTTCAACAGACAATCCATTACACTGGTC F2: 3 TTAAACCGTTTCGTGGAAGCTTATTCAAACATAAATTTTAG 2 Unidirectional alignment (log-probability: -75) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAgAT-----------------------------TTTAaatacaaacttattcgaaggtgctttgccAAATtTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAAATTTGGCAAAGTACCTTCGAATAAGTTTGTATTTA-----------------------------AAATCTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Template switch alignment (log-probability: -26.4) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|GATTTTAAATACAAACTTATTCGAAGGTgCTTTGCCAAATT|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|GATTTTAAATACAAACTTATTCGAAGGTACTTTGCCAAATT|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Gorilla > Chimp --------------- chr18:56391320-56391360 Template switch process: F1: L GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA 1 F3: 4 TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG R RF: GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAGATTTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATTTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG RR: CTTCCTCGATCATTATAACTCCTTGTCTTCAATGCTTTTATCTAAAATTTATGTTTGAATAAGCTTCCACGAAACGGTTTAAATTGTCTCCTTCTTTCAACAGACAATCCATTACACTGGTC F2: 3 CTAAAATTTATGTTTGAATAAGCTTCCACGAAACGGTTTAA 2 Unidirectional alignment (log-probability: -75) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAaATttggcaaagcaccttcgaataagtttgtaTTTA-----------------------------AAATcTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAGAT-----------------------------TTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATTTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Template switch alignment (log-probability: -20.9) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|AATTTGGCAAAGCACCTTCGAATAAGTTTGTATTTAAAATC|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|AATTTGGCAAAGCACCTTCGAATAAGTTTGTATTTAAAATC|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Chimp > Gorilla --------------- chr18:56316928-56316968 Template switch process: F1: L GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA 1 F3: 4 TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG R RF: GAAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAAATTTGGCAAAGCACCTTCGAATAAGTTTGTATTTAAAATCTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG RR: CTTCCTCGATCATTATAACTCCTTGTCTTCAATGCTTTTATTTAAACCGTTTCGTGGAAGCTTATTCAAACATAAATTTTAGATTGTCTCCTTCTTTCAACAGACAATCCATTACACTGGTC F2: 3 TTAAACCGTTTCGTGGAAGCTTATTCAAACATAAATTTTAG 2 Unidirectional alignment (log-probability: -75) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAgAT-----------------------------TTTAaatacaaacttattcgaaggtgctttgccAAATtTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATAAATTTGGCAAAGCACCTTCGAATAAGTTTGTATTTA-----------------------------AAATCTAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG Template switch alignment (log-probability: -20.9) AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|GATTTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATT|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG AAGGAGCTAGTAATATTGAGGAACAGAAGTTACGAAAATA|GATTTTAAATACAAACTTATTCGAAGGTGCTTTGCCAAATT|TAACAGAGGAAGAAAGTTGTCTGTTAGGTAATGTGACCAG ========== Event 1538 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGTGATGGCATTACTTGGGTGAAT--------------------------------------------------------------------------------------------------------AAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAAGATACTTTAACTATTTTAGCTAAAATTACATAA ↓ 4 3 1 2 Chimp: TGGTGATGGCATTACTTGGGTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAATAGTTAAAGTATCTTAAGAGGGTTTTTCTGTACTTCAAATGTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAAGATACTTTAACTATTTTAGCTAAAATTACATAA ↑ 4 3 1 2 Gorilla: TGGTGATGGCATTACTTGGGTGAAT--------------------------------------------------------------------------------------------------------AAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAAGATAATTTAACTATTTTAGCTAAAATTACATAA Human: TGGTGATGGCATTACTTGGGTGAAT--------------------------------------------------------------------------------------------------------AAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAAGATACTTTAACTATTTTAGCTAAAATTACATAA Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human > Chimp ------------- chr18:56365156-56365195 Template switch process: F1: L AAGGTAAAGATAGTGGTGGTGATGGCATTACTTGGGTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAA 1 F3: 4 GTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGT R RF: AAGGTAAAGATAGTGGTGGTGATGGCATTACTTGGGTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAAACAGTAAAACCCTCTTAAGATACTTTAACTA RR: TTCCATTTCTATCACCACCACTACCGTAATGAACCCACTTATTTTCGTACCCTCTACGTAAAGTAGTAAGAGTAAACTTCATGTCATTTTGGGAGAATTTGTCATTTTGGGAGAATTCTATGAAATTGAT F2: 3 TAAACTTCATGTCTTTTTGGGAGAATTCTATGAAATTGAT 2 Unidirectional alignment (log-probability: -157) TTTCATCATTCTCATTTGAAGTacagtaaaaccctcttaatagttaaagtatcttaagagggtttttctgtacttcaaatgtgaataaaagcatgggagatgcatttcatcattctcatt TTTCATCATTCTCATTTGAAGT-------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -27.2) TTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAA|TAGTTAAAGTATCTTAAGAGGGTTTTtCTGTACTTCAAAT|GTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATT TTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAA|TAGTTAAAGTATCTTAAGAGGGTTTTACTGTACTTCAAAT|GTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATT Gorilla > Chimp --------------- chr18:56365156-56365195 Template switch process: F1: L AAGGTAAAGATAGTGGTGGTGATGGCATTACTTGGGTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAA 1 F3: 4 GTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGT R RF: AAGGTAAAGATAGTGGTGGTGATGGCATTACTTGGGTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAAACAGTAAAACCCTCTTAAGATAATTTAACTA RR: TTCCATTTCTATCACCACCACTACCGTAATGAACCCACTTATTTTCGTACCCTCTACGTAAAGTAGTAAGAGTAAACTTCATGTCATTTTGGGAGAATTTGTCATTTTGGGAGAATTCTATTAAATTGAT F2: 3 TAAACTTCATGTCTTTTTGGGAGAATTCTATGAAATTGAT 2 Unidirectional alignment (log-probability: -157) TTTCATCATTCTCATTTGAAGTacagtaaaaccctcttaatagttaaagtatcttaagagggtttttctgtacttcaaatgtgaataaaagcatgggagatgcatttcatcattctcatt TTTCATCATTCTCATTTGAAGT-------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -33.2) TTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAA|TAGTTAAAgTATCTTAAGAGGGTTTTtCTGTACTTCAAAT|GTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATT TTTCATCATTCTCATTTGAAGTACAGTAAAACCCTCTTAA|TAGTTAAATTATCTTAAGAGGGTTTTACTGTACTTCAAAT|GTGAATAAAAGCATGGGAGATGCATTTCATCATTCTCATT ========== Event 1539 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGGAAAATATATTCTTGGTACAAGTTCTTTACTGGCTAAGTGGCAAGATT--------------------------TTATCGGGGTGGAGCCAGATGACTTGAAAACTTGTCTGAAAACGGCAATCGTTG ↑ 1 4 3 2 Chimp: CTTGAAAATATATTCTTGGTATGAGGTCTTTACTGGCTAAGTGGCAAGATT-------------TTATAATTTGCTTTTATCGGGGTGGAGCCAGATGACTTGAAAACTTGTCTGAAAACGGCAATCGTTG Gorilla: CTGGAAAATATATTCTTGGTACGAGGTCTTTACTGGATAAGTGGCAAGATTTTATAATTTGCTT-------------TTATCGGGGTGGAGCCCGATGACTTGAAAACTTGTCTGAAAATGGCAGTCGTTG Human: CTGGAAAATATATTCTTGGTACAAGTTCTTTACTGGCTAAGTGGCAAGATT--------------------------TTATCGGGGTGGAGCCAGATGACTTGAAAACTTGTCTGAAAACGGCAATCGTTG Cluster: [ ] Orangutan: CTGGAAAATATATTCTTGGTACGAGGTTTTTACTGGATAAGTGGCAAGATTTTATAATTTGCTC-------------TTATCAGGGTGGAGCCAGATGGCTTGAAAACTTGTCTAAAAATGGCAATCTTTG Chimp > Human ------------- chr18:59142345-59142349 Template switch process: F1: L TTCAAGCATGGGAAATTATACTGGAAAATATATTCTTGGTA 1 F3: 4 TCTTTACTGGCTAAGTGGCAAGATTTT R RF: TTCAAGCATGGGAAATTATACTTGAAAATATATTCTTGGTATGAGGTCTTTACTGGCTAAGTGGCAAGATTTTATAATTTGCTTTTATCGGGGTGGAGCCAGATGACTTGAAAACTTG RR: AAGTTCGTACCCTTTAATATGAACTTTTATATAAGAACCATACTCCAGAAATGACCGATTCACCGTTCTAAAATATTAAACGAAAATAGCCCCACCTCGGTCTACTGAACTTTTGAAC F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -32.5) TCAAGCATGGGAAATTATACTgGAAAATATATTCTTGGTAcaAGtTCTTTACTGGCTAAGTGGCAAGATTTT------------- TCAAGCATGGGAAATTATACTTGAAAATATATTCTTGGTATGAGGTCTTTACTGGCTAAGTGGCAAGATTTTATAATTTGCTTTT Template switch alignment (log-probability: -21.6) TCAAGCATGGGAAATTATACTgGAAAATATATTCTTGGTA|CAAGT|TCTTTACTGGCTAAGTGGCAAGATTTT TCAAGCATGGGAAATTATACTTGAAAATATATTCTTGGTA|CAAGT|TCTTTACTGGCTAAGTGGCAAGATTTT ========== Event 1540 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTTTTGTCAGCTAATTGGCATGTGTGTGTGCAGGCGCACATGAGCATGTAAAACTGCAA Chimp: GGTTTTGTCAGCTAATTGGCATGTGTGTGTGCACG--CGCATGAGCATGTAAAACTGCAA Gorilla: GGTTTTGTCAGCTAATTGGCATGTGTGTGTGCACACATGCATGAGCATGTAAGACTGCAA ↑ 3 2 1 4 Human: GGTTTTGTCAGCTAATTGGCATGTGTGTGTGCAGGCGCACATGAGCATGTAAAACTGCAA Cluster: [ ] Orangutan: GGTTTTGCCAGCTAATTGACGT--GTGTGTGCATGCGCATGTGAGCATGTAAAACTGCAA Human > Gorilla --------------- chr18:21082060-21082065 Template switch process: F1: L CTTCTGTAGGTTTTGTCAGCTAATTGGCATGTGTGTGTGCA 1 F3: 4 CATGAGCATGTAAGACTGCAACACGTTTCCTTTTCCTGTA R RF: CTTCTGTAGGTTTTGTCAGCTAATTGGCATGTGTGTGTGCAGGCGCACATGAGCATGTAAAACTGCAACACGTTTCCTTTTCCTGTA RR: GAAGACATCCAAAACAGTCGATTAACCGTACACACACACGTCCGCGTGTACTCGTACATTTTGACGTTGTGCAAAGGAAAAGGACAT F2: 3 GTACAC 2 Unidirectional alignment (log-probability: -32.1) TTCTGTAGGTTTTGTCAGCTAATTGGCATGTGTGTGTGCA----CAcatgCATGAGCATGTAAgACTGCAACACGTTTCCTTTTCCTGTA TTCTGTAGGTTTTGTCAGCTAATTGGCATGTGTGTGTGCAGGCGCA----CATGAGCATGTAAAACTGCAACACGTTTCCTTTTCCTGTA Template switch alignment (log-probability: -22) TTCTGTAGGTTTTGTCAGCTAATTGGCATGTGTGTGTGCA|CACATG|CATGAGCATGTAAgACTGCAACACGTTTCCTTTTCCTGTA TTCTGTAGGTTTTGTCAGCTAATTGGCATGTGTGTGTGCA|CACATG|CATGAGCATGTAAAACTGCAACACGTTTCCTTTTCCTGTA ========== Event 1541 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: ctctgtgtgtctgcagagcacctggatcatagtggtgcttgataagtatttggcgaatgaaCAACAAACCTAAGAAATGCCCAGGTCTAAGAAATGCCTTCTGCAACCGTGGATCTTT Chimp: ctctgtgtgtctgcagagcacctggatcatagtggtgcttgataagtatttggcaaatgaaCAACAAACCTAAG-----------------AAATGCCTTCTGCAACCGTGGATCTTT ↓ 3 2 4 1 Gorilla: ctctgtgtgtctgcagagcacctggatcatagtggtgcttgataagtatttggcgaatgaacaaCAAACCTAAGAAATGCCCAGGTCTAAGAAATGCCTTCTGCAACCGTGGATCTTT Human: ctctgtgtgtctgcagagcacctggatcatagtggtgcttgataagtatttggcgaatgaaCAACAAACCTAAGAAATGCCCAGGTCTAAGAAATGCCTTCTGCAACCGTGGATCTTT Cluster: [ ] Orangutan: ctctgtgtgtctgcagagcacctggatcatagtggtgcttgataagtatttggcgaatgaaCAACAAACCTAAGAAATGCCGAGGTCTAAGAAATGCCTTCTGCAACCCTGGATCTTT Chimp > Gorilla --------------- chr18:21388722-21388726 Template switch process: F1: L GGTGCTTGATAAGTATTTGGCGAATGAACAACAAACCTAAGAAATGCC 1 F3: 4 CTAAGAAATGCCTTCTGCAACCGTGGATCTTTGGAGACGCATTAA R RF: ACCTGGATCATAGTGGTGCTTGATAAGTATTTGGCAAATGAACAACAAACCTAAGAAATGCCTTCTGCAACCGTGGATCTTTGGAGATGCATTAA RR: TGGACCTAGTATCACCACGAACTATTCATAAACCGTTTACTTGTTGTTTGGATTCTTTACGGAAGACGTTGGCACCTAGAAACCTCTACGTAATT F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -46.4) ATAAGTATTTGGCgAATGAACAACAAACctaagaaatgcccaggtCTAAGAAATGCCTTCTGCAACCGTGGATCTTTGGAGAcGC ATAAGTATTTGGCAAATGAACAACAAAC-----------------CTAAGAAATGCCTTCTGCAACCGTGGATCTTTGGAGATGC Template switch alignment (log-probability: -27.7) ATAAGTATTTGGCgAATGAACAACAAACCTAAGAAATGCC|CAGGT|CTAAGAAATGCCTTCTGCAACCGTGGATCTTTGGAGAcGC ATAAGTATTTGGCAAATGAACAACAAACCTAAGAAATGCC|CAGGT|CTAAGAAATGCCTTCTGCAACCGTGGATCTTTGGAGATGC ========== Event 1542 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAA--AAGTAAACAGCTATAACATCTGCA ↓ 13 24 ↑ 1 3 24 Chimp: ATCACATTCTGTTTTAGATTAC--TTTTTCATCCCGCAAATAAAAGCAATAAACAGCTATAACATCTGCA ↓ 1 3 24 ↑ 13 24 Gorilla: ATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAA--AAGTAAACAGCTATAACATCTGCA Human: ATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAA--AAGTAAACAGCTATAACATCTGCA Cluster: [ ] Orangutan: ATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAA--AAGTAAACAGCTATAACATCTGCA Chimp > Human ------------- chr18:20682917-20682942 Template switch process: F1: L TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA 1 F3: 4 TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG R RF: TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTACTTTTTCATCCCGCAAATAAAAGCAATAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG RR: ACTCATAGATCTCTTGTTTCTAGTGTAAGACAAAATCTAATGAAAAAGTAGGGCGTTTATTTTCGTTATTTGTCGATATTGTAGACGTCAAGGAGAAGACGGTTCAC F2: 3 GAAAAAGTAGGGCGTTTATTTTCGTT 2 Unidirectional alignment (log-probability: -59.8) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATT--------------------------AttgcttttatttgcgggatgaaaaagTAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTACTTTTTCATCCCGCAAATAAAAGCAA--------------------------TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Template switch alignment (log-probability: -18.5) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|TTGCTTTTATTTGCGGGATGAAAAAG|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|TTGCTTTTATTTGCGGGATGAAAAAG|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Human > Chimp ------------- chr18:21089409-21089434 Template switch process: F1: L TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA 1 F3: 4 TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG R RF: TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAAAAGTAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG RR: ACTCATAGATCTCTTGTTTCTAGTGTAAGACAAAATCTAATAACGAAAATAAACGCCCTACTTTTTCATTTGTCGATATTGTAGACGTCAAGGAGAAGACGGTTCAC F2: 3 AACGAAAATAAACGCCCTACTTTTTC 2 Unidirectional alignment (log-probability: -59.8) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA--------------------------ctttttcatcccgcaaataaaagcaaTAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAAAAG--------------------------TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Template switch alignment (log-probability: -18.5) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|CTTTTTCATCCCGCAAATAAAAGCAA|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|CTTTTTCATCCCGCAAATAAAAGCAA|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Gorilla > Chimp --------------- chr18:21089409-21089434 Template switch process: F1: L TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA 1 F3: 4 TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG R RF: TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAAAAGTAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG RR: ACTCATAGATCTCTTGTTTCTAGTGTAAGACAAAATCTAATAACGAAAATAAACGCCCTACTTTTTCATTTGTCGATATTGTAGACGTCAAGGAGAAGACGGTTCAC F2: 3 AACGAAAATAAACGCCCTACTTTTTC 2 Unidirectional alignment (log-probability: -59.3) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA--------------------------ctttttcatcccgcaaataaaagcaaTAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTATTGCTTTTATTTGCGGGATGAAAAAG--------------------------TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Template switch alignment (log-probability: -19) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|CTTTTTCATCCCGCAAATAAAAGCAA|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|CTTTTTCATCCCGCAAATAAAAGCAA|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Chimp > Gorilla --------------- chr18:20857717-20857742 Template switch process: F1: L TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA 1 F3: 4 TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG R RF: TGAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTACTTTTTCATCCCGCAAATAAAAGCAATAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG RR: ACTCATAGATCTCTTGTTTCTAGTGTAAGACAAAATCTAATGAAAAAGTAGGGCGTTTATTTTCGTTATTTGTCGATATTGTAGACGTCAAGGAGAAGACGGTTCAC F2: 3 GAAAAAGTAGGGCGTTTATTTTCGTT 2 Unidirectional alignment (log-probability: -59.3) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATT--------------------------AttgcttttatttgcgggatgaaaaagTAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTACTTTTTCATCCCGCAAATAAAAGCAA--------------------------TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG Template switch alignment (log-probability: -19) GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|TTGCTTTTATTTGCGGGATGAAAAAG|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG GAGTATCTAGAGAACAAAGATCACATTCTGTTTTAGATTA|TTGCTTTTATTTGCGGGATGAAAAAG|TAAACAGCTATAACATCTGCAGTTCCTCTTCTGCCAAGTG ========== Event 1543 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TTGAAAGCACCAAGTTGTCACTGATCCAATAGAAGTCTGCTCCCTTGTCTGTTATTCAAAAACTACTGTAGCAGAAAGGCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTAC--------------------CAAAATGGCAGAGGTGAAGGAG ↓ 3 2 4 1 Chimp: TTGAAAGCACCAAGTTGTCACTGATCCAATAGAAGTCTGCTCCCTTGTCTGTTATTCAAAAACTACTGTAGCAGAAAGGCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTAC----------CAGATCAGTCCAAAATGGCAGAGGTGAAGGAG Gorilla: Human: TTGAAAGCACCAAGTTGTCACTGATCCAATAGAAGTCTGCTCCCTTGTCTGTTATTCAAAAACTACTGTAGCAGAAAGGCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTAC--------------------CAAAATGGCAGAGGTGAAGGAG Cluster: [ ] Orangutan: TTGAAAGCACTAAGTTGTCACCGATCCAATAGAGTTCTGCTCCCTCGTCTGTTATTCAAAAACTACTGTAGCAGAAAGGCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTACCAGATCGGTC----------CAAAATGGCAGAGGTGAAGGAG Human > Chimp ------------- chr18:20274020-20274026 Template switch process: F1: L AAGGCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTACCA 1 F3: 4 CCAAAATGGCAGAGGTGAAGGAGACACCTGTAATGACTTCA R RF: ACTGATCCAATAGAAGTCTGCTCCCTTGTCTGTTATTCAAAAACTACTGTAGCAGAAAGGCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTACCAAAATGGCAGAGGTGAAGGAGACACCTGAAATGACTTCA RR: TGACTAGGTTATCTTCAGACGAGGGAACAGACAATAAGTTTTTGATGACATCGTCTTTCCGTACCCTGACCCGACTCACAACCACTGTACCTCGATGGTTTTACCGTCTCCACTTCCTCTGTGGACTTTACTGAAGT F2: 3 TGACTAG 2 Unidirectional alignment (log-probability: -31.3) GCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTAccagatcagtCCAAAATGGCAGAGGTGAAGGAGACACCTGtAATGACTTC GCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTA----------CCAAAATGGCAGAGGTGAAGGAGACACCTGAAATGACTTC Template switch alignment (log-probability: -22.2) GCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTACCA|GATCAGT|CCAAAATGGCAGAGGTGAAGGAGACACCTGtAATGACTTC GCATGGGACTGGGCTGAGTGTTGGTGACATGGAGCTACCA|GATCAGT|CCAAAATGGCAGAGGTGAAGGAGACACCTGAAATGACTTC ========== Event 1544 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: aagaatcatagaacAATTTCTTTAGAAGTTCATTCTAAAGAATTCTCCCTATGAAGGGCAT ↑ 3 2 1 4 Chimp: AAGAATCATAGAACAATTTCTTTAGAAGTTCATTTGT--AAATTCTCCCTATGAAGGGCAT Gorilla: aagaatcatagaacaatttctttagaagttcatttgt--aaattctccctataaagggcgt Human: aagaatcatagaacAATTTCTTTAGAAGTTCATTCTAAAGAATTCTCCCTATGAAGGGCAT Cluster: [ ] Orangutan: aagaatcatagaacaatttctctagaagttaatttgc--aaattctccctatgaagggcat Chimp > Human ------------- chr18:61151372-61151377 Template switch process: F1: L GTGATCCAAGAATCATAGAACAATTTCTTTAGAAGTTCATT 1 F3: 4 AATTCTCCCTATGAAGGGCATGTCTGATAGCTGCTTTGGT R RF: GTGATCCAAGAATCATAGAACAATTTCTTTAGAAGTTCATTTGTAAATTCTCCCTATGAAGGGCATGTCTGATAGCTGCTTTGGT RR: CACTAGGTTCTTAGTATCTTGTTAAAGAAATCTTCAAGTAAACATTTAAGAGGGATACTTCCCGTACAGACTATCGACGAAACCA F2: 3 GAAATC 2 Unidirectional alignment (log-probability: -30) TGATCCAAGAATCATAGAACAATTTCTTTAGAAGTTCATTctaaag----AATTCTCCCTATGAAGGGCATGTCTGATAGCTGCTTTGGT TGATCCAAGAATCATAGAACAATTTCTTTAGAAGTTCATT------TGTAAATTCTCCCTATGAAGGGCATGTCTGATAGCTGCTTTGGT Template switch alignment (log-probability: -16) TGATCCAAGAATCATAGAACAATTTCTTTAGAAGTTCATT|CTAAAG|AATTCTCCCTATGAAGGGCATGTCTGATAGCTGCTTTGGT TGATCCAAGAATCATAGAACAATTTCTTTAGAAGTTCATT|CTAAAG|AATTCTCCCTATGAAGGGCATGTCTGATAGCTGCTTTGGT ========== Event 1545 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGGTTGGTTACCTTGAAAGCATGGGAATGGAGATATCACTAAA------CATAAAATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAAATGAAAT ↓ 1 3 4 2 Chimp: CAGGTTGATTACCTTGAAAGTATGGGAATGGAGATATCATTAAA------TATTTTATATTTAATGATATCTCCATTCCCATACTTTCCCACtaaaatgaaat Gorilla: CAGGTTGATTACCTTGAAAGTATGGGAATGGAGATATCATTAAA------TATAAAATATTTAATGATATCTCCATTCCCATACTTTCCCACtaaaatgaaat Human: CAGGTTGGTTACCTTGAAAGCATGGGAATGGAGATATCACTAAA------CATAAAATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAAATGAAAT Cluster: [ ] Orangutan: CAGGTTGATTACCTTGAAAGTATGGGAATGGAGATATCACTAAATATAAATATAAAATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAAATGAAAT Human > Chimp ------------- chr1:142043522-142043551 Template switch process: F1: L CACAGGTTGATTACCTTGAAAG 1 F3: 4 ATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAA R RF: CACAGGTTGGTTACCTTGAAAGCATGGGAATGGAGATATCACTAAACATAAAATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAA RR: GTGTCCAACCAATGGAACTTTCGTACCCTTACCTCTATAGTGATTTGTATTTTATAAATTACTATAGAGGTAAGGGTATGAAAGGGTGATTT F2: 3 TTTTATAAATTACTATAGAGGTAAGGGTAT 2 Unidirectional alignment (log-probability: -42.7) CACAGGTTGaTTACCTTGAAAGtATGGGAATGGAGATATCAtTAAAtATtttATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAA CACAGGTTGGTTACCTTGAAAGCATGGGAATGGAGATATCACTAAACATAAAATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAA Template switch alignment (log-probability: -24.6) CACAGGTTGaTTACCTTGAAAG|TATGGGAATGGAGATATCATTAAATATTTT|ATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAA CACAGGTTGGTTACCTTGAAAG|TATGGGAATGGAGATATCATTAAATATTTT|ATATTTAATGATATCTCCATTCCCATACTTTCCCACTAAA ========== Event 1546 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TACCTAGGAGTACTGTCTGAGGGGCTATATAGGAAACTT---AATTTAAAACCATGGGTCTCCTTGTTACACACA Chimp: TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTT---AATTTAAAACCATGGGTCTCCTTGTTACACACA ↓ 3 2 1 4 Gorilla: TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTT------ACAGCCCCTTGGGTCTCCTTGTTACACACA Human: TACCTAGGAGTACTGTCTGAGGGGCTATATAGGAAACTT---AATTTAAAACCATGGGTCTCCTTGTTACACACA Cluster: [ ] Orangutan: TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTAAT---TTAAAACCATGGGTCTCCTTGTCTCACACA Chimp > Gorilla --------------- chr18:58806387-58806394 Template switch process: F1: L TATACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTA 1 F3: 4 TGGGTCTCCTTGTTACACACAGTGTGACATAAT-------------CTCTGCC R RF: TATACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTAATTTAAAACCATGGGTCTCCTTGTTACACACAGTGTGACATAATCCAAGAACATACACTCTGCC RR: ATATGGATCCTCATGACAGACTCCCCGACATATCCTTTGAATTAAATTTTGGTACCCAGAGGAACAATGTGTGTCACACTGTATTAGGTTCTTGTATGTGAGACGG F2: 3 TCCCCGAC 2 Unidirectional alignment (log-probability: -50.7) TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTA---------CAgcccctTGGGTCTCCTTGTTACACACAGTGTGACATAATCtctgCc TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTAATTTAAAACCA------TGGGTCTCCTTGTTACACACAGTGTGACATAATC----CA Template switch alignment (log-probability: -27.2) TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTA|CAGCCCCT|TGGGTCTCCTTGTTACACACAGTGTGACATAAT-------------CTCTGCC TACCTAGGAGTACTGTCTGAGGGGCTGTATAGGAAACTTA|CAGCCCCT|TGGGTCTCCTTGTTACACACAGTGTGACATAATCCAAGAACATACACTCTGCC ========== Event 1547 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AGGCACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACCCTGCTGACCTCAGTATACACCTAATGCCAGTCACCTTTCC ↑ 3 2 4 1 Chimp: GGGCACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCA-------------------GTATACACCTAATGCCAGTCACCTTTCC ↓ 4 3 2 1 Gorilla: GGGCACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACTCTGCTGACCTCAGTATACACCTAATGCCAGTCACCTTTCC Human: AGGCACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACCCTGCTGACCTCAGTATACACCTAATGCCAGTCACCTTTCC Cluster: [ ] Orangutan: AGGCACACTGGGTGAAACACTCCACAGGCTTTCATTTTTGCCTCAGTATACTCTGCTGACCTCAGTATACACCTAATGCCAGTCACCTTTCC Chimp > Human ------------- chr18:63481808-63481816 Template switch process: F1: L ACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATAC 1 F3: 4 CTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGTGTGAT R RF: ACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGTGTGAT RR: TGTGACCCACTTTGTGAGTTGTCCGAAAGTAAAAACGGAGTCATATGTGGATTACGGTCAGTGGAAAGGGACCCCACACTA F2: 3 CAGTCGTCC 2 Unidirectional alignment (log-probability: -38.2) GTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATAccctgctgacctcagtataCACCTAATGCCAGTCACCTTTCCCTGGGGTG GTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATA-------------------CACCTAATGCCAGTCACCTTTCCCTGGGGTG Template switch alignment (log-probability: -28.6) GTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATAC|CCTGcTGAc|CTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGTG GTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATAC|CCTGTTGAG|CTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGTG Chimp > Gorilla --------------- chr18:60988110-60988115 Template switch process: F1: L ACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACTC 1 F3: 4 CCTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGTGTGAT R RF: ACACTGGGTGAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGTGTGAT RR: TGTGACCCACTTTGTGAGTTGTCCGAAAGTAAAAACGGAGTCATATGTGGATTACGGTCAGTGGAAAGGGACCCCACACTA F2: 3 AGTCGT 2 Unidirectional alignment (log-probability: -38.2) GAAACACTCAACAGGCTTTCATTTTTGCCTcagtatactctgctgacctCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGT GAAACACTCAACAGGCTTTCATTTTTGCCT-------------------CAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGT Template switch alignment (log-probability: -27.8) GAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACtC|TgCTGA|CCTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGT GAAACACTCAACAGGCTTTCATTTTTGCCTCAGTATACAC|TACTGA|CCTCAGTATACACCTAATGCCAGTCACCTTTCCCTGGGGT ========== Event 1548 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AAGGAACCATAGTGCTTTAATTGCATGTTTAAGAATCTATTACATTTTCCTTTTAATGTTATGAGATGGAAGTTGTTTGATGAGT ↓ 3 2 1 4 Chimp: AAGGAACCATAGTGCTTTAATTGCATGTTTAAGAAT------------------CATGCAA--TCATGGAAGTTGTTTGATGAGT Gorilla: Human: AAGGAACCATAGTGCTTTAATTGCATGTTTAAGAATCTATTACATTTTCCTTTTAATGTTATGAGATGGAAGTTGTTTGATGAGT Cluster: [ ] Orangutan: Human > Chimp ------------- chr1:86946045-86946051 Template switch process: F1: L GTGAAAAGGAACCATAGTGCTTTAATTGCATGTTTAAGAATC 1 F3: 4 CATGGAAGTTGTTTGATGAGTCTCTGGTTCTTTGGGGAAAA R RF: GTGAAAAGGAACCATAGTGCTTTAATTGCATGTTTAAGAATCTATTACATTTTCCTTTTAATGTTATGAGATGGAAGTTGTTTGATGAGTCTCTGGTTCTTTGGGGAAAA RR: CACTTTTCCTTGGTATCACGAAATTAACGTACAAATTCTTAGATAATGTAAAAGGAAAATTACAATACTCTACCTTCAACAAACTACTCAGAGACCAAGAAACCCCTTTT F2: 3 TAACGTA 2 Unidirectional alignment (log-probability: -34.1) GAAAAGGAACCATAGTGCTTTAATTGCATGTTTAAGaatcatgcAATC----------------------------ATGGAAGTTGTTTGATGAGTCTCTGGTTCTTTGGGGAAA GAAAAGGAACCATAGTGCTTTAATTGCATGTTTAAG--------AATCTATTACATTTTCCTTTTAATGTTATGAGATGGAAGTTGTTTGATGAGTCTCTGGTTCTTTGGGGAAA Template switch alignment (log-probability: -22.2) GAAAAGGAACCATAGTGCTTTAATTGCATGTTTAAGAATC|ATGCAAT|cATGGAAGTTGTTTGATGAGTCTCTGGTTCTTTGGGGAAA GAAAAGGAACCATAGTGCTTTAATTGCATGTTTAAGAATC|ATGCAAT|GATGGAAGTTGTTTGATGAGTCTCTGGTTCTTTGGGGAAA ========== Event 1549 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCATAATTGGGATTGGATCCAT----TTACTGTACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAA ↑ 1 4 3 2 Chimp: GCATAATTGGGATTGGATCCAC--TCATAACATACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAA Gorilla: GCATAATTGGGATTGGATCCATTA--ATAACATACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAA ↓ 1 4 3 2 Human: GCATAATTGGGATTGGATCCAT----TTACTGTACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAA Cluster: [ ] Orangutan: GCATAATTGGGATTGGATCCATTA--ATAACATACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAA Chimp > Human ------------- chr1:86744012-86744018 Template switch process: F1: L TTCAGTTGGCACAATTTAATGCATAATTGGGATTGGATCCA 1 F3: 4 TACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG R RF: TTCAATTGGCACAATTTAATGCATAATTGGGATTGGATCCACTCATAACATACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG RR: AAGTTAACCGTGTTAAATTACGTATTAACCCTAACCTAGGTGAGTATTGTATGACACCATGTCATTTCTCTTACACAAGAATAACTTGTC F2: 3 GTCATTT 2 Unidirectional alignment (log-probability: -37.7) TCAgTTGGCACAATTTAATGCATAATTGGGATTGGATC---------CATttactgtACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG TCAATTGGCACAATTTAATGCATAATTGGGATTGGATCCACTCATAACAT-------ACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG Template switch alignment (log-probability: -22.1) TCAgTTGGCACAATTTAATGCATAATTGGGATTGGATCCA|TTTACTG|TACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG TCAATTGGCACAATTTAATGCATAATTGGGATTGGATCCA|TTTACTG|TACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG Gorilla > Human --------------- chr1:86744014-86744020 Template switch process: F1: L TCAGTTGGCACAATTTAATGCATAATTGGGATTGGATCCATT 1 F3: 4 CTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG R RF: TCAATTGGCACAATTTAATGCATAATTGGGATTGGATCCATTAATAACATACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG RR: AGTTAACCGTGTTAAATTACGTATTAACCCTAACCTAGGTAATTATTGTATGACACCATGTCATTTCTCTTACACAAGAATAACTTGTC F2: 3 ATGTCAT 2 Unidirectional alignment (log-probability: -33.1) AgTTGGCACAATTTAATGCATAATTGGGATTGGATCCATT--TActgTACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG AATTGGCACAATTTAATGCATAATTGGGATTGGATCCATTAATAACATACTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG Template switch alignment (log-probability: -22.1) AgTTGGCACAATTTAATGCATAATTGGGATTGGATCCATT|TACTGTA|CTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG AATTGGCACAATTTAATGCATAATTGGGATTGGATCCATT|TACTGTA|CTGTGGTACAGTAAAGAGAATGTGTTCTTATTGAACAG ========== Event 1550 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCATGTCATAGGCACAGATCCTTGGAACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAG ↑ 1 4 3 2 Chimp: ACCATGTCATAGGCACAGATCTAT--GACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAG Gorilla: ACCATGTCATAGGCACAGATCTAT--GACCTTTTTGTTCCAAAGCAGGACTGTTTTCCCTAAG Human: ACCATGTCATAGGCACAGATCCTTGGAACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAG Cluster: [ ] Orangutan: CCCATGTCATAGGCACAGATCTAT--GACCTTTGCATTCCAAAGCGGGACTGTTTTCCCTAAG Chimp > Human ------------- chr18:65802934-65802939 Template switch process: F1: L TGAACATGAAGCTCTAAGTAACCATGTCATAGGCACAGATC 1 F3: 4 ACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAGGAAT R RF: TGAACATGAAGCTCTAAGTAACCATGTCATAGGCACAGATCTATGACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAGGAAT RR: ACTTGTACTTCGAGATTCATTGGTACAGTATCCGTGTCTAGATACTGGAAAACCAAGGTTCCGTCCTGACAAAAGGGATTCCTTA F2: 3 AGGTTC 2 Unidirectional alignment (log-probability: -25.8) GAACATGAAGCTCTAAGTAACCATGTCATAGGCACAGATCctTGgaACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAGGAAT GAACATGAAGCTCTAAGTAACCATGTCATAGGCACAGATCTATG--ACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAGGAAT Template switch alignment (log-probability: -16) GAACATGAAGCTCTAAGTAACCATGTCATAGGCACAGATC|CTTGGA|ACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAGGAAT GAACATGAAGCTCTAAGTAACCATGTCATAGGCACAGATC|CTTGGA|ACCTTTTGGTTCCAAGGCAGGACTGTTTTCCCTAAGGAAT ========== Event 1551 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAGTGCTGGGTGAAAAGGGATGATCAGTAGTGGCAGAGAGCAAAGACAACAGTGGAAGAACCACTCTCCTGGTGAAGCATTCAGGAGACAATACGTGTAAGTTAGACAATAATGAGAATGCATTCTGATCATCCATTCCTTAACCCATGATGTTTAAA ↑ 3 2 4 1 Chimp: AGAGTGCTGGGTGAAAAGGGATGATCAGTAGTGGCAGAGGGCAAAGACAACAGTGGAAGAACCACTCTCCTGGTGAAGCATTCAGGAGACAATATGTGTAAGTTAGACAATAATGAGAATGCA-------------TTCCTTAACCCATGATGTTTAAA ↓ 3 2 4 1 Gorilla: AGAGTGCTGGGTGAAAAGGGATGATCAGTAGTGGCAGAGAGCAAAGACAACAGTGGAAGAACCTCTCTCCTGGTGAAGCATTCAGGAGACAATATGTGTAAGTTAGACAATAATAAGAATGCATTCTGATCATCCATTCCTTAACCCATGATGTTTAAA Human: AGAGTGCTGGGTGAAAAGGGATGATCAGTAGTGGCAGAGAGCAAAGACAACAGTGGAAGAACCACTCTCCTGGTGAAGCATTCAGGAGACAATACGTGTAAGTTAGACAATAATGAGAATGCATTCTGATCATCCATTCCTTAACCCATGATGTTTAAA Cluster: [ ] Orangutan: AGAGTGCTGGGTGAAAAGGGATGATCAGTAGTGGCAGAGAGCAAAGACAACAGTGGAAGAACCACTCTCCTGGTGAAGCATTCAGGAGACCATATGTGTAAGTTAGACAATAATGAGAATGCATTCTGATCATCCATTTCTTAACCCATGATGTTTAAA Chimp > Human ------------- chr18:13718214-13718221 Template switch process: F1: L CAGGAGACAATACGTGTAAGTTAGACAATAATGAGAATGCATTC 1 F3: 4 CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGGTG R RF: GATGATCAGTAGTGGCAGAGGGCAAAGACAACAGTGGAAGAACCACTCTCCTGGTGAAGCATTCAGGAGACAATATGTGTAAGTTAGACAATAATGAGAATGCATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGGTG RR: CTACTAGTCATCACCGTCTCCCGTTTCTGTTGTCACCTTCTTGGTGAGAGGACCACTTCGTAAGTCCTCTGTTATACACATTCAATCTGTTATTACTCTTACGTAAGGAATTGGGTACTACAAATTTAATGTTCACCTTACCAC F2: 3 CTACTAGT 2 Unidirectional alignment (log-probability: -35.6) AGACAATAcGTGTAAGTTAGACAATAATGAGAATGCAttctgatcatccaTTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG AGACAATATGTGTAAGTTAGACAATAATGAGAATGCA-------------TTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG Template switch alignment (log-probability: -22.4) AGACAATAcGTGTAAGTTAGACAATAATGAGAATGCATTC|TGATCATC|CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG AGACAATATGTGTAAGTTAGACAATAATGAGAATGCATTC|TGATCATC|CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG Chimp > Gorilla --------------- chr18:13720792-13720799 Template switch process: F1: L TGAAGCATTCAGGAGACAATATGTGTAAGTTAGACAATAATAAGAATGCATTC 1 F3: 4 CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGGTG R RF: GATGATCAGTAGTGGCAGAGGGCAAAGACAACAGTGGAAGAACCACTCTCCTGGTGAAGCATTCAGGAGACAATATGTGTAAGTTAGACAATAATGAGAATGCATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGGTG RR: CTACTAGTCATCACCGTCTCCCGTTTCTGTTGTCACCTTCTTGGTGAGAGGACCACTTCGTAAGTCCTCTGTTATACACATTCAATCTGTTATTACTCTTACGTAAGGAATTGGGTACTACAAATTTAATGTTCACCTTACCAC F2: 3 CTACTAGT 2 Unidirectional alignment (log-probability: -35.2) AGACAATATGTGTAAGTTAGACAATAATaAGAATGcattctgatcatcCATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG AGACAATATGTGTAAGTTAGACAATAATGAGAATG-------------CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG Template switch alignment (log-probability: -22.6) AGACAATATGTGTAAGTTAGACAATAATaAGAATGCATTC|TGATCATC|CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG AGACAATATGTGTAAGTTAGACAATAATGAGAATGCATTC|TGATCATC|CATTCCTTAACCCATGATGTTTAAATTACAAGTGGAATGG ========== Event 1552 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGCAAGAACTTGTTTCAGGTATATTAGCATATAAACTCATCATTTATATGCTAATACATGTCCTCCAGTGGTTT ↑ 4 1 3 2 Chimp: TGGCAAGAACTTGTTTCAGGT----------ATAAACTCATCATTTATATGCTAATACATGTCCTCCAGTGGTTT Gorilla: TGACAAGAACTTGTTTCAGGT----------ATAAACTCATCATTTATATGCTAATACATGTCCTCCAGTGGTTT Human: TGGCAAGAACTTGTTTCAGGTATATTAGCATATAAACTCATCATTTATATGCTAATACATGTCCTCCAGTGGTTT Cluster: [ ] Orangutan: TGGCAGGAACTTGTTTCAGGT----------ATAAACTCATCATTTATATGCTAATACATGTCCTCCAATGGTTT Chimp > Human ------------- chr18:73461883-73461888 Template switch process: F1: L AAGAAAAGAAAAGAAAAATATGGCAAGAACTTGTTTCAGGTATA 1 F3: 4 TATAAACTCATCATTTATATGCTAATACATGTCCTCCAGTG R RF: AAGAAAAGAAAAGAAAAATATGGCAAGAACTTGTTTCAGGTATAAACTCATCATTTATATGCTAATACATGTCCTCCAGTG RR: TTCTTTTCTTTTCTTTTTATACCGTTCTTGAACAAAGTCCATATTTGAGTAGTAAATATACGATTATGTACAGGAGGTCAC F2: 3 ACGATT 2 Unidirectional alignment (log-probability: -25.3) AAAGAAAAGAAAAATATGGCAAGAACTTGTTTCAGGtatattagcaTATAAACTCATCATTTATATGCTAATACATGTCCTCCAGT AAAGAAAAGAAAAATATGGCAAGAACTTGTTTCAGG----------TATAAACTCATCATTTATATGCTAATACATGTCCTCCAGT Template switch alignment (log-probability: -16.1) AAAGAAAAGAAAAATATGGCAAGAACTTGTTTCAGGTATA|TTAGCA|TATAAACTCATCATTTATATGCTAATACATGTCCTCCAGT AAAGAAAAGAAAAATATGGCAAGAACTTGTTTCAGGTATA|TTAGCA|TATAAACTCATCATTTATATGCTAATACATGTCCTCCAGT ========== Event 1553 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCGCTCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGGTTAAAGCCCAGCCTCGCCTCTGGCTTTTG Chimp: CCCGCTCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGGG--TCGTCCAGCCTCGCCTCTGGCTTTTG Gorilla: CCCGCTCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGGG--TCGTCCAGCCTCGCCTCTGGCTTTTG ↓ 3 2 1 4 Human: CCCGCTCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGGTTAAAGCCCAGCCTCGCCTCTGGCTTTTG Cluster: [ ] Orangutan: CCCGCTCTTCGCAGTCTTAGGCTTTAACCTCCTCGGGCTTCGGGGG--TCGTCCAGCCTCGCCTCTGGCTTTTG Gorilla > Human --------------- chr18:73255872-73255879 Template switch process: F1: L CTCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGG 1 F3: 4 CAGCCTCGCCTCTGGCTTTTGCGGGACTTCGCGACCCAG R RF: CTCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGGGTCGTCCAGCCTCGCCTCTGGCTTTTGCGGGACTTCGCGACCCAG RR: GAGAAACGTCCGAATCCGAAATTGGAGGAGCCCGAAACCCCCAGCAGGTCGGAGCGGAGACCGAAAACGCCCTGAAGCGCTGGGTC F2: 3 CCGAAATT 2 Unidirectional alignment (log-probability: -29.5) TCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGG----GTtaaagcCCAGCCTCGCCTCTGGCTTTTGCGGGACTTCGCGACCCAG TCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGGGTCGT------CCAGCCTCGCCTCTGGCTTTTGCGGGACTTCGCGACCCAG Template switch alignment (log-probability: -16.7) TCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGG|TTAAAGCC|CAGCCTCGCCTCTGGCTTTTGCGGGACTTCGCGACCCAG TCTTTGCAGGCTTAGGCTTTAACCTCCTCGGGCTTTGGGG|TTAAAGCC|CAGCCTCGCCTCTGGCTTTTGCGGGACTTCGCGACCCAG ========== Event 1554 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAACCCAGCCTATGCTATATCTCAGCAAATATTTGTATGATT---------------------------------------------TATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGATAGAATAATCAAATGCACACACAAA Chimp: AAAACCCAGCCTATGCTATATCTCAGCAAATATTTGTATGATT---------------------------------------------TATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGACAGAATAATCAAATGCACACACAAA ↓ 3 2 1 4 Gorilla: AAAACCCAGCCTATGCTATATCTCAGCAAATATTTG-CTGAGA------------------------------------------------------------------------------------------TATAATCAAATGCACACACAAA ↑ 3 2 1 4 Human: AAAACCCAGCCTATGCTATATCTCAGCAAATATTTGTATGATT---------------------------------------------TATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGATAGAATAATCAAATGCACACACAAA Cluster: [ ] Orangutan: AAAACCCAGCCTATGCTATATCTCAGCAAATATTTGTATGATTTATATATGCACTGGTAATAATTAATGGTCATCTTTATCTAGACAG---------------------------------------------AATAATCAAATGCACACACAAA Human > Gorilla --------------- chr18:8141455-8141461 Template switch process: F1: L TTTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG 1 F3: 4 ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT R RF: TTTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTGTATGATTTATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGATAGAATAATCAAATGCACACACAAACACATTCATATGCGCAAAT RR: AAAAATTTTGGGTCGGATACGATATAGAGTCGTTTATAAACATACTAAATATATACGTAACCATTATTAATTACCAGTAGAAATAGATCTATCTTATTAGTTTACGTGTGTGTTTGTGTAAGTATACGCGTTTA F2: 3 TAGAGTC 2 Unidirectional alignment (log-probability: -31.9) TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTGctgagaT----------------------------------------------------ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG------TATGATTTATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGATAGAATAATCAAATGCACACACAAACACATTCATATGCGCAAAT Template switch alignment (log-probability: -16.6) TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG|CTGAGAT|ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG|CTGAGAT|ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT Chimp > Gorilla --------------- chr18:8141455-8141461 Template switch process: F1: L TTTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG 1 F3: 4 ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT R RF: TTTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTGTATGATTTATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGACAGAATAATCAAATGCACACACAAACACATTCATATGCGCAAAT RR: AAAAATTTTGGGTCGGATACGATATAGAGTCGTTTATAAACATACTAAATATATACGTAACCATTATTAATTACCAGTAGAAATAGATCTGTCTTATTAGTTTACGTGTGTGTTTGTGTAAGTATACGCGTTTA F2: 3 TAGAGTC 2 Unidirectional alignment (log-probability: -31.9) TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTGctgagaT----------------------------------------------------ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG------TATGATTTATATATGCATTGGTAATAATTAATGGTCATCTTTATCTAGACAGAATAATCAAATGCACACACAAACACATTCATATGCGCAAAT Template switch alignment (log-probability: -16.6) TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG|CTGAGAT|ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT TTTTAAAACCCAGCCTATGCTATATCTCAGCAAATATTTG|CTGAGAT|ATAATCAAATGCACACACAAACACATTCATATGCGCAAAT ========== Event 1555 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTTGTAGATGCCTAAAATGT----TAAAAGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGATTA ↓ 1 4 3 2 Chimp: TGTTGTAGGTGCCTAAAATGTTCTTAGACAGCAAATATATGCCTGTCTAAGAACTGCTGATGGAAAGATTA Gorilla: TGTTGTAGATGCCTAAAATGT----TAAAAGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGATTA Human: TGTTGTAGATGCCTAAAATGT----TAAAAGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGATTA Cluster: [ ] Orangutan: TGTTGTAGATGCCTAAAATGT----TAAAAGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGATTA Human > Chimp ------------- chr18:66451079-66451085 Template switch process: F1: L TTGAATACAAGTGTAATTTCTGTTGTAGGTGCCTAAAATGTT 1 F3: 4 AGCAAATATATGCCTGTCTAAGAACTGCTGATGGAAAGATTAGCAATTG R RF: TTGAATACAAGTGTAATTTCTGTTGTAGATGCCTAAAATGTTAAAAGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGATTAGCAATTG RR: AACTTATGTTCACATTAAAGACAACATCTACGGATTTTACAATTTTCGTTTATGTACGGACAGATTCTTGACGACTACCTTTCTAATCGTTAAC F2: 3 CAGATTC 2 Unidirectional alignment (log-probability: -40.8) GAATACAAGTGTAATTTCTGTTGTAGgTGCCTAAAATGTTcttagAcAGCAAATAtATGCCTGTCTAAGAACTGCTGATGGAAAGAT GAATACAAGTGTAATTTCTGTTGTAGATGCCTAAAATGTT----AAAAGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGAT Template switch alignment (log-probability: -28.3) GAATACAAGTGTAATTTCTGTTGTAGgTGCCTAAAATGTT|CTTAGAC|AGCAAATAtATGCCTGTCTAAGAACTGCTGATGGAAAGAT GAATACAAGTGTAATTTCTGTTGTAGATGCCTAAAATGTT|CTTAGAC|AGCAAATACATGCCTGTCTAAGAACTGCTGATGGAAAGAT ========== Event 1556 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTATCATCAATAATAGTTACTGCTGTTCAACTGAGA-TGTGATTTAATATTACTAACAAAAT ↓ 3 2 1 4 Chimp: TTTATCATCAATAATAGTTACTGCTGTTCAACTGACAGCAGTATTTAATATTACTAACAAAAT ↑ 3 2 1 4 Gorilla: TTTATCATCAATAATAGTTACTGCTGTTCAACTGAGA-TATGATTTAATATTACTAACAAAAT Human: TTTATCATCAATAATAGTTACTGCTGTTCAACTGAGA-TGTGATTTAATATTACTAACAAAAT Cluster: [ ] Orangutan: TTTTTCATCAATAATAGTTACTACTGTTCAACTGAGA-TATGGTTTAATATT----ACAAAAT Human > Chimp ------------- chr1:87489990-87489996 Template switch process: F1: L TAGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA 1 F3: 4 ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC R RF: TAGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGAGATGTGATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC RR: ATCATTAAATAGTAGTTATTATCAATGACGACAAGTTGACTCTACACTAAATTATAATGATTGTTTTAACAAGAATTAAAAGGTATG F2: 3 TGACGAC 2 Unidirectional alignment (log-probability: -31.5) AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGAcagcagt------ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA-------GATGTGATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC Template switch alignment (log-probability: -16.2) AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA|CAGCAGT|ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA|CAGCAGT|ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC Gorilla > Chimp --------------- chr1:87489990-87489996 Template switch process: F1: L TAGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA 1 F3: 4 ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC R RF: TAGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGAGATATGATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC RR: ATCATTAAATAGTAGTTATTATCAATGACGACAAGTTGACTCTATACTAAATTATAATGATTGTTTTAACAAGAATTAAAAGGTATG F2: 3 TGACGAC 2 Unidirectional alignment (log-probability: -31) AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA------cagcagtATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGAGATATG-------ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC Template switch alignment (log-probability: -16.6) AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA|CAGCAGT|ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC AGTAATTTATCATCAATAATAGTTACTGCTGTTCAACTGA|CAGCAGT|ATTTAATATTACTAACAAAATTGTTCTTAATTTTCCATAC ========== Event 1557 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGCCTCGCATTGGTGTTAGGGGTGCAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATTTCTCCCACAGAAATATTCAATAGGCGTCACTGACTGAGCCTTTCAGTGCTGCTCTCCTAGACAACTAAAGGGCTGCAAGAACTTTTTTTCCTTGGAGTT ↑ 4 1 3 2 Chimp: AGGATGGATTGCACTCGTGTTGGTGTCAGG----------------------GGTGCAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATTTCTCCCACAGAAATATTCAATAGGCGTCACTGACTGAGCCTTTCAGTGCTGCTCTCCTAGACAACTGAAGGGCTGCAAGAACtttttttCCTTGGAGTT Gorilla: AGGATGGATTGCActcgtgttggtgtcaggggtgcctcgcgttggtgttaggggtgcAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATTTCTCCCACAGAAATACTCAATAGGCGTCACTGACTGAGCCTTTCAGTGCTGCTCTCCTAGACAACTGAAGGACTGCAAGAACtttttttCCTTGGAGTT Human: AGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGCCTCGCATTGGTGTTAGGGGTGCAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATTTCTCCCACAGAAATATTCAATAGGCGTCACTGACTGAGCCTTTCAGTGCTGCTCTCCTAGACAACTAAAGGGCTGCAAGAACTTTTTTTCCTTGGAGTT Cluster: [ ] Orangutan: AGGATgggttgcactcgtgttggtgtcaggggtgcctcgcgttggtgttaggggtgcAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATTTCTCCCACGGAAATATTCAATAGGTGTCACTGACTGAGCCTTTCAGTGCTGCTCTCCCAGACAACTGAAGGGCTGCAAGAACTT-TTTTCCTTGGAGTT Chimp > Human ------------- chr18:70414371-70414376 Template switch process: F1: L GCCATCGGGGCAGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGC 1 F3: 4 TTGGTGTTAGGGGTGCAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATT R RF: GCCATCGGGGCAGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGCAAAGGTCGCTGCTGCCCAGCCTGCAGTGGTTGATTTCTCCCACAGAAATATTCAATAGGCGTCACTGACTGAGCCTTTCAGTGCTGCTCTCCTAGACAACTGAAGGGCTGCAAG RR: CGGTAGCCCCGTCCTACCTAACGTGAGCACAACCACAGTCCCCACGTTTCCAGCGACGACGGGTCGGACGTCACCAACTAAAGAGGGTGTCTTTATAAGTTATCCGCAGTGACTGACTCGGAAAGTCACGACGAGAGGATCTGTTGACTTCCCGACGTTC F2: 3 ACGCTC 2 Unidirectional alignment (log-probability: -42.6) GGGGCAGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGCctcgcattggtgttaggggtgcAAAGGTCGCTGCTGCCCAGCCTGC GGGGCAGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGC----------------------AAAGGTCGCTGCTGCCCAGCCTGC Template switch alignment (log-probability: -28.3) GGGGCAGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGC|CTcGCA|TTGGTGTtAGGGGTGCAAAGGTCGCTGCTGCCCAGCCTGC GGGGCAGGATGGATTGCACTCGTGTTGGTGTCAGGGGTGC|CTTGCA|TTGGTGTCAGGGGTGCAAAGGTCGCTGCTGCCCAGCCTGC ========== Event 1558 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAATGGTGCACCTGAGAGAAACTGCGTCTGCCTTCCACAGACAGAACATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCACAGT-TGGCAATTTTATTGTTATTATT ↑ 3 2 1 4 Chimp: TAATGGTGCACCTGAGAGAAACTGCGTCTGCCTTCCACAGACAGAACATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTC--AGTCAGGCAATTTTATTGTTATTATT Gorilla: TAATGGTGCACCTGAGAGAAACTGCGTCTGCCTTCCACAGACAGAACATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCACAGTCAGGCAATTTTATTGTTATTATT Human: TAATGGTGCACCTGAGAGAAACTGCGTCTGCCTTCCACAGACAGAACATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCACAGT-TGGCAATTTTATTGTTATTATT Cluster: [ ] Orangutan: TAACGGTGCACCTGAGAGAAACCGTGTCTGCCTTCCACACACAGAACATTAGCAGTAACAGGAAACCACAAGTCTGTTAGGAGGTCACAGTCAGGCAATTTTATTGTTATTATT Chimp > Human ------------- chr18:9700480-9700484 Template switch process: F1: L ACATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCA 1 F3: 4 GGCAATTTTATTGTTATTATTGAGGATGGTGATCAGAGGC R RF: AACTGCGTCTGCCTTCCACAGACAGAACATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCAGTCAGGCAATTTTATTGTTATTATTGAGGATGGTGATCAGAGGC RR: TTGACGCAGACGGAAGGTGTCTGTCTTGTAATCGTTATTGTCCTTTGGTGTTCAGACAATCCTCCAGTCAGTCCGTTAAAATAACAATAATAACTCCTACCACTAGTCTCCG F2: 3 TTGAC 2 Unidirectional alignment (log-probability: -25.6) ATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCA--CAgttGGCAATTTTATTGTTATTATTGAGGATGGTGATCAGAGGC ATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCAGTCA---GGCAATTTTATTGTTATTATTGAGGATGGTGATCAGAGGC Template switch alignment (log-probability: -15.9) ATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCA|CAGTT|GGCAATTTTATTGTTATTATTGAGGATGGTGATCAGAGGC ATTAGCAATAACAGGAAACCACAAGTCTGTTAGGAGGTCA|CAGTT|GGCAATTTTATTGTTATTATTGAGGATGGTGATCAGAGGC ========== Event 1559 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTCAGTAGGAGTCTCTCTGTATCTCCTGCTGATAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAATAGAAGATAAGACTCTTTCTTTAGCTCTCACTCCACTTTATTTCTGGGGTCTTTTAGAAACACTATACTGGTTCAGTCTCAAGACTTTCCATGAGAATTAGTC ↓ 1 4 3 2 Chimp: CGTCAGTAGGAGTCTCTCTGTC----TT-----GAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAATAGAAGATAAGACTCTTTCTTTAGCTCTCACTCCACTTTATTTTTGGGGTCTTTTAGAAACACTATACTGGTTCAGTCTCAAGACTTTCCATGAGAATTAGTC ↑ 1 4 3 2 Gorilla: CGTCAGTAGGAGTCTCTCTGTATCCCCTGCTGACAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAAAAGAAGATAAGACTCTTTCTTTAGCTGTCACTCCACTTTATTTTTGGGGTCTTTTAGAAACACTGTACTGGTTCAGTCTCAAGACTTTCCATGAGAATTAGTC Human: TGTCAGTAGGAGTCTCTCTGTATCTCCTGCTGATAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAATAGAAGATAAGACTCTTTCTTTAGCTCTCACTCCACTTTATTTCTGGGGTCTTTTAGAAACACTATACTGGTTCAGTCTCAAGACTTTCCATGAGAATTAGTC Cluster: [ ] Orangutan: AGTCAGTAGGAGTCTCTCTGTATCCCCAGCTGATAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAATAGAAGATAAGACTCTTTCTTTAGCTCTCACTCCATTTTATTTTTGGGGTCTTTTAGAAACACTATACTGGTTCAGTCTCAAGACTTTCCATGAGAATTAGTC Human > Chimp ------------- chr18:9790012-9790016 Template switch process: F1: L TATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGT 1 F3: 4 GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT R RF: TATGTGTGCATGAAGGCTGATGTCAGTAGGAGTCTCTCTGTATCTCCTGCTGATAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAATAGAAGATAAGACTCTTTCTTTAGCTCTCACTCCACTTTATTTCTGGGGTCTTTTAGAAACACTATACTGGTTCAGTCTCAAG RR: ATACACACGTACTTCCGACTACAGTCATCCTCAGAGAGACATAGAGGACGACTATCCTAGGGGAGTTCTGTAGTTTTTGCTGGGACCTGTTGTACATCTTTATCTTCTATTCTGAGAAAGAAATCGAGAGTGAGGTGAAATAAAGACCCCAGAAAATCTTTGTGATATGACCAAGTCAGAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -33.5) ATGTGTGCATGAAGGCTGAcGTCAGTAGGAGTCTCTCTGTcttgA-------------GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT ATGTGTGCATGAAGGCTGATGTCAGTAGGAGTCTCTCTGT----ATCTCCTGCTGATAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT Template switch alignment (log-probability: -21.9) ATGTGTGCATGAAGGCTGAcGTCAGTAGGAGTCTCTCTGT|CTTGA|GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT ATGTGTGCATGAAGGCTGATGTCAGTAGGAGTCTCTCTGT|CTTGA|GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT Gorilla > Chimp --------------- chr18:9790012-9790016 Template switch process: F1: L TATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGT 1 F3: 4 GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT R RF: TATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGTATCCCCTGCTGACAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACATGTAGAAAAAGAAGATAAGACTCTTTCTTTAGCTGTCACTCCACTTTATTTTTGGGGTCTTTTAGAAACACTGTACTGGTTCAGTCTCAAG RR: ATACACACGTACTTCCGACTGCAGTCATCCTCAGAGAGACATAGGGGACGACTGTCCTAGGGGAGTTCTGTAGTTTTTGCTGGGACCTGTTGTACATCTTTTTCTTCTATTCTGAGAAAGAAATCGACAGTGAGGTGAAATAAAAACCCCAGAAAATCTTTGTGACATGACCAAGTCAGAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -25.6) ATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGT------------CttgAGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT ATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGTATCCCCTGCTGAC---AGGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT Template switch alignment (log-probability: -16.3) ATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGT|CTTGA|GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT ATGTGTGCATGAAGGCTGACGTCAGTAGGAGTCTCTCTGT|CTTGA|GGATCCCCTCAAGACATCAAAAACGACCCTGGACAACAT ========== Event 1560 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: accgcacccggccAAAAAGAGTTATT---------------TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC ↓ 4 1 3 2 Chimp: accgcacccggccAAAAAGAGCTATTTTTTAAATTGTTACATTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC ↑ 4 1 3 2 Gorilla: accgcacccggccAAAAAGAGCTATT---------------TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC Human: accgcacccggccAAAAAGAGTTATT---------------TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC Cluster: [ ] Orangutan: accgcaccctgccaaaaagagttatt---------------ttttaagccaacataacaatttgcctctgaatagaattta Human > Chimp ------------- chr18:68504936-68504944 Template switch process: F1: L TGGGATTACAGGCGTGAGCCACCGCACCCGGCCAAAAAGAGCTATTTTTTAA 1 F3: 4 TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC R RF: TGGGATTACAGGCGTGAGCCACCGCACCCGGCCAAAAAGAGTTATTTTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC RR: ACCCTAATGTCCGCACTCGGTGGCGTGGGCCGGTTTTTCTCAATAAAAAATTCGGTTACATTGTTAAACGGAGACTTATCTTAATG F2: 3 ACATTGTTA 2 Unidirectional alignment (log-probability: -38.5) CGTGAGCCACCGCACCCGGCCAAAAAGAGcTATTTTTTAAattgttacattttaaGCCAATGTAACAATTTGCCTCTGAATAGAATTAC CGTGAGCCACCGCACCCGGCCAAAAAGAGTTATTTTTTAA---------------GCCAATGTAACAATTTGCCTCTGAATAGAATTAC Template switch alignment (log-probability: -22.6) CGTGAGCCACCGCACCCGGCCAAAAAGAGcTATTTTTTAA|ATTGTTACA|TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC CGTGAGCCACCGCACCCGGCCAAAAAGAGTTATTTTTTAA|ATTGTTACA|TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC Gorilla > Chimp --------------- chr18:68504936-68504944 Template switch process: F1: L TTACAGGCGTGAGCCACCGCACCCGGCCAAAAAGAGCTATTTTTTAA 1 F3: 4 TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC R RF: TTACAGGCGTGAGCCACCGCACCCGGCCAAAAAGAGCTATTTTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC RR: AATGTCCGCACTCGGTGGCGTGGGCCGGTTTTTCTCGATAAAAAATTCGGTTACATTGTTAAACGGAGACTTATCTTAATG F2: 3 ACATTGTTA 2 Unidirectional alignment (log-probability: -32.5) CGTGAGCCACCGCACCCGGCCAAAAAGAGCTATTttttaaattgttacaTTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC CGTGAGCCACCGCACCCGGCCAAAAAGAGCTATT---------------TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC Template switch alignment (log-probability: -17) CGTGAGCCACCGCACCCGGCCAAAAAGAGCTATTTTTTAA|ATTGTTACA|TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC CGTGAGCCACCGCACCCGGCCAAAAAGAGCTATTTTTTAA|ATTGTTACA|TTTTAAGCCAATGTAACAATTTGCCTCTGAATAGAATTAC ========== Event 1561 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCGATGTATCTATCAATTATCTATCTAT--CGGAGAGAGAAGataaatatttaaagttt--ttt--ttttttaaataaaCAAGATTCTGAGATGAACTGAGTCCTGCAGCTGAGCTTCGATATTAGTTTCAGTGTTCTGGTA ↑ 1 4 3 2 Chimp: TCGATGTATCTATCAATTATC----TAT--CAGAGAGAGAAGATAAATATTTAAAGttt-----ttttttttAAATAAACAAGATTCTGAGATGAACTGAGTCCTGCAGCTGAGCTTCGATAATAGTTTCAGTGTTCTGGTA Gorilla: TCGATGTATCTATCAATTATC----TAT----CAGAGAGAAGATAAATATGTAAAGTTTAtttt--ttttttAAATCAACAAGATTCTGAGATGAACTGAGTCCTGCAGCTGAGCTTTGATATTAGTTTCAGTGTTCTGGTA Human: TCGATGTATCTATCAATTATCTATCTAT--CGGAGAGAGAAGataaatatttaaagttt--ttt--ttttttaaataaaCAAGATTCTGAGATGAACTGAGTCCTGCAGCTGAGCTTCGATATTAGTTTCAGTGTTCTGGTA Cluster: [ ] Orangutan: TCTATGTATCTATCAATTATC----TATCT--GAGAGAGAAGGTAAATATTTAAAGTTT--Att--ttttttAAATAAACAAGATTCTGAGATGAACTGAGTTCTGCAGCtgagcttcaatattagtttcagtgttctggta Chimp > Human ------------- chr18:71143015-71143019 Template switch process: F1: L TGATACATGTTATCTTTATCTCGATGTATCTATCAATTATCTATC 1 F3: 4 GAGAGAGAAGATAAATATTTAAAGTTTTTTTTTTTTAA R RF: TGATACATGTTATCTTTATCTCGATGTATCTATCAATTATCTATCAGAGAGAGAAGATAAATATTTAAAGTTTTTTTTTTTAAATAAACAAGATTCTGAGATGAACTGAGTCCTGCAGCTGAGCTTCGATA RR: ACTATGTACAATAGAAATAGAGCTACATAGATAGTTAATAGATAGTCTCTCTCTTCTATTTATAAATTTCAAAAAAAAAAATTTATTTGTTCTAAGACTCTACTTGACTCAGGACGTCGACTCGAAGCTAT F2: 3 GCTAT 2 Unidirectional alignment (log-probability: -34.3) CATGTTATCTTTATCTCGATGTATCTATCAATtatcTATCTATCgGAGAGAGAAGATAAATATTTAAAGTTTTTTTTTTTtAA CATGTTATCTTTATCTCGATGTATCTATCAAT----TATCTATCAGAGAGAGAAGATAAATATTTAAAGTTTTTTTTTTT-AA Template switch alignment (log-probability: -21.9) CATGTTATCTTTATCTCGATGTATCTATCAATTATCTATC|TATCG|GAGAGAGAAGATAAATATTTAAAGTTTTTTTTTTTtAA CATGTTATCTTTATCTCGATGTATCTATCAATTATCTATC|TATCG|GAGAGAGAAGATAAATATTTAAAGTTTTTTTTTTTAAA ========== Event 1562 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTAAGAATCAGATTACATATA----------AAAATGTGACATCTTAGACTTTACTACAAGAAATAAT ↓ 1 4 2 Chimp: TTTAAGAATCAGATTACATATCTAAGATGTCACATATGTGACATCTTAGACTTTACTACAAGAAATAAT Gorilla: TTTAAGAATCAGATTACATATA----------AAAATGTGACATCTTAGACTTTACTACAAGAAATAAT Human: TTTAAGAATCAGATTACATATA----------AAAATGTGACATCTTAGACTTTACTACAAGAAATAAT Cluster: [ ] Orangutan: TTTAAGAATCAGATTACATATA----------AAAATGTGACATCTTAGACTTTACTACGAGAAATAAT Human > Chimp ------------- chr18:68776446-68776459 Template switch process: F1: L TAAATTCAACAAATAGACTTTTTAAGAATCAGATTACATAT 1 F3: 4 ATGTGACATCTTAGACTTTACTACAAGAAATAATGTTATT R RF: TAAATTCAACAAATAGACTTTTTAAGAATCAGATTACATATAAAAATGTGACATCTTAGACTTTACTACAAGAAATAATGTTATT RR: ATTTAAGTTGTTTATCTGAAAAATTCTTAGTCTAATGTATATTTTTACACTGTAGAATCTGAAATGATGTTCTTTATTACAATAA F2: 3 TACACTGTAGAATC 2 Unidirectional alignment (log-probability: -37.3) AAATTCAACAAATAGACTTTTTAAGAATCAGATTACATATctaagatgtcAcAtATGTGACATCTTAGACTTTACTACAAGAAATAATGTTATT AAATTCAACAAATAGACTTTTTAAGAATCAGATTACATAT----------AAAAATGTGACATCTTAGACTTTACTACAAGAAATAATGTTATT Template switch alignment (log-probability: -17) AAATTCAACAAATAGACTTTTTAAGAATCAGATTACATAT|CTAAGATGTCACAT|ATGTGACATCTTAGACTTTACTACAAGAAATAATGTTATT AAATTCAACAAATAGACTTTTTAAGAATCAGATTACATAT|CTAAGATGTCACAT|ATGTGACATCTTAGACTTTACTACAAGAAATAATGTTATT ========== Event 1563 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGATTTTGATTTCAGAATAT-----AAAACGTATAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATTC Chimp: TAGATTTTGATTTCAGAATAT-----AAAACGTATAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATTC ↑ 1 4 3 2 Gorilla: TAGATTTTGATTTCAGAATAT---GATAAAATTACAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATTC ↓ 1 4 3 2 Human: TAGATTTTGATTTCAGAATAT-----AAAACGTATAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATTC Cluster: [ ] Orangutan: TAGATTTTGATTTTAGAATATGAT--AAAACTTATAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATTC Gorilla > Human --------------- chr18:71184508-71184516 Template switch process: F1: L TCAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT 1 F3: 4 AAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT R RF: TCAGAATATTTTATATTTAATAGATTTTGATTTCAGAATATGATAAAATTACAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT RR: AGTCTTATAAAATATAAATTATCTAAAACTAAAGTCTTATACTATTTTAATGTTTTACAGTTAATATTCAAAACAGTAAGTATTTTAAGTAA F2: 3 TATGCAAAA 2 Unidirectional alignment (log-probability: -33.2) CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT--aAAAcgTAtAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATATGATAAAATTACAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT Template switch alignment (log-probability: -22.4) CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT|AAAACgTAT|AAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT|AAAACTTAT|AAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT Gorilla > Chimp --------------- chr18:68854076-68854084 Template switch process: F1: L TCAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT 1 F3: 4 AAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT R RF: TCAGAATATTTTATATTTAATAGATTTTGATTTCAGAATATGATAAAATTACAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT RR: AGTCTTATAAAATATAAATTATCTAAAACTAAAGTCTTATACTATTTTAATGTTTTACAGTTAATATTCAAAACAGTAAGTATTTTAAGTAA F2: 3 TATGCAAAA 2 Unidirectional alignment (log-probability: -33.2) CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT--aAAAcgTAtAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATATGATAAAATTACAAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT Template switch alignment (log-probability: -22.4) CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT|AAAACgTAT|AAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT CAGAATATTTTATATTTAATAGATTTTGATTTCAGAATAT|AAAACTTAT|AAAATGTCAATTATAAGTTTTGTCATTCATAAAATTCATT ========== Event 1564 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACATTTTGATAGCTGGATAGTCTG--------TGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCA Chimp: AACGTTTTGATAGCTGGATAGTCTG--------TGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCA ↓ 1 4 3 2 Gorilla: AACATTTTGATAGCTGGATAGCTGA----------------TGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCA ↑ 1 4 3 2 Human: AACATTTTGATAGCTGGATAGTCTG--------TGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCA Cluster: [ ] Orangutan: AACATTTTGATAGCTGGATAGTCTGTGAAACCC--------AGCATGTGGCATCACCTCTTCCCCTGAGCCACCCA Human > Gorilla --------------- chr18:70210366-70210370 Template switch process: F1: L TAATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAG 1 F3: 4 GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT R RF: TAATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAGTCTGTGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT RR: ATTACTCTCTTATTTTTAGGTTGTAAAACTATCGACCTATCAGACACTTTGGGTCGTACACCGTAGTCGAGAAGGGGACTCGGTGGGTCAACAA F2: 3 TAGTC 2 Unidirectional alignment (log-probability: -27) AATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAGctgaT------------GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT AATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAG----TCTGTGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT Template switch alignment (log-probability: -16.4) AATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAG|CTGAT|GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT AATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAG|CTGAT|GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT Chimp > Gorilla --------------- chr18:70210366-70210370 Template switch process: F1: L TAATGAGAGAATAAAAATCCAACATTTTGATAGCTGGATAG 1 F3: 4 GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT R RF: TAATGAGAGAATAAAAATCCAACGTTTTGATAGCTGGATAGTCTGTGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT RR: ATTACTCTCTTATTTTTAGGTTGCAAAACTATCGACCTATCAGACACTTTGGGTCGTACACCGTAGTCGAGAAGGGGACTCGGTGGGTCAACAA F2: 3 TAGTC 2 Unidirectional alignment (log-probability: -32.5) AATGAGAGAATAAAAATCCAACaTTTTGATAGCTGGATAGctgaT------------GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT AATGAGAGAATAAAAATCCAACGTTTTGATAGCTGGATAG----TCTGTGAAACCCAGCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT Template switch alignment (log-probability: -21.9) AATGAGAGAATAAAAATCCAACaTTTTGATAGCTGGATAG|CTGAT|GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT AATGAGAGAATAAAAATCCAACGTTTTGATAGCTGGATAG|CTGAT|GCATGTGGCATCAGCTCTTCCCCTGAGCCACCCAGTTGTT ========== Event 1565 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGTTATTTAGCCTGGGAAATGCTATGTGTACATTTACCTGTACACATAGCAAGCATGCTTTTAAGGGCT Chimp: GGTTATTTAGCCTGGGAAATGCTATGTGTACATTTACCTGTACACATAGCAAGCATGCTTTTAAGGGCT ↑ 1 4 3 2 Gorilla: GGTTATTTAGCCTGGGAAATGGT-----GACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT ↓ 1 4 3 2 Human: GGTTATTTAGCCTGGGAAATGCTATGTGTACATTTACCTGTACACATAGCAAGCATGCTTTTAAGGGCT Cluster: [ ] Orangutan: GGTTATTTAGCCTGGGAAATGGT-----GACATTTACCTGTACACATAGCAAGCATGCTTTTAAGGGCT Gorilla > Human --------------- chr18:71580521-71580528 Template switch process: F1: L GTATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG 1 F3: 4 ACATTTACCTGTACACATAGCAAGCATGCTTTTAAGGGCT R RF: GTATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATGGTGACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT RR: CATAATCAGAAATTTTCCAACCAATAAATCGGACCCTTTACCACTGTAAATGGACATGTGTATCGTTCGCACGAAAATTCCCGA F2: 3 TGTGTATC 2 Unidirectional alignment (log-probability: -33.4) TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATGctatGTGtACATTTACCTGTACACATAGCAAGCaTGCTTTTAAGGGCT TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG----GTG-ACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT Template switch alignment (log-probability: -22.3) TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG|CTATGTGT|ACATTTACCTGTACACATAGCAAGCaTGCTTTTAAGGGCT TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG|CTATGTGT|ACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT Gorilla > Chimp --------------- chr18:69266189-69266196 Template switch process: F1: L GTATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG 1 F3: 4 ACATTTACCTGTACACATAGCAAGCATGCTTTTAAGGGCT R RF: GTATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATGGTGACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT RR: CATAATCAGAAATTTTCCAACCAATAAATCGGACCCTTTACCACTGTAAATGGACATGTGTATCGTTCGCACGAAAATTCCCGA F2: 3 TGTGTATC 2 Unidirectional alignment (log-probability: -33.4) TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATGctatGTGtACATTTACCTGTACACATAGCAAGCaTGCTTTTAAGGGCT TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG----GTG-ACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT Template switch alignment (log-probability: -22.3) TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG|CTATGTGT|ACATTTACCTGTACACATAGCAAGCaTGCTTTTAAGGGCT TATTAGTCTTTAAAAGGTTGGTTATTTAGCCTGGGAAATG|CTATGTGT|ACATTTACCTGTACACATAGCAAGCGTGCTTTTAAGGGCT ========== Event 1566 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTGTGTTTGTTAGGGTTTCTT--------------CCCTAGG-GTTCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTCCCCTGAAGTTATTTCACTCTTCTGCGTGACACATTTCCTGGAGAGGTCCATGTCAACCCCTTCCCTCTCGGACTCTAGGACTCTCCATGGGGTCCCCTC Chimp: TCCTGTGTTTGTTAGGGTTTCTT-------CATCCCACCGCAGCATCTCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTCCCCTGAAGTTATTTCACTCTTCTGCGTGACACATTTCCTGGAGAGGTCCATGTCAACCCCTTCCCTCTCGGACTCTAGGGCTCTCCATGGGGTCCCCTC Gorilla: TCCTGTGTTTGTTAGGGTTTCCTCATCCCA-------CCGCAGCATCTCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTCCCCTGAAGTTATTTCACTCTTCTGCGTGACACATTTCCTGGAGAGGTCCATGTCAACCCCTTCCCTCTCGGACTCTAGGACTCTCCATGGGGTCCCCTC ↓ 1 4 3 2 Human: TCCTGTGTTTGTTAGGGTTTCTT--------------CCCTAGG-GTTCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTCCCCTGAAGTTATTTCACTCTTCTGCGTGACACATTTCCTGGAGAGGTCCATGTCAACCCCTTCCCTCTCGGACTCTAGGACTCTCCATGGGGTCCCCTC Cluster: [ ] Orangutan: TCCTGTGTTTGTTAGGGTTTCTTCAT-CCA-------CCGCACCATCTCCCTGTTTATATTTCTTGCTCTGGCTCCCATTCAGATTCCCCTGAAGTTATTTCACTCTTCTGCGTGACACCTTTCCTGGAGAGGTCCATGTCAACCCCTTCCCTCTCGGACTCTAGGACTCTCCGTGGGGTCCCCTC Gorilla > Human --------------- chr18:7249446-7249453 Template switch process: F1: L CATCACTTTTCCTATAAGTCTCCTGTGTTTGTTAGGGTTTCTTC 1 F3: 4 TCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTC R RF: CATCACTTTTCCTATAAGTCTCCTGTGTTTGTTAGGGTTTCCTCATCCCACCGCAGCATCTCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTCCCCTGAAGTTATTTCACTCTTCTGCGTGACACATTTCCTGGAGAGGTCCATGTCAACCCCTTCCCTCTCGGACTCTAGG RR: GTAGTGAAAAGGATATTCAGAGGACACAAACAATCCCAAAGGAGTAGGGTGGCGTCGTAGAGGGACAAAGATAAAGAGTGAGACCGACGGTAAGTCTAAGGGGACTTCAATAAAGTGAGAAGACGCACTGTGTAAAGGACCTCTCCAGGTACAGTTGGGGAAGGGAGAGCCTGAGATCC F2: 3 TGGGATCC 2 Unidirectional alignment (log-probability: -37) ACTTTTCCTATAAGTCTCCTGTGTTTGTTAGGGTTTCtTC---------------CctagggtTCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTC ACTTTTCCTATAAGTCTCCTGTGTTTGTTAGGGTTTCCTCATCCCACCGCAGCATC-------TCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTC Template switch alignment (log-probability: -27.9) ACTTTTCCTATAAGTCTCCTGTGTTTGTTAGGGTTTCtTC|CCTAGgGT|TCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTC ACTTTTCCTATAAGTCTCCTGTGTTTGTTAGGGTTTCCTC|CCTAGAGT|TCCCTGTTTCTATTTCTCACTCTGGCTGCCATTCAGATTC ========== Event 1567 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGTGAATTTATTGATAGGCTTAGGAAGTGGCCTTCCTAAGCCTATCAAAATGCATGTA ↑ 1 3 4 2 Chimp: ATGTGAATTTATTGATAGGCTTAGAAAGGCCACTTCCTAAGCCTATCAAAATGCATGTA Gorilla: ATGTGAATTTATTGATAGGCTCAGGAAGGCCACTTCCTAAGCCTATCAAAATGCATGTA ↓ 1 3 4 2 Human: ATGTGAATTTATTGATAGGCTTAGGAAGTGGCCTTCCTAAGCCTATCAAAATGCATGTA Cluster: [ ] Orangutan: ATGTGAATTTATTGATAGGTTTAGGAAGGCCACTTCCTAAGCCTATCAAAATGCATGTA Chimp > Human ------------- chr18:6133416-6133423 Template switch process: F1: L TGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTTAG 1 F3: 4 CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT R RF: TGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTTAGAAAGGCCACTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT RR: ACCCAGAGAAATATTTATACACTTAAATAACTATCCGAATCTTTCCGGTGAAGGATTCGGATAGTTTTACGTACATAAATATTTTTTCA F2: 3 CGGTGAAG 2 Unidirectional alignment (log-probability: -30.2) GGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTTAGgAAgtGGC--CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT GGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTTAGAAA--GGCCACTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT Template switch alignment (log-probability: -16.3) GGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTTAG|GAAGTGGC|CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT GGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTTAG|GAAGTGGC|CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT Gorilla > Human --------------- chr18:6133413-6133423 Template switch process: F1: L CTCTGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCT 1 F3: 4 CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT R RF: CTCTGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTCAGGAAGGCCACTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT RR: GAGACCCAGAGAAATATTTATACACTTAAATAACTATCCGAGTCCTTCCGGTGAAGGATTCGGATAGTTTTACGTACATAAATATTTTTTCA F2: 3 CGGTGAAGGAT 2 Unidirectional alignment (log-probability: -28.9) TCTGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTtAGGAAGtggcCTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT TCTGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCTCAGGAAGGCCACTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT Template switch alignment (log-probability: -17.1) TCTGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCT|TAGGAAGTGGC|CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT TCTGGGTCTCTTTATAAATATGTGAATTTATTGATAGGCT|TAGGAAGTGGC|CTTCCTAAGCCTATCAAAATGCATGTATTTATAAAAAAGT ========== Event 1568 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: Chimp: ↓ Gorilla: ↑ Human: Cluster: Orangutan: Human > Gorilla --------------- chr18:5181762-5181771 Template switch process: F1: L AGGTAATAGAACAGTCAG 1 F3: 4 ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAA----------------------------------------------------------------------------------------------------A R RF: AGGTAATAGAACAGTCAGTGATGAACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAATCGGTGTAAATTAACAGACTTTTTAAATTAAAAAAATTAGTAACAGATTTTATTTCCTGTAAGAACATAAAAGCTAGTAAGCTTACTTACATTTTGAGTA RR: TCCATTATCTTGTCAGTCACTACTTGATATGAAGAGTCGATTCCTTAGGTTCTGTTTAATATTTAGCCACATTTAATTGTCTGAAAAATTTAATTTTTTTAATCATTGTCTAAAATAAAGGACATTCTTGTATTTTCGATCATTCGAATGAATGTAAAACTCAT F2: 3 TTATCTTGTC 2 Unidirectional alignment (log-probability: -33.5) AGGTAATAGAACAGTCAGctgttctatT-----ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAA AGGTAATAGAACAGTCAG---------TGATGAACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAA Template switch alignment (log-probability: -16.4) AGGTAATAGAACAGTCAG|CTGTTCTATT|ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAA----------------------------------------------------------------------------------------------------A AGGTAATAGAACAGTCAG|CTGTTCTATT|ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAATCGGTGTAAATTAACAGACTTTTTAAATTAAAAAAATTAGTAACAGATTTTATTTCCTGTAAGAACATAAAAGCTAGTAAGCTTACTTACATTTTGAGTA Chimp > Gorilla --------------- chr18:5181762-5181771 Template switch process: F1: L AGGTAATAGAACAGTCAG 1 F3: 4 ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAA----------------------------------------------------------------------------------------------------A R RF: AGGTAATAGAACAGTCAGTGATGAACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAATCAGTGTAAATTAACAGACTTTTTAAATTAAAAAAATTAGTAACAGATTTTATTTCCTGTAAGAACATAAAAGCTAGTAAGCTTACTTACATTTTGAGTA RR: TCCATTATCTTGTCAGTCACTACTTGATATGAAGAGTCGATTCCTTAGGTTCTGTTTAATATTTAGTCACATTTAATTGTCTGAAAAATTTAATTTTTTTAATCATTGTCTAAAATAAAGGACATTCTTGTATTTTCGATCATTCGAATGAATGTAAAACTCAT F2: 3 TTATCTTGTC 2 Unidirectional alignment (log-probability: -33.5) AGGTAATAGAACAGTCAGctgttctatT-----ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAA AGGTAATAGAACAGTCAG---------TGATGAACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAA Template switch alignment (log-probability: -16.4) AGGTAATAGAACAGTCAG|CTGTTCTATT|ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAA----------------------------------------------------------------------------------------------------A AGGTAATAGAACAGTCAG|CTGTTCTATT|ACTATACTTCTCAGCTAAGGAATCCAAGACAAATTATAAATCAGTGTAAATTAACAGACTTTTTAAATTAAAAAAATTAGTAACAGATTTTATTTCCTGTAAGAACATAAAAGCTAGTAAGCTTACTTACATTTTGAGTA ========== Event 1569 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCATTACCCTTCTACCTTTGGTCCAGGTTACATTATCGAGTGGCACCCA------------------------------------------------CTCATTTACCTAATGTATTTTTCTAGATGGGTTTGGGATGCCAAATACCTAGACACAGCGGCGTAACGCACGGCTTTCAGTTTTC Chimp: GCATTACCCCTCTACCTTTGGTCCAGGTGACATTATCGAGTGGCACCCA------------------------TGTATAAAATGAAGAAATGGAAAGTTCATTTACCTAATGTATTTTTCTAGATGGGTTTGGGATGCCAAATGCCTAGACACAGCGGCGTAACGCACGGCTTTCAGTTTTC ↓ 1 4 3 2 Gorilla: GCATTACCCCTCTACCTTTGGCCCAGGTTACGTTATCGAGTGGCACCCATGCATAAAATGAAGAAATGGAAAG------------------------TTCATTTACCTAATGTATTTTTCTAGATGGGTTTGGGATGCCAAATGCCTAGACACAGCGGCGTAACGCACGGCTTTCAGTTTTC Human: GCATTACCCTTCTACCTTTGGTCCAGGTTACATTATCGAGTGGCACCCA------------------------------------------------CTCATTTACCTAATGTATTTTTCTAGATGGGTTTGGGATGCCAAATACCTAGACACAGCGGCGTAACGCACGGCTTTCAGTTTTC Cluster: [ ] Orangutan: GTATTACCCCTCTACCTTTGGTCCAGGTTACATTATCGAGTGGCACCCATGTATAAAATGAAGAAATGGAAAG------------------------TTCATTTACCTAATGTATTTTTCTAGATGGGTTTGGGATGCCAAATGCCTAGATACAGCAGCGTAGCGCACGGCTTTCAGTTTTC Chimp > Gorilla --------------- chr18:73673052-73673055 Template switch process: F1: L AACTCCCTATAGAACTACCTGCATTACCCCTCTACCTTTGGCCCAGGT 1 F3: 4 TTATCGAGTGGCACCCATGCATAAAATGAAGAAATGGAAA R RF: AACTCCCTATAGAACTACCTGCATTACCCCTCTACCTTTGGTCCAGGTGACATTATCGAGTGGCACCCATGTATAAAATGAAGAAATGGAAAGTTCATTTACCTAATGTATTTTTCTAGATGGGTTTGGGATGCCAAATGCCTAGACACAGCGGCGTA RR: TTGAGGGATATCTTGATGGACGTAATGGGGAGATGGAAACCAGGTCCACTGTAATAGCTCACCGTGGGTACATATTTTACTTCTTTACCTTTCAAGTAAATGGATTACATAAAAAGATCTACCCAAACCCTACGGTTTACGGATCTGTGTCGCCGCAT F2: 3 GCAT 2 Unidirectional alignment (log-probability: -57.3) ATAGAACTACCTGCATTACCCCTCTACCTTTGGcCCAGGTtACgTTATCGAGTGGCACCCAtgcataaaatgaagaaatggaaa ATAGAACTACCTGCATTACCCCTCTACCTTTGGTCCAGGTGACATTATCGAGTGGCACCCA----------------------- Template switch alignment (log-probability: -27.4) ATAGAACTACCTGCATTACCCCTCTACCTTTGGcCCAGGT|TACG|TTATCGAGTGGCACCCATGcATAAAATGAAGAAATGGAAA ATAGAACTACCTGCATTACCCCTCTACCTTTGGTCCAGGT|TACG|TTATCGAGTGGCACCCATGTATAAAATGAAGAAATGGAAA ========== Event 1570 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCCATTGGCATTTTTTGCTCCCAGAGCTTAATCTGTCAGAGgattctgtccctta Chimp: AGCCATTGGCATTTTTTGCTC---CAGCTTAATCTGTCAGAGgattctgtccctta ↓ 1 4 3 2 Gorilla: AGCCATTGGCATTTTTTGCTCCCAGATTTTAATCTGTCAGAGgattctctccctta Human: AGCCATTGGCATTTTTTGCTCCCAGAGCTTAATCTGTCAGAGgattctgtccctta Cluster: [ ] Orangutan: AGCCACTGGCATCTTTTGCTCCCAGAGCTTAATCTGTCAGAGggttctgtccctta Chimp > Gorilla --------------- chr1:140239041-140239046 Template switch process: F1: L TTCATCTTAGAACAGAGTCAAGCCATTGGCATTTTTTGCTCC 1 F3: 4 TTAATCTGTCAGAGGATTCTCTCCCTTACTTGCACTGTGA R RF: TTCATCTTAGAACAGAGTCAAGCCATTGGCATTTTTTGCTCCAGCTTAATCTGTCAGAGGATTCTGTCCCTTACTTGCACTGTGA RR: AAGTAGAATCTTGTCTCAGTTCGGTAACCGTAAAAAACGAGGTCGAATTAGACAGTCTCCTAAGACAGGGAATGAACGTGACACT F2: 3 TTAGAC 2 Unidirectional alignment (log-probability: -31.8) CATCTTAGAACAGAGTCAAGCCATTGGCATTTTTTGCTCCcagAttTTAATCTGTCAGAGGATTCTcTCCCTTACTTGCACTGTGA CATCTTAGAACAGAGTCAAGCCATTGGCATTTTTTGCTCC---AGCTTAATCTGTCAGAGGATTCTGTCCCTTACTTGCACTGTGA Template switch alignment (log-probability: -22) CATCTTAGAACAGAGTCAAGCCATTGGCATTTTTTGCTCC|CAGATT|TTAATCTGTCAGAGGATTCTcTCCCTTACTTGCACTGTGA CATCTTAGAACAGAGTCAAGCCATTGGCATTTTTTGCTCC|CAGATT|TTAATCTGTCAGAGGATTCTGTCCCTTACTTGCACTGTGA ========== Event 1571 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTGAGATGAAGCCGGAGGA--------------------------------------------CCTGGTCTTCAAAGGTCCTTAAGG Chimp: TATTGAGATGAAGCCGGAGGG----------------------TGGAGCATGAGCTGTGCCAGCTGCTGGTCTTCAAAGGTCCTTAAGG ↑ 1 34 2 Gorilla: TATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGCGAGCA----------------------GCTGGTCTTCAGAGGTCCTTAAGG Human: TATTGAGATGAAGCCGGAGGA--------------------------------------------CCTGGTCTTCAAAGGTCCTTAAGG Cluster: [ ] Orangutan: TATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGCGAGCT----------------------GCTGGTCTTCAAAGGTCCTTAAGG Gorilla > Chimp --------------- chr18:74423481-74423485 Template switch process: F1: L CATAAATTTCTGGAATCCCGTATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGC 1 F3: 4 GCTGGTCTTCAAAGGTCCTTAAGGGTCTGGCTCACAGAGT R RF: CATAAATTTCTGGAATCCCGTATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGCGAGCAGCTGGTCTTCAGAGGTCCTTAAGGGTCTGGCTCACAGAGG RR: GTATTTAAAGACCTTAGGGCATAACTCTACTTCGGCCTCCCACCTCGTACTCGACACGCTCGTCGACCAGAAGTCTCCAGGAATTCCCAGACCGAGTGTCTCC F2: 3 TCGAC 2 Unidirectional alignment (log-probability: -33.3) CGTATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGCcAGCtGCTGGTCTTCAaAGGTCCTTAAGGGTCTGGCTCAcagagt CGTATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGCGAGCAGCTGGTCTTCAGAGGTCCTTAAGGGTCTGGCTCA------ Template switch alignment (log-probability: -27.8) CGTATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGC|CAGCT|GCTGGTCTTCAaAGGTCCTTAAGGGTCTGGCTCACAGAGt CGTATTGAGATGAAGCCGGAGGGTGGAGCATGAGCTGTGC|CAGCT|GCTGGTCTTCAGAGGTCCTTAAGGGTCTGGCTCACAGAGG ========== Event 1572 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAGGAGGGCAAGAAATGCTATGTACGGGGTTTGCAAATATAttttcttttctttctt-ttt---ttttttttttttttttgagactgggactcgttccatcacccgggctggagtacagtgttgtgatcacaattca Chimp: TAGGAGGGCAAGAAATGCTATCTACGAGGTTTGCAAATATAttttcttttctttctt-tcttttttttttttttttttttgagactgggactcgttccatcacccgggctggagtacagtgttgtgatcacaattca Gorilla: TAGGAGGGGAAGAAATGCTATCTATGGGGTTTGCAAATATAttttcttttctttctt----------------tttttttgagactgggactcgttccatcacccgggctggagtacagtgttgtgatcacaattca ↓ 1 4 3 2 Human: TAGGAGGGCAAGAAATGCTATGTACGGGGTTTGCAAATATAttttcttttctttctt-ttt---ttttttttttttttttgagactgggactcgttccatcacccgggctggagtacagtgttgtgatcacaattca Cluster: [ ] Orangutan: TAGGAGGGCAAGAAATGCTATCTACGGGGTTTGCAAATATAttttcttttctttcttt---------------tttttttgagactgggactcgttccatcacccgggctagagtacagtgttgtgatcacaattca Gorilla > Human --------------- chr18:7889300-7889303 Template switch process: F1: L AAAATAAAAGCAGTCACTTGTAGGAGGGCAAGAAATGCTAT 1 F3: 4 GGGGTTTGCAAATATATTTTCTTTTCTTTCTTTTTTTTTT R RF: AAAATAAAAGCAGTCACTTGTAGGAGGGGAAGAAATGCTATCTATGGGGTTTGCAAATATATTTTCTTTTCTTTCTTTTTTTTTGAGACTGGGACTCGTTCCATCACCCGGGCTGGAGTAC RR: TTTTATTTTCGTCAGTGAACATCCTCCCCTTCTTTACGATAGATACCCCAAACGTTTATATAAAAGAAAAGAAAGAAAAAAAAACTCTGACCCTGAGCAAGGTAGTGGGCCCGACCTCATG F2: 3 CATG 2 Unidirectional alignment (log-probability: -35.9) AAATAAAAGCAGTCACTTGTAGGAGGGcAAGAAATGCTATgTAcGGGGTTTGCAAATATATTTTCTTTTCTTTCTTtttttttt AAATAAAAGCAGTCACTTGTAGGAGGGGAAGAAATGCTATCTATGGGGTTTGCAAATATATTTTCTTTTCTTTCTT-------- Template switch alignment (log-probability: -27.3) AAATAAAAGCAGTCACTTGTAGGAGGGcAAGAAATGCTAT|GTAC|GGGGTTTGCAAATATATTTTCTTTTCTTTCTTTTTTTTTt AAATAAAAGCAGTCACTTGTAGGAGGGGAAGAAATGCTAT|GTAC|GGGGTTTGCAAATATATTTTCTTTTCTTTCTTTTTTTTTG ========== Event 1573 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCTATGAAGCTCCTTTATTTGCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCTAGATTGTCCAAAAACAAGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTTGTTTTTGGGCAATCTAGCCAAGGTGTCACATAATGGAGAAAAATGCAGATGGTCCTGTGGCTGGTGTGAATGAAGAATGACCTGGGCCCAACATAGAA ↓ 1 3 2 4 Chimp: ATCTATGAAGCTCCTTTATTTATT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCTAGATTGCCCAAAAACAAGTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCTTGTTTTTGACAGAAGTAAAtttctttgtcttctttttttgaggtggagtctcacctatcacccaggctggagtgcagtggcacgatctcagctcactgcaagcttcgcctccccagttcatgccatcctcccacctcagcctcccgaggagctgggactacaggcacccgccacTGTTTGTGGCTTGTGAGCTTGTTTTTGGGCAATCTAGCCAATGTGTCACATAATGGGGAAAAATGCAGATGGTCCTGTGGCTGGTGTGAATGAAGAATGACCTGGGCCCAACATAGAA Gorilla: ATCTATGAAGCTCCTTTATTTATT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTAGATTGCCCAAAAACAAGTG----AGCTTGTTTTTGACAGAAGTAAAtttctttttcttctttttttgagatggagtctcacctatcacccaggctggagtgcagtggcgtgatctcagctcactgcaagcttcgcctccccagttcatgccatcctcccacctcagcctcccgaggaactgggactacaggcgcctgccacTGTTTGTGGCTTGTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCTTGTTTTTGGGCAATCTAGCCAATGTGTCACATAATGGGGAAAAATGCAGATGGTCCTGTGACTGGTGTGAATGAAGAATGACCTGGGCCCAACATAGAA Human: ATCTATGAAGCTCCTTTATTTGCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCTAGATTGTCCAAAAACAAGCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTTGTTTTTGGGCAATCTAGCCAAGGTGTCACATAATGGAGAAAAATGCAGATGGTCCTGTGGCTGGTGTGAATGAAGAATGACCTGGGCCCAACATAGAA Cluster: [] Orangutan: ATCTATGAAGCTCCTTTTTTTGCTCATCTCTGCAAGTGGCTCACCCCACTGCTATTTTTTTAACTAAACTTCTACCAGTCTTTAAATTGTAACTTTGTTTTGACGATAGTTGTTACTTTTTGAAGGCTACTCCATTCAAAGAGGACATTCCTCTGTTGTTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTCATTCCAAAAGACATTTATCATTTTTTAACTATCATGGCATACAGGCGCGGGATTGATAAATATCT----AGTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCTCGTTCCTGGACAATCTAGCCAACGTGTCACATAATGGGGAAAAATGCAGATGGTCCTGTGGCTGGTGCTAATGAAGAACGACCTGGGCCCAACATAGAA Human > Chimp ------------- chr18:75030659-75030695 Template switch process: F1: L TCATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTA 1 F3: 4 GACA R RF: TCATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTGCCATATACCACAGTACTGTATTTCAAAATATTGGATATTGATTATGAACACTGGAACTATTTATGTGTCATCATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTGCTGGCTAGATTGTCCAAAAACAAGCTCACTTGTTTTTGGGCAATCTAGCCAA RR: AGTAAGGTTTCTGGTAACACTAGATACTTCGAGGAAATAAACGGTATATGGTGTCATGACATAAAGTTTTATAACCTATAACTAATACTTGTGACCTTGATAAATACACAGTAGTAAGGTTTCTGGTAACACTAGATACTTCGAGGAAATAAACGACCGATCTAACAGGTTTTTGTTCGAGTGAACAAAAACCCGTTAGATCGGTT F2: 3 TTTTTGTTCGAGTGAACAAAAACCCGTTAGATCGGTT 2 Unidirectional alignment (log-probability: -56.3) ATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTatTGGCTAGATTGcCCAAAAACAAGtgagcttgtttttgaCa ATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTGCTGGCTAGATTGTCCAAAAACAAG---------------CT Template switch alignment (log-probability: -25.2) ATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTa|TTGGCTAGATTGCCCAAAAACAAGTGAGCTTGTTTTT|GACA ATTCCAAAGACCATTGTGATCTATGAAGCTCCTTTATTTG|TTGGCTAGATTGCCCAAAAACAAGTGAGCTTGTTTTT|GACA ========== Event 1574 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: CAATCAGTGAGCACACGTTTCCACTGTGCTCTGTGTTGCCACTGTGTTGGCAAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATTTTGAAATAAAAGCAAAACTGAAAAGTATACTTTACAATGTTAAT ↓ 1 4 3 2 Chimp: CAATCAGTGAGCACACGTTTC-------------CTTTCC---------AGAAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATTTTGAAATAAAAGCAAAACTGAAAAGTATAATTTACAATGTTAAT Gorilla: CAATCAGTGAGCACACGTTTC-------------CTTTCC---------AGAAACGGATCCAATGCCAACAGCAACCCAAAACTGCATATTTTGAAATAAAAGCAAAACTGAAAAGTATAATTTACAATGTTAAT Human: CAATCAGTGAGCACACGTTTCCACTGTGCTCTGTGTTGCCACTGTGTTGGCAAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATTTTGAAATAAAAGCAAAACTGAAAAGTATACTTTACAATGTTAAT Cluster: [ ] Orangutan: CAATCAGTGAGCACACATTTC-------------CTTTCC---------AGAAACAGATCCAACGCCAACAGCAACCCAAAACAGCATATTTTGAAATAAAAGCAAAACTGAAAAGTATAATTTGCAATGTTAAT Human > Chimp ------------- chr18:76139160-76139166 Template switch process: F1: L TTAAGAAACTCAATGCATGCCAATCAGTGAGCACACGTTTCC 1 F3: 4 AAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATT R RF: TTAAGAAACTCAATGCATGCCAATCAGTGAGCACACGTTTCCACTGTGCTCTGTGTTGCCACTGTGTTGGCAAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATTTTGAAATAAAAGCAAAACTGAAAA RR: AATTCTTTGAGTTACGTACGGTTAGTCACTCGTGTGCAAAGGTGACACGAGACACAACGGTGACACAACCGTTTGCCTAGGTTACGGTTGTCGTTGGGTTTTGTCGTATAAAACTTTATTTTCGTTTTGACTTTT F2: 3 GACCTTT 2 Unidirectional alignment (log-probability: -32.7) AAGAAACTCAATGCATGCCAATCAGTGAGCACACGTTTCCtttccag-----------------------------AAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATT AAGAAACTCAATGCATGCCAATCAGTGAGCACACGTTTCC-------ACTGTGCTCTGTGTTGCCACTGTGTTGGCAAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATT Template switch alignment (log-probability: -22.2) AAGAAACTCAATGCATGCCAATCAGTGAGCACACGTTTCC|TTTcCAG|AAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATT AAGAAACTCAATGCATGCCAATCAGTGAGCACACGTTTCC|TTTTCAG|AAACGGATCCAATGCCAACAGCAACCCAAAACAGCATATT ========== Event 1575 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTAAAAACTGCACCATTAGCTGAAAA--------TCTTGCATGAGTGCAGATCATT Chimp: CTAAAAACTGCACCATTAGCTGGATT----TTCAGATTGCATGAGTGCAGATCATT Gorilla: CTAAAAACTGCACCATTAGCTGGATTTTCA----GATTGCATGAGTGCAGATCATT ↑ 3 1 4 Human: CTAAAAACTGCACCATTAGCTGAAAA--------TCTTGCATGAGTGCAGATCATT Cluster: [ ] Orangutan: CTAAAAACTGCACCATTAGCTGGATTTTCA----GATTGCATGAGTGCAGAGCATT Human > Gorilla --------------- chr18:76199449-76199457 Template switch process: F1: L CTTGCTGTTTGTGCAATCACTAAAAACTGCACCATTAGCTG 1 F3: 4 ATTGCATGAGTGCAGATCATTAAGTGTTATTACAGTATTAA R RF: CTTGCTGTTTGTGCAATCACTAAAAACTGCACCATTAGCTGAAAATCTTGCATGAGTGCAGATCATTAAGTGTTATTACAGTATTAA RR: GAACGACAAACACGTTAGTGATTTTTGACGTGGTAATCGACTTTTAGAACGTACTCACGTCTAGTAATTCACAATAATGTCATAATT F2: 3 GACTTTTAG 2 Unidirectional alignment (log-probability: -33.8) TTGCTGTTTGTGCAATCACTAAAAACTGCACCATTAGCTggattttcaGA-----TTGCATGAGTGCAGATCATTAAGTGTTATTACAGTATTA TTGCTGTTTGTGCAATCACTAAAAACTGCACCATTAGCT---------GAAAATCTTGCATGAGTGCAGATCATTAAGTGTTATTACAGTATTA Template switch alignment (log-probability: -22.4) TTGCTGTTTGTGCAATCACTAAAAACTGCACCATTAGCTG|GATTTTCAG|aTTGCATGAGTGCAGATCATTAAGTGTTATTACAGTATTA TTGCTGTTTGTGCAATCACTAAAAACTGCACCATTAGCTG|GATTTTCAG|CTTGCATGAGTGCAGATCATTAAGTGTTATTACAGTATTA ========== Event 1576 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GGCCTAAAGCGAGGCCCATCCATCCCACAGGACCGGGAGTCCCACAGCCTGCACTGCTGTGAATAATGCAGCTTCTCTCCCATGGCCAGTTGAGAAGGTCCCAGTCTCTCCAGGCCGCATGCACGA Chimp: GGCCTAAAGCGAGGCCCATCCATCCCACAGGACTGGGAGTCCCACAGCCTGCAATGCTGTGAATAATGCAGCTTCTCTCCCATGGCCAGTTGAGAAGGTCCCAGTCTCTCCAGGCCACATGCACGA ↑ 4 1 3 2 Gorilla: GGCCTAAAGCGAGGCCCATCCGTC-----------------CCACAGCCTGCACTGCTGTGAATAATGCAGCTTCTCTCCCACGGCCAGTTGAGAAGGTCCCAGTCTCTCCAGGCCGCATGCACGA Human: GGCCTAAAGCGAGGCCCATCCATCCCACAGGACCGGGAGTCCCACAGCCTGCACTGCTGTGAATAATGCAGCTTCTCTCCCATGGCCAGTTGAGAAGGTCCCAGTCTCTCCAGGCCGCATGCACGA Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr18:76463556-76463563 Template switch process: F1: L TGCCCACACTGGCTTCAAGTGGCCTAAAGCGAGGCCCATCCATCCCACAG 1 F3: 4 GTCCCACAGCCTGCAATGCTGTGAATAATGCAGCTTCTCTCCC R RF: TGCCCACACTGGCTTCAAGTGGCCTAAAGCGAGGCCCATCCGTCCCACAGCCTGCACTGCTGTGAATAATGCAGCTTCTCTCCCACGGCCAGTTGAGAAGGTCCCAGTC RR: ACGGGTGTGACCGAAGTTCACCGGATTTCGCTCCGGGTAGGCAGGGTGTCGGACGTGACGACACTTATTACGTCGAAGAGAGGGTGCCGGTCAACTCTTCCAGGGTCAG F2: 3 AGGGTCAG 2 Unidirectional alignment (log-probability: -40.9) GGCTTCAAGTGGCCTAAAGCGAGGCCCATCCatcccacaggactgggaGTCCCACAGCCTGCAaTGCTGTGAATAATGCAGCTTCTCT GGCTTCAAGTGGCCTAAAGCGAGGCCCATCC-----------------GTCCCACAGCCTGCACTGCTGTGAATAATGCAGCTTCTCT Template switch alignment (log-probability: -28.1) GGCTTCAAGTGGCCTAAAGCGAGGCCCATCCaTCCCACAG|GACTGGGA|GTCCCACAGCCTGCAaTGCTGTGAATAATGCAGCTTCTCT GGCTTCAAGTGGCCTAAAGCGAGGCCCATCCGTCCCACAG|GACTGGGA|GTCCCACAGCCTGCACTGCTGTGAATAATGCAGCTTCTCT ========== Event 1577 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: tcagcttgaagaaaggaGATGTTATGAACATATTCATAACAGCCCACATCTCTATTTTT Chimp: tcagcttgaagaaaggagatgag----ctatgttcataacagcccacatctctatTTTT Gorilla: tcagcttgaagaaaggaGATGAG----CTATGTTCATAACAGCCCACATCTCTATTTTT ↓ 1 3 4 2 Human: tcagcttgaagaaaggaGATGTTATGAACATATTCATAACAGCCCACATCTCTATTTTT Cluster: [ ] Orangutan: tcagcttgaagaaaggagatgag----ctatgttcataacagcccacatctctatTTTT Gorilla > Human --------------- chr18:79785429-79785439 Template switch process: F1: L GCTGACAGAATTGGAATTACTCAGCTTGAAGAAAGGAGATG 1 F3: 4 TTCATAACAGCCCACATCTCTATTTTTAGCCCCTGCAATT R RF: GCTGACAGAATTGGAATTATTCAGCTTGAAGAAAGGAGATGAGCTATGTTCATAACAGCCCACATCTCTATTTTTAGCCCCTGCAATT RR: CGACTGTCTTAACCTTAATAAGTCGAACTTCTTTCCTCTACTCGATACAAGTATTGTCGGGTGTAGAGATAAAAATCGGGGACGTTAA F2: 3 ATACAAGTATT 2 Unidirectional alignment (log-probability: -40.5) CTGACAGAATTGGAATTAcTCAGCTTGAAGAAAGGAGAT--GtTATGaacataTTCATAACAGCCCACATCTCTATTTTTAGCCCCTGCAATT CTGACAGAATTGGAATTATTCAGCTTGAAGAAAGGAGATGAGCTATG------TTCATAACAGCCCACATCTCTATTTTTAGCCCCTGCAATT Template switch alignment (log-probability: -22.6) CTGACAGAATTGGAATTAcTCAGCTTGAAGAAAGGAGATG|TTATGAACATA|TTCATAACAGCCCACATCTCTATTTTTAGCCCCTGCAATT CTGACAGAATTGGAATTATTCAGCTTGAAGAAAGGAGATG|TTATGAACATA|TTCATAACAGCCCACATCTCTATTTTTAGCCCCTGCAATT ========== Event 1578 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGCTGGGGGCTGGGCAGGTGCATCCGCTGCTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCCCTGCGCGCCCCACATGATGTCACATGCCTCCA Chimp: TGTGCTGTGGGCCGGGCAGGTGCATCCGCTGCTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCCCTGTGTGCCCCACATGATGTCACATGCCTCCA ↓ 3 2 1 4 Gorilla: TGTGCTGGGGGCCAGGTAGGTGTATCTGCTGCTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTG-CCCTGCACGCCCCCCATGATGTCACATTCCTCCA Human: TGTGCTGGGGGCTGGGCAGGTGCATCCGCTGCTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCCCTGCGCGCCCCACATGATGTCACATGCCTCCA Cluster: [ ] Orangutan: TGTGCTGGGGGCTGGGCAGGTGCATCCACTGCTCCAAAAAGCACTTGTTTTTCCTTTCCACTAAAGTGCCCCTGCACACCCACCATGATGTCACATGCCTCCA Chimp > Gorilla --------------- chr18:77375290-77375294 Template switch process: F1: L GCTGCTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCC 1 F3: 4 GCCCCCCATGATGTCACATTCCTCCACATGCTCCCCATGTCCCCCT R RF: GTGCATCCGCTGCTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCCCTGTGTGCCCCACATGATGTCACATGCCTCCACATGCTCCCCATGTCCCCCT RR: CACGTAGGCGACGAGGTTTTTCGTGAACAAGGAGGAAAGGTGATTTCACGGGGACACACGGGGTGTACTACAGTGTACGGAGGTGTACGAGGGGTACAGGGGGA F2: 3 CACGT 2 Unidirectional alignment (log-probability: -37.8) CTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCC-----TgcacGCCCCcCATGATGTCACATtCCTCCACATGCTCCCCATGT CTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCCCTGTGT----GCCCCACATGATGTCACATGCCTCCACATGCTCCCCATGT Template switch alignment (log-probability: -27.6) CTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCC|TGCAC|GCCCCcCATGATGTCACATtCCTCCACATGCTCCCCATGT CTCCAAAAAGCACTTGTTCCTCCTTTCCACTAAAGTGCCC|TGCAC|GCCCCACATGATGTCACATGCCTCCACATGCTCCCCATGT ========== Event 1579 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCCCTCAGTTCCTGGTACCCTCATGTATTTGCC------TCTCTCTTCAGGACAGAAGTTTCTTATGG Chimp: GGCCCTCAGTGCCTGGTACCATCATGTAAATACATGATGTCCTCTCTTTAGGACAGAAGTTTCTTATGG ↑ 3 4 1 2 Gorilla: GGCCCTCAGTGCCTGGTACCATCATGTATTTGCC------TCTCTCTTCAGGACAGAAGTTTCTTATGG Human: GGCCCTCAGTTCCTGGTACCCTCATGTATTTGCC------TCTCTCTTCAGGACAGAAGTTTCTTATGG Cluster: [ ] Orangutan: GGCCCTCAGTGCCTGCTACCATCATGTATTTGCC------TCTCTCTTCAGGACAGAAGTTTCTTATGG Gorilla > Chimp --------------- chr18:9918845-9918855 Template switch process: F1: L GCAAAAAGCTGGAGGCCCTCAGTGCCTGGTACCATCATGTA 1 F3: 4 TC------------CTCTCTTTAGGACAGAAGTTTCTTATGGTAGAGATCCCAAGGAGGCTG R RF: GCAAAAAGCTGGAGGCCCTCAGTGCCTGGTACCATCATGTATTTGCCTCTCTCTTCAGGACAGAAGTTTCTTATGGTAGAGATCCCAAGGAGGCTG RR: CGTTTTTCGACCTCCGGGAGTCACGGACCATGGTAGTACATAAACGGAGAGAGAAGTCCTGTCTTCAAAGAATACCATCTCTAGGGTTCCTCCGAC F2: 3 GTAGTACATAA 2 Unidirectional alignment (log-probability: -45.3) CAAAAAGCTGGAGGCCCTCAGTGCCTGGTACCATCATGTA-------aatacatgatgtcCTCTCTTtAGGACAGAAGTTTCTTATGGTAGAGATCCC CAAAAAGCTGGAGGCCCTCAGTGCCTGGTACCATCATGTATTTGCCT-------------CTCTCTTCAGGACAGAAGTTTCTTATGGTAGAGATCCC Template switch alignment (log-probability: -33.2) CAAAAAGCTGGAGGCCCTCAGTGCCTGGTACCATCATGTA|AATACATGATG|TC------------CTCTCTTtAGGACAGAAGTTTCTTATGGTAGAGATCCC CAAAAAGCTGGAGGCCCTCAGTGCCTGGTACCATCATGTA|AATACATGATG|TCATGTATTTGCCTCTCTCTTCAGGACAGAAGTTTCTTATGGTAGAGATCCC ========== Event 1580 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGGCTGATGTCACTGGGGGATGATATCCTCTGGCTTCT-------------GACCACAGAAGCCAGAGGATATCTTCTCTAGTCACATCCACAAATCC Chimp: CAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCT-----------------------------------GTGGTCTAGTCACATCTACAAATCC ↓ 3 1 4 Gorilla: CAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCT-------------GACCACAGAAGCCAGAGGATATCTTCTCTAGTCACATCCACAAATCC Human: CAGGCTGATGTCACTGGGGGATGATATCCTCTGGCTTCT-------------GACCACAGAAGCCAGAGGATATCTTCTCTAGTCACATCCACAAATCC Cluster: [ ] Orangutan: CAAGCTGATGTCATTGGGAGATGATATCCTCCGGCTTCTGTGGTCAGACCCAGACCACAGAAGCCAGAGGCTATCTTCTCTGGTCGCATCCACAAATCC Chimp > Gorilla --------------- chr18:76693590-76693614 Template switch process: F1: L TACAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCTG 1 F3: 4 TCTAGTCACATCCACAAATCCCATAAATCATGGCACCTAC R RF: TACAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCTGTGGTCTAGTCACATCTACAAATCCCATAAATCATGGCACCTAC RR: ATGTCCGACTACAGTAACCCCCTACTATAGGAGACCGAAGACACCAGATCAGTGTAGATGTTTAGGGTATTTAGTACCGTGGATG F2: 3 CTTCTATAGGAGACCGAAGACACCA 2 Unidirectional alignment (log-probability: -59.1) CAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCTGaccacagaagccagaggatatcTtcTCTAGTCACATCcACAAATCCCATAAATCATGGCACCTAC CAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCTG----------------------TGGTCTAGTCACATCTACAAATCCCATAAATCATGGCACCTAC Template switch alignment (log-probability: -30) CAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCTG|ACCACAGAAGCCAGAGGATATCtTC|TCTAGTCACATCcACAAATCCCATAAATCATGGCACCTAC CAGGCTGATGTCATTGGGGGATGATATCCTCTGGCTTCTG|ACCACAGAAGCCAGAGGATATCATC|TCTAGTCACATCTACAAATCCCATAAATCATGGCACCTAC ========== Event 1581 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCCTGGGTTCTCACAAAGAGGCT--ACTCTCTTCTCTTTTCAAATTTA ↓ 13 42 Chimp: CCCCTGGGTTCTCACAAAGAGAGTAGCCTCTCTTCTCTTTTCAAATTTA Gorilla: CCCCTGGGTTCTCACAAAGAGGCT--ACTCTCTTCTCTTTTCAAATTTA Human: CCCCTGGGTTCTCACAAAGAGGCT--ACTCTCTTCTCTTTTCAAATTTA Cluster: [ ] Orangutan: CCCCTGGGTTCCCACAAAGAGGCT--ACTCTCTTCTCTTTTCTTATTTA Human > Chimp ------------- chr1:88984570-88984575 Template switch process: F1: L TCTGCTGACAGTCAGTTCTGCCCCTGGGTTCTCACAAAGAG 1 F3: 4 CTCTCTTCTCTTTTCAAATTTATCATTTTAGCGCCCTCAG R RF: TCTGCTGACAGTCAGTTCTGCCCCTGGGTTCTCACAAAGAGGCTACTCTCTTCTCTTTTCAAATTTATCATTTTAGCACCCTCAG RR: AGACGACTGTCAGTCAAGACGGGGACCCAAGAGTGTTTCTCCGATGAGAGAAGAGAAAAGTTTAAATAGTAAAATCGTGGGAGTC F2: 3 CGATGA 2 Unidirectional alignment (log-probability: -31.8) CTGCTGACAGTCAGTTCTGCCCCTGGGTTCTCACAAAGAGagTAgcCTCTCTTCTCTTTTCAAATTTATCATTTTAGCgCCCTCAG CTGCTGACAGTCAGTTCTGCCCCTGGGTTCTCACAAAGAGGCTA--CTCTCTTCTCTTTTCAAATTTATCATTTTAGCACCCTCAG Template switch alignment (log-probability: -22) CTGCTGACAGTCAGTTCTGCCCCTGGGTTCTCACAAAGAG|AGTAGC|CTCTCTTCTCTTTTCAAATTTATCATTTTAGCgCCCTCAG CTGCTGACAGTCAGTTCTGCCCCTGGGTTCTCACAAAGAG|AGTAGC|CTCTCTTCTCTTTTCAAATTTATCATTTTAGCACCCTCAG ========== Event 1582 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCCTAGAGCCATAAAGTATGTTCAAC------AGGGGCCTTGCACTCTGAGTGAGTTA ↓ 3 1 2 4 Chimp: GCCTAGGGCCATAAAGTATGTTCAACCCCTGTTGAACCCTTGCACTCTGAGTGAGTTA ↑ 3 1 2 4 Gorilla: GCCTAGGGCCATAAAGTATGTTCAAC------AGGGGCCTTGCACTCTGAGTGAGTTA Human: GCCTAGAGCCATAAAGTATGTTCAAC------AGGGGCCTTGCACTCTGAGTGAGTTA Cluster: [ ] Orangutan: GCCTAGGGCCATAAAGTATGTTCAAC------AGGGGCCTTGCACTCTGAGTGAGTTA Human > Chimp ------------- chr1:89030423-89030433 Template switch process: F1: L ACTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAAC 1 F3: 4 CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC R RF: ACTGGCACTGCTAGTGCCTAGAGCCATAAAGTATGTTCAACAGGGGCCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC RR: TGACCGTGACGATCACGGATCTCGGTATTTCATACAAGTTGTCCCCGGAACGTGAGACTCACTCAATAAAGAAACCACTGAATAGG F2: 3 CAAGTTGTCCC 2 Unidirectional alignment (log-probability: -43.2) CTGGCACTGCTAGTGCCTAGgGCCATAAAGTATGTTCAAC-----CCctgttgaacccTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC CTGGCACTGCTAGTGCCTAGAGCCATAAAGTATGTTCAACAGGGGCC-----------TTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC Template switch alignment (log-probability: -22.6) CTGGCACTGCTAGTGCCTAGgGCCATAAAGTATGTTCAAC|CCCTGTTGAAC|CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC CTGGCACTGCTAGTGCCTAGAGCCATAAAGTATGTTCAAC|CCCTGTTGAAC|CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC Gorilla > Chimp --------------- chr1:89030423-89030433 Template switch process: F1: L ACTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAAC 1 F3: 4 CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC R RF: ACTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAACAGGGGCCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC RR: TGACCGTGACGATCACGGATCCCGGTATTTCATACAAGTTGTCCCCGGAACGTGAGACTCACTCAATAAAGAAACCACTGAATAGG F2: 3 CAAGTTGTCCC 2 Unidirectional alignment (log-probability: -36.7) CTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAAC-----ccctgttgaacCCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC CTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAACAGGGG-----------CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC Template switch alignment (log-probability: -17.1) CTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAAC|CCCTGTTGAAC|CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC CTGGCACTGCTAGTGCCTAGGGCCATAAAGTATGTTCAAC|CCCTGTTGAAC|CCTTGCACTCTGAGTGAGTTATTTCTTTGGTGACTTATCC ========== Event 1583 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tgtactgtaccacatGATACA--------TATGTACATATGTACCACACGTGTGTGTGCACA----------------------------------CATGTGATCTCAAATCACTCCCATCC Chimp: tgtactgtaccacatGATACA--------TATGTACATATGTACCACACGTGTATGTGCACA-----------------CGTGTGCCCATTGCACACGTGTGATCTCAAATCACTCCCATCC ↓ 1 4 3 2 Gorilla: tgtactgtaccacatGATACA----------------TATGTACCACACGTGTGTGTGCACACATGTGCCCATTGCACA-----------------CGTGTGGTCTCAAAGCACTCCCATCC Human: tgtactgtaccacatGATACA--------TATGTACATATGTACCACACGTGTGTGTGCACA----------------------------------CATGTGATCTCAAATCACTCCCATCC Cluster: [ ] Orangutan: tgtactgtgcca--cGATCCATATGTACA--------TATGTACCACACATGTGTG--------TGTGCCCACTGCACA-----------------CGTGTGACCTCAAATCACTCCCATCC Chimp > Gorilla --------------- chr18:76792671-76792680 Template switch process: F1: L GGCTGCATAGTATTCCATGGTGTACTGTACCACATGATACATATGTAC 1 F3: 4 TGTGCACACATGTGCCCATTGCA R RF: GGCTGCATAGTATTCCATGGTGTACTGTACCACATGATACATATGTACATATGTACCACACGTGTATGTGCACACGTGTGCCCATTGCACACGTGTG RR: CCGACGTATCATAAGGTACCACATGACATGGTGTACTATGTATACATGTATACATGGTGTGCACATACACGTGTGCACACGGGTAACGTGTGCACAC F2: 3 GTGTGCACAC 2 Unidirectional alignment (log-probability: -44.9) AGTATTCCATGGTGTACTGTACCACATGATACATATGTAC--------CACACGTGTgTGTGCACAcatgtgcccattgca AGTATTCCATGGTGTACTGTACCACATGATACATATGTACATATGTACCACACGTGTATGTGCACA--------------- Template switch alignment (log-probability: -22.3) AGTATTCCATGGTGTACTGTACCACATGATACATATGTAC|CACACGTGTG|TGTGCACACaTGTGCCCATTGCA AGTATTCCATGGTGTACTGTACCACATGATACATATGTAC|CACACGTGTG|TGTGCACACGTGTGCCCATTGCA ========== Event 1584 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAGGATTCCGAGTTTGTAAACTTCTGAACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT ↑ 1 4 3 2 Chimp: TTAGGATTCCGAGTTTGTAAA------TACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT Gorilla: TTAGGATTCCGAGTTTGTAAA------TACTAGTAAACTGTGCAGAAGATTAATATTTTGCTTTATAT Human: TTAGGATTCCGAGTTTGTAAACTTCTGAACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT Cluster: [ ] Orangutan: TTAGGATTCTGAGTTTGTAAA------TACTAGTAAACTGTGCAGAAGATTAATATTTTGCTTTATAT Chimp > Human ------------- chr1:160263086-160263092 Template switch process: F1: L AGCAATGACAAAAACTGTATTTAGGATTCCGAGTTTGTAAA 1 F3: 4 ACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT R RF: AGCAATGACAAAAACTGTATTTAGGATTCCGAGTTTGTAAATACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT RR: TCGTTACTGTTTTTGACATAAATCCTAAGGCTCAAACATTTATGATCATTTGACAAGTCTTCTAATTATAAAACGAAATATA F2: 3 AGTCTTC 2 Unidirectional alignment (log-probability: -25.6) GCAATGACAAAAACTGTATTTAGGATTCCGAGTTTGTAAActtctgaACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT GCAATGACAAAAACTGTATTTAGGATTCCGAGTTTGTAAA------TACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT Template switch alignment (log-probability: -16.2) GCAATGACAAAAACTGTATTTAGGATTCCGAGTTTGTAAA|CTTCTGA|ACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT GCAATGACAAAAACTGTATTTAGGATTCCGAGTTTGTAAA|CTTCTGA|ACTAGTAAACTGTTCAGAAGATTAATATTTTGCTTTATAT ========== Event 1585 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCCTCTCTGCCCTCTGACCACCGAGCTGCAGAGCTCCGGAGCTGCAGGAGGAGGACCTGCAGGGCCT ↑ 4 3 2 1 Chimp: TCCTCTCTGCCCTCTGACCACCGAGC----------------TGCAGGAGGAGGACCTGCAGGGCCT ↓ 4 3 2 1 Gorilla: TCCTCTCTGCCCTCTGACCACTGAGCTGCAGAGCTCCGGAGCTGCAGGAGGAGGACCTGCAGGGCCT Human: TCCTCTCTGCCCTCTGACCACCGAGCTGCAGAGCTCCGGAGCTGCAGGAGGAGGACCTGCAGGGCCT Cluster: [ ] Orangutan: TCCTCTCTGCCCTCTGCCCACCGAGCTGCAGAGCTCCGGAGCTACAGGAGGAGGACCTGCAGGGCCT Chimp > Human ------------- chr18:9088135-9088139 Template switch process: F1: L AGATCCTGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCAG 1 F3: 4 CGGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCAACTGTA R RF: AGATCCTGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCAACTGTA RR: TCTAGGACTGTTCGGAGGAGAGACGGGAGACTGGTGGCTCGACGTCCTCCTCCTGGACGTCCCGGACACCCACGTTGACAT F2: 3 CTCGA 2 Unidirectional alignment (log-probability: -33.9) TGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCagagctccggagctgcAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA TGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGC----------------AGGAGGAGGACCTGCAGGGCCTGTGGGTGCA Template switch alignment (log-probability: -22.1) TGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCAG|AGCTC|CgGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA TGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCAG|AGCTC|CCGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA Chimp > Gorilla --------------- chr18:72153673-72153677 Template switch process: F1: L CCCATAGATCCTGACAAGCCTCCTCTCTGCCCTCTGACCACTGAGCTGCAG 1 F3: 4 CGGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCAACTGTA R RF: CCCATAGATCCTGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCAACTGTA RR: GGGTATCTAGGACTGTTCGGAGGAGAGACGGGAGACTGGTGGCTCGACGTCCTCCTCCTGGACGTCCCGGACACCCACGTTGACAT F2: 3 CTCGA 2 Unidirectional alignment (log-probability: -39.5) TGACAAGCCTCCTCTCTGCCCTCTGACCActgagctgcagagctcCgGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA TGACAAGCCTCCTCTCTGCCCTCTGACCA----------------CCGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA Template switch alignment (log-probability: -27.8) TGACAAGCCTCCTCTCTGCCCTCTGACCACtGAGCTGCAG|AGCTC|CgGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA TGACAAGCCTCCTCTCTGCCCTCTGACCACCGAGCTGCAG|AGCTC|CCGAGCTGCAGGAGGAGGACCTGCAGGGCCTGTGGGTGCA ========== Event 1586 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACTGAAA--TAAAGTTAGGAACTTGCATTC- Chimp: CCTGAAA-GGGCTGCAGCTCAGTGGAAGCTGGAACTGAAA--TAAAGTTAGGAACTTGCATTCC Gorilla: CCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACTTCCACTGCAAGTTAGGAACTTGCATTC- ↑ 3 2 1 4 Human: CCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACTGAAA--TAAAGTTAGGAACTTGCATTC- Cluster: [ ] Orangutan: CCTGAAAGTGGCTGCAGCTCAGTGGAAGCTGGAACTGAAA--TAAAGTTAGGAACTTGCATTC- Human > Gorilla --------------- chr18:72217434-72217440 Template switch process: F1: L TTTGCCCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACT 1 F3: 4 CAAGTTAGGAACTTGCATTCCATGCTCAGAGTTCTCTCTTT R RF: TTTGCCCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACTGAAATAAAGTTAGGAACTTGCATTCCTTGCTCAGAGTTCTCTCTTT RR: AAACGGGACTTTCGCCGACGTCGAGTCACCTTCGACCTTGACTTTATTTCAATCCTTGAACGTAAGGAACGAGTCTCAAGAGAGAAA F2: 3 GTCACCT 2 Unidirectional alignment (log-probability: -38) TTGCCCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACT------tccactgcAAGTTAGGAACTTGCATTCCaTGCTCAGAGTTCTCTCTT TTGCCCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACTGAAATA--------AAGTTAGGAACTTGCATTCCTTGCTCAGAGTTCTCTCTT Template switch alignment (log-probability: -27.7) TTGCCCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACT|TCCACTG|cAAGTTAGGAACTTGCATTCCaTGCTCAGAGTTCTCTCTT TTGCCCTGAAAGCGGCTGCAGCTCAGTGGAAGCTGGAACT|TCCACTG|AAAGTTAGGAACTTGCATTCCTTGCTCAGAGTTCTCTCTT ========== Event 1587 ========== Phylogenetic placement: unresolved Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ctttataaattacccagtctcaggtatttctttatagcaatgtgagaacagactaatacaGTACTTAAATACCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGGGCTGGGGAAGTGAGGGAGTGGGGTTA ↓ 3 2 1 4 Chimp: ctttataaattacccagtctcaggtatttctttatagcaatgtgagaatagactaatacaGTACTTAAATACCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGG-GGGGCTGAGGAAGTGAGGGAGTGGGGTTA Gorilla: ctttataaattacccagtctcaggtatttctttatagcaatgtgagaacagactaatacaGTACTTAAATACCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGG-GGGGCTGGGGAAGTGAGGGAGTGGGGTTA Human: ctttataaattacccagtctcaggtatttctttatagcaatgtgagaacagactaatacaGTACTTAAATACCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGGGCTGGGGAAGTGAGGGAGTGGGGTTA Cluster: [ ] Orangutan: ctttataaattacccagtctcaggtatttctttatatcaatgtgagaatagactaatacaGTACTTAAATACCAGCATACTT----CTGCAAAGA--GACAGGAAGG-GGGACTGGGGAAGTGAGGGAGTGGGGTTA Human > Chimp ------------- chr18:8046978-8046981 Template switch process: F1: L AAATACCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGG 1 F3: 4 GGAAGTGAGGGAGTGGGGTTAAGACACACTAAAAAAAAA R RF: TCAGGTATTTCTTTATAGCAATGTGAGAACAGACTAATACAGTACTTAAATACCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGGGCTGGGGAAGTGAGGGAGTGGGGTTAAAACACACTAAAAAAAAA RR: AGTCCATAAAGAAATATCGTTACACTCTTGTCTGATTATGTCATGAATTTATGGTCGCATGAAGAAAGACGTTTCTCTATGTCCTTCCCCCCCGACCCCTTCACTCCCTCACCCCAATTTTGTGTGATTTTTTTTT F2: 3 AGTC 2 Unidirectional alignment (log-probability: -33.1) CCAGCGTACTTCTTTCTGCAAAGAGATACAGGAA-GGGGGGCTGaGGAAGTGAGGGAGTGGGGTTAAgACACACTAAAAAAAaa CCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGGGCTGGGGAAGTGAGGGAGTGGGGTTAAAACACACTAAAAAAA-- Template switch alignment (log-probability: -21.8) CCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGG|CTGA|GGAAGTGAGGGAGTGGGGTTAAgACACACTAAAAAAAAA CCAGCGTACTTCTTTCTGCAAAGAGATACAGGAAGGGGGG|CTGA|GGAAGTGAGGGAGTGGGGTTAAAACACACTAAAAAAAAA ========== Event 1588 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGGGTGGTGATGGTGGCAGGTGT-----------------ATGTTACTAAATAATGATTTTGGGGGCACA Chimp: CTGGGTGGTGATGGTGGCAGGTGT-----------------ATGTTACTAAATAATGGTTTTGGGGGCACA ↓ 3 41 2 Gorilla: CTGGGTGGTGATGGTGGCAGGTGTATTTAGTAACATACACCATGTTACTAAATAATGGTTTTGGGGGCACA ↑ 3 41 2 Human: CTGGGTGGTGATGGTGGCAGGTGT-----------------ATGTTACTAAATAATGATTTTGGGGGCACA Cluster: [ ] Orangutan: CTGCGTGGTGATGGTGGCAGGTGT-----------------CTGTTACTAAATAATGGTTTTGGGGGCACA Human > Gorilla --------------- chr1:90995662-90995676 Template switch process: F1: L CTTTGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTAT 1 F3: 4 ATGTTACTAAATAATGGTTTTGGGGGCACACTTAGTAGTT R RF: CTTTGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTATGTTACTAAATAATGATTTTGGGGGCACACTTAGTAGTT RR: GAAACGTGGATCGATTTGACCCACCACTACCACCGTCCACATACAATGATTTATTACTAAAACCCCCGTGTGAATCATCAA F2: 3 CCACATACAATGATT 2 Unidirectional alignment (log-probability: -40.8) TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTatttagtaacatacaccATGTTACTAAATAATGgTTTTGGGGGCACACTTAGTAGTT TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGT-----------------ATGTTACTAAATAATGATTTTGGGGGCACACTTAGTAGTT Template switch alignment (log-probability: -23.2) TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTAT|TTAGTAACATACACC|ATGTTACTAAATAATGgTTTTGGGGGCACACTTAGTAGTT TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTAT|TTAGTAACATACACC|ATGTTACTAAATAATGATTTTGGGGGCACACTTAGTAGTT Chimp > Gorilla --------------- chr1:90995662-90995676 Template switch process: F1: L CTTTGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTAT 1 F3: 4 ATGTTACTAAATAATGGTTTTGGGGGCACACTTAGTAGTT R RF: CTTTGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTATGTTACTAAATAATGGTTTTGGGGGCACACGTAGTAGTT RR: GAAACGTGGATCGATTTGACCCACCACTACCACCGTCCACATACAATGATTTATTACCAAAACCCCCGTGTGCATCATCAA F2: 3 CCACATACAATGATT 2 Unidirectional alignment (log-probability: -40.8) TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTatttagtaacatacaccATGTTACTAAATAATGGTTTTGGGGGCACACtTAGTAGTT TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGT-----------------ATGTTACTAAATAATGGTTTTGGGGGCACACGTAGTAGTT Template switch alignment (log-probability: -23.2) TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTAT|TTAGTAACATACACC|ATGTTACTAAATAATGGTTTTGGGGGCACACtTAGTAGTT TGCACCTAGCTAAACTGGGTGGTGATGGTGGCAGGTGTAT|TTAGTAACATACACC|ATGTTACTAAATAATGGTTTTGGGGGCACACGTAGTAGTT ========== Event 1589 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCGGATGATTAGGCTTTCATCCGGCACCCAGGAAACCTTCAAAACCAACTTCAGTC Chimp: GTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCGGATGATGAGGCTTTCTTTTTGCA------CAGCCTTCAAAACCAACTTCACTC Gorilla: GTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCGGATGATGAGGCTTTCTTTTTGCA------CAGCCTTCAAAACCAACTTCACTC ↓ 3 2 1 4 Human: GTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCGGATGATTAGGCTTTCATCCGGCACCCAGGAAACCTTCAAAACCAACTTCAGTC Cluster: [ ] Orangutan: GTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCAGATGATGAGGCTTTCTTTTTGCA------CAGCCTTCAAAACCAACTTCACTC Gorilla > Human --------------- chr1:90362327-90362343 Template switch process: F1: L AGGTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCGGATGATTAGGCTTTC 1 F3: 4 CCTTCAAAACCAACTTCAGTCTAAGTTTTCTCACACTCTG R RF: AGGTTCTTTTGGCTCTTTGCATTTCCTGGGTGCCGGATGATGAGGCTTTCTTTTTGCACAGCCTTCAAAACCAACTTCACTCTAAGTTTTCTCACACTCTG RR: TCCAAGAAAACCGAGAAACGTAAAGGACCCACGGCCTACTACTCCGAAAGAAAAACGTGTCGGAAGTTTTGGTTGAAGTGAGATTCAAAAGAGTGTGAGAC F2: 3 AAAGGACCCACGGCCTA 2 Unidirectional alignment (log-probability: -56.8) GGCTCTTTGCATTTCCTGGGTGCCGGATGATtAGGCTTTCatccggcacccaggaaa-----------CCTTCAAAACCAACTTCAgTCTAAGTTTTCTCACACTCTG GGCTCTTTGCATTTCCTGGGTGCCGGATGATGAGGCTTTC-----------------TTTTTGCACAGCCTTCAAAACCAACTTCACTCTAAGTTTTCTCACACTCTG Template switch alignment (log-probability: -29.1) GGCTCTTTGCATTTCCTGGGTGCCGGATGATtAGGCTTTC|ATCCGGCACCCAGGAAA|CCTTCAAAACCAACTTCAgTCTAAGTTTTCTCACACTCTG GGCTCTTTGCATTTCCTGGGTGCCGGATGATGAGGCTTTC|ATCCGGCACCCAGGAAA|CCTTCAAAACCAACTTCACTCTAAGTTTTCTCACACTCTG ========== Event 1590 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: atgattcgtttgtta------caatTTGTGTCCACTGTTAGTGGACACAAATAAACAACTTTGTCCACA Chimp: atgattcgtttgtta------caatTTGTGTCCACTGTTAGTGGACACAAATAAACAACTTTGTCCACA ↑ 1 3 4 2 Gorilla: atgattcgtttgttacaatTACAATTTGTGTCCACTAACAGTGGACACAAATAAACAACTTTGTCCACA ↓ 1 3 4 2 Human: atgattcgtttgtta------caatTTGTGTCCACTGTTAGTGGACACAAATAAACAACTTTGTCCACA Cluster: [ ] Orangutan: atgattcatttgttacaatTACAATTTGTGTCCACCAACAGTGGACACAAATAAACAACTTTGTCCACA Gorilla > Human --------------- chr1:157783507-157783519 Template switch process: F1: L CCAGAATGATTCGTTTGTTACAATT 1 F3: 4 AGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT R RF: CCAGAATGATTCGTTTGTTACAATTACAATTTGTGTCCACTAACAGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT RR: GGTCTTACTAAGCAAACAATGTTAATGTTAAACACAGGTGATTGTCACCTGTGTTTATTTGTTGAAACAGGTGTCGAAAGAGGA F2: 3 TTGTCACCTGTGT 2 Unidirectional alignment (log-probability: -27.7) CCAGAATGATTCGTTTGTTACAAT------TTGTGTCCACTgttAGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT CCAGAATGATTCGTTTGTTACAATTACAATTTGTGTCCACTAACAGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT Template switch alignment (log-probability: -17) CCAGAATGATTCGTTTGTTACAATT|TGTGTCCACTGTT|AGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT CCAGAATGATTCGTTTGTTACAATT|TGTGTCCACTGTT|AGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT Gorilla > Chimp --------------- chr1:136927061-136927073 Template switch process: F1: L CCAGAATGATTCGTTTGTTACAATT 1 F3: 4 AGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT R RF: CCAGAATGATTCGTTTGTTACAATTACAATTTGTGTCCACTAACAGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT RR: GGTCTTACTAAGCAAACAATGTTAATGTTAAACACAGGTGATTGTCACCTGTGTTTATTTGTTGAAACAGGTGTCGAAAGAGGA F2: 3 TTGTCACCTGTGT 2 Unidirectional alignment (log-probability: -27.7) CCAGAATGATTCGTTTGTTACAAT------TTGTGTCCACTgttAGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT CCAGAATGATTCGTTTGTTACAATTACAATTTGTGTCCACTAACAGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT Template switch alignment (log-probability: -17) CCAGAATGATTCGTTTGTTACAATT|TGTGTCCACTGTT|AGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT CCAGAATGATTCGTTTGTTACAATT|TGTGTCCACTGTT|AGTGGACACAAATAAACAACTTTGTCCACAGCTTTCTCCT ========== Event 1591 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CTAGAGAGTAA----CGGGAATGTTTGATCACGAGGATCAAACATTCAAACATTCAAATGATCAAACGT ↑ 3 2 1 4 Chimp: CTAGAGAGTAA--CAGGGGAATGTTTGATCACGAGAATCAA--------ACATTCAAATGATCAAACGT Gorilla: CTAGAGAGTAA----CGGGAATGTTTGATTACGAGGATCAAACATTCAAACATTCAAATGATCAAACGT Human: CTAGAGAGTAA----CGGGAATGTTTGATCACGAGGATCAAACATTCAAACATTCAAATGATCAAACGT Cluster: [ ] Orangutan: CTAAAAAGTAACA--GGGGAATGTTTGATCTTTAAGATGAATCCTTCAAACCTTCAAATGATCCAACCT Chimp > Human ------------- chr19:47028402-47028412 Template switch process: F1: L GATGGGGTCTAGAGAGTAAC--GGGAATGTTTGATCACGAG 1 F3: 4 CAAACATTCAAATGATCAAACGTTCAAATCATTGAGGAAAGAG R RF: GACGGGGTCTAGAGAGTAACAGGGGAATGTTTGATCACGAGAATCAAACATTCAAATGATCAAACGTTCAAATCATTGAGGAAAGAG RR: CTGCCCCAGATCTCTCATTGTCCCCTTACAAACTAGTGCTCTTAGTTTGTAAGTTTACTAGTTTGCAAGTTTAGTAACTCCTTTCTC F2: 3 TTACAAACTAG 2 Unidirectional alignment (log-probability: -44.8) GAtGGGGTCTAGAGAGTAAC--GGGAATGTTTGATCACGAGgATCAAACATTCAAacattcaaATGATCAAACGTTCAAATCATTGAGGAAA GACGGGGTCTAGAGAGTAACAGGGGAATGTTTGATCACGAGAATCAAACATTCAA--------ATGATCAAACGTTCAAATCATTGAGGAAA Template switch alignment (log-probability: -33) GAtGGGGTCTAGAGAGTAAC--GGGAATGTTTGATCACGAG|GATCAAACATT|CAAACATTCAAATGATCAAACGTTCAAATCATTGAGGAAA GACGGGGTCTAGAGAGTAACAGGGGAATGTTTGATCACGAG|GATCAAACATT|CAAACATTCAAATGATCAAACGTTCAAATCATTGAGGAAA ========== Event 1592 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CATAAGATGTTCACGATGATTCTGT--------GATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTC-TAACTCTTTGGCCACACTCCCTC--AGTAGTTTATGAACACACGAAAATTATTTCTACACTTTCACTGTGATCACAATCATATTGCTTTCCAATGG Chimp: CATAAGATGTTCACGATGATTCTGT--------GATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTTAACTCTTTGGCCACACTCCCTCAGAGTAGTTTATGAACACACGAAAATTATTTCTACACTTTCACTGTGATCACAATCATATTGCTTTCCAATGG ↓ 1 4 3 2 ↑ 1 4 3 2 Gorilla: CATAAGATGTTCACGATGATTTATTCATAGAATAAATTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTC-TAACTCTTTGGCCACACTCCCTC--AGTAGTTTATGAACACACGAAAATTATTTCTACACTTTCACTGTGATCACAATCATATTGCTTTCCAATGG ↓ 1 4 3 2 ↑ 1 4 3 2 Human: CATAAGATGTTCACGATGATTCTGT--------GATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTC-TAACTCTTTGGCCACACTCCCTC--AGTAGTTTATGAACACACGAAAATTATTTCTACACTTTCACTGTGATCACAATCATATTGCTTTCCAATGG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr19:12250460-12250466 Template switch process: F1: L CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTC 1 F3: 4 TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA R RF: CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTTATTCATAGAATAAATTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAACTCTTTGGCCACACTCCCTCAGTAGTTTATGAACACACGAAAATTATTTCTACACTTTCACTGTGATCACA RR: GACCTGTAGATATGAGCTCAGTATTCTACAAGTGCTACTAAATAAGTATCTTATTTAAGGTCTCTAAATAAGATACTTAAACAACAGTCTTGAGATTGAGAAACCGGTGTGAGGGAGTCATCAAATACTTGTGTGCTTTTAATAAAGATGTGAAAGTGACACTAGTGT F2: 3 CTAGTGT 2 Unidirectional alignment (log-probability: -33) GGACATCTATACTCGAGTCATAAGATGTTCACGATGAT----------------TctgtgatcTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTTATTCATAGAATAAAT--------TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA Template switch alignment (log-probability: -22.2) GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTc|TGTGATC|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTT|TGTGATC|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA Human > Gorilla --------------- chr19:12002059-12002073 Template switch process: F1: L CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTT 1 F3: 4 TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA R RF: CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTCTGTGATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA RR: GACCTGTAGATATGAGCTCAGTATTCTACAAGTGCTACTAAGACACTAGAGGTCTCTAAATAAGATACTTAAACAACAGTCTTGAGATT F2: 3 TAAATAAGATACTTA 2 Unidirectional alignment (log-probability: -44) GGACATCTATACTCGAGTCATAAGATGTTCACGATGATttattcatagaataaaT--------TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA GGACATCTATACTCGAGTCATAAGATGTTCACGATGAT----------------TCTGTGATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA Template switch alignment (log-probability: -23.2) GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTt|ATTCATAGAATAAAT|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTC|ATTCATAGAATAAAT|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA Gorilla > Chimp --------------- chr19:12941430-12941436 Template switch process: F1: L CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTC 1 F3: 4 TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTTA R RF: CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTTATTCATAGAATAAATTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAACTCTTTGGCCACACTCCCTCAGTAGTTTATGAACACACGAAAATTATTTCTACACTTTCACTGTGATCACA RR: GACCTGTAGATATGAGCTCAGTATTCTACAAGTGCTACTAAATAAGTATCTTATTTAAGGTCTCTAAATAAGATACTTAAACAACAGTCTTGAGATTGAGAAACCGGTGTGAGGGAGTCATCAAATACTTGTGTGCTTTTAATAAAGATGTGAAAGTGACACTAGTGT F2: 3 CTAGTGT 2 Unidirectional alignment (log-probability: -44.1) GGACATCTATACTCGAGTCATAAGATGTTCACGATGAT----------------TctgtgatcTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCtTA GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTTATTCATAGAATAAAT--------TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTC-TA Template switch alignment (log-probability: -27.7) GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTc|TGTGATC|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTtA GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTT|TGTGATC|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTAA Chimp > Gorilla --------------- chr19:12002059-12002073 Template switch process: F1: L CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTT 1 F3: 4 TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTA R RF: CTGGACATCTATACTCGAGTCATAAGATGTTCACGATGATTCTGTGATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTT RR: GACCTGTAGATATGAGCTCAGTATTCTACAAGTGCTACTAAGACACTAGAGGTCTCTAAATAAGATACTTAAACAACAGTCTTGAGAA F2: 3 TAAATAAGATACTTA 2 Unidirectional alignment (log-probability: -53.8) GGACATCTATACTCGAGTCATAAGATGTTCACGATGATttattcatagaataaaT--------TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTC-TA GGACATCTATACTCGAGTCATAAGATGTTCACGATGAT----------------TCTGTGATCTCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTTA Template switch alignment (log-probability: -28.7) GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTt|ATTCATAGAATAAAT|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTa GGACATCTATACTCGAGTCATAAGATGTTCACGATGATTC|ATTCATAGAATAAAT|TCCAGAGATTTATTCTATGAATTTGTTGTCAGAACTCTT ========== Event 1593 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GGGCCAGAGCGCTGCATACACACACACGTGTGTTCACATGCACATGTACAACTGCTG ↑ 3 1 2 4 Chimp: GGGCCAGAGCGCTGCATACACACACGTGT---GTCATATGCACATGTACAACTGCTG Gorilla: GGGCCAGAGCGCTGCATACACACACACGTGTGTTCATATGCACATGTACAACTGCTG Human: GGGCCAGAGCGCTGCATACACACACACGTGTGTTCACATGCACATGTACAACTGCTG Cluster: [ ] Orangutan: AGGCCAGAGCGCTGCATACACACACATGTGTGTTCATATGCACATGTACAACTGCTG Chimp > Human ------------- chr19:57298291-57298298 Template switch process: F1: L GTCCCAGTGGCCGGCCGGGCCAGAGCGCTGCATACACACAC 1 F3: 4 TCACATGCACATGTACAACTGCTGGGGGATTTTCCCCCCTTCTT R RF: GTCCCAGTGGCCGGCCGGGCCAGAGCGCTGCATACACACACGTGTGTCATATGCACATGTACAACTGCTGGGGGATTTTCCCCCCTTCTT RR: CAGGGTCACCGGCCGGCCCGGTCTCGCGACGTATGTGTGTGCACACAGTATACGTGTACATGTTGACGACCCCCTAAAAGGGGGGAAGAA F2: 3 TGTGTGCA 2 Unidirectional alignment (log-probability: -31.5) TCCCAGTGGCCGGCCGGGCCAGAGCGCTGCATacACACACACGTGTGtTCAcATGCACATGTACAACTGCTGGGGGATTTTCCCCCCT TCCCAGTGGCCGGCCGGGCCAGAGCGCTGCAT--ACACACACGTGTG-TCATATGCACATGTACAACTGCTGGGGGATTTTCCCCCCT Template switch alignment (log-probability: -22.3) TCCCAGTGGCCGGCCGGGCCAGAGCGCTGCATACACACAC|ACGTGTGT|TCAcATGCACATGTACAACTGCTGGGGGATTTTCCCCCCT TCCCAGTGGCCGGCCGGGCCAGAGCGCTGCATACACACAC|ACGTGTGT|TCATATGCACATGTACAACTGCTGGGGGATTTTCCCCCCT ========== Event 1594 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACTCACCATCTTGGGAGCTGCCTACTGGTCCTCAGCCTCGGGGCGGACGATCAGAAACTGGCCTTGTGAACACACTGCACTGTCCTGAC Chimp: CTACTCACCATCTTGGGAGCTGCCTACTGGTCCTCACCCTCAGGGCGGACGATTAGAAACTGGCCTTGTGAACACACTGCCCTGTCCTGAC Gorilla: CTACTCACCATCTTGGGAGCTGCCTACTGGTCCTCACCCTCAGGGCGGACGATCAGAAACTGGCCTTGT-GCCAGTCTGCCCTGTCCTGAC ↑ 4 3 2 1 Human: CTACTCACCATCTTGGGAGCTGCCTACTGGTCCTCAGCCTCGGGGCGGACGATCAGAAACTGGCCTTGTGAACACACTGCACTGTCCTGAC Cluster: [ ] Orangutan: Human > Gorilla --------------- chr19:44406068-44406072 Template switch process: F1: L GCTGTCTACTCACCATCTTGGGAGCTGCCTACTGGTCCTCACCCTCAGGGCGGACGATCAGAAACTGGCCTTGTG 1 F3: 4 CTGCCC R RF: GCTGTCTACTCACCATCTTGGGAGCTGCCTACTGGTCCTCAGCCTCGGGGCGGACGATCAGAAACTGGCCTTGTGAACACACTGCACTGTCCTGACCTCTTGTGGAGCCTGGCAGAGGGTCCACAGGCTTCCC RR: CGACAGATGAGTGGTAGAACCCTCGACGGATGACCAGGAGTCGGAGCCCCGCCTGCTAGTCTTTGACCGGAACACTTGTGTGACGTGACAGGACTGGAGAACACCTCGGACCGTCTCCCAGGTGTCCGAAGGG F2: 3 TGACC 2 Unidirectional alignment (log-probability: -43.5) TCCTCAcCCTCaGGGCGGACGATCAGAAACTGGCCTTGTG-----------Ccagtctgccc TCCTCAGCCTCGGGGCGGACGATCAGAAACTGGCCTTGTGAACACACTGCAC---------- Template switch alignment (log-probability: -32.9) TCCTCAcCCTCaGGGCGGACGATCAGAAACTGGCCTTGTG|CCAGT|CTgCCC TCCTCAGCCTCGGGGCGGACGATCAGAAACTGGCCTTGTG|CCAGT|CTTCCC ========== Event 1595 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCGGGGCGGACGATCAGAAACTGGCCTTGTGAACACACTGCACTGTCCTGACCTCTTG Chimp: TCAGGGCGGACGATTAGAAACTGGCCTTGTGAACACACTGCCCTGTCCTGACCTCTTG ↓ 3 2 1 4 Gorilla: TCAGGGCGGACGATCAGAAACTGGCCTTGT-GCCAGTCTGCCCTGTCCTGACCTCTTG Human: TCGGGGCGGACGATCAGAAACTGGCCTTGTGAACACACTGCACTGTCCTGACCTCTTG Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr19:44406068-44406072 Template switch process: F1: L GGTCCTCACCCTCAGGGCGGACGATCAGAAACTGGCCTTGTG 1 F3: 4 CTGCCCTGTCCTGACCTCTTGCGGAGCCTGGCAGAGGGTC R RF: GGTCCTCACCCTCAGGGCGGACGATTAGAAACTGGCCTTGTGAACACACTGCCCTGTCCTGACCTCTTGCGGAGCCTGGCAGAGGGTC RR: CCAGGAGTGGGAGTCCCGCCTGCTAATCTTTGACCGGAACACTTGTGTGACGGGACAGGACTGGAGAACGCCTCGGACCGTCTCCCAG F2: 3 TGACC 2 Unidirectional alignment (log-probability: -33.1) TCCTCACCCTCAGGGCGGACGATcAGAAACTGGCCTTGTG-cCAgtCTGCCCTGTCCTGACCTCTTGCGGAGCCTGGCAGAGGGTC TCCTCACCCTCAGGGCGGACGATTAGAAACTGGCCTTGTGAACACACTGCCCTGTCCTGACCTCTTGCGGAGCCTGGCAGAGGGTC Template switch alignment (log-probability: -21.9) TCCTCACCCTCAGGGCGGACGATcAGAAACTGGCCTTGTG|CCAGT|CTGCCCTGTCCTGACCTCTTGCGGAGCCTGGCAGAGGGTC TCCTCACCCTCAGGGCGGACGATTAGAAACTGGCCTTGTG|CCAGT|CTGCCCTGTCCTGACCTCTTGCGGAGCCTGGCAGAGGGTC ========== Event 1596 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGGCAATATAACATGTCTGT----TTGTATACTTTATATGTCATTTTAAGTaaa-aaaaaGGGA ↓ 1 4 3 2 Chimp: AGGGCAATATAACATGTCTGTTATGACATATACTTTATATGTCATTTTAAGTaaa--aaaaGGGA Gorilla: AGGGCAATATAACATGTCTGT----CTGTATACTTTATATGTCATTTTAAGTAAT--AAAAGGGA Human: AGGGCAATATAACATGTCTGT----TTGTATACTTTATATGTCATTTTAAGTaaa-aaaaaGGGA Cluster: [ ] Orangutan: AGGGCAATATAACATGTCTGT----CTGTATATTTTATATGTCATTTTAAGTAAAA-ATAAGGGA Human > Chimp ------------- chr1:136356194-136356199 Template switch process: F1: L AGTGGAAGCATGGGAATTTGAGGGCAATATAACATGTCTGTT 1 F3: 4 TATACTTTATATGTCATTTTAAGT-AAAAAAAGGGAAAGT R RF: AGTGGAAGCATGGGAATTTGAGGGCAATATAACATGTCTGTTTGTATACTTTATATGTCATTTTAAGTAAAAAAAAGGGAAAGTTTATTATACATATGTACTGTGTGTGTTAATAATTTAAACATTAGACTAACTGTACAGTTATAGACTAGGCATACTTAGTATGTAACTACTTACATGTCAT RR: TCACCTTCGTACCCTTAAACTCCCGTTATATTGTACAGACAAACATATGAAATATACAGTAAAATTCATTTTTTTTCCCTTTCAAATAATATGTATACATGACACACACAATTATTAAATTTGTAATCTGATTGACATGTCAATATCTGATCCGTATGAATCATACATTGATGAATGTACAGTA F2: 3 ACAGTA 2 Unidirectional alignment (log-probability: -37.2) TGGAAGCATGGGAATTTGAGGGCAATATAACATGTCTGTTaTGacaTATACTTTATATGTCATTTTAAGTAAAAAA-AGGGAAAGT TGGAAGCATGGGAATTTGAGGGCAATATAACATGTCTGTT-TG---TATACTTTATATGTCATTTTAAGTAAAAAAAAGGGAAAGT Template switch alignment (log-probability: -26.3) TGGAAGCATGGGAATTTGAGGGCAATATAACATGTCTGTT|ATGACA|TATACTTTATATGTCATTTTAAGT-AAAAAAAGGGAAAGT TGGAAGCATGGGAATTTGAGGGCAATATAACATGTCTGTT|ATGACA|TATACTTTATATGTCATTTTAAGTAAAAAAAAGGGAAAGT ========== Event 1597 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: caggcatgagccaccATGTTATCTGAGATA--------------------GATAACATACTGTATGTGATCCTG Chimp: caggcatgagccaccgtgTTATCTGAGATA--------------------GATAACATACTGTATGTGATCCTG ↓ 3 4 2 Gorilla: caggcatgagccaccATGTTATCTGAGATAGACATATCTATCTCAGATAAGATAACATACTGTATGTGATCCTG ↑ 3 4 2 Human: caggcatgagccaccATGTTATCTGAGATA--------------------GATAACATACTGTATGTGATCCTG Cluster: [ ] Orangutan: caggcatgagccactgc--------------------------------------------------------- Human > Gorilla --------------- chr19:42788999-42789013 Template switch process: F1: L TGCTGGGATTACAGGCATGAGCCACCATGTTATCTGAGATAGACA 1 F3: 4 AGATAACATACTGTATGTGATCCTGACATCATCTCCAATAA R RF: TGCTGGGATTACAGGCATGAGCCACCATGTTATCTGAGATAGATAACATACTGTATGTGATCCTGACATCATCTCCAATAA RR: ACGACCCTAATGTCCGTACTCGGTGGTACAATAGACTCTATCTATTGTATGACATACACTAGGACTGTAGTAGAGGTTATT F2: 3 ATAGACTCTATCTAT 2 Unidirectional alignment (log-probability: -39.6) GGATTACAGGCATGAGCCACCATGTTATCTGAGATagacatatctatctcagataAGATAACATACTGTATGTGATCCTGACATCATCTCCAATA GGATTACAGGCATGAGCCACCATGTTATCTGAGAT--------------------AGATAACATACTGTATGTGATCCTGACATCATCTCCAATA Template switch alignment (log-probability: -23.3) GGATTACAGGCATGAGCCACCATGTTATCTGAGATAGAcA|TATCTATCTCAGATA|AGATAACATACTGTATGTGATCCTGACATCATCTCCAATA GGATTACAGGCATGAGCCACCATGTTATCTGAGATAGATA|TATCTATCTCAGATA|AGATAACATACTGTATGTGATCCTGACATCATCTCCAATA Chimp > Gorilla --------------- chr19:42788999-42789013 Template switch process: F1: L TGCTGGGATTACAGGCATGAGCCACCATGTTATCTGAGATAGACA 1 F3: 4 AGATAACATACTGTATGTGATCCTGACATCATCTCCAATAA R RF: TGCTGGGATTACAGGCATGAGCCACCGTGTTATCTGAGATAGATAACATACTGTATGTGATCCTGACATCATCTCCAATAA RR: ACGACCCTAATGTCCGTACTCGGTGGCACAATAGACTCTATCTATTGTATGACATACACTAGGACTGTAGTAGAGGTTATT F2: 3 ATAGACTCTATCTAT 2 Unidirectional alignment (log-probability: -45.2) GGATTACAGGCATGAGCCACCaTGTTATCTGAGATagacatatctatctcagataAGATAACATACTGTATGTGATCCTGACATCATCTCCAATA GGATTACAGGCATGAGCCACCGTGTTATCTGAGAT--------------------AGATAACATACTGTATGTGATCCTGACATCATCTCCAATA Template switch alignment (log-probability: -28.8) GGATTACAGGCATGAGCCACCaTGTTATCTGAGATAGAcA|TATCTATCTCAGATA|AGATAACATACTGTATGTGATCCTGACATCATCTCCAATA GGATTACAGGCATGAGCCACCGTGTTATCTGAGATAGATA|TATCTATCTCAGATA|AGATAACATACTGTATGTGATCCTGACATCATCTCCAATA ========== Event 1598 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGGAACCAAGACAGGTCCTACCTGGGCAAGCAGCATGCCCCCTGCACTTGGTCCCAAGAAAATCCCACCCTGACCTTTGTCCTGAATCCTCAGGCT------------------------------GGGACATCCCTGCCCCAGCTGGGAGC ↓ 3 2 4 1 Chimp: GGGAACCAAGACAGGTCCTACCTGGGCAAGCAGCATGCCCCCTGCACTTGGTCCCAAGAAAATCCCACCCTGACCTTTGTCCTGAATCCTCAGGCT---------------GGGACACAGGTGGCTGGGACATCCCTGCCCCAGCTGGGAGC Gorilla: GGGAACCAAGACAGGTCCTACCTGGGCAAGCAGCATGCCCCCTGCACTTGGTCCCAAGAAAATCCCACCCTGAACTTTGTCCTGAATCCTCAGGCTGGGACACAGGTGGCT---------------GGGACATCCCTGCCCCAGCTGGGAGC ↑ 3 2 4 1 Human: GGGAACCAAGACAGGTCCTACCTGGGCAAGCAGCATGCCCCCTGCACTTGGTCCCAAGAAAATCCCACCCTGACCTTTGTCCTGAATCCTCAGGCT------------------------------GGGACATCCCTGCCCCAGCTGGGAGC Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:45587504-45587508 Template switch process: F1: L AAGAAAATCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACA 1 F3: 4 GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGAGGCA R RF: ACCTGGGCAAGCAGCATGCCCCCTGCACTTGGTCCCAAGAAAATCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGAGGCA RR: TGGACCCGTTCGTCGTACGGGGGACGTGAACCAGGGTTCTTTTAGGGTGGGACTGGAAACAGGACTTAGGAGTCCGACCCTGTAGGGACGGGGTCGACCCTCGACGGGTCCCTCCGT F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -32.5) TCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACacaggtggctgggacATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA TCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGAC---------------ATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA Template switch alignment (log-probability: -16.1) TCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACA|CAGGT|GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA TCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACA|CAGGT|GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA Human > Gorilla --------------- chr19:43386601-43386605 Template switch process: F1: L AAGAAAATCCCACCCTGAACTTTGTCCTGAATCCTCAGGCTGGGACA 1 F3: 4 GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGAGGCA R RF: ACCTGGGCAAGCAGCATGCCCCCTGCACTTGGTCCCAAGAAAATCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGAGGCA RR: TGGACCCGTTCGTCGTACGGGGGACGTGAACCAGGGTTCTTTTAGGGTGGGACTGGAAACAGGACTTAGGAGTCCGACCCTGTAGGGACGGGGTCGACCCTCGACGGGTCCCTCCGT F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -38) TCCCACCCTGAaCTTTGTCCTGAATCCTCAggctgggacacaggtGGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA TCCCACCCTGACCTTTGTCCTGAATCCTCA---------------GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA Template switch alignment (log-probability: -22.1) TCCCACCCTGAaCTTTGTCCTGAATCCTCAGGCTGGGACA|CAGGT|GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA TCCCACCCTGACCTTTGTCCTGAATCCTCAGGCTGGGACA|CAGGT|GGCTGGGACATCCCTGCCCCAGCTGGGAGCTGCCCAGGGA ========== Event 1599 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: tgtgaatgcatgctcacctgtat--gcatgtgtgttcatgtgcaaacaggtgcatgcat Chimp: TGTGAATGCATGCTCACCTGTAT--GCATGTGTGTTCACGTGCAAACAGGTGCATGCAT ↓ 1 4 3 2 Gorilla: TGTGAATGCATGCTCACCTGTGTGAACATGTGTGTTCACGTGCAAACAGGTGCATGCAT Human: tgtgaatgcatgctcacctgtat--gcatgtgtgttcatgtgcaaacaggtgcatgcat Cluster: [ ] Orangutan: TGTGAATGCATGCTCACCTGTAT--GCACGTGTGTTCACGTGCAAACAGGTGCATGCAT Chimp > Gorilla --------------- chr19:16188256-16188261 Template switch process: F1: L TGTGATGCAGTATGTATGTGAATGCATGCTCACCTGT 1 F3: 4 ATGTGTGTTCACGTGCAAACAGGTGCATGCATGCG R RF: TGTGATGCAGTATGTATGTGAATGCATGCTCACCTGTATGCATGTGTGTTCACGTGCAAACAGGTGCATGCATGCA RR: ACACTACGTCATACATACACTTACGTACGAGTGGACATACGTACACACAAGTGCACGTTTGTCCACGTACGTACGT F2: 3 CAAGTG 2 Unidirectional alignment (log-probability: -29.2) TGTGATGCAGTATGTATGTGAATGCATGCTCACCTGTgTGaaCATGTGTGTTCACGTGCAAACAGGTGCATGCATGC----G TGTGATGCAGTATGTATGTGAATGCATGCTCACCTGTATG--CATGTGTGTTCACGTGCAAACAGGTGCATGCATGCATGTG Template switch alignment (log-probability: -21.8) TGTGATGCAGTATGTATGTGAATGCATGCTCACCTGT|GTGAAC|ATGTGTGTTCACGTGCAAACAGGTGCATGCATGCg TGTGATGCAGTATGTATGTGAATGCATGCTCACCTGT|GTGAAC|ATGTGTGTTCACGTGCAAACAGGTGCATGCATGCA ========== Event 1600 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT-----------ACTTGGCACAGTCCTGCTGGGA ↓ 43 2 1 Chimp: ATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGTGAGAAACTCACTGTTGGCACAGTCCTGCTGGGA Gorilla: ATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT-----------ACTTGGCACAGTCCTGCTGGGA Human: ATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT-----------ACTTGGCACAGTCCTGCTGGGA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----------NNNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr19:43552048-43552057 Template switch process: F1: L GAATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT 1 F3: 4 CTG-------------------TTGGCACAGTCCTGCTGGGAGGATAGAGGTATAGAAACTC R RF: GAATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGTACTTGGCACAGTCCTGCTGGGAGGATAGAGGTATAGAAACTC RR: CTTAACCTGTCACTCCCTAAAGACTCAAAGAGTGGTTGTCATGAACCGTGTCAGGACGACCCTCCTATCTCCATATCTTTGAG F2: 3 ACTCAAAGAG 2 Unidirectional alignment (log-probability: -37) AATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGTgagaaactcACTgtTGGCACAGTCCTGCTGGGAGGATAGAGGTATAGAAA AATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT---------ACT--TGGCACAGTCCTGCTGGGAGGATAGAGGTATAGAAA Template switch alignment (log-probability: -27.8) AATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT|GAGAAACTCA|CTG-------------------TTGGCACAGTCCTGCTGGGAGGATAGAGGTATAGAAA AATTGGACAGTGAGGGATTTCTGAGTTTCTCACCAACAGT|GAGAAACTCA|CTGAGTTTCTCACCAACAGTACTTGGCACAGTCCTGCTGGGAGGATAGAGGTATAGAAA ========== Event 1601 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGGATAATTTGTTATTTTCT------CAATTcccagga-------------------taaatactttgtatccttcaatccaatcaagttg Chimp: TGGGATAATTTGTTATTTTCT---CCTTAATTcccagga-------------------taaatactttgtatccttcaatccaatcaagttg ↓ 3 4 2 1 Gorilla: TGGGATAATTTGTTATTTTCTCCT---TAATTCCCAGGATAAAGTATTATCCTGGgaataaatactttgtatccttcaatccaatcaagttg Human: TGGGATAATTTGTTATTTTCT------CAATTcccagga-------------------taaatactttgtatccttcaatccaatcaagttg Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr19:37119655-37119664 Template switch process: F1: L CAGATAATTAGTAAATGTTATGGGATAATTTGTTATTTTCTCCTTAATTCCCAGGATAAA------GTAT 1 F3: 4 ATAAATACTT R RF: CAGATAATTAGTAAATGTTATGGGATAATTTGTTATTTTCTCCTTAATTCCCAGGATAAATACTTTGTAT RR: GTCTATTAATCATTTACAATACCCTATTAAACAATAAAAGAGGAATTAAGGGTCCTATTTATGAAACATA F2: 3 AGGGTCCTAT 2 Unidirectional alignment (log-probability: -38) ATAATTTGTTATTTTCTCCTTAATTCCCAGGataaagtattatcctgggaATAAATACTT ATAATTTGTTATTTTCTCCTTAATTCCCAGG-------------------ATAAATACTT Template switch alignment (log-probability: -26.9) ATAATTTGTTATTTTCTCCTTAATTCCCAGGATAAA------GTAT|TATCCTGGGA|ATAAATACTT ATAATTTGTTATTTTCTCCTTAATTCCCAGGATAAATACTTTGTAT|TATCCTGGGA|ATAAATACTT ========== Event 1602 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AGGAGGGTGCCCACTGGTCTCCAT------------------------------GGTAATTTCTGTAATGGTGGTAAAACTGGGCGACCAGAATAGGGCACACATGCTGATTTAATCAGAATAAGA ↑ 1 4 3 2 Chimp: AGGAGGGTGCCCACTGGTCTCTGTAATGGTGGTAAAACTGGGTGTAAAAATGGGTGTAATTTCTGTAATGGTGGTAAAACTGGGCAACCAGAATAGGGCACACATGCTGATTTAATCAGAATAAGA Gorilla: Human: AGGAGGGTGCCCACTGGTCTCCAT------------------------------GGTAATTTCTGTAATGGTGGTAAAACTGGGCGACCAGAATAGGGCACACATGCTGATTTAATCAGAATAAGA Cluster: [ ] Orangutan: Chimp > Human ------------- chr19:36128521-36128524 Template switch process: F1: L TTCATGATAATGTTAATTCTAGGAGGGTGCCCACTGGTCTC 1 F3: 4 GTAATTTCTGTAATGGTGGTAAAACTGGGCGACCAGAATA R RF: TTCATGATAATGTTAATTCTAGGAGGGTGCCCACTGGTCTCTGTAATGGTGGTAAAACTGGGTGTAAAAATGGGTGTAATTTCTGTAATGGTGGTAAAACTGGGCAACCAGAATAGGGCACACATG RR: AAGTACTATTACAATTAAGATCCTCCCACGGGTGACCAGAGACATTACCACCATTTTGACCCACATTTTTACCCACATTAAAGACATTACCACCATTTTGACCCGTTGGTCTTATCCCGTGTGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -31.7) TCATGATAATGTTAATTCTAGGAGGGTGCCCACTGGTCTCcaTG--------------------------------GTAATTTCTGTAATGGTGGTAAAACTGGGCgACCAGAATA TCATGATAATGTTAATTCTAGGAGGGTGCCCACTGGTCTC--TGTAATGGTGGTAAAACTGGGTGTAAAAATGGGTGTAATTTCTGTAATGGTGGTAAAACTGGGCAACCAGAATA Template switch alignment (log-probability: -21.8) TCATGATAATGTTAATTCTAGGAGGGTGCCCACTGGTCTC|CATG|GTAATTTCTGTAATGGTGGTAAAACTGGGCgACCAGAATA TCATGATAATGTTAATTCTAGGAGGGTGCCCACTGGTCTC|CATG|GTAATTTCTGTAATGGTGGTAAAACTGGGCAACCAGAATA ========== Event 1603 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAAGATGGGACAGAACTTTGTGGGACAGCTGGA-------TCAAGGCCAAGGATGCCTGAAGAATACAGAGA Chimp: TCAAGATGGGACAGAACTTTGTGGGACAGCTGGATGTCCCACAAAGGCCAAGCATGCCTGAAGAATACAGAGA ↑ 3 2 1 4 Gorilla: TCAAGATGGGACAGAACTTTGTGGGACAGCTGGA-------TCAAGGCCAAGGATGCCTGAAGAATACAGAGA Human: TCAAGATGGGACAGAACTTTGTGGGACAGCTGGA-------TCAAGGCCAAGGATGCCTGAAGAATACAGAGA Cluster: [ ] Orangutan: TCAAGATGGGACAGAACTTTGTGGGACAGCTGGA-------TCAAGGCCAAGGATGCCTGAAGAATACAGAGA Gorilla > Chimp --------------- chr1:92862413-92862420 Template switch process: F1: L TGCA--GTCAAGATGGGACAGAACTTTGTGGGACAGCTGGAT 1 F3: 4 AAGGCCAAGCATGCCTGAAGAATACAGAGAAAGCAGAAAAGGGGAGGGAG R RF: TGCAGAGTCAAGATGGGACAGAACTTTGTGGGACAGCTGGATCAAGGCCAAGGATGCCTGAAGAATACAGAGAAAGCAGAAAAGGGGAGGGAG RR: ACGTCTCAGTTCTACCCTGTCTTGAAACACCCTGTCGACCTAGTTCCGGTTCCTACGGACTTCTTATGTCTCTTTCGTCTTTTCCCCTCCCTC F2: 3 ACACCCTG 2 Unidirectional alignment (log-probability: -42) TGCAG--TCAAGATGGGACAGAACTTTGTGGGACAGCTGGATgtcccacaAAGGCCAAGcATGCCTGAAGAATACAGAGAAAGCAGAAAA TGCAGAGTCAAGATGGGACAGAACTTTGTGGGACAGCTGGAT-------CAAGGCCAAGGATGCCTGAAGAATACAGAGAAAGCAGAAAA Template switch alignment (log-probability: -32.3) TGCA--GTCAAGATGGGACAGAACTTTGTGGGACAGCTGGAT|GTCCCACA|AAGGCCAAGcATGCCTGAAGAATACAGAGAAAGCAGAAAA TGCAGAGTCAAGATGGGACAGAACTTTGTGGGACAGCTGGAT|GTCCCACA|AAGGCCAAGGATGCCTGAAGAATACAGAGAAAGCAGAAAA ========== Event 1604 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGAGACTGTAAGCATCCCATTGGTATCAGTGGCCAGGTACCCAATGCCTGTTCTCTGCAGCAACCTT Chimp: GGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCA-GT-ACCAATGCCTGTTCTCTGCAGCAACCTT ↑ 3 2 1 4 Gorilla: GGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAGGTACCCAGTCCCTGTTCTCTGCAGCAACCTT Human: GGAGAGACTGTAAGCATCCCATTGGTATCAGTGGCCAGGTACCCAATGCCTGTTCTCTGCAGCAACCTT Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr19:36330607-36330614 Template switch process: F1: L CAGTGGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAG 1 F3: 4 CCTGTTCTCTGCAGCAACCTTTGCAGTCCCATACATGGGA R RF: CAGTGGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAGGTACCCAGTCCCTGTTCTCTGCAGCAACCTTTGCAGTCCCATACATGGGA RR: GTCACCTGTCTGACATTCGTAGGGTAACCATAGTCACCGGTCCATGGGTCAGGGACAAGAGACGTCGTTGGAAACGTCAGGGTATGTACCCT F2: 3 GTAACCAT 2 Unidirectional alignment (log-probability: -31.2) GTGGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAGtaccaatG---------CCTGTTCTCTGCAGCAACCTTTGCAGTCCCATACATGGGA GTGGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAG-------GTACCCAGTCCCTGTTCTCTGCAGCAACCTTTGCAGTCCCATACATGGGA Template switch alignment (log-probability: -16.8) GTGGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAG|TACCAATG|CCTGTTCTCTGCAGCAACCTTTGCAGTCCCATACATGGGA GTGGACAGACTGTAAGCATCCCATTGGTATCAGTGGCCAG|TACCAATG|CCTGTTCTCTGCAGCAACCTTTGCAGTCCCATACATGGGA ========== Event 1605 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGAAATACTTCCTGCTCACAACTTGATTGTACTTGTTGTGTAATTGTTGTTGTGCTCACAACATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCCAATTACTCAAGGTGTGTGAATCTTGACTCCCCAGTATTTGCAGGGCTT ↓ 1 4 3 2 Chimp: AGAAATACTTCCTGCTCACAA-----------------------------------CAGTCCATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCCAATTACTCAAGGTGTGTGAATCTTGACTCCCCAGTATTTGCAGGGCTT Gorilla: AGAAATACTTCCTGCTCACAA-----------------------------------CAGTCCATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCCAATTACTCAAGGTGTGTGAATCTTGACTCCCCAGTATTTGCAGGGCTT ↑ 1 4 3 2 Human: AGAAATACTTCCTGCTCACAACTTGATTGTACTTGTTGTGTAATTGTTGTTGTGCTCACAACATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCCAATTACTCAAGGTGTGTGAATCTTGACTCCCCAGTATTTGCAGGGCTT Cluster: [ ] Orangutan: AGAAATACTTCCTGCTCACAA-----------------------------------CAGTCCATTTTG--TTTGATTACATATTCTGCTCTGTGGTGCCCTAATTACTCAAGGTGTGTGAATCTTGACTCCTCAGTATTTGCAGGGCTT Human > Chimp ------------- chr19:31143908-31143911 Template switch process: F1: L TCCTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC 1 F3: 4 CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC R RF: TCCTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAACTTGATTGTACTTGTTGTGTAATTGTTGTTGTGCTCACAACATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCCAATTACTCAAGGTGTGTGAATCTTGACT RR: AGGAAATAGAGAGGGAAAGGTCTTTATGAAGGACGAGTGTTGAACTAACATGAACAACACATTAACAACAACACGAGTGTTGTAAAACATGAACTAATGTATAAGACGAGACACCACGGGGTTAATGAGTTCCACACACTTAGAACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -27.4) CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC--------------------------------------AgtcCATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAACTTGATTGTACTTGTTGTGTAATTGTTGTTGTGCTCACAA---CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC Template switch alignment (log-probability: -15.8) CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC|AGTC|CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC|AGTC|CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC Human > Gorilla --------------- chr19:30150612-30150615 Template switch process: F1: L TCCTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC 1 F3: 4 CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC R RF: TCCTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAACTTGATTGTACTTGTTGTGTAATTGTTGTTGTGCTCACAACATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCCAATTACTCAAGGTGTGTGAATCTTGACT RR: AGGAAATAGAGAGGGAAAGGTCTTTATGAAGGACGAGTGTTGAACTAACATGAACAACACATTAACAACAACACGAGTGTTGTAAAACATGAACTAATGTATAAGACGAGACACCACGGGGTTAATGAGTTCCACACACTTAGAACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -26.9) CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC--------------------------------------AgtcCATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAACTTGATTGTACTTGTTGTGTAATTGTTGTTGTGCTCACAA---CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC Template switch alignment (log-probability: -16.3) CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC|AGTC|CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC CTTTATCTCTCCCTTTCCAGAAATACTTCCTGCTCACAAC|AGTC|CATTTTGTACTTGATTACATATTCTGCTCTGTGGTGCCCC ========== Event 1606 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: aagtgagTCTCACTCCAATCTTCATAC---TGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGCCTGATC Chimp: aagtgagTCTCACTCCAATCTC-CCACTGGAGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGATC ↑ 1 4 3 2 Gorilla: aagtgagTCTCACTCCAATCTTCATAC---TGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGATT Human: aagtgagTCTCACTCCAATCTTCATAC---TGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGCCTGATC Cluster: [ ] Orangutan: aagtgggTCTCACTCCAATCTTCATAC---TGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGAGC Gorilla > Chimp --------------- chr1:93535285-93535292 Template switch process: F1: L CTGTTTTGGATTCCTGACATAAGTGAGTCTCACTCCAATCT 1 F3: 4 AGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGAT R RF: CTGTTTTGGATTCCTGACATAAGTGAGTCTCACTCCAATCTTCATACTGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGAT RR: GACAAAACCTAAGGACTGTATTCACTCAGAGTGAGGTTAGAAGTATGACGGAGGGTGAGGGGGTCACCCGTACACTGGGTTCAGACTA F2: 3 GGTCACCC 2 Unidirectional alignment (log-probability: -33.9) TGTTTTGGATTCCTGACATAAGTGAGTCTCACTCCAAT-------CTcccactggaGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGA TGTTTTGGATTCCTGACATAAGTGAGTCTCACTCCAATCTTCATACT---------GCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGA Template switch alignment (log-probability: -22.3) TGTTTTGGATTCCTGACATAAGTGAGTCTCACTCCAATCT|CCCACTGG|aGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGA TGTTTTGGATTCCTGACATAAGTGAGTCTCACTCCAATCT|CCCACTGG|TGCCTCCCACTCCCCCAGTGGGCATGTGACCCAAGTCTGA ========== Event 1607 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: tgctttttaagccaaccagactgcaggactttgttatggcagccccagaaaattaatacaGACAGCAAACGGCCAGATGTCCCACTTGAAAAATGGATCCAGGAACAGAAAAGTAAATGTTGTGAGAATGACGTTTGATGGCAGGGTTTTATTCTGCAGTTGCCTACAGGAATGACAACAG Chimp: tgctttttaagccaaccagactgcaggactttgttatggcagccccagaaaattaatacaGACAGCAAACGGCCAGATGTCCCACTTGAAAAATGGATCCAGGAACAGAAAAGTAAATGTTGTGGGAATGACGTTTGATGGCAGGGTTTTAC----AGGATGCCTACAGGAATGACAACAG ↓ 3 2 1 4 Gorilla: tgctttttaagccaaccagactgcaggactttgttatggcagccccagaaaattaatacaGACAGCAAACGGCCAGATGTCCCACTTGAAAAATGGATCCAGGAACATAAAAGTAAATGTTGTGGGAATGACGTTTGATGGCAGGATTTTATTCTGCAGTTGCCTACAGGAATGACAACAG Human: tgctttttaagccaaccagactgcaggactttgttatggcagccccagaaaattaatacaGACAGCAAACGGCCAGATGTCCCACTTGAAAAATGGATCCAGGAACAGAAAAGTAAATGTTGTGAGAATGACGTTTGATGGCAGGGTTTTATTCTGCAGTTGCCTACAGGAATGACAACAG Cluster: [ ] Orangutan: tgttgtttaagccaaccagactgcaggactttgttatggcagccccagaaaattaatacaGACAGCAAATGGCCAGATGTCCCACTTGAAAAATGGATCCAGGAACAGAAAAGTATATGTTGTGGGAATGATGTTTGATGGCACGGTTTTATTCTGTAGTTGCCTACAGGAAGGACAACAG Chimp > Gorilla --------------- chr19:28313822-28313830 Template switch process: F1: L ACATAAAAGTAAATGTTGTGGGAATGACGTTTGATGGCAGGATTTTA 1 F3: 4 TGCCTACAGGAATGACAACAGAAAACTTAAGATGGTGTGT R RF: ACTGCAGGACTTTGTTATGGCAGCCCCAGAAAATTAATACAGACAGCAAACGGCCAGATGTCCCACTTGAAAAATGGATCCAGGAACAGAAAAGTAAATGTTGTGGGAATGACGTTTGATGGCAGGGTTTTACAGGATGCCTACAGGAATGACAACAGAAAACTTAAGATGGTGTGT RR: TGACGTCCTGAAACAATACCGTCGGGGTCTTTTAATTATGTCTGTCGTTTGCCGGTCTACAGGGTGAACTTTTTACCTAGGTCCTTGTCTTTTCATTTACAACACCCTTACTGCAAACTACCGTCCCAAAATGTCCTACGGATGTCCTTACTGTTGTCTTTTGAATTCTACCACACA F2: 3 TGACGTCTT 2 Unidirectional alignment (log-probability: -44.6) AGTAAATGTTGTGGGAATGACGTTTGATGGCAGGaTTTTAttctgCA-GtTGCCTACAGGAATGACAACAGAAAACTTAAGATGGTGTGT AGTAAATGTTGTGGGAATGACGTTTGATGGCAGGGTTTTA-----CAGGATGCCTACAGGAATGACAACAGAAAACTTAAGATGGTGTGT Template switch alignment (log-probability: -33.6) AGTAAATGTTGTGGGAATGACGTTTGATGGCAGGaTTTTA|TtCTGCAGT|TGCCTACAGGAATGACAACAGAAAACTTAAGATGGTGTGT AGTAAATGTTGTGGGAATGACGTTTGATGGCAGGGTTTTA|TCCTGCAGT|TGCCTACAGGAATGACAACAGAAAACTTAAGATGGTGTGT ========== Event 1608 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATTGGGCTGTGAGCCCAGCTTGGTCGT--GGAGGCACAGACCTGCTTGTCACTATTACTTCTGGGACATATG ↓ 1 4 3 2 Chimp: CATTGGGCTGTGAGCCCAGCTGTGGTGTGACAAGCCACAGACCTGCTTGTCACTATTACTTCTGGGACATATG Gorilla: CATTGGGCTGTGAGCCCAGCTTGGTCGT--GGAGGCACAGACCTGCTTGTCACTATTACTTCTGGGACATATG Human: CATTGGGCTGTGAGCCCAGCTTGGTCGT--GGAGGCACAGACCTGCTTGTCACTATTACTTCTGGGACATATG Cluster: [ ] Orangutan: CATTGGGCTCTGAGCCCAGCTTGGTCGT--GGAGGCACAGACCTGCTTGTCACTATTACTTCTGGGACATATG Human > Chimp ------------- chr19:30411094-30411102 Template switch process: F1: L AGCAGAGAGAACCAAGGTCTCATTGGGCTGTGAGCCCAGCTGTGGT 1 F3: 4 CACAGACCTGCTTGTCACTATTACTTCTGGGACATATGCA R RF: AGCAGAGAGAACCAAGGTCTCATTGGGCTGTGAGCCCAGCT-TGGTCGTGGAGGCACAGACCTGCTTGTCACTATTACTTCTGGGACATATGCA RR: TCGTCTCTCTTGGTTCCAGAGTAACCCGACACTCGGGTCGA-ACCAGCACCTCCGTGTCTGGACGAACAGTGATAATGAAGACCCTGTATACGT F2: 3 CGAACAGTG 2 Unidirectional alignment (log-probability: -37.5) GAGAACCAAGGTCTCATTGGGCTGTGAGCCCAGCT-----GTGGtgtgacaAGcCACAGACCTGCTTGTCACTATTACTTCTGGGACATATGCA GAGAACCAAGGTCTCATTGGGCTGTGAGCCCAGCTTGGTCGTGG-------AGGCACAGACCTGCTTGTCACTATTACTTCTGGGACATATGCA Template switch alignment (log-probability: -28.1) GAGAACCAAGGTCTCATTGGGCTGTGAGCCCAGCTgTGGT|GTGACAAGC|CACAGACCTGCTTGTCACTATTACTTCTGGGACATATGCA GAGAACCAAGGTCTCATTGGGCTGTGAGCCCAGCT-TGGT|GTGACAAGC|CACAGACCTGCTTGTCACTATTACTTCTGGGACATATGCA ========== Event 1609 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCCTCTGTCACCTTGCTTAT---ATGGTTATCTCATACCTACCCATGCTCTT Chimp: TGCCTCTGTCACCTTGCTTAT---ATGGTTATCTCATACCTACCCATACTCTT ↓ 1 3 4 2 Gorilla: TGCCTCTGTCACCTTGCTTATGATAACCATATCTCATACCTACCCATGCTCTT ↑ 1 3 4 2 Human: TGCCTCTGTCACCTTGCTTAT---ATGGTTATCTCATACCTACCCATGCTCTT Cluster: [ ] Orangutan: TGCCTCTGTCACCTTGCTTAT---ATGGTTATCTCATACCTACCCATGCTCTT Human > Gorilla --------------- chr19:29386377-29386384 Template switch process: F1: L CATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT 1 F3: 4 TATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA R RF: CATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTATATGGTTATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA RR: GTATGCGTTACGGGGAAGAGACGGAGACAGTGGAACGAATATACCAATAGAGTATGGATGGGTACGAGAAAGGAGACGAGACACAT F2: 3 ACCAATAG 2 Unidirectional alignment (log-probability: -30.9) ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTATgataaccA----TATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT-------ATGGTTATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA Template switch alignment (log-probability: -16.7) ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT|GATAACCA|TATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT|GATAACCA|TATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA Chimp > Gorilla --------------- chr19:29386377-29386384 Template switch process: F1: L CATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT 1 F3: 4 TATCTCATACCTACCCATGCTCTTTCCTCTGCTCTGTGTA R RF: CATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTATATGGTTATCTCATACCTACCCATACTCTTTCCTCTGCTCTGTGTA RR: GTATGCGTTACGGGGAAGAGACGGAGACAGTGGAACGAATATACCAATAGAGTATGGATGGGTATGAGAAAGGAGACGAGACACAT F2: 3 ACCAATAG 2 Unidirectional alignment (log-probability: -36.4) ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTATgataaccA----TATCTCATACCTACCCATgCTCTTTCCTCTGCTCTGTGTA ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT-------ATGGTTATCTCATACCTACCCATACTCTTTCCTCTGCTCTGTGTA Template switch alignment (log-probability: -22.3) ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT|GATAACCA|TATCTCATACCTACCCATgCTCTTTCCTCTGCTCTGTGTA ATACGCAATGCCCCTTCTCTGCCTCTGTCACCTTGCTTAT|GATAACCA|TATCTCATACCTACCCATACTCTTTCCTCTGCTCTGTGTA ========== Event 1610 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: gagaccaagagttggaggctgcagagagctgtgattgcaccactgcactccagcctgggagacagagtgagactctgtctcaaaaaaagaaaa-aaaaaaaagacaaTATGCTTCCTTCTCCCCAGATACATGAGGACAGAAATGTCCTCATCATTTCTGG ↓ 3 2 1 4 Chimp: gagaccaagagttggaggctgcagagagctgtgattgcaccactgcactccagcctgggagacagagtgagactctgtctcaaaaaaagaaaa-aaaaaaaagacaaTATGCTTCCTTCTCCCCAGATACATGCTG--CAAAATGTCCTCATCATTTCTGG Gorilla: gagaccaagagttggaggctgcagagagctgtgattgcaccactgcactccagcctgggagacagagtgaga--ctgtctcaaaaaaagaaaaaaaaaaaaagacaaTATGCTTCCTTCTCCCCAGATACATGCTG--CAAAATGTCCTCATCATTTCTGG Human: gagaccaagagttggaggctgcagagagctgtgattgcaccactgcactccagcctgggagacagagtgagactctgtctcaaaaaaagaaaa-aaaaaaaagacaaTATGCTTCCTTCTCCCCAGATACATGAGGACAGAAATGTCCTCATCATTTCTGG Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:29936702-29936706 Template switch process: F1: L AAAAAAAAAAGACAATATGCTTCCTTCTCCCCAGATACATG 1 F3: 4 AAATGTCCTCATCATTTCTGGCCCTGCTTGTCCTCTTCCT R RF: TGCAGAGAGCTGTGATTGCACCACTGCACTCCAGCCTGGGAGACAGAGTGAGACTCTGTCTCAAAAAAAGAAAAAAAAAAAAGACAATATGCTTCCTTCTCCCCAGATACATGAGGACAGAAATGTCCTCATCATTTCTGGCCCTGCTTGTCCTCTTCCT RR: ACGTCTCTCGACACTAACGTGGTGACGTGAGGTCGGACCCTCTGTCTCACTCTGAGACAGAGTTTTTTTCTTTTTTTTTTTTCTGTTATACGAAGGAAGAGGGGTCTATGTACTCCTGTCTTTACAGGAGTAGTAAAGACCGGGACGAACAGGAGAAGGA F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -27.2) AAAAAAAAAGACAATATGCTTCCTTCTCCCCAGATACATGctgcA------AAATGTCCTCATCATTTCTGGCCCTGCTTGTCCTCTTCCT AAAAAAAAAGACAATATGCTTCCTTCTCCCCAGATACATG----AGGACAGAAATGTCCTCATCATTTCTGGCCCTGCTTGTCCTCTTCCT Template switch alignment (log-probability: -15.9) AAAAAAAAAGACAATATGCTTCCTTCTCCCCAGATACATG|CTGCA|AAATGTCCTCATCATTTCTGGCCCTGCTTGTCCTCTTCCT AAAAAAAAAGACAATATGCTTCCTTCTCCCCAGATACATG|CTGCA|AAATGTCCTCATCATTTCTGGCCCTGCTTGTCCTCTTCCT ========== Event 1611 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGAGGA----------------------------TTCCACCAGGTCTTAGCCGACCAG ↑ 3 2 1 4 Chimp: CCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGACGA--------------GGTCCCAGAAATCAAACCACCAGGTCTTAGCCGACCAG Gorilla: CCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGAGGAGGTCCCAGAAATCA--------------AACCACCAGGTCTTAGCCGACCAG Human: CCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGAGGA----------------------------TTCCACCAGGTCTTAGCCGACCAG Cluster: [ ] Orangutan: CCTGGCTCTTTGAATGCTGGAATCCTGAAGGAGGAGGAGGTCCCAGAAATCA--------------AACCACCAGGTCTTAGCTGACCAG Chimp > Human ------------- chr19:31356165-31356170 Template switch process: F1: L CTGAACCCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGA 1 F3: 4 CACCAGGTCTTAGCCGACCAGATAGCCCAGCTTTCTGAG R RF: CTGAACCCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGACGAGGTCCCAGAAATCAAACCACCAGGTCTTAGCCGACCAGATAGCCCAGCTTTCTGAG RR: GACTTGGGGTCGAGAAACTTACGACCTTAGGACTTCCTCCTGCTCCAGGGTCTTTAGTTTGGTGGTCCAGAATCGGCTGGTCTATCGGGTCGAAAGACTC F2: 3 CTTAGG 2 Unidirectional alignment (log-probability: -29.3) TGAACCCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGAggatt-------------------CCACCAGGTCTTAGCCGACCAGATAGCCCAGCTTTCTGAG TGAACCCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGA-----CGAGGTCCCAGAAATCAAACCACCAGGTCTTAGCCGACCAGATAGCCCAGCTTTCTGAG Template switch alignment (log-probability: -16) TGAACCCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGA|GGATTC|CACCAGGTCTTAGCCGACCAGATAGCCCAGCTTTCTGAG TGAACCCCAGCTCTTTGAATGCTGGAATCCTGAAGGAGGA|GGATTC|CACCAGGTCTTAGCCGACCAGATAGCCCAGCTTTCTGAG ========== Event 1612 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCCATGTTTCCGTCCTGAGTTGTCTTTCCTGCACTTTGCAGGCATGGAAACCTTGTTCCACACATTG Chimp: GTCCATGTTTCTGTCCTGAGTTGTCTTTCCTGCACTTTGCAGGCATGGAAATCTTGTTCCACACATTG ↓ 1 4 3 2 Gorilla: GTCCATGTTTCTGTCCTGAGT-TCCATGCCTGCACTTTGCAGGCATGGAAACCTAGTTCCACACATTG ↑ 1 4 3 2 Human: GTCCATGTTTCCGTCCTGAGTTGTCTTTCCTGCACTTTGCAGGCATGGAAACCTTGTTCCACACATTG Cluster: [ ] Orangutan: GTCCATGTTTCTGTCCTGAGTTGTCTTTCCTGCACTTTGCAGGCATGGAAACCTTATTCCACACATTG Human > Gorilla --------------- chr19:30600624-30600628 Template switch process: F1: L TTTTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGTT 1 F3: 4 CCTGCACTTTGCAGGCATGGAAACCTAGTTCCACACATTG R RF: TTTTTCCCAGCTTCTTGGCTGTCCATGTTTCCGTCCTGAGTTGTCTTTCCTGCACTTTGCAGGCATGGAAACCTTGTTCCACACATTG RR: AAAAAGGGTCGAAGAACCGACAGGTACAAAGGCAGGACTCAACAGAAAGGACGTGAAACGTCCGTACCTTTGGAACAAGGTGTGTAAC F2: 3 GTACC 2 Unidirectional alignment (log-probability: -37.7) TTTCCCAGCTTCTTGGCTGTCCATGTTTCtGTCCTGAGTtccaTG-----CCTGCACTTTGCAGGCATGGAAACCTaGTTCCACACATTG TTTCCCAGCTTCTTGGCTGTCCATGTTTCCGTCCTGAGT----TGTCTTTCCTGCACTTTGCAGGCATGGAAACCTTGTTCCACACATTG Template switch alignment (log-probability: -27.4) TTTCCCAGCTTCTTGGCTGTCCATGTTTCtGTCCTGAGTT|CCATG|CCTGCACTTTGCAGGCATGGAAACCTaGTTCCACACATTG TTTCCCAGCTTCTTGGCTGTCCATGTTTCCGTCCTGAGTT|CCATG|CCTGCACTTTGCAGGCATGGAAACCTTGTTCCACACATTG Chimp > Gorilla --------------- chr19:30600624-30600628 Template switch process: F1: L TTTTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGTT 1 F3: 4 CCTGCACTTTGCAGGCATGGAAACCTAGTTCCACACATTG R RF: TTTTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGTTGTCTTTCCTGCACTTTGCAGGCATGGAAATCTTGTTCCACACATTG RR: AAAAAGGGTCGAAGAACCGACAGGTACAAAGACAGGACTCAACAGAAAGGACGTGAAACGTCCGTACCTTTAGAACAAGGTGTGTAAC F2: 3 GTACC 2 Unidirectional alignment (log-probability: -37.7) TTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGTtccaTG-----CCTGCACTTTGCAGGCATGGAAAcCTaGTTCCACACATTG TTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGT----TGTCTTTCCTGCACTTTGCAGGCATGGAAATCTTGTTCCACACATTG Template switch alignment (log-probability: -27.4) TTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGTT|CCATG|CCTGCACTTTGCAGGCATGGAAAcCTaGTTCCACACATTG TTTCCCAGCTTCTTGGCTGTCCATGTTTCTGTCCTGAGTT|CCATG|CCTGCACTTTGCAGGCATGGAAATCTTGTTCCACACATTG ========== Event 1613 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAGCACTGAGTTCTTCCAGGAGGAGGCTCT ↑ 3 2 1 4 Chimp: GGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG-GCT-GGTTCTTCCAGGAGGAGGCTCT Gorilla: GGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG-GCT-GGTTCTTCCAGGAGGAGGCTCT ↓ 3 2 1 4 Human: GGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAGCACTGAGTTCTTCCAGGAGGAGGCTCT Cluster: [ ] Orangutan: ---------------------------------------------------------------- Chimp > Human ------------- chr19:30594968-30594973 Template switch process: F1: L CCAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG 1 F3: 4 GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA R RF: CCAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAGGCTGGTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA RR: GGTCCCCTCGGTACGGACACACGAGTCACGACGGGACCGTCCGACCAAGAAGGTCCTCCTCCGAGAAGACGTAGGACGAACCCGT F2: 3 AGTCAC 2 Unidirectional alignment (log-probability: -30) CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAGcactga----GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG------GCTGGTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA Template switch alignment (log-probability: -16) CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG|CACTGA|GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG|CACTGA|GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA Gorilla > Human --------------- chr19:30594968-30594973 Template switch process: F1: L CCAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG 1 F3: 4 GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA R RF: CCAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAGGCTGGTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA RR: GGTCCCCTCGGTACGGACACACGAGTCACGACGGGACCGTCCGACCAAGAAGGTCCTCCTCCGAGAAGACGTAGGACGAACCCGT F2: 3 AGTCAC 2 Unidirectional alignment (log-probability: -29.1) CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAGcaCTGaGTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG-GCTG-GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA Template switch alignment (log-probability: -16.5) CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG|CACTGA|GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA CAGGGGAGCCATGCCTGTGTGCTCAGTGCTGCCCTGGCAG|CACTGA|GTTCTTCCAGGAGGAGGCTCTTCTGCATCCTGCTTGGGCA ========== Event 1614 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAAAGTGTGGCTGGATGAAC-------CAAGGCCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCT Chimp: ACAAAGTGTGGCTGGATGAACCTTGGTTTAGAGCCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCT ↑ 4 3 2 Gorilla: ACAAAGTGTGGCTGGATGAAC-------CAAGGGCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCT Human: ACAAAGTGTGGCTGGATGAAC-------CAAGGCCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCT Cluster: [ ] Orangutan: ACAAAGTGTGGCTGGATGAAC-------CAAGGCCTCCTTTGCTCTAAACCTCATCTCTGAATATCTTCT Gorilla > Chimp --------------- chr19:32444080-32444088 Template switch process: F1: L AGGCATGTGGGTGTCTGGATACAAAGTGTGGCTGGATGAACC----------TTG 1 F3: 4 CTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCTTTAT R RF: AGGCATGTGGGTGTCTGGATACAAAGTGTGGCTGGATGAACCAAGGGCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCTTTAT RR: TCCGTACACCCACAGACCTATGTTTCACACCGACCTACTTGGTTCCCGAGGAAACGAGATTTGGGGTAGAGACTTATAAAAGAAATA F2: 3 CGAGATTTG 2 Unidirectional alignment (log-probability: -37.6) TGTGGGTGTCTGGATACAAAGTGTGGCTGGATGAACCttggtttAgaGcCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCTTTAT TGTGGGTGTCTGGATACAAAGTGTGGCTGGATGAACC-------AAGGGCTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCTTTAT Template switch alignment (log-probability: -27.2) TGTGGGTGTCTGGATACAAAGTGTGGCTGGATGAACC----------TTG|GTTTAGAGC|CTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCTTTAT TGTGGGTGTCTGGATACAAAGTGTGGCTGGATGAACCAAGGGCTCCTTTG|GTTTAGAGC|CTCCTTTGCTCTAAACCCCATCTCTGAATATTTTCTTTAT ========== Event 1615 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGAGTCCAAGCACCCATGAC----CATCTCTAGAGGCTCTATGCAGCTCCCAGATCCGTGTGC----TGCTCCAATAGGGTTACAAAAACAagttgagctaacatctaaaaattaaaagctttcatagaaagaagggattt Chimp: TAGAGTCCAAGCACCCATGAC----CGTCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGC--TGTGCTCCAATAGGGTTACAAAAACAagttgagctaacatctaaaaattaaaagctttcataggaagaagggattt ↓ 14 3 2 Gorilla: TAGAGTCCAAGCACCCATGACCAGCTATCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCTG--TGCTCCAATAGGGTTACAAAAACAagttgagctaacatctaaaaattaaaagctttcatagaaagaagggattt Human: CAGAGTCCAAGCACCCATGAC----CATCTCTAGAGGCTCTATGCAGCTCCCAGATCCGTGTGC----TGCTCCAATAGGGTTACAAAAACAagttgagctaacatctaaaaattaaaagctttcatagaaagaagggattt Cluster: [ ] Orangutan: TAGAGTCCAAGCACCCATGAC----CATCTCTAGAGGCTCTATGCAGCTTCCAGATCTGTGTGCTG--TGCTCCAATAGGGTTACAAAAACAagttgagctaacatctaaaaattaaaagctttcatagaaagaagggattt Chimp > Gorilla --------------- chr19:30931317-30931320 Template switch process: F1: L ATCAACAGATGGAAAGTTCTTAGAGTCCAAGCACCCATGACC 1 F3: 4 ATCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCTG R RF: ATCTACAGATGGAAAGTTCTTAGAGTCCAAGCACCCATGACCGTCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCTGTGCTCCAATAGGGTTACAAAAACAAGTTGAGCTAACATCTAAAAATTAAAAGCT RR: TAGATGTCTACCTTTCAAGAATCTCAGGTTCGTGGGTACTGGCAGAGATCTCCGAGATACGTCGAGGGTCTAGACACACGACACGAGGTTATCCCAATGTTTTTGTTCAACTCGATTGTAGATTTTTAATTTTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -35.9) CaACAGATGGAAAGTTCTTAGAGTCCAAGCACCCATGACCagctaTCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCTg CTACAGATGGAAAGTTCTTAGAGTCCAAGCACCCATGACCG----TCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCT- Template switch alignment (log-probability: -27.3) CaACAGATGGAAAGTTCTTAGAGTCCAAGCACCCATGACC|AGCT|aTCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCTG CTACAGATGGAAAGTTCTTAGAGTCCAAGCACCCATGACC|AGCT|GTCTCTAGAGGCTCTATGCAGCTCCCAGATCTGTGTGCTG ========== Event 1616 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCAGCCTTCCCTGGCCCTCC--CCCTGCCCCAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCCAATTAGATTTGCCCA Chimp: ACAAGCCTTCCCTGGCCCTCC--CCCTGCCTCAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCCAGTTAGATTTGCCCA ↓ 1 4 3 2 Gorilla: ACTAGCCTTCCCTGGCCCTCC---CCTGGCCAAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCCAATTAGATTTGCCCA Human: ACCAGCCTTCCCTGGCCCTCC--CCCTGCCCCAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCCAATTAGATTTGCCCA Cluster: [ ] Orangutan: ACCAGCCTTCCCTGCCACTCCCGCCCCACCCCAGGAGGCTGGCCCTGCAGGCtgcccatgctggccagtgccaattagatttgccca Chimp > Gorilla --------------- chr19:26481237-26481242 Template switch process: F1: L CCACCCCCCATCACCCATTTACTAGCCTTCCCTGGCCCTCCCC 1 F3: 4 AGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCC R RF: CCACCCCCCATCACCCATTTACAAGCCTTCCCTGGCCCTCCCCCTGCCTCAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCC RR: GGTGGGGGGTAGTGGGTAAATGTTCGGAAGGGACCGGGAGGGGGACGGAGTCCTCGGACCGGGACGTCCGACGGGTACGACCGGTCACGG F2: 3 ACCGGT 2 Unidirectional alignment (log-probability: -33.1) CCCCCCATCACCCATTTACtAGCCTTCCCTGGCCCT-CCCCTGgCcaAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCC CCCCCCATCACCCATTTACAAGCCTTCCCTGGCCCTCCCCCTGCCTCAGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCC Template switch alignment (log-probability: -22.1) CCCCCCATCACCCATTTACtAGCCTTCCCTGGCCCTCCCC|TGGCCA|AGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCC CCCCCCATCACCCATTTACAAGCCTTCCCTGGCCCTCCCC|TGGCCA|AGGAGCCTGGCCCTGCAGGCTGCCCATGCTGGCCAGTGCC ========== Event 1617 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAATTTATTTGATTTTTTGGCTATATG--------------------ATATCTTTTACTGTTATCTTCTCAATCTTCTTTTTCt------ Chimp: CCAATTTATTtgattttttggctatatg--------------------atatcttttactgttatcttctcaatcttcttcttct------ Gorilla: CCAATTTATTTGATTTTTTGG-CATATA----------------------------------------GCCAAtcttcttcttct------ ↑ 31 2 4 Human: CCAATTTATTTGATTTTTTGGCTATATG--------------------ATATCTTTTACTGTTATCTTCTCAATCTTCTTTTTCt------ Cluster: [ ] Orangutan: CCAATTTATTTGATTTTTTGGCTATATGATATCTTTTACTGTTAtctt--------------------ctcaatcttcttcttcttcttct Human > Gorilla --------------- chr19:25725698-25725704 Template switch process: F1: L AAAACTGAATAAATCTTTAGCCAATTTATTTGATTTTTTGGC 1 F3: 4 CAATCTTCTTCTTCTTCTTCTTTTTTTT R RF: AAAACTGAATAAATCTTTAGCCAATTTATTTGATTTTTTGGCTATATGATATCTTTTACTGTTATCTTCTCAATCTTCTTTTTCTTCTTCTTTTTTTT RR: TTTTGACTTATTTAGAAATCGGTTAAATAAACTAAAAAACCGATATACTATAGAAAATGACAATAGAAGAGTTAGAAGAAAAAGAAGAAGAAAAAAAA F2: 3 CGATATA 2 Unidirectional alignment (log-probability: -44.3) AACTGAATAAATCTTTAGCCAATTTATTTGATTTTTTGGC----------------------------atatagcCAATCTTCTTcTTCTTCTTCTTTTTTTT- AACTGAATAAATCTTTAGCCAATTTATTTGATTTTTTGGCTATATGATATCTTTTACTGTTATCTTCT-------CAATCTTCTTTTTCTTCTTCTTTTTTTTT Template switch alignment (log-probability: -21.8) AACTGAATAAATCTTTAGCCAATTTATTTGATTTTTTGGC|ATATAGC|CAATCTTCTTcTTCTTCTTCTTTTTTTT AACTGAATAAATCTTTAGCCAATTTATTTGATTTTTTGGC|ATATAGC|CAATCTTCTTTTTCTTCTTCTTTTTTTT ========== Event 1618 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAAGGGTGAGGCCTGGGCCGGCTCCACTGCACCTGGAgccgggtgcagtggctcacgcctgtaatcccaacact ↑ 4 3 2 1 Chimp: AGAAAGGGTGAGGCCTGGGCCTTAT-AAAGGAACCTGGAgccgggtgcagtggctcacgcctgtaatcccaacact Gorilla: AGAAAGGGTGAGGCCTGGGCCTTAT-AAAGGAACCTGGAgccgggtgcagtggctcacacctgtaatcccaacact Human: AGAAAGGGTGAGGCCTGGGCCGGCTCCACTGCACCTGGAgccgggtgcagtggctcacgcctgtaatcccaacact Cluster: [ ] Orangutan: AGAAAGGGTGAGGCCTGGGCCTTAT-AAAGGCCCCTGGAgccaggtgcagtggctcacgcctgtaatcccaacact Chimp > Human ------------- chr19:25350650-25350655 Template switch process: F1: L CCTGGGAATGTGAGGTCTGGAGAAAGGGTGAGGCCTGGGCC-----------------------------GGCTC 1 F3: 4 ACCTGGAGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAA R RF: CCTGGGAATGTGAGGTCTGGAGAAAGGGTGAGGCCTGGGCCTTATAAAGGAACCTGGAGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAA RR: GGACCCTTACACTCCAGACCTCTTTCCCACTCCGGACCCGGAATATTTCCTTGGACCTCGGCCCACGTCACCGAGTGCGGACATTAGGGTT F2: 3 CGTCAC 2 Unidirectional alignment (log-probability: -37.5) AATGTGAGGTCTGGAGAAAGGGTGAGGCCTGGGCC----------ggctccactgcACCTGGAGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAA AATGTGAGGTCTGGAGAAAGGGTGAGGCCTGGGCCTTATAAAGGA-----------ACCTGGAGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAA Template switch alignment (log-probability: -27.8) AATGTGAGGTCTGGAGAAAGGGTGAGGCCTGGGCC-----------------------------GGCTC|CACTGC|ACCTGGAGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAA AATGTGAGGTCTGGAGAAAGGGTGAGGCCTGGGCCTTATAAAGGAACCTGGAGCCGGGTGCAGTGGCTC|CACTGC|ACCTGGAGCCGGGTGCAGTGGCTCACGCCTGTAATCCCAA ========== Event 1619 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTCCTCACCTTGCTCCTTACACTC----------CAGCAAATTTAACTACTTGGAATTACCTGTATCAATAGGCCT Chimp: TCTCCTCACCTTGCTCCTTACACTC----------CAGCAAATTTAACTACTTGGAATTACCTGTATCAACAGGCCT ↓ 3 1 2 4 Gorilla: TCTCCTCACCTTGCTCCTTACACTT--------------------TGCTGGAGTGTATTACCTGTATCAATAGGCCT ↑ 3 1 2 4 Human: TCTCCTCACCTTGCTCCTTACACTC----------CAGCAAATTTAACTACTTGGAATTACCTGTATCAATAGGCCT Cluster: [ ] Orangutan: TCTCCTCACCTTGCTCCTTACCCTCCAGCAAATTT----------AACTACTTGGAATTACCTGTATCAATAGGCCT Human > Gorilla --------------- chr1:94825865-94825876 Template switch process: F1: L CCAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT 1 F3: 4 ATTACCTGTATCAATAGGCCTGGGGTCCCCATCTTCTTCT R RF: CCAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACTCCAGCAAATTTAACTACTTGGAATTACCTGTATCAATAGGCCTGGGGTCCCCATCCTCTTCT RR: GGTTGAGTGGTCGGATTAGAGGAGTGGAACGAGGAATGTGAGGTCGTTTAAATTGATGAACCTTAATGGACATAGTTATCCGGACCCCAGGGGTAGGAGAAGA F2: 3 TGTGAGGTCGTT 2 Unidirectional alignment (log-probability: -42.7) CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT-----------------TTGctggagtGtATTACCTGTATCAATAGGCCTGGGGTCCCCATCtTCTTCT CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACTCCAGCAAATTTAACTACTTG-------GAATTACCTGTATCAATAGGCCTGGGGTCCCCATCCTCTTCT Template switch alignment (log-probability: -22.8) CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT|TTGCTGGAGTGT|ATTACCTGTATCAATAGGCCTGGGGTCCCCATCtTCTTCT CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT|TTGCTGGAGTGT|ATTACCTGTATCAATAGGCCTGGGGTCCCCATCCTCTTCT Chimp > Gorilla --------------- chr1:94825865-94825876 Template switch process: F1: L CCAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT 1 F3: 4 ATTACCTGTATCAATAGGCCTGGGGTCCCCATCTTCTTCT R RF: CCAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACTCCAGCAAATTTAACTACTTGGAATTACCTGTATCAACAGGCCTGGGGTCCCCATCTTCTTCT RR: GGTTGAGTGGTCGGATTAGAGGAGTGGAACGAGGAATGTGAGGTCGTTTAAATTGATGAACCTTAATGGACATAGTTGTCCGGACCCCAGGGGTAGAAGAAGA F2: 3 TGTGAGGTCGTT 2 Unidirectional alignment (log-probability: -42.7) CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT-----------------TTGctggagtGtATTACCTGTATCAAtAGGCCTGGGGTCCCCATCTTCTTCT CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACTCCAGCAAATTTAACTACTTG-------GAATTACCTGTATCAACAGGCCTGGGGTCCCCATCTTCTTCT Template switch alignment (log-probability: -22.8) CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT|TTGCTGGAGTGT|ATTACCTGTATCAAtAGGCCTGGGGTCCCCATCTTCTTCT CAACTCACCAGCCTAATCTCCTCACCTTGCTCCTTACACT|TTGCTGGAGTGT|ATTACCTGTATCAACAGGCCTGGGGTCCCCATCTTCTTCT ========== Event 1620 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CAGTTACTATATTATAATAATTATGTAAATTACGTAATTTACATTATGTAGCTCTTAAAATTATAGGA Chimp: CAGTTACTATATTATAATAATTATGTAAATTACATAATTTACATTATGTAGCTCTTAAAATTATAGGA Gorilla: CAGTTACTATATTATAATAATTATGTAAATTACATAG--------CAGTAGCTCTTAAGATTATAGGA ↓ 3 2 4 Human: CAGTTACTATATTATAATAATTATGTAAATTACGTAATTTACATTATGTAGCTCTTAAAATTATAGGA Cluster: [ ] Orangutan: CAGTTACTATATTATAGTAATTATGTAAATTACATAG--------CAGTAGCTCTTAAAATTATAGGA Gorilla > Human --------------- chr19:24465030-24465043 Template switch process: F1: L GAAAAGAACAGTTACTATATTATAATAATTATGTAAATTAC 1 F3: 4 GTAGCTCTTAAAATTATAGGATGCCTTGCTACAAGTACTA R RF: GAAAAGAACAGTTACTATATTATAATAATTATGTAAATTACATAGCAGTAGCTCTTAAGATTATAGGATGCCTTGCTACAAGTACTA RR: CTTTTCTTGTCAATGATATAATATTATTAATACATTTAATGTATCGTCATCGAGAATTCTAATATCCTACGGAACGATGTTCATGAT F2: 3 TATTACATTTAATG 2 Unidirectional alignment (log-probability: -43.6) AAAAGAACAGTTACTATATTATAATAATTATGTAAATTACgtaatttacattAT----GTAGCTCTTAAaATTATAGGATGCCTTGCTACAAGTACTA AAAAGAACAGTTACTATATTATAATAATTATGTAAATTAC------------ATAGCAGTAGCTCTTAAGATTATAGGATGCCTTGCTACAAGTACTA Template switch alignment (log-probability: -28.5) AAAAGAACAGTTACTATATTATAATAATTATGTAAATTAC|GTAATTTACATtAT|GTAGCTCTTAAaATTATAGGATGCCTTGCTACAAGTACTA AAAAGAACAGTTACTATATTATAATAATTATGTAAATTAC|GTAATTTACATAAT|GTAGCTCTTAAGATTATAGGATGCCTTGCTACAAGTACTA ========== Event 1621 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTGCACAAACCCCATCACTGAGCATGTCCCTCCCAGGGCAATGCAGATCAGCCACTGGGAGGGACATGCTCCAAGCCCTGGGAGGCCCAGAGG Chimp: CTACACAAACCCCATCACTGAGCATGTCCCTCCCAGGGCAATGCAGATCAGCCACT-GGAGGGACATGCTCCTAGCCCTGGGAGGCCCAGAGG ↑ 3 2 1 4 Gorilla: CTACACAAACCCCGTCACTGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCACA-G-----------GTCTAGCCCTGGGAGGCCCAGAGG ↓ 3 2 1 4 Human: CTGCACAAACCCCATCACTGAGCATGTCCCTCCCAGGGCAATGCAGATCAGCCACTGGGAGGGACATGCTCCAAGCCCTGGGAGGCCCAGAGG Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr19:24020568-24020583 Template switch process: F1: L TCACTGAGCATGTCCCTCCCAGGGCAATGCAGATCAGCCAC 1 F3: 4 CAAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGAAG R RF: TCACTGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCACAGGTCTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGAAG RR: AGTGACTCGTACAGGGAGGGTCCCGTTGCGTCTAGTCGGTGTCCAGATCGGGACCCTCCGGGTCTCCCCGGAGTCCAGGAGTCCTTC F2: 3 CTCGTACAGGGAGGGT 2 Unidirectional alignment (log-probability: -50.3) CACTGAGCATGTCCCTCCCAGGGCAAtGCAGATCAGCCACtGGgagggacatgctcCaAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA CACTGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCACAGG------------TCTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA Template switch alignment (log-probability: -28.9) CACTGAGCATGTCCCTCCCAGGGCAAtGCAGATCAGCCAC|TGGGAGGGACATGCTC|CaAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA CACTGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCAC|TGGGAGGGACATGCTC|CTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA Gorilla > Chimp --------------- chr19:24770722-24770733 Template switch process: F1: L TCACTGAGCATGTCCCTCCCAGGGCAATGCAGATCAGCCACTGG 1 F3: 4 CTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA R RF: TCACTGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCACAGGTCTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA RR: AGTGACTCGTACAGGGAGGGTCCCGTTGCGTCTAGTCGGTGTCCAGATCGGGACCCTCCGGGTCTCCCCGGAGTCCAGGAGTCCT F2: 3 CTCGTACAGGGA 2 Unidirectional alignment (log-probability: -43.3) TGAGCATGTCCCTCCCAGGGCAAtGCAGATCAGCCACtGGagggacatgctcCTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA TGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCACAGG-----------TCTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA Template switch alignment (log-probability: -28.4) TGAGCATGTCCCTCCCAGGGCAAtGCAGATCAGCCACtGG|AGGGACATGCTC|CTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA TGAGCATGTCCCTCCCAGGGCAACGCAGATCAGCCACAGG|AGGGACATGCTC|CTAGCCCTGGGAGGCCCAGAGGGGCCTCAGGTCCTCAGGA ========== Event 1622 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: atgttataAAATTTAACTTGTCATTAAAATTTTACGTATTTTAAACTCAATTACATGTACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATA------------------------AAAGTTGCAATATATCATCATTG ↓ 3 2 41 Chimp: atgttataAAATTTAACTTGTCATTAAAATTTTATGTATTTTAAACTCAATTACATGTACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATA------------AAATTTTAATGACAAGTTGCAATATATCATCATTG Gorilla: atgttatacaatttaacttgtcattaaaaTTTTATGTATTTTAAACTCAATTACATGTACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAATTTTAATGA------------CAAGTTGCAATATATCATCATTG ↑ 3 2 41 Human: atgttataAAATTTAACTTGTCATTAAAATTTTACGTATTTTAAACTCAATTACATGTACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATA------------------------AAAGTTGCAATATATCATCATTG Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:24375477-24375486 Template switch process: F1: L ACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAA 1 F3: 4 AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG R RF: GTCATTAAAATTTTACGTATTTTAAACTCAATTACATGTACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG RR: CAGTAATTTTAAAATGCATAAAATTTGAGTTAATGTACATGTTAAAGTACATATTTTTGAGTTAATCAAATTTTATGTATTTTCAACGTTATATAGTAGTAACAATTTTGATAAAATTGTC F2: 3 CAGTAATTTT 2 Unidirectional alignment (log-probability: -28.2) TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAaattttaatgacAAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAA------------AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG Template switch alignment (log-probability: -16.6) TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAA|TTTTAATGAC|AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAA|TTTTAATGAC|AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG Human > Gorilla --------------- chr19:23456172-23456181 Template switch process: F1: L ACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAA 1 F3: 4 AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG R RF: GTCATTAAAATTTTACGTATTTTAAACTCAATTACATGTACAATTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG RR: CAGTAATTTTAAAATGCATAAAATTTGAGTTAATGTACATGTTAAAGTACATATTTTTGAGTTAATCAAATTTTATGTATTTTCAACGTTATATAGTAGTAACAATTTTGATAAAATTGTC F2: 3 CAGTAATTTT 2 Unidirectional alignment (log-probability: -28.2) TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAaattttaatgacAAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAA------------AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG Template switch alignment (log-probability: -17.1) TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAA|TTTTAATGAC|AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG TTTCATGTATAAAAACTCAATTAGTTTAAAATACATAAAA|TTTTAATGAC|AAGTTGCAATATATCATCATTGTTAAAACTATTTTAACAG ========== Event 1623 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTCAGGCATTGAATTAAGCAGA--------GAAGGATCTTCCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACACTTCAGGACAGCATCACTGCCTGAGAGTAGGGCT Chimp: TGTCAGGCATTGAATTAAGCAGA--------GAAGGATCTTCCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACACTTCAGGACAGCATCACTGCCTGAGAGTAGGGCT ↓ 1 4 3 2 Gorilla: TGTCAGGCATTGAATTAAGCAAT----------------GCCCCTAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACACTTCAGGACAGCATCACTGCCTGAGAGTAGGGCT ↑ 1 4 3 2 Human: TGTCAGGCATTGAATTAAGCAGA--------GAAGGATCTTCCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACACTTCAGGACAGCATCACTGCCTGAGAGTAGGGCT Cluster: [ ] Orangutan: TGTCAGCCATTGAATTAAGCAGAGAAGGACC--------TTCCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACGCTTCAGGACAGCATCACTGCCTGAGAGTAGGGCT Human > Gorilla --------------- chr19:34738656-34738659 Template switch process: F1: L ACCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCA 1 F3: 4 CCCTAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCA R RF: ACCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCAGAGAAGGATCTTCCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACACTTCAGGACAGCAT RR: TGGGGGTCCGTCAAAGGAATACAGTCCGTAACTTAATTCGTCTCTTCCTAGAAGGGGTTCTTACCTTCTCTTCATGGTCTCACGGTACCCTACCAGTGTGAAGTCCTGTCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -32.6) CCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCA------------atgcCCCtAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG CCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCAGAGAAGGATCTT----CCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG Template switch alignment (log-probability: -21.8) CCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCA|ATGC|CCCtAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG CCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCA|ATGC|CCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG Chimp > Gorilla --------------- chr19:34738656-34738659 Template switch process: F1: L ACCCCCAGGCAGTTTCCTTATGTCAGGCATTGAATTAAGCA 1 F3: 4 CCCTAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCA R RF: ACCCCCAGGCAGTTTCCTTCTGTCAGGCATTGAATTAAGCAGAGAAGGATCTTCCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATGGTCACACTTCAGGACAGCAT RR: TGGGGGTCCGTCAAAGGAAGACAGTCCGTAACTTAATTCGTCTCTTCCTAGAAGGGGTTCTTACCTTCTCTTCATGGTCTCACGGTACCCTACCAGTGTGAAGTCCTGTCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -38.1) CCCCCAGGCAGTTTCCTTaTGTCAGGCATTGAATTAAGCA------------atgcCCCtAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG CCCCCAGGCAGTTTCCTTCTGTCAGGCATTGAATTAAGCAGAGAAGGATCTT----CCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG Template switch alignment (log-probability: -27.4) CCCCCAGGCAGTTTCCTTaTGTCAGGCATTGAATTAAGCA|ATGC|CCCtAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG CCCCCAGGCAGTTTCCTTCTGTCAGGCATTGAATTAAGCA|ATGC|CCCCAAGAATGGAAGAGAAGTACCAGAGTGCCATGGGATG ========== Event 1624 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GACCCCTGTCACCCTCTTCCAAGTGCACCATGCACTT----GAGTGCAC------------CTTGAGTCTCCAGCCTCTCAA Chimp: GACCCCTGTCGCCCTCTTCCAAGTGCACCATGCTGCA--GGCAGGAGAC------CTAGGAGTTGAGTCTCCAGCCTCTCAA Gorilla: GACCCCTGTCACCCTCTTCCAAGTGCACCATGCTGCAGG--CAGGAGACCTAGGA------GTTGAGTCTCCAGCCTCTCAA ↓ 3 4 2 1 Human: GACCCCTGTCACCCTCTTCCAAGTGCACCATGCACTT----GAGTGCAC------------CTTGAGTCTCCAGCCTCTCAA Cluster: [ ] Orangutan: GACCCCTGTCACCCTCTTCCGAGTGCACTATGCTGCAGG--CAG-GGACCTAGGA------GTTGAGTCTCCAGCCTCTCAA Gorilla > Human --------------- chr19:35855864-35855868 Template switch process: F1: L GATATTCTGACCCCTGTCACCCTCTTCCAAGTGCACCATGC 1 F3: 4 AGTGCACC-------------------------TTGAGTCTCCAGCCTCTCAAGGAACCGGGAGATCAGGCCA R RF: GATATTCTGACCCCTGTCACCCTCTTCCAAGTGCACCATGCTGCAGGCAGGAGACCTAGGAGTTGAGTCTCCAGCCTCTCAAGGAACCGGGAGATCAGGCCA RR: CTATAAGACTGGGGACAGTGGGAGAAGGTTCACGTGGTACGACGTCCGTCCTCTGGATCCTCAACTCAGAGGTCGGAGAGTTCCTTGGCCCTCTAGTCCGGT F2: 3 GTTCA 2 Unidirectional alignment (log-probability: -40.4) ATATTCTGACCCCTGTCACCCTCTTCCAAGTGCACCATGC---------------------acttgagtgcaccTTGAGTCTCCAGCCTCTCAAGGAACCGGGAGA ATATTCTGACCCCTGTCACCCTCTTCCAAGTGCACCATGCTGCAGGCAGGAGACCTAGGAG-------------TTGAGTCTCCAGCCTCTCAAGGAACCGGGAGA Template switch alignment (log-probability: -27.6) ATATTCTGACCCCTGTCACCCTCTTCCAAGTGCACCATGC|ACTTG|AGTGCACC-------------------------TTGAGTCTCCAGCCTCTCAAGGAACCGGGAGA ATATTCTGACCCCTGTCACCCTCTTCCAAGTGCACCATGC|ACTTG|AGTGCACCATGCTGCAGGCAGGAGACCTAGGAGTTGAGTCTCCAGCCTCTCAAGGAACCGGGAGA ========== Event 1625 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tgaaaaaaagcaaggttctaaatagACTAT--------CTCAGCTTTTAGTCATTGTGGtag Chimp: tgaaaaaaagcaaggttctaaatagACTAT--------CTCAGCTTTTAGTCATTGTGGTAG ↓ 3 2 1 4 Gorilla: TGaaaaaaaGCAAGGTTCTAAATAGACTATTTAGTCTATTTAGCTTTTAGTCATTGTGGTAG ↑ 3 2 1 4 Human: tgaaaaaaagcaaggttctaaatagACTAT--------CTCAGCTTTTAGTCATTGTGGtag Cluster: [ ] Orangutan: tgaaaaaaagcaaggttctaaatagACTAT--------CTCAGCTTTTAGTCATTGTGGtag Human > Gorilla --------------- chr19:35551007-35551015 Template switch process: F1: L CACACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATTT 1 F3: 4 AGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCTATG R RF: CACACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATCTCAGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCCATG RR: GTGTGTAATACACTTTTTTTCGTTCCAAGATTTATCTGATAGAGTCGAAAATCAGTAACACCATCGGGGGTTTTCGATAGGTAC F2: 3 TTTATCTGA 2 Unidirectional alignment (log-probability: -39) ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATttagtctatTtAGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCtATG ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTAT--------CTCAGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCCATG Template switch alignment (log-probability: -28) ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATtT|AGTCTATTT|AGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCtATG ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATCT|AGTCTATTT|AGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCCATG Chimp > Gorilla --------------- chr19:35551007-35551015 Template switch process: F1: L CACACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATTT 1 F3: 4 AGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCTATG R RF: CACACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATCTCAGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCCATG RR: GTGTGTAATACACTTTTTTTCGTTCCAAGATTTATCTGATAGAGTCGAAAATCAGTAACACCATCGGGGGTTTTCGATAGGTAC F2: 3 TTTATCTGA 2 Unidirectional alignment (log-probability: -39) ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATttagtctatTtAGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCtATG ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTAT--------CTCAGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCCATG Template switch alignment (log-probability: -28) ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATtT|AGTCTATTT|AGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCtATG ACATTATGTGAAAAAAAGCAAGGTTCTAAATAGACTATCT|AGTCTATTT|AGCTTTTAGTCATTGTGGTAGCCCCCAAAAGCTATCCATG ========== Event 1626 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAGCAGTCCACGCTTTGCCATATCATGGCTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAAGTCCACGGTGGTGGTGTCCCCATCTGCAACAGGGGAAACTGAGGACCCATGAACAGGCTTGCCCAAgctgggtatggtggcctgcacctataatcccggctactc ↓ 1 4 3 2 Chimp: CCAGCAGTCCACGCTTTGCCAGCAGTCCACTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAAGTCCACGGTGGTGGTGTCCCCATTTGCAACAGGGGAAACTGAGGACCCATGAACAGGCTTGCCCAAgctgggtatggtggcctgcacccataatcccggctactc Gorilla: CCAGCAGTCCATGCTTTGCCATATCATGTCTCAGGGCCTCTGGGCCAAGGCCACACTAGATTCCACAAAGTCCACGGTGGTGTTGTCCCCATCCGCAGCAGGGGAAACTGAGGACCCATGAACAGGCTTGCCCAAgctgggtatggtggcctgcacctataatcctggctactc Human: CCAGCAGTCCACGCTTTGCCATATCATGGCTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAAGTCCACGGTGGTGGTGTCCCCATCTGCAACAGGGGAAACTGAGGACCCATGAACAGGCTTGCCCAAgctgggtatggtggcctgcacctataatcccggctactc Cluster: [ ] Orangutan: CCAGCAGTCCACGCTTTGCCATATCATGGCTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAAGTCCACGGTGGTGGTGTCCCCATCCGCAACAGGGGAAACTGAGGACCTATGAACAGGCTTGCCCAAgctgggtatggtggcctgcacctataatcccggctactc Human > Chimp ------------- chr19:38059864-38059871 Template switch process: F1: L TCACCATGTGCCTACCTTGCCCAGCAGTCCACGCTTTGCCA 1 F3: 4 CTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAA R RF: TCACCATGTGCCTACCTTGCCCAGCAGTCCACGCTTTGCCATATCATGGCTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAAGTCCACGGTGGTGGTGTCCCCATCTGCAACAGGGGAAACTGAGGACCCATGAACAGGCTTGCCCAAGCTGGGTATGGTGGCCTGC RR: AGTGGTACACGGATGGAACGGGTCGTCAGGTGCGAAACGGTATAGTACCGAGTCCCGGAGACCCGGTTCCGGTGTGATCTAGGGTGTTTCAGGTGCCACCACCACAGGGGTAGACGTTGTCCCCTTTGACTCCTGGGTACTTGTCCGAACGGGTTCGACCCATACCACCGGACG F2: 3 ACCTGACG 2 Unidirectional alignment (log-probability: -31.6) CACCATGTGCCTACCTTGCCCAGCAGTCCACGCTTTGCCA-------GcagtccaCTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAA CACCATGTGCCTACCTTGCCCAGCAGTCCACGCTTTGCCATATCATGG-------CTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAA Template switch alignment (log-probability: -22.3) CACCATGTGCCTACCTTGCCCAGCAGTCCACGCTTTGCCA|GCAGtCCA|CTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAA CACCATGTGCCTACCTTGCCCAGCAGTCCACGCTTTGCCA|GCAGGCCA|CTCAGGGCCTCTGGGCCAAGGCCACACTAGATCCCACAAA ========== Event 1627 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCTTCCTCCTTCCTTCCCCT-----------TTCTC-Agtacatatgtatgtatgtgtatatgtatatgtatgttcatatgtgtttgttttgtttttgtctttgtttttgtttttgttttttgagacagagtctcgctctgtcacccaggctggagtgcagtggcacgatctcggctcactgcaacctccgcctc Chimp: CCCTTCCTCCTTCCTTCCCCTCAGTACATATGTACTGAGGTACatatgtatgtatgtgtatatgtatatgtatgttcatatgtgtttgttttgtttttgtctttgtttttgtttttgttttttgagacagagtctcgctctgtcacccaggctggagtgcagtggcatgatctcagctcactgcaacctccgtctc ↑ 4 1 3 2 Gorilla: CCCTTCCTCCTTCCTTCCCCT-----------TTCTC-AGTACatatgtatgtatgtgtatatgtatatgtatgttcatatgtgtttgttttgtttttgtctttgtttttgtttttgttttttgagacagagtctcgctctgtcacccaggctggagtgcagtggcatgatctcagctcactgcaacctccgcctc Human: CCCTTCCTCCTTCCTTCCCCT-----------TTCTC-Agtacatatgtatgtatgtgtatatgtatatgtatgttcatatgtgtttgttttgtttttgtctttgtttttgtttttgttttttgagacagagtctcgctctgtcacccaggctggagtgcagtggcacgatctcggctcactgcaacctccgcctc Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Gorilla > Chimp --------------- chr19:39250044-39250048 Template switch process: F1: L TGTGCTCTTTTGCATGCATACCCTTCCTCCTTCCTTCCC----CTCAGTACATATGTA 1 F3: 4 GTACATATGTATGTATGTGTATATGTATATGTATGTTCAT R RF: TGTGCTCTTTTGCATGCATACCCTTCCTCCTTCCTTCCCCTTTCTCAGTACATATGTATGTATGTGTATATGTATATGTATGTTCATATGTGTTTGTTTTGTTTTTGTCTTTGTTTTTGTTTTTGTTTTTTGAGACAGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCAG RR: ACACGAGAAAACGTACGTATGGGAAGGAGGAAGGAAGGGGAAAGAGTCATGTATACATACATACACATATACATATACATACAAGTATACACAAACAAAACAAAAACAGAAACAAAAACAAAAACAAAAAACTCTGTCTCAGAGCGAGACAGTGGGTCCGACCTCACGTCACCGTACTAGAGTC F2: 3 GAGTC 2 Unidirectional alignment (log-probability: -43.9) TGCATACCCTTCCTCCTTCCTTCCC----CTCAgtacatatgtactgagGTACATATGTATGTATGTGTATATGTATATGTATGTTCAT TGCATACCCTTCCTCCTTCCTTCCCCTTTCTCA----------------GTACATATGTATGTATGTGTATATGTATATGTATGTTCAT Template switch alignment (log-probability: -26.6) TGCATACCCTTCCTCCTTCCTTCCC----CTCAGTACATATGTA|CTGAG|GTACATATGTATGTATGTGTATATGTATATGTATGTTCAT TGCATACCCTTCCTCCTTCCTTCCCCTTTCTCAGTACATATGTA|CTGAG|GTACATATGTATGTATGTGTATATGTATATGTATGTTCAT ========== Event 1628 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGTACTTCAGACCTACTAATAGGT Chimp: AAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGTACTTCAGACCTACTAATAGGT ↓ 3 2 1 4 Gorilla: AAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC--------TGACACTTCAGACCTACTAATAGGT ↑ 3 2 1 4 Human: AAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGTACTTCAGACCTACTAATAGGT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr19:36903894-36903897 Template switch process: F1: L AATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC 1 F3: 4 ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT R RF: AATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGTACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT RR: TTAAATGTTTTCCATCTTTCTGGAACACAGTCCGAAAGGGGGGAGATGATCCATGAAGTCTGGATGATTATCCAAGATACATAAACTTATATA F2: 3 CAGT 2 Unidirectional alignment (log-probability: -25.5) ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC-----------TgacACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGT---ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT Template switch alignment (log-probability: -16.2) ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC|TGAC|ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC|TGAC|ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT Chimp > Gorilla --------------- chr19:36903894-36903897 Template switch process: F1: L AATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC 1 F3: 4 ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT R RF: AATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGTACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT RR: TTAAATGTTTTCCATCTTTCTGGAACACAGTCCGAAAGGGGGGAGATGATCCATGAAGTCTGGATGATTATCCAAGATACATAAACTTATATA F2: 3 CAGT 2 Unidirectional alignment (log-probability: -25.5) ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC-----------TgacACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCCCCTCTACTAGGT---ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT Template switch alignment (log-probability: -16.2) ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC|TGAC|ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT ATTTACAAAAGGTAGAAAGACCTTGTGTCAGGCTTTCCCC|TGAC|ACTTCAGACCTACTAATAGGTTCTATGTATTTGAATATAT ========== Event 1629 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CATTGTGATGTGATTGATAGAT----AGGACTAATGTACTAATTATGGCCAT--------------------ATAG-TCTATTTGGATAATGGTAAAATTA ↓ 13 24 ↑ 13 24 Chimp: CATTGTGATGTGATTGATAGAT-----AGACT----------ATATGGCCAT----------AATTAGTACATTAGTCCTATTTGGATAATGGTAAAATTA Gorilla: CATTGTGATGTGATTGATAGAG-----GGACT----------ATATGGCCATAATTAGTACA----------TTAGTCCTATTTGGATAATGGTAAAATTA ↓ 1 3 4 2 ↑ 3 4 Human: CATTGTGATGTGATTGATAGAT----AGGACTAATGTACTAATTATGGCCAT--------------------ATAG-TCTATTTGGATAATGGTAAAATTA Cluster: [ ] Orangutan: CATTGTGATGTGATTGACAGATAGAG-GGACT----------ATATGGCCATAATT-ATACA----------TTAGTCCTATTTGGCTAATGGTAAAATTA Chimp > Human ------------- chr19:21045586-21045614 Template switch process: F1: L GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG 1 F3: 4 CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA R RF: GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGACTATATGGCCATAATTAGTACATTAGTCCTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA RR: CACTATACACTTAAAAAGAGTAACACTACACTAACTATCTATCTGATATACCGGTATTAATCATGTAATCAGGATAAACCTATTACCATTTTAATCTAGTATTTTTTTCTAT F2: 3 TGATATACCGGTATTAATCATGTAATCAG 2 Unidirectional alignment (log-probability: -58.1) ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGgactaatgtACTAatTATGGCCATA----------TAGT-CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG---------ACTA--TATGGCCATAATTAGTACATTAGTCCTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA Template switch alignment (log-probability: -18.9) ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG|GACTAATGTACTAATTATGGCCATATAGT|CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG|GACTAATGTACTAATTATGGCCATATAGT|CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA Human > Chimp ------------- chr19:21816186-21816214 Template switch process: F1: L GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG 1 F3: 4 CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA R RF: GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGGACTAATGTACTAATTATGGCCATATAGTCTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA RR: CACTATACACTTAAAAAGAGTAACACTACACTAACTATCTATCCTGATTACATGATTAATACCGGTATATCAGATAAACCTATTACCATTTTAATCTAGTATTTTTTTCTAT F2: 3 CTGATTACATGATTAATACCGGTATATCA 2 Unidirectional alignment (log-probability: -58.1) ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATA-GACTA----------TATGGCCATAatTAGTacattagtcCTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGGACTAATGTACTAATTATGGCCATA--TAGT---------CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA Template switch alignment (log-probability: -18.9) ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG|ACTATATGGCCATAATTAGTACATTAGTC|CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA ATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAG|ACTATATGGCCATAATTAGTACATTAGTC|CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA Gorilla > Human --------------- chr19:21045583-21045614 Template switch process: F1: L TGTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGA 1 F3: 4 CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA R RF: TGTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGAGGGACTATATGGCCATAATTAGTACATTAGTCCTATTTGGATAATGGTAAAATTAGATCATAAAACAAGATA RR: ACACTATACACTTAAAAAGAGTAACACTACACTAACTATCTCCCTGATATACCGGTATTAATCATGTAATCAGGATAAACCTATTACCATTTTAATCTAGTATTTTGTTCTAT F2: 3 TGATATACCGGTATTAATCATGTAATCAGGAT 2 Unidirectional alignment (log-probability: -67.8) GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGAtaGGACTAatgtactaatTATGGCCATA----------TAGT-CTATTTGGATAATGGTAAAATTAGATCATAAAAaAAGATA GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGA-GGGACTA----------TATGGCCATAATTAGTACATTAGTCCTATTTGGATAATGGTAAAATTAGATCATAAAACAAGATA Template switch alignment (log-probability: -25.3) GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGA|TAGGACTAATGTACTAATTATGGCCATATAGT|CTATTTGGATAATGGTAAAATTAGATCATAAAAaAAGATA GTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGA|TAGGACTAATGTACTAATTATGGCCATATAGT|CTATTTGGATAATGGTAAAATTAGATCATAAAACAAGATA Human > Gorilla --------------- chr19:20839835-20839864 Template switch process: F1: L TGTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAG--AGG 1 F3: 4 CTATTTGGATAATGGTAAAATTAGATCATAAAACAAGATA R RF: TGTGATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGGACTAATGTACTAATTATGGCCATATAGTCTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA RR: ACACTATACACTTAAAAAGAGTAACACTACACTAACTATCTATCCTGATTACATGATTAATACCGGTATATCAGATAAACCTATTACCATTTTAATCTAGTATTTTTTTCTAT F2: 3 CTGATTACATGATTAATACCGGTATATCAG 2 Unidirectional alignment (log-probability: -67.8) GATATGTGAATTTTTCTCATTGTGATGTGATTGATAGA-gGGACTA----------TATGGCCATAattagtacatTAGTcCTATTTGGATAATGGTAAAATTAGATCATAAAAcAAGATA GATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGGACTAATGTACTAATTATGGCCATA----------TAGT-CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA Template switch alignment (log-probability: -35) GATATGTGAATTTTTCTCATTGTGATGTGATTGATAG--AGG|GACTATATGGCCATAATTAGTACATTAGTC|CTATTTGGATAATGGTAAAATTAGATCATAAAAcAAGATA GATATGTGAATTTTTCTCATTGTGATGTGATTGATAGATAGG|GACTATATGGCCATAATTAGTACATTAGTC|CTATTTGGATAATGGTAAAATTAGATCATAAAAAAAGATA ========== Event 1630 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: acagctcagaaagcccactgcaattccgggattcTGGTTTTGTTTTGAGGTTGCCCCGGGCTTCTGAGGAGGGGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGG------CTGGAGGAAGATGCAGCGAGGCTG ↓ 3 2 1 4 Chimp: acagctcagaaagcccactgcaattccgggattcTGGTTTTGTTTTCAGGTTGCCCCGGGCTTCTGAGGAGGAGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGG---AATTGCGAGGAAGATGCAGCGAGGCTG Gorilla: acagctcagaaagcccactgcaattccgggattcTGGTTTTGTTTTCAGGTTGCCCCGGGCTTCTGAGGAGGAGTCAGTGGGCTCAGCATGGAGAGGAAGGAAGCCGGAAGGAAT---TGCGAGGAAGATGCAGCGAGGCTG Human: acagctcagaaagcccactgcaattccgggattcTGGTTTTGTTTTGAGGTTGCCCCGGGCTTCTGAGGAGGGGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGG------CTGGAGGAAGATGCAGCGAGGCTG Cluster: [ ] Orangutan: acagctcagaaagcccactgcaattccgggattcTGGTTTTGTTTTCAGGTTGCCCCGGGCTTCTGAGGAGGAGTCAGTGGGCTCAGCATGGAGAGGAAGGAAGCCGGAAGGAAT---TGCGAGGAAGATGCAGCGAGGCTG Human > Chimp ------------- chr19:41092262-41092267 Template switch process: F1: L GAGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGG 1 F3: 4 GAGGAAGATGCAGCGAGGCTGGAAAGGTTGGGGATCCCCC R RF: GCAATTCCGGGATTCTGGTTTTGTTTTGAGGTTGCCCCGGGCTTCTGAGGAGGGGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGGCTGGAGGAAGATGCAGCGAGGCTGGAAAGGTTGGGGATCCCCC RR: CGTTAAGGCCCTAAGACCAAAACAAAACTCCAACGGGGCCCGAAGACTCCTCCCCAGTCACCCGAGTCGTACCTTTCCTTCCTTCGGCCTTCCGACCTCCTTCTACGTCGCTCCGACCTTTCCAACCCCTAGGGGG F2: 3 CGTTAA 2 Unidirectional alignment (log-probability: -34.4) aGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGgaattGC--GAGGAAGATGCAGCGAGGCTGGAAAGGTTGGGGATCCCCC GGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAG-----GCTGGAGGAAGATGCAGCGAGGCTGGAAAGGTTGGGGATCCCCC Template switch alignment (log-probability: -22) aGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGG|AATTGC|GAGGAAGATGCAGCGAGGCTGGAAAGGTTGGGGATCCCCC GGTCAGTGGGCTCAGCATGGAAAGGAAGGAAGCCGGAAGG|AATTGC|GAGGAAGATGCAGCGAGGCTGGAAAGGTTGGGGATCCCCC ========== Event 1631 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TGTGTTTTTAAATTCATGTGATCATTGAAGTCTCGTTATCTTGAGACTTCCTTCCTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTCCCTAGTTACAGTGAAGGATAGTGCCAAA ↓ 3 2 1 4 Chimp: TGTGTTTTTAAATTCATGTGATCATTGAAGTCTCATTATCTTGAGACTTCCTTCCTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACT--CTGATCACAGTGAAGGATAGTGCCAAA Gorilla: TGTGTTTTTAAATTCATGTGATCATTGAAGTCTCATTATCTTGAGACTTCCTTCCTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACT--CTGGTCACAGTGAAGGATAGTGCCAAA Human: TGTGTTTTTAAATTCATGTGATCATTGAAGTCTCGTTATCTTGAGACTTCCTTCCTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTCCCTAGTTACAGTGAAGGATAGTGCCAAA Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:42002498-42002502 Template switch process: F1: L TCCTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTC 1 F3: 4 ACAGTGAAGGATAGTGCCAAATAGCCTAGTGTCTTCCTCA R RF: GATCATTGAAGTCTCGTTATCTTGAGACTTCCTTCCTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTCCCTAGTTACAGTGAAGGATAGTGCCAAATAGCCTAGTGTCTTCCTCA RR: CTAGTAACTTCAGAGCAATAGAACTCTGAAGGAAGGATTCTGTTGGGACAACACCTTGGACGAGGGATCAATGAGGGATCAATGTCACTTCCTATCACGGTTTATCGGATCACAGAAGGAGT F2: 3 CTAGT 2 Unidirectional alignment (log-probability: -27.2) CTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTCtgatC------ACAGTGAAGGATAGTGCCAAATAGCCTAGTGTCTTCCTCA CTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTC----CCTAGTTACAGTGAAGGATAGTGCCAAATAGCCTAGTGTCTTCCTCA Template switch alignment (log-probability: -15.9) CTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTC|TGATC|ACAGTGAAGGATAGTGCCAAATAGCCTAGTGTCTTCCTCA CTAAGACAACCCTGTTGTGGAACCTGCTCCCTAGTTACTC|TGATC|ACAGTGAAGGATAGTGCCAAATAGCCTAGTGTCTTCCTCA ========== Event 1632 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GGAAGCAGTGGGGTGGGGGTGGCTGTGGCTACACTTGGTGGCT----ATGTCACTGCCACTGAAAAGCCAGGCCCCTGTC Chimp: GGAAGCAGTGGGGTGGGGGTGGCAGTGAC-----ATAGCCACC--AAGTGTAGCCACAGCTGAAAAGCCAGGCCCCTGTC Gorilla: GGAAGCAGTGGGGTGGGGGTGGCAGTGAC-----ATAGCCACCAA--GTGTAGCCACAGCTGAAAAGCCAGGCCCCTGTC ↓ 3 1 2 4 ↑ 3 2 4 Human: GGAAGCAGTGGGGTGGGGGTGGCTGTGGCTACACTTGGTGGCT----ATGTCACTGCCACTGAAAAGCCAGGCCCCTGTC Cluster: [ ] Orangutan: GGAAGCAGTGGGGTGGGGGTGGCAGTGAC-----ATAGCCACCAA--GTGTAGCCACAGCTGAAAAGCCAGGCCCCTGTC Gorilla > Human --------------- chr1:94339782-94339813 Template switch process: F1: L ATGTAAGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGC 1 F3: 4 CTGAAAAGCCAGGCCCCTGTCCGCGGAAGTCCAGGTTGAT R RF: ATGTACGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGCAGTGACATAGCCACCAAGTGTAGCCACAGCTGAAAAGCCAGGCCCCTGTCCGCAGAAGTCCAGGTTGAT RR: TACATGCGAGACACCGTTCCTTCGTCACCCCACCCCCACCGTCACTGTATCGGTGGTTCACATCGGTGTCGACTTTTCGGTCCGGGGACAGGCGTCTTCAGGTCCAACTA F2: 3 ACCGTCACTGTATCGGTGGTTCACATCGGTGT 2 Unidirectional alignment (log-probability: -77.3) TGTAaGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGCtGTGgctacacttggtggctatgtcactgccA------------------------CTGAAAAGCCAGGCCCCTGTCCGCgGAAGTCCAGGTTGAT TGTACGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGCAGTG---------------------------ACATAGCCACCAAGTGTAGCCACAGCTGAAAAGCCAGGCCCCTGTCCGCAGAAGTCCAGGTTGAT Template switch alignment (log-probability: -30.8) TGTAaGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGC|TGTGGCTACACTTGGTGGCTATGTCACTGCCA|CTGAAAAGCCAGGCCCCTGTCCGCgGAAGTCCAGGTTGAT TGTACGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGC|TGTGGCTACACTTGGTGGCTATGTCACTGCCA|CTGAAAAGCCAGGCCCCTGTCCGCAGAAGTCCAGGTTGAT Human > Gorilla --------------- chr1:95545370-95545398 Template switch process: F1: L ATGTACGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGC 1 F3: 4 CTGAAAAGCCAGGCCCCTGTCCGCAGAAGTCCAGGTTGAT R RF: ATGTAAGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGCTGTGGCTACACTTGGTGGCTATGTCACTGCCACTGAAAAGCCAGGCCCCTGTCCGCGGAAGTCCAGGTTGAT RR: TACATTCGAGACACCGTTCCTTCGTCACCCCACCCCCACCGACACCGATGTGAACCACCGATACAGTGACGGTGACTTTTCGGTCCGGGGACAGGCGCCTTCAGGTCCAACTA F2: 3 GACACCGATGTGAACCACCGATACAGTGA 2 Unidirectional alignment (log-probability: -73.1) TGTAcGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGCaGTGacatagccaccaagtgtagccacaG---------------------------CTGAAAAGCCAGGCCCCTGTCCGCaGAAGTCCAGGTTGAT TGTAAGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGCTGTG------------------------GCTACACTTGGTGGCTATGTCACTGCCACTGAAAAGCCAGGCCCCTGTCCGCGGAAGTCCAGGTTGAT Template switch alignment (log-probability: -30.5) TGTAcGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGC|AGTGACATAGCCACCAAGTGTAGCCACAG|CTGAAAAGCCAGGCCCCTGTCCGCaGAAGTCCAGGTTGAT TGTAAGCTCTGTGGCAAGGAAGCAGTGGGGTGGGGGTGGC|AGTGACATAGCCACCAAGTGTAGCCACAG|CTGAAAAGCCAGGCCCCTGTCCGCGGAAGTCCAGGTTGAT ========== Event 1633 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTCACAAGcagggaaggcttc--ctgtgcaagtgacatgtcaggaaaacttcaagggacaggaaggttttcaccaggtgggtggcagagggtc Chimp: GGTCACAAGCAGGGAAGGCTTC--CTGTGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGGTTGTCACCAGGTGGGTGGCAGAgggta ↓ 1 4 3 2 Gorilla: GGTCACAAGCAGGGAAGGCTTGTGACATGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGGTTGTCACCAGGTGGGTGGCAGAGGGTA Human: GGTCACAAGcagggaaggcttc--ctgtgcaagtgacatgtcaggaaaacttcaagggacaggaaggttttcaccaggtgggtggcagagggtc Cluster: [ ] Orangutan: GGTCACAAGcagggaaggcttc--ctgtgcaagtgacatctcaggaaaacttcaagggacaggaaggttgtcaccaggtgggtggcagagggta Chimp > Gorilla --------------- chr19:40018559-40018564 Template switch process: F1: L GAATGACTAGAGCCAACTGGGGTCACAAGCAGGGAAGGCTT 1 F3: 4 TGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGG R RF: GAATGACTAGAGCCAACTGGGGTCACAAGCAGGGAAGGCTTCCTGTGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGGTTGTCAC RR: CTTACTGATCTCGGTTGACCCCAGTGTTCGTCCCTTCCGAAGGACACGTTCACTGTACAGTCCTTTTGAAGTTCCCTGTCCTTCCAACAGTG F2: 3 ACAGTG 2 Unidirectional alignment (log-probability: -28) AATGACTAGAGCCAACTGGGGTCACAAGCAGGGAAGGCT---TGtgacaTGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGG AATGACTAGAGCCAACTGGGGTCACAAGCAGGGAAGGCTTCCTG-----TGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGG Template switch alignment (log-probability: -16.5) AATGACTAGAGCCAACTGGGGTCACAAGCAGGGAAGGCTT|GTGACA|TGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGG AATGACTAGAGCCAACTGGGGTCACAAGCAGGGAAGGCTT|GTGACA|TGCAAGTGACATGTCAGGAAAACTTCAAGGGACAGGAAGG ========== Event 1634 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACATTTGGTCCCACGGAGACCACA------------------------------------------------TGCAGCCTCAACCAGACCAGTCACACCAACACACTGTTTT Chimp: ACATTTGGTCCCACGGAGACCACA------------------------TGCAGGAACAGCTGCATGTGGACATGCAGCCTCAACTAGACCAGTCACACCAACACACTGTTTT Gorilla: ACATTTGGTCCCACGGAGACCACATGCAGGAACAGCTGCATGTGGACA------------------------TGCAGCCTCAACCAGACCAGTCACACCAACACACTGTTTT ↑ 3 4 2 1 Human: ACATTTGGTCCCACGGAGACCACA------------------------------------------------TGCAGCCTCAACCAGACCAGTCACACCAACACACTGTTTT Cluster: [ ] Orangutan: ACATTTGGTCCCACGGAGACCACATGCA-GAACAGCTGCACGTGGACA------------------------TGCAGCCTCAACCAGACCAGTCACACCAACACACTGTTTT Human > Gorilla --------------- chr19:40226139-40226148 Template switch process: F1: L TGCACACGGACAGACACACATTTGGTCCCACGGAGACCACATGCAG---------GAACAG 1 F3: 4 ACATGCAGCCTCAACCAGACCAGTCACACCAACACACTGTTTT R RF: TGCACACGGACAGACACACATTTGGTCCCACGGAGACCACATGCAGCCTCAACCAGACCAGTCACACCAACACACTGTTTT RR: ACGTGTGCCTGTCTGTGTGTAAACCAGGGTGCCTCTGGTGTACGTCGGAGTTGGTCTGGTCAGTGTGGTTGTGTGACAAAA F2: 3 GGTGTACGTC 2 Unidirectional alignment (log-probability: -45.4) GACACACATTTGGTCCCACGGAGACCAcatgcaggaacagctgcatgtggaCATGCAGCCTCAACCAGACCAGTCACACCAACACACTGT GACACACATTTGGTCCCACGGAGACCA------------------------CATGCAGCCTCAACCAGACCAGTCACACCAACACACTGT Template switch alignment (log-probability: -33.1) GACACACATTTGGTCCCACGGAGACCACATGCAG---------GAaCAG|CTGCATGTGG|ACATGCAGCCTCAACCAGACCAGTCACACCAACACACTGT GACACACATTTGGTCCCACGGAGACCACATGCAGCCTCAACCAGACCAG|CTGCATGTGG|ACATGCAGCCTCAACCAGACCAGTCACACCAACACACTGT ========== Event 1635 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: acatttgtgtcagtagggttcttcagaaaaacagaataaattatatatat----------------------------------------------------------------------------------------------------------agctaagttatacgtataatttaattaagttatgcgtataa----------ttatatatataatttattCTGTTTTTCTGGAGGACCCAatttatatatataaat ↓ 3 2 1 4 Chimp: acatttgtgtcagtagggttctccagaaaaacagaataaattatatatat---------------------------------------------------------------------------------------------------------------aattatacgcataatttaattaaattatacgtataa-----cttagctatatatataatttattCTGTTTTTCTGAAGAACCCAatttatatatataaat Gorilla: acatTTGTGTCAGTAGGGTTCTCCAGAAAAACAGAATAAATTATATATATAATTATannnnnnnnnnnnnnnnnnnnnnnnnGCACATGAAAAGATGCTCAACATTtgtgtcagtagggttctccagaaaaacagaataaattatatatatagcta-----agttatacgtataatttaattaaattatacgtataacttag-----ctatatatataatttattCTGTTTTTCTGAAGAACCCAatttatatatataaat ↑ 3 2 1 4 Human: acatttgtgtcagtagggttcttcagaaaaacagaataaattatatatat----------------------------------------------------------------------------------------------------------agctaagttatacgtataatttaattaagttatgcgtataa----------ttatatatataatttattCTGTTTTTCTGGAGGACCCAatttatatatataaat Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:43475012-43475049 Template switch process: F1: L CGTATAA 1 F3: 4 ACCCAATTTATATATATAAATTGGCTCATGTAGTTATGGA R RF: TCTTCAGAAAAACAGAATAAATTATATATATAGCTAAGTTATACGTATAATTTAATTAAGTTATGCGTATAATTATATATATAATTTATTCTGTTTTTCTGGAGGACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA RR: AGAAGTCTTTTTGTCTTATTTAATATATATATCGATTCAATATGCATATTAAATTAATTCAATACGCATATTAATATATATATTAAATAAGACAAAAAGACCTCCTGGGTTAAATATATATATTTAACCGAGTACATTAATACCT F2: 3 AGAAGTCTTTTTGTCTTATTTAATATATATATCGATTC 2 Unidirectional alignment (log-probability: -42.1) CGTATAActtagcTATATATATAATTTATTCTGTTTTTCTGaAGaACCCAATTTATATATATAAATTGGCTCATGTAgTTATGGA CGTATAA-----TTATATATATAATTTATTCTGTTTTTCTGGAGGACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA Template switch alignment (log-probability: -25.3) CGTATAA|CTTAGCTATATATATAATTTATTCTGTTTTTCTGAAGA|ACCCAATTTATATATATAAATTGGCTCATGTAgTTATGGA CGTATAA|CTTAGCTATATATATAATTTATTCTGTTTTTCTGAAGA|ACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA Human > Gorilla --------------- chr19:40918849-40918886 Template switch process: F1: L CGTATAA 1 F3: 4 ACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA R RF: TCTTCAGAAAAACAGAATAAATTATATATATAGCTAAGTTATACGTATAATTTAATTAAGTTATGCGTATAATTATATATATAATTTATTCTGTTTTTCTGGAGGACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA RR: AGAAGTCTTTTTGTCTTATTTAATATATATATCGATTCAATATGCATATTAAATTAATTCAATACGCATATTAATATATATATTAAATAAGACAAAAAGACCTCCTGGGTTAAATATATATATTTAACCGAGTACATTAATACCT F2: 3 AGAAGTCTTTTTGTCTTATTTAATATATATATCGATTC 2 Unidirectional alignment (log-probability: -34.6) CGTATAActtagcTATATATATAATTTATTCTGTTTTTCTGaAGaACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA CGTATAA-----TTATATATATAATTTATTCTGTTTTTCTGGAGGACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA Template switch alignment (log-probability: -19.7) CGTATAA|CTTAGCTATATATATAATTTATTCTGTTTTTCTGAAGA|ACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA CGTATAA|CTTAGCTATATATATAATTTATTCTGTTTTTCTGAAGA|ACCCAATTTATATATATAAATTGGCTCATGTAATTATGGA ========== Event 1636 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCAGGCTCACCATCAATGATGCTGGGACCTTGTG---CATCCACAGGGCCTGGCACCCAGGGCCTGTGGAGAGACAGGGTGGGTGGGTCAGGGACTGGGGATGGTGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAGCACTCCTGGGAAGA---------- Chimp: CCCAGGCTCACCATCAATGATGCTGGGACCTTGTG---CATCCACAGGGCCTGGCACCCAGGGCCTGTGGAGAGACCGGGTGGGTGGGTCAGGGACTGGGGATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAACACTCCTgggaaga---------- ↓ 3 2 1 4 Gorilla: CCCAGGCTCACCATCAATGATGCTGGGACCTTGTG---CATCCACAGGGCCTGGCACCCAGGGCCTGTGAAGAGACAGGGTGGGTGGGTCAGGGACTGGGGATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAGCATTCCTgggaaga---------- Human: CCCAGGCTCACCATCAATGATGCTGGGACCTTGTG---CATCCACAGGGCCTGGCACCCAGGGCCTGTGGAGAGACAGGGTGGGTGGGTCAGGGACTGGGGATGGTGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAGCACTCCTGGGAAGA---------- Cluster: [ ] Orangutan: CCCAGGCTCACCATCAATGATGTTGGGACCCTGTGCACCACCCACAGGGCCTGGCACCCAGGGCCTGTGGAGAGACAGGGTGGGTGGGTCAGGGACTGGGGATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGCTCCAGCACTCCTAggaagagggtgaggac Chimp > Gorilla --------------- chr19:16648288-16648291 Template switch process: F1: L GATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCA 1 F3: 4 TCCTGGGAAGAGGATGAGGACACGCCTGGGTGGGGAGGGG R RF: ATGCTGGGACCTTGTGCATCCACAGGGCCTGGCACCCAGGGCCTGTGGAGAGACCGGGTGGGTGGGTCAGGGACTGGGGATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAACACTCCTGGGAAGAGGGTGAGGACACGCCTGGGTGGGGAGGGG RR: TACGACCCTGGAACACGTAGGTGTCCCGGACCGTGGGTCCCGGACACCTCTCTGGCCCACCCACCCAGTCCCTGACCCCTACCGCTGTGTAAAGGGGTCGGGACCGGGGACGTCAAGGTTGTGAGGACCCTTCTCCCACTCCTGTGCGGACCCACCCCTCCCC F2: 3 TACG 2 Unidirectional alignment (log-probability: -60.3) ATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAgCAtTCCTGGGAAGAggatgaggacacgcctgggtggggagggg ATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCAACACTCCTGGGAAGA----------------------------- Template switch alignment (log-probability: -21.7) ATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCA|GCAT|TCCTGGGAAGAGGaTGAGGACACGCCTGGGTGGGGAGGGG ATGGCGACACATTTCCCCAGCCCTGGCCCCTGCAGTTCCA|GCAT|TCCTGGGAAGAGGGTGAGGACACGCCTGGGTGGGGAGGGG ========== Event 1637 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAGACCCAGATGATTCCAGATGAT--------------------------------------TTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAGATTAGAGACAGCTGTCTTGGCATGAGGGCCTGAGCCAGGGATCCC-AGCTGGGTCTCATCTCTCCAGCATCACAGTAGAGGGCTGGTCTGG-TCTGCAGCTGTCA Chimp: CCAAACCCAGATGATTCCAGATGAT-------------------TTCCCTCAGCACTGATGATTTCCCTAAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAGATTAGAGACAGCTGTCTTGGCATGAGGGCCTGAGCCAGGGATCCC-AGCTGAGTCTCATCTCTCCAGCATCACAGTAGAGGGCTGGTCTGG-TCTGCCGCTGTCA Gorilla: CCAGACCCAGATGATTCCAGATGATTTCCCTCAGCACTGATGAT-------------------TTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAGATTAGAGACAGCTGTCTTGGTATGAGGACCTGAGCCAGGGATCCC-AGCTGGGTCTCATCTCTCCAGCATCACAGTAGAGGGCTGGTCTGG-TCTGCAGCTGTCA ↑ 4 1 3 2 Human: CCAGACCCAGATGATTCCAGATGAT--------------------------------------TTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAGATTAGAGACAGCTGTCTTGGCATGAGGGCCTGAGCCAGGGATCCC-AGCTGGGTCTCATCTCTCCAGCATCACAGTAGAGGGCTGGTCTGG-TCTGCAGCTGTCA Cluster: [ ] Orangutan: CCAGACCCAGATGATTCCAGATGATTTCCCTCAGCACTGATGAT-------------------TTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAGATTAGAGACAGCTGTCTTGGCATGAGGGCCTGAGCCAGGGATCCCACGCTGAGTCTCATCTCTCCAGCATCACAGTAGAGGGCTGGTCTGGTCCTGCAGCTGTCA Human > Gorilla --------------- chr19:15259289-15259295 Template switch process: F1: L TGCTTGTAAAAAATAACCAGACCCAGATGATTCCAGATGATTTCCCT 1 F3: 4 GATGATTTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAG R RF: TGCTTGTGAAAAATAACCAGACCCAGATGATTCCAGATGATTTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCACCGGCAGATTAGAGACAGCTGTCTTGGCATGAGGGCCTGAGCCAGGGATCCCAGCTGGGTCTCATCTCTCCAGCATCACAGTAGAGGGCTG RR: ACGAACACTTTTTATTGGTCTGGGTCTACTAAGGTCTACTAAAGGGACTCATCTTACCCGACCGACCCGACAGTGGCCGTCTAATCTCTGTCGACAGAACCGTACTCCCGGACTCGGTCCCTAGGGTCGACCCAGAGTAGAGAGGTCGTAGTGTCATCTCCCGAC F2: 3 TCACGAC 2 Unidirectional alignment (log-probability: -43.7) aAAAAATAACCAGACCCAGATGATTCCAgatgatttccctcagcactGATGATTTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCAC GAAAAATAACCAGACCCAGATGATTCCA-------------------GATGATTTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCAC Template switch alignment (log-probability: -27.9) aAAAAATAACCAGACCCAGATGATTCCAGATGATTTCCCT|CAGCaCT|GATGATTTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCAC GAAAAATAACCAGACCCAGATGATTCCAGATGATTTCCCT|CAGCCCT|GATGATTTCCCTGAGTAGAATGGGCTGGCTGGGCTGTCAC ========== Event 1638 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAATTAAGGTCCTGAGGCCA-TAGTGTCCCT----AAAGGAGGCCTGTTGTTGTGCCCTCAG Chimp: GGAATTAAGGTCCTGAGGCCA-TAGTGTCCCT----AAAGGAGGCCTGTTGTTGTGCCCTCGG ↓ 31 2 4 Gorilla: GGAATTAAGGTCCTGAGGCCATTAAGGACACT--------ATGGCCTGTTGTTGTGCCCTCAG ↑ 31 2 4 Human: GGAATTAAGGTCCTGAGGCCA-TAGTGTCCCT----AAAGGAGGCCTGTTGTTGTGCCCTCAG Cluster: [ ] Orangutan: GGAATTAAGGTCCTGAGGCCA-TAGTGTCCCTAAAG----GAGGCCTGTTGTTGTACCCTCAG Human > Gorilla --------------- chr1:95818469-95818480 Template switch process: F1: L AAAGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCAT 1 F3: 4 GGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA R RF: AAAGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCATAGTGTCCCTAAAGGAGGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA RR: TTTCTCTTGTCTTCGTAAACCCTTAATTCCAGGACTCCGGTATCACAGGGATTTCCTCCGGACAACAACACGGGAGTCTGTGGGAGGTACCGGGAGT F2: 3 TATCACAGGAAT 2 Unidirectional alignment (log-probability: -35.3) AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCA---------TtAAGGAcactatGGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCATAGTGTCCCTAAAGGA------GGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA Template switch alignment (log-probability: -22.8) AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCAT|TAaGGACACTAT|GGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCAT|TAGGGACACTAT|GGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA Chimp > Gorilla --------------- chr1:95818469-95818480 Template switch process: F1: L AAAGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCAT 1 F3: 4 GGCCTGTTGTTGTGCCCTCAGACACCCTCCATGGCCCTCA R RF: AAAGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCATAGTGTCCCTAAAGGAGGCCTGTTGTTGTGCCCTCGGACACCCTCCATGGCCCTCA RR: TTTCTCTTGTCTTCGTAAACCCTTAATTCCAGGACTCCGGTATCACAGGGATTTCCTCCGGACAACAACACGGGAGCCTGTGGGAGGTACCGGGAGT F2: 3 TATCACAGGAAT 2 Unidirectional alignment (log-probability: -40.9) AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCA---------TtAAGGAcactatGGCCTGTTGTTGTGCCCTCaGACACCCTCCATGGCCCTCA AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCATAGTGTCCCTAAAGGA------GGCCTGTTGTTGTGCCCTCGGACACCCTCCATGGCCCTCA Template switch alignment (log-probability: -28.3) AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCAT|TAaGGACACTAT|GGCCTGTTGTTGTGCCCTCaGACACCCTCCATGGCCCTCA AGAGAACAGAAGCATTTGGGAATTAAGGTCCTGAGGCCAT|TAGGGACACTAT|GGCCTGTTGTTGTGCCCTCGGACACCCTCCATGGCCCTCA ========== Event 1639 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGACAGTCCACCAATGGTTGT------------------GCGAAAGCCAGCCCGCTTTCGCACA--ACTGTCCGATGGAATT ↑ 1 4 3 2 Chimp: CAGACAGTCCACCAATGGTTGG---------AGGCCAGACCCCAGAGCCAGTCCGCTTTCGCACA--AGTGTCCGATGGAATT Gorilla: CAGACAGTCCACCAATGGTTGGAGGCCAGAC---------CCCAGAGCCAGTCCGCTTTCGCACA--AGTGTCCGATGGAATT ↓ 1 4 3 2 Human: CAGACAGTCCACCAATGGTTGT------------------GCGAAAGCCAGCCCGCTTTCGCACA--ACTGTCCGATGGAATT Cluster: [ ] Orangutan: CAGACAGTCCACCAGTGGTTGGAGGCCAGAC---------CCCAGAGCCAGTCCGCTTTCGCACAAGAGTGTCCGGTGGAATT Chimp > Human ------------- chr1:9654481-9654486 Template switch process: F1: L CCCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG 1 F3: 4 AGCCAGCCCGCTTTCGCACAACTGTCCGATGGAATTCATGGAGGTGG R RF: CCCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTGGAGGCCAGACCCCAGAGCCAGTCCGCTTTCGCACAAGTGTCCGATGGAATTCATGGAGGTGG RR: GGGGACCCCCCGAATGTCCTGTCTGTCAGGTGGTTACCAACCTCCGGTCTGGGGTCTCGGTCAGGCGAAAGCGTGTTCACAGGCTACCTTAAGTACCTCCACC F2: 3 AAGCGT 2 Unidirectional alignment (log-probability: -42.6) CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTGtgcgaa---------------AGCCAGcCCGCTTTCGCACAAcTGTCCGATGGAATTCATG CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG------GAGGCCAGACCCCAGAGCCAGTCCGCTTTCGCACAAGTGTCCGATGGAATTCATG Template switch alignment (log-probability: -28.1) CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG|TGCGAA|AGCCAGcCCGCTTTCGCACAAcTGTCCGATGGAATTCATG CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG|TGCGAA|AGCCAGTCCGCTTTCGCACAAGTGTCCGATGGAATTCATG Gorilla > Human --------------- chr1:9654481-9654486 Template switch process: F1: L CCCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG 1 F3: 4 AGCCAGCCCGCTTTCGCACAACTGTCCGATGGAATTCATGGAGGTGG R RF: CCCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTGGAGGCCAGACCCCAGAGCCAGTCCGCTTTCGCACAAGTGTCCGATGGAATTCATGGAGGTGG RR: GGGGACCCCCCGAATGTCCTGTCTGTCAGGTGGTTACCAACCTCCGGTCTGGGGTCTCGGTCAGGCGAAAGCGTGTTCACAGGCTACCTTAAGTACCTCCACC F2: 3 AAGCGT 2 Unidirectional alignment (log-probability: -41.2) CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTT---------------GtgcgaaAGCCAGcCCGCTTTCGCACAAcTGTCCGATGGAATTCATG CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTGGAGGCCAGACCCCAG------AGCCAGTCCGCTTTCGCACAAGTGTCCGATGGAATTCATG Template switch alignment (log-probability: -27.7) CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG|TGCGAA|AGCCAGcCCGCTTTCGCACAAcTGTCCGATGGAATTCATG CCCTGGGGGGCTTACAGGACAGACAGTCCACCAATGGTTG|TGCGAA|AGCCAGTCCGCTTTCGCACAAGTGTCCGATGGAATTCATG ========== Event 1640 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GCTACCAGTCTCTCCTCTTCCGCGTAGAGGAAGAGGGGGGCAGACaaaa Chimp: GCTACCAGTCTCTCCTCTTCCACGTGGAGGAAGAGGGGGGCAG--aaaa Gorilla: GCTACCAGTCTCTCCTCTTCCTCTACGCGGAAGAGGGGGGCAGaaaaaa ↓ 13 24 ↑ 13 24 Human: GCTACCAGTCTCTCCTCTTCCGCGTAGAGGAAGAGGGGGGCAGACaaaa Cluster: [ ] Orangutan: GCTACCAGTCTCTCCTCTTCCGCATAGAGGAAGAGGGGGGCAGa-aaaa Gorilla > Human --------------- chr19:12906561-12906567 Template switch process: F1: L TGTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCC 1 F3: 4 GGAAGAGGGGGGCAGACAAAAAAAAAGCTGAAGTATAAAA R RF: TGTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCCTCTACGCGGAAGAGGGGGGCAGAAAAAAAAAAAGCTGAAGTATAAAA RR: ACAAAAGAGGAATTGGAGTTCGATGGTCAGAGAGGAGAAGGAGATGCGCCTTCTCCCCCCGTCTTTTTTTTTTTCGACTTCATATTTT F2: 3 AGATGCG 2 Unidirectional alignment (log-probability: -33.6) GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTC-----CGCgtagaGGAAGAGGGGGGCAGAcAAAAAAAAAGCTGAAGTATAAAA GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCCTCTACGC-----GGAAGAGGGGGGCAGAAAAAAAAAAAGCTGAAGTATAAAA Template switch alignment (log-probability: -22.1) GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCC|GCGTAGA|GGAAGAGGGGGGCAGAcAAAAAAAAAGCTGAAGTATAAAA GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCC|GCGTAGA|GGAAGAGGGGGGCAGAAAAAAAAAAAGCTGAAGTATAAAA Human > Gorilla --------------- chr19:12962619-12962625 Template switch process: F1: L TGTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCC 1 F3: 4 GGAAGAGGGGGGCAGAAAAAAAAAAAGCTGAAGTATAAAA R RF: TGTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCCGCGTAGAGGAAGAGGGGGGCAGACAAAAAAAAAGCTGAAGTATAAAA RR: ACAAAAGAGGAATTGGAGTTCGATGGTCAGAGAGGAGAAGGCGCATCTCCTTCTCCCCCCGTCTGTTTTTTTTTCGACTTCATATTTT F2: 3 CGCATCT 2 Unidirectional alignment (log-probability: -33.6) GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCctctaCGC-----GGAAGAGGGGGGCAGAaAAAAAAAAAGCTGAAGTATAAAA GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTC-----CGCGTAGAGGAAGAGGGGGGCAGACAAAAAAAAAGCTGAAGTATAAAA Template switch alignment (log-probability: -22.1) GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCC|TCTACGC|GGAAGAGGGGGGCAGAaAAAAAAAAAGCTGAAGTATAAAA GTTTTCTCCTTAACCTCAAGCTACCAGTCTCTCCTCTTCC|TCTACGC|GGAAGAGGGGGGCAGACAAAAAAAAAGCTGAAGTATAAAA ========== Event 1641 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGTGCCTTTCTTATAAGCCGG--------------TGGCACAAAGAGGTGCCTCTGGTGGC-----AGCCCAGG ↑ 1 4 3 2 Chimp: TTGTGCCTTTCTTATAAGCCGA-------GGACGGCGGGCTTAAAGAGGTGCCTCTGGTGGC-----AGCCCAGG Gorilla: TTGTGCCTTTCTTATAAGCCGAGGACGGT-------GGGCTTAAAGAGGTGCCTCTGGTGGC----------AGA Human: TTGTGCCTTTCTTATAAGCCGG--------------TGGCACAAAGAGGTGCCTCTGGTGGC-----AGCCCAGG Cluster: [ ] Orangutan: TTGTGCCTTTCTTATAAGCCAAGGACGGC-------GGGCTTAAAGAGGTGCCTCTGGTGGCAGCCC-----AGG Chimp > Human ------------- chr19:5016856-5016862 Template switch process: F1: L CCCGGGTTTAGTTCCTTTTCTTGTGCCTTTCTTATAAGCCG 1 F3: 4 AAAGAGGTGCCTCTGGTGGCAGCCCAGGGGGACCACTCAG R RF: CCCGGGTTTAGTTCCTTTTCTTGTGCCTTTCTTATAAGCCGAGGACGGCGGGCTTAAAGAGGTGCCTCTGGTGGCAGCCCAGGGGGACCACTCAG RR: GGGCCCAAATCAAGGAAAAGAACACGGAAAGAATATTCGGCTCCTGCCGCCCGAATTTCTCCACGGAGACCACCGTCGGGTCCCCCTGGTGAGTC F2: 3 CACGGTG 2 Unidirectional alignment (log-probability: -31.9) CCGGGTTTAGTTCCTTTTCTTGTGCCTTTCTTATAAGCCGgtggcac--------------AAAGAGGTGCCTCTGGTGGCAGCCCAGGGGGACCACTCAG CCGGGTTTAGTTCCTTTTCTTGTGCCTTTCTTATAAGCCG-------AGGACGGCGGGCTTAAAGAGGTGCCTCTGGTGGCAGCCCAGGGGGACCACTCAG Template switch alignment (log-probability: -22.1) CCGGGTTTAGTTCCTTTTCTTGTGCCTTTCTTATAAGCCG|GtGGCAC|AAAGAGGTGCCTCTGGTGGCAGCCCAGGGGGACCACTCAG CCGGGTTTAGTTCCTTTTCTTGTGCCTTTCTTATAAGCCG|GAGGCAC|AAAGAGGTGCCTCTGGTGGCAGCCCAGGGGGACCACTCAG ========== Event 1642 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: ACACACATACAATTCTGCTTAGA-CTACAAAGTCTTCTCTA-CTTGTAGGAATTTCTATAGTTTGTTTTGCGG Chimp: Gorilla: acacacaTAAAATTCTGCTTATTCCTAC-AAGTAGAGACGACTTTGTA-GTCTTTCTATAGTTTGTTTTGCGG ↓ 13 24 ↑ 13 24 Human: ACACACATACAATTCTGCTTAGA-CTACAAAGTCTTCTCTA-CTTGTAGGAATTTCTATAGTTTGTTTTGCGG Cluster: [ ] Orangutan: ACACACATACAATTCTGCTTATTCCTAC-AAGTAGA---GACTTTGTA-GTCTTTCTACAGTTTGTTTTGTGA Gorilla > Human --------------- chr1:153827684-153827712 Template switch process: F1: L CCCTGCCACCCCCACCACACACACACATACAATTCTGCTTA 1 F3: 4 TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG R RF: CCCTGCCACCCCCACCACACACACACATAAAATTCTGCTTATTCCTACAAGTAGAGACGACTTTGTAGTCTTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG RR: GGGACGGTGGGGGTGGTGTGTGTGTGTATTTTAAGACGAATAAGGATGTTCATCTCTGCTGAAACATCAGAAAGATATCAAACAAAACGCCCTCGTTTTCTCAAGACAAC F2: 3 AAGGATGTTCATCTCTTCTGAAACATCAG 2 Unidirectional alignment (log-probability: -69.3) CCTGCCACCCCCACCACACACACACATAcAATTCTGCTTagactacaaagtcttctctacttgtaggaA-----------------------------TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG CCTGCCACCCCCACCACACACACACATAAAATTCTGCTT-----------------------------ATTCCTACAAGTAGAGACGACTTTGTAGTCTTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG Template switch alignment (log-probability: -30.5) CCTGCCACCCCCACCACACACACACATAcAATTCTGCTTA|GACTACAAAGTCtTCTCTACTTGTAGGAA|TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG CCTGCCACCCCCACCACACACACACATAAAATTCTGCTTA|GACTACAAAGTCGTCTCTACTTGTAGGAA|TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG Human > Gorilla --------------- chr1:132559429-132559457 Template switch process: F1: L CCCTGCCACCCCCACCACACACACACATAAAATTCTGCTTA 1 F3: 4 TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG R RF: CCCTGCCACCCCCACCACACACACACATACAATTCTGCTTAGACTACAAAGTCTTCTCTACTTGTAGGAATTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG RR: GGGACGGTGGGGGTGGTGTGTGTGTGTATGTTAAGACGAATCTGATGTTTCAGAAGAGATGAACATCCTTAAAGATATCAAACAAAACGCCCTCGTTTTCTCAAGACAAC F2: 3 CTGATGTTTCAGCAGAGATGAACATCCTT 2 Unidirectional alignment (log-probability: -69.3) CCTGCCACCCCCACCACACACACACATAaAATTCTGCTTAttcctacaagtagagacgactttgtagtc-----------------------------TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG CCTGCCACCCCCACCACACACACACATACAATTCTGCTTA-----------------------------GACTACAAAGTCTTCTCTACTTGTAGGAATTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG Template switch alignment (log-probability: -30.5) CCTGCCACCCCCACCACACACACACATAaAATTCTGCTTA|TTCCTACAAGTAGAGAcGACTTTGTAGTC|TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG CCTGCCACCCCCACCACACACACACATACAATTCTGCTTA|TTCCTACAAGTAGAGAAGACTTTGTAGTC|TTTCTATAGTTTGTTTTGCGGGAGCAAAAGAGTTCTGTTG ========== Event 1643 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGAGGTTGGAGATGGG-ACT--GGGGTT-GAGGAACAGGCTG-GAGTACT--TGGTATGGT-TA Chimp: ATGAGGTTGGAGATGGG-ACT--GGGGTT-GAGGAACAGGCTG-GAGTACT--TGGTATGGT-TA ↓ 1 4 3 2 Gorilla: ATGAGGTTGGAGATGGG-ACTCCAGCCTG-GAGGAACAGGCTG-GAGTACT--TGGTATGGT-TA ↑ 1 4 3 2 Human: ATGAGGTTGGAGATGGG-ACT--GGGGTT-GAGGAACAGGCTG-GAGTACT--TGGTATGGT-TA Cluster: [ ] Orangutan: ATGAAGTTGGAGATGGGAACT--GGGGTTGAAGGAACAGGCTGGAAGTACTTTGGGTATGGTTTA Human > Gorilla --------------- chr19:7564387-7564394 Template switch process: F1: L GTGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACT 1 F3: 4 GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGTTGGAT R RF: GTGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACTGGGGTTGAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGATGGAT RR: CACAACTCTCGATTTGGACTCTACTCCAACCTCTACCCTGACCCCAACTCCTTGTCCGACCTCATGAACCATACCAATCCCTACCTA F2: 3 GTCCGACC 2 Unidirectional alignment (log-probability: -36.5) TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGActccagcCTG-----GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGtTGGAT TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGA-------CTGGGGTTGAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGATGGAT Template switch alignment (log-probability: -22.3) TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACT|CCAGCCTG|GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGtTGGAT TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACT|CCAGCCTG|GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGATGGAT Chimp > Gorilla --------------- chr19:7564387-7564394 Template switch process: F1: L GTGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACT 1 F3: 4 GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGTTGGAT R RF: GTGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACTGGGGTTGAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGATGGAT RR: CACAACTCTCGATTTGGACTCTACTCCAACCTCTACCCTGACCCCAACTCCTTGTCCGACCTCATGAACCATACCAATCCCTACCTA F2: 3 GTCCGACC 2 Unidirectional alignment (log-probability: -36.5) TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGActccagcCTG-----GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGtTGGAT TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGA-------CTGGGGTTGAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGATGGAT Template switch alignment (log-probability: -22.3) TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACT|CCAGCCTG|GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGtTGGAT TGTTGAGAGCTAAACCTGAGATGAGGTTGGAGATGGGACT|CCAGCCTG|GAGGAACAGGCTGGAGTACTTGGTATGGTTAGGGATGGAT ========== Event 1644 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGGATGGAAGAGAATTCACCT----------------GCTGGGCTCAGGCCCTGCTGGGCTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGTGTTAGCAGAACACCTGATTCTGGTGGGGGCGCCTTAGGCAAGGGAAGAGTGGGCTGAGGACACCCCCACCTCTGTCTT Chimp: GGGGATGGAAGAGAATTCACCT----------------GCCGGGCTCAGGCCCTGCTGGGCTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGTGTTAGCAGAACAGCTGATTCTGGTGGGGGCGACTTAGGCAAGGGAAGAGTGGACTGAGGACACCCCCACCTCTGTCTT Gorilla: GGGGATGGAAGAGAATTCACCT--------------------------------GCTGGGTTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGTGTTAGCAGAACACCTGATTCTGGTGGGGGCGCCTTAGGCAAGGGAAGAGTGGGCTGAGGACACCCCCACCTCTGTCTT ↓ 4 1 3 2 Human: GGGGATGGAAGAGAATTCACCT----------------GCTGGGCTCAGGCCCTGCTGGGCTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGTGTTAGCAGAACACCTGATTCTGGTGGGGGCGCCTTAGGCAAGGGAAGAGTGGGCTGAGGACACCCCCACCTCTGTCTT Cluster: [ ] Orangutan: GGGGATG-----GAATTCACCTGCTGGGCTCAGGCCCT----------------GCTGGGCTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGTGTTAGCAGAACACCTGCTTCGGGTGGGGGCGCCTTAGGCAAGGGAAGAGTGGGCTGAGGACACCCCCACCTCTGTCTT Gorilla > Human --------------- chr19:7191130-7191136 Template switch process: F1: L GCTGCCCCAGGTGGTTTTAGGGGATGGAAGAGAATTCACCTGCTGGG 1 F3: 4 CCTGCTGGGCTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGT R RF: GCTGCCCCAGGTGGTTTTAGGGGATGGAAGAGAATTCACCTGCTGGGTTCCCACCCCATCTCCCTGAGCCTGGCTGTGCAGGGTGAGTGTTAGCAGAACACCTGATTCTGGTGGGGGCGCCTTAGGCAAGGGAAGAGTGGGCTGAG RR: CGACGGGGTCCACCAAAATCCCCTACCTTCTCTTAAGTGGACGACCCAAGGGTGGGGTAGAGGGACTCGGACCGACACGTCCCACTCACAATCGTCTTGTGGACTAAGACCACCCCCGCGGAATCCGTTCCCTTCTCACCCGACTC F2: 3 CGGACTC 2 Unidirectional alignment (log-probability: -39.5) CAGGTGGTTTTAGGGGATGGAAGAGAATTCACctgctgggctcaggccCTGCTGGGcTCCCACCCCATCTCCCTGAGCCTGGCTGTG CAGGTGGTTTTAGGGGATGGAAGAGAATTCAC----------------CTGCTGGGTTCCCACCCCATCTCCCTGAGCCTGGCTGTG Template switch alignment (log-probability: -28) CAGGTGGTTTTAGGGGATGGAAGAGAATTCACCTGCTGGG|CTCAGgC|CCTGCTGGGcTCCCACCCCATCTCCCTGAGCCTGGCTGTG CAGGTGGTTTTAGGGGATGGAAGAGAATTCACCTGCTGGG|CTCAGCC|CCTGCTGGGTTCCCACCCCATCTCCCTGAGCCTGGCTGTG ========== Event 1645 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TAACCCTGGAGTCGGCTGCCCCAGCAATC-------TAACCTGCTCTGTGCCTTGGGC Chimp: Gorilla: TAACCCTGGAGTCGGCTGCCCCAGCTAGATTGCTGGGCACCTGCTCTGTGCCTTGGGC ↑ 3 1 4 Human: TAACCCTGGAGTCGGCTGCCCCAGCAATC-------TAACCTGCTCTGTGCCTTGGGC Cluster: [ ] Orangutan: TAACCCTGGAGTCGGCTGCCACAGCAATC-------TAACCTGCTGTGTGCCCTGGGC Human > Gorilla --------------- chr19:50812122-50812133 Template switch process: F1: L GACATCTTCATCCCAATAACCCTGGAGTCGGCTGCCCCAGC 1 F3: 4 CACCTGCTCTGTGCCTTGGGCCTGTGAGCAGGGGATGCCTC R RF: GACATCTTCATCCCAATAACCCTGGAGTCGGCTGCCCCAGCAATCTAACCTGCTCTGTGCCTTGGGCCTGTGAGCAGGGGATGCCTC RR: CTGTAGAAGTAGGGTTATTGGGACCTCAGCCGACGGGGTCGTTAGATTGGACGAGACACGGAACCCGGACACTCGTCCCCTACGGAG F2: 3 GGGTCGTTAGAT 2 Unidirectional alignment (log-probability: -36.7) ACATCTTCATCCCAATAACCCTGGAGTCGGCTGCCCCAG----CTAgattgctgggcACCTGCTCTGTGCCTTGGGCCTGTGAGCAGGGGATGCCT ACATCTTCATCCCAATAACCCTGGAGTCGGCTGCCCCAGCAATCTA-----------ACCTGCTCTGTGCCTTGGGCCTGTGAGCAGGGGATGCCT Template switch alignment (log-probability: -22.8) ACATCTTCATCCCAATAACCCTGGAGTCGGCTGCCCCAGC|TAGATTGCTGGG|cACCTGCTCTGTGCCTTGGGCCTGTGAGCAGGGGATGCCT ACATCTTCATCCCAATAACCCTGGAGTCGGCTGCCCCAGC|TAGATTGCTGGG|AACCTGCTCTGTGCCTTGGGCCTGTGAGCAGGGGATGCCT ========== Event 1646 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: gGCTtggcaaacctggcccatctaaaaataaataaaattgaacttctatctcatctcagactatatacaaaaatacatgc Chimp: gGCTTGGCAAACCTGGCCCATTCTGAG----------ATGAACTTCTATCTCATCTCAGACTATACACAAAAATACACGC ↑ 1 4 3 2 Gorilla: GGCTTGGCAAACCTGGCCCATCTAAAAATAAATAAAATTGAACTTCTATCTCATCTCAGACTATATACAAAAATACATGC Human: gGCTtggcaaacctggcccatctaaaaataaataaaattgaacttctatctcatctcagactatatacaaaaatacatgc Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr19:53890649-53890655 Template switch process: F1: L AATTAATTTAAACTTAAATGGGCTTGGCAAACCTGGCCCAT 1 F3: 4 TGAACTTCTATCTCATCTCAGACTATACACAAAAATACAC R RF: AATTAATTTAAACTTAAATGGGCTTGGCAAACCTGGCCCATCTAAAAATAAATAAAATTGAACTTCTATCTCATCTCAGACTATATACAAAAATACAT RR: TTAATTAAATTTGAATTTACCCGAACCGTTTGGACCGGGTAGATTTTTATTTATTTTAACTTGAAGATAGAGTAGAGTCTGATATATGTTTTTATGTA F2: 3 AGAGTCT 2 Unidirectional alignment (log-probability: -41.1) ATTAATTTAAACTTAAATGGGCTTGGCAAACCTGGCCCAT----------------TctgagaTGAACTTCTATCTCATCTCAGACTATAcACAAAAATACAc ATTAATTTAAACTTAAATGGGCTTGGCAAACCTGGCCCATCTAAAAATAAATAAAAT------TGAACTTCTATCTCATCTCAGACTATATACAAAAATACAT Template switch alignment (log-probability: -27.7) ATTAATTTAAACTTAAATGGGCTTGGCAAACCTGGCCCAT|TCTGAGA|TGAACTTCTATCTCATCTCAGACTATAcACAAAAATACAc ATTAATTTAAACTTAAATGGGCTTGGCAAACCTGGCCCAT|TCTGAGA|TGAACTTCTATCTCATCTCAGACTATATACAAAAATACAT ========== Event 1647 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTCAAGAAAAGAGTGGGCAGTACTCAAGAAAAGAATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTATTCTC ↓ 1 4 3 2 Chimp: TGTCAAGAAAAGAGTGGGCAGACT--------GCAATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTATTCTC Gorilla: TGTCAAGAAAAGAGTGGGCAGAAT--------GCAGTAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTATTCTC Human: TGTCAAGAAAAGAGTGGGCAGTACTCAAGAAAAGAATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTATTCTC Cluster: [ ] Orangutan: TGTCAAGAAAAGAGTAGGCAGCAT--------GCAATAAGCATGACAGCTTCAAGCAGTCATCATTTTATGTTATTGTC Human > Chimp ------------- chr19:6558978-6558982 Template switch process: F1: L GCACAGAAGTACTGCACCCTTGTCAAGAAAAGAGTGGGCAG 1 F3: 4 AATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTA R RF: GCACAGAAGTACTGCATCCTTGTCAAGAAAAGAGTGGGCAGTACTCAAGAAAAGAATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTA RR: CGTGTCTTCATGACGTAGGAACAGTTCTTTTCTCACCCGTCATGAGTTCTTTTCTTATTCGCACTGACGAAGTTCGTCAGTAGTAAAATACAAT F2: 3 CGTCA 2 Unidirectional alignment (log-probability: -35) CACAGAAGTACTGCAcCCTTGTCAAGAAAAGAGTGGGC-------------AGactgcAATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTA CACAGAAGTACTGCATCCTTGTCAAGAAAAGAGTGGGCAGTACTCAAGAAAAG-----AATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTA Template switch alignment (log-probability: -21.9) CACAGAAGTACTGCAcCCTTGTCAAGAAAAGAGTGGGCAG|ACTGC|AATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTA CACAGAAGTACTGCATCCTTGTCAAGAAAAGAGTGGGCAG|ACTGC|AATAAGCGTGACTGCTTCAAGCAGTCATCATTTTATGTTA ========== Event 1648 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TGATTGTCCAAGATGAGTCACATGTCTGCTCATCATCTGTCTGGGGATGATGAGCCATCT ↓ 3 2 1 4 Chimp: TGATTGTCCAAGATGAGTCACATGTCTGC-CA--TGTTGCCTGGGGATGATGAGCCATCT Gorilla: TGATTGTCCAAGATGAGTCACATGTCTGC-CA--TGTTGCCTGGGGATGATGAGCTATCT Human: TGATTGTCCAAGATGAGTCACATGTCTGCTCATCATCTGTCTGGGGATGATGAGCCATCT Cluster: [ ] Orangutan: tgattgtccaaggtgagtcacatgtctgc-ca--tcttgcctggggatgatgagccatct Human > Chimp ------------- chr1:95937131-95937135 Template switch process: F1: L GAAGGAAGTATCTGATTGTCCAAGATGAGTCACATGTCTGC 1 F3: 4 TGCCTGGGGATGATGAGCCATCTTGATTAATAGACATAGCATA R RF: GAAGGAAGTATCTGATTGTCCAAGATGAGTCACATGTCTGCTCATCATCTGTCTGGGGATGATGAGCCATCTTGATTAATAGACATAGCATA RR: CTTCCTTCATAGACTAACAGGTTCTACTCAGTGTACAGACGAGTAGTAGACAGACCCCTACTACTCGGTAGAACTAATTATCTGTATCGTAT F2: 3 TGTAC 2 Unidirectional alignment (log-probability: -33.2) AAGGAAGTATCTGATTGTCCAAGATGAGTCACATGTCtgccatgtTGC-----------CTGGGGATGATGAGCCATCTTGATTAATAGACATAGC AAGGAAGTATCTGATTGTCCAAGATGAGTCACATGTC--------TGCTCATCATCTGTCTGGGGATGATGAGCCATCTTGATTAATAGACATAGC Template switch alignment (log-probability: -22) AAGGAAGTATCTGATTGTCCAAGATGAGTCACATGTCTGC|CATGT|TGcCTGGGGATGATGAGCCATCTTGATTAATAGACATAGC AAGGAAGTATCTGATTGTCCAAGATGAGTCACATGTCTGC|CATGT|TGTCTGGGGATGATGAGCCATCTTGATTAATAGACATAGC ========== Event 1649 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGCAGCAGGGAAGGACATCTGATCCAGGCAGACTAGACCACCTGGGATGAACAGACAATCCTCAGAAGAACGATCG------------------------------------ATTAGTGATGTCTGCTTCAGGCACCA Chimp: CAGCAGCAGGGAAGGACATCTGATCCAGGCAGACTAGACCACCTGGGATGAACAGACAATCCTCAGAAGAACGATCG----------------ATTAGTATCAGTTAGTATCGATTAGTGATGTCTGCTTCAGGCACCA Gorilla: CAGCAGCAGGGAAGGACATCTGATCCAGGCAGACTAGACCACCTGGGATGAACAGACAATCCTCAGAAGAACGATCGATTAGTATCAGTATCG--------------------ATTAGTGATGTCTGCTTCAGGCACCA ↑ 3 2 4 1 Human: CAGCAGCAGGGAAGGACATCTGATCCAGGCAGACTAGACCACCTGGGATGAACAGACAATCCTCAGAAGAACGATCG------------------------------------ATTAGTGATGTCTGCTTCAGGCACCA Cluster: [ ] Orangutan: CAGCAGCAGGGAAGGACATCTGATCCAGGCAGACTAAACCACCTGGGATGAACAGACAATCATCA---GAACgatcg------------------------------------attagtgatgtctgctgtaggcacca Human > Gorilla --------------- chr19:54407043-54407047 Template switch process: F1: L GACCACCTGGGATGAACAGACAATCCTCAGAAGAACGATCGATTAGT 1 F3: 4 TATCGATTAGTGATGTCTGCTTCAGGCACCAGAAGCGGGCAGCGT R RF: CTGATCCAGGCAGACTAGACCACCTGGGATGAACAGACAATCCTCAGAAGAACGATCGATTAGTGATGTCTGCTTCAGGCACCAGAAGCGGGCAGCGT RR: GACTAGGTCCGTCTGATCTGGTGGACCCTACTTGTCTGTTAGGAGTCTTCTTGCTAGCTAATCACTACAGACGAAGTCCGTGGTCTTCGCCCGTCGCA F2: 3 GACTA 2 Unidirectional alignment (log-probability: -33.9) TGGGATGAACAGACAATCCTCAGAAGAACGATcgattagtatcagtatCGATTAGTGATGTCTGCTTCAGGCACCAGAAGCGGGC TGGGATGAACAGACAATCCTCAGAAGAACGAT----------------CGATTAGTGATGTCTGCTTCAGGCACCAGAAGCGGGC Template switch alignment (log-probability: -22.2) TGGGATGAACAGACAATCCTCAGAAGAACGATCGATTAGT|ATCAG|tATCGATTAGTGATGTCTGCTTCAGGCACCAGAAGCGGGC TGGGATGAACAGACAATCCTCAGAAGAACGATCGATTAGT|ATCAG|GATCGATTAGTGATGTCTGCTTCAGGCACCAGAAGCGGGC ========== Event 1650 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGGGGGACTGGGAAATCTCACAGGAGCCAA-----------TAGGCTCCTGTGTGCACtttattttattttatttt Chimp: ATGGGGGACTGGGAAATCTCACAGGAGCCAA-----------TAGGCTCCTGTGTGCACtttattttattttatttt ↑ 3 1 4 Gorilla: ATGGGGGACTGGGAAATCTCACAGGAGCCTA----------------------TTGTACtttattttattttatttt ↓ 3 1 4 Human: ATGGGGGACTGGGAAATCTCACAGGAGCCAA-----------TAGGCTCCTGTGTGCACtttattttattttatttt Cluster: [ ] Orangutan: ATGGGGGACTGGGAAATCTCACAGGAGCCAATAGGTTCCTGT-----------GTGCACtttattttattttatttt Gorilla > Human --------------- chr19:55282733-55282746 Template switch process: F1: L TCAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCC 1 F3: 4 TGCACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCTCAC R RF: TCAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCCTATTGTACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCTCAC RR: AGTTCCACAACTTACCCCCTGACCCTTTAGAGTGTCCTCGGATAACATGAAATAAAATAAAATAAAAACAATCTCTGTCCCGGAGTG F2: 3 GTGTCCTCGGATAA 2 Unidirectional alignment (log-probability: -37.8) CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCCaATaggctcctgtgTGcACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCCTAT-----------TGTACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT Template switch alignment (log-probability: -23.1) CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCC|AATAGGCTCCTGTG|TGcACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCC|AATAGGCTCCTGTG|TGTACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT Gorilla > Chimp --------------- chr19:57685978-57685991 Template switch process: F1: L TCAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCC 1 F3: 4 TGCACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCTCAC R RF: TCAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCCTATTGTACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCTCAC RR: AGTTCCACAACTTACCCCCTGACCCTTTAGAGTGTCCTCGGATAACATGAAATAAAATAAAATAAAAACAATCTCTGTCCCGGAGTG F2: 3 GTGTCCTCGGATAA 2 Unidirectional alignment (log-probability: -37.8) CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCCaATaggctcctgtgTGcACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCCTAT-----------TGTACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT Template switch alignment (log-probability: -23.1) CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCC|AATAGGCTCCTGTG|TGcACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT CAAGGTGTTGAATGGGGGACTGGGAAATCTCACAGGAGCC|AATAGGCTCCTGTG|TGTACTTTATTTTATTTTATTTTTGTTAGAGACAGGGCCT ========== Event 1651 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TGAATCAGCACGTCTTGGCCTACGTCCCTGGGAGGCTTGTGCTTTTGGGTCTCCGAGTTTGC ↓ 3 2 1 4 Chimp: TGAATCAGCACGTCTTGGCCTACGTCCCTGGGACG---TAGCTTTTGGGTCTCCGAGTTTGC Gorilla: Human: TGAATCAGCACGTCTTGGCCTACGTCCCTGGGAGGCTTGTGCTTTTGGGTCTCCGAGTTTGC Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:57872367-57872371 Template switch process: F1: L AGGGGCCCTGAATCAGCACGTCTTGGCCTACGTCCCTGGGA 1 F3: 4 CTTTTGGGTCTCCGAGTTTGCTGCACAAGTGAGGGTTTG R RF: AGGGGCCCTGAATCAGCACGTCTTGGCCTACGTCCCTGGGAGGCTTGTGCTTTTGGGTCTCCGAGTTTGCTGCACAAGTGAGGGTTTG RR: TCCCCGGGACTTAGTCGTGCAGAACCGGATGCAGGGACCCTCCGAACACGAAAACCCAGAGGCTCAAACGACGTGTTCACTCCCAAAC F2: 3 GATGC 2 Unidirectional alignment (log-probability: -27.2) GGGGCCCTGAATCAGCACGTCTTGGCCTACGTCCCTGGGacgtA-------GCTTTTGGGTCTCCGAGTTTGCTGCACAAGTGAGGGTTTG GGGGCCCTGAATCAGCACGTCTTGGCCTACGTCCCTGGG----AGGCTTGTGCTTTTGGGTCTCCGAGTTTGCTGCACAAGTGAGGGTTTG Template switch alignment (log-probability: -15.9) GGGGCCCTGAATCAGCACGTCTTGGCCTACGTCCCTGGGA|CGTAG|CTTTTGGGTCTCCGAGTTTGCTGCACAAGTGAGGGTTTG GGGGCCCTGAATCAGCACGTCTTGGCCTACGTCCCTGGGA|CGTAG|CTTTTGGGTCTCCGAGTTTGCTGCACAAGTGAGGGTTTG ========== Event 1652 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: -------------------ATATTATCCAAAAAAAGGTATGAAGCCG----T----------CTCAGATA------------------ Chimp: -------------------atctgag-------acggcttcatacct--tgt-----tttggataatata------------------ Gorilla: -------------------ATCTGAG-------ACGGCTTCATACCTTG--TTTTGG-----ATAATATA------------------ ↓ 13 24 ↑ 13 24 Human: -------------------ATATTATCCAAAAAAAGGTATGAAGCCG----T----------CTCAGATA------------------ Cluster: [ ] Orangutan: ttgctttggataatataacatctgag-------ccagcttcataccttg--ctttgg-----ataatataacatctgaaccagcttca Gorilla > Human --------------- chr19:2739108-2739139 Template switch process: F1: L TCTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT 1 F3: 4 ATAACAATGGAAGCAAGATTAGGAGAGTTCTGAGCCACCA R RF: TCTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACATCTGAGACGGCTTCATACCTTGTTTTGGATAATATAACAATGGAAGCAAGGTTAGGAGAGTTCTGAGCCACCA RR: AGATAAAGGCCGAAGTATGGAACGAAACCTATTATATTGTAGACTCTGCCGAAGTATGGAACAAAACCTATTATATTGTTACCTTCGTTCCAATCCTCTCAAGACTCGGTGGT F2: 3 GACTCTGCCGAAGTATGGAAAAAAACCTATTA 2 Unidirectional alignment (log-probability: -70.8) CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT------------------------------ATtatccaaaaaaaggtatgaagccgtctcagATAACAATGGAAGCAAGaTTAGGAGAGTTCTGAGCCACCA CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACATCTGAGACGGCTTCATACCTTGTTTTGGATAAT------------------------------ATAACAATGGAAGCAAGGTTAGGAGAGTTCTGAGCCACCA Template switch alignment (log-probability: -30.8) CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT|ATTATCCAAAAaAAGGTATGAAGCCGTCTCAG|ATAACAATGGAAGCAAGaTTAGGAGAGTTCTGAGCCACCA CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT|ATTATCCAAAACAAGGTATGAAGCCGTCTCAG|ATAACAATGGAAGCAAGGTTAGGAGAGTTCTGAGCCACCA Human > Gorilla --------------- chr19:2730869-2730900 Template switch process: F1: L TCTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT 1 F3: 4 ATAACAATGGAAGCAAGGTTAGGAGAGTTCTGAGCCACCA R RF: TCTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACATATTATCCAAAAAAAGGTATGAAGCCGTCTCAGATAACAATGGAAGCAAGATTAGGAGAGTTCTGAGCCACCA RR: AGATAAAGGCCGAAGTATGGAACGAAACCTATTATATTGTATAATAGGTTTTTTTCCATACTTCGGCAGAGTCTATTGTTACCTTCGTTCTAATCCTCTCAAGACTCGGTGGT F2: 3 TAATAGGTTTTGTTCCATACTTCGGCAGAGTC 2 Unidirectional alignment (log-probability: -70.8) CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACATctgagacggcttcataccttgttttggataAT------------------------------ATAACAATGGAAGCAAGgTTAGGAGAGTTCTGAGCCACCA CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT------------------------------ATTATCCAAAAAAAGGTATGAAGCCGTCTCAGATAACAATGGAAGCAAGATTAGGAGAGTTCTGAGCCACCA Template switch alignment (log-probability: -30.8) CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT|CTGAGACGGCTTCATACCTTgTTTTGGATAAT|ATAACAATGGAAGCAAGgTTAGGAGAGTTCTGAGCCACCA CTATTTCCGGCTTCATACCTTGCTTTGGATAATATAACAT|CTGAGACGGCTTCATACCTTTTTTTGGATAAT|ATAACAATGGAAGCAAGATTAGGAGAGTTCTGAGCCACCA ========== Event 1653 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GTCTTTATTTCGTTATCTGAACAGCTCTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACAC ↑ 1 4 3 2 Chimp: GTCTTTATTTCGTTATCTGAA--CCCTTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACAC Gorilla: GTCTTTATTTCGTTATCTGAACAGCTCTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACAC Human: GTCTTTATTTCGTTATCTGAACAGCTCTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACAC Cluster: [ ] Orangutan: GTCTTTATTTTGTTATCTGAACAGCTCTGAGGCTGCCTGAGCTGTCGCTGCC-CGTCCCACAC Chimp > Human ------------- chr19:56096898-56096902 Template switch process: F1: L TCCCTCCTCAGAAGCGGAATGTCTTTATTTCGTTATCTGAAC 1 F3: 4 TGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACACCCCT R RF: TCCCTCCTCAGAAGCGGAATGTCTTTATTTCGTTATCTGAACCCTTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACACCCCT RR: AGGGAGGAGTCTTCGCCTTACAGAAATAAAGCAATAGACTTGGGAACTCCGACGGACTCGACAGCGACGGGCCAGGGTGTGGGGA F2: 3 CTCGA 2 Unidirectional alignment (log-probability: -25.8) CCTCCTCAGAAGCGGAATGTCTTTATTTCGTTATCTGAACagCtcTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACACCCCT CCTCCTCAGAAGCGGAATGTCTTTATTTCGTTATCTGAAC--CCTTGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACACCCCT Template switch alignment (log-probability: -15.9) CCTCCTCAGAAGCGGAATGTCTTTATTTCGTTATCTGAAC|AGCTC|TGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACACCCCT CCTCCTCAGAAGCGGAATGTCTTTATTTCGTTATCTGAAC|AGCTC|TGAGGCTGCCTGAGCTGTCGCTGCCCGGTCCCACACCCCT ========== Event 1654 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGGTATGGGTCGGATTTGGTCCGATTCTTCCTGCTGCATTGGTACAGTAGCAGAAGACTAGAAACAGGCAG Chimp: AGGGTGTGGGTCGGATTTGGTG------CTACTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCAG ↑ 1 4 3 2 Gorilla: AGGGTGTGGGTCGGATTTGGTCAGATTCTTCCTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCAG Human: AGGGTATGGGTCGGATTTGGTCCGATTCTTCCTGCTGCATTGGTACAGTAGCAGAAGACTAGAAACAGGCAG Cluster: [ ] Orangutan: AGGGTGTGGGTCAGATTTCATCGGATTCTTCCTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCAG Gorilla > Chimp --------------- chr19:58542458-58542461 Template switch process: F1: L CCTGTCAGGACAAGCAGCACAGGGTGTGGGTCGGATTTGGT 1 F3: 4 CTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCA R RF: CCTGTCAGGACAAGCAGCACAGGGTGTGGGTCGGATTTGGTCAGATTCTTCCTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCA RR: GGACAGTCCTGTTCGTCGTGTCCCACACCCAGCCTAAACCAGTCTAAGAAGGACGACGTAACGATGTCATCGTCTTCTGATCTTTGTCCGT F2: 3 ATCG 2 Unidirectional alignment (log-probability: -26.9) CTGTCAGGACAAGCAGCACAGGGTGTGGGTCGGATTTGGT----------gctaCTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCA CTGTCAGGACAAGCAGCACAGGGTGTGGGTCGGATTTGGTCAGATTCTTC----CTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCA Template switch alignment (log-probability: -16.2) CTGTCAGGACAAGCAGCACAGGGTGTGGGTCGGATTTGGT|GCTA|CTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCA CTGTCAGGACAAGCAGCACAGGGTGTGGGTCGGATTTGGT|GCTA|CTGCTGCATTGCTACAGTAGCAGAAGACTAGAAACAGGCA ========== Event 1655 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGTTCAGCACCACAGGCAGCCCCCC-----------------------AGGCTCGCAGGACAGTTCCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTCTTCCGGTATCACGAAGAGCCCTGCTGGACTGGTTCTGCAACATGGATAGGAACAAGTGTCATTTCGCCATCACCTGTGCTAGATGTAGACGCTCTTC Chimp: GGTTCAGCACCACAGGCAGCCCCCC-----------------------AGCCTCGCAGGACAGTTCCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCCGGTATCACGAAGAGCCCTGCTGGACTGGTTCTGCAACATGGATGGGAACAAGTG-TATTTCGCCATCACCTGTGCTAGATGTAGACGCTCTTC ↑ 4 1 3 2 Gorilla: GGTTCAGCACCACAGGCAGCCCCCC----------------------------------------------AGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCCGGTATCACGAAGAGCCCTGCTGGACTGGTTCTGCAACATGGATAGGAACAAGTGTCATTTCGCCATCACCTGTGCTAGATGTAGACGCTCTTC Human: GGTTCAGCACCACAGGCAGCCCCCC-----------------------AGGCTCGCAGGACAGTTCCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTCTTCCGGTATCACGAAGAGCCCTGCTGGACTGGTTCTGCAACATGGATAGGAACAAGTGTCATTTCGCCATCACCTGTGCTAGATGTAGACGCTCTTC Cluster: [ ] Orangutan: ggttcagcaccacgggcagcccCCCAGCCTCGCAGGACAGTCCCCGCA-----------------------AGCCTCGCAGGGTAGCCTGTGCCTGGACTATTCCAGCATCACGGAGATCCCTGCTGGACTGGTTCTGCAACATGGATAGGAACAAGTGTCATTTCGCCACCACCTGTGCTAGATGTAGGCGCTCTTC Gorilla > Chimp --------------- chr19:59152057-59152062 Template switch process: F1: L CGGCTCAGGCCAGAATGGTTCAGCACCACAGGCAGCCCCCCAGCCTCGCAGG 1 F3: 4 CCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCCGGTATC R RF: CGGCTCAGGCCAGAATGGTTCAGCACCACAGGCAGCCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCCGGTATCACGAAGAGCCCTGCTGGACTGGTTCTGCAACATGGATAGGAACAAGTGTCATTTCGCCATCACCTGT RR: GCCGAGTCCGGTCTTACCAAGTCGTGGTGTCCGTCGGGGGGTCGGAGCGTCCCATCGGACACGACCCTGATAAGGCCATAGTGCTTCTCGGGACGACCTGACCAAGACGTTGTACCTATCCTTGTTCACAGTAAAGCGGTAGTGGACA F2: 3 TTGACA 2 Unidirectional alignment (log-probability: -44) GAATGGTTCAGCACCACAGGCAGCCCCccagcctcgcaggacagttccccCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCC GAATGGTTCAGCACCACAGGCAGCCCC-----------------------CCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCC Template switch alignment (log-probability: -22.4) GAATGGTTCAGCACCACAGGCAGCCCCCCAGCCTCGCAGG|ACAGtT|CCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCC GAATGGTTCAGCACCACAGGCAGCCCCCCAGCCTCGCAGG|ACAGGT|CCCCCCAGCCTCGCAGGGTAGCCTGTGCTGGGACTATTCC ========== Event 1656 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTCTTTAAGGTGATTCCTGCTTTGCCTATCCTCAGAGTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCT ↑ 1 4 3 2 Chimp: ATTCTTTAAGGTGATTCCTGCACA----GACCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCT ↓ 1 4 3 2 Gorilla: ATTCTTTAAGGTGATTCCTGCTTTGCCTATCCTCAGAGTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCT Human: ATTCTTTAAGGTGATTCCTGCTTTGCCTATCCTCAGAGTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCT Cluster: [ ] Orangutan: ATTCTTTAAGGTGATTCCTGCTTTGCCTATCCTCAGAGTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCT Chimp > Human ------------- chr1:96001878-96001886 Template switch process: F1: L TGCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC 1 F3: 4 CCTCAGAGTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCTTTA R RF: TGCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGCACAGACCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCTTTA RR: ACGAATCACTTGTAGGGGAATAAGAAATTCCACTAAGGACGTGTCTGGAGTCTGACACCAGTTTTCCGTTTGAAAGGGTGAACGGAAAAGAAAT F2: 3 TATCCGTTT 2 Unidirectional alignment (log-probability: -40.4) GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGCtttgcctat-----CCTCAGAgTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC---------ACAGACCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT Template switch alignment (log-probability: -28.5) GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC|TTTGCCTaT|CCTCAGAgTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC|TTTGCCTTT|CCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT Chimp > Gorilla --------------- chr1:97266897-97266905 Template switch process: F1: L TGCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC 1 F3: 4 CCTCAGAGTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCTTTA R RF: TGCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGCACAGACCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCTTTTCTTTA RR: ACGAATCACTTGTAGGGGAATAAGAAATTCCACTAAGGACGTGTCTGGAGTCTGACACCAGTTTTCCGTTTGAAAGGGTGAACGGAAAAGAAAT F2: 3 TATCCGTTT 2 Unidirectional alignment (log-probability: -39.5) GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC-----tttgcctatCCTCAGAgTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGCACAGA---------CCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT Template switch alignment (log-probability: -28.1) GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC|TTTGCCTaT|CCTCAGAgTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT GCTTAGTGAACATCCCCTTATTCTTTAAGGTGATTCCTGC|TTTGCCTTT|CCTCAGACTGTGGTCAAAAGGCAAACTTTCCCACTTGCCT ========== Event 1657 ========== Phylogenetic placement: unresolved Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GGGACAACAGGACTAGGAGACGTGCATGGGGGTTCAGCTGATTCCACT ↑ 13 24 Chimp: GGGACAACAGGACTAGGAGACATGCACGGGGGTTCAGCTGATTCCACT Gorilla: GGGACAACAGGACTAGGAGACGTGCACGGGGGTTCAGCTGATTCCACT Human: GGGACAACAGGACTAGGAGACGTGCATGGGGGTTCAGCTGATTCCACT Cluster: [ ] Orangutan: Chimp > Human ------------- chr19:577789-577794 Template switch process: F1: L TGGGGTGTCAGGCAGAGCGGGGGACAACAGGACTAGGAGAC 1 F3: 4 GGGGGTTCAGCTGATTCCACTGGTTGTTCCTTTTTTTTTT R RF: TGGGGTGTCAGGCAGAGCGGGGGACAACAGGACTAGGAGACATGCACGGGGGTTCAGCTGATTCCACTGGTTATTCCTTTTTTTTTT RR: ACCCCACAGTCCGTCTCGCCCCCTGTTGTCCTGATCCTCTGTACGTGCCCCCAAGTCGACTAAGGTGACCAATAAGGAAAAAAAAAA F2: 3 TACGTG 2 Unidirectional alignment (log-probability: -33.1) GGGGTGTCAGGCAGAGCGGGGGACAACAGGACTAGGAGACgTGCAtGGGGGTTCAGCTGATTCCACTGGTTgTTCCTTTTTttttt GGGGTGTCAGGCAGAGCGGGGGACAACAGGACTAGGAGACATGCACGGGGGTTCAGCTGATTCCACTGGTTATTCCTTTTT----- Template switch alignment (log-probability: -22) GGGGTGTCAGGCAGAGCGGGGGACAACAGGACTAGGAGAC|GTGCAT|GGGGGTTCAGCTGATTCCACTGGTTgTTCCTTTTTTTTTT GGGGTGTCAGGCAGAGCGGGGGACAACAGGACTAGGAGAC|GTGCAT|GGGGGTTCAGCTGATTCCACTGGTTATTCCTTTTTTTTTT ========== Event 1658 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACACACTAGGCACAGGCCCCA--------------------------------------CTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCC ↓ 4 3 1 2 Chimp: ACACACTAGGCACAGGCCCCA-------------------CACTGGTGGCCGAGGCCTCCTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCC Gorilla: ACACACTAGGCACAGGCCCCACATTGGTGGCCGAGGCCTC-------------------CTCTGGTGGCCTCATCAAGCCCCTGTGTGTGCC Human: ACACACTAGGCACAGGCCCCA--------------------------------------CTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCC Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:6133291-6133298 Template switch process: F1: L TCCTGAGATGCTCTCTTCTGACACACTAGGCACAGGCCCCACACTGGTGGCC 1 F3: 4 CTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCCTCAAAGC R RF: TCCTGAGATGCTCTCTTCTGACACACTAGGCACAGGCCCCACTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCCTCAAAGC RR: AGGACTCTACGAGAGAAGACTGTGTGATCCGTGTCCGGGGTGAGACCACCGGAGTGGTTCGGGAAGACACACGGAGTTTCG F2: 3 CTCCGGAG 2 Unidirectional alignment (log-probability: -38.2) CTCTTCTGACACACTAGGCACAGGCCCCACactggtggccgaggcctccTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCCTCAAAGC CTCTTCTGACACACTAGGCACAGGCCCCAC-------------------TCTGGTGGCCTCACCAAGCCCTTCTGTGTGCCTCAAAGC Template switch alignment (log-probability: -28.5) CTCTTCTGACACACTAGGCACAGGCCCCACaCTGGTGGCC|GAGGCCtC|CTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCCTCAAAGC CTCTTCTGACACACTAGGCACAGGCCCCACTCTGGTGGCC|GAGGCCAC|CTCTGGTGGCCTCACCAAGCCCTTCTGTGTGCCTCAAAGC ========== Event 1659 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAAGACCTCCCCCTGGAATCATA----------------------------------------------CGCAGATCTCCTGCCCTCCTCCAACTCTGCC ↓ 4 3 21 Chimp: CAAAGACCTCCCCCTGGAATCATA-----------------------CGCAGATCTCCGAGATCTCCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCC ↑ 4 3 21 Gorilla: CAAAGACCTCCCCCTGGAATCATA----------------------------------------------CGCAGATCTCCTGCCCTCCTCCAACTCTGCC Human: CAAAGACCTCCCCCTGGAATCATA----------------------------------------------CGCAGATCTCCTGCCCTCCTCCAACTCTGCC Cluster: [ ] Orangutan: CAAAGACCTCCGCCTGGAATCATACGCAGACCTCAGAGATCTCCATA-----------------------CGCAGATCTCCTGCCCTCCTCCAACTCTGCC Human > Chimp ------------- chr19:219696-219702 Template switch process: F1: L ATGCCCCAGCCCTGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCC 1 F3: 4 CCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGGCACAC R RF: ATGCCCCAGCCGTGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGGCACAC RR: TACGGGGTCGGCACGTAGTTTCTGGAGGGGGACCTTAGTATGCGTCTAGAGGACGGGAGGAGGTTGAGACGGGACCGTGTG F2: 3 TCTAGAG 2 Unidirectional alignment (log-probability: -50) TGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCtccgagatctccatacgcagatcTCCTGCCCTCCTCCAACTCTGCCCTGG TGCATCAAAGACCTCCCCCTGGAATCATACGCAGATC-----------------------TCCTGCCCTCCTCCAACTCTGCCCTGG Template switch alignment (log-probability: -28.4) TGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCC|GAGATCT|cCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGG TGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCC|GAGATCT|TCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGG Gorilla > Chimp --------------- chr19:219696-219702 Template switch process: F1: L ATGCCCCAGCCCTGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCC 1 F3: 4 CCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGGCACAC R RF: ATGCCCCAGCCCTGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGGCACAC RR: TACGGGGTCGGGACGTAGTTTCTGGAGGGGGACCTTAGTATGCGTCTAGAGGACGGGAGGAGGTTGAGACGGGACCGTGTG F2: 3 TCTAGAG 2 Unidirectional alignment (log-probability: -44) TGCATCAAAGACCTCCCCCTGGAATCAtacgcagatctccgagatctccaTACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGG TGCATCAAAGACCTCCCCCTGGAATCA-----------------------TACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGG Template switch alignment (log-probability: -22.5) TGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCC|GAGATCT|cCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGG TGCATCAAAGACCTCCCCCTGGAATCATACGCAGATCTCC|GAGATCT|TCATACGCAGATCTCCTGCCCTCCTCCAACTCTGCCCTGG ========== Event 1660 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAGGTTTGAAGAGGCTAGATGAC-AAACCTAGTTAAGGAACAAACATAC ↓ 3 1 2 4 Chimp: ATAGGTTTGAAGAGGCTAGATGTTGTCATCTAGTTAAGGAACAAACATAC ↑ 3 1 2 4 Gorilla: ATAGGTTTGAAGAGGCTAGATGAC-AAACCTAGTTAAGGAACAAACATAC Human: ATAGGTTTGAAGAGGCTAGATGAC-AAACCTAGTTAAGGAACAAACATAC Cluster: [ ] Orangutan: Human > Chimp ------------- chr19:54073049-54073055 Template switch process: F1: L CTGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG 1 F3: 4 CTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA R RF: CTGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATGACAAACCTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA RR: GACCGAACCGGGGTGTCTTTATCCAAACTTCTCCGATCTACTGTTTGGATCAATTCCTTGTTTGTATGTGATAAAACGTATTCGAAT F2: 3 TACTGTT 2 Unidirectional alignment (log-probability: -31.5) TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATGttgtcat------CTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG-------ACAAACCTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA Template switch alignment (log-probability: -16.2) TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG|TTGTCAT|CTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG|TTGTCAT|CTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA Gorilla > Chimp --------------- chr19:54073049-54073055 Template switch process: F1: L CTGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG 1 F3: 4 CTAGTTAAGGAACAAACATACACTATTTTGCATAAGCTTA R RF: CTGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATGACAAACCTAGTTAAGGAACAAACATACGCTATTTTGCATAAGCTTA RR: GACCGAACCGGGGTGTCTTTATCCAAACTTCTCCGATCTACTGTTTGGATCAATTCCTTGTTTGTATGCGATAAAACGTATTCGAAT F2: 3 TACTGTT 2 Unidirectional alignment (log-probability: -36.5) TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG------ttgtcatCTAGTTAAGGAACAAACATACaCTATTTTGCATAAGCTTA TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATGACAAAC-------CTAGTTAAGGAACAAACATACGCTATTTTGCATAAGCTTA Template switch alignment (log-probability: -22.1) TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG|TTGTCAT|CTAGTTAAGGAACAAACATACaCTATTTTGCATAAGCTTA TGGCTTGGCCCCACAGAAATAGGTTTGAAGAGGCTAGATG|TTGTCAT|CTAGTTAAGGAACAAACATACGCTATTTTGCATAAGCTTA ========== Event 1661 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATAACTAGGGAGAACAGGAA--AATTGAGCCAAAGCATATTCAGTATAGAAGAATCTCATACAT ↓ 1 4 3 2 Chimp: AATAACTAGGGAGAACAGGAACTGAATATGCCAAAGCATATTCAGTATAGAAGAATCTCATACAT ↑ 1 4 3 2 Gorilla: GATAACTAGGGAGAACAGGAA--AGTTGAGCCAAAGCATATTCAGTATAGAAGAATCTCATACAT Human: GATAACTAGGGAGAACAGGAA--AATTGAGCCAAAGCATATTCAGTATAGAAGAATCTCATACAT Cluster: [ ] Orangutan: GATAACTAGGGGGAACAGCAA--AGTTGAGCCAAAGTATATTCAATATAGAAGAATCTCATACAT Human > Chimp ------------- chr1:98370233-98370240 Template switch process: F1: L AGAAAGAATTTAAGTAGAATAATAACTAGGGAGAACAGGAA 1 F3: 4 GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT R RF: AGAAAGAATTTAAGTAGAATGATAACTAGGGAGAACAGGAAAATTGAGCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT RR: TCTTTCTTAAATTCATCTTACTATTGATCCCTCTTGTCCTTTTAACTCGGTTTCGTATAAGTCATATCTTCTTAGAGTATGTACGAA F2: 3 TATAAGTC 2 Unidirectional alignment (log-probability: -38.9) GAAAGAATTTAAGTAGAATaATAACTAGGGAGAACAGGA------ActgaatatGCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT GAAAGAATTTAAGTAGAATGATAACTAGGGAGAACAGGAAAATTGA--------GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT Template switch alignment (log-probability: -22.3) GAAAGAATTTAAGTAGAATaATAACTAGGGAGAACAGGAA|CTGAATAT|GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT GAAAGAATTTAAGTAGAATGATAACTAGGGAGAACAGGAA|CTGAATAT|GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT Gorilla > Chimp --------------- chr1:98370233-98370240 Template switch process: F1: L AGAAAGAATTTAAGTAGAATAATAACTAGGGAGAACAGGAA 1 F3: 4 GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT R RF: AGAAAGAATTTAAGTAGAATGATAACTAGGGAGAACAGGAAAGTTGAGCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT RR: TCTTTCTTAAATTCATCTTACTATTGATCCCTCTTGTCCTTTCAACTCGGTTTCGTATAAGTCATATCTTCTTAGAGTATGTACGAA F2: 3 TATAAGTC 2 Unidirectional alignment (log-probability: -37.6) GAAAGAATTTAAGTAGAATaATAACTAGGGAGAACAGGAA--cTGAatatGCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT GAAAGAATTTAAGTAGAATGATAACTAGGGAGAACAGGAAAGTTGA----GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT Template switch alignment (log-probability: -22.3) GAAAGAATTTAAGTAGAATaATAACTAGGGAGAACAGGAA|CTGAATAT|GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT GAAAGAATTTAAGTAGAATGATAACTAGGGAGAACAGGAA|CTGAATAT|GCCAAAGCATATTCAGTATAGAAGAATCTCATACATGCTT ========== Event 1662 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTAT---------------TGTCAGGTAGTGATAGGATTTATCACTACCTGACAATACAGTATGTGTTTGttttat Chimp: TGTAT---------------TGTCAGGTAGTGATAGGATTTACCACTACCTGACAATACAGTATGTGTTTGTTTTAT ↑ 3 1 2 4 Gorilla: TGTAT---------------TGTCAGGTAGTGATAAATCCTATCACCACCTGACATTACAGTATGTGTTTGttttat ↓ 3 1 2 4 Human: TGTAT---------------TGTCAGGTAGTGATAGGATTTATCACTACCTGACAATACAGTATGTGTTTGttttat Cluster: [ ] Orangutan: TTTATTATATTTATATTATTTATCAGGTAGTGATAAATTCTATCACTACCTGACAATACAGTATGTGTTTGttttat Gorilla > Human --------------- chr19:50228280-50228300 Template switch process: F1: L AGAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATA 1 F3: 4 TACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG R RF: AGAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATAAATCCTATCACCACCTGACATTACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG RR: TCTTTTATTTTGTGTATGACGACATAACAGTCCATCACTATTTAGGATAGTGGTGGACTGTAATGTCATACACAAACAAAATATATAAATCCCACATGTCGC F2: 3 AACAGTCCATCACTATTTAGG 2 Unidirectional alignment (log-probability: -39.3) GAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATA-----ggattTATCACtACCTGACAaTACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG GAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATAAATCC-----TATCACCACCTGACATTACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG Template switch alignment (log-probability: -18.4) GAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATA|GGATTTATCACTACCTGACAA|TACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG GAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATA|GGATTTATCACTACCTGACAA|TACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG Gorilla > Chimp --------------- chr19:52535166-52535186 Template switch process: F1: L AGAAAATAAAATACATACTGCTGTATTGTCAGGTAGTGATA 1 F3: 4 TACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG R RF: AGAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATAAATCCTATCACCACCTGACATTACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG RR: TCTTTTATTTTGTGTATGACGACATAACAGTCCATCACTATTTAGGATAGTGGTGGACTGTAATGTCATACACAAACAAAATATATAAATCCCACATGTCGC F2: 3 AACAGTCCATCACCATTTAGG 2 Unidirectional alignment (log-probability: -49.3) GAAAATAAAAtACATACTGCTGTATTGTCAGGTAGTGATA--------ggatttacCACtACCTGACAaTACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG GAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATAAATCCTAT--------CACCACCTGACATTACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG Template switch alignment (log-probability: -29.4) GAAAATAAAAtACATACTGCTGTATTGTCAGGTAGTGATA|GGATTTAcCACTACCTGACAA|TACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG GAAAATAAAACACATACTGCTGTATTGTCAGGTAGTGATA|GGATTTATCACTACCTGACAA|TACAGTATGTGTTTGTTTTATATATTTAGGGTGTACAGCG ========== Event 1663 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAAATAATCAAATACACCCACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTT--------------------------------------------------------------------------------------------------GTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATCACGGCTACCATCAGG ↓ 3 4 2 1 Chimp: ACAAATAATCAAATACACCCACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCAAAATAACCTGGATAGAGACATCTACTGGAGATGGGAAGTGGATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATCATGGCTACCATCAGG ↑ 3 4 2 1 Gorilla: ACAAATAATCAAATACACCCACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTT--------------------------------------------------------------------------------------------------GTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATCACGGCTACCATCAGG Human: ACAAATAATCAAATACACCCACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTT--------------------------------------------------------------------------------------------------GTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATCACGGCTACCATCAGG Cluster: [ ] Orangutan: ACAAATAATCAGATACACCCACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTT--------------------------------------------------------------------------------------------------GTGTGATCTCTGCCTCTATCCCTTAGGAACATCCATTATCACAGCTACCATCAGG Human > Chimp ------------- chr1:128788435-128788474 Template switch process: F1: L CACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA 1 F3: 4 GATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATC R RF: CACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATC RR: GTGAAGGGTAGAGGTCATCTACAGAGATAGGTCCAATAAAACACACTAGAGATGGAGATAGGGAATCCTCGTAGGTAATAG F2: 3 GTGAAGGGTAGAGGTCATCTACAGAGATAGGTCCAATAAA 2 Unidirectional alignment (log-probability: -152) ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCAaaataacctggatagagacatctactggagatgggaagtggatgtctctatccaggttattttgtgtgatctctacctct ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA-------------------------------------------------------------------------------- Template switch alignment (log-probability: -21.1) ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA|AAATAACCTGGATAGAGACATCTACTGGAGATGGGAAGTG|GATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCT ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA|AAATAACCTGGATAGAGACATCTACTGGAGATGGGAAGTG|GATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCT Gorilla > Chimp --------------- chr1:128788435-128788474 Template switch process: F1: L CACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA 1 F3: 4 GATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATC R RF: CACTTCCCATCTCCAGTAGATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCATTATC RR: GTGAAGGGTAGAGGTCATCTACAGAGATAGGTCCAATAAAACACACTAGAGATGGAGATAGGGAATCCTCGTAGGTAATAG F2: 3 GTGAAGGGTAGAGGTCATCTACAGAGATAGGTCCAATAAA 2 Unidirectional alignment (log-probability: -152) ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCaaaataacctggatagagacatctactggagatgggaagtggatgtctctatccaggttattttgtgtgatctctacctct ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCC--------------------------------------------------------------------------------- Template switch alignment (log-probability: -22) ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA|AAATAACCTGGATAGAGACATCTACTGGAGATGGGAAGTG|GATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCT ATTTTGTGTGATCTCTACCTCTATCCCTTAGGAGCATCCA|AAATAACCTGGATAGAGACATCTACTGGAGATGGGAAGTG|GATGTCTCTATCCAGGTTATTTTGTGTGATCTCTACCTCT ========== Event 1664 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATCCTCATTGAGCCCAGAGGC---TACTGTATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAGTATTGCAATCATAACAGTAAAAAGAAGTATGTCTTCAG Chimp: ATCCTCATTGAGCCCAGAGGC---TACTGTATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAGTATTGCAATCATAACAGTAAAAAGAAGTATGTCTTCAG Gorilla: ATCCTCACTGAGCCCAGAGGC------TCAATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAGTATTGCAATCATAACAGTAAAAAGAAGTATGTCTTCAG ↓ 1 4 3 2 Human: ATCCTCATTGAGCCCAGAGGC---TACTGTATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAGTATTGCAATCATAACAGTAAAAAGAAGTATGTCTTCAG Cluster: [ ] Orangutan: ATCCTCATTGAGCCCAGAGGCTAC---TGTATGTTCTAGTCTCACTGTCACACCCCCAGAACAGTGTCAGTATTACAATCATAACAGTAAAAAGAAGTATGTCTTCAG Gorilla > Human --------------- chr1:149692635-149692639 Template switch process: F1: L TGAATGCACAGGTAATGGGCATCCTCATTGAGCCCAGAGGCT 1 F3: 4 ATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAG R RF: TGAATGCACAGGTAATGGGCATCCTCACTGAGCCCAGAGGCTCAATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAGTATTGCAATCATAACAGT RR: ACTTACGTGTCCATTACCCGTAGGAGTGACTCGGGTCTCCGAGTTACAAGATTAGAGTGACAGTGTGGGGGTCTTGTCACAGTCATAACGTTAGTATTGTCA F2: 3 TGTCA 2 Unidirectional alignment (log-probability: -31.8) AATGCACAGGTAATGGGCATCCTCAtTGAGCCCAGAGGctaCTgtATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAG AATGCACAGGTAATGGGCATCCTCACTGAGCCCAGAGG---CTCAATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAG Template switch alignment (log-probability: -21.9) AATGCACAGGTAATGGGCATCCTCAtTGAGCCCAGAGGCT|ACTGT|ATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAG AATGCACAGGTAATGGGCATCCTCACTGAGCCCAGAGGCT|ACTGT|ATGTTCTAATCTCACTGTCACACCCCCAGAACAGTGTCAG ========== Event 1665 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCAGTGATAGCAGACAGCAAAGATGACCCTCCAGGGTCATCTTTTGGGGACTGGGGTTTAG ↑ 1 4 3 2 Chimp: GCAGTGATAGCAGACAGCAAAACCATGCCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAG Gorilla: GCAGTGATAGCAGACAGCAAAACCATGCCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAG ↓ 1 4 3 2 Human: GCAGTGATAGCAGACAGCAAAGATGACCCTCCAGGGTCATCTTTTGGGGACTGGGGTTTAG Cluster: [ ] Orangutan: GCAGTGATAGCAGACAGCAAAACCATGCCTCTAGGGTCATCTTTTGGGGACCGGGGTTTAG Chimp > Human ------------- chr20:52031484-52031489 Template switch process: F1: L TATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA 1 F3: 4 CCTCCAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGGGACAC R RF: TATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAAACCATGCCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGGGACAC RR: ATAAAAGAGGATTCCGTCGTCGTCACTATCGTCTGTCGTTTTGGTACGGAGATCCCAGTAGAAAACCCCTGACCCCAAATCCTTTCCCTGTG F2: 3 CAGTAG 2 Unidirectional alignment (log-probability: -33.1) ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAAgatgAC----CCTCcAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA----ACCATGCCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG Template switch alignment (log-probability: -22.1) ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA|GATGAC|CCTCcAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA|GATGAC|CCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG Gorilla > Human --------------- chr20:52031484-52031489 Template switch process: F1: L TATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA 1 F3: 4 CCTCCAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGGGACAC R RF: TATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAAACCATGCCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGGGACAC RR: ATAAAAGAGGATTCCGTCGTCGTCACTATCGTCTGTCGTTTTGGTACGGAGATCCCAGTAGAAAACCCCTGACCCCAAATCCTTTCCCTGTG F2: 3 CAGTAG 2 Unidirectional alignment (log-probability: -32.2) ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAAgatgAC----CCTCcAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA----ACCATGCCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG Template switch alignment (log-probability: -22.1) ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA|GATGAC|CCTCcAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG ATTTTCTCCTAAGGCAGCAGCAGTGATAGCAGACAGCAAA|GATGAC|CCTCTAGGGTCATCTTTTGGGGACTGGGGTTTAGGAAAGG ========== Event 1666 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: TGCTTTCTATAATTAGTAGTT----ATCAATATTAAATTACTATTA----ACAGTTATCAACCTGGCTTTAACTTCAGGTAA Chimp: TGCTTTCTATAATTAGTAGTT----ATCAATATTAAATTACTATTA----ACAGTTATCAACCTGGCTTTAACTTCAGGTAA ↓ 13 24 ↑ 13 24 Gorilla: TGCTTTCTATAATTAGTAGTTAACTGTTAATAGTAATTTAATATTG--------ATATCAATCTGGCTTTAACTTCAGGTAA Human: TGCTTTCTATAATTAGTAGTT----ATCAATATTAAATTACTATTA----ACAGTTATCAACCTGGCTTTAACTTCAGGTAA Cluster: [ ] Orangutan: TGCTTTCTATAATTAGTAGTT----ATCAATATTAAATTACTACTAACAG----TTATCAACCTTGCTTTAACTTCAGGTAA Gorilla > Chimp --------------- chr20:54003579-54003603 Template switch process: F1: L TTTTTAATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA 1 F3: 4 TATCAACCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATTATGGGAC R RF: TTTTTCATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTAACTGTTAATAGTAATTTAATATTGATATCAATCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATTATGGGAC RR: AAAAAGTACGGTTTATCAAGACGAAAGATATTAATCATCAATTGACAATTATCATTAAATTATAACTATAGTTAGACCGAAATTGAAGTCCATTCTCGTTTCCGTAATACCCTG F2: 3 TGACAATTATCATTAAATTATAACT 2 Unidirectional alignment (log-probability: -62.3) TTTaATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTAtcaatattaaattACTaTTAAcAGT-------------TATCAAcCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT TTTCATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA-------------ACTGTTAATAGTAATTTAATATTGATATCAATCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT Template switch alignment (log-probability: -30.1) TTTaATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA|TCAATATTAAATTACTATTAACAGT|TATCAAcCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT TTTCATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA|TCAATATTAAATTACTATTAACAGT|TATCAATCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT Chimp > Gorilla --------------- chr20:50486940-50486964 Template switch process: F1: L TTTTTCATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA 1 F3: 4 TATCAATCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATTATGGGAC R RF: TTTTTAATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTATCAATATTAAATTACTATTAACAGTTATCAACCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATTATGGGAC RR: AAAAATTACGGTTTATCAAGACGAAAGATATTAATCATCAATAGTTATAATTTAATGATAATTGTCAATAGTTGGACCGAAATTGAAGTCCATTCTCGTTTCCGTAATACCCTG F2: 3 AGTTATAATTTAATGATAATTGTCA 2 Unidirectional alignment (log-probability: -62.3) TTTcATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA-------------ACTgTTAAtAGTaatttaatattgaTATCAAtCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT TTTAATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTATCAATATTAAATTACTATTAACAGT-------------TATCAACCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT Template switch alignment (log-probability: -30.1) TTTcATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA|ACTGTTAATAGTAATTTAATATTGA|TATCAAtCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT TTTAATGCCAAATAGTTCTGCTTTCTATAATTAGTAGTTA|ACTGTTAATAGTAATTTAATATTGA|TATCAACCTGGCTTTAACTTCAGGTAAGAGCAAAGGCATT ========== Event 1667 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTGGCCAAGTCCCTGTATCTG-------------AGATTATGGAAGCCATATTGATTACTGCCAATACCCATGGC Chimp: AGTGGCCAAGTCCCTGTATCTG-------------AGATTATGGAAGCCATATTGATTACTGCCAATACCCATGGC ↓ 4 13 2 Gorilla: AGTGGCCAAGTCCCTGTATCTTATGGAATCAATATGGCTTATGGAAGCCATATTGATTACTGCCAATACCCATGGC Human: AGTGGCCAAGTCCCTGTATCTG-------------AGATTATGGAAGCCATATTGATTACTGCCAATACCCATGGC Cluster: [ ] Orangutan: AGTAGCCAAGTCCCTGTATCTA-------------AGATTATGGAAGCCATATTGATTACTGCCAATACCCATGGT Chimp > Gorilla --------------- chr20:52222824-52222833 Template switch process: F1: L GAACAAGCTGTATAGCCCATAGTGGCCAAGTCCCTGTATC-----TTATGGAA 1 F3: 4 TTATGGAAGCCATATTGATTACTGCCAATACCCATGGCAA R RF: GAACAAGCTGTATAGCCCATAGTGGCCAAGTCCCTGTATCTGAGATTATGGAAGCCATATTGATTACTGCCAATACCCATGGCGA RR: CTTGTTCGACATATCGGGTATCACCGGTTCAGGGACATAGACTCTAATACCTTCGGTATAACTAATGACGGTTATGGGTACCGCT F2: 3 CGGTATAACT 2 Unidirectional alignment (log-probability: -46.2) TGTATAGCCCATAGTGGCCAAGTCCCTGTATCTtAtggaatcaatatgGcTTATGGAAGCCATATTGATTACTGCCAATACCCATGGCaA TGTATAGCCCATAGTGGCCAAGTCCCTGTATCTGA-------------GATTATGGAAGCCATATTGATTACTGCCAATACCCATGGCGA Template switch alignment (log-probability: -32.7) TGTATAGCCCATAGTGGCCAAGTCCCTGTATC-----TTATGGAA|TCAATATGGC|TTATGGAAGCCATATTGATTACTGCCAATACCCATGGCaA TGTATAGCCCATAGTGGCCAAGTCCCTGTATCTGAGATTATGGAA|TCAATATGGC|TTATGGAAGCCATATTGATTACTGCCAATACCCATGGCGA ========== Event 1668 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AACTGGTGGCAAAGGAACTTGAGAGTAAAGACAACTTCGTTCCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT ↓ 1 4 3 2 Chimp: AACTGGTGGCAAAGGAACTTGGGAG---------ATTGTCCCCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT Gorilla: AACTAGTGGCAAAGGAACTTGAGAGTAAAAACAACTCCGTTCCCATCATGGAGGGGACAATAAACCCTCGTTTGCCCTATT Human: AACTGGTGGCAAAGGAACTTGAGAGTAAAGACAACTTCGTTCCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT Cluster: [ ] Orangutan: AACTAGTGGCAAAGGAAAATGAGAGTAAAGACAACTTCGTTCCCATCATGGAGCGGACAATAAG-CCACGTTTGCCCTATT Human > Chimp ------------- chr20:53653385-53653391 Template switch process: F1: L TAAAGGGTCCCAAGGATCAAAACTGGTGGCAAAGGAACTTGGGAG 1 F3: 4 CCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT R RF: TAAAGGGTCCCAAGGATCAAAACTGGTGGCAAAGGAACTTGAGAGTAAAGACAACTTCGTTCCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT RR: ATTTCCCAGGGTTCCTAGTTTTGACCACCGTTTCCTTGAACTCTCATTTCTGTTGAAGCAAGGGTAGTACCTCCCCTGTTATTCGGGAGCAAACGGGATAA F2: 3 CCTGTTA 2 Unidirectional alignment (log-probability: -38) GGTCCCAAGGATCAAAACTGGTGGCAAAGGAACTTG--------------------ggagattgtccCCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT GGTCCCAAGGATCAAAACTGGTGGCAAAGGAACTTGAGAGTAAAGACAACTTCGTT-----------CCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT Template switch alignment (log-probability: -22.2) GGTCCCAAGGATCAAAACTGGTGGCAAAGGAACTTGgGAG|ATTGTCC|CCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT GGTCCCAAGGATCAAAACTGGTGGCAAAGGAACTTGAGAG|ATTGTCC|CCCATCATGGAGGGGACAATAAGCCCTCGTTTGCCCTATT ========== Event 1669 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCCATCCACCCGTTTACCTCATGGATAAAGGTTAACACAACGTAGTGTCCAAAATAGAAAGAATGATTATCACTATCTATCATGAACTATCTATGGATCCTCAAATATACCTCTTAC---CATGGCTTATGCTTTCCCCAGAGAT Chimp: TCCATCCACCCGTTTACCTCATGGATAAAGGTTAACACAACATAGTATCCAAAATAGAAAGAATGATTATCACTATCTATCATGAGCTATCTATAGATCCTCAAATATACCTCTTAC---CATGGCTTATGCTTTCCCCAGAGAT ↓ 3 2 1 4 ↑ 3 2 1 4 Gorilla: CCCATCCACCCATTTACCTCATGGATAAAGGTTAACACAACGTAGTGTCCAAAATAGAAAGAATGATTATCACTGTCTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTATAGCTTATGCTTATGCTTTCCCCAGAGAT ↓ 3 2 1 4 Human: TCCATCCACCCGTTTACCTCATGGATAAAGGTTAACACAACGTAGTGTCCAAAATAGAAAGAATGATTATCACTATCTATCATGAACTATCTATGGATCCTCAAATATACCTCTTAC---CATGGCTTATGCTTTCCCCAGAGAT Cluster: [ ] Orangutan: TCCATCCACCCATTTACCTCCTGGATAAAGGTCAACACAACGTGGTGTCCAAAATAGAAAGAATGATTATCACTATCTATCATGAGCTACCTATGGATCCTCAAATATACCTCTTAC---CATGGCTTATGCTTTCCCCAGAGAT Gorilla > Human --------------- chr20:51540476-51540480 Template switch process: F1: L TCTATCATGAACTATCTATGGATCCTCAAATATACCTCTTA 1 F3: 4 GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA R RF: CATGGATAAAGGTTAACACAACGTAGTGTCCAAAATAGAAAGAATGATTATCACTGTCTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTATAGCTTATGCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA RR: GTACCTATTTCCAATTGTGTTGCATCACAGGTTTTATCTTTCTTACTAATAGTGACAGATAGTACTCGATAGATACCTAGGAGTTTATATGGAGAATATCGAATACGAATACGAAAGGGGTCTCTACAACCAAAACTCTTATAAT F2: 3 GTACC 2 Unidirectional alignment (log-probability: -33.7) CTATCATGAaCTATCTATGGATCCTCAAATATACCTCTTA--------ccatgGCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA CTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTATAGCTTAT-----GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA Template switch alignment (log-probability: -21.9) CTATCATGAaCTATCTATGGATCCTCAAATATACCTCTTA|CCATG|GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA CTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTA|CCATG|GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA Gorilla > Chimp --------------- chr20:53761956-53761960 Template switch process: F1: L TCTATCATGAGCTATCTATAGATCCTCAAATATACCTCTTA 1 F3: 4 GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA R RF: CATGGATAAAGGTTAACACAACGTAGTGTCCAAAATAGAAAGAATGATTATCACTGTCTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTATAGCTTATGCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA RR: GTACCTATTTCCAATTGTGTTGCATCACAGGTTTTATCTTTCTTACTAATAGTGACAGATAGTACTCGATAGATACCTAGGAGTTTATATGGAGAATATCGAATACGAATACGAAAGGGGTCTCTACAACCAAAACTCTTATAAT F2: 3 GTACC 2 Unidirectional alignment (log-probability: -33.7) CTATCATGAGCTATCTATaGATCCTCAAATATACCTCTTA--------ccatgGCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA CTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTATAGCTTAT-----GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA Template switch alignment (log-probability: -21.9) CTATCATGAGCTATCTATaGATCCTCAAATATACCTCTTA|CCATG|GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA CTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTA|CCATG|GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA Chimp > Gorilla --------------- chr20:50241418-50241425 Template switch process: F1: L TCTATCATGAGCTATCTATGGATCCTCAAATATACCTCTTA 1 F3: 4 GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA R RF: TCTATCATGAGCTATCTATAGATCCTCAAATATACCTCTTACCATGGCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA RR: AGATAGTACTCGATAGATATCTAGGAGTTTATATGGAGAATGGTACCGAATACGAAAGGGGTCTCTACAACCAAAACTCTTATAAT F2: 3 TATTCGAT 2 Unidirectional alignment (log-probability: -37.9) CTATCATGAGCTATCTATgGATCCTCAAATATACCTCTTA-----tagcttatGCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA CTATCATGAGCTATCTATAGATCCTCAAATATACCTCTTACCATG--------GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA Template switch alignment (log-probability: -27.8) CTATCATGAGCTATCTATgGATCCTCAAATATACCTCTTA|TAGCTtAT|GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA CTATCATGAGCTATCTATAGATCCTCAAATATACCTCTTA|TAGCTCAT|GCTTATGCTTTCCCCAGAGATGTTGGTTTTGAGAATATTA ========== Event 1670 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGTGCTCATTCCTTCAGAAAAAGCatatatat---------atatatatatatatGTTTAAAAAATTACATATATATGg Chimp: AAGTGCTCATTCCTTCAGAAAAAGCATGtatatatataatatatatatatatatatgtttaaaaaattatatatatatGg Gorilla: AAGTGCTCATTCCTTCAGAAAGTGCatatatat---------ata----------tGTTTAAAAAATTACATATATATGg ↓ 1 4 2 Human: AAGTGCTCATTCCTTCAGAAAAAGCatatatat---------atatatatatatatGTTTAAAAAATTACATATATATGg Cluster: [] Orangutan: AAGTGCTCATTCCTTCAGAAAGAGCATATATGT---------ATA----------TATTTTAAAAATTACATATATATGa Gorilla > Human --------------- chr20:49847730-49847744 Template switch process: F1: L AAATATTTTAGTTAAGTCATAAGTGCTCATTCCTTCAGAAA 1 F3: 4 TATATATATATGTTTAAAAAATTACAT R RF: AAATATTTTAGTTAAGTCGTAAGTGCTCATTCCTTCAGAAAGTGCATATATATATATGTTTAAAAAATTACAT RR: TTTATAAAATCAATTCAGCATTCACGAGTAAGGAAGTCTTTCACGTATATATATATACAAATTTTTTAATGTA F2: 3 ATATATATATACGAA 2 Unidirectional alignment (log-probability: -41.7) AATATTTTAGTTAAGTCaTAAGTGCTCATTCCTTCAGAAAaaGCatatatatatATATATATATATGTTTAAAAAATTACAT AATATTTTAGTTAAGTCGTAAGTGCTCATTCCTTCAGAAAGTGC----------ATATATATATATGTTTAAAAAATTACAT Template switch alignment (log-probability: -28.3) AATATTTTAGTTAAGTCaTAAGTGCTCATTCCTTCAGAAA|AAgCATATATATATA|TATATATATATGTTTAAAAAATTACAT AATATTTTAGTTAAGTCGTAAGTGCTCATTCCTTCAGAAA|AAACATATATATATA|TATATATATATGTTTAAAAAATTACAT ========== Event 1671 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGTAGTCACTGTGCTAAAACC----------------------TTGCCATAGGCTCCATCCTAGGTGCCCgggagggaggtgggcactgaggtcataggacgcactccagaatcgg ↓ 4 1 3 2 Chimp: TGTAGTCACTGTGCTAAAACC-----------TTGATGACCCCTTGCCGTAGGCTCCATCCTAGGTGCCCGGGAGGGAGGTGGGCACTGAGGTCATAGGATGCACTCCAGAATCAG Gorilla: TGTAGTCACTGTGCTAAAACCTTGATGACCCC-----------TTGCCATAGGCTCCATCCTAGGTGCCTGGGAGGGAGGTGGGCACTGAGGTCATAGGATGCGCTCCAGAATCAG ↑ 4 1 3 2 Human: TGTAGTCACTGTGCTAAAACC----------------------TTGCCATAGGCTCCATCCTAGGTGCCCgggagggaggtgggcactgaggtcataggacgcactccagaatcgg Cluster: [ ] Orangutan: TGTAGTCACTGTGCTAAAACCTTGATGGCCCC-----------TTGCCATAGGCTCCATCCTAGGTGCCCgggagggaggtgggcactgaggttatagaatgcactctagaatcac Human > Chimp ------------- chr20:1393077-1393082 Template switch process: F1: L TGTGTCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTG 1 F3: 4 CCTTGCCGTAGGCTCCATCCTAGGTGCCCGGGAGGGAGGTGGGCACTG R RF: TGTGTCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTGCCATAGGCTCCATCCTAGGTGCCCGGGAGGGAGGTGGGCACTGAGGTCAT RR: ACACAGACCCGACACTAAGGACATCAGTGACACGATTTTGGAACGGTATCCGAGGTAGGATCCACGGGCCCTCCCTCCACCCGTGACTCCAGTA F2: 3 CCAGTA 2 Unidirectional alignment (log-probability: -32.8) TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAAccttgatgaccCCTTGCCgTAGGCTCCATCCTAGGTGCCCGGGAGGGAGGT TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAA-----------CCTTGCCATAGGCTCCATCCTAGGTGCCCGGGAGGGAGGT Template switch alignment (log-probability: -22.2) TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTG|ATGACC|CCTTGCCgTAGGCTCCATCCTAGGTGCCCGGGAGGGAGGT TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTG|ATGACC|CCTTGCCATAGGCTCCATCCTAGGTGCCCGGGAGGGAGGT Human > Gorilla --------------- chr20:1465667-1465672 Template switch process: F1: L TGTGTCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTG 1 F3: 4 CCTTGCCATAGGCTCCATCCTAGGTGCCTGGGAGGGAGGTGG R RF: TGTGTCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTGCCATAGGCTCCATCCTAGGTGCCCGGGAGGGAGGTGGGCACTGAGGTCAT RR: ACACAGACCCGACACTAAGGACATCAGTGACACGATTTTGGAACGGTATCCGAGGTAGGATCCACGGGCCCTCCCTCCACCCGTGACTCCAGTA F2: 3 CCAGTA 2 Unidirectional alignment (log-probability: -32.2) TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAAccttgatgaccCCTTGCCATAGGCTCCATCCTAGGTGCCtGGGAGGGAGGT TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAA-----------CCTTGCCATAGGCTCCATCCTAGGTGCCCGGGAGGGAGGT Template switch alignment (log-probability: -22.1) TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTG|ATGACC|CCTTGCCATAGGCTCCATCCTAGGTGCCtGGGAGGGAGGT TCTGGGCTGTGATTCCTGTAGTCACTGTGCTAAAACCTTG|ATGACC|CCTTGCCATAGGCTCCATCCTAGGTGCCCGGGAGGGAGGT ========== Event 1672 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTA-----------TCTTTAGAATCAGGATTCTGATTCTAAAATCCTATCAAGAAT-TACCTTGAAACCC ↑ 4 2 1 Chimp: TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTA---------------------------------------------TCAAGAAT-TACCTTGAAACCC Gorilla: TTATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATCTTTTCAATT----------------------------------ACCAGAAT-TACCTTGAAACCC Human: TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTA-----------TCTTTAGAATCAGGATTCTGATTCTAAAATCCTATCAAGAAT-TACCTTGAAACCC Cluster: [ ] Orangutan: TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATCTTTTCAATT----------------------------------ACCAGAATTCTCCTTGAAACCC Chimp > Human ------------- chr20:49328537-49328549 Template switch process: F1: L TTTTCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATC 1 F3: 4 TTCTGATTCTAAAATCCTATCAAGAATTACCTTGAAACCCTGCATGTTTGGGTAACACT R RF: TTTTCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATCAAGAATTACCTTGAAACCCTGCATGTTTGGGTAACACT RR: AAAAGTACATAGTAAAGGTCTGAAGACTAAGATTTTAGGATAGTTCTTAATGGAACTTTGGGACGTACAAACCCATTGTGA F2: 3 AGGACTAAGATTT 2 Unidirectional alignment (log-probability: -59.8) TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATctttagaatcaggattctgattctaaaatcctatCAAGAATTACCTTGAAACCC TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTAT----------------------------------CAAGAATTACCTTGAAACCC Template switch alignment (log-probability: -23.3) TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATC|TTTAGAATCAGgA|TTCTGATTCTAAAATCCTATCAAGAATTACCTTGAAACCC TCATGTATCATTTCCAGACTTCTGATTCTAAAATCCTATC|TTTAGAATCAGAA|TTCTGATTCTAAAATCCTATCAAGAATTACCTTGAAACCC ========== Event 1673 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCCATAGTACTTATGAGTAACTACTCCACACTGAGTTTCTCATTTTC---------TCAGTGTGGAGTAGTTAAATTCagtcaggaggcctgt Chimp: GTTCATAGTACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTC------------------TGTTAGAAAATTCagtcaggaggcctgt ↓ 3 2 1 4 Gorilla: GTCCATAGTACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCTCAGTGTGC---------AGTAGTTAAATTCagtcaggaggcctgt Human: GTCCATAGTACTTATGAGTAACTACTCCACACTGAGTTTCTCATTTTC---------TCAGTGTGGAGTAGTTAAATTCagtcaggaggcctgt Cluster: [ ] Orangutan: GTCCATAGTACTTATGAGTAACTACTCCACACTGAGTTTCTCATTTTC------------------TGTTAGAAAATCCagtcaggaggcctgt Chimp > Gorilla --------------- chr20:47835002-47835016 Template switch process: F1: L GTACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCT 1 F3: 4 AAATTCAGTCAGGAGGCCTGTCTTTGAATTCCAGTTCCAG R RF: GTACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCTGTTAGAAAATTCAGTCAGGAGGCCTGTCTTTGAATTCCACTTCCAG RR: CATGAATACTCATTGATGAGGTGTGACTCAAAGAGCAAAAGACAATCTTTTAAGTCAGTCCTCCGGACAGAAACTTAAGGTGAAGGTC F2: 3 TTGATGACGTGTGAC 2 Unidirectional alignment (log-probability: -43.6) ACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCTcagtgtgcagtaGTT---AAATTCAGTCAGGAGGCCTGTCTTTGAATTCCAgTTCCAG ACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCT------------GTTAGAAAATTCAGTCAGGAGGCCTGTCTTTGAATTCCACTTCCAG Template switch alignment (log-probability: -28.7) ACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCT|CAGTGTGcAGTAGTT|AAATTCAGTCAGGAGGCCTGTCTTTGAATTCCAgTTCCAG ACTTATGAGTAACTACTCCACACTGAGTTTCTCGTTTTCT|CAGTGTGGAGTAGTT|AAATTCAGTCAGGAGGCCTGTCTTTGAATTCCACTTCCAG ========== Event 1674 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACAGTTCATTCATTTCAACCTCTGTACCTAAAGGTACAGAGGTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGGTTCAAA ↑ 4 3 2 1 Chimp: AACAGTTCATTCATTTCAACCATTC----------------TGTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGGTTCAAA Gorilla: AACAGTTCATTCATTTCAACCATTC----------------TGTATTTTATAACCTCTGTACCTAAAGTAAAATATTTGGGGTTCAAA Human: AACAGTTCATTCATTTCAACCTCTGTACCTAAAGGTACAGAGGTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGGTTCAAA Cluster: [ ] Orangutan: AACAGTTCATTCATTTCAACCATTC----------------TGTATTTTATAAACTCTGTACCTAAAGTAAAATATTTAGGGTTCAAA Chimp > Human ------------- chr20:48665487-48665494 Template switch process: F1: L AATGGCATACTATCTAAGATAACAGTTCATTCATTTCAAC------------------CTCTGTACCTAAAG 1 F3: 4 GTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGG R RF: AATGGCATACTATCTAAGATAACAGTTCATTCATTTCAACCATTCTGTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGG RR: TTACCGTATGATAGATTCTATTGTCAAGTAAGTAAAGTTGGTAAGACATAAAATATTGGAGACATGGATTTCATTTTATAAATCCC F2: 3 GAGACATG 2 Unidirectional alignment (log-probability: -47.1) TAAGATAACAGTTCATTCATTTCAACC--TCTGTacctaaaggtacagaggtATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGG TAAGATAACAGTTCATTCATTTCAACCATTCTGT------------------ATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGG Template switch alignment (log-probability: -27.7) TAAGATAACAGTTCATTCATTTCAAC------------------CTCTGTACCTAAAG|GTACAGAG|GTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGG TAAGATAACAGTTCATTCATTTCAACCATTCTGTATTTTATAACCTCTGTACCTAAAG|GTACAGAG|GTATTTTATAACCTCTGTACCTAAAGTAAAATATTTAGGG ========== Event 1675 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATGGTTTTCTGTGAGGCGAAG-TCCATAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAACCTCACTCTTTCATTAAAAAGGGTTTCTTCTTTTCTTTCTATTTTTAAAccttcggacttttcgtcctttcatcttcc Chimp: AATGGTTTTCTGTGAGGCGAAG-TCCATAGGCTTAAAATCAATGTCAtttttgagtttttggtttaacctcattctttcattaaaaagggtttcttcttttctttctatttttaaaccttcagacttttcgtcctttcatcttcc ↑ 1 4 3 2 Gorilla: AATGGTTTTCTGTGAGGCGAAAACTCGTAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAACCTCATTCTTTCATTAAAAAGGGTTTCTTCTAGtctttctatttttaaacctttggacttttcgtcctttcatcttcc ↓ 1 4 3 2 Human: AATGGTTTTCTGTGAGGCGAAG-TCCATAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAACCTCACTCTTTCATTAAAAAGGGTTTCTTCTTTTCTTTCTATTTTTAAAccttcggacttttcgtcctttcatcttcc Cluster: [ ] Orangutan: AATGATTTTCTGTGAGGTGAAG-TCCACAGGCTTAAAATCAAGGTCATTTTTTAGTTTTTGGTTTAACCTCATTCTTTCATTAAAAAGGGTTTCTTCTTTTCTTTCTATTTTTAAAccttcagacttttcgttctttcatcttcc Gorilla > Human --------------- chr20:48570329-48570333 Template switch process: F1: L AACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA 1 F3: 4 TAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA R RF: AACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAAAACTCGTAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAACCTCATTCTTTCATTAAAAAGGGTTTCTTCTAGTCTTTCTATTTTTAAACCTTTGGAC RR: TTGTTAGATTAATCTTTATTTTACCAAAAGACACTCCGCTTTTGAGCATCCGAATTTTAGTTCCAGTAAAAACTCAAAAACCAAATTGGAGTAAGAAAGTAATTTTTCCCAAAGAAGATCAGAAAGATAAAAATTTGGAAACCTG F2: 3 ACCTG 2 Unidirectional alignment (log-probability: -26.7) ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA-----GtccaTAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAAAACTCG----TAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA Template switch alignment (log-probability: -16.4) ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA|GTCCA|TAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA|GTCCA|TAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA Gorilla > Chimp --------------- chr20:50725568-50725572 Template switch process: F1: L AACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA 1 F3: 4 TAGGCTTAAAATCAATGTCATTTTTGAGTTTTTGGTTTAA R RF: AACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAAAACTCGTAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAACCTCATTCTTTCATTAAAAAGGGTTTCTTCTAGTCTTTCTATTTTTAAACCTTTGGAC RR: TTGTTAGATTAATCTTTATTTTACCAAAAGACACTCCGCTTTTGAGCATCCGAATTTTAGTTCCAGTAAAAACTCAAAAACCAAATTGGAGTAAGAAAGTAATTTTTCCCAAAGAAGATCAGAAAGATAAAAATTTGGAAACCTG F2: 3 ACCTG 2 Unidirectional alignment (log-probability: -32.2) ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA-----GtccaTAGGCTTAAAATCAAtGTCATTTTTGAGTTTTTGGTTTAA ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAAAACTCG----TAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA Template switch alignment (log-probability: -21.9) ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA|GTCCA|TAGGCTTAAAATCAAtGTCATTTTTGAGTTTTTGGTTTAA ACAATCTAATTAGAAATAAAATGGTTTTCTGTGAGGCGAA|GTCCA|TAGGCTTAAAATCAAGGTCATTTTTGAGTTTTTGGTTTAA ========== Event 1676 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TAGTCTCTCTGTTTCCTCCAGGTGGAATGACCTAAAAACATTGAGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGTGGTCAAGGCTGATAGTTTTGCTTCATACAACTTCACCTACATTTTATGAGATATCAGATAATAAGTTGACACTGCTTCAAAAGTCAGTGGTGTTTGGCTTCATCTCTGTTTTGGG Chimp: TAGTCTCTCTGTTTCCTCCAGG------------------------TGGAATGACCAGAGATTAGACCAAAATCCACTGAGGTGGTCAGGGCTGATAGTTTTGCTTCATACAACTTTACCTACATTTTATGAGATATCAGATAATAAGTTGACACTGCTTCGAAAGTCA---GTGTTTGGCTTCATCTCTGTCTTGGG ↓ 4 1 3 2 Gorilla: TAGTCTCTCTGTTTCCTCCAGGTGGAATGACCTAAAAACATTGAGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGTGGTCAGGGCTGATAGTTTTGCTTCATACAACTTCACCTACATTTTATGAGATATCAGATAATAAGTTGACACTGCTTCAAAAGTCAGTGGTGTTTGGCTTCATCTCTGTCTTGGG Human: TAGTCTCTCTGTTTCCTCCAGGTGGAATGACCTAAAAACATTGAGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGTGGTCAAGGCTGATAGTTTTGCTTCATACAACTTCACCTACATTTTATGAGATATCAGATAATAAGTTGACACTGCTTCAAAAGTCAGTGGTGTTTGGCTTCATCTCTGTTTTGGG Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr20:46674200-46674207 Template switch process: F1: L CGATGAAGATAAAATTCTCTAGTCTCTCTGTTTCCTCCAGGTGGAATGACCTAA 1 F3: 4 AGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGTGGT R RF: CGATGAAGATAAAATTCTCTAGTCTCTCTGTTTCCTCCAGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGTGGTCAGGGCTGATAGTTTTGCTTCATACAACTTTACCTACATTTTATGAGATATCAGATAATAAGTTGACACTGCTTCGAAAGTCAGTGTTT RR: GCTACTTCTATTTTAAGAGATCAGAGAGACAAAGGAGGTCCACCTTACTGGTCTCTAATCTGGTTTTAGGTGACTCCACCAGTCCCGACTATCAAAACGAAGTATGTTGAAATGGATGTAAAATACTCTATAGTCTATTATTCAACTGTGACGAAGCTTTCAGTCACAAA F2: 3 GTTACAAA 2 Unidirectional alignment (log-probability: -45.4) TTCTCTAGTCTCTCTGTTTCCTCCAggtggaatgacctaaaaacattgaGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGT TTCTCTAGTCTCTCTGTTTCCTCCA------------------------GGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGT Template switch alignment (log-probability: -33.7) TTCTCTAGTCTCTCTGTTTCCTCCAGGTGGAATGACCtaA|AAACAtTG|AGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGT TTCTCTAGTCTCTCTGTTTCCTCCAGGTGGAATGACCAGA|AAACACTG|AGGTGGAATGACCAGAGATTAGACCAAAATCCACTGAGGT ========== Event 1677 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGACAACATTTTAATCCCT----GATGATGTATATGATCCACCAGTGGAGAGAAAATGTATATGAGAATTTTGAGAGTGTGAAAACATTTAAGATTTCCATCACCCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCTTCTATATCGCTATGATAATCTGCAACGTATCTACATTCTAGCTC Chimp: TGTGACAACATTTTAATCCCT----GATGATGTATATGATCCACCAGTGCAGAGAAAATGTATATGAGAATTTTGAGAGTGTGAAAACATTTAAGATTTCCATCACCCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCCTCTATATCGCTATGATAATCTGCAACGTATCTACATTCTAGCTC ↓ 1 4 3 2 Gorilla: TGTGACAACATTTTAATCCCT--------GTGCAG-AGATCCACCAGTGCAGAGAAAATGTATATGAGAGTTTTGAGAGTGTGAAAACATTTAAGATTTCCATCACCCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCCTCTATATCGCTATGATAATCTGCAACGTATCTACATTCTAGCTC ↑ 1 4 3 2 Human: TGTGACAACATTTTAATCCCT----GATGATGTATATGATCCACCAGTGGAGAGAAAATGTATATGAGAATTTTGAGAGTGTGAAAACATTTAAGATTTCCATCACCCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCTTCTATATCGCTATGATAATCTGCAACGTATCTACATTCTAGCTC Cluster: [ ] Orangutan: TGTGACAACATTTTAATCCCTGATG----ATGTATATGATCCACCAGTGCAGAGAAAATGTATATGAGAATTTTGAGAGTGCGAAAACATTTAAGATTTCCGTCACTCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCCTCTATATCGCTATGATAATCTGTAATGTATCTACATTCTAGCTC Human > Gorilla --------------- chr20:46121034-46121039 Template switch process: F1: L ATTTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG 1 F3: 4 GATCCACCAGTGCAGAGAAAATGTATATGAGAGTTTTGAG R RF: ATTTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTGATGATGTATATGATCCACCAGTGGAGAGAAAATGTATATGAGAATTTTGAGAGTGTGAAAACATTTAAGATTTCCATCACCCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCTTCTATATCGCTATGATAATCTGCA RR: TAAAGACTAGTAAAACTGAAACACTGTTGTAAAATTAGGGACTACTACATATACTAGGTGGTCACCTCTCTTTTACATATACTCTTAAAACTCTCACACTTTTGTAAATTCTAAAGGTAGTGGGAGTGGTGTGAAGAGAGGGACAATGAGTCGAGGAAAAGGGAAGATATAGCGATACTATTAGACGT F2: 3 AGACGT 2 Unidirectional alignment (log-probability: -39.4) TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG----------TgcagaGATCCACCAGTGcAGAGAAAATGTATATGAGAgTTTTGAG TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTGATGATGTATAT-----GATCCACCAGTGGAGAGAAAATGTATATGAGAATTTTGAG Template switch alignment (log-probability: -27.5) TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG|TGCAGA|GATCCACCAGTGcAGAGAAAATGTATATGAGAgTTTTGAG TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG|TGCAGA|GATCCACCAGTGGAGAGAAAATGTATATGAGAATTTTGAG Chimp > Gorilla --------------- chr20:46121034-46121039 Template switch process: F1: L ATTTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG 1 F3: 4 GATCCACCAGTGCAGAGAAAATGTATATGAGAGTTTTGAG R RF: ATTTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTGATGATGTATATGATCCACCAGTGCAGAGAAAATGTATATGAGAATTTTGAGAGTGTGAAAACATTTAAGATTTCCATCACCCTCACCACACTTCTCTCCCTGTTACTCAGCTCCTTTTCCCCTCTATATCGCTATGATAATCTGCA RR: TAAAGACTAGTAAAACTGAAACACTGTTGTAAAATTAGGGACTACTACATATACTAGGTGGTCACGTCTCTTTTACATATACTCTTAAAACTCTCACACTTTTGTAAATTCTAAAGGTAGTGGGAGTGGTGTGAAGAGAGGGACAATGAGTCGAGGAAAAGGGGAGATATAGCGATACTATTAGACGT F2: 3 AGACGT 2 Unidirectional alignment (log-probability: -33.9) TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG----------TgcagaGATCCACCAGTGCAGAGAAAATGTATATGAGAgTTTTGAG TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTGATGATGTATAT-----GATCCACCAGTGCAGAGAAAATGTATATGAGAATTTTGAG Template switch alignment (log-probability: -22) TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG|TGCAGA|GATCCACCAGTGCAGAGAAAATGTATATGAGAgTTTTGAG TTCTGATCATTTTGACTTTGTGACAACATTTTAATCCCTG|TGCAGA|GATCCACCAGTGCAGAGAAAATGTATATGAGAATTTTGAG ========== Event 1678 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGGTGCCAGGCACTCCCAGCCCAGGGGATCAGGCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGGCTCCCTGCAGGAACGCTGAAGCCAGAACGGAACAAACTG ↑ 4 1 3 2 Chimp: GGGGTGCCAGGCACTCCCAGCCCA--------------GGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGGCTCCCTGCAGGAACGCTGAAGCCAGAACGGAACAAACTG Gorilla: GGGGTGCCAGGCACTCCCAGCCCGGGGTGTCAGGCCCAGGGGAAGGAGGGACT-GAGGTATGTTCAGCTGGGGCTCCCTGCAGGAACGCTGAAGCCAGAACGGAACAAACTG Human: GGGGTGCCAGGCACTCCCAGCCCAGGGGATCAGGCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGGCTCCCTGCAGGAACGCTGAAGCCAGAACGGAACAAACTG Cluster: [ ] Orangutan: GGGGTGCCAGGCACTCCCAGCCCAGGGGGTCAGGCCCAGGGGAAGGAGGGACTGGCGGTATGTTCAGCCGGGGCTCCCTGTAGGAACACTGAAGCCAGAACGGAATAAACTG Chimp > Human ------------- chr20:18093604-18093607 Template switch process: F1: L GCTGCTCCCGTCCCTGGGGGGTGCCAGGCACTCCCAGCCCAGGGGA 1 F3: 4 GCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGGCTCCC R RF: GCTGCTCCCGTCCCTGGGGGGTGCCAGGCACTCCCAGCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGGCTCCCTGCAGGAACGCTGA RR: CGACGAGGGCAGGGACCCCCCACGGTCCGTGAGGGTCGGGTCCCCTTCCTCCCTGACCTCCATACAAGTCGACCCCGAGGGACGTCCTTGCGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -31.1) CCCGTCCCTGGGGGGTGCCAGGCACTCCCAgcccaggggatcagGCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGG CCCGTCCCTGGGGGGTGCCAGGCACTCCCA--------------GCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGG Template switch alignment (log-probability: -16) CCCGTCCCTGGGGGGTGCCAGGCACTCCCAGCCCAGGGGA|TCAG|GCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGG CCCGTCCCTGGGGGGTGCCAGGCACTCCCAGCCCAGGGGA|TCAG|GCCCAGGGGAAGGAGGGACTGGAGGTATGTTCAGCTGGGG ========== Event 1679 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GACCTTCCTCTG-GGGACTCATGGTGACAGCCCCATGCTGCCAGGAAGCAGCCTTCCACCTGACGAGTGAAGAAGAAACCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGCAGATGGCTGTGTGTCTCTCAAGGCAACTGGGGGCTGT Chimp: GACCTTCCTCCG-GGGACTCATGGTGACAGCCCCATGCTGCCAGGAAGCAGCCTTCCACCTGACGAGTGAAGAAGAAACCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGCAGACGGCTCCAT---GCTCAAGGCAACTGGGGGCTGT Gorilla: GACCTTCCTCCG-GGGACTCATGGTGACAGCCCCATGCTGCCAGGAAGCAGCCTTCCACCTGACGAGTGAAGAAGAAACCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGCAGACGGCTCCAT---GCTCAAGGCAACTGGGGGCTGT ↑ 3 2 1 4 Human: GACCTTCCTCTG-GGGACTCATGGTGACAGCCCCATGCTGCCAGGAAGCAGCCTTCCACCTGACGAGTGAAGAAGAAACCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGCAGATGGCTGTGTGTCTCTCAAGGCAACTGGGGGCTGT Cluster: [ ] Orangutan: GACCTTCCTCCGGGGGACTCATGGTGACAGCCCCATGCTGCCAGGAAGCAGCCTTCCACCTGACGAGTGAAGAAGAAACCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGTAGACGGCTCCAT---GCTCAAGGCAACTGGGGGCTGT Human > Gorilla --------------- chr20:19029059-19029063 Template switch process: F1: L CCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGCAGACGGCT 1 F3: 4 CTCAAGGCAACTGGGGGCTGTGGGCCACGTGGCGTTCAGC R RF: CATGGTGACAGCCCCATGCTGCCAGGAAGCAGCCTTCCACCTGACGAGTGAAGAAGAAACCCCAGCTCCTGCTTGTTCATGCTTCTGCACACACTGCAGATGGCTGTGTGTCTCTCAAGGCAACTGGGGGCTGTGGGCCACGTGGCATTCAGC RR: GTACCACTGTCGGGGTACGACGGTCCTTCGTCGGAAGGTGGACTGCTCACTTCTTCTTTGGGGTCGAGGACGAACAAGTACGAAGACGTGTGTGACGTCTACCGACACACAGAGAGTTCCGTTGACCCCCGACACCCGGTGCACCGTAAGTCG F2: 3 GTACC 2 Unidirectional alignment (log-probability: -37.9) CTCCTGCTTGTTCATGCTTCTGCACACACTGCAGAcGGCtccaTG-------CTCAAGGCAACTGGGGGCTGTGGGCCACGTGGCgTTCAGC CTCCTGCTTGTTCATGCTTCTGCACACACTGCAGATGGC----TGTGTGTCTCTCAAGGCAACTGGGGGCTGTGGGCCACGTGGCATTCAGC Template switch alignment (log-probability: -27.5) CTCCTGCTTGTTCATGCTTCTGCACACACTGCAGAcGGCT|CCATG|CTCAAGGCAACTGGGGGCTGTGGGCCACGTGGCgTTCAGC CTCCTGCTTGTTCATGCTTCTGCACACACTGCAGATGGCT|CCATG|CTCAAGGCAACTGGGGGCTGTGGGCCACGTGGCATTCAGC ========== Event 1680 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGCCATGGATATTCTTCTTTACTATACTCTAAAGCAAGGCCAGATGCTTGCTTTAGAGTACTCAggacaacattgtagttaaaagcctgggctctggagtccaagaaaa Chimp: AGGCCGTGGATATTCTTCTTT---ATCCTC------TAGGCCAGATGCTTGCTTTAGAGTACTCAggacaacattgtagttaaaagcctaggctctggagtccaagaaaa Gorilla: AGGCCATGGATATTCTTCTTT---ATCCTC------TGGGCCAGATGCTTGCTTTAGAGTACTCAggacaacattgtagttaaaagcctaggctctggagtccaagaaaa ↓ 4 3 2 1 Human: AGGCCATGGATATTCTTCTTTACTATACTCTAAAGCAAGGCCAGATGCTTGCTTTAGAGTACTCAggacaacattgtagttaaaagcctgggctctggagtccaagaaaa Cluster: [ ] Orangutan: AGGCCTTGGATATT---CTTT---ATCCTC------TAGGCCAGATGCTTGCTTTACAGTACTcaggacaatattgtggttaaaagcctgggctctggagtccaagaaaa Gorilla > Human --------------- chr20:19492202-19492214 Template switch process: F1: L AGAGCTTTCTGGCCTTGACAAGGCCATGGATATTCTTCTTTA--------------------------------------------------------CTA 1 F3: 4 GGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTA R RF: AGAGCTTTCTGGCCTTGACAAGGCCATGGATATTCTTCTTTATCCTCTGGGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTAGTTAAAAGCCTA RR: TCTCGAAAGACCGGAACTGTTCCGGTACCTATAAGAAGAAATAGGAGACCCGGTCTACGAACGAAATCTCATGAGTCCTGTTGTAACATCAATTTTCGGAT F2: 3 AACGAAATCTCAT 2 Unidirectional alignment (log-probability: -44) TTTCTGGCCTTGACAAGGCCATGGATATTCTTCTTTactatactctaaagcaA-------GGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTA TTTCTGGCCTTGACAAGGCCATGGATATTCTTCTTT----------------ATCCTCTGGGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTA Template switch alignment (log-probability: -30.1) TTTCTGGCCTTGACAAGGCCATGGATATTCTTCTTTA--------------------------------------------------------CTA|TACTCTAAAGCAA|GGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTA TTTCTGGCCTTGACAAGGCCATGGATATTCTTCTTTATCCTCTGGGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTAGTTAAAAGCCTA|TACTCTAAAGCAA|GGCCAGATGCTTGCTTTAGAGTACTCAGGACAACATTGTA ========== Event 1681 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGAGAGAAGATGCAAGGTAG----------------------TCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCG Chimp: GTGAGAGAAGATGCAAGGTAG-----------TCTGCTGCCAGTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCTG Gorilla: GTGAGAGAAGATGCAAGGTAGTCTGCTGCCAG-----------TCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCG ↑ 4 1 3 2 Human: GTGAGAGAAGATGCAAGGTAG----------------------TCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCG Cluster: [ ] Orangutan: GTGAGGGAAGATGCAAGGTAGTCTGCCGCCAG-----------TCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCG Human > Gorilla --------------- chr20:19914024-19914030 Template switch process: F1: L ACATTACACTGCTATAGAGGGTGAGAGAAGATGCAAGGTAGTCT 1 F3: 4 GTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCGGT R RF: ATGTTACACTGCTATAGAGGGTGAGAGAAGATGCAAGGTAGTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCGGT RR: TACAATGTGACGATATCTCCCACTCTCTTCTACGTTCCATCAGATGAGTTATACCGTCGGTTGTACTCGGTCGGTAGGCCA F2: 3 ACCGTCG 2 Unidirectional alignment (log-probability: -37.7) TACACTGCTATAGAGGGTGAGAGAAGATGCAAGGTagtctgctgccAGTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCGG TACACTGCTATAGAGGGTGAGAGAAGATGCAAGGT-----------AGTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCGG Template switch alignment (log-probability: -27.8) TACACTGCTATAGAGGGTGAGAGAAGATGCAAGGTAGTCT|GCTGCCA|GTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCGG TACACTGCTATAGAGGGTGAGAGAAGATGCAAGGTAGTCT|GCTGCCA|GTCTACTCAATATGGCAGCCAACATGAGCCAGCCATCCGG ========== Event 1682 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: tatcagccgccgcacctggcTGAGAATGGACTTTGTAATAACTTTCCCTATGCAGGCCCATTTGAGATGAACGGGAGATGCCAGAAGTGCCCTTGTACTGATGCCCCCACCACCAAGCACTTTCCAGACCCAGGCTCAGCTTCATCTCCA------------------------------CCCCTGGGATCTCCAGGTTTAATACT Chimp: tatcagccgccgcatctggcTGAGAATGGACTTTGTAATAACTTTCCCTATGCGGGCCCATTTGAGATGAACGGGAGATGCCAGAAGTGCCCTTGTACTGATGCCCCCACCACCAAGCACTTTCCAGACCCAGGCTCAGCTTCGTCTCCA---------------CCTCTGCTCAGTCTACCCCTGGGATCTCCAGGTTTAATACT Gorilla: tatcagccgccgcacctggcTGAGAATGGACTTTGTAATAACTTTCCCTATGCAGGCCCATTTGAGATGAACGGGAGATGCCAGAAGTGCCCTTGTACTGATGCCCCCACCACCAAGCACTTTCCAGACCCAGGCTCAGCTTCATCTCCACCCCTGCTCAGTCTA---------------CCCCTGGGATCTCCAGGTTTAATACT ↑ 3 2 4 1 Human: tatcagccgccgcacctggcTGAGAATGGACTTTGTAATAACTTTCCCTATGCAGGCCCATTTGAGATGAACGGGAGATGCCAGAAGTGCCCTTGTACTGATGCCCCCACCACCAAGCACTTTCCAGACCCAGGCTCAGCTTCATCTCCA------------------------------CCCCTGGGATCTCCAGGTTTAATACT Cluster: [ ] Orangutan: tatcagccgccgcacctggctGAGAATGGACTTTGTAATACCTTTCCCTATGCAGGACCATTTGAGATGAACGGGAGATGCCAGAAGTGCCCTTGTACTGATGCCCCCACCACCAAGCACTCTCCAGACCCAGGCTCAGCTTTGTCTCCACCCCTGTTCAGTCTA---------------GCCCTGGGATCTCCAGGTTTAATACT Human > Gorilla --------------- chr20:42230588-42230592 Template switch process: F1: L CCACCAAGCACTTTCCAGACCCAGGCTCAGCTTCATCTCCACCCCTG 1 F3: 4 TCTACCCCTGGGATCTCCAGGTTTAATACTTTAGGGAAACTTCC R RF: CTGAGAATGGACTTTGTAATAACTTTCCCTATGCAGGCCCATTTGAGATGAACGGGAGATGCCAGAAGTGCCCTTGTACTGATGCCCCCACCACCAAGCACTTTCCAGACCCAGGCTCAGCTTCATCTCCACCCCTGGGATCTCCAGGTTTAATACTTTAGGGAAACTTCA RR: GACTCTTACCTGAAACATTATTGAAAGGGATACGTCCGGGTAAACTCTACTTGCCCTCTACGGTCTTCACGGGAACATGACTACGGGGGTGGTGGTTCGTGAAAGGTCTGGGTCCGAGTCGAAGTAGAGGTGGGGACCCTAGAGGTCCAAATTATGAAATCCCTTTGAAGT F2: 3 GACTC 2 Unidirectional alignment (log-probability: -38) GCACTTTCCAGACCCAGGCTCAGCTTCATCTCCacccctgctcagtctACCCCTGGGATCTCCAGGTTTAATACTTTAGGGAAAC GCACTTTCCAGACCCAGGCTCAGCTTCATCTCC---------------ACCCCTGGGATCTCCAGGTTTAATACTTTAGGGAAAC Template switch alignment (log-probability: -27.6) GCACTTTCCAGACCCAGGCTCAGCTTCATCTCCACCCCTG|CTCAG|TCtACCCCTGGGATCTCCAGGTTTAATACTTTAGGGAAAC GCACTTTCCAGACCCAGGCTCAGCTTCATCTCCACCCCTG|CTCAG|TCCACCCCTGGGATCTCCAGGTTTAATACTTTAGGGAAAC ========== Event 1683 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCCAGGTTTTCTCACTCCATGTCAAGGGCTAttcttcttctctctctctgtctctAACAATATTGCAACGATATTCTGAATTTAGTTGTAAAT-TTAGTTGGAATTTGATATAAGCTAT Chimp: AGCCAGGTTTTCTCACTCCATGTCAAGGGCTATTCTTCTTCTCTCTGTCTGTCTCTAACAATAATGCAATGATATTCTGAATTTAGTTGTAAATGACATTTGGAATTTGATATAAGCTAT Gorilla: AGCCAGATTTTCTCACTCCATGTCAAGGGCTATTCTTCT-TTCTCTCTCTGTCTCTAACAATAATGCAATGATATTCTGAATTTAGTTGTAAATGACATTTGGAATTTGATATAAGCTAT ↑ 3 2 1 4 Human: AGCCAGGTTTTCTCACTCCATGTCAAGGGCTAttcttcttctctctctctgtctctAACAATATTGCAACGATATTCTGAATTTAGTTGTAAAT-TTAGTTGGAATTTGATATAAGCTAT Cluster: [ ] Orangutan: agccaggttttctcactccatgtcaagggctattcttcttctctctctctgtctctAACAATAATGCAATGATATTCTGAATTTGGTTGTAAATGACATTTGGAATTTGATATAAGCTAT Human > Gorilla --------------- chr20:22071938-22071942 Template switch process: F1: L TCTAACAATAATGCAATGATATTCTGAATTTAGTTGTAAAT 1 F3: 4 TTGGAATTTGATATAAGCTATTTGATTTTCCTTCACAAAT R RF: ATGTCAAGGGCTATTCTTCTTCTCTCTCTCTGTCTCTAACAATATTGCAACGATATTCTGAATTTAGTTGTAAATTTAGTTGGAATTTGATATAAGCTATTTGATTTTCCTTCACAAAT RR: TACAGTTCCCGATAAGAAGAAGAGAGAGAGACAGAGATTGTTATAACGTTGCTATAAGACTTAAATCAACATTTAAATCAACCTTAAACTATATTCGATAAACTAAAAGGAAGTGTTTA F2: 3 TACAG 2 Unidirectional alignment (log-probability: -37.6) CTAACAATAaTGCAAtGATATTCTGAATTTAGTTGTAAAT---GacatTTGGAATTTGATATAAGCTATTTGATTTTCCTTCACAAAT CTAACAATATTGCAACGATATTCTGAATTTAGTTGTAAATTTAG----TTGGAATTTGATATAAGCTATTTGATTTTCCTTCACAAAT Template switch alignment (log-probability: -27.4) CTAACAATAaTGCAAtGATATTCTGAATTTAGTTGTAAAT|GACAT|TTGGAATTTGATATAAGCTATTTGATTTTCCTTCACAAAT CTAACAATATTGCAACGATATTCTGAATTTAGTTGTAAAT|GACAT|TTGGAATTTGATATAAGCTATTTGATTTTCCTTCACAAAT ========== Event 1684 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTGATGCTTCTGATGTGTAGCTTACTTAGGAGCATTCCTAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATG Chimp: TCTGATGCTTCTGATGTGTAGTTTACTTAGGAGCATTCCTAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATG ↑ 1 3 4 2 Gorilla: TCTGATGCTTCTGATGTGTAGTTTAATGTGCAGCATTAGGAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATG ↓ 1 3 4 2 Human: TCTGATGCTTCTGATGTGTAGCTTACTTAGGAGCATTCCTAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATG Cluster: [ ] Orangutan: TCTGATGCTTCTGATGTGTAGTTTACTTAGGAGCATTCCTAATGCTCTTAAGTAAGTTGATTTGAAAG----AGTC Gorilla > Human --------------- chr20:62147572-62147590 Template switch process: F1: L AGTCACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAG 1 F3: 4 AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT R RF: AGTCACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTAATGTGCAGCATTAGGAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT RR: TCAGTGAATGTGTCTCGGACAGACTACGAAGACTACACATCAAATTACACGTCGTAATCCTTACGAGGATTCATTCAACTAAACTTTATTTGTTACCAAA F2: 3 TCCTTACGAGGATTCATTC 2 Unidirectional alignment (log-probability: -45.2) GTCACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGcTTA---------cTTAGGagcattcctAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT GTCACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTAATGTGCAGCATTAGG---------AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT Template switch alignment (log-probability: -18.2) GTCACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAG|CTTACTTAGGAGCATTCCT|AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT GTCACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAG|CTTACTTAGGAGCATTCCT|AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT Gorilla > Chimp --------------- chr20:64370657-64370671 Template switch process: F1: L ACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTA 1 F3: 4 AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT R RF: ACTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTAATGTGCAGCATTAGGAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT RR: TGAATGTGTCTCGGACAGACTACGAAGACTACACATCAAATTACACGTCGTAATCCTTACGAGGATTCATTCAACTAAACTTTATTTGTTACCAAA F2: 3 TCCTTACGAGGATTC 2 Unidirectional alignment (log-probability: -39.6) CTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTA---------cTTAGGagcattcctAATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT CTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTAATGTGCAGCATTAGG---------AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT Template switch alignment (log-probability: -17.6) CTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTA|CTTAGGAGCATTCCT|AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT CTTACACAGAGCCTGTCTGATGCTTCTGATGTGTAGTTTA|CTTAGGAGCATTCCT|AATGCTCCTAAGTAAGTTGATTTGAAATAAACAATGGTTT ========== Event 1685 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: TAGAGAGGACACATGTGGGTGTTTAAGGAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGGTGCACTCTTTCAAAAGCAAGTACTGAGACCTCTTTTTGGATCAGACTGATTCATGCAGTTTTTAAGGGGATGCCTCAAGGTGGAACTGACTCAGTGGTGCTTTGTTCT ↓ 1 4 3 2 Chimp: TAGAGAGGACACATGTGGGTG-TCAGTGAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGGTGCCCTCTTTCAAAAGCAAGTACTGAGACCTCTTTTTGGATCAGACTGATTCATGCAGTTTTTAAGGGGATGCCTCAAGGTGGAACTGACTCAGTGGTGCTTTGTTCT Gorilla: TAGAGAGGACACTTGTGGGTG-TCAGTGAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGGTGCACTCTTTCAAAAGCAAATACTGAGACCTCTTTTTGGATCAGACTGATTCATGCAGTTTTTAAGGGGATGCCTCAAGGTGGAACTGACTCAGTGGTGCTTTGTTCT Human: TAGAGAGGACACATGTGGGTGTTTAAGGAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGGTGCACTCTTTCAAAAGCAAGTACTGAGACCTCTTTTTGGATCAGACTGATTCATGCAGTTTTTAAGGGGATGCCTCAAGGTGGAACTGACTCAGTGGTGCTTTGTTCT Cluster: [ ] Orangutan: TAGAGAGGACACCTGTGGGTG-TCAGTGAAGTCCCTCTATTATGTCTCCAATGGTCAGTGGGCCTGATGCACTCTTTCAAAAGCAAGTACTGAGACCTCTTTTTAGATCAGACTGATTCATGCAGTTTTTAAGGGGATGCCTCAAGGTGGAACTGACTCAATGGTGCTTTGTTCT Human > Chimp ------------- chr20:24302923-24302926 Template switch process: F1: L GTATACAGTGAGATGTGTGGTAGAGAGGACACATGTGGGTGT 1 F3: 4 GAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGG R RF: ATATACAGTGAGATGTGTGGTAGAGAGGACACATGTGGGTGTTTAAGGAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGGTGCACTCTTTCAAAAGCAAGTACTGAGACCTCTTTTTGGATCAGACTGATTCATGCAGTTTTTAAGGGGATGCCTCAAGGTGGAACTG RR: TATATGTCACTCTACACACCATCTCTCCTGTGTACACCCACAAATTCCTTCGGGGAGGTCATACAGAGGTTACCAGTCACCCGGACCACGTGAGAAAGTTTTCGTTCATGACTCTGGAGAAAAACCTAGTCTGACTAAGTACGTCAAAAATTCCCCTACGGAGTTCCACCTTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -31.7) ATACAGTGAGATGTGTGGTAGAGAGGACACATGTGGGTGTcagT----GAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGG ATACAGTGAGATGTGTGGTAGAGAGGACACATGTGGGTGT---TTAAGGAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGG Template switch alignment (log-probability: -21.8) ATACAGTGAGATGTGTGGTAGAGAGGACACATGTGGGTGT|CAGT|GAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGG ATACAGTGAGATGTGTGGTAGAGAGGACACATGTGGGTGT|CAGT|GAAGCCCCTCCAGTATGTCTCCAATGGTCAGTGGGCCTGG ========== Event 1686 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGACAATGGTTCAAAATCCCTGCCATCTGGCAGGCCTACCACATTTCTTCTGAAT ↑ 3 2 1 4 Chimp: CAGACAATGGTTCAAAATCCCTGCCATCCAGTATCCCTACCACATTTCTTCTGAAT ↓ 3 2 1 4 Gorilla: CAGACAATGGTTCAAAATCCCTGCCATCTGGCAGGCCTACCACATTTCTTCTGAAT Human: CAGACAATGGTTCAAAATCCCTGCCATCTGGCAGGCCTACCACATTTCTTCTGAAT Cluster: [ ] Orangutan: CAGACAATGGTTCAAAATCCCTGCCATCTGGCAGGCCTACCACATTTCTTCTGAAT Chimp > Human ------------- chr20:24833871-24833877 Template switch process: F1: L TGCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATC 1 F3: 4 CCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA R RF: TGCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATCCAGTATCCCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA RR: ACGCACGTCCTTCGTCTGTTACCAAGTTTTAGGGACGGTAGGTCATAGGGATGGTGTAAAGAAGACTTACGTCACTAGATTCGACATT F2: 3 GGACGGT 2 Unidirectional alignment (log-probability: -30.7) GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATCtgGcAggCCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATCCAGTATCCCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA Template switch alignment (log-probability: -16.2) GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATC|TGGCAGG|CCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATC|TGGCAGG|CCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA Chimp > Gorilla --------------- chr20:25151346-25151352 Template switch process: F1: L TGCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATC 1 F3: 4 CCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA R RF: TGCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATCCAGTATCCCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA RR: ACGCACGTCCTTCGTCTGTTACCAAGTTTTAGGGACGGTAGGTCATAGGGATGGTGTAAAGAAGACTTACGTCACTAGATTCGACATT F2: 3 GGACGGT 2 Unidirectional alignment (log-probability: -28.8) GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATCtgGcAggCCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATCCAGTATCCCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA Template switch alignment (log-probability: -16.6) GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATC|TGGCAGG|CCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA GCGTGCAGGAAGCAGACAATGGTTCAAAATCCCTGCCATC|TGGCAGG|CCTACCACATTTCTTCTGAATGCAGTGATCTAAGCTGTAA ========== Event 1687 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GCGCAGGATCCTTGG-GGCCG-CGCACCCTGCAGCGGcccctcccctcccctcc ↓ 13 24 ↑ 13 24 Chimp: GCGCAGGATCCTTGG-GGCCGCTGCAGGGTG-CGCGGcccctcccctcccctcc Gorilla: GCGCAGGATCCTTGG-GGCCGCTGCAGGGTG-CGCGGcccctcccctcccctcc ↓ 13 24 ↑ 13 24 Human: GCGCAGGATCCTTGG-GGCCG-CGCACCCTGCAGCGGcccctcccctcccctcc Cluster: [ ] Orangutan: GCTCAGGATCCTTGGGGGCCGCTGAAGGGTG-CGCGGcccctcccctccc---- Chimp > Human ------------- chr20:61275788-61275797 Template switch process: F1: L ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC 1 F3: 4 GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA R RF: ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGCTGCAGGGTGCGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA RR: TAAGAAACGCCCCAAGCCGTCCGCGTCCTAGGAACCCCGGCGACGTCCCACGCGCCGGGGAGGGGAGGGGAGGGGGGAGGGTGGACACCCTT F2: 3 ACGTCCCACG 2 Unidirectional alignment (log-probability: -30.1) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGcgcaccCTGCA------GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCG------CTGCAGGGTGCGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Template switch alignment (log-probability: -16.5) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|GCACCCTGCA|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|GCACCCTGCA|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Human > Chimp ------------- chr20:63505618-63505627 Template switch process: F1: L ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC 1 F3: 4 GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA R RF: ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGCGCACCCTGCAGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA RR: TAAGAAACGCCCCAAGCCGTCCGCGTCCTAGGAACCCCGGCGCGTGGGACGTCGCCGGGGAGGGGAGGGGAGGGGGGAGGGTGGACACCCTT F2: 3 CGTGGGACGT 2 Unidirectional alignment (log-probability: -30.1) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCG------CTGCAgggtgcGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGCGCACCCTGCA------GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Template switch alignment (log-probability: -16.5) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|TGCAGGGTGC|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|TGCAGGGTGC|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Gorilla > Human --------------- chr20:61275788-61275797 Template switch process: F1: L ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC 1 F3: 4 GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA R RF: ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGCTGCAGGGTGCGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA RR: TAAGAAACGCCCCAAGCCGTCCGCGTCCTAGGAACCCCGGCGACGTCCCACGCGCCGGGGAGGGGAGGGGAGGGGGGAGGGTGGACACCCTT F2: 3 ACGTCCCACG 2 Unidirectional alignment (log-probability: -29.6) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGcgcaccCTGCA------GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCG------CTGCAGGGTGCGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Template switch alignment (log-probability: -17) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|GCACCCTGCA|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|GCACCCTGCA|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Human > Gorilla --------------- chr20:60180505-60180514 Template switch process: F1: L ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC 1 F3: 4 GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA R RF: ATTCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGCGCACCCTGCAGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA RR: TAAGAAACGCCCCAAGCCGTCCGCGTCCTAGGAACCCCGGCGCGTGGGACGTCGCCGGGGAGGGGAGGGGAGGGGGGAGGGTGGACACCCTT F2: 3 CGTGGGACGT 2 Unidirectional alignment (log-probability: -29.6) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCG------CTGCAgggtgcGCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGCGCACCCTGCA------GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA Template switch alignment (log-probability: -17) TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|TGCAGGGTGC|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA TCTTTGCGGGGTTCGGCAGGCGCAGGATCCTTGGGGCCGC|TGCAGGGTGC|GCGGCCCCTCCCCTCCCCTCCCCCCTCCCACCTGTGGGAA ========== Event 1688 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAATTACCTATTTCTTCCAAGCACTTATCCTCTCCTTGCAATACTA Chimp: GTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAATAGGTAATTTCTTCCAAGCACTTATCCTCTCCTTGCAATACTA Gorilla: GTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAATAGGTAATTTCTTCCAAGCACCTATCCTCTCCTTGCAATACTA ↓ 3 1 2 4 Human: GTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAATTACCTATTTCTTCCAAGCACTTATCCTCTCCTTGCAATACTA Cluster: [ ] Orangutan: TAATTTCTAGCAGAGGA--GGAGCTTTGAAAAAAT-------------AAANNNNNNNNNNTCTCCTTGCAATACTA Gorilla > Human --------------- chr20:32461772-32461792 Template switch process: F1: L ACAGTAGTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAAT 1 F3: 4 TATCCTCTCCTTGCAATACTACTG R RF: ACAGTAGTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAATAGGTAATTTCTTCCAAGCACCTATCCTCTCCTTGCAATACTACTG RR: TGTCATCATAACGTTCCTCTCCTATTCACGAACCTTCTTTATCCATTAAAGAAGGTTCGTGGATAGGAGAGGAACGTTATGATGAC F2: 3 TCACGAACCTTCTTTATCCAT 2 Unidirectional alignment (log-probability: -30.6) CAGTAGTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAAT---TAcctATTTCTTCCAAGCACtTATCCTCTCCTTGCAATACTACTG CAGTAGTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAATAGGTA---ATTTCTTCCAAGCACCTATCCTCTCCTTGCAATACTACTG Template switch alignment (log-probability: -18) CAGTAGTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAAT|TACCTATTTCTTCCAAGCACT|TATCCTCTCCTTGCAATACTACTG CAGTAGTATTGCAAGGAGAGGATAAGTGCTTGGAAGAAAT|TACCTATTTCTTCCAAGCACT|TATCCTCTCCTTGCAATACTACTG ========== Event 1689 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GCTAGGAAAGACGGCCTGTGTTCTAGGCCCTCAGAAGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGC ↑ 4 3 1 2 Chimp: GCTAGGAAAGACGGCCTGTGT-----------------TCTAAGGGCCATCTTGGTTTCTCCCCCAGC ↓ 4 3 1 2 Gorilla: GCTAGGAAAGACGGCCTGTGTTCTAGGCCCTCAGAAGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGC Human: GCTAGGAAAGACGGCCTGTGTTCTAGGCCCTCAGAAGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGC Cluster: [ ] Orangutan: GCTAGGAAAGATGGCCTGTGTTCTAGGCCCTCAGAAGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGC Chimp > Human ------------- chr20:31991366-31991376 Template switch process: F1: L TGGCGGCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTA 1 F3: 4 GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCTCT R RF: TGGCGGCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCTCT RR: ACCGCCGTCACCCCTACCTCCGATCCTTTCTGCCGGACACAAGATTCCCGGTAGAACCAAAGAGGGGGTCGGGGGTGGAGA F2: 3 AAGACTCCCGG 2 Unidirectional alignment (log-probability: -35.4) GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTctaggccctcagaagttCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTT-----------------CTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT Template switch alignment (log-probability: -22.8) GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTA|GGCCCTcAGAA|GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTA|GGCCCTTAGAA|GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT Chimp > Gorilla --------------- chr20:30659943-30659953 Template switch process: F1: L TGGCGGCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTA 1 F3: 4 GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCTCT R RF: TGGCGGCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCTCT RR: ACCGCCGTCACCCCTACCTCCGATCCTTTCTGCCGGACACAAGATTCCCGGTAGAACCAAAGAGGGGGTCGGGGGTGGAGA F2: 3 AAGACTCCCGG 2 Unidirectional alignment (log-probability: -35.3) GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTgttctaggccctcagaaGTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGT-----------------GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT Template switch alignment (log-probability: -22.8) GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTA|GGCCCTcAGAA|GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT GCAGTGGGGATGGAGGCTAGGAAAGACGGCCTGTGTTCTA|GGCCCTTAGAA|GTTCTAAGGGCCATCTTGGTTTCTCCCCCAGCCCCCACCT ========== Event 1690 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: ATCTCTTGCCTCTGAACAACAATGCTGTTGTTCACGTATATGCATACGTCTTAAGGGACAGGCCATGCAACcacccattcaacactta ↓ 1 4 3 2 Chimp: ATCTCTTGCCTCTGAACAACA--------------GC----ATATACATCTTAAGGGACAGGCCATGCAACcacccattcaacactta Gorilla: ATCTCTTGCCTCTGAACAACA--------------GC----ATATACGTCTTAAGGGACAGGCCATGCAACcacccattcaacactta Human: ATCTCTTGCCTCTGAACAACAATGCTGTTGTTCACGTATATGCATACGTCTTAAGGGACAGGCCATGCAACcacccattcaacactta Cluster: [ ] Orangutan: ATCTCTTGCCTCTGAACAACA--------------GC----ATATACGTCTTAAGGGACAGGCCATGCAACcacccattcaacactta Human > Chimp ------------- chr20:33223760-33223763 Template switch process: F1: L TGGGGAGGCCAGCCCCCAGAATCTCTTGCCTCTGAACAACA 1 F3: 4 ATACATCTTAAGGGACAGGCCATGCAACCACCCATTCAACACTTA R RF: TGGGGAGGCCAGCCCCCAGAATCTCTTGCCTCTGAACAACAATGCTGTTGTTCACGTATATGCATACGTCTTAAGGGACAGGCCATGCAACCACCCATTCAACACTTA RR: ACCCCTCCGGTCGGGGGTCTTAGAGAACGGAGACTTGTTGTTACGACAACAAGTGCATATACGTATGCAGAATTCCCTGTCCGGTACGTTGGTGGGTAAGTTGTGAAT F2: 3 TACG 2 Unidirectional alignment (log-probability: -31.1) GGGGAGGCCAGCCCCCAGAATCTCTTGCCTCTGAACAACAgcAT--------------------ATACaTCTTAAGGGACAGGCCATGCAACCACCCATTCAAC GGGGAGGCCAGCCCCCAGAATCTCTTGCCTCTGAACAACA--ATGCTGTTGTTCACGTATATGCATACGTCTTAAGGGACAGGCCATGCAACCACCCATTCAAC Template switch alignment (log-probability: -21.9) GGGGAGGCCAGCCCCCAGAATCTCTTGCCTCTGAACAACA|GCAT|ATACaTCTTAAGGGACAGGCCATGCAACCACCCATTCAAC GGGGAGGCCAGCCCCCAGAATCTCTTGCCTCTGAACAACA|GCAT|ATACGTCTTAAGGGACAGGCCATGCAACCACCCATTCAAC ========== Event 1691 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CGCAAGCAACAGGTTTAATGCA--------TCTCCAGGGGAAGTCCAGGACTGAAACTGCTA Chimp: CGTAAGCAACAGGTTTAATGCA--------TCTCCAGGGGAAGTCCAAGACTGAAACTGCTA Gorilla: CGCAAGCAACAGGTTTAATGCTTCCCCTGGACTCCAGGGGAAGTCCAGGACTGAAACTGCTA ↑ 1 43 2 Human: CGCAAGCAACAGGTTTAATGCA--------TCTCCAGGGGAAGTCCAGGACTGAAACTGCTA Cluster: [ ] Orangutan: CGCAAGCAACAGGTTTAATGCA--------CCTCCAGGGGAAGTCCAGGACCGAAACTGCTA Human > Gorilla --------------- chr20:30366168-30366177 Template switch process: F1: L TAATGGATGACACAGGGCACCGCAAGCAACAGGTTTAATGC 1 F3: 4 CTCCAGGGGAAGTCCAGGACTGAAACTGCTAATGCGTGAT R RF: TAATGGATGACACAGGGCACCGCAAGCAACAGGTTTAATGCATCTCCAGGGGAAGTCCAGGACTGAAACTGCTAATGCGTGAT RR: ATTACCTACTGTGTCCCGTGGCGTTCGTTGTCCAAATTACGTAGAGGTCCCCTTCAGGTCCTGACTTTGACGATTACGCACTA F2: 3 AGGTCCCCTT 2 Unidirectional alignment (log-probability: -27.9) AATGGATGACACAGGGCACCGCAAGCAACAGGTTTAATGCtTcccctggaCTCCAGGGGAAGTCCAGGACTGAAACTGCTAATGCGTGAT AATGGATGACACAGGGCACCGCAAGCAACAGGTTTAATGCAT--------CTCCAGGGGAAGTCCAGGACTGAAACTGCTAATGCGTGAT Template switch alignment (log-probability: -17) AATGGATGACACAGGGCACCGCAAGCAACAGGTTTAATGC|TTCCCCTGGA|CTCCAGGGGAAGTCCAGGACTGAAACTGCTAATGCGTGAT AATGGATGACACAGGGCACCGCAAGCAACAGGTTTAATGC|TTCCCCTGGA|CTCCAGGGGAAGTCCAGGACTGAAACTGCTAATGCGTGAT ========== Event 1692 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTGGTGCAGTTCCCTGATGAGGCTCCGGGTCCAGGCCCTGCCCGCCTTCCAACCCACATCCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTA-AATTAGCCTCCAAATCTCAAATCTCATTTTTGGCTTCA ↓ 3 2 1 4 Chimp: CCTGGTGCAGTTCCCTGATGAGGCTCCGGGTCCAGGCCCTGCCCACCTTCCAACCCACATCCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAAAGGAGCCTCCAAAT-------CTCATTTTTGGCTTCA Gorilla: CCTGGTGCAGTTCCCTGATGAGGCTCCGGGTCCAGGCCCTGCCCACCTTCCAACCCACATCCCCTACATCCCAAAGAGGAGACATCCGAGTCCTCTAAAAGTAGCCTCCAAATCTCAAATCTCATTTTTGGCTTCA Human: CCTGGTGCAGTTCCCTGATGAGGCTCCGGGTCCAGGCCCTGCCCGCCTTCCAACCCACATCCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTA-AATTAGCCTCCAAATCTCAAATCTCATTTTTGGCTTCA Cluster: [ ] Orangutan: Human > Chimp ------------- chr20:34113464-34113471 Template switch process: F1: L ACATCCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAAA 1 F3: 4 CAAATCTCATTTTTGGCTTCAATGATA R RF: GAGGCTCCGGGTCCAGGCCCTGCCCGCCTTCCAACCCACATCCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAATTAGCCTCCAAATCTCAAATCTCATTTTTGGCTTCAATGATA RR: CTCCGAGGCCCAGGTCCGGGACGGGCGGAAGGTTGGGTGTAGGGGATGTAGGGTTTCTCCTCTGTAGGTTCAGGAGATTTAATCGGAGGTTTAGAGTTTAGAGTAAAAACCGAAGTTACTAT F2: 3 CTCCGAGG 2 Unidirectional alignment (log-probability: -34.7) CCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAAaggagcctc---------------CAAATCTCATTTTTGGCTTCAATGATA CCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAA---------TTAGCCTCCAAATCTCAAATCTCATTTTTGGCTTCAATGATA Template switch alignment (log-probability: -22.1) CCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAAa|GGAGCCTC|CAAATCTCATTTTTGGCTTCAATGATA CCCCTACATCCCAAAGAGGAGACATCCAAGTCCTCTAAAT|GGAGCCTC|CAAATCTCATTTTTGGCTTCAATGATA ========== Event 1693 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATAAGAGCACACATTTTCCC--------CGTACATGTGACTATGCACACACACTCACATGCATGTATCAAC----ACAACCCTCATCCACACATGTGCATATGCAAATTCCTTCATGCG Chimp: CATAAGAGCACACATTTTCCC--------TGTACATGTGACTATGCACACACACTCACATGCATGTATCAAC----ACAACCCTCATCCACACATGTGCATATGCAAATTCCTTCATGCG Gorilla: CATAAGAGCACACATTTTCCCTGCACATGTGTACATGTGACTATGcacacacactcacatgcacgtatcaacacacacaaccctcatccacacaTGTGCATATGCAAATTCCTTCATGTG ↑ 1 4 3 2 Human: CATAAGAGCACACATTTTCCC--------CGTACATGTGACTATGCACACACACTCACATGCATGTATCAAC----ACAACCCTCATCCACACATGTGCATATGCAAATTCCTTCATGCG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr20:31663912-31663920 Template switch process: F1: L ATTTCATGTCCACACTCACACATAAGAGCACACATTTTCCC 1 F3: 4 GTACATGTGACTATGCACACACACTCACATGCACGTATCA R RF: ATTTCATGTCCACACTCACACATAAGAGCACACATTTTCCCCGTACATGTGACTATGCACACACACTCACATGCATGTATCAACACAACCCTCATCCACACATGTGCA RR: TAAAGTACAGGTGTGAGTGTGTATTCTCGTGTGTAAAAGGGGCATGTACACTGATACGTGTGTGTGAGTGTACGTACATAGTTGTGTTGGGAGTAGGTGTGTACACGT F2: 3 TGTACACGT 2 Unidirectional alignment (log-probability: -33.4) TTTCATGTCCACACTCACACATAAGAGCACACATTTTCCCtgcacatgtGTACATGTGACTATGCACACACACTCACATGCAcGTATCA TTTCATGTCCACACTCACACATAAGAGCACACATTTTCCC--------CGTACATGTGACTATGCACACACACTCACATGCATGTATCA Template switch alignment (log-probability: -22.4) TTTCATGTCCACACTCACACATAAGAGCACACATTTTCCC|TGCACATGT|GTACATGTGACTATGCACACACACTCACATGCAcGTATCA TTTCATGTCCACACTCACACATAAGAGCACACATTTTCCC|TGCACATGT|GTACATGTGACTATGCACACACACTCACATGCATGTATCA ========== Event 1694 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCCAGAGTTTCTAAAATTC--CT--CGAGTGGCTCTCCCAGCAAGCAATTTTCTGACTTCTGCCTATTCCATTGACTGGGAAGTCACT---------------------------------------------ACttttttttt---tttttttttttgagatggaatctcactctattgcccagactggagtgcagtggtgcgatctcggctccctgcaacctctgcctccagagttcaagcgattctcctgcctcagcct Chimp: TGCCAGAGTTTCTAAAATTCTAGTCAGGCGTGGCTCTCCCAGCA---------------------------------------------AGCAATTTTCTGACTTCTGCCTATTCCATTGACTGGGAAGTCACTACttttttttt--ttttttttttttgagatggaatctcactctattgcccagactggagtgcagtggtgcgatctcggctccctgcaacctctgcctccagagttcaagcgattctcctgcttcagcct ↓ 1 4 3 2 Gorilla: TGCCAGAGTTTCTAAAATTC--CT--TGAGTGGCTCTCCCAGCAAGCAATCTTCTGACTTCTGCCTATTCCATTGACTGGGAAGTCACT---------------------------------------------ACttttttttt---tttttttttttgagatggaatctcactctattgcccagactggagtgcagtgttgtgatctcggctccctgcaacctctgcctccagagttcaagcgattctcctgcctcagcct Human: TGCCAGAGTTTCTAAAATTC--CT--CGAGTGGCTCTCCCAGCAAGCAATTTTCTGACTTCTGCCTATTCCATTGACTGGGAAGTCACT---------------------------------------------ACttttttttt---tttttttttttgagatggaatctcactctattgcccagactggagtgcagtggtgcgatctcggctccctgcaacctctgcctccagagttcaagcgattctcctgcctcagcct Cluster: [ ] Orangutan: TGCCAGAGTTTCTAAAATTC--CT--TGAGTGGCTCTCCCAGCAAGCAATTTTCTGACCTCCGCTTATTCCATTGACTGGAAAGTCACT---------------------------------------------ACttttttttttt-tttttttttgtgagatagaatctcactctattgcccaggctggagtgcagtggtgcaatctcagctcactgcaacctctgcctccagagttcaagcgattcttctgcctcagcct Chimp > Gorilla --------------- chr20:31887173-31887177 Template switch process: F1: L CAGAGTTTCTAAAATTC 1 F3: 4 GTGGCTCTCCCAGCAAGCAATCTTCTGACTTCTGCCTATTCCATTGACTGGGAAGTCACTAC-TTTTTTTTTTTTTTTTTTTTGAGATGGAATCTCACTC R RF: CAGAGTTTCTAAAATTCTAGTCAGGCGTGGCTCTCCCAGCAAGCAATTTTCTGACTTCTGCCTATTCCATTGACTGGGAAGTCACTACTTTTTTTTTTTTTTTTTTTTTGAGATGGAATCTCACTCTATTGCCCAGACTGGAGTGCAGTGGTGCGATCTCGGCTCCCTGCAACCTCTGCCTCCAGAGTTCAAG RR: GTCTCAAAGATTTTAAGATCAGTCCGCACCGAGAGGGTCGTTCGTTAAAAGACTGAAGACGGATAAGGTAACTGACCCTTCAGTGATGAAAAAAAAAAAAAAAAAAAAACTCTACCTTAGAGTGAGATAACGGGTCTGACCTCACGTCACCACGCTAGAGCCGAGGGACGTTGGAGACGGAGGTCTCAAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -42.6) CAGAGTTTCTAAAATTC--------CttgaGTGGCTCTCCCAGCAAGCAATcTTCTGACTTCTGCCTATT CAGAGTTTCTAAAATTCTAGTCAGGC----GTGGCTCTCCCAGCAAGCAATTTTCTGACTTCTGCCTATT Template switch alignment (log-probability: -32.5) CAGAGTTTCTAAAATTC|CTTGA|GTGGCTCTCCCAGCAAGCAATcTTCTGACTTCTGCCTATT CAGAGTTTCTAAAATTC|CTTGA|GTGGCTCTCCCAGCAAGCAATTTTCTGACTTCTGCCTATT ========== Event 1695 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GTTCTCGGCAAATATCTCACTTGAATTTGACCTTGAATTGAGACCGTGAGTCATACAGAAGCAGAATCTGAGA ↑ 4 1 3 2 Chimp: GTTCTCGGCAAATATCTCACTT------------GAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGAGA ↓ 4 1 3 2 Gorilla: GTTCTCGGCAAACATCTCACTTGAATTTGACCTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGAGA Human: GTTCTCGGCAAATATCTCACTTGAATTTGACCTTGAATTGAGACCGTGAGTCATACAGAAGCAGAATCTGAGA Cluster: [ ] Orangutan: GTTCTCGGCAAACATCTCACTTGAATTTGACCTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGAGA Chimp > Human ------------- chr20:33224445-33224448 Template switch process: F1: L TATCATTCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAATT 1 F3: 4 CTTGAATTGAGACCGTGAGTCATACAGAAGCAGAATCTGAGAG R RF: TGTCATTCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGAGAG RR: ACAGTAAGGTATTCCTCACCAAGAGCCGTTTATAGAGTGAACTTAACTCTGGCACTCAGTATGTCTTCGTCGTAGACTCTC F2: 3 CAGT 2 Unidirectional alignment (log-probability: -40.2) TCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAatttgaccttgaATTGAGACCGTGAGTCATACAGAAGCAGaATCTGA TCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGA------------ATTGAGACCGTGAGTCATACAGAAGCAGCATCTGA Template switch alignment (log-probability: -27.9) TCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAATT|TGAC|CTTGAATTGAGACCGTGAGTCATACAGAAGCAGaATCTGA TCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAATT|TGAC|CTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGA Chimp > Gorilla --------------- chr20:31905019-31905022 Template switch process: F1: L TGTCATTCCATAAGGAGTGGTTCTCGGCAAACATCTCACTTGAATT 1 F3: 4 CTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGAGAG R RF: TGTCATTCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGAGAG RR: ACAGTAAGGTATTCCTCACCAAGAGCCGTTTATAGAGTGAACTTAACTCTGGCACTCAGTATGTCTTCGTCGTAGACTCTC F2: 3 CAGT 2 Unidirectional alignment (log-probability: -33.7) TCCATAAGGAGTGGTTCTCGGCAAAcATCTCActtgaatttgacCTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGA TCCATAAGGAGTGGTTCTCGGCAAATATCTCA------------CTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGA Template switch alignment (log-probability: -21.9) TCCATAAGGAGTGGTTCTCGGCAAAcATCTCACTTGAATT|TGAC|CTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGA TCCATAAGGAGTGGTTCTCGGCAAATATCTCACTTGAATT|TGAC|CTTGAATTGAGACCGTGAGTCATACAGAAGCAGCATCTGA ========== Event 1696 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCACGCCAGCTTCCTCTGCC--CGTATCTCCACATCATGTCCACATGCCACCTAACTgtt Chimp: CCCACGCCAGCTTCCTCTGCC--CATATCTCCACATCATGTCCACATGCCACCTAACTgtt Gorilla: CCCATGCCAGCTTCCTCTGCCACATCATGTCCACATCATGTCCACATGCCACCTAACTgtt ↑ 1 4 3 2 Human: CCCACGCCAGCTTCCTCTGCC--CGTATCTCCACATCATGTCCACATGCCACCTAACTgtt Cluster: [ ] Orangutan: CCCCCGCCAGCTTCCTCTGCC--CATGTCTCCACATCATGTCCACATGCCACCTAACTgtt Human > Gorilla --------------- chr20:30660460-30660468 Template switch process: F1: L CACGTTTCCCTCTCTCCCCTCCCATGCCAGCTTCCTCTGCC 1 F3: 4 CCACATCATGTCCACATGCCACCTAACTGTTTGGGTTCC R RF: CACGTTTCCCTCTCTCCCCTCCCACGCCAGCTTCCTCTGCCCGTATCTCCACATCATGTCCACATGCCACCTAACTGTTTGGGTTCC RR: GTGCAAAGGGAGAGAGGGGAGGGTGCGGTCGAAGGAGACGGGCATAGAGGTGTAGTACAGGTGTACGGTGGATTGACAAACCCAAGG F2: 3 TGTACTACA 2 Unidirectional alignment (log-probability: -37.6) ACGTTTCCCTCTCTCCCCTCCCAtGCCAGCTTCCTCTGCCacatC--ATgTCCACATCATGTCCACATGCCACCTAACTGTTTGGGTTCC ACGTTTCCCTCTCTCCCCTCCCACGCCAGCTTCCTCTGCC----CGTATCTCCACATCATGTCCACATGCCACCTAACTGTTTGGGTTCC Template switch alignment (log-probability: -27.9) ACGTTTCCCTCTCTCCCCTCCCAtGCCAGCTTCCTCTGCC|ACATcATGT|CCACATCATGTCCACATGCCACCTAACTGTTTGGGTTCC ACGTTTCCCTCTCTCCCCTCCCACGCCAGCTTCCTCTGCC|ACATGATGT|CCACATCATGTCCACATGCCACCTAACTGTTTGGGTTCC ========== Event 1697 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGTGAGGGCTGGTCCCAAGGCATCTGGGTAGATGCCACGGGCCCAGGCCATGC Chimp: TGGTGAAGGCTGGTCCCAAGG-CTCTACCCAGATGCCACGGGCCCAGGCCGTGC Gorilla: TGGTGAGGGCTGGTCCCAAGG-CTCTACCCAGATGCCACGGGCCCAGGCCATGC ↓ 1 3 4 2 Human: TGGTGAGGGCTGGTCCCAAGGCATCTGGGTAGATGCCACGGGCCCAGGCCATGC Cluster: [ ] Orangutan: TGGTGAGGGCTGGTCCCAAGG-CTCTACCCAGATGCCACGGGCCCAGGCCATGC Gorilla > Human --------------- chr20:60790584-60790591 Template switch process: F1: L GCCTTGAAATGACACATCATTGGTGAGGGCTGGTCCCAAGGC 1 F3: 4 AGATGCCACGGGCCCAGGCCATGCAGTCGAAGCTGTGGAC R RF: GCCTTGAAATGACACATCATTGGTGAGGGCTGGTCCCAAGGCTCTACCCAGATGCCACGGGCCCAGGCCATGCAGTCGAAGCTGTGGAC RR: CGGAACTTTACTGTGTAGTAACCACTCCCGACCAGGGTTCCGAGATGGGTCTACGGTGCCCGGGTCCGGTACGTCAGCTTCGACACCTG F2: 3 TGGGTCTA 2 Unidirectional alignment (log-probability: -31) CTTGAAATGACACATCATTGGTGAGGGCTGGTCCCAAGGCatctgggT------AGATGCCACGGGCCCAGGCCATGCAGTCGAAGCTGTGGAC CTTGAAATGACACATCATTGGTGAGGGCTGGTCCCAAGGC-------TCTACCCAGATGCCACGGGCCCAGGCCATGCAGTCGAAGCTGTGGAC Template switch alignment (log-probability: -16.8) CTTGAAATGACACATCATTGGTGAGGGCTGGTCCCAAGGC|ATCTGGGT|AGATGCCACGGGCCCAGGCCATGCAGTCGAAGCTGTGGAC CTTGAAATGACACATCATTGGTGAGGGCTGGTCCCAAGGC|ATCTGGGT|AGATGCCACGGGCCCAGGCCATGCAGTCGAAGCTGTGGAC ========== Event 1698 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCCTGGTAAAGAAGCTGCCTTC-------TCCTT-----AGGATGAGCCTTTCTTTCTCCCCAGCATCAC Chimp: GGCCTGGTAAAGAAGCTGCCTTC-------TCCTT-----AGGATGAGCCTTTCTTTCTCCCCAGCATCAC ↓ 31 4 2 Gorilla: GGCCTGGTAAAGAAGCTGCCTCCTAGGCTCATCCTATGGAGGGATGAGCCTTTCTTTCTCCCCAGCATCAC Human: GGCCTGGTAAAGAAGCTGCCTTC-------TCCTT-----AGGATGAGCCTTTCTTTCTCCCCAGCATCAC Cluster: [ ] Orangutan: GGCCTGGTAAAGAAGCTGCCTCC-------TCCCT-----AGGATGAGCCTTTCCTTCTCCCCAGCATCAC Chimp > Gorilla --------------- chr20:34925068-34925084 Template switch process: F1: L TGAGAGCCATGGCATTCAGGGGCCTGGTAAAGAAGCTGCCTCCT 1 F3: 4 GGATGAGCCTTTCTTTCTCCCCAGCATCACCACATCACTA R RF: TGAGAGCCATGGCATTCAGGGGCCTGGTAAAGAAGCTGCCTTCTCCTTAGGATGAGCCTTTCTTTCTCCCCAGCATCACCACATCACTA RR: ACTCTCGGTACCGTAAGTCCCCGGACCATTTCTTCGACGGAAGAGGAATCCTACTCGGAAAGAAAGAGGGGTCGTAGTGGTGTAGTGAT F2: 3 GAGGTATCCTACTCGGA 2 Unidirectional alignment (log-probability: -49.4) AGCCATGGCATTCAGGGGCCTGGTAAAGAAGCTGCCT----CcTAggctcatcctatggagGGATGAGCCTTTCTTTCTCCCCAGCATCACCACATCACTA AGCCATGGCATTCAGGGGCCTGGTAAAGAAGCTGCCTTCTCCTTA----------------GGATGAGCCTTTCTTTCTCCCCAGCATCACCACATCACTA Template switch alignment (log-probability: -29) AGCCATGGCATTCAGGGGCCTGGTAAAGAAGCTGCCTcCT|AGGCTCATCCTAtGGAG|GGATGAGCCTTTCTTTCTCCCCAGCATCACCACATCACTA AGCCATGGCATTCAGGGGCCTGGTAAAGAAGCTGCCTTCT|AGGCTCATCCTAAGGAG|GGATGAGCCTTTCTTTCTCCCCAGCATCACCACATCACTA ========== Event 1699 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GGGGCTGAAGTTTAGGAAATGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCCAGCCTCAAGCTCAGCATGGGCACCACAT ↑ 3 2 1 4 Chimp: GGGGCTGAAGTTTAGGAAATGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCC----CT-CAGCTCAGCATGGGCACCACAT ↓ 3 2 1 4 Gorilla: GGGGCTGAAGTTTAGGAAATGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCCAGCCTCAAGCTCAGCATGGGCACCACAT Human: GGGGCTGAAGTTTAGGAAATGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCCAGCCTCAAGCTCAGCATGGGCACCACAT Cluster: [ ] Orangutan: GGGGCTGAAGTTTAGGAAATGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATCCCAGCCCTGTGGGCTCCTCTGTCCCAGCATCAAGCTCAGCATGGGCACCACAT Chimp > Human ------------- chr20:60745205-60745211 Template switch process: F1: L GTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCC 1 F3: 4 AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG R RF: TGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCCTCAGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG RR: ACTCCGACCCCGGAAGAGATGGAGGGGTACAGAAATGGGAGGTTACGGTCGGGACACCCGAGGAGACAGGGAGTCGAGTCGTACCCGTGGTGTAGGTACGAAACAGGAGTACC F2: 3 ACTCCGA 2 Unidirectional alignment (log-probability: -28.4) CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCccagCCTCaAGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTC----CCTC-AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG Template switch alignment (log-probability: -16.2) CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCC|AGCCTCA|AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCC|AGCCTCA|AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG Chimp > Gorilla --------------- chr20:59689558-59689564 Template switch process: F1: L GTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCC 1 F3: 4 AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG R RF: TGAGGCTGGGGCCTTCTCTACCTCCCCATGTCTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCCTCAGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG RR: ACTCCGACCCCGGAAGAGATGGAGGGGTACAGAAATGGGAGGTTACGGTCGGGACACCCGAGGAGACAGGGAGTCGAGTCGTACCCGTGGTGTAGGTACGAAACAGGAGTACC F2: 3 ACTCCGA 2 Unidirectional alignment (log-probability: -27.9) CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCccagCCTCaAGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTC----CCTC-AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG Template switch alignment (log-probability: -16.6) CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCC|AGCCTCA|AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG CTTTACCCTCCAATGCCAGCCCTGTGGGCTCCTCTGTCCC|AGCCTCA|AGCTCAGCATGGGCACCACATCCATGCTTTGTCCTCATGG ========== Event 1700 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAAGAGGTGGGTTATAAATCCTTCGCCA-------------CCCTCCTGTGGCGAAGGAGG-GGAAGTGGGAGCCGGGAAGTA Chimp: GAAAGAGGTGGGTTATAAATCCTTCGCCA-------------CCCTCCTGTGGCGAAGGAGG-GGAAGTGGGAGCCGGTAAGTA ↑ 3 1 4 Gorilla: GAAAGAGGTGGGTTATAAATCCTTCGCCA--------------------------CAGGAGGGTGAAGTGGGAGCCGGGAAGTA ↓ 3 1 4 Human: GAAAGAGGTGGGTTATAAATCCTTCGCCA-------------CCCTCCTGTGGCGAAGGAGG-GGAAGTGGGAGCCGGGAAGTA Cluster: [ ] Orangutan: GAAAGAGGTGGGTTATAAATCCTTCGCCACCCTCCTGTGGCG-------------AAGGAGG-GGAAGTGGGAGTCGGGAAGTA Gorilla > Human --------------- chr20:60555453-60555469 Template switch process: F1: L TGGCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC 1 F3: 4 GGGGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAGGAG R RF: TGGCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCACAGGAGGGTGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAGGAG RR: ACCGTTGACTTTCTTTCTCCACCCAATATTTAGGAAGCGGTGTCCTCCCACTTCACCCTCGGCCCTTCATCTCAACCGGAAAACGTCCTC F2: 3 AGGAAGCGGTGTCCTCC 2 Unidirectional alignment (log-probability: -39.5) GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCACcctcctgtggcgaAGGAGGG-GAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAG GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC-------------AGGAGGGTGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAG Template switch alignment (log-probability: -23.5) GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC|CCTCCTGTGGCGAAGGA|GGgGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAG GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC|CCTCCTGTGGCGAAGGA|GGTGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAG Gorilla > Chimp --------------- chr20:62772490-62772506 Template switch process: F1: L TGGCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC 1 F3: 4 GGGGAAGTGGGAGCCGGTAAGTAGAGTTGGCCTTTTGCAGGAG R RF: TGGCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCACAGGAGGGTGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAGGAG RR: ACCGTTGACTTTCTTTCTCCACCCAATATTTAGGAAGCGGTGTCCTCCCACTTCACCCTCGGCCCTTCATCTCAACCGGAAAACGTCCTC F2: 3 AGGAAGCGGTGTCCTCC 2 Unidirectional alignment (log-probability: -45) GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCACcctcctgtggcgaAGGAGGG-GAAGTGGGAGCCGGtAAGTAGAGTTGGCCTTTTGCAG GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC-------------AGGAGGGTGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAG Template switch alignment (log-probability: -29) GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC|CCTCCTGTGGCGAAGGA|GGgGAAGTGGGAGCCGGtAAGTAGAGTTGGCCTTTTGCAG GCAACTGAAAGAAAGAGGTGGGTTATAAATCCTTCGCCAC|CCTCCTGTGGCGAAGGA|GGTGAAGTGGGAGCCGGGAAGTAGAGTTGGCCTTTTGCAG ========== Event 1701 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCCATGGAGTTCCTGGTAGTGGGGACTCCA-------------GCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGT ↓ 3 2 4 1 Chimp: GGCCATGGAGTTCCTGGTAGTGGGGACTCCATGGCTGGAGTCCCCACTCATGCCATGGCTGGACTTTGTTGAATTATCACTGT ↑ 3 2 4 1 Gorilla: GGCCATGGAGTTCCTGGTAGTGGGGACTCCA-------------GCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGT Human: GGCCATGGAGTTCCTGGTAGTGGGGACTCCA-------------GCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGT Cluster: [ ] Orangutan: GGCCATGGAGTTCCTGGTAGTGGGGACTCCA-------------GCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGT Human > Chimp ------------- chr20:40372045-40372052 Template switch process: F1: L GACCTCTAAAGGCCATGGAGTTCCTGGTAGTGGGGACTCCA-----------TGGCTGGA 1 F3: 4 TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA R RF: GACCTCTAAAGGCCATGGAGTTCCTGGTAGTGGGGACTCCAGCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA RR: CTGGAGATTTCCGGTACCTCAAGGACCATCACCCCTGAGGTCGTAGTACGGTACCGACCTGAAACAACTTAATAGTGACAATCT F2: 3 CACCCCTG 2 Unidirectional alignment (log-probability: -44.3) AGGCCATGGAGTTCCTGGTAGTGGGGACTC---CAtggctggagtccccacTCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA AGGCCATGGAGTTCCTGGTAGTGGGGACTCCAGCA----------------TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA Template switch alignment (log-probability: -27.2) AGGCCATGGAGTTCCTGGTAGTGGGGACTCCA-----------TGGCTGGA|GTCCCCAC|TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA AGGCCATGGAGTTCCTGGTAGTGGGGACTCCAGCATCATGCCATGGCTGGA|GTCCCCAC|TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA Gorilla > Chimp --------------- chr20:40372045-40372052 Template switch process: F1: L GACCTCTAAAGGCCATGGAGTTCCTGGTAGTGGGGACTCC-----------ATGGCTGGA 1 F3: 4 TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA R RF: GACCTCTAAAGGCCATGGAGTTCCTGGTAGTGGGGACTCCAGCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA RR: CTGGAGATTTCCGGTACCTCAAGGACCATCACCCCTGAGGTCGTAGTACGGTACCGACCTGAAACAACTTAATAGTGACAATCT F2: 3 CACCCCTG 2 Unidirectional alignment (log-probability: -43.8) AGGCCATGGAGTTCCTGGTAGTGGGGACTCCAtggctggagtccccac---TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA AGGCCATGGAGTTCCTGGTAGTGGGGACTCCA----------------GCATCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA Template switch alignment (log-probability: -27.2) AGGCCATGGAGTTCCTGGTAGTGGGGACTCC-----------ATGGCTGGA|GTCCCCAC|TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA AGGCCATGGAGTTCCTGGTAGTGGGGACTCCAGCATCATGCCATGGCTGGA|GTCCCCAC|TCATGCCATGGCTGGACTTTGTTGAATTATCACTGTTAGA ========== Event 1702 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAAATGAAGTTGTCCTAATTGTTACTGATATACAGTAACAATTTGGACCCTTAATCAATGAT ↑ 3 2 1 4 Chimp: CAAAATGAAGTTGTCCTAATTGTTACTGATATACACT---GCTTTGGACCCTTAATCAATGAT Gorilla: CAAAATGAAGTTGTCCTAATTGTTACTGATATACACT---GCTTTGGACCCTTAATCAATGAT ↓ 3 2 1 4 Human: CAAAATGAAGTTGTCCTAATTGTTACTGATATACAGTAACAATTTGGACCCTTAATCAATGAT Cluster: [ ] Orangutan: CAAAATGAAGTTGTCCTAATTGTTACTGATATATACT---GCTTTGGACCCTTAATCAATGAT Chimp > Human ------------- chr20:24301374-24301380 Template switch process: F1: L TTTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA 1 F3: 4 TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT R RF: TTTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACACTGCTTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT RR: AAACGGGTTTTACTTCAACAGGATTAACAATGACTATATGTGACGAAACCTGGGAATTAGTTACTACAATCGTCAAAAGTTACAA F2: 3 AACAATG 2 Unidirectional alignment (log-probability: -31.4) TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACagtaacaA----TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATAC-------ACTGCTTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT Template switch alignment (log-probability: -16.2) TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA|GTAACAA|TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA|GTAACAA|TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT Gorilla > Human --------------- chr20:24301374-24301380 Template switch process: F1: L TTTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA 1 F3: 4 TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT R RF: TTTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACACTGCTTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT RR: AAACGGGTTTTACTTCAACAGGATTAACAATGACTATATGTGACGAAACCTGGGAATTAGTTACTACAATCGTCAAAAGTTACAA F2: 3 AACAATG 2 Unidirectional alignment (log-probability: -30.9) TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA----gtaacaaTTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACACTGC-------TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT Template switch alignment (log-probability: -16.6) TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA|GTAACAA|TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT TTGCCCAAAATGAAGTTGTCCTAATTGTTACTGATATACA|GTAACAA|TTTGGACCCTTAATCAATGATGTTAGCAGTTTTCAATGTT ========== Event 1703 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GAGACACCCTCTATTTCTGCCTCAAGAAGGCAAATCTTGAGGCAGAAATAGAGGGTGTCT Chimp: GAGACACCCTCTATTTCTGCCTCAAGAAGGCAAATCTTGAGGCAGAAATAGAGGGTGTCT ↑ 1 3 4 2 Gorilla: GAGACACCCTCTATTTCTGCCCCAAGATTTGCCTTCTTGAGGCAGAAATAGAGGGTGTCT Human: GAGACACCCTCTATTTCTGCCTCAAGAAGGCAAATCTTGAGGCAGAAATAGAGGGTGTCT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr20:24761831-24761843 Template switch process: F1: L ATCTATCTTTCAGAAGTCCAGAGACACCCTCTATTTCTGCC 1 F3: 4 TCTTGAGGCAGAAATAGAGGGTGTCTCTGGACTCTGAAAG R RF: ATCTATCTTTCAGAAGTCCAGAGACACCCTCTATTTCTGCCCCAAGATTTGCCTTCTTGAGGCAGAAATAGAGGGTGTCTCTGGACTCTGAAAG RR: TAGATAGAAAGTCTTCAGGTCTCTGTGGGAGATAAAGACGGGGTTCTAAACGGAAGAACTCCGTCTTTATCTCCCACAGAGACCTGAGACTTTC F2: 3 AAACGGAAGAACT 2 Unidirectional alignment (log-probability: -36.7) TCTATCTTTCAGAAGTCCAGAGACACCCTCTATTTCTGCCtCAAGA-------aggcaaaTCTTGAGGCAGAAATAGAGGGTGTCTCTGGACTCTGAAAG TCTATCTTTCAGAAGTCCAGAGACACCCTCTATTTCTGCCCCAAGATTTGCCT-------TCTTGAGGCAGAAATAGAGGGTGTCTCTGGACTCTGAAAG Template switch alignment (log-probability: -17.4) TCTATCTTTCAGAAGTCCAGAGACACCCTCTATTTCTGCC|TCAAGAAGGCAAA|TCTTGAGGCAGAAATAGAGGGTGTCTCTGGACTCTGAAAG TCTATCTTTCAGAAGTCCAGAGACACCCTCTATTTCTGCC|TCAAGAAGGCAAA|TCTTGAGGCAGAAATAGAGGGTGTCTCTGGACTCTGAAAG ========== Event 1704 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTGGTTAGTGGCCAGGCTTGCACAAGCCTCATCATGCCTCT--------GAATTGAATATTGCCTCTCCTTCCTCA------------GAGCCTGCAACAGAGCCCACTTTGGCCCCACGGTCCT Chimp: TCTTGGTTAGTGGCCAGGCTTGCACAAGCCTCATCATGCCTCT----GATTGAATTGAATATTGCCTCTCCTTCCTCA------------GAGCCTGCAACAGAGCCCACTTTGGCCCCACGGTCCT ↑ 3 2 4 1 Gorilla: TCTTGGTTAGTGGCCAGGCTTGCACAAGCCTCATCATGCCTCTGATT----GAATTGAATGTTGTCTCTCCTTCCTCA------------------------GAGCCCACTTTGGCCCCACGGTCCT Human: TCTTGGTTAGTGGCCAGGCTTGCACAAGCCTCATCATGCCTCT--------GAATTGAATATTGCCTCTCCTTCCTCA------------GAGCCTGCAACAGAGCCCACTTTGGCCCCACGGTCCT Cluster: [ ] Orangutan: TCTTGGTTAGTGGCCAGGCTTTCACAAGCCTCATCATGCCTCTGATT----GAATTGAATATTGTCTCTCCTACCTCAGAGACTGCAACA------------GAGCCCACTTTGGCCCCACGGTTCT Gorilla > Chimp --------------- chr20:25021617-25021621 Template switch process: F1: L TTGGTTAGTGGCCAGGCTTGCACAAGCCTCATCATGCCTCTGATTGAATTGAATATTGCCTCTCCTTCCTCAGAGCC 1 F3: 4 CAGAGCCCACTTTGGCC R RF: TTGGTTAGTGGCCAGGCTTGCACAAGCCTCATCATGCCTCTGATTGAATTGAATGTTGTCTCTCCTTCCTCAGAGCCCACTTTGGCC RR: AACCAATCACCGGTCCGAACGTGTTCGGAGTAGTACGGAGACTAACTTAACTTACAACAGAGAGGAAGGAGTCTCGGGTGAAACCGG F2: 3 AACGT 2 Unidirectional alignment (log-probability: -39.3) CTCTGATTGAATTGAATaTTGcCTCTCCTTCCTcagagcctgcaaCAGAGCCCACTTTGGCC CTCTGATTGAATTGAATGTTGTCTCTCCTTCCT------------CAGAGCCCACTTTGGCC Template switch alignment (log-probability: -27.7) CTCTGATTGAATTGAATaTTGcCTCTCCTTCCTCAGAGCC|TGCAA|CAGAGCCCACTTTGGCC CTCTGATTGAATTGAATGTTGTCTCTCCTTCCTCAGAGCC|TGCAA|CAGAGCCCACTTTGGCC ========== Event 1705 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAGCTGCCTAGACACGTACCGGCCCTGAGCTGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAAACTGCAGA ↑ 41 3 2 Chimp: AGAGCTGCCTAGACACGTACC-----------GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAAACTGTAGA ↓ 41 3 2 Gorilla: AGAGCTGCCTAGACACGTACCGGCCCTGAGCTGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAAACTGTAGA Human: AGAGCTGCCTAGACACGTACCGGCCCTGAGCTGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAAACTGCAGA Cluster: [ ] Orangutan: AGAGCTGCCTAGACACATACTGGCCCTGAGCTGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAAACTGCAGA Chimp > Human ------------- chr20:40990778-40990786 Template switch process: F1: L AAGTGAGGAAAGAGCTGGATAGAGCTGCCTAGACACGTACCGG 1 F3: 4 GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA R RF: AAGTGAGGAAAGAGCTGGACAGAGCTGCCTAGACACGTACCGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA RR: TTCACTCCTTTCTCGACCTGTCTCGACGGATCTGTGCATGGCCCTATCCAACCTCCGGTATCGAGTCCCTTTCTGAACCTT F2: 3 TCGAGTCCC 2 Unidirectional alignment (log-probability: -32.7) TGAGGAAAGAGCTGGAtAGAGCTGCCTAGACACGTACCggccctgagctGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA TGAGGAAAGAGCTGGACAGAGCTGCCTAGACACGTACC-----------GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA Template switch alignment (log-probability: -22.4) TGAGGAAAGAGCTGGAtAGAGCTGCCTAGACACGTACCGG|CCCTGAGCT|GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA TGAGGAAAGAGCTGGACAGAGCTGCCTAGACACGTACCGG|CCCTGAGCT|GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA Chimp > Gorilla --------------- chr20:39721018-39721026 Template switch process: F1: L AAGTGAGGAAAGAGCTGGATAGAGCTGCCTAGACACGTACCGG 1 F3: 4 GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA R RF: AAGTGAGGAAAGAGCTGGACAGAGCTGCCTAGACACGTACCGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA RR: TTCACTCCTTTCTCGACCTGTCTCGACGGATCTGTGCATGGCCCTATCCAACCTCCGGTATCGAGTCCCTTTCTGAACCTT F2: 3 TCGAGTCCC 2 Unidirectional alignment (log-probability: -32.2) TGAGGAAAGAGCTGGAtAGAGCTGCCTAGACACGTACCggccctgagctGGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA TGAGGAAAGAGCTGGACAGAGCTGCCTAGACACGTACC-----------GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA Template switch alignment (log-probability: -22.4) TGAGGAAAGAGCTGGAtAGAGCTGCCTAGACACGTACCGG|CCCTGAGCT|GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA TGAGGAAAGAGCTGGACAGAGCTGCCTAGACACGTACCGG|CCCTGAGCT|GGGATAGGTTGGAGGCCATAGCTCAGGGAAAGACTTGGAA ========== Event 1706 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTCACTCAGACTCATAATCTACTGGTTTCAAATGAACCAGTATTTATTTTAGGGGAATATATA Chimp: CTCACTCAGACTCATAATCTACTGGTTTCAAATGAACCAGTATTTATTTTAGGGGAATATATA ↑ 3 2 1 4 Gorilla: CTCACTCAGACTCATAATCTACTGGTTTCAAATGA-----CTTTTATTTTAGGGGAATATATA ↓ 3 2 1 4 Human: CTCACTCAGACTCATAATCTACTGGTTTCAAATGAACCAGTATTTATTTTAGGGGAATATATA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr20:23169472-23169478 Template switch process: F1: L CTGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA 1 F3: 4 TTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG R RF: CTGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGACTTTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG RR: GACGGGGAGTGAGTCTGAGTATTAGATGACCAAAGTTTACTGAAAATAAAATCCCCTTATATATGAAAGGAACGTTAACGCTC F2: 3 ATGACCA 2 Unidirectional alignment (log-probability: -29.1) TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGAaccagtaTTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA-----CTTTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG Template switch alignment (log-probability: -16.6) TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA|ACCAGTA|TTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA|ACCAGTA|TTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG Gorilla > Chimp --------------- chr20:23641708-23641714 Template switch process: F1: L CTGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA 1 F3: 4 TTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG R RF: CTGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGACTTTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG RR: GACGGGGAGTGAGTCTGAGTATTAGATGACCAAAGTTTACTGAAAATAAAATCCCCTTATATATGAAAGGAACGTTAACGCTC F2: 3 ATGACCA 2 Unidirectional alignment (log-probability: -29.1) TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGAaccagtaTTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA-----CTTTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG Template switch alignment (log-probability: -16.6) TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA|ACCAGTA|TTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG TGCCCCTCACTCAGACTCATAATCTACTGGTTTCAAATGA|ACCAGTA|TTTATTTTAGGGGAATATATACTTTCCTTGCAATTGCGAG ========== Event 1707 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATCATGAGAGTGGGGCCTAT---------------GGCCCAGTATCCTGAGTAGCAGGTCAG Chimp: AAATCATGAGAGTGGGGCCTAT---------------GGCCCAGTATCCTGAGTAGCAGGTCGG ↓ 3 4 12 Gorilla: AAATCATGAGAGTGGGGCCTATGCCCCACTGGGCCATAGCCCAGTATCCTGAGTAGCAGGTCGG ↑ 3 4 12 Human: AAATCATGAGAGTGGGGCCTAT---------------GGCCCAGTATCCTGAGTAGCAGGTCAG Cluster: [ ] Orangutan: AAATCATGAGAGTGTGGCCTAT---------------GGCCCAGTGTCCTGAGTAGCAGGTCAG Human > Gorilla --------------- chr20:21888875-21888884 Template switch process: F1: L CTCCTTATCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGCCCCA 1 F3: 4 GCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC R RF: CTCCTTATCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGGCCCAGTATCCTGAGTAGCAGGTCAGGGTGTTCTTGATGC RR: GAGGAATAGAGAGTCGGACTTTAGTACTCTCACCCCGGATACCGGGTCATAGGACTCATCGTCCAGTCCCACAAGAACTACG F2: 3 ATACCGGGTC 2 Unidirectional alignment (log-probability: -38) TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGccccactgggccataGCCCAGTATCCTGAGTAGCAGGTCgGGGTGTTCTTGATGC TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATG---------------GCCCAGTATCCTGAGTAGCAGGTCAGGGTGTTCTTGATGC Template switch alignment (log-probability: -28.2) TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGcCCCA|CTGGGCCATA|GCCCAGTATCCTGAGTAGCAGGTCgGGGTGTTCTTGATGC TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGGCCCA|CTGGGCCATA|GCCCAGTATCCTGAGTAGCAGGTCAGGGTGTTCTTGATGC Chimp > Gorilla --------------- chr20:21888875-21888884 Template switch process: F1: L CTCCTTATCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGCCCCA 1 F3: 4 GCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC R RF: CTCCTTATCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGGCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC RR: GAGGAATAGAGAGTCGGACTTTAGTACTCTCACCCCGGATACCGGGTCATAGGACTCATCGTCCAGCCCCACAAGAACTACG F2: 3 ATACCGGGTC 2 Unidirectional alignment (log-probability: -32.5) TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGccccactgggccataGCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATG---------------GCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC Template switch alignment (log-probability: -22.7) TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGcCCCA|CTGGGCCATA|GCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC TCTCTCAGCCTGAAATCATGAGAGTGGGGCCTATGGCCCA|CTGGGCCATA|GCCCAGTATCCTGAGTAGCAGGTCGGGGTGTTCTTGATGC ========== Event 1708 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCAGGGGAGAGAGACACGCATC----------------CCTCTCACTGTTATTCCCTTAGACATTTGGCTGGTGGT Chimp: GCAGGGGAGAGAGACACACATAGGGAATAACAGTGAGAGGGCTCACTGTTATTCCCCTAGACATTTGGCTGGTGGT ↑ 3 4 2 Gorilla: GCAGGGGAGAGAGACACACATC----------------CCTCTCACTGTTATTCCCCTAGACATTTGGCTGGTGGT Human: GCAGGGGAGAGAGACACGCATC----------------CCTCTCACTGTTATTCCCTTAGACATTTGGCTGGTGGT Cluster: [ ] Orangutan: GCAGGGGAGAGAGACACACATC----------------CCTCTCACTGTTATTCCCCTAAACATTTGGCTGGTGGT Gorilla > Chimp --------------- chr20:22363082-22363100 Template switch process: F1: L GTGTCTAGCAAAGCAAAAGTGCAGGGGAGAGAGACACACATA 1 F3: 4 CTCACTGTTATTCCCCTAGACATTTGGCTGGTGGTGGTCT R RF: GTGTCTAGCAAAGCAAAAGTGCAGGGGAGAGAGACACACATCCCTCTCACTGTTATTCCCCTAGACATTTGGCTGGTGGTGGTCT RR: CACAGATCGTTTCGTTTTCACGTCCCCTCTCTCTGTGTGTAGGGAGAGTGACAATAAGGGGATCTGTAAACCGACCACCACCAGA F2: 3 GGGAGAGTGACAATAAGGG 2 Unidirectional alignment (log-probability: -49.6) GTCTAGCAAAGCAAAAGTGCAGGGGAGAGAGACACACATagggaataacagtgagaggg----CTCACTGTTATTCCCCTAGACATTTGGCTGGTGGTGGTCT GTCTAGCAAAGCAAAAGTGCAGGGGAGAGAGACACACAT--------------------CCCTCTCACTGTTATTCCCCTAGACATTTGGCTGGTGGTGGTCT Template switch alignment (log-probability: -23.7) GTCTAGCAAAGCAAAAGTGCAGGGGAGAGAGACACACATa|GGGAATAACAGTGAGAGGG|CTCACTGTTATTCCCCTAGACATTTGGCTGGTGGTGGTCT GTCTAGCAAAGCAAAAGTGCAGGGGAGAGAGACACACATC|GGGAATAACAGTGAGAGGG|CTCACTGTTATTCCCCTAGACATTTGGCTGGTGGTGGTCT ========== Event 1709 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGCAAAAGGGATTTTAAATC-------ACAAAGTATAAGTAAAAATGACTAATcaggtgatgcccatgttgctggctcagggccgacattttgtgtagcaaggTTCTAAGGGA Chimp: ttgcaaaagggattttaaatc----aaaacaaaatataagtaaaaatGACTAATcaggtgatacccatgttgctggctcagggacgacattttgtgtagcaaggTTCTAAGGGA Gorilla: TTGCAAAAGGGATTTTAAATCACAA---ACAAAATGTAACTAAAAATGACTAATcaggtgatgcccatgttgctggctcagggaccacattttgtgtagcaaggTTCTAAGGGA ↑ 1 4 3 2 Human: TTGCAAAAGGGATTTTAAATC-------ACAAAGTATAAGTAAAAATGACTAATcaggtgatgcccatgttgctggctcagggccgacattttgtgtagcaaggTTCTAAGGGA Cluster: [ ] Orangutan: TTGCAAAAGGGATTTTAAATCACAA---ACAAAATGTAAGTAAAAATGACTAATcaggtgatggccatgttgctggctcagggatcacattttgtgtagcaaagTTCTAAGGGG Human > Gorilla --------------- chr20:21462660-21462666 Template switch process: F1: L AAAGTTTTTAAAAATCTGTATTGCAAAAGGGATTTTAAATCACAAA 1 F3: 4 TAACTAAAAATGACTAATCAGGTGATGCCCATGTTGCTGGCTCA R RF: AAAGTTTTTAAAAATCTGTATTGCAAAAGGGATTTTAAATCACAAAGTATAAGTAAAAATGACTAATCAGGTGATGCCCATGTTGCTGGCTCAGGGCCGACATTTTG RR: TTTCAAAAATTTTTAGACATAACGTTTTCCCTAAAATTTAGTGTTTCATATTCATTTTTACTGATTAGTCCACTACGGGTACAACGACCGAGTCCCGGCTGTAAAAC F2: 3 GTAAAAC 2 Unidirectional alignment (log-probability: -33.4) TTTAAAAATCTGTATTGCAAAAGGGATTTTAAATCacaaACAAAaTgTAAcTAAAAATGACTAATCAGGTGATGCCCATGTTGCTGG TTTAAAAATCTGTATTGCAAAAGGGATTTTAAATC----ACAAAGTATAAGTAAAAATGACTAATCAGGTGATGCCCATGTTGCTGG Template switch alignment (log-probability: -22.4) TTTAAAAATCTGTATTGCAAAAGGGATTTTAAATCACAAA|CAAAATG|TAAcTAAAAATGACTAATCAGGTGATGCCCATGTTGCTGG TTTAAAAATCTGTATTGCAAAAGGGATTTTAAATCACAAA|CAAAATG|TAAGTAAAAATGACTAATCAGGTGATGCCCATGTTGCTGG ========== Event 1710 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCTCCGGCAATCAGTGGGTGCTCAATACAAGCGAGCTGTGCCTGCCAAG--------- Chimp: GGCTCTGGCAATCAGTGGGTGCTCAATACAAGCGAGCTGTGCCTGCCAAG--------- ↓ 3 2 1 4 Gorilla: GGCTCTGGCAATCAGTGGGTGCTCAATACAAGTGAGCAGTGCCTGCCAAGCAAAAGAAA Human: GGCTCCGGCAATCAGTGGGTGCTCAATACAAGCGAGCTGTGCCTGCCAAG--------- Cluster: [ ] Orangutan: GGCTCCGGCAATCAGTGGGTGCTCAATACAAGCGAGCTGTGCCTGCCAAGCAAAAGAAA Chimp > Gorilla --------------- chr20:20734899-20734904 Template switch process: F1: L TTAAGCACTGGCTCTGGCAATCAGTGGGTGCTCAATACAAG 1 F3: 4 GTGCCTGCCAAGCAAAAGAAAACAGAACGGTCTGGGGCAA R RF: TTAAGCACTGGCTCTGGCAATCAGTGGGTGCTCAATACAAGCGAGCTGTGCCTGCCAAGCACAAGAAAACAGAACGGTCTGGGGTAA RR: AATTCGTGACCGAGACCGTTAGTCACCCACGAGTTATGTTCGCTCGACACGGACGGTTCGTGTTCTTTTGTCTTGCCAGACCCCATT F2: 3 ACGAGT 2 Unidirectional alignment (log-probability: -58.9) TAAGCACTGGCTCTGGCAATCAGTGGGTGCTCAATACAAGtGAGCaGTGCCTGCCAAGcaaaagaaaacagaacggtctggggcaa TAAGCACTGGCTCTGGCAATCAGTGGGTGCTCAATACAAGCGAGCTGTGCCTGCCAAG---------------------------- Template switch alignment (log-probability: -27.5) TAAGCACTGGCTCTGGCAATCAGTGGGTGCTCAATACAAG|TGAGCA|GTGCCTGCCAAGCAaAAGAAAACAGAACGGTCTGGGGcAA TAAGCACTGGCTCTGGCAATCAGTGGGTGCTCAATACAAG|TGAGCA|GTGCCTGCCAAGCACAAGAAAACAGAACGGTCTGGGGTAA ========== Event 1711 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCT-----ATTGTTACTGTGGATCCTTTGGGAGATGACTT Chimp: CTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCT-----ATTGTTACTGTGGATCCTTTGGGAGATGACTT ↓ 3 2 1 4 Gorilla: CTTGGCCTTTCCCACATCCCAGTCATGGGCAGCT----------GACT-GGGATCCTTTGGGAGATGACTT ↑ 3 2 1 4 Human: CTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCT-----ATTGTTACTGTGGATCCTTTGGGAGATGACTT Cluster: [ ] Orangutan: CTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCTATTGT-----TACTGTGGATCCTTTGGGAGATGACTT Human > Gorilla --------------- chr20:20286685-20286689 Template switch process: F1: L TTCCTTGCTTGGCCTTTCCCACATCCCAGTCATGGGCAGCT 1 F3: 4 GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG R RF: TTCCTTGCTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCTATTGTTACTGTGGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG RR: AAGGAACGAACCGGAAAGGGTGCAGGGTCAGTACCCGTCGATAACAATGACACCTAGGAAACCCTCTACTGAAATCGAGTCTCCCTCAGGTC F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -32) TCCTTGCTTGGCCTTTCCCACaTCCCAGTCATGGGCAGC-----TgACTG-GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG TCCTTGCTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCTATTGTTACTGTGGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG Template switch alignment (log-probability: -21.9) TCCTTGCTTGGCCTTTCCCACaTCCCAGTCATGGGCAGCT|GACTG|GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG TCCTTGCTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCT|GACTG|GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG Chimp > Gorilla --------------- chr20:20286685-20286689 Template switch process: F1: L TTCCTTGCTTGGCCTTTCCCACATCCCAGTCATGGGCAGCT 1 F3: 4 GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG R RF: TTCCTTTCTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCTATTGTTACTGTGGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG RR: AAGGAAAGAACCGGAAAGGGTGCAGGGTCAGTACCCGTCGATAACAATGACACCTAGGAAACCCTCTACTGAAATCGAGTCTCCCTCAGGTC F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -37.6) TCCTTgCTTGGCCTTTCCCACaTCCCAGTCATGGGCAGC-----TgACTG-GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG TCCTTTCTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCTATTGTTACTGTGGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG Template switch alignment (log-probability: -27.4) TCCTTgCTTGGCCTTTCCCACaTCCCAGTCATGGGCAGCT|GACTG|GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG TCCTTTCTTGGCCTTTCCCACGTCCCAGTCATGGGCAGCT|GACTG|GGATCCTTTGGGAGATGACTTTAGCTCAGAGGGAGTCCAG ========== Event 1712 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTCCACGTTCCCAACTGCTGGAGGGCGAGCAGGGCCGTCTACCTCCAAGGCAAACCTAGTCAGATTAGTTCTCCCTGGTGAGCCTTGGGGACAACTAATCTGACTGGGTTTACCTTGGAGGTAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-CGCCCTGCTCG-CCTCCGGCAGTTGGGTTTGCCTCCCAA Chimp: TTTCCACGTTCCCAACTGCTGGAGGGCGAGCAGGGCCGTCTACCTCCAAGGCAAACCTAGTCAGATTAGTTCTCCCTGGTGAGCCTTGGGGACAACTAATCTGACTGGGTTTACCTTGGAGGTAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAGCCCTGCTCGCCCTCCAGCAGTTGGGTTTGCCTCCGAA Gorilla: TTTCCACGTTCCCAACTGCTGGAGGGCGAGCAGGGCCGTCTACCTCCAAGGCAAACCTAGTCAGATTAGTTCTTCCTGGTGAGCCTTGGGGACAACCAATCTGACTGGGTTTACCTTGGAGGTAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGGCCCTGCTCGCCCTCCAGCAGTTGGGTTTGCCTCCCAA ↑ 3 2 1 4 Human: TTTCCACGTTCCCAACTGCTGGAGGGCGAGCAGGGCCGTCTACCTCCAAGGCAAACCTAGTCAGATTAGTTCTCCCTGGTGAGCCTTGGGGACAACTAATCTGACTGGGTTTACCTTGGAGGTAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-CGCCCTGCTCG-CCTCCGGCAGTTGGGTTTGCCTCCCAA Cluster: [ ] Orangutan: TTTCCATGTTCCCAACTGCTGGAGGGCGAGCCGG-----GTTCTTCCTAGGCGGACTG------AAGAGT--------------TT-----CGAAATCACCTGTTAGGGTGTGCCACCCAGCTCGACCCTGCAAAGGGAGAGGAGTAGGGTCTTGATCCTACGGGCAGGGCCAAGCGCTGTCGCTGCTAAAACCTGGCATTCCTGATAATAAGGGCCAAGTGGGGTAAAACAACAATGTCCCATTCGAGTAACAAACTGTGTGTGCATCTCATCATGAGGCACCACTCCGCTTTTTAGCCAGTCTGACTTAATGTTTGCGATGGGAGCCGCCTATCAAAGTGGCTCAGTCCATATGATAAAGTGCTGTTATTTACGAGGATTCTGCCGTGGTAAGGAGAgggggggggCTTGTCGGATGGTTTCCAGCCTTGTTTTTAATCAAACGATGTCTTGGCTCCCCATTCCGCCTTGTCCTGGATTTGTAATGTTTTTTAGTGTTNNNNNNNNNNACCCTCCGGCAGTTGGGTTTGCCTCCCAA Human > Gorilla --------------- chr20:43457105-43457121 Template switch process: F1: L AATCTGACTGGGTTTACCTTGGAGGTAGACG 1 F3: 4 GCAGTTGGGTTTGCCTCCCAAACACATCGCTCTGTTTTGT R RF: TGGAGGGCGAGCAGGGCCGTCTACCTCCAAGGCAAACCTAGTCAGATTAGTTCTCCCTGGTGAGCCTTGGGGACAACTAATCTGACTGGGTTTACCTTGGAGGTAGACGCCCTGCTCGCCTCCGGCAGTTGGGTTTGCCTCCCAAACACATCGCTCTGTTTTGT RR: ACCTCCCGCTCGTCCCGGCAGATGGAGGTTCCGTTTGGATCAGTCTAATCAAGAGGGACCACTCGGAACCCCTGTTGATTAGACTGACCCAAATGGAACCTCCATCTGCGGGACGAGCGGAGGCCGTCAACCCAAACGGAGGGTTTGTGTAGCGAGACAAAACA F2: 3 ACCTCCCGCTCGTCCCG 2 Unidirectional alignment (log-probability: -29.1) AATCTGACTGGGTTTACCTTGGAGGTAGACgGCCCTGCTCGcCCTCCaGCAGTTGGGTTTGCCTCCCAAACACATCGCTCTGTTTTGT AATCTGACTGGGTTTACCTTGGAGGTAGAC-GCCCTGCTCG-CCTCCGGCAGTTGGGTTTGCCTCCCAAACACATCGCTCTGTTTTGT Template switch alignment (log-probability: -17.6) AATCTGACTGGGTTTACCTTGGAGGTAGACG|GCCCTGCTCGCCCTCCA|GCAGTTGGGTTTGCCTCCCAAACACATCGCTCTGTTTTGT AATCTGACTGGGTTTACCTTGGAGGTAGACG|GCCCTGCTCGCCCTCCA|GCAGTTGGGTTTGCCTCCCAAACACATCGCTCTGTTTTGT ========== Event 1713 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TGAAGCTGTCTGCCTTCTCTAGACACAAacctcatgtttcagtctctccatctgtaaattgggaagaataatgctgTTATTGGTATATATGTTGGATCTGGAGATTTCCAGTCTGTCTAAGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAA ↑ 3 2 4 1 Chimp: TGAAGCTGTCTGCCTTCTCTAGACACAAacctcatgtttcagtctctccatctgtaaattgggaagaataatgctgTTATTGGTATATATGTTGGATCTGGA---------------------GATCTCCAGTCATCTCATCCCCAAGCCAGAA ↓ 3 2 4 1 Gorilla: TGAAGCTGTCTGCCTTCTCTAGACACAAacctcatgtttcagtctctccatctgtaaattgggaagaataatgctgTTATTGGTATATATGTTGGATCTGGAGATTTCCAGTCTGTCTAAGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAA Human: TGAAGCTGTCTGCCTTCTCTAGACACAAacctcatgtttcagtctctccatctgtaaattgggaagaataatgctgTTATTGGTATATATGTTGGATCTGGAGATTTCCAGTCTGTCTAAGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAA Cluster: [ ] Orangutan: TGAAGCTGTCTGCCTCCTCTAGACCCAaacctcatgtttcagtctctccatctgtaaattgggaagaataatGCTGTTATTGGTATATATGTTGGATCTGGAGATTTCCAGTCTGTCTAAGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAA Chimp > Human ------------- chr20:46025309-46025314 Template switch process: F1: L GGAAGAATAATGCTGTTATTGGTATATATGTTGGATCTGGAGATTTCCAGTC 1 F3: 4 AGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAGAACC R RF: TAGACACAAACCTCATGTTTCAGTCTCTCCATCTGTAAATTGGGAAGAATAATGCTGTTATTGGTATATATGTTGGATCTGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAGAACC RR: ATCTGTGTTTGGAGTACAAAGTCAGAGAGGTAGACATTTAACCCTTCTTATTACGACAATAACCATATATACAACCTAGACCTCTAGAGGTCAGTAGAGTAGGGGTTCGGTCTTGAGTCTTGG F2: 3 ATCTGT 2 Unidirectional alignment (log-probability: -41.1) CTGTTATTGGTATATATGTTGGATCTGGAGatttccagtctgtctaaggagATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG CTGTTATTGGTATATATGTTGGATCTGGAG---------------------ATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG Template switch alignment (log-probability: -28.3) CTGTTATTGGTATATATGTTGGATCTGGAGATtTCCAGTC|TGTCTA|aGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG CTGTTATTGGTATATATGTTGGATCTGGAGATCTCCAGTC|TGTCTA|TGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG Chimp > Gorilla --------------- chr20:44893315-44893320 Template switch process: F1: L GGAAGAATAATGCTGTTATTGGTATATATGTTGGATCTGGAGATTTCCAGTC 1 F3: 4 AGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAGAACC R RF: TAGACACAAACCTCATGTTTCAGTCTCTCCATCTGTAAATTGGGAAGAATAATGCTGTTATTGGTATATATGTTGGATCTGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAGAACC RR: ATCTGTGTTTGGAGTACAAAGTCAGAGAGGTAGACATTTAACCCTTCTTATTACGACAATAACCATATATACAACCTAGACCTCTAGAGGTCAGTAGAGTAGGGGTTCGGTCTTGAGTCTTGG F2: 3 ATCTGT 2 Unidirectional alignment (log-probability: -41.1) CTGTTATTGGTATATATGTTGGATCTGgagatttccagtctgtctaagGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG CTGTTATTGGTATATATGTTGGATCTG---------------------GAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG Template switch alignment (log-probability: -27.9) CTGTTATTGGTATATATGTTGGATCTGGAGATtTCCAGTC|TGTCTA|aGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG CTGTTATTGGTATATATGTTGGATCTGGAGATCTCCAGTC|TGTCTA|TGGAGATCTCCAGTCATCTCATCCCCAAGCCAGAACTCAG ========== Event 1714 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CAGTTCTGGACCAGGTTTGACACTGTAA------------------------------AATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGTATCTATCTGGGAAGGGTTCTGACAGATCTCAGCTGCCTCATGGAACAAGCACAACTCTTACTG ↓ 4 1 3 2 Chimp: CAGTTCTGGACCAGGTTTGACGCTGTAA---------------AATATGCCATGGTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGT----ATCTGGGAAGGGTTCTGACAGATCTCAGCTGCCTCATGGAACAAGCACAACTCTTACTG Gorilla: CAGTTCTGGACCAGGTTTGACACTGTAAAATATGCCATGGTAA---------------AATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGT----ATCTGGGAAGGGTTCTGACAGATCTCAGCTGCCTCATGGAACAAGCACAACTCTTATTG ↑ 4 1 3 2 Human: CAGTTCTGGACCAGGTTTGACACTGTAA------------------------------AATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGTATCTATCTGGGAAGGGTTCTGACAGATCTCAGCTGCCTCATGGAACAAGCACAACTCTTACTG Cluster: [ ] Orangutan: CAGTTCTGGACCAGGTTTGACACTGTAAAATATGCCATGGTAA---------------AATATGACTGTTAAGGTGATTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGT----ATCTGGGAAGAGTTCTGACAGATCTGAGCTGCCTCATGGAACAAGCACAACTCTTATTG Human > Chimp ------------- chr20:48743628-48743632 Template switch process: F1: L CGAAGGGTCCAAACTAGGGCCAGTTCTGGACCAGGTTTGACGCTGTAAAATATG 1 F3: 4 GTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTG R RF: CGAAGGGTCCAAACTAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGTATCTATCTGGGAAGGGTTCTGACAGATCTCAGCTGCCTCATGG RR: GCTTCCCAGGTTTGATCCCGGTCAAGACCTGGTCCAAACTGTGACATTTTATACTGACAATTCCACTCAAGTTCTCAAGTCGTCGAACCACTTGAGAACACATAGATAGACCCTTCCCAAGACTGTCTAGAGTCGACGGAGTACC F2: 3 GTACC 2 Unidirectional alignment (log-probability: -38.5) TAGGGCCAGTTCTGGACCAGGTTTGACgCTGTAAAATAtgccatggtaaaataTGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG TAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATA---------------TGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG Template switch alignment (log-probability: -22.2) TAGGGCCAGTTCTGGACCAGGTTTGACgCTGTAAAATATG|CCATG|GTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG TAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATATG|CCATG|GTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG Human > Gorilla --------------- chr20:45864825-45864829 Template switch process: F1: L TCCAAACTAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATATG 1 F3: 4 GTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTG R RF: TCCAAACTAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAGCTTGGTGAACTCTTGTGTATCTATCTGGGAAGGGTTCTGACAGATCTCAGCTGCCTCATGG RR: AGGTTTGATCCCGGTCAAGACCTGGTCCAAACTGTGACATTTTATACTGACAATTCCACTCAAGTTCTCAAGTCGTCGAACCACTTGAGAACACATAGATAGACCCTTCCCAAGACTGTCTAGAGTCGACGGAGTACC F2: 3 GTACC 2 Unidirectional alignment (log-probability: -32.5) TAGGGCCAGTTCTGGACCAGGTTTGACACTGTaaaatatgccatggtAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG TAGGGCCAGTTCTGGACCAGGTTTGACACTGT---------------AAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG Template switch alignment (log-probability: -16.6) TAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATATG|CCATG|GTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG TAGGGCCAGTTCTGGACCAGGTTTGACACTGTAAAATATG|CCATG|GTAAAATATGACTGTTAAGGTGAGTTCAAGAGTTCAGCAG ========== Event 1715 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGGTTCATGCAAAAGAAAAG------------AGAAATCAGAAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCTTCCTAAGCT Chimp: AAGGTTGATGCAAAAGAAAAG------------AGAAATCAGAAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCTTCCTAAGCT ↑ 4 1 3 2 Gorilla: AAGGTTGATGCAAAAGAAAAG------------------------AGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCTTCCTAAGCT ↓ 4 1 3 2 Human: AAGGTTCATGCAAAAGAAAAG------------AGAAATCAGAAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCTTCCTAAGCT Cluster: [ ] Orangutan: AAGGTTGGTGCAAAAGAAAAGAGAAATCAGAAG------------AGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCTTCCTAAGTT Gorilla > Human --------------- chr20:47067216-47067220 Template switch process: F1: L TGCCCTGAGTCATCATTCAGAAGGTTCATGCAAAAGAAAAGAGAAA 1 F3: 4 AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCT R RF: TGCCCTGAGTCATCATTCAGAAGGTTGATGCAAAAGAAAAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCT RR: ACGGGACTCAGTAGTAAGTCTTCCAACTACGTTTTCTTTTCTCTTTTGTGACGTCAGTCCTCAGAAGACTCTGTCCACCGA F2: 3 AGACT 2 Unidirectional alignment (log-probability: -33.7) GAGTCATCATTCAGAAGGTTcATGCAAAAGAAaagagaaatcagAAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG GAGTCATCATTCAGAAGGTTGATGCAAAAGAA------------AAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG Template switch alignment (log-probability: -22.1) GAGTCATCATTCAGAAGGTTcATGCAAAAGAAAAGAGAAA|TCAGA|AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG GAGTCATCATTCAGAAGGTTGATGCAAAAGAAAAGAGAAA|TCAGA|AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG Gorilla > Chimp --------------- chr20:48764172-48764176 Template switch process: F1: L TGCCCTGAGTCATCATTCAGAAGGTTGATGCAAAAGAAAAGAGAAA 1 F3: 4 AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCT R RF: TGCCCTGAGTCATCATTCAGAAGGTTGATGCAAAAGAAAAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGGCT RR: ACGGGACTCAGTAGTAAGTCTTCCAACTACGTTTTCTTTTCTCTTTTGTGACGTCAGTCCTCAGAAGACTCTGTCCACCGA F2: 3 AGACT 2 Unidirectional alignment (log-probability: -28.1) GAGTCATCATTCAGAAGGTTGATGCAAAAGAAAagagaaatcagaAGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG GAGTCATCATTCAGAAGGTTGATGCAAAAGAAA------------AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG Template switch alignment (log-probability: -16.5) GAGTCATCATTCAGAAGGTTGATGCAAAAGAAAAGAGAAA|TCAGA|AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG GAGTCATCATTCAGAAGGTTGATGCAAAAGAAAAGAGAAA|TCAGA|AGAGAAAACACTGCAGTCAGGAGTCTTCTGAGACAGGTGG ========== Event 1716 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: ttatctagaaacaaggcaagacccaggccccaaatcctgggacgatacaaggtGTCAACATGCA Chimp: ttatctagaaaCAAGGCAAGACCCAGGCCCCAAAT-CTGGG-ACATACAAGGTGTCAACATGCA ↓ 3 2 1 4 Gorilla: ttatctagaaaCAAGGCAAGACCCAGGCCCCAAATCCTGGGACCATACAAGGTGTCAACGTGCA Human: ttatctagaaacaaggcaagacccaggccccaaatcctgggacgatacaaggtGTCAACATGCA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr20:17026434-17026440 Template switch process: F1: L ACCAGATTATCTAGAAACAAGGCAAGACCCAGGCCCCAAATC 1 F3: 4 CATACAAGGTGTCAACGTGCACTTAAATCTTTTTTTTTTT R RF: ACCAGATTATCTAGAAACAAGGCAAGACCCAGGCCCCAAATCTGGGACATACAAGGTGTCAACATGCACTTAAATCTTTTTTTTTTT RR: TGGTCTAATAGATCTTTGTTCCGTTCTGGGTCCGGGGTTTAGACCCTGTATGTTCCACAGTTGTACGTGAATTTAGAAAAAAAAAAA F2: 3 CAGGGTC 2 Unidirectional alignment (log-probability: -43) CAGATTATCTAGAAACAAGGCAAGACCCAGGCCCCAAATcCTGGGAcCATACAAGGTGTCAACgTGCACTTAAATCTTTTTTttttt CAGATTATCTAGAAACAAGGCAAGACCCAGGCCCCAAAT-CTGGGA-CATACAAGGTGTCAACATGCACTTAAATCTTTTTT----- Template switch alignment (log-probability: -27.7) CAGATTATCTAGAAACAAGGCAAGACCCAGGCCCCAAATC|CTGGGaC|CATACAAGGTGTCAACgTGCACTTAAATCTTTTTTTTTTT CAGATTATCTAGAAACAAGGCAAGACCCAGGCCCCAAATC|CTGGGTC|CATACAAGGTGTCAACATGCACTTAAATCTTTTTTTTTTT ========== Event 1717 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGTCTTTCCTGTCCATCATCCCCTGATGATCACCCCTGCCCTGCTCA ↑ 31 2 4 Chimp: CAGTCTTTCCTGTCCATCATCAGGGGGTGATCACCCCTGCCCTGCTCA Gorilla: CAGTCTTTCCTGTCCATCATCAGGGGGTGATCACCCCTGCCCTGCTCA ↓ 31 2 4 Human: CAGTCTTTCCTGTCCATCATCCCCTGATGATCACCCCTGCCCTGCTCA Cluster: [ ] Orangutan: CAGTCTTTCCTGTCCATCATCAggggatgatcacccctgccctgctca Chimp > Human ------------- chr20:47669682-47669687 Template switch process: F1: L CCCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC 1 F3: 4 TGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC R RF: CCCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATCAGGGGGTGATCACCCCTGCCCTGCTCACAGGGCTTTTGAGAGGTGC RR: GGGTTTAGTCGGTGCACTGGGTCAGAAAGGACAGGTAGTAGTCCCCCACTAGTGGGGACGGGACGAGTGTCCCGAAAACTCTCCACG F2: 3 AGTCCC 2 Unidirectional alignment (log-probability: -34.6) CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATCccctgA-----TGATCACCCCTGCCCTGCTCACAGGGCTgTTGAGAGGTGC CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC-----AGGGGGTGATCACCCCTGCCCTGCTCACAGGGCTTTTGAGAGGTGC Template switch alignment (log-probability: -22) CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC|CCCTGA|TGATCACCCCTGCCCTGCTCACAGGGCTgTTGAGAGGTGC CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC|CCCTGA|TGATCACCCCTGCCCTGCTCACAGGGCTTTTGAGAGGTGC Gorilla > Human --------------- chr20:47669682-47669687 Template switch process: F1: L CCCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC 1 F3: 4 TGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC R RF: CCCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATCAGGGGGTGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC RR: GGGTTTAGTCGGTGCACTGGGTCAGAAAGGACAGGTAGTAGTCCCCCACTAGTGGGGACGGGACGAGTGTCCCGACAACTCTCCACG F2: 3 AGTCCC 2 Unidirectional alignment (log-probability: -28.1) CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATCccctgA-----TGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC-----AGGGGGTGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC Template switch alignment (log-probability: -16.5) CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC|CCCTGA|TGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC CCAAATCAGCCACGTGACCCAGTCTTTCCTGTCCATCATC|CCCTGA|TGATCACCCCTGCCCTGCTCACAGGGCTGTTGAGAGGTGC ========== Event 1718 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGAGAGTGTGGAAATCTCTATGAAAGCCA--------CCAGTCACCACCCTAACATGAAAGAGGG Chimp: AAGAGAGTATGGAAATCTCTGTGAAAGCCA--------CCAGTCACCACCCTAACATGAAAGAGGG ↑ 1 3 4 2 Gorilla: AAGAGAGTATGGAAATCTCTATGAAAGCCACACTGGTGGCTTTCACCACCCTAACGTGAAAGAGGG Human: AAGAGAGTGTGGAAATCTCTATGAAAGCCA--------CCAGTCACCACCCTAACATGAAAGAGGG Cluster: [ ] Orangutan: AAGAGAGTACGGAAATCTCTATGAAAGCCA--------TCAGTCACCACCCTAACATGAAAGAGGG Gorilla > Chimp --------------- chr20:17004238-17004252 Template switch process: F1: L AATTTGTTCTAAAGAGAGTATGGAAATCTCT 1 F3: 4 CACCACCCTAACATGAAAGAGGGACATTCGAAAGGAGAT R RF: AATTTGTTCTAAAGAGAGTATGGAAATCTCTATGAAAGCCACACTGGTGGCTTTCACCACCCTAACGTGAAAGAGGGACATTCGAAAGGACAT RR: TTAAACAAGATTTCTCTCATACCTTTAGAGATACTTTCGGTGTGACCACCGAAAGTGGTGGGATTGCACTTTCTCCCTGTAAGCTTTCCTGTA F2: 3 TGACCACCGAAAGTG 2 Unidirectional alignment (log-probability: -38.9) AATTTGTTCTAAAGAGAGTATGGAAATCTCTgTGAAAGCCAC--------CagTCACCACCCTAACaTGAAAGAGGGACATTCGAAAGGAgAT AATTTGTTCTAAAGAGAGTATGGAAATCTCTATGAAAGCCACACTGGTGGCTTTCACCACCCTAACGTGAAAGAGGGACATTCGAAAGGACAT Template switch alignment (log-probability: -28.4) AATTTGTTCTAAAGAGAGTATGGAAATCTCT|GTGAAAGCCACCAGT|CACCACCCTAACaTGAAAGAGGGACATTCGAAAGGAgAT AATTTGTTCTAAAGAGAGTATGGAAATCTCT|GTGAAAGCCACCAGT|CACCACCCTAACGTGAAAGAGGGACATTCGAAAGGACAT ========== Event 1719 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTGTATTAGTTCAGTCAGAATTTGCCGCTAAGATTGGCTGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTTGCAAGTTAGTGCATATAGTCTCTGTTCC ↑ 3 2 1 4 Chimp: TTTGTATTAGTTCAGTCAGAATTTGCCACTAAGATTGGCTGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTTAA---ACAGTGCATATAGTCTCTGTTCC Gorilla: TTTGTATTAGGTCAGTCAGAATTTGCCACtaagattggctggggagtttccctcctttcacagagctctggaacagtttaa---acagtgcatatagtctctcttcc Human: TTTGTATTAGTTCAGTCAGAATTTGCCGCTAAGATTGGCTGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTTGCAAGTTAGTGCATATAGTCTCTGTTCC Cluster: [ ] Orangutan: TTTGTATTAGTTCAGTCAGAATTTGCCACtaagattggctggagagtttccctcctttcacagagctctggaacagtttaa---acagtgcatatattctctcttcc Chimp > Human ------------- chr20:4880218-4880224 Template switch process: F1: L CTGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTT 1 F3: 4 AGTGCATATAGTCTCTGTTCCTTGAAGACTGAATGCACTC R RF: AATTTGCCACTAAGATTGGCTGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTTAAACAGTGCATATAGTCTCTGTTCCTTGAAGACTGAATGCACTC RR: TTAAACGGTGATTCTAACCGACCCCTCAAAGGGAGGAAAGTGTCTCGAGACCTTGTCAAATTTGTCACGTATATCAGAGACAAGGAACTTCTGACTTACGTGAG F2: 3 TTGAACG 2 Unidirectional alignment (log-probability: -31.4) TGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTttgcaagTT----AGTGCATATAGTCTCTGTTCCTTGAAGACTGAATGCACTC TGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGT-------TTAAACAGTGCATATAGTCTCTGTTCCTTGAAGACTGAATGCACTC Template switch alignment (log-probability: -22.1) TGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTT|GCAAgTT|AGTGCATATAGTCTCTGTTCCTTGAAGACTGAATGCACTC TGGGGAGTTTCCCTCCTTTCACAGAGCTCTGGAACAGTTT|GCAAATT|AGTGCATATAGTCTCTGTTCCTTGAAGACTGAATGCACTC ========== Event 1720 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: agccAATACCTGTTTTTAAACTATGCTTCTATGTAGATG------------GGTTGTGCTTGAAATTATTTCACTAGTGGGGAAACACAC Chimp: ggccAATACCTGTTTTTAAACTATGCTTCTATGAAGATG------------GGTTGTGCTTGAAATTATTTCACTAGTGGAGAAACACAC Gorilla: agccAATACCTGTTTTTAAACTATGCTTCTATGAAGAAG------------------------CATAGTTTCACTAGTGGGGAAACACAC ↑ 3 2 1 4 Human: agccAATACCTGTTTTTAAACTATGCTTCTATGTAGATG------------GGTTGTGCTTGAAATTATTTCACTAGTGGGGAAACACAC Cluster: [ ] Orangutan: agccAATACCTGGTTTTTAACTATGCTTCTATGAAGATGGGTTGTGCTTGA------------AATTATTTCACTAGTGGGGAAACACGC Human > Gorilla --------------- chr20:49685262-49685269 Template switch process: F1: L CCGCACCCAGCCAATACCTGTTTTTAAACTATGCTTCTATGAAGA 1 F3: 4 TTCACTAGTGGGGAAACACACTAAGTAGGAGAGTGACTT R RF: CCGCACCCAGCCAATACCTGTTTTTAAACTATGCTTCTATGTAGATGGGTTGTGCTTGAAATTATTTCACTAGTGGGGAAACACACTAAGTAGGAGAGCGACTT RR: GGCGTGGGTCGGTTATGGACAAAAATTTGATACGAAGATACATCTACCCAACACGAACTTTAATAAAGTGATCACCCCTTTGTGTGATTCATCCTCTCGCTGAA F2: 3 TGATACGA 2 Unidirectional alignment (log-probability: -38.7) CCCAGCCAATACCTGTTTTTAAACTATGCTTCTATGaagaagcaTAG--------------------TTTCACTAGTGGGGAAACACACTAAGTAGGAGAGtGACTT CCCAGCCAATACCTGTTTTTAAACTATGCTTCTATG--------TAGATGGGTTGTGCTTGAAATTATTTCACTAGTGGGGAAACACACTAAGTAGGAGAGCGACTT Template switch alignment (log-probability: -27.9) CCCAGCCAATACCTGTTTTTAAACTATGCTTCTATGaAGA|AGCATAGT|TTCACTAGTGGGGAAACACACTAAGTAGGAGAGtGACTT CCCAGCCAATACCTGTTTTTAAACTATGCTTCTATGTAGA|AGCATAGT|TTCACTAGTGGGGAAACACACTAAGTAGGAGAGCGACTT ========== Event 1721 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCTTATTTATTTCTTTGTTGCTAAGTGTTTGGCAAAACCTCTTTGCTGTGAGCACAAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTG-------------------------------TCCAGCGCTGTAGTTATGTATTTGAGCAGTGTCCAGTGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGT Chimp: TTCTTATTTATTTCTTTGTTGCTAAGTGTTTGGTAAAACCTCTTTGCTGTGAGCACAAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTG-------------------------------TCCAGCGCTGTAGTTATGTGTTTGAGCAGTGTCCAGTGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGT ↑ 3 2 4 1 Gorilla: TTTTTATTTATTTCTTTGTTGCTCAGTGTTTGGTAAAACCTCTTTGCTGTGAGCACAAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTG--------------------------------------------------------------TCCAGCGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGT ↓ 3 2 4 1 Human: TTCTTATTTATTTCTTTGTTGCTAAGTGTTTGGCAAAACCTCTTTGCTGTGAGCACAAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTG-------------------------------TCCAGCGCTGTAGTTATGTATTTGAGCAGTGTCCAGTGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGT Cluster: [ ] Orangutan: TTTTTATTTATTTCTTTGTTGCTAAGTGTTTGGTAAAACCTCTTTGCTGTGAGCACGAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGgagcggtgtccagcgctgtagttatgtgtttgagcagtg-------------------------------tccagtgctgtagttatgtgttCCAGCCTCACCAGGCCCTGT Gorilla > Human --------------- chr20:50571108-50571113 Template switch process: F1: L TTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTATT 1 F3: 4 GTGTCCAGTGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGTGCTT R RF: TGCTCAGTGTTTGGTAAAACCTCTTTGCTGTGAGCACAAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGTGCTT RR: ACGAGTCACAAACCATTTTGGAGAAACGACACTCGTGTTCCAAACGAAATCGTTAACAACAGTGTAATGTCGTTCCTCACCACAGGTCGCGACATCAATACACAAGGTCGGAGTGGTCCGGGACACGAA F2: 3 ACGAGT 2 Unidirectional alignment (log-probability: -55.5) TTACAGCAAGGAGTGGTGTCCAGCgctgtagttatgtatttgagcagtgtccagtGCTGTAGTTATGTGTTCCAGCCTCACCAGGC TTACAGCAAGGAGTGGTGTCCAGC-------------------------------GCTGTAGTTATGTGTTCCAGCCTCACCAGGC Template switch alignment (log-probability: -28.3) TTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTaTT|TGAGCA|GTGTCCAGtGCTGTAGTTATGTGTTCCAGCCTCACCAGGC TTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTGTT|TGAGCA|GTGTCCAGCGCTGTAGTTATGTGTTCCAGCCTCACCAGGC Gorilla > Chimp --------------- chr20:52345615-52345620 Template switch process: F1: L TTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTGTT 1 F3: 4 GTGTCCAGTGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGTGCTT R RF: TGCTCAGTGTTTGGTAAAACCTCTTTGCTGTGAGCACAAGGTTTGCTTTAGCAATTGTTGTCACATTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTGTTCCAGCCTCACCAGGCCCTGTGCTT RR: ACGAGTCACAAACCATTTTGGAGAAACGACACTCGTGTTCCAAACGAAATCGTTAACAACAGTGTAATGTCGTTCCTCACCACAGGTCGCGACATCAATACACAAGGTCGGAGTGGTCCGGGACACGAA F2: 3 ACGAGT 2 Unidirectional alignment (log-probability: -55.5) TTACAGCAAGGAGTGGTGTCCAGCgctgtagttatgtgtttgagcagtgtccagtGCTGTAGTTATGTGTTCCAGCCTCACCAGGC TTACAGCAAGGAGTGGTGTCCAGC-------------------------------GCTGTAGTTATGTGTTCCAGCCTCACCAGGC Template switch alignment (log-probability: -22.7) TTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTGTT|TGAGCA|GTGTCCAGtGCTGTAGTTATGTGTTCCAGCCTCACCAGGC TTACAGCAAGGAGTGGTGTCCAGCGCTGTAGTTATGTGTT|TGAGCA|GTGTCCAGCGCTGTAGTTATGTGTTCCAGCCTCACCAGGC ========== Event 1722 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCAGCAAATCTAGGAAATTGCACTGGGCACTCTTCGTTCA--AGCCTGGAGCCCCTGCCCCATCCC Chimp: GGCAGCAAATCTAGGAAATTGCACTGGGCACTCTTCATTCA--AGCCTGGAGCCCCTGCCCCATCCC Gorilla: GGCAGCAAATCTAGGAAATTGCACTGGGCACTCTCCATTGC----ACTGGAGCCCCTGCCCCATCCC ↑ 3 2 1 4 Human: GGCAGCAAATCTAGGAAATTGCACTGGGCACTCTTCGTTCA--AGCCTGGAGCCCCTGCCCCATCCC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr20:49589967-49589974 Template switch process: F1: L ACAACAAGGCAGCAAATCTAGGAAATTGCACTGGGCACTCT 1 F3: 4 CTGGAGCCCCTGCCCCATCCCAGGGCAGCCAGCCTCCACC R RF: ACGACAAGGCAGCAAATCTAGGAAATTGCACTGGGCACTCTTCGTTCAAGCCTGGAGCCCCTGCCCCATCCCAGGGCAGCCAGCCTCCACC RR: TGCTGTTCCGTCGTTTAGATCCTTTAACGTGACCCGTGAGAAGCAAGTTCGGACCTCGGGGACGGGGTAGGGTCCCGTCGGTCGGAGGTGG F2: 3 ACGTTACC 2 Unidirectional alignment (log-probability: -36.7) CaACAAGGCAGCAAATCTAGGAAATTGCACTGGGCACTCT---------CcattgcaCTGGAGCCCCTGCCCCATCCCAGGGCAGCCAGCCTCCACC CGACAAGGCAGCAAATCTAGGAAATTGCACTGGGCACTCTTCGTTCAAGC-------CTGGAGCCCCTGCCCCATCCCAGGGCAGCCAGCCTCCACC Template switch alignment (log-probability: -27.8) CaACAAGGCAGCAAATCTAGGAAATTGCACTGGGCACTCT|CCAtTGCA|CTGGAGCCCCTGCCCCATCCCAGGGCAGCCAGCCTCCACC CGACAAGGCAGCAAATCTAGGAAATTGCACTGGGCACTCT|CCAGTGCA|CTGGAGCCCCTGCCCCATCCCAGGGCAGCCAGCCTCCACC ========== Event 1723 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CATGCAATGAAATGCctgttttcc---------------------ccagtgtgtgtctgtatttccccagtgtgtgtAGTTAGAGAAAAAATCCAGAAGAAAACACTCCACCATTTCAACCCCAGTACTCCAGCCCAgttctcaggcaggggt Chimp: CATGCAACGAAATGCCTATTTTCC---------------------CCAGTGTGTGTCTGTATTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAAAACACTCCACCATTTTAACCCCAGTACTCCAGCCCAgttctcaggcaggggt ↑ 4 1 3 2 Gorilla: CATGCAACGCAATGCCTATTTTCC------------------------------------------CCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAAAACACTCCACCATTTCAACCCCAGTACTCCAGCCCAgttctcaggcaggggc Human: CATGCAATGAAATGCctgttttcc---------------------ccagtgtgtgtctgtatttccccagtgtgtgtAGTTAGAGAAAAAATCCAGAAGAAAACACTCCACCATTTCAACCCCAGTACTCCAGCCCAgttctcaggcaggggt Cluster: [ ] Orangutan: CATGCAACAAAATGCCTATTTTCCAGTGTGTGTCTCTGTATTTCC---------------------CCAGTGTGTGTAGTTAGGGAAAAAATCCAGAAGAAAACACTCCACCATTTCAACCCCAGTACTCCAGCCCAgttctcaggcaggggc Gorilla > Chimp --------------- chr20:14711109-14711113 Template switch process: F1: L AAAGAGAAAATGCAAGGCATGCAACGAAATGCCTATTTTCCCCAGTGTGTGT 1 F3: 4 TTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAAAACAC R RF: AAAGAGAAAATGCAAGGCATGCAACGCAATGCCTATTTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAAAACACTCCACCATTTCAACCCCAGTACTCCAG RR: TTTCTCTTTTACGTTCCGTACGTTGCGTTACGGATAAAAGGGGTCACACACATCAATCTCTTTTTTAGGTCTTCTTTTGTGAGGTGGTAAAGTTGGGGTCATGAGGTC F2: 3 ATGTC 2 Unidirectional alignment (log-probability: -46.6) CAAGGCATGCAACGaAATGCCTATtttccccagtgtgtgtctgtaTTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAA CAAGGCATGCAACGCAATGCCTAT---------------------TTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAA Template switch alignment (log-probability: -27.8) CAAGGCATGCAACGaAATGCCTATTTTCCCCAGTGTGTGT|CTGtA|TTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAA CAAGGCATGCAACGCAATGCCTATTTTCCCCAGTGTGTGT|CTGGA|TTTCCCCAGTGTGTGTAGTTAGAGAAAAAATCCAGAAGAA ========== Event 1724 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AATGCTTTCCAAAAATTTGAGTCCTTTTGTATTTTAATACAAAAGGATTAAACTCACCACAGGTAGTTCT ↑ 3 1 2 4 Chimp: AATGCTTTCCAAAAATTTGAGTCCTTTTGTATTAAAATACA--------AAACTCACCACAGGTAGTTCT ↓ 3 1 2 4 Gorilla: aatgctttccAAAACTTTGAGTCCTTTTGTATTTTAATACAAAAGGATTAAACTCACCACAGGTAGTTCT Human: AATGCTTTCCAAAAATTTGAGTCCTTTTGTATTTTAATACAAAAGGATTAAACTCACCACAGGTAGTTCT Cluster: [ ] Orangutan: aatactttccAAAAATTTGAGTCCTTTTGTATTAAAATACAAAAGGATTAAACTCACCACAGGTAGTTGT Chimp > Human ------------- chr20:13264592-13264607 Template switch process: F1: L ATTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATT 1 F3: 4 AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT R RF: ATTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATTAAAATACAAAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT RR: TAATATACTTACGAAAGGTTTTTAAACTCAGGAAAACATAATTTTATGTTTTGAGTGGTGTCCATCAAGATTACACACAATTATACAAA F2: 3 TTAGGAAAACATAATT 2 Unidirectional alignment (log-probability: -34.5) TTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATTttAATACAAaaggattaAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT TTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATTAAAATACAA--------AACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT Template switch alignment (log-probability: -23.3) TTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATT|TTAATACAAAAGGAtT|AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT TTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATT|TTAATACAAAAGGACT|AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT Chimp > Gorilla --------------- chr20:13144802-13144817 Template switch process: F1: L ATTATATGAATGCTTTCCAAAACTTTGAGTCCTTTTGTATT 1 F3: 4 AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT R RF: ATTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATTAAAATACAAAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT RR: TAATATACTTACGAAAGGTTTTTAAACTCAGGAAAACATAATTTTATGTTTTGAGTGGTGTCCATCAAGATTACACACAATTATACAAA F2: 3 TTAGGAAAACATAATT 2 Unidirectional alignment (log-probability: -39.1) TTATATGAATGCTTTCCAAAAcTTTGAGTCCTTTTGTATTttAATACAaaaggattAAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT TTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATTAAAATACA--------AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT Template switch alignment (log-probability: -28.8) TTATATGAATGCTTTCCAAAAcTTTGAGTCCTTTTGTATT|TTAATACAAAAGGAtT|AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT TTATATGAATGCTTTCCAAAAATTTGAGTCCTTTTGTATT|TTAATACAAAAGGACT|AAACTCACCACAGGTAGTTCTAATGTGTGTTAATATGTTT ========== Event 1725 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTTTATCTGGGACAATTAA----------ATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTT Chimp: TATTTTATCTGGGACAATTAA----------ATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTT ↓ 1 3 4 2 Gorilla: TATTTTATCTGGGACAATTAAAAGATCGAAAAGAGCACTTTTCGATCTCCCGTTTTTCTTCTGGGTTT ↑ 1 3 4 2 Human: TATTTTATCTGGGACAATTAA----------ATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTT Cluster: [ ] Orangutan: TATTTTATCTGGGACAATTAA----------ATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTT Human > Gorilla --------------- chr20:12135961-12135975 Template switch process: F1: L ACAAGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAA 1 F3: 4 CTTTTCGATCTCCCGTTTTTCTTCTGGGTTTGATACCGGT R RF: ACAAGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTTGATACCGGT RR: TGTTCATATGAACATTTAGAATAAAATAGACCCTGTTAATTTAACGAGAAAAGCTAGAGGGTAAAAAGAAGACCCAAACTATGGCCA F2: 3 ACGAGAAAAGCTAGA 2 Unidirectional alignment (log-probability: -47.4) AAGTATACTTGTAAATCTTATTTTATCTGGGACAATTaaaagatcgaAAAgaGCaCTTTTCGATCTCCCgTTTTTCTTCTGGGTTTGATACCGGT AAGTATACTTGTAAATCTTATTTTATCTGGGACAATT----------AAATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTTGATACCGGT Template switch alignment (log-probability: -23.2) AAGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAA|AGATCGAAAAGAGCA|CTTTTCGATCTCCCgTTTTTCTTCTGGGTTTGATACCGGT AAGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAA|AGATCGAAAAGAGCA|CTTTTCGATCTCCCATTTTTCTTCTGGGTTTGATACCGGT Chimp > Gorilla --------------- chr20:12135961-12135975 Template switch process: F1: L ACAAGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAA 1 F3: 4 CTTTTCGATCTCCCGTTTTTCTTCTGGGTTTGATACCGGT R RF: ACAGGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTTGATACCGGT RR: TGTCCATATGAACATTTAGAATAAAATAGACCCTGTTAATTTAACGAGAAAAGCTAGAGGGTAAAAAGAAGACCCAAACTATGGCCA F2: 3 ACGAGAAAAGCTAGA 2 Unidirectional alignment (log-probability: -52.9) AaGTATACTTGTAAATCTTATTTTATCTGGGACAATTaaaagatcgaAAAgaGCaCTTTTCGATCTCCCgTTTTTCTTCTGGGTTTGATACCGGT AGGTATACTTGTAAATCTTATTTTATCTGGGACAATT----------AAATTGCTCTTTTCGATCTCCCATTTTTCTTCTGGGTTTGATACCGGT Template switch alignment (log-probability: -28.7) AaGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAA|AGATCGAAAAGAGCA|CTTTTCGATCTCCCgTTTTTCTTCTGGGTTTGATACCGGT AGGTATACTTGTAAATCTTATTTTATCTGGGACAATTAAA|AGATCGAAAAGAGCA|CTTTTCGATCTCCCATTTTTCTTCTGGGTTTGATACCGGT ========== Event 1726 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GAGCCACGGAAAGCTTTCACACTGTTCTCCCTGGCAGTCAAGGAGCCGTTGCTATGATGTGCAGTCTCAGCACGTGCATCCTGAGCCAGCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTCA----GTGCTCCCAATAAACTTGAAAGCT ↑ 3 2 1 4 Chimp: GAGCCACGGAAAGCTTTCACACTGTTCT-CCTGGCAGTCAAGGAGCCGTTGCTATGATGTGCAGTCTCAGCACGTGCATCCTGAGCCAGCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTTGAAATAAACTCCCAATAAACTTGAAAGCT ↓ 3 2 1 4 Gorilla: GAGCCACGGAAAGCTTTCACACTGTTCTCCCTGGCAGTCAAGGAGCCGTTGCTATGATGTGCAGTCTCAGCACGTGCATCCTGAGCCAGTCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTCA----GTGCTCCCAATAAACTTGAAAGCT Human: GAGCCACGGAAAGCTTTCACACTGTTCTCCCTGGCAGTCAAGGAGCCGTTGCTATGATGTGCAGTCTCAGCACGTGCATCCTGAGCCAGCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTCA----GTGCTCCCAATAAACTTGAAAGCT Cluster: [ ] Orangutan: GAGCCACGGAAAGCTTTCACACTGTTCTCTCTGGCAGTCAAGGAGCCATTGCTATGATGTGCAGTCTCAGCACGCGTATCCTGAGCCAGCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTCA----GTGCTCCCAATAAACTTGGAAGCT Chimp > Human ------------- chr20:11355250-11355254 Template switch process: F1: L GCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT 1 F3: 4 CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA R RF: CACTGTTCTCCTGGCAGTCAAGGAGCCGTTGCTATGATGTGCAGTCTCAGCACGTGCATCCTGAGCCAGCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTTGAAATAAACTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA RR: GTGACAAGAGGACCGTCAGTTCCTCGGCAACGATACTACACGTCAGAGTCGTGCACGTAGGACTCGGTCGGCTTCTTACGTCTTGTTGGATTAACGATAGGAACCTTGAACTTTATTTGAGGGTTATTTGAACTTTCGACTTATCGTTGTAAAGTGTT F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -25.8) CCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTcagTG-------CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA CCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT---TGAAATAAACTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA Template switch alignment (log-probability: -15.9) CCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT|CAGTG|CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA CCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT|CAGTG|CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA Chimp > Gorilla --------------- chr20:11122254-11122258 Template switch process: F1: L GTCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT 1 F3: 4 CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA R RF: CACTGTTCTCCTGGCAGTCAAGGAGCCGTTGCTATGATGTGCAGTCTCAGCACGTGCATCCTGAGCCAGCCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTTGAAATAAACTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA RR: GTGACAAGAGGACCGTCAGTTCCTCGGCAACGATACTACACGTCAGAGTCGTGCACGTAGGACTCGGTCGGCTTCTTACGTCTTGTTGGATTAACGATAGGAACCTTGAACTTTATTTGAGGGTTATTTGAACTTTCGACTTATCGTTGTAAAGTGTT F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -30.8) tCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACTcagTG-------CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA CCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT---TGAAATAAACTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA Template switch alignment (log-probability: -21.9) tCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT|CAGTG|CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA CCGAAGAATGCAGAACAACCTAATTGCTATCCTTGGAACT|CAGTG|CTCCCAATAAACTTGAAAGCTGAATAGCAACATTTCACAA ========== Event 1727 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTATTATTTGGAGTACTCATTTAAGAGTCACCTACTGTTAAGGTGACTCTTAAATACAAATACAAGACATCTTTT Chimp: CTATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAAGGTGACTCTTAAATACAAATACAAGACATCTTTT ↑ 3 2 1 4 Gorilla: CTATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAA--------ATACTTACAAATACAAGACATCTTTT ↓ 3 2 1 4 Human: CTATTATTTGGAGTACTCATTTAAGAGTCACCTACTGTTAAGGTGACTCTTAAATACAAATACAAGACATCTTTT Cluster: [ ] Orangutan: CTATTATTTGGAGTACTCATTTAAGCGTCACCTACAGTTAA--------ATACTTATAAATACAAGACATCTTTT Gorilla > Human --------------- chr20:11455134-11455146 Template switch process: F1: L CTTATCCTATTATTTGGAGTACTCATTTAAGAGTCACCTACTGTTAA 1 F3: 4 TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC R RF: CTTATCCTATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAAATACTTACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC RR: GAATAGGATAATAAACCTCATGAGTAAATTCTCAGTGGATGTCAATTTATGAATGTTTATGTTCTGTAGAAAATCTGTAGAACTGGTATTTG F2: 3 AAATTCTCAGTGG 2 Unidirectional alignment (log-probability: -43.7) TATTATTTGGAGTACTCATTTAAGAGTCACCTACtGttaaggtgactcTTAAA----TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC TATTATTTGGAGTACTCATTTAAGAGTCACCTACAG------------TTAAATACTTACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC Template switch alignment (log-probability: -23.1) TATTATTTGGAGTACTCATTTAAGAGTCACCTACtGTTAA|GGTGACTCTTAAA|TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC TATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAA|GGTGACTCTTAAA|TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC Gorilla > Chimp --------------- chr20:11697574-11697586 Template switch process: F1: L CTATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAA 1 F3: 4 TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC R RF: CTATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAAATACTTACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC RR: GATAATAAACCTCATGAGTAAATTCTCAGTGGATGTCAATTTATGAATGTTTATGTTCTGTAGAAAATCTGTAGAACTGGTATTTG F2: 3 AAATTCTCAGTGG 2 Unidirectional alignment (log-probability: -38.1) TATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTaaggtgactcttAAA----TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC TATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTT------------AAATACTTACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC Template switch alignment (log-probability: -17.4) TATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAA|GGTGACTCTTAAA|TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC TATTATTTGGAGTACTCATTTAAGAGTCACCTACAGTTAA|GGTGACTCTTAAA|TACAAATACAAGACATCTTTTAGACATCTTGACCATAAAC ========== Event 1728 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: aTGAAAAATGGCCAAAGTTTTATTGGCAATAGCCAATTAATTAAGCTCTAACCTTAATTAAATTGTTA ↑ 3 1 4 2 Chimp: aTGAAAAATGGCCAAAGTTTTATTGGC-----------TATTAAGCTTTAACCTTAATTAAATTGTTA Gorilla: aTGAAAAATGGCCAAAGTTTTATTGGC-----------TATTAAGCTTTAACCTTAATTAAATTGTTA ↓ 3 1 4 2 Human: aTGAAAAATGGCCAAAGTTTTATTGGCAATAGCCAATTAATTAAGCTCTAACCTTAATTAAATTGTTA Cluster: [ ] Orangutan: aTGAAAAATGGCCAAAGTTTTATTGGC-----------TATTAAGCTTTAACCTTAATTAAATTGTTA Chimp > Human ------------- chr20:10125844-10125855 Template switch process: F1: L AAAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC 1 F3: 4 ATTAAGCTCTAACCTTAATTAAATTGTTACAAATTTAATTGTAAACAAA R RF: AAAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGCTATTAAGCTTTAACCTTAATTAAATTGTTACAAATTTAATTGTAAACAAA RR: TTTTTATCGGTATCTACTTTTTACCGGTTTCAAAATAACCGATAATTCGAAATTGGAATTAATTTAACAATGTTTAAATTAACATTTGTTT F2: 3 ATTAACCGATAA 2 Unidirectional alignment (log-probability: -38.8) AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGCaATagccaattaatTAAGCTcTAACCTTAATTAAATTGTTACAAATTTAATT AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGCTAT-----------TAAGCTTTAACCTTAATTAAATTGTTACAAATTTAATT Template switch alignment (log-probability: -28.9) AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC|AATAGCCAATtA|ATTAAGCTcTAACCTTAATTAAATTGTTACAAATTTAATT AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC|AATAGCCAATAA|ATTAAGCTTTAACCTTAATTAAATTGTTACAAATTTAATT Gorilla > Human --------------- chr20:10125844-10125855 Template switch process: F1: L AAAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC 1 F3: 4 ATTAAGCTCTAACCTTAATTAAATTGTTACAAATTTAATTGTAAACAAA R RF: AAAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGCTATTAAGCTTTAACCTTAATTAAATTGTTACAAATTTAATTGTAAACAAA RR: TTTTTATCGGTATCTACTTTTTACCGGTTTCAAAATAACCGATAATTCGAAATTGGAATTAATTTAACAATGTTTAAATTAACATTTGTTT F2: 3 ATTAACCGATAA 2 Unidirectional alignment (log-probability: -37.9) AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGCaatagccaattaATTAAGCTcTAACCTTAATTAAATTGTTACAAATTTAATT AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC-----------TATTAAGCTTTAACCTTAATTAAATTGTTACAAATTTAATT Template switch alignment (log-probability: -28.5) AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC|AATAGCCAATtA|ATTAAGCTcTAACCTTAATTAAATTGTTACAAATTTAATT AAAATAGCCATAGATGAAAAATGGCCAAAGTTTTATTGGC|AATAGCCAATAA|ATTAAGCTTTAACCTTAATTAAATTGTTACAAATTTAATT ========== Event 1729 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GAGGCTGAGTCAAAAAAAGATATAAGAATGGAGACAGGAGAAGATAGAAATGGAGatttcattttctcttctcaaaaagaagacaactttctgattccacaataggaggccaaggt Chimp: GAGGCTGAGTCaaaaaaaGATGTAAGAATGGAGACAGGAGAAGATAGAAAATGAAATCTCCATTTCTCTTCTCAAAAAGAAGACAACTTTCTGATTCCACAATAGGAGGCCAAGGT Gorilla: GAGGCTGAGTCaaaaaaaGATGAAAGAATGGAGACAGGAGAAGAGAGAAAATGAAATCTCCATTTCTCTTCTCAAAAAGAAGACAACTTTCTGATTCCACAATAGGAGGCCAAGGT ↑ 1 3 2 4 Human: GAGGCTGAGTCAAAAAAAGATATAAGAATGGAGACAGGAGAAGATAGAAATGGAGatttcattttctcttctcaaaaagaagacaactttctgattccacaataggaggccaaggt Cluster: [] Orangutan: AAGGCTGAGTCAAAAAAAGATA--TGAGTGGAGACAGGAGAAGATAGAAATGGAGATTTCATTTTCTCTTCTCAAAAAGGAGACAACTTTCTAATTCCACAATAGGAGGCCAAGAT Human > Gorilla --------------- chr20:54693303-54693318 Template switch process: F1: L AACTTATGATTCCTTTCATCGAGGCTGAGTCAAAAAAAGATGAAAGAATGGAGACAGGAGAAGA 1 F3: 4 CAT R RF: AACTTATGATTCCTTTCATCGAGGCTGAGTCAAAAAAAGATATAAGAATGGAGACAGGAGAAGATAGAAATGGAGATTTCATTTTCTCTTCTCAAAAAGAAGACAACTTTCTGATTCCACAATAGGAGGCCAAGGTGTTATGAACCTCAT RR: TTGAATACTAAGGAAAGTAGCTCCGACTCAGTTTTTTTCTATATTCTTACCTCTGTCCTCTTCTATCTTTACCTCTAAAGTAAAAGAGAAGAGTTTTTCTTCTGTTGAAAGACTAAGGTGTTATCCTCCGGTTCCACAATACTTGGAGTA F2: 3 CTCTAAAGTAAAAGAG 2 Unidirectional alignment (log-probability: -50.8) CTGAGTCAAAAAAAGATgaAAGAATGGAGACAGGAGAAGAgAGAAAatGAaATcTCcaT CTGAGTCAAAAAAAGATATAAGAATGGAGACAGGAGAAGATAGAAATGGAGATTTCATT Template switch alignment (log-probability: -28.4) CTGAGTCAAAAAAAGATgaAAGAATGGAGACAGGAGAAGA|GAGAAAATGAAATCTC|CAT CTGAGTCAAAAAAAGATATAAGAATGGAGACAGGAGAAGA|GAGAAAATGAAATCTC|CAT ========== Event 1730 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAGGGGGCTCAGTGTTGAAAAGGAACTCACAGGTTCCTACTCACAGACTCTCTCAGTAGGACATTG ↓ 1 3 42 Chimp: AAGGGGGCTCAGTGTTGAAAATGAACCT------------GTGAAGACTCTCTCAGTAGGACATTG Gorilla: AAGGGGGCTCAGTGTTGAAAATGAACCT------------GTGAAGACTCTCTCAGTAGGACATTG ↑ 1 3 42 Human: AAGGGGGCTCAGTGTTGAAAAGGAACTCACAGGTTCCTACTCACAGACTCTCTCAGTAGGACATTG Cluster: [ ] Orangutan: AAGGGGGCTCAGTGTTGAAAACGAACCT------------GTGAAGACTCTCTCAGTAGGACATTG Human > Chimp ------------- chr20:59366693-59366698 Template switch process: F1: L TTAAAGTCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAATGAAC 1 F3: 4 AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA R RF: TTAAAGTCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAGGAACTCACAGGTTCCTACTCACAGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA RR: AATTTCAGGACCCCACAATTTTCCCCCGAGTCACAACTTTTCCTTGAGTGTCCAAGGATGAGTGTCTGAGAGAGTCATCCTGTAACTACTGTGTGACCATGGTT F2: 3 AGTGTC 2 Unidirectional alignment (log-probability: -35.2) TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAtGAAC-----------------CtgtgaAGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAGGAACTCACAGGTTCCTACTCAC-----AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA Template switch alignment (log-probability: -22.1) TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAtGAAC|CTGTGA|AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAGGAAC|CTGTGA|AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA Human > Gorilla --------------- chr20:56328451-56328456 Template switch process: F1: L TTAAAGTCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAATGAAC 1 F3: 4 AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA R RF: TTAAAGTCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAGGAACTCACAGGTTCCTACTCACAGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA RR: AATTTCAGGACCCCACAATTTTCCCCCGAGTCACAACTTTTCCTTGAGTGTCCAAGGATGAGTGTCTGAGAGAGTCATCCTGTAACTACTGTGTGACCATGGTT F2: 3 AGTGTC 2 Unidirectional alignment (log-probability: -34.3) TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAtGAAC-----------------CtgtgaAGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAGGAACTCACAGGTTCCTACTCAC-----AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA Template switch alignment (log-probability: -22.1) TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAtGAAC|CTGTGA|AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA TCCTGGGGTGTTAAAAGGGGGCTCAGTGTTGAAAAGGAAC|CTGTGA|AGACTCTCTCAGTAGGACATTGATGACACACTGGTACCAA ========== Event 1731 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTTGACCCTTCTCCCACCCCT----CAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGG Chimp: TGTTGACCCTTCTCCCACCCCT----CAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGG ↓ 1 4 3 2 Gorilla: TGTTGACCCTTCTCCCACCCCACTGTAATGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGG ↑ 1 4 3 2 Human: TGTTGACCCTTCTCCCACCCCT----CAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGG Cluster: [ ] Orangutan: TGTTGACCCTTCTCCCATCCCT----CAGGATGTGGCCATTAGAGTCAGGCTTGAAGAAGCAGAGG Human > Gorilla --------------- chr20:57390520-57390527 Template switch process: F1: L CAGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC 1 F3: 4 GATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA R RF: CAGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCCTCAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA RR: GTCGTGCACACACTGAAGGAACAACTGGGAAGAGGGTGGGGAGTCCTACACCGGTAATGTCAGTCCGAACTTCGTCCTCTCCTCT F2: 3 TAATGTCA 2 Unidirectional alignment (log-probability: -27.7) AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCCactgTaAtGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC----TCAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA Template switch alignment (log-probability: -16.7) AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC|ACTGTAAT|GATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC|ACTGTAAT|GATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA Chimp > Gorilla --------------- chr20:57390520-57390527 Template switch process: F1: L CAGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC 1 F3: 4 GATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA R RF: CAGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCCTCAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA RR: GTCGTGCACACACTGAAGGAACAACTGGGAAGAGGGTGGGGAGTCCTACACCGGTAATGTCAGTCCGAACTTCGTCCTCTCCTCT F2: 3 TAATGTCA 2 Unidirectional alignment (log-probability: -27.7) AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCCactgTaAtGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC----TCAGGATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA Template switch alignment (log-probability: -16.7) AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC|ACTGTAAT|GATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA AGCACGTGTGTGACTTCCTTGTTGACCCTTCTCCCACCCC|ACTGTAAT|GATGTGGCCATTACAGTCAGGCTTGAAGCAGGAGAGGAGA ========== Event 1732 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCGGGAAGCTCCGCTGTAGT--------------------GTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACTAACAAGGTGTGTCACCTAGAGCAAGGTACTTCTGCTCACTCAGGTGCACGGGTaaa-aaaaaaTCGGATGTGACAGCTAGACCAATGGTTTGCG ↓ 4 1 3 2 Chimp: GTCGGGAAGCTCCGCTGTAGT----------GTAGTCACATGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACTAACAAGGTGTGTCACCTAGAGCAAGGTACTTCTGCTCACTCAGGTGCACGGGTaaa-aaaaaaTCGGATGTGACAGCTAGACCAATGGTTTGCG Gorilla: GTCGGGAAGCTCCGCTGTAGTGTAGTCACAT----------GTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACTAACAAGGTGTGTCACCTAGAGCAAGGTACTTCTGCTCACTCAGGTGCACGGGTaaa-aaaaaaTCGGATGTGACAGCTAGACCAATGGTTTGCA Human: GTCGGGAAGCTCCGCTGTAGT--------------------GTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACTAACAAGGTGTGTCACCTAGAGCAAGGTACTTCTGCTCACTCAGGTGCACGGGTaaa-aaaaaaTCGGATGTGACAGCTAGACCAATGGTTTGCG Cluster: [ ] Orangutan: GTCGGGAAGCTCTGTTGTAGTGTAGTCACAT----------GTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACTAACAAGGTGTGTCACCTAGAGCAAGGTACTTCTGCTCACTCAGGTGCACGGGTaaaaaaaaaaTCGGATGTGACACCTAGACCAATGGTTTGCG Human > Chimp ------------- chr20:61052582-61052587 Template switch process: F1: L CGCTGGCTTGACCTCAGCAAGTCGGGAAGCTCCGCTGTAGTGTA 1 F3: 4 TGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACT R RF: CGCTGGCTTGACCTCAGCAAGTCGGGAAGCTCCGCTGTAGTGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAACTAACAAGGTGTGTCACCTAGAGCAAGGTACTTCTGCTCACTCAGGTGCACGGGTAAAAAAAAATCGGATGTGAC RR: GCGACCGAACTGGAGTCGTTCAGCCCTTCGAGGCGACATCACATGGGTGTTTTACATTTCACGATGTGGTAGGTCAGTTGATTGTTCCACACAGTGGATCTCGTTCCATGAAGACGAGTGAGTCCACGTGCCCATTTTTTTTTAGCCTACACTG F2: 3 ACACTG 2 Unidirectional alignment (log-probability: -25.3) GGCTTGACCTCAGCAAGTCGGGAAGCTCCGCTGTAGtgtagtcacaTGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAAC GGCTTGACCTCAGCAAGTCGGGAAGCTCCGCTGTAG----------TGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAAC Template switch alignment (log-probability: -16.1) GGCTTGACCTCAGCAAGTCGGGAAGCTCCGCTGTAGTGTA|GTCACA|TGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAAC GGCTTGACCTCAGCAAGTCGGGAAGCTCCGCTGTAGTGTA|GTCACA|TGTACCCACAAAATGTAAAGTGCTACACCATCCAGTCAAC ========== Event 1733 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CAAAGGCAATCTTAAGTAATGTCTTTTTGACAAAAATGTCAAAAAGAATGGCCAACAAATATAAAAA Chimp: CAAAGGCAATCTTAAGTAATGTCTTTTTGACAAAAATATCAAAAAGAATGGCCAACAAATATAAAAA ↑ 1 4 3 2 Gorilla: CAAAGGCAATCTTAAGTAATGGTCAGACACCAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAA ↓ 1 4 3 2 Human: CAAAGGCAATCTTAAGTAATGTCTTTTTGACAAAAATGTCAAAAAGAATGGCCAACAAATATAAAAA Cluster: [ ] Orangutan: CAAAGGCAATGTTAAGTAATGGTCAGACACCAAAAATGTCAAAAAGAATGGCCAACAGATATAAAAA Gorilla > Human --------------- chr20:6404702-6404710 Template switch process: F1: L TTTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG 1 F3: 4 CAAAAATGTCAAAAAGAATGGCCAACAAATATAAAAACCA R RF: TTTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATGGTCAGACACCAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAACCA RR: AAAACCTTCCTTCGTTCTGTGTTTCCGTTAGAATTCATTACCAGTCTGTGGTTTTTACAGTTTTTCTTACCGATTGTTTATATTTTTGGT F2: 3 AGTTTTTCT 2 Unidirectional alignment (log-probability: -39.5) TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG---------tctttttgaCAAAAATGTCAAAAAGAATGGCcAACAAATATAAAAACCA TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATGGTCAGACAC---------CAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAACCA Template switch alignment (log-probability: -22.4) TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG|TCTTTTTGA|CAAAAATGTCAAAAAGAATGGCcAACAAATATAAAAACCA TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG|TCTTTTTGA|CAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAACCA Gorilla > Chimp --------------- chr20:6278962-6278970 Template switch process: F1: L TTTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG 1 F3: 4 CAAAAATATCAAAAAGAATGGCCAACAAATATAAAAACCAACTAGCCA R RF: TTTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATGGTCAGACACCAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAACCAACTAGCCA RR: AAAACCTTCCTTCGTTCTGTGTTTCCGTTAGAATTCATTACCAGTCTGTGGTTTTTACAGTTTTTCTTACCGATTGTTTATATTTTTGGTTGATCGGT F2: 3 AGTTTTTCT 2 Unidirectional alignment (log-probability: -45.2) TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG---------tctttttgaCAAAAATaTCAAAAAGAATGGCcAACAAATATAAAAACCA TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATGGTCAGACAC---------CAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAACCA Template switch alignment (log-probability: -28.1) TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG|TCTTTTTGA|CAAAAATaTCAAAAAGAATGGCcAACAAATATAAAAACCA TTTGGAAGGAAGCAAGACACAAAGGCAATCTTAAGTAATG|TCTTTTTGA|CAAAAATGTCAAAAAGAATGGCTAACAAATATAAAAACCA ========== Event 1734 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGGTAGGATGGAGCAATTACC-TC-ATGGGAGAACGCACCATGAGGACAAATACGGAGCTGGCTT ↑ 1 4 3 2 Chimp: AGGGTAGGATGGAGCAATTACTCTGACCTCGAGAACGCACCATGAGGACAAATACGGAGCTGGCTT Gorilla: AGGGTAGGATGGAGCAATTACTCTGACCTCGAGAACGCACCATGAGGACAAATACGGAGCTGGCTT ↓ 1 4 3 2 Human: AGGGTAGGATGGAGCAATTACC-TC-ATGGGAGAACGCACCATGAGGACAAATACGGAGCTGGCTT Cluster: [ ] Orangutan: ACGGTAGGATGGAGCAATTACTCTGACCTCGAGAACGCACCATGAGGACAAATATGGAGCTGGCTT Chimp > Human ------------- chr20:4669077-4669083 Template switch process: F1: L CCCGAGCCCCGGAGTCCTCAAGGGTAGGATGGAGCAATTAC 1 F3: 4 GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA R RF: CCCGAGCCCTGGAGTCCTCAAGGGTAGGATGGAGCAATTACTCTGACCTCGAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA RR: GGGCTCGGGACCTCAGGAGTTCCCATCCTACCTCGTTAATGAGACTGGAGCTCTTGCGTGGTACTCCTGTTTATGCCTCGACCGAAGGTT F2: 3 GGTACTC 2 Unidirectional alignment (log-probability: -33.2) CCGAGCCCcGGAGTCCTCAAGGGTAGGATGGAGCAATT------ACCTCatggGAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA CCGAGCCCTGGAGTCCTCAAGGGTAGGATGGAGCAATTACTCTGACCTC----GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA Template switch alignment (log-probability: -22.1) CCGAGCCCcGGAGTCCTCAAGGGTAGGATGGAGCAATTAC|CTCATGG|GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA CCGAGCCCTGGAGTCCTCAAGGGTAGGATGGAGCAATTAC|CTCATGG|GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA Gorilla > Human --------------- chr20:4669077-4669083 Template switch process: F1: L CCCGAGCCCCGGAGTCCTCAAGGGTAGGATGGAGCAATTAC 1 F3: 4 GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA R RF: CCCGAACCCCGGAGTCCTCAAGGGTAGGATGGAGCAATTACTCTGACCTCGAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA RR: GGGCTTGGGGCCTCAGGAGTTCCCATCCTACCTCGTTAATGAGACTGGAGCTCTTGCGTGGTACTCCTGTTTATGCCTCGACCGAAGGTT F2: 3 GGTACTC 2 Unidirectional alignment (log-probability: -32.2) CCGAgCCCCGGAGTCCTCAAGGGTAGGATGGAGCAATT------ACCTCatggGAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA CCGAACCCCGGAGTCCTCAAGGGTAGGATGGAGCAATTACTCTGACCTC----GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA Template switch alignment (log-probability: -22.1) CCGAgCCCCGGAGTCCTCAAGGGTAGGATGGAGCAATTAC|CTCATGG|GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA CCGAACCCCGGAGTCCTCAAGGGTAGGATGGAGCAATTAC|CTCATGG|GAGAACGCACCATGAGGACAAATACGGAGCTGGCTTCCAA ========== Event 1735 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATATTTCCAAAAGATTATAA------------------------------------------AGTACAATGGCATGtgtacaagttatctcttact ↓ 4 3 1 2 Chimp: CATATTTCCAAAAGATTATAA---------------------AGTCCAACCTGCCATTGTAAAAGTACAATGGCATGtgtacaagttatctcttact Gorilla: CATATTCCCAAAAGATTATAAAGTTCAACCTGCCATTGTAAA---------------------AGTACAATGGCATGtgtactagttatctcttact Human: CATATTTCCAAAAGATTATAA------------------------------------------AGTACAATGGCATGtgtacaagttatctcttact Cluster: [ ] Orangutan: CATATTTCCAAAAGATTATAAAGTCCAAACTGCCATTGTAAA---------------------AGTACAATGGCATGtgtactagttatctcttact Human > Chimp ------------- chr20:62647567-62647578 Template switch process: F1: L ATGGAAGTTTTAAAAATAAACATATTTCCAAAAGATTATAAAGTCCAA 1 F3: 4 AAAGTACAATGGCATGTGTACAAGTTATCTCTTACTGTGTAA R RF: ATGGAAGTTTTAAAAATAAACATATTTCCAAAAGATTATAAAGTACAATGGCATGTGTACAAGTTATCTCTTACTGTGTAA RR: TACCTTCAAAATTTTTATTTGTATAAAGGTTTTCTAATATTTCATGTTACCGTACACATGTTCAATAGAGAATGACACATT F2: 3 ATGTTACCGTCC 2 Unidirectional alignment (log-probability: -41.1) TTTAAAAATAAACATATTTCCAAAAGATTATAAAgtccaacctgccattgtaaaaGTACAATGGCATGTGTACAAGTTATCTCTTACTGTGT TTTAAAAATAAACATATTTCCAAAAGATTATAAA---------------------GTACAATGGCATGTGTACAAGTTATCTCTTACTGTGT Template switch alignment (log-probability: -28.9) TTTAAAAATAAACATATTTCCAAAAGATTATAAAGTcCAA|CcTGCCATTGTA|AAAGTACAATGGCATGTGTACAAGTTATCTCTTACTGTGT TTTAAAAATAAACATATTTCCAAAAGATTATAAAGTACAA|CATGCCATTGTA|AAAGTACAATGGCATGTGTACAAGTTATCTCTTACTGTGT ========== Event 1736 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TACTCCCGTGTCCTGTCTGAA---TAGTCCATTTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTTAGATTATAAGGTCACCATTGAGACCACATCCCACTTCCCAAGATAACCAAATTCCATAAAGAAGTCAAGCAACATTGGTGCATTTTAATGGAATAAAACACTCCGGTGACTTCAT Chimp: TACTCCCGTGTCCTGTCTGAA---TAGTCCATTTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTATAAGGTCACCATTGAGACCACATCCCACTTCCCAAGATAACCAAATTCCATAAAGAAGTCAAGCAACATTGGTGCATTTTAATGGAATAAAACACTCCGGTGACTTCAT ↑ 1 4 3 2 Gorilla: TACTCCCGTGTCCTGTCTGAA------CTTACTTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTATAAGGTCACCATTGAGACCACATCCCACTTCCCAAGATAACCAAATTCCATAAAGAAGTCAAGCAACATTGGTGCATTTTAATGGAATAAAACACTCCGGTGACTTCAT Human: TACTCCCGTGTCCTGTCTGAA---TAGTCCATTTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTTAGATTATAAGGTCACCATTGAGACCACATCCCACTTCCCAAGATAACCAAATTCCATAAAGAAGTCAAGCAACATTGGTGCATTTTAATGGAATAAAACACTCCGGTGACTTCAT Cluster: [ ] Orangutan: TACTCCCGTGTCCTGTCTGAACAG---TCCATTTAGGGAGTAGCTTGCAGTGACCTGGGCTTGTTCAGATTATAAGGTCGCCATTGAGACCACATCCCACTTCCCAAGATCACCAAATTCCATAAAGAAGTCAAGCAGCATTGGTGCATTTTAATGGAATGAAACACTCTGGTGACTTCAT Gorilla > Chimp --------------- chr20:62563067-62563074 Template switch process: F1: L TTACAACAAGTGAAGGCAGGTACTCCCGTGTCCTGTCTGAA 1 F3: 4 TTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTA R RF: TTACGACAAGTGAAGGCAGGTACTCCCGTGTCCTGTCTGAACTTACTTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTATAAGGTCACCATTGAGACCACATCCCACTTCCCAAGATAACCAAATTCCATAAAGAAGTCAAGCAACATTGGTGCATTTTAATGGAATA RR: AATGCTGTTCACTTCCGTCCATGAGGGCACAGGACAGACTTGAATGAATCCCTCATCGAACGTCACTGGGCCCGAACAAGTCTAATATTCCAGTGGTAACTCTGGTGTAGGGTGAAGGGTTCTATTGGTTTAAGGTATTTCTTCAGTTCGTTGTAACCACGTAAAATTACCTTAT F2: 3 TACCTGAT 2 Unidirectional alignment (log-probability: -37.9) TACaACAAGTGAAGGCAGGTACTCCCGTGTCCTGTCTGAA-----tagtccatTTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTA TACGACAAGTGAAGGCAGGTACTCCCGTGTCCTGTCTGAACTTAC--------TTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTA Template switch alignment (log-probability: -27.8) TACaACAAGTGAAGGCAGGTACTCCCGTGTCCTGTCTGAA|TAgTCCAT|TTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTA TACGACAAGTGAAGGCAGGTACTCCCGTGTCCTGTCTGAA|TATTCCAT|TTAGGGAGTAGCTTGCAGTGACCCGGGCTTGTTCAGATTA ========== Event 1737 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GACACACATGAAGGTACACATTTACAGGGAAACCTGTAAATCAGGGAAATCGGGACAGCCCCACACCCC ↑ 3 4 2 1 Chimp: GACACACATGAAGGTACACATTTACAG-----------------GGAAATCGGGACAGCCCCACACCCC ↓ 3 4 2 1 Gorilla: GATACACATGAAGGTACACATTTACAGGGAAACCTGTAAATCAGGGAAATCGGGACAGCCCCACACCCC Human: GACACACATGAAGGTACACATTTACAGGGAAACCTGTAAATCAGGGAAATCGGGACAGCCCCACACCCC Cluster: [ ] Orangutan: GATACACATGAAGGTACACATTTACAGGGAAACCTGTAAATCAGGGAAATCGGGACAGCCCCACACCCC Chimp > Human ------------- chr20:61179044-61179052 Template switch process: F1: L CTCCAGTGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAA 1 F3: 4 CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCACTT R RF: CTCCAGTGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCACTT RR: GAGGTCACTCGACACTGTGTGTACTTCCATGTGTAAATGTCCCTTTAGCCCTGTCGGGGTGTGGGGAAGAGTTCCGGTGAA F2: 3 TAAATGTCC 2 Unidirectional alignment (log-probability: -35.4) TGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAAcctgtaaatcagggaaaTCGGGACAGCCCCACACCCCTTCTCAAGGCCA TGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAA-----------------TCGGGACAGCCCCACACCCCTTCTCAAGGCCA Template switch alignment (log-probability: -16.6) TGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAA|CCTGTAAAT|CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCA TGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAA|CCTGTAAAT|CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCA Chimp > Gorilla --------------- chr20:60214059-60214067 Template switch process: F1: L CTCCAATGAGCTGTGATACACATGAAGGTACACATTTACAGGGAAA 1 F3: 4 CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCACTT R RF: CTCCAGTGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCACTT RR: GAGGTCACTCGACACTGTGTGTACTTCCATGTGTAAATGTCCCTTTAGCCCTGTCGGGGTGTGGGGAAGAGTTCCGGTGAA F2: 3 TAAATGTCC 2 Unidirectional alignment (log-probability: -46.4) TGAGCTGTGAtACACATGAAGGTACACATTTAcagggaaacctgtaaatCAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCA TGAGCTGTGACACACATGAAGGTACACATTTA-----------------CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCA Template switch alignment (log-probability: -28.1) TGAGCTGTGAtACACATGAAGGTACACATTTACAGGGAAA|CCTGTAAAT|CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCA TGAGCTGTGACACACATGAAGGTACACATTTACAGGGAAA|CCTGTAAAT|CAGGGAAATCGGGACAGCCCCACACCCCTTCTCAAGGCCA ========== Event 1738 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CACTGGGGATGCCAGGCGTCATGCCATTTCACCTGT-TTAAAGGCTGAGGTCTACATCATTGCTTTTGACTGTTCACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCACATGGTACAATGTGTCAGTGGAATT ↑ 3 2 1 4 Chimp: CACTGGGGATGCCAGGCGTCATGCCATTTCACCTGTTTTAAAGGCTGAGGTCTACGTCATTGCTTTTGACTGTTCACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTC-A-GTGTACAATGTGTCAGTGGAATT Gorilla: CACTGGGGATGCCAGGCATCATGCCATTTCACCTGT-TTAAAGGCTGAGGTCTATGTCATTGCTTTTGACTGTTCACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCAT-GTGTACAATGTGTCAGTGGAATT Human: CACTGGGGATGCCAGGCGTCATGCCATTTCACCTGT-TTAAAGGCTGAGGTCTACATCATTGCTTTTGACTGTTCACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCACATGGTACAATGTGTCAGTGGAATT Cluster: [ ] Orangutan: CACTGGGGATGCCAGGCATCATGCCATTTCACCTGT-TTAAAGGCTGAGGTCTACGTCATTGCTTTTGACTGTTCACTTTCTTTACCCCTGAGTCATCTGCTGCTGCCTTTGTCGC-GTGTACAATGTGTCAGTGGAATT Chimp > Human ------------- chr20:61537203-61537206 Template switch process: F1: L TCACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCA 1 F3: 4 GTACAATGTGTCAGTGGAATTGTTAAAATAATTTTTCTTA R RF: CATGCCATTTCACCTGTTTTAAAGGCTGAGGTCTACGTCATTGCTTTTGACTGTTCACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCAGTGTACAATGTGTCAGTGGAATTGTTAAAATAATTTTTCTTA RR: GTACGGTAAAGTGGACAAAATTTCCGACTCCAGATGCAGTAACGAAAACTGACAAGTGAAAGAAAGGGGGACTCGATAGACGACGACGGAAACAGTCACATGTTACACAGTCACCTTAACAATTTTATTAAAAAGAAT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -25.5) ACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCAcatG-GTACAATGTGTCAGTGGAATTGTTAAAATAATTTTTCTTA ACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCA---GTGTACAATGTGTCAGTGGAATTGTTAAAATAATTTTTCTTA Template switch alignment (log-probability: -15.8) ACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCA|CATG|GTACAATGTGTCAGTGGAATTGTTAAAATAATTTTTCTTA ACTTTCTTTCCCCCTGAGCTATCTGCTGCTGCCTTTGTCA|CATG|GTACAATGTGTCAGTGGAATTGTTAAAATAATTTTTCTTA ========== Event 1739 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ggaagccttgGGGCCAGAGCCTGGAGACTCCAGAGGGAGTCTCCTACAGACGATGCCGCCA Chimp: ggaagccttgGGGCCAGAGCCTGGAGACTCCAGAGGGAGTCTCCTACAGACGATGCCGCCA ↑ 1 3 4 2 Gorilla: GGAAGCCTTGGGGCCAGAGCCCGGATCCTC----TGGAGTCTCCTACAGACGATGCCGCCA ↓ 1 3 4 2 Human: ggaagccttgGGGCCAGAGCCTGGAGACTCCAGAGGGAGTCTCCTACAGACGATGCCGCCA Cluster: [ ] Orangutan: ggaagcctcggggctggagCCCGGATCCTC----TGGAGTCTCCTACAGACGATGCCGCCA Gorilla > Human --------------- chr20:62604616-62604625 Template switch process: F1: L AAGGTCTGCAGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCTGGA 1 F3: 4 GGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC R RF: AAGGTCTGCGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCCGGATCCTCTGGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC RR: TTCCAGACGCCGGAGGAGCCCCTTCGGAACCCCGGTCTCGGGCCTAGGAGACCTCAGAGGATGTCTGCTACGGCGGTAGTCACCCTGGACG F2: 3 GAGACCTCAG 2 Unidirectional alignment (log-probability: -44.4) CTGCaGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCtGGAgaCTCcagagGGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC CTGCGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCCGGATCCTC----TGGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC Template switch alignment (log-probability: -28.1) CTGCaGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCtGGA|GACTCCAGAG|GGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC CTGCGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCCGGA|GACTCCAGAG|GGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC Gorilla > Chimp --------------- chr20:64713455-64713464 Template switch process: F1: L AAGGTCTGTGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCTGGA 1 F3: 4 GGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC R RF: AAGGTCTGCGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCCGGATCCTCTGGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC RR: TTCCAGACGCCGGAGGAGCCCCTTCGGAACCCCGGTCTCGGGCCTAGGAGACCTCAGAGGATGTCTGCTACGGCGGTAGTCACCCTGGACG F2: 3 GAGACCTCAG 2 Unidirectional alignment (log-probability: -44.4) CTGtGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCtGGAgaCTCcagagGGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC CTGCGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCCGGATCCTC----TGGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC Template switch alignment (log-probability: -28.1) CTGtGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCtGGA|GACTCCAGAG|GGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC CTGCGGCCTCCTCGGGGAAGCCTTGGGGCCAGAGCCCGGA|GACTCCAGAG|GGAGTCTCCTACAGACGATGCCGCCATCAGTGGGACCTGC ========== Event 1740 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCACGGCTGCCGCTGTCCTGGAGAGAGGCAGCAGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGCCCAGGGCCGCTGAGATCACTGGGCAGTTCCCAGGCTGGCTGGGCTG Chimp: CCACGGCTGCCGCTGTCCTGGAGAGACGCAGCAGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGCCCAGGGCCGCTGAGATCACTGGGCAGTTCCCAGGCTGGCTGGGCTG ↓ 1 4 3 2 Gorilla: CCACGGCTGCCGCTGTCCTGG----CTGCCCAAGCCCGGGAGAGGCAGTAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGCCCAGGGCCGCTGAGATCACTGGGCAGTTCCCAGGCTGGTTGGGCTG ↑ 1 4 3 2 Human: CCACGGCTGCCGCTGTCCTGGAGAGAGGCAGCAGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGCCCAGGGCCGCTGAGATCACTGGGCAGTTCCCAGGCTGGCTGGGCTG Cluster: [ ] Orangutan: CCACGGCTACTGCTGTCCTGG----CCACCCAAGCTGGGGAAAGGCAGCAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGTCCAGGGCCGCTGAGATCACTGGGCTTTTCCCAGGCTGGCTGGGCTG Human > Gorilla --------------- chr20:61508893-61508899 Template switch process: F1: L CAGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGG 1 F3: 4 AGCCCGGGAGAGGCAGTAGCCCTGGCCACACCCCTGCCAA R RF: CAGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGGAGAGAGGCAGCAGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGCCCAGGGCCGCTGAGATCACTGGGCAG RR: GTCGTCCCGTCATTCTTTCAGGTGCCGACGGCGACAGGACCTCTCTCCGTCGTCGGGCCCTCTCCGTCGTCGGGACCGGTGTGGGGACGGTTCTCGGTCGAGTCCCCGGGTCCCGGCGACTCTAGTGACCCGTC F2: 3 ACCCGTC 2 Unidirectional alignment (log-probability: -35.3) AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTG----------GCtgcccaAGCCCGGGAGAGGCAGtAGCCCTGGCCACACCCCTGCCAA AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGGAGAGAGGCAGC------AGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAA Template switch alignment (log-probability: -22.1) AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGG|CTGCCCA|AGCCCGGGAGAGGCAGtAGCCCTGGCCACACCCCTGCCAA AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGG|CTGCCCA|AGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAA Chimp > Gorilla --------------- chr20:61508893-61508899 Template switch process: F1: L CAGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGG 1 F3: 4 AGCCCGGGAGAGGCAGTAGCCCTGGCCACACCCCTGCCAA R RF: CAGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGGAGAGACGCAGCAGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAAGAGCCAGCTCAGGGGCCCAGGGCCGCTGAGATCACTGGGCAG RR: GTCGTCCCGTCATTCTTTCAGGTGCCGACGGCGACAGGACCTCTCTGCGTCGTCGGGCCCTCTCCGTCGTCGGGACCGGTGTGGGGACGGTTCTCGGTCGAGTCCCCGGGTCCCGGCGACTCTAGTGACCCGTC F2: 3 ACCCGTC 2 Unidirectional alignment (log-probability: -35.3) AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTG----------GCtgcccaAGCCCGGGAGAGGCAGtAGCCCTGGCCACACCCCTGCCAA AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGGAGAGACGCAGC------AGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAA Template switch alignment (log-probability: -22.1) AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGG|CTGCCCA|AGCCCGGGAGAGGCAGtAGCCCTGGCCACACCCCTGCCAA AGCAGGGCAGTAAGAAAGTCCACGGCTGCCGCTGTCCTGG|CTGCCCA|AGCCCGGGAGAGGCAGCAGCCCTGGCCACACCCCTGCCAA ========== Event 1741 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TGCCTCCACATGGGGCCTCAGCACCGGCTGGTGCCTGGCACCCCGCACGCGG Chimp: TGCCTCCACATGGGGCCTCAGCACCGGCTGGTGCCTGGCACCCCGCACGCAG Gorilla: TGCCTCCACGTGGGGCCTCAG--CTAGCCGGTGCCTGGCACCCCGCACGCGG ↓ 1 3 4 2 Human: TGCCTCCACATGGGGCCTCAGCACCGGCTGGTGCCTGGCACCCCGCACGCGG Cluster: [ ] Orangutan: TGCCTCCACATGGGGCCTCAG--CTAGCCGGTGCCTGGCACCCCGCACGCAG Gorilla > Human --------------- chr20:1709126-1709132 Template switch process: F1: L TGCTGCCCATCATGCAGGGCTGCCTCCACATGGGGCCTCAGC 1 F3: 4 GGTGCCTGGCACCCCGCACGCGGCACCCCACCCCAAGGGG R RF: TGCTGCCCATCACGCAGGGCTGCCTCCACGTGGGGCCTCAGCTAGCCGGTGCCTGGCACCCCGCACGCGGCACCCCACCCCAAGGGG RR: ACGACGGGTAGTGCGTCCCGACGGAGGTGCACCCCGGAGTCGATCGGCCACGGACCGTGGGGCGTGCGCCGTGGGGTGGGGTTCCCC F2: 3 TCGGCCA 2 Unidirectional alignment (log-probability: -40.5) CTGCCCATCAtGCAGGGCTGCCTCCACaTGGGGCCTCAgcaccgGCT----GGTGCCTGGCACCCCGCACGCGGCACCCCACCCCAAGGGG CTGCCCATCACGCAGGGCTGCCTCCACGTGGGGCCTCA------GCTAGCCGGTGCCTGGCACCCCGCACGCGGCACCCCACCCCAAGGGG Template switch alignment (log-probability: -27.7) CTGCCCATCAtGCAGGGCTGCCTCCACaTGGGGCCTCAGC|ACCGGCT|GGTGCCTGGCACCCCGCACGCGGCACCCCACCCCAAGGGG CTGCCCATCACGCAGGGCTGCCTCCACGTGGGGCCTCAGC|ACCGGCT|GGTGCCTGGCACCCCGCACGCGGCACCCCACCCCAAGGGG ========== Event 1742 ========== Phylogenetic placement: unresolved Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GATTTCTCTACATTATTTTGGTACACATTTCACTCAGCAGGTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGGTACCCTGCGCAAGATAGAGGCATGT ↑ 3 2 1 4 Chimp: GATTTCTCTACATTATTTTGGTACACATTTCACTCAGCAGGTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGATA-CCTGCGCAAGATAGAGGCATGT Gorilla: GATTTCTCTACATTATTTTGGTACACATTTCACTCAGCAGGTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGGTA-CCTGCGCAAGACAGAGGCATGT Human: GATTTCTCTACATTATTTTGGTACACATTTCACTCAGCAGGTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGGTACCCTGCGCAAGATAGAGGCATGT Cluster: [ ] Orangutan: GATTTCTCTACATTATTTTGGTACACATTTCACTCAGCAGGTCTTTTCCAGTGTGACCAGGCACTACTGAAGGTGCTGGGGTACCCTGGGCAAGACAGAGGCATGT Chimp > Human ------------- chr20:1593156-1593160 Template switch process: F1: L GGTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGG 1 F3: 4 CTGCGCAAGATAGAGGCATGTCTGGCATGGAGGGAG R RF: GGTACACATTTCACTCAGCAGGTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGATACCTGCGCAAGATAGAGGCATGTCTGGCATGGAGGGAG RR: CCATGTGTAAAGTGAGTCGTCCAGAAAAGGTCACACTGGTCCGTGACGACTTCCACGACCCTATGGACGCGTTCTATCTCCGTACAGACCGTACCTCCCTC F2: 3 CCATG 2 Unidirectional alignment (log-probability: -25.7) GTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGgTAcCCTGCGCAAGATAGAGGCATGTCTGGCATGGAGGGAG--- GTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGGATA-CCTGCGCAAGATAGAGGCATGTCTGGCATGGAGGGAGGCA Template switch alignment (log-probability: -15.8) GTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGG|GTACC|CTGCGCAAGATAGAGGCATGTCTGGCATGGAGGGAG GTCTTTTCCAGTGTGACCAGGCACTGCTGAAGGTGCTGGG|GTACC|CTGCGCAAGATAGAGGCATGTCTGGCATGGAGGGAG ========== Event 1743 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACCCAATTTGTCAGGCCAGACT-CGGGGCCAGGCACCCATGCCCCTGGCTCCCCCCACCAGGGCCCTGTGGCTGGTGCTGTCATTATCTCAGTCTATGGGGGCACAAGGCTGGGCTCAGCATAGAAGGCTTGAAAACAGGGCAGCTCCGGCCTGGCCCCGACCGT---------------- Chimp: ACCCAATTTGTCAGGCTAGACT-CGGGGCCAGGCACCCATGCCCATGGCTCCCCCTACCAGGGCCCTGTGGCTGGTGCTGTCATTATCTCAGTCTATGGGGGTACAAGGCTGGGCTCAGCATAGAAGGCTTGAaaacagggcagctccggcctggccccgaccgt---------------- Gorilla: ACCCAATTTGTCAGGCCAGACACCCTGGCCTGGCACCCATGCCCATGGCTCCCCCCACCAGGGCCCTGTGGCTGGTGCTGTCATTATCTCAGTCTATGGGGGCACAAGGCTGGGATCAGCATAGAAGGCTTGAaaacagggcagctccggcctggccccgaccgt---------------- ↓ 1 4 3 2 Human: ACCCAATTTGTCAGGCCAGACT-CGGGGCCAGGCACCCATGCCCCTGGCTCCCCCCACCAGGGCCCTGTGGCTGGTGCTGTCATTATCTCAGTCTATGGGGGCACAAGGCTGGGCTCAGCATAGAAGGCTTGAAAACAGGGCAGCTCCGGCCTGGCCCCGACCGT---------------- Cluster: [ ] Orangutan: ACCCAATTTGTCAGGCCAGACT-CGGGGCCAGGCACCCATGCCCATGGCTCCCCCCACCAGGGCCCTGTGGCTGGTGCTGTCATTATCTCAGTCTACGAGGGCACAAGGCTGGGCTCAGCATAGAAGGCTTGAaaacagggcagctctggcctggccctgaccatctcccagcgggcgagg Gorilla > Human --------------- chr20:1614032-1614040 Template switch process: F1: L AGAACTCAGGCATACCCTGGACCCAATTTGTCAGGCCAGAC 1 F3: 4 GGCACCCATGCCCCTGGCTCCCCCCACCAGGGCCCTGTGG R RF: AGAACTCAGGCATGCCCTGGACCCAATTTGTCAGGCCAGACACCCTGGCCTGGCACCCATGCCCATGGCTCCCCCCACCAGGGCCCTGTGGCTGGTGCTGTCATTATCTCAGTCTATGGGGGCACAAGGCTGGGATCAGCATAGAAGGCTTGAAAACAGGGCAGCTCCGGCCTGGCCCCGA RR: TCTTGAGTCCGTACGGGACCTGGGTTAAACAGTCCGGTCTGTGGGACCGGACCGTGGGTACGGGTACCGAGGGGGGTGGTCCCGGGACACCGACCACGACAGTAATAGAGTCAGATACCCCCGTGTTCCGACCCTAGTCGTATCTTCCGAACTTTTGTCCCGTCGAGGCCGGACCGGGGCT F2: 3 ACCGGGGCT 2 Unidirectional alignment (log-probability: -41.8) GAACTCAGGCATaCCCTGGACCCAATTTGTCAGGCCAGA----CTcggGGCCaGGCACCCATGCCCcTGGCTCCCCCCACCAGGGCCCTGTGG GAACTCAGGCATGCCCTGGACCCAATTTGTCAGGCCAGACACCCT---GGCCTGGCACCCATGCCCATGGCTCCCCCCACCAGGGCCCTGTGG Template switch alignment (log-probability: -27.9) GAACTCAGGCATaCCCTGGACCCAATTTGTCAGGCCAGAC|TCGGGGCCA|GGCACCCATGCCCcTGGCTCCCCCCACCAGGGCCCTGTGG GAACTCAGGCATGCCCTGGACCCAATTTGTCAGGCCAGAC|TCGGGGCCA|GGCACCCATGCCCATGGCTCCCCCCACCAGGGCCCTGTGG ========== Event 1744 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGTCGAGGGGACTGGCGAGCACTCGGTGGTCGCGGCTGGAACGGTTCCGAGGGTGGGAGTCGGGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGGCGAGTGCGGCCCGGGGCTCG--G--GGGCTGCGTAGCTGGCTTGT Chimp: AGGTCGAGGCGACTGGCGAGCACTCGGTGGTCGCGGCTGGAACGGTTCCGAGGGTGGGAGTCGGGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTG---------------GGGCTCG---GGGGGCTGCGTAGCTGGCTTGT ↓ 3 2 4 1 Gorilla: AGGTCGAGGCGACTGGCGAGCACTCGGTGGTCGCGGCTGGAACGGTTCCGAGGGTGGGAGTCGGGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGGCGAGTGCGGCCCGGGGCTCGGG---GGGCTGCGTAGCTGGCTTGT Human: AGGTCGAGGGGACTGGCGAGCACTCGGTGGTCGCGGCTGGAACGGTTCCGAGGGTGGGAGTCGGGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGGCGAGTGCGGCCCGGGGCTCG--G--GGGCTGCGTAGCTGGCTTGT Cluster: [ ] Orangutan: AGGTCGAGGCGACTGGCGAGCACTCGGTGGTCGCGGCTGGAACGGTTCCGAGGGTGGGAGTTGGGGCGGCCGTTCGCGGGGAAGAGCGCAGGGCTGGCCTGGGCGAGTGCGGCCCGGGTCTCGGG---GGGCTGCGTAGCTGGCTTGT Chimp > Gorilla --------------- chr20:1349941-1349947 Template switch process: F1: L TCGGGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGG 1 F3: 4 GGCCCGGGGCTCGGGGGGCTGCGTAGCTGGCTTGTAAGTGCAGCTGGTTTCCCTA R RF: GCACTCGGTGGTCGCGGCTGGAACGGTTCCGAGGGTGGGAGTCGGGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGGGCTCGGGGGGCTGCGTAGCTGGCTTGTAAGCGCAGCTGGTTTCCCTA RR: CGTGAGCCACCAGCGCCGACCTTGCCAAGGCTCCCACCCTCAGCCCCGCCGGCGAGCGCCCCTTCTCGCGTCCCGACCGGACCCCGAGCCCCCCGACGCATCGACCGAACATTCGCGTCGACCAAAGGGAT F2: 3 CGTGAGC 2 Unidirectional alignment (log-probability: -38.1) GGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTgggcgagtgcggcccGGGGCTCGGGGGGCTGCGTAGCTGGCTTGTAAGtG GGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCT---------------GGGGCTCGGGGGGCTGCGTAGCTGGCTTGTAAGCG Template switch alignment (log-probability: -28.1) GGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGG|CGAGTGC|GGCCcGGGGCTCGGGGGGCTGCGTAGCTGGCTTGTAAGtG GGGCGGCCGCTCGCGGGGAAGAGCGCAGGGCTGGCCTGGG|CGAGTGC|GGCCTGGGGCTCGGGGGGCTGCGTAGCTGGCTTGTAAGCG ========== Event 1745 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ttctttttttttAGATGGAGTTTCTCTCTTGTTGCCCAGTTTGTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCCGACCTCGGTGGGCTTGCGCAACACACAGGCATGATGTAGCC ↑ 4 1 3 2 Chimp: ttctttttttttAGATGGAGTTTCTC-------------------TCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCCGACCTCGGTGGGCTTGCGCAACACACAGGCATGATGTGGCC ↓ 4 1 3 2 Gorilla: TTCtttttttttAGATGGAGTTTCTCTCTTGTTGCCCAGTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCCGACCTCGGTGGGCTGGTGCAACACACAGGCATGATGTGGCC Human: ttctttttttttAGATGGAGTTTCTCTCTTGTTGCCCAGTTTGTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCCGACCTCGGTGGGCTTGCGCAACACACAGGCATGATGTAGCC Cluster: [ ] Orangutan: TTCTTTTTTGTTAGATGGAGTTTCTCTCTTGTTGCCCAGTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCAGACCTCGGTGGGCTTGTGCAACACACAGGCATGATGTGGCC Chimp > Human ------------- chr20:815198-815204 Template switch process: F1: L TCTTGGAGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG 1 F3: 4 GTTTGTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAG R RF: TCTTGGAGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCCGACCTCGGTGGGCTTGCGCAA RR: AGAACCTCCACTAAAAAGAAAAAAAAATCTACCTCAAAGAGAGAACCTCGGGGTCTCACTTCCTCCGTCTTGTCCGGGGTCCCGAGTGGGGTCCGGCTGGAGCCACCCGAACGCGTT F2: 3 ACCCGTT 2 Unidirectional alignment (log-probability: -38.2) AGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTGttgcccagtttgtctcttgGAGCCCCAGAGTGAAGGAGGCAGAACAG AGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG-------------------GAGCCCCAGAGTGAAGGAGGCAGAACAG Template switch alignment (log-probability: -28.4) AGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG|TTGCcCA|GTTTgTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAG AGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG|TTGCGCA|GTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAG Chimp > Gorilla --------------- chr20:649483-649489 Template switch process: F1: L TCTTGGAGGTGATGTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG 1 F3: 4 GTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAG R RF: TCTTGGAGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAGGCCCCAGGGCTCACCCCAGGCCGACCTCGGTGGGCTTGCGCAA RR: AGAACCTCCACTAAAAAGAAAAAAAAATCTACCTCAAAGAGAGAACCTCGGGGTCTCACTTCCTCCGTCTTGTCCGGGGTCCCGAGTGGGGTCCGGCTGGAGCCACCCGAACGCGTT F2: 3 ACCCGTT 2 Unidirectional alignment (log-probability: -43.7) AGGTGATgTTTCTTTTTTTTTAGATGGagtttctctcttgttgcccAGTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAG AGGTGATTTTTCTTTTTTTTTAGATGG-------------------AGTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAG Template switch alignment (log-probability: -27.9) AGGTGATgTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG|TTGCcCA|GTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAG AGGTGATTTTTCTTTTTTTTTAGATGGAGTTTCTCTCTTG|TTGCGCA|GTTTCTCTCTTGGAGCCCCAGAGTGAAGGAGGCAGAACAG ========== Event 1746 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTCTTTTGCCAAAAGGTCCTTACT--------------------------------TGACTTCTGAAGGCTGTTTGTACCAAA ↓ 3 4 1 2 Chimp: TCTCTTTTGCCAAAAGGTCCTTACT----------------TGCCGAAGTCAAGTAAGGACATCTGAAGGCTGTTTGTACCAAA Gorilla: TCTCTTTTGCCAAAAGGTCCTTACTTGCCGAAGTCAAGTAA----------------GGACATCTGAAGGCTGTTTGTACCAAA Human: TCTCTTTTGCCAAAAGGTCCTTACT--------------------------------TGACTTCTGAAGGCTGTTTGTACCAAA Cluster: [ ] Orangutan: TCTCTTTTGCCAAAAGGTCC----TTGCCGAAGTCAAGTAA----------------GGACATCTGAAGGCTGTTTGTACCAAA Human > Chimp ------------- chr20:66079547-66079559 Template switch process: F1: L ACTTGACTTGGTGGTTTCTCTTTTGCCAAAAGGTCCTTACTTGCC 1 F3: 4 GACATCTGAAGGCTGTTTGTACCAAATACTTTTCAAAAGCCCAG R RF: ACTTGACTTGGTGGTTTCTCTTTTGCCAAAAGGTCCTTACTTGACTTCTGAAGGCTGTTTGTACCAAATACTTTTCAAAAGCCCAA RR: TGAACTGAACCACCAAAGAGAAAACGGTTTTCCAGGAATGAACTGAAGACTTCCGACAAACATGGTTTATGAAAAGTTTTCGGGTT F2: 3 GAATGAACTGAAG 2 Unidirectional alignment (log-probability: -46) ACTTGGTGGTTTCTCTTTTGCCAAAAGGTCCTTACTTgccgaagtcaagtaagGACaTCTGAAGGCTGTTTGTACCAAATACTTTTCAAAAGC ACTTGGTGGTTTCTCTTTTGCCAAAAGGTCCTTACTT----------------GACTTCTGAAGGCTGTTTGTACCAAATACTTTTCAAAAGC Template switch alignment (log-probability: -35) ACTTGGTGGTTTCTCTTTTGCCAAAAGGTCCTTACTTGcC|GAAGTCAAGTAAG|GACaTCTGAAGGCTGTTTGTACCAAATACTTTTCAAAAGC ACTTGGTGGTTTCTCTTTTGCCAAAAGGTCCTTACTTGAC|GAAGTCAAGTAAG|GACTTCTGAAGGCTGTTTGTACCAAATACTTTTCAAAAGC ========== Event 1747 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATGTATTCACGTACATAAAACGGTTGGGCATTCCCAACTGTCTTAAAAATTATTTCTCATC Chimp: AATGTATTCACGTACATAAAATGGTTGGGCATTCCCAACCGTCTTAAAAATTATTTCTCATC ↑ 3 1 2 4 Gorilla: AATGTATTCATGTACATAAAACGGTTGGGAATG------ATTCTTAAAAATTATTTCTCATC ↓ 3 1 2 4 Human: AATGTATTCACGTACATAAAACGGTTGGGCATTCCCAACTGTCTTAAAAATTATTTCTCATC Cluster: [ ] Orangutan: AATGTATTCACATACATAAAATGGTTGGGAATG------ATTCTTAAAAATTATTTCTCATC Gorilla > Human --------------- chr20:196173-196184 Template switch process: F1: L CCGGTGAACTCGAATGTATTCACGTACATAAAACGGTTGGG 1 F3: 4 TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC R RF: CCGGTGAACTCGAATGTATTCATGTACATAAAACGGTTGGGAATGATTCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC RR: GGCCACTTGAGCTTACATAAGTACATGTATTTTGCCAACCCTTACTAAGAATTTTTAATAAAGAGTAGAATTTTGTTTGGTGAAATG F2: 3 GTCAACCCTTAC 2 Unidirectional alignment (log-probability: -43.3) CGGTGAACTCGAATGTATTCAcGTACATAAAACGGTTGGGcattcccaAcTG--TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC CGGTGAACTCGAATGTATTCATGTACATAAAACGGTTGGG--------AATGATTCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC Template switch alignment (log-probability: -28.3) CGGTGAACTCGAATGTATTCAcGTACATAAAACGGTTGGG|CATTCCCAACtG|TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC CGGTGAACTCGAATGTATTCATGTACATAAAACGGTTGGG|CATTCCCAACCG|TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC Gorilla > Chimp --------------- chr20:41117-41128 Template switch process: F1: L TGAAAATACCGGTGAACTCGAATGTATTCACGTACATAAAATGGTTGGG 1 F3: 4 TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC R RF: TGAAAATACCGGTGAACTCGAATGTATTCATGTACATAAAACGGTTGGGAATGATTCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC RR: ACTTTTATGGCCACTTGAGCTTACATAAGTACATGTATTTTGCCAACCCTTACTAAGAATTTTTAATAAAGAGTAGAATTTTGTTTGGTGAAATG F2: 3 GCCAACCCTTAC 2 Unidirectional alignment (log-probability: -49) CGGTGAACTCGAATGTATTCAcGTACATAAAAtGGTTGGGcATtcccaaccG--TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC CGGTGAACTCGAATGTATTCATGTACATAAAACGGTTGGGAAT--------GATTCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC Template switch alignment (log-probability: -28.5) CGGTGAACTCGAATGTATTCAcGTACATAAAAtGGTTGGG|CATTCCCAACCG|TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC CGGTGAACTCGAATGTATTCATGTACATAAAACGGTTGGG|CATTCCCAACCG|TCTTAAAAATTATTTCTCATCTTAAAACAAACCACTTTAC ========== Event 1748 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGATTTCATCACCACTCCTC-ACCTACATATTC-TCAATCCCCAGATCACTAACTCACTGAACCAAG Chimp: GAGATTTCATCACCACTCCTC-ACCTACATATTC-TCAATCCCCAGATCACTAACTCACTGAACCAAG ↓ 1 3 4 2 Gorilla: GAGATTTCATCACCACTCCTCAATCTGGGGATTGAGAAATCCCCAGATCACTAACTCACTGAACCAAG ↑ 1 3 4 2 Human: GAGATTTCATCACCACTCCTC-ACCTACATATTC-TCAATCCCCAGATCACTAACTCACTGAACCAAG Cluster: [ ] Orangutan: GAGATTTCATCACCACTCTTC-ACCTACATATTC-TCAATCCCCAGATCACTAACTCACTGAACCAAG Human > Gorilla --------------- chr20:6416644-6416658 Template switch process: F1: L GCCATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA 1 F3: 4 AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG R RF: GCCATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCACCTACATATTCTCAATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG RR: CGGTAGTCCCGGGTTTGGTTCTCTAAAGTAGTGGTGAGGAGTGGATGTATAAGAGTTAGGGGTCTAGTGATTGAGTGACTTGGTTCTACTCAACC F2: 3 AGAGTTAGGGGTCTA 2 Unidirectional alignment (log-probability: -42.9) CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA-------------atctggggattgagaAATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCACCTACATATTCTC---------------AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG Template switch alignment (log-probability: -17.7) CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA|ATCTGGGGATTGAGA|AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA|ATCTGGGGATTGAGA|AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG Chimp > Gorilla --------------- chr20:6416644-6416658 Template switch process: F1: L GCCATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA 1 F3: 4 AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG R RF: GCCATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCACCTACATATTCTCAATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG RR: CGGTAGTCCCGGGTTTGGTTCTCTAAAGTAGTGGTGAGGAGTGGATGTATAAGAGTTAGGGGTCTAGTGATTGAGTGACTTGGTTCTACTCAACC F2: 3 AGAGTTAGGGGTCTA 2 Unidirectional alignment (log-probability: -42.9) CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA-------------atctggggattgagaAATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCACCTACATATTCTC---------------AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG Template switch alignment (log-probability: -17.7) CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA|ATCTGGGGATTGAGA|AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG CATCAGGGCCCAAACCAAGAGATTTCATCACCACTCCTCA|ATCTGGGGATTGAGA|AATCCCCAGATCACTAACTCACTGAACCAAGATGAGTTGG ========== Event 1749 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCAAACCTTTTGCATCTTTTAGAACC---TCAATAAGCTGTTCTCTCTGGGACTA Chimp: ACCAAGCCTTTCGCATCTTTTAGAACCTGTTCTAAAAGCTGTTCTCTCTGGGACCA ↑ 3 2 1 4 Gorilla: ACCAAGCCTTTTGCATCTTTTAGAACC---TCAATAAGCTGTTCTCTCTGGGACTA Human: ACCAAACCTTTTGCATCTTTTAGAACC---TCAATAAGCTGTTCTCTCTGGGACTA Cluster: [ ] Orangutan: ACTAAGTCTTTTGCATCTTTTAGAACC---TCAATAAGCTGTTCTCTCTGGGACCA Gorilla > Chimp --------------- chr20:7165160-7165166 Template switch process: F1: L CAATAAATAACTTGACCAAGCCTTTCGCATCTTTTAGAACCT 1 F3: 4 AAGCTGTTCTCTCTGGGACCAGGAATTTATGTGATATATG R RF: CAATAAATAACTTGACCAAGCCTTTTGCATCTTTTAGAACCTCAATAAGCTGTTCTCTCTGGGACTAGGAATTTATGTGATATATG RR: GTTATTTATTGAACTGGTTCGGAAAACGTAGAAAATCTTGGAGTTATTCGACAAGAGAGACCCTGATCCTTAAATACACTATATAC F2: 3 AATCTTG 2 Unidirectional alignment (log-probability: -37.3) ATAAATAACTTGACCAAGCCTTTcGCATCTTTTAGAACCtgtTCtAaAAGCTGTTCTCTCTGGGACcAGGAATTTATGTGATATATG ATAAATAACTTGACCAAGCCTTTTGCATCTTTTAGAACC---TCAATAAGCTGTTCTCTCTGGGACTAGGAATTTATGTGATATATG Template switch alignment (log-probability: -27.7) ATAAATAACTTGACCAAGCCTTTcGCATCTTTTAGAACCT|GTTCTAA|AAGCTGTTCTCTCTGGGACcAGGAATTTATGTGATATATG ATAAATAACTTGACCAAGCCTTTTGCATCTTTTAGAACCT|GTTCTAA|AAGCTGTTCTCTCTGGGACTAGGAATTTATGTGATATATG ========== Event 1750 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTCTCTCGGGTGATCAACGTTCA----------------------------ACCTAGAGATGAGAACCATCACTGTTCAACCTGGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGCGAATGATAAATTAGCAAAGATAAACTCACggccgggtgcggtggctcacgcct-gtaatccca Chimp: GTCTCTCGGGTGATCAACGTTCA----------------------------ACCTAGAGATGAGAACCATCACTGTTCAACCTGGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGCGAATGATAAATTAGCAAAGATAAACTCACggccgggtgcggtggctcacgcct-gtaatccca ↑ 4 1 3 2 Gorilla: GTCTCTCGGGTGATCAACGTTCA--------------------------------------------------------ACCTAGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGTGAATGATAAATTAGCAAAGATAAACTCACggccgggtgcagtggctcacgcctggtaatccca ↓ 4 1 3 2 Human: GTCTCTCGGGTGATCAACGTTCA----------------------------ACCTAGAGATGAGAACCATCACTGTTCAACCTGGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGCGAATGATAAATTAGCAAAGATAAACTCACggccgggtgcggtggctcacgcct-gtaatccca Cluster: [ ] Orangutan: GTC--TCAGGTGatcagcgttcaacctagagatgagaaccatcagtgttca----------------------------acctagagatgagaaccatTACAAGGGCTTTAGGGTTAAACTGCGAATGATAAATTAGCAAAGATAAACTCACggccgggtgcggtggctcacgcct-gtaatccca Gorilla > Human --------------- chr20:410280-410284 Template switch process: F1: L AGGCTGAAGAGAAGCCAAGTCTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCAT 1 F3: 4 TTCAACCTGGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGCG R RF: AGGCTGAAGAGAAGCCAAGTCTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGTGAATGATAAATTAGCAAAGATAAACTCACGGCCGGGTGCAGTG RR: TCCGACTTCTCTTCGGTTCAGAGAGCCCACTAGTTGCAAGTTGGATCTCTACTCTTGGTAATGTTCCCGAAATCCCAATTTGACACTTACTATTTAATCGTTTCTATTTGAGTGCCGGCCCACGTCAC F2: 3 GTCAC 2 Unidirectional alignment (log-probability: -56.7) CTCTCGGGTGATCAACGTTCAACCTAgagatgagaaccatcactgttcaacctgGAGATGAGAACCATTACAAGGGCTTTAGGGT CTCTCGGGTGATCAACGTTCAACCTA----------------------------GAGATGAGAACCATTACAAGGGCTTTAGGGT Template switch alignment (log-probability: -28.1) CTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCAT|CACTG|TTCAACCTgGAGATGAGAACCATTACAAGGGCTTTAGGGT CTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCAT|CACTG|TTCAACCTAGAGATGAGAACCATTACAAGGGCTTTAGGGT Gorilla > Chimp --------------- chr20:296021-296025 Template switch process: F1: L AGGCTGAAGAGAAGCCAAGTCTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCAT 1 F3: 4 TTCAACCTGGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGCG R RF: AGGCTGAAGAGAAGCCAAGTCTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCATTACAAGGGCTTTAGGGTTAAACTGTGAATGATAAATTAGCAAAGATAAACTCACGGCCGGGTGCAGTG RR: TCCGACTTCTCTTCGGTTCAGAGAGCCCACTAGTTGCAAGTTGGATCTCTACTCTTGGTAATGTTCCCGAAATCCCAATTTGACACTTACTATTTAATCGTTTCTATTTGAGTGCCGGCCCACGTCAC F2: 3 GTCAC 2 Unidirectional alignment (log-probability: -56.7) CTCTCGGGTGATCAACGTTCAACCTAgagatgagaaccatcactgttcaacctgGAGATGAGAACCATTACAAGGGCTTTAGGGT CTCTCGGGTGATCAACGTTCAACCTA----------------------------GAGATGAGAACCATTACAAGGGCTTTAGGGT Template switch alignment (log-probability: -28.1) CTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCAT|CACTG|TTCAACCTgGAGATGAGAACCATTACAAGGGCTTTAGGGT CTCTCGGGTGATCAACGTTCAACCTAGAGATGAGAACCAT|CACTG|TTCAACCTAGAGATGAGAACCATTACAAGGGCTTTAGGGT ========== Event 1751 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGATGGAAGAATGCAGTTTACA----------------GTCAAACCAAGATAACTATTTTTG Chimp: AGATGGAAGAATGCAGTTTACA----------------GTCAAACCAAGATGACTATTTTTG ↑ 1 3 24 Gorilla: AGATGGAAGAATGCAGTTTACGACTGTAAACTGGTTTGACTAAACCAAGATAACCATTTTTG ↓ 1 3 24 Human: AGATGGAAGAATGCAGTTTACA----------------GTCAAACCAAGATAACTATTTTTG Cluster: [ ] Orangutan: AGATGGAAGGATGCAGTTTACA----------------GTCAAACCAAGAAAACTATTTTTG Gorilla > Human --------------- chr20:56260222-56260225 Template switch process: F1: L AGAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC 1 F3: 4 AAACCAAGATAACTATTTTTGGTTCTTTTTTAACCAATAT R RF: AGAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTACGACTGTAAACTGGTTTGACTAAACCAAGATAACCATTTTTGGTTCTTTTTTAACCAGTAT RR: TCTTTTTAAGTTTTAAAAGTTCTACCTTCTTACGTCAAATGCTGACATTTGACCAAACTGATTTGGTTCTATTGGTAAAAACCAAGAAAAAATTGGTCATA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -38.4) GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC--------------------agtcAAACCAAGATAACtATTTTTGGTTCTTTTTTAACCAaTAT GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTACGACTGTAAACTGGTTTGACT----AAACCAAGATAACCATTTTTGGTTCTTTTTTAACCAGTAT Template switch alignment (log-probability: -27.3) GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC|AGTC|AAACCAAGATAACtATTTTTGGTTCTTTTTTAACCAaTAT GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC|AGTC|AAACCAAGATAACCATTTTTGGTTCTTTTTTAACCAGTAT Gorilla > Chimp --------------- chr20:58474552-58474555 Template switch process: F1: L AGAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC 1 F3: 4 AAACCAAGATGACTATTTTTGGTTCTTTTTTAACCAGTAT R RF: AGAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTACGACTGTAAACTGGTTTGACTAAACCAAGATAACCATTTTTGGTTCTTTTTTAACCAGTAT RR: TCTTTTTAAGTTTTAAAAGTTCTACCTTCTTACGTCAAATGCTGACATTTGACCAAACTGATTTGGTTCTATTGGTAAAAACCAAGAAAAAATTGGTCATA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -38.4) GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC--------------------agtcAAACCAAGATgACtATTTTTGGTTCTTTTTTAACCAGTAT GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTACGACTGTAAACTGGTTTGACT----AAACCAAGATAACCATTTTTGGTTCTTTTTTAACCAGTAT Template switch alignment (log-probability: -27.3) GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC|AGTC|AAACCAAGATgACtATTTTTGGTTCTTTTTTAACCAGTAT GAAAAATTCAAAATTTTCAAGATGGAAGAATGCAGTTTAC|AGTC|AAACCAAGATAACCATTTTTGGTTCTTTTTTAACCAGTAT ========== Event 1752 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAAAGCAAATTTTTCTTAAACATGTAAGACAAA--------CTTAGATCCAGATTGGGTGCTC ↓ 3 2 1 4 Chimp: TTAAAGCAAATTTTTCTTAAACATGTAAGACAAATTACATGTTTTAGATCCAGATTGGGTGCTC ↑ 3 2 1 4 Gorilla: TTAAAGCAAATTTTTCTTAAACATGTAAGACAAA--------CTTAGATCCAGATTGGGTGCTC Human: TTAAAGCAAATTTTTCTTAAACATGTAAGACAAA--------CTTAGATCCAGATTGGGTGCTC Cluster: [ ] Orangutan: TTAAAGCAAATTTTTCTTAAACATGTAAGACAAA--------CCTAGATCCAGATTGGGTGCTC Human > Chimp ------------- chr20:57812041-57812049 Template switch process: F1: L AAATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA 1 F3: 4 TTAGATCCAGATTGGGTGCTCTAGGGGGCTATTTCCTGCA R RF: AAATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAACTTAGATCCAGATTGGGTGCTCTAGGGGGCTGTTTCCTGCA RR: TTTATTTAATTTCGTTTAAAAAGAATTTGTACATTCTGTTTGAATCTAGGTCTAACCCACGAGATCCCCCGACAAAGGACGT F2: 3 TTGTACATT 2 Unidirectional alignment (log-probability: -34.4) AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAAttacatgttTTAGATCCAGATTGGGTGCTCTAGGGGGCTaTTTCCTGCA AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA--------CTTAGATCCAGATTGGGTGCTCTAGGGGGCTGTTTCCTGCA Template switch alignment (log-probability: -22.4) AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA|TTACATGTT|TTAGATCCAGATTGGGTGCTCTAGGGGGCTaTTTCCTGCA AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA|TTACATGTT|TTAGATCCAGATTGGGTGCTCTAGGGGGCTGTTTCCTGCA Gorilla > Chimp --------------- chr20:57812041-57812049 Template switch process: F1: L AAATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA 1 F3: 4 TTAGATCCAGATTGGGTGCTCTAGGGGGCTATTTCCTGCA R RF: AAATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAACTTAGATCCAGATTGGGTGCTCTAGGGGGTTGTTTCCTGCA RR: TTTATTTAATTTCGTTTAAAAAGAATTTGTACATTCTGTTTGAATCTAGGTCTAACCCACGAGATCCCCCAACAAAGGACGT F2: 3 TTGTACATT 2 Unidirectional alignment (log-probability: -39) AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAAttacatgttTTAGATCCAGATTGGGTGCTCTAGGGGGcTaTTTCCTGCA AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA--------CTTAGATCCAGATTGGGTGCTCTAGGGGGTTGTTTCCTGCA Template switch alignment (log-probability: -27.9) AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA|TTACATGTT|TTAGATCCAGATTGGGTGCTCTAGGGGGcTaTTTCCTGCA AATAAATTAAAGCAAATTTTTCTTAAACATGTAAGACAAA|TTACATGTT|TTAGATCCAGATTGGGTGCTCTAGGGGGTTGTTTCCTGCA ========== Event 1753 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: caaagtcaGTAAGTTGTAGAATAGTATATTCTGTTAAA--------------------------------------AGTGAATTTAACAGAATATAAAAGTATATTCTGTTAAAAGTGACCTCAGAGAAAAGATAGGGTT Chimp: caaagtcaGTACGTTGTAGAATAGTATATTCTGTTAAA--------------------------------------AGTGAATTTAACAGAATATAAAAGTATATTCTGTTAAAAGTGACCTCAGAGCAAAGATAGGGTT Gorilla: caaagtcagtaagttgtagaatagTATATTCTGTTAAA----------------------------------------------------------------------------AGTGACCTCAGAGCAAAGATAGGGTT ↓ 4 3 2 1 Human: caaagtcaGTAAGTTGTAGAATAGTATATTCTGTTAAA--------------------------------------AGTGAATTTAACAGAATATAAAAGTATATTCTGTTAAAAGTGACCTCAGAGAAAAGATAGGGTT Cluster: [ ] Orangutan: caaagtcaGTAAGTTGTAGAATAGTATATTCTGTTAAAAGTGAATTTAACAGAATATAAAGGTATGTTCTGTTAAA--------------------------------------AGTGACCTCAGAGCAAAGATAGGGTT Gorilla > Human --------------- chr20:55405467-55405479 Template switch process: F1: L GCCCAAAGTCAGTAAGTTGTAGAATAGTATATTCTGTTAAAAGTGAA 1 F3: 4 AAAAGTATATTCTGTTAAAAGTGACCTCAGAGAAAAGATAGGGTTGTGAAAAAATAATA R RF: GCCCAAAGTCAGTAAGTTGTAGAATAGTATATTCTGTTAAAAGTGACCTCAGAGCAAAGATAGGGTTGTGAAAAAATAATA RR: CGGGTTTCAGTCATTCAACATCTTATCATATAAGACAATTTTCACTGGAGTCTCGTTTCTATCCCAACACTTTTTTATTAT F2: 3 TATAAGACAATTT 2 Unidirectional alignment (log-probability: -71) GTCAGTAAGTTGTAGAATagtatattctgttaaaagtgaatttaacagaatataaaAGTATATTCTGTTAAAAGTGACCTCAGAGaAAAGATA GTCAGTAAGTTGTAGAAT--------------------------------------AGTATATTCTGTTAAAAGTGACCTCAGAGCAAAGATA Template switch alignment (log-probability: -34.5) GTCAGTAAGTTGTAGAATAGTATATTCTGTTAAAAGTGAa|TTTAACAGAATAT|AAaAGTATATTCTGTTAAAAGTGACCTCAGAGaAAAGATA GTCAGTAAGTTGTAGAATAGTATATTCTGTTAAAAGTGAC|TTTAACAGAATAT|AATAGTATATTCTGTTAAAAGTGACCTCAGAGCAAAGATA ========== Event 1754 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTAAATAGATGAAGATTAATGCAGTGGAGAGCATGA-ACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTA---------AAAATTTCGCATGCTGCAACAATTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCATTTCTCTCAGAAAATTAAGG ↓ 1 4 3 2 Chimp: GTAAATAGATGAAGATTAATG----------CATGA-ACAA--------CAGAGATAAGACTCaaaataagtaaattgtaattttaaaaattttaaaaattttGCATGCTGCGACAATTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCATTTCTCTCAGAAAATTAAGG ↑ 1 4 3 2 Gorilla: GTAAATAGATGAAGATTAATGCAGTGGAGAGCATGA-ACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTA---------AAAATTTCGCATGCTGCAACAGTTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCATTTCTCTCAGAAAATTAAGG Human: GTAAATAGATGAAGATTAATGCAGTGGAGAGCATGA-ACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTA---------AAAATTTCGCATGCTGCAACAATTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCATTTCTCTCAGAAAATTAAGG Cluster: [ ] Orangutan: GTAAATAGATGAAGATTAATGCAGTGGAGAGCATGAATCAATATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTA---------AAAGTTTCGCATGCTGCAACAATTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCATTTCTCTCAGAAAATTAAGG Human > Chimp ------------- chr20:57444558-57444564 Template switch process: F1: L ATAAACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA 1 F3: 4 CAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAAA R RF: ATAAACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCAGTGGAGAGCATGAACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAAATTTCGCATGCTGCAACAATTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCA RR: TATTTGTCCAACTGACTTTACATTTATCTACTTCTAATTACGTCACCTCTCGTACTTGTTGTACGTCCTTCTCTATTCTGAGTTTTATTCATTTAACATTAAAATTTTTAAAGCGTACGACGTTGTTAACAGACTTTATTATTTTTAGACCCTCTGGACCGTAAATCTTATGGTTAAAAACAAGT F2: 3 AACAAGT 2 Unidirectional alignment (log-probability: -35.1) AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA----------TGAACAAC--------AGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAaaa AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCAGTGGAGAGCATGAACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTA--- Template switch alignment (log-probability: -22.2) AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA|TGAACAA|cAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAA AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA|TGAACAA|AAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAA Gorilla > Chimp --------------- chr20:57444558-57444564 Template switch process: F1: L ATAAACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA 1 F3: 4 CAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAAA R RF: ATAAACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCAGTGGAGAGCATGAACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAAATTTCGCATGCTGCAACAGTTGTCTGAAATAATAAAAATCTGGGAGACCTGGCATTTAGAATACCAATTTTTGTTCA RR: TATTTGTCCAACTGACTTTACATTTATCTACTTCTAATTACGTCACCTCTCGTACTTGTTGTACGTCCTTCTCTATTCTGAGTTTTATTCATTTAACATTAAAATTTTTAAAGCGTACGACGTTGTCAACAGACTTTATTATTTTTAGACCCTCTGGACCGTAAATCTTATGGTTAAAAACAAGT F2: 3 AACAAGT 2 Unidirectional alignment (log-probability: -34.1) AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA----------TGAACAAC--------AGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAaaa AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCAGTGGAGAGCATGAACAACATGCAGGAAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTA--- Template switch alignment (log-probability: -22.2) AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA|TGAACAA|cAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAA AACAGGTTGACTGAAATGTAAATAGATGAAGATTAATGCA|TGAACAA|AAGAGATAAGACTCAAAATAAGTAAATTGTAATTTTAAAA ========== Event 1755 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAATATTGAGTTCAGTCTTTCATAATGAAGTA---CTCTTC-------ATTATGAGGGAGAAAACTCTGTTCCTT- Chimp: AAATATTGAGTTCAGTCTTTCATAATGAAGTA---CTCTTC-------ATTATGAGGGAGAAAACTCTGTTCCTT- ↑ 3 1 2 4 Gorilla: AAATGTTGAGTTCAGTCTTTCATAATGAAGAGTAAATTTTT---AGAGGTCACTGGGGAGAAAACTCTGTTCCTT- ↓ 3 1 2 4 Human: AAATATTGAGTTCAGTCTTTCATAATGAAGTA---CTCTTC-------ATTATGAGGGAGAAAACTCTGTTCCTT- Cluster: [ ] Orangutan: AAATATTGAGTTCAGTCTTTCATAATGAAGAGTAAATTTTTAGG----GTCACTGTGGAGAAAACTCTGTTCCttg Gorilla > Human --------------- chr20:54460708-54460722 Template switch process: F1: L TTAATTGGAAAAAATATTGAGTTCAGTCTTTCATAATGAAG 1 F3: 4 GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA R RF: TTAATTGGAAAAAATGTTGAGTTCAGTCTTTCATAATGAAGAGTAAATTTTTAGAGGTCACTGGGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA RR: AATTAACCTTTTTTACAACTCAAGTCAGAAAGTATTACTTCTCATTTAAAAATCTCCAGTGACCCCTCTTTTGAGACAAGGAAATTCTTAAACAAGGTAGTTT F2: 3 AGTATTACTTCTCAT 2 Unidirectional alignment (log-probability: -47.4) TAATTGGAAAAAATaTTGAGTTCAGTCTTTCATAATGAAgtactcttcattatGA---------------------GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA TAATTGGAAAAAATGTTGAGTTCAGTCTTTCATAATGAA--------------GAGTAAATTTTTAGAGGTCACTGGGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA Template switch alignment (log-probability: -23.2) TAATTGGAAAAAATaTTGAGTTCAGTCTTTCATAATGAAG|TACTCTTCATTATGA|GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA TAATTGGAAAAAATGTTGAGTTCAGTCTTTCATAATGAAG|TACTCTTCATTATGA|GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA Gorilla > Chimp --------------- chr20:56687379-56687393 Template switch process: F1: L TTAATTGGAAAAAATATTGAGTTCAGTCTTTCATAATGAAG 1 F3: 4 GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA R RF: TTAATTGGAAAAAATGTTGAGTTCAGTCTTTCATAATGAAGAGTAAATTTTTAGAGGTCACTGGGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA RR: AATTAACCTTTTTTACAACTCAAGTCAGAAAGTATTACTTCTCATTTAAAAATCTCCAGTGACCCCTCTTTTGAGACAAGGAAATTCTTAAACAAGGTAGTTT F2: 3 AGTATTACTTCTCAT 2 Unidirectional alignment (log-probability: -47.4) TAATTGGAAAAAATaTTGAGTTCAGTCTTTCATAATGAAgtactcttcattatGA---------------------GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA TAATTGGAAAAAATGTTGAGTTCAGTCTTTCATAATGAA--------------GAGTAAATTTTTAGAGGTCACTGGGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA Template switch alignment (log-probability: -23.2) TAATTGGAAAAAATaTTGAGTTCAGTCTTTCATAATGAAG|TACTCTTCATTATGA|GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA TAATTGGAAAAAATGTTGAGTTCAGTCTTTCATAATGAAG|TACTCTTCATTATGA|GGGAGAAAACTCTGTTCCTTTAAGAATTTGTTCCATCAAA ========== Event 1756 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGCCATCCGCTTCCTGCTTCTGCAGCATTCGGCCATTTGCCCAATGCTCCCTGATGCCACggttctcaaagtgtggtccctgtccctggcctgggagcatcagcttcctgtggggactctagaaatgcaagttctccggccccacactagact ↓ 1 4 3 2 Chimp: AGCCATCTGCTTCCTGCTTCTA---ACTTGGGCTATTTGCCCAATGCTCCCTGATGCCACggttctcaaagtgtggtccctgtccctggcctgggagcatcagcttcctgtggggactctagaaatgcaagttctccggccccacactagact Gorilla: AGCCATCCGCTTCCTGCTTCTG---ACTTGGGCCATTTGCCCAGTGCTCCCTGATGCCACggttctcaaagtgtggtccctgtccctggcctgggagcatcagcttcctgtggggactctagaaatgcaagttctccggccccacactagact ↑ 1 4 3 2 Human: AGCCATCCGCTTCCTGCTTCTGCAGCATTCGGCCATTTGCCCAATGCTCCCTGATGCCACggttctcaaagtgtggtccctgtccctggcctgggagcatcagcttcctgtggggactctagaaatgcaagttctccggccccacactagact Cluster: [ ] Orangutan: AGCCATCCGCTTCCTGCTTCTG---ACTTGGGCCATTTGCCCAACGCTCCCTGATGCCACggttctcaaagtgtggtccctgtccctggcctgggagcatcagcttcccgtggggactctagaaatgcaagttctccggccccacactagact Human > Chimp ------------- chr2A:10322396-10322401 Template switch process: F1: L GAACAGAGGAAGGCGAGGAGAGCCATCTGCTTCCTGCTTCT 1 F3: 4 GGCTATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAAGTGT R RF: GAACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCTGCAGCATTCGGCCATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAAGTGTGGTCCCTGTCCCTGGCCTGGGAGCATCAGCTTCCTGTGGGGACTCTAGAAATGCAAGTT RR: CTTGTCTCCTTCCGCTCCTCTCGGTAGGCGAAGGACGAAGACGTCGTAAGCCGGTAAACGGGTTACGAGGGACTACGGTGCCAAGAGTTTCACACCAGGGACAGGGACCGGACCCTCGTAGTCGAAGGACACCCCTGAGATCTTTACGTTCAA F2: 3 GTTCAA 2 Unidirectional alignment (log-probability: -40.8) AACAGAGGAAGGCGAGGAGAGCCATCtGCTTCCTGCTTCtaactTG--------GGCtATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAA AACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTC-----TGCAGCATTCGGCCATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAA Template switch alignment (log-probability: -28.1) AACAGAGGAAGGCGAGGAGAGCCATCtGCTTCCTGCTTCT|AACTTG|GGCtATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAA AACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCT|AACTTG|GGCCATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAA Human > Gorilla --------------- chr2A:10329037-10329041 Template switch process: F1: L AACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCTG 1 F3: 4 GGCCATTTGCCCAGTGCTCCCTGATGCCACGGTTCTCAAA R RF: AACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCTGCAGCATTCGGCCATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAAGTGTGGTCCCTGTCCCTGGCCTGGGAGCATCAGCTTCCTGTGGGGACTCTAGAAATGCAAGT RR: TTGTCTCCTTCCGCTCCTCTCGGTAGGCGAAGGACGAAGACGTCGTAAGCCGGTAAACGGGTTACGAGGGACTACGGTGCCAAGAGTTTCACACCAGGGACAGGGACCGGACCCTCGTAGTCGAAGGACACCCCTGAGATCTTTACGTTCA F2: 3 GTTCA 2 Unidirectional alignment (log-probability: -33.2) ACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCT---GacTTgGGCCATTTGCCCAgTGCTCCCTGATGCCACGGTTCTCAAA ACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCTGCAGCATTCGGCCATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAA Template switch alignment (log-probability: -21.9) ACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCTG|ACTTG|GGCCATTTGCCCAgTGCTCCCTGATGCCACGGTTCTCAAA ACAGAGGAAGGCGAGGAGAGCCATCCGCTTCCTGCTTCTG|ACTTG|GGCCATTTGCCCAATGCTCCCTGATGCCACGGTTCTCAAA ========== Event 1757 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATACTACATTGAAATGAAACATT----------TCAATGACAACAAAAATAGAAACTAAGTTAGAAAACAGTCATAG Chimp: TTATACTACATTGAAATGAAACGTT-----TCTATTCAATGACAACAAAAATAGAAACTAAGTTAGAAAACAGTCATAG Gorilla: TTATACTACATTGAAATGAAAAGTTTCTAT-----TCAGTGACAACAAAAATAGAAACTAAGTTAGAAAACAGTCATAG ↑ 1 4 3 2 Human: TTATACTACATTGAAATGAAACATT----------TCAATGACAACAAAAATAGAAACTAAGTTAGAAAACAGTCATAG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr2A:101153654-101153661 Template switch process: F1: L ATAATCTTTAAAATGATACATTATACTACATTGAAATGAAA 1 F3: 4 TTCAGTGACAACAAAAATAGAAACTAAGTTAGAAAACAGTCATAG R RF: ATAATCTTTAAAATGATACATTATACTACATTGAAATGAAACATTTCAATGACAACAAAAATAGAAACTAAGTTAGAAAACAGTCATAG RR: TATTAGAAATTTTACTATGTAATATGATGTAACTTTACTTTGTAAAGTTACTGTTGTTTTTATCTTTGATTCAATCTTTTGTCAGTATC F2: 3 ATCTTTGA 2 Unidirectional alignment (log-probability: -34.7) TAATCTTTAAAATGATACATTATACTACATTGAAATGAAAagtttCtaTTCAgTGACAACAAAAATAGAAACTAAGTTAGAAAACAGT TAATCTTTAAAATGATACATTATACTACATTGAAATGAAA-----CATTTCAATGACAACAAAAATAGAAACTAAGTTAGAAAACAGT Template switch alignment (log-probability: -22.4) TAATCTTTAAAATGATACATTATACTACATTGAAATGAAA|AGTTTCTA|TTCAgTGACAACAAAAATAGAAACTAAGTTAGAAAACAGT TAATCTTTAAAATGATACATTATACTACATTGAAATGAAA|AGTTTCTA|TTCAATGACAACAAAAATAGAAACTAAGTTAGAAAACAGT ========== Event 1758 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAAGACTAAAAATGAACCAGA---AACTAAGAAGGTTGCTCTATCAAAGGGGATAACGGT ↓ 13 24 ↑ 13 24 Chimp: AAAGACTAAAAATGAACCAGAGCAACCTTCTTAG---TTTCTATCAAAGGGGATAACGGT ↓ 13 24 ↑ 13 24 Gorilla: AAAGACTAAAAATGAACCAGA---AACTAAGAAGGTTGCTCTATCAAAGGGGATAACGGT Human: AAAGACTAAAAATGAACCAGA---AACTAAGAAGGTTGCTCTATCAAAGGGGATAACGGT Cluster: [ ] Orangutan: AAAGACTAAAAGTGAACCAGA---AACTAAGAAGGTTGCTCTATCAAAGGGGATAACGGC Chimp > Human ------------- chr2:101786456-101786470 Template switch process: F1: L CATACATTTTCCTGAAATTTAAAGACTAAAAATGAACCAGA 1 F3: 4 TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT R RF: CATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGAGCAACCTTCTTAGTTTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT RR: GTATGTAAAAAGACTTTAAATTTCTGATTTTTACTTGGTCTCGTTGGAAGAATCAAAGATAGTTTCCCCTATTGCCAAGACCAATAAACTCGGTAA F2: 3 CGTTGGAAGAATCAA 2 Unidirectional alignment (log-probability: -46.5) ATACATTTTcCTGAAATTTAAAGACTAAAAATGAACCAGAaactaagaaggttGC-------------TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA-------------GCAACCTTCTTAGTTTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Template switch alignment (log-probability: -23.1) ATACATTTTcCTGAAATTTAAAGACTAAAAATGAACCAGA|AACTAAGAAGGTTGC|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA|AACTAAGAAGGTTGC|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Human > Chimp ------------- chr2A:100806039-100806053 Template switch process: F1: L CATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA 1 F3: 4 TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT R RF: CATACATTTTCCTGAAATTTAAAGACTAAAAATGAACCAGAAACTAAGAAGGTTGCTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT RR: GTATGTAAAAGGACTTTAAATTTCTGATTTTTACTTGGTCTTTGATTCTTCCAACGAGATAGTTTCCCCTATTGCCAAGACCAATAAACTCGGTAA F2: 3 TTGATTCTTCCAACG 2 Unidirectional alignment (log-probability: -46.5) ATACATTTTtCTGAAATTTAAAGACTAAAAATGAACCAGA-------------GCaaccttcttagttTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTCCTGAAATTTAAAGACTAAAAATGAACCAGAAACTAAGAAGGTTGC-------------TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Template switch alignment (log-probability: -23.1) ATACATTTTtCTGAAATTTAAAGACTAAAAATGAACCAGA|GCAACCTTCTTAGTT|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTCCTGAAATTTAAAGACTAAAAATGAACCAGA|GCAACCTTCTTAGTT|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Gorilla > Chimp --------------- chr2A:100806039-100806053 Template switch process: F1: L CATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA 1 F3: 4 TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT R RF: AATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGAAACTAAGAAGGTTGCTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT RR: TTATGTAAAAAGACTTTAAATTTCTGATTTTTACTTGGTCTTTGATTCTTCCAACGAGATAGTTTCCCCTATTGCCAAGACCAATAAACTCGGTAA F2: 3 TTGATTCTTCCAACG 2 Unidirectional alignment (log-probability: -45.5) ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA-------------GCaaccttcttagttTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGAAACTAAGAAGGTTGC-------------TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Template switch alignment (log-probability: -23.2) ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA|GCAACCTTCTTAGTT|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA|GCAACCTTCTTAGTT|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Chimp > Gorilla --------------- chr2A:6746147-6746161 Template switch process: F1: L AATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA 1 F3: 4 TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT R RF: CATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGAGCAACCTTCTTAGTTTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT RR: GTATGTAAAAAGACTTTAAATTTCTGATTTTTACTTGGTCTCGTTGGAAGAATCAAAGATAGTTTCCCCTATTGCCAAGACCAATAAACTCGGTAA F2: 3 CGTTGGAAGAATCAA 2 Unidirectional alignment (log-probability: -45.5) ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGAaactaagaaggttGC-------------TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA-------------GCAACCTTCTTAGTTTCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT Template switch alignment (log-probability: -23.2) ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA|AACTAAGAAGGTTGC|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ATACATTTTTCTGAAATTTAAAGACTAAAAATGAACCAGA|AACTAAGAAGGTTGC|TCTATCAAAGGGGATAACGGTTCTGGTTATTTGAGCCATT ========== Event 1759 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCTTGCTGTCTGGTCCCCCC-------ACCTGCCATCTGTCCTAGAACACAGCA---------- Chimp: AGCTTGCTGTCTGGTCCCCCC-------ACCTGCCATCTGTCCTAGAACACAGCA---------- Gorilla: AGCTTGCTGTCTGGTCCCCCCTAGGACAGGTTGCCATCTGTCCTAGAACACAGCA---------- ↑ 1 4 3 2 Human: AGCTTGCTGTCTGGTCCCCCC-------ACCTGCCATCTGTCCTAGAACACAGCA---------- Cluster: [ ] Orangutan: AGCTTGCTGTCTGGTCCCCCC-------ACCTGCCATCTGTCCTAGAACACAGCACACAGCTGTA Human > Gorilla --------------- chr2A:6741738-6741747 Template switch process: F1: L AGCTCCTCGAACTGGAACTGAGCTTGCTGTCTGGTCCCCCC 1 F3: 4 TGCCATCTGTCCTAGAACACAGCACACAGCTGTAAATGAC R RF: AGCTCCTCGAACTGGAACTGAGCTTGCTGTCTGGTCCCCCCACCTGCCATCTGTCCTAGAACACAGCACACAGCTGTAAATGAC RR: TCGAGGAGCTTGACCTTGACTCGAACGACAGACCAGGGGGGTGGACGGTAGACAGGATCTTGTGTCGTGTGTCGACATTTACTG F2: 3 TGGACAGGAT 2 Unidirectional alignment (log-probability: -35.2) GCTCCTCGAACTGGAACTGAGCTTGCTGTCTGGTCCCC---CCtaggacaggtTGCCATCTGTCCTAGAACACAGCACACAGCTGTAAATGAC GCTCCTCGAACTGGAACTGAGCTTGCTGTCTGGTCCCCCCACC----------TGCCATCTGTCCTAGAACACAGCACACAGCTGTAAATGAC Template switch alignment (log-probability: -22.5) GCTCCTCGAACTGGAACTGAGCTTGCTGTCTGGTCCCCCC|TAGGACAGgT|TGCCATCTGTCCTAGAACACAGCACACAGCTGTAAATGAC GCTCCTCGAACTGGAACTGAGCTTGCTGTCTGGTCCCCCC|TAGGACAGAT|TGCCATCTGTCCTAGAACACAGCACACAGCTGTAAATGAC ========== Event 1760 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAGCTTCTTATACATTTGCAGAAATCTAGAAGATTTCTGCACAGACCGTGGTGTTGGAAAGTAGAATT ↑ 3 2 1 4 Chimp: CAAGCTTCTTATACATTTGCAGAAATCTAGAAGTTAATAGCACAGACCATGGTGTTGGAAAGTAGAATT Gorilla: CAAGCTTCTTATACATTTGCAGAAATCTAGAAGATAATAGCACAGACTATGGTGTTGGAAAGTAGAATT Human: CAAGCTTCTTATACATTTGCAGAAATCTAGAAGATTTCTGCACAGACCGTGGTGTTGGAAAGTAGAATT Cluster: [ ] Orangutan: CAAGCATCTTATACATTTGCAGAAATCTAGAAGATAATAGCACAGACTATGGTGTTGGAAAGTAGAATT Chimp > Human ------------- chr2:103818877-103818883 Template switch process: F1: L TGTTGATGCAAGCTTCTTATACATTTGCAGAAATCTAGAAG 1 F3: 4 CACAGACCGTGGTGTTGGAAAGTAGAATTGAAGCCAATGTTACTTTACT R RF: TGTTGATGCAAGCTTCTTATACATTTGCAGAAATCTAGAAGTTAATAGCACAGACCATGGTGTTGGAAAGTAGAATTGAAACCAATGTTACTTTACT RR: ACAACTACGTTCGAAGAATATGTAAACGTCTTTAGATCTTCAATTATCGTGTCTGGTACCACAACCTTTCATCTTAACTTTGGTTACAATGAAATGA F2: 3 GTCTTTA 2 Unidirectional alignment (log-probability: -40.7) GTTGATGCAAGCTTCTTATACATTTGCAGAAATCTAGAAGatttcT-----GCACAGACCgTGGTGTTGGAAAGTAGAATTGAAgCCAATGT GTTGATGCAAGCTTCTTATACATTTGCAGAAATCTAGAAG-----TTAATAGCACAGACCATGGTGTTGGAAAGTAGAATTGAAACCAATGT Template switch alignment (log-probability: -28.3) GTTGATGCAAGCTTCTTATACATTTGCAGAAATCTAGAAG|ATTTCTG|CACAGACCgTGGTGTTGGAAAGTAGAATTGAAgCCAATGT GTTGATGCAAGCTTCTTATACATTTGCAGAAATCTAGAAG|ATTTCTG|CACAGACCATGGTGTTGGAAAGTAGAATTGAAACCAATGT ========== Event 1761 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: -----CTCTTAGATACCTCTTTTTGCACACCTACTATAAtttattta---------------------taggtctccctcactaga------- Chimp: -----CTCTTAGATACCTCTTTTTGCACACCTACTATAATTTATTTATAGGTGTGCAAAAATTATTTATAGGTCTCCCTCACTAGA------- ↑ 3 2 4 1 Gorilla: -----CTCTTAGATACCTCTTTTTGCACACCTACTATAATTTACTTA---------------------TAGGTCTCCCTCACTAGACAAGTAT Human: -----CTCTTAGATACCTCTTTTTGCACACCTACTATAAtttattta---------------------taggtctccctcactaga------- Cluster: [ ] Orangutan: ctgataccttaaatacc------------------ctgatttaa------------------------------------------------- Gorilla > Chimp --------------- chr2A:100316910-100316918 Template switch process: F1: L TGCCTCTTAGATACCTCTTTTTGCACACCTACTATAATTTATTTATAGGT 1 F3: 4 TTATTTATAGGTCTCCCTCACTAGA R RF: TGCCTCTTAGATACCTCTTTTTGCACACCTACTATAATTTACTTATAGGTCTCCCTCACTAGA RR: ACGGAGAATCTATGGAGAAAAACGTGTGGATGATATTAAATGAATATCCAGAGGGAGTGATCT F2: 3 AAAAACGTG 2 Unidirectional alignment (log-probability: -54.2) ATACCTCTTTTTGCACACCTACTATAATTtatttataggtgtgcaaaaatTAtTTATAGGTCTCCCTCACTAGA---------------------- ATACCTCTTTTTGCACACCTACTATAATT---------------------TACTTATAGGTCTCCCTCACTAGACAAGTATTACCTGTTCTTATTT Template switch alignment (log-probability: -27.8) ATACCTCTTTTTGCACACCTACTATAATTTAtTTATAGGT|GTGCAAAAA|TTAtTTATAGGTCTCCCTCACTAGA ATACCTCTTTTTGCACACCTACTATAATTTACTTATAGGT|GTGCAAAAA|TTACTTATAGGTCTCCCTCACTAGA ========== Event 1762 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTTCCCTCTTGAAAACATGAGGAGACttttttttttt---tttttt--ttttttttttttgagacagtctcactctgttacccaggctggagtgcagtggcgcgatctcagctcaccgcaacctctgcctatcaggttcaagcaagtctcctgcctcgccctccagagta Chimp: gttttCCCTCTTGAAAACATG---AGACttttttttttt---------ttttttttttttttgagacagtctcactctgttacccaggctagagtgcagtggcgcgatctcagctcaccacaacctctgcctatcaggttcaagcaagtctcctgcctcgccctccagagta ↓ 1 4 3 2 Gorilla: gttttCCCTCTTGAAAACATGAGGAGACtttttttttttttt--------ttttttttttttgagacagtctcactctgttacccaggctggagtgcagtggtgtgatctcagctcaccgcaacctctgcctgtcaggttcaagcaagtctcctgcctcgccctccagagta Human: GTTTTCCCTCTTGAAAACATGAGGAGACttttttttttt---tttttt--ttttttttttttgagacagtctcactctgttacccaggctggagtgcagtggcgcgatctcagctcaccgcaacctctgcctatcaggttcaagcaagtctcctgcctcgccctccagagta Cluster: [ ] Orangutan: CTTTTCCCTCTTGAAAACATGAGGAGACtttttttttt---------------tttttttttgagacagtctcactctgttacccaggctggagtgcagtgacgcgatctcggctcaccgcaacctctgcctaccgggttcaagcaagtctcctgcctcgccctccggagta Chimp > Gorilla --------------- chr2A:10907470-10907475 Template switch process: F1: L AAATATAACATATATTTATAGTTTTCCCTCTTGAAAACATGAG 1 F3: 4 TTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGT R RF: AAATATAAGATATATTTATAGTTTTCCCTCTTGAAAACATGAGACTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGTCTCACTCTGTTACCCAGGCTAGAGTGCAGTGGCGCGATCTCAGCTCACCACAACCTCTGCCTATCAGGTTCAAGCAAGTCTC RR: TTTATATTCTATATAAATATCAAAAGGGAGAACTTTTGTACTCTGAAAAAAAAAAAAAAAAAAAAAAAAACTCTGTCAGAGTGAGACAATGGGTCCGATCTCACGTCACCGCGCTAGAGTCGAGTGGTGTTGGAGACGGATAGTCCAAGTTCGTTCAGAG F2: 3 TCAGAG 2 Unidirectional alignment (log-probability: -31.9) TATAAcATATATTTATAGTTTTCCCTCTTGAAAACATgagGAGACtTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGT TATAAGATATATTTATAGTTTTCCCTCTTGAAAACAT---GAGAC-TTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGT Template switch alignment (log-probability: -21.9) TATAAcATATATTTATAGTTTTCCCTCTTGAAAACATGAG|GAGACT|TTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGT TATAAGATATATTTATAGTTTTCCCTCTTGAAAACATGAG|GAGACT|TTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGT ========== Event 1763 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTCCATTGCACAGGTTTGTA-----CTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCATTGTGAATAAACATT- ↓ 1 4 3 2 Chimp: GTTTCCATTGCACAGGTTTGTGATTCCATTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCATTGTGAATAAACATT- ↑ 1 4 3 2 Gorilla: GTTTCCATTGCACAGGTTTGTA-----CTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCATTGTGAATAAACATT- Human: GTTTCCATTGCACAGGTTTGTA-----CTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCATTGTGAATAAACATT- Cluster: [ ] Orangutan: GTTTCCATTGCACAGGTTTGTA-----CTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAAACTTCATTGTGAATAAACATTT Human > Chimp ------------- chr2A:6794297-6794303 Template switch process: F1: L AAATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGT 1 F3: 4 TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA R RF: AAATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGTACTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA RR: TTTAGTGAGGTACACGAGAACAAAGGTAACGTGTCCAAACATGAAAGGTCTACACTAGGAGAACCCGAAGGAACCTTAGAAGT F2: 3 ACCTTAG 2 Unidirectional alignment (log-probability: -29.8) AATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGTgattccA-TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA AATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGT------ACTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA Template switch alignment (log-probability: -16.2) AATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGT|GATTCCA|TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA AATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGT|GATTCCA|TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA Gorilla > Chimp --------------- chr2A:6794297-6794303 Template switch process: F1: L AAATCACTCCATGTGCTCTTGTTTCCATTGCACAGGTTTGT 1 F3: 4 TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA R RF: AAATCACTCCATGTACTCTTGTTTCCATTGCACAGGTTTGTACTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA RR: TTTAGTGAGGTACATGAGAACAAAGGTAACGTGTCCAAACATGAAAGGTCTACACTAGGAGAACCCGAAGGAACCTTAGAAGT F2: 3 ACCTTAG 2 Unidirectional alignment (log-probability: -34.7) AATCACTCCATGTgCTCTTGTTTCCATTGCACAGGTTTGTgattccaTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA AATCACTCCATGTACTCTTGTTTCCATTGCACAGGTTTGTA-----CTTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA Template switch alignment (log-probability: -22.1) AATCACTCCATGTgCTCTTGTTTCCATTGCACAGGTTTGT|GATTCCA|TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA AATCACTCCATGTACTCTTGTTTCCATTGCACAGGTTTGT|GATTCCA|TTTCCAGATGTGATCCTCTTGGGCTTCCTTGGAATCTTCA ========== Event 1764 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACATATTGGACAATTAAGGAAGGGGTCCC----------TTGAAAAAAATATGAGGGTGCTTGACTGGCATTCTATGTTTTCTGAG Chimp: AACATATTGGACAATTAAGGAGGGGGTCCC----------TTGaaaaaaaTATGAGGGTGCCTGACTGGCATTCTATGTTTTCTGAG ↓ 1 4 3 2 Gorilla: AACATATTGGACAATTAAGGAGGGGGTCCC--------------------AGTCAGGGTGCCTGACTGGCATTCTATGTTTTCTGAG ↑ 1 4 3 2 Human: AACATATTGGACAATTAAGGAAGGGGTCCC----------TTGAAAAAAATATGAGGGTGCTTGACTGGCATTCTATGTTTTCTGAG Cluster: [ ] Orangutan: AACGTATTGGACAATTAAGGAGGGAGTCCCTTGAAAAAAA----------TATGAGGGTGCCTGGCTGGCATTCTATGTTTTCTGAC Human > Gorilla --------------- chr2A:97021078-97021081 Template switch process: F1: L AATATTATGTTTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCC 1 F3: 4 AGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTGGTAACCTA R RF: AATATTATGTTTTCTTTAGAAACATATTGGACAATTAAGGAAGGGGTCCCTTGAAAAAAATATGAGGGTGCTTGACTGGCATTCTATGTTTTCTGAGGGAACTGGTAACCTA RR: TTATAATACAAAAGAAATCTTTGTATAACCTGTTAATTCCTTCCCCAGGGAACTTTTTTTATACTCCCACGAACTGACCGTAAGATACAAAAGACTCCCTTGACCATTGGAT F2: 3 CTGA 2 Unidirectional alignment (log-probability: -38.4) TTTCTTTAGAAACATATTGGACAATTAAGGAgGGGGTCCC--------------agtcAGGGTGCcTGACTGGCATTCTATGTTTTCTGAGGGAACTG TTTCTTTAGAAACATATTGGACAATTAAGGAAGGGGTCCCTTGAAAAAAATATG----AGGGTGCTTGACTGGCATTCTATGTTTTCTGAGGGAACTG Template switch alignment (log-probability: -27.7) TTTCTTTAGAAACATATTGGACAATTAAGGAgGGGGTCCC|AGTC|AGGGTGCcTGACTGGCATTCTATGTTTTCTGAGGGAACTG TTTCTTTAGAAACATATTGGACAATTAAGGAAGGGGTCCC|AGTC|AGGGTGCTTGACTGGCATTCTATGTTTTCTGAGGGAACTG Chimp > Gorilla --------------- chr2A:97021078-97021081 Template switch process: F1: L TTTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCC 1 F3: 4 AGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTG R RF: TTTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCCTTGAAAAAAATATGAGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTG RR: AAAAGAAATCTTTGTATAACCTGTTAATTCCTCCCCCAGGGAACTTTTTTTATACTCCCACGGACTGACCGTAAGATACAAAAGACTCCCTTGAC F2: 3 CTGA 2 Unidirectional alignment (log-probability: -27.1) TTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCC--------------agtcAGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTG TTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCCTTGAAAAAAATATG----AGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTG Template switch alignment (log-probability: -16.2) TTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCC|AGTC|AGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTG TTTCTTTAGAAACATATTGGACAATTAAGGAGGGGGTCCC|AGTC|AGGGTGCCTGACTGGCATTCTATGTTTTCTGAGGGAACTG ========== Event 1765 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCCAGCTCAGGACAAAATGCACC---------------------------------------------CTGGCCCGCTCTGATGGCCTGGTCACTGTCC ↓ 3 42 1 Chimp: TCCCAGCTCAGGACAAAATGCACC---------------------------CTGGCCCACTCAGGGTGCCTGGCCCGCTCTGATGGCCTGGTCACTGTCC Gorilla: TCCCAGCTCAGGACAAAATGCACc---------ctggcccgctcagggtgc------------------ctggcccgctccgatggcctggTCACTGTCC Human: TCCCAGCTCAGGACAAAATGCACC---------------------------------------------CTGGCCCGCTCTGATGGCCTGGTCACTGTCC Cluster: [ ] Orangutan: TCCCAGCTCAGGACAAAATGCAC-CCAGGGTGC------------------------------------CTGGTCCGCTCTGATGGCCTGGTCACTGTTC Human > Chimp ------------- chr2A:6321470-6321476 Template switch process: F1: L GCCTGTGCTATGTGCTGTCCCAGCTCAGGACAAAATGCACCCTGGCCCACTC 1 F3: 4 CTGGCCCGCTCTGATGGCCTGGTCACTGTCCTGTGCCTGC R RF: GCCTGTGCTATGTGCTGTCCCAGCTCAGGACAAAATGCACCCTGGCCCGCTCTGATGGCCTGGTCACTGTCCTGTGCCTGC RR: CGGACACGATACACGACAGGGTCGAGTCCTGTTTTACGTGGGACCGGGCGAGACTACCGGACCAGTGACAGGACACGGACG F2: 3 CGTGGGA 2 Unidirectional alignment (log-probability: -36.8) TGCTGTCCCAGCTCAGGACAAAATGCACCCTGGCccactcagggtgcctggcCCGCTCTGATGGCCTGGTCACTGTCCTGTGCCTGC TGCTGTCCCAGCTCAGGACAAAATGCACCCTGGC------------------CCGCTCTGATGGCCTGGTCACTGTCCTGTGCCTGC Template switch alignment (log-probability: -22.4) TGCTGTCCCAGCTCAGGACAAAATGCACCCTGGCCCaCTC|AGGGTGC|CTGGCCCGCTCTGATGGCCTGGTCACTGTCCTGTGCCTGC TGCTGTCCCAGCTCAGGACAAAATGCACCCTGGCCCGCTC|AGGGTGC|CTGGCCCGCTCTGATGGCCTGGTCACTGTCCTGTGCCTGC ========== Event 1766 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CGTGTGCTTGGAGGTGGTACCACCTTT------------------------------------------GGATAAGGCTTTTGCATAAAGCCACCTTTGCATAAGGCTTTTCGAACTCTGCGTTCACAAGCCTTATGCAAAGAACAGAGCAGAAAAAT ↑ 4 1 3 2 Chimp: CGTGTGCTTGGAGGTGGTACCACCTTT-----------------------------------------------------------------------GCATAAGGCTTTTCGAACTCTGCGTTCACAAGCCTTATGCAAAGAACAGAGCAGAAAAAT Gorilla: TGTGTGTTTGGAGGTGGTACCACCttt-----------------------------ggataaggctttt-----------------------------gcataaggcttttTGAACTCTGAGTTCACAAGCCTTATGCAAGGAACAGAGCAGAAAAAT Human: CGTGTGCTTGGAGGTGGTACCACCTTT------------------------------------------GGATAAGGCTTTTGCATAAAGCCACCTTTGCATAAGGCTTTTCGAACTCTGCGTTCACAAGCCTTATGCAAAGAACAGAGCAGAAAAAT Cluster: [ ] Orangutan: TGTGTGCTTGGAGGTGGTACCACCTTTGGATAAGGCTTTTGCATAAAGCCACCTTT------------------------------------------GCATAAGGCTTTTTGAACTCTGAGTTCAAAAGCCTTATGCAAAGAACAGAGCAGAAAAAT Chimp > Human ------------- chr2:135550002-135550009 Template switch process: F1: L TCATAAAGATTCATCGTGTGCTTGGAGGTGGTACCACCTTTGGATAAGGCTTTT 1 F3: 4 CCACCTTTGCATAAGGCTTTTCGAACTCTGCGTTCACAAGCCTTATGC R RF: TCATAAAGATTCATCGTGTGCTTGGAGGTGGTACCACCTTTGCATAAGGCTTTTCGAACTCTGCGTTCACAAGCCTTATGC RR: AGTATTTCTAAGTAGCACACGAACCTCCACCATGGTGGAAACGTATTCCGAAAAGCTTGAGACGCAAGTGTTCGGAATACG F2: 3 GAAATACG 2 Unidirectional alignment (log-probability: -52.6) CGTGTGCTTGGAGGTGGTACCACCTTTGgataaggcttttgcataaagccacctttgCATAAGGCTTTTCGAACTCTGCGTTCACAAG CGTGTGCTTGGAGGTGGTACCACCTTTG-----------------------------CATAAGGCTTTTCGAACTCTGCGTTCACAAG Template switch alignment (log-probability: -28.7) CGTGTGCTTGGAGGTGGTACCACCTTTGgATAAGGCTTTT|GCATAAaG|CCACCTTTGCATAAGGCTTTTCGAACTCTGCGTTCACAAG CGTGTGCTTGGAGGTGGTACCACCTTTGCATAAGGCTTTT|GCATAAGG|CCACCTTTGCATAAGGCTTTTCGAACTCTGCGTTCACAAG ========== Event 1767 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGCACTTTGGCATTAGATGAC-----TAATGCTCACAAGTGTGCTATTGTAACTGG Chimp: AAAGCACTTTGGCATTAGATGAC-----TAATGCTCACAAGTGTGCTACTGTAACTGG ↓ 1 3 2 4 Gorilla: AAAGCACTTTGGCATTAGATGGC----------ATTACAAGTGTGCTACTGTAACTGG ↑ 1 3 2 4 Human: AAAGCACTTTGGCATTAGATGAC-----TAATGCTCACAAGTGTGCTATTGTAACTGG Cluster: [ ] Orangutan: AAAGCACTTTGGCATTAGATGACTAATG-----CTCACAAGTGTGCTGCTGTAACTGG Human > Gorilla --------------- chr2A:11866767-11866772 Template switch process: F1: L CTGCCCACCAATTCTGCACAAAAGCACTTTGGCATTAGATG 1 F3: 4 CAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA R RF: CTGCCCACCGATTCTGCACAAAAGCACTTTGGCATTAGATGACTAATGCTCACAAGTGTGCTATTGTAACTGGGTATCAACGTGGTGTTCA RR: GACGGGTGGCTAAGACGTGTTTTCGTGAAACCGTAATCTACTGATTACGAGTGTTCACACGATAACATTGACCCATAGTTGCACCACAAGT F2: 3 ATTACG 2 Unidirectional alignment (log-probability: -38.8) TGCCCACCaATTCTGCACAAAAGCACTTTGGCATTAGATGgC-----aTtACAAGTGTGCTAcTGTAACTGGGTATCAACGTGGTGTTCA TGCCCACCGATTCTGCACAAAAGCACTTTGGCATTAGATGACTAATGCTCACAAGTGTGCTATTGTAACTGGGTATCAACGTGGTGTTCA Template switch alignment (log-probability: -27.5) TGCCCACCaATTCTGCACAAAAGCACTTTGGCATTAGATG|GCATTA|CAAGTGTGCTAcTGTAACTGGGTATCAACGTGGTGTTCA TGCCCACCGATTCTGCACAAAAGCACTTTGGCATTAGATG|GCATTA|CAAGTGTGCTATTGTAACTGGGTATCAACGTGGTGTTCA Chimp > Gorilla --------------- chr2A:11866767-11866772 Template switch process: F1: L CTGCCCACCAATTCTGCACAAAAGCACTTTGGCATTAGATG 1 F3: 4 CAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA R RF: CTGCCCACCGATTCTGCACAAAAGCACTTTGGCATTAGATGACTAATGCTCACAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA RR: GACGGGTGGCTAAGACGTGTTTTCGTGAAACCGTAATCTACTGATTACGAGTGTTCACACGATGACATTGACCCATAGTTGCACCACAAGT F2: 3 ATTACG 2 Unidirectional alignment (log-probability: -33.3) TGCCCACCaATTCTGCACAAAAGCACTTTGGCATTAGATGgC-----aTtACAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA TGCCCACCGATTCTGCACAAAAGCACTTTGGCATTAGATGACTAATGCTCACAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA Template switch alignment (log-probability: -22) TGCCCACCaATTCTGCACAAAAGCACTTTGGCATTAGATG|GCATTA|CAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA TGCCCACCGATTCTGCACAAAAGCACTTTGGCATTAGATG|GCATTA|CAAGTGTGCTACTGTAACTGGGTATCAACGTGGTGTTCA ========== Event 1768 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATTATAAAATGCTCATAAACTAAGAAGATA--------------ATAAGTAGTCAGCTATCACATTG Chimp: AATTATAAAATGCTCATAAACTAATAAGATA--------------ATAAGTAGTCAGCTATCACATTG ↓ 3 1 4 2 Gorilla: AATTATAAAATGCTCATAAACTAATAAGATTATTATCTTATTAGTATTAGTAGTCAGCTATCACATTG Human: AATTATAAAATGCTCATAAACTAAGAAGATA--------------ATAAGTAGTCAGCTATCACATTG Cluster: [ ] Orangutan: AAATATAAAATGCTCATAAACTAATAAGATA--------------ATAAGTAGTCAGCTATCACACTG Chimp > Gorilla --------------- chr2A:94550247-94550261 Template switch process: F1: L TATTACCAAAAAATTATAAAATGCTCATAAACTAATAAGAT 1 F3: 4 ATTAGTAGTCAGCTATCACATTGGCATATATACTTAAACGCAC R RF: TATTACCAAAAAATTATAAAATGCTCATAAACTAATAAGATAATAAGTAGTCAGCTATCACATTGGCATATATACTTAAATGCAC RR: ATAATGGTTTTTTAATATTTTACGAGTATTTGATTATTCTATTATTCATCAGTCGATAGTGTAACCGTATATATGAATTTACGTG F2: 3 TGATTATTCTATTAT 2 Unidirectional alignment (log-probability: -47.6) ATTACCAAAAAATTATAAAATGCTCATAAACTAATAAGATtattatcttattagtATtAGTAGTCAGCTATCACATTGGCATATATACTTAAAcG ATTACCAAAAAATTATAAAATGCTCATAAACTAATAAGAT--------------AATAAGTAGTCAGCTATCACATTGGCATATATACTTAAATG Template switch alignment (log-probability: -28.7) ATTACCAAAAAATTATAAAATGCTCATAAACTAATAAGAT|TATTATCTTATTAGT|ATtAGTAGTCAGCTATCACATTGGCATATATACTTAAAcG ATTACCAAAAAATTATAAAATGCTCATAAACTAATAAGAT|TATTATCTTATTAGT|ATAAGTAGTCAGCTATCACATTGGCATATATACTTAAATG ========== Event 1769 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: CAGCTCCCAGCAGGATGCTCCTTAGAAGACTAAGCGTTTGCCTTGGCAAGAAGCCT Chimp: Gorilla: CAGCTCCCAGCAGGATGCTCC--TGTCTTCTAAGGGTTTGCCTTGGCAAGAAGCCT ↑ 3 1 2 4 Human: CAGCTCCCAGCAGGATGCTCCTTAGAAGACTAAGCGTTTGCCTTGGCAAGAAGCCT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr2A:13268465-13268475 Template switch process: F1: L AGAGATGTCTGCCTGGCAATCAGCTCCCAGCAGGATGCTCCT 1 F3: 4 GTTTGCCTTGGCAAGAAGCCTTTGGACATTCAGCCCGGTG R RF: AGAGATGTCTGCCTGGCAATCAGCTCCCAGCAGGATGCTCCTTAGAAGACTAAGCGTTTGCCTTGGCAAGAAGCCTTTGGACATTCAGCCCGGTG RR: TCTCTACAGACGGACCGTTAGTCGAGGGTCGTCCTACGAGGAATCTTCTGATTCGCAAACGGAACCGTTCTTCGGAAACCTGTAAGTCGGGCCAC F2: 3 GGAATCTTCTG 2 Unidirectional alignment (log-probability: -32.3) AGATGTCTGCCTGGCAATCAGCTCCCAGCAGGATGCTCctgtCTT------CTAAGgGTTTGCCTTGGCAAGAAGCCTTTGGACATTCAGCCCGGTG AGATGTCTGCCTGGCAATCAGCTCCCAGCAGGATGCTC----CTTAGAAGACTAAGCGTTTGCCTTGGCAAGAAGCCTTTGGACATTCAGCCCGGTG Template switch alignment (log-probability: -17.2) AGATGTCTGCCTGGCAATCAGCTCCCAGCAGGATGCTCCT|GTCTTCTAAGG|GTTTGCCTTGGCAAGAAGCCTTTGGACATTCAGCCCGGTG AGATGTCTGCCTGGCAATCAGCTCCCAGCAGGATGCTCCT|GTCTTCTAAGG|GTTTGCCTTGGCAAGAAGCCTTTGGACATTCAGCCCGGTG ========== Event 1770 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: TGTCAAAAGTCTGGTGGTTCAGTCTCC------------AAACCAAAGTTTAGAGGTCCTGAGGCCACACTGAAAGTTTAGAGGTCCTGAGGTCAGCTGGCCACGTTCTTCCACCCGTCACctg Chimp: ---------------------------------------------------------------------------------------------------------------------------- Gorilla: TGTCAAAAGTCTGGTGGTTCAGTCTCCAAACCAAAGTTT----------------------------------------AGAGGTCCTGAGATCAGCTGGCCACGTTCTTCCACCCGTCACCTG ↓ 3 2 4 1 Human: TGTCAAAAGTCTGGTGGTTCAGTCTCC------------AAACCAAAGTTTAGAGGTCCTGAGGCCACACTGAAAGTTTAGAGGTCCTGAGGTCAGCTGGCCACGTTCTTCCACCCGTCACctg Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr2:108318919-108318922 Template switch process: F1: L AAACTGTGGAACCTTGTCAAAAGTCTGGTGGTTCAGTCTCCAAACCAAAGTTTAGAGGTCCTGA--------GGCCAC 1 F3: 4 AAAGTTTAGAGGTCCTGAGGTCAGCTGGCCACGTTCTTCCACCCGTC R RF: AAACTGTGGAACCTTGTCAAAAGTCTGGTGGTTCAGTCTCCAAACCAAAGTTTAGAGGTCCTGAGATCAGCTGGCCACGTTCTTCCACCCGTC RR: TTTGACACCTTGGAACAGTTTTCAGACCACCAAGTCAGAGGTTTGGTTTCAAATCTCCAGGACTCTAGTCGACCGGTGCAAGAAGGTGGGCAG F2: 3 GTCA 2 Unidirectional alignment (log-probability: -56.8) GTTCAGTCTCCAAACCaaagtttagaggtcctgaggccacactgAAAGTTTAGAGGTCCTGAGgTCAGCTGGCCACGTTCTTCC GTTCAGTCTCCAAACC----------------------------AAAGTTTAGAGGTCCTGAGATCAGCTGGCCACGTTCTTCC Template switch alignment (log-probability: -32.8) GTTCAGTCTCCAAACCAAAGTTTAGAGGTCCTGA--------GGCCAC|ACTG|AAAGTTTAGAGGTCCTGAGgTCAGCTGGCCACGTTCTTCC GTTCAGTCTCCAAACCAAAGTTTAGAGGTCCTGAGATCAGCTGGCCAC|ACTG|AAAGTTTAGAGGTCCTGAGATCAGCTGGCCACGTTCTTCC ========== Event 1771 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAACACCCGACATGGGTGATCTTAAGCGACC------------------------------GCTTAA--------------------GATTGGTTTAGTTCAGTTTGGAG ↑ 3 1 2 4 Chimp: GAACACCCGACGTGGGTGATCTTAAGCGGTC---------------ATTCTCTGTGGTCAGACTCAA----------GCCACACATCCTTTGGTTTAGTTCAGTTTGGAG Gorilla: GAACACCCGACGTGGGTGATCTTAAGCGGTCATTCTCTGTGGTCAG---------------ACTCAAGCCACACATC----------CTTTGGTTTAGTTCAGTTTGGAG ↓ 3 1 2 4 Human: GAACACCCGACATGGGTGATCTTAAGCGACC------------------------------GCTTAA--------------------GATTGGTTTAGTTCAGTTTGGAG Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:109019601-109019611 Template switch process: F1: L TTCTCCAAGGGAAGAACACCCGACATGGGTGATCTTAAGCG 1 F3: 4 TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT R RF: TTCTCCAAGGGAAGAACACCCGACGTGGGTGATCTTAAGCGGTCATTCTCTGTGGTCAGACTCAAGCCACACATCCTTTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT RR: AAGAGGTTCCCTTCTTGTGGGCTGCACCCACTAGAATTCGCCAGTAAGAGACACCAGTCTGAGTTCGGTGTGTAGGAAACCAAATCAAGTCAAACCTCTCGTTAAACTACACGACCA F2: 3 AGAATTCGCCA 2 Unidirectional alignment (log-probability: -44.8) TCTCCAAGGGAAGAACACCCGACaTGGGTGATCTTAAGCG------------------------------------accgcttaagaTTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT TCTCCAAGGGAAGAACACCCGACGTGGGTGATCTTAAGCGGTCATTCTCTGTGGTCAGACTCAAGCCACACATCCT-----------TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT Template switch alignment (log-probability: -22.6) TCTCCAAGGGAAGAACACCCGACaTGGGTGATCTTAAGCG|ACCGCTTAAGA|TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT TCTCCAAGGGAAGAACACCCGACGTGGGTGATCTTAAGCG|ACCGCTTAAGA|TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT Gorilla > Human --------------- chr2:109019601-109019611 Template switch process: F1: L TTCTCCAAGGGAAGAACACCCGACATGGGTGATCTTAAGCG 1 F3: 4 TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT R RF: TTCTCCAAGGGAAGAACACCCGACGTGGGTGATCTTAAGCGGTCATTCTCTGTGGTCAGACTCAAGCCACACATCCTTTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT RR: AAGAGGTTCCCTTCTTGTGGGCTGCACCCACTAGAATTCGCCAGTAAGAGACACCAGTCTGAGTTCGGTGTGTAGGAAACCAAATCAAGTCAAACCTCTCGTTAAACTACACGACCA F2: 3 AGAATTCGCCA 2 Unidirectional alignment (log-probability: -43.8) TCTCCAAGGGAAGAACACCCGACaTGGGTGATCTTAAGCG------------------------------------accgcttaagaTTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT TCTCCAAGGGAAGAACACCCGACGTGGGTGATCTTAAGCGGTCATTCTCTGTGGTCAGACTCAAGCCACACATCCT-----------TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT Template switch alignment (log-probability: -22.6) TCTCCAAGGGAAGAACACCCGACaTGGGTGATCTTAAGCG|ACCGCTTAAGA|TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT TCTCCAAGGGAAGAACACCCGACGTGGGTGATCTTAAGCG|ACCGCTTAAGA|TTGGTTTAGTTCAGTTTGGAGAGCAATTTGATGTGCTGGT ========== Event 1772 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCAGCCCGTGGGAAGGCAGATTTCCT---TATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATC Chimp: TGCAGCCCGTGGGAAGGCAGATTTCCT---TATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATC ↓ 1 4 3 2 Gorilla: TGCAGCCCGTGGGAAGGCAGACATGTT------TTATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATC ↑ 1 4 3 2 Human: TGCAGCCCGTGGGAAGGCAGATTTCCT---TATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATC Cluster: [ ] Orangutan: TGCAGCCCGTGGGAAGGCAGATTTCCTTAT---GCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATC Human > Gorilla --------------- chr2A:14568174-14568181 Template switch process: F1: L CCACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGA 1 F3: 4 ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC R RF: CCACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGATTTCCTTATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC RR: GGTGGGATGACACAGATGGTACGTCGGGCACCCTTCCGTCTAAAGGAATACGTACAGTAGTATTTTGTACGAGGTCTTACACGTCCTTAGTG F2: 3 TTTTGTAC 2 Unidirectional alignment (log-probability: -28.3) CACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGAcatgtTTT--------ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC CACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGA-----TTTCCTTATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC Template switch alignment (log-probability: -16.7) CACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGA|CATGTTTT|ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC CACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGA|CATGTTTT|ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC Chimp > Gorilla --------------- chr2A:14568174-14568181 Template switch process: F1: L CCACCCTACTGTGTCTACCATGCAGCCCGTGGGAAGGCAGA 1 F3: 4 ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC R RF: CCACCCTACTGTGTCTCCCATGCAGCCCGTGGGAAGGCAGATTTCCTTATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC RR: GGTGGGATGACACAGAGGGTACGTCGGGCACCCTTCCGTCTAAAGGAATACGTACAGTAGTATTTTGTACGAGGTCTTACACGTCCTTAGTG F2: 3 TTTTGTAC 2 Unidirectional alignment (log-probability: -33.8) CACCCTACTGTGTCTaCCATGCAGCCCGTGGGAAGGCAGAcatgtTTT--------ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC CACCCTACTGTGTCTCCCATGCAGCCCGTGGGAAGGCAGA-----TTTCCTTATGCATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC Template switch alignment (log-probability: -22.3) CACCCTACTGTGTCTaCCATGCAGCCCGTGGGAAGGCAGA|CATGTTTT|ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC CACCCTACTGTGTCTCCCATGCAGCCCGTGGGAAGGCAGA|CATGTTTT|ATGTCATCATAAAACATGCTCCAGAATGTGCAGGAATCAC ========== Event 1773 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGATGAGTGGTTCC Chimp: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTCC ↓ 4 3 2 1 Gorilla: TCAGCCAGCAGTTGGCCTGGATAGACACAGGGAATGTGTCTACCAGTTGGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTCC Human: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGATGAGTGGTTCC Cluster: [ ] Orangutan: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTCC Chimp > Gorilla --------------- chr2A:88150926-88150934 Template switch process: F1: L TGTTTCTTTTTGCTCTCTCTTCAGCCAGCAGTTGGCCTGGA----------TAGACACAGGGAATGT 1 F3: 4 TTGGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTC R RF: TGTTTCTTTTTGCTCTCTCTTCAGCCAGCAGTTGGCCTGGATCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTC RR: ACAAAGAAAAACGAGAGAGAAGTCGGTCGTCAACCGGACCTAGAAACGACCATCTGTGTCCCTTACAAGAGGAACTCCTCACCAAG F2: 3 GACCATCTG 2 Unidirectional alignment (log-probability: -55.1) TCTTCAGCCAGCAGTTGGCCTGGATagacacagggaatgtgtctaccagTTgGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG TCTTCAGCCAGCAGTTGGCCTGGAT-----------------------CTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG Template switch alignment (log-probability: -33.1) TCTTCAGCCAGCAGTTGGCCTGGA----------TAGACACAGGGAATGT|GTCTACCAG|TTgGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG TCTTCAGCCAGCAGTTGGCCTGGATCTTTGCTGGTAGACACAGGGAATGT|GTCTACCAG|TTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG ========== Event 1774 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAAGAGGATGTAAAGCAACTAT---CTTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATT ↓ 1 4 3 2 Chimp: CAAAGAGGATGTAAAGCAACTGTCAGTTAACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATT ↑ 1 4 3 2 Gorilla: CAAAGAGGATGTAAAGCAACTAT---CTTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATT Human: CAAAGAGGATGTAAAGCAACTAT---CTTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATT Cluster: [ ] Orangutan: CAAA-GGGATGTAAAGCAACTAT---CTTACCGCCCAAGTTAATTGACATTCAAATATGCTGCAGATT Human > Chimp ------------- chr2A:2158513-2158520 Template switch process: F1: L AAAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACT 1 F3: 4 ACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC R RF: AAAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACTATCTTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC RR: TTTTTTTACAAACTTTTTGAGTTTCTCCTACATTTCGTTGATAGAATGGTGGGTTCAATTGACTGTAAGTTTATACGACGTCTAAG F2: 3 ATTGACTG 2 Unidirectional alignment (log-probability: -27.3) AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACTgTCagtTaACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACTATC---TTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC Template switch alignment (log-probability: -16.3) AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACT|GTCAGTTA|ACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACT|GTCAGTTA|ACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC Gorilla > Chimp --------------- chr2A:2158513-2158520 Template switch process: F1: L AAAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACT 1 F3: 4 ACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC R RF: CAAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACTATCTTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC RR: GTTTTTTACAAACTTTTTGAGTTTCTCCTACATTTCGTTGATAGAATGGTGGGTTCAATTGACTGTAAGTTTATACGACGTCTAAG F2: 3 ATTGACTG 2 Unidirectional alignment (log-probability: -31.8) AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACTgTCagtTaACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACTATC---TTACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC Template switch alignment (log-probability: -22.3) AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACT|GTCAGTTA|ACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC AAAAAATGTTTGAAAAACTCAAAGAGGATGTAAAGCAACT|GTCAGTTA|ACCACCCAAGTTAACTGACATTCAAATATGCTGCAGATTC ========== Event 1775 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GCATGTCCTTGAGCCAGGGACTCAC------------CTGCAGGTGAGTCTGTGTGCCTTAACCTCCTCATC Chimp: GCGTGTCCTTGAGCCAGGGACTCAC------------CTGCAGGTGAGTCTGTGTGCCTTAACCTCTTCATC Gorilla: GCATGTCCTTGATCCAGGGACTCAC------------------------CTGTGTGCCTTAACCTCCTCATC ↓ 3 4 2 Human: GCATGTCCTTGAGCCAGGGACTCAC------------CTGCAGGTGAGTCTGTGTGCCTTAACCTCCTCATC Cluster: [ ] Orangutan: GCGTGTCCTTCAGCCAGGGACTCACCTGCAGGTGAGT------------CTGTGTGCCTTAACCTCCTCATC Gorilla > Human --------------- chr2:131317647-131317655 Template switch process: F1: L CTACTGTTTCTTTCCTGCATGTCCTTGAGCCAGGGACTCACCTG 1 F3: 4 CTGTGTGCCTTAACCTCCTCATCCATTGTAGAGGTTACAA R RF: CTACTGTTTCTTTCCTGCATGTCCTTGATCCAGGGACTCACCTGTGTGCCTTAACCTCCTCATCCCTTGTAGAGGTTACAA RR: GATGACAAAGAAAGGACGTACAGGAACTAGGTCCCTGAGTGGACACACGGAATTGGAGGAGTAGGGAACATCTCCAATGTT F2: 3 TGAGTGGAC 2 Unidirectional alignment (log-probability: -39.2) TGTTTCTTTCCTGCATGTCCTTGAgCCAGGGACTCACctgcaggtgagtCTGTGTGCCTTAACCTCCTCATCCaTTGTAGAGGTTACAA TGTTTCTTTCCTGCATGTCCTTGATCCAGGGACTCAC------------CTGTGTGCCTTAACCTCCTCATCCCTTGTAGAGGTTACAA Template switch alignment (log-probability: -28) TGTTTCTTTCCTGCATGTCCTTGAgCCAGGGACTCACCTG|CAGGTGAGT|CTGTGTGCCTTAACCTCCTCATCCaTTGTAGAGGTTACAA TGTTTCTTTCCTGCATGTCCTTGATCCAGGGACTCACCTG|CAGGTGAGT|CTGTGTGCCTTAACCTCCTCATCCCTTGTAGAGGTTACAA ========== Event 1776 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTCTGAAGTTAGAGATGTACCCTTGTAATC----------TATGTTACAAAACAAAGAGCACCA Chimp: tATTCTGAAGTTAGAGATGTACCCTTGTAATC----------TATGTTACAAAACAAAGAGCACCA ↓ 3 1 2 4 Gorilla: tATTCTGAAGTTAGAGATGTACCCTTGTAAGATTACAAGGGTAATCTTACAAAACAAAGAGCACTA ↑ 3 1 2 4 Human: TATTCTGAAGTTAGAGATGTACCCTTGTAATC----------TATGTTACAAAACAAAGAGCACCA Cluster: [ ] Orangutan: TATTCTGAAGTTAGAGATGTACCCTTGTAATC----------TATGTTACAAAACAAAGAGCACCA Human > Gorilla --------------- chr2A:11466982-11466994 Template switch process: F1: L AGTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAA 1 F3: 4 ATCTTACAAAACAAAGAGCACTATTACACAGAACACAATGTCC R RF: AGTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAATCTATGTTACAAAACAAAGAGCACCATTACACAGAACACAATGTCC RR: TCATTTTGTTAATAAGACTTCAATCTCTACATGGGAACATTAGATACAATGTTTTGTTTCTCGTGGTAATGTGTCTTGTGTTACAGG F2: 3 ATGGGAACATTAG 2 Unidirectional alignment (log-probability: -46.5) GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTaagattacaagggtAATC----TTACAAAACAAAGAGCACtATTACACAGAACACAATG GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGT--------------AATCTATGTTACAAAACAAAGAGCACCATTACACAGAACACAATG Template switch alignment (log-probability: -28.5) GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAA|GATTACAAGGGTA|ATcTTACAAAACAAAGAGCACtATTACACAGAACACAATG GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAA|GATTACAAGGGTA|ATGTTACAAAACAAAGAGCACCATTACACAGAACACAATG Chimp > Gorilla --------------- chr2A:11466982-11466994 Template switch process: F1: L AGTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAA 1 F3: 4 ATCTTACAAAACAAAGAGCACTATTACACAGAACACAATGTCC R RF: AGTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAATCTATGTTACAAAACAAAGAGCACCATTACACAGAACACAATGTCC RR: TCATTTTGTTAATAAGACTTCAATCTCTACATGGGAACATTAGATACAATGTTTTGTTTCTCGTGGTAATGTGTCTTGTGTTACAGG F2: 3 ATGGGAACATTAG 2 Unidirectional alignment (log-probability: -46.5) GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTaagattacaagggtAATC----TTACAAAACAAAGAGCACtATTACACAGAACACAATG GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGT--------------AATCTATGTTACAAAACAAAGAGCACCATTACACAGAACACAATG Template switch alignment (log-probability: -28.5) GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAA|GATTACAAGGGTA|ATcTTACAAAACAAAGAGCACtATTACACAGAACACAATG GTAAAACAATTATTCTGAAGTTAGAGATGTACCCTTGTAA|GATTACAAGGGTA|ATGTTACAAAACAAAGAGCACCATTACACAGAACACAATG ========== Event 1777 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: CAGGAGGCTGTGTTATACACC-------TGTGTCCGCTCATATTACATATGACCCAAAACATG ↓ 1 3 4 2 Chimp: CAGGAGGCTGTGTTATACACCGTATATGAGCGGACGCTCATATTACATATGACCCAAAACATG Gorilla: --------------------------------------------------------------- Human: CAGGAGGCTGTGTTATACACC-------TGTGTCCGCTCATATTACATATGACCCAAAACATG Cluster: [ ] Orangutan: --------------------------------------------------------------- Human > Chimp ------------- chr21:795025-795035 Template switch process: F1: L ATGAATCTCGTATTTGGTATCAGGAGGCTGTGTTATACACC-GT 1 F3: 4 CGCTCATATTACATATGACCCAAAACATGAATTTTCAGGG R RF: ATGAATCTCGTATTTGGTATCAGGAGGCTGTGTTATACACCTGTGTCCGCTCATATTACATATGACCCAAAACATGAATTTTCAGGG RR: TACTTAGAGCATAAACCATAGTCCTCCGACACAATATGTGGACACAGGCGAGTATAATGTATACTGGGTTTTGTACTTAAAAGTCCC F2: 3 AGGCGAGTATA 2 Unidirectional alignment (log-probability: -40.1) AATCTCGTATTTGGTATCAGGAGGCTGTGTTATACAC------CgtatatgagcggaCGCTCATATTACATATGACCCAAAACATGAATTTTCAGGG AATCTCGTATTTGGTATCAGGAGGCTGTGTTATACACCTGTGTC-------------CGCTCATATTACATATGACCCAAAACATGAATTTTCAGGG Template switch alignment (log-probability: -26.9) AATCTCGTATTTGGTATCAGGAGGCTGTGTTATACACC-GT|ATATGAGCGGA|CGCTCATATTACATATGACCCAAAACATGAATTTTCAGGG AATCTCGTATTTGGTATCAGGAGGCTGTGTTATACACCTGT|ATATGAGCGGA|CGCTCATATTACATATGACCCAAAACATGAATTTTCAGGG ========== Event 1778 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TGGTTTTTATGCATATTTACTTAAATGTGTGAGACATTTAAAAAAATATCTTCAGGCTCTTCA Chimp: TAGTTTTTATGCATATTTACTAAA----CTCACACATTTAAGAAAATATCTTCAGGCTCTTCA Gorilla: TGGTTTTTATGCATATTTACTAAA----CTCACACATTTAAGAAAATATCTTCAGGCTCTTCA ↑ 3 1 2 4 Human: TGGTTTTTATGCATATTTACTTAAATGTGTGAGACATTTAAAAAAATATCTTCAGGCTCTTCA Cluster: [ ] Orangutan: TGGTTTTTAAGCATATTTACTAAA----CTCACACATTTAAGAAAATATCTTCAGGCTCTTCA Human > Gorilla --------------- chr21:5644990-5645003 Template switch process: F1: L TAGTTGGCCATGAAATGGTTTGGTTTTTATGCATATTTACTAAA 1 F3: 4 AAAATATCTTCAGGCTCTTCAGCCTATTCAATGTTTCTTT R RF: TAGTTGGCCATGAAATGGTTTGGTTTTTATGCATATTTACTTAAATGTGTGAGACATTTAAAAAAATATCTTCAGGCTCTTCAGCCTATTCAATTTTTCTTT RR: ATCAACCGGTACTTTACCAAACCAAAAATACGTATAAATGAATTTACACACTCTGTAAATTTTTTTATAGAAGTCCGAGAAGTCGGATAAGTTAAAAAGAAA F2: 3 GAATTTACACACTC 2 Unidirectional alignment (log-probability: -43.9) TGGCCATGAAATGGTTTGGTTTTTATGCATATTTACT------------aaactcacACATTTAAgAAAATATCTTCAGGCTCTTCAGCCTATTCAATgTTTCTTT TGGCCATGAAATGGTTTGGTTTTTATGCATATTTACTTAAATGTGTGAG--------ACATTTAAAAAAATATCTTCAGGCTCTTCAGCCTATTCAATTTTTCTTT Template switch alignment (log-probability: -28.6) TGGCCATGAAATGGTTTGGTTTTTATGCATATTTACTaAA|CTCACACATTTAAG|AAAATATCTTCAGGCTCTTCAGCCTATTCAATgTTTCTTT TGGCCATGAAATGGTTTGGTTTTTATGCATATTTACTTAA|CTCACACATTTAAG|AAAATATCTTCAGGCTCTTCAGCCTATTCAATTTTTCTTT ========== Event 1779 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCAGTTGTCTTTATCaatatttat--------------------gaatcatctagcgttagatgctgggtgtcgggaacacaaggattaactaggtaggagctcataggctagtgagagagactgagataaatattgccaattcta Chimp: AATCAGTTGTCTTTATCAATATTTAT--------------------GAATCATCTAGCGTTAGATGCTGGGTGTCAGGAACACAAGGATTAACTAGGCAGGAGCTCATAGGCTAGTGAGAGAGACTGAGATAAATACTGCCAATTCTA ↓ 4 1 3 2 Gorilla: AATCAGTTGTCTTTATCAATATTTATGAATCATCTTCAGTATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCGGGAACACAAGGATTAACTAGGTAGGAGCTCGTAGGCTAGTGAGAGAGACTGAGATAAATATTGCCAATTCTA Human: AATCAGTTGTCTTTATCaatatttat--------------------gaatcatctagcgttagatgctgggtgtcgggaacacaaggattaactaggtaggagctcataggctagtgagagagactgagataaatattgccaattcta Cluster: [ ] Orangutan: AATCAGTTGTCTTTATCaatatttat--------------------gaatcatctagcgttagatgctgggtgtcaggaacacaaggattaactaggtaggggctcataggctagtgagagagactgagataaacattgccaattCTA Chimp > Gorilla --------------- chr21:5319830-5319833 Template switch process: F1: L TCTGCCAATAATATTAATCAGTTGTCTTTATCAATATTTATGAATCATCT 1 F3: 4 TATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCGGGAACACAAG R RF: TCTGCCAATAATACTAATCAGTTGTCTTTATCAATATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCAGGAACACAAGGATTAACTAGGCAGGAGCTCATAGGCTAGTGAGAGAGACTGA RR: AGACGGTTATTATGATTAGTCAACAGAAATAGTTATAAATACTTAGTAGATCGCAATCTACGACCCACAGTCCTTGTGTTCCTAATTGATCCGTCCTCGAGTATCCGATCACTCTCTCTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -50.7) ATAtTAATCAGTTGTCTTTATCAAtatttatgaatcatcttcagTATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCgGGA ATACTAATCAGTTGTCTTTATCAA--------------------TATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCAGGA Template switch alignment (log-probability: -27.7) ATAtTAATCAGTTGTCTTTATCAATATTTATGAATCATCT|TCAG|TATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCgGGA ATACTAATCAGTTGTCTTTATCAATATTTATGAATCATCT|TCAG|TATTTATGAATCATCTAGCGTTAGATGCTGGGTGTCAGGA ========== Event 1780 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: tttt--tt------ttttttttCTGTATATAAACTTCCATGCTATTAGCAGGTGGATATGTTTCATTaaa---a-aaaaaaTAGTGCTTAACCTAAGCTTATTAGTTATCTGTCTTGTTGGAACACTTAGTTTATATACAGGATTTTTTCCATGCCTCCCT ↑ 1 4 3 2 Chimp: tt------ttttttttttttttCTGTGTATAGCCTTCCATGCTATTAGCAGGTGGATATGTTTCATTaaa---aaaaaaaaTAGTGCTTAACCTAAGCTAATTAGTTATCTGTCTTGTTGGAACACTTAGTTTATATACAGGATTTTTTCCATGCCTCCCT Gorilla: tttt---t------ttttttttCTGTATATAGCCTTCCATGCTATTAGCAGGTGGATATGTTTCATTaaa------aaaaGTAGTGCTTAACCTAAGCTAATTAGTTATCTGCCTTGTTGGAACACTTAGTTTATATACAGGATTTTTTCCATGCCTCCCT ↓ 1 4 3 2 Human: tttt--tt------ttttttttCTGTATATAAACTTCCATGCTATTAGCAGGTGGATATGTTTCATTaaa---a-aaaaaaTAGTGCTTAACCTAAGCTTATTAGTTATCTGTCTTGTTGGAACACTTAGTTTATATACAGGATTTTTTCCATGCCTCCCT Cluster: [ ] Orangutan: tttttttt------ttttttttCTGTATATAGCCTTCCATGCTATTAGCAGGTGGATACGTTTCATTaaaaaa---aaaaaTAGTGCTTAACCTTAGCTAATTAGTTATCTGTCTTGTTGGAACACTTAGTTTATATACAGGATTTTTTCCATGCCTCCCT Chimp > Human ------------- chr21:15421138-15421148 Template switch process: F1: L AGTTATCTCAGTTCTTTTTTTTTTTTTTTTT 1 F3: 4 CTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAA R RF: AGTTATCTCAGTTCTTTTTTTTTTTTTTTTTTTCTGTGTATAGCCTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAAAAAAAATAGTGCTTAACCTAAGCTAATTAGTTATCTGTCTTGTTGGAACACTTAGTTTATATACAG RR: TCAATAGAGTCAAGAAAAAAAAAAAAAAAAAAAGACACATATCGGAAGGTACGATAATCGTCCACCTATACAAAGTAATTTTTTTTTTTATCACGAATTGGATTCGATTAATCAATAGACAGAACAACCTTGTGAATCAAATATATGTC F2: 3 AAATATATGTC 2 Unidirectional alignment (log-probability: -36.3) AGTTATCTCAGTTC--TTTTTTTTTTTTTTTTTCTGTaTATAaaCTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAA- AGTTATCTCAGTTCTTTTTTTTTTTTTTTTTTTCTGTGTATAGCCTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAAA Template switch alignment (log-probability: -16.4) AGTTATCTCAGTTCTTTTTTTTTTTTTTTTT|CTGTATATAAA|CTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAA AGTTATCTCAGTTCTTTTTTTTTTTTTTTTT|CTGTATATAAA|CTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAA Gorilla > Human --------------- chr21:15421138-15421148 Template switch process: F1: L GAGTTATCTCAGTTCTTTTTTTTTTTTTTTTT 1 F3: 4 CTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAAA R RF: GAGTTATCTCAGTTCTTTTTTTTTTTTTTTTCTGTATATAGCCTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAAAAGTAGTGCTTAACCTAAGCTAATTAGTTATCTGCCTTGTTGGAACACTTAGTTTATATACAG RR: CTCAATAGAGTCAAGAAAAAAAAAAAAAAAAGACATATATCGGAAGGTACGATAATCGTCCACCTATACAAAGTAATTTTTTTCATCACGAATTGGATTCGATTAATCAATAGACGGAACAACCTTGTGAATCAAATATATGTC F2: 3 AAATATATGTC 2 Unidirectional alignment (log-probability: -33) GAGTTATCTCAGTTCTTTTTTTTTTTTTTtTTCTGTATATAaaCTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAaa GAGTTATCTCAGTTCTTTTTTTTTTTTTT-TTCTGTATATAGCCTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAA-- Template switch alignment (log-probability: -22.4) GAGTTATCTCAGTTCTTTTTTTTTTTTTTTTt|CTGTATATAAA|CTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAAA GAGTTATCTCAGTTCTTTTTTTTTTTTTTTTC|CTGTATATAAA|CTTCCATGCTATTAGCAGGTGGATATGTTTCATTAAAAAA ========== Event 1781 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGTGGTCCTTTTGACACCTGTGACATTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGTTAGGACAAGTTTTCCAATATCCACCCAGTTGCCACTAGAGTTGTGTTAAAACAGAGTACTGTTGAGATGCCACCCTACTTAAAATCTGTCACTCAACTCATCGAAACTGAT ↑ 1 4 3 2 Chimp: TTGTGGTCCTTTTGACACCTGCAGTGTTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGTTAGGACAGGTTTTCCAATATCCACCCAGCAGCCACTAGAGTTGTGTTAAAACAGAGTACTGTTGAGATGCCACCCTACTTAAAATCTGTCACTCAACTCATCGAAACTGAT Gorilla: TTGTGGTCCTTTTGACATCTGTGACGTTGACTCTCTACAAGATACTTGAGGGCACAGACTTTTTGTTAGGACAGGTTTTCCAATATCCACCCAGTAGCCACTAGAGTTGTGTTAAAACAGAGTACTATTGAGATGCCACCCTACTTAAAATCTGTCACTCAACTCATCGAAACTGAT Human: TTGTGGTCCTTTTGACACCTGTGACATTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGTTAGGACAAGTTTTCCAATATCCACCCAGTTGCCACTAGAGTTGTGTTAAAACAGAGTACTGTTGAGATGCCACCCTACTTAAAATCTGTCACTCAACTCATCGAAACTGAT Cluster: [ ] Orangutan: TCGTGGTCCTTTTGACACCTGTGATGTTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGTTAGGACAGGTTTTCCAATATCCACCCAGTAGCCAGTAGAGTTGTGTTAAAACAGAGTACTGTTGAGATGCCACCCTACTTAAAATCTGTCACTCAACTC------------ Chimp > Human ------------- chr21:15216508-15216512 Template switch process: F1: L ACAAAGTACTAGTTCATGGTTTGTGGTCCTTTTGACACCTG 1 F3: 4 TTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGT R RF: ACAAAGTACTAGTTTATGGTTTGTGGTCCTTTTGACACCTGCAGTGTTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGTTAGGACAGGTTTTCCAATATCCACCCAGCAGCCACTAGAGTTGTGTTAAAACAGAGTACTGTTGAGATGCCACCCTACTTAAAATCTGTCA RR: TGTTTCATGATCAAATACCAAACACCAGGAAAACTGTGGACGTCACAACTGAGAGATGTTCTAGGAACTCCCGTGTCTGAAAAACAATCCTGTCCAAAAGGTTATAGGTGGGTCGTCGGTGATCTCAACACAATTTTGTCTCATGACAACTCTACGGTGGGATGAATTTTAGACAGT F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -31.6) CAAAGTACTAGTTcATGGTTTGTGGTCCTTTTGACACCT---GTGacaTTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGT CAAAGTACTAGTTTATGGTTTGTGGTCCTTTTGACACCTGCAGTG---TTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGT Template switch alignment (log-probability: -21.9) CAAAGTACTAGTTcATGGTTTGTGGTCCTTTTGACACCTG|TGACA|TTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGT CAAAGTACTAGTTTATGGTTTGTGGTCCTTTTGACACCTG|TGACA|TTGACTCTCTACAAGATCCTTGAGGGCACAGACTTTTTGT ========== Event 1782 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAGTATACACTAGGGATCCTTAGGGAGGCC--CAGTGATCTTTACATCAAGGTTTGC ↓ 3 2 1 4 Chimp: GAAGTATACACTAGGGATCCTTAGGGAGGCCCCTAAGGATCTTTACATCAAGGTTTGC Gorilla: GAAGTATACACTAGGGATCCTTAGGGAGGCC--CAGGGATCTTTACATCAAGGTTTGC Human: GAAGTATACACTAGGGATCCTTAGGGAGGCC--CAGTGATCTTTACATCAAGGTTTGC Cluster: [ ] Orangutan: GAAGTATACATTAGGGATCCTTAGAGAGGCC--CAGTGATCTTTACATCAAAGTTTGC Human > Chimp ------------- chr21:1585548-1585552 Template switch process: F1: L TAGTGTTTGGGAAGTATACACTAGGGATCCTTAGGGAGGCCC 1 F3: 4 GATCTTTACATCAAGGTTTGCTCTCAGCCCTTTGTGATAA R RF: TAGTGTTTGGGAAGTATACACTAGGGATCCTTAGGGAGGCCCAGTGATCTTTACATCAAGGTTTGCTCTCAGCCCTTTGTGATAA RR: ATCACAAACCCTTCATATGTGATCCCTAGGAATCCCTCCGGGTCACTAGAAATGTAGTTCCAAACGAGAGTCGGGAAACACTATT F2: 3 GAATC 2 Unidirectional alignment (log-probability: -25.5) GTGTTTGGGAAGTATACACTAGGGATCCTTAGGGAGGCCCctaAG-GATCTTTACATCAAGGTTTGCTCTCAGCCCTTTGTGATAA GTGTTTGGGAAGTATACACTAGGGATCCTTAGGGAGGCCC---AGTGATCTTTACATCAAGGTTTGCTCTCAGCCCTTTGTGATAA Template switch alignment (log-probability: -15.9) GTGTTTGGGAAGTATACACTAGGGATCCTTAGGGAGGCCC|CTAAG|GATCTTTACATCAAGGTTTGCTCTCAGCCCTTTGTGATAA GTGTTTGGGAAGTATACACTAGGGATCCTTAGGGAGGCCC|CTAAG|GATCTTTACATCAAGGTTTGCTCTCAGCCCTTTGTGATAA ========== Event 1783 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGATGCTTTAAAAGGATCATCATAAAATACATTTAGATGTATTTTACAT--------------------------------------------------------------------------------AACCCTGACTTGGCTCTTGAGACATATTGAGCCAGAACTAGGCAATTAGTCAATCAGTAAACACATATGAAGTACTCCTGTGTGTGTCAGGCATTTGGTGCAGGTCAGAGAA Chimp: ATGATGCTTTAAAGGGATcatcataaaatacatttagatgtattttacat----------------------------------------aagcctgacatcataaaatacatttagatgtattttacataaccctgacTTGCCTCTTGAGACATATTGAGCCAGAACTAGGCAATTAGTCAATCAGTAAACACATATGAAGTCCTCCTGCGTGTGTCAGGCATTTGGTGCAGGTCAGGGAA Gorilla: ATGATGCTTTAAAAGGATCATCATAAAATACATTTAGATGTATTTTACATAAGCCTGACATCATAAAATACATTTAGATGTATTTTACAT----------------------------------------AACCCTGACTTGCCTCTTGAGACATATTGAGCCAGAACTAGGCAATTAGTCAATCAGTAAACACATATGAAGTCCTCCTGTGTGTGTCAGGCATTTGGTGCAGGTCAGGGAA ↑ 4 1 3 2 Human: ATGATGCTTTAAAAGGATCATCATAAAATACATTTAGATGTATTTTACAT--------------------------------------------------------------------------------AACCCTGACTTGGCTCTTGAGACATATTGAGCCAGAACTAGGCAATTAGTCAATCAGTAAACACATATGAAGTACTCCTGTGTGTGTCAGGCATTTGGTGCAGGTCAGAGAA Cluster: [ ] Orangutan: ---ATGCTTTAAAAGGATcatcataaaatacatttagatgtattttacataactctgacatcataaaatacatttagatgtattttacat----------------------------------------aaccctgacTTGCCTCTTGAGACATATTGAGCCAGAGCTAGGCAATTTGTCAATCAGTAAACACATATGAAGTCTTCCTGTGTGTGTCAGGCATTTGGTGCAGGTCAGGGGA Human > Gorilla --------------- chr21:6255222-6255228 Template switch process: F1: L TAAAAGGATCATCATAAAATACATTTAGATGTATTTTACATAA 1 F3: 4 ATCATAAAATACATTTAGATGTATTTTACATAACCCTGACTTGCCTCTTGAGACATATTGAGCCAGAACTA R RF: TAAAAGGATCATCATAAAATACATTTAGATGTATTTTACATAACCCTGACTTGGCTCTTGAGACATATTGAGCCAGAACTAGGCAATTAGTCAATCAGTAAACACATATGAAGTACTCCTGTGTGTGTCAGGC RR: ATTTTCCTAGTAGTATTTTATGTAAATCTACATAAAATGTATTGGGACTGAACCGAGAACTCTGTATAACTCGGTCTTGATCCGTTAATCAGTTAGTCATTTGTGTATACTTCATGAGGACACACACAGTCCG F2: 3 CAGTCCG 2 Unidirectional alignment (log-probability: -73.9) AAGGATcatcataaaatacatttagatgtattttacataagcctgaCATCATAAAATACATTTAGATGTATTTTACATAACCCTGAC AAGGAT----------------------------------------CATCATAAAATACATTTAGATGTATTTTACATAACCCTGAC Template switch alignment (log-probability: -22.9) AAGGATCATCATAAAATACATTTAGATGTATTTTACATAA|GCCTGAC|ATCATAAAATACATTTAGATGTATTTTACATAACCCTGAC AAGGATCATCATAAAATACATTTAGATGTATTTTACATAA|GCCTGAC|ATCATAAAATACATTTAGATGTATTTTACATAACCCTGAC ========== Event 1784 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGGGTTCAAAGATGTCCATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCC ↑ 3 4 2 1 Chimp: AGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGA-------------------------------GGATTCATTGAAAACTGAATCC Gorilla: AGCCAGAAGCATGCAAAATGGCATCTTCGAACAGTGAGGGTTCAAAGATCTTCATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCC Human: AGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGGGTTCAAAGATGTCCATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCC Cluster: [ ] Orangutan: AGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGGGG---------------------------------TTTGAAAACTGAATCC Chimp > Human ------------- chr2:126346262-126346274 Template switch process: F1: L CTGCAGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGG 1 F3: 4 CATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCCAAAGAGATGATGATGAAC R RF: CTGCAGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCCAAAGACATGATGATGAAC RR: GACGTCGGTCTTCGTACGTTTTACCGTAGAAACTTGTCACTCCTAAGTAACTTTTGACTTAGGTTTCTGTACTACTACTTG F2: 3 CTGTAGAAACTTG 2 Unidirectional alignment (log-probability: -61.5) CAGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGggttcaaagatgtccatctttgaacagtgagGATTCATTGAAAACTGAATCCAA CAGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAG-------------------------------GATTCATTGAAAACTGAATCCAA Template switch alignment (log-probability: -29.2) CAGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGG|GTTCAAAGATGtC|CATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCCAA CAGCCAGAAGCATGCAAAATGGCATCTTTGAACAGTGAGG|GTTCAAAGATGCC|CATCTTTGAACAGTGAGGATTCATTGAAAACTGAATCCAA ========== Event 1785 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GATGCTTCATCTCAGCATTATACGAACTCAAAGTTCGTATGAAGTGGGTCTGAGTTAGAGA ↑ 3 2 1 4 Chimp: GATGCTTCATCTCAGCATTATACGAACTCAAAGGT--AACGAAGTGGGTCTGAGTTAGAGA Gorilla: GATGCTTCATCTCAGCATTATACGAACTCAAAGGT--AACGAAGTGGGTCTGAGTTAGAGA ↓ 3 2 1 4 Human: GATGCTTCATCTCAGCATTATACGAACTCAAAGTTCGTATGAAGTGGGTCTGAGTTAGAGA Cluster: [ ] Orangutan: GATGCTTCATCTCAGCATTATACGAACTCAAAGGT--AATGAAGTGGGTCTGAGTTAGAGA Chimp > Human ------------- chr21:30396707-30396713 Template switch process: F1: L TGATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG 1 F3: 4 GAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG R RF: TGATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAGGTAACGAAGTGGGTCTGAGTTAGAGACACTTTCAAAGGATGTCTG RR: ACTAATTTCTACGAAGTAGAGTCGTAATATGCTTGAGTTTCCATTGCTTCACCCAGACTCAATCTCTGTGAAAGTTTCCTACAGAC F2: 3 TATGCTT 2 Unidirectional alignment (log-probability: -37.4) GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAGttcgtat-----GAAGTGGGTCTGAGTTAGAGACACTTTtAAAGGATGTCTG GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG-------GTAACGAAGTGGGTCTGAGTTAGAGACACTTTCAAAGGATGTCTG Template switch alignment (log-probability: -22.1) GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG|TTCGTAT|GAAGTGGGTCTGAGTTAGAGACACTTTtAAAGGATGTCTG GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG|TTCGTAT|GAAGTGGGTCTGAGTTAGAGACACTTTCAAAGGATGTCTG Gorilla > Human --------------- chr21:30396707-30396713 Template switch process: F1: L TGATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG 1 F3: 4 GAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG R RF: TGATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAGGTAACGAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG RR: ACTAATTTCTACGAAGTAGAGTCGTAATATGCTTGAGTTTCCATTGCTTCACCCAGACTCAATCTCTGTGAAAATTTCCTACAGAC F2: 3 TATGCTT 2 Unidirectional alignment (log-probability: -30.4) GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAGtTcgtAtGAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAGGT--AACGAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG Template switch alignment (log-probability: -16.6) GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG|TTCGTAT|GAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG GATTAAAGATGCTTCATCTCAGCATTATACGAACTCAAAG|TTCGTAT|GAAGTGGGTCTGAGTTAGAGACACTTTTAAAGGATGTCTG ========== Event 1786 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GATTCCAAGTTATATAAATGACAATACTAATTTTTCTAAGCAATCCACTTAAAACTAT------------------------------------TAGACTTCTGTTTGATATTCAAATTAATGTACAATATGAACAATCATGAAAACTAATTAGTTTAGAAATAACATTGCAATATTTAAACTTTCATTA Chimp: GATTCCAAGTTATATAAATGATAATACTAATTTTTCTAAGCAATCCACTTAAAACTAT------------------TGTGGATTAGGCTTTATATAGACTTCTGTTTGATATTCAAATTAATGTACAATATGAACAATCATGAAAACTAATTAGTTTAGAAATAACATTGCAATATTTAAACTTTCATTA ↓ 1 4 3 2 Gorilla: GATTCCAAGTTATATAAATGACAATGCTAATTTTTCTAAGCAATCCACTTAAAACTATTGTGGATTAGGCTTTATA------------------TAGACTTCTGTTTGATACTCAAATTAATGTACAATATGAACAATCATGAAAACTAATTAGTTTAGAAATAACATTGCAATATTTAAACTTTCATTA Human: GATTCCAAGTTATATAAATGACAATACTAATTTTTCTAAGCAATCCACTTAAAACTAT------------------------------------TAGACTTCTGTTTGATATTCAAATTAATGTACAATATGAACAATCATGAAAACTAATTAGTTTAGAAATAACATTGCAATATTTAAACTTTCATTA Cluster: [ ] Orangutan: GATTCCAAGTTATATAAATGACAATACTAATTTTTCTAAGCAATCCACTTAAAACTATTGTGGATTAGGCTTTATA------------------TAGACTTCTGTTTGATATTCAAATTAATGTACAATATGAACAATCATGAAAACTAATTAGTTTAGAAATAACATTGCAATATTTAAACTTTCATTA Chimp > Gorilla --------------- chr21:30279045-30279049 Template switch process: F1: L TCTTCAGATAATCTTCTTTGGATTCCAAGTTATATAAATGA 1 F3: 4 CTAATTTTTCTAAGCAATCCACTTAAAACTATTGTGGATT R RF: TCTTCAGAGAATCTTCTTTGGATTCCAAGTTATATAAATGATAATACTAATTTTTCTAAGCAATCCACTTAAAACTATTGTGGATTAGGCTTTATATAGACTTCTGTTTGATATTCAAATTAATGTACAATATGAACAATCATGAAAACTAATTAGTTTAGAAATAACATTG RR: AGAAGTCTCTTAGAAGAAACCTAAGGTTCAATATATTTACTATTATGATTAAAAAGATTCGTTAGGTGAATTTTGATAACACCTAATCCGAAATATATCTGAAGACAAACTATAAGTTTAATTACATGTTATACTTGTTAGTACTTTTGATTAATCAAATCTTTATTGTAAC F2: 3 GTAAC 2 Unidirectional alignment (log-probability: -35.9) CTTCAGAtAATCTTCTTTGGATTCCAAGTTATATAAATGAcAATgCTAATTTTTCTAAGCAATCCACTTAAAACTATtgtggatt CTTCAGAGAATCTTCTTTGGATTCCAAGTTATATAAATGATAATACTAATTTTTCTAAGCAATCCACTTAAAACTAT-------- Template switch alignment (log-probability: -21.9) CTTCAGAtAATCTTCTTTGGATTCCAAGTTATATAAATGA|CAATG|CTAATTTTTCTAAGCAATCCACTTAAAACTATTGTGGATT CTTCAGAGAATCTTCTTTGGATTCCAAGTTATATAAATGA|CAATG|CTAATTTTTCTAAGCAATCCACTTAAAACTATTGTGGATT ========== Event 1787 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTTTATCTACTCTATTCTCT---------ATGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTCGA ↓ 1 4 3 2 Chimp: CTTTTATCTACTCTATTCTCTACTCTCTTGAAGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTCAA ↑ 1 4 3 2 Gorilla: CTTTTATCTACTCTATTCTCT---------ATGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGGTCAA Human: CTTTTATCTACTCTATTCTCT---------ATGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTCGA Cluster: [ ] Orangutan: Human > Chimp ------------- chr2B:2996163-2996172 Template switch process: F1: L AAAATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA 1 F3: 4 GTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC R RF: AAAATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTATGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC RR: TTTTATCCAGACTTTAAGTAGAAAATAGATGAGATAAGAGATACACATCTACATGAAGTTCTCTCATACTCTCAACTCCCGAG F2: 3 AAGTTCTCTC 2 Unidirectional alignment (log-probability: -29.9) AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTActctcttgaaGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA---------TGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC Template switch alignment (log-probability: -16.5) AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA|CTCTCTTGAA|GTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA|CTCTCTTGAA|GTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC Gorilla > Chimp --------------- chr2B:2996163-2996172 Template switch process: F1: L AAAATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA 1 F3: 4 GTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGCTC R RF: AAAATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTATGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGGTC RR: TTTTATCCAGACTTTAAGTAGAAAATAGATGAGATAAGAGATACACATCTACATGAAGTTCTCTCATACTCTCAACTCCCCAG F2: 3 AAGTTCTCTC 2 Unidirectional alignment (log-probability: -34.9) AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTactctcttgAaGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGcTC AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCT---------ATGTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGGTC Template switch alignment (log-probability: -22.5) AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA|CTCTCTTGAA|GTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGcTC AATAGGTCTGAAATTCATCTTTTATCTACTCTATTCTCTA|CTCTCTTGAA|GTGTAGATGTACTTCAAGAGAGTATGAGAGTTGAGGGGTC ========== Event 1788 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATTAATCTTGGCCTCAAAAATGCCCATGCATTCTGTAATAATATTTGGAG ↑ 1 3 4 2 Chimp: AATTAATCTTGGCCTCAAAAA--CATGGGCATTCTGTAATAATATTTGGAG Gorilla: AATTAATCTTGGCCTCAAAAA--CATGGGCATTCTGTAATAATATTTGGAG ↓ 1 3 4 2 Human: AATTAATCTTGGCCTCAAAAATGCCCATGCATTCTGTAATAATATTTGGAG Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:116822676-116822682 Template switch process: F1: L CCAGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAA 1 F3: 4 GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT R RF: CCGGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAACATGGGCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT RR: GGCCGGTGTCATTGAACCTGTTAATTAGAACCGGAGTTTTTGTACCCGTAAGACATTATTATAAACCTCCCACAGTATTACCGTTA F2: 3 TACCCGT 2 Unidirectional alignment (log-probability: -33) CaGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAAtgccCATG--CATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT CGGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAA----CATGGGCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT Template switch alignment (log-probability: -22.1) CaGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAA|TGCCCAT|GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT CGGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAA|TGCCCAT|GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT Gorilla > Human --------------- chr2:116822676-116822682 Template switch process: F1: L CCAGCCACAGTAACTTGGACAATTAATCTTGGCCTCAAAAA 1 F3: 4 GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT R RF: CCGGCCACAGTAACTCGGACAATTAATCTTGGCCTCAAAAACATGGGCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT RR: GGCCGGTGTCATTGAGCCTGTTAATTAGAACCGGAGTTTTTGTACCCGTAAGACATTATTATAAACCTCCCACAGTATTACCGTTA F2: 3 TACCCGT 2 Unidirectional alignment (log-probability: -37.6) CaGCCACAGTAACTtGGACAATTAATCTTGGCCTCAAAAAtgccCAT--GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT CGGCCACAGTAACTCGGACAATTAATCTTGGCCTCAAAAA----CATGGGCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT Template switch alignment (log-probability: -27.7) CaGCCACAGTAACTtGGACAATTAATCTTGGCCTCAAAAA|TGCCCAT|GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT CGGCCACAGTAACTCGGACAATTAATCTTGGCCTCAAAAA|TGCCCAT|GCATTCTGTAATAATATTTGGAGGGTGTCATAATGGCAAT ========== Event 1789 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCCCCTCCGCCACGCTTAGAA------GCTTCCTCCCTATTGTCTCCGTGGACTGC ↓ 3 1 2 4 Chimp: GCCCCTCCGCCACGCTTAGAA---GAAGCTT----CCTATTGTCTCCGTGGACTGC Gorilla: GCCCCTCCGCCACGCTTAGAAGAA---GCTTCCTCCCTATTGTCTCCGTGGACTGC Human: GCCCCTCCGCCACGCTTAGAA------GCTTCCTCCCTATTGTCTCCGTGGACTGC Cluster: [ ] Orangutan: GCCCCTCCGCCACGCTTAGAAGAA---GCTTCCTCCCTATTGTCTCCGTGGACTGC Human > Chimp ------------- chr2B:129555282-129555287 Template switch process: F1: L TGAGCCTCTTTCCCTGGGTTGCCCCTCCGCCACGCTTAGAAG 1 F3: 4 CCTATTGTCTCCGTGGACTGCAAGATGAATATGTTCAAGA R RF: TGAGCCTCTTTCCCTGGGTTGCCCCTCCGCCACGCTTAGAAGCTTCCTCCCTATTGTCTCCGTGGACTGCAAGATGAATATGTTCAAGA RR: ACTCGGAGAAAGGGACCCAACGGGGAGGCGGTGCGAATCTTCGAAGGAGGGATAACAGAGGCACCTGACGTTCTACTTATACAAGTTCT F2: 3 TTCGAA 2 Unidirectional alignment (log-probability: -25.7) AGCCTCTTTCCCTGGGTTGCCCCTCCGCCACGCTTagaAGAAGCTT----CCTATTGTCTCCGTGGACTGCAAGATGAATATGTTCAAGA AGCCTCTTTCCCTGGGTTGCCCCTCCGCCACGCTT---AGAAGCTTCCTCCCTATTGTCTCCGTGGACTGCAAGATGAATATGTTCAAGA Template switch alignment (log-probability: -16) AGCCTCTTTCCCTGGGTTGCCCCTCCGCCACGCTTAGAAG|AAGCTT|CCTATTGTCTCCGTGGACTGCAAGATGAATATGTTCAAGA AGCCTCTTTCCCTGGGTTGCCCCTCCGCCACGCTTAGAAG|AAGCTT|CCTATTGTCTCCGTGGACTGCAAGATGAATATGTTCAAGA ========== Event 1790 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: acagccaaacctggtactaaTACATTTCCATTATTTCATTTGTATATTGTTGCGTGATTTATTAAT------------------------------------------------------------------TAGTCAAACACAGTGGCCCACAGAT Chimp: ACAGCCAAACCTGGTACTAATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATTGACTAATTAATAAATCAAGCAACAATATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATTTATTAATTAGTCAAACACAGTGGCCCACAGAT ↑ 4 3 1 2 Gorilla: ACAGCCAAACCTAGTACTAATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATTTATTAAT------------------------------------------------------------------TAGTCAAACACAGTGGCCCACAGAT Human: acagccaaacctggtactaaTACATTTCCATTATTTCATTTGTATATTGTTGCGTGATTTATTAAT------------------------------------------------------------------TAGTCAAACACAGTGGCCCACAGAT Cluster: [ ] Orangutan: acagccaaacgtagtactaaTACATTTCCATTATTTCATTTATATATTGTTGCTTGATTTATTAAT------------------------------------------------------------------TAATCAAACACAGCGGCCCACAGAT Gorilla > Chimp --------------- chr2B:129488905-129488930 Template switch process: F1: L AATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT 1 F3: 4 ATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATTTATTAATTAGTCAAACACAGTGGCCCACAGATGAGGAGTAGTTTCAT R RF: AATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATTTATTAATTAGTCAAACACAGTGGCCCACAGATGAGGAGTAGTTTCAT RR: TTATGTAAAGGTAATAAAGTAAACATATAACAACGAACTAAATAATTAATCAGTTTGTGTCACCGGGTGTCTACTCCTCATCAAAGTA F2: 3 TAACAACGAACTAAATAATTAATCAG 2 Unidirectional alignment (log-probability: -106) atacatttccattatttcatttgtatattgttgcttgattgactaattaataaatcaagcaacaatATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT ------------------------------------------------------------------ATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT Template switch alignment (log-probability: -20.1) ATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT|GACTAATTAATAAATCAAGCAACAAT|ATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT ATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT|GACTAATTAATAAATCAAGCAACAAT|ATACATTTCCATTATTTCATTTGTATATTGTTGCTTGATT ========== Event 1791 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTACCCTTGAGAGAATCTTACAATATACT--------------------------------------------------------------------------CATCATACTCATATGCTATACACATTATACTCATCATATGGTATATGGATACTGTAATGTAGTatc ↓ 4 1 3 2 Chimp: TCTACCCTTGAGAGAATCTTACAATATACT-------------------------------------CATCAATATGCCATATGATGAGTATACACAATATACTCATCATACTCATATGCTATACACATTATACTCATCATATGGTATATGGATACCATAATGTAGTATC ↑ 4 1 3 2 Gorilla: TCTACCCTTGAGAGAATCTTACAATATACT--------------------------------------------------------------------------CATCATACTCATATGCTATACACATTATACTCATCATATGGTATATGGATACCATAATGTAGTATC Human: TCTACCCTTGAGAGAATCTTACAATATACT--------------------------------------------------------------------------CATCATACTCATATGCTATACACATTATACTCATCATATGGTATATGGATACTGTAATGTAGTatc Cluster: [ ] Orangutan: TCTACCCTTGAGAGAATCTTACAATATACTCATCAGTATGCCATATGATGAGTATACACAATATACT-------------------------------------CATCACACTCATATGCTATACACATTATACTCATCATATGGTATATGGATACCATAATGTAGTatc Human > Chimp ------------- chr2B:129197230-129197250 Template switch process: F1: L TATTGTGAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA 1 F3: 4 CACAATATACTCATCATACTCATATGCTATACACATTATACTCATCATATG R RF: TATTGTGAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCATACTCATATGCTATACACATTATACTCATCATATGGTATAT RR: ATAACACTCCAAGATGGGAACTCTCTTAGAATGTTATATGAGTAGTATGAGTATACGATATGTGTAATATGAGTAGTATACCATATA F2: 3 ATATGAGTAGTATACCGTATA 2 Unidirectional alignment (log-probability: -64.1) GAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCAatatgccatatgatgagtatacacaatatactcatcaTACTCATATGCTATACACATTATA GAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA-------------------------------------TACTCATATGCTATACACATTATA Template switch alignment (log-probability: -30.1) GAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA|ATATgCCATATGATGAGTATA|cACAATATACTCATCATACTCATATGCTATACACATTATA GAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA|ATATACCATATGATGAGTATA|TACAATATACTCATCATACTCATATGCTATACACATTATA Gorilla > Chimp --------------- chr2B:129197230-129197250 Template switch process: F1: L TATTGTGAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA 1 F3: 4 CACAATATACTCATCATACTCATATGCTATACACATTATACTCATCATATG R RF: TATTGTGAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCATACTCATATGCTATACACATTATACTCATCATATGGTATAT RR: ATAACACTCCAAGATGGGAACTCTCTTAGAATGTTATATGAGTAGTATGAGTATACGATATGTGTAATATGAGTAGTATACCATATA F2: 3 ATATGAGTAGTATACCGTATA 2 Unidirectional alignment (log-probability: -64.1) GAGGTTCTACCCTTGAGAGAATCTTACAATATActcatcaatatgccatatgatgagtatacacaatataCTCATCATACTCATATGCTATACACATTATA GAGGTTCTACCCTTGAGAGAATCTTACAATATA-------------------------------------CTCATCATACTCATATGCTATACACATTATA Template switch alignment (log-probability: -29.8) GAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA|ATATgCCATATGATGAGTATA|cACAATATACTCATCATACTCATATGCTATACACATTATA GAGGTTCTACCCTTGAGAGAATCTTACAATATACTCATCA|ATATACCATATGATGAGTATA|TACAATATACTCATCATACTCATATGCTATACACATTATA ========== Event 1792 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGCCCATCATTAATCCAATCCGGGAAGAAGAGAACAGAAACATTAAAAGGAAGACCGGTTCTAACTTAAAT-CCATGAAACCATAACTAATTTCTTAT Chimp: GAAGCCCATCATTAATCCAATTCAGGAAGAAGAGAACAGAAACATTAAAAGGAAGACCGGTTCTAACTTAAAT-CCATGAAACCATAACTAATTTCTTAT Gorilla: GAAGCCCATGATTAATCCAATTCATGAAGAAGAGTACAGAAACATTAAAAGGAAGACCGGTTCTAACTTAAATCACATGAAACCATAACTAATTTCTTAT ↑ 1 4 3 2 Human: GAAGCCCATCATTAATCCAATCCGGGAAGAAGAGAACAGAAACATTAAAAGGAAGACCGGTTCTAACTTAAAT-CCATGAAACCATAACTAATTTCTTAT Cluster: [ ] Orangutan: GAAGCCCGTCATTAATCAAATTCAGGAAGAAGAGAACAGAAACATTAAAAGGAAGACAAGTTGTAACTTAAATCACATGAAACTGTAACTAATTTCTTAT Human > Gorilla --------------- chr21:10206451-10206455 Template switch process: F1: L TCAGAACTGAGTCAGTTTCAGAAGCCCATGATTAATCCAAT 1 F3: 4 AAGAAGAGTACAGAAACATTAAAAGGAAGACCGGTTCTAACTTAAATCA R RF: TCAGAACTGAGTCAGTTTCAGAAGCCCATCATTAATCCAATCCGGGAAGAAGAGAACAGAAACATTAAAAGGAAGACCGGTTCTAACTTAAATCCATGA RR: AGTCTTGACTCAGTCAAAGTCTTCGGGTAGTAATTAGGTTAGGCCCTTCTTCTCTTGTCTTTGTAATTTTCCTTCTGGCCAAGATTGAATTTAGGTACT F2: 3 GTACT 2 Unidirectional alignment (log-probability: -37.1) CAGAACTGAGTCAGTTTCAGAAGCCCATgATTAATCCAATtCatGAAGAAGAGtACAGAAACATTAAAAGGAAGACCGGTTCTAA CAGAACTGAGTCAGTTTCAGAAGCCCATCATTAATCCAATCCGGGAAGAAGAGAACAGAAACATTAAAAGGAAGACCGGTTCTAA Template switch alignment (log-probability: -33.1) CAGAACTGAGTCAGTTTCAGAAGCCCATgATTAATCCAAT|TCATG|AAGAAGAGtACAGAAACATTAAAAGGAAGACCGGTTCTAA CAGAACTGAGTCAGTTTCAGAAGCCCATCATTAATCCAAT|TCATG|AAGAAGAGAACAGAAACATTAAAAGGAAGACCGGTTCTAA ========== Event 1793 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTATTTTGCAGTCTAATATCTAACAGCCAGTTAAAACTGGCTGAATTGAAACACTTAGCAc ↑ 1 3 4 2 Chimp: GTATTTTGCAGTCTAATATCTGACAA---TGTTTAACTGGCTGAATTGAAACACTTAGCac Gorilla: GTATTTTGCAGTCTAATATCTAACAA---TGTTTAACTGGCTGAATTGAAATACGTAGCAC Human: GTATTTTGCAGTCTAATATCTAACAGCCAGTTAAAACTGGCTGAATTGAAACACTTAGCAc Cluster: [ ] Orangutan: GTATTTTGCAGTCTAATATCTAACAA---TGTTTAACTGGCTGAATTGAAACACTTAGCAC Chimp > Human ------------- chr2:122934529-122934537 Template switch process: F1: L GGTGAGCTGCTCTGACTGGAGTATTTTGCAGTCTAATATCTAACA 1 F3: 4 AACTGGCTGAATTGAAACACTTAGCACAACCCAAACCAAA R RF: GGTGAGCTGCTCTGACTGGAGTATTTTGCAGTCTAATATCTGACAATGTTTAACTGGCTGAATTGAAACACTTAGCACAACCCAAACCAAA RR: CCACTCGACGAGACTGACCTCATAAAACGTCAGATTATAGACTGTTACAAATTGACCGACTTAACTTTGTGAATCGTGTTGGGTTTGGTTT F2: 3 AATTGACCG 2 Unidirectional alignment (log-probability: -38.9) GCTGCTCTGACTGGAGTATTTTGCAGTCTAATATCTaACagccagttAA-----AACTGGCTGAATTGAAACACTTAGCACAACCCAAACCAAA GCTGCTCTGACTGGAGTATTTTGCAGTCTAATATCTGAC--------AATGTTTAACTGGCTGAATTGAAACACTTAGCACAACCCAAACCAAA Template switch alignment (log-probability: -22.5) GCTGCTCTGACTGGAGTATTTTGCAGTCTAATATCTaACA|GCCAGTTAA|AACTGGCTGAATTGAAACACTTAGCACAACCCAAACCAAA GCTGCTCTGACTGGAGTATTTTGCAGTCTAATATCTGACA|GCCAGTTAA|AACTGGCTGAATTGAAACACTTAGCACAACCCAAACCAAA ========== Event 1794 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGATATATTTGAGTTTTATGTCAAGTTTACTTATGGTTTAATCTTAGTCCAGAATATACATTTTTCTCCTAGAGCGTAAC-TTTACTTCTAGAGCTTACATCTTCTGGCCCCTGAAAAATGCTTCATGACTT--------GACCATGACATGCCCATACTTTAAT Chimp: ATGATATATTTGAGTTTTATGTCAAGTTTACTTATGGTTTAATCTTAGTCCAGAATATACATTTTTCTCCTAGAGCATAAC-TTTACTTCTAGAGTTTACATCTTCTGGCCCCTGAAAAACGCATCATGACTT----GACTGACCATGACATGCCCATACTTTAAT Gorilla: ATGATATATTTGAGTTTTATGTCGAGTTTATTTATGGTTTAATCTTAGTCCAGAATATACATTTTTCTCCTAGAGCGTAAC-TTTACTTCTAGAGCTTACATCTTCTGGCCCCTGAAAAACGCATCATGACTTGACT----GACAATGACATGCCCATACTTTAAT ↑ 3 2 1 4 Human: ATGATATATTTGAGTTTTATGTCAAGTTTACTTATGGTTTAATCTTAGTCCAGAATATACATTTTTCTCCTAGAGCGTAAC-TTTACTTCTAGAGCTTACATCTTCTGGCCCCTGAAAAATGCTTCATGACTT--------GACCATGACATGCCCATACTTTAAT Cluster: [ ] Orangutan: atggtatgtttgaGTTTTATGTCGAGTTTATTTATGGTTTAATCTTAGTCCAGAATATACATTTTTCTCCTAGAGCATAGCTTTTACCTCTAGAGCTTACATCTTCTGGCCCCTGAAAGACGCATCATGACTT--------GACCATGACATGCCCATATTTTAAT Human > Gorilla --------------- chr21:10715914-10715918 Template switch process: F1: L AACTTTACTTCTAGAGCTTACATCTTCTGGCCCCTGAAAAACGCATCATGACTTGAC 1 F3: 4 ATGACATGCCCATACTTTAATCTAGGCTCTTCAGGAC R RF: TGTCAAGTTTACTTATGGTTTAATCTTAGTCCAGAATATACATTTTTCTCCTAGAGCGTAACTTTACTTCTAGAGCTTACATCTTCTGGCCCCTGAAAAATGCTTCATGACTTGACCATGACATGCCCATACTTTAATCTAGGCTCTTCAGGAC RR: ACAGTTCAAATGAATACCAAATTAGAATCAGGTCTTATATGTAAAAAGAGGATCTCGCATTGAAATGAAGATCTCGAATGTAGAAGACCGGGGACTTTTTACGAAGTACTGAACTGGTACTGTACGGGTATGAAATTAGATCCGAGAAGTCCTG F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -40.3) TTACATCTTCTGGCCCCTGAAAAAcGCaTCATGACTtgacTGACaATGACATGCCCATACTTTAATCTAGGCTCTTCAGGAC--- TTACATCTTCTGGCCCCTGAAAAATGCTTCATGACT----TGACCATGACATGCCCATACTTTAATCTAGGCTCTTCAGGACAAC Template switch alignment (log-probability: -27.7) TTACATCTTCTGGCCCCTGAAAAAcGCaTCATGACTTGAC|TGACA|ATGACATGCCCATACTTTAATCTAGGCTCTTCAGGAC TTACATCTTCTGGCCCCTGAAAAATGCTTCATGACTTGAC|TGACA|ATGACATGCCCATACTTTAATCTAGGCTCTTCAGGAC ========== Event 1795 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGTAATCACTCTTATTTTTA----------------------------------TTATTCAATAGTTTAAAGATCCTTATGTGTTTTCttataaaatttactatttttcatttacaaaattaaaaagaatatatata Chimp: TAGCAATCACTCTTATTTTTA-----------------TTATTCATTGTCAATTATTATTCAATAGTTTAAAGATCCTTATATGTTTTCTTATAAAATTTACTATTTTTCATTTACAAAATTAAAAAGAatatatata ↑ 4 1 3 2 Gorilla: TAGCAATCACTCTTATTTTTA----------------------------------TTATTCAATAGTTTAAAGATCCTTATGTGTTTTCTTATAAAATTTACTATTTTTCATTTACAAAATTAAAAAGAatatatata Human: TAGTAATCACTCTTATTTTTA----------------------------------TTATTCAATAGTTTAAAGATCCTTATGTGTTTTCttataaaatttactatttttcatttacaaaattaaaaagaatatatata Cluster: [ ] Orangutan: TAGTAATCACCTTTATTTTTATTATCCATTGTCAATTA-----------------TTATTCAATAGTTTAAAGATCCTTATGTGTTTTCTTATAAAGTTTACTATTTTTCATTTACAAAATTAAAAAGAATATATATA Gorilla > Chimp --------------- chr21:6179506-6179513 Template switch process: F1: L AAACATTATACAATTTGTAATAGCAATCACTCTTATTTTTATTATTCA 1 F3: 4 TATTATTCAATAGTTTAAAGATCCTTATATGTTTTCTTATAA R RF: AAACATTATACAATTTGTAATAGCAATCACTCTTATTTTTATTATTCAATAGTTTAAAGATCCTTATGTGTTTTCTTATAAAATTTACTATTTTTCATTTACAA RR: TTTGTAATATGTTAAACATTATCGTTAGTGAGAATAAAAATAATAAGTTATCAAATTTCTAGGAATACACAAAAGAATATTTTAAATGATAAAAAGTAAATGTT F2: 3 TAACTGTT 2 Unidirectional alignment (log-probability: -40.8) TACAATTTGTAATAGCAATCACTCTTATTTttattattcattgtcaaTTATTATTCAATAGTTTAAAGATCCTTATaTGTTTTCTTAT TACAATTTGTAATAGCAATCACTCTTATTT-----------------TTATTATTCAATAGTTTAAAGATCCTTATGTGTTTTCTTAT Template switch alignment (log-probability: -28) TACAATTTGTAATAGCAATCACTCTTATTTTTATTATTCA|TTGTcAAT|TATTATTCAATAGTTTAAAGATCCTTATaTGTTTTCTTAT TACAATTTGTAATAGCAATCACTCTTATTTTTATTATTCA|TTGTAAAT|TATTATTCAATAGTTTAAAGATCCTTATGTGTTTTCTTAT ========== Event 1796 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTAAAATATTTCTGGGATATTTCAGATTTCATTTG--------ACCCTTTAAATCTTTTGCTTCTTC Chimp: CTTAAAATATTTCTGGGATATTTCAGATTTCATTTG--------ACCCTTTAAATCTTTTGCTTCTTC ↓ 3 2 1 4 Gorilla: CTTAAAATATTTCTGGGGTATTTCAGATTTCATTTGAAATCTGAAATCTTTAAATCTTTTGCTTGTTC Human: CTTAAAATATTTCTGGGATATTTCAGATTTCATTTG--------ACCCTTTAAATCTTTTGCTTCTTC Cluster: [ ] Orangutan: CTTAAAATATTTCTGGGATATTTCAGATTTCGTTTG--------ACCCTTTAAATCTTTTGCTTCTTC Chimp > Gorilla --------------- chr21:10686103-10686112 Template switch process: F1: L CTTATCTTAAAATATTTCTGGGGTATTTCAGATTTCATTTGA 1 F3: 4 CTTTAAATCTTTTGCTTGTTCTTTCCTGTAGTAAGTCAGG R RF: CTTATCTTAAAATATTTCTGGGATATTTCAGATTTCATTTGACCCTTTAAATCTTTTGCTTCTTCTTTCCTGTAGTAAGTCAGG RR: GAATAGAATTTTATAAAGACCCTATAAAGTCTAAAGTAAACTGGGAAATTTAGAAAACGAAGAAGAAAGGACATCATTCAGTCC F2: 3 TAAAGTCTAA 2 Unidirectional alignment (log-probability: -44.5) TATCTTAAAATATTTCTGGGgTATTTCAGATTTCATTTGaaatctgaAatCTTTAAATCTTTTGCTTgTTCTTTCCTGTAGTAAGTCAGG TATCTTAAAATATTTCTGGGATATTTCAGATTTCATTTG--------ACCCTTTAAATCTTTTGCTTCTTCTTTCCTGTAGTAAGTCAGG Template switch alignment (log-probability: -28.1) TATCTTAAAATATTTCTGGGgTATTTCAGATTTCATTTGA|AATCTGAAAT|CTTTAAATCTTTTGCTTgTTCTTTCCTGTAGTAAGTCAGG TATCTTAAAATATTTCTGGGATATTTCAGATTTCATTTGA|AATCTGAAAT|CTTTAAATCTTTTGCTTCTTCTTTCCTGTAGTAAGTCAGG ========== Event 1797 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCCACTGCCCACCTCCACCCCTCTGCTCTCCTT Chimp: GTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCCACTGCCCACCTCCACCCCTCTGCTCTCCTT ↓ 3 2 1 4 Gorilla: GTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCCTGGTCCC-ACTCCACCCCTCTGCTCTCCTT ↑ 3 2 1 4 Human: GTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCCACTGCCCACCTCCACCCCTCTGCTCTCCTT Cluster: [ ] Orangutan: ------------------------------------------------------------------- Human > Gorilla --------------- chr2B:126949987-126949994 Template switch process: F1: L TGCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCC 1 F3: 4 CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA R RF: TGCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCCACTGCCCACCTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA RR: ACGTCAGAGGGGACCCAGGACTCACCCTGGTCCGGATTGGGTGACGGGTGGAGGTGGGGAGACGAGAGGAACGACTGGGGATGCTCGGTT F2: 3 ACCCTGGT 2 Unidirectional alignment (log-probability: -31.1) GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACcctggtcCCA--------CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAAC-------CCACTGCCCACCTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA Template switch alignment (log-probability: -16.7) GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCC|TGGTCCCA|CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCC|TGGTCCCA|CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA Chimp > Gorilla --------------- chr2B:126949987-126949994 Template switch process: F1: L TGCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCC 1 F3: 4 CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA R RF: TGCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCCACTGCCCACCTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA RR: ACGTCAGAGGGGACCCAGGACTCACCCTGGTCCGGATTGGGTGACGGGTGGAGGTGGGGAGACGAGAGGAACGACTGGGGATGCTCGGTT F2: 3 ACCCTGGT 2 Unidirectional alignment (log-probability: -31.1) GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACcctggtcCCA--------CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAAC-------CCACTGCCCACCTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA Template switch alignment (log-probability: -16.7) GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCC|TGGTCCCA|CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA GCAGTCTCCCCTGGGTCCTGAGTGGGACCAGGCCTAACCC|TGGTCCCA|CTCCACCCCTCTGCTCTCCTTGCTGACCCCTACGAGCCAA ========== Event 1798 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGCATAATTCTAACAACCTG-------CCA---GATAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCGCTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTggccgggcgtagtggctcatg Chimp: ATGCATAATTCTAACAACCTG-------CCA---GATAGTTCCGTCTTGAAAGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCGCTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTggccaggcgtggtggctcaag ↑ 1 4 3 2 Gorilla: ATGCATAATTCTAACAACCTGCATTTGGACGGACAAGAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCACTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTggccaggcgtggtggctcacg ↓ 1 4 3 2 Human: ATGCATAATTCTAACAACCTG-------CCA---GATAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCGCTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTggccgggcgtagtggctcatg Cluster: [ ] Orangutan: ----------------------------------GATAGTTCCATCTTGAAGGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCACTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTggccgggcgtgatggcttatg Gorilla > Human --------------- chr21:19886546-19886550 Template switch process: F1: L ATTCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC 1 F3: 4 AGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA R RF: ATTCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGCATTTGGACGGACAAGAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCACTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTG RR: TAAGTGACGCAACTCTTCTTTACGTATTAAGATTGTTGGACGTAAACCTGCCTGTTCTCAAGGCAGAACTTCCAGATTTCAGTAAAGTTGTTCTGGTTGTCTCACTATTAATGAGAAAAGTGATGGTTTTGAACAAGAATTAAGGGTTGAAACATAGGTCAATTTTTATAATCACGACTAGAC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -25.7) TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGCcagAT-------------AGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC---ATTTGGACGGACAAGAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA Template switch alignment (log-probability: -16.4) TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC|CAGAT|AGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC|CAGAT|AGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA Gorilla > Chimp --------------- chr21:6378926-6378930 Template switch process: F1: L ATTCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC 1 F3: 4 AGTTCCGTCTTGAAAGTCTAAAGTCATTTCAACAAGACCA R RF: ATTCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGCATTTGGACGGACAAGAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCAACAGAGTGATAATTACTCTTTTCACTACCAAAACTTGTTCTTAATTCCCAACTTTGTATCCAGTTAAAAATATTAGTGCTGATCTG RR: TAAGTGACGCAACTCTTCTTTACGTATTAAGATTGTTGGACGTAAACCTGCCTGTTCTCAAGGCAGAACTTCCAGATTTCAGTAAAGTTGTTCTGGTTGTCTCACTATTAATGAGAAAAGTGATGGTTTTGAACAAGAATTAAGGGTTGAAACATAGGTCAATTTTTATAATCACGACTAGAC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -31.2) TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGCcagAT-------------AGTTCCGTCTTGAAaGTCTAAAGTCATTTCAACAAGACCA TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC---ATTTGGACGGACAAGAGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA Template switch alignment (log-probability: -21.9) TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC|CAGAT|AGTTCCGTCTTGAAaGTCTAAAGTCATTTCAACAAGACCA TCACTGCGTTGAGAAGAAATGCATAATTCTAACAACCTGC|CAGAT|AGTTCCGTCTTGAAGGTCTAAAGTCATTTCAACAAGACCA ========== Event 1799 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CATCTATTTATAGAAGTTTTAGGCTATCTGTCTATAT------------AAGATAGCC--------------------------TAAATAAGAAAAGTCAAAACAGG ↑ 3 2 1 4 Chimp: catctatTTATAGAAGTTTTAGGCTATCTGTCTATAT------ATACGCTGGATATTT-------------TTCTTCCTTTGTGGCAATAAGAAAAGTCAAAACAGG Gorilla: CATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATATACGC------TGGATATTTTTCTTCCTTTGTG-------------GCAATAAGAAAAGTCAAAACAGG ↓ 3 2 1 4 Human: CATCTATTTATAGAAGTTTTAGGCTATCTGTCTATAT------------AAGATAGCC--------------------------TAAATAAGAAAAGTCAAAACAGG Cluster: [ ] Orangutan: CATCTATTTATAGAGGTTTTAGGGTATCTGTCTATATATACGC------TGGATATTTTTCTTCCTTTGTG-------------GCAATAAGAAAAGTCAAAACAGG Chimp > Human ------------- chr21:20993448-20993457 Template switch process: F1: L GGATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA 1 F3: 4 AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA R RF: GGATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATATACGCTGGATATTTTTCTTCCTTTGTGGCAATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA RR: CCTAGTAGATAAATATCTTCAAAATCCGATAGACAGATATATATGCGACCTATAAAAAGAAGGAAACACCGTTATTCTTTTCAGTTTTGTCCGTTAAAAGATCTGTTCATT F2: 3 ATCCGATAGA 2 Unidirectional alignment (log-probability: -34) ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATAagatagccTA---------------------------AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA--------TACGCTGGATATTTTTCTTCCTTTGTGGCAATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA Template switch alignment (log-probability: -16.5) ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA|AGATAGCCTA|AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA|AGATAGCCTA|AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA Gorilla > Human --------------- chr21:20993448-20993457 Template switch process: F1: L GGATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA 1 F3: 4 AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA R RF: GGATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATATACGCTGGATATTTTTCTTCCTTTGTGGCAATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA RR: CCTAGTAGATAAATATCTTCAAAATCCGATAGACAGATATATATGCGACCTATAAAAAGAAGGAAACACCGTTATTCTTTTCAGTTTTGTCCGTTAAAAGATCTGTTCATT F2: 3 ATCCGATAGA 2 Unidirectional alignment (log-probability: -33.6) ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATAagatagccTA---------------------------AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA--------TACGCTGGATATTTTTCTTCCTTTGTGGCAATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA Template switch alignment (log-probability: -17) ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA|AGATAGCCTA|AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA ATCATCTATTTATAGAAGTTTTAGGCTATCTGTCTATATA|AGATAGCCTA|AATAAGAAAAGTCAAAACAGGCAATTTTCTAGACAAGTAA ========== Event 1800 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GCAAATGAATTCTTTATAGCAAGCATAATAATAAAAAGGACATGAGCAAGCCATGAAAGGAGGCTAACAGGAAGCACTGACAGTT----------------AATACAATACTTGGTTAATACAGCCcccaggagaaaacggaa Chimp: GCAAATGAATTCTTTATAGCAAGCATAATAATAAAAAGGACATGAGCAAGCCATGAAAGGAGGCTAACAGGAAGCACTGACAGTT----------------AATACAATACTTGGTTAATACAGCCCTCAGGAGAAAACGGAA Gorilla: GCAAATGAACTCTTTATAGCAAGCATAATAATAAAAAGGACATGAGCAAGCCATGAAAGGAGGCTAACGGGAAGCACTGACAGTT--------------------------------AATACAGCCCCCAGGAGAAAACGGAA ↓ 3 2 4 1 Human: GCAAATGAATTCTTTATAGCAAGCATAATAATAAAAAGGACATGAGCAAGCCATGAAAGGAGGCTAACAGGAAGCACTGACAGTT----------------AATACAATACTTGGTTAATACAGCCcccaggagaaaacggaa Cluster: [ ] Orangutan: gCAAATGAATTCTTTATAGTAAGCAT---AATAAAAAGGATATGAGCAAGCCATGAAAGGAGGCTAACGGGAAGCACTGACAGTTAACGCAATACTTGGTT----------------AATACAGCCCCCAGGAGAAAATGGAA Gorilla > Human --------------- chr2:230123170-230123176 Template switch process: F1: L AGCAAGCCATGAAAGGAGGCTAACAGGAAGCACTGACAGTTAATACA 1 F3: 4 GTTAATACAGCCCCCAGGAGAAAACGGAAACAGAGTGCCTTGT R RF: CAAGCATAATAATAAAAAGGACATGAGCAAGCCATGAAAGGAGGCTAACGGGAAGCACTGACAGTTAATACAGCCCCCAGGAGAAAACGGAAACAGAGTGCCTTGT RR: GTTCGTATTATTATTTTTCCTGTACTCGTTCGGTACTTTCCTCCGATTGCCCTTCGTGACTGTCAATTATGTCGGGGGTCCTCTTTTGCCTTTGTCTCACGGAACA F2: 3 GTTCATA 2 Unidirectional alignment (log-probability: -39.4) CATGAAAGGAGGCTAACaGGAAGCACTGACAgttaatacaatacttgGTTAATACAGCCCCCAGGAGAAAACGGAAACAGAGTGCCT CATGAAAGGAGGCTAACGGGAAGCACTGACA----------------GTTAATACAGCCCCCAGGAGAAAACGGAAACAGAGTGCCT Template switch alignment (log-probability: -27.9) CATGAAAGGAGGCTAACaGGAAGCACTGACAGTTAATACA|ATaCTTG|GTTAATACAGCCCCCAGGAGAAAACGGAAACAGAGTGCCT CATGAAAGGAGGCTAACGGGAAGCACTGACAGTTAATACA|ATGCTTG|GTTAATACAGCCCCCAGGAGAAAACGGAAACAGAGTGCCT ========== Event 1801 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAGGCAG----------------------------------------CCTCTGTGTGGCACCTCTCATGC-TGATTTCCACAGAGGGCGAGGCTGTGCCGG ↓ 3 2 1 4 Chimp: ATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAGAGAG------------------------------------------------------------GGCTGGATTTCCAGAGAGGGCGAGGCTGTGCCGG Gorilla: ATTCCTCCTTCCCCCTGTTCAGCCCACTCTCCAGGCAG--------------------CCTCTATGTGGCGCCTCTCA--------------------TGC-TGATTTCCACAGAGGGCGAGGCTGTGCCGG Human: ATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAGGCAG----------------------------------------CCTCTGTGTGGCACCTCTCATGC-TGATTTCCACAGAGGGCGAGGCTGTGCCGG Cluster: [ ] Orangutan: ATTACTCCTCCCCCCTGTTCAGTCCACTCTCCAGGCAGCCTCTGTGTGGCTCCTCTCA----------------------------------------TGC-TGATTTCCACAGAGGGCGAGGCTGTGCCAG Human > Chimp ------------- chr2B:7114197-7114205 Template switch process: F1: L ATGGGGGATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAG 1 F3: 4 GATTTCCAGAGAGGGCGAGGCTGTGCCGGCCAGAAACGTGGGTCTAGGA R RF: ATGGGGGATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAGGCAGCCTCTGTGTGGCACCTCTCATGCTGATTTCCACAGAGGGCGAGGCTGTGCCGGCCAGAAACGTGGGTCTAGGA RR: TACCCCCTAATGAGGAAGGGGGACAAGTCGGGTGAGAGGTCCGTCGGAGACACACCGTGGAGAGTACGACTAAAGGTGTCTCCCGCTCCGACACGGCCGGTCTTTGCACCCAGATCCT F2: 3 GTCGGGAGA 2 Unidirectional alignment (log-probability: -40.1) TGGGGGATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAGagagggctG---------------------------GATTTCCAgAGAGGGCGAGGCTGTGCCGGCCAGAAACGTG TGGGGGATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAG--------GCAGCCTCTGTGTGGCACCTCTCATGCTGATTTCCACAGAGGGCGAGGCTGTGCCGGCCAGAAACGTG Template switch alignment (log-probability: -28.6) TGGGGGATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAG|AGaGGGCTG|GATTTCCAgAGAGGGCGAGGCTGTGCCGGCCAGAAACGTG TGGGGGATTACTCCTTCCCCCTGTTCAGCCCACTCTCCAG|AGTGGGCTG|GATTTCCACAGAGGGCGAGGCTGTGCCGGCCAGAAACGTG ========== Event 1802 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GACAGTGGATGTGTCTGCTCCTAGCTCCCCCAGCTGCAG------------------------------AATGAGCCACCTGCCAGTATGGGTGGTGCATGGAATGTGGAGGTCTTGGGGCCACAGGTTCTCCAGAACCTCCCCAGCTGGGACTGGGGCCCAGAGCCATTGCATG Chimp: GACAGTGGATGTGTCTGCTCCCAGCTCCCCCAGCTGCAG---------------------------------------------AGTATGGGTGGTGCATGGAATGTGGAGGTCTTGGGGCCACAGGTTCTCCAGAACCTCCCCAGCTGGGACTGGGGCCCAGAGCCATTGCATG Gorilla: GACAGTGGATGTGTCTGCTCCCAGTTCCCCCAGCTGCAG---------------AATGAGCCACCTGCC---------------AGTATGGGTGGTGCATGGAATATGGAGGTCTTGGGGCCACAGGTTCTCCAGAACCTCCCCAGCTGGGACTGGGGCCCAGAACCATTGCATG ↑ 1 4 3 2 Human: GACAGTGGATGTGTCTGCTCCTAGCTCCCCCAGCTGCAG------------------------------AATGAGCCACCTGCCAGTATGGGTGGTGCATGGAATGTGGAGGTCTTGGGGCCACAGGTTCTCCAGAACCTCCCCAGCTGGGACTGGGGCCCAGAGCCATTGCATG Cluster: [ ] Orangutan: GACAGTGGATGTGTCTGCTCCCAGCTCCCCCAGCTGCAGAAGGAGCCACCTGCC------------------------------AGCATGGGTGGTGCATGGAATGTGGAGGTCTTGGGGCCACAGGTTCTCCAGAACCTCCCCAGCTGGCAGTGGGGCCCAGAGCCATTGCATG Human > Gorilla --------------- chr2B:10857891-10857894 Template switch process: F1: L GGGGGACATCATTGCTGAGGGACAGTGGATGTGTCTGCTCC 1 F3: 4 TCCCCCAGCTGCAGAATGAGCCACCTGCC R RF: GGGGGACATCATTGCTGAGGGACAGTGGATGTGTCTGCTCCTAGCTCCCCCAGCTGCAGAATGAGCCACCTGCCAGTATGGGTGGTGCATGGAATGTGGAGGTCTTGGGGCCACAGGTTCTCCAGAACCTCCCCAGCTGGGACTG RR: CCCCCTGTAGTAACGACTCCCTGTCACCTACACAGACGAGGATCGAGGGGGTCGACGTCTTACTCGGTGGACGGTCATACCCACCACGTACCTTACACCTCCAGAACCCCGGTGTCCAAGAGGTCTTGGAGGGGTCGACCCTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -24.5) GGGGACATCATTGCTGAGGGACAGTGGATGTGTCTGCTCCcAGtTCCCCCAGCTGCAGAATGAGCCACCtgcc GGGGACATCATTGCTGAGGGACAGTGGATGTGTCTGCTCCTAGCTCCCCCAGCTGCAGAATGAGCCACC---- Template switch alignment (log-probability: -15.9) GGGGACATCATTGCTGAGGGACAGTGGATGTGTCTGCTCC|CAGT|TCCCCCAGCTGCAGAATGAGCCACCTGCC GGGGACATCATTGCTGAGGGACAGTGGATGTGTCTGCTCC|CAGT|TCCCCCAGCTGCAGAATGAGCCACCTGCC ========== Event 1803 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCGGGCACCAGAAGAGGTGCCATGTATCCATGTGCCCACTGGGG-------G-------ATGTAGCTGGATGCTTCCAC Chimp: ACCGGGCACCAGAAGAAGTGCCATGTATCCATGTGCCCACTGGGG-------G-------ATGTAGCTGGATGCTTCCAC ↓ 3 4 2 1 Gorilla: ACCGGGCACCAGAAGAAGTGCAGTGTATCCATGTGCCCACTGGGGGCACATGGATACATGTGGTAGCTGGATGCTTCCAC Human: ACCGGGCACCAGAAGAGGTGCCATGTATCCATGTGCCCACTGGGG-------G-------ATGTAGCTGGATGCTTCCAC Cluster: [] Orangutan: ACCAGGCACCAGAAGAAGTGCAATGTATCCACGTGCTCACTGGGG-------G-------ATGTAGCTGGATGCTTCCAC Chimp > Gorilla --------------- chr2B:11018769-11018781 Template switch process: F1: L GGGAGCCACTAGCCTCATGGACCGGGCACCAGAAGAAGTGCAGTGTATCCATGTGCCCACTGGGGG 1 F3: 4 GTGG R RF: GGGAGCCACTAGCCTCATGGACCGGGCACCAGAAGAAGTGCCATGTATCCATGTGCCCACTGGGGGAATCATTGGGACATACTTTCTCTACCTGGACATAAGCTGAAAACAATACCAACCCTCAGCCCTGGGGAGCCACTAGCCTCATGGACCGGGCACCAGAAGAAGTGCCATGTATCCATGTG RR: CCCTCGGTGATCGGAGTACCTGGCCCGTGGTCTTCTTCACGGTACATAGGTACACGGGTGACCCCCTTAGTAACCCTGTATGAAAGAGATGGACCTGTATTCGACTTTTGTTATGGTTGGGAGTCGGGACCCCTCGGTGATCGGAGTACCTGGCCCGTGGTCTTCTTCACGGTACATAGGTACAC F2: 3 TACATAGGTACAC 2 Unidirectional alignment (log-probability: -48.6) CACCAGAAGAAGTGCagTGTATCCATGTGCCCACTGGGGGcacatggatacATGtgg CACCAGAAGAAGTGCCATGTATCCATGTGCCCACTGGGGG-----------ATG--- Template switch alignment (log-probability: -28.1) CACCAGAAGAAGTGCagTGTATCCATGTGCCCACTGGGGG|CACATGGATACAT|GTGG CACCAGAAGAAGTGCCATGTATCCATGTGCCCACTGGGGG|CACATGGATACAT|GTGG ========== Event 1804 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCAGGGATATCTTCATTTATCCTTGCAGTTGCAAGGAACAGCCCTCACcagtaag ↑ 1 3 4 2 Chimp: TGCAGGGATATCTTCATTTAT-CTAGCAACTGCAAGGAACAGCCCTCACcagtaag Gorilla: AGCAGGGATATCTTCATTTAT-CTAGCAATTGCAAGGAACAGCCCTCACcagtaag Human: AGCAGGGATATCTTCATTTATCCTTGCAGTTGCAAGGAACAGCCCTCACcagtaag Cluster: [ ] Orangutan: AGCAGGGATATCTTCATTTAT-CTAGCAACTGCAAGGAACAgccctcaccagtaag Chimp > Human ------------- chr2:119853895-119853902 Template switch process: F1: L CCGTCTCCTGACGCTGTTTCAGCAGGGATATCTTCATTTATC 1 F3: 4 TGCAAGGAACAGCCCTCACCAGTAAGTAAAACCTTGAACT R RF: CCGTCTCCTGACGCTGTTTCTGCAGGGATATCTTCATTTATCTAGCAACTGCAAGGAACAGCCCTCACCAGTAAGTAAAACCTTGAACT RR: GGCAGAGGACTGCGACAAAGACGTCCCTATAGAAGTAAATAGATCGTTGACGTTCCTTGTCGGGAGTGGTCATTCATTTTGGAACTTGA F2: 3 TGACGTTC 2 Unidirectional alignment (log-probability: -36.4) GTCTCCTGACGCTGTTTCaGCAGGGATATCTTCATTTATcCTtGCAgtTGCAAGGAACAGCCCTCACCAGTAAGTAAAACCTTGAACT GTCTCCTGACGCTGTTTCTGCAGGGATATCTTCATTTAT-CTAGCAACTGCAAGGAACAGCCCTCACCAGTAAGTAAAACCTTGAACT Template switch alignment (log-probability: -22.3) GTCTCCTGACGCTGTTTCaGCAGGGATATCTTCATTTATC|CTTGCAGT|TGCAAGGAACAGCCCTCACCAGTAAGTAAAACCTTGAACT GTCTCCTGACGCTGTTTCTGCAGGGATATCTTCATTTATC|CTTGCAGT|TGCAAGGAACAGCCCTCACCAGTAAGTAAAACCTTGAACT ========== Event 1805 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAAGCATCAGCAAGCACTCTGTGATTTA-------TTACCAATAATTGCTTATTATT Chimp: TAAAGCATCAGCAAGCACTCTGTGATTTA-------TTACCAATAATTGCTTATTATT ↓ 3 1 4 2 Gorilla: TAAAGCATCAGCAAGCACTCTGTAATAAATCACAGATAACCAATAATTGCTTATTATT Human: TAAAGCATCAGCAAGCACTCTGTGATTTA-------TTACCAATAATTGCTTATTATT Cluster: [ ] Orangutan: TAAAGCATCAGCAAGCACTCTGTGATTTA-------TTACCAGTAATTTCTTATTATT Chimp > Gorilla --------------- chr2B:11832842-11832853 Template switch process: F1: L TAATGTAAAGCTATGGTGTAAAGCATCAGCAAGCACTCTGT 1 F3: 4 ATAACCAATAATTGCTTATTATTTACATTTTAATTCTTTTTAG R RF: TAATGTAAAGCTATGGTGTAAAGCATCAGCAAGCACTCTGTGATTTATTACCAATAATTGCTTATTATTTACATTTTAATTCTTTTTAA RR: ATTACATTTCGATACCACATTTCGTAGTCGTTCGTGAGACACTAAATAATGGTTATTAACGAATAATAAATGTAAAATTAAGAAAAATT F2: 3 GACACTAAATAA 2 Unidirectional alignment (log-probability: -47.7) AATGTAAAGCTATGGTGTAAAGCATCAGCAAGCACTCTGTaataaatcacaG----ATaACCAATAATTGCTTATTATTTACATTTTAATTCTTTT AATGTAAAGCTATGGTGTAAAGCATCAGCAAGCACTCTGT-----------GATTTATTACCAATAATTGCTTATTATTTACATTTTAATTCTTTT Template switch alignment (log-probability: -28.4) AATGTAAAGCTATGGTGTAAAGCATCAGCAAGCACTCTGT|AATAAATCACAG|ATaACCAATAATTGCTTATTATTTACATTTTAATTCTTTT AATGTAAAGCTATGGTGTAAAGCATCAGCAAGCACTCTGT|AATAAATCACAG|ATTACCAATAATTGCTTATTATTTACATTTTAATTCTTTT ========== Event 1806 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATTATTTGTTTTTTGTTGT-CCGATTATTTAAGCATaatcagaaccagtatttattgagtg Chimp: AAATTATTTGTTTTTTGTTGT-CCGATTATTTAAGCATAATCGGAACCAATATTTATTGAGTG ↑ 1 4 3 2 Gorilla: AAATTATTTGTTTTTTGTTGTCACTCTAATTTAAGCATAATCGGGACCAGTATTTATTGAGTG Human: AAATTATTTGTTTTTTGTTGT-CCGATTATTTAAGCATaatcagaaccagtatttattgagtg Cluster: [ ] Orangutan: AAATTATTTGTTTTTTGTTGT-C----ACTCTAAGCATAATCAGAACCAGTATTTATTG---T Gorilla > Chimp --------------- chr21:9884269-9884273 Template switch process: F1: L CTAAAAATCCCATTTAACCAAAATTATTTGTTTTTTGTTGTC 1 F3: 4 ATTTAAGCATAATCGGAACCAATATTTATTGAGTGTTTTT R RF: CTAAAAATCCCATTTAACCAAAATTATTTGTTTTTTGTTGTCACTCTAATTTAAGCATAATCGGGACCAGTATTTATTGAGTGTTTTT RR: GATTTTTAGGGTAAATTGGTTTTAATAAACAAAAAACAACAGTGAGATTAAATTCGTATTAGCCCTGGTCATAAATAACTCACAAAAA F2: 3 TTAGC 2 Unidirectional alignment (log-probability: -38.6) AAAAATCCCATTTAACCAAAATTATTTGTTTTTTGTTGTC-CgaTtATTTAAGCATAATCGGaACCAaTATTTATTGAGTGTTTTT AAAAATCCCATTTAACCAAAATTATTTGTTTTTTGTTGTCACTCTAATTTAAGCATAATCGGGACCAGTATTTATTGAGTGTTTTT Template switch alignment (log-probability: -27.4) AAAAATCCCATTTAACCAAAATTATTTGTTTTTTGTTGTC|CGATT|ATTTAAGCATAATCGGaACCAaTATTTATTGAGTGTTTTT AAAAATCCCATTTAACCAAAATTATTTGTTTTTTGTTGTC|CGATT|ATTTAAGCATAATCGGGACCAGTATTTATTGAGTGTTTTT ========== Event 1807 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGGATATATTCAAATATTTG----------TTTACTTGTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATAATTGCAAAGTACGTTTACTATGTATTGTATAGAGCAGCTATTCTCATGGTAACCATGCCAACAAgtatatcagaacccccggagga Chimp: ATGGATATATTCAAATATTTG-----TTTTATTTATTTGTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATAATTGCAAAGTACGTTTACTATGTATCGTATAGAGCAGCTATTCTCATGGTAACCATGCCAACAAgtatatcagaacccccggagga Gorilla: ATGGATATATTCAAATATTTGTTTTA-----TTTATT-TTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATAATTGCAAAGTACGTTTACTATGTATTGTATAGAGCAGCTATTCTCATGGTAACCATGCCAACAAgtatatcagaacccccggagga ↓ 1 4 3 2 Human: ATGGATATATTCAAATATTTG----------TTTACTTGTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATAATTGCAAAGTACGTTTACTATGTATTGTATAGAGCAGCTATTCTCATGGTAACCATGCCAACAAgtatatcagaacccccggagga Cluster: [ ] Orangutan: ATGGATATATTCAAATATTTGTTT---------TATTTGTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATAATTGCAAGGTACGTTTACTATGTATTGTACACAGCAGCTATTCTCATGGTAACCGTGCCAACAAgtatatcagaacccccggagga Gorilla > Human --------------- chr2:124185942-124185946 Template switch process: F1: L TGAGCAGTTGCTTTATGTTAATGGATATATTCAAATATTTGTTT 1 F3: 4 TTAGCATAGGACATACGTGTATACTCCTATAAATAAGATA R RF: TGAGCAGTTGCTTTATGTTAATGGATATATTCAAATATTTGTTTTATTTATTTTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATAATTGCAAAGTACGTTTACTATGTATTGTATAGAGCAGCTATTCTCATGGTAACCATGCCAACAAGT RR: ACTCGTCAACGAAATACAATTACCTATATAAGTTTATAAACAAAATAAATAAAAATCGTATCCTGTATGCACATATGAGGATATTTATTCTATTAACGTTTCATGCAAATGATACATAACATATCTCGTCGATAAGAGTACCATTGGTACGGTTGTTCA F2: 3 GTTCA 2 Unidirectional alignment (log-probability: -27.8) CAGTTGCTTTATGTTAATGGATATATTCAAATATTTGTT----TacTTgTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATA CAGTTGCTTTATGTTAATGGATATATTCAAATATTTGTTTTATTTATTTTTAGCATAGGACATACGTGTATACTCCTATAAATAAGATA Template switch alignment (log-probability: -16.4) CAGTTGCTTTATGTTAATGGATATATTCAAATATTTGTTT|ACTTG|TTAGCATAGGACATACGTGTATACTCCTATAAATAAGATA CAGTTGCTTTATGTTAATGGATATATTCAAATATTTGTTT|ACTTG|TTAGCATAGGACATACGTGTATACTCCTATAAATAAGATA ========== Event 1808 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAGTAACTGGGTGATCAGCTAAGAGTCCATTAAGACCAAACACAGAGAAAATTACCACCCT Chimp: TGAGTAACTGGGTGATCAGCTAAGAGTCCATTAAGACCAAACACAGAGAAAATTACCACCCT Gorilla: TGAGTAACTGGGTGATCAGCTAAGAGTCCATTAACTCTTAGCACAGAGAAAATTATCACCCT ↑ 3 2 1 4 Human: TGAGTAACTGGGTGATCAGCTAAGAGTCCATTAAGACCAAACACAGAGAAAATTACCACCCT Cluster: [ ] Orangutan: -------------------------------------------------------------- Human > Gorilla --------------- chr21:22527891-22527897 Template switch process: F1: L ACCTCGCTGAGTAACTGGGTGATCAGCTAAGAGTCCATTAA 1 F3: 4 CACAGAGAAAATTATCACCCTACAAGAACAAAATACCATT R RF: ACCTCGCTGAGTAACTGGGTGATCAGCTAAGAGTCCATTAAGACCAAACACAGAGAAAATTACCACCCTACAAGAACAAAATACCATT RR: TGGAGCGACTCATTGACCCACTAGTCGATTCTCAGGTAATTCTGGTTTGTGTCTCTTTTAATGGTGGGATGTTCTTGTTTTATGGTAA F2: 3 GATTCTC 2 Unidirectional alignment (log-probability: -34.4) CCTCGCTGAGTAACTGGGTGATCAGCTAAGAGTCCATTAActCttAgCACAGAGAAAATTAtCACCCTACAAGAACAAAATACCATT CCTCGCTGAGTAACTGGGTGATCAGCTAAGAGTCCATTAAGACCAAACACAGAGAAAATTACCACCCTACAAGAACAAAATACCATT Template switch alignment (log-probability: -22.1) CCTCGCTGAGTAACTGGGTGATCAGCTAAGAGTCCATTAA|CTCTTAG|CACAGAGAAAATTAtCACCCTACAAGAACAAAATACCATT CCTCGCTGAGTAACTGGGTGATCAGCTAAGAGTCCATTAA|CTCTTAG|CACAGAGAAAATTACCACCCTACAAGAACAAAATACCATT ========== Event 1809 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACACTTTTAGGGGAGGGTGTGAACAGCTTTAACTTGATTACAGTTTTTGTAGACATTGCAACATCAATGAAAGTTAGCAGTAATACTTCTCGTGCATACTGCTTATATGTCTGAAGATTATCTAACTCTGA---TAATAACTGTTCATTGTATTA--GTATACGCTTTG Chimp: ACACTTCTAGGGGAGGGTGTGAACAGCTTTAACTTGATTACAGTTTTTGCAGACATTGCAACATCAATGAAAGTTAGCAGTAATACTTCTCACGCATACTGCTTATATGTCTGAAGATTATCTAACCCTGA---TAATAACTGTT----CTATTA--GTATATGCTTTG ↓ 3 2 1 4 Gorilla: ACACTTCTAGGGAAGGGTGTGAACAGCTTTAACTTGATTACAGTTTTTGCAGACATTGCAACATCAATGAAAGTTAGCAGTAATACTTCTCACGCATACTGCTTATATGTCTGAAGATTATCTAACTCTGA------TAACTGTTCATTCTATTA--GTATACGCTTTG Human: ACACTTTTAGGGGAGGGTGTGAACAGCTTTAACTTGATTACAGTTTTTGTAGACATTGCAACATCAATGAAAGTTAGCAGTAATACTTCTCGTGCATACTGCTTATATGTCTGAAGATTATCTAACTCTGA---TAATAACTGTTCATTGTATTA--GTATACGCTTTG Cluster: [ ] Orangutan: ACACTTCTAGGGGAGGGGGTGAACAACTTTAACTTGATTACAGTTTTTGCAGACATTGCAACATCAATGAAAGTTAGCAGTAATACTTCTCACGCATACTGCTAATATGTCTGAAGATTATCTAACTCTGATAA---TAACTGTTCATTCTATTAGTGTATATGCTTTG Chimp > Gorilla --------------- chr21:22570129-22570135 Template switch process: F1: L CTTCTCACGCATACTGCTTATATGTCTGAAGATTATCTAACTCTGATAA 1 F3: 4 TTCTATTAGTATACGCTTTGCAAGAACTCTTGTCAACACCTG R RF: TGAACAGCTTTAACTTGATTACAGTTTTTGCAGACATTGCAACATCAATGAAAGTTAGCAGTAATACTTCTCACGCATACTGCTTATATGTCTGAAGATTATCTAACCCTGATAATAACTGTTCTATTAGTATATGCTTTGCAAGAACTCTTGTCAACACCTG RR: ACTTGTCGAAATTGAACTAATGTCAAAAACGTCTGTAACGTTGTAGTTACTTTCAATCGTCATTATGAAGAGTGCGTATGACGAATATACAGACTTCTAATAGATTGGGACTATTATTGACAAGATAATCATATACGAAACGTTCTTGAGAACAGTTGTGGAC F2: 3 ACTTGTC 2 Unidirectional alignment (log-probability: -37.8) CATACTGCTTATATGTCTGAAGATTATCTAACtCTG---ATAACTGttcaTTCTATTAGTATAcGCTTTGCAAGAACTCTTGTCAACACC CATACTGCTTATATGTCTGAAGATTATCTAACCCTGATAATAACTG----TTCTATTAGTATATGCTTTGCAAGAACTCTTGTCAACACC Template switch alignment (log-probability: -27.9) CATACTGCTTATATGTCTGAAGATTATCTAACtCTGATAA|CTGTTCA|TTCTATTAGTATAcGCTTTGCAAGAACTCTTGTCAACACC CATACTGCTTATATGTCTGAAGATTATCTAACCCTGATAA|CTGTTCA|TTCTATTAGTATATGCTTTGCAAGAACTCTTGTCAACACC ========== Event 1810 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATATTCATCTCACAAAGTGGGTATATAAGTAATATATAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACAGAAATCAAAAGTGATGATAGAACCATATTGAGCAGAGGGAAAAGAGGAAGTGTGGGGTACAAGTGAGCTAAAAAGTCTAAATCTGATAACATGACAG ↓ 1 4 3 2 Chimp: ATATATTCATCTCACAAAGTGAGTA------TGACTTTGAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACAGAAATCAAAAGTGATGATAGAACCATATTGAGCAGAGGGAAAAGAGGAAGTGTGGGGTACAAGTGAGCTAAAAAGTCTAAATCTGATAACATGACAG Gorilla: ATATATTCATCTCACAAAGTGCGTA------TGATTTTGAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACAGAAATCAAAAGTGATGATAGAACCATACTGAGCAGAGGGAAAAGAGGAAGTGTGGGGTACAAGTGAGCTAAAAAGTCTAAATCTGATAACATGACAG Human: ATATATTCATCTCACAAAGTGGGTATATAAGTAATATATAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACAGAAATCAAAAGTGATGATAGAACCATATTGAGCAGAGGGAAAAGAGGAAGTGTGGGGTACAAGTGAGCTAAAAAGTCTAAATCTGATAACATGACAG Cluster: [ ] Orangutan: ATATATTCATGTTACAAAGTGGGTA------CGACTTCGAAGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACAGAAATCAAAAGTGATGATAGAACCATATTGAGCAGAGGGAAAAGAGGAAGTGTGGGGTGCAAGTGAGCTAAAAAGTCTAAATCTGATAACATGACAG Human > Chimp ------------- chr21:11841337-11841342 Template switch process: F1: L AAAGTTCTTTTTTCTTTGTAATATATTCATCTCACAAAGTGAGTAT 1 F3: 4 GAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACA R RF: AAAGTTCTTTTTTCTTTGTAATATATTCATCTCACAAAGTGGGTATATAAGTAATATATAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATACAGAAATCAAAAGTGATGATAGAACCATATTGAGCAGAGGGAAAAGAGGAAGTGTGGGGTACAAGTGAGCTAAAAAGTC RR: TTTCAAGAAAAAAGAAACATTATATAAGTAGAGTGTTTCACCCATATATTCATTATATATCCAGTTTTCATTATTTCTCTATGTTACCATTGGTTATGTCTTTAGTTTTCACTACTATCTTGGTATAACTCGTCTCCCTTTTCTCCTTCACACCCCATGTTCACTCGATTTTTCAG F2: 3 TTTCAG 2 Unidirectional alignment (log-probability: -37.8) CTTTTTTCTTTGTAATATATTCATCTCACAAAGTGagtatgactttG-----------------AGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATAC CTTTTTTCTTTGTAATATATTCATCTCACAAAGTG-----------GGTATATAAGTAATATATAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATAC Template switch alignment (log-probability: -28.1) CTTTTTTCTTTGTAATATATTCATCTCACAAAGTGaGTAT|GACTTT|gAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATAC CTTTTTTCTTTGTAATATATTCATCTCACAAAGTGGGTAT|GACTTT|TAGGTCAAAAGTAATAAAGAGATACAATGGTAACCAATAC ========== Event 1811 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGCTGAAACAGAGTAGAAGCCACCTCTGTCTGTTGGACAGAGGTGGCCTTAACAC-TGAGTATCA ↑ 1 4 3 2 Chimp: TGGCTGAAACAGAGTAGAAGCAA----AGTCTGTTGGACAGAGGTGGCCTTAACACTTGAGTATCA Gorilla: TGGCTGAAACAGAGTAGAAGCAA----AGTCTGTTGGACAGAGGTGGCCTTAACAC-TGAGTATCA ↓ 1 4 3 2 Human: TGGCTGAAACAGAGTAGAAGCCACCTCTGTCTGTTGGACAGAGGTGGCCTTAACAC-TGAGTATCA Cluster: [ ] Orangutan: TGGCTGAAACAGAGTAGAAGCAA----AGTCTGTTGGACAGAGGTGGCCTTAACAC-TGAGTATCA Chimp > Human ------------- chr21:20549898-20549905 Template switch process: F1: L AGAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGC 1 F3: 4 TCTGTTGGACAGAGGTGGCCTTAACAC-TGAGTATCAAT R RF: AGAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGCAAAGTCTGTTGGACAGAGGTGGCCTTAACACTTGAGTATCAAT RR: TCTCATCGGTACACTCATAAACCGACTTTGTCTCATCTTCGTTTCAGACAACCTGTCTCCACCGGAATTGTGAACTCATAGTTA F2: 3 GTCTCCAC 2 Unidirectional alignment (log-probability: -38.9) GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGCcAcctctGTCTGTTGGACAGAGGTGGCCTTAACACT-GAGTATCAAT GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGCAA----AGTCTGTTGGACAGAGGTGGCCTTAACACTTGAGTATCAAT Template switch alignment (log-probability: -26.5) GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGC|CACCTCTG|TCTGTTGGACAGAGGTGGCCTTAACAC-TGAGTATCAAT GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGC|CACCTCTG|TCTGTTGGACAGAGGTGGCCTTAACACTTGAGTATCAAT Gorilla > Human --------------- chr21:20549898-20549905 Template switch process: F1: L AGAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGC 1 F3: 4 TCTGTTGGACAGAGGTGGCCTTAACACTGAGTATCAATC R RF: AGAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGCAAAGTCTGTTGGACAGAGGTGGCCTTAACACTGAGTATCAATC RR: TCTCATCGGTACACTCATAAACCGACTTTGTCTCATCTTCGTTTCAGACAACCTGTCTCCACCGGAATTGTGACTCATAGTTAG F2: 3 GTCTCCAC 2 Unidirectional alignment (log-probability: -27.7) GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGCcAcctctGTCTGTTGGACAGAGGTGGCCTTAACACTGAGTATCAATC GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGCAAA----GTCTGTTGGACAGAGGTGGCCTTAACACTGAGTATCAATC Template switch alignment (log-probability: -16.7) GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGC|CACCTCTG|TCTGTTGGACAGAGGTGGCCTTAACACTGAGTATCAATC GAGTAGCCATGTGAGTATTTGGCTGAAACAGAGTAGAAGC|CACCTCTG|TCTGTTGGACAGAGGTGGCCTTAACACTGAGTATCAATC ========== Event 1812 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTCTTGAAGCACAGAATTT-------------ATC---TATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA Chimp: TTTTCTTGAAGCACAGAATTT-------------ATC---TATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA ↓ 4 3 1 2 Gorilla: TTTTCTTGAAGCACAGAATTTAGGTCCTAGAATCATCTAGGACCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCG ↑ 4 3 1 2 Human: TTTTCTTGAAGCACAGAATTT-------------ATC---TATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA Cluster: [ ] Orangutan: TTTTCTTGAAGCACAGAATTT-------------ATC---TATCTGTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA Human > Gorilla --------------- chr21:20762813-20762824 Template switch process: F1: L ATGAGTGGGCTTTGCTGATATTTTCTTGAAGCACAGAATT------------TAGGTCCTAGA 1 F3: 4 CTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCG R RF: ATGAGTGGGCTTTGCTGATATTTTCTTGAAGCACAGAATTTATCTATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA RR: TACTCACCCGAAACGACTATAAAAGAACTTCGTGTCTTAAATAGATAGAGACATCCAGGATCTACTATCCACTCTTTTTCTTTGGGT F2: 3 CAGGATCTACTA 2 Unidirectional alignment (log-probability: -54.8) TTGCTGATATTTTCTTGAAGCACAGAATTTaggtcctagaatcATCTaggAcCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCg TTGCTGATATTTTCTTGAAGCACAGAATTT-------------ATCT---ATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA Template switch alignment (log-probability: -33.4) TTGCTGATATTTTCTTGAAGCACAGAATT------------TAGGTCCTAGA|ATCATCTAGGAC|CTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCg TTGCTGATATTTTCTTGAAGCACAGAATTTATCTATCTCTGTAGGTCCTAGA|ATCATCTAGGAC|CTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA Chimp > Gorilla --------------- chr21:20762813-20762824 Template switch process: F1: L ATGAGTGGGCTTTGCTGATATTTTCTTGAAGCACAGAATT------------TAGGTCCTAGA 1 F3: 4 CTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCG R RF: ATGAGTGGGCTTTGCTGATATTTTCTTGAAGCACAGAATTTATCTATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA RR: TACTCACCCGAAACGACTATAAAAGAACTTCGTGTCTTAAATAGATAGAGACATCCAGGATCTACTATCCACTCTTTTTCTTTGGGT F2: 3 CAGGATCTACTA 2 Unidirectional alignment (log-probability: -54.8) TTGCTGATATTTTCTTGAAGCACAGAATTTaggtcctagaatcATCTaggAcCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCg TTGCTGATATTTTCTTGAAGCACAGAATTT-------------ATCT---ATCTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA Template switch alignment (log-probability: -33.4) TTGCTGATATTTTCTTGAAGCACAGAATT------------TAGGTCCTAGA|ATCATCTAGGAC|CTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCg TTGCTGATATTTTCTTGAAGCACAGAATTTATCTATCTCTGTAGGTCCTAGA|ATCATCTAGGAC|CTCTGTAGGTCCTAGATGATAGGTGAGAAAAAGAAACCCA ========== Event 1813 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: ↑ Gorilla: Human: Cluster: Orangutan: Gorilla > Chimp --------------- chr21:20900136-20900140 Template switch process: F1: L TGTGTACTTAAACAATGATCCTGCATG 1 F3: 4 AAAATAAAATATTGATTATGCATATTGACAAATGCATATTA----------------------------------------------------------------------------------------------------T R RF: TGTGTACTTAAACAATGATCCTGCATGCGATTATATTCACTACCTGAATATAATATAATAAAATATTGATTATGCAAATTGACAAATGCATATTATCTATGATGCCACTGCAGAGTATTGAACTGAATTCCAGTCTGAAGAGTTCCAGCCTGTCTGTTCACAAACTATTTGATGTTAGGTAAATTATTAATGTCTA RR: ACACATGAATTTGTTACTAGGACGTACGCTAATATAAGTGATGGACTTATATTATATTATTTTATAACTAATACGTTTAACTGTTTACGTATAATAGATACTACGGTGACGTCTCATAACTTGACTTAAGGTCAGACTTCTCAAGGTCGGACAGACAAGTGTTTGATAAACTACAATCCATTTAATAATTACAGAT F2: 3 ACATG 2 Unidirectional alignment (log-probability: -37.5) TGTGTACTTAAACAATGATCCTGCATG-----------------------------gtacaaaAATAAAATATTGATTATGCAtATTGACAAATGCATATT TGTGTACTTAAACAATGATCCTGCATGCGATTATATTCACTACCTGAATATAATAT-------AATAAAATATTGATTATGCAAATTGACAAATGCATATT Template switch alignment (log-probability: -27.1) TGTGTACTTAAACAATGATCCTGCATG|GTACA|AaAATAAAATATTGATTATGCAtATTGACAAATGCATATT TGTGTACTTAAACAATGATCCTGCATG|GTACA|ATAATAAAATATTGATTATGCAAATTGACAAATGCATATT ========== Event 1814 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATAAGTTATATTTTATTACTAATGCTGAAGACTGTAT--AA----TATAGCTTTCAGAAACAGATTGA ↓ 3 1 2 4 Chimp: GATAAGTTATATTTTATTACTAATGCTGAATACAGTCTTCAGCATTAGTAGCTTTCAGAAACAGATTGA ↑ 3 1 2 4 Gorilla: GATAAGTTATATTTTATTACTAATGCTGAAGACTGTAT--AA----TGTAGCTTTCAGAAACAGATTGA Human: GATAAGTTATATTTTATTACTAATGCTGAAGACTGTAT--AA----TATAGCTTTCAGAAACAGATTGA Cluster: [ ] Orangutan: GATTAGTTATACTTTATTACTAATGCTGAAGACTGTAT--AA----TGTAGCTTTCAGAAACAGATTGA Human > Chimp ------------- chr2B:120221462-120221479 Template switch process: F1: L CTGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAA 1 F3: 4 TAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAGG R RF: CTGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAAGACTGTATAATATAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAGG RR: GACCAAAAGAACTATTCAATATAAAATAATGATTACGACTTCTGACATATTATATCGAAAGTCTTTGTCTAACTTACACAACCCCGAAGCTCC F2: 3 GATTACGACTTCTGACAT 2 Unidirectional alignment (log-probability: -44.7) TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTG----------AATAcagtcttcagcattagTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAGG TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAAGACTGTATAATA----------------TAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAGG Template switch alignment (log-probability: -17.5) TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAA|TACAGTCTTCAGCATTAG|TAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAGG TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAA|TACAGTCTTCAGCATTAG|TAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAGG Gorilla > Chimp --------------- chr2B:120221462-120221478 Template switch process: F1: L CTGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAA 1 F3: 4 GTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAG R RF: CTGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAAGACTGTATAATGTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAG RR: GACCAAAAGAACTATTCAATATAAAATAATGATTACGACTTCTGACATATTACATCGAAAGTCTTTGTCTAACTTACACAACCCCGAAGCTC F2: 3 ATTACGACTTCTGACAT 2 Unidirectional alignment (log-probability: -44.2) TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTG----------AATacagtcttcagcattaGTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAG TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAAGACTGTATAAT----------------GTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAG Template switch alignment (log-probability: -17.9) TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAA|TACAGTCTTCAGCATTA|GTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAG TGGTTTTCTTGATAAGTTATATTTTATTACTAATGCTGAA|TACAGTCTTCAGCATTA|GTAGCTTTCAGAAACAGATTGAATGTGTTGGGGCTTCGAG ========== Event 1815 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTAATCAGCTTTTTGACTTA-----TTCTGTTTTCTGATGCTCCTGGATC ↓ 3 1 4 Chimp: CTCTAATCAGCATTTTGACTTATCAGAATAAGTTTTCTGATGCTCCTGGATC ↑ 3 1 4 Gorilla: CTCTAATCAGCATTTTGACTTA-----TTCTGTTTTCTGATGCTCCTGGATC Human: CTCTAATCAGCTTTTTGACTTA-----TTCTGTTTTCTGATGCTCCTGGATC Cluster: [ ] Orangutan: CTCTAATCAGCATTTTGACTTG-----TTCTGTTTTCTGATGCTCCTGGATC Human > Chimp ------------- chr2B:120039865-120039872 Template switch process: F1: L AGTCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTAT 1 F3: 4 GTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT R RF: AGTCTGCTGGGCCACGTGTCTCTAATCAGCTTTTTGACTTATTCTGTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT RR: TCAGACGACCCGGTGCACAGAGATTAGTCGAAAAACTGAATAAGACAAAAGACTACGAGGACCTAGAGGGGAAGGAATGATCCGA F2: 3 AATAAGAC 2 Unidirectional alignment (log-probability: -36.1) TCTGCTGGGCCACGTGTCTCTAATCAGCaTTTTGACTTATcagaaTaaGTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT TCTGCTGGGCCACGTGTCTCTAATCAGCTTTTTGACTTAT-----TCTGTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT Template switch alignment (log-probability: -22.3) TCTGCTGGGCCACGTGTCTCTAATCAGCaTTTTGACTTAT|CAGAATAA|GTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT TCTGCTGGGCCACGTGTCTCTAATCAGCTTTTTGACTTAT|CAGAATAA|GTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT Gorilla > Chimp --------------- chr2B:120039865-120039872 Template switch process: F1: L AGTCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTAT 1 F3: 4 GTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT R RF: AGTCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTATTCTGTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT RR: TCAGACGACCCGGTGCACAGAGATTAGTCGTAAAACTGAATAAGACAAAAGACTACGAGGACCTAGAGGGGAAGGAATGATCCGA F2: 3 AATAAGAC 2 Unidirectional alignment (log-probability: -29.2) TCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTATcagaaTaaGTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT TCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTAT-----TCTGTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT Template switch alignment (log-probability: -16.8) TCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTAT|CAGAATAA|GTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT TCTGCTGGGCCACGTGTCTCTAATCAGCATTTTGACTTAT|CAGAATAA|GTTTTCTGATGCTCCTGGATCTCCCCTTCCTTACTAGGCT ========== Event 1816 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTTTCTGTGTGCAGGATAA-------------ACATGCATGCACACAGAAAAATGACTTCAgatttgcatagttgtatcttatttattttttctgtgtgcatgtatgtttactctgcttggtgtttg Chimp: ttttttctGTGTGCAGGATAA-------------ACATGCATGCACACAGAAAAATGACTTCAgatttgcatagttgtatcttatttattttttctgtgtgcatgtatgtttactctgcttggtgtttg ↑ 1 4 3 2 Gorilla: ttttttctGTGTGCAGGATAA--------------------------AATAAAAATGACTTCAgatttgcatagttgtatcttatttattttttctgtgtgcatgtatgtttactctgcttggtgtttg ↓ 1 4 3 2 Human: TTTTTTCTGTGTGCAGGATAA-------------ACATGCATGCACACAGAAAAATGACTTCAgatttgcatagttgtatcttatttattttttctgtgtgcatgtatgtttactctgcttggtgtttg Cluster: [ ] Orangutan: TTTTTTCTGTGTGCAGGATAAACATGCATGCACA-------------CAGAAAAATGACTTCAgatttgcatagttgtatcttatttattttttctgtgtgcatgtatgtttactctgcttggtgtttg Gorilla > Human --------------- chr21:27098283-27098297 Template switch process: F1: L TTTTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA 1 F3: 4 AAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT R RF: TTTTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAAATAAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATTTTTTCTGTGTGCATGTATG RR: AAAAGAAAGGAGGAATAAATAAAAAAGACACACGTCCTATTTTATTTTTACTGAAGTCTAAACGTATCAACATAGAATAAATAAAAAAGACACACGTACATAC F2: 3 GACACACGTACGTAC 2 Unidirectional alignment (log-probability: -35.1) TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAAcatgcatgcacacAgAAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA-------------ATAAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT Template switch alignment (log-probability: -23.2) TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA|CATgCATGCACACAG|AAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA|CATACATGCACACAG|AAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT Gorilla > Chimp --------------- chr21:13440037-13440051 Template switch process: F1: L TTTTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA 1 F3: 4 AAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT R RF: TTTTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAAATAAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATTTTTTCTGTGTGCATGTATG RR: AAAAGAAAGGAGGAATAAATAAAAAAGACACACGTCCTATTTTATTTTTACTGAAGTCTAAACGTATCAACATAGAATAAATAAAAAAGACACACGTACATAC F2: 3 GACACACGTACGTAC 2 Unidirectional alignment (log-probability: -35.1) TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAAcatgcatgcacacAgAAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA-------------ATAAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT Template switch alignment (log-probability: -23.2) TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA|CATgCATGCACACAG|AAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT TTCTTTCCTCCTTATTTATTTTTTCTGTGTGCAGGATAAA|CATACATGCACACAG|AAAAATGACTTCAGATTTGCATAGTTGTATCTTATTTATT ========== Event 1817 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAGGTCTAGCCCAAGTGTGATTT----TTTATGGGTTTACTGTCAAAATTTCTGAGTCACTT Chimp: TTAGGTCTAGCCCAAGTGTGATTT----TTTATGGGTTTACTGTCAAAATTTCTGAGTCACTT ↓ 1 3 4 2 Gorilla: TTAGGTCTAGCCCAAGTGTGACAGTAAACCCATAGGTTTACTGTCAAAATTTCTGAGTCACTT ↑ 1 3 4 2 Human: TTAGGTCTAGCCCAAGTGTGATTT----TTTATGGGTTTACTGTCAAAATTTCTGAGTCACTT Cluster: [ ] Orangutan: TTAGGTCTAGTCCAAGTGTAATTT----TTTATGGGTTTACTGTCAAAATTTCTGAGTCACTT Human > Gorilla --------------- chr21:18131117-18131129 Template switch process: F1: L GTATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA 1 F3: 4 GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT R RF: GTATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGATTTTTTATGGGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT RR: CATAACGAATATTCTCAAGAAATCCAGATCGGGTTCACACTAAAAAATACCCAAATGACAGTTTTAAAGACTCAGTGAATTTTTTTCTTA F2: 3 ATACCCAAATGAC 2 Unidirectional alignment (log-probability: -39.8) TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA---------cagtaaacccataGGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGATTTTTTATG-------------GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT Template switch alignment (log-probability: -17.4) TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA|CAGTAAACCCATA|GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA|CAGTAAACCCATA|GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT Chimp > Gorilla --------------- chr21:18131117-18131129 Template switch process: F1: L GTATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA 1 F3: 4 GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT R RF: GTATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGATTTTTTATGGGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT RR: CATAACGAATATTCTCAAGAAATCCAGATCGGGTTCACACTAAAAAATACCCAAATGACAGTTTTAAAGACTCAGTGAATTTTTTTCTTA F2: 3 ATACCCAAATGAC 2 Unidirectional alignment (log-probability: -39.8) TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA---------cagtaaacccataGGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGATTTTTTATG-------------GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT Template switch alignment (log-probability: -17.4) TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA|CAGTAAACCCATA|GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT TATTGCTTATAAGAGTTCTTTAGGTCTAGCCCAAGTGTGA|CAGTAAACCCATA|GGTTTACTGTCAAAATTTCTGAGTCACTTAAAAAAAGAAT ========== Event 1818 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTGCAGGGTGGATCCTCTGGAAGGCTGGTGACTTGCCCGGGGCTGCGGGTC-----------AGTGGGAGGCCCTTGCTGCCCCCTGCAGCATGCCCCTGAGCTGGTGGCTGGCCTCAGGGCTGAGCCTGGTGGTGCTAGGGACTGCGGGCAGGTGTTTGGGGCCTTTAGTCAGCAGCACTGCCTCCCACACG Chimp: ACTGCAGGGTGAATCCTCTGGAAGGCTGGCGACTTGCCTGG-----------GGCTGCAGGTCAGTGGGAGGCCCTTGCTGCCCCCTGCAGCATGCCTCTGAGCTGGTGGCTGGCCTCAGGGCTGAGCCTGGTGGTGCTAGGGACTGCGGGCAGGTGTTTGGGGCCTTTAGTCGGCAGCACTGCCTCCCACACG Gorilla: ACCGCAGGGTGGATCCTCTGGTGACTTGGTGACTTGCCCGGGGCTGCGGGTC-----------AGTGGGAGGCCCTTGCTGCCCCCTGCAGCATGCCCCTGAGCTGGTGGCTGGCCTCAGGGCTGAGCCTGGTGGTGCTAGGGACTGCGGGCAGGTGTTTGGGGCCTTTAGTCAGCAGCACTGCCTCCCACACG ↑ 1 4 3 2 Human: ACTGCAGGGTGGATCCTCTGGAAGGCTGGTGACTTGCCCGGGGCTGCGGGTC-----------AGTGGGAGGCCCTTGCTGCCCCCTGCAGCATGCCCCTGAGCTGGTGGCTGGCCTCAGGGCTGAGCCTGGTGGTGCTAGGGACTGCGGGCAGGTGTTTGGGGCCTTTAGTCAGCAGCACTGCCTCCCACACG Cluster: [ ] Orangutan: ACTGCAGGGCGGATCCTCTGGAAGGCTGGTGACTAGCCCAGGGCTGCGGGTC-----------AGTGGGAGGCCCTTGCTGCCCCCTGCAGTGTGCCCCTGAGCTGGTGGCTGGCCTCAGGGCTGAGCCTGGTGGTGCTAGGGACTGCGGGCAGGTGTTT-GGGCCTTTAGTCAGCAGCACTGCCTCCCACACG Human > Gorilla --------------- chr2B:119450079-119450083 Template switch process: F1: L CTTTCTAGATGGTGACTGGGACCGCAGGGTGGATCCTCTGG 1 F3: 4 TGGTGACTTGCCCGGGGCTGCGGGTCAGTGGGAGGCCCTT R RF: CTTTCTAGATGATGACTGGGACTGCAGGGTGGATCCTCTGGAAGGCTGGTGACTTGCCCGGGGCTGCGGGTCAGTGGGAGGCCCTTGCTGCCCCCTGCAGCATGCCCCTGAGCTGGTGGCTGGCCTCAGGGCTGAGCCTGGTGGTGCTAGGGACTGCGGGCAGGTGTTTGGGGCCTTTAGTCA RR: GAAAGATCTACTACTGACCCTGACGTCCCACCTAGGAGACCTTCCGACCACTGAACGGGCCCCGACGCCCAGTCACCCTCCGGGAACGACGGGGGACGTCGTACGGGGACTCGACCACCGACCGGAGTCCCGACTCGGACCACCACGATCCCTGACGCCCGTCCACAAACCCCGGAAATCAGT F2: 3 TCAGT 2 Unidirectional alignment (log-probability: -39.1) TTTCTAGATGgTGACTGGGACcGCAGGGTGGATCCTCTGGtgact-----TGGTGACTTGCCCGGGGCTGCGGGTCAGTGGGAGGCCCTT TTTCTAGATGATGACTGGGACTGCAGGGTGGATCCTCTGG-----AAGGCTGGTGACTTGCCCGGGGCTGCGGGTCAGTGGGAGGCCCTT Template switch alignment (log-probability: -27.4) TTTCTAGATGgTGACTGGGACcGCAGGGTGGATCCTCTGG|TGACT|TGGTGACTTGCCCGGGGCTGCGGGTCAGTGGGAGGCCCTT TTTCTAGATGATGACTGGGACTGCAGGGTGGATCCTCTGG|TGACT|TGGTGACTTGCCCGGGGCTGCGGGTCAGTGGGAGGCCCTT ========== Event 1819 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CCCGGCATGGGCAAGGTCAGCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCAGCCAAC-TGCCCGTGGCCACAGAACAGGGGC ↑ 3 2 1 4 Chimp: CCCGGCATGGGCAAGGTCAGCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCACAGAACAGGGCCGTGGCCACAGAACAGGGGC Gorilla: CCCGGCATGGGCAAGGTCAGCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAGCTGTCAGCCAAC-TGCCCATGGCCACAGAACAGGGGC Human: CCCGGCATGGGCAAGGTCAGCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCAGCCAAC-TGCCCGTGGCCACAGAACAGGGGC Cluster: [ ] Orangutan: CCCGGCGTGGGCAAGGTCAGCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAGCTGTCAGCCAAC-TGCCCGTGGCCACAGAACAGGGGC Chimp > Human ------------- chr2:127105028-127105036 Template switch process: F1: L GCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCA 1 F3: 4 CCGTGGCCACAGAACAGGGGCTCAAGAGAGAGGGATGGTG R RF: GCTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCACAGAACAGGGCCGTGGCCACAGAACAGGGGCTCAAGAGAGAGGGATGGTG RR: CGACAACCGGTTCTGGTCGTACGGATCGACTGGTTGACAGTGTCTTGTCCCGGCACCGGTGTCTTGTCCCCGAGTTCTCTCTCCCTACCAC F2: 3 CGTCAACCG 2 Unidirectional alignment (log-probability: -33.1) CTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCAgccaactgC---------CCGTGGCCACAGAACAGGGGCTCAAGAGAGAGGGATGGTG CTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCA--------CAGAACAGGGCCGTGGCCACAGAACAGGGGCTCAAGAGAGAGGGATGGTG Template switch alignment (log-probability: -22.4) CTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCA|GCCAACtGC|CCGTGGCCACAGAACAGGGGCTCAAGAGAGAGGGATGGTG CTGTTGGCCAAGACCAGCATGCCTAGCTGACCAACTGTCA|GCCAACAGC|CCGTGGCCACAGAACAGGGGCTCAAGAGAGAGGGATGGTG ========== Event 1820 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGCTATGCCTAGTAAACAATAAACAT-----------TCAAAAATGTTTATTGAAAGACATGAATAA------ Chimp: TGCTATGCCTAGTAAACAATAAACAT-----------TCAAAAATGTTTATTGAAAGACATGAATAA------ ↑ 3 1 4 2 Gorilla: TGCTATGCCTAGTAAACAATAAACAT----------------------TTTTGAAAGACATGAATAA------ ↓ 3 1 4 2 Human: TGCTATGCCTAGTAAACAATAAACAT-----------TCAAAAATGTTTATTGAAAGACATGAATAA------ Cluster: [ ] Orangutan: TGCTATGCCTAGTAAACAATAAACATTCAAAAATGTT-----------TATtgaaagacatgaataataaatt Gorilla > Human --------------- chr2:127512847-127512858 Template switch process: F1: L GTTTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATT 1 F3: 4 TTGAAAGACATGAATAATAAATTATCACACATTATATAAA R RF: GTTTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATTTTTGAAAGACATGAATAATAAATTATCACACATTATATAAA RR: CAAAATTCAAACGTAACGATACGGATCATTTGTTATTTGTAAAAACTTTCTGTACTTATTATTTAATAGTGTGTAATATATTT F2: 3 ATTTGTAAAAAC 2 Unidirectional alignment (log-probability: -32.2) TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACAttcaaaaatgtTTaTTGAAAGACATGAATAATAAATTATCACACATTATATAAA TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACA-----------TTTTTGAAAGACATGAATAATAAATTATCACACATTATATAAA Template switch alignment (log-probability: -17.3) TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATT|CAAAAATGTTTA|TTGAAAGACATGAATAATAAATTATCACACATTATATAAA TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATT|CAAAAATGTTTA|TTGAAAGACATGAATAATAAATTATCACACATTATATAAA Gorilla > Chimp --------------- chr2B:14055553-14055564 Template switch process: F1: L GTTTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATT 1 F3: 4 TTGAAAGACATGAATAATAAATTATCACACATTATATAAA R RF: GTTTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATTTTTGAAAGACATGAATAATAAATTATCACACATTATATAAA RR: CAAAATTCAAACGTAACGATACGGATCATTTGTTATTTGTAAAAACTTTCTGTACTTATTATTTAATAGTGTGTAATATATTT F2: 3 ATTTGTAAAAAC 2 Unidirectional alignment (log-probability: -32.2) TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACAttcaaaaatgtTTaTTGAAAGACATGAATAATAAATTATCACACATTATATAAA TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACA-----------TTTTTGAAAGACATGAATAATAAATTATCACACATTATATAAA Template switch alignment (log-probability: -17.3) TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATT|CAAAAATGTTTA|TTGAAAGACATGAATAATAAATTATCACACATTATATAAA TTTAAGTTTGCATTGCTATGCCTAGTAAACAATAAACATT|CAAAAATGTTTA|TTGAAAGACATGAATAATAAATTATCACACATTATATAAA ========== Event 1821 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATAGAACTTACCTGGGAACCAGATTTTAAAAGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAAC Chimp: TGATAGAACTTACCTGGGAACCAGATTTTAAAAGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAAC ↓ 1 4 3 2 Gorilla: TGATAGAACTTACCTGGGAACTCAA-----TGGGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAAC ↑ 1 4 3 2 Human: TGATAGAACTTACCTGGGAACCAGATTTTAAAAGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAAC Cluster: [ ] Orangutan: ---------------------------------------------------------------------- Human > Gorilla --------------- chr2B:15711109-15711114 Template switch process: F1: L AACTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACT 1 F3: 4 GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC R RF: AACTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACCAGATTTTAAAAGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC RR: TTGAAGAGGGAACCTTAATTACTATCTTGAATGGACCCTTGGTCTAAAATTTTCGTGACAAACGGGTAACCCTTCACTTAATCAGTCTTGAAG F2: 3 GGTAAC 2 Unidirectional alignment (log-probability: -31.3) CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAAC------------tcaatggGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACCAGATTTTAAAA-------GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC Template switch alignment (log-probability: -22) CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACt|CAATGG|GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACC|CAATGG|GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC Chimp > Gorilla --------------- chr2B:15711109-15711114 Template switch process: F1: L AACTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACT 1 F3: 4 GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC R RF: GACTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACCAGATTTTAAAAGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC RR: CTGAAGAGGGAACCTTAATTACTATCTTGAATGGACCCTTGGTCTAAAATTTTCGTGACAAACGGGTAACCCTTCACTTAATCAGTCTTGAAG F2: 3 GGTAAC 2 Unidirectional alignment (log-probability: -36.8) CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAAC------------tcaatggGCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACCAGATTTTAAAA-------GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC Template switch alignment (log-probability: -27.5) CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACt|CAATGG|GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC CTTCTCCCTTGGAATTAATGATAGAACTTACCTGGGAACC|CAATGG|GCACTGTTTGCCCATTGGGAAGTGAATTAGTCAGAACTTC ========== Event 1822 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGGCAGCCAACCCTACAGCTGAGGTGGCACTGAGGAGGGAGGATGGTGGTGGGTCACATATGCCACTCACTCACAAATCAGCAGTC ↑ 4 1 3 2 Chimp: CAGGCAGCCAACCCTACAGCT-----------GAGAAGGGAGGATGGTGGTGGGTCACATATGCCACTCACTCACAAATCAGCAGTG Gorilla: CAGGCAGCCAACCCTACAGCTGAGGTGGCACTGAGGAGGGAGGATGGTGGTGGGTCACGTATGCCACTCACTCAAAAATCAGCAGTC Human: CAGGCAGCCAACCCTACAGCTGAGGTGGCACTGAGGAGGGAGGATGGTGGTGGGTCACATATGCCACTCACTCACAAATCAGCAGTC Cluster: [ ] Orangutan: CAGGCAGCCATCCCTACAGCTGAGGTGGCACTGAGGAGGGAGGATGGTGGTGGGTCACATATGCCACTCACTCACAAATCAGCAGTC Chimp > Human ------------- chr2:113990400-113990405 Template switch process: F1: L AGTGAGATGTTCCAAGAGTGCAGGCAGCCAACCCTACAGCTGAG 1 F3: 4 CTGAGGAGGGAGGATGGTGGTGGGTCACATATGCCACTCACTCACA R RF: AGTGAGATGTTCCAAGAGTGCAGGCAGCCAACCCTACAGCTGAGAAGGGAGGATGGTGGTGGGTCACATATGCCACTCACTCACA RR: TCACTCTACAAGGTTCTCACGTCCGTCGGTTGGGATGTCGACTCTTCCCTCCTACCACCACCCAGTGTATACGGTGAGTGAGTGT F2: 3 ACGGTG 2 Unidirectional alignment (log-probability: -32.8) AGATGTTCCAAGAGTGCAGGCAGCCAACCCTACAGctgaggtggcaCTGAGgAGGGAGGATGGTGGTGGGTCACATATGCCACTCA AGATGTTCCAAGAGTGCAGGCAGCCAACCCTACAG-----------CTGAGAAGGGAGGATGGTGGTGGGTCACATATGCCACTCA Template switch alignment (log-probability: -22.2) AGATGTTCCAAGAGTGCAGGCAGCCAACCCTACAGCTGAG|GTGGCA|CTGAGgAGGGAGGATGGTGGTGGGTCACATATGCCACTCA AGATGTTCCAAGAGTGCAGGCAGCCAACCCTACAGCTGAG|GTGGCA|CTGAGAAGGGAGGATGGTGGTGGGTCACATATGCCACTCA ========== Event 1823 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTTAGGTAAATATCCATATTTGCTTTATGT----AAATATCCATAAAGCAAAAACTTCCAAAATTGTTC ↑ 1 4 3 2 Chimp: TTTAGGTAAATATCCATATTTTCTCTCTGTAAATAAATATCCATAAAGCAAAGACTTCCAAAATTGTTC ↓ 1 4 3 2 Gorilla: TTTAGGTAAATATCCATATTTGCTTTATGT----AAATATCCATAAAGCAAAGACTTCCAAAATTGTTC Human: TTTAGGTAAATATCCATATTTGCTTTATGT----AAATATCCATAAAGCAAAAACTTCCAAAATTGTTC Cluster: [ ] Orangutan: TTTATGTAAATATCCATATTTGCTTTATGT----AAATATCCATAAAGCAAAGACTTCCAAAATTGTTC Chimp > Human ------------- chr21:28431027-28431034 Template switch process: F1: L AATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTT 1 F3: 4 TAAATATCCATAAAGCAAAAACTTCCAAAATTGTTCTCAGG R RF: AATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTTTCTCTCTGTAAATAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAGG RR: TTAATCCGGAACCAGGTCGGAAATCCATTTATAGGTATAAAAGAGAGACATTTATTTATAGGTATTTCGTTTCTGAAGGTTTTAACAAGAGTCC F2: 3 GTATTTCG 2 Unidirectional alignment (log-probability: -35.2) ATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTTgCTtTaTG----TAAATATCCATAAAGCAAAaACTTCCAAAATTGTTCTCAG ATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTTTCTCTCTGTAAATAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAG Template switch alignment (log-probability: -22.3) ATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTT|GCTTTATG|TAAATATCCATAAAGCAAAaACTTCCAAAATTGTTCTCAG ATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTT|GCTTTATG|TAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAG Chimp > Gorilla --------------- chr21:19482426-19482433 Template switch process: F1: L AATTAGGCCTTGGTCTAGCCTTTAGGTAAATATCCATATTT 1 F3: 4 TAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAGG R RF: AATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTTTCTCTCTGTAAATAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAGG RR: TTAATCCGGAACCAGGTCGGAAATCCATTTATAGGTATAAAAGAGAGACATTTATTTATAGGTATTTCGTTTCTGAAGGTTTTAACAAGAGTCC F2: 3 GTATTTCG 2 Unidirectional alignment (log-probability: -33.3) ATTAGGCCTTGGTCtAGCCTTTAGGTAAATATCCATATTTgCTtTaTG----TAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAG ATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTTTCTCTCTGTAAATAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAG Template switch alignment (log-probability: -22.3) ATTAGGCCTTGGTCtAGCCTTTAGGTAAATATCCATATTT|GCTTTATG|TAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAG ATTAGGCCTTGGTCCAGCCTTTAGGTAAATATCCATATTT|GCTTTATG|TAAATATCCATAAAGCAAAGACTTCCAAAATTGTTCTCAG ========== Event 1824 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTTTACTTTGAGGTAAAAG---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGA Chimp: ACTTTTACTTTGAGGTAAAAT---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAG--- Gorilla: ACTTTTACTTTGAGGTAAAAGTCCTCACTCCTAGGACTCTAGGAGTGATTAAAATGGTAAAAAGAGA ↑ 3 41 2 Human: ACTTTTACTTTGAGGTAAAAG---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGA Cluster: [ ] Orangutan: ACTTTTACTTTGAGGTAAAAG---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGA Human > Gorilla --------------- chr21:19504797-19504809 Template switch process: F1: L CAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGT------CCT 1 F3: 4 CTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAAT R RF: CAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGTTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAAT RR: GTTCCTGCATTCAAATCTACTGAAAATGAAACTCCATTTTCAACCTCAGGATCCTCACTAATTTTACCATTTTTCTCTTCCTCCGTTTA F2: 3 TCAGGATCCTCAC 2 Unidirectional alignment (log-probability: -42.5) ACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGTcctcactcctaggacT------CTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAAT ACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGT---------------TGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAAT Template switch alignment (log-probability: -27.5) ACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGT------CCT|CACTCCTAGGACT|CTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAAT ACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGTTGGAGTCCT|CACTCCTAGGACT|CTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAAT ========== Event 1825 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GATTTGCACTGCTCAGTTTGAGGTAGAACAGGTAGCTGGAAAAGGAGAATGGGAGCTTTGCAGGGAGAGATGGCCAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAG---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAAATCAAG Chimp: GATTTGCACTGCTCAGTTTGAGGTAGAACAGGCAGCTGGAAAAGGAGAATGGGATCTTTGCAGGGAGAGATGGCCAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAT---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAG---AGGAGGCAAATTAAATCAAG ↑ 1 3 4 Gorilla: GATTTGCACTGCTCAGTTTGAGGTAGAACAGGTAGCTGGAAAAGGAGAATGGGAGCTTTGCAGGGAGAGATGGCCAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGTCCTCACTCCTAGGACTCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAAATCAAG Human: GATTTGCACTGCTCAGTTTGAGGTAGAACAGGTAGCTGGAAAAGGAGAATGGGAGCTTTGCAGGGAGAGATGGCCAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAG---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAAATCAAG Cluster: [ ] Orangutan: GGTTTGCACTGCTCAGTTTGAGGTAGAACAGGTAGCTGGAAAAGGAGAATGGGAGCTTTGCAGGGAGAGATGGCCAAGGACATAAGTTTAGATGACTTTTACTTTGAGGTAAAAG---------TTGGAGTCCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAAACCAAG Gorilla > Chimp --------------- chr21:14841820-14841824 Template switch process: F1: L TTG 1 F3: 4 CTAGGAGTGATTAAAATGGTAAAAAG---AGGAGGCAAATTAAATCAAGTACTGATAGTTGTGGATCAA R RF: TTGAGGTAGAACAGGTAGCTGGAAAAGGAGAATGGGAGCTTTGCAGGGAGAGATGGCCAAGGACGTAAGTTTAGATGACTTTTACTTTGAGGTAAAAGTCCTCACTCCTAGGACTCTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAAATCAAGTACTGATAGTTGTGGATCAA RR: AACTCCATCTTGTCCATCGACCTTTTCCTCTTACCCTCGAAACGTCCCTCTCTACCGGTTCCTGCATTCAAATCTACTGAAAATGAAACTCCATTTTCAGGAGTGAGGATCCTGAGATCCTCACTAATTTTACCATTTTTCTCTTCCTCCGTTTAATTTAGTTCATGACTATCAACACCTAGTT F2: 3 CTGAG 2 Unidirectional alignment (log-probability: -35.7) TtggagtcCTAGGAGTGATTAAAATGGTAAAAAG---AGGAGGCAAATTAA T-------CTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAA Template switch alignment (log-probability: -25.9) TTG|GAGTC|CTAGGAGTGATTAAAATGGTAAAAAG---AGGAGGCAAATTAA TTG|GAGTC|CTAGGAGTGATTAAAATGGTAAAAAGAGAAGGAGGCAAATTAA ========== Event 1826 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ----ACACTTACGTCACAAAG-------CTATATATGTTCTAAGAACAGGGTCCACACA Chimp: ----ACACTTATGTCACAAAG-------CTATATATGTTCTAAGAACAGGGTCCACACA ↓ 13 4 2 Gorilla: ----ACACTTACGTCACAAAGAACATATATAGATATGTTCTAAGAACAGGGTCCACACA ↑ 13 4 2 Human: ----ACACTTACGTCACAAAG-------CTATATATGTTCTAAGAACAGGGTCCACACA Cluster: [ ] Orangutan: GCATACACTTATGTCACAAAG-------CTATATATGTTCTAAGAACAGGGTCCACACA Human > Gorilla --------------- chr21:19904038-19904048 Template switch process: F1: L TATGTTAAATCTTT---CTGTTTAACACTTACGTCACAAAG 1 F3: 4 ATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT R RF: TATGTTAAATCTTTCTACTGTTTAACACTTACGTCACAAAGCTATATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT RR: ATACAATTTAGAAAGATGACAAATTGTGAATGCAGTGTTTCGATATATACAAGATTCTTGTCCCAGGTGTGTCAGGTGACAAGTA F2: 3 GATATATACAA 2 Unidirectional alignment (log-probability: -41.9) TATGTTAAATCTTTC---TGTTTAACACTTACGTCACAAAGaacatataTAgATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT TATGTTAAATCTTTCTACTGTTTAACACTTACGTCACAAAG-------CTATATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT Template switch alignment (log-probability: -26.9) TATGTTAAATCTTT---CTGTTTAACACTTACGTCACAAAG|AACATATATAG|ATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT TATGTTAAATCTTTCTACTGTTTAACACTTACGTCACAAAG|AACATATATAG|ATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT Chimp > Gorilla --------------- chr21:19904038-19904048 Template switch process: F1: L CTCTATGTTAAATCTTTCTGTTTAACACTTACGTCACAAAG 1 F3: 4 ATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT R RF: CTCTATGTTAAATCTTTCTGTTTAACACTTATGTCACAAAGCTATATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT RR: GAGATACAATTTAGAAAGACAAATTGTGAATACAGTGTTTCGATATATACAAGATTCTTGTCCCAGGTGTGTCAGGTGACAAGTA F2: 3 GATATATACAA 2 Unidirectional alignment (log-probability: -37.6) TCTATGTTAAATCTTTCTGTTTAACACTTAcGTCACAAAGaacatataTAgATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT TCTATGTTAAATCTTTCTGTTTAACACTTATGTCACAAAGC-------TATATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT Template switch alignment (log-probability: -22.6) TCTATGTTAAATCTTTCTGTTTAACACTTAcGTCACAAAG|AACATATATAG|ATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT TCTATGTTAAATCTTTCTGTTTAACACTTATGTCACAAAG|AACATATATAG|ATATGTTCTAAGAACAGGGTCCACACAGTCCACTGTTCAT ========== Event 1827 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: aaaTTTTTTATATAGTATTTCTGAAAGATGAAAACTG---CGACAAAATATAAAGATTACAGGGACAAAT ↓ 3 2 1 4 Chimp: aaaTTTTTTATATAGTATTTCTGAAAGATGAAAACTTTCAGAACAAAATGTAAAGATTACAGGGACAAAT Gorilla: Human: aaaTTTTTTATATAGTATTTCTGAAAGATGAAAACTG---CGACAAAATATAAAGATTACAGGGACAAAT Cluster: [ ] Orangutan: aGATTTTTTATATCGTATTTCTGAAAGATGAAAACTG---TGACAAAATATGAAGATTACAGGGACAAAT Human > Chimp ------------- chr21:18096775-18096780 Template switch process: F1: L AGTTAAAATTTTTTATATAGTATTTCTGAAAGATGAAAACT 1 F3: 4 ACAAAATGTAAAGATTACAGGGACAAATGACAAAATGGGAGATGACAT R RF: AGTTAAAATTTTTTATATAGTATTTCTGAAAGATGAAAACTGCGACAAAATATAAAGATTACAGGGACAAATGACAAAATGGGAGATGACAT RR: TCAATTTTAAAAAATATATCATAAAGACTTTCTACTTTTGACGCTGTTTTATATTTCTAATGTCCCTGTTTACTGTTTTACCCTCTACTGTA F2: 3 AGACTT 2 Unidirectional alignment (log-probability: -36) GTTAAAATTTTTTATATAGTATTTCTGAAAGATGAAAACTttcaga---ACAAAATgTAAAGATTACAGGGACAAATGACAAAATGGGA GTTAAAATTTTTTATATAGTATTTCTGAAAGATGAAAACT------GCGACAAAATATAAAGATTACAGGGACAAATGACAAAATGGGA Template switch alignment (log-probability: -22.2) GTTAAAATTTTTTATATAGTATTTCTGAAAGATGAAAACT|TTCAGA|ACAAAATgTAAAGATTACAGGGACAAATGACAAAATGGGA GTTAAAATTTTTTATATAGTATTTCTGAAAGATGAAAACT|TTCAGA|ACAAAATATAAAGATTACAGGGACAAATGACAAAATGGGA ========== Event 1828 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATCTTATCAAGCCTCAATCAGTAATTCATTTACTGTA-TCTTAATATGTAATTTATAACTAA Chimp: TGATCTTATCAAGCCTCCATCAGTAATTCATTTACTGTA-TCTTAATATGTAATTTATAACTAA ↓ 3 2 1 4 Gorilla: TGATCTTATCAAGCCTCAATCAGTAATTCATTTATATTACTGATAATATGTAATTTATAACTAA ↑ 3 2 1 4 Human: TGATCTTATCAAGCCTCAATCAGTAATTCATTTACTGTA-TCTTAATATGTAATTTATAACTAA Cluster: [ ] Orangutan: TGATCTTACCAAGCCTCAATCAATAATTTATTTACTATA-GCTTAATATGTAATTTATAACTAA Human > Gorilla --------------- chr21:20316176-20316183 Template switch process: F1: L CTGCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTAT 1 F3: 4 TAATATGTAATTTATAACTAATATATAACATCAATGTATA R RF: CTGCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTACTGTATCTTAATATGTAATTTATAACTAATATATAACATCAATGTATA RR: GACGTTGACTAGAATAGTTCGGAGTTAGTCATTAAGTAAATGACATAGAATTATACATTAAATATTGATTATATATTGTAGTTACATAT F2: 3 AGTCATTA 2 Unidirectional alignment (log-probability: -32.5) GCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTA-------TattactgaTAATATGTAATTTATAACTAATATATAACATCAATGTATA GCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTACTGTATCT--------TAATATGTAATTTATAACTAATATATAACATCAATGTATA Template switch alignment (log-probability: -22.3) GCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTAt|ATTACTGA|TAATATGTAATTTATAACTAATATATAACATCAATGTATA GCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTAC|ATTACTGA|TAATATGTAATTTATAACTAATATATAACATCAATGTATA Chimp > Gorilla --------------- chr21:20316176-20316183 Template switch process: F1: L CTGCAACTGATCTTATCAAGCCTCAATCAGTAATTCATTTAT 1 F3: 4 TAATATGTAATTTATAACTAATATATAACATCAATGTATA R RF: CTGCAACTGATCTTATCAAGCCTCCATCAGTAATTCATTTACTGTATCTTAATATGTAATTTATAACTAATATATAACATCAATGTATA RR: GACGTTGACTAGAATAGTTCGGAGGTAGTCATTAAGTAAATGACATAGAATTATACATTAAATATTGATTATATATTGTAGTTACATAT F2: 3 AGTCATTA 2 Unidirectional alignment (log-probability: -38) GCAACTGATCTTATCAAGCCTCaATCAGTAATTCATTTA-------TattactgaTAATATGTAATTTATAACTAATATATAACATCAATGTATA GCAACTGATCTTATCAAGCCTCCATCAGTAATTCATTTACTGTATCT--------TAATATGTAATTTATAACTAATATATAACATCAATGTATA Template switch alignment (log-probability: -27.8) GCAACTGATCTTATCAAGCCTCaATCAGTAATTCATTTAt|ATTACTGA|TAATATGTAATTTATAACTAATATATAACATCAATGTATA GCAACTGATCTTATCAAGCCTCCATCAGTAATTCATTTAC|ATTACTGA|TAATATGTAATTTATAACTAATATATAACATCAATGTATA ========== Event 1829 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAGGTTGGGTCCACCTGTGT-----CCAATATGCACATTTGTTCTGTTGTTGG Chimp: TCAAGGTTGGGTCCACCTGTGT-----CCAATATGCACATTTGTTCTGTTGTTGG ↓ 3 4 2 Gorilla: TCAAGGTTGGGTCCACCTGTGCATATTGGACTATGCACATTTGTTCTGTTGTTGG ↑ 3 4 2 Human: TCAAGGTTGGGTCCACCTGTGT-----CCAATATGCACATTTGTTCTGTTGTTGG Cluster: [ ] Orangutan: tcaaggttgggtccacctgtgt-----ccaatatgcacacttgttctgttgTTGG Human > Gorilla --------------- chr2B:18778839-18778848 Template switch process: F1: L GCAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG 1 F3: 4 TATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT R RF: GCAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTGTCCAATATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT RR: CGTTCACCACGTCGATCGTGAGTTCCAACCCAGGTGGACACAGGTTATACGTGTAAACAAGACAACAACCCGACGTGTGTTGTCTA F2: 3 CAGGTTATAC 2 Unidirectional alignment (log-probability: -34.7) CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTGcatatTggAcTATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG-----TCCAATATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT Template switch alignment (log-probability: -17) CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG|CATATTGGAC|TATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG|CATATTGGAC|TATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT Chimp > Gorilla --------------- chr2B:18778839-18778848 Template switch process: F1: L GCAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG 1 F3: 4 TATGCACATTTGTTCTGTTGTTGGGCTGCACACAACAGAT R RF: GCAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTGTCCAATATGCACATTTGTTCTGTTGTTGGGCTGCATACAACAGAT RR: CGTTCACCACGTCGATCGTGAGTTCCAACCCAGGTGGACACAGGTTATACGTGTAAACAAGACAACAACCCGACGTATGTTGTCTA F2: 3 CAGGTTATAC 2 Unidirectional alignment (log-probability: -40.2) CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTGcatatTggAcTATGCACATTTGTTCTGTTGTTGGGCTGCAcACAACAGAT CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG-----TCCAATATGCACATTTGTTCTGTTGTTGGGCTGCATACAACAGAT Template switch alignment (log-probability: -22.5) CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG|CATATTGGAC|TATGCACATTTGTTCTGTTGTTGGGCTGCAcACAACAGAT CAAGTGGTGCAGCTAGCACTCAAGGTTGGGTCCACCTGTG|CATATTGGAC|TATGCACATTTGTTCTGTTGTTGGGCTGCATACAACAGAT ========== Event 1830 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGCTGTTTGAAACACATATGGCATTTATTCTATTCAGGGTACTGCTTAATTCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACC------------------------------TAGACCATATTTTCAAGTCTCTAC Chimp: CAGCTGTTTGAAACACATATGGCATTTATTCTATTCAGGGTACTGCTTAATTCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACC------------------------------TAGACCATATTTTCAAGTCTCTAC ↓ 3 2 4 1 Gorilla: CAGCTGTTTGAAACACATATGGCATTTATTCTATTCAGGGTACTGCTTAATTCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGATGCCATGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTCTCTAC ↑ 3 2 4 1 Human: CAGCTGTTTGAAACACATATGGCATTTATTCTATTCAGGGTACTGCTTAATTCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACC------------------------------TAGACCATATTTTCAAGTCTCTAC Cluster: [ ] Orangutan: CAGCTGTTTGAAACACATATGGCATTTATTCTATTCAGGGTACAGCTTACTTCATAGTGTGACATGTGGTTTGTTTGACAAATATCTAGACCTAGATGCCATGTTTGACAAATATCTAGACCTAGACCATATTTTCATGTCTCTAC Human > Gorilla --------------- chr21:21133814-21133818 Template switch process: F1: L TCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGA 1 F3: 4 TGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTCTCTACATCTTTGGAGGCATTT R RF: TGGCATTTATTCTATTCAGGGTACTGCTTAATTCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTCTCTACATCTTTGGAGGCATTT RR: ACCGTAAATAAGATAAGTCCCATGACGAATTAAGTATCACACTGTGCACCAAACAAACTGTTTATAGATCTGGATCTGGTATAAAAGTTCAGAGATGTAGAAACCTCCGTAAA F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -54) GTGTGACACGTGGTTTGTTTGACAAATATCTAGAcctagatgccatgtttgacaaatatctagaCCTAGACCATATTTTCAAGTC GTGTGACACGTGGTTTGTTTGACAAATATCTAGA------------------------------CCTAGACCATATTTTCAAGTC Template switch alignment (log-probability: -17) GTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGA|TGCCA|TGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTC GTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGA|TGCCA|TGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTC Chimp > Gorilla --------------- chr21:21133814-21133818 Template switch process: F1: L TCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGA 1 F3: 4 TGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTCTCTACATCTTTGGAGGCATTT R RF: TGGCATTTATTCTATTCAGGGTACTGCTTAATTCATAGTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTCTCTACATCTTTGGAGGCATTT RR: ACCGTAAATAAGATAAGTCCCATGACGAATTAAGTATCACACTGTGCACCAAACAAACTGTTTATAGATCTGGATCTGGTATAAAAGTTCAGAGATGTAGAAACCTCCGTAAA F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -54) GTGTGACACGTGGTTTGTTTGACAAATATCTAGAcctagatgccatgtttgacaaatatctagaCCTAGACCATATTTTCAAGTC GTGTGACACGTGGTTTGTTTGACAAATATCTAGA------------------------------CCTAGACCATATTTTCAAGTC Template switch alignment (log-probability: -17) GTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGA|TGCCA|TGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTC GTGTGACACGTGGTTTGTTTGACAAATATCTAGACCTAGA|TGCCA|TGTTTGACAAATATCTAGACCTAGACCATATTTTCAAGTC ========== Event 1831 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTGTGCAGTCACTTTGGCAGAGTTTCATAAATAAAGCAGATAGCATAAGATGGTGCTGGCTTATGGAAACCTA ↓ 1 3 4 2 Chimp: TATTGTGCAGTCACTTTGGCA---TCTTA--------------TGCTTAAGATGATGCTGGCTTATGGAAACCTA Gorilla: TACTGTGCAGTCACTTTGGCAGAGTTTCATAAATAAAGCAGATAGCATAAGATGGTGCTGGCTTATGGAAACCTA Human: TATTGTGCAGTCACTTTGGCAGAGTTTCATAAATAAAGCAGATAGCATAAGATGGTGCTGGCTTATGGAAACCTA Cluster: [ ] Orangutan: Human > Chimp ------------- chr2B:16426171-16426179 Template switch process: F1: L ACCACACATTAGCCTTACTATATTGTGCAGTCACTTTGGCA 1 F3: 4 TAAGATGATGCTGGCTTATGGAAACCTAATCAGAACATCTCAGCCTGG R RF: ACCACACATTAGCCTTACTATATTGTGCAGTCACTTTGGCAGAGTTTCATAAATAAAGCAGATAGCATAAGATGGTGCTGGCTTATGGAAACCTAATCAGAACATCTCAGTCTGG RR: TGGTGTGTAATCGGAATGATATAACACGTCAGTGAAACCGTCTCAAAGTATTTATTTCGTCTATCGTATTCTACCACGACCGAATACCTTTGGATTAGTCTTGTAGAGTCAGACC F2: 3 TCGTATTCT 2 Unidirectional alignment (log-probability: -47.5) CCACACATTAGCCTTACTATATTGTGCAGTCACTTTGGCAtcttatgct--------------------------TAAGATGaTGCTGGCTTATGGAAACCTAATCAGAACATCT CCACACATTAGCCTTACTATATTGTGCAGTCACTTTGGCA---------GAGTTTCATAAATAAAGCAGATAGCATAAGATGGTGCTGGCTTATGGAAACCTAATCAGAACATCT Template switch alignment (log-probability: -28.5) CCACACATTAGCCTTACTATATTGTGCAGTCACTTTGGCA|TCTTATGCT|TAAGATGaTGCTGGCTTATGGAAACCTAATCAGAACATCT CCACACATTAGCCTTACTATATTGTGCAGTCACTTTGGCA|TCTTATGCT|TAAGATGGTGCTGGCTTATGGAAACCTAATCAGAACATCT ========== Event 1832 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTAATGTTCACATTTAAATGCATATATAATTTATAAGAGTAGA----------TTATATGCaa-aaaatatttaatcattat Chimp: TTTAATGTTCACATTTAAATGCatatataatttataagagtaga-----ttatattatatgcaa-aaaatatttaatcattat Gorilla: TTTAATGTTCACATTTAAATGCATATATAATTTATAAGAGTAGATTATA-----TTATATGCaaaaaaaTATTTAATCATTAT ↑ 3 2 1 4 Human: TTTAATGTTCACATTTAAATGCATATATAATTTATAAGAGTAGA----------TTATATGCaa-aaaatatttaatcattat Cluster: [ ] Orangutan: TTTTATGTTTACATTTAAATGCATATATAGTTTA--TGAGTAGATTATA-----TTATATGCAA-AAAATATTTAATAGTTAT Human > Gorilla --------------- chr21:21785831-21785838 Template switch process: F1: L AATGTTCACATTTAAATGCATATATAATTTATAAGAGTAGATTATAT 1 F3: 4 AAAAAATATTTAATCATTATAGATTTATGTA R RF: AATGTTCACATTTAAATGCATATATAATTTATAAGAGTAGATTATATGCAAAAAATATTTAATCATTATAGATTTATGTA RR: TTACAAGTGTAAATTTACGTATATATTAAATATTCTCATCTAATATACGTTTTTTATAAATTAGTAATATCTAAATACAT F2: 3 ACGTATAT 2 Unidirectional alignment (log-probability: -29.2) ACATTTAAATGCATATATAATTTATAAGAGTAGattatATTATATGCaAAAAAATATTTAATCATTATAGATTTATGTA ACATTTAAATGCATATATAATTTATAAGAGTAG-----ATTATATGC-AAAAAATATTTAATCATTATAGATTTATGTA Template switch alignment (log-probability: -16.7) ACATTTAAATGCATATATAATTTATAAGAGTAGATTATAT|TATATGCA|AAAAAATATTTAATCATTATAGATTTATGTA ACATTTAAATGCATATATAATTTATAAGAGTAGATTATAT|TATATGCA|AAAAAATATTTAATCATTATAGATTTATGTA ========== Event 1833 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: tgttagccaagatggtctcgatct----gctgacttcgtgatctgcccgtctcggcctcccaaagtgctgggattacaggcgtgagccaccgtgcccagccTTTTCAAGAGAACAGAACTACACTCACATACTGCATTTGATTTAGAAAGAAAAA---GAAGACCATCTCAAAGAATACACAACTA Chimp: tgttagccaggatggtctcgatct----gctgacttcgtgatctgcccgtctcggcctcccaaagtgctgggattacaggcgtgagccaccgcgaccggccTTTTCAAGAGAACAGAACTACACTCACATACTGCATTTGATTTAGAAAGAAAAA---GAAGATCATCTCAAAGAAGACACAACTA ↑ 3 2 1 4 Gorilla: tgttagccaagatggtctcgatctgcttgctgacttagtgatccgcccgtctcggcctcccaaagtgctgggattacaggcgtgagccaccgctccccgccTTTTCAAGAGAACAGAACTACACTCACATACTGCATTTGATTTAGAAAGAAAAA------GACTATCTCAAAGAAGACACAACTA Human: tgttagccaagatggtctcgatct----gctgacttcgtgatctgcccgtctcggcctcccaaagtgctgggattacaggcgtgagccaccgtgcccagccTTTTCAAGAGAACAGAACTACACTCACATACTGCATTTGATTTAGAAAGAAAAA---GAAGACCATCTCAAAGAATACACAACTA Cluster: [ ] Orangutan: tgttagccaggatggtctcgatct----gctgacctcgtgatccgcccgtcttggcctcccaaagtgctgggattacaggcgtgagccaccacgcccggccTTTTCAAGAGAAGAGAACTACAGCCACATACTGCATTTGATCTAGAAAGAAAAAGAA---AACCATCTCAAAGAAGACACAACAA Gorilla > Chimp --------------- chr21:17139025-17139029 Template switch process: F1: L AGAACTACACTCACATACTGCATTTGATTTAGAAAGAAAAAGA 1 F3: 4 ATCTCAAAGAAGACACAACTATGCCCCTACAGGTCATAGA R RF: GATCTGCTTGCTGACTTAGTGATCCGCCCGTCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCTCCCCGCCTTTTCAAGAGAACAGAACTACACTCACATACTGCATTTGATTTAGAAAGAAAAAGACTATCTCAAAGAAGACACAACTATGCCCCTACAGGTCATAGA RR: CTAGACGAACGACTGAATCACTAGGCGGGCAGAGCCGGAGGGTTTCACGACCCTAATGTCCGCACTCGGTGGCGAGGGGCGGAAAAGTTCTCTTGTCTTGATGTGAGTGTATGACGTAAACTAAATCTTTCTTTTTCTGATAGAGTTTCTTCTGTGTTGATACGGGGATGTCCAGTATCT F2: 3 CTAGA 2 Unidirectional alignment (log-probability: -26.3) ACTACACTCACATACTGCATTTGATTTAGAAAGAAAAAGAagatcATCTCAAAGAAGACACAACTATGCCCCTACAGGTCATAGA ACTACACTCACATACTGCATTTGATTTAGAAAGAAAAAGACT---ATCTCAAAGAAGACACAACTATGCCCCTACAGGTCATAGA Template switch alignment (log-probability: -16.4) ACTACACTCACATACTGCATTTGATTTAGAAAGAAAAAGA|AGATC|ATCTCAAAGAAGACACAACTATGCCCCTACAGGTCATAGA ACTACACTCACATACTGCATTTGATTTAGAAAGAAAAAGA|AGATC|ATCTCAAAGAAGACACAACTATGCCCCTACAGGTCATAGA ========== Event 1834 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: --------------------TTTAATAGCAGTTTAACCTGTATCCAAACTAGTACCCTCAGTTTTCTATATCTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTAAGTATCTCTCTTTTTCTTCTGCCAAATGTGGCA-------------------GAGAAGATATAGAAAATTGAGGATACTAGTTTGGATGTGGGTTAAGCTGCCATTACTAATTCTTGCCAAATTCTCCA Chimp: TGGAGAATTTGGCAAGAATTAGTAATGGCAGCTTAACCCACATCCAAACTAGTATCCTCAATTTTCTGTATCTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCTGCCACATTTGGCAGAAGAAAAAGAGATACTTAGAAAAGATATAGAAAACTGAGGGTACTAGTTTGGATACAGGTTAAACTGCTATTAAAAAA----------------- ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: --------------------tttaatagCAGTTTAACCTGTATCCAAACTAGTACCCTCAGTTTTCTATATCTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTAAGTATC--TCTTTTTCTTCTGCCAAATGTGGCA-------------------GAGAAGATATAGAAAATTGAGGATACTAGTTTGGATGTGGGTTAAGCTGCCATTACTAATTCTTGCCAAATTCTCCA Human: --------------------TTTAATAGCAGTTTAACCTGTATCCAAACTAGTACCCTCAGTTTTCTATATCTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTAAGTATCTCTCTTTTTCTTCTGCCAAATGTGGCA-------------------GAGAAGATATAGAAAATTGAGGATACTAGTTTGGATGTGGGTTAAGCTGCCATTACTAATTCTTGCCAAATTCTCCA Cluster: [ ] Orangutan: --------------------TTTAATAGCAGTTTAACCTGTATCCAAACCAGTACCCTCAGttttcttttttttttttttttttctgagacggagtctccctctgttgcccaggctggagtgcagtggcgcgatcttggctcactgcaagctccgcctcctgggttcacgccattctcctgcctcagcctcccgagtagctgggactacacgcacccgccaccacgcccggctaattttttgtatttttagtagagacggggtttcaccatgttagccaggatggtctcgatctcctgacctcgtgatccactcaccttggcctcccaaagtgctgggattacaggcatgagccaccgcgcccggccCTCAGTTTTCTATATATTTTCTAAGTATC--TCTTTTTCTTCTGCCAAATGTGGCA-------------------GAGAAGATATAGAAAATTGAGGATACTAGTTTGGATGTGGGTTAAGCTGCCATTACTAATTCTTGCCAAATTCTCCA Gorilla > Chimp --------------- chr21:15443924-15444059 Template switch process: F1: L 1 F3: 4 GGTT R RF: TGTATCCAAACTAGTACCCTCAGTTTTCTATATCTTTTCTAAGTATCTCTTTTTCTTCTGCCAAATGTGGCAGAGAAGATATAGAAAATTGAGGATACTAGTTTGGATGTGGGTTAAGCTGCCATTACTAATTCTAAGCTGCCATTACTAATTCTT RR: ACATAGGTTTGATCATGGGAGTCAAAAGATATAGAAAAGATTCATAGAGAAAAAGAAGACGGTTTACACCGTCTCTTCTATATCTTTTAACTCCTATGATCAAACCTACACCCAATTCGACGGTAATGATTAAGATTCGACGGTAATGATTAAGAA F2: 3 ACATAGGTTTGATCATGGGAGTCAAAAGATATAGAAAAGATTCATAGAGAAAAAGAAGACGGTTTACACCGTCTCTTCTATGTCTTTTAACTCCTATGATCAAACCTACACCCAATTCGACGGTAATGATTAAGAA 2 Unidirectional alignment (log-probability: -167) aagaaTTagTAATgGCAGcTTAACCcacATCCAAACTAGTAtCCTCAaTTTTCTgTATCTT-------------------cTCTGCCAcATtTGGCAGAagaaaaagagatacttagaaAAGATATAGAAAAcTGAGGgTACTAGTTTGGATacaGGTT -----TT--TAATAGCAGTTTAACCTGTATCCAAACTAGTACCCTCAGTTTTCTATATCTTTTCTAAGTATCTCTTTTTCTTCTGCCAAATGTGGCAGA-------------------GAAGATATAGAAAATTGAGGATACTAGTTTGGATGTGGGTT Template switch alignment (log-probability: -36.6) |AAGAATTAGTAATGGCAGCTTAACCCACATCCAAACTAGTATCCTCAATTTTCTgTATCTTCTCTGCCACATTTGGCAGAAGAAAAAGAGATACTTAGAAAAGATATAGAAAACTGAGGGTACTAGTTTGGATACA|GGTT |AAGAATTAGTAATGGCAGCTTAACCCACATCCAAACTAGTATCCTCAATTTTCTATATCTTCTCTGCCACATTTGGCAGAAGAAAAAGAGATACTTAGAAAAGATATAGAAAACTGAGGGTACTAGTTTGGATACA|GGTT Chimp > Gorilla --------------- chr21:15214143-15214270 Template switch process: F1: L T 1 F3: 4 GGTT R RF: TGGGGTGAGAAAAACTAGGTACCAATAATAAAGCAGGTGTAGTTGGCCATATGGAAAATAGTGTTCAGATGAGTTTTATAATTCAGTTGGAGAATTTGGCAAGAATTAGTAATGGCAGCTTAACCCACATCCAAACTAGTATCCTCAATTTTCTGTATCTTCTCTGCCACATTTGGCAGAAGAAAAAGAGATACTTAGAAAAGATATAGAAAACTGAGGGTACTAGTTTGGATACAGGTTAAACTGCTATTAA RR: ACCCCACTCTTTTTGATCCATGGTTATTATTTCGTCCACATCAACCGGTATACCTTTTATCACAAGTCTACTCAAAATATTAAGTCAACCTCTTAAACCGTTCTTAATCATTACCGTCGAATTGGGTGTAGGTTTGATCATAGGAGTTAAAAGACATAGAAGAGACGGTGTAAACCGTCTTCTTTTTCTCTATGAATCTTTTCTATATCTTTTGACTCCCATGATCAAACCTATGTCCAATTTGACGATAATT F2: 3 GTGTAGGTTTGATCATAGGAGTTAAAAGATATAGAAGAGACGGTGTAAACCGTCTTCTTTTTCTCTATGAATCTTTTCTATATCTTTTGACTCCCATGATCAAACCTATGTCCAATTTGACGATAATT 2 Unidirectional alignment (log-probability: -158) TT--TAATaGCAGtTTAACCtgtATCCAAACTAGTAcCCTCAgTTTTCTaTATCTTttctaagtatctctttttctTCTGCCAaATgTGGC-------------------AGAgAAGATATAGAAAAtTGAGGaTACTAGTTTGGATgtgGGTT TTAGTAATGGCAGCTTAACCCACATCCAAACTAGTATCCTCAATTTTCTGTATCTT-------------------CTCTGCCACATTTGGCAGAAGAAAAAGAGATACTTAGAAAAGATATAGAAAACTGAGGGTACTAGTTTGGATACAGGTT Template switch alignment (log-probability: -35.7) T|TTAATAGCAGTTTAACCTGTATCCAAACTAGTACCCTCAGTTTTCTATATCTTTTCTAAGTATCTCTTTTTCTTCTGCCAAATGTGGCAGAGAAGATAtAGAAAATTGAGGATACTAGTTTGGATGTG|GGTT T|TTAATAGCAGTTTAACCTGTATCCAAACTAGTACCCTCAGTTTTCTATATCTTTTCTAAGTATCTCTTTTTCTTCTGCCAAATGTGGCAGAGAAGATACAGAAAATTGAGGATACTAGTTTGGATGTG|GGTT ========== Event 1835 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATGGGCTTTCTTTCTGACAGAAG----------ATCTACAGACCAATGTTTGAGAAGCACAAAAAGCACC Chimp: CATGGGCTTTCTTTCTGACAGCAG----------ATCTACAGACCAATGTTTGAGAAGCACAAAAAGCACC ↓ 1 3 4 2 Gorilla: CATGGGCTTTCTTTCTGACAGAAGAAACATTGGTCTGTAGAGACCAATGTTTGAGAAGCACAAAAAGCACC ↑ 1 3 4 2 Human: CATGGGCTTTCTTTCTGACAGAAG----------ATCTACAGACCAATGTTTGAGAAGCACAAAAAGCACC Cluster: [ ] Orangutan: CCTGGGCTTTCTTTCTGACAGAAG----------ATCTACAGGCCAATGTTTGAGAAGCACAAAAAGCACC Human > Gorilla --------------- chr21:14967531-14967545 Template switch process: F1: L CATTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGA 1 F3: 4 AGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA R RF: CATTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGATCTACAGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA RR: GTAACTCCATATAAAGAGTACCCGAAAGAAAGACTGTCTTCTAGATGTCTGGTTACAAACTCTTCGTGTTTTTCGTGGTACCAAACT F2: 3 GATGTCTGGTTACAA 2 Unidirectional alignment (log-probability: -36.4) TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGAaacattggtcTgTAgAGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGA----------TCTACAGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA Template switch alignment (log-probability: -17.7) TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGA|AACATTGGTCTGTAG|AGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGA|AACATTGGTCTGTAG|AGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA Chimp > Gorilla --------------- chr21:14967531-14967545 Template switch process: F1: L TATCATTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGAAGA 1 F3: 4 AGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA R RF: TATCATTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGCAGATCTACAGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA RR: ATAGTAACTCCATATAAAGAGTACCCGAAAGAAAGACTGTCGTCTAGATGTCTGGTTACAAACTCTTCGTGTTTTTCGTGGTACCAAACT F2: 3 GATGTCTGGTTACAA 2 Unidirectional alignment (log-probability: -41.9) TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGaAGAaacattggtcTgTAgAGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGCAGA----------TCTACAGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA Template switch alignment (log-probability: -23.3) TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGaAGA|AACATTGGTCTGTAG|AGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA TTGAGGTATATTTCTCATGGGCTTTCTTTCTGACAGCAGA|AACATTGGTCTGTAG|AGACCAATGTTTGAGAAGCACAAAAAGCACCATGGTTTGA ========== Event 1836 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTAGGGAAAGAACATTCATTGAATAACAC-----------AAGTAAGGTAACTCTACAGTTTATG Chimp: CTGTAGGGAAAGAACATTCGTTGAATAACAC-GCATGTTATTCAACAAGGTAACTCTACAGTTTATG ↑ 3 2 1 4 Gorilla: CTGTAGGGAAAGAACATTCGTTGAATAACACA----------CAGTAAGGTAACTCTACAGTTTGTG Human: CTGTAGGGAAAGAACATTCATTGAATAACAC-----------AAGTAAGGTAACTCTACAGTTTATG Cluster: [ ] Orangutan: CTATAGGGAAAGAACATTTGTTGAATAACACA----------CAATAAGGTAACTCTACAGTTTATG Gorilla > Chimp --------------- chr21:14930037-14930047 Template switch process: F1: L CAAGGTAGAACTGTAGGGAAAGAACATTCGTTGAATAACACGCA 1 F3: 4 AAGGTAACTCTACAGTTTATGGTAAAAACTGGCTTCAAAG R RF: CAAGGTAGAACTGTAGGGAAAGAACATTCGTTGAATAACACACAGTAAGGTAACTCTACAGTTTGTGGTAAAAACTGGCTTCAAAG RR: GTTCCATCTTGACATCCCTTTCTTGTAAGCAACTTATTGTGTGTCATTCCATTGAGATGTCAAACACCATTTTTGACCGAAGTTTC F2: 3 CAACTTATTGT 2 Unidirectional alignment (log-probability: -43.6) GTAGAACTGTAGGGAAAGAACATTCGTTGAATAACACgcatgttattcaAC---AAGGTAACTCTACAGTTTaTGGTAAAAACTGGCTTCAAAG GTAGAACTGTAGGGAAAGAACATTCGTTGAATAACAC------------ACAGTAAGGTAACTCTACAGTTTGTGGTAAAAACTGGCTTCAAAG Template switch alignment (log-probability: -28.2) GTAGAACTGTAGGGAAAGAACATTCGTTGAATAACACgCA|TGTTATTCAAC|AAGGTAACTCTACAGTTTaTGGTAAAAACTGGCTTCAAAG GTAGAACTGTAGGGAAAGAACATTCGTTGAATAACACACA|TGTTATTCAAC|AAGGTAACTCTACAGTTTGTGGTAAAAACTGGCTTCAAAG ========== Event 1837 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AATACATTCCTTCATTATGAATAGCATTAAGTGCTATCATTTTAAACTCATTTACA ↑ 1 4 3 2 Chimp: AATACATTCCTTCATTATGAAGGCTCTTAAGTGCTATCATTTTAAACTCATTTACG Gorilla: Human: AATACATTCCTTCATTATGAATAGCATTAAGTGCTATCATTTTAAACTCATTTACA Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:110344510-110344514 Template switch process: F1: L GGTCCTGTTATCTAAGTTGGAATACATTCCTTCATTATGAA 1 F3: 4 TTAAGTGCTATCATTTTAAACTCATTTACATGACCTCTTC R RF: GGTCCTGTTATCTAAGTTGGAATACATTCCTTCATTATGAAGGCTCTTAAGTGCTATCATTTTAAACTCATTTACGTGACCTCTTC RR: CCAGGACAATAGATTCAACCTTATGTAAGGAAGTAATACTTCCGAGAATTCACGATAGTAAAATTTGAGTAAATGCACTGGAGAAG F2: 3 ACGAT 2 Unidirectional alignment (log-probability: -34.6) GTCCTGTTATCTAAGTTGGAATACATTCCTTCATTATGAatagcA-----TTAAGTGCTATCATTTTAAACTCATTTACaTGACCTCTTC GTCCTGTTATCTAAGTTGGAATACATTCCTTCATTATGA-----AGGCTCTTAAGTGCTATCATTTTAAACTCATTTACGTGACCTCTTC Template switch alignment (log-probability: -21.9) GTCCTGTTATCTAAGTTGGAATACATTCCTTCATTATGAA|TAGCA|TTAAGTGCTATCATTTTAAACTCATTTACaTGACCTCTTC GTCCTGTTATCTAAGTTGGAATACATTCCTTCATTATGAA|TAGCA|TTAAGTGCTATCATTTTAAACTCATTTACGTGACCTCTTC ========== Event 1838 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TATATGATTCATACTCTATTCTGGATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------CCAACCCAGAA---ATGGGT------------------------------------------------------CACCACAGAGTGTGTGAATATAAGATTGTGGCAGTAATTGTCACGATCAGGAAATTCATGCTTCAG---TGA-------TACTTT---------------CCTAT-ACCTTACTCTTAATGAAATGGT-A--GAAATATATAGGAATTCATTTACACA--GTCATTCAGGTTTCATTAAGACTAAAGATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAGTTTTAAAGTTGTGTAAAGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTAGGACAAAGGCCTAAAACCCAGACTTTCTAGATAGGAAAACAAATCTAAATAACCAATTGGGATGAAAAAGTTACTTACTTGCAATGTT Chimp: TATATGATTCATACTCTATTCTGGATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------CCAACCCAGAA---ATGGGT------------------------------------------------------CACCACAGAGTGTGTGAATATAAGATTGTGGCAGTAATTGTCACGATCAGGAAATTCATGCTTCAG---TGA-------TACTTT---------------CCTAT-ACCTTACTCTTAATGAAATGGT-A--GAAATATATAGGAATTCATTTACACA--GTCATTCAGGTTTCATTAAGACTAAAGATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAGTTTTAAAGTTGTGTAAAGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTAGGACAAAGGCCTAAAACCCAGACTTTCTAGATAGGAAAACAAATCTAAATAACCAATTGGGATGAAAAAGTTACTTACTTGCAATGTT ↓ 1 3 2 4 ↑ 1 3 2 4 Gorilla: TATATGATTCATACTCttttttttttttttttttttttttttttAGATTAATAAACAGACATAAACTTGAAACATCCTCTACCACATAATCTGCGCATGGCTGTAGAAAGTATAATTTTTGTGGAGCCTCACAACATTGCAAGTAAGTAACTTTTTCATCCCAATTTGTTATTTAGATTTGTTTTCCTATCTAGAAAGTCTGGGT------------------------------------------------------------------------------------------------------------TTTAGGCCTTTG------TCCTAAAAACTTTACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATT----T-CTACCATTTCATTAAGAGTA-AGGTATAGGAAAGTATCACTGAAGCATGAATTTCCTGATCGTGACAATTACTGCCACAATCTTATATTCACACACTCTGTGGTGACCnnnnnnnnnntAATGTTTAtgaaactggcccaattgtcctatagaactgatgtttatggtttcttttgaaaaaaaaaataaataaaaagttgaccctctcagtcttaaaactgaagaaact----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ↓ 1 3 2 4 ↑ 1 3 2 4 Human: TATATGATTCATACTCTATTCTGGATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------CCAACCCAGAA---ATGGGT------------------------------------------------------CACCACAGAGTGTGTGAATATAAGATTGTGGCAGTAATTGTCACGATCAGGAAATTCATGCTTCAG---TGA-------TACTTT---------------CCTAT-ACCTTACTCTTAATGAAATGGT-A--GAAATATATAGGAATTCATTTACACA--GTCATTCAGGTTTCATTAAGACTAAAGATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAGTTTTAAAGTTGTGTAAAGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTAGGACAAAGGCCTAAAACCCAGACTTTCTAGATAGGAAAACAAATCTAAATAACCAATTGGGATGAAAAAGTTACTTACTTGCAATGTT Cluster: [ ] Orangutan: TATATGATTCATACTCTGTTCTGGATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------CCAACCCAGAA---ATGGGTCACCGCAGAGTGTGTGAATATAAGATTGTGGCAGTAATTGTCACGATCAGGAAA------------------------------------------------------TTCATGCTTCAGTGA----------TACTTT---------------CCTAA-TCCTTACTCTTAATGAAATGGT-A--GAAATGTATAGGAATTCATTTACACAGT--CATTCAGGTTTCATTAAGACTAAAGATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCAGTTTTAAAGTTGTGTAAAGTTTTTAGGACAAAGGCCTAAAACCCAGACTTTCTAGATAGGAAAACAAATCTAAATAACCAACTGGGATGAAAAAGTTACTTACTTGCAATGTTGTGAGGCTCCACAAAAATTATACTTTCTACAGCCATGCGCAGATTATGTGGTAGAGGATGTTTCAAGTTTATGTCTGTTTATTAATCTAATTTGATAACTTCAATTTTCTTAATAGACTTATTTTTAATCTTTTTAAAATAACACAGTTTAGAAAATTTTGCACAAGAAATATAAAAAAGCTAATCTTGTGTCGGGCCCAAATGAATATCTGAGAGTCATTATACTGGAGAGCAGGGAATGTTGGATGGAGTAACTGGGAAAATTAACATaaaaa--------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr2:13409863-13409943 Template switch process: F1: L TT 1 F3: 4 ATA R RF: TTACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAAGCATGAATTTCCTGATCGTGACAATTACTGCCACAATCTTATA RR: AATGTGTTGAAATTTTGACTTATAGAAATCAGAATTACTTTGGACTTACTGACACATTTACTTAAGGATATATAAAGATGGTAAAGTAATTCTCATTCCATATCCTTTCATAGTGACTTCGTACTTAAAGGACTAGCACTGTTAATGACGGTGTTAGAATAT F2: 3 GAAATCAGAATTACTTTGGACTTACTGACACATTTACTTAAGGATATATAAAGATGGTAAAGTAATTCTCATTCCATATCC 2 Unidirectional alignment (log-probability: -136) TTCCTATaccttactcttaatgaaatggtagaaatatataggaattcatttacacagtcattcaggtttcattaagactaaagATA------------------------------------------------ TTCCTAT----------------------------------------------------------------------------ATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAAGC Template switch alignment (log-probability: -24.2) TT|CCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAG|ATA TT|CCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAG|ATA Human > Gorilla --------------- chr2A:13588279-13588395 Template switch process: F1: L TT 1 F3: 4 GC R RF: TTCTGGATTTCCAACCCAGAAATGGGTCACCACAGAGTGTGTGAATATAAGATTGTGGCAGTAATTGTCACGATCAGGAAATTCATGCTTCAGTGATACTTTCCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAGATATTCAGTTTTAAAGTTGTGTAAAGTTTTTAGGACAAAGGC RR: AAGACCTAAAGGTTGGGTCTTTACCCAGTGGTGTCTCACACACTTATATTCTAACACCGTCATTAACAGTGCTAGTCCTTTAAGTACGAAGTCACTATGAAAGGATATGGAATGAGAATTACTTTACCATCTTTATATATCCTTAAGTAAATGTGTCAGTAAGTCCAAAGTAATTCTGATTTCTATAAGTCAAAATTTCAACACATTTCAAAAATCCTGTTTCCG F2: 3 AAGTCACTATGAAAGGATATGGAATGAGAATTACTTTACCATCTTTATATATCCTTAAGTAAATGTGTCAGTAAGTCCAAAGTAATTCTGATTTCTATAAGTCAAAATTTCAACACA 2 Unidirectional alignment (log-probability: -184) ttacacaactttaaaactgaatatctttagtcttaatgaaacctgaatgactgtgtaaatgaaTTCCTAT----------------------------------------------------------------------------ATAtttctaccatttcattaagagtaaggtataggaaagtatcactgaagc ---------------------------------------------------------------TTCCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAGATA------------------------------------------------ Template switch alignment (log-probability: -28.7) TT|ACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAA|GC TT|ACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAA|GC Gorilla > Chimp --------------- chr2A:13615680-13615760 Template switch process: F1: L TT 1 F3: 4 ATA R RF: TTACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAAGCATGAATTTCCTGATCGTGACAATTACTGCCACAATCTTATA RR: AATGTGTTGAAATTTTGACTTATAGAAATCAGAATTACTTTGGACTTACTGACACATTTACTTAAGGATATATAAAGATGGTAAAGTAATTCTCATTCCATATCCTTTCATAGTGACTTCGTACTTAAAGGACTAGCACTGTTAATGACGGTGTTAGAATAT F2: 3 GAAATCAGAATTACTTTGGACTTACTGACACATTTACTTAAGGATATATAAAGATGGTAAAGTAATTCTCATTCCATATCC 2 Unidirectional alignment (log-probability: -136) TTCCTATaccttactcttaatgaaatggtagaaatatataggaattcatttacacagtcattcaggtttcattaagactaaagATA------------------------------------------------ TTCCTAT----------------------------------------------------------------------------ATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAAGC Template switch alignment (log-probability: -24.2) TT|CCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAG|ATA TT|CCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAG|ATA Chimp > Gorilla --------------- chr2A:13588279-13588395 Template switch process: F1: L TT 1 F3: 4 GC R RF: TTCTGGATTTCCAACCCAGAAATGGGTCACCACAGAGTGTGTGAATATAAGATTGTGGCAGTAATTGTCACGATCAGGAAATTCATGCTTCAGTGATACTTTCCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAGATATTCAGTTTTAAAGTTGTGTAAAGTTTTTAGGACAAAGGC RR: AAGACCTAAAGGTTGGGTCTTTACCCAGTGGTGTCTCACACACTTATATTCTAACACCGTCATTAACAGTGCTAGTCCTTTAAGTACGAAGTCACTATGAAAGGATATGGAATGAGAATTACTTTACCATCTTTATATATCCTTAAGTAAATGTGTCAGTAAGTCCAAAGTAATTCTGATTTCTATAAGTCAAAATTTCAACACATTTCAAAAATCCTGTTTCCG F2: 3 AAGTCACTATGAAAGGATATGGAATGAGAATTACTTTACCATCTTTATATATCCTTAAGTAAATGTGTCAGTAAGTCCAAAGTAATTCTGATTTCTATAAGTCAAAATTTCAACACA 2 Unidirectional alignment (log-probability: -184) ttacacaactttaaaactgaatatctttagtcttaatgaaacctgaatgactgtgtaaatgaaTTCCTAT----------------------------------------------------------------------------ATAtttctaccatttcattaagagtaaggtataggaaagtatcactgaagc ---------------------------------------------------------------TTCCTATACCTTACTCTTAATGAAATGGTAGAAATATATAGGAATTCATTTACACAGTCATTCAGGTTTCATTAAGACTAAAGATA------------------------------------------------ Template switch alignment (log-probability: -28.7) TT|ACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAA|GC TT|ACACAACTTTAAAACTGAATATCTTTAGTCTTAATGAAACCTGAATGACTGTGTAAATGAATTCCTATATATTTCTACCATTTCATTAAGAGTAAGGTATAGGAAAGTATCACTGAA|GC ========== Event 1839 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATGACTGAAGCGTGAATTCAAGGAGGGGAAAGAAGACTGTACTTGTAATAACTTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAAC--ATGTGATAGTGTGACTTCTGAGTACAT Chimp: AAATGACTGAAGCGTCAATTCAAGGAGGGGAAAGAAGATTGTACTTGTAATAACTTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAAT--ATGTGGTAGTGTGACTTCTGAGTACAT ↓ 3 2 1 4 Gorilla: AAATGACTGAAGCATGAATTCAAGGAGGGGAAAGAAGACTTTACTTGTAATAACTTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAAC----TTGATAGTGTGACTTCTGAGTACAT Human: AAATGACTGAAGCGTGAATTCAAGGAGGGGAAAGAAGACTGTACTTGTAATAACTTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAAC--ATGTGATAGTGTGACTTCTGAGTACAT Cluster: [ ] Orangutan: AAATGACTGAAGCGTGAATTCAAGGAGGGGAAAGGAGACTTTACTTGTAATAACTTCACTACAAAATAA-----TAAATGTGACAACACAGTAACAT--GTGACAGTGTGACTTCTGAGTACAT Chimp > Gorilla --------------- chr2B:111012916-111012920 Template switch process: F1: L CTTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAA 1 F3: 4 TAGTGTGACTTCTGAGTACATGTAATAATACTATTCTCTG R RF: TCAAGGAGGGGAAAGAAGATTGTACTTGTAATAACTTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAATATGTGGTAGTGTGACTTCTGAGTACATGTAATAATACTATTCTCTG RR: AGTTCCTCCCCTTTCTTCTAACATGAACATTATTGAAGTGATCTTTTATTATTTTATTTACACTGTTGTGTCATTATACACCATCACACTGAAGACTCATGTACATTATTATGATAAGAGAC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -27.6) TTCACTAGAAAATAATAAAATAAATGTGACAACACAGTA--ActTGaTAGTGTGACTTCTGAGTACATGTAATAATACTATTCTCTG TTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAATATGTGGTAGTGTGACTTCTGAGTACATGTAATAATACTATTCTCTG Template switch alignment (log-probability: -16.4) TTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAA|CTTGA|TAGTGTGACTTCTGAGTACATGTAATAATACTATTCTCTG TTCACTAGAAAATAATAAAATAAATGTGACAACACAGTAA|CTTGA|TAGTGTGACTTCTGAGTACATGTAATAATACTATTCTCTG ========== Event 1840 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: -----------------------ACGGGTTCCTGGTGACGTCACTCACCTGTCTGCTTGTTAAGAAACTGCACAACTTC ↓ 1 4 3 2 Chimp: --------------------CAGGTGAGTTCCTGGTGACGTCACTCACCTGTCTGC---TTAAGAAACTGCACAACTTC Gorilla: caaaggcacctacccacCAG---GTGAGTTCCTGGTGACGTCACTCACCTGTCTGCTTGTTAAGAAACTGCACAACTTC Human: -----------------------ACGGGTTCCTGGTGACGTCACTCACCTGTCTGCTTGTTAAGAAACTGCACAACTTC Cluster: [ ] Orangutan: Human > Chimp ------------- chr21:19018521-19018527 Template switch process: F1: L CCCAC 1 F3: 4 GTTCCTGGTGACGTCACTCACCTGTCTGC---TTAAGAAACTGCACAACTTCCAAACCATCAGGGTAGGTCG R RF: CCCACACGGGTTCCTGGTGACGTCACTCACCTGTCTGCTTGTTAAGAAACTGCACAACTTCCAAACCATCAGGGTAGGTCG RR: GGGTGTGCCCAAGGACCACTGCAGTGAGTGGACAGACGAACAATTCTTTGACGTGTTGAAGGTTTGGTAGTCCCATCCAGC F2: 3 AGTGGAC 2 Unidirectional alignment (log-probability: -37.6) CCCACcaGGtgaGTTCCTGGTGACGTCACTCACCTGTCTGCTT---AAGAAACTG CCCACACGG---GTTCCTGGTGACGTCACTCACCTGTCTGCTTGTTAAGAAACTG Template switch alignment (log-probability: -26.4) CCCAC|CAGGTGA|GTTCCTGGTGACGTCACTCACCTGTCTGC---TTAAGAAACTG CCCAC|CAGGTGA|GTTCCTGGTGACGTCACTCACCTGTCTGCTTGTTAAGAAACTG ========== Event 1841 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGGAGTCACTGCTCCCTTCTAACATTTGATTCTGGTATCTAATGTTAGATGGGTACAGGACCCATCACCT Chimp: AGGGAGTCACTGCTCCCTTCTAACATTTGATTCTGGTATCAAATGTTAGATGGGTACAGGACCCATCACCT ↑ 3 2 41 Gorilla: AGGGAGCCACTGCTCCCTTCTAACATTTGATTCTGGT------------ATGGGTACAGGACCCATCACCT Human: AGGGAGTCACTGCTCCCTTCTAACATTTGATTCTGGTATCTAATGTTAGATGGGTACAGGACCCATCACCT Cluster: [ ] Orangutan: AGAGAGTCACTGCTCCCTTTTAACATTTGATTCTGGT------------ATGGATACAGGACCCA-TACCT Gorilla > Chimp --------------- chr21:14105370-14105379 Template switch process: F1: L GGGGAGGGAGTCACTGCTCCCTTCTAACATTTGATTCTGGTAT 1 F3: 4 ATGGGTACAGGACCCATCACCTAATCTGCCCTAGTAGAAC R RF: GGGGAGGGAGCCACTGCTCCCTTCTAACATTTGATTCTGGTATGGGTACAGGACCCATCACCTAATCTGCCCTAGTAGAAC RR: CCCCTCCCTCGGTGACGAGGGAAGATTGTAAACTAAGACCATACCCATGTCCTGGGTAGTGGATTAGACGGGATCATCTTG F2: 3 GATTGTAAAC 2 Unidirectional alignment (log-probability: -33.7) GAGGGAGtCACTGCTCCCTTCTAACATTTGATTCTGGTatcaaatgttagATGGGTACAGGACCCATCACCTAATCTGCCCTAGTAGAAC GAGGGAGCCACTGCTCCCTTCTAACATTTGATTCTGGT------------ATGGGTACAGGACCCATCACCTAATCTGCCCTAGTAGAAC Template switch alignment (log-probability: -22.6) GAGGGAGtCACTGCTCCCTTCTAACATTTGATTCTGGTAT|CAAATGTTAG|ATGGGTACAGGACCCATCACCTAATCTGCCCTAGTAGAAC GAGGGAGCCACTGCTCCCTTCTAACATTTGATTCTGGTAT|CAAATGTTAG|ATGGGTACAGGACCCATCACCTAATCTGCCCTAGTAGAAC ========== Event 1842 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCCATCACTTGACTAAGCC---AGAGGTTA---ACTCACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTCTCAA Chimp: CTTCCATCACTTGACTAAGCC---AGAGGTTA---ACTGACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTCTCAA ↓ 3 1 2 4 Gorilla: TTTCCATCACTTGACTAAGCC------AGTTAACCTCTGGCTTAGTCAAGTGATGGAAACTTTACTCACTTTAGTTTTTCTCAA ↑ 3 1 2 4 Human: CTTCCATCACTTGACTAAGCC---AGAGGTTA---ACTCACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTCTCAA Cluster: [ ] Orangutan: TTTCCATCACTTGACTAAGCCAGA---GGTTA---ACTGGCTTAGACAAGTGATGGAAAGTTTACTCACTTTAGTTTTTCTCAA Human > Gorilla --------------- chr2B:25190760-25190770 Template switch process: F1: L TAAGCCAG 1 F3: 4 CTTAGTCAAGTGATGGAAACTTTACTCACTTTAGTTTTTCTCAAAAAAGTGACACTTTAATTAC R RF: TAAGCCAGAGGTTAACTCACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTCTCAAAAAAGTGACACTTTAATTAT RR: ATTCGGTCTCCAATTGAGTGAATCAGTTCACTACCTTTCAAAGGAGTGAAATCAAAAAGAGTTTTTTCACTGTGAAATTAATA F2: 3 GGTCTCCAATT 2 Unidirectional alignment (log-probability: -52.7) TAAGCCA---GTTAAcctCTggCTTAGTCAAGTGATGGAAAcTTTaCTCACTTTAGTTTTTC TAAGCCAGAGGTTAA---CTCACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTC Template switch alignment (log-probability: -33.5) TAAGCCAG|TTAACCTCTGG|CTTAGTCAAGTGATGGAAAcTTTaCTCACTTTAGTTTTTC TAAGCCAG|TTAACCTCTGG|CTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTC Chimp > Gorilla --------------- chr2B:25190760-25190770 Template switch process: F1: L TAAGCCAG 1 F3: 4 CTTAGTCAAGTGATGGAAACTTTACTCACTTTAGTTTTTCTCAAAAAAGTGACACTTTAATTAC R RF: TAAGCCAGAGGTTAACTGACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTCTCAAAAAAGTGACACTTTAATTAT RR: ATTCGGTCTCCAATTGACTGAATCAGTTCACTACCTTTCAAAGGAGTGAAATCAAAAAGAGTTTTTTCACTGTGAAATTAATA F2: 3 GGTCTCCAATT 2 Unidirectional alignment (log-probability: -47.2) TAAGCCA---GTTAAcctCTGgCTTAGTCAAGTGATGGAAAcTTTaCTCACTTTAGTTTTTC TAAGCCAGAGGTTAA---CTGACTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTC Template switch alignment (log-probability: -33.5) TAAGCCAG|TTAACCTCTGG|CTTAGTCAAGTGATGGAAAcTTTaCTCACTTTAGTTTTTC TAAGCCAG|TTAACCTCTGG|CTTAGTCAAGTGATGGAAAGTTTCCTCACTTTAGTTTTTC ========== Event 1843 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCGATGTTCTCATCTCTGGAGTTTCCACAGAAT-GCCCATAGGAAAGGAAGCTCTGG ↓ 3 2 1 4 Chimp: GCGATGTTCTCATCTCTGGAGTTTCCACAGGAAACTCCATAGGAAAGGAAGCTCTGG ↑ 3 2 1 4 Gorilla: GCGATGTTTTCATCTCTGGAGTTTCCACAGAAT-GCCCATAGGAAAGGAAGCTCTGG Human: GCGATGTTCTCATCTCTGGAGTTTCCACAGAAT-GCCCATAGGAAAGGAAGCTCTGG Cluster: [ ] Orangutan: GCAACGTTCTTACCTCTGGAGTTGCCACAGAAT-GCCTACAAGCAAGGAAGCTCTGG Human > Chimp ------------- chr2B:23216004-23216009 Template switch process: F1: L TTTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAG 1 F3: 4 CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC R RF: TTTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAGAATGCCCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC RR: AAAAGGTAAGACGCTACAAGAGTAGAGACCTCAAAGGTGTCTTACGGGTATCCTTTCCTTCGAGACCCGGGTTACCGTATTTTTGG F2: 3 TCAAAG 2 Unidirectional alignment (log-probability: -30) TTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAGgaaact-----CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC TTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAG------AATGCCCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC Template switch alignment (log-probability: -16) TTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAG|GAAACT|CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC TTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAG|GAAACT|CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC Gorilla > Chimp --------------- chr2B:23216004-23216009 Template switch process: F1: L TTTTCCATTCTGCGATGTTCTCATCTCTGGAGTTTCCACAG 1 F3: 4 CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC R RF: TTTTCCATTCTGCGATGTTTTCATCTCTGGAGTTTCCACAGAATGCCCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC RR: AAAAGGTAAGACGCTACAAAAGTAGAGACCTCAAAGGTGTCTTACGGGTATCCTTTCCTTCGAGACCCGGGTTACCGTATTTTTGG F2: 3 TCAAAG 2 Unidirectional alignment (log-probability: -34.5) TTTCCATTCTGCGATGTTcTCATCTCTGGAGTTTCCACAgGAAactCCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC TTTCCATTCTGCGATGTTTTCATCTCTGGAGTTTCCACA-GAATGCCCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC Template switch alignment (log-probability: -22) TTTCCATTCTGCGATGTTcTCATCTCTGGAGTTTCCACAG|GAAACT|CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC TTTCCATTCTGCGATGTTTTCATCTCTGGAGTTTCCACAG|GAAACT|CCATAGGAAAGGAAGCTCTGGGCCCAATGGCATAAAAACC ========== Event 1844 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACCAAAGCTAAGCTTGCATG---------------TCTGGAGATGACAGCTGAATAATGGAGGAGAT Chimp: AACCAAAGCTAAGCTTGCATG---------------TCTGGAGATGACAGCTGAATAATagaggagat ↓ 4 31 2 Gorilla: AACCAAAGCTAAGCTTGCATGTCTGGAGGGCATCTGTCTGGAGATGACAGCTGAATAATggaggagat ↑ 4 31 2 Human: AACCAAAGCTAAGCTTGCATG---------------TCTGGAGATGACAGCTGAATAATGGAGGAGAT Cluster: [ ] Orangutan: AACCAAAGCTAAGCTTGCATGTATGGAGGGCATCTGTCTGGAGATGACAGCTGAATAATGGAGGAGAT Human > Gorilla --------------- chr2B:25383867-25383873 Template switch process: F1: L AGATGAAAGCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAG 1 F3: 4 GTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAAC R RF: AGATGAAAGCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAAC RR: TCTACTTTCGAATCTTCTCATTGGTTTCGATTCGAACGTACAGACCTCTACTGTCGACTTATTACCTCCTCTACTCTGTTG F2: 3 TCTACGG 2 Unidirectional alignment (log-probability: -32.5) GCTTAGAAGAGTAACCAAAGCTAAGCTTGCAtgtctggagggcatcTGTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAA GCTTAGAAGAGTAACCAAAGCTAAGCTTGCA---------------TGTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAA Template switch alignment (log-probability: -22.3) GCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAG|GgCATCT|GTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAA GCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAG|GTCATCT|GTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAA Chimp > Gorilla --------------- chr2B:25383867-25383873 Template switch process: F1: L AGATGAAAGCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAG 1 F3: 4 GTCTGGAGATGACAGCTGAATAATGGAGGAGATGAGACAAC R RF: AGATGAAAGCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAGATGACAGCTGAATAATAGAGGAGATGAGACAAC RR: TCTACTTTCGAATCTTCTCATTGGTTTCGATTCGAACGTACAGACCTCTACTGTCGACTTATTATCTCCTCTACTCTGTTG F2: 3 TCTACGG 2 Unidirectional alignment (log-probability: -38) GCTTAGAAGAGTAACCAAAGCTAAGCTTGCAtgtctggagggcatcTGTCTGGAGATGACAGCTGAATAATgGAGGAGATGAGACAA GCTTAGAAGAGTAACCAAAGCTAAGCTTGCA---------------TGTCTGGAGATGACAGCTGAATAATAGAGGAGATGAGACAA Template switch alignment (log-probability: -27.9) GCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAG|GgCATCT|GTCTGGAGATGACAGCTGAATAATgGAGGAGATGAGACAA GCTTAGAAGAGTAACCAAAGCTAAGCTTGCATGTCTGGAG|GTCATCT|GTCTGGAGATGACAGCTGAATAATAGAGGAGATGAGACAA ========== Event 1845 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATGTA----------------------------AAAGCATAATTTGCcttttctttactt Chimp: GGTCTGCATTGCATAAAACTGcttttactttttgaaaaatgta----------------------------aaagcataatttgccttttctttactt Gorilla: GGTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATGGC--------------AGCGTTTTACCCTTTGAACGTAATTTGCcttttctttactt ↓ 3 2 1 4 Human: GGTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATGTA----------------------------AAAGCATAATTTGCcttttctttactt Cluster: [ ] Orangutan: GGTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATGGCAGCGTTTTACCCTT--------------TGAACATAATTTGCcttttctttactt Gorilla > Human --------------- chr21:33798050-33798057 Template switch process: F1: L GGTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATG 1 F3: 4 TAATTTGCCTTTTCTTTACTTCTCTTTTCTTTCTTCTCTT R RF: GGTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATGGCAGCGTTTTACCCTTTGAACGTAATTTGCCTTTTCTTTACTTCTCTTTTCTTTCTTCTCTT RR: CCAGACGTAACGTATTTTGACGAAAATGAAAAACTTTTTACCGTCGCAAAATGGGAAACTTGCATTAAACGGAAAAGAAATGAAGAGAAAAGAAAGAAGAGAA F2: 3 ACGAAAAT 2 Unidirectional alignment (log-probability: -28.8) GTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATGtaaaaGCA-------------------TAATTTGCCTTTTCTTTACTTCTCTTTTCTTTCTTCTCTT GTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATG-----GCAGCGTTTTACCCTTTGAACGTAATTTGCCTTTTCTTTACTTCTCTTTTCTTTCTTCTCTT Template switch alignment (log-probability: -16.7) GTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATG|TAAAAGCA|TAATTTGCCTTTTCTTTACTTCTCTTTTCTTTCTTCTCTT GTCTGCATTGCATAAAACTGCTTTTACTTTTTGAAAAATG|TAAAAGCA|TAATTTGCCTTTTCTTTACTTCTCTTTTCTTTCTTCTCTT ========== Event 1846 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGACTTC----------------ATCTTTCCAGAAGTATTTATAAGTACATTTAAATGACAGCCTATTGTGGTCCCACTGGAAATGAGTGTAAGATGAAGTTGATTTTTTAAAAAGAAT ↓ 1 3 2 4 ↑ 3 1 4 2 Chimp: CCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGACCAC--------AATAGGCTGTCAT-TTAAATGTACTTATAAATACTTCT-----------------------------------GGAAAGATGAAGTTGATTTTTTAAAAAGAAT Gorilla: CCTTCATTCTGAAGATGATACACTCATTTCCAGTGGGACCACAATAGGCT--------GTCAT-TTAAATGTACTTATAGGTACTTCT-----------------------------------GGAAATACGAAGTTGATTTTTTAAAAAGAAT Human: CCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGACTTC----------------ATCTTTCCAGAAGTATTTATAAGTACATTTAAATGACAGCCTATTGTGGTCCCACTGGAAATGAGTGTAAGATGAAGTTGATTTTTTAAAAAGAAT Cluster: [ ] Orangutan: TCTTCATTCAGGAGATGATACAATCATTTCCAGTGGGACCACAATAGGCT--------GTCAT-TTAAATGTACTTATAAATACTTCT-----------------------------------GGGAAGATGAAGTTGATTTTTTTAAAAGAAT Chimp > Human ------------- chr2:134926953-134927023 Template switch process: F1: L TACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAC 1 F3: 4 AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA R RF: TACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGACCACAATAGGCTGTCATTTAAATGTACTTATAAATACTTCTGGAAAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA RR: ATGGAAGTAAGTCTTCTACTATGTGAGTAAAGGTCACCCTGGTGTTATCCGACAGTAAATTTACATGAATATTTATGAAGACCTTTCTACTTCAACTAAAAAATTTTTCTTATTTAGTGAACTT F2: 3 TGTGAGTAAAGGTCACCCTGGTGTTATCCGACAGTAAATTTACATGAATATTTATGAAGACCTTTCTACTT 2 Unidirectional alignment (log-probability: -125) ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGActtcatctttccagaagtatttataagtacatttaaatgacagcctattgtggtcCCA------------------------------------CTGGAaatgagtgtAAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGA-------------------------------------------------------CCACAATAGGCTGTCATTTAAATGTACTTATAAATACTTCTGGA---------AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA Template switch alignment (log-probability: -23.9) ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAC|TTCATCTTTCCAGAAGTATTTATAAGTACATTTAAATGACAGCCTATTGTGGTCCCACTGGAAATGAGTGT|AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAC|TTCATCTTTCCAGAAGTATTTATAAGTACATTTAAATGACAGCCTATTGTGGTCCCACTGGAAATGAGTGT|AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA Human > Chimp ------------- chr2B:24543599-24543641 Template switch process: F1: L TACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAC 1 F3: 4 AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA R RF: TACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGACTTCATCTTTCCAGAAGTATTTATAAGTACATTTAAATGACAGCCTATTGTGGTCCCACTGGAAATGAGTGTAAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA RR: ATGGAAGTAAGTCTTCTACTATGTGAGTAAAGGTCACCCTGAAGTAGAAAGGTCTTCATAAATATTCATGTAAATTTACTGTCGGATAACACCAGGGTGACCTTTACTCACATTCTACTTCAACTAAAAAATTTTTCTTATTTAGTGAACTT F2: 3 AGGTCTTCATAAATATTCATGTAAATTTACTGTCGGATAACAC 2 Unidirectional alignment (log-probability: -86.4) ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAccacaataggctgtcatttaaatgtacttataaataCTT-------------------------------------------------------CTGGA---------AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGA------------------------------------CTTCATCTTTCCAGAAGTATTTATAAGTACATTTAAATGACAGCCTATTGTGGTCCCACTGGAAATGAGTGTAAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA Template switch alignment (log-probability: -20.6) ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAC|CACAATAGGCTGTCATTTAAATGTACTTATAAATACTTCTGGA|AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA ACCTTCATTCAGAAGATGATACACTCATTTCCAGTGGGAC|CACAATAGGCTGTCATTTAAATGTACTTATAAATACTTCTGGA|AAGATGAAGTTGATTTTTTAAAAAGAATAAATCACTTGAA ========== Event 1847 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ttctttttaattttcaatttttacGGGTACGTAGTACCCGTAAATGTAGGTACCTAGGCATTTAGGTGC ↑ 3 2 1 4 Chimp: ttctttttaattttcaatttttACGGGTACGTAGTAGGTG----TGTATGTACCTAGGCATTTAGGTGC Gorilla: ttctttttaattttcagtttttaTGGGTACGTAGTAGGTG----TGTAGGTACCTAGGCATTTAGGTGC Human: ttctttttaattttcaatttttacGGGTACGTAGTACCCGTAAATGTAGGTACCTAGGCATTTAGGTGC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr21:11715333-11715340 Template switch process: F1: L TATTTTTCTTTTTAATTTTCAATTTTTACGGGTACGTAGTA 1 F3: 4 TGTAGGTACCTAGGCATTTAGGTGCATAGTAGGTGTATACGCATA R RF: TATTTTTCTTTTTAATTTTCAATTTTTACGGGTACGTAGTAGGTGTGTATGTACCTAGGCATTTAGGTGCATAGTAGGTGTATACGCATA RR: ATAAAAAGAAAAATTAAAAGTTAAAAATGCCCATGCATCATCCACACATACATGGATCCGTAAATCCACGTATCATCCACATATGCGTAT F2: 3 AAATGCCC 2 Unidirectional alignment (log-probability: -38.8) ATTTTTCTTTTTAATTTTCAATTTTTACGGGTACGTAgtacccgtaaatGTAGGT--------ACCTAGGCATTTAGGTGCATAGTAGGTGTATAC ATTTTTCTTTTTAATTTTCAATTTTTACGGGTACGTA------------GTAGGTGTGTATGTACCTAGGCATTTAGGTGCATAGTAGGTGTATAC Template switch alignment (log-probability: -22.4) ATTTTTCTTTTTAATTTTCAATTTTTACGGGTACGTAGTA|CCCGTAAA|TGTAgGTACCTAGGCATTTAGGTGCATAGTAGGTGTATAC ATTTTTCTTTTTAATTTTCAATTTTTACGGGTACGTAGTA|CCCGTAAA|TGTATGTACCTAGGCATTTAGGTGCATAGTAGGTGTATAC ========== Event 1848 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AGTTTGCAATACGTATGCATTACTTGTGTATTTTGCAACTATTTACTTGCAAAAATAGACAAGTAATGCATGTGTCTGTAGTTGCACCTG ↑ 3 2 4 1 Chimp: AGTTTGCAATACGTATGCATTACTTGTCTATTTTGCAACTATTTACTT-------------------GCATGTGTCTGTAGTTGCACCTG Gorilla: AGTTTGCAATCCATATGCATTACTTGTCTATTTTGCAACTATTTACTTGCAAAAATAGACAAGTAATGCATGTGTCTGTAGTTGCACCTG Human: AGTTTGCAATACGTATGCATTACTTGTGTATTTTGCAACTATTTACTTGCAAAAATAGACAAGTAATGCATGTGTCTGTAGTTGCACCTG Cluster: [ ] Orangutan: AGTTTGCAATACACATGCATTACTTGTCTATTTTGCAACTATTTACTTGCAAAAATAGACAAGTAATGCATGTGTCTGTAGTTGCACCTG Chimp > Human ------------- chr21:11248319-11248333 Template switch process: F1: L AATACGTATGCATTACTTGTGTATTTTGCAACTATTTACTTGCA 1 F3: 4 TGCATGTGTCTGTAGTTGCACCTGAGTTCCAGTGCAACAGG R RF: AATACGTATGCATTACTTGTCTATTTTGCAACTATTTACTTGCATGTGTCTGTAGTTGCACCTGAGTTCCAGTGCAACAAG RR: TTATGCATACGTAATGAACAGATAAAACGTTGATAAATGAACGTACACAGACATCAACGTGGACTCAAGGTCACGTTGTTC F2: 3 AATGAACAGATAAAA 2 Unidirectional alignment (log-probability: -50.2) CGTATGCATTACTTGTgTATTTTGCAACTATTTACTTgcaaaaatagacaagtaatGCATGTGTCTGTAGTTGCACCTGAGTTCCAGTGCAACAg CGTATGCATTACTTGTCTATTTTGCAACTATTTACTT-------------------GCATGTGTCTGTAGTTGCACCTGAGTTCCAGTGCAACAA Template switch alignment (log-probability: -29.2) CGTATGCATTACTTGTgTATTTTGCAACTATTTACTTGCA|AAAATAGACAAGTAA|TGCATGTGTCTGTAGTTGCACCTGAGTTCCAGTGCAACAg CGTATGCATTACTTGTCTATTTTGCAACTATTTACTTGCA|AAAATAGACAAGTAA|TGCATGTGTCTGTAGTTGCACCTGAGTTCCAGTGCAACAA ========== Event 1849 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAGTTCACACACATTATTCACATTCAAGG----------------------TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATGTGCTAGACTCCTGGACCTGTTTTCTAAGGACTTGTTctcataatccctgctgag ↓ 4 1 3 2 Chimp: CCAGTTCACACACATTATTCAAATTCAAGG-----------TCTTAACAAGTTCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCTGCTAGACTCCTGGACCTGTGttctaaggacttgttctcataatccgtgctgag ↑ 4 1 3 2 Gorilla: CCAGTTCACACACATTATTCAAATTCAAGG----------------------TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCTGCTAGACTCCTGGACCTGTTTTCTAAGGACTTGTTctcataatccctgctgag Human: CCAGTTCACACACATTATTCACATTCAAGG----------------------TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATGTGCTAGACTCCTGGACCTGTTTTCTAAGGACTTGTTctcataatccctgctgag Cluster: [ ] Orangutan: CCAGTTCACACACATTATTCAACTTCAAGGTCGTAACAAGT-----------TCTTAATGATTCACACCTGTTGGCATGCTTTAGCGCATCTGCTAGACTCCTGGACCTGTTTTCTAAGGACTTGTTctcataatcccttctgag Human > Chimp ------------- chr21:11482534-11482538 Template switch process: F1: L ACATGTTCCATGAGCTCTGCCCAGTTCACACACATTATTCAAATTCAAGGTCTTAA 1 F3: 4 TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCT R RF: ACGTGTTTCATGAGCTCTGCCCAGTTCACACACATTATTCACATTCAAGGTCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATGTGCTAGACTCCTGGACCTGTTTTCTAAGGACTTG RR: TGCACAAAGTACTCGAGACGGGTCAAGTGTGTGTAATAAGTGTAAGTTCCAGAATTACTAAGTGTGGACTACCGTACGAAATCGCGTACACGATCTGAGGACCTGGACAAAAGATTCCTGAAC F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -50.8) CTGCCCAGTTCACACACATTATTCAaATTCAAGGTCTTAacaagttcttaATGATTCACACCTGATGGCATGCTTTAGCGCATcT CTGCCCAGTTCACACACATTATTCACATTCAAGGTCTTA-----------ATGATTCACACCTGATGGCATGCTTTAGCGCATGT Template switch alignment (log-probability: -40.2) CTGCCCAGTTCACACACATTATTCAaATTCAAGGTCTTAA|CAAGT|TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATcT CTGCCCAGTTCACACACATTATTCACATTCAAGGTCTTAA|CAAGT|TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATGT Gorilla > Chimp --------------- chr21:11482534-11482538 Template switch process: F1: L ATGAGCTCTGCCCAGTTCACACACATTATTCAAATTCAAGGTCTTAA 1 F3: 4 TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCT R RF: ATGAGCTCTGCCCAGTTCACACACATTATTCAAATTCAAGGTCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCTGCTAGACTCCTGGACCTGTTTTCTAAGGACTTG RR: TACTCGAGACGGGTCAAGTGTGTGTAATAAGTTTAAGTTCCAGAATTACTAAGTGTGGACTACCGTACGAAATCGCGTAGACGATCTGAGGACCTGGACAAAAGATTCCTGAAC F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -26.7) CTGCCCAGTTCACACACATTATTCAAATTCAAGGtcttaacaagtTCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCT CTGCCCAGTTCACACACATTATTCAAATTCAAGG-----------TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCT Template switch alignment (log-probability: -16.5) CTGCCCAGTTCACACACATTATTCAAATTCAAGGTCTTAA|CAAGT|TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCT CTGCCCAGTTCACACACATTATTCAAATTCAAGGTCTTAA|CAAGT|TCTTAATGATTCACACCTGATGGCATGCTTTAGCGCATCT ========== Event 1850 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGTAGCAAGGAGCAATGGTCAACTTTGCTCCTTG Chimp: TAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGCAGCAAGGAGCAATGGTCAACTTTGCTCCTTG ↓ 3 2 1 4 Gorilla: TAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTCGTTA-----TTTAATGGTCAACTTTGCTCCTTG ↑ 3 2 1 4 Human: TAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGTAGCAAGGAGCAATGGTCAACTTTGCTCCTTG Cluster: [ ] Orangutan: TAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGTTA-----TTTAATGGTCAACTTTGCTCCTTC Human > Gorilla --------------- chr21:11714037-11714044 Template switch process: F1: L GCTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT 1 F3: 4 AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC R RF: GCTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGTAGCAAGGAGCAATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC RR: CGATTTTTACCCTTAAATGTTTTTATTGCCCATCCACACAACCATCGTTCCTCGTTACCAGTTGAAACGAGGAACGAGGGATGTCTTTTCTACG F2: 3 TTTATTGC 2 Unidirectional alignment (log-probability: -31.3) CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT------------CgttatttAATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGTAGCAAGGAGC-------AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC Template switch alignment (log-probability: -16.7) CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT|CGTTATTT|AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT|CGTTATTT|AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC Chimp > Gorilla --------------- chr21:11714037-11714044 Template switch process: F1: L GCTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT 1 F3: 4 AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC R RF: GCTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGCAGCAAGGAGCAATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC RR: CGATTTTTACCCTTAAATGTTTTTATTGCCCATCCACACAACCGTCGTTCCTCGTTACCAGTTGAAACGAGGAACGAGGGATGTCTTTTCTACG F2: 3 TTTATTGC 2 Unidirectional alignment (log-probability: -31.3) CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT------------CgttatttAATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTTGGCAGCAAGGAGC-------AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC Template switch alignment (log-probability: -16.7) CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT|CGTTATTT|AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC CTAAAAATGGGAATTTACAAAAATAACGGGTAGGTGTGTT|CGTTATTT|AATGGTCAACTTTGCTCCTTGCTCCCTACAGAAAAGATGC ========== Event 1851 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTCAGAATGTAATCATTTGCAAC-----------TTACTGTCTTTTGAAGGCAGGAAAAGGTATTCTATTTTGTGA Chimp: TTTCAGAATGTAATCATTTGCAAC-----------TTACTGTCTTTTGAAGGCAGGAAAAGGTATTCTATTTTGTGA ↓ 3 1 2 4 Gorilla: TTTCAGAATGTAATCATTTGCAAC----------------------AGTAAGTTGCAAAAGGTATTCTATTTTGTGA Human: TTTCAGAATGTAATCATTTGCAAC-----------TTACTGTCTTTTGAAGGCAGGAAAAGGTATTCTATTTTGTGA Cluster: [ ] Orangutan: TTTTAGAATGTAATCATTTGCAACTCACTGTCTTT-----------TGAAGGCAGGAAAAGGTATTCTATTTTGTGA Chimp > Gorilla --------------- chr21:11003192-11003201 Template switch process: F1: L GCACATATTAAAGTTATATACTAAAAAAAACCTCATTACAAAGAGTTTAAATATCAGGATTGTGAACATTCCTCTATTTTCAGAATGTAATCATTTGCAAC 1 F3: 4 AAAAGGTATTCTATTTTGTGAATATTTGTGTATGTTTTTTGAGATATTCTGAAACTAATGTAGCATATCAATTAAATTACATTTTTAATTTGTC R RF: GCACATATTAAAGTTATATACTAAAAAAAACCTCATTACAAAGAGTTTAAATATCAGGATTGTGAACATTCCTCTATTTTCAGAATGTAATCATTTGCAACTTACTGTCTTTTGAAGGCAGGAAAAGGTATTCTATTTTGTGAATATTTGTGTATGTTTTTTGAGATATTCTGAAACTAATGTAGCATATCAATTAAATTACATTTTTAATTTGTC RR: CGTGTATAATTTCAATATATGATTTTTTTTGGAGTAATGTTTCTCAAATTTATAGTCCTAACACTTGTAAGGAGATAAAAGTCTTACATTAGTAAACGTTGAATGACAGAAAACTTCCGTCCTTTTCCATAAGATAAAACACTTATAAACACATACAAAAAACTCTATAAGACTTTGATTACATCGTATAGTTAATTTAATGTAAAAATTAAACAG F2: 3 CGTTGAATGA 2 Unidirectional alignment (log-probability: -37.3) GTGAACATTCCTCTATTTTCAGAATGTAATCATTTGCAACagtaagTT-----------------GcAAAAGGTATTCTATTTTGTGAATATTTGTGTATGTTTTTT GTGAACATTCCTCTATTTTCAGAATGTAATCATTTGCAAC------TTACTGTCTTTTGAAGGCAGGAAAAGGTATTCTATTTTGTGAATATTTGTGTATGTTTTTT Template switch alignment (log-probability: -19.4) GTGAACATTCCTCTATTTTCAGAATGTAATCATTTGCAAC|AGTAAGTTGC|AAAAGGTATTCTATTTTGTGAATATTTGTGTATGTTTTTT GTGAACATTCCTCTATTTTCAGAATGTAATCATTTGCAAC|AGTAAGTTGC|AAAAGGTATTCTATTTTGTGAATATTTGTGTATGTTTTTT ========== Event 1852 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTAATACACTTGTGTGCAGCATGTACAGGTGATCCTGAATGCATGCGCATGCCCA ↓ 3 1 2 4 Chimp: CTAATACACTTGTGTGCAGCATGTGTAC---ATGCTGAATGCATGCACATGCCCA Gorilla: CTAATACACTTGTGTGCAGCATGTACAGGTGATCCTGAATGCATGCGCATGCCCA Human: CTAATACACTTGTGTGCAGCATGTACAGGTGATCCTGAATGCATGCGCATGCCCA Cluster: [ ] Orangutan: CTAATACACTTGTGTGCAGCATGTACAGGTGATCCTGAATGCACGCGCATGCCCA Human > Chimp ------------- chr2B:25444398-25444404 Template switch process: F1: L TCTCCTGTAGAACCTGACTAATACACTTGTGTGCAGCATGT 1 F3: 4 CTGAATGCATGCACATGCCCACAGGGAGACCTGGGGCTTC R RF: TCTCCTGTAGAACCTGACTAATACACTTGTGTGCAGCATGTACAGGTGATCCTGAATGCATGCGCATGCCCACAGGGAGACCTGGGGCTTC RR: AGAGGACATCTTGGACTGATTATGTGAACACACGTCGTACATGTCCACTAGGACTTACGTACGCGTACGGGTGTCCCTCTGGACCCCGAAG F2: 3 GTACATG 2 Unidirectional alignment (log-probability: -36.3) CTCCTGTAGAACCTGACTAATACACTTGTGTGCAGCAtgTGTAC-----ATgCTGAATGCATGCaCATGCCCACAGGGAGACCTGGGGCTTC CTCCTGTAGAACCTGACTAATACACTTGTGTGCAGCA--TGTACAGGTGATCCTGAATGCATGCGCATGCCCACAGGGAGACCTGGGGCTTC Template switch alignment (log-probability: -22.1) CTCCTGTAGAACCTGACTAATACACTTGTGTGCAGCATGT|GTACATG|CTGAATGCATGCaCATGCCCACAGGGAGACCTGGGGCTTC CTCCTGTAGAACCTGACTAATACACTTGTGTGCAGCATGT|GTACATG|CTGAATGCATGCGCATGCCCACAGGGAGACCTGGGGCTTC ========== Event 1853 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAACCGAACT-TCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG------------AATGCATATGATTACCAAGAGG ↓ 3 2 1 4 Chimp: TAACCGAACT-TCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTGGCCCTAGCTTTCTATGCATATGATTACCAAGAGG ↑ 3 2 1 4 Gorilla: TAACCAAACT-TCCCAAACAGAAAGCTACGGCCAGTGTTGACTCCAGTG------------AATGCATATGATTACCAAGAGG Human: TAACCGAACT-TCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG------------AATGCATATGATTACCAAGAGG Cluster: [ ] Orangutan: TAACCGAACTTGCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAAAG------------AATGCACGTGATTACCAAGAGG Human > Chimp ------------- chr21:10716100-10716112 Template switch process: F1: L ACTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG 1 F3: 4 ATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC R RF: ACTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTGAATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC RR: TGAAGGGTTTGTCTTTCGATCCCGGTCACAACTGAGGTCACTTACGTATACTAATGGTTCTCCGTTCTTTTTTAAGATTAAG F2: 3 TCTTTCGATCCCG 2 Unidirectional alignment (log-probability: -34.2) CTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTGgccctagctttctATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC CTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG------------AATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC Template switch alignment (log-probability: -16.9) CTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG|GCCCTAGCTTTCT|ATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC CTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG|GCCCTAGCTTTCT|ATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC Gorilla > Chimp --------------- chr21:10716100-10716112 Template switch process: F1: L ACTTCCCAAACAGAAAGCTAGGGCCAGTGTTGACTCCAGTG 1 F3: 4 ATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC R RF: ACTTCCCAAACAGAAAGCTACGGCCAGTGTTGACTCCAGTGAATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC RR: TGAAGGGTTTGTCTTTCGATGCCGGTCACAACTGAGGTCACTTACGTATACTAATGGTTCTCCGTTCTTTTTTAAGATTAAG F2: 3 TCTTTCGATCCCG 2 Unidirectional alignment (log-probability: -39.2) CTTCCCAAACAGAAAGCTAgGGCCAGTGTTGACTCCAGTGgccctagctttctATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC CTTCCCAAACAGAAAGCTACGGCCAGTGTTGACTCCAGTG------------AATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC Template switch alignment (log-probability: -28.4) CTTCCCAAACAGAAAGCTAgGGCCAGTGTTGACTCCAGTG|GCCcTAGCTTTCT|ATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC CTTCCCAAACAGAAAGCTACGGCCAGTGTTGACTCCAGTG|GCCGTAGCTTTCT|ATGCATATGATTACCAAGAGGCAAGAAAAAATTCTAATTC ========== Event 1854 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGGGGGAAAGTCAGAAATGAGAATTAGAATTTGCAGAGAATCCTCTGCAAATGGATTCTTCTATTAAAATT ↑ 4 1 3 2 Chimp: CTGGGGGAAAGTCAGAAATGAGAATTAGAAGAACCTCT-GAGCCTCTGCAAATGGATTCTTCTATTAAAATT Gorilla: CTGGGGGAAAGTCAGAAATGAGAATTAGAAGAACCTCT-GAGCCTCTGCAAATGGATTCTTCTATTAAAATT ↓ 4 1 3 2 Human: CTGGGGGAAAGTCAGAAATGAGAATTAGAATTTGCAGAGAATCCTCTGCAAATGGATTCTTCTATTAAAATT Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:136633174-136633179 Template switch process: F1: L AAACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA 1 F3: 4 GAGAAT----------------CCTCTGCAAATGGATTCTTCTATTAAAATTGAAAACAAAT R RF: AAACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAAGAACCTCTGAGCCTCTGCAAATGGATTCTTCTATTAAAATTGAAAACAAAT RR: TTTGTCAGCTCGACCCCCTTTCAGTCTTTACTCTTAATCTTCTTGGAGACTCGGAGACGTTTACCTAAGAAGATAATTTTAACTTTTGTTTA F2: 3 ACGTTT 2 Unidirectional alignment (log-probability: -39) AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA-----------tttgcagagaatCCTCTGCAAATGGATTCTTCTATTAAAATTGAAA AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAAGAACCTCTGAG------------CCTCTGCAAATGGATTCTTCTATTAAAATTGAAA Template switch alignment (log-probability: -27.2) AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA|TTTGCA|GAGAAT----------------CCTCTGCAAATGGATTCTTCTATTAAAATTGAAA AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA|TTTGCA|GAGAATTAGAAGAACCTCTGAGCCTCTGCAAATGGATTCTTCTATTAAAATTGAAA Gorilla > Human --------------- chr2:136633174-136633179 Template switch process: F1: L AAACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA 1 F3: 4 GAGAAT----------------CCTCTGCAAATGGATTCTTCTATTAAAATTGAAAACAAAT R RF: AAACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAAGAACCTCTGAGCCTCTGCAAATGGATTCTTCTATTAAAATTGAAAACAAAT RR: TTTGTCAGCTCGACCCCCTTTCAGTCTTTACTCTTAATCTTCTTGGAGACTCGGAGACGTTTACCTAAGAAGATAATTTTAACTTTTGTTTA F2: 3 ACGTTT 2 Unidirectional alignment (log-probability: -38.1) AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAatttgcagAGA-------AtCCTCTGCAAATGGATTCTTCTATTAAAATTGAAA AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGA--------AGAACCTCTGAGCCTCTGCAAATGGATTCTTCTATTAAAATTGAAA Template switch alignment (log-probability: -27.2) AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA|TTTGCA|GAGAAT----------------CCTCTGCAAATGGATTCTTCTATTAAAATTGAAA AACAGTCGAGCTGGGGGAAAGTCAGAAATGAGAATTAGAA|TTTGCA|GAGAATTAGAAGAACCTCTGAGCCTCTGCAAATGGATTCTTCTATTAAAATTGAAA ========== Event 1855 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAACCCATTCCAGGTTCTTTGGAGTGCTGAACATAATTCAGCACTCTTTTCTAAGAAAAATCATAT ↑ 1 4 3 2 Chimp: TAACCCATTCCAGGTTCTTTGTAGTGCTGATCATAATTCAGCACTCTTTTCTAAGAAAAATCATAG Gorilla: TAACCCATTCCAGGTTCTTTGTAGTGCTGATCATAATTCAGCACTCTTTTCTAAGAAAAATCATAT Human: TAACCCATTCCAGGTTCTTTGGAGTGCTGAACATAATTCAGCACTCTTTTCTAAGAAAAATCATAT Cluster: [ ] Orangutan: TAACCCATTCCAGGTTCTTTGTAGTGCTGAACATAATTCAGCATTCTTTTCTAAGAAAAATCATAT Chimp > Human ------------- chr2:105374917-105374926 Template switch process: F1: L AAGGGACTATAGTCAATTCCTAACCCATTCCAGGTTCTTTG 1 F3: 4 CATAATTCAGCACTCTTTTCTAAGAAAAATCATATTCTTT R RF: AAGGGACTATAGTCAATTCCTAACCCATTCCAGGTTCTTTGTAGTGCTGATCATAATTCAGCACTCTTTTCTAAGAAAAATCATAGTCTTT RR: TTCCCTGATATCAGTTAAGGATTGGGTAAGGTCCAAGAAACATCACGACTAGTATTAAGTCGTGAGAAAAGATTCTTTTTAGTATCAGAAA F2: 3 AAGTCGTGAG 2 Unidirectional alignment (log-probability: -33.1) AGGGACTATAGTCAATTCCTAACCCATTCCAGGTTCTTTGgAGTGCTGAaCATAATTCAGCACTCTTTTCTAAGAAAAATCATAttcttt AGGGACTATAGTCAATTCCTAACCCATTCCAGGTTCTTTGTAGTGCTGATCATAATTCAGCACTCTTTTCTAAGAAAAATCATAG----- Template switch alignment (log-probability: -22.5) AGGGACTATAGTCAATTCCTAACCCATTCCAGGTTCTTTG|GAGTGCTGAA|CATAATTCAGCACTCTTTTCTAAGAAAAATCATAtTCTTT AGGGACTATAGTCAATTCCTAACCCATTCCAGGTTCTTTG|GAGTGCTGAA|CATAATTCAGCACTCTTTTCTAAGAAAAATCATAGTCTTT ========== Event 1856 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: CCATGATCTCCTATTTGGATATGAGTTAATCCAAAATTAACTCACATCCAATATTAACTCTAAAAA ↓ 13 24 ↑ 13 24 Chimp: CCATGATCTCCTATTTGGATGTGAGTTAATTTTGGATTAACTCATATCCAATATTAACTCTAAAAA ↓ 13 24 ↑ 13 24 Gorilla: CCATGATCTCCTATTTGGATATGAGTTAATCCAAAATTAACTCACATCCAATATTAACTCTAAAAA Human: CCATGATCTCCTATTTGGATATGAGTTAATCCAAAATTAACTCACATCCAATATTAACTCTAAAAA Cluster: [ ] Orangutan: CCATGATCTCCTATTTGGATATGAGTTAATCCAAAATTAACTCACATCCAATATTAACTCTAAAAA Chimp > Human ------------- chr2:105140241-105140265 Template switch process: F1: L TCTTAGCTTAGCCATGATCTCCTATTTGGAT 1 F3: 4 ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA R RF: TCTTAGCTTAGCCATGATCTCCTATTTGGATGTGAGTTAATTTTGGATTAACTCATATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA RR: AGAATCGAATCGGTACTAGAGGATAAACCTACACTCAATTAAAACCTAATTGAGTATAGGTTATAATTGAGATTTTTAATAGGTTTCCTTATAATT F2: 3 CACTCAATTAAAACCTAATTGAGTA 2 Unidirectional alignment (log-probability: -40.6) TCTTAGCTTAGCCATGATCTCCTATTTGGATaTGAGTTAAT-----ccaaaATTAACTCAcATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGATGTGAGTTAATTTTGG-----ATTAACTCATATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Template switch alignment (log-probability: -18.2) TCTTAGCTTAGCCATGATCTCCTATTTGGAT|ATGAGTTAATCCAAAATTAACTCAC|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGAT|ATGAGTTAATCCAAAATTAACTCAC|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Human > Chimp ------------- chr2B:106496030-106496054 Template switch process: F1: L TCTTAGCTTAGCCATGATCTCCTATTTGGAT 1 F3: 4 ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA R RF: TCTTAGCTTAGCCATGATCTCCTATTTGGATATGAGTTAATCCAAAATTAACTCACATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA RR: AGAATCGAATCGGTACTAGAGGATAAACCTATACTCAATTAGGTTTTAATTGAGTGTAGGTTATAATTGAGATTTTTAATAGGTTTCCTTATAATT F2: 3 TACTCAATTAGGTTTTAATTGAGTG 2 Unidirectional alignment (log-probability: -40.6) TCTTAGCTTAGCCATGATCTCCTATTTGGATgTGAGTTAAT-----tttggATTAACTCAtATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGATATGAGTTAATCCAAA-----ATTAACTCACATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Template switch alignment (log-probability: -18.2) TCTTAGCTTAGCCATGATCTCCTATTTGGAT|GTGAGTTAATTTTGGATTAACTCAT|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGAT|GTGAGTTAATTTTGGATTAACTCAT|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Gorilla > Chimp --------------- chr2B:106496030-106496054 Template switch process: F1: L TCTTAGCTTAGCCATGATCTCCTATTTGGAT 1 F3: 4 ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA R RF: TCTTAGCTTAGCCATGATCTCCTATTTGGATATGAGTTAATCCAAAATTAACTCACATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA RR: AGAATCGAATCGGTACTAGAGGATAAACCTATACTCAATTAGGTTTTAATTGAGTGTAGGTTATAATTGAGATTTTTAATAGGTTTCCTTATAATT F2: 3 TACTCAATTAGGTTTTAATTGAGTG 2 Unidirectional alignment (log-probability: -39.3) TCTTAGCTTAGCCATGATCTCCTATTTGGATgTGAGTTAAT-----tttggATTAACTCAtATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGATATGAGTTAATCCAAA-----ATTAACTCACATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Template switch alignment (log-probability: -18.7) TCTTAGCTTAGCCATGATCTCCTATTTGGAT|GTGAGTTAATTTTGGATTAACTCAT|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGAT|GTGAGTTAATTTTGGATTAACTCAT|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Chimp > Gorilla --------------- chr2B:106460478-106460502 Template switch process: F1: L TCTTAGCTTAGCCATGATCTCCTATTTGGAT 1 F3: 4 ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA R RF: TCTTAGCTTAGCCATGATCTCCTATTTGGATGTGAGTTAATTTTGGATTAACTCATATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA RR: AGAATCGAATCGGTACTAGAGGATAAACCTACACTCAATTAAAACCTAATTGAGTATAGGTTATAATTGAGATTTTTAATAGGTTTCCTTATAATT F2: 3 CACTCAATTAAAACCTAATTGAGTA 2 Unidirectional alignment (log-probability: -39.3) TCTTAGCTTAGCCATGATCTCCTATTTGGATaTGAGTTAAT-----ccaaaATTAACTCAcATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGATGTGAGTTAATTTTGG-----ATTAACTCATATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA Template switch alignment (log-probability: -18.7) TCTTAGCTTAGCCATGATCTCCTATTTGGAT|ATGAGTTAATCCAAAATTAACTCAC|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA TCTTAGCTTAGCCATGATCTCCTATTTGGAT|ATGAGTTAATCCAAAATTAACTCAC|ATCCAATATTAACTCTAAAAATTATCCAAAGGAATATTAA ========== Event 1857 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TGAGAACTAAAGCCATATTCA-AC----TGCAGCCTCCCACacttttatcatacttttcttatatctgttcgttctttctttcttcttt------tttttcggagtctcgctctgtcacccaggctggagtgcagtggcacgatctcggctcacta ↑ 1 4 3 2 Chimp: TGAGAACTAAAGCCATATTCACACTTTTATCAGCCTCCCACActtttatcatacttttcttatatctgttcattctttctttcttcttt----tttttttcggagtctcgctctgtcacccaggctggagtgcagtggcacgatctcggctcacta ↓ 1 4 3 2 Gorilla: TGAGAACTAAAGCCATATTCA-AC----TGCAGCCTCCCACActtttatcatacttttcttatatctgtttgttctttct-tcttcttt--tt--tttttcggagtctcactctgtcacccaggctggagtgcagtggcacgatctcggctcacta Human: TGAGAACTAAAGCCATATTCA-AC----TGCAGCCTCCCACacttttatcatacttttcttatatctgttcgttctttctttcttcttt------tttttcggagtctcgctctgtcacccaggctggagtgcagtggcacgatctcggctcacta Cluster: [ ] Orangutan: TGAGAACTAAAGCCATATTCA-AC----AGCGGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTTCGTTCGttctttcttcttttt----tttttcggagtctcgctctgtcacccaggctggagtgcagtggcacgatctcggctcacta Chimp > Human ------------- chr2:137883425-137883428 Template switch process: F1: L TGTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA 1 F3: 4 CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT R RF: TGTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCACACTTTTATCAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTTCATTCTTTCTTTCTTCTTTTTTTTTTCGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGT RR: ACAATGTAACTACAAGTTTTACTCTTGATTTCGGTATAAGTGTGAAAATAGTCGGAGGGTGTGAAAATAGTATGAAAAGAATATAGACAAGTAAGAAAGAAAGAAGAAAAAAAAAAGCCTCAGAGCGAGACAGTGGGTCCGACCTCACGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -27.4) GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCAactg---------CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA----CACTTTTATCAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT Template switch alignment (log-probability: -15.8) GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA|ACTG|CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA|ACTG|CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT Chimp > Gorilla --------------- chr2B:29827253-29827256 Template switch process: F1: L TGTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA 1 F3: 4 CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT R RF: TGTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCACACTTTTATCAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTTCATTCTTTCTTTCTTCTTTTTTTTTTCGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGT RR: ACAATGTAACTACAAGTTTTACTCTTGATTTCGGTATAAGTGTGAAAATAGTCGGAGGGTGTGAAAATAGTATGAAAAGAATATAGACAAGTAAGAAAGAAAGAAGAAAAAAAAAAGCCTCAGAGCGAGACAGTGGGTCCGACCTCACGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -26.5) GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA-ACTg----CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCACACTTTTATCAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT Template switch alignment (log-probability: -16.2) GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA|ACTG|CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT GTTACATTGATGTTCAAAATGAGAACTAAAGCCATATTCA|ACTG|CAGCCTCCCACACTTTTATCATACTTTTCTTATATCTGTT ========== Event 1858 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGTCTGAAGACACGGTGAGC--CTGAAATTGGCTGTGAACCAAACCTATTTCATTCTCCTTCTTTCTCTCTGAAATGCAAACCAGGCAGGACA Chimp: ATGTCTGAAGACATGGTGAGCTCAGGAAATTGGCTGTGAACGAAACCTATTTCATTCTC---CTTTCTCTCTGAAATGCAAACCAGGCAGGACA ↑ 1 4 3 2 Gorilla: ATGTCTGAAGACATGGTGAGC--CTGAAATTGGCTGTGAACCAAATCTATTTCATTCTCCTTCTTTCTCTCTGAAATGCAAACCAGGCAGGACA Human: ATGTCTGAAGACACGGTGAGC--CTGAAATTGGCTGTGAACCAAACCTATTTCATTCTCCTTCTTTCTCTCTGAAATGCAAACCAGGCAGGACA Cluster: [ ] Orangutan: ATGTCTGAAGACATGGTGAGC--CTGAAATTGGCTGTGAACCAAGCCTATTTCATTCTCCTTCTTTCTCTCCGAAATGCAAACCAGGCAGGACA Gorilla > Chimp --------------- chr21:9414336-9414339 Template switch process: F1: L CCCGGAACCTCAGCCTCATAATGTCTGAAGACATGGTGAGC 1 F3: 4 GAAATTGGCTGTGAACGAAACCTATTTCATTCTCCTT R RF: CCCGGAACCTCAGCCTCATAATGTCTGAAGACATGGTGAGCCTGAAATTGGCTGTGAACCAAATCTATTTCATTCTCCTTCTTTCTCTCTGA RR: GGGCCTTGGAGTCGGAGTATTACAGACTTCTGTACCACTCGGACTTTAACCGACACTTGGTTTAGATAAAGTAAGAGGAAGAAAGAGAGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -42.7) CCGGAACCTCAGCCTCATAATGTCTGAAGACATGGTGAGctCagGAAATTGGCTGTGAACgAAAcCTATTTCATTCTCCTT--- CCGGAACCTCAGCCTCATAATGTCTGAAGACATGGTGAG--CCTGAAATTGGCTGTGAACCAAATCTATTTCATTCTCCTTCTT Template switch alignment (log-probability: -27.2) CCGGAACCTCAGCCTCATAATGTCTGAAGACATGGTGAGC|TCAG|GAAATTGGCTGTGAACgAAAcCTATTTCATTCTCCTT CCGGAACCTCAGCCTCATAATGTCTGAAGACATGGTGAGC|TCAG|GAAATTGGCTGTGAACCAAATCTATTTCATTCTCCTT ========== Event 1859 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tgatttgaatgaaATGAGGATGATTAT------TAAATAGCTCCTCctatgctccagatgcttttcatgtatttctc ↓ 1 4 3 2 Chimp: tgatttgaATGAAATGAGGATCTGGAG------------CATCCTCctatgctccagatgcttttcatgtatttctc ↑ 1 4 3 2 Gorilla: tgatttgaATGAAATGAGGATGATTATTAAATA------GCTCCTCCTAtgctccagatgcttttcatgtatttctc Human: tgatttgaatgaaATGAGGATGATTAT------TAAATAGCTCCTCctatgctccagatgcttttcatgtatttctc Cluster: [ ] Orangutan: Human > Chimp ------------- chr2B:105469643-105469650 Template switch process: F1: L TTGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT 1 F3: 4 TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT R RF: TTGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGATGATTATTAAATAGCTCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT RR: AACGTCTAAGAATTTTTATAACTAAACTTACTTTACTCCTACTAATAATTTATCGAGGAGGATACGAGGTCTACGAAAAGTACATAAAGAGTCAA F2: 3 ACGAGGTC 2 Unidirectional alignment (log-probability: -31.9) TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT-------------CtggagcaTCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGATGATTATTAAATAGC-------TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT Template switch alignment (log-probability: -16.3) TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT|CTGGAGCA|TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT|CTGGAGCA|TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT Gorilla > Chimp --------------- chr2B:105469643-105469650 Template switch process: F1: L TTGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT 1 F3: 4 TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT R RF: TTGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGATGATTATTAAATAGCTCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT RR: AACGTCTAAGAATTTTTATAACTAAACTTACTTTACTCCTACTAATAATTTATCGAGGAGGATACGAGGTCTACGAAAAGTACATAAAGAGTCAA F2: 3 ACGAGGTC 2 Unidirectional alignment (log-probability: -31.4) TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT-------------CtggagcaTCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGATGATTATTAAATAGC-------TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT Template switch alignment (log-probability: -16.7) TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT|CTGGAGCA|TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT TGCAGATTCTTAAAAATATTGATTTGAATGAAATGAGGAT|CTGGAGCA|TCCTCCTATGCTCCAGATGCTTTTCATGTATTTCTCAGTT ========== Event 1860 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gacagaatggttgaggtaCGGATGCTCGAGCTCTCA--Aggccacaagtcggcaggggctacattcct Chimp: gacagaatggttgaggtaCGGATGCT---CCTCTCA--AGGCCACAAGTCGGCAGGGGCTACATTCCT ↓ 3 2 1 4 Gorilla: gacagaatggttgaggtaCGGATGCT---CCTCACG----AGCATCCGTCGGCAGGGGCTACATTCCT Human: gacagaatggttgaggtaCGGATGCTCGAGCTCTCA--Aggccacaagtcggcaggggctacattcct Cluster: [ ] Orangutan: gacagaatggttgaggtaccaatgct---cctctccag--gccacaagtcggcaggggctacattcct Chimp > Gorilla --------------- chr21:29244193-29244200 Template switch process: F1: L TGGGGCAGGAGGACAGAATGGTTGAGGTACGGATGCTCCTCAC 1 F3: 4 GTCGGCAGGGGCTACATTCCTGTGTGAAGCTCACTACCCC R RF: TGGGGCAGGAGGACAGAATGGTTGAGGTACGGATGCTCCTCTCAAGGCCACAAGTCGGCAGGGGCTACATTCCTGTGTGAAGCTCACTACCCC RR: ACCCCGTCCTCCTGTCTTACCAACTCCATGCCTACGAGGAGAGTTCCGGTGTTCAGCCGTCCCCGATGTAAGGACACACTTCGAGTGATGGGG F2: 3 CCTACGAG 2 Unidirectional alignment (log-probability: -34.1) GGCAGGAGGACAGAATGGTTGAGGTACGGATGCTCCTC-----------AcgagcatccGTCGGCAGGGGCTACATTCCTGTGTGAAGCTCACTACCCC GGCAGGAGGACAGAATGGTTGAGGTACGGATGCTCCTCTCAAGGCCACAA---------GTCGGCAGGGGCTACATTCCTGTGTGAAGCTCACTACCCC Template switch alignment (log-probability: -22.3) GGCAGGAGGACAGAATGGTTGAGGTACGGATGCTCCTCaC|GAGCATCC|GTCGGCAGGGGCTACATTCCTGTGTGAAGCTCACTACCCC GGCAGGAGGACAGAATGGTTGAGGTACGGATGCTCCTCTC|GAGCATCC|GTCGGCAGGGGCTACATTCCTGTGTGAAGCTCACTACCCC ========== Event 1861 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCCGGCCAACGTCATTGGAT----GAAGGCTTCAGTCGTGTTTCCACAAAACATAGACGTGTTCTC Chimp: GGCCGGCCAGCGTCATTGGAT----GAAGGCTTCAGTCGTGTTTCCACAAAACACAGACGTGTTCTC ↓ 1 4 3 2 Gorilla: GGCCGGCCAGCGTCATTGGATGTGGAAACATGTCAGTCGTGTTTCCACAAAACACAGACGTGTTCTC Human: GGCCGGCCAACGTCATTGGAT----GAAGGCTTCAGTCGTGTTTCCACAAAACATAGACGTGTTCTC Cluster: [ ] Orangutan: GGCCAGCCAACCTCATTGGAT----GAAGGCTTCAGTCATGTTTCCACAAAACACAGACGTGTTCTC Chimp > Gorilla --------------- chr21:8375750-8375759 Template switch process: F1: L TGATGGCACGAGGAGAGCGGGGCCGGCCAGCGTCATTGGATG 1 F3: 4 TCAGTCGTGTTTCCACAAAACACAGACGTGTTCTCCTTTG R RF: TGATGGCACGAGGAGAGCGGGGCCGGCCAGCGTCATTGGATGAAGGCTTCAGTCGTGTTTCCACAAAACACAGACGTGTTCTCCTTTG RR: ACTACCGTGCTCCTCTCGCCCCGGCCGGTCGCAGTAACCTACTTCCGAAGTCAGCACAAAGGTGTTTTGTGTCTGCACAAGAGGAAAC F2: 3 GTACAAAGGT 2 Unidirectional alignment (log-probability: -33.9) ATGGCACGAGGAGAGCGGGGCCGGCCAGCGTCATTGGATG-----TggaaacatgTCAGTCGTGTTTCCACAAAACACAGACGTGTTCTCCTTTG ATGGCACGAGGAGAGCGGGGCCGGCCAGCGTCATTGGATGAAGGCT---------TCAGTCGTGTTTCCACAAAACACAGACGTGTTCTCCTTTG Template switch alignment (log-probability: -22.5) ATGGCACGAGGAGAGCGGGGCCGGCCAGCGTCATTGGATG|TGGAAACAtG|TCAGTCGTGTTTCCACAAAACACAGACGTGTTCTCCTTTG ATGGCACGAGGAGAGCGGGGCCGGCCAGCGTCATTGGATG|TGGAAACACG|TCAGTCGTGTTTCCACAAAACACAGACGTGTTCTCCTTTG ========== Event 1862 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTTGGATCCTG-----AAATATACATCT---------TTTTGCTGATATAGGTATTTATACCCTGGGCACCG Chimp: TGACATATATTTTAAAGTTGCCATCAATCAGATTCATTTTTGGATCCTG-----AAATATACATCT---------TTTTGCTGATATAGATATTTATACCCTGGGCACCG Gorilla: TGACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTTTGAATCTG----------GGCATCA------------------ATCAGATATTTATACCCTGGGCACCG ↑ 4 3 2 1 Human: TGACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTTGGATCCTG-----AAATATACATCT---------TTTTGCTGATATAGGTATTTATACCCTGGGCACCG Cluster: [ ] Orangutan: TGACATATATTTTAAAGTTGGCATCAGTCAGATTCATTTTTGGATCCTGAAATA-----TACATCTTTTTGCTGA---------TATAGATATTTATACCCTGGGCACCG Human > Gorilla --------------- chr2B:30505646-30505653 Template switch process: F1: L TGACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTT 1 F3: 4 GGCATCAATCAGA--------------------------------------------TATTTATACCCTGGGCACCGTATTTAGCATAGGTGGGCAA R RF: TGACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTTGGATCCTGAAATATACATCTTTTTGCTGATATAGGTATTTATACCCTGGGCACCGTATTTAGCATAGGTGGGCAA RR: ACTGTATATAAAATTTCAACCGTAGTTAGTCTAAGTAAAAACCTAGGACTTTATATGTAGAAAAACGACTATATCCATAAATATGGGACCCGTGGCATAAATCGTATCCACCCGTT F2: 3 GTCTAAGT 2 Unidirectional alignment (log-probability: -51.9) GACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTTtGA---------------------------ATctgggcatcaatcAGaTATTTATACCCTGGGCACCGTATTTAG GACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTTGGATCCTGAAATATACATCTTTTTGCTGATAT-------------AGGTATTTATACCCTGGGCACCGTATTTAG Template switch alignment (log-probability: -29.1) GACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTT|TGAATCTG|GGCATCAATCAGA--------------------------------------------TATTTATACCCTGGGCACCGTATTTAG GACATATATTTTAAAGTTGGCATCAATCAGATTCATTTTT|TGAATCTG|GGCATCAATCAGATTCATTTTTGGATCCTGAAATATACATCTTTTTGCTGATATAGGTATTTATACCCTGGGCACCGTATTTAG ========== Event 1863 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACAG--AGACTTTTGGCTGTGAGCAATAG-A Chimp: GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACAG--AGACTTTTGGCTGTGAGCAATAGAA ↓ 3 2 1 4 Gorilla: GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACACATTAGATTTTGGCTGTGAGCAATAGAA Human: GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACAG--AGACTTTTGGCTGTGAGCAATAG-A Cluster: [ ] Orangutan: -------------------------------------------------------------------- Chimp > Gorilla --------------- chr21:30548016-30548022 Template switch process: F1: L TGACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACA 1 F3: 4 TTTTGGCTGTGAGCAATAGAAAGCCAAATTAGCATCAACC R RF: TGACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACAGAGACTTTTGGCTGTGAGCAATAGAAACCCAAATTAGCATCAACC RR: ACTGTCCTGAGAAGTCACTTAGATTACACTCTGTCTCGTGTCTCTGAAAACCGACACTCGTTATCTTTGGGTTTAATCGTAGTTGG F2: 3 AGATTAC 2 Unidirectional alignment (log-probability: -33.5) GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACacattAGA---TTTTGGCTGTGAGCAATAGAAAgCCAAATTAGCATCAACC GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCAC-----AGAGACTTTTGGCTGTGAGCAATAGAAACCCAAATTAGCATCAACC Template switch alignment (log-probability: -22.1) GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACA|CATTAGA|TTTTGGCTGTGAGCAATAGAAAgCCAAATTAGCATCAACC GACAGGACTCTTCAGTGAATCTAATGTGAGACAGAGCACA|CATTAGA|TTTTGGCTGTGAGCAATAGAAACCCAAATTAGCATCAACC ========== Event 1864 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CTGCAACAAGCACAATTTGCTCGCCTAAAGAGGCATAACTGCCCATGACAGCGC Chimp: CTGCAACAAGCACAATTTGCTCGCCTAAAGAGGCATAACTGCCCATGACAGCGC Gorilla: CTGCAACAAGCACAATTTGCTTTCTT---TAGGCATAACTGCCCATGACAGGGC ↓ 13 4 2 Human: CTGCAACAAGCACAATTTGCTCGCCTAAAGAGGCATAACTGCCCATGACAGCGC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr21:7023245-7023253 Template switch process: F1: L CCTACATCTCACCAATCTCACTGCAACAAGCACAATTTGCTC 1 F3: 4 GGCATAACTGCCCATGACAGCGCAAATCTCTAACACGCA R RF: CCTACATCTCACCAATCTCACTGCAACAAGCACAATTTGCTTTCTTTAGGCATAACTGCCCATGACAGGGCAAATCTCTAACACGCA RR: GGATGTAGAGTGGTTAGAGTGACGTTGTTCGTGTTAAACGAAAGAAATCCGTATTGACGGGTACTGTCCCGTTTAGAGATTGTGCGT F2: 3 AGAAATCCG 2 Unidirectional alignment (log-probability: -39.4) TACATCTCACCAATCTCACTGCAACAAGCACAATTTGC------TcgcctaaagAGGCATAACTGCCCATGACAGcGCAAATCTCTAACACGCA TACATCTCACCAATCTCACTGCAACAAGCACAATTTGCTTTCTTT---------AGGCATAACTGCCCATGACAGGGCAAATCTCTAACACGCA Template switch alignment (log-probability: -27.9) TACATCTCACCAATCTCACTGCAACAAGCACAATTTGCTc|GCCTAAAGA|GGCATAACTGCCCATGACAGcGCAAATCTCTAACACGCA TACATCTCACCAATCTCACTGCAACAAGCACAATTTGCTT|GCCTAAAGA|GGCATAACTGCCCATGACAGGGCAAATCTCTAACACGCA ========== Event 1865 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCATTAAACAGTCATTGCACT--------------------------------------------------------GTCACTGGAGAATAGGAGAAGCACAGGCAATACACTATTTGAGCCATGACAATGTTAGAGGATTTCT---- Chimp: CTCATTAAACAGTCATTGCACC------------------------------CAAAGTGTAAATCAAACCTAAGTGAGCCCCCTGGAGAATAGGAGAAGCACAGGCAATACACTATTTGAGCCATGATAATGTTAGAGGATTTCT---- Gorilla: CTCATTAAACAGTCATTGCACCCAAAGTGTAAATCAAAC----CTAAGTGAG--------------------------CCCCCTGGAGAATAGGAGAAGCACAGGCAATACGCTATTTGAGCCATGACAAACTTAGAGGATTTCT---- ↓ 1 4 3 2 Human: CTCATTAAACAGTCATTGCACT--------------------------------------------------------GTCACTGGAGAATAGGAGAAGCACAGGCAATACACTATTTGAGCCATGACAATGTTAGAGGATTTCT---- Cluster: [ ] Orangutan: CTCATTAAACAGTCATTGCACCCAAAGTGTAAATCAAATCTGACTAAGTGAG--------------------------CCCCCTGAAGAATAGGAGAAGCACAGGCAATACACTACTTGAGCCATGACAAACTTAAAGGATTTCTATCT Gorilla > Human --------------- chr2:140808218-140808222 Template switch process: F1: L CTTGAAAGGTGTTAACAGTCCTCATTAAACAGTCATTGCAC 1 F3: 4 CTGGAGAATAGGAGAAGCACAGGCAATACACTATTTGAGC R RF: CTTGAAAGGTGTTAACAGTCCTCATTAAACAGTCATTGCACCCAAAGTGTAAATCAAACCTAAGTGAGCCCCCTGGAGAATAGGAGAAGCACAGGCAATACGCTATTTGAGCCATGACA RR: GAACTTTCCACAATTGTCAGGAGTAATTTGTCAGTAACGTGGGTTTCACATTTAGTTTGGATTCACTCGGGGGACCTCTTATCCTCTTCGTGTCCGTTATGCGATAAACTCGGTACTGT F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -33.1) TTGAAAGGTGTTAACAGTCCTCATTAAACAGTCATTGCAC------TGT--------------------CaCTGGAGAATAGGAGAAGCACAGGCAATACaCTATTTGAGC TTGAAAGGTGTTAACAGTCCTCATTAAACAGTCATTGCACCCAAAGTGTAAATCAAACCTAAGTGAGCCCCCTGGAGAATAGGAGAAGCACAGGCAATACGCTATTTGAGC Template switch alignment (log-probability: -21.9) TTGAAAGGTGTTAACAGTCCTCATTAAACAGTCATTGCAC|TGTCA|CTGGAGAATAGGAGAAGCACAGGCAATACaCTATTTGAGC TTGAAAGGTGTTAACAGTCCTCATTAAACAGTCATTGCAC|TGTCA|CTGGAGAATAGGAGAAGCACAGGCAATACGCTATTTGAGC ========== Event 1866 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: caaagtaaacagcagaaATGACTTTTTATGGTAAGATTCTACTACATATTGAA-AAAACCCTAGTG ↓ 3 2 1 4 Chimp: caaagtaaacagcagaaATGACTTTTTATGGTAAAA-----AGTCATATTGAA-AAAACCCTAGTG Gorilla: CAAAGTAAACAGCAGAAATGACTTTTTATGGTAAGATTCTACTACATATTGaaaaaaaCCCTAGTG Human: caaagtaaacagcagaaATGACTTTTTATGGTAAGATTCTACTACATATTGAA-AAAACCCTAGTG Cluster: [ ] Orangutan: CAAAATAAACAGCAGAAATGAC--------------------TAAATATTGAA-AAAACCCTAGTG Human > Chimp ------------- chr2B:30069008-30069013 Template switch process: F1: L TAGTGAACAAAGTAAACAGCAGAAATGACTTTTTATGGTAA 1 F3: 4 ATATTGAAAAAACCCTAGTGACATACAAGTATGTAAGTT R RF: TAGTGAACAAAGTAAACAGCAGAAATGACTTTTTATGGTAAGATTCTACTACATATTGAAAAAACCCTAGTGACATACAAGTATGTAGGTT RR: ATCACTTGTTTCATTTGTCGTCTTTACTGAAAAATACCATTCTAAGATGATGTATAACTTTTTTGGGATCACTGTATGTTCATACATCCAA F2: 3 CTGAAA 2 Unidirectional alignment (log-probability: -33.3) AGTGAACAAAGTAAACAGCAGAAATGACTTTTTATGGTAA---------AaagtCATATTGAAAAAACCCTAGTGACATACAAGTATGTAaGTT AGTGAACAAAGTAAACAGCAGAAATGACTTTTTATGGTAAGATTCTACTA----CATATTGAAAAAACCCTAGTGACATACAAGTATGTAGGTT Template switch alignment (log-probability: -22) AGTGAACAAAGTAAACAGCAGAAATGACTTTTTATGGTAA|AAAGTC|ATATTGAAAAAACCCTAGTGACATACAAGTATGTAaGTT AGTGAACAAAGTAAACAGCAGAAATGACTTTTTATGGTAA|AAAGTC|ATATTGAAAAAACCCTAGTGACATACAAGTATGTAGGTT ========== Event 1867 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 345 Detected in comparisons: 3456 Multiple sequence alignment: Human: AGATAGATACATATTTTCTTA-------AGTAAAATGTATTGATATTTTAC-------TAATCATTTATCACTAAGAGGATCAATT Chimp: AGATAGATACATATTTTCTTA-------AGTAAAATGTATTGATATTTTAC-------TAATCATTTATCACTAAGACGATCAATT ↑ 13 24 Gorilla: AGATAGATACATATTTTCTTAAATGATTAGTAAAATATCAATACATTTTAC--------------TTATCACTAAGAGGATCAATT ↓ 13 24 ↑ 13 24 Human: AGATAGATACATATTTTCTTA-------AGTAAAATGTATTGATATTTTAC-------TAATCATTTATCACTAAGAGGATCAATT Cluster: [ ] Orangutan: AGATAGATACATATTTTCTTA-------AGTAAAATGTATTGATATTTTACTAATCAT-------TTATCACTAAGAGGATCAATT Gorilla > Human --------------- chr2:140279937-140279965 Template switch process: F1: L TTGAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA 1 F3: 4 TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT R RF: TTGAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAAATGATTAGTAAAATATCAATACATTTTACTTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT RR: AACTTTCATCGGAAATATTTTCTATCTATGTATAAAAGAATTTACTAATCATTTTATAGTTATGTAAAATGAATAGTGATTCTCCTAGTTAATAAACATACTTGAATGGAA F2: 3 TACTAATCATTTTATAGTTATGTAAAATG 2 Unidirectional alignment (log-probability: -59.7) GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTA-------AGTAAAATgtattgAT------ATTTTACtaatcatTTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAAATGATTAGTAAAAT------ATCAATACATTTTAC-------TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT Template switch alignment (log-probability: -19.4) GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA|GTAAAATGTATTGATATTTTACTAATCAT|TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA|GTAAAATGTATTGATATTTTACTAATCAT|TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT Human > Gorilla --------------- chr2B:32265429-32265457 Template switch process: F1: L TTGAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA 1 F3: 4 TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT R RF: TTGAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAAGTAAAATGTATTGATATTTTACTAATCATTTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT RR: AACTTTCATCGGAAATATTTTCTATCTATGTATAAAAGAATTCATTTTACATAACTATAAAATGATTAGTAAATAGTGATTCTCCTAGTTAATAAACATACTTGAATGGAA F2: 3 CATTTTACATAACTATAAAATGATTAGTA 2 Unidirectional alignment (log-probability: -59.7) GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAaatgattAGTAAAAT------ATcaatacATTTTAC-------TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTA-------AGTAAAATGTATTGAT------ATTTTACTAATCATTTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT Template switch alignment (log-probability: -19.4) GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA|ATGATTAGTAAAATATCAATACATTTTAC|TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA|ATGATTAGTAAAATATCAATACATTTTAC|TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT Gorilla > Chimp --------------- chr2B:29990669-29990697 Template switch process: F1: L TTGAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA 1 F3: 4 TTATCACTAAGACGATCAATTATTTGTATGAACTTACCTT R RF: TTGAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAAATGATTAGTAAAATATCAATACATTTTACTTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT RR: AACTTTCATCGGAAATATTTTCTATCTATGTATAAAAGAATTTACTAATCATTTTATAGTTATGTAAAATGAATAGTGATTCTCCTAGTTAATAAACATACTTGAATGGAA F2: 3 TACTAATCATTTTATAGTTATGTAAAATG 2 Unidirectional alignment (log-probability: -65.2) GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTA-------AGTAAAATgtattgAT------ATTTTACtaatcatTTATCACTAAGAcGATCAATTATTTGTATGAACTTACCTT GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAAATGATTAGTAAAAT------ATCAATACATTTTAC-------TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT Template switch alignment (log-probability: -25) GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA|GTAAAATGTATTGATATTTTACTAATCAT|TTATCACTAAGAcGATCAATTATTTGTATGAACTTACCTT GAAAGTAGCCTTTATAAAAGATAGATACATATTTTCTTAA|GTAAAATGTATTGATATTTTACTAATCAT|TTATCACTAAGAGGATCAATTATTTGTATGAACTTACCTT ========== Event 1868 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAATCACCATGAAATGTGAA----------------------------GGTATGAAAGAAACATTTAACAAACAAACCCTTAAT-TAATGCTGAGATGTCGTTAAATTTAGGGGAA Chimp: AAAATCACCATGAAATGTGAA----------------------------GGTATGAAAGAAACATTTAACAAACAAACCCTTAAC-TAATGCTGAGATGTCGTTAAATTTAGGGGAA ↓ 1 3 4 2 Gorilla: AAAATCACCATGAAATGTGAA--------------------------------------------------------GCATTAGTTAAATGCTGAGGTGTCGTTAAATTTAGGGGAA Human: AAAATCACCATGAAATGTGAA----------------------------GGTATGAAAGAAACATTTAACAAACAAACCCTTAAT-TAATGCTGAGATGTCGTTAAATTTAGGGGAA Cluster: [ ] Orangutan: AAAATAAACATGAAATGTGAAGGTATGAGAGAAACGTTTAACAAACAAA----------------------------CCCTTAAC-TAATGCTGAGGTGTCGTTAGGTTTAGGGGAA Chimp > Gorilla --------------- chr2B:32448471-32448479 Template switch process: F1: L GAAGTACATGGAGCTAATAAAAAATCACCATGAAATGTGAAG 1 F3: 4 AATGCTGAGGTGTCGTTAAATTTAGGGGAAAAGTAGTCAATGTTGCCTAA R RF: GAAGTACATGGAGCTAATAAAAAATCACCATGAAATGTGAAGGTATGAAAGAAACATTTAACAAACAAACCCTTAACTAATGCTGAGATGTCGTTAAATTTAGGGGAAAAGTAGTCAATGTTGCCTAA RR: CTTCATGTACCTCGATTATTTTTTAGTGGTACTTTACACTTCCATACTTTCTTTGTAAATTGTTTGTTTGGGAATTGATTACGACTCTACAGCAATTTAAATCCCCTTTTCATCAGTTACAACGGATT F2: 3 ATTGATTAC 2 Unidirectional alignment (log-probability: -41.1) AGTACATGGAGCTAATAAAAAATCACCATGAAATGTGAAG------------------------------------cattagttaAATGCTGAGgTGTCGTTAAATTTAGGGGAAAAGTAGTCAA AGTACATGGAGCTAATAAAAAATCACCATGAAATGTGAAGGTATGAAAGAAACATTTAACAAACAAACCCTTAACT---------AATGCTGAGATGTCGTTAAATTTAGGGGAAAAGTAGTCAA Template switch alignment (log-probability: -22.7) AGTACATGGAGCTAATAAAAAATCACCATGAAATGTGAAG|CATTAGTTA|AATGCTGAGgTGTCGTTAAATTTAGGGGAAAAGTAGTCAA AGTACATGGAGCTAATAAAAAATCACCATGAAATGTGAAG|CATTAGTTA|AATGCTGAGATGTCGTTAAATTTAGGGGAAAAGTAGTCAA ========== Event 1869 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: gcttgtacaacaatatgaatgtacttaataccactgaaatgtgcacttaaaatctttaagatggtaaattttgtgctatgagtattttagaacaattaaaaCAATGTTCTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGT--------------------------ATTTATGTACAGTATTTATTGGTATCTTGTTTTCTATGT ↑ 3 2 4 1 Chimp: gcttgtacaacaatatgaatgtacgtaataccactgaaatgtgcacttaaaatctttaagatggtcaattttgtgctatgagtattttagaacaattaaaaCAATGTTCTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGT---------------------------------------ATTTATTGGTATCTTGTTTTCTATGT Gorilla: gcttgtacaacaatatgaatgtacttaataccactgaaatgtgcaattaaaatctttaagatggtaaattttgtgctatgagtattttagaacaattaaaaCAATGTTCTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGT-------------ATTTATGTACAGT-------------ATTTACTGGTATCTTGTTTTCTATGT Human: gcttgtacaacaatatgaatgtacttaataccactgaaatgtgcacttaaaatctttaagatggtaaattttgtgctatgagtattttagaacaattaaaaCAATGTTCTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGT--------------------------ATTTATGTACAGTATTTATTGGTATCTTGTTTTCTATGT Cluster: [ ] Orangutan: gcttgtacaacaatatgaatgtacttaataccactgaaatgtgcacttaaaatctttaagatggtaaattttgtgctatgagtgttttagaacaattaaaaCAACGTTCTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGTATTTATGTACAGT--------------------------ATTTATTGGTATCTTGTTTTCTATGT Chimp > Human ------------- chr2:140937687-140937691 Template switch process: F1: L CTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGTATTTAT 1 F3: 4 GTATTTATTGGTATCTTGTTTTCTATGTGATAAGGATTCAAG R RF: TGTACGTAATACCACTGAAATGTGCACTTAAAATCTTTAAGATGGTCAATTTTGTGCTATGAGTATTTTAGAACAATTAAAACAATGTTCTCATGAAAGAAACAGAAGAGGTGACTGAGTCAGTATTTGTATTTATTGGTATCTTGTTTTCTATGTGATAAGGATCCAAG RR: ACATGCATTATGGTGACTTTACACGTGAATTTTAGAAATTCTACCAGTTAAAACACGATACTCATAAAATCTTGTTAATTTTGTTACAAGAGTACTTTCTTTGTCTTCTCCACTGACTCAGTCATAAACATAAATAACCATAGAACAAAAGATACACTATTCCTAGGTTC F2: 3 ACATG 2 Unidirectional alignment (log-probability: -35.6) AAGAAACAGAAGAGGTGACTGAGTCAGTATTTgtatttatgtacaGTATTTATTGGTATCTTGTTTTCTATGTGATAAGGATtCA AAGAAACAGAAGAGGTGACTGAGTCAGTATTT-------------GTATTTATTGGTATCTTGTTTTCTATGTGATAAGGATCCA Template switch alignment (log-probability: -22.1) AAGAAACAGAAGAGGTGACTGAGTCAGTATTTGTATTTAT|GTACA|GTATTTATTGGTATCTTGTTTTCTATGTGATAAGGATtCA AAGAAACAGAAGAGGTGACTGAGTCAGTATTTGTATTTAT|GTACA|GTATTTATTGGTATCTTGTTTTCTATGTGATAAGGATCCA ========== Event 1870 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAACTGAATGTCATAGAGTGATGATCTGTA----TCCCCTGACCCATTGAGAGTGACAG Chimp: ATAACTGAATGTCATAGAGTGATGATCTGTA----TCCCCTGACCCATTGAGAGTGACAG ↓ 3 1 2 4 Gorilla: ATAACTGAATGTCATAGAGTGATGATCTACAGATCATCACTGACCCATTGAGAGTGAGAG ↑ 3 1 2 4 Human: ATAACTGAATGTCATAGAGTGATGATCTGTA----TCCCCTGACCCATTGAGAGTGACAG Cluster: [ ] Orangutan: ATAAATGAATGTCATAGAGTGATGATCTGTA----TCCCCTGACCCATTGAGAGTGACAG Human > Gorilla --------------- chr2B:102431553-102431563 Template switch process: F1: L TATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT 1 F3: 4 CTGACCCATTGAGAGTGAGAGTTTGCATTGGATAATGGAA R RF: TATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCTGTATCCCCTGACCCATTGAGAGTGACAGTTTGCATTGGATAATGGAA RR: ATAGTTTCTATTTTATTGACTTACAGTATCTCACTACTAGACATAGGGGACTGGGTAACTCTCACTGTCAAACGTAACCTATTACCTT F2: 3 ACTACTAGACA 2 Unidirectional alignment (log-probability: -42.3) ATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT-------acagatcatcaCTGACCCATTGAGAGTGAgAGTTTGCATTGGATAATGGAA ATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCTGTATCCC-----------CTGACCCATTGAGAGTGACAGTTTGCATTGGATAATGGAA Template switch alignment (log-probability: -22.6) ATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT|ACAGATCATCA|CTGACCCATTGAGAGTGAgAGTTTGCATTGGATAATGGAA ATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT|ACAGATCATCA|CTGACCCATTGAGAGTGACAGTTTGCATTGGATAATGGAA Chimp > Gorilla --------------- chr2B:102431553-102431563 Template switch process: F1: L TATCAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT 1 F3: 4 CTGACCCATTGAGAGTGAGAGTTTGCATTGGATAATGGAA R RF: TATTAAAGATAAAATAACTGAATGTCATAGAGTGATGATCTGTATCCCCTGACCCATTGAGAGTGACAGTTTGCATTGGATAATGGAA RR: ATAATTTCTATTTTATTGACTTACAGTATCTCACTACTAGACATAGGGGACTGGGTAACTCTCACTGTCAAACGTAACCTATTACCTT F2: 3 ACTACTAGACA 2 Unidirectional alignment (log-probability: -47.8) ATcAAAGATAAAATAACTGAATGTCATAGAGTGATGATCTacagatcatca-------CTGACCCATTGAGAGTGAgAGTTTGCATTGGATAATGGAA ATTAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT-----------GTATCCCCTGACCCATTGAGAGTGACAGTTTGCATTGGATAATGGAA Template switch alignment (log-probability: -28.2) ATcAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT|ACAGATCATCA|CTGACCCATTGAGAGTGAgAGTTTGCATTGGATAATGGAA ATTAAAGATAAAATAACTGAATGTCATAGAGTGATGATCT|ACAGATCATCA|CTGACCCATTGAGAGTGACAGTTTGCATTGGATAATGGAA ========== Event 1871 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCCCACACACCCAGTTTCTCCTTCTCCTGTGAC---------------CTATGCCCTGCAGTCAGGAGAAT Chimp: ATCCCACACACCCAGTTTCTCCTTCTCCTGTGTTAGGACACAGGAGAAGGACTGCCCTGCAGTCAGGAGAAT ↑ 3 1 4 Gorilla: ATCCCACACACCCAGTTTCTCCTTCTCCTGTGTC---------------CTATGCCCTGCAGTCAGGAGAAT Human: ATCCCACACACCCAGTTTCTCCTTCTCCTGTGAC---------------CTATGCCCTGCAGTCAGGAGAAT Cluster: [ ] Orangutan: ATTCCACAAGCCCAGTTTCTCCTTCTCCTGTGTC---------------TTATGCCCTGC---------AAT Gorilla > Chimp --------------- chr21:5854675-5854692 Template switch process: F1: L TTGCACTGATCCCACACACCCAGTTTCTCCTTCTCCTGTGT 1 F3: 4 CTGCCCTGCAGTCAGGAGAATCTTTCCGTAGTGCAGCCGTG R RF: TTGCATTGATCCCACACACCCAGTTTCTCCTTCTCCTGTGTCCTATGCCCTGCAGTCAGGAGAATCTTTCCGTAGTGCAGCCGTG RR: AACGTAACTAGGGTGTGTGGGTCAAAGAGGAAGAGGACACAGGATACGGGACGTCAGTCCTCTTAGAAAGGCATCACGTCGGCAC F2: 3 AGGAAGAGGACACAGGAT 2 Unidirectional alignment (log-probability: -50.7) TGCAcTGATCCCACACACCCAGTTTCTCCTTCTCCTGTGT--TAggacacaggagaaggacTGCCCTGCAGTCAGGAGAATCTTTCCGTAGTGCAGCCGT TGCATTGATCCCACACACCCAGTTTCTCCTTCTCCTGTGTCCTA-----------------TGCCCTGCAGTCAGGAGAATCTTTCCGTAGTGCAGCCGT Template switch alignment (log-probability: -29.1) TGCAcTGATCCCACACACCCAGTTTCTCCTTCTCCTGTGT|TAGGACACAGGAGAAGGA|cTGCCCTGCAGTCAGGAGAATCTTTCCGTAGTGCAGCCGT TGCATTGATCCCACACACCCAGTTTCTCCTTCTCCTGTGT|TAGGACACAGGAGAAGGA|ATGCCCTGCAGTCAGGAGAATCTTTCCGTAGTGCAGCCGT ========== Event 1872 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATATCTGCTGATAGATAACTATT----------------------------------------------------------TTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAGTAATTAAGCAAACAAACATTATTGAAG ↓ 4 3 1 2 Chimp: TATATCTGCTGATAGATAACTATTTTTCACCTATACAAATGGAATTCCTTTATTACTAAATTGAATCTGATGGAATTCTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAGTAATTAAGCAAACAAACATTATTGAAG ↑ 4 3 1 2 Gorilla: TATATCTGCTGATAGATAACTATT----------------------------------------------------------TTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAGTAATTAAGCAAACAAACATTATTGAAG Human: TATATCTGCTGATAGATAACTATT----------------------------------------------------------TTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAGTAATTAAGCAAACAAACATTATTGAAG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNN----------------------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACATTATTGAAG Human > Chimp ------------- chr2B:31253189-31253217 Template switch process: F1: L TATTATATCAAGCCATCTATATCTGCTGATAGATAACTATTTTTCACCTATACAAATGGAATTCC 1 F3: 4 CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAG R RF: TATTATATCAAGCCATCTATATCTGCTGATAGATAACTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAGTAATTAA RR: ATAATATAGTTCGGTAGATATAGACGACTATCTATTGATAAAAAGTGGATATGTTTACCTTAAGGTAGTCTAAGTTAAATCATTAATT F2: 3 TTAAGGTAGTCTAAGTTAAATCATTATTT 2 Unidirectional alignment (log-probability: -94.3) CTGATAGATAActatttttcacctatacaaatggaattcctttattactaaattgaatctgatggaattCTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA CTGATAGATAA----------------------------------------------------------CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA Template switch alignment (log-probability: -25.3) CTGATAGATAACTATTTTTCACCTATACAAATGGAATTCC|TTtATTACTAAATTGAATCTGATGGAATT|CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA CTGATAGATAACTATTTTTCACCTATACAAATGGAATTCC|TTAATTACTAAATTGAATCTGATGGAATT|CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA Gorilla > Chimp --------------- chr2B:31253189-31253217 Template switch process: F1: L TATTATATCAAGCCATCTATATCTGCTGATAGATAACTATTTTTCACCTATACAAATGGAATTCC 1 F3: 4 CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAG R RF: TATTATATCAAGCCATCTATATCTGCTGATAGATAACTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAATTTAGTAATTAA RR: ATAATATAGTTCGGTAGATATAGACGACTATCTATTGATAAAAAGTGGATATGTTTACCTTAAGGTAGTCTAAGTTAAATCATTAATT F2: 3 TTAAGGTAGTCTAAGTTAAATCATTATTT 2 Unidirectional alignment (log-probability: -94.3) CTGATAGATAActatttttcacctatacaaatggaattcctttattactaaattgaatctgatggaattCTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA CTGATAGATAA----------------------------------------------------------CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA Template switch alignment (log-probability: -25.6) CTGATAGATAACTATTTTTCACCTATACAAATGGAATTCC|TTtATTACTAAATTGAATCTGATGGAATT|CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA CTGATAGATAACTATTTTTCACCTATACAAATGGAATTCC|TTAATTACTAAATTGAATCTGATGGAATT|CTATTTTTCACCTATACAAATGGAATTCCATCAGATTCAA ========== Event 1873 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTCACCACCATATCCTGGTG------TGACC----TAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCAAGAGGCATTTTGATGAATAA ↑ 1 4 3 2 Chimp: GGTCACCACCATATCCTGGTG---ATCAAACC--TTCAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCAAGAGGCATTTTGATGAATAA Gorilla: GGTCACCACCATATCCTGGTGATC---AAATCTT--CAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCAAGAGGCATTTTGAAGAATAA ↓ 1 4 3 2 Human: GGTCACCACCATATCCTGGTG------TGACC----TAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCAAGAGGCATTTTGATGAATAA Cluster: [ ] Orangutan: GGTCACCACCATATTCTGGTTATC---AAACCTT--CAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCAAGAGGCATTTTGATGAATAA Chimp > Human ------------- chr2:99931582-99931587 Template switch process: F1: L TCCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG 1 F3: 4 AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT R RF: TCCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTGATCAAACCTTCAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCA RR: AGGAAGTGTAAGTAAAGAGACCAGTGGTGGTATAGGACCACTAGTTTGGAAGTTTCCGGATTTCCAGATTTACATCCTGACAATCGTCTTCAATATTATTTACTTAGGTTCCAGT F2: 3 TCCAGT 2 Unidirectional alignment (log-probability: -30.3) CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTGtgacct-----------AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG------ATCAAACCTTCAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT Template switch alignment (log-probability: -16) CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG|TGACCT|AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG|TGACCT|AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT Gorilla > Human --------------- chr2:99931582-99931587 Template switch process: F1: L TCCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG 1 F3: 4 AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT R RF: TCCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTGATCAAATCTTCAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGTTATAATAAATGAATCCAAGGTCA RR: AGGAAGTGTAAGTAAAGAGACCAGTGGTGGTATAGGACCACTAGTTTAGAAGTTTCCGGATTTCCAGATTTACATCCTGACAATCGTCTTCAATATTATTTACTTAGGTTCCAGT F2: 3 TCCAGT 2 Unidirectional alignment (log-probability: -29.8) CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG-----------tgacctAAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTGATCAAATCTTC------AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT Template switch alignment (log-probability: -16.5) CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG|TGACCT|AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT CCTTCACATTCATTTCTCTGGTCACCACCATATCCTGGTG|TGACCT|AAAGGCCTAAAGGTCTAAATGTAGGACTGTTAGCAGAAGT ========== Event 1874 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: acatatatatataatctctttgtcactatatatat----atatat-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atataGTGAC--AGAGATAATTTCATTAAAAATT ↓ 3 2 1 4 Chimp: acatatatatataatctctttgtcactatatatat--atatatat-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atataGTGACAAATAGATAATTTCATTAAAAATT Gorilla: atatatatataaaatctctttgtcactatatatat----atatat--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: acatatatatataatctctttgtcactatatatat----atatat-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atataGTGAC--AGAGATAATTTCATTAAAAATT Cluster: [ ] Orangutan: ------------------------tctACATATATAT--ATATACATGTAGTGACAAAGAGATAATTTCATTAAAAATTTATATTAGCAACCTGGCATTAAAAGCTTTATCTATTTTGATATAGGGACCAGTCCCCTTTCTCACCATTAAAAAATTATTTTTATAACATATTAGGCCGTCTGTAGAGGTGGCAAGTCATCATCCCTTGTGGATAATTTTTCCGTAACTGTTATAATATTCACCTGCTGTTTTCATTGTTTTGTGGTACATGCCTAATTTTTTAACCACTAAACTTTGTGGAATCTCCTTCAGTTCTCACAGGCAGATGAatttatttatttttaatttttatttttgagacagtgtctcactctgtcacccaggctggagtgcaatggtacaatcacaattcactgcagcctcaacttcctgagttcaagtgatcctctgatctcagcctttcgagtagaagggaccataggcatgcaccactacacccagctaatttttttattttttgtagagacgagtctcactatgttgcccaggctggtctcgaactcctgagttcaagtgattctcctgcctctgcctcccaaagggctgaaattacagacaggagccaccacacccggctACTTTttatcattcccatttatagctgagggaactgaagcacaTAAGATAGCTGAGCTTCTCAGTGAAATATGTGTGACTCTAGAGTCAATTTCTTGACACTAGTAAATGACCCTTACTGCCTCTACAGCTGTTGATTTAAACACCTGGAACTCCTCGATTCCATAAATTGGCAATTTATTCCATTCAGTTCAATGTTTAAATACCTTCTTTATATAAAAATGTGTAAGCATCCAGTGCCTGGTGCTGAAAAGTGAAGATCAGGTGGAGGAGGAGAACAATGAGTAGCAGAAAATGCTCACAATGAGCTGTATGTAATCTAAAGTGTTATTAGAATGGTAATATAGACTGTGATAAAACACAGATTAAGTTAGGAGGTGGCGTTTTAACTGAACTGTAAACAGTGGCATACATTTTTGCCAGGAGGCTAAAGCAAAGAAGACAAAATGTGCAAAGATATGAGTCCTTAGAGTAAATAGTACACATAGGGGATGAGATGAAGCTTGTCATAGTTGTTGGTTTAGAGCAGGTAAGCAGGGCTTACAAGGTGAGTTCTGTGTTCTTTGTCCAATGTGTTTATTTCAATATGTATTTTATTCCAGGTTATATTATAAATCTGTGAAAAACACTTTTTTCATGCATGCCTAATatgtttttactaacagatgtttttactaacaagattttttttgtttaatgtttAGGTCTAAGAGACCTTAACTCTTATGTTCTGGGCTTTAGACTATTGGGATAAATCCTGAATTCTTTAGATTCTTTTCCACACCCTTTTCTTAGTATTTAAGGATTAATAATTAAGTATTCTTATGACATTATTTTGGATGCTAGCTGACTTAGATTTTCTTTGGAAAAGTTTATGGCCTTTAAGACTACATTATCATTCTGAAATGAATGAATATAATGTAAAAGAAAAATGTGTATATTTCACTACTCTGAAACCCTTAAGTGTAAAATTTCCTTAGTTTCCTGTAATTACTAGGTTTGAAAAATTAAAGTAGAATTATTCTTTATGATGCCAAGATTTTTGAATGGAATATTTGCTTTCTATTGAATTATATGATGTTTTTAAGAATAGGAAATATTTCTTTTATTTGGTAAATTAAAACAAATTAAACTATTTTATTTATAATTGAGAAGCATTAGGGTAAAAGCTAAGTTTA---------------------------------- Human > Chimp ------------- chr2B:101567368-101567376 Template switch process: F1: L AATCTCTTTGTCACTATATATATATATATATATA 1 F3: 4 ATAGATAATTTCATTAAAAATTTATATTAGCAACCTGGCATT R RF: AATCTCTTTGTCACTATATATATATATATATATAGTGACAGAGATAATTTCATTAAAAATTTATATTAGCAACCTGGCATT RR: TTAGAGAAACAGTGATATATATATATATATATATCACTGTCTCTATTAAAGTAATTTTTAAATATAATCGTTGGACCGTAA F2: 3 AACAGTGAT 2 Unidirectional alignment (log-probability: -32.9) AATCTCTTTGTCACtaTATATATATATATATATATAGTGACAaAtaGATAATTTCATTAAAAATTTATATTAGCAACCTGGCA AATCTCTTTGTCAC--TATATATATATATATATATAGTGACAGA--GATAATTTCATTAAAAATTTATATTAGCAACCTGGCA Template switch alignment (log-probability: -22.3) AATCTCTTTGTCACTATATATATATATATATATA|TAGTGACAA|AtAGATAATTTCATTAAAAATTTATATTAGCAACCTGGCA AATCTCTTTGTCACTATATATATATATATATATA|TAGTGACAA|AGAGATAATTTCATTAAAAATTTATATTAGCAACCTGGCA ========== Event 1875 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCATTCTATAACCACCAGGGGGAAGAAAGATTCCTTTCTT------TCTGGTGGTTAAGTACCAACTT Chimp: TGCATTCTATAACCACCAGGGGGAAGAAAGATTCCTTTCTT---CCCCCTGGTGGTTAAGTACCAACTT Gorilla: TGCATTCTATAACCACCAGGGGGAAGAAAGGAATCTTTCTTCCC---CCTGGTGGTTAAGTACCAACTT ↑ 3 1 2 4 Human: TGCATTCTATAACCACCAGGGGGAAGAAAGATTCCTTTCTT------TCTGGTGGTTAAGTACCAACTT Cluster: [ ] Orangutan: TGCATTCTATAACCACCAGGGGGAAGAAAGGAATCTTTCTTCCC---CCTGGTGGTTAAGTACCAATTT Human > Gorilla --------------- chr2B:101347402-101347416 Template switch process: F1: L TATGTTGAGGCTGCATTCTATAACCACCAGGGGGAAGAAAG 1 F3: 4 CTGGTGGTTAAGTACCAACTTATTTTTATTAGCATCTAGT R RF: TATGTTGAGGCTGCATTCTATAACCACCAGGGGGAAGAAAGATTCCTTTCTTTCTGGTGGTTAAGTACCAACTTATTTTTATTAGCATCTAGT RR: ATACAACTCCGACGTAAGATATTGGTGGTCCCCCTTCTTTCTAAGGAAAGAAAGACCACCAATTCATGGTTGAATAAAAATAATCGTAGATCA F2: 3 CCCCTTCTTTCTAAG 2 Unidirectional alignment (log-probability: -42.8) ATGTTGAGGCTGCATTCTATAACCACCAGGGGGAAGAAAG------------gaatctttcttccccCTGGTGGTTAAGTACCAACTTATTTTTATTAGCATCTAGT ATGTTGAGGCTGCATTCTATAACCACCAGGGGGAAGAAAGATTCCTTTCTTT---------------CTGGTGGTTAAGTACCAACTTATTTTTATTAGCATCTAGT Template switch alignment (log-probability: -17.6) ATGTTGAGGCTGCATTCTATAACCACCAGGGGGAAGAAAG|GAATCTTTCTTCCCC|CTGGTGGTTAAGTACCAACTTATTTTTATTAGCATCTAGT ATGTTGAGGCTGCATTCTATAACCACCAGGGGGAAGAAAG|GAATCTTTCTTCCCC|CTGGTGGTTAAGTACCAACTTATTTTTATTAGCATCTAGT ========== Event 1876 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTGAAAGGCTTGGAATCCACATCGATGGATCCTTCCCATCGATCAGCAAAATCCAAAAACCT Chimp: ATTGAAAGGCTTGGAATCCAC------AAATCCTTCCCATTGATCAGCAAAATCCAAAAACCT Gorilla: ATTGAAAGGCTTGGAATCCAC------AAATCCTTCCCATCGATCAGCAAAATCCAAaaacct ↓ 1 4 3 2 Human: ATTGAAAGGCTTGGAATCCACATCGATGGATCCTTCCCATCGATCAGCAAAATCCAAAAACCT Cluster: [ ] Orangutan: ATTGAAAGGCTTGGAATCCAC------AAATCCTTCCCATCGATCAGCAAAATCCAAAAACCT Gorilla > Human --------------- chr21:42051540-42051546 Template switch process: F1: L ACAACATCAAAGTCGCTTTTATTGAAAGGCTTGGAATCCACA 1 F3: 4 ATCCTTCCCATCGATCAGCAAAATCCAAAAACCTAT R RF: ACAACATCAAGGTCGCTTTTATTGAAAGGCTTGGAATCCACAAATCCTTCCCATCGATCAGCAAAATCCAAAAACCTAT RR: TGTTGTAGTTCCAGCGAAAATAACTTTCCGAACCTTAGGTGTTTAGGAAGGGTAGCTAGTCGTTTTAGGTTTTTGGATA F2: 3 GGTAGCT 2 Unidirectional alignment (log-probability: -37.5) AACATCAAaGTCGCTTTTATTGAAAGGCTTGGAATCCACAtcgatggATCCTTCCCATCGATCAGCAAAATCCAAAAACCTAT---- AACATCAAGGTCGCTTTTATTGAAAGGCTTGGAATCCACAA------ATCCTTCCCATCGATCAGCAAAATCCAAAAACCTATCCGC Template switch alignment (log-probability: -22.1) AACATCAAaGTCGCTTTTATTGAAAGGCTTGGAATCCACA|TCGATGG|ATCCTTCCCATCGATCAGCAAAATCCAAAAACCTAT AACATCAAGGTCGCTTTTATTGAAAGGCTTGGAATCCACA|TCGATGG|ATCCTTCCCATCGATCAGCAAAATCCAAAAACCTAT ========== Event 1877 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CATGGCAGACGTGCCCTTTCAGGTGTGTTAGCCAGGGGCTGGAATTTGAAACGGGGGCAAGAGTTCTCCTGTACACCCTTTATATCGAGTAAGAGGACCTGCCAGGGATGCAGGGTGACA-- ↑ 3 2 1 4 Chimp: CATGGCGGACGTGCCCTTTCAGGTGTGTTAGCCAGGGGCTGGAATTTGAAACGGGGGCAAGAGTTCTCCTATACACCCTTTATATCGAGTAAGAGGGCCTTCCAGGGATGCAGGGTGACA-- Gorilla: CATGGCGGACGTGCCCTTTCAGGTGTGTTAGCCAGGGGCTGGAATTTGAAATGGGGGCAAGAGTTCTCCTGTACCCCCTTTATATCGAGTAAGAGGGCCTGCCAGGGATGCAGGGTGACA-- Human: CATGGCAGACGTGCCCTTTCAGGTGTGTTAGCCAGGGGCTGGAATTTGAAACGGGGGCAAGAGTTCTCCTGTACACCCTTTATATCGAGTAAGAGGACCTGCCAGGGATGCAGGGTGACA-- Cluster: [ ] Orangutan: CATGGCGGACGTGCCCTTTCAGGTGTGTTAGCTGGGGGCTGGAATTGGAAACGGGGGCAAGAGTTCTCCTGTACACCCTTTATATCGAGTAAGAGGGCCTGCCAGGGATGCAGAGTGACATg Chimp > Human ------------- chr21:42291267-42291271 Template switch process: F1: L GGCAAGAGTTCTCCTGTACACCCTTTATATCGAGTAAGAGG 1 F3: 4 CCAGGGATGCAGGGTGACATGGCCCGACTTCGGGAGCTCT R RF: CAGGTGTGTTAGCCAGGGGCTGGAATTTGAAACGGGGGCAAGAGTTCTCCTATACACCCTTTATATCGAGTAAGAGGGCCTTCCAGGGATGCAGGGTGACATGGCCCGACTTCGGGAGCTCT RR: GTCCACACAATCGGTCCCCGACCTTAAACTTTGCCCCCGTTCTCAAGAGGATATGTGGGAAATATAGCTCATTCTCCCGGAAGGTCCCTACGTCCCACTGTACCGGGCTGAAGCCCTCGAGA F2: 3 GTCCA 2 Unidirectional alignment (log-probability: -55.9) GCAAGAGTTCTCCTgTACACCCTTTATATCGAGTAAGAGGaCCTgCCAGGGATGCAGGGTGACAtggcccgacttcgggagctct GCAAGAGTTCTCCTATACACCCTTTATATCGAGTAAGAGGGCCTTCCAGGGATGCAGGGTGACA--------------------- Template switch alignment (log-probability: -21.9) GCAAGAGTTCTCCTgTACACCCTTTATATCGAGTAAGAGG|ACCTG|CCAGGGATGCAGGGTGACATGGCCCGACTTCGGGAGCTCT GCAAGAGTTCTCCTATACACCCTTTATATCGAGTAAGAGG|ACCTG|CCAGGGATGCAGGGTGACATGGCCCGACTTCGGGAGCTCT ========== Event 1878 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTAGACG-CTTTGGAATTTAAGTTCTAGAACTACAG-GCCCGACTGAGaaatgcaataggcaa ↓ 3 2 1 4 Chimp: TTTAGACG-CTTTGGAATTTAAGTTCTAGAACTATAGAACTTAACTGAGaaatgcaataggcaa Gorilla: TTTAGACA-CTTTGGAATTTAAATTCTAGAACTATAG-GCCCGACTGAGaaatacaataggcaa Human: TTTAGACG-CTTTGGAATTTAAGTTCTAGAACTACAG-GCCCGACTGAGaaatgcaataggcaa Cluster: [ ] Orangutan: TTTTGATGCCTTTGTAATTTAAGTTCTAGAACTATAG-GCCAGACTGAGaaataccatagccaa Human > Chimp ------------- chr2B:100857887-100857895 Template switch process: F1: L CTCTATAATTTAGACGCTTTGGAATTTAAGTTCTAGAACTA 1 F3: 4 ACTGAGAAATGCAATAGGCAAAATACATTAGCCAAAATGC R RF: CTCTATAATTTAGACGCTTTGGAATTTAAGTTCTAGAACTACAGGCCCGACTGAGAAATGCAATAGGCAAAATACATTAGCCAAAATGC RR: GAGATATTAAATCTGCGAAACCTTAAATTCAAGATCTTGATGTCCGGGCTGACTCTTTACGTTATCCGTTTTATGTAATCGGTTTTACG F2: 3 ATTCAAGAT 2 Unidirectional alignment (log-probability: -34.5) TCTATAATTTAGACGCTTTGGAATTTAAGTTCTAGAACtatagaactTA--------ACTGAGAAATGCAATAGGCAAAATACATTAGCCAAAATGC TCTATAATTTAGACGCTTTGGAATTTAAGTTCTAGAAC---------TACAGGCCCGACTGAGAAATGCAATAGGCAAAATACATTAGCCAAAATGC Template switch alignment (log-probability: -16.4) TCTATAATTTAGACGCTTTGGAATTTAAGTTCTAGAACTA|TAGAACTTA|ACTGAGAAATGCAATAGGCAAAATACATTAGCCAAAATGC TCTATAATTTAGACGCTTTGGAATTTAAGTTCTAGAACTA|TAGAACTTA|ACTGAGAAATGCAATAGGCAAAATACATTAGCCAAAATGC ========== Event 1879 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACACCTTAGGTAGGAAAGAGGTTCTT---CAGTAGCCTGACTTGTGGGTTATGTT Chimp: ACACCTTAGGTAGGAAAGAGGTTCTT---CAGTAGCCTGACTTGTGGGTTATGTT ↓ 1 3 4 2 Gorilla: ACACCTTAGGTAGGAAAGAGGCTACTGAAGAGTAGCCTGACTTGTGGGTTATGTT ↑ 1 3 4 2 Human: ACACCTTAGGTAGGAAAGAGGTTCTT---CAGTAGCCTGACTTGTGGGTTATGTT Cluster: [ ] Orangutan: ACACCTTAGGTAGGAAAGAGGTTCTT---CAGTAGTCTGACCTGTGGGTTATGTT Human > Gorilla --------------- chr2B:100856971-100856979 Template switch process: F1: L AAAAAGCATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG 1 F3: 4 AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACCGCTGT R RF: AAAAAGTATGTGTCATCTGGACACCTTAGGTAGGAAAGAGGTTCTTCAGTAGCCTGACTTGTGGGTTATGTTCCCATCCACAGCTGT RR: TTTTTCATACACAGTAGACCTGTGGAATCCATCCTTTCTCCAAGAAGTCATCGGACTGAACACCCAATACAAGGGTAGGTGTCGACA F2: 3 GAAGTCATC 2 Unidirectional alignment (log-probability: -43.4) AAAAGcATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG-----CtactgaagAGTAGCCTGACTTGTGGGTTATGTTCCCATCCACcGCTGT AAAAGTATGTGTCATCTGGACACCTTAGGTAGGAAAGAGGTTCTTC--------AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACAGCTGT Template switch alignment (log-probability: -27.9) AAAAGcATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG|CTACTGAAG|AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACcGCTGT AAAAGTATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG|CTACTGAAG|AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACAGCTGT Chimp > Gorilla --------------- chr2B:100856971-100856979 Template switch process: F1: L AAAAAGCATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG 1 F3: 4 AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACCGCTGT R RF: AAAAAGTATGTGTCATCTGGACACCTTAGGTAGGAAAGAGGTTCTTCAGTAGCCTGACTTGTGGGTTATGTTCCCATCCACAGCTGT RR: TTTTTCATACACAGTAGACCTGTGGAATCCATCCTTTCTCCAAGAAGTCATCGGACTGAACACCCAATACAAGGGTAGGTGTCGACA F2: 3 GAAGTCATC 2 Unidirectional alignment (log-probability: -43.4) AAAAGcATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG-----CtactgaagAGTAGCCTGACTTGTGGGTTATGTTCCCATCCACcGCTGT AAAAGTATGTGTCATCTGGACACCTTAGGTAGGAAAGAGGTTCTTC--------AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACAGCTGT Template switch alignment (log-probability: -27.9) AAAAGcATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG|CTACTGAAG|AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACcGCTGT AAAAGTATGTGTCATCTGGACACCTTAGGTAGGAAAGAGG|CTACTGAAG|AGTAGCCTGACTTGTGGGTTATGTTCCCATCCACAGCTGT ========== Event 1880 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAATTGTTGCCTCCTTGATAA----TGGGTAACATGACTCAATATGATGCtaaaatggaaaataaattgag Chimp: AATAATTGTTGCCTCCTTGATAA----TGGGTAACATGACTCAATATGATGCtaaaatggaaaataagttgag ↓ 1 4 3 2 Gorilla: AATAATTGTTGCCTCCTTGATGA--------TAGCATC-ATCAATATGATGCtaaaatggaaaataaattgag ↑ 1 4 3 2 Human: AATAATTGTTGCCTCCTTGATAA----TGGGTAACATGACTCAATATGATGCtaaaatggaaaataaattgag Cluster: [ ] Orangutan: AATAATTGTTGCCTTTTTGATAATGGG----TAACATGACTCAATATAATGCtaaaatggaaaata-attgag Human > Gorilla --------------- chr2A:93046109-93046115 Template switch process: F1: L TAGAAATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATGAT 1 F3: 4 TCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT R RF: TAGAAATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATAATGGGTAACATGACTCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT RR: ATCTTTAATCCTTCTTCAATTTATTAACAACGGAGGAACTATTACCCATTGTACTGAGTTATACTACGATTTTACCTTTTATTTAACTCCTGAAAA F2: 3 ACTACGA 2 Unidirectional alignment (log-probability: -34.3) AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATgatagcatcA--------------TCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGAT---------AATGGGTAACATGACTCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT Template switch alignment (log-probability: -22.2) AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATgAT|AGCATCA|TCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATAAT|AGCATCA|TCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT Chimp > Gorilla --------------- chr2A:93046109-93046115 Template switch process: F1: L TAGAAATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATGAT 1 F3: 4 TCAATATGATGCTAAAATGGAAAATAAATTGAGGACTTTT R RF: TAGAAATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATAATGGGTAACATGACTCAATATGATGCTAAAATGGAAAATAAGTTGAGGACTTTT RR: ATCTTTAATCCTTCTTCAATTTATTAACAACGGAGGAACTATTACCCATTGTACTGAGTTATACTACGATTTTACCTTTTATTCAACTCCTGAAAA F2: 3 ACTACGA 2 Unidirectional alignment (log-probability: -39.8) AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATgatagcatcA--------------TCAATATGATGCTAAAATGGAAAATAAaTTGAGGACTTTT AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGAT---------AATGGGTAACATGACTCAATATGATGCTAAAATGGAAAATAAGTTGAGGACTTTT Template switch alignment (log-probability: -27.7) AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATgAT|AGCATCA|TCAATATGATGCTAAAATGGAAAATAAaTTGAGGACTTTT AATTAGGAAGAAGTTAAATAATTGTTGCCTCCTTGATAAT|AGCATCA|TCAATATGATGCTAAAATGGAAAATAAGTTGAGGACTTTT ========== Event 1881 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TTACTTATTTTGAAATAATGGATTTTGGCATAAGACCTCTGCCAAAATCCCCTTCTGGTGGTGTTTCTGATGAA ↑ 3 2 4 1 Chimp: TGACTTATTTTGAAATAATGGATTTTGGCATAAGAC---------------CTTCTGGTGGTGTTTCTGATGAA Gorilla: -------------------------------------------------------------------------- Human: TTACTTATTTTGAAATAATGGATTTTGGCATAAGACCTCTGCCAAAATCCCCTTCTGGTGGTGTTTCTGATGAA Cluster: [ ] Orangutan: -------------------------------------------------------------------------- Chimp > Human ------------- chr21:2778223-2778233 Template switch process: F1: L TGGTTTTACTTATTTTGAAATAATGGATTTTGGCATAAGACCTC 1 F3: 4 CCTTCTGGTGGTGTTTCTGATGAACGGGAGCTGCACTGTCT R RF: TGGTTTGACTTATTTTGAAATAATGGATTTTGGCATAAGACCTTCTGGTGGTGTTTCTGATGAACGGGAGCTGCACTGTCT RR: ACCAAACTGAATAAAACTTTATTACCTAAAACCGTATTCTGGAAGACCACCACAAAGACTACTTGCCCTCGACGTGACAGA F2: 3 CCTAAAACCGT 2 Unidirectional alignment (log-probability: -38.5) TTtACTTATTTTGAAATAATGGATTTTGGCATAAGACctctgccaaaatcccCTTCTGGTGGTGTTTCTGATGAACGGGAGCTGCACTGTC TTGACTTATTTTGAAATAATGGATTTTGGCATAAGAC---------------CTTCTGGTGGTGTTTCTGATGAACGGGAGCTGCACTGTC Template switch alignment (log-probability: -28.7) TTtACTTATTTTGAAATAATGGATTTTGGCATAAGACCTc|TGCCAAAATCC|CCTTCTGGTGGTGTTTCTGATGAACGGGAGCTGCACTGTC TTGACTTATTTTGAAATAATGGATTTTGGCATAAGACCTT|TGCCAAAATCC|CCTTCTGGTGGTGTTTCTGATGAACGGGAGCTGCACTGTC ========== Event 1882 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: acccacttcggcctcccaaagtgctgggattacagatgtgagccaccacacctggccGACCCGCTCTCTTTTAAAGATGGTTGGAGACTGTTATCACTGAGCTCACTGGCTTCAAG--- Chimp: acccacttcggcctcccaaagtgctgggattacagatgtgagccaccacacctggccGACCCGCTCTCTTTTAAAGATGGTTGGAGAC--TTAGCACTGAGCTCACTGGCTTCAAG--- ↑ 3 2 1 4 Gorilla: acccacttcggcctcccaaagtgctgggattacaggcgtaagccaccacacctggccGACCCGCTCTCTTTTAAAGATGGTTGGAGACTGTTATCATGGAGCTCACTGGCTTCAAG--- Human: acccacttcggcctcccaaagtgctgggattacagatgtgagccaccacacctggccGACCCGCTCTCTTTTAAAGATGGTTGGAGACTGTTATCACTGAGCTCACTGGCTTCAAG--- Cluster: [ ] Orangutan: acccacttcggcctcccaaagtgctgggattacaggcgtgagccaccacacctggctGACCCGCTCTCTTTTAAAGATGGTTAGAGACTGTTAACACTGAGCTCACCGGCTTCAAGAGA Gorilla > Chimp --------------- chr21:2955277-2955282 Template switch process: F1: L ACACCTGGCCGACCCGCTCTCTTTTAAAGATGGTTGGAGACTT 1 F3: 4 GAGCTCACTGGCTTCAAGATATTTTTTCTAGTTGATCTCT R RF: AGTGCTGGGATTACAGGCGTAAGCCACCACACCTGGCCGACCCGCTCTCTTTTAAAGATGGTTGGAGACTGTTATCATGGAGCTCACTGGCTTCAAGATATTTTTTCTAGTTGACCTCT RR: TCACGACCCTAATGTCCGCATTCGGTGGTGTGGACCGGCTGGGCGAGAGAAAATTTCTACCAACCTCTGACAATAGTACCTCGAGTGACCGAAGTTCTATAAAAAAGATCAACTGGAGA F2: 3 TCACGA 2 Unidirectional alignment (log-probability: -42.8) CCTGGCCGACCCGCTCTCTTTTAAAGATGGTTGGAGAC--TTAgCActGAGCTCACTGGCTTCAAGATATTTTTTCTAGTTGAtCTct CCTGGCCGACCCGCTCTCTTTTAAAGATGGTTGGAGACTGTTATCATGGAGCTCACTGGCTTCAAGATATTTTTTCTAGTTGACCT-- Template switch alignment (log-probability: -27.6) CCTGGCCGACCCGCTCTCTTTTAAAGATGGTTGGAGACTt|AGCACT|GAGCTCACTGGCTTCAAGATATTTTTTCTAGTTGAtCTCT CCTGGCCGACCCGCTCTCTTTTAAAGATGGTTGGAGACTG|AGCACT|GAGCTCACTGGCTTCAAGATATTTTTTCTAGTTGACCTCT ========== Event 1883 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ----ACACGGCTCCATGGGG-AGGGGTGGCCATGCTGGAGGAGTCTGTGCGCCT Chimp: ----ACACGGCTCCGTGGGGAAGGGGTGGCCATGCTGGAGGAGTCTGTGCGCCT ↓ 13 2 4 Gorilla: CCGGACACGGCTCCGTGGGGA-AGGGTGGCCACGCTGGAGGAGTCTGTGCGCCT Human: ----ACACGGCTCCATGGGG-AGGGGTGGCCATGCTGGAGGAGTCTGTGCGCCT Cluster: [ ] Orangutan: ----ACACGGCTTCGTGGGG-AGGGGTGGCCATGCTGGAGGAGTCTGTGTGCCT Chimp > Gorilla --------------- chr21:2916861-2916867 Template switch process: F1: L ----------------------------------------------------------------------------ACCACAAGCCCCCTCTGCCTCCGGACACGGCTCCGTGGGGAAGGG 1 F3: 4 GCTGGAGGAGTCTGTGCGCCTCGTGGGGAGGGGTGGCTAT R RF: CGGAGCTGGAAGGGCTCAGTCCCTGGTGCCCCCTGAGCGCGGTGCAGTGAGGGGCGGGAGGCATGGGTTCTCTGCCACCACAAGCCCCCTCTGCCTCCGGACACGGCTCCGTGGGGAAGGGGTGGCCATGCTGGAGGAGTCTGTGCGCCTCGTGGGGAGGGGTGGCTAT RR: GCCTCGACCTTCCCGAGTCAGGGACCACGGGGGACTCGCGCCACGTCACTCCCCGCCCTCCGTACCCAAGAGACGGTGGTGTTCGGGGGAGACGGAGGCCTGTGCCGAGGCACCCCTTCCCCACCGGTACGACCTCCTCAGACACGCGGAGCACCCCTCCCCACCGATA F2: 3 CACCGGT 2 Unidirectional alignment (log-probability: -55.2) aagccccctctgcctccggACACGGCTCCGTGGGGAA-GGGTGGCCAcGCTGGAGGAGTCTGTGCGCCTCGTGGGGAGGGGTGGCTAT -------------------ACACGGCTCCGTGGGGAAGGGGTGGCCATGCTGGAGGAGTCTGTGCGCCTCGTGGGGAGGGGTGGCTAT Template switch alignment (log-probability: -30.4) AAGCCCCCTCTGCCTCCGGACACGGCTCCGTGGGGAAGGG|TGGCCAC|GCTGGAGGAGTCTGTGCGCCTCGTGGGGAGGGGTGGCTAT AAGCCCCCTCTGCCTCCGGACACGGCTCCGTGGGGAAGGG|TGGCCAC|GCTGGAGGAGTCTGTGCGCCTCGTGGGGAGGGGTGGCTAT ========== Event 1884 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGTGGTTGCCATACCAAATTGAGATACAGTTAA-----TGGTCATTCTTGTCAGCCTGTTCACACTTGATACCACTCT Chimp: ATGTGGTTGCCATACCAAATTGAGATACAGTTAA-----TGGTCATTCTTGTCAGCCTATTCACACTTGATACCACTCT ↓ 3 2 1 4 Gorilla: ATGTGGTTGCCATACCAAATTGAGATAGGCTGTA----------TCTCAAGTCAGCCTATTCACACTTGATACCACTCT ↑ 3 2 1 4 Human: ATGTGGTTGCCATACCAAATTGAGATACAGTTAA-----TGGTCATTCTTGTCAGCCTGTTCACACTTGATACCACTCT Cluster: [ ] Orangutan: ACATGGTTGCCATACCAAATTGAGATACAGTTAATGGTC-----ATTCTTGTCAGCCTATTCACACTTGATACCACTCT Human > Gorilla --------------- chr2B:99117505-99117515 Template switch process: F1: L AATGGATGCTACCTATGTGGTTGCCATACCAAATTGAGATA--------GG 1 F3: 4 GTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGAGGTATACCT R RF: AATGGATGCTACCTATGTGGTTGCCATACCAAATTGAGATACAGTTAATGGTCATTCTTGTCAGCCTGTTCACACTTGATACCACTCTATTGGTTGTGAGGTATACCT RR: TTACCTACGATGGATACACCAACGGTATGGTTTAACTCTATGTCAATTACCAGTAAGAACAGTCGGACAAGTGTGAACTATGGTGAGATAACCAACACTCCATATGGA F2: 3 AACTCTATGTC 2 Unidirectional alignment (log-probability: -45.9) GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATA------------------ggctgtatctcaaGTCAGCCTaTTCACACTTGATACCACTCTATTGGTTGTGA GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATACAGTTAATGGTCATTCTT-------------GTCAGCCTGTTCACACTTGATACCACTCTATTGGTTGTGA Template switch alignment (log-probability: -33.1) GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATA--------GG|CTGTATCTCAA|GTCAGCCTaTTCACACTTGATACCACTCTATTGGTTGTGA GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATACAGTTAATGG|CTGTATCTCAA|GTCAGCCTGTTCACACTTGATACCACTCTATTGGTTGTGA Chimp > Gorilla --------------- chr2B:99117505-99117515 Template switch process: F1: L AATGGATGCTACCTATGTGGTTGCCATACCAAATTGAGATA--------GG 1 F3: 4 GTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGA R RF: AATGGATGCTACCTATGTGGTTGCCATACCAAATTGAGATACAGTTAATGGTCATTCTTGTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGA RR: TTACCTACGATGGATACACCAACGGTATGGTTTAACTCTATGTCAATTACCAGTAAGAACAGTCGGATAAGTGTGAACTATGGTGAGATAACCAACACT F2: 3 AACTCTATGTC 2 Unidirectional alignment (log-probability: -40.2) GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATA------------------ggctgtatctcaaGTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGA GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATACAGTTAATGGTCATTCTT-------------GTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGA Template switch alignment (log-probability: -27.3) GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATA--------GG|CTGTATCTCAA|GTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGA GGATGCTACCTATGTGGTTGCCATACCAAATTGAGATACAGTTAATGG|CTGTATCTCAA|GTCAGCCTATTCACACTTGATACCACTCTATTGGTTGTGA ========== Event 1885 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: atatatgcttacatt-tttaca--------------tgcacagatgcaca--tgcatgcctgtacacatgtggatacacatgcagatacacag--------gcctgctcatgtatacatacac--atgtatacctacacacacgtatgtatgcatgcaaccat-------------------------gcatctgtgtccatgtgcatatgtgt Chimp: ATATATGCTTACATT-TTTACA--------------TGCACGCCTGTACA--C----GTGGATACACATGCAGATACACAGGC--CTGCTcat----gtatacatacacatgtacacctacac--acgtacacctacacacaTGTATGTACGCATGCAACCAT-------------------------GCATCTGTGTCCACGTGCATATGTGT ↓ 4 1 3 2 Gorilla: acatatgcttacatt-tttacatgcacagatgcacatgcacGCCTGTACACAT----GTGGAtacacatgcagatacacaggc--ctgctcatgtat----acatacacatgtacacctacacacatgtacacctacacacatgtatgtatgcatgcaaccat-------------------------gcatCTGTGTCCATGTGCATATGTGT Human: atatatgcttacatt-tttaca--------------tgcacagatgcaca--tgcatgcctgtacacatgtggatacacatgcagatacacag--------gcctgctcatgtatacatacac--atgtatacctacacacacgtatgtatgcatgcaaccat-------------------------gcatctgtgtccatgtgcatatgtgt Cluster: [ ] Orangutan: ATATATGCTTACATTTTTTACA--------------TGCACAGATATGCA--T----GCCCACACACATGTGGATACACAGAT--CTGCTCATGTAT----ACATACACATATACAC----------------CTACACACATGTATATATGCATGCAACCATGACTTGcatgtgtgtacatgtgtacacacgtgtgcacatgtgCATATGTGT Chimp > Gorilla --------------- chr21:35652584-35652589 Template switch process: F1: L TTACATTTTTACATGCAC 1 F3: 4 ACATGCACGCCTGTACACATGTGGATACACATGCAGATACACAGGCCTGCTCATGTAT R RF: TTACATTTTTACATGCACGCCTGTACACGTGGATACACATGCAGATACACAGGCCTGCTCATGTATACATACACATGTACACCTACACACGTACACCTACACACATGTATGTACGCATGCAACCATGCATCT RR: AATGTAAAAATGTACGTGCGGACATGTGCACCTATGTGTACGTCTATGTGTCCGGACGAGTACATATGTATGTGTACATGTGGATGTGTGCATGTGGATGTGTGTACATACATGCGTACGTTGGTACGTAGA F2: 3 CGTAGA 2 Unidirectional alignment (log-probability: -53) TTACATTTTTAcatgcacagatgcaCATGCACGCCTGTACACatGTGGATACACATGCAGATAC TTACATTTTTA--------------CATGCACGCCTGTACAC--GTGGATACACATGCAGATAC Template switch alignment (log-probability: -28.9) TTACATTTTTACATGCAC|AGATGC|ACATGCACGCCTGTACACatGTGGATACACATGCAGATAC TTACATTTTTACATGCAC|AGATGC|ACATGCACGCCTGTACAC--GTGGATACACATGCAGATAC ========== Event 1886 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGCAGGGGCTGGGCTCACAGACCGCCTGGCAGCAGGGGCTGGACACACAGCTCACACAGCTAGACTGCTGGCAGCACGAAGAGGAAATCCCAGAGCAGACAGGCTTGCAGCAGACGGGCACACAGCAGGCCTGCTGGCAGGGGGAGGAGGTGCAGCAAGCTGACTGGCAGCTAGACTGCTGGCA ↓ 1 4 3 2 Chimp: TGGCAGGGGCTGGGCTCACAGGTCACTTGGCAGCAGGGGCTGGACACACAG-------------------------------------------------------------------------------------------------------------------------------------- Gorilla: TGGCAGGGGCTGGGCTCACAGGCCACCTGGCAGCAGGGGCTGGACGCACAG-------------------------------------------------------------------------------------------------------------------------------------- Human: TGGCAGGGGCTGGGCTCACAGACCGCCTGGCAGCAGGGGCTGGACACACAGCTCACACAGCTAGACTGCTGGCAGCACGAAGAGGAAATCCCAGAGCAGACAGGCTTGCAGCAGACGGGCACACAGCAGGCCTGCTGGCAGGGGGAGGAGGTGCAGCAAGCTGACTGGCAGCTAGACTGCTGGCA Cluster: [ ] Orangutan: Human > Chimp ------------- chr21:31145310-31145313 Template switch process: F1: L AGGAGCTGGTGCAGCCTGATTGGCAGGGGCTGGGCTCACAG 1 F3: 4 CTTGGCAGCAGGGGCTGGACACACAG R RF: AGGAGCTGGTGCAGCCTGATTGGCAGGGGCTGGGCTCACAGACCGCCTGGCAGCAGGGGCTGGACACACAGCTCACACAGCTAGACTGCTGGCAGCACGAAGAGGAAATCCCAGAGCAGACAGGCTTGCAGCAGACGGGCACACAGCAGGCCTGCTGGCAGGGGGAGGAGGTGCAGCAAGCTGAC RR: TCCTCGACCACGTCGGACTAACCGTCCCCGACCCGAGTGTCTGGCGGACCGTCGTCCCCGACCTGTGTGTCGAGTGTGTCGATCTGACGACCGTCGTGCTTCTCCTTTAGGGTCTCGTCTGTCCGAACGTCGTCTGCCCGTGTGTCGTCCGGACGACCGTCCCCCTCCTCCACGTCGTTCGACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -32.6) GGAGCTGGTGCAGCCTGATTGGCAGGGGCTGGGCTCACAGgtCaCtTGGCAGCAGGGGCTGGACACACAG---------------- GGAGCTGGTGCAGCCTGATTGGCAGGGGCTGGGCTCACAGACCGCCTGGCAGCAGGGGCTGGACACACAGCTCACACAGCTAGACT Template switch alignment (log-probability: -21.5) GGAGCTGGTGCAGCCTGATTGGCAGGGGCTGGGCTCACAG|GTCA|CtTGGCAGCAGGGGCTGGACACACAG GGAGCTGGTGCAGCCTGATTGGCAGGGGCTGGGCTCACAG|GTCA|CCTGGCAGCAGGGGCTGGACACACAG ========== Event 1887 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTTAAATCCTTTCAACATGTGCTATAAATAATAGCACATATTAAAGATCTGTGGCTATTA ↑ 3 2 4 1 Chimp: TGTTAAATCCTTTCAACATGTGCTATAAA----------TATTAAAGATCTATGGCTATTA Gorilla: TGTTAAATCCTTTCAACATGTGCTATAAA----------TATTAAAGATCTATGGCTATTA Human: TGTTAAATCCTTTCAACATGTGCTATAAATAATAGCACATATTAAAGATCTGTGGCTATTA Cluster: [ ] Orangutan: TGTTAAATCCTTTCAACATGTGCTATAAA----------TATTAAAGATCTATGGCTATTA Chimp > Human ------------- chr2:144756567-144756573 Template switch process: F1: L GATCACTACATATGTTAAATCCTTTCAACATGTGCTATAAATA 1 F3: 4 ATATTAAAGATCTGTGGCTATTAAATTACGTGAGAGCAAAT R RF: GATCACTACATATGTTAAATCCTTTCAACATGTGCTATAAATATTAAAGATCTATGGCTATTAAATTACGTGAGAGCAAAT RR: CTAGTGATGTATACAATTTAGGAAAGTTGTACACGATATTTATAATTTCTAGATACCGATAATTTAATGCACTCTCGTTTA F2: 3 CACGATA 2 Unidirectional alignment (log-probability: -31.3) CACTACATATGTTAAATCCTTTCAACATGTGCTATAAataatagcacATATTAAAGATCTgTGGCTATTAAATTACGTGAGAGCAAA CACTACATATGTTAAATCCTTTCAACATGTGCTATAA----------ATATTAAAGATCTATGGCTATTAAATTACGTGAGAGCAAA Template switch alignment (log-probability: -22.2) CACTACATATGTTAAATCCTTTCAACATGTGCTATAAATA|ATAGCAC|ATATTAAAGATCTgTGGCTATTAAATTACGTGAGAGCAAA CACTACATATGTTAAATCCTTTCAACATGTGCTATAAATA|ATAGCAC|ATATTAAAGATCTATGGCTATTAAATTACGTGAGAGCAAA ========== Event 1888 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GGATGGTGGACGTTCCCTTTG------TTGGGAACGTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGGGTCTGGGCAGGGGACACACAGGGAATCACACAGGATGGAGTGAGTTCCCAGGGACCCAGGGTGGCTTGGC Chimp: Gorilla: GGATGGTGGATGTTCCCTTTGTGTAGTCAGGGGAGGTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGGGTCTGGGCAGGGGACACACAGGGAATCACGCAGGATGCAGTGAGTTCCCAGGGACCCAGGGTGGCTTGGC ↓ 1 4 3 2 Human: GGATGGTGGACGTTCCCTTTG------TTGGGAACGTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGGGTCTGGGCAGGGGACACACAGGGAATCACACAGGATGGAGTGAGTTCCCAGGGACCCAGGGTGGCTTGGC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr21:45327879-45327885 Template switch process: F1: L AATGAAGTGGGCGGGTTCTGGGATGGTGGACGTTCCCTTTGT 1 F3: 4 GTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGG R RF: AATAAAGTGGGCGGGTTCTGGGATGGTGGATGTTCCCTTTGTGTAGTCAGGGGAGGTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGGGTCTGGGCAGGGGACACACAGGGAATCACGCAGGATGCAGTGAGTTCCCA RR: TTATTTCACCCGCCCAAGACCCTACCACCTACAAGGGAAACACATCAGTCCCCTCCACAACCACGGTTCGACGGTAAACTCAAACCGAGACTCCCCAGACCCGTCCCCTGTGTGTCCCTTAGTGCGTCCTACGTCACTCAAGGGT F2: 3 CAAGGGT 2 Unidirectional alignment (log-probability: -38.9) TgAAGTGGGCGGGTTCTGGGATGGTGGAcGTTCCCTTTGT------tGGGaAcGTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGG TAAAGTGGGCGGGTTCTGGGATGGTGGATGTTCCCTTTGTGTAGTCAGGGGAGGTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGG Template switch alignment (log-probability: -27.7) TgAAGTGGGCGGGTTCTGGGATGGTGGAcGTTCCCTTTGT|TGGGAAC|GTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGG TAAAGTGGGCGGGTTCTGGGATGGTGGATGTTCCCTTTGT|TGGGAAC|GTGTTGGTGCCAAGCTGCCATTTGAGTTTGGCTCTGAGGG ========== Event 1889 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGAGGCCCATTTGCCCTGACTGCACAGTCCTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCTGTTGCCCACCGTAGCTGCTGTGGGGCCACAGCCTTGAGCCTGGACACTGGCCATGACTGGATACCACCG-------GTG ↑ 4 1 3 2 Chimp: GGGAGGCCCACTTGCCCTGAC----------TGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCTGTTGCCCACCGTGGCTGCTGTGGGGCCACAGCCTTGAGCCTGGACACTGGCCATGACTGGATGCCACCA-------GTG Gorilla: GGGAGACCCACTTGCCCTGACCGCATAGTCCTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCTGTTGCCCACCATGGCTGCTGTGGGGCCACAGCCTTGAGCCTGGACACTGGCCATGACTGGATGCCACCCGCTGCACGTG Human: GGGAGGCCCATTTGCCCTGACTGCACAGTCCTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCTGTTGCCCACCGTAGCTGCTGTGGGGCCACAGCCTTGAGCCTGGACACTGGCCATGACTGGATACCACCG-------GTG Cluster: [ ] Orangutan: GGGAGGCCCACTTGCCCTGACCGCACAGTCCTGCAGCTCGGCTGTGCCCTTGAGTGGGCGGCGCTGCCCTGTTGCCCACCGTGGCTGCTGTGGGGCCACAGCCTTGGGCCTGGACACTGGCCATGACTGGATGCCACCCGCTGCACACG Chimp > Human ------------- chr21:45442099-45442103 Template switch process: F1: L CTCATCCACGCAGTCCTGCGGGGAGGCCCATTTGCCCTGACTGCA 1 F3: 4 CTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCTG R RF: CTCATCCACACAGTCCTGCGGGGAGGCCCACTTGCCCTGACTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCTGTTGCCCACCGTGGCTGCTGTGGGGCCACAGCCTTGAGCCTGGACACTGGCCATGACTG RR: GAGTAGGTGTGTCAGGACGCCCCTCCGGGTGAACGGGACTGACGTCGAGCCGACACGGGAACTCACCCACCGCGACGGGACAACGGGTGGCACCGACGACACCCCGGTGTCGGAACTCGGACCTGTGACCGGTACTGAC F2: 3 CTGAC 2 Unidirectional alignment (log-probability: -37.3) CCACgCAGTCCTGCGGGGAGGCCCAtTTGCCCTGACTGCacagtcctgcAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCT CCACACAGTCCTGCGGGGAGGCCCACTTGCCCTGACTGC----------AGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCT Template switch alignment (log-probability: -28) CCACgCAGTCCTGCGGGGAGGCCCAtTTGCCCTGACTGCA|CAGTC|CTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCT CCACACAGTCCTGCGGGGAGGCCCACTTGCCCTGACTGCA|CAGTC|CTGCAGCTCGGCTGTGCCCTTGAGTGGGTGGCGCTGCCCT ========== Event 1890 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CATTCTACTGTTTTCTGTCTCTTATGCCATAAAAATAAATTTATGGCATAAGATATGTCTATGATATTCTATTT ↑ 3 1 2 4 Chimp: CATTCTACTGTTTTCTGTCTCTAATGCCATA------AATTTAT-------TTTATGTCTATGATATTCTATTT Gorilla: CATTCTACTGTTTTCTGTCTCTTATGCCATA------AATTTAT-------TTTATGTCTATGATATTCTATTT ↓ 3 1 2 4 Human: CATTCTACTGTTTTCTGTCTCTTATGCCATAAAAATAAATTTATGGCATAAGATATGTCTATGATATTCTATTT Cluster: [ ] Orangutan: CATTCTACTGTTTTCTCTCTCTTATGCCATA------AATTTAT-------TTTATGTCTATGATATTCTATTT Chimp > Human ------------- chr2:146082948-146082967 Template switch process: F1: L TTTTCTCCTCAAGATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAAA 1 F3: 4 TATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT R RF: TTTTCTCCTCAAGATTAACCATTCTACTGTTTTCTGTCTCTAATGCCATAAATTTATTTTATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT RR: AAAAGAGGAGTTCTAATTGGTAAGATGACAAAAGACAGAGATTACGGTATTTAAATAAAATACAGATACTATAAGATAAATATTACAAAAGTAATCGTA F2: 3 AGAATACGGTATTTAAATAA 2 Unidirectional alignment (log-probability: -56.3) GATTAACCATTCTACTGTTTTCTGTCTCTtATGCCATAAA-------aataaatttatggcataagaTATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT GATTAACCATTCTACTGTTTTCTGTCTCTAATGCCATAAATTTATTT--------------------TATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT Template switch alignment (log-probability: -29.9) GATTAACCATTCTACTGTTTTCTGTCTCTtATGCCATAAA|AATAAATTTATGGCATaAGA|TATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT GATTAACCATTCTACTGTTTTCTGTCTCTAATGCCATAAA|AATAAATTTATGGCATTAGA|TATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT Gorilla > Human --------------- chr2:146082948-146082967 Template switch process: F1: L CAAGATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAAA 1 F3: 4 TATGTCTATGATATTCTATTTATAATGTTTTCATTAGCAT R RF: CAAGATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAAATTTATTTTATGTCTATGATATTCTATTTATAATATCTTCATTAGCAT RR: GTTCTAATTGGTAAGATGACAAAAGACAGAGAATACGGTATTTAAATAAAATACAGATACTATAAGATAAATATTATAGAAGTAATCGTA F2: 3 AGAATACGGTATTTAAATAA 2 Unidirectional alignment (log-probability: -60.8) GATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAAaaataaatttatggcataagA-------TATGTCTATGATATTCTATTTATAATgTtTTCATTAGCAT GATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAA--------------------ATTTATTTTATGTCTATGATATTCTATTTATAATATCTTCATTAGCAT Template switch alignment (log-probability: -29.4) GATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAAA|AATAAATTTATGGCATAAGA|TATGTCTATGATATTCTATTTATAATgTtTTCATTAGCAT GATTAACCATTCTACTGTTTTCTGTCTCTTATGCCATAAA|AATAAATTTATGGCATAAGA|TATGTCTATGATATTCTATTTATAATATCTTCATTAGCAT ========== Event 1891 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTCCAGGCCACCCACAGTAGCTCCTCCTTCAGCCTTACAGAGGGGCTGCCTGGTCT--------------------------------GCTTTCCTGGCCGTGGGTTGCCCC Chimp: AGTCCAGGCCACCCACAGTAGCTCCTCCTTCAGCCTTACAGAGGGGCTGCCTGGTCT----------------GCTCGGAGCCTTGCCTGCTTTCCTGGCCGTGGGTTGCCCC Gorilla: AGTCCAGGCCACCCACAGTAGCTCCTCCTTCAGCTTTACAGAGGGGCTGCCTGGTCTGCTTGGAGCTTTGTCT----------------GCTTTCCTGGCCGTGGGTTGCCCC ↑ 3 2 4 1 Human: AGTCCAGGCCACCCACAGTAGCTCCTCCTTCAGCCTTACAGAGGGGCTGCCTGGTCT--------------------------------GCTTTCCTGGCCGTGGGTTGCCCC Cluster: [ ] Orangutan: AGTCCAGGCCACCCACAGTAGCTCCTCCTTCAGCCTTACAGAGGAGCTGCCTGGTCTGCTCGGAGCTTTGTGT----------------GCTTTCCTGGCTGTGGGCTGCCCC Human > Gorilla --------------- chr21:37016182-37016187 Template switch process: F1: L AGTAGCTCCTCCTTCAGCTTTACAGAGGGGCTGCCTGGTCTGCTT 1 F3: 4 TTGTCTGCTTTCCTGGCCGTGGGTTGCCCCTCTCTGGGGGCCGATG R RF: AGTAGCTCCTCCTTCAGCCTTACAGAGGGGCTGCCTGGTCTGCTTTCCTGGCCGTGGGTTGCCCCTCTCTGGGGGCCGATG RR: TCATCGAGGAGGAAGTCGGAATGTCTCCCCGACGGACCAGACGAAAGGACCGGCACCCAACGGGGAGAGACCCCCGGCTAC F2: 3 TCGAGG 2 Unidirectional alignment (log-probability: -39.4) CTCCTCCTTCAGCtTTACAGAGGGGCTGCCTGgtctgcttggagctttGTCTGCTTTCCTGGCCGTGGGTTGCCCCTCTCTGGGGG CTCCTCCTTCAGCCTTACAGAGGGGCTGCCTG----------------GTCTGCTTTCCTGGCCGTGGGTTGCCCCTCTCTGGGGG Template switch alignment (log-probability: -27.8) CTCCTCCTTCAGCtTTACAGAGGGGCTGCCTGGTCTGCTT|GGAGCT|TtGTCTGCTTTCCTGGCCGTGGGTTGCCCCTCTCTGGGGG CTCCTCCTTCAGCCTTACAGAGGGGCTGCCTGGTCTGCTT|GGAGCT|TGGTCTGCTTTCCTGGCCGTGGGTTGCCCCTCTCTGGGGG ========== Event 1892 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTAAAAACTGGCT--TTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAGGAGTTAATATTCTTTTAAGAAGATGATTTTCTTTATTCAGTAGATGA ↓ 1 4 3 2 Chimp: GTAAAAACTGGCT-TTTAAAATCATCTTCTTA-AAAGAATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAGGAGTTAATATTCTTTTAAGAAGATGATTTTCTTTATTCAGTAGATGA ↑ 1 4 3 2 Gorilla: GTAAAAACTGGCT--TTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAGGAGTTAATATTCTTTTAAGAAGATGATTTTCTTTATTCAGTAGATGA Human: GTAAAAACTGGCT--TTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAGGAGTTAATATTCTTTTAAGAAGATGATTTTCTTTATTCAGTAGATGA Cluster: [ ] Orangutan: GTAAAAACTGGCTT-TTAAAATCATCTTCTTA-AAAGAATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAAGAGTTAATATTCTTTTAAGAAGATGATTTTCTTTATTCAGTAGATGA Human > Chimp ------------- chr2B:35071501-35071517 Template switch process: F1: L GAAATTAACAAAGTAAAAACTGGCTTTTAAA 1 F3: 4 ATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA R RF: GAAATTAACAAAGTAAAAACTGGCTTTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAGGAGTTAATATTCTTTTAAGAAGATGAT RR: CTTTAATTGTTTCATTTTTGACCGAAATTTTAGTAGAAGATTTTTTCATATAATTGTGAAGAAAGATAAAAAGAATAAAAATTTCTTTTCATCTTTCTCCTCAATTATAAGAAAATTCTTCTACTA F2: 3 AGAAAATTCTTCTACTA 2 Unidirectional alignment (log-probability: -34.7) GAAATTAACAAAGTAAAAACTGGCtTTTAAAATCATCTTCT-tAAAAGaATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA GAAATTAACAAAGTAAAAACTGGC-TTTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA Template switch alignment (log-probability: -23.2) GAAATTAACAAAGTAAAAACTGGCTTTtAAA|ATCATCTTCTTAAAAGA|ATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA GAAATTAACAAAGTAAAAACTGGCTTTAAAA|ATCATCTTCTTAAAAGA|ATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA Gorilla > Chimp --------------- chr2B:35071501-35071517 Template switch process: F1: L GAAATTAACAAAGTAAAAACTGGCTTTTAAA 1 F3: 4 ATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA R RF: GAAATTAACAAAGTAAAAACTGGCTTTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAAAGTAGAAAGAGGAGTTAATATTCTTTTAAGAAGATGAT RR: CTTTAATTGTTTCATTTTTGACCGAAATTTTAGTAGAAGATTTTTTCATATAATTGTGAAGAAAGATAAAAAGAATAAAAATTTCTTTTCATCTTTCTCCTCAATTATAAGAAAATTCTTCTACTA F2: 3 AGAAAATTCTTCTACTA 2 Unidirectional alignment (log-probability: -33.2) GAAATTAACAAAGTAAAAACTGGCTtTTAAAATCATCTTCTt-AAAAGaATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA GAAATTAACAAAGTAAAAACTGGCT-TTAAAATCATCTTCTAAAAAAGTATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA Template switch alignment (log-probability: -23.2) GAAATTAACAAAGTAAAAACTGGCTTTtAAA|ATCATCTTCTTAAAAGA|ATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA GAAATTAACAAAGTAAAAACTGGCTTTAAAA|ATCATCTTCTTAAAAGA|ATATTAACACTTCTTTCTATTTTTCTTATTTTTAAAGAAA ========== Event 1893 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGCCCTGTGGAAGAGGAAGTG------TTCAGCAGCTAAATGCAGGATTGAAAAGAAGAAAGGAGACGGTTCTTGCCACTTTCACAAAGCCAGTTTGTGGTAACAAGAATGGTGATCCCCCAGTGTGTAAGCTTGGCCGTATGCCTACTTATTATCCTACTGAACATGTGCCTCAAAAGCCATTGA Chimp: AGAGCCCTGTCGAAGAGGAAGTG------TTCAGCAGCTAAATGCAGGATTGAAAAGAAGAAAGGAGATGGTTCTTGCCACTTTCACAAAGCCAGTTGCTGGTAACAAGAATGGTGATCCCCCAGTGTGTAAGCTTGGCCGTATGCCTACTTATTATCCTACTGAACATGTGCCTCAAAAGCCATTGA Gorilla: AGTGCCCTGTGGAAGAGGAAGGG------------CACTAAATGCAGGATTGAAAAGAAGAAAGGAGATGGTTCTTGCCACTTTCGCAAAGCCAGTTGGTGGTAACAAGAATGGTGATCCCCCAGTGTGTAAGCTTGGCCGTATGCCTACTTATTATCCTACTGAACATGTGCCTCAAAAGCCATTGA ↓ 1 4 3 2 Human: AGTGCCCTGTGGAAGAGGAAGTG------TTCAGCAGCTAAATGCAGGATTGAAAAGAAGAAAGGAGACGGTTCTTGCCACTTTCACAAAGCCAGTTTGTGGTAACAAGAATGGTGATCCCCCAGTGTGTAAGCTTGGCCGTATGCCTACTTATTATCCTACTGAACATGTGCCTCAAAAGCCATTGA Cluster: [ ] Orangutan: AGTGCCCTGTGGAAGAGGAAGTGTTCAGC------AGCTAAATGCAGGATTGAAAAGAAGAAAGGAGATGGTTCTTGCCCCTTTCACAAAGCAAGTTGGTGGTAACAAGAATGGTGATCCCCCAGTGTGTAAGCTTGGCCATATGCCTACTTATTATCCTACTGAAGATGTGCCTCAAAAGCCATTGA Gorilla > Human --------------- chr2:145337432-145337441 Template switch process: F1: L CAGATATTCCTAATCCGAGGAGTGCCCTGTGGAAGAGGAAG 1 F3: 4 CTAAATGCAGGATTGAAAAGAAGAAAGGAGACGGTTCTTG R RF: CAGATATTCCTAATCCGAGGAGTGCCCTGTGGAAGAGGAAGGGCACTAAATGCAGGATTGAAAAGAAGAAAGGAGATGGTTCTTGCCACTTTCGCAAAGCCAGTTGGTGGTAACAAGAATGGTGATCCCCCAGTGTGTAAGCTTGGCCGTATGCCTACTTATTATCCTACTGAACA RR: GTCTATAAGGATTAGGCTCCTCACGGGACACCTTCTCCTTCCCGTGATTTACGTCCTAACTTTTCTTCTTTCCTCTACCAAGAACGGTGAAAGCGTTTCGGTCAACCACCATTGTTCTTACCACTAGGGGGTCACACATTCGAACCGGCATACGGATGAATAATAGGATGACTTGT F2: 3 GACGACTTGT 2 Unidirectional alignment (log-probability: -39.3) AGATATTCCTAATCCGAGGAGTGCCCTGTGGAAGAGGAAGtgttcagcaG---CTAAATGCAGGATTGAAAAGAAGAAAGGAGAcGGTTCTTG AGATATTCCTAATCCGAGGAGTGCCCTGTGGAAGAGGAAG---------GGCACTAAATGCAGGATTGAAAAGAAGAAAGGAGATGGTTCTTG Template switch alignment (log-probability: -28) AGATATTCCTAATCCGAGGAGTGCCCTGTGGAAGAGGAAG|TGTTCAGcAG|CTAAATGCAGGATTGAAAAGAAGAAAGGAGAcGGTTCTTG AGATATTCCTAATCCGAGGAGTGCCCTGTGGAAGAGGAAG|TGTTCAGTAG|CTAAATGCAGGATTGAAAAGAAGAAAGGAGATGGTTCTTG ========== Event 1894 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATGGTACAGCCACCAATCTACAAAAAGAGGATATATGACC-----AAGAAGGTCTCTTCATTAACTTCCGAA Chimp: TGATGGTACAGCCACCAATCTACAAAAAGAGGATATATGACC-----AAGAAAGTCTCTTCATTAACTTCTGAA ↓ 3 2 1 4 Gorilla: TGATGGTATAGCCACCAATCTACAAAAAGAGGATATATGACCTCTTTTTGTAGCTCTCTTCATTAACTTCTGAA Human: TGATGGTACAGCCACCAATCTACAAAAAGAGGATATATGACC-----AAGAAGGTCTCTTCATTAACTTCCGAA Cluster: [ ] Orangutan: TGATGGTACAGCCACCAATCTACAGAAAGAGGATATATGACC-----AAGAAGTTCTCTTCATTAACTTCCGAA Chimp > Gorilla --------------- chr2B:37378356-37378366 Template switch process: F1: L GATGGTATAGCCACCAATCTACAAAAAGAGGATATATGACC 1 F3: 4 CTCTCTTCATTAACTTCTGAAAACATCAAAGCCATAGTTTA R RF: GATGGTACAGCCACCAATCTACAAAAAGAGGATATATGACCAAGAAAGTCTCTTCATTAACTTCTGAAAACATCAAAGCCATAGTTTA RR: CTACCATGTCGGTGGTTAGATGTTTTTCTCCTATATACTGGTTCTTTCAGAGAAGTAATTGAAGACTTTTGTAGTTTCGGTATCAAAT F2: 3 GATGTTTTTCT 2 Unidirectional alignment (log-probability: -56.2) ATGGTAtAGCCACCAATCTACAAAAAGAGGATATATGACctctttttgtagC-------TCTCTTCATTAACTTCTGAAAACATCAAAGCCATAGttt ATGGTACAGCCACCAATCTACAAAAAGAGGATATATGAC------------CAAGAAAGTCTCTTCATTAACTTCTGAAAACATCAAAGCCATAG--- Template switch alignment (log-probability: -28.2) ATGGTAtAGCCACCAATCTACAAAAAGAGGATATATGACC|TCTTTTTGTAG|cTCTCTTCATTAACTTCTGAAAACATCAAAGCCATAGTTT ATGGTACAGCCACCAATCTACAAAAAGAGGATATATGACC|TCTTTTTGTAG|GTCTCTTCATTAACTTCTGAAAACATCAAAGCCATAGTTT ========== Event 1895 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTTTGCAGTCTAGTCAAGAGGC-----AATATAGACATCAACAATGTCATAGTAATGA Chimp: AGTTTGCAGTCTAGTCAAGAGGC-----AATATAGACATCAACAATGTCATAGTAATGA ↓ 1 3 4 2 Gorilla: AGTTTGCAGTCTAGTCAAGAGATGTCTATATTTAGACATCAACAATGTCATAGTAATGA ↑ 1 3 4 2 Human: AGTTTGCAGTCTAGTCAAGAGGC-----AATATAGACATCAACAATGTCATAGTAATGA Cluster: [ ] Orangutan: AGTTTGCAGTCTAGTCAAGAGGC-----AATATAGACATCAACAATGTCATAGTAATGA Human > Gorilla --------------- chr2B:38564857-38564867 Template switch process: F1: L ACATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG 1 F3: 4 TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGG R RF: ACATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAGGCAATATAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGC RR: TGTACAAATTTTTACTCAGGTCAAACGTCAGATCAGTTCTCCGTTATATCTGTAGTTGTTACAGTATCATTACTTCCATGATCCCCG F2: 3 TTATATCTGTA 2 Unidirectional alignment (log-probability: -40.8) CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG-----AtgtctatattTAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGg CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAGGCAATA----------TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGC Template switch alignment (log-probability: -22.6) CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG|ATGTCTATATT|TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGg CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG|ATGTCTATATT|TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGC Chimp > Gorilla --------------- chr2B:38564857-38564867 Template switch process: F1: L ACATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG 1 F3: 4 TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGG R RF: ACATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAGGCAATATAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGC RR: TGTACAAATTTTTACTCAGGTCAAACGTCAGATCAGTTCTCCGTTATATCTGTAGTTGTTACAGTATCATTACTTCCATGATCCCCG F2: 3 TTATATCTGTA 2 Unidirectional alignment (log-probability: -40.8) CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG-----AtgtctatattTAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGg CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAGGCAATA----------TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGC Template switch alignment (log-probability: -22.6) CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG|ATGTCTATATT|TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGg CATGTTTAAAAATGAGTCCAGTTTGCAGTCTAGTCAAGAG|ATGTCTATATT|TAGACATCAACAATGTCATAGTAATGAAGGTACTAGGGGC ========== Event 1896 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AAATATTGTGTGAAGGAAAAG-------GCCTTTAGAAACATAACAGAAAAGTGTCAGTCATCAAAGAATCTCACCAATACAGAATGCTTTGTTAATATGAGTGATCCAAAGGCAAACAGAAGACACTTTGTTT Chimp: AAATATTGTGTGAAGGAAAAG-------GCCTTTAGAAACATAACAGAAAAGTGTCAGTCATCAAAGAATCTCACCAATACAGAATGCTTTGTTAATATGAGTGATCCAAAGGCAAACAGAAGACACTTTGTTT Gorilla: AAATATTGTGTGAAGGAAAAG--------------ATAACATAACAGAAAAGTGTCAGTCATCAAAGGATCTCACCAATACAGAATGCTTCGTGAATATGAGTGATCCAAAGGCAAACAGAAGACACTTTGTTT ↓ 1 4 3 2 Human: AAATATTGTGTGAAGGAAAAG-------GCCTTTAGAAACATAACAGAAAAGTGTCAGTCATCAAAGAATCTCACCAATACAGAATGCTTTGTTAATATGAGTGATCCAAAGGCAAACAGAAGACACTTTGTTT Cluster: [ ] Orangutan: AAATATTGTGTGAAGGAAAAGGCCTTTA-------GAAACATAACAGAAAAGTGTCAGTCATCAAAGGATGTCACCAATACAGAATGCTTTGTTAGTATGAGTGATCCAAAGGCAAACAGAAGACACTTTGTTT Gorilla > Human --------------- chr2:146561308-146561316 Template switch process: F1: L GTATATTAATGAGTTTTGCAAAATATTGTGTGAAGGAAAAG 1 F3: 4 AACATAACAGAAAAGTGTCAGTCATCAAAGAATCTCACCA R RF: GTATATTAATGAGTTTTGCAAAATATTGTGTGAAGGAAAAGATAACATAACAGAAAAGTGTCAGTCATCAAAGGATCTCACCAATACAGAATGCTTCGTGAATATGAGTGATCCAAAGGC RR: CATATAATTACTCAAAACGTTTTATAACACACTTCCTTTTCTATTGTATTGTCTTTTCACAGTCAGTAGTTTCCTAGAGTGGTTATGTCTTACGAAGCACTTATACTCACTAGGTTTCCG F2: 3 AGATTTCCG 2 Unidirectional alignment (log-probability: -37.5) TATATTAATGAGTTTTGCAAAATATTGTGTGAAGGAAAAGgcctttagaAACATAACAGAAAAGTGTCAGTCATCAAAGaATCTCACCA TATATTAATGAGTTTTGCAAAATATTGTGTGAAGGAAAAG-------ATAACATAACAGAAAAGTGTCAGTCATCAAAGGATCTCACCA Template switch alignment (log-probability: -27.9) TATATTAATGAGTTTTGCAAAATATTGTGTGAAGGAAAAG|GCCTTTaGA|AACATAACAGAAAAGTGTCAGTCATCAAAGaATCTCACCA TATATTAATGAGTTTTGCAAAATATTGTGTGAAGGAAAAG|GCCTTTGGA|AACATAACAGAAAAGTGTCAGTCATCAAAGGATCTCACCA ========== Event 1897 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCCCTACTTCTCAGAGCCTTG----CGG----ACTTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGC Chimp: CTCCCTATTTCTCAGAGCCTTG----CGG----ACTTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGC ↓ 1 4 3 2 Gorilla: CTCCCTATTTCTCAGAGCCTTTCTCTAGGATATTTCTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGC Human: CTCCCTACTTCTCAGAGCCTTG----CGG----ACTTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGC Cluster: [ ] Orangutan: CTCCCTATTTCTCAGAGCCTCG----CGG----ACTTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGC Chimp > Gorilla --------------- chr2B:38821433-38821445 Template switch process: F1: L TTTGGTTAATGCTTTGCTATCTCCCTATTTCTCAGAGCCTTTC 1 F3: 4 TCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGCAAGA R RF: TTTGGTTAATGCTTTGCTATCTCCCTATTTCTCAGAGCCTTGCGGACTTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGCAAGA RR: AAACCAATTACGAAACGATAGAGGGATAAAGAGTCTCGGAACGCCTGAAGTCTGTATAGGATCTTACAGTCAAAAAGATTTTCGTTCT F2: 3 CTTTATAGGATCT 2 Unidirectional alignment (log-probability: -41.1) GGTTAATGCTTTGCTATCTCCCTATTTCTCAGAGCCTT------TctctaggatatttcTCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGCAAGA GGTTAATGCTTTGCTATCTCCCTATTTCTCAGAGCCTTGCGGACT--------------TCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGCAAGA Template switch alignment (log-probability: -28.5) GGTTAATGCTTTGCTATCTCCCTATTTCTCAGAGCCTTtC|TCTAGGATATtTC|TCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGCAAGA GGTTAATGCTTTGCTATCTCCCTATTTCTCAGAGCCTTGC|TCTAGGATATGTC|TCAGACATATCCTAGAATGTCAGTTTTTCTAAAAGCAAGA ========== Event 1898 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAAATGAGGAAATGTAGACTTAGAGAACAGGAAACGTAACCCAACCACAGGTTGACAGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTT-ATCTCTGAGCCAAATCACttttttttttt- Chimp: AAAAATGAGGAAATGCAGACTTAGAGAACAGGAATCGTAACCCAACCACAGGTTGACAGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTT-ATCTCTG-ACCAAATCACTGttttttttt- Gorilla: AAAAATGAGGAAATGCAGACTTAGAGAACAGGAATCGTAACCCAACCATAGGTTGACAGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTTAATCGCTG-ACCAAATCACtttttttttttt ↓ 3 2 1 4 Human: AAAAATGAGGAAATGTAGACTTAGAGAACAGGAAACGTAACCCAACCACAGGTTGACAGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTT-ATCTCTGAGCCAAATCACttttttttttt- Cluster: [ ] Orangutan: AAAAATGAGGAAATGCAGACTTAGAGAACAGGAATCGTAACCCAACCACAGGTTGACAGTTTTCATCCTGGTTATTCCCAAGGCAAATAAGCACTTGATCTCTG-ACCAAATCACttttttt----- Gorilla > Human --------------- chr21:418751-418758 Template switch process: F1: L ACAGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTTA 1 F3: 4 CCAAATCACTTTTTTTTTTTTTTTTTTT R RF: CTTAGAGAACAGGAATCGTAACCCAACCATAGGTTGACAGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTTAATCGCTGACCAAATCACTTTTTTTTTTTTTTTTTTT RR: GAATCTCTTGTCCTTAGCATTGGGTTGGTATCCAACTGTCCAAAGTAGGACCAATTAGGGTTCCGTTTATTCGTGAATTAGCGACTGGTTTAGTGAAAAAAAAAAAAAAAAAAA F2: 3 GAGTCTCT 2 Unidirectional alignment (log-probability: -34.7) AGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTT-ATCtCTGAgCCAAATCACTTTTTTTTTTTTTTTTTTT-------- AGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTTAATCGCTGA-CCAAATCACTTTTTTTTTTTTTTTTTTTTGAGACGG Template switch alignment (log-probability: -22) AGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTTA|TCTCTgAG|CCAAATCACTTTTTTTTTTTTTTTTTTT AGGTTTCATCCTGGTTAATCCCAAGGCAAATAAGCACTTA|TCTCTAAG|CCAAATCACTTTTTTTTTTTTTTTTTTT ========== Event 1899 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCTGGAGAGAGGTTCATGTCTTAGTAGGAAAGAAATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTCATTTTTTGCAGTTTATATTACATAGAAAGGAAATCTATggccgg Chimp: ACCTGGAGAGAGGTTCATGTCTTAGTAGGAAAGAAATACTAGCTAATTTATAAAATAATTTGGGTTTATATTTCATTTTTTGCAGTTTATATTACATAGAAAGGAAATCTATggccag Gorilla: ACCTGGAGAGAGGTTCATGTCTTAGTAGGAAAGAAATATTAGCTAATTTATAAAATAATTTGGGTTTATATTT---------------CTACTATGAAGAAAGGAAATCTATggccgg ↑ 3 2 1 4 Human: ACCTGGAGAGAGGTTCATGTCTTAGTAGGAAAGAAATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTCATTTTTTGCAGTTTATATTACATAGAAAGGAAATCTATggccgg Cluster: [ ] Orangutan: ACCTGGAGAGAAGTTCATGTCTTAGTAGGAAAGAAATATTAGCTAATTTATAAAATAATTTGGGTTTATATTT---------------CTACTATGAAGAAAGGAAATCTATggccgg Human > Gorilla --------------- chr2B:39142503-39142510 Template switch process: F1: L GAAATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTC 1 F3: 4 AGAAAGGAAATCTATGGCCGGGTGTGGTGGCTCAGGCCTG R RF: TCTTAGTAGGAAAGAAATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTCATTTTTTGCAGTTTATATTACATAGAAAGGAAATCTATGGCCGGGTGTGGTGGCTCAGGCCTG RR: AGAATCATCCTTTCTTTATAATCGATTAAATATTTTATTAAACCCAAATATAAAGTAAAAAACGTCAAATATAATGTATCTTTCCTTTAGATACCGGCCCACACCACCGAGTCCGGAC F2: 3 AGTATCAT 2 Unidirectional alignment (log-probability: -31.8) AATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTC----------------------TactatgaAGAAAGGAAATCTATGGCCGGGTGTGGTGGCTCAGGCCTG AATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTCATTTTTTGCAGTTTATATTACAT-------AGAAAGGAAATCTATGGCCGGGTGTGGTGGCTCAGGCCTG Template switch alignment (log-probability: -22.3) AATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTC|TACTAtGA|AGAAAGGAAATCTATGGCCGGGTGTGGTGGCTCAGGCCTG AATATTAGCTAATTTATAAAATAATTTGGGTTTATATTTC|TACTAAGA|AGAAAGGAAATCTATGGCCGGGTGTGGTGGCTCAGGCCTG ========== Event 1900 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATGAGCAAATTACATGCAAGAATG------ACTGGGCAGGCCATACAAACTGT Chimp: CATGAGCAAATTACATGCAAGAATG------ACTGGGCAGGCCATACAAACTGT ↓ 3 1 4 Gorilla: CATGAGCAAATTACATGCAAGAATAGTCATTCTTGGGCAGGCCATACAAACTGT Human: CATGAGCAAATTACATGCAAGAATG------ACTGGGCAGGCCATACAAACTGT Cluster: [ ] Orangutan: TATGAGCAAATTACATGCAAGAATG------ACTGGGCAGGTCATACTCACTGT Chimp > Gorilla --------------- chr2B:38972871-38972879 Template switch process: F1: L TTCCTACTCCCAGAGTACATGAGCAAATTACATGCAAGAAT 1 F3: 4 TGGGCAGGCCATACAAACTGTAATTATAATTTAACACACT R RF: TTCCTACTCCCAGAGTACATGAGCAAATTACATGCAAGAATGACTGGGCAGGCCATACAAACTGTAATTATAATTTAACACACT RR: AAGGATGAGGGTCTCATGTACTCGTTTAATGTACGTTCTTACTGACCCGTCCGGTATGTTTGACATTAATATTAAATTGTGTGA F2: 3 TCTTACTGA 2 Unidirectional alignment (log-probability: -33.7) TCCTACTCCCAGAGTACATGAGCAAATTACATGCAAGAAT---agtcattctTGGGCAGGCCATACAAACTGTAATTATAATTTAACACACT TCCTACTCCCAGAGTACATGAGCAAATTACATGCAAGAATGAC---------TGGGCAGGCCATACAAACTGTAATTATAATTTAACACACT Template switch alignment (log-probability: -16.9) TCCTACTCCCAGAGTACATGAGCAAATTACATGCAAGAAT|AGTCATTCT|TGGGCAGGCCATACAAACTGTAATTATAATTTAACACACT TCCTACTCCCAGAGTACATGAGCAAATTACATGCAAGAAT|AGTCATTCT|TGGGCAGGCCATACAAACTGTAATTATAATTTAACACACT ========== Event 1901 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCCCACACCAAACCCCAGTACTACTGAAC---T---------------------TAGCACCATCTGCTAAGTTCTCATCAAAATAGATTCC Chimp: TTCCCACACCAAACCCCAGTACTACTGAAC---T---------------------TAGCACCATCTGCTAAGTTCCCATCAAAACAGATTCC Gorilla: TTCCCACACCAAACCCCAGTATTACTGAATGGCT-----------TTTTGATGAGAGTCACCATCTGCTAAGTTCTCATCAAAATAGATTCC ↓ 1 4 3 2 Human: TTCCCACACCAAACCCCAGTACTACTGAAC---T---------------------TAGCACCATCTGCTAAGTTCTCATCAAAATAGATTCC Cluster: [ ] Orangutan: TTCCCACACCAAACCCCAGTATTACTGAACCGCTTTTTGATGGTG----------AGTCACCATTTGCTAAGTTGTCATCAAAATAGATTCC Gorilla > Human --------------- chr2:1603111-1603115 Template switch process: F1: L TTTTAAGGAAGAAAGTGAATTTCCCACACCAAACCCCAGTACTACTGAA 1 F3: 4 CACCATCTGCTAAGTTCTCATCAAAATAGATTCCACAGGT R RF: TTGTAAGGAAGAAAGTGAACTTCCCACACCAAACCCCAGTATTACTGAATGGCTTTTTGATGAGAGTCACCATCTGCTAAGTTCTCATCAAAATAGATTCCACAGGT RR: AACATTCCTTCTTTCACTTGAAGGGTGTGGTTTGGGGTCATAATGACTTACCGAAAAACTACTCTCAGTGGTAGACGATTCAAGAGTAGTTTTATCTAAGGTGTCCA F2: 3 GATTC 2 Unidirectional alignment (log-probability: -45.4) AGAAAGTGAAtTTCCCACACCAAACCCCAGTAcTACTGAActtag------------------CACCATCTGCTAAGTTCTCATCAAAATAGATTCCACAGGT AGAAAGTGAACTTCCCACACCAAACCCCAGTATTACTGAA-----TGGCTTTTTGATGAGAGTCACCATCTGCTAAGTTCTCATCAAAATAGATTCCACAGGT Template switch alignment (log-probability: -33.1) AGAAAGTGAAtTTCCCACACCAAACCCCAGTAcTACTGAA|CTTAG|CACCATCTGCTAAGTTCTCATCAAAATAGATTCCACAGGT AGAAAGTGAACTTCCCACACCAAACCCCAGTATTACTGAA|CTTAG|CACCATCTGCTAAGTTCTCATCAAAATAGATTCCACAGGT ========== Event 1902 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGGCCTAGAGAAAGGGAGCCCG-CGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCTCAGTGAGTGACCACAGCAGGGCTCCCCGGCCCTGGCACCAGCC Chimp: GAGGCCTAGAGAAAGGGAGCCCG-CGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCTCAGTGAGTGACCACAGCAGGGCTCCCTGGCCTTGGCACCAGCC ↓ 1 4 3 2 Gorilla: GAGGCCTAGAGAAAGGGAGCCAGCCCTGGCCCGACCTGGGAAGAGGCCGTGTGTGCTGCATGGGTGCTCAGTGAGTGACCACAGCAGGGCTCCCCGGCCTTGGCGCCAGCC ↑ 1 4 3 2 Human: GAGGCCTAGAGAAAGGGAGCCCG-CGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCTCAGTGAGTGACCACAGCAGGGCTCCCCGGCCCTGGCACCAGCC Cluster: [ ] Orangutan: GAGGCCTAGAGAAAGGGAGCCAA-CGGGGCCCGAGCTGGGAAGTGGCTGTGTGTGCTGCGTGGGTGCTCAGTGAGTGACCACAGCAGGGCTCCCCGGCCTCGGCACCAGCC Human > Gorilla --------------- chr2A:1397697-1397703 Template switch process: F1: L CTCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCC 1 F3: 4 GCCCGACCTGGGAAGAGGCCGTGTGTGCTGCATGGGTGCTCAGTGAG R RF: CTCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCCCGCGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCTCAGTGAGTGACCACAGCAGGGCT RR: GAGATCACTCTTTCCTTGACCTCCGGATCTCTTTCCCTCGGGCGCCCCGGGCTAGACCCTTCTCCGGCACACACGACGCACCCACGAGTCACTCACTGGTGTCGTCCCGA F2: 3 GTCCCGA 2 Unidirectional alignment (log-probability: -40.1) TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCCaGcCctGGCCCGAcCTGGGAAGAGGCCGTGTGTGCTGCaTGGGTGCT TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCCCG-CGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCT Template switch alignment (log-probability: -27.8) TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCC|AGCCCTG|GCCCGAcCTGGGAAGAGGCCGTGTGTGCTGCaTGGGTGCT TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCC|AGCCCTG|GCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCT Chimp > Gorilla --------------- chr2A:1397697-1397703 Template switch process: F1: L CTCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCC 1 F3: 4 GCCCGACCTGGGAAGAGGCCGTGTGTGCTGCATGGGTGCTCAGTGAG R RF: CTCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCCCGCGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCTCAGTGAGTGACCACAGCAGGGCT RR: GAGATCACTCTTTCCTTGACCTCCGGATCTCTTTCCCTCGGGCGCCCCGGGCTAGACCCTTCTCCGGCACACACGACGCACCCACGAGTCACTCACTGGTGTCGTCCCGA F2: 3 GTCCCGA 2 Unidirectional alignment (log-probability: -40.1) TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCCaGcCctGGCCCGAcCTGGGAAGAGGCCGTGTGTGCTGCaTGGGTGCT TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCCCG-CGGGGCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCT Template switch alignment (log-probability: -27.8) TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCC|AGCCCTG|GCCCGAcCTGGGAAGAGGCCGTGTGTGCTGCaTGGGTGCT TCTAGTGAGAAAGGAACTGGAGGCCTAGAGAAAGGGAGCC|AGCCCTG|GCCCGATCTGGGAAGAGGCCGTGTGTGCTGCGTGGGTGCT ========== Event 1903 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAATGAGGGGAGGATACAT-TAA---------------------TGG-------------------------------------AGGGGAACAGGTGTACAAAAATTAAAACATATAAATTTAGAGCAATTAACATAGTTTGCATGAATCAATGAATAAAAGACCACAAA--------------------ATATGTAAGAATTTAATACAAT----------CAAGGAAACATTT-------------------------------------------------CCAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCATGCAAACTATGTTAATTGCTCTAAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATTAATTTTTCCCCAGATTTTTA ↑ 1 3 4 2 Chimp: AAATGAGGGGAGGATACAT-TTC-----------TTTCCTTAAATGG-------------------------------CTATCC------------------------------------------------------------------TGTTTATTGAATACCCCAAC----------CCCTTTATTC-------------------CCT-----CACAAATTGGAAATGTTT-------------------------------------CCTTGATTGTATTAAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCATGCAAACTATGTTAATTGCTCTAAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATTAATTTTTCCCCAGATTTTTA Gorilla: AAATGAGGGGAGGATACAT-TTCTTTCCTTAAA-----------TGGCTGTC-------------------------C------------------------------------------------------------------------TATTTATTGAATACCCCAACCCCTTTATTC-----------------------------CCTCACAA-----ATTGGAAATGTTT-------------------------CCTTGATTGTAT------------TAAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCATGCAAACTATGTTAATTGCTCTAAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATTAATTTTTCCCCAGATTTTTA ↓ 1 3 4 2 Human: AAATGAGGGGAGGATACAT-TAA---------------------TGG-------------------------------------AGGGGAACAGGTGTACAAAAATTAAAACATATAAATTTAGAGCAATTAACATAGTTTGCATGAATCAATGAATAAAAGACCACAAA--------------------ATATGTAAGAATTTAATACAAT----------CAAGGAAACATTT-------------------------------------------------CCAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCATGCAAACTATGTTAATTGCTCTAAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATTAATTTTTCCCCAGATTTTTA Cluster: [ ] Orangutan: AAATGAGGAGAGGATACATTTTCTTTCCTTAAAT----------TGGCTATCCTGTTTATGAATANNNNNNNNNNTCC------------------------------------------------------------------------TGTTTATTGAATACCCCACCCCCTTTATTC-----------------------------CCTCTCCC-----AGTGTCCCTGTTTCCTTGATTGAAGTATGCCCGAAGGT------------------------TAAATTCTTACCTATTTTGTGGCCTATTATTCCTTGATTCCTGCACACTATTTTACTTGCTCTGAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATTAAtttttccccagattttta Chimp > Human ------------- chr2:150288901-150289028 Template switch process: F1: L CTGAATTGATTGTGGATTAGGAAATGAGGGGAGGATACATT 1 F3: 4 AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT R RF: CTGAATTGATTGTGGATTAAGAAATGAGGGGAGGATACATTTCTTTCCTTAAATGGCTATCCTGTTTATTGAATACCCCAACCCCTTTATTCCCTCACAAATTGGAAATGTTTCCTTGATTGTATTAAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCATGCAAACTATGTTAATTGCTCTAAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATT RR: GACTTAACTAACACCTAATTCTTTACTCCCCTCCTATGTAAAGAAAGGAATTTACCGATAGGACAAATAACTTATGGGGTTGGGGAAATAAGGGAGTGTTTAACCTTTACAAAGGAACTAACATAATTTAAGAATGTATAAAACACCAGAAAATAAGTAACTAAGTACGTTTGATACAATTAACGAGATTTAAATATACAAAATTAAAAACATGTGGACAAGGGGAGGTAA F2: 3 CCTTTACAAAGGAACTAACATAATTTAAGAATGTATAAAACACCAGAAAATAAGTAACTAAGTACGTTTGATACAATTAACGAGATTTAAATATACAAAATTAAAAACATGTGGACAAGGGGAGGTAA 2 Unidirectional alignment (log-probability: -212) TGAATTGATTGTGGATTAgGAAATGAGGGGAGGATACATT-----------------------------------------------------------------AATGgaggggaacaggtgtacaaaaattaaaacatataaatttagagcaattaacatagtttgcatgaatcaatgaataaaagaccacaaaatatgtaagaatttaatacaatcaaggaaacaTTTCC------------AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT TGAATTGATTGTGGATTAAGAAATGAGGGGAGGATACATTTCTTTCCTTAAATGGCTATCCTGTTTATTGAATACCCCAACCCCTTTATTCCCTCACAAATTGGAAATG-----------------------------------------------------------------------------------------------------------------------TTTCCTTGATTGTATTAAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT Template switch alignment (log-probability: -36.7) TGAATTGATTGTGGATTAgGAAATGAGGGGAGGATACATT|AATGGAGGGGAACAGGTGTACAAAAATTAAAACATATAAATTTAGAGCAATTAACATAGTTTGCATGAATCAATGAATAAAAGACCACAAAATATGTAAGAATTTAATACAATCAAGGAAACATTTCC|AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT TGAATTGATTGTGGATTAAGAAATGAGGGGAGGATACATT|AATGGAGGGGAACAGGTGTACAAAAATTAAAACATATAAATTTAGAGCAATTAACATAGTTTGCATGAATCAATGAATAAAAGACCACAAAATATGTAAGAATTTAATACAATCAAGGAAACATTTCC|AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT Gorilla > Human --------------- chr2:150288901-150289028 Template switch process: F1: L CTGAATTGATTGTGGATTAGGAAATGAGGGGAGGATACATT 1 F3: 4 AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT R RF: CTGAATTGATTGTGGATTAAGAAATGAGGGGAGGATACATTTCTTTCCTTAAATGGCTGTCCTATTTATTGAATACCCCAACCCCTTTATTCCCTCACAAATTGGAAATGTTTCCTTGATTGTATTAAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCATGCAAACTATGTTAATTGCTCTAAATTTATATGTTTTAATTTTTGTACACCTGTTCCCCTCCATT RR: GACTTAACTAACACCTAATTCTTTACTCCCCTCCTATGTAAAGAAAGGAATTTACCGACAGGATAAATAACTTATGGGGTTGGGGAAATAAGGGAGTGTTTAACCTTTACAAAGGAACTAACATAATTTAAGAATGTATAAAACACCAGAAAATAAGTAACTAAGTACGTTTGATACAATTAACGAGATTTAAATATACAAAATTAAAAACATGTGGACAAGGGGAGGTAA F2: 3 CCTTTACAAAGGAACTAACATAATTTAAGAATGTATAAAACACCAGAAAATAAGTAACTAAGTACGTTTGATACAATTAACGAGATTTAAATATACAAAATTAAAAACATGTGGACAAGGGGAGGTAA 2 Unidirectional alignment (log-probability: -211) TGAATTGATTGTGGATTAgGAAATGAGGGGAGGATACATT-----------------------------------------------------------------AATGgaggggaacaggtgtacaaaaattaaaacatataaatttagagcaattaacatagtttgcatgaatcaatgaataaaagaccacaaaatatgtaagaatttaatacaatcaaggaaacaTTTCC------------AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT TGAATTGATTGTGGATTAAGAAATGAGGGGAGGATACATTTCTTTCCTTAAATGGCTGTCCTATTTATTGAATACCCCAACCCCTTTATTCCCTCACAAATTGGAAATG-----------------------------------------------------------------------------------------------------------------------TTTCCTTGATTGTATTAAATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT Template switch alignment (log-probability: -37.2) TGAATTGATTGTGGATTAgGAAATGAGGGGAGGATACATT|AATGGAGGGGAACAGGTGTACAAAAATTAAAACATATAAATTTAGAGCAATTAACATAGTTTGCATGAATCAATGAATAAAAGACCACAAAATATGTAAGAATTTAATACAATCAAGGAAACATTTCC|AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT TGAATTGATTGTGGATTAAGAAATGAGGGGAGGATACATT|AATGGAGGGGAACAGGTGTACAAAAATTAAAACATATAAATTTAGAGCAATTAACATAGTTTGCATGAATCAATGAATAAAAGACCACAAAATATGTAAGAATTTAATACAATCAAGGAAACATTTCC|AATTCTTACATATTTTGTGGTCTTTTATTCATTGATTCAT ========== Event 1904 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTATTAAAGATTTAAGCTTTCTTAGATGATTTCATCTAAGAAATAATACAACTAAGA-AACAA ↑ 3 2 1 4 Chimp: TTTATTAAAGATTTAAGCTTTCTTAGATGATTTCATGTT--TTATAATACAACTAAGAAAACAA Gorilla: TTTATTAAACATTTAAGCTTTCTTAGATGATTTCATGTT--TTATAATACAACTAAGAAAACAA Human: TTTATTAAAGATTTAAGCTTTCTTAGATGATTTCATCTAAGAAATAATACAACTAAGA-AACAA Cluster: [ ] Orangutan: TTTATTAAAGATTTAAGCTTTCTTAGATGATTTCGTGTT--TTATAATACAACTAAGAAAACAA Chimp > Human ------------- chr2:153995091-153995097 Template switch process: F1: L ACCATTTTATTAAAGATTTAAGCTTTCTTAGATGATTTCAT 1 F3: 4 ATAATACAACTAAG-AAACAATTAATTAGATTAGATCTCA R RF: ACCATTTTATTAAAGATTTAAGCTTTCTTAGATGATTTCATGTTTTATAATACAACTAAGAAAACAATTAATTAGATTAGATCTCA RR: TGGTAAAATAATTTCTAAATTCGAAAGAATCTACTAAAGTACAAAATATTATGTTGATTCTTTTGTTAATTAATCTAATCTAGAGT F2: 3 AAGAATC 2 Unidirectional alignment (log-probability: -41.7) CCATTTTATTAAAGATTTAAGCTTTCTTAGATGATTTCATctaagaa-----ATAATACAACTAAGAA-ACAATTAATTAGATTAGATCTCA CCATTTTATTAAAGATTTAAGCTTTCTTAGATGATTTCAT-------GTTTTATAATACAACTAAGAAAACAATTAATTAGATTAGATCTCA Template switch alignment (log-probability: -26.4) CCATTTTATTAAAGATTTAAGCTTTCTTAGATGATTTCAT|CTAAGAA|ATAATACAACTAAG-AAACAATTAATTAGATTAGATCTCA CCATTTTATTAAAGATTTAAGCTTTCTTAGATGATTTCAT|CTAAGAA|ATAATACAACTAAGAAAACAATTAATTAGATTAGATCTCA ========== Event 1905 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAACTAGCACAAGATTTCCTTGGAACATTAAGAAATGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACTAGAACATAATTCCACTCTTCTTAAGTTCCTTTTTGTTAATGTAGAGGGAttt-ttttttCTA Chimp: AAACTAGCACAAGATTTCCTTGGAACATTAAGAAATGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACTAGAACATAATTCCGCTCTTCTTAAGTTCCTTTTTGTTAATGTAGAGGGAttttttttttCTA ↑ 4 1 3 2 Gorilla: AAACTAGCACAAGATTTCCTT---------------GGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACCAGAACATAATTCCACTCTTCTTAAGTTCCTTTTTGTTAATGTAGAGGGAttt-ttttttCTA ↓ 4 1 3 2 Human: AAACTAGCACAAGATTTCCTTGGAACATTAAGAAATGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACTAGAACATAATTCCACTCTTCTTAAGTTCCTTTTTGTTAATGTAGAGGGAttt-ttttttCTA Cluster: [ ] Orangutan: AAACTAGCACAAGATTTCCTTGGAACATTAAGAAATGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACTAGAACATAATTCCACTCTTCTTAAGTTCCTTTTTGTTAATGTAGAGGGAttt-ttttttCTA Gorilla > Human --------------- chr2:87416552-87416562 Template switch process: F1: L GGTTGGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGA 1 F3: 4 TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAA R RF: GGTTGGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACCAGAACATAATTCCACTCTTCTTAAGTTCCTTTTTGTTAATGT RR: CCAACCTCTCTGAAGACCTATTTGATCGTGTTCTAAAGGAACCTCACACGGACCATACACACTACAGTAAAATTTTATCTTGTGGTCTTGTATTAAGGTGAGAAGAATTCAAGGAAAAACAATTACA F2: 3 AAAGAATTACA 2 Unidirectional alignment (log-probability: -32.5) GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTtggaacattaagaaaTGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCT---------------TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA Template switch alignment (log-probability: -22.7) GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGA|ACATTAAgAAA|TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGA|ACATTAACAAA|TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA Gorilla > Chimp --------------- chr2B:88584569-88584579 Template switch process: F1: L GGTTGGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGA 1 F3: 4 TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAA R RF: GGTTGGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGAACACCAGAACATAATTCCACTCTTCTTAAGTTCCTTTTTGTTAATGT RR: CCAACCTCTCTGAAGACCTATTTGATCGTGTTCTAAAGGAACCTCACACGGACCATACACACTACAGTAAAATTTTATCTTGTGGTCTTGTATTAAGGTGAGAAGAATTCAAGGAAAAACAATTACA F2: 3 AAAGAATTACA 2 Unidirectional alignment (log-probability: -32.5) GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTtggaacattaagaaaTGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCT---------------TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA Template switch alignment (log-probability: -22.7) GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGA|ACATTAAgAAA|TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA GGAGAGACTTCTGGATAAACTAGCACAAGATTTCCTTGGA|ACATTAACAAA|TGGAGTGTGCCTGGTATGTGTGATGTCATTTTAAAATAGA ========== Event 1906 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCATCTTTTTCTAAATGTTACATGCAAAGTACAATAATCAAATACTTAGGTTAATTTCTGTTTTCAAAGATTACTAAAGCCTTG------------------------------CTTTACAATGTCATGCTTTACAATGTTACatttatataaaataaac Chimp: TCATCTTTTTCTAAATGTTACATGCAAAGTACAATAATCAAATACTTAGGTTAATTTCTGTTTCCAAAGATTACTAAAGCCTTG---------------------------------------------CTTTACAATGTTACATTTatataaaataaac ↓ 3 2 4 1 Gorilla: TCATCTTTTTCTAAATGTTACATGCAAAGTACAATAATCAAATGCTTAGGTTAATTTCTGTTTTCAAAGATTACTAAAGCCTTG---------------CTTTACAATGTCATG---------------TTTTACAATGTTACATTTatataaaataaac Human: TCATCTTTTTCTAAATGTTACATGCAAAGTACAATAATCAAATACTTAGGTTAATTTCTGTTTTCAAAGATTACTAAAGCCTTG------------------------------CTTTACAATGTCATGCTTTACAATGTTACatttatataaaataaac Cluster: [ ] Orangutan: TCATCTTTTTCTAAATGTTACATGCAAAGTACAATAATCAAACGCTTAGATTAATTTCTGTTTTCAAAGATTACTAAAGCCTtgctttacgatgttatg------------------------------ctttacaatgttaCATTTATataaaataaac Chimp > Gorilla --------------- chr2B:88439528-88439532 Template switch process: F1: L GCTTAGGTTAATTTCTGTTTTCAAAGATTACTAAAGCCTTGCTTTACAATGT 1 F3: 4 TTTACAATGTTACATTTATATAAAATAAACAAATAAAATT R RF: ACATGCAAAGTACAATAATCAAATACTTAGGTTAATTTCTGTTTCCAAAGATTACTAAAGCCTTGCTTTACAATGTTACATTTATATAAAATAAACAAATAAAATT RR: TGTACGTTTCATGTTATTAGTTTATGAATCCAATTAAAGACAAAGGTTTCTAATGATTTCGGAACGAAATGTTACAATGTAAATATATTTTATTTGTTTATTTTAA F2: 3 TGTAC 2 Unidirectional alignment (log-probability: -43.5) TTCTGTTTtCAAAGATTACTAAAGCCTTGCtttacaatgtcatgtTTTACAATGTTACATTTATATAAAATAAACAAATAAAATT TTCTGTTTCCAAAGATTACTAAAGCCTTGC---------------TTTACAATGTTACATTTATATAAAATAAACAAATAAAATT Template switch alignment (log-probability: -27.7) TTCTGTTTtCAAAGATTACTAAAGCCTTGCTTTACAATGT|CATGT|TTTACAATGTTACATTTATATAAAATAAACAAATAAAATT TTCTGTTTCCAAAGATTACTAAAGCCTTGCTTTACAATGT|CATGT|TTTACAATGTTACATTTATATAAAATAAACAAATAAAATT ========== Event 1907 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAGCCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTATATT-TAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTC Chimp: AGAGCCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTATATT-TAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTC ↓ 3 2 1 4 Gorilla: AGAGCCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTACACCTTA------GGAT---AAATTATCCCCTCCCCTGCCTC ↑ 3 2 1 4 Human: AGAGCCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTATATT-TAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTC Cluster: [ ] Orangutan: AGAGCCACAGAGATATACGTTTCCTAAGGTATAAGAAATATTTTATATT-TAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTC Human > Gorilla --------------- chr2B:85922694-85922705 Template switch process: F1: L CCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTA 1 F3: 4 AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT R RF: CCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTATATTTAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT RR: GGTGTCTCTATATGGAAAGGATTCCACATTCTTTATAAAATATAAATCTCCCTCTTGTCTATTAATAGGGGAGGGGACGGAGGTTGTAACTTTTCGTACGA F2: 3 ATAGGATTCCAC 2 Unidirectional alignment (log-probability: -36) CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTacaccttaggATA------------------AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTT----------ATATTTAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT Template switch alignment (log-probability: -22.8) CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTA|CACCTTAGGAtA|AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTA|CACCTTAGGAAA|AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT Chimp > Gorilla --------------- chr2B:85922694-85922705 Template switch process: F1: L CCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTA 1 F3: 4 AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT R RF: CCACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTATATTTAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT RR: GGTGTCTCTATATGGAAAGGATTCCACATTCTTTATAAAATATAAATCTCCCTCTTGTCTATTAATAGGGGAGGGGACGGAGGTTGTAACTTTTCGTACGA F2: 3 ATAGGATTCCAC 2 Unidirectional alignment (log-probability: -36) CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTacaccttaggATA------------------AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTT----------ATATTTAGAGGGAGAACAGATAATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT Template switch alignment (log-probability: -22.8) CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTA|CACCTTAGGAtA|AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT CACAGAGATATACCTTTCCTAAGGTGTAAGAAATATTTTA|CACCTTAGGAAA|AATTATCCCCTCCCCTGCCTCCAACATTGAAAAGCATGCT ========== Event 1908 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAATTGTGGCACCCTCGCAAAGTATCATGTAATTACTTAATTACATGATACTTTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGTAAACTGGAAGCCATGGATTTTTAGTATCATTTTGCCATTCACCTAGGATTCACATCTTCTTTTAAAG ↓ 1 4 3 2 ↑ 3 2 1 4 Chimp: AAATTGTGGCACCCTCGCAAAGTATCATGTAATTATTTAACC--------TAGTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGCAAACTGGAAGCCATGGATTTTTAGTATCAGTTTGCCATTCACGTAGGATTCACATCTTCTTTTAAAG Gorilla: AAATTGTAGCACCCTCGCAAAGTATCACGTAATTATTTAACC--------TAGTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGTAAACTGGAAGCCATGGATTTTTAGTATCATTTTGCCATTCACCTAGGATTCACATCTTCTTTTAAAG Human: AAATTGTGGCACCCTCGCAAAGTATCATGTAATTACTTAATTACATGATACTTTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGTAAACTGGAAGCCATGGATTTTTAGTATCATTTTGCCATTCACCTAGGATTCACATCTTCTTTTAAAG Cluster: [ ] Orangutan: AAATTGTGGCACCCTCGCAAAGTATCATATAATTATTTAACC--------TAGTTATACACTATAATCAATTTCCCATTTGCATGTCTTGAGCAAACTGGAAGCCATGGATTTTTAGTATCAGTTTGCCATTCACCTAGGATTCACATCTTCTTTTAAAG Chimp > Human ------------- chr2:85395039-85395051 Template switch process: F1: L -CTGAAAAATTGTGGCACCCTCGCAAAGTATCATGTAATTACTTAA 1 F3: 4 TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGT R RF: TTTGAAAAATTGTGGCACCCTCGCAAAGTATCATGTAATTATTTAACCTAGTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGC RR: AAACTTTTTAACACCGTGGGAGCGTTTCATAGTACATTAATAAATTGGATCAATATGTAATATTAGTTAAAGGGTAAACGTACAGAACTCG F2: 3 TTCATAGTACATT 2 Unidirectional alignment (log-probability: -61) AAATTGTGGCACCCTCGCAAAGTATCATGTAATTActtaattacatgatacTT--------TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGt AAATTGTGGCACCCTCGCAAAGTATCATGTAATTA----------------TTTAACCTAGTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGC Template switch alignment (log-probability: -45.2) AAATTGTGGCACCCTCGCAAAGTATCATGTAATTAcTTAA|TTACATGATACTT|TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGt AAATTGTGGCACCCTCGCAAAGTATCATGTAATTATTTAA|TTACATGATACTT|TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGC Human > Chimp ------------- chr2B:86514028-86514032 Template switch process: F1: L TT---------------------------------------------------------------------------------------------------TGAAAAATTGTGGCACCCTCGCAAAGTATCATGTAATTATTTAA 1 F3: 4 TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGC R RF: TTTTTAACCTTTCCTATGGTGCTGATAAACTGTTTTCTTTAGCTATTCTCTCTATATAGTATGCATAAGTCTCTTTTTCTTTCACTGCTATCAATATAGACTGAAAAATTGTGGCACCCTCGCAAAGTATCATGTAATTACTTAATTACATGATACTTTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGTAAACTGGAAGCCATGGATTTTTAGTATCATTTTGCCATTCACCTAGG RR: AAAAATTGGAAAGGATACCACGACTATTTGACAAAAGAAATCGATAAGAGAGATATATCATACGTATTCAGAGAAAAAGAAAGTGACGATAGTTATATCTGACTTTTTAACACCGTGGGAGCGTTTCATAGTACATTAATGAATTAATGTACTATGAAAATATGTAATATTAGTTAAAGGGTAAACGTACAGAACTCATTTGACCTTCGGTACCTAAAAATCATAGTAAAACGGTAAGTGGATCC F2: 3 GATCC 2 Unidirectional alignment (log-probability: -51.3) AAATTGTGGCACCCTCGCAAAGTATCATGTAATTA----------------TTtaacctagTTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGc AAATTGTGGCACCCTCGCAAAGTATCATGTAATTACTTAATTACATGATACTT--------TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGT Template switch alignment (log-probability: -43.3) AAATTGTGGCACCCTCGCAAAGTATCATGTAATTAtTTAA|CCTAG|TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGc AAATTGTGGCACCCTCGCAAAGTATCATGTAATTACTTAA|CCTAG|TTATACATTATAATCAATTTCCCATTTGCATGTCTTGAGT ========== Event 1909 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TCCTGACTTTTCAAGGTGTTGAAAAGAGCCTTATGATTCAGCCAA----------ACTTTCCAACAGCTCTGATGGGCAGTT ↓ 13 24 ↑ 13 24 Chimp: TCCTGACTTTTCAAGGTGTTGGAAA-----GTTTGGCTGAATCAT-----AAGGCTCTTTTCAACAGCTCTGATGGGCAGTT Gorilla: TCCTGACTTTTCAAGGTGTTGGAAA-----GTTTGGCTGAATCATAAGGC-----TCTTTTCAACAGCTCTGATGGGCAGTT ↓ 13 24 ↑ 13 24 Human: TCCTGACTTTTCAAGGTGTTGAAAAGAGCCTTATGATTCAGCCAA----------ACTTTCCAACAGCTCTGATGGGCAGTT Cluster: [ ] Orangutan: TCCTGACTTTTCAAGGTGTTGGAAA-----GTTTGGCTGAATCATAAGAC-----TCTTTTCAACAGCTCTGATGGGCAGTT Chimp > Human ------------- chr2:82956963-82956992 Template switch process: F1: L TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG 1 F3: 4 CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA R RF: TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGGAAAGTTTGGCTGAATCATAAGGCTCTTTTCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA RR: AGTAGAGACCCATGGACAAAAGGACTGAAAAGTTCCACAACCTTTCAAACCGACTTAGTATTCCGAGAAAAGTTGTCGAGACTACCCGTCAAATAGGAGTGAGGGTGAGAT F2: 3 CTTTCAAACCGACTTAGTATTCCGAGAAAA 2 Unidirectional alignment (log-probability: -61.6) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGaAAAG---------------AGcCTtatgattcagccaaaCTTTcCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGGAAAGTTTGGCTGAATCATAAGGCT---------------CTTTTCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Template switch alignment (log-probability: -19) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|AAAAGAGCCTTATGATTCAGCCAAACTTTC|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|AAAAGAGCCTTATGATTCAGCCAAACTTTC|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Human > Chimp ------------- chr2B:83963381-83963410 Template switch process: F1: L TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG 1 F3: 4 CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA R RF: TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGAAAAGAGCCTTATGATTCAGCCAAACTTTCCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA RR: AGTAGAGACCCATGGACAAAAGGACTGAAAAGTTCCACAACTTTTCTCGGAATACTAAGTCGGTTTGAAAGGTTGTCGAGACTACCCGTCAAATAGGAGTGAGGGTGAGAT F2: 3 TTTTCTCGGAATACTAAGTCGGTTTGAAAG 2 Unidirectional alignment (log-probability: -61.6) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGgAAAGtttggctgaatcataAGgCT---------------CTTTtCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGAAAAG---------------AGCCTTATGATTCAGCCAAACTTTCCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Template switch alignment (log-probability: -19) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|GAAAGTTTGGCTGAATCATAAGGCTCTTTT|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|GAAAGTTTGGCTGAATCATAAGGCTCTTTT|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Gorilla > Human --------------- chr2:82956963-82956992 Template switch process: F1: L TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG 1 F3: 4 CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA R RF: TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGGAAAGTTTGGCTGAATCATAAGGCTCTTTTCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA RR: AGTAGAGACCCATGGACAAAAGGACTGAAAAGTTCCACAACCTTTCAAACCGACTTAGTATTCCGAGAAAAGTTGTCGAGACTACCCGTCAAATAGGAGTGAGGGTGAGAT F2: 3 CTTTCAAACCGACTTAGTATTCCGAGAAAA 2 Unidirectional alignment (log-probability: -59.7) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGaAAAG---------------AGcCTtatgattcagccaaaCTTTcCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGGAAAGTTTGGCTGAATCATAAGGCT---------------CTTTTCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Template switch alignment (log-probability: -19.5) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|AAAAGAGCCTTATGATTCAGCCAAACTTTC|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|AAAAGAGCCTTATGATTCAGCCAAACTTTC|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Human > Gorilla --------------- chr2B:83984900-83984929 Template switch process: F1: L TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG 1 F3: 4 CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA R RF: TCATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGAAAAGAGCCTTATGATTCAGCCAAACTTTCCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA RR: AGTAGAGACCCATGGACAAAAGGACTGAAAAGTTCCACAACTTTTCTCGGAATACTAAGTCGGTTTGAAAGGTTGTCGAGACTACCCGTCAAATAGGAGTGAGGGTGAGAT F2: 3 TTTTCTCGGAATACTAAGTCGGTTTGAAAG 2 Unidirectional alignment (log-probability: -59.7) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGgAAAGtttggctgaatcataAGgCT---------------CTTTtCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTGAAAAG---------------AGCCTTATGATTCAGCCAAACTTTCCAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA Template switch alignment (log-probability: -19.5) CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|GAAAGTTTGGCTGAATCATAAGGCTCTTTT|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA CATCTCTGGGTACCTGTTTTCCTGACTTTTCAAGGTGTTG|GAAAGTTTGGCTGAATCATAAGGCTCTTTT|CAACAGCTCTGATGGGCAGTTTATCCTCACTCCCACTCTA ========== Event 1910 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTCATTGGTTTTTCATATTTCAGGATGTATCCATCCTGAATGGATGCAGCAGACAATCTGGCT ↑ 3 4 1 2 Chimp: GTCATTGGTTTTTCATATTTCAGGATGGA------------TAATGCAGCAGACAATCTGGCT Gorilla: GTCATTGGTGTTTCATATTTCAGGATGGA------------TAATGCAGCAGACAATCTGGCT Human: GTCATTGGTTTTTCATATTTCAGGATGTATCCATCCTGAATGGATGCAGCAGACAATCTGGCT Cluster: [ ] Orangutan: ATCATTGGTGTTTCATATTTCAGGATAGA------------TAATGCAGCAGACAATCTGGCT Chimp > Human ------------- chr2:161618486-161618497 Template switch process: F1: L TATTTCTTCATTTAGTCATTGGTTTTTCATATTTCAGGATG 1 F3: 4 ATGG---ATGCAGCAGACAATCTGGCTTTAAGTTTCAGAAGCCTTAA R RF: TATTTCTTCATTTAGTCATTGGTTTTTCATATTTCAGGATGGATAATGCAGCAGACAATCTGGCTTTAAGTTTCAGAAGCCTTAA RR: ATAAAGAAGTAAATCAGTAACCAAAAAGTATAAAGTCCTACCTATTACGTCGTCTGTTAGACCGAAATTCAAAGTCTTCGGAATT F2: 3 AGTCCTACCTAT 2 Unidirectional alignment (log-probability: -40.2) ATTTCTTCATTTAGTCATTGGTTTTTCATATTTCAGGATGtATccatcctgaatggATGCAGCAGACAATCTGGCTTTAAGTTTCAGAAGCC ATTTCTTCATTTAGTCATTGGTTTTTCATATTTCAGGATGGATA------------ATGCAGCAGACAATCTGGCTTTAAGTTTCAGAAGCC Template switch alignment (log-probability: -27.2) ATTTCTTCATTTAGTCATTGGTTTTTCATATTTCAGGATG|TATCCATCCTGA|ATGG---ATGCAGCAGACAATCTGGCTTTAAGTTTCAGAAGCC ATTTCTTCATTTAGTCATTGGTTTTTCATATTTCAGGATG|TATCCATCCTGA|ATGGATAATGCAGCAGACAATCTGGCTTTAAGTTTCAGAAGCC ========== Event 1911 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTTCCAAAGGCTGTAATTCTGTAAATAGCC-ACGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGA Chimp: TCTTCCAAAGGCTGTAATTCTGTAAATAGCC-ACGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGA ↑ 1 4 3 2 Gorilla: TCTTCCAAAGGCTGTAATTCT------GGCCACCGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGA ↓ 1 4 3 2 Human: TCTTCCAAAGGCTGTAATTCTGTAAATAGCC-ACGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGA Cluster: [ ] Orangutan: TCTTCCAAAGGCTTTAATTCT------GGCCACCGTATCAGTGGCTATTTAGCTGAAAACATGGAGTAAGA Gorilla > Human --------------- chr2:162002414-162002423 Template switch process: F1: L TTTTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG 1 F3: 4 CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC R RF: TTTTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTGGCCACCGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC RR: AAAATAATTTTTGACGTAAAAGAAGGTTTCCGACATTAAGACCGGTGGCATAGTCACCGATAAATCGACTTTTGTACCTGATTCTAG F2: 3 ACCGATAAAT 2 Unidirectional alignment (log-probability: -29.4) TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTGtaaataGCCA-CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG------GCCACCGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC Template switch alignment (log-probability: -17) TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG|TAAATAGCCA|CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG|TAAATAGCCA|CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC Gorilla > Chimp --------------- chr2B:52086091-52086100 Template switch process: F1: L TTTTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG 1 F3: 4 CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC R RF: TTTTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTGGCCACCGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC RR: AAAATAATTTTTGACGTAAAAGAAGGTTTCCGACATTAAGACCGGTGGCATAGTCACCGATAAATCGACTTTTGTACCTGATTCTAG F2: 3 ACCGATAAAT 2 Unidirectional alignment (log-probability: -29.4) TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTGtaaataGCCA-CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG------GCCACCGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC Template switch alignment (log-probability: -17) TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG|TAAATAGCCA|CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC TTATTAAAAACTGCATTTTCTTCCAAAGGCTGTAATTCTG|TAAATAGCCA|CGTATCAGTGGCTATTTAGCTGAAAACATGGACTAAGATC ========== Event 1912 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CAGCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC-------AGACATGGGCAGATGCCTTGCTTGGCCAATAGCATGTGAGCAGACATGAAA Chimp: CAGCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC-------AGACATGGGCAGATGCCTTGCTTGGCCAATAGCATGTGAGCAGACATGAAA ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: CAGCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC------------------------ATGTCTGGGCAGCAGCATGTGAGCAGACATGAAA ↓ 3 1 2 4 ↑ 3 1 2 4 Human: CAGCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC-------AGACATGGGCAGATGCCTTGCTTGGCCAATAGCATGTGAGCAGACATGAAA Cluster: [ ] Orangutan: gagct--------------ctt------------cg-------tactttC-----------------TTGCTTGGCCAATAGCATGTGAGCAGACATGAAA Gorilla > Human --------------- chr2:225991692-225991720 Template switch process: F1: L GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA 1 F3: 4 AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA R RF: GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCATGTCTGGGCAGCAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA RR: CGGGTGGTAGTACAGGATAACCGGTTCGTTCCGTAGACGGGTACAGACCCGTCGTCGTACACTCGTCTGTACTTTGTCTGAAAGCTACAAGAGT F2: 3 TAACCGGTTCGTTCCGTAGACGGGTACAG 2 Unidirectional alignment (log-probability: -61.5) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCagacatgggcagatgccttgcttggccaAT-----------AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC----------------------------ATGTCTGGGCAGCAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA Template switch alignment (log-probability: -19.4) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|GACATGGGCAGATGCCTTGCTTGGCCAAT|AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|GACATGGGCAGATGCCTTGCTTGGCCAAT|AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA Human > Gorilla --------------- chr2A:91302117-91302127 Template switch process: F1: L GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA 1 F3: 4 CAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA R RF: GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCAGACATGGGCAGATGCCTTGCTTGGCCAATAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA RR: CGGGTGGTAGTACAGGATAACCGGTTCGTTCCGTAGACGGGTCTGTACCCGTCTACGGAACGAACCGGTTATCGTACACTCGTCTGTACTTTGTCTGAAAGCTACAAGAGT F2: 3 GACGGGTCTGT 2 Unidirectional alignment (log-probability: -37.9) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC----------------------------ATgtctgggcagcAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCAGACATGGGCAGATGCCTTGCTTGGCCAAT-----------AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC Template switch alignment (log-probability: -22.7) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|TGTCTGGGCAG|cAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|TGTCTGGGCAG|TAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC Gorilla > Chimp --------------- chr2A:94986861-94986889 Template switch process: F1: L GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA 1 F3: 4 AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA R RF: GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCATGTCTGGGCAGCAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA RR: CGGGTGGTAGTACAGGATAACCGGTTCGTTCCGTAGACGGGTACAGACCCGTCGTCGTACACTCGTCTGTACTTTGTCTGAAAGCTACAAGAGT F2: 3 TAACCGGTTCGTTCCGTAGACGGGTACAG 2 Unidirectional alignment (log-probability: -61.5) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCagacatgggcagatgccttgcttggccaAT-----------AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC----------------------------ATGTCTGGGCAGCAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA Template switch alignment (log-probability: -19.4) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|GACATGGGCAGATGCCTTGCTTGGCCAAT|AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|GACATGGGCAGATGCCTTGCTTGGCCAAT|AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA Chimp > Gorilla --------------- chr2A:91302117-91302127 Template switch process: F1: L GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA 1 F3: 4 CAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA R RF: GCCCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCAGACATGGGCAGATGCCTTGCTTGGCCAATAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTCA RR: CGGGTGGTAGTACAGGATAACCGGTTCGTTCCGTAGACGGGTCTGTACCCGTCTACGGAACGAACCGGTTATCGTACACTCGTCTGTACTTTGTCTGAAAGCTACAAGAGT F2: 3 GACGGGTCTGT 2 Unidirectional alignment (log-probability: -37.9) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCC----------------------------ATgtctgggcagcAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCAGACATGGGCAGATGCCTTGCTTGGCCAAT-----------AGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC Template switch alignment (log-probability: -22.7) CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|TGTCTGGGCAG|cAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC CCACCATCATGTCCTATTGGCCAAGCAAGGCATCTGCCCA|TGTCTGGGCAG|TAGCATGTGAGCAGACATGAAACAGACTTTCGATGTTCTC ========== Event 1913 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: tggttctaAGGGTATATATAGCTTAT----------AATAGTCTATTCCTACAGAAAATGA Chimp: tggttctaAGGGT----ATAGCTTATTATTATAAGCTATAATCTATCCCTACAGAAAATGA ↑ 3 1 4 2 Gorilla: tggttctaAGGGT----ATAGCTTAT----------AATAGTCTATCCCTACAGAAAATGA Human: tggttctaAGGGTATATATAGCTTAT----------AATAGTCTATTCCTACAGAAAATGA Cluster: [ ] Orangutan: tggttctaAGGGT----ATACCTTAT----------AATAGTCTATCCCTACAGAAAATGA Gorilla > Chimp --------------- chr2B:53409301-53409311 Template switch process: F1: L TTCCAACTTTGACAGTCTATGGTTCTAAGGGTATAGCTTAT 1 F3: 4 ATAATCTATCCCTACAGAAAATGACCAAGCCACAACTGGTAGTA R RF: TTCCAACTTTGACAGTCTATGGTTCTAAGGGTATAGCTTATAATAGTCTATCCCTACAGAAAATGACCAAGCCACAACTGGTAGTA RR: AAGGTTGAAACTGTCAGATACCAAGATTCCCATATCGAATATTATCAGATAGGGATGTCTTTTACTGGTTCGGTGTTGACCATCAT F2: 3 TCGAATATTAT 2 Unidirectional alignment (log-probability: -36.4) TCCAACTTTGACAGTCTATGGTTCTAAGGGTATAGCTTATtattataagctATAaTCTATCCCTACAGAAAATGACCAAGCCACAACTGGT TCCAACTTTGACAGTCTATGGTTCTAAGGGTATAGCTTAT----------AATAGTCTATCCCTACAGAAAATGACCAAGCCACAACTGGT Template switch alignment (log-probability: -22.7) TCCAACTTTGACAGTCTATGGTTCTAAGGGTATAGCTTAT|TATTATAAGCT|ATAaTCTATCCCTACAGAAAATGACCAAGCCACAACTGGT TCCAACTTTGACAGTCTATGGTTCTAAGGGTATAGCTTAT|TATTATAAGCT|ATAGTCTATCCCTACAGAAAATGACCAAGCCACAACTGGT ========== Event 1914 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGTATTAAATCACCTTGAAATCTTGTCATGATAATGACATGATTAGCCAACTTTTGAAGATAAAA Chimp: CAGTATGAAATCACCTTGAAATCTTGTCATTAT--------CTTAAGCCAACTTTTGAAGATAAAA Gorilla: CAGTATTAAATCACCTTGAAATCTTGTCATTAT--------CTTAAGCCAACTTTTGAAGATAAAA ↓ 3 1 2 4 Human: CAGTATTAAATCACCTTGAAATCTTGTCATGATAATGACATGATTAGCCAACTTTTGAAGATAAAA Cluster: [ ] Orangutan: CAGTATTAAATCACCTTGAAACCTTGTCATTAT--------CTTAAGCCAACTTTTGAAGATAAAA Gorilla > Human --------------- chr2:164496184-164496198 Template switch process: F1: L TATCCAAATTTCAGTATTAAATCACCTTGAAATCTTGTCAT 1 F3: 4 AGCCAACTTTTGAAGATAAAAGATCCCATCACCACTTGTT R RF: TATCCAAATTTCAGTATTAAATCACCTTGAAATCTTGTCATTATCTTAAGCCAACTTTTGAAGATAAAAGATCCCATCACCACTTGTT RR: ATAGGTTTAAAGTCATAATTTAGTGGAACTTTAGAACAGTAATAGAATTCGGTTGAAAACTTCTATTTTCTAGGGTAGTGGTGAACAA F2: 3 TTAGTACAGTAATAG 2 Unidirectional alignment (log-probability: -41.1) ATCCAAATTTCAGTATTAAATCACCTTGAAATCTTGTCatgataatgacatgATT------AGCCAACTTTTGAAGATAAAAGATCCCATCACCACTTGTT ATCCAAATTTCAGTATTAAATCACCTTGAAATCTTGTC--------------ATTATCTTAAGCCAACTTTTGAAGATAAAAGATCCCATCACCACTTGTT Template switch alignment (log-probability: -23.2) ATCCAAATTTCAGTATTAAATCACCTTGAAATCTTGTCAT|GATAATGACAtGATT|AGCCAACTTTTGAAGATAAAAGATCCCATCACCACTTGTT ATCCAAATTTCAGTATTAAATCACCTTGAAATCTTGTCAT|GATAATGACAAGATT|AGCCAACTTTTGAAGATAAAAGATCCCATCACCACTTGTT ========== Event 1915 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCGTGTCTATGTTCCCCCATAGCACTTATAGCACCCAGTAGCACAACAGCACTTAACACATGGTGCTGGACTGTCTACCACATTCATGTTATACTTATCTGCTTATAGGACAACTCTAATGTCCTAAACTGTA-----------AGATGAGTCAGGAAACAGAT Chimp: AATCGTGTCTATGTTCCCCCATAGCACTTATAGCACCCAGTAGCACAACAGCACTTAACACATGGTGCTGGACTGTCTACCACATTCATGTTATACTTATCTACTTATAGGACAACTCTAATGT-----------CCTAAACTGTAAGATGAGTCAGGAAAGAGAT ↓ 3 2 1 4 Gorilla: AATCGTGTCTATGTTCCCCCATAGCACTTATAGCACCCAGTAGCACAACAGCACTTAACACATGATGCTGGACTGTCTACCACATTCATGCTATGCTTATCTATTTATAGGACAACTCTAATGTCCTAAACTGTA-----------AGATGAGTCAGGAAAGAGAT Human: AATCGTGTCTATGTTCCCCCATAGCACTTATAGCACCCAGTAGCACAACAGCACTTAACACATGGTGCTGGACTGTCTACCACATTCATGTTATACTTATCTGCTTATAGGACAACTCTAATGTCCTAAACTGTA-----------AGATGAGTCAGGAAACAGAT Cluster: [ ] Orangutan: AATAGTGTCTATGTTCCCCCATAGCACTTATAGCACCCAGTAGCACAACAGCACTTAACAAATGGTGCTGGACTGTCTACCACATTCATGCTATACTTATCTACTTATATGACAACTCTAATGTCCTAAACTGTA-----------AGATGAGTCAGGAAAGAGAT Chimp > Gorilla --------------- chr2B:56726963-56726967 Template switch process: F1: L ATTCATG 1 F3: 4 CTTATCTATTTATAGGACAACTCTAATGTCCTAAACTGTAAGATGAGTCAGGAAAGAGATAACGACTTTTTTTTTTTTTT R RF: CATAGCACTTATAGCACCCAGTAGCACAACAGCACTTAACACATGGTGCTGGACTGTCTACCACATTCATGTTATACTTATCTACTTATAGGACAACTCTAATGTCCTAAACTGTAAGATGAGTCAGGAAAGAGATAACGACTTTTTTTTTTTTTT RR: GTATCGTGAATATCGTGGGTCATCGTGTTGTCGTGAATTGTGTACCACGACCTGACAGATGGTGTAAGTACAATATGAATAGATGAATATCCTGTTGAGATTACAGGATTTGACATTCTACTCAGTCCTTTCTCTATTGCTGAAAAAAAAAAAAAA F2: 3 GTATC 2 Unidirectional alignment (log-probability: -33.1) ATTCATGcTATgCTTATCTAtTTATAGGACAACTCTAATGTCCTAAACTGTA ATTCATGTTATACTTATCTACTTATAGGACAACTCTAATGTCCTAAACTGTA Template switch alignment (log-probability: -22) ATTCATG|CTATG|CTTATCTAtTTATAGGACAACTCTAATGTCCTAAACTGTA ATTCATG|CTATG|CTTATCTACTTATAGGACAACTCTAATGTCCTAAACTGTA ========== Event 1916 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TACTCTTGTCATTATAATATTGTCT--------ATATTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGACAAAAAAATATAAACACCAACTTTAGCTCTCCAGC ↑ 1 4 3 2 Chimp: TACTCTTGTCATTATAATATTCCAC----AAGATTGTTGTTGGCTATGTGTCACAATGAATAGAGAATCTGAGGACAACAAAATATAGACACCAACTTTAGCTCTCCAGC Gorilla: TACTCTTGTCATTATAATATTCCACAAGA----CTGTTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGACAACAAAATATAGACACCAACTTTAGCTCTCCAGC ↓ 1 4 3 2 Human: TACTCTTGTCATTATAATATTGTCT--------ATATTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGACAAAAAAATATAAACACCAACTTTAGCTCTCCAGC Cluster: [ ] Orangutan: TACTCTTGTCATTATAATATTCCACAAGA----TTGTTGTTGGCTATGCGTCACAATGAATAGAGTATCTGAGGACAACAAAATATAGACACCAACTTTAGCTCTCCAGT Chimp > Human ------------- chr2:163746616-163746622 Template switch process: F1: L AGTTAAACATGCATTATATCTACTCTTGTCATTATAATATT 1 F3: 4 TTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGAC R RF: AGTTAAACATGCATTATATCTACTCTTGTCATTATAATATTCCACAAGATTGTTGTTGGCTATGTGTCACAATGAATAGAGAATCTGAGGACAACAAAATATAGAC RR: TCAATTTGTACGTAATATAGATGAGAACAGTAATATTATAAGGTGTTCTAACAACAACCGATACACAGTGTTACTTATCTCTTAGACTCCTGTTGTTTTATATCTG F2: 3 ATATCTG 2 Unidirectional alignment (log-probability: -36.3) GTTAAACATGCATTATATCTACTCTTGTCATTATAAT----------ATTGtctataTTGTTGGCTATGTGTCACAATGAATAGAGtATCTGAGGAC GTTAAACATGCATTATATCTACTCTTGTCATTATAATATTCCACAAGATTG------TTGTTGGCTATGTGTCACAATGAATAGAGAATCTGAGGAC Template switch alignment (log-probability: -22.1) GTTAAACATGCATTATATCTACTCTTGTCATTATAATATT|GTCTATA|TTGTTGGCTATGTGTCACAATGAATAGAGtATCTGAGGAC GTTAAACATGCATTATATCTACTCTTGTCATTATAATATT|GTCTATA|TTGTTGGCTATGTGTCACAATGAATAGAGAATCTGAGGAC Gorilla > Human --------------- chr2:163746616-163746622 Template switch process: F1: L AGTTAAACATGCATTATATCTACTCTTGTCATTATAATATT 1 F3: 4 TTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGAC R RF: AGTTAAACATGCATTATATCTACTCTTGTCATTATAATATTCCACAAGACTGTTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGACAACAAAATATAGAC RR: TCAATTTGTACGTAATATAGATGAGAACAGTAATATTATAAGGTGTTCTGACAACAACCGATACACAGTGTTACTTATCTCATAGACTCCTGTTGTTTTATATCTG F2: 3 ATATCTG 2 Unidirectional alignment (log-probability: -29.8) GTTAAACATGCATTATATCTACTCTTGTCATTATAATAT----------TGtctataTTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGAC GTTAAACATGCATTATATCTACTCTTGTCATTATAATATTCCACAAGACTG------TTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGAC Template switch alignment (log-probability: -16.6) GTTAAACATGCATTATATCTACTCTTGTCATTATAATATT|GTCTATA|TTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGAC GTTAAACATGCATTATATCTACTCTTGTCATTATAATATT|GTCTATA|TTGTTGGCTATGTGTCACAATGAATAGAGTATCTGAGGAC ========== Event 1917 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTTTAACCCCAGAAATTATTGTACTATG------TCATGTTC--CTAATGCTATGTTTTAACCTGC Chimp: ATTTTAACCCCAGAAATTATTGTATTATG------TCATGTTC--CTAATGCTATGTTTTAACCTGC ↓ 3 1 2 4 Gorilla: ATTTTAACCCCAGAAATTATTGTATTATGTACATGACATAATACAATAATGCTATGTTTTAACCTGC Human: ATTTTAACCCCAGAAATTATTGTACTATG------TCATGTTC--CTAATGCTATGTTTTAACCTGC Cluster: [ ] Orangutan: ATTTTAACCCCAGAAATTATTGTACTATG------TCATGTTC--CTAATGCTATGTTTTAACCTGC Chimp > Gorilla --------------- chr2B:56419685-56419700 Template switch process: F1: L AGACATCATCTAATTTTAACCCCAGAAATTATTGTATTATGT 1 F3: 4 TAATGCTATGTTTTAACCTGCTTCTATTACTATTGTATCA R RF: AGACATCATCTAATTTTAACCCCAGAAATTATTGTATTATGTCATGTTCCTAATGCTATGTTTTAACCTGCTTCTATTATTATTGTATCA RR: TCTGTAGTAGATTAAAATTGGGGTCTTTAATAACATAATACAGTACAAGGATTACGATACAAAATTGGACGAAGATAATAATAACATAGT F2: 3 AACATAATACAGTACA 2 Unidirectional alignment (log-probability: -49.6) ACATCATCTAATTTTAACCCCAGAAATTATTGTATTATGTacatgacataatacaa--------TAATGCTATGTTTTAACCTGCTTCTATTAcTATTGTATCA ACATCATCTAATTTTAACCCCAGAAATTATTGTATTATGT----------------CATGTTCCTAATGCTATGTTTTAACCTGCTTCTATTATTATTGTATCA Template switch alignment (log-probability: -23.3) ACATCATCTAATTTTAACCCCAGAAATTATTGTATTATGT|ACATGACATAATACAA|TAATGCTATGTTTTAACCTGCTTCTATTAcTATTGTATCA ACATCATCTAATTTTAACCCCAGAAATTATTGTATTATGT|ACATGACATAATACAA|TAATGCTATGTTTTAACCTGCTTCTATTATTATTGTATCA ========== Event 1918 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GCGGCCTCCCTGGGGTCGCCAGC---------------CCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCGGAGATCTTGGCGGCAAGGCCGCCCCTGACAGCGGAGCCAGAGGGACCCAGGGGGCTGCCAGAGGCGGGGAAGCACTGCAGTCGCCCCTTTGTCTGACCGTGAGTCCCGGCTCCAATGCT ↓ 4 1 3 2 Chimp: GCGGCCGCCCTGGGGTCGCCAGCCCGCGCGGTCACAGCCCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCGGAGATCTTGGCGGCAAGGCCGCCCCTGACAGCGGAGCCAGAGGGACCCAGGGGGCTGCCAGAGGCGGGGAAGCACTGCAGTCGCCCCTTTGTCTGACCGTGGGTCCCGGCTCCAGTGCT Gorilla: Human: GCGGCCTCCCTGGGGTCGCCAGC---------------CCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCGGAGATCTTGGCGGCAAGGCCGCCCCTGACAGCGGAGCCAGAGGGACCCAGGGGGCTGCCAGAGGCGGGGAAGCACTGCAGTCGCCCCTTTGTCTGACCGTGAGTCCCGGCTCCAATGCT Cluster: [ ] Orangutan: Human > Chimp ------------- chr2B:66812025-66812030 Template switch process: F1: L TCAACAGTGAAGGGCGGTGCGGCCGCCCTGGGGTCGCCAGCCCGCG 1 F3: 4 CAGCCCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCGGAGA R RF: TCAACAGTGAAGGGCGGTGCGGCCTCCCTGGGGTCGCCAGCCCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCGGAGATCTTGGCGGCAAGGCCGCCCCTGACAGCGGAGCCAGAGGGACCCAGGGGGCTGCCAGAGGCGGGGAAGCACTGCAGTCGCCCCTTTGTCTGACCG RR: AGTTGTCACTTCCCGCCACGCCGGAGGGACCCCAGCGGTCGGGCGAAAGTCTGCGTCGGATCGCGGAGGCTTTCGGCCTCTAGAACCGCCGTTCCGGCGGGGACTGTCGCCTCGGTCTCCCTGGGTCCCCCGACGGTCTCCGCCCCTTCGTGACGTCAGCGGGGAAACAGACTGGC F2: 3 ACTGGC 2 Unidirectional alignment (log-probability: -38.5) GTGAAGGGCGGTGCGGCCgCCCTGGGGTCGCCAGCCCGcgcggtcacagcccgCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCG GTGAAGGGCGGTGCGGCCTCCCTGGGGTCGCCAGCCCG---------------CTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCG Template switch alignment (log-probability: -28.2) GTGAAGGGCGGTGCGGCCgCCCTGGGGTCGCCAGCCCGCg|CGGTCA|CAGCCCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCG GTGAAGGGCGGTGCGGCCTCCCTGGGGTCGCCAGCCCGCT|CGGTCA|CAGCCCGCTTTCAGACGCAGCCTAGCGCCTCCGAAAGCCG ========== Event 1919 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: --CAAAGA-AAAATGAG-ACT--------------------CTATA-ACT-GTATGT-TTGATATG-ATTA-- ↑ 1 3 2 4 Chimp: --CAAAGA-AAAATGAG-ACTGGGATTACATACAGTTATAGAGATA-A---CTATGT-TTGATATG-ATTA-- ↓ 1 3 2 4 Gorilla: --CAAAGA-AAAATGAG-ACT--------------------CTATA-ACT-GTATGT-TTGATATG-ATTA-- Human: --CAAAGA-AAAATGAG-ACT--------------------CTATA-ACT-GTATGT-TTGATATG-ATTA-- Cluster: [ ] Orangutan: TCCAAAGAAGAAATGAGAAAT--------------------CTATAAGCTGTTATGTTGTGATATGAATTATT Chimp > Human ------------- chr2:167494528-167494536 Template switch process: F1: L GAAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT 1 F3: 4 TATGTTTGATATGATTATATCTACATAAAATAGCATATGT R RF: GAAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACTGGGATTACATACAGTTATAGAGATAACTATGTTTGATATGATTATATCTACATAAAATAGCATATGT RR: CTTCATAGATTTTATTTTGATACAGTTTCTTTTTACTCTGACCCTAATGTATGTCAATATCTCTATTGATACAAACTATACTAATATAGATGTATTTTATCGTATACA F2: 3 GTCAATATC 2 Unidirectional alignment (log-probability: -34) AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGactctataACTG--------------------------TATGTTTGATATGATTATATCTACATAAAATAGCATATGT AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAG--------ACTGGGATTACATACAGTTATAGAGATAACTATGTTTGATATGATTATATCTACATAAAATAGCATATGT Template switch alignment (log-probability: -16.4) AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT|CTATAACTG|TATGTTTGATATGATTATATCTACATAAAATAGCATATGT AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT|CTATAACTG|TATGTTTGATATGATTATATCTACATAAAATAGCATATGT Chimp > Gorilla --------------- chr2B:59830391-59830399 Template switch process: F1: L GAAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT 1 F3: 4 TATGTTTGATATGATTATATCTACCTAAAATAGCATATGT R RF: GAAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACTGGGATTACATACAGTTATAGAGATAACTATGTTTGATATGATTATATCTACATAAAATAGCATATGT RR: CTTCATAGATTTTATTTTGATACAGTTTCTTTTTACTCTGACCCTAATGTATGTCAATATCTCTATTGATACAAACTATACTAATATAGATGTATTTTATCGTATACA F2: 3 GTCAATATC 2 Unidirectional alignment (log-probability: -39) AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT--------------------------CtataactgTATGTTTGATATGATTATATCTACcTAAAATAGCATATGT AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACTGGGATTACATACAGTTATAGAGATAAC--------TATGTTTGATATGATTATATCTACATAAAATAGCATATGT Template switch alignment (log-probability: -22.4) AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT|CTATAACTG|TATGTTTGATATGATTATATCTACcTAAAATAGCATATGT AAGTATCTAAAATAAAACTATGTCAAAGAAAAATGAGACT|CTATAACTG|TATGTTTGATATGATTATATCTACATAAAATAGCATATGT ========== Event 1920 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATCTCATCTTGTTTTTGCCAA---TGCTAGCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATACTGCGTTCATGTCATAGCAGTCACCTTCCAGGACAGTG Chimp: atctcatcttgtttttgccaa---tgctagcagttggattAAATTGCTGAAACAAAACAAGCAAACATACTGCGTTCATGTCATAGCAGTCACCTTCCAGGACAGTG Gorilla: ATCTCATCTTGTTTTTGCCAATTGGATTGGCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATACTGCATTCATGTCATAGCAGTCACCTTCCAGGACAGTG ↓ 1 4 3 2 Human: ATCTCATCTTGTTTTTGCCAA---TGCTAGCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATACTGCGTTCATGTCATAGCAGTCACCTTCCAGGACAGTG Cluster: [ ] Orangutan: atctcatcttgtttttgccaa---tgctagcagttggattAAATTGCTGAAACAAAACAAGCAAACACACTGCGTTCATGTCATAGCAGTCACCTTCCAGGACAGTG Gorilla > Human --------------- chr2:167133720-167133723 Template switch process: F1: L GGGATCTGCACCTTCTATTTATCTCATCTTGTTTTTGCCAAT 1 F3: 4 GCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATA R RF: GGCATCTGCACCTTCTATTTATCTCATCTTGTTTTTGCCAATTGGATTGGCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATACTGCATTCATGTCATAGC RR: CCGTAGACGTGGAAGATAAATAGAGTAGAACAAAAACGGTTAACCTAACCGTCAACCTAATTTAACGACTTTGTTTTGTTCGTTTGTATGACGTAAGTACAGTATCG F2: 3 ATCG 2 Unidirectional alignment (log-probability: -30.8) gATCTGCACCTTCTATTTATCTCATCTTGTTTTTGCCAA------TGctaGCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATA CATCTGCACCTTCTATTTATCTCATCTTGTTTTTGCCAATTGGATTG---GCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATA Template switch alignment (log-probability: -21.8) gATCTGCACCTTCTATTTATCTCATCTTGTTTTTGCCAAT|GCTA|GCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATA CATCTGCACCTTCTATTTATCTCATCTTGTTTTTGCCAAT|GCTA|GCAGTTGGATTAAATTGCTGAAACAAAACAAGCAAACATA ========== Event 1921 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGATGCATAGATGCTACTATTTCTTTAGTTAC ↑ 3 2 1 4 Chimp: CTAAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA--GATGGTTGCTACTATTTCTTTAGTTAC Gorilla: CTAAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA--GATGGTTGCTACTATTTCTTTAGTTAC ↓ 3 2 1 4 Human: CTAAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGATGCATAGATGCTACTATTTCTTTAGTTAC Cluster: [ ] Orangutan: CTAAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA--GATGGTTGCTACTATTTCTTTAGTTAC Chimp > Human ------------- chr2:166069333-166069340 Template switch process: F1: L AAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA 1 F3: 4 TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC R RF: AAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGAGATGGTTGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC RR: TTTTTGGAAGATTACGAAGATACGTAGTCCTTACAAGTACTCTACCAACGATGATAAAGAAATCAATGATGATGTTATAATGACTTG F2: 3 AGATACGT 2 Unidirectional alignment (log-probability: -30) AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGatgcatAGA----TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATG------AGATGGTTGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC Template switch alignment (log-probability: -16.3) AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA|TGCATAGA|TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA|TGCATAGA|TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC Gorilla > Human --------------- chr2:166069333-166069340 Template switch process: F1: L AAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA 1 F3: 4 TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC R RF: AAAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGAGATGGTTGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC RR: TTTTTGGAAGATTACGAAGATACGTAGTCCTTACAAGTACTCTACCAACGATGATAAAGAAATCAATGATGATGTTATAATGACTTG F2: 3 AGATACGT 2 Unidirectional alignment (log-probability: -29.5) AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGatgcatAGA----TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATG------AGATGGTTGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC Template switch alignment (log-probability: -16.7) AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA|TGCATAGA|TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC AAAACCTTCTAATGCTTCTATGCATCAGGAATGTTCATGA|TGCATAGA|TGCTACTATTTCTTTAGTTACTACTACAATATTACTGAAC ========== Event 1922 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAACAGAGCTAAAGAGACAATTCTGCCTTTCTGATATTTCCCTATGAAAACAGTATCACATATGCTGATTACTTTCTATCATGCTGGTA-----------------------AAGGAAAACAGAATTTCCTGGTAAAGGAAAATAGGATGTCCATTTGAACTA Chimp: GGAACAGAGCTAAAGAGACAATTCTGCCTTTCTGATATTTCCCTATGAAAACAGTATCACATATGCTGATTGCTTTCTATCATGCTGGTA-----------------------AAGGAAAACAGAATTTCCTGGTAAAGGAAAATAGGATGTCTATTTGAACTA ↑ 3 2 4 1 Gorilla: GGAACAGAGCTAAAGAGACAATTCTGCCTTTCTGATATTTCCCTATGAAAACAGTATCACATATGCTGATTACTTTCTATCATGCTGGTA----------------------------------------------AAGGAAAATAGGATGTCTATTTGAACTA Human: GGAACAGAGCTAAAGAGACAATTCTGCCTTTCTGATATTTCCCTATGAAAACAGTATCACATATGCTGATTACTTTCTATCATGCTGGTA-----------------------AAGGAAAACAGAATTTCCTGGTAAAGGAAAATAGGATGTCCATTTGAACTA Cluster: [ ] Orangutan: GGAACAGAGCTAAAGAAACAATTCTGCCTTTCTGATATTTCCCTATGAAAACAGTATCACGTATGCTGATTACTTTCTATCATGCTGGTAAAGGAAAACAGAATTTACTGGTA-----------------------AAGGAAAACAGGATGTCTATTTGAACTA Gorilla > Chimp --------------- chr2B:56020527-56020533 Template switch process: F1: L AACAGTATCACATATGCTGATTGCTTTCTATCATGCTGGTAAAGGAAAA 1 F3: 4 TCCTGGTAAAGGAAAATAGGATGTCTATTTGAACTAGAGGCCCAACTA R RF: AATTCTGCCTTTCTGATATTTCCCTATGAAAACAGTATCACATATGCTGATTACTTTCTATCATGCTGGTAAAGGAAAATAGGATGTCTATTTGAACTAGATGCCCAACTA RR: TTAAGACGGAAAGACTATAAAGGGATACTTTTGTCATAGTGTATACGACTAATGAAAGATAGTACGACCATTTCCTTTTATCCTACAGATAAACTTGATCTACGGGTTGAT F2: 3 TTAAGAC 2 Unidirectional alignment (log-probability: -55) ACATATGCTGATTgCTTTCTATCATGctggtaaaggaaaacagaatttcCTGGTAAAGGAAAATAGGATGTCTATTTGAACTAGAgG ACATATGCTGATTACTTTCTATCATG-----------------------CTGGTAAAGGAAAATAGGATGTCTATTTGAACTAGATG Template switch alignment (log-probability: -33.6) ACATATGCTGATTgCTTTCTATCATGCTGGTAAAGGAAAA|CAGAATT|TcCTGGTAAAGGAAAATAGGATGTCTATTTGAACTAGAgG ACATATGCTGATTACTTTCTATCATGCTGGTAAAGGAAAA|CAGAATT|TGCTGGTAAAGGAAAATAGGATGTCTATTTGAACTAGATG ========== Event 1923 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTATGTTTTAAGAATAACTTGTACACACAGTTACTTTCAAATGAATCT--CTCTCTGTGTGTACATACAAATACATACATATAA ↑ 1 4 3 2 Chimp: GTTATGTTTTAAGAATAACTTATA--CGCAGTTACTTTCAAATGAATCT--CTCTCTGTGTGTACATACAAATACATACATATAA Gorilla: GTTATGTTTTAAGAATAACTTGTACACACAGTTACTTTCAAATGAATCT----CTCTGTGTGTACATACAAATACATACATATAA Human: GTTATGTTTTAAGAATAACTTGTACACACAGTTACTTTCAAATGAATCT--CTCTCTGTGTGTACATACAAATACATACATATAA Cluster: [ ] Orangutan: GTTATGTTTTAAGAATAACTTGTACCCACAGTTACTTTCAAATGAATCTCT--TTCTGTGTATACATATAAATACACACATATAA Chimp > Human ------------- chr2:166799397-166799404 Template switch process: F1: L TATTAATCTTGCTTTTATTAGTTATGTTTTAAGAATAACTT 1 F3: 4 AGTTACTTTCAAATGAATCTCTCTCTGTGTGTACATACA R RF: TATGAATCTTGCTTTTATTAGTTATGTTTTAAGAATAACTTATACGCAGTTACTTTCAAATGAATCTCTCTCTGTGTGTACATACA RR: ATACTTAGAACGAAAATAATCAATACAAAATTCTTATTGAATATGCGTCAATGAAAGTTTACTTAGAGAGAGACACACATGTATGT F2: 3 CACACATG 2 Unidirectional alignment (log-probability: -31.8) ATtAATCTTGCTTTTATTAGTTATGTTTTAAGAATAACTtgTAcACaCAGTTACTTTCAAATGAATCTCTCTCTGTGTGTACATACA ATGAATCTTGCTTTTATTAGTTATGTTTTAAGAATAACT--TATACGCAGTTACTTTCAAATGAATCTCTCTCTGTGTGTACATACA Template switch alignment (log-probability: -22.2) ATtAATCTTGCTTTTATTAGTTATGTTTTAAGAATAACTT|GTACACAC|AGTTACTTTCAAATGAATCTCTCTCTGTGTGTACATACA ATGAATCTTGCTTTTATTAGTTATGTTTTAAGAATAACTT|GTACACAC|AGTTACTTTCAAATGAATCTCTCTCTGTGTGTACATACA ========== Event 1924 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ttGGGGAAGGGGCAGGAACAC----------------------CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTTTCCAGTTAATGTGTTGCCAGGGCTGTAATGAGACAATAAACAATCTA Chimp: ttGGGGAAGGGGCAGGAACAC-----------CTTTTTACAGCCCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTTTCCAGTTAATGTGTTGCCAGGGCTGTAATGAGACAATAAACAATCTA Gorilla: TTGGGGAAGGGGCAGGAACACCCTTTTACAGC-----------CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTTTCCAGTTAATGTGTTGCCAGGGCTGTAATGAGACAATAAACAATCTA ↑ 4 1 3 2 Human: ttGGGGAAGGGGCAGGAACAC----------------------CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTTTCCAGTTAATGTGTTGCCAGGGCTGTAATGAGACAATAAACAATCTA Cluster: [ ] Orangutan: TTGGGGAAGGGGCAG-GCCACCCTTTTACAGC-----------CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTTTCCAGTTAATGTGTTGCCAGGGCTGTAATGAGACAATAAACAATCTA Human > Gorilla --------------- chr2B:59061804-59061809 Template switch process: F1: L CATTCACTAAGGTTAATAGATTGGGGAAGGGGCAGGAACACCCTTT 1 F3: 4 CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTT R RF: CATTCACTGAGGTTAATAGATTGGGGAAGGGGCAGGAACACCCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTTTCCAGTTAATGTGTTGCCAGGGCTGTA RR: GTAAGTGACTCCAATTATCTAACCCCTTCCCCGTCCTTGTGGGAAATTTTAGTGTCAAATCCATCGAAATAAAACAAGAAAAGGTCAATTACACAACGGTCCCGACAT F2: 3 CGACAT 2 Unidirectional alignment (log-probability: -32.2) CTaAGGTTAATAGATTGGGGAAGGGGCAGGAACAcccttttacagCCCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTT CTGAGGTTAATAGATTGGGGAAGGGGCAGGAACA-----------CCCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTT Template switch alignment (log-probability: -22.1) CTaAGGTTAATAGATTGGGGAAGGGGCAGGAACACCCTTT|TACAGC|CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTT CTGAGGTTAATAGATTGGGGAAGGGGCAGGAACACCCTTT|TACAGC|CCTTTAAAATCACAGTTTAGGTAGCTTTATTTTGTTCTTT ========== Event 1925 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTTTTGGAGGGTTCTGGTCTTGGTACAAGACCAGAATATTAAAACAT Chimp: CTTTTTGGAGGGTTCTGGTCTTGTACCAAGACCAGAATATTAAAACAT ↑ 1 3 42 Gorilla: CTTTTTGGAGGGTTCTGGTCTCAGTACAAGACCAGAATATTAAAACAT Human: CTTTTTGGAGGGTTCTGGTCTTGGTACAAGACCAGAATATTAAAACAT Cluster: [ ] Orangutan: CTTTTTGGAGGGTTCTGGTCTTGGTACAAGATCAGAATATTAAAACAT Gorilla > Chimp --------------- chr2B:56615882-56615886 Template switch process: F1: L GTTATACCGCATCTAGATCTCTTTTTGGAGGGTTCTGGTCT 1 F3: 4 CAAGACCAGAATATTAAAACATAGCACTGATCACAATCAG R RF: GTTATACCGCATCTAGATCTCTTTTTGGAGGGTTCTGGTCTCAGTACAAGACCAGAATATTAAAACATAGCACTGATCACAATCAG RR: CAATATGGCGTAGATCTAGAGAAAAACCTCCCAAGACCAGAGTCATGTTCTGGTCTTATAATTTTGTATCGTGACTAGTGTTAGTC F2: 3 CATGT 2 Unidirectional alignment (log-probability: -26.6) TTATACCGCATCTAGATCTCTTTTTGGAGGGTTCTGGTCTtgtaC----CAAGACCAGAATATTAAAACATAGCACTGATCACAATCAG TTATACCGCATCTAGATCTCTTTTTGGAGGGTTCTGGTCT----CAGTACAAGACCAGAATATTAAAACATAGCACTGATCACAATCAG Template switch alignment (log-probability: -16.4) TTATACCGCATCTAGATCTCTTTTTGGAGGGTTCTGGTCT|TGTAC|CAAGACCAGAATATTAAAACATAGCACTGATCACAATCAG TTATACCGCATCTAGATCTCTTTTTGGAGGGTTCTGGTCT|TGTAC|CAAGACCAGAATATTAAAACATAGCACTGATCACAATCAG ========== Event 1926 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: atcccacctacatttcgaaacagcttcttaattatgaggctggttactgctcccAGCCTCATATTAAGAACATTTAGTCTAGGGTAA Chimp: ATCCCACCTACATTTCCAAACAGCCTCTTA-ATATGAGGCTGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCTAGGGTAA ↑ 4 3 1 2 Gorilla: ATCCCACCTACATTTCCAAAC----ACTAA-GTAAGA-ATTGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCTAGGGTAA Human: atcccacctacatttcgaaacagcttcttaattatgaggctggttactgctcccAGCCTCATATTAAGAACATTTAGTCTAGGGTAA Cluster: [ ] Orangutan: atcccacctacatttccaaaC----ACTAA-GTAAGA-ATTGGTTACTGCTCCCAGCCTCATATTAAGAAAATTTAGTCTAGGGTAA Gorilla > Chimp --------------- chr2B:73220564-73220575 Template switch process: F1: L AGTCACTGTGACAATGAAAAATCCCACCTACATTTCCAAA---------------------------CAGCCTC 1 F3: 4 TGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCT R RF: AGTCACTGTGACAATGAAAAATCCCACCTACATTTCCAAACACTAAGTAAGAATTGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCT RR: TCAGTGACACTGTTACTTTTTAGGGTGGATGTAAAGGTTTGTGATTCATTCTTAACCAATGACGAGGGTCGGAGTATAATTCTTGTAAATCAGA F2: 3 CGGAGTATAATT 2 Unidirectional alignment (log-probability: -44.2) GTGACAATGAAAAATCCCACCTACATTTCCAAACAgcctcttaatatgaggC-----------TGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCT GTGACAATGAAAAATCCCACCTACATTTCCAAACA----------------CTAAGTAAGAATTGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCT Template switch alignment (log-probability: -28.5) GTGACAATGAAAAATCCCACCTACATTTCCAAA---------------------------CAGCCTC|TTAATATGAGGC|TGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCT GTGACAATGAAAAATCCCACCTACATTTCCAAACACTAAGTAAGAATTGGTTACTGCTCCCAGCCTC|TTAATATGAGGC|TGGTTACTGCTCCCAGCCTCATATTAAGAACATTTAGTCT ========== Event 1927 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCTAGTTAAgagacagggtctcac ↓ 3 2 1 4 Chimp: TTGCCATTTCCCACTCACTTGTTCACTTAAGTGA----ACAAGTTAAgagacagggtctcac ↑ 3 2 1 4 Gorilla: TTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCTAGTTAAgagacagggtctcac Human: TTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCTAGTTAAgagacagggtctcac Cluster: [ ] Orangutan: TTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCTAGTTAAgagacagggtctcac Human > Chimp ------------- chr2B:72624599-72624605 Template switch process: F1: L GATGCCTCTACTTGCCATTTCCCACTCACTTGTTCACTTAA 1 F3: 4 AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG R RF: GATGCCTCTACTTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCTAGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG RR: CTACGGAGATGAACGGTAAAGAGTGAGTGAACAAGTGAATTGATTATTTAGATCAATTCTCTGTCCCAGAGTGAGACAACAGGTCCGACCTC F2: 3 ACAAGTG 2 Unidirectional alignment (log-probability: -37.8) ATGCCTCTACTTGCCATTTCcCACTCACTTGTTCACTTAA-----------gtgaacaAGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG ATGCCTCTACTTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCT-------AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG Template switch alignment (log-probability: -22.1) ATGCCTCTACTTGCCATTTCcCACTCACTTGTTCACTTAA|GTGAACA|AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG ATGCCTCTACTTGCCATTTCTCACTCACTTGTTCACTTAA|GTGAACA|AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG Gorilla > Chimp --------------- chr2B:72624599-72624605 Template switch process: F1: L GATGCCTCTACTTGCCATTTCCCACTCACTTGTTCACTTAA 1 F3: 4 AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG R RF: GATGCCTCTACTTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCTAGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG RR: CTACGGAGATGAACGGTAAAGAGTGAGTGAACAAGTGAATTGATTATTTAGATCAATTCTCTGTCCCAGAGTGAGACAACAGGTCCGACCTC F2: 3 ACAAGTG 2 Unidirectional alignment (log-probability: -36.8) ATGCCTCTACTTGCCATTTCcCACTCACTTGTTCACTTAA-----------gtgaacaAGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG ATGCCTCTACTTGCCATTTCTCACTCACTTGTTCACTTAACTAATAAATCT-------AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG Template switch alignment (log-probability: -22.1) ATGCCTCTACTTGCCATTTCcCACTCACTTGTTCACTTAA|GTGAACA|AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG ATGCCTCTACTTGCCATTTCTCACTCACTTGTTCACTTAA|GTGAACA|AGTTAAGAGACAGGGTCTCACTCTGTTGTCCAGGCTGGAG ========== Event 1928 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCATCTTCAGTTCTAGAGGAACTGAAGCTCTTCTTTAAGAGCTGCTGGGAAGTTTCACCTCCAACAT Chimp: CCATCTTCAGTTCTAGAGGAAGGAAA---------GAAGAGCTGCTGGGAAGTTTCACCTCCAACAT Gorilla: CCATCTTCAGTTCTAGAGGAAGGAAA---------GAAGAGCTGCTGGGAAGTTTCACCTCCAACAT ↓ 1 3 4 2 Human: CCATCTTCAGTTCTAGAGGAACTGAAGCTCTTCTTTAAGAGCTGCTGGGAAGTTTCACCTCCAACAT Cluster: [ ] Orangutan: CCATCTTCAATTCTAGAGGAAGGAAA---------GAAGAGCTGCTGGGAAGTTTCACCTCCAACAT Gorilla > Human --------------- chr2:170955621-170955635 Template switch process: F1: L GTTTTGTCTACACAGTTTGGCCATCTTCAGTTCTAGAGGAA 1 F3: 4 AAGAGCTGCTGGGAAGTTTCACCTCCAACATTGGCTCATG R RF: GTTTTGTCTACACAGTTTGGCCATCTTCAGTTCTAGAGGAAGGAAAGAAGAGCTGCTGGGAAGTTTCACCTCCAACATTGGCTCATG RR: CAAAACAGATGTGTCAAACCGGTAGAAGTCAAGATCTCCTTCCTTTCTTCTCGACGACCCTTCAAAGTGGAGGTTGTAACCGAGTAC F2: 3 TTTCTTCTCGAAGTC 2 Unidirectional alignment (log-probability: -40.5) TTTTGTCTACACAGTTTGGCCATCTTCAGTTCTAGAGGAActgAAGctcttctttAAGAGCTGCTGGGAAGTTTCACCTCCAACATTGGCTCATG TTTTGTCTACACAGTTTGGCCATCTTCAGTTCTAGAGGAAGGAAAG---------AAGAGCTGCTGGGAAGTTTCACCTCCAACATTGGCTCATG Template switch alignment (log-probability: -28.7) TTTTGTCTACACAGTTTGGCCATCTTCAGTTCTAGAGGAA|CtGaAGCTCTTCTTT|AAGAGCTGCTGGGAAGTTTCACCTCCAACATTGGCTCATG TTTTGTCTACACAGTTTGGCCATCTTCAGTTCTAGAGGAA|CAGCAGCTCTTCTTT|AAGAGCTGCTGGGAAGTTTCACCTCCAACATTGGCTCATG ========== Event 1929 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AGCTGTGGTCTCACAACTTTTGACCCATTGTGACACTCACAATGGAGTAACATACTCCTGTATCa ↑ 4 1 3 2 Chimp: AGCTGTGGTCTCACAACTTTT----------GACACTCACAATGGAGTAACATACTCCTGTATCA Gorilla: ----------------------------------------------------------------- Human: AGCTGTGGTCTCACAACTTTTGACCCATTGTGACACTCACAATGGAGTAACATACTCCTGTATCa Cluster: [ ] Orangutan: ----------------------------------------------------------------- Chimp > Human ------------- chr2:171067010-171067015 Template switch process: F1: L CTTGTAATAGTCAAATTCAGAGCTGTGGTCTCACAACTTTTGAC 1 F3: 4 TGACACTCACAATGGAGTAACATACTCCTGTATCATACCCC R RF: CTTGTAATAGTCAAATTCAGAGCTGTGGTCTCACAACTTTTGACACTCACAATGGAGTAACATACTCCTGTATCATACCCC RR: GAACATTATCAGTTTAAGTCTCGACACCAGAGTGTTGAAAACTGTGAGTGTTACCTCATTGTATGAGGACATAGTATGGGG F2: 3 GTTACC 2 Unidirectional alignment (log-probability: -25.3) TAATAGTCAAATTCAGAGCTGTGGTCTCACAACTTTtgacccattgTGACACTCACAATGGAGTAACATACTCCTGTATCATACCC TAATAGTCAAATTCAGAGCTGTGGTCTCACAACTTT----------TGACACTCACAATGGAGTAACATACTCCTGTATCATACCC Template switch alignment (log-probability: -16.1) TAATAGTCAAATTCAGAGCTGTGGTCTCACAACTTTTGAC|CCATTG|TGACACTCACAATGGAGTAACATACTCCTGTATCATACCC TAATAGTCAAATTCAGAGCTGTGGTCTCACAACTTTTGAC|CCATTG|TGACACTCACAATGGAGTAACATACTCCTGTATCATACCC ========== Event 1930 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: aaGACTTGGTATTATCCTACA----GTG----CAAAAGCTGCTTAAATGCTCACCTTACTGC ↑ 3 1 2 4 Chimp: aaGACTTGGTATTATCCTACAGCTTTTGCACTTAAATGC-TCTTAAATGCTCACCTTACTTC ↓ 3 1 2 4 Gorilla: aaGACTTGGTATTATCCTACA----GTG----CAAAAGCTGCTTAAATGCTCACCTTACTTC Human: aaGACTTGGTATTATCCTACA----GTG----CAAAAGCTGCTTAAATGCTCACCTTACTGC Cluster: [ ] Orangutan: aaGACTTGGTATTATCCTACA----GTG----CAAAAGCTGCTTAAATGCTCACTTTACTTC Chimp > Human ------------- chr2:70420437-70420447 Template switch process: F1: L TAAGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG 1 F3: 4 CTTAAATGCTCACCTTACTGCTCTAGGTTCTGGCTTTTCC R RF: TAAGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAGCTTTTGCACTTAAATGCTCTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC RR: ATTCCTACAATCATGTGAACTTCTGAACCATAATAGGATGTCGAAAACGTGAATTTACGAGAATTTACGAGTGGAATGAAGAGATCCAAGACCGAAAAGG F2: 3 GTCGAAAACGT 2 Unidirectional alignment (log-probability: -42.4) AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG-----------------TgcaaaagctgCTTAAATGCTCACCTTACTgCTCTAGGTTCTGGCTTTTCC AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAGCTTTTGCACTTAAATGCT----------CTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC Template switch alignment (log-probability: -22.7) AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG|TGCAAAAGCTG|CTTAAATGCTCACCTTACTgCTCTAGGTTCTGGCTTTTCC AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG|TGCAAAAGCTG|CTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC Chimp > Gorilla --------------- chr2B:71261896-71261906 Template switch process: F1: L TAAGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG 1 F3: 4 CTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC R RF: TAAGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAGCTTTTGCACTTAAATGCTCTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC RR: ATTCCTACAATCATGTGAACTTCTGAACCATAATAGGATGTCGAAAACGTGAATTTACGAGAATTTACGAGTGGAATGAAGAGATCCAAGACCGAAAAGG F2: 3 GTCGAAAACGT 2 Unidirectional alignment (log-probability: -35.9) AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG-----------------TgcaaaagctgCTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAGCTTTTGCACTTAAATGCT----------CTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC Template switch alignment (log-probability: -17.2) AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG|TGCAAAAGCTG|CTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC AGGATGTTAGTACACTTGAAGACTTGGTATTATCCTACAG|TGCAAAAGCTG|CTTAAATGCTCACCTTACTTCTCTAGGTTCTGGCTTTTCC ========== Event 1931 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGACAAGGCTTCCCTGACCTG---------------ATGTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAG Chimp: GGGACAAGGCTTCCCTGACCTTGGGACTGACTTGAGTCAGTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAG ↑ 4 3 2 Gorilla: GGGACAAGGCTTCCCTGACCTG---------------ATGTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAG Human: GGGACAAGGCTTCCCTGACCTG---------------ATGTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAG Cluster: [ ] Orangutan: GGGACAAGGCTTCCCTGACCTG---------------ATGTCTTGGGACTGGCTCTGAGTGTTGGGTTAAATCAG Gorilla > Chimp --------------- chr2B:70947419-70947425 Template switch process: F1: L TGGGAACTGTGCAGGCTTGAGGGACAAGGCTTCCCTGAC-------CTTGGGACTGACTT 1 F3: 4 TCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAGAAGT R RF: TGGGAACTGTGCAGGCTTGAGGGACAAGGCTTCCCTGACCTGATGTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAGAAGT RR: ACCCTTGACACGTCCGAACTCCCTGTTCCGAAGGGACTGGACTACAGAACCCTGACTGAGACTCACAACCCAATTTCGTCTTCA F2: 3 GACTGAG 2 Unidirectional alignment (log-probability: -45.2) GGCTTGAGGGACAAGGCTTCCCTGACCT--TgggactgacttgagtcaGTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAGAAGT GGCTTGAGGGACAAGGCTTCCCTGACCTGAT-----------------GTCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAGAAGT Template switch alignment (log-probability: -32.5) GGCTTGAGGGACAAGGCTTCCCTGAC-------CTTGGGACTGACTt|GAGTCAG|TCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAGAAGT GGCTTGAGGGACAAGGCTTCCCTGACCTGATGTCTTGGGACTGACTC|GAGTCAG|TCTTGGGACTGACTCTGAGTGTTGGGTTAAAGCAGAAGT ========== Event 1932 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTCCAAGAAAAAGTGTAAACA-GTATTAGTACACAATAGTACACTGTTGTGTACTAATACTTAACAGATATGTCATGAG ↑ 1 4 3 2 Chimp: GTCCAAGAAAAAGTGTAAACAGCTATTCCTGACTGCTC-ATCACTGTTGTGTACTAATACTTAACAGATATGTCATGAG Gorilla: GTCCaaaaaaaaGTGTAAACAGCTATTCCTGACTGCTC-ATCACtgttgtgtactaatacttaacagatatgtcatgag Human: GTCCAAGAAAAAGTGTAAACA-GTATTAGTACACAATAGTACACTGTTGTGTACTAATACTTAACAGATATGTCATGAG Cluster: [ ] Orangutan: GTCCAAGAAAAAGTGTAAACAGCTATTCCTGACTGTTC-ATCACTGTTGTGTACTAAGACTTAACAGATATGTCATAAG Chimp > Human ------------- chr2:69578535-69578551 Template switch process: F1: L GCCAGACCAGGCAAAGTTATGTCCAAGAAAAAGTGTAAACAG 1 F3: 4 ACACTGTTGTGTACTAATACTTAACAGATATGTCATGAGGC R RF: GCCAGACCAGGCAAAGTTATGTCCAAGAAAAAGTGTAAACAGCTATTCCTGACTGCTCATCACTGTTGTGTACTAATACTTAACAGATATGTCATGAGGC RR: CGGTCTGGTCCGTTTCAATACAGGTTCTTTTTCACATTTGTCGATAAGGACTGACGAGTAGTGACAACACATGATTATGAATTGTCTATACAGTACTCCG F2: 3 TGATAACACATGATTAT 2 Unidirectional alignment (log-probability: -46.5) CAGACCAGGCAAAGTTATGTCCAAGAAAAAGTGTAAACAG-----------------TattagtacacaatagtaCACTGTTGTGTACTAATACTTAACAGATATGTCATGAGG CAGACCAGGCAAAGTTATGTCCAAGAAAAAGTGTAAACAGCTATTCCTGACTGCTCAT-----------------CACTGTTGTGTACTAATACTTAACAGATATGTCATGAGG Template switch alignment (log-probability: -29.4) CAGACCAGGCAAAGTTATGTCCAAGAAAAAGTGTAAACAG|TATTAGTACACAAtAGT|aCACTGTTGTGTACTAATACTTAACAGATATGTCATGAGG CAGACCAGGCAAAGTTATGTCCAAGAAAAAGTGTAAACAG|TATTAGTACACAACAGT|TCACTGTTGTGTACTAATACTTAACAGATATGTCATGAGG ========== Event 1933 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTCGCTTGAATCACAGTGCATAGGACGTGGGCAATTTGCTCCAGCTAATGGTTCGTGTGGGATAGGTAT ↓ 1 4 3 2 Chimp: TCTTCGCTTGAATCACAGTGC-AATTAGCTGGGCAATTTGCTCCAGCTAATGCTTCGTGTGGGATAGGTAT ↑ 1 4 3 2 Gorilla: TCTTCGCTTGAATCACAGTGCATAGGATGTGGGCAATTTGCTCCAGCTAATGGTTTGTGTGGGATAGGTAT Human: TCTTCGCTTGAATCACAGTGCATAGGACGTGGGCAATTTGCTCCAGCTAATGGTTCGTGTGGGATAGGTAT Cluster: [ ] Orangutan: TCTTTGCTTGAATCACAGTGCATAGGACGTGGGCAATTCGCTCCAGCTAATGGTTCATGTGGGATAGGTAT Human > Chimp ------------- chr2B:68154531-68154536 Template switch process: F1: L CACTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA 1 F3: 4 TGGGCAATTTGCTCCAGCTAATGCTTCGTGTGGGATAGGT R RF: CACTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCATAGGACGTGGGCAATTTGCTCCAGCTAATGGTTCGTGTGGGATAGGT RR: GTGAAAAAGGGTTATTAATGAGAAGCGAACTTAGTGTCACGTATCCTGCACCCGTTAAACGAGGTCGATTACCAAGCACACCCTATCCA F2: 3 CGATTA 2 Unidirectional alignment (log-probability: -36.1) CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCAattagc-------TGGGCAATTTGCTCCAGCTAATGcTTCGTGTGGGATAGGT CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA------TAGGACGTGGGCAATTTGCTCCAGCTAATGGTTCGTGTGGGATAGGT Template switch alignment (log-probability: -22) CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA|ATTAGC|TGGGCAATTTGCTCCAGCTAATGcTTCGTGTGGGATAGGT CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA|ATTAGC|TGGGCAATTTGCTCCAGCTAATGGTTCGTGTGGGATAGGT Gorilla > Chimp --------------- chr2B:68154531-68154536 Template switch process: F1: L CACTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA 1 F3: 4 TGGGCAATTTGCTCCAGCTAATGCTTCGTGTGGGATAGGT R RF: CACTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCATAGGATGTGGGCAATTTGCTCCAGCTAATGGTTTGTGTGGGATAGGT RR: GTGAAAAAGGGTTATTAATGAGAAGCGAACTTAGTGTCACGTATCCTACACCCGTTAAACGAGGTCGATTACCAAACACACCCTATCCA F2: 3 CGATTA 2 Unidirectional alignment (log-probability: -40.3) CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCAatTAG---cTGGGCAATTTGCTCCAGCTAATGcTTcGTGTGGGATAGGT CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA--TAGGATGTGGGCAATTTGCTCCAGCTAATGGTTTGTGTGGGATAGGT Template switch alignment (log-probability: -27.5) CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA|ATTAGC|TGGGCAATTTGCTCCAGCTAATGcTTcGTGTGGGATAGGT CTTTTTCCCAATAATTACTCTTCGCTTGAATCACAGTGCA|ATTAGC|TGGGCAATTTGCTCCAGCTAATGGTTTGTGTGGGATAGGT ========== Event 1934 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ------GATGGTTATTACACTGAGCAAGAACTT--------TTTGTTGTTATTCCTTTCAAATGC-ACACTCAGTAG Chimp: ------GATGGTTATTACACTGAGCAAGAACTT--------TTTGTTATTATTCCTTTCAAATGC-ACACTCAGTAG ↓ 3 2 1 4 Gorilla: ---------------------GAGCAAGAACTT----------------TGCTCAGTTCAAATGC-ACACTCAGTAG ↑ 3 2 1 4 Human: ------GATGGTTATTACACTGAGCAAGAACTT--------TTTGTTGTTATTCCTTTCAAATGC-ACACTCAGTAG Cluster: [ ] Orangutan: TACACT---------------GAG-CAGAACTTTTTGTTGT--------TATTCCTTTCAAATGCAACACTCAGTAG Human > Gorilla --------------- chr2B:68386279-68386284 Template switch process: F1: L TAACAATATGATCC---------------GAGCAAGAACTTT 1 F3: 4 TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG R RF: TAACAATATGATCCGATGGTTATTACACTGAGCAAGAACTTTTTGTTGTTATTCCTTTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG RR: ATTGTTATACTAGGCTACCAATAATGTGACTCGTTCTTGAAAAACAACAATAAGGAAAGTTTACGTGTGAGTCATCGATATCGCAGAATCGCTCAC F2: 3 GACTCG 2 Unidirectional alignment (log-probability: -40.3) TAACAATATGATCCG---------------AGCAAGAACTTTgctcag--------------TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG TAACAATATGATCCGATGGTTATTACACTGAGCAAGAACTTT------TTGTTGTTATTCCTTTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG Template switch alignment (log-probability: -26.6) TAACAATATGATCC---------------GAGCAAGAACTTT|GCTCAG|TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG TAACAATATGATCCGATGGTTATTACACTGAGCAAGAACTTT|GCTCAG|TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG Chimp > Gorilla --------------- chr2B:68386279-68386284 Template switch process: F1: L TAACAATATGATCC---------------GAGCAAGAACTTT 1 F3: 4 TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG R RF: TAACAATATGATCCGATGGTTATTACACTGAGCAAGAACTTTTTGTTATTATTCCTTTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG RR: ATTGTTATACTAGGCTACCAATAATGTGACTCGTTCTTGAAAAACAATAATAAGGAAAGTTTACGTGTGAGTCATCGATATCGCAGAATCGCTCAC F2: 3 GACTCG 2 Unidirectional alignment (log-probability: -40.3) TAACAATATGATCCG---------------AGCAAGAACTTTgctcag--------------TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG TAACAATATGATCCGATGGTTATTACACTGAGCAAGAACTTT------TTGTTATTATTCCTTTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG Template switch alignment (log-probability: -26.6) TAACAATATGATCC---------------GAGCAAGAACTTT|GCTCAG|TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG TAACAATATGATCCGATGGTTATTACACTGAGCAAGAACTTT|GCTCAG|TTCAAATGCACACTCAGTAGCTATAGCGTCTTAGCGAGTG ========== Event 1935 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAGTAAACTCTATGTTTCTTTGAGGCACAAATAGCCTCAAAGCATTTTGAGATAGCATATGT Chimp: TTAGTAAACTCTATGTTTCTTTGAGGCACAAATA------GGGCATTTTGAGATAGCATATGT Gorilla: TTAGTAAACTCTATGTTTCTTTGAGGCACAAATA------TGGCATTTTGAGATAGCATATGT ↓ 3 2 1 4 Human: TTAGTAAACTCTATGTTTCTTTGAGGCACAAATAGCCTCAAAGCATTTTGAGATAGCATATGT Cluster: [ ] Orangutan: TTAGTAAACTATATGTTTCTTTGAGGCACAAATA------TGGCATTTTGAGATAGCATATGT Gorilla > Human --------------- chr2:66879048-66879055 Template switch process: F1: L GATTGCTTTAGTAAACTCTATGTTTCTTTGAGGCACAAATA 1 F3: 4 GCATTTTGAGATAGCATATGTTTCTAAGATATTTCTCACT R RF: GATTGCTTTAGTAAACTCTATGTTTCTTTGAGGCACAAATATGGCATTTTGAGATAGCATATGTTTCTAAGATATTTCTCACT RR: CTAACGAAATCATTTGAGATACAAAGAAACTCCGTGTTTATACCGTAAAACTCTATCGTATACAAAGATTCTATAAAGAGTGA F2: 3 AAACTCCG 2 Unidirectional alignment (log-probability: -30.6) ATTGCTTTAGTAAACTCTATGTTTCTTTGAGGCACAAATagcctcAaaGCATTTTGAGATAGCATATGTTTCTAAGATATTTCTCACT ATTGCTTTAGTAAACTCTATGTTTCTTTGAGGCACAAAT------ATGGCATTTTGAGATAGCATATGTTTCTAAGATATTTCTCACT Template switch alignment (log-probability: -16.7) ATTGCTTTAGTAAACTCTATGTTTCTTTGAGGCACAAATA|GCCTCAAA|GCATTTTGAGATAGCATATGTTTCTAAGATATTTCTCACT ATTGCTTTAGTAAACTCTATGTTTCTTTGAGGCACAAATA|GCCTCAAA|GCATTTTGAGATAGCATATGTTTCTAAGATATTTCTCACT ========== Event 1936 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAAAAGCCTTCTCTCACTAA----------------------AGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCCCT ↓ 4 13 2 Chimp: GAAAAAGCCTTCTCTCACTAAAGAAACCCCTAGCACGACTAAAAGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCCCT Gorilla: GAAAAAGCCTTCTCTCACTAA----------------------AGAAACTCCTAGCATGGTGGTAGGTACACTCCAAAGCCCT Human: GAAAAAGCCTTCTCTCACTAA----------------------AGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCCCT Cluster: [ ] Orangutan: GAAAAAGCCTTCTCTCGCTAA----------------------AGAAACTCCTAGCATAGTGGTAGGTATACTCCAAAGCCCT Human > Chimp ------------- chr2B:66127252-66127257 Template switch process: F1: L ACATGATGTCTTTGCTTAATGAAAAAGCCTTCTCTCACTAAAGAAACCCCTAGCA 1 F3: 4 AAAGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCCCT R RF: ACATGATGTCTTTGCTTAATGAAAAAGCCTTCTCTCACTAAAGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCCCT RR: TGTACTACAGAAACGAATTACTTTTTCGGAAGAGAGTGATTTCTTTGAGGATCGTATCACCATCCATGTGAGGTTTCGGGA F2: 3 ATCAGC 2 Unidirectional alignment (log-probability: -42.6) TTAATGAAAAAGCCTTCTCTCACTAAAGAAAcccctagcacgactaaaagaaaCTCCTAGCATAGTGGTAGGTACACTCCAAAGCC TTAATGAAAAAGCCTTCTCTCACTAAAGAAA----------------------CTCCTAGCATAGTGGTAGGTACACTCCAAAGCC Template switch alignment (log-probability: -28.3) TTAATGAAAAAGCCTTCTCTCACTAAAGAAACcCCTAGCA|CgACTA|AAAGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCC TTAATGAAAAAGCCTTCTCTCACTAAAGAAACTCCTAGCA|CCACTA|AAAGAAACTCCTAGCATAGTGGTAGGTACACTCCAAAGCC ========== Event 1937 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACATTGCATGAACTGTCATTTAATGCATG--------CAT---TAAGGTTTCCTTCACCCGAAG ↓ 1 3 4 2 Chimp: ACATTGCATGAACTGTCA-TTAATGCATG----CATTCAT---TAAGGTTTCCTTCACCCGAAG Gorilla: ACATTGCATGAGCTGTCATTTAATGCATGCATT----CAT------TGTTTCCTTCACCCGAAG Human: ACATTGCATGAACTGTCATTTAATGCATG--------CAT---TAAGGTTTCCTTCACCCGAAG Cluster: [ ] Orangutan: ACATTGCATGAACTGTCATTTAATGCATGCATT----CACTAA---GGTTTCCTTCACCCGAAG Human > Chimp ------------- chr2B:65690244-65690255 Template switch process: F1: L AGACTTTTTAATACATTGCATGAACTGTCATT 1 F3: 4 CATTAAGGTTTCCTTCACCCGAAGTTCTTAAATAAGGGGC R RF: AGACTTTTTAACACATTGCATGAACTGTCATTTAATGCATGCATTAAGGTTTCCTTCACCCGAAGTTCTTAAATAAGGGGC RR: TCTGAAAAATTGTGTAACGTACTTGACAGTAAATTACGTACGTAATTCCAAAGGAAGTGGGCTTCAAGAATTTATTCCCCG F2: 3 TTACGTACGTAA 2 Unidirectional alignment (log-probability: -32.9) AGACTTTTTAAtACATTGCATGAACTGTCA-TTAATGCATGCATtcatTAAGGTTTCCTTCACCCGAAGTTCTTAAATAAGGGGC AGACTTTTTAACACATTGCATGAACTGTCATTTAATGCATGCAT----TAAGGTTTCCTTCACCCGAAGTTCTTAAATAAGGGGC Template switch alignment (log-probability: -22.6) AGACTTTTTAAtACATTGCATGAACTGTCATT|AATGCATGCATT|CATTAAGGTTTCCTTCACCCGAAGTTCTTAAATAAGGGGC AGACTTTTTAACACATTGCATGAACTGTCATT|AATGCATGCATT|CATTAAGGTTTCCTTCACCCGAAGTTCTTAAATAAGGGGC ========== Event 1938 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAAGAAGAGATAAAACACAATTCTG---AGTTGGATGTGAGGTTGGAGGTAGAAAGCC----TCCAAGTTTCAAAACAAAAGGAAAACAAGTCAGAAAACTGCTGTGGCAAGTGCG Chimp: AGAAGAAGAGATAAAACACAATTCTG---AATTGGATGTGAGGTTGGAGGTAGAAAGAC--AAATAAAGTTTCAAAACAAAAGGAAAACAAGTCAGAAAACTGCTGTGGCAAGTGCT ↑ 1 4 3 2 Gorilla: AGAAGAAGAGATAAAACACAA-TGTG------AGGATGTGAGGTTGGAGGTAGAAAGCCAA--ATAAAGTTTCAAAACAAAAGGAAAACAAGTCAGAAAACTGCTGTGGCAAGTGCT Human: AGAAGAAGAGATAAAACACAATTCTG---AGTTGGATGTGAGGTTGGAGGTAGAAAGCC----TCCAAGTTTCAAAACAAAAGGAAAACAAGTCAGAAAACTGCTGTGGCAAGTGCG Cluster: [ ] Orangutan: AGAAGGAGA--GAGAACACAATTCTGAGT---TGGATGTGAGGTTGGAGGTAGAAAGCCAA--ATAAAGTTTCAAAACAAAAGGAAAACAAGTCAGAAAACTGCTGTGGCAAGAGCT Gorilla > Chimp --------------- chr2B:65400572-65400579 Template switch process: F1: L TGGTCAAGCAGCTGAAAGTGAGAAGAAGAGATAAAACACAAT 1 F3: 4 GGATGTGAGGTTGGAGGTAGAAAGACAAATAAAGTTTC R RF: TGGTCAAGCAGCTGAAAGTGAGAAGAAGAGATAAAACACAATGTGAGGATGTGAGGTTGGAGGTAGAAAGCCAAATAAAGTTTCAAAACAAAAGGAAAACAAGTCAGA RR: ACCAGTTCGTCGACTTTCACTCTTCTTCTCTATTTTGTGTTACACTCCTACACTCCAACCTCCATCTTTCGGTTTATTTCAAAGTTTTGTTTTCCTTTTGTTCAGTCT F2: 3 TTAAGTCT 2 Unidirectional alignment (log-probability: -37.5) GTCAAGCAGCTGAAAGTGAGAAGAAGAGATAAAACACAATtcTGAattGGATGTGAGGTTGGAGGTAGAAAGaCAAATAAAGTTTC GTCAAGCAGCTGAAAGTGAGAAGAAGAGATAAAACACAATG-TGA---GGATGTGAGGTTGGAGGTAGAAAGCCAAATAAAGTTTC Template switch alignment (log-probability: -27.8) GTCAAGCAGCTGAAAGTGAGAAGAAGAGATAAAACACAAT|TCTGAaTT|GGATGTGAGGTTGGAGGTAGAAAGaCAAATAAAGTTTC GTCAAGCAGCTGAAAGTGAGAAGAAGAGATAAAACACAAT|TCTGACTT|GGATGTGAGGTTGGAGGTAGAAAGCCAAATAAAGTTTC ========== Event 1939 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACTGATAGGATAAATCCAAA----ACCCTCTGTGGAGTCCCTGATGAGCTGGTTCTTGCCT Chimp: AACTGATAGGATAAATCCAAA----ACCCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCT ↓ 1 4 3 2 Gorilla: AACTGATAGGATAAATCCAAAGGGACTCCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCT ↑ 1 4 3 2 Human: AACTGATAGGATAAATCCAAA----ACCCTCTGTGGAGTCCCTGATGAGCTGGTTCTTGCCT Cluster: [ ] Orangutan: AACTGATAGGATAAATCCAAA----ACCCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCT Human > Gorilla --------------- chr2B:64536834-64536839 Template switch process: F1: L ATTTACCAGTTAAAACTGTTAACTGATAGGATAAATCCAAA 1 F3: 4 CCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTAATCA R RF: ATTTACCAGTTAAAATTGTTAACTGATAGGATAAATCCAAAACCCTCTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTAATCA RR: TAAATGGTCAATTTTAACAATTGACTATCCTATTTAGGTTTTGGGAGACACCTCAGGGACTACTCGACCAAGAACGGATGAATTAGT F2: 3 TCAGGG 2 Unidirectional alignment (log-probability: -37.5) TTTACCAGTTAAAAcTGTTAACTGATAGGATAAATCCAAAgggACtCCTtTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA TTTACCAGTTAAAATTGTTAACTGATAGGATAAATCCAAA---AC-CCTCTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA Template switch alignment (log-probability: -27.6) TTTACCAGTTAAAAcTGTTAACTGATAGGATAAATCCAAA|GGGACT|CCTtTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA TTTACCAGTTAAAATTGTTAACTGATAGGATAAATCCAAA|GGGACT|CCTCTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA Chimp > Gorilla --------------- chr2B:64536834-64536839 Template switch process: F1: L ATTTACCAGTTAAAACTGTTAACTGATAGGATAAATCCAAA 1 F3: 4 CCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA R RF: ATTTACCAGTTAAAATTGTTAACTGATAGGATAAATCCAAAACCCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA RR: TAAATGGTCAATTTTAACAATTGACTATCCTATTTAGGTTTTGGGAAACACCTCAGGGACTACTCGACCAAGAACGGATGAAT F2: 3 TCAGGG 2 Unidirectional alignment (log-probability: -31.9) TTTACCAGTTAAAAcTGTTAACTGATAGGATAAATCCAAAgggACtCCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA TTTACCAGTTAAAATTGTTAACTGATAGGATAAATCCAAA---AC-CCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA Template switch alignment (log-probability: -22) TTTACCAGTTAAAAcTGTTAACTGATAGGATAAATCCAAA|GGGACT|CCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA TTTACCAGTTAAAATTGTTAACTGATAGGATAAATCCAAA|GGGACT|CCTTTGTGGAGTCCCTGATGAGCTGGTTCTTGCCTACTTA ========== Event 1940 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAATGCCATAGTTGTTTGCCATAGTAAATGAAGAGAGAGACTTTAAGCCCAACCGCAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGCGAT----TTATGTGATTTATGAAAACATGTTAT ↓ 3 2 1 4 Chimp: TCAATGCCATAGTTGTTTGCCATAGTAAATGAAGAGAGAGACTTTAAGCCCAACCGCAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGCCTA--TGGTATGCGATTTATGAAAACATGTTAT Gorilla: TCAGCGCTATAGTTGTTTGCCATAGTAAATGAAGAGAGAGACTTTAAGCCCAACCGCAACACATCAAAATTGGGGAAACATGTTTTTAAGGAAAGCCTATG--GTATGCGATTTATGAAAACGTGTTAT Human: TCAATGCCATAGTTGTTTGCCATAGTAAATGAAGAGAGAGACTTTAAGCCCAACCGCAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGCGAT----TTATGTGATTTATGAAAACATGTTAT Cluster: [ ] Orangutan: TCAACACCATAGTTGTTTGCCATAGTAAATGAAGAGAGAGACTTTAAGCCCAACTGCAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGCCTATA--GTATGCAATTTATGAAAACGTGTTAT Human > Chimp ------------- chr2B:68307346-68307351 Template switch process: F1: L GCAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGC 1 F3: 4 TATGCGATTTATGAAAACATGTTATTTCAAAAAGACAGGATATGA R RF: CCATAGTAAATGAAGAGAGAGACTTTAAGCCCAACCGCAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGCGATTTATGTGATTTATGAAAACATGTTATTTCAAAAAGACAGGATATGA RR: GGTATCATTTACTTCTCTCTCTGAAATTCGGGTTGGCGTTGTGTAGTTTTAACCCCTTTGCACAAAAATTCCTTTCGCTAAATACACTAAATACTTTTGTACAATAAAGTTTTTCTGTCCTATACT F2: 3 GGTATC 2 Unidirectional alignment (log-probability: -34.5) CAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGCctatgG---TATGcGATTTATGAAAACATGTTATTTCAAAAAGACAGGA CAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGC-----GATTTATGTGATTTATGAAAACATGTTATTTCAAAAAGACAGGA Template switch alignment (log-probability: -22.1) CAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGC|CTATGG|TATGcGATTTATGAAAACATGTTATTTCAAAAAGACAGGA CAACACATCAAAATTGGGGAAACGTGTTTTTAAGGAAAGC|CTATGG|TATGTGATTTATGAAAACATGTTATTTCAAAAAGACAGGA ========== Event 1941 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAGGAGTATAAAATGTAGAGTAA------------GAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGTGGCTTA ↓ 4 1 3 2 Chimp: ACAGGAGTATAAAATGTAGAGTAAGAAATCTGATAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGTGGCTTA ↑ 4 1 3 2 Gorilla: ACAGGAGTATAAAATGTAGAGGAA------------GAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGTGGCTTA Human: ACAGGAGTATAAAATGTAGAGTAA------------GAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGTGGCTTA Cluster: [ ] Orangutan: ACAGGAGTATAAAATGTAGAGTAA------------GAAATTTGAATTATTTGAAGTATCAGTCATATAAAATTGTGGCTTA Human > Chimp ------------- chr2B:69228422-69228426 Template switch process: F1: L CATTTTGATCAATGAATACAGGAGTATAAAATGTAGAGTAAGAAAT 1 F3: 4 AAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGT R RF: CATTTTGATCAATGAATACAGGAGTATAAAATGTAGAGTAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGT RR: GTAAAACTAGTTACTTATGTCCTCATATTTTACATCTCATTCTTTAAACTTAATAAACTTCATAGTCAATATATTTTAACA F2: 3 TAGTC 2 Unidirectional alignment (log-probability: -28.2) GATCAATGAATACAGGAGTATAAAATGTAGAGtaagaaatctgaTAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATT GATCAATGAATACAGGAGTATAAAATGTAGAG------------TAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATT Template switch alignment (log-probability: -16) GATCAATGAATACAGGAGTATAAAATGTAGAGTAAGAAAT|CTGAT|AAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATT GATCAATGAATACAGGAGTATAAAATGTAGAGTAAGAAAT|CTGAT|AAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATT Gorilla > Chimp --------------- chr2B:69228422-69228427 Template switch process: F1: L AAACATTTTGATCAATGAATACAGGAGTATAAAATGTAGAGTAAGAAAT 1 F3: 4 AGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGT R RF: AAACATTTTGATCAATGAATACAGGAGTATAAAATGTAGAGGAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTGT RR: TTTGTAAAACTAGTTACTTATGTCCTCATATTTTACATCTCCTTCTTTAAACTTAATAAACTTCATAGTCAATATATTTTAACA F2: 3 ATAGTC 2 Unidirectional alignment (log-probability: -33.7) GATCAATGAATACAGGAGTATAAAATGTAGAGtaagaaatctgatAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTG GATCAATGAATACAGGAGTATAAAATGTAGAG------------GAAGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTG Template switch alignment (log-probability: -22.2) GATCAATGAATACAGGAGTATAAAATGTAGAGtAAGAAAT|CTGATA|AGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTG GATCAATGAATACAGGAGTATAAAATGTAGAGGAAGAAAT|CTGATA|AGAAATTTGAATTATTTGAAGTATCAGTTATATAAAATTG ========== Event 1942 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAGGCTCAGAAACAAGGCTACATCTAAGGTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTGAT--GGTTAGGAATCCATCTTACAGG ↓ 3 1 2 4 Chimp: ACAGGCTCAGAAACAAGGCTACATCTAAGTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGATCTGTTTGCAAATTAATATTTTTACAGTTTGCTCTTAACTTAGATGTAGTTAGGAATCCATCTTACAGG ↑ 3 1 2 4 Gorilla: ACAGGCTCAGAAACAAGGCTACATCTAAGTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTGAT--GGTTAGGAATCCATCTTACAGG Human: ACAGGCTCAGAAACAAGGCTACATCTAAGGTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTTGAT--GGTTAGGAATCCATCTTACAGG Cluster: [ ] Orangutan: ACAGGCTCAGAAACAAGGCTACATGTAA-GTAAGAGCAAACTGTAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------------------------------NNNNNNNN--NNNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr2A:92961752-92961804 Template switch process: F1: L AAGTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT 1 F3: 4 GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT R RF: TACATCTAAGGTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGATCTTTGATGGTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT RR: ATGTAGATTCCATTCTCGTTTGACATTTTTATAATTAAACGTTTGTCTAGAAACTACCAATCCTTAGGTAGAATGTCCACAGATCTATGAGACTTGA F2: 3 ATGTAGATTCAATTCTCGTTTGACATTTTTATAATTAAACGTTTGTCTAGAAA 2 Unidirectional alignment (log-probability: -97.9) GtTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGATaaagatctgtttgcaaattaatatttttacagtttgctcttaaCTTaGATGtaGTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT GGTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT-------------------------------------------CTTTGATG--GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT Template switch alignment (log-probability: -33.8) GtTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT|AAAGATCTGTTTGCAAATTAATATTTTTACAGTTTGCTCTTAaCTTAGATGTA|GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT GGTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT|AAAGATCTGTTTGCAAATTAATATTTTTACAGTTTGCTCTTACCTTAGATGTA|GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT Gorilla > Chimp --------------- chr2A:92961752-92961804 Template switch process: F1: L AAGTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT 1 F3: 4 GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT R RF: TACATCTAAGTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGATCTTTGATGGTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT RR: ATGTAGATTCAATTCTCGTTTGACATTTTTATAATTAAACGTTTGTCTAGAAACTACCAATCCTTAGGTAGAATGTCCACAGATCTATGAGACTTGA F2: 3 ATGTAGATTCAATTCTCGTTTGACATTTTTATAATTAAACGTTTGTCTAGAAA 2 Unidirectional alignment (log-probability: -91) GTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGATaaagatctgtttgcaaattaatatttttacagtttgctcttaaCTTaGATGtaGTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT GTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT-------------------------------------------CTTTGATG--GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT Template switch alignment (log-probability: -22.5) GTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT|AAAGATCTGTTTGCAAATTAATATTTTTACAGTTTGCTCTTAACTTAGATGTA|GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT GTTAAGAGCAAACTGTAAAAATATTAATTTGCAAACAGAT|AAAGATCTGTTTGCAAATTAATATTTTTACAGTTTGCTCTTAACTTAGATGTA|GTTAGGAATCCATCTTACAGGTGTCTAGATACTCTGAACT ========== Event 1943 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: agcacttacctcatggtcttgttgcaagaattaaataatttagataaagcacttacaacaatgtcaagcatatatgtaaTATTATTATTGCACAGTGTCTATT--------------------------------------CCAATGGGTCCAAACTACTTTTAAA Chimp: agcacttacctcatggtcttgttgtaagaattaaataatttagataaagcacttaaaacaatgtcaagcacatatgtaaTAATATTATTGCACAGTTTCTATT-------------------CCAATTGCAACAGCACATTCCAATGGGTCCAAACTACTTTTAAA Gorilla: agcacttacctcatggtcttgttgtaagaattaaataatttagataaagcacttaaaacaatgtcaagcatatatgtaaTATTATTATTGCACAGTTTCTATTCCAATTGCAACAGCACATT-------------------CCAATGGGTCCAAACTACTTTTAAA ↑ 3 2 4 1 Human: agcacttacctcatggtcttgttgcaagaattaaataatttagataaagcacttacaacaatgtcaagcatatatgtaaTATTATTATTGCACAGTGTCTATT--------------------------------------CCAATGGGTCCAAACTACTTTTAAA Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------------------------------------------------NNNNNNNNN Human > Gorilla --------------- chr2A:89506185-89506191 Template switch process: F1: L AAACAATGTCAAGCATATATGTAATATTATTATTGCACAGTTTCTATTCCAAT 1 F3: 4 GCAC-------ATTCCAATGGGTCCAAACTACTTTTAAAACTCCAGCTTTATTA R RF: TGTTGCAAGAATTAAATAATTTAGATAAAGCACTTACAACAATGTCAAGCATATATGTAATATTATTATTGCACAGTGTCTATTCCAATGGGTCCAAACTACTTTTAAAACTCCAGCTTTATTA RR: ACAACGTTCTTAATTTATTAAATCTATTTCGTGAATGTTGTTACAGTTCGTATATACATTATAATAATAACGTGTCACAGATAAGGTTACCCAGGTTTGATGAAAATTTTGAGGTCGAAATAAT F2: 3 ACAACGT 2 Unidirectional alignment (log-probability: -49.3) CATATATGTAATATTATTATTGCACAGTtTCTattccaattgcaacagcacATTCCAATGGGTCCAAACTACTTTTAAAACTCCAGC CATATATGTAATATTATTATTGCACAGTGTCT-------------------ATTCCAATGGGTCCAAACTACTTTTAAAACTCCAGC Template switch alignment (log-probability: -38.2) CATATATGTAATATTATTATTGCACAGTtTCTATTCCAAT|TGCAACA|GCAC-------ATTCCAATGGGTCCAAACTACTTTTAAAACTCCAGC CATATATGTAATATTATTATTGCACAGTGTCTATTCCAAT|TGCAACA|GCACAGTGTCTATTCCAATGGGTCCAAACTACTTTTAAAACTCCAGC ========== Event 1944 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAGGTCTGCTTGACTTCGATGAAACTAAT----------ACAATTAGAACTTTGGTGAAAT Chimp: CAAGGTCTGCTTGACTTCGATGAAACTAGAATTAGTTTCATCAATTAGAACTTTGGTGAAAT ↑ 3 1 4 Gorilla: CAAGGTCTGCTTGACTTCGATGAAACTAAT----------ACAATTAGAACTTTGGTGAAAT Human: CAAGGTCTGCTTGACTTCGATGAAACTAAT----------ACAATTAGAACTTTGGTGAAAT Cluster: [ ] Orangutan: CAAGGTCTGCTTGACTTCGATGAAACTAAT----------ACAATTAGAACTTTGGTGAAAT Gorilla > Chimp --------------- chr2B:69647381-69647393 Template switch process: F1: L CCAATAATTGTAGCAAGGTCTGCTTGACTTCGATGAAACTA 1 F3: 4 CAATTAGAACTTTGGTGAAATGAATCTAAAGAAAAATAGC R RF: CCAATAATCGTAGCAAGGTCTGCTTGACTTCGATGAAACTAATACAATTAGAACTTTGGTGAAATGAATCTAAAGAAAAATAGC RR: GGTTATTAGCATCGTTCCAGACGAACTGAAGCTACTTTGATTATGTTAATCTTGAAACCACTTTACTTAGATTTCTTTTTATCG F2: 3 TACTTTGATTAAG 2 Unidirectional alignment (log-probability: -41.9) CAATAATtGTAGCAAGGTCTGCTTGACTTCGATGAAACTAgaAttagtttcatCAATTAGAACTTTGGTGAAATGAATCTAAAGAAAAATAGC CAATAATCGTAGCAAGGTCTGCTTGACTTCGATGAAACTAATA----------CAATTAGAACTTTGGTGAAATGAATCTAAAGAAAAATAGC Template switch alignment (log-probability: -28.4) CAATAATtGTAGCAAGGTCTGCTTGACTTCGATGAAACTA|GaATTAGTTTCAT|CAATTAGAACTTTGGTGAAATGAATCTAAAGAAAAATAGC CAATAATCGTAGCAAGGTCTGCTTGACTTCGATGAAACTA|GTATTAGTTTCAT|CAATTAGAACTTTGGTGAAATGAATCTAAAGAAAAATAGC ========== Event 1945 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCTCTGCATGAGAAAAGGAGAGGAGTTCtttttttttttttttCCTTCCAAAAAAGGGCAGAGAGAAGAGTAGAGAACAAATAATCCAGGGAGAAGTAAATGAGAGGGAGGGAAGGGGAGCCAGAGGAGGCTGTGAGACTAGGAACTGTATGGAGGAGGAGTAAAGA Chimp: TGCTCTGCATGAGAAAAGGAG---AGTTCtttttt-ttttttttCCTTCCAAAAAAGGGCAG--AGAAGAGTAGAGAACAAATAATCCAGGGAGAAGTAAATGAGAGGGAGGGAAGGGGAGCCAAAGGAGGCTGTGAGACTAGGAACTGTATGGAGGAGGAGTAAAGA ↓ 1 4 3 2 Gorilla: TGCTCTGCATGAGAAAAGGAGAGGAGTTCttttt--ttttttttCCTTCCAAAAAAGGGCAGAGAGAAGAGTAGAGAACAAATAATCCAGGGAGAAGTAAATGAAAGGGAGGGAAGGGGAGCCAGAGGCGGCTGTGAGACTAGGAACTGTATGGAGGAGGAGTAAAGA Human: TGCTCTGCATGAGAAAAGGAGAGGAGTTCtttttttttttttttCCTTCCAAAAAAGGGCAGAGAGAAGAGTAGAGAACAAATAATCCAGGGAGAAGTAAATGAGAGGGAGGGAAGGGGAGCCAGAGGAGGCTGTGAGACTAGGAACTGTATGGAGGAGGAGTAAAGA Cluster: [ ] Orangutan: TGCTCTGCATGAGAAAAGGAGAGGAGTTCTTT----ATTTTTCTCCTTCCAAAAAAGGGCAGAGAGAAGAGTAGAGAATAAATAATCCAGGGAGAAGTAAACGAGAGGAAGGGAAGGGGAGCCAGAGGAGGCTGTGAGACTAGGAACTGTATGGAGGAGGAGTGAAGA Chimp > Gorilla --------------- chr2B:71968186-71968190 Template switch process: F1: L TTCAGAGAACAGGGTAGAATTGCTCTGCATGAGAAAAGGAGAGG 1 F3: 4 TTTTTTTTTTTTTCCTTCCAAAAAAGGGCAGAGA R RF: TTCAGAGAACAGGGTAGAATTGCTCTGCATGAGAAAAGGAGAGTTCTTTTTTTTTTTTTTCCTTCCAAAAAAGGGCAGAGAAGAGTAGAGAACAAATAATCCAGGGAGAAGTAAATGAGAGGGAGGGAAGGGGAGCCAAAGGAGGCTGTGAGACTAGGAACT RR: AAGTCTCTTGTCCCATCTTAACGAGACGTACTCTTTTCCTCTCAAGAAAAAAAAAAAAAAGGAAGGTTTTTTCCCGTCTCTTCTCATCTCTTGTTTATTAGGTCCCTCTTCATTTACTCTCCCTCCCTTCCCCTCGGTTTCCTCCGACACTCTGATCCTTGA F2: 3 CTTGA 2 Unidirectional alignment (log-probability: -34.6) GAGAACAGGGTAGAATTGCTCTGCATGAGAAAAGGAgagGAGTTC-TTTTTTTTTTTTTCCTTCCAAAAAAGGGCAGAga GAGAACAGGGTAGAATTGCTCTGCATGAGAAAAGGA---GAGTTCTTTTTTTTTTTTTTCCTTCCAAAAAAGGGCAGA-- Template switch alignment (log-probability: -21.8) GAGAACAGGGTAGAATTGCTCTGCATGAGAAAAGGAGAGg|AGTTC|TTTTTTTTTTTTTCCTTCCAAAAAAGGGCAGAGA GAGAACAGGGTAGAATTGCTCTGCATGAGAAAAGGAGAGT|AGTTC|TTTTTTTTTTTTTCCTTCCAAAAAAGGGCAGAGA ========== Event 1946 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTGGAAAGATGACTGTCACTCTATCCTCCAC-GGACTCATACCCCATTCTCTTGGAGAATTAAGTAGGTATGGTATGAGTTA Chimp: CTGGAAAGATGACTGTCACTCTATCCTCCAT-GGACTCATACCCCATTCTCTTGGAGAATTAAGTAGGTATGGTATGAGTTA ↓ 1 3 4 2 ↑ 3 1 2 4 Gorilla: CTGGAAAGATGACTGTCACTCAATTCTCCAAGAGAATGGGGTATGAG-TCCGTGGAGGATCAAGTAGGTATGGTATGAGTTA ↓ 3 1 2 4 ↑ 1 3 4 2 Human: CTGGAAAGATGACTGTCACTCTATCCTCCAC-GGACTCATACCCCATTCTCTTGGAGAATTAAGTAGGTATGGTATGAGTTA Cluster: [ ] Orangutan: CTGGAAAGATGACTGTCATTCTATCCTCCAC-GGACTCATATCCCATTCTCTTGGAGAACTAAGTAGGTATGGTATGAGTTA Gorilla > Human --------------- chr2:62130648-62130683 Template switch process: F1: L GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCTAT 1 F3: 4 AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC R RF: GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCAATTCTCCAAGAGAATGGGGTATGAGTCCGTGGAGGATCAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC RR: CAATGACTGGTTTTAGTTAGGACCTTTCTACTGACAGTGAGTTAAGAGGTTCTCTTACCCCATACTCAGGCACCTCCTAGTTCATCCATACCATACTCAATTCTACTTGGATATATAAGG F2: 3 TTAAGAGGTTCTCTTACCCCATACTCAGGCACCTCC 2 Unidirectional alignment (log-probability: -71.3) CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCtATcCTCCA-------------------CGgactcataccccattctctTGGAGaATtAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCAATTCTCCAAGAGAATGGGGTATGAGTCCG-------------------TGGAGGATCAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC Template switch alignment (log-probability: -25.9) CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCtAT|CCTCCACGGACTCATACCCCATTCTCTTGGAGAATT|AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCAAT|CCTCCACGGACTCATACCCCATTCTCTTGGAGAATT|AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC Human > Gorilla --------------- chr2B:62769990-62770025 Template switch process: F1: L GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC 1 F3: 4 ATCAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC R RF: GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCTATCCTCCACGGACTCATACCCCATTCTCTTGGAGAATTAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC RR: CAATGACTGGTTTTAGTTAGGACCTTTCTACTGACAGTGAGATAGGAGGTGCCTGAGTATGGGGTAAGAGAACCTCTTAATTCATCCATACCATACTCAATTCTACTTGGATATATAAGG F2: 3 GGAGGTGCCTGAGTATGGGGTAAGAGAACCTCTTAA 2 Unidirectional alignment (log-probability: -71.3) TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCaATtCTCCAagagaatggggtatgagtcCG-------------------TGGAGgATcAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCTATCCTCCA-------------------CGGACTCATACCCCATTCTCTTGGAGAATTAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT Template switch alignment (log-probability: -25.9) TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC|AATTCTCCAAGAGAATGGGGTATGAGTCCGTGGAGG|ATcAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC|AATTCTCCAAGAGAATGGGGTATGAGTCCGTGGAGG|ATTAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT Gorilla > Chimp --------------- chr2B:62782782-62782817 Template switch process: F1: L GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCTAT 1 F3: 4 AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC R RF: GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCAATTCTCCAAGAGAATGGGGTATGAGTCCGTGGAGGATCAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC RR: CAATGACTGGTTTTAGTTAGGACCTTTCTACTGACAGTGAGTTAAGAGGTTCTCTTACCCCATACTCAGGCACCTCCTAGTTCATCCATACCATACTCAATTCTACTTGGATATATAAGG F2: 3 TTAAGAGGTTCTCTTACCCCATACTCAGGTACCTCC 2 Unidirectional alignment (log-probability: -72.8) CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCtatcctccatggactcataccccattctcttggagAATT-----------------------------------AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC-----------------------------------AATTCTCCAAGAGAATGGGGTATGAGTCCGTGGAGGATCAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC Template switch alignment (log-probability: -31.4) CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCtAT|CCTCCAtGGACTCATACCCCATTCTCTTGGAGAATT|AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC CTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCAAT|CCTCCACGGACTCATACCCCATTCTCTTGGAGAATT|AAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC Chimp > Gorilla --------------- chr2B:62769990-62770025 Template switch process: F1: L GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC 1 F3: 4 ATCAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC R RF: GTTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCTATCCTCCATGGACTCATACCCCATTCTCTTGGAGAATTAAGTAGGTATGGTATGAGTTAAGATGAACCTATATATTCC RR: CAATGACTGGTTTTAGTTAGGACCTTTCTACTGACAGTGAGATAGGAGGTACCTGAGTATGGGGTAAGAGAACCTCTTAATTCATCCATACCATACTCAATTCTACTTGGATATATAAGG F2: 3 GGAGGTGCCTGAGTATGGGGTAAGAGAACCTCTTAA 2 Unidirectional alignment (log-probability: -72.8) TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC-----------------------------------AATTctccaagagaatggggtatgagtccgtggaggatcAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTCTATCCTCCATGGACTCATACCCCATTCTCTTGGAGAATT-----------------------------------AAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT Template switch alignment (log-probability: -31.4) TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC|AATTCTCCAAGAGAATGGGGTATGAGTCCgTGGAGG|ATcAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT TTACTGACCAAAATCAATCCTGGAAAGATGACTGTCACTC|AATTCTCCAAGAGAATGGGGTATGAGTCCATGGAGG|ATTAAGTAGGTATGGTATGAGTTAAGATGAACCTATATAT ========== Event 1947 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCAGAAAATTGCTCCAAATGATTTGATGGTTTACACCCATCAAATCTGCTGAACTTTTATTTCCACCT Chimp: CTCAGAAAATTGCTCCAAATGATTTGATGGTTTACACCCATCAAATCACCTGAACTTTTATTTCCACCT Gorilla: CTCAGAAAATTGCTCCAAATGATTTGATGGGTGTAAACCATCAAATCACCTGAACTTTTATTTCCACCT ↑ 3 1 2 4 Human: CTCAGAAAATTGCTCCAAATGATTTGATGGTTTACACCCATCAAATCTGCTGAACTTTTATTTCCACCT Cluster: [ ] Orangutan: CTCAGAAAACTGCTCCAAATGAATTGATGGTTTACACCCATCAAATCACCTGAACCTTTATTTCCACTT Human > Gorilla --------------- chr2B:72500012-72500029 Template switch process: F1: L ACTTACCACAGCTCAGAAAATTGCTCCAAATGATTTGATGG 1 F3: 4 CCTGAACTTTTATTTCCACCTCTCACTCA R RF: ACTTACCACAGCTCAGAAAATTGCTCCAAATGATTTGATGGTTTACACCCATCAAATCTGCTGAACTTTTATTTCCACCTCTCACTCA RR: TGAATGGTGTCGAGTCTTTTAACGAGGTTTACTAAACTACCAAATGTGGGTAGTTTAGACGACTTGAAAATAAAGGTGGAGAGTGAGT F2: 3 ACTAAACTACCAAATGTG 2 Unidirectional alignment (log-probability: -39.9) CTTACCACAGCTCAGAAAATTGCTCCAAATGATTTGATGGgTgtaAaCCATCAAATCacCTGAACTTTTATTTCCACCTCTCACTCA CTTACCACAGCTCAGAAAATTGCTCCAAATGATTTGATGGTTTACACCCATCAAATCTGCTGAACTTTTATTTCCACCTCTCACTCA Template switch alignment (log-probability: -23.3) CTTACCACAGCTCAGAAAATTGCTCCAAATGATTTGATGG|GTGTAAACCATCAAATCA|cCTGAACTTTTATTTCCACCTCTCACTCA CTTACCACAGCTCAGAAAATTGCTCCAAATGATTTGATGG|GTGTAAACCATCAAATCA|GCTGAACTTTTATTTCCACCTCTCACTCA ========== Event 1948 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAATACTGCTTTTCTTAAATGACTTTTCTTAAAAGTCATTTAATGTTCATCTCTAGAAAGCTG ↑ 3 2 4 1 Chimp: CTAATACTGCTTTTCTTAAATGACTTTGCT-----------TAATGTTCATCTCTAGAAAGCTG Gorilla: CTAATACTGCTTTTCTTAAATGATTTTGCT-----------TAATGTTCATCTCTAGAAAGCTG Human: CTAATACTGCTTTTCTTAAATGACTTTTCTTAAAAGTCATTTAATGTTCATCTCTAGAAAGCTG Cluster: [ ] Orangutan: CTAATACTGCTTTTCTTAAATGACTTTGCT-----------TAATGTTCATCTCTAGAAAGCTG Chimp > Human ------------- chr2:179591503-179591509 Template switch process: F1: L AGGGGTTGGCCTGGCTAATACTGCTTTTCTTAAATGACTTTTCTTAA 1 F3: 4 TTAATGTTCATCTCTAGAAAGCTGTTCTTTGCTGATGAAAT R RF: AGGGGTTGGCCTGGCTAATACTGCTTTTCTTAAATGACTTTGCTTAATGTTCATCTCTAGAAAGCTGTTCTTTGCTGATGAAAT RR: TCCCCAACCGGACCGATTATGACGAAAAGAATTTACTGAAACGAATTACAAGTAGAGATCTTTCGACAAGAAACGACTACTTTA F2: 3 TACTGAA 2 Unidirectional alignment (log-probability: -32.8) GGCCTGGCTAATACTGCTTTTCTTAAATGACTTTtCTtaaaagtcattTAATGTTCATCTCTAGAAAGCTGTTCTTTGCTGATGAAA GGCCTGGCTAATACTGCTTTTCTTAAATGACTTTGCT-----------TAATGTTCATCTCTAGAAAGCTGTTCTTTGCTGATGAAA Template switch alignment (log-probability: -22.3) GGCCTGGCTAATACTGCTTTTCTTAAATGACTTTtCTTAA|AAGTCAT|TTAATGTTCATCTCTAGAAAGCTGTTCTTTGCTGATGAAA GGCCTGGCTAATACTGCTTTTCTTAAATGACTTTGCTTAA|AAGTCAT|TTAATGTTCATCTCTAGAAAGCTGTTCTTTGCTGATGAAA ========== Event 1949 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATCCAGAACTTTCAAACCCTATGAAAACGAACTCAAAAGTTCATTTTCAAAATCTATCCTTTGTATCAT Chimp: ATCCAGAACTTTCAAACCCTATGAAAATGAACTCAAAAGTTCATTTTCAAAATCTATCCTTTGTATCAT Gorilla: ATCCAGAACTTTCAAACCCTAAT----ATCACTCAAAAGTTCATTTTCAAAATCGATCCTTTGTATCAT ↓ 1 4 3 2 Human: ATCCAGAACTTTCAAACCCTATGAAAACGAACTCAAAAGTTCATTTTCAAAATCTATCCTTTGTATCAT Cluster: [ ] Orangutan: ATCCAGAACTTTCAAACCCTAAT----ATCACTCAAACTTTCATTTTCAAAATCTATCCTTTGTTTCAT Gorilla > Human --------------- chr2:179691236-179691244 Template switch process: F1: L GTAATTCTAATAAACTAGTCATCCAGAACTTTCAAACCCTA 1 F3: 4 ACTCAAAAGTTCATTTTCAAAATCTATCCTTTGTATCATT R RF: GTAATTCTAATAAACTAGTCATCCAGAACTTTCAAACCCTAATATCACTCAAAAGTTCATTTTCAAAATCGATCCTTTGTATCATT RR: CATTAAGATTATTTGATCAGTAGGTCTTGAAAGTTTGGGATTATAGTGAGTTTTCAAGTAAAAGTTTTAGCTAGGAAACATAGTAA F2: 3 AGCAAAAGT 2 Unidirectional alignment (log-probability: -37.9) TAATTCTAATAAACTAGTCATCCAGAACTTTCAAACCCTAtgaaaacgA----ACTCAAAAGTTCATTTTCAAAATCtATCCTTTGTATCATT TAATTCTAATAAACTAGTCATCCAGAACTTTCAAACCCTA--------ATATCACTCAAAAGTTCATTTTCAAAATCGATCCTTTGTATCATT Template switch alignment (log-probability: -27.9) TAATTCTAATAAACTAGTCATCCAGAACTTTCAAACCCTA|TGAAAAcGA|ACTCAAAAGTTCATTTTCAAAATCtATCCTTTGTATCATT TAATTCTAATAAACTAGTCATCCAGAACTTTCAAACCCTA|TGAAAATGA|ACTCAAAAGTTCATTTTCAAAATCGATCCTTTGTATCATT ========== Event 1950 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATCCACTATATGCCCAGTT-A-----GTCATATTCAAAAAGGAAAATAATCTACCTAAGTCTTGATTCCAAGGAA Chimp: ATCCACTATATGCCCAGTT-A-----GTCATATTCAAAAAGGAAAATAATCAACCTAAGTCTTGATTCCAAGGAA ↓ 13 24 ↑ 13 24 Gorilla: ATCCACTATATGCCCAGTT-AGGTTGATTATTTTCCTTTTTGAATATG-----ACTAAGTCTTGATTCCAAGGAA Human: ATCCACTATATGCCCAGTT-A-----GTCATATTCAAAAAGGAAAATAATCTACCTAAGTCTTGATTCCAAGGAA Cluster: [ ] Orangutan: ATCCACTATGTGCCCAGTTAAGGTTGATTATTTTCCTTTTTGAATATG-----ACTAAGTCTTGATTCCAAGGAA Gorilla > Chimp --------------- chr2B:62642916-62642942 Template switch process: F1: L GGCTGCAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG 1 F3: 4 CTAAGTCTTGATTCCAAGGAAGGTAGAAAAACTTTAAACA R RF: GGCTGAAAAATCTATTTAAAGATCCACTATATGCCCAGTTAGGTTGATTATTTTCCTTTTTGAATATGACTAAGTCTTGATTCCAAGGAAGGTAAAAAAACTTTAAACA RR: CCGACTTTTTAGATAAATTTCTAGGTGATATACGGGTCAATCCAACTAATAAAAGGAAAAACTTATACTGATTCAGAACTAAGGTTCCTTCCATTTTTTTGAAATTTGT F2: 3 CAACTAATAAAAGGAAAAACTTATACT 2 Unidirectional alignment (log-probability: -71.9) CTGcAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG---------------------------tcatattcaaaaaggaaaataatcaacCTAAGTCTTGATTCCAAGGAAGGTAgAAAAACTTTAAACA CTGAAAAATCTATTTAAAGATCCACTATATGCCCAGTTAGGTTGATTATTTTCCTTTTTGAATATGA---------------------------CTAAGTCTTGATTCCAAGGAAGGTAAAAAAACTTTAAACA Template switch alignment (log-probability: -30.2) CTGcAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG|TCATATTCAAAAAGGAAAATAATCAAC|CTAAGTCTTGATTCCAAGGAAGGTAgAAAAACTTTAAACA CTGAAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG|TCATATTCAAAAAGGAAAATAATCAAC|CTAAGTCTTGATTCCAAGGAAGGTAAAAAAACTTTAAACA Chimp > Gorilla --------------- chr2B:62632787-62632813 Template switch process: F1: L GGCTGAAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG 1 F3: 4 CTAAGTCTTGATTCCAAGGAAGGTAAAAAAACTTTAAACA R RF: GGCTGCAAAATCTATTTAAAGATCCACTATATGCCCAGTTAGTCATATTCAAAAAGGAAAATAATCAACCTAAGTCTTGATTCCAAGGAAGGTAGAAAAACTTTAAACA RR: CCGACGTTTTAGATAAATTTCTAGGTGATATACGGGTCAATCAGTATAAGTTTTTCCTTTTATTAGTTGGATTCAGAACTAAGGTTCCTTCCATCTTTTTGAAATTTGT F2: 3 AGTATAAGTTTTTCCTTTTATTAGTTG 2 Unidirectional alignment (log-probability: -71.9) CTGaAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG---------------------------gttgattattttcctttttgaatatgaCTAAGTCTTGATTCCAAGGAAGGTAaAAAAACTTTAAACA CTGCAAAATCTATTTAAAGATCCACTATATGCCCAGTTAGTCATATTCAAAAAGGAAAATAATCAAC---------------------------CTAAGTCTTGATTCCAAGGAAGGTAGAAAAACTTTAAACA Template switch alignment (log-probability: -30.2) CTGaAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG|GTTGATTATTTTCCTTTTTGAATATGA|CTAAGTCTTGATTCCAAGGAAGGTAaAAAAACTTTAAACA CTGCAAAATCTATTTAAAGATCCACTATATGCCCAGTTAG|GTTGATTATTTTCCTTTTTGAATATGA|CTAAGTCTTGATTCCAAGGAAGGTAGAAAAACTTTAAACA ========== Event 1951 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TCTGTGGTTTATGCTAATAAGAGAAGAGAA--CTGAAATAACAGTTA-------------------TTCTTAA---------TTCTCATTTTGTTAAAATCA ↓ 13 24 ↑ 13 24 Chimp: TCTGTGGTTTATGCTAATAAG----AATAA--CTGTTATTTCAGTTC-----------------TC-------TTCTCTTAATTCTCATTTTGTCAAAATCA Gorilla: TCTGTGGTTTATGCTAATAAG----AATAA--CAGTTATTTCAGTTC------TCTTCTCTTAA------------------TTCTCATTTTGTCAAAATCA ↓ 13 24 ↑ 13 24 Human: TCTGTGGTTTATGCTAATAAGAGAAGAGAA--CTGAAATAACAGTTA-------------------TTCTTAA---------TTCTCATTTTGTTAAAATCA Cluster: [ ] Orangutan: TCTGTGGTTTATGCCAATAAG----AATAACTCTGTTATTTCAGTTCTCTTAA-----------------------------TTCTCATTTTGTCAAAATCA Chimp > Human ------------- chr2:180176805-180176828 Template switch process: F1: L ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA 1 F3: 4 TCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTTTTTTCT R RF: ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGAATAACTGTTATTTCAGTTCTCTTCTCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTTTTTTCT RR: TAATTAACCGAAACACACCGAGACACCAAATACGATTATTCTTATTGACAATAAAGTCAAGAGAAGAGAATTAAGAGTAAAACAGTTTTAGTCCCAACCATTTAAAAAAAGA F2: 3 TATTGACAATAAAGTCAAGAGAAG 2 Unidirectional alignment (log-probability: -52.6) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGagaagagaactgaAATAACaGTTAT-------------TCTTAATTCTCATTTTGTtAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAG-------------AATAACTGTTATTTCAGTTCTCTTCTCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTT Template switch alignment (log-probability: -24.4) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|GAAGAGAACTGAAATAACAGTTAT|TCTTAATTCTCATTTTGTtAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|GAAGAGAACTGAAATAACAGTTAT|TCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTT Human > Chimp ------------- chr2B:70547630-70547653 Template switch process: F1: L ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA 1 F3: 4 TCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTTTTTTCT R RF: ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGAGAAGAGAACTGAAATAACAGTTATTCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTTTTTTCT RR: TAATTAACCGAAACACACCGAGACACCAAATACGATTATTCTCTTCTCTTGACTTTATTGTCAATAAGAATTAAGAGTAAAACAATTTTAGTCCCAACCATTTAAAAAAAGA F2: 3 CTTCTCTTGACTTTATTGTCAATA 2 Unidirectional alignment (log-probability: -52.6) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAG-------------AATAACtGTTATTtcagttctcttctCTTAATTCTCATTTTGTcAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGAGAAGAGAACTGAAATAACAGTTATT-------------CTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTT Template switch alignment (log-probability: -24.4) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|ATAACTGTTATTTCAGTTCTCTTC|TCTTAATTCTCATTTTGTcAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|ATAACTGTTATTTCAGTTCTCTTC|TCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTT Gorilla > Human --------------- chr2:180176805-180176828 Template switch process: F1: L ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA 1 F3: 4 TCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTTTTTTCT R RF: ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGAATAACAGTTATTTCAGTTCTCTTCTCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTTTTTTCT RR: TAATTAACCGAAACACACCGAGACACCAAATACGATTATTCTTATTGTCAATAAAGTCAAGAGAAGAGAATTAAGAGTAAAACAGTTTTAGTCCCAACCATTTAAAAAAAGA F2: 3 TATTGACAATAAAGTCAAGAGAAG 2 Unidirectional alignment (log-probability: -45.8) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGagaagagaactgaAATAACAGTTAT-------------TCTTAATTCTCATTTTGTtAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAG-------------AATAACAGTTATTTCAGTTCTCTTCTCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTT Template switch alignment (log-probability: -30) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|GAAGAGAACTGAAATAACaGTTAT|TCTTAATTCTCATTTTGTtAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|GAAGAGAACTGAAATAACTGTTAT|TCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTT Human > Gorilla --------------- chr2B:72790116-72790139 Template switch process: F1: L ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA 1 F3: 4 TCTTAATTCTCATTTTGTCAAAATCAGGGTTGGTAAATTTTTTTCT R RF: ATTAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGAGAAGAGAACTGAAATAACAGTTATTCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTTTTTTCT RR: TAATTAACCGAAACACACCGAGACACCAAATACGATTATTCTCTTCTCTTGACTTTATTGTCAATAAGAATTAAGAGTAAAACAATTTTAGTCCCAACCATTTAAAAAAAGA F2: 3 CTTCTCTTGACTTTATTGACAATA 2 Unidirectional alignment (log-probability: -45.8) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAG-------------AATAACAGTTATttcagttctcttcTCTTAATTCTCATTTTGTcAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGAGAAGAGAACTGAAATAACAGTTAT-------------TCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTT Template switch alignment (log-probability: -30) TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|ATAACaGTTATTTCAGTTCTCTTC|TCTTAATTCTCATTTTGTcAAAATCAGGGTTGGTAAATTT TAATTGGCTTTGTGTGGCTCTGTGGTTTATGCTAATAAGA|ATAACTGTTATTTCAGTTCTCTTC|TCTTAATTCTCATTTTGTTAAAATCAGGGTTGGTAAATTT ========== Event 1952 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: agggacactactaatgcACAAAGTAG-------------ACAATTGGAGCCACCAATTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACTGGTATTCCAGG Chimp: agggacactactaatgcacaaagtag-------------acaattggaaccacCAATTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACTGGTATTCCAGG Gorilla: agggacactactaatgcACAA-ATGC--------------------------ACAATTCAGAGGAACCCTCCAACCCCCGTGCAGCTGAAACTGGTATTCCAGG ↑ 1 4 3 2 Human: agggacactactaatgcACAAAGTAG-------------ACAATTGGAGCCACCAATTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACTGGTATTCCAGG Cluster: [ ] Orangutan: agggacactactaatgcACAAACTAGACAATTGGAACCA-------------CCAGTTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACTGGTATTCCAGG Human > Gorilla --------------- chr2B:73292300-73292303 Template switch process: F1: L GTATTTCTAATAAACTGCTAAGGGACACTACTAATGCACAAA 1 F3: 4 CAATTCAGAGGAACCCTCCAACCCCCGTGCAGCTGAAACT R RF: GTATTTCTAATAAACTGCTAAGGGACACTACTAATGCACAAAGTAGACAATTGGAGCCACCAATTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACT RR: CATAAAGATTATTTGACGATTCCCTGTGATGATTACGTGTTTCATCTGTTAACCTCGGTGGTTAAGTCTCATTGGGAGGTTGGGGTCACGTCGACTTTGA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -38) ATTTCTAATAAACTGCTAAGGGACACTACTAATGCACAAA---------TGcA-----CAATTCAGAGgAACCCTCCAACCCCcGTGCAGCTGAAACT ATTTCTAATAAACTGCTAAGGGACACTACTAATGCACAAAGTAGACAATTGGAGCCACCAATTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACT Template switch alignment (log-probability: -27.3) ATTTCTAATAAACTGCTAAGGGACACTACTAATGCACAAA|TGCA|CAATTCAGAGgAACCCTCCAACCCCcGTGCAGCTGAAACT ATTTCTAATAAACTGCTAAGGGACACTACTAATGCACAAA|TGCA|CAATTCAGAGTAACCCTCCAACCCCAGTGCAGCTGAAACT ========== Event 1953 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCTTCATGTCATCATTTGATACTATTTGCCCATTAAATATGGGCAAATAGTATTTGTACTATTACGTAGACCCA Chimp: TGCTTCATGTCATCATTTGATACTATTTGCCCATATTTAATGGGCAAATAGTATTTGTACTATTATGTAGACCCA ↑ 3 1 2 4 Gorilla: TGCTTCATGTCATCATTTGATACTATTTGCCCATTAAATATGGGCAAATAGTACTTGTACTATTATGTAGACCCA Human: TGCTTCATGTCATCATTTGATACTATTTGCCCATTAAATATGGGCAAATAGTATTTGTACTATTACGTAGACCCA Cluster: [ ] Orangutan: TGCTTTATGCCATCATTTGATACTATTTGCCCATTACATATGGGCAAATAGTATTTGTACTATTATGTAGACCCA Gorilla > Chimp --------------- chr2B:71069279-71069298 Template switch process: F1: L TTTAAACTGCTTCATGTCATCATTTGATACTATTTGCCCAT 1 F3: 4 TTGTACTATTATGTAGACCCAGAAA R RF: TTTAAACTGCTTCATGTCATCATTTGATACTATTTGCCCATTAAATATGGGCAAATAGTACTTGTACTATTATGTAGACCCAGAAA RR: AAATTTGACGAAGTACAGTAGTAAACTATGATAAACGGGTAATTTATACCCGTTTATCATGAACATGATAATACATCTGGGTCTTT F2: 3 TATGATAAACGGGTAATTTA 2 Unidirectional alignment (log-probability: -30.6) TTAAACTGCTTCATGTCATCATTTGATACTATTTGCCCAT---ATttaATGGGCAAATAGTAtTTGTACTATTATGTAGACCCAGAAA TTAAACTGCTTCATGTCATCATTTGATACTATTTGCCCATTAAAT---ATGGGCAAATAGTACTTGTACTATTATGTAGACCCAGAAA Template switch alignment (log-probability: -17.9) TTAAACTGCTTCATGTCATCATTTGATACTATTTGCCCAT|ATTTAATGGGCAAATAGTAT|TTGTACTATTATGTAGACCCAGAAA TTAAACTGCTTCATGTCATCATTTGATACTATTTGCCCAT|ATTTAATGGGCAAATAGTAT|TTGTACTATTATGTAGACCCAGAAA ========== Event 1954 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gccacactgtcttccacaatggctgaactaatttacactcccaccaacagtgtaaaagcgttcctatttctccacatcctctccagcatctgttgtttcctgactAAACAGTTCTTCTGAAGCAGCCAAAAAGAAAATACATAACTGAT Chimp: gccacactgtcttccacaatggctgaactaatttacactcccaccaacggtgtaaaagcgttcctatttctccacatcctctccagcatctgttgtttcctgactAAACAGTTCTTCTGAACCAGCTGAAAAGAAAATACATAACTGAT ↓ 3 2 1 4 Gorilla: gccacactgtcttccacaatggctgaactaatttacactcccaccaacagtgtaaaagtgttcctatttctccacatcctctccagcatctgttgtttcctgactAAACAGTTCTTCTG-ATCAGCCAAAAAGAAAATACATAACTGAT Human: gccacactgtcttccacaatggctgaactaatttacactcccaccaacagtgtaaaagcgttcctatttctccacatcctctccagcatctgttgtttcctgactAAACAGTTCTTCTGAAGCAGCCAAAAAGAAAATACATAACTGAT Cluster: [ ] Orangutan: accacactgtcttccacaatggttgaactaatttacactcccaccaacaatgtaaaagcgttcctatttctccacgtcctctccagcatctgttgtttcctgactAAACAGTTCTTCTGAATCAGCCAAAAAGAAAATACATAACTGAT Chimp > Gorilla --------------- chr2B:61495974-61495980 Template switch process: F1: L CTCTCCAGCATCTGTTGTTTCCTGACTAAACAGTTCTTCTGA 1 F3: 4 AAAAGAAAATACATAACTGATTCAAATTTTTGCTTTGTTT R RF: TGGCTGAACTAATTTACACTCCCACCAACGGTGTAAAAGCGTTCCTATTTCTCCACATCCTCTCCAGCATCTGTTGTTTCCTGACTAAACAGTTCTTCTGAACCAGCTGAAAAGAAAATACATAACTGATTCAAATTTTTGCTTTGTTT RR: ACCGACTTGATTAAATGTGAGGGTGGTTGCCACATTTTCGCAAGGATAAAGAGGTGTAGGAGAGGTCGTAGACAACAAAGGACTGATTTGTCAAGAAGACTTGGTCGACTTTTCTTTTATGTATTGACTAAGTTTAAAAACGAAACAAA F2: 3 ACCGACT 2 Unidirectional alignment (log-probability: -27.6) CTCCAGCATCTGTTGTTTCCTGACTAAACAGTTCTTCTGAt-CAGCcaAAAAGAAAATACATAACTGATTCAAATTTTTGCTTTGTTT CTCCAGCATCTGTTGTTTCCTGACTAAACAGTTCTTCTGAACCAGCTGAAAAGAAAATACATAACTGATTCAAATTTTTGCTTTGTTT Template switch alignment (log-probability: -16.6) CTCCAGCATCTGTTGTTTCCTGACTAAACAGTTCTTCTGA|TCAGCCA|AAAAGAAAATACATAACTGATTCAAATTTTTGCTTTGTTT CTCCAGCATCTGTTGTTTCCTGACTAAACAGTTCTTCTGA|TCAGCCA|AAAAGAAAATACATAACTGATTCAAATTTTTGCTTTGTTT ========== Event 1955 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ccctcttctttgTTTTACCAGCAAGGTCCCT-GACCTTGCTGATTTTATTCTTTTCCAAGGA ↑ 3 2 1 4 Chimp: ccctcttctttgTTTTACCAGCAAGGTCCCTATAGGAAGCAGATTTTATTCTTTTCCAAGGA ↓ 3 2 1 4 Gorilla: ccctcttctttgTTTTACCAGCAAGGTCCCT-GACCTTGCTGATTTTATTCTTTTCCAAGGA Human: ccctcttctttgTTTTACCAGCAAGGTCCCT-GACCTTGCTGATTTTATTCTTTTCCAAGGA Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:58555964-58555972 Template switch process: F1: L GCCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT 1 F3: 4 GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC R RF: GCCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCTATAGGAAGCAGATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC RR: CGGGTGGAGGGGGAGAAGAAACAAAATGGTCGTTCCAGGGATATCCTTCGTCTAAAATAAGAAAAGGTTCCTACCCGTGACAATCGTACTG F2: 3 TCGTTCCAG 2 Unidirectional alignment (log-probability: -34.6) CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCctgaccttgCT----------GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCC---------CTATAGGAAGCAGATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC Template switch alignment (log-probability: -16.4) CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT|GACCTTGCT|GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT|GACCTTGCT|GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC Chimp > Gorilla --------------- chr2B:59151246-59151254 Template switch process: F1: L GCCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT 1 F3: 4 GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC R RF: GCCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCTATAGGAAGCAGATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC RR: CGGGTGGAGGGGGAGAAGAAACAAAATGGTCGTTCCAGGGATATCCTTCGTCTAAAATAAGAAAAGGTTCCTACCCGTGACAATCGTACTG F2: 3 TCGTTCCAG 2 Unidirectional alignment (log-probability: -34.1) CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT----------gaccttgctGATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCTATAGGAAGCA---------GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC Template switch alignment (log-probability: -16.9) CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT|GACCTTGCT|GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC CCCACCTCCCCCTCTTCTTTGTTTTACCAGCAAGGTCCCT|GACCTTGCT|GATTTTATTCTTTTCCAAGGATGGGCACTGTTAGCATGAC ========== Event 1956 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAG Chimp: GATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTATCACCCCAAGGAAAAG ↓ 1 4 3 2 Gorilla: GATTTCAGGATTTATTTGAAGGGTA-CCTGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAG ↑ 1 4 3 2 Human: GATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAG Cluster: [ ] Orangutan: GATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTGTGCAGGTACCCTTACCACCCCAAGGAAAAG Human > Gorilla --------------- chr2B:60320314-60320319 Template switch process: F1: L AATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAG 1 F3: 4 TGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG R RF: AATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG RR: TTACTCTATGACTTTCCCTCCTAAAGTCCTAAATAAACTTCACTCGAGACAGTCATACGTCCATGGGAATGGTGGGGTTCCTTTTCC F2: 3 CCATGG 2 Unidirectional alignment (log-probability: -27.6) ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAGgGtaC-CTGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG Template switch alignment (log-probability: -16.5) ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAG|GGTACC|TGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAG|GGTACC|TGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG Chimp > Gorilla --------------- chr2B:60320314-60320319 Template switch process: F1: L AATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAG 1 F3: 4 TGTCAGTATGCAGGTACCCTTACCACCCCAAGGAAAAGG R RF: AATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTATCACCCCAAGGAAAAGG RR: TTACTCTATGACTTTCCCTCCTAAAGTCCTAAATAAACTTCACTCGAGACAGTCATACGTCCATGGGAATAGTGGGGTTCCTTTTCC F2: 3 CCATGG 2 Unidirectional alignment (log-probability: -33.1) ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAGgGtaC-CTGTCAGTATGCAGGTACCCTTAcCACCCCAAGGAAAAGG ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAGTGAGCTCTGTCAGTATGCAGGTACCCTTATCACCCCAAGGAAAAGG Template switch alignment (log-probability: -22) ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAG|GGTACC|TGTCAGTATGCAGGTACCCTTAcCACCCCAAGGAAAAGG ATGAGATACTGAAAGGGAGGATTTCAGGATTTATTTGAAG|GGTACC|TGTCAGTATGCAGGTACCCTTATCACCCCAAGGAAAAGG ========== Event 1957 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCATAACTAGGGCTGAGCATA-----------------------GGCTAGGTTCAGTAGTAGCAAAATAATGGACA ↓ 4 3 2 1 Chimp: GCATAACTAGGGCTGAGCATATGCTAGGTTCAGGAACCTAGCTAGGCTAGGTTCAGTAGTAGCAAAATAATGGACA ↑ 4 3 2 1 Gorilla: GCATAACTAGGGCTGAGCATA-----------------------GGCTAGGTTCAGTAGTAGCAAAATAATGGACA Human: GCATAACTAGGGCTGAGCATA-----------------------GGCTAGGTTCAGTAGTAGCAAAATAATGGACA Cluster: [ ] Orangutan: GCAAAACTAGGGCTGAGCATA-----------------------TGCTAGGTTCAGTAGCAGCAAAATAATGGACA Human > Chimp ------------- chr2B:74512616-74512624 Template switch process: F1: L GCAGAGGTCTGAGGGTGATAGCATAACTAGGGCTGAGCATATGCTAGGTTCAG 1 F3: 4 TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTTTG R RF: GCAGAGGTCTGAGGGTGATAGCATAACTAGGGCTGAGCATAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTTTG RR: CGTCTCCAGACTCCCACTATCGTATTGATCCCGACTCGTATCCGATCCAAGTCATCATCGTTTTATTACCTGTACCAAAAC F2: 3 CGATCCAAG 2 Unidirectional alignment (log-probability: -44) GGTGATAGCATAACTAGGGCTGAGCATatgctaggttcaggaacctagctAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT GGTGATAGCATAACTAGGGCTGAGCAT-----------------------AGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT Template switch alignment (log-probability: -22.7) GGTGATAGCATAACTAGGGCTGAGCATAtGCTAGGTTCAG|GAACCTAGC|TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT GGTGATAGCATAACTAGGGCTGAGCATAGGCTAGGTTCAG|GAACCTAGC|TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT Gorilla > Chimp --------------- chr2B:74512616-74512624 Template switch process: F1: L GCAGAGGTCTGAGGGTGATAGCATAACTAGGGCTGAGCATATGCTAGGTTCAG 1 F3: 4 TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTTTG R RF: GCAGAGGTCTGAGGGTGATAGCATAACTAGGGCTGAGCATAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTTTG RR: CGTCTCCAGACTCCCACTATCGTATTGATCCCGACTCGTATCCGATCCAAGTCATCATCGTTTTATTACCTGTACCAAAAC F2: 3 CGATCCAAG 2 Unidirectional alignment (log-probability: -44) GGTGATAGCATAACTAGGGCTGAGCAtatgctaggttcaggaacctagcTAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT GGTGATAGCATAACTAGGGCTGAGCA-----------------------TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT Template switch alignment (log-probability: -22.7) GGTGATAGCATAACTAGGGCTGAGCATAtGCTAGGTTCAG|GAACCTAGC|TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT GGTGATAGCATAACTAGGGCTGAGCATAGGCTAGGTTCAG|GAACCTAGC|TAGGCTAGGTTCAGTAGTAGCAAAATAATGGACATGGTTT ========== Event 1958 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: agtaatgacaTGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACT Chimp: AGTAATGACATGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACT ↓ 13 24 ↑ 13 24 Gorilla: AGTAATGACATGAAGATCTAGCATTAGAAGATTTAATACTAGATCTTCATGTCATTACT ↓ 13 24 ↑ 13 24 Human: agtaatgacaTGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACT Cluster: [ ] Orangutan: AGTAATGTCATGAAAATCTAGCATTAAATCTTCTAATGCTAGATCTTCATGTCATTACT Gorilla > Human --------------- chr2:57036274-57036290 Template switch process: F1: L CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG 1 F3: 4 CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT R RF: CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGCATTAGAAGATTTAATACTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT RR: GTGATAGTTCGATCTTTTATTCATTACTGTACTTCTAGATCGTAATCTTCTAAATTATGATCTAGAAGTACAGTAATGAATAAAGGATCGAACAGTTA F2: 3 GTAATCTTCTAAATTAT 2 Unidirectional alignment (log-probability: -40) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGtATTAaAtctTcTAATgCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGCATTAGAAGATTTAATACTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Template switch alignment (log-probability: -17.9) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|TATTAAATCTTCTAATG|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|TATTAAATCTTCTAATG|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Human > Gorilla --------------- chr2B:57572760-57572776 Template switch process: F1: L CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG 1 F3: 4 CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT R RF: CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT RR: GTGATAGTTCGATCTTTTATTCATTACTGTACTTCTAGATCATAATTTAGAAGATTACGATCTAGAAGTACAGTAATGAATAAAGGATCGAACAGTTA F2: 3 ATAATTTAGAAGATTAC 2 Unidirectional alignment (log-probability: -40) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGcATTAgAagaTtTAATaCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Template switch alignment (log-probability: -17.9) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|CATTAGAAGATTTAATA|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|CATTAGAAGATTTAATA|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Gorilla > Chimp --------------- chr2B:57597072-57597088 Template switch process: F1: L CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG 1 F3: 4 CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT R RF: CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGCATTAGAAGATTTAATACTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT RR: GTGATAGTTCGATCTTTTATTCATTACTGTACTTCTAGATCGTAATCTTCTAAATTATGATCTAGAAGTACAGTAATGAATAAAGGATCGAACAGTTA F2: 3 GTAATCTTCTAAATTAT 2 Unidirectional alignment (log-probability: -40) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGtATTAaAtctTcTAATgCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGCATTAGAAGATTTAATACTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Template switch alignment (log-probability: -17.9) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|TATTAAATCTTCTAATG|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|TATTAAATCTTCTAATG|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Chimp > Gorilla --------------- chr2B:57572760-57572776 Template switch process: F1: L CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG 1 F3: 4 CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT R RF: CACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT RR: GTGATAGTTCGATCTTTTATTCATTACTGTACTTCTAGATCATAATTTAGAAGATTACGATCTAGAAGTACAGTAATGAATAAAGGATCGAACAGTTA F2: 3 ATAATTTAGAAGATTAC 2 Unidirectional alignment (log-probability: -40) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGcATTAgAagaTtTAATaCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAGTATTAAATCTTCTAATGCTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT Template switch alignment (log-probability: -17.9) ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|CATTAGAAGATTTAATA|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ACTATCAAGCTAGAAAATAAGTAATGACATGAAGATCTAG|CATTAGAAGATTTAATA|CTAGATCTTCATGTCATTACTTATTTCCTAGCTTGTCAAT ========== Event 1959 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAATTTCTTTTGTACATCCGGGGATCTCTTCTAATAACT----AGTGGAAAGGAATTAGGGACTTCA Chimp: CAATTTCTTTTGTACATCCGGGGATCTCTTCTAATAACT----AGTGGAAGGGAATTAGGGACTTCA Gorilla: CAATTTCTTTTGTATATCCGGGGATCTCTTATTGGAAGAGATCCCCGGAAAGGAATTAGGGACTTCA ↑ 3 1 2 4 Human: CAATTTCTTTTGTACATCCGGGGATCTCTTCTAATAACT----AGTGGAAAGGAATTAGGGACTTCA Cluster: [ ] Orangutan: CAATTTCTTTTGTATATCCTGGGATCTCTTCTAATAACT----AGTGGAAAGGAATTAGGGACTTCA Human > Gorilla --------------- chr2B:56344054-56344069 Template switch process: F1: L TTTGGGGATTACAATTTCTTTTGTATATCCGGGGATCTCTT 1 F3: 4 GGAAAGGAATTAGGGACTTCAACATTGTTGATTTATGTGT R RF: TTTGGGGATTACAATTTCTTTTGTACATCCGGGGATCTCTTCTAATAACTAGTGGAAAGGAATTAGGGACTTCAACATTGTTGATTTATGTGT RR: AAACCCCTAATGTTAAAGAAAACATGTAGGCCCCTAGAGAAGATTATTGATCACCTTTCCTTAATCCCTGAAGTTGTAACAACTAAATACACA F2: 3 CCCCTAGAGAAGGTTA 2 Unidirectional alignment (log-probability: -48.3) TTGGGGATTACAATTTCTTTTGTAtATCCGGGGATCTCTTattggaagagatcccC-----------GGAAAGGAATTAGGGACTTCAACATTGTTGATTTATGTGT TTGGGGATTACAATTTCTTTTGTACATCCGGGGATCTCTT---------------CTAATAACTAGTGGAAAGGAATTAGGGACTTCAACATTGTTGATTTATGTGT Template switch alignment (log-probability: -28.8) TTGGGGATTACAATTTCTTTTGTAtATCCGGGGATCTCTT|ATTgGAAGAGATCCCC|GGAAAGGAATTAGGGACTTCAACATTGTTGATTTATGTGT TTGGGGATTACAATTTCTTTTGTACATCCGGGGATCTCTT|ATTAGAAGAGATCCCC|GGAAAGGAATTAGGGACTTCAACATTGTTGATTTATGTGT ========== Event 1960 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATCTCCGAGGGGTCAAAAA---TAACAATTTTTTAAAAAGTTGTCTCGTT-GGTACGTAATATCCTAGA Chimp: AAATCTCCGAGGGGTCAAAAAATGAGACAA------CCAAAGTTGTCTCATT-GGTACCTAATATCCTAGA ↑ 1 4 3 2 Gorilla: AAATCTCCGAGGGGTCAAAAA---TAACAATTTTTTGAAAAGTTGTCTCATT-GGTACCTAATATCCTAGA Human: AAATCTCCGAGGGGTCAAAAA---TAACAATTTTTTAAAAAGTTGTCTCGTT-GGTACGTAATATCCTAGA Cluster: [ ] Orangutan: AAATCTCCGAGGGGTCAAAAA---TAACAATTTTTTAAAAAGTTGTCTCATTGGGTACCTAATATCCTATA Gorilla > Chimp --------------- chr2B:77444703-77444712 Template switch process: F1: L TGAGCTGTTGGAAAACTGACAAATCTCCGAGGGGTCAAAAA 1 F3: 4 CAAAGTTGTCTCATTGGTACCTAATATCCTAGAGCCTGAAT R RF: TGAGCTGTTGGAAAACTGACAAATCTCCGAGGGGTCAAAAATAACAATTTTTTGAAAAGTTGTCTCATTGGTACCTAATATCCTAGAGCCTGAAT RR: ACTCGACAACCTTTTGACTGTTTAGAGGCTCCCCAGTTTTTATTGTTAAAAAACTTTTCAACAGAGTAACCATGGATTATAGGATCTCGGACTTA F2: 3 CAACAGAGTA 2 Unidirectional alignment (log-probability: -35.7) GAGCTGTTGGAAAACTGACAAATCTCCGAGGGGTCAAAAA-------------AtgagacaaccAAAGTTGTCTCATTGGTACCTAATATCCTAGAGCCTGAA GAGCTGTTGGAAAACTGACAAATCTCCGAGGGGTCAAAAATAACAATTTTTTGA----------AAAGTTGTCTCATTGGTACCTAATATCCTAGAGCCTGAA Template switch alignment (log-probability: -22.5) GAGCTGTTGGAAAACTGACAAATCTCCGAGGGGTCAAAAA|ATGAGACAAC|cAAAGTTGTCTCATTGGTACCTAATATCCTAGAGCCTGAA GAGCTGTTGGAAAACTGACAAATCTCCGAGGGGTCAAAAA|ATGAGACAAC|AAAAGTTGTCTCATTGGTACCTAATATCCTAGAGCCTGAA ========== Event 1961 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGATAAATATACTGACAGACAAATGCA----------------------------------------------TACATACATAGATTGATCACATGGTTGGTG ↓ 3 4 2 1 Chimp: AGATAAATATACTGACAGACAAATGCA-----------------------TACATACATATATGCATCTGACATACATACATAGATTGATCACATGGTTGGTG Gorilla: AGataaatatactgacagacaaatgcatacatacatatatgcatctgaca-----------------------tacatatataGATTGATCACATGGTTGGTG Human: AGATAAATATACTGACAGACAAATGCA----------------------------------------------TACATACATAGATTGATCACATGGTTGGTG Cluster: [ ] Orangutan: AGATAAATATACTGACAGACAAATGCATACATACATATATGCATCTGACA-----------------------TACATACATAGATTGATCACATGGTTGGTG Human > Chimp ------------- chr2B:54933520-54933529 Template switch process: F1: L TGAATTTTGAAGAAAGATAAATATACTGACAGACAAATGCATACATACATA 1 F3: 4 ACATACATACATAGATTGATCACATGGTTGGTGGAGAATGCAA R RF: TGAATTTTGAAGAAAGATAAATATACTGACAGACAAATGCATACATACATAGATTGATCACATGGTTGGTGGAGAATGCAA RR: ACTTAAAACTTCTTTCTATTTATATGACTGTCTGTTTACGTATGTATGTATCTAACTAGTGTACCAACCACCTCTTACGTT F2: 3 GTCTACGTAT 2 Unidirectional alignment (log-probability: -44) GAAAGATAAATATACTGACAGACAAATGCATACATACATatatgcatctgacatacatacatAGATTGATCACATGGTTGGTGGAGAATG GAAAGATAAATATACTGACAGACAAATGCATACATACAT-----------------------AGATTGATCACATGGTTGGTGGAGAATG Template switch alignment (log-probability: -28.8) GAAAGATAAATATACTGACAGACAAATGCATACATACATA|TATGCATcTG|aCATACATACATAGATTGATCACATGGTTGGTGGAGAATG GAAAGATAAATATACTGACAGACAAATGCATACATACATA|TATGCATTTG|GCATACATACATAGATTGATCACATGGTTGGTGGAGAATG ========== Event 1962 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AACTGCTTCTGAAATATGTCAATGTTAAGTCATTGAATCTCATTCCTTTCATTTTGTAGGTTTGTAACTTTACCAACTTCAATAAATTTTATATTCTTTTATAGACATGATCACATAACCACAGAGAG Chimp: AACTGCTTCTGAAATATGTCAATGT---------CTATCTCATTCCTTTCATTTTGTAGGTTTGTAACTTTACCAACTTCAATAAATTTTATATTCTTTTATAGACATGATCACATAACCACAGAGAG ↑ 1 4 3 2 Gorilla: AACTGCTTCTGAAATATGTCAGTGTTAAGTCATTGAATCTCATTCCTTTAATTTTGTAGGTTTGTAACTTTACCAACTTCAATAAATTTTATATTCTTTTATAGACATGATCACATAACCACAGAGAG Human: AACTGCTTCTGAAATATGTCAATGTTAAGTCATTGAATCTCATTCCTTTCATTTTGTAGGTTTGTAACTTTACCAACTTCAATAAATTTTATATTCTTTTATAGACATGATCACATAACCACAGAGAG Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr2B:53927959-53927965 Template switch process: F1: L TTCCATTTTCATTGGTTGGAAACTGCTTCTGAAATATGTCA 1 F3: 4 TCTCATTCCTTTCATTTTGTAGGTTTGTAACTTTACCAA R RF: TTCCATTTTCATTGGTTGGAAACTGCTTCTGAAATATGTCAGTGTTAAGTCATTGAATCTCATTCCTTTAATTTTGTAGGTTTGTAACTTTACCAACTTCAATAAATTTTATATTCTTTTATAGACAT RR: AAGGTAAAAGTAACCAACCTTTGACGAAGACTTTATACAGTCACAATTCAGTAACTTAGAGTAAGGAAATTAAAACATCCAAACATTGAAATGGTTGAAGTTATTTAAAATATAAGAAAATATCTGTA F2: 3 ATCTGTA 2 Unidirectional alignment (log-probability: -33.5) TCCATTTTCATTGGTTGGAAACTGCTTCTGAAATATGTCAaTG---------TctATCTCATTCCTTTcATTTTGTAGGTTTGTAACTTTACCAA TCCATTTTCATTGGTTGGAAACTGCTTCTGAAATATGTCAGTGTTAAGTCATTGAATCTCATTCCTTTAATTTTGTAGGTTTGTAACTTTACCAA Template switch alignment (log-probability: -22.1) TCCATTTTCATTGGTTGGAAACTGCTTCTGAAATATGTCA|ATGTCTA|TCTCATTCCTTTcATTTTGTAGGTTTGTAACTTTACCAA TCCATTTTCATTGGTTGGAAACTGCTTCTGAAATATGTCA|ATGTCTA|TCTCATTCCTTTAATTTTGTAGGTTTGTAACTTTACCAA ========== Event 1963 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAAATTTATTATGAAAGCACTGATGAGACTAAGTAGATACTAATGTGATCATTTATTAGTTCATTGATTCTAGATCATTAATTTATATCCTTACTCATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGA-------------------ATGTAAGCAGTGAAGATGAATGTAAGAAtaccagtaaatgtttcac Chimp: GAAAATTTATTATGAAAGCACTGATGAGACTAAGTAGATACTAATGTGATCATTTATTAGTTCATTGATTCTAGATCATGAATTTATATCCTTACTCATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGA-------------------ATGTAAGCAGTGAAGATGAATGTAAGAAtaccagtaaatgtttcac ↑ 3 2 4 1 Gorilla: GAAAATTTATTATGAAAGCACTGATGAGACTAAGTAGATACTAATGTGATCATTTATTAGTTCATTGATTCTAGATCATTAATTTATATACTTACTCATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGA--------------------------------------ATGTAAGAAtaccagtaaatgtttcac ↓ 3 2 4 1 Human: GAAAATTTATTATGAAAGCACTGATGAGACTAAGTAGATACTAATGTGATCATTTATTAGTTCATTGATTCTAGATCATTAATTTATATCCTTACTCATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGA-------------------ATGTAAGCAGTGAAGATGAATGTAAGAAtaccagtaaatgtttcac Cluster: [ ] Orangutan: GAAAATTTATTATGAAAGCACTGATGAGACTAAGTAGATACTAATGTAATCATTTATTAGTTCATTGATTCTAGATCATTAATTTATATACTTACTGATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAGCAGTGAAGGTGA-------------------ATGTAAGAAtaccagtaaatgtttcaa Gorilla > Human --------------- chr2:18929970-18929973 Template switch process: F1: L GTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAG 1 F3: 4 GAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTGTTTTTTGG R RF: ACTGATGAGACTAAGTAGATACTAATGTGATCATTTATTAGTTCATTGATTCTAGATCATTAATTTATATACTTACTCATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTGTTTTTTGG RR: TGACTACTCTGATTCATCTATGATTACACTAGTAAATAATCAAGTAACTAAGATCTAGTAATTAAATATATGAATGAGTAAATCAAAAACCATTTGTGATAAAGTCTTGGACACGATCCAAAACTTCTACTTACATTCTTATGGTCATTTACAAAGTGTTAACAAAAAACC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -46.4) TATTTCAGAACCTGTGCTAGGTTTTGAAGATgaatgtaagcagtgaagatGAATGTAAGAATACCAGTAAATGTTTCACAATTG TATTTCAGAACCTGTGCTAGGTTTTGAAGAT-------------------GAATGTAAGAATACCAGTAAATGTTTCACAATTG Template switch alignment (log-probability: -16.6) TATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAG|CAGT|GAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTG TATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAG|CAGT|GAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTG Gorilla > Chimp --------------- chr2A:19257980-19257983 Template switch process: F1: L GTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAG 1 F3: 4 GAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTGTTTTTTGG R RF: ACTGATGAGACTAAGTAGATACTAATGTGATCATTTATTAGTTCATTGATTCTAGATCATTAATTTATATACTTACTCATTTAGTTTTTGGTAAACACTATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTGTTTTTTGG RR: TGACTACTCTGATTCATCTATGATTACACTAGTAAATAATCAAGTAACTAAGATCTAGTAATTAAATATATGAATGAGTAAATCAAAAACCATTTGTGATAAAGTCTTGGACACGATCCAAAACTTCTACTTACATTCTTATGGTCATTTACAAAGTGTTAACAAAAAACC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -46.4) TATTTCAGAACCTGTGCTAGGTTTTGAAGATgaatgtaagcagtgaagatGAATGTAAGAATACCAGTAAATGTTTCACAATTG TATTTCAGAACCTGTGCTAGGTTTTGAAGAT-------------------GAATGTAAGAATACCAGTAAATGTTTCACAATTG Template switch alignment (log-probability: -16.6) TATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAG|CAGT|GAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTG TATTTCAGAACCTGTGCTAGGTTTTGAAGATGAATGTAAG|CAGT|GAAGATGAATGTAAGAATACCAGTAAATGTTTCACAATTG ========== Event 1964 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTAGAATCAGACTCAAAACA---------------TTCTGTGACTATTAATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCATAAAAAGGAAAGCAACTCAGAGAATAAAATTCAGTGGCCATGGTGACCATTAATAGTCATGTTTTAGGTTGGaatttaa Chimp: ATTAGAATCAGACTCAAAACA---------------TTCTGTGACTACTAATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCATAAAAAGGAAAGCAACTCAGAGAATAAAATTCAGTGGCCATGGTGACCATTAATAGTCATGTTTTAGGTTGGAATTTAA Gorilla: ATTAGAGTCAGACTCAAAACA------------------------------TTCTTAATACTGGTCTGAAGACCACAGGATATGAATCATAAAAAGGAAAGCAACTCAGAGAATAAAATTCAGTGGCCATGGTGACCATTAATAGTCATGTTTTAGGTTGGAATTTAA ↓ 4 1 3 2 Human: ATTAGAATCAGACTCAAAACA---------------TTCTGTGACTATTAATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCATAAAAAGGAAAGCAACTCAGAGAATAAAATTCAGTGGCCATGGTGACCATTAATAGTCATGTTTTAGGTTGGaatttaa Cluster: [ ] Orangutan: ATTCGAATCAGACTCAAAACATTCTGTGACTACTAA---------------TTCTTAATACTGGTCTGAAGACCACAGGATAGGAATCATAAAAAGGAAAGCAACTCAGAGAATAAAATTCAGTGGCCATGGTGACCATTAATAGTCATGCTTTAGGTTGGAATTTAA Gorilla > Human --------------- chr2:189408465-189408473 Template switch process: F1: L AAATAGAGTTGCCATACTACATTAGAATCAGACTCAAAACATTCTG 1 F3: 4 ATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCATA R RF: AAATAGAGTTGCCATACTACATTAGAGTCAGACTCAAAACATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCATAAAAAGGAAAGCAACTCAGAGAATAAAATTCAGTGGCCATGGTGACCATTAATAGTCA RR: TTTATCTCAACGGTATGATGTAATCTCAGTCTGAGTTTTGTAAGAATTATGACCAGACTTCTGGTGTCCTATACTTAGTATTTTTCCTTTCGTTGAGTCTCTTATTTTAAGTCACCGGTACCACTGGTAATTATCAGT F2: 3 ATTATCAGT 2 Unidirectional alignment (log-probability: -38) AGTTGCCATACTACATTAGAaTCAGACTCAAAACattctgtgactattaATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCAT AGTTGCCATACTACATTAGAGTCAGACTCAAAAC---------------ATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCAT Template switch alignment (log-probability: -28.1) AGTTGCCATACTACATTAGAaTCAGACTCAAAACATTCTg|TGACTATTA|ATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCAT AGTTGCCATACTACATTAGAGTCAGACTCAAAACATTCTT|TGACTATTA|ATTCTTAATACTGGTCTGAAGACCACAGGATATGAATCAT ========== Event 1965 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGAGGGGTCAGAAAATTCAAGGACTCAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAA ↑ 1 4 3 2 Chimp: CAGAGGGGTCAGAAAATTCAA----ATAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAA Gorilla: CAGAGGGGTCAGAAAATTCAA----ATAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAA ↓ 1 4 3 2 Human: CAGAGGGGTCAGAAAATTCAAGGACTCAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAA Cluster: [ ] Orangutan: CAGAGGGGTCAAAAAATTCAA----ATAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAA Chimp > Human ------------- chr2:19276936-19276941 Template switch process: F1: L CCATTATAAATTGGCAATTTCAGAGGGGTCAGAAAATTCAA 1 F3: 4 AGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG R RF: CCATTATAACTTGGCAATTTCAGAGGGGTCAGAAAATTCAAATAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG RR: GGTAATATTGAACCGTTAAAGTCTCCCCAGTCTTTTAAGTTTATCGGTGAACTCAGGAAGTCATATAAGGAAGGGTTTCCTTC F2: 3 CTCAGG 2 Unidirectional alignment (log-probability: -34.7) CATTATAAaTTGGCAATTTCAGAGGGGTCAGAAAATTCAAggActcaGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG CATTATAACTTGGCAATTTCAGAGGGGTCAGAAAATTCAAATA----GCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG Template switch alignment (log-probability: -22) CATTATAAaTTGGCAATTTCAGAGGGGTCAGAAAATTCAA|GGACTC|AGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG CATTATAACTTGGCAATTTCAGAGGGGTCAGAAAATTCAA|GGACTC|AGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG Gorilla > Human --------------- chr2:19276936-19276941 Template switch process: F1: L CCATTATAAATTGGCAATTTCAGAGGGGTCAGAAAATTCAA 1 F3: 4 AGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG R RF: CCATTATAACTTGGCAATTTCAGAGGGGTCAGAAAATTCAAATAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG RR: GGTAATATTGAACCGTTAAAGTCTCCCCAGTCTTTTAAGTTTATCGGTGAACTCAGGAAGTCATATAAGGAAGGGTTTCCTTC F2: 3 CTCAGG 2 Unidirectional alignment (log-probability: -33.2) CATTATAAaTTGGCAATTTCAGAGGGGTCAGAAAATTCAAggactcAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG CATTATAACTTGGCAATTTCAGAGGGGTCAGAAAATTCAAA----TAGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG Template switch alignment (log-probability: -22) CATTATAAaTTGGCAATTTCAGAGGGGTCAGAAAATTCAA|GGACTC|AGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG CATTATAACTTGGCAATTTCAGAGGGGTCAGAAAATTCAA|GGACTC|AGCCACTTGAGTCCTTCAGTATATTCCTTCCCAAAGGAAG ========== Event 1966 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGTTTAGAAATAGTATCAGA--ATACTCTAGATAGTTCACTTCTACA-----------------------------------------TTTAATAAGTATGAAGCTCATTTCT Chimp: TTGTTTATAAATAGTATCAGA--ATACTCTAGATAGTTCACTTCTACA-----------------------------------------TTTAATAAGTATGAAGCTCATTTCT ↓ 3 2 1 4 Gorilla: TTGTTTATAAATAGTATCAGA----ACTCTAGATAGTTCACTTCTATCTAGagtataagtatgaagtaatacttatgaagtaagtatgaagtaataagtatgaagCTCATTTCT Human: TTGTTTAGAAATAGTATCAGA--ATACTCTAGATAGTTCACTTCTACA-----------------------------------------TTTAATAAGTATGAAGCTCATTTCT Cluster: [ ] Orangutan: TTGTTTATAAATAGTATCAGAAT--ACTCTAGATAGTTCACTTCTACA-----------------------------------------TTTAATAAGTATGAAGCTCATTTCT Chimp > Gorilla --------------- chr2B:82585901-82585908 Template switch process: F1: L ATTTCTAATCTTTAATGGAATTGTTTATAAATAGTATCAGA--ACTCTAGATAGTTCACTTCTA 1 F3: 4 ATAAGTATGAA R RF: ATTTCTAATCTTTAATGGAATTGTTTATAAATAGTATCAGAATACTCTAGATAGTTCACTTCTACATTTAATAAGTATGAA RR: TAAAGATTAGAAATTACCTTAACAAATATTTATCATAGTCTTATGAGATCTATCAAGTGAAGATGTAAATTATTCATACTT F2: 3 TGAGATCT 2 Unidirectional alignment (log-probability: -50.4) GTTTATAAATAGTATCAGA--ACTCTAGATAGTTCACTTCTAtctagagtataagtatgaA GTTTATAAATAGTATCAGAATACTCTAGATAGTTCACTTCTA-----------------CA Template switch alignment (log-probability: -26.4) GTTTATAAATAGTATCAGA--ACTCTAGATAGTTCACTTCTA|TCTAGAGT|ATAAGTATGAA GTTTATAAATAGTATCAGAATACTCTAGATAGTTCACTTCTA|TCTAGAGT|ATAAGTATGAA ========== Event 1967 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTGCCATTAAACAAAAATTAT--------------------------------------------------------------------------------------AATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGtagaccaacctccaatccattttattatc ↓ 3 4 2 1 Chimp: TTTGCCATTAAACAAAAATTATAATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAACATTGTGTGGACCTAAATAAGTAATGATT-ATAATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGtagaccaacctccaatccattttattatc ↑ 3 4 2 1 Gorilla: TTTGCCATTAAACAAAAATTAT--------------------------------------------------------------------------------------AATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGtagaccaacctccaatccattttattatc Human: TTTGCCATTAAACAAAAATTAT--------------------------------------------------------------------------------------AATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGtagaccaacctccaatccattttattatc Cluster: [ ] Orangutan: TTTGCCATTaa-aaaaaaTTAT--------------------------------------------------------------------------------------AAGCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGtagaccaacctccaatccattttattatc Human > Chimp ------------- chr2B:80733152-80733182 Template switch process: F1: L TTTCAGT------TTTTGTTTTGCCATTAAACAAAAATTATAATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC 1 F3: 4 ATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAA R RF: TTTCAGTTTTTAATTTTGTTTTGCCATTAAACAAAAATTATAATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC RR: AAAGTCAAAAATTAAAACAAAACGGTAATTTGTTTTTAATATTAGTAATGAATAAATCCAGGTGTGTTACAACATTGTTTTCCTACGAAATTTTAACATCTGGTTG F2: 3 ATATTAGTAATGAATAAATCCAGGTGTGTTA 2 Unidirectional alignment (log-probability: -141) AATGTTGTAACAAAAGGATGCTTTAAaattgtagaccaacattgtgtggacctaaataagtaatgattataatttaggtccacacaatgttgtaacaaaaggatgctttaa AATGTTGTAACAAAAGGATGCTTTAA------------------------------------------------------------------------------------- Template switch alignment (log-probability: -30.6) AATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC|ATTGTGTGGACCTAAATAAGTAATGATTATA|ATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAA AATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC|ATTGTGTGGACCTAAATAAGTAATGATTATA|ATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAA Gorilla > Chimp --------------- chr2B:80733152-80733182 Template switch process: F1: L TTTCAGT------TTTTGTTTTGCCATTAAACAAAAATTATAATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC 1 F3: 4 ATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAA R RF: TTTCAGTTTTTAATTTTGTTTTGCCATTAAACAAAAATTATAATCATTACTTATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC RR: AAAGTCAAAAATTAAAACAAAACGGTAATTTGTTTTTAATATTAGTAATGAATAAATCCAGGTGTGTTACAACATTGTTTTCCTACGAAATTTTAACATCTGGTTG F2: 3 ATATTAGTAATGAATAAATCCAGGTGTGTTA 2 Unidirectional alignment (log-probability: -140) AATGTTGTAACAAAAGGATGCTTTAAaattgtagaccaacattgtgtggacctaaataagtaatgattataatttaggtccacacaatgttgtaacaaaaggatgctttaa AATGTTGTAACAAAAGGATGCTTTAA------------------------------------------------------------------------------------- Template switch alignment (log-probability: -31) AATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC|ATTGTGTGGACCTAAATAAGTAATGATTATA|ATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAA AATGTTGTAACAAAAGGATGCTTTAAAATTGTAGACCAAC|ATTGTGTGGACCTAAATAAGTAATGATTATA|ATTTAGGTCCACACAATGTTGTAACAAAAGGATGCTTTAA ========== Event 1968 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: atcatttaagattttggattttcagat-tagggatgctcaacctATAGTTTGATTATTTCCCTCATCTCTCCCTTCTCAGCCTTTCCTTATCAATGCTGTTTGGGAATCTGAGGCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTTTCTGAAATGTCCTCCCTGGAATACATTT ↑ 3 2 1 4 Chimp: atcatttaagattttggattttcagat-tagggatgctcaacctATAGTTTGATTATTTCCCTCATCTCTCCCTTCTCAGCCTTTCCTTATCAATGCTGTTTGGGAATCTGAGGCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGT-TCT---CAGTCCTCCCTGGAATACATTT Gorilla: atcatttaagattttggattttcagat-tagggatgctcaacctATAGTTTGATTATTTCCCTCATCTCTCCCTTCTCAGCCTTTCCTTATCAATGCTGTTCGGGAATCTGAGGCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGT-ACT---CAGTCCTCCCTGGAATACATTT Human: atcatttaagattttggattttcagat-tagggatgctcaacctATAGTTTGATTATTTCCCTCATCTCTCCCTTCTCAGCCTTTCCTTATCAATGCTGTTTGGGAATCTGAGGCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTTTCTGAAATGTCCTCCCTGGAATACATTT Cluster: [ ] Orangutan: atcatttaagattttggattttcagattaagggatgctcaacctATAGTTTGATTATTTCCCTCATCTCTCCCTTCTCAGCCTTTCCTTATCAATGCTGTTTGGGAATCTGAGGCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGT-ACT---CAGTCCTCCCTGGAATACATTT Chimp > Human ------------- chr2:50892257-50892263 Template switch process: F1: L GCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTT 1 F3: 4 TGTCCTCCCTGGAATACATTTTTTACCTTCCTTATTTTCAA R RF: TTTCAGATTAGGGATGCTCAACCTATAGTTTGATTATTTCCCTCATCTCTCCCTTCTCAGCCTTTCCTTATCAATGCTGTTTGGGAATCTGAGGCAGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTTCTCAGTCCTCCCTGGAATACATTTTTTACCTTCCTTATTTTCAA RR: AAAGTCTAATCCCTACGAGTTGGATATCAAACTAATAAAGGGAGTAGAGAGGGAAGAGTCGGAAAGGAATAGTTACGACAAACCCTTAGACTCCGTCAAGAGTTACTTAGGTCAATGACTCAAAAGACTTTACAAGAGTCAGGAGGGACCTTATGTAAAAAATGGAAGGAATAAAAGTT F2: 3 AAAGTCT 2 Unidirectional alignment (log-probability: -32.9) AGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTttctgaaaT----GTCCTCCCTGGAATACATTTTTTACCTTCCTTATTTTCA AGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGT--------TCTCAGTCCTCCCTGGAATACATTTTTTACCTTCCTTATTTTCA Template switch alignment (log-probability: -22.2) AGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTT|TCTGAAA|tGTCCTCCCTGGAATACATTTTTTACCTTCCTTATTTTCA AGTTCTCAATGAATCCAGTTACTGAGTTTTCTGAAATGTT|TCTGAAA|AGTCCTCCCTGGAATACATTTTTTACCTTCCTTATTTTCA ========== Event 1969 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCAGATTTTAGGCATCTGATTT--------------TAATCATCTTGgggtggcagaggttgcagtgagctgagatggtgccactgcactccagcctgggtgaaagagtgagatcctgtctcaaaa-------aa Chimp: GTCAGATTTTAGGCATCTGATTT--------------TAATCATCTTGgggtggcagaggttgcagtgagctgagatggtgccactgcactccagcctgggtgaaagagtgagatcctgtctcaaaa-------aa ↓ 4 1 3 2 Gorilla: GTCAGATTTTAGGCATCTGATTTTAATCAGATCATTTTAATCATCTTGgggtggcagaggttgcagtgagctgagatggtgccactgcactccagcctgggtgaaagagtgagatcctgtctcaaaa--------- ↑ 4 1 3 2 Human: GTCAGATTTTAGGCATCTGATTT--------------TAATCATCTTGgggtggcagaggttgcagtgagctgagatggtgccactgcactccagcctgggtgaaagagtgagatcctgtctcaaaa-------aa Cluster: [ ] Orangutan: GTCAGATTTTAGGCATCTGATTT--------------TAATCATCTTGgggtggcagagattgtagtgagctgagatggtgccactgcactccagcctgggtgaaagagtgaggtcctgtctcaaaaaaaaaaa-- Human > Gorilla --------------- chr2B:51460736-51460739 Template switch process: F1: L TAAAATCTAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCA 1 F3: 4 ATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTGAGAT R RF: TAAAATCTAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTGAGATGGTGCCACTGCACTCCAGCCTGGGTGAAAGAGTGAGATC RR: ATTTTAGATTACGGATTTCAGTCTAAAATCCGTAGACTAAAATTAGTAGAACCCCACCGTCTCCAACGTCACTCGACTCTACCACGGTGACGTGAGGTCGGACCCACTTTCTCACTCTAG F2: 3 CTAG 2 Unidirectional alignment (log-probability: -31) TAATGCCTAAAGTCAGATTTTAGGCATCTGATtttaatcagatcatTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG TAATGCCTAAAGTCAGATTTTAGGCATCTGAT--------------TTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG Template switch alignment (log-probability: -16.5) TAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCA|GATC|ATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG TAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCA|GATC|ATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG Chimp > Gorilla --------------- chr2B:51460736-51460739 Template switch process: F1: L TAAAATCTAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCA 1 F3: 4 ATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTGAGAT R RF: TAAAATCTAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTGAGATGGTGCCACTGCACTCCAGCCTGGGTGAAAGAGTGAGATC RR: ATTTTAGATTACGGATTTCAGTCTAAAATCCGTAGACTAAAATTAGTAGAACCCCACCGTCTCCAACGTCACTCGACTCTACCACGGTGACGTGAGGTCGGACCCACTTTCTCACTCTAG F2: 3 CTAG 2 Unidirectional alignment (log-probability: -31) TAATGCCTAAAGTCAGATTTTAGGCATCTGATtttaatcagatcatTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG TAATGCCTAAAGTCAGATTTTAGGCATCTGAT--------------TTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG Template switch alignment (log-probability: -16.5) TAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCA|GATC|ATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG TAATGCCTAAAGTCAGATTTTAGGCATCTGATTTTAATCA|GATC|ATTTTAATCATCTTGGGGTGGCAGAGGTTGCAGTGAGCTG ========== Event 1970 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGTTTGGGAAGACTTGTAGAT-----------AGAGCATGAATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAATCCCAATGTTGTCTGCAGTGTGGCTTAGTGTACCCTGTAGTCATAAAGTTCATATCCATTGAAAACATCAGGACTAAAATAGGTGTTTCATGTTAAGACCTGGACTTGGCTC Chimp: AGTTTGGGAAGACTTGTAGAT-----------AGAGCATGAATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAATCCCAATGTAGTCTGCAGTGTGGCTTAGTGTACCCTGTAGTCATAAAG-TCATATCCATTGAAAACATCAGGACTAAAATAGGTGTTTCATGTTAAGACCTGGACTTGGCTC ↑ 4 1 3 2 Gorilla: AGTTTGGGAAGACTTGTAGAT----------------------AGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAATCCCAATGTAGTTTGCAGTGTGGCTTAGTGTACCCTGTAGTCATGAAG-TCATATCCATTGAAAACATCAGGACTAAAATAGGTGTTTCATGTTAAGACCTGGACTGGGCTC ↓ 4 1 3 2 Human: AGTTTGGGAAGACTTGTAGAT-----------AGAGCATGAATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAATCCCAATGTTGTCTGCAGTGTGGCTTAGTGTACCCTGTAGTCATAAAGTTCATATCCATTGAAAACATCAGGACTAAAATAGGTGTTTCATGTTAAGACCTGGACTTGGCTC Cluster: [ ] Orangutan: AGTTTGGGAAGACTTGTAGATAGAGCATGAAT-----------AGAGTGCAGTTTGATGTGGTGTGGCTGATCGCAAAGGAATCCCGATGTAGTTTGCAGTGTGGCTTAGTGTACCCTGTAGTCATAAAG-TCATATCCATTGAAAACATCAGGACTAAAGTAGGTGTTTCATGTTAAGACCTGGACTTGGCTC Gorilla > Human --------------- chr2:191563443-191563447 Template switch process: F1: L TTTAGCAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAG 1 F3: 4 ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAAT R RF: TTTAGCAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAATCCCAATGTAGTTTGCAGTGTGGCTTAGTGTACCCTGTAGTCATGAAGTCATATCCATTGAAAACATCAGGACTAAAATAGGTGTTTCATG RR: AAATCGTTCTTTTCTTCTATTCAAACCCTTCTGAACATCTATCTCACGTCAAACTACACCACACCAACTAGCGTTTCCTTAGGGTTACATCAAACGTCACACCGAATCACATGGGACATCAGTACTTCAGTATAGGTAACTTTTGTAGTCCTGATTTTATCCACAAAGTAC F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -26.7) CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGatagagcatgaATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAG-----------ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA Template switch alignment (log-probability: -16.5) CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAG|CATGA|ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAG|CATGA|ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA Gorilla > Chimp --------------- chr2B:82119844-82119848 Template switch process: F1: L TTTAGCAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAG 1 F3: 4 ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAAT R RF: TTTAGCAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGAATCCCAATGTAGTTTGCAGTGTGGCTTAGTGTACCCTGTAGTCATGAAGTCATATCCATTGAAAACATCAGGACTAAAATAGGTGTTTCATG RR: AAATCGTTCTTTTCTTCTATTCAAACCCTTCTGAACATCTATCTCACGTCAAACTACACCACACCAACTAGCGTTTCCTTAGGGTTACATCAAACGTCACACCGAATCACATGGGACATCAGTACTTCAGTATAGGTAACTTTTGTAGTCCTGATTTTATCCACAAAGTAC F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -26.7) CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGatagagcatgaATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAG-----------ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA Template switch alignment (log-probability: -16.5) CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAG|CATGA|ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA CAAGAAAAGAAGATAAGTTTGGGAAGACTTGTAGATAGAG|CATGA|ATAGAGTGCAGTTTGATGTGGTGTGGTTGATCGCAAAGGA ========== Event 1971 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: GGGTAGCAGCTATTTGTATATTACTTAAAGGAATGTACATgatttttttacattat ↓ 31 2 4 ↑ 3 1 2 4 Chimp: GGGTAGCAGCTATTTGTATATTCCTTTAAGTAA--TACATGAtttttttACATTAT Gorilla: GGGTAGCAGCTATTTGTATATTCCTTTAAGTAA--TACATGAtttttttACGTTAT Human: GGGTAGCAGCTATTTGTATATTACTTAAAGGAATGTACATgatttttttacattat Cluster: [ ] Orangutan: GGGTAGCAGCTATTTGTATATTCCTTTAAGTAA--TACATGatttttttacattat Chimp > Human ------------- chr2:191943589-191943600 Template switch process: F1: L TAACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATT 1 F3: 4 GTACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA R RF: TAACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATTCCTTTAAGTAATACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA RR: ATTGAAGTCGAGTCCATTACCCATCGTCGATAAACATATAAGGAAATTCATTATGTACTAAAAAAATGTAATAAAAATTAATAAGTTAAAAT F2: 3 TAAGGAAATTCA 2 Unidirectional alignment (log-probability: -31.9) AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATTaCTTaAAGgAAtgTACATGATTTTTTTACATTATTTTTAATTATTCAATTTT AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATTCCTTTAAGTAA--TACATGATTTTTTTACATTATTTTTAATTATTCAATTTT Template switch alignment (log-probability: -22.8) AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATT|ACTTAAAGGAAT|gTACATGATTTTTTTACATTATTTTTAATTATTCAATTTT AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATT|ACTTAAAGGAAT|ATACATGATTTTTTTACATTATTTTTAATTATTCAATTTT Human > Chimp ------------- chr2B:82496096-82496106 Template switch process: F1: L TAACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATT 1 F3: 4 TACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA R RF: TAACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATTACTTAAAGGAATGTACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA RR: ATTGAAGTCGAGTCCATTACCCATCGTCGATAAACATATAATGAATTTCCTTACATGTACTAAAAAAATGTAATAAAAATTAATAAGTTAAAAT F2: 3 AATGAATTTCC 2 Unidirectional alignment (log-probability: -29.1) AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATTcCTTtAAGtAA--TACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATTACTTAAAGGAATGTACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA Template switch alignment (log-probability: -16.6) AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATT|CCTTTAAGTAA|TACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA AACTTCAGCTCAGGTAATGGGTAGCAGCTATTTGTATATT|CCTTTAAGTAA|TACATGATTTTTTTACATTATTTTTAATTATTCAATTTTA ========== Event 1972 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CAGCCAAGGGTGTCACTTGTGA--AACCTGCTTTTAAAAACATATACTACACATCAGTTTTAGTGCAGCT Chimp: CAGCCAAGGGTGTCACTTGTGA--AACCTGCTTTTAAAAACATATACTACACATCAGTTTTAGTGCAGCT ↑ 13 24 Gorilla: CAGCCAAGGGTGTCACTTGTGTAGTATATGTTTTTAAAAGCAGG--TTTCACATCAGTTTTAGTGCAGCT ↓ 13 24 Human: CAGCCAAGGGTGTCACTTGTGA--AACCTGCTTTTAAAAACATATACTACACATCAGTTTTAGTGCAGCT Cluster: [ ] Orangutan: CAGCCAAGGGTGTCACTTGTGTAGTATATGTTTTTAAAAGCAGG--TTTCACATCAGTTTTAGTGCAGCT Gorilla > Human --------------- chr2:192073366-192073391 Template switch process: F1: L GTGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG 1 F3: 4 CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT R RF: GTGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTGTAGTATATGTTTTTAAAAGCAGGTTTCACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT RR: CACCCACCCTATCCTACATTGTCGGTTCCCACAGTGAACACATCATATACAAAAATTTTCGTCCAAAGTGTAGTCAAAATCACGTCGACCCTTACTAAAGTTGAAAA F2: 3 ATCATATACAAAAATTTTCGTCCAAA 2 Unidirectional alignment (log-probability: -56.4) TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTGaaacctgcttttaaaaacatatacTA------------------------CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG------------------------TAGTATATGTTTTTAAAAGCAGGTTTCACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT Template switch alignment (log-probability: -19) TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG|AAACCTGCTTTTAAAAACATATACTA|CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG|AAACCTGCTTTTAAAAACATATACTA|CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT Gorilla > Chimp --------------- chr2B:82636938-82636963 Template switch process: F1: L GTGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG 1 F3: 4 CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT R RF: GTGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTGTAGTATATGTTTTTAAAAGCAGGTTTCACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT RR: CACCCACCCTATCCTACATTGTCGGTTCCCACAGTGAACACATCATATACAAAAATTTTCGTCCAAAGTGTAGTCAAAATCACGTCGACCCTTACTAAAGTTGAAAA F2: 3 ATCATATACAAAAATTTTCGTCCAAA 2 Unidirectional alignment (log-probability: -56.4) TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTGaaacctgcttttaaaaacatatacTA------------------------CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG------------------------TAGTATATGTTTTTAAAAGCAGGTTTCACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT Template switch alignment (log-probability: -19) TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG|AAACCTGCTTTTAAAAACATATACTA|CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT TGGGTGGGATAGGATGTAACAGCCAAGGGTGTCACTTGTG|AAACCTGCTTTTAAAAACATATACTA|CACATCAGTTTTAGTGCAGCTGGGAATGATTTCAACTTTT ========== Event 1973 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATAAACCAAAAAGTTATTTTCAGAAAGTTAC-----CATTTCATGTTATTTTCTGTTC Chimp: TAATAAACCAAAAAGTTATTTTCAGAAAGTTAC-----CATTTCATGTTATTTTCTGTTC ↓ 3 2 1 4 Gorilla: TAATAAACCAAAAAGTTATTTTCAGAAAGTTTTCTGAAATTTTCATGTTATTTTCTGTTC ↑ 3 2 1 4 Human: TAATAAACCAAAAAGTTATTTTCAGAAAGTTAC-----CATTTCATGTTATTTTCTGTTC Cluster: [ ] Orangutan: ------------------------------------------------------------ Human > Gorilla --------------- chr2B:84874324-84874331 Template switch process: F1: L TATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT 1 F3: 4 TTTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTTA R RF: TATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTTACCATTTCATGTTATTTTCTGTTCTAAAACACTGACAACACTTA RR: ATATTGAACTATTATTTGGTTTTTCAATAAAAGTCTTTCAATGGTAAAGTACAATAAAAGACAAGATTTTGTGACTGTTGTGAAT F2: 3 AAAGTCTT 2 Unidirectional alignment (log-probability: -39.3) ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT----ttctgaaatTTTCATGTTATTTTCTGTTCTAAAACACTGACAAtACTT ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTTACCA---------TTTCATGTTATTTTCTGTTCTAAAACACTGACAACACTT Template switch alignment (log-probability: -27.8) ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT|TTCTGAAA|tTTTCATGTTATTTTCTGTTCTAAAACACTGACAAtACTT ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT|TTCTGAAA|ATTTCATGTTATTTTCTGTTCTAAAACACTGACAACACTT Chimp > Gorilla --------------- chr2B:84874324-84874331 Template switch process: F1: L TATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT 1 F3: 4 TTTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTTA R RF: TATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTTACCATTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTTA RR: ATATTGAACTATTATTTGGTTTTTCAATAAAAGTCTTTCAATGGTAAAGTACAATAAAAGACAAGATTTTGTGACTGTTATGAAT F2: 3 AAAGTCTT 2 Unidirectional alignment (log-probability: -33.8) ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT----ttctgaaatTTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTT ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTTACCA---------TTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTT Template switch alignment (log-probability: -22.3) ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT|TTCTGAAA|tTTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTT ATAACTTGATAATAAACCAAAAAGTTATTTTCAGAAAGTT|TTCTGAAA|ATTTCATGTTATTTTCTGTTCTAAAACACTGACAATACTT ========== Event 1974 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGAGCAGCACTTCGGGGTGGCA---AAGCATTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGCACCAATTAAGAATTTGTTAGCCACATGCAATAGAAGCAATTCTTTAACGATGCTTTTGAAAATCAACAAAATTAAA Chimp: TGAGCAACACTTCGGGGTGGCA---AAGCATTTGTAAAGCTTGTTAATTATAATTCATGGACATGAGAGCACCAATTAAGAATTTGTTAGCCACATGCAATAGAAGCAATTCTTTAACGATGCTTTTGAAAATCAACAAAATTAAA ↑ 1 4 3 2 Gorilla: TGAGCAACACTTCGGGGTGGCC------ATTTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGCACCAATTAAGAATTTGTTAGCCACATGCAATAGAAGCAATTCTTTAACGATGCTTTTGAAAATCAACAAAATTAAA ↓ 1 4 3 2 Human: TGAGCAGCACTTCGGGGTGGCA---AAGCATTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGCACCAATTAAGAATTTGTTAGCCACATGCAATAGAAGCAATTCTTTAACGATGCTTTTGAAAATCAACAAAATTAAA Cluster: [ ] Orangutan: TGAGTAACACTTCGGGGTGGCAAAG---CATTTGTAAAGCTTGTTAATTATAATTCATAGACACAAGAACACCAATTAAGAATTTGTTAGCCACATGCAAAAGGAGCAATTCTTTAACGATGCTTTTGAAAATCAACAAAATTAAA Gorilla > Human --------------- chr2:192380736-192380742 Template switch process: F1: L TGAAGGGAACCATTTGAGGGTGAGCAGCACTTCGGGGTGGC 1 F3: 4 TTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC R RF: TGAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGCCATTTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGCACCAATTAAGAATTTGTTAGCCACATGCAATAGAAGCAATTCTTTAACGATGCTTT RR: ACTTCCCTTGGTAAACTCCCACTCGTTGTGAAGCCCCACCGGTAAAACATTTCGAACAATTAATATTAAGTATCTGTACTCTCGTGGTTAATTCTTAAACAATCGGTGTACGTTATCTTCGTTAAGAAATTGCTACGAAA F2: 3 TACGAAA 2 Unidirectional alignment (log-probability: -31.8) GAAGGGAACCATTTGAGGGTGAGCAgCACTTCGGGGTGGCaAagcaTTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC GAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGCCAT---TTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC Template switch alignment (log-probability: -22.1) GAAGGGAACCATTTGAGGGTGAGCAgCACTTCGGGGTGGC|AAAGCAT|TTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC GAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGC|AAAGCAT|TTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC Gorilla > Chimp --------------- chr2B:82940053-82940059 Template switch process: F1: L TGAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGC 1 F3: 4 TTGTAAAGCTTGTTAATTATAATTCATGGACATGAGAGC R RF: TGAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGCCATTTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGCACCAATTAAGAATTTGTTAGCCACATGCAATAGAAGCAATTCTTTAACGATGCTTT RR: ACTTCCCTTGGTAAACTCCCACTCGTTGTGAAGCCCCACCGGTAAAACATTTCGAACAATTAATATTAAGTATCTGTACTCTCGTGGTTAATTCTTAAACAATCGGTGTACGTTATCTTCGTTAAGAAATTGCTACGAAA F2: 3 TACGAAA 2 Unidirectional alignment (log-probability: -31.8) GAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGCaAagcaTTTGTAAAGCTTGTTAATTATAATTCATgGACATGAGAGC GAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGCCAT---TTTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC Template switch alignment (log-probability: -22.1) GAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGC|AAAGCAT|TTGTAAAGCTTGTTAATTATAATTCATgGACATGAGAGC GAAGGGAACCATTTGAGGGTGAGCAACACTTCGGGGTGGC|AAAGCAT|TTGTAAAGCTTGTTAATTATAATTCATAGACATGAGAGC ========== Event 1975 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGAGAGAAATGAGCATGGATACTC------------------------ATTCATGAGTATCTGGAGCTGTATGTATACCTC ↑ 3 1 2 4 Chimp: CTGAGAGAAATGAGCATGGATACTC------------ATGAATTTCATTATTAATGAAGAACTGGAGCTGTATGTATACCTC Gorilla: CTGAGACAAATGAGCATGGATACTCATGAATTTCATT------------ATTAATGAAGAACTGGAGCTGTATGTATACCTC ↓ 3 1 2 4 Human: CTGAGAGAAATGAGCATGGATACTC------------------------ATTCATGAGTATCTGGAGCTGTATGTATACCTC Cluster: [ ] Orangutan: CTGAGAGGAATGAGCATGCATACTCATGAATTTTATT------------ATTAATGAAGAACTGGAGCTCTATGTACACCTC Chimp > Human ------------- chr2:193625357-193625366 Template switch process: F1: L AAATCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCAT 1 F3: 4 CTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT R RF: AAATCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCATGAATTTCATTATTAATGAAGAACTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT RR: TTTAGACTCCTTTTATGACTCTCTTTACTCGTACCTATGAGTACTTAAAGTAATAATTACTTCTTGACCTCGACATACATATGGAGATCCAATCATCTATATTGA F2: 3 TATGAGTACT 2 Unidirectional alignment (log-probability: -35.6) TCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCAT------------TcATGAgtAtCTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT TCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCATGAATTTCATTATTAATGAAGAACTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT Template switch alignment (log-probability: -16.6) TCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCAT|TCATGAGTAT|CTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT TCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCAT|TCATGAGTAT|CTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT Gorilla > Human --------------- chr2:193625357-193625366 Template switch process: F1: L AAATCTGAGGAAAATACTGAGAGAAATGAGCATGGATACTCAT 1 F3: 4 CTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT R RF: AAATCTGAGGAAAATACTGAGACAAATGAGCATGGATACTCATGAATTTCATTATTAATGAAGAACTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT RR: TTTAGACTCCTTTTATGACTCTGTTTACTCGTACCTATGAGTACTTAAAGTAATAATTACTTCTTGACCTCGACATACATATGGAGATCCAATCATCTATATTGA F2: 3 TATGAGTACT 2 Unidirectional alignment (log-probability: -39.3) TCTGAGGAAAATACTGAGAgAAATGAGCATGGATACTC------------ATTcATGAgtAtCTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT TCTGAGGAAAATACTGAGACAAATGAGCATGGATACTCATGAATTTCATTATTAATGAAGAACTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT Template switch alignment (log-probability: -22.6) TCTGAGGAAAATACTGAGAgAAATGAGCATGGATACTCAT|TCATGAGTAT|CTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT TCTGAGGAAAATACTGAGACAAATGAGCATGGATACTCAT|TCATGAGTAT|CTGGAGCTGTATGTATACCTCTAGGTTAGTAGATATAACT ========== Event 1976 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAATTTTTTTCTGGGAGTGCTGT--------TTACTTATAATCTTATTTGTATTG Chimp: TTAAtttttttCTGGGAGTGCTGT--------TTACTTATAATCTTATTTGTATTG ↓ 3 1 42 Gorilla: TTAAtttttttCTGGGAGTGCTGTTGTAAACAGCACTTATAATCTTATTTGTATTG ↑ 3 1 42 Human: TTAATTTTTTTCTGGGAGTGCTGT--------TTACTTATAATCTTATTTGTATTG Cluster: [ ] Orangutan: TTAATTTTTTTCTGGGAGTGCTGTTG---------TAAACAATCTTATTTGTATTG Human > Gorilla --------------- chr2B:86536369-86536377 Template switch process: F1: L ACCTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTT 1 F3: 4 ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC R RF: ACCTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTTTACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC RR: TGGAAATTGGATCTTAAAATTAAAAAAAGACCCTCACGACAAATGAATATTAGAATAAACATAACTTTTCTCTTGTATTCTGG F2: 3 CGACAAATG 2 Unidirectional alignment (log-probability: -27.9) CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTTgtaaacagcACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTTT--------ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC Template switch alignment (log-probability: -16.9) CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTT|GTAAACAGC|ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTT|GTAAACAGC|ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC Chimp > Gorilla --------------- chr2B:86536369-86536377 Template switch process: F1: L ACCTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTT 1 F3: 4 ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC R RF: ACCTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTTTACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC RR: TGGAAATTGGATCTTAAAATTAAAAAAAGACCCTCACGACAAATGAATATTAGAATAAACATAACTTTTCTCTTGTATTCTGG F2: 3 CGACAAATG 2 Unidirectional alignment (log-probability: -27.9) CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTTgtaaacagcACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTTT--------ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC Template switch alignment (log-probability: -16.9) CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTT|GTAAACAGC|ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC CTTTAACCTAGAATTTTAATTTTTTTCTGGGAGTGCTGTT|GTAAACAGC|ACTTATAATCTTATTTGTATTGAAAAGAGAACATAAGACC ========== Event 1977 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: AACCAAGTTACTCAAATACATATCTTAGCAAGATATCTGCTATACATAGA-AAT------------GTATGTGTTAATGATAATCATC ↓ 3 2 4 ↑ 1 3 24 Chimp: AATCAAGTTACTCAAATACATATCTTA----GA---TTTCTATGTATAGCAGAT------ATCTTGCTATGTGTTAATGATAATCATC Gorilla: AACCAAGTTACTCAAATACATTTCTTA----CA---TTTCTATGTATAGCAGATATCTTG------CTATGTGTTAATGATAATCATC ↓ 13 24 ↑ 13 24 Human: AACCAAGTTACTCAAATACATATCTTAGCAAGATATCTGCTATACATAGA-AAT------------GTATGTGTTAATGATAATCATC Cluster: [ ] Orangutan: AACCAAGTTACTCAAATACATATCTTA----CA---TTTCTATGTATAGCAGATATCTTG------CTATGTGTTAATGATAATCACC Chimp > Human ------------- chr2:194378251-194378275 Template switch process: F1: L AAAAGGTATTTACAAACCAAGTTACTCAAATACATATCTTAG 1 F3: 4 GTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC R RF: AAAAGGTATTTACAAATCAAGTTACTCAAATACATATCTTAGATTTCTATGTATAGCAGATATCTTGCTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC RR: TTTTCCATAAATGTTTAGTTCAATGAGTTTATGTATAGAATCTAAAGATACATATCGTCTATAGAACGATACACAATTACTATTAGTAGTTATATTACGGTTCAAAAG F2: 3 TAAAGATACATATCGTCTATAGAAC 2 Unidirectional alignment (log-probability: -64.4) AAGGTATTTACAAAcCAAGTTACTCAAATACATATCTTA-------------------------GCaagatatctgctatacatagaaatgTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTT AAGGTATTTACAAATCAAGTTACTCAAATACATATCTTAGATTTCTATGTATAGCAGATATCTTGC-------------------------TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTT Template switch alignment (log-probability: -30.4) AAGGTATTTACAAAcCAAGTTACTCAAATACATATCTTAG|CAAGATATCTGCTATACATAGAAAT|gTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTT AAGGTATTTACAAATCAAGTTACTCAAATACATATCTTAG|CAAGATATCTGCTATACATAGAAAT|CTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTT Human > Chimp ------------- chr2B:84940270-84940295 Template switch process: F1: L AAAAGGTATTTACAAATCAAGTTACTCAAATACATATCTTAG 1 F3: 4 TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC R RF: AAAAGGTATTTACAAACCAAGTTACTCAAATACATATCTTAGCAAGATATCTGCTATACATAGAAATGTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC RR: TTTTCCATAAATGTTTGGTTCAATGAGTTTATGTATAGAATCGTTCTATAGACGATATGTATCTTTACATACACAATTACTATTAGTAGTTATATTACGGTTCAAAAG F2: 3 CGTTCTATAGACGATATGTATCTTTA 2 Unidirectional alignment (log-probability: -64.4) AAGGTATTTACAAAtCAAGTTACTCAAATACATATCTTAgatttctatgtatagcagatatcttGC-------------------------TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC AAGGTATTTACAAACCAAGTTACTCAAATACATATCTTA-------------------------GCAAGATATCTGCTATACATAGAAATGTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC Template switch alignment (log-probability: -24.5) AAGGTATTTACAAAtCAAGTTACTCAAATACATATCTTAG|ATTTCTATGTATAGCAGATATCTTGC|TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC AAGGTATTTACAAACCAAGTTACTCAAATACATATCTTAG|ATTTCTATGTATAGCAGATATCTTGC|TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC Gorilla > Human --------------- chr2:194378250-194378276 Template switch process: F1: L ATTTTTAAAAGGTATTTACAAACCAAGTTACTCAAATACATATCTTA 1 F3: 4 TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC R RF: ATTTTTAAAAGGTATTTACAAACCAAGTTACTCAAATACATTTCTTACATTTCTATGTATAGCAGATATCTTGCTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC RR: TAAAAATTTTCCATAAATGTTTGGTTCAATGAGTTTATGTAAAGAATGTAAAGATACATATCGTCTATAGAACGATACACAATTACTATTAGTAGTTATATTACGGTTCAAAAG F2: 3 GTAAAGATACATATCGTCTATAGAACG 2 Unidirectional alignment (log-probability: -63.5) AAAGGTATTTACAAACCAAGTTACTCAAATACATaTCTTA-------------------------GCaagatatctgctatacatagaaatgTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC AAAGGTATTTACAAACCAAGTTACTCAAATACATTTCTTACATTTCTATGTATAGCAGATATCTTGC-------------------------TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC Template switch alignment (log-probability: -24.8) AAAGGTATTTACAAACCAAGTTACTCAAATACATaTCTTA|GCAAGATATCTGCTATACATAGAAATG|TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC AAAGGTATTTACAAACCAAGTTACTCAAATACATTTCTTA|GCAAGATATCTGCTATACATAGAAATG|TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC Human > Gorilla --------------- chr2B:87103191-87103217 Template switch process: F1: L ATTTTTAAAAGGTATTTACAAACCAAGTTACTCAAATACATTTCTTA 1 F3: 4 TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC R RF: ATTTTTAAAAGGTATTTACAAACCAAGTTACTCAAATACATATCTTAGCAAGATATCTGCTATACATAGAAATGTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC RR: TAAAAATTTTCCATAAATGTTTGGTTCAATGAGTTTATGTATAGAATCGTTCTATAGACGATATGTATCTTTACATACACAATTACTATTAGTAGTTATATTACGGTTCAAAAG F2: 3 CGTTCTATAGACGATATGTATCTTTAC 2 Unidirectional alignment (log-probability: -63.5) AAAGGTATTTACAAACCAAGTTACTCAAATACATtTCTTAcatttctatgtatagcagatatcttGC-------------------------TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC AAAGGTATTTACAAACCAAGTTACTCAAATACATATCTTA-------------------------GCAAGATATCTGCTATACATAGAAATGTATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC Template switch alignment (log-probability: -24.8) AAAGGTATTTACAAACCAAGTTACTCAAATACATtTCTTA|CATTTCTATGTATAGCAGATATCTTGC|TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC AAAGGTATTTACAAACCAAGTTACTCAAATACATATCTTA|CATTTCTATGTATAGCAGATATCTTGC|TATGTGTTAATGATAATCATCAATATAATGCCAAGTTTTC ========== Event 1978 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ----ACACTTGCACATGTATATAACACTCACATCCACTTAAATATAACTGTGCACACATGCACAGTTATATTTATTTATAGATTGTGTCCTTTGAAAatattttcctagattttgttttttatttttctgctttctacac Chimp: ACACACACTTGCACATGTATATAACACTCACATCCACTTAAATATAACTGTGCACACATGCACAGTtatatttatttgtagattgtgtcctttgaaaatattttcctagattttgttttttatttttctgctttctacac ↑ 3 1 2 4 Gorilla: ----ACACTTGCACATGTATACAACACTGACATCCACTTAAATATAACTGTGCATGTGTGTATACt-ttttttatttgtagattgtgtcctttgaaaatattttcctagattttgttttttatttttctgctttctacac Human: ----ACACTTGCACATGTATATAACACTCACATCCACTTAAATATAACTGTGCACACATGCACAGTTATATTTATTTATAGATTGTGTCCTTTGAAAatattttcctagattttgttttttatttttctgctttctacac Cluster: [ ] Orangutan: ----ACACTTGCACATGTATACAACATTCACATCCACTTAAATATAACTGTGCATGTGTGTATACt-ttttttatttgtagattgtgtccttttaaaatattttcctagattttgt---ttatttttcTGCTTTCTACAC Gorilla > Chimp --------------- chr2B:84726698-84726708 Template switch process: F1: L AATGGTTCAAAATTACACACACACTTGCACATGTATATAACACTCACATCCACTTAAATATAACTGTGCA 1 F3: 4 TTAT R RF: AATGGTTCAAAATTACACACACACTTGCACATGTATACAACACTGACATCCACTTAAATATAACTGTGCATGTGTGTATACTTTTTTTATTTGTAGATTGTGTCCTTTGAAAATATTTTCCTAGATTTTGTTTTTTAT RR: TTACCAAGTTTTAATGTGTGTGTGAACGTGTACATATGTTGTGACTGTAGGTGAATTTATATTGACACGTACACACATATGAAAAAAATAAACATCTAACACAGGAAACTTTTATAAAAGGATCTAAAACAAAAAATA F2: 3 GACACGTACAC 2 Unidirectional alignment (log-probability: -49.3) ATGTATAtAACACTcACATCCACTTAAATATAACTGTGCacacatgcacagttAT------------- ATGTATACAACACTGACATCCACTTAAATATAACTGTGC--------------ATGTGTGTATACTTT Template switch alignment (log-probability: -28) ATGTATAtAACACTcACATCCACTTAAATATAACTGTGCA|CACATGCACAG|TTAT ATGTATACAACACTGACATCCACTTAAATATAACTGTGCA|CACATGCACAG|TTAT ========== Event 1979 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAAAATTAATACACTGGCACATAAGCAAAGTAAATCAATCTAGATTTAAATAAGCAA------ Chimp: GAAAAATTAATACACTGGCACATAAGCAAAGTAAATCAATCTAGATTTAAATAAGCAA------ ↓ 1 4 3 2 Gorilla: GAAAAATTAATACACTGGCACCTAGGCAAAGTAAATCAATCTAGATTTAAATAAGCAACATAAT Human: GAAAAATTAATACACTGGCACATAAGCAAAGTAAATCAATCTAGATTTAAATAAGCAA------ Cluster: [ ] Orangutan: GAAAAATTAATACACTGGCACATAAGCAAAGTAAATCAATCTAGATTTAAATAAGCAACATAAT Chimp > Gorilla --------------- chr2B:88022446-88022449 Template switch process: F1: L AAATTCAATAATGCTATGAAGAAAAATTAATACACTGGCAC 1 F3: 4 GCAAAGTAAATCAATCTAGATTTAAATAAGCAACATAATG R RF: AAATTCAATAATGCTATGAAGAAAAATTAATACACTGGCACATAAGCAAAGTAAATCAATCTAGATTTAAATAAGCAACATAATG RR: TTTAAGTTATTACGATACTTCTTTTTAATTATGTGACCGTGTATTCGTTTCATTTAGTTAGATCTAAATTTATTCGTTGTATTAC F2: 3 GATC 2 Unidirectional alignment (log-probability: -29) AATTCAATAATGCTATGAAGAAAAATTAATACACTGGCACcTAgGCAAAGTAAATCAATCTAGATTTAAATAAGCAAcataatg AATTCAATAATGCTATGAAGAAAAATTAATACACTGGCACATAAGCAAAGTAAATCAATCTAGATTTAAATAAGCAA------- Template switch alignment (log-probability: -16.2) AATTCAATAATGCTATGAAGAAAAATTAATACACTGGCAC|CTAG|GCAAAGTAAATCAATCTAGATTTAAATAAGCAACATAATG AATTCAATAATGCTATGAAGAAAAATTAATACACTGGCAC|CTAG|GCAAAGTAAATCAATCTAGATTTAAATAAGCAACATAATG ========== Event 1980 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAAATTATTTTTCATTCTCTAC--------------------------------------------------------AAAGTACAAGCCAAAATAACTAATTATGGCTTGTACTTTGTAACAtctgtatctcccataa ↑ 1 4 3 2 Chimp: TAAAATTATTTTTCATTCTCTCT----------------------------AGCCTCTTTCCAGAGGCAGCACTTGCCACAATTACAA--TTAAATAACTAATTATGGCTTGTACTTTGTAACAtctgtacctcccataa Gorilla: TAAAATTATTTTTCATTCTCTCTAGCCTCTTTCCAGAGGCAGCACTTGCCA----------------------------CAATTACAA--TTAAATAACTAATTATGGCTTGTACTTTGTAACAtctgtatctcccataa ↓ 1 4 3 2 Human: TAAAATTATTTTTCATTCTCTAC--------------------------------------------------------AAAGTACAAGCCAAAATAACTAATTATGGCTTGTACTTTGTAACAtctgtatctcccataa Cluster: [ ] Orangutan: TAAAATTATTTTTCATTCTCTCTAGCCTCTTTCCAGAGGCAGCACTTGCCA----------------------------CAATTACAA--TTAAATAACTAATTATGGCTTGTACTTTGTAACAtctgtatctcccataa Chimp > Human ------------- chr2:44068723-44068737 Template switch process: F1: L CAGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCT 1 F3: 4 AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC R RF: CAGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCTCTAGCCTCTTTCCAGAGGCAGCACTTGCCACAATTACAATTAAATAACTAATTATGGCTTGTACTTTGTAACATCTGTACC RR: GTCGTTCTATTACTTAATTTATTTTAATAAAAAGTAAGAGAGATCGGAGAAAGGTCTCCGTCGTGAACGGTGTTAATGTTAATTTATTGATTAATACCGAACATGAAACATTGTAGACATGG F2: 3 ACCGAACATGAAACA 2 Unidirectional alignment (log-probability: -50.8) AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTC-----------------------------------------TAcaaagtacaagccaaAATAACTAATTATGGCTTGTACTTTGTAACATCTGTAtC AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCTCTAGCCTCTTTCCAGAGGCAGCACTTGCCACAATTACAATTA---------------AATAACTAATTATGGCTTGTACTTTGTAACATCTGTACC Template switch alignment (log-probability: -23.1) AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCT|ACAAAGTACAAGCCA|AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTAtC AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCT|ACAAAGTACAAGCCA|AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTACC Gorilla > Human --------------- chr2:44068723-44068737 Template switch process: F1: L CAGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCT 1 F3: 4 AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC R RF: CAGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCTCTAGCCTCTTTCCAGAGGCAGCACTTGCCACAATTACAATTAAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC RR: GTCGTTCTATTACTTAATTTATTTTAATAAAAAGTAAGAGAGATCGGAGAAAGGTCTCCGTCGTGAACGGTGTTAATGTTAATTTATTGATTAATACCGAACATGAAACATTGTAGACATAG F2: 3 ACCGAACATGAAACA 2 Unidirectional alignment (log-probability: -44.3) AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTC-----------------------------------------TacaaagtacaagccaAAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCTCTAGCCTCTTTCCAGAGGCAGCACTTGCCACAATTACAATT---------------AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC Template switch alignment (log-probability: -17.6) AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCT|ACAAAGTACAAGCCA|AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC AGCAAGATAATGAATTAAATAAAATTATTTTTCATTCTCT|ACAAAGTACAAGCCA|AAATAACTAATTATGGCTTGTACTTTGTAACATCTGTATC ========== Event 1981 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCTCTCTTAGAATAACAATCTAGACTAGTCTCTAGTCTCTAGACTAGAGACTTTGAATCGTAACCATATT Chimp: TTCTCTCATAGAATAACAATCTAGACTAGTCTCTAGTCTCTAGACTAGAGACTTTGAATCGTAACCATATT ↑ 4 3 1 2 Gorilla: TTCTCTCATAGAATAACAATCTAG-------------------ACTAGAGACTTTGAATCGTAACCATATC Human: TTCTCTCTTAGAATAACAATCTAGACTAGTCTCTAGTCTCTAGACTAGAGACTTTGAATCGTAACCATATT Cluster: [ ] Orangutan: TTCTCTCACAGAATAACAATCTAG-------------------ACCAGAGACTTTGAATCGTAACCATATC Gorilla > Chimp --------------- chr2B:44504536-44504544 Template switch process: F1: L TTCTAAGGATTCCTCATTTCTCTCATAGAATAACAATCTAGACTAG 1 F3: 4 TCTAGACTAGAGACTTTGAATCGTAACCATATTGCCATTCTTATA R RF: TTCTAAGGATTCCTCATTTCTCTCATAGAATAACAATCTAGACTAGAGACTTTGAATCGTAACCATATCGCCATTCTTATA RR: AAGATTCCTAAGGAGTAAAGAGAGTATCTTATTGTTAGATCTGATCTCTGAAACTTAGCATTGGTATAGCGGTAAGAATAT F2: 3 CTGATCTCT 2 Unidirectional alignment (log-probability: -43.7) GGATTCCTCATTTCTCTCATAGAATAACAATCTagactagtctctagtctctAGACTAGAGACTTTGAATCGTAACCATATtGCCATTC GGATTCCTCATTTCTCTCATAGAATAACAATCT-------------------AGACTAGAGACTTTGAATCGTAACCATATCGCCATTC Template switch alignment (log-probability: -22.6) GGATTCCTCATTTCTCTCATAGAATAACAATCTAGACTAG|TCTCTAGTC|TCTAGACTAGAGACTTTGAATCGTAACCATATtGCCATTC GGATTCCTCATTTCTCTCATAGAATAACAATCTAGACTAG|TCTCTAGTC|TCTAGACTAGAGACTTTGAATCGTAACCATATCGCCATTC ========== Event 1982 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCATCTGTGTCCCTTCCCTTAAATTTTGC ↓ 3 2 1 4 Chimp: AGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCTAGCTAGTCCCTTCCCTTAAATTTTGC ↑ 3 2 1 4 Gorilla: AGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCATCTGTGTCCCTTCCCTTAAATTTTGC Human: AGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCATCTGTGTCCCTTCCCTTAAATTTTGC Cluster: [ ] Orangutan: AGCTACAGTTGCCCCTTACTAGCTAGCACTGAGCATCTGTGTCCCTTCCCTTAAATTTTGC Human > Chimp ------------- chr2B:42162767-42162772 Template switch process: F1: L GCTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC 1 F3: 4 GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG R RF: GCTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCATCTGTGTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG RR: CGACCGTTCGATGTCAACGGGGCATGATCGATCGTGACTCGTAGACACAGGGAAGGGAATTTAAAACGGGTGATCAACGTTCCGTCC F2: 3 ATCGAT 2 Unidirectional alignment (log-probability: -28.6) CTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCtagctA-----GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG CTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC-----ATCTGTGTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG Template switch alignment (log-probability: -16) CTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC|TAGCTA|GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG CTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC|TAGCTA|GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG Gorilla > Chimp --------------- chr2B:42162767-42162772 Template switch process: F1: L GCTGGCAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC 1 F3: 4 GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG R RF: GCTGGGAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCATCTGTGTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG RR: CGACCCTTCGATGTCAACGGGGCATGATCGATCGTGACTCGTAGACACAGGGAAGGGAATTTAAAACGGGTGATCAACGTTCCGTCC F2: 3 ATCGAT 2 Unidirectional alignment (log-probability: -33.6) CTGGcAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC-----TagctaGTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG CTGGGAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGCATCTGT-----GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG Template switch alignment (log-probability: -22) CTGGcAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC|TAGCTA|GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG CTGGGAAGCTACAGTTGCCCCGTACTAGCTAGCACTGAGC|TAGCTA|GTCCCTTCCCTTAAATTTTGCCCACTAGTTGCAAGGCAGG ========== Event 1983 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCAGAATGGTTTGGAACAAGACCAAT--------AGCTAGCCAGTAAAATCATCTAAATGTGA Chimp: GCAGAATGGTTTGGAACAAGATGGCTAGCTATTGAGCTAGCCAGTAAAATCGTCTAAATGTGA ↑ 1 3 4 2 Gorilla: GCAGAATGGTTTGGAACAAGACCAAT--------AGCTAGCCAGTAAAATCATCTAAATGTGA Human: GCAGAATGGTTTGGAACAAGACCAAT--------AGCTAGCCAGTAAAATCATCTAAATGTGA Cluster: [ ] Orangutan: GCAGAATGGTTTGGAACAAGACCAAT--------AGCGAGCCAGTAAAATCATCTAAATGTGA Gorilla > Chimp --------------- chr2B:41807416-41807428 Template switch process: F1: L TGTTGAGAAAGATTATCTTGGCAGAATGGTTTGGAACAAGA 1 F3: 4 AGCTAGCCAGTAAAATCGTCTAAATGTGAAGTTACAGGAG R RF: TGTTGAGAAAGATTATCTTGGCAGAATGGTTTGGAACAAGACCAATAGCTAGCCAGTAAAATCATCTAAATGTGAAGTTACAGGAG RR: ACAACTCTTTCTAATAGAACCGTCTTACCAAACCTTGTTCTGGTTATCGATCGGTCATTTTAGTAGATTTACACTTCAATGTCCTC F2: 3 GTTATCGATCGGT 2 Unidirectional alignment (log-probability: -43.6) GTTGAGAAAGATTATCTTGGCAGAATGGTTTGGAACAAG----ATggctagctattgAGCTAGCCAGTAAAATCgTCTAAATGTGAAGTTACAGGAG GTTGAGAAAGATTATCTTGGCAGAATGGTTTGGAACAAGACCAAT------------AGCTAGCCAGTAAAATCATCTAAATGTGAAGTTACAGGAG Template switch alignment (log-probability: -22.9) GTTGAGAAAGATTATCTTGGCAGAATGGTTTGGAACAAGA|TGGCTAGCTATTG|AGCTAGCCAGTAAAATCgTCTAAATGTGAAGTTACAGGAG GTTGAGAAAGATTATCTTGGCAGAATGGTTTGGAACAAGA|TGGCTAGCTATTG|AGCTAGCCAGTAAAATCATCTAAATGTGAAGTTACAGGAG ========== Event 1984 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCTAATAATTCCTTGTCATTGTCTAAGCAGCATTTGCTGG----GTGTGTGACTTTGAACCAGTTA Chimp: CCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCTGG----GTGTGTGACTTTGAACCAATTA ↓ 3 2 1 4 Gorilla: CCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCTTAGACAATGTGTGACTTTGAACCAGTTA ↑ 3 2 1 4 Human: CCCTAATAATTCCTTGTCATTGTCTAAGCAGCATTTGCTGG----GTGTGTGACTTTGAACCAGTTA Cluster: [ ] Orangutan: CCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCTGG----GTGTGTGACTTTGGACCAGTTA Human > Gorilla --------------- chr2B:43973481-43973487 Template switch process: F1: L TATTCTCACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCT 1 F3: 4 TGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC R RF: TATTCTCACCCTAATAATTCCTTGTCATTGTCTAAGCAGCATTTGCTGGGTGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC RR: ATAAGAGTGGGATTATTAAGGAACAGTAACAGATTCGTCGTAAACGACCCACACACTGAAACTTGGTCAATCACACTTCGTCAGGGGTTG F2: 3 AACAGAT 2 Unidirectional alignment (log-probability: -33.3) ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCAcTTGCTtaGacaaTGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCATTTGCTGGG----TGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC Template switch alignment (log-probability: -22.3) ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCAcTTGCT|TAGACAA|TGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCATTTGCT|TAGACAA|TGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC Chimp > Gorilla --------------- chr2B:43973481-43973487 Template switch process: F1: L CACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCT 1 F3: 4 TGTGTGACTTTGAACCAGTTAGTGTGAAGCAGTCCCCAAC R RF: CACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCTGGGTGTGTGACTTTGAACCAATTAGTGTGAAGCAGTCCCCAAC RR: GTGGGATTATTAAGGAACAGTAACAGATTCGTCGTGAACGACCCACACACTGAAACTTGGTTAATCACACTTCGTCAGGGGTTG F2: 3 AACAGAT 2 Unidirectional alignment (log-probability: -33.2) ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCTtaGacaaTGTGTGACTTTGAACCAgTTAGTGTGAAGCAGTCCCCAAC ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCTGGG----TGTGTGACTTTGAACCAATTAGTGTGAAGCAGTCCCCAAC Template switch alignment (log-probability: -22.1) ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCT|TAGACAA|TGTGTGACTTTGAACCAgTTAGTGTGAAGCAGTCCCCAAC ACCCTAATAATTCCTTGTCATTGTCTAAGCAGCACTTGCT|TAGACAA|TGTGTGACTTTGAACCAATTAGTGTGAAGCAGTCCCCAAC ========== Event 1985 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AGTTAAGCCTTCGTGCAGTAGAG------------------------------------------GCTGTATTATAAGAGCCTCTCTTTGTGGAATGGATTAACTTGATTCACCTGCAATTTGGGCAGCCTCATTCTGCACCCCTCCAAAAAGCAATGGCTGAATGAAAAATCTCCTCCTTCGGCCTGGGGAAATTTGCTTTCCCAG ↑ 1 4 3 2 Chimp: AGTTAAGCCTTCGTGCAGTAGGG---------------------AAAGAGTTAACAGATTCCATTCCTCTATTATAAGAGCCTCTCTTTGTGGAATGGATGAACTTGATTCACCTGCAATTTGGGCAGCCTCATTCTGCACCCCACCAAAAAGCAATGGCTGAATGAAAAATCT---CCTTCAGCCTGGGGAAATTTGCTTTCCCAG Gorilla: Human: AGTTAAGCCTTCGTGCAGTAGAG------------------------------------------GCTGTATTATAAGAGCCTCTCTTTGTGGAATGGATTAACTTGATTCACCTGCAATTTGGGCAGCCTCATTCTGCACCCCTCCAAAAAGCAATGGCTGAATGAAAAATCTCCTCCTTCGGCCTGGGGAAATTTGCTTTCCCAG Cluster: [ ] Orangutan: AGTTAAGCCTTCATGCAGTAGGGAAAGAGTTAACAGATTCAATT---------------------CATCTATTATAAGAGCCTCTCTTTGTGGAATGGATGAACTTGATTCACCTGCAGTTTGGACAGCCTCATTCCACACCCCTCCAAAAAGCAATGGCTGAATGAAAGATCT---TCTTCAGCCTGGGGAAATTTGCTTTCCCAG Chimp > Human ------------- chr2:19726414-19726419 Template switch process: F1: L GTTGTTGACACTTTAAAGGGAGTTAAGCCTTCGTGCAGTAG 1 F3: 4 TATTATAAGAGCCTCTCTTTGTGGAATGGATTAACTTGAT R RF: GTTGTTGACACTTTAAAGGGAGTTAAGCCTTCGTGCAGTAGGGAAAGAGTTAACAGATTCCATTCCTCTATTATAAGAGCCTCTCTTTGTGGAATGGATGAACTTGATTCACCTGCAATTTGGGCAGCCTCATTCTGCACCCCACCAAAAAGCAATGGCTGAATGAAAAATCTCCTTCAGCCT RR: CAACAACTGTGAAATTTCCCTCAATTCGGAAGCACGTCATCCCTTTCTCAATTGTCTAAGGTAAGGAGATAATATTCTCGGAGAGAAACACCTTACCTACTTGAACTAAGTGGACGTTAAACCCGTCGGAGTAAGACGTGGGGTGGTTTTTCGTTACCGACTTACTTTTTAGAGGAAGTCGGA F2: 3 GTCGGA 2 Unidirectional alignment (log-probability: -35.7) TTGTTGACACTTTAAAGGGAGTTAAGCCTTCGTGCAGTAGaggctG--------------------------TATTATAAGAGCCTCTCTTTGTGGAATGGATtAACTTGAT TTGTTGACACTTTAAAGGGAGTTAAGCCTTCGTGCAGTAG-----GGAAAGAGTTAACAGATTCCATTCCTCTATTATAAGAGCCTCTCTTTGTGGAATGGATGAACTTGAT Template switch alignment (log-probability: -22) TTGTTGACACTTTAAAGGGAGTTAAGCCTTCGTGCAGTAG|AGGCTG|TATTATAAGAGCCTCTCTTTGTGGAATGGATtAACTTGAT TTGTTGACACTTTAAAGGGAGTTAAGCCTTCGTGCAGTAG|AGGCTG|TATTATAAGAGCCTCTCTTTGTGGAATGGATGAACTTGAT ========== Event 1986 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCTGCCTCTGAGACTTGTTAC-----------GGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGAGATCTACCTTAGCAGGAGGGTGCCACAGCAGGA Chimp: GCCTGCCTCTGAGACTTGTTAC-----------AGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGAGATCTACCTTAGCAGGAGGGTGCCACAGCAGGA Gorilla: GCCTGCCTCTGAGACTTGTTAAGGGTTCGCTAAGGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGAGATCTACCTTAGCAGGAGGGTGCCACAGCAGGA ↑ 4 1 3 2 Human: GCCTGCCTCTGAGACTTGTTAC-----------GGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGAGATCTACCTTAGCAGGAGGGTGCCACAGCAGGA Cluster: [ ] Orangutan: GCCTGCATCTGAGACTTGTTAT-----------GGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGAGATCTACCTTAGCAGGACGGTGCCACAGCAGGA Human > Gorilla --------------- chr2B:96728153-96728157 Template switch process: F1: L CTGGCCTAGTTCCTCCTACGGCCTGCCTCTGAGACTTGTTAAGGGTTC 1 F3: 4 GGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGA R RF: CTGGCCTAGCTCCTCCTACGGCCTGCCTCTGAGACTTGTTACGGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGAGATCTACCTTAGC RR: GACCGGATCGAGGAGGATGCCGGACGGAGACTCTGAACAATGCCCAAGTCCGAGGTAAGTCCGTCCGCAGTGACACGTGTCTCTAGATGGAATCG F2: 3 AATCG 2 Unidirectional alignment (log-probability: -37.8) GtTCCTCCTACGGCCTGCCTCTGAGACTTGTtaagggttcgcTAaGGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGA GCTCCTCCTACGGCCTGCCTCTGAGACTTGT-----------TACGGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGA Template switch alignment (log-probability: -27.6) GtTCCTCCTACGGCCTGCCTCTGAGACTTGTTAaGGGTTC|GCTAA|GGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGA GCTCCTCCTACGGCCTGCCTCTGAGACTTGTTACGGGTTC|GCTAA|GGGTTCAGGCTCCATTCAGGCAGGCGTCACTGTGCACAGA ========== Event 1987 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GTTGGATCATGCTAATATACATGTATGCATGTATATGCTTGTATGCATAAATGTGAATACATACATGTGGACACCCTGAACATGGCACTAGCAGAGCTCATGACAAGGAATCATAAGCATATACCTCGCCTGCCTGCTCTATTC ↑ 4 1 3 2 Chimp: GTTGGATCATGCTAATATACACGTA------------------TGCATAAATGTGAATGCATACATGTGGACACCCTGAACATGGCACTAGTAGAGCTCATGACAAGGAATCATAAGCATATACCTTGCCTACCTGCTCTATTC Gorilla: Human: GTTGGATCATGCTAATATACATGTATGCATGTATATGCTTGTATGCATAAATGTGAATACATACATGTGGACACCCTGAACATGGCACTAGCAGAGCTCATGACAAGGAATCATAAGCATATACCTCGCCTGCCTGCTCTATTC Cluster: [ ] Orangutan: GTTGGATCATGCTAATATACATGTATGCATGTATATGCTTGTATGCATAAATGTGAATACATACATGTGGACACCCTGAACATGGCACTAGCAGAGCTCATGACAAGGAATCATAAGCATATACCTCGCGTGCCTGCTCTATTC Chimp > Human ------------- chr2:204303105-204303114 Template switch process: F1: L TCATGATTTTAGCACAATAGGTTGGATCATGCTAATATACATGTATGCAT 1 F3: 4 GTATGCATAAATGTGAATACATACATGTGGACACCCTGAACAT R RF: TCATGATTTTAGCACAATAGGTTGGATCATGCTAATATACACGTATGCATAAATGTGAATGCATACATGTGGACACCCTGAACATGGCACTAGTAGAGCTCATGACAAGGAATCATAAGCATATAC RR: AGTACTAAAATCGTGTTATCCAACCTAGTACGATTATATGTGCATACGTATTTACACTTACGTATGTACACCTGTGGGACTTGTACCGTGATCATCTCGAGTACTGTTCCTTAGTATTCGTATATG F2: 3 TTCGTATATG 2 Unidirectional alignment (log-probability: -48.8) AGCACAATAGGTTGGATCATGCTAATATACAtGTATGCatgtatatgcttgtatgcATAAATGTGAATaCATACATGTGGACACCCTGAA AGCACAATAGGTTGGATCATGCTAATATACACGTATGC------------------ATAAATGTGAATGCATACATGTGGACACCCTGAA Template switch alignment (log-probability: -28.7) AGCACAATAGGTTGGATCATGCTAATATACAtGTATGCAT|GTATATGCTT|GTATGCATAAATGTGAATaCATACATGTGGACACCCTGAA AGCACAATAGGTTGGATCATGCTAATATACACGTATGCAT|GTATATGCTT|GTATGCATAAATGTGAATGCATACATGTGGACACCCTGAA ========== Event 1988 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCCCTATAGCTATTTGGGTTTATTCACATGGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTT Chimp: CCCCTATAGCTATTTGGGTTTATTCACATGGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTT ↑ 1 4 3 2 Gorilla: CCCCTATAGCTATTTGGGTTT------GCAGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTT ↓ 1 4 3 2 Human: CCCCTATAGCTATTTGGGTTTATTCACATGGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTT Cluster: [ ] Orangutan: CCCCTATAGCTATTTGGGTTT------GCAGTCCCTGACCCTTGTGAATAATTCTTGCTCTCTAGATTT Gorilla > Human --------------- chr2:36599027-36599035 Template switch process: F1: L TCACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT 1 F3: 4 GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC R RF: TCACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTTGCAGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC RR: AGTGACTGTAAAGGGTACACGGGGATATCGATAAACCCAAACGTCAGGGACTGGGTACACTTATTTAGAACGAGAGATCTAAAG F2: 3 GTACACTTA 2 Unidirectional alignment (log-probability: -32.2) CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT--AttcacatgGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTTGCA--------GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC Template switch alignment (log-probability: -16.9) CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT|ATTCACATG|GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT|ATTCACATG|GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC Gorilla > Chimp --------------- chr2B:36933123-36933131 Template switch process: F1: L TCACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT 1 F3: 4 GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC R RF: TCACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTTGCAGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC RR: AGTGACTGTAAAGGGTACACGGGGATATCGATAAACCCAAACGTCAGGGACTGGGTACACTTATTTAGAACGAGAGATCTAAAG F2: 3 GTACACTTA 2 Unidirectional alignment (log-probability: -32.2) CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT--AttcacatgGTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTTGCA--------GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC Template switch alignment (log-probability: -16.9) CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT|ATTCACATG|GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC CACTGACATTTCCCATGTGCCCCTATAGCTATTTGGGTTT|ATTCACATG|GTCCCTGACCCATGTGAATAAATCTTGCTCTCTAGATTTC ========== Event 1989 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCAGATGTATCTGCTTCTAGTTGTTAA----CGTTTTAAAATGTAATTTAatg ↑ 3 1 2 4 Chimp: CCCAGATGTATCTGCTTCTAG---TTAA--CAAGTTTTAAAATGTAATTTAATG Gorilla: TCCAGATGTATCTGCTTCTAGTTGTTAACA--AGTTTTAAAATGTAATTTAATG Human: CCCAGATGTATCTGCTTCTAGTTGTTAA----CGTTTTAAAATGTAATTTAatg Cluster: [ ] Orangutan: CCCAGATGTATCTGCTTCTAGTTGTT---A--AGTTTTAAAATGTAATTTAatg Chimp > Human ------------- chr2:37066640-37066645 Template switch process: F1: L AAACCTCTCATAACCAATATCCCAGATGTATCTGCTTCTAGTT 1 F3: 4 GTTTTAAAATGTAATTTAATGATACTGCACAAATAATTTT R RF: AAACCTCTCATAACCGATATCCCAGATGTATCTGCTTCTAGTTAACAAGTTTTAAAATGTAATTTAATGATACTGCACAAATAATTTT RR: TTTGGAGAGTATTGGCTATAGGGTCTACATAGACGAAGATCAATTGTTCAAAATTTTACATTAAATTACTATGACGTGTTTATTAAAA F2: 3 CAATTG 2 Unidirectional alignment (log-probability: -31.6) CCTCTCATAACCaATATCCCAGATGTATCTGCTTCTAgttGTTAAC--GTTTTAAAATGTAATTTAATGATACTGCACAAATAATTTT CCTCTCATAACCGATATCCCAGATGTATCTGCTTCTA---GTTAACAAGTTTTAAAATGTAATTTAATGATACTGCACAAATAATTTT Template switch alignment (log-probability: -22.1) CCTCTCATAACCaATATCCCAGATGTATCTGCTTCTAGTT|GTTAAC|GTTTTAAAATGTAATTTAATGATACTGCACAAATAATTTT CCTCTCATAACCGATATCCCAGATGTATCTGCTTCTAGTT|GTTAAC|GTTTTAAAATGTAATTTAATGATACTGCACAAATAATTTT ========== Event 1990 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCAGATTCAGTTCCAATCAAG--------AGATTAGAGAGGAG-CTGCAGTCAAAGCCTGGCAATTAGCA Chimp: TCCAGATTCAGTTCCAATCAAG--------AGATTAGAGAGGAG-CTGCAGTCAAAGCCTGGCAATTAGCA Gorilla: TCCAGATTCAGTTCCAATCAAT----------------CTGCAGCTTGCAGTCAAAGCCTGGCAATTAGCA ↑ 1 3 4 2 Human: TCCAGATTCAGTTCCAATCAAG--------AGATTAGAGAGGAG-CTGCAGTCAAAGCCTGGCAATTAGCA Cluster: [ ] Orangutan: TCCAGGTTCAGTTCCAATCAAGAGATTAGA--------GAGGAG-CTGCAGTCAAAGCCTGGCAATTAGCA Human > Gorilla --------------- chr2B:38064812-38064819 Template switch process: F1: L GAAGGGCTGGCGAATGAGCTTCCAGATTCAGTTCCAATCAAT 1 F3: 4 TGCAGTCAAAGCCTGGCAATTAGCATGTTTGAAGCTGTGG R RF: GAAGGGCTGGCTAATGAGCTTCCAGATTCAGTTCCAATCAAGAGATTAGAGAGGAGCTGCAGTCAAAGCCTGGCAATTAGCATGTTTGAAGCTGTGG RR: CTTCCCGACCGATTACTCGAAGGTCTAAGTCAAGGTTAGTTCTCTAATCTCTCCTCGACGTCAGTTTCGGACCGTTAATCGTACAAACTTCGACACC F2: 3 TCGACGTC 2 Unidirectional alignment (log-probability: -39.9) AGGGCTGGCgAATGAGCTTCCAGATTCAGTTCCAATCAA----------------tctgcagctTGCAGTCAAAGCCTGGCAATTAGCATGTTTGAAGCTGTGG AGGGCTGGCTAATGAGCTTCCAGATTCAGTTCCAATCAAGAGATTAGAGAGGAGC---------TGCAGTCAAAGCCTGGCAATTAGCATGTTTGAAGCTGTGG Template switch alignment (log-probability: -27.8) AGGGCTGGCgAATGAGCTTCCAGATTCAGTTCCAATCAAt|CTGCAGCT|TGCAGTCAAAGCCTGGCAATTAGCATGTTTGAAGCTGTGG AGGGCTGGCTAATGAGCTTCCAGATTCAGTTCCAATCAAG|CTGCAGCT|TGCAGTCAAAGCCTGGCAATTAGCATGTTTGAAGCTGTGG ========== Event 1991 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAACATAGGAAAGGTGAGGAG-GATTTGTGCAGGCACACAGTCCAGCACCCACAGTTACCTCTGGAGACCTACTTACC ↓ 1 3 4 2 Chimp: GAACATAGGAAAGGTGAGGAGGTAACTGTG----------------------GAGTTACCTCTGGAGACCTACTTACC Gorilla: GAACATAGGATAGGTGAGGAG-GATTTGTGCAGGCACACAGTCCAGCACCCACAGTTACCTCTGGAGACCTACTTACC Human: GAACATAGGAAAGGTGAGGAG-GATTTGTGCAGGCACACAGTCCAGCACCCACAGTTACCTCTGGAGACCTACTTACC Cluster: [ ] Orangutan: GAACATAGGAAAGGTGAGGAG-GATTTGTGCAGGCACACAGTCCAGCACCCACAGTTACCTCTGGAAACCTACTTACC Human > Chimp ------------- chr2A:21144686-21144694 Template switch process: F1: L CAACTGAACAAGAGACAAAAGAACATAGGAAAGGTGAGGAGG 1 F3: 4 AGTTACCTCTGGAGACCTACTTACCGGGAGCTCAGGTACT R RF: CAACTGAACAAGAGACAAAAGAACATAGGAAAGGTGAGGAGGATTTGTGCAGGCACACAGTCCAGCACCCACAGTTACCTCTGGAGACCTACTTACCGGGAGCTCAGGGACT RR: GTTGACTTGTTCTCTGTTTTCTTGTATCCTTTCCACTCCTCCTAAACACGTCCGTGTGTCAGGTCGTGGGTGTCAATGGAGACCTCTGGATGAATGGCCCTCGAGTCCCTGA F2: 3 GGTGTCAAT 2 Unidirectional alignment (log-probability: -41.6) ACTGAACAAGAGACAAAAGAACATAGGAAAGGTGAGGAGG------------------------------taactgtggAGTTACCTCTGGAGACCTACTTACCGGGAGCTCAGGtACT ACTGAACAAGAGACAAAAGAACATAGGAAAGGTGAGGAGGATTTGTGCAGGCACACAGTCCAGCACCCAC---------AGTTACCTCTGGAGACCTACTTACCGGGAGCTCAGGGACT Template switch alignment (log-probability: -22.4) ACTGAACAAGAGACAAAAGAACATAGGAAAGGTGAGGAGG|TAACTGTGG|AGTTACCTCTGGAGACCTACTTACCGGGAGCTCAGGtACT ACTGAACAAGAGACAAAAGAACATAGGAAAGGTGAGGAGG|TAACTGTGG|AGTTACCTCTGGAGACCTACTTACCGGGAGCTCAGGGACT ========== Event 1992 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAAGGTGATGCATAAATAGTTTTCTAAAGTA----------------GAACTGCAAGGTGGCAAGCCAAGTT Chimp: GGAAGGTGATGCATAAATAGTTTTCTAAAGTAGAACTTTAGAAAACTAGAACTGCAAGGTGGCAAGCCAAGTT ↑ 3 2 4 1 Gorilla: GGAAGGTGATGCATAAATAGTTTTCTAAAGTA----------------GAACTGCAAGGTGGCAAGCCAAGTT Human: GGAAGGTGATGCATAAATAGTTTTCTAAAGTA----------------GAACTGCAAGGTGGCAAGCCAAGTT Cluster: [ ] Orangutan: GGAAGGTGATGCATAAATAGTTTTCTAAAGTA----------------GAACTGCAAGGTGGCAAGCCAAGTT Gorilla > Chimp --------------- chr2A:21094892-21094900 Template switch process: F1: L TCATAAAATGGAAGGTGATGCATAAATAGTTTTCTAAAGTAGAACT 1 F3: 4 TAGAACTGCAAGGTGGCAAGCCAAGTTGTGCTGCTGTTTTGG R RF: TCATAAAATGGAAGGTGATGCATAAATAGTTTTCTAAAGTAGAACTGCAAGGTGGCAAGCCAAGTTGTGCTGCTGTTTTGG RR: AGTATTTTACCTTCCACTACGTATTTATCAAAAGATTTCATCTTGACGTTCCACCGTTCGGTTCAACACGACGACAAAACC F2: 3 CAAAAGATT 2 Unidirectional alignment (log-probability: -33.9) AATGGAAGGTGATGCATAAATAGTTTTCTAAAGtagaactttagaaaacTAGAACTGCAAGGTGGCAAGCCAAGTTGTGCTGCTGTTTT AATGGAAGGTGATGCATAAATAGTTTTCTAAAG----------------TAGAACTGCAAGGTGGCAAGCCAAGTTGTGCTGCTGTTTT Template switch alignment (log-probability: -17) AATGGAAGGTGATGCATAAATAGTTTTCTAAAGTAGAACT|TTAGAAAAC|TAGAACTGCAAGGTGGCAAGCCAAGTTGTGCTGCTGTTTT AATGGAAGGTGATGCATAAATAGTTTTCTAAAGTAGAACT|TTAGAAAAC|TAGAACTGCAAGGTGGCAAGCCAAGTTGTGCTGCTGTTTT ========== Event 1993 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAGTACAATTTAGTAACATG-------------TTCCAGGTGAATGTTCAAGTATTAATGAATACAAGTTTGAAGTTTCACCTGGAATTGCTAAGAATCACAAA Chimp: GAAGTACAATTTAGTAACATG-------------TTCCAGGTGAATGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCATCTGGAATTGCTAAGAATCACAAA ↑ 4 1 3 2 Gorilla: GAAGTACAATTTAGTAACATG--------------------------TTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTGGAATTGCTAAGAATCACAAA ↓ 4 1 3 2 Human: GAAGTACAATTTAGTAACATG-------------TTCCAGGTGAATGTTCAAGTATTAATGAATACAAGTTTGAAGTTTCACCTGGAATTGCTAAGAATCACAAA Cluster: [ ] Orangutan: GAAGTACAATTTAGTAACACGTTCCAGGTGAATG-------------TTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTGGAATTGCTAAGAATCACAAA Gorilla > Human --------------- chr2:34660517-34660524 Template switch process: F1: L TCCATGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTC 1 F3: 4 TGTTCAAGTATTAATGAATACAAGTTTGAAGTTTCACCTGGA R RF: CCCATGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTGGA RR: GGGTACCGACCTTGTCACGTCTTCATGTTAAATCATTGTACAAGTTCATAATTACTTATATTCAAACTTCAAAGTGGACCT F2: 3 AAGTGGAC 2 Unidirectional alignment (log-probability: -40.6) TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACatgttccaggtgaATGTTCAAGTATTAATGAATAcAAGTTTGAAGTTTCACCTG TGGCTGGAACAGTGCAGAAGTACAATTTAGTAAC-------------ATGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTG Template switch alignment (log-probability: -27.9) TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTC|CAGGTGAA|TGTTCAAGTATTAATGAATAcAAGTTTGAAGTTTCACCTG TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTC|CAGGTGAA|TGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTG Gorilla > Chimp --------------- chr2B:34948273-34948280 Template switch process: F1: L CCCATGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTC 1 F3: 4 TGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCATCTGGA R RF: CCCATGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTGGA RR: GGGTACCGACCTTGTCACGTCTTCATGTTAAATCATTGTACAAGTTCATAATTACTTATATTCAAACTTCAAAGTGGACCT F2: 3 AAGTGGAC 2 Unidirectional alignment (log-probability: -35.1) TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACAtgttccaggtgaaTGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCAtCTG TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACA-------------TGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTG Template switch alignment (log-probability: -22.4) TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTC|CAGGTGAA|TGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCAtCTG TGGCTGGAACAGTGCAGAAGTACAATTTAGTAACATGTTC|CAGGTGAA|TGTTCAAGTATTAATGAATATAAGTTTGAAGTTTCACCTG ========== Event 1994 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCTAACATAGGCCTGCATGTCAGCCCAG-----TCTTCTGGGCTGAGCTGCTGCACTGTTGCTGGCC Chimp: TCTAACATAGGCCTGCATGTCAGCCCAG-----TCTTCTGGGCTGAGCTGCTGCACTGTTGCTGGCC ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: TCTAACATAGGCCTGCATGTCAGCCCAG----------AAGACTGGGCTGCTGCACTGTTGCTGGCC ↓ 3 1 2 4 ↑ 3 1 2 4 Human: TCTAACATAGGCCTGCATGTCAGCCCAG-----TCTTCTGGGCTGAGCTGCTGCACTGTTGCTGGCC Cluster: [ ] Orangutan: TCTAACATAGGCCTGCATGTCAGCCCACTCTTC-----TGGGCTGAGCTGCTGCACTGTTGCTGGCC Gorilla > Human --------------- chr2:34954887-34954899 Template switch process: F1: L TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG 1 F3: 4 GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC R RF: TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAGAAGACTGGGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC RR: AAGGGTTCTCTGCAGATTGTATCCGGACGTACAGTCGGGTCTTCTGACCCGACGACGTGACAACGACCGGAACTACCGACTTGGACTAG F2: 3 AGTCGGGTCTTCT 2 Unidirectional alignment (log-probability: -38.3) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAgtcttctgggctGA-------GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCA------------GAAGACTGGGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Template switch alignment (log-probability: -17.4) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|TCTTCTGGGCTGA|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|TCTTCTGGGCTGA|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Human > Gorilla --------------- chr2B:35274797-35274804 Template switch process: F1: L TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG 1 F3: 4 GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC R RF: TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAGTCTTCTGGGCTGAGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC RR: AAGGGTTCTCTGCAGATTGTATCCGGACGTACAGTCGGGTCAGAAGACCCGACTCGACGACGTGACAACGACCGGAACTACCGACTTGGACTAG F2: 3 GGTCAGAA 2 Unidirectional alignment (log-probability: -31.3) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCA------------GAagactggGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAGTCTTCTGGGCTGA-------GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Template switch alignment (log-probability: -16.7) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|AAGACTGG|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|AAGACTGG|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Gorilla > Chimp --------------- chr2B:35249972-35249984 Template switch process: F1: L TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG 1 F3: 4 GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC R RF: TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAGAAGACTGGGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC RR: AAGGGTTCTCTGCAGATTGTATCCGGACGTACAGTCGGGTCTTCTGACCCGACGACGTGACAACGACCGGAACTACCGACTTGGACTAG F2: 3 AGTCGGGTCTTCT 2 Unidirectional alignment (log-probability: -38.3) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAgtcttctgggctGA-------GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCA------------GAAGACTGGGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Template switch alignment (log-probability: -17.4) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|TCTTCTGGGCTGA|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|TCTTCTGGGCTGA|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Chimp > Gorilla --------------- chr2B:35274797-35274804 Template switch process: F1: L TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG 1 F3: 4 GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC R RF: TTCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAGTCTTCTGGGCTGAGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC RR: AAGGGTTCTCTGCAGATTGTATCCGGACGTACAGTCGGGTCAGAAGACCCGACTCGACGACGTGACAACGACCGGAACTACCGACTTGGACTAG F2: 3 GGTCAGAA 2 Unidirectional alignment (log-probability: -31.3) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCA------------GAagactggGCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAGTCTTCTGGGCTGA-------GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC Template switch alignment (log-probability: -16.7) TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|AAGACTGG|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC TCCCAAGAGACGTCTAACATAGGCCTGCATGTCAGCCCAG|AAGACTGG|GCTGCTGCACTGTTGCTGGCCTTGATGGCTGAACCTGATC ========== Event 1995 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ccCCAAATCCTCCAACAGCTCCAACAGGCATTATCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGGGTCTG ↑ 4 1 3 2 Chimp: ccCCAAATCCTCCAACAGCTC------CCCATCTCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGGGTCTG Gorilla: ccCCAAATCCTCCAACAGCTC------CCCATCTCAAAATATAAGTTTTTATAATGCCTGAAGTGCCCATAGGGTCTG Human: ccCCAAATCCTCCAACAGCTCCAACAGGCATTATCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGGGTCTG Cluster: [ ] Orangutan: ccCCAAATCCTCCAACAGCTC------CCCATCTCAAAACATAAGTTTTTATAATGCCTGAAGTGCCTATAGGGTCTg Chimp > Human ------------- chr2:33757163-33757169 Template switch process: F1: L CTTTATTTTTGACACAATAGCCCCAAATCCTCCAACAGCTCC---------AACA 1 F3: 4 TCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGG R RF: CTTTATTTTTGACACAATAGCCCCAAATCCTCCAACAGCTCCCCATCTCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGG RR: GAAATAAAAACTGTGTTATCGGGGTTTAGGAGGTTGTCGAGGGGTAGAGTTTTGTATTCAAAAATATTACGGACTTCACGGGTATCC F2: 3 ATTACGG 2 Unidirectional alignment (log-probability: -37.2) TTTTGACACAATAGCCCCAAATCCTCCAACAGCTC-----CaacaggcattaTCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGG TTTTGACACAATAGCCCCAAATCCTCCAACAGCTCCCCATC-----------TCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGG Template switch alignment (log-probability: -26.9) TTTTGACACAATAGCCCCAAATCCTCCAACAGCTCC---------AACA|GGCATTA|TCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGG TTTTGACACAATAGCCCCAAATCCTCCAACAGCTCCCCATCTCAAAACA|GGCATTA|TCAAAACATAAGTTTTTATAATGCCTGAAGTGCCCATAGG ========== Event 1996 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAATACAACTATGACAACAGTTACCATGGAAG------CTTCTTGGTAACTGCCTTCCTGAATAGTAACAT ↑ 3 2 1 4 Chimp: AAATACAACTATGACAACAGTTACCATGGAAG---CGGTTTCT-TTCGGCTGCCTTCCTGAATAGTAACAT Gorilla: AAATACAACTATGACAACAGTTACCATGGAAGCGG---TTTCT-TTCGGCTGCCTTCCTGAATAGTAACAT Human: AAATACAACTATGACAACAGTTACCATGGAAG------CTTCTTGGTAACTGCCTTCCTGAATAGTAACAT Cluster: [ ] Orangutan: AAATACAACTATGACAACAGTTACCATGGAAGCGG---TTTCT-TTCGGCTGCCTTCCTGAATAGTAACAT Chimp > Human ------------- chr2:35721701-35721706 Template switch process: F1: L GATGAGTAAAAATACAACTATGACAACAGTTACCATGGAAGC---TTCTT 1 F3: 4 TGCCTTCCTGAATAGTAACATTTAATGTGGTGCATTAAT R RF: GATGAGTAAAAATACAACTATGACAACAGTTACCATGGAAGCGGTTTCTTTCGGCTGCCTTCCTGAATAGTAACATTTAATGTGGTGCATTAAT RR: CTACTCATTTTTATGTTGATACTGTTGTCAATGGTACCTTCGCCAAAGAAAGCCGACGGAAGGACTTATCATTGTAAATTACACCACGTAATTA F2: 3 CAATGG 2 Unidirectional alignment (log-probability: -36) AAAAATACAACTATGACAACAGTTACCATGGAAGC---TTCTT--GGtaaCTGCCTTCCTGAATAGTAACATTTAATGTGGTGCATTAAT AAAAATACAACTATGACAACAGTTACCATGGAAGCGGTTTCTTTCGG---CTGCCTTCCTGAATAGTAACATTTAATGTGGTGCATTAAT Template switch alignment (log-probability: -26.5) AAAAATACAACTATGACAACAGTTACCATGGAAGC---TTCTT|GGTAAC|TGCCTTCCTGAATAGTAACATTTAATGTGGTGCATTAAT AAAAATACAACTATGACAACAGTTACCATGGAAGCGGTTTCTT|GGTAAC|TGCCTTCCTGAATAGTAACATTTAATGTGGTGCATTAAT ========== Event 1997 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAGCAAATCATTGATATCCCTGCAAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTA----TGTGTTCATGAAGAATCATTCTGATTGAATGaaaaaaaaaTAGCTTAACCATACACAGCTTGGAAATTTGGTAAA Chimp: AGAGCAAATCATTGATATCCCCGCAAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTA--TAGGTGTTCATGAAGAATCATTCTGATTGAATGaaaaaaaaaTAGCTTAACCATACACAGCTTGGAAATTTGGTAAA Gorilla: AGAGCAAATCATTGATATCCCCC-CAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTATA--GGTGTTCATGAAGAGTCATTCTGATTGAATGaaaaaaaaaTAGCATAACCATGCACAGCTTGGAAATTTGGTAAA ↓ 1 4 3 2 Human: AGAGCAAATCATTGATATCCCTGCAAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTA----TGTGTTCATGAAGAATCATTCTGATTGAATGaaaaaaaaaTAGCTTAACCATACACAGCTTGGAAATTTGGTAAA Cluster: [ ] Orangutan: AGAGCAAATCATTGATATCCCCTCAAATCCTAAGATTAAATAGGATTCCTTCCAGAAATTATA--GGTGTTCATGAAGAATCATTCTGGTTGAATTaaaaaaaaaCAGCTTAACCATACACAGCTTGGAAATTTGGTAAA Gorilla > Human --------------- chr2:209921235-209921238 Template switch process: F1: L TATTTGATCATAATATTTAAAGAGCAAATCATTGATATCCC 1 F3: 4 AATCCTGAGATGAAATAGGATTCCTTCCAGAAATTATG R RF: TATTTGATCATAATATTTAAAGAGCAAATCATTGATATCCCCCCAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTATAGGTGTTCATGAAGAGTCATTCTGATTGAATGAAAAAAAAATAGCATAACCATGCA RR: ATAAACTAGTATTATAAATTTCTCGTTTAGTAACTATAGGGGGGTTAGGACTCTACTTTATCCTAAGGAAGGTCTTTAATATCCACAAGTACTTCTCAGTAAGACTAACTTACTTTTTTTTTATCGTATTGGTACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -33.2) ATTTGATCATAATATTTAAAGAGCAAATCATTGATATCCCtgCaAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTAT--G ATTTGATCATAATATTTAAAGAGCAAATCATTGATATCCC-CCCAATCCTGAGATGAAATAGGATTCCTTCCAGAAATTATAGG Template switch alignment (log-probability: -21.7) ATTTGATCATAATATTTAAAGAGCAAATCATTGATATCCC|TGCA|AATCCTGAGATGAAATAGGATTCCTTCCAGAAATTATg ATTTGATCATAATATTTAAAGAGCAAATCATTGATATCCC|TGCA|AATCCTGAGATGAAATAGGATTCCTTCCAGAAATTATA ========== Event 1998 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTATAATAATACTCTTCCCCTTAGTGACAGCAATACCTATAGTCACTAAGCCTTAGTT-------TATTCTT-------TATTATTATTACATGAAATCTTATAACTATAATAATGCCCTCAGCATGTCAGAAATATATCAACTAACTAA ↑ 41 3 2 Chimp: GTTATAATAATACTCTTCCCC------TCAGCAATACCTATAGTCACTAAGCCTTAGTT--------------TATTCTTTATTATTATTACATGAAATCTTATAACTATAATAATGCCCTCAGCATGTCAGAAATATATCAATTAACTAA Gorilla: GTTATAATAATACTCTTCCTC------TCAGCAATACCTATAGTCACTAAGCCTTAATT---------------------TATTGTTATTACACGAAATCTTATAACTATAGTAATGCTCTCAGCATGTCAGAAATATATCAACTAACTAA Human: GTTATAATAATACTCTTCCCCTTAGTGACAGCAATACCTATAGTCACTAAGCCTTAGTT-------TATTCTT-------TATTATTATTACATGAAATCTTATAACTATAATAATGCCCTCAGCATGTCAGAAATATATCAACTAACTAA Cluster: [ ] Orangutan: GTTATAATAATACTCTTCCCC------TCAGCAATACCTATAGTCACTAAGCCTTAGTTTATTCTT--------------TATTATTATTATATAAAATCTTATAACTATAATAATGCCCTCAGCATGTTAGAAATATATCAACTAACTAA Chimp > Human ------------- chr2:211162289-211162292 Template switch process: F1: L TTAAAACACAGCTTCTTTGAGTTATAATAATACTCTTCCCCTTAG 1 F3: 4 AGCAATACCTATAGTCACTAAGCCTTAGTTTATTCTT R RF: TTAAAACACAGCTTCTTTGAGTTATAATAATACTCTTCCCCTCAGCAATACCTATAGTCACTAAGCCTTAGTTTATTCTTTATTATTATTACATGAAATCTTATAACTATAATAATGCCCTCAGCATGTCA RR: AATTTTGTGTCGAAGAAACTCAATATTATTATGAGAAGGGGAGTCGTTATGGATATCAGTGATTCGGAATCAAATAAGAAATAATAATAATGTACTTTAGAATATTGATATTATTACGGGAGTCGTACAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -33.9) ACACAGCTTCTTTGAGTTATAATAATACTCTTCCCCTtagtgaCAGCAATACCTATAGTCACTAAGCCTTAGTTTAttctt ACACAGCTTCTTTGAGTTATAATAATACTCTTCCCCT------CAGCAATACCTATAGTCACTAAGCCTTAGTTTA----- Template switch alignment (log-probability: -21.8) ACACAGCTTCTTTGAGTTATAATAATACTCTTCCCCTtAG|TGAC|AGCAATACCTATAGTCACTAAGCCTTAGTTTATTCTT ACACAGCTTCTTTGAGTTATAATAATACTCTTCCCCTCAG|TGAC|AGCAATACCTATAGTCACTAAGCCTTAGTTTATTCTT ========== Event 1999 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTCTCTCCCTGAGCTCATGTT--------------TATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAATATGCAACATGTTGTAAGTG ↓ 3 4 2 1 Chimp: ATTTCTCTCCCTGAGCTCATGATAAACATTTTCAGATAAACTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAATATGCAACATGTTGTAAGTG ↑ 3 4 2 1 Gorilla: ATTTCTCTCCCTGAGCTCATGTT--------------TATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAATATGCAACATGTTGTAAGTG Human: ATTTCTCTCCCTGAGCTCATGTT--------------TATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAATATGCAACATGTTGTAAGTG Cluster: [ ] Orangutan: ATTTCTCTCCCTGAGCTCATTTT--------------TATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAATATGCAACATGTTGTAAGTG Human > Chimp ------------- chr2B:101930109-101930122 Template switch process: F1: L GGCCGTAGCCATTCAAAGTCATTTCTCTCCCTGAGCTCA----------------------------------------TGATAAA 1 F3: 4 CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA R RF: GGCCGTAGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATGTTTATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA RR: CCGGCATCGGTAAGTTTCAGTAAAGAGAGGGACTCGAGTACAAATAGACTTTTACTTATGTCAAACCCGTACAACAGATACTATTT F2: 3 AAATAGACTTTTAC 2 Unidirectional alignment (log-probability: -45.7) AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATG---ATaaacattttcagataaaCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATGTTTAT-----------------CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA Template switch alignment (log-probability: -29.4) AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCA----------------------------------------TGATAAA|CATTTTCAGATAAA|CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATGTTTATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA|CATTTTCAGATAAA|CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA Gorilla > Chimp --------------- chr2B:101930109-101930122 Template switch process: F1: L GGCCGTAGCCATTCAAAGTCATTTCTCTCCCTGAGCTC----------------------------------------ATGATAAA 1 F3: 4 CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA R RF: GGCCGTAGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATGTTTATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA RR: CCGGCATCGGTAAGTTTCAGTAAAGAGAGGGACTCGAGTACAAATAGACTTTTACTTATGTCAAACCCGTACAACAGATACTATTT F2: 3 AAATAGACTTTTAC 2 Unidirectional alignment (log-probability: -45.3) AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATG---ATaaacattttcagataaaCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATGTTTAT-----------------CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA Template switch alignment (log-probability: -29.4) AGCCATTCAAAGTCATTTCTCTCCCTGAGCTC----------------------------------------ATGATAAA|CATTTTCAGATAAA|CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA AGCCATTCAAAGTCATTTCTCTCCCTGAGCTCATGTTTATCTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA|CATTTTCAGATAAA|CTGAAAATGAATACAGTTTGGGCATGTTGTCTATGATAAA ========== Event 2000 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAGTAAAGCATCAAATGACTTAACTGATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTTCTTAATATACGGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGACTAGAAATTAAAATCACCTTT ↓ 1 4 3 2 Chimp: AAGTAAAGCATCAAATGACTTGT-CAATTTACCTTAACTGATTAAAATATGCTCAGGGCATGACTTCTTAATATACAGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGACTAGAAATTAAAATCACCTTT Gorilla: AAGTAAAGCATCAAATGACTTGT-CAATTTACCTTAACTGATTAAAATATGCTCAGGGCATGACTTCTCAATATACGGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGACTAGAAATTAAAATCACCTTT ↑ 1 4 3 2 Human: AAGTAAAGCATCAAATGACTTAACTGATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTTCTTAATATACGGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGACTAGAAATTAAAATCACCTTT Cluster: [ ] Orangutan: AAGTAAAGCATCAAATGACTTGT-CAATTTACCTTAACTGATTAAAATATGCTCAGGGCATGACTTCTCAATGTACGGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGACTAGAAATTAAAATCACCTTT Human > Chimp ------------- chr2A:21627864-21627867 Template switch process: F1: L GATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTT 1 F3: 4 ATTTACCTTAACTGATTAAAATATGCTCAGGGCATGACTT R RF: GATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTTAACTGATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTTCTTAATATACGGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGAC RR: CTATAATATTTAAATCGTTCTTCATTTCGTAGTTTACTGAATTGACTAAATGGAATTGACTAATTTTATACGAGTCTCGTACTGAAGAATTATATGCCCAGTTTATAGTATCCCTCTCAAAAGTCACAAGTACTCTTTATACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -31.7) ATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTTgtcA----ATTTACCTTAACTGATTAAAATATGCTCAGgGCATGACTT ATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTT---AACTGATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTT Template switch alignment (log-probability: -21.8) ATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTT|GTCA|ATTTACCTTAACTGATTAAAATATGCTCAGgGCATGACTT ATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTT|GTCA|ATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTT Human > Gorilla --------------- chr2A:21338788-21338791 Template switch process: F1: L GATATTATAAATTTACCAAGAAGTAAAGCATCAAATGACTT 1 F3: 4 ATTTACCTTAACTGATTAAAATATGCTCAGGGCATGACTT R RF: GATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTTAACTGATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTTCTTAATATACGGGTCAAATATCATAGGGAGAGTTTTCAGTGTTCATGAGAAATATGAC RR: CTATAATATTTAAATCGTTCTTCATTTCGTAGTTTACTGAATTGACTAAATGGAATTGACTAATTTTATACGAGTCTCGTACTGAAGAATTATATGCCCAGTTTATAGTATCCCTCTCAAAAGTCACAAGTACTCTTTATACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -36.2) ATATTATAAATTTAcCAAGAAGTAAAGCATCAAATGACT----TGtcaATTTACCTTAACTGATTAAAATATGCTCAGgGCATGACTT ATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTTAACTG---ATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTT Template switch alignment (log-probability: -27.3) ATATTATAAATTTAcCAAGAAGTAAAGCATCAAATGACTT|GTCA|ATTTACCTTAACTGATTAAAATATGCTCAGgGCATGACTT ATATTATAAATTTAGCAAGAAGTAAAGCATCAAATGACTT|GTCA|ATTTACCTTAACTGATTAAAATATGCTCAGAGCATGACTT ========== Event 2001 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGGTTCACAAACAAGC-TCATCATAATGACC------------AGAAGGCTTTTTCCTCCATCCCTGC Chimp: CTGGTTCACAAACAAGCTGCATCATAGTGACCTTCTGGTCATTATGCAGGCTTTTTCCTCCATCCCTGC ↓ 1 3 2 4 Gorilla: CTGGTTCACAAACAAGCTGCAACATAATGACC------------AGAAGGCTTTTTCCTCCATCCCTGC Human: CTGGTTCACAAACAAGC-TCATCATAATGACC------------AGAAGGCTTTTTCCTCCATCCCTGC Cluster: [ ] Orangutan: Ctggttcacaaacaagcttcatcataataacc------------agagggctttttcctccatccctgc Chimp > Gorilla --------------- chr2B:30043019-30043028 Template switch process: F1: L AGATCAGTAGTTCCAAAATTCTGGTTCACAAACAAGCTGCAACATA 1 F3: 4 GGCTTTTTCCTCCATCCCTGCAAACTGGGGTTCTGATTT R RF: AGATCAGTAGTTCCAAAATTCTGGTTCACAAACAAGCTGCATCATAGTGACCTTCTGGTCATTATGCAGGCTTTTTCCTCCATCCCTGCAAACTGGGGTTCTGATTT RR: TCTAGTCATCAAGGTTTTAAGACCAAGTGTTTGTTCGACGTAGTATCACTGGAAGACCAGTAATACGTCCGAAAAAGGAGGTAGGGACGTTTGACCCCAAGACTAAA F2: 3 AAGACCAGTA 2 Unidirectional alignment (log-probability: -33.8) GTAGTTCCAAAATTCTGGTTCACAAACAAGCTGCAaCATAaTGACC------------aGaAGGCTTTTTCCTCCATCCCTGCAAACTGGGGTTCTGATTT GTAGTTCCAAAATTCTGGTTCACAAACAAGCTGCATCATAGTGACCTTCTGGTCATTATGCAGGCTTTTTCCTCCATCCCTGCAAACTGGGGTTCTGATTT Template switch alignment (log-probability: -22.6) GTAGTTCCAAAATTCTGGTTCACAAACAAGCTGCAaCATA|ATGACCAGAA|GGCTTTTTCCTCCATCCCTGCAAACTGGGGTTCTGATTT GTAGTTCCAAAATTCTGGTTCACAAACAAGCTGCATCATA|ATGACCAGAA|GGCTTTTTCCTCCATCCCTGCAAACTGGGGTTCTGATTT ========== Event 2002 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGCAAGGCATCAAG----------CAAAGCACCCTTGATTCACATCTTATAAATCACAGCATCT--CTGTTTGGGCCATGCTTCTT Chimp: GAAGCAAGGCATCAAG----------CAAAGCACCCTTGATTCACATCTTATAAATCACAGCAT--CTCTGTTTGGGCCATGCTTCTT ↓ 1 3 4 2 Gorilla: GAATCAAGGCATCAAGTTGCTGTGAATCAAGGGTGCTTGATTCACATCTTATAAATCACAGCATGT--CTGTTTGGGCCATGCTTCTT Human: GAAGCAAGGCATCAAG----------CAAAGCACCCTTGATTCACATCTTATAAATCACAGCATCT--CTGTTTGGGCCATGCTTCTT Cluster: [ ] Orangutan: GAATCAAGGCATCAAGTTGCTGTGAATCAAGGGTGCTTGATTCACATCTTATAAATCACAGCATCT--CTGTTTGGGCCATGCTTCTT Chimp > Gorilla --------------- chr2B:28758888-28758902 Template switch process: F1: L CTTGTGGCTCTTTTAAATGAAAGGGCAAGTTGCCTTTGAATCAAGGCATCAAGTTGC 1 F3: 4 CTTGATTCACATCTTATAAATCACAGCATGTCTGTTTGGGCCATGCTTCTTCTGGGTATTAGCTATCTTCAGCTGGCTTCCATAATCATAGGCATACAGTGGCAGACATTCTAAGTGTTGCAGCTTAGCGT R RF: CTTGTGGCTCTTTTAAATGAAAGGGCAAGTTGCCTTTGAAGCAAGGCATCAA---GCAAAGCACCCTTGATTCACATCTTATAAATCACAGCATCTCTGTTTGGGCCATGCTTCTTCTGGGTATTAGCTATCTTCAGCTGGCTTCCATAATCATAGGCATACAGTGGCAGACATTCTAAGTGTTGCAGCTTAGCAT RR: GAACACCGAGAAAATTTACTTTCCCGTTCAACGGAAACTTCGTTCCGTAGTT---CGTTTCGTGGGAACTAAGTGTAGAATATTTAGTGTCGTAGAGACAAACCCGGTACGAAGAAGACCCATAATCGATAGAAGTCGACCGAAGGTATTAGTATCCGTATGTCACCGTCTGTAAGATTCACAACGTCGAATCGTA F2: 3 GTGGGAACTAAGTGT 2 Unidirectional alignment (log-probability: -66.4) TGAAAGGGCAAGTTGCCTTTGAAtCAAGGCATCAAgttgctgtgaatcaagggtG---------CTTGATTCACATCTTATAAATCACAGCATgTCTGTTTGGG TGAAAGGGCAAGTTGCCTTTGAAGCAAGGCATCAA-------------------GCAAAGCACCCTTGATTCACATCTTATAAATCACAGCATCTCTGTTTGGG Template switch alignment (log-probability: -50.5) TGAAAGGGCAAGTTGCCTTTGAAtCAAGGCATCAAgttGC|TGTGAATCAAGGGTG|CTTGATTCACATCTTATAAATCACAGCATgTCTGTTTGGG TGAAAGGGCAAGTTGCCTTTGAAGCAAGGCATCAA---GC|TGTGAATCAAGGGTG|CTTGATTCACATCTTATAAATCACAGCATCTCTGTTTGGG ========== Event 2003 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATGGATTCAAAAATAAATAAT----T-TATTGCCTTTGGGTAATTTTATTATTCATCATGTTGCTTAA ↓ 1 3 24 ↑ 13 24 Chimp: ATGGATTCAAAAATAAATAAT----AAAATTACCCAAAGGCAA-TAAATTATTCATCATGTTGCTTAA Gorilla: ATGGATTCAAAAATAAATAAT----AAAATTACCCAAAGGCAA-TAAATTATTCATCATGTTGCTTAA ↓ 13 24 ↑ 1 3 24 Human: ATGGATTCAAAAATAAATAAT----T-TATTGCCTTTGGGTAATTTTATTATTCATCATGTTGCTTAA Cluster: [ ] Orangutan: ATGGATTCAAAAATAAATAATAAATAAAATTATCCAAAGACAA-TAAATTATTCATCATGTTGCTTAA Chimp > Human ------------- chr2:214619897-214619917 Template switch process: F1: L GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT 1 F3: 4 ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG R RF: GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATAAAATTACCCAAAGGCAATAAATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAA RR: CGAATTAAAAAGTACGAAAATACCTAAGTTTTTATTTATTATTTTAATGGGTTTCCGTTATTTAATAAGTAGTACAACGAATTAGAATTTAGGGACCAATTT F2: 3 TTTTAATGGGTTTCCGTTATT 2 Unidirectional alignment (log-probability: -58.4) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT---------------------ttattgcctttgggtaattttATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAg CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATAAAATTACCCAAAGGCAATAA---------------------ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAA Template switch alignment (log-probability: -23.9) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|TTATTGCCTTTGGGTAATTTT|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAg CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|TTATTGCCTTTGGGTAATTTT|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAA Human > Chimp ------------- chr2B:105460122-105460142 Template switch process: F1: L GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT 1 F3: 4 ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAA R RF: GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATTTATTGCCTTTGGGTAATTTTATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG RR: CGAATTAAAAAGTACGAAAATACCTAAGTTTTTATTTATTAAATAACGGAAACCCATTAAAATAATAAGTAGTACAACGAATTAGAATTTAGGGACCAATTC F2: 3 AATAACGGAAACCCATTAAAA 2 Unidirectional alignment (log-probability: -58.4) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAA---------------------TaaaattacccaaaggcaataaATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAa CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATTTATTGCCTTTGGGTAATTTT---------------------ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG Template switch alignment (log-probability: -23.9) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|AAAATTACCCAAAGGCAATAA|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAa CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|AAAATTACCCAAAGGCAATAA|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG Gorilla > Human --------------- chr2:214619897-214619917 Template switch process: F1: L GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT 1 F3: 4 ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG R RF: GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATAAAATTACCCAAAGGCAATAAATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAT RR: CGAATTAAAAAGTACGAAAATACCTAAGTTTTTATTTATTATTTTAATGGGTTTCCGTTATTTAATAAGTAGTACAACGAATTAGAATTTAGGGACCAATTA F2: 3 TTTTAATGGGTTTCCGTTATT 2 Unidirectional alignment (log-probability: -57.4) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT---------------------ttattgcctttgggtaattttATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAg CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATAAAATTACCCAAAGGCAATAA---------------------ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAT Template switch alignment (log-probability: -23.9) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|TTATTGCCTTTGGGTAATTTT|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAg CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|TTATTGCCTTTGGGTAATTTT|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAT Human > Gorilla --------------- chr2B:107734753-107734773 Template switch process: F1: L GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT 1 F3: 4 ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAT R RF: GCTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATTTATTGCCTTTGGGTAATTTTATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG RR: CGAATTAAAAAGTACGAAAATACCTAAGTTTTTATTTATTAAATAACGGAAACCCATTAAAATAATAAGTAGTACAACGAATTAGAATTTAGGGACCAATTC F2: 3 AATAACGGAAACCCATTAAAA 2 Unidirectional alignment (log-probability: -57.4) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAA---------------------TaaaattacccaaaggcaataaATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAt CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAATTTATTGCCTTTGGGTAATTTT---------------------ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG Template switch alignment (log-probability: -23.9) CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|AAAATTACCCAAAGGCAATAA|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAt CTTAATTTTTCATGCTTTTATGGATTCAAAAATAAATAAT|AAAATTACCCAAAGGCAATAA|ATTATTCATCATGTTGCTTAATCTTAAATCCCTGGTTAAG ========== Event 2004 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAGGCAGTACCTTTTCTGAGCTCATCTGTATTTCCAGAGcatggaaatgtatcatcatgaaaatgtatcatcatgaaaatTATTAAGGACCTGTTTGAAACTGAGACGTGAAGAATAAACACTTCTTACCTTTAGAAGTCTGTATCTggccgggtgcagtggctcatgcctataatcccagcactttg Chimp: TTAAGCAATACCTTTTCTGAGTTCATCTGTATTTCCAGAGCATGGAAATGTA-------------------TCATGAAAATTATTAAGGACCTGTTTGAAACTGAGATGTGAAGAATAAACACTTCTTACTTTTAGAAGTCTGTATCTggccgggtgcagtggctcatgcctataatcccagcactttg ↓ 4 1 3 2 Gorilla: TTAAGCAATACCTTTTCTGAGCTCATCTATATTTCCAGAGcatggaaatgtatcatcatgaaaatgtatcatcatgaaaatTATTAAGGACCTGTTTGAAACTGAGACGTGAAGAATAAACACTTCTTACCATTAAAAGTCTTTATCTggccgggtgcagtggctcatgcctataatcccagcactttg Human: TTAGGCAGTACCTTTTCTGAGCTCATCTGTATTTCCAGAGcatggaaatgtatcatcatgaaaatgtatcatcatgaaaatTATTAAGGACCTGTTTGAAACTGAGACGTGAAGAATAAACACTTCTTACCTTTAGAAGTCTGTATCTggccgggtgcagtggctcatgcctataatcccagcactttg Cluster: [ ] Orangutan: TTAAGCAATACCTTTTCTGAGCTCATCTGTATTTCCAGAGCATGAAAATGTA----------------TCATCATGAAAATTATTAAGGACCTGTTTGAAACTGAGACATGAAGAATAAACACTTCTTACCTTTAGAAGTCTGTATCTggccaggtgcagtggctcacgcctataatcccagcactttg Chimp > Gorilla --------------- chr2B:107598900-107598904 Template switch process: F1: L AATTCCATACCAATGAGCTTTTAAGCAATACCTTTTCTGAGCTCATCTATATTTCCAGAGCATGGAAATGTATCAT 1 F3: 4 AAATGTAT R RF: AATTCCATACCAATGAGCTTTTAAGCAATACCTTTTCTGAGTTCATCTGTATTTCCAGAGCATGGAAATGTATCATCATGAAAATTATTAAGGACCTGTTTGAAACTGAGATGTGAAGAATAAACACTTCTTACTTTTAGAAGTCTGTATCTGGCCGGGTGCAGTGGCTCATG RR: TTAAGGTATGGTTACTCGAAAATTCGTTATGGAAAAGACTCAAGTAGACATAAAGGTCTCGTACCTTTACATAGTAGTACTTTTAATAATTCCTGGACAAACTTTGACTCTACACTTCTTATTTGTGAAGAATGAAAATCTTCAGACATAGACCGGCCCACGTCACCGAGTAC F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -43.2) CTGAGcTCATCTaTATTTCCAGAGCATGGAAATGTAtcatcatgaaaatgtat CTGAGTTCATCTGTATTTCCAGAGCATGGAAATGTA----------------- Template switch alignment (log-probability: -27.5) CTGAGcTCATCTaTATTTCCAGAGCATGGAAATGTATCAT|CATGA|AAATGTAT CTGAGTTCATCTGTATTTCCAGAGCATGGAAATGTATCAT|CATGA|AAATGTAT ========== Event 2005 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTATATTTGAGTTTCAGCCCTCACATCTAATGGACTGACATCTTGACAAAGCCAAGA---------------------TGTCAGTCCATTAGATGTGAGTGCTGGAACTTAAATATAAGTTTGAGTT Chimp: CTATATTTGAGTTTCAGCCCTCACATCTAATGGACTGACATCTTGACAAAGCCAAGA---------------------TGTCAGTCCATTAGATGTGAGTGCTGGAGCTTAAATATAAGTTTGAGTT ↑ 3 2 41 Gorilla: CTATATTTGAGTTTCAGCACTCACATCTAATGGACTGACATCTTGACAAAGCCAAGA------------------------------------------TGCTGGAACTTAAATATAAGTTTGAGTT ↓ 3 2 41 Human: CTATATTTGAGTTTCAGCCCTCACATCTAATGGACTGACATCTTGACAAAGCCAAGA---------------------TGTCAGTCCATTAGATGTGAGTGCTGGAACTTAAATATAAGTTTGAGTT Cluster: [ ] Orangutan: CTATATTTGAATTTCAGCCCTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATGTCAGTCCATTAGATGTGAA---------------------TGCTGGAACTTAAATATAAGTTTGAGTT Gorilla > Human --------------- chr2:24734382-24734400 Template switch process: F1: L GCCCTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATG 1 F3: 4 TGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG R RF: GCACTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG RR: CGTGAGTGTAGATTACCTGACTGTAGAACTGTTTCGGTTCTACGACCTTGAATTTATATTCAAACTCAAACCGAGTTTCCC F2: 3 GAGTGTAGATTACCTGACT 2 Unidirectional alignment (log-probability: -46.6) CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGAtgtcagtccattagatgtgagTGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGA---------------------TGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG Template switch alignment (log-probability: -23.7) CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATG|TCAGTCCATTAGATGTGAG|TGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATG|TCAGTCCATTAGATGTGAG|TGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG Gorilla > Chimp --------------- chr2B:24853357-24853375 Template switch process: F1: L GCCCTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATG 1 F3: 4 TGCTGGAGCTTAAATATAAGTTTGAGTTTGGCTCAAAGGGTGAGTTTG R RF: GCACTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGGTGAATTTG RR: CGTGAGTGTAGATTACCTGACTGTAGAACTGTTTCGGTTCTACGACCTTGAATTTATATTCAAACTCAAACCGAGTTTCCCACTTAAAC F2: 3 GAGTGTAGATTACCTGACT 2 Unidirectional alignment (log-probability: -57.7) CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGAtgtcagtccattagatgtgagTGCTGGAgCTTAAATATAAGTTTGAGTTTGGCTCAAAGGG CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGA---------------------TGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG Template switch alignment (log-probability: -34.9) CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATG|TCAGTCCATTAGATGTGAG|TGCTGGAgCTTAAATATAAGTTTGAGTTTGGCTCAAAGGG CTCACATCTAATGGACTGACATCTTGACAAAGCCAAGATG|TCAGTCCATTAGATGTGAG|TGCTGGAACTTAAATATAAGTTTGAGTTTGGCTCAAAGGG ========== Event 2006 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: GAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGT-----AA-----CAACAAAGAAGAAAAACACCAT ↓ 13 24 ↑ 13 24 Chimp: GAGGAAGGTCACAGAGATTGT-----TGTT-----ACTTTTGTGGAAAAGGAAAGTTACCAGTGAACAAAGAAGAAAAACACCAT ↓ 13 24 ↑ 13 24 Gorilla: GAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGT-----AA-----CAACAAAGAAGAAAAACACCAT Human: GAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGT-----AA-----CAACAAAGAAGAAAAACACCAT Cluster: [ ] Orangutan: GAGGAGGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGT-----AA-----CAACAAAGAAGAAAAACACCAT Chimp > Human ------------- chr2:25188141-25188172 Template switch process: F1: L AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT 1 F3: 4 AACAAAGAAGAAAAACACCATGAAATCCTGTGAGCAGGCA R RF: AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTGTTACTTTTGTGGAAAAGGAAAGTTACCAGTGAACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA RR: TTCGTATAAAAACCCTAACTCTCCTTCCAGTGTCTCTAACAACAATGAAAACACCTTTTCCTTTCAATGGTCACTTGTTTCTTCTTTTTGTGGTACTTTAGGACACTTGTCCGT F2: 3 CAATGAAAACACCTTTTCCTTTCAATGGTCAC 2 Unidirectional alignment (log-probability: -73.4) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT---------------------------CAcTGgtaactttccttttccacaaaagtaacAACAAAGAAGAAAAACACCATGAAATCCTGTGAgCAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTGTTACTTTTGTGGAAAAGGAAAGTTACCAGTG---------------------------AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA Template switch alignment (log-probability: -25.2) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|CACTGGTAACTTTCCTTTTCCACAAAAGTAAC|AACAAAGAAGAAAAACACCATGAAATCCTGTGAgCAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|CACTGGTAACTTTCCTTTTCCACAAAAGTAAC|AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA Human > Chimp ------------- chr2B:25308250-25308281 Template switch process: F1: L AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT 1 F3: 4 AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA R RF: AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGTAACAACAAAGAAGAAAAACACCATGAAATCCTGTGAGCAGGCA RR: TTCGTATAAAAACCCTAACTCTCCTTCCAGTGTCTCTAACAAGTGACCATTGAAAGGAAAAGGTGTTTTCATTGTTGTTTCTTCTTTTTGTGGTACTTTAGGACACTCGTCCGT F2: 3 GTGACCATTGAAAGGAAAAGGTGTTTTCATTG 2 Unidirectional alignment (log-probability: -73.4) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT---------------------------GTtACttttgtggaaaaggaaagttaccagtgAACAAAGAAGAAAAACACCATGAAATCCTGTGAaCAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGTAAC---------------------------AACAAAGAAGAAAAACACCATGAAATCCTGTGAGCAGGCA Template switch alignment (log-probability: -25.2) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|GTTACTTTTGTGGAAAAGGAAAGTTACCAGTG|AACAAAGAAGAAAAACACCATGAAATCCTGTGAaCAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|GTTACTTTTGTGGAAAAGGAAAGTTACCAGTG|AACAAAGAAGAAAAACACCATGAAATCCTGTGAGCAGGCA Gorilla > Chimp --------------- chr2B:25308250-25308281 Template switch process: F1: L AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT 1 F3: 4 AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA R RF: AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGTAACAACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA RR: TTCGTATAAAAACCCTAACTCTCCTTCCAGTGTCTCTAACAAGTGACCATTGAAAGGAAAAGGTGTTTTCATTGTTGTTTCTTCTTTTTGTGGTACTTTAGGACACTTGTCCGT F2: 3 GTGACCATTGAAAGGAAAAGGTGTTTTCATTG 2 Unidirectional alignment (log-probability: -66.4) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT---------------------------GTtACttttgtggaaaaggaaagttaccagtgAACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTCACTGGTAACTTTCCTTTTCCACAAAAGTAAC---------------------------AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA Template switch alignment (log-probability: -19.8) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|GTTACTTTTGTGGAAAAGGAAAGTTACCAGTG|AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|GTTACTTTTGTGGAAAAGGAAAGTTACCAGTG|AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA Chimp > Gorilla --------------- chr2B:25235503-25235534 Template switch process: F1: L AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT 1 F3: 4 AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA R RF: AAGCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTGTTACTTTTGTGGAAAAGGAAAGTTACCAGTGAACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA RR: TTCGTATAAAAACCCTAACTCTCCTTCCAGTGTCTCTAACAACAATGAAAACACCTTTTCCTTTCAATGGTCACTTGTTTCTTCTTTTTGTGGTACTTTAGGACACTTGTCCGT F2: 3 CAATGAAAACACCTTTTCCTTTCAATGGTCAC 2 Unidirectional alignment (log-probability: -66.4) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT---------------------------CAcTGgtaactttccttttccacaaaagtaacAACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTTGTTACTTTTGTGGAAAAGGAAAGTTACCAGTG---------------------------AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA Template switch alignment (log-probability: -19.8) GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|CACTGGTAACTTTCCTTTTCCACAAAAGTAAC|AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA GCATATTTTTGGGATTGAGAGGAAGGTCACAGAGATTGTT|CACTGGTAACTTTCCTTTTCCACAAAAGTAAC|AACAAAGAAGAAAAACACCATGAAATCCTGTGAACAGGCA ========== Event 2007 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAGGCCACAAACACATTCTAGGGAGTCTAGAATAGACTCCCTTGAGCTCTTTTAATTCTTaaaa ↓ 3 1 2 4 Chimp: ACAGGCCACAAACACATTCTAGGGAGTCTATTCTAGACTCCCTAGAGCTCTTTTAATTCTTaaaa Gorilla: ACAGGCCACAAACACATTCTAGGGAGTCTAGAGTAGACTCCCTAGAGCTCTTTTAATTCTTaaaa Human: ACAGGCCACAAACACATTCTAGGGAGTCTAGAATAGACTCCCTTGAGCTCTTTTAATTCTTaaaa Cluster: [ ] Orangutan: ACAGGCCACAAACACATTCTAGGGAGTCTAGAATAGACTCCCCAGAGCTCTTTTAATTCTTTaaa Human > Chimp ------------- chr22:4618424-4618437 Template switch process: F1: L GAAAATTCTGGACAGGCCACAAACACATTCTAGGGAGTCTA 1 F3: 4 GAGCTCTTTTAATTCTTAAAAAAAAAA R RF: GAAAATTCTGGACAGGCCACAAACACATTCTAGGGAGTCTAGAATAGACTCCCTTGAGCTCTTTTAATTCTTAAAAAAAAAA RR: CTTTTAAGACCTGTCCGGTGTTTGTGTAAGATCCCTCAGATCTTATCTGAGGGAACTCGAGAAAATTAAGAATTTTTTTTTT F2: 3 ATCCCTCAGATCTT 2 Unidirectional alignment (log-probability: -32) AAAATTCTGGACAGGCCACAAACACATTCTAGGGAGTCTAttcTAGACTCCCTaGAGCTCTTTTAATTCTTAAAAAAAAAA-- AAAATTCTGGACAGGCCACAAACACATTCTAGGGAGTCTAGAATAGACTCCCTTGAGCTCTTTTAATTCTTAAAAAAAAAAAA Template switch alignment (log-probability: -16.8) AAAATTCTGGACAGGCCACAAACACATTCTAGGGAGTCTA|TTCTAGACTCCCTA|GAGCTCTTTTAATTCTTAAAAAAAAAA AAAATTCTGGACAGGCCACAAACACATTCTAGGGAGTCTA|TTCTAGACTCCCTA|GAGCTCTTTTAATTCTTAAAAAAAAAA ========== Event 2008 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCTGCTTGCCATCCTTGGGCAGCTACATTTTTGACCTCTTAGCCAGTTTGAGtctttcttt-ttttttttttttcactcagtctcactctgtcaccaaagctgaagtgcaggggcatgatcacggctcactgatcatgccagcccca Chimp: ACCTGCTTGCCATCCTTGGGCAGCTACATTTTTGACCTCTTAGCCAGTTTGAGTCtttcttt-----ttttttttcactcagtctcactctgttaccaaagctgaagtgcaggggcatgatcacggctcactgatcatgccagcccca Gorilla: ACCTGCTTGCCATCCTTGGGCCACCACATTTTTGACCTCTTAGCCAGTTTGAGTCtttcttt-----ttttttttcactcagtctcactctgtcaccaaagctgaagtgcaggggcatgatcacagctcactgatcatgccagcccca ↓ 1 4 3 2 Human: ACCTGCTTGCCATCCTTGGGCAGCTACATTTTTGACCTCTTAGCCAGTTTGAGtctttcttt-ttttttttttttcactcagtctcactctgtcaccaaagctgaagtgcaggggcatgatcacggctcactgatcatgccagcccca Cluster: [ ] Orangutan: ACCTGCTTGCCATCC-TGGGCAGCTACAttttttacctcttagccagtttgagtctttctttc----ttttttttcactcagtctca--ctgtcaccaaagctgaagtgcaggagcatgatcacggctcactggtcatgccagcctca Gorilla > Human --------------- chr2:218380157-218380160 Template switch process: F1: L CCTCTCTCATAGTTTATCTTACCTGCTTGCCATCCTTGGGC 1 F3: 4 ACATTTTTGACCTCTTAGCCAGTTTGAGTCTTTCTTTTTT R RF: CCTCTCTCATAGTTTATCTTACCTGCTTGCCATCCTTGGGCCACCACATTTTTGACCTCTTAGCCAGTTTGAGTCTTTCTTTTTTTTTTTCACTCAGTCTCACTCTGTCACCAAAGCTGAAGTGCAGGGGCATGATCACAGCT RR: GGAGAGAGTATCAAATAGAATGGACGAACGGTAGGAACCCGGTGGTGTAAAAACTGGAGAATCGGTCAAACTCAGAAAGAAAAAAAAAAAGTGAGTCAGAGTGAGACAGTGGTTTCGACTTCACGTCCCCGTACTAGTGTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -28.8) CTCTCTCATAGTTTATCTTACCTGCTTGCCATCCTTGGGCagCtACATTTTTGACCTCTTAGCCAGTTTGAGTCTTTCTTTttt CTCTCTCATAGTTTATCTTACCTGCTTGCCATCCTTGGGCCACCACATTTTTGACCTCTTAGCCAGTTTGAGTCTTTCTTT--- Template switch alignment (log-probability: -16.2) CTCTCTCATAGTTTATCTTACCTGCTTGCCATCCTTGGGC|AGCT|ACATTTTTGACCTCTTAGCCAGTTTGAGTCTTTCTTTTTT CTCTCTCATAGTTTATCTTACCTGCTTGCCATCCTTGGGC|AGCT|ACATTTTTGACCTCTTAGCCAGTTTGAGTCTTTCTTTTTT ========== Event 2009 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ATGGTATCTGTTCTAGGTGGGG-------ACAGTGCCCAGGAGGAACGGCTTGAG ↓ 31 4 2 Chimp: ATGGTATCTGTTCTAGGTGGGCACTGTCCCCAGTGCCCAGGAGGAACGGCTTGAG Gorilla: Human: ATGGTATCTGTTCTAGGTGGGG-------ACAGTGCCCAGGAGGAACGGCTTGAG Cluster: [ ] Orangutan: ATGGTATCTGTTCTA-GTGGGG-------ACAGTGCCCAGCAGGAATGGCTTGAG Human > Chimp ------------- chr2B:110129849-110129857 Template switch process: F1: L GTTTTGTGAGATTTGAATTCATGGTATCTGTTCTAGGTGGG 1 F3: 4 CAGTGCCCAGGAGGAACGGCTTGAGCATACACAAGGCAGG R RF: GTTTTGTGAGATTTGAATTCATGGTATCTGTTCTAGGTGGGGACAGTGCCCAGGAGGAACGGCTTGAGCATACACAAGGCAGG RR: CAAAACACTCTAAACTTAAGTACCATAGACAAGATCCACCCCTGTCACGGGTCCTCCTTGCCGAACTCGTATGTGTTCCGTCC F2: 3 CCCTGTCAC 2 Unidirectional alignment (log-probability: -27) TTTTGTGAGATTTGAATTCATGGTATCTGTTCTAGGTGGGcActgtcccCAGTGCCCAGGAGGAACGGCTTGAGCATACACAAGGCAGG TTTTGTGAGATTTGAATTCATGGTATCTGTTCTAGGTGGGGA-------CAGTGCCCAGGAGGAACGGCTTGAGCATACACAAGGCAGG Template switch alignment (log-probability: -16.4) TTTTGTGAGATTTGAATTCATGGTATCTGTTCTAGGTGGG|CACTGTCCC|CAGTGCCCAGGAGGAACGGCTTGAGCATACACAAGGCAGG TTTTGTGAGATTTGAATTCATGGTATCTGTTCTAGGTGGG|CACTGTCCC|CAGTGCCCAGGAGGAACGGCTTGAGCATACACAAGGCAGG ========== Event 2010 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGTCTTATCTCCACTGTGGGCTGGTAATCTCTCAAGGAGAGTTGATTCACAGGCTTGGGT ↑ 1 3 4 2 Chimp: ATGTCTTATCTCCACTGTGGGTTGGTAATCCCC--TTGAGAGTTGATTCACAGGCTTGGGT Gorilla: ATGTCTTATCTCCACTGTGGGTTGGTAATCCCC--TTGAGAGTTGATTCACAGGCTTGGGT Human: ATGTCTTATCTCCACTGTGGGCTGGTAATCTCTCAAGGAGAGTTGATTCACAGGCTTGGGT Cluster: [ ] Orangutan: Chimp > Human ------------- chr22:31542445-31542451 Template switch process: F1: L TGCCTAGTGTCATCCTGCACATGTCTTATCTCCACTGTGGGCTGGTAATC 1 F3: 4 GAGAGTTGATTCACAGGCTTGGGTGGATCTATTACAGGCG R RF: TGCCTAGTGTCATCCTGCACATGTCTTATCTCCACTGTGGGTTGGTAATCCCCTTGAGAGTTGATTCACAGGCTTGGGTGGATCTATTACAGGCG RR: ACGGATCACAGTAGGACGTGTACAGAATAGAGGTGACACCCAACCATTAGGGGAACTCTCAACTAAGTGTCCGAACCCACCTAGATAATGTCCGC F2: 3 GAACTCT 2 Unidirectional alignment (log-probability: -36) CATCCTGCACATGTCTTATCTCCACTGTGGGcTGGTAATC----TctcaagGAGAGTTGATTCACAGGCTTGGGTGGATCTATTACAGGCG CATCCTGCACATGTCTTATCTCCACTGTGGGTTGGTAATCCCCTT------GAGAGTTGATTCACAGGCTTGGGTGGATCTATTACAGGCG Template switch alignment (log-probability: -22.3) CATCCTGCACATGTCTTATCTCCACTGTGGGcTGGTAATC|TCTCAAG|GAGAGTTGATTCACAGGCTTGGGTGGATCTATTACAGGCG CATCCTGCACATGTCTTATCTCCACTGTGGGTTGGTAATC|TCTCAAG|GAGAGTTGATTCACAGGCTTGGGTGGATCTATTACAGGCG ========== Event 2011 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCGGTGTTTTGGAGGCCTGGGCACCC---------AGCATAGTTCTGCACATGGAGGACAGTGGCGTGGGAT Chimp: CCAGTGTTTTAGAGGCCTGGGCACCC---------AGCATGGTTCTGCACATGGAGGACAGTGGCGTGGGAT Gorilla: CCGGTGTTTTGGAGGCCTGGGTGCAG------------------AAGCACCAGGAGGACAGTGGCGTGGGAT ↑ 1 3 4 2 Human: CCGGTGTTTTGGAGGCCTGGGCACCC---------AGCATAGTTCTGCACATGGAGGACAGTGGCGTGGGAT Cluster: [ ] Orangutan: CCGGTGTTTTGGAGGCCTGGGCACCCAGCATGGTT---------CTGCACATGGAGGACAGCGGCATGGGAT Human > Gorilla --------------- chr22:31544735-31544741 Template switch process: F1: L AGGAGGCGTTGGGGGAGGGGCCGGTGTTTTGGAGGCCTGGG 1 F3: 4 GCACCAGGAGGACAGTGGCGTGGGATGGCCAAGCATGGAGGCCCGA R RF: AGGAGGCGTTGGGGGAGGGGCCGGTGTTTTGGAGGCCTGGGCACCCAGCATAGTTCTGCACATGGAGGACAGTGGCGTGGGATGGCCAAGCATGGAGGCCCGA RR: TCCTCCGCAACCCCCTCCCCGGCCACAAAACCTCCGGACCCGTGGGTCGTATCAAGACGTGTACCTCCTGTCACCGCACCCTACCGGTTCGTACCTCCGGGCT F2: 3 AAGACGT 2 Unidirectional alignment (log-probability: -37.5) GGAGGCGTTGGGGGAGGGGCCGGTGTTTTGGAGGCCTGGGtgcagaagcacCA--------------------GGAGGACAGTGGCGTGGGATGGCCAAGCATGGAG GGAGGCGTTGGGGGAGGGGCCGGTGTTTTGGAGGCCTGGG-----------CACCCAGCATAGTTCTGCACATGGAGGACAGTGGCGTGGGATGGCCAAGCATGGAG Template switch alignment (log-probability: -27.8) GGAGGCGTTGGGGGAGGGGCCGGTGTTTTGGAGGCCTGGG|TGCAGAA|GCACcaGGAGGACAGTGGCGTGGGATGGCCAAGCATGGAG GGAGGCGTTGGGGGAGGGGCCGGTGTTTTGGAGGCCTGGG|TGCAGAA|GCACATGGAGGACAGTGGCGTGGGATGGCCAAGCATGGAG ========== Event 2012 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GAGGGCGGGTTGGCAAGGTTT-TCTTTCCCCCATGTGTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAGCCA Chimp: GAGGGTGAGTTGGCAAGGTTTCTTTTTCCCCCATG--TGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAGCCA Gorilla: GAGGGTGGGTTGGCAAGGTTTTTGTTCCCCCCATG--TGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAGCCA ↓ 1 4 3 2 Human: GAGGGCGGGTTGGCAAGGTTT-TCTTTCCCCCATGTGTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAGCCA Cluster: [ ] Orangutan: GAGGGTGGGTTGGCAAGGTTTTTT-------TGTG--TGTGTGTCCACACGGGGGAAGGTGTTGTCTTGGGCTGAGCCA Gorilla > Human --------------- chr22:30588669-30588681 Template switch process: F1: L GAGTCCAGGCCCCTTTGCTAGAGGGCGGGTTGGCAAGGTTTT 1 F3: 4 GTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAGC R RF: GAGTCCAGGCCCCTTTGCTAGAGGGTGGGTTGGCAAGGTTTTTGTTCCCCCCATGTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAGC RR: CTCAGGTCCGGGGAAACGATCTCCCACCCAACCGTTCCAAAAACAAGGGGGGTACACACACAGGTGTACCCCCTTCCACAACAGAACCCGACTCG F2: 3 TGTACCCCCTTTC 2 Unidirectional alignment (log-probability: -40.1) GTCCAGGCCCCTTTGCTAGAGGGcGGGTTGGCAAGGTTTTctTTCCCCCatgTGTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAG GTCCAGGCCCCTTTGCTAGAGGGTGGGTTGGCAAGGTTTTTGTTCCCCC-CATGTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAG Template switch alignment (log-probability: -28.5) GTCCAGGCCCCTTTGCTAGAGGGcGGGTTGGCAAGGTTTT|CtTTCCCCCATGT|GTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAG GTCCAGGCCCCTTTGCTAGAGGGTGGGTTGGCAAGGTTTT|CCTTCCCCCATGT|GTGTGTGTCCACATGGGGGAAGGTGTTGTCTTGGGCTGAG ========== Event 2013 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGGAGGCAATGGTGCCTCTT-------GAAGGGCAGGGCACACAGCCACAGG Chimp: TCAGGAGGCAATGGTGCCTCTT-------GAAGGGCAGGGCACACAGCCACAGG ↓ 3 1 4 2 Gorilla: TCAGGAGGCAATGGTGCCTCTTGCCTTCAAGAGGGCAGGGCATACAGCCACAGG ↑ 3 1 4 2 Human: TCAGGAGGCAATGGTGCCTCTT-------GAAGGGCAGGGCACACAGCCACAGG Cluster: [ ] Orangutan: TCAAGAGGCAATGGTGCCTCTT-------GAAGGGCAGGGCACACAGCCGCAGG Human > Gorilla --------------- chr22:31181180-31181187 Template switch process: F1: L GCAGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTG 1 F3: 4 AGGGCAGGGCATACAGCCACAGGGCCACCTTCTGCATGGC R RF: GCAGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTGAAGGGCAGGGCACACAGCCACAGGGCCACCTTCTGCATGGC RR: CGTCTGTTCCTTTGTCCGAAGTCCTCCGTTACCACGGAGAACTTCCCGTCCCGTGTGTCGGTGTCCCGGTGGAAGACGTACCG F2: 3 GAACTTCC 2 Unidirectional alignment (log-probability: -32) AGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTGccttcaagAGGGCAGGGCAtACAGCCACAGGGCCACCTTCTGCATGGC AGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTGA-------AGGGCAGGGCACACAGCCACAGGGCCACCTTCTGCATGGC Template switch alignment (log-probability: -22.3) AGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTG|CCTTCAAG|AGGGCAGGGCAtACAGCCACAGGGCCACCTTCTGCATGGC AGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTG|CCTTCAAG|AGGGCAGGGCACACAGCCACAGGGCCACCTTCTGCATGGC Chimp > Gorilla --------------- chr22:31181180-31181187 Template switch process: F1: L GCAGACAAGGAAACAGGCTTCAGGAGGCAATGGTGCCTCTTG 1 F3: 4 AGGGCAGGGCATACAGCCACAGGGCCACCTTCTGCATGGC R RF: GCAGACAAGGAAACAAGCTTCAGGAGGCAATGGTGCCTCTTGAAGGGCAGGGCACACAGCCACAGGGCCACCTTCTGCATGGC RR: CGTCTGTTCCTTTGTTCGAAGTCCTCCGTTACCACGGAGAACTTCCCGTCCCGTGTGTCGGTGTCCCGGTGGAAGACGTACCG F2: 3 GAACTTCC 2 Unidirectional alignment (log-probability: -37.5) AGACAAGGAAACAgGCTTCAGGAGGCAATGGTGCCTCTTGccttcaagAGGGCAGGGCAtACAGCCACAGGGCCACCTTCTGCATGGC AGACAAGGAAACAAGCTTCAGGAGGCAATGGTGCCTCTTGA-------AGGGCAGGGCACACAGCCACAGGGCCACCTTCTGCATGGC Template switch alignment (log-probability: -27.8) AGACAAGGAAACAgGCTTCAGGAGGCAATGGTGCCTCTTG|CCTTCAAG|AGGGCAGGGCAtACAGCCACAGGGCCACCTTCTGCATGGC AGACAAGGAAACAAGCTTCAGGAGGCAATGGTGCCTCTTG|CCTTCAAG|AGGGCAGGGCACACAGCCACAGGGCCACCTTCTGCATGGC ========== Event 2014 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCGTTAATGAAGGAGTGCACTGAAATAAAGGTGTGAGGTAGGGGCATTTCCTATGCAGTGCCTGTGCGGTTGCTTGCCTGTTCAATCATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAATCAGGTCTATTTAACCCAGTCCATA ↑ 3 2 1 4 Chimp: GCGTTAATGAAGGAGTGCACTGAAATAAAGGTGTGAGGTAGGGGCATTTCCTATGCAGTGCCTGTGCGGTTGCTTGCCTGTTCAATCATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAAATGAGTCTATTTAACCCAGTCCATA Gorilla: GCATTAATGAAGGAGTGCACTGAAATAAAGGTGTGAGGTAGGGGCATTTCCTATGCAGTGCCTGTGCGGTTGCTTGCCTGTTCAATCGTGTGTTCATTTACACCTCCAAGACATTTCTTAATTGAAACGGGTCTATTTAACCCAGTCCATA Human: GCGTTAATGAAGGAGTGCACTGAAATAAAGGTGTGAGGTAGGGGCATTTCCTATGCAGTGCCTGTGCGGTTGCTTGCCTGTTCAATCATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAATCAGGTCTATTTAACCCAGTCCATA Cluster: [ ] Orangutan: GTGTTAATGAAGGAGTGCACTGAACTAAAGGTGTGAGGTAGGGGCATTTCCTGTGCAGTGCCTGTACGGTTGCTTGCCTGTTCAATCGTGTGTTCATTTACACCTCCAAGACATTTCTTAATTGAAACGGGTCTATTTAACCCAGTCCATA Chimp > Human ------------- chr2:220799249-220799252 Template switch process: F1: L TCATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAA 1 F3: 4 GTCTATTTAACCCAGTCCATATAATACCTAAAAGCAGCCT R RF: CTGAAATAAAGGTGTGAGGTAGGGGCATTTCCTATGCAGTGCCTGTGCGGTTGCTTGCCTGTTCAATCATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAAATGAGTCTATTTAACCCAGTCCATATAATACATAAAAGCAGCCT RR: GACTTTATTTCCACACTCCATCCCCGTAAAGGATACGTCACGGACACGCCAACGAACGGACAAGTTAGTACACAAGTAAATATGGAGGTTCTGTAAAGAATTAACTTTACTCAGATAAATTGGGTCAGGTATATTATGTATTTTCGTCGGA F2: 3 GACT 2 Unidirectional alignment (log-probability: -30.7) CATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAAtcagGTCTATTTAACCCAGTCCATATAATACcTAAAAGCAGCCT CATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAAATGAGTCTATTTAACCCAGTCCATATAATACATAAAAGCAGCCT Template switch alignment (log-probability: -21.8) CATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAA|TCAG|GTCTATTTAACCCAGTCCATATAATACcTAAAAGCAGCCT CATGTGTTCATTTATACCTCCAAGACATTTCTTAATTGAA|TCAG|GTCTATTTAACCCAGTCCATATAATACATAAAAGCAGCCT ========== Event 2015 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGAGTAGGGTATGTGTTCTCC--------CAAT--TCCCTCCCTTGTAGCCTCTGAAGACCCAACTC Chimp: TAAGAGTAGGGTATGTGTTCTCC--------CAAT--TCCCTCCCTTGTAGCCTCTGAAGACCCAACTC ↓ 1 3 4 2 Gorilla: TAAGAGTAGGGTATGTGTTCTACAAGGGAGGGAAT----TCTCCCTTGTAGCCTCTGAAGACCCAACTC ↑ 1 3 4 2 Human: TAAGAGTAGGGTATGTGTTCTCC--------CAAT--TCCCTCCCTTGTAGCCTCTGAAGACCCAACTC Cluster: [ ] Orangutan: TAAGAGTAGGGTATGTGTTCTCC--------CAATTC--CTTCCCTTGTAGCCTCTGAAGACCCAACTC Human > Gorilla --------------- chr2B:113602913-113602927 Template switch process: F1: L TTGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCT 1 F3: 4 CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG R RF: TTGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCTCCCAATTCCCTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG RR: AACCCAGTTTCCTACCACTTATTCTCATCCCATACACAAGAGGGTTAAGGGAGGGAACATCGGAGACTTCTGGGTTGAGGACAGGGGGCC F2: 3 TTAAGGGAGGGAACA 2 Unidirectional alignment (log-probability: -42.7) TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCtacaagggagggaatT---------CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTC---------------TCCCAATTCCCTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG Template switch alignment (log-probability: -17.6) TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCT|ACAAGGGAGGGAATT|CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCT|ACAAGGGAGGGAATT|CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG Chimp > Gorilla --------------- chr2B:113602913-113602927 Template switch process: F1: L TTGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCT 1 F3: 4 CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCGG R RF: TTGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCTCCCAATTCCCTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCAG RR: AACCCAGTTTCCTACCACTTATTCTCATCCCATACACAAGAGGGTTAAGGGAGGGAACATCGGAGACTTCTGGGTTGAGGACAGGGGGTC F2: 3 TTAAGGGAGGGAACA 2 Unidirectional alignment (log-probability: -48.2) TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCtacaagggagggaatT---------CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCgG TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTC---------------TCCCAATTCCCTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCAG Template switch alignment (log-probability: -23.2) TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCT|ACAAGGGAGGGAATT|CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCgG TGGGTCAAAGGATGGTGAATAAGAGTAGGGTATGTGTTCT|ACAAGGGAGGGAATT|CTCCCTTGTAGCCTCTGAAGACCCAACTCCTGTCCCCCAG ========== Event 2016 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGAAGAGTAAGGCAAAATTTTAAAAATGATGGTGGACAAAGGCCACCATCAATGCAGAAAACCACCCA ↑ 1 3 4 2 Chimp: TGAAGAGTAAGGCAAAATTTTTAAAATGACGGTGGCCTTTGTCCACCATCAATGCAGAAAACCACCCA Gorilla: TGAAGAGTAACGCAAAATTTTAAAAATGATGGTGGCCTTTGTCCACCATCAATGCAGAAAACCACCCA Human: TGAAGAGTAAGGCAAAATTTTAAAAATGATGGTGGACAAAGGCCACCATCAATGCAGAAAACCACCCA Cluster: [ ] Orangutan: TGAAGAGTAAGGCAAAATTTTAAAAATGATAGTGGCCTTTGTCCATCATCAATGCAGAAAACCCCCCA Chimp > Human ------------- chr2:221575048-221575060 Template switch process: F1: L ACCTAGCAGATATGATTCCTTGAAGAGTAAGGCAAAATTTTAAAAATGA 1 F3: 4 CCACCATCAATGCAGAAAACCACCCACATTATGGGAAGAC R RF: ACCTAGGAGATATGATTCCTTGAAGAGTAAGGCAAAATTTTTAAAATGACGGTGGCCTTTGTCCACCATCAATGCAGAAAACCACCCACATTATGGGAAGAC RR: TGGATCCTCTATACTAAGGAACTTCTCATTCCGTTTTAAAAATTTTACTGCCACCGGAAACAGGTGGTAGTTACGTCTTTTGGTGGGTGTAATACCCTTCTG F2: 3 GGAAACAGGTGGT 2 Unidirectional alignment (log-probability: -48.8) ATATGATTCCTTGAAGAGTAAGGCAAAATTTTaAAAATGAtGGTGGaCaaaGgCCACCATCAATGCAGAAAACCACCCACATTATGGGAAGAC ATATGATTCCTTGAAGAGTAAGGCAAAATTTTTAAAATGACGGTGGCCTTTGTCCACCATCAATGCAGAAAACCACCCACATTATGGGAAGAC Template switch alignment (log-probability: -29) ATATGATTCCTTGAAGAGTAAGGCAAAATTTTaAAAATGA|TGGTGGACAAAGG|CCACCATCAATGCAGAAAACCACCCACATTATGGGAAGAC ATATGATTCCTTGAAGAGTAAGGCAAAATTTTTAAAATGA|TGGTGGACAAAGG|CCACCATCAATGCAGAAAACCACCCACATTATGGGAAGAC ========== Event 2017 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: aactgtccttggcTCCTTGGAACTTT----------------------------------------------------------------------------------------CTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAACACATTTAGACATagaagaaattcttttaactgctacttaacag ↓ 4 3 1 2 Chimp: aactgtccttggctccatggaACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAGAATTTCTTCTATGTCTAAATGTGTTTTATATTTGATTAACGTGAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAACACATTTAGACATAGAAGAAATTCTTTTAACCGCTACTTAACAA ↑ 4 3 1 2 Gorilla: aactgtccttggctccatggaACTTT----------------------------------------------------------------------------------------CTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAACACATTTAGACACAGAAGAAATTCTTTTAACCACTACTTAACAG Human: aactgtccttggcTCCTTGGAACTTT----------------------------------------------------------------------------------------CTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAACACATTTAGACATagaagaaattcttttaactgctacttaacag Cluster: [ ] Orangutan: aactgtccttggctccatggaACTTT----------------------------------------------------------------------------------------CTATCTGGCAAGGGAGATTCACGTTAATCAAATATTAAACACATTTAGACATagaagaaattcttttaaccgctacttaacag Human > Chimp ------------- chr2B:112805401-112805443 Template switch process: F1: L CCTTCTATACATAGGAACTGTCCTTGGCTCCATGGAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA 1 F3: 4 GAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAAC R RF: CCTCCTATACATAGGAACTGTCCTTGGCTCCTTGGAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAACACATTTAGACATAGAAGAAATTC RR: GGAGGATATGTATCCTTGACAGGAACCGAGGAACCTTGAAAGATAGACCGTTTCCTCTAAGTGCAATTAGTTTATAATTTGTGTAAATCTGTATCTTCTTTAAG F2: 3 TGCAATTAGTTTATATTTTGTGTAAATCTGTATCTTCTTTAAG 2 Unidirectional alignment (log-probability: -149) TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAgaatttcttctatgtctaaatgtgttttatatttgattaacgtgaactttctatctggcaaaggagattcacgttaatcaaat TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA----------------------------------------------------------------------------------- Template switch alignment (log-probability: -39.2) TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA|GAATTTCTTCTATGTCTAAATGTGTTTtATATTTGATTAACGT|GAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAAT TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA|GAATTTCTTCTATGTCTAAATGTGTTTAATATTTGATTAACGT|GAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAAT Gorilla > Chimp --------------- chr2B:112805401-112805443 Template switch process: F1: L CCTTCTATACATAGGAACTGTCCTTGGCTCCATGGAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA 1 F3: 4 GAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAAC R RF: CCTCCTATACATAGGAACTGTCCTTGGCTCCATGGAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAAACACATTTAGACACAGAAGAAATTC RR: GGAGGATATGTATCCTTGACAGGAACCGAGGTACCTTGAAAGATAGACCGTTTCCTCTAAGTGCAATTAGTTTATAATTTGTGTAAATCTGTGTCTTCTTTAAG F2: 3 TGCAATTAGTTTATATTTTGTGTAAATCTGTATCTTCTTTAAG 2 Unidirectional alignment (log-probability: -143) TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAagaatttcttctatgtctaaatgtgttttatatttgattaacgtgaactttctatctggcaaaggagattcacgttaatcaaat TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTA------------------------------------------------------------------------------------ Template switch alignment (log-probability: -38.7) TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA|GAATTTCTTCTaTGTCTAAATGTGTTTtATATTTGATTAACGT|GAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAAT TTCTATCTGGCAAAGGAGATTCACGTTAATCAAATATTAA|GAATTTCTTCTGTGTCTAAATGTGTTTAATATTTGATTAACGT|GAACTTTCTATCTGGCAAAGGAGATTCACGTTAATCAAAT ========== Event 2018 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTAATTGATGAATTTTGATCGAGAAATTTGATC--------G------AGTATTTTAAATGTCTAAAGCC Chimp: ATTAATTGATGAATTTTGATCGAGAAATTTGAAA----GTTTG---AAATGTATTTTAAATGTCTAAAGCC Gorilla: ATTAATTGATGAATTTTGATCGAGAAATTTGAAAGTTT----GAAA---TGTATTTTAAATGTCTAAAGCC ↓ 3 2 1 4 Human: ATTAATTGATGAATTTTGATCGAGAAATTTGATC--------G------AGTATTTTAAATGTCTAAAGCC Cluster: [ ] Orangutan: ATTAATTGATGAATTTCGATCGAGAAATTTGAAAGTTT----GAAA---TGTATTTTAAATGTCTAAAGCC Gorilla > Human --------------- chr2:221552804-221552807 Template switch process: F1: L TGTCCTAAAATTAATTGATGAATTTTGATCGAGAAATTTGA 1 F3: 4 GTATTTTAAATGTCTAAAGCCTGTGAATGCATCATAACCA R RF: TGTCCTAAAATTAATTGATGAATTTTGATCGAGAAATTTGAAAGTTTGAAATGTATTTTAAATGTCTAAAGCCTGTGAATGCATCATAACCA RR: ACAGGATTTTAATTAACTACTTAAAACTAGCTCTTTAAACTTTCAAACTTTACATAAAATTTACAGATTTCGGACACTTACGTAGTATTGGT F2: 3 AGCT 2 Unidirectional alignment (log-probability: -25.5) GTCCTAAAATTAATTGATGAATTTTGATCGAGAAATTTG----------ATcgaGTATTTTAAATGTCTAAAGCCTGTGAATGCATCATAACCA GTCCTAAAATTAATTGATGAATTTTGATCGAGAAATTTGAAAGTTTGAAAT---GTATTTTAAATGTCTAAAGCCTGTGAATGCATCATAACCA Template switch alignment (log-probability: -16.2) GTCCTAAAATTAATTGATGAATTTTGATCGAGAAATTTGA|TCGA|GTATTTTAAATGTCTAAAGCCTGTGAATGCATCATAACCA GTCCTAAAATTAATTGATGAATTTTGATCGAGAAATTTGA|TCGA|GTATTTTAAATGTCTAAAGCCTGTGAATGCATCATAACCA ========== Event 2019 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATAAATATTTTGAACATCTGGATGAGAATTTTTTGTTGG-GGA--CAGGGGGAATCATTTCTCTACAA Chimp: AAATAAATATTTTGAGCATCTGGATGATAATTTTTTGTTGG-GGG--CAGGGGGAATCATTTCTCTACAA ↓ 3 2 1 4 Gorilla: AAATAAATATTTTGAGCATCTGGATGAGAATTTTTTGTTCT-CATCCAGGGGGGAATCATTTCTCTACAA ↑ 3 2 1 4 Human: AAATAAATATTTTGAACATCTGGATGAGAATTTTTTGTTGG-GGA--CAGGGGGAATCATTTCTCTACAA Cluster: [ ] Orangutan: AAATAAATATTTTGAGCATCTGGATGAGAATTTTTTGTTGGGGGG--CAGGGGGAATCATTTCTCTACAA Human > Gorilla --------------- chr2B:114896481-114896489 Template switch process: F1: L CCAAATAAATATTTTGAGCATCTGGATGAGAATTTTTTGTT 1 F3: 4 GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT R RF: CCAAATAAATATTTTGAACATCTGGATGAGAATTTTTTGTTGGGGACAGGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT RR: GGTTTATTTATAAAACTTGTAGACCTACTCTTAAAAAACAACCCCTGTCCCCCTTAGTAAAGAGATGTTCCCTATCTAACGTACATAA F2: 3 GACCTACTC 2 Unidirectional alignment (log-probability: -38) CAAATAAATATTTTGAgCATCTGGATGAGAATTTTTTGTTctcatccaG------GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT CAAATAAATATTTTGAACATCTGGATGAGAATTTTTTGTT--------GGGGACAGGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT Template switch alignment (log-probability: -22.4) CAAATAAATATTTTGAgCATCTGGATGAGAATTTTTTGTT|CTCATCCAG|GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT CAAATAAATATTTTGAACATCTGGATGAGAATTTTTTGTT|CTCATCCAG|GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT Chimp > Gorilla --------------- chr2B:114896482-114896489 Template switch process: F1: L CCAAATAAATATTTTGAGCATCTGGATGAGAATTTTTTGTTC 1 F3: 4 GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT R RF: CCAAATAAATATTTTGAGCATCTGGATGATAATTTTTTGTTGGGGGCAGGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT RR: GGTTTATTTATAAAACTCGTAGACCTACTATTAAAAAACAACCCCCGTCCCCCTTAGTAAAGAGATGTTCCCTATCTAACGTACATAA F2: 3 GACCTACT 2 Unidirectional alignment (log-probability: -38) AAATAAATATTTTGAGCATCTGGATGAgAATTTTTTGTTctcatccaG------GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT AAATAAATATTTTGAGCATCTGGATGATAATTTTTTGTT--------GGGGGCAGGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT Template switch alignment (log-probability: -27.8) AAATAAATATTTTGAGCATCTGGATGAgAATTTTTTGTTc|TCATCCAG|GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT AAATAAATATTTTGAGCATCTGGATGATAATTTTTTGTTG|TCATCCAG|GGGGGAATCATTTCTCTACAAGGGATAGATTGCATGTATT ========== Event 2020 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGTCATCTCTGGGTCATCTGACAGCCATGTCTTAAATATAGGGCTGCCACTGGTATGTGCTTGTTGTAGGAAATTCAGCCTGTCA------------CTAGGCGGGACCCGCAGCAGTGCCCTG Chimp: AAGGTCATCTCTGGGTCATTTGACAGCCATGTCTTAAATATAGGGCTGCCACTGGTATGTGCTTGTTGTAGGAAATTCAGCCTGTCA------------CTAGGCGGGACCCGCAGCAGTGCCCTG Gorilla: AAGGTCATCTCTGGGTCATTTGACAGCCATGTCTTAAATATAGGGCTGCCACTGGTATGTGCTTGTTGTAGGAAATTCAGCCTGTCAGTAGGCGTGTCAGTAGGCGGGACCCGCAGCAGTGCCCTG ↑ 3 2 4 1 Human: AAGGTCATCTCTGGGTCATCTGACAGCCATGTCTTAAATATAGGGCTGCCACTGGTATGTGCTTGTTGTAGGAAATTCAGCCTGTCA------------CTAGGCGGGACCCGCAGCAGTGCCCTG Cluster: [ ] Orangutan: AAGGTCATCTCTGGGTCATTTAACAGCCATGTCTTAAATATAGGGCTGCCACTGGTATGTGCTTGTTGTAAGAAATTCAGCCTGTCA------------CTAGGCGGGACCTGCAGCAGTGCCCTG Human > Gorilla --------------- chr22:5051035-5051040 Template switch process: F1: L TGCCACTGGTATGTGCTTGTTGTAGGAAATTCAGCCTGTCAGTAGGCG 1 F3: 4 TAGGCGGGACCCGCAGCAGTGCCCTGTGTCCTTCCTAGGG R RF: CTGACAGCCATGTCTTAAATATAGGGCTGCCACTGGTATGTGCTTGTTGTAGGAAATTCAGCCTGTCACTAGGCGGGACCCGCAGCAGTGCCCTGTGTCCTTCCTAGGG RR: GACTGTCGGTACAGAATTTATATCCCGACGGTGACCATACACGAACAACATCCTTTAAGTCGGACAGTGATCCGCCCTGGGCGTCGTCACGGGACACAGGAAGGATCCC F2: 3 GACTGT 2 Unidirectional alignment (log-probability: -33.7) GTATGTGCTTGTTGTAGGAAATTCAGCCTGTcagtaggcgtgtCAgTAGGCGGGACCCGCAGCAGTGCCCTGTGTCCTTCCTAGGG GTATGTGCTTGTTGTAGGAAATTCAGCCTGT------------CACTAGGCGGGACCCGCAGCAGTGCCCTGTGTCCTTCCTAGGG Template switch alignment (log-probability: -22.2) GTATGTGCTTGTTGTAGGAAATTCAGCCTGTCAgTAGGCG|TGTCAG|TAGGCGGGACCCGCAGCAGTGCCCTGTGTCCTTCCTAGGG GTATGTGCTTGTTGTAGGAAATTCAGCCTGTCACTAGGCG|TGTCAG|TAGGCGGGACCCGCAGCAGTGCCCTGTGTCCTTCCTAGGG ========== Event 2021 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: CAGTGATGGAAGCCACAAAAATGGG----------------ATCCCCAGTTACAGTTCTCAGGATCCAGCTA Chimp: Gorilla: CAGTGATGGAAGCCACAAAAAGGGGATCCCCATAACTGGGGATCCCCAGTTACAGTTCTCAGGATCCAGCTA ↑ 4 31 2 Human: CAGTGATGGAAGCCACAAAAATGGG----------------ATCCCCAGTTACAGTTCTCAGGATCCAGCTA Cluster: [ ] Orangutan: CAGTGATGGAAGCCACATAAAGGGG----------------ATCCCCAGTTACAGTTCTCAGGATCCAGCTA Human > Gorilla --------------- chr22:5531102-5531107 Template switch process: F1: L TGGTACTTGATGTATGTTACCAGTGATGGAAGCCACAAAAAGGGGATCCCCA 1 F3: 4 GGGATCCCCAGTTACAGTTCTCAGGATCCAGCTATGGGGCTGA R RF: TGGTACTTGATGTATGTTACCAGTGATGGAAGCCACAAAAATGGGATCCCCAGTTACAGTTCTCAGGATCCAGCTATGGGGCTGA RR: ACCATGAACTACATACAATGGTCACTACCTTCGGTGTTTTTACCCTAGGGGTCAATGTCAAGAGTCCTAGGTCGATACCCCGACT F2: 3 GTCAAT 2 Unidirectional alignment (log-probability: -39.5) TATGTTACCAGTGATGGAAGCCACAAAAAggggatccccataactgGGGATCCCCAGTTACAGTTCTCAGGATCCAGCTATGGGGC TATGTTACCAGTGATGGAAGCCACAAAAA----------------TGGGATCCCCAGTTACAGTTCTCAGGATCCAGCTATGGGGC Template switch alignment (log-probability: -22.4) TATGTTACCAGTGATGGAAGCCACAAAAAgGGGATCCCCA|TAACTG|GGGATCCCCAGTTACAGTTCTCAGGATCCAGCTATGGGGC TATGTTACCAGTGATGGAAGCCACAAAAATGGGATCCCCA|TAACTG|GGGATCCCCAGTTACAGTTCTCAGGATCCAGCTATGGGGC ========== Event 2022 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: gaCTCCTGAATCAGAAAAATCTTAATGCTTAATATTTATTAAGCAAACTAGAAGTAGAGTCCCTT Chimp: gaCTCCTGAATCAGAAAAATCTTAATGCTTAATATTTATTAAGCAAACTAGAAGTAGAGTCCCTT ↑ 3 4 1 2 Gorilla: gaCTCCTGAATCAGAAAAATCAAA-----------ATATTAAGCAAACTAGAAGTAGAGTCCCTT ↓ 3 4 1 2 Human: gaCTCCTGAATCAGAAAAATCTTAATGCTTAATATTTATTAAGCAAACTAGAAGTAGAGTCCCTT Cluster: [ ] Orangutan: gaCTCCTGAATCAGAAAAATCAAA-----------ATATTAAACAAACTAGAAGTAGAGCCCCTT Gorilla > Human --------------- chr2:222622896-222622906 Template switch process: F1: L TCAACAAATGTTGAATGAATGACTCCTGAATCAGAAAAATC------TTAA 1 F3: 4 TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA R RF: TCAACAAATGTTGAATGAATGACTCCTGAATCAGAAAAATCAAAATATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA RR: AGTTGTTTACAACTTACTTACTGAGGACTTAGTCTTTTTAGTTTTATAATTCGTTTGATCTTCATCTCAGGGAATTTATGAGATT F2: 3 TTATAATTCGT 2 Unidirectional alignment (log-probability: -37.8) AAATGTTGAATGAATGACTCCTGAATCAGAAAAATCttAAtgcttaatattTATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA AAATGTTGAATGAATGACTCCTGAATCAGAAAAATCAAAA-----------TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA Template switch alignment (log-probability: -27.3) AAATGTTGAATGAATGACTCCTGAATCAGAAAAATC------TTAA|TGCTTAATATT|TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA AAATGTTGAATGAATGACTCCTGAATCAGAAAAATCAAAATATTAA|TGCTTAATATT|TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA Gorilla > Chimp --------------- chr2B:113536323-113536333 Template switch process: F1: L TCAACAAATGTTGAATGAATGACTCCTGAATCAGAAAAATC------TTAA 1 F3: 4 TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA R RF: TCAACAAATGTTGAATGAATGACTCCTGAATCAGAAAAATCAAAATATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA RR: AGTTGTTTACAACTTACTTACTGAGGACTTAGTCTTTTTAGTTTTATAATTCGTTTGATCTTCATCTCAGGGAATTTATGAGATT F2: 3 TTATAATTCGT 2 Unidirectional alignment (log-probability: -37.8) AAATGTTGAATGAATGACTCCTGAATCAGAAAAATCttAAtgcttaatattTATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA AAATGTTGAATGAATGACTCCTGAATCAGAAAAATCAAAA-----------TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA Template switch alignment (log-probability: -27.3) AAATGTTGAATGAATGACTCCTGAATCAGAAAAATC------TTAA|TGCTTAATATT|TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA AAATGTTGAATGAATGACTCCTGAATCAGAAAAATCAAAATATTAA|TGCTTAATATT|TATTAAGCAAACTAGAAGTAGAGTCCCTTAAATACTCTAA ========== Event 2023 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GGGTCTTTAGACATCTATAATTGCTAAACACCCACATGGGTGTTTAGCAATTATAGATGTCTAAAAATGAAA ↑ 3 2 1 4 Chimp: GGGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGT---------CTATAGATGTCTAAAAATGAAA ↓ 3 2 1 4 Gorilla: GGGTCTTTAGACATCTATAATTGCTAAACACCCACATGGGTGTTTAGCAATTATAGATGTCTAAAAATGAAA Human: GGGTCTTTAGACATCTATAATTGCTAAACACCCACATGGGTGTTTAGCAATTATAGATGTCTAAAAATGAAA Cluster: [ ] Orangutan: GGGTCTTTAGAG-----------------GGCCACGTGGGTGTTTAGCAATTATAGATGTCTAAAAATGAAA Chimp > Human ------------- chr2:22792107-22792116 Template switch process: F1: L ACTGTGGGGTCTTTAGACATCTATAATTGCTAAACACCCACATGGGT 1 F3: 4 TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC R RF: ACTGTGGGGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGTCTATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC RR: TGACACCCCAGAAATCTGTAGATATTAACGATTTGTGGGTGCACCCAGATATCTACAGATTTTTACTTTCCTATAAAATCATCAGGAG F2: 3 TAACGATTTG 2 Unidirectional alignment (log-probability: -35.9) GGTCTTTAGACATCTATAATTGCTAAACACCCACaTGGGTgtttagcaatTATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC GGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGTC---------TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC Template switch alignment (log-probability: -22.6) GGTCTTTAGACATCTATAATTGCTAAACACCCACaTGGGT|GTTTAGCAAT|TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC GGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGT|GTTTAGCAAT|TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC Chimp > Gorilla --------------- chr2A:22937584-22937593 Template switch process: F1: L ACTGTGGGGTCTTTAGACATCTATAATTGCTAAACACCCACATGGGT 1 F3: 4 TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC R RF: ACTGTGGGGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGTCTATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC RR: TGACACCCCAGAAATCTGTAGATATTAACGATTTGTGGGTGCACCCAGATATCTACAGATTTTTACTTTCCTATAAAATCATCAGGAG F2: 3 TAACGATTTG 2 Unidirectional alignment (log-probability: -35) GGTCTTTAGACATCTATAATTGCTAAACACCCACaTGGGTgtttagcaatTATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC GGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGT---------CTATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC Template switch alignment (log-probability: -22.7) GGTCTTTAGACATCTATAATTGCTAAACACCCACaTGGGT|GTTTAGCAAT|TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC GGTCTTTAGACATCTATAATTGCTAAACACCCACGTGGGT|GTTTAGCAAT|TATAGATGTCTAAAAATGAAAGGATATTTTAGTAGTCCTC ========== Event 2024 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGCCCTATATTTTGGTTCCAGTTCAGTCAACACTTAACAGTCTATCTAGTTCATACTGTAT Chimp: AAGCCCTATATTTTGGTTCCAGTTCAGT-----GT---TGATCTATCTAGTTCATACTGTAT Gorilla: AAGCCCTATATTTTGGTTCCAGTTAAGT-----GT---TGATCTATCTAGTTCATACTGTAT ↓ 3 1 2 4 Human: AAGCCCTATATTTTGGTTCCAGTTCAGTCAACACTTAACAGTCTATCTAGTTCATACTGTAT Cluster: [ ] Orangutan: AAGCCCTATATTTTGGTTCCAGTTAAGT-----GT---TGATCTATCTAGTTCATACTGTAT Gorilla > Human --------------- chr2:224183566-224183578 Template switch process: F1: L TAGAATGATTATTTCATAAGCCCTATATTTTGGTTCCAGTTCAGT 1 F3: 4 TCTATCTAGTTCATACTGTATATTAAACACATTATGCAAA R RF: TAGAATGATTATTTCATAAGCCCTATATTTTGGTTCCAGTTAAGTGTTGATCTATCTAGTTCATACTGTATATTAAACACATTATGCAAA RR: ATCTTACTAATAAAGTATTCGGGATATAAAACCAAGGTCAATTCACAACTAGATAGATCAAGTATGACATATAATTTGTGTAATACGTTT F2: 3 GACAATTCACAAC 2 Unidirectional alignment (log-probability: -43.7) TGATTATTTCATAAGCCCTATATTTTGGTTCCAGTTcAGTcaacacttaacaG----TCTATCTAGTTCATACTGTATATTAAACACATTATGCAAA TGATTATTTCATAAGCCCTATATTTTGGTTCCAGTTAAGT------------GTTGATCTATCTAGTTCATACTGTATATTAAACACATTATGCAAA Template switch alignment (log-probability: -28.5) TGATTATTTCATAAGCCCTATATTTTGGTTCCAGTTcAGT|CAACACTTAACaG|TCTATCTAGTTCATACTGTATATTAAACACATTATGCAAA TGATTATTTCATAAGCCCTATATTTTGGTTCCAGTTAAGT|CAACACTTAACTG|TCTATCTAGTTCATACTGTATATTAAACACATTATGCAAA ========== Event 2025 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCAAGAGTTCCTGACATTCCTTATGGGAG-------------CGGCTACACCTTGAAATCAACCACG Chimp: CCCAAGAGTTCCTGACATTCCTTAT-GGAG-------------CGACTACACCTTGAAATCAACCACG ↓ 3 1 42 Gorilla: CCCAAGAGTTCCTGACATTCCTTAT-GGAGCAGCCGCTCCATAAGGCTACACCTTGAAATCAACCACG Human: CCCAAGAGTTCCTGACATTCCTTATGGGAG-------------CGGCTACACCTTGAAATCAACCACG Cluster: [ ] Orangutan: CCCAAGAGTTCCTGACATT-CTTAT-GGAG-------------TGGCTACACCTTGAAATCAACCACG Chimp > Gorilla --------------- chr2B:117417688-117417702 Template switch process: F1: L GCCAGCAGGATACCCAAGAGTTCCTGACATTCCTTATGGAGC 1 F3: 4 CTACACCTTGAAATCAACCACGGAGGCCGCGGGGCTCCAC R RF: GCCAGCAGGATACCCAAGAGTTCCTGACATTCCTTATGGAGCGACTACACCTTGAAATCAACCACGGAGGCCGCGGGGCTCCAC RR: CGGTCGTCCTATGGGTTCTCAAGGACTGTAAGGAATACCTCGCTGATGTGGAACTTTAGTTGGTGCCTCCGGCGCCCCGAGGTG F2: 3 GGAATACCTCGCCGA 2 Unidirectional alignment (log-probability: -35.1) CAGCAGGATACCCAAGAGTTCCTGACATTCCTTATGGAGCagccgctccataaGgCTACACCTTGAAATCAACCACGGAGGCCGCGGGGCTCCAC CAGCAGGATACCCAAGAGTTCCTGACATTCCTTATGGAGC-------------GACTACACCTTGAAATCAACCACGGAGGCCGCGGGGCTCCAC Template switch alignment (log-probability: -23.2) CAGCAGGATACCCAAGAGTTCCTGACATTCCTTATGGAGC|AGcCGCTCCATAAGG|CTACACCTTGAAATCAACCACGGAGGCCGCGGGGCTCCAC CAGCAGGATACCCAAGAGTTCCTGACATTCCTTATGGAGC|AGTCGCTCCATAAGG|CTACACCTTGAAATCAACCACGGAGGCCGCGGGGCTCCAC ========== Event 2026 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TGCAAACCAAACTACAGGGTA-CACTCTTAGTGAGCCAGCCA-AACTGCAGGGTAGACTGCCCGCCAGGTCT Chimp: TGCAAACCAAACTACAGGGTAGTACTCTTAGTGAGCCAGCCAAAACTGCA-GGTAGACTGC--CCCAGGTCT ↓ 1 3 4 Gorilla: TGCAAACCAAACTACAGGGTA-GACTCTTAGTGAGCCAGCCA-AACTGCAGGGTAGACTGCCTGCCAGGTCT Human: TGCAAACCAAACTACAGGGTA-CACTCTTAGTGAGCCAGCCA-AACTGCAGGGTAGACTGCCCGCCAGGTCT Cluster: [] Orangutan: TGCAAACCAAACTACAGGGTA-GACTCTTAGGGAGCCAGCCA-AACTGCACGGTAGACTTCCCGCCAGGTCT Chimp > Gorilla --------------- chr22:7320290-7320295 Template switch process: F1: L GGCTTCCCAAAGATCTTGGGTGCAAACCAAACTACAGGGTAG-ACTCTTAGTGAGCCAGCCAAA 1 F3: 4 GGTAGACTGCCT R RF: GGCTTCCCAAAGATCTTGGGTGCAAACCAAACTACAGGGTAGTACTCTTAGTGAGCCAGCCAAAACTGCAGGTAGACTGCCC RR: CCGAAGGGTTTCTAGAACCCACGTTTGGTTTGATGTCCCATCATGAGAATCACTCGGTCGGTTTTGACGTCCATCTGACGGG F2: 3 GACGTC 2 Unidirectional alignment (log-probability: -41.5) AAACCAAACTACAGGGTAG-ACTCTTAGTGAGCCAGCC-AAACTGCAgGGTAGACTGCct AAACCAAACTACAGGGTAGTACTCTTAGTGAGCCAGCCAAAACTGCA-GGTAGACTGC-- Template switch alignment (log-probability: -31.6) AAACCAAACTACAGGGTAG-ACTCTTAGTGAGCCAGCCAAA|CTGCAG|GGTAGACTGCCt AAACCAAACTACAGGGTAGTACTCTTAGTGAGCCAGCCAAA|CTGCAG|GGTAGACTGCCC ========== Event 2027 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCCTAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCTG---GCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAG Chimp: GGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCTG---GCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAG ↓ 3 2 1 4 Gorilla: GGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCAT-----AATGAGGCGGCTACACGTCTTGGCAAGACACCAACAG ↑ 3 2 1 4 Human: GGCCTAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCTG---GCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAG Cluster: [ ] Orangutan: GG-CCAGTGAACTCAGGGGG-CTC-ATATG-CAGAGC---TGC--CCTCA-GTTGCTACACATC-TGGCAAGACA-CAACAG Human > Gorilla --------------- chr22:27101963-27101972 Template switch process: F1: L GATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC 1 F3: 4 GGCTACACGTCTTGGCAAGACACCAACAGCTGAGAGGCCCAGACCAAAA R RF: GATGGCCTAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCTGGCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAGCTGAGAGGCCCAGACCAAAA RR: CTACCGGATCACTTGAGTCCCCCGGAGTAATACCTTTTCGGACCGGGAGTCCACCGATGTGTAGAACCGTTCTGTGGTTGTCGACTCTCCGGGTCTGGTTTT F2: 3 CGGAGTAATA 2 Unidirectional alignment (log-probability: -43.5) ATGGCCcAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCataaTG------AGGcGGCTACACgTCTTGGCAAGACACCAACAGCTGAGAGGCCC ATGGCCTAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC----TGGCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAGCTGAGAGGCCC Template switch alignment (log-probability: -28.3) ATGGCCcAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC|ATAATGAGGC|GGCTACACgTCTTGGCAAGACACCAACAGCTGAGAGGCCC ATGGCCTAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC|ATAATGAGGC|GGCTACACATCTTGGCAAGACACCAACAGCTGAGAGGCCC Chimp > Gorilla --------------- chr22:27101963-27101972 Template switch process: F1: L GATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC 1 F3: 4 GGCTACACGTCTTGGCAAGACACCAACAGCTGAGAGGCCCAGACCAAAA R RF: GATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCTGGCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAGCTGAGAGGCCCAGACCAAAA RR: CTACCGGGTCACTTGAGTCCCCCGGAGTAATACCTTTTCGGACCGGGAGTCCACCGATGTGTAGAACCGTTCTGTGGTTGTCGACTCTCCGGGTCTGGTTTT F2: 3 CGGAGTAATA 2 Unidirectional alignment (log-probability: -37.9) ATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCCataaTG------AGGcGGCTACACgTCTTGGCAAGACACCAACAGCTGAGAGGCCC ATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC----TGGCCCTCAGGTGGCTACACATCTTGGCAAGACACCAACAGCTGAGAGGCCC Template switch alignment (log-probability: -22.7) ATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC|ATAATGAGGC|GGCTACACgTCTTGGCAAGACACCAACAGCTGAGAGGCCC ATGGCCCAGTGAACTCAGGGGGCCTCATTATGGAAAAGCC|ATAATGAGGC|GGCTACACATCTTGGCAAGACACCAACAGCTGAGAGGCCC ========== Event 2028 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTGATTCTTATAACCAATACTGCACCCTTCCTCAGGTTTTGTTAAATACATAG Chimp: CTTTGATTCTTATAACCAATACTGCACCCTTCCTTAGGTTTTGTTAAATACATAG ↓ 13 24 Gorilla: CTTTGATTCTTATAACCAATAGTGCAGCCTTCCTCAGGTTTTGTTAACTACATAG Human: CTTTGATTCTTATAACCAATACTGCACCCTTCCTCAGGTTTTGTTAAATACATAG Cluster: [ ] Orangutan: CTTTCATTCTTATAACCAATACTGCAGCCTTCCTCAGGTTTTGTTAAATACATAG Chimp > Gorilla --------------- chr2B:118732802-118732807 Template switch process: F1: L CTAGATTAGACCCCATTGTTCTTTGATTCTTATAACCAATA 1 F3: 4 CCTTCCTCAGGTTTTGTTAACTACATAGAGGTTTTTGTTTGTTTGT R RF: CTAGATTAGACCCCATTGTTCTTTGATTCTTATAACCAATACTGCACCCTTCCTTAGGTTTTGTTAAATACATAGAGGTTTTTGTTTGTTTGT RR: GATCTAATCTGGGGTAACAAGAAACTAAGAATATTGGTTATGACGTGGGAAGGAATCCAAAACAATTTATGTATCTCCAAAAACAAACAAACA F2: 3 GACGTG 2 Unidirectional alignment (log-probability: -38.7) TAGATTAGACCCCATTGTTCTTTGATTCTTATAACCAATAgTGCAgCCTTCCTcAGGTTTTGTTAAcTACATAGAGGTTTTTGTTT TAGATTAGACCCCATTGTTCTTTGATTCTTATAACCAATACTGCACCCTTCCTTAGGTTTTGTTAAATACATAGAGGTTTTTGTTT Template switch alignment (log-probability: -27.7) TAGATTAGACCCCATTGTTCTTTGATTCTTATAACCAATA|GTGCAG|CCTTCCTcAGGTTTTGTTAAcTACATAGAGGTTTTTGTTT TAGATTAGACCCCATTGTTCTTTGATTCTTATAACCAATA|GTGCAG|CCTTCCTTAGGTTTTGTTAAATACATAGAGGTTTTTGTTT ========== Event 2029 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GCCAACTGCAAGGGCGAGCAGTTTGTGTTTGAGAAGGGCGAGTACGCCCACTGGGACTGGTGGACCAGCAGCCAGAGGACAGACTCAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCC Chimp: Gorilla: GCCAACTGCAAGGGCGAGCAGTTTGTGTTTGAGAAGGGCGAGTACGCCCACTGGGACTGGTGGACCAG--------------------CAGCCTGAGGCCCATCAAAGTGGTGAGCCC ↓ 3 2 4 1 Human: GCCAACTGCAAGGGCGAGCAGTTTGTGTTTGAGAAGGGCGAGTACGCCCACTGGGACTGGTGGACCAGCAGCCAGAGGACAGACTCAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr22:25455809-25455815 Template switch process: F1: L TTTGAGAAGGGCGAGTACGCCCACTGGGACTGGTGGACCAGCAGCCAGAGG 1 F3: 4 CAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCCCCTGCCATCA R RF: AGTTTGTGTTTGAGAAGGGCGAGTACGCCCACTGGGACTGGTGGACCAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCCCCTGCCATCA RR: TCAAACACAAACTCTTCCCGCTCATGCGGGTGACCCTGACCACCTGGTCGTCGGACTCCGGGTAGTTTCACCACTCGGGGGACGGTAGT F2: 3 TCAGACA 2 Unidirectional alignment (log-probability: -39.6) CGAGTACGCCCACTGGGACTGGTGGACCagcagccagaggacagactcAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCCCCTGCCA CGAGTACGCCCACTGGGACTGGTGGACC--------------------AGCAGCCTGAGGCCCATCAAAGTGGTGAGCCCCCTGCCA Template switch alignment (log-probability: -28) CGAGTACGCCCACTGGGACTGGTGGACCAGCAGCCaGAGG|ACAgACT|CAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCCCCTGCCA CGAGTACGCCCACTGGGACTGGTGGACCAGCAGCCTGAGG|ACAAACT|CAGCAGCCTGAGGCCCATCAAAGTGGTGAGCCCCCTGCCA ========== Event 2030 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tttaataaatagttactgctgacagaggtatcacaaggttgggtcagaagacacttttcctgtcctctcggagtttacaggataatggaTTTAAATGAAAAATAATGGAAAGAAAAGAAAGGCCCTTGAACAGATGTCACTGATG ↓ 3 2 1 4 Chimp: TTTAATAAATAGTTACTGCTGACAGAGGTATCACAAGGTTGGGTCAGAAGACCCTTTTCCTGTCCTCTTGGAGTTTATAGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAG-ATGTCACTTGAACAGATGTCACTGATG Gorilla: TTTAATAAATAGTTACTGCTGACAGAGGTATCACAAGGTTGGGTCAGAAGACCCTTTTCCTGTCCTCTTGGAGTTTATAGGataatggatttaaatgaaaaataatggaaagaaaagaaaGGCCCTTGAACAGATGTCACTGATG Human: tttaataaatagttactgctgacagaggtatcacaaggttgggtcagaagacacttttcctgtcctctcggagtttacaggataatggaTTTAAATGAAAAATAATGGAAAGAAAAGAAAGGCCCTTGAACAGATGTCACTGATG Cluster: [ ] Orangutan: GTTAATAAATAGTTACTGCTGACAGAGGCATcacaagggtgggtcagaagacccttttcctgtcctcttggagtttataggataatggATTTAAATGAAAAATAATGGAAAGGAAAGAAAGGCCCTTGAACAGATGTCACTGATG Human > Chimp ------------- chr2B:117182496-117182500 Template switch process: F1: L ATAGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAGA 1 F3: 4 CTTGAACAGATGTCACTGATGCCTCTGCATATCACTGAAG R RF: TGACAGAGGTATCACAAGGTTGGGTCAGAAGACACTTTTCCTGTCCTCTCGGAGTTTACAGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAGAAAGGCCCTTGAACAGATGTCACTGATGCCTCTGCATATCACTGAAG RR: ACTGTCTCCATAGTGTTCCAACCCAGTCTTCTGTGAAAAGGACAGGAGAGCCTCAAATGTCCTATTACCTAAATTTACTTTTTATTACCTTTCTTTTCTTTCCGGGAACTTGTCTACAGTGACTACGGAGACGTATAGTGACTTC F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -33.2) AGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAGAtgtcA-----CTTGAACAGATGTCACTGATGCCTCTGCATATCACTGAAG AGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAGA----AAGGCCCTTGAACAGATGTCACTGATGCCTCTGCATATCACTGAAG Template switch alignment (log-probability: -21.9) AGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAGA|TGTCA|CTTGAACAGATGTCACTGATGCCTCTGCATATCACTGAAG AGGATAATGGATTTAAATGAAAAATAATGGAAAGAAAAGA|TGTCA|CTTGAACAGATGTCACTGATGCCTCTGCATATCACTGAAG ========== Event 2031 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGACAATCTAGCATCCAAATATACTGATAGTAT------------TTCCAAACCATTTATTGAGCCATGGGCTTATTTG Chimp: GGACAATCTAGCATCCAAATATACTGATAGTAT------------TTCCAAACCATT-TTTGAGCCATGGGCTTATTTG ↓ 3 1 2 4 Gorilla: GGACAATCTAGCATCCAAATATACTATCAGTAT------------------------ATTTGAGCCATGGGCTTATTTG Human: GGACAATCTAGCATCCAAATATACTGATAGTAT------------TTCCAAACCATTTATTGAGCCATGGGCTTATTTG Cluster: [ ] Orangutan: GGACAATCTAGCATCCAAATATACTGATAGTATTTCCAAACCATT------------TTTCGAGCCATGGGCTTATTTG Chimp > Gorilla --------------- chr2B:119121215-119121223 Template switch process: F1: L CCAAGAAGTCACATTGGGACAATCTAGCATCCAAATATACT 1 F3: 4 TTTGAGCCATGGGCTTATTTGAACATTCCTTCAAAGCTAT R RF: CCAAGAAGTCACGTTGGGACAATCTAGCATCCAAATATACTGATAGTATTTCCAAACCATTTTTGAGCCATGGGCTTATTTGAACATTCCTTGAAAGCTAT RR: GGTTCTTCAGTGCAACCCTGTTAGATCGTAGGTTTATATGACTATCATAAAGGTTTGGTAAAAACTCGGTACCCGAATAAACTTGTAAGGAACTTTCGATA F2: 3 ATATGACTA 2 Unidirectional alignment (log-probability: -44.7) CAAGAAGTCACaTTGGGACAATCTAGCATCCAAATATACTatcAGT-----------ATaTTTGAGCCATGGGCTTATTTGAACATTCCTTcAAAGCTAT CAAGAAGTCACGTTGGGACAATCTAGCATCCAAATATACTGATAGTATTTCCAAACCATTTTTGAGCCATGGGCTTATTTGAACATTCCTTGAAAGCTAT Template switch alignment (log-probability: -27.9) CAAGAAGTCACaTTGGGACAATCTAGCATCCAAATATACT|ATCAGTATA|TTTGAGCCATGGGCTTATTTGAACATTCCTTcAAAGCTAT CAAGAAGTCACGTTGGGACAATCTAGCATCCAAATATACT|ATCAGTATA|TTTGAGCCATGGGCTTATTTGAACATTCCTTGAAAGCTAT ========== Event 2032 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATCAGGTTTGAGGGAGTTACTTGCTTTCATCAGGTCACCTTGTCCCCTACCTCAGGGAGCCCCACAGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGG------------GTGTGCAAGTGGGTGTGTATGGGTGGAGGAATCTGAC Chimp: TATCAGGTTTGAGGGAGTTACTTGCTTTCATCAGGTCACCTTGTCCCGTACCTCAGGGAACCCCACAGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGG------------GTGTGCAAGTGGGTGTGTATGGGTGGAGGAATCTGAC ↑ 3 2 4 1 Gorilla: TATCAGGTTTGAGGGAGTTACTTGCTTTCATCAGGTCACTTTGTCCCCTACCTCAGGGAGCCCCACAGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGG------------------------GTGTGTATGGGTGGAGAAATCTGAC ↓ 3 2 4 1 Human: TATCAGGTTTGAGGGAGTTACTTGCTTTCATCAGGTCACCTTGTCCCCTACCTCAGGGAGCCCCACAGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGG------------GTGTGCAAGTGGGTGTGTATGGGTGGAGGAATCTGAC Cluster: [ ] Orangutan: AACCAGGTTTGAGGGAGTTATTTGCTTTCATCAGGTCACCTTGTCCCCTACCTCAGGGAGCCCCACAGCTCTGAGTGCTTTGGCTGTGAGAGAATTCCATCCTCTGGGTGTGCAAGTGG------------GTGTGTATGGGTGGAGGAATCTGAC Gorilla > Human --------------- chr2:14483920-14483924 Template switch process: F1: L AGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTG 1 F3: 4 GGGTGTGTATGGGTGGAGGAATCTGACCAAATAAGGCTTTAC R RF: ACTTGCTTTCATCAGGTCACTTTGTCCCCTACCTCAGGGAGCCCCACAGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTGTATGGGTGGAGAAATCTGACCAAATAAGGCTTTAC RR: TGAACGAAAGTAGTCCAGTGAAACAGGGGATGGAGTCCCTCGGGGTGTCGAGACTCACGAAACCGACACCCTCTTAAGGTAGGAGACCCACACATACCCACCTCTTTAGACTGGTTTATTCCGAAATG F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -33.7) GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTgggtgtgcaagtGGGTGTGTATGGGTGGAGgAATCTGACCAAATAAGGCTTT GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCT------------GGGTGTGTATGGGTGGAGAAATCTGACCAAATAAGGCTTT Template switch alignment (log-probability: -22.1) GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTG|CAAGT|GGGTGTGTATGGGTGGAGgAATCTGACCAAATAAGGCTTT GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTG|CAAGT|GGGTGTGTATGGGTGGAGAAATCTGACCAAATAAGGCTTT Gorilla > Chimp --------------- chr2B:14498469-14498473 Template switch process: F1: L AGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTG 1 F3: 4 GGGTGTGTATGGGTGGAGGAATCTGACCAAATAAGGCTTTAC R RF: ACTTGCTTTCATCAGGTCACTTTGTCCCCTACCTCAGGGAGCCCCACAGCTCTGAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTGTATGGGTGGAGAAATCTGACCAAATAAGGCTTTAC RR: TGAACGAAAGTAGTCCAGTGAAACAGGGGATGGAGTCCCTCGGGGTGTCGAGACTCACGAAACCGACACCCTCTTAAGGTAGGAGACCCACACATACCCACCTCTTTAGACTGGTTTATTCCGAAATG F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -33.7) GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTgggtgtgcaagtGGGTGTGTATGGGTGGAGgAATCTGACCAAATAAGGCTTT GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCT------------GGGTGTGTATGGGTGGAGAAATCTGACCAAATAAGGCTTT Template switch alignment (log-probability: -22.1) GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTG|CAAGT|GGGTGTGTATGGGTGGAGgAATCTGACCAAATAAGGCTTT GAGTGCTTTGGCTGTGGGAGAATTCCATCCTCTGGGTGTG|CAAGT|GGGTGTGTATGGGTGGAGAAATCTGACCAAATAAGGCTTT ========== Event 2033 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: cattgagatccactgCTCTACAGAAA----------------------------------TCTAAGGGATTTCTGTAGAAATCCCCACATCATAGCACTGTGGAAAA Chimp: cattgagatccactgCTCTACAGAAA-------------------------------------------------------TCCTCACATCATAGCACTCTGGAAAA ↓ 3 4 2 1 Gorilla: cattgagatccactgCTCTACAGAAA-------------TCCCTCAGATTTCTGTAGAAA---------------------TCCTCACATCATAGCACTCTGGAAAA Human: cattgagatccactgCTCTACAGAAA----------------------------------TCTAAGGGATTTCTGTAGAAATCCCCACATCATAGCACTGTGGAAAA Cluster: [ ] Orangutan: cattgagatccactgCTCTACAGAAATCTAAGGGAGAAT------------------------------------------ACCCCACATCATAGCACTCTGGAAAA Chimp > Gorilla --------------- chr2B:14449844-14449852 Template switch process: F1: L GGCAAAATTGCCCCTCATTGAGATCCACTGCTCTACAGAAATCCCTCA 1 F3: 4 AGAAATCCTCACATCATAGCACTCTGGAAAAGGATGCCAGTTTAG R RF: GGCAAAATTGCCCCTCATTGAGATCCACTGCTCTACAGAAAT-CCTCACATCATAGCACTCTGGAAAAGGATGCCAGTTTAG RR: CCGTTTTAACGGGGAGTAACTCTAGGTGACGAGATGTCTTTA-GGAGTGTAGTATCGTGAGACCTTTTCCTACGGTCAAATC F2: 3 TGTCTTTAG 2 Unidirectional alignment (log-probability: -41.1) TGCCCCTCATTGAGATCCACTGCTCTACAGAaatccctcagatttctgtagaAATCCTCACATCATAGCACTCTGGAAAAGGATGCCAG TGCCCCTCATTGAGATCCACTGCTCTACAGA---------------------AATCCTCACATCATAGCACTCTGGAAAAGGATGCCAG Template switch alignment (log-probability: -28.3) TGCCCCTCATTGAGATCCACTGCTCTACAGAAATcCCTCA|GATTTCTGT|AGAAATCCTCACATCATAGCACTCTGGAAAAGGATGCCAG TGCCCCTCATTGAGATCCACTGCTCTACAGAAAT-CCTCA|GATTTCTGT|AGAAATCCTCACATCATAGCACTCTGGAAAAGGATGCCAG ========== Event 2034 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGAGAGAGGAAAGACTGCAACTTGCTTGTGTTTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGC--------------------TAATGAGTCCTTAGGATCTCTAG ↓ 3 2 4 1 Chimp: GAGAAAGAGGAAAGACTGCAACTTGCTTGTGTTTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGC----------TAACAAGTTCTAATGAGTCCTTAGGATCTCTAG Gorilla: GAGAGAGAGGGAAGACTGCAACTTGCTTGTGTTTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGCTAACAAGTTC----------TAATGAGTCCTTAGGATCTCTAG Human: GAGAGAGAGGAAAGACTGCAACTTGCTTGTGTTTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGC--------------------TAATGAGTCCTTAGGATCTCTAG Cluster: [ ] Orangutan: GAGAGAGAGGAAAGACTGCAACTTGCTTATGTTTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGCTAACAAGTTC----------TAATGAGTCCTTAGGATCTCTAG Human > Chimp ------------- chr22:23212790-23212795 Template switch process: F1: L TTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGCTAA 1 F3: 4 CTAATGAGTCCTTAGGATCTCTAGCAGGTTATGTGGCTTGA R RF: AACTTGCTTGTGTTTCCCATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGCTAATGAGTCCTTAGGATCTCTAGCAGGTTATGTGGCTTGA RR: TTGAACGAACACAAAGGGTACAATTGGTAAAGGGGAGACGAGATATGTCTCTCGATTACTCAGGAATCCTAGAGATCGTCCAATACACCGAACT F2: 3 TTGAAC 2 Unidirectional alignment (log-probability: -25.3) CATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGctaacaagttCTAATGAGTCCTTAGGATCTCTAGCAGGTTATGTGGCTTG CATGTTAACCATTTCCCCTCTGCTCTATACAGAGAG----------CTAATGAGTCCTTAGGATCTCTAGCAGGTTATGTGGCTTG Template switch alignment (log-probability: -16.1) CATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGCTAA|CAAGTT|CTAATGAGTCCTTAGGATCTCTAGCAGGTTATGTGGCTTG CATGTTAACCATTTCCCCTCTGCTCTATACAGAGAGCTAA|CAAGTT|CTAATGAGTCCTTAGGATCTCTAGCAGGTTATGTGGCTTG ========== Event 2035 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGA Chimp: TAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGA ↓ 3 2 1 4 Gorilla: TAAAAATAACTATGATAAGCTAGAAATTGCTATATTTCTAGCATGGGTTTGGGATTTTCAAA ↑ 3 2 1 4 Human: TAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGA Cluster: [ ] Orangutan: TAAAAATAACTATGATAAGCTAGAAATTGCTAT--AAACAACATGGGTTTGGGATTTTCAGA Human > Gorilla --------------- chr22:22663953-22663958 Template switch process: F1: L TATACATAAAAATAACTATGATAAGCTAGAAATTGCTATAT 1 F3: 4 CATGGGTTTGGGATTTTCAAATACAGTCTAAAAGTTGTGA R RF: TATACATAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGATACAGTCTAAAAGTTGTGA RR: ATATGTATTTTTATTGATACTATTCGATCTTTAACGATATATTTGTTGTACCCAAACCCTAAAAGTCTATGTCAGATTTTCAACACT F2: 3 GATCTT 2 Unidirectional alignment (log-probability: -34.3) ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATATttctAgCATGGGTTTGGGATTTTCAaATACAGTCTAAAAGTTGTGA ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGATACAGTCTAAAAGTTGTGA Template switch alignment (log-probability: -22) ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATAT|TTCTAG|CATGGGTTTGGGATTTTCAaATACAGTCTAAAAGTTGTGA ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATAT|TTCTAG|CATGGGTTTGGGATTTTCAGATACAGTCTAAAAGTTGTGA Chimp > Gorilla --------------- chr22:22663953-22663958 Template switch process: F1: L TATACATAAAAATAACTATGATAAGCTAGAAATTGCTATAT 1 F3: 4 CATGGGTTTGGGATTTTCAAATACAGTCTAAAAGTTGTGA R RF: TATACATAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGATACAGTCTAAAAGTTGTGA RR: ATATGTATTTTTATTGATACTATTCGATCTTTAACGATATATTTGTTGTACCCAAACCCTAAAAGTCTATGTCAGATTTTCAACACT F2: 3 GATCTT 2 Unidirectional alignment (log-probability: -34.3) ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATATttctAgCATGGGTTTGGGATTTTCAaATACAGTCTAAAAGTTGTGA ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATATAAACAACATGGGTTTGGGATTTTCAGATACAGTCTAAAAGTTGTGA Template switch alignment (log-probability: -22) ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATAT|TTCTAG|CATGGGTTTGGGATTTTCAaATACAGTCTAAAAGTTGTGA ATACATAAAAATAACTATGATAAGCTAGAAATTGCTATAT|TTCTAG|CATGGGTTTGGGATTTTCAGATACAGTCTAAAAGTTGTGA ========== Event 2036 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: tggaggagatcacctgggaagATCTTTGAAGCTTATGAAGCGA----------------------------TCTTCCCAGGTACCAAATCAATAA ↑ 3 2 1 4 Chimp: tggaggagatcacctgggaagATCTTTGAAGCTTATGAAGCTT--------------TTCTCTATAGCTCTACCTCCCAGGTACCAAATCAATAA Gorilla: tggatgagatcacctgggaagATCTTTGAAGCTTATGAAGCTTTTCTCTATAGCTCT--------------ACCTCCCAGGTACCAAATCAATAA Human: tggaggagatcacctgggaagATCTTTGAAGCTTATGAAGCGA----------------------------TCTTCCCAGGTACCAAATCAATAA Cluster: [ ] Orangutan: tggatgagatcacctggggagATCTTTGAAGCTTATGAAGCTTTTCTCTATAGCTCT--------------ACCTCCCAGATACCAAAACAATAA Chimp > Human ------------- chr2:23354851-23354855 Template switch process: F1: L TGGAGGAGATCACCTGGGAAGATCTTTGAAGCTTATGAAGC 1 F3: 4 TCCCAGGTACCAAATCAATAAGCCAGTTCTGCCCGTTTGG R RF: TGGAGGAGATCACCTGGGAAGATCTTTGAAGCTTATGAAGCTTTTCTCTATAGCTCTACCTCCCAGGTACCAAATCAATAAGCCAGTTCTGCCCGTTTGG RR: ACCTCCTCTAGTGGACCCTTCTAGAAACTTCGAATACTTCGAAAAGAGATATCGAGATGGAGGGTCCATGGTTTAGTTATTCGGTCAAGACGGGCAAACC F2: 3 TCTAG 2 Unidirectional alignment (log-probability: -27.8) GGAGGAGATCACCTGGGAAGATCTTTGAAGCTTATGAAGcgatCT------------------TCCCAGGTACCAAATCAATAAGCCAGTTCTGCCCGTTTGG GGAGGAGATCACCTGGGAAGATCTTTGAAGCTTATGAAG----CTTTTCTCTATAGCTCTACCTCCCAGGTACCAAATCAATAAGCCAGTTCTGCCCGTTTGG Template switch alignment (log-probability: -15.9) GGAGGAGATCACCTGGGAAGATCTTTGAAGCTTATGAAGC|GATCT|TCCCAGGTACCAAATCAATAAGCCAGTTCTGCCCGTTTGG GGAGGAGATCACCTGGGAAGATCTTTGAAGCTTATGAAGC|GATCT|TCCCAGGTACCAAATCAATAAGCCAGTTCTGCCCGTTTGG ========== Event 2037 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTAAAGACAAAAAGGTAAAGCATGGCAAAAAGTTTTTGCCATGGTTTTCCCATACCTAGATT Chimp: TTTAAAGACAAAAAGGTAAAGCATGGCAAAAAGTTTTTGCCATGGTTTTCCCATACCTAGATT ↑ 1 43 2 Gorilla: TGTAAAGACAAAAAGGTAAAG---------CTGTTTTTGCCATGGTTTTCCCATACCTAGATT ↓ 1 43 2 Human: TTTAAAGACAAAAAGGTAAAGCATGGCAAAAAGTTTTTGCCATGGTTTTCCCATACCTAGATT Cluster: [ ] Orangutan: TTTAAAGACAAAAAGGTAAAG---------CTGTTTTTGCCATGGTTTTCCTATACCTAGATT Gorilla > Human --------------- chr2:23370629-23370638 Template switch process: F1: L CGAAAATGAATACATTAAATTTTAAAGACAAAAAGGTAAAGC 1 F3: 4 GTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT R RF: CGAAAATGAATACATTAAATTGTAAAGACAAAAAGGTAAAGCTGTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT RR: GCTTTTACTTATGTAATTTAACATTTCTGTTTTTCCATTTCGACAAAAACGGTACCAAAAGGGTATGGATCTAAATGAAACAA F2: 3 AAAAACGGTA 2 Unidirectional alignment (log-probability: -34.9) AAAATGAATACATTAAATTtTAAAGACAAAAAGGTAAAGCatggcaaaaaGTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT AAAATGAATACATTAAATTGTAAAGACAAAAAGGTAAAGC---------TGTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT Template switch alignment (log-probability: -22.5) AAAATGAATACATTAAATTtTAAAGACAAAAAGGTAAAGC|ATGGCAAAAA|GTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT AAAATGAATACATTAAATTGTAAAGACAAAAAGGTAAAGC|ATGGCAAAAA|GTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT Gorilla > Chimp --------------- chr2A:23835831-23835840 Template switch process: F1: L CAAAAATGAATACATTAAATTTTAAAGACAAAAAGGTAAAGC 1 F3: 4 GTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT R RF: CGAAAATGAATACATTAAATTGTAAAGACAAAAAGGTAAAGCTGTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT RR: GCTTTTACTTATGTAATTTAACATTTCTGTTTTTCCATTTCGACAAAAACGGTACCAAAAGGGTATGGATCTAAATGAAACAA F2: 3 AAAAACGGTA 2 Unidirectional alignment (log-probability: -40.4) AAAATGAATACATTAAATTtTAAAGACAAAAAGGTAAAGCatggcaaaaaGTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT AAAATGAATACATTAAATTGTAAAGACAAAAAGGTAAAGC---------TGTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT Template switch alignment (log-probability: -28.1) AAAATGAATACATTAAATTtTAAAGACAAAAAGGTAAAGC|ATGGCAAAAA|GTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT AAAATGAATACATTAAATTGTAAAGACAAAAAGGTAAAGC|ATGGCAAAAA|GTTTTTGCCATGGTTTTCCCATACCTAGATTTACTTTGTT ========== Event 2038 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTGCATCCTGGCGCCTGGGAGGGAGGTCACCACGCTGCCTT--------------------------CTGCCTTGATTAGGCCGGTAACA Chimp: GCTGCATCCCGGCGCCTGGGAGGGAGGTCACCACGCTGCCTT--------------------------CTGCCTTGATTAGGCCGGTAACA ↓ 3 24 1 Gorilla: GCTGCATCCCGGGGCCTGGGAGGGAGGTCACCACGCTGCCTTCTGAAGGCAGCGTGGTGACCTCCCTCCTGCCTTGATTAGGCCGGTAACA ↑ 3 24 1 Human: GCTGCATCCTGGCGCCTGGGAGGGAGGTCACCACGCTGCCTT--------------------------CTGCCTTGATTAGGCCGGTAACA Cluster: [ ] Orangutan: GCTGCATCCCGGCGCCTGGGAG--GGGTCACCACGCTGCCTT--------------------------CTGCCTTGATTAGGCCGGTAACA Human > Gorilla --------------- chr2A:23520913-23520935 Template switch process: F1: L CTGCATCCCGGGGCCTGGGAGGGAGGTCACCACGCTGCCTTCTG 1 F3: 4 CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG R RF: CTGCATCCTGGCGCCTGGGAGGGAGGTCACCACGCTGCCTTCTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG RR: GACGTAGGACCGCGGACCCTCCCTCCAGTGGTGCGACGGAAGACGGAACTAATCCGGCCATTGTCAGTCCTTTCGGGACCC F2: 3 CTCCCTCCAGTGGTGCGACGGAA 2 Unidirectional alignment (log-probability: -59.3) ATCCcGGgGCCTGGGAGGGAGGTCACCACGCTGCCTTctgaaggcagcgtggtgacctccctcCTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG ATCCTGGCGCCTGGGAGGGAGGTCACCACGCTGCCTT--------------------------CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG Template switch alignment (log-probability: -29.8) ATCCcGGgGCCTGGGAGGGAGGTCACCACGCTGCCTTCTG|AAGGCAGCGTGGTGACCTCCCTC|CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG ATCCTGGCGCCTGGGAGGGAGGTCACCACGCTGCCTTCTG|AAGGCAGCGTGGTGACCTCCCTC|CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG Chimp > Gorilla --------------- chr2A:23520913-23520935 Template switch process: F1: L CTGCATCCCGGGGCCTGGGAGGGAGGTCACCACGCTGCCTTCTG 1 F3: 4 CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG R RF: CTGCATCCCGGCGCCTGGGAGGGAGGTCACCACGCTGCCTTCTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG RR: GACGTAGGGCCGCGGACCCTCCCTCCAGTGGTGCGACGGAAGACGGAACTAATCCGGCCATTGTCAGTCCTTTCGGGACCC F2: 3 CTCCCTCCAGTGGTGCGACGGAA 2 Unidirectional alignment (log-probability: -53.8) ATCCCGGgGCCTGGGAGGGAGGTCACCACGCTGCCTTctgaaggcagcgtggtgacctccctcCTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG ATCCCGGCGCCTGGGAGGGAGGTCACCACGCTGCCTT--------------------------CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG Template switch alignment (log-probability: -24.2) ATCCCGGgGCCTGGGAGGGAGGTCACCACGCTGCCTTCTG|AAGGCAGCGTGGTGACCTCCCTC|CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG ATCCCGGCGCCTGGGAGGGAGGTCACCACGCTGCCTTCTG|AAGGCAGCGTGGTGACCTCCCTC|CTGCCTTGATTAGGCCGGTAACAGTCAGGAAAGCCCTGGG ========== Event 2039 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGTGGCCCAGGAAAAAGTAAAGGTTGTCACCTTTACAGCTAAATGTAAATGAATA Chimp: AAGTGGCCCAGGAAAAAGTAAAGGTTGTCACCTTTACAGCTAAATGTAAATGAATA ↑ 3 1 2 4 Gorilla: AAGTGGCCCAGGAAAAAGTAAAGGTGA-C----AAACAGCTAAATGTAAATGAATA ↓ 3 1 2 4 Human: AAGTGGCCCAGGAAAAAGTAAAGGTTGTCACCTTTACAGCTAAATGTAAATGAATA Cluster: [ ] Orangutan: AAGTGG-----CAAAAAGTAAAGGTGA-C----AAACAGCTAAATGTAAATGAATA Gorilla > Human --------------- chr2:229896119-229896128 Template switch process: F1: L TCCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT 1 F3: 4 ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA R RF: TCCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGTGACAAACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA RR: AGGTGGTCGTCTTTTCTTCACCGGGTCCTTTTTCATTTCCACTGTTTGTCGATTTACATTTACTTATAATTGAGATATAATATGAT F2: 3 TTTCCACTGT 2 Unidirectional alignment (log-probability: -35.3) CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT-----tgtcacctttACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGTGACAA----------ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA Template switch alignment (log-probability: -17) CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT|TGTCACCTTT|ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT|TGTCACCTTT|ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA Gorilla > Chimp --------------- chr2B:120966784-120966793 Template switch process: F1: L TCCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT 1 F3: 4 ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA R RF: TCCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGTGACAAACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA RR: AGGTGGTCGTCTTTTCTTCACCGGGTCCTTTTTCATTTCCACTGTTTGTCGATTTACATTTACTTATAATTGAGATATAATATGAT F2: 3 TTTCCACTGT 2 Unidirectional alignment (log-probability: -35.3) CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT-----tgtcacctttACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGTGACAA----------ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA Template switch alignment (log-probability: -17) CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT|TGTCACCTTT|ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA CCACCAGCAGAAAAGAAGTGGCCCAGGAAAAAGTAAAGGT|TGTCACCTTT|ACAGCTAAATGTAAATGAATATTAACTCTATATTATACTA ========== Event 2040 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ttggcttattatttcctaAGCTTTCTCCT------CAAA---CTCACTCCTGAAAAAGGCCAAGTTAAGgggattct Chimp: TTGGCTTATTATTTCCTAAGCTTTTTCCT------CAAA---CTCACTCCTGAAAAAGGCCAAGTTAAGgggattct Gorilla: TTGGCTTATTATTTCCTAAGCTTTCTCCTCTTTTTCAGGCTTTTCACTCCTAAAAAAGGCCAAGTTAAGgggattct ↑ 4 1 3 2 Human: ttggcttattatttcctaAGCTTTCTCCT------CAAA---CTCACTCCTGAAAAAGGCCAAGTTAAGgggattct Cluster: [ ] Orangutan: TTGGCTTATTATTTCCTAAGCTTTCTCCT------CAAA---CTCACCCCTGAAAAAGGCCAAGTTAAGgggattct Human > Gorilla --------------- chr2B:12172537-12172544 Template switch process: F1: L AGACACAAAAATTTGGCTTATTATTTCCTAAGCTTTCTCCTC 1 F3: 4 GCTTT----------TCACTCCTAAAAAAGGCCAAGTTAAGGGGATTCTTGGCAGAGATGCAGG R RF: AGACACAAAAATTTGGCTTATTATTTCCTAAGCTTTCTCCTCAAACTCACTCCTGAAAAAGGCCAAGTTAAGGGGATTCTTGGCAGAGATGCAGG RR: TCTGTGTTTTTAAACCGAATAATAAAGGATTCGAAAGAGGAGTTTGAGTGAGGACTTTTTCCGGTTCAATTCCCCTAAGAACCGTCTCTACGTCC F2: 3 GACTTTTT 2 Unidirectional alignment (log-probability: -45.2) ACACAAAAATTTGGCTTATTATTTCCTAAGCTTTCTCCT----CtttttcaggctttTCACTCCTaAAAAAGGCCAAGTTAAGGGGATTCTT ACACAAAAATTTGGCTTATTATTTCCTAAGCTTTCTCCTCAAAC-------------TCACTCCTGAAAAAGGCCAAGTTAAGGGGATTCTT Template switch alignment (log-probability: -32.9) ACACAAAAATTTGGCTTATTATTTCCTAAGCTTTCTCCTC|TTTTTCAG|GCTTT----------TCACTCCTaAAAAAGGCCAAGTTAAGGGGATTCTT ACACAAAAATTTGGCTTATTATTTCCTAAGCTTTCTCCTC|TTTTTCAG|GCTTTCTCCTCAAACTCACTCCTGAAAAAGGCCAAGTTAAGGGGATTCTT ========== Event 2041 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GAATGGAGAGAGGGACTTCAT------------------GTCAGCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCACACATTTTCCCTGACTCATGAAAACTTAGAGCTGG Chimp: GAATGGAGAGAGGGACTTCAT---------GAATTAGCCCTGGGCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCACACATTTTCCCTGACTCATGAAAACTTAGAGCTGG Gorilla: GAATGGAGAGAGGGACTTCATAAATTAGCT---------CTGGGCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCACACATTTTCCCTGACTCATGAAAACTTAGAGCTGG ↓ 1 4 3 2 Human: GAATGGAGAGAGGGACTTCAT------------------GTCAGCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCACACATTTTCCCTGACTCATGAAAACTTAGAGCTGG Cluster: [ ] Orangutan: GAATGGAGAGAGGGACTTCATAAATTAGCC---------CTGGGCTGGCTAAGCATGTCTGACAAGCTTCTTTTCAGAGTGCACACATTTTCCCTGACTCATGAAAACTTAGCGCTGG Gorilla > Human --------------- chr22:20658473-20658476 Template switch process: F1: L AGAATGTGGATGGAAAAGAAGAATGGAGAGAGGGACTTCAT 1 F3: 4 GCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCA R RF: AGAATGTGGATGGAAAAGAAGAATGGAGAGAGGGACTTCATAAATTAGCTCTGGGCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCACACATTTTCCCTGAC RR: TCTTACACCTACCTTTTCTTCTTACCTCTCTCCCTGAAGTATTTAATCGAGACCCGACCGACTCGTACAGACTGTTCGAAGAAAAGTCTCACGTGTGTAAAAGGGACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -25.6) GAATGTGGATGGAAAAGAAGAATGGAGAGAGGGACTTCAT------------GtcaGCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCA GAATGTGGATGGAAAAGAAGAATGGAGAGAGGGACTTCATAAATTAGCTCTGG---GCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCA Template switch alignment (log-probability: -16.2) GAATGTGGATGGAAAAGAAGAATGGAGAGAGGGACTTCAT|GTCA|GCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCA GAATGTGGATGGAAAAGAAGAATGGAGAGAGGGACTTCAT|GTCA|GCTGGCTGAGCATGTCTGACAAGCTTCTTTTCAGAGTGCA ========== Event 2042 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: ACATTGTTTGTGGAGACCCCTAGGTCCCCAGGGACCTAGGAGGATGGAAAGGTCATAAAGGGGATGGAAGAGCATCAAAGACACAGTATC----CACCTAGCAATTTGAATTAAGGGTTCTC Chimp: Gorilla: ATATTGTTTTTGGAGACCCCTAGGTCCCCAGGGACCTAGGAGGATGGAAAGGTCATAAAGGGGATGGACGAGCATCAAAGACACAGTATC--------CCACAATTTGAATTAAGGGTTCTC ↓ 3 2 1 4 Human: ACATTGTTTGTGGAGACCCCTAGGTCCCCAGGGACCTAGGAGGATGGAAAGGTCATAAAGGGGATGGAAGAGCATCAAAGACACAGTATC----CACCTAGCAATTTGAATTAAGGGTTCTC Cluster: [ ] Orangutan: ATATTGTTTTTGGAGACCCCTAGGTCCCCAGGGACCTAGGAGGATGGAAAGGTCATAAAGGGGATGGAAGAGCATCAAAGACACAGTATCCACC----TCACAATTTGAATTAACGGTTCTC Gorilla > Human --------------- chr2:11581699-11581704 Template switch process: F1: L AGGTCATAAAGGGGATGGAAGAGCATCAAAGACACAGTATCC 1 F3: 4 CAATTTGAATTAAGGGTTCTCTGCGTAGGCCATAAACCCA R RF: CTAGGTCCCCAGGGACCTAGGAGGATGGAAAGGTCATAAAGGGGATGGACGAGCATCAAAGACACAGTATCCCACAATTTGAATTAAGGGTTCTCTGCATAGGCCATAAACCCA RR: GATCCAGGGGTCCCTGGATCCTCCTACCTTTCCAGTATTTCCCCTACCTGCTCGTAGTTTCTGTGTCATAGGGTGTTAAACTTAATTCCCAAGAGACGTATCCGGTATTTGGGT F2: 3 GATCCA 2 Unidirectional alignment (log-probability: -38.8) GTCATAAAGGGGATGGAaGAGCATCAAAGACACAGTATCCacctagCAATTTGAATTAAGGGTTCTCTGCgTAGGCCATAAACCCA GTCATAAAGGGGATGGACGAGCATCAAAGACACAGTATCC----CACAATTTGAATTAAGGGTTCTCTGCATAGGCCATAAACCCA Template switch alignment (log-probability: -27.5) GTCATAAAGGGGATGGAaGAGCATCAAAGACACAGTATCC|ACCTAG|CAATTTGAATTAAGGGTTCTCTGCgTAGGCCATAAACCCA GTCATAAAGGGGATGGACGAGCATCAAAGACACAGTATCC|ACCTAG|CAATTTGAATTAAGGGTTCTCTGCATAGGCCATAAACCCA ========== Event 2043 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTCCAAGAGATGTGGCCTGAGGCTTTGGACACAAAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTCTG-GGATGAGCTGGGATTTGGAAGGTC ↓ 3 2 1 4 Chimp: TTCCAAGAGATGTGGCCTGAGGCTTTGGACACAAAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTAAAGCCTTGAGCTGGGATTTGGAAGGTC Gorilla: TTCCAAGAGATGTGGCCTGAGGCTTTGGACACAAAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTAAAGCCTTGAGCTGGGATTTGGAAAGTA ↑ 3 2 1 4 Human: TTCCAAGAGATGTGGCCTGAGGCTTTGGACACAAAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTCTG-GGATGAGCTGGGATTTGGAAGGTC Cluster: [ ] Orangutan: TTCCAAGAGATGTGGCCTAAGGCTTTGGACA--CAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTAAAGCCTTGAGCAGGGATTTGGAAGGTC Human > Chimp ------------- chr22:17214896-17214902 Template switch process: F1: L GGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT 1 F3: 4 TGAGCTGGGATTTGGAAGGTCATGGGTCAGGTCTAAGTCT R RF: AGGCTTTGGACACAAAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTCTGGGATGAGCTGGGATTTGGAAGGTCAGGGGTCAGGTCTAAGTCT RR: TCCGAAACCTGTGTTTCCTTTCGGTCTTTCGTACCCGGTCCCTCTCTTTTCCTCCCAGACCCTACTCGACCCTAAACCTTCCAGTCCCCAGTCCAGATTCAGA F2: 3 TCCGAAA 2 Unidirectional alignment (log-probability: -34.5) GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTaaagcCT----TGAGCTGGGATTTGGAAGGTCAtGGGTCAGGTCTAAGTCT GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT-----CTGGGATGAGCTGGGATTTGGAAGGTCAGGGGTCAGGTCTAAGTCT Template switch alignment (log-probability: -22.1) GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT|AAAGCCT|TGAGCTGGGATTTGGAAGGTCAtGGGTCAGGTCTAAGTCT GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT|AAAGCCT|TGAGCTGGGATTTGGAAGGTCAGGGGTCAGGTCTAAGTCT Human > Gorilla --------------- chr22:14166266-14166272 Template switch process: F1: L GGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT 1 F3: 4 TGAGCTGGGATTTGGAAAGTAAGGGGTCAGGTCTAAGTCT R RF: AGGCTTTGGACACAAAGGAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTCTGGGATGAGCTGGGATTTGGAAGGTCAGGGGTCAGGTCTAAGTCT RR: TCCGAAACCTGTGTTTCCTTTCGGTCTTTCGTACCCGGTCCCTCTCTTTTCCTCCCAGACCCTACTCGACCCTAAACCTTCCAGTCCCCAGTCCAGATTCAGA F2: 3 TCCGAAA 2 Unidirectional alignment (log-probability: -39.1) GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGTaaagcCT----TGAGCTGGGATTTGGAAaGTaAGGGGTCAGGTCTAAGTCT GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT-----CTGGGATGAGCTGGGATTTGGAAGGTCAGGGGTCAGGTCTAAGTCT Template switch alignment (log-probability: -27.7) GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT|AAAGCCT|TGAGCTGGGATTTGGAAaGTaAGGGGTCAGGTCTAAGTCT GAAAGCCAGAAAGCATGGGCCAGGGAGAGAAAAGGAGGGT|AAAGCCT|TGAGCTGGGATTTGGAAGGTCAGGGGTCAGGTCTAAGTCT ========== Event 2044 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCT-TAGACTTCAGTGGGTCTAAGCTCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTA ↑ 1 4 3 2 Chimp: ATTCT-TAGACTTCAGTGGGTTGA--ATCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTA Gorilla: ATTCT-TAGACTTCAGTGGGTTGA--ATCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTA Human: ATTCT-TAGACTTCAGTGGGTCTAAGCTCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTA Cluster: [ ] Orangutan: ATTCTTAAGACTTCAGTGGGTTGA--ATCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTA Chimp > Human ------------- chr22:31438453-31438458 Template switch process: F1: L AATGCATGAGTCTTAAGGGAAATTCTTAGACTTCAGTGGGT 1 F3: 4 TCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTAAA R RF: AGTGCATGAGTCTTAAGGGAAATTCTTAGACTTCAGTGGGTTGAATCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTAAA RR: TCACGTACTCAGAATTCCCTTTAAGAATCTGAAGTCACCCAACTTAGTCTTGAGACTCGAATCTCTTTGTCCTACGGGGTCATTT F2: 3 CGAATC 2 Unidirectional alignment (log-probability: -31.8) aTGCATGAGTCTTAAGGGAAATTCTTAGACTTCAGTGGGTctAAgcTCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTAAA GTGCATGAGTCTTAAGGGAAATTCTTAGACTTCAGTGGGTTGAA--TCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTAAA Template switch alignment (log-probability: -22) aTGCATGAGTCTTAAGGGAAATTCTTAGACTTCAGTGGGT|CTAAGC|TCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTAAA GTGCATGAGTCTTAAGGGAAATTCTTAGACTTCAGTGGGT|CTAAGC|TCAGAACTCTGAGCTTAGAGAAACAGGATGCCCCAGTAAA ========== Event 2045 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTATAATGCTTTATAGGATAGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTT ↓ 1 4 2 Chimp: ATTTATAATGCTTTATAGGATGA--AACTGAAATGTCAGTTTCATTGTCTGGGCCTGTATGTT ↑ 1 4 2 Gorilla: ATTTATAATGCTTTATAGGATAGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTT Human: ATTTATAATGCTTTATAGGATAGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTT Cluster: [ ] Orangutan: ATTTATAATGCTTTATAGGATAGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTT Human > Chimp ------------- chr2B:123209264-123209273 Template switch process: F1: L AAGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT 1 F3: 4 TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA R RF: AAGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGATAGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA RR: TTCTCTTCTTAACGGGACCGTAAATATTACGAAATATCCTATCACAGGATCGAACAGTCAAAGTAACAGACCCGGACATACAATCTTTCATAT F2: 3 AAAGTCAAAG 2 Unidirectional alignment (log-probability: -34.6) AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGATgaaactgaaA-----------TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT---------AGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA Template switch alignment (log-probability: -22.5) AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT|GAAACTGAaA|TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT|GAAACTGACA|TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA Gorilla > Chimp --------------- chr2B:123209264-123209273 Template switch process: F1: L AAGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT 1 F3: 4 TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA R RF: AAGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGATAGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA RR: TTCTCTTCTTAACGGGACCGTAAATATTACGAAATATCCTATCACAGGATCGAACAGTCAAAGTAACAGACCCGGACATACAATCTTTCATAT F2: 3 AAAGTCAAAG 2 Unidirectional alignment (log-probability: -34.1) AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGATgaaactgaaA-----------TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT---------AGTGTCCTAGCTTGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA Template switch alignment (log-probability: -22.5) AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT|GAAACTGAaA|TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA AGAGAAGAATTGCCCTGGCATTTATAATGCTTTATAGGAT|GAAACTGACA|TGTCAGTTTCATTGTCTGGGCCTGTATGTTAGAAAGTATA ========== Event 2046 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAAAACACTATGAGGGGACACAGACCCTGAAGCACAGTCACACACGACTGTCCCC-ATGCTGCTCCTGGGCGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTGCCAG-----------------GCCTCGGTCTATGCCAGGCCTCACGCCACATCTTGCAGGCCCAT Chimp: TAAAAACACCATGAGGGGACACAGACCCTGAAGCACAGTCACACACGACTGTCCCCATTGCTGCTCCTGGGCGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTGCCAG-----------------GCCTCGGTCTATGCCAGGCCTCATGCCACATCTTGCAGGCCCAT ↑ 3 2 4 1 Gorilla: TAAAAACCCTATGAGGGGACACAGACCCTGACGCACAGTCACACACGACTGTCCCC-ATGCTGCTCCTGGGCGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTACCAG----------------------------------GCCTCACGCCACATCTTGCAGGCCCAT ↓ 3 2 4 1 Human: TAAAAACACTATGAGGGGACACAGACCCTGAAGCACAGTCACACACGACTGTCCCC-ATGCTGCTCCTGGGCGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTGCCAG-----------------GCCTCGGTCTATGCCAGGCCTCACGCCACATCTTGCAGGCCCAT Cluster: [ ] Orangutan: TAAAAATCCTAGGAGGGGACACAGACCCTGAAGCACAGTCACACACGACTGTCCCC-GTGCTGCTCCCGGGTGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTGCCAGGCCTCGGTCTATGCCAG-----------------GCCCCACGCCACATCTTGCAGGGTCAT Gorilla > Human --------------- chr2:233468945-233468952 Template switch process: F1: L TGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTGCCAGGCCTC 1 F3: 4 CCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCCCAGG R RF: CACAGACCCTGACGCACAGTCACACACGACTGTCCCCATGCTGCTCCTGGGCGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTACCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCCCAGG RR: GTGTCTGGGACTGCGTGTCAGTGTGTGCTGACAGGGGTACGACGAGGACCCGCCCACGACGGTGAGCAGACGTCCCTCGTAACCCTCCCCACCAACCCATGGTCCGGAGTGCGGTGTAGAACGTCCGGGTACGGGGACGGGTCC F2: 3 GTATCTGG 2 Unidirectional alignment (log-probability: -40.9) TGCAGGGAGCATTGGGAGGGGTGGTTGGGtgccaggcctcggtctaTgCCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCC TGCAGGGAGCATTGGGAGGGGTGGTTGGG-----------------TACCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCC Template switch alignment (log-probability: -28.1) TGCAGGGAGCATTGGGAGGGGTGGTTGGGTgCCAGGCCTC|GGTCTaTG|CCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCC TGCAGGGAGCATTGGGAGGGGTGGTTGGGTACCAGGCCTC|GGTCTGTG|CCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCC Gorilla > Chimp --------------- chr2B:124541727-124541734 Template switch process: F1: L TGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTGCCAGGCCTC 1 F3: 4 CCAGGCCTCATGCCACATCTTGCAGGCCCATGCCCCTGCCCAGGTTGGCCT R RF: CACAGACCCTGACGCACAGTCACACACGACTGTCCCCATGCTGCTCCTGGGCGGGTGCTGCCACTCGTCTGCAGGGAGCATTGGGAGGGGTGGTTGGGTACCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCCCAGGTTGGCCT RR: GTGTCTGGGACTGCGTGTCAGTGTGTGCTGACAGGGGTACGACGAGGACCCGCCCACGACGGTGAGCAGACGTCCCTCGTAACCCTCCCCACCAACCCATGGTCCGGAGTGCGGTGTAGAACGTCCGGGTACGGGGACGGGTCCAACCGGA F2: 3 GTATCTGG 2 Unidirectional alignment (log-probability: -46.5) TGCAGGGAGCATTGGGAGGGGTGGTTGGGtgccaggcctcggtctaTgCCAGGCCTCAtGCCACATCTTGCAGGCCCATGCCCCTGCC TGCAGGGAGCATTGGGAGGGGTGGTTGGG-----------------TACCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCC Template switch alignment (log-probability: -33.8) TGCAGGGAGCATTGGGAGGGGTGGTTGGGTgCCAGGCCTC|GGTCTaTG|CCAGGCCTCAtGCCACATCTTGCAGGCCCATGCCCCTGCC TGCAGGGAGCATTGGGAGGGGTGGTTGGGTACCAGGCCTC|GGTCTGTG|CCAGGCCTCACGCCACATCTTGCAGGCCCATGCCCCTGCC ========== Event 2047 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CCCAGAACCCCAAGGGGATCATTGCAGAGGGACTGATAGATGGACAGGATGGCCTGGTGAGGCCTGCGCCATCTGTGCCTTCAACCCGGCGGATCAAAGATGAATGTGTGATTGAGTGAGGCCTCACTGATGACAATGCACCCTGGCTGGAAAATGCAC Chimp: CCCAGAACCCCAAGGGGATCATTGCAGAGGGACTGATAGATGGGCAGGATGGCCTGGTGAGGCCTGCGCCATCTGTGCCTTCAACCCGGCGGATCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGACAATGCACCCTGGCTGGAAAATGCAC ↑ 3 2 1 4 Gorilla: CCCAGAACCCCAAGGGGATCATTGCAGAGGGACTGATAGATGGACAGGATGGCTTGGTGAGGCCTGCGCCATCTGTGCCTTCAACCCGGCGGATCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGAGGCCTCACCCTGGCTGGAAAATGCAC Human: CCCAGAACCCCAAGGGGATCATTGCAGAGGGACTGATAGATGGACAGGATGGCCTGGTGAGGCCTGCGCCATCTGTGCCTTCAACCCGGCGGATCAAAGATGAATGTGTGATTGAGTGAGGCCTCACTGATGACAATGCACCCTGGCTGGAAAATGCAC Cluster: [ ] Orangutan: CCCAGAACCCCAAGGGGATCGTTGCAAAGGGACTGATAGATGGACAGGATGGCCTGGTGAGGCCTACGCTATCTGTGCTTTCAACCTGGCAGATCAAAGATGAATGTGTAGTTGAGTGAGGCCTCACCAATGACAATGCACCCTGGCTGGAAAATGCAC Gorilla > Chimp --------------- chr22:17441245-17441249 Template switch process: F1: L ATCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGA 1 F3: 4 CACCCTGGCTGGAAAATGCACAGCAGGAGGCTCTCGTTTG R RF: CATTGCAGAGGGACTGATAGATGGACAGGATGGCTTGGTGAGGCCTGCGCCATCTGTGCCTTCAACCCGGCGGATCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGAGGCCTCACCCTGGCTGGAAAATGCACAGCAGGAGGCTCTGGTTTG RR: GTAACGTCTCCCTGACTATCTACCTGTCCTACCGAACCACTCCGGACGCGGTAGACACGGAAGTTGGGCCGCCTAGTTTCTACTTGCACACTAACTCACTCCGGAGTGATTACTCCGGAGTGGGACCGACCTTTTACGTGTCGTCCTCCGAGACCAAAC F2: 3 GTAAC 2 Unidirectional alignment (log-probability: -32.1) TCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGAcaatG----CACCCTGGCTGGAAAATGCACAGCAGGAGGCTCTcGTTTG TCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGA----GGCCTCACCCTGGCTGGAAAATGCACAGCAGGAGGCTCTGGTTTG Template switch alignment (log-probability: -21.9) TCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGA|CAATG|CACCCTGGCTGGAAAATGCACAGCAGGAGGCTCTcGTTTG TCAAAGATGAACGTGTGATTGAGTGAGGCCTCACTAATGA|CAATG|CACCCTGGCTGGAAAATGCACAGCAGGAGGCTCTGGTTTG ========== Event 2048 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAACATAATCCCAGGAGAAAGTGTTCATCAAAACATGTACCTGATGGGATACTTAT Chimp: AAACATAATCCCAGGAGAAAGT----ATGAATACTTGTACCTGATGGGATACTTAT ↑ 3 1 2 4 Gorilla: AAACATAATCCCAGGAGAAAGTATTCATCAAAACATGTACCTGATGAGATACTTAT Human: AAACATAATCCCAGGAGAAAGTGTTCATCAAAACATGTACCTGATGGGATACTTAT Cluster: [ ] Orangutan: AAACATAATCCCAGGAGAAAGTATTCATCAAAACACGTACCTGATGGGATACTTAT Gorilla > Chimp --------------- chr22:20702006-20702012 Template switch process: F1: L CCCTCATGAGTGCATTGGGAAACATAATCCCAGGAGAAAGTAT 1 F3: 4 TGTACCTGATGGGATACTTATTTGAAACCTAGTCCGGTAG R RF: CCCTCATGAGTGCATTGGGAAACATAATCCCAGGAGAAAGTATTCATCAAAACATGTACCTGATGAGATACTTATTTGAAACCTAGTCTGGTAG RR: GGGAGTACTCACGTAACCCTTTGTATTAGGGTCCTCTTTCATAAGTAGTTTTGTACATGGACTACTCTATGAATAAACTTTGGATCAGACCATC F2: 3 TCATAAG 2 Unidirectional alignment (log-probability: -38.8) TCATGAGTGCATTGGGAAACATAATCCCAGGAGAAAGTATg----AAtACtTGTACCTGATGgGATACTTATTTGAAACCTAGTCcGGTAG TCATGAGTGCATTGGGAAACATAATCCCAGGAGAAAGTATTCATCAAAACATGTACCTGATGAGATACTTATTTGAAACCTAGTCTGGTAG Template switch alignment (log-probability: -27.7) TCATGAGTGCATTGGGAAACATAATCCCAGGAGAAAGTAT|GAATACT|TGTACCTGATGgGATACTTATTTGAAACCTAGTCcGGTAG TCATGAGTGCATTGGGAAACATAATCCCAGGAGAAAGTAT|GAATACT|TGTACCTGATGAGATACTTATTTGAAACCTAGTCTGGTAG ========== Event 2049 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTCAGGCCACAGGCCCATGCCATGGTCT--TTCTTCCATGTGACCTAGCAGACCTCCTCC ↓ 3 1 2 4 Chimp: GTTCAGGCCACAGGCCCATGCCATGACCATGGCCTTCCATATGACCTAGCAGACCTCCTCC ↑ 3 1 2 4 Gorilla: GTTCAGGCCACAGGCCCATGCCATGGTCT--TTCTTCCATGTGACCTAGCAGACCTCCTCC Human: GTTCAGGCCACAGGCCCATGCCATGGTCT--TTCTTCCATGTGACCTAGCAGACCTCCTCC Cluster: [ ] Orangutan: GTTCAGGCCACAGGCCCATGCCATGGTCT--TTCTTCCATGTGACCTAGCAGACCTCCTCC Human > Chimp ------------- chr2B:8217242-8217249 Template switch process: F1: L ATCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG 1 F3: 4 CTTCCATATGACCTAGCAGACCTCCTCCTGTCCCACCGGTACCTCAGC R RF: ATCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATGGTCTTTCTTCCATGTGACCTAGCAGACCTCCTCCTGTCCCACCGGTACCTCAGC RR: TAGTGTCTCGGGGTCCCAAGTCCGGTGTCCGGGTACGGTACCAGAAAGAAGGTACACTGGATCGTCTGGAGGAGGACAGGGTGGCCATGGAGTCG F2: 3 CGGTACCA 2 Unidirectional alignment (log-probability: -39) TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATGaccatggc------CTTCCATaTGACCTAGCAGACCTCCTCCTGTCCCACCGGT TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG--------GTCTTTCTTCCATGTGACCTAGCAGACCTCCTCCTGTCCCACCGGT Template switch alignment (log-probability: -22.4) TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG|ACCATGGC|CTTCCATaTGACCTAGCAGACCTCCTCCTGTCCCACCGGT TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG|ACCATGGC|CTTCCATGTGACCTAGCAGACCTCCTCCTGTCCCACCGGT Gorilla > Chimp --------------- chr2B:8217242-8217249 Template switch process: F1: L ATCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG 1 F3: 4 CTTCCATATGACCTAGCAGACCTCCTCCTGTCCCACCGGTACCTCAGC R RF: ATCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATGGTCTTTCTTCCATGTGACCTAGCAGACCTCCTCCTGTCCCACCGGTACCTCAGC RR: TAGTGTCTCGGGGTCCCAAGTCCGGTGTCCGGGTACGGTACCAGAAAGAAGGTACACTGGATCGTCTGGAGGAGGACAGGGTGGCCATGGAGTCG F2: 3 CGGTACCA 2 Unidirectional alignment (log-probability: -38.1) TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG------accatggcCTTCCATaTGACCTAGCAGACCTCCTCCTGTCCCACCGGT TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATGGTCTTT--------CTTCCATGTGACCTAGCAGACCTCCTCCTGTCCCACCGGT Template switch alignment (log-probability: -22.5) TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG|ACCATGGC|CTTCCATaTGACCTAGCAGACCTCCTCCTGTCCCACCGGT TCACAGAGCCCCAGGGTTCAGGCCACAGGCCCATGCCATG|ACCATGGC|CTTCCATGTGACCTAGCAGACCTCCTCCTGTCCCACCGGT ========== Event 2050 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCTTGTAAAAGTGATTGATGGACAGGTTTCCC----TCTTCGAAGAACAAATTTATCTC Chimp: GTCTTGTAAAAGTGATTGATGGACAGGTTTCCC----TCTTTGAAGAACAAATTTATCTC Gorilla: GTCTTGTAAAAGTGATTGATGGACAGGGAAACCTGTCCATTCGAAGAACAAATTTATCTC ↑ 3 1 2 4 Human: ATCTTGTAAAAGTGATTGATGGACAGGTTTCCC----TCTTCGAAGAACAAATTTATCTC Cluster: [ ] Orangutan: GTCTTGTAAAAGTGATTGATGGACAGGTTTCCC----TCTTCGAAGAACAAATTTATCTC Human > Gorilla --------------- chr22:18127842-18127853 Template switch process: F1: L ATGATCAGACTTGTGTCTTGTAAAAGTGATTGATGGACAGG 1 F3: 4 TTCGAAGAACAAATTTATCTCATGCTGGGAGTGAGAGATG R RF: ATGATCAGACTTGCATCTTGTAAAAGTGATTGATGGACAGGTTTCCCTCTTCGAAGAACAAATTTATCTCATGCTGGGAGTGAGAGATG RR: TACTAGTCTGAACGTAGAACATTTTCACTAACTACCTGTCCAAAGGGAGAAGCTTCTTGTTTAAATAGAGTACGACCCTCACTCTCTAC F2: 3 ACCTGTCCAAAG 2 Unidirectional alignment (log-probability: -49.3) TGATCAGACTTGtgTCTTGTAAAAGTGATTGATGGACAGGgaaacctgtcca--------TTCGAAGAACAAATTTATCTCATGCTGGGAGTGAGAGATG TGATCAGACTTGCATCTTGTAAAAGTGATTGATGGACAGG------------TTTCCCTCTTCGAAGAACAAATTTATCTCATGCTGGGAGTGAGAGATG Template switch alignment (log-probability: -28.3) TGATCAGACTTGtgTCTTGTAAAAGTGATTGATGGACAGG|GAAACCTGTCCA|TTCGAAGAACAAATTTATCTCATGCTGGGAGTGAGAGATG TGATCAGACTTGCATCTTGTAAAAGTGATTGATGGACAGG|GAAACCTGTCCA|TTCGAAGAACAAATTTATCTCATGCTGGGAGTGAGAGATG ========== Event 2051 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGATTCTAGGTGATGGATCAGACCTGGTTCTAGGAGTAGAAA-------AATTCTTCAAGAAGAATAAGA Chimp: TGATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAAGCAGGTCTTATTCTTCAAGAAGAATAAGA ↑ 3 2 1 4 Gorilla: TGATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAAA-------AATTCTTCAAGAAGAATAAGA Human: TGATTCTAGGTGATGGATCAGACCTGGTTCTAGGAGTAGAAA-------AATTCTTCAAGAAGAATAAGA Cluster: [ ] Orangutan: TGATTCTAGGTGATGGATCAGACCTGGTTCTAGGAGTAGAAA-------AATTCTTCAAGAAGAATAAGA Gorilla > Chimp --------------- chr2B:7668457-7668464 Template switch process: F1: L TGATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAA 1 F3: 4 TATTCTTCAAGAAGAATAAGAGCGACTGATTCATTATGGGG R RF: TGATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAAAAATTCTTCAAGAAGAATAAGAGCGACTGATTCATTATGGGG RR: ACTAAGATCCACTACCTAGTCTGGACGAAGATCCTCATCTTTTTAAGAAGTTCTTCTTATTCTCGCTGACTAAGTAATACCCC F2: 3 TCTGGACG 2 Unidirectional alignment (log-probability: -32) GATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAAgcaggtcttATTCTTCAAGAAGAATAAGAGCGACTGATTCATTATGGG GATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAA-------AAATTCTTCAAGAAGAATAAGAGCGACTGATTCATTATGGG Template switch alignment (log-probability: -22.3) GATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAA|GCAGGTCT|tATTCTTCAAGAAGAATAAGAGCGACTGATTCATTATGGG GATTCTAGGTGATGGATCAGACCTGCTTCTAGGAGTAGAA|GCAGGTCT|AATTCTTCAAGAAGAATAAGAGCGACTGATTCATTATGGG ========== Event 2052 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ataTTAGCTGACAACAAGGACACAGTTGTCCTTGTTGCACAGTCAATGAATAAAGTACTGAACTTCAGGGGTTTAGGGCAGTGGTTTC Chimp: ataTTAGCTGACAACA----------------------------AATGAATGAAGTACTGAACTTCAGGGGTTTAGGGCAGTGGTTTC Gorilla: ataTTATCTGACAACAAGGACC----------T-GAGCACAGTCAATGAATGAAGTACTGAACTTCAGGGGTTTAGGGCAGTGGTTTC ↑ 1 4 3 2 Human: ataTTAGCTGACAACAAGGACACAGTTGTCCTTGTTGCACAGTCAATGAATAAAGTACTGAACTTCAGGGGTTTAGGGCAGTGGTTTC Cluster: [ ] Orangutan: GTATTAGCTGACAACAAGGACC----------T-GTGCACAGTCAATGAATGAAGTACTGAACTTCAGGGGTTTAGGGCAGTGGTTTC Human > Gorilla --------------- chr2B:7480781-7480784 Template switch process: F1: L CTGGAAGGTTCCAAACTAAGATATTATCTGACAACAAGGAC 1 F3: 4 GCACAGTCAATGAATGAAGTACTGAACTTCAGGGGTTTAG R RF: CTGGAAGGTTCCAAACTAAGATATTAGCTGACAACAAGGACACAGTTGTCCTTGTTGCACAGTCAATGAATAAAGTACTGAACTTCAGGGGTTTAG RR: GACCTTCCAAGGTTTGATTCTATAATCGACTGTTGTTCCTGTGTCAACAGGAACAACGTGTCAGTTACTTATTTCATGACTTGAAGTCCCCAAATC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -36.7) TGGAAGGTTCCAAACTAAGATATTAtCTGACAACAAGGACctgA--------------GCACAGTCAATGAATgAAGTACTGAACTTCAGGGGTTTAG TGGAAGGTTCCAAACTAAGATATTAGCTGACAACAAGGAC---ACAGTTGTCCTTGTTGCACAGTCAATGAATAAAGTACTGAACTTCAGGGGTTTAG Template switch alignment (log-probability: -27.3) TGGAAGGTTCCAAACTAAGATATTAtCTGACAACAAGGAC|CTGA|GCACAGTCAATGAATgAAGTACTGAACTTCAGGGGTTTAG TGGAAGGTTCCAAACTAAGATATTAGCTGACAACAAGGAC|CTGA|GCACAGTCAATGAATAAAGTACTGAACTTCAGGGGTTTAG ========== Event 2053 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TCCTCGGGGAAGGAAGAATGTGCT-TCAATATTCTGGGAGCAGAGAGTGGCAGGAGCTAGAGCCTGGGGCATGGGTTGAAGCCATGTAGAGTCTGAAAGACC ↑ 1 4 3 2 Chimp: TCCTCGGGGAAGGAAGAATGTTCTGGGAATATTCTGGGAGCAGACAGTGGCAGGAGCTAGAGCCTGGGGCATGGGTTGAAGCCATGTAGAGTCTGAAAGACC Gorilla: TCCTCGGGGAAGGAAGAATGTGCT-TCAATATTCTGGGAGCCGAGAGTGGCAGGAGCTAGAGCCTGGGGCATGGGTTGAAGCTATGTAGAGTCTGAAAGACC Human: TCCTCGGGGAAGGAAGAATGTGCT-TCAATATTCTGGGAGCAGAGAGTGGCAGGAGCTAGAGCCTGGGGCATGGGTTGAAGCCATGTAGAGTCTGAAAGACC Cluster: [ ] Orangutan: TCCTCGGGGAGGGAAGAATGTGCT-TCAATATTCTGGGAGCAGAGAGTGGCAGGAGCTAGAGCCTGGGGCGTGGGTTGAAGCCACGAAGAGTCTGAAAGACC Chimp > Human ------------- chr2:6826840-6826845 Template switch process: F1: L GGTGGTCAGGAAGCTGTCCTTCCTCGGGGAAGGAAGAATGT 1 F3: 4 ATATTCTGGGAGCAGAGAGTGGCAGGAGCTAGAGCCTGG R RF: GGTGGTCAGGAAGCTGTCCTTCCTCGGGGAAGGAAGAATGTTCTGGGAATATTCTGGGAGCAGACAGTGGCAGGAGCTAGAGCCTGGGGCATGGGTTGAAGC RR: CCACCAGTCCTTCGACAGGAAGGAGCCCCTTCCTTCTTACAAGACCCTTATAAGACCCTCGTCTGTCACCGTCCTCGATCTCGGACCCCGTACCCAACTTCG F2: 3 ACTTCG 2 Unidirectional alignment (log-probability: -31.7) GTGGTCAGGAAGCTGTCCTTCCTCGGGGAAGGAAGAATGtgcTTC----AATATTCTGGGAGCAGAgAGTGGCAGGAGCTAGAGCCTGG GTGGTCAGGAAGCTGTCCTTCCTCGGGGAAGGAAGAATG---TTCTGGGAATATTCTGGGAGCAGACAGTGGCAGGAGCTAGAGCCTGG Template switch alignment (log-probability: -22) GTGGTCAGGAAGCTGTCCTTCCTCGGGGAAGGAAGAATGT|GCTTCA|ATATTCTGGGAGCAGAgAGTGGCAGGAGCTAGAGCCTGG GTGGTCAGGAAGCTGTCCTTCCTCGGGGAAGGAAGAATGT|GCTTCA|ATATTCTGGGAGCAGACAGTGGCAGGAGCTAGAGCCTGG ========== Event 2054 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATATGTAGATAGTT-TTTTACATACGTAAAAAACCTACTATTGACGTATGTAAACCTACACACATTGGCTT Chimp: ACATATGTAGATAGTT-TTTTACATATGTAAAAAACCTACTGTTGACGTATGTAAACCTACACACATTGGCTT Gorilla: ACATATGTAGATAGtttttttACATATACAAAAAACCTACTATTGACGTATGTAAACCTACACACATTGGCTT ↓ 1 4 3 2 Human: ACATATGTAGATAGTT-TTTTACATACGTAAAAAACCTACTATTGACGTATGTAAACCTACACACATTGGCTT Cluster: [ ] Orangutan: ACATATGTAGATAGTT-TTTTACATATGTAAAAAGCCTACTAATAACGTATGTAAACCTACACACATTGGCTT Gorilla > Human --------------- chr22:35428570-35428577 Template switch process: F1: L ATATGTAAACTATCTACATATGTAGATAGTTTTTT 1 F3: 4 AAAAAACCTACTATTGACGTATGTAAACCTACACACATTG R RF: ATATGTAAACTATCTACATATGTAGATAGTTTTTTTACATATACAAAAAACCTACTATTGACGTATGTAAACCTACACACATTG RR: TATACATTTGATAGATGTATACATCTATCAAAAAAATGTATATGTTTTTTGGATGATAACTGCATACATTTGGATGTGTGTAAC F2: 3 TGCATACA 2 Unidirectional alignment (log-probability: -27.5) ATATGTAAACTATCTACATATGTAGATAGTTTT-TTACATAcgtAAAAAACCTACTATTGACGTATGTAAACCTACACACATTG ATATGTAAACTATCTACATATGTAGATAGTTTTTTTACATATACAAAAAACCTACTATTGACGTATGTAAACCTACACACATTG Template switch alignment (log-probability: -16.6) ATATGTAAACTATCTACATATGTAGATAGTTTTTT|ACATACGT|AAAAAACCTACTATTGACGTATGTAAACCTACACACATTG ATATGTAAACTATCTACATATGTAGATAGTTTTTT|ACATACGT|AAAAAACCTACTATTGACGTATGTAAACCTACACACATTG ========== Event 2055 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: AATACTGCGGTTAAGAGCAAGCAGACAGACGT----GCCTGCCCGCAAGCCAGGCTTATT Chimp: AATACTGCGGTTAAGAGCAAGAAGACAGACGT----GCCTGCCCGCAAGCCAGGCTTATT ↓ 3 4 2 ↑ 3 2 4 Gorilla: AATACTGCGGTTAAGAGCAAGAAGACAGGCACGTCTTCTTGCCCGCAAGCCAGGCTTATT ↓ 3 2 4 Human: AATACTGCGGTTAAGAGCAAGCAGACAGACGT----GCCTGCCCGCAAGCCAGGCTTATT Cluster: [ ] Orangutan: AATACTGCGGTTAAGAGCAAGAAGACAGACGT----GCCTGCCCgcaagccaggcttatc Gorilla > Human --------------- chr2:6524609-6524615 Template switch process: F1: L CCCATGACAACAGACAGGAGAATACTGCGGTTAAGAGCAAGCAGACAG 1 F3: 4 TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT R RF: CCCATGACAACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAGGCACGTCTTCTTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT RR: GGGTACTGTTGTCTGTCCTCTTATGACGCCAATTCTCGTTCTTCTGTCCGTGCAGAAGAACGGGCGTTCGGTCCGAATAAGTGACTGTTTGGTGAACGA F2: 3 CCGTGCA 2 Unidirectional alignment (log-probability: -36.9) AACAGACAGGAGAATACTGCGGTTAAGAGCAAGcAGACAG-----------acgtgccTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAGGCACGTCTTCT-------TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT Template switch alignment (log-probability: -22.3) AACAGACAGGAGAATACTGCGGTTAAGAGCAAGcAGACAG|ACGTGCC|TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG|ACGTGCC|TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT Gorilla > Chimp --------------- chr2B:6444639-6444645 Template switch process: F1: L CAACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG 1 F3: 4 TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT R RF: CAACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAGGCACGTCTTCTTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT RR: GTTGTCTGTCCTCTTATGACGCCAATTCTCGTTCTTCTGTCCGTGCAGAAGAACGGGCGTTCGGTCCGAATAAGTGACTGTTTGGTGAACGA F2: 3 CCGTGCA 2 Unidirectional alignment (log-probability: -31.3) AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG-----------acgtgccTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAGGCACGTCTTCT-------TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT Template switch alignment (log-probability: -16.6) AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG|ACGTGCC|TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG|ACGTGCC|TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT Chimp > Gorilla --------------- chr2B:6404285-6404291 Template switch process: F1: L CAACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG 1 F3: 4 TTCTTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT R RF: CAACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAGACGTGCCTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACTTGCT RR: GTTGTCTGTCCTCTTATGACGCCAATTCTCGTTCTTCTGTCTGCACGGACGGGCGTTCGGTCCGAATAAGTGACTGTTTGGTGAACGA F2: 3 CTGCACG 2 Unidirectional alignment (log-probability: -36.8) AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG-------gcacgtcttctTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACT AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAGACGTGCC-----------TGCCCGCAAGCCAGGCTTATTCACTGACAAACCACT Template switch alignment (log-probability: -27.8) AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG|GCACGTC|TtCtTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACT AACAGACAGGAGAATACTGCGGTTAAGAGCAAGAAGACAG|GCACGTC|TGCCTGCCCGCAAGCCAGGCTTATTCACTGACAAACCACT ========== Event 2056 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CGTGGACAAAGTGTGCTGA-----TGTCTACACTGGCTATGTATGGACTTTCTGCGTCTTCAGGTTGGCAGATGG Chimp: CGTGGACAAAGTGTGCTGA-----TGTCTACACTGGCTATGTATGGACTTTCTACGTCTTCAGGTTGGCAGATGG Gorilla: TGTGGACAAAGTGTGCTGATAGCCAGTGTAGACTGGCTATGTATGGACTTTCTATGTCTTCAGGTTGGCAGATGG ↑ 1 3 4 2 Human: CGTGGACAAAGTGTGCTGA-----TGTCTACACTGGCTATGTATGGACTTTCTGCGTCTTCAGGTTGGCAGATGG Cluster: [] Orangutan: CGTGCACAAAGTGTGCTGA-----TGTCTACACTGGCTATGTATGTACTTTCTATGTCTTCAGGTTGGCAGATGG Human > Gorilla --------------- chr2B:6062783-6062793 Template switch process: F1: L GTGCTGAT 1 F3: 4 ACTGGCTATGTATGGACTTTCTATGTCTTCAGGTTGGCAGATGGGATGGGTGTCACTCCACTCA R RF: GTGCTGATGTCTACACTGGCTATGTATGGACTTTCTGCGTCTTCAGGTTGGCAGATGGGATGGGTGTCACTCCACTCA RR: CACGACTACAGATGTGACCGATACATACCTGAAAGACGCAGAAGTCCAACCGTCTACCCTACCCACAGTGAGGTGAGT F2: 3 GATGTGACCGA 2 Unidirectional alignment (log-probability: -40.1) GTGCTGATagccaGTgTAgACTGGCTATGTATGGACTTTCTatGTCTTCAGGTTGGCAG GTGCTGAT-----GTCTACACTGGCTATGTATGGACTTTCTGCGTCTTCAGGTTGGCAG Template switch alignment (log-probability: -27.9) GTGCTGAT|AGCCAGTGTAG|ACTGGCTATGTATGGACTTTCTatGTCTTCAGGTTGGCAG GTGCTGAT|AGCCAGTGTAG|ACTGGCTATGTATGGACTTTCTGCGTCTTCAGGTTGGCAG ========== Event 2057 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAACCCTTTGGTGCCAATTTTTC-------TATTAGGTAGGACCCTTTGGATGCAAGTAGAACATAGcaaagcaaaac Chimp: CAACCCTTTGGTGCCAATTTTTC-------TATTAGGTAGGACCCTTTGGATgcaagtagaacacagcaaagcaaaac ↓ 1 4 3 2 Gorilla: CAACCCTTTGGTGCCAATTTTAC--------------TTGCACCCTTTGGATGCAAGTAGAACATAgcaaagcaaaac ↑ 1 4 3 2 Human: CAACCCTTTGGTGCCAATTTTTC-------TATTAGGTAGGACCCTTTGGATGCAAGTAGAACATAGcaaagcaaaac Cluster: [ ] Orangutan: CAACACTTTGGTGCCAATTTTTCTATTAGG-------TAGGACCCTTTCGATGCAAGTAGAACACAGcaaagcaaaac Human > Gorilla --------------- chr22:14879737-14879743 Template switch process: F1: L GGGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTT 1 F3: 4 CCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA R RF: GAGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTTTCTATTAGGTAGGACCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA RR: CTCCGAAACACCAGACGTTGGTTGGGAAACCACGGTTAAAAAGATAATCCATCCTGGGAAACCTACGTTCATCTTGTATCGTTTCGTTTTGGTT F2: 3 ACGTTCA 2 Unidirectional alignment (log-probability: -33.4) gGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTTaC-------TtGcACCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA AGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTTTCTATTAGGTAGGACCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA Template switch alignment (log-probability: -22.1) gGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTT|ACTTGCA|CCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA AGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTT|ACTTGCA|CCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA Chimp > Gorilla --------------- chr22:14879737-14879743 Template switch process: F1: L GGGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTT 1 F3: 4 CCCTTTGGATGCAAGTAGAACATAGCAAAGCAAAACCAA R RF: GGGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTTTCTATTAGGTAGGACCCTTTGGATGCAAGTAGAACACAGCAAAGCAAAACCAA RR: CCCCGAAACACCAGACGTTGGTTGGGAAACCACGGTTAAAAAGATAATCCATCCTGGGAAACCTACGTTCATCTTGTGTCGTTTCGTTTTGGTT F2: 3 ACGTTCA 2 Unidirectional alignment (log-probability: -33.4) GGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTTaC-------TtGcACCCTTTGGATGCAAGTAGAACAtAGCAAAGCAAAACCAA GGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTTTCTATTAGGTAGGACCCTTTGGATGCAAGTAGAACACAGCAAAGCAAAACCAA Template switch alignment (log-probability: -22.1) GGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTT|ACTTGCA|CCCTTTGGATGCAAGTAGAACAtAGCAAAGCAAAACCAA GGGCTTTGTGGTCTGCAACCAACCCTTTGGTGCCAATTTT|ACTTGCA|CCCTTTGGATGCAAGTAGAACACAGCAAAGCAAAACCAA ========== Event 2058 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGAACAAGGGAGAGGCTTATGGTAGTGATTCTCACTCATTTTGCTTCTTCTCAATCCACTTTATGATTTGCACTTGACCCTTTATAATTGTATTGTTGAATGATTCATCTTGTATACACATTCACCATTTCTAATGTACTTTCCATTTT Chimp: AAGAAAAAGGGAGAGGCTTATGGTAGTGATTCTCACTCATTTTGCTTCTTCTCAATCCACTTTATGATTTGCACTTGACCCTTTATAATTGTATTGCTGAATGACTCATCTTGTATACACATTTGCCATTTCTAATGTACTTTCCATTTT ↑ 3 2 1 4 Gorilla: AAGAACAAGGGAGAGGCTTATGGCAGTGATTCTCACTCATTTTGCTTCTTATCAATCCACTTTATGATTTGCACTTGACCCTTTATAATTGTATTGTTGAATGATTCATCTTGTATACACATTCACTAATTCTAATGTACTTTCCATTTT Human: AAGAACAAGGGAGAGGCTTATGGTAGTGATTCTCACTCATTTTGCTTCTTCTCAATCCACTTTATGATTTGCACTTGACCCTTTATAATTGTATTGTTGAATGATTCATCTTGTATACACATTCACCATTTCTAATGTACTTTCCATTTT Cluster: [ ] Orangutan: AAGAAAAAGGGAGAGGCTTATGGTAGTGATTCTCACTCATTTTGCTTCTTCTCAACCCACTTTATGATTTGCACTTGACCCTTTATAATTGTATTGTTGAATGATTCATCTTGTATAGACATTCACCATTTCTAATGTACTTTTCATTTT Gorilla > Chimp --------------- chr22:22621473-22621478 Template switch process: F1: L TTATAATTGTATTGCTGAATGACTCATCTTGTATACACATT 1 F3: 4 TTCTAATGTACTTTCCATTTTTAATCATCTCTTCA R RF: ATGGCAGTGATTCTCACTCATTTTGCTTCTTATCAATCCACTTTATGATTTGCACTTGACCCTTTATAATTGTATTGTTGAATGATTCATCTTGTATACACATTCACTAATTCTAATGTACTTTCCATTTTTAATCATCTCTTCA RR: TACCGTCACTAAGAGTGAGTAAAACGAAGAATAGTTAGGTGAAATACTAAACGTGAACTGGGAAATATTAACATAACAACTTACTAAGTAGAACATATGTGTAAGTGATTAAGATTACATGAAAGGTAAAAATTAGTAGAGAAGT F2: 3 TACCGT 2 Unidirectional alignment (log-probability: -41.1) TATAATTGTATTGcTGAATGAcTCATCTTGTATACACATTtgCcAtTTCTAATGTACTTTCCATTTTTAATCATCTCTTCA- TATAATTGTATTGTTGAATGATTCATCTTGTATACACATTCACTAATTCTAATGTACTTTCCATTTTTAATCATCTCTTCAT Template switch alignment (log-probability: -27.4) TATAATTGTATTGcTGAATGAcTCATCTTGTATACACATT|TGCCAT|TTCTAATGTACTTTCCATTTTTAATCATCTCTTCA TATAATTGTATTGTTGAATGATTCATCTTGTATACACATT|TGCCAT|TTCTAATGTACTTTCCATTTTTAATCATCTCTTCA ========== Event 2059 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTTGTCTGGGTTATTAATCAGGAAGAGAAGTCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAACTA------------------------------CAGAAATTGGCCAGGCACCTCTGCTGACA Chimp: TCTTTGTCTGGGTTATTAATCAGGAAGAGAAGTCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAGCTACAGAAATTGCTGAAGCTACTTTATGAACTACAGAAATTGGCCAGGCACCTCTGCTGACA ↑ 3 2 4 1 Gorilla: TCTTTGTCTGGGTTATTAATCAGGAAGAGAAGTCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAGCTA------------------------------CAGAAATTGGCCAGGCACCTCTGCTGACA Human: TCTTTGTCTGGGTTATTAATCAGGAAGAGAAGTCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAACTA------------------------------CAGAAATTGGCCAGGCACCTCTGCTGACA Cluster: [ ] Orangutan: TCTTTGTCTGGGTTATTAATCAGGAAGACAAGTCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAGCTA------------------------------CAGAAATTGGCCAGGCACCCCTGCTGACA Gorilla > Chimp --------------- chr2B:127460558-127460561 Template switch process: F1: L TCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAGCTACAGAAATTG 1 F3: 4 AGCTAC------------TTTATGAACTACAGAAATTGGCCAGGCACCTCTGCTGACACCTGGACTAGC R RF: TCAGGAAGAGAAGTCTTCTTCTATGAGCTACAGAAACATACCTTTTATGAGCTACAGAAATTGGCCAGGCACCTCTGCTGACACCTGGACTAGC RR: AGTCCTTCTCTTCAGAAGAAGATACTCGATGTCTTTGTATGGAAAATACTCGATGTCTTTAACCGGTCCGTGGAGACGACTGTGGACCTGATCG F2: 3 AGTC 2 Unidirectional alignment (log-probability: -54) TGAGCTACAGAAACATACCTTTTATGAGCtacagaaattgctgaagctactttatgaacTACAGAAATTGGCCAGGCACCTCTG TGAGCTACAGAAACATACCTTTTATGAGC------------------------------TACAGAAATTGGCCAGGCACCTCTG Template switch alignment (log-probability: -32.7) TGAGCTACAGAAACATACCTTTTATGAGCTACAGAAATTG|CTGA|AGCTAC------------TTTATGAaCTACAGAAATTGGCCAGGCACCTCTG TGAGCTACAGAAACATACCTTTTATGAGCTACAGAAATTG|CTGA|AGCTACAGAAACATACCTTTTATGAGCTACAGAAATTGGCCAGGCACCTCTG ========== Event 2060 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAAATTCAGGTCTGCCCCAGTCCCAGCCCACACCCGGGCTACGGCGGCCACCACAGGCCTGTAGAGGGCTCTTCTCAGGGCCAG--------------------------------GGGCTGGATATGAGGTCCCACTTAGAG ↓ 3 2 4 1 Chimp: TCAAATTCAGGTCTGCCCCAGTCCCAGCCCACACCCGGGCTACGGCGGCCACCACAGGCCTGTAGAGGGCTCTTCTCGGGGCCAG----------------GGGCTGGGACTGCCAGGGGCTGGATATGAGGTCCCACTTAGAG Gorilla: TCAAATTCAGGTCTGCCCCAGTCCCAGCCCACACCCGGGCTACGGCGGCCACCACAGGCCTGTAGAGAGCTCTTCTCAGGGCTAGGGGCTGGGACTGCCAG----------------GGGCTGGATATGAGGTCCCACTTAGAG Human: TCAAATTCAGGTCTGCCCCAGTCCCAGCCCACACCCGGGCTACGGCGGCCACCACAGGCCTGTAGAGGGCTCTTCTCAGGGCCAG--------------------------------GGGCTGGATATGAGGTCCCACTTAGAG Cluster: [ ] Orangutan: TTAAATTCAGGTCTGCCCCAGTCCCAGCCCACACCTGGGCTACCGTGGCCACCACAGGCCTGTAGAGGGCTCTTCTCAGGGCCAGGGGCTGGGACTGCCAG----------------GGGCTGGATATGAGGTCCCACTTAGAG Human > Chimp ------------- chr2B:128068719-128068722 Template switch process: F1: L GGGCTACGGCGGCCACCACAGGCCTGTAGAGGGCTCTTCTCGGGGCCAGGGGCTGG 1 F3: 4 GCCAGGGGCTGGATATGAGGTCCCACTTAGAGGTGATAAGTGACA R RF: AGTCCCAGCCCACACCCGGGCTACGGCGGCCACCACAGGCCTGTAGAGGGCTCTTCTCAGGGCCAGGGGCTGGATATGAGGTCCCACTTAGAGGTGATAAGTGACA RR: TCAGGGTCGGGTGTGGGCCCGATGCCGCCGGTGGTGTCCGGACATCTCCCGAGAAGAGTCCCGGTCCCCGACCTATACTCCAGGGTGAATCTCCACTATTCACTGT F2: 3 TCAG 2 Unidirectional alignment (log-probability: -40) CACAGGCCTGTAGAGGGCTCTTCTCgGGGCCAGGGGCTGGgactgccaggggctggATATGAGGTCCCACTTAGAGGTGATAAG CACAGGCCTGTAGAGGGCTCTTCTCAGGGCCAGGGGCTGG----------------ATATGAGGTCCCACTTAGAGGTGATAAG Template switch alignment (log-probability: -22.2) CACAGGCCTGTAGAGGGCTCTTCTCgGGGCCAGGGGCTGG|GACT|GCCAGGGGCTGGATATGAGGTCCCACTTAGAGGTGATAAG CACAGGCCTGTAGAGGGCTCTTCTCAGGGCCAGGGGCTGG|GACT|GCCAGGGGCTGGATATGAGGTCCCACTTAGAGGTGATAAG ========== Event 2061 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCAAGCTGGTTCCTTGATCTGAATAGCATTGGCCTGAAGAAAAGAGGAGCCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAG--------AAGAATTTAGAAAGATGAGAGAGGGGACCATG Chimp: CCTCAAGCTGGTTCTTTGATCTGAATAGCATTGGCCTGAAGAAAAGAGGAGCCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAG--------AAGAATTTAGAAAGATGAGAGAGGGGACCATG ↓ 3 2 4 1 Gorilla: CCTCAAGCTGGTTCCTTGATCTGAATAGCATTGACCTGAAGAAAAGAGGAGCCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAATTTAGAATTCAGAAAGAATTTAGAAAGATGAGAGAGGGGACCATG ↑ 3 2 4 1 Human: CCTCAAGCTGGTTCCTTGATCTGAATAGCATTGGCCTGAAGAAAAGAGGAGCCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAG--------AAGAATTTAGAAAGATGAGAGAGGGGACCATG Cluster: [ ] Orangutan: CCTCAAGCTGGTTCCTTGATCTGAATAGCATTGGCCTGAAGAAAAGAGGAGGCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAG--------AAGAATTTAGAAAGATGAGAGAGGGGACCATG Human > Gorilla --------------- chr2B:130763147-130763152 Template switch process: F1: L TTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGG----------AATTTAGAA 1 F3: 4 AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA R RF: TCTGAATAGCATTGGCCTGAAGAAAAGAGGAGCCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAGAAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA RR: AGACTTATCGTAACCGGACTTCTTTTCTCCTCGGAAGGGAAGTGTAAGGACCTCGTCACCCCCAGTTCTTCTTACCCTCCCCCCTTGGGTCTTCTTAAATCTTTCTACTCTCTCCCCTGGTACTTATTAAT F2: 3 AGACTT 2 Unidirectional alignment (log-probability: -39) GCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAAtttAGaattcagaAAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA GCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAG--------AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA Template switch alignment (log-probability: -26.9) GCAGTGGGGGTCAAGAAGAATGGGAGGGGGG----------AATTTAGAA|TTCAGA|AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA GCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAGAAGAATTTAGAA|TTCAGA|AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA Chimp > Gorilla --------------- chr2B:130763147-130763152 Template switch process: F1: L TTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGG----------AATTTAGAA 1 F3: 4 AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA R RF: TCTGAATAGCATTGGCCTGAAGAAAAGAGGAGCCTTCCCTTCACATTCCTGGAGCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAGAAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA RR: AGACTTATCGTAACCGGACTTCTTTTCTCCTCGGAAGGGAAGTGTAAGGACCTCGTCACCCCCAGTTCTTCTTACCCTCCCCCCTTGGGTCTTCTTAAATCTTTCTACTCTCTCCCCTGGTACTTATTAAT F2: 3 AGACTT 2 Unidirectional alignment (log-probability: -39) GCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAAtttAGaattcagaAAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA GCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAG--------AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA Template switch alignment (log-probability: -26.9) GCAGTGGGGGTCAAGAAGAATGGGAGGGGGG----------AATTTAGAA|TTCAGA|AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA GCAGTGGGGGTCAAGAAGAATGGGAGGGGGGAACCCAGAAGAATTTAGAA|TTCAGA|AAGAATTTAGAAAGATGAGAGAGGGGACCATGAATAATTA ========== Event 2062 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAGGACACCTCCCAGGGGTTGTAGTGAGCCC-------------------------------TCAGCACCCGGCCCACAATGGGCACAGCTCAGCGATCTCCCAGCATTCCCTGATCCTCGGACCCTGGGACGCAATGCAACCCCTGCTCAGGCCCAGATGCAGCCAGCAT ↓ 4 1 3 2 Chimp: CCAGGACACCTCCCAGGGGTTGTAGTGAGCCC---------TCAGTGAGCCTGTAGTGAGCCCTCAGCACCCGGCCCACAATGGGCACAGCTCAGCGATCTCCCAGCATTCCCTGATCCTCGGACCCTGGGACGCAATGCAACCCCTGCTCAGGCCCAGATGCAGCCAGCAT Gorilla: CCAGGACACCTCCCAGGGGTTGTAATGAGCCCTCAGGGTCA----------------------CATGCACCCGGCCCACAATGGGCACAGCTCAGCGATCTCCCAGCATTCCCTGATCCTCGGACCCTGGGACGCAATGCAACCCCTGCTCAGGCCCAGATGCAGCCAGCAC Human: CCAGGACACCTCCCAGGGGTTGTAGTGAGCCC-------------------------------TCAGCACCCGGCCCACAATGGGCACAGCTCAGCGATCTCCCAGCATTCCCTGATCCTCGGACCCTGGGACGCAATGCAACCCCTGCTCAGGCCCAGATGCAGCCAGCAT Cluster: [ ] Orangutan: CCAGGACACCTCCCAGGGGTTGTAGTGAGCCCTCGGGGTCA----------------------CATGCACCTGGCCCACAGTGGGCACAGCTCAGCGATCTCCCAGCATTCCCTGATCCTCGGACCCCGGGACGCAATGCACCCCCTGCTCAGGCCCAGATGCAGCCAGCAT Human > Chimp ------------- chr2B:129027231-129027235 Template switch process: F1: L ACAGGGGTGCCAGGACACCTCCCAGGGGTTGTAGTGAGCCCTCAG 1 F3: 4 CTGTAGTGAGCCCTCAGCACCCGGCCCACAATGGGCACAGCTCAGCGATCTCC R RF: ACAGGGGTGCCAGGACACCTCCCAGGGGTTGTAGTGAGCCCTCAGCACCCGGCCCACAATGGGCACAGCTCAGCGATCTCCCAGCATTCCCTGATCCTCGGACCCTGGGACGCAATGCAACCCCTGCTCA RR: TGTCCCCACGGTCCTGTGGAGGGTCCCCAACATCACTCGGGAGTCGTGGGCCGGGTGTTACCCGTGTCGAGTCGCTAGAGGGTCGTAAGGGACTAGGAGCCTGGGACCCTGCGTTACGTTGGGGACGAGT F2: 3 CGAGT 2 Unidirectional alignment (log-probability: -42.6) GGTGCCAGGACACCTCCCAGGGGTTGTAGTGAGCCCTcagtgagcctgtagtgagccctCAGCACCCGGCCCACAATGGGCACAG GGTGCCAGGACACCTCCCAGGGGTTGTAGTGAGCCCT----------------------CAGCACCCGGCCCACAATGGGCACAG Template switch alignment (log-probability: -22.2) GGTGCCAGGACACCTCCCAGGGGTTGTAGTGAGCCCTCAG|TGAGC|cTGTAGTGAGCCCTCAGCACCCGGCCCACAATGGGCACAG GGTGCCAGGACACCTCCCAGGGGTTGTAGTGAGCCCTCAG|TGAGC|TTGTAGTGAGCCCTCAGCACCCGGCCCACAATGGGCACAG ========== Event 2063 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGCGCACGGATCAGGAAAGCC-------AGCCAGAGGGTAGCCCTAGGGAGGGCAGGCAC ↓ 1 3 4 2 Chimp: GAGCGCACGGATCAGGAAAGCTACCCTCTGGCTAGAGGGTAGCCCTCGGGAGGGCAGGCAC ↑ 1 3 4 2 Gorilla: GAGCGCACGGATCAGGAAAGCC-------AGCCAGAGGGTAGCCCTAGGGAGGGCAGGCAC Human: GAGCGCACGGATCAGGAAAGCC-------AGCCAGAGGGTAGCCCTAGGGAGGGCAGGCAC Cluster: [ ] Orangutan: GAGAGCACGGATCAGGAAAGCT-------AGCCAGAGGGTAGCCCTAGGGAGGGCAGGCAC Human > Chimp ------------- chr2B:129563947-129563958 Template switch process: F1: L GTGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGC 1 F3: 4 AGAGGGTAGCCCTCGGGAGGGCAGGCACTTTTTCACCATT R RF: GTGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGCCAGCCAGAGGGTAGCCCTAGGGAGGGCAGGCACTTTTTCACCATT RR: CACCCGGTGGAAGGTCGAGACTCGCGTGCCTAGTCCTTTCGGTCGGTCTCCCATCGGGATCCCTCCCGTCCGTGAAAAAGTGGTAA F2: 3 TCGGTCTCCCAT 2 Unidirectional alignment (log-probability: -39) TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGCtAccctctgGCtAGAGGGTAGCCCTcGGGAGGGCAGGCACTTTTTCACCATT TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGCCA-------GCCAGAGGGTAGCCCTAGGGAGGGCAGGCACTTTTTCACCATT Template switch alignment (log-probability: -22.8) TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGC|TACCCTCTGGCT|AGAGGGTAGCCCTcGGGAGGGCAGGCACTTTTTCACCATT TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGC|TACCCTCTGGCT|AGAGGGTAGCCCTAGGGAGGGCAGGCACTTTTTCACCATT Gorilla > Chimp --------------- chr2B:129563947-129563958 Template switch process: F1: L GTGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGC 1 F3: 4 AGAGGGTAGCCCTCGGGAGGGCAGGCACTTTTTCACCATT R RF: GTGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGCCAGCCAGAGGGTAGCCCTAGGGAGGGCAGGCACTTTTTCACCATT RR: CACCCGGTGGAAGGTCGAGACTCGCGTGCCTAGTCCTTTCGGTCGGTCTCCCATCGGGATCCCTCCCGTCCGTGAAAAAGTGGTAA F2: 3 TCGGTCTCCCAT 2 Unidirectional alignment (log-probability: -37.6) TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGCtAccctctgGCtAGAGGGTAGCCCTcGGGAGGGCAGGCACTTTTTCACCATT TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGCCA-------GCCAGAGGGTAGCCCTAGGGAGGGCAGGCACTTTTTCACCATT Template switch alignment (log-probability: -22.8) TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGC|TACCCTCTGGCT|AGAGGGTAGCCCTcGGGAGGGCAGGCACTTTTTCACCATT TGGGCCACCTTCCAGCTCTGAGCGCACGGATCAGGAAAGC|TACCCTCTGGCT|AGAGGGTAGCCCTAGGGAGGGCAGGCACTTTTTCACCATT ========== Event 2064 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTACCCCCAGGCTACACAGCTGCTGTACTTTATTTGCATTTGGCACAGTTCTCATTC ↓ 3 1 2 4 Chimp: TTACCCCCAGGCTACACAGCTACTG-----TGTACACATTTGGCACAGTTCTCATTC ↑ 3 1 2 4 Gorilla: TTACCCCCAGGCTACACAGCTGCTGTACTTTATTTGCATTTGGCACAGTTCTCATTC Human: TTACCCCCAGGCTACACAGCTGCTGTACTTTATTTGCATTTGGCACAGTTCTCATTC Cluster: [ ] Orangutan: Human > Chimp ------------- chr22:13413049-13413053 Template switch process: F1: L CAACAGCAAAACCTGGACTTTTACCCCCAGGCTACACAGCTACTGT 1 F3: 4 CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC R RF: CAACAGCAAAACCTGGACTTTTACCCCCAGGCTACACAGCTGCTGTACTTTATTTGCATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC RR: GTTGTCGTTTTGGACCTGAAAATGGGGGTCCGATGTGTCGACGACATGAAATAAACGTAAACCGTGTCAAGAGTAAGCTGGAACTTGTCGTTGAGG F2: 3 ACATG 2 Unidirectional alignment (log-probability: -33.4) CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTaCTGTgtacAC---------ATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTGCTGT----ACTTTATTTGCATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC Template switch alignment (log-probability: -22) CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTaCTGT|GTACA|CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTGCTGT|GTACA|CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC Gorilla > Chimp --------------- chr22:13413049-13413053 Template switch process: F1: L CAACAGCAAAACCTGGACTTTTACCCCCAGGCTACACAGCTACTGT 1 F3: 4 CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC R RF: CAATAGCAAAACCTGGACTTTTACCCCCAGGCTACACAGCTGCTGTACTTTATTTGCATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC RR: GTTATCGTTTTGGACCTGAAAATGGGGGTCCGATGTGTCGACGACATGAAATAAACGTAAACCGTGTCAAGAGTAAGCTGGAACTTGTCGTTGAGG F2: 3 ACATG 2 Unidirectional alignment (log-probability: -38) CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTaCTGTgtacA---------CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTGCTGT----ACTTTATTTGCATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC Template switch alignment (log-probability: -27.5) CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTaCTGT|GTACA|CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC CAAAACCTGGACTTTTACCCCCAGGCTACACAGCTGCTGT|GTACA|CATTTGGCACAGTTCTCATTCGACCTTGAACAGCAACTCC ========== Event 2065 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACATAATTAAGAAGGAATCCTAGGTTTATAAAAGAACCTAGGTAAAAAGAAACCTCCGAGAGT ↑ 3 2 1 4 Chimp: AAAATAATTAAGAAGGAATCCTAGGTTTATAAG-------AGCTAAAAAGAAACCTCCGAGAGT Gorilla: AAAATAATTAAGAAGGAATCCTAGGTTTATAAG-------AGCTAAAAAGAAACCTCCGAGAGT Human: AACATAATTAAGAAGGAATCCTAGGTTTATAAAAGAACCTAGGTAAAAAGAAACCTCCGAGAGT Cluster: [ ] Orangutan: aaAATAATTAAGAAGGAATCCTAGGTTTATAAG-------AGCTAAAAAGAAGCCTCCAAGAGT Chimp > Human ------------- chr2:238800595-238800602 Template switch process: F1: L CAAACGTGAAACATAATTAAGAAGGAATCCTAGGTTTATAAAAG 1 F3: 4 TAAAAAGAAACCTCCGAGAGTCGACGTGATGTCGCTGAAG R RF: CAAACGTGAAAAATAATTAAGAAGGAATCCTAGGTTTATAAGAGCTAAAAAGAAACCTCCGAGAGTCGACGTGATGTCGCTGAAG RR: GTTTGCACTTTTTATTAATTCTTCCTTAGGATCCAAATATTCTCGATTTTTCTTTGGAGGCTCTCAGCTGCACTACAGCGACTTC F2: 3 GGATCCAA 2 Unidirectional alignment (log-probability: -39) CGTGAAAcATAATTAAGAAGGAATCCTAGGTTTATAAaAGaacctaggTAAAAAGAAACCTCCGAGAGTCGACGTGATGTCGCTGAAG CGTGAAAAATAATTAAGAAGGAATCCTAGGTTTATAAGAGC-------TAAAAAGAAACCTCCGAGAGTCGACGTGATGTCGCTGAAG Template switch alignment (log-probability: -28.3) CGTGAAAcATAATTAAGAAGGAATCCTAGGTTTATAAaAG|AACCTAGG|TAAAAAGAAACCTCCGAGAGTCGACGTGATGTCGCTGAAG CGTGAAAAATAATTAAGAAGGAATCCTAGGTTTATAAGAG|AACCTAGG|TAAAAAGAAACCTCCGAGAGTCGACGTGATGTCGCTGAAG ========== Event 2066 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CGAAGCTGAGCAAAGTGTCCA--CACACACGTGCACCCTCGCACACGCATACACATATGGG Chimp: TGAAGCTGAGCAAAGTGTCCA--CACACACGTGTACCCTCACACACGCATACACATATGGG ↑ 3 1 2 4 Gorilla: TGAAGCTGAGCAAAGTGTCCA----CACACGTGCACCCTCGCACACGCATACACATATGGG Human: CGAAGCTGAGCAAAGTGTCCA--CACACACGTGCACCCTCGCACACGCATACACATATGGG Cluster: [ ] Orangutan: TGAAGCTGAGCAAAGTGTCCACA--CACACGTGCACCCTCACACACGCATACACATATGGG Gorilla > Chimp --------------- chr2B:130667514-130667519 Template switch process: F1: L ATGTCCTTACGAGCTGGAGATGAAGCTGAGCAAAGTGTCCACACAC 1 F3: 4 ACCCTCACACACGCATACACATATGGGCAGCCCCACGCGGC R RF: ATGTCCTTACGAGCTGGAGATGAAGCTGAGCAAAGTGTCCACACACGTGCACCCTCGCACACGCATACACATATGGGCAGCCCCACGCGGC RR: TACAGGAATGCTCGACCTCTACTTCGACTCGTTTCACAGGTGTGTGCACGTGGGAGCGTGTGCGTATGTGTATACCCGTCGGGGTGCGCCG F2: 3 TGTGCA 2 Unidirectional alignment (log-probability: -32) TTACGAGCTGGAGATGAAGCTGAGCAAAGTGTCCACACacACGTGtACCCTCaCACACGCATACACATATGGGCAGCCCCACGCGG TTACGAGCTGGAGATGAAGCTGAGCAAAGTGTCCACAC--ACGTGCACCCTCGCACACGCATACACATATGGGCAGCCCCACGCGG Template switch alignment (log-probability: -22.2) TTACGAGCTGGAGATGAAGCTGAGCAAAGTGTCCACACAC|ACGTGT|ACCCTCaCACACGCATACACATATGGGCAGCCCCACGCGG TTACGAGCTGGAGATGAAGCTGAGCAAAGTGTCCACACAC|ACGTGT|ACCCTCGCACACGCATACACATATGGGCAGCCCCACGCGG ========== Event 2067 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 156 Detected in comparisons: 1256 Multiple sequence alignment: Human: CTGACCTCCGAGGGGCTTCACGGG------CT-------TGCTGTAGccacatgcaca----cacacacaaacatat ↑ 13 2 4 Chimp: CTGACCTCCGAGGGGCTTCACAGCATGTGGCTACAGCAAGCCTGTAGCcacattcaca--cacacacacaaacatat ↓ 13 2 4 ↑ 1 3 4 2 Gorilla: CTGACCTCTGAGGGGCTTCACAGG------CT-------TGCTGTAGCcacatgcacaca--cacacacaaacatat Human: CTGACCTCCGAGGGGCTTCACGGG------CT-------TGCTGTAGccacatgcaca----cacacacaaacatat Cluster: [ ] Orangutan: CTGACCTCCGAGGGGCTTCACAGG------CT-------TGCTGTAGccacatgcaca----cacacacaaacatat Chimp > Human ------------- chr2:239590570-239590587 Template switch process: F1: L CGTCAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACGG 1 F3: 4 CACACACACACAAACATATGCACAC R RF: CGTCAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACAGCATGTGGCTACAGCAAGCCTGTAGCCACATTCACACACACACACAAACATATGCACAC RR: GCAGTCCACCTAGACGTGTGGACTGGAGGCTCCCCGAAGTGTCGTACACCGATGTCGTTCGGACATCGGTGTAAGTGTGTGTGTGTGTTTGTATACGTGTG F2: 3 GTACACCGATGTCGTTCG 2 Unidirectional alignment (log-probability: -48.5) CAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACgggcttg--------------------CTGTAGCCACATg--CACACACACACAAACATATGCACAC CAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCAC-------AGCATGTGGCTACAGCAAGCCTGTAGCCACATTCACACACACACACAAACATATGCACAC Template switch alignment (log-probability: -23.2) CAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACgG|GCTTGCTGTAGCCACATG|CACACACACACAAACATATGCACAC CAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACAG|GCTTGCTGTAGCCACATG|CACACACACACAAACATATGCACAC Gorilla > Chimp --------------- chr2B:130748113-130748130 Template switch process: F1: L TCAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACAG 1 F3: 4 CTGTAGCCACATTCACACACACACACAAACATATGCAC R RF: TCAGGTGGATCTGCACACCTGACCTCTGAGGGGCTTCACAGGCTTGCTGTAGCCACATGCACACACACACACAAACATATGCAC RR: AGTCCACCTAGACGTGTGGACTGGAGACTCCCCGAAGTGTCCGAACGACATCGGTGTACGTGTGTGTGTGTGTTTGTATACGTG F2: 3 CGAACGACATCGGTGTAC 2 Unidirectional alignment (log-probability: -54.8) CAGGTGGATCTGCACACCTGACCTCcGAGGGGCTTCACAGcatgtggctacagcaaGC---CTGTAGCCACATtCACACACACACACAAACATATGCAC CAGGTGGATCTGCACACCTGACCTCTGAGGGGCTTCACAG----------------GCTTGCTGTAGCCACATGCACACACACACACAAACATATGCAC Template switch alignment (log-probability: -29) CAGGTGGATCTGCACACCTGACCTCcGAGGGGCTTCACAG|CATGTGGCTACAGCAAGC|CTGTAGCCACATtCACACACACACACAAACATATGCAC CAGGTGGATCTGCACACCTGACCTCTGAGGGGCTTCACAG|CATGTGGCTACAGCAAGC|CTGTAGCCACATGCACACACACACACAAACATATGCAC Chimp > Gorilla --------------- chr2B:132985009-132985026 Template switch process: F1: L TCAGGTGGATCTGCACACCTGACCTCTGAGGGGCTTCACAG 1 F3: 4 CACACACACACACAAACATATGCAC R RF: TCAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACAGCATGTGGCTACAGCAAGCCTGTAGCCACATTCACACACACACACAAACATATGCAC RR: AGTCCACCTAGACGTGTGGACTGGAGGCTCCCCGAAGTGTCGTACACCGATGTCGTTCGGACATCGGTGTAAGTGTGTGTGTGTGTTTGTATACGTG F2: 3 GTACACCGATGTCGTTCG 2 Unidirectional alignment (log-probability: -36.8) CAGGTGGATCTGCACACCTGACCTCtGAGGGGCTTCACAG----------------GCttgCTGTAGCCACATgCACACACACACACAAACATATGCAC CAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACAGCATGTGGCTACAGCAAGC---CTGTAGCCACATTCACACACACACACAAACATATGCAC Template switch alignment (log-probability: -23.2) CAGGTGGATCTGCACACCTGACCTCtGAGGGGCTTCACAG|GCTTGCTGTAGCCACATG|CACACACACACACAAACATATGCAC CAGGTGGATCTGCACACCTGACCTCCGAGGGGCTTCACAG|GCTTGCTGTAGCCACATG|CACACACACACACAAACATATGCAC ========== Event 2068 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: ttttttgttaactcaggatagg-------tataaccatcctggctaagacaaaaaatccaagttttg Chimp: TTTTTTGTTAACTCAGGATAGG-------TATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTG ↓ 1 4 3 2 Gorilla: TTTTTTGTTAACTCAGGATAGTTACCCAGGATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTG Human: ttttttgttaactcaggatagg-------tataaccatcctggctaagacaaaaaatccaagttttg Cluster: [ ] Orangutan: ttttttgttaactcaggatagg-------tataaccattctgggtaagacaaaaaatccaagttttg Chimp > Gorilla --------------- chr22:11482310-11482318 Template switch process: F1: L TTATAAGAAAATATGGAATATTTTTTGTTAACTCAGGATAG 1 F3: 4 ATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTGTAA R RF: TTATAAGAAAATATGGAATATTTTTTGTTAACTCAGGATAGGTATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTGTAA RR: AATATTCTTTTATACCTTATAAAAAACAATTGAGTCCTATCCATATTGGTAGGACCCATTCTGTTTTTTAGGTTCAAAACATT F2: 3 GGACCCATT 2 Unidirectional alignment (log-probability: -26.5) TATAAGAAAATATGGAATATTTTTTGTTAACTCAGGATAGttacccaGgATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTGTAA TATAAGAAAATATGGAATATTTTTTGTTAACTCAGGATAG-------GTATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTGTAA Template switch alignment (log-probability: -16.9) TATAAGAAAATATGGAATATTTTTTGTTAACTCAGGATAG|TTACCCAGG|ATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTGTAA TATAAGAAAATATGGAATATTTTTTGTTAACTCAGGATAG|TTACCCAGG|ATAACCATCCTGGGTAAGACAAAAAATCCAAGTTTTGTAA ========== Event 2069 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTTACACAGTGTTCCTTATTTAATAGCAGATGGTTTTGTAAAGAGAATCACTATAAAATTATTCTATAAA Chimp: TATTTACACAGTGTTCCTTATGTAATAGCAGATGGTTTTGTAAAGAGAATCACTATAAAATTATTTTATAAA ↓ 1 4 3 2 Gorilla: TATTTACACAGTGTTCCTTATTTAATAG-TGATTCTCTTGTAAAGAGAATCACTATAAAATTATTTTATAAA ↑ 1 4 3 2 Human: TATTTACACAGTGTTCCTTATTTAATAGCAGATGGTTTTGTAAAGAGAATCACTATAAAATTATTCTATAAA Cluster: [ ] Orangutan: TATTTACACATTGTTCCTCATTCAACAGCGGATGGTTTTGTAAAGAGAATCACTATAAAATTATTTTATAAA Human > Gorilla --------------- chr22:11215323-11215330 Template switch process: F1: L TTAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAG 1 F3: 4 TTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT R RF: TTAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAGCAGATGGTTTTGTAAAGAGAATCACTATAAAATTATTCTATAAAGTTTT RR: AATCCACCAGGAGATAAATGTGTCACAAGGAATAAATTATCGTCTACCAAAACATTTCTCTTAGTGATATTTTAATAAGATATTTCAAAA F2: 3 CTCTTAGT 2 Unidirectional alignment (log-probability: -36.3) TAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAG----TGaTTctcTTGTAAAGAGAATCACTATAAAATTATTtTATAAAGTTTT TAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAGCAGATGGTT---TTGTAAAGAGAATCACTATAAAATTATTCTATAAAGTTTT Template switch alignment (log-probability: -22.3) TAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAG|TGATTCTC|TTGTAAAGAGAATCACTATAAAATTATTtTATAAAGTTTT TAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAG|TGATTCTC|TTGTAAAGAGAATCACTATAAAATTATTCTATAAAGTTTT Chimp > Gorilla --------------- chr22:11215323-11215330 Template switch process: F1: L AATATACTTAGGTGGTCCTCTATTTACACAGTGTTCCTTATTTAATAG 1 F3: 4 TTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT R RF: AATATACTTAGGTGGTCCTCTATTTACACAGTGTTCCTTATGTAATAGCAGATGGTTTTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT RR: TTATATGAATCCACCAGGAGATAAATGTGTCACAAGGAATACATTATCGTCTACCAAAACATTTCTCTTAGTGATATTTTAATAAAATATTTCAAAA F2: 3 CTCTTAGT 2 Unidirectional alignment (log-probability: -36.4) TAGGTGGTCCTCTATTTACACAGTGTTCCTTATtTAATAG----TGaTTctcTTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT TAGGTGGTCCTCTATTTACACAGTGTTCCTTATGTAATAGCAGATGGTT---TTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT Template switch alignment (log-probability: -22.4) TAGGTGGTCCTCTATTTACACAGTGTTCCTTATtTAATAG|TGATTCTC|TTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT TAGGTGGTCCTCTATTTACACAGTGTTCCTTATGTAATAG|TGATTCTC|TTGTAAAGAGAATCACTATAAAATTATTTTATAAAGTTTT ========== Event 2070 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AACGACGCCCCAAAAGGTAAGAAGG----AGGACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGTTAA Chimp: AATGATGCCCCAAAAGGTAAGAAGTTTTTCTAACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGTTAA ↑ 1 4 3 2 Gorilla: AATGATGCCCCAAAAGGTAAGGAGG----AGGACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGTTAA Human: AACGACGCCCCAAAAGGTAAGAAGG----AGGACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGTTAA Cluster: [ ] Orangutan: AATGATGCCCCAAAAGGTAAGAAGG----AGGACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAG--AGTTAA Gorilla > Chimp --------------- chr22:11158241-11158251 Template switch process: F1: L GGGATAGAAGTCAGGAAAGGAATGATGCCCCAAAAGGTAAG 1 F3: 4 ACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGT R RF: GGGATAGAAGTCAGGAAAGGAATGATGCCCCAAAAGGTAAGGAGGAGGACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGT RR: CCCTATCTTCAGTCCTTTCCTTACTACGGGGTTTTCCATTCCTCCTCCTGTCATGCTACAATCTTTTTGAATTCTTTTCCGTCTCTCA F2: 3 ATCTTTTTGAA 2 Unidirectional alignment (log-probability: -36.8) GGATAGAAGTCAGGAAAGGAATGATGCCCCAAAAGGTAA-------GaagtttttctaACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGT GGATAGAAGTCAGGAAAGGAATGATGCCCCAAAAGGTAAGGAGGAGG-----------ACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGT Template switch alignment (log-probability: -17.1) GGATAGAAGTCAGGAAAGGAATGATGCCCCAAAAGGTAAG|AAGTTTTTCTA|ACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGT GGATAGAAGTCAGGAAAGGAATGATGCCCCAAAAGGTAAG|AAGTTTTTCTA|ACAGTACGATGTTAGAAAAACTTAAGAAAAGGCAGAGAGT ========== Event 2071 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTGCCACGCAGGGCAGAGGAGAGCAGCTGTCAAGAAGCAGCCCTGGCTCTCACGCTGGGGT Chimp: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACTGAGAAGCCCTTACTCCTGGTTCAGTCCCACGCAGGGCAGAGGAGAGCAGCTGTCAAGAAGCAGCCCTGGCTCTCACGCTGGGGT Gorilla: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGTCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTCCCACACAGGGCAGAGGAGAG--------------CAGCCCTGGCTCTCACACTGGGGT ↓ 3 2 4 1 Human: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTGCCACGCAGGGCAGAGGAGAGCAGCTGTCAAGAAGCAGCCCTGGCTCTCACGCTGGGGT Cluster: [ ] Orangutan: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCTCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCCTACTCCTGGTTCAGTCCCACCCAGAGCAGAGGAGAG--------------CAGCCCTGGCTCTCACGCTGGGGT Gorilla > Human --------------- chr22:10407277-10407284 Template switch process: F1: L CTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTGCCACGCAGGGCAGAGGAGAGCAGC 1 F3: 4 AGCAGCCCTGGCT R RF: TCTTGACAATCACAGTCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTCCCACACAGGGCAGAGGAGAGCAGCCCTGGCT RR: AGAACTGTTAGTGTCAGGGACGAAAAAGGGAAGGGACCCTCCGATCTTGTCTCTTCGGGAATGAGGACCAAGTCAGGGTGTGTCCCGTCTCCTCTCGTCGGGACCGA F2: 3 AGAACTGT 2 Unidirectional alignment (log-probability: -41.9) TACTCCTGGTTCAGTgCCACgCAGGGCAGAGGAGagcagctgtcaagaAGCAGCCCTGGCT TACTCCTGGTTCAGTCCCACACAGGGCAGAGGAG--------------AGCAGCCCTGGCT Template switch alignment (log-probability: -27.7) TACTCCTGGTTCAGTgCCACgCAGGGCAGAGGAGAGCAGC|TGTCAAGA|AGCAGCCCTGGCT TACTCCTGGTTCAGTCCCACACAGGGCAGAGGAGAGCAGC|TGTCAAGA|AGCAGCCCTGGCT ========== Event 2072 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTGCCACGCAGGGCAGAGGAGAGCAGCTGTCAAGAAGCAGCCCTGGCTCTCACGCTGGGGT Chimp: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACTGAGAAGCCCTTACTCCTGGTTCAGTCCCACGCAGGGCAGAGGAGAGCAGCTGTCAAGAAGCAGCCCTGGCTCTCACGCTGGGGT ↑ 3 2 4 1 Gorilla: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGTCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTCCCACACAGGGCAGAGGAGAG--------------CAGCCCTGGCTCTCACACTGGGGT Human: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTGCCACGCAGGGCAGAGGAGAGCAGCTGTCAAGAAGCAGCCCTGGCTCTCACGCTGGGGT Cluster: [ ] Orangutan: CTCTCCACATGGTTGTGAGTCTTGACAATCACAGCTCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCCTACTCCTGGTTCAGTCCCACCCAGAGCAGAGGAGAG--------------CAGCCCTGGCTCTCACGCTGGGGT Gorilla > Chimp --------------- chr22:10789774-10789781 Template switch process: F1: L GCCCTTACTCCTGGTTCAGTCCCACGCAGGGCAGAGGAGAGCAGC 1 F3: 4 AGCAGCCCTGGCTCTCACGCTGGGGTTTTGGACACACGGTC R RF: TCTTGACAATCACAGTCCCTGCTTTTTCCCTTCCCTGGGAGGCTAGAACAGAGAAGCCCTTACTCCTGGTTCAGTCCCACACAGGGCAGAGGAGAGCAGCCCTGGCTCTCACACTGGGGTTTTGGACACACGGTC RR: AGAACTGTTAGTGTCAGGGACGAAAAAGGGAAGGGACCCTCCGATCTTGTCTCTTCGGGAATGAGGACCAAGTCAGGGTGTGTCCCGTCTCCTCTCGTCGGGACCGAGAGTGTGACCCCAAAACCTGTGTGCCAG F2: 3 AGAACTGT 2 Unidirectional alignment (log-probability: -48.8) TACTCCTGGTTCAGTCCCACgCAGGGCAGAGGAGagcagctgtcaagaAGCAGCCCTGGCTCTCACgCTGGGGTTTTGGACACACGGT TACTCCTGGTTCAGTCCCACACAGGGCAGAGGAG--------------AGCAGCCCTGGCTCTCACACTGGGGTTTTGGACACACGGT Template switch alignment (log-probability: -27.9) TACTCCTGGTTCAGTCCCACgCAGGGCAGAGGAGAGCAGC|TGTCAAGA|AGCAGCCCTGGCTCTCACgCTGGGGTTTTGGACACACGGT TACTCCTGGTTCAGTCCCACACAGGGCAGAGGAGAGCAGC|TGTCAAGA|AGCAGCCCTGGCTCTCACACTGGGGTTTTGGACACACGGT ========== Event 2073 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGGCTACCTTCCAACACAGCTGGGAGACTTTGACACTGGCTGCCCAGCCCCTTGCTTCTTCCCTTTGGCCACGCAGCTTCCCATTCCAGAAGCAGGGCCACAGCCA----------------GCTTCCAGAGCCAGGATTCTGTAGAGTACCCATTTCC Chimp: AGTGGCTACCTTCCAACACAGCTGGGAGACTTTGACACTGGCTGCCCAGCCCCTTGCTTCTTCCCTCTGGCCACACAGCTTCCCATTCCAGAAGCAGGGCCACAGCAG--------GTCCCTAATCACCCAGAGCCAGGAGTCTGTAGAGTACCCATTTCC Gorilla: AGTGGCTACCTTCCAACACAGCTGGGAGACTTTGACACTGGCTGCCCAGCCCCTTGCTTCTTCCCGCTGGCCACACAGCTTCCCATTCCAGAAGCAGGGCCACAGCAGGTCCCTAA--------TCATCCAGAGCCAGAAGTCTGTAGAGTACCCATTTCC ↓ 3 2 1 4 Human: AGTGGCTACCTTCCAACACAGCTGGGAGACTTTGACACTGGCTGCCCAGCCCCTTGCTTCTTCCCTTTGGCCACGCAGCTTCCCATTCCAGAAGCAGGGCCACAGCCA----------------GCTTCCAGAGCCAGGATTCTGTAGAGTACCCATTTCC Cluster: [ ] Orangutan: AGTGGCTACCTTCCAACACAGCTGGGAGACTTTGACACTGGCTGCCCAGCCCCTTGCTTCTTCCCTCTGGCCACACAGCTTCCCATTCCAGAAGCACG-GCACAGCAGGTCCCTAA--------TCACCCAGAGCCAAGAGTCTGTACAGTACCCATTGCC Gorilla > Human --------------- chr2:240339973-240339977 Template switch process: F1: L AGAAGCAGGGCCACAGC 1 F3: 4 TCCAGAGCCAGGATTCTGTAGAGTACCCATTTCCCAGGCAGCATCTGCCCACCA R RF: AGCTGGGAGACTTTGACACTGGCTGCCCAGCCCCTTGCTTCTTCCCGCTGGCCACACAGCTTCCCATTCCAGAAGCAGGGCCACAGCAGGTCCCTAATCATCCAGAGCCAGAAGTCTGTAGAGTACCCATTTCCCAGGCAGCATCTGCCCACCA RR: TCGACCCTCTGAAACTGTGACCGACGGGTCGGGGAACGAAGAAGGGCGACCGGTGTGTCGAAGGGTAAGGTCTTCGTCCCGGTGTCGTCCAGGGATTAGTAGGTCTCGGTCTTCAGACATCTCATGGGTAAAGGGTCCGTCGTAGACGGGTGGT F2: 3 TCGAC 2 Unidirectional alignment (log-probability: -36.4) AGAAGCAGGGCCACAGC-----------CAgctTCCAGAGCCAGgAtTCTGTAGAGTACCCATTTCCCAGGCA AGAAGCAGGGCCACAGCAGGTCCCTAATCA---TCCAGAGCCAGAAGTCTGTAGAGTACCCATTTCCCAGGCA Template switch alignment (log-probability: -27.1) AGAAGCAGGGCCACAGC|CAGCT|TCCAGAGCCAGgAtTCTGTAGAGTACCCATTTCCCAGGCA AGAAGCAGGGCCACAGC|CAGCT|TCCAGAGCCAGAAGTCTGTAGAGTACCCATTTCCCAGGCA ========== Event 2074 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTGTGTATGTGCGTGTTCACCTGTGC--------CCGTGGCACAGGTGCACACGTGGGTGTGGGCCAA Chimp: TCTATGTATGTGCGTGTTCACCTGTGC--------CCGTGGCACAGGTGCACACGTGGGTGTGGGCCAG ↑ 3 1 2 4 Gorilla: TCTATGTATGTGCGTGTTCACCTGTGC----------------CATGGGCACACGTGGGTGTGGGCCAG Human: TCTGTGTATGTGCGTGTTCACCTGTGC--------CCGTGGCACAGGTGCACACGTGGGTGTGGGCCAA Cluster: [ ] Orangutan: TCTGT--GTGTGCGTGTTCACCTGTGCCCGTGGCA--------CAGGTACACACGTGGGCGTGGGCCAG Gorilla > Chimp --------------- chr2B:131629126-131629137 Template switch process: F1: L CATGCAGAATGGCCTCTATGTATGTGCGTGTTCACCTGTGCC 1 F3: 4 GCACACGTGGGTGTGGGCCAGGCTGAGTGCACGTGGCCTG R RF: CATGCAGAATGGCCTCTATGTATGTGCGTGTTCACCTGTGCCATGGGCACACGTGGGTGTGGGCCAGGCTGAGTGCACGTGGCCTG RR: GTACGTCTTACCGGAGATACATACACGCACAAGTGGACACGGTACCCGTGTGCACCCACACCCGGTCCGACTCACGTGCACCGGAC F2: 3 TGGACACGGTGC 2 Unidirectional alignment (log-probability: -33.5) TGCAGAATGGCCTCTATGTATGTGCGTGTTCACCTGTGCccgtggcaCAgGtGCACACGTGGGTGTGGGCCAGGCTGAGTGCACGTGGCCTG TGCAGAATGGCCTCTATGTATGTGCGTGTTCACCTGTGC--------CATGGGCACACGTGGGTGTGGGCCAGGCTGAGTGCACGTGGCCTG Template switch alignment (log-probability: -22.8) TGCAGAATGGCCTCTATGTATGTGCGTGTTCACCTGTGCC|CgTGGCACAGGT|GCACACGTGGGTGTGGGCCAGGCTGAGTGCACGTGGCCTG TGCAGAATGGCCTCTATGTATGTGCGTGTTCACCTGTGCC|CATGGCACAGGT|GCACACGTGGGTGTGGGCCAGGCTGAGTGCACGTGGCCTG ========== Event 2075 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGAGTCTATTTAGGTGTGACTACCACTC--ATATGACGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCA-----AATTTATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACAGTTGTACAAA------TAGTTGTACTAACATTTAATGGCGACAACATGTCATGTTCCCACACTCAAAATAAG Chimp: ATGAGTCTATTTAGGTGTGACAACCACTC--ATATGACGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCA-----AATTTATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACagttgtacaaa---tattagttgtactaatattTAATGGCGACAACATGTCATGTTCCCACACTCAAAATAAG ↑ 1 4 3 2 Gorilla: ATGAGTCTATTTAGGTGTGACTACCACTC----ATGATGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCA----------ATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACagttgtacaaatat---tagttgtactaatattTAATGGCGACAACATGTCATGTTCCCACACTCAAAATAAG ↓ 1 4 3 2 Human: ATGAGTCTATTTAGGTGTGACTACCACTC--ATATGACGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCA-----AATTTATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACAGTTGTACAAA------TAGTTGTACTAACATTTAATGGCGACAACATGTCATGTTCCCACACTCAAAATAAG Cluster: [ ] Orangutan: ATGAGTCTATTTAGGTGTGACTACCACTCAT--ATGACCTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAATTT-----ATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACagttgtacaaatat---tagttgtactaatattTAATGGCGACAACATGTCATGTTCCCACCCTCAAAATAAG Gorilla > Human --------------- chr22:9925742-9925746 Template switch process: F1: L AAGTACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCAT 1 F3: 4 GTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAATTTA R RF: AAGTACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCATGATGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACAGTTGTACAAATATTAGTTGTACTAATATTTAATGGCGACAACATGTCAT RR: TTCATGTAACTTTACTCAGATAAATCCACACTGATGGTGAGTACTACATTCGGACCCCCTGAGTTATAAAACCCCAGGGTTAAAAGATCAACATCATTTCGTCAACATGTTTACTTTGTCAACATGTTTATAATCAACATGATTATAAATTACCGCTGTTGTACAGTA F2: 3 CAGTA 2 Unidirectional alignment (log-probability: -33.2) TACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCatATGAcGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAattta TACATTGAAATGAGTCTATTTAGGTGTGACTACCACTC--ATGATGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAA----- Template switch alignment (log-probability: -27.4) TACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCAT|ATGAC|GTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAaTTTa TACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCAT|ATGAC|GTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAATTTTC Gorilla > Chimp --------------- chr22:10285733-10285737 Template switch process: F1: L ATTCTGGAAAGTACATTGAAATGAGTCTATTTAGGTGTGACAACCACTCAT 1 F3: 4 GTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAATTTA R RF: ATTCTGGAAAGTACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCATGATGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAATTTTCTAGTTGTAGTAAAGCAGTTGTACAAATGAAACAGTTGTACAAATATTAGTTGTACTAATATTTAATGGCGACAACATGTCAT RR: TAAGACCTTTCATGTAACTTTACTCAGATAAATCCACACTGATGGTGAGTACTACATTCGGACCCCCTGAGTTATAAAACCCCAGGGTTAAAAGATCAACATCATTTCGTCAACATGTTTACTTTGTCAACATGTTTATAATCAACATGATTATAAATTACCGCTGTTGTACAGTA F2: 3 CAGTA 2 Unidirectional alignment (log-probability: -38.8) TACATTGAAATGAGTCTATTTAGGTGTGACaACCACTCatATGAcGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAattta TACATTGAAATGAGTCTATTTAGGTGTGACTACCACTC--ATGATGTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAA----- Template switch alignment (log-probability: -33.2) TACATTGAAATGAGTCTATTTAGGTGTGACaACCACTCAT|ATGAC|GTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAAaTTTa TACATTGAAATGAGTCTATTTAGGTGTGACTACCACTCAT|ATGAC|GTAAGCCTGGGGGACTCAATATTTTGGGGTCCCAATTTTC ========== Event 2076 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGGAGGCGGGGGCAGCAGTGCATAGGCCATGTGGCCCTCGGGGTCCCTCAACT--TCTCTGAGCCGCTCATTCCTCTCTAACTGGGGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGC----------------------GGTCCTCAGCGAAGGCAGTG Chimp: GGGGAGGCGGGGGCAGCAGTGCGTAGGCCATGTGGCCCTCAGGGTCCCTCAACC--TCTCTGAGCCGCTCATTCCTCTCTAACTGGGGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGC-----------GGCCCATGCAGGGTCCTCAGCGAAGGCAGTG Gorilla: GGGGAGGCGGGGGCAGCAGTGCGGAGGCCATGTGGCCCTCGGGGTCCCTCAACC----TCTGAGCCGCTCATTCCTCTCTAACTGGGGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGTGGCCTATGCAG-----------GGTCCTCAGCGAAGGCAGTG ↑ 3 2 1 4 Human: GGGGAGGCGGGGGCAGCAGTGCATAGGCCATGTGGCCCTCGGGGTCCCTCAACT--TCTCTGAGCCGCTCATTCCTCTCTAACTGGGGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGC----------------------GGTCCTCAGCGAAGGCAGTG Cluster: [ ] Orangutan: GGGGAGGTGGGGGCAGCAGTGCGGAGGCCATGTGGCCCTCGGGGTCCCTCGACCTC--TCTGAGCCACTCATTCCTCTCTAACTGGGGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGCGGCCCATGCAG-----------GGTCCTCAGCGAAGGCAGTG Human > Gorilla --------------- chr2B:1282847-1282857 Template switch process: F1: L GGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAG 1 F3: 4 GGGTCCTCAGCGAAGGCAGTGATGGAGGCTGCAGGAACTGA R RF: TGCATAGGCCATGTGGCCCTCGGGGTCCCTCAACTTCTCTGAGCCGCTCATTCCTCTCTAACTGGGGCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGCGGTCCTCAGCGAAGGCAGTGATGGAGGCTGCAGGAACTGA RR: ACGTATCCGGTACACCGGGAGCCCCAGGGAGTTGAAGAGACTCGGCGAGTAAGGAGAGATTGACCCCGCTCCTGGGGTGGGACGAGGGGACCTTCCAGTGGGACTCGCCAGGAGTCGCTTCCGTCACTACCTCCGACGTCCTTGACT F2: 3 ACGTATCCGGT 2 Unidirectional alignment (log-probability: -32.2) GCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAGtggcctatgcagGGTCCTCAGCGAAGGCAGTGATGGAGGCTGCAGGAACTG GCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAG-----------CGGTCCTCAGCGAAGGCAGTGATGGAGGCTGCAGGAACTG Template switch alignment (log-probability: -22.7) GCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAG|TGGCCTATGCA|gGGTCCTCAGCGAAGGCAGTGATGGAGGCTGCAGGAACTG GCGAGGACCCCACCCTGCTCCCCTGGAAGGTCACCCTGAG|TGGCCTATGCA|CGGTCCTCAGCGAAGGCAGTGATGGAGGCTGCAGGAACTG ========== Event 2077 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CATGTGGCCTGGGGCCTCCCCAGTTAGCAGCTGACCAGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCATCCCCTCCATGGCAA ↑ 4 1 3 2 Chimp: CCTGTGGCCTGGGGCCTCCCCGGTTA-----------GCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCATCCCCTCCATGGCAA ↓ 4 1 3 2 Gorilla: CATGTGGCCTGGGGCCTCCCCAGTTAGCAGCTGACCAGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCATCCCCTCCATGGCAA Human: CATGTGGCCTGGGGCCTCCCCAGTTAGCAGCTGACCAGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCATCCCCTCCATGGCAA Cluster: [ ] Orangutan: CATGTGACCTGGGGCCTCCCCAGTTAGCAGCTGACCAGCAGCCCAAGAATCTCAGCCTGGTCAGAGGGGTCAGAGCGTCCCCTCCATGGCAA Chimp > Human ------------- chr2:241010563-241010567 Template switch process: F1: L GTCACTGCAGCTCCAGGTTCCATGTGGCCTGGGGCCTCCCCAGTTAGCAGC 1 F3: 4 AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCA R RF: GTCACTGCAGCTCCAGGTTCCCTGTGGCCTGGGGCCTCCCCGGTTAGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCA RR: CAGTGACGTCGAGGTCCAAGGGACACCGGACCCCGGAGGGGCCAATCGTCGGGTTCTTAGAGTCGGACGAGTCTCCCCAGTCTCGT F2: 3 CCAGT 2 Unidirectional alignment (log-probability: -38.8) TCCAGGTTCCaTGTGGCCTGGGGCCTCCCCaGTTAGCagctgaccagcAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC TCCAGGTTCCCTGTGGCCTGGGGCCTCCCCGGTTAGC-----------AGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC Template switch alignment (log-probability: -28.1) TCCAGGTTCCaTGTGGCCTGGGGCCTCCCCaGTTAGCAGC|TGACC|AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC TCCAGGTTCCCTGTGGCCTGGGGCCTCCCCGGTTAGCAGC|TGACC|AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC Chimp > Gorilla --------------- chr2B:134384522-134384526 Template switch process: F1: L GTCACTGCAGCTCCAGGTTCCATGTGGCCTGGGGCCTCCCCAGTTAGCAGC 1 F3: 4 AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCA R RF: GTCACTGCAGCTCCAGGTTCCCTGTGGCCTGGGGCCTCCCCGGTTAGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGCA RR: CAGTGACGTCGAGGTCCAAGGGACACCGGACCCCGGAGGGGCCAATCGTCGGGTTCTTAGAGTCGGACGAGTCTCCCCAGTCTCGT F2: 3 CCAGT 2 Unidirectional alignment (log-probability: -37.8) TCCAGGTTCCaTGTGGCCTGGGGCCTCCCCaGTTagcagctgaccAGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC TCCAGGTTCCCTGTGGCCTGGGGCCTCCCCGGTT-----------AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC Template switch alignment (log-probability: -27.7) TCCAGGTTCCaTGTGGCCTGGGGCCTCCCCaGTTAGCAGC|TGACC|AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC TCCAGGTTCCCTGTGGCCTGGGGCCTCCCCGGTTAGCAGC|TGACC|AGCAGCCCAAGAATCTCAGCCTGCTCAGAGGGGTCAGAGC ========== Event 2078 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAGATGCCCGCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTGCACATAGTGTCATCTCTCTGGGCATCCAGGAAGCATGTCACACAC ↑ 4 1 3 2 Chimp: TTTGTGAAACAAAAGGTATGCCCTCCACTCTGTG----------------------------TTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTGCACACAGTGTCATCTCTCTGGGCATCCAGGAAGCATGTCACACAC Gorilla: TTTGTGAAACAAAAGGTATGCCCTCCACTCTGTG----------------------------TTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTGCACATAGTGTCATCTCTCTGGGCATCCAGGAAGCATGTCACACAC ↓ 4 1 3 2 Human: TTTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAGATGCCCGCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTGCACATAGTGTCATCTCTCTGGGCATCCAGGAAGCATGTCACACAC Cluster: [ ] Orangutan: TTTGTGAAACAAAAGGTATGCCCTCCACTCTGTG-----------------------------TATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTTCACATAGTGTCATCTCTCTGGTCATCCAGGAAGCATGTCACACAC Chimp > Human ------------- chr2:955482-955487 Template switch process: F1: L CTCTGCATTTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAG 1 F3: 4 GCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCC R RF: CTCTGCATTTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTGCACACAGTGTCATCTCTCTGGGCAT RR: GAGACGTAAACACTTTGTTTTCCATACGGGAGGTGAGACACAATAGTCAGAACCAACTCGACAAACCCGCCGTCCACCGGGACGTCGGACGACTCACGTGTGTCACAGTAGAGAGACCCGTA F2: 3 CCCGTA 2 Unidirectional alignment (log-probability: -51.2) TTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCagatgcccgccctccactctgtgttatcAGTCTTGGTTGAGCTGTTTG TTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATC----------------------------AGTCTTGGTTGAGCTGTTTG Template switch alignment (log-probability: -16.4) TTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAG|ATGCCC|GCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTG TTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAG|ATGCCC|GCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTG Gorilla > Human --------------- chr2:955482-955487 Template switch process: F1: L CTCTGCATTTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAG 1 F3: 4 GCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCC R RF: CTCTGCATTTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTGGGCGGCAGGTGGCCCTGCAGCCTGCTGAGTGCACATAGTGTCATCTCTCTGGGCAT RR: GAGACGTAAACACTTTGTTTTCCATACGGGAGGTGAGACACAATAGTCAGAACCAACTCGACAAACCCGCCGTCCACCGGGACGTCGGACGACTCACGTGTATCACAGTAGAGAGACCCGTA F2: 3 CCCGTA 2 Unidirectional alignment (log-probability: -51.1) TTGTGAAACAAAAGGTATGCCCTCCACTCTGtgttatcagatgcccgccctccactctgTGTTATCAGTCTTGGTTGAGCTGTTTG TTGTGAAACAAAAGGTATGCCCTCCACTCTG----------------------------TGTTATCAGTCTTGGTTGAGCTGTTTG Template switch alignment (log-probability: -17) TTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAG|ATGCCC|GCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTG TTGTGAAACAAAAGGTATGCCCTCCACTCTGTGTTATCAG|ATGCCC|GCCCTCCACTCTGTGTTATCAGTCTTGGTTGAGCTGTTTG ========== Event 2079 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGTCATGGTGAATGCCAAGTGTCAG-AATA-------------------------------------------TC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGACACTTGGCATTCACCATGACC Chimp: AGGTCATGGTGAATGCCAAGTGTCAG-AATA-------------------------------------------TC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGACACTTGGCATTCACCATGACC ↑ 1 3 4 2 Gorilla: AGGTCATGGTGAATGCCAAGTTTCAAAGATA---------------TTCTGACACTTGAGTATTTGTCAGAGATAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGACACTTGGCATTCACCATGACC Human: AGGTCATGGTGAATGCCAAGTGTCAG-AATA-------------------------------------------TC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGACACTTGGCATTCACCATGACC Cluster: [ ] Orangutan: AGGTCATGGTGAATGCCAAGTGTCAAAGATATTCTGACACTTGGGT----------------------------ATTTGTCAGAGATATTCTGTGGGATCCCCGGGTACCGAGCTCGAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCATTCACCATGACC Gorilla > Chimp --------------- chr2B:628812-628822 Template switch process: F1: L GTCACCCAAAGGCTTCCACTAGGTCATGGTGAATGCCAAGT 1 F3: 4 TCTGACACTTGGCATTCACCATGACCCAGCGGGATAACAG R RF: GTCACCCAAAGGCTTCCACTAGGTCATGGTGAATGCCAAGTTTCAAAGATATTCTGACACTTGAGTATTTGTCAGAGATATTCTGACACTTGGCATTCACCATGACCCAGCGGGATAACAG RR: CAGTGGGTTTCCGAAGGTGATCCAGTACCACTTACGGTTCAAAGTTTCTATAAGACTGTGAACTCATAAACAGTCTCTATAAGACTGTGAACCGTAAGTGGTACTGGGTCGCCCTATTGTC F2: 3 CTATAAGACTG 2 Unidirectional alignment (log-probability: -33.5) TCACCCAAAGGCTTCCACTAGGTCATGGTGAATGCCAAG-----------------------------TGTCAGA-ATATcTCTGACACTTGGCATTCACCATGACCCAGCGGGATAACAG TCACCCAAAGGCTTCCACTAGGTCATGGTGAATGCCAAGTTTCAAAGATATTCTGACACTTGAGTATTTGTCAGAGATAT-TCTGACACTTGGCATTCACCATGACCCAGCGGGATAACAG Template switch alignment (log-probability: -17.1) TCACCCAAAGGCTTCCACTAGGTCATGGTGAATGCCAAGT|GTCAGAATATC|TCTGACACTTGGCATTCACCATGACCCAGCGGGATAACAG TCACCCAAAGGCTTCCACTAGGTCATGGTGAATGCCAAGT|GTCAGAATATC|TCTGACACTTGGCATTCACCATGACCCAGCGGGATAACAG ========== Event 2080 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTCACTCCACCCCGATTATTC-----------AGTGTGCGATCAGTGTGAGCATATTGTGGTGAGGGGCTTTAGAAAA Chimp: GTCACTCCACCCCGATTATTC-----------AGTGTGCGATCAGTGTGAGCATATTGTGGTGAGGGGCTTTAGAAAA ↑ 4 1 3 2 Gorilla: GTCACTCCACCCCGATTATTC----------------------AGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAA ↓ 4 1 3 2 Human: GTCACTCCACCCCGATTATTC-----------AGTGTGCGATCAGTGTGAGCATATTGTGGTGAGGGGCTTTAGAAAA Cluster: [ ] Orangutan: GTCACTCCACCCCCATTATTCAGTTTGTGATC-----------AGTATGAGCGTATCGTGGTGAGGGGCTTTGGAAAA Gorilla > Human --------------- chr22:7967708-7967711 Template switch process: F1: L GGCCTCTTTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTG 1 F3: 4 CAGTGTGAGCATATTGTGGTGAGGGGCTTTAGAAAACCCAC R RF: GGCCTCTTTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAACCCAC RR: CCGGAGAAAAACACAGTCAACAGTGAGGTGGGGCTAATAAGTCACACTCGTATAGCACCACTCCCCGAAATCTTTTGGGTG F2: 3 TAGC 2 Unidirectional alignment (log-probability: -32.2) TTTTGTGTCAGTTGTCACTCCACCCCGATTATtcagtgtgcgaTCAGTGTGAGCATATtGTGGTGAGGGGCTTTAGAAAACCCA TTTTGTGTCAGTTGTCACTCCACCCCGATTAT-----------TCAGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAACCCA Template switch alignment (log-probability: -21.9) TTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTG|CGAT|CAGTGTGAGCATATtGTGGTGAGGGGCTTTAGAAAACCCA TTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTG|CGAT|CAGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAACCCA Gorilla > Chimp --------------- chr22:8229163-8229166 Template switch process: F1: L GGCCTCTTTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTG 1 F3: 4 CAGTGTGAGCATATTGTGGTGAGGGGCTTTAGAAAACCCAC R RF: GGCCTCTTTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAACCCAC RR: CCGGAGAAAAACACAGTCAACAGTGAGGTGGGGCTAATAAGTCACACTCGTATAGCACCACTCCCCGAAATCTTTTGGGTG F2: 3 TAGC 2 Unidirectional alignment (log-probability: -32.2) TTTTGTGTCAGTTGTCACTCCACCCCGATTATtcagtgtgcgaTCAGTGTGAGCATATtGTGGTGAGGGGCTTTAGAAAACCCA TTTTGTGTCAGTTGTCACTCCACCCCGATTAT-----------TCAGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAACCCA Template switch alignment (log-probability: -21.9) TTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTG|CGAT|CAGTGTGAGCATATtGTGGTGAGGGGCTTTAGAAAACCCA TTTTGTGTCAGTTGTCACTCCACCCCGATTATTCAGTGTG|CGAT|CAGTGTGAGCATATCGTGGTGAGGGGCTTTAGAAAACCCA ========== Event 2081 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAAGGATAAAACTGTGGGTGTTATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAA Chimp: TTAAGGATAAAACTGTGGGTGTTATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAA ↓ 1 4 3 2 Gorilla: TTAAGGATAAAACTGTGGGTG-TATGCA-TAGAACATTCTATGCATACAAAATGGAAAAAACATAA ↑ 1 4 3 2 Human: TTAAGGATAAAACTGTGGGTGTTATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAA Cluster: [ ] Orangutan: TTAAGGATAAAACTGTGGGTGTTACACTTGGGAACATTCTATGCATACAAAATGGAAAAAACATAA Human > Gorilla --------------- chr22:6953527-6953533 Template switch process: F1: L GATTGAAAATGGAAGAAGAGTTAAGGATAAAACTGTGGGTGT 1 F3: 4 GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA R RF: GATTGAAAAGGGAAGAATAGTTAAGGATAAAACTGTGGGTGTTATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA RR: CTAACTTTTCCCTTCTTATCAATTCCTATTTTGACACCCACAATATGAGCCCTTGTAAGATACGTATGTTTTACCTTTTTTGTATTATTCT F2: 3 ATACGTA 2 Unidirectional alignment (log-probability: -39.3) TTGAAAAtGGAAGAAgAGTTAAGGATAAAACTGTGGGTGTatgcaTA-------GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA TTGAAAAGGGAAGAATAGTTAAGGATAAAACTGTGGGTGT-----TATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA Template switch alignment (log-probability: -27.7) TTGAAAAtGGAAGAAgAGTTAAGGATAAAACTGTGGGTGT|ATGCATA|GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA TTGAAAAGGGAAGAATAGTTAAGGATAAAACTGTGGGTGT|ATGCATA|GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA Chimp > Gorilla --------------- chr22:6953527-6953533 Template switch process: F1: L GATTGAAAATGGAAGAAGAGTTAAGGATAAAACTGTGGGTGT 1 F3: 4 GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA R RF: GATTGAAAAGGGAAGAATAGTTAAGGATAAAACTGTGGGTGTTATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA RR: CTAACTTTTCCCTTCTTATCAATTCCTATTTTGACACCCACAATATGAGCCCTTGTAAGATACGTATGTTTTACCTTTTTTGTATTATTCT F2: 3 ATACGTA 2 Unidirectional alignment (log-probability: -39.3) TTGAAAAtGGAAGAAgAGTTAAGGATAAAACTGTGGGTGTatgcaTA-------GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA TTGAAAAGGGAAGAATAGTTAAGGATAAAACTGTGGGTGT-----TATACTCGGGAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA Template switch alignment (log-probability: -27.7) TTGAAAAtGGAAGAAgAGTTAAGGATAAAACTGTGGGTGT|ATGCATA|GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA TTGAAAAGGGAAGAATAGTTAAGGATAAAACTGTGGGTGT|ATGCATA|GAACATTCTATGCATACAAAATGGAAAAAACATAATAAGA ========== Event 2082 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGTAATTTATAATAAAACATAC------GATTATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAATTAGGTATCGTTCAACTGAAAAGACAAAAGG Chimp: TTGTAATTTATAATAAAACATAC---TTAATTTATGATTTCGTAACTTACTGaaaaaaaCTTTAAGAAAATTAGGTATCATTCAACTGAAAAGACAAAAGG Gorilla: TTGTAATTTATAATAAAACATGCTTA---ATTTATGATTTCGTAACTTACTGaaaaaaaCTTTAAGAAAATTAGGTATCGTTCAACTGAAAAGACAAAAGG ↓ 1 4 3 2 Human: TTGTAATTTATAATAAAACATAC------GATTATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAATTAGGTATCGTTCAACTGAAAAGACAAAAGG Cluster: [ ] Orangutan: TTGTAATTTATAATAAAACATGCTTA---ATTTATGATTTCGTAACTTATGGAAAAAAACTTTAAGAAAATTAGGTATCGTTCGATTGAAAAGACAAAAGG Gorilla > Human --------------- chr2:24594258-24594262 Template switch process: F1: L TGAATTCAATAAATGGTAATTTGTAATTTATAATAAAACAT 1 F3: 4 TATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAAT R RF: TGACTTCAATAAATGGTAATTTGTAATTTATAATAAAACATGCTTAATTTATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAATTAGGTATCGT RR: ACTGAAGTTATTTACCATTAAACATTAAATATTATTTTGTACGAATTAAATACTAAAGCATTGAATGACTTTTTTTGAAATTCTTTTAATCCATAGCA F2: 3 TAGCA 2 Unidirectional alignment (log-probability: -32.3) GAaTTCAATAAATGGTAATTTGTAATTTATAATAAAAC-------ATacgaTTATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAAT GACTTCAATAAATGGTAATTTGTAATTTATAATAAAACATGCTTAAT----TTATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAAT Template switch alignment (log-probability: -21.8) GAaTTCAATAAATGGTAATTTGTAATTTATAATAAAACAT|ACGAT|TATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAAT GACTTCAATAAATGGTAATTTGTAATTTATAATAAAACAT|ACGAT|TATGATTTCGTAACTTACTGAAAAAAACTTTAAGAAAAT ========== Event 2083 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGGCCAGCGGCACCTGAGAGTCAGGAGGAAGTGGCCGATGGGACTCTGAGCCCCGTGCAAAGGCCCCCTGCCTTGTGGCAGCCACCAGGACCACCCACTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCCCACGTCAGAGGAGAGGAAGCAGAGGTCA ↓ 3 2 1 4 Chimp: AGGGCCGGCGGCACCTGAGAGTCAGGAGGAAGTGGCCGATGGGACTCTGAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCA----CTGACTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCCCACGTCAGAGGAGAGGAAGCAGAGGTCA ↑ 1 4 3 2 Gorilla: AGGGCCGGCGGCACCTGAGAGTCAGGAGGAAGTGGCCGATGGGACTTTGAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCAGGACCACCCTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCCCACGTCAGAGGAGAGGAAGCAGAGGTCA Human: AGGGCCAGCGGCACCTGAGAGTCAGGAGGAAGTGGCCGATGGGACTCTGAGCCCCGTGCAAAGGCCCCCTGCCTTGTGGCAGCCACCAGGACCACCCACTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCCCACGTCAGAGGAGAGGAAGCAGAGGTCA Cluster: [ ] Orangutan: AGGGCTGGCGGCACCTGGGAGTCAGGAGGAAGTGGCCGATGGGACTCTGAGCCCCATGCAAAGGTCCCCTGCCTGGTGGCAGGCACCAGGACCACCCTCCGGGTCAGCAGTCCCCAGGAGGGGAGGGGCTGCCATGCCCACGTCAGAGGAGAGGAAGCAGAGGTCA Human > Chimp ------------- chr22:6103638-6103643 Template switch process: F1: L TGAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCA 1 F3: 4 CTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCC R RF: AGTCAGGAGGAAGTGGCCGATGGGACTCTGAGCCCCGTGCAAAGGCCCCCTGCCTTGTGGCAGCCACCAGGACCACCCACTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCC RR: TCAGTCCTCCTTCACCGGCTACCCTGAGACTCGGGGCACGTTTCCGGGGGACGGAACACCGTCGGTGGTCCTGGTGGGTGACCCAGTCGTCAGGGGTCCTCCCCTGCCCGACGGTACGG F2: 3 TCAGTC 2 Unidirectional alignment (log-probability: -36.3) GAGCCCCGTGCAAAGGCCCCCTGCCTcGTGGCAGCCA----------CCACTGactctgGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCC GAGCCCCGTGCAAAGGCCCCCTGCCTTGTGGCAGCCACCAGGACCACCCACTG------GGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCC Template switch alignment (log-probability: -22) GAGCCCCGTGCAAAGGCCCCCTGCCTcGTGGCAGCCACCA|CTGACT|CTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCC GAGCCCCGTGCAAAGGCCCCCTGCCTTGTGGCAGCCACCA|CTGACT|CTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCC Gorilla > Chimp --------------- chr22:6103638-6103641 Template switch process: F1: L TGAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCA 1 F3: 4 CTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATG R RF: TGAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCAGGACCACCCTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATGCCCACGTCAG RR: ACTCGGGGCACGTTTCCGGGGGACGGAGCACCGTCGGTGGTCCTGGTGGGAGACCCAGTCGTCAGGGGTCCTCCCCTGCCCGACGGTACGGGTGCAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -25.3) GAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCA-------CtgaCTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATG GAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCAGGACCACC---CTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATG Template switch alignment (log-probability: -16.2) GAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCA|CTGA|CTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATG GAGCCCCGTGCAAAGGCCCCCTGCCTCGTGGCAGCCACCA|CTGA|CTCTGGGTCAGCAGTCCCCAGGAGGGGACGGGCTGCCATG ========== Event 2084 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATCCCTTCACTCCCCTTCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTCGGCTCACCCTTGGCACTCTCA Chimp: catccCTTCACTCCCCTTCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTCGGCTCACCCTTGGCACTCTCA ↓ 3 2 1 4 Gorilla: catccCTTCACTCCCCTTCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGCTGAAGGCTCACCCTTGGCACTCTCA ↑ 3 2 1 4 Human: CATCCCTTCACTCCCCTTCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTCGGCTCACCCTTGGCACTCTCA Cluster: [ ] Orangutan: CATCCCTTCACTCCCCTTCTTCAGCCAACTCCCCAAGCCCCCATACCTGTGCTAAAGGGCCTCGGCTCACCCTTGGCACTCTCA Human > Gorilla --------------- chr22:6752721-6752725 Template switch process: F1: L TCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG 1 F3: 4 GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT R RF: TCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTCGGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT RR: AGAAGTCGGTTGAGGGGCTCGGGGGTACGGACACGACTTCCCGGAGCCGAGTGGGAACCGTGAGAGTTCCTTCGTCTCCTCCTTCA F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -26.6) CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG----CtgaaGGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTC----GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT Template switch alignment (log-probability: -16.4) CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG|CTGAA|GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG|CTGAA|GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT Chimp > Gorilla --------------- chr22:6752721-6752725 Template switch process: F1: L TCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG 1 F3: 4 GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT R RF: TCTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTCGGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT RR: AGAAGTCGGTTGAGGGGCTCGGGGGTACGGACACGACTTCCCGGAGCCGAGTGGGAACCGTGAGAGTTCCTTCGTCTCCTCCTTCA F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -26.6) CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG----CtgaaGGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGGGCCTC----GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT Template switch alignment (log-probability: -16.4) CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG|CTGAA|GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT CTTCAGCCAACTCCCCGAGCCCCCATGCCTGTGCTGAAGG|CTGAA|GGCTCACCCTTGGCACTCTCAAGGAAGCAGAGGAGGAAGT ========== Event 2085 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCCCTCCAAAGTACTGAATGA-----AACATCCACACCTCCCTTTGGAACAT Chimp: CTCCCTCCAAAGTACTGAATGA-----AACATCCACACCTCCCTTTGGAACAT ↓ 3 4 2 Gorilla: CTCCCTCCAAAGTACTGAATGGATGTTTCCATCCACACCTCCCTTCGGAACAT ↑ 3 4 2 Human: CTCCCTCCAAAGTACTGAATGA-----AACATCCACACCTCCCTTTGGAACAT Cluster: [ ] Orangutan: CTCCCTCCAAAGTACTGAATGA-----AACATCCACACCTCCCTTTGGAACAT Human > Gorilla --------------- chr22:5325086-5325093 Template switch process: F1: L GAGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATG 1 F3: 4 CATCCACACCTCCCTTCGGAACATTCTCCAGAGGCCTTGA R RF: GAGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATGAAACATCCACACCTCCCTTTGGAACATTCTCCAGAGGCCTTGA RR: CTCTTTCTTGGGTAAAGAAAGAGGGAGGTTTCATGACTTACTTTGTAGGTGTGGAGGGAAACCTTGTAAGAGGTCTCCGGAACT F2: 3 CTTTGTAG 2 Unidirectional alignment (log-probability: -34.7) AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATGgAtgtttcCATCCACACCTCCCTTcGGAACATTCTCCAGAGGCCTTGA AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATGAAA-----CATCCACACCTCCCTTTGGAACATTCTCCAGAGGCCTTGA Template switch alignment (log-probability: -22.3) AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATG|GATGTTTC|CATCCACACCTCCCTTcGGAACATTCTCCAGAGGCCTTGA AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATG|GATGTTTC|CATCCACACCTCCCTTTGGAACATTCTCCAGAGGCCTTGA Chimp > Gorilla --------------- chr22:5325086-5325093 Template switch process: F1: L GAGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATG 1 F3: 4 CATCCACACCTCCCTTCGGAACATTCTCCAGAGGCCTTGA R RF: GAGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATGAAACATCCACACCTCCCTTTGGAACATTCTCCAGAGGCCTTGA RR: CTCTTTCTTGGGTAAAGAAAGAGGGAGGTTTCATGACTTACTTTGTAGGTGTGGAGGGAAACCTTGTAAGAGGTCTCCGGAACT F2: 3 CTTTGTAG 2 Unidirectional alignment (log-probability: -34.7) AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATGgAtgtttcCATCCACACCTCCCTTcGGAACATTCTCCAGAGGCCTTGA AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATGAAA-----CATCCACACCTCCCTTTGGAACATTCTCCAGAGGCCTTGA Template switch alignment (log-probability: -22.3) AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATG|GATGTTTC|CATCCACACCTCCCTTcGGAACATTCTCCAGAGGCCTTGA AGAAAGAACCCATTTCTTTCTCCCTCCAAAGTACTGAATG|GATGTTTC|CATCCACACCTCCCTTTGGAACATTCTCCAGAGGCCTTGA ========== Event 2086 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGTCACCCTGGAACCACAGAGGCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAG--------------------------GGCTGAGCAATTCAGGGACCTGAGg ↓ 3 2 4 1 Chimp: AGTCACCCTGGAACCACAGAGGCCTGGGCTAGGTCCTGGGTCAGCAGTACGACGAG-------------GGCTGCAGGCCTGGGCTGAGCAATTCAGGGACCTGAGg Gorilla: AGTCACCCTGGAACCACAGAGGCCTGGGCTAGGCCCTGGGTCAGCAGTACAATGAGGGCTGCAGGCCTG-------------GGCTGAGCAATTCAgggacctgagg ↑ 3 2 4 1 Human: AGTCACCCTGGAACCACAGAGGCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAG--------------------------GGCTGAGCAATTCAGGGACCTGAGg Cluster: [ ] Orangutan: AGTCATCCTGGAACCACAGAGGCCTGGGCTGGGCCCTGGGTCAGCAGTACAATGAGGGCTGCAGGCCTG-------------GGCTGAGCAATTCAGGGACCTGAGG Human > Chimp ------------- chr22:33067961-33067967 Template switch process: F1: L AACCACAGAGGCCTGGGCTAGGTCCTGGGTCAGCAGTACGACGAGGGCTG 1 F3: 4 GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGGC R RF: AACCACAGAGGCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAGGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGGC RR: TTGGTGTCTCCGGACCCGATCCGGGACCCAGTCGTCATGCTACTCCCGACTCGTTAAGTCCCTGGACTCCCTCCCGTACCGTCCG F2: 3 TCCGGAC 2 Unidirectional alignment (log-probability: -41.6) GCCTGGGCTAGGtCCTGGGTCAGCAGTACGAcGAGGGCtgcaggcctgggcTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG GCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAGGGC-------------TGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG Template switch alignment (log-probability: -28.3) GCCTGGGCTAGGtCCTGGGTCAGCAGTACGAcGAGGGCTG|CAGGCCT|GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG GCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAGGGCTG|CAGGCCT|GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG Human > Gorilla --------------- chr22:29934806-29934812 Template switch process: F1: L GGAACCACAGAGGCCTGGGCTAGGCCCTGGGTCAGCAGTACAATGAGGGCTG 1 F3: 4 GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGGC R RF: GGAACCACAGAGGCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAGGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGGC RR: CCTTGGTGTCTCCGGACCCGATCCGGGACCCAGTCGTCATGCTACTCCCGACTCGTTAAGTCCCTGGACTCCCTCCCGTACCGTCCG F2: 3 TCCGGAC 2 Unidirectional alignment (log-probability: -35.2) GCCTGGGCTAGGCCCTGGGTCAGCAGTACaATGAgggctgcaggcctGGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG GCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGA-------------GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG Template switch alignment (log-probability: -22.4) GCCTGGGCTAGGCCCTGGGTCAGCAGTACaATGAGGGCTG|CAGGCCT|GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG GCCTGGGCTAGGCCCTGGGTCAGCAGTACGATGAGGGCTG|CAGGCCT|GGGCTGAGCAATTCAGGGACCTGAGGGAGGGCATGGCAGG ========== Event 2087 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGTTTCAGGGATGGGAGAGGGAGTCCAGACTGCAGCCTGTGAGCCCAGACTGCGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCCCCTGCACTGAGGGGTGCACGTGGCCTGGTGAGGGGTTGGGGAGGAGTGTT-GGGCTGG----------GACTCACACCGCAGGCTGTTGGGGCCTGGGGCACACCG Chimp: CAGTTTCAGGGATGGGAGAGGGAGTCCA--------------------GACTGTGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCCTCTGCGCTGAGGGGTGCACGTGGCCTGGTGAGGGGTTAGGGCGGAGTGTT-GGGCTGG-----GTCTCCACTCACACGGCAGGCTGTTGGGGCCTGGGGCACACCG ↓ 4 1 3 2 Gorilla: CAGTTTCAGGGATGGGAGAGGGAGTCCAGACTGCAGCCTGTGAGCCCAGACTGCGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCCTCTACACTGAGGGGTGCACGTGGCCTGGTGAGGGGTTGGGGCGGAGTGTT-GGGCTGGGTCTC-----CACTCACACCGCAGGCTGTTGGGGCCTGGGGCACACCG Human: AAGTTTCAGGGATGGGAGAGGGAGTCCAGACTGCAGCCTGTGAGCCCAGACTGCGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCCCCTGCACTGAGGGGTGCACGTGGCCTGGTGAGGGGTTGGGGAGGAGTGTT-GGGCTGG----------GACTCACACCGCAGGCTGTTGGGGCCTGGGGCACACCG Cluster: [ ] Orangutan: CAGTTTCAGGGATGGGAGGGGGAGTCCAGACTGCAGCCTGTGAGCCCAGACTACGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCGCCTGCGCTGAGAGGTGCACGCGGCATGGGGAGGGGTTGGGGCGGAGTGTTGGGGCTGGGTCTC-----CACCCACACCGCAGGCTGTTGGGGCCTGGGGCACACTG Chimp > Gorilla --------------- chr22:4490237-4490242 Template switch process: F1: L TGGCACAGCCAGCCAGTTTCAGGGATGGGAGAGGGAGTCCAGACTG 1 F3: 4 GTGAGCCCAGACTGCGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCCTC R RF: TGGCACAGCCAGCCAGTTTCAGGGATGGGAGAGGGAGTCCAGACTGTGGGCGAGGCAGGAGGAGGAGGCGGGTCACAGCGGGGCCTCTGCGCTGAGGGGTGCACGTGGCCTGGTGAGGGGTTAGGGCGGAGTGTTGGGCTGGGTCTCCACTCACACGGCAGGCTG RR: ACCGTGTCGGTCGGTCAAAGTCCCTACCCTCTCCCTCAGGTCTGACACCCGCTCCGTCCTCCTCCTCCGCCCAGTGTCGCCCCGGAGACGCGACTCCCCACGTGCACCGGACCACTCCCCAATCCCGCCTCACAACCCGACCCAGAGGTGAGTGTGCCGTCCGAC F2: 3 TCCGAC 2 Unidirectional alignment (log-probability: -45.2) AGCCAGCCAGTTTCAGGGATGGGAGAGGGAGTCcagactgcagcctgtgagccCAGACTGcGGGCGAGGCAGGAGGAGGAGGCGGG AGCCAGCCAGTTTCAGGGATGGGAGAGGGAGTC--------------------CAGACTGTGGGCGAGGCAGGAGGAGGAGGCGGG Template switch alignment (log-probability: -33.5) AGCCAGCCAGTTTCAGGGATGGGAGAGGGAGTCCAGACTG|CAGCCT|GtGAGcCCAGACTGcGGGCGAGGCAGGAGGAGGAGGCGGG AGCCAGCCAGTTTCAGGGATGGGAGAGGGAGTCCAGACTG|CAGCCT|GGGAGTCCAGACTGTGGGCGAGGCAGGAGGAGGAGGCGGG ========== Event 2088 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ggggtggggtgtgttcctcactgtgtgcagcccaagcacaggctcagggacCACCCATGGCGCAGCAAACACTCTCAGGGGC ↓ 3 2 1 4 Chimp: ggggtggggtgtgttcctcactgtgtgcagcccaagcacaggctcagggacCACC-CCAGTGCAGCAAACACTCTCAGGGGC Gorilla: ggggtggggtgtgttcctcactgtgtgcagcccaagcacaggctcagggacCACCCACGGTGCAGCAAACACTCTCAGGGGC Human: ggggtggggtgtgttcctcactgtgtgcagcccaagcacaggctcagggacCACCCATGGCGCAGCAAACACTCTCAGGGGC Cluster: [ ] Orangutan: agggtggggtatgttcctcactgtatacagcacaagcacaggctcagggacCACCCACAGCACAGCAAACACTCCCAGGGGC Human > Chimp ------------- chr22:3762140-3762143 Template switch process: F1: L TCCTCACTGTGTGCAGCCCAAGCACAGGCTCAGGGACCACCC 1 F3: 4 GCAGCAAACACTCTCAGGGGCTGGGCCAAGCCCCAGAGGA R RF: TCCTCACTGTGTGCAGCCCAAGCACAGGCTCAGGGACCACCCATGGCGCAGCAAACACTCTCAGGGGCTGGGCCAAGCCCCAGAGGA RR: AGGAGTGACACACGTCGGGTTCGTGTCCGAGTCCCTGGTGGGTACCGCGTCGTTTGTGAGAGTCCCCGACCCGGTTCGGGGTCTCCT F2: 3 TGAC 2 Unidirectional alignment (log-probability: -25.7) CTCACTGTGTGCAGCCCAAGCACAGGCTCAGGGACCACCC----CagtGCAGCAAACACTCTCAGGGGCTGGGCCAAGCCCCAGAGGA CTCACTGTGTGCAGCCCAAGCACAGGCTCAGGGACCACCCATGGC---GCAGCAAACACTCTCAGGGGCTGGGCCAAGCCCCAGAGGA Template switch alignment (log-probability: -15.8) CTCACTGTGTGCAGCCCAAGCACAGGCTCAGGGACCACCC|CAGT|GCAGCAAACACTCTCAGGGGCTGGGCCAAGCCCCAGAGGA CTCACTGTGTGCAGCCCAAGCACAGGCTCAGGGACCACCC|CAGT|GCAGCAAACACTCTCAGGGGCTGGGCCAAGCCCCAGAGGA ========== Event 2089 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCATGACCAGATGATGTCCACGG-------TAGGGACGGAGCCCGTGAATGCACA Chimp: CCATGACCAGATGATGTCCACGG-------TAGGGACGGAGCCCGTGAATGCACA ↓ 3 1 42 Gorilla: CCATGACCAGATGATGTCCACAGTCCCTACCGTGGACGGAGCCCGTGAATGCACA ↑ 3 1 42 Human: CCATGACCAGATGATGTCCACGG-------TAGGGACGGAGCCCGTGAATGCACA Cluster: [ ] Orangutan: CCATGACCAGATGATGTCCACAG-------TAGGGACAGAGCCCGTGAATGCACA Human > Gorilla --------------- chr22:3792718-3792726 Template switch process: F1: L GCTTGCACAAACCACATCTGCCATGACCAGATGATGTCCACAGT 1 F3: 4 GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA R RF: GCTTGCACAAACCACATCTGCCATGACCAGATGATGTCCACGGTAGGGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA RR: CGAACGTGTTTGGTGTAGACGGTACTGGTCTACTACAGGTGCCATCCCTGCCTCGGGCACTTACGTGTTTGGGTGTGGTCCCCGAT F2: 3 TGCCATCCC 2 Unidirectional alignment (log-probability: -35.2) GCACAAACCACATCTGCCATGACCAGATGATGTCCAC---AGtccctaccgtGGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA GCACAAACCACATCTGCCATGACCAGATGATGTCCACGGTAG----------GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA Template switch alignment (log-probability: -22.5) GCACAAACCACATCTGCCATGACCAGATGATGTCCACaGT|CCCTACCGT|GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA GCACAAACCACATCTGCCATGACCAGATGATGTCCACGGT|CCCTACCGT|GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA Chimp > Gorilla --------------- chr22:3792718-3792726 Template switch process: F1: L GCTTGCACAAACCACATCTGCCATGACCAGATGATGTCCACAGT 1 F3: 4 GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA R RF: GCTTGCACAAACCACATCTGCCATGACCAGATGATGTCCACGGTAGGGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA RR: CGAACGTGTTTGGTGTAGACGGTACTGGTCTACTACAGGTGCCATCCCTGCCTCGGGCACTTACGTGTTTGGGTGTGGTCCCCGAT F2: 3 TGCCATCCC 2 Unidirectional alignment (log-probability: -35.2) GCACAAACCACATCTGCCATGACCAGATGATGTCCAC---AGtccctaccgtGGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA GCACAAACCACATCTGCCATGACCAGATGATGTCCACGGTAG----------GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA Template switch alignment (log-probability: -22.5) GCACAAACCACATCTGCCATGACCAGATGATGTCCACaGT|CCCTACCGT|GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA GCACAAACCACATCTGCCATGACCAGATGATGTCCACGGT|CCCTACCGT|GGACGGAGCCCGTGAATGCACAAACCCACACCAGGGGCTA ========== Event 2090 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cgtttgagatttttttaataatg----------acagtggctttgtggcaggtatctggtatat Chimp: CGTTTGAGATT-TTTTAATAAAAAGCCACTGTCGTAGTGGCTTTGTGGCAGGTATCTGGTATAT ↑ 3 4 2 Gorilla: CGTTTGAGATT-TTTTAATAATG----------ACAGTGGCTTTGTGGCAGGTATCTGGTATAT Human: cgtttgagatttttttaataatg----------acagtggctttgtggcaggtatctggtatat Cluster: [ ] Orangutan: cgtttgagatt-ttttaataatg----------acagtggctttgtggcaggtatctggtatat Gorilla > Chimp --------------- chr22:2792898-2792911 Template switch process: F1: L TCTCTGTGTCTATTTTTATGCCGTTTGAGATTTTTTAATAA 1 F3: 4 AGTGGCTTTGTGGCAGGTATCTGGTATATGGAGTGCTTTC R RF: TCTCTGTGTCTATTTTTATGCCGTTTGAGATTTTTTAATAATGACAGTGGCTTTGTGGCAGGTATCTGGTATATGGAGTGCTTTC RR: AGAGACACAGATAAAAATACGGCAAACTCTAAAAAATTATTACTGTCACCGAAACACCGTCCATAGACCATATACCTCACGAAAG F2: 3 TGCTGTCACCGAAA 2 Unidirectional alignment (log-probability: -39.5) CTCTGTGTCTATTTTTATGCCGTTTGAGATTTTTTAATAAaaagccactgtcgT---AGTGGCTTTGTGGCAGGTATCTGGTATATGGAGTGCTTTC CTCTGTGTCTATTTTTATGCCGTTTGAGATTTTTTAATAA-------------TGACAGTGGCTTTGTGGCAGGTATCTGGTATATGGAGTGCTTTC Template switch alignment (log-probability: -23) CTCTGTGTCTATTTTTATGCCGTTTGAGATTTTTTAATAA|AAAGCCACTGTCgT|AGTGGCTTTGTGGCAGGTATCTGGTATATGGAGTGCTTTC CTCTGTGTCTATTTTTATGCCGTTTGAGATTTTTTAATAA|AAAGCCACTGTCAT|AGTGGCTTTGTGGCAGGTATCTGGTATATGGAGTGCTTTC ========== Event 2091 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: CCATTTGCCCTGCGGAGGCCCTGG----GGCCAGTGTTCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCAGGGCTGGCATCTCCATCCCTGAGGCTGCACTGGC ↓ 1 4 3 2 Chimp: CCATTTGCCCTGCGGAGGCCCGGA--------GATGCTCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCAGGGCTGGCATCCCCATCCCTGAGGTTGCACTGGC Gorilla: CCATTTGCCCTGCGGAGGCCCAGA--------GATGCTCACGCCTGGAGCCACAGTCACATCTAGCGCTAGGGAGCAGGGCTGGCATCCCCATCCCTGAGGCTGCACTGGC Human: CCATTTGCCCTGCGGAGGCCCTGG----GGCCAGTGTTCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCAGGGCTGGCATCTCCATCCCTGAGGCTGCACTGGC Cluster: [ ] Orangutan: CCATTTGCCCTGCAGAGGCCTGGGGGCC----GGTGCTCACACCTGGAACCACAGTCACATCTAGCGCTAGGGAGCAGGGCTGGCATCCCCATCCCTGAGGCCGCACTGGC Human > Chimp ------------- chr22:2245885-2245892 Template switch process: F1: L CTCCCTGGCCACAAGGCTGCCCATTTGCCCTGCGGAGGCCC 1 F3: 4 TCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCA R RF: CTCCCTGGCCACAAGGCTGCCCATTTGCCCTGCGGAGGCCCTGGGGCCAGTGTTCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCAGGGCTGGCATCTCC RR: GAGGGACCGGTGTTCCGACGGGTAAACGGGACGCCTCCGGGACCCCGGTCACAAGTGTGGACCTCGGTGTCAGTGTAGGTCGCGATCCCTCGTCCCGACCGTAGAGG F2: 3 CGTAGAGG 2 Unidirectional alignment (log-probability: -33.3) TCCCTGGCCACAAGGCTGCCCATTTGCCCTGCGGAGGCCcggagatgC------------TCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCA TCCCTGGCCACAAGGCTGCCCATTTGCCCTGCGGAGGCC--------CTGGGGCCAGTGTTCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCA Template switch alignment (log-probability: -16.3) TCCCTGGCCACAAGGCTGCCCATTTGCCCTGCGGAGGCCC|GGAGATGC|TCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCA TCCCTGGCCACAAGGCTGCCCATTTGCCCTGCGGAGGCCC|GGAGATGC|TCACACCTGGAGCCACAGTCACATCCAGCGCTAGGGAGCA ========== Event 2092 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CAGAACCGATAAGACTGCAAATATTGATATATTGATATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCTGGTCTGCCTCCTGATTCCTGCCCTGAAATATGCTC ↓ 1 4 3 2 Chimp: CAGAACCGATAAGACTGCAAA------TATATCAGGATCACAGTTACG-GTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCCAGTCTGCCTCCTGATTCCTGCCCTGAAATATGCTC Gorilla: CAGAACCGATAAGACTGCAAA------TATATCAGGATCACAGTTATGGCTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCCAGTCTACCTCCTGATTCCTGCCCTGAAATACGCTC ↑ 1 4 3 2 Human: CAGAACCGATAAGACTGCAAATATTGATATATTGATATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCTGGTCTGCCTCCTGATTCCTGCCCTGAAATATGCTC Cluster: [ ] Orangutan: CAGAACCAATAAGACTGCAAA------TATATCAGGATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCCGGTCTGCCTCCTGATTCCTGCCCTGAAATATGCTC Human > Chimp ------------- chr22:2315606-2315611 Template switch process: F1: L CTAACACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT 1 F3: 4 ATCACAGTTACGG-TATTTCAGGAAATGGAATTTTATTAG R RF: CTAACACGCAATACCCATGTCAGAACCGATAAGACTGCAAATATTGATATATTGATATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCTGGTCTGCCTCCTGAT RR: GATTGTGCGTTATGGGTACAGTCTTGGCTATTCTGACGTTTATAACTATATAACTATAGTGTCAATGCCGATAAAGTCCTTTACCTTAAAATAATCTTCAAAAGGTTAGAAAGGAGGGAAGGAGGACCAGACGGAGGACTA F2: 3 GGACTA 2 Unidirectional alignment (log-probability: -37.7) CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT----------ATcaggATCACAGTTACGG-TATTTCAGGAAATGGAATTTTATTAG CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATATTGATATATTGAT----ATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAG Template switch alignment (log-probability: -26.3) CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT|ATCAGG|ATCACAGTTACGG-TATTTCAGGAAATGGAATTTTATTAG CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT|ATCAGG|ATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAG Human > Gorilla --------------- chr22:2303768-2303773 Template switch process: F1: L CTAACACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT 1 F3: 4 ATCACAGTTATGGCTATTTCAGGAAATGGAATTTTATTAG R RF: CTAACACGCAATACCCATGTCAGAACCGATAAGACTGCAAATATTGATATATTGATATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAGAAGTTTTCCAATCTTTCCTCCCTTCCTCCTGGTCTGCCTCCTGAT RR: GATTGTGCGTTATGGGTACAGTCTTGGCTATTCTGACGTTTATAACTATATAACTATAGTGTCAATGCCGATAAAGTCCTTTACCTTAAAATAATCTTCAAAAGGTTAGAAAGGAGGGAAGGAGGACCAGACGGAGGACTA F2: 3 GGACTA 2 Unidirectional alignment (log-probability: -32.5) CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT----------ATcaggATCACAGTTAtGGCTATTTCAGGAAATGGAATTTTATTAG CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATATTGATATATTGAT----ATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAG Template switch alignment (log-probability: -22.1) CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT|ATCAGG|ATCACAGTTAtGGCTATTTCAGGAAATGGAATTTTATTAG CACGCAATACCCATGTCAGAACCGATAAGACTGCAAATAT|ATCAGG|ATCACAGTTACGGCTATTTCAGGAAATGGAATTTTATTAG ========== Event 2093 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TGCCCCGGCACCCACGCCAGTCA---------------------TCCAAGGTCTCAGAAGGAAACATCTGAGACACTC Chimp: Gorilla: TGCCCTGGCACCCACGCCAGTCATCCAAGGTGACTTGGATGTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTC ↑ 4 3 2 1 Human: TGCCCCGGCACCCACGCCAGTCA---------------------TCCAAGGTCTCAGAAGGAAACATCTGAGACACTC Cluster: [ ] Orangutan: TGCCCCGGCACCCACACCAGTCATCCAAGGTGACTTGGATGTCATCCAAGGTCTCAGAAGGAAGCATCTGAGACACTC Human > Gorilla --------------- chr22:32539603-32539609 Template switch process: F1: L GGCCAGCAGCTGCCCCCATGCCCTGGCACCCACGCCAGTCATCCAAGGT----GA 1 F3: 4 GTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTCCTCCAG R RF: GGCCAGCAGCTGCCCCCATGCCCCGGCACCCACGCCAGTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTCCTCCAG RR: CCGGTCGTCGACGGGGGTACGGGGCCGTGGGTGCGGTCAGTAGGTTCCAGAGTCTTCCTTTGTAGACTCTGTGAGGAGGTC F2: 3 TAGGTTC 2 Unidirectional alignment (log-probability: -46.6) GCCCCCATGCCCtGGCACCCACGCCAgtcatccaaggtgacttggatGTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTCCT GCCCCCATGCCCCGGCACCCACGCCA---------------------GTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTCCT Template switch alignment (log-probability: -32.4) GCCCCCATGCCCtGGCACCCACGCCAGTCATCCAAGGT----GA|CTTGGAT|GTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTCCT GCCCCCATGCCCCGGCACCCACGCCAGTCATCCAAGGTCTCAGA|CTTGGAT|GTCATCCAAGGTCTCAGAAGGAAACATCTGAGACACTCCT ========== Event 2094 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGCTATCTGTGGCGTCCCATCCCTGGGGACAGCCCAGCCTTCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGCCCCGCAAGGAGGACTCAGGATC ↑ 4 3 2 1 Chimp: TGCTATCTGTGGCGTCCCATCCC---------------------TGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGCCCCGCAAGGAGGACTCAGGATC Gorilla: TGCTATCTGTGGCGTCCCATCCCTGGGGACAGCCCAGCCTTCCCTGGGGAGGCTCTAGCAAGACAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGCCCCGCAAGGAGGACTCAGGATC Human: TGCTATCTGTGGCGTCCCATCCCTGGGGACAGCCCAGCCTTCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGCCCCGCAAGGAGGACTCAGGATC Cluster: [ ] Orangutan: TGCTATCTGTGGCGTCCCATCCCTGCGGACAGCCCAGCCTTCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGC-CCGCAAGGAGAACTCGGGATC Chimp > Human ------------- chr22:2014491-2014495 Template switch process: F1: L ACCTTGGGGAAGGCCTCCTGCTATCTGTGGCGTCCCATCCCTGGGG--------------------------------------------------------ACAGCCC 1 F3: 4 TCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGG R RF: ACCTTGGGGAAGGCCTCCTGCTATCTGTGGCGTCCCATCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGCCC RR: TGGAACCCCTTCCGGAGGACGATAGACACCGCAGGGTAGGGACCCCTCCGAGATCGTTCCGTCTTTTCTCCGTAGCTCTCCTTTTCTTTGTGTCCTCGTGTCTGTCGGG F2: 3 TCCGA 2 Unidirectional alignment (log-probability: -41.1) CCTCCTGCTATCTGTGGCGTCCCATCCCTGGGGacagcccagccttccctggggAGGCTCTAGCAAGGCAGAAAAGAGGCATCGA CCTCCTGCTATCTGTGGCGTCCCATCCCTGGGG---------------------AGGCTCTAGCAAGGCAGAAAAGAGGCATCGA Template switch alignment (log-probability: -29.3) CCTCCTGCTATCTGTGGCGTCCCATCCCTGGGG--------------------------------------------------------ACAGCCC|AGCCT|TCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGA CCTCCTGCTATCTGTGGCGTCCCATCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGAGAGGAAAAGAAACACAGGAGCACAGACAGCCC|AGCCT|TCCCTGGGGAGGCTCTAGCAAGGCAGAAAAGAGGCATCGA ========== Event 2095 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CCTCCCCACCACGAGCAGCTGGTGGCCCCCAGGATCACTCACCgcccacgcagaaaggaagcccacgcagaaaggaagcGGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCAGGGCTACCACCGAGAAGCCCAGCTAATGGC ↑ 3 2 1 4 Chimp: CCTCCCCACCACGAGCAGCTGGTGGCCCCCAGGATCACCCACCGCCCACGCAG-----------------AAAGGAAGCGGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCAT-----TAGCCGAGAAGCCCAGCTAATGGC Gorilla: Human: CCTCCCCACCACGAGCAGCTGGTGGCCCCCAGGATCACTCACCgcccacgcagaaaggaagcccacgcagaaaggaagcGGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCAGGGCTACCACCGAGAAGCCCAGCTAATGGC Cluster: [ ] Orangutan: CCTCCCCACCATGAGCAGCTGGTGGCCCCCAGGATCACCCACTGCCCACGCAG-----------------AAAGGAAGTGGGTGCAGGAGCCAGGTGAGGACAGGCCGTGGAGCACTCAGGGCTACCACCGAGAAGCCCAGCTAATGGC Chimp > Human ------------- chr22:1045634-1045642 Template switch process: F1: L CGGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCA 1 F3: 4 CCGAGAAGCCCAGCTAATGGCGGGTGCAGTTTGCACCCCT R RF: TGGTGGCCCCCAGGATCACCCACCGCCCACGCAGAAAGGAAGCGGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCATTAGCCGAGAAGCCCAGCTAATGGCGGGTGCAGTTTGCACCCCT RR: ACCACCGGGGGTCCTAGTGGGTGGCGGGTGCGTCTTTCCTTCGCCCACGTCCTCGGTCCACCCCTGTCCGGCACCTCGTGAGTAATCGGCTCTTCGGGTCGATTACCGCCCACGTCAAACGTGGGGA F2: 3 ACCATCGGG 2 Unidirectional alignment (log-probability: -32.8) GGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTC---AGggctaccaCCGAGAAGCCCAGCTAATGGCGGGTGCAGTTTGCACCCCT GGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCATTAG--------CCGAGAAGCCCAGCTAATGGCGGGTGCAGTTTGCACCCCT Template switch alignment (log-probability: -22.4) GGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCA|GGGCtACCA|CCGAGAAGCCCAGCTAATGGCGGGTGCAGTTTGCACCCCT GGGTGCAGGAGCCAGGTGGGGACAGGCCGTGGAGCACTCA|GGGCCACCA|CCGAGAAGCCCAGCTAATGGCGGGTGCAGTTTGCACCCCT ========== Event 2096 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTCCTGTCTCACAGCAGGAG---------------------------------ACAGTCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCCCTGCTTCCTCCCCTCAGCTCATCCCACACGGAACAGACTGTTGAGGGGGACCCTGGGCATG Chimp: AGTCCTGTCTCACAGCAGGAG---------ACAGCCCTTGTGTCACAGCAGGAGACAGTCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCCCTGCTTCCTCCCCTCAGCTCATCCCACACGGAACAGACTGTTGAGGGGGACCCTGGGCATG Gorilla: AGTCCTGTCTCACAGCAGGAGCTAAGGCCT------------------------GC-AGCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCCCTGCTTCCTCCCCTCAGCTCATCCCACACGGAACAGACTGTTGAGGGGGACCCTGGGCATG ↓ 1 4 3 2 Human: AGTCCTGTCTCACAGCAGGAG---------------------------------ACAGTCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCCCTGCTTCCTCCCCTCAGCTCATCCCACACGGAACAGACTGTTGAGGGGGACCCTGGGCATG Cluster: [ ] Orangutan: AGTCCTGTCTCACAGCAGGAGCTAAGGCCT------------------------GC-AGCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGGCCCCTGCTTCCTCCCCTCAGCTCATCCCACACGGAACAGACTGTTGAGGGGGACCCTGGGCATG Gorilla > Human --------------- chr22:848155-848159 Template switch process: F1: L ATGCCTGCCAGCCCCTGCCCAGTCCTGTCTCACAGCAGGAG 1 F3: 4 CCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCC R RF: ATGCCTGCCAGCCCCTGCCCAGTCCTGTCTCACAGCAGGAGCTAAGGCCTGCAGCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCCCTGCTTCCTCCCCTCAGCTCATCCCACACGGAACAGACTGT RR: TACGGACGGTCGGGGACGGGTCAGGACAGAGTGTCGTCCTCGATTCCGGACGTCGGGGTCCCGAGACGAGTCCCGGGAACACGAAGACTCTGGGGACGAAGGAGGGGAGTCGAGTAGGGTGTGCCTTGTCTGACA F2: 3 TGACA 2 Unidirectional alignment (log-probability: -28.1) TGCCTGCCAGCCCCTGCCCAGTCCTGTCTCACAGCAGGAG---------aCAGtCCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCC TGCCTGCCAGCCCCTGCCCAGTCCTGTCTCACAGCAGGAGCTAAGGCCTGCAG-CCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCC Template switch alignment (log-probability: -16.4) TGCCTGCCAGCCCCTGCCCAGTCCTGTCTCACAGCAGGAG|ACAGT|CCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCC TGCCTGCCAGCCCCTGCCCAGTCCTGTCTCACAGCAGGAG|ACAGT|CCCCAGGGCTCTGCTCAGGGCCCTTGTGCTTCTGAGACCC ========== Event 2097 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGGGACCCTCGGTGGCTGGTCAGT----------------------------------------GGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCC--CACCCCACCCCCAGCACCCCTGTGC ↓ 4 1 3 2 Chimp: AGGGACCCTCGGTGGCTGGTCAGT--------------------GGCCACGGGTGGCCATCGGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCC--CACCCCACCCCCAGCACCCCTGTGC Gorilla: AGGGACCCTCGGTGGCTGGTCAGTGGCCACGGGTGGCCATCAGT--------------------GGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCC----ACCCACCCCCAGCACCCCTGTGC ↑ 4 1 3 2 Human: AGGGACCCTCGGTGGCTGGTCAGT----------------------------------------GGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCC--CACCCCACCCCCAGCACCCCTGTGC Cluster: [ ] Orangutan: AGGGACCCTCGGTGGCTGGTCAGTGGCCATGGGTGGCCATCGGT--------------------GGCCACCAGTCACCTCCTGGGCGCCTCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCCCA--CCCC----ACAGCACCCGTGTGC Human > Chimp ------------- chr22:865377-865385 Template switch process: F1: L GAGCTTCTGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAC 1 F3: 4 TCGGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGG R RF: GAGCTTCTGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCCCACCC RR: CTCGAAGACGTCGGTAATCCCTGGGAGCCACCGACCAGTCACCGGTGGTCAGTGGAGGACCCACGTAGGGTCCTGAGGACCAGATTCCGGCACCGGTCTTAGTGAGCCACGGGTGGG F2: 3 ACCGGTGGG 2 Unidirectional alignment (log-probability: -39.7) TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAcgggtggccatcggtggccaCCAGTCACCTCCTGGGTGCATCCCAGGACT TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCA--------------------CCAGTCACCTCCTGGGTGCATCCCAGGACT Template switch alignment (log-probability: -28.6) TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAC|GGGTGGcCA|TCgGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACT TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAC|GGGTGGGCA|TCAGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACT Human > Gorilla --------------- chr22:705708-705716 Template switch process: F1: L GAGCTTCTGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAC 1 F3: 4 TCAGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGG R RF: GAGCTTCTGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACTCCTGGTCTAAGGCCGTGGCCAGAATCACTCGGTGCCCACCC RR: CTCGAAGACGTCGGTAATCCCTGGGAGCCACCGACCAGTCACCGGTGGTCAGTGGAGGACCCACGTAGGGTCCTGAGGACCAGATTCCGGCACCGGTCTTAGTGAGCCACGGGTGGG F2: 3 ACCGGTGGG 2 Unidirectional alignment (log-probability: -39.6) TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAgtggccacgggtggccatcaGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACT TGCAGCCATTAGGGACCCTCGGTGGCTGGTCA--------------------GTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACT Template switch alignment (log-probability: -22.7) TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAC|GGGTGGcCA|TCAGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACT TGCAGCCATTAGGGACCCTCGGTGGCTGGTCAGTGGCCAC|GGGTGGGCA|TCAGTGGCCACCAGTCACCTCCTGGGTGCATCCCAGGACT ========== Event 2098 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCACCTGTGGGCTGGTGACCT----------TCAGTCTATTTCACTGGCCAG------------TCTATT------------------TCACTGGTGGCACCCACCCTAG Chimp: CCACCTGTGGGCTGGTGACCT----------TCAGTCTATTTCACTGGCCAG------GTGTCCCCAAGT---------TCTGCATACACACTGGTGGCACCCACCCTAG ↑ 4 1 3 2 Gorilla: CCACCTGTGGGCTGGTGACCT--------------------TCACTGGCCAGATGTCC------CCAAGTTCTGCATAC---------ACACTGGTGGCACCCACCCTAG Human: CCACCTGTGGGCTGGTGACCT----------TCAGTCTATTTCACTGGCCAG------------TCTATT------------------TCACTGGTGGCACCCACCCTAG Cluster: [ ] Orangutan: CCACCTGTGGGCTGGTGACCTGCAGTCTATT----------TCACTGGCCAGATGTCC------CCAAGTTCTGCATAC---------ACACTGGTGGTACCCACCCTAG Gorilla > Chimp --------------- chr2A:26718824-26718829 Template switch process: F1: L TTGCCTCACAGCCAAGGCTGCCACCTGTGGGCTGGTGACCTTCA 1 F3: 4 TTCACTGGCCAGGTGTCCCCAAGTTC R RF: TTGCCTCACAGCCAAGGCTGCCACCTGTGGGCTGGTGACCTTCACTGGCCAGATGTCCCCAAGTTCTGCATACAC RR: AACGGAGTGTCGGTTCCGACGGTGGACACCCGACCACTGGAAGTGACCGGTCTACAGGGGTTCAAGACGTATGTG F2: 3 TATCTG 2 Unidirectional alignment (log-probability: -37.7) CTCACAGCCAAGGCTGCCACCTGTGGGCTGGTGACCttcagtctatTTCACTGGCCAGgTGTCCCCAAGTTC------- CTCACAGCCAAGGCTGCCACCTGTGGGCTGGTGACC----------TTCACTGGCCAGATGTCCCCAAGTTCTGCATAC Template switch alignment (log-probability: -27.2) CTCACAGCCAAGGCTGCCACCTGTGGGCTGGTGACCTTCA|GTcTAT|TTCACTGGCCAGgTGTCCCCAAGTTC CTCACAGCCAAGGCTGCCACCTGTGGGCTGGTGACCTTCA|GTGTAT|TTCACTGGCCAGATGTCCCCAAGTTC ========== Event 2099 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: CAGTGTGCATTTTCGTGCCTTTCGTGTAGATCAGCCCACAGAGATGTGCTGGT-CACAAAGAGGATCAAACTCTGAC Chimp: cagtgtgcattttcgtgccttg-----tgaccagcacatctctgtgggctgatctacaaaggggatcaaactctgac Gorilla: CAGTGTGCATTTTCGTGCCTTG-----TGACCAGCACATCTCTGTGGGCTGATCTACAAAGAGGATCAAACTCGGAC ↑ 1 3 42 Human: CAGTGTGCATTTTCGTGCCTTTCGTGTAGATCAGCCCACAGAGATGTGCTGGT-CACAAAGAGGATCAAACTCTGAC Cluster: [ ] Orangutan: cagtgtgagttttcgtgccttg-----tgaccagcacatctctgtgggctgatctacaaagaggatcaaactctgac Human > Gorilla --------------- chr2A:81027883-81027911 Template switch process: F1: L AGTACAACCATCACACAGGGCAGTGTGCATTTTCGTGCCTT 1 F3: 4 ACAAAGAGGATCAAACTCGGACTGGGAAGTCCTTTGATAT R RF: AGTACAACCATCACACAGGGCAGTGTGCATTTTCGTGCCTTTCGTGTAGATCAGCCCACAGAGATGTGCTGGTCACAAAGAGGATCAAACTCTGACTGGGAAGTCCCTTGATAT RR: TCATGTTGGTAGTGTGTCCCGTCACACGTAAAAGCACGGAAAGCACATCTAGTCGGGTGTCTCTACACGACCAGTGTTTCTCCTAGTTTGAGACTGACCCTTCAGGGAACTATA F2: 3 TCTAGTCGGGTGTCTCTACACGACCAGTG 2 Unidirectional alignment (log-probability: -73.6) GTACAACCATCACACAGGGCAGTGTGCATTTTCGTGCCTTgtgaccagcacatctctgtgggctgatcT--------------------------------ACAAAGAGGATCAAACTCgGACTGGGAAGTCCtTTGATAT GTACAACCATCACACAGGGCAGTGTGCATTTTCGTGCCTT----------------------------TCGTGTAGATCAGCCCACAGAGATGTGCTGGTCACAAAGAGGATCAAACTCTGACTGGGAAGTCCCTTGATAT Template switch alignment (log-probability: -30.5) GTACAACCATCACACAGGGCAGTGTGCATTTTCGTGCCTT|GTGACCAGCACATCTCTGTGGGCTGATCT|ACAAAGAGGATCAAACTCgGACTGGGAAGTCCtTTGATAT GTACAACCATCACACAGGGCAGTGTGCATTTTCGTGCCTT|GTGACCAGCACATCTCTGTGGGCTGATCT|ACAAAGAGGATCAAACTCTGACTGGGAAGTCCCTTGATAT ========== Event 2100 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTGGCCTGGCTCTGCCTGCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGC---------------CTTGCCCGAGCTGGCCTTGCTGTCTCTGTCCCCACCGCCA Chimp: TCTGGCCTGGCTCTGCCTGCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGC---------------CTTGCCCGAGCTGGCCTTGCTGTCTCTGTCCCCACCGCCA ↑ 3 2 4 1 Gorilla: TCTGGCCTGGCTCTGCCTGCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGC------------------------------CTTGCTGTCTCTGTCCCCACCGCCA ↓ 3 2 4 1 Human: TCTGGCCTGGCTCTGCCTGCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGC---------------CTTGCCCGAGCTGGCCTTGCTGTCTCTGTCCCCACCGCCA Cluster: [ ] Orangutan: TCTGTCCTGGCTCTGCCCGCGGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGCCCGAGCTGGC---------------CTTGCTGTCTCTGTCCCCACCGTCA Gorilla > Human --------------- chr22:359719-359726 Template switch process: F1: L GCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGC 1 F3: 4 GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACAGG R RF: GCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACAGG RR: CGTCGAACCGGAGACAGGAGCACACAGGACCAAGGAACCCGGAACGACAGAGACAGGGGTGGCGGTGCGTGTGAAGTGTCC F2: 3 GTCGAGCC 2 Unidirectional alignment (log-probability: -32.5) TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGgccttgcccgagctgGCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGG---------------GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA Template switch alignment (log-probability: -22.4) TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGC|CCgAGCTG|GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGC|CCAAGCTG|GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA Gorilla > Chimp --------------- chr22:351622-351629 Template switch process: F1: L GCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGC 1 F3: 4 GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACAGG R RF: GCAGCTTGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACAGG RR: CGTCGAACCGGAGACAGGAGCACACAGGACCAAGGAACCCGGAACGACAGAGACAGGGGTGGCGGTGCGTGTGAAGTGTCC F2: 3 GTCGAGCC 2 Unidirectional alignment (log-probability: -32.5) TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGgccttgcccgagctgGCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGG---------------GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA Template switch alignment (log-probability: -22.4) TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGC|CCgAGCTG|GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA TGGCCTCTGTCCTCGTGTGTCCTGGTTCCTTGGGCCTTGC|CCAAGCTG|GCCTTGCTGTCTCTGTCCCCACCGCCACGCACACTTCACA ========== Event 2101 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: gCTGCAAAC--TCTACTGAAGTACCCTTGTACTGCAGTCAAGTCCAGAGAAACT ↑ 3 1 2 4 Chimp: gTTGCAAAC--TCTACTGAAGTACA---AGGAAGCAGTCAAGTCCAGAGAAACT Gorilla: ACTGCAAAC--TCTACTGAAGTACA---AGGAAGCAGTCAAGTCCAGAGAAACT ↓ 3 1 2 4 Human: gCTGCAAAC--TCTACTGAAGTACCCTTGTACTGCAGTCAAGTCCAGAGAAACT Cluster: [ ] Orangutan: GCTGCAAACTCACTACTGAAGTACA---AGGAAGCAGTCAAGTCCAGAGAAACT Chimp > Human ------------- chr2:214819322-214819330 Template switch process: F1: L GGGGTGGGGAGTTAGGGGGGCTGCAAACTCTACTGAAGTAC 1 F3: 4 GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC R RF: GGGGTGGGGAGTTAGGGGGGTTGCAAACTCTACTGAAGTACAAGGAAGCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC RR: CCCCACCCCTCAATCCCCCCAACGTTTGAGATGACTTCATGTTCCTTCGTCAGTTCAGGTCTCTTTGAGTGTTCTTTTCCGAGGTAG F2: 3 TCATGTTCC 2 Unidirectional alignment (log-probability: -40.4) GGGTGGGGAGTTAGGGGGGcTGCAAACTCTACTGAAGTAC------ccttgtactGCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC GGGTGGGGAGTTAGGGGGGTTGCAAACTCTACTGAAGTACAAGGAA---------GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC Template switch alignment (log-probability: -22.4) GGGTGGGGAGTTAGGGGGGcTGCAAACTCTACTGAAGTAC|CCTTGTACT|GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC GGGTGGGGAGTTAGGGGGGTTGCAAACTCTACTGAAGTAC|CCTTGTACT|GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC Gorilla > Human --------------- chr2:214819322-214819330 Template switch process: F1: L GGGGTGGGGAGTTAGGGGGGCTGCAAACTCTACTGAAGTAC 1 F3: 4 GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC R RF: GGGGTGGGGAGTTAGAGGGACTGCAAACTCTACTGAAGTACAAGGAAGCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC RR: CCCCACCCCTCAATCTCCCTGACGTTTGAGATGACTTCATGTTCCTTCGTCAGTTCAGGTCTCTTTGAGTGTTCTTTTCCGAGGTAG F2: 3 TCATGTTCC 2 Unidirectional alignment (log-probability: -44.9) GGGTGGGGAGTTAGgGGGgCTGCAAACTCTACTGAAGTACccttgtact------GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC GGGTGGGGAGTTAGAGGGACTGCAAACTCTACTGAAGTAC---------AAGGAAGCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC Template switch alignment (log-probability: -27.9) GGGTGGGGAGTTAGgGGGgCTGCAAACTCTACTGAAGTAC|CCTTGTACT|GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC GGGTGGGGAGTTAGAGGGACTGCAAACTCTACTGAAGTAC|CCTTGTACT|GCAGTCAAGTCCAGAGAAACTCACAAGAAAAGGCTCCATC ========== Event 2102 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAACAACAACATGATGAAGG--ACTGCATGCAGGACTCAGTGATGGATGG Chimp: GGAACAACAACATGATGAAGG--ACTGCATGCAGGACTCAGTGATGAATGG ↑ 1 3 4 Gorilla: GGAACAACAACATGATGAAGGAAAATGC-AGCAGGACTCAGTGATGGATGG Human: GGAACAACAACATGATGAAGG--ACTGCATGCAGGACTCAGTGATGGATGG Cluster: [ ] Orangutan: GGAACAACAACATGATGAAGGAAAATGC-AGCAGGACTCAGTGATGGATGG Gorilla > Chimp --------------- chr2A:83536778-83536783 Template switch process: F1: L CAACAAAACAAAGTAATCCAGGAACAACAACATGATGAAGGA 1 F3: 4 GCAGGACTCAGTGATGAATGGTGGAAGACAGCCAGGAAGT R RF: CAACAAAACAAAGTAATCCAGGAACAACAACATGATGAAGGAAAATGCAGCAGGACTCAGTGATGGATGGTGGAAGACAGCCAGGAAGT RR: GTTGTTTTGTTTCATTAGGTCCTTGTTGTTGTACTACTTCCTTTTACGTCGTCCTGAGTCACTACCTACCACCTTCTGTCGGTCCTTCA F2: 3 TACGTC 2 Unidirectional alignment (log-probability: -33.3) ACAAAACAAAGTAATCCAGGAACAACAACATGATGAAGGAc--TGCAtGCAGGACTCAGTGATGaATGGTGGAAGACAGCCAGGAAGT ACAAAACAAAGTAATCCAGGAACAACAACATGATGAAGGAAAATGCA-GCAGGACTCAGTGATGGATGGTGGAAGACAGCCAGGAAGT Template switch alignment (log-probability: -22) ACAAAACAAAGTAATCCAGGAACAACAACATGATGAAGGA|CTGCAT|GCAGGACTCAGTGATGaATGGTGGAAGACAGCCAGGAAGT ACAAAACAAAGTAATCCAGGAACAACAACATGATGAAGGA|CTGCAT|GCAGGACTCAGTGATGGATGGTGGAAGACAGCCAGGAAGT ========== Event 2103 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CACACACCAAACGCACCAGTGCGGCACAGCCTGAAGGAGGGCAGACGGGCCACACGAGGCCCCACC ↓ 3 2 1 4 Chimp: CACACACCAAACGCACCAGTGCGGCACAGCCTGGTGCCGCAGAGATGGGCCACACGAGGCCCCACC Gorilla: CACACACCAAACGCACCAGTGCGGCACAGCCTGAAGGAGGGCAGACGGGCCACACGAGACCCCACC Human: CACACACCAAACGCACCAGTGCGGCACAGCCTGAAGGAGGGCAGACGGGCCACACGAGGCCCCACC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---- Human > Chimp ------------- chr2A:3115380-3115387 Template switch process: F1: L TCACCAAGCACACACCAAACGCACCAGTGCGGCACAGCCTG 1 F3: 4 GAGATGGGCCACACGAGGCCCCACCCTTCAGGCTCCACTAAACAG R RF: TCACCAAGCACACACCAAACGCACCAGTGCGGCACAGCCTGAAGGAGGGCAGACGGGCCACACGAGGCCCCACCCTTCAGGCTCCACTAAACAG RR: AGTGGTTCGTGTGTGGTTTGCGTGGTCACGCCGTGTCGGACTTCCTCCCGTCTGCCCGGTGTGCTCCGGGGTGGGAAGTCCGAGGTGATTTGTC F2: 3 ACGCCGTG 2 Unidirectional alignment (log-probability: -40.5) CACCAAGCACACACCAAACGCACCAGTGCGGCACAGCCTG-------------gtgccgcagagatGGGCCACACGAGGCCCCACCCTTCAGGCTCCACTA CACCAAGCACACACCAAACGCACCAGTGCGGCACAGCCTGAAGGAGGGCAGAC-------------GGGCCACACGAGGCCCCACCCTTCAGGCTCCACTA Template switch alignment (log-probability: -28.4) CACCAAGCACACACCAAACGCACCAGTGCGGCACAGCCTG|GTGCCGCA|gAGAtGGGCCACACGAGGCCCCACCCTTCAGGCTCCACTA CACCAAGCACACACCAAACGCACCAGTGCGGCACAGCCTG|GTGCCGCA|CAGACGGGCCACACGAGGCCCCACCCTTCAGGCTCCACTA ========== Event 2104 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TTCACTTAAGAAATAAAGAACTGTGTAGTATTTTAAAAAATTTTTAGTGACCAAGAATAAATATAGTAAACCTAAAAAAAGATAGATT Chimp: TTCACTTAAGAAATAAAGAACTGTGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATAT-ATAAACCTaaaaaaaGATAGATT ↓ 3 2 1 4 Gorilla: TTCACTTAAGAAATAAAGAACTGTGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATACAGTAAACCTaaaaaaaGATAGATT Human: TTCACTTAAGAAATAAAGAACTGTGTAGTATTTTAAAAAATTTTTAGTGACCAAGAATAAATATAGTAAACCTAAAAAAAGATAGATT Cluster: [ ] Orangutan: TTCACTTGAGAAATAAAGAACTGTGTAGTATTTTTAAAAATTTTTAGTGACCAATAATAAATATAGTAAACCTAAAAAAAGATAGATT Chimp > Gorilla --------------- chr2A:32916643-32916646 Template switch process: F1: L GTGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATA 1 F3: 4 AAACCTAAAAAAAGATAGATTACTAGGAAATGCATATTA R RF: ACTGTGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATATATAAACCTAAAAAAAGATAGATTACTAGGAAATGCGTATTA RR: TGACACATCATAAAAATTTTTAAAAATCACTGGTTCTTATTTATATATTTGGATTTTTTTCTATCTAATGATCCTTTACGCATAAT F2: 3 TGAC 2 Unidirectional alignment (log-probability: -35.8) TGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATAcAgTAAACCTAAAAAAAGATAGATTACTAGGAAATGCaTatta TGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATATA-TAAACCTAAAAAAAGATAGATTACTAGGAAATGCGT---- Template switch alignment (log-probability: -21.7) TGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATA|CAGT|AAACCTAAAAAAAGATAGATTACTAGGAAATGCaTATTA TGTAGTATTTTTAAAAATTTTTAGTGACCAAGAATAAATA|CAGT|AAACCTAAAAAAAGATAGATTACTAGGAAATGCGTATTA ========== Event 2105 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: aaagataataATGCTGT-AAG-GTC----------------------------------------------------------ACTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTAATTACTTCCCACTCCTGCCTCCAGTAGAGAATGACATATTTACCATTCATTTCCC ↑ 1 4 3 2 Chimp: aaagataataATGCTGT-AAGCCTC-----------------------------ACTCTTATTCTGGCCCATTGTAACCCAATTCTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTAATTACTTCCCAGTCCTGCCTCCAGTAGAGAATGACATATTTACCATTCATTTCCC Gorilla: aaagataataATGCTGT-AAGCCTCACTCTTATTCTGGCCCATTGTAACCCAAT-----------------------------TCTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTAATTACTTCCCACTGCTGCCTCCAGTAGAGAATGACATATTTACCATTCATTTCCC ↓ 1 4 3 2 Human: aaagataataATGCTGT-AAG-GTC----------------------------------------------------------ACTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTAATTACTTCCCACTCCTGCCTCCAGTAGAGAATGACATATTTACCATTCATTTCCC Cluster: [ ] Orangutan: aaagatagtaATGCTGTACAGCCTCACTCTTATTCTAGCCCATTGTAACCCAAT-----------------------------TCTTATTCTGACCTTAGCCAGTTCCCACTCCTCTCCAGCTAATTACTTCCCACTGCTGCCTCCAGTAGAGAATGACATATTTACCATTCATTTCCC Chimp > Human ------------- chr2:33419885-33419888 Template switch process: F1: L ATAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG 1 F3: 4 CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA R RF: ATAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAGCCTCACTCTTATTCTGGCCCATTGTAACCCAATTCTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTAATTACTTCCCAGTCCTGCCTCCAGTAGAGAATGAC RR: TATCTTCACATAAACTTAAACTTTCTATTATTACGACATTCGGAGTGAGAATAAGACCGGGTAACATTGGGTTAAGACAAAGACTGGAATCGGTCGAGGGTGAGGAGGGGTCGATTAATGAAGGGTCAGGACGGAGGTCATCTCTTACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -28.6) TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAGgtca----------------------------------CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG----CCTCACTCTTATTCTGGCCCATTGTAACCCAATTCTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA Template switch alignment (log-probability: -15.8) TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG|GTCA|CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG|GTCA|CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA Gorilla > Human --------------- chr2:33419885-33419888 Template switch process: F1: L ATAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG 1 F3: 4 CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA R RF: ATAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAGCCTCACTCTTATTCTGGCCCATTGTAACCCAATTCTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTAATTACTTCCCACTGCTGCCTCCAGTAGAGAATGAC RR: TATCTTCACATAAACTTAAACTTTCTATTATTACGACATTCGGAGTGAGAATAAGACCGGGTAACATTGGGTTAAGACAAAGACTGGAATCGGTCGAGGGTGAGGAGGGGTCGATTAATGAAGGGTGACGACGGAGGTCATCTCTTACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -27.7) TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG-----------------------GTcA-------CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAGCCTCACTCTTATTCTGGCCCATTGTAACCCAATTCTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA Template switch alignment (log-probability: -16.2) TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG|GTCA|CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA TAGAAGTGTATTTGAATTTGAAAGATAATAATGCTGTAAG|GTCA|CTGTTTCTGACCTTAGCCAGCTCCCACTCCTCCCCAGCTA ========== Event 2106 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAACACACTCAGGGTCACAT-----------TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGT ↓ 4 3 2 Chimp: GAAACACACTCAGGGTCACATTTTAAATGACATCTTCCTGTGTCATTTAAAACGTTTTCCTTTCCTTGGT ↑ 4 3 2 Gorilla: GAAACACACTCAGGGTCACAT-----------TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGT Human: GAAACACACTCAGGGTCACAT-----------TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGT Cluster: [ ] Orangutan: GAAACACACTCAGGGTCACAT-----------TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGT Human > Chimp ------------- chr2A:33903053-33903062 Template switch process: F1: L CTTAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATT 1 F3: 4 TCTTCCTGTGTCATTTAAAACGTTTTCCTTTCCTTGGTTG R RF: CTTAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATTCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGTTG RR: GAATTCACTGAGTGAGGGTTCTTTGTGTGAGTCCCAGTGTAAGAAGGACACAGTAAATTTTTCAAAAGGAAAGGAACCAAC F2: 3 ACAGTAAATT 2 Unidirectional alignment (log-probability: -32.7) TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATtttaaatgacaTCTTCCTGTGTCATTTAAAAcGTTTTCCTTTCCTTGGTTG TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACAT-----------TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGTTG Template switch alignment (log-probability: -22.5) TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATT|TTAAATGACA|TCTTCCTGTGTCATTTAAAAcGTTTTCCTTTCCTTGGTTG TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATT|TTAAATGACA|TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGTTG Gorilla > Chimp --------------- chr2A:33903053-33903062 Template switch process: F1: L CTTAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATT 1 F3: 4 TCTTCCTGTGTCATTTAAAACGTTTTCCTTTCCTTGGTTG R RF: CTTAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATTCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGTTG RR: GAATTCACTGAGTGAGGGTTCTTTGTGTGAGTCCCAGTGTAAGAAGGACACAGTAAATTTTTCAAAAGGAAAGGAACCAAC F2: 3 ACAGTAAATT 2 Unidirectional alignment (log-probability: -32.2) TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATtttaaatgacaTCTTCCTGTGTCATTTAAAAcGTTTTCCTTTCCTTGGTTG TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACAT-----------TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGTTG Template switch alignment (log-probability: -22.5) TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATT|TTAAATGACA|TCTTCCTGTGTCATTTAAAAcGTTTTCCTTTCCTTGGTTG TAAGTGACTCACTCCCAAGAAACACACTCAGGGTCACATT|TTAAATGACA|TCTTCCTGTGTCATTTAAAAAGTTTTCCTTTCCTTGGTTG ========== Event 2107 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTCACCATCCCAGGCCAGTA----AGTAGTTCAGCTATTCAAGTACCATAAAGTCCCATTCTTTACGGTACTT Chimp: GGTCACCATCCCAGGCCAGTA----AGTCGTTCAGCTAT-----------GGCATCCCATTCTTTATGgtactt ↓ 1 4 3 2 Gorilla: GGTCACCATCCCAGGCCAGTAATGCCATAGTTCAGCTAT-----------GGCATCCCATTCTTTATGgtactt Human: GGTCACCATCCCAGGCCAGTA----AGTAGTTCAGCTATTCAAGTACCATAAAGTCCCATTCTTTACGGTACTT Cluster: [ ] Orangutan: -GTCACCATCCCAGGCCAGTA----AATAGTTCAGCTGT-----------GGCATCCCATTCTTTATGGTACTT Chimp > Gorilla --------------- chr2A:33341710-33341716 Template switch process: F1: L AAACTTTACTTAATCATCCTGGTCACCATCCCAGGCCAGTAA 1 F3: 4 GTTCAGCTATGGCATCCCATTCTTTATGGTACTTGTAGCA R RF: AAACTTTACTTAATCATCCTGGTCACCATCCCAGGCCAGTAAGTCGTTCAGCTATGGCATCCCATTCTTTATGGTACTTGTAGCA RR: TTTGAAATGAATTAGTAGGACCAGTGGTAGGGTCCGGTCATTCAGCAAGTCGATACCGTAGGGTAAGAAATACCATGAACATCGT F2: 3 ATACCGT 2 Unidirectional alignment (log-probability: -27.7) ACTTTACTTAATCATCCTGGTCACCATCCCAGGCCAGTAAtgccaTaGTTCAGCTATGGCATCCCATTCTTTATGGTACTTGTAGCA ACTTTACTTAATCATCCTGGTCACCATCCCAGGCCAGTAAG----TCGTTCAGCTATGGCATCCCATTCTTTATGGTACTTGTAGCA Template switch alignment (log-probability: -16.6) ACTTTACTTAATCATCCTGGTCACCATCCCAGGCCAGTAA|TGCCATA|GTTCAGCTATGGCATCCCATTCTTTATGGTACTTGTAGCA ACTTTACTTAATCATCCTGGTCACCATCCCAGGCCAGTAA|TGCCATA|GTTCAGCTATGGCATCCCATTCTTTATGGTACTTGTAGCA ========== Event 2108 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CATCACTTCTCTCATCTGCCT--TTCCTTAACT--TCAGGACATACTGGGTTCCAGTATG-------------------------TCCTTAACTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGCTCTGCCCCTCACA ↑ 4 3 2 1 Chimp: CATCACTTCTCTCATCTGCCT-------------------------------------------------------------------------TTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGCTCTGCCCCTCACA Gorilla: CATCACTTCTCTCATCTGCCT--TTCCTTAACT---------------------------TCAGGATATACTGGGTTCCAGTATGTCCTTAACTTTGCTTAACTTCAGGACATACTGGGTTCTAGCCCAGGCTCTGCCCCTCACA Human: CATCACTTCTCTCATCTGCCT--TTCCTTAACT--TCAGGACATACTGGGTTCCAGTATG-------------------------TCCTTAACTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGCTCTGCCCCTCACA Cluster: [ ] Orangutan: CATCACTTCTCTCATCTGCCTCGATCCTGG---GA-----------------------------------------------------AAACCTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGCTCTGCCCCTCACA Chimp > Human ------------- chr2:33731897-33731907 Template switch process: F1: L GTCTTTGGTTCTGGCTCCCACATCACTTCTCTCATCTGCCTTTCCTTAACTTCAGGACATACTGGGTTCCAG 1 F3: 4 CTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGCTC R RF: GTCTTTGGTTCTGGCTCCCACATCACTTCTCTCATCTGCCTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGCTC RR: CAGAAACCAAGACCGAGGGTGTAGTGAAGAGAGTAGACGGAAAGGAATTGAAGTCCTGTATGACCCAAGGTCGGGTCCGAG F2: 3 AATTCCTGTAT 2 Unidirectional alignment (log-probability: -74.2) CATCTGCctttccttaacttcaggacatactgggttccagtatgtccttaaCTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGC CATCTGC--------------------------------------------CTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGC Template switch alignment (log-probability: -23.2) CATCTGCCTTTCCTTAACTTCAGGACATACTGGGTTCCAG|TATGTCCTtAA|CTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGC CATCTGCCTTTCCTTAACTTCAGGACATACTGGGTTCCAG|TATGTCCTGAA|CTTTCCTTAACTTCAGGACATACTGGGTTCCAGCCCAGGC ========== Event 2109 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTATTTGTTGATGCCTAAGATCAGT------------------------------------------TATAGTAAATTAAGCTTTCTTAATGGGATT ↓ 4 3 2 1 Chimp: GTATTTGTTGATGCCTAAGATCAGT---------------------TATAGTAAATAACTGATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATT Gorilla: GTATTTGTTGATGCCTAAGATCAGTTATAGTAAATAACTGATCAGT---------------------TATAGTAAATTAAGCTTTCTTCATGGGATT ↑ 4 3 2 1 Human: GTATTTGTTGATGCCTAAGATCAGT------------------------------------------TATAGTAAATTAAGCTTTCTTAATGGGATT Cluster: [ ] Orangutan: Human > Chimp ------------- chr2A:35501211-35501215 Template switch process: F1: L AAAGTAGTCACTATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAT 1 F3: 4 ATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATTGTTATGCTTT R RF: AAAGTAGTCACTATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATTCTGATGCTTT RR: TTTCATCAGTGATACACATAAACAACTACGGATTCTAGTCAATATCATTTAATTCGAAAGAATTACCCTAAGACTACGAAA F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -53.1) TATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAtaactgatcagttatagtaaaTTAAGCTTTCTTAATGGGATTgTtA TATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAA---------------------TTAAGCTTTCTTAATGGGATTCTGA Template switch alignment (log-probability: -28.2) TATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAT|AACTG|ATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATTgTtA TATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAT|AACTG|ATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATTCTGA Human > Gorilla --------------- chr2A:35139178-35139182 Template switch process: F1: L AAAGTAGTCACTATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAT 1 F3: 4 ATCAGTTATAGTAAATTAAGCTTTCTTCATGGGATTCTTATGCTTT R RF: AAAGTAGTCACTATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATTCTGATGCTTT RR: TTTCATCAGTGATACACATAAACAACTACGGATTCTAGTCAATATCATTTAATTCGAAAGAATTACCCTAAGACTACGAAA F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -52.1) TATGTGTATTTGTTGATGCCTAAGATCAgttatagtaaataactgatcaGTTATAGTAAATTAAGCTTTCTTcATGGGATTCTtA TATGTGTATTTGTTGATGCCTAAGATCA---------------------GTTATAGTAAATTAAGCTTTCTTAATGGGATTCTGA Template switch alignment (log-probability: -27.8) TATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAT|AACTG|ATCAGTTATAGTAAATTAAGCTTTCTTcATGGGATTCTtA TATGTGTATTTGTTGATGCCTAAGATCAGTTATAGTAAAT|AACTG|ATCAGTTATAGTAAATTAAGCTTTCTTAATGGGATTCTGA ========== Event 2110 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCAATGCTCTGAACTAACAG-------------AGCATTTCAGAAAGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTC Chimp: TTCAATGCTCTGAACTAACAG-------------AGCATTGCAGAAAGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTC ↑ 41 3 2 Gorilla: TTCAATGCTCTGAACTAACAG-------------------------AGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTC Human: TTCAATGCTCTGAACTAACAG-------------AGCATTTCAGAAAGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTC Cluster: [ ] Orangutan: TTCAATGCTCTGAACTAACAGAGCATTGCAGAAA------------AGCTAGTTTTCTGCAATGCTCTGTTAGTGCTAGTCTTC Gorilla > Chimp --------------- chr2A:35591245-35591254 Template switch process: F1: L AATGTGGTTTCAAAGATTACTTCAATGCTCTGAACTAACAGAG 1 F3: 4 AGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTCTA R RF: AATGTGGTTTCAAAGATTACTTCAATGCTCTGAACTAACAGAGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTCTA RR: TTACACCAAAGTTTCTAATGAAGTTACGAGACTTGATTGTCTCCATCAAAAGACGTTACGAGACAATCACGATCGGAAGAT F2: 3 AAGACGTTAC 2 Unidirectional alignment (log-probability: -28.1) GTGGTTTCAAAGATTACTTCAATGCTCTGAACTAACAGagcattgcagaaAGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTCTA GTGGTTTCAAAGATTACTTCAATGCTCTGAACTAACAG------------AGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTCTA Template switch alignment (log-probability: -17.1) GTGGTTTCAAAGATTACTTCAATGCTCTGAACTAACAGAG|CATTGCAGAA|AGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTCTA GTGGTTTCAAAGATTACTTCAATGCTCTGAACTAACAGAG|CATTGCAGAA|AGGTAGTTTTCTGCAATGCTCTGTTAGTGCTAGCCTTCTA ========== Event 2111 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACAAAGCCTGAAAAGGTCTGGGTCACACAAGGAAACTAGGActcaaggtggacttatttctcaaggtggacttatttctcaaggtggacttatttcCCTATTACTGTTCCTTTTCATTTCTCCGTCTTGTCCAATTTACCTGTACAGTTTTAGTTTTCTCCCTATGACCCTCCTTTTCCTTATTTCCTT ↑ 1 4 3 2 Chimp: AACAAAGCCTGAAAAGGTCTGCGTCCCACAAGGAAACTAGGActcaaggtggatttatt------------------tctcaaggtggacttatttcCCTATTACTGTTCCTTTTCATTTCTCCCTCTTGTCCAA-TTACCTGTACTGTTTTAGTTTTCTCCCTATGACCCTCCTTTTCCTTATGTCCTT Gorilla: AACAAAGGCTGAAAAGGTCTGGGTCCCACAAGGAAACTAGTActcaaggtggacttatt------------------tctcaaggtggacttatttcCCTATTACTGTTCCTTTTCATTTCTCCCTCTTGTCCAG-TTACCTGTACTGTTTTAGTTTTCTCCCTATGACCCTCCTTTTCCTTATGTCCTT Human: AACAAAGCCTGAAAAGGTCTGGGTCACACAAGGAAACTAGGActcaaggtggacttatttctcaaggtggacttatttctcaaggtggacttatttcCCTATTACTGTTCCTTTTCATTTCTCCGTCTTGTCCAATTTACCTGTACAGTTTTAGTTTTCTCCCTATGACCCTCCTTTTCCTTATTTCCTT Cluster: [ ] Orangutan: AACAAAGCCTGAAAAGGTCCAGGTCCCACAAGGAAACTAGGACTC--------------------------------------AGTGGACTTATTTCCCTATTACTGTCCCTTTTCATTTCTCCCTCTTGTCCAA-TTACCTGTACTGTTTTAATTTCCTCCCTATGACCCTCCTTTTCCTTATTTCCTT Chimp > Human ------------- chr2:35457533-35457537 Template switch process: F1: L GCACAAATGTGTTTCTCTGGAACAAAGCCTGAAAAGGTCTG 1 F3: 4 CACAAGGAAACTAGGACTCAAGGTGGACTTATTTCTCAAG R RF: GCACAAATGTGTTTCTCTGGAACAAAGCCTGAAAAGGTCTGCGTCCCACAAGGAAACTAGGACTCAAGGTGGATTTATTTCTCAAGGTGGACTTATTTCCCTATTACTGTTCCTTTTCATTTCTCCCTCTTGTCCAATTACCTGTACTGTTTTAGTTTTCTCCCTATGACC RR: CGTGTTTACACAAAGAGACCTTGTTTCGGACTTTTCCAGACGCAGGGTGTTCCTTTGATCCTGAGTTCCACCTAAATAAAGAGTTCCACCTGAATAAAGGGATAATGACAAGGAAAAGTAAAGAGGGAGAACAGGTTAATGGACATGACAAAATCAAAAGAGGGATACTGG F2: 3 ACTGG 2 Unidirectional alignment (log-probability: -35.9) CACAAATGTGTTTCTCTGGAACAAAGCCTGAAAAGGTCTGgGTCaCACAAGGAAACTAGGACTCAAGGTGGAcTTATTtctcaag CACAAATGTGTTTCTCTGGAACAAAGCCTGAAAAGGTCTGCGTCCCACAAGGAAACTAGGACTCAAGGTGGATTTATT------- Template switch alignment (log-probability: -21.9) CACAAATGTGTTTCTCTGGAACAAAGCCTGAAAAGGTCTG|GGTCA|CACAAGGAAACTAGGACTCAAGGTGGAcTTATTTCTCAAG CACAAATGTGTTTCTCTGGAACAAAGCCTGAAAAGGTCTG|GGTCA|CACAAGGAAACTAGGACTCAAGGTGGATTTATTTCTCAAG ========== Event 2112 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAATTCAAATTAAGATGAAG-----------CAGCCTAAGAATTAAGAGAATGAATTGATTTGACGG Chimp: ACAATTCAAATTAAGATGAAG-----------CAGCCTAAGAATTAAGAGAATGAATTGATTTGACGG ↓ 13 4 2 Gorilla: ACAATTCAAATTAAGATGAAGCCTTAATTCTTAGGCTTAAGAATTAAGAGAATGAATTGATTTGACGG ↑ 13 4 2 Human: ACAATTCAAATTAAGATGAAG-----------CAGCCTAAGAATTAAGAGAATGAATTGATTTGACGG Cluster: [ ] Orangutan: ACAATTCAGATTAAGATGAAG-----------CAGCCTAAGAATTAAGAGAATGAATTGATTTGACGG Human > Gorilla --------------- chr2A:35749118-35749132 Template switch process: F1: L CTGGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGC 1 F3: 4 TAAGAATTAAGAGAATGAATTGATTTGACGGTATTCTATT R RF: CTGGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGCAGCCTAAGAATTAAGAGAATGAATTGATTTGACGGTACTCTATT RR: GACCTACCGGACCAAGTGGTTGTTAAGTTTAATTCTACTTCGTCGGATTCTTAATTCTCTTACTTAACTAAACTGCCATGAGATAA F2: 3 TCGGATTCTTAATTC 2 Unidirectional alignment (log-probability: -43.3) GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGCcttaattcttagGCtTAAGAATTAAGAGAATGAATTGATTTGACGGTAtTCTATT GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGCA-----------GCCTAAGAATTAAGAGAATGAATTGATTTGACGGTACTCTATT Template switch alignment (log-probability: -23.2) GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGC|CTTAATTCTTAGGCT|TAAGAATTAAGAGAATGAATTGATTTGACGGTAtTCTATT GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGC|CTTAATTCTTAGGCT|TAAGAATTAAGAGAATGAATTGATTTGACGGTACTCTATT Chimp > Gorilla --------------- chr2A:35749118-35749132 Template switch process: F1: L CTGGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGC 1 F3: 4 TAAGAATTAAGAGAATGAATTGATTTGACGGTATTCTATT R RF: CTGGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGCAGCCTAAGAATTAAGAGAATGAATTGATTTGACGGTACTCTATT RR: GACCTACCGGACCAAGTGGTTGTTAAGTTTAATTCTACTTCGTCGGATTCTTAATTCTCTTACTTAACTAAACTGCCATGAGATAA F2: 3 TCGGATTCTTAATTC 2 Unidirectional alignment (log-probability: -43.3) GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGCcttaattcttagGCtTAAGAATTAAGAGAATGAATTGATTTGACGGTAtTCTATT GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGCA-----------GCCTAAGAATTAAGAGAATGAATTGATTTGACGGTACTCTATT Template switch alignment (log-probability: -23.2) GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGC|CTTAATTCTTAGGCT|TAAGAATTAAGAGAATGAATTGATTTGACGGTAtTCTATT GGATGGCCTGGTTCACCAACAATTCAAATTAAGATGAAGC|CTTAATTCTTAGGCT|TAAGAATTAAGAGAATGAATTGATTTGACGGTACTCTATT ========== Event 2113 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: catATAGAGGATGAAAAGAACCAGTGTTCTTTTCATCCTGTACATA ↓ 13 24 ↑ 13 24 Chimp: catgTAGAGGATGAAAAGAACACTGGTTCTTTTCATCCTGTACATA Gorilla: catgTAGAGGATGAAAAGAACCAGTGTTCTTTTCATCCTGTACATA Human: catATAGAGGATGAAAAGAACCAGTGTTCTTTTCATCCTGTACATA Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:3567814-3567817 Template switch process: F1: L AAATATAAAAATTATCCGGGCATATAGAGGATGAAAAGAAC 1 F3: 4 GTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT R RF: AAATATAAAAATTATCCGGGCATGTAGAGGATGAAAAGAACACTGGTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT RR: TTTATATTTTTAATAGGCCCGTACATCTCCTACTTTTCTTGTGACCAAGAAAAGTAGGACATGTATAAAACACTGTTAATTACCA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -30.7) AATATAAAAATTATCCGGGCATaTAGAGGATGAAAAGAACcagtGTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT AATATAAAAATTATCCGGGCATGTAGAGGATGAAAAGAACACTGGTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT Template switch alignment (log-probability: -21.8) AATATAAAAATTATCCGGGCATaTAGAGGATGAAAAGAAC|CAGT|GTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT AATATAAAAATTATCCGGGCATGTAGAGGATGAAAAGAAC|CAGT|GTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT Human > Chimp ------------- chr2A:3656651-3656654 Template switch process: F1: L AAATATAAAAATTATCCGGGCATGTAGAGGATGAAAAGAAC 1 F3: 4 GTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT R RF: AAATATAAAAATTATCCGGGCATATAGAGGATGAAAAGAACCAGTGTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT RR: TTTATATTTTTAATAGGCCCGTATATCTCCTACTTTTCTTGGTCACAAGAAAAGTAGGACATGTATAAAACACTGTTAATTACCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -30.7) AATATAAAAATTATCCGGGCATgTAGAGGATGAAAAGAACactgGTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT AATATAAAAATTATCCGGGCATATAGAGGATGAAAAGAACCAGTGTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT Template switch alignment (log-probability: -21.8) AATATAAAAATTATCCGGGCATgTAGAGGATGAAAAGAAC|ACTG|GTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT AATATAAAAATTATCCGGGCATATAGAGGATGAAAAGAAC|ACTG|GTTCTTTTCATCCTGTACATATTTTGTGACAATTAATGGT ========== Event 2114 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAATCACTCAAGTGGACTACCAGTTAAAGAATATAAACGGATTTGGGTTTGGAAGAACTAATGA Chimp: TCAAATCATTCAAGTGGACTACCAGTTAAAGAACATAAACGGATTTGGGTTTGGAAGAACTAATGa ↓ 3 2 1 4 Gorilla: TCAAATCACTCAAGTGGACTACCAGTTAAAGAACATAAC-TGGTATGGGTTTGGAAGAACTAATGa ↑ 3 2 1 4 Human: TCAAATCACTCAAGTGGACTACCAGTTAAAGAATATAAACGGATTTGGGTTTGGAAGAACTAATGA Cluster: [ ] Orangutan: TCAAATCACTCAGGTGGACTACCAGTTAAAGAACATAAGTGGATTTGGGTTTGGAAGAACTAATGA Human > Gorilla --------------- chr2A:36229807-36229812 Template switch process: F1: L ATACTGAGTCAAATCACTCAAGTGGACTACCAGTTAAAGAACATAA 1 F3: 4 TGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC R RF: ATACTGAGTCAAATCACTCAAGTGGACTACCAGTTAAAGAATATAAACGGATTTGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC RR: TATGACTCAGTTTAGTGAGTTCACCTGATGGTCAATTTCTTATATTTGCCTAAACCCAAACCTTCTTGATTACTTTTTTTACATTTGGAATAG F2: 3 ATGGTC 2 Unidirectional alignment (log-probability: -33.2) AGTCAAATCACTCAAGTGGACTACCAGTTAAAGAAcAT-AACtGgTaTGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC AGTCAAATCACTCAAGTGGACTACCAGTTAAAGAATATAAACGGATTTGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC Template switch alignment (log-probability: -22.1) AGTCAAATCACTCAAGTGGACTACCAGTTAAAGAAcATAA|CTGGTA|TGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC AGTCAAATCACTCAAGTGGACTACCAGTTAAAGAATATAA|CTGGTA|TGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC Chimp > Gorilla --------------- chr2A:36229807-36229812 Template switch process: F1: L GAGTCAAATCACTCAAGTGGACTACCAGTTAAAGAACATAA 1 F3: 4 TGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC R RF: GAGTCAAATCATTCAAGTGGACTACCAGTTAAAGAACATAAACGGATTTGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC RR: CTCAGTTTAGTAAGTTCACCTGATGGTCAATTTCTTGTATTTGCCTAAACCCAAACCTTCTTGATTACTTTTTTTACATTTGGAATAG F2: 3 ATGGTC 2 Unidirectional alignment (log-probability: -33.1) AGTCAAATCAcTCAAGTGGACTACCAGTTAAAGAACAT-AACtGgTaTGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC AGTCAAATCATTCAAGTGGACTACCAGTTAAAGAACATAAACGGATTTGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC Template switch alignment (log-probability: -22) AGTCAAATCAcTCAAGTGGACTACCAGTTAAAGAACATAA|CTGGTA|TGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC AGTCAAATCATTCAAGTGGACTACCAGTTAAAGAACATAA|CTGGTA|TGGGTTTGGAAGAACTAATGAAAAAAATGTAAACCTTATC ========== Event 2115 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAGGGCCAAGCCTAGGGAAA----GAGGCTTTCTCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGG Chimp: GTAGCGCCAAGCCTAGGGAAA----GAGGCTTTCTCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGG ↓ 1 4 3 2 Gorilla: GTAGGGCCAAGCCTAGGGAAA--------GCTCAGCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGG Human: GTAGGGCCAAGCCTAGGGAAA----GAGGCTTTCTCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGG Cluster: [ ] Orangutan: GTAGGGCCAAGCCTAGGGAAAGAGG----CTTTCTCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGA Chimp > Gorilla --------------- chr2A:36439019-36439023 Template switch process: F1: L CAGCACCGATCAGATGCTAGGTAGGGCCAAGCCTAGGGAAAG 1 F3: 4 CTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGGGCTAG R RF: CAGCACCGATCAGATGCTTGGTAGCGCCAAGCCTAGGGAAAGAGGCTTTCTCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGGGCTAG RR: GTCGTGGCTAGTCTACGAACCATCGCGGTTCGGATCCCTTTCTCCGAAAGAGATTGGTGTCGACTCGTTCCGATCTCTTCAGTCCCCGATC F2: 3 GACTC 2 Unidirectional alignment (log-probability: -36.4) GCACCGATCAGATGCTaGGTAGgGCCAAGCCTAGGGAAAG-------CTcagCTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGGGCTAG GCACCGATCAGATGCTTGGTAGCGCCAAGCCTAGGGAAAGAGGCTTTCT---CTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGGGCTAG Template switch alignment (log-probability: -27.4) GCACCGATCAGATGCTaGGTAGgGCCAAGCCTAGGGAAAG|CTCAG|CTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGGGCTAG GCACCGATCAGATGCTTGGTAGCGCCAAGCCTAGGGAAAG|CTCAG|CTAACCACAGCTGAGCAAGGCTAGAGAAGTCAGGGGCTAG ========== Event 2116 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCACCCTGACACCCACTCCTCAAATGCCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCGTCTCCCTAAAGCCTCCAGCTGGCTTGGCCTTTGTCTCAGCCTCCACCTGCTTCCCGGGGTCAGGGAACCCTGCCAGCTCCCTG Chimp: TCACCCTGACACCCACTCCTCAAATGCCCACAGTGCGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCGTCTCCCTAAAGCCTCCAGCTGGCTTGGCCTTTGTCTCAGCCTCCACCTGCTGCCCGGGGTCAGGGAACCCTGCCAGCTCCCTG ↓ 1 4 3 2 Gorilla: TCACCCTGACACCCACTCCTCCTGACCCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCATCTCCCTAAAGCCTCCAGCTGGCTTGGCCTTTGTCTCAGCCTCCACCTGCTGCCCGGGGTCAGGGAACCCTGCCAGCTCCCTG ↑ 1 4 3 2 Human: TCACCCTGACACCCACTCCTCAAATGCCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCGTCTCCCTAAAGCCTCCAGCTGGCTTGGCCTTTGTCTCAGCCTCCACCTGCTTCCCGGGGTCAGGGAACCCTGCCAGCTCCCTG Cluster: [ ] Orangutan: CCGCCCTGACACCCACTCCTCAAATGCCCACAGTGAGCCTGGGGCCCTGCTGCCTGTGGAGTGGACCCAGTGCATCTCCCTAAAGCCTCTGGCTGGCTCGGCCTTTGTCTCAGCCTCCACCTGCTGCCCAGTGTCAGGGAACCCCGCCAGCTCCCTG Human > Gorilla --------------- chr2A:3483411-3483415 Template switch process: F1: L TCCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC 1 F3: 4 CCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC R RF: TCCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTCAAATGCCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCGTCTCCCTAAAGCCTCCAGCTGGCTTGGCCTTTGTCTCAGCCTCCACCTGCTTCCCGGGGTCAG RR: AGGTGGGACCGAGGAAGACCAGTGGGACTGTGGGTGAGGAGTTTACGGGTGTCACTCGGACCCCAGGACGACGGACACCTCACCTGGGTCACGCAGAGGGATTTCGGAGGTCGACCGAACCGGAAACAGAGTCGGAGGTGGACGAAGGGCCCCAGTC F2: 3 CAGTC 2 Unidirectional alignment (log-probability: -28.1) CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC-----ctgacCCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTCAAATG-----CCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC Template switch alignment (log-probability: -16.4) CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC|CTGAC|CCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC|CTGAC|CCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC Chimp > Gorilla --------------- chr2A:3483411-3483415 Template switch process: F1: L TCCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC 1 F3: 4 CCCACAGTGAGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCATC R RF: TCCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTCAAATGCCCACAGTGCGCCTGGGGTCCTGCTGCCTGTGGAGTGGACCCAGTGCGTCTCCCTAAAGCCTCCAGCTGGCTTGGCCTTTGTCTCAGCCTCCACCTGCTGCCCGGGGTCAG RR: AGGTGGGACCGAGGAAGACCAGTGGGACTGTGGGTGAGGAGTTTACGGGTGTCACGCGGACCCCAGGACGACGGACACCTCACCTGGGTCACGCAGAGGGATTTCGGAGGTCGACCGAACCGGAAACAGAGTCGGAGGTGGACGACGGGCCCCAGTC F2: 3 CAGTC 2 Unidirectional alignment (log-probability: -39.3) CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC-----ctgacCCCACAGTGaGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTCAAATG-----CCCACAGTGCGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC Template switch alignment (log-probability: -27.6) CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC|CTGAC|CCCACAGTGaGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC CCACCCTGGCTCCTTCTGGTCACCCTGACACCCACTCCTC|CTGAC|CCCACAGTGCGCCTGGGGTCCTGCTGCCTGTGGAGTGGAC ========== Event 2117 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAA--------ATAAAGAATCCAAGTGTTCAAA ↓ 13 24 ↑ 13 24 Chimp: ACCCAATCCTCCCTCCATTTATTT--------CAAACTTGGAAATGGTAGATTAAAGAATCCAAGTGTTCAAA ↓ 13 24 ↑ 13 24 Gorilla: ACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAA--------ATAAAGAATCCAAGTGTTCAAA Human: ACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAA--------ATAAAGAATCCAAGTGTTCAAA Cluster: [ ] Orangutan: ACCCAATCCCCCCTCCATTTAATCTACCATTTCCAAGTTTGAA--------AT-AAGAATCCAAGTGTTCAAA Chimp > Human ------------- chr2:36568456-36568478 Template switch process: F1: L ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA 1 F3: 4 TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT R RF: ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTATTTCAAACTTGGAAATGGTAGATTAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT RR: TATTGCGTCATATAGTCTTTTGGGTTAGGAGGGAGGTAAATAAAGTTTGAACCTTTACCATCTAATTTCTTAGGTTCACAAGTTTAAGTTTCACTTCTTGACCA F2: 3 AAAGTTTGAACCTTTACCATCTA 2 Unidirectional alignment (log-probability: -51) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTAatctaccatttccaagTTTgAAA----------------TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA----------------TTTCAAACTTGGAAATGGTAGATTAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Template switch alignment (log-probability: -18.1) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|ATCTACCATTTCCAAGTTTGAAA|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|ATCTACCATTTCCAAGTTTGAAA|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Human > Chimp ------------- chr2A:37319546-37319568 Template switch process: F1: L ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA 1 F3: 4 TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT R RF: ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAAATAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT RR: TATTGCGTCATATAGTCTTTTGGGTTAGGAGGGAGGTAAATTAGATGGTAAAGGTTCAAACTTTATTTCTTAGGTTCACAAGTTTAAGTTTCACTTCTTGACCA F2: 3 TAGATGGTAAAGGTTCAAACTTT 2 Unidirectional alignment (log-probability: -51) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA----------------TTTcAAActtggaaatggtagatTAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAAA----------------TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Template switch alignment (log-probability: -18.1) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|TTTCAAACTTGGAAATGGTAGAT|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|TTTCAAACTTGGAAATGGTAGAT|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Gorilla > Chimp --------------- chr2A:37319546-37319568 Template switch process: F1: L ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA 1 F3: 4 TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT R RF: ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAAATAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT RR: TATTGCGTCATATAGTCTTTTGGGTTAGGAGGGAGGTAAATTAGATGGTAAAGGTTCAAACTTTATTTCTTAGGTTCACAAGTTTAAGTTTCACTTCTTGACCA F2: 3 TAGATGGTAAAGGTTCAAACTTT 2 Unidirectional alignment (log-probability: -49.3) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTT--------ATTTCaAAcTTgGAAAtggtagatTAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTAATCTACCATTTCCAAGTTTGAAA--------TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Template switch alignment (log-probability: -18.7) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|TTTCAAACTTGGAAATGGTAGAT|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|TTTCAAACTTGGAAATGGTAGAT|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Chimp > Gorilla --------------- chr2A:36970196-36970218 Template switch process: F1: L ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA 1 F3: 4 TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT R RF: ATAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTATTTCAAACTTGGAAATGGTAGATTAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT RR: TATTGCGTCATATAGTCTTTTGGGTTAGGAGGGAGGTAAATAAAGTTTGAACCTTTACCATCTAATTTCTTAGGTTCACAAGTTTAAGTTTCACTTCTTGACCA F2: 3 AAAGTTTGAACCTTTACCATCTA 2 Unidirectional alignment (log-probability: -49.3) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTaatctaccATTTCcAAgTTtGAAA--------TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTT--------ATTTCAAACTTGGAAATGGTAGATTAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT Template switch alignment (log-probability: -18.7) TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|ATCTACCATTTCCAAGTTTGAAA|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT TAACGCAGTATATCAGAAAACCCAATCCTCCCTCCATTTA|ATCTACCATTTCCAAGTTTGAAA|TAAAGAATCCAAGTGTTCAAATTCAAAGTGAAGAACTGGT ========== Event 2118 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GACACCATAGAAAATTAGATGTCTATGGGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGTAAATAAAGTTTATTTTGTCTC Chimp: GACACCATAGAAAATTAGATGTCTATGGGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGTAAATAAAGTTTATTTTGTCTC ↓ 3 2 1 4 ↑ 3 2 1 4 Gorilla: GACACCATAGAAAATTAGATGTCTATGGGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGCTTAGACAAAATAAAGTTTATTTTGTCTC ↓ 3 2 1 4 ↑ 3 2 1 4 Human: GACACCATAGAAAATTAGATGTCTATGGGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGTAAATAAAGTTTATTTTGTCTC Cluster: [ ] Orangutan: GACACCATAGAAAATTAGATGTCTATGAGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTATGTGCAGGGTAAATAAAGTTTATTTTGTCTC Gorilla > Human --------------- chr2:205530456-205530463 Template switch process: F1: L TTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG 1 F3: 4 AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC R RF: ACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGCTTAGACAAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC RR: TGGGAGGTTCAATTGAATGAAAAGATTAAATGAAGATTCCTCACCGAATCCGAATCTGTTTTATTTCAAATAAAACAGAGGCAAGAAGGTAAAGAGACG F2: 3 TGGGACGT 2 Unidirectional alignment (log-probability: -32.5) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG--------tgcagggtAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGCTTAGACA--------AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Template switch alignment (log-probability: -22.3) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|TGcAGGGT|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|TGGAGGGT|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Human > Gorilla --------------- chr2A:70573720-70573727 Template switch process: F1: L TTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG 1 F3: 4 AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC R RF: TGTCTATGGGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGTAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC RR: ACAGATACCCATGGGAGGTTCAATTGAATGAAAAGATTAAATGAAGATTCCTCACCGAATCCACGTCCCATTTATTTCAAATAAAACAGAGGCAAGAAGGTAAAGAGACG F2: 3 ACAGATTC 2 Unidirectional alignment (log-probability: -32.5) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG--------cttagacaAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGT--------AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Template switch alignment (log-probability: -22.3) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|CtTAGACA|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|CATAGACA|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Gorilla > Chimp --------------- chr2A:74087655-74087662 Template switch process: F1: L TTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG 1 F3: 4 AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC R RF: ACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGCTTAGACAAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC RR: TGGGAGGTTCAATTGAATGAAAAGATTAAATGAAGATTCCTCACCGAATCCGAATCTGTTTTATTTCAAATAAAACAGAGGCAAGAAGGTAAAGAGACG F2: 3 TGGGACGT 2 Unidirectional alignment (log-probability: -32.5) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG--------tgcagggtAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGCTTAGACA--------AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Template switch alignment (log-probability: -22.3) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|TGcAGGGT|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|TGGAGGGT|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Chimp > Gorilla --------------- chr2A:70573720-70573727 Template switch process: F1: L TTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG 1 F3: 4 AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC R RF: TGTCTATGGGTACCCTCCAAGTTAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGTAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC RR: ACAGATACCCATGGGAGGTTCAATTGAATGAAAAGATTAAATGAAGATTCCTCACCGAATCCACGTCCCATTTATTTCAAATAAAACAGAGGCAAGAAGGTAAAGAGACG F2: 3 ACAGATTC 2 Unidirectional alignment (log-probability: -32.5) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG--------cttagacaAAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGGTGCAGGGT--------AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC Template switch alignment (log-probability: -22.3) TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|CtTAGACA|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC TAACTTACTTTTCTAATTTACTTCTAAGGAGTGGCTTAGG|CATAGACA|AAATAAAGTTTATTTTGTCTCCGTTCTTCCATTTCTCTGC ========== Event 2119 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TATCTCATAAGCACATTATCT----CAAGTTTTTCCTGAGAGGGCTACTCAAAGAGATACATATA--TATATATAGCAAGTTCGATCTGAATTACATAATCAGCGAGACTCAAAGTACAATCATCACAGAAGATTGTGAATTATAAGCAGCATTATATCAAATTAAAACTTGTACTAGCAAAGAATTTCCTT Chimp: TATCTCATAAGCACATTATCT----CAAGTTTTTCCTGAGAGGGCTACTCAAAGAGATACatatatatatatataGCAAGTTCGATCTGAATTACATAATCAGCGAGACTCAAAGTACAATCATCACAGAAGATTGTGAATTATAAGCAGCATTATATCAAATTAAAACTTGTACTAGCAAAGAATTTCCTT Gorilla: TATCTCATAAGCACATTATCTGAATGAAGTTCTTCCTGAGAGGGCTACTCAAAGAGCTACATAT----ATATATAGCAAGTTCGATGTGAATTACATAATCAGCGAGACTCAAAGTACAATCATCACAGAAGATTGTGAATTATAAGCAGCATTATATCAAATTAAAACTTGTACTAGCAAAGAATTTCCTT ↓ 1 4 3 2 Human: TATCTCATAAGCACATTATCT----CAAGTTTTTCCTGAGAGGGCTACTCAAAGAGATACATATA--TATATATAGCAAGTTCGATCTGAATTACATAATCAGCGAGACTCAAAGTACAATCATCACAGAAGATTGTGAATTATAAGCAGCATTATATCAAATTAAAACTTGTACTAGCAAAGAATTTCCTT Cluster: [ ] Orangutan: TACCTCATAAGCACATTATCT----CAAGTTTTTCCTGAGAGGGCTACTCAAAGAGATACATA------TATATAGCAAGTTCGATTTGAATTACATAATCAGCGAGACTCAAAGTACAATCATCACAGAAAATTGTGAATTATAAGCAGCATTATATCAAATTAAAACTTGTACTAGCAAATAATTTCCTT Gorilla > Human --------------- chr2:37322729-37322735 Template switch process: F1: L TTCCTACATTAAAATGAAAATATCTCATAAGCACATTATCT 1 F3: 4 TTCCTGAGAGGGCTACTCAAAGAGATACATATATATATAT R RF: TCCCTACATTAAAATGAAAATATCTCATAAGCACATTATCTGAATGAAGTTCTTCCTGAGAGGGCTACTCAAAGAGCTACATATATATATAGCAAGTTCGATGTGAATTACATAATCAGCGAGACTCAAAGTACAATCATCACAGAAGATTGTGAATTATAAGCAGCATTATATCAAATTAAAACTTG RR: AGGGATGTAATTTTACTTTTATAGAGTATTCGTGTAATAGACTTACTTCAAGAAGGACTCTCCCGATGAGTTTCTCGATGTATATATATATCGTTCAAGCTACACTTAATGTATTAGTCGCTCTGAGTTTCATGTTAGTAGTGTCTTCTAACACTTAATATTCGTCGTAATATAGTTTAATTTTGAAC F2: 3 TTTGAAC 2 Unidirectional alignment (log-probability: -42.9) tCCTACATTAAAATGAAAATATCTCATAAGCACATTATC----TcAAGTTtTTCCTGAGAGGGCTACTCAAAGAGaTACATATATATATat CCCTACATTAAAATGAAAATATCTCATAAGCACATTATCTGAATGAAGTTCTTCCTGAGAGGGCTACTCAAAGAGCTACATATATATAT-- Template switch alignment (log-probability: -33.2) tCCTACATTAAAATGAAAATATCTCATAAGCACATTATCT|CAAGTTT|TTCCTGAGAGGGCTACTCAAAGAGaTACATATATATATAt CCCTACATTAAAATGAAAATATCTCATAAGCACATTATCT|CAAGTTT|TTCCTGAGAGGGCTACTCAAAGAGCTACATATATATATAG ========== Event 2120 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTTCCTTCTCTTTAGATCTTGTTTAGGAAGATTCTGAACGTCCTGAAA------AATAAACTGCCATTTAATATAGGACCA ↑ 1 3 4 2 Chimp: ATTTCCTTCTCTTTAGATCTTCATTA---TTTTTCAGGACGTTCAGAAT---CTTCCTAAACTGCCATTTAATATAGGACCA Gorilla: ATTTCCTTCTCTTTAGATCTTGATTA---TTTTTCAGGACGTTCAGAATCTT---CCTAAACTGCCATTTAATATAGGACCA ↓ 1 3 4 2 Human: ATTTCCTTCTCTTTAGATCTTGTTTAGGAAGATTCTGAACGTCCTGAAA------AATAAACTGCCATTTAATATAGGACCA Cluster: [ ] Orangutan: ATTTCCTTCTCTTTAGATCTTGATTA---TTTTTCAGGACGTTCAGAATCTT---CCTAAACTGCCATTTAATATAGGACCA Chimp > Human ------------- chr2:204878054-204878083 Template switch process: F1: L CTTTTTTTT-------ATCCATTTCCTTCTCTTTAGATCTT 1 F3: 4 TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT R RF: CTTTTTTTTTTTTTTAATCCATTTCCTTCTCTTTAGATCTTCATTATTTTTCAGGACGTTCAGAATCTTCCTAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT RR: GAAAAAAAAAAAAAATTAGGTAAAGGAAGAGAAATCTAGAAGTAATAAAAAGTCCTGCAAGTCTTAGAAGGATTTGACGGTAAATTATATCCTGGTACGAAAGACAGAAAA F2: 3 AAAAAGTCCTGCAAGTCTTAGAAGGATTTG 2 Unidirectional alignment (log-probability: -76.3) CTTTTTTTT-------ATCCATTTCCTTCTCTTTAGATCTTgtttaggaagattctgaacgtcctgaaaaa------------------------------TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT CTTTTTTTTTTTTTTAATCCATTTCCTTCTCTTTAGATCTT------------------------------CATTATTTTTCAGGACGTTCAGAATCTTCCTAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT Template switch alignment (log-probability: -29.4) CTTTTTTTT-------ATCCATTTCCTTCTCTTTAGATCTT|GTTTAGGAAGATTCTGAACGTCCTGAAAAA|TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT CTTTTTTTTTTTTTTAATCCATTTCCTTCTCTTTAGATCTT|GTTTAGGAAGATTCTGAACGTCCTGAAAAA|TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT Gorilla > Human --------------- chr2:204878055-204878083 Template switch process: F1: L CTC----TTTTTTTTATCCATTTCCTTCTCTTTAGATCTTG 1 F3: 4 TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT R RF: CTCTTTTTTTTTTTTATCCATTTCCTTCTCTTTAGATCTTGATTATTTTTCAGGACGTTCAGAATCTTCCTAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT RR: GAGAAAAAAAAAAAATAGGTAAAGGAAGAGAAATCTAGAACTAATAAAAAGTCCTGCAAGTCTTAGAAGGATTTGACGGTAAATTATATCCTGGTACGAAAGACAGAAAA F2: 3 AAAAAGTCCTGCAAGTCTTAGAAGGATTT 2 Unidirectional alignment (log-probability: -72.2) CTCTTTTTTT----TATCCATTTCCTTCTCTTTAGATCTTGtttaggaagattctgaacgtcctgaaaaA----------------------------TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT CTCTTTTTTTTTTTTATCCATTTCCTTCTCTTTAGATCTTG----------------------------ATTATTTTTCAGGACGTTCAGAATCTTCCTAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT Template switch alignment (log-probability: -29.3) CTC----TTTTTTTTATCCATTTCCTTCTCTTTAGATCTTG|TTTAGGAAGATTCTGAACGTCCTGAAAAA|TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT CTCTTTTTTTTTTTTATCCATTTCCTTCTCTTTAGATCTTG|TTTAGGAAGATTCTGAACGTCCTGAAAAA|TAAACTGCCATTTAATATAGGACCATGCTTTCTGTCTTTT ========== Event 2121 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGCAACTTTCTACCCCAAGCCACCATAGTGGCTGCACTATGGTCAGACAAGTGGTCATCATC ↑ 1 3 4 2 Chimp: AGGCAACTTTCTACCCCAAGCAATGATTCA---GCCACTATGGTCAGACAAGTGGTCATCATC Gorilla: AGGCAACTTTCTACCCCAAGCAATGATTCA---GCCACTATGGTCAGACAAGTGGTCATCATC ↓ 1 3 4 2 Human: AGGCAACTTTCTACCCCAAGCCACCATAGTGGCTGCACTATGGTCAGACAAGTGGTCATCATC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr2:37711902-37711913 Template switch process: F1: L TCCCAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCCA 1 F3: 4 CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC R RF: TCCCAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCAATGATTCAGCCACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC RR: AGGGTTTCCGGTTTTTATTTTCCGTTGAAAGATGGGGTTCGTTACTAAGTCGGTGATACCAGTCTGTTCACCAGTAGTAGGACCAGACATTG F2: 3 GTCGGTGATACC 2 Unidirectional alignment (log-probability: -40.3) CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGC----------CaccatagtggctgCACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCAATGATTCAGC-------------CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC Template switch alignment (log-probability: -22.8) CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCcA|CCATAGTGGCTG|CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCAA|CCATAGTGGCTG|CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC Gorilla > Human --------------- chr2:37711902-37711913 Template switch process: F1: L TCCCAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCCA 1 F3: 4 CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC R RF: TCCCAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCAATGATTCAGCCACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC RR: AGGGTTTCCGGTTTTTATTTTCCGTTGAAAGATGGGGTTCGTTACTAAGTCGGTGATACCAGTCTGTTCACCAGTAGTAGGACCAGACATTG F2: 3 GTCGGTGATACC 2 Unidirectional alignment (log-probability: -39.8) CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGC----------CaccatagtggctgCACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCAATGATTCAGC-------------CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC Template switch alignment (log-probability: -22.8) CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCcA|CCATAGTGGCTG|CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC CAAAGGCCAAAAATAAAAGGCAACTTTCTACCCCAAGCAA|CCATAGTGGCTG|CACTATGGTCAGACAAGTGGTCATCATCCTGGTCTGTAAC ========== Event 2122 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGGAAACATCTACAGGATACAGATGTTTCTATAAAACTTAACATAATACAACTGGCACAGGAGAA-AAAATGATAAATTCTATCAGGGAGGGTGGGAGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTC---ATCATCTGTAGAATTAAGATCTTCCATAAC Chimp: TTGGAAACATCTACAGGATACAGATGTTTCTATAAAACTTAACATAATACAACTGGCACAGGAGAA-AAAATGATAAATTCTATCAGGGAGGGTGGGAGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTC---ATCATCTGCAGAGTTAAGATCTTCCATAAC Gorilla: TTGGAAACATCTACAGGATACAGATGTTTCTATAAAACTTAACAGAATACAACTGGCACAGGAGaaaaaaaTGATAAATTCTATCAGGGAGGGTGGGAGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTC------ATCTAAAGAATTAAGATCTtccataac ↓ 3 2 1 4 Human: TTGGAAACATCTACAGGATACAGATGTTTCTATAAAACTTAACATAATACAACTGGCACAGGAGAA-AAAATGATAAATTCTATCAGGGAGGGTGGGAGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTC---ATCATCTGTAGAATTAAGATCTTCCATAAC Cluster: [ ] Orangutan: TTGGAAATATCTACAGGATACAGATGTTTCTATAAAATTTAACAGAATACAACGGGCACAGGAGAA-AAAATGATAAATTCTACCAGGGAGTGTGGGAGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATC---ATCTACAGAAATAAGATCTTTCATAAC Gorilla > Human --------------- chr2:37848243-37848248 Template switch process: F1: L AGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATC 1 F3: 4 AGAATTAAGATCTTCCATAACATGCCCCTAGCTACCCATT R RF: ACAGATGTTTCTATAAAACTTAACAGAATACAACTGGCACAGGAGAAAAAAATGATAAATTCTATCAGGGAGGGTGGGAGCAATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATCTAAAGAATTAAGATCTTCCATAACATGCCCCTAGCTACCCATT RR: TGTCTACAAAGATATTTTGAATTGTCTTATGTTGACCGTGTCCTCTTTTTTTACTATTTAAGATAGTCCCTCCCACCCTCGTTAATATCTTTAGTGAGTTTTAAATATACACCGAGGAGTAGATTTCTTAATTCTAGAAGGTATTGTACGGGGATCGATGGGTAA F2: 3 TGTCTA 2 Unidirectional alignment (log-probability: -26.3) ATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATCatcTgtAGAATTAAGATCTTCCATAACATGCCCCTAGCTACCCATT ATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATC---TAAAGAATTAAGATCTTCCATAACATGCCCCTAGCTACCCATT Template switch alignment (log-probability: -16.6) ATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATC|ATCTGT|AGAATTAAGATCTTCCATAACATGCCCCTAGCTACCCATT ATTATAGAAATCACTCAAAATTTATATGTGGCTCCTCATC|ATCTGT|AGAATTAAGATCTTCCATAACATGCCCCTAGCTACCCATT ========== Event 2123 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGATCACAAAATACAGTTCTCTA------------------AA----G---GAAATAGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAATCTAGTTTGTATACT Chimp: AAGATCACAAAATACAGTTCTCTA------------------AA----G---GAAATAGCTTTACTTTTATTCTTACTGCATAAGTGAGGCTATGAATCTAGTTTGTATACT Gorilla: AAGATCACAAAATACAGTTCTTTACTTTTATTCTGACTGCATAAGTGAGGCTTATGCAGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAATCTAGTTTGTATACT ↑ 4 3 2 1 Human: AAGATCACAAAATACAGTTCTCTA------------------AA----G---GAAATAGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAATCTAGTTTGTATACT Cluster: [ ] Orangutan: AAGATCACAAAATACAGTNNNNNN------------------NN----N---NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr2A:38362370-38362374 Template switch process: F1: L ATCGATATGAATGCATCATAAAGATCACAAAATACAGTT---------------CTTTACTTTTATTCTGACTGCATAAGTGAGGCT 1 F3: 4 AGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAA R RF: ATCGATATGAATGCATCATAAAGATCACAAAATACAGTTCTCTAAAGGAAATAGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAA RR: TAGCTATACTTACGTAGTATTTCTAGTGTTTTATGTCAAGAGATTTCCTTTATCGAAATGAAAATAAGACTGACGTATTCACTCCGATACTT F2: 3 CGTAT 2 Unidirectional alignment (log-probability: -71.5) TACAGTTCTttacttttattctgactgcataagtgaggcttatgC----------AGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAA TACAGTTCT-----------------------------------CTAAAGGAAATAGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAA Template switch alignment (log-probability: -27.6) TACAGTT---------------CTTTACTTTTATTCTGACTGCATAAGTGAGGCT|TATGC|AGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAA TACAGTTCTCTAAAGGAAATAGCTTTACTTTTATTCTGACTGCATAAGTGAGGCT|TATGC|AGCTTTACTTTTATTCTGACTGCATAAGTGAGGCTATGAA ========== Event 2124 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GAGGGGCaataatataataaat-------------atattttCAAGATATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGTATTTATCTCCCTGTATCTTGAAAACAGGTGGGTAATGAAA Chimp: GAGGGGCAATAATATAATAAAT-------------ATATTTTCAAGATATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGTATTTATCTCCCTGTATCTTGAAAACAGGTGGGTAATGAAA ↑ 4 1 3 2 Gorilla: GAGGGGCAATAATATAATAAAC--------------------------ATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGTATTTATCTCCCTGTATCTTGAAAACAGGTGGGTAATGAAA Human: GAGGGGCaataatataataaat-------------atattttCAAGATATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGTATTTATCTCCCTGTATCTTGAAAACAGGTGGGTAATGAAA Cluster: [ ] Orangutan: GAGAGGCAATAATATAATAAATATATTTTCAAGAT-------------ATATTTTTGTTGAAATCCGTGGTACTAATATTAGGATTGTATTTATCTCCCTGTATCTTGAAAACAGGTGGGTAACGAAA Gorilla > Chimp --------------- chr2A:71070758-71070763 Template switch process: F1: L GGGCTGGTGTTGGGGAGTTGGAGGGGCAATAATATAATAAATATATTTT 1 F3: 4 ATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGT R RF: GGGCTGGTGTTGGGGAGTTGGAGGGGCAATAATATAATAAACATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGTATTTATCTCCCTGTATCTTG RR: CCCGACCACAACCCCTCAACCTCCCCGTTATTATATTATTTGTATAAAAACAACTTTAGACACCATGATTATAATCCTAACATAAATAGAGGGACATAGAAC F2: 3 TAGAAC 2 Unidirectional alignment (log-probability: -35.1) TTGGGGAGTTGGAGGGGCAATAATATAATAAatatattttcaagAtATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGT TTGGGGAGTTGGAGGGGCAATAATATAATAA-------------ACATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGT Template switch alignment (log-probability: -22.2) TTGGGGAGTTGGAGGGGCAATAATATAATAAAtATATTTT|CAAGAT|ATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGT TTGGGGAGTTGGAGGGGCAATAATATAATAAACATATTTT|CAAGAT|ATATTTTTGTTGAAATCTGTGGTACTAATATTAGGATTGT ========== Event 2125 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAATAAA-AACCAAACCCATC-----------------CTAGAGAAAGTCAGGCTGGTAT-AATTTACTAGGCTGA-AA ↓ 4 1 3 2 Chimp: GAATAAA-AACCAAACCCATC--CTATACCAGCCTGACCTAGAGAAAGTCAGGCtggtat-aatttactaggctga-aa ↑ 4 1 3 2 Gorilla: GAATAAA-AACCAAACCCATC-----------------CTAGAGAAAGTCAGGCtggtat-aatttactaggctga-aa Human: GAATAAA-AACCAAACCCATC-----------------CTAGAGAAAGTCAGGCTGGTAT-AATTTACTAGGCTGA-AA Cluster: [ ] Orangutan: GAATAAAACACCAAACCCATCCT----------------AAGAGAAAGTCAGGCTGGTATAAATTTACTAGGCTGAAAA Human > Chimp ------------- chr2A:40528559-40528569 Template switch process: F1: L TCATTTTCAGTCAATCACCTGGAATAAAAACCAAACCCATCCTA 1 F3: 4 CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAAG R RF: TCATTTTCAATCAATCACCTGGAATAAAAACCAAACCCATCCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAAG RR: AGTAAAAGTTAGTTAGTGGACCTTATTTTTGGTTTGGGTAGGATCTCTTTCAGTCCGACCATATTAAATGATCCGACTTTC F2: 3 AGTCCGACCAT 2 Unidirectional alignment (log-probability: -38.5) TTTCAgTCAATCACCTGGAATAAAAACCAAACCCATCctataccagcctgacCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA TTTCAATCAATCACCTGGAATAAAAACCAAACCCATC---------------CTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA Template switch alignment (log-probability: -22.7) TTTCAgTCAATCACCTGGAATAAAAACCAAACCCATCCTA|TACCAGCCTGA|CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA TTTCAATCAATCACCTGGAATAAAAACCAAACCCATCCTA|TACCAGCCTGA|CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA Gorilla > Chimp --------------- chr2A:40528559-40528569 Template switch process: F1: L TCATTTTCAGTCAATCACCTGGAATAAAAACCAAACCCATCCTA 1 F3: 4 CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAAG R RF: TCATTTTCAATCAATCACTTGGAATAAAAACCAAACCCATCCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAAG RR: AGTAAAAGTTAGTTAGTGAACCTTATTTTTGGTTTGGGTAGGATCTCTTTCAGTCCGACCATATTAAATGATCCGACTTTC F2: 3 AGTCCGACCAT 2 Unidirectional alignment (log-probability: -43.5) TTTCAgTCAATCACcTGGAATAAAAACCAAACCCATcctataccagcctgaCCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA TTTCAATCAATCACTTGGAATAAAAACCAAACCCAT---------------CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA Template switch alignment (log-probability: -28.3) TTTCAgTCAATCACcTGGAATAAAAACCAAACCCATCCTA|TACCAGCCTGA|CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA TTTCAATCAATCACTTGGAATAAAAACCAAACCCATCCTA|TACCAGCCTGA|CCTAGAGAAAGTCAGGCTGGTATAATTTACTAGGCTGAAA ========== Event 2126 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTATGGTTCTGTCCCATCTACAATGTGCAT-----------------------------------GTCTTTTTTATTATCCACAGGCAA ↓ 3 4 1 2 Chimp: TCCTATGGTTCTGTCCCATCTACAATGTGCAT---------GAGACATGCACATTGTAGATATGCATGTCTTTTTTATTATCCACAGGCAA Gorilla: TCCTACGGTTCTGTCCCATCTACAATTTGCATGTCTCAATC--------------------------TTCTTTTTTATTATCCACAGGCAA Human: TCCTATGGTTCTGTCCCATCTACAATGTGCAT-----------------------------------GTCTTTTTTATTATCCACAGGCAA Cluster: [ ] Orangutan: TCCTATGGTTCTGTCCCATCTACAATTTGCATGTCTCAATC--------------------------TTCTTTTTTATTATCCACAGGCAA Human > Chimp ------------- chr2A:42872411-42872427 Template switch process: F1: L TCATATGTCTCCTATGGTTCTGTCCCATCTACAATGTGCATG 1 F3: 4 ATATGCATGTCTTTTTTATTATCCACAGGCAAAATATTATTCAGTGCA R RF: TCATATGTCTCCTATGGTTCTGTCCCATCTACAATGTGCATGTCTTTTTTATTATCCACAGGCAAAATATTATTCAGTGCA RR: AGTATACAGAGGATACCAAGACAGGGTAGATGTTACACGTACAGAAAAAATAATAGGTGTCCGTTTTATAATAAGTCACGT F2: 3 GATGTTACACGTACAGA 2 Unidirectional alignment (log-probability: -48.3) ATATGTCTCCTATGGTTCTGTCCCATCTACAATGTGCATGagacatgcacattgtagatatgcatgTCTTTTTTATTATCCACAGGCAAAATATTAT ATATGTCTCCTATGGTTCTGTCCCATCTACAATGTGCATG--------------------------TCTTTTTTATTATCCACAGGCAAAATATTAT Template switch alignment (log-probability: -23.5) ATATGTCTCCTATGGTTCTGTCCCATCTACAATGTGCATG|AGACATGCACATTGTAG|ATaTGCATGTCTTTTTTATTATCCACAGGCAAAATATTAT ATATGTCTCCTATGGTTCTGTCCCATCTACAATGTGCATG|AGACATGCACATTGTAG|ATGTGCATGTCTTTTTTATTATCCACAGGCAAAATATTAT ========== Event 2127 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTGGTGTGAGTTACTTGGGTGCAAAACGATATTCTAGTTTTGCACTAGAAGTGCTCAGCTAAAACT Chimp: GGTGGTGTGAGTTATTTGGGTGCAAAACGGTATTCTAG-------AAAGAAGTGCTCAGCTAAAACT Gorilla: GGTGGTGTGAGTTATTTGGGTGCAAAACGATATTCTAG-------AAAGAAGTGCTCAGCTAAAACT ↓ 3 2 1 4 Human: GGTGGTGTGAGTTACTTGGGTGCAAAACGATATTCTAGTTTTGCACTAGAAGTGCTCAGCTAAAACT Cluster: [ ] Orangutan: GGTGGTGTGAGTTATTTGGGTGCAAAACGATATTCTAG-------AAAGAAGTGCTCAGCTAAAACT Gorilla > Human --------------- chr2:199399599-199399606 Template switch process: F1: L GAAGGTGGTGTGAGTTACTTGGGTGCAAAACGATATTCTAG 1 F3: 4 TAGAAGTGCTCAGCTAAAACTGTGCTAGATAAATAACTAAA R RF: GAAGGTGGTGTGAGTTATTTGGGTGCAAAACGATATTCTAGAAAGAAGTGCTCAGCTAAAACTGTGCTAGATAAATAACTAAA RR: CTTCCACCACACTCAATAAACCCACGTTTTGCTATAAGATCTTTCTTCACGAGTCGATTTTGACACGATCTATTTATTGATTT F2: 3 CACGTTTT 2 Unidirectional alignment (log-probability: -37.5) AAGGTGGTGTGAGTTAcTTGGGTGCAAAACGATATTCTAGttttgcactAGAAGTGCTCAGCTAAAACTGTGCTAGATAAATAACTAA AAGGTGGTGTGAGTTATTTGGGTGCAAAACGATATTCTAGA-------AAGAAGTGCTCAGCTAAAACTGTGCTAGATAAATAACTAA Template switch alignment (log-probability: -27.8) AAGGTGGTGTGAGTTAcTTGGGTGCAAAACGATATTCTAG|TTTTGCAC|tAGAAGTGCTCAGCTAAAACTGTGCTAGATAAATAACTAA AAGGTGGTGTGAGTTATTTGGGTGCAAAACGATATTCTAG|TTTTGCAC|AAGAAGTGCTCAGCTAAAACTGTGCTAGATAAATAACTAA ========== Event 2128 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCATAGCCAGTCTACCTTGCT-TGTACTACACTGTACTTGGAATGACTTAACTGAGGCTTACCTTTTAGTTTTCATtttttaaataaacttttaatgttgaaataatttcagatttacagaaaagtttgcaaaggtagtacagagtcttccccatctaccc Chimp: CCATAGCCAGTCTACCTTGCT-TGTACTACACTGTACTTGGAATGACTTAACTGAGGCTTACCTTTTAGTTTTCATtttttaaataaacttttaatgttgaaataatttcagatttacagaaaagtttgcaaaggtagtacagagtcttccccatctaccc ↑ 1 4 3 2 Gorilla: CCATAGCCAGTCTACCTTGCTTCATCCAACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTAGTTTTCATtttttaaataaacttttaatgttgaaataatttcagatttacagaaaagtttgcaaaggtagtacagagtcttccccatctaccc ↓ 1 4 3 2 Human: CCATAGCCAGTCTACCTTGCT-TGTACTACACTGTACTTGGAATGACTTAACTGAGGCTTACCTTTTAGTTTTCATtttttaaataaacttttaatgttgaaataatttcagatttacagaaaagtttgcaaaggtagtacagagtcttccccatctaccc Cluster: [ ] Orangutan: CCATAGCCAGTCCACCTTGCTTCATCCAACACTGTACTTGGAATGACTTAACTGAGGCTTACCTTTTAGTTTTCATtttttaaataaacttttaatgttgaaataatttcagatttacagaaaagtttgcaaaggtagtacagagtcttccccatctaccc Gorilla > Human --------------- chr2:44196960-44196964 Template switch process: F1: L ATCACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT 1 F3: 4 ACACTGTACTTGGAATGACTTAACTGAGGCTTACCTTTTAGTTT R RF: ATCACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTTCATCCAACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTAGTTTTCATTTTTTAAATAAACTTTTAATGTTGAAATAATTTCAGATTTACAGAAAAGTTTGCAAAGGTAGTAC RR: TAGTGTCCACCTCTCTAAAAGGTATCGGTCAGATGGAACGAAGTAGGTTGTAACATGAACCTTAGTGAATTGACTCCGAATGGAAAATCAAAAGTAAAAAATTTATTTGAAAATTACAACTTTATTAAAGTCTAAATGTCTTTTCAAACGTTTCCATCATG F2: 3 TCATG 2 Unidirectional alignment (log-probability: -38.1) CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTTgtactacaC---------TGTACTTGGAATgACTTAACTGAGGCTTACCTTTTA CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT--------CATCCAACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTA Template switch alignment (log-probability: -27.5) CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT|GTACT|ACAcTGTACTTGGAATgACTTAACTGAGGCTTACCTTTTA CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT|GTACT|ACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTA Gorilla > Chimp --------------- chr2A:45199122-45199126 Template switch process: F1: L ATCACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT 1 F3: 4 ACACTGTACTTGGAATGACTTAACTGAGGCTTACCTTTTAGTTT R RF: ATCACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTTCATCCAACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTAGTTTTCATTTTTTAAATAAACTTTTAATGTTGAAATAATTTCAGATTTACAGAAAAGTTTGCAAAGGTAGTAC RR: TAGTGTCCACCTCTCTAAAAGGTATCGGTCAGATGGAACGAAGTAGGTTGTAACATGAACCTTAGTGAATTGACTCCGAATGGAAAATCAAAAGTAAAAAATTTATTTGAAAATTACAACTTTATTAAAGTCTAAATGTCTTTTCAAACGTTTCCATCATG F2: 3 TCATG 2 Unidirectional alignment (log-probability: -38.1) CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTTgtactacaC---------TGTACTTGGAATgACTTAACTGAGGCTTACCTTTTA CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT--------CATCCAACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTA Template switch alignment (log-probability: -27.5) CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT|GTACT|ACAcTGTACTTGGAATgACTTAACTGAGGCTTACCTTTTA CACAGGTGGAGAGATTTTCCATAGCCAGTCTACCTTGCTT|GTACT|ACATTGTACTTGGAATCACTTAACTGAGGCTTACCTTTTA ========== Event 2129 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: GTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCTTTATATAACTCAAGACTGACTTGAGTTATATAA ↓ 3 2 1 4 Chimp: GTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCT------A--GCTAGACTGACTTGAGTTATATAA Gorilla: GTAGTTCTGCAGTAAAGAAAGCTTCTTGCTTAGGGCT------A--GCTAGACTGACTTGAGTTATATAA Human: GTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCTTTATATAACTCAAGACTGACTTGAGTTATATAA Cluster: [ ] Orangutan: GTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCT------A--GCTAGACTGACTTGAGTTGTATAA Human > Chimp ------------- chr2A:64975926-64975929 Template switch process: F1: L CTTGGTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCT 1 F3: 4 AGACTGACTTGAGTTATATAAAGAAGGATTCTTCTTGCAA R RF: CTTGGTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCTTTATATAACTCAAGACTGACTTGAGTTATATAAAGAAGGATTCTTGTTGCAA RR: GAACCATCAAGAAGTCATTTCTTTCGAAGAACGAATCCCGAAATATATTGAGTTCTGACTGAACTCAATATATTTCTTCCTAAGAACAACGTT F2: 3 TCGA 2 Unidirectional alignment (log-probability: -32) TTGGTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCTagcT-----------AGACTGACTTGAGTTATATAAAGAAGGATTCTTcTTGCAA TTGGTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCT---TTATATAACTCAAGACTGACTTGAGTTATATAAAGAAGGATTCTTGTTGCAA Template switch alignment (log-probability: -21.8) TTGGTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCT|AGCT|AGACTGACTTGAGTTATATAAAGAAGGATTCTTcTTGCAA TTGGTAGTTCTTCAGTAAAGAAAGCTTCTTGCTTAGGGCT|AGCT|AGACTGACTTGAGTTATATAAAGAAGGATTCTTGTTGCAA ========== Event 2130 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GATTTGTGACTGTTACATCTCATGAA----CTATAGGTTTATTCAGAATGGAAT Chimp: GATTTGTGACTGTTACATCTCATGAA----CTATAGGTTTATTCAGAATGGAAT ↓ 3 1 4 ↑ 1 3 4 Gorilla: GATTTGTGACTGTTACATCTCCTGAATAGTTCATAGGTTTATTCAGAATGGAAT ↓ 1 3 4 ↑ 3 1 4 Human: GATTTGTGACTGTTACATCTCATGAA----CTATAGGTTTATTCAGAATGGAAT Cluster: [ ] Orangutan: gatttgtgactgttacatctcctgaatagttcataggtttattcagaatggaat Gorilla > Human --------------- chr2:196777157-196777164 Template switch process: F1: L CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTC 1 F3: 4 TAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT R RF: CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCCTGAATAGTTCATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG RR: GACTATTAATCCATGAACTTCTAAACACTGACAATGTAGAGGACTTATCAAGTATCCAAATAAGTCTTACCTTATAACGATGGTGTAAATTC F2: 3 ATCAAGTA 2 Unidirectional alignment (log-probability: -33.3) TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCaTGAA----ctATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAt TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCCTGAATAGTTCATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG Template switch alignment (log-probability: -22.2) TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTC|ATGAACTA|TAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAt TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTC|ATGAACTA|TAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG Human > Gorilla --------------- chr2A:61769481-61769486 Template switch process: F1: L CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCCTGAA 1 F3: 4 ATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG R RF: CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCATGAACTATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT RR: GACTATTAATCCATGAACTTCTAAACACTGACAATGTAGAGTACTTGATATCCAAATAAGTCTTACCTTATAACGATGGTGTAAATTA F2: 3 CTTGAT 2 Unidirectional alignment (log-probability: -38.8) ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCcTGAAtagttcATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAg ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCATGAA----CTATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT Template switch alignment (log-probability: -27.6) ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCcTGAA|TAGTTC|ATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAg ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCATGAA|TAGTTC|ATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT Gorilla > Chimp --------------- chr2A:65063683-65063690 Template switch process: F1: L CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTC 1 F3: 4 TAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT R RF: CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCCTGAATAGTTCATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG RR: GACTATTAATCCATGAACTTCTAAACACTGACAATGTAGAGGACTTATCAAGTATCCAAATAAGTCTTACCTTATAACGATGGTGTAAATTC F2: 3 ATCAAGTA 2 Unidirectional alignment (log-probability: -33.3) TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCaTGAA----ctATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAt TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCCTGAATAGTTCATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG Template switch alignment (log-probability: -22.2) TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTC|ATGAACTA|TAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAt TGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTC|ATGAACTA|TAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG Chimp > Gorilla --------------- chr2A:61769481-61769486 Template switch process: F1: L CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCCTGAA 1 F3: 4 ATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAG R RF: CTGATAATTAGGTACTTGAAGATTTGTGACTGTTACATCTCATGAACTATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT RR: GACTATTAATCCATGAACTTCTAAACACTGACAATGTAGAGTACTTGATATCCAAATAAGTCTTACCTTATAACGATGGTGTAAATTA F2: 3 CTTGAT 2 Unidirectional alignment (log-probability: -38.8) ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCcTGAAtagttcATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAg ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCATGAA----CTATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT Template switch alignment (log-probability: -27.6) ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCcTGAA|TAGTTC|ATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAg ATTAGGTACTTGAAGATTTGTGACTGTTACATCTCATGAA|TAGTTC|ATAGGTTTATTCAGAATGGAATATTGCTACCACATTTAAT ========== Event 2131 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTACACAACGATCTCTTTGTCCCCA-----ATGTTCTGTGTCTCTGTGGATGTTTAGTA Chimp: TTACACAACGATCTCTTTGTCCCCA-----ATGTTCTGTGTCTCTGTGGATGTTTAGTA ↓ 1 3 4 2 Gorilla: TTACACAACGATCTCTTTGTCACAGAACATTGGTTCTGTGTCTCTGTGGATGTTTAGTA ↑ 1 3 4 2 Human: TTACACAACGATCTCTTTGTCCCCA-----ATGTTCTGTGTCTCTGTGGATGTTTAGTA Cluster: [ ] Orangutan: TTACACAACGATCTCTTTGTCCCCA-----ACGTTCTGTGTCTCTGTGGATGTTTAGTA Human > Gorilla --------------- chr2A:61364123-61364133 Template switch process: F1: L ATATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC 1 F3: 4 GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA R RF: ATATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTCCCCAATGTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA RR: TATATTAAACTCAGTAAAGAAATGTGTTGCTAGAGAAACAGGGGTTACAAGACACAGAGACACCTACAAATCATTGTGGATGACAAT F2: 3 GTTACAAGACA 2 Unidirectional alignment (log-probability: -36.8) TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC------acagaacattgGTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTCCCCAAT-----------GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA Template switch alignment (log-probability: -17.1) TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC|ACAGAACATTG|GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC|ACAGAACATTG|GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA Chimp > Gorilla --------------- chr2A:61364123-61364133 Template switch process: F1: L ATATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC 1 F3: 4 GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTACTGTTA R RF: ATATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTCCCCAATGTTCTGTGTCTCTGTGGATGTTTAGTAACACCTGCTGTTA RR: TATATTAAACTCAGTAAAGAAATGTGTTGCTAGAGAAACAGGGGTTACAAGACACAGAGACACCTACAAATCATTGTGGACGACAAT F2: 3 GTTACAAGACA 2 Unidirectional alignment (log-probability: -42.3) TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC------acagaacattgGTTCTGTGTCTCTGTGGATGTTTAGTAACACCTaCTGTTA TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTCCCCAAT-----------GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTGCTGTTA Template switch alignment (log-probability: -22.6) TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC|ACAGAACATTG|GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTaCTGTTA TATAATTTGAGTCATTTCTTTACACAACGATCTCTTTGTC|ACAGAACATTG|GTTCTGTGTCTCTGTGGATGTTTAGTAACACCTGCTGTTA ========== Event 2132 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAGATCTTAACCATCTTCAGGTATATGTACTAAGTTTTAGGTTATTCCCTAT Chimp: TCAAGATCTTAACCATCTTCAGGTATATGTACTAAGTTTTAGGTTATTCCCTAT ↓ 3 2 1 4 Gorilla: TCAAGATCTTAACCATCTTCAGGTATATACCTGAAGTTTTAGGTTATTCCCTAT ↑ 3 2 1 4 Human: TCAAGATCTTAACCATCTTCAGGTATATGTACTAAGTTTTAGGTTATTCCCTAT Cluster: [ ] Orangutan: TCAAGATCTTAACCATCTTCAGGTATATGTACTAAGTTTTAGGTTATTCCCTAT Human > Gorilla --------------- chr2A:427081-427085 Template switch process: F1: L ATTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAT 1 F3: 4 AAGTTTTAGGTTATTCCCTATAGATATCTGTCAGTCGTAA R RF: ATTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATATGTACTAAGTTTTAGGTTATTCCCTATAGACATCTGTCAGTCTTAA RR: TAAACGTGACAGGAGTTCTAGAATTGGTAGAAGTCCATATACATGATTCAAAATCCAATAAGGGATATCTGTAGACAGTCAGAATT F2: 3 GTCCA 2 Unidirectional alignment (log-probability: -37.6) TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAtaccTG----AAGTTTTAGGTTATTCCCTATAGAtATCTGTCAGTCgTAA TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATA----TGTACTAAGTTTTAGGTTATTCCCTATAGACATCTGTCAGTCTTAA Template switch alignment (log-probability: -27.4) TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAT|ACCTG|AAGTTTTAGGTTATTCCCTATAGAtATCTGTCAGTCgTAA TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAT|ACCTG|AAGTTTTAGGTTATTCCCTATAGACATCTGTCAGTCTTAA Chimp > Gorilla --------------- chr2A:427081-427085 Template switch process: F1: L ATTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAT 1 F3: 4 AAGTTTTAGGTTATTCCCTATAGATATCTGTCAGTCGTAA R RF: ATTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATATGTACTAAGTTTTAGGTTATTCCCTATAGACATCTGTCAGTCTTAA RR: TAAACGTGACAGGAGTTCTAGAATTGGTAGAAGTCCATATACATGATTCAAAATCCAATAAGGGATATCTGTAGACAGTCAGAATT F2: 3 GTCCA 2 Unidirectional alignment (log-probability: -37.6) TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAtaccTG----AAGTTTTAGGTTATTCCCTATAGAtATCTGTCAGTCgTAA TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATA----TGTACTAAGTTTTAGGTTATTCCCTATAGACATCTGTCAGTCTTAA Template switch alignment (log-probability: -27.4) TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAT|ACCTG|AAGTTTTAGGTTATTCCCTATAGAtATCTGTCAGTCgTAA TTTGCACTGTCCTCAAGATCTTAACCATCTTCAGGTATAT|ACCTG|AAGTTTTAGGTTATTCCCTATAGACATCTGTCAGTCTTAA ========== Event 2133 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: tttt------------ttttttCCTTCTCTTCCATTCATAGAGAAATATGCATAGAAACAACAGTTGGGGACATGTTTTGCAAAATATTGTACCATAATACAGTTTCCAGAAAACTGTATCCCCAAGTGTGACATAATC Chimp: tttt---------tttttttttCCTTCTCTTCCATTCATAGAGAAATACGCATAGAAACAACATTTGGGGACATGTTTTGCAAAATATTGTACCATAA--ATGTTTGCAGAAAACTGTATCCCCAAGTGTGACATAATC Gorilla: tttt-----tttt---ttttttCCTTCTCTTCCATTCATAGAGAAATATGCATAGAAACAACATTTGCGGACATGTTTTGCAAAATATTGTACCATAA--ATGTTTGCAGAAAACTGTATCCCCAAGTGTGACATAATC ↓ 4 1 3 2 Human: tttt------------ttttttCCTTCTCTTCCATTCATAGAGAAATATGCATAGAAACAACAGTTGGGGACATGTTTTGCAAAATATTGTACCATAATACAGTTTCCAGAAAACTGTATCCCCAAGTGTGACATAATC Cluster: [ ] Orangutan: ttttttttc-------ttttttCCTTCTCTTCCATTCATAGAGAAATACGCATAGAAACAACATTTGCGGACATATTTTACAAAATATTGTATCATAA--ATGTTTGCAGAAAACTGTATCCCCAAGTGTGACATAATC Gorilla > Human --------------- chr2:237532949-237532953 Template switch process: F1: L CCTTCTCTTCCATTCATAGAGAAATATGCATAGAAACAACAGTTGGGGACATGTTTTGCAAAATATTGTACCATAA 1 F3: 4 TTTCC R RF: CCTTCTCTTCCATTCATAGAGAAATATGCATAGAAACAACATTTGCGGACATGTTTTGCAAAATATTGTACCATAATTCTCTTCCATTCATAGAGAAATATGCATAGAAACAACATTTGCGGACATGTTTTGCAAAATATTGTACCATAAATGTTTGCAGAAAACTGTA RR: GGAAGAGAAGGTAAGTATCTCTTTATACGTATCTTTGTTGTAAACGCCTGTACAAAACGTTTTATAACATGGTATTAAGAGAAGGTAAGTATCTCTTTATACGTATCTTTGTTGTAAACGCCTGTACAAAACGTTTTATAACATGGTATTTACAAACGTCTTTTGACAT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -41.4) CAACAgTTGgGGACATGTTTTGCAAAATATTGTACCATAatAcaGTTTcC CAACATTTGCGGACATGTTTTGCAAAATATTGTACCATA--AATGTTTGC Template switch alignment (log-probability: -27.4) CAACAgTTGgGGACATGTTTTGCAAAATATTGTACCATAA|TACAG|TTTCC CAACATTTGCGGACATGTTTTGCAAAATATTGTACCATAA|TACAG|TTTCC ========== Event 2134 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAAGAGAGGGGAGAGTGGAGGTACATTCGTTTTTCACTACAGCTTCTTATGA-TTATTCGTGCTGCTTCTAACAACAGAT Chimp: TGAAGAGGGGGGAGAGTGGAGGTACATTCGTTTTTCACTACAGCTTCTTATGATATACCCGTGCTGCTTCTAACAACAGAT Gorilla: TGAAGAGGGGGGAGAGTGGAGGTACATTCATTTTTCACTACAGCTTCTTATGATGTACCTGTGCTGCTTCTAACAACAGAT ↑ 3 2 1 4 Human: TGAAGAGAGGGGAGAGTGGAGGTACATTCGTTTTTCACTACAGCTTCTTATGA-TTATTCGTGCTGCTTCTAACAACAGAT Cluster: [ ] Orangutan: TGAGGAGGGGGGAGAGTGAAGGTACATTCGTTTTTCACTACAGCTTCTTATGATGTACCTGTGCTGCTTCTAACAACAGAT Human > Gorilla --------------- chr2A:4857139-4857144 Template switch process: F1: L AGAGTGGAGGTACATTCATTTTTCACTACAGCTTCTTATGAT 1 F3: 4 GTGCTGCTTCTAACAACAGATGCCACCCTTGAACAGGCAG R RF: AGAGTGGAGGTACATTCGTTTTTCACTACAGCTTCTTATGATTATTCGTGCTGCTTCTAACAACAGATGCCACCCTTGAACAGGCAG RR: TCTCACCTCCATGTAAGCAAAAAGTGATGTCGAAGAATACTAATAAGCACGACGAAGATTGTTGTCTACGGTGGGAACTTGTCCGTC F2: 3 TCCATG 2 Unidirectional alignment (log-probability: -33.6) AGTGGAGGTACATTCaTTTTTCACTACAGCTTCTTATGATgtaccT----GTGCTGCTTCTAACAACAGATGCCACCCTTGAACAGGCAG AGTGGAGGTACATTCGTTTTTCACTACAGCTTCTTATGAT-----TATTCGTGCTGCTTCTAACAACAGATGCCACCCTTGAACAGGCAG Template switch alignment (log-probability: -22) AGTGGAGGTACATTCaTTTTTCACTACAGCTTCTTATGAT|GTACCT|GTGCTGCTTCTAACAACAGATGCCACCCTTGAACAGGCAG AGTGGAGGTACATTCGTTTTTCACTACAGCTTCTTATGAT|GTACCT|GTGCTGCTTCTAACAACAGATGCCACCCTTGAACAGGCAG ========== Event 2135 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGATTTTGTCTGAGAAGAGTG--TGTACTGTATCTAGAGTTTGCTGCTTTGTAAACGAAAAAGAACATGTATGTAAGTTGAAAATCTTGATCGTTAAGGTTTTACAGTAAGCTAGAATCACAGGATACATACCTTTGAAAAATACAGGTAACAATGGGATCTA-AAATAAAG Chimp: GGATTTTGTCTGAGAAGAGTG--TGTT-ACTATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAATATGTATGTAAGTTGAAAATCTTGATCGTTAAGGTTTTACAGTAAGCTAGAATGACAGGATACATACCTTTGAAAAATACAGGTAACAATGGGATCTA-AAATAAAG ↑ 1 4 3 2 Gorilla: GGATTTTGTCTGAGAAGAGTG----TAGCATATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAACATGTATGTAAGTTGAAAATCTTGATCGTTAAGGTTTTACAGTAAGCTAGAATCACAGGATACATACCTTTGAAAAATACAGGTAACAATGGGATCTA-AAATAAAG Human: GGATTTTGTCTGAGAAGAGTG--TGTACTGTATCTAGAGTTTGCTGCTTTGTAAACGAAAAAGAACATGTATGTAAGTTGAAAATCTTGATCGTTAAGGTTTTACAGTAAGCTAGAATCACAGGATACATACCTTTGAAAAATACAGGTAACAATGGGATCTA-AAATAAAG Cluster: [ ] Orangutan: GGATTTTGTCTGAGAAGAGTGTG--TAGTCTATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAACATGTATGTAAGTTGAAAATCTTGATCGTTAAGGTTTTACAGTAAGCTAGAATCACAGGATACATGCCTTTGAAAAATACAGATAACAATGGGATCTAAAAATAAAG Gorilla > Chimp --------------- chr2A:60924730-60924734 Template switch process: F1: L CAAAAATTGATGCATGATTGGGATTTTGTCTGAGAAGAGTGT 1 F3: 4 TATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAATATGT R RF: CAAAAATTGATGCATGATTGGGATTTTGTCTGAGAAGAGTGTAGCATATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAACATGTATGTAAGTTGAAAATCTTGATCGTTAAGGTTTTACAGTAAGCTAGAATCACAGGATACATACCTTTGAAAAATACAGGTAAC RR: GTTTTTAACTACGTACTAACCCTAAAACAGACTCTTCTCACATCGTATAGATCACAAACGACGAAACATTTACTTTTTCTTGTACATACATTCAACTTTTAGAACTAGCAATTCCAAAATGTCATTCGATCTTAGTGTCCTATGTATGGAAACTTTTTATGTCCATTG F2: 3 CATTG 2 Unidirectional alignment (log-probability: -33.6) AAAATTGATGCATGATTGGGATTTTGTCTGAGAAGAGTGT----gttacTATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAAtATGT AAAATTGATGCATGATTGGGATTTTGTCTGAGAAGAGTGTAGCA-----TATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAACATGT Template switch alignment (log-probability: -21.9) AAAATTGATGCATGATTGGGATTTTGTCTGAGAAGAGTGT|GTTAC|TATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAAtATGT AAAATTGATGCATGATTGGGATTTTGTCTGAGAAGAGTGT|GTTAC|TATCTAGTGTTTGCTGCTTTGTAAATGAAAAAGAACATGT ========== Event 2136 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTTAAGAAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTT----------------------------ATTTAGGAATATTTTCTTtatatat Chimp: CCTTTAAGAAAATGTTCCTTAAATTGTGGCTCATATGAGAGCCACTT--------------AATATGAGCCACAATTTAAGGAatattttatttatatat Gorilla: CCTTTAAGAAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTAATATGAGCCACAA--------------TTTAAGGAATATTTTCTTtatatat ↑ 3 2 1 4 Human: CCTTTAAGAAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTT----------------------------ATTTAGGAATATTTTCTTtatatat Cluster: [ ] Orangutan: CCTTTAAGAAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTT----------------------------ATTTAGGAATATTT---Ttatatat Human > Gorilla --------------- chr2A:56840239-56840255 Template switch process: F1: L AGAAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTA 1 F3: 4 AGGAATATTTTCTTTATATATATATATAT R RF: AGAAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTATTTAGGAATATTTTCTTTATATATATATATAA RR: TCTTTTATAAGGAATTTAACACCGAGTATACTCTCGGTGAATAAATCCTTATAAAAGAAATATATATATATATT F2: 3 ATTTAACACCGAGTATA 2 Unidirectional alignment (log-probability: -49.3) AAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTAatatgagccacaatTTaAGGAATATTTTCTTTATATATATATATAt----------- AAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTA--------------TTTAGGAATATTTTCTTTATATATATATATAATATATTATATA Template switch alignment (log-probability: -23.2) AAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTA|ATATGAGCCACAATTTA|AGGAATATTTTCTTTATATATATATATAt AAAATATTCCTTAAATTGTGGCTCATATGAGAGCCACTTA|ATATGAGCCACAATTTA|AGGAATATTTTCTTTATATATATATATAA ========== Event 2137 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAACAATTAAATTATTTCACTAGGTTGTTAGAAAAAATAGCATTTTGTGGGAAACCATGGA Chimp: AGAACAATTAGATTATTTGACTAGGTTGTTAGAAACAATAGCATTTTGTGGGAAACCATGGA ↓ 3 2 1 4 Gorilla: AGAACAATTAAATTATTTGACTAGGTTGTTAGAAACCTAGTCATTTTGTGGGAAACCATGGA ↑ 3 2 1 4 Human: AGAACAATTAAATTATTTCACTAGGTTGTTAGAAAAAATAGCATTTTGTGGGAAACCATGGA Cluster: [ ] Orangutan: AGAACAATTAAATTATTTGACTAGGTTGTTAGAAACAATAGCATTTTTTGGGAAACCATGGA Human > Gorilla --------------- chr2A:55958693-55958698 Template switch process: F1: L AAGTGAAGAACAATTAAATTATTTGACTAGGTTGTTAGAAA 1 F3: 4 CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT R RF: AAGTGAAGAACAATTAAATTATTTCACTAGGTTGTTAGAAAAAATAGCATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT RR: TTCACTTCTTGTTAATTTAATAAAGTGATCCAACAATCTTTTTTATCGTAAAACACCCTTTGGTACCTGAATCGTCTCTGACACTAA F2: 3 TGATCC 2 Unidirectional alignment (log-probability: -35.1) AGTGAAGAACAATTAAATTATTTgACTAGGTTGTTAGAAA------cctagtCATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT AGTGAAGAACAATTAAATTATTTCACTAGGTTGTTAGAAAAAATAG------CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT Template switch alignment (log-probability: -22) AGTGAAGAACAATTAAATTATTTgACTAGGTTGTTAGAAA|CCTAGT|CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT AGTGAAGAACAATTAAATTATTTCACTAGGTTGTTAGAAA|CCTAGT|CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT Chimp > Gorilla --------------- chr2A:55958694-55958698 Template switch process: F1: L AGTGAAGAACAATTAAATTATTTGACTAGGTTGTTAGAAAC 1 F3: 4 CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT R RF: AGTGAAGAACAATTAGATTATTTGACTAGGTTGTTAGAAACAATAGCATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT RR: TCACTTCTTGTTAATCTAATAAACTGATCCAACAATCTTTGTTATCGTAAAACACCCTTTGGTACCTGAATCGTCTCTGACACTAA F2: 3 TGATC 2 Unidirectional alignment (log-probability: -33.2) GTGAAGAACAATTAaATTATTTGACTAGGTTGTTAGAAAC-cTAGtCATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT GTGAAGAACAATTAGATTATTTGACTAGGTTGTTAGAAACAATAG-CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT Template switch alignment (log-probability: -21.9) GTGAAGAACAATTAaATTATTTGACTAGGTTGTTAGAAAC|CTAGT|CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT GTGAAGAACAATTAGATTATTTGACTAGGTTGTTAGAAAC|CTAGT|CATTTTGTGGGAAACCATGGACTTAGCAGAGACTGTGATT ========== Event 2138 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAGCTTCACTTCTTGGTGCAATGAACAATGGTTCATTGATCCTCACAGTGCTTAAT ↑ 31 4 2 Chimp: AAAGCTTCACTTCTTGGTGCAT--------TGTTCATTGATCCTCACAGTGCTTAAT Gorilla: AAACCTTCACTTCTTGGTGCAT--------TGTTCATTGATCCTCACAGTGCTTAAT Human: AAAGCTTCACTTCTTGGTGCAATGAACAATGGTTCATTGATCCTCACAGTGCTTAAT Cluster: [ ] Orangutan: AAAGCTTCACTtcttggtgcat--------tgttcattgatcctcacagtgcttaat Chimp > Human ------------- chr2:190955457-190955466 Template switch process: F1: L ACAAAATCCAGGGGCCATAAAAAGCTTCACTTCTTGGTGCA 1 F3: 4 GTTCATTGATCCTCACAGTGCTTAATGGGTGGGAAGTGGC R RF: ACAAAATCCAGTGGCCATAAAAAGCTTCACTTCTTGGTGCATTGTTCATTGATCCTCACAGTGCTTAATGGGTGGGAAGTGGC RR: TGTTTTAGGTCACCGGTATTTTTCGAAGTGAAGAACCACGTAACAAGTAACTAGGAGTGTCACGAATTACCCACCCTTCACCG F2: 3 GTAACAAGTA 2 Unidirectional alignment (log-probability: -34.4) CAAAATCCAGgGGCCATAAAAAGCTTCACTTCTTGGTGCaatgaacaATgGTTCATTGATCCTCACAGTGCTTAATGGGTGGGAAGTGGC CAAAATCCAGTGGCCATAAAAAGCTTCACTTCTTGGTGC--------ATTGTTCATTGATCCTCACAGTGCTTAATGGGTGGGAAGTGGC Template switch alignment (log-probability: -22.5) CAAAATCCAGgGGCCATAAAAAGCTTCACTTCTTGGTGCA|ATGAACAATG|GTTCATTGATCCTCACAGTGCTTAATGGGTGGGAAGTGGC CAAAATCCAGTGGCCATAAAAAGCTTCACTTCTTGGTGCA|ATGAACAATG|GTTCATTGATCCTCACAGTGCTTAATGGGTGGGAAGTGGC ========== Event 2139 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CACATTTGGAACTTGCTTTTTGTCTGATAATATCAATACCATTGATATTATCAGACAAATACCACATGCATGTCTG Chimp: CACATTTGGAACTTGCTTTTTGTCTGATAATATCAATGGTATTGATATTATCAGACAAATACCACATGCATGTCTG ↑ 1 4 3 2 Gorilla: CACATTTGGAACTTGCTTTTT---------------AGGTATTGATATTATCAGACAAATACCACATGCATGTCTG ↓ 1 3 4 2 Human: CACATTTGGAACTTGCTTTTTGTCTGATAATATCAATACCATTGATATTATCAGACAAATACCACATGCATGTCTG Cluster: [ ] Orangutan: CACATTTGGAACTTGCTTTTT---------------AGGTATTGATATTATCAGACAAATACCACATGCACGTCTG Gorilla > Human --------------- chr2:190884277-190884295 Template switch process: F1: L GTGTATTTGTGCAAAGTAGTCACATTTGGAACTTGCTTTTT 1 F3: 4 ATTGATATTATCAGACAAATACCACATGCATGTCTGTAGG R RF: GTGTATTTGTGCAAAGTATTCACATTTGGAACTTGCTTTTTAGGTATTGATATTATCAGACAAATACCACATGCATGTCTGTAGG RR: CACATAAACACGTTTCATAAGTGTAAACCTTGAACGAAAAATCCATAACTATAATAGTCTGTTTATGGTGTACGTACAGACATCC F2: 3 CCATAACTATAATAGTCTG 2 Unidirectional alignment (log-probability: -50.7) TGTATTTGTGCAAAGTAgTCACATTTGGAACTTGCTTTTT--GTctgataatatcaataccATTGATATTATCAGACAAATACCACATGCATGTCTGTAGG TGTATTTGTGCAAAGTATTCACATTTGGAACTTGCTTTTTAGGT-----------------ATTGATATTATCAGACAAATACCACATGCATGTCTGTAGG Template switch alignment (log-probability: -23.7) TGTATTTGTGCAAAGTAgTCACATTTGGAACTTGCTTTTT|GTCTGATAATATCAATACC|ATTGATATTATCAGACAAATACCACATGCATGTCTGTAGG TGTATTTGTGCAAAGTATTCACATTTGGAACTTGCTTTTT|GTCTGATAATATCAATACC|ATTGATATTATCAGACAAATACCACATGCATGTCTGTAGG Gorilla > Chimp --------------- chr2A:58999611-58999626 Template switch process: F1: L GTGTATTTGTGCAAAGTAGTCACATTTGGAACTTGCTTTTT 1 F3: 4 GGTATTGATATTATCAGACAAATACCACATGCATGTCTGT R RF: GTGTATTTGTGCAAAGTATTCACATTTGGAACTTGCTTTTTAGGTATTGATATTATCAGACAAATACCACATGCATGTCTGT RR: CACATAAACACGTTTCATAAGTGTAAACCTTGAACGAAAAATCCATAACTATAATAGTCTGTTTATGGTGTACGTACAGACA F2: 3 TAACTATAATAGTCTG 2 Unidirectional alignment (log-probability: -43.5) TGTATTTGTGCAAAGTAgTCACATTTGGAACTTGCTTTTTgtctgataatatcaatGGTATTGATATTATCAGACAAATACCACATGCATGTCTGT TGTATTTGTGCAAAGTATTCACATTTGGAACTTGCTTTTT---------------AGGTATTGATATTATCAGACAAATACCACATGCATGTCTGT Template switch alignment (log-probability: -23.3) TGTATTTGTGCAAAGTAgTCACATTTGGAACTTGCTTTTT|GTCTGATAATATCAAT|GGTATTGATATTATCAGACAAATACCACATGCATGTCTGT TGTATTTGTGCAAAGTATTCACATTTGGAACTTGCTTTTT|GTCTGATAATATCAAT|GGTATTGATATTATCAGACAAATACCACATGCATGTCTGT ========== Event 2140 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: TAATAAAATGGGAACAAAATG--GACAT-AAAGATC------ACATTATCTTCTAGGATAAAAATCTATTTCC Chimp: TAATAAAATGGGAACAAAATGGGAACATAGAAGATAATGTGATCTTTATCTTCTAGGATAAAAATCTATTTCC ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: TAATAAAATGGGAACAAAATG--GACAT-AAAGATC------ACATTATCTTCTAGGATAAAAATCTATTTCC Human: TAATAAAATGGGAACAAAATG--GACAT-AAAGATC------ACATTATCTTCTAGGATAAAAATCTATTTCC Cluster: [ ] Orangutan: TAATAAAATGGGAACAAAATG--GACAT-AAAGATC------ACATTATCTGCTAGGATAAAAATCTATTTCC Gorilla > Chimp --------------- chr2A:58586129-58586144 Template switch process: F1: L ATAAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGGGAACATA 1 F3: 4 TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT R RF: ATAAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGG--ACATAAAGATCACATTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT RR: TATTTAAAGTTTCCCACCATATTATTTTACCCTTGTTTTACC--TGTATTTCTAGTGTAATAGAAGATCCTATTTTTAGATAAAGGACAATTAGAACA F2: 3 TCTAGTGTAATAGAAG 2 Unidirectional alignment (log-probability: -54.4) AAAGGGTGGTATAATAAAATGGGAACAAAATGGgaacatagaagataatgtgatct--------------TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT AAAGGGTGGTATAATAAAATGGGAACAAAATGG-----------------------ACATAAAGATCACATTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT Template switch alignment (log-probability: -30.5) AAAGGGTGGTATAATAAAATGGGAACAAAATGGgaACATA|GAAGATAATGTGATCT|TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT AAAGGGTGGTATAATAAAATGGGAACAAAATGG--ACATA|GAAGATAATGTGATCT|TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT Chimp > Gorilla --------------- chr2A:55343460-55343473 Template switch process: F1: L ATAAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGG 1 F3: 4 TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT R RF: ATAAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGGGAACATAGAAGATAATGTGATCTTTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT RR: TATTTAAAGTTTCCCACCATATTATTTTACCCTTGTTTTACCCTTGTATCTTCTATTACACTAGAAATAGAAGATCCTATTTTTAGATAAAGGACAATTAGAACA F2: 3 ACACTAGAAATACA 2 Unidirectional alignment (log-probability: -41.9) AAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGG-----------------------acataaagatcacaTTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT AAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGGGAACATAGAAGATAATGTGATCT--------------TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT Template switch alignment (log-probability: -23.1) AAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGG|AcATAAAGATCACA|TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT AAATTTCAAAGGGTGGTATAATAAAATGGGAACAAAATGG|AGATAAAGATCACA|TTATCTTCTAGGATAAAAATCTATTTCCTGTTAATCTTGT ========== Event 2141 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTCTTACACTATTTTCATCTGTCATAACAGATGCCTCTTCTTATCCCCAAGAT ↑ 3 1 4 2 Chimp: AGTCTTACACTATTTTCATCTGTT-------ATGCCTCTTCTTATCCCCAAGAT Gorilla: AGTCTTACACTATTTTCATCTGTT-------ATGCCTCTTCTTATCCCCAAGAT ↓ 3 1 4 2 Human: AGTCTTACACTATTTTCATCTGTCATAACAGATGCCTCTTCTTATCCCCAAGAT Cluster: [ ] Orangutan: AGTCTTGCACTATTTTTGTCTCTT-------ATGCCTCTTCCTATCCCCAGGAT Chimp > Human ------------- chr2:189353004-189353011 Template switch process: F1: L CCCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT 1 F3: 4 ATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC R RF: CCCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGTTATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC RR: GGGTACCCTTCTTAACTCTCAGAATGTGATAAAAGTAGACAATACGGAGAAGAATAGGGGTTCTAAGTAGTGTTAAGTGAGG F2: 3 GACAATAC 2 Unidirectional alignment (log-probability: -27) CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGTcataacagATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT-------TATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC Template switch alignment (log-probability: -16.3) CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT|CATAACAG|ATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT|CATAACAG|ATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC Gorilla > Human --------------- chr2:189353004-189353011 Template switch process: F1: L CCCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT 1 F3: 4 ATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC R RF: CCCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGTTATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC RR: GGGTACCCTTCTTAACTCTCAGAATGTGATAAAAGTAGACAATACGGAGAAGAATAGGGGTTCTAAGTAGTGTTAAGTGAGG F2: 3 GACAATAC 2 Unidirectional alignment (log-probability: -26.5) CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGTcataacagATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT-------TATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC Template switch alignment (log-probability: -16.7) CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT|CATAACAG|ATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC CCATGGGAAGAATTGAGAGTCTTACACTATTTTCATCTGT|CATAACAG|ATGCCTCTTCTTATCCCCAAGATTCATCACAATTCACTCC ========== Event 2142 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATGAAATACAAAATAGCTTT------AATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAA Chimp: AATGAAATACAAAATAGCTTT------AATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAA ↓ 1 4 3 2 Gorilla: AATGAAATACAAAATAGCTTTTTTGTTCACATTGCATTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAA ↑ 1 4 3 2 Human: AATGAAATACAAAATAGCTTT------AATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAA Cluster: [ ] Orangutan: AATGAAATACAAAATAACTTT------AATCATGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTCATTAGAA Human > Gorilla --------------- chr2A:54582360-54582369 Template switch process: F1: L TTCATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT 1 F3: 4 TTGCATTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAAGCTG R RF: TTTATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTTAATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAAGCTG RR: AAATAGAAAACAAAAAAGATTTACTTTATGTTTTATCGAAATTAGAACGTCACGGTTACACTTGTTTTCTTCGGTTTCACTAATCTTCGAC F2: 3 ACACTTGTTT 2 Unidirectional alignment (log-probability: -44.9) TcATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTTtttgttcacA---TTGCAtTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG TTATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT---------AATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG Template switch alignment (log-probability: -28.2) TcATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT|TTTGTTCACA|TTGCAtTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG TTATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT|TTTGTTCACA|TTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG Chimp > Gorilla --------------- chr2A:54582360-54582369 Template switch process: F1: L TTCATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT 1 F3: 4 TTGCATTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAAGCTG R RF: TTTATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTTAATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAGAAGCTG RR: AAATAGAAAACAAAAAAGATTTACTTTATGTTTTATCGAAATTAGAACGTCACGGTTACACTTGTTTTCTTCGGTTTCACTAATCTTCGAC F2: 3 ACACTTGTTT 2 Unidirectional alignment (log-probability: -44.9) TcATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTTtttgttcacA---TTGCAtTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG TTATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT---------AATCTTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG Template switch alignment (log-probability: -28.2) TcATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT|TTTGTTCACA|TTGCAtTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG TTATCTTTTGTTTTTTCTAAATGAAATACAAAATAGCTTT|TTTGTTCACA|TTGCAGTGCCAATGTGAACAAAAGAAGCCAAAGTGATTAG ========== Event 2143 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATCAT-AGAGTAACAAAATAGCTTGAAGTGCTTGCCTGGTAACAGAGACAAGTTACTATAGAACAATGCCTAAGATTTAATGTTTACTCATTTACCACTATTACTCATAATTGAATAATAGATGGT Chimp: CGTCAT-AGAGTAACAAAATAGCTTGAAGTGCTTGCCTGGTAACAGAGACAAGTTACTATAGAACAATGCCTAAGATTTAATGTTTACTCATTTAC----------CATAATTGAATAATAGATGGT ↓ 3 2 4 1 Gorilla: CATCAT-AGAGTAACAAAATAGCTTGAAGTGCTTGCCTGGTAACAGAGACAAGTTACTATAGTACAATACCTAAGATTTAATGTTTACTCATTTACCGCTATTACTCATAATTGAATAATAGATGGT Human: CATCAT-AGAGTAACAAAATAGCTTGAAGTGCTTGCCTGGTAACAGAGACAAGTTACTATAGAACAATGCCTAAGATTTAATGTTTACTCATTTACCACTATTACTCATAATTGAATAATAGATGGT Cluster: [ ] Orangutan: CATCATGGGAGTAACAAAATAGCTTGAAGTGCTTGCCTGGTAACAGAGACAAGGTACTATAGAACAATGCCTAAGATTTAATGTTTACTCATTAACCACTATTANNNNNNNNNNNNNNNNNNNNNNN Chimp > Gorilla --------------- chr2A:53829836-53829839 Template switch process: F1: L GCTTGAAGTGCTTGCCTGGTAACAGAGACAAGTTACTATAGTACAATACCTAAGATTTAATGTTTACTCATTTACC 1 F3: 4 TTACTCAT R RF: TAGCTTGAAGTGCTTGCCTGGTAACAGAGACAAGTTACTATAGAACAATGCCTAAGATTTAATGTTTACTCATTTACC RR: ATCGAACTTCACGAACGGACCATTGTCTCTGTTCAATGATATCTTGTTACGGATTCTAAATTACAAATGAGTAAATGG F2: 3 ATCG 2 Unidirectional alignment (log-probability: -36.3) TATAGtACAATaCCTAAGATTTAATGTTTACTCATTTACcgctattactCAT TATAGAACAATGCCTAAGATTTAATGTTTACTCATTTAC----------CAT Template switch alignment (log-probability: -27.3) TATAGtACAATaCCTAAGATTTAATGTTTACTCATTTACC|GCTA|TTACTCAT TATAGAACAATGCCTAAGATTTAATGTTTACTCATTTACC|GCTA|TTACTCAT ========== Event 2144 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCAGCTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAATTCAGACCTCTTCTGTTACAGA Chimp: ACCAGCTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAATTCAGACCTCTTCCGTTACAGA ↓ 3 2 1 4 Gorilla: ACCAGCTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCAC------TGGTCAGACCTCTTCCGTTACAGA ↑ 3 2 1 4 Human: ACCAGCTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAATTCAGACCTCTTCTGTTACAGA Cluster: [ ] Orangutan: ACCAGCTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCAC------TGTTCAGACCTCTTCCATTACAGA Human > Gorilla --------------- chr2A:53294640-53294644 Template switch process: F1: L CTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC 1 F3: 4 TCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA R RF: CTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAATTCAGACCTCTTCTGTTACAGACTGTTTTTTAATTCCTTAA RR: GATTATGAAATTACGGTCAATTACACAACGGACATACCTAGACAAAAAATTAAGTCTGGAGAAGACAATGTCTGACAAAAAATTAAGGAATT F2: 3 GGTCA 2 Unidirectional alignment (log-probability: -33.9) TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC-----------actggTCAGACCTCTTCcGTTACAGACTGTTTTTTAATTCCTTAA TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAAT-----TCAGACCTCTTCTGTTACAGACTGTTTTTTAATTCCTTAA Template switch alignment (log-probability: -21.9) TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC|ACTGG|TCAGACCTCTTCcGTTACAGACTGTTTTTTAATTCCTTAA TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC|ACTGG|TCAGACCTCTTCTGTTACAGACTGTTTTTTAATTCCTTAA Chimp > Gorilla --------------- chr2A:53294640-53294644 Template switch process: F1: L CTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC 1 F3: 4 TCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA R RF: CTAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAATTCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA RR: GATTATGAAATTACGGTCAATTACACAACGGACATACCTAGACAAAAAATTAAGTCTGGAGAAGGCAATGTCTGACAAAAAATTAAGGAATT F2: 3 GGTCA 2 Unidirectional alignment (log-probability: -28.4) TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC-----------actggTCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATCTGTTTTTTAAT-----TCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA Template switch alignment (log-probability: -16.4) TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC|ACTGG|TCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA TAATACTTTAATGCCAGTTAATGTGTTGCCTGTATGGATC|ACTGG|TCAGACCTCTTCCGTTACAGACTGTTTTTTAATTCCTTAA ========== Event 2145 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTACCATAAGCATATGAACATGCACATAAACATGCACTAATATGTGCATATAAATATGCACTAATACCAATTAAAAGTCATCTCAT Chimp: TTACTATAAGCATATGAACATGCACATAAACATGCACTAATATGTGCATATAAATATGCACTAATACCAATTAAAAGCCATCCCAT ↑ 3 4 1 Gorilla: TTACTATAAGCATATGAACATGCAC------------------------ATAAATATGCACTAATACCAATTAAAAGTCATCTCAT ↓ 3 4 1 Human: TTACCATAAGCATATGAACATGCACATAAACATGCACTAATATGTGCATATAAATATGCACTAATACCAATTAAAAGTCATCTCAT Cluster: [ ] Orangutan: TTACTATAAGCATATGAACATGCAC------------------------ATAAATATGCACTAATACCAATTAAAAGTCATCTCAT Gorilla > Human --------------- chr2:54348753-54348759 Template switch process: F1: L ATATGTGCCAGATTTTTTACCATAAGCATATGAACATGCACATAAACATGCACTAATA 1 F3: 4 ATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT R RF: ATATGTGCCAGATTTTTTACTATAAGCATATGAACATGCACATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT RR: TATACACGGTCTAAAAAATGATATTCGTATACTTGTACGTGTATTTATACGTGATTATGGTTAATTTTCAGTAGAGTATCA F2: 3 TACGTGT 2 Unidirectional alignment (log-probability: -50.9) ACcATAAGCATATGAACATGCACataaacatgcactaatatgtgcatATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT ACTATAAGCATATGAACATGCAC------------------------ATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT Template switch alignment (log-probability: -28.1) ACcATAAGCATATGAACATGCACATAAAcATGCACTAATA|TGTGCAT|ATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT ACTATAAGCATATGAACATGCACATAAATATGCACTAATA|TGTGCAT|ATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT Gorilla > Chimp --------------- chr2A:55567657-55567663 Template switch process: F1: L ATATGTGCCAGATTTTTTACTATAAGCATATGAACATGCACATAAACATGCACTAATA 1 F3: 4 ATAAATATGCACTAATACCAATTAAAAGCCATCCCATAGT R RF: ATATGTGCCAGATTTTTTACTATAAGCATATGAACATGCACATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT RR: TATACACGGTCTAAAAAATGATATTCGTATACTTGTACGTGTATTTATACGTGATTATGGTTAATTTTCAGTAGAGTATCA F2: 3 TACGTGT 2 Unidirectional alignment (log-probability: -56.4) ACTATAAGCATATGAACATGCACataaacatgcactaatatgtgcatATAAATATGCACTAATACCAATTAAAAGcCATCcCATAGT ACTATAAGCATATGAACATGCAC------------------------ATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT Template switch alignment (log-probability: -33.6) ACTATAAGCATATGAACATGCACATAAAcATGCACTAATA|TGTGCAT|ATAAATATGCACTAATACCAATTAAAAGcCATCcCATAGT ACTATAAGCATATGAACATGCACATAAATATGCACTAATA|TGTGCAT|ATAAATATGCACTAATACCAATTAAAAGTCATCTCATAGT ========== Event 2146 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GAATGGCAATTTGTGTTAATCAA--AGGGATCAAAAATAGATTTTTTGGGCAAAGTTTA Chimp: GAATGGCAATTTGTGTTAATCAA--AGGGATCAAAAATAGATTTTTTGGGCAAAGTTTA Gorilla: GAATGGCAATTTGTGTTAATCTATTTTTGATCA-AAATAGATTTTTTGGGCAAAGTTTA ↑ 1 3 4 2 Human: GAATGGCAATTTGTGTTAATCAA--AGGGATCAAAAATAGATTTTTTGGGCAAAGTTTA Cluster: [ ] Orangutan: GAATGGCAATTTGTATTAATCAA--AGGGATCA-AAATAGATTTTTTGGGCAAAGTTTA Human > Gorilla --------------- chr2A:54915139-54915149 Template switch process: F1: L TCCCCCAGGAAAAGTACAGAGAATGGCAATTTGTGTTAATC 1 F3: 4 AAAATAGATTTTTTGGGCAAAGTTTAAGAACTTAAGTTTTC R RF: TCCCCCAGGAAAAGTACAGAGAATGGCAATTTGTGTTAATCAAAGGGATCAAAAATAGATTTTTTGGGCAAAGTTTAAGAACTTAAGTTTTC RR: AGGGGGTCCTTTTCATGTCTCTTACCGTTAAACACAATTAGTTTCCCTAGTTTTTATCTAAAAAACCCGTTTCAAATTCTTGAATTCAAAAG F2: 3 CTAGTTTTTAT 2 Unidirectional alignment (log-probability: -37) CCCCCAGGAAAAGTACAGAGAATGGCAATTTGTGTTAATC----------tatttttgatcAAAATAGATTTTTTGGGCAAAGTTTAAGAACTTAAGTTTT CCCCCAGGAAAAGTACAGAGAATGGCAATTTGTGTTAATCAAAGGGATCA-----------AAAATAGATTTTTTGGGCAAAGTTTAAGAACTTAAGTTTT Template switch alignment (log-probability: -17.2) CCCCCAGGAAAAGTACAGAGAATGGCAATTTGTGTTAATC|TATTTTTGATC|AAAATAGATTTTTTGGGCAAAGTTTAAGAACTTAAGTTTT CCCCCAGGAAAAGTACAGAGAATGGCAATTTGTGTTAATC|TATTTTTGATC|AAAATAGATTTTTTGGGCAAAGTTTAAGAACTTAAGTTTT ========== Event 2147 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTGAGTGGGAAAGTTACTTCA----TTCATTCATTCATGGGTACTTTTCTGTGCCGGGGG ↓ 1 4 3 2 Chimp: AGTGAGTGGGAAAGTTACTTCCCATGAATATTCATTCATGGGTACTTTTCTGTGCCGGGGG ↑ 1 4 3 2 Gorilla: AGTGAGTGGGAAAGTTACTTCA----TTCATTCATTCATGGGTACTTTTCTGTGCCGGGGG Human: AGTGAGTGGGAAAGTTACTTCA----TTCATTCATTCATGGGTACTTTTCTGTGCCGGGGG Cluster: [ ] Orangutan: AGTGAGTGGGAAAGTTACTTCA----TTCATTCATTCACGGGTACTTTTCTGTGCCGCGGG Human > Chimp ------------- chr2A:57453071-57453078 Template switch process: F1: L GTGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC 1 F3: 4 ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAGCTTCT R RF: GTGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTCATTCATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAACTTCT RR: CACACTATGTCCGGAATTTGTCACTCACCCTTTCAATGAAGTAAGTAAGTAAGTACCCATGAAAAGACACGGCCCCCTTTGAAGA F2: 3 TAAGTACC 2 Unidirectional alignment (log-probability: -35.9) TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTCccatgaAT--ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAgCTTCT TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC------ATTCATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAACTTCT Template switch alignment (log-probability: -22.3) TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC|CCATGAAT|ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAgCTTCT TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC|CCATGAAT|ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAACTTCT Gorilla > Chimp --------------- chr2A:57453071-57453078 Template switch process: F1: L GTGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC 1 F3: 4 ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAGCTTCT R RF: GTGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTCATTCATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAACTTCT RR: CACACTATGTCCGGAATTTGTCACTCACCCTTTCAATGAAGTAAGTAAGTAAGTACCCATGAAAAGACACGGCCCCCTTTGAAGA F2: 3 TAAGTACC 2 Unidirectional alignment (log-probability: -34.9) TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTCccatgaAT--ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAgCTTCT TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC------ATTCATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAACTTCT Template switch alignment (log-probability: -22.3) TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC|CCATGAAT|ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAgCTTCT TGTGATACAGGCCTTAAACAGTGAGTGGGAAAGTTACTTC|CCATGAAT|ATTCATTCATGGGTACTTTTCTGTGCCGGGGGAAACTTCT ========== Event 2148 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAGAGATAAAACATTTGTTTAGTC--ATGATTTTCTCTTTATACTAGAGTATAGCTGACTTTT-TTCATCGAGACAGATG Chimp: GAAGAGATAAAACATTTGTTTAGTC--ATGATTTTCTCTTTATACTAGAGTATAGCTGACTTTT-TTCATCGAGACAGATG ↑ 1 4 3 2 Gorilla: GAAGAGATAAAACATTTGTTTTATCTTCTTATTTTCTCTTTATACTAGAGTATAGCTGACTTTT-TTCATCGAGACGGATG ↓ 1 4 3 2 Human: GAAGAGATAAAACATTTGTTTAGTC--ATGATTTTCTCTTTATACTAGAGTATAGCTGACTTTT-TTCATCGAGACAGATG Cluster: [ ] Orangutan: GAAGAGATAAAACATTTGTTTAGTC--ATGATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTGTCATCCAGACAGATG Gorilla > Human --------------- chr2:55800560-55800564 Template switch process: F1: L AAAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTT 1 F3: 4 TGATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCATC R RF: AAAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTTTATCTTCTTATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCATC RR: TTTCAAAATTTATGAAATATCTTCTCTATTTTGTAAACAAAATAGAAGAATAAAAGAGAAATATGATCTCATATCGACTGAAAAAAGTAG F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -31.2) AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGT---------TTagtcatgATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTTTATCTTCTT-------ATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA Template switch alignment (log-probability: -21.9) AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTT|AGTCA|TgATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTT|AGTCA|TTATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA Gorilla > Chimp --------------- chr2A:57058760-57058764 Template switch process: F1: L AAAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTT 1 F3: 4 TGATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCATC R RF: AAAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTTTATCTTCTTATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCATC RR: TTTCAAAATTTATGAAATATCTTCTCTATTTTGTAAACAAAATAGAAGAATAAAAGAGAAATATGATCTCATATCGACTGAAAAAAGTAG F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -31.2) AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGT---------TTagtcatgATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTTTATCTTCTT-------ATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA Template switch alignment (log-probability: -21.9) AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTT|AGTCA|TgATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA AAGTTTTAAATACTTTATAGAAGAGATAAAACATTTGTTT|AGTCA|TTATTTTCTCTTTATACTAGAGTATAGCTGACTTTTTTCA ========== Event 2149 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGAAGAAATCATGCACTGGCCCACACTAGTTGGATATCTGGGGCTGCTCTGtttttttttt----tttttt------ttttttttttAAATCTCTTTCTAAACCTGGTTCTAGCTATTTGTTTGATTCTGCGA ↑ 1 4 3 2 Chimp: CTGAAGAAATCATGCACTGGCACACAGTACTTGGATATCTGGGGCTGCTCTGtttttttttt----------ttttttttttttttttAAATCTCTTTCTAAACCTAGTTCTAGCTATTTCTTTGATTCTGCGA Gorilla: CTGAAGAAATCATGCACTGGCACACACTACTTGGATATCTGGGGCTGCTCTGtttttttttttttt------------ttttttttttAAATCTCTTTCTAAACCTAGTTCTAGCTATTTCTTTGATTCTGCGA Human: CTGAAGAAATCATGCACTGGCCCACACTAGTTGGATATCTGGGGCTGCTCTGtttttttttt----tttttt------ttttttttttAAATCTCTTTCTAAACCTGGTTCTAGCTATTTGTTTGATTCTGCGA Cluster: [ ] Orangutan: CTGAAGAAATCATGCACTGGCACACACTACTTGGGTATCTGTGGCTGCTCTGtttttttttt----------------------tttttAATCTCTTTCTAGATCTAGTTCTAGCTATTTCTTTGATTCTGTGA Chimp > Human ------------- chr2:56643214-56643217 Template switch process: F1: L CACAGCTCTAGCAGAGTTCTCTGAAGAAATCATGCACTGGCCCACA 1 F3: 4 TTGGATATCTGGGGCTGCTCTGTTTTTTTTTTTTTTTT R RF: CACAGCTCTAGCAGAGTTCTCTGAAGAAATCATGCACTGGCACACAGTACTTGGATATCTGGGGCTGCTCTGTTTTTTTTTTTTTTTTTTTTTTTTTTAAATCTCTTTCTAAACCTAGTTCTAG RR: GTGTCGAGATCGTCTCAAGAGACTTCTTTAGTACGTGACCGTGTGTCATGAACCTATAGACCCCGACGAGACAAAAAAAAAAAAAAAAAAAAAAAAAATTTAGAGAAAGATTTGGATCAAGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -31.7) TCTAGCAGAGTTCTCTGAAGAAATCATGCACTGGCcCACAcTAgTTGGATATCTGGGGCTGCTCTGTTTTTTTTTTTTtttt TCTAGCAGAGTTCTCTGAAGAAATCATGCACTGGCACACAGTACTTGGATATCTGGGGCTGCTCTGTTTTTTTTTTTT---- Template switch alignment (log-probability: -21.8) TCTAGCAGAGTTCTCTGAAGAAATCATGCACTGGCcCACA|CTAG|TTGGATATCTGGGGCTGCTCTGTTTTTTTTTTTTTTTT TCTAGCAGAGTTCTCTGAAGAAATCATGCACTGGCACACA|CTAG|TTGGATATCTGGGGCTGCTCTGTTTTTTTTTTTTTTTT ========== Event 2150 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGGCAATAATTTAAATCAC---AATTTCCTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCACTTGGGGGAAGCAATGTGTCCTGGATGTAGCCCAA Chimp: AGAGGCAATAATTTAAATCAC---AATTGCTTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCACTTGGGGGAAGCAGTGTGTCCTGGATGTAGCCCAA ↑ 1 4 3 2 Gorilla: AGAGGCAATAATTTAAATCAC------ATCCTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCACTTGCGGGAAGCAATGTGTCCTGGATGTAGCCCAA Human: AGAGGCAATAATTTAAATCAC---AATTTCCTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCACTTGGGGGAAGCAATGTGTCCTGGATGTAGCCCAA Cluster: [ ] Orangutan: AGAGGCAATAATTTAAATCACAAT---TTCCTGATGCTAAACAAGTGTACCATGTTCTCCTAGAACCAGCACTTGGGGGAAGCACTGTGTCCTGGATGTAGCCCAA Gorilla > Chimp --------------- chr2A:58804621-58804626 Template switch process: F1: L GCCACTTTCCAGGAGAAAGAAGAGGCAATAATTTAAATCACA 1 F3: 4 TGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCA R RF: GCCACTTTCCAGGAGAAAGAAGAGGCAATAATTTAAATCACATCCTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCACTTGCGGGAAGCAAT RR: CGGTGAAAGGTCCTCTTTCTTCTCCGTTATTAAATTTAGTGTAGGACTACGATTTGTTCACATGGTACAAGAGGGTCTTGATCGTGAACGCCCTTCGTTA F2: 3 TCGTTA 2 Unidirectional alignment (log-probability: -26.3) CACTTTCCAGGAGAAAGAAGAGGCAATAATTTAAATCACAattgCtTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCA CACTTTCCAGGAGAAAGAAGAGGCAATAATTTAAATCACAT---CCTGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCA Template switch alignment (log-probability: -16.5) CACTTTCCAGGAGAAAGAAGAGGCAATAATTTAAATCACA|ATTGCT|TGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCA CACTTTCCAGGAGAAAGAAGAGGCAATAATTTAAATCACA|ATTGCT|TGATGCTAAACAAGTGTACCATGTTCTCCCAGAACTAGCA ========== Event 2151 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: --------TATTTCTTGCATACGTCAT-------ATGAATGACAGAAGTATACTGAAAAGCATA Chimp: --------TATTTCTTGCATATGTCAT-------ATGAATGACAGAAGTATACTGAAAAGCATA ↑ 1 4 3 2 Gorilla: --------TATTTCTTGCATACATCATATAGGTGATGAATGACAGAAGTATACTGAAAAGCATA Human: --------TATTTCTTGCATACGTCAT-------ATGAATGACAGAAGTATACTGAAAAGCATA Cluster: [ ] Orangutan: ATTTGAAATATTTCTTGCATACGTCATATAGGTGATGAATGGCAGAAGTATATTGAAAAGCATA Gorilla > Chimp --------------- chr2A:60905145-60905150 Template switch process: F1: L TAAAAGGATGTCTCAGCTTTTGAGGAAATATTTCTTGCATA 1 F3: 4 ATGAATGACAGAAGTATACTGAAAAGCATATTAGCAA R RF: TAAAAGGATGTCTCAGCTTTTGAGGAAATATTTCTTGCATACATCATATAGGTGATGAATGACAGAAGTATACTGAAAAGCATATTAGCAA RR: ATTTTCCTACAGAGTCGAAAACTCCTTTATAAAGAACGTATGTAGTATATCCACTACTTACTGTCTTCATATGACTTTTCGTATAATCGTT F2: 3 TACTGT 2 Unidirectional alignment (log-probability: -29.2) AAAAGGATGTCTCAGCTTTTGAGGAAATATTTCTTGCATAtgTCAT-------ATGAATGACAGAAGTATACTGAAAAGCATATTAGCAA--- AAAAGGATGTCTCAGCTTTTGAGGAAATATTTCTTGCATACATCATATAGGTGATGAATGACAGAAGTATACTGAAAAGCATATTAGCAAACA Template switch alignment (log-probability: -16.4) AAAAGGATGTCTCAGCTTTTGAGGAAATATTTCTTGCATA|TGTCAT|ATGAATGACAGAAGTATACTGAAAAGCATATTAGCAA AAAAGGATGTCTCAGCTTTTGAGGAAATATTTCTTGCATA|TGTCAT|ATGAATGACAGAAGTATACTGAAAAGCATATTAGCAA ========== Event 2152 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGACTTGAACTGAATTTCAGTCAGTAAAGGAACAACTGTC ↑ 4 3 2 1 Chimp: GTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGA---G--------AGCACTCAGTAAAGGAACAACTGTC Gorilla: GTTTCTGGAATCATAGTTCAATTTCATTTCAAGTTACGA---G--------AGCACTCAGTAAAGGAACAACTGTC Human: GTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGACTTGAACTGAATTTCAGTCAGTAAAGGAACAACTGTC Cluster: [ ] Orangutan: GTTTCTGAAATCATAGTTCAATTTCAGTTCAAGTTAAGA---G--------AGCACTCAGTAAAGGAACAACTGTC Chimp > Human ------------- chr2:58612861-58612869 Template switch process: F1: L TTGTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGA 1 F3: 4 AATTTCAG------------------TCAGTAAAGGAACAACTGTCAAAAAGGTTCTGTCTTGATA R RF: TTGTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGAGAGCACTCAGTAAAGGAACAACTGTCAAAAAGGTTCTGTCTTGATA RR: AACAAAGACCTTAGTATCAAGTTAAAGTCAAGTTCAATCCTCTCGTGAGTCATTTCCTTGTTGACAGTTTTTCCAAGACAGAACTAT F2: 3 GTCAAGTTC 2 Unidirectional alignment (log-probability: -44.4) TGTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGG-----ACttgaactgaatttcagTCAGTAAAGGAACAACTGTCAAAAAGGTTCTG TGTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGAGAGCAC----------------TCAGTAAAGGAACAACTGTCAAAAAGGTTCTG Template switch alignment (log-probability: -27.7) TGTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGA|CTTGAACTG|AATTTCAG------------------TCAGTAAAGGAACAACTGTCAAAAAGGTTCTG TGTTTCTGGAATCATAGTTCAATTTCAGTTCAAGTTAGGA|CTTGAACTG|AATTTCAGTTCAAGTTAGGAGAGCACTCAGTAAAGGAACAACTGTCAAAAAGGTTCTG ========== Event 2153 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AATTGTAGATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAATTTTAATTACACTTTAGTGTAATTAAAGTGTAAAGTAAAATTAAAGTGTAAATTGCACTGGCCAAGTGAGAG ↓ 3 2 1 4 Chimp: AATTGTAGATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTA--------------------------------------------AAAGCCTCCATTGCACTGGCCAAGTGAGAG Gorilla: AATTGTAGATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTA--------------------------------------------AAAGCCTCCATTGCACTGGCCAAGTGAGAG ↑ 3 2 1 4 Human: AATTGTAGATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAATTTTAATTACACTTTAGTGTAATTAAAGTGTAAAGTAAAATTAAAGTGTAAATTGCACTGGCCAAGTGAGAG Cluster: [ ] Orangutan: AATTGTAGATAGGTGTGAAGTAGGCTAAAACAATATAATTAAAGTGTA--------------------------------------------AAAGCCTCCATTGCACTGGCCAAATGAGAG Human > Chimp ------------- chr2A:60116908-60116914 Template switch process: F1: L GATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA 1 F3: 4 ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG R RF: GATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAATTTTAATTACACTTTAGTGTAATTAAAGTGTAAAGTAAAATTAAAGTGTAAATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG RR: CTATCCACACTTCATCCGATTTTGTTATGTTAATTTCACATTTAAAATTAATGTGAAATCACATTAATTTCACATTTCATTTTAATTTCACATTTAACGTGACCGGTTCACTCTCTTGACCCGTCTTGTGTCCC F2: 3 CCTCCGA 2 Unidirectional alignment (log-probability: -32.4) AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA--------------------------------------------------AgcctccATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAATTTTAATTACACTTTAGTGTAATTAAAGTGTAAAGTAAAATTAAAGTGTAA------ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG Template switch alignment (log-probability: -22.2) AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA|AGCCTcC|ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA|AGCCTAC|ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG Human > Gorilla --------------- chr2A:59554340-59554346 Template switch process: F1: L GATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA 1 F3: 4 ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG R RF: GATAGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAATTTTAATTACACTTTAGTGTAATTAAAGTGTAAAGTAAAATTAAAGTGTAAATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG RR: CTATCCACACTTCATCCGATTTTGTTATGTTAATTTCACATTTAAAATTAATGTGAAATCACATTAATTTCACATTTCATTTTAATTTCACATTTAACGTGACCGGTTCACTCTCTTGACCCGTCTTGTGTCCC F2: 3 CCTCCGA 2 Unidirectional alignment (log-probability: -31.9) AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAA--------------------------------------------------AAgcctccATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAATTTTAATTACACTTTAGTGTAATTAAAGTGTAAAGTAAAATTAAAGTGTAA------ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG Template switch alignment (log-probability: -22.2) AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA|AGCCTcC|ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG AGGTGTGAAGTAGGCTAAAACAATACAATTAAAGTGTAAA|AGCCTAC|ATTGCACTGGCCAAGTGAGAGAACTGGGCAGAACACAGGG ========== Event 2154 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGGGCTAAACTGAAAGACACAGATACTGTAAGGCCAAGAATGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCGTCTGTATTTATGTTCACTTTTCCACC Chimp: AAGGGCTAAACTGAAAGACACAGATACTGTAAGGCCAAGAATGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCATCTGTATTTATGTTCACTTT------ ↑ 3 2 1 4 Gorilla: AAGGGCTAAACTGAAAGACACAGATACTGTAAGGCCAAGAATGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCGTCCATATTTATGTTCACTTTTCCACC Human: AAGGGCTAAACTGAAAGACACAGATACTGTAAGGCCAAGAATGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCGTCTGTATTTATGTTCACTTTTCCACC Cluster: [ ] Orangutan: AAGGGCTAAACTGAAAGACACAGATACTGTAAGGCCAAGAATGTGGATATGGTTTTTAGTAATTACCTTCCCCTGCTGTGTATCTGTATTTATGTTCACTTTTCCACC Gorilla > Chimp --------------- chr2A:60263100-60263105 Template switch process: F1: L ATGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGC 1 F3: 4 ATTTATGTTCACTTTTCCA R RF: ACAGATACTGTAAGGCCAAGAATGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCGTCCATATTTATGTTCACTTTTCCA RR: TGTCTATGACATTCCGGTTCTTACACCTACACCAAAAATCATTAAAGGAAGGGGACGACACGCAGGTATAAATACAAGTGAAAAGGT F2: 3 TGTCTA 2 Unidirectional alignment (log-probability: -25.3) TGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCaTCtgTATTTATGTTCACTTTTCCA-------------------- TGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGCGTCCATATTTATGTTCACTTTTCCACCACCTCTTTTGGGTTTCCA Template switch alignment (log-probability: -15.9) TGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGC|ATCTGT|ATTTATGTTCACTTTTCCA TGTGGATGTGGTTTTTAGTAATTTCCTTCCCCTGCTGTGC|ATCTGT|ATTTATGTTCACTTTTCCA ========== Event 2155 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGAAAACGATACCCCATACATTACATGTTCGGTTGTGGGATAGAAATG Chimp: ATGAT-------------------------------------------- Gorilla: ATGAAAAAGATACCCCATACA---TGTATTCGGTTGTGGGATAGAAATG ↓ 3 1 24 Human: ATGAAAACGATACCCCATACATTACATGTTCGGTTGTGGGATAGAAATG Cluster: [ ] Orangutan: ATGAAAAAGATACCCCATACA---TGTATTCGGTTGTGGGATAGAAATG Gorilla > Human --------------- chr2:61569061-61569066 Template switch process: F1: L AGTTAAAATTAAAATCTGAAATGAAAACGATACCCCATACAT 1 F3: 4 TTCGGTTGTGGGATAGAAATGTCTCTTAAATTATTTTTTG R RF: AGTTAAAATTAAAATCTGAAATGAAAAAGATACCCCATACATGTATTCGGTTGTGGGATAGAAATGTCTCTTAAATTATTTTTTG RR: TCAATTTTAATTTTAGACTTTACTTTTTCTATGGGGTATGTACATAAGCCAACACCCTATCTTTACAGAGAATTTAATAAAAAAC F2: 3 GTACAT 2 Unidirectional alignment (log-probability: -31.8) TTAAAATTAAAATCTGAAATGAAAAcGATACCCCATACATtacaTgTTCGGTTGTGGGATAGAAATGTCTCTTAAATTATTTTTTG TTAAAATTAAAATCTGAAATGAAAAAGATACCCCATACATG---TATTCGGTTGTGGGATAGAAATGTCTCTTAAATTATTTTTTG Template switch alignment (log-probability: -22) TTAAAATTAAAATCTGAAATGAAAAcGATACCCCATACAT|TACATG|TTCGGTTGTGGGATAGAAATGTCTCTTAAATTATTTTTTG TTAAAATTAAAATCTGAAATGAAAAAGATACCCCATACAT|TACATG|TTCGGTTGTGGGATAGAAATGTCTCTTAAATTATTTTTTG ========== Event 2156 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: -------------GTAAAATAATTACACTAGTAATTA-AGGTGGCACTAAGACTAACAAGTATTCCTT Chimp: gattctcatttcagtaaaatAGTGCCAA-CTTAATTACTAGTGTAATTAAGACTAACAAGTATTCCTT Gorilla: -------------GTAAAATAGTGCCAA-TTTAATTACTAGTGTAATTAAGACTAACAAGTATTCCTT ↓ 13 24 ↑ 13 24 Human: -------------GTAAAATAATTACACTAGTAATTA-AGGTGGCACTAAGACTAACAAGTATTCCTT Cluster: [ ] Orangutan: -------------GTAAAATAGTACCAA-CTTAATTACTAGTGTAATTAAGACTAACAA--GTTCCTT Gorilla > Human --------------- chr2:178303217-178303241 Template switch process: F1: L AATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATA 1 F3: 4 TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT R RF: AATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATAGTGCCAATTTAATTACTAGTGTAATTAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT RR: TTATCACTAGGATAAAATTTCTAAGAGTAAAGTCATTTTATCACGGTTAAATTAATGATCACATTAATTCTGATTGTTCATAAGGAATTTCATTTACATTTAAATA F2: 3 CACGGTGGAATTAATGATCACATTA 2 Unidirectional alignment (log-probability: -54.9) ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAAT-----------------------AATtacactagtaattaaggtggcacTAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATAGTGCCAATTTAATTACTAGTGTAAT-----------------------TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT Template switch alignment (log-probability: -29.9) ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATA|ATTACACTAGTAATTAAggTGGCAC|TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATA|ATTACACTAGTAATTAAATTGGCAC|TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT Human > Gorilla --------------- chr2A:42990204-42990228 Template switch process: F1: L AATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATA 1 F3: 4 TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT R RF: AATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATAATTACACTAGTAATTAAGGTGGCACTAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT RR: TTATCACTAGGATAAAATTTCTAAGAGTAAAGTCATTTTATTAATGTGATCATTAATTCCACCGTGATTCTGATTGTTCATAAGGAATTTCATTTACATTTAAATA F2: 3 TAATGTGATCATTAATTTAACCGTG 2 Unidirectional alignment (log-probability: -54.9) ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAAtagtgccaatttaattactagtgTAAT-----------------------TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAA-----------------------TAATTACACTAGTAATTAAGGTGGCACTAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT Template switch alignment (log-probability: -29.9) ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATA|GTGCCAatTTAATTACTAGTGTAAT|TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT ATAGTGATCCTATTTTAAAGATTCTCATTTCAGTAAAATA|GTGCCACCTTAATTACTAGTGTAAT|TAAGACTAACAAGTATTCCTTAAAGTAAATGTAAATTTAT ========== Event 2157 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: TGTGCTATTCCACTAGATAGT-GCTACCACCCACTTCCAA---CAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTG ↓ 13 24 ↑ 13 24 Chimp: TGTGCTATTCCACTAGATAGTCTCCCCCATCCACAGCCCATCATGGCTGCTCAAC---TGTTGGAAGTGGGTGGTA-GCACTAACAGTCAGCTCAGAGTG ↓ 13 24 ↑ 13 24 Gorilla: TGTGCTATTCCACTAGATAGT-GCTACCACCCACTTCCAA---CAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTG Human: TGTGCTATTCCACTAGATAGT-GCTACCACCCACTTCCAA---CAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTG Cluster: [ ] Orangutan: TGTGCTATTCCACTAGATAGT-GCTACCACCGACTTCCAA---CAGTTGAGCAGCCATGATGGGCTATGGATGGGGGAGACTAACAGTCAGCTCAGAGTG Chimp > Human ------------- chr2:64582265-64582318 Template switch process: F1: L TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT 1 F3: 4 ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC R RF: TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTCTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGCACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC RR: AGGACTCTTAAGTGACCAAAACACGATAAGGTGATCTATCAGAGGGGGTAGGTGTCGGGTAGTACCGACGAGTTGACAACCTTCACCCACCATCGTGATTGTCAGTCGAGTCTCACTTGGACCCTGGATCCTACG F2: 3 GAGGGGGTAGGTGTCGGGTAGTACCGACGAGTTGACAACCTTCACCCACCATCG 2 Unidirectional alignment (log-probability: -98.6) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT----------------------------------------------------GCtaccacccacttccaacagttgagcagccatgatgggctgtggatgggggagACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTCTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGC----------------------------------------------------ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Template switch alignment (log-probability: -21.9) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|GCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAG|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|GCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAG|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Human > Chimp ------------- chr2A:65943946-65943999 Template switch process: F1: L TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT 1 F3: 4 ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC R RF: TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTGCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC RR: AGGACTCTTAAGTGACCAAAACACGATAAGGTGATCTATCACGATGGTGGGTGAAGGTTGTCAACTCGTCGGTACTACCCGACACCTACCCCCTCTGATTGTCAGTCGAGTCTCACTTGGACCCTGGATCCTACG F2: 3 CGATGGTGGGTGAAGGTTGTCAACTCGTCGGTACTACCCGACACCTACCCCCTC 2 Unidirectional alignment (log-probability: -98.6) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTctcccccatccacagcccatcatggctgctcaactgttggaagtgggtggtaGC----------------------------------------------------ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT----------------------------------------------------GCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Template switch alignment (log-probability: -21.9) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|CTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGC|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|CTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGC|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Gorilla > Chimp --------------- chr2A:65943946-65943999 Template switch process: F1: L TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT 1 F3: 4 ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC R RF: TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTGCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC RR: AGGACTCTTAAGTGACCAAAACACGATAAGGTGATCTATCACGATGGTGGGTGAAGGTTGTCAACTCGTCGGTACTACCCGACACCTACCCCCTCTGATTGTCAGTCGAGTCTCACTTGGACCCTGGATCCTACG F2: 3 CGATGGTGGGTGAAGGTTGTCAACTCGTCGGTACTACCCGACACCTACCCCCTC 2 Unidirectional alignment (log-probability: -98.1) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTctcccccatccacagcccatcatggctgctcaactgttggaagtgggtggtaGC----------------------------------------------------ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT----------------------------------------------------GCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAGACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Template switch alignment (log-probability: -22.6) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|CTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGC|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|CTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGC|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Chimp > Gorilla --------------- chr2A:65360393-65360446 Template switch process: F1: L TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT 1 F3: 4 ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC R RF: TCCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTCTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGCACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC RR: AGGACTCTTAAGTGACCAAAACACGATAAGGTGATCTATCAGAGGGGGTAGGTGTCGGGTAGTACCGACGAGTTGACAACCTTCACCCACCATCGTGATTGTCAGTCGAGTCTCACTTGGACCCTGGATCCTACG F2: 3 GAGGGGGTAGGTGTCGGGTAGTACCGACGAGTTGACAACCTTCACCCACCATCG 2 Unidirectional alignment (log-probability: -98.1) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT----------------------------------------------------GCtaccacccacttccaacagttgagcagccatgatgggctgtggatgggggagACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGTCTCCCCCATCCACAGCCCATCATGGCTGCTCAACTGTTGGAAGTGGGTGGTAGC----------------------------------------------------ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC Template switch alignment (log-probability: -22.6) CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|GCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAG|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC CCTGAGAATTCACTGGTTTTGTGCTATTCCACTAGATAGT|GCTACCACCCACTTCCAACAGTTGAGCAGCCATGATGGGCTGTGGATGGGGGAG|ACTAACAGTCAGCTCAGAGTGAACCTGGGACCTAGGATGC ========== Event 2158 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGTGAGGGGAGAGGCTGCCCA------CTCCTCTGAGGGACATGCATCGAGCCCAG Chimp: AGGTGAGGGGAGAGGCTGCCCG------CTCCTCTGAGGGACATGCATCGAGCCCAG ↓ 1 3 4 2 Gorilla: AGGTGAGGGGAGAGGCTGCCCTCAGAGGAGCCTCTGAGGGACATGCATCGAGCCCAG Human: AGGTGAGGGGAGAGGCTGCCCA------CTCCTCTGAGGGACATGCATCGAGCCCAG Cluster: [ ] Orangutan: AGGTGAGGGGAGAGGCTGCCTG------CTCCTCTGAGGGACATGCATCAAGCCCAG Chimp > Gorilla --------------- chr2A:66089288-66089297 Template switch process: F1: L ACAGAAAGGCACTGTGGAGGAGGTGAGGGGAGAGGCTGCCC 1 F3: 4 CTCTGAGGGACATGCATCGAGCCCAGCCTCTGTAGTGAC R RF: ACAGAAAGGCACTGTGGAGGAGGTGAGGGGAGAGGCTGCCCGCTCCTCTGAGGGACATGCATCGAGCCCAGCCTCTGTAGTGAC RR: TGTCTTTCCGTGACACCTCCTCCACTCCCCTCTCCGACGGGCGAGGAGACTCCCTGTACGTAGCTCGGGTCGGAGACATCACTG F2: 3 CGAGGAGACT 2 Unidirectional alignment (log-probability: -30.6) CAGAAAGGCACTGTGGAGGAGGTGAGGGGAGAGGCTGCCCtcagagGagCCTCTGAGGGACATGCATCGAGCCCAGCCTCTGTAGTGAC CAGAAAGGCACTGTGGAGGAGGTGAGGGGAGAGGCTGCCC------GCTCCTCTGAGGGACATGCATCGAGCCCAGCCTCTGTAGTGAC Template switch alignment (log-probability: -17) CAGAAAGGCACTGTGGAGGAGGTGAGGGGAGAGGCTGCCC|TCAGAGGAGC|CTCTGAGGGACATGCATCGAGCCCAGCCTCTGTAGTGAC CAGAAAGGCACTGTGGAGGAGGTGAGGGGAGAGGCTGCCC|TCAGAGGAGC|CTCTGAGGGACATGCATCGAGCCCAGCCTCTGTAGTGAC ========== Event 2159 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATAAAAGCAGAGAGGAGTTTGGACAGTTTAATCACAATCT----ACACGTGGCCCAGCAGCTTGAAGAGGT Chimp: TATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCACAATCT----ACACGTGGCCCAGCAGCTTGAAGGGGT ↓ 3 2 1 4 Gorilla: TATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCACTGTCC--------AAGGCCCAGCAGCTTGAAGGGGT ↑ 3 2 1 4 Human: TATAAAAGCAGAGAGGAGTTTGGACAGTTTAATCACAATCT----ACACGTGGCCCAGCAGCTTGAAGAGGT Cluster: [ ] Orangutan: TATAAAAGCGGACAAGACTTTGGACAGTTTAATCACAATCTACAT----GTGGCCCAGCACCTTGAAGGGGT Human > Gorilla --------------- chr2A:100558148-100558154 Template switch process: F1: L CAAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCAC 1 F3: 4 GGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA R RF: CAAATTATAAAAGCAGAGAGGAGTTTGGACAGTTTAATCACAATCTACACGTGGCCCAGCAGCTTGAAGAGGTGCGCAGGTGATGCTAATGA RR: GTTTAATATTTTCGTCTCTCCTCAAACCTGTCAAATTAGTGTTAGATGTGCACCGGGTCGTCGAACTTCTCCACGCGTCCACTACGATTACT F2: 3 AACCTGT 2 Unidirectional alignment (log-probability: -39.3) AAATTATAAAAGCAGAGAaGAGTTTGGACAGTTTAATCActgtcCAA---------GGCCCAGCAGCTTGAAGgGGTGCGCAGGTGATGCTAATGA AAATTATAAAAGCAGAGAGGAGTTTGGACAGTTTAATCA-----CAATCTACACGTGGCCCAGCAGCTTGAAGAGGTGCGCAGGTGATGCTAATGA Template switch alignment (log-probability: -27.7) AAATTATAAAAGCAGAGAaGAGTTTGGACAGTTTAATCAC|TGTCCAA|GGCCCAGCAGCTTGAAGgGGTGCGCAGGTGATGCTAATGA AAATTATAAAAGCAGAGAGGAGTTTGGACAGTTTAATCAC|TGTCCAA|GGCCCAGCAGCTTGAAGAGGTGCGCAGGTGATGCTAATGA Chimp > Gorilla --------------- chr2A:100558148-100558154 Template switch process: F1: L CAAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCAC 1 F3: 4 GGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA R RF: CAAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCACAATCTACACGTGGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA RR: GTTTAATATTTTCGTCTCTTCTCAAACCTGTCAAATTAGTGTTAGATGTGCACCGGGTCGTCGAACTTCCCCACGCGTCCACTACGATTACT F2: 3 AACCTGT 2 Unidirectional alignment (log-probability: -28.3) AAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCActgtcCAA---------GGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA AAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCA-----CAATCTACACGTGGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA Template switch alignment (log-probability: -16.6) AAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCAC|TGTCCAA|GGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA AAATTATAAAAGCAGAGAAGAGTTTGGACAGTTTAATCAC|TGTCCAA|GGCCCAGCAGCTTGAAGGGGTGCGCAGGTGATGCTAATGA ========== Event 2160 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGTAGGGAAAGTGCCTCCAAAAGTTAGACAACTTTTGTTGTCTGGCCAGTGGAGACGGGACTA ↑ 3 4 1 2 Chimp: CAGTAGGGAAAGTGCCTCCAAAA--------------GTTGTCTGGCCAGTGGAGAAGGGACTA Gorilla: CAGTAGGGAAAGTGCCTCCAAAA--------------GTTGTCTGGCCAGTGGAGAAGGGACTA ↓ 3 4 1 2 Human: CAGTAGGGAAAGTGCCTCCAAAAGTTAGACAACTTTTGTTGTCTGGCCAGTGGAGACGGGACTA Cluster: [ ] Orangutan: CAGTAGGGAAAGTGCCTCCAAAA--------------GTTGTCTGGCCAGTGGAGAAGGGACTA Chimp > Human ------------- chr2:66422526-66422536 Template switch process: F1: L TGCCTTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTT 1 F3: 4 GTTGTCTGGCCAGTGGAGACGGGACTAAGTGTTTTAACTT R RF: TGCCTTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTTGTCTGGCCAGTGGAGAAGGGACTAAGTGTTTTAACTT RR: ACGGAATCGTACGAATCCGTCATCCCTTTCACGGAGGTTTTCAACAGACCGGTCACCTCTTCCCTGATTCACAAAATTGAA F2: 3 TTTTCAACAGA 2 Unidirectional alignment (log-probability: -37) TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAgttagacaacttttGTTGTCTGGCCAGTGGAGAcGGGACTAAGTGTTTTAACTT TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAA--------------GTTGTCTGGCCAGTGGAGAAGGGACTAAGTGTTTTAACTT Template switch alignment (log-probability: -22.7) TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTT|AGACAACTTTT|GTTGTCTGGCCAGTGGAGAcGGGACTAAGTGTTTTAACTT TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTT|AGACAACTTTT|GTTGTCTGGCCAGTGGAGAAGGGACTAAGTGTTTTAACTT Gorilla > Human --------------- chr2:66422526-66422536 Template switch process: F1: L TGCCTTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTT 1 F3: 4 GTTGTCTGGCCAGTGGAGACGGGACTAAGTGTTTTAACTT R RF: TGCCTTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTTGTCTGGCCAGTGGAGAAGGGACTAAGTGTTTTAACTT RR: ACGGAATCGTACGAATCCGTCATCCCTTTCACGGAGGTTTTCAACAGACCGGTCACCTCTTCCCTGATTCACAAAATTGAA F2: 3 TTTTCAACAGA 2 Unidirectional alignment (log-probability: -36.5) TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAgttagacaacttttGTTGTCTGGCCAGTGGAGAcGGGACTAAGTGTTTTAACTT TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAA--------------GTTGTCTGGCCAGTGGAGAAGGGACTAAGTGTTTTAACTT Template switch alignment (log-probability: -22.7) TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTT|AGACAACTTTT|GTTGTCTGGCCAGTGGAGAcGGGACTAAGTGTTTTAACTT TTAGCATGCTTAGGCAGTAGGGAAAGTGCCTCCAAAAGTT|AGACAACTTTT|GTTGTCTGGCCAGTGGAGAAGGGACTAAGTGTTTTAACTT ========== Event 2161 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AGCAAACTGTCTCTGGTTGGTTTGCCTTTGTCAATAAAATAACTCCTGTCATACCACCAGCTGCATTTGGTT ↓ 1 4 3 2 Chimp: AGCAAACTGTCTCTGGTTGGT-----TATGAC--AGGTATAACTCCTGTCATACCACCAGCTGCATTTGGTT Gorilla: Human: AGCAAACTGTCTCTGGTTGGTTTGCCTTTGTCAATAAAATAACTCCTGTCATACCACCAGCTGCATTTGGTT Cluster: [ ] Orangutan: AGCAAAATGTCTCTGGTTGGTTTGCCTTTGTCAATAAAATAACTCCTGTCATACCACCAGCTGCATTTGATT Human > Chimp ------------- chr2A:69386394-69386401 Template switch process: F1: L GCCAGGTGTCCCCTCTTGGGAGCAAACTGTCTCTGGTTGGTT 1 F3: 4 TATAACTCCTGTCATACCACCAGCTGCATTTGGTTCCATTT R RF: GCCAGGTGTCCCCTCTTGGGAGCAAACTGTCTCTGGTTGGTTTGCCTTTGTCAATAAAATAACTCCTGTCATACCACCAGCTGCATTTGGTTCCATTT RR: CGGTCCACAGGGGAGAACCCTCGTTTGACAGAGACCAACCAAACGGAAACAGTTATTTTATTGAGGACAGTATGGTGGTCGACGTAAACCAAGGTAAA F2: 3 GGACAGTA 2 Unidirectional alignment (log-probability: -33.4) CAGGTGTCCCCTCTTGGGAGCAAACTGTCTCTGGTTGGTTatgacaggT---------------ATAACTCCTGTCATACCACCAGCTGCATTTGGTTCCATT CAGGTGTCCCCTCTTGGGAGCAAACTGTCTCTGGTTGGTT--------TGCCTTTGTCAATAAAATAACTCCTGTCATACCACCAGCTGCATTTGGTTCCATT Template switch alignment (log-probability: -22.3) CAGGTGTCCCCTCTTGGGAGCAAACTGTCTCTGGTTGGTT|ATGACAGG|tATAACTCCTGTCATACCACCAGCTGCATTTGGTTCCATT CAGGTGTCCCCTCTTGGGAGCAAACTGTCTCTGGTTGGTT|ATGACAGG|AATAACTCCTGTCATACCACCAGCTGCATTTGGTTCCATT ========== Event 2162 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCCTCTAGGAAGGCTAAACTAGACTTCTTGCAATATACTGTAAGAT-GCAACACCCCAGTCTGTCTCCACCTT ↓ 13 24 ↑ 13 24 Chimp: CCCTCTAGGAAGGCTAAACTA-GCATCTTACAGTATATTGCAAGAAGTCAACTCCCCAGTCTGTCTCCACCTT Gorilla: CCCTCTAGGAAGGCTAAACTA-GCATCTTACAGTATATTGCAAGAAGTCAACTCCCCAGTCTGTCTCCACCTT ↓ 13 24 ↑ 13 24 Human: CCCTCTAGGAAGGCTAAACTAGACTTCTTGCAATATACTGTAAGAT-GCAACACCCCAGTCTGTCTCCACCTT Cluster: [ ] Orangutan: CCCTCTGGGAAGGCTAAACTA-GCATCTTACAGTATATTGCAAGAAGTCAACTCCCCAGTCTGTCTCCACCTT Chimp > Human ------------- chr2:67647549-67647573 Template switch process: F1: L CTACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG 1 F3: 4 CAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC R RF: CTACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGCATCTTACAGTATATTGCAAGAAGTCAACTCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC RR: GATGGTCCGAAGAGAGAATGGGGAGATCCTTCCGATTTGATCGTAGAATGTCATATAACGTTCTTCAGTTGAGGGGTCAGACAGAGGTGGAATTCGTAGGTAATAATAGGAG F2: 3 GTAGAATGTCATATAACGTTCTTCA 2 Unidirectional alignment (log-probability: -61.4) ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG---------------------------ACTtcttgcaatatactgtaagatgcaacaCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGCATCTTACAGTATATTGCAAGAAGTCAACT---------------------------CCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Template switch alignment (log-probability: -24.5) ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|ACTTCTTGCAATATACTGTAAGATG|CAACaCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|ACTTCTTGCAATATACTGTAAGATG|CAACTCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Human > Chimp ------------- chr2A:69061282-69061306 Template switch process: F1: L CTACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG 1 F3: 4 CAACTCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC R RF: CTACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGACTTCTTGCAATATACTGTAAGATGCAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC RR: GATGGTCCGAAGAGAGAATGGGGAGATCCTTCCGATTTGATCTGAAGAACGTTATATGACATTCTACGTTGTGGGGTCAGACAGAGGTGGAATTCGTAGGTAATAATAGGAG F2: 3 TGAAGAACGTTATATGACATTCTAC 2 Unidirectional alignment (log-probability: -61.4) ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGcatcttacagtatattgcaagaagtcaACT---------------------------CCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG---------------------------ACTTCTTGCAATATACTGTAAGATGCAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Template switch alignment (log-probability: -24.5) ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|CATCTTACAGTATATTGCAAGAAGT|CAACtCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|CATCTTACAGTATATTGCAAGAAGT|CAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Gorilla > Human --------------- chr2:67647549-67647573 Template switch process: F1: L CTACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG 1 F3: 4 CAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC R RF: CTACCAGGTTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGCATCTTACAGTATATTGCAAGAAGTCAACTCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC RR: GATGGTCCAAAGAGAGAATGGGGAGATCCTTCCGATTTGATCGTAGAATGTCATATAACGTTCTTCAGTTGAGGGGTCAGACAGAGGTGGAATTCGTAGGTAATAATAGGAG F2: 3 GTAGAATGTCATATAACGTTCTTCA 2 Unidirectional alignment (log-probability: -66.4) ACCAGGcTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG---------------------------ACTtcttgcaatatactgtaagatgcaacaCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGTTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGCATCTTACAGTATATTGCAAGAAGTCAACT---------------------------CCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Template switch alignment (log-probability: -30.1) ACCAGGcTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|ACTTCTTGCAATATACTGTAAGATG|CAACaCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGTTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|ACTTCTTGCAATATACTGTAAGATG|CAACTCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Human > Gorilla --------------- chr2A:68412385-68412409 Template switch process: F1: L CTACCAGGTTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG 1 F3: 4 CAACTCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC R RF: CTACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGACTTCTTGCAATATACTGTAAGATGCAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTATCCTC RR: GATGGTCCGAAGAGAGAATGGGGAGATCCTTCCGATTTGATCTGAAGAACGTTATATGACATTCTACGTTGTGGGGTCAGACAGAGGTGGAATTCGTAGGTAATAATAGGAG F2: 3 TGAAGAACGTTATATGACATTCTAC 2 Unidirectional alignment (log-probability: -66.4) ACCAGGtTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAGcatcttacagtatattgcaagaagtcaACT---------------------------CCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG---------------------------ACTTCTTGCAATATACTGTAAGATGCAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA Template switch alignment (log-probability: -30.1) ACCAGGtTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|CATCTTACAGTATATTGCAAGAAGT|CAACtCCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ACCAGGCTTCTCTCTTACCCCTCTAGGAAGGCTAAACTAG|CATCTTACAGTATATTGCAAGAAGT|CAACACCCCAGTCTGTCTCCACCTTAAGCATCCATTATTA ========== Event 2163 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: GCCAGTCACTCACACTTGGGCTATTCAGTGGCCTTCCTCTCACATCATCTC Chimp: GCCAGTCACTCACACTTGGGCTATTCAATGGCCTTCCTCTCACATCATCTC Gorilla: GCCAGTCACTCACACTTGGGCCACTGAATAGCCTTCCTCTCACATCATCTC ↓ 13 24 ↑ 13 24 Human: GCCAGTCACTCACACTTGGGCTATTCAGTGGCCTTCCTCTCACATCATCTC Cluster: [ ] Orangutan: GCCAGTCACTCACACTTGGGCCATTGAATAGCCTTCCTCTCACATCATCTC Gorilla > Human --------------- chr2:67801613-67801621 Template switch process: F1: L CACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGC 1 F3: 4 GCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCACC R RF: CACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGCCACTGAATAGCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAAC RR: GTGAGACCTCCTACTGTCTCCGGTCAGTGAGTGTGAACCCGGTGACTTATCGGAAGGAGAGTGTAGTAGAGGACCAAAGACCCGAAGTTG F2: 3 GTGACTTAT 2 Unidirectional alignment (log-probability: -34.4) ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGCtAtTcAgTgGCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAcC ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGCCACTGAATAGCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAAC Template switch alignment (log-probability: -22.4) ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGC|TATTCAGTG|GCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAcC ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGC|TATTCAGTG|GCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAAC Human > Gorilla --------------- chr2A:68566448-68566456 Template switch process: F1: L CACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGC 1 F3: 4 GCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAAC R RF: CACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGCTATTCAGTGGCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCACC RR: GTGAGACCTCCTACTGTCTCCGGTCAGTGAGTGTGAACCCGATAAGTCACCGGAAGGAGAGTGTAGTAGAGGACCAAAGACCCGAAGTGG F2: 3 ATAAGTCAC 2 Unidirectional alignment (log-probability: -34.4) ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGCcAcTgAaTaGCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAaC ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGCTATTCAGTGGCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCACC Template switch alignment (log-probability: -22.4) ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGC|CACTGAATA|GCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCAaC ACTCTGGAGGATGACAGAGGCCAGTCACTCACACTTGGGC|CACTGAATA|GCCTTCCTCTCACATCATCTCCTGGTTTCTGGGCTTCACC ========== Event 2164 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ----------AGGCTGAATATCTGAGTTTGAATCCTAATTCTGCAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCAGATATTCAGCCTCAAAGTTCATTT Chimp: ----------AGGCTGAATATCTGAGTTTGAATCCTAATTCTGCAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCAGACATTCAGCCTCAAAGTTCATTT ↓ 3 1 2 4 ↑ 13 24 Gorilla: ----------AGGCTGAATATCTGAAAATGCAGAATTAGGATTCAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGATATTCAGCCTCAAAGTTCATTT ↓ 13 24 ↑ 13 24 Human: ----------AGGCTGAATATCTGAGTTTGAATCCTAATTCTGCAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCAGATATTCAGCCTCAAAGTTCATTT Cluster: [ ] Orangutan: CTTTTTTTGTAGACTCAATACCTCAAAATTTA-----GTCAAACACTTTCAAACTTCCCATACCTTGGATGCATATTCTGATGATCGCCCAGCAGTTATATCTATGCACGTCAGTCACATTTGATAGATAGCACCTCAGGATTAGTAGATACACATCTTAAGAGCCATCTACTGACGCACCTATTTCAGAGAGTGATGGCTCACTCGTTTGACCTAGTAGATCATGAATAGGTGTGTAGCTCTGACCCAGCTGTGACGCTGGCATTTTCGAGTCTCAGGACGTATGATGTGATGTCATCAGTTCTACCACATCGTCTTGAATGGAGGGTGGCTAATGCGACGACGGGGCAGATCACATCGATCTTATGACAACGGGATCTGATGTTGCCTTGATGATCAGCTGTTCAGACCTCGTATCACATCACTTGCTCACATCCTACGCTANNNNNNNNNNTT Gorilla > Human --------------- chr2:70036030-70036052 Template switch process: F1: L AATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA 1 F3: 4 TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC R RF: AATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGAAAATGCAGAATTAGGATTCAAACTCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC RR: TTATTTCTTTACTCTTTACTTGAAACTCCGACTTATAGACTTTTACGTCTTAATCCTAAGTTTGAGTCTATAAGTCGGAGTTTCAAGTAAAGAGTAAAGAGGTG F2: 3 TTTACGTCTTAATCCTAAGTTTG 2 Unidirectional alignment (log-probability: -54.9) ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA-----------------------gtttgaatcctaattctgcatttTCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGAAAATGCAGAATTAGGATTCAAAC-----------------------TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC Template switch alignment (log-probability: -18.7) ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA|GTTTGAATCCTAATTCTGCATTT|TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA|GTTTGAATCCTAATTCTGCATTT|TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC Human > Gorilla --------------- chr2A:70799359-70799381 Template switch process: F1: L AATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA 1 F3: 4 TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC R RF: AATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGAGTTTGAATCCTAATTCTGCATTTTCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC RR: TTATTTCTTTACTCTTTACTTGAAACTCCGACTTATAGACTCAAACTTAGGATTAAGACGTAAAAGTCTATAAGTCGGAGTTTCAAGTAAAGAGTAAAGAGGTG F2: 3 CAAACTTAGGATTAAGACGTAAA 2 Unidirectional alignment (log-probability: -54.9) ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA-----------------------aaatgcagaattaggattcaaacTCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGAGTTTGAATCCTAATTCTGCATTT-----------------------TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC Template switch alignment (log-probability: -18.7) ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA|AAATGCAGAATTAGGATTCAAAC|TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA|AAATGCAGAATTAGGATTCAAAC|TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC Gorilla > Chimp --------------- chr2A:71459351-71459373 Template switch process: F1: L AATAAAGAAATTAGAAATGAACTTTGAGGCTGAATATCTGA 1 F3: 4 TCAGACATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG R RF: AATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGAAAATGCAGAATTAGGATTCAAACTCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG RR: TTATTTCTTTACTCTTTACTTGAAACTCCGACTTATAGACTTTTACGTCTTAATCCTAAGTTTGAGTCTATAAGTCGGAGTTTCAAGTAAAGAGTAAAGAGGTGAGGGAC F2: 3 TTTACGTCTTAATCCTAAGTTTG 2 Unidirectional alignment (log-probability: -66) ATAAAGAAATtAGAAATGAACTTTGAGGCTGAATATCTGA-----------------------gtttgaatcctaattctgcatttTCAGAcATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGAAAATGCAGAATTAGGATTCAAAC-----------------------TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC Template switch alignment (log-probability: -29.8) ATAAAGAAATtAGAAATGAACTTTGAGGCTGAATATCTGA|GTTTGAATCCTAATTCTGCATTT|TCAGAcATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC ATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA|GTTTGAATCCTAATTCTGCATTT|TCAGATATTCAGCCTCAAAGTTCATTTCTCATTTCTCCAC Chimp > Gorilla --------------- chr2A:70799359-70799387 Template switch process: F1: L AATAAAGAAATGAGAAATGAACTTTGAGGCTGAATATCTGA 1 F3: 4 ATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG R RF: AATAAAGAAATTAGAAATGAACTTTGAGGCTGAATATCTGAGTTTGAATCCTAATTCTGCATTTTCAGACATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG RR: TTATTTCTTTAATCTTTACTTGAAACTCCGACTTATAGACTCAAACTTAGGATTAAGACGTAAAAGTCTGTAAGTCGGAGTTTCAAGTAAAGAGTAAAGAGGTGAGGGAC F2: 3 TAGACTCAAACTTAGGATTAAGACGTAAA 2 Unidirectional alignment (log-probability: -66) ATAAAGAAATgAGAAATGAACTTTGAGGCTGAATATCTGA-----------------------aaatgcagaattaggattcaaacTCAGAtATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG ATAAAGAAATTAGAAATGAACTTTGAGGCTGAATATCTGAGTTTGAATCCTAATTCTGCATTT-----------------------TCAGACATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG Template switch alignment (log-probability: -24.9) ATAAAGAAATgAGAAATGAACTTTGAGGCTGAATATCTGA|AAATGCAGAATTAGGATTCAAACTCAGAT|ATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG ATAAAGAAATTAGAAATGAACTTTGAGGCTGAATATCTGA|AAATGCAGAATTAGGATTCAAACTCAGAT|ATTCAGCCTCAAAGTTCATTTCTCATTTCTCCACTCCCTG ========== Event 2165 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: atctcaaaaacaaaaaGGACAGTCGTATACtttt------------------- Chimp: atctcaaaaacaaaaaGGACAATAGTATACtttt------------------- Gorilla: atctcaaaaacaaaaaGGACAATAGTATACtttttttttttttttttggagat ↑ 1 3 2 4 Human: atctcaaaaacaaaaaGGACAGTCGTATACtttt------------------- Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNt-------------------- Human > Gorilla --------------- chr2A:37451183-37451189 Template switch process: F1: L GCCAACAACAGTGAGACTCCATCTCAAAAACAAAAAGGACAAT 1 F3: 4 TTTTTTTTTTTTTTTTTGGAGATGGAGTCTTGCT R RF: GCCAACAACAGTGAGACTCCATCTCAAAAACAAAAAGGACAGTCGTATACTTTTTTTTTTTTTTTTTTTGGAGATGGAGTCTTGCT RR: CGGTTGTTGTCACTCTGAGGTAGAGTTTTTGTTTTTCCTGTCAGCATATGAAAAAAAAAAAAAAAAAAACCTCTACCTCAGAACGA F2: 3 CATATGA 2 Unidirectional alignment (log-probability: -61.7) AACAACAGTGAGACTCCATCTCAAAAACAAAAAGGACAaTaGTATACTTTTtttttttttttttggagatggagtcttgct AACAACAGTGAGACTCCATCTCAAAAACAAAAAGGACAGTCGTATACTTTT------------------------------ Template switch alignment (log-probability: -22) AACAACAGTGAGACTCCATCTCAAAAACAAAAAGGACAaT|AGTATAC|TTTTTTTTTTTTTTTTTGGAGATGGAGTCTTGCT AACAACAGTGAGACTCCATCTCAAAAACAAAAAGGACAGT|AGTATAC|TTTTTTTTTTTTTTTTTGGAGATGGAGTCTTGCT ========== Event 2166 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGCATTGCAGGACTAATATAAAGACCAGCTGGAAGTT----------------------------------------------------------GGTCTTTAAACTTCTATAGAAAAGCAGTa Chimp: AGGCATTGCAGGACTAATATAAAGACCAGCTGGAAGTT-----------------------------CCCTGCAGGAATAGCATCCTCTGAAAGACACAATTTAAACTTCTATAGAAAAGCAGTG Gorilla: AGGCATTGCAGGACTAATGTAAAGACCAGCTGGAAGTTCCATGCAGGAATAGCATCCTCTGAAAGAC-----------------------------ACAACTTTAACTTCTATAGAAAAGCAGTG ↓ 3 2 1 4 Human: AGGCATTGCAGGACTAATATAAAGACCAGCTGGAAGTT----------------------------------------------------------GGTCTTTAAACTTCTATAGAAAAGCAGTa Cluster: [ ] Orangutan: AGGCATTACAGGACTAATATAAAGACCAGCTGGAAGTTCCATGCAGGAATAGCATCCTCTGAAAGAC-----------------------------ACAATTTAAACTTCTATAGAAAAGCAGTG Gorilla > Human --------------- chr2:67051078-67051085 Template switch process: F1: L GAGAGGCATTGCAGGACTAATATAAAGACCAGCTGGAAGTT 1 F3: 4 AACTTCTATAGAAAAGCAGTAATCCTGGTTCTCTGCTGTC R RF: GAGAGGCATTGCAGGACTAATGTAAAGACCAGCTGGAAGTTCCATGCAGGAATAGCATCCTCTGAAAGACACAACTTTAACTTCTATAGAAAAGCAGTGATCCTGGTTCTCTGCTGTC RR: CTCTCCGTAACGTCCTGATTACATTTCTGGTCGACCTTCAAGGTACGTCCTTATCGTAGGAGACTTTCTGTGTTGAAATTGAAGATATCTTTTCGTCACTAGGACCAAGAGACGACAG F2: 3 ATTTCTGG 2 Unidirectional alignment (log-probability: -45.1) AGAGGCATTGCAGGACTAATaTAAAGACCAGCTGGAAG-------------------------------------TTggtctttaAACTTCTATAGAAAAGCAGTaATCCTGGTTCTCTGCTGTC AGAGGCATTGCAGGACTAATGTAAAGACCAGCTGGAAGTTCCATGCAGGAATAGCATCCTCTGAAAGACACAACTTT--------AACTTCTATAGAAAAGCAGTGATCCTGGTTCTCTGCTGTC Template switch alignment (log-probability: -27.8) AGAGGCATTGCAGGACTAATaTAAAGACCAGCTGGAAGTT|GGTCTTTA|AACTTCTATAGAAAAGCAGTaATCCTGGTTCTCTGCTGTC AGAGGCATTGCAGGACTAATGTAAAGACCAGCTGGAAGTT|GGTCTTTA|AACTTCTATAGAAAAGCAGTGATCCTGGTTCTCTGCTGTC ========== Event 2167 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCTAAAAGCCTCAAGCTGCCTA----TTCTTAGGCATTTTCATGAAACTGTAGTGT ↑ 3 1 2 4 Chimp: ATTCTAAAAGCCTCAAGCTGCCTA--AGAAGTAAGTCATTTTCATGAAACTGTAGTGT Gorilla: ATTCTAAAAGCCTCAAGCTGCCTAAG--AAGTAAGTTATTTTCATGAAACTGTAGTGT ↓ 3 1 2 4 Human: ATTCTAAAAGCCTCAAGCTGCCTA----TTCTTAGGCATTTTCATGAAACTGTAGTGT Cluster: [ ] Orangutan: ATCCTAAAAGCCTCAAGCTGCCTAAG--AAGTAAGTCGTTTTCATGAAACTGTAGTGT Chimp > Human ------------- chr2:170221028-170221035 Template switch process: F1: L TTTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTA 1 F3: 4 CATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGAT R RF: TTTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTAAGAAGTAAGTCATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGAT RR: AAAACTTTTCATAGTTGTAAGATTTTCGGAGTTCGACGGATTCTTCATTCAGTAAAAGTACTTTGACATCACAAAGTCCTCGTGTCCACTA F2: 3 GGATTCTT 2 Unidirectional alignment (log-probability: -31.7) TTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTA---------TtcttaggCATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGAT TTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTAAGAAGTAAGT-------CATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGAT Template switch alignment (log-probability: -16.3) TTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTA|TTCTTAGG|CATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGAT TTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTA|TTCTTAGG|CATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGAT Gorilla > Human --------------- chr2:170221028-170221036 Template switch process: F1: L TTTTGAAAAGTATCAACATTCTAAAAGCCTCAAGCTGCCTA 1 F3: 4 ATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGATT R RF: TTTTGAAAAATATCAACATTCTAAAAGCCTCAAGCTGCCTAAGAAGTAAGTTATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGATT RR: AAAACTTTTTATAGTTGTAAGATTTTCGGAGTTCGACGGATTCTTCATTCAATAAAAGTACTTTGACATCACAAAGTCCTCGTGTCCACTAA F2: 3 CGGATTCTT 2 Unidirectional alignment (log-probability: -36.7) TTTGAAAAgTATCAACATTCTAAAAGCCTCAAGCTGCCTA---------TTcttaggcATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGATT TTTGAAAAATATCAACATTCTAAAAGCCTCAAGCTGCCTAAGAAGTAAGTT-------ATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGATT Template switch alignment (log-probability: -22.4) TTTGAAAAgTATCAACATTCTAAAAGCCTCAAGCTGCCTA|TTCTTAGGC|ATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGATT TTTGAAAAATATCAACATTCTAAAAGCCTCAAGCTGCCTA|TTCTTAGGC|ATTTTCATGAAACTGTAGTGTTTCAGGAGCACAGGTGATT ========== Event 2168 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAGAACAGAGGTTTGGAGGCCCTGTCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTG Chimp: TGAGAACAGAGGTTTGGAGGCCCTGTCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTG ↓ 1 4 3 2 Gorilla: TGAGAACAGAGGTTTGGAGGC-TGCTAATGGGAATTAGCAGCCCGGCAGCCATGTAGGTG ↑ 1 4 3 2 Human: TGAGAACAGAGGTTTGGAGGCCCTGTCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTG Cluster: [ ] Orangutan: TGAGAACAGAGGTTTGGAGGCCCTGTCCTGGGAATTAGCAGCCTGGCAGCTATGTAGGTG Human > Gorilla --------------- chr2A:35083466-35083470 Template switch process: F1: L GACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGC 1 F3: 4 ATGGGAATTAGCAGCCCGGCAGCCATGTAGGTGCCCAAAG R RF: GACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGCCCTGTCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTGCCCAAAG RR: CTGTCACCTACCTCCGACCGACTCTTGTCTCCAAACCTCCGGGACAGTACCCTTAATCGTCGGACCGTCGGTACATCCACGGGTTTC F2: 3 ATCGT 2 Unidirectional alignment (log-probability: -33.3) ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGG--CTGcTaATGGGAATTAGCAGCCcGGCAGCCATGTAGGTGCCCAAAG ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGCCCTG-TCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTGCCCAAAG Template switch alignment (log-probability: -21.9) ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGC|TGCTA|ATGGGAATTAGCAGCCcGGCAGCCATGTAGGTGCCCAAAG ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGC|TGCTA|ATGGGAATTAGCAGCCTGGCAGCCATGTAGGTGCCCAAAG Chimp > Gorilla --------------- chr2A:35083466-35083470 Template switch process: F1: L GACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGC 1 F3: 4 ATGGGAATTAGCAGCCCGGCAGCCATGTAGGTGCCCAAAG R RF: GACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGCCCTGTCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTGCCCAAAG RR: CTGTCACCTACCTCCGACCGACTCTTGTCTCCAAACCTCCGGGACAGTACCCTTAATCGTCGGACCGTCGGTACATCCACGGGTTTC F2: 3 ATCGT 2 Unidirectional alignment (log-probability: -33.3) ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGG--CTGcTaATGGGAATTAGCAGCCcGGCAGCCATGTAGGTGCCCAAAG ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGCCCTG-TCATGGGAATTAGCAGCCTGGCAGCCATGTAGGTGCCCAAAG Template switch alignment (log-probability: -21.9) ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGC|TGCTA|ATGGGAATTAGCAGCCcGGCAGCCATGTAGGTGCCCAAAG ACAGTGGATGGAGGCTGGCTGAGAACAGAGGTTTGGAGGC|TGCTA|ATGGGAATTAGCAGCCTGGCAGCCATGTAGGTGCCCAAAG ========== Event 2169 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GAGGCTCCGTTCAGCCCCTGC---T----TAGA--CTGTGCCACTTGGCAAGGGAGC Chimp: GAGGCTCTATTCAGCCTCTGC---T----TAGA--CTGTGCCACTTGGCAAGGGAGC Gorilla: GAGGCTCCATTCAGCCCCTGCTGTCTAAGCAGTCTATGTGCCACTTGGCAAGGGAGC ↓ 1 3 24 Human: GAGGCTCCGTTCAGCCCCTGC---T----TAGA--CTGTGCCACTTGGCAAGGGAGC Cluster: [ ] Orangutan: GAGGCTCCATTCAGCCCCTGC---T----TAGA--CTGTGCCACTTGGCAAGGGAGC Gorilla > Human --------------- chr2:169085364-169085368 Template switch process: F1: L CCATGAATTGTGGCCTGCAAGAGGCTCCGTTCAGCCCCTGCT 1 F3: 4 TGTGCCACTTGGCAAGGGAGCTCGGAGAGCTGAGGCTGTG R RF: CCATGAATTGTGGCCTGCAAGAGGCTCCATTCAGCCCCTGCTGTCTAAGCAGTCTATGTGCCACTTGGCAAGGGAGCTCGGACAGCTGAGGCTGTG RR: GGTACTTAACACCGGACGTTCTCCGAGGTAAGTCGGGGACGACAGATTCGTCAGATACACGGTGAACCGTTCCCTCGAGCCTGTCGACTCCGACAC F2: 3 CAGAT 2 Unidirectional alignment (log-probability: -36.6) ATGAATTGTGGCCTGCAAGAGGCTCCgTTCAGCCCCTGCT------------TAgacTGTGCCACTTGGCAAGGGAGCTCGGAgAGCTGAGGCTGTG ATGAATTGTGGCCTGCAAGAGGCTCCATTCAGCCCCTGCTGTCTAAGCAGTCTA---TGTGCCACTTGGCAAGGGAGCTCGGACAGCTGAGGCTGTG Template switch alignment (log-probability: -27.4) ATGAATTGTGGCCTGCAAGAGGCTCCgTTCAGCCCCTGCT|TAGAC|TGTGCCACTTGGCAAGGGAGCTCGGAgAGCTGAGGCTGTG ATGAATTGTGGCCTGCAAGAGGCTCCATTCAGCCCCTGCT|TAGAC|TGTGCCACTTGGCAAGGGAGCTCGGACAGCTGAGGCTGTG ========== Event 2170 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CACACGGGAGCCCAGTAGCGAGGGCACGCCTGGGCGCTTTTGGGTGTGCTC----------------ACCTGCCATATGAGTCAGAATTATCGCATGCATGCTAGCCTATGAGGCCATGTTC Chimp: CACACGGGAGCCCAGTAGCGAGGGCATGCCTGGGCGCTTTTGGGTGTGCTC----------------ACCTGCCATATGAGTCAGAATTATCGCATGCATGCTAGCCTATGAGGCCATGTTC ↑ 1 4 3 2 Gorilla: CACACGGGAGCCCAGTAGCGA-GGCACGCCTGGGCGCTTTTGGGTGTGCTCACCCAGGAATGTGCACACCTGCCATATGAGTCAGAATTATCGCATGCATGCTAGCCTATGAGGCCATGTTC Human: CACACGGGAGCCCAGTAGCGAGGGCACGCCTGGGCGCTTTTGGGTGTGCTC----------------ACCTGCCATATGAGTCAGAATTATCGCATGCATGCTAGCCTATGAGGCCATGTTC Cluster: [ ] Orangutan: CACATGGGAGCCCAGTAGCGAGGGCACGCCTGGGCGCTCTTGGGTGTGCTCACCCAGGAATGTGCACACCTGCCATATGAGTCAGAATTACCGCGTGCATGCTAGCCTATGAGGCCATGTTC Gorilla > Chimp --------------- chr2A:37140958-37140961 Template switch process: F1: L TTCACCCACCTCCCTGTCATCACACGGGAGCCCAGTAGCGAGG 1 F3: 4 GCCTGGGCGCTTTTGGGTGTGCTC R RF: TTCACCCACCTCCCTGTCATCACACGGGAGCCCAGTAGCGAGGCACGCCTGGGCGCTTTTGGGTGTGCTCACCCAGGAATGTGCACACCTGCCATATGAGTCAGAATTATCGCATGCATGC RR: AAGTGGGTGGAGGGACAGTAGTGTGCCCTCGGGTCATCGCTCCGTGCGGACCCGCGAAAACCCACACGAGTGGGTCCTTACACGTGTGGACGGTATACTCAGTCTTAATAGCGTACGTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -25.3) ACCCACCTCCCTGTCATCACACGGGAGCCCAGTAGCGAgGGCAtGCCTGGGCGCTTTTGGGTGTGCTC---------------- ACCCACCTCCCTGTCATCACACGGGAGCCCAGTAGCGA-GGCACGCCTGGGCGCTTTTGGGTGTGCTCACCCAGGAATGTGCAC Template switch alignment (log-probability: -15.8) ACCCACCTCCCTGTCATCACACGGGAGCCCAGTAGCGAGG|GCAT|GCCTGGGCGCTTTTGGGTGTGCTC ACCCACCTCCCTGTCATCACACGGGAGCCCAGTAGCGAGG|GCAT|GCCTGGGCGCTTTTGGGTGTGCTC ========== Event 2171 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GATACTAGCGGATGTCTGGGTGGCTGAAG----CCAACCAGTGCATGTGTCCAG Chimp: GATACTAGCGGATGTCTGGGTGGCTGAAG----CCAACCAGTGCATGTGTCCAG ↓ 3 1 2 4 Gorilla: GATACTAGCGGATGTCTGGGTGGCTTCAGCCACCCAACCAGTGCATGTGTCCAG ↑ 3 1 2 4 Human: GATACTAGCGGATGTCTGGGTGGCTGAAG----CCAACCAGTGCATGTGTCCAG Cluster: [ ] Orangutan: GATACTAGCGGATGTCTGGGTGGCTGAAG----CCAACCAGTGCATGTGTCCAG Human > Gorilla --------------- chr2A:33049513-33049520 Template switch process: F1: L GAAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCT 1 F3: 4 CCAACCAGTGCATGTGTCCAGTATGAAAGCCACTGGTCAC R RF: GAAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCTGAAGCCAACCAGTGCATGTGTCCAGTATGAAGGCCACTGGTCAC RR: CTTCCCTTCTTCTCTGCTATGATCGCCTACAGACCCACCGACTTCGGTTGGTCACGTACACAGGTCATACTTCCGGTGACCAGTG F2: 3 CACCGACT 2 Unidirectional alignment (log-probability: -33.3) AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCTtcAGccacCCAACCAGTGCATGTGTCCAGTATGAAaGCCACTGGTCAC AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCTGAAG----CCAACCAGTGCATGTGTCCAGTATGAAGGCCACTGGTCAC Template switch alignment (log-probability: -22.3) AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCT|TCAGCCAC|CCAACCAGTGCATGTGTCCAGTATGAAaGCCACTGGTCAC AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCT|TCAGCCAC|CCAACCAGTGCATGTGTCCAGTATGAAGGCCACTGGTCAC Chimp > Gorilla --------------- chr2A:33049513-33049520 Template switch process: F1: L GAAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCT 1 F3: 4 CCAACCAGTGCATGTGTCCAGTATGAAAGCCACTGGTCAC R RF: GAAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCTGAAGCCAACCAGTGCATGTGTCCAGTATGAAGGCCACTGGTCAC RR: CTTCCCTTCTTCTCTGCTATGATCGCCTACAGACCCACCGACTTCGGTTGGTCACGTACACAGGTCATACTTCCGGTGACCAGTG F2: 3 CACCGACT 2 Unidirectional alignment (log-probability: -33.3) AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCTtcAGccacCCAACCAGTGCATGTGTCCAGTATGAAaGCCACTGGTCAC AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCTGAAG----CCAACCAGTGCATGTGTCCAGTATGAAGGCCACTGGTCAC Template switch alignment (log-probability: -22.3) AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCT|TCAGCCAC|CCAACCAGTGCATGTGTCCAGTATGAAaGCCACTGGTCAC AAGGGAAGAAGAGACGATACTAGCGGATGTCTGGGTGGCT|TCAGCCAC|CCAACCAGTGCATGTGTCCAGTATGAAGGCCACTGGTCAC ========== Event 2172 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ---aaaaaaaaaaaaaGTTTCACCTGAACTTAACCAAGTATTTAGATCCTTCAGCATACGGTTCTCTTTTTTCTCACAGTGAAACAAGGTTTACTAACCTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA------------TCTTTACCCTACTTACATTCAT ↓ 3 2 1 4 Chimp: aaaaaaaaaaaaaaaaGTTTCACCTGAACTTAACCAAGTATTTAGATCCTTCAGCATACGGTTCTCTTTTTTCTCACAGTGAAACAAGGTTTACTAACCTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA------CAGGTGACTTTACCCTACTTACATTCAT Gorilla: -------aaaaaaaaaGTTTCACCTGAACTTAACCAAGTATTTAGATCCTTCAGCATATGGTTCTCTTTTTTCTCACAGTGAAACAAGGTTTACTAACCTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAACAGGTG------ACTTTACCCTACTTACATTCAT Human: ---aaaaaaaaaaaaaGTTTCACCTGAACTTAACCAAGTATTTAGATCCTTCAGCATACGGTTCTCTTTTTTCTCACAGTGAAACAAGGTTTACTAACCTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA------------TCTTTACCCTACTTACATTCAT Cluster: [ ] Orangutan: -------aaaaaaaaaGTTTCACCTGAACTTAACCAAGTATTTAGATCCTTCAGCATATGGTTCTCTTTTTTCTCACAGTGAAACAAGGTTTACTAACCTTCTTGGTGCTCTTTAATGCTATTCAATCTTAAATTCAACAGGCG------ACTTTACCCTACTTACATTCAT Human > Chimp ------------- chr2A:35972484-35972490 Template switch process: F1: L CCTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA 1 F3: 4 CTTTACCCTACTTACATTCATTGTTATAACATATATTTCT R RF: TCACCTGAACTTAACCAAGTATTTAGATCCTTCAGCATACGGTTCTCTTTTTTCTCACAGTGAAACAAGGTTTACTAACCTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAATCTTTACCCTACTTACATTCATTGTTATAACATATATTTCC RR: AGTGGACTTGAATTGGTTCATAAATCTAGGAAGTCGTATGCCAAGAGAAAAAAGAGTGTCACTTTGTTCCAAATGATTGGAAGAACCACGACAAATTACGATAAGTTAGAATTTAAGTTAGAAATGGGATGAATGTAAGTAACAATATTGTATATAAAGG F2: 3 AGTGGAC 2 Unidirectional alignment (log-probability: -31.5) CTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAAcaggtgaCTTTACCCTACTTACATTCATTGTTATAACATATATTTCt CTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA------TCTTTACCCTACTTACATTCATTGTTATAACATATATTTCC Template switch alignment (log-probability: -22.1) CTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA|CAGGTGA|CTTTACCCTACTTACATTCATTGTTATAACATATATTTCt CTTCTTGGTGCTGTTTAATGCTATTCAATCTTAAATTCAA|CAGGTGA|CTTTACCCTACTTACATTCATTGTTATAACATATATTTCC ========== Event 2173 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: --TCCAGCAAATCTTATAATGGACCTTTCATTTCCTACAAGGTCTAAACAACTCTCTGTCTCCTCTCATATATTTGCCTTCATCCCCAACTACCTTTCCCTTTGCTCAGAGAAGCAGG-------------------------TGTCTCTTCTCCAGTCCAAAGCTGGTGTCTCCTCCCCATAACCCCACTATGGTCTAGG Chimp: --TCCAGCAAATCTTATAATGGACCTTTCATTTCCTACAAGGTCTAAACAACTCTCTGTCTCCTCTCATATATTTGCCTTCATCCCCAACTACCTTTCCCTTTGCTCAGAGAAGCAGG-------------------------TGTCTCTTCTCCAGTCCAAAGCTGGTGTCTCCTCCCCATAACCCCACTATGCTCTAGG ↑ 3 2 4 1 Gorilla: --TCCAGCAAATCTTATAATGGACCTTTCATTTCCTACAAGATCTAAACAACTCTCTGTCTCCTCTCATATATTTGCCTTCATCCCCAACTACCTTTCCCTTTGCTCAGAGAAGCAGG--------------------------------------------------TGTCTCCTCCCCATAACCCCACTATGCTCTAGG Human: --TCCAGCAAATCTTATAATGGACCTTTCATTTCCTACAAGGTCTAAACAACTCTCTGTCTCCTCTCATATATTTGCCTTCATCCCCAACTACCTTTCCCTTTGCTCAGAGAAGCAGG-------------------------TGTCTCTTCTCCAGTCCAAAGCTGGTGTCTCCTCCCCATAACCCCACTATGGTCTAGG Cluster: [ ] Orangutan: TGTCCAGCAAATCTTATAATGGACCTTTCATTTCCTACAAGATCTAAACAACTCTCTGTCTTCTCTCATATATTTGCCTTCATCCCCAACTACATTTCCCTTTGCTCAGAGAAGCAGGTGTCTCTTCTCCAGACCAAAGCTGG-------------------------TGTCTCCTCCCCACAAACCCACTATGCTCTAGG Gorilla > Chimp --------------- chr2A:77070063-77070067 Template switch process: F1: L CTTCATCCCCAACTACCTTTCCCTTTGCTCAGAGAAGCAGGTGTCTCTTCTCCA 1 F3: 4 AAGCTGGTGTCTCCTCCCCATAACCCCACTATGCTCTAGGTCCTCTT R RF: TGGACCTTTCATTTCCTACAAGATCTAAACAACTCTCTGTCTCCTCTCATATATTTGCCTTCATCCCCAACTACCTTTCCCTTTGCTCAGAGAAGCAGGTGTCTCCTCCCCATAACCCCACTATGCTCTAGGTCCTCTT RR: ACCTGGAAAGTAAAGGATGTTCTAGATTTGTTGAGAGACAGAGGAGAGTATATAAACGGAAGTAGGGGTTGATGGAAAGGGAAACGAGTCTCTTCGTCCACAGAGGAGGGGTATTGGGGTGATACGAGATCCAGGAGAA F2: 3 ACCTG 2 Unidirectional alignment (log-probability: -46.8) ACCTTTCCCTTTGCTCAGAGAAGCAggtgtctcttctccagtccaaagctGGTGTCTCCTCCCCATAACCCCACTATGCTCTAGG ACCTTTCCCTTTGCTCAGAGAAGCA-------------------------GGTGTCTCCTCCCCATAACCCCACTATGCTCTAGG Template switch alignment (log-probability: -33.4) ACCTTTCCCTTTGCTCAGAGAAGCAGGTGTCTCtTCtCCA|GTCCA|AAGCtGGTGTCTCCTCCCCATAACCCCACTATGCTCTAGG ACCTTTCCCTTTGCTCAGAGAAGCAGGTGTCTCCTCCCCA|GTCCA|AAGCAGGTGTCTCCTCCCCATAACCCCACTATGCTCTAGG ========== Event 2174 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AATTTATGTATAACTGCTTAA---AGGCTATTTTGTTGCCCATTTTCTTATGTCTGGTG--------TTGACATCTAGTGAGCTTTAGATGGGCAATACGGTCTTAATTTTTTATTGAGGTA Chimp: AATTTATGTATAACTGCTTAAAACTGTATATTTTGTTGCCCATTTTCTTATGTCTGGTG----TTATTTGACATCTAGTGAGCTTTAGATGGGCAATACGGTCTTAATTTTTTATTGAGGTA ↑ 1 4 3 2 Gorilla: AATTTATGTATAACTGCTTAA---AGGCTATTTTGTTGCCCATTTTCTTATGTCTGGTGTTAT----TTGACATCTAGTGAGCTTTAGATGGGCAATACAGTCTTAATTTTTTATTGAGGTA Human: AATTTATGTATAACTGCTTAA---AGGCTATTTTGTTGCCCATTTTCTTATGTCTGGTG--------TTGACATCTAGTGAGCTTTAGATGGGCAATACGGTCTTAATTTTTTATTGAGGTA Cluster: [ ] Orangutan: AATTTATGTATAACTGCTTAA---AGGCTATTTTGTTGCCCATTTTCTTATGTCTGGTGTTAT----TTGACATCTAGTGAGCTTTAGATTGGCAATAAGGTCTTAATTTTTTATTGAGGTA Gorilla > Chimp --------------- chr2A:78026537-78026542 Template switch process: F1: L AAGATCTTCCAGGGAGGATTAATTTATGTATAACTGCTTAAA 1 F3: 4 TATTTTGTTGCCCATTTTCTTATGTCTGGTGTTATT R RF: AAGATCTTCCAGGGAGGATTAATTTATGTATAACTGCTTAAAGGCTATTTTGTTGCCCATTTTCTTATGTCTGGTGTTATTTGACATCTAGTGAGCTTTAGATGGGCAATACAGT RR: TTCTAGAAGGTCCCTCCTAATTAAATACATATTGACGAATTTCCGATAAAACAACGGGTAAAAGAATACAGACCACAATAAACTGTAGATCACTCGAAATCTACCCGTTATGTCA F2: 3 ATGTCA 2 Unidirectional alignment (log-probability: -26.2) GATCTTCCAGGGAGGATTAATTTATGTATAACTGCTTAAAactGtaTATTTTGTTGCCCATTTTCTTATGTCTGGTGTTATT GATCTTCCAGGGAGGATTAATTTATGTATAACTGCTTAAA---GGCTATTTTGTTGCCCATTTTCTTATGTCTGGTGTTATT Template switch alignment (log-probability: -16.4) GATCTTCCAGGGAGGATTAATTTATGTATAACTGCTTAAA|ACTGTA|TATTTTGTTGCCCATTTTCTTATGTCTGGTGTTATT GATCTTCCAGGGAGGATTAATTTATGTATAACTGCTTAAA|ACTGTA|TATTTTGTTGCCCATTTTCTTATGTCTGGTGTTATT ========== Event 2175 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAAAACTAAAAACCAGAAAGATACTCTGGTATCTTTTTTACTTCTTACAATGTAT ↑ 3 2 1 4 Chimp: TTAAAACTAAAAACCAGAAAGATACTCT-GT---ATTTTTACTTCTTACAATGTAT Gorilla: TTAAAACGAAAAACCAGAAAGATACTCT-GT---ATTTTTACTTCTTAGGATGTAT Human: TTAAAACTAAAAACCAGAAAGATACTCTGGTATCTTTTTTACTTCTTACAATGTAT Cluster: [ ] Orangutan: TTAAAACTAAAAACCAGAAAGATACTCT-GT---ATTTTTACTTCTTACAATGTAT Chimp > Human ------------- chr2:77184835-77184840 Template switch process: F1: L TGGTCCTATGCTATTAAAACTAAAAACCAGAAAGATACTCTG 1 F3: 4 TTTTTACTTCTTACAATGTATTTTGAAAATAAGATAGCGT R RF: TGGTCCTATGCTATTAAAACTAAAAACCAGAAAGATACTCTGTATTTTTACTTCTTACAATGTATTTTGAAAATAAGATAGCGT RR: ACCAGGATACGATAATTTTGATTTTTGGTCTTTCTATGAGACATAAAAATGAAGAATGTTACATAAAACTTTTATTCTATCGCA F2: 3 TCTATG 2 Unidirectional alignment (log-probability: -26.9) GTCCTATGCTATTAAAACTAAAAACCAGAAAGATACTCTgGTAtctTTTTTACTTCTTACAATGTATTTTGAAAATAAGATAGCGT GTCCTATGCTATTAAAACTAAAAACCAGAAAGATACTCT-GTA---TTTTTACTTCTTACAATGTATTTTGAAAATAAGATAGCGT Template switch alignment (log-probability: -16) GTCCTATGCTATTAAAACTAAAAACCAGAAAGATACTCTG|GTATCT|TTTTTACTTCTTACAATGTATTTTGAAAATAAGATAGCGT GTCCTATGCTATTAAAACTAAAAACCAGAAAGATACTCTG|GTATCT|TTTTTACTTCTTACAATGTATTTTGAAAATAAGATAGCGT ========== Event 2176 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAACAGACAGAAGAAAGAACCATATGCAGACA-CGCA---ATTTAGAGCAATATGTACGGGAC Chimp: CAACAGACAGAAGAAAGAACCATATGCAGACACAGCA---ATTTGGAGCAATATGTACGGGAC Gorilla: CAACAGACAGAAGAAAGAACCATATGCAGACACAGCATATGGTTAGAGCAATATGTACGGGAC ↑ 3 2 1 4 Human: CAACAGACAGAAGAAAGAACCATATGCAGACA-CGCA---ATTTAGAGCAATATGTACGGGAC Cluster: [ ] Orangutan: CAACAGACAGAAGAAAGAACCATATGCAGACACAGCA---ATTTAGACCAATATGTATGGGAC Human > Gorilla --------------- chr2A:79769400-79769407 Template switch process: F1: L GTATCTTGGCAACAGACAGAAGAAAGAACCATATGCAGACACA 1 F3: 4 TTAGAGCAATATGTACGGGACAATGTGGGAACTTGAACTG R RF: TTATCTTGGCAACAGACAGAAGAAAGAACCATATGCAGACACGCAATTTAGAGCAATATGTACGGGACAATGTGGGAACTTGAACTG RR: AATAGAACCGTTGTCTGTCTTCTTTCTTGGTATACGTCTGTGCGTTAAATCTCGTTATACATGCCCTGTTACACCCTTGAACTTGAC F2: 3 GGTATACG 2 Unidirectional alignment (log-probability: -37.9) TCTTGGCAACAGACAGAAGAAAGAACCATATGCAGACACagcatatgG----TTAGAGCAATATGTACGGGACAATGTGGGAACTTGAACTG TCTTGGCAACAGACAGAAGAAAGAACCATATGCAGACAC--------GCAATTTAGAGCAATATGTACGGGACAATGTGGGAACTTGAACTG Template switch alignment (log-probability: -27.8) TCTTGGCAACAGACAGAAGAAAGAACCATATGCAGACACa|GCATATGG|TTAGAGCAATATGTACGGGACAATGTGGGAACTTGAACTG TCTTGGCAACAGACAGAAGAAAGAACCATATGCAGACACG|GCATATGG|TTAGAGCAATATGTACGGGACAATGTGGGAACTTGAACTG ========== Event 2177 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: TTATTTCAAGAGGAAAAGGGGTCCTAGCT--AAACTCTCAATGCTTGCATTTT Chimp: Gorilla: TTATTTCAAGAGGAAAAGGGG-TTTAGCTAGGAACTCTCAATGCTTGCATTTT ↓ 1 3 24 ↑ 13 4 Human: TTATTTCAAGAGGAAAAGGGGTCCTAGCT--AAACTCTCAATGCTTGCATTTT Cluster: [ ] Orangutan: TTATTTCAAGAGGAAAAGGGA-TTTAGCTAGGAACTCTCAATGCTTGCATTTT Gorilla > Human --------------- chr2:234335796-234335803 Template switch process: F1: L ATTCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGT 1 F3: 4 AACTCTCAATGCTTGCATTTTGCTTATCAGGACTCAAGGC R RF: ATTCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGTTTAGCTAGGAACTCTCAATGCTTGCATTTTGTTTATCAGGACTCAAGGC RR: TAAGACATCGGTCCGTTATCAATAAAGTTCTCCTTTTCCCCAAATCGATCCTTGAGAGTTACGAACGTAAAACAAATAGTCCTGAGTTCCG F2: 3 ATCGATCC 2 Unidirectional alignment (log-probability: -33.3) TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGTccTAGCTA--AACTCTCAATGCTTGCATTTTGcTTATCAGGACTCAAGGC TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGTT-TAGCTAGGAACTCTCAATGCTTGCATTTTGTTTATCAGGACTCAAGGC Template switch alignment (log-probability: -22.3) TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGT|CCTAGCTA|AACTCTCAATGCTTGCATTTTGcTTATCAGGACTCAAGGC TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGT|CCTAGCTA|AACTCTCAATGCTTGCATTTTGTTTATCAGGACTCAAGGC Human > Gorilla --------------- chr2A:99706670-99706678 Template switch process: F1: L ATTCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGT 1 F3: 4 AACTCTCAATGCTTGCATTTTGTTTATCAGGACTCAAGGC R RF: ATTCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGTCCTAGCTAAACTCTCAATGCTTGCATTTTGCTTATCAGGACTCAAGGC RR: TAAGACATCGGTCCGTTATCAATAAAGTTCTCCTTTTCCCCAGGATCGATTTGAGAGTTACGAACGTAAAACGAATAGTCCTGAGTTCCG F2: 3 GGATCGATT 2 Unidirectional alignment (log-probability: -34.7) TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGTt-TAGCTAggAACTCTCAATGCTTGCATTTTGtTTATCAGGACTCAAGGC TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGTCCTAGCTA--AACTCTCAATGCTTGCATTTTGCTTATCAGGACTCAAGGC Template switch alignment (log-probability: -22.4) TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGT|TTAGCTAGG|AACTCTCAATGCTTGCATTTTGtTTATCAGGACTCAAGGC TCTGTAGCCAGGCAATAGTTATTTCAAGAGGAAAAGGGGT|TTAGCTAGG|AACTCTCAATGCTTGCATTTTGCTTATCAGGACTCAAGGC ========== Event 2178 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AATCAATTGAGTAGTACATTAAACACAGTCATTTCATAGACTCCTCTTTTATCTTCTACTAAATGGCATTTCTCTTATTAGCATTCATAAAATAATCACTGTGTTTATACTAGAAATTATTTAAAGTA Chimp: AATCAATTGAGTAGTACATTAAACACAGTCATTTCATAGACTCCTCTTTTATCTTCTACTAAATGTCATTTCCCTTATTAGCATTCATAAAATAATC--AGTGT--TTACTAGAAATTATTTAAAGTA ↓ 3 2 1 4 Gorilla: AATCAATTGAGTAGTACATTAAACACAGTCATTTCATAGACTCCTCTTTTATCTTCTACTAAATGGCATTTCTCTTATTAGCATTCATAAAATAATCACTGTGTTTATACTAGAAATTATTTAAAGTA Human: AATCAATTGAGTAGTACATTAAACACAGTCATTTCATAGACTCCTCTTTTATCTTCTACTAAATGGCATTTCTCTTATTAGCATTCATAAAATAATCACTGTGTTTATACTAGAAATTATTTAAAGTA Cluster: [ ] Orangutan: AATCAATTGAGTACTACATTAAACACAGTCATTTCATAGACTCCTCATTTGTCTTCTACTAAATGGCATTTCTTTTATTAGCATTCATAAAATAATCACTGTGTTTATACTAAAAATTATTTAAAGTA Chimp > Gorilla --------------- chr2A:27158114-27158122 Template switch process: F1: L ACAGTCATTTCATAGACTCCTCTTTTATCTTCTACTAAATGGCATTTCTCTTATTAGCATTCATAAAATAATCA 1 F3: 4 TACTAG R RF: TAAACACAGTCATTTCATAGACTCCTCTTTTATCTTCTACTAAATGTCATTTCCCTTATTAGCATTCATAAAATAATCAGTGTTTACTAG RR: ATTTGTGTCAGTAAAGTATCTGAGGAGAAAATAGAAGATGATTTACAGTAAAGGGAATAATCGTAAGTATTTTATTAGTCACAAATGATC F2: 3 ATTTGTGTC 2 Unidirectional alignment (log-probability: -37.5) CTAAATGgCATTTCtCTTATTAGCATTCATAAAATAATCActGTGTTtaTACTAG CTAAATGTCATTTCCCTTATTAGCATTCATAAAATAATCA--GTGTT--TACTAG Template switch alignment (log-probability: -27.9) CTAAATGgCATTTCtCTTATTAGCATTCATAAAATAATCA|CTGTGTTTA|TACTAG CTAAATGTCATTTCCCTTATTAGCATTCATAAAATAATCA|CTGTGTTTA|TACTAG ========== Event 2179 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTTAGCATTTCTCTTAAGTTCAGAAAGGGAGATGTCTGAACTACAGTTGTCCGAAGGAGTC ↑ 3 2 1 4 Chimp: GGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATGG--AGGCTACAGTTGTCCGAAGGAGTC Gorilla: GGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATGG--AGGCTACAGTTGTCCAAAGGAGTC ↓ 3 2 1 4 Human: GGTTAGCATTTCTCTTAAGTTCAGAAAGGGAGATGTCTGAACTACAGTTGTCCGAAGGAGTC Cluster: [ ] Orangutan: GGTTAGCATTTCTCCTAAGTTCAGAAAGAGAGATGG--AGGCTACAGTTGTCCAGAGGAGTC Chimp > Human ------------- chr2:233684126-233684131 Template switch process: F1: L GCTTCTGGTTAGCATTTCTCTTAAGTTCAGAAAGGGAGATG 1 F3: 4 CTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT R RF: GCTTCTGGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATGGAGGCTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT RR: CGAAGACCAATCGTAAAGAGGATTCAAGTCTTTCCCTCTACCTCCGATGTCAACAGGCTTCCTCAGGATCCACTCAGAACTAGAA F2: 3 AAGTCT 2 Unidirectional alignment (log-probability: -36) CTTCTGGTTAGCATTTCTCtTAAGTTCAGAAAGGGAGAT----GtctgaaCTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT CTTCTGGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATGGAGG------CTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT Template switch alignment (log-probability: -22) CTTCTGGTTAGCATTTCTCtTAAGTTCAGAAAGGGAGATG|TCTGAA|CTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT CTTCTGGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATG|TCTGAA|CTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT Gorilla > Human --------------- chr2:233684126-233684131 Template switch process: F1: L GCTTCTGGTTAGCATTTCTCTTAAGTTCAGAAAGGGAGATG 1 F3: 4 CTACAGTTGTCCGAAGGAGTCCTAGGTGAGTCTTGATCTT R RF: GCTTCTGGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATGGAGGCTACAGTTGTCCAAAGGAGTCCTAGGTGAGTCTTGATCTT RR: CGAAGACCAATCGTAAAGAGGATTCAAGTCTTTCCCTCTACCTCCGATGTCAACAGGTTTCCTCAGGATCCACTCAGAACTAGAA F2: 3 AAGTCT 2 Unidirectional alignment (log-probability: -40.5) CTTCTGGTTAGCATTTCTCtTAAGTTCAGAAAGGGAGAT----GtctgaaCTACAGTTGTCCgAAGGAGTCCTAGGTGAGTCTTGATCTT CTTCTGGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATGGAGG------CTACAGTTGTCCAAAGGAGTCCTAGGTGAGTCTTGATCTT Template switch alignment (log-probability: -27.5) CTTCTGGTTAGCATTTCTCtTAAGTTCAGAAAGGGAGATG|TCTGAA|CTACAGTTGTCCgAAGGAGTCCTAGGTGAGTCTTGATCTT CTTCTGGTTAGCATTTCTCCTAAGTTCAGAAAGGGAGATG|TCTGAA|CTACAGTTGTCCAAAGGAGTCCTAGGTGAGTCTTGATCTT ========== Event 2180 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTATGTACTGGAAGCAAGAGCTTGACCTA----ACTTTATCAATTCATTCATCTG Chimp: TTTATGTACTGGAAGCAAGAGCTTGACCTA----ACTTTATCAATTCAATCATCTG ↓ 3 1 2 4 Gorilla: TTTATGTACTGAAAGCAAGAGCTTGAGGTCAAGCTCTTTATCAATTCAATCATCTG ↑ 3 1 2 4 Human: TTTATGTACTGGAAGCAAGAGCTTGACCTA----ACTTTATCAATTCATTCATCTG Cluster: [ ] Orangutan: TTTACATACTGGAAGCAGGAGCTTGACCTA----ACTTTATCAATTAAATCATCTG Human > Gorilla --------------- chr2A:24984830-24984838 Template switch process: F1: L AACACCTCTAAATTTTTTATGTACTGAAAGCAAGAGCTTGA 1 F3: 4 CTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA R RF: AACACCTCTAAATTTTTTATGTACTGGAAGCAAGAGCTTGACCTAACTTTATCAATTCATTCATCTGCCTCTTTTAGTCAAAACTA RR: TTGTGGAGATTTAAAAAATACATGACCTTCGTTCTCGAACTGGATTGAAATAGTTAAGTAAGTAGACGGAGAAAATCAGTTTTGAT F2: 3 TCGAACTGG 2 Unidirectional alignment (log-probability: -44.3) ACACCTCTAAATTTTTTATGTACTGaAAGCAAGAGCTTGAggTcAagctCTTTATCAATTCAaTCATCTGCCTCTTTTAGTCAAAACTA ACACCTCTAAATTTTTTATGTACTGGAAGCAAGAGCTTGACCTAA----CTTTATCAATTCATTCATCTGCCTCTTTTAGTCAAAACTA Template switch alignment (log-probability: -27.9) ACACCTCTAAATTTTTTATGTACTGaAAGCAAGAGCTTGA|GGTCAAGCT|CTTTATCAATTCAaTCATCTGCCTCTTTTAGTCAAAACTA ACACCTCTAAATTTTTTATGTACTGGAAGCAAGAGCTTGA|GGTCAAGCT|CTTTATCAATTCATTCATCTGCCTCTTTTAGTCAAAACTA Chimp > Gorilla --------------- chr2A:24984830-24984838 Template switch process: F1: L AACACCTCTAAATTTTTTATGTACTGAAAGCAAGAGCTTGA 1 F3: 4 CTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA R RF: AACACCTCTAAATTTTTTATGTACTGGAAGCAAGAGCTTGACCTAACTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA RR: TTGTGGAGATTTAAAAAATACATGACCTTCGTTCTCGAACTGGATTGAAATAGTTAAGTTAGTAGACGGAGAAAATCAGTTTTGAT F2: 3 TCGAACTGG 2 Unidirectional alignment (log-probability: -38.8) ACACCTCTAAATTTTTTATGTACTGaAAGCAAGAGCTTGAggTcAagctCTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA ACACCTCTAAATTTTTTATGTACTGGAAGCAAGAGCTTGACCTAA----CTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA Template switch alignment (log-probability: -22.4) ACACCTCTAAATTTTTTATGTACTGaAAGCAAGAGCTTGA|GGTCAAGCT|CTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA ACACCTCTAAATTTTTTATGTACTGGAAGCAAGAGCTTGA|GGTCAAGCT|CTTTATCAATTCAATCATCTGCCTCTTTTAGTCAAAACTA ========== Event 2181 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTAGTTGAAGTATCTGGGGTGATCTTAAAGTCAAATATTAAAGGTAATTTCATTCTCCTAACAA----------------TGATCAGAGCTTATCAGAAAAGGTCAT Chimp: GTAGTTGAGGTATCTGGGGTGATCTTAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAA----------------TGATCAGAGCTTATCAGAAAAGGTCAT ↑ 3 2 1 4 Gorilla: GTAGTTGAAGTATCTGGGGTGATCTTAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAATTTCAATAAGCTCCTAAGTTAGGAGCTTATCAGAAAAGGTCAT ↓ 3 2 1 4 Human: GTAGTTGAAGTATCTGGGGTGATCTTAAAGTCAAATATTAAAGGTAATTTCATTCTCCTAACAA----------------TGATCAGAGCTTATCAGAAAAGGTCAT Cluster: [ ] Orangutan: GTATTTGAAGTATCTGCAGTGATCTTAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAA----------------TGATCAGAGCTTATCATAAAAGGTCAT Gorilla > Human --------------- chr2:159328961-159328965 Template switch process: F1: L CTTAAAGTCAAATATTAAAGGTAATTTCATTCTCCTAACAAT 1 F3: 4 GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT R RF: TGATCTTAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAATTTCAATAAGCTCCTAAGTTAGGAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT RR: ACTAGAATTTCAGTTTATAATTTCCATTAAAGTTAGAGGATTGTTAAAGTTATTCGAGGATTCAATCCTCGAATAGTCTTTTCCAGTAACAATCGTGTTGAAAATAA F2: 3 ACTAG 2 Unidirectional alignment (log-probability: -33) TAAAGTCAAATATTAAAGGTAATTTCAtTCTCCTAACAAT--------------------GatcaGAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT TAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAATTTCAATAAGCTCCTAAGTTAG----GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT Template switch alignment (log-probability: -21.9) TAAAGTCAAATATTAAAGGTAATTTCAtTCTCCTAACAAT|GATCA|GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT TAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAAT|GATCA|GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT Gorilla > Chimp --------------- chr2A:26956569-26956573 Template switch process: F1: L CTTAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAAT 1 F3: 4 GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT R RF: TGATCTTAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAATTTCAATAAGCTCCTAAGTTAGGAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT RR: ACTAGAATTTCAGTTTATAATTTCCATTAAAGTTAGAGGATTGTTAAAGTTATTCGAGGATTCAATCCTCGAATAGTCTTTTCCAGTAACAATCGTGTTGAAAATAA F2: 3 ACTAG 2 Unidirectional alignment (log-probability: -27.4) TAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAAT--------------------GatcaGAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT TAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAATTTCAATAAGCTCCTAAGTTAG----GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT Template switch alignment (log-probability: -16.4) TAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAAT|GATCA|GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT TAAAGTCAAATATTAAAGGTAATTTCAATCTCCTAACAAT|GATCA|GAGCTTATCAGAAAAGGTCATTGTTAGCACAACTTTTATT ========== Event 2182 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTTTAATTTTTAGTTTGTATAG-----------------AATCTCAAAATATCTCACGTTGTCATTGTAAATAATTTGTCATTGTAAAATAGGTGCATTTTCCAGAACAATACTGATTCTATGTGCTCTATTCACTCTTGAATAATTTCAGTCTTATGCCAATGCTGATAGGCTAAATGTGGACTGTTCTTTTCAA Chimp: TCTTTAATTTTTAGTTTGTATAG-----------------AATCTCAAAATATCTCACGCTGTCATTGTAAATAATTTGTCATTGTAAAATAGTTGCATTTTCCAGAACAATACTGATTCTATGTGCTCTATTCACTCTTGAATAATTTCAATCTTATGCCAGTGCTGATAGGCTAAATGTGGACTGTTCTTTTCAA Gorilla: TCTTTAATTTTTAGTTTGTATTT----------------------------------AGCTGTCATTGTAAATAATTTGTCATTGTAAAATAGTTGCATTTTCCAGAACAATACTGATTCTATGTGCTCTATTCACTCTTGAATAATTTCAATCTTATGCCAATGCTGATAGGCTAAATGTGGACTGTTCTTTTCAA ↑ 1 4 3 2 Human: TCTTTAATTTTTAGTTTGTATAG-----------------AATCTCAAAATATCTCACGTTGTCATTGTAAATAATTTGTCATTGTAAAATAGGTGCATTTTCCAGAACAATACTGATTCTATGTGCTCTATTCACTCTTGAATAATTTCAGTCTTATGCCAATGCTGATAGGCTAAATGTGGACTGTTCTTTTCAA Cluster: [ ] Orangutan: TCTTTAATTTTTAGTTTGCATAGAATCTCAAAATATCTCA-----------------CGCTGTCATTGTAAATAATTTGGCATTGTAAAATAGTTGCATTTTCTAGAACAATACTGATTCTATGTGCTCTATTCACTCTTGAATAATTTCAATCTTATGCCAATGCTGATAGGCTAAATGTGGACTGTTCTTTTCAA Human > Gorilla --------------- chr2A:84517780-84517784 Template switch process: F1: L GTATGCTAGGAACTTCCATTTCTTTAATTTTTAGTTTGTAT 1 F3: 4 TGTCATTGTAAATAATTTGTCATTGTAAAATAGTTGCATT R RF: GTATGCTAGGAACTTCCATTTCTTTAATTTTTAGTTTGTATAGAATCTCAAAATATCTCACGTTGTCATTGTAAATAATTTGTCATTGTAAAATAGGTGCATTTTCCAGAACAATACTGATTCTATGTGCTCTATTCACTCTTGAATAATTTCAGTCTTATGCCAATGCTGATAGGCTAA RR: CATACGATCCTTGAAGGTAAAGAAATTAAAAATCAAACATATCTTAGAGTTTTATAGAGTGCAACAGTAACATTTATTAAACAGTAACATTTTATCCACGTAAAAGGTCTTGTTATGACTAAGATACACGAGATAAGTGAGAACTTATTAAAGTCAGAATACGGTTACGACTATCCGATT F2: 3 CGATT 2 Unidirectional alignment (log-probability: -33) TATGCTAGGAACTTCCATTTCTTTAATTTTTAGTTTGTAT---------------------TtagcTGTCATTGTAAATAATTTGTCATTGTAAAATAGtTGCATT TATGCTAGGAACTTCCATTTCTTTAATTTTTAGTTTGTATAGAATCTCAAAATATCTCACGT----TGTCATTGTAAATAATTTGTCATTGTAAAATAGGTGCATT Template switch alignment (log-probability: -21.9) TATGCTAGGAACTTCCATTTCTTTAATTTTTAGTTTGTAT|TTAGC|TGTCATTGTAAATAATTTGTCATTGTAAAATAGtTGCATT TATGCTAGGAACTTCCATTTCTTTAATTTTTAGTTTGTAT|TTAGC|TGTCATTGTAAATAATTTGTCATTGTAAAATAGGTGCATT ========== Event 2183 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TACATATGTCAGGCATTTGTTTACTATCAAATATGTACATGTAGAGGAAGAAAATGAGCATGC Chimp: TACATATGTCAGGCATTTGTTCACTATCAAATATGTACATGTAGAGGAAGAAAATGAGCATGC ↓ 1 4 3 2 Gorilla: TACATATGTCAGGCATTTGTTTA-TA-TGTACATGTACATGTAGAGGAAGAAAATGAGCATGC Human: TACATATGTCAGGCATTTGTTTACTATCAAATATGTACATGTAGAGGAAGAAAATGAGCATGC Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr2A:84778593-84778601 Template switch process: F1: L ATAAGGGTGCATCCAGCACTTACATATGTCAGGCATTTGTT 1 F3: 4 ATGTACATGTAGAGGAAGAAAATGAGCATGCATTTAGAGC R RF: ATGAGGGTGCATCCAGCACTTACATATGTCAGGCATTTGTTCACTATCAAATATGTACATGTAGAGGAAGAAAATGAGCATGCATTTAGAGC RR: TACTCCCACGTAGGTCGTGAATGTATACAGTCCGTAAACAAGTGATAGTTTATACATGTACATCTCCTTCTTTTACTCGTACGTAAATCTCG F2: 3 CATGTATAT 2 Unidirectional alignment (log-probability: -38.2) TaAGGGTGCATCCAGCACTTACATATGTCAGGCATTTGTT----------TatatgtacATGTACATGTAGAGGAAGAAAATGAGCATGCATTTAGAGC TGAGGGTGCATCCAGCACTTACATATGTCAGGCATTTGTTCACTATCAAAT--------ATGTACATGTAGAGGAAGAAAATGAGCATGCATTTAGAGC Template switch alignment (log-probability: -27.9) TaAGGGTGCATCCAGCACTTACATATGTCAGGCATTTGTT|TAtATGTAC|ATGTACATGTAGAGGAAGAAAATGAGCATGCATTTAGAGC TGAGGGTGCATCCAGCACTTACATATGTCAGGCATTTGTT|TACATGTAC|ATGTACATGTAGAGGAAGAAAATGAGCATGCATTTAGAGC ========== Event 2184 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTGCTATTACTTCCCTCATTGCTGACCTAGAGATCAGCAATC----------TGGAACTCT ↑ 3 2 1 4 Chimp: TGTGCTATTACTTCCCTCATTGCTGACTTAGGGAAGATCTCTC----------TGGAACTCT Gorilla: TATGCTATTACTTCCGTCATTGCTGACCTAGGGAAGATCTCTC----------TGGAACTCT Human: TGTGCTATTACTTCCCTCATTGCTGACCTAGAGATCAGCAATC----------TGGAACTCT Cluster: [ ] Orangutan: TGTGCTATTACTTTCCTCATTGCTGACCTAGGGAAGATctctctggaactctctggaactct Chimp > Human ------------- chr2:84250879-84250885 Template switch process: F1: L CTTAGTCTGGCGGCTGTGCTATTACTTCCCTCATTGCTGACCTAGAGA 1 F3: 4 TCTGGAACTCTCTATGAAGGAAATAGAAAATCTTTCTAGG R RF: CTTAGTCTGGCGGCTGTGCTATTACTTCCCTCATTGCTGACTTAGGGAAGATCTCTCTGGAACTCTCTATGAAGGAAATAGAAAATCTTTCTAGG RR: GAATCAGACCGCCGACACGATAATGAAGGGAGTAACGACTGAATCCCTTCTAGAGAGACCTTGAGAGATACTTCCTTTATCTTTTAGAAAGATCC F2: 3 AACGACT 2 Unidirectional alignment (log-probability: -40.5) GGCGGCTGTGCTATTACTTCCCTCATTGCTGAC-------------CtagagatcagcaaTCTGGAACTCTCTATGAAGGAAATAGAAAATCTTTCTAGG GGCGGCTGTGCTATTACTTCCCTCATTGCTGACTTAGGGAAGATCTC-------------TCTGGAACTCTCTATGAAGGAAATAGAAAATCTTTCTAGG Template switch alignment (log-probability: -28.3) GGCGGCTGTGCTATTACTTCCCTCATTGCTGACcTAGaGA|TCAGCAA|TCTGGAACTCTCTATGAAGGAAATAGAAAATCTTTCTAGG GGCGGCTGTGCTATTACTTCCCTCATTGCTGACTTAGGGA|TCAGCAA|TCTGGAACTCTCTATGAAGGAAATAGAAAATCTTTCTAGG ========== Event 2185 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGGCCACAGTTATAACAAGGATCCAGTGAAGGATCCTTGTTATAACTGTGAGCTGTG ↑ 3 1 2 4 Chimp: GGGGCCACAGTTATAACAAGGATCCTTCACTGGATCTTTGTTATAACTGTGAGCTGTG Gorilla: GGGGCCACAGTTATAACAAGGATCCTTCACTGGATCCTTGTTATAACTGTGAGCTGTG Human: GGGGCCACAGTTATAACAAGGATCCAGTGAAGGATCCTTGTTATAACTGTGAGCTGTG Cluster: [ ] Orangutan: GGGGC-------------------------------TGTGATATAACTGTGAGCTGTG Chimp > Human ------------- chr2:156956194-156956205 Template switch process: F1: L ACCAGGGCTCCAATCAGGGGCCACAGTTATAACAAGGATCC 1 F3: 4 TTGTTATAACTGTGAGCTGTGATTGCACCACTGCATCCTT R RF: ACCAGGGCTCCAATCAGGGGCCACAGTTATAACAAGGATCCTTCACTGGATCTTTGTTATAACTGTGAGCTGTGATTGCACCACTGCATCCTT RR: TGGTCCCGAGGTTAGTCCCCGGTGTCAATATTGTTCCTAGGAAGTGACCTAGAAACAATATTGACACTCGACACTAACGTGGTGACGTAGGAA F2: 3 CCTAGGAAGTGA 2 Unidirectional alignment (log-probability: -36.1) CCAGGGCTCCAATCAGGGGCCACAGTTATAACAAGGATCCagtgaa------GGATCcTTGTTATAACTGTGAGCTGTGATTGCACCACTGCATCCTT CCAGGGCTCCAATCAGGGGCCACAGTTATAACAAGGATCC------TTCACTGGATCTTTGTTATAACTGTGAGCTGTGATTGCACCACTGCATCCTT Template switch alignment (log-probability: -16.8) CCAGGGCTCCAATCAGGGGCCACAGTTATAACAAGGATCC|AGTGAAGGATCC|TTGTTATAACTGTGAGCTGTGATTGCACCACTGCATCCTT CCAGGGCTCCAATCAGGGGCCACAGTTATAACAAGGATCC|AGTGAAGGATCC|TTGTTATAACTGTGAGCTGTGATTGCACCACTGCATCCTT ========== Event 2186 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGTCGAGGACCCCTCAGTGT--------------------GCAGGGGTAAGAAGAGAAAGGGGACCCCTAgtcatatctaggtggagacctcctaggatcctgagaattctaaatttcaacccggccttccagatttttaggaaggtacatttgtcaaggtaggcagatacagcatt ↓ 4 1 3 2 Chimp: GTGTCGAGGACCCCTCAGTGT----------GCATGACAGTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAgtcatatctaggcggagacctcctgggatcctgagaattctaaatttcaacccggccttccagatttttaggaaggtacatttgtcaaggtaggcagatagagcttt Gorilla: GTGTCTAGGACCCCTCAGTGTGCATGACAGT----------ACAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATCTAggtggagacctcctaggatcctgagaattctaaatttcaacccggccttccagatttttaggaaggtacatttgtcaaggtaggcagatagagcatt Human: GTGTCGAGGACCCCTCAGTGT--------------------GCAGGGGTAAGAAGAGAAAGGGGACCCCTAgtcatatctaggtggagacctcctaggatcctgagaattctaaatttcaacccggccttccagatttttaggaaggtacatttgtcaaggtaggcagatacagcatt Cluster: [ ] Orangutan: GTGTCGAGGACCCTTCAGTGTGCATGACAGT----------GCAGGGGTAAGAAGAGAGAGGGGACCCCTAGTCATATCTAGGTGGAgacctcctaggatcctgagaattctaaatttcaacccggccttccagatttttaggaaggtacatttgtcaaggtaggcagatagagcatt Human > Chimp ------------- chr2A:87291543-87291547 Template switch process: F1: L GTGCCCTTGGGTGTAAGCAGGTGTCGAGGACCCCTCAGTGTGCA 1 F3: 4 GTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATCTA R RF: GTACCCTTGGGTGTAAGCAGGTGTCGAGGACCCCTCAGTGTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATCTAGGTGGAGACCTCCTAGGATCCTGAGAATTCTAAATTTCAACCCGGCCTTCCAGATTTTTAGGAAGGTACATTTGTCA RR: CATGGGAACCCACATTCGTCCACAGCTCCTGGGGAGTCACACGTCCCCATTCTTCTCTTTCCCCTGGGGATCAGTATAGATCCACCTCTGGAGGATCCTAGGACTCTTAAGATTTAAAGTTGGGCCGGAAGGTCTAAAAATCCTTCCATGTAAACAGT F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -31.3) CCTTGGGTGTAAGCAGGTGTCGAGGACCCCTCAGTgtgcatgacaGTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATC CCTTGGGTGTAAGCAGGTGTCGAGGACCCCTCAGT----------GTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATC Template switch alignment (log-probability: -22) CCTTGGGTGTAAGCAGGTGTCGAGGACCCCTCAGTGTGCA|TGACA|GTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATC CCTTGGGTGTAAGCAGGTGTCGAGGACCCCTCAGTGTGCA|TGACA|GTGCAGGGGTAAGAAGAGAAAGGGGACCCCTAGTCATATC ========== Event 2187 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGACGAGTGGTTCC Chimp: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTCC ↓ 4 3 2 1 Gorilla: TCAGCCAGCAGTTGGCCTGGATAGACACAGGGAATGTGTCTACCAGTTGGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTCC Human: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGACGAGTGGTTCC Cluster: [ ] Orangutan: TCAGCCAGCAGTTGGCCTGGA-----------------------TCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTCC Chimp > Gorilla --------------- chr2A:88150926-88150934 Template switch process: F1: L TGTTTCTTTTTGCTCTCTCTTCAGCCAGCAGTTGGCCTGGA----------TAGACACAGGGAATGT 1 F3: 4 TTGGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTC R RF: TGTTTCTTTTTGCTCTCTCTTCAGCCAGCAGTTGGCCTGGATCTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGGTTC RR: ACAAAGAAAAACGAGAGAGAAGTCGGTCGTCAACCGGACCTAGAAACGACCATCTGTGTCCCTTACAAGAGGAACTCCTCACCAAG F2: 3 GACCATCTG 2 Unidirectional alignment (log-probability: -55.1) TCTTCAGCCAGCAGTTGGCCTGGATagacacagggaatgtgtctaccagTTgGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG TCTTCAGCCAGCAGTTGGCCTGGAT-----------------------CTTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG Template switch alignment (log-probability: -33.1) TCTTCAGCCAGCAGTTGGCCTGGA----------TAGACACAGGGAATGT|GTCTACCAG|TTgGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG TCTTCAGCCAGCAGTTGGCCTGGATCTTTGCTGGTAGACACAGGGAATGT|GTCTACCAG|TTTGCTGGTAGACACAGGGAATGTTCTCCTTGAGGAGTGG ========== Event 2188 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTTAGGAAGCCCAGGATGTAGCATAGAGCAGTAGCCCCTGCGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGA-------------TCAGTGCTAGGGATCAGGCTCAAGGGTCAGGCCTGGC Chimp: CTTTAGGAAGCCCAGGATGTAGCATAGAGCAGTAGCCCCTGCGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGA-------------TCAGTGCTAGGGATCAGGCTCAAGGGTCAGGCCTGGC ↑ 3 2 4 1 Gorilla: CTTTAGGAAGCCCAGGATGTAGCATAGAGCAGTAGCCCCTGCGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGA--------------------------TCAGGCTCAAAGGTCAGGCCTGGC ↓ 3 2 4 1 Human: CTTTAGGAAGCCCAGGATGTAGCATAGAGCAGTAGCCCCTGCGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGA-------------TCAGTGCTAGGGATCAGGCTCAAGGGTCAGGCCTGGC Cluster: [ ] Orangutan: CTTTAGGAAGCCCAGGATGTAGCATAGAGCAGTAGGCCCTGTGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCTAGATGCCATACTGGGATCAGTGCTAGGGA-------------TCAGGCTCAAGGGTCAGGCCTGGC Gorilla > Human --------------- chr2:88082527-88082531 Template switch process: F1: L GCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAG 1 F3: 4 GGGATCAGGCTCAAGGGTCAGGCCTGGCCTTTGGGCTGGTCCTT R RF: TAGCATAGAGCAGTAGCCCCTGCGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAGGCTCAAAGGTCAGGCCTGGCCTTTGGGCTGGTCCTT RR: ATCGTATCTCGTCATCGGGGACGCCACGGGAGTCGACCGAGACGTGGACAGATAGGGGAAGGTCTACGGTACGACCCTAGTCCGAGTTTCCAGTCCGGACCGGAAACCCGACCAGGAA F2: 3 ATCGT 2 Unidirectional alignment (log-probability: -35.1) GCACCTGTCTATCCCCTTCCAGATGCCATGCTGGgatcagtgctaggGATCAGGCTCAAgGGTCAGGCCTGGCCTTTGGGCTGGT GCACCTGTCTATCCCCTTCCAGATGCCATGCTGG-------------GATCAGGCTCAAAGGTCAGGCCTGGCCTTTGGGCTGGT Template switch alignment (log-probability: -22.1) GCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAG|TGCTA|GGGATCAGGCTCAAgGGTCAGGCCTGGCCTTTGGGCTGGT GCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAG|TGCTA|GGGATCAGGCTCAAAGGTCAGGCCTGGCCTTTGGGCTGGT Gorilla > Chimp --------------- chr2A:88822158-88822162 Template switch process: F1: L GCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAG 1 F3: 4 GGGATCAGGCTCAAGGGTCAGGCCTGGCCTTTGGGCTGGTCCTT R RF: TAGCATAGAGCAGTAGCCCCTGCGGTGCCCTCAGCTGGCTCTGCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAGGCTCAAAGGTCAGGCCTGGCCTTTGGGCTGGTCCTT RR: ATCGTATCTCGTCATCGGGGACGCCACGGGAGTCGACCGAGACGTGGACAGATAGGGGAAGGTCTACGGTACGACCCTAGTCCGAGTTTCCAGTCCGGACCGGAAACCCGACCAGGAA F2: 3 ATCGT 2 Unidirectional alignment (log-probability: -35.1) GCACCTGTCTATCCCCTTCCAGATGCCATGCTGGgatcagtgctaggGATCAGGCTCAAgGGTCAGGCCTGGCCTTTGGGCTGGT GCACCTGTCTATCCCCTTCCAGATGCCATGCTGG-------------GATCAGGCTCAAAGGTCAGGCCTGGCCTTTGGGCTGGT Template switch alignment (log-probability: -22.1) GCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAG|TGCTA|GGGATCAGGCTCAAgGGTCAGGCCTGGCCTTTGGGCTGGT GCACCTGTCTATCCCCTTCCAGATGCCATGCTGGGATCAG|TGCTA|GGGATCAGGCTCAAAGGTCAGGCCTGGCCTTTGGGCTGGT ========== Event 2189 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CTACTATGTTGAGGACAATTGTGAATGGTATGAAGTACCATTCATGATGGTATGAAGTTCCAATCCTGGCTCTGTCCC Chimp: CTACTATGTTGAGGACAATCGTGAATGGT----------------------ATGAAgttctaatcctggctctgtccc ↓ 3 4 2 1 Gorilla: CTACTATGTTGAGGACAATCGTGAATGGTATGAAGTACCATTCATGATGGTATGAAgttctaatcctggctctgtccc Human: CTACTATGTTGAGGACAATTGTGAATGGTATGAAGTACCATTCATGATGGTATGAAGTTCCAATCCTGGCTCTGTCCC Cluster: [ ] Orangutan: CTACTGTGATGAGGAGAATCGTGAATGGTATGAAGTACCATTCATGATGGTATGAAgttctaatcctggctctgtccc Chimp > Gorilla --------------- chr2A:88605717-88605726 Template switch process: F1: L AACCAGGCAAGACTACTATGTTGAGGACAATCGTGAATGGTATGAAGT 1 F3: 4 ATGGTATGAAGTTCTAATCCTGGCTCTGTCCCGAAAGTGTTGTGG R RF: AACCAGGCAAGGCTACTATGTTGAGGACAATCGTGAATGGTATGAAGTTCTAATCCTGGCTCTGTCCCGAAAGTGTTGTGG RR: TTGGTCCGTTCCGATGATACAACTCCTGTTAGCACTTACCATACTTCAAGATTAGGACCGAGACAGGGCTTTCACAACACC F2: 3 GTACTTACCA 2 Unidirectional alignment (log-probability: -48) AAGaCTACTATGTTGAGGACAATCGTGAatggtatgaagtaccattcatgATGGTATGAAGTTCTAATCCTGGCTCTGTCCCGAAAGTGT AAGGCTACTATGTTGAGGACAATCGTGA----------------------ATGGTATGAAGTTCTAATCCTGGCTCTGTCCCGAAAGTGT Template switch alignment (log-probability: -28.3) AAGaCTACTATGTTGAGGACAATCGTGAATGGTATGAAGT|ACCATTCAtG|ATGGTATGAAGTTCTAATCCTGGCTCTGTCCCGAAAGTGT AAGGCTACTATGTTGAGGACAATCGTGAATGGTATGAAGT|ACCATTCACG|ATGGTATGAAGTTCTAATCCTGGCTCTGTCCCGAAAGTGT ========== Event 2190 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGAAAAGGACTTTCTCCTGGGCAATG------------------------CCAGGCTGTATCCTGGCACTG---------------------CCAGGCTTCTTGATGAATGGTTTCC Chimp: AGAAAAGGACTTTCTCCTGGGCACTG---------------------------------------------CCAGGCTGTATCCTGGCACTGCCAGGCTTCTTGATGAATGCTTTCC Gorilla: AGAAAAGGACTTTCTCCTGGGCAATGCCAGGATACAGCC--------------------------------------------------------TGCTTCTTGATGAATGGTTTCC ↓ 4 3 1 2 ↑ 3 1 2 4 Human: AGAAAAGGACTTTCTCCTGGGCAATG------------------------CCAGGCTGTATCCTGGCACTG---------------------CCAGGCTTCTTGATGAATGGTTTCC Cluster: [ ] Orangutan: AGAAAAGGACTTTCTCCTGGGCAATGCCAAGCTGTATCCTGGCACTGCCA---------------------------------------------GGCTTCTTGATGAATGGTTTCC Gorilla > Human --------------- chr2:98300266-98300274 Template switch process: F1: L AGTAGATTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG 1 F3: 4 GGCACTGCCAG----------GCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCCC R RF: AGTAGATTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGGATACAGCCTGCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCCT RR: TCATCTAAAAGTAAATCTTTTCCTGAAAGAGGACCCGTTACGGTCCTATGTCGGACGAAGAACTACTTACCAAAGGGACCGACGTAGACGACGGA F2: 3 TCCTATGTC 2 Unidirectional alignment (log-probability: -55.1) TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG-------CTgtatcctggcactgccagGCTTCTTGATGAATGGTTTCCCTGGCTGC TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGGATACAGCCT------------------GCTTCTTGATGAATGGTTTCCCTGGCTGC Template switch alignment (log-probability: -38.6) TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG|CTGTATCCT|GGCAcTGCCAG----------GCTTCTTGATGAATGGTTTCCCTGGCTGC TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG|CTGTATCCT|GGCAATGCCAGGATACAGCCTGCTTCTTGATGAATGGTTTCCCTGGCTGC Human > Gorilla --------------- chr2A:3167565-3167573 Template switch process: F1: L AGTAGATTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG 1 F3: 4 GCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCC R RF: AGTAGATTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGGCTGTATCCTGGCACTGCCAGGCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCC RR: TCATCTAAAAGTAAATCTTTTCCTGAAAGAGGACCCGTTACGGTCCGACATAGGACCGTGACGGTCCGAAGAACTACTTACCAAAGGGACCGACGTAGACGACGG F2: 3 TCCGACATA 2 Unidirectional alignment (log-probability: -38.5) TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGGatacagcCT------------------GCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCC- TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG-------CTGTATCCTGGCACTGCCAGGCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCCC Template switch alignment (log-probability: -17) TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG|ATACAGCCT|GCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCC TTTTCATTTAGAAAAGGACTTTCTCCTGGGCAATGCCAGG|ATACAGCCT|GCTTCTTGATGAATGGTTTCCCTGGCTGCATCTGCTGCC ========== Event 2191 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAACCAGAACTGTCAGTTT----------GCT--------GAGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTATCCTT ↑ 1 4 3 2 Chimp: AGAAACCAGAACTGTCAGTTT-----GTCCCACT----GTGCTTGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTATCCTT Gorilla: AGAAACCAGAACTGTCAGTTTGTCCC-----ACTGTGC----TTGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTATCCTT ↓ 1 4 3 2 Human: AGAAACCAGAACTGTCAGTTT----------GCT--------GAGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTATCCTT Cluster: [ ] Orangutan: Chimp > Human ------------- chr2:98459962-98459965 Template switch process: F1: L GCCCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG 1 F3: 4 GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA R RF: GCCCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTGTCCCACTGTGCTTGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA RR: CGGGGTCATTCAAGAGTCCCTCTTTGGTCTTGACAGTCAAACAGGGTGACACGAACAGTTTCCGTCTTCGGACAAGAGTCGTCACTGGAAAAAAT F2: 3 AGTC 2 Unidirectional alignment (log-probability: -27.6) CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTGctga-------------GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG----TCCCACTGTGCTTGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA Template switch alignment (log-probability: -15.8) CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG|CTGA|GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG|CTGA|GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA Gorilla > Human --------------- chr2:98459962-98459965 Template switch process: F1: L GCCCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG 1 F3: 4 GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA R RF: GCCCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTGTCCCACTGTGCTTGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA RR: CGGGGTCATTCAAGAGTCCCTCTTTGGTCTTGACAGTCAAACAGGGTGACACGAACAGTTTCCGTCTTCGGACAAGAGTCGTCACTGGAAAAAAT F2: 3 AGTC 2 Unidirectional alignment (log-probability: -26.7) CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG-----CTGa----GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTGTCCCACTGTGCTTGTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA Template switch alignment (log-probability: -16.3) CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG|CTGA|GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA CCCAGTAAGTTCTCAGGGAGAAACCAGAACTGTCAGTTTG|CTGA|GTCAAAGGCAGAAGCCTGTTCTCAGCAGTGACCTTTTTTA ========== Event 2192 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTCAAGATCAAAACCTGACTAGT----TTGTGGGATGTGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGAA Chimp: CCTTCAAGATCAAAACCTGACCAGT----TTGTGGGATGTGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGAA ↓ 1 4 3 2 Gorilla: CCTTCAAGATCAAAACCTGACTAGT--------TGTACGGGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGAA ↑ 1 4 3 2 Human: CCTTCAAGATCAAAACCTGACTAGT----TTGTGGGATGTGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGAA Cluster: [ ] Orangutan: CCTTCAAGATCAAAACCTGACTAGTTTGT----GGGATGTGCTTGTCTGTAGTGCCTGTACAACTTCAGCAATTGTTTGAA Human > Gorilla --------------- chr2A:103246271-103246276 Template switch process: F1: L TACCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGTT 1 F3: 4 GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA R RF: TACCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGTTTGTGGGATGTGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA RR: ATGGAACCACTCTCAGGGAAGTTCTAGTTTTGGACTGATCAAACACCCTACACGTACAGACATCACGGGCATGTTGAAGTCGTTAACAAACT F2: 3 GGCATG 2 Unidirectional alignment (log-probability: -26.8) CCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGT--------TGTacggGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA CCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGTTTGTGGGATGT----GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA Template switch alignment (log-probability: -16.5) CCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGTT|GTACGG|GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA CCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGTT|GTACGG|GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA Chimp > Gorilla --------------- chr2A:103246271-103246276 Template switch process: F1: L TATATACCTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACTAGTT 1 F3: 4 GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA R RF: TATATACTTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACCAGTTTGTGGGATGTGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA RR: ATATATGAAACCACTCTCAGGGAAGTTCTAGTTTTGGACTGGTCAAACACCCTACACGTACAGACATCACGGGCATGTTGAAGTCGTTAACAAACT F2: 3 GGCATG 2 Unidirectional alignment (log-probability: -37.9) CcTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACtAGT--------TGTacggGCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA CTTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACCAGTTTGTGGGATGT----GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA Template switch alignment (log-probability: -27.6) CcTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACtAGTT|GTACGG|GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA CTTTGGTGAGAGTCCCTTCAAGATCAAAACCTGACCAGTT|GTACGG|GCATGTCTGTAGTGCCCGTACAACTTCAGCAATTGTTTGA ========== Event 2193 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTTATTGTTTGATATACCTA----------------TGTTTCCACAGGGAAACAGACAAATGATAAAAATGTTC ↑ 1 3 4 2 Chimp: ATTTATTGTTTGATATACCTA--------CGCCTATCTGTTTCCCTGTGGAAACAGACAAATGATAAAAATGTTC ↓ 1 3 4 2 Gorilla: ATTTATTGTTTGATATACCTA----------------TGTTTCCACAGGGAAACAGACAAATGATAAAAATGTTC Human: ATTTATTGTTTGATATACCTA----------------TGTTTCCACAGGGAAACAGACAAATGATAAAAATGTTC Cluster: [ ] Orangutan: GTTTATTGTTTGATATACCTATGCCCATC--------TGTTTCCTTGTGGAAACAGACAAATGATAAAAACGTTC Chimp > Human ------------- chr2:142517658-142517668 Template switch process: F1: L TTGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA 1 F3: 4 GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG R RF: TTGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTACGCCTATCTGTTTCCCTGTGGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG RR: AACTTGTGAAAACAAACAAATAAATAACAAACTATATGGATGCGGATAGACAAAGGGACACCTTTGTCTGTTTACTATTTTTACAAGGGGTCCCAAACCC F2: 3 GACACCTTTGT 2 Unidirectional alignment (log-probability: -33.5) TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA----------------TGTttccacagGGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTACGCCTATCTGTTTCCCTGT--------GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG Template switch alignment (log-probability: -16.6) TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA|TGTTTCCACAG|GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA|TGTTTCCACAG|GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG Chimp > Gorilla --------------- chr2A:103041923-103041933 Template switch process: F1: L TTGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA 1 F3: 4 GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG R RF: TTGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTACGCCTATCTGTTTCCCTGTGGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG RR: AACTTGTGAAAACAAACAAATAAATAACAAACTATATGGATGCGGATAGACAAAGGGACACCTTTGTCTGTTTACTATTTTTACAAGGGGTCCCAAACCC F2: 3 GACACCTTTGT 2 Unidirectional alignment (log-probability: -33) TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA----------------TGTttccacagGGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTACGCCTATCTGTTTCCCTGT--------GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG Template switch alignment (log-probability: -17.1) TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA|TGTTTCCACAG|GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG TGAACACTTTTGTTTGTTTATTTATTGTTTGATATACCTA|TGTTTCCACAG|GGAAACAGACAAATGATAAAAATGTTCCCCAGGGTTTGGG ========== Event 2194 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGTCTCCACATCGTTTGAAA----------TCTGTTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGGTTTGGACTCAGAGGCAAAAGCACATATATGGATCAAGTTCTTAAGGCATTTCTACGGTGATCACTAATTAGAG ↓ 1 4 3 2 Chimp: TTGTCTCCACATCGTTTGAAA-----CAGAAATGCTTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGATTTGGACTCAGAGGCAAAAGCACATATATGGATCAAGTTCTTAAGGCATTTCTACGGTGATCACTAATTAGAG Gorilla: TTGTCTCCACATCGTCTGAAACAGAA-----ATACTTCCCCTAAACTCCCAAAATGTGGTATTTAGACAAATAGGTTTGGACTCAGAGGCAAAAGCACATATATGGATCAAGTTCTTAAGGCATTTCTATGGTGATCACTAATTAGAG Human: TTGTCTCCACATCGTTTGAAA----------TCTGTTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGGTTTGGACTCAGAGGCAAAAGCACATATATGGATCAAGTTCTTAAGGCATTTCTACGGTGATCACTAATTAGAG Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------------------------------------------------------------- Human > Chimp ------------- chr2A:12669970-12669977 Template switch process: F1: L GTGGTGGTCTTTCTCAGTGCTTGTCTCCACATCGTTTGAAAC 1 F3: 4 TTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGA R RF: GTGGTGGTCTTTCTCAGTGCTTGTCTCCACATCGTTTGAAATCTGTTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGGTTTGGACTCAGAGGCAAAAGCACATATATGGATCAAGTTCTTAAGGCATTTCT RR: CACCACCAGAAAGAGTCACGAACAGAGGTGTAGCAAACTTTAGACAAGGGGGTTTGAGGGTTTTACACCATAAATCTGTTTATCCAAACCTGAGTCTCCGTTTTCGTGTATATACCTAGTTCAAGAATTCCGTAAAGA F2: 3 CGTAAAGA 2 Unidirectional alignment (log-probability: -40.3) GGTGGTCTTTCTCAGTGCTTGTCTCCACATCGTTTGAAAcagaaatgc----TTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGa GGTGGTCTTTCTCAGTGCTTGTCTCCACATCGTTTGAAA---------TCTGTTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGG Template switch alignment (log-probability: -28.3) GGTGGTCTTTCTCAGTGCTTGTCTCCACATCGTTTGAAAc|AGAAATGC|TTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGa GGTGGTCTTTCTCAGTGCTTGTCTCCACATCGTTTGAAAT|AGAAATGC|TTCCCCCAAACTCCCAAAATGTGGTATTTAGACAAATAGG ========== Event 2195 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACT--TTTATTTTTATCCCAAGATGTGGAACTGTCA Chimp: GGAAGGAGCTTTTCTGGGATGATAACTGCTTCTACT--TTTATTTTTATCCCAAGATGTGGAACTGTCA Gorilla: GGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACT----TGTTATCGTCCCAAGATGTGGAACTGTCA ↑ 3 2 1 4 Human: GGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACT--TTTATTTTTATCCCAAGATGTGGAACTGTCA Cluster: [ ] Orangutan: GGAAGGAGCTTTTCTGGGATGATGACTGCTTCTACTTT--TATTTTTATCCCAAGATGTGGAACTGTCA Human > Gorilla --------------- chr2A:103066934-103066940 Template switch process: F1: L CCTTAGGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACTT 1 F3: 4 TCCCAAGATGTGGAACTGTCACCAAGGATGTATTTTATTT R RF: CCTTAGGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACTTTTATTTTTATCCCAAGATGTGGAACTGTCACCAAGGGTGTATTTTATTT RR: GGAATCCTTCCTCGAAAAGACCCTGCTATTGACGAAGATGAAAATAAAAATAGGGTTCTACACCTTGACAGTGGTTCCCACATAAAATAAA F2: 3 GCTATTG 2 Unidirectional alignment (log-probability: -36.3) TTAGGAAGGAGCTTTTCTGGGACGATAACTGCTTCTAC-----TTgTTAtcgTCCCAAGATGTGGAACTGTCACCAAGGaTGTATTTTATTT TTAGGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACTTTTATTTTTA---TCCCAAGATGTGGAACTGTCACCAAGGGTGTATTTTATTT Template switch alignment (log-probability: -22.2) TTAGGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACTT|GTTATCG|TCCCAAGATGTGGAACTGTCACCAAGGaTGTATTTTATTT TTAGGAAGGAGCTTTTCTGGGACGATAACTGCTTCTACTT|GTTATCG|TCCCAAGATGTGGAACTGTCACCAAGGGTGTATTTTATTT ========== Event 2196 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTTTTATATTTTGAG-TTTCTAAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCGTATTTTAAAAAATAGGCTGCttttctttt Chimp: TTTTTATATTTTGAG-TTTCTAAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCCTATTTTAGAAAATAGACTGcttttctttt Gorilla: TTTTTATATTTTGAGTTTTCTAAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCCTATTTTAGAAAATAGGCTGcttttctttt ↑ 3 2 1 4 Human: TTTTTATATTTTGAG-TTTCTAAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCGTATTTTAAAAAATAGGCTGCttttctttt Cluster: [ ] Orangutan: Human > Gorilla --------------- chr2A:103404733-103404741 Template switch process: F1: L TAAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACC 1 F3: 4 AAAATAGGCTGCTTTTCTTTTTCTT---TTTCTTTTTTTT R RF: CTAAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCGTATTTTAAAAAATAGGCTGCTTTTCTTTTTCTTTTCTTTCTTTTTTTT RR: GATTTTATCTCATGCAATATACCGAAAATGGACATGGGATGGCATAAAATTTTTTATCCGACGAAAAGAAAAAGAAAAGAAAGAAAAAAAA F2: 3 GATTTTATC 2 Unidirectional alignment (log-probability: -38.7) AAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCcTATTTTAgAAAATAGGCTGCTTTTCTTTTTCTTtttcTTtTTTtT AAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACCGTATTTTAAAAAATAGGCTGCTTTTCTTTTTCTT----TTCTTTCT Template switch alignment (log-probability: -26.7) AAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACC|CTATTTTAG|AAAATAGGCTGCTTTTCTTTTTCTT---TTTCTTTTTTTT AAAATAGAGTACGTTATATGGCTTTTACCTGTACCCTACC|CTATTTTAG|AAAATAGGCTGCTTTTCTTTTTCTTTTCTTTCTTTTTTTT ========== Event 2197 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGGATTAAGCAGGAGAGCATTTC-----TAGGCCTAGaaaaaaaaTTGCATT ↓ 3 1 24 Chimp: GTGGATTAAGCAGGAGAGCATTTCCTAGAAATGCCTAGaaaaaaaaTTGCATT ↑ 3 1 24 Gorilla: GTGGATTAAGCAGGAGAGCATTTC-----TAGGCCTAGaaaaaaaaTTGCATT Human: GTGGATTAAGCAGGAGAGCATTTC-----TAGGCCTAGaaaaaaaaTTGCATT Cluster: [ ] Orangutan: GTGGATTAAGCAGGAGAGCATTTC-----TAGGCCTAGAA--AAAATTGCATT Human > Chimp ------------- chr3:99035123-99035130 Template switch process: F1: L TTGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTC 1 F3: 4 GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT R RF: TTATGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTCTAGGCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT RR: AATACGTAGAAACCTAACACCTAATTCGTCCTCTCGTAAAGATCCGGATCTTTTTTTTAACGTAAGAAGTCGATTTACTAAAAA F2: 3 TAAAGATC 2 Unidirectional alignment (log-probability: -34.3) TgTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTcCTAGaaatGCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT TATGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTT-CTAG----GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT Template switch alignment (log-probability: -22.3) TgTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTC|CTAGAAAT|GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT TATGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTC|CTAGAAAT|GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT Gorilla > Chimp --------------- chr3:99035123-99035130 Template switch process: F1: L TTGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTC 1 F3: 4 GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT R RF: TTGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTCTAGGCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT RR: AACACGTAGAAACCTAACACCTAATTCGTCCTCTCGTAAAGATCCGGATCTTTTTTTTAACGTAAGAAGTCGATTTACTAAAAA F2: 3 TAAAGATC 2 Unidirectional alignment (log-probability: -27.9) TGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTcCTAGaaatGCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT TGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTT-CTAG----GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT Template switch alignment (log-probability: -16.7) TGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTC|CTAGAAAT|GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT TGTGCATCTTTGGATTGTGGATTAAGCAGGAGAGCATTTC|CTAGAAAT|GCCTAGAAAAAAAATTGCATTCTTCAGCTAAATGATTTTT ========== Event 2198 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAAATCCAGAGATTTTTGTAGGACTCTTTTAT--------GGCAGTTGGGGGCTCATTCTGAGGCT Chimp: GTAAATCCAGAGATTTTTGTAGGACTCTTATAT--------GGCAGCTGGGGGCTCATTCTGAGGCT ↓ 3 1 2 4 Gorilla: GTAAATCCAGAGATTTTTGTAGGACTC-TATATAAGAGTCCTACAGTTGGGGGCTCATTCTGAGGCT ↑ 3 1 2 4 Human: GTAAATCCAGAGATTTTTGTAGGACTCTTTTAT--------GGCAGTTGGGGGCTCATTCTGAGGCT Cluster: [ ] Orangutan: GTAAATCCAGAGATTTTTGGAGGACTCTCATAT--------GGCAGTTGGGGGCTCATTCTGAGGCT Human > Gorilla --------------- chr3:99414638-99414651 Template switch process: F1: L GAGGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT 1 F3: 4 CAGTTGGGGGCTCATTCTGAGGCTCAAGTTTTGATGCTTA R RF: GAGGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCTTTTATGGCAGTTGGGGGCTCATTCTGAGGCTCAAGTCTTGATGCTTA RR: CTCCCCACTTGATACATTTAGGTCTCTAAAAACATCCTGAGAAAATACCGTCAACCCCCGAGTAAGACTCCGAGTTCAGAACTACGAAT F2: 3 ATCCTGAGAATATA 2 Unidirectional alignment (log-probability: -46.3) GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCTaTataagagtccTA---CAGTTGGGGGCTCATTCTGAGGCTCAAGTtTTGATGCTTA GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCTTT----------TATGGCAGTTGGGGGCTCATTCTGAGGCTCAAGTCTTGATGCTTA Template switch alignment (log-probability: -28.6) GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT|ATAtAAGAGTCCTA|CAGTTGGGGGCTCATTCTGAGGCTCAAGTtTTGATGCTTA GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT|ATAAAAGAGTCCTA|CAGTTGGGGGCTCATTCTGAGGCTCAAGTCTTGATGCTTA Chimp > Gorilla --------------- chr3:99414638-99414651 Template switch process: F1: L GAGGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT 1 F3: 4 CAGTTGGGGGCTCATTCTGAGGCTCAAGTTTTGATGCTTACAGA R RF: GAGGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCTTATATGGCAGCTGGGGGCTCATTCTGAGGCTCAAGTCTTGATGCTTACAGA RR: CTCCCCACTTGATACATTTAGGTCTCTAAAAACATCCTGAGAATATACCGTCGACCCCCGAGTAAGACTCCGAGTTCAGAACTACGAATGTCT F2: 3 ATCCTGAGAATATA 2 Unidirectional alignment (log-probability: -49.3) GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCTatataagagtccTA-----CAGtTGGGGGCTCATTCTGAGGCTCAAGTtTTGATGCTTA GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT------------TATATGGCAGCTGGGGGCTCATTCTGAGGCTCAAGTCTTGATGCTTA Template switch alignment (log-probability: -28.7) GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT|ATATAAGAGTCCTA|CAGtTGGGGGCTCATTCTGAGGCTCAAGTtTTGATGCTTA GGGGTGAACTATGTAAATCCAGAGATTTTTGTAGGACTCT|ATATAAGAGTCCTA|CAGCTGGGGGCTCATTCTGAGGCTCAAGTCTTGATGCTTA ========== Event 2199 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCAGTTCTACTACATATCTAAGCATGCTGGGCAACATGCTTAGGGAACAGCTTAACTCTCTTT ↑ 3 2 1 4 Chimp: TTCAGTTCTACTACATATCTAAGCATGCTGGGCAAC------TGGGAACAGCTTAACTCTCTTT Gorilla: TTCAGTTCTACTACATATCTAAGCATGCTGGGCAAC------TGGGAACAGCTTAACTCTCTTT Human: TTCAGTTCTACTACATATCTAAGCATGCTGGGCAACATGCTTAGGGAACAGCTTAACTCTCTTT Cluster: [ ] Orangutan: TTCAGTTCTACTACATATCTAAGCACGCTGGGCAAC------TGGGAACAGCTTAACTCTCTTT Chimp > Human ------------- chr3:101501579-101501585 Template switch process: F1: L ACACTTTCAGTTCTACTACATATCTAAGCATGCTGGGCAAC 1 F3: 4 GGGAACAGCTTAACTCTCTTT R RF: ACACTTTCAGTTCTACTACATATCTAAGCATGCTGGGCAACTGGGAACAGCTTAACTCTCTTT RR: TGTGAAAGTCAAGATGATGTATAGATTCGTACGACCCGTTGACCCTTGTCGAATTGAGAGAAA F2: 3 ATTCGTA 2 Unidirectional alignment (log-probability: -25.4) CACTTTCAGTTCTACTACATATCTAAGCATGCTGGGCAACatgcttaGGGAACAGCTTAACTCTCTTT CACTTTCAGTTCTACTACATATCTAAGCATGCTGGGCAAC------TGGGAACAGCTTAACTCTCTTT Template switch alignment (log-probability: -15.7) CACTTTCAGTTCTACTACATATCTAAGCATGCTGGGCAAC|ATGCTTA|GGGAACAGCTTAACTCTCTTT CACTTTCAGTTCTACTACATATCTAAGCATGCTGGGCAAC|ATGCTTA|GGGAACAGCTTAACTCTCTTT ========== Event 2200 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGTTTAAATGAAGCCATATCAAAGATTAA---------------TAAAGTAGTATTTGATTCCAT ↓ 3 4 1 2 Chimp: GGTTTAAATGAAGCCATATCAAAGATTATTAATCTTTGATTAATAAAAGTAGTATTTGATTCCAT ↑ 3 4 1 2 Gorilla: GGTTTAAATGAAGCCATATCAAAGATTAA---------------TAAAGTAGTATTTGATTCCAT Human: GGTTTAAATGAAGCCATATCAAAGATTAA---------------TAAAGTAGTATTTGATTCCAT Cluster: [ ] Orangutan: GGTTTAAATGAAGCAATATCAAAGATTAA---------------TAAAGTAGTATTTGATTCCAT Human > Chimp ------------- chr3:104031962-104031971 Template switch process: F1: L GATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTA 1 F3: 4 ATTAATAAAAGTAGTATTTGATTCCATTTCTTACAGCAATCACATCA R RF: GATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTAATAAAGTAGTATTTGATTCCATTTCTTACAGCAATCACATCA RR: CTATAAAATTTTGCCAAATTTACTTCGGTATAGTTTCTAATTATTTCATCATAAACTAAGGTAAAGAATGTCGTTAGTGTAGT F2: 3 GTTTCTAATT 2 Unidirectional alignment (log-probability: -38.5) ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTAtTAatctttgattaataaAAGTAGTATTTGATTCCATTTCTTACAGCAAT ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTAATA---------------AAGTAGTATTTGATTCCATTTCTTACAGCAAT Template switch alignment (log-probability: -28.3) ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTA|TTAATCTTTG|ATTAATaAAAGTAGTATTTGATTCCATTTCTTACAGCAAT ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTA|TTAATCTTTG|ATTAAT-AAAGTAGTATTTGATTCCATTTCTTACAGCAAT Gorilla > Chimp --------------- chr3:104031962-104031971 Template switch process: F1: L GATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTA 1 F3: 4 ATTAATAAAAGTAGTATTTGATTCCATTTCTTACAGCAATCACATCA R RF: GATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTAATAAAGTAGTATTTGATTCCATTTCTTACAGCAATCACATCA RR: CTATAAAATTTTGCCAAATTTACTTCGGTATAGTTTCTAATTATTTCATCATAAACTAAGGTAAAGAATGTCGTTAGTGTAGT F2: 3 GTTTCTAATT 2 Unidirectional alignment (log-probability: -38) ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTAtTaatctttgattaataAAAGTAGTATTTGATTCCATTTCTTACAGCAAT ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTAAT---------------AAAGTAGTATTTGATTCCATTTCTTACAGCAAT Template switch alignment (log-probability: -28.3) ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTA|TTAATCTTTG|ATTAATaAAAGTAGTATTTGATTCCATTTCTTACAGCAAT ATATTTTAAAACGGTTTAAATGAAGCCATATCAAAGATTA|TTAATCTTTG|ATTAAT-AAAGTAGTATTTGATTCCATTTCTTACAGCAAT ========== Event 2201 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TACACCACACCTTTGCAAAAACTAAGGG-----GAAGAT--GGAGGTGGGTAAGATGAAGGTAG Chimp: TACACCACACCTTTCCAAAAACTAAGGG-----GAAGAT--GGAGGTGGGTAAGATGAAGGTAG ↓ 3 1 2 4 Gorilla: TACACCACACCTTTCCAAAAACTAAGGTTCCTCTTAGTT----GGGTGGGTAAGATGAAGGTAG Human: TACACCACACCTTTGCAAAAACTAAGGG-----GAAGAT--GGAGGTGGGTAAGATGAAGGTAG Cluster: [ ] Orangutan: TACACCACACCTTTCCAAAAAC--TGGG-----GAAGACGG--AGGTGGGAAAGGTGAAGGTAG Chimp > Gorilla --------------- chr3:99066587-99066598 Template switch process: F1: L AAATGGCATTGGCTTACACCACACCTTTCCAAAAACTAAGG 1 F3: 4 GGGTGGGTAAGATGAAGGTAGGCTACAGGATGACCTCATAT R RF: AAATGGCATTGGCTTACACCACACCTTTCCAAAAACTAAGGGGAAGATGGAGGTGGGTAAGATGAAGGTAGGCTACAGGATGACCTCATAT RR: TTTACCGTAACCGAATGTGGTGTGGAAAGGTTTTTGATTCCCCTTCTACCTCCACCCATTCTACTTCCATCCGATGTCCTACTGGAGTATA F2: 3 TTGATTCTCCTT 2 Unidirectional alignment (log-probability: -38.4) AATGGCATTGGCTTACACCACACCTTTCCAAAAACTAAGGttcctcttagttG---------GGTGGGTAAGATGAAGGTAGGCTACAGGATGACCTCATA AATGGCATTGGCTTACACCACACCTTTCCAAAAACTAAGG------------GGAAGATGGAGGTGGGTAAGATGAAGGTAGGCTACAGGATGACCTCATA Template switch alignment (log-probability: -28.3) AATGGCATTGGCTTACACCACACCTTTCCAAAAACTAAGG|TTCCtCTTAGTT|gGGTGGGTAAGATGAAGGTAGGCTACAGGATGACCTCATA AATGGCATTGGCTTACACCACACCTTTCCAAAAACTAAGG|TTCCCCTTAGTT|AGGTGGGTAAGATGAAGGTAGGCTACAGGATGACCTCATA ========== Event 2202 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cagccaactgtggttgaggaaagc-----aggatacctgagagaggctccgtgagg Chimp: CAGCCAACTGTGGTTGAGGAAAGCAATCCTGCTTTCCTGAGAGAGGCTCCGTGAGG ↑ 3 1 2 4 Gorilla: CAGCCAACTGTGGTTGAGGAAAGC-----AGGATACCTGAGAGAGGCTCCGTGAGG Human: cagccaactgtggttgaggaaagc-----aggatacctgagagaggctccgtgagg Cluster: [ ] Orangutan: cagccaactgtggttgaggaaagc-----aggatacctgagagaggctccctgagg Gorilla > Chimp --------------- chr3:97807330-97807339 Template switch process: F1: L ACTGAGTACAAAGGCAGCAGCCAACTGTGGTTGAGGAAAGCA 1 F3: 4 CCTGAGAGAGGCTCCGTGAGGCATGGGCATGTGGGGCCTG R RF: ACTGAGTACAAAGGCAGCAGCCAACTGTGGTTGAGGAAAGCAGGATACCTGAGAGAGGCTCCGTGAGGCATGCGCATGTGGGGCCTG RR: TGACTCATGTTTCCGTCGTCGGTTGACACCAACTCCTTTCGTCCTATGGACTCTCTCCGAGGCACTCCGTACGCGTACACCCCGGAC F2: 3 TTTCGTCCTA 2 Unidirectional alignment (log-probability: -39.3) TGAGTACAAAGGCAGCAGCCAACTGTGGTTGAGGAAAGCA----AtcctgctttCCTGAGAGAGGCTCCGTGAGGCATGgGCATGTGGGGCCTG TGAGTACAAAGGCAGCAGCCAACTGTGGTTGAGGAAAGCAGGATA---------CCTGAGAGAGGCTCCGTGAGGCATGCGCATGTGGGGCCTG Template switch alignment (log-probability: -22.5) TGAGTACAAAGGCAGCAGCCAACTGTGGTTGAGGAAAGCA|ATCCTGCTTT|CCTGAGAGAGGCTCCGTGAGGCATGgGCATGTGGGGCCTG TGAGTACAAAGGCAGCAGCCAACTGTGGTTGAGGAAAGCA|ATCCTGCTTT|CCTGAGAGAGGCTCCGTGAGGCATGCGCATGTGGGGCCTG ========== Event 2203 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tTTATCTCTACTGCTATACTGCCAAAGAAAAG----TGTAATCATTAAAATTTGTGAG Chimp: TTTATCTCTACTGCTATACTGCCAAAGAAAAG----TGTAATCATTAAAATTTGTGAG ↓ 3 1 2 4 Gorilla: TTTATCTCTACTGCTATACTGCCAATTTTCTTTGGCATTAATCATTAAAATTTGTGAG ↑ 3 1 2 4 Human: tTTATCTCTACTGCTATACTGCCAAAGAAAAG----TGTAATCATTAAAATTTGTGAG Cluster: [ ] Orangutan: TTTATCTCTACTGCTATACTTCCAAAGGGAAG----TGTAATCATTAAAATTTGTGAG Human > Gorilla --------------- chr3:97693923-97693934 Template switch process: F1: L AAGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA 1 F3: 4 TTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTGG R RF: AAGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAAAGAAAAGTGTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTGG RR: TTCTTTTTTAACTTTTAAATAGAGATGACGATATGACGGTTTCTTTTCACATTAGTAATTTTAAACACTCCCTCGTTAATCTTACCCACC F2: 3 ACGGTTTCTTTT 2 Unidirectional alignment (log-probability: -39.8) AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA---------ttttctttggcatTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAAAGAAAAGTG-------------TAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG Template switch alignment (log-probability: -22.8) AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA|TTTTCTTTGGCA|tTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA|TTTTCTTTGGCA|GTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG Chimp > Gorilla --------------- chr3:97693923-97693934 Template switch process: F1: L AAGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA 1 F3: 4 TTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTGG R RF: AAGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAAAGAAAAGTGTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTGG RR: TTCTTTTTTAACTTTTAAATAGAGATGACGATATGACGGTTTCTTTTCACATTAGTAATTTTAAACACTCCCTCGTTAATCTTACCCACC F2: 3 ACGGTTTCTTTT 2 Unidirectional alignment (log-probability: -39.8) AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA---------ttttctttggcatTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAAAGAAAAGTG-------------TAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG Template switch alignment (log-probability: -22.8) AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA|TTTTCTTTGGCA|tTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG AGAAAAAATTGAAAATTTATCTCTACTGCTATACTGCCAA|TTTTCTTTGGCA|GTAATCATTAAAATTTGTGAGGGAGCAATTAGAATGGGTG ========== Event 2204 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGGTGATGCTCTGTGCACATGCTCACTGCCTTATCTTGAGAGAACAAGAACCAGGGAATAATGTTTCCTGATTTCCTGCTTGAAATCCCTTAGGTGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAAGCATAACAAAATAAAATCCAGAAGATTGAG ↑ 3 2 4 1 Chimp: CAGGTGATGCTCTGTGCACATGCCCACTGCCTTATCTTGAGGGAGCAAGAACCAGGGGATAATGTTTCCTGATTTCCTGCTTGAAATCCCTTAGGTGAACATTATCTCCCATCTCCCTATTTACTTGTAAA----------CAAAATAAAATCCAGAAGATTGAG Gorilla: CAGGTGATGCTCTGTGCACATGCTCGCTGCCTTAGCTTGAGGGAACAAGAACCAGGGAATAATGTTTCCTGATTTCCTACTTGAAATCCCTTAGGTGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAAGCATAACAAAATAAAATCCAGAAGATTGAG Human: CAGGTGATGCTCTGTGCACATGCTCACTGCCTTATCTTGAGAGAACAAGAACCAGGGAATAATGTTTCCTGATTTCCTGCTTGAAATCCCTTAGGTGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAAGCATAACAAAATAAAATCCAGAAGATTGAG Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Chimp > Human ------------- chr3:1068749-1068752 Template switch process: F1: L TTAGGTGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAA 1 F3: 4 AACAAAATAAAATCCAGAAGATTGAGAGTGTTGGTTCTTTCA R RF: ATGCCCACTGCCTTATCTTGAGGGAGCAAGAACCAGGGGATAATGTTTCCTGATTTCCTGCTTGAAATCCCTTAGGTGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAAATAAAATCCAGAAGATTGAGAGTGTTGCTTCTTTCA RR: TACGGGTGACGGAATAGAACTCCCTCGTTCTTGGTCCCCTATTACAAAGGACTAAAGGACGAACTTTAGGGAATCCACTTGTAATAGAGGGTAGAGGGATAAATGAACATTTGTTTTATTTTAGGTCTTCTAACTCTCACAACGAAGAAAGT F2: 3 TACG 2 Unidirectional alignment (log-probability: -31.3) TGAACATTATCTCCCATCTCCCTATTTACTTGTAaacaaagcatAACAAAATAAAATCCAGAAGATTGAGAGTGTTGgTTCTTT TGAACATTATCTCCCATCTCCCTATTTACTTGTA----------AACAAAATAAAATCCAGAAGATTGAGAGTGTTGCTTCTTT Template switch alignment (log-probability: -21.9) TGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAA|GCAT|AACAAAATAAAATCCAGAAGATTGAGAGTGTTGgTTCTTT TGAACATTATCTCCCATCTCCCTATTTACTTGTAAACAAA|GCAT|AACAAAATAAAATCCAGAAGATTGAGAGTGTTGCTTCTTT ========== Event 2205 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGTTCTCT--------TTAGCTAGTTTCATCACTAGCTAAACTGGATGATatttattcaa Chimp: GTGTTCTTT--------TTAGCTAG---------TGATGAAACTGGATGATATTTATTCAA Gorilla: GTGTTCTCT--------TTAGCTAG---------TGAAGAAACTGGATGATATTTATTCAA ↓ 3 1 42 Human: GTGTTCTCT--------TTAGCTAGTTTCATCACTAGCTAAACTGGATGATatttattcaa Cluster: [ ] Orangutan: GTGTTCTCTTTGCTTTGTTAGCTAG---------TGATGAAACTGGATGATATTTATTCAA Gorilla > Human --------------- chr3:104006024-104006036 Template switch process: F1: L GATCGTGGATTCCATCTGGTTTAGGTGTTCTCTTTAGCTAGT 1 F3: 4 AAACTGGATGATATTTATTCAACAAACACTGAGTCTGTAC R RF: GATCGTGGATTCCATCTGGTTTAGGTGTTCTCTTTAGCTAGTGAAGAAACTGGATGATATTTATTCAACAAACACTGAGTCTGTAC RR: CTAGCACCTAAGGTAGACCAAATCCACAAGAGAAATCGATCACTTCTTTGACCTACTATAAATAAGTTGTTTGTGACTCAGACATG F2: 3 TCGATCACTACTT 2 Unidirectional alignment (log-probability: -39.5) TCGTGGATTCCATCTGGTTTAGGTGTTCTCTTTAGCTAGtttcatcactagcT----AAACTGGATGATATTTATTCAACAAACACTGAGTCTGTAC TCGTGGATTCCATCTGGTTTAGGTGTTCTCTTTAGCTAG-------------TGAAGAAACTGGATGATATTTATTCAACAAACACTGAGTCTGTAC Template switch alignment (log-probability: -22.9) TCGTGGATTCCATCTGGTTTAGGTGTTCTCTTTAGCTAGT|TTCaTCACTAGCT|AAACTGGATGATATTTATTCAACAAACACTGAGTCTGTAC TCGTGGATTCCATCTGGTTTAGGTGTTCTCTTTAGCTAGT|TTCTTCACTAGCT|AAACTGGATGATATTTATTCAACAAACACTGAGTCTGTAC ========== Event 2206 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACGGTTTTGAAAATATTGCAAAGTAGTGGCCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCCCCCAA ↑ 1 4 3 2 Chimp: ACGGTTTTGAAAATATTGCAA--------GCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCCCCCAA Gorilla: ACGGTTTTGAAAATATTGCAA--------GCCTCACTGAGGTGGGGGCCGCTACTTGAGACTGAAAATCCCCCAA Human: ACGGTTTTGAAAATATTGCAAAGTAGTGGCCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCCCCCAA Cluster: [ ] Orangutan: ATGGTTTTGAAAATATTGCAA--------GCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCCCCCAA Chimp > Human ------------- chr3:10883837-10883845 Template switch process: F1: L TCAACACAGAGACATTATATACGGTTTTGAAAATATTGCAA 1 F3: 4 CCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCC R RF: TCAACACAGAGACATTATATACGGTTTTGAAAATATTGCAAGCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCC RR: AGTTGTGTCTCTGTAATATATGCCAAAACTTTTATAACGTTCGGAGTGACTCCACCCCCGGTGATGAACTCTGACTTTTAGG F2: 3 CGGTGATGA 2 Unidirectional alignment (log-probability: -28.4) CAACACAGAGACATTATATACGGTTTTGAAAATATTGCAAagtagtggcCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCC CAACACAGAGACATTATATACGGTTTTGAAAATATTGCAA--------GCCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCC Template switch alignment (log-probability: -16.4) CAACACAGAGACATTATATACGGTTTTGAAAATATTGCAA|AGTAGTGGC|CCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCC CAACACAGAGACATTATATACGGTTTTGAAAATATTGCAA|AGTAGTGGC|CCTCACTGAGGTGGGGGCCACTACTTGAGACTGAAAATCC ========== Event 2207 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTGTAGGGCATTTTTGTTGACATATATGCAACA-----GAATAATTTGTCAACAtt-ttt Chimp: AGTGTAGGGCATTTTTGTTGACATATATGCAACA-----GAATAATTTGTCAACAtt---t ↓ 3 2 1 4 Gorilla: AGTGTAGGGCATTTTTGTTGACATATATGCAATATATGTCAATAATTTGTCAACAtt---t ↑ 3 2 1 4 Human: AGTGTAGGGCATTTTTGTTGACATATATGCAACA-----GAATAATTTGTCAACAtt-ttt Cluster: [ ] Orangutan: AGTGTAGGGCATTTTTGTTGATATATATGCAACA-----GAATAATTTGTCAACAttt--t Human > Gorilla --------------- chr3:93779967-93779974 Template switch process: F1: L ACCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAA 1 F3: 4 AATAATTTGTCAACA--TTTTTTTTGTTTGAGTCTCACTA R RF: ACCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAACAGAATAATTTGTCAACATTTTTTTTTTGTTTGAGTCTCACTA RR: TGGACAACGTCACATCCCGTAAAAACAACTGTATATACGTTGTCTTATTAAACAGTTGTAAAAAAAAAACAAACTCAGAGTGAT F2: 3 CTGTATAT 2 Unidirectional alignment (log-probability: -39) CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAAtAtatgtcAATAATTTGTCAACA--TTTTTTTTGTTTGAGTCTCACTA CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAACAG-----AATAATTTGTCAACATTTTTTTTTTGTTTGAGTCTCACTA Template switch alignment (log-probability: -26.5) CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAA|TATATGTC|AATAATTTGTCAACA--TTTTTTTTGTTTGAGTCTCACTA CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAA|TATATGTC|AATAATTTGTCAACATTTTTTTTTTGTTTGAGTCTCACTA Chimp > Gorilla --------------- chr3:93779967-93779974 Template switch process: F1: L ACCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAA 1 F3: 4 AATAATTTGTCAACATTTTTTTTGTTTGAGTCTCACTATT R RF: ACCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAACAGAATAATTTGTCAACATTTTTTTTGTTTGAGTCTCACTATT RR: TGGACAACGTCACATCCCGTAAAAACAACTGTATATACGTTGTCTTATTAAACAGTTGTAAAAAAAACAAACTCAGAGTGATAA F2: 3 CTGTATAT 2 Unidirectional alignment (log-probability: -29.2) CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAAtAtatgtcAATAATTTGTCAACATTTTTTTTGTTTGAGTCTCACTATT CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAACAG-----AATAATTTGTCAACATTTTTTTTGTTTGAGTCTCACTATT Template switch alignment (log-probability: -16.7) CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAA|TATATGTC|AATAATTTGTCAACATTTTTTTTGTTTGAGTCTCACTATT CCTGTTGCAGTGTAGGGCATTTTTGTTGACATATATGCAA|TATATGTC|AATAATTTGTCAACATTTTTTTTGTTTGAGTCTCACTATT ========== Event 2208 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGCAGCTGCACCCTTACATGCA---CTAAATATG----TACAAAGTGATGCCCCTTGGCTTGGTATC Chimp: ATGCAGCTGCACCCTTACATGCA---CTAAATATG----TACAAAGTGATGCCCCTTGGCTTGGTATC ↑ 31 4 2 Gorilla: ATGCAGCTGCACCCTTACATGTA------CATATT--------TAGTGATGCCCCTTGGCTTGGTATC Human: ATGCAGCTGCACCCTTACATGCA---CTAAATATG----TACAAAGTGATGCCCCTTGGCTTGGTATC Cluster: [ ] Orangutan: ATGCAGCTGCACCCTTACATGCACTA---AATAAGCACA----AAGTGATGCCCCTTGGCTTGGTATC Gorilla > Chimp --------------- chr3:93587160-93587174 Template switch process: F1: L CCTTAAAAGTCATATGCACTATGCAGCTGCACCCTTACATG 1 F3: 4 AAGTGATGCCCCTTGGCTTGGTATCAAGTGTTGGGTTGAAA R RF: CCTTAAAAGTCATATGCACTATGCAGCTGCACCCTTACATGTACATATTTAGTGATGCCCCTTGGCTTGGTATCAAGTGTTGGGTTCAAA RR: GGAATTTTCAGTATACGTGATACGTCGACGTGGGAATGTACATGTATAAATCACTACGGGGAACCGAACCATAGTTCACAACCCAAGTTT F2: 3 ACATGTATAAATCAC 2 Unidirectional alignment (log-probability: -47.4) CTTAAAAGTCATATGCACTATGCAGCTGCACCCTTACATGcacTAaATATgTacaaAGTGATGCCCCTTGGCTTGGTATCAAGTGTTGGGTTgAA CTTAAAAGTCATATGCACTATGCAGCTGCACCCTTACATG---TACATATTT----AGTGATGCCCCTTGGCTTGGTATCAAGTGTTGGGTTCAA Template switch alignment (log-probability: -28.7) CTTAAAAGTCATATGCACTATGCAGCTGCACCCTTACATG|CACTAAATATGTACA|aAGTGATGCCCCTTGGCTTGGTATCAAGTGTTGGGTTgAA CTTAAAAGTCATATGCACTATGCAGCTGCACCCTTACATG|CACTAAATATGTACA|TAGTGATGCCCCTTGGCTTGGTATCAAGTGTTGGGTTCAA ========== Event 2209 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCTGCAATTTCATACCACACTCCTCTTCCt ↑ 3 2 1 4 Chimp: ATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCTA--CTGTCATACCACACTCCTCTTCCt Gorilla: ATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCTA--CTGTCATACCACACTCCTCTTCCt Human: ATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCTGCAATTTCATACCACACTCCTCTTCCt Cluster: [ ] Orangutan: ATTGATATTTAACAATTGAAATTGCAGAGATCTGACTCTA--CTGTCATACCACACTCCTCTTCCT Chimp > Human ------------- chr3:91689586-91689591 Template switch process: F1: L AAATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCT 1 F3: 4 TCATACCACACTCCTCTTCCTCATTCATTCATTTATTCAT R RF: AAATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCTACTGTCATACCACACTCCTCTTCCTCATTCATTCATTTATTCAT RR: TTTAACTATAAATTGTTAACTTTAACGTCTCTAGAGTGAGATGACAGTATGGTGTGAGGAGAAGGAGTAAGTAAGTAAATAAGTA F2: 3 TTAACG 2 Unidirectional alignment (log-probability: -25.8) AATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCTgcAaTtTCATACCACACTCCTCTTCCTCATTCATTCATTTATTCAT AATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCT--ACTGTCATACCACACTCCTCTTCCTCATTCATTCATTTATTCAT Template switch alignment (log-probability: -16) AATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCT|GCAATT|TCATACCACACTCCTCTTCCTCATTCATTCATTTATTCAT AATTGATATTTAACAATTGAAATTGCAGAGATCTCACTCT|GCAATT|TCATACCACACTCCTCTTCCTCATTCATTCATTTATTCAT ========== Event 2210 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: taaaaattaaatGATTAGATATCAATAATCGCCCTAATGGAGTTTCCATTAGGGTGATTATTGATAGATA----GAT------ Chimp: TAAAAATTAAATGAGTAGATATCAATAATCGCCCTAATGGA--GTCCATTAGGGCGATTATTGATAGATA----GAT----TG Gorilla: TAAAAATTAAATGATTAGATATCAATAATCACCCTAATGGAGACTCCATTAGGGCGATGATTGATAGATAGACAGATAGAT-- ↓ 3 1 2 4 Human: taaaaattaaatGATTAGATATCAATAATCGCCCTAATGGAGTTTCCATTAGGGTGATTATTGATAGATA----GAT------ Cluster: [] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNN------ Gorilla > Human --------------- chr3:91680273-91680308 Template switch process: F1: L AAAAATTAAATGATTAGATATCAATAATC 1 F3: 4 GATAGATAGA R RF: AAAAATTAAATGATTAGATATCAATAATCACCCTAATGGAGACTCCATTAGGGCGATGATTGATAGATAGA RR: TTTTTAATTTACTAATCTATAGTTATTAGTGGGATTACCTCTGAGGTAATCCCGCTACTAACTATCTATCT F2: 3 ATAGTTATTAGTGGGATTACCTTTGAGGTAATCCCG 2 Unidirectional alignment (log-probability: -41.3) AAAAATTAAATGATTAGATATCAATAATCgCCCTAATGGAGttTCCATTAGGGtGATtATTGATAGATAGAtAGA-------- AAAAATTAAATGATTAGATATCAATAATCACCCTAATGGAGACTCCATTAGGGCGATGATTGATAGATAGACAGATAGATTGA Template switch alignment (log-probability: -24.8) AAAAATTAAATGATTAGATATCAATAATC|GCCCTAATGGAGTtTCCATTAGGGTGATTATTGATA|GATAGATAGA AAAAATTAAATGATTAGATATCAATAATC|GCCCTAATGGAGTCTCCATTAGGGTGATTATTGATA|GATAGATAGA ========== Event 2211 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: TCAAGGCTGAGGGTCCTGCCTGTGATAAGTCTATCACAGGCCTTTGAGTTCTCTGACAGC ↓ 13 2 4 ↑ 3 1 24 Chimp: TCAAGGCTGAGGGTCCTGCCTGTGATAG-AC-------TGCCTTTGAGTTCTCTGACAGC Gorilla: TCAAGGCTGAGGGTCCTGCCTGTGATAG-AC-------TGCCTTTGAGTTCTCTGACAGC Human: TCAAGGCTGAGGGTCCTGCCTGTGATAAGTCTATCACAGGCCTTTGAGTTCTCTGACAGC Cluster: [ ] Orangutan: TCAAGGCTGAGGGTCCTGCCTGTGATAG-AC-------TGCCATTGAGTTCTCTTATAGC Chimp > Human ------------- chr3:90651677-90651688 Template switch process: F1: L AGCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATA 1 F3: 4 GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA R RF: AGCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATAGACTGCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA RR: TCGTCTGTAGTCAAAGTTCCGACTCCCAGGACGGACACTATCTGACGGAAACTCAAGAGACTGTCGGTTTGTCTTTGTGAGGTTT F2: 3 GACACTATCTGA 2 Unidirectional alignment (log-probability: -37.1) GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATaagtctatcacAG---GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGAT-----------AGACTGCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA Template switch alignment (log-probability: -16.8) GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATA|AGTCTATCACAG|GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATA|AGTCTATCACAG|GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA Human > Chimp ------------- chr3:91984712-91984715 Template switch process: F1: L AGCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATA 1 F3: 4 GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA R RF: AGCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATAAGTCTATCACAGGCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA RR: TCGTCTGTAGTCAAAGTTCCGACTCCCAGGACGGACACTATTCAGATAGTGTCCGGAAACTCAAGAGACTGTCGGTTTGTCTTTGTGAGGTTT F2: 3 TCAG 2 Unidirectional alignment (log-probability: -26) GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGAT-----------AGactGCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATAAGTCTATCACAG---GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA Template switch alignment (log-probability: -15.8) GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATA|GACT|GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA GCAGACATCAGTTTCAAGGCTGAGGGTCCTGCCTGTGATA|GACT|GCCTTTGAGTTCTCTGACAGCCAAACAGAAACACTCCAAA ========== Event 2212 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AACTTTTGAGTTTCATTTCAATTAGACAGTAAACTATTGTCT-----AATCACTAGGAAATATTTTGT Chimp: AACTTTTGAGTTTCATTTCAATTAGACAGTAAACTACTGTCT-----AATCACTAGGAAATATTTTGT ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: AACTTTTGAGTTTCATTTCAATTAGACAGTAGTTTACTGTCTAATTCAATCACTAGGAAATATTTTGT ↓ 3 1 2 4 ↑ 3 1 2 4 Human: AACTTTTGAGTTTCATTTCAATTAGACAGTAAACTATTGTCT-----AATCACTAGGAAATATTTTGT Cluster: [ ] Orangutan: AACTTTTGAGTTTCATTTCAATTAGACAGTAGTTTACTGTCTAATTCAATCACTAGGAGATATTTTGT Gorilla > Human --------------- chr3:91064178-91064188 Template switch process: F1: L ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA 1 F3: 4 AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCATAGG R RF: ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAGTTTACTGTCTAATTCAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG RR: TGTTCCAGGGTTGAAAACTCAAAGTAAAGTTAATCTGTCATCAAATGACAGATTAAGTTAGTGATCCTTTATAAAACACTCACAAAGTAACGCATCC F2: 3 TCTGTTATCAA 2 Unidirectional alignment (log-probability: -38.9) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAaacTAtTGTCT-----AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCaTAGG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAGTTTACTGTCTAATTCAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG Template switch alignment (log-probability: -28.2) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|AACTAtTGTCT|AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCaTAGG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|AACTACTGTCT|AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG Human > Gorilla --------------- chr3:92792723-92792737 Template switch process: F1: L ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA 1 F3: 4 CAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG R RF: ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAAACTATTGTCTAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCATAGG RR: TGTTCCAGGGTTGAAAACTCAAAGTAAAGTTAATCTGTCATTTGATAACAGATTAGTGATCCTTTATAAAACACTCACAAAGTAACGTATCC F2: 3 TTAATCTGTCATTTG 2 Unidirectional alignment (log-probability: -45.8) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAgttTAcTGTCTaattcAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCgTAG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAAACTATTGTCT-----AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCATAG Template switch alignment (log-probability: -28.7) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|GTTTACTGTCTAATT|cAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCgTAG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|GTTTACTGTCTAATT|TAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCATAG Gorilla > Chimp --------------- chr3:92400176-92400186 Template switch process: F1: L ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA 1 F3: 4 AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGCAGG R RF: ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAGTTTACTGTCTAATTCAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG RR: TGTTCCAGGGTTGAAAACTCAAAGTAAAGTTAATCTGTCATCAAATGACAGATTAAGTTAGTGATCCTTTATAAAACACTCACAAAGTAACGCATCC F2: 3 TCTGTCATCAA 2 Unidirectional alignment (log-probability: -33.4) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAaacTACTGTCT-----AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGcAGG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAGTTTACTGTCTAATTCAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG Template switch alignment (log-probability: -22.6) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|AACTACTGTCT|AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGcAGG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|AACTACTGTCT|AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG Chimp > Gorilla --------------- chr3:92792723-92792737 Template switch process: F1: L ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA 1 F3: 4 CAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGTAGG R RF: ACAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAAACTACTGTCTAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGCAGG RR: TGTTCCAGGGTTGAAAACTCAAAGTAAAGTTAATCTGTCATTTGATGACAGATTAGTGATCCTTTATAAAACACTCACAAAGTAACGCGTCC F2: 3 TTAATCTGTCATTTG 2 Unidirectional alignment (log-probability: -40.3) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAgttTACTGTCTaattcAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGtAG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTAAACTACTGTCT-----AATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGCAG Template switch alignment (log-probability: -28.7) CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|GTTTACTGTCTAATT|cAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGtAG CAAGGTCCCAACTTTTGAGTTTCATTTCAATTAGACAGTA|GTTTACTGTCTAATT|TAATCACTAGGAAATATTTTGTGAGTGTTTCATTGCGCAG ========== Event 2213 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGCTGCACTGTGGGCAGAGTGGACCTGCACAGGTCCACAGGACCTGTGTCCTGTGTCTCTACCAGTCA ↑ 34 1 2 Chimp: AAGCTGCACTGTGGGCAGAGTGGAC-------------------CTGTGTCCTGTGTCTCTACCAGTCA Gorilla: AAGCTGCACTGTGGGCAGAGTGGAC------------------------CCCTGTGTCTCTACCAGTCA Human: AAGCTGCACTGTGGGCAGAGTGGACCTGCACAGGTCCACAGGACCTGTGTCCTGTGTCTCTACCAGTCA Cluster: [ ] Orangutan: AAGCTGCCCTGTGGGCAGAGTGGAC------------------------CCCTGTGTCTCTACCAGTCA Chimp > Human ------------- chr3:90254677-90254687 Template switch process: F1: L GGAGGGTGTTGTAGTTAAGCTGCACTGTGGGCAGAGTGGACCTG 1 F3: 4 AGGACCTGTGTCCTGTGTCTCTACCAGTCATCATATATGTCACAG R RF: GGAGGGTGTTGTAGTTAAGCTGCACTGTGGGCAGAGTGGACCTGTGTCCTGTGTCTCTACCAGTCATCATATATGTCACAG RR: CCTCCCACAACATCAATTCGACGTGACACCCGTCTCACCTGGACACAGGACACAGAGATGGTCAGTAGTATATACAGTGTC F2: 3 CACCTGGACAC 2 Unidirectional alignment (log-probability: -38.2) GGTGTTGTAGTTAAGCTGCACTGTGGGCAGAGTGGACCtgcacaggtccacaggaccTGTGTCCTGTGTCTCTACCAGTCATCATATATGT GGTGTTGTAGTTAAGCTGCACTGTGGGCAGAGTGGACC-------------------TGTGTCCTGTGTCTCTACCAGTCATCATATATGT Template switch alignment (log-probability: -22.8) GGTGTTGTAGTTAAGCTGCACTGTGGGCAGAGTGGACCTG|CACAGGTCCAC|aGGACCTGTGTCCTGTGTCTCTACCAGTCATCATATATGT GGTGTTGTAGTTAAGCTGCACTGTGGGCAGAGTGGACCTG|CACAGGTCCAC|TGGACCTGTGTCCTGTGTCTCTACCAGTCATCATATATGT ========== Event 2214 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGCCAGGAGGGCTGGGACTCC---------------CAGGAAGACTGATCCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCCACTGGGGGCTT Chimp: AGCCAGGAGGGCTGGGACTCC---------------CAGGAAGACTGATCCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCCACTGGGGGCTT Gorilla: AGCCAGGAGGGCTGGGACTCC------------------------------CAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCCACTGGGGGCTT ↓ 4 1 3 2 Human: AGCCAGGAGGGCTGGGACTCC---------------CAGGAAGACTGATCCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCCACTGGGGGCTT Cluster: [ ] Orangutan: AGCCCGGAGGGCTGGGACTCCCAGGAAGACTGATGC---------------CAGGGAAGACATTCAAGTTCGTGAGTCTTTCCTCCGCCACTGGGGGCTT Gorilla > Human --------------- chr3:90317710-90317718 Template switch process: F1: L AAGTCCTGGAGCTGTGTTCCAGCCAGGAGGGCTGGGACTCCCAGG 1 F3: 4 CCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCCAC R RF: AAGTCCTGGAGCTGTGTTCCAGCCAGGAGGGCTGGGACTCCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCCAC RR: TTCAGGACCTCGACACAAGGTCGGTCCTCCCGACCCTGAGGGTCCCTTCTGTAAGTTCAAGTACTCAGAAAGGAGTCGGTG F2: 3 TAGTCAGAA 2 Unidirectional alignment (log-probability: -32.5) CTGGAGCTGTGTTCCAGCCAGGAGGGCTGGGACTcccaggaagactgatCCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCC CTGGAGCTGTGTTCCAGCCAGGAGGGCTGGGACT---------------CCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCC Template switch alignment (log-probability: -22.5) CTGGAGCTGTGTTCCAGCCAGGAGGGCTGGGACTCCCAGG|AAGACTgAT|CCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCC CTGGAGCTGTGTTCCAGCCAGGAGGGCTGGGACTCCCAGG|AAGACTCAT|CCCAGGGAAGACATTCAAGTTCATGAGTCTTTCCTCAGCC ========== Event 2215 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTTTACCCTAACTAGCAATGT-TTGCATAACTAGTTTGTAGTTGCATTGCTAGTTTGTATGGCTGGA ↓ 31 2 4 Chimp: GTTTACCCTAACTAGCAATGTTATGCA---------------AACATTGCTAGTTTGTATGGCTGGA Gorilla: GTTTACCCTAACTAGCAATGTTATGCA---------------AACACTGCTAGTTTGTATGGCTGGA ↑ 31 2 4 Human: GTTTACCCTAACTAGCAATGT-TTGCATAACTAGTTTGTAGTTGCATTGCTAGTTTGTATGGCTGGA Cluster: [ ] Orangutan: GTTTACCCTAACTAGCAATGTTATGCA---------------AACATTGCTAGTTTGTATGGCTGGA Human > Chimp ------------- chr3:111799656-111799662 Template switch process: F1: L AATTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT 1 F3: 4 CATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA R RF: AATTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTTTGCATAACTAGTTTGTAGTTGCATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA RR: TTAAATTCAATTATGTTTTTCAAATGGGATTGATCGTTACAAACGTATTGATCAAACATCAACGTAACGATCAAACATACCGACCTTTAACAGGTTCTTTTTT F2: 3 AAACGTA 2 Unidirectional alignment (log-probability: -29.4) TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTTaTGCAaA---------------CATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT-TGCATAACTAGTTTGTAGTTGCATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA Template switch alignment (log-probability: -16.2) TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT|ATGCAAA|CATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT|ATGCAAA|CATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA Human > Gorilla --------------- chr3:110204359-110204365 Template switch process: F1: L AATTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT 1 F3: 4 CACTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAAATG R RF: AATTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTTTGCATAACTAGTTTGTAGTTGCATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAAATG RR: TTAAATTCAATTATGTTTTTCAAATGGGATTGATCGTTACAAACGTATTGATCAAACATCAACGTAACGATCAAACATACCGACCTTTAACAGGTTCTTTTTTTAC F2: 3 AAACGTA 2 Unidirectional alignment (log-probability: -33.3) TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT----------------------ATgcaaacacTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTTTGCATAACTAGTTTGTAGTTGCAT--------TGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA Template switch alignment (log-probability: -22.2) TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT|ATGCAAA|CAcTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA TTTAAGTTAATACAAAAAGTTTACCCTAACTAGCAATGTT|ATGCAAA|CATTGCTAGTTTGTATGGCTGGAAATTGTCCAAGAAAAAA ========== Event 2216 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGACTACACTTCCAATCACAATGTTACAATGGTCTTTGTAACATTAGCAAAGGCAATAAATCTAG ↑ 1 4 3 2 Chimp: AGTGACTACACTTCCAATCACC-------TTTGGTCTTTGTAACATTAACAAAGGCAATAAATCTAG Gorilla: AGTGACTACACTTCCAATCACC-------TTTGGTCTTTGTAACATTAACAAAGGCAATAAATCTAG ↓ 1 4 3 2 Human: AGTGACTACACTTCCAATCACAATGTTACAATGGTCTTTGTAACATTAGCAAAGGCAATAAATCTAG Cluster: [ ] Orangutan: AGTGGCTACACTTCCAATCACC-------TTTGGTCTTTGTAACATTAACAAAGGCAATATATCTAG Chimp > Human ------------- chr3:89792508-89792517 Template switch process: F1: L TTCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC 1 F3: 4 TGGTCTTTGTAACATTAGCAAAGGCAATAAATCTAGTGGG R RF: TTCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCACCTTTGGTCTTTGTAACATTAACAAAGGCAATAAATCTAGTGGG RR: AAGGAGAAGGAGTACAATCTTCACTGATGTGAAGGTTAGTGGAAACCAGAAACATTGTAATTGTTTCCGTTATTTAGATCACCC F2: 3 AACATTGTAA 2 Unidirectional alignment (log-probability: -39) TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCACaatgttaCaaTGGTCTTTGTAACATTAgCAAAGGCAATAAATCTAGTGGG TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC-------CTTTGGTCTTTGTAACATTAACAAAGGCAATAAATCTAGTGGG Template switch alignment (log-probability: -22.5) TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC|AATGTTACAA|TGGTCTTTGTAACATTAgCAAAGGCAATAAATCTAGTGGG TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC|AATGTTACAA|TGGTCTTTGTAACATTAACAAAGGCAATAAATCTAGTGGG Gorilla > Human --------------- chr3:89792508-89792517 Template switch process: F1: L TTCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC 1 F3: 4 TGGTCTTTGTAACATTAGCAAAGGCAATAAATCTAGTGGG R RF: TTCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCACCTTTGGTCTTTGTAACATTAACAAAGGCAATAAATCTAGTGGG RR: AAGGAGAAGGAGTACAATCTTCACTGATGTGAAGGTTAGTGGAAACCAGAAACATTGTAATTGTTTCCGTTATTTAGATCACCC F2: 3 AACATTGTAA 2 Unidirectional alignment (log-probability: -37.5) TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCACaatgttaCaaTGGTCTTTGTAACATTAgCAAAGGCAATAAATCTAGTGGG TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC-------CTTTGGTCTTTGTAACATTAACAAAGGCAATAAATCTAGTGGG Template switch alignment (log-probability: -22.5) TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC|AATGTTACAA|TGGTCTTTGTAACATTAgCAAAGGCAATAAATCTAGTGGG TCCTCTTCCTCATGTTAGAAGTGACTACACTTCCAATCAC|AATGTTACAA|TGGTCTTTGTAACATTAACAAAGGCAATAAATCTAGTGGG ========== Event 2217 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATAAGCATTTTATTTCCTGACATCTATAGAAGTG----TCCACACATTTGGACATATGCTACAACTGCTA Chimp: TAATAAGCATTTTATTTCCTGACATCTATAGAGGTG----TCCACACATTTGGACATATGCTACAAGTGCTA Gorilla: TAATAAGCATTTTATTTCCTGACATCTATAGAAGTG--------GATGTCAGGACATATGCTGCAAGTGCTA ↑ 3 2 1 4 Human: TAATAAGCATTTTATTTCCTGACATCTATAGAAGTG----TCCACACATTTGGACATATGCTACAACTGCTA Cluster: [ ] Orangutan: TAATAAGCATTTTATTTCCTGACGTCTATAGATGTGTCCA----CACATTTGGACATATGCTACAAGTGCTA Human > Gorilla --------------- chr3:110460569-110460575 Template switch process: F1: L TATTTTAATAAGCATTTTATTTCCTGACATCTATAGAAGTG 1 F3: 4 GGACATATGCTGCAAGTGCTATTTGAGGAAGCCAACAGGC R RF: TATTTTAATAAGCATTTTATTTCCTGACATCTATAGAAGTGTCCACACATTTGGACATATGCTACAACTGCTATTTGAGGAAGCCAACAGGC RR: ATAAAATTATTCGTAAAATAAAGGACTGTAGATATCTTCACAGGTGTGTAAACCTGTATACGATGTTGACGATAAACTCCTTCGGTTGTCCG F2: 3 ACTGTAG 2 Unidirectional alignment (log-probability: -42.3) ATTTTAATAAGCATTTTATTTCCTGACATCTATAGAAGTG-----------gatgtcaGGACATATGCTgCAAgTGCTATTTGAGGAAGCCAACAGGC ATTTTAATAAGCATTTTATTTCCTGACATCTATAGAAGTGTCCACACATTT-------GGACATATGCTACAACTGCTATTTGAGGAAGCCAACAGGC Template switch alignment (log-probability: -27.7) ATTTTAATAAGCATTTTATTTCCTGACATCTATAGAAGTG|GATGTCA|GGACATATGCTgCAAgTGCTATTTGAGGAAGCCAACAGGC ATTTTAATAAGCATTTTATTTCCTGACATCTATAGAAGTG|GATGTCA|GGACATATGCTACAACTGCTATTTGAGGAAGCCAACAGGC ========== Event 2218 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCATTCTCTTCTTTACCTCCTC-------ACCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTTGAAGAAACCCCAATGCCATTGCTTTCAAAGATTTATCATATGTTAGGGGAGAGATGGAGGAGAAG Chimp: CCATTCTCTTCTTTACCTCCTC-------ACAACACACAAATACTCTCTTCATTCCTTTCATTGTCACTTGAAGAAACCTCAATGCCATTGCTTTCAAAGATTTATCATATGTTAGGGGAGAGATGGAGGAGAAG Gorilla: CCATTCTCATCTTTACCTCCTTAACATATGCCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTTGAAGAAACCCCAGTGCCATTGCTTTCAAAGATTTATCATATGTTAGGGGAGAGATGGAGGAGAAG ↑ 1 4 3 2 Human: CCATTCTCTTCTTTACCTCCTC-------ACCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTTGAAGAAACCCCAATGCCATTGCTTTCAAAGATTTATCATATGTTAGGGGAGAGATGGAGGAGAAG Cluster: [ ] Orangutan: CCATTCTCTTCTTTACCTCCTCACCGTATGCCACACACAAATACTCTCCTCATTCCTTCCATTGTCACTTGAAGAAACCCCAATGCCATTGCTTTCAAAGATTTATCATATGTTAGGGGAGAGATGGAGGAGAAG Human > Gorilla --------------- chr3:111096324-111096332 Template switch process: F1: L TTTGTTGCCATTCTCTTCCACCATTCTCATCTTTACCTCCT 1 F3: 4 CCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTT R RF: TTTGTTGCCATTCTCTTCCACCATTCTCTTCTTTACCTCCTCACCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTTGAAGAAACCCCAATGCCATTGCTTTCAAAGATTTATCATATGTTA RR: AAACAACGGTAAGAGAAGGTGGTAAGAGAAGAAATGGAGGAGTGGTGTGTGTTTATGAGAGGAGTAAGGAAAGTAACAGTGAACTTCTTTGGGGTTACGGTAACGAAAGTTTCTAAATAGTATACAAT F2: 3 GTATACAAT 2 Unidirectional alignment (log-probability: -32) TTGTTGCCATTCTCTTCCACCATTCTCaTCTTTACCTCCTtAacatatgCCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTT TTGTTGCCATTCTCTTCCACCATTCTCTTCTTTACCTCCTCA-------CCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTT Template switch alignment (log-probability: -22.4) TTGTTGCCATTCTCTTCCACCATTCTCaTCTTTACCTCCT|TAACATATG|CCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTT TTGTTGCCATTCTCTTCCACCATTCTCTTCTTTACCTCCT|TAACATATG|CCACACACAAATACTCTCCTCATTCCTTTCATTGTCACTT ========== Event 2219 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAATAACTGGACTAGCATGAAAACATTTTGTTTCTGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGAC Chimp: TAATAACTGGACTAGCATGAAAGCATTTTGTTTCTGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGAC Gorilla: TAATAACTGGACTAGCATGAAT----------ACGGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGAC ↓ 1 4 3 2 Human: TAATAACTGGACTAGCATGAAAACATTTTGTTTCTGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGAC Cluster: [ ] Orangutan: TAATAACTGGACTAGCATGAAT----------ACGGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTAAC Gorilla > Human --------------- chr3:110274100-110274110 Template switch process: F1: L CAGGCAGAATCTTTACTTTATAATAACTGGACTAGCATGAAAAC 1 F3: 4 GTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGACTAA R RF: CAGGCAGAATCTTTACTTTATAATAACTGGACTAGCATGAATACGGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGACTAA RR: GTCCGTCTTAGAAATGAAATATTATTGACCTGATCGTACTTATGCCATTCGTCTTTGTTTTAGGTTTGACTGGAAAGAACTGATT F2: 3 TCTTTGTTTTA 2 Unidirectional alignment (log-probability: -36.4) CAGAATCTTTACTTTATAATAACTGGACTAGCATGAAaacattttgtTtCtGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGACTAA CAGAATCTTTACTTTATAATAACTGGACTAGCATGAA----------TACGGTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGACTAA Template switch alignment (log-probability: -22.7) CAGAATCTTTACTTTATAATAACTGGACTAGCATGAAaAC|ATTTTGTTTCT|GTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGACTAA CAGAATCTTTACTTTATAATAACTGGACTAGCATGAATAC|ATTTTGTTTCT|GTAAGCAGAAACAAAATCCAAACTGACCTTTCTTGACTAA ========== Event 2220 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tttaagctgtatcaTCTGTTTGTGTCATTTGTGAAT--ATTAAAAGGTAC-ACAGAACTAGAATGTAGAGTGT Chimp: tttaagctgtatcaTCTGTTTGTGTCATTTGTGAAT--ATTAAAAGGTAC-ACAGAACTAGAATGTAGAGTGT ↓ 3 2 1 4 Gorilla: tttaagctgtatcaTCTGTTTGTGTCATTTGTGAAT----AGAATGACACAATAGAACTAGAATGTAGAGTGT ↑ 3 2 1 4 Human: tttaagctgtatcaTCTGTTTGTGTCATTTGTGAAT--ATTAAAAGGTAC-ACAGAACTAGAATGTAGAGTGT Cluster: [ ] Orangutan: TTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAT--TAAAAGGTAC-ACAGAACTAGAATGTAGAGTGT Human > Gorilla --------------- chr3:111647788-111647797 Template switch process: F1: L ACATATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAG 1 F3: 4 TAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTTA R RF: ACATATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATATTAAAAGGTACACAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTTA RR: TGTATAAATTCGACATAGTAGACAAACACAGTAAACACTTATAATTTTCCATGTGTCTTGATCTTACATCTCACACTAAGAGAGAAAACAACAAT F2: 3 AACACAGTAA 2 Unidirectional alignment (log-probability: -37.1) TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATagaatgacacaAT------------AGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAAT-----------ATTAAAAGGTACACAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT Template switch alignment (log-probability: -28.1) TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAg|AATGACACAA|tAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAT|AATGACACAA|CAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT Chimp > Gorilla --------------- chr3:111647788-111647797 Template switch process: F1: L ACATATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAG 1 F3: 4 TAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTTA R RF: ACATATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATATTAAAAGGTACACAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTTA RR: TGTATAAATTCGACATAGTAGACAAACACAGTAAACACTTATAATTTTCCATGTGTCTTGATCTTACATCTCACACTAAGAGAGAAAACAACAAT F2: 3 AACACAGTAA 2 Unidirectional alignment (log-probability: -37.1) TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATagaatgacacaAT------------AGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAAT-----------ATTAAAAGGTACACAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT Template switch alignment (log-probability: -28.1) TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAg|AATGACACAA|tAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT TATTTAAGCTGTATCATCTGTTTGTGTCATTTGTGAATAT|AATGACACAA|CAGAACTAGAATGTAGAGTGTGATTCTCTCTTTTGTTGTT ========== Event 2221 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CACGCTTCCGGTGGGAGGACGTCTGTTTACAG----------CTCGGGGAAGCTATGACAGCACAATGTGGTGTGGACACATGCGGGAACGTGGCTGGCTGCCCCCACGGGCTGCCAGAGCTATTTTCCAGATATGGCAGCA Chimp: CACGCTTCCGGTGGGAGGACGCCTGTTTACGTTCCCTCTGTTGTGGGGGAAGCTGTGACAGCACAATGTGGTGTGGACACATGCCGGAACGTGGCTGGCTGCCCCCACGGGCTGCCAGAGCTATTTTCCAGATATGGCAGCA ↓ 1 4 3 2 Gorilla: CACGCTTCCGGTGGGAGGACGTCTGTTTACAG----------CTCGGGGAAGCTATGACAGCACAATGTGGTGTGGACACATGCCGGAACGTGGCTGGCTGCCCCCACGGGCTGCCAGAGCTATTTTCCAGATATGGCAGCA Human: CACGCTTCCGGTGGGAGGACGTCTGTTTACAG----------CTCGGGGAAGCTATGACAGCACAATGTGGTGTGGACACATGCGGGAACGTGGCTGGCTGCCCCCACGGGCTGCCAGAGCTATTTTCCAGATATGGCAGCA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr3:11341917-11341921 Template switch process: F1: L TCCAAGAGACAGGAGAAAAGCACGCTTCCGGTGGGAGGACGTCTGTTTAC 1 F3: 4 GGGGAAGCTATGACAGCACAATGTGGTGTGGACACATGCCGGAACGTGGC R RF: TCCAAGAGACAGGAGAAAAGCACGCTTCCGGTGGGAGGACGCCTGTTTACGTTCCCTCTGTTGTGGGGGAAGCTGTGACAGCACAATGTGGTGTGGACACATGCCGGAACGTGGCTGGCTGCCCCCACGGGCTGCCAGAGCT RR: AGGTTCTCTGTCCTCTTTTCGTGCGAAGGCCACCCTCCTGCGGACAAATGCAAGGGAGACAACACCCCCTTCGACACTGTCGTGTTACACCACACCTGTGTACGGCCTTGCACCGACCGACGGGGGTGCCCGACGGTCTCGA F2: 3 CTCGA 2 Unidirectional alignment (log-probability: -39.5) AGGAGAAAAGCACGCTTCCGGTGGGAGGACGtCTGTTTACaGcTC-----------GGGGAAGCTaTGACAGCACAATGTGGTGTGGACACATGCC AGGAGAAAAGCACGCTTCCGGTGGGAGGACGCCTGTTTAC-GTTCCCTCTGTTGTGGGGGAAGCTGTGACAGCACAATGTGGTGTGGACACATGCC Template switch alignment (log-probability: -27.9) AGGAGAAAAGCACGCTTCCGGTGGGAGGACGtCTGTTTAC|AGCTC|GGGGAAGCTaTGACAGCACAATGTGGTGTGGACACATGCC AGGAGAAAAGCACGCTTCCGGTGGGAGGACGCCTGTTTAC|AGCTC|GGGGAAGCTGTGACAGCACAATGTGGTGTGGACACATGCC ========== Event 2222 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: ACAAAACTCTAGGTACAATCTTCCTAGACTTACTTCCTACAAAGCGTTTAGAATGACACTTTCCAAACCTCCAGG----------GTAACCCTTTtgtgaagtcctaattagagaaaaggagttaggctggtgagagcacgggaaagcaaagaaagaaagaaagcagataagctatgagtctgcctttctttgtggtccag Chimp: Gorilla: ACAAAACTCTAGGTACAATCTT-------------CCTACAAAGTGTTTAGAATGACACTTTCCAAACCTCCAGGGTCTGAATATGTAACCCTTTtgcgaagtcctaattagagaaaaggagttaggctggtgggagcatgggaaagcaaaga----aagaaagcagataagctataagtctgcctttctttgtggtccag ↓ 4 1 3 2 Human: ACAAAACTCTAGGTACAATCTTCCTAGACTTACTTCCTACAAAGCGTTTAGAATGACACTTTCCAAACCTCCAGG----------GTAACCCTTTtgtgaagtcctaattagagaaaaggagttaggctggtgagagcacgggaaagcaaagaaagaaagaaagcagataagctatgagtctgcctttctttgtggtccag Cluster: [ ] Orangutan: Gorilla > Human --------------- chr3:11853438-11853443 Template switch process: F1: L TTGTTCAGACCCAGAACTGACAAAACTCTAGGTACAATCTTCCTA 1 F3: 4 CTTCCTACAAAGCGTTTAGAATGACACTTTCCAAACCTCCAGG R RF: TTGTTCAGACCCAGAACTGACAAAACTCTAGGTACAATCTTCCTACAAAGTGTTTAGAATGACACTTTCCAAACCTCCAGGGTCTGAATATGTAACCCTTTTGCGAAGTCCTAATTAGAGAAAAGGAGTTAGGCTGGTGGGAGCATGGGAAAGCAAAGAAAGAAAGCAGATAAGCTATAAGTC RR: AACAAGTCTGGGTCTTGACTGTTTTGAGATCCATGTTAGAAGGATGTTTCACAAATCTTACTGTGAAAGGTTTGGAGGTCCCAGACTTATACATTGGGAAAACGCTTCAGGATTAATCTCTTTTCCTCAATCCGACCACCCTCGTACCCTTTCGTTTCTTTCTTTCGTCTATTCGATATTCAG F2: 3 ATTCAG 2 Unidirectional alignment (log-probability: -42.4) CAGACCCAGAACTGACAAAACTCTAGGTACAATCttcctagacttacTTCCTACAAAGcGTTTAGAATGACACTTTCCAAACCTCC CAGACCCAGAACTGACAAAACTCTAGGTACAATC-------------TTCCTACAAAGTGTTTAGAATGACACTTTCCAAACCTCC Template switch alignment (log-probability: -22.2) CAGACCCAGAACTGACAAAACTCTAGGTACAATCTTCCTA|GACTTA|CTTCCTACAAAGcGTTTAGAATGACACTTTCCAAACCTCC CAGACCCAGAACTGACAAAACTCTAGGTACAATCTTCCTA|GACTTA|CTTCCTACAAAGTGTTTAGAATGACACTTTCCAAACCTCC ========== Event 2223 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTATAGTTAAGTCAACTTAC--------AGTGTTTTTCACATTCCTCTCTTCTCCATTTAT Chimp: TGTATAGTTAAGTCAACTTAC--------AGTGTTTTTCACATTCCTCTCTTCTCCATTTAT ↑ 1 3 42 Gorilla: TGTATAGTTAAGTCAACTTACAAGAGAGGAATGTGAAAAACATTCCTCTCTTCTCCATTTAT ↓ 1 3 42 Human: TGTATAGTTAAGTCAACTTAC--------AGTGTTTTTCACATTCCTCTCTTCTCCATTTAT Cluster: [ ] Orangutan: TGTATAGTTAAGTCAACTTAC--------AGTGTTTTTCACATTCCTCTCTTCTCCATTTAT Gorilla > Human --------------- chr3:86379028-86379036 Template switch process: F1: L AAATATCATTAAGATTGTTCTGTATAGTTAAGTCAACTTACAG 1 F3: 4 CATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA R RF: AAATATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAAGAGAGGAATGTGAAAAACATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA RR: TTTATAGTAATTCTAACAAAACATATCAATTCAGTTGAATGTTCTCTCCTTACACTTTTTGTAAGGAGAGAAGAGGTAAATAGGGATTTAGCTAATAAT F2: 3 ACTTTTTGT 2 Unidirectional alignment (log-probability: -40) TATCATTAAGATTGTTcTGTATAGTTAAGTCAACTTAC-----------------AgtgtttttcACATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA TATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAAGAGAGGAATGTGAAAA---------ACATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA Template switch alignment (log-probability: -27.9) TATCATTAAGATTGTTcTGTATAGTTAAGTCAACTTACAg|TGTTTTTCA|CATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA TATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAA|TGTTTTTCA|CATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA Gorilla > Chimp --------------- chr3:87601128-87601136 Template switch process: F1: L AAATATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAG 1 F3: 4 CATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA R RF: AAATATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAAGAGAGGAATGTGAAAAACATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA RR: TTTATAGTAATTCTAACAAAACATATCAATTCAGTTGAATGTTCTCTCCTTACACTTTTTGTAAGGAGAGAAGAGGTAAATAGGGATTTAGCTAATAAT F2: 3 ACTTTTTGT 2 Unidirectional alignment (log-probability: -34.5) TATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTAC-----------------AgtgtttttcACATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA TATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAAGAGAGGAATGTGAAAA---------ACATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA Template switch alignment (log-probability: -22.4) TATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAg|TGTTTTTCA|CATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA TATCATTAAGATTGTTTTGTATAGTTAAGTCAACTTACAA|TGTTTTTCA|CATTCCTCTCTTCTCCATTTATCCCTAAATCGATTATTA ========== Event 2224 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTCTCAAGTCTGGATAAAGC---------------------------TTTAGAGTTTCTGGATAAAGCAATTTTATTTTAAGAATTCT Chimp: ACTCTCAAGTCTGGATAAAGC---------------------------TTTAGAGTTTCTGGATAAAGCAATTTTATTTTAAGAATTCT ↓ 3 4 2 1 Gorilla: ACTCTCAAGTCTGGATAAAGCTTTAGAGTTTCTGGATAAAGCTTTATCCATAAATTGTATGGATAAAGCAATTTTATTTTAAGAATTCT Human: ACTCTCAAGTCTGGATAAAGC---------------------------TTTAGAGTTTCTGGATAAAGCAATTTTATTTTAAGAATTCT Cluster: [ ] Orangutan: ACTCTCAAGTCTGGATAAAGCTTTAGAGTTTCTGGATAAAGCTTTATCCATAAATTGTATGGATAAAGCAATTTTATTTTAAGAATTCT Chimp > Gorilla --------------- chr3:86988424-86988440 Template switch process: F1: L AACGTAATGTCTTGCTGAAAACTCTCAAGTCTGGATAAAGCTTTAGAGTTTCTGGATAAAGC 1 F3: 4 TGGATAAAGCAATTTTATTTTAAGAATTCTCAAACTATTA R RF: AACGTAATGTCTTGCTGAAAACTCTCAAGTCTGGATAAAGCTTTAGAGTTTCTGGATAAAGCAATTTTATTTTAAGAATTCTCAAACTATTA RR: TTGCATTACAGAACGACTTTTGAGAGTTCAGACCTATTTCGAAATCTCAAAGACCTATTTCGTTAAAATAAAATTCTTAAGAGTTTGATAAT F2: 3 ATGTTAAATACCTATTT 2 Unidirectional alignment (log-probability: -49.9) TCTCAAGTCTGGATAAAGCTTTAGAGTTTCtggataaagctttatccataaattgtaTGGATAAAGCAATTTTATTTTAAGAATTCTCAAACTATTA TCTCAAGTCTGGATAAAGCTTTAGAGTTTC---------------------------TGGATAAAGCAATTTTATTTTAAGAATTCTCAAACTATTA Template switch alignment (log-probability: -34.9) TCTCAAGTCTGGATAAAGCTTTAGAGTTTCTGGATAAAGC|TTTATCCAtAAAtTgTA|TGGATAAAGCAATTTTATTTTAAGAATTCTCAAACTATTA TCTCAAGTCTGGATAAAGCTTTAGAGTTTCTGGATAAAGC|TTTATCCAGAAACTCTA|TGGATAAAGCAATTTTATTTTAAGAATTCTCAAACTATTA ========== Event 2225 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AATTATTTAGGTATGGGGAAAATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTA ↓ 1 4 3 2 Chimp: AATTATTTAGGTATGGGGAAAG-CTATGCTTTAGCATAGCTTTCATCATTGTTATCACTA ↑ 1 4 3 2 Gorilla: AATTATTTAGGTATGGGGAAAATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTA Human: AATTATTTAGGTATGGGGAAAATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTA Cluster: [ ] Orangutan: AATTATTCAGGTATGGGGAAAATGCCTGCTTTAGCATAACTTTCATCATTGTTATTACTA Human > Chimp ------------- chr3:117163901-117163904 Template switch process: F1: L CTATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA 1 F3: 4 TGCTTTAGCATAGCTTTCATCATTGTTATCACTATCAAAC R RF: CTATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAAATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTATCAAAC RR: GATAATTCTTTTAAAGGACTTTAATAAATCCATACCCCTTTTACGGACGAAATCGTATCGAAAGTAGTAACAATAATGATAGTTTG F2: 3 ATCG 2 Unidirectional alignment (log-probability: -31.7) TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAAgctA----TGCTTTAGCATAGCTTTCATCATTGTTATcACTATCAAAC TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA---ATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTATCAAAC Template switch alignment (log-probability: -21.8) TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA|GCTA|TGCTTTAGCATAGCTTTCATCATTGTTATcACTATCAAAC TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA|GCTA|TGCTTTAGCATAGCTTTCATCATTGTTATTACTATCAAAC Gorilla > Chimp --------------- chr3:117163901-117163904 Template switch process: F1: L CTATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA 1 F3: 4 TGCTTTAGCATAGCTTTCATCATTGTTATCACTATCAAAC R RF: CTATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAAATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTATCAAAC RR: GATAATTCTTTTAAAGGACTTTAATAAATCCATACCCCTTTTACGGACGAAATCGTATCGAAAGTAGTAACAATAATGATAGTTTG F2: 3 ATCG 2 Unidirectional alignment (log-probability: -30.7) TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAAgctA----TGCTTTAGCATAGCTTTCATCATTGTTATcACTATCAAAC TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA---ATGCCTGCTTTAGCATAGCTTTCATCATTGTTATTACTATCAAAC Template switch alignment (log-probability: -21.7) TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA|GCTA|TGCTTTAGCATAGCTTTCATCATTGTTATcACTATCAAAC TATTAAGAAAATTTCCTGAAATTATTTAGGTATGGGGAAA|GCTA|TGCTTTAGCATAGCTTTCATCATTGTTATTACTATCAAAC ========== Event 2226 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCAGCTTGTGTGATAAGCTAATATTACTGGATGATATTGTAGTGCCCT-TTTATCATGGTGAGATTAAGACACTATAAAAGATCTCTGGGGAAATACTTTTTGATAAATGGAGAATTTTAACCTTAATGtgaattcacaaagattgggatctgatttctacttctgtcgattcat Chimp: TGCAGCTTGTGTGATAAGCTA-AATTATTGGATGATATTGTAGTGCCCT-TTTATC-AGGTGAGATTAAGACACTATAAAAGATCTCTGGGGAAATACTTTTTGATAAATGGAGAATTTTAACCTTAATGtgaattcacaaagattgggatctgatttctacttctatcgattcat ↑ 1 4 3 2 Gorilla: TGCAGCTTGTGTGATAAGCTAATATTATTGGATGATATTGTAGTGCCCTTTTTATCATGATGAGATTAAGACACTATAAAAGATCTCTGGGGAAATACTTTTTGATAAATGGAGAATTTTAACCTTAATGtgaattcacaaagattgggatctgatttctacttctatcggttcat Human: TGCAGCTTGTGTGATAAGCTAATATTACTGGATGATATTGTAGTGCCCT-TTTATCATGGTGAGATTAAGACACTATAAAAGATCTCTGGGGAAATACTTTTTGATAAATGGAGAATTTTAACCTTAATGtgaattcacaaagattgggatctgatttctacttctgtcgattcat Cluster: [] Orangutan: CGCAGCTTGTGTGATAAGCTAATATTAATGGATGATATTGTAGTGCCCT-TTTATCATGGTGAGATTAAGACACTATAAAAGATCTCTGGGGAAATACTTTTTGATAAATGGAGAATTTTAACCTTAATGTAAATtcacaaagattgggatctgatttctgcttctgtcggttcat Gorilla > Chimp --------------- chr3:81650764-81650768 Template switch process: F1: L GCTGCTTTCACTAGGGCATTTGCAGCTTGTGTGATAAGCTAA-ATTATTGGATGATATTGTAGTGCCCTTTT 1 F3: 4 GTGA R RF: GCTGCTTTCACTAGGGCATTTGCAGCTTGTGTGATAAGCTAATATTATTGGATGATATTGTAGTGCCCTTTTTATCATGATGAGATTAAGACACTATAAAAGATCTCTGGGGAAATACTTTTTGATAAATGGAGAATTTTAACCTTAATGTGAATTCACAAAGATTGGGATCTGAT RR: CGACGAAAGTGATCCCGTAAACGTCGAACACACTATTCGATTATAATAACCTACTATAACATCACGGGAAAAATAGTACTACTCTAATTCTGTGATATTTTCTAGAGACCCCTTTATGAAAAACTATTTACCTCTTAAAATTGGAATTACACTTAAGTGTTTCTAACCCTAGACTA F2: 3 GACTA 2 Unidirectional alignment (log-probability: -36) TGATAAGCTAA-ATTATTGGATGATATTGTAGTGCCC-TTTTATCA-GgTGA TGATAAGCTAATATTATTGGATGATATTGTAGTGCCCTTTTTATCATGATGA Template switch alignment (log-probability: -26) TGATAAGCTAA-ATTATTGGATGATATTGTAGTGCCCTTTT|ATCAG|GTGA TGATAAGCTAATATTATTGGATGATATTGTAGTGCCCTTTT|ATCAG|GTGA ========== Event 2227 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: tggaatAGGAAGAAAAGATTTTCTTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGGTATG-----------------------------------------------GATCTTCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAAACCTGACATCAGAAGACAACCATG Chimp: tggaatGGGAAGAAAAGATTTTCTTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGATCCA-----------------------------------------------TACCTTCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAAACCTGACATCAGAAGACAACCATG ↑ 3 2 4 1 Gorilla: TGGAATAGGAAGAAAAGATTTTCTTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGATCCA----------------------------------------------------------------------------------------------TACCTGACATCAGAAGACAACCATG ↓ 3 1 42 Human: tggaatAGGAAGAAAAGATTTTCTTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGGTATG-----------------------------------------------GATCTTCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAAACCTGACATCAGAAGACAACCATG Cluster: [ ] Orangutan: tggaatAGGAAGAAAAGATTTTCTTTCCTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----------------------------------------------NNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr3:12105495-12105547 Template switch process: F1: L TTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAG 1 F3: 4 ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG R RF: TTTCTTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGATCCATACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG RR: AAAGAAAGGAAAAGTCCCCGATGGATCCTGTTTGTGGTGATCTTCTAGGTATGGACTGTAGTCTTCTGTTGGTACGAGATCCCGTTGAGGC F2: 3 AAAGAAAGGAAAAGTCCCCGATGGATCCTGTTTGTGGTGATCTTCTAGGTATG 2 Unidirectional alignment (log-probability: -95.7) TTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGgtatggatcttctagtggtgtttgtcctaggtagcccctgaaaaggaaagaaA-----ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG TTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAG----------------------------------------------------ATCCATACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG Template switch alignment (log-probability: -22.4) TTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAG|GTATGGATCTTCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAA|ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG TTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAG|GTATGGATCTTCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAA|ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG Gorilla > Chimp --------------- chr3:12397851-12397893 Template switch process: F1: L TTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGATCCATACCT 1 F3: 4 ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCA R RF: TTTCTTTCCTTTTCAGGGGCTACCTAGGACAAACACCACTAGAAGATCCATACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG RR: AAAGAAAGGAAAAGTCCCCGATGGATCCTGTTTGTGGTGATCTTCTAGGTATGGACTGTAGTCTTCTGTTGGTACGAGATCCCGTTGAGGC F2: 3 AAAGAAAGGAAAAGTCCCCGATGGATCCTGTTTGTGGTGATCT 2 Unidirectional alignment (log-probability: -84) GGGGCTACCTAGGACAAACACCACTAGAAGATCCATaccttctagtggtgtttgtcctaggtagcccctgaaaaggaaagaaaACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCa GGGGCTACCTAGGACAAACACCACTAGAAGATCCAT-----------------------------------------------ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG Template switch alignment (log-probability: -26.8) GGGGCTACCTAGGACAAACACCACTAGAAGATCCATACCT|TCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAA|ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCa GGGGCTACCTAGGACAAACACCACTAGAAGATCCATACCT|TCTAGTGGTGTTTGTCCTAGGTAGCCCCTGAAAAGGAAAGAAA|ACCTGACATCAGAAGACAACCATGCTCTAGGGCAACTCCG ========== Event 2228 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAACAGCTCTGATTACACAT------AGTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCC ↓ 1 4 3 2 Chimp: TTAACAGCTCTGATTACACATGAGCCTTTTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCC ↑ 1 4 3 2 Gorilla: TTAACAGCTCTGATTACACAT------AGTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCC Human: TTAACAGCTCTGATTACACAT------AGTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCC Cluster: [ ] Orangutan: TTAACAGCTCTGATTACACAT------AGTCATGAGAAAAGGCTCCTATAGCAAGCATAAGCCCC Human > Chimp ------------- chr3:80897684-80897691 Template switch process: F1: L TCCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT 1 F3: 4 TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA R RF: TCCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACATAGTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA RR: AGGATCGTACTTACTCTCTAAATTGTCGAGACTAATGTGTATCAGTACTCTTTTCCGAGGATACCGTTCGTGTTCGGGGAGTT F2: 3 TTTCCGAG 2 Unidirectional alignment (log-probability: -29.8) CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACATgAGcctttTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT-AG-----TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA Template switch alignment (log-probability: -16.3) CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT|GAGCCTTT|TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT|GAGCCTTT|TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA Gorilla > Chimp --------------- chr3:80897684-80897691 Template switch process: F1: L TCCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT 1 F3: 4 TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA R RF: TCCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACATAGTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA RR: AGGATCGTACTTACTCTCTAAATTGTCGAGACTAATGTGTATCAGTACTCTTTTCCGAGGATACCGTTCGTGTTCGGGGAGTT F2: 3 TTTCCGAG 2 Unidirectional alignment (log-probability: -29.3) CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACATgAGcctttTCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT-AG-----TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA Template switch alignment (log-probability: -16.7) CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT|GAGCCTTT|TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA CCTAGCATGAATGAGAGATTTAACAGCTCTGATTACACAT|GAGCCTTT|TCATGAGAAAAGGCTCCTATGGCAAGCACAAGCCCCTCAA ========== Event 2229 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCGTGTAAGGTTCCAAACACAAATAAGTTCCATCGTCTGGAGCTTATTTGTACACTttaaaaatgtacaga Chimp: TCGTGTAAGGTTCCAAACACAAATAAGCTCCATCGTCTGGAGCTTATTTGTACActttaaaaatgtacaga Gorilla: TCGTGTAAGCTTCCAAACACAAATAAGCTCCATCGTCT----------GCTACACTttaaaaatgtacaga ↓ 3 2 1 4 Human: TCGTGTAAGGTTCCAAACACAAATAAGTTCCATCGTCTGGAGCTTATTTGTACACTttaaaaatgtacaga Cluster: [ ] Orangutan: TCGTGTAAGGTTCCAAACAC----AAGCTCCATCGTGT----------GGTACACTttaaaaatgtacaga Gorilla > Human --------------- chr3:79502767-79502777 Template switch process: F1: L GTGTCGTGTAAGGTTCCAAACACAAATAAGTTCCATCGTCTG 1 F3: 4 TACACTTTAAAAATGTACAGATCCCTAGGCTCAATATCCA R RF: GTGTCGTGTAAGCTTCCAAACACAAATAAGCTCCATCGTCTGCTACACTTTAAAAATGTACAGATCCCTAGGCTCAATATCCA RR: CACAGCACATTCGAAGGTTTGTGTTTATTCGAGGTAGCAGACGATGTGAAATTTTTACATGTCTAGGGATCCGAGTTATAGGT F2: 3 GTTTATTCGAG 2 Unidirectional alignment (log-probability: -41.8) GTCGTGTAAGgTTCCAAACACAAATAAGtTCCATCGTCTGgagcttatttgTACACTTTAAAAATGTACAGATCCCTAGGCTCAATATCCA GTCGTGTAAGCTTCCAAACACAAATAAGCTCCATCGTCTG----------CTACACTTTAAAAATGTACAGATCCCTAGGCTCAATATCCA Template switch alignment (log-probability: -28.2) GTCGTGTAAGgTTCCAAACACAAATAAGtTCCATCGTCTG|GAGCTTATTTG|TACACTTTAAAAATGTACAGATCCCTAGGCTCAATATCCA GTCGTGTAAGCTTCCAAACACAAATAAGCTCCATCGTCTG|GAGCTTATTTG|TACACTTTAAAAATGTACAGATCCCTAGGCTCAATATCCA ========== Event 2230 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCTGATAAACTGCAAAGGGGATAGAGGGTATTATGGACATTATGGAACAAATTACTGTTT Chimp: AATCTGATAAACTGCAAAGGGGATAGAGGGTATTATGGACATTATGGAACAAAATACTGTTT ↓ 1 34 2 Gorilla: AATCTGATAAACTGCAAAGGGAATAATGTCCATAATGGACATTATGGAACAAAATACTGTTT ↑ 1 34 2 Human: AATCTGATAAACTGCAAAGGGGATAGAGGGTATTATGGACATTATGGAACAAATTACTGTTT Cluster: [ ] Orangutan: AGTTTGATAAACTGCAAAGGGGATAGAGGGTATTATGGACACTATGGAACAAAATACTGTTT Human > Gorilla --------------- chr3:81258850-81258858 Template switch process: F1: L AACAGAATAGTAGACTATACAATCTGATAAACTGCAAAGGGAATA 1 F3: 4 ATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT R RF: AACAGAATAGTAGACTATACAATCTGATAAACTGCAAAGGGGATAGAGGGTATTATGGACATTATGGAACAAATTACTGTTTCTACTTCTCTTT RR: TTGTCTTATCATCTGATATGTTAGACTATTTGACGTTTCCCCTATCTCCCATAATACCTGTAATACCTTGTTTAATGACAAAGATGAAGAGAAA F2: 3 ATACCTGTA 2 Unidirectional alignment (log-probability: -45.1) AATAGTAGACTATACAATCTGATAAACTGCAAAGGGaATA---------atgtccataATGGACATTATGGAACAAAaTACTGTTTCTACTTCTCTTT AATAGTAGACTATACAATCTGATAAACTGCAAAGGGGATAGAGGGTATT---------ATGGACATTATGGAACAAATTACTGTTTCTACTTCTCTTT Template switch alignment (log-probability: -28) AATAGTAGACTATACAATCTGATAAACTGCAAAGGGaATA|ATGTCCATA|ATGGACATTATGGAACAAAaTACTGTTTCTACTTCTCTTT AATAGTAGACTATACAATCTGATAAACTGCAAAGGGGATA|ATGTCCATA|ATGGACATTATGGAACAAATTACTGTTTCTACTTCTCTTT Chimp > Gorilla --------------- chr3:81258850-81258858 Template switch process: F1: L AACAGAATAGTAGACTATACAATCTGATAAACTGCAAAGGGAATA 1 F3: 4 ATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT R RF: AACAGAATAGTAGACTATACAATCTGATAAACTGCAAAGGGGATAGAGGGTATTATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT RR: TTGTCTTATCATCTGATATGTTAGACTATTTGACGTTTCCCCTATCTCCCATAATACCTGTAATACCTTGTTTTATGACAAAGATGAAGAGAAA F2: 3 ATACCTGTA 2 Unidirectional alignment (log-probability: -39.6) AATAGTAGACTATACAATCTGATAAACTGCAAAGGGaATA---------atgtccataATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT AATAGTAGACTATACAATCTGATAAACTGCAAAGGGGATAGAGGGTATT---------ATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT Template switch alignment (log-probability: -22.5) AATAGTAGACTATACAATCTGATAAACTGCAAAGGGaATA|ATGTCCATA|ATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT AATAGTAGACTATACAATCTGATAAACTGCAAAGGGGATA|ATGTCCATA|ATGGACATTATGGAACAAAATACTGTTTCTACTTCTCTTT ========== Event 2231 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGCAGAGAAACGCAGAGGGTAGTCAGT--GTGTCTCTGGCTTAGCCTCACACCA Chimp: CTGCAGAGAAATGCAGAGGGTAGTCAGT--GTGTCTCTGGCTTAGCCTCACACCA Gorilla: CTGCAGAGAAACGCAGAGGGTAGTCACTGACTACCTCTGGCTTAGCCTCACAGCA ↑ 3 12 4 Human: CTGCAGAGAAACGCAGAGGGTAGTCAGT--GTGTCTCTGGCTTAGCCTCACACCA Cluster: [ ] Orangutan: CTGCAGAGAAACGCAGAGGGTAGTCAGT--GTGTCTCTGGCTTAGCCTCACACCA Human > Gorilla --------------- chr3:80316325-80316332 Template switch process: F1: L TGTGGTCAATGATCGCTGCAGAGAAACGCAGAGGGTAGTCA 1 F3: 4 CTCTGGCTTAGCCTCACAGCAGGCTGCTTTGGTGAGATGG R RF: TGTGGTCAATGATCACTGCAGAGAAACGCAGAGGGTAGTCAGTGTGTCTCTGGCTTAGCCTCACACCAGGCTGCTTTGGTGAGATGG RR: ACACCAGTTACTAGTGACGTCTCTTTGCGTCTCCCATCAGTCACACAGAGACCGAATCGGAGTGTGGTCCGACGAAACCACTCTACC F2: 3 CATCAGTC 2 Unidirectional alignment (log-probability: -41.4) GTGGTCAATGATCgCTGCAGAGAAACGCAGAGGGTAGTCAcTGacTacCTCTGGCTTAGCCTCACAgCAGGCTGCTTTGGTGAGATGG GTGGTCAATGATCACTGCAGAGAAACGCAGAGGGTAGTCAGTG--TGTCTCTGGCTTAGCCTCACACCAGGCTGCTTTGGTGAGATGG Template switch alignment (log-probability: -27.8) GTGGTCAATGATCgCTGCAGAGAAACGCAGAGGGTAGTCA|CTGACTAC|CTCTGGCTTAGCCTCACAgCAGGCTGCTTTGGTGAGATGG GTGGTCAATGATCACTGCAGAGAAACGCAGAGGGTAGTCA|CTGACTAC|CTCTGGCTTAGCCTCACACCAGGCTGCTTTGGTGAGATGG ========== Event 2232 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAATTCAGAACTAAACCTGTCCTGGGGGAAAACATACACACATGTCTACATATGCTTGTTTTAA Chimp: ATAATTCAGAACTAAAGCTGTCATGT------GTATATACACATGTCTACATATGCTTGTTTTAA ↑ 1 4 3 2 Gorilla: ATAATTCAGAAGTAAAGCTGTTCTGGGGGAAAACATACACACATGTCTACATATGCTTGTTTTAA Human: ATAATTCAGAACTAAACCTGTCCTGGGGGAAAACATACACACATGTCTACATATGCTTGTTTTAA Cluster: [ ] Orangutan: ATAATTCAGAACTAAAGCTGTCCTGGGGGAAAACATATACACATGTCTACATATGCTTGTTTTAA Gorilla > Chimp --------------- chr3:122641839-122641845 Template switch process: F1: L TTTATCCTCATTATATGGAGATAATTCAGAACTAAAGCTGT 1 F3: 4 ATATACACATGTCTACATATGCTTGTTTTAAAGGAAAAAGATGG R RF: TTTATCCTCATTATATGGAGATAATTCAGAAGTAAAGCTGTTCTGGGGGAAAACATACACACATGTCTACATATGCTTGTTTTAAAGGAAAAAGATGG RR: AAATAGGAGTAATATACCTCTATTAAGTCTTCATTTCGACAAGACCCCCTTTTGTATGTGTGTACAGATGTATACGAACAAAATTTCCTTTTTCTACC F2: 3 TGTGTAC 2 Unidirectional alignment (log-probability: -41) TTATCCTCATTATATGGAGATAATTCAGAAcTAAAGCTGT------------CatgtgtATAtACACATGTCTACATATGCTTGTTTTAAAGGAAAAAG TTATCCTCATTATATGGAGATAATTCAGAAGTAAAGCTGTTCTGGGGGAAAAC------ATACACACATGTCTACATATGCTTGTTTTAAAGGAAAAAG Template switch alignment (log-probability: -27.8) TTATCCTCATTATATGGAGATAATTCAGAAcTAAAGCTGT|CATGTGT|ATAtACACATGTCTACATATGCTTGTTTTAAAGGAAAAAG TTATCCTCATTATATGGAGATAATTCAGAAGTAAAGCTGT|CATGTGT|ATACACACATGTCTACATATGCTTGTTTTAAAGGAAAAAG ========== Event 2233 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTTTGGTGCATCCATTCTCCTACAGAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATG----------------AAAATGACAAATGCTGAAAATGAAGAAACCACTGTGCATGTGCCCATGACCAATATTAATACaacatgggaggtctgctgtaggaacatgggcctacgtatg Chimp: ACTTTGGTGCATCCATTCTCCTACAGAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATG----------------AAAATGACAAATGCTGAAAATGAAGAAACCACTGTGCATGTGCCCATGACCAatattagtacaacatgggaggtctgctgtaggaacatgggcctacgtatg ↑ 1 4 3 2 Gorilla: ACTTTGGTGCATCCATTCTCCCACACAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATG--------------------------------AAAATGAAGAAACCACTGTGCATGTGCCCATGACCAatattagtacaacatgggaggtctgctgtaggaacatgggcctacgtatg ↓ 1 4 3 2 Human: ACTTTGGTGCATCCATTCTCCTACAGAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATG----------------AAAATGACAAATGCTGAAAATGAAGAAACCACTGTGCATGTGCCCATGACCAATATTAATACaacatgggaggtctgctgtaggaacatgggcctacgtatg Cluster: [ ] Orangutan: ACTTTGGTGCATCCATTCTCCTACAGAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATGACAAATGCTA----------------AAAATGAAGAAACTACTGTACATGTGCCCATGACCAatattagtacaacatgggaggtctgctgtaggaacatgggcctacgtatg Gorilla > Human --------------- chr3:75892180-75892184 Template switch process: F1: L TAATTTCTGGACTACTATTTACTTTGGTGCATCCATTCTCC 1 F3: 4 AAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATG R RF: TAATTTCTGGACTACTGTTTACTTTGGTGCATCCATTCTCCCACACAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATGAAGAAACCACTGTGCATGTGCCCATGACCAATATTAGTACAACATGGGAGGTCTGCTGTA RR: ATTAAAGACCTGATGACAAATGAAACCACGTAGGTAAGAGGGTGTGTTTCGAGGTCAGGTTGGGATGTCCGTTCTTCTACTTTTACTTCTTTGGTGACACGTACACGGGTACTGGTTATAATCATGTTGTACCCTCCAGACGACAT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -33.1) AATTTCTGGACTACTaTTTACTTTGGTGCATCCATTCTCCtACAgAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGaaaatg AATTTCTGGACTACTGTTTACTTTGGTGCATCCATTCTCCCACACAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATG------ Template switch alignment (log-probability: -21.9) AATTTCTGGACTACTaTTTACTTTGGTGCATCCATTCTCC|TACAG|AAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATG AATTTCTGGACTACTGTTTACTTTGGTGCATCCATTCTCC|TACAG|AAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATG Gorilla > Chimp --------------- chr3:77045170-77045174 Template switch process: F1: L TAATTTCTGGACTACTATTTACTTTGGTGCATCCATTCTCC 1 F3: 4 AAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATG R RF: TAATTTCTGGACTACTGTTTACTTTGGTGCATCCATTCTCCCACACAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATGAAGAAACCACTGTGCATGTGCCCATGACCAATATTAGTACAACATGGGAGGTCTGCTGTA RR: ATTAAAGACCTGATGACAAATGAAACCACGTAGGTAAGAGGGTGTGTTTCGAGGTCAGGTTGGGATGTCCGTTCTTCTACTTTTACTTCTTTGGTGACACGTACACGGGTACTGGTTATAATCATGTTGTACCCTCCAGACGACAT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -33.1) AATTTCTGGACTACTaTTTACTTTGGTGCATCCATTCTCCtACAgAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGaaaatg AATTTCTGGACTACTGTTTACTTTGGTGCATCCATTCTCCCACACAAAGCTCCAGTCCAACCCTACAGGCAAGAAGATG------ Template switch alignment (log-probability: -21.9) AATTTCTGGACTACTaTTTACTTTGGTGCATCCATTCTCC|TACAG|AAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATG AATTTCTGGACTACTGTTTACTTTGGTGCATCCATTCTCC|TACAG|AAAGCTCCAGTCCAACCCTACAGGCAAGAAGATGAAAATG ========== Event 2234 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTcccccccccGTCTCCACCAGGGCATG------------------------------------------------------------------------TTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCTGATTTTATTACTTGAAGCATTTCTAGGG Chimp: CTCCCCTCCCTGTCTCCACCAGGGCATG------------------------------------------------------------------------TTGGTGGCCATGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCTGATTTTATTACTTGAAGCATTTCTAGGG ↓ 3 4 1 2 Gorilla: CTCCCCTCCCCGTCTCCACCAGGGCATGTTGGATAAAATCAGGATGACTTAAGAAATCCATTACCCCTCTTGGCCTCCCACGGCCACCAACATGCCCTGGTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCTGATTTTATTACTTGAAGCATTTCTAGGG ↑ 3 4 1 2 Human: CTcccccccccGTCTCCACCAGGGCATG------------------------------------------------------------------------TTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCTGATTTTATTACTTGAAGCATTTCTAGGG Cluster: [ ] Orangutan: CTCCCCTCCCCATCTCCACCAGGGTATG------------------------------------------------------------------------TTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGGTTTCTTAAGTCATCCTGATTTTATTACTTGAAGCATTTCTAGGG Human > Gorilla --------------- chr3:124719588-124719654 Template switch process: F1: L GGTCCCCAGGCCTCTCCCCTCCCCGTCTCCACCAGGGCATGTTGG 1 F3: 4 GTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCTT R RF: GGTCCCCAGGCCTCTCCCCCCCCCGTCTCCACCAGGGCATGTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCTGATTTTAT RR: CCAGGGGTCCGGAGAGGGGGGGGGCAGAGGTGGTCCCGTACAACCACCGGCACCCTCCGGTTCTCCCCATTACCTAAAGAATTCAGTAGGACTAAAATA F2: 3 GTCCCGTACAACCACCGGCACCCTCCGGTTCTCCCCATTACCTAAAGAATTCAGTAGGACTAAAATA 2 Unidirectional alignment (log-probability: -120) CCAGGCCTCTCCCCtCCCCGTCTCCACCAGGGCATgttggataaaatcaggatgacttaagaaatccattacccctcttggcctcccacggccaccaacatgccctgGTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCT CCAGGCCTCTCCCCCCCCCGTCTCCACCAGGGCAT------------------------------------------------------------------------GTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCT Template switch alignment (log-probability: -29.8) CCAGGCCTCTCCCCtCCCCGTCTCCACCAGGGCATGTTGG|ATAAAATCAGGATGACTTAAGAAATCCATTACCCCTCTTGGCCTCCCACGGCCACCAACATGCCCTG|GTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCT CCAGGCCTCTCCCCCCCCCGTCTCCACCAGGGCATGTTGG|ATAAAATCAGGATGACTTAAGAAATCCATTACCCCTCTTGGCCTCCCACGGCCACCAACATGCCCTG|GTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCT Chimp > Gorilla --------------- chr3:124719588-124719654 Template switch process: F1: L GGTCCCCAGGCCTCTCCCCTCCCCGTCTCCACCAGGGCATGTTGG 1 F3: 4 GTTGGTGGCCGTGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCT R RF: GGTCCCCAGGCCTCTCCCCTCCCTGTCTCCACCAGGGCATGTTGGTGGCCATGGGAGGCCAAGAGGGGTAATGGATTTCTTAAGTCATCCTGATTTTAT RR: CCAGGGGTCCGGAGAGGGGAGGGACAGAGGTGGTCCCGTACAACCACCGGTACCCTCCGGTTCTCCCCATTACCTAAAGAATTCAGTAGGACTAAAATA F2: 3 GTCCCGTACAACCACCGGCACCCTCCGGTTCTCCCCATTACCTAAAGAATTCAGTAGGACTAAAATA 2 Unidirectional alignment (log-probability: -126) CCAGGCCTCTCCCCTCCCcGTCTCCACCAGGGCATgttggataaaatcaggatgacttaagaaatccattacccctcttggcctcccacggccaccaacatgccctgGTTGGTGGCCgTGGGAGGCCAAGAGGGGTAATGGATTTCT CCAGGCCTCTCCCCTCCCTGTCTCCACCAGGGCAT------------------------------------------------------------------------GTTGGTGGCCATGGGAGGCCAAGAGGGGTAATGGATTTCT Template switch alignment (log-probability: -41) CCAGGCCTCTCCCCTCCCcGTCTCCACCAGGGCATGTTGG|ATAAAATCAGGATGACTTAAGAAATCCATTACCCCTCTTGGCCTCCCAcGGCCACCAACATGCCCTG|GTTGGTGGCCgTGGGAGGCCAAGAGGGGTAATGGATTTCT CCAGGCCTCTCCCCTCCCTGTCTCCACCAGGGCATGTTGG|ATAAAATCAGGATGACTTAAGAAATCCATTACCCCTCTTGGCCTCCCATGGCCACCAACATGCCCTG|GTTGGTGGCCATGGGAGGCCAAGAGGGGTAATGGATTTCT ========== Event 2235 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CACTCACTTTCAATCTTATAATTCTGTAATACAGAATTGGGTAAAGGTTCTCCATG ↑ 1 34 2 Chimp: CACTCACTTTCAATCTTATAA------ATTACAGAATTGGGTAAAGGTTCTCCATG Gorilla: CACTCACTTTCAATCTTATAA------ATTACAGAATTGGGTAAAGGTTCTCCATG Human: CACTCACTTTCAATCTTATAATTCTGTAATACAGAATTGGGTAAAGGTTCTCCATG Cluster: [ ] Orangutan: CACTCACTTTCAATCTTATAA------ATTACAGAATTGGGTAAAGGTTCTCCATG Chimp > Human ------------- chr3:75019950-75019957 Template switch process: F1: L GTGCCAATCCAAGGATAGCACACTCACTTTCAATCTTATAA 1 F3: 4 TACAGAATTGGGTAAAGGTTCTCCATGTCTTAAGGCATTT R RF: GTGCCAATCCAGGGATAGCACACTCACTTTCAATCTTATAAATTACAGAATTGGGTAAAGGTTCTCCATGTCTTAAGGCATTT RR: CACGGTTAGGTCCCTATCGTGTGAGTGAAAGTTAGAATATTTAATGTCTTAACCCATTTCCAAGAGGTACAGAATTCCGTAAA F2: 3 AATGTCTT 2 Unidirectional alignment (log-probability: -31.6) TGCCAATCCAaGGATAGCACACTCACTTTCAATCTTATAAttctgtAaTACAGAATTGGGTAAAGGTTCTCCATGTCTTAAGGCATTT TGCCAATCCAGGGATAGCACACTCACTTTCAATCTTATAA------ATTACAGAATTGGGTAAAGGTTCTCCATGTCTTAAGGCATTT Template switch alignment (log-probability: -22.3) TGCCAATCCAaGGATAGCACACTCACTTTCAATCTTATAA|TTCTGTAA|TACAGAATTGGGTAAAGGTTCTCCATGTCTTAAGGCATTT TGCCAATCCAGGGATAGCACACTCACTTTCAATCTTATAA|TTCTGTAA|TACAGAATTGGGTAAAGGTTCTCCATGTCTTAAGGCATTT ========== Event 2236 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCAGCTGGAACAGGTCTTCCGCTTGGAAGAGGGAGCAGGAAGCACTGC ↑ 3 1 2 4 Chimp: ATTCAGCTGGAACAGGTCTTCCAAGC-GGAGAGGGAGCAGGAAGCACTGC Gorilla: ATTCAGCTGGAACAGGTCTTCCAAGC-GGAGAGGGAGCAGGAAGCACTGC ↓ 3 1 2 4 Human: ATTCAGCTGGAACAGGTCTTCCGCTTGGAAGAGGGAGCAGGAAGCACTGC Cluster: [ ] Orangutan: ATTCAGCTGGAACAGGTCTTCCAAGG-GGAGAGGGAACAGGAAGCACTGC Chimp > Human ------------- chr3:123804936-123804942 Template switch process: F1: L TTCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC 1 F3: 4 AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCGGT R RF: TTCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCCAAGCGGAGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGTGGT RR: AAGGTACACTCGGATTCGGTAAGTCGACCTTGTCCAGAAGGTTCGCCTCTCCCTCGTCCTTCGTGACGACTGTCCTCCCCGACACCA F2: 3 AGGTTCG 2 Unidirectional alignment (log-probability: -36) TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCCgcttggA-----AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGcGGT TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC------AAGCGGAGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGTGGT Template switch alignment (log-probability: -22.1) TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC|GCTTGGA|AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGcGGT TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC|GCTTGGA|AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGTGGT Gorilla > Human --------------- chr3:123804936-123804942 Template switch process: F1: L TTCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC 1 F3: 4 AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCGGT R RF: TTCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCCAAGCGGAGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCAGT RR: AAGGTACACTCGGATTCGGTAAGTCGACCTTGTCCAGAAGGTTCGCCTCTCCCTCGTCCTTCGTGACGACTGTCCTCCCCGACGTCA F2: 3 AGGTTCG 2 Unidirectional alignment (log-probability: -35) TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC-----GcttggaAGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCgGT TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCCAAGCGG------AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCAGT Template switch alignment (log-probability: -22.1) TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC|GCTTGGA|AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCgGT TCCATGTGAGCCTAAGCCATTCAGCTGGAACAGGTCTTCC|GCTTGGA|AGAGGGAGCAGGAAGCACTGCTGACAGGAGGGGCTGCAGT ========== Event 2237 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATGATAAAAATGAGCATCTATTGTGCTGAGCATGGCATGATGTAAATACTTTCTCTAGAC Chimp: AAATGATAAAAATGAGCATCTATTGTGCTGAGCATGGCATGATGTAAATACTTTCTCTAGAC ↓ 3 2 1 4 Gorilla: AAATGATAAAAATGAGCATCTATTGTGTGGAGCACAAT-AGATGTAAATACTTTCTCTAGAC Human: AAATGATAAAAATGAGCATCTATTGTGCTGAGCATGGCATGATGTAAATACTTTCTCTAGAC Cluster: [ ] Orangutan: AAATGATAAAAATGAGCATCTATTGTGCTGAGCATGGCATGATGTAAATACTTTCTCTAGAC Chimp > Gorilla --------------- chr3:74152407-74152416 Template switch process: F1: L GTAGCAAACTTAAAAAATGATAAAAATGAGCATCTATTGTG-------TGG 1 F3: 4 ATGTAAATACTTTCTCTAGACTTTATTTGGAGACTGA R RF: GTAGCAAACTTAAAAAATGATAAAAATGAGCATCTATTGTGCTGAGCATGGCATGATGTAAATACTTTCTCTAGACTTTATTTGGAGACTGA RR: CATCGTTTGAATTTTTTACTATTTTTACTCGTAGATAACACGACTCGTACCGTACTACATTTATGAAAGAGATCTGAAATAAACCTCTGACT F2: 3 GATAACACGA 2 Unidirectional alignment (log-probability: -49.5) CAAACTTAAAAAATGATAAAAATGAGCATCTATTGTG------------TggagcacaataGATGTAAATACTTTCTCTAGACTTTATTTGGAGActga CAAACTTAAAAAATGATAAAAATGAGCATCTATTGTGCTGAGCATGGCAT-----------GATGTAAATACTTTCTCTAGACTTTATTTGGAGA---- Template switch alignment (log-probability: -27.1) CAAACTTAAAAAATGATAAAAATGAGCATCTATTGTG-------TGG|AGCACAATAG|ATGTAAATACTTTCTCTAGACTTTATTTGGAGACTGA CAAACTTAAAAAATGATAAAAATGAGCATCTATTGTGCTGAGCATGG|AGCACAATAG|ATGTAAATACTTTCTCTAGACTTTATTTGGAGACTGA ========== Event 2238 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGCTGTAATTTGAAAGTTTATGTGTATTTCTATCT-----ATAGGGTTTTCCTTAATGTGAAG Chimp: TGGCTGTAATTTGAAAGTTTATGTGTATTTCTATCT-----ATAGGGTTTTCCTTAATGTAAAG Gorilla: TGGCTGTAATTTGAAAGTTTATGTGTCTTTCTAAAGACACATAAGGGTTTTCCTTAATGTGAAG ↑ 3 2 1 4 Human: TGGCTGTAATTTGAAAGTTTATGTGTATTTCTATCT-----ATAGGGTTTTCCTTAATGTGAAG Cluster: [ ] Orangutan: TAGCTGTAATTTGAAAGTTTATGTGTCTTTCTATCT-----GTAGGG-TTTCCTTAATGTGAAG Human > Gorilla --------------- chr3:125833553-125833562 Template switch process: F1: L TTTGATCACCACATATGGCTGTAATTTGAAAGTTTATGTGTCTTTCTA 1 F3: 4 AGGGTTTTCCTTAATGTGAAGTTTTAGACCAGTAGCTCTT R RF: TTTGATCACCACATATGGCTGTAATTTGAAAGTTTATGTGTATTTCTATCTATAGGGTTTTCCTTAATGTGAAGTTTTAGACCAGTAGCTCTT RR: AAACTAGTGGTGTATACCGACATTAAACTTTCAAATACACATAAAGATAGATATCCCAAAAGGAATTACACTTCAAAATCTGGTCATCGAGAA F2: 3 ATACACAGAA 2 Unidirectional alignment (log-probability: -40.9) CCACATATGGCTGTAATTTGAAAGTTTATGTGTcTTTCtaaagacacaTA-----AGGGTTTTCCTTAATGTGAAGTTTTAGACCAGTAGCTCTT CCACATATGGCTGTAATTTGAAAGTTTATGTGTATTTC----------TATCTATAGGGTTTTCCTTAATGTGAAGTTTTAGACCAGTAGCTCTT Template switch alignment (log-probability: -28.2) CCACATATGGCTGTAATTTGAAAGTTTATGTGTcTTTCTA|AAgACACATA|AGGGTTTTCCTTAATGTGAAGTTTTAGACCAGTAGCTCTT CCACATATGGCTGTAATTTGAAAGTTTATGTGTATTTCTA|AATACACATA|AGGGTTTTCCTTAATGTGAAGTTTTAGACCAGTAGCTCTT ========== Event 2239 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGATTTCCTTTACAATCAG--TCATAA----GAATGATTTATCATCATC------------------------------------------TCCTAGGTAGTACATAGTTC Chimp: GGATTTCCTTTACAATCAGAATGATAAATCATTCTGATTTATCATCATC---------------------TCCTAGGGATGTTGAATAACCTCCTAGGTAGTACATAGTCC ↑ 1 3 4 2 Gorilla: GGATTTCCTTTACAATCAG--TCATAA----GAATGATTTATCATCATCTCCTAGGGATGATGAATAACC---------------------TCCTAGGTAGTACATAGTCC Human: GGATTTCCTTTACAATCAG--TCATAA----GAATGATTTATCATCATC------------------------------------------TCCTAGGTAGTACATAGTTC Cluster: [ ] Orangutan: GGATTCCCTTTACAATCAG--TCATGA----GAATGATTTATCATCATCTCCTAGGGATGATGAATAACC---------------------TCCTAGGTAGTACATAGTCC Gorilla > Chimp --------------- chr3:127700168-127700181 Template switch process: F1: L TTTACAATCAGA 1 F3: 4 TGATTTATCATCATCTCCTAGGGATGTTGAATAACCTCCTAGGTAGTACATAGTCCCAAAAACTGGTTTCAGAAAA R RF: TTTACAATCAGTCATAAGAATGATTTATCATCATCTCCTAGGGATGATGAATAACCTCCTAGGTAGTACATAGTCCCAAAAACTGGTTTCAGAAAA RR: AAATGTTAGTCAGTATTCTTACTAAATAGTAGTAGAGGATCCCTACTACTTATTGGAGGATCCATCATGTATCAGGGTTTTTGACCAAAGTCTTTT F2: 3 CTTACTAAATAGTA 2 Unidirectional alignment (log-probability: -45.3) TTTACAATCA-------GAAtgataaatcattcTGATTTATCATCATCTCCTAGGGATGtTGAATAACCTCCT TTTACAATCAGTCATAAGAA-------------TGATTTATCATCATCTCCTAGGGATGATGAATAACCTCCT Template switch alignment (log-probability: -28.7) TTTACAATCAGa|ATGATAAATCATTC|TGATTTATCATCATCTCCTAGGGATGtTGAATAACCTCCT TTTACAATCAGT|ATGATAAATCATTC|TGATTTATCATCATCTCCTAGGGATGATGAATAACCTCCT ========== Event 2240 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAATTCTTTTAGGAATGTGTCATCAGATGTGTCTCTCACTCCCCTTGCCTCCACCCTTTTCTTAGGGCGTGCACATTTCCTCTGTTGCTGGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCT------AAACAACTTTGGGTTGTTTAGCCttt Chimp: AGAATTCTTTTAGGAATGTGTCATCAGATGTGTCTCTCACTCCCCTTGCCTCCACCCTTTTCTTAGGGCGTGCACATTTCCTCTGTTGCTGGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATGATTGCT---CTCATGACACTTTGGGTTGTTTAGCCttt Gorilla: AGAATTCTTTCAGGAATGTGTCATCAGATGTGTCTCTCACTCCCCTTGCCTCCACCCTTTTCTTAGGGCGTGCACATTTCCTCTGTTGCTGGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCTCTA---ATGACACTTTGGGTTGTTTAGCCttt ↑ 3 2 1 4 Human: AGAATTCTTTTAGGAATGTGTCATCAGATGTGTCTCTCACTCCCCTTGCCTCCACCCTTTTCTTAGGGCGTGCACATTTCCTCTGTTGCTGGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCT------AAACAACTTTGGGTTGTTTAGCCttt Cluster: [ ] Orangutan: AGAATTCTTTTAGGAATGTGTCATCAGACGTGTCTCTCTCTCCTCTTGCCTCCACCCTTTTCTTAGGGCGTGCACATTTCCTCTGTTGCTGGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCTCTC---ATGACACTTTGGGTTGTTTGGCCTTT Human > Gorilla --------------- chr3:74671027-74671034 Template switch process: F1: L GGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCT 1 F3: 4 ACTTTGGGTTGTTTAGCCTTTTTTCTATTTTTAAAATAAA R RF: GTCATCAGATGTGTCTCTCACTCCCCTTGCCTCCACCCTTTTCTTAGGGCGTGCACATTTCCTCTGTTGCTGGAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCTAAACAACTTTGGGTTGTTTAGCCTTTTTTCTATTTTTAAAATAAA RR: CAGTAGTCTACACAGAGAGTGAGGGGAACGGAGGTGGGAAAAGAATCCCGCACGTGTAAAGGAGACAACGACCTTCAAATGCAACCAAGGAGGAGTGTCAAAGTATTAACGATTTGTTGAAACCCAACAAATCGGAAAAAAGATAAAAATTTTATTT F2: 3 CAGTAATC 2 Unidirectional alignment (log-probability: -32.4) GAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCT-----ctaatgacACTTTGGGTTGTTTAGCCTTTTTTCTATTTTTAAAATAAA GAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCTAAACA--------ACTTTGGGTTGTTTAGCCTTTTTTCTATTTTTAAAATAAA Template switch alignment (log-probability: -22.3) GAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCT|CTaATGAC|ACTTTGGGTTGTTTAGCCTTTTTTCTATTTTTAAAATAAA GAAGTTTACGTTGGTTCCTCCTCACAGTTTCATAATTGCT|CTGATGAC|ACTTTGGGTTGTTTAGCCTTTTTTCTATTTTTAAAATAAA ========== Event 2241 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTGAAGGCCTCCTCAAAGTAG----CCCCTCTTATTCCCAGGGAGCCTTTTTT Chimp: TATGAAGGCCTCCTCAAAGTAGCGGGCTACTCTTATTCCCAGGGAGCCtttttt ↑ 3 1 24 Gorilla: TATGAAGGCCTCCTCAAAGTAG----CCCCTCTGATTCCCAGGGAGCCtttttt Human: TTTGAAGGCCTCCTCAAAGTAG----CCCCTCTTATTCCCAGGGAGCCTTTTTT Cluster: [ ] Orangutan: TATGAAGGCCTCCTCAAAGTAG----CCCCTCTTATTCCCAGGGAGCCTTTTTT Gorilla > Chimp --------------- chr3:74406231-74406236 Template switch process: F1: L AATTTACCTTTGGTGCTACTATGAAGGCCTCCTCAAAGTAGC 1 F3: 4 CTCTTATTCCCAGGGAGCCTTTTTTTGAGATCCAACTGGTCACTT R RF: AATTTACCTTTGGTGCTACTATGAAGGCCTCCTCAAAGTAGCCCCTCTGATTCCCAGGGAGCCTTTTTTTGAGATCCAACTGATCACTT RR: TTAAATGGAAACCACGATGATACTTCCGGAGGAGTTTCATCGGGGAGACTAAGGGTCCCTCGGAAAAAAACTCTAGGTTGACTAGTGAA F2: 3 ATCGGG 2 Unidirectional alignment (log-probability: -38.8) TTTACCTTTGGTGCTACTATGAAGGCCTCCTCAAAGTAgcggGCtaCTCTtATTCCCAGGGAGCCTTTTTTTGAGATCCAACTGgT TTTACCTTTGGTGCTACTATGAAGGCCTCCTCAAAGTA----GCCCCTCTGATTCCCAGGGAGCCTTTTTTTGAGATCCAACTGAT Template switch alignment (log-probability: -27.7) TTTACCTTTGGTGCTACTATGAAGGCCTCCTCAAAGTAGC|GGGCTA|CTCTtATTCCCAGGGAGCCTTTTTTTGAGATCCAACTGgT TTTACCTTTGGTGCTACTATGAAGGCCTCCTCAAAGTAGC|GGGCTA|CTCTGATTCCCAGGGAGCCTTTTTTTGAGATCCAACTGAT ========== Event 2242 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: cctgaaagagctccaagccccaatgttgagtggcaagagctagttccagaaGTTAGGACCATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTG--------------------GAGACGTCGGTTTCTTCAATTTATAT ↓ 3 2 4 1 Chimp: cctgaaagagctccaagccccaatgttgagtggcaagagctagttccagaaGTTAGGACCATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTG----------GAGCAGTGGGGAGACTTCGGTTTCTTCAATTTATAT Gorilla: cctgaaagagctccaagccccaatgttgagtggcaagagctagttccagaaGTTAGGACCATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTGGAGCAGTGGG----------GAGACTTCAGTTTCTTCAATTTATAT Human: cctgaaagagctccaagccccaatgttgagtggcaagagctagttccagaaGTTAGGACCATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTG--------------------GAGACGTCGGTTTCTTCAATTTATAT Cluster: [ ] Orangutan: CCTGAAAGAGCTCCAAGCCCCAATGTTGAGTGGCAAGAGCTAGTTCCAGAAGTTAGGACCATTTTCTTACCAGACGGAGTGAGT--CGGGCTGGTGGAGCAGTGGA----------GAGACTTCGGTTTCTTCAATTTGTAT Human > Chimp ------------- chr3:13119622-13119627 Template switch process: F1: L GGACCATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTGGAG 1 F3: 4 GGAGACTTCGGTTTCTTCAATTTATATCTTTCTATATCATTTTTTA R RF: CCAATGTTGAGTGGCAAGAGCTAGTTCCAGAAGTTAGGACCATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTGGAGACGTCGGTTTCTTCAATTTATATCTTTCTATATCATTTTTTT RR: GGTTACAACTCACCGTTCTCGATCAAGGTCTTCAATCCTGGTAAAAGAATTGTCTGTCTCACTCAGACCCCGACCACCTCTGCAGCCAAAGAAGTTAAATATAGAAAGATATAGTAAAAAAA F2: 3 GGTGAC 2 Unidirectional alignment (log-probability: -41.6) CATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTggagcagtggGGAGACtTCGGTTTCTTCAATTTATATCTTTCTATATCAT CATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGT----------GGAGACGTCGGTTTCTTCAATTTATATCTTTCTATATCAT Template switch alignment (log-probability: -34.2) CATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTGGAG|CAgTGG|GGAGACtTCGGTTTCTTCAATTTATATCTTTCTATATCAT CATTTTCTTAACAGACAGAGTGAGTCTGGGGCTGGTGGAG|CATTGG|GGAGACGTCGGTTTCTTCAATTTATATCTTTCTATATCAT ========== Event 2243 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCATTCCATGCTGCCCCTGAC---------------CCCAGCCCTCAGGACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGGTGTCCTCTCCTGGCCACAGG Chimp: TCCATTCCATGCTGCCCCTGAC---------------CCCAGCCCTCAGGACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGGTGTCCTCTCCTGGCCACAGG ↑ 4 1 3 2 Gorilla: TCCATTCCATGCTGCCCCTGAC------------------------------CCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGGTGTCCTCTCCTGGCCACAGG ↓ 4 1 3 2 Human: TCCATTCCATGCTGCCCCTGAC---------------CCCAGCCCTCAGGACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGGTGTCCTCTCCTGGCCACAGG Cluster: [ ] Orangutan: TCCATTCCATGCTGCCCCTGACCCCAGCCCTCAGGAC---------------CCCAGGGGACCTGACTGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGGTGTCCTCTCCTGGCCACAGG Gorilla > Human --------------- chr3:127195692-127195698 Template switch process: F1: L CAGCTGTGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAG 1 F3: 4 GACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGC R RF: CAGCTGTGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGG RR: GTCGACACGGAGTCAAAGAAGGTAAGGTACGACGGGGACTGGGGTCCCCAGGACTGGCGTGGTCGGAGGCGAGGAACTACGACCCCGACCCCC F2: 3 GACTCCC 2 Unidirectional alignment (log-probability: -32.5) TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGaccccagccctcaggACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTG---------------ACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA Template switch alignment (log-probability: -22.3) TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAG|CCCtCAG|GACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAG|CCCCCAG|GACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA Gorilla > Chimp --------------- chr3:130395184-130395190 Template switch process: F1: L CAGCTGTGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAG 1 F3: 4 GACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGC R RF: CAGCTGTGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGATGCTGGGGCTGGGGG RR: GTCGACACGGAGTCAAAGAAGGTAAGGTACGACGGGGACTGGGGTCCCCAGGACTGGCGTGGTCGGAGGCGAGGAACTACGACCCCGACCCCC F2: 3 GACTCCC 2 Unidirectional alignment (log-probability: -32.5) TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGaccccagccctcaggACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTG---------------ACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA Template switch alignment (log-probability: -22.3) TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAG|CCCtCAG|GACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA TGCCTCAGTTTCTTCCATTCCATGCTGCCCCTGACCCCAG|CCCCCAG|GACCCCAGGGGTCCTGACCGCACCAGCCTCCGCTCCTTGA ========== Event 2244 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGAGGAGTCTAGTGACATTCCGGATGTCTTAGGCATTATATGTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAATAAAAGGATTGTGTTCA Chimp: TTGAGGAGTCTAGTGACATTCCGGATGTA----------T-AGTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAATAAAAGGATTGTGTTCA Gorilla: TTGAGGAGTCTAGTGACATTCTGGCTGTA----------T-AGTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAATAAAAGGATTGTGTTCA ↑ 1 4 3 2 Human: TTGAGGAGTCTAGTGACATTCCGGATGTCTTAGGCATTATATGTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAATAAAAGGATTGTGTTCA Cluster: [ ] Orangutan: TTGAGGAGTCTAGTGACATTCCGGATGTA----------T-AGTCTTAGGCATACAAATAAGGAATCACAGACAGCCATAATAAAAGGATTGTGTTCA Human > Gorilla --------------- chr3:71770763-71770772 Template switch process: F1: L GTTTTTCTAATCTGGAATATTTGAGGAGTCTAGTGACATTC 1 F3: 4 GTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAAT R RF: GTTTTTCTAATCTGGAATATTTGAGGAGTCTAGTGACATTCCGGATGTCTTAGGCATTATATGTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAAT RR: CAAAAAGATTAGACCTTATAAACTCCTCAGATCACTGTAAGGCCTACAGAATCCGTAATATACAGAATCCGTATATTTATTCCTTAGTATCTGTCGGTATTA F2: 3 ATATGTCGGT 2 Unidirectional alignment (log-probability: -32.4) TTTTTCTAATCTGGAATATTTGAGGAGTCTAGTGACATTCtGGcTG----------TATA-GTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAAT TTTTTCTAATCTGGAATATTTGAGGAGTCTAGTGACATTCCGGATGTCTTAGGCATTATATGTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAAT Template switch alignment (log-probability: -22.5) TTTTTCTAATCTGGAATATTTGAGGAGTCTAGTGACATTC|TGGCTGTaTA|GTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAAT TTTTTCTAATCTGGAATATTTGAGGAGTCTAGTGACATTC|TGGCTGTCTA|GTCTTAGGCATATAAATAAGGAATCATAGACAGCCATAAT ========== Event 2245 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACATTCCACAGCTTATGTGGCATCTATCTTATAGACATA---CTCCCTTTGGAAGATTTATGTTGCG Chimp: ACATTCCACAGCTTATGTGGCATCTATCTTATAGACATA---CTCCCTTTGGAAGATTTATGTTGCG ↓ 3 2 1 4 Gorilla: ACATTCCACAGCTTATGTGGCATCTATCTTATAGACAGATAGATGCCTTTGGAAGATTTATGTTGCG ↑ 3 2 1 4 Human: ACATTCCACAGCTTATGTGGCATCTATCTTATAGACATA---CTCCCTTTGGAAGATTTATGTTGCG Cluster: [ ] Orangutan: ACATTCCACAGCTTATGTGGCATCTATCTTATAGACATA---CTCCCTTTGGAAGATTTATGTTGCG Human > Gorilla --------------- chr3:71351286-71351294 Template switch process: F1: L TAATACATTCCACAGCTTATGTGGCATCTATCTTATAGACA 1 F3: 4 CTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG R RF: TAATACATTCCACAGCTTATGTGGCATCTATCTTATAGACATACTCCCTTTGGAAGATTTATGTTGCGATTACAAAAGAGTAAAAG RR: ATTATGTAAGGTGTCGAATACACCGTAGATAGAATATCTGTATGAGGGAAACCTTCTAAATACAACGCTAATGTTTTCTCATTTTC F2: 3 CGTAGATAG 2 Unidirectional alignment (log-probability: -37.3) AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACAgAtagaTgCCTTTGGAAGATTTATGTTGCGATTACAAAAGAtTAAAAG AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACATAC---TCCCTTTGGAAGATTTATGTTGCGATTACAAAAGAGTAAAAG Template switch alignment (log-probability: -22.4) AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACA|GATAGATGC|CTTTGGAAGATTTATGTTGCGATTACAAAAGAtTAAAAG AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACA|GATAGATGC|CTTTGGAAGATTTATGTTGCGATTACAAAAGAGTAAAAG Chimp > Gorilla --------------- chr3:71351286-71351294 Template switch process: F1: L TAATACATTCCACAGCTTATGTGGCATCTATCTTATAGACA 1 F3: 4 CTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG R RF: TAATACATTCCACAGCTTATGTGGCATCTATCTTATAGACATACTCCCTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG RR: ATTATGTAAGGTGTCGAATACACCGTAGATAGAATATCTGTATGAGGGAAACCTTCTAAATACAACGCTAATGTTTTCTAATTTTC F2: 3 CGTAGATAG 2 Unidirectional alignment (log-probability: -31.8) AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACAgAtagaTgCCTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACATAC---TCCCTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG Template switch alignment (log-probability: -16.8) AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACA|GATAGATGC|CTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG AATACATTCCACAGCTTATGTGGCATCTATCTTATAGACA|GATAGATGC|CTTTGGAAGATTTATGTTGCGATTACAAAAGATTAAAAG ========== Event 2246 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTGAAGGAAGATTTGGCCACCACGATAGTTTTGCAGCTTCATCAGTTTCTCGGCATGTTCCCTCTCCTCATGAGATTGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACA------TCATCGCGG----TCAAAGTTGTAAGACACGGACA Chimp: CCTGAAGGAAGATTTGGCCACCTCGATGGTTTTGCAGCTTCATCAGTTTCTCGGCATGTTCCCTCTCCTCATGAGATTGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACA------TCATCGCGG----TCAAAGTTGTGAGACATGGACA Gorilla: CCTGAAGGAAGATTTGGCCACCTCGATGGTTTTGCAGCTTCATCAGTTCCTCGGCATGTTCCCTCTCCTCATGAGATTGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACATTTGTGGCTTTGTTGTCAAACAAAGTTGTAAGACACGGACA ↓ 3 2 1 4 Human: CCTGAAGGAAGATTTGGCCACCACGATAGTTTTGCAGCTTCATCAGTTTCTCGGCATGTTCCCTCTCCTCATGAGATTGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACA------TCATCGCGG----TCAAAGTTGTAAGACACGGACA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr3:128764882-128764890 Template switch process: F1: L ATTGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACAT 1 F3: 4 CAAAGTTGTAAGACACGGACAGGTAAACGTAGGAGGCGTA R RF: ACCTCGATGGTTTTGCAGCTTCATCAGTTCCTCGGCATGTTCCCTCTCCTCATGAGATTGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACATTTGTGGCTTTGTTGTCAAACAAAGTTGTAAGACACGGACAGGTAAACATAGGAGGCGTA RR: TGGAGCTACCAAAACGTCGAAGTAGTCAAGGAGCCGTACAAGGGAGAGGAGTACTCTAACCACTTCTTTCATACACCGTTTCAAGGAGTTTCGGTGTAAACACCGAAACAACAGTTTGTTTCAACATTCTGTGCCTGTCCATTTGTATCCTCCGCAT F2: 3 TGGCGCTAC 2 Unidirectional alignment (log-probability: -38.6) TGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACATcatcgcggT------------------CAAAGTTGTAAGACACGGACAGGTAAACgTAGGAGGCGTA TGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACAT--------TTGTGGCTTTGTTGTCAAACAAAGTTGTAAGACACGGACAGGTAAACATAGGAGGCGTA Template switch alignment (log-probability: -27.9) TGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACAT|CATCGcGGT|CAAAGTTGTAAGACACGGACAGGTAAACgTAGGAGGCGTA TGGTGAAGAAAGTATGTGGCAAAGTTCCTCAAAGCCACAT|CATCGAGGT|CAAAGTTGTAAGACACGGACAGGTAAACATAGGAGGCGTA ========== Event 2247 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACAGGCTGCAACTGGAGATCCC----------------CAGACAGCTCTGGCCCCAGATGGTTTCTGTGTGACCTGAGctggatttggggcttcctgtgaa Chimp: ACAGGCTGCAACTGGAGATCCC----------------CAGACAGCTCTGGCCCCAGATGGTTTCTGTGTGACCCGAGCTGGATTTGGGGCTTCCTGTGAA Gorilla: ACAGGCTACAACTGGAGATCCC--------------------------------CAGATGGTTTCTGTGTGACCTGAGctggatttggggcttcctgtgaa ↓ 4 1 3 2 Human: ACAGGCTGCAACTGGAGATCCC----------------CAGACAGCTCTGGCCCCAGATGGTTTCTGTGTGACCTGAGctggatttggggcttcctgtgaa Cluster: [ ] Orangutan: ACAGGCTGCAACTGGAGGTCCCCAGACAGCTCTGGCCC----------------CAGATGGTTTCTGCGTGACCTGAGCTGGATTTGGGGCTTCCTGTGAA Gorilla > Human --------------- chr3:12981981-12981989 Template switch process: F1: L GACACTAAGACCCCAGGTCACAGGCTGCAACTGGAGATCCCCAGA 1 F3: 4 CCCCAGATGGTTTCTGTGTGACCTGAGCTGGATTTGGGGCTTC R RF: GACACTAAGACCCCAGGTCACAGGCTACAACTGGAGATCCCCAGATGGTTTCTGTGTGACCTGAGCTGGATTTGGGGCTTC RR: CTGTGATTCTGGGGTCCAGTGTCCGATGTTGACCTCTAGGGGTCTACCAAAGACACACTGGACTCGACCTAAACCCCGAAG F2: 3 GGTCTCGAC 2 Unidirectional alignment (log-probability: -39.4) TAAGACCCCAGGTCACAGGCTgCAACTGGAGATccccagacagctctggCCCCAGATGGTTTCTGTGTGACCTGAGCTGGATTTGGGGC TAAGACCCCAGGTCACAGGCTACAACTGGAGAT----------------CCCCAGATGGTTTCTGTGTGACCTGAGCTGGATTTGGGGC Template switch alignment (log-probability: -28.1) TAAGACCCCAGGTCACAGGCTgCAACTGGAGATCCCCAGA|CAGCTCtGG|CCCCAGATGGTTTCTGTGTGACCTGAGCTGGATTTGGGGC TAAGACCCCAGGTCACAGGCTACAACTGGAGATCCCCAGA|CAGCTCAGG|CCCCAGATGGTTTCTGTGTGACCTGAGCTGGATTTGGGGC ========== Event 2248 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ataaaaataagggtggagctggactggcccacaggctgtagtttgctaaccccGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTGTCTCCCTATGGAGGCAAACATGTTTAATGAGC ↓ 3 2 1 4 Chimp: ataaaaataagggtggggctggactggcccacaggctgtagtttgctaaccccGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTAGTC------CAAGGCAAACATGTTTAATGAGC Gorilla: ataaaaataagggtggagctgtactggcccacaggctgtagtttgctaaccccGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTAGTC------CAAGGCAAACATGTATAATGAGC ↑ 3 2 1 4 Human: ataaaaataagggtggagctggactggcccacaggctgtagtttgctaaccccGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTGTCTCCCTATGGAGGCAAACATGTTTAATGAGC Cluster: [ ] Orangutan: ataaaaataagggtggagctggactggcccacaggctgtagtttgctaaccccGGATTTAACTGATGACTTCTGCTCCCTGTGGAGACAATTTAGTC------CAAGGCAAACATGTTTAATGAGC Human > Chimp ------------- chr3:70343583-70343588 Template switch process: F1: L CGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT 1 F3: 4 AGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA R RF: TGGACTGGCCCACAGGCTGTAGTTTGCTAACCCCGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTGTCTCCCTATGGAGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA RR: ACCTGACCGGGTGTCCGACATCAAACGATTGGGGCCTAAATTGACTACTGAAGACGAGGGATACCTCTGTTAAACAGAGGGATACCTCCGTTTGTACAAATTACTCGGACCTCTTGACTCCAGAGT F2: 3 ACCTGA 2 Unidirectional alignment (log-probability: -30.4) GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTagtcca------------AGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT------GTCTCCCTATGGAGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA Template switch alignment (log-probability: -16) GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT|AGTCCA|AGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT|AGTCCA|AGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA Human > Gorilla --------------- chr3:70450856-70450861 Template switch process: F1: L CGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT 1 F3: 4 AGGCAAACATGTATAATGAGCCTGGAGAACTGAGGTCTCA R RF: TGGACTGGCCCACAGGCTGTAGTTTGCTAACCCCGGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTGTCTCCCTATGGAGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA RR: ACCTGACCGGGTGTCCGACATCAAACGATTGGGGCCTAAATTGACTACTGAAGACGAGGGATACCTCTGTTAAACAGAGGGATACCTCCGTTTGTACAAATTACTCGGACCTCTTGACTCCAGAGT F2: 3 ACCTGA 2 Unidirectional alignment (log-probability: -35.4) GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT------------agtccaAGGCAAACATGTaTAATGAGCCTGGAGAACTGAGGTCTCA GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTTGTCTCCCTATGG------AGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA Template switch alignment (log-probability: -22) GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT|AGTCCA|AGGCAAACATGTaTAATGAGCCTGGAGAACTGAGGTCTCA GGATTTAACTGATGACTTCTGCTCCCTATGGAGACAATTT|AGTCCA|AGGCAAACATGTTTAATGAGCCTGGAGAACTGAGGTCTCA ========== Event 2249 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTGAGGTCTTTCATGGTACAGAGATG-----------------GGGAGAGTATTTGTGGGGGGTTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAA Chimp: TCTGAGGTCTTTCATggtacagagatg-----------------gggagagtatttgtggggggttgtgccacatgagcgaagtcagggagatgagaaaa Gorilla: TCTGAGGTCTTTCATGGTACAACGCTC----------------------------------ATGTTGTGCCAcatgagcgaagtcagggagatgagaaaa ↑ 1 4 3 2 Human: TCTGAGGTCTTTCATGGTACAGAGATG-----------------GGGAGAGTATTTGTGGGGGGTTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAA Cluster: [ ] Orangutan: TCTGAGGTCTTTCATGGTACAGACATGGGGAGAGTATTTGTGGG-----------------GGGTTGTACTACATGAGCAAAGTCAGGGAGATGAGAAAA Human > Gorilla --------------- chr3:131190935-131190942 Template switch process: F1: L TCTCATATCAGTTTTTTGCTTCTGAGGTCTTTCATGGTACAA 1 F3: 4 TTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAATGC R RF: TCTCATATCAGTTTTTTGCTTCTGAGGTCTTTCATGGTACAGAGATGGGGAGAGTATTTGTGGGGGGTTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAATGC RR: AGAGTATAGTCAAAAAACGAAGACTCCAGAAAGTACCATGTCTCTACCCCTCTCATAAACACCCCCCAACACGGTGTACTCGCTTCAGTCCCTCTACTCTTTTACG F2: 3 GTACTCGC 2 Unidirectional alignment (log-probability: -33.4) TCATATCAGTTTTTTGCTTCTGAGGTCTTTCATGGTACA-------------------------acgctcatGTTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAATGC TCATATCAGTTTTTTGCTTCTGAGGTCTTTCATGGTACAGAGATGGGGAGAGTATTTGTGGGGG--------GTTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAATGC Template switch alignment (log-probability: -22.3) TCATATCAGTTTTTTGCTTCTGAGGTCTTTCATGGTACAa|CGCTCATG|TTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAATGC TCATATCAGTTTTTTGCTTCTGAGGTCTTTCATGGTACAG|CGCTCATG|TTGTGCCACATGAGCGAAGTCAGGGAGATGAGAAAATGC ========== Event 2250 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGGAAAGAATACAGGCACTGACCTTCAGACACTAAATTATGTCTTGCTTTCCAAGAAATACAGTAAGTAACAAAGACTGCTTATTTAGGTACTGCCTACCTCAATGGAATCA------------------------------TGTACCACCCAGGGGACTCAAAGGTGCT Chimp: TCAGGAAAGAATACAGGCACTGACCTTTAGACACTAAATTATGTCTTGCTTTCCAAGAAATACAGTAAGTAACAAAGACTGCTTATTTAGGTACTGCCTACCTCAATGGAATCA---------------TGTACCACAATGTCATGTACCACCCAGGGGACTCAAAGGTGCT Gorilla: TCAGGAAAGAATACAGGCACTGACCTTTAGACACTAAATTATGTCTTGCTTTCCAAGAAATACAGTAAATAACAAAGACTGCTTATTTAGGCACTGCCTACCTCAATGGAATCATGTACCACAATGTCA---------------GGTACCACCCAGGGGACTCAAAGGTGCT ↑ 3 2 4 1 Human: TCAGGAAAGAATACAGGCACTGACCTTCAGACACTAAATTATGTCTTGCTTTCCAAGAAATACAGTAAGTAACAAAGACTGCTTATTTAGGTACTGCCTACCTCAATGGAATCA------------------------------TGTACCACCCAGGGGACTCAAAGGTGCT Cluster: [ ] Orangutan: TCAGGAAAGAATACAGGCACTGACCTTTAGACACTAAATTATGTCTTGCTTTCCAAGAAATACAGTAAGTAACAAAGACTGCTTATTTAGGCACTGCCTACCTCAATGGAATCATGTACCACAATGTCA---------------TGTACCACCCATGGGACTCAAAGGTGCT Human > Gorilla --------------- chr3:131640557-131640564 Template switch process: F1: L AAAGACTGCTTATTTAGGCACTGCCTACCTCAATGGAATCATGTACCAC 1 F3: 4 GTACCACCCAGGGGACTCAAAGGTGCTGCAGAGAGCTGTT R RF: CTGACCTTCAGACACTAAATTATGTCTTGCTTTCCAAGAAATACAGTAAGTAACAAAGACTGCTTATTTAGGTACTGCCTACCTCAATGGAATCATGTACCACCCAGGGGACTCAAAGGTGCTGCAGAGAGCTGTT RR: GACTGGAAGTCTGTGATTTAATACAGAACGAAAGGTTCTTTATGTCATTCATTGTTTCTGACGAATAAATCCATGACGGATGGAGTTACCTTAGTACATGGTGGGTCCCCTGAGTTTCCACGACGTCTCTCGACAA F2: 3 GACTGTAA 2 Unidirectional alignment (log-probability: -38) TTATTTAGGcACTGCCTACCTCAATGGAATCATgtaccacaatgtcagGTACCACCCAGGGGACTCAAAGGTGCTGCAGAGAGCTGTT TTATTTAGGTACTGCCTACCTCAATGGAATCAT---------------GTACCACCCAGGGGACTCAAAGGTGCTGCAGAGAGCTGTT Template switch alignment (log-probability: -28) TTATTTAGGcACTGCCTACCTCAATGGAATCATGTACCAC|AAtGTCAG|GTACCACCCAGGGGACTCAAAGGTGCTGCAGAGAGCTGTT TTATTTAGGTACTGCCTACCTCAATGGAATCATGTACCAC|AAGGTCAG|GTACCACCCAGGGGACTCAAAGGTGCTGCAGAGAGCTGTT ========== Event 2251 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGTGACTTTTCCTCACAGTGTCTGCAATCCCTTTCCAAAGCTACCT----------------------GACAGCCTTCGGT------ATACTATAATGATTATTAAGGATTTTTTTCCTTTCTCCCCATTTGTAATAGCCTGTCTGGTTTCCTAGCCATATAGTCCCTTCCCTCATACCAGTCACAGGCTCTACTCTAaataacag ↑ 41 3 2 Chimp: CAGTGACTTTTCCTCACAGTG-------TCCCTTTCCAAAGCTACCT----------------------GACAGCCTTCGGT---ATAATACTGTAATGATTATTAAGGAtttttttCCTTTCTCCCCATTTGTAATAGCCTGTCTGGTTTCCTAGCCATATAGTCCCTTCTCCCATACCAGTTGCAGGCTCTACTCTAaataacag Gorilla: CAGTGACTTTTCCTCACAGTGTCTGCAATCCCTTTCCAAAGCTACCT----------------------GACAGCCTTCAGTATA---ATACTATAATGATTATGAAGGAtttttttCCTTTCTCCCCATTTGTAATAGCCTGTCTGGTTTCCTAGCCATATAGTCCCTTCTTCCGTACCAGTTGCAGGCTCTACTCTAaataacag Human: CAGTGACTTTTCCTCACAGTGTCTGCAATCCCTTTCCAAAGCTACCT----------------------GACAGCCTTCGGT------ATACTATAATGATTATTAAGGATTTTTTTCCTTTCTCCCCATTTGTAATAGCCTGTCTGGTTTCCTAGCCATATAGTCCCTTCCCTCATACCAGTCACAGGCTCTACTCTAaataacag Cluster: [ ] Orangutan: cagtgatttttcctcacagtgtctgcaatccttttccaaagctaccttcagtatgatacaatccctttccaaagccttcagtgtg---atacTATAATGATTATTAAGGATTTTTTTCCTTTCTCCCCTTTTGTAATAGCCTGCCTGGTTTCCTAGCCATATAGTCCCTTCTCCCATACCAGTTGCAGGCTCTACTCTAaataacag Chimp > Human ------------- chr3:67503246-67503250 Template switch process: F1: L ACAAAACTATAAAATTCTGACAGTGACTTTTCCTCACAGTGTC 1 F3: 4 TCCCTTTCCAAAGCTACCTGACAGCCTTCGGTATACT R RF: ACAAAACTATAAAATTCTGACAGTGACTTTTCCTCACAGTGTCCCTTTCCAAAGCTACCTGACAGCCTTCGGTATAATACTGTAATGATTATTAAGGATTTTTTTCCTTTCTCCCCATTTGTAATAGCCTGTCTGGTTTCCTAGCCATATAGTCCCTTCTCCCATACCAGTTGCA RR: TGTTTTGATATTTTAAGACTGTCACTGAAAAGGAGTGTCACAGGGAAAGGTTTCGATGGACTGTCGGAAGCCATATTATGACATTACTAATAATTCCTAAAAAAAGGAAAGAGGGGTAAACATTATCGGACAGACCAAAGGATCGGTATATCAGGGAAGAGGGTATGGTCAACGT F2: 3 AACGT 2 Unidirectional alignment (log-probability: -31.3) AAACTATAAAATTCTGACAGTGACTTTTCCTCACAGTGtctgcaaTCCCTTTCCAAAGCTACCTGACAGCCTTCGGT---ATACT AAACTATAAAATTCTGACAGTGACTTTTCCTCACAGTG-------TCCCTTTCCAAAGCTACCTGACAGCCTTCGGTATAATACT Template switch alignment (log-probability: -21.9) AAACTATAAAATTCTGACAGTGACTTTTCCTCACAGTGTC|TGCAA|TCCCTTTCCAAAGCTACCTGACAGCCTTCGGTATAcT AAACTATAAAATTCTGACAGTGACTTTTCCTCACAGTGTC|TGCAA|TCCCTTTCCAAAGCTACCTGACAGCCTTCGGTATAAT ========== Event 2252 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACAAAGGCATCAAGTAAACACA-------GAAATGGGATA--------ATATCTAATTATC----------CCATTTCTGACCCGTTACAATTCTCAGGATG Chimp: ACAAAGGCATCAAGTAAATACA-------GAAATGGGATA--------ATATCTAATTATC----------CCATTTCTGACCCGTTACAATTCTCAGGATG ↑ 3 1 2 4 Gorilla: ACAAAGGCATCAAGTAAACTCA-------GAAATGGGATAATTAGATGTTATCTAATTATC--------------------CCCGTTACAATTCTCAGGATG ↓ 3 1 2 4 Human: ACAAAGGCATCAAGTAAACACA-------GAAATGGGATA--------ATATCTAATTATC----------CCATTTCTGACCCGTTACAATTCTCAGGATG Cluster: [ ] Orangutan: ACAAAGGCATCAAGTAAACCCAAGatatatatatataata--------atatCTAATTATCCCATTTCTGA----------CCCATTACAATTCTCAGGATG Gorilla > Human --------------- chr3:67465036-67465056 Template switch process: F1: L GTAAACACAGAAATGGGATAAT 1 F3: 4 CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA R RF: GTAAACTCAGAAATGGGATAATTAGATGTTATCTAATTATCCCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA RR: CATTTGAGTCTTTACCCTATTAATCTACAATAGATTAATAGGGGCAATGTTAAGAGTCCTACAAACGATAAATCGAAAATT F2: 3 AGTCTTTACCCTATTAATCTA 2 Unidirectional alignment (log-probability: -40.8) GTAAACaCAGAAATGGGATAA--------TATCTAATTATCccatttctgaCCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA GTAAACTCAGAAATGGGATAATTAGATGTTATCTAATTATC----------CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA Template switch alignment (log-probability: -23.4) GTAAACaCAGAAATGGGATAAT|ATCTAATTATCCCATTTCTGA|CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA GTAAACTCAGAAATGGGATAAT|ATCTAATTATCCCATTTCTGA|CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA Gorilla > Chimp --------------- chr3:68497450-68497470 Template switch process: F1: L GTAAATACAGAAATGGGATAAT 1 F3: 4 CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA R RF: GTAAACTCAGAAATGGGATAATTAGATGTTATCTAATTATCCCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA RR: CATTTGAGTCTTTACCCTATTAATCTACAATAGATTAATAGGGGCAATGTTAAGAGTCCTACAAACGATAAATCGAAAATT F2: 3 AGTCTTTACCCTATTAATCTA 2 Unidirectional alignment (log-probability: -46.3) GTAAAtaCAGAAATGGGATAA--------TATCTAATTATCccatttctgaCCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA GTAAACTCAGAAATGGGATAATTAGATGTTATCTAATTATC----------CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA Template switch alignment (log-probability: -29) GTAAAtaCAGAAATGGGATAAT|ATCTAATTATCCCATTTCTGA|CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA GTAAACTCAGAAATGGGATAAT|ATCTAATTATCCCATTTCTGA|CCCGTTACAATTCTCAGGATGTTTGCTATTTAGCTTTTAA ========== Event 2253 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTACAAAGGCATCAAGTAAACACA-------GAAATGGGATA--------ATATCTAATTATC----------CCATTTCTGACCCGTTACAATTCTCAGGAT Chimp: GTTACAAAGGCATCAAGTAAATACA-------GAAATGGGATA--------ATATCTAATTATC----------CCATTTCTGACCCGTTACAATTCTCAGGAT ↓ 1 34 2 Gorilla: GTTACAAAGGCATCAAGTAAACTCA-------GAAATGGGATAATTAGATGTTATCTAATTATC--------------------CCCGTTACAATTCTCAGGAT Human: GTTACAAAGGCATCAAGTAAACACA-------GAAATGGGATA--------ATATCTAATTATC----------CCATTTCTGACCCGTTACAATTCTCAGGAT Cluster: [] Orangutan: GTTACAAAGGCATCAAGTAAACCCAAGatatatatatataata--------atatCTAATTATCCCATTTCTGA----------CCCATTACAATTCTCAGGAT Chimp > Gorilla --------------- chr3:68571191-68571213 Template switch process: F1: L ATATGTCAATTGTGCAGACTGTTACAAAGGCATCAAGTAAAC 1 F3: 4 TATCTAATTATC R RF: ATATGTCAATTGTGCAGACTGTTACAAAGGCATCAAGTAAATACAGAAATGGGATAATATCTAATTATCCCATTTCTGA RR: TATACAGTTAACACGTCTGACAATGTTTCCGTAGTTCATTTATGTCTTTACCCTATTATAGATTAATAGGGTAAAGACT F2: 3 TGTAGATTAATAGGGTAAAGACT 2 Unidirectional alignment (log-probability: -40.3) ATGTCAATTGTGCAGACTGTTACAAAGGCATCAAGTAAActCAGAAATGGGATAAttagatgtTATCTAATTATC------ ATGTCAATTGTGCAGACTGTTACAAAGGCATCAAGTAAATACAGAAATGGGATAA--------TATCTAATTATCCCATTT Template switch alignment (log-probability: -29) ATGTCAATTGTGCAGACTGTTACAAAGGCATCAAGTAAAc|TCAGAAATGGGATAATTAGATgT|TATCTAATTATC ATGTCAATTGTGCAGACTGTTACAAAGGCATCAAGTAAAT|TCAGAAATGGGATAATTAGATAT|TATCTAATTATC ========== Event 2254 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CATCCGCTACTACTCTATTTCTGAAGGTGCCTTCAGAAGATTACCACAGCCTTCATCT ↑ 3 2 1 4 Chimp: CATCCGCTACTACTCTATTTCTGAAGGTGC------TAGATTACCACAGCCTTCATCT Gorilla: CATCCGCTACTACTCTATTTCTGAAGGTGC------TAGATTACCACAGCCTTCATCT Human: CATCCGCTACTACTCTATTTCTGAAGGTGCCTTCAGAAGATTACCACAGCCTTCATCT Cluster: [ ] Orangutan: ---------------------------------------------------------- Chimp > Human ------------- chr3:131688291-131688297 Template switch process: F1: L AGAGTCTGGAACATCCGCTACTACTCTATTTCTGAAGGTGC 1 F3: 4 AGATTACCACAGCCTTCATCTTGTCAAGACCCCAAAATGG R RF: AGAGTCTGGAACATCCGCTACTACTCTATTTCTGAAGGTGCTAGATTACCACAGCCTTCATCTTGTCAAGACCCCAAAATGG RR: TCTCAGACCTTGTAGGCGATGATGAGATAAAGACTTCCACGATCTAATGGTGTCGGAAGTAGAACAGTTCTGGGGTTTTACC F2: 3 AGACTTC 2 Unidirectional alignment (log-probability: -25.6) GAGTCTGGAACATCCGCTACTACTCTATTTCTGAAGGTGCcttcagaAGATTACCACAGCCTTCATCTTGTCAAGACCCCAAAATGG GAGTCTGGAACATCCGCTACTACTCTATTTCTGAAGGTGC------TAGATTACCACAGCCTTCATCTTGTCAAGACCCCAAAATGG Template switch alignment (log-probability: -16.2) GAGTCTGGAACATCCGCTACTACTCTATTTCTGAAGGTGC|CTTCAGA|AGATTACCACAGCCTTCATCTTGTCAAGACCCCAAAATGG GAGTCTGGAACATCCGCTACTACTCTATTTCTGAAGGTGC|CTTCAGA|AGATTACCACAGCCTTCATCTTGTCAAGACCCCAAAATGG ========== Event 2255 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAAGCTATAAATAGTTTCCTGAAATCACGTTTTTGCCTAAGATCTTGGGAAACTATTTC Chimp: AAAAGCTATAAATAGTTTCCTGAAATCACGTTTTTGCCTAAGATCTTGGGAAACTATTTC ↓ 1 4 3 2 Gorilla: AAAAGCTATAAATAGTTTCCTTAG-GCAAGTTTTTGCCTAAGATCTTGGGAAACTATTTC ↑ 1 4 3 2 Human: AAAAGCTATAAATAGTTTCCTGAAATCACGTTTTTGCCTAAGATCTTGGGAAACTATTTC Cluster: [ ] Orangutan: AAAAGCTATAAATAGTTTCCTGAAATCCCGTTTTTGCCTAAGATCTTGGGAAACTATTTC Human > Gorilla --------------- chr3:133578448-133578454 Template switch process: F1: L ATCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT 1 F3: 4 GTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC R RF: ATCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCTGAAATCACGTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC RR: TAGTTATCTCGAAAGGGAACTTTTCGATATTTATCAAAGGACTTTAGTGCAAAAACGGATTCTAGAACCCTTTGATAAAGGTCATCGAG F2: 3 AACGGAT 2 Unidirectional alignment (log-probability: -30.7) TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT----TaggCAaGTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCTGAAAT---CACGTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC Template switch alignment (log-probability: -16.6) TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT|TAGGCAA|GTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT|TAGGCAA|GTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC Chimp > Gorilla --------------- chr3:133578448-133578454 Template switch process: F1: L ATCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT 1 F3: 4 GTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC R RF: ATCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCTGAAATCACGTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC RR: TAGTTATCTCGAAAGGGAACTTTTCGATATTTATCAAAGGACTTTAGTGCAAAAACGGATTCTAGAACCCTTTGATAAAGGTCATCGAG F2: 3 AACGGAT 2 Unidirectional alignment (log-probability: -30.7) TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT----TaggCAaGTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCTGAAAT---CACGTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC Template switch alignment (log-probability: -16.6) TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT|TAGGCAA|GTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC TCAATAGAGCTTTCCCTTGAAAAGCTATAAATAGTTTCCT|TAGGCAA|GTTTTTGCCTAAGATCTTGGGAAACTATTTCCAGTAGCTC ========== Event 2256 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: GTGCTGCAGCCAGGGGTTCCT-------GAGGACGGCTCTGCCTTGTGAGACGGAGGTCTGTCCCCTGAT Chimp: GTGCTGCAGCCAGGGGTTCCT-------GAGGACGGCTCTGCCTTGTGAGACGGAGGTCTGTCCCCTGAC Gorilla: GTGCTGCAGCCAGGGGTTCCTGGCTCACAAGGCAGAGCCGTCCTTGTGAGACAGAGGTCTGTCCCCTGAT ↓ 1 3 4 2 ↑ 1 3 4 2 Human: GTGCTGCAGCCAGGGGTTCCT-------GAGGACGGCTCTGCCTTGTGAGACGGAGGTCTGTCCCCTGAT Cluster: [ ] Orangutan: GTGCTGCAGCCAGGGGTTCCT-------GAGGACGGCTCTGCCTTGTGAGACGGAGGTCTGTCCCCTGAT Gorilla > Human --------------- chr3:13255286-13255297 Template switch process: F1: L AGACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTG 1 F3: 4 CCTTGTGAGACGGAGGTCTGTCCCCTGATCCTGAGGACAC R RF: AGACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGGCTCACAAGGCAGAGCCGTCCTTGTGAGACAGAGGTCTGTCCCCTGATCCTGAGGACAC RR: TCTGGCCTGTGACCCGAAGCCACGACGTCGGTCCCCAAGGACCGAGTGTTCCGTCTCGGCAGGAACACTCTGTCTCCAGACAGGGGACTAGGACTCCTGTG F2: 3 GTCTCGGCAGGA 2 Unidirectional alignment (log-probability: -42.9) ACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGaggacggctctG------------------CCTTGTGAGACgGAGGTCTGTCCCCTGATCCTGAGGACAC ACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTG-----------GCTCACAAGGCAGAGCCGTCCTTGTGAGACAGAGGTCTGTCCCCTGATCCTGAGGACAC Template switch alignment (log-probability: -22.8) ACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTG|AGGACGGCTCTG|CCTTGTGAGACgGAGGTCTGTCCCCTGATCCTGAGGACAC ACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTG|AGGACGGCTCTG|CCTTGTGAGACAGAGGTCTGTCCCCTGATCCTGAGGACAC Human > Gorilla --------------- chr3:13511350-13511367 Template switch process: F1: L AGACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGG 1 F3: 4 CCTTGTGAGACAGAGGTCTGTCCCCTGATCCTGAGGACAC R RF: AGACCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGAGGACGGCTCTGCCTTGTGAGACGGAGGTCTGTCCCCTGATCCTGAGGACAC RR: TCTGGCCTGTGACCCGAAGCCACGACGTCGGTCCCCAAGGACTCCTGCCGAGACGGAACACTCTGCCTCCAGACAGGGGACTAGGACTCCTGTG F2: 3 TGCCGAGACGGAACACTC 2 Unidirectional alignment (log-probability: -52.6) CCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTG-----------GctcacaaggcagagccgtCCTTGTGAGACaGAGGTCTGTCCCCTGATCCTGAGGACAC CCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGAGGACGGCTCTG------------------CCTTGTGAGACGGAGGTCTGTCCCCTGATCCTGAGGACAC Template switch alignment (log-probability: -29.1) CCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGg|CTCACAAGGCAGAGCCGT|CCTTGTGAGACaGAGGTCTGTCCCCTGATCCTGAGGACAC CCGGACACTGGGCTTCGGTGCTGCAGCCAGGGGTTCCTGA|CTCACAAGGCAGAGCCGT|CCTTGTGAGACGGAGGTCTGTCCCCTGATCCTGAGGACAC ========== Event 2257 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CTAAATGGTATAACTGTCAAGTCCTTAACATGGAACATGTTAACATGGAAATAACTATAAGGAAgtggct ↑ 4 3 2 1 Chimp: CTAAATGGTATAACTGTCAAGCCCTTAAC---------------ATGGAAATAACTATAAGGAAgtggct ↓ 4 3 2 1 Gorilla: CTAAATGGTATAACTGTCAAGCCCTTAACATGGAACATGTTAACATGGAAATAACTATAAGGAAgtggct Human: CTAAATGGTATAACTGTCAAGTCCTTAACATGGAACATGTTAACATGGAAATAACTATAAGGAAgtggct Cluster: [ ] Orangutan: CTAAATGGTATAACTGTCAAGCCCTTAACATGGAACATGTTAACATGGAAATAACTATAAGGAAgtggca Chimp > Human ------------- chr3:133644762-133644765 Template switch process: F1: L TAAGAAAAAAATTAACAAGTCTAAATGGTATAACTGTCAAGTCCTTAACATGGAA 1 F3: 4 TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCCTAAAA R RF: TAAGAAAAAAATTAACAAGTCTAAATGGTATAACTGTCAAGCCCTTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCCTAAAA RR: ATTCTTTTTTTAATTGTTCAGATTTACCATATTGACAGTTCGGGAATTGTACCTTTATTGATATTCCTTCACCGACCGTTTAGGATTTT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -38.6) CAAGTCTAAATGGTATAACTGTCAAGtCCTTAACATGgaacatgttaacatgGAAATAACTATAAGGAAGTGGCTGGCAAATCC CAAGTCTAAATGGTATAACTGTCAAGCCCTTAACATG---------------GAAATAACTATAAGGAAGTGGCTGGCAAATCC Template switch alignment (log-probability: -22.1) CAAGTCTAAATGGTATAACTGTCAAGtCCTTAACATGGAA|CATG|TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCC CAAGTCTAAATGGTATAACTGTCAAGCCCTTAACATGGAA|CATG|TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCC Chimp > Gorilla --------------- chr3:135706842-135706845 Template switch process: F1: L AATTAACAAAGTCTAAATGGTATAACTGTCAAGCCCTTAACATGGAA 1 F3: 4 TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCCTAAAA R RF: AATTAACA-AGTCTAAATGGTATAACTGTCAAGCCCTTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCCTAAAA RR: TTAATTGT-TCAGATTTACCATATTGACAGTTCGGGAATTGTACCTTTATTGATATTCCTTCACCGACCGTTTAGGATTTT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -43.6) aAAGTCTAAATGGTATAACTGTCAAGCCCttaacatggaacatgTTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCC -AAGTCTAAATGGTATAACTGTCAAGCCC---------------TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCC Template switch alignment (log-probability: -27.7) AaAGTCTAAATGGTATAACTGTCAAGCCCTTAACATGGAA|CATG|TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCC A-AGTCTAAATGGTATAACTGTCAAGCCCTTAACATGGAA|CATG|TTAACATGGAAATAACTATAAGGAAGTGGCTGGCAAATCC ========== Event 2258 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGAAGGCTGTGCTTTCCTCACATAACCGCT----AGCTAGCACTTTGGGCAGCCCAGGTATG Chimp: AGGAAGGCTGTGCTTTCCTCACATAACTGCTAGCTAGCTAGCACTTTGGGCAGCCCAGGTATG ↑ 1 4 3 2 Gorilla: AGGAAGGCTGTGCTTTCCTCATATAACCACT----AGCTAGCACTTTGGGCAGCCCAGGTATG Human: AGGAAGGCTGTGCTTTCCTCACATAACCGCT----AGCTAGCACTTTGGGCAGCCCAGGTATG Cluster: [ ] Orangutan: AGGAAGGCTATGCTTTCCTCACATAACCGCT----ACCTAGCACTTTGGGCAGCCCAGGTACG Gorilla > Chimp --------------- chr3:137814509-137814514 Template switch process: F1: L GCCTGGCTGGCCAGAATCCCAGGAAGGCTGTGCTTTCCTCACATAAC 1 F3: 4 CTAGCTAGCACTTTGGGCAGCCCAGGTATGCAGAATCACTTT R RF: GCCTGGCTGGCCAGAATCCCAGGAAGGCTGTGCTTTCCTCATATAACCACTAGCTAGCACTTTGGGCAGCCCAGGTATGCAGAAGCACTTT RR: CGGACCGACCGGTCTTAGGGTCCTTCCGACACGAAAGGAGTATATTGGTGATCGATCGTGAAACCCGTCGGGTCCATACGTCTTCGTGAAA F2: 3 GATCGT 2 Unidirectional alignment (log-probability: -38.9) TGGCCAGAATCCCAGGAAGGCTGTGCTTTCCTCAcATAACtgctagCTAGCTAGCACTTTGGGCAGCCCAGGTATGCAGAAtCACT TGGCCAGAATCCCAGGAAGGCTGTGCTTTCCTCATATAAC----CACTAGCTAGCACTTTGGGCAGCCCAGGTATGCAGAAGCACT Template switch alignment (log-probability: -27.7) TGGCCAGAATCCCAGGAAGGCTGTGCTTTCCTCAcATAAC|TGCTAG|CTAGCTAGCACTTTGGGCAGCCCAGGTATGCAGAAtCACT TGGCCAGAATCCCAGGAAGGCTGTGCTTTCCTCATATAAC|TGCTAG|CTAGCTAGCACTTTGGGCAGCCCAGGTATGCAGAAGCACT ========== Event 2259 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: aGATAGGCCACAATAAAGGATATATAT-G------TATGTGTGTGTGTATacacacaca------------cacac Chimp: aGATAGGCCACAATAAAGGATATATAT-G------TATGTGTGTGTGTATacacacaca----------------- ↑ 3 1 4 2 Gorilla: aGATAGGCCACAATAAAGGATCTATAT-G------------TGTGTGTATacacacacacacacgcgcgcg----- ↓ 3 1 4 2 Human: aGATAGGCCACAATAAAGGATATATAT-G------TATGTGTGTGTGTATacacacaca------------cacac Cluster: [ ] Orangutan: agataggccataataaaggatATATATGGTATGTG------TGTGTGTATACACACA------------------- Gorilla > Human --------------- chr3:136574336-136574349 Template switch process: F1: L CACACTTTTAATATAAGAGCAGATAGGCCACAATAAAGGATATATATGTATGTGT 1 F3: 4 ACACACACACACA R RF: CACACTTTTAATATAAGAGCAGATAGGCCACAATAAAGGATCTATATGTGTGTGTATACACACACACACA RR: GTGTGAAAATTATATTCTCGTCTATCCGGTGTTATTTCCTAGATATACACACACATATGTGTGTGTGTGT F2: 3 CACACATATGTGTG 2 Unidirectional alignment (log-probability: -46) AGAGCAGATAGGCCACAATAAAGGATaTATAtgtatgTGTGTGTGTATACACACACACACACa------CACa AGAGCAGATAGGCCACAATAAAGGATCTATA------TGTGTGTGTATACACACACACACACGCGCGCGCACG Template switch alignment (log-probability: -28.2) AGAGCAGATAGGCCACAATAAAGGATaTATATGTaTGTGT|GTGTGTATACACAC|ACACACACACACA AGAGCAGATAGGCCACAATAAAGGATCTATATGTGTGTGT|GTGTGTATACACAC|ACACACACACACA Gorilla > Chimp --------------- chr3:139946110-139946123 Template switch process: F1: L CACACTTTTAATATAAGAGCAGATAGGCCACAATAAAGGATATATATGTATGTGT 1 F3: 4 ACACACACACACA R RF: CACACTTTTAATATAAGAGCAGATAGGCCACAATAAAGGATCTATATGTGTGTGTATACACACACACACA RR: GTGTGAAAATTATATTCTCGTCTATCCGGTGTTATTTCCTAGATATACACACACATATGTGTGTGTGTGT F2: 3 CACACATATGTGTG 2 Unidirectional alignment (log-probability: -46) AGAGCAGATAGGCCACAATAAAGGATaTATAtgtatgTGTGTGTGTATACACACACACACACa------CACa AGAGCAGATAGGCCACAATAAAGGATCTATA------TGTGTGTGTATACACACACACACACGCGCGCGCACG Template switch alignment (log-probability: -28.2) AGAGCAGATAGGCCACAATAAAGGATaTATATGTaTGTGT|GTGTGTATACACAC|ACACACACACACA AGAGCAGATAGGCCACAATAAAGGATCTATATGTGTGTGT|GTGTGTATACACAC|ACACACACACACA ========== Event 2260 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGGCACAAGGACCCTACCTAAAGGCCTGGGAGAACCTATACAGGAGGTCTGCTTGGGGTCTCAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGGGC--CTTCAGGTCAAGTGTTCTGCACAAAG Chimp: TTGGCACAAGGACCCTACCTGAAGGCCTGGGAGAACCTATACAGGAGGTCTGCTTGGGGTCTCAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGGGC--CTTCAGGTCAAGTGTTCTGCACAAAG ↑ 3 2 1 4 Gorilla: TTGGCAGAAGGACCCTACCTGAAGGCCTGGGAGAACCTATACGGGAGGTCTGCTTGGGGTCTCAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGGAA----AAGGGTCAAGTGTTCTGCACAAAG Human: TTGGCACAAGGACCCTACCTAAAGGCCTGGGAGAACCTATACAGGAGGTCTGCTTGGGGTCTCAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGGGC--CTTCAGGTCAAGTGTTCTGCACAAAG Cluster: [ ] Orangutan: TTGGCACAAGGACCCTACCTGAAGGCCTGGGAGAACCTATATAGGAGGTCTGCTTGGGATCTCAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCCCAGGGCCT--TCAGGTCAAGTGTTCTGCACAAAG Gorilla > Chimp --------------- chr3:138474144-138474150 Template switch process: F1: L CAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGG 1 F3: 4 GGTCAAGTGTTCTGCACAAAGTCTTTTTTTTTTTTAATTG R RF: TGAAGGCCTGGGAGAACCTATACGGGAGGTCTGCTTGGGGTCTCAGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGGAAAAGGGTCAAGTGTTCTGCACAAAGTCTTTTTTTTCTTTAATTG RR: ACTTCCGGACCCTCTTGGATATGCCCTCCAGACGAACCCCAGAGTCCCCGGGATCCGTTCCTCTACAAAAAGGACGAAGTGTCCTTTTCCCAGTTCACAAGACGTGTTTCAGAAAAAAAAGAAATTAAC F2: 3 ACTTCCG 2 Unidirectional alignment (log-probability: -35) AGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGG----GccttcaGGTCAAGTGTTCTGCACAAAGTCTTTTTTTTtTTTAATTG AGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGGAAAAG------GGTCAAGTGTTCTGCACAAAGTCTTTTTTTTCTTTAATTG Template switch alignment (log-probability: -22.1) AGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGG|GCCTTCA|GGTCAAGTGTTCTGCACAAAGTCTTTTTTTTtTTTAATTG AGGGGCCCTAGGCAAGGAGATGTTTTTCCTGCTTCACAGG|GCCTTCA|GGTCAAGTGTTCTGCACAAAGTCTTTTTTTTCTTTAATTG ========== Event 2261 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCTACCTCCCACAGAGAATGCTAAACTCCCC-------GTATGAGGGGAGCTTCTCAGGTC ↓ 3 2 1 4 Chimp: CCCTACCTCCCATAGAGAATGCTAAACTCCCCAGTTTAGCAATGAGGGGAGCTTCTCAGGTC ↑ 3 2 1 4 Gorilla: CCCTACCTCCCGTAGAGAATGCTAAACTCCCC-------GTATGAGGGGAGCTTCTCAGGTC Human: CCCTACCTCCCACAGAGAATGCTAAACTCCCC-------GTATGAGGGGAGCTTCTCAGGTC Cluster: [ ] Orangutan: CCCCACCTCCCATAGAGAATGCTAAACTTCCT-------GTATGAGGGGAGCTTCTCAGGTC Human > Chimp ------------- chr3:143912900-143912908 Template switch process: F1: L CTGCCCCTGCCCTACCTCCCATAGAGAATGCTAAACTCCCC 1 F3: 4 ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT R RF: CTGCCCCTGCCCTACCTCCCACAGAGAATGCTAAACTCCCCGTATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT RR: GACGGGGACGGGATGGAGGGTGTCTCTTACGATTTGAGGGGCATACTCCCCTCGAAGAGTCCAGGGGTCGTCGGGAAGTGGTA F2: 3 ACGATTTGA 2 Unidirectional alignment (log-probability: -37.2) TGCCCCTGCCCTACCTCCCAtAGAGAATGCTAAACTCCCCaGTttagcaATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT TGCCCCTGCCCTACCTCCCACAGAGAATGCTAAACTCCCC-GT------ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT Template switch alignment (log-probability: -22.4) TGCCCCTGCCCTACCTCCCAtAGAGAATGCTAAACTCCCC|AGTTTAGCA|ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT TGCCCCTGCCCTACCTCCCACAGAGAATGCTAAACTCCCC|AGTTTAGCA|ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT Gorilla > Chimp --------------- chr3:143912900-143912908 Template switch process: F1: L CTGCCCCTGCCCTACCTCCCATAGAGAATGCTAAACTCCCC 1 F3: 4 ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAT R RF: CTGCCCCTGCCCTACCTCCCGTAGAGAATGCTAAACTCCCCGTATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAC RR: GACGGGGACGGGATGGAGGGCATCTCTTACGATTTGAGGGGCATACTCCCCTCGAAGAGTCCAGGGGTCGTCGGGAAGTGGTG F2: 3 ACGATTTGA 2 Unidirectional alignment (log-probability: -41.8) TGCCCCTGCCCTACCTCCCaTAGAGAATGCTAAACTCCCCaGTttagcaATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAt TGCCCCTGCCCTACCTCCCGTAGAGAATGCTAAACTCCCC-GT------ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAC Template switch alignment (log-probability: -27.9) TGCCCCTGCCCTACCTCCCaTAGAGAATGCTAAACTCCCC|AGTTTAGCA|ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAt TGCCCCTGCCCTACCTCCCGTAGAGAATGCTAAACTCCCC|AGTTTAGCA|ATGAGGGGAGCTTCTCAGGTCCCCAGCAGCCCTTCACCAC ========== Event 2262 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGACTGTCCTGGTTCTTTTTATTA-------GAGTCTGTGGGTAACTTGAAGTTAGGTACC Chimp: AGACTGTCCTGGTTCTTTTTATTA-------GAGTCTGTGGGTAACTTGAAGTTAGGTACC ↓ 1 3 4 2 Gorilla: AGACTGTCCTGGTTCTTTTTACCACAGACTCTAGTCTGTGGGTAACTTGAAGTTAGGTACC ↑ 1 3 4 2 Human: AGACTGTCCTGGTTCTTTTTATTA-------GAGTCTGTGGGTAACTTGAAGTTAGGTACC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNN-------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr3:142069797-142069807 Template switch process: F1: L ATTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA 1 F3: 4 AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC R RF: ATTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTATTAGAGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC RR: TAAGAGGGGACACTGTGGGATCTGACAGGACCAAGAAAAATAATCTCAGACACCCATTGAACTTCAATCCATGGATGTCTCACTG F2: 3 TCTCAGACACC 2 Unidirectional alignment (log-probability: -35.2) TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTAccacagactcT---AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA----------TTAGAGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC Template switch alignment (log-probability: -17.1) TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA|CCACAGACTCT|AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA|CCACAGACTCT|AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC Chimp > Gorilla --------------- chr3:142069797-142069807 Template switch process: F1: L ATTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA 1 F3: 4 AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC R RF: ATTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTATTAGAGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC RR: TAAGAGGGGACACTGTGGGATCTGACAGGACCAAGAAAAATAATCTCAGACACCCATTGAACTTCAATCCATGGATGTCTCACTG F2: 3 TCTCAGACACC 2 Unidirectional alignment (log-probability: -35.2) TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTAccacagactcT---AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA----------TTAGAGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC Template switch alignment (log-probability: -17.1) TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA|CCACAGACTCT|AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC TTCTCCCCTGTGACACCCTAGACTGTCCTGGTTCTTTTTA|CCACAGACTCT|AGTCTGTGGGTAACTTGAAGTTAGGTACCTACAGAGTGAC ========== Event 2263 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ccttatccaggcatttgacaaggtgtcacaagatcaccttggcaatgaggtgggaaatgtatgctggaccaggctgcaggcaaatggagttgtaTTCTCCCTGTATTCTGCATGCATT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAGTATGCATTTGGACCAGGTTGCAGGCAGGTAGTCTAAATGCATGCATCCCTCTTCTGGTGAAGTGGGCCTGAATGCTCAGAGTCAGCAAGTCCTATCACTGGATGAGGATCTGGGCTGAGAATCAGGTTGCTGAGAGATTCTAGCAGTTGCTTTTCCACAGGGTGTCTGAAGATTCCT Chimp: --------------------------------------------------------------------------------------nnnnnnnnttca-tgtgtcttttggctgcataaatatcttcttttgagaagtgtctgttcatatccttcacccactttgtgatggggttgtttgattttttcttgtaaatttgtttgagttcattgtagattccggatattagccctttgtcagatgagtagattgcaaaaattttatcccattctgtaggttgcccgttcactctgagggtagtttcttttgctgtgcagaagctctttagtttaattagatcccatttgtcaattttggcttttgttgccattgcttttagtgttttagacatgaagtccttgcccatgcctatgtcctgtatggtattgcctaggttttcttccagggtttttatggttttagatctaacatttaggtctttaatccatcttgaattgatatttgtataaggtgtaaggaagagatccagtttcagctttctacatatggctagccagttttcccagcaccatttattaaatagggaatcctttccccattgcttgtttttctcaggtttgtcaaagatcagatagttgtagataggtggcattatttctgagggctctgttctgttccattggtctatatctctgttttggtaccagtaccatgctgttttgGAAAGTCTTTAACCAACTCGCTCACCATGTGCTTACTAGGCCATGGGAGGAGCCTTAGCAAGGAATCTTCAGACACCCTGTGGAAAAGCAACTGCTAGAATCTCTCAGCAACCTGATTCTCAGCCCAGATCCTCATCCAGTGATAGGACTTGCTGACTCTGAGCATTCAGGCCCACTTCACCAGAAGAGGGATGCATGCATTTGGACTACCTGCCTGCAACCTGGTCCAAATGCATAC------------------------------------------------------------------------------------------------------------------------------------- ↑ 1 3 2 4 Gorilla: ccttatccaggcatttgacaaggtgtcacaagatcaccttggcaatgaggtgggaaatgtatgctggaccaggctgcaggcaaatggagttgtaTTCGCCCTGTATTCTGCATGCATT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAGTATGCATTTGGACCAGGTTGCAGGCAGGTAGTCCAAATGCATGCATCCCTCTTCTGGTGAAGTGGGCCCGAATGCTCAGAGTCAGCAAGTCCTATCACTGGATGAGGATCTGGGCTGAGAATCAGGTTGCTGAGAGATTCTAGCAGTTGCTTTTCCACAGGGTGTCTGAAGATTCCT Human: ccttatccaggcatttgacaaggtgtcacaagatcaccttggcaatgaggtgggaaatgtatgctggaccaggctgcaggcaaatggagttgtaTTCTCCCTGTATTCTGCATGCATT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAGTATGCATTTGGACCAGGTTGCAGGCAGGTAGTCTAAATGCATGCATCCCTCTTCTGGTGAAGTGGGCCTGAATGCTCAGAGTCAGCAAGTCCTATCACTGGATGAGGATCTGGGCTGAGAATCAGGTTGCTGAGAGATTCTAGCAGTTGCTTTTCCACAGGGTGTCTGAAGATTCCT Cluster: [ ] Orangutan: ccttatccaggcatttgacaaggtgtcacaagatcaccttggcaatgaggtgggaaatgtatagtggaCCAGGCTGCAGGCAAATGGAGTTGTATTCTCCCTGTATTCTGCATGCATT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAGTATGCATTTGGACCAGGTTGCAGGCAGGTAGTCCAAATGCATGCATCCCTCTTCTGGTGAAGTGGGCCTGAATGTTCAGAGTCAGCAAGTCCTACCACTGGATGAGGATCTGGGCTGAGAATCAGGTTGCTGAGAGATTCTAGCAGTTGCTTTTCCACAGGGTGTCTGAAGATTCCT Gorilla > Chimp --------------- chr3:143045452-143045517 Template switch process: F1: L TCAG 1 F3: 4 AC R RF: CCAGTATGCATTTGGACCAGGTTGCAGGCAGGTAGTCCAAATGCATGCATCCCTCTTCTGGTGAAGTGGGCCCGAATGCTCAGAGTCAGCAAGTCCTATCACTGGATGAGGATCTGGGCTGAGAATCAGGTTGCTGAGAGATTCTAGCAGTTGCTTTTCCAC RR: GGTCATACGTAAACCTGGTCCAACGTCCGTCCATCAGGTTTACGTACGTAGGGAGAAGACCACTTCACCCGGGCTTACGAGTCTCAGTCGTTCAGGATAGTGACCTACTCCTAGACCCGACTCTTAGTCCAACGACTCTCTAAGATCGTCAACGAAAAGGTG F2: 3 TACGTAAACCTGGTCCAACGTCCGTCCATCAGGTTTACGTACGTAGGGAGAAGACCACTTCACCCG 2 Unidirectional alignment (log-probability: -110) tcaggcccacttcaCCAgaagagggatGcATGCATTTGGAC---------------TAcctgcctgcaacctgGTCCAAATGCATaC-------------------------- --------------CCA----------GTATGCATTTGGACCAGGTTGCAGGCAGGTA---------------GTCCAAATGCATGCATCCCTCTTCTGGTGAAGTGGGCCCG Template switch alignment (log-probability: -27.8) tCAG|GCCCACTTCACCAGAAGAGGGATGCATGCATTTGGACTACCTGCCTGCAACCTGGTCCAAATGCAT|AC CCAG|GCCCACTTCACCAGAAGAGGGATGCATGCATTTGGACTACCTGCCTGCAACCTGGTCCAAATGCAT|AC ========== Event 2264 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ttTGTTGGTTTGCTTCATCTCTGAGAAAAACTCAGTGATGAGTTTTTCTCAGTGATTGTAATGTGCGTCAGTGG Chimp: ttTGTTGGTTTGCTTCATCTCTGAGAAAATCTCAGTGATGAGTTTTTCTCAGTGATTGTAATGTGCGTCAGTGG Gorilla: ttTGTTGGTTTGCTTCATCTCTGAGAAAAACTCATCACTGAGTTTTTCTCAGAGATTGTAATGTGCATCAGTGG ↑ 3 1 2 4 Human: ttTGTTGGTTTGCTTCATCTCTGAGAAAAACTCAGTGATGAGTTTTTCTCAGTGATTGTAATGTGCGTCAGTGG Cluster: [ ] Orangutan: ttTGTTGGTTTGCTTCATCTCTGAGAAAAACTCAGTGATGAGTTTTTCTCAGTGATTGTAATGTGCATCAGTGG Human > Gorilla --------------- chr3:140999738-140999756 Template switch process: F1: L GTTTTTGTTTGTTGGTTTGCTTCATCTCTGAGAAAAACTCA 1 F3: 4 GATTGTAATGTGCATCAGTGGCTGA R RF: GTTTTTGTTTGTTGGTTTGCTTCATCTCTGAGAAAAACTCAGTGATGAGTTTTTCTCAGTGATTGTAATGTGCGTCAGTGGCTGA RR: CAAAAACAAACAACCAAACGAAGTAGAGACTCTTTTTGAGTCACTACTCAAAAAGAGTCACTAACATTACACGCAGTCACCGACT F2: 3 AGACTCTTTTTGAGTCACT 2 Unidirectional alignment (log-probability: -34.3) TTTTTGTTTGTTGGTTTGCTTCATCTCTGAGAAAAACTCAtcacTGAGTTTTTCTCAGaGATTGTAATGTGCaTCAGTGGCTGA TTTTTGTTTGTTGGTTTGCTTCATCTCTGAGAAAAACTCAGTGATGAGTTTTTCTCAGTGATTGTAATGTGCGTCAGTGGCTGA Template switch alignment (log-probability: -23.3) TTTTTGTTTGTTGGTTTGCTTCATCTCTGAGAAAAACTCA|TCACTGAGTTTTTCTCAGA|GATTGTAATGTGCaTCAGTGGCTGA TTTTTGTTTGTTGGTTTGCTTCATCTCTGAGAAAAACTCA|TCACTGAGTTTTTCTCAGA|GATTGTAATGTGCGTCAGTGGCTGA ========== Event 2265 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGTATTAGAAGAGGGGGCCAAGG---------------------------CATGGCTCAGGCTGGAGTTCAGCAAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGGGCTCTTCATGCCCAGCTGGTGAGGACCCCTGGCTTCTGGTCT Chimp: GGTATTAGAAGAGGGGGCCAAGG---------------------------CATGGCTCAGGCTGGAGTTCAGCAAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGGGCTCTTCATGCCCAGCTGGTGAGGACCCCTGGCTTCTGGTCT Gorilla: GGTATTAGAAGAGGGGGCCAAGG------------------------------------------------------CACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGGGCTCTTCATGCCCAGCTGCTGAGGACCCCTGGCTTCTGGTCT ↓ 4 1 3 2 Human: GGTATTAGAAGAGGGGGCCAAGG---------------------------CATGGCTCAGGCTGGAGTTCAGCAAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGGGCTCTTCATGCCCAGCTGGTGAGGACCCCTGGCTTCTGGTCT Cluster: [ ] Orangutan: ggtattagaaGAGGGGGCCAAGGCACGGCTCAGGCTGGAGTTCAGCAAGG---------------------------CACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGGGCTCTTCATGCCCAGCTGGTGAGGACCCTTGGCTTCTGTTCT Gorilla > Human --------------- chr3:57201713-57201717 Template switch process: F1: L CACATGGGAGACCTGTGTGGTATTAGAAGAGGGGGCCAAGGCATGGCTCAGGCT-------------GGAGT 1 F3: 4 AAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGG R RF: CACATGGGAGACCTGTGTGGTATTAGAAGAGGGGGCCAAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCACAGGGCTCTTCATGCCCAGCTGCTGA RR: GTGTACCCTCTGGACACACCATAATCTTCTCCCCCGGTTCCGTGCCGAGTCCGAGACCTCCCGACCTCCTCACCCGTGTCCCGAGAAGTACGGGTCGACGACT F2: 3 CGACT 2 Unidirectional alignment (log-probability: -49.7) GTATTAGAAGAGGGGGCCAAggcatggctcaggctggagttcagcaaGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCA GTATTAGAAGAGGGGGCCAA---------------------------GGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCA Template switch alignment (log-probability: -32.8) GTATTAGAAGAGGGGGCCAAGGCAtGGCTCAGGCT-------------GGAGT|TCAGC|AAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCA GTATTAGAAGAGGGGGCCAAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGT|TCAGC|AAGGCACGGCTCAGGCTCTGGAGGGCTGGAGGAGTGGGCA ========== Event 2266 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTG-----GCTGAGGCAGGGCGTTGCCTCA Chimp: ATGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTG-----GCTGAGGCAGGGCGTTGCCTCA ↓ 3 2 1 4 Gorilla: ACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTACCTGCCCTGAGGCAGGGCATTGCCTCA ↑ 3 2 1 4 Human: ACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTG-----GCTGAGGCAGGGCGTTGCCTCA Cluster: [ ] Orangutan: ACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTG-----GCTGAGGCAGGGCGTTGCCTCA Human > Gorilla --------------- chr3:57926629-57926635 Template switch process: F1: L AAGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT 1 F3: 4 CTGAGGCAGGGCATTGCCTCAGGAGTCAATCTTCTCATTG R RF: AAGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTGGCTGAGGCAGGGCGTTGCCTCAGGAGTGAATCTTCTCATTG RR: TTCATGCCCGTACGGATAGACTCCCGTCCATTCTCGAGGAACCGACTCCGTCCCGCAACGGAGTCCTCACTTAGAAGAGTAAC F2: 3 CCGTCCA 2 Unidirectional alignment (log-probability: -40.2) AGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTacctgccCTGAGGCAGGGCaTTGCCTCAGGAGTcAATCTTCTCATTG AGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT-----GGCTGAGGCAGGGCGTTGCCTCAGGAGTGAATCTTCTCATTG Template switch alignment (log-probability: -27.7) AGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT|ACCTGCC|CTGAGGCAGGGCaTTGCCTCAGGAGTcAATCTTCTCATTG AGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT|ACCTGCC|CTGAGGCAGGGCGTTGCCTCAGGAGTGAATCTTCTCATTG Chimp > Gorilla --------------- chr3:57926629-57926635 Template switch process: F1: L AAGTACGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT 1 F3: 4 CTGAGGCAGGGCATTGCCTCAGGAGTCAATCTTCTCATTG R RF: AAGTATGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTGGCTGAGGCAGGGCGTTGCCTCAGGAGTCAATCTTCTCATTG RR: TTCATACCCGTACGGATAGACTCCCGTCCATTCTCGAGGAACCGACTCCGTCCCGCAACGGAGTCCTCAGTTAGAAGAGTAAC F2: 3 CCGTCCA 2 Unidirectional alignment (log-probability: -40.2) AGTAcGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTTacctgccCTGAGGCAGGGCaTTGCCTCAGGAGTCAATCTTCTCATTG AGTATGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT-----GGCTGAGGCAGGGCGTTGCCTCAGGAGTCAATCTTCTCATTG Template switch alignment (log-probability: -27.7) AGTAcGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT|ACCTGCC|CTGAGGCAGGGCaTTGCCTCAGGAGTCAATCTTCTCATTG AGTATGGGCATGCCTATCTGAGGGCAGGTAAGAGCTCCTT|ACCTGCC|CTGAGGCAGGGCGTTGCCTCAGGAGTCAATCTTCTCATTG ========== Event 2267 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: tgatggaatataagctagattctgaggattctctc--agaatgagcaaagcatagagagtaa Chimp: TGATGGAATATAAGCTAGATTCTGAGGATTCTCTC--AGAATGAGCAAAGCATAGAGAGTAA ↑ 3 2 1 4 Gorilla: TGATGGAATATAAGCTAGATTCTGAGGATTCTTTCTAGCCATGAGCAAAGCATAGAGAGTAA Human: tgatggaatataagctagattctgaggattctctc--agaatgagcaaagcatagagagtaa Cluster: [ ] Orangutan: TGATGGAATATAAGCTAGATTCTGAGGATTCTCTCTAGCCATGAGCAAAGCATAGAGAGTAA Gorilla > Chimp --------------- chr3:57703531-57703537 Template switch process: F1: L CAAGGGGCGTGATGGAATATAAGCTAGATTCTGAGGATTCT 1 F3: 4 TGAGCAAAGCATAGAGAGTAACCTGATTACCCATAATAA R RF: CAAGGGGCGTGATGGAATATAAGCTAGATTCTGAGGATTCTTTCTAGCCATGAGCAAAGCATAGAGAGTAACCTGATTACCCATAATAA RR: GTTCCCCGCACTACCTTATATTCGATCTAAGACTCCTAAGAAAGATCGGTACTCGTTTCGTATCTCTCATTGGACTAATGGGTATTATT F2: 3 AAGACTC 2 Unidirectional alignment (log-probability: -28.2) AAGGGGCGTGATGGAATATAAGCTAGATTCTGAGGATTCT-------CtcagaATGAGCAAAGCATAGAGAGTAACCTGATTACCCATAATAA AAGGGGCGTGATGGAATATAAGCTAGATTCTGAGGATTCTTTCTAGCC-----ATGAGCAAAGCATAGAGAGTAACCTGATTACCCATAATAA Template switch alignment (log-probability: -16.6) AAGGGGCGTGATGGAATATAAGCTAGATTCTGAGGATTCT|CTCAGAA|TGAGCAAAGCATAGAGAGTAACCTGATTACCCATAATAA AAGGGGCGTGATGGAATATAAGCTAGATTCTGAGGATTCT|CTCAGAA|TGAGCAAAGCATAGAGAGTAACCTGATTACCCATAATAA ========== Event 2268 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTGAAACTTGTTCTGAAGTTTCAATAGAAACTTTCTATTGAAAGCAATAGAAAGTACTCCCTAAATCTTGTAAT ↑ 4 3 12 Chimp: GTTGAAACTTGTTCTGAAGTT-----------------TTCAAAGCAATAGAAAGTACTCCCTAAATCTTGTAAT Gorilla: GTTGAAACTTGTTCTGAAGTT-----------------TTCAAAGCAATAGAAAGTACTCCCTAAATCTTGTAAT ↓ 4 3 12 Human: GTTGAAACTTGTTCTGAAGTTTCAATAGAAACTTTCTATTGAAAGCAATAGAAAGTACTCCCTAAATCTTGTAAT Cluster: [ ] Orangutan: GTTGAAACTTGTTCTGAAGTT-----------------TTCAAAGCAATAGAAAATACTCCCTAAATCTTGTAAT Chimp > Human ------------- chr3:55740208-55740217 Template switch process: F1: L TCCATTTGTTTAGGTAGTAAGTTGAAACTTGTTCTGAAGTTT------CAATAGAAA 1 F3: 4 AAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG R RF: TCCATTTGTTTAGGTAGTAAGTTGAAACTTGTTCTGAAGTTTTCAAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG RR: AGGTAAACAAATCCATCATTCAACTTTGAACAAGACTTCAAAAGTTTCGTTATCTTTCATGAGGGATTTAGAACATTACATTCC F2: 3 GTTATCTTTC 2 Unidirectional alignment (log-probability: -41.4) AGGTAGTAAGTTGAAACTTGTTCTGAAGTTTcaatagaaactttctatTgAAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG AGGTAGTAAGTTGAAACTTGTTCTGAAGTTT-----------------TCAAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG Template switch alignment (log-probability: -27.2) AGGTAGTAAGTTGAAACTTGTTCTGAAGTTT------CAATAGAAA|CTTTCTATTG|AAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG AGGTAGTAAGTTGAAACTTGTTCTGAAGTTTTCAAAGCAATAGAAA|CTTTCTATTG|AAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG Gorilla > Human --------------- chr3:55740208-55740217 Template switch process: F1: L TCCATTTGTTTAGGTAGTAAGTTGAAACTTGTTCTGAAGTTT------CAATAGAAA 1 F3: 4 AAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG R RF: TCCATTTGTTTAGGTAGTAAGTTGAAACTTGTTCTGAAGTTTTCAAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG RR: AGGTAAACAAATCCATCATTCAACTTTGAACAAGACTTCAAAAGTTTCGTTATCTTTCATGAGGGATTTAGAACATTACATTCC F2: 3 GTTATCTTTC 2 Unidirectional alignment (log-probability: -40.9) AGGTAGTAAGTTGAAACTTGTTCTGAAGTTtcaatagaaactttctaTTgAAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG AGGTAGTAAGTTGAAACTTGTTCTGAAGTT-----------------TTCAAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG Template switch alignment (log-probability: -27.3) AGGTAGTAAGTTGAAACTTGTTCTGAAGTTT------CAATAGAAA|CTTTCTATTG|AAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG AGGTAGTAAGTTGAAACTTGTTCTGAAGTTTTCAAAGCAATAGAAA|CTTTCTATTG|AAAGCAATAGAAAGTACTCCCTAAATCTTGTAATGTAAGG ========== Event 2269 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TGATGACTAGAAAGTCATTTAAAAAGCTGATAAAAAGGAATGAGAGCAAATTCCCAATTTTTGTTTGTTTTTAATGTAAGGGTGGGCAGTGTTGTGGTGAGCTATACTGGCAATCAGGGGCCGGGATTCTGGCAGCC ↑ 4 1 3 2 Chimp: TGATGACTAGAAAGTCATTTA-----------AAAAGGAATGAGAGCAAATTCCCAttttttgtttgtttttAATGTAAGGGTGGGCAGTATTGTGGTGAGCTATACTGACAATCAGGGGCCGGGATTCTGGCAGCC ↓ 4 1 3 2 Gorilla: TGATGACTAGAAAGTCATTTAAAAAGCTGATAAAAAGGAATGAGAGCAAATTCCCAttttttgtttgtttttAATGTAAGGGTGGGCAGTGTTGTGGTGAGCTATACTGGCAATCAGGGGCCGGGATTCTGGCAGCC Human: TGATGACTAGAAAGTCATTTAAAAAGCTGATAAAAAGGAATGAGAGCAAATTCCCAATTTTTGTTTGTTTTTAATGTAAGGGTGGGCAGTGTTGTGGTGAGCTATACTGGCAATCAGGGGCCGGGATTCTGGCAGCC Cluster: [ ] Orangutan: TGATGACTAGAAAGTCATTTAAAAAGCTGATAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTTTTAATGTAAGGGTGGGCAGTGTTGTGGTGAGCTATACTGGCAATCAGGGGCTGGGATTCTGGCACCC Chimp > Human ------------- chr3:143366044-143366047 Template switch process: F1: L TGATAGTGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAG 1 F3: 4 TAAAAAGGAATGAGAGCAAATTCCCAATTTTTGTTTGTTTTT R RF: TGATAGTGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTTTTAATGTAAGGGTGGGCAGTATTGTGGTGAGCTATACTGACAATCAG RR: ACTATCACCTATTATAGATGACTACTGATCTTTCAGTAAATTTTTCCTTACTCTCGTTTAAGGGTAAAAAACAAACAAAAATTACATTCCCACCCGTCATAACACCACTCGATATGACTGTTAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -32.7) TGGATAATATCTACTGATGACTAGAAAGTCATTtaaaaagctgaTAAAAAGGAATGAGAGCAAATTCCCAaTTTTTGTTTGTTT TGGATAATATCTACTGATGACTAGAAAGTCATT-----------TAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTT Template switch alignment (log-probability: -21.9) TGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAG|CTGA|TAAAAAGGAATGAGAGCAAATTCCCAaTTTTTGTTTGTTT TGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAG|CTGA|TAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTT Chimp > Gorilla --------------- chr3:145522251-145522254 Template switch process: F1: L TGATAGTGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAG 1 F3: 4 TAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTTTT R RF: TGATAGTGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTTTTAATGTAAGGGTGGGCAGTATTGTGGTGAGCTATACTGACAATCAG RR: ACTATCACCTATTATAGATGACTACTGATCTTTCAGTAAATTTTTCCTTACTCTCGTTTAAGGGTAAAAAACAAACAAAAATTACATTCCCACCCGTCATAACACCACTCGATATGACTGTTAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -26.7) TGGATAATATCTACTGATGACTAGAAAGTCATTtaaaaagctgaTAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTT TGGATAATATCTACTGATGACTAGAAAGTCATT-----------TAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTT Template switch alignment (log-probability: -16.4) TGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAG|CTGA|TAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTT TGGATAATATCTACTGATGACTAGAAAGTCATTTAAAAAG|CTGA|TAAAAAGGAATGAGAGCAAATTCCCATTTTTTGTTTGTTT ========== Event 2270 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCACAAGCAACTCACTGAGTA--------GATGTTCAGCAAGTACTTGATGTTTAATGCT ↓ 1 3 4 2 Chimp: AGCACAAGCAACTCACTGAGTTGCTGAACATCTGTTCAGCAAGTACTTGATGTTTAATGCT ↑ 1 3 4 2 Gorilla: AGCACAAGCAACTCACTGAGTA--------GATGTTCAGCAAGTACTTGATGTTTAATGCT Human: AGCACAAGCAACTCACTGAGTA--------GATGTTCAGCAAGTACTTGATGTTTAATGCT Cluster: [ ] Orangutan: AGCACAAGCAACTCACTGAGTA--------GATGTTCAGTAAGTACTTGATGTTTAATGCT Human > Chimp ------------- chr3:51651285-51651295 Template switch process: F1: L GTTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT 1 F3: 4 TGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC R RF: GTTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGTAGATGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC RR: CAATGAAAACAACTTAAGTATCGTGTTCGTTGAGTGACTCATCTACAAGTCGTTCATGAACTACAAATTACGAAATTAAGTGTG F2: 3 CTACAAGTCGT 2 Unidirectional alignment (log-probability: -34.4) TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGTtgctgaacAtcTGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT--------AGATGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC Template switch alignment (log-probability: -16.6) TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT|TGCTGAACATC|TGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT|TGCTGAACATC|TGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC Gorilla > Chimp --------------- chr3:51651285-51651295 Template switch process: F1: L GTTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT 1 F3: 4 TGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC R RF: GTTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGTAGATGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC RR: CAATGAAAACAACTTAAGTATCGTGTTCGTTGAGTGACTCATCTACAAGTCGTTCATGAACTACAAATTACGAAATTAAGTGTG F2: 3 CTACAAGTCGT 2 Unidirectional alignment (log-probability: -33.5) TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGTtgctgaacAtcTGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT--------AGATGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC Template switch alignment (log-probability: -17.1) TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT|TGCTGAACATC|TGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC TTACTTTTGTTGAATTCATAGCACAAGCAACTCACTGAGT|TGCTGAACATC|TGTTCAGCAAGTACTTGATGTTTAATGCTTTAATTCACAC ========== Event 2271 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGTTGTCCCCTTTGCCTTGTGGGATCCCTGGATCCCACAACCCTTGCCCTGCAATTCT Chimp: AGTTGTCCCCTTTGCCTTGTGGGATCCCTGGATCCCACAACCCTTGCCCTGCAATTCT ↑ 3 1 2 4 Gorilla: AGTTGTCCCCTTTGCCTTGTGGGATCCAGGAA----TCAACCCTTGCCCTGCATTTCT ↓ 3 1 2 4 Human: AGTTGTCCCCTTTGCCTTGTGGGATCCCTGGATCCCACAACCCTTGCCCTGCAATTCT Cluster: [ ] Orangutan: AGTTGTCCCCTTTGCCTTGTGGGATCCAGGAA----TCAACCCTTGCCCTGCATTTCT Gorilla > Human --------------- chr3:148948138-148948147 Template switch process: F1: L GCCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCC 1 F3: 4 CAACCCTTGCCCTGCAATTCTGAAGTTCTGCAATTCACAT R RF: GCCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCCAGGAATCAACCCTTGCCCTGCATTTCTGAAGTTCTGCAATTCACAT RR: CGGACCGGACCCCGTCAACAGGGGAAACGGAACACCCTAGGTCCTTAGTTGGGAACGGGACGTAAAGACTTCAAGACGTTAAGTGTA F2: 3 ACCCTAGGTC 2 Unidirectional alignment (log-probability: -38.8) CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCCctGgATcccaCAACCCTTGCCCTGCAaTTCTGAAGTTCTGCAATTCACAT CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCCAGGAAT----CAACCCTTGCCCTGCATTTCTGAAGTTCTGCAATTCACAT Template switch alignment (log-probability: -22.5) CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCC|CTGGATCCCA|CAACCCTTGCCCTGCAaTTCTGAAGTTCTGCAATTCACAT CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCC|CTGGATCCCA|CAACCCTTGCCCTGCATTTCTGAAGTTCTGCAATTCACAT Gorilla > Chimp --------------- chr3:152444996-152445005 Template switch process: F1: L GCCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCC 1 F3: 4 CAACCCTTGCCCTGCAATTCTGAAGTTCTGCAATTCACAT R RF: GCCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCCAGGAATCAACCCTTGCCCTGCATTTCTGAAGTTCTGCAATTCACAT RR: CGGACCGGACCCCGTCAACAGGGGAAACGGAACACCCTAGGTCCTTAGTTGGGAACGGGACGTAAAGACTTCAAGACGTTAAGTGTA F2: 3 ACCCTAGGTC 2 Unidirectional alignment (log-probability: -38.8) CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCCctGgATcccaCAACCCTTGCCCTGCAaTTCTGAAGTTCTGCAATTCACAT CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCCAGGAAT----CAACCCTTGCCCTGCATTTCTGAAGTTCTGCAATTCACAT Template switch alignment (log-probability: -22.5) CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCC|CTGGATCCCA|CAACCCTTGCCCTGCAaTTCTGAAGTTCTGCAATTCACAT CCTGGCCTGGGGCAGTTGTCCCCTTTGCCTTGTGGGATCC|CTGGATCCCA|CAACCCTTGCCCTGCATTTCTGAAGTTCTGCAATTCACAT ========== Event 2272 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAAC------------CCTTCACATAAAGGAGACTGGC Chimp: ACTTGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAAC------------CCTTCACATAAAGGAGACTGGC ↓ 3 2 14 Gorilla: ACTTGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACCTTTGGCATCTCTCTTCACATAAAGGAGACTGGC ↑ 3 2 14 Human: ACTTGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAAC------------CCTTCACATAAAGGAGACTGGC Cluster: [ ] Orangutan: ACTTGGCTTAGTGAAGAAGAGAGATGCCAAAGTAATGAACCAAC------------GCTTCACATAAAGGAGACTGGC Human > Gorilla --------------- chr3:14735418-14735429 Template switch process: F1: L TGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC 1 F3: 4 CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC R RF: TGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACCCTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC RR: ACCGAATCACTTCTTCTCTCTACGGTTTCCTTACTTGGTTGGGAAGTGTATTTCCTCTGACCGACTTCGACTTACTCCTCCG F2: 3 TCTCTACGGTTT 2 Unidirectional alignment (log-probability: -28.2) GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACCtttggcatctctCTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC------------CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC Template switch alignment (log-probability: -17.3) GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC|TTTGGCATCTCT|CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC|TTTGGCATCTCT|CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC Chimp > Gorilla --------------- chr3:14735418-14735429 Template switch process: F1: L TGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC 1 F3: 4 CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC R RF: TGGCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACCCTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC RR: ACCGAATCACTTCTTCTCTCTACGGTTTCCTTACTTGGTTGGGAAGTGTATTTCCTCTGACCGACTTCGACTTACTCCTCCG F2: 3 TCTCTACGGTTT 2 Unidirectional alignment (log-probability: -28.2) GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACCtttggcatctctCTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC------------CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC Template switch alignment (log-probability: -17.3) GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC|TTTGGCATCTCT|CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC GCTTAGTGAAGAAGAGAGATGCCAAAGGAATGAACCAACC|TTTGGCATCTCT|CTTCACATAAAGGAGACTGGCTGAAGCTGAATGAGGAGGC ========== Event 2273 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTAGCCATTTCTTTCTATAGACATGTAAGAAATGTCT-ATAAATGTAAGAATATGAAAATAGATTGGATTT ↑ 3 2 4 1 Chimp: TCCTAGCCATTTCTTTCTATAGACAT---------GGCTACTAAATGTAAGAATATGAAAATAGATTGGATTT Gorilla: TCCTAGCCATTTCTTTCTATAGACAT---------GGCTACTAAATGTAAGAATATGAAAATAGATTGGATTT ↓ 3 2 4 1 Human: TCCTAGCCATTTCTTTCTATAGACATGTAAGAAATGTCT-ATAAATGTAAGAATATGAAAATAGATTGGATTT Cluster: [ ] Orangutan: TCCTAGCCATTTCTTTCTATAGACAT---------GGCTACTAAATGTAAGAATATGAAAATAGATTGGATTT Chimp > Human ------------- chr3:49587942-49587948 Template switch process: F1: L ATAGTGCAGTCTCATTCCTAGCCATTTCTTTCTATAGACAT-----------GTAAGAA 1 F3: 4 TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT R RF: ATAGTGCAGTCTCATTCCTAGCCATTTCTTTCTATAGACATGGCTACTAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT RR: TATCACGTCAGAGTAAGGATCGGTAAAGAAAGATATCTGTACCGATGATTTACATTCTTATACTTTTATCTAACCTAAAAATGAACA F2: 3 ATCTGTA 2 Unidirectional alignment (log-probability: -40.1) GTCTCATTCCTAGCCATTTCTTTCTATAGACATG-----taagaaatgtctaTAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT GTCTCATTCCTAGCCATTTCTTTCTATAGACATGGCTAC-------------TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT Template switch alignment (log-probability: -27.1) GTCTCATTCCTAGCCATTTCTTTCTATAGACAT-----------GTAAGAA|ATGTCTA|TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT GTCTCATTCCTAGCCATTTCTTTCTATAGACATGGCTACTAAATGTAAGAA|ATGTCTA|TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT Gorilla > Human --------------- chr3:49587942-49587948 Template switch process: F1: L ATAGTGCAGTCTCATTCCTAGCCATTTCTTTCTATAGACA-----------TGTAAGAA 1 F3: 4 TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT R RF: ATAGTGCAGTCTCATTCCTAGCCATTTCTTTCTATAGACATGGCTACTAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT RR: TATCACGTCAGAGTAAGGATCGGTAAAGAAAGATATCTGTACCGATGATTTACATTCTTATACTTTTATCTAACCTAAAAATGAACA F2: 3 ATCTGTA 2 Unidirectional alignment (log-probability: -39.2) GTCTCATTCCTAGCCATTTCTTTCTATAGACatgtaagaaATGtCTA-TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT GTCTCATTCCTAGCCATTTCTTTCTATAGAC---------ATGGCTACTAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT Template switch alignment (log-probability: -27.1) GTCTCATTCCTAGCCATTTCTTTCTATAGACA-----------TGTAAGAA|ATGTCTA|TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT GTCTCATTCCTAGCCATTTCTTTCTATAGACATGGCTACTAAATGTAAGAA|ATGTCTA|TAAATGTAAGAATATGAAAATAGATTGGATTTTTACTTGT ========== Event 2274 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAATAGCTTAATTCCTAGATATTATCTCTCTTAAACAAAACAGATTTTAATGCAttt-tt--tttttCAAATGCATGTCCCAACCAGTTACTTCTGAGGAGTAAGAACACATTCTACATCTCTGGAAATTCTACTAAAACCAGTAGGTTACCAGTTTGAGAATACAGTCTTTTAT Chimp: TGAATAGCTTAATTCCTAGATACTGTCTCTCTTAAACAAAACAGATTTTAATGCAttt---tttttttCAAATGCATGTCCCAACCAGTTACTTCTGAGGAGTAAGAACACATTCTACATCTCTGGAAATTCTACTAAAACCAGTAGGTTACCAGTTTGAGAATACAGTCTTTTAT ↑ 1 4 3 2 Gorilla: TGAATAGCTTAATTCCTAGATGTTATCTCTCTTAAACAAAACAGATTTTAATGCAtttt----tttttCAAATGCATGTCCCAACCAGTTACTTCTGAGGAGTAAGAACACATTCTACATCTCTGGAAATTCTACTAAAACCAGTAGGTTATCAGTTTGAGAATACAGTCTTTTAT Human: TGAATAGCTTAATTCCTAGATATTATCTCTCTTAAACAAAACAGATTTTAATGCAttt-tt--tttttCAAATGCATGTCCCAACCAGTTACTTCTGAGGAGTAAGAACACATTCTACATCTCTGGAAATTCTACTAAAACCAGTAGGTTACCAGTTTGAGAATACAGTCTTTTAT Cluster: [ ] Orangutan: TGAATAGCTTAATTCCTAGGTATTATCTCTCTTAAACAAAACAGATTTTAATGCAtttt----tttttCAAACACATGTCCCAACCAGTTACTTCTGAGGAGTAAGAACACATTCTACATCTCTGGAAATTCTACTAAAACCAGTAGGTTACCAGTTTGAGAATACAGGTTTTTAT Gorilla > Chimp --------------- chr3:50552548-50552551 Template switch process: F1: L CTAGAAAGAAAAGGAAATAATGAATAGCTTAATTCCTAGAT 1 F3: 4 TCTCTCTTAAACAAAACAGATTTTAATGCATTTTTTTTT R RF: GTAGAAAGAAAAGGAAATAATGAATAGCTTAATTCCTAGATGTTATCTCTCTTAAACAAAACAGATTTTAATGCATTTTTTTTTCAAATGCATGTCCCAACCAGTTACTTCTGAGGAGTAAGAACACATTCTACATCTCTGGAAATTCTACTAAAACCAGTAGGTTATCAGT RR: CATCTTTCTTTTCCTTTATTACTTATCGAATTAAGGATCTACAATAGAGAGAATTTGTTTTGTCTAAAATTACGTAAAAAAAAAGTTTACGTACAGGGTTGGTCAATGAAGACTCCTCATTCTTGTGTAAGATGTAGAGACCTTTAAGATGATTTTGGTCATCCAATAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -31.4) TAGAAAGAAAAGGAAATAATGAATAGCTTAATTCCTAGATacTgTCTCTCTTAAACAAAACAGATTTTAATGCATTTTTTTTt TAGAAAGAAAAGGAAATAATGAATAGCTTAATTCCTAGATGTTATCTCTCTTAAACAAAACAGATTTTAATGCATTTTTTTT- Template switch alignment (log-probability: -21.7) TAGAAAGAAAAGGAAATAATGAATAGCTTAATTCCTAGAT|ACTG|TCTCTCTTAAACAAAACAGATTTTAATGCATTTTTTTTT TAGAAAGAAAAGGAAATAATGAATAGCTTAATTCCTAGAT|ACTG|TCTCTCTTAAACAAAACAGATTTTAATGCATTTTTTTTT ========== Event 2275 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TTAGACAACAGGTAAGCCTATCT------------GTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGAT Chimp: ------------------------------------------------------------------------ Gorilla: TTAGACAACAGGTAAGCCTATCTGTCTTAGCATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGAT ↑ 4 1 3 2 Human: TTAGACAACAGGTAAGCCTATCT------------GTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGAT Cluster: [ ] Orangutan: TTAGACAACAGGTAAGCCTATCT------------GTCTGTTCTGGATGCTAAATAACTCTTCTGGAAGGAT Human > Gorilla --------------- chr3:48905550-48905553 Template switch process: F1: L GGGGACTGAAACTTTATTTTAGACAACAGGTAAGCCTATCTGTCT 1 F3: 4 ATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGATACA R RF: GGGGATTGAAACTTTATTTTAGACAACAGGTAAGCCTATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGATACA RR: CCCCTAACTTTGAAATAAAATCTGTTGTCCATTCGGATAGACAGACAAGACCTACGATTTCTTGAGAAGACCTTCCTATGT F2: 3 CGAT 2 Unidirectional alignment (log-probability: -33.7) cTGAAACTTTATTTTAGACAACAGGTAAGCCTatctgtcttagcATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGA TTGAAACTTTATTTTAGACAACAGGTAAGCCT------------ATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGA Template switch alignment (log-probability: -21.9) cTGAAACTTTATTTTAGACAACAGGTAAGCCTATCTGTCT|TAGC|ATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGA TTGAAACTTTATTTTAGACAACAGGTAAGCCTATCTGTCT|TAGC|ATCTGTCTGTTCTGGATGCTAAAGAACTCTTCTGGAAGGA ========== Event 2276 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCACCAGGAAAAATATTATGCATGCTCAGTGAATTATTCCTACTCAGCAATATTGGCCTAGTGATGTCCATGAATCATGACTAGGGAAGCATCTATGACTTTTGTAGCTAAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTCCATTggccaggcatggtggctcatgcc---------ggtaa Chimp: TCCACAAGGAAAAATATTATTCATGCTCAGTAAATTATTCCTACTCAGCAATATTGGCCTAGTGATGTCCATGAATCATGACTAGGGAAGCATCTATGACTTTTGTAGCTAAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTCCATTggccaggcatcgtggctcatgcc---------tgtaa Gorilla: TCCACAAGGAAAAATATTATTCATGCTCAGTGAATTATTCCTACTCAGCAATATTGGCCTAGTGATGTCCATGAATCATGACTAGGGAAGCATCTATGACTTTTGTCGCTAAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTTTATTGGCCAGGCATGAGCCACCATGcc-------------- ↑ 4 3 1 2 Human: TCCACCAGGAAAAATATTATGCATGCTCAGTGAATTATTCCTACTCAGCAATATTGGCCTAGTGATGTCCATGAATCATGACTAGGGAAGCATCTATGACTTTTGTAGCTAAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTCCATTggccaggcatggtggctcatgcc---------ggtaa Cluster: [] Orangutan: TCCACAAGGAAAAATATTATTCATGCTCAGTGAATTATTCCTACTCAGCAATATTGGCCTAGTGATGTCCATGAATCATGACTAGCAAAGCATCTATGACTTTTGTAGCTAAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTCCATTggccaggc-aggtggctcatgcctgtaatccc----- Human > Gorilla --------------- chr3:50966476-50966488 Template switch process: F1: L AAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTTTATTGGCCAGGCATG 1 F3: 4 GCAC R RF: AAATTACCCAGGAAGAGATTAATTTTTAAAATGCTTAAGCTCCATTGGCCAGGCATGGTGGCTCATGCCGGTAATCCCAGCAC RR: TTTAATGGGTCCTTCTCTAATTAAAAATTTTACGAATTCGAGGTAACCGGTCCGTACCACCGAGTACGGCCATTAGGGTCGTG F2: 3 TCCGTACCACCGA 2 Unidirectional alignment (log-probability: -49.7) ATTAATTTTTAAAATGCTTAAGCTttATTGGCCAGGCATG---------------------AgccaccatgcctGCAC ATTAATTTTTAAAATGCTTAAGCTCCATTGGCCAGGCATGGTGGCTCATGCCGGTAATCCCA------------GCAC Template switch alignment (log-probability: -27.9) ATTAATTTTTAAAATGCTTAAGCTttATTGGCCAGGCATG|AGCCACCATGCCT|GCAC ATTAATTTTTAAAATGCTTAAGCTCCATTGGCCAGGCATG|AGCCACCATGCCT|GCAC ========== Event 2277 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tgGTCTTTCAGGCAAACAGTGG--------------------CAGCTCTTGAGATGTGGGCTCTG ↓ 34 21 Chimp: tgGTCTTTCAGGCAAACAGTGG----------CAGTGCCAGGCAGCTCTTGAGATGTGGGCTCTG Gorilla: tgGTCTTTCAGGCAAACAGTGGCAGTGCCAGG----------CAGCTCTTGAGATGTGGGCTCTG Human: tgGTCTTTCAGGCAAACAGTGG--------------------CAGCTCTTGAGATGTGGGCTCTG Cluster: [ ] Orangutan: tggtctttcaggcaaacagtggcagtgccagg----------CAGCTCTTGAGATGTGGGCTCTG Human > Chimp ------------- chr3:154275438-154275442 Template switch process: F1: L AAATCAAGGCCCTGGGAGGTGGTCTTTCAGGCAAACAGTGGCAG 1 F3: 4 GGCAGCTCTTGAGATGTGGGCTCTGGTACTTTATTCAACGTT R RF: AAATCAAGGCCCTGGGAGGTGGTCTTTCAGGCAAACAGTGGCAGCTCTTGAGATGTGGGCTCTGGTACTTTATTCAACGTT RR: TTTAGTTCCGGGACCCTCCACCAGAAAGTCCGTTTGTCACCGTCGAGAACTCTACACCCGAGACCATGAAATAAGTTGCAA F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -25.3) CAAGGCCCTGGGAGGTGGTCTTTCAGGCAAACAGTggcagtgccaGGCAGCTCTTGAGATGTGGGCTCTGGTACTTTATTCAACG CAAGGCCCTGGGAGGTGGTCTTTCAGGCAAACAGT----------GGCAGCTCTTGAGATGTGGGCTCTGGTACTTTATTCAACG Template switch alignment (log-probability: -16) CAAGGCCCTGGGAGGTGGTCTTTCAGGCAAACAGTGGCAG|TGCCA|GGCAGCTCTTGAGATGTGGGCTCTGGTACTTTATTCAACG CAAGGCCCTGGGAGGTGGTCTTTCAGGCAAACAGTGGCAG|TGCCA|GGCAGCTCTTGAGATGTGGGCTCTGGTACTTTATTCAACG ========== Event 2278 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TAAAACATCAGTTTGAGATTATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGA Chimp: TAAAACATCAGTTTGAGATTATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGA ↓ 13 24 ↑ 13 24 Gorilla: TAAAACATCAGTTTGAGATTAGTATATTTTAGTGTTAATGTCATAAAGATTACCAATTTATGGA ↓ 13 24 ↑ 13 24 Human: TAAAACATCAGTTTGAGATTATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGA Cluster: [ ] Orangutan: TAAAACATCACTCTGAGATTAGTATACTTCAGTGTTAATTTCATAAAGATTACCAATTTATGGA Gorilla > Human --------------- chr3:46769164-46769185 Template switch process: F1: L TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA 1 F3: 4 TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA R RF: TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTAGTATATTTTAGTGTTAATGTCATAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA RR: AAAGTAATATGGTTCAGAAAATTTTGTAGTCAAACTCTAATCATATAAAATCACAATTACAGTATTTCTAATGGTTAAATACCTGTTTCAATATGTTGACTTT F2: 3 CATATAAAGTCGCAATTACAGT 2 Unidirectional alignment (log-probability: -51.5) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATT-----------------ATGaCAttaacgctgaaatatacTAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTAGTATATTTTAGTGTTAATGTCA-----------------TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Template switch alignment (log-probability: -29.6) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|TGACATTAACgCTgAAATATAC|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|TGACATTAACACTAAAATATAC|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Human > Gorilla --------------- chr3:47553441-47553462 Template switch process: F1: L TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA 1 F3: 4 TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA R RF: TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA RR: AAAGTAATATGGTTCAGAAAATTTTGTAGTCAAACTCTAATACTGTAATTGCGACTTTATATGATTTCTAATGGTTAAATACCTGTTTCAATATGTTGACTTT F2: 3 ACTGTAATTGTGATTTTATATG 2 Unidirectional alignment (log-probability: -51.5) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTagtatattttagtgttaATGtCA-----------------TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATT-----------------ATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Template switch alignment (log-probability: -29.6) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|GTATATTTtAGtGTTAATGTCA|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|GTATATTTCAGCGTTAATGTCA|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Gorilla > Chimp --------------- chr3:47566894-47566915 Template switch process: F1: L TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA 1 F3: 4 TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA R RF: TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTAGTATATTTTAGTGTTAATGTCATAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA RR: AAAGTAATATGGTTCAGAAAATTTTGTAGTCAAACTCTAATCATATAAAATCACAATTACAGTATTTCTAATGGTTAAATACCTGTTTCAATATGTTGACTTT F2: 3 CATATAAAGTCGCAATTACAGT 2 Unidirectional alignment (log-probability: -51.5) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATT-----------------ATGaCAttaacgctgaaatatacTAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTAGTATATTTTAGTGTTAATGTCA-----------------TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Template switch alignment (log-probability: -29.6) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|TGACATTAACgCTgAAATATAC|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|TGACATTAACACTAAAATATAC|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Chimp > Gorilla --------------- chr3:47553441-47553462 Template switch process: F1: L TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA 1 F3: 4 TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA R RF: TTTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA RR: AAAGTAATATGGTTCAGAAAATTTTGTAGTCAAACTCTAATACTGTAATTGCGACTTTATATGATTTCTAATGGTTAAATACCTGTTTCAATATGTTGACTTT F2: 3 ACTGTAATTGTGATTTTATATG 2 Unidirectional alignment (log-probability: -51.5) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTagtatattttagtgttaATGtCA-----------------TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATT-----------------ATGACATTAACGCTGAAATATACTAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA Template switch alignment (log-probability: -29.6) TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|GTATATTTtAGtGTTAATGTCA|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA TTCATTATACCAAGTCTTTTAAAACATCAGTTTGAGATTA|GTATATTTCAGCGTTAATGTCA|TAAAGATTACCAATTTATGGACAAAGTTATACAACTGAAA ========== Event 2279 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATTTTAAACATAGAAAAGGCAGAATATCAATGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTTTCCACAAATAAGTTAACTGATTGATTAATATTCTAATTTATAAAGAGCATC-- ↑ 1 4 3 2 Chimp: ATTTTAAACATAGAAAAGGCAA------CGTGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTTTCCACAAATAAGTTAACTGATTGATTAATATTCTAATTTATAAAGAGCATC-- ↓ 1 4 3 2 Gorilla: ATTTTAAACATAGAAAAGGCAGAATATCAATGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTT-TCACAAATAAGTTGACTGATTGATTAATATTCTAATTTATAAAGAGCATCTA Human: ATTTTAAACATAGAAAAGGCAGAATATCAATGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTTTCCACAAATAAGTTAACTGATTGATTAATATTCTAATTTATAAAGAGCATC-- Cluster: [ ] Orangutan: ATTTTAAACATAGAAAAGGCAGAATATCAATGCAAAAGACTAATATATTTGGGCACATACAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTTTCCACAAATAAGTTAAATGATTGATTAATATTCTAATTTATAAAGAGCATCTA Chimp > Human ------------- chr3:151616575-151616583 Template switch process: F1: L CTTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA 1 F3: 4 TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA R RF: CTTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCAACGTGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTTTCCACAAATAAGTTAACTGATTGATTAATATTC RR: GAATCCGGGGAAATTTCCTATAAAATTTGTATCTTTTCCGTTGCACGTTTTCTGATTATATAAACCCGTGTATTTTCAATTTGTTTTTGGAAAAGATGTAATTTTATAAATTTAAGTAATAACTGTTCGACTCATTTTTACGAAAGGTGTTTATTCAATTGACTAACTAATTATAAG F2: 3 AACTATAAG 2 Unidirectional alignment (log-probability: -32.8) TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGcagaatatCAA--TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGG--------CAACGTGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA Template switch alignment (log-probability: -22.4) TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA|GAATATcAA|TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA|GAATATTAA|TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA Chimp > Gorilla --------------- chr3:153934642-153934650 Template switch process: F1: L CTTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA 1 F3: 4 TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA R RF: CTTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCAACGTGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACAAAAACCTTTTCTACATTAAAATATTTAAATTCATTATTGACAAGCTGAGTAAAAATGCTTTCCACAAATAAGTTAACTGATTGATTAATATTC RR: GAATCCGGGGAAATTTCCTATAAAATTTGTATCTTTTCCGTTGCACGTTTTCTGATTATATAAACCCGTGTATTTTCAATTTGTTTTTGGAAAAGATGTAATTTTATAAATTTAAGTAATAACTGTTCGACTCATTTTTACGAAAGGTGTTTATTCAATTGACTAACTAATTATAAG F2: 3 AACTATAAG 2 Unidirectional alignment (log-probability: -32.2) TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA--GaatatcaaTGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCAACG--------TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA Template switch alignment (log-probability: -22.4) TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA|GAATATcAA|TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA TTAGGCCCCTTTAAAGGATATTTTAAACATAGAAAAGGCA|GAATATTAA|TGCAAAAGACTAATATATTTGGGCACATAAAAGTTAAACA ========== Event 2280 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTGGCATTTAAATGTATACT------CTACTTCTTCCTTGTGAAATTCTGAAGC------ATATTTTTGAATGTTGAGTTCCT Chimp: TTTGGCATTTAAATGTATACT------CTACTTCTTCCTTGTGAAATTCTGAAGC------ATATTTTTGAATGTTGAGTTCCT ↓ 13 24 ↑ 13 24 Gorilla: TTTGGCATTTAAATGTATACT------------CATGCTTCAGAATTTCACAAGGAAGAAGTAATTTTTGAATGTTGAGTTCCT ↓ 13 24 ↑ 13 24 Human: TTTGGCATTTAAATGTATACT------CTACTTCTTCCTTGTGAAATTCTGAAGC------ATATTTTTGAATGTTGAGTTCCT Cluster: [ ] Orangutan: TTTGGCATTTAAATGTATACTCTACTT------CTTCCTTGTGAAATTCTGAACC------ATATTTTTGAATGTTGAGTTCCT Gorilla > Human --------------- chr3:152437148-152437176 Template switch process: F1: L ATTGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC 1 F3: 4 ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC R RF: ATTGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTCATGCTTCAGAATTTCACAAGGAAGAAGTAATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT RR: TAACTGGTTTACAAACCAGTAAACCGTAAATTTACATATGAGTACGAAGTCTTAAAGTGTTCCTTCTTCATTAAAAACTTACAACTCAAGGAAGACTCCACTTTTTAAAAA F2: 3 TACGAAGTCTTAAAGTGTTCCTTCTTCAT 2 Unidirectional alignment (log-probability: -66.4) TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC---------------------------TActtcttccttgtgaaattctgaagcatATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTc TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTCATGCTTCAGAATTTCACAAGGAAGAAGTA---------------------------ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT Template switch alignment (log-probability: -25) TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC|TACTTCTTCCTTGTGAAATTCTGAAGCAT|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTc TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC|TACTTCTTCCTTGTGAAATTCTGAAGCAT|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT Human > Gorilla --------------- chr3:154779691-154779719 Template switch process: F1: L ATTGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC 1 F3: 4 ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT R RF: ATTGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTCTACTTCTTCCTTGTGAAATTCTGAAGCATATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC RR: TAACTGGTTTACAAACCAGTAAACCGTAAATTTACATATGAGATGAAGAAGGAACACTTTAAGACTTCGTATAAAAACTTACAACTCAAGGAAGACTCCACTTTTTAAAAG F2: 3 ATGAAGAAGGAACACTTTAAGACTTCGTA 2 Unidirectional alignment (log-probability: -66.4) TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACT---------------------------CATgcttcagaatttcacaaggaagaagtaATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTt TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTCTACTTCTTCCTTGTGAAATTCTGAAGCAT---------------------------ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC Template switch alignment (log-probability: -25) TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC|ATGCTTCAGAATTTCACAAGGAAGAAGTA|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTt TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC|ATGCTTCAGAATTTCACAAGGAAGAAGTA|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC Gorilla > Chimp --------------- chr3:155969418-155969446 Template switch process: F1: L ATTGACCAAACGTTTGGTCATTTGGCATTTAAATGTATACTC 1 F3: 4 ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC R RF: ATTGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTCATGCTTCAGAATTTCACAAGGAAGAAGTAATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT RR: TAACTGGTTTACAAACCAGTAAACCGTAAATTTACATATGAGTACGAAGTCTTAAAGTGTTCCTTCTTCATTAAAAACTTACAACTCAAGGAAGACTCCACTTTTTAAAAA F2: 3 TACGAAGTCTTAAAGTGTTCCTTCTTCAT 2 Unidirectional alignment (log-probability: -71.9) TGACCAAAcGTTTGGTCATTTGGCATTTAAATGTATACTC---------------------------TActtcttccttgtgaaattctgaagcatATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTc TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTCATGCTTCAGAATTTCACAAGGAAGAAGTA---------------------------ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT Template switch alignment (log-probability: -30.5) TGACCAAAcGTTTGGTCATTTGGCATTTAAATGTATACTC|TACTTCTTCCTTGTGAAATTCTGAAGCAT|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTc TGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC|TACTTCTTCCTTGTGAAATTCTGAAGCAT|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT Chimp > Gorilla --------------- chr3:154779691-154779719 Template switch process: F1: L ATTGACCAAATGTTTGGTCATTTGGCATTTAAATGTATACTC 1 F3: 4 ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTT R RF: ATTGACCAAACGTTTGGTCATTTGGCATTTAAATGTATACTCTACTTCTTCCTTGTGAAATTCTGAAGCATATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC RR: TAACTGGTTTGCAAACCAGTAAACCGTAAATTTACATATGAGATGAAGAAGGAACACTTTAAGACTTCGTATAAAAACTTACAACTCAAGGAAGACTCCACTTTTTAAAAG F2: 3 ATGAAGAAGGAACACTTTAAGACTTCGTA 2 Unidirectional alignment (log-probability: -71.9) TGACCAAAtGTTTGGTCATTTGGCATTTAAATGTATACT---------------------------CATgcttcagaatttcacaaggaagaagtaATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTt TGACCAAACGTTTGGTCATTTGGCATTTAAATGTATACTCTACTTCTTCCTTGTGAAATTCTGAAGCAT---------------------------ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC Template switch alignment (log-probability: -30.5) TGACCAAAtGTTTGGTCATTTGGCATTTAAATGTATACTC|ATGCTTCAGAATTTCACAAGGAAGAAGTA|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTt TGACCAAACGTTTGGTCATTTGGCATTTAAATGTATACTC|ATGCTTCAGAATTTCACAAGGAAGAAGTA|ATTTTTGAATGTTGAGTTCCTTCTGAGGTGAAAAATTTTC ========== Event 2281 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCTCATTTATCTTGGATATGGCATAAATTCTTAAACAAGTTCTTGAGTTAATGCTGCAGAGAGGTTAGACCGAATCAAAT Chimp: ATTCTCATTTATCTCGGATATGGCATAAACTCTTATG--------------------CCATAGAGGTTAGACCGAATCAAAT ↑ 3 2 1 4 Gorilla: ATTCTCATTTATCTTGGATATGGCATAAACTCTTAAACAAGTTCTTGAGTTAATGCTGCAGAGAGGTTAGACCGAATCAAAT Human: ATTCTCATTTATCTTGGATATGGCATAAATTCTTAAACAAGTTCTTGAGTTAATGCTGCAGAGAGGTTAGACCGAATCAAAT Cluster: [ ] Orangutan: ATCCTCATTTATCTTGGATATGACATAAACTCTTAAACAAGTTCTTGAGTTAATGCTGCAGAGAGGTTAGACCGAATCAAAT Gorilla > Chimp --------------- chr3:46495414-46495419 Template switch process: F1: L AGGCCAATTCTCATTTATCTCGGATATGGCATAAACTCTTA 1 F3: 4 AGAGGTTAGACCGAATCAAATCCTTAAGTGTCTCCAAAAC R RF: AGGCCAATTCTCATTTATCTTGGATATGGCATAAACTCTTAAACAAGTTCTTGAGTTAATGCTGCAGAGAGGTTAGACCGAATCAAATCCTTAAGTGTCTCCAAAAC RR: TCCGGTTAAGAGTAAATAGAACCTATACCGTATTTGAGAATTTGTTCAAGAACTCAATTACGACGTCTCTCCAATCTGGCTTAGTTTAGGAATTCACAGAGGTTTTG F2: 3 TACCGT 2 Unidirectional alignment (log-probability: -32.8) GGCCAATTCTCATTTATCTcGGATATGGCATAAACTCTT------------------ATGC--CAtAGAGGTTAGACCGAATCAAATCCTTAAGTGTCTCCAAAAC GGCCAATTCTCATTTATCTTGGATATGGCATAAACTCTTAAACAAGTTCTTGAGTTAATGCTGCAGAGAGGTTAGACCGAATCAAATCCTTAAGTGTCTCCAAAAC Template switch alignment (log-probability: -22) GGCCAATTCTCATTTATCTcGGATATGGCATAAACTCTTA|TGCCAT|AGAGGTTAGACCGAATCAAATCCTTAAGTGTCTCCAAAAC GGCCAATTCTCATTTATCTTGGATATGGCATAAACTCTTA|TGCCAT|AGAGGTTAGACCGAATCAAATCCTTAAGTGTCTCCAAAAC ========== Event 2282 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAACCTTGGCCTACAGTGGGTA----GGACACATCCTCAACTTGGGGGGC Chimp: ACAACCTTGGCCTACAGTGGGTA----GGACACATCCTCAACTTGGGGGGC ↓ 3 1 4 Gorilla: ACAACCTTGGCCTACAGTGGGTGTCCTACCCACATCCTCAACTTGGGGGGC ↑ 3 1 4 Human: ACAACCTTGGCCTACAGTGGGTA----GGACACATCCTCAACTTGGGGGGC Cluster: [ ] Orangutan: ACAACCTCAGCCTACAGTGGGTA----GGACACATCCTCAACTTGGGGGGC Human > Gorilla --------------- chr3:15576508-15576515 Template switch process: F1: L GTTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT 1 F3: 4 CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA R RF: GTTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGTAGGACACATCCTCAACTTGGGGGGCATCTCAAAGATTAATCCAA RR: CAAAGTCCAGTTCTTACTATGTTGGAACCGGATGTCACCCATCCTGTGTAGGAGTTGAACCCCCCGTAGAGTTTCTAATTAGGTT F2: 3 CCATCCTG 2 Unidirectional alignment (log-probability: -37.9) TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT----gtcctaccCACATCCTCAACTTGGGGGGCATCTCAAAGATTAATgCAA TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGTAGGA--------CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATCCAA Template switch alignment (log-probability: -22.3) TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT|GTCCTACC|CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATgCAA TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT|GTCCTACC|CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATCCAA Chimp > Gorilla --------------- chr3:15576508-15576515 Template switch process: F1: L GTTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT 1 F3: 4 CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA R RF: GTTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGTAGGACACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA RR: CAAAGTCCAGTTCTTACTATGTTGGAACCGGATGTCACCCATCCTGTGTAGGAGTTGAACCCCCCGTAGAGTTTCTAATTACGTT F2: 3 CCATCCTG 2 Unidirectional alignment (log-probability: -32.3) TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT----gtcctaccCACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGTAGGA--------CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA Template switch alignment (log-probability: -16.7) TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT|GTCCTACC|CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA TTTCAGGTCAAGAATGATACAACCTTGGCCTACAGTGGGT|GTCCTACC|CACATCCTCAACTTGGGGGGCATCTCAAAGATTAATGCAA ========== Event 2283 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CTTTTCAGTACCCTTAAAGACAAATGCTATACAAACAGCAAGAACTTGAAATGTACAACTTTTCTAAATATATAATATCAAAAACTAAATTTAAAAAGTACATACCCATATATGCTGCCCAATGGATAGCACGCCTATCTTTCTTGTCAAA ↑ 4 1 3 2 Chimp: CTTTTCAGTACCCTTAAAGAC-----------AAACAGCAAGAACTTAAAATGTACAACTTTTCTAAATATATAATATCAAAAACTAAATTTAAAAAGTACATACCCATATATGCTGCCCAATGGATAGCACGCCTATCTTTCTTGTCAAA Gorilla: CTTTTCAGTACCCTTAAAGACAAATGTTATACAAACAGCAAGAACTTAAAATGTACAACTTTTCTAAATATATAATATCAAAAACTAAATTTAAAAAGTACATACCCATATATGCTGCCCAATGGATAGCACGCCTATCTTTCTTGTCAAA Human: CTTTTCAGTACCCTTAAAGACAAATGCTATACAAACAGCAAGAACTTGAAATGTACAACTTTTCTAAATATATAATATCAAAAACTAAATTTAAAAAGTACATACCCATATATGCTGCCCAATGGATAGCACGCCTATCTTTCTTGTCAAA Cluster: [ ] Orangutan: CTTTTCAGTACCCTTAAAGACAAATGTTATACAAACAGCAAGAACTTAAAATGTACAACTTTTCTAAATATATAATATCAAAAACTAAATTTAAAAAGTACATACCCATATATGCTGCCCAATGGATAGCACGCCTATCTTTCTTGTCAAA Chimp > Human ------------- chr3:15735329-15735334 Template switch process: F1: L CAAACTCAGATACTGTGTAGCTTTTCAGTACCCTTAAAGACAAA 1 F3: 4 ACAAACAGCAAGAACTTGAAATGTACAACTTTTCTAAATATA R RF: CAAACTCAGATACTGTGTAGCTTTTCAGTACCCTTAAAGACAAACAGCAAGAACTTAAAATGTACAACTTTTCTAAATATATAATATCAAAAACTAAATTTAAAAAGTACATACCCATATATGCTGCCCAATGGATAGCA RR: GTTTGAGTCTATGACACATCGAAAAGTCATGGGAATTTCTGTTTGTCGTTCTTGAATTTTACATGTTGAAAAGATTTATATATTATAGTTTTTGATTTAAATTTTTCATGTATGGGTATATACGACGGGTTACCTATCGT F2: 3 TATCGT 2 Unidirectional alignment (log-probability: -32.7) CTCAGATACTGTGTAGCTTTTCAGTACCCTTAAAGacaaatgctatACAAACAGCAAGAACTTgAAATGTACAACTTTTCTAAATA CTCAGATACTGTGTAGCTTTTCAGTACCCTTAAAG-----------ACAAACAGCAAGAACTTAAAATGTACAACTTTTCTAAATA Template switch alignment (log-probability: -22.1) CTCAGATACTGTGTAGCTTTTCAGTACCCTTAAAGACAAA|TGCTAT|ACAAACAGCAAGAACTTgAAATGTACAACTTTTCTAAATA CTCAGATACTGTGTAGCTTTTCAGTACCCTTAAAGACAAA|TGCTAT|ACAAACAGCAAGAACTTAAAATGTACAACTTTTCTAAATA ========== Event 2284 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTCCGTATTAGATATATTTAAGTTCTGTATGCTATAGCCGCATACAGAACTAacttcctt--------ccttccttct Chimp: TTTCTGTATTAGATATATTTAAGTTCTGTATGCTGTAGCCGCATACAGAACTAActtcctt----ccttccttccttct Gorilla: TTTCCATATTAGATATATTTAAGTTCTGTATGCGGCTATAGCATACAGAACTAActtccttcctt----ccttccttct ↓ 3 1 2 4 Human: TTTCCGTATTAGATATATTTAAGTTCTGTATGCTATAGCCGCATACAGAACTAacttcctt--------ccttccttct Cluster: [ ] Orangutan: TTTCCGTATTAGATGTATTTAAGTTCTGTATGCTATAGCCACATACAGAACTAActtcc------------ttccttct Gorilla > Human --------------- chr3:154686354-154686374 Template switch process: F1: L TCTTCCATTTTCCGTATTAGATATATTTAAGTTCTGTATGC 1 F3: 4 CTTCCTTCCTTCCTTCTTTCCT R RF: TCTTCCATTTTCCATATTAGATATATTTAAGTTCTGTATGCGGCTATAGCATACAGAACTAACTTCCTTCCTTCCTTCCTTCTTTCCT RR: AGAAGGTAAAAGGTATAATCTATATAAATTCAAGACATACGCCGATATCGTATGTCTTGATTGAAGGAAGGAAGGAAGGAAGAAAGGA F2: 3 AATCAAGACATACGCCGATAT 2 Unidirectional alignment (log-probability: -40.6) CTTCCATTTTCCgTATTAGATATATTTAAGTTCTGTAT---GCTATAgccGCATACAGAACTAA----CTTCCTTCCTTCCTTCTTTCCT CTTCCATTTTCCATATTAGATATATTTAAGTTCTGTATGCGGCTATA---GCATACAGAACTAACTTCCTTCCTTCCTTCCTTCTTTCCT Template switch alignment (log-probability: -29) CTTCCATTTTCCgTATTAGATATATTTAAGTTCTGTATGC|TATAGCCGCATACAGAACTaA|CTTCCTTCCTTCCTTCTTTCCT CTTCCATTTTCCATATTAGATATATTTAAGTTCTGTATGC|TATAGCCGCATACAGAACTTA|CTTCCTTCCTTCCTTCTTTCCT ========== Event 2285 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCACAAAGAGAAAGTGAAATGG---------TGGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTT ↓ 1 4 3 2 Chimp: TTCACAAAGAGAAAGTGAAATTGTTTAGGGGCAAGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTT ↑ 1 4 3 2 Gorilla: TTCACAAAGAGAAAGTGAAATGG---------TGGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTT Human: TTCACAAAGAGAAAGTGAAATGG---------TGGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTT Cluster: [ ] Orangutan: TTCACAAAGAGAAAGTGAAATGG---------TAGTGATTCTTGC-CCTAAAATAATAGATAGTGTAGGTT Human > Chimp ------------- chr3:43898283-43898292 Template switch process: F1: L GCAGCACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATTGT 1 F3: 4 GTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC R RF: GCAGCACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATGGTGGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC RR: CGTCGTGTCTCTTCTCTTTTAAGTGTTTCTCTTTCACTTTACCACCACTAAGAACGGGGATTTTATTATCTATCACATCCAATGG F2: 3 AACGGGGATT 2 Unidirectional alignment (log-probability: -35.9) CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATtGTttaggggcaaGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATGGT---------GGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC Template switch alignment (log-probability: -22.6) CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATtGT|TTAGGGGCAA|GTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATGGT|TTAGGGGCAA|GTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC Gorilla > Chimp --------------- chr3:43898283-43898292 Template switch process: F1: L GCAGCACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATTGT 1 F3: 4 GTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC R RF: GCAGCACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATGGTGGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC RR: CGTCGTGTCTCTTCTCTTTTAAGTGTTTCTCTTTCACTTTACCACCACTAAGAACGGGGATTTTATTATCTATCACATCCAATGG F2: 3 AACGGGGATT 2 Unidirectional alignment (log-probability: -34.9) CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATtGTttaggggcaaGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATGGT---------GGTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC Template switch alignment (log-probability: -22.6) CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATtGT|TTAGGGGCAA|GTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC CACAGAGAAGAGAAAATTCACAAAGAGAAAGTGAAATGGT|TTAGGGGCAA|GTGATTCTTGCCCCTAAAATAATAGATAGTGTAGGTTACC ========== Event 2286 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GATCAACTTTGGGAAACTTACCGCAAAACCTTCTTCAGAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAGAGAAGAATGTGCCACTCTCA Chimp: GATCAACTTTGGGAAACTTACCGCAAAACCTTCTTCAGAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAGAGAAGAATGTGCCACTCTCA ↑ 1 4 3 2 Gorilla: GATCAACTTTGGGAAACTTACTGCAAAATCTTTGCGGTAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAGAGAAGAATGTGCCACTCTCA ↓ 1 4 3 2 Human: GATCAACTTTGGGAAACTTACCGCAAAACCTTCTTCAGAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAGAGAAGAATGTGCCACTCTCA Cluster: [ ] Orangutan: GATCAACTTTGGGAAACTTACCACAAAACCTTCTTCAGAAGGAACAGCTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAGAGAAGAATGTGCCACTCTCA Gorilla > Human --------------- chr3:42182937-42182942 Template switch process: F1: L AAGGAAAAAACAGGGGAAGAGATCAACTTTGGGAAACTTACCGCAAAACCTT 1 F3: 4 AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA R RF: AAGGAAAAAACAGGGGAAGAGATCAACTTTGGGAAACTTACTGCAAAATCTTTGCGGTAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAG RR: TTCCTTTTTTGTCCCCTTCTCTAGTTGAAACCCTTTGAATGACGTTTTAGAAACGCCATTCCTTGTTGAAATTCCCATCTTCTAGAACATTTTGTCATAAAAGTTTGACTTC F2: 3 GACTTC 2 Unidirectional alignment (log-probability: -40.8) GGGGAAGAGATCAACTTTGGGAAACTTACcGCAAAAcCTTcttcag------AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA GGGGAAGAGATCAACTTTGGGAAACTTACTGCAAAATCTT------TGCGGTAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA Template switch alignment (log-probability: -27.8) GGGGAAGAGATCAACTTTGGGAAACTTACcGCAAAAcCTT|CTTCAG|AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA GGGGAAGAGATCAACTTTGGGAAACTTACTGCAAAATCTT|CTTCAG|AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA Gorilla > Chimp --------------- chr3:42945109-42945114 Template switch process: F1: L AAGGAAAAAACAGGGGAAGAGATCAACTTTGGGAAACTTACCGCAAAACCTT 1 F3: 4 AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA R RF: AAGGAAAAAACAGGGGAAGAGATCAACTTTGGGAAACTTACTGCAAAATCTTTGCGGTAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTATTTTCAAACTGAAG RR: TTCCTTTTTTGTCCCCTTCTCTAGTTGAAACCCTTTGAATGACGTTTTAGAAACGCCATTCCTTGTTGAAATTCCCATCTTCTAGAACATTTTGTCATAAAAGTTTGACTTC F2: 3 GACTTC 2 Unidirectional alignment (log-probability: -40.8) GGGGAAGAGATCAACTTTGGGAAACTTACcGCAAAAcCTTcttcag------AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA GGGGAAGAGATCAACTTTGGGAAACTTACTGCAAAATCTT------TGCGGTAAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA Template switch alignment (log-probability: -27.8) GGGGAAGAGATCAACTTTGGGAAACTTACcGCAAAAcCTT|CTTCAG|AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA GGGGAAGAGATCAACTTTGGGAAACTTACTGCAAAATCTT|CTTCAG|AAGGAACAACTTTAAGGGTAGAAGATCTTGTAAAACAGTA ========== Event 2287 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gagataatgcacgacaagaca--------ttttataaacaaggatactacaaattgtaggTATTT Chimp: gagataatgcacgACAAGACA--------TCTTATAAACAAGGATACTACAAATTGTAGGTATTT ↓ 1 4 3 2 Gorilla: gagataatgcacgACAAGACATATCCTTGTTTTATAAACAAGGATACTACAAATTGTAGGTATTT Human: gagataatgcacgacaagaca--------ttttataaacaaggatactacaaattgtaggTATTT Cluster: [ ] Orangutan: gagatattgcacaagaagaca--------ttttataaacaaggatactacaaattgtaggTATTT Chimp > Gorilla --------------- chr3:42737193-42737201 Template switch process: F1: L TATGTTGTGTGAAGGCAAATGAGATAATGCACGACAAGACAT 1 F3: 4 TTATAAACAAGGATACTACAAATTGTAGGTATTTGTGTTA R RF: TATGTTGTGTGAAGGCAAATGAGATAATGCACGACAAGACATCTTATAAACAAGGATACTACAAATTGTAGGTATTTGTGTTA RR: ATACAACACACTTCCGTTTACTCTATTACGTGCTGTTCTGTAGAATATTTGTTCCTATGATGTTTAACATCCATAAACACAAT F2: 3 TTGTTCCTA 2 Unidirectional alignment (log-probability: -27.9) TGTTGTGTGAAGGCAAATGAGATAATGCACGACAAGACAtatccttgTtTTATAAACAAGGATACTACAAATTGTAGGTATTTGTGTTA TGTTGTGTGAAGGCAAATGAGATAATGCACGACAAGACA--------TCTTATAAACAAGGATACTACAAATTGTAGGTATTTGTGTTA Template switch alignment (log-probability: -16.9) TGTTGTGTGAAGGCAAATGAGATAATGCACGACAAGACAT|ATCCTTGTT|TTATAAACAAGGATACTACAAATTGTAGGTATTTGTGTTA TGTTGTGTGAAGGCAAATGAGATAATGCACGACAAGACAT|ATCCTTGTT|TTATAAACAAGGATACTACAAATTGTAGGTATTTGTGTTA ========== Event 2288 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTGTTAGTTCTTTGTAATCCCATCTGTAAAACTAATC ↑ 3 2 1 4 Chimp: AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG---------AACCATCCCATCTGTAAAACTAATC Gorilla: AGACTTCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG---------AACCATCCCATCTGTAAAACTAATC ↓ 3 2 1 4 Human: AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTGTTAGTTCTTTGTAATCCCATCTGTAAAACTAATC Cluster: [ ] Orangutan: AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG---------AACCATCCCATCTGTAAAACTAATC Chimp > Human ------------- chr3:156770809-156770821 Template switch process: F1: L AAGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG 1 F3: 4 ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA R RF: AAGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTGAACCATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA RR: TTCTGAGGATTCCCGAACCAATGTTTCTTGATTAATCTGACTTGGTAGGGTAGACATTTTGATTAGGTCTCTAAAATGTGGGTAT F2: 3 ATGTTTCTTGATT 2 Unidirectional alignment (log-probability: -38.6) AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTGttagttctttgtA---ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG------------AACCATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA Template switch alignment (log-probability: -16.9) AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG|TTAGTTCTTTGTA|ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA AGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG|TTAGTTCTTTGTA|ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA Gorilla > Human --------------- chr3:156770809-156770821 Template switch process: F1: L AAGACTCCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG 1 F3: 4 ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA R RF: AAGACTTCTAAGGGCTTGGTTACAAAGAACTAATTAGACTGAACCATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA RR: TTCTGAAGATTCCCGAACCAATGTTTCTTGATTAATCTGACTTGGTAGGGTAGACATTTTGATTAGGTCTCTAAAATGTGGGTAT F2: 3 ATGTTTCTTGATT 2 Unidirectional alignment (log-probability: -43.6) AGACTcCTAAGGGCTTGGTTACAAAGAACTAATTAGACTGttagttctttgtA---ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA AGACTTCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG------------AACCATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA Template switch alignment (log-probability: -22.9) AGACTcCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG|TTAGTTCTTTGTA|ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA AGACTTCTAAGGGCTTGGTTACAAAGAACTAATTAGACTG|TTAGTTCTTTGTA|ATCCCATCTGTAAAACTAATCCAGAGATTTTACACCCATA ========== Event 2289 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTTGTTTTCTGAAACCCTCAAATTGCCTCAAAGATATAATATCTTTGTGCTAAAAATACTTGTTAGT Chimp: ACTTGTTTTCTGAAACCCTCAGATTGCCTCAAAGATATAATATCTTCGTGCTAAAAATACTTGTCAGT ↑ 134 2 Gorilla: ACTTGTTTTCTGAAACCCTCAAATTGCCT---------TATATCTTTGTGCTAAAAATACTTGTCAGT ↓ 134 2 Human: ACTTGTTTTCTGAAACCCTCAAATTGCCTCAAAGATATAATATCTTTGTGCTAAAAATACTTGTTAGT Cluster: [ ] Orangutan: ACTTGTTTTCTGAAACCCTCAAATTACCT---------TATTTCTTTGTGCTAAAAATACTTGTCAGT Gorilla > Human --------------- chr3:157135627-157135636 Template switch process: F1: L TTTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCT 1 F3: 4 ATATCTTTGTGCTAAAAATACTTGTTAGTCAAACATTGGT R RF: TTTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCTTATATCTTTGTGCTAAAAATACTTGTCAGTCAAACATTGGT RR: AAAGGTCTGTCGTGAACAAAAGACTTTGGGAGTTTAACGGAATATAGAAACACGATTTTTATGAACAGTCAGTTTGTAACCA F2: 3 ATATAGAAAC 2 Unidirectional alignment (log-probability: -34.9) TTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCtcaaagataTaATATCTTTGTGCTAAAAATACTTGTtAGTCAAACATTGGT TTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCC---------TTATATCTTTGTGCTAAAAATACTTGTCAGTCAAACATTGGT Template switch alignment (log-probability: -22.5) TTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCT|CAAAGATATA|ATATCTTTGTGCTAAAAATACTTGTtAGTCAAACATTGGT TTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCT|CAAAGATATA|ATATCTTTGTGCTAAAAATACTTGTCAGTCAAACATTGGT Gorilla > Chimp --------------- chr3:160693194-160693203 Template switch process: F1: L TATTTGGGTTTCCAGACAGCACTTGTTTTCTGAAACCCTCAGATTGCCT 1 F3: 4 ATATCTTCGTGCTAAAAATACTTGTCAGTCAAACATTGGTTGAACTCA R RF: TATTTGGGTTTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCTTATATCTTTGTGCTAAAAATACTTGTCAGTCAAACATTGGTTGAACTCA RR: ATAAACCCAAAGGTCTGTCGTGAACAAAAGACTTTGGGAGTTTAACGGAATATAGAAACACGATTTTTATGAACAGTCAGTTTGTAACCAACTTGAGT F2: 3 ATATAGAAAC 2 Unidirectional alignment (log-probability: -40.6) TTCCAGACAGCACTTGTTTTCTGAAACCCTCAgATTGCCtcaaagataTaATATCTTcGTGCTAAAAATACTTGTCAGTCAAACATTGGT TTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCC---------TTATATCTTTGTGCTAAAAATACTTGTCAGTCAAACATTGGT Template switch alignment (log-probability: -28.4) TTCCAGACAGCACTTGTTTTCTGAAACCCTCAgATTGCCT|CAAAGATATA|ATATCTTcGTGCTAAAAATACTTGTCAGTCAAACATTGGT TTCCAGACAGCACTTGTTTTCTGAAACCCTCAAATTGCCT|CAAAGATATA|ATATCTTTGTGCTAAAAATACTTGTCAGTCAAACATTGGT ========== Event 2290 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCGTTCTGAACTCACGCAATG-TTTAATA----TTAGCAGTCCTTTTGAAAAAATTTT ↓ 1 3 4 2 Chimp: TCGTTCTGAACTCACGCAATGTGCTAATATTAATTAGCAGTCCTTTTGAAAAAATTTT Gorilla: TCGTTCTGAACTCATGCAATG-TTTAATA----TTAGCATTCCTTTTGAAAAAATTTT Human: TCGTTCTGAACTCACGCAATG-TTTAATA----TTAGCAGTCCTTTTGAAAAAATTTT Cluster: [ ] Orangutan: TCGTTCTGAACTCACGCAATG-TTTAATA----TTAGCAGTCCTTTTGAAAAAATTTT Human > Chimp ------------- chr3:39744333-39744342 Template switch process: F1: L TTAACTGTCAATTTTGCATATCGTTCTGAACTCACGCAATGT 1 F3: 4 ATTAGCAGTCCTTTTGAAAAAATTTTAAATCCCCAAACCAG R RF: TTAACTGTCAATTTTGCATATCGTTCTGAACTCACGCAATGTTTAATATTAGCAGTCCTTTTGAAAAAATTTTAAATCCCCAAACCAG RR: AATTGACAGTTAAAACGTATAGCAAGACTTGAGTGCGTTACAAATTATAATCGTCAGGAAAACTTTTTTAAAATTTAGGGGTTTGGTC F2: 3 ATTATAATCG 2 Unidirectional alignment (log-probability: -31.3) AACTGTCAATTTTGCATATCGTTCTGAACTCACGCAATGTgctaataTTA--ATTAGCAGTCCTTTTGAAAAAATTTTAAATCCCCAAACCA AACTGTCAATTTTGCATATCGTTCTGAACTCACGCAATGT-------TTAATATTAGCAGTCCTTTTGAAAAAATTTTAAATCCCCAAACCA Template switch alignment (log-probability: -16.6) AACTGTCAATTTTGCATATCGTTCTGAACTCACGCAATGT|GCTAATATTA|ATTAGCAGTCCTTTTGAAAAAATTTTAAATCCCCAAACCA AACTGTCAATTTTGCATATCGTTCTGAACTCACGCAATGT|GCTAATATTA|ATTAGCAGTCCTTTTGAAAAAATTTTAAATCCCCAAACCA ========== Event 2291 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCCACAGATGAAGCCTAGGCCGCTTAAATGGA--AGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGA ↓ 1 4 3 2 Chimp: GCCACAGATGAAGCCTAGGCCGCTTAAATGCACTCAGGCATGCCTGAGTGCAGGGCCAGCCTGACAGGGA ↑ 1 4 3 2 Gorilla: GCCACAGATGAAGCCTAGGCCTCTTAAATGGA--AGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGA Human: GCCACAGATGAAGCCTAGGCCGCTTAAATGGA--AGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGA Cluster: [ ] Orangutan: GCCACAGATGAAGCCTAGGCCCCTTAAATGGA--AGGTCATGCCTGAGTGCAGGGCCAGCCTGACAGGGA Human > Chimp ------------- chr3:16611856-16611863 Template switch process: F1: L TGAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAATG 1 F3: 4 CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT R RF: TGAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAATGGAAGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT RR: ACTCAAACGTACGGTGTCTACTTCGGATCCGGCGAATTTACCTTCCTGTACGGACTCACGTCCCGGTCGGACTGTCCCTTCGGGGTA F2: 3 GGACTCAC 2 Unidirectional alignment (log-probability: -31.5) GAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAATgcactcaGG-----CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT GAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAAT-------GGAAGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT Template switch alignment (log-probability: -16.3) GAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAATG|CACTCAGG|CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT GAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAATG|CACTCAGG|CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT Gorilla > Chimp --------------- chr3:16611856-16611863 Template switch process: F1: L AGTTAGATGTGAGTTTGCATGCCACAGATGAAGCCTAGGCCGCTTAAATG 1 F3: 4 CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT R RF: AGTTAGATGTGAGTTTGCATGCCACAGATGAAGCCTAGGCCTCTTAAATGGAAGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT RR: TCAATCTACACTCAAACGTACGGTGTCTACTTCGGATCCGGAGAATTTACCTTCCTGTACGGACTCACGTCCCGGTCGGACTGTCCCTTCGGGGTA F2: 3 GGACTCAC 2 Unidirectional alignment (log-probability: -36.2) GAGTTTGCATGCCACAGATGAAGCCTAGGCCgCTTAAATGcActcAGG-CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT GAGTTTGCATGCCACAGATGAAGCCTAGGCCTCTTAAATGGA---AGGACATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT Template switch alignment (log-probability: -22.5) GAGTTTGCATGCCACAGATGAAGCCTAGGCCgCTTAAATG|CACTCAGG|CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT GAGTTTGCATGCCACAGATGAAGCCTAGGCCTCTTAAATG|CACTCAGG|CATGCCTGAGTGCAGGGCCAGCCTGACAGGGAAGCCCCAT ========== Event 2292 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TATGAAAATTAGACACAGTCAT-----GTACTGGCC--------------ATAAAGCACAAGGCCATTATTTAGCTAGCCACACACAAACTTGTTTCTTCC Chimp: TATGAAAATTAGACACAGTCAG-----GTACTGGCC--------------ATAAAGCACAAGGCCATTATTTAGCTGGCCACACACAAACGTGTTTcttcc ↓ 1 4 3 2 Gorilla: TATGAAAATTAGACACAGTCAT----------GGCC----------------------------AGTTATTTAGCTGGCCACACACAAACTTGTTTcttcc Human: TATGAAAATTAGACACAGTCAT-----GTACTGGCC--------------ATAAAGCACAAGGCCATTATTTAGCTAGCCACACACAAACTTGTTTCTTCC Cluster: [ ] Orangutan: TATGAAAATTAGATACAGTCATGTACT-----GGCCATCAAGCACAAGGC--------------CATTATTTACGTGACAACACACAAACTTGTTTCTTCC Chimp > Gorilla --------------- chr3:16605184-16605190 Template switch process: F1: L AAGTTGGAAGTATATTCACGTATGAAAATTAGACACAGTCA 1 F3: 4 TTATTTAGCTGGCCACACACAAACTTGTTTCTTCCCTGTT R RF: AAGTTGGAAGTATATTCACGTATGAAAATTAGACACAGTCAGGTACTGGCCATAAAGCACAAGGCCATTATTTAGCTGGCCACACACAAACGTGTTTCTTCCCTGTT RR: TTCAACCTTCATATAAGTGCATACTTTTAATCTGTGTCAGTCCATGACCGGTATTTCGTGTTCCGGTAATAAATCGACCGGTGTGTGTTTGCACAAAGAAGGGACAA F2: 3 GACCGGT 2 Unidirectional alignment (log-probability: -32.7) AGTTGGAAGTATATTCACGTATGAAAATTAGACACAGTCA-----TGGCCAg--------------TTATTTAGCTGGCCACACACAAACtTGTTTCTTCCCTGTT AGTTGGAAGTATATTCACGTATGAAAATTAGACACAGTCAGGTACTGGCCATAAAGCACAAGGCCATTATTTAGCTGGCCACACACAAACGTGTTTCTTCCCTGTT Template switch alignment (log-probability: -22.1) AGTTGGAAGTATATTCACGTATGAAAATTAGACACAGTCA|TGGCCAG|TTATTTAGCTGGCCACACACAAACtTGTTTCTTCCCTGTT AGTTGGAAGTATATTCACGTATGAAAATTAGACACAGTCA|TGGCCAG|TTATTTAGCTGGCCACACACAAACGTGTTTCTTCCCTGTT ========== Event 2293 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAACAGCACTGAAACCTATGAGA-----GAACCAGTTTAGAATTGGGAGAAATAAGTGCT Chimp: ACAACAGCACTGAAACCTATGAGA-----GAACCAGTTTAGAATTGGGAGAAATAAGTGCT ↓ 1 4 3 2 Gorilla: ACAACAGCACTGAAACCTATGCTAAACTGAAACCAGTTTAGAATTGGGAGAAATAAGTGCT ↑ 1 4 3 2 Human: ACAACAGCACTGAAACCTATGAGA-----GAACCAGTTTAGAATTGGGAGAAATAAGTGCT Cluster: [ ] Orangutan: ACAACAGCACTGAAACCTATGAGA-----GAACCTGTTTAGAATTGGGAGAAATAAGTGCT Human > Gorilla --------------- chr3:163312328-163312335 Template switch process: F1: L GGGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATG 1 F3: 4 AAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTACATG R RF: GGGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATGAGAGAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTGCATG RR: CCCGATTTTATTTAAACTTTTGTTGTCGTGACTTTGGATACTCTCTTGGTCAAATCTTAACCCTCTTTATTCACGATCCACGTAC F2: 3 GTCAAATC 2 Unidirectional alignment (log-probability: -37.8) GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTAtgctaaacTGA---AACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTaCAT GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTA--------TGAGAGAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTGCAT Template switch alignment (log-probability: -27.8) GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATG|CTAAACTG|aAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTaCAT GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATG|CTAAACTG|GAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTGCAT Chimp > Gorilla --------------- chr3:163312328-163312335 Template switch process: F1: L GGGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATG 1 F3: 4 AAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTACATG R RF: GGGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATGAGAGAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTGCATG RR: CCCGATTTTATTTAAACTTTTGTTGTCGTGACTTTGGATACTCTCTTGGTCAAATCTTAACCCTCTTTATTCACGATCCACGTAC F2: 3 GTCAAATC 2 Unidirectional alignment (log-probability: -37.8) GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTAtgctaaacTGA---AACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTaCAT GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTA--------TGAGAGAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTGCAT Template switch alignment (log-probability: -27.8) GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATG|CTAAACTG|aAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTaCAT GGCTAAAATAAATTTGAAAACAACAGCACTGAAACCTATG|CTAAACTG|GAACCAGTTTAGAATTGGGAGAAATAAGTGCTAGGTGCAT ========== Event 2294 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: TAGAAGGGCCAGAACTGACGGCAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACA----TGTGCCTGTGGTTTGGGGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGATAACTTGTTAGGAATCCTTTTCATGAA ↓ 1 3 42 ↑ 1 4 3 2 Chimp: TAGAAGGGCCAGAACTGACGGTTCGAT-AAGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACA----TGTGCCTGTGGTTTGGTGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGACAACTTGTTAGGAATCCTTTTCATGAA ↓ 1 4 3 2 ↑ 1 3 42 Gorilla: TAGAAGGGCCAGAACTGACGGCAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACA----TGTGCCTGTGGTTTGGTGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGATAACTTGTTAGGAATCCTTTTCATGAA Human: TAGAAGGGCCAGAACTGACGGCAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACA----TGTGCCTGTGGTTTGGGGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGATAACTTGTTAGGAATCCTTTTCATGAA Cluster: [ ] Orangutan: TAGAAGGGCCAGAAATGACGGCAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTATGTGCCTGTGGTTTGGTGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGATAACTTGTTAGGAATCCTTTTCATGAA Chimp > Human ------------- chr3:37396928-37396936 Template switch process: F1: L ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG 1 F3: 4 GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC R RF: ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGTTCGATAAGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGCCTGTGGTTTGGTGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGACAACTTG RR: TGAACCAAGTGGACCAGGGGATCTTCCCGGTCTTGACTGCCAAGCTATTCTGAACCACTCCGTTCAGGAGTTCTTCGGGGTTGTACACGGACACCAAACCACTCCAGTCTCGTTAACTCCGGAGTGTTAATTTTTCGTTAGAATACACTCCAATAGAACAACCTGTTGAAC F2: 3 CTATTGAAC 2 Unidirectional alignment (log-probability: -34.5) CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGcaagttatc--------GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG---------TTCGATAAGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Template switch alignment (log-probability: -22.4) CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG|CAAGTTaTC|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG|CAAGTTGTC|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Human > Chimp ------------- chr3:38117790-38117796 Template switch process: F1: L ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGT 1 F3: 4 GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC R RF: ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGCAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC RR: TGAACCAAGTGGACCAGGGGATCTTCCCGGTCTTGACTGCCGTTCAATAGCTGAACCACTCCGTTCAGGAGTTCTTCGGGGTTGTACACG F2: 3 AATAGCT 2 Unidirectional alignment (log-probability: -33.1) TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGttcgataa---------GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG--------CAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Template switch alignment (log-probability: -22.2) TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGt|TCGATAA|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGC|TCGATAA|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Gorilla > Chimp --------------- chr3:38117790-38117796 Template switch process: F1: L ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGT 1 F3: 4 GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC R RF: ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGCAAGTTATCGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC RR: TGAACCAAGTGGACCAGGGGATCTTCCCGGTCTTGACTGCCGTTCAATAGCTGAACCACTCCGTTCAGGAGTTCTTCGGGGTTGTACACG F2: 3 AATAGCT 2 Unidirectional alignment (log-probability: -32.6) TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG---------ttcgataaGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGCAAGTTATC--------GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Template switch alignment (log-probability: -22.2) TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGt|TCGATAA|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC TTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGC|TCGATAA|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Chimp > Gorilla --------------- chr3:37906233-37906241 Template switch process: F1: L ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG 1 F3: 4 GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC R RF: ACTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGTTCGATAAGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGCCTGTGGTTTGGTGAGGTCAGAGCAATTGAGGCCTCACAATTAAAAAGCAATCTTATGTGAGGTTATCTTGTTGGACAACTTG RR: TGAACCAAGTGGACCAGGGGATCTTCCCGGTCTTGACTGCCAAGCTATTCTGAACCACTCCGTTCAGGAGTTCTTCGGGGTTGTACACGGACACCAAACCACTCCAGTCTCGTTAACTCCGGAGTGTTAATTTTTCGTTAGAATACACTCCAATAGAACAACCTGTTGAAC F2: 3 CTATTGAAC 2 Unidirectional alignment (log-probability: -34) CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG--------caagttatcGACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGGTTCGATAA---------GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC Template switch alignment (log-probability: -22.4) CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG|CAAGTTaTC|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC CTTGGTTCACCTGGTCCCCTAGAAGGGCCAGAACTGACGG|CAAGTTGTC|GACTTGGTGAGGCAAGTCCTCAAGAAGCCCCAACATGTGC ========== Event 2295 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: ATGTACTTCTGGTCTCTCAAAAGTTCCATTTGAGAGACCAGAATGGCAGTGGAGtctcccttctagacaccaggaaactaagctcaaggggcagagggctttgtccaggggctggaactgctaaatgatggagcctgga ↓ 13 24 ↑ 1 4 3 2 Chimp: ATGTACTTCTGGTCTCTCAAATGGAACTTTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGACACCAGGAAACTAAGCTCAAGGGTCAGAGGGCTTTGTCCAGGGGCTGGAACTGCTAAATGATGGAGCCTGGA Gorilla: Human: ATGTACTTCTGGTCTCTCAAAAGTTCCATTTGAGAGACCAGAATGGCAGTGGAGtctcccttctagacaccaggaaactaagctcaaggggcagagggctttgtccaggggctggaactgctaaatgatggagcctgga Cluster: [ ] Orangutan: ATGTGCTTCTGGTCTCTCAAGAGTTCCATTTGAGAGATCAGAATGGCAGTGGAGTCTCCCTTCTAGACACCAGGAAACTAAGCTCAAGGGGCAGAGAGCTTTGTC-TGGGGCTGGAACTGCTAAATGATGGAGCCTGGA Chimp > Human ------------- chr3:181890595-181890601 Template switch process: F1: L CATTGTGCACGTTTTCTGGCATGTACTTCTGGTCTCTCAAA 1 F3: 4 TTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC R RF: CATTGTGCACATTTTCTGGCATGTACTTCTGGTCTCTCAAATGGAACTTTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGACACCAGGAAACTAAGCTCAAGGGTCAGAGGGCTTTGTCCAGGGGCTGGAACT RR: GTAACACGTGTAAAAGACCGTACATGAAGACCAGAGAGTTTACCTTGAAAACTCTCTGGTCTTACCGTCACCTCAGAGGGAAGATCTGTGGTCCTTTGATTCGAGTTCCCAGTCTCCCGAAACAGGTCCCCGACCTTGA F2: 3 ACCTTGA 2 Unidirectional alignment (log-probability: -36.7) ATTGTGCACgTTTTCTGGCATGTACTTCTGGTCTCTCAAAaGttcCaTTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC ATTGTGCACATTTTCTGGCATGTACTTCTGGTCTCTCAAATGGAACTTTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC Template switch alignment (log-probability: -22.1) ATTGTGCACgTTTTCTGGCATGTACTTCTGGTCTCTCAAA|AGTTCCA|TTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC ATTGTGCACATTTTCTGGCATGTACTTCTGGTCTCTCAAA|AGTTCCA|TTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC Human > Chimp ------------- chr3:185818532-185818538 Template switch process: F1: L CATTGTGCACATTTTCTGGCATGTACTTCTGGTCTCTCAAA 1 F3: 4 TTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC R RF: CATTGTGCACGTTTTCTGGCATGTACTTCTGGTCTCTCAAAAGTTCCATTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC RR: GTAACACGTGCAAAAGACCGTACATGAAGACCAGAGAGTTTTCAAGGTAAACTCTCTGGTCTTACCGTCACCTCAGAGGGAAGATCTG F2: 3 TCAAGGT 2 Unidirectional alignment (log-probability: -36.7) ATTGTGCACaTTTTCTGGCATGTACTTCTGGTCTCTCAAAtGgaaCtTTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC ATTGTGCACGTTTTCTGGCATGTACTTCTGGTCTCTCAAAAGTTCCATTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC Template switch alignment (log-probability: -22.1) ATTGTGCACaTTTTCTGGCATGTACTTCTGGTCTCTCAAA|TGGAACT|TTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC ATTGTGCACGTTTTCTGGCATGTACTTCTGGTCTCTCAAA|TGGAACT|TTTGAGAGACCAGAATGGCAGTGGAGTCTCCCTTCTAGAC ========== Event 2296 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAATAGGCAATTGCCTTAAAAGTG--T-AA------AAGGCTAA-CCAATATTTGAAA-AC-A ↓ 13 4 2 Chimp: GAATAGGCAATTGCCTTAAAAATG--T-TAGCCTTTTAGGCTAA-CCAATATTTGAAA-AC-A ↑ 13 4 2 Gorilla: GAATAGGCAATTGCCTTAAAAATG--T-AA------AAGGCTAA-CCAATATTTGAAA-AC-A Human: GAATAGGCAATTGCCTTAAAAGTG--T-AA------AAGGCTAA-CCAATATTTGAAA-AC-A Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNAAAAATGTGTAAA------AGGGCTAACCCAATATTTGAAAAACAC Human > Chimp ------------- chr3:16836949-16836957 Template switch process: F1: L TTTAAACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGT 1 F3: 4 AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT R RF: TTTAAACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAGTGTAAAAGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT RR: AAATTTGCCCTTTTTATATACTTATCCGTTAACGGAATTTTCACATTTTCCGATTGGTTATAAACTTTTGTGTGAAATTAAGTCGTAA F2: 3 TTTTCCGAT 2 Unidirectional alignment (log-probability: -37.6) ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAaTGTtAgccttttAGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAGTGTAAA------AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT Template switch alignment (log-probability: -22.5) ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAaTGT|TAGCCTTTT|AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAGTGT|TAGCCTTTT|AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT Gorilla > Chimp --------------- chr3:16836949-16836957 Template switch process: F1: L AACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGT 1 F3: 4 AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT R RF: AACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGTAAAAGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT RR: TTGCCCTTTTTATATACTTATCCGTTAACGGAATTTTTACATTTTCCGATTGGTTATAAACTTTTGTGTGAAATTAAGTCGTAA F2: 3 TTTTCCGAT 2 Unidirectional alignment (log-probability: -30.6) ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGTtAgccttttAGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGTAAA------AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT Template switch alignment (log-probability: -16.9) ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGT|TAGCCTTTT|AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT ACGGGAAAAATATATGAATAGGCAATTGCCTTAAAAATGT|TAGCCTTTT|AGGCTAACCAATATTTGAAAACACACTTTAATTCAGCATT ========== Event 2297 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AAGGTATAGGCATTGAACAGCATATATTTTAGGCTTATATCTGATTCTACTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCTG----TATGTTATTTTATGCATTttgtgttt ↓ 3 2 1 4 Chimp: AAGGTATAGGCATTGAACAGCATATATTTTAGGCTTATATCTCATTCTACTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCTA--TATATGCTATTTTATGCATTttgtgttt Gorilla: Human: AAGGTATAGGCATTGAACAGCATATATTTTAGGCTTATATCTGATTCTACTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCTG----TATGTTATTTTATGCATTttgtgttt Cluster: [ ] Orangutan: AAGGTATAGGCATTGAACAGCATATATTTTAGGCTTATATCTGATTCTACTTTGTCCCCACCCTTGTATTTCCTTCTTTACTGCAATCTATA--TATGCTATTTTACATATTttgtgttt Human > Chimp ------------- chr3:34009666-34009673 Template switch process: F1: L ACTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCT 1 F3: 4 TATTTTATGCATTTTGTGTTTATATGTCTACATTGTAGTT R RF: GCATATATTTTAGGCTTATATCTGATTCTACTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCTGTATGTTATTTTATGCATTTTGTGTTTATACGTCTACATTGTAGTT RR: CGTATATAAAATCCGAATATAGACTAAGATGAAACAGGGGTGGGAACATAAAGGAAGAAATAACGTTAGACATACAATAAAATACGTAAAACACAAATATGCAGATGTAACATCAA F2: 3 CGTATATA 2 Unidirectional alignment (log-probability: -31.8) CTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCtaTaTATGcTATTTTATGCATTTTGTGTTTATAtGTCTACATTGTAGTT CTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATC--TGTATGTTATTTTATGCATTTTGTGTTTATACGTCTACATTGTAGTT Template switch alignment (log-probability: -22.3) CTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCT|ATATATGC|TATTTTATGCATTTTGTGTTTATAtGTCTACATTGTAGTT CTTTGTCCCCACCCTTGTATTTCCTTCTTTATTGCAATCT|ATATATGC|TATTTTATGCATTTTGTGTTTATACGTCTACATTGTAGTT ========== Event 2298 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTGTAATAATACTTTCACATACGTGTTATTACACGTATTAATTGTTCCAGTGTCCGTATC ↑ 3 1 42 Chimp: GTTGTAATAATACTTTCACATACGTG----------TAATAATTGTTCCAGTGTCCGTATC Gorilla: GTTGTAATAACACTTTCACATACGTG----------TAATAATTGTTCCAGTGTCTGTATC Human: GTTGTAATAATACTTTCACATACGTGTTATTACACGTATTAATTGTTCCAGTGTCCGTATC Cluster: [ ] Orangutan: GTTGTAATAATACTTTCACATACGTG----------TAATAATTATTCCAGTGTCCGTATC Chimp > Human ------------- chr3:33098109-33098120 Template switch process: F1: L GGTCGCCTCTGTAATGTTGTAATAATACTTTCACATACGTGT 1 F3: 4 TAATTGTTCCAGTGTCCGTATCTAATTTATCGCGAAATGG R RF: GGTCGCCTCTGTAATGTTGTAATAATACTTTCACATACGTGTAATAATTGTTCCAGTGTCCGTATCTAATTTATCGCGAAATGG RR: CCAGCGGAGACATTACAACATTATTATGAAAGTGTATGCACATTATTAACAAGGTCACAGGCATAGATTAAATAGCGCTTTACC F2: 3 TATGCACATTAT 2 Unidirectional alignment (log-probability: -31.3) TCGCCTCTGTAATGTTGTAATAATACTTTCACATACGTgttattacacGTAtTAATTGTTCCAGTGTCCGTATCTAATTTATCGCGAAATGG TCGCCTCTGTAATGTTGTAATAATACTTTCACATACGT----------GTAATAATTGTTCCAGTGTCCGTATCTAATTTATCGCGAAATGG Template switch alignment (log-probability: -16.8) TCGCCTCTGTAATGTTGTAATAATACTTTCACATACGTGT|TATTACACGTAT|TAATTGTTCCAGTGTCCGTATCTAATTTATCGCGAAATGG TCGCCTCTGTAATGTTGTAATAATACTTTCACATACGTGT|TATTACACGTAT|TAATTGTTCCAGTGTCCGTATCTAATTTATCGCGAAATGG ========== Event 2299 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CTGCCAATAGAACAATAAAGCCTGTGTAGCTTTATTGTCTTGATACAGC ↓ 13 24 ↑ 13 24 Chimp: CTGCCAATAGAACAATAAAGCTACACAGGCTTTATTGTCTTGATACAGC Gorilla: CTGCCAATAGAACAATAAAGCTACACAGGCTTTATTGTCTTGATACAGC ↓ 13 24 ↑ 13 24 Human: CTGCCAATAGAACAATAAAGCCTGTGTAGCTTTATTGTCTTGATACAGC Cluster: [ ] Orangutan: CTGCCAGTAGAACAATAAAGCTACACAGGCTTTATCGTCTTGATACAGC Chimp > Human ------------- chr3:32815750-32815756 Template switch process: F1: L ACTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGC 1 F3: 4 GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG R RF: ACTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGCTACACAGGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG RR: TGACCATTAAATTGTTAGCTGACGGTTATCTTGTTATTTCGATGTGTCCGAAATAACAGAACTATGTCGCGTATTAAAAACTGTCTTC F2: 3 ATGTGTC 2 Unidirectional alignment (log-probability: -34.6) CTGGTAATTTAACAATgGACTGCCAATAGAACAATAAAGCctgtgTA-----GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGC-----TACACAGGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Template switch alignment (log-probability: -22.1) CTGGTAATTTAACAATgGACTGCCAATAGAACAATAAAGC|CTGTGTA|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGC|CTGTGTA|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Human > Chimp ------------- chr3:33471950-33471956 Template switch process: F1: L ACTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGC 1 F3: 4 GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG R RF: ACTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGCCTGTGTAGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG RR: TGACCATTAAATTGTTACCTGACGGTTATCTTGTTATTTCGGACACATCGAAATAACAGAACTATGTCGCGTATTAAAAACTGTCTTC F2: 3 GACACAT 2 Unidirectional alignment (log-probability: -34.6) CTGGTAATTTAACAATcGACTGCCAATAGAACAATAAAGC-----TAcacagGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGCCTGTGTA-----GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Template switch alignment (log-probability: -22.1) CTGGTAATTTAACAATcGACTGCCAATAGAACAATAAAGC|TACACAG|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGC|TACACAG|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Gorilla > Human --------------- chr3:32815750-32815756 Template switch process: F1: L ACTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGC 1 F3: 4 GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG R RF: ACTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGCTACACAGGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG RR: TGACCATTAAATTGTTAGCTGACGGTTATCTTGTTATTTCGATGTGTCCGAAATAACAGAACTATGTCGCGTATTAAAAACTGTCTTC F2: 3 ATGTGTC 2 Unidirectional alignment (log-probability: -33.6) CTGGTAATTTAACAATgGACTGCCAATAGAACAATAAAGCctgtgTA-----GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGC-----TACACAGGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Template switch alignment (log-probability: -22.1) CTGGTAATTTAACAATgGACTGCCAATAGAACAATAAAGC|CTGTGTA|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGC|CTGTGTA|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Human > Gorilla --------------- chr3:33283769-33283775 Template switch process: F1: L ACTGGTAATTTAACAATCGACTGCCAATAGAACAATAAAGC 1 F3: 4 GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG R RF: ACTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGCCTGTGTAGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG RR: TGACCATTAAATTGTTACCTGACGGTTATCTTGTTATTTCGGACACATCGAAATAACAGAACTATGTCGCGTATTAAAAACTGTCTTC F2: 3 GACACAT 2 Unidirectional alignment (log-probability: -33.6) CTGGTAATTTAACAATcGACTGCCAATAGAACAATAAAGC-----TAcacagGCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGCCTGTGTA-----GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG Template switch alignment (log-probability: -22.1) CTGGTAATTTAACAATcGACTGCCAATAGAACAATAAAGC|TACACAG|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG CTGGTAATTTAACAATGGACTGCCAATAGAACAATAAAGC|TACACAG|GCTTTATTGTCTTGATACAGCGCATAATTTTTGACAGAAG ========== Event 2300 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTGaagaatcacaagacaccagag--aaaagcctgcaacatgaaggggaaacgcaaaatgaacatatta Chimp: TATTGAAGAATCACAAGACACCAGAG--AAAAGCCTGCAACATGAAGGGGAAACGCAAAATGAACATATTA ↓ 1 4 3 2 Gorilla: TATTGAAGAATCACAAGACACAATCACCTTCATGCTGCAACATGAAGGGGAAACGCAAAATGAACATATTA Human: TATTGaagaatcacaagacaccagag--aaaagcctgcaacatgaaggggaaacgcaaaatgaacatatta Cluster: [ ] Orangutan: tattgaagaatcacgagacaccagag--aaaagcctgcaacatgaaggggaaaagcaaaacgaacatgtta Chimp > Gorilla --------------- chr3:168883181-168883191 Template switch process: F1: L TTTAATTGTTAATTATAAGATATTGAAGAATCACAAGACACAA 1 F3: 4 CTGCAACATGAAGGGGAAACGCAAAATGAACATATTAGAA R RF: TTTAATTGTTAATTATAAGATATTGAAGAATCACAAGACACCAGAGAAAAGCCTGCAACATGAAGGGGAAACGCAAAATGAACATATTAGAA RR: AAATTAACAATTAATATTCTATAACTTCTTAGTGTTCTGTGGTCTCTTTTCGGACGTTGTACTTCCCCTTTGCGTTTTACTTGTATAATCTT F2: 3 GTACTTCCACT 2 Unidirectional alignment (log-probability: -39.5) AATTGTTAATTATAAGATATTGAAGAATCACAAGACAC-------AAtCaccttcatgCTGCAACATGAAGGGGAAACGCAAAATGAACATATTAGAA AATTGTTAATTATAAGATATTGAAGAATCACAAGACACCAGAGAAAAGC---------CTGCAACATGAAGGGGAAACGCAAAATGAACATATTAGAA Template switch alignment (log-probability: -28.2) AATTGTTAATTATAAGATATTGAAGAATCACAAGACACaA|TCaCCTTCATG|CTGCAACATGAAGGGGAAACGCAAAATGAACATATTAGAA AATTGTTAATTATAAGATATTGAAGAATCACAAGACACCA|TCCCCTTCATG|CTGCAACATGAAGGGGAAACGCAAAATGAACATATTAGAA ========== Event 2301 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GATATTATTAACACCATAGAAGCTGGATACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCAGCTTACAAAAAGAAGTCAAAGG ↑ 1 4 3 2 Chimp: GATATTATTAACACCATAGAATAGTGTTACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCAGCTTACAAAAAGAAGTCAAAGG Gorilla: gatattattaacaccatagaaactggataccctagtttgagggcagcatcaccttctatcaattccagcttacaaaaagaagTCAAAGG Human: GATATTATTAACACCATAGAAGCTGGATACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCAGCTTACAAAAAGAAGTCAAAGG Cluster: [ ] Orangutan: GATATTATTAACACCATAGAAACTGGATACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCAGCTTACAAAAAGAAGTCAAAGG Chimp > Human ------------- chr3:166767458-166767463 Template switch process: F1: L CGTAGTTTCTGTCTTTCTGAGATATTATTAACACCATAGAA 1 F3: 4 TACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCA R RF: CGTAGTTTCTGTCTTTCTGAGATATTATTAACACCATAGAATAGTGTTACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCAGC RR: GCATCAAAGACAGAAAGACTCTATAATAATTGTGGTATCTTATCACAATGGGATCAAACTCCCGTCGTAGTGGAAGATAGTTAAGGTCG F2: 3 AGGTCG 2 Unidirectional alignment (log-probability: -30.1) GTAGTTTCTGTCTTTCTGAGATATTATTAACACCATAGAagctggA------TACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCA GTAGTTTCTGTCTTTCTGAGATATTATTAACACCATAGA------ATAGTGTTACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCA Template switch alignment (log-probability: -16) GTAGTTTCTGTCTTTCTGAGATATTATTAACACCATAGAA|GCTGGA|TACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCA GTAGTTTCTGTCTTTCTGAGATATTATTAACACCATAGAA|GCTGGA|TACCCTAGTTTGAGGGCAGCATCACCTTCTATCAATTCCA ========== Event 2302 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTATGCAGCATAGTAAGAGCATGGAAAAGTAACAACTTTTCCAAATGAAATTCATTATGAATA ↑ 1 3 4 2 Chimp: TTATGCAGCATAGTAAGAGCACTG--------TTACTTTTCCAAATGAAATTCATTATGAATA Gorilla: TTATGCAGCACAGTAAGAGCACTG--------TTACTTTTCCAAATGAAATTCATTATGAATA ↓ 1 3 4 2 Human: TTATGCAGCATAGTAAGAGCATGGAAAAGTAACAACTTTTCCAAATGAAATTCATTATGAATA Cluster: [ ] Orangutan: TTATGCAGCATAGTCAGAGCACTG--------TTACTTTTCCAAATGAAATTCATTCTGAATA Chimp > Human ------------- chr3:30990188-30990200 Template switch process: F1: L ATGATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCA 1 F3: 4 ACTTTTCCAAATGAAATTCATTATGAATAATAC R RF: ATAATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCACTGTTACTTTTCCAAATGAAATTCATTATGAATAATAC RR: TATTATGAAATTCCGGGTGGAATACGTCGTATCATTCTCGTGACAATGAAAAGGTTTACTTTAAGTAATACTTATTATG F2: 3 ACAATGAAAAGGT 2 Unidirectional alignment (log-probability: -52.1) TgATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCA----TggaaaagtaacaACTTTTCCAAATGAAATTCATTATGAATAATAC------- TAATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCACTGTT------------ACTTTTCCAAATGAAATTCATTATGAATAATACATAATAC Template switch alignment (log-probability: -22.7) TgATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCA|TGGAAAAGTAACA|ACTTTTCCAAATGAAATTCATTATGAATAATAC TAATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCA|TGGAAAAGTAACA|ACTTTTCCAAATGAAATTCATTATGAATAATAC Gorilla > Human --------------- chr3:30990188-30990200 Template switch process: F1: L ATGATACTTTAAGGCCCACCTTATGCAGCATAGTAAGAGCA 1 F3: 4 ACTTTTCCAAATGAAATTCATTATGAATAATACAGTATAA R RF: ATAATACTTTAAGGCCCACCTTATGCAGCACAGTAAGAGCACTGTTACTTTTCCAAATGAAATTCATTATGAATAATACAGTATAA RR: TATTATGAAATTCCGGGTGGAATACGTCGTGTCATTCTCGTGACAATGAAAAGGTTTACTTTAAGTAATACTTATTATGTCATATT F2: 3 ACAATGAAAAGGT 2 Unidirectional alignment (log-probability: -49.1) TgATACTTTAAGGCCCACCTTATGCAGCAtAGTAAGAGCA----TggaaaagtaacaACTTTTCCAAATGAAATTCATTATGAATAATACAGTATAA TAATACTTTAAGGCCCACCTTATGCAGCACAGTAAGAGCACTGTT------------ACTTTTCCAAATGAAATTCATTATGAATAATACAGTATAA Template switch alignment (log-probability: -28.4) TgATACTTTAAGGCCCACCTTATGCAGCAtAGTAAGAGCA|TGGAAAAGTAACA|ACTTTTCCAAATGAAATTCATTATGAATAATACAGTATAA TAATACTTTAAGGCCCACCTTATGCAGCACAGTAAGAGCA|TGGAAAAGTAACA|ACTTTTCCAAATGAAATTCATTATGAATAATACAGTATAA ========== Event 2303 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: TGGAAAATATTTTGTGTCTAAATTTGTGTCTAGGTTAGAGCCATAAAGAAAATCA ↓ 3 2 4 ↑ 1 3 4 Chimp: TGGAAAATATTTTGTGTCTAAGCTAGACACAAATTTAGAGCCATAAAGAAAATCA Gorilla: Human: TGGAAAATATTTTGTGTCTAAATTTGTGTCTAGGTTAGAGCCATAAAGAAAATCA Cluster: [ ] Orangutan: TGGAAGATATTTTGTGTCTAAGCTAGACACAAATTTAGAGCCATAAAGAAAATCA Chimp > Human ------------- chr3:167584862-167584873 Template switch process: F1: L TAACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAA 1 F3: 4 GTTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT R RF: TAACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAAGCTAGACACAAATTTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT RR: ATTGAATGTTTATCCTCTACACCTTTTATAAAACACAGATTCGATCTGTGTTTAAATCTCGGTATTTCTTTTAGTAAGGAATCTGAGTAAAAAA F2: 3 GATCTGTGTTTA 2 Unidirectional alignment (log-probability: -37.5) AACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCT-----------AAATTtgtgtctaggtTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTT AACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAAGCTAGACACAAATT-----------TAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTT Template switch alignment (log-probability: -22.8) AACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAA|ATTTGTGTCTAG|gTTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTT AACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAA|ATTTGTGTCTAG|TTTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTT Human > Chimp ------------- chr3:171270975-171270986 Template switch process: F1: L TAACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAAG 1 F3: 4 TTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT R RF: TAACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAAATTTGTGTCTAGGTTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT RR: ATTGAATGTTTATCCTCTACACCTTTTATAAAACACAGATTTAAACACAGATCCAATCTCGGTATTTCTTTTAGTAAGGAATCTGAGTAAAAAA F2: 3 TAAACACAGATC 2 Unidirectional alignment (log-probability: -37.5) ACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTaagctagacacAAATT-----------TAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT ACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCT-----------AAATTTGTGTCTAGGTTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT Template switch alignment (log-probability: -22.8) ACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAAg|CTAGACACAAAT|TTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT ACTTACAAATAGGAGATGTGGAAAATATTTTGTGTCTAAA|CTAGACACAAAT|TTAGAGCCATAAAGAAAATCATTCCTTAGACTCATTTTTT ========== Event 2304 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCCTAATGGCTCATCTTCATGCAGCTGGGATTCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGTTTCCTAGTATCATATCTAGCATGCACCCGCATC---CTAGACATTTCTCAAAAGAGAAGGCCCAGGgactggacctggtggctcgcacctgtaatcccagcactttgggaggccaaggtg ↑ 4 1 3 2 Chimp: TCCTAATGGCTCATCTTCATG-----------CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGTTTCCTAGTATCATATCTAGCATGTACCCGCATC---CTAGACATTTCTCAAAAGAGAAGGCCCAGGgactggacctggtggcttgcacctgtaatcccagcactttgggaggccaaggtg ↓ 4 1 3 2 Gorilla: TCCTAATGGCTCATCTTCATGCAGCTGGGATTCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGTTCCCTAGTATCATATCTAGCAtgtacccgcatcctactagacatttctcaaaagagaaggcccagggactggacctggtggctcgcacctgtaatcccagcactttgggaggccaaggtg Human: TCCTAATGGCTCATCTTCATGCAGCTGGGATTCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGTTTCCTAGTATCATATCTAGCATGCACCCGCATC---CTAGACATTTCTCAAAAGAGAAGGCCCAGGgactggacctggtggctcgcacctgtaatcccagcactttgggaggccaaggtg Cluster: [ ] Orangutan: TCCTAATGGCTCATCTTCATGCAGCTGGGATTCAGAGATGATGCCCTAGTCCCATTGTGTGGCCTCAACAGTTTCCTAGTATCATATCCAGCATGTACCCGCATC---CTAGACATTTCTCAAAAGAGAAGGCCCAGGgactggacctggtggctcgcacctgtaatcccagcactttgggaggccaaggtg Chimp > Human ------------- chr3:167685019-167685026 Template switch process: F1: L CTTTGAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAG 1 F3: 4 CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT R RF: CTTTGAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGTTTCCTAGTATCATATCTAGCATGTACCCGCATCCTAGACATTTCTCAAAAGAGAAGGCCCAGGGACTGGACCTGGTGGCTTGCACCTGTAATCCCAG RR: GAAACTCGGGGTGGTGTAAGAGGATTACCGAGTAGAAGTACGTCTCTACTACGGGATCAGGGTGACACACCGGAGTTGTCAAAGGATCATAGTATAGATCGTACATGGGCGTAGGATCTGTAAAGAGTTTTCTCTTCCGGGTCCCTGACCTGGACCACCGAACGTGGACATTAGGGTC F2: 3 TTAGGGTC 2 Unidirectional alignment (log-probability: -26.7) GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGcagctgggattCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATG-----------CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT Template switch alignment (log-probability: -16.3) GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAG|CTGGGATT|CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAG|CTGGGATT|CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT Chimp > Gorilla --------------- chr3:170371476-170371483 Template switch process: F1: L CTTTGAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAG 1 F3: 4 CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT R RF: CTTTGAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGTTTCCTAGTATCATATCTAGCATGTACCCGCATCCTAGACATTTCTCAAAAGAGAAGGCCCAGGGACTGGACCTGGTGGCTTGCACCTGTAATCCCAG RR: GAAACTCGGGGTGGTGTAAGAGGATTACCGAGTAGAAGTACGTCTCTACTACGGGATCAGGGTGACACACCGGAGTTGTCAAAGGATCATAGTATAGATCGTACATGGGCGTAGGATCTGTAAAGAGTTTTCTCTTCCGGGTCCCTGACCTGGACCACCGAACGTGGACATTAGGGTC F2: 3 TTAGGGTC 2 Unidirectional alignment (log-probability: -26.7) GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGcagctgggattCAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATG-----------CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT Template switch alignment (log-probability: -16.8) GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAG|CTGGGATT|CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT GAGCCCCACCACATTCTCCTAATGGCTCATCTTCATGCAG|CTGGGATT|CAGAGATGATGCCCTAGTCCCACTGTGTGGCCTCAACAGT ========== Event 2305 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCAGAATCAGAGTAATTCAACTGCTGTCCGTGGTATGGTTTTGTCTGTGGCAGTAGATATCCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCA---------------ACAG---TCTCTTTGGAGACAGGAACGAA ↑ 3 2 1 4 Chimp: TCAGAATCAGAGTAATTCAACTGCTTTCTGTGGTATGGTTTTGTCTGTGGCAGTAGATATCCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCA---------------AAGGACTCCTCTTTGGAGACAGGAACGAA Gorilla: TCAGAATCAGAGTAATTCAACTGCTGTCCGTGGTATGGTTTTGTCTGTGGCAGTAGATATCCAAGGAAGCGTGGTTGTCCGGAGAAGTCAACAGCGGCA------------------------------AAGACAGGAACGAA Human: TCAGAATCAGAGTAATTCAACTGCTGTCCGTGGTATGGTTTTGTCTGTGGCAGTAGATATCCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCA---------------ACAG---TCTCTTTGGAGACAGGAACGAA Cluster: [ ] Orangutan: TCAGAATCAGAGTAATTCAACTGCTTTCCGTAGTACGGTTTTGTCTGTGGCAGTAGATATCCAAGGAAGTGTGGTTGTGCTGAGAAGTCAACAGCAGCAAAGGACTCCTCTTTG---------------GAGACATGAATGAA Chimp > Human ------------- chr3:167996792-167996795 Template switch process: F1: L TCCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCAA 1 F3: 4 CTCTTTGGAGACAGGAACGAACATGAGACCAAGATATGTT R RF: ACTGCTTTCTGTGGTATGGTTTTGTCTGTGGCAGTAGATATCCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCAAAGGACTCCTCTTTGGAGACAGGAACGAACATGAGACCAAGGTATGTT RR: TGACGAAAGACACCATACCAAAACAGACACCGTCATCTATAGGTTCCTTCACACCAACAGGACTCTTCAGTTGTCGCCGTTTCCTGAGGAGAAACCTCTGTCCTTGCTTGTACTCTGGTTCCATACAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -31.8) CCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCAA------CagtCTCTTTGGAGACAGGAACGAACATGAGACCAAGaTATGTT CCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCAAAGGACTC---CTCTTTGGAGACAGGAACGAACATGAGACCAAGGTATGTT Template switch alignment (log-probability: -21.8) CCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCAA|CAGT|CTCTTTGGAGACAGGAACGAACATGAGACCAAGaTATGTT CCAAGGAAGTGTGGTTGTCCTGAGAAGTCAACAGCGGCAA|CAGT|CTCTTTGGAGACAGGAACGAACATGAGACCAAGGTATGTT ========== Event 2306 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTTTTAATACAAGTATACCAAAATCAGAGACAC------------------------------------------------------------------------------------------ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGTTTTACAATGGTTACCACGT Chimp: CCTTTTAATACAAGTATACCAAAATCAGAGACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGATTAGGTAACCAACCAAGACAGATAACCATGCGTCTCTGATTTTGGACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGTTTTACAATGGTTACCACGT ↑ 3 4 2 1 Gorilla: CCTTTTAATACAAGTATACCAAAATCAGAGACGC------------------------------------------------------------------------------------------ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGTTTTACAATGGTTACCACGT Human: CCTTTTAATACAAGTATACCAAAATCAGAGACAC------------------------------------------------------------------------------------------ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGTTTTACAATGGTTACCACGT Cluster: [ ] Orangutan: CCTTTTAATACAAGTATACCAAAATCAGAGAGAC------------------------------------------------------------------------------------------ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGTTGTACAATGGTTATCACAT Gorilla > Chimp --------------- chr3:170200465-170200509 Template switch process: F1: L AATTTAACCTTTTAATACAAGTATACCAAAATCAGAGACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATG 1 F3: 4 GACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATG R RF: AATTTAACCTTTTAATACAAGTATACCAAAATCAGAGACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATG RR: TTAAATTGGAAAATTATGTTCATATGGTTTTAGTCTCTGCGTACCATTAGACAGAACCAACCATTGGATTAGTATTCTTAC F2: 3 GTTTTAGTCTCTGCGTACCAATAGACAGAACCAACCAATGGATTA 2 Unidirectional alignment (log-probability: -137) ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATGattaggtaaccaaccaagacagataaccatgcgtctctgattttggacgcatggtaatctgtcttggttggtaacctaatcataa ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATG------------------------------------------------------------------------------------- Template switch alignment (log-probability: -33.4) ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATG|ATTAGGTaACCAACCAAGACAGATaACCATGCGTCTCTGATTTTG|GACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAA ATGGTAATCTGTCTTGGTTGGTAACCTAATCATAAGAATG|ATTAGGTTACCAACCAAGACAGATTACCATGCGTCTCTGATTTTG|GACGCATGGTAATCTGTCTTGGTTGGTAACCTAATCATAA ========== Event 2307 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGTTTGTGTTTCAGTTAAGTGAGTATTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACAAGTGAGCTTAATACTCACTTA------------------ ↑ 3 1 2 4 Chimp: TGTTTGTGTTTCAGTTAAGTGAGTATTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTTGTGAGCT-----------TA------------------ Gorilla: TGTTTGTGTTTCAATTAAGTGAGTATTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACAAgtgagcttaatactcactta----------------at Human: TGTTTGTGTTTCAGTTAAGTGAGTATTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACAAGTGAGCTTAATACTCACTTA------------------ Cluster: [ ] Orangutan: TGTTTGTGTTTCAATTAAGCGAATGCTGTCTGGCCCTGTGCCTTCCAATGGGTCGCTTGAACTCTAGTGCTGCAGTCAAGGTAAAGGATTCCCTGGGATGACAGTTGAGGTGGGTTTAAATGAAGCCTATTTTCACCCTGGGAGGTTCCAGATTCTGCCTCTCTGACTATCCCTGGAGGGTATACTCACCTGGCTCTGATGTTCTATTTCACAACCAGAATCTGTGTTTGCTAGAATCGCACCTCCCTTTCCAGAAGAAACCCAGGCTTTGACCTACCCTTGCTTTTTGTGTGTTTAGCACAAACTGAGTCTGCTCCCCAANNNNNNNNNNAGGATTAACGgaaaggatgaaaagaaagctgaatattaatagtctaaaaatatttttaaaaaattaaaaaCATTCAAATCTTGGTAACTATTTTCATTGTGTTCAAATACAATGCATTTGGTATTCTAAATATTTTTGTAGTGTTGTATACTAACAGCTAGTAAACCCAGTTTTTTGGAGGTCTTTGTTAAAACGGTAAGTTAATAACTTGGTGATTTTACCATGGGATATTCCATTCTAGAACAAGAACTCAAGGAGAACCATAATAAATCAactaaattgactactcacttaattgaatactgactta-- Chimp > Human ------------- chr3:29172402-29172419 Template switch process: F1: L TTTGAGTGTTTGTGTTTCAGTTAAGTGAGTATTAAGCTCAC 1 F3: 4 CTTAATTGACTACTCACTTAATTGTGAGCTTAATACTCACTT R RF: TTTGAGTGTTTGTGTTTCAGTTAAGTGAGTATTAAGCTCACTTGTGAGCTTAATTGACTACTCACTTAATTGTGAGCTTAATACTCACTT RR: AAACTCACAAACACAAAGTCAATTCACTCATAATTCGAGTGAACACTCGAATTAACTGATGAGTGAATTAACACTCGAATTATGAGTGAA F2: 3 ACTCATAATTCGAGTGAA 2 Unidirectional alignment (log-probability: -38.8) TTGAGTGTTTGTGTTTCAGTTAAGTGAGTATTAAGCTCACaaGTGAGCTTAatactcacttaATTGACTACTCACTTAATTGTGAGCTTAATACTCAC TTGAGTGTTTGTGTTTCAGTTAAGTGAGTATTAAGCTCACTTGTGAGCTTA-----------ATTGACTACTCACTTAATTGTGAGCTTAATACTCAC Template switch alignment (log-probability: -17.5) TTGAGTGTTTGTGTTTCAGTTAAGTGAGTATTAAGCTCAC|AAGTGAGCTTAATACTCA|CTTAATTGACTACTCACTTAATTGTGAGCTTAATACTCAC TTGAGTGTTTGTGTTTCAGTTAAGTGAGTATTAAGCTCAC|AAGTGAGCTTAATACTCA|CTTAATTGACTACTCACTTAATTGTGAGCTTAATACTCAC ========== Event 2308 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTATGATATATATAAGATACATGAAACAACAAGTTTGAGGAGAAAATAATAGCATTTACtttt----------ttttttGAGCTTGAATCCAAATTTAAAAGAATGAGGGAGCTATGGCCCTCTTGTGGAGAACTTCAGCAATGCACTTTTCTTAAAAGTCTCAACGTCTAAAT- ↓ 1 4 3 2 Chimp: ATTTATGATATATATAAGATATACGAAA---CAAGTTTGAGGAGAAAATAATAGCATTTACtttt-------tttttttttGAGCTTGAATCCAAATTTAAAAGAATGAGGGAGCTATGGCCCTCTTGTGGAGAACTTCAGCAATGCACTTTTCTTAAAAGTCTCAACGTCTAAAT- Gorilla: ATTTATGATATATATAAGATATATGAAACAACAAGTTTGAGGAGAAAATAATAGCATTTACtttt------t---ttttCTGAGCTTGAATCCAAATTTAAAAGAATGAGGGAGCTATGGCCCTCTTGTGGAGAACTTCAGCAATGCACTTTTCTTAAAAGTCTCAACGTCTAAATT Human: ATTTATGATATATATAAGATACATGAAACAACAAGTTTGAGGAGAAAATAATAGCATTTACtttt----------ttttttGAGCTTGAATCCAAATTTAAAAGAATGAGGGAGCTATGGCCCTCTTGTGGAGAACTTCAGCAATGCACTTTTCTTAAAAGTCTCAACGTCTAAAT- Cluster: [ ] Orangutan: ATTTATGATCTATATAAGATATATGAAACAACAAGTTTGAGGAGAAAATAATAGCATTTACttttttttttt---ttttttGAGCTTGAATCCAAATTTAAAAGAATGAGGGAGCTATGGCCCTCTTGTGGAGAACTTCAGCAATGCACTTTTCTTAAAAGTCTCAACGTCTAAATT Human > Chimp ------------- chr3:30068437-30068441 Template switch process: F1: L AATTATTCTTATTATCACATATTTATGATATATATAAGATA 1 F3: 4 AACAAGTTTGAGGAGAAAATAATAGCATTTACTTTTTTTTTT R RF: AATTATTCTTATTATCACATATTTATGATATATATAAGATACATGAAACAACAAGTTTGAGGAGAAAATAATAGCATTTACTTTTTTTTTTGAGCTTGAATCCAAATTTAAAAGAATGAGGGAGCTATGGCCCTCTTGTGGAGAACTTCAGCAATGCACTTTTCTTA RR: TTAATAAGAATAATAGTGTATAAATACTATATATATTCTATGTACTTTGTTGTTCAAACTCCTCTTTTATTATCGTAAATGAAAAAAAAAACTCGAACTTAGGTTTAAATTTTCTTACTCCCTCGATACCGGGAGAACACCTCTTGAAGTCGTTACGTGAAAAGAAT F2: 3 AGCAT 2 Unidirectional alignment (log-probability: -34.6) ATTATTCTTATTATCACATATTTATGATATATATAAGATAtAcGA---AACAAGTTTGAGGAGAAAATAATAGCATTTACTTTTTTTt ATTATTCTTATTATCACATATTTATGATATATATAAGATACATGAAACAACAAGTTTGAGGAGAAAATAATAGCATTTACTTTTTTT- Template switch alignment (log-probability: -21.9) ATTATTCTTATTATCACATATTTATGATATATATAAGATA|TAcGA|AACAAGTTTGAGGAGAAAATAATAGCATTTACTTTTTTTT ATTATTCTTATTATCACATATTTATGATATATATAAGATA|TAAGA|AACAAGTTTGAGGAGAAAATAATAGCATTTACTTTTTTTT ========== Event 2309 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GCAGGCAGTCCTGTGACAGGACTCTCAGGATTGAGAGTCAGGAATTTGTGGAGTTGC Chimp: GCAGGCAGTCCTGTGACAGGAATC------CTGAGAGTCAGGAATTTGTGGAGTTGC Gorilla: GCAGGCAGTCCTGTGACAGGAATC------CTGAGAGTCAGGAATTTGTGGAGTTGC ↓ 13 4 2 Human: GCAGGCAGTCCTGTGACAGGACTCTCAGGATTGAGAGTCAGGAATTTGTGGAGTTGC Cluster: [ ] Orangutan: GCAGGCAGTCCTGTGACAGGAATC------CTGAGAGTCAGGAATTTGTGGAGTTGC Gorilla > Human --------------- chr3:29053289-29053298 Template switch process: F1: L AGAAACCAGGACTGATTGCCGCAGGCAGTCCTGTGACAGGA 1 F3: 4 TGAGAGTCAGGAATTTGTGGAGTTGCTGTGCTGAGATGCA R RF: AGGAACCAGGACTGATTGCCGCAGGCAGTCCTGTGACAGGAATCCTGAGAGTCAGGAATTTGTGGAGTTGCTGTGCTGAGATGCA RR: TCCTTGGTCCTGACTAACGGCGTCCGTCAGGACACTGTCCTTAGGACTCTCAGTCCTTAAACACCTCAACGACACGACTCTACGT F2: 3 TAGGACTCTC 2 Unidirectional alignment (log-probability: -36.1) GaAACCAGGACTGATTGCCGCAGGCAGTCCTGTGACAGGAcTCtcaggatTGAGAGTCAGGAATTTGTGGAGTTGCTGTGCTGAGATGCA GGAACCAGGACTGATTGCCGCAGGCAGTCCTGTGACAGGAATC------CTGAGAGTCAGGAATTTGTGGAGTTGCTGTGCTGAGATGCA Template switch alignment (log-probability: -22.5) GaAACCAGGACTGATTGCCGCAGGCAGTCCTGTGACAGGA|CTCTCAGGAT|TGAGAGTCAGGAATTTGTGGAGTTGCTGTGCTGAGATGCA GGAACCAGGACTGATTGCCGCAGGCAGTCCTGTGACAGGA|CTCTCAGGAT|TGAGAGTCAGGAATTTGTGGAGTTGCTGTGCTGAGATGCA ========== Event 2310 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GACTAAATAATGGACACCTAT---GTATCTGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTAATCTTGCTTCAGATGGATTAAgtgtgcgtgcctgtgtgtggtgtgtgtTTTacattacagattagaacttaggtcctctggattcacaaccccgaatcccatttg Chimp: GACTAAATAATGGACACCTAT---GTATCTGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTAATCTTGCTTCAGATGGATTAAgtgtgtgtgcctgcgtgtggtgtgtgtTTTacattacagattagaacttaggtcctctggatacacaaccctgaatcccatttg ↑ 1 4 3 2 Gorilla: GACTAAATAATGGACACCTAT------AATGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTAATCTTGCTTCAGATGGATTAAgtgtgtgtgcctgtgtgtggtgtgtgtTTTacattacagattagaacttaggtcctctggatacacaaccccgaatcccatttg ↓ 1 4 3 2 Human: GACTAAATAATGGACACCTAT---GTATCTGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTAATCTTGCTTCAGATGGATTAAgtgtgcgtgcctgtgtgtggtgtgtgtTTTacattacagattagaacttaggtcctctggattcacaaccccgaatcccatttg Cluster: [ ] Orangutan: gactaaataATGGACACCTATGTA---TCTGCAAATACGCATTCAGTTGTCTTTAATAATGCTTTGCTAATCTTGCTTCAGATGGATTAAgtgtgtgtgtctgtgtgtggtgtgtgtTTTACATTACAGATTAGAActtaggtcctctggattcacagccccgaatcccatttg Gorilla > Human --------------- chr3:28733770-28733774 Template switch process: F1: L GTTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT 1 F3: 4 TGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA R RF: GTTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTATAATGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTAATCTTGCTTCAGATGGATTAAGTGTGTGTGCCTGTGTGTGGTGTGTGTTTTACATTACAGATTAGAACTTAGGTCCTCTGGATAC RR: CAATTTATAATTCTTTTTTTCTGATTTATTACCTGTGGATATTACGTTTATGCGTAAGTCAACAGAAATTATTAGGAAACGATTAGAACGAAGTCTACCTAATTCACACACACGGACACACACCACACACAAAATGTAATGTCTAATCTTGAATCCAGGAGACCTATG F2: 3 CTATG 2 Unidirectional alignment (log-probability: -26.3) TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTATgtatcTGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT---AATGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA Template switch alignment (log-probability: -16.4) TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT|GTATC|TGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT|GTATC|TGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA Gorilla > Chimp --------------- chr3:29374713-29374717 Template switch process: F1: L GTTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT 1 F3: 4 TGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA R RF: GTTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTATAATGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTAATCTTGCTTCAGATGGATTAAGTGTGTGTGCCTGTGTGTGGTGTGTGTTTTACATTACAGATTAGAACTTAGGTCCTCTGGATAC RR: CAATTTATAATTCTTTTTTTCTGATTTATTACCTGTGGATATTACGTTTATGCGTAAGTCAACAGAAATTATTAGGAAACGATTAGAACGAAGTCTACCTAATTCACACACACGGACACACACCACACACAAAATGTAATGTCTAATCTTGAATCCAGGAGACCTATG F2: 3 CTATG 2 Unidirectional alignment (log-probability: -26.3) TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTATgtatcTGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT---AATGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA Template switch alignment (log-probability: -16.4) TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT|GTATC|TGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA TTAAATATTAAGAAAAAAAGACTAAATAATGGACACCTAT|GTATC|TGCAAATACGCATTCAGTTGTCTTTAATAATCCTTTGCTA ========== Event 2311 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: agtattgttATACTTGTATGTACATGTACATGTTATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTACACATAAA----CGTACATACAAGTCTATAGGTCAT ↑ 1 4 3 2 Chimp: agtattgttATACTTGTATGT------ACATGCTATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTACACATAAA--CATGTACATACAAGTCTATGGGTCAT Gorilla: agtattgttatacttgtatgt------acatgttatacatgttatGTAAGGGTAAGTATGTTACTTGTATGTACACATAAA----CGTACATACAAGTCTATGGGTCAT Human: agtattgttATACTTGTATGTACATGTACATGTTATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTACACATAAA----CGTACATACAAGTCTATAGGTCAT Cluster: [ ] Orangutan: agtattgttatacttgtatgt------acatgttatacatgttatgtaagggtaagtatgttacttgtatgtacatgtaaaca--tgtacatagaagtctatgggtcat Chimp > Human ------------- chr3:28209426-28209432 Template switch process: F1: L TTGCATGATATGTAAGGGTAAGTATTGTTATACTTGTATGTACATG 1 F3: 4 TATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTA R RF: TTGCATGATATGTAAGGGTAAGTATTGTTATACTTGTATGTACATGCTATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTACACATAAACATGTA RR: AACGTACTATACATTCCCATTCATAACAATATGAACATACATGTACGATATGTACAATACATTCCCATTCATACAATGAACATACATGTGTATTTGTACAT F2: 3 TGTACAT 2 Unidirectional alignment (log-probability: -25.6) GATATGTAAGGGTAAGTATTGTTATACTTGTatgtacATGTACATGtTATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTA GATATGTAAGGGTAAGTATTGTTATACTTGT------ATGTACATGCTATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTA Template switch alignment (log-probability: -16.3) GATATGTAAGGGTAAGTATTGTTATACTTGTATGTACATG|TACATGT|TATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTA GATATGTAAGGGTAAGTATTGTTATACTTGTATGTACATG|TACATGT|TATACATGTTATGTAAGGGTAAGTATGTTACTTGTATGTA ========== Event 2312 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTCTCGCCTCCAAACTGTTAATTGAAAATTTCCTTTAAGTTTAAT--------TGTTATTTCTAATGTTTCAGGGC ↓ 13 24 ↑ 13 24 Chimp: GTCTCGCCTCCAAACTGTTAA----CAATTAAACTTAAAGGAAAT----TTTCAATTATTTCTAATGTTTCAGGGC Gorilla: GTCTCGCCTCCAAACTGTTAA----CAATTAAACTTAAAGGAAATTTTC----AATTATTTCTAATGTTTCAGGGC ↓ 13 24 ↑ 13 24 Human: GTCTCGCCTCCAAACTGTTAATTGAAAATTTCCTTTAAGTTTAAT--------TGTTATTTCTAATGTTTCAGGGC Cluster: [ ] Orangutan: GTCTCGCCTCCAAACTGTTAA----CAATTAAACTTAAAGGAAATTTTC----AATTATTTCTAATGTTTCAGGGC Chimp > Human ------------- chr3:27191472-27191497 Template switch process: F1: L TCATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAA 1 F3: 4 TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA R RF: CCATAGGGATTCTCGTATATGTCTCGCCTCCAAACTGTTAACAATTAAACTTAAAGGAAATTTTCAATTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA RR: GGTATCCCTAAGAGCATATACAGAGCGGAGGTTTGACAATTGTTAATTTGAATTTCCTTTAAAAGTTAATAAAGATTACAAAGTCCCGTCTCTCGAAAAATCATTGT F2: 3 GTTAATTTGAATTTCCTTTAAAAGTT 2 Unidirectional alignment (log-probability: -70.4) CATAGGGATTCTgGTATATGTCTCGCCTCCAAACTGTTAA---------------------TTgAAaatttcctttaagtttaattgTTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTCGTATATGTCTCGCCTCCAAACTGTTAACAATTAAACTTAAAGGAAATTTTCAA---------------------TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Template switch alignment (log-probability: -30.5) CATAGGGATTCTgGTATATGTCTCGCCTCCAAACTGTTAA|TTGAAAATTTCCTTTAAGTTTAATTG|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTCGTATATGTCTCGCCTCCAAACTGTTAA|TTGAAAATTTCCTTTAAGTTTAATTG|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Human > Chimp ------------- chr3:27795133-27795158 Template switch process: F1: L CCATAGGGATTCTCGTATATGTCTCGCCTCCAAACTGTTAA 1 F3: 4 TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA R RF: TCATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAATTGAAAATTTCCTTTAAGTTTAATTGTTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA RR: AGTATCCCTAAGACCATATACAGAGCGGAGGTTTGACAATTAACTTTTAAAGGAAATTCAAATTAACAATAAAGATTACAAAGTCCCGTCTCTCGAAAAATCATTGT F2: 3 AACTTTTAAAGGAAATTCAAATTAAC 2 Unidirectional alignment (log-probability: -70.4) CATAGGGATTCTcGTATATGTCTCGCCTCCAAACTGTTAAcaattaaacttaaaggaaattTTcAA---------------------TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAA---------------------TTGAAAATTTCCTTTAAGTTTAATTGTTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Template switch alignment (log-probability: -30.5) CATAGGGATTCTcGTATATGTCTCGCCTCCAAACTGTTAA|CAATTAAACTTAAAGGAAATTTTCAA|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAA|CAATTAAACTTAAAGGAAATTTTCAA|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Gorilla > Human --------------- chr3:27191472-27191497 Template switch process: F1: L TCATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAA 1 F3: 4 TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA R RF: TCATAGGGATTCTTGTATATGTCTCGCCTCCAAACTGTTAACAATTAAACTTAAAGGAAATTTTCAATTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA RR: AGTATCCCTAAGAACATATACAGAGCGGAGGTTTGACAATTGTTAATTTGAATTTCCTTTAAAAGTTAATAAAGATTACAAAGTCCCGTCTCTCGAAAAATCATTGT F2: 3 GTTAATTTGAATTTCCTTTAAAAGTT 2 Unidirectional alignment (log-probability: -63) CATAGGGATTCTgGTATATGTCTCGCCTCCAAACTGTTAA---------------------TTgAAaatttcctttaagtttaattgTTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTTGTATATGTCTCGCCTCCAAACTGTTAACAATTAAACTTAAAGGAAATTTTCAA---------------------TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Template switch alignment (log-probability: -24.6) CATAGGGATTCTgGTATATGTCTCGCCTCCAAACTGTTAA|TTGAAAATTTCCTTTAAGTTTAATTG|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTTGTATATGTCTCGCCTCCAAACTGTTAA|TTGAAAATTTCCTTTAAGTTTAATTG|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Human > Gorilla --------------- chr3:27466944-27466969 Template switch process: F1: L TCATAGGGATTCTTGTATATGTCTCGCCTCCAAACTGTTAA 1 F3: 4 TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA R RF: TCATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAATTGAAAATTTCCTTTAAGTTTAATTGTTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA RR: AGTATCCCTAAGACCATATACAGAGCGGAGGTTTGACAATTAACTTTTAAAGGAAATTCAAATTAACAATAAAGATTACAAAGTCCCGTCTCTCGAAAAATCATTGT F2: 3 AACTTTTAAAGGAAATTCAAATTAAC 2 Unidirectional alignment (log-probability: -63) CATAGGGATTCTtGTATATGTCTCGCCTCCAAACTGTTAAcaattaaacttaaaggaaattTTcAA---------------------TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAA---------------------TTGAAAATTTCCTTTAAGTTTAATTGTTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA Template switch alignment (log-probability: -24.6) CATAGGGATTCTtGTATATGTCTCGCCTCCAAACTGTTAA|CAATTAAACTTAAAGGAAATTTTCAA|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA CATAGGGATTCTGGTATATGTCTCGCCTCCAAACTGTTAA|CAATTAAACTTAAAGGAAATTTTCAA|TTATTTCTAATGTTTCAGGGCAGAGAGCTTTTTAGTAACA ========== Event 2313 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GGCTTGGACAGTGCCAGGCCACTGAGGGTTGCTGCATACCAAGTGGCCTCTCTACCACTCTCATTTCCTAATTGTCAATGCCAACTACAGCCAAAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGGCCTAGCTG------CTTCAGCCAGTGCTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTA Chimp: GgcttggacagtgccaggccactgagggttgctgcatgccaagtggcctctctaccactctcatttcctaattgtcAATGCCAACTACAGCCAAAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGG-------------------------------CCTAGTGCTTCAGCACTAATCTGTCATTCATTTA ↓ 3 2 4 1 Gorilla: GgcttggacagtgccaggccactgagggttgctgcataccaagtggcctctctaccactctcatttcctaattgtcAATGCCAACTACAGCCAAAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGGCCTAGCTG------CTTCAGCCAGTGCTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTA Human: GGCTTGGACAGTGCCAGGCCACTGAGGGTTGCTGCATACCAAGTGGCCTCTCTACCACTCTCATTTCCTAATTGTCAATGCCAACTACAGCCAAAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGGCCTAGCTG------CTTCAGCCAGTGCTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTA Cluster: [ ] Orangutan: GGCTTGGACAGCGCCAGGCCACTGAGGGTTGCTGCATACCAAGTGGCCTCTCTACCACTCTCATTTCCTAATTGTCAATGCCAACTACAGCCAAAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGGCGTAGCTGCTTCAGCTAG------TGCTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTA Chimp > Gorilla --------------- chr3:27604738-27604742 Template switch process: F1: L AAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGGCCTAGCTGCTTCAGC 1 F3: 4 CTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTAAGAGTG R RF: CACTGAGGGTTGCTGCATGCCAAGTGGCCTCTCTACCACTCTCATTTCCTAATTGTCAATGCCAACTACAGCCAAAGTACCACTTAGCTGAAGGCACCAGCATCTTTTATTTTGGCCTAG-TGCTTCAGCACTAATCTGTCATTCATTTAAGAGTG RR: GTGACTCCCAACGACGTACGGTTCACCGGAGAGATGGTGAGAGTAAAGGATTAACAGTTACGGTTGATGTCGGTTTCATGGTGAATCGACTTCCGTGGTCGTAGAAAATAAAACCGGATC-ACGAAGTCGTGATTAGACAGTAAGTAAATTCTCAC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -46.8) AAGGCACCAGCATCTTTTATTTTggcctagctgcttcagccagtgcttGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTAA AAGGCACCAGCATCTTTTATTTT-------------------------GGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTAA Template switch alignment (log-probability: -33.5) AAGGCACCAGCATCTTTTATTTTGGCCTAGcTGCTTCAGC|CAGTG|cTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTAA AAGGCACCAGCATCTTTTATTTTGGCCTAG-TGCTTCAGC|CAGTG|TTTGGCCTAGTGCTTCAGCACTAATCTGTCATTCATTTAA ========== Event 2314 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCCACAGTTTACCCAGTGCATGCCAGCCTTCCATCCTCATAGACCAGCAGCAGGTGGCAACA ↓ 3 2 1 4 Chimp: GGCCACAGTTTACCCAGTGCATGCCAG--------CCTCATGGACCAGCAGCAGGTGGCAACA Gorilla: GGCCACAGTTTACCCAGTGCATGCCAGCCTTCCATCCTCATGGACCAGCAGCAGGTGGCAACA Human: GGCCACAGTTTACCCAGTGCATGCCAGCCTTCCATCCTCATAGACCAGCAGCAGGTGGCAACA Cluster: [ ] Orangutan: GGCCACAGTTTACCCAGTGCATGCCAGCCTTCCATCCTCATGGACCAGCAGCAGGTGGCAACA Human > Chimp ------------- chr3:28400105-28400108 Template switch process: F1: L ACAGAAGACACTGCGGCCACAGTTTACCCAGTGCATGCCAGCCT 1 F3: 4 GACCAGCAGCAGGTGGCAACACTCACACCATAAAA R RF: ACAGAAGACACTGCGGCCACAGTTTACCCAGTGCATGCCAGCCTTCCATCCTCATAGACCAGCAGCAGGTGGCAACACTCACGCCATAAAA RR: TGTCTTCTGTGACGCCGGTGTCAAATGGGTCACGTACGGTCGGAAGGTAGGAGTATCTGGTCGTCGTCCACCGTTGTGAGTGCGGTATTTT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -30.8) AAGACACTGCGGCCACAGTTTACCCAGTGCATGCCAG--------CCTCATgGACCAGCAGCAGGTGGCAACACTCACaCCATAAAA----- AAGACACTGCGGCCACAGTTTACCCAGTGCATGCCAGCCTTCCATCCTCATAGACCAGCAGCAGGTGGCAACACTCACGCCATAAAATGCAA Template switch alignment (log-probability: -21.7) AAGACACTGCGGCCACAGTTTACCCAGTGCATGCCAGCCT|CATG|GACCAGCAGCAGGTGGCAACACTCACaCCATAAAA AAGACACTGCGGCCACAGTTTACCCAGTGCATGCCAGCCT|CATG|GACCAGCAGCAGGTGGCAACACTCACGCCATAAAA ========== Event 2315 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAAATCAGCCATTAGAACTGCATCAACGTACAGTCACATCTATAGAGACT Chimp: CCAAATCAGCCATTAGAACTGTACGTTGGTACAGTCACATCTATAGAGACT ↑ 1 3 4 2 Gorilla: CCAAATCAGCCATTAGAACTGCATCAACGTACAGTCACATCTATAGAGACT Human: CCAAATCAGCCATTAGAACTGCATCAACGTACAGTCACATCTATAGAGACT Cluster: [ ] Orangutan: CCAAATCAGCCATTAGAACTGCATCAACTTACAGTCACATCTATAGAGACT Gorilla > Chimp --------------- chr3:28060751-28060757 Template switch process: F1: L AATCATTTTGATTTTATTTTCCAAATCAGCCATTAGAACTG 1 F3: 4 GTACAGTCACATCTATAGAGACTATATTAATTTCTAGAGC R RF: AATCATTTTGATTTTATTTTCCAAATCAGCCATTAGAACTGCATCAACGTACAGTCACATCTATAGAGACTATATTAATTTCTAGAGC RR: TTAGTAAAACTAAAATAAAAGGTTTAGTCGGTAATCTTGACGTAGTTGCATGTCAGTGTAGATATCTCTGATATAATTAAAGATCTCG F2: 3 GTTGCAT 2 Unidirectional alignment (log-probability: -31.1) ATCATTTTGATTTTATTTTCCAAATCAGCCATTAGAACTG-------tacgttgGTACAGTCACATCTATAGAGACTATATTAATTTCTAGAGC ATCATTTTGATTTTATTTTCCAAATCAGCCATTAGAACTGCATCAAC-------GTACAGTCACATCTATAGAGACTATATTAATTTCTAGAGC Template switch alignment (log-probability: -16.6) ATCATTTTGATTTTATTTTCCAAATCAGCCATTAGAACTG|TACGTTG|GTACAGTCACATCTATAGAGACTATATTAATTTCTAGAGC ATCATTTTGATTTTATTTTCCAAATCAGCCATTAGAACTG|TACGTTG|GTACAGTCACATCTATAGAGACTATATTAATTTCTAGAGC ========== Event 2316 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: CACACTGGTTCAGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCAC-CGTCTCTACCCCAGAGTGGACTCAAATCCTCAAGTCAGTCCTCTGAACATTGAAGTC---AGAAA--------- Chimp: CACACTGGTTCAGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCAC-CGTCTCTACCCCAGAGTGGACTCAAATCCTCAAGTCAGTCCTCTGAACATTCAAGTC---AGAAA--------- ↓ 4 1 3 2 ↑ 1 3 24 Gorilla: CACACTGGTTCAGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACTTGAATGTTCAGAGGACTGACTTGAGGATTTGAGTC------CA--------- ↓ 1 3 24 Human: CACACTGGTTCAGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCAC-CGTCTCTACCCCAGAGTGGACTCAAATCCTCAAGTCAGTCCTCTGAACATTGAAGTC---AGAAA--------- Cluster: [] Orangutan: CACACTGGTTCAGGGACTCACTGGACGGTTTTTTGTCCACTGTGGCCCGCACCCGTCTCTACCCCAGAGTGGACTCAAATCCTCAAGTCAGTCCTCTGAACATTCAAGTCAGA---AATTATAAAAG Gorilla > Human --------------- chr3:172353330-172353343 Template switch process: F1: L AGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACT 1 F3: 4 AGTCC R RF: AGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACTTGAATGTTCAGAGGACTGACTTGAGGATTTGAGTCC RR: TCCCTGAGTGACCTGCCAAAACACAGGTGAGATTGGACGTGGACAGAGATGGGGTCTCACCTGAACTTACAAGTCTCCTGACTGAACTCCTAAACTCAGG F2: 3 CTGAACTCCTAAAC 2 Unidirectional alignment (log-probability: -55.5) GTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACTcaaatcctcaagtcagtcc------------------- GTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACT-------------------TGAATGTTCAGAGGACTGA Template switch alignment (log-probability: -27) GTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACT|CAAATCCTCAAGTC|AGTCC GTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACT|CAAATCCTCAAGTC|AGTCC Gorilla > Chimp --------------- chr3:176102258-176102271 Template switch process: F1: L AGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACT 1 F3: 4 AGTCC R RF: AGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACTTGAATGTTCAGAGGACTGACTTGAGGATTTGAGTCC RR: TCCCTGAGTGACCTGCCAAAACACAGGTGAGATTGGACGTGGACAGAGATGGGGTCTCACCTGAACTTACAAGTCTCCTGACTGAACTCCTAAACTCAGG F2: 3 CTGAACTCCTAAAC 2 Unidirectional alignment (log-probability: -55.5) GTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACTcaaatcctcaagtcagtcc------------------- GTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACT-------------------TGAATGTTCAGAGGACTGA Template switch alignment (log-probability: -27) GTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACT|CAAATCCTCAAGTC|AGTCC GTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACT|CAAATCCTCAAGTC|AGTCC Chimp > Gorilla --------------- chr3:175227402-175227416 Template switch process: F1: L AGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACCTGTCTCTACCCCAGAGTGGACT 1 F3: 4 CTGA R RF: AGGGACTCACTGGACGGTTTTGTGTCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACTCAAATCCTCAAGTCAGTCCTCTGAACATTCA RR: TCCCTGAGTGACCTGCCAAAACACAGGTGAGATTGGACGTGG-CAGAGATGGGGTCTCACCTGAGTTTAGGAGTTCAGTCAGGAGACTTGTAAGT F2: 3 AGGAGACTTGTAAGT 2 Unidirectional alignment (log-probability: -56.8) TCCACTCTAACCTGCACCtGTCTCTACCCCAGAGTGGACTtgaatgttcagaggactga------------------- TCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACT-------------------CAAATCCTCAAGTCAGTCC Template switch alignment (log-probability: -28.5) TCCACTCTAACCTGCACCtGTCTCTACCCCAGAGTGGACT|TGAATGTTCAGAGGA|CTGA TCCACTCTAACCTGCACC-GTCTCTACCCCAGAGTGGACT|TGAATGTTCAGAGGA|CTGA ========== Event 2317 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GCAATTAAAATGAGGCTGTAAAACCTCTGTACCAGAGgttttcttcgtctt Chimp: GCAATTAAAATGAGGCTGTAATA---CAGTACCAGAGGttttcttcgtctt Gorilla: GCAATTAAAATGAGGCTGTAATA---CAGTACCAGAGGTTTTCTTCGTCTT ↑ 1 3 42 Human: GCAATTAAAATGAGGCTGTAAAACCTCTGTACCAGAGgttttcttcgtctt Cluster: [ ] Orangutan: GCAATTAAAATGAGGCTGTAATA---CAGTACCAGAGgttttcttggtc-- Human > Gorilla --------------- chr3:175356425-175356429 Template switch process: F1: L AAATCAAAATCAGCATGAAAGCAATTAAAATGAGGCTGTAA 1 F3: 4 TACCAGAGGTTTTCTTCGTCTTCTTTCCTTTCCTT R RF: AAATCAAAATCAGCATGAAAGCAATTAAAATGAGGCTGTAAAACCTCTGTACCAGAGGTTTTCTTCGTCTTCTTTTCTTTTCTT RR: TTTAGTTTTAGTCGTACTTTCGTTAATTTTACTCCGACATTTTGGAGACATGGTCTCCAAAAGAAGCAGAAGAAAAGAAAAGAA F2: 3 GACAT 2 Unidirectional alignment (log-probability: -40.1) AATCAAAATCAGCATGAAAGCAATTAAAATGAGGCTGTAAtA---CaGTACCAGAGGTTTTCTTCGTCTTCTTTcCTTTcCTT---- AATCAAAATCAGCATGAAAGCAATTAAAATGAGGCTGTAAAACCTCTGTACCAGAGGTTTTCTTCGTCTTCTTTTCTTTTCTTTCCT Template switch alignment (log-probability: -27.3) AATCAAAATCAGCATGAAAGCAATTAAAATGAGGCTGTAA|TACAG|TACCAGAGGTTTTCTTCGTCTTCTTTcCTTTcCTT AATCAAAATCAGCATGAAAGCAATTAAAATGAGGCTGTAA|TACAG|TACCAGAGGTTTTCTTCGTCTTCTTTTCTTTTCTT ========== Event 2318 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ctcttcttTTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTTCTGACTTTCTTAAAGCCTAtttttttttctc ↑ 3 2 4 1 Chimp: ctcttcttTTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTT-----------TCTTAAAGCCTAttt-tttttctc Gorilla: ctcttcttTTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTTCTGACTTTCTTAAAGCCTAtttttttttctc Human: ctcttcttTTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTTCTGACTTTCTTAAAGCCTAtttttttttctc Cluster: [ ] Orangutan: ctcttcttttGAGCAATACTCAATTTGGCTCCTGTATATCCCTTTCTTCTGACTTTCTTAAAGCCTACttttttttCTC Chimp > Human ------------- chr3:26700681-26700684 Template switch process: F1: L TTCTTTTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTT 1 F3: 4 CTTTCTTAAAGCCTATTTTTTTTTCTCCTAAGTAGCCTTCTTT R RF: TTCTTTTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTTAAAGCCTATTTTTTTTCTCCTAAGTAGCCTTCTTT RR: AAGAAAACTCGTTATGAGTCAAACCGAGGACATATAGGGAAAGAATTTCGGATAAAAAAAAGAGGATTCATCGGAAGAAA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -38.4) TTGAGCAATACTCAGTTTGGCTCCTGTATATCCctttcttctgaCTTTCTTAAAGCCTATTTTTTTtTCTCCTAAGTAGCCTTC TTGAGCAATACTCAGTTTGGCTCCTGTATATCC-----------CTTTCTTAAAGCCTATTTTTTT-TCTCCTAAGTAGCCTTC Template switch alignment (log-probability: -27.6) TTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTT|CTGA|CTTTCTTAAAGCCTAtTTTTTTTTCTCCTAAGTAGCCTTC TTGAGCAATACTCAGTTTGGCTCCTGTATATCCCTTTCTT|CTGA|CTTTCTTAAAGCCTA-TTTTTTTTCTCCTAAGTAGCCTTC ========== Event 2319 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAGGATAGCTGATCTTCTGAATGCATTTAATTTCTTTCTGAAGGGTGCTTCTGGGCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGG-TT--------------------------------------------GACCTTCAGAAAGAAGAGAAGCAAAATTTTTTCCCTA Chimp: AGAGGATAGCTGATCTTCTGAATGCATTTAATTTCTTTCTGAAGGGTGCTTCTGGGCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGG-TT--------------------------------------------GACCTTCAGAAAGAAGAGAAGCAAAATTTTTTCCCTA ↓ 3 12 4 Gorilla: AGAGGATAGCTGATCTTCTGAATGCATTTAATTTCTTTCTGAAGGGTGCTTCTGGGCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCACTGATTGTATAGGAGAAATTGCTTGCAGCTATCCTGCTATGCCCAGAAGCACCCTTCAGAAAGAAATTA-----AATGCATT---CA ↑ 3 12 4 Human: AGAGGATAGCTGATCTTCTGAATGCATTTAATTTCTTTCTGAAGGGTGCTTCTGGGCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGG-TT--------------------------------------------GACCTTCAGAAAGAAGAGAAGCAAAATTTTTTCCCTA Cluster: [ ] Orangutan: ----------------------------------------------------------------------------------------catcatc---------------------------------------------------------------------------------------- Human > Gorilla --------------- chr3:27032557-27032634 Template switch process: F1: L GCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA 1 F3: 4 AGAAGA R RF: GAATGCATTTAATTTCTTTCTGAAGGGTGCTTCTGGGCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGGTTGACCTTCAGAAAGAAGA RR: CTTACGTAAATTAAAGAAAGACTTCCCACGAAGACCCGTATCGTCCTATCGACGTTCGTTAAAGAGGATATGTTAGTCCCAACTGGAAGTCTTTCTTCT F2: 3 CTTACGTAAATTAAAGAAAGACTTCCCACGAAGACCCGTATCGTCCTATCGACGTTCGTTAAAGAGGATATGTTAGTC 2 Unidirectional alignment (log-probability: -137) CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA---------------------------------------CTgattgtataggagaaattgcttgcagctatcctgctatgcccagaagcacccttcagaaagaaattaaatgcattcAGAAgA CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGGTTGACCTTCAGAAAGAAGAGAAGCAAAATTTTTTCCCT----------------------------------------------------------------------------AGAAAA Template switch alignment (log-probability: -24.8) CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA|CTGATTGTATAGGAGAAATTGCTTGCAGCTATCCTGCTATGCCCAGAAGCACCCTTCAGAAAGAAATTAAATGCATTC|AGAAGA CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA|CTGATTGTATAGGAGAAATTGCTTGCAGCTATCCTGCTATGCCCAGAAGCACCCTTCAGAAAGAAATTAAATGCATTC|AGAAGA Chimp > Gorilla --------------- chr3:27032557-27032634 Template switch process: F1: L GCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA 1 F3: 4 AGAAGA R RF: GAATGCATTTAATTTCTTTCTGAAGGGTGCTTCTGGGCATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGGTTGACCTTCAGAAAGAAGA RR: CTTACGTAAATTAAAGAAAGACTTCCCACGAAGACCCGTATCGTCCTATCGACGTTCGTTAAAGAGGATATGTTAGTCCCAACTGGAAGTCTTTCTTCT F2: 3 CTTACGTAAATTAAAGAAAGACTTCCCACGAAGACCCGTATCGTCCTATCGACGTTCGTTAAAGAGGATATGTTAGTC 2 Unidirectional alignment (log-probability: -137) CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA---------------------------------------CTgattgtataggagaaattgcttgcagctatcctgctatgcccagaagcacccttcagaaagaaattaaatgcattcAGAAgA CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCAGGGTTGACCTTCAGAAAGAAGAGAAGCAAAATTTTTTCCCT----------------------------------------------------------------------------AGAAAA Template switch alignment (log-probability: -24.8) CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA|CTGATTGTATAGGAGAAATTGCTTGCAGCTATCCTGCTATGCCCAGAAGCACCCTTCAGAAAGAAATTAAATGCATTC|AGAAGA CATAGCAGGATAGCTGCAAGCAATTTCTCCTATACAATCA|CTGATTGTATAGGAGAAATTGCTTGCAGCTATCCTGCTATGCCCAGAAGCACCCTTCAGAAAGAAATTAAATGCATTC|AGAAGA ========== Event 2320 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CTGCTAGCCTATGCTTTAAAA---CAT---TGCTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAGAAATTGGTTATGCAATGCTTAGGAAAAACAGCTTCC ↑ 1 4 3 2 Chimp: CTGCTAGCCTATGCTTTAAAACTGAATAGACATTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAGAAATTGGTTATGCAATGCTTAGGAAAAACAGCTTCC ↓ 1 4 3 2 Gorilla: CTGCTAGCCTATGCTTTAAAA---CAT---TGCTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAGAAATTGGTTACGCAATGCTTAGGAAAAACAGCTTCC Human: CTGCTAGCCTATGCTTTAAAA---CAT---TGCTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAGAAATTGGTTATGCAATGCTTAGGAAAAACAGCTTCC Cluster: [ ] Orangutan: CTGCTAGCCTATGCTTTAAAA---CAT---TGCTTATTACTGAAATGTCTATTAGAGTAGAGTGAGAAGAAAGAAATTGGTTATGCAATGCTTAGGAAAAACATCTTCC Chimp > Human ------------- chr3:17645152-17645156 Template switch process: F1: L TATAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAAC 1 F3: 4 TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG R RF: TATAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAACTGAATAGACATTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAGAAATTGGTTATGCAAT RR: ATATTTATATTATATCTTATGACGATCGGATACGAAATTTTGACTTATCTGTAAATAATGACTTTACAGATAACCTCATCTCACTCTTCTTTCTTTAACCAATACGTTA F2: 3 CGTTA 2 Unidirectional alignment (log-probability: -25.9) TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAA---------ACATtgcTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAACTGAATAGACAT---TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG Template switch alignment (log-probability: -15.9) TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAAC|ATTGC|TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAAC|ATTGC|TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG Chimp > Gorilla --------------- chr3:17960508-17960512 Template switch process: F1: L TATAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAAC 1 F3: 4 TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG R RF: TATAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAACTGAATAGACATTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAGAAATTGGTTATGCAAT RR: ATATTTATATTATATCTTATGACGATCGGATACGAAATTTTGACTTATCTGTAAATAATGACTTTACAGATAACCTCATCTCACTCTTCTTTCTTTAACCAATACGTTA F2: 3 CGTTA 2 Unidirectional alignment (log-probability: -25.4) TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAA---------ACATtgcTTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAACTGAATAGACAT---TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG Template switch alignment (log-probability: -16.4) TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAAC|ATTGC|TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG TAAATATAATATAGAATACTGCTAGCCTATGCTTTAAAAC|ATTGC|TTATTACTGAAATGTCTATTGGAGTAGAGTGAGAAGAAAG ========== Event 2321 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACCCTGTTTTGGTTCTAATGGGTTGAGACA-------CTTGGGCACGTCATCTGCATTA Chimp: ACCCTGTTTTGGTTCTAATGGGTTGAGACA-------CTTGGGCACGTCATCTGCATTA Gorilla: ACCCTGTTTTGGTTCTAATGGGTCTCAACCCATTAGGGTTGGGCACGTTATCTGCATTA ↓ 3 1 2 4 Human: ACCCTGTTTTGGTTCTAATGGGTTGAGACA-------CTTGGGCACGTCATCTGCATTA Cluster: [ ] Orangutan: ACCCTGTTTTGGTTCTAATGGGTTGAGACA-------CTTGGGCACGTCATCTGCATTA Gorilla > Human --------------- chr3:17417949-17417956 Template switch process: F1: L AAGATACAGTGTTCAACTACCCTGTTTTGGTTCTAATGGGT 1 F3: 4 TTGGGCACGTCATCTGCATTAGTTTCCTAATCTGAAAAGG R RF: AAGATACAGTGTTCAACTACCCTGTTTTGGTTCTAATGGGTCTCAACCCATTAGGGTTGGGCACGTTATCTGCATTAGTTTCCTAATCTGAAAAGG RR: TTCTATGTCACAAGTTGATGGGACAAAACCAAGATTACCCAGAGTTGGGTAATCCCAACCCGTGCAATAGACGTAATCAAAGGATTAGACTTTTCC F2: 3 CACAGAGT 2 Unidirectional alignment (log-probability: -36.9) AGATACAGTGTTCAACTACCCTGTTTTGGTTCTAATGGGTtgagacaC--------------TTGGGCACGTcATCTGCATTAGTTTCCTAATCTGAAAAGG AGATACAGTGTTCAACTACCCTGTTTTGGTTCTAATGGGT-------CTCAACCCATTAGGGTTGGGCACGTTATCTGCATTAGTTTCCTAATCTGAAAAGG Template switch alignment (log-probability: -27.8) AGATACAGTGTTCAACTACCCTGTTTTGGTTCTAATGGGT|TGAGACaC|TTGGGCACGTcATCTGCATTAGTTTCCTAATCTGAAAAGG AGATACAGTGTTCAACTACCCTGTTTTGGTTCTAATGGGT|TGAGACCC|TTGGGCACGTTATCTGCATTAGTTTCCTAATCTGAAAAGG ========== Event 2322 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: tatgactGTGCTCTTGAACTTCAGCACAGCTGAAGTTTGGTTTGGCAGCTGTGCT ↑ 3 1 2 4 Chimp: tatgactGTGCTCTTGAACTTCAGCTGTGCTTTCGTTTGGTTTGGCAGCTGTGCT Gorilla: tatgactGTGCTCTTGAACTTCAGCAGTGCTTTCGTTTGGTTTGGCAGCTGTGCT Human: tatgactGTGCTCTTGAACTTCAGCACAGCTGAAGTTTGGTTTGGCAGCTGTGCT Cluster: [ ] Orangutan: tatgactGTGCTCTTGAACTTCAGCAATGCTTTCATTTGGTTTGGCAGCTGTGCT Chimp > Human ------------- chr3:174496046-174496054 Template switch process: F1: L TAAAATTTTTTGATTGTATGACTGTGCTCTTGAACTTCAGC 1 F3: 4 GTTTGGTTTGGCAGCTGTGCTAGGTGGGGCACCTCTGGCT R RF: TAAAATTTTTTGATTGTATGACTGTGCTCTTGAACTTCAGCTGTGCTTTCGTTTGGTTTGGCAGCTGTGCTAGGTGGGGCACCTCTGGCT RR: ATTTTAAAAAACTAACATACTGACACGAGAACTTGAAGTCGACACGAAAGCAAACCAAACCGTCGACACGATCCACCCCGTGGAGACCGA F2: 3 AAGTCGACA 2 Unidirectional alignment (log-probability: -34.5) AAAATTTTTTGATTGTATGACTGTGCTCTTGAACTTCAGCacagctgaa---------GTTTGGTTTGGCAGCTGTGCTAGGTGGGGCACCTCTGGCT AAAATTTTTTGATTGTATGACTGTGCTCTTGAACTTCAGC---------TGTGCTTTCGTTTGGTTTGGCAGCTGTGCTAGGTGGGGCACCTCTGGCT Template switch alignment (log-probability: -16.4) AAAATTTTTTGATTGTATGACTGTGCTCTTGAACTTCAGC|ACAGCTGAA|GTTTGGTTTGGCAGCTGTGCTAGGTGGGGCACCTCTGGCT AAAATTTTTTGATTGTATGACTGTGCTCTTGAACTTCAGC|ACAGCTGAA|GTTTGGTTTGGCAGCTGTGCTAGGTGGGGCACCTCTGGCT ========== Event 2323 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCTAAAATCCTTTCTGGCTCTGGAAAGGATATTCTTCGCAGGGCCAGAAAGGaatatctatat Chimp: TCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTTCACAGGGCCAGAAAGGAatatctatat ↓ 3 2 1 4 Gorilla: TCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTTTGCAGAGCCAGAAAGGAatatctatat Human: TCCTAAAATCCTTTCTGGCTCTGGAAAGGATATTCTTCGCAGGGCCAGAAAGGaatatctatat Cluster: [ ] Orangutan: ---------------------------------------------------------------- Chimp > Gorilla --------------- chr3:177825280-177825285 Template switch process: F1: L TGCGTCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTT 1 F3: 4 GCCAGAAAGGAATATCTATATCTATATCTATATCTGTATC R RF: TGTGTCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTTCACAGGGCCAGAAAGGAATATCTATATCTATATCTATATCTGTATC RR: ACACAGGATTTTAGGAAAGACCGAGACGTTTCCTATAAGAAGTGTCCCGGTCTTTCCTTATAGATATAGATATAGATATAGACATAG F2: 3 AGACGT 2 Unidirectional alignment (log-probability: -40) GcGTCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTTtgCAGaGCCAGAAAGGAATATCTATATCTATATCTATATctgtatc GTGTCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTTCACAGGGCCAGAAAGGAATATCTATATCTATATCTATAT------- Template switch alignment (log-probability: -22) GcGTCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTT|TGCAGA|GCCAGAAAGGAATATCTATATCTATATCTATATCTGTATC GTGTCCTAAAATCCTTTCTGGCTCTGCAAAGGATATTCTT|TGCAGA|GCCAGAAAGGAATATCTATATCTATATCTATATCTGTATC ========== Event 2324 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: TATGAGCATATTTTATTAATAACATCTTATCATTAAATTGAATATGGATA-TTTAACATTCAATAAGCACATA Chimp: TATGAGCATATTTTATTAATA-AATATCCATATTCAATTTAATGATAAGATGTTAACATTTAATAAGCACAGA ↓ 13 24 ↑ 13 24 Gorilla: TATGAGCATATTTTATTAATAACATCTTATCATTAAATTGAATATGGATA-TTTAACATTTAATAAGCATAGA Human: TATGAGCATATTTTATTAATAACATCTTATCATTAAATTGAATATGGATA-TTTAACATTCAATAAGCACATA Cluster: [ ] Orangutan: TATG-ACATA-TTTATTAATAACATCTTATCATGACATA-GATAAGAGTA-TT-TACATT-TATAAGCACAGA Gorilla > Chimp --------------- chr3:179650140-179650168 Template switch process: F1: L CAGGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA 1 F3: 4 TTAACATTTAATAAGCACAGAATGTATATGTAGAAATGTA R RF: CAGGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAACATCTTATCATTAAATTGAATATGGATATTTAACATTTAATAAGCATAGAATGTATATTTAGAAATGTG RR: GTCCTAATTAGACATTGAAAATACTCGTATAAAATAATTATTGTAGAATAGTAATTTAACTTATACCTATAAATTGTAAATTATTCGTATCTTACATATAAATCTTTACAC F2: 3 GTAGAATAGTAATTTAACTTATACCTATA 2 Unidirectional alignment (log-probability: -74.5) GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA-------------------------ATATccatattcaatttaatgataagatgTTAACATTTAATAAGCAcAGAATGTATATgTAGAAATGTa GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAACATCTTATCATTAAATTGAATATGGATAT-------------------------TTAACATTTAATAAGCATAGAATGTATATTTAGAAATGTG Template switch alignment (log-probability: -36) GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA|ATATCCATATTCAATTTAATGATAAGATG|TTAACATTTAATAAGCAcAGAATGTATATgTAGAAATGTa GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA|ATATCCATATTCAATTTAATGATAAGATG|TTAACATTTAATAAGCATAGAATGTATATTTAGAAATGTG Chimp > Gorilla --------------- chr3:178768702-178768730 Template switch process: F1: L CAGGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA 1 F3: 4 TTAACATTTAATAAGCATAGAATGTATATTTAGAAATGTG R RF: CAGGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAAATATCCATATTCAATTTAATGATAAGATGTTAACATTTAATAAGCACAGAATGTATATGTAGAAATGTA RR: GTCCTAATTAGACATTGAAAATACTCGTATAAAATAATTATTTATAGGTATAAGTTAAATTACTATTCTACAATTGTAAATTATTCGTGTCTTACATATACATCTTTACAT F2: 3 TATAGGTATAAGTTAAATTACTATTCTAC 2 Unidirectional alignment (log-probability: -74.5) GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAAcatcttatcattaaattgaatatggATAT-------------------------TTAACATTTAATAAGCAtAGAATGTATATtTAGAAATGTg GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA-------------------------ATATCCATATTCAATTTAATGATAAGATGTTAACATTTAATAAGCACAGAATGTATATGTAGAAATGTA Template switch alignment (log-probability: -36) GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA|CATCTTATCATTAAATTGAATATGGATAT|TTAACATTTAATAAGCAtAGAATGTATATtTAGAAATGTg GGATTAATCTGTAACTTTTATGAGCATATTTTATTAATAA|CATCTTATCATTAAATTGAATATGGATAT|TTAACATTTAATAAGCACAGAATGTATATGTAGAAATGTA ========== Event 2325 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGTAAATGTTAAGCCTATT------------AGAACCATCCCTGGAGATGGGAGTGGGCT Chimp: TAAGTAAACTTTAAGCCTATT------------AGAACCATCCCTGGAGATGGGAGTGGGCT ↓ 3 4 2 Gorilla: TAAGTAAACTTTAAGCCTATTAAAGATGGTTCTAAAACCATCCCTGGAGATGGGAGTGGGCT Human: TAAGTAAATGTTAAGCCTATT------------AGAACCATCCCTGGAGATGGGAGTGGGCT Cluster: [ ] Orangutan: -------------------------------------------------------------- Chimp > Gorilla --------------- chr3:178893699-178893709 Template switch process: F1: L CAATTACTGTCAAAAAAGACTAAGTAAACTTTAAGCCTATTAAA 1 F3: 4 AACCATCCCTGGAGATGGGAGTGGGCTCTAGTGAAAAGCA R RF: CAATTACTGTCAAAAAAGACTAAGTAAACTTTAAGCCTATTAGAACCATCCCTGGAGATGGGAGTGGGCTCCAGTGAAAAGCG RR: GTTAATGACAGTTTTTTCTGATTCATTTGAAATTCGGATAATCTTGGTAGGGACCTCTACCCTCACCCGAGGTCACTTTTCGC F2: 3 AATCTTGGTAG 2 Unidirectional alignment (log-probability: -44.7) TACTGTCAAAAAAGACTAAGTAAACTTTAAGCCTATtaaagatggttcTAaAACCATCCCTGGAGATGGGAGTGGGCTCtAGTGAAAAGCa TACTGTCAAAAAAGACTAAGTAAACTTTAAGCCTAT------------TAGAACCATCCCTGGAGATGGGAGTGGGCTCCAGTGAAAAGCG Template switch alignment (log-probability: -33.8) TACTGTCAAAAAAGACTAAGTAAACTTTAAGCCTATTAaA|GATGGTTCTAA|AACCATCCCTGGAGATGGGAGTGGGCTCtAGTGAAAAGCa TACTGTCAAAAAAGACTAAGTAAACTTTAAGCCTATTAGA|GATGGTTCTAA|AACCATCCCTGGAGATGGGAGTGGGCTCCAGTGAAAAGCG ========== Event 2326 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AACACTCCAAAGGGAACATAAGGTCTTAACTTGTTT-TCTGTTATCTCGTCCCCCACCTTAT Chimp: AAGACTCCAAAGGGAACATAAGGTCTTAACTTGTTT-TCTGTTATCTCGTCCCCCACCTTAT ↓ 13 24 ↑ 13 24 Gorilla: AAGACTCCAAAGGGAACATAACA-GAAAACAAGTTAAGACCTTATCTCGTCCCCCACCTTAT ↓ 13 24 ↑ 13 24 Human: AACACTCCAAAGGGAACATAAGGTCTTAACTTGTTT-TCTGTTATCTCGTCCCCCACCTTAT Cluster: [ ] Orangutan: -------------------------------------------------------------- Gorilla > Human --------------- chr3:177672846-177672864 Template switch process: F1: L GGGAAGTTGTTAGAACTCAGAACACTCCAAAGGGAACATAA 1 F3: 4 TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC R RF: GGGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAACAGAAAACAAGTTAAGACCTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC RR: CCCTTCAACAATCTTGAGTCTTCTGAGGTTTCCCTTGTATTGTCTTTTGTTCAATTCTGGAATAGAGCAGGGGGTGGAATAAGAGTTGGACTTTTCTCGG F2: 3 GTCTTTTGTTCAATTCTGG 2 Unidirectional alignment (log-probability: -60) GGAAGTTGTTAGAACTCAGAAcACTCCAAAGGGAACATAA-------------------ggtcttaacttgttttctgTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAaCC GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAACAGAAAACAAGTTAAGACC-------------------TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC Template switch alignment (log-probability: -29.2) GGAAGTTGTTAGAACTCAGAAcACTCCAAAGGGAACATAA|GGTCTTAACTTGTTTTCTG|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAaCC GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA|GGTCTTAACTTGTTTTCTG|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC Human > Gorilla --------------- chr3:180711851-180711869 Template switch process: F1: L GGGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA 1 F3: 4 TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC R RF: GGGAAGTTGTTAGAACTCAGAACACTCCAAAGGGAACATAAGGTCTTAACTTGTTTTCTGTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC RR: CCCTTCAACAATCTTGAGTCTTGTGAGGTTTCCCTTGTATTCCAGAATTGAACAAAAGACAATAGAGCAGGGGGTGGAATAAGAGTTGGACTTTTCTTGG F2: 3 CCAGAATTGAACAAAAGAC 2 Unidirectional alignment (log-probability: -60) GGAAGTTGTTAGAACTCAGAAgACTCCAAAGGGAACATAA-------------------cagaaaacaagttaagaccTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAgCC GGAAGTTGTTAGAACTCAGAACACTCCAAAGGGAACATAAGGTCTTAACTTGTTTTCTG-------------------TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC Template switch alignment (log-probability: -29.2) GGAAGTTGTTAGAACTCAGAAgACTCCAAAGGGAACATAA|CAGAAAACAAGTTAAGACC|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAgCC GGAAGTTGTTAGAACTCAGAACACTCCAAAGGGAACATAA|CAGAAAACAAGTTAAGACC|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC Gorilla > Chimp --------------- chr3:181578011-181578029 Template switch process: F1: L GGGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA 1 F3: 4 TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC R RF: GGGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAACAGAAAACAAGTTAAGACCTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC RR: CCCTTCAACAATCTTGAGTCTTCTGAGGTTTCCCTTGTATTGTCTTTTGTTCAATTCTGGAATAGAGCAGGGGGTGGAATAAGAGTTGGACTTTTCTCGG F2: 3 GTCTTTTGTTCAATTCTGG 2 Unidirectional alignment (log-probability: -54.4) GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA-------------------ggtcttaacttgttttctgTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAaCC GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAACAGAAAACAAGTTAAGACC-------------------TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC Template switch alignment (log-probability: -23.7) GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA|GGTCTTAACTTGTTTTCTG|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAaCC GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA|GGTCTTAACTTGTTTTCTG|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC Chimp > Gorilla --------------- chr3:180711851-180711869 Template switch process: F1: L GGGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA 1 F3: 4 TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAGCC R RF: GGGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAAGGTCTTAACTTGTTTTCTGTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC RR: CCCTTCAACAATCTTGAGTCTTCTGAGGTTTCCCTTGTATTCCAGAATTGAACAAAAGACAATAGAGCAGGGGGTGGAATAAGAGTTGGACTTTTCTTGG F2: 3 CCAGAATTGAACAAAAGAC 2 Unidirectional alignment (log-probability: -54.4) GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA-------------------cagaaaacaagttaagaccTTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAgCC GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAAGGTCTTAACTTGTTTTCTG-------------------TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC Template switch alignment (log-probability: -23.7) GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA|CAGAAAACAAGTTAAGACC|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAgCC GGAAGTTGTTAGAACTCAGAAGACTCCAAAGGGAACATAA|CAGAAAACAAGTTAAGACC|TTATCTCGTCCCCCACCTTATTCTCAACCTGAAAAGAACC ========== Event 2327 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAAGTATAAATTGTCAGTTTTG--A--CCAATTTTTGTTGTGgttttcgatctcattcatttttgccattaattttattattttcttcctcatttctttgggtttgctctatttatcctttgagttgaatgttcagctcaaatttttggtcatctttgttttgtgataaatg ↑ 1 4 3 2 Chimp: AAAAGTATAAATTGTCAGTTTATAAACCACAAtttttgttgtggttttcgatctcattcatttttgccattaattttattattttcttcctcatttctttgggtttgctctatttatcctttgagttgaatgttcagctcaaatttttggtcatctttgttttgtgataaatg Gorilla: AAAAGTATAAATTGTCAGttttg--a--ccaatttttgttgcggttttcaatctcattcatttttgccattaattttattattttCTTCCTCGTTTCTTTCGGtttgctctatttatcctttgagttgaatgttcagctcaaatttttggtcatctttgttttgtgataaatg Human: AAAAGTATAAATTGTCAGTTTTG--A--CCAATTTTTGTTGTGgttttcgatctcattcatttttgccattaattttattattttcttcctcatttctttgggtttgctctatttatcctttgagttgaatgttcagctcaaatttttggtcatctttgttttgtgataaatg Cluster: [ ] Orangutan: aaaagtattaattgtcagttttg--a--ccaatttttgttgtggttttcgatctcattcatttttgccattaattttattattttcttcttcacttctttgggtttgctctatttatcctttgagttgaatgttcagctcaaatttttggtcatctttgttttgtgataaata Chimp > Human ------------- chr3:19641004-19641007 Template switch process: F1: L ATGTATGTAAAAGTTCTTTGAAAAGTATAAATTGTCAGTTT 1 F3: 4 CAATTTTTGTTGTGGTTTTCGATCTCATTCATTTTTGCCA R RF: ATGTATGTAAAAGTTCTTTGAAAAGTATAAATTGTCAGTTTATAAACCACAATTTTTGTTGTGGTTTTCGATCTCATTCATTTTTGCCATTAATTTTATTATTTTCTTCCTCATTTCTTTGGGTTTGCTCTATTTATCCTTTGAGTTGAATGTTCAGCTCAAATTTTTGGTCA RR: TACATACATTTTCAAGAAACTTTTCATATTTAACAGTCAAATATTTGGTGTTAAAAACAACACCAAAAGCTAGAGTAAGTAAAAACGGTAATTAAAATAATAAAAGAAGGAGTAAAGAAACCCAAACGAGATAAATAGGAAACTCAACTTACAAGTCGAGTTTAAAAACCAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -27.3) TGTATGTAAAAGTTCTTTGAAAAGTATAAATTGTCAGTTTtgac--------CAATTTTTGTTGTGGTTTTCGATCTCATTCATTTTTGCCA TGTATGTAAAAGTTCTTTGAAAAGTATAAATTGTCAGTTT----ATAAACCACAATTTTTGTTGTGGTTTTCGATCTCATTCATTTTTGCCA Template switch alignment (log-probability: -15.8) TGTATGTAAAAGTTCTTTGAAAAGTATAAATTGTCAGTTT|TGAC|CAATTTTTGTTGTGGTTTTCGATCTCATTCATTTTTGCCA TGTATGTAAAAGTTCTTTGAAAAGTATAAATTGTCAGTTT|TGAC|CAATTTTTGTTGTGGTTTTCGATCTCATTCATTTTTGCCA ========== Event 2328 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TACCTCTCCAAAATAAAGTTTCAGAGGTAAATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACATGCACAATTG-AAATGTGTTTGGTTAACAtttt Chimp: TACCTCTCCAAAATGAAGTTTCAGAGGTAAATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAATTG-AAATGTGTTTGGTTAACAtttt ↓ 3 2 1 4 Gorilla: TACCTCTCCAAAATAAAGTTTCAGAGGTAAATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAACTGAAAATGTGTTTGGTTAACAtttt ↑ 3 2 1 4 Human: TACCTCTCCAAAATAAAGTTTCAGAGGTAAATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACATGCACAATTG-AAATGTGTTTGGTTAACAtttt Cluster: [ ] Orangutan: TACCTCTCCAAAATAAAGTTTCAGAAGTAAATAAAAGGGGAACAGTGAGACAAGCTCTTCATGAACAACATGCACAATTT-AAATGTGTTTGGTTAACAtttt Human > Gorilla --------------- chr3:181903075-181903079 Template switch process: F1: L AATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAA 1 F3: 4 AATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT R RF: TTCAGAGGTAAATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACATGCACAATTGAAATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT RR: AAGTCTCCATTTATTTTCCCCTTCTCACTCTGTTCGAGAAGTACTTGTTGTACGTGTTAACTTTACACAAACCAATTGTAAAAACAAACAAAATAAAACAA F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -33.1) GGGAAGAGTGAGACAAGCTCTTCATGAACAACAcGCACAAcTGaAAATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGtt GGGAAGAGTGAGACAAGCTCTTCATGAACAACATGCACAATTG-AAATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTG-- Template switch alignment (log-probability: -22) GGGAAGAGTGAGACAAGCTCTTCATGAACAACAcGCACAA|CTGAA|AATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT GGGAAGAGTGAGACAAGCTCTTCATGAACAACATGCACAA|CTGAA|AATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT Chimp > Gorilla --------------- chr3:181903075-181903079 Template switch process: F1: L GGGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAA 1 F3: 4 AATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT R RF: TTCAGAGGTAAATAAAAGGGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAATTGAAATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT RR: AAGTCTCCATTTATTTTCCCCTTCTCACTCTGTTCGAGAAGTACTTGTTGTGCGTGTTAACTTTACACAAACCAATTGTAAAAACAAACAAAATAAAACAA F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -27.5) GGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAAcTGaAAATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGtt GGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAATTG-AAATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTG-- Template switch alignment (log-probability: -16.3) GGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAA|CTGAA|AATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT GGGAAGAGTGAGACAAGCTCTTCATGAACAACACGCACAA|CTGAA|AATGTGTTTGGTTAACATTTTTGTTTGTTTTATTTTGTT ========== Event 2329 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGTCAAAAAGGCATCACTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGA-----------------------------------------------------------------------------------------------------------------------TATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTAAAGC ↓ 3 4 2 1 Chimp: TCATGTCAAAAAGGCATCACTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAGAAAGCTTAGGGCAAGGCAAGCATGCTTATATCATCAATAAGACAAATTTGAGATGCATTAAAGATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTAAAGC ↑ 3 4 2 1 Gorilla: TCGTGTCAAAAAGGCATCACTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGA-----------------------------------------------------------------------------------------------------------------------TATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTAAAGC Human: TCATGTCAAAAAGGCATCACTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGA-----------------------------------------------------------------------------------------------------------------------TATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTAAAGC Cluster: [ ] Orangutan: TCATGTCAAAAAGGCATTACTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGA-----------------------------------------------------------------------------------------------------------------------TATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTAAAGC Human > Chimp ------------- chr3:18101427-18101489 Template switch process: F1: L GATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAG 1 F3: 4 ATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTA R RF: CTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTA RR: GAAATTACGTAGAGTTTAAACAGAATAACTACTATATTCGTACGAACGGAACGGGATTCGAAAATCTGATCTATATTACGTTAACAACTTTCTGTCAGAAGTATGGTAAAAT F2: 3 GAAATTACGTAGAGTTTAAACAGAATAACTACTATATTCGTACGAACGGAACGGGATTCGAAA 2 Unidirectional alignment (log-probability: -182) AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACagaaagcttagggcaaggcaagcatgcttatatcatcaataagacaaatttgagatgcattaaagatgcttgccttgccctaagcttttagactagatataatgc AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGAC--------------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -23.8) AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAG|AAAGCTTAGGGCAAGGCAAGCATGCTTATATCATCAATAAGACAAATTTGAGATGCATTAAAG|ATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGC AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAG|AAAGCTTAGGGCAAGGCAAGCATGCTTATATCATCAATAAGACAAATTTGAGATGCATTAAAG|ATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGC Gorilla > Chimp --------------- chr3:18101427-18101489 Template switch process: F1: L GATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAG 1 F3: 4 ATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTA R RF: CTTTAATGCATCTCAAATTTGTCTTATTGATGATATAAGCATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAGTCTTCATACCATTTTA RR: GAAATTACGTAGAGTTTAAACAGAATAACTACTATATTCGTACGAACGGAACGGGATTCGAAAATCTGATCTATATTACGTTAACAACTTTCTGTCAGAAGTATGGTAAAAT F2: 3 GAAATTACGTAGAGTTTAAACAGAATAACTACTATATTCGTACGAACGGAACGGGATTCGAAA 2 Unidirectional alignment (log-probability: -182) AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAgaaagcttagggcaaggcaagcatgcttatatcatcaataagacaaatttgagatgcattaaagatgcttgccttgccctaagcttttagactagatataatgc AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACA-------------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -24.8) AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAG|AAAGCTTAGGGCAAGGCAAGCATGCTTATATCATCAATAAGACAAATTTGAGATGCATTAAAG|ATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGC AAGCTTTTAGACTAGATATAATGCAATTGTTGAAAGACAG|AAAGCTTAGGGCAAGGCAAGCATGCTTATATCATCAATAAGACAAATTTGAGATGCATTAAAG|ATGCTTGCCTTGCCCTAAGCTTTTAGACTAGATATAATGC ========== Event 2330 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TACATTGATTTTTAATAATTGAAATACTGTTAAAG---------TATTTCTATAATGAAAGAAAATTTTTAA Chimp: TACATTGATTTTTAATAATTGAAATACTGTTAAAG---------TATTTCTATAATGAAAGAAAATTTTTAA ↓ 3 2 1 4 Gorilla: TACATTGATTTTTAATAATTGACATACTGTTAAAGTATTAACAGTATTTCAATAATGAAAGAAAATTTTTAA ↑ 3 2 1 4 Human: TACATTGATTTTTAATAATTGAAATACTGTTAAAG---------TATTTCTATAATGAAAGAAAATTTTTAA Cluster: [ ] Orangutan: TACATTGATTTTTAATAATTGAAATACTGTTAAAG---------TATTTCTATAATGAAAGAAAATTTTTAA Human > Gorilla --------------- chr3:17539260-17539271 Template switch process: F1: L CATCTGTACATTGATTTTTAATAATTGACATACTGTTAAAGTATT 1 F3: 4 ATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA R RF: CATCTGTACATTGATTTTTAATAATTGAAATACTGTTAAAGTATTTCTATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA RR: GTAGACATGTAACTAAAAATTATTAACTTTATGACAATTTCATAAAGATATTACTTTCTTTTAAAAATTCACCATATAAAACAAAGTT F2: 3 ACTTTATGACAA 2 Unidirectional alignment (log-probability: -35) GTACATTGATTTTTAATAATTGAcATACTGTTAAagtattaacAGTATTTCaATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA GTACATTGATTTTTAATAATTGAAATACTGTTAA---------AGTATTTCTATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA Template switch alignment (log-probability: -22.9) GTACATTGATTTTTAATAATTGAcATACTGTTAAAGTATT|AACAGTATTTCA|ATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA GTACATTGATTTTTAATAATTGAAATACTGTTAAAGTATT|AACAGTATTTCA|ATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA Chimp > Gorilla --------------- chr3:17539260-17539271 Template switch process: F1: L CATCTGTACATTGATTTTTAATAATTGACATACTGTTAAAGTATT 1 F3: 4 ATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA R RF: CATCTGTACATTGATTTTTAATAATTGAAATACTGTTAAAGTATTTCTATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA RR: GTAGACATGTAACTAAAAATTATTAACTTTATGACAATTTCATAAAGATATTACTTTCTTTTAAAAATTCACCATATAAAACAAAGTT F2: 3 ACTTTATGACAA 2 Unidirectional alignment (log-probability: -35) GTACATTGATTTTTAATAATTGAcATACTGTTAAagtattaacAGTATTTCaATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA GTACATTGATTTTTAATAATTGAAATACTGTTAA---------AGTATTTCTATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA Template switch alignment (log-probability: -22.9) GTACATTGATTTTTAATAATTGAcATACTGTTAAAGTATT|AACAGTATTTCA|ATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA GTACATTGATTTTTAATAATTGAAATACTGTTAAAGTATT|AACAGTATTTCA|ATAATGAAAGAAAATTTTTAAGTGGTATATTTTGTTTCAA ========== Event 2331 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGAATAATTTTTAAATGTATAAA--TACTGCTCACAGTTTACTTCCC---- Chimp: AAAGAATAATTTTTAAATGTATAAA--TACTGCTCACCGTTTACTTCCC---- ↓ 1 4 3 2 Gorilla: GAAGAATAATTTTTAAATGTAGCAGTAAACTGCTCACCGTTTACTTCCC---- Human: GAAGAATAATTTTTAAATGTATAAA--TACTGCTCACAGTTTACTTCCC---- Cluster: [ ] Orangutan: GAAGAATAATTTTTAAATGTATAAA--tactgctcacagtttacttcccttta Chimp > Gorilla --------------- chr3:16407583-16407587 Template switch process: F1: L TATTAAAATCTCTAATATCCGAAGAATAATTTTTAAATGTA 1 F3: 4 AAACTGCTCACCGTTTACTTCCCTTTAGCTGATCCTTTTTTT R RF: TATTAAAATCTCTAATATCCAAAGAATAATTTTTAAATGTATAAATACTGCTCACCGTTTACTTCCCTTTAGCTGATCCTTTTTTA RR: ATAATTTTAGAGATTATAGGTTTCTTATTAAAAATTTACATATTTATGACGAGTGGCAAATGAAGGGAAATCGACTAGGAAAAAAT F2: 3 TGACG 2 Unidirectional alignment (log-probability: -40.2) ATTAAAATCTCTAATATCCgAAGAATAATTTTTAAATGTAgcagTAA--ACTGCTCACCGTTTACTTCCCTTTAGCTGATCCTTTTT ATTAAAATCTCTAATATCCAAAGAATAATTTTTAAATGTA----TAAATACTGCTCACCGTTTACTTCCCTTTAGCTGATCCTTTTT Template switch alignment (log-probability: -33) ATTAAAATCTCTAATATCCgAAGAATAATTTTTAAATGTA|GCAGT|AaACTGCTCACCGTTTACTTCCCTTTAGCTGATCCTTTTT ATTAAAATCTCTAATATCCAAAGAATAATTTTTAAATGTA|GCAGT|ATACTGCTCACCGTTTACTTCCCTTTAGCTGATCCTTTTT ========== Event 2332 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATATTGCTTTTGCTCAAATTTGATTAGACTTAAAGTCTAATTGATTAGACTTAAATAAGCATTTAAGACTTATTTTGT Chimp: ATATTGCTTTTGCTCAAATTTGATTAGACTTAAAGTCTAATTGATTAGACTTAAATAAGCATTTAAGACTTATTTTGT Gorilla: ATATTGCTTTTGCTCAAATTTGATTAGACTT-------------------------AAGCATTTAAGACTTATTTTGT ↓ 4 3 2 1 Human: ATATTGCTTTTGCTCAAATTTGATTAGACTTAAAGTCTAATTGATTAGACTTAAATAAGCATTTAAGACTTATTTTGT Cluster: [ ] Orangutan: ATATTGCTTTTGCTCAAATTTGAGTAGA----------------------------------------CTTATTTTGT Gorilla > Human --------------- chr3:14433870-14433876 Template switch process: F1: L GAATTGCAAAATATTGCTTTTGCTCAAATTTGATTAGACTTAA 1 F3: 4 TTGATTAGACTTAAATAAGCATTTAAGACTTATTTTGTACTCTTAATTTTCTGTAC R RF: GAATTGCAAAATATTGCTTTTGCTCAAATTTGATTAGACTTAAGCATTTAAGACTTATTTTGTACTCTTAATTTTCTGTAC RR: CTTAACGTTTTATAACGAAAACGAGTTTAAACTAATCTGAATTCGTAAATTCTGAATAAAACATGAGAATTAAAAGACATG F2: 3 AATCTGA 2 Unidirectional alignment (log-probability: -46.8) TTGCAAAATATTGCTTTTGCTCAAATTTGATTAGACTtaaagtctaattgattagacttaaaTAAGCATTTAAGACTTATTTTGTAC TTGCAAAATATTGCTTTTGCTCAAATTTGATTAGACT-------------------------TAAGCATTTAAGACTTATTTTGTAC Template switch alignment (log-probability: -32.5) TTGCAAAATATTGCTTTTGCTCAAATTTGATTAGACTTAA|AGTCTAA|TTGATTAGACTtaaaTAAGCATTTAAGACTTATTTTGTAC TTGCAAAATATTGCTTTTGCTCAAATTTGATTAGACTTAA|AGTCTAA|TTGATTAGACT----TAAGCATTTAAGACTTATTTTGTAC ========== Event 2333 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: tatgatcatgtcactgtactccagcctgggtgacagagcgagatcctgtttcttaa--aaataaataaaTAACGCAATTGGGTTTTAG-------CTGGAAAAAAGCAGTGAAGGAGGAGG ↑ 3 2 1 4 Chimp: tatgatcatgtcactgtactccagcctgggtgacagagcgagatcctgtttcttaa--aaataaataaaTAACGCAATTGGGTTTTAGTTTAGTTTTAGCAAAAAGCAGTGAAGGAGGAGG ↓ 3 2 1 4 Gorilla: tatgatcatgtcaccgtactccagcctgggtgacagagcgagatcctgtttcttaa--aaataaataaaTAACGCAATTGGGTTTTAG-------CTGGAAAAAAGCAGTGAAGGAGGAGG Human: tatgatcatgtcactgtactccagcctgggtgacagagcgagatcctgtttcttaa--aaataaataaaTAACGCAATTGGGTTTTAG-------CTGGAAAAAAGCAGTGAAGGAGGAGG Cluster: [ ] Orangutan: tatgatcatgtcactgtactccagcatgggtgacagagcgagatcctatttcttaaataaataaataaaTAATGCAATTGGGTTTTAG-------CTGGAAAAAAGCAGTGGAGGAGGAGG Chimp > Human ------------- chr3:12800136-12800140 Template switch process: F1: L CTGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAG 1 F3: 4 AAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC R RF: TCCAGCCTGGGTGACAGAGCGAGATCCTGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAGTTTAGTTTTAGCAAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC RR: AGGTCGGACCCACTGTCTCGCTCTAGGACAAAGAATTTTTATTTATTTATTGCGTTAACCCAAAATCAAATCAAAATCGTTTTTCGTCACTTCCTCCTCCCTTGGATACTGAGAGTCCG F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -27.5) TGTTTCTTAAAAATAAATAAATAACGCAATTGG-----------GTTTTAGCtggaAAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAGTTTAGTTTTAGC----AAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC Template switch alignment (log-probability: -15.9) TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAG|CTGGA|AAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAG|CTGGA|AAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC Chimp > Gorilla --------------- chr3:12769351-12769355 Template switch process: F1: L CTGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAG 1 F3: 4 AAAAAGCAGTGAAGGAGGAGGGAACCTACGACTCTCAGGC R RF: TCCAGCCTGGGTGACAGAGCGAGATCCTGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAGTTTAGTTTTAGCAAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC RR: AGGTCGGACCCACTGTCTCGCTCTAGGACAAAGAATTTTTATTTATTTATTGCGTTAACCCAAAATCAAATCAAAATCGTTTTTCGTCACTTCCTCCTCCCTTGGATACTGAGAGTCCG F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -32.5) TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTT-----------TAGCtggaAAAAAGCAGTGAAGGAGGAGGGAACCTAcGACTCTCAGGC TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAGTTTAGTTTTAGC----AAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC Template switch alignment (log-probability: -21.9) TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAG|CTGGA|AAAAAGCAGTGAAGGAGGAGGGAACCTAcGACTCTCAGGC TGTTTCTTAAAAATAAATAAATAACGCAATTGGGTTTTAG|CTGGA|AAAAAGCAGTGAAGGAGGAGGGAACCTATGACTCTCAGGC ========== Event 2334 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTGTACTGTCAATAGAGTAAGAAGCCCCAGG----CGTCTTAATTAAAGGAACAAAAAATTAGTGTGTGG Chimp: GTGTACTGTCAATAGAGTAAGAAGCCCCAGG----CGTCTTAATTAAAGGAACAAAAAATTAGTGTGTGG ↑ 3 1 4 Gorilla: GTGTACTGTCAATAGAGTAAGACGCCTGGGG--------CTAATTAAAGTAACAAAAAATTAGTGTGTGG ↓ 3 1 4 Human: GTGTACTGTCAATAGAGTAAGAAGCCCCAGG----CGTCTTAATTAAAGGAACAAAAAATTAGTGTGTGG Cluster: [ ] Orangutan: GTGTACTGTCAATAGAGTAAGAAGCCCCAGGCATC----TTAATTAAAGTAACAAAAAATTAGTGTGTGG Gorilla > Human --------------- chr3:185721085-185721098 Template switch process: F1: L CTCATAAATGCCACCTCCTGTGTACTGTCAATAGAGTAAGA 1 F3: 4 TAATTAAAGGAACAAAAAATTAGTGTGTGGATTTTAACCAATTAATGAAT R RF: CTCATAAATGCCACCCCCTGTGTACTGTCAATAGAGTAAGACGCCTGGGGCTAATTAAAGTAACAAAAAATTAGTGTGTGGATTTTAACCAATTAATGAAT RR: GAGTATTTACGGTGGGGGACACATGACAGTTATCTCATTCTGCGGACCCCGATTAATTTCATTGTTTTTTAATCACACACCTAAAATTGGTTAATTACTTA F2: 3 TCTGCGGACCCCGA 2 Unidirectional alignment (log-probability: -50) TCATAAATGCCACCtCCTGTGTACTGTCAATAGAGTAAGAaGCCccaGGCgtctTAATTAAAGgAACAAAAAATTAGTGTGTGGATTTTAACCA TCATAAATGCCACCCCCTGTGTACTGTCAATAGAGTAAGACGCCTGGGGC----TAATTAAAGTAACAAAAAATTAGTGTGTGGATTTTAACCA Template switch alignment (log-probability: -28.8) TCATAAATGCCACCtCCTGTGTACTGTCAATAGAGTAAGA|AGCCCCAGGCGTCT|TAATTAAAGgAACAAAAAATTAGTGTGTGGATTTTAACCA TCATAAATGCCACCCCCTGTGTACTGTCAATAGAGTAAGA|AGCCCCAGGCGTCT|TAATTAAAGTAACAAAAAATTAGTGTGTGGATTTTAACCA Gorilla > Chimp --------------- chr3:189808761-189808774 Template switch process: F1: L CTCATAAATGCCACCTCCTGTGTACTGTCAATAGAGTAAGA 1 F3: 4 TAATTAAAGGAACAAAAAATTAGTGTGTGGATTTTAACCAATTAATGAAT R RF: CTCATAAATGCCACCCCCTGTGTACTGTCAATAGAGTAAGACGCCTGGGGCTAATTAAAGTAACAAAAAATTAGTGTGTGGATTTTAACCAATTAATGAAT RR: GAGTATTTACGGTGGGGGACACATGACAGTTATCTCATTCTGCGGACCCCGATTAATTTCATTGTTTTTTAATCACACACCTAAAATTGGTTAATTACTTA F2: 3 TCTGCGGACCCCGA 2 Unidirectional alignment (log-probability: -50) TCATAAATGCCACCtCCTGTGTACTGTCAATAGAGTAAGAaGCCccaGGCgtctTAATTAAAGgAACAAAAAATTAGTGTGTGGATTTTAACCA TCATAAATGCCACCCCCTGTGTACTGTCAATAGAGTAAGACGCCTGGGGC----TAATTAAAGTAACAAAAAATTAGTGTGTGGATTTTAACCA Template switch alignment (log-probability: -28.8) TCATAAATGCCACCtCCTGTGTACTGTCAATAGAGTAAGA|AGCCCCAGGCGTCT|TAATTAAAGgAACAAAAAATTAGTGTGTGGATTTTAACCA TCATAAATGCCACCCCCTGTGTACTGTCAATAGAGTAAGA|AGCCCCAGGCGTCT|TAATTAAAGTAACAAAAAATTAGTGTGTGGATTTTAACCA ========== Event 2335 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TCAGACCCGTGACCACATTTCCCCAGACTTGGAGGAATCTGGGGAATGGTGCACCTGGgagactcc Chimp: TCAGACCCATGACCACATTTCCCCAGACTTGGAGGAATCTGGGGAATGGTGCACCTGGgagactcc ↑ 3 2 1 4 Gorilla: TCAGACCCATGACCACATTTCCCCAGACTTGGAGAAAGGA-TGGGATGGTGCACCTGGgagactcc Human: TCAGACCCGTGACCACATTTCCCCAGACTTGGAGGAATCTGGGGAATGGTGCACCTGGgagactcc Cluster: [ ] Orangutan: TCAGACCCGTGACCACATTTCCCCAGACTCGGAGGAAGGA-TGGGA-TATGCACCTGGgagactcc Gorilla > Chimp --------------- chr3:190519316-190519323 Template switch process: F1: L ACTTCTATCAGACCCATGACCACATTTCCCCAGACTTGGAGGAA 1 F3: 4 ATGGTGCACCTGGGAGACTCCTGGCCTCTGTAATAACCCT R RF: ACTTCTATCAGACCCATGACCACATTTCCCCAGACTTGGAGAAAGGATGGGATGGTGCACCTGGGAGACTCCTGGCCTCTGTAATAACCCT RR: TGAAGATAGTCTGGGTACTGGTGTAAAGGGGTCTGAACCTCTTTCCTACCCTACCACGTGGACCCTCTGAGGACCGGAGACATTATTGGGA F2: 3 AGGGGTCT 2 Unidirectional alignment (log-probability: -33.6) CTATCAGACCCATGACCACATTTCCCCAGACTTGGAGgAAtctggGGA----ATGGTGCACCTGGGAGACTCCTGGCCTCTGTAATAACCCT CTATCAGACCCATGACCACATTTCCCCAGACTTGGAGAAA-----GGATGGGATGGTGCACCTGGGAGACTCCTGGCCTCTGTAATAACCCT Template switch alignment (log-probability: -22.3) CTATCAGACCCATGACCACATTTCCCCAGACTTGGAGgAA|TCTGGGGA|ATGGTGCACCTGGGAGACTCCTGGCCTCTGTAATAACCCT CTATCAGACCCATGACCACATTTCCCCAGACTTGGAGAAA|TCTGGGGA|ATGGTGCACCTGGGAGACTCCTGGCCTCTGTAATAACCCT ========== Event 2336 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATGTGGCTGGGTAAAACCCACCC-----ACCATACTGCTTACATCCTATTCTAATAAG ↓ 1 3 4 2 Chimp: AATGTGGCTGGGTAAAACCCAGCAGTATGGTGATACTGCTTACATCCTATTCTAATAAG Gorilla: AATGTGGCTAGGTAAAACCCACCC-----ACCATACTGCTTACATCCTATTCTAATAAG Human: AATGTGGCTGGGTAAAACCCACCC-----ACCATACTGCTTACATCCTATTCTAATAAG Cluster: [ ] Orangutan: CATGTTGCTGGGTAAAACCCAG---------CATACTGCTTACATCCTATTCTAAGAAG Human > Chimp ------------- chr3:183365008-183365018 Template switch process: F1: L TGAACTAACTTAAGAAATTAAATGTGGCTGGGTAAAACCCA 1 F3: 4 ATACTGCTTACATCCTATTCTAATAAGTGAAAATGTGTTT R RF: TGAACTAACTTAAGAAATTAAATGTGGCTGGGTAAAACCCACCCACCATACTGCTTACATCCTATTCTAATAAGTGAAAATGTGTTT RR: ACTTGATTGAATTCTTTAATTTACACCGACCCATTTTGGGTGGGTGGTATGACGAATGTAGGATAAGATTATTCACTTTTACACAAA F2: 3 GTGGTATGACG 2 Unidirectional alignment (log-probability: -37.3) GAACTAACTTAAGAAATTAAATGTGGCTGGGTAAAACCCA------gcagtatggtgATACTGCTTACATCCTATTCTAATAAGTGAAAATGTGTTT GAACTAACTTAAGAAATTAAATGTGGCTGGGTAAAACCCACCCACC-----------ATACTGCTTACATCCTATTCTAATAAGTGAAAATGTGTTT Template switch alignment (log-probability: -16.6) GAACTAACTTAAGAAATTAAATGTGGCTGGGTAAAACCCA|GCAGTATGGTG|ATACTGCTTACATCCTATTCTAATAAGTGAAAATGTGTTT GAACTAACTTAAGAAATTAAATGTGGCTGGGTAAAACCCA|GCAGTATGGTG|ATACTGCTTACATCCTATTCTAATAAGTGAAAATGTGTTT ========== Event 2337 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGTCTCTGTGGTTTGAACTGCTTGATGTTTACATCAAGCAGAGTGAACAACTCTGCTTCCCA Chimp: CTGTCTCTGTGGTTTGAACTGCTTGGTGTTTA-------CTGGGTGAACAACTCTGCTTCCCA Gorilla: CTGTCTCTGTGGTTTGAACTGCTTGATGTTTA-------CTGGGTGAACAACTCTGCTTCCCA ↓ 3 2 1 4 Human: CTGTCTCTGTGGTTTGAACTGCTTGATGTTTACATCAAGCAGAGTGAACAACTCTGCTTCCCA Cluster: [ ] Orangutan: C------TGTGGTTTGAACTGCTTGATGTTTA-------CTGGGTGAACAACTCTGCTTCCCA Gorilla > Human --------------- chr3:10684169-10684176 Template switch process: F1: L TGGAAAATCCTGTCTCTGTGGTTTGAACTGCTTGATGTTTAC 1 F3: 4 GAGTGAACAACTCTGCTTCCCAGACTTTAGAAGAGTCATGTC R RF: TGGAAAATCCTGTCTCTGTGGTTTGAACTGCTTGATGTTTACTGGGTGAACAACTCTGCTTCCCAGACTTTAGAAGAGTCATGTC RR: ACCTTTTAGGACAGAGACACCAAACTTGACGAACTACAAATGACCCACTTGTTGAGACGAAGGGTCTGAAATCTTCTCAGTACAG F2: 3 ACGAACTA 2 Unidirectional alignment (log-probability: -32) GAAAATCCTGTCTCTGTGGTTTGAACTGCTTGATGTTTAcatcaagCaGaGTGAACAACTCTGCTTCCCAGACTTTAGAAGAGTCATG GAAAATCCTGTCTCTGTGGTTTGAACTGCTTGATGTTTA-------CTGGGTGAACAACTCTGCTTCCCAGACTTTAGAAGAGTCATG Template switch alignment (log-probability: -22.3) GAAAATCCTGTCTCTGTGGTTTGAACTGCTTGATGTTTAC|ATCAAGCA|GaGTGAACAACTCTGCTTCCCAGACTTTAGAAGAGTCATG GAAAATCCTGTCTCTGTGGTTTGAACTGCTTGATGTTTAC|ATCAAGCA|GGGTGAACAACTCTGCTTCCCAGACTTTAGAAGAGTCATG ========== Event 2338 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTACCTGTTTTTCTTCTGAC------CCGTCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTGACAGTCAAAGTCATTTGCAAAGCATAGAATAAGTGGTTTAGATGCTTAGGTATATTTTTCACTTTGAATGTTCATTCTGAGCCAGTTTTGTTTATGTATTAAAATA Chimp: TTTACCTGTTTTTCTTCTGAC---CACTGGTCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTGAGAGTCAAAGTCATTTGCAAAGCATAGAATAAGTGGTTTAGATGCTTAGGTATATTTTTCACCTTGAATGCTCATTCTGAGCCAGTTTTGTTTATGTATTAAAATA ↑ 1 4 3 2 Gorilla: TTTACCTGTTTTTCTTCTGAC------CCATCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTGACAGTCAAAGTCATTTGCAAAGCATAGAATAAGTGGTTTAGATGCTTAGGTATATTTTTCACTTTGAATGTTCATTCTGAGCCAGTTTTGTTTATGTATTAAAATA Human: TTTACCTGTTTTTCTTCTGAC------CCGTCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTGACAGTCAAAGTCATTTGCAAAGCATAGAATAAGTGGTTTAGATGCTTAGGTATATTTTTCACTTTGAATGTTCATTCTGAGCCAGTTTTGTTTATGTATTAAAATA Cluster: [ ] Orangutan: TTTACCTGTTTTTCTTCTGACCAC---TGGTCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTGAGAGTCAAAGTCATTTGCAAAGCATAGAACAAGTGGTTTAGATGCTCAGGTATACTTTTCACTTTGAATGTTCATTCTGAGCCAGTTTTGTTATTTTATTAAAATA Gorilla > Chimp --------------- chr3:10491054-10491058 Template switch process: F1: L TCTTGTTTTCTGAATCAATTTTTACCTGTTTTTCTTCTGACC 1 F3: 4 TCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTG R RF: TCTTGTTTTCTGAATCAATTTTTACCTGTTTTTCTTCTGACCCATCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTGACAGTCAAAGTCATTTGCAAAGCATAGAATAAGTGGTTTAGATGCTTAGGTATATTTTTCACTTTGAATGTTCATTCTGAGCCAGT RR: AGAACAAAAGACTTAGTTAAAAATGGACAAAAAGAAGACTGGGTAGGACTATTTAAAAGTCTATCGTTTGGAAAACCATATCACTGTCAGTTTCAGTAAACGTTTCGTATCTTATTCACCAAATCTACGAATCCATATAAAAAGTGAAACTTACAAGTAAGACTCGGTCA F2: 3 GGTCA 2 Unidirectional alignment (log-probability: -26.3) TTGTTTTCTGAATCAATTTTTACCTGTTTTTCTTCTGACCactggTCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTG TTGTTTTCTGAATCAATTTTTACCTGTTTTTCTTCTGACCCA---TCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTG Template switch alignment (log-probability: -16.4) TTGTTTTCTGAATCAATTTTTACCTGTTTTTCTTCTGACC|ACTGG|TCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTG TTGTTTTCTGAATCAATTTTTACCTGTTTTTCTTCTGACC|ACTGG|TCCTGATAAATTTTCAGATAGCAAACCTTTTGGTATAGTG ========== Event 2339 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAATCTTTGACTTCCTTCAAGAGAATATGATCGTTTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTG ↓ 1 4 3 2 Chimp: ATAATCTTTGACTTCCTTCAATA-------GTTACATTGTAAAATGTAACTATGGCCATTGCCTGACTCTTG ↑ 1 4 3 2 Gorilla: ATAATCTTTGACTTCCTTCAAGAGAATATGATCGTTTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTG Human: ATAATCTTTGACTTCCTTCAAGAGAATATGATCGTTTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTG Cluster: [ ] Orangutan: ATAATCTTTGACTTCCTTCAAGAGAATATGATCGTTTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTG Human > Chimp ------------- chr3:8351640-8351648 Template switch process: F1: L CTTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA 1 F3: 4 TGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT R RF: CTTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAAGAGAATATGATCGTTTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT RR: GAACGGAGTTCCGGGTGTATTATTAGAAACTGAAGGAAGTTCTCTTATACTAGCAAAACATTTTACATTGATACCGGTAACGGACTGAGAACTTTA F2: 3 TACATTGAT 2 Unidirectional alignment (log-probability: -31.9) TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA--------------TagttacaTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAAGAGAATATGATCGTT-------TTGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT Template switch alignment (log-probability: -16.4) TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA|TAGTTACAT|TGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA|TAGTTACAT|TGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT Gorilla > Chimp --------------- chr3:8351640-8351648 Template switch process: F1: L CTTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA 1 F3: 4 TGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT R RF: CTTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAAGAGAATATGATCGTTTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT RR: GAACGGAGTTCCGGGTGTATTATTAGAAACTGAAGGAAGTTCTCTTATACTAGCAAAACATTTTACATTGATACCGGTAACGGACTGAGAACTTTA F2: 3 TACATTGAT 2 Unidirectional alignment (log-probability: -31) TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCA----------ATaGTTacaTTGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAAGAGAATATGATCGTT---TTGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT Template switch alignment (log-probability: -16.8) TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA|TAGTTACAT|TGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT TTGCCTCAAGGCCCACATAATAATCTTTGACTTCCTTCAA|TAGTTACAT|TGTAAAATGTAACTATGGCCATTGCCTGACTCTTGAAAT ========== Event 2340 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTTCTCTGTGCTTTGGTTGAGAAATTCTCATCCCACAGATGAGAATTTCACCAGAAGCAACACGAGAAT Chimp: TTTTTCTCTGTGCTTTGGTTGAGAAATTCTCATCCCACAGATGAGAATTTCACCAGAAGCAACACGAGAAT Gorilla: TTTTTCTCTGTGCTTTGGTTGTT------ACTTCTGTGGGATGAGAATTTCACCAGAAGCAACACGAGAAT ↓ 1 3 4 2 Human: TTTTTCTCTGTGCTTTGGTTGAGAAATTCTCATCCCACAGATGAGAATTTCACCAGAAGCAACACGAGAAT Cluster: [ ] Orangutan: TTTTTCTTTGTGCTTTGGTTGTT------ACTTCTGTGGGATGAGAATTTCACCAGAAGCAACACGAGAAT Gorilla > Human --------------- chr3:8210421-8210437 Template switch process: F1: L CCCCCAAGCAAAAGTCATGATTTTTCTCTGTGCTTTGGTTGA 1 F3: 4 GATGAGAATTTCACCAGAAGCAACACGAGAATAATTCAAC R RF: CCCCCAAGCAAAAGTCATGATTTTTCTCTGTGCTTTGGTTGTTACTTCTGTGGGATGAGAATTTCACCAGAAGCAACACGAGAATAATTCAAC RR: GGGGGTTCGTTTTCAGTACTAAAAAGAGACACGAAACCAACAATGAAGACACCCTACTCTTAAAGTGGTCTTCGTTGTGCTCTTATTAAGTTG F2: 3 ACACCCTACTCTTAAAG 2 Unidirectional alignment (log-probability: -47.1) CCCAAGCAAAAGTCATGATTTTTCTCTGTGCTTTGGTTGagaaattctcatcccaca------------GATGAGAATTTCACCAGAAGCAACACGAGAATAATTCAAC CCCAAGCAAAAGTCATGATTTTTCTCTGTGCTTTGGTTG------------------TTACTTCTGTGGGATGAGAATTTCACCAGAAGCAACACGAGAATAATTCAAC Template switch alignment (log-probability: -23.4) CCCAAGCAAAAGTCATGATTTTTCTCTGTGCTTTGGTTGa|GAAATTCTCATCCCACA|GATGAGAATTTCACCAGAAGCAACACGAGAATAATTCAAC CCCAAGCAAAAGTCATGATTTTTCTCTGTGCTTTGGTTGT|GAAATTCTCATCCCACA|GATGAGAATTTCACCAGAAGCAACACGAGAATAATTCAAC ========== Event 2341 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCCCCCAAAGATAACAATAATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTA-------------------------------------------------------TCCTTTGAAACATAACTTTCA ↓ 3 4 2 1 Chimp: tttCCCCCAAAGATAACAATAATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTATAAAATCCATCATATTTGCCTTATTAATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAACATAACTTTCA ↑ 3 4 2 1 Gorilla: TTTCCCCCAAAGATAACAATAATAAGGCCAATATGATGGATTTTATTATTGACTCCAATTA-------------------------------------------------------TCCTTTGAAACATAACTTTCA Human: TTTCCCCCAAAGATAACAATAATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTA-------------------------------------------------------TCCTTTGAAACATAACTTTCA Cluster: [ ] Orangutan: TTTCCCCCAAAGATAACAATAATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTA-------------------------------------------------------TCCTTTGAAACATAACTTTCA Human > Chimp ------------- chr3:183025209-183025233 Template switch process: F1: L AATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTAT 1 F3: 4 ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAACATAACTTTCAGCTCCCACTCACTGTGGGA R RF: TAATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAACATAACTTTCAGCTCCCACTCACTGTGGGA RR: ATTATTCCGTTTATACTACCTAAAATAATAACTGAGGTTAATAGGAAACTTTGTATTGAAAGTCGAGGGTGAGTGACACCCT F2: 3 ATTATTCCGTTTATACTACCTAAAA 2 Unidirectional alignment (log-probability: -90) TAAGGCAAATatgatggattttattattgactccaattataaaatccatcatatttgccttattaATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC TAAGGCAAAT-------------------------------------------------------ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC Template switch alignment (log-probability: -18.9) TAAGGCAAATATGATGGATTTTATTATTGACTCCAATTAT|AAAATCCATCATATTTGCCTTATTA|ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC TAAGGCAAATATGATGGATTTTATTATTGACTCCAATTAT|AAAATCCATCATATTTGCCTTATTA|ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC Gorilla > Chimp --------------- chr3:183025209-183025233 Template switch process: F1: L AATAAGGCAAATATGATGGATTTTATTATTGACTCCAATTAT 1 F3: 4 ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAACATAACTTTCAGCTCCCACTCACTGTGGGA R RF: TAATAAGGCCAATATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAACATAACTTTCAGCGCCCACTCACTGTGGGA RR: ATTATTCCGGTTATACTACCTAAAATAATAACTGAGGTTAATAGGAAACTTTGTATTGAAAGTCGCGGGTGAGTGACACCCT F2: 3 ATTATTCCGTTTATACTACCTAAAA 2 Unidirectional alignment (log-probability: -101) TAAGGCaAATatgatggattttattattgactccaattataaaatccatcatatttgccttattaATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC TAAGGCCAAT-------------------------------------------------------ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC Template switch alignment (log-probability: -36.1) TAAGGCaAATATGATGGATTTTATTATTGACTCCAATTAT|AAAATCCATCATATTtGCCTTATTA|ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC TAAGGCCAATATGATGGATTTTATTATTGACTCCAATTAT|AAAATCCATCATATTGGCCTTATTA|ATGATGGATTTTATTATTGACTCCAATTATCCTTTGAAAC ========== Event 2342 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCTGTATTCAGCCGTCTCCCAATGATGCTTACTCAGTGCCAAACTTCCCGTTTAAAGTTCTCATCCTAATTCAACAAAGCCTGAAGATAAAAA--AGGCATAGGAATAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTGCCTGTTAATCACTGGTTAAAGGAAAGTGGACACAGGGCT ↑ 3 2 4 1 Chimp: CCTGTATTCAGCCGTCTCCCAGTGATGCTTACTCAGTGCCAAACTTCCCGTTTAAAGTTCTCATCCTAATTCAACAAAGCCTGAAGATAAAAA--AGGCATAGGAATAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTTCCTG-----------TTAAAGGAAAGTggacacagg--- ↓ 3 2 4 1 Gorilla: CCTGTATTCAGCCGTCTCCCAATGATGCTTACTCAGTGCCAAACTTCCCGTTTAAAATTCTCATCCTAATTCAACaaagcctgaagataaaaa--aggcatagaaatagtgaaaaagcttcaaactataaaattaaaaaTTGCGCTTGCCTGTTAATCACTGGTTAAAGGAAAGTGGACACAGGGCT Human: CCTGTATTCAGCCGTCTCCCAATGATGCTTACTCAGTGCCAAACTTCCCGTTTAAAGTTCTCATCCTAATTCAACAAAGCCTGAAGATAAAAA--AGGCATAGGAATAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTGCCTGTTAATCACTGGTTAAAGGAAAGTGGACACAGGGCT Cluster: [ ] Orangutan: CATGTATTCAGCAGTCTCCCAACGATGCTTGCTCAGTGCCAAACTTCCCATTTAAAGTTTTGATCCTAATTCAACAAAGCCTGAAGATAAAAAAAGGGCATAG-GATAGCGA-AAAGCTCAAACCTATAAAATTAAA--ATGCACTTG-CTGTT-AT----CGCTAAA--GAAGTGGATACAGGGTT Chimp > Human ------------- chr3:7385403-7385408 Template switch process: F1: L TAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTGCCTGTTAA 1 F3: 4 GTTAAAGGAAAGTGGACACAGGGCTTCCAAA R RF: CAGTGATGCTTACTCAGTGCCAAACTTCCCGTTTAAAGTTCTCATCCTAATTCAACAAAGCCTGAAGATAAAAAAGGCATAGGAATAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTTCCTGTTAAAGGAAAGTGGACACAGGGCTTCCAAA RR: GTCACTACGAATGAGTCACGGTTTGAAGGGCAAATTTCAAGAGTAGGATTAAGTTGTTTCGGACTTCTATTTTTTCCGTATCCTTATCACTTTTTCGAAGTTTGATATTTTAATTTTTAACGCGAAAGGACAATTTCCTTTCACCTGTGTCCCGAAGGTTT F2: 3 GTCACT 2 Unidirectional alignment (log-probability: -40) GCTTCAAACTATAAAATTAAAAATTGCGCTTgCCTGTTaatcactggttAAAGGAAAGTGGACACAGGGCTTCCAAA- GCTTCAAACTATAAAATTAAAAATTGCGCTTTCCTGTT-----------AAAGGAAAGTGGACACAGGGCTTCCAAAG Template switch alignment (log-probability: -22) GCTTCAAACTATAAAATTAAAAATTGCGCTTgCCTGTTAA|TCACTG|GTTAAAGGAAAGTGGACACAGGGCTTCCAAA GCTTCAAACTATAAAATTAAAAATTGCGCTTTCCTGTTAA|TCACTG|GTTAAAGGAAAGTGGACACAGGGCTTCCAAA Chimp > Gorilla --------------- chr3:7175914-7175919 Template switch process: F1: L TAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTGCCTGTTAA 1 F3: 4 GTTAAAGGAAAGTGGACACAGGGCTTCCAAAGCATGCGGGG R RF: CAGTGATGCTTACTCAGTGCCAAACTTCCCGTTTAAAGTTCTCATCCTAATTCAACAAAGCCTGAAGATAAAAAAGGCATAGGAATAGTGAAAAAGCTTCAAACTATAAAATTAAAAATTGCGCTTTCCTGTTAAAGGAAAGTGGACACAGGGCTTCCAAAGCGTGCGGGG RR: GTCACTACGAATGAGTCACGGTTTGAAGGGCAAATTTCAAGAGTAGGATTAAGTTGTTTCGGACTTCTATTTTTTCCGTATCCTTATCACTTTTTCGAAGTTTGATATTTTAATTTTTAACGCGAAAGGACAATTTCCTTTCACCTGTGTCCCGAAGGTTTCGCACGCCCC F2: 3 GTCACT 2 Unidirectional alignment (log-probability: -66.1) GCTTCAAACTATAAAATTAAAAATTGCGCTTgCCTgttaatcactgGTTAAAGGAAAGTGGACACAGGgcttccaaagcatgcggg GCTTCAAACTATAAAATTAAAAATTGCGCTTTCCT-----------GTTAAAGGAAAGTGGACACAGG------------------ Template switch alignment (log-probability: -27.8) GCTTCAAACTATAAAATTAAAAATTGCGCTTgCCTGTTAA|TCACTG|GTTAAAGGAAAGTGGACACAGGGCTTCCAAAGCaTGCGGG GCTTCAAACTATAAAATTAAAAATTGCGCTTTCCTGTTAA|TCACTG|GTTAAAGGAAAGTGGACACAGGGCTTCCAAAGCGTGCGGG ========== Event 2343 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGAC-------------AGTACATATCAAAGTACATCATG ↓ 3 2 1 4 Chimp: TTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACATATTGATTTTTACATACATATCAAAGTACATCATG ↑ 3 2 1 4 Gorilla: TTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGAC-------------AGTACATATCAAAGTACATCATG Human: TTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGAC-------------AGTACATATCAAAGTACATCATG Cluster: [ ] Orangutan: TTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGAC-------------AGTACATATCAAAATACATCACG Human > Chimp ------------- chr3:7300004-7300017 Template switch process: F1: L ATGTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA 1 F3: 4 TACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA R RF: ATGTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACAGTACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA RR: TACAAGAAACATAAGGTCTTTAACATTTTTAGTTATTTCTGTCATGTATAGTTTCATGTAGTACTTAACGTAACAAGGTCCGT F2: 3 ACATTTTTAGTTAT 2 Unidirectional alignment (log-probability: -35.6) GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACAtattgatttttacaTACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA-------------GTACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA Template switch alignment (log-probability: -17) GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA|TATTGATTTTTACA|TACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA|TATTGATTTTTACA|TACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA Gorilla > Chimp --------------- chr3:7300004-7300017 Template switch process: F1: L ATGTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA 1 F3: 4 TACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA R RF: ATGTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACAGTACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA RR: TACAAGAAACATAAGGTCTTTAACATTTTTAGTTATTTCTGTCATGTATAGTTTCATGTAGTACTTAACGTAACAAGGTCCGT F2: 3 ACATTTTTAGTTAT 2 Unidirectional alignment (log-probability: -35.1) GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACAtattgatttttacaTACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA-------------GTACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA Template switch alignment (log-probability: -17.5) GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA|TATTGATTTTTACA|TACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA GTTCTTTGTATTCCAGAAATTGTAAAAATCAATAAAGACA|TATTGATTTTTACA|TACATATCAAAGTACATCATGAATTGCATTGTTCCAGGCA ========== Event 2344 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATCTTGGGTAGCTCAAAAGGCTCT-TAGAGTCCTCCTTTTGATAGCATCTTTTC Chimp: AAATCTTGGGTAGCTCAAAAGGCTCT-TACAGTCCTCCTTTTGATAGCATCTTTTC ↓ 3 2 1 4 Gorilla: AAATCTTGGGTAGCTCAAAAGGCTCCTAAGAGCCTTCCTTTTGATAGCATCTTTTC ↑ 3 1 2 4 Human: AAATCTTGGGTAGCTCAAAAGGCTCT-TAGAGTCCTCCTTTTGATAGCATCTTTTC Cluster: [ ] Orangutan: AAATCTTGGGTAGCTCAAAAGGCTCT-TAGAGTCCTCCTTTTGATAGCATCTTTTT Human > Gorilla --------------- chr3:194851952-194851961 Template switch process: F1: L GCCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTC 1 F3: 4 TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC R RF: GCCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTCTTAGAGTCCTCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC RR: CGGGTGACTCTTGTAATTTAGAACCCATCGAGTTTTCCGAGAATCTCAGGAGGAAAACTATCGTAGAAAAGTTAAGGAATGAGTAAACCG F2: 3 TCCGAGAATC 2 Unidirectional alignment (log-probability: -29) CCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTcCTaAGAGcCtTCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC CCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCT-CTTAGAGTCCTCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC Template switch alignment (log-probability: -17) CCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTC|CTAAGAGCCT|TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC CCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTC|CTAAGAGCCT|TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC Chimp > Gorilla --------------- chr3:194851955-194851961 Template switch process: F1: L GCCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTCCTA 1 F3: 4 TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC R RF: GCCCACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTCTTACAGTCCTCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC RR: CGGGTGACTCTTGTAATTTAGAACCCATCGAGTTTTCCGAGAATGTCAGGAGGAAAACTATCGTAGAAAAGTTAAGGAATGAGTAAACCG F2: 3 TCCGAGA 2 Unidirectional alignment (log-probability: -34) ACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGC--------TCCtaagagcctTCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC ACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTCTTACAGTCC---------TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC Template switch alignment (log-probability: -22.2) ACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTCcTA|AGAGCCT|TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC ACTGAGAACATTAAATCTTGGGTAGCTCAAAAGGCTCTTA|AGAGCCT|TCCTTTTGATAGCATCTTTTCAATTCCTTACTCATTTGGC ========== Event 2345 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGATTAAAGAAAGGTACAATATTTCACAGTAAGC--GTAAGTTTTTACTGTCTTAAGCTGGATT Chimp: AGATTAAAGAAAGGTACAATATTTCACAGTAATCTGTGAAATATTTACTGTCTTAAGCTGGATT ↑ 3 2 1 4 Gorilla: AGATTGAAGAAAGGTACAATATTTCACAGTAAGG--GTAAGTTTTTACTGTCTTAAGCTGGATT Human: AGATTAAAGAAAGGTACAATATTTCACAGTAAGC--GTAAGTTTTTACTGTCTTAAGCTGGATT Cluster: [ ] Orangutan: AGATTAAAGAAAGGTACAATATTTCACAGTAAGC--ATAAGTTTTTACTGTCTTAAGCTGGATT Gorilla > Chimp --------------- chr3:195565540-195565549 Template switch process: F1: L TATATTAAAAGATTAAAGAAAGGTACAATATTTCACAGTAAT 1 F3: 4 TTTACTGTCTTAAGCTGGATTTCTGGGTCTATTTCATCCT R RF: TATATTAAAAGATTGAAGAAAGGTACAATATTTCACAGTAAGGGTAAGTTTTTACTGTCTTAAGCTGGATTTCTGGGTCTATTTCATCCT RR: ATATAATTTTCTAACTTCTTTCCATGTTATAAAGTGTCATTCCCATTCAAAAATGACAGAATTCGACCTAAAGACCCAGATAAAGTAGGA F2: 3 ATAAAGTGTC 2 Unidirectional alignment (log-probability: -40.9) TATTAAAAGATTaAAGAAAGGTACAATATTTCACAGTAA--------TctgtgaaataTTTACTGTCTTAAGCTGGATTTCTGGGTCTATTTCATCCT TATTAAAAGATTGAAGAAAGGTACAATATTTCACAGTAAGGGTAAGTT----------TTTACTGTCTTAAGCTGGATTTCTGGGTCTATTTCATCCT Template switch alignment (log-probability: -28.1) TATTAAAAGATTaAAGAAAGGTACAATATTTCACAGTAAt|CTGTGAAATA|TTTACTGTCTTAAGCTGGATTTCTGGGTCTATTTCATCCT TATTAAAAGATTGAAGAAAGGTACAATATTTCACAGTAAG|CTGTGAAATA|TTTACTGTCTTAAGCTGGATTTCTGGGTCTATTTCATCCT ========== Event 2346 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGACATTAGGAGATCTCACCA-G------------TACCTCATTCAGTACCTCAAGAGAAGGAGGTAGGA ↑ 1 4 3 2 Chimp: TGACATTAGGAGATCTCACCAAG------TGACTGATACTCATTCAGTACCTCAAGAGAAGGAGGTAGGA Gorilla: TGACATTAGGAGATCTCACCAAGTGGCTG------ATACTCATTCAGTACCTCAAGAGAAGGAGGTAGGA ↓ 1 4 3 2 Human: TGACATTAGGAGATCTCACCA-G------------TACCTCATTCAGTACCTCAAGAGAAGGAGGTAGGA Cluster: [ ] Orangutan: TGACATTAGGAGATCTCACCAAGTGACTG------ACACTCGTTCAGTACCTCAAGAGAAGGAGGTAGGA Chimp > Human ------------- chr3:5233652-5233655 Template switch process: F1: L ATTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA 1 F3: 4 CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG R RF: ATTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCAAGTGACTGATACTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG RR: TAAGAAAAATCTAGTAGACCACTGTAATCCTCTAGAGTGGTTCACTGACTATGAGTAAGTCATGGAGTTCTCTTCCTCCATCCTTAATTCTC F2: 3 CATG 2 Unidirectional alignment (log-probability: -27.5) TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCAgtac-----------CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA----AGTGACTGATACTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG Template switch alignment (log-probability: -15.8) TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA|GTAC|CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA|GTAC|CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG Gorilla > Human --------------- chr3:5233652-5233655 Template switch process: F1: L ATTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA 1 F3: 4 CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG R RF: ATTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCAAGTGGCTGATACTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG RR: TAAGAAAAATCTAGTAGACCACTGTAATCCTCTAGAGTGGTTCACCGACTATGAGTAAGTCATGGAGTTCTCTTCCTCCATCCTTAATTCTC F2: 3 CATG 2 Unidirectional alignment (log-probability: -26.9) TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACC-----------AgtacCTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCAAGTGGCTGATA----CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG Template switch alignment (log-probability: -16.2) TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA|GTAC|CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG TTCTTTTTAGATCATCTGGTGACATTAGGAGATCTCACCA|GTAC|CTCATTCAGTACCTCAAGAGAAGGAGGTAGGAATTAAGAG ========== Event 2347 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCTTTTACCATCTGGGCCCTTGCACCATATCC---TCACCACCACCACTGCCACTTTG ↓ 3 2 1 4 Chimp: TTTCTTTTACCATCTGGGCCCTTGCACCATAGTGCAAGGACCACCACCACTGCCACTTTG ↑ 3 2 1 4 Gorilla: TTTCTTTTACCATCTGGGCCCTTGCACCATATCC---TCACCACCACCACTGCCACTTTG Human: TTTCTTTTACCATCTGGGCCCTTGCACCATATCC---TCACCACCACCACTGCCACTTTG Cluster: [ ] Orangutan: GTTCTTTTACCATCTGGGTCCTTGCACCATATCC---TCACCACCACCACTGCCACTTTG Human > Chimp ------------- chr3:198038574-198038581 Template switch process: F1: L AAGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA 1 F3: 4 ACCACCACCACTGCCACTTTGCCATCTGCCCCTCGGCAAG R RF: AAGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATATCCTCACCACCACCACTGCCACTTTGCCATCTGCCCCTCAGCAAG RR: TTCGGTCACAAAAGAAAATGGTAGACCCGGGAACGTGGTATAGGAGTGGTGGTGGTGACGGTGAAACGGTAGACGGGGAGTCGTTC F2: 3 GGAACGTG 2 Unidirectional alignment (log-probability: -38.9) AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATAgtgcaagg-----ACCACCACCACTGCCACTTTGCCATCTGCCCCTCgGCAAG AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA--------TCCTCACCACCACCACTGCCACTTTGCCATCTGCCCCTCAGCAAG Template switch alignment (log-probability: -22.3) AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA|GTGCAAGG|ACCACCACCACTGCCACTTTGCCATCTGCCCCTCgGCAAG AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA|GTGCAAGG|ACCACCACCACTGCCACTTTGCCATCTGCCCCTCAGCAAG Gorilla > Chimp --------------- chr3:198038574-198038581 Template switch process: F1: L AAGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA 1 F3: 4 ACCACCACCACTGCCACTTTGCCATCTGCCCCTCGGCAAG R RF: AAGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATATCCTCACCACCACCACTGCCACTTTGCCATCTGCCCCTCAGCAAG RR: TTCGGTCACAAAAGAAAATGGTAGACCCGGGAACGTGGTATAGGAGTGGTGGTGGTGACGGTGAAACGGTAGACGGGGAGTCGTTC F2: 3 GGAACGTG 2 Unidirectional alignment (log-probability: -37.9) AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA-----gtgcaaggACCACCACCACTGCCACTTTGCCATCTGCCCCTCgGCAAG AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATATCCTC--------ACCACCACCACTGCCACTTTGCCATCTGCCCCTCAGCAAG Template switch alignment (log-probability: -22.3) AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA|GTGCAAGG|ACCACCACCACTGCCACTTTGCCATCTGCCCCTCgGCAAG AGCCAGTGTTTTCTTTTACCATCTGGGCCCTTGCACCATA|GTGCAAGG|ACCACCACCACTGCCACTTTGCCATCTGCCCCTCAGCAAG ========== Event 2348 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTGGTCAGCA-CGTGCTCCTGTGGCCCTGGAGGATGtcacaggtgtcttgtggagcggggagctaataagagccgatcgggattggtggtagatttccagatcacaggtgtcttgtggagcggggagctaataagagccgatcgggattggtggtggatttccaaagcacag-----------------------------------------------------------------gtgtcttgtggagcggggagctaataagagccgatcgggattggtcgtggatttccagatcCCCGTGGAGTCAGCTGA Chimp: CCTGGTCAGCA-CGTGCTCCTATGGCCCTGGGGGATGtcacaggtgtcttgtggagtggtgagccaataagagccgatcgggattggtggtggatttccagatcagag-----------------------------------------------------------------gtgtcttgtggagcggggagctaataagagccgatcgggattggtggtagatttccagatcacaggtgtcttgtggagcggggagctaataagagccgatcgggatcggtggtggatttccagatcCCTGTGGAGTCAGCTGA Gorilla: CCTGGTCAGCA-CGTGCTCCTATGGCCGTGGGGGATGTCACAGGTGTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTGGAGCGGGGAGCTAATAAGAGCCGATCGGGATTGGTGGTGGATTTCCAGATCCCCGTGGAGTCAGCTGA ↓ 1 4 3 2 Human: ACTGGTCAGCA-CGTGCTCCTGTGGCCCTGGAGGATGtcacaggtgtcttgtggagcggggagctaataagagccgatcgggattggtggtagatttccagatcacaggtgtcttgtggagcggggagctaataagagccgatcgggattggtggtggatttccaaagcacag-----------------------------------------------------------------gtgtcttgtggagcggggagctaataagagccgatcgggattggtcgtggatttccagatcCCCGTGGAGTCAGCTGA Cluster: [ ] Orangutan: CCTGGTCAGCACTGTGCTCCTATGGCCCTGGGGGATGTCACAGGTGTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTGGAGCGGGGAGCTAATAAGAGCCGATCGGGATTGGTGGTGGATTTCCAGATCCCCACGGAGTCAGCTGA Gorilla > Human --------------- chr3:194357209-194357213 Template switch process: F1: L GTGCAGGAACTGGAAGGGAAAACTGGTCAGCACGTGCTCCTGTGGCC 1 F3: 4 GGATGTCACAGGTGTCTTGTGGAGCGGGGAGCTAATAAGA R RF: GTGCAGGAACTGGAAGGGAAACCTGGTCAGCACGTGCTCCTATGGCCGTGGGGGATGTCACAGGTGTCTTGTGGAGCGGGGAGCTAATAAGAGCCGATCGGGATTGGTGGTGGATTTCCAG RR: CACGTCCTTGACCTTCCCTTTGGACCAGTCGTGCACGAGGATACCGGCACCCCCTACAGTGTCCACAGAACACCTCGCCCCTCGATTATTCTCGGCTAGCCCTAACCACCACCTAAAGGTC F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -64.3) AACTGGAAGGGAAAaCTGGTCAGCACGTGCTCCTgTGGCCcTGGaGGATGTCACAGGTGTCttgtggagcggggagctaataaga AACTGGAAGGGAAACCTGGTCAGCACGTGCTCCTATGGCCGTGGGGGATGTCACAGGTGTC------------------------ Template switch alignment (log-probability: -27.5) AACTGGAAGGGAAAaCTGGTCAGCACGTGCTCCTgTGGCC|CTGGA|GGATGTCACAGGTGTCTTGTGGAGCGGGGAGCTAATAAGA AACTGGAAGGGAAACCTGGTCAGCACGTGCTCCTATGGCC|CTGGA|GGATGTCACAGGTGTCTTGTGGAGCGGGGAGCTAATAAGA ========== Event 2349 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: cccacctgGCTGGGCTGGCTCTGTGCCATCTGCCCA-------------------------ATGCCCTGTCTGGCCGCTGGCAGCCTCTCCCTCCCTGGGGCTGTAGGGAATGCTCCCCTCACTGGCCAGCCAGGGGTGGGGTTCAAATGGGGGAAGCCAGGAGCAACCCTTGCAGTCAGGGCTCCAGGCAGGAATCAG Chimp: cccacctgGCTGGGCTGGCTCTGTGCCATCTGCCCAATGCTGACAGTCTGTCATCTGCCCAATGCCCTGTCTGGCCGCTGGCAGCCTCTCCCTCCCTGGGGCTGTAGGGAATGCTCCCCTCACTGGCCAGCCAGGGGTGGGGTTCAAATGGGGGAAGCCAGGAGCAACCCTTGCAGTCAGGGCTCCAGGCAGGAATCAG ↑ 4 1 3 2 Gorilla: cccacctgGCTGGGCTGGCTCTGTGCCATCTGCCCA-------------------------ATGCCCTGTCTGGCCGCTGGCAGCCTCTCCCTCCCTGGGGCTGTAGGGAATGCTCCCCTCACTGGCCAGCCAGGGGTGGGGTTCAAATGGGGGAAGCCAGGAGCAACCCTTGCAGTCAGGGCTCCAGGCAGGAATCAG Human: cccacctgGCTGGGCTGGCTCTGTGCCATCTGCCCA-------------------------ATGCCCTGTCTGGCCGCTGGCAGCCTCTCCCTCCCTGGGGCTGTAGGGAATGCTCCCCTCACTGGCCAGCCAGGGGTGGGGTTCAAATGGGGGAAGCCAGGAGCAACCCTTGCAGTCAGGGCTCCAGGCAGGAATCAG Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Gorilla > Chimp --------------- chr3:198665072-198665077 Template switch process: F1: L GTTTCCCCACCTGGCTGGGCTGGCTCTGTGCCATCTGCCCAATGC 1 F3: 4 TCTGT--CATCTGCCCAATGCCCTGTCTGGCCGCTGGCAGCCTCTCCCTCCCTGGGG R RF: GTTTCCCCACCTGGCTGGGCTGGCTCTGTGCCATCTGCCCAATGCCCTGTCTGGCCGCTGGCAGCCTCTCCCTCCCTGGGGCTGTAGGGAATGCTCCCCTCACTGGCCAGCCAGGGGTGGGGTTCAAATGGGGGAAGCCAGGAGCAACCCTTGCAGTCA RR: CAAAGGGGTGGACCGACCCGACCGAGACACGGTAGACGGGTTACGGGACAGACCGGCGACCGTCGGAGAGGGAGGGACCCCGACATCCCTTACGAGGGGAGTGACCGGTCGGTCCCCACCCCAAGTTTACCCCCTTCGGTCCTCGTTGGGAACGTCAGT F2: 3 GACAGT 2 Unidirectional alignment (log-probability: -46.8) CCCACCTGGCTGGGCTGGCTCTGTGCCATCTGCCcaatgctgacagtctgtcatctgccCAATGCCCTGTCTGGCCGCTGGCAGCC CCCACCTGGCTGGGCTGGCTCTGTGCCATCTGCC-------------------------CAATGCCCTGTCTGGCCGCTGGCAGCC Template switch alignment (log-probability: -32.3) CCCACCTGGCTGGGCTGGCTCTGTGCCATCTGCCCAATGC|TGACaG|TCTGT--CATCTGCCCAATGCCCTGTCTGGCCGCTGGCAGCC CCCACCTGGCTGGGCTGGCTCTGTGCCATCTGCCCAATGC|TGACTG|TCTGTGCCATCTGCCCAATGCCCTGTCTGGCCGCTGGCAGCC ========== Event 2350 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTATGgatacaacaaaaggtactacaacagatact---acc----------------------------------acaaatactacCATGCATACTAC Chimp: ATCATGGATACAACAAAAGGTACTACAACAGATACT---ACC--ACATATCTGTTGTGTACCACAACAGATACTACACAAATACTACCATGCATACTAC ↑ 4 3 2 1 Gorilla: ATCATGGATACAACAAAAGGTACCACAACAGATACT------AC--------------------------------ACAAATACTACCATGCATACTAC Human: ATTATGgatacaacaaaaggtactacaacagatact---acc----------------------------------acaaatactacCATGCATACTAC Cluster: [ ] Orangutan: ataatgtatacaacaacAGGTACTACAACAGATACTACC-------------------------------------ATAAATGCTACCACGCATACTAT Gorilla > Chimp --------------- chr3:3428607-3428616 Template switch process: F1: L ATATAATCATGGATACAACAAAAGGTACTACAACAGATACTACCACA 1 F3: 4 GTACCACAACAGATACTACACAAATACTACCATGCATACTACAATGGGTAGTGCAAGGA R RF: ATATAATCATGGATACAACAAAAGGTACCACAACAGATACTA-CACAAATACTACCATGCATACTACAATGGGTAGTGCAAGGA RR: TATATTAGTACCTATGTTGTTTTCCATGGTGTTGTCTATGAT-GTGTTTATGATGGTACGTATGATGTTACCCATCACGTTCCT F2: 3 TGTTGTCTAT 2 Unidirectional alignment (log-probability: -58.4) CATGGATACAACAAAAGgtactacaacagatactaccacatatctgttgtGTACCACAACAGATACTACACAAATACTACCATGCATACT CATGGATACAACAAAAG---------------------------------GTACCACAACAGATACTACACAAATACTACCATGCATACT Template switch alignment (log-probability: -34.3) CATGGATACAACAAAAGGTACtACAACAGATACTAcCACA|TATCTGTTGT|GTACCACAACAGATACTACACAAATACTACCATGCATACT CATGGATACAACAAAAGGTACCACAACAGATACTA-CACA|TATCTGTTGT|GTACCACAACAGATACTACACAAATACTACCATGCATACT ========== Event 2351 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGGAATC-CCCACCTCCCCTGATGAAGATGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAG------------GGTGTCAGAGAGGGTAGTATTGGCATGTTTGGTTC Chimp: TGGAATC-CCCACCTCCCGTGATGAAGATGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAG------------GGTGTCAGAGAGGGTAGTATTGGCATGTTTGGTTC ↑ 3 2 4 1 Gorilla: TCGAATC-CCCACCTCCCGTGACGAAGATGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAG------------------------GGTAGTATTGGCATGTTTGGTTC ↓ 3 2 4 1 Human: TGGAATC-CCCACCTCCCCTGATGAAGATGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAG------------GGTGTCAGAGAGGGTAGTATTGGCATGTTTGGTTC Cluster: [ ] Orangutan: TCGACTCCCCCACCTCTTGTGATGAAGGTGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGTATCAGAGAG------------GGCAGTATTGGCATGTTTGGTTC Gorilla > Human --------------- chr3:3227438-3227441 Template switch process: F1: L ACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGT 1 F3: 4 GAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAATCATTT R RF: TGACGAAGATGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAATCATTT RR: ACTGCTTCTACTCACGAATGTCCTCTAGGATTCCTGGTTCCTCTCCCGTGTAGACTCTCCCATCATAACCGTACAAACCAAGTTTCGTTCCTTAGTAAA F2: 3 ACTG 2 Unidirectional alignment (log-probability: -28.1) GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGagggtgtcagagAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAG------------AGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT Template switch alignment (log-probability: -16.4) GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGT|GTCA|GAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGT|GTCA|GAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT Gorilla > Chimp --------------- chr3:3179166-3179169 Template switch process: F1: L ACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGT 1 F3: 4 GAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAATCATTT R RF: TGACGAAGATGAGTGCTTACAGGAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAATCATTT RR: ACTGCTTCTACTCACGAATGTCCTCTAGGATTCCTGGTTCCTCTCCCGTGTAGACTCTCCCATCATAACCGTACAAACCAAGTTTCGTTCCTTAGTAAA F2: 3 ACTG 2 Unidirectional alignment (log-probability: -28.1) GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGagggtgtcagagAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAG------------AGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT Template switch alignment (log-probability: -16.4) GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGT|GTCA|GAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT GAGATCCTAAGGACCAAGGAGAGGGCACATCTGAGAGGGT|GTCA|GAGAGGGTAGTATTGGCATGTTTGGTTCAAAGCAAGGAAT ========== Event 2352 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAGAGGGTCCGGTCCCAGCTCTGGCAGCAGCTGCTCACGTAGTAGCAGTCAGGGGAGGTG Chimp: AGAGAGGGTCCGGTCCCAGCTCTGGCAGCAGCTGCTCACGTAGTAGCAGTCAGGGGAGGTG Gorilla: AGAGAGGGTCCGGTCCCAGCTCTGGCAGCTGCTGCCAGAGTAGTAGCAGTCAGGGGAGGTG ↑ 3 12 4 Human: GGAGAGGGTCCGGTCCCAGCTCTGGCAGCAGCTGCTCACGTAGTAGCAGTCAGGGGAGGTG Cluster: [ ] Orangutan: AGAGAGGTTCCGGTCCCAGCTCTGGCAGCAGCTGCTCACATAGTAGCAGTCAGGGGAGGTG Human > Gorilla --------------- chr3:199945121-199945131 Template switch process: F1: L AGCCCCTTTAGCAGAGAGGGTCCGGTCCCAGCTCTGGCAGC 1 F3: 4 TAGTAGCAGTCAGGGGAGGTGGGGGTGGGGACGGTAAGG R RF: AGCCCCTTTAGCGGAGAGGGTCCGGTCCCAGCTCTGGCAGCAGCTGCTCACGTAGTAGCAGTCAGGGGAGGTGGGGGTGGGGACGGTAAGG RR: TCGGGGAAATCGCCTCTCCCAGGCCAGGGTCGAGACCGTCGTCGACGAGTGCATCATCGTCAGTCCCCTCCACCCCCACCCCTGCCATTCC F2: 3 GAGACCGTCGT 2 Unidirectional alignment (log-probability: -34.4) GCCCCTTTAGCaGAGAGGGTCCGGTCCCAGCTCTGGCAGCtGCTGCcagaGTAGTAGCAGTCAGGGGAGGTGGGGGTGGGGACGGTAAGG GCCCCTTTAGCGGAGAGGGTCCGGTCCCAGCTCTGGCAGCAGCTGCTCACGTAGTAGCAGTCAGGGGAGGTGGGGGTGGGGACGGTAAGG Template switch alignment (log-probability: -22.6) GCCCCTTTAGCaGAGAGGGTCCGGTCCCAGCTCTGGCAGC|TGCTGCCAGAG|TAGTAGCAGTCAGGGGAGGTGGGGGTGGGGACGGTAAGG GCCCCTTTAGCGGAGAGGGTCCGGTCCCAGCTCTGGCAGC|TGCTGCCAGAG|TAGTAGCAGTCAGGGGAGGTGGGGGTGGGGACGGTAAGG ========== Event 2353 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TAATCTCACTGCCCACGGCTTC--------------------------AGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACTGACA ↓ 4 1 3 2 Chimp: TAATCTCACTGCCCACGGCTTC-------------AGGCTTAGCGTTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACTGACA Gorilla: TAATCTCACTGCCCACGGCTTCAGGCTTAGCGTTC-------------AGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACTGACA ↑ 4 1 3 2 Human: TAATCTCACTGCCCACGGCTTC--------------------------AGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACTGACA Cluster: [ ] Orangutan: TAATCTCACTGCCCACGGCTTCAGGCTTAGCGTTC-------------AGGCTCCCCAGGAGAGCAACGCTACCCTCCTATCTTCACTGACA Human > Chimp ------------- chr3:201944394-201944398 Template switch process: F1: L TCAGAGGAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCT 1 F3: 4 TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACT R RF: TCAGAGGAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACT RR: AGTCTCCTTTGATCCCCTAATTAGAGTGACGGGTGCCGAAGTCCGAGGGCTCCTCTCGTTGCGATGGGAGGATAGAAGTGA F2: 3 GCGAT 2 Unidirectional alignment (log-probability: -29.6) GAAACTAGGGGATTAATCTCACTGCCCACGGCttcaggcttagcgTTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC GAAACTAGGGGATTAATCTCACTGCCCACGGC-------------TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC Template switch alignment (log-probability: -16.1) GAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCT|TAGCG|TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC GAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCT|TAGCG|TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC Human > Gorilla --------------- chr3:200797433-200797437 Template switch process: F1: L TCAGAGGAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCT 1 F3: 4 TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACT R RF: TCAGAGGAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTCACT RR: AGTCTCCTTTGATCCCCTAATTAGAGTGACGGGTGCCGAAGTCCGAGGGCTCCTCTCGTTGCGATGGGAGGATAGAAGTGA F2: 3 GCGAT 2 Unidirectional alignment (log-probability: -29.6) GAAACTAGGGGATTAATCTCACTGCCCACGGCTtcaggcttagcgtTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC GAAACTAGGGGATTAATCTCACTGCCCACGGCT-------------TCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC Template switch alignment (log-probability: -16.6) GAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCT|TAGCG|TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC GAAACTAGGGGATTAATCTCACTGCCCACGGCTTCAGGCT|TAGCG|TTCAGGCTCCCGAGGAGAGCAACGCTACCCTCCTATCTTC ========== Event 2354 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCATCAGGGGCCTCCCACAGCTCCTCCTGGCCCTGGGAACAGAGGGGTTGGAAGTGGATTGCATTTGGCCCAGCCCGGGAAGCCGAGGCGGATCTGGGACCAGTT Chimp: GGCATCAGGGGCCTCCCACAGCTCCTGCTGGCCCTGGGAACAGAGGGGTTGGAAGTGGATTGCATTTGGCCCAGCTGGGGAAGCCGAGGCGGATCTGGGACCAGTT ↑ 3 2 1 4 Gorilla: GGCATCAGGGGCCTCCCACAGCTCCTCCTGGCCCTGGGAACAGAGGGGTTCGAAGTGGATTGCATTTGGCCCGGCCGGGGAAGCCCAGGCGGATCTGGGACCAGTT Human: GGCATCAGGGGCCTCCCACAGCTCCTCCTGGCCCTGGGAACAGAGGGGTTGGAAGTGGATTGCATTTGGCCCAGCCCGGGAAGCCGAGGCGGATCTGGGACCAGTT Cluster: [ ] Orangutan: GGCATCAGGGGCCTCCCACAGCTCCTCCTGGCCCCGGGAACAGAGGGGTTGGAAGTGGATTGCATTTGGCCCGGCCGGGGAAGCCCAGGCGGATCTGGGACCAGTT Gorilla > Chimp --------------- chr3:201932723-201932726 Template switch process: F1: L CCCTGGGAACAGAGGGGTTGGAAGTGGATTGCATTTGGCCC 1 F3: 4 GGGGAAGCCGAGGCGGATCTGGGACCAGTTTTCCTGGGAGGGAACTCAGC R RF: AGCTCCTCCTGGCCCTGGGAACAGAGGGGTTCGAAGTGGATTGCATTTGGCCCGGCCGGGGAAGCCCAGGCGGATCTGGGACCAGTTTTCCTGGGAGGGAACTCAGC RR: TCGAGGAGGACCGGGACCCTTGTCTCCCCAAGCTTCACCTAACGTAAACCGGGCCGGCCCCTTCGGGTCCGCCTAGACCCTGGTCAAAAGGACCCTCCCTTGAGTCG F2: 3 TCGA 2 Unidirectional alignment (log-probability: -44.4) CCTGGGAACAGAGGGGTTgGAAGTGGATTGCATTTGGCCCaGCtGGGGAAGCCgAGGCGGATCTGGGACCAGTTTTCCTGGGAG CCTGGGAACAGAGGGGTTCGAAGTGGATTGCATTTGGCCCGGCCGGGGAAGCCCAGGCGGATCTGGGACCAGTTTTCCTGGGAG Template switch alignment (log-probability: -27.5) CCTGGGAACAGAGGGGTTgGAAGTGGATTGCATTTGGCCC|AGCT|GGGGAAGCCgAGGCGGATCTGGGACCAGTTTTCCTGGGAG CCTGGGAACAGAGGGGTTCGAAGTGGATTGCATTTGGCCC|AGCT|GGGGAAGCCCAGGCGGATCTGGGACCAGTTTTCCTGGGAG ========== Event 2355 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTCTAGTTTTATGCAAAGATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAG--------------------------------------------------------------------------TCATGTATCAAGATTACCCACTTCTTCTTTGGGGCCCAAAGAATATCCAACAACTACT-AC-TGCGAACACTTAAGGCTTAAAAAACCATGAATAACTAACCG Chimp: GCTCTAGTTTTATGCAAAGAAAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCACGTTTTATGCATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCATGTATCAAGATTACCCACTTCTTCTTTGGGGCCCAAAGAATATCCAACAACTACTAAC-TGCGAACACTTAAGGCTTAAAAAACCATGAATAACTAACCG ↑ 4 1 3 2 Gorilla: GCTCTAGTTTTATGCAAAGATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAG--------------------------------------------------------------------------TCACGTATCAAGATTACCCACTTCTTCTTTGGGGCCCAAAGAATATCCAACAACTACT-AC-TGCAAACACTTAAGGCTTAAAAAACCATGAATAACTAACCG Human: GCTCTAGTTTTATGCAAAGATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAG--------------------------------------------------------------------------TCATGTATCAAGATTACCCACTTCTTCTTTGGGGCCCAAAGAATATCCAACAACTACT-AC-TGCGAACACTTAAGGCTTAAAAAACCATGAATAACTAACCG Cluster: [ ] Orangutan: GCTCTAGTTTTATGCAAAGATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTGTGCAGTGACTAG--------------------------------------------------------------------------TCACGTATCA----AACCCACTT---CTTTGGGGCCCAAAGAATATCCAACAACTACT-ACTAGAGAACACTTAAGGCTTAAAAAACCATGAATAACTAACCG Gorilla > Chimp --------------- chr3:182205380-182205386 Template switch process: F1: L TGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCACGT 1 F3: 4 ATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCATGTATCAAGATTACCCACTTCTTCTTTGGGGCCCAAAGAAT R RF: TGAGAAAAGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCACGTATCAAGATTACCCACTTCTTCTTTGGGGCCCAAAGAATATCCAACAACTACTACTGCAAACACTTAAGGCTTAAA RR: ACTCTTTTCGACTTCCACAGACTATTAATACGTCACTGATCAGTGCATAGTTCTAATGGGTGAAGAAGAAACCCCGGGTTTCTTATAGGTTGTTGATGATGACGTTTGTGAATTCCGAATTT F2: 3 CGTATTT 2 Unidirectional alignment (log-probability: -117) AGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCACgttttatgcataaagaacagttttttgactgagaaaagctgaaggtgtc AGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCAC------------------------------------------------- Template switch alignment (log-probability: -29.3) AGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCACGT|TTTAtGC|ATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTC AGCTGAAGGTGTCTGATAATTATGCAGTGACTAGTCACGT|TTTAAGC|ATAAAGAACAGTTTTTTGACTGAGAAAAGCTGAAGGTGTC ========== Event 2356 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGAGAGCTAACCTCAAGCTTTAGAGGTGCAAGATGACTACTTGCACATCTCTGACAGCAGGTGAACAGGG Chimp: TGAGAGCTAACCTCAAGCTTTCT--CT---GCCTGGCTACTTGCACATCTCTGACAGCAGGTGAACAGGG Gorilla: TGAGAGCTAACCTCAAGCTTTCT--CT---GCCTGACTACTTGCACATCTCTGACAGCAGGTGAACAGGG ↓ 1 4 3 2 Human: TGAGAGCTAACCTCAAGCTTTAGAGGTGCAAGATGACTACTTGCACATCTCTGACAGCAGGTGAACAGGG Cluster: [ ] Orangutan: TGAGAGCTAACCTCAAGCTTTCT--CT---GCCTGACTGCTTGCACATCTCTGACAGGAGGTGAACAGGG Gorilla > Human --------------- chr3:20650568-20650578 Template switch process: F1: L CTGAAAGTGAGAAGTGCTCATGAGAGCTAACCTCAAGCTTT 1 F3: 4 ATGACTACTTGCACATCTCTGACAGCAGGTGAACAGGGAAC R RF: CTGAAAGTGAGAAGTGCTCATGAGAGCTAACCTCAAGCTTTCTCTGCCTGACTACTTGCACATCTCTGACAGCAGGTGAACAGGGAAC RR: GACTTTCACTCTTCACGAGTACTCTCGATTGGAGTTCGAAAGAGACGGACTGATGAACGTGTAGAGACTGTCGTCCACTTGTCCCTTG F2: 3 GAACGTGGAGA 2 Unidirectional alignment (log-probability: -38.2) TGAAAGTGAGAAGTGCTCATGAGAGCTAACCTCAAGCTTT-------agaggtgcaagaTGACTACTTGCACATCTCTGACAGCAGGTGAACAGGGAA TGAAAGTGAGAAGTGCTCATGAGAGCTAACCTCAAGCTTTCTCTGCC------------TGACTACTTGCACATCTCTGACAGCAGGTGAACAGGGAA Template switch alignment (log-probability: -28.2) TGAAAGTGAGAAGTGCTCATGAGAGCTAACCTCAAGCTTT|AGAgGTGCAAG|aTGACTACTTGCACATCTCTGACAGCAGGTGAACAGGGAA TGAAAGTGAGAAGTGCTCATGAGAGCTAACCTCAAGCTTT|AGATGTGCAAG|CTGACTACTTGCACATCTCTGACAGCAGGTGAACAGGGAA ========== Event 2357 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTGAAATTTATATCTACTGGTCC-AAGATATGTCAGAGGCAGAGGTTGTAGA Chimp: TTCTGAAATTTATATCTACTGGTCCTTGGACCAGTCAGAGGCAGAGGTTGTAGA ↑ 3 1 2 4 Gorilla: TTCTGAAATTTATATCTACTGGTCC-AAGATATGTCAGAGGCAGAGGTTGTAGA Human: TTCTGAAATTTATATCTACTGGTCC-AAGATATGTCAGAGGCAGAGGTTGTAGA Cluster: [ ] Orangutan: TTCTGAAATTTATATCTACTGGTCC-AAGATATGTCAGAGGCAGAGGCTGTAGA Gorilla > Chimp --------------- chr3:22105662-22105669 Template switch process: F1: L AAGTAAACTATGAGGATTCTGAAATTTATATCTACTGGTCC 1 F3: 4 GTCAGAGGCAGAGGTTGTAGAGCAAACCCACATAGAAGCC R RF: AAGTAAACTATGAGGATTCTGAAATTTATATCTACTGGTCCAAGATATGTCAGAGGCAGAGGTTGTAGAGCAAACCCACACAGAAGCC RR: TTCATTTGATACTCCTAAGACTTTAAATATAGATGACCAGGTTCTATACAGTCTCCGTCTCCAACATCTCGTTTGGGTGTGTCTTCGG F2: 3 ACCAGGTT 2 Unidirectional alignment (log-probability: -36.5) AGTAAACTATGAGGATTCTGAAATTTATATCTACTGGTCC------TtggaccaGTCAGAGGCAGAGGTTGTAGAGCAAACCCACAtAGAAGCC AGTAAACTATGAGGATTCTGAAATTTATATCTACTGGTCCAAGATAT-------GTCAGAGGCAGAGGTTGTAGAGCAAACCCACACAGAAGCC Template switch alignment (log-probability: -22.3) AGTAAACTATGAGGATTCTGAAATTTATATCTACTGGTCC|TTGGACCA|GTCAGAGGCAGAGGTTGTAGAGCAAACCCACAtAGAAGCC AGTAAACTATGAGGATTCTGAAATTTATATCTACTGGTCC|TTGGACCA|GTCAGAGGCAGAGGTTGTAGAGCAAACCCACACAGAAGCC ========== Event 2358 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGTAATCCCATCCTAAAGGGT-TAACTGCACAAAGAAATTTTTACTGAGTTATTTTTCAACCATACATCTTTTCCTTTTAAAAAATATTATTGAATCTGAAGTGAAAAGACATAAAAACAATGCAAAGTGGAGACACAGTTATAAGCAACTAATATTAACA Chimp: GGTAATCCCATCCTAAAGGGT-TAACTGCACAAAGAAATTTTTACTGAGATATTTTTCAACCATACGTCTTTTCCTTTTAAAAAATATTATTGAATCTGAAGTGAAAAGACATAAAAACAATGCAAAGTGGAGACACAGTTATAAGCAACTAATATTAACA ↑ 1 4 3 2 Gorilla: GGTAATCCCATCCTAAAGGGTTTTAGGACACAAAGAAATTTTTACTGAGATATTTTTCAACCACACATCTTTTCCTTTTAAAAAATATTATTGAATCTGAAGTGAAAAGACATAAAAACAATGCAAAGCGGAGACACAGTTATAAGCAACTAATATTAACA ↓ 1 4 3 2 Human: GGTAATCCCATCCTAAAGGGT-TAACTGCACAAAGAAATTTTTACTGAGTTATTTTTCAACCATACATCTTTTCCTTTTAAAAAATATTATTGAATCTGAAGTGAAAAGACATAAAAACAATGCAAAGTGGAGACACAGTTATAAGCAACTAATATTAACA Cluster: [ ] Orangutan: GGTAATCCCATCCTAAAGGGT-TAACTGCACAAAGAAATTTTCACTGAGATATTTTTCAACCATACATCTTTTCCTTTTAAAAAGTAGTATTGAATCTGAAGTGAAAAGACATA-AAACAATGCAAAGCGGAGACACAGTTATAAGCAACTGATATTAACA Gorilla > Human --------------- chr3:175945214-175945218 Template switch process: F1: L GGTGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT 1 F3: 4 CACAAAGAAATTTTTACTGAGTTATTTTTCAACCATACAT R RF: GGTGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTTTTAGGACACAAAGAAATTTTTACTGAGATATTTTTCAACCACACATCTTTTCCTTTTAAAAAATATTATTGAATCTGAAGTGAAAAGACATAAAAACAATGCAAAGCGGAGACACAGTT RR: CCACTCATTAATTTGTGTACCCATTAGGGTAGGATTTCCCAAAATCCTGTGTTTCTTTAAAAATGACTCTATAAAAAGTTGGTGTGTAGAAAAGGAAAATTTTTTATAATAACTTAGACTTCACTTTTCTGTATTTTTGTTACGTTTCGCCTCTGTGTCAA F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -37.7) TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT-----AactgCACAAAGAAATTTTTACTGAGtTATTTTTCAACCAtACAT TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTTTTAGGA----CACAAAGAAATTTTTACTGAGATATTTTTCAACCACACAT Template switch alignment (log-probability: -27.4) TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT|AACTG|CACAAAGAAATTTTTACTGAGtTATTTTTCAACCAtACAT TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT|AACTG|CACAAAGAAATTTTTACTGAGATATTTTTCAACCACACAT Gorilla > Chimp --------------- chr3:179767508-179767512 Template switch process: F1: L GGTGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT 1 F3: 4 CACAAAGAAATTTTTACTGAGATATTTTTCAACCATACGT R RF: GGTGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTTTTAGGACACAAAGAAATTTTTACTGAGATATTTTTCAACCACACATCTTTTCCTTTTAAAAAATATTATTGAATCTGAAGTGAAAAGACATAAAAACAATGCAAAGCGGAGACACAGTT RR: CCACTCATTAATTTGTGTACCCATTAGGGTAGGATTTCCCAAAATCCTGTGTTTCTTTAAAAATGACTCTATAAAAAGTTGGTGTGTAGAAAAGGAAAATTTTTTATAATAACTTAGACTTCACTTTTCTGTATTTTTGTTACGTTTCGCCTCTGTGTCAA F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -37.7) TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT-----AactgCACAAAGAAATTTTTACTGAGATATTTTTCAACCAtACgT TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTTTTAGGA----CACAAAGAAATTTTTACTGAGATATTTTTCAACCACACAT Template switch alignment (log-probability: -27.4) TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT|AACTG|CACAAAGAAATTTTTACTGAGATATTTTTCAACCAtACgT TGAGTAATTAAACACATGGGTAATCCCATCCTAAAGGGTT|AACTG|CACAAAGAAATTTTTACTGAGATATTTTTCAACCACACAT ========== Event 2359 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TATGTACCCATTGAATATAAAGATATTCCTCAGGAATATCTATTCCTCTCCAAAAATAAT ↑ 1 4 3 2 Chimp: TATGTACCCATTGAATATAAATGT---ACTCAGGAATATCTATTCCTCTCCAAATATAAT Gorilla: TATGTACCCATTGAATATAAAGATATTCCTCAGGAATATCTATTCCTCTCCAAAAATAAT Human: TATGTACCCATTGAATATAAAGATATTCCTCAGGAATATCTATTCCTCTCCAAAAATAAT Cluster: [ ] Orangutan: TATGTACCCATTGAATATAAAGATATTCCTCAGGAATATGTATTCCTCTCCAAAAATAAT Chimp > Human ------------- chr3:23391931-23391937 Template switch process: F1: L CCCCTCCACCATTGTTCTATTATGTACCCATTGAATATAAA 1 F3: 4 CTCAGGAATATCTATTCCTCTCCAAAAATAATTGTCACAG R RF: CCCCTCCACCATTGTTCTATTATGTACCCATTGAATATAAATGTACTCAGGAATATCTATTCCTCTCCAAATATAATTGTCACAG RR: GGGGAGGTGGTAACAAGATAATACATGGGTAACTTATATTTACATGAGTCCTTATAGATAAGGAGAGGTTTATATTAACAGTGTC F2: 3 CTTATAG 2 Unidirectional alignment (log-probability: -33.2) CCCTCCACCATTGTTCTATTATGTACCCATTGAATATAAAgaTAttcCTCAGGAATATCTATTCCTCTCCAAAaATAATTGTCACAG CCCTCCACCATTGTTCTATTATGTACCCATTGAATATAAATGTA---CTCAGGAATATCTATTCCTCTCCAAATATAATTGTCACAG Template switch alignment (log-probability: -22.1) CCCTCCACCATTGTTCTATTATGTACCCATTGAATATAAA|GATATTC|CTCAGGAATATCTATTCCTCTCCAAAaATAATTGTCACAG CCCTCCACCATTGTTCTATTATGTACCCATTGAATATAAA|GATATTC|CTCAGGAATATCTATTCCTCTCCAAATATAATTGTCACAG ========== Event 2360 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATACAATGATTCTTAAGTAAGAT-----ATTCACCTTTCCCAATTATTGCttt ↓ 3 1 24 Chimp: AACACAATGATTCTTAAGTAAGATGAATATCTTACCTTTCCCA----------- Gorilla: AATACAATGATTCTTAAGTAAGAT-----GTTCACCTTTCCCA----------- Human: AATACAATGATTCTTAAGTAAGAT-----ATTCACCTTTCCCAATTATTGCttt Cluster: [ ] Orangutan: AATACAATGATTCTTAAGTAAGAT-----ATTCACCTTTCCCA----------- Human > Chimp ------------- chr3:23252516-23252524 Template switch process: F1: L AATAGGTAAGATCCCAGAACACAATGATTCTTAAGTAAGAT 1 F3: 4 ACCTTTCCCA R RF: AATAGGTAAGATCCCAGAATACAATGATTCTTAAGTAAGATATTCACCTTTCCCA RR: TTATCCATTCTAGGGTCTTATGTTACTAAGAATTCATTCTATAAGTGGAAAGGGT F2: 3 TTCTATAAG 2 Unidirectional alignment (log-probability: -48.8) ATAGGTAAGATCCCAGAAcACAATGATTCTTAAGTAAGAT----gaatatcttACCTTTCCCA------------------------------ ATAGGTAAGATCCCAGAATACAATGATTCTTAAGTAAGATATTC---------ACCTTTCCCAATTATTGCTTTTTTTTTTAAGTTTTTTTTC Template switch alignment (log-probability: -21.7) ATAGGTAAGATCCCAGAAcACAATGATTCTTAAGTAAGAT|GAATATCTT|ACCTTTCCCA ATAGGTAAGATCCCAGAATACAATGATTCTTAAGTAAGAT|GAATATCTT|ACCTTTCCCA ========== Event 2361 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTGTCCTGTCTTAACCACCTGTGCACTATAAATGTACCTCACTGTGACCTGTTT------------------------------GGATTTGTTGTTGAGCTTCCTAAAGTGAATATAATACCTTGACTTTGCAGGATGGACCCAGCTTCCATACATAGCATTATAGAGATTGATATTGTTT Chimp: ATTGTCCTGTCTTAACCACCTGTGTGCTATAAATGTACCTCACTGTGATCTGTTT------------------------------GGATTTGTTGTTCAGCTTCCTAAAGTGAATATAATACCTTGACTTTGCAGGATGGACCCAGCCTCCATAAATAGCATTATAGAGATTGATATTGTTT ↓ 1 4 3 2 Gorilla: ATTGTCCTGTCTTAACCACCTATGCGCTATAAAtgtacctcactgtgatctgtttggatttgttgtacctcactgtgatctgtttggatttgttgtTGAGCTTCCTAAAGTGAATATAATACCTTGACTTTGCAGGATGGACCCAGCTTCCATACATAGCATTATAGAGATTGATATTGTTT Human: ATTGTCCTGTCTTAACCACCTGTGCACTATAAATGTACCTCACTGTGACCTGTTT------------------------------GGATTTGTTGTTGAGCTTCCTAAAGTGAATATAATACCTTGACTTTGCAGGATGGACCCAGCTTCCATACATAGCATTATAGAGATTGATATTGTTT Cluster: [ ] Orangutan: ATTATCCTGTCTTAACCACATGTGTGCTATAAATGTATCTCACTGTGATCCGTTT------------------------------GGATTTGTTGTTCAGCTTCCTAAAGTGAATATAGTACCTTGACTTTGCAGGATGGACCCAGCCTCCATACATAGCATTATAGAGATTGATACTGTTT Chimp > Gorilla --------------- chr3:25457501-25457504 Template switch process: F1: L TCTCAGTACTAACAGATGGTATTGTCCTGTCTTAACCACCT 1 F3: 4 GCTATAAATGTACCTCACTGTGATCTGTTTGGATTTGTTG R RF: TCTCAGTACTAACAGATGGTATTGTCCTGTCTTAACCACCTGTGTGCTATAAATGTACCTCACTGTGATCTGTTTGGATTTGTTGTTCAGCTTCCTAAAGTGAATATAATACCTTGACTTTGCAGGATGGACCCAGCCTCCATAAATAGCAT RR: AGAGTCATGATTGTCTACCATAACAGGACAGAATTGGTGGACACACGATATTTACATGGAGTGACACTAGACAAACCTAAACAACAAGTCGAAGGATTTCACTTATATTATGGAACTGAAACGTCCTACCTGGGTCGGAGGTATTTATCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -33.2) CTCAGTACTAACAGATGGTATTGTCCTGTCTTAACCACCTaTGcGCTATAAATGTACCTCACTGTGATCTGTTTggatttgttg CTCAGTACTAACAGATGGTATTGTCCTGTCTTAACCACCTGTGTGCTATAAATGTACCTCACTGTGATCTGTTT---------- Template switch alignment (log-probability: -16.2) CTCAGTACTAACAGATGGTATTGTCCTGTCTTAACCACCT|ATGC|GCTATAAATGTACCTCACTGTGATCTGTTTGGATTTGTTG CTCAGTACTAACAGATGGTATTGTCCTGTCTTAACCACCT|ATGC|GCTATAAATGTACCTCACTGTGATCTGTTTGGATTTGTTG ========== Event 2362 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATATTCCAAATTTTCTCCAATAA-TGTATGCTATTATTTTCTCTTTTTTCaattt ↑ 1 3 4 2 Chimp: atattccaaattttcTCCAATGATAGCAT-ACATTAttttctcttttttcaattt Gorilla: atattccaaattttcTGCAATGATAGCAT-ACATTATTTTCTCTTTTTTCAACTT Human: ATATTCCAAATTTTCTCCAATAA-TGTATGCTATTATTTTCTCTTTTTTCaattt Cluster: [ ] Orangutan: ATATTCCAAATTTTCTGCAATGATAACAT-ACattattttctcttttttcaattt Chimp > Human ------------- chr3:25846402-25846411 Template switch process: F1: L CTCCAGTGTATTTTTTCTGCATATTCCAAATTTTCTCCAAT 1 F3: 4 ATTATTTTCTCTTTTTTCAATTTTTATTGAATGTAAAATA R RF: CTCCCGTGTATTTTTTCTGCATATTCCAAATTTTCTCCAATGATAGCATACATTATTTTCTCTTTTTTCAATTTTTATTGAATGTAAAATA RR: GAGGGCACATAAAAAAGACGTATAAGGTTTAAAAGAGGTTACTATCGTATGTAATAAAAGAGAAAAAAGTTAAAAATAACTTACATTTTAT F2: 3 TCGTATGTAA 2 Unidirectional alignment (log-probability: -42) TCCaGTGTATTTTTTCTGCATATTCCAAATTTTCTCCAAT----------aatgtatgctATTATTTTCTCTTTTTTCAATTTTTATTGAATGTAAAATA TCCCGTGTATTTTTTCTGCATATTCCAAATTTTCTCCAATGATAGCATAC----------ATTATTTTCTCTTTTTTCAATTTTTATTGAATGTAAAATA Template switch alignment (log-probability: -22.5) TCCaGTGTATTTTTTCTGCATATTCCAAATTTTCTCCAAT|AATGTATGCT|ATTATTTTCTCTTTTTTCAATTTTTATTGAATGTAAAATA TCCCGTGTATTTTTTCTGCATATTCCAAATTTTCTCCAAT|AATGTATGCT|ATTATTTTCTCTTTTTTCAATTTTTATTGAATGTAAAATA ========== Event 2363 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTGATAGAAATAGGAAAGATCGGAAATCTACC--TGCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAATA Chimp: ATTGATAGAAATAGGAAAGATGGGAAATCTA--CCTGCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAATA ↑ 1 4 3 2 Gorilla: ATTGATAGAAATAGGAAAGATGGGAAAGGGA----ATCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAATA ↓ 1 4 3 2 Human: ATTGATAGAAATAGGAAAGATCGGAAATCTACC--TGCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAATA Cluster: [ ] Orangutan: ATTGATAGAAATAGGAAAGTTGGGAAAGAGA----ATCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAATA Gorilla > Human --------------- chr3:25703150-25703157 Template switch process: F1: L TCATGATGTAAGTTGGCATTATTGATAGAAATAGGAAAGATCGGAAA 1 F3: 4 CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA R RF: TCATGATGTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAAGGGAATCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA RR: AGTACTACATTCAACCGTAATAACTATCTTTATCCTTTCTACCCTTTCCCTTAGAGAACGTCAACTCGTCCATCTAAAACCCAACCACACCTT F2: 3 GTCCATCT 2 Unidirectional alignment (log-probability: -36.6) GTAAGTTGGCATTATTGATAGAAATAGGAAAGATcGGA-----AATctacctgCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA GTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAAGGGAAT-------CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA Template switch alignment (log-probability: -22.4) GTAAGTTGGCATTATTGATAGAAATAGGAAAGATcGGAAA|TCTACCTG|CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA GTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAA|TCTACCTG|CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA Gorilla > Chimp --------------- chr3:26270784-26270791 Template switch process: F1: L TGTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAA 1 F3: 4 CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA R RF: TGTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAAGGGAATCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA RR: ACATTCAACCGTAATAACTATCTTTATCCTTTCTACCCTTTCCCTTAGAGAACGTCAACTCGTCCATCTAAAACCCAACCACACCTT F2: 3 GTCCATCT 2 Unidirectional alignment (log-probability: -31) GTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGA-----AATctacctgCTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA GTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAAGGGAAT-------CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA Template switch alignment (log-probability: -16.7) GTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAA|TCTACCTG|CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA GTAAGTTGGCATTATTGATAGAAATAGGAAAGATGGGAAA|TCTACCTG|CTCTTGCAGTTGAGCAGGTAGATTTTGGGTTGGTGTGGAA ========== Event 2364 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CATGAGAGGGGAAGGAAATTGCAGATATTTTCATATAGAATGTTAGTGAA------------ATCAATCAGAAATACTTTCCAAA ↑ 13 24 Chimp: CATGAGAGGGGAAGGAAATTG------ATTTCACTAACATTCTATATGAA------AATATCTGCAATCAGAAATACTTTCCAAA Gorilla: CATGAGAGGGGAAGGAAATTG------ATTTCACTAACATTCTATATGAAAATATC------TGCAATCAGAAATACTTTCCAAA ↓ 13 24 Human: CATGAGAGGGGAAGGAAATTGCAGATATTTTCATATAGAATGTTAGTGAA------------ATCAATCAGAAATACTTTCCAAA Cluster: [ ] Orangutan: CATGAGAAGGGAAGGAAATTG------ATTTCACTAACATTCTATATGAAAATATC------TGCAATCAGAAATACTTTCCAAA Chimp > Human ------------- chr3:25097445-25097475 Template switch process: F1: L AAGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG 1 F3: 4 CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA R RF: AAGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTGATTTCACTAACATTCTATATGAAAATATCTGCAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA RR: TTCATCATTATATTAAAGTAGTACTCTCCCCTTCCTTTAACTAAAGTGATTGTAAGATATACTTTTATAGACGTTAGTCTTTATGAAAGGTTTTCGGTCCACGTCACCACGT F2: 3 TAAAGTGATTGTAAGATATACTTTTATAGAC 2 Unidirectional alignment (log-probability: -64.3) AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTGcagatattttcatatagaatgttagtgaaAT-----------------------------CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG-----------------------------ATTTCACTAACATTCTATATGAAAATATCTGCAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA Template switch alignment (log-probability: -19.1) AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG|CAGATATTTTCATATAGAATGTTAGTGAAAT|CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG|CAGATATTTTCATATAGAATGTTAGTGAAAT|CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA Gorilla > Human --------------- chr3:25097445-25097475 Template switch process: F1: L AAGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG 1 F3: 4 CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA R RF: AAGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTGATTTCACTAACATTCTATATGAAAATATCTGCAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA RR: TTCATCATTATATTAAAGTAGTACTCTCCCCTTCCTTTAACTAAAGTGATTGTAAGATATACTTTTATAGACGTTAGTCTTTATGAAAGGTTTTCGGTCCACGTCACCACGT F2: 3 TAAAGTGATTGTAAGATATACTTTTATAGAC 2 Unidirectional alignment (log-probability: -63.8) AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTGcagatattttcatatagaatgttagtgaaAT-----------------------------CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG-----------------------------ATTTCACTAACATTCTATATGAAAATATCTGCAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA Template switch alignment (log-probability: -19.7) AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG|CAGATATTTTCATATAGAATGTTAGTGAAAT|CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA AGTAGTAATATAATTTCATCATGAGAGGGGAAGGAAATTG|CAGATATTTTCATATAGAATGTTAGTGAAAT|CAATCAGAAATACTTTCCAAAAGCCAGGTGCAGTGGTGCA ========== Event 2365 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGTCCTCTTAGAGCCGTCGGGCATCTCCATTC----------------------CTGTCTTGCCCTCTTCAACCACA ↓ 3 2 4 1 Chimp: GGTCCTCCTAGAGCCGTCGGGCATCTCCATTC-----------CTGAGATGCCCCTGTCTTGCCCTCTTCAACCACA Gorilla: GGTCCTCCTAGAGCCGTCGGGCATCTCCATTCCTGAGATGCCC-----------CTGTCTTGCCCTCTTCAACCACA ↑ 3 2 4 1 Human: GGTCCTCTTAGAGCCGTCGGGCATCTCCATTC----------------------CTGTCTTGCCCTCTTCAACCACA Cluster: [ ] Orangutan: GGTCCTCCTAGAGCCATCAGGCATCTCCATTCCTGAGATGCCC-----------CTGGCTTGCCCTCTTCGACCATA Human > Chimp ------------- chr3:26089782-26089788 Template switch process: F1: L AGGTCTGTGGGTCCTCCTAGAGCCGTCGGGCATCTCCATTCCTG 1 F3: 4 CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTGA R RF: AGGTCTGCGGGTCCTCTTAGAGCCGTCGGGCATCTCCATTCCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTGA RR: TCCAGACGCCCAGGAGAATCTCGGCAGCCCGTAGAGGTAAGGACAGAACGGGAGAAGTTGGTGTGGACTCCATATAAAACT F2: 3 CCGTAGA 2 Unidirectional alignment (log-probability: -38.7) CTGtGGGTCCTCcTAGAGCCGTCGGGCATCTCCATTCCTGagatgcccctgTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG CTGCGGGTCCTCTTAGAGCCGTCGGGCATCTCCATTCCTG-----------TCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG Template switch alignment (log-probability: -28.2) CTGtGGGTCCTCcTAGAGCCGTCGGGCATCTCCATTCCTG|AGATGCC|CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG CTGCGGGTCCTCTTAGAGCCGTCGGGCATCTCCATTCCTG|AGATGCC|CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG Human > Gorilla --------------- chr3:26074062-26074068 Template switch process: F1: L AGGTCTGCGGGTCCTCCTAGAGCCGTCGGGCATCTCCATTCCTG 1 F3: 4 CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTGA R RF: AGGTCTGCGGGTCCTCTTAGAGCCGTCGGGCATCTCCATTCCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTGA RR: TCCAGACGCCCAGGAGAATCTCGGCAGCCCGTAGAGGTAAGGACAGAACGGGAGAAGTTGGTGTGGACTCCATATAAAACT F2: 3 CCGTAGA 2 Unidirectional alignment (log-probability: -32.2) CTGCGGGTCCTCcTAGAGCCGTCGGGCATCTCCATTcctgagatgccCCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG CTGCGGGTCCTCTTAGAGCCGTCGGGCATCTCCATT-----------CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG Template switch alignment (log-probability: -22.2) CTGCGGGTCCTCcTAGAGCCGTCGGGCATCTCCATTCCTG|AGATGCC|CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG CTGCGGGTCCTCTTAGAGCCGTCGGGCATCTCCATTCCTG|AGATGCC|CCTGTCTTGCCCTCTTCAACCACACCTGAGGTATATTTTG ========== Event 2366 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTTCCTTTTGCTTTTAAGAT----------------------------------------------------------------------------------------------GCATAGATTTAT-TTTAAATGATTGATAGAGACATAGATGGACTCTATGAATGAATAAATGAATGAATATTGGTATCAATTGTGAGTGAATCAAATTGGGTTTATGACATTATTAGATCACAAGGA ↑ 1 4 3 2 Chimp: GTTTCCTTTTGCTTTTAAGAT-----------------------------------------------GGCCAACAAACTGTAATGTGTGGTGTTGGAAACTCTAGATATGAAAGGCCAAGGTTTAT-TTTAAATGATTGATAGAGACATAGATGGACTCTATGAATGAATAAATGAATGAATATTGTTATCAATTGTGAGTGAATCAAATTGGGTCTATGACATTGTTAGATCACAAGGA Gorilla: GTTTCCTTTTGCTTTTAAGATGGCCAACAAACTGAAATGTGTGGTGTTGGAAACTCTAGATATGTAAG-----------------------------------------------GCCAAGGTTTAT-TTTAAATGATTGATAGAGACATAGATGGACTCTATGAATGAATAAATGAATGAATCTTGGTATCAATTGTGAGTGAATCAAATTGGGTTTATGACATTATTAGATCACAAGGA ↓ 1 4 3 2 Human: GTTTCCTTTTGCTTTTAAGAT----------------------------------------------------------------------------------------------GCATAGATTTAT-TTTAAATGATTGATAGAGACATAGATGGACTCTATGAATGAATAAATGAATGAATATTGGTATCAATTGTGAGTGAATCAAATTGGGTTTATGACATTATTAGATCACAAGGA Cluster: [ ] Orangutan: GTTTCCTTTTGCTTTTAAGATGGCCAACAAACTGAAATGTGTGGTGTTGGAAACTCTAGATAAGTAAG-----------------------------------------------GCCAAGGTTTATTTTTAAATG---AATAGAGACGTAGATGGACTCTATGAATGAATAAATGAATGAATATGGGTACCAGTTTTGAGTGAATCAAATTGGGTTTATGACATTATTAGATCACAA-GA Chimp > Human ------------- chr3:24188487-24188492 Template switch process: F1: L CTTGTATTCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG 1 F3: 4 TTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT R RF: CTTGTATCCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATGGCCAACAAACTGTAATGTGTGGTGTTGGAAACTCTAGATATGAAAGGCCAAGGTTTATTTTAAATGATTGATAGAGACATAGATGGACTCTATGAATGAATAAATGAATGAATATTGTTATCAATTGTGAGTGAATCAAATTGGGTCTATG RR: GAACATAGGTTTGTCTCTGACAAAGGAAAACGAAAATTCTACCGGTTGTTTGACATTACACACCACAACCTTTGAGATCTATACTTTCCGGTTCCAAATAAAATTTACTAACTATCTCTGTATCTACCTGAGATACTTACTTATTTACTTACTTATAACAATAGTTAACACTCACTTAGTTTAACCCAGATAC F2: 3 AGATAC 2 Unidirectional alignment (log-probability: -37.1) TGTATtCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG------------------------------------------------CAtAGaTTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT TGTATCCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATGGCCAACAAACTGTAATGTGTGGTGTTGGAAACTCTAGATATGAAAGGCCA-AGGTTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT Template switch alignment (log-probability: -22) TGTATtCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG|CATAGA|TTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT TGTATCCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG|CATAGA|TTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT Gorilla > Human --------------- chr3:24188487-24188492 Template switch process: F1: L CTTGTATTCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG 1 F3: 4 TTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT R RF: CTTGTATCCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATGGCCAACAAACTGAAATGTGTGGTGTTGGAAACTCTAGATATGTAAGGCCAAGGTTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT RR: GAACATAGGTTTGTCTCTGACAAAGGAAAACGAAAATTCTACCGGTTGTTTGACTTTACACACCACAACCTTTGAGATCTATACATTCCGGTTCCAAATAAAATTTACTAACTATCTCTGTATCTACCTGAGATA F2: 3 AGATAC 2 Unidirectional alignment (log-probability: -35.5) TGTATtCAAACAGAGACTGTTTCCTTTTGCTTTTAAGAT-----------------------------------------------GCatAGaTTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT TGTATCCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATGGCCAACAAACTGAAATGTGTGGTGTTGGAAACTCTAGATATGTAAGGCCAAGGTTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT Template switch alignment (log-probability: -22) TGTATtCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG|CATAGA|TTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT TGTATCCAAACAGAGACTGTTTCCTTTTGCTTTTAAGATG|CATAGA|TTTATTTTAAATGATTGATAGAGACATAGATGGACTCTAT ========== Event 2367 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGGTC----TCTCTCAACATCGTGAAATTATCC ↓ 3 2 1 4 Chimp: AATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGGCCTGAGTTTCTCAACATCATGAAATTATCC Gorilla: AATTTCGTGGTTGTTATCTAAACTCAGGCTACTTTGGGCC----TCTCTCAACATCGTGAAATTATCC Human: AATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGGTC----TCTCTCAACATCGTGAAATTATCC Cluster: [ ] Orangutan: AATTTTGTGGTTGTCATCTAAACTCAGGCTACTTTGGGCC----TCTCTCAACATCGTGAAATTATCC Human > Chimp ------------- chr3:24659786-24659794 Template switch process: F1: L GGAAATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGG 1 F3: 4 CTCAACATCATGAAATTATCCTGCCATTTCCTTGTTACT R RF: GGAAATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGGTCTCTCTCAACATCGTGAAATTATCCTGCCATTTCCTTGTTACT RR: CCTTTAAAACACCAACAATAGATTTGAGTCCGATGAAACCCAGAGAGAGTTGTAGCACTTTAATAGGACGGTAAAGGAACAATGA F2: 3 TTTGAGTCC 2 Unidirectional alignment (log-probability: -34.7) GAAATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGGcCTgagttTCTCAACATCaTGAAATTATCCTGCCATTTCCTTGTTACT GAAATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGGTCT----CTCTCAACATCGTGAAATTATCCTGCCATTTCCTTGTTACT Template switch alignment (log-probability: -22.4) GAAATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGG|CCTGAGTTT|CTCAACATCaTGAAATTATCCTGCCATTTCCTTGTTACT GAAATTTTGTGGTTGTTATCTAAACTCAGGCTACTTTGGG|CCTGAGTTT|CTCAACATCGTGAAATTATCCTGCCATTTCCTTGTTACT ========== Event 2368 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tggataaccaGTAAATTTGAGAATATAAGCCTAATTCTAG---------------TGCCTCTTAAGAAAAGTTTTCC ↓ 3 2 4 1 Chimp: tggataaccaGTAAATTTGAGAATATAAGCCTAATTCTAGTAGGCTTATATTCTTTCCCTCTTAAGAAAAGTTTTCC Gorilla: tggataaccaGTAAATTTGAGAATATAAGCCTAATTCTAG---------------TGCCTCTTAAGAAAATTTTTCC Human: tggataaccaGTAAATTTGAGAATATAAGCCTAATTCTAG---------------TGCCTCTTAAGAAAAGTTTTCC Cluster: [ ] Orangutan: tggataaccaGTAAATTTGAGAATATAAGCCTAATTCTAG---------------TGCCTCTTAAGAAAAGTTTTCC Human > Chimp ------------- chr3:174138990-174139002 Template switch process: F1: L ATGGATAACCAGTAAATTTGAGAATATAAGCCTAATTCTAGT 1 F3: 4 TTC-----CCTCTTAAGAAAAGTTTTCCTGTCTTGTCTCATTTTGAAA R RF: ATGGATAACCAGTAAATTTGAGAATATAAGCCTAATTCTAGTGCCTCTTAAGAAAAGTTTTCCTGTCTTGTCTCATTTTGAAA RR: TACCTATTGGTCATTTAAACTCTTATATTCGGATTAAGATCACGGAGAATTCTTTTCAAAAGGACAGAACAGAGTAAAACTTT F2: 3 TCTTATATTCGGA 2 Unidirectional alignment (log-probability: -38.5) GGATAACCAGTAAATTTGAGAATATAAGCCTAATTCTAGtaggcttatattcttTcCCTCTTAAGAAAAGTTTTCCTGTCTTGTCTCATTTTG GGATAACCAGTAAATTTGAGAATATAAGCCTAATTCTAG---------------TGCCTCTTAAGAAAAGTTTTCCTGTCTTGTCTCATTTTG Template switch alignment (log-probability: -27.4) GGATAACCAGTAAATTTGAGAATATAAGCCTAATTCTAGT|AGGCTTATATTCT|TTC-----CCTCTTAAGAAAAGTTTTCCTGTCTTGTCTCATTTTG GGATAACCAGTAAATTTGAGAATATAAGCCTAATTCTAGT|AGGCTTATATTCT|TTCTAGTGCCTCTTAAGAAAAGTTTTCCTGTCTTGTCTCATTTTG ========== Event 2369 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGATGGGTTTACAGGAAAAGATA-------TGGACCTTGAAATTCTGAATTATAATTGTCATTATTT ↓ 1 4 3 2 Chimp: AAGATGGGTTTACAGGAAAAGGTCAGAATTTCAGACCTTGAAATTCTGAATTATAATTGTCATTATTT Gorilla: AAGATGGGTTTACAGGAAAAGATA-------TGGACCTTGAAGTTCTGAATTATAATTGTCATTATTT Human: AAGATGGGTTTACAGGAAAAGATA-------TGGACCTTGAAATTCTGAATTATAATTGTCATTATTT Cluster: [ ] Orangutan: Human > Chimp ------------- chr3:173680906-173680915 Template switch process: F1: L ACTGAGAAGCCTCTTTTCAAAAGATGGGTTTACAGGAAAAGGT 1 F3: 4 GACCTTGAAATTCTGAATTATAATTGTCATTATTTATATT R RF: ACTGAGAAGCCTCTTTTCAAAAGATGGGTTTACAGGAAAAGATATGGACCTTGAAATTCTGAATTATAATTGTCATTATTTATATT RR: TGACTCTTCGGAGAAAAGTTTTCTACCCAAATGTCCTTTTCTATACCTGGAACTTTAAGACTTAATATTAACAGTAATAAATATAA F2: 3 ACTTTAAGAC 2 Unidirectional alignment (log-probability: -37.2) GAGAAGCCTCTTTTCAAAAGATGGGTTTACAGGAAAAG----GtcagaatttcaGACCTTGAAATTCTGAATTATAATTGTCATTATTTATATT GAGAAGCCTCTTTTCAAAAGATGGGTTTACAGGAAAAGATATG-----------GACCTTGAAATTCTGAATTATAATTGTCATTATTTATATT Template switch alignment (log-probability: -22.6) GAGAAGCCTCTTTTCAAAAGATGGGTTTACAGGAAAAGgT|CAGAATTTCA|GACCTTGAAATTCTGAATTATAATTGTCATTATTTATATT GAGAAGCCTCTTTTCAAAAGATGGGTTTACAGGAAAAGAT|CAGAATTTCA|GACCTTGAAATTCTGAATTATAATTGTCATTATTTATATT ========== Event 2370 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTACTGAAAAATACACAAATCTATTTCTACAGGTTCGCATAGGTAATGACTTT ↓ 1 3 4 2 Chimp: TATTACTGAAAAATACACAAACCTG--TAGACAGGTTCGCATAGGTAATGACTTT ↑ 1 3 4 2 Gorilla: TATTACTGATAAATACACAAATCTATTTCTACAGGTTCGCATAGGTAATGACTTT Human: TATTACTGAAAAATACACAAATCTATTTCTACAGGTTCGCATAGGTAATGACTTT Cluster: [ ] Orangutan: TATTACTGATAAATACACAAATCTATTTCTACAGGTTTGCATAGGTAATGACTTT Human > Chimp ------------- chr3:199728040-199728046 Template switch process: F1: L AATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAA 1 F3: 4 ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC R RF: AATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAATCTATTTCTACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC RR: TTAAGGGACCAATAAAATAAATAATGACTTTTTATGTGTTTAGATAAAGATGTCCAAGCGTATCCATTACTGAAAAGAGAGGGTAGACTG F2: 3 GATGTCC 2 Unidirectional alignment (log-probability: -31.7) ATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAAcctgtag---------ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC ATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAA-------TCTATTTCTACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC Template switch alignment (log-probability: -16.2) ATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAA|CCTGTAG|ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC ATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAA|CCTGTAG|ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC Gorilla > Chimp --------------- chr3:199728040-199728046 Template switch process: F1: L AATTCCCTGGTTATTTTATTTATTACTGAAAAATACACAAA 1 F3: 4 ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC R RF: AATTCCCTGGTTATTTTATTTATTACTGATAAATACACAAATCTATTTCTACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC RR: TTAAGGGACCAATAAAATAAATAATGACTATTTATGTGTTTAGATAAAGATGTCCAAGCGTATCCATTACTGAAAAGAGAGGGTAGACTG F2: 3 GATGTCC 2 Unidirectional alignment (log-probability: -36.7) ATTCCCTGGTTATTTTATTTATTACTGAaAAATACACAAA---------cctgtagACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC ATTCCCTGGTTATTTTATTTATTACTGATAAATACACAAATCTATTTCT-------ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC Template switch alignment (log-probability: -22.1) ATTCCCTGGTTATTTTATTTATTACTGAaAAATACACAAA|CCTGTAG|ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC ATTCCCTGGTTATTTTATTTATTACTGATAAATACACAAA|CCTGTAG|ACAGGTTCGCATAGGTAATGACTTTTCTCTCCCATCTGAC ========== Event 2371 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTTGACAACTGCAGTTGTCCTCAGATTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGTCAGTCATGTAATTCTGAAAATCAGCTGTCTTATGACC ↑ 1 4 3 2 Chimp: GGTTGACAACTGCAGTTGTCCGCGGGTTACTGTATCCAGTTAAATCCAAAATTGtttttttCTG----TCATGTAATTCTGAAAATCAGCTCTCTTATGACC Gorilla: GGTTGACAACTGCAGTTGTCCTCAGATTACTGTATCCAGTTAAATCCAAAATTGtttttttCTG----TCATGTAATTCTGAAAATCAGCTCTCTTATGACC Human: GGTTGACAACTGCAGTTGTCCTCAGATTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGTCAGTCATGTAATTCTGAAAATCAGCTGTCTTATGACC Cluster: [ ] Orangutan: GGTTGACAACTGCAGTTGTCCTCAAATTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTG----TCACGTAATTCTGAAAATCAGCTGTCTTATGACC Chimp > Human ------------- chr3:195143518-195143522 Template switch process: F1: L ATTGAATGAAAGGAAGAAAAGGTTGACAACTGCAGTTGTCC 1 F3: 4 TTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGTC R RF: ATTGAATGAAAGGAAGAAAAGGTTGACAACTGCAGTTGTCCGCGGGTTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGTCATGTAATTCTGA RR: TAACTTACTTTCCTTCTTTTCCAACTGTTGACGTCAACAGGCGCCCAATGACATAGGTCAATTTAGGTTTTAACAAAAAAAGACAGTACATTAAGACT F2: 3 AGACT 2 Unidirectional alignment (log-probability: -28.8) TTGAATGAAAGGAAGAAAAGGTTGACAACTGCAGTTGTCCtCaGaTTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGtc TTGAATGAAAGGAAGAAAAGGTTGACAACTGCAGTTGTCCGCGGGTTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTG-- Template switch alignment (log-probability: -15.9) TTGAATGAAAGGAAGAAAAGGTTGACAACTGCAGTTGTCC|TCAGA|TTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGTC TTGAATGAAAGGAAGAAAAGGTTGACAACTGCAGTTGTCC|TCAGA|TTACTGTATCCAGTTAAATCCAAAATTGTTTTTTTCTGTC ========== Event 2372 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAATATA-CTACTATCCCTTTCATGT-TTTTAGAAAAATACTATTTTAATGATATGCCGATGTATATTAGAGTATTTTCCTTTCAAAAAATAGACCTTGACATAGATATGAGAAGATATGATTAGAAAGACAGCAATTATAGAAAATTGTGTATAATTGTTCATGatgaccaagggaataatagga ↑ 1 4 3 2 Chimp: AAAATATA-CTACTATCCCTTATTTGTTTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATACTAGAGTATTTTCCTTTCAAAAAATAGACCTTGACATAGATATGAGAAGATATGATTAGAAAGACAGCAATTATAGAAAATTGTGTATAATTGTTCATGatgaccaagggaataatagga Gorilla: AAAATATACTTACTATCCCTTTCATGT-TTTTAGAAAAATACTATTTTAATGATATGCCAATGTATACTAGAGTACTTTCCTTTCAAAAAATAGACCTTGACATAGATATGAGAAGATATGATTAGAAAGACAGCAATTATAGAAAATTGTGTGTAATTGTTCATGatgaccaagggaataatagga Human: AAAATATA-CTACTATCCCTTTCATGT-TTTTAGAAAAATACTATTTTAATGATATGCCGATGTATATTAGAGTATTTTCCTTTCAAAAAATAGACCTTGACATAGATATGAGAAGATATGATTAGAAAGACAGCAATTATAGAAAATTGTGTATAATTGTTCATGatgaccaagggaataatagga Cluster: [ ] Orangutan: AAAATATA-CTACTATCCCTTTCATAT-TTTTAGAAAAATACTATTTTAATGATATGCTGATATGTATTAGAGTATTTTCCTTTCAAAAAATAGACCTTGACATAGTTATGAGAAGATATGATTAGAAAGACAGCAATTATAGAAAATTGTATATAATTGTTCGTGatgaccaagggaataatagga Chimp > Human ------------- chr3:29492233-29492237 Template switch process: F1: L TAAGTCAGCAAATCATGATCAAAAATATACTACTATCCCTT 1 F3: 4 TTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATAT R RF: TAAGTCAGCAAATCATGATCAAAAATATACTACTATCCCTTATTTGTTTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATACTAGAGTATTTTCCTTTCAAAAAATAGACCTTGACATAGATATGAGAAGATATGATTAGAAAGACAGCAATTATAGAAAATTGTGTATAATTGTTCATGA RR: ATTCAGTCGTTTAGTACTAGTTTTTATATGATGATAGGGAATAAACAAAAAATCTTTTTATGATAAAATTACTATACGGCTACATATGATCTCATAAAAGGAAAGTTTTTTATCTGGAACTGTATCTATACTCTTCTATACTAATCTTTCTGTCGTTAATATCTTTTAACACATATTAACAAGTACT F2: 3 GTACT 2 Unidirectional alignment (log-probability: -33.2) AAGTCAGCAAATCATGATCAAAAATATACTACTATCCCTT-----TcatgTTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATA AAGTCAGCAAATCATGATCAAAAATATACTACTATCCCTTATTTGT----TTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATA Template switch alignment (log-probability: -21.9) AAGTCAGCAAATCATGATCAAAAATATACTACTATCCCTT|TCATG|TTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATA AAGTCAGCAAATCATGATCAAAAATATACTACTATCCCTT|TCATG|TTTTTAGAAAAATACTATTTTAATGATATGCCGATGTATA ========== Event 2373 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: cttttaTAGGCTATTGGAAGCCACTATAGA----GTAATAGGCGTAAGAGCATTGC ↓ 3 1 2 4 Chimp: cttttaTAGGCTATTGGAAGCCACTCTATAGTGGCTAATAGGCGTAAGAGCATTGC ↑ 3 1 2 4 Gorilla: cttttaTAGGCTATTGGAAGCCACTATAGA----GTAATAGGCGTAAGAGCATTGC Human: cttttaTAGGCTATTGGAAGCCACTATAGA----GTAATAGGCGTAAGAGCATTGC Cluster: [ ] Orangutan: ctCTTATAGGCTATTGGAAGCCACTATAGA----GTAATAGGCATAACAGCATTGC Human > Chimp ------------- chr3:29943976-29943985 Template switch process: F1: L GAAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACT 1 F3: 4 TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA R RF: GAAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACTATAGAGTAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA RR: CTTTTAAACTCTAAATGAAAATATCCGATAACCTTCGGTGATATCTCATTATCCGCATTCTCGTAACGTAACTTTAGATGTAAATCT F2: 3 CGGTGATATC 2 Unidirectional alignment (log-probability: -28.7) AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACTcTAtAGtggcTAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACTATAGAG----TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA Template switch alignment (log-probability: -16.5) AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACT|CTATAGTGGC|TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACT|CTATAGTGGC|TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA Gorilla > Chimp --------------- chr3:29943976-29943985 Template switch process: F1: L GAAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACT 1 F3: 4 TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA R RF: GAAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACTATAGAGTAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA RR: CTTTTAAACTCTAAATGAAAATATCCGATAACCTTCGGTGATATCTCATTATCCGCATTCTCGTAACGTAACTTTAGATGTAAATCT F2: 3 CGGTGATATC 2 Unidirectional alignment (log-probability: -27.8) AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACTcTAtAGtggcTAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACTATAGAG----TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA Template switch alignment (log-probability: -17) AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACT|CTATAGTGGC|TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA AAAATTTGAGATTTACTTTTATAGGCTATTGGAAGCCACT|CTATAGTGGC|TAATAGGCGTAAGAGCATTGCATTGAAATCTACATTTAGA ========== Event 2374 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCCTGTAAGTCAGCAAATCATGATCAAAAATATA-CTACTATCCCTTTCATGT-TTTTAGAAAAATACTATTTT Chimp: GCCCTGTAAGTCAGCAAATCATGATCAAAAATATA-CTACTATCCCTTATTTGTTTTTTAGAAAAATACTATTTT ↓ 3 2 1 4 Gorilla: GCCCTGTAAGTCAGCAAATCATGATCAAAAATATACTTACTATCCCTTTCATGT-TTTTAGAAAAATACTATTTT Human: GCCCTGTAAGTCAGCAAATCATGATCAAAAATATA-CTACTATCCCTTTCATGT-TTTTAGAAAAATACTATTTT Cluster: [] Orangutan: GCCTTGTAAGTCAGCAAATCATGATCAAAAATATA-CTACTATCCCTTTCATAT-TTTTAGAAAAATACTATTTT Chimp > Gorilla --------------- chr3:29993265-29993269 Template switch process: F1: L GGAGGTGCCCTGTAAGTCAGCAAATCATGATCAAAAATATACTTACTATCCCTT 1 F3: 4 TTTTTAGAAAAATACTATTTTAA R RF: GGAGGTGCCCTGTAAGTCAGCAAATCATGATCAAAAATATAC-TACTATCCCTTATTTGTTTTTTAGAAAAATACTATTTTAA RR: CCTCCACGGGACATTCAGTCGTTTAGTACTAGTTTTTATATG-ATGATAGGGAATAAACAAAAAATCTTTTTATGATAAAATT F2: 3 GTACT 2 Unidirectional alignment (log-probability: -37.8) AGTCAGCAAATCATGATCAAAAATATACtTACTATCCCTT-----TcatgTTTTTAGAAAAATACTATTTTAA AGTCAGCAAATCATGATCAAAAATATAC-TACTATCCCTTATTTGT----TTTTTAGAAAAATACTATTTTAA Template switch alignment (log-probability: -27.4) AGTCAGCAAATCATGATCAAAAATATACtTACTATCCCTT|TCATG|TTTTTAGAAAAATACTATTTTAA AGTCAGCAAATCATGATCAAAAATATAC-TACTATCCCTT|TCATG|TTTTTAGAAAAATACTATTTTAA ========== Event 2375 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCATGACAGAGGCATGGTTACCCTGTATCCACAGGGTATGCACTGTGCCTTTTGGAAAT Chimp: TCATGACAGAGGCATGGTTACCCTGTATCCACAGGGTATGCACTGTGCCTTTTGGAAAT ↑ 3 1 42 Gorilla: TCATGACAGAGGCATGGTTACCCTG---------TGGATGCACTGTGCCTTTTGGTAAT ↓ 3 1 42 Human: TCATGACAGAGGCATGGTTACCCTGTATCCACAGGGTATGCACTGTGCCTTTTGGAAAT Cluster: [ ] Orangutan: TCATGACAGAGGCATGGTTACCCTG---------TGGATGCACTGTGCCTTTTGGAAAT Gorilla > Human --------------- chr3:168008124-168008134 Template switch process: F1: L TACAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT 1 F3: 4 ATGCACTGTGCCTTTTGGAAATGGAGTATGTTAATCAATG R RF: TACAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGTGGATGCACTGTGCCTTTTGGTAATGGAGTATGTTAAACAATG RR: ATGTCACTTTTACGACAGTACTGTCTCCGTACCAATGGGACACCTACGTGACACGGAAAACCATTACCTCATACAATTTGTTAC F2: 3 TGGGACACCTA 2 Unidirectional alignment (log-probability: -40.4) CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGTatccacaggGtATGCACTGTGCCTTTTGGaAATGGAGTATGTTAAtCAATG CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT---------GGATGCACTGTGCCTTTTGGTAATGGAGTATGTTAAACAATG Template switch alignment (log-probability: -28.2) CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT|ATCCACAGGGT|ATGCACTGTGCCTTTTGGaAATGGAGTATGTTAAtCAATG CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT|ATCCACAGGGT|ATGCACTGTGCCTTTTGGTAATGGAGTATGTTAAACAATG Gorilla > Chimp --------------- chr3:171646777-171646787 Template switch process: F1: L TACAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT 1 F3: 4 ATGCACTGTGCCTTTTGGAAATGGAGTATGTTAAACAATG R RF: TACAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGTGGATGCACTGTGCCTTTTGGTAATGGAGTATGTTAAACAATG RR: ATGTCACTTTTACGACAGTACTGTCTCCGTACCAATGGGACACCTACGTGACACGGAAAACCATTACCTCATACAATTTGTTAC F2: 3 TGGGACACCTA 2 Unidirectional alignment (log-probability: -34.9) CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGTatccacaggGtATGCACTGTGCCTTTTGGaAATGGAGTATGTTAAACAATG CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT---------GGATGCACTGTGCCTTTTGGTAATGGAGTATGTTAAACAATG Template switch alignment (log-probability: -22.7) CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT|ATCCACAGGGT|ATGCACTGTGCCTTTTGGaAATGGAGTATGTTAAACAATG CAGTGAAAATGCTGTCATGACAGAGGCATGGTTACCCTGT|ATCCACAGGGT|ATGCACTGTGCCTTTTGGTAATGGAGTATGTTAAACAATG ========== Event 2376 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CAGAATTCACTTAAAATAATACATT-----------------TCTTGAAGATGATTGAAAGTTATTT--TTATTCTTTCCAGGAAAAAATACTC ↓ 13 24 ↑ 13 24 Chimp: CAGAATTCACTTAAAATAATAACTT----------TCAATCATCTTCA-------AGAAATGTATTT--TTATCCTTTCCAGGAAAAAATACTC Gorilla: CAGAATTCACTTAAAATAATAACTT---TCAATCA-------TCTTCA-------AGAAATGTATTT------TCTTTTCAGGAAAAAATACTC Human: CAGAATTCACTTAAAATAATACATT-----------------TCTTGAAGATGATTGAAAGTTATTT--TTATTCTTTCCAGGAAAAAATACTC Cluster: [ ] Orangutan: CAGAATTCACTTAAAATAATAACTTTCA--------------TCTTCA-------AGAAATGTATTTTT-----GTTTTCAGGA-AAAATATTC Chimp > Human ------------- chr3:30783392-30783415 Template switch process: F1: L TCAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA 1 F3: 4 TATTTTTATTCTTTCCAGGAAAAAATACTCAAGTACTGGGTATTGTCTTG R RF: TCAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATAACTTTCAATCATCTTCAAGAAATGTATTTTTATCCTTTCCAGGAAAAAATACTCAAGTACTGGGTATTGTCTTG RR: AGTCCCCGGATACTTATTAAGTCTTAAGTGAATTTTATTATTGAAAGTTAGTAGAAGTTCTTTACATAAAAATAGGAAAGGTCCTTTTTTATGAGTTCATGACCCATAACAGAAC F2: 3 TGAAAGTTAGTAGAAGTTCTTTAC 2 Unidirectional alignment (log-probability: -62.9) CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA------------------------catttcttgaagatgattgaaagtTATTTTTATtCTTTCCAGGAAAAAATACTCAAGTACTGGG CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATAACTTTCAATCATCTTCAAGAAATG------------------------TATTTTTATCCTTTCCAGGAAAAAATACTCAAGTACTGGG Template switch alignment (log-probability: -24.4) CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA|CATTTCTTGAAGATGATTGAAAGT|TATTTTTATtCTTTCCAGGAAAAAATACTCAAGTACTGGG CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA|CATTTCTTGAAGATGATTGAAAGT|TATTTTTATCCTTTCCAGGAAAAAATACTCAAGTACTGGG Human > Chimp ------------- chr3:31471382-31471405 Template switch process: F1: L TCAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA 1 F3: 4 TATTTTTATCCTTTCCAGGAAAAAATACTCAAGTACTGGGTATTGTCTTG R RF: TCAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATACATTTCTTGAAGATGATTGAAAGTTATTTTTATTCTTTCCAGGAAAAAATACTCAAGTACTGGGTATTGTCTTG RR: AGTCCCCGGATACTTATTAAGTCTTAAGTGAATTTTATTATGTAAAGAACTTCTACTAACTTTCAATAAAAATAAGAAAGGTCCTTTTTTATGAGTTCATGACCCATAACAGAAC F2: 3 GTAAAGAACTTCTACTAACTTTCA 2 Unidirectional alignment (log-probability: -62.9) CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA------------------------actttcaatcatcttcaagaaatgTATTTTTATcCTTTCCAGGAAAAAATACTCAAGTACTGGG CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATACATTTCTTGAAGATGATTGAAAGT------------------------TATTTTTATTCTTTCCAGGAAAAAATACTCAAGTACTGGG Template switch alignment (log-probability: -24.4) CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA|ACTTTCAATCATCTTCAAGAAATG|TATTTTTATcCTTTCCAGGAAAAAATACTCAAGTACTGGG CAGGGGCCTATGAATAATTCAGAATTCACTTAAAATAATA|ACTTTCAATCATCTTCAAGAAATG|TATTTTTATTCTTTCCAGGAAAAAATACTCAAGTACTGGG ========== Event 2377 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: aagA--CACTTCTCTAGATAATTCTGTGCTTGCTAGGCC----CTCTTATTTATAGGATCAACAGAT Chimp: AAGA--CACTTCTCTAGATAAG--AGGGCCTAGCAAGCA--CAGAATTATTTATAGGATCAACAGAT Gorilla: AAGA--CACTTCTCTAGATAAG--AGGGCCTAGCAAGCACA--GAATTATTTATAGGATCAACGGAT ↓ 1 3 24 ↑ 13 24 Human: aagA--CACTTCTCTAGATAATTCTGTGCTTGCTAGGCC----CTCTTATTTATAGGATCAACAGAT Cluster: [ ] Orangutan: AAGATGTGCTTCTCTAGATAAG--AGGGCCTAGCAAGCACA--AAATTATTTATAGGATCAACAGAT Gorilla > Human --------------- chr3:30778081-30778101 Template switch process: F1: L TCATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA 1 F3: 4 TTATTTATAGGATCAACAGATAATGTACACTGAATCTACT R RF: CCATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAAGAGGGCCTAGCAAGCACAGAATTATTTATAGGATCAACGGATAATGTACACTGAATCTACT RR: GGTAATGAAAAATTGTTTGATCTTCTGTGAAGAGATCTATTCTCCCGGATCGTTCGTGTCTTAATAAATATCCTAGTTGCCTATTACATGTGACTTAGATGA F2: 3 CTCCCGGATCGTTCGTGTCTT 2 Unidirectional alignment (log-probability: -62.9) CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGAT---------------------AAttctgtgcttgctaggccctcTTATTTATAGGATCAACaGATAATGTACACTGAATCTACT CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAAGAGGGCCTAGCAAGCACAGAA---------------------TTATTTATAGGATCAACGGATAATGTACACTGAATCTACT Template switch alignment (log-probability: -29.4) CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA|TTCTGTGCTTGCTAGGCCCTC|TTATTTATAGGATCAACaGATAATGTACACTGAATCTACT CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA|TTCTGTGCTTGCTAGGCCCTC|TTATTTATAGGATCAACGGATAATGTACACTGAATCTACT Human > Gorilla --------------- chr3:31299085-31299105 Template switch process: F1: L CCATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA 1 F3: 4 TTATTTATAGGATCAACGGATAATGTACACTGAATCTACT R RF: TCATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAATTCTGTGCTTGCTAGGCCCTCTTATTTATAGGATCAACAGATAATGTACACTGAATCTACT RR: AGTAATGAAAAATTGTTTGATCTTCTGTGAAGAGATCTATTAAGACACGAACGATCCGGGAGAATAAATATCCTAGTTGTCTATTACATGTGACTTAGATGA F2: 3 AAGACACGAACGATCCGGGAG 2 Unidirectional alignment (log-probability: -62.9) CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA---------------------gagggcctagcaagcacagaaTTATTTATAGGATCAACgGATAATGTACACTGAATCTACT CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAATTCTGTGCTTGCTAGGCCCTC---------------------TTATTTATAGGATCAACAGATAATGTACACTGAATCTACT Template switch alignment (log-probability: -29.4) CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA|GAGGGCCTAGCAAGCACAGAA|TTATTTATAGGATCAACgGATAATGTACACTGAATCTACT CATTACTTTTTAACAAACTAGAAGACACTTCTCTAGATAA|GAGGGCCTAGCAAGCACAGAA|TTATTTATAGGATCAACAGATAATGTACACTGAATCTACT ========== Event 2378 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCATTTGACACATGTGTCCCAAACTACTGATTTGGGACATCAGTGGTTCACACAGAGGGCAGAAAACA ↑ 1 4 3 2 Chimp: GCATTTGACACATGTGTCCCA------GGTTTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACA Gorilla: GCATTTGACACATGTGTCCCA------GGTTTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACA ↓ 1 4 3 2 Human: GCATTTGACACATGTGTCCCAAACTACTGATTTGGGACATCAGTGGTTCACACAGAGGGCAGAAAACA Cluster: [ ] Orangutan: gcatttgacacatgtgtccca------ggttttgggccatcactagttcacacagagggcagaaaaca Chimp > Human ------------- chr3:166835210-166835218 Template switch process: F1: L TGAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA 1 F3: 4 TTTGGGACATCAGTGGTTCACACAGAGGGCAGAAAACAGA R RF: TGAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCAGGTTTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACAGA RR: ACTTGTCCATAAAAACATCTCGTAAACTGTGTACACAGGGTCCAAAACCCTGTAGTCATCAAGTGTGTCTCCCGTCTTTTGTCT F2: 3 AGTCATCAA 2 Unidirectional alignment (log-probability: -37.5) GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCAaactactGaTTTGGGACATCAGTgGTTCACACAGAGGGCAGAAAACAGA GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA------GGTTTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACAGA Template switch alignment (log-probability: -22.4) GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA|AACTACTGA|TTTGGGACATCAGTgGTTCACACAGAGGGCAGAAAACAGA GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA|AACTACTGA|TTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACAGA Gorilla > Human --------------- chr3:166835210-166835218 Template switch process: F1: L TGAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA 1 F3: 4 TTTGGGACATCAGTGGTTCACACAGAGGGCAGAAAACAGA R RF: TGAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCAGGTTTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACAGA RR: ACTTGTCCATAAAAACATCTCGTAAACTGTGTACACAGGGTCCAAAACCCTGTAGTCATCAAGTGTGTCTCCCGTCTTTTGTCT F2: 3 AGTCATCAA 2 Unidirectional alignment (log-probability: -36.1) GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCAaactactGaTTTGGGACATCAGTgGTTCACACAGAGGGCAGAAAACAGA GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA------GGTTTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACAGA Template switch alignment (log-probability: -22.4) GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA|AACTACTGA|TTTGGGACATCAGTgGTTCACACAGAGGGCAGAAAACAGA GAACAGGTATTTTTGTAGAGCATTTGACACATGTGTCCCA|AACTACTGA|TTTGGGACATCAGTAGTTCACACAGAGGGCAGAAAACAGA ========== Event 2379 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAGATCTCCCAGCCTGAGGAAG--------ATGCATGGAAGGATTGATTATTTGATGt-------------------------------------------------------------tttttttttttttGGCTTCTCTTAGCTGTTAGGCCAAATGAAGAAGTAACTT ↓ 1 4 3 2 Chimp: GAAGATCTCCCAGCCTGAGGACT----AACTGTGCATGGAAGGATTGATTATTTGATGt-------------------------------------------------------------tttt--tttttttAGCTTCTCTTAGCTGTTAGGCCAAATGAAGAAGTAACTT Gorilla: GAAGATCTCCCAGCCTGAGGACTAACC----ATGCATGGAAGGATTGATTATTTGATGT------TCtttttttttttttttnnnnnnnnnnnnnnnnnnnnnnnnntgatttttttttttttt--tttttttAGCTTCTCTTAGCTGTTAGGCCAAATGAAGAAGTAACTT Human: GAAGATCTCCCAGCCTGAGGAAG--------ATGCATGGAAGGATTGATTATTTGATGt-------------------------------------------------------------tttttttttttttGGCTTCTCTTAGCTGTTAGGCCAAATGAAGAAGTAACTT Cluster: [ ] Orangutan: GAAGATCTCCCAGCCTGAGGACTAACC----GTGTATGGAAGGACTGATTATTTGATGttttttt-------------------------------------------------------tttt--tttttttAGCTTCTCTTAGCTGTTAGGCCAAATGAAGAAGTAACTT Human > Chimp ------------- chr3:170260756-170260762 Template switch process: F1: L CAATTTGTGGAATTTCAAATGAAGATCTCCCAGCCTGAGGA 1 F3: 4 TGCATGGAAGGATTGATTATTTGATGTTTTTTTTTTTT R RF: CAATTTGTGGAATTTCAAATGAAGATCTCCCAGCCTGAGGAAGATGCATGGAAGGATTGATTATTTGATGTTTTTTTTTTTTTTGGCTTCTCTTAGCTGTTAG RR: GTTAAACACCTTAAAGTTTACTTCTAGAGGGTCGGACTCCTTCTACGTACCTTCCTAACTAATAAACTACAAAAAAAAAAAAAACCGAAGAGAATCGACAATC F2: 3 GTCAATC 2 Unidirectional alignment (log-probability: -36) AATTTGTGGAATTTCAAATGAAGATCTCCCAGCCTGAGGActAactgTGCATGGAAGGATTGATTATTTGATGTTTTTTTTTTTT-- AATTTGTGGAATTTCAAATGAAGATCTCCCAGCCTGAGGAAGA----TGCATGGAAGGATTGATTATTTGATGTTTTTTTTTTTTTT Template switch alignment (log-probability: -22.1) AATTTGTGGAATTTCAAATGAAGATCTCCCAGCCTGAGGA|CTAACtG|TGCATGGAAGGATTGATTATTTGATGTTTTTTTTTTTT AATTTGTGGAATTTCAAATGAAGATCTCCCAGCCTGAGGA|CTAACAG|TGCATGGAAGGATTGATTATTTGATGTTTTTTTTTTTT ========== Event 2380 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCATATCAGTTGATTGTAATCTGTTCTTTTCCATTTAATATTATTTTAT-AGCATGATTTTATAAACATACAGTTCATATAGTTATTTTTAGTAA ↓ 1 4 3 2 Chimp: GCATATCAGTTGATTGTAATCAAC---------TGTAATATTATTTTAT-AGCATGATTTTATAAACATACAGTTCATATAGTTATTTTTAGTAA Gorilla: GCATATCAGTTGATTGTAATCTGTTCTTTTCCATTTAATATTATTTTATAGGCATGAT-TTATAAACATACAGTTCATATAGTTATTTTTAGTAA Human: GCATATCAGTTGATTGTAATCTGTTCTTTTCCATTTAATATTATTTTAT-AGCATGATTTTATAAACATACAGTTCATATAGTTATTTTTAGTAA Cluster: [ ] Orangutan: GCATATCAGTTGATTGTAATCTGTTCTTTTCCATTTAATATTATTTTATAGGCATGATTTTATAAACATACAATTCATATAGTTATTTTTAGTAA Human > Chimp ------------- chr3:34613702-34613706 Template switch process: F1: L TTAGTATTATTATAATGAATGCATATCAGTTGATTGTAATC 1 F3: 4 TAATATTATTTTATAGCATGATTTTATAAACATACAGTTC R RF: TTAGTGTTATTATAATGAATGCATATCAGTTGATTGTAATCTGTTCTTTTCCATTTAATATTATTTTATAGCATGATTTTATAAACATACAGTTC RR: AATCACAATAATATTACTTACGTATAGTCAACTAACATTAGACAAGAAAAGGTAAATTATAATAAAATATCGTACTAAAATATTTGTATGTCAAG F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -32.1) TAGTaTTATTATAATGAATGCATATCAGTTGATTGTAATcaaCTG------------TAATATTATTTTATAGCATGATTTTATAAACATACAGTTC TAGTGTTATTATAATGAATGCATATCAGTTGATTGTAAT---CTGTTCTTTTCCATTTAATATTATTTTATAGCATGATTTTATAAACATACAGTTC Template switch alignment (log-probability: -21.9) TAGTaTTATTATAATGAATGCATATCAGTTGATTGTAATC|AACTG|TAATATTATTTTATAGCATGATTTTATAAACATACAGTTC TAGTGTTATTATAATGAATGCATATCAGTTGATTGTAATC|AACTG|TAATATTATTTTATAGCATGATTTTATAAACATACAGTTC ========== Event 2381 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: aTTCATCTTGGTTAACCATTTTATTGTCATGTGT---------TCATGACAATAAAACCTATTCAATGTT-TCGGTC Chimp: aTTCATCTTGGTTAACCATTTTATTGT-CTGTGT---------TCATGACAATAAAACC-TTTCAATCTTTGTGGTC Gorilla: aTTCATCTTGGTTAACCATTTTATTGTCATGTGT------------------TATCACCTATTCAATGTT-TCGGTC ↓ 3 2 1 4 Human: aTTCATCTTGGTTAACCATTTTATTGTCATGTGT---------TCATGACAATAAAACCTATTCAATGTT-TCGGTC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---------NNNNNNNNATACAAGGTT-TCGGAA Gorilla > Human --------------- chr3:165568758-165568769 Template switch process: F1: L AAAAAAAATTCATCTTGGTTAACCATTTTATTGTCATGTGTT 1 F3: 4 ACCTATTCAATGTTTCGGTCTACCTTGATTTATAATACAT R RF: AAAAAAAATTCATCTTGGTTAACCATTTTATTGTCATGTGTTATCACCTATTCAATGTTTCGGTCTACCTTGATTTATAATACAT RR: TTTTTTTTAAGTAGAACCAATTGGTAAAATAACAGTACACAATAGTGGATAAGTTACAAAGCCAGATGGAACTAAATATTATGTA F2: 3 AAATAACAGTAC 2 Unidirectional alignment (log-probability: -34.9) AAAAAATTCATCTTGGTTAACCATTTTATTGTCATGTGTtcatgacaaTAaaACCTATTCAATGTTTCGGTCTACCTTGATTTATAATACAT AAAAAATTCATCTTGGTTAACCATTTTATTGTCATGTGT---------TATCACCTATTCAATGTTTCGGTCTACCTTGATTTATAATACAT Template switch alignment (log-probability: -17.3) AAAAAATTCATCTTGGTTAACCATTTTATTGTCATGTGTT|CATGACAATAAA|ACCTATTCAATGTTTCGGTCTACCTTGATTTATAATACAT AAAAAATTCATCTTGGTTAACCATTTTATTGTCATGTGTT|CATGACAATAAA|ACCTATTCAATGTTTCGGTCTACCTTGATTTATAATACAT ========== Event 2382 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCTCAGGCGATGCCACAGTGTCG--AGGGCACCGGTGTCGAGGAGACACCAGCAGGGTAAG Chimp: TCCTCAGGCGATGCCACAGTGTCG--AGGGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAG ↑ 1 4 3 2 Gorilla: TCCTCAGGCGATGCCACAGTGAAGGCTGAGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAG Human: TCCTCAGGCGATGCCACAGTGTCG--AGGGCACCGGTGTCGAGGAGACACCAGCAGGGTAAG Cluster: [ ] Orangutan: TCCTCAGGCGATGCCACAGTGAAGGGTGGGCACCGGTGTCAAGGAAACGCCAGCAGGGTAAG Gorilla > Chimp --------------- chr3:169040278-169040281 Template switch process: F1: L GCTGACACCAGTGGTTAAGTTCCTCAGGCGATGCCACAGTG 1 F3: 4 GGGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAGGA R RF: GCTGACACCAGTGGTTAAGTTCCTCAGGCGATGCCACAGTGAAGGCTGAGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAGGC RR: CGACTGTGGTCACCAATTCAAGGAGTCCGCTACGGTGTCACTTCCGACTCGTGGCCACAGCTCCTCTGCGGTCGTCCCATTCCG F2: 3 AGCT 2 Unidirectional alignment (log-probability: -39.2) CTGACACCAGTGGTTAAGTTCCTCAGGCGATGCCACAGTGtcgAGG----GCACCGGTGTCGAGGAGACGCCAGCAGGGTAAGG-----A CTGACACCAGTGGTTAAGTTCCTCAGGCGATGCCACAGTG--AAGGCTGAGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAGGCATTTA Template switch alignment (log-probability: -27.2) CTGACACCAGTGGTTAAGTTCCTCAGGCGATGCCACAGTG|TCGA|GgGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAGGa CTGACACCAGTGGTTAAGTTCCTCAGGCGATGCCACAGTG|TCGA|GAGCACCGGTGTCGAGGAGACGCCAGCAGGGTAAGGC ========== Event 2383 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTAGCATATACCTTGACTTAGAAAC----AATAAACCAATGGGCCAGAGTAGTACTAT----CAttttttataat Chimp: GTAGCATATACCTTGACTTAGTACT--ACTCTGGCCCATTGGTTTATT--GTTTCTATCAATCattttttataat Gorilla: GTAGCATATACCTTGACTTAGTACTAC--TCTGGCCCATTGGTTTATT--GTTTCTAT----CAttttttataat ↓ 13 24 ↑ 13 24 Human: GTAGCATATACCTTGACTTAGAAAC----AATAAACCAATGGGCCAGAGTAGTACTAT----CAttttttataat Cluster: [ ] Orangutan: GTAGCATATACTTCGACTTAGTACTAC--TCTGGCTCATTGGTTTATT--GTTTCTAt----tattttttataat Gorilla > Human --------------- chr3:34666621-34666649 Template switch process: F1: L TACAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAG 1 F3: 4 CTATCATTTTTTATAATATGAAAACCCCTAATTTTTATTT R RF: TATAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAGTACTACTCTGGCCCATTGGTTTATTGTTTCTATCATTTTTTATAATATGAAAACCCCTAATTTTTATTT RR: ATATCTACAAAGAGGTCCTTCATCGTATATGGAACTGAATCATGATGAGACCGGGTAACCAAATAACAAAGATAGTAAAAAATATTATACTTTTGGGGATTAAAAATAAA F2: 3 ATGATGAGACCGGGTAACCAAATAACAAA 2 Unidirectional alignment (log-probability: -78.8) AcAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTtagaaacaataaaccaatgggccagagTAGTA---------------------------CTATCATTTTTTATAATATGAAAACCCCTAATTTTTattt ATAGATGTTTCTCCAGGAAGTAGCATATACCTTGACT---------------------------TAGTACTACTCTGGCCCATTGGTTTATTGTTTCTATCATTTTTTATAATATGAAAACCCCTAATTTTT---- Template switch alignment (log-probability: -24.9) AcAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAG|AAACAATAAACCAATGGGCCAGAGTAGTA|CTATCATTTTTTATAATATGAAAACCCCTAATTTTTATTT ATAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAG|AAACAATAAACCAATGGGCCAGAGTAGTA|CTATCATTTTTTATAATATGAAAACCCCTAATTTTTATTT Human > Gorilla --------------- chr3:35241999-35242027 Template switch process: F1: L TATAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAG 1 F3: 4 CTATCATTTTTTATAATATGAAAACCCCTAATTTTT R RF: TACAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAGAAACAATAAACCAATGGGCCAGAGTAGTACTATCATTTTTTATAATATGAAAACCCCTAATTTTT RR: ATGTCTACAAAGAGGTCCTTCATCGTATATGGAACTGAATCTTTGTTATTTGGTTACCCGGTCTCATCATGATAGTAAAAAATATTATACTTTTGGGGATTAAAAA F2: 3 TTTGTTATTTGGTTACCCGGTCTCATCAT 2 Unidirectional alignment (log-probability: -73.3) AtAGATGTTTCTCCAGGAAGTAGCATATACCTTGACT---------------------------TAGTActactctggcccattggtttattgtttCTATCATTTTTTATAATATGAAAACCCCTAATTTTT---- ACAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAGAAACAATAAACCAATGGGCCAGAGTAGTA---------------------------CTATCATTTTTTATAATATGAAAACCCCTAATTTTTATTT Template switch alignment (log-probability: -24.8) AtAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAG|TACTACTCTGGCCCATTGGTTTATTGTTT|CTATCATTTTTTATAATATGAAAACCCCTAATTTTT ACAGATGTTTCTCCAGGAAGTAGCATATACCTTGACTTAG|TACTACTCTGGCCCATTGGTTTATTGTTT|CTATCATTTTTTATAATATGAAAACCCCTAATTTTT ========== Event 2384 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTTTAGAGCTCAATGCTGAGTGAGCTTCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCCGCCATTTGGAGATtgtggcagcagtgaaggtacatagctcagctccctcacttcgagaaag Chimp: TCTTTAGAGCTCAATGCTGAGTGAGCTTCTTACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCCGCCGTTTGGAGATtgtggcagcagtgaaggtacatagctcagctccctcacttcgagaaag Gorilla: TCTTTAGAGCTCAATGCTGAGCTCA-CTCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCCACCGTTTGGAGATtgtggcagcagtgaaggtacatagctcagctccctcacttcaagaaag ↓ 1 4 3 2 Human: TCTTTAGAGCTCAATGCTGAGTGAGCTTCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCCGCCATTTGGAGATtgtggcagcagtgaaggtacatagctcagctccctcacttcgagaaag Cluster: [ ] Orangutan: TCTTTAGAGCTCAATGCTGAGTGAGCTTCTCACTCCCACCAGGCCCTTCCAGTTATGAAAATTTGCTGCCGTTTGGAGATtgtggcagcagtgaaggtacatagctcagctctctcacttcgagaaag Gorilla > Human --------------- chr3:163917479-163917484 Template switch process: F1: L ACTGCCAGAGGGCAAAGGCTTCTTTAGAGCTCAATGCTGAG 1 F3: 4 TCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCC R RF: ACTGCCAGAGGGCAAAGGCTTCTTTAGAGCTCAATGCTGAGCTCACTCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCCACCGTTTGGAGATTGTGGCAGCAGTGAAGGTACATAGCTCA RR: TGACGGTCTCCCGTTTCCGAAGAAATCTCGAGTTACGACTCGAGTGAGAGTGAGAGTGGTCCGGGAAGGTCAATACTTTTAAACGGTGGCAAACCTCTAACACCGTCGTCACTTCCATGTATCGAGT F2: 3 TCGAGT 2 Unidirectional alignment (log-probability: -26.6) CTGCCAGAGGGCAAAGGCTTCTTTAGAGCTCAATGCTGagtgAGCT---TCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCC CTGCCAGAGGGCAAAGGCTTCTTTAGAGCTCAATGCTG----AGCTCACTCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCC Template switch alignment (log-probability: -16.5) CTGCCAGAGGGCAAAGGCTTCTTTAGAGCTCAATGCTGAG|TGAGCT|TCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCC CTGCCAGAGGGCAAAGGCTTCTTTAGAGCTCAATGCTGAG|TGAGCT|TCTCACTCTCACCAGGCCCTTCCAGTTATGAAAATTTGCC ========== Event 2385 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCAATCTTTTCAGTATGGTTA-TCT--------GTCTTTGAATCCTCCTTAACAAAATTAATTGTTCCttttttgtttaaa-aaattttttttCTAAGATGCTTTTGTTATAGCATACTCCTTTATTT-TTAA-AAAAGTCCACAGCAATTTCTATATATCTCTCTTTTAGCACATCAGATTGCATTGTATTTATTTGGGT ↑ 1 4 3 2 Chimp: TTCAATCTTTTCAGTATGGTTCTTTT--------ATCTTTGAATACTCCTTAACAAAATTAATTGTTCCttttttgtttaaa--aattttttttCTAAGATGCTTTTGTTATAGCATACTCCTTTATTT-TTaaaaaaaGTCCACAGCAATTTCTATATATCTCTCTTTTAGCACATCAGATTGCATTGTATTTATTTGGGT Gorilla: TTCAATCTTTTCAGTATGGTTCTTTT----ATCTGTCTTTGAATCCTCCTTAACAAAATTAATTGTTCtttttttgtttaaa--atttttttttCTAAGATGCTTTTGTTATAGCATACTCCTTTATTTTTTaaaaaaaaTCCACAGCAATTTCTATATATCTCTCTTTTAGCACATCAGATTGCATTGTATTTATTTGGGT Human: TTCAATCTTTTCAGTATGGTTA-TCT--------GTCTTTGAATCCTCCTTAACAAAATTAATTGTTCCttttttgtttaaa-aaattttttttCTAAGATGCTTTTGTTATAGCATACTCCTTTATTT-TTAA-AAAAGTCCACAGCAATTTCTATATATCTCTCTTTTAGCACATCAGATTGCATTGTATTTATTTGGGT Cluster: [ ] Orangutan: TTCAATCTTTTCAGTATGGTTCTTTTATCT----GTCTTTGAATCCTCCTTAACAAA----ATTGTTCCttttttgtttaaaa-aattttttttCTAAGATGCTTTTGTTATAGCATACTCCCTTCTTT-TTAA-AAAAATCCACAGCAATTTCTATATATCTCTCTTTTAGCACATCAGATTGCATTGTATTTATTTTGGT Chimp > Human ------------- chr3:34202292-34202296 Template switch process: F1: L CTGTGTTAAAAACCTTCATTTTCAATCTTTTCAGTATGGTT 1 F3: 4 TCTTTGAATCCTCCTTAACAAAATTAATTGTTCCTTTTTTGTTTAAAAAA R RF: CTGTGTTAAAAACCTTCATTTTCAATCTTTTCAGTATGGTTCTTTTATCTTTGAATACTCCTTAACAAAATTAATTGTTCCTTTTTTGTTTAAAAATTTTTTTTCTAAGATGCTTTTGTTATAGCATACTCCTTTATTTTTAAAAAAAGTCCACAGCAATTTCTATATATCTCTCTTTTAGCACATCAGAT RR: GACACAATTTTTGGAAGTAAAAGTTAGAAAAGTCATACCAAGAAAATAGAAACTTATGAGGAATTGTTTTAATTAACAAGGAAAAAACAAATTTTTAAAAAAAAGATTCTACGAAAACAATATCGTATGAGGAAATAAAAATTTTTTTCAGGTGTCGTTAAAGATATATAGAGAGAAAATCGTGTAGTCTA F2: 3 GTCTA 2 Unidirectional alignment (log-probability: -41.9) TGTGTTAAAAACCTTCATTTTCAATCTTTTCAGTATGG-----TTAtctgTCTTTGAATcCTCCTTAACAAAATTAATTGTTCCTTTTTT TGTGTTAAAAACCTTCATTTTCAATCTTTTCAGTATGGTTCTTTTA----TCTTTGAATACTCCTTAACAAAATTAATTGTTCCTTTTTT Template switch alignment (log-probability: -28.1) TGTGTTAAAAACCTTCATTTTCAATCTTTTCAGTATGGTT|ATCTG|TCTTTGAATcCTCCTTAACAAAATTAATTGTTCCTTTTTT TGTGTTAAAAACCTTCATTTTCAATCTTTTCAGTATGGTT|ATCTG|TCTTTGAATACTCCTTAACAAAATTAATTGTTCCTTTTTT ========== Event 2386 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: caaggcaaagcctcatgtggTAGTCAGCTCTCCTTGGTGC-----CTCTCCTCCAAGAGGATCCAGCT ↓ 3 2 1 4 Chimp: caaggcaaagcctgatgtggTAGTCAGCTCTCCTTGGTGCTGACTACCTCCTCCAAGAGGATCCAGCT Gorilla: caaggcaaagcctcatgtggtagtcagctctcgttggtgc-----ctctcctccaagaggacccagct Human: caaggcaaagcctcatgtggTAGTCAGCTCTCCTTGGTGC-----CTCTCCTCCAAGAGGATCCAGCT Cluster: [ ] Orangutan: caaggcaaagcctcatgtggttgtcagctctccttggtgc-----ctctcctccaagaggacccagct Human > Chimp ------------- chr3:167729808-167729814 Template switch process: F1: L TCAAGGCAAAGCCTGATGTGGTAGTCAGCTCTCCTTGGTGC 1 F3: 4 CTCCTCCAAGAGGATCCAGCTGCTTCCACCTCAAACACAT R RF: TCAAGGCAAAGCCTCATGTGGTAGTCAGCTCTCCTTGGTGCCTCTCCTCCAAGAGGATCCAGCTGCTTCCACCTCAAACACAT RR: AGTTCCGTTTCGGAGTACACCATCAGTCGAGAGGAACCACGGAGAGGAGGTTCTCCTAGGTCGACGAAGGTGGAGTTTGTGTA F2: 3 CATCAGT 2 Unidirectional alignment (log-probability: -34.3) CAAGGCAAAGCCTgATGTGGTAGTCAGCTCTCCTTGGTGCtgaCTacCTCCTCCAAGAGGATCCAGCTGCTTCCACCTCAAACACAT CAAGGCAAAGCCTCATGTGGTAGTCAGCTCTCCTTGGTGC---CT--CTCCTCCAAGAGGATCCAGCTGCTTCCACCTCAAACACAT Template switch alignment (log-probability: -22.1) CAAGGCAAAGCCTgATGTGGTAGTCAGCTCTCCTTGGTGC|TGACTAC|CTCCTCCAAGAGGATCCAGCTGCTTCCACCTCAAACACAT CAAGGCAAAGCCTCATGTGGTAGTCAGCTCTCCTTGGTGC|TGACTAC|CTCCTCCAAGAGGATCCAGCTGCTTCCACCTCAAACACAT ========== Event 2387 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: gtgagcggaagaaccatccaggtaacctacagaagcatg------agaaacaataatttgctgCAATAGA Chimp: GTGCGCGGAAGAACCATCCAGGTAACCTACAGAAGCATGTAGGTAACCTACAATAATTTGCTGCAATAGA ↑ 3 2 1 4 Gorilla: GTGAGCGGAAGAACCATCCAGGTAACCTACAGAAGCATG------AGAAACAATAATTTGCTGCAATAGA Human: gtgagcggaagaaccatccaggtaacctacagaagcatg------agaaacaataatttgctgCAATAGA Cluster: [ ] Orangutan: GTGAGTGGAAGAACTATCCAGGTAACCTACAGAAGCATG------AGAAACAATAATTTGCTGCAATAGA Gorilla > Chimp --------------- chr3:198899258-198899267 Template switch process: F1: L ACGTGCGCGGAAGAACCATCCAGGTAACCTACAGAAGCATG 1 F3: 4 ACAATAATTTGCTGCAATAGATTCTAAAACAGAGTATGTA R RF: ACGTGAGCGGAAGAACCATCCAGGTAACCTACAGAAGCATGAGAAACAATAATTTGCTGCAATAGATTCTAAAACAGAGTATGTA RR: TGCACTCGCCTTCTTGGTAGGTCCATTGGATGTCTTCGTACTCTTTGTTATTAAACGACGTTATCTAAGATTTTGTCTCATACAT F2: 3 TCCAATGGAT 2 Unidirectional alignment (log-probability: -40.7) CGTGcGCGGAAGAACCATCCAGGTAACCTACAGAAGCATGtaggtaacct----ACAATAATTTGCTGCAATAGATTCTAAAACAGAGTATGTA CGTGAGCGGAAGAACCATCCAGGTAACCTACAGAAGCATG----------AGAAACAATAATTTGCTGCAATAGATTCTAAAACAGAGTATGTA Template switch alignment (log-probability: -28) CGTGcGCGGAAGAACCATCCAGGTAACCTACAGAAGCATG|TAGGTaACCT|ACAATAATTTGCTGCAATAGATTCTAAAACAGAGTATGTA CGTGAGCGGAAGAACCATCCAGGTAACCTACAGAAGCATG|TAGGTTACCT|ACAATAATTTGCTGCAATAGATTCTAAAACAGAGTATGTA ========== Event 2388 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ttatttttGACTTGCTTTGTA-------TTTACTATGTCATACAGTTAGCTGTTTAACCAGCttt-t Chimp: TTATTTTTGACTTGCTTTGTATAACTGTATAACTATGTCATACAGTTAGCTGTTTAACCAGCttt-t ↑ 14 3 2 Gorilla: TTATTTTTGACTTGCTTTGTA-------TTTACTATGTCATACAGTTAGCTGTTTAACCAGCttttt Human: ttatttttGACTTGCTTTGTA-------TTTACTATGTCATACAGTTAGCTGTTTAACCAGCttt-t Cluster: [ ] Orangutan: TTATTTTTGACTTGCTTTGTA-------TTTACTATGTCATACAGTTAGCTGTTTAACCAGCTTT-T Gorilla > Chimp --------------- chr3:38016299-38016305 Template switch process: F1: L TTGTAATATTTTAAAAATAATTATTTTTGACTTGCTTTGTAT 1 F3: 4 TAACTATGTCATACAGTTAGCTGTTTAACCAGCTTTTTTTT R RF: TTGTAATATTTTAAAAATAATTATTTTTGACTTGCTTTGTATTTACTATGTCATACAGTTAGCTGTTTAACCAGCTTTTTTTT RR: AACATTATAAAATTTTTATTAATAAAAACTGAACGAAACATAAATGATACAGTATGTCAATCGACAAATTGGTCGAAAAAAAA F2: 3 ATGTCAA 2 Unidirectional alignment (log-probability: -33.3) GTAATATTTTAAAAATAATTATTTTTGACTTGCTTTGTATaactgtaTaACTATGTCATACAGTTAGCTGTTTAACCAGCTTTTTTT GTAATATTTTAAAAATAATTATTTTTGACTTGCTTTGTAT-------TTACTATGTCATACAGTTAGCTGTTTAACCAGCTTTTTTT Template switch alignment (log-probability: -22.2) GTAATATTTTAAAAATAATTATTTTTGACTTGCTTTGTAT|AACTGTA|TaACTATGTCATACAGTTAGCTGTTTAACCAGCTTTTTTT GTAATATTTTAAAAATAATTATTTTTGACTTGCTTTGTAT|AACTGTA|TTACTATGTCATACAGTTAGCTGTTTAACCAGCTTTTTTT ========== Event 2389 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAAGGCTTATACTTGATCTTTGTATCCAGAATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTCTGT Chimp: GGAAGGCTTATACTTGATCTTTGTATCCAGAATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTCTGT ↑ 1 4 3 2 Gorilla: GGAAGGCTTATACTTGATCTT---------CATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTCTGT ↓ 1 4 3 2 Human: GGAAGGCTTATACTTGATCTTTGTATCCAGAATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTCTGT Cluster: [ ] Orangutan: GGAAGGCTTATACTTGATCTT---------CATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTGTCTGT Gorilla > Human --------------- chr3:37724973-37724982 Template switch process: F1: L TTGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT 1 F3: 4 ATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC R RF: TTGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTTCATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC RR: AACTCATACAATTCTGGGGTCCTTCCGAATATGAACTAGAAGTACAACGGTTGTAAGACCTATGTTTCTTTTCGTGGGAGAG F2: 3 AGACCTATGT 2 Unidirectional alignment (log-probability: -29.4) TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTTtgtatccagaATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT---------CATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC Template switch alignment (log-probability: -17) TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT|TGTATCCAGA|ATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT|TGTATCCAGA|ATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC Gorilla > Chimp --------------- chr3:38466889-38466898 Template switch process: F1: L TTGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT 1 F3: 4 ATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC R RF: TTGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTTCATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC RR: AACTCATACAATTCTGGGGTCCTTCCGAATATGAACTAGAAGTACAACGGTTGTAAGACCTATGTTTCTTTTCGTGGGAGAG F2: 3 AGACCTATGT 2 Unidirectional alignment (log-probability: -29.4) TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTTtgtatccagaATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT---------CATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC Template switch alignment (log-probability: -17) TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT|TGTATCCAGA|ATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC TGAGTATGTTAAGACCCCAGGAAGGCTTATACTTGATCTT|TGTATCCAGA|ATGTTGCCAACATTCTGGATACAAAGAAAAGCACCCTCTC ========== Event 2390 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGGCCAGTTATAGAGTACAGT---------GGCTAAGAGCATAggccttgtgaactcagctggaccttggttagggtccgtttcatcaattgtgacatggccataataatacctatgtcacaagacgactgtaaatattaaacaggggatgcacaaaaaggttagcctagtCTATTATCTCCTATTC Chimp: TGGCCAGTTATAGAGTACAGT---------GGCTAAGAGCATAggccttgtgaactcagctggaccttggttagggtccatttcatcaattgtgacatggccataataatacctatgtcacaagacgactgtaaatattaaacaggggatgcacaaaaaggttagcctagtCTATTATCTCCTATTC ↑ 1 4 3 2 Gorilla: TGGCCAGTTATAGAGTACAGTATAGAGTATAGAGTACAGCATAggccttgtgaactcagctggaccttggttagggtccgtttcatcaattgtgacatggccgtaataatacctatgtcacaagacgactgtaaatattaaacagaggatgcacaaaaaggttagcctagtCTATTATCTCCTATTC ↓ 1 4 3 2 Human: TGGCCAGTTATAGAGTACAGT---------GGCTAAGAGCATAggccttgtgaactcagctggaccttggttagggtccgtttcatcaattgtgacatggccataataatacctatgtcacaagacgactgtaaatattaaacaggggatgcacaaaaaggttagcctagtCTATTATCTCCTATTC Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr3:159481952-159481956 Template switch process: F1: L GGAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT 1 F3: 4 AGAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGGGT R RF: GGAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGTATAGAGTATAGAGTACAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGGGTCCGTTTCATCAATTGTGACATGGCCGTAATAATACCTATGTCACAAGACGACTGTAAATATTAAACAGAGGATGCACAAAAAGGTTAGCC RR: CCTTCCTCAGTCTCACCGGTACCGGTCAATATCTCATGTCATATCTCATATCTCATGTCGTATCCGGAACACTTGAGTCGACCTGGAACCAATCCCAGGCAAAGTAGTTAACACTGTACCGGCATTATTATGGATACAGTGTTCTGCTGACATTTATAATTTGTCTCCTACGTGTTTTTCCAATCGG F2: 3 ATCGG 2 Unidirectional alignment (log-probability: -31.5) GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT----------------ggctaagAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGTATAGAGTATAGAGTAC-------AGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG Template switch alignment (log-probability: -21.9) GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT|GGCTA|AgAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT|GGCTA|ACAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG Gorilla > Chimp --------------- chr3:163032539-163032543 Template switch process: F1: L GGAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT 1 F3: 4 AGAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGGGT R RF: GGAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGTATAGAGTATAGAGTACAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGGGTCCGTTTCATCAATTGTGACATGGCCGTAATAATACCTATGTCACAAGACGACTGTAAATATTAAACAGAGGATGCACAAAAAGGTTAGCC RR: CCTTCCTCAGTCTCACCGGTACCGGTCAATATCTCATGTCATATCTCATATCTCATGTCGTATCCGGAACACTTGAGTCGACCTGGAACCAATCCCAGGCAAAGTAGTTAACACTGTACCGGCATTATTATGGATACAGTGTTCTGCTGACATTTATAATTTGTCTCCTACGTGTTTTTCCAATCGG F2: 3 ATCGG 2 Unidirectional alignment (log-probability: -31.5) GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT----------------ggctaagAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGTATAGAGTATAGAGTAC-------AGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG Template switch alignment (log-probability: -21.9) GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT|GGCTA|AgAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG GAAGGAGTCAGAGTGGCCATGGCCAGTTATAGAGTACAGT|GGCTA|ACAGCATAGGCCTTGTGAACTCAGCTGGACCTTGGTTAGG ========== Event 2391 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTGTGGGTTAGAAAATACAT---ATTTCTA--TTCTTCTAGaaattaccagtaaagtaaagtacca Chimp: TTTGTGGGTTAGAAAATACAT---ATTTCTA--TTCTTCTAGaaattaccagtaaagtaaagtacca ↓ 1 3 4 2 Gorilla: TTTGTGGGTTAGAAAATACATAGAATTTCTAGAAAATTCTAGaaattaccagtaaagtaaagtacca ↑ 1 3 4 2 Human: TTTGTGGGTTAGAAAATACAT---ATTTCTA--TTCTTCTAGaaattaccagtaaagtaaagtacca Cluster: [ ] Orangutan: TTTGTGGGTTAGAAAATANNN---NNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr3:41058534-41058546 Template switch process: F1: L CTTTTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATAG 1 F3: 4 TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT R RF: CTTTTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATATTTCTATTCTTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT RR: GAAAAAAGGAGAAGTACGGAAAACACCCAATCTTTTATGTATAAAGATAAGAAGATCTTTAATGGTCATTTCATTTCATGGTCATTTCATA F2: 3 AAAAGATCTTTAA 2 Unidirectional alignment (log-probability: -41.2) TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATA---------gaatttctagaaaaTTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATATTTCTATTC--------------TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT Template switch alignment (log-probability: -28.5) TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATAg|AATTTCTAGAAaA|TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATAT|AATTTCTAGAAGA|TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT Chimp > Gorilla --------------- chr3:41058534-41058546 Template switch process: F1: L CTTTTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATAG 1 F3: 4 TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT R RF: CTTTTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATATTTCTATTCTTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT RR: GAAAAAAGGAGAAGTACGGAAAACACCCAATCTTTTATGTATAAAGATAAGAAGATCTTTAATGGTCATTTCATTTCATGGTCATTTCATA F2: 3 AAAAGATCTTTAA 2 Unidirectional alignment (log-probability: -41.2) TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATA---------gaatttctagaaaaTTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATATTTCTATTC--------------TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT Template switch alignment (log-probability: -28.5) TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATAg|AATTTCTAGAAaA|TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT TTTTCCTCTTCATGCCTTTTGTGGGTTAGAAAATACATAT|AATTTCTAGAAGA|TTCTAGAAATTACCAGTAAAGTAAAGTACCAGTAAAGTAT ========== Event 2392 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CCCCATTATGACAGGAGTGTCATAAAACCTGTTTTTA-----TGACACTCAGTTAACAGCATCTTA Chimp: CCCCATTATGACAGGAGCGTCATAAAACCTGTTTTTA-----TGACACTCAGTTAACAGCATCTTA Gorilla: CCCCATTATGACAGGATTGTCATAAAAACAGGTCATATTAAATATCACTCAGTTAACAGCATCTTA ↓ 3 1 2 4 Human: CCCCATTATGACAGGAGTGTCATAAAACCTGTTTTTA-----TGACACTCAGTTAACAGCATCTTA Cluster: [ ] Orangutan: CCCCATTATGACAGGATTGTCATAAAAACAGTTCATATTAAATATCACTCAGTTGACAGCATCTTA Gorilla > Human --------------- chr3:41915567-41915579 Template switch process: F1: L CTATCACTTAATAGCCCCATTATGACAGGAGTGTCATAAAA 1 F3: 4 CACTCAGTTAACAGCATCTTAACTTGACAATATCATCCCT R RF: CTATCACTTAATATCCCCATTATGACAGGATTGTCATAAAAACAGGTCATATTAAATATCACTCAGTTAACAGCATCTTAACTTGACAATATCATCCCT RR: GATAGTGAATTATAGGGGTAATACTGTCCTAACAGTATTTTTGTCCAGTATAATTTATAGTGAGTCAATTGTCGTAGAATTGAACTGTTATAGTAGGGA F2: 3 AGTATTTTTGTCC 2 Unidirectional alignment (log-probability: -49.8) TATCACTTAATAgCCCCATTATGACAGGAgTGTCATAAAAcctgtttttatgA-----------------CACTCAGTTAACAGCATCTTAACTTGACAATATCATCCCT TATCACTTAATATCCCCATTATGACAGGATTGTCATAAAA------------ACAGGTCATATTAAATATCACTCAGTTAACAGCATCTTAACTTGACAATATCATCCCT Template switch alignment (log-probability: -28.4) TATCACTTAATAgCCCCATTATGACAGGAgTGTCATAAAA|CCTGTTTTTATGA|CACTCAGTTAACAGCATCTTAACTTGACAATATCATCCCT TATCACTTAATATCCCCATTATGACAGGATTGTCATAAAA|CCTGTTTTTATGA|CACTCAGTTAACAGCATCTTAACTTGACAATATCATCCCT ========== Event 2393 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: gaagAGGCAGGTATAGATATC-----------TGAAGTGGCTCTGGTTGGAATATGGAAGGAGAAACAGCCCTTAttt----------------t--------tttttttttttgagacggagtcttgctctgtcgcccaggctggagtgcagtggcacgatcttggctcactgcaacttccacctcccgggttcaagtg Chimp: GAAGAGGCAGGTATAGATATC-----------TGAAGTGGCTCTGGTTGGAATATGGAAGGAGAAACAGCCCttattt---------tatttta-ttttattttttttttttttgagacggagtcttgctctgtcgcccaggctggagtgcagtggcacgatcttggctcactgcaacttccacctcccgggttcaagtg ↑ 4 1 3 2 Gorilla: GAAGAGGCAGGTATAGATATC----------------------TGGTTGGAATATGGAAGGAGAAACAGCCCTTAtttt-----ttt----------------tttttttttttgagacggagtcttgctctgttgcccaggctggagtgcagtggcacgatcttggctcactgcaacttccacctcccgggttcaagtg ↓ 4 1 3 2 Human: gaagAGGCAGGTATAGATATC-----------TGAAGTGGCTCTGGTTGGAATATGGAAGGAGAAACAGCCCTTAttt----------------t--------tttttttttttgagacggagtcttgctctgtcgcccaggctggagtgcagtggcacgatcttggctcactgcaacttccacctcccgggttcaagtg Cluster: [ ] Orangutan: GAAGAGGCAGGTATAGATATCTGAAGTGGCTC-----------CAGTTGGAATATGGA-AGAGAAACAGCACttctttttttttttt----------------tttttttttttgaaacggagtcttgctctgtcg-tcaggctggagtgcagtggcacgatcttggctcactgcaacctccgcctcccaggttc-agtg Gorilla > Human --------------- chr3:155950613-155950619 Template switch process: F1: L CTAGGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTG 1 F3: 4 TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT R RF: CTAGGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACGATCTTGGCTCACTGCAACTT RR: GATCCCCCTCGAGGTTCAAACTTCTCCGTCCATATCTATAGACCAACCTTATACCTTCCTCTTTGTCGGGAATAAAAAAAAAAAAAAAAAACTCTGCCTCAGAACGAGACAACGGGTCCGACCTCACGTCACCGTGCTAGAACCGAGTGACGTTGAA F2: 3 CGGTGAA 2 Unidirectional alignment (log-probability: -33.5) GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATAtctgaagtggcTCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT--- GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATA-----------TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTTTTT Template switch alignment (log-probability: -22.1) GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTG|AAGTgGC|TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTG|AAGTTGC|TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT Gorilla > Chimp --------------- chr3:159378436-159378442 Template switch process: F1: L CTAGGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTG 1 F3: 4 TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT R RF: CTAGGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACGATCTTGGCTCACTGCAACTT RR: GATCCCCCTCGAGGTTCAAACTTCTCCGTCCATATCTATAGACCAACCTTATACCTTCCTCTTTGTCGGGAATAAAAAAAAAAAAAAAAAACTCTGCCTCAGAACGAGACAACGGGTCCGACCTCACGTCACCGTGCTAGAACCGAGTGACGTTGAA F2: 3 CGGTGAA 2 Unidirectional alignment (log-probability: -33.5) GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATAtctgaagtggcTCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT--- GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATA-----------TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTTTTT Template switch alignment (log-probability: -22.1) GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTG|AAGTgGC|TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT GGGGGAGCTCCAAGTTTGAAGAGGCAGGTATAGATATCTG|AAGTTGC|TCTGGTTGGAATATGGAAGGAGAAACAGCCCTTATTTT ========== Event 2394 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAGTTAAGACTTTAGACATGAAATTGCTAAAATTTCACGTCTAAGAAATTGCTTTAGAC Chimp: GGAAGTTAAGACTTTAGACATGAAATTGCTAAAATTTCATGTCTAAGAAATTGCTTTAGAC Gorilla: GGAAATTAAGACTTTAGACATGAAATTTTAGCAATTTCATGTCTAAGAAATTGCTTTAGAC ↑ 3 1 2 4 Human: GGAAGTTAAGACTTTAGACATGAAATTGCTAAAATTTCACGTCTAAGAAATTGCTTTAGAC Cluster: [ ] Orangutan: GGAAGTTAAGACTTTAGACATGAAATTGCTAAAATTTCATGTCTAAGAAATTGCTTTAGAC Human > Gorilla --------------- chr3:39840795-39840807 Template switch process: F1: L GTTTCTTTTCCTGTGGAAATTAAGACTTTAGACATGAAATT 1 F3: 4 GTCTAAGAAATTGCTTTAGACATCAATCAGAGAAGCCGTC R RF: GTTTCTTTTCCTGTGGAAGTTAAGACTTTAGACATGAAATTGCTAAAATTTCACGTCTAAGAAATTGCTTTAGACATCAATCAGAGAAGCCGTC RR: CAAAGAAAAGGACACCTTCAATTCTGAAATCTGTACTTTAACGATTTTAAAGTGCAGATTCTTTAACGAAATCTGTAGTTAGTCTCTTCGGCAG F2: 3 TACTTTAACGATT 2 Unidirectional alignment (log-probability: -36.3) TTTCTTTTCCTGTGGAAaTTAAGACTTTAGACATGAAATTttaGC---AATTTCAtGTCTAAGAAATTGCTTTAGACATCAATCAGAGAAGCCGTC TTTCTTTTCCTGTGGAAGTTAAGACTTTAGACATGAAATT---GCTAAAATTTCACGTCTAAGAAATTGCTTTAGACATCAATCAGAGAAGCCGTC Template switch alignment (log-probability: -22.9) TTTCTTTTCCTGTGGAAaTTAAGACTTTAGACATGAAATT|TTAGCAATTTCAT|GTCTAAGAAATTGCTTTAGACATCAATCAGAGAAGCCGTC TTTCTTTTCCTGTGGAAGTTAAGACTTTAGACATGAAATT|TTAGCAATTTCAT|GTCTAAGAAATTGCTTTAGACATCAATCAGAGAAGCCGTC ========== Event 2395 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGCGGAGCCGTGTGACAGAAGGA------------------GAGGCGGAGTTCAGTGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAATGTGCGGCTACCTGAAGGAGGTCCCGCGCTAGGCTTTGGCTGAACAGCAGGCGCGCAGGAGCTC Chimp: GGCGGAGACGTGTGACAGAAGGA------------------GAGGCGGAGTTCAGTGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAATGTGCGGCTACCTGAAGGAGGTCCCGCGCTAGGCTTTGGCTGAACAGCAGGCGCGCAGGAGTTC ↑ 4 1 3 2 Gorilla: GGCGGAGCCGTGTGACAGAAGGA------------------------------------GAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAATGTGCGGCTACCTGAAGGAGGTCCCGCGCTAGGCTTTGGCTGAACAGCAGGGGCGCAGGAGCTC ↓ 4 1 3 2 Human: GGCGGAGCCGTGTGACAGAAGGA------------------GAGGCGGAGTTCAGTGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAATGTGCGGCTACCTGAAGGAGGTCCCGCGCTAGGCTTTGGCTGAACAGCAGGCGCGCAGGAGCTC Cluster: [ ] Orangutan: GGCGGAGCCGTGTGATAGAAGGAGGGGCGGAGTTCAGTGGA------------------GAGGCGGAGAGGGCAGCGGGTCCCAGAGCCTTGAGCAGAATGTGCGGCTACCTGAAGGAGGTTCCGCGCTAGGCTTTGGCTGAACAGCAGGCGCGCAGGAGTTC Gorilla > Human --------------- chr3:155794128-155794132 Template switch process: F1: L CGGCAGGATAGAGTGGCTGGCGGAGCCGTGTGACAGAAGGAGAGGCGGAG 1 F3: 4 TGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAA R RF: CGGCAGGATAGAGTGGCTGGCGGAGCCGTGTGACAGAAGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAATGTGCGGCTACCTGAAGGAGGTCCCGCGCTAGGCTTTGGCTGAA RR: GCCGTCCTATCTCACCGACCGCCTCGGCACACTGTCTTCCTCTCCGCCTCTCCCGTCGCCCAGGGTCTCGGGACTCGTCTTACACGCCGATGGACTTCCTCCAGGGCGCGATCCGAAACCGACTT F2: 3 GACTT 2 Unidirectional alignment (log-probability: -36.8) GAGTGGCTGGCGGAGCCGTGTGACAGAAGgagaggcggagttcagtgGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC GAGTGGCTGGCGGAGCCGTGTGACAGAAG------------------GAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC Template switch alignment (log-probability: -22.2) GAGTGGCTGGCGGAGCCGTGTGACAGAAGGAGAGGCGGAG|TTCAG|tGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC GAGTGGCTGGCGGAGCCGTGTGACAGAAGGAGAGGCGGAG|TTCAG|AGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC Gorilla > Chimp --------------- chr3:159221342-159221346 Template switch process: F1: L CGGCAGGATAGAGTGGCTGGCGGAGACGTGTGACAGAAGGAGAGGCGGAG 1 F3: 4 TGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAA R RF: CGGCAGGATAGAGTGGCTGGCGGAGCCGTGTGACAGAAGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGCAGAATGTGCGGCTACCTGAAGGAGGTCCCGCGCTAGGCTTTGGCTGAA RR: GCCGTCCTATCTCACCGACCGCCTCGGCACACTGTCTTCCTCTCCGCCTCTCCCGTCGCCCAGGGTCTCGGGACTCGTCTTACACGCCGATGGACTTCCTCCAGGGCGCGATCCGAAACCGACTT F2: 3 GACTT 2 Unidirectional alignment (log-probability: -42.3) GAGTGGCTGGCGGAGaCGTGTGACAGAAggagaggcggagttcagtGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC GAGTGGCTGGCGGAGCCGTGTGACAGAA------------------GGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC Template switch alignment (log-probability: -27.7) GAGTGGCTGGCGGAGaCGTGTGACAGAAGGAGAGGCGGAG|TTCAG|tGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC GAGTGGCTGGCGGAGCCGTGTGACAGAAGGAGAGGCGGAG|TTCAG|AGGAGAGGCGGAGAGGGCAGCGGGTCCCAGAGCCCTGAGC ========== Event 2396 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TCCCACCCATCCCAGCCCCCTCCAGG----CTGGAATGCTGGAGGTGCTGCTGcccccac ↓ 3 2 1 4 Chimp: TCCCACCCATCCCAGCCCCCTCCAGG--CTCTGGA---GTGGAGGTGCTGCTGCCCCCAC Gorilla: TCCCACCCATCCCAGCCCCCTCCAGGCT--CTGGA---GTGGAGGTGCTTCTGCCCCCAC ↑ 3 2 1 4 Human: TCCCACCCATCCCAGCCCCCTCCAGG----CTGGAATGCTGGAGGTGCTGCTGcccccac Cluster: [ ] Orangutan: TCCCACCCATCCCAGCCCCCTCCAGGCT--CTGGA---GTGGAGGTGCTGCTGCCCCCAC Human > Chimp ------------- chr3:159003442-159003447 Template switch process: F1: L CTGTCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT 1 F3: 4 TGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC R RF: CTGTCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCTGGAATGCTGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC RR: GACAGACTGGAGGGTAGGGTGGGTAGGGTCGGGGGAGGTCCGACCTTACGACCTCCACGACGACGGGGGTGACGTGGGAGAAAGTTGTGG F2: 3 GAGGTC 2 Unidirectional alignment (log-probability: -28.7) TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCTctggaG------TGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT-----GGAATGCTGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC Template switch alignment (log-probability: -16.1) TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT|CTGGAG|TGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT|CTGGAG|TGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC Human > Gorilla --------------- chr3:157927220-157927225 Template switch process: F1: L CTGTCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT 1 F3: 4 TGGAGGTGCTTCTGCCCCCACTGCAGCCTCTTTCAACACC R RF: CTGTCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCTGGAATGCTGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC RR: GACAGACTGGAGGGTAGGGTGGGTAGGGTCGGGGGAGGTCCGACCTTACGACCTCCACGACGACGGGGGTGACGTGGGAGAAAGTTGTGG F2: 3 GAGGTC 2 Unidirectional alignment (log-probability: -39.2) TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT------CtggagTGGAGGTGCTtCTGCCCCCACTGCAgCCTCTTTCAACACC TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCTGGAATGC-----TGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC Template switch alignment (log-probability: -27.6) TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT|CTGGAG|TGGAGGTGCTtCTGCCCCCACTGCAgCCTCTTTCAACACC TCTGACCTCCCATCCCACCCATCCCAGCCCCCTCCAGGCT|CTGGAG|TGGAGGTGCTGCTGCCCCCACTGCACCCTCTTTCAACACC ========== Event 2397 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAGGAAAGCAAACAAATAAGGATCA------AGGTTGTTGGGTCCCCTTTGAATC ↓ 3 1 24 Chimp: AAAGGAAAGCAAACAAATAAGGATCCCTTGATCCTTTGTTGGGTCCCCTTTGAAGC ↑ 3 1 24 Gorilla: AAAGGAAAGCAAACAAATAAGGATCA------AGGTTGTTGGGTCCCCTTTGAAGC Human: AAAGGAAAGCAAACAAATAAGGATCA------AGGTTGTTGGGTCCCCTTTGAATC Cluster: [ ] Orangutan: AAAGGAAAGCAAACAAATAAGGATCA------AGGTTGTTGGGTCCCCTTTGAAGC Human > Chimp ------------- chr3:158634803-158634812 Template switch process: F1: L TTACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATC 1 F3: 4 TTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA R RF: TTACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATCAAGGTTGTTGGGTCCCCTTTGAATCCCTTTTGTCTCCTTCAAGA RR: AATGGAGGCGAAAAGATTTCCTTTCGTTTGTTTATTCCTAGTTCCAACAACCCAGGGGAAACTTAGGGAAAACAGAGGAAGTTCT F2: 3 TCCTAGTTCC 2 Unidirectional alignment (log-probability: -41.7) TACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATC----ccttgatcctTTGTTGGGTCCCCTTTGAAgCCCTTTTGTCTCCTTCAAGA TACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATCAAGG----------TTGTTGGGTCCCCTTTGAATCCCTTTTGTCTCCTTCAAGA Template switch alignment (log-probability: -22.5) TACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATC|CCTTGATCCT|TTGTTGGGTCCCCTTTGAAgCCCTTTTGTCTCCTTCAAGA TACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATC|CCTTGATCCT|TTGTTGGGTCCCCTTTGAATCCCTTTTGTCTCCTTCAAGA Gorilla > Chimp --------------- chr3:158634803-158634812 Template switch process: F1: L TTACCTCCGCTTTTCTAAAGGAAAGCAAACAAATAAGGATC 1 F3: 4 TTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA R RF: TTACCTCCACTTTTCTAAAGGAAAGCAAACAAATAAGGATCAAGGTTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA RR: AATGGAGGTGAAAAGATTTCCTTTCGTTTGTTTATTCCTAGTTCCAACAACCCAGGGGAAACTTCGGGAAAACAGAGGAAGTTCT F2: 3 TCCTAGTTCC 2 Unidirectional alignment (log-probability: -40.7) TACCTCCgCTTTTCTAAAGGAAAGCAAACAAATAAGGATCccttgatcct----TTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA TACCTCCACTTTTCTAAAGGAAAGCAAACAAATAAGGATC----------AAGGTTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA Template switch alignment (log-probability: -22.5) TACCTCCgCTTTTCTAAAGGAAAGCAAACAAATAAGGATC|CCTTGATCCT|TTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA TACCTCCACTTTTCTAAAGGAAAGCAAACAAATAAGGATC|CCTTGATCCT|TTGTTGGGTCCCCTTTGAAGCCCTTTTGTCTCCTTCAAGA ========== Event 2398 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GCAGGTCAGAAAGAGCTTAGA------------------GCAAGATCCATTAACAAATTTGTGACAAAAATTTAACTAAATTGTTTAGGGTAGGGTATGTTTTAATAAAGAGTTCATTTTTCTCTTTGGGAGATAAGTCAGTAGTGAATAATAGTGGCT ↓ 4 1 3 2 Chimp: GCAGGTCAGAAAGAGCTTAGA---------GCAGACTGAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAA--CAATTGTTTAGGGTAGGGTATGTTTTAATAAAGAGTTCATTTTTCTCTTTGGGAGGTAAGTCAGTAGTGAGTAATAGTGGCT Gorilla: GCAGGTCAGAAAGAGCTTAGAGCAGACTGA---------GCAAGATCCATTAACAAATTTGTGACAAAAATTTAA--CAATTGTTTAGGGTAGGGTATGTTTTAATAAAGAGGTCATTCTTCTCTTTGGGAGGTAAGTCAGTAGTGAATAATAGTGGCA ↑ 4 1 3 2 Human: GCAGGTCAGAAAGAGCTTAGA------------------GCAAGATCCATTAACAAATTTGTGACAAAAATTTAACTAAATTGTTTAGGGTAGGGTATGTTTTAATAAAGAGTTCATTTTTCTCTTTGGGAGATAAGTCAGTAGTGAATAATAGTGGCT Cluster: [ ] Orangutan: GCAGGTCAGAAAGAGCTTAGAGCAGACTGA---------GCAAGATCCATTAACAAATTTGTGACAAAAATTTAA--CAATTGTTTAGGGTAGGGTATGTTCTAATAAAGAGTTCATTTTTCTCTTTGGGAGGTAAGTCAATAGTGAATAATAGTGGCT Human > Chimp ------------- chr3:44607696-44607699 Template switch process: F1: L TCCTACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCA 1 F3: 4 GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACA R RF: TCCTACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACTAAATTGTTTAGGGTAGGGTATGTTTTAATAAAGAGTTCATTTTTCTCTTTGGGAGATAAGTC RR: AGGATGGACAAAAACCCAATCGTCCAGTCTTTCTCGAATCTCGTTCTAGGTAATTGTTTAAACACTGTTTTTAAATTGATTTAACAAATCCCATCCCATACAAAATTATTTCTCAAGTAAAAAGAGAAACCCTCTATTCAG F2: 3 TCAG 2 Unidirectional alignment (log-probability: -34.2) ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAgagcagactGAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAAC--A ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTA---------GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACTAA Template switch alignment (log-probability: -21.8) ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCA|GACT|GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACa ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCA|GACT|GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACT Human > Gorilla --------------- chr3:44487572-44487575 Template switch process: F1: L TCCTACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCA 1 F3: 4 GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACA R RF: TCCTACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACTAAATTGTTTAGGGTAGGGTATGTTTTAATAAAGAGTTCATTTTTCTCTTTGGGAGATAAGTC RR: AGGATGGACAAAAACCCAATCGTCCAGTCTTTCTCGAATCTCGTTCTAGGTAATTGTTTAAACACTGTTTTTAAATTGATTTAACAAATCCCATCCCATACAAAATTATTTCTCAAGTAAAAAGAGAAACCCTCTATTCAG F2: 3 TCAG 2 Unidirectional alignment (log-probability: -33.6) ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAgagcagactGAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAAC--A ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTA---------GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACTAA Template switch alignment (log-probability: -21.8) ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCA|GACT|GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACa ACCTGTTTTTGGGTTAGCAGGTCAGAAAGAGCTTAGAGCA|GACT|GAGCAAGATCCATTAACAAATTTGTGACAAAAATTTAACT ========== Event 2399 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATGTCAAGTATTCTGTGACTTG----------GTCTCACAAATCC--TTGGTGAGATGTAGCTATGTCAAAGGGTCACATCTTG ↓ 1 3 24 ↑ 1 3 24 Chimp: ATGTCAAGTATTCTGTGACTTA-----GCTACATCTCACCAAGGA--TTTGTGAG-----ACCATGTCAAAGGGTCACATCTTG Gorilla: ATGTCAAGTATTCTGTGACTTAGCTAC-----ATCTCACCAAGGA--TTTGTGAG-----ACCATGTCAAAGGGTCACATCTTG ↓ 13 24 ↑ 1 3 24 Human: ATGTCAAGTATTCTGTGACTTG----------GTCTCACAAATCC--TTGGTGAGATGTAGCTATGTCAAAGGGTCACATCTTG Cluster: [ ] Orangutan: ATGTCAAGTATTCTGTGACTTAGCTAC-----ATCTCACCAAGGATTTTTGTGAG-----ACCGTGTCAAAGGGTCACATCTTG Chimp > Human ------------- chr3:44156110-44156139 Template switch process: F1: L ATTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT 1 F3: 4 ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC R RF: ATTCCCACAAGAAACTACTCATGTCAAGTATTCTGTGACTTAGCTACATCTCACCAAGGATTTGTGAGACCATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC RR: TAAGGGTGTTCTTTGATGAGTACAGTTCATAAGACACTGAATCGATGTAGAGTGGTTCCTAAACACTCTGGTACAGTTTCCCAGTGTAGAACCTTGTCCACCGGAAATCCG F2: 3 TCGATGTAGAGTGGTTCCTAAACACTCTGG 2 Unidirectional alignment (log-probability: -65.9) TTCCCACAAGAAtCTACTCATGTCAAGTATTCTGTGACTTggtctcacaaatccttggtgagatgtAGCT--------------------------ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAAACTACTCATGTCAAGTATTCTGTGACTT--------------------------AGCTACATCTCACCAAGGATTTGTGAGACCATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Template switch alignment (log-probability: -25) TTCCCACAAGAAtCTACTCATGTCAAGTATTCTGTGACTT|GGTCTCACAAATCCTTGGTGAGATGTAGCT|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAAACTACTCATGTCAAGTATTCTGTGACTT|GGTCTCACAAATCCTTGGTGAGATGTAGCT|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Human > Chimp ------------- chr3:45054597-45054626 Template switch process: F1: L ATTCCCACAAGAAACTACTCATGTCAAGTATTCTGTGACTT 1 F3: 4 ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC R RF: ATTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTTGGTCTCACAAATCCTTGGTGAGATGTAGCTATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC RR: TAAGGGTGTTCTTAGATGAGTACAGTTCATAAGACACTGAACCAGAGTGTTTAGGAACCACTCTACATCGATACAGTTTCCCAGTGTAGAACCTTGTCCACCGGAAATCCG F2: 3 CCAGAGTGTTTAGGAACCACTCTACATCGA 2 Unidirectional alignment (log-probability: -65.9) TTCCCACAAGAAaCTACTCATGTCAAGTATTCTGTGACT--------------------------TAGCTacatctcaccaaggatttgtgagaccATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTTGGTCTCACAAATCCTTGGTGAGATGTAGCT--------------------------ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Template switch alignment (log-probability: -25) TTCCCACAAGAAaCTACTCATGTCAAGTATTCTGTGACTT|AGCTACATCTCACCAAGGATTTGTGAGACC|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT|AGCTACATCTCACCAAGGATTTGTGAGACC|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Gorilla > Human --------------- chr3:44156110-44156139 Template switch process: F1: L ATTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT 1 F3: 4 ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC R RF: ATTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTTAGCTACATCTCACCAAGGATTTGTGAGACCATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC RR: TAAGGGTGTTCTTAGATGAGTACAGTTCATAAGACACTGAATCGATGTAGAGTGGTTCCTAAACACTCTGGTACAGTTTCCCAGTGTAGAACCTTGTCCACCGGAAATCCG F2: 3 TCGATGTAGAGTGGTTCCTAAACACTCTGG 2 Unidirectional alignment (log-probability: -59.4) TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTtggtctcacaaatccttggtgagatgTAGCT--------------------------ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACT--------------------------TAGCTACATCTCACCAAGGATTTGTGAGACCATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Template switch alignment (log-probability: -19.5) TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT|GGTCTCACAAATCCTTGGTGAGATGTAGCT|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT|GGTCTCACAAATCCTTGGTGAGATGTAGCT|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Human > Gorilla --------------- chr3:44958204-44958233 Template switch process: F1: L ATTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT 1 F3: 4 ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC R RF: ATTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTTGGTCTCACAAATCCTTGGTGAGATGTAGCTATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC RR: TAAGGGTGTTCTTAGATGAGTACAGTTCATAAGACACTGAACCAGAGTGTTTAGGAACCACTCTACATCGATACAGTTTCCCAGTGTAGAACCTTGTCCACCGGAAATCCG F2: 3 CCAGAGTGTTTAGGAACCACTCTACATCGA 2 Unidirectional alignment (log-probability: -59.4) TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACT--------------------------TAGCTacatctcaccaaggatttgtgagaccATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTTGGTCTCACAAATCCTTGGTGAGATGTAGCT--------------------------ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC Template switch alignment (log-probability: -19.5) TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT|AGCTACATCTCACCAAGGATTTGTGAGACC|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC TTCCCACAAGAATCTACTCATGTCAAGTATTCTGTGACTT|AGCTACATCTCACCAAGGATTTGTGAGACC|ATGTCAAAGGGTCACATCTTGGAACAGGTGGCCTTTAGGC ========== Event 2400 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACGGACATCCCTTATAGCTGCTTATCTGCTTTGCACTGTTAGTGCCTCTACAACAGTATCATAGGATCATTAGTTTGCAGATGAGGATCCTGAGGCTTGGCAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGGGTAAGTTAGGCTTTGATTTCTGGTCTT Chimp: ACGGACATCCCTTATAGCTGCTTATCTGCTTTGCACtcttagtgcctctacaacagtatcataggatcattagtttgcagatgaggatcctgaggcTTGGCAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGGGTAAATTAGGCTTTGATTTCTGGTCTT ↓ 3 2 1 4 Gorilla: ACGGACATCCCTTATAGCTGCTTATCTGCTTTGCACTCTTAGTGCCTCTACAACTGTATCATAGGATCGTTAGTTTGCAGATGAGGATCCTGAGGCTTGGCAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGAC-GGTAAGCTAGGCTTTGATTTCTGGTCTT Human: ACGGACATCCCTTATAGCTGCTTATCTGCTTTGCACTGTTAGTGCCTCTACAACAGTATCATAGGATCATTAGTTTGCAGATGAGGATCCTGAGGCTTGGCAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGGGTAAGTTAGGCTTTGATTTCTGGTCTT Cluster: [ ] Orangutan: ACGGACATCCCTTATAGCTGCTTATCCGCTTTGCACT-CCAGTGCCTCTACAACAGTATCATAGGATCATTAGTTTGCAGATGAGGACCCTGAGGCTTGGCAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGGGTAAGTTAGACTTTGATTTCTGGTCTT Chimp > Gorilla --------------- chr3:156021101-156021105 Template switch process: F1: L CAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGG 1 F3: 4 TAGGCTTTGATTTCTGGTCTTTAGACCATTCCTCCTTC R RF: GCTTATCTGCTTTGCACTCTTAGTGCCTCTACAACAGTATCATAGGATCATTAGTTTGCAGATGAGGATCCTGAGGCTTGGCAAACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGGGTAAATTAGGCTTTGATTTCTGGTCTTTAGACCATTCCTTCTTC RR: CGAATAGACGAAACGTGAGAATCACGGAGATGTTGTCATAGTATCCTAGTAATCAAACGTCTACTCCTAGGACTCCGAACCGTTTGTCGGATCATCGACTCATTGTAAAATGACCGACTCTGCCCATTTAATCCGAAACTAAAGACCAGAAATCTGGTAAGGAAGAAG F2: 3 CGAAT 2 Unidirectional alignment (log-probability: -34.4) ACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGG-TAAgcTAGGCTTTGATTTCTGGTCTTTAGACCATTCCTcCTTC-- ACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGGGTAAATTAGGCTTTGATTTCTGGTCTTTAGACCATTCCTTCTTCTC Template switch alignment (log-probability: -21.9) ACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGG|TAAGC|TAGGCTTTGATTTCTGGTCTTTAGACCATTCCTcCTTC ACAGCCTAGTAGCTGAGTAACATTTTACTGGCTGAGACGG|TAAGC|TAGGCTTTGATTTCTGGTCTTTAGACCATTCCTTCTTC ========== Event 2401 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAAGAGGTAAACCCAGAGTGCTACCAAGGCAGA---GGTAGCACTGTGAGAGGGCTGCTCCATG Chimp: GGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGA---GGTAGCACTGTGAGAGGGCTGCTCCATG ↑ 3 2 1 4 Gorilla: GGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAGAAGGAGGGCCTGTGAGAGGGCTGCTGCATG Human: GGAAGAGGTAAACCCAGAGTGCTACCAAGGCAGA---GGTAGCACTGTGAGAGGGCTGCTCCATG Cluster: [ ] Orangutan: ggaagaagtaaacccagagtgctatcaaggcagagaagaaggGCCTGTGAGAGGGCTGCTCCATG Gorilla > Chimp --------------- chr3:5012153-5012158 Template switch process: F1: L AGTCCCTGGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAG 1 F3: 4 CTGTGAGAGGGCTGCTCCATGGCCTAACACCAGAGGGGTC R RF: AGTCCCTGGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAGAAGGAGGGCCTGTGAGAGGGCTGCTGCATGGCCTAACACCAGAGGAGTC RR: TCAGGGACCTTCTTCATTTGGGTCTCACGATGGTTCCGTCTCTTCCTCCCGGACACTCTCCCGACGACGTACCGGATTGTGGTCTCCTCAG F2: 3 ACGATG 2 Unidirectional alignment (log-probability: -39.3) TCCCTGGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAGgtagcA--------CTGTGAGAGGGCTGCTcCATGGCCTAACACCAGAGGgGTC TCCCTGGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAG-----AAGGAGGGCCTGTGAGAGGGCTGCTGCATGGCCTAACACCAGAGGAGTC Template switch alignment (log-probability: -27.5) TCCCTGGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAG|GTAGCA|CTGTGAGAGGGCTGCTcCATGGCCTAACACCAGAGGgGTC TCCCTGGAAGAAGTAAACCCAGAGTGCTACCAAGGCAGAG|GTAGCA|CTGTGAGAGGGCTGCTGCATGGCCTAACACCAGAGGAGTC ========== Event 2402 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACTCAAGAAATGGGAAGAGATATTCTAGGG Chimp: TAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACTCAAGAAATGGGAAGAGATATTCTAGGG ↑ 3 2 1 4 Gorilla: TAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC------CATGGGAAGAGATATTCTAGGG ↓ 3 2 1 4 Human: TAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACTCAAGAAATGGGAAGAGATATTCTAGGG Cluster: [ ] Orangutan: TAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC------CATGGGAAGAGATATTCTAGGG Gorilla > Human --------------- chr3:153252847-153252853 Template switch process: F1: L TTGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC 1 F3: 4 ATGGGAAGAGATATTCTAGGGCTGATGAG-TTTTTTTCCA R RF: TTGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACCATGGGAAGAGATATTCTAGGGCTGATGAGTTTTTTTTCCA RR: AACGAGTTATCGATCTCACCATCCTTAAAGAACTCCTTCTGGTACCCTTCTCTATAAGATCCCGACTACTCAAAAAAAAGGT F2: 3 AAGAACT 2 Unidirectional alignment (log-probability: -34.8) TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACtcaagaaATGGGAAGAGATATTCTAGGGCTGATGAG-TTTTTTTCCA TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC------CATGGGAAGAGATATTCTAGGGCTGATGAGTTTTTTTTCCA Template switch alignment (log-probability: -26.4) TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC|TCAAGAA|ATGGGAAGAGATATTCTAGGGCTGATGAG-TTTTTTTCCA TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC|TCAAGAA|ATGGGAAGAGATATTCTAGGGCTGATGAGTTTTTTTTCCA Gorilla > Chimp --------------- chr3:156604716-156604722 Template switch process: F1: L TTGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC 1 F3: 4 ATGGGAAGAGATATTCTAGGGCTGATGAG-TTTTTTTCCA R RF: TTGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACCATGGGAAGAGATATTCTAGGGCTGATGAGTTTTTTTTCCA RR: AACGAGTTATCGATCTCACCATCCTTAAAGAACTCCTTCTGGTACCCTTCTCTATAAGATCCCGACTACTCAAAAAAAAGGT F2: 3 AAGAACT 2 Unidirectional alignment (log-probability: -34.8) TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGACtcaagaaATGGGAAGAGATATTCTAGGGCTGATGAG-TTTTTTTCCA TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC------CATGGGAAGAGATATTCTAGGGCTGATGAGTTTTTTTTCCA Template switch alignment (log-probability: -26.4) TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC|TCAAGAA|ATGGGAAGAGATATTCTAGGGCTGATGAG-TTTTTTTCCA TGCTCAATAGCTAGAGTGGTAGGAATTTCTTGAGGAAGAC|TCAAGAA|ATGGGAAGAGATATTCTAGGGCTGATGAGTTTTTTTTCCA ========== Event 2403 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TAACACAGGTAAACATCCTTT--------------------ATCAGTCCCTCTCATCTCTTATGGAA ↑ 1 3 24 Chimp: TAACACAGGTAAACATCCTTTTGATAAAAGGATGAGAGGGACTGATTCCCTCTCATCTCTTATGGAA ↓ 1 3 24 Gorilla: TAACACAGGCAAACATCCTTT--------------------ATCAGTCCCTCTCATCTCTTATGGAA Human: TAACACAGGTAAACATCCTTT--------------------ATCAGTCCCTCTCATCTCTTATGGAA Cluster: [ ] Orangutan: TAACACAGGCAAACATCCTTT--------------------ATCAGTACCTCTCATCTCTTATGGAA Chimp > Human ------------- chr3:152630546-152630550 Template switch process: F1: L AACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTT 1 F3: 4 TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG R RF: AACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTTTGATAAAAGGATGAGAGGGACTGATTCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG RR: TTGAGAACGAAGGTATTCCGATTGTGTCCATTTGTAGGAAAACTATTTTCCTACTCTCCCTGACTAAGGGAGAGTAGAGAATACCTTTTGTGTTACCCCGACACTC F2: 3 GACTA 2 Unidirectional alignment (log-probability: -26.6) ACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTT-----------------------ATcagTCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG ACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTTTGATAAAAGGATGAGAGGGACTGAT---TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG Template switch alignment (log-probability: -15.9) ACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTT|ATCAG|TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG ACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTT|ATCAG|TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG Chimp > Gorilla --------------- chr3:154859512-154859516 Template switch process: F1: L AACTCTTGCTTCCATAAGGCTAACACAGGCAAACATCCTTT 1 F3: 4 TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG R RF: AACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTTTGATAAAAGGATGAGAGGGACTGATTCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG RR: TTGAGAACGAAGGTATTCCGATTGTGTCCATTTGTAGGAAAACTATTTTCCTACTCTCCCTGACTAAGGGAGAGTAGAGAATACCTTTTGTGTTACCCCGACACTC F2: 3 GACTA 2 Unidirectional alignment (log-probability: -31.7) ACTCTTGCTTCCATAAGGCTAACACAGGcAAACATCCTTT-----------------------ATcagTCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG ACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTTTGATAAAAGGATGAGAGGGACTGAT---TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG Template switch alignment (log-probability: -21.9) ACTCTTGCTTCCATAAGGCTAACACAGGcAAACATCCTTT|ATCAG|TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG ACTCTTGCTTCCATAAGGCTAACACAGGTAAACATCCTTT|ATCAG|TCCCTCTCATCTCTTATGGAAAACACAATGGGGCTGTGAG ========== Event 2404 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTTTGAGTTCATGGCAAGAGTCCATCAGCCTTTAAATGATGAAATGTACAGATTATTTTTTACCATTGTCTACTGGTAAAAATCAAGGAAGAAGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAGCACTAAAACTGTACCTCACCCCTACCACTGCCTG Chimp: TCTTTGAGTTCATGGCAAGAGTCCATCAGCCTTTAAATGATGAAATGTACAGATTATTTTTTACCATTGTCTACTGGTAAAAATCAAGGAAGAAGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAGCG----G---ACCCCTCACCCCTACCACTGCCTG Gorilla: TCTTTGAGTTCATGGCAAGAGTCCATCAGCCTTTAAATGACGAAATGTACAGATTATTTTTTACCATCGTCTACTGGTAAAAATCAAGGAAGAAGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAGTG----G---ACTCCTCACCCCTACCACTGCCTG ↑ 3 2 1 4 Human: TCTTTGAGTTCATGGCAAGAGTCCATCAGCCTTTAAATGATGAAATGTACAGATTATTTTTTACCATTGTCTACTGGTAAAAATCAAGGAAGAAGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAGCACTAAAACTGTACCTCACCCCTACCACTGCCTG Cluster: [ ] Orangutan: TCTTTGAGTTCACGGCAAGAGTCCATCAGCCTTTAAATGATGAAATGTACAGATTATATTTTACCATTGTCCACTGGTAAAAATCAAGGAAGAAGTATAACTTGAGGCAAATAGCACTAAAACTGTACCCGAGTG----G---ACCCCTCACCCCTACCACTGCCTG Human > Gorilla --------------- chr3:155182365-155182370 Template switch process: F1: L AAGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAG 1 F3: 4 CCTCACCCCTACCACTGCCTGCTCTTTGCTTGCGAGGACC R RF: AGTCCATCAGCCTTTAAATGATGAAATGTACAGATTATTTTTTACCATTGTCTACTGGTAAAAATCAAGGAAGAAGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAGCACTAAAACTGTACCTCACCCCTACCACTGCCTGCTCTTTGCTTGCGAGGACC RR: TCAGGTAGTCGGAAATTTACTACTTTACATGTCTAATAAAAAATGGTAACAGATGACCATTTTTAGTTCCTTCTTCCTATTGAACTCCGTTTATCGTGATTTTGACATGGGTTCGTGATTTTGACATGGAGTGGGGATGGTGACGGACGAGAAACGAACGCTCCTGG F2: 3 TCAGGT 2 Unidirectional alignment (log-probability: -29.5) AGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAG---------TGgActCCTCACCCCTACCACTGCCTGCTCTTTGCTTGCGAGGACC AGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAGCACTAAAACTGTA--CCTCACCCCTACCACTGCCTGCTCTTTGCTTGCGAGGACC Template switch alignment (log-probability: -16.5) AGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAG|TGGACT|CCTCACCCCTACCACTGCCTGCTCTTTGCTTGCGAGGACC AGGATAACTTGAGGCAAATAGCACTAAAACTGTACCCAAG|TGGACT|CCTCACCCCTACCACTGCCTGCTCTTTGCTTGCGAGGACC ========== Event 2405 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTATGTTTAGAATATCAATGAGGACAAATTTTATT-----AGTTTCATTTATTGATTCGTTAT ↓ 3 2 1 4 Chimp: TGTATGTTTAGAATATCAATGAGGACAAATTTTATTGTCCTCATTTCATTTATTGATTCATTAT ↑ 3 2 1 4 Gorilla: TGTATGTTTAGAATATCAATGAGGACAAATTTTATT-----AGTTTCATTTATTGATTCATTAT Human: TGTATGTTTAGAATATCAATGAGGACAAATTTTATT-----AGTTTCATTTATTGATTCGTTAT Cluster: [ ] Orangutan: TGTATGTTTAGAATATCAATGAGGACAAATTTTATT-----AGTTTCATTTATTGATTCATTAT Human > Chimp ------------- chr3:155090463-155090469 Template switch process: F1: L ATCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT 1 F3: 4 TTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA R RF: ATCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATTAGTTTCATTTATTGATTCGTTATACATAAACTTTCAAACAAA RR: TAGTGACATACAAATCTTATAGTTACTCCTGTTTAAAATAATCAAAGTAAATAACTAAGCAATATGTATTTGAAAGTTTGTTT F2: 3 ACTCCTG 2 Unidirectional alignment (log-probability: -35.8) TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATTgtcctcA-TTTCATTTATTGATTCaTTATACATAAACTTTCAAACAAA TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT------AGTTTCATTTATTGATTCGTTATACATAAACTTTCAAACAAA Template switch alignment (log-probability: -22.1) TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT|GTCCTCA|TTTCATTTATTGATTCaTTATACATAAACTTTCAAACAAA TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT|GTCCTCA|TTTCATTTATTGATTCGTTATACATAAACTTTCAAACAAA Gorilla > Chimp --------------- chr3:155090463-155090469 Template switch process: F1: L ATCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT 1 F3: 4 TTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA R RF: ATCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATTAGTTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA RR: TAGTGACATACAAATCTTATAGTTACTCCTGTTTAAAATAATCAAAGTAAATAACTAAGTAATATGTATTTGAAAGTTTGTTT F2: 3 ACTCCTG 2 Unidirectional alignment (log-probability: -29.1) TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATtgtccTcaTTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTAT-----TAGTTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA Template switch alignment (log-probability: -16.6) TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT|GTCCTCA|TTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA TCACTGTATGTTTAGAATATCAATGAGGACAAATTTTATT|GTCCTCA|TTTCATTTATTGATTCATTATACATAAACTTTCAAACAAA ========== Event 2406 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTCGCCATACAAGGTGGAGCAGTGAGTGACCCGAACCAGGGGCTGACCCCTGCCAGAGCCCCCACAGCGACTCACTGcccc----------ccccTCC Chimp: TGTCGCCATACAAGGTGGAGCAGTGAGTGACCCGAACCAGGGGCTGACCCCTGCCAGAGCCCCCACAGCGACTCACTGcccc---cccccacccccTCC Gorilla: TGTCGCCATACAAGGTGGAGCAGTGAGTGACCCGAACCAGGGGCTGACTCCCGCCAGAGCCCCCACAGCGATTCATTGccccccc-------tcccccc ↓ 3 2 1 4 Human: TGTCGCCATACAAGGTGGAGCAGTGAGTGACCCGAACCAGGGGCTGACCCCTGCCAGAGCCCCCACAGCGACTCACTGcccc----------ccccTCC Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr3:47475155-47475162 Template switch process: F1: L ATACAAGGTGGAGCAGTGAGTGACCCGAACCAGGGGCTGACCCCTGCCAGAGCCCCCACAGCGA 1 F3: 4 CCCCCCCTCC R RF: ATACAAGGTGGAGCAGTGAGTGACCCGAACCAGGGGCTGACTCCCGCCAGAGCCCCCACAGCGATTCATTGCCCCCCCTCC RR: TATGTTCCACCTCGTCACTCACTGGGCTTGGTCCCCGACTGAGGGCGGTCTCGGGGGTGTCGCTAAGTAACGGGGGGGAGG F2: 3 CGTCACTC 2 Unidirectional alignment (log-probability: -38.6) CCGAACCAGGGGCTGACcCCtGCCAGAGCCCCCACAGCGAcTCAcTGCCCCC---CCCtCC CCGAACCAGGGGCTGACTCCCGCCAGAGCCCCCACAGCGATTCATTGCCCCCCCTCCCCCC Template switch alignment (log-probability: -27.6) CCGAACCAGGGGCTGACcCCtGCCAGAGCCCCCACAGCGA|CTCACTGC|CCCCCCCTCC CCGAACCAGGGGCTGACTCCCGCCAGAGCCCCCACAGCGA|CTCACTGC|CCCCCCCTCC ========== Event 2407 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: --------------------GTGTTAGGAAACCTTCATTTTAC--TGTGTCACATTAGCCAAATTTC ↓ 1 4 3 2 Chimp: --------------------GCAG-----TACCTTCATTTTAC--TGTGTCACATTAGCCAAATTTC Gorilla: --------------------GTAG-----TACCTTCATTTTAC----TGTCACATTAGCCAAATTTC Human: --------------------GTGTTAGGAAACCTTCATTTTAC--TGTGTCACATTAGCCAAATTTC Cluster: [ ] Orangutan: actcacttttcctaacctctgtaG-----TACCTTCGTTTCACTG--TGTCACATTAGCCAAATTTC Human > Chimp ------------- chr3:49057360-49057363 Template switch process: F1: L AGCCTGATTCCCACCATCATACTCACTTTTCCTAACCACTG 1 F3: 4 ACCTTCATTTTACTGTGTCACATTAGCCAAATTTCTACCG R RF: AGCCTGATTCCCACCATCATACTCACTTTTCCTAACCACTGTGTTAGGAAACCTTCATTTTACTGTGTCACATTAGCCAAATTTCTACCG RR: TCGGACTAAGGGTGGTAGTATGAGTGAAAAGGATTGGTGACACAATCCTTTGGAAGTAAAATGACACAGTGTAATCGGTTTAAAGATGGC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -25.9) GCCTGATTCCCACCATCATACTCACTTTTCCTAACCACTgcaGT--------ACCTTCATTTTACTGTGTCACATTAGCCAAATTTCTACCG GCCTGATTCCCACCATCATACTCACTTTTCCTAACCACT---GTGTTAGGAAACCTTCATTTTACTGTGTCACATTAGCCAAATTTCTACCG Template switch alignment (log-probability: -15.8) GCCTGATTCCCACCATCATACTCACTTTTCCTAACCACTG|CAGT|ACCTTCATTTTACTGTGTCACATTAGCCAAATTTCTACCG GCCTGATTCCCACCATCATACTCACTTTTCCTAACCACTG|CAGT|ACCTTCATTTTACTGTGTCACATTAGCCAAATTTCTACCG ========== Event 2408 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGAGCCCTCCCTGCATATGTGAGTAGGAAGCCTCCTACTCACATTTGGGGGCTTAATAAATCT ↑ 3 1 2 4 Chimp: GGGAGCCCTCCCTGCATATGTGAGTAGGAG-GCTGCTGCTAGGATTTGGGGGCTTAATAAATCT Gorilla: GGGAGCCCTCCCTGCATATGTGAGTAGGAG-GCTGCTGCTAGGATTTGGGGGCTTAATAAATCT ↓ 3 1 2 4 Human: GGGAGCCCTCCCTGCATATGTGAGTAGGAAGCCTCCTACTCACATTTGGGGGCTTAATAAATCT Cluster: [ ] Orangutan: GGGAGCCCTCCCTGCATATGTGAGTAGGAG-GCTGCTGCTAGGATTTGGGGGCTTAATAAATC- Chimp > Human ------------- chr3:49560140-49560153 Template switch process: F1: L ACCCCAGTGTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA 1 F3: 4 ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC R RF: ACCCCAGTTTGGGGGAGCCCTCCCTGCATATGTGAGTAGGAGGCTGCTGCTAGGATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC RR: TGGGGTCAAACCCCCTCGGGAGGGACGTATACACTCATCCTCCGACGACGATCCTAAACCCCCGAATTATTTAGAAAGGGGAATAGTGTCCAGG F2: 3 CACTCATCCTCCGA 2 Unidirectional alignment (log-probability: -47.9) CCCCAGTgTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA-------------agcctcctactcacATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC CCCCAGTTTGGGGGAGCCCTCCCTGCATATGTGAGTAGGAGGCTGCTGCTAGG--------------ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC Template switch alignment (log-probability: -23) CCCCAGTgTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA|AGCCTCCTACTCAC|ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC CCCCAGTTTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA|AGCCTCCTACTCAC|ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC Gorilla > Human --------------- chr3:49560140-49560153 Template switch process: F1: L ACCCCAGTGTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA 1 F3: 4 ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC R RF: ACCCCAGTTTGGGGGAGCCCTCCCTGCATATGTGAGTAGGAGGCTGCTGCTAGGATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC RR: TGGGGTCAAACCCCCTCGGGAGGGACGTATACACTCATCCTCCGACGACGATCCTAAACCCCCGAATTATTTAGAAAGGGGAATAGTGTCCAGG F2: 3 CACTCATCCTCCGA 2 Unidirectional alignment (log-probability: -46.9) CCCCAGTgTGGGGGAGCCCTCCCTGCATATGTGAGTAGGAagcctcctactcac-------------ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC CCCCAGTTTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA--------------GGCTGCTGCTAGGATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC Template switch alignment (log-probability: -23) CCCCAGTgTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA|AGCCTCCTACTCAC|ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC CCCCAGTTTGGGGGAGCCCTCCCTGCATATGTGAGTAGGA|AGCCTCCTACTCAC|ATTTGGGGGCTTAATAAATCTTTCCCCTTATCACAGGTCC ========== Event 2409 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GCATAAGAAAGGAAAAGGCCAGTAAAGAAAACACTATGCAACAGTAAAGAAAACTGTAggccaagcacagtggctcacgcctg--ttcccaacactttgggaggccaaggcaggaggattgcttgagcccatgagtttgaaaccagcctgggtaatatagtctgtatctcttcaacaaaatttacaaattagcctggtgtggtggc Chimp: GCATAAGAAAGGAAAAGGCCAGTA----------------------AAGAAAACTGTAggccaagcacagtggctcacgcctg--ttcccaacactttgggaggccaaggcaggaggattgcttgagcccatgagtttgaaaccagcctgggtaatatagtctgtatctcttcaacaaaatttgcaaattagcctggtgtggtggc ↓ 4 1 3 2 Gorilla: GCATAAGAAAGGAAAAGGCCAGTAAAGAAAACACTATGCAACAGTAAAGAAAACTGTAggccaagcacagtggctcacgcctg--ttcccaacactttgggaggccaaggcaggaggattgcttgagcccatgagtttgaaaccagcctgggtaatatagtctgtatctgttcaacaaaatttacaaattagcctggtttggtggc Human: GCATAAGAAAGGAAAAGGCCAGTAAAGAAAACACTATGCAACAGTAAAGAAAACTGTAggccaagcacagtggctcacgcctg--ttcccaacactttgggaggccaaggcaggaggattgcttgagcccatgagtttgaaaccagcctgggtaatatagtctgtatctcttcaacaaaatttacaaattagcctggtgtggtggc Cluster: [ ] Orangutan: GCATAAGAAAGGAAAAGGCGAGTAAAGAAAACACTATGCAACAGTAAAGAAAACTGTAggccaagcacagtggctcactcctgcaatcccaacactttgggaggccaaggcaggaggattgcttgagcccatgagtttgaaaccagcctgggtaatatagtctgtatctcttcaacagaatttacaaattagcctggtgtggtggc Chimp > Gorilla --------------- chr3:50508189-50508193 Template switch process: F1: L AAAAAAAGGATTAAAATGCATAAGAAAGGAAAAGGCCAGTAAAGAAAACACTA 1 F3: 4 CAGTAAAGAAAACTGTAGGCCAAGCACAGTGGCTCACGCCTGTTC R RF: AAAAAAAGGATTAAAATGCATAAGAAAGGAAAAGGCCAGTAAAGAAAACTGTAGGCCAAGCACAGTGGCTCACGCCTGTTCCCAACACTTTGGGAGGCCAAGGCAGGAGGATTGCTTGAGCCCATGAGTTTGAAACCAGCCTGGGTAATATAGTCTGTATCTCTTCAACAAAATTTGCA RR: TTTTTTTCCTAATTTTACGTATTCTTTCCTTTTCCGGTCATTTCTTTTGACATCCGGTTCGTGTCACCGAGTGCGGACAAGGGTTGTGAAACCCTCCGGTTCCGTCCTCCTAACGAACTCGGGTACTCAAACTTTGGTCGGACCCATTATATCAGACATAGAGAAGTTGTTTTAAACGT F2: 3 AACGT 2 Unidirectional alignment (log-probability: -42.5) AAATGCATAAGAAAGGAAAAGGCCAGtaaagaaaacactatgcaacagTAAAGAAAACTGTAGGCCAAGCACAGTGGCTCACGCC AAATGCATAAGAAAGGAAAAGGCCAG----------------------TAAAGAAAACTGTAGGCCAAGCACAGTGGCTCACGCC Template switch alignment (log-probability: -27.8) AAATGCATAAGAAAGGAAAAGGCCAGTAAAGAAAACacTA|TGCAA|CAGTAAAGAAAACTGTAGGCCAAGCACAGTGGCTCACGCC AAATGCATAAGAAAGGAAAAGGCCAGTAAAGAAAACTGTA|TGCAA|CAGTAAAGAAAACTGTAGGCCAAGCACAGTGGCTCACGCC ========== Event 2410 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCATTTTCAGGAAAACTAGGCCATTGACTAATGGCCTCCCTCATTCTAAGTGAGTT ↑ 3 1 2 4 Chimp: TCATTTTCAGGAAAACTAGGCCATT-AGTCATTTACTCCCTCATTCTAAGTGAGTT Gorilla: TCATTTTCAGGAAAACTAGGCCATT-AGTCATTTACTCCCTCATTCTAAGTGAGTT ↓ 3 1 2 4 Human: TCATTTTCAGGAAAACTAGGCCATTGACTAATGGCCTCCCTCATTCTAAGTGAGTT Cluster: [ ] Orangutan: TCATTTTCAGGAAAACTAGGCCATT-AGTTATTTACTCCCTCATTCTAAGTGAGTT Chimp > Human ------------- chr3:147006867-147006876 Template switch process: F1: L TCCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT 1 F3: 4 CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG R RF: TCCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATTAGTCATTTACTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG RR: AGGAAAAGAAAGTTTGAGTAAAAGTCCTTTTGATCCGGTAATCAGTAAATGAGGGAGTAAGATTCACTCAAAAACAGTGAACAATGAGAC F2: 3 CGGTAATCAG 2 Unidirectional alignment (log-probability: -36) CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT---------gactaatggcCTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATTAGTCATTTA----------CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG Template switch alignment (log-probability: -16.5) CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT|GACTAATGGC|CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT|GACTAATGGC|CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG Gorilla > Human --------------- chr3:147006867-147006876 Template switch process: F1: L TCCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT 1 F3: 4 CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG R RF: TCCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATTAGTCATTTACTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG RR: AGGAAAAGAAAGTTTGAGTAAAAGTCCTTTTGATCCGGTAATCAGTAAATGAGGGAGTAAGATTCACTCAAAAACAGTGAACAATGAGAC F2: 3 CGGTAATCAG 2 Unidirectional alignment (log-probability: -35.5) CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT---------gactaatggcCTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATTAGTCATTTA----------CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG Template switch alignment (log-probability: -17) CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT|GACTAATGGC|CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG CCTTTTCTTTCAAACTCATTTTCAGGAAAACTAGGCCATT|GACTAATGGC|CTCCCTCATTCTAAGTGAGTTTTTGTCACTTGTTACTCTG ========== Event 2411 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACAGCCATCCTAACTGAGGCTCTC---TGAAGTCTGTGGTGCCCCACAGTGAG Chimp: CTACAGCCATCCTAACTGAGGCTCTC---TGAAGTCTGTGGTGCCCCACAGTGAG ↓ 1 3 4 2 Gorilla: CTACAGCCATCCTAACTGAGGACTTCAGAGGAAGTCTGTGGTGCCCCACAGTGAG ↑ 1 3 4 2 Human: CTACAGCCATCCTAACTGAGGCTCTC---TGAAGTCTGTGGTGCCCCACAGTGAG Cluster: [ ] Orangutan: CTACAGCCATCCTAACTGAGGC--TC---TGAAGTCTGTGGTGCCCCACAGAGAG Human > Gorilla --------------- chr3:149151249-149151257 Template switch process: F1: L TACACAGAGACCTCCTCTCACTACAGCCATCCTAACTGAGG 1 F3: 4 GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG R RF: TACACAGAGACCACCTCTCACTACAGCCATCCTAACTGAGGCTCTCTGAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG RR: ATGTGTCTCTGGTGGAGAGTGATGTCGGTAGGATTGACTCCGAGAGACTTCAGACACCACGGGGTGTCACTCTAGAAAGATTGTGAC F2: 3 GAGACTTCA 2 Unidirectional alignment (log-probability: -39.4) ACACAGAGACCtCCTCTCACTACAGCCATCCTAACTGAGG------acttcagagGAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG ACACAGAGACCACCTCTCACTACAGCCATCCTAACTGAGGCTCTCT---------GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG Template switch alignment (log-probability: -22.4) ACACAGAGACCtCCTCTCACTACAGCCATCCTAACTGAGG|ACTTCAGAG|GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG ACACAGAGACCACCTCTCACTACAGCCATCCTAACTGAGG|ACTTCAGAG|GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG Chimp > Gorilla --------------- chr3:149151249-149151257 Template switch process: F1: L TACACAGAGACCTCCTCTCACTACAGCCATCCTAACTGAGG 1 F3: 4 GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG R RF: TACACAGAGACCACCTCTCACTACAGCCATCCTAACTGAGGCTCTCTGAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG RR: ATGTGTCTCTGGTGGAGAGTGATGTCGGTAGGATTGACTCCGAGAGACTTCAGACACCACGGGGTGTCACTCTAGAAAGATTGTGAC F2: 3 GAGACTTCA 2 Unidirectional alignment (log-probability: -39.4) ACACAGAGACCtCCTCTCACTACAGCCATCCTAACTGAGG------acttcagagGAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG ACACAGAGACCACCTCTCACTACAGCCATCCTAACTGAGGCTCTCT---------GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG Template switch alignment (log-probability: -22.4) ACACAGAGACCtCCTCTCACTACAGCCATCCTAACTGAGG|ACTTCAGAG|GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG ACACAGAGACCACCTCTCACTACAGCCATCCTAACTGAGG|ACTTCAGAG|GAAGTCTGTGGTGCCCCACAGTGAGATCTTTCTAACACTG ========== Event 2412 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGGATGGTTAACAGAGGACTGGAGATTTTATGACCATC----ATTCCTACAGCTTCAGAACCATGAGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGTTCTCCAGCATCTTGACAGGCCACTCAGA Chimp: GGGGATGGTTAACAGAGGACTGGAGATTTTATGACCATC----ATTCCTACAGCTTCAGAACCATGAGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGTTCTCCAGCATCTTGACAGGCCACTCAGA ↑ 3 2 1 4 Gorilla: GGGGATGGTTAACAGAGGACTGGAGATTTTATGACCATCATTCATTCCTACAGCTTCAGAACCATGAGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGTCAAG-TTCATCTTGACAGGCCACTCAGA Human: GGGGATGGTTAACAGAGGACTGGAGATTTTATGACCATC----ATTCCTACAGCTTCAGAACCATGAGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGTTCTCCAGCATCTTGACAGGCCACTCAGA Cluster: [ ] Orangutan: GGGGATGGTTAACAGAGGACTGGAGATTTTATAACCATC----ATTCCTACAGCTTCAGAGCCATGAGCTCAGCTGAAAGCAGACTTCGCTTGAAATAATAATAGTTCTCTAGCATCTTGACATGGCACTCAGA Gorilla > Chimp --------------- chr3:150222029-150222035 Template switch process: F1: L GAGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGT 1 F3: 4 CATCTTGACAGGCCACTCAGAACTCTACAATATCACAGGA R RF: CTGGAGATTTTATGACCATCATTCATTCCTACAGCTTCAGAACCATGAGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGTCAAGTTCATCTTGACAGGCCACTCAGAACTCTACAATATCACAGGA RR: GACCTCTAAAATACTGGTAGTAAGTAAGGATGTCGAAGTCTTGGTACTCGAGTCGACTTTCGTCTGAAGTGAACTTTATTATTATCAGTTCAAGTAGAACTGTCCGGTGAGTCTTGAGATGTTATAGTGTCCT F2: 3 GACCTCT 2 Unidirectional alignment (log-probability: -29.5) AGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAAT-----AGTTctccagCATCTTGACAGGCCACTCAGAACTCTACAATATCACAGGA AGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGTCAAGTT------CATCTTGACAGGCCACTCAGAACTCTACAATATCACAGGA Template switch alignment (log-probability: -16.6) AGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGT|TCTCCAG|CATCTTGACAGGCCACTCAGAACTCTACAATATCACAGGA AGCTCAGCTGAAAGCAGACTTCACTTGAAATAATAATAGT|TCTCCAG|CATCTTGACAGGCCACTCAGAACTCTACAATATCACAGGA ========== Event 2413 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGAGAGATCAGGTGGTGCACCCCCCACCAACAGTCTTGGGC Chimp: GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGAGAGATCAGGTGGTGCACCCCCCACCAACAGTCTTGGGC ↑ 3 2 1 4 Gorilla: GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGAT-----ATTTGGTGCACTCCCCACCAACAGTCTTGGGC ↓ 3 2 1 4 Human: GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGAGAGATCAGGTGGTGCACCCCCCACCAACAGTCTTGGGC Cluster: [ ] Orangutan: GTGACCCTGGGGGCTCAGACCTGATCTCTCAAAGACCTGAT-----ATTTGGTGCACTCCCCACCAACAGTCTTGGGC Gorilla > Human --------------- chr3:146004395-146004403 Template switch process: F1: L TGTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA 1 F3: 4 TGGTGCACCCCCCACCAACAGTCTTGGGCCAATGTGGTACCACACCTGA R RF: CGTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGATATTTGGTGCACTCCCCACCAACAGTCTTGGGCCAATGTGGTACCACACCTGA RR: GCACTGGGGCCCCCGAGTCTGGACTAGAGAGCTTCTGGACTATAAACCACGTGAGGGGTGGTTGTCAGAACCCGGTTACACCATGGTGTGGACT F2: 3 GGACTAGAG 2 Unidirectional alignment (log-probability: -44.9) GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA----gagatcaggTGGTGCACcCCCCACCAACAGTCTTGGGCCAATGTGGTAC GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGATATT---------TGGTGCACTCCCCACCAACAGTCTTGGGCCAATGTGGTAC Template switch alignment (log-probability: -28.1) GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA|GAGATCAGG|TGGTGCACcCCCCACCAACAGTCTTGGGCCAATGTGGTAC GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA|GAGATCAGG|TGGTGCACTCCCCACCAACAGTCTTGGGCCAATGTGGTAC Gorilla > Chimp --------------- chr3:149215921-149215929 Template switch process: F1: L TGTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA 1 F3: 4 TGGTGCACCCCCCACCAACAGTCTTGGGCCAATGTGGTACCACACCTGA R RF: CGTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGATATTTGGTGCACTCCCCACCAACAGTCTTGGGCCAATGTGGTACCACACCTGA RR: GCACTGGGGCCCCCGAGTCTGGACTAGAGAGCTTCTGGACTATAAACCACGTGAGGGGTGGTTGTCAGAACCCGGTTACACCATGGTGTGGACT F2: 3 GGACTAGAG 2 Unidirectional alignment (log-probability: -44.9) GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA----gagatcaggTGGTGCACcCCCCACCAACAGTCTTGGGCCAATGTGGTAC GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGATATT---------TGGTGCACTCCCCACCAACAGTCTTGGGCCAATGTGGTAC Template switch alignment (log-probability: -28.1) GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA|GAGATCAGG|TGGTGCACcCCCCACCAACAGTCTTGGGCCAATGTGGTAC GTGACCCCGGGGGCTCAGACCTGATCTCTCGAAGACCTGA|GAGATCAGG|TGGTGCACTCCCCACCAACAGTCTTGGGCCAATGTGGTAC ========== Event 2414 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GC--TCTCCTAAAGGTAAAAAATTTAACAGAGTCCGACCTATAAGCCATGCTATGAATGACTGAAC ↓ 1 4 3 2 Chimp: GC--TCTCCTAAAGGTAAAAAGCTTATCAGAGTCAGACCTGTAAGCCATGCTATGAATGACTGAAC Gorilla: GCTCTCTCCTAAAGGTAAAAAATTTATCAGAGTCAGACCTGTAAGCCATGCTATGAATCACTGAAt Human: GC--TCTCCTAAAGGTAAAAAATTTAACAGAGTCCGACCTATAAGCCATGCTATGAATGACTGAAC Cluster: [ ] Orangutan: CG--TCTCCTAAAGGTAAAAAATGTAACAGAATCAGACCTGTAAGCCATGCTATGAATGACTGAAC Human > Chimp ------------- chr3:5360399-5360404 Template switch process: F1: L AAGTGTTCACTTTTAATGATCTGCTCTCCTAAAGGTAAAAA 1 F3: 4 CAGAGTCAGACCTGTAAGCCATGCTATGAATGACTGAACGTGTGTGTGTG R RF: AAGTGTTCACTTTTAATGATCTGCTCTCCTAAAGGTAAAAAATTTAACAGAGTCCGACCTATAAGCCATGCTATGAATGACTGAACGTGTGTGTGTG RR: TTCACAAGTGAAAATTACTAGACGAGAGGATTTCCATTTTTTAAATTGTCTCAGGCTGGATATTCGGTACGATACTTACTGACTTGCACACACACAC F2: 3 TATTCG 2 Unidirectional alignment (log-probability: -38.2) AGTGTTCACTTTTAATGATCTGCTCTCCTAAAGGTAAAAAgcTTAtCAGAGTCaGACCTgTAAGCCATGCTATGAATGACTGAACG AGTGTTCACTTTTAATGATCTGCTCTCCTAAAGGTAAAAAATTTAACAGAGTCCGACCTATAAGCCATGCTATGAATGACTGAACG Template switch alignment (log-probability: -28.2) AGTGTTCACTTTTAATGATCTGCTCTCCTAAAGGTAAAAA|GCTTAT|CAGAGTCaGACCTgTAAGCCATGCTATGAATGACTGAACG AGTGTTCACTTTTAATGATCTGCTCTCCTAAAGGTAAAAA|GCTTAT|CAGAGTCCGACCTATAAGCCATGCTATGAATGACTGAACG ========== Event 2415 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGGCACGGTACAGCGCCTAAGCATGG--AGAGAGGGGGGTCTTGGCATCATGTCCAAGCTCCAGATTCTCCCAGAGGGACCTCC Chimp: GTGGCACGGGACAGCGCCTAA--CTGG--AGAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCTCCCAGAGGGACCTCC ↑ 1 4 3 2 Gorilla: GTGGCACGGGACAGCGCCTAAGCATGG----AGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCTCCCAGAGGGACCTCC Human: GTGGCACGGTACAGCGCCTAAGCATGG--AGAGAGGGGGGTCTTGGCATCATGTCCAAGCTCCAGATTCTCCCAGAGGGACCTCC Cluster: [ ] Orangutan: GTGGCACGGGACAGTGCCTAAGCATGGAG--AGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCTCCCAGAGGGACCTCC Gorilla > Chimp --------------- chr3:148671046-148671050 Template switch process: F1: L TCGCTAGGGGGCAGGCACAGGTGGCACGGGACAGCGCCTAA 1 F3: 4 GAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCTC R RF: TCGCTAGGGGGCAGGCACAGGTGGCACGGGACAGCGCCTAAGCATGGAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCTC RR: AGCGATCCCCCGTCCGTGTCCACCGTGCCCTGTCGCGGATTCGTACCTCTCCCCCCAGAACCATAGTACAGGTTCGAGGTCTAAGAG F2: 3 AGGTC 2 Unidirectional alignment (log-probability: -28.1) CGCTAGGGGGCAGGCACAGGTGGCACGGGACAGCGCCTAA-----ctggaGAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCT CGCTAGGGGGCAGGCACAGGTGGCACGGGACAGCGCCTAAGCATG-----GAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCT Template switch alignment (log-probability: -16.4) CGCTAGGGGGCAGGCACAGGTGGCACGGGACAGCGCCTAA|CTGGA|GAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCT CGCTAGGGGGCAGGCACAGGTGGCACGGGACAGCGCCTAA|CTGGA|GAGAGGGGGGTCTTGGTATCATGTCCAAGCTCCAGATTCT ========== Event 2416 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TATCTGACTTACGTCTCCTCTAAGCACA------------GTACTTTTGTACTGTGAATATTGTTGTCAAGAAG ↑ 1 4 3 2 Chimp: TATCTGACTTACGTCTCCTCTAAGCAGA------AGATAATCACTTTTGTACTGTGAATATTGTTGTCAAGAAG Gorilla: TATCTGACTTACGTCTCCTCTCAGCAGAAGATAA------TCACTTTTGTACTGTGAATATTGTTGTCAAGAAG ↓ 1 4 3 2 Human: TATCTGACTTACGTCTCCTCTAAGCACA------------GTACTTTTGTACTGTGAATATTGTTGTCAAGAAG Cluster: [ ] Orangutan: TATCTGACTTGTGTCTCCTCTCAGTAGAAGATAA------TCACTTTTGTACTGTGAATATTGTTGTCAAGAAG Chimp > Human ------------- chr3:145290642-145290646 Template switch process: F1: L TGAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCA 1 F3: 4 CTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC R RF: TGAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCAGAAGATAATCACTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC RR: ACTTTTCAATGTCGAATAGACTGAATGCAGAGGAGATTCGTCTTCTATTAGTGAAAACATGACACTTATAACAACAGTTCTTCCTTCGGAG F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -25.9) GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCA---------CagtACTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCAGAAGATAATC---ACTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC Template switch alignment (log-probability: -15.9) GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCA|CAGTA|CTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCA|CAGTA|CTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC Gorilla > Human --------------- chr3:145290642-145290646 Template switch process: F1: L TTTTGTGAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTAAGCA 1 F3: 4 CTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC R RF: TTTTGTGAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTCAGCAGAAGATAATCACTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC RR: AAAACACTTTTCAATGTCGAATAGACTGAATGCAGAGGAGAGTCGTCTTCTATTAGTGAAAACATGACACTTATAACAACAGTTCTTCCTTCGGAG F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -31) GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTaAGCA---------CagtACTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTCAGCAGAAGATAATC---ACTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC Template switch alignment (log-probability: -22) GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTaAGCA|CAGTA|CTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC GAAAAGTTACAGCTTATCTGACTTACGTCTCCTCTCAGCA|CAGTA|CTTTTGTACTGTGAATATTGTTGTCAAGAAGGAAGCCTC ========== Event 2417 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTAGAAAGACCTCGTCTCTGAGGTTGGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT Chimp: TCTAGAAAGACCTCGTCTCTGAGGTTGGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT ↓ 1 4 3 2 Gorilla: TCTAGAAAGACCTCGTCTCTGGATACAGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT ↑ 1 4 3 2 Human: TCTAGAAAGACCTCGTCTCTGAGGTTGGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT Cluster: [ ] Orangutan: TCTAGAAAGACCTCGTCTCTGAGATTGGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT Human > Gorilla --------------- chr3:147069804-147069809 Template switch process: F1: L CCATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG 1 F3: 4 GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT R RF: CCATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTGAGGTTGGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT RR: GGTACCCTTCCCTACCGGAGAGATCTTTCTGGAGCAGAGACTCCAACCCACACGGTGTAGGACATAGGAGTCAAATAGACAAAGCCA F2: 3 ACATAG 2 Unidirectional alignment (log-probability: -28.1) CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG-----GatacaGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTGAGGTTG-----GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT Template switch alignment (log-probability: -16.5) CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG|GATACA|GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG|GATACA|GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT Chimp > Gorilla --------------- chr3:147069804-147069809 Template switch process: F1: L CCATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG 1 F3: 4 GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT R RF: CCATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTGAGGTTGGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT RR: GGTACCCTTCCCTACCGGAGAGATCTTTCTGGAGCAGAGACTCCAACCCACACGGTGTAGGACATAGGAGTCAAATAGACAAAGCCA F2: 3 ACATAG 2 Unidirectional alignment (log-probability: -28.1) CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG-----GatacaGGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTGAGGTTG-----GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT Template switch alignment (log-probability: -16.5) CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG|GATACA|GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT CATGGGAAGGGATGGCCTCTCTAGAAAGACCTCGTCTCTG|GATACA|GGTGTGCCACATCCTGTATCCTCAGTTTATCTGTTTCGGT ========== Event 2418 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATGCTTTTATTATTCTTTTATACCCACCCACAGAA----CATGGGTGGGGAT-AAATGAATTAAGAAAGCTTCAT Chimp: AATGCTTTTATTATTCTTTTATCCCCACCCACAGAA----CATGGGTGGGGAT-AAATGAATTAAGAAAGCTTCAT ↑ 3 1 2 4 Gorilla: AATGCTTTTATTATTCTTTTATCCCCACCCATGTTC--------TGTGGGTACAGAATGAATTAAGAAAGCTTCAT ↓ 3 1 2 4 Human: AATGCTTTTATTATTCTTTTATACCCACCCACAGAA----CATGGGTGGGGAT-AAATGAATTAAGAAAGCTTCAT Cluster: [ ] Orangutan: AATGCTTTTATTATTCTTTTATCCCCACCCACAGAACATG----GGTGGGGAT-AAATGAATTAAGAAAGCTCCAT Gorilla > Human --------------- chr3:144197284-144197302 Template switch process: F1: L TTTTATTCCTTCAACAGGCAATGCTTTTATTATTCTTTTATACCCACCCA 1 F3: 4 AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT R RF: TTTTATTCCTTAAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCATGTTCTGTGGGTACAGAATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT RR: AAAATAAGGAATTTGTCCGTTACGAAAATAATAAGAAAATAGGGGTGGGTACAAGACACCCATGTCTTACTTAATTCTTTCGAAGTACTTGAAAAATGTATATTTA F2: 3 ATAGGGGTGGGTACAAGAC 2 Unidirectional alignment (log-probability: -55.5) TcAACAGGCAATGCTTTTATTATTCTTTTATaCCCACCC-------------ACAGaacatgggtggggataAATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT TAAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCATGTTCTGTGGGTACAG----------------AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT Template switch alignment (log-probability: -29.4) TcAACAGGCAATGCTTTTATTATTCTTTTATaCCCACCCA|CAGAACATGGGTGGGGATA|AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT TAAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCA|CAGAACATGGGTGGGGATA|AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT Gorilla > Chimp --------------- chr3:147393399-147393417 Template switch process: F1: L TTCAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCA 1 F3: 4 AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT R RF: TTAAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCATGTTCTGTGGGTACAGAATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT RR: AATTTGTCCGTTACGAAAATAATAAGAAAATAGGGGTGGGTACAAGACACCCATGTCTTACTTAATTCTTTCGAAGTACTTGAAAAATGTATATTTA F2: 3 ATAGGGGTGGGTACAAGAC 2 Unidirectional alignment (log-probability: -49.9) TcAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCC-------------ACAGaacatgggtggggataAATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT TAAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCATGTTCTGTGGGTACAG----------------AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT Template switch alignment (log-probability: -23.7) TcAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCA|CAGAACATGGGTGGGGATA|AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT TAAACAGGCAATGCTTTTATTATTCTTTTATCCCCACCCA|CAGAACATGGGTGGGGATA|AATGAATTAAGAAAGCTTCATGAACTTTTTACATATAAAT ========== Event 2419 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAGATAAATTAAGGAATTAGAAATTATAGAACAGAAATTCTGTTCTATAATTCTATTAATCCCTAATAGATA ↑ 1 43 2 Chimp: ATAGATAAATTAAGGAATTAG--------------GCATTCTGTTCTATAATTCTATTAATCCCTAATAGATA Gorilla: ATAGATAAATTAAGGAATTAG--------------GCATTCTGTTCTATAATTCTATTAATCCCTAATAGATA ↓ 1 43 2 Human: ATAGATAAATTAAGGAATTAGAAATTATAGAACAGAAATTCTGTTCTATAATTCTATTAATCCCTAATAGATA Cluster: [ ] Orangutan: ATAGGTAAATTAAGGAATTAG--------------GCATTCTGTTCTATAATTTTATTAATCCCTAATAGATA Chimp > Human ------------- chr3:143165996-143166010 Template switch process: F1: L TTCATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGA 1 F3: 4 ATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA R RF: TTCATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGGCATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA RR: AAGTAGGATACTTATAAATCTATCTATTTAATTCCTTAATCCGTAAGACAAGATATTAAGATAATTAGGGATTATCTATCCTT F2: 3 AAGACAAGATATTAA 2 Unidirectional alignment (log-probability: -43.1) CATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGaaAttatagaacagaaaTTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA CATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGGCA--------------TTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA Template switch alignment (log-probability: -23.2) CATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGa|AATTATAGAACAGAA|ATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA CATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGG|AATTATAGAACAGAA|ATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA Gorilla > Human --------------- chr3:143165996-143166010 Template switch process: F1: L TTCATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGA 1 F3: 4 ATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA R RF: TTCATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGGCATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA RR: AAGTAGGATACTTATAAATCTATCTATTTAATTCCTTAATCCGTAAGACAAGATATTAAGATAATTAGGGATTATCTATCCTT F2: 3 AAGACAAGATATTAA 2 Unidirectional alignment (log-probability: -42.1) CATCCTATGAATATTTAGATAGATAAATTAAGGAATTagaaattatagaacAGaaATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA CATCCTATGAATATTTAGATAGATAAATTAAGGAATT--------------AGGCATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA Template switch alignment (log-probability: -23.2) CATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGa|AATTATAGAACAGAA|ATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA CATCCTATGAATATTTAGATAGATAAATTAAGGAATTAGG|AATTATAGAACAGAA|ATTCTGTTCTATAATTCTATTAATCCCTAATAGATAGGAA ========== Event 2420 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: CTCAACTCACTTTTGATCGTT-AGAGGTTAGAACCTCTAACGTTTGATCGTTTCTTGGTTAAAACCAAGAAATAGGAGGACAG Chimp: CTCAACCCACTTTTGATCGTT-AGAGGTT-------------------------------CTAACCAAGAAATAGGAGGACAG Gorilla: CTCAACCCACTTTTGATCGTTAAGAGGTT-------------------------------CTAACCAAGAAATAGGAGGACAG ↑ 1 3 2 4 Human: CTCAACTCACTTTTGATCGTT-AGAGGTTAGAACCTCTAACGTTTGATCGTTTCTTGGTTAAAACCAAGAAATAGGAGGACAG Cluster: [ ] Orangutan: CTCAACTCACTTTTGATCATT-AGAGGTT-------------------------------CTAACCAAGAAATAGCAGGACAG Human > Gorilla --------------- chr3:144441366-144441374 Template switch process: F1: L GAACTAATCTCTTAAAGCTCCTCAACCCACTTTTGATCGTTA 1 F3: 4 AACCAAGAAATAGGAGGACAGAAAGCCAAGCAGTCCTTTC R RF: GAACTAATCTCTTAAAGCTCCTCAACTCACTTTTGATCGTTAGAGGTTAGAACCTCTAACGTTTGATCGTTTCTTGGTTAAAACCAAGAAATAGGAGGACAGAAAGCCAAGCAGTCCTTTC RR: CTTGATTAGAGAATTTCGAGGAGTTGAGTGAAAACTAGCAATCTCCAATCTTGGAGATTGCAAACTAGCAAAGAACCAATTTTGGTTCTTTATCCTCCTGTCTTTCGGTTCGTCAGGAAAG F2: 3 TCTTGGAGA 2 Unidirectional alignment (log-probability: -38.9) ACTAATCTCTTAAAGCTCCTCAACcCACTTTTGATCGTTA------AGA------------------------GGTTctAACCAAGAAATAGGAGGACAGAAAGCCAAGCAGTCCTTTC ACTAATCTCTTAAAGCTCCTCAACTCACTTTTGATCGTTAGAGGTTAGAACCTCTAACGTTTGATCGTTTCTTGGTTAAAACCAAGAAATAGGAGGACAGAAAGCCAAGCAGTCCTTTC Template switch alignment (log-probability: -22.4) ACTAATCTCTTAAAGCTCCTCAACcCACTTTTGATCGTTA|AGAGGTTCT|AACCAAGAAATAGGAGGACAGAAAGCCAAGCAGTCCTTTC ACTAATCTCTTAAAGCTCCTCAACTCACTTTTGATCGTTA|AGAGGTTCT|AACCAAGAAATAGGAGGACAGAAAGCCAAGCAGTCCTTTC ========== Event 2421 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: CTAGGAAAGTACTAAGAAAAATTTAAGACATATTCAAGAAACTTTATAGAA------CTAAGTGCAGGAATTACTAATTTGG ↓ 1 3 4 2 ↑ 13 24 Chimp: CTAGGAAAGTACTAAGAAAAACTTA------GTTCTATAAAGTTTCTTGAATATGTCTTAAGTGCAGGAATTACTAATTTGG ↓ 13 24 ↑ 1 3 4 2 Gorilla: CTAGGAAAGTACTAAGAAAAAGTTAAGACATATTCAAGAAACTTTATGGAA------CTAAGTGCAGGAATTACTAATTTGG Human: CTAGGAAAGTACTAAGAAAAATTTAAGACATATTCAAGAAACTTTATAGAA------CTAAGTGCAGGAATTACTAATTTGG Cluster: [ ] Orangutan: CTAGGAAAGTACTAAGCAAAATTTAAGACATATTCAAGAAACTTTGTAGAA------CTAAGTGCAGGAATTACTAATTTGG Chimp > Human ------------- chr3:141675911-141675937 Template switch process: F1: L CATTATAATAAGTATGTATCCTAGGAAAGTACTAAGAAAAATTTA 1 F3: 4 TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGA R RF: CATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAACTTAGTTCTATAAAGTTTCTTGAATATGTCTTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG RR: GTAATATTATTTATACATAGGATCCTTTCATGATTCTTTTTGAATCAAGATATTTCAAAGAACTTATACAGAATTCACGTCCTTAATGATTAAACCTTAAATTTCAACAACC F2: 3 CAAGATATTTCAAAGAACTTATACAGA 2 Unidirectional alignment (log-probability: -81.9) TAATAAgTATGTATCCTAGGAAAGTACTAAGAAAAAtttaagacatattcaagaaactttatagaaC------------------------------TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTga TAATAAATATGTATCCTAGGAAAGTACTAAGAAAAA------------------------------CTTAGTTCTATAAAGTTTCTTGAATATGTCTTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTT-- Template switch alignment (log-probability: -36.7) TAATAAgTATGTATCCTAGGAAAGTACTAAGAAAAAtTTA|AGACATATTCAAGAAACTTTATAGAAC|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGa TAATAAATATGTATCCTAGGAAAGTACTAAGAAAAACTTA|AGACATATTCAAGAAACTTTATAGAAC|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG Human > Chimp ------------- chr3:144864894-144864924 Template switch process: F1: L CATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAA 1 F3: 4 TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTT R RF: CATTATAATAAGTATGTATCCTAGGAAAGTACTAAGAAAAATTTAAGACATATTCAAGAAACTTTATAGAACTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTT RR: GTAATATTATTCATACATAGGATCCTTTCATGATTCTTTTTAAATTCTGTATAAGTTCTTTGAAATATCTTGATTCACGTCCTTAATGATTAAACCTTAAATTTCAACAA F2: 3 TCTGTATAAGTTCTTTGAAATATCTTGATTC 2 Unidirectional alignment (log-probability: -79.1) ATTATAATAAaTATGTATCCTAGGAAAGTACTAAGAAAAActtagttctataaagtttcttgaatatgtcT------------------------------TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTT-- ATTATAATAAGTATGTATCCTAGGAAAGTACTAAGAAAAA------------------------------TTTAAGACATATTCAAGAAACTTTATAGAACTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGA Template switch alignment (log-probability: -25.1) ATTATAATAAaTATGTATCCTAGGAAAGTACTAAGAAAAA|CTTAGTTCTATAAAGTTTCTTGAATATGTCT|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTT ATTATAATAAGTATGTATCCTAGGAAAGTACTAAGAAAAA|CTTAGTTCTATAAAGTTTCTTGAATATGTCT|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTT Gorilla > Chimp --------------- chr3:144864894-144864924 Template switch process: F1: L CATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAA 1 F3: 4 TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG R RF: CATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAAGTTAAGACATATTCAAGAAACTTTATGGAACTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG RR: GTAATATTATTTATACATAGGATCCTTTCATGATTCTTTTTCAATTCTGTATAAGTTCTTTGAAATACCTTGATTCACGTCCTTAATGATTAAACCTTAAATTTCAACAACC F2: 3 TCTGTATAAGTTCTTTGAAATATCTTGATTC 2 Unidirectional alignment (log-probability: -65.3) ATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAA------------------------------ACttagttctataaagtttcttgaatatgtctTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG ATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAAGTTAAGACATATTCAAGAAACTTTATGGAAC------------------------------TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG Template switch alignment (log-probability: -25.2) ATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAA|CTTAGTTCtATAAAGTTTCTTGAATATGTCT|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG ATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAA|CTTAGTTCCATAAAGTTTCTTGAATATGTCT|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG Chimp > Gorilla --------------- chr3:143675896-143675922 Template switch process: F1: L CATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAAGTTA 1 F3: 4 TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG R RF: CATTATAATAAATATGTATCCTAGGAAAGTACTAAGAAAAACTTAGTTCTATAAAGTTTCTTGAATATGTCTTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG RR: GTAATATTATTTATACATAGGATCCTTTCATGATTCTTTTTGAATCAAGATATTTCAAAGAACTTATACAGAATTCACGTCCTTAATGATTAAACCTTAAATTTCAACAACC F2: 3 CAAGGTATTTCAAAGAACTTATACAGA 2 Unidirectional alignment (log-probability: -65.3) TAATAAATATGTATCCTAGGAAAGTACTAAGAAAaagttaagacatattcaagaaactttatggAAC------------------------------TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG TAATAAATATGTATCCTAGGAAAGTACTAAGAAA------------------------------AACTTAGTTCTATAAAGTTTCTTGAATATGTCTTAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG Template switch alignment (log-probability: -30.3) TAATAAATATGTATCCTAGGAAAGTACTAAGAAAAAgTTA|AGACATATTCAAGAAACTTTATgGAAC|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG TAATAAATATGTATCCTAGGAAAGTACTAAGAAAAACTTA|AGACATATTCAAGAAACTTTATAGAAC|TAAGTGCAGGAATTACTAATTTGGAATTTAAAGTTGTTGG ========== Event 2422 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAAATGAGAAGGAGAGAATCCTAAAAGCAAGTTAAATATTGCTTTTAGATCAGCTAAGttttttt--- ↑ 1 4 3 2 Chimp: ATAAATGAGAAGGAGAGAATCTCAGGGTATAGTTAAATATTGCTTTTAGATCAGC-----------TAA Gorilla: ATAAATGAGAAGGAGAGAATCTCAGGGTATAGTTAAATATTGCTTTTAGATCAGCTAAGttt------- Human: ATAAATGAGAAGGAGAGAATCCTAAAAGCAAGTTAAATATTGCTTTTAGATCAGCTAAGttttttt--- Cluster: [ ] Orangutan: ATAAATG---AGGAGAGAATCTCAGGATATAGTTAAATATTGCTTTTAGATCAGCTAAGttt------- Chimp > Human ------------- chr3:141158858-141158866 Template switch process: F1: L TTTGCAGAGGTTTTTCATGGATAAATGAGAAGGAGAGAATC 1 F3: 4 AGTTAAATATTGCTTTTAGATCAGCTAAGTTTTTTT R RF: TTTGCAGAGGTTTTTCATGGATAAATGAGAAGGAGAGAATCTCAGGGTATAGTTAAATATTGCTTTTAGATCAGCTAAGTTTTGTT RR: AAACGTCTCCAAAAAGTACCTATTTACTCTTCCTCTCTTAGAGTCCCATATCAATTTATAACGAAAATCTAGTCGATTCAAAACAA F2: 3 ACGAAAATC 2 Unidirectional alignment (log-probability: -51.7) TTGCAGAGGTTTTTCATGGATAAATGAGAAGGAGAGAATCctaaaagca---------AGTTAAATATTGCTTTTAGATCAGCTAAGttttttt TTGCAGAGGTTTTTCATGGATAAATGAGAAGGAGAGAATC---------TCAGGGTATAGTTAAATATTGCTTTTAGATCAGCTAAG------- Template switch alignment (log-probability: -22.3) TTGCAGAGGTTTTTCATGGATAAATGAGAAGGAGAGAATC|CTAAAAGCA|AGTTAAATATTGCTTTTAGATCAGCTAAGTTTTtTT TTGCAGAGGTTTTTCATGGATAAATGAGAAGGAGAGAATC|CTAAAAGCA|AGTTAAATATTGCTTTTAGATCAGCTAAGTTTTGTT ========== Event 2423 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAGTAAAGGGCTTAGGTTGCATTGAGGCCTCTCAATGCATAATCACTGCTAAAGCAGGA Chimp: TAAGTAAAGGGCTTAGGTTGCATTGAGGCCTCT---GGAATAATCACTGCTAAAGCAGGA Gorilla: TAAATAAAGAGCTTAGGTTGCATTGAGGCCTCT---GGAATAATCACTGCTAAAGCAGGA ↓ 3 2 1 4 Human: TAAGTAAAGGGCTTAGGTTGCATTGAGGCCTCTCAATGCATAATCACTGCTAAAGCAGGA Cluster: [ ] Orangutan: TAAGTAAAGGGCTTAGGTTGCATTGAGGCCTCT---GGAATAATCACTGCTAAAGCAGGA Gorilla > Human --------------- chr3:141177134-141177139 Template switch process: F1: L AATCAATGTAAGTAAAGGGCTTAGGTTGCATTGAGGCCTCT 1 F3: 4 ATAATCACTGCTAAAGCAGGATTGTAAAAGTTGCGGTTAC R RF: AATCAATGTAAATAAAGAGCTTAGGTTGCATTGAGGCCTCTGGAATAATCACTGCTAAAGCAGGATTGTAAAAGTTGCGGTTAC RR: TTAGTTACATTTATTTCTCGAATCCAACGTAACTCCGGAGACCTTATTAGTGACGATTTCGTCCTAACATTTTCAACGCCAATG F2: 3 CGTAAC 2 Unidirectional alignment (log-probability: -37.3) ATCAATGTAAgTAAAGgGCTTAGGTTGCATTGAGGCCTCTcaatGcATAATCACTGCTAAAGCAGGATTGTAAAAGTTGCGGTTAC ATCAATGTAAATAAAGAGCTTAGGTTGCATTGAGGCCTCTG---GAATAATCACTGCTAAAGCAGGATTGTAAAAGTTGCGGTTAC Template switch alignment (log-probability: -27.5) ATCAATGTAAgTAAAGgGCTTAGGTTGCATTGAGGCCTCT|CAATGC|ATAATCACTGCTAAAGCAGGATTGTAAAAGTTGCGGTTAC ATCAATGTAAATAAAGAGCTTAGGTTGCATTGAGGCCTCT|CAATGC|ATAATCACTGCTAAAGCAGGATTGTAAAAGTTGCGGTTAC ========== Event 2424 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTTAAAATAATTCAGGCAAATGTGACAGCACATTAATT--------------ATGTGCTGTCACATTTGTCACTACTGTAGTTTTTTA Chimp: ACTTAAAATAATTCAGGCAAATGTGACAGCACATTAATT--------------ATGTGCTGTCACATTTGTCACTACTGTAGTTTTTTA ↑ 3 1 2 4 Gorilla: ACTTAAAATAATTCAGGCAAATGTGACAGCACATAATTA----------------------------ATGTCACTACTGTAGTTTTTTA ↓ 3 1 2 4 Human: ACTTAAAATAATTCAGGCAAATGTGACAGCACATTAATT--------------ATGTGCTGTCACATTTGTCACTACTGTAGTTTTTTA Cluster: [ ] Orangutan: ACTTAAAATAATTCAGGCAAATGTGACAGCACATTGATTATGTGCTGTCACAT--------------TGGTCACTATTGTAGTTTTTTA Gorilla > Human --------------- chr3:140503169-140503188 Template switch process: F1: L TCCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACAT 1 F3: 4 TGTCACTACTGTAGTTTTTTAACTATGTTTTTATTTAAAA R RF: TCCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACATAATTAATGTCACTACTGTAGTTTTTTAACTATGTTTTTTTTTAAAT RR: AGGGGATTGAATTTTATTAAGTCCGTTTACACTGTCGTGTATTAATTACAGTGATGACATCAAAAAATTGATACAAAAAAAAATTTA F2: 3 TTACACTGTCGTGTATTAAT 2 Unidirectional alignment (log-probability: -58.9) CCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCAC---ATTAAttatgtgctgtcacattTGTCACTACTGTAGTTTTTTAACTATGTTTTTaTTTAAAa CCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACATAATTAA-----------------TGTCACTACTGTAGTTTTTTAACTATGTTTTTTTTTAAA- Template switch alignment (log-probability: -29.3) CCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACAT|TAATTATGTGCTGTCACATT|TGTCACTACTGTAGTTTTTTAACTATGTTTTTaTTTAAAa CCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACAT|TAATTATGTGCTGTCACATT|TGTCACTACTGTAGTTTTTTAACTATGTTTTTTTTTAAAT Gorilla > Chimp --------------- chr3:143641665-143641684 Template switch process: F1: L TCCCCTGACTTAAAATAATTCAGGCAAATGTGACAGCACAT 1 F3: 4 TGTCACTACTGTAGTTTTTTAACTATGTTTTTCTTTAAAA R RF: TCCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACATAATTAATGTCACTACTGTAGTTTTTTAACTATGTTTTTTTTTAAAT RR: AGGGGATTGAATTTTATTAAGTCCGTTTACACTGTCGTGTATTAATTACAGTGATGACATCAAAAAATTGATACAAAAAAAAATTTA F2: 3 TTACACTGTCGTGTATTAAT 2 Unidirectional alignment (log-probability: -64.5) CCCCTgACTTAAAATAATTCAGGCAAATGTGACAGCAC---ATTAAttatgtgctgtcacattTGTCACTACTGTAGTTTTTTAACTATGTTTTTcTTTAAAa CCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACATAATTAA-----------------TGTCACTACTGTAGTTTTTTAACTATGTTTTTTTTTAAA- Template switch alignment (log-probability: -34.8) CCCCTgACTTAAAATAATTCAGGCAAATGTGACAGCACAT|TAATTATGTGCTGTCACATT|TGTCACTACTGTAGTTTTTTAACTATGTTTTTcTTTAAAa CCCCTAACTTAAAATAATTCAGGCAAATGTGACAGCACAT|TAATTATGTGCTGTCACATT|TGTCACTACTGTAGTTTTTTAACTATGTTTTTTTTTAAAT ========== Event 2425 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGACACAGTTTGGAATCCCTCCTG--------------------------GTTCACCTGCAGCCCAGGATCCCACCTCTTTGCGAAGACTTTGAAAGTTTCAGAAG Chimp: TGACACAGTTTGGAATCCCTCCTG--------------------------GTTCACCTGCAGCCCAGGATCCCACCTCTTTGCGAAGACTTTGAAAGTTTCAGAAG ↓ 1 3 4 2 Gorilla: TGACACAGTTTGGAATCCCTCTTC----------------------------------------------------GCAAAGAGAAGACTTTGAAAGTTTCAGAAG ↑ 1 3 4 2 Human: TGACACAGTTTGGAATCCCTCCTG--------------------------GTTCACCTGCAGCCCAGGATCCCACCTCTTTGCGAAGACTTTGAAAGTTTCAGAAG Cluster: [ ] Orangutan: TGACACAGTTTGGAATCCCTCCTGGTTCCCCTGCAGCCCAGGATCCCACC--------------------------TCTTTGCGAAGACTTTGAAAGTTTCAGAAA Human > Gorilla --------------- chr3:60168368-60168377 Template switch process: F1: L TGCTGAGACTGAGGCATCACTGACACAGTTTGGAATCCCTC 1 F3: 4 GAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT R RF: TGCTGAGATTGAGGCATCACTGACACAGTTTGGAATCCCTCCTGGTTCACCTGCAGCCCAGGATCCCACCTCTTTGCGAAGACTTTGAAAGTTTCAGAAGTGAATTCTCATTCTAGT RR: ACGACTCTAACTCCGTAGTGACTGTGTCAAACCTTAGGGAGGACCAAGTGGACGTCGGGTCCTAGGGTGGAGAAACGCTTCTGAAACTTTCAAAGTCTTCACTTAAGAGTAAGATCA F2: 3 AGAAACGCTT 2 Unidirectional alignment (log-probability: -46) GCTGAGAcTGAGGCATCACTGACACAGTTTGGAATC-------------------------------CCTCTTcGCaaagaGAAGACTTTGAAAGTTTCAGAAGcGAATTCTCATTCTAGT GCTGAGATTGAGGCATCACTGACACAGTTTGGAATCCCTCCTGGTTCACCTGCAGCCCAGGATCCCACCTCTTTGC-----GAAGACTTTGAAAGTTTCAGAAGTGAATTCTCATTCTAGT Template switch alignment (log-probability: -28) GCTGAGAcTGAGGCATCACTGACACAGTTTGGAATCCCTC|TTCGCAAAGA|GAAGACTTTGAAAGTTTCAGAAGcGAATTCTCATTCTAGT GCTGAGATTGAGGCATCACTGACACAGTTTGGAATCCCTC|TTCGCAAAGA|GAAGACTTTGAAAGTTTCAGAAGTGAATTCTCATTCTAGT Chimp > Gorilla --------------- chr3:60168368-60168377 Template switch process: F1: L TGCTGAGACTGAGGCATCACTGACACAGTTTGGAATCCCTC 1 F3: 4 GAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT R RF: TGCTGAGATTGAGGCATCACTGACACAGTTTGGAATCCCTCCTGGTTCACCTGCAGCCCAGGATCCCACCTCTTTGCGAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT RR: ACGACTCTAACTCCGTAGTGACTGTGTCAAACCTTAGGGAGGACCAAGTGGACGTCGGGTCCTAGGGTGGAGAAACGCTTCTGAAACTTTCAAAGTCTTCGCTTAAGAGTAAGATCA F2: 3 AGAAACGCTT 2 Unidirectional alignment (log-probability: -40.5) GCTGAGAcTGAGGCATCACTGACACAGTTTGGAATC-------------------------------CCTCTTcGCaaagaGAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT GCTGAGATTGAGGCATCACTGACACAGTTTGGAATCCCTCCTGGTTCACCTGCAGCCCAGGATCCCACCTCTTTGC-----GAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT Template switch alignment (log-probability: -22.5) GCTGAGAcTGAGGCATCACTGACACAGTTTGGAATCCCTC|TTCGCAAAGA|GAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT GCTGAGATTGAGGCATCACTGACACAGTTTGGAATCCCTC|TTCGCAAAGA|GAAGACTTTGAAAGTTTCAGAAGCGAATTCTCATTCTAGT ========== Event 2426 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ACAAACTGCCTATTGCTAGTC--CCCATACTGTCAAGTCCTTGCCAGTATGTGTTTATCCTCTTCAGCTA ↑ 1 4 3 2 Chimp: ACAAACTGCCTATTGCTAGTC-CCCCAGA--CCCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTA ↓ 1 4 3 2 Gorilla: ACAAACTGCCTATTGCTAGTC--CCCATACTGTCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTA Human: ACAAACTGCCTATTGCTAGTC--CCCATACTGTCAAGTCCTTGCCAGTATGTGTTTATCCTCTTCAGCTA Cluster: [ ] Orangutan: ACAAGCTGCCTTGTGCTAGTCT-CCCAGA--CCCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTA Chimp > Human ------------- chr3:138842609-138842615 Template switch process: F1: L CCAAACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC 1 F3: 4 CAAGTCCTTGCCAGTATGTGTTTATCCTCTTCAGCTACAG R RF: CCAAACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCCCAGACCCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG RR: GGTTTGGTAAAAACGTAAACTGTTTGACGGATAACGATCAGGGGGTCTGGGTTCAGGAACTGTCATACACAAATAGGAGAAGTCGATGTC F2: 3 TGTCATA 2 Unidirectional alignment (log-probability: -37.5) ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCCatactgt------CAAGTCCTTGcCAGTATGTGTTTATCCTCTTCAGCTACAG ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC-------CAGACCCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG Template switch alignment (log-probability: -22.2) ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC|ATACTGT|CAAGTCCTTGcCAGTATGTGTTTATCCTCTTCAGCTACAG ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC|ATACTGT|CAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG Chimp > Gorilla --------------- chr3:140855359-140855365 Template switch process: F1: L CCAAACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC 1 F3: 4 CAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG R RF: CCAAACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCCCAGACCCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG RR: GGTTTGGTAAAAACGTAAACTGTTTGACGGATAACGATCAGGGGGTCTGGGTTCAGGAACTGTCATACACAAATAGGAGAAGTCGATGTC F2: 3 TGTCATA 2 Unidirectional alignment (log-probability: -31) ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCC------CatactgtCAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCCCAGACC-------CAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG Template switch alignment (log-probability: -16.7) ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC|ATACTGT|CAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG ACCATTTTTGCATTTGACAAACTGCCTATTGCTAGTCCCC|ATACTGT|CAAGTCCTTGACAGTATGTGTTTATCCTCTTCAGCTACAG ========== Event 2427 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAGTTAGTAGACACAGCACCATTGTCTGATCTACATGGTATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTA-------------------------------------------------------------------------------------------------------------------TTTAAATGTG-AGGAAATACAG-GTAA ↓ 3 4 2 1 Chimp: ACAGTTAGTAGACACAGCACCATTGTCTCATCTACATGGTATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTA-----------------------------------TTTAAATATTTGCTGAATATACCATGAAGATGAGACAATGGATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAATGTG-AGGAAATACAG-GTAA ↑ 3 4 2 1 Gorilla: ACAGTTAGCAGACACAGCACCATTGTCTCATCTACATGGTATATTCAGCAAATACTCAACTAGAAATTTATCCACTCTA-------------------------------------------------------------------------------------------------------------------TTTAAATGTG-AGGAAATACAG-GTAA Human: ACAGTTAGTAGACACAGCACCATTGTCTGATCTACATGGTATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTA-------------------------------------------------------------------------------------------------------------------TTTAAATGTG-AGGAAATACAG-GTAA Cluster: [ ] Orangutan: ACAGTTAGTAGAGACAGCACCATTGTCTCATCTACATTGGCTA-----------------------------TAT----TCAGCAAATATTCAACTAGAAATTTATCCACTCTA--------------------------------------------------------------------------------TTTAAATGTGAAGGAAATACAGGTTAA Human > Chimp ------------- chr3:141924975-141925008 Template switch process: F1: L GTATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAAT 1 F3: 4 ATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAATGTGAGGAAATACAGGTAATTAAGCAAGGCTCAG R RF: CCATTGTCTGATCTACATGGTATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAATGTGAGGAAATACAGGTAATTAAGCAAGGCTCGG RR: GGTAACAGACTAGATGTACCATATAAGTCGTTTATAAGTTGATCTTTAAATAGGTGAGATAAATTTACACTCCTTTATGTCCATTAATTCGTTCCGAGCC F2: 3 GGTAACAGAGTAGAAGTACCATATAAGTCGTTTA 2 Unidirectional alignment (log-probability: -132) agcaaatattcaactagaaatttatccactctatttaaatatttgctgaatataccatgaagatgagacaatggATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTAT --------------------------------------------------------------------------ATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTAT Template switch alignment (log-probability: -38.2) AGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAAT|ATTTGCTGAATATACCATGaAGATgAGACAATGG|ATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTAT AGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAAT|ATTTGCTGAATATACCATGTAGATCAGACAATGG|ATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTAT Gorilla > Chimp --------------- chr3:141924975-141925008 Template switch process: F1: L GTATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAAT 1 F3: 4 ATATTCAGCAAATATTCAACTAGAAATTTATCCACTCTATTTAAATGTGAGGAAATACAGGTAATTAAGCAAGGCTCAG R RF: CCATTGTCTCATCTACATGGTATATTCAGCAAATACTCAACTAGAAATTTATCCACTCTATTTAAATGTGAGGAAATACAGGTAATTAAGCAAGGCTCGG RR: GGTAACAGAGTAGATGTACCATATAAGTCGTTTATGAGTTGATCTTTAAATAGGTGAGATAAATTTACACTCCTTTATGTCCATTAATTCGTTCCGAGCC F2: 3 GGTAACAGAGTAGAAGTACCATATAAGTCGTTTA 2 Unidirectional alignment (log-probability: -137) AGCAAATAtTCAACTAGAAATTTATCCACTCTATTTAAAtatttgctgaatataccatgaagatgagacaatggatattcagcaaatattcaactagaaatttatccactctat AGCAAATACTCAACTAGAAATTTATCCACTCTATTTAAA--------------------------------------------------------------------------- Template switch alignment (log-probability: -43.1) AGCAAATAtTCAACTAGAAATTTATCCACTCTATTTAAAT|ATTTGCTGAATATACCATGaAGATGAGACAATGG|ATATTCAGCAAATAtTCAACTAGAAATTTATCCACTCTAT AGCAAATACTCAACTAGAAATTTATCCACTCTATTTAAAT|ATTTGCTGAATATACCATGTAGATGAGACAATGG|ATATTCAGCAAATACTCAACTAGAAATTTATCCACTCTAT ========== Event 2428 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGGAAGAGTTGGTATTCAACTGGGAGGGATTTTATCAGTAGAGGAGCTGAGATTGAGAATGGGGTTGAGGAAGAGATAAGTCAGGAGCAAAAATA Chimp: TCATGGAAGAGTTGGTATTCAACTGGAAGAG-----------------------------------------------ATAAGTCAGGAGCAAAAATA ↑ 1 3 2 4 Gorilla: TCATGGAAGAGTTGGTATTCACCTGGGAGGGATTTTATCAGTAGAGGAGCTGAGATTGAGAATGGGGTTGAGGAAGAGATAAGTCAGGAGCAAAAATA Human: TCATGGAAGAGTTGGTATTCAACTGGGAGGGATTTTATCAGTAGAGGAGCTGAGATTGAGAATGGGGTTGAGGAAGAGATAAGTCAGGAGCAAAAATA Cluster: [ ] Orangutan: TCATGGAAGAGTTGGCATTCAACTGGGAGGGATTTTATCAGTAGAGGAGCTGAGATTGAGAATGGGGTTGAGGAAGAGAGAAGTCAGGAGCAAAAATA Gorilla > Chimp --------------- chr3:141442491-141442494 Template switch process: F1: L ACACCCTGTCTAGCTGAGGTTCATGGAAGAGTTGGTATTCA 1 F3: 4 GAAGAGATAAGTCAGGAGCAAAAATACGGAAGTGAGGGAGC R RF: ACACCCTGTCTAGCTGAGGTTCATGGAAGAGTTGGTATTCACCTGGGAGGGATTTTATCAGTAGAGGAGCTGAGATTGAGAATGGGGTTGAGGAAGAGATAAGTCAGGAGCAAAAATACGGAAGTGAGGTAGC RR: TGTGGGACAGATCGACTCCAAGTACCTTCTCAACCATAAGTGGACCCTCCCTAAAATAGTCATCTCCTCGACTCTAACTCTTACCCCAACTCCTTCTCTATTCAGTCCTCGTTTTTATGCCTTCACTCCATCG F2: 3 GTCA 2 Unidirectional alignment (log-probability: -31.4) CACCCTGTCTAGCTGAGGTTCATGGAAGAGTTGGTATTCAaCT-----------------------------------------------GGAAGAGATAAGTCAGGAGCAAAAATACGGAAGTGAGGgAG CACCCTGTCTAGCTGAGGTTCATGGAAGAGTTGGTATTCACCTGGGAGGGATTTTATCAGTAGAGGAGCTGAGATTGAGAATGGGGTTGAGGAAGAGATAAGTCAGGAGCAAAAATACGGAAGTGAGGTAG Template switch alignment (log-probability: -21.8) CACCCTGTCTAGCTGAGGTTCATGGAAGAGTTGGTATTCA|ACTG|GAAGAGATAAGTCAGGAGCAAAAATACGGAAGTGAGGgAG CACCCTGTCTAGCTGAGGTTCATGGAAGAGTTGGTATTCA|ACTG|GAAGAGATAAGTCAGGAGCAAAAATACGGAAGTGAGGTAG ========== Event 2429 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GATCTTCTCTTTCCTCTGTGTCTTTCACTTTCTTTAGTGACAGACATCTGCTCAAATCCTCCTTTTTTCCTCT Chimp: GATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGTGATAGACATCTGCTGAAATCCTCCTTTTTTCCTCT ↑ 3 2 1 4 Gorilla: GATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAG-TACAAAAATCTGCTCAAATCCTCCTTTTTTCCTCT Human: GATCTTCTCTTTCCTCTGTGTCTTTCACTTTCTTTAGTGACAGACATCTGCTCAAATCCTCCTTTTTTCCTCT Cluster: [ ] Orangutan: GATCTTCTCCTTCCTCTGTGTCTATCACTTTCTTCAA-TACAAAAATCTGCTCAAATCCTCCTTTTTTCTTCT Gorilla > Chimp --------------- chr3:140654949-140654955 Template switch process: F1: L CATAGATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGT 1 F3: 4 ATCTGCTGAAATCCTCCTTTTTTCCTCTCCGGCTGCTTCTTCATCAAT R RF: CGTAGATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGTACAAAAATCTGCTCAAATCCTCCTTTTTTCCTCTCCGGCTGCTTCTTCATCAAT RR: GCATCTAGAAGAGAAAGGAGACACAGATAGTGAAAGAAGTCATGTTTTTAGACGAGTTTAGGAGGAAAAAAGGAGAGGCCGACGAAGAAGTAGTTA F2: 3 CAGATAG 2 Unidirectional alignment (log-probability: -39.2) TAGATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGTgatagAC----ATCTGCTgAAATCCTCCTTTTTTCCTCTCCGGCTGCTTCT TAGATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGT-----ACAAAAATCTGCTCAAATCCTCCTTTTTTCCTCTCCGGCTGCTTCT Template switch alignment (log-probability: -27.9) TAGATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGT|GATAGAC|ATCTGCTgAAATCCTCCTTTTTTCCTCTCCGGCTGCTTCT TAGATCTTCTCTTTCCTCTGTGTCTATCACTTTCTTCAGT|GATAGAC|ATCTGCTCAAATCCTCCTTTTTTCCTCTCCGGCTGCTTCT ========== Event 2430 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CACATGCCTGAAATGACAATGTAGCACAtggaatggacctctgctg ↑ 3 4 Chimp: CACATGCCTGAAATGACAATG--CTACATGGAATGGACCTCTGCTG Gorilla: CACATGGCTGAAATGACAATG--CTACAtggaatggacctctgctg Human: CACATGCCTGAAATGACAATGTAGCACAtggaatggacctctgctg Cluster: [ ] Orangutan: CACACGCCTGAAATGACAATG--CTACATGGAATGGACCTCTGCTG Chimp > Human ------------- chr3:60169960-60169963 Template switch process: F1: L AAGAAAAAGAGGAAGTACTACACATGCCTGAAATGACAATG 1 F3: 4 ACATGGAATGGACCTCTGCTGTTTTCGATGATCCAGCATT R RF: AAGAAAAAGAGGAAGTACTACACATGCCTGAAATGACAATGCTACATGGAATGGACCTCTGCTGTTTTCGATGATCCAGCATT RR: TTCTTTTTCTCCTTCATGATGTGTACGGACTTTACTGTTACGATGTACCTTACCTGGAGACGACAAAAGCTACTAGGTCGTAA F2: 3 CGAT 2 Unidirectional alignment (log-probability: -25.5) AGAAAAAGAGGAAGTACTACACATGCCTGAAATGACAATgtaGC-ACATGGAATGGACCTCTGCTGTTTTCGATGATCCAGCATT AGAAAAAGAGGAAGTACTACACATGCCTGAAATGACAAT---GCTACATGGAATGGACCTCTGCTGTTTTCGATGATCCAGCATT Template switch alignment (log-probability: -15.8) AGAAAAAGAGGAAGTACTACACATGCCTGAAATGACAATG|TAGC|ACATGGAATGGACCTCTGCTGTTTTCGATGATCCAGCATT AGAAAAAGAGGAAGTACTACACATGCCTGAAATGACAATG|TAGC|ACATGGAATGGACCTCTGCTGTTTTCGATGATCCAGCATT ========== Event 2431 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGTTTGTTTGGCTTTCTAGCAGACTCTTTGTTAAAAAGGACAGATCAAGAGtttgtttgtttgttgtttgagatggagtctcgctcttgttgcccaggctg Chimp: AGGTTTGTTTGGCTTTCTAGCAGACTCTTTGTTAAAAAGGACAGATCAAGAGtttgtttgtttgttgtttgagatggagtctcgctcttgttgcccaggctg ↑ 1 4 3 2 Gorilla: AGGTTTGTTTGGCTTTCTAGCCA-AACTTTGTTAAAAAGGACAGATCAAGAgtttgtttgtttgttttttgagatggagtctcgctcttgtcgcccaggctg ↓ 1 4 3 2 Human: AGGTTTGTTTGGCTTTCTAGCAGACTCTTTGTTAAAAAGGACAGATCAAGAGtttgtttgtttgttgtttgagatggagtctcgctcttgttgcccaggctg Cluster: [ ] Orangutan: AGGTTTGTTTGGCGTTCTAGCAGACCCTTTGTTAAAAAGGACAGATCAAGAGtttgtttgtttgttttttgagatggagtttcgctcttgttgtccaggctg Gorilla > Human --------------- chr3:61541354-61541358 Template switch process: F1: L GAGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC 1 F3: 4 CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT R RF: GAGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGCCAAACTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTTTTTTGAGATGGAGTCT RR: CTCCGATCTAGTAAAGGTTCTCCAAACAAACCGAAAGATCGGTTTGAAACAATTTTTCCTGTCTAGTTCTCAAACAAACAAACAAAAAACTCTACCTCAGA F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -26.5) AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC---AgactCTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGCCAAA----CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT Template switch alignment (log-probability: -16.4) AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC|AGACT|CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC|AGACT|CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT Gorilla > Chimp --------------- chr3:62761313-62761317 Template switch process: F1: L GAGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC 1 F3: 4 CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT R RF: GAGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGCCAAACTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTTTTTTGAGATGGAGTCT RR: CTCCGATCTAGTAAAGGTTCTCCAAACAAACCGAAAGATCGGTTTGAAACAATTTTTCCTGTCTAGTTCTCAAACAAACAAACAAAAAACTCTACCTCAGA F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -26.5) AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC---AgactCTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGCCAAA----CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT Template switch alignment (log-probability: -16.4) AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC|AGACT|CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT AGGCTAGATCATTTCCAAGAGGTTTGTTTGGCTTTCTAGC|AGACT|CTTTGTTAAAAAGGACAGATCAAGAGTTTGTTTGTTTGTT ========== Event 2432 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAGAAAAAAGGGGAGATTCTTAAGTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCAGTAC------------------- Chimp: AAGAAAAAAGGGGAGATTCTTAAGTTTAACCATTTCACTAGAACAGATTAAacaaatgttaaattcttccccacctaaacaaaatcagtacaaatgttaaattcttcccc ↓ 3 1 2 4 ↑ 13 24 Gorilla: AAGAAAAAAGGGGAGATTCTTAATCTGTTCTAGTGAAATGGTTAAACTTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCAGGAC------------------- ↓ 13 24 ↑ 13 24 Human: AAGAAAAAAGGGGAGATTCTTAAGTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCAGTAC------------------- Cluster: [ ] Orangutan: AAGAAAAAAGGGGAGATTCTTAAGTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCAGTAC------------------- Gorilla > Human --------------- chr3:62287198-62287221 Template switch process: F1: L GATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA 1 F3: 4 TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA R RF: GCTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAATCTGTTCTAGTGAAATGGTTAAACTTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA RR: CGATCGAAACTTTCTCGATTCTTTTTTCCCCTCTAAGAATTAGACAAGATCACTTTACCAATTTGAATTTGTTTACAATTTAAGAAGGGGAGGATTTGTTTTAGT F2: 3 AGACAAGATCACTTTACCAATTTG 2 Unidirectional alignment (log-probability: -57.1) aTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA-----------------GTTtAACcatttcactagaacagaTTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA CTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAATCTGTTCTAGTGAAATGGTTAAAC-----------------TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA Template switch alignment (log-probability: -24.3) aTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|GTTTAACCATTTCACTAGAACAGA|TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA CTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|GTTTAACCATTTCACTAGAACAGA|TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA Human > Gorilla --------------- chr3:63343515-63343538 Template switch process: F1: L GCTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA 1 F3: 4 TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA R RF: GATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAAGTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA RR: CTATCGAAACTTTCTCGATTCTTTTTTCCCCTCTAAGAATTCAAATTGGTAAAGTGATCTTGTCTAATTTGTTTACAATTTAAGAAGGGGAGGATTTGTTTTAGT F2: 3 CAAATTGGTAAAGTGATCTTGTCT 2 Unidirectional alignment (log-probability: -57.1) cTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAAtctgttctagtgaaatgGTTaAAC-----------------TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA ATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA-----------------GTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA Template switch alignment (log-probability: -24.3) cTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|TCTGTTCTAGTGAAATGGTTAAAC|TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA ATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|TCTGTTCTAGTGAAATGGTTAAAC|TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA Gorilla > Chimp --------------- chr3:63508170-63508193 Template switch process: F1: L GATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA 1 F3: 4 TTAAACAAATGTTAAATTCTTCCCCACCTAAACAAAATCA R RF: GCTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAATCTGTTCTAGTGAAATGGTTAAACTTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA RR: CGATCGAAACTTTCTCGATTCTTTTTTCCCCTCTAAGAATTAGACAAGATCACTTTACCAATTTGAATTTGTTTACAATTTAAGAAGGGGAGGATTTGTTTTAGT F2: 3 AGACAAGATCACTTTACCAATTTG 2 Unidirectional alignment (log-probability: -62.6) aTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA-----------------GTTtAACcatttcactagaacagaTTAAACAAATGTTAAATTCTTCCCCaCCTAAACAAAATCA CTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAATCTGTTCTAGTGAAATGGTTAAAC-----------------TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA Template switch alignment (log-probability: -29.8) aTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|GTTTAACCATTTCACTAGAACAGA|TTAAACAAATGTTAAATTCTTCCCCaCCTAAACAAAATCA CTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|GTTTAACCATTTCACTAGAACAGA|TTAAACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA Chimp > Gorilla --------------- chr3:63343515-63343542 Template switch process: F1: L GCTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA 1 F3: 4 ACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA R RF: GATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAAGTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCACCTAAACAAAATCAGTACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA RR: CTATCGAAACTTTCTCGATTCTTTTTTCCCCTCTAAGAATTCAAATTGGTAAAGTGATCTTGTCTAATTTGTTTACAATTTAAGAAGGGGTGGATTTGTTTTAGTCATGTTTACAATTTAAGAAGGGGAGGATTTGTTTTAGT F2: 3 AATTCAAATTGGTAAAGTGATCTTGTCT 2 Unidirectional alignment (log-probability: -62.6) cTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAAtctgttctagtgaaatgGTTaAAC-----------------TTAAACAAATGTTAAATTCTTCCCCtCCTAAACAAAATCA ATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA-----------------GTTTAACCATTTCACTAGAACAGATTAAACAAATGTTAAATTCTTCCCCACCTAAACAAAATCA Template switch alignment (log-probability: -24.7) cTAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|TCTGTTCTAGTGAAATGGTTAAACTTAA|ACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA ATAGCTTTGAAAGAGCTAAGAAAAAAGGGGAGATTCTTAA|TCTGTTCTAGTGAAATGGTTAAACTTAA|ACAAATGTTAAATTCTTCCCCTCCTAAACAAAATCA ========== Event 2433 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA----------------------------------------------------------------------------------CATTAGAAGAATACTCTTCCCTTCCACTT ↑ 3 2 1 4 Chimp: GACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA-----------------------------------------TTCGGGGAGCCAGAATCTCCATTAGGTCAATTCTGGGGTCCTAACAAGGGAATACTCTTCCCTTCCACTT Gorilla: GACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCATTCGGGGAGCCAGAATCTCCATTAGGTCAATTCTGGGGTCC-----------------------------------------TAACAAGGGAATACTCTTCCCTTCCACTT ↓ 3 2 1 4 Human: GACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA----------------------------------------------------------------------------------CATTAGAAGAATACTCTTCCCTTCCACTT Cluster: [ ] Orangutan: GACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCATTCAGGGAGCCAGAATCTCCATTAGGTCAATTCTGAGGTCC-----------------------------------------TAACAAGGGAATACTCTTCCCTTCCACTT Chimp > Human ------------- chr3:62714379-62714386 Template switch process: F1: L TGTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA 1 F3: 4 GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT R RF: TGTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCATTCGGGGAGCCAGAATCTCCATTAGGTCAATTCTGGGGTCCTAACAAGGGAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT RR: ACACTGACCCATGACATGTACAAAGATTACACCTCTCTAGTAAGCCCCTCGGTCTTAGAGGTAATCCAGTTAAGACCCCAGGATTGTTCCCTTATGAGAAGGGAAGGTGAATGACAAAACCTTGACGACA F2: 3 AAGATTAC 2 Unidirectional alignment (log-probability: -33.5) GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA-------------------CATTAG--------------------AA--GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCATTCGGGGAGCCAGAATCTCCATTAGGTCAATTCTGGGGTCCTAACAAGGGAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT Template switch alignment (log-probability: -16.3) GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA|CATTAGAA|GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA|CATTAGAA|GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT Gorilla > Human --------------- chr3:62714379-62714386 Template switch process: F1: L TGTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA 1 F3: 4 GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT R RF: TGTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCATTCGGGGAGCCAGAATCTCCATTAGGTCAATTCTGGGGTCCTAACAAGGGAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT RR: ACACTGACCCATGACATGTACAAAGATTACACCTCTCTAGTAAGCCCCTCGGTCTTAGAGGTAATCCAGTTAAGACCCCAGGATTGTTCCCTTATGAGAAGGGAAGGTGAATGACAAAACCTTGACGACA F2: 3 AAGATTAC 2 Unidirectional alignment (log-probability: -32.6) GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA-------------------CATTAG--------------------AA--GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCATTCGGGGAGCCAGAATCTCCATTAGGTCAATTCTGGGGTCCTAACAAGGGAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT Template switch alignment (log-probability: -16.7) GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA|CATTAGAA|GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT GTGACTGGGTACTGTACATGTTTCTAATGTGGAGAGATCA|CATTAGAA|GAATACTCTTCCCTTCCACTTACTGTTTTGGAACTGCTGT ========== Event 2434 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGCGGGGAGTTGCACACATACAGT-TCTGTAAGAACTGTACCAGGAAGGCATTAAAGAATT ↑ 3 2 1 4 Chimp: CAGCGGGGAGTTGCACACATACAGT-TCTGTAAGAG---CCCCAGGAAGGCATTAAAGAATT Gorilla: CAGCGGAGAGTTGCACACATACAGT-TCTGTAAGAG---CCCCAGGAAGGCATTAAAGAATT ↓ 3 2 1 4 Human: CAGCGGGGAGTTGCACACATACAGT-TCTGTAAGAACTGTACCAGGAAGGCATTAAAGAATT Cluster: [ ] Orangutan: CAGCGGGGAGTTGCACACATACAGTTACTGTAAGAG---CCCCAGGAAGGCATTAAAGAATT Chimp > Human ------------- chr3:63995322-63995327 Template switch process: F1: L GCAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGA 1 F3: 4 CCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG R RF: GCAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGAGCCCCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG RR: CGTTATCGTCGCCCCTCAACGTGTGTATGTCAAGACATTCTCGGGGTCCTTCCGTAATTTCTTAAACTTCCTCTCTCCACTGTC F2: 3 ATGTCA 2 Unidirectional alignment (log-probability: -27.2) CAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGAactGtaCCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG CAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGA---GCCCCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG Template switch alignment (log-probability: -16) CAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGA|ACTGTA|CCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG CAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGA|ACTGTA|CCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG Gorilla > Human --------------- chr3:63995322-63995327 Template switch process: F1: L GCAATAGCAGCGGGGAGTTGCACACATACAGTTCTGTAAGA 1 F3: 4 CCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG R RF: GCAATAGCAGCGGAGAGTTGCACACATACAGTTCTGTAAGAGCCCCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG RR: CGTTATCGTCGCCTCTCAACGTGTGTATGTCAAGACATTCTCGGGGTCCTTCCGTAATTTCTTAAACTTCCTCTCTCCACTGTC F2: 3 ATGTCA 2 Unidirectional alignment (log-probability: -31.8) CAATAGCAGCGGgGAGTTGCACACATACAGTTCTGTAAGAactGtaCCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG CAATAGCAGCGGAGAGTTGCACACATACAGTTCTGTAAGA---GCCCCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG Template switch alignment (log-probability: -22) CAATAGCAGCGGgGAGTTGCACACATACAGTTCTGTAAGA|ACTGTA|CCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG CAATAGCAGCGGAGAGTTGCACACATACAGTTCTGTAAGA|ACTGTA|CCAGGAAGGCATTAAAGAATTTGAAGGAGAGAGGTGACAG ========== Event 2435 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTATAATCTAAGCATAATATGTTAATTTAGCTAATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGTAAAAGCAATA ↑ 1 4 3 2 Chimp: CCTATAATCTAAGCATAATATATTAATT-A--GAATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGTAAAAGCAATA Gorilla: TCTATAATCTAAGCATAATATATTAATT-A--GAATGCAGTTAACTAAAGACATCGCTAGCTAATAAACATGTAAAAGCAATA Human: CCTATAATCTAAGCATAATATGTTAATTTAGCTAATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGTAAAAGCAATA Cluster: [ ] Orangutan: GCTATAATCTAAGCATAATATATTAATT-A--GAATGCAATTAACTAAAGACATCGCTAGCTAATTAACATATAAAAGCaata Chimp > Human ------------- chr3:64888065-64888069 Template switch process: F1: L GCTAATAGTGAGGCTTCCCACCTATAATCTAAGCATAATATGTTAATT 1 F3: 4 AATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGT R RF: GCTAATAGTGAGGCTTCCCACCTATAATCTAAGCATAATATATTAATTAGAATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGT RR: CGATTATCACTCCGAAGGGTGGATATTAGATTCGTATTATATAATTAATCTTACGTTAATTGATTTCTGTAGCGATCGATTATTTGTACA F2: 3 TCGAT 2 Unidirectional alignment (log-probability: -31.5) TGAGGCTTCCCACCTATAATCTAAGCATAATATgTTAAtTTAGctAATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGT TGAGGCTTCCCACCTATAATCTAAGCATAATATATTAA-TTAG--AATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGT Template switch alignment (log-probability: -22) TGAGGCTTCCCACCTATAATCTAAGCATAATATgTTAATT|TAGCT|AATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGT TGAGGCTTCCCACCTATAATCTAAGCATAATATATTAATT|TAGCT|AATGCAATTAACTAAAGACATCGCTAGCTAATAAACATGT ========== Event 2436 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGCTTCACTTGACAACTGCTG---TTATCTTGACACATCCACTTAAAAATTATTTCTGACAAGAA Chimp: TTTCTTCACTTGGCAACTGCTG---TTATCTTGACAAGATAACAGAAAAATTATTTCTGACAAGAA ↑ 3 2 1 4 Gorilla: TTTCTTCACTTGACAACTGCTG---TTATCTTGACACATCCACTTAAAAATTATTTCTGACAAGAA Human: TTGCTTCACTTGACAACTGCTG---TTATCTTGACACATCCACTTAAAAATTATTTCTGACAAGAA Cluster: [ ] Orangutan: TTTCTTCACTTGACAACTGCTGTTTTTATCTTGACACATCCACTTAAAAATTATTTCTGACAAGAA Gorilla > Chimp --------------- chr3:66403822-66403830 Template switch process: F1: L ATTACCGTTTTCTTCACTTGGCAACTGCTGTTATCTTGACA 1 F3: 4 AAAAATTATTTCTGACAAGAATCTTAACAGCTTTAAATCA R RF: ATTACCGTTTTCTTCACTTGACAACTGCTGTTATCTTGACACATCCACTTAAAAATTATTTCTGACAAGAATCTTAACAGCTTTAAATCA RR: TAATGGCAAAAGAAGTGAACTGTTGACGACAATAGAACTGTGTAGGTGAATTTTTAATAAAGACTGTTCTTAGAATTGTCGAAATTTAGT F2: 3 GACAATAGA 2 Unidirectional alignment (log-probability: -39.5) TTACCGTTTTCTTCACTTGgCAACTGCTGTTATCTTGACA---------agataacagAAAAATTATTTCTGACAAGAATCTTAACAGCTTTAAATCA TTACCGTTTTCTTCACTTGACAACTGCTGTTATCTTGACACATCCACTT---------AAAAATTATTTCTGACAAGAATCTTAACAGCTTTAAATCA Template switch alignment (log-probability: -22.4) TTACCGTTTTCTTCACTTGgCAACTGCTGTTATCTTGACA|AGATAACAG|AAAAATTATTTCTGACAAGAATCTTAACAGCTTTAAATCA TTACCGTTTTCTTCACTTGACAACTGCTGTTATCTTGACA|AGATAACAG|AAAAATTATTTCTGACAAGAATCTTAACAGCTTTAAATCA ========== Event 2437 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CACTTCCGTGTCAGCCTTGTTACACACAGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCTAAGCTCTTGCCTTTGTGGTTTCTGAGTATTTCTCTAATATCCCTTCCTGCTTCACAACTCCTGTTACCTATGATGATACAAAAGTTA ↓ 1 4 3 2 Chimp: CACTTCCGTGTCAGCCTTGTTGTAACAAGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCTAAGCTCTTGCCTTTGTGGTTTCTGAGTATTTCTCTAATATCCCTTCCTGCTTCACAACTCCTGTTACCTATGATGATACAAAAGTTA Gorilla: CACTTCCGTGTCAGCCTTGTTACACACAGGGCAGGCTCACCGGCCCTCTCTTACTTGCTTGTCCTCTAAGCTCTTGCCTGTGTGGTTTCTGAGTATTTCTCTAATATCCCTTCCTGCTTCACAACTCCTGTTACCTATGATGATAGAAAAGTTA Human: CACTTCCGTGTCAGCCTTGTTACACACAGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCTAAGCTCTTGCCTTTGTGGTTTCTGAGTATTTCTCTAATATCCCTTCCTGCTTCACAACTCCTGTTACCTATGATGATACAAAAGTTA Cluster: [ ] Orangutan: CATTTCCGTGTCAGCCTTGTTACACACAGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCTAAGCTCTTGCCTTTGTGGTTTCTGACTCTTTCTCTAATATCCCTTCCTGCTTCACAACTCCTGTTACCTATGACGATACAAAAGTTA Human > Chimp ------------- chr3:134921035-134921040 Template switch process: F1: L CCCTTTAGGTGTGTGGCAGGCACTTCCGTGTCAGCCTTGTT 1 F3: 4 AGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCT R RF: CCCTTTAGGTGTGCGGCAGGCACTTCCGTGTCAGCCTTGTTACACACAGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCTAAGCTCTTGCCTTTGTGGTTTCTGAGTATTTCTCTAATATCCCTTCCTGCTTCACAACTCCTGTTAC RR: GGGAAATCCACACGCCGTCCGTGAAGGCACAGTCGGAACAATGTGTGTCCCGTCCGAGTGGTCGGGAGAGAATGAACGAACAGGAGATTCGAGAACGGAAACACCAAAGACTCATAAAGAGATTATAGGGAAGGACGAAGTGTTGAGGACAATG F2: 3 ACAATG 2 Unidirectional alignment (log-probability: -31.6) CCTTTAGGTGTGtGGCAGGCACTTCCGTGTCAGCCTTGTTgtaACA---AGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCT CCTTTAGGTGTGCGGCAGGCACTTCCGTGTCAGCCTTGTT---ACACACAGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCT Template switch alignment (log-probability: -22) CCTTTAGGTGTGtGGCAGGCACTTCCGTGTCAGCCTTGTT|GTAACA|AGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCT CCTTTAGGTGTGCGGCAGGCACTTCCGTGTCAGCCTTGTT|GTAACA|AGGGCAGGCTCACCAGCCCTCTCTTACTTGCTTGTCCTCT ========== Event 2438 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: aataaaagcttcctaaaaactttagcagcaactgctaaagtggcttattctcacatttcat Chimp: AATAAAAGCTTCCTAAAAACTTTAGCAGCAACTGCTAAAGTGGcttcttctcacatttcat ↑ 3 2 1 4 Gorilla: AATAAAAGCTTCCTAAAAACTTTAGCAGCAG--------TTGGcttcttctcacatttcat Human: aataaaagcttcctaaaaactttagcagcaactgctaaagtggcttattctcacatttcat Cluster: [ ] Orangutan: aataaaagcttcctaaaaactttagcagcag--------ttggcttcttctcacatttcat Gorilla > Chimp --------------- chr3:135269058-135269066 Template switch process: F1: L TTTAGTAAGAAAATAAAAGCTTCCTAAAAACTTTAGCAGCAA 1 F3: 4 TGGCTTCTTCTCACATTTCATGGGCTAAAACTGGGTCATA R RF: TTTAGTAAGAAAATAAAAGCTTCCTAAAAACTTTAGCAGCAGTTGGCTTCTTCTCACATTTCATGGGCTAAAACTGGGTCATA RR: AAATCATTCTTTTATTTTCGAAGGATTTTTGAAATCGTCGTCAACCGAAGAAGAGTGTAAAGTACCCGATTTTGACCCAGTAT F2: 3 GAAATCGTC 2 Unidirectional alignment (log-probability: -33.5) TAGTAAGAAAATAAAAGCTTCCTAAAAACTTTAGCAGCaactgctaAagTGGCTTCTTCTCACATTTCATGGGCTAAAACTGGGTCATA TAGTAAGAAAATAAAAGCTTCCTAAAAACTTTAGCAGC--------AGTTGGCTTCTTCTCACATTTCATGGGCTAAAACTGGGTCATA Template switch alignment (log-probability: -22.4) TAGTAAGAAAATAAAAGCTTCCTAAAAACTTTAGCAGCAa|CTGCTAAAG|TGGCTTCTTCTCACATTTCATGGGCTAAAACTGGGTCATA TAGTAAGAAAATAAAAGCTTCCTAAAAACTTTAGCAGCAG|CTGCTAAAG|TGGCTTCTTCTCACATTTCATGGGCTAAAACTGGGTCATA ========== Event 2439 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT---GAGCACAACGAACCACAGGAAAGCCAACT Chimp: TTCTTCACTGCAGTTTGAGAGGCAAGAGTGAAACT---GAGCACAACGAACCACAGGAAAGCCAACT Gorilla: TTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT------TGCATCGAACCACAGGAAAGCCAACT ↑ 3 2 1 4 Human: TTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT---GAGCACAACGAACCACAGGAAAGCCAACT Cluster: [ ] Orangutan: TTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACTGAG---CGCAACGAACCACAGGAAAGCCAACT Human > Gorilla --------------- chr3:132217176-132217180 Template switch process: F1: L TATGTATTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT 1 F3: 4 CGAACCACAGGAAAGCCAACTTGGGTGACATCTACTATTT R RF: TATGTATTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACTGAGCACAACGAACCACAGGAAAGCCAACTTGGGTGACATCTACTATTT RR: ATACATAAGAAGTGACGTCAAACTCTACGTTCTCACTTTGACTCGTGTTGCTTGGTGTCCTTTCGGTTGAACCCACTGTAGATGATAAA F2: 3 TACGT 2 Unidirectional alignment (log-probability: -27.7) ATGTATTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT---tgCAtCGAACCACAGGAAAGCCAACTTGGGTGACATCTACTATTT ATGTATTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACTGAGCACAACGAACCACAGGAAAGCCAACTTGGGTGACATCTACTATTT Template switch alignment (log-probability: -16.4) ATGTATTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT|TGCAT|CGAACCACAGGAAAGCCAACTTGGGTGACATCTACTATTT ATGTATTCTTCACTGCAGTTTGAGATGCAAGAGTGAAACT|TGCAT|CGAACCACAGGAAAGCCAACTTGGGTGACATCTACTATTT ========== Event 2440 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCTCAATATTTGGGTTGCTTTCCAGGGGCAGATTTTGTAAGGGGGTTGGGTGAAGCCTCATCACAGATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTCT-------GG---AACTTGTTAAATCCAAGACTGAG Chimp: CCTCAATATTTGGGTTGCTTTCCAGGGGCAGATTTTGTAAGGGGGTTGGGTGAAGCCTCATCACAGATTTTAATTTCCACTCATTCTAAGAGAAAGCTATTGATCTCT-------GG---AACTTGTTAAATCCAAGACTGAG ↑ 3 2 1 4 Gorilla: CCTCAATATTTGGGTTGCTTTCCAGGGGCAGATTTTGTAAGGGGGTTGGGTGAAGCCTCATCACAGATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTTAGACTGAGGGAATAGATTGTTAAATCCAAGACTGAG ↓ 3 2 1 4 Human: CCTCAATATTTGGGTTGCTTTCCAGGGGCAGATTTTGTAAGGGGGTTGGGTGAAGCCTCATCACAGATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTCT-------GG---AACTTGTTAAATCCAAGACTGAG Cluster: [ ] Orangutan: CCTCAATATTTGGGTTGCTTTCCAGGGGCAGATTTTGCAAGGGGGTTGGGTGAAGCCTCATCACAGGTTTTAATTTCCACTCATTCTAAGAGAAAGCTATTGATCTCT-------GG---AACTTGTTAAATCCAAGACTGAG Gorilla > Human --------------- chr3:130137559-130137564 Template switch process: F1: L GATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCT 1 F3: 4 CTTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAAG R RF: TTCCAGGGGCAGATTTTGTAAGGGGGTTGGGTGAAGCCTCATCACAGATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTTAGACTGAGGGAATAGATTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAAG RR: AAGGTCCCCGTCTAAAACATTCCCCCAACCCACTTCGGAGTAGTGTCTAAAATTAAAGGCGAGTAAGATTCTCTTTCGATAACTAGAATCTGACTCCCTTATCTAACAATTTAGGTTCTGACTCCCTTATCTAACTCTCATTTC F2: 3 AAGGTC 2 Unidirectional alignment (log-probability: -31.6) ATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCT-----------------ctggaacTTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA ATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTTAGACTGAGGGAATAGA-------TTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA Template switch alignment (log-probability: -22) ATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCT|CTGGAA|cTTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA ATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCT|CTGGAA|ATTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA Gorilla > Chimp --------------- chr3:133171171-133171176 Template switch process: F1: L GATTTTAATTTCCACTCATTCTAAGAGAAAGCTATTGATCT 1 F3: 4 CTTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAAG R RF: TTCCAGGGGCAGATTTTGTAAGGGGGTTGGGTGAAGCCTCATCACAGATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTTAGACTGAGGGAATAGATTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAAG RR: AAGGTCCCCGTCTAAAACATTCCCCCAACCCACTTCGGAGTAGTGTCTAAAATTAAAGGCGAGTAAGATTCTCTTTCGATAACTAGAATCTGACTCCCTTATCTAACAATTTAGGTTCTGACTCCCTTATCTAACTCTCATTTC F2: 3 AAGGTC 2 Unidirectional alignment (log-probability: -37.1) ATTTTAATTTCCaCTCATTCTAAGAGAAAGCTATTGATCT-----------------ctggaacTTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA ATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCTTAGACTGAGGGAATAGA-------TTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA Template switch alignment (log-probability: -27.5) ATTTTAATTTCCaCTCATTCTAAGAGAAAGCTATTGATCT|CTGGAA|cTTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA ATTTTAATTTCCGCTCATTCTAAGAGAAAGCTATTGATCT|CTGGAA|ATTGTTAAATCCAAGACTGAGGGAATAGATTGAGAGTAAA ========== Event 2441 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTGGTATTTGGGGTGACAGTCCTTAATGCTGGCTTTGCCTGTAGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCATATCTGCTAGG-CACATAGGAAGACAAAAGGGTC ↓ 3 2 1 4 Chimp: TTCT-GTATTTGGGGTGACAGTCCTTAATGCTGGCTTTGCCTGTAGCTAGCTTGTTGCACTTTGG-ATCCAAAGGTCATATCTGCAGGACTACATAGGAAGACAAAAGGGTC Gorilla: TTCTGGTATTT-GGGTGACAGTCCTTAATGCTGTCTTTGCCTGTAGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCGTATCTGCTAGG-CACATAGGAAGACAAAAGGGTC Human: TTCTGGTATTTGGGGTGACAGTCCTTAATGCTGGCTTTGCCTGTAGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCATATCTGCTAGG-CACATAGGAAGACAAAAGGGTC Cluster: [ ] Orangutan: TTCTGGTATTTGGGGTGACAATCCTTAATGCTTGCTTTGCCTGTAGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCGTATCTGCTAGG-CACATAGGAAGACACAAGGGTC Human > Chimp ------------- chr3:68951488-68951493 Template switch process: F1: L AGCTAGCTTGTTGCACTTTGGA-TCCAAAGGTCATATCTGC 1 F3: 4 ACATAGGAAGACAAAAGGGTCTAGATTCTTGGCCTTTTTT R RF: AGTCCTTAATGCTGGCTTTGCCTGTAGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCATATCTGCTAGGCACATAGGAAGACAAAAGGGTCTAGATTCTTGGCCTTTTTT RR: TCAGGAATTACGACCGAAACGGACATCGATCGAACAACGTGAAACCTCAGGTTTCCAGTATAGACGATCCGTGTATCCTTCTGTTTTCCCAGATCTAAGAACCGGAAAAAA F2: 3 TCAGGA 2 Unidirectional alignment (log-probability: -38.8) AGCTAGCTTGTTGCACTTTGGA-TCCAAAGGTCATATCTGcaggaCTA----CATAGGAAGACAAAAGGGTCTAGATTCTTGGCCTTTTTT AGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCATATCTG-----CTAGGCACATAGGAAGACAAAAGGGTCTAGATTCTTGGCCTTTTTT Template switch alignment (log-probability: -26.3) AGCTAGCTTGTTGCACTTTGGA-TCCAAAGGTCATATCTGC|AGGACT|ACATAGGAAGACAAAAGGGTCTAGATTCTTGGCCTTTTTT AGCTAGCTTGTTGCACTTTGGAGTCCAAAGGTCATATCTGC|AGGACT|ACATAGGAAGACAAAAGGGTCTAGATTCTTGGCCTTTTTT ========== Event 2442 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: TGTCTTTGTGTGTTTTACAGTCTAGCTGGGAGCCAGGCATTAATCAGTTTCACAGAGAAATA Chimp: TGTCTTTGTGTGTTTTACAGTAATGCCTGGCTCCCAGCTAGAATCAGTTTCACAGAGAAATA ↓ 13 24 ↑ 13 24 Gorilla: TGTCTTTGTGTGTTTTACAGTCTAGCTGGGAGCCAGGCATTAATCAGTTTCACAGAGAAATA Human: TGTCTTTGTGTGTTTTACAGTCTAGCTGGGAGCCAGGCATTAATCAGTTTCACAGAGAAATA Cluster: [ ] Orangutan: TGTCTTTGTGTCTTTTACAGTCTAGCTGGGAGCCAGGCATTAATCAGTTTCACAGAGAAATA Gorilla > Chimp --------------- chr3:130310509-130310528 Template switch process: F1: L GGGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT 1 F3: 4 AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA R RF: GGGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGTCTAGCTGGGAGCCAGGCATTAATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA RR: CCCACACCTTAGTTGGTCGGACAGAAACACACAAAATGTCAGATCGACCCTCGGTCCGTAATTAGTCAAAGTGTCTCTTTATACTTTCAGGTTCACAATGT F2: 3 GATCGACCCTCGGTCCGTAA 2 Unidirectional alignment (log-probability: -44.5) GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGTaatgcctggctcccagCTAG----------------AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT----------------CTAGCTGGGAGCCAGGCATTAATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA Template switch alignment (log-probability: -18.3) GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT|AATGCCTGGCTCCCAGCTAG|AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT|AATGCCTGGCTCCCAGCTAG|AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA Chimp > Gorilla --------------- chr3:129391074-129391093 Template switch process: F1: L GGGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT 1 F3: 4 AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA R RF: GGGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGTAATGCCTGGCTCCCAGCTAGAATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA RR: CCCACACCTTAGTTGGTCGGACAGAAACACACAAAATGTCATTACGGACCGAGGGTCGATCTTAGTCAAAGTGTCTCTTTATACTTTCAGGTTCACAATGT F2: 3 TTACGGACCGAGGGTCGATC 2 Unidirectional alignment (log-probability: -44.5) GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT----------------CTAGctgggagccaggcattAATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGTAATGCCTGGCTCCCAGCTAG----------------AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA Template switch alignment (log-probability: -18.3) GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT|CTAGCTGGGAGCCAGGCATT|AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA GGTGTGGAATCAACCAGCCTGTCTTTGTGTGTTTTACAGT|CTAGCTGGGAGCCAGGCATT|AATCAGTTTCACAGAGAAATATGAAAGTCCAAGTGTTACA ========== Event 2443 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTGAAAATGTTTCCATTCTAGTCTGGAACCCATCTGCTTCTATCCCCACAGAAAACCCGTGAATCCATTGC Chimp: TGTGAAAATGTTTCCATTCTAGTCTGGAACCCATCAGAC----------TAGAAAACCCGTGAGTCCATTGC ↑ 3 2 1 4 Gorilla: TGTGAAAATGTTTCCATTCTAGTCTGGAACCCATCTGCTTCTATCCCCACAGAAAACCCGTGAGTCCATTGC Human: TGTGAAAATGTTTCCATTCTAGTCTGGAACCCATCTGCTTCTATCCCCACAGAAAACCCGTGAATCCATTGC Cluster: [ ] Orangutan: TGTGAAAATGTTTCCATTCTAGTCTGGAACCCATCTGCTTCTATCCCCACAGAAAACCCGTGAGTCCATTGC Gorilla > Chimp --------------- chr3:130632100-130632105 Template switch process: F1: L TCCTTCTGTGAAAATGTTTCCATTCTAGTCTGGAACCCATC 1 F3: 4 GAAAACCCGTGAGTCCATTGCCTTCTACTGTATCTTCGA R RF: TCCTTCTGTGAAAATGTTTCCATTCTAGTCTGGAACCCATCTGCTTCTATCCCCACAGAAAACCCGTGAGTCCATTGCCTTCTATTGTATCTTCGA RR: AGGAAGACACTTTTACAAAGGTAAGATCAGACCTTGGGTAGACGAAGATAGGGGTGTCTTTTGGGCACTCAGGTAACGGAAGATAACATAGAAGCT F2: 3 ATCAGA 2 Unidirectional alignment (log-probability: -32.6) CCTTCTGTGAAAATGTTTCCATTCTAGTCTGGAACCCATcagaCT--------------AGAAAACCCGTGAGTCCATTGCCTTCTAcTGTATCTTCGA CCTTCTGTGAAAATGTTTCCATTCTAGTCTGGAACCCAT----CTGCTTCTATCCCCACAGAAAACCCGTGAGTCCATTGCCTTCTATTGTATCTTCGA Template switch alignment (log-probability: -22) CCTTCTGTGAAAATGTTTCCATTCTAGTCTGGAACCCATC|AGACTA|GAAAACCCGTGAGTCCATTGCCTTCTAcTGTATCTTCGA CCTTCTGTGAAAATGTTTCCATTCTAGTCTGGAACCCATC|AGACTA|GAAAACCCGTGAGTCCATTGCCTTCTATTGTATCTTCGA ========== Event 2444 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGGCCAAACGGAAGACCAGCCAGTACAACCAGTTGTAGTTACAACTGTTCTTTCAAAGCTTTGGATT ↑ 3 4 1 2 Chimp: AAGGCCAAACGGAAGACCAGCA----------------ACTACAACTGTTCTTTCAAAGCTTTGGATT Gorilla: AAGGCCAAACGGAAGACCAGCA----------------ACTACAACTGTTCTTTCAAAGCTTTGGATT ↓ 3 4 1 2 Human: AAGGCCAAACGGAAGACCAGCCAGTACAACCAGTTGTAGTTACAACTGTTCTTTCAAAGCTTTGGATT Cluster: [ ] Orangutan: AAGGCCAAACGGAAGATCAGCA----------------ACTACAACTGTTCTTTCAAAGCTTTGGATT Chimp > Human ------------- chr3:69472469-69472478 Template switch process: F1: L GCCAATAATTAATCACTAAAAAGGCCAAACGGAAGACCAGCCAGTACAAC 1 F3: 4 TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA R RF: GCCAATAATTAATCACTAAAAAGGCCAAACGGAAGACCAGCAACTACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA RR: CGGTTATTAATTAGTGATTTTTCCGGTTTGCCTTCTGGTCGTTGATGTTGACAAGAAAGTTTCGAAACCTAAGGAACTGTAAGT F2: 3 TGATGTTGAC 2 Unidirectional alignment (log-probability: -44.2) AATCACTAAAAAGGCCAAACGGAAGACCAGccagtaCAACcagttgtagtTACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA AATCACTAAAAAGGCCAAACGGAAGACCAG------CAAC----------TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA Template switch alignment (log-probability: -28.7) AATCACTAAAAAGGCCAAACGGAAGACCAGCcAgTACAAC|CAGTTGTAGT|TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA AATCACTAAAAAGGCCAAACGGAAGACCAGCAACTACAAC|CAGTTGTAGT|TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA Gorilla > Human --------------- chr3:69472469-69472478 Template switch process: F1: L GCCAATAATTAATCACTAAAAAGGCCAAACGGAAGACCAGCCAGTACAAC 1 F3: 4 TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA R RF: GCCAATAATTAATCACTAAAAAGGCCAAACGGAAGACCAGCAACTACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA RR: CGGTTATTAATTAGTGATTTTTCCGGTTTGCCTTCTGGTCGTTGATGTTGACAAGAAAGTTTCGAAACCTAAGGAACTGTAAGT F2: 3 TGATGTTGAC 2 Unidirectional alignment (log-probability: -43.7) AATCACTAAAAAGGCCAAACGGAAGACCAGccagtaCAACcagttgtagtTACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA AATCACTAAAAAGGCCAAACGGAAGACCAG------CAAC----------TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA Template switch alignment (log-probability: -28.3) AATCACTAAAAAGGCCAAACGGAAGACCAGCcAgTACAAC|CAGTTGTAGT|TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA AATCACTAAAAAGGCCAAACGGAAGACCAGCAACTACAAC|CAGTTGTAGT|TACAACTGTTCTTTCAAAGCTTTGGATTCCTTGACATTCA ========== Event 2445 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTGTAGCCACACAGCACAAAAGTCTCCCTTTCTCCTCCCCCTCCCTCCCT-AGAC------TTTATTTCACTATGGGACTTTGCA ↑ 3 2 1 4 Chimp: TCTGTAGCCACACAGCACAAAAGTCTCCCTTTCTCCTCCCTCTCCCTCCCT-AACC---TCTTTAATTTCACTATGGGACTTTGCA Gorilla: TCTGTAGCCACACAGCACAAAAGTCTCCCTTTCTCCTCCCCCTCCCTCCCTATACCTCT---TTAATTTCACTATGGGACTTTGCA Human: TCTGTAGCCACACAGCACAAAAGTCTCCCTTTCTCCTCCCCCTCCCTCCCT-AGAC------TTTATTTCACTATGGGACTTTGCA Cluster: [ ] Orangutan: TCTGTAGCCACACAGCACAAAAGTCTCCCTTTCTCCTCCCCCTCCCTCCCTAGACCTCT---TTAATTTCACTATGGGACTTTGCA Chimp > Human ------------- chr3:126779935-126779940 Template switch process: F1: L ACAGCACAAAAGTCTCCCTTTCTCCTCCCCCTCCCTCCCTA 1 F3: 4 ATTTCACTATGGGACTTTGCAGTAATGTTAGATTGGCTCT R RF: ACAGCACAAAAGTCTCCCTTTCTCCTCCCTCTCCCTCCCTAACCTCTTTAATTTCACTATGGGACTTTGCAGTAATGTTAGATTGGCTCT RR: TGTCGTGTTTTCAGAGGGAAAGAGGAGGGAGAGGGAGGGATTGGAGAAATTAAAGTGATACCCTGAAACGTCATTACAATCTAACCGAGA F2: 3 TTTCAG 2 Unidirectional alignment (log-probability: -34.8) CAGCACAAAAGTCTCCCTTTCTCCTCCCcCTCCCTCCCTAgAC----TTtATTTCACTATGGGACTTTGCAGTAATGTTAGATTGGCTCT CAGCACAAAAGTCTCCCTTTCTCCTCCCTCTCCCTCCCTA-ACCTCTTTAATTTCACTATGGGACTTTGCAGTAATGTTAGATTGGCTCT Template switch alignment (log-probability: -22) CAGCACAAAAGTCTCCCTTTCTCCTCCCcCTCCCTCCCTA|GACTTT|ATTTCACTATGGGACTTTGCAGTAATGTTAGATTGGCTCT CAGCACAAAAGTCTCCCTTTCTCCTCCCTCTCCCTCCCTA|GACTTT|ATTTCACTATGGGACTTTGCAGTAATGTTAGATTGGCTCT ========== Event 2446 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCCTGTTTGTTTTCTTCCTC-----CAGCGGGGAGCAACAGCTGCTAATTG Chimp: TTCCTGTTTGTTTTCTTCCTC-----CAGCGGGGAGCAACAGCTGCTAATTG ↓ 3 1 42 Gorilla: TTCCTGTTTGTTTTCTTCCTCCCCGCTGGAGGGGAGCAACGGCTGCTAATTG ↑ 3 1 42 Human: TTCCTGTTTGTTTTCTTCCTC-----CAGCGGGGAGCAACAGCTGCTAATTG Cluster: [ ] Orangutan: TTCCTGTTTGTTTTCTTCCTC-----CAGCGGGGAGCAACGGCTGTTAATTG Human > Gorilla --------------- chr3:128199816-128199823 Template switch process: F1: L AAACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCC 1 F3: 4 GGGGAGCAACGGCTGCTAATTGGATAGTGAAGTGACCGAT R RF: AAACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCCAGCGGGGAGCAACAGCTGCTAATTGGATAGTGAAGTGACCGAT RR: TTTGTTTTGTCCCGTCCCAGAAGGACAAACAAAAGAAGGAGGTCGCCCCTCGTTGTCGACGATTAACCTATCACTTCACTGGCTA F2: 3 AGGTCGCC 2 Unidirectional alignment (log-probability: -34.7) ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCCccgctgGaGGGGAGCAACgGCTGCTAATTGGATAGTGAAGTGACCGAT ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCCA-----GCGGGGAGCAACAGCTGCTAATTGGATAGTGAAGTGACCGAT Template switch alignment (log-probability: -22.3) ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCC|CCGCTGGA|GGGGAGCAACgGCTGCTAATTGGATAGTGAAGTGACCGAT ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCC|CCGCTGGA|GGGGAGCAACAGCTGCTAATTGGATAGTGAAGTGACCGAT Chimp > Gorilla --------------- chr3:128199816-128199823 Template switch process: F1: L AAACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCC 1 F3: 4 GGGGAGCAACGGCTGCTAATTGGATAGTGAAGTGACCGAT R RF: AAACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCCAGCGGGGAGCAACAGCTGCTAATTGGATAGTGAAGTGACCGAT RR: TTTGTTTTGTCCCGTCCCAGAAGGACAAACAAAAGAAGGAGGTCGCCCCTCGTTGTCGACGATTAACCTATCACTTCACTGGCTA F2: 3 AGGTCGCC 2 Unidirectional alignment (log-probability: -34.7) ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCCccgctgGaGGGGAGCAACgGCTGCTAATTGGATAGTGAAGTGACCGAT ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCCA-----GCGGGGAGCAACAGCTGCTAATTGGATAGTGAAGTGACCGAT Template switch alignment (log-probability: -22.3) ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCC|CCGCTGGA|GGGGAGCAACgGCTGCTAATTGGATAGTGAAGTGACCGAT ACAAAACAGGGCAGGGTCTTCCTGTTTGTTTTCTTCCTCC|CCGCTGGA|GGGGAGCAACAGCTGCTAATTGGATAGTGAAGTGACCGAT ========== Event 2447 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAACCTCCCAAGAGCTAAGAGACTTGCTCCCAGC ↑ 3 2 1 4 Chimp: GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAA-----CGATGGCTAAGAGACTTGCTCCCAGC Gorilla: GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTcacgaaa-----cgatggctaagagacttgctcccagc Human: GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAACCTCCCAAGAGCTAAGAGACTTGCTCCCAGC Cluster: [ ] Orangutan: GGGGATTTAAGGCAATACTTCTTGGGAGGTGTCACAGAA-----CAACGGCTAAGAGACTTGCTCCCAGC Chimp > Human ------------- chr3:72285054-72285062 Template switch process: F1: L GGGGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAAC 1 F3: 4 GCTAAGAGACTTGCTCCCAGCTGTACCCTGGCTCTGCCAT R RF: GGGGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAACGATGGCTAAGAGACTTGCTCCCAGCAGTACCCTGGCTCTGCCAT RR: CCCCCCTAAATTCCGTCATGAAGAACCCTCCACAGTGCTTTGCTACCGATTCTCTGAACGAGGGTCGTCATGGGACCGAGACGGTA F2: 3 AGAACCCTC 2 Unidirectional alignment (log-probability: -37.3) GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAACctcccaaGA--GCTAAGAGACTTGCTCCCAGCtGTACCCTGGCTCTGCCAT GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAAC-------GATGGCTAAGAGACTTGCTCCCAGCAGTACCCTGGCTCTGCCAT Template switch alignment (log-probability: -22.4) GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAAC|CTCCCAAGA|GCTAAGAGACTTGCTCCCAGCtGTACCCTGGCTCTGCCAT GGGGATTTAAGGCAGTACTTCTTGGGAGGTGTCACGAAAC|CTCCCAAGA|GCTAAGAGACTTGCTCCCAGCAGTACCCTGGCTCTGCCAT ========== Event 2448 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCACTTTTGCCACATTCTGACCTTGGAATAGTGAAATTGTCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACACTCAGCAGAATTTCTGTGACTGA--GACAACAGTGGTCACACCTCTCTCAGATAAAAGCAGTTAAGATGC Chimp: CCACTTTTGCCACATTCTGACCTTGGAATAGTGAAATTGTCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACGCTTAGCAGAATTTCTGTGACTGA--GAGAGGTGTGACCACTGTTGTCTCAGATAAAAGCAGTTAAGATGC Gorilla: CCACTTTTGCCACATTCTGACCTTGGAATAGTGAAATTGTCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACGCTTAGCAGAATTTCTGTGACAGA----GAGATGTGACCACTGTTGTCTCAGATAAAAGCAGTTAAGATGC ↓ 4 1 3 2 Human: CCACTTTTGCCACATTCTGACCTTGGAATAGTGAAATTGTCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACACTCAGCAGAATTTCTGTGACTGA--GACAACAGTGGTCACACCTCTCTCAGATAAAAGCAGTTAAGATGC Cluster: [ ] Orangutan: CCACTTTTGCCACATTCTGACCTTGGAATAGTAAAATTGTCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACGCTTGGCAGAATTTCTGTGATTGAGA--GAGGTGTGACCACTGTTGTCTCAGATAAAAGCAGTTAAGATGC Gorilla > Human --------------- chr3:127327765-127327782 Template switch process: F1: L TCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACACTCAGCAGAATTTCTGTGAC 1 F3: 4 ACCTC R RF: TCTTATGAGAGCTTATCTTATGGTATTTCCAGTGGAAAGACGCTTAGCAGAATTTCTGTGACAGAGAGATGTGACCACTGTTGTCTCA RR: AGAATACTCTCGAATAGAATACCATAAAGGTCACCTTTCTGCGAATCGTCTTAAAGACACTGTCTCTCTACACTGGTGACAACAGAGT F2: 3 CACTGGTGACAACAGAGT 2 Unidirectional alignment (log-probability: -59.6) GTATTTCCAGTGGAAAGACaCTcAGCAGAATTTCTGTGAC-------------------TGagacaacagtggtcacacctc GTATTTCCAGTGGAAAGACGCTTAGCAGAATTTCTGTGACAGAGAGATGTGACCACTGTTG--------------------- Template switch alignment (log-probability: -34.2) GTATTTCCAGTGGAAAGACaCTcAGCAGAATTTCTGTGAC|TGAGACAACAGTGGTCAC|ACCtC GTATTTCCAGTGGAAAGACGCTTAGCAGAATTTCTGTGAC|TGAGACAACAGTGGTCAC|ACCAC ========== Event 2449 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AATTTTGATTCTCTGGTTACATTCTATTCTTCTATTAACTTCTTATTTAAATCTTGAATCAttttttttttCCACCACAGACCAGCATGGGAGAGTGAACACAGAAAG Chimp: AATTTTGATTCTCTGGTTACAATCTTT---TCTATTAACTTCTTATTTAAATCTTGAATCAtttt-tttttCCACCACAGACCAGCATGGGAGAGTGAACACAGAAAG ↓ 1 4 3 2 Gorilla: AATTTTGATTCTCTGGTTACATTCTATGCTTCTATTAACTTCTTATTTAAATCTTGAATCAttttttttttCCACCACAGACCAGCATGGGAGAGTGAACACAGAAAG Human: AATTTTGATTCTCTGGTTACATTCTATTCTTCTATTAACTTCTTATTTAAATCTTGAATCAttttttttttCCACCACAGACCAGCATGGGAGAGTGAACACAGAAAG Cluster: [ ] Orangutan: AATTTTGACTCTCTGGTTACATTCTATTCTTCTATTAACTTCTTATTTAAATCTTGAATCAGTTT-TTTATCCACCACACACTAGCATGGGAGAGTGAACACAGAAAG Chimp > Gorilla --------------- chr3:75396607-75396611 Template switch process: F1: L GTATATTTATAGACTACAGAAATTTTGATTCTCTGGTTACATTCT 1 F3: 4 TCTATTAACTTCTTATTTAAATCTTGAATCATTTTTTTTT R RF: GTATATTTATAGACTACAGAAATTTTGATTCTCTGGTTACAATCTTTTCTATTAACTTCTTATTTAAATCTTGAATCATTTTTTTTTCCACCACAGACCAGCAT RR: CATATAAATATCTGATGTCTTTAAAACTAAGAGACCAATGTTAGAAAAGATAATTGAAGAATAAATTTAGAACTTAGTAAAAAAAAAGGTGGTGTCTGGTCGTA F2: 3 TCGTA 2 Unidirectional alignment (log-probability: -34.5) TTTATAGACTACAGAAATTTTGATTCTCTGGTTACAtTCTatgcTTCTATTAACTTCTTATTTAAATCTTGAATCATTTTTTTTt TTTATAGACTACAGAAATTTTGATTCTCTGGTTACAATCTT---TTCTATTAACTTCTTATTTAAATCTTGAATCATTTTTTTT- Template switch alignment (log-probability: -22) TTTATAGACTACAGAAATTTTGATTCTCTGGTTACAtTCT|ATGCT|TCTATTAACTTCTTATTTAAATCTTGAATCATTTTTTTTT TTTATAGACTACAGAAATTTTGATTCTCTGGTTACAATCT|ATGCT|TCTATTAACTTCTTATTTAAATCTTGAATCATTTTTTTTT ========== Event 2450 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCTGACCTTGATCTAAGTGTC------------------------------------------------------ACAGTGACGCACTGTGGAGCTCAGTAGAATACTTT ↑ 1 4 3 2 Chimp: ACTGACCTTGATCTAAGTGTC---------------------------TACCATCATGAAAGGCACCCAGCATGACCCTTCACCCACTGTGGAGCTCAGTAGAATACTTT Gorilla: ACTGACCTTGATCTAAGTGTCTACCATCATTAAAGGCACCCAACATGA---------------------------CCTTTCACCCACTGTGGAGCTCAGTAGAATACTTT ↓ 1 4 3 2 Human: GCTGACCTTGATCTAAGTGTC------------------------------------------------------ACAGTGACGCACTGTGGAGCTCAGTAGAATACTTT Cluster: [ ] Orangutan: ACTGACCTTGATCTAAGTGTCTACCATCATTAAAGGCACAAAGCATGA---------------------------CCCTTCACCCACTGTGGAGCTCAGTAGAATACTTT Chimp > Human ------------- chr3:7514783-7514788 Template switch process: F1: L CAATATAAATCCACTGTGAGGCTGACCTTGATCTAAGTGTC 1 F3: 4 ACGCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGCAGG R RF: CAATATAAATCCACTGTGAGACTGACCTTGATCTAAGTGTCTACCATCATGAAAGGCACCCAGCATGACCCTTCACCCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGCAGG RR: GTTATATTTAGGTGACACTCTGACTGGAACTAGATTCACAGATGGTAGTACTTTCCGTGGGTCGTACTGGGAAGTGGGTGACACCTCGAGTCATCTTATGAAAGGTATTTCGCGTCC F2: 3 GTGACA 2 Unidirectional alignment (log-probability: -41.9) AATATAAATCCACTGTGAGgCTGACCTTGATCTAAGTGT------------------------------------CacagtgacgCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC AATATAAATCCACTGTGAGACTGACCTTGATCTAAGTGTCTACCATCATGAAAGGCACCCAGCATGACCCTTCACC---------CACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC Template switch alignment (log-probability: -28.1) AATATAAATCCACTGTGAGgCTGACCTTGATCTAAGTGTC|ACAGTG|ACgCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC AATATAAATCCACTGTGAGACTGACCTTGATCTAAGTGTC|ACAGTG|ACCCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC Gorilla > Human --------------- chr3:7514783-7514788 Template switch process: F1: L CAATATAAATCCACTGTGAGGCTGACCTTGATCTAAGTGTC 1 F3: 4 ACGCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGCAGG R RF: CAATATAAATCCACTGTGAGACTGACCTTGATCTAAGTGTCTACCATCATTAAAGGCACCCAACATGACCTTTCACCCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGCAGG RR: GTTATATTTAGGTGACACTCTGACTGGAACTAGATTCACAGATGGTAGTAATTTCCGTGGGTTGTACTGGAAAGTGGGTGACACCTCGAGTCATCTTATGAAAGGTATTTCGCGTCC F2: 3 GTGACA 2 Unidirectional alignment (log-probability: -40.9) AATATAAATCCACTGTGAGgCTGACCTTGATCTAAGTGT------------------------------------CacagtgacgCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC AATATAAATCCACTGTGAGACTGACCTTGATCTAAGTGTCTACCATCATTAAAGGCACCCAACATGACCTTTCACC---------CACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC Template switch alignment (log-probability: -27.6) AATATAAATCCACTGTGAGgCTGACCTTGATCTAAGTGTC|ACAGTG|ACgCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC AATATAAATCCACTGTGAGACTGACCTTGATCTAAGTGTC|ACAGTG|ACCCACTGTGGAGCTCAGTAGAATACTTTCCATAAAGCGC ========== Event 2451 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TTGTTGATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCCATAAAATACAACTTTGCATTCATGATACTAAG ↓ 3 2 1 4 Chimp: TTGTTCATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCCT-----TTCAGCTTTGCATTCATGATACTAAG Gorilla: Human: TTGTTGATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCCATAAAATACAACTTTGCATTCATGATACTAAG Cluster: [ ] Orangutan: TTGTTGATTCTTAATCTTGCTGAAAGGTAAGAGAGAGCCATAAAATACAACTTTGCATTCATGACACTAAG Human > Chimp ------------- chr3:76347483-76347488 Template switch process: F1: L GTTTGTTCATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCC 1 F3: 4 CTTTGCATTCATGATACTAAGTTCACCTCCCTTGAATAGT R RF: GTTTGTTGATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCCATAAAATACAACTTTGCATTCATGATACTAAGTTCACCTCCCTTGAATAGT RR: CAAACAACTAAGAATTAGAACGACTTTCCGTTCTCTCTCGGTATTTTATGTTGAAACGTAAGTACTATGATTCAAGTGGAGGGAACTTATCA F2: 3 GACTTT 2 Unidirectional alignment (log-probability: -35.2) TTTGTTcATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCC-----tTtCAgCTTTGCATTCATGATACTAAGTTCACCTCCCTTGAATAGT TTTGTTGATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCCATAAAATACAACTTTGCATTCATGATACTAAGTTCACCTCCCTTGAATAGT Template switch alignment (log-probability: -22) TTTGTTcATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCC|TTTCAG|CTTTGCATTCATGATACTAAGTTCACCTCCCTTGAATAGT TTTGTTGATTCTTAATCTTGCTGAAAGGCAAGAGAGAGCC|TTTCAG|CTTTGCATTCATGATACTAAGTTCACCTCCCTTGAATAGT ========== Event 2452 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTACCCTGTTTTCAGTTTCAG------------------------GGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTACAAATTTAAAACGTCACTTGAACCATACCCATTTAATA ↓ 4 1 3 2 Chimp: ATTACCCTGTTTTCAGTTTCAG------------GGCAGTGACCAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTACAAATTTAAAACGTCACTTGA-ACATACCCATTTAATA Gorilla: ATTACCCTGTTTTCAGTTTCAGGGCAGTGACCAG------------GACCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTACAAATTTAAAACGTCACTTGA-ACATACCCATTTAATA Human: ATTACCCTGTTTTCAGTTTCAG------------------------GGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTACAAATTTAAAACGTCACTTGAACCATACCCATTTAATA Cluster: [ ] Orangutan: ATTACCCTGTTTTCAGTTTCAGGGAAGTGACCAG------------GGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTACAAATTTAAAACGTCACTTGA-ACATACCCATTTAACA Human > Chimp ------------- chr3:127460736-127460741 Template switch process: F1: L CACATCACGTGTTCCTCCAATTACCCTGTTTTCAGTTTCAGGGC 1 F3: 4 CAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTAC R RF: CACATCACGTGTTCCTCCAATTACCCTGTTTTCAGTTTCAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACACTACAAATTTAAAACGTCACT RR: GTGTAGTGCACAAGGAGGTTAATGGGACAAAAGTCAAAGTCCCGGCGAGTTTTCCATTTGTCCGTCGACTGTATTGTGATGTTTAAATTTTGCAGTGA F2: 3 CAGTGA 2 Unidirectional alignment (log-probability: -28.2) TCACGTGTTCCTCCAATTACCCTGTTTTCAGTTTcagggcagtgacCAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACAC TCACGTGTTCCTCCAATTACCCTGTTTTCAGTTT------------CAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACAC Template switch alignment (log-probability: -16.1) TCACGTGTTCCTCCAATTACCCTGTTTTCAGTTTCAGGGC|AGTGAC|CAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACAC TCACGTGTTCCTCCAATTACCCTGTTTTCAGTTTCAGGGC|AGTGAC|CAGGGCCGCTCAAAAGGTAAACAGGCAGCTGACATAACAC ========== Event 2453 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TGTTACATTTATTTATATTGTACACATGATCTCAAAGTTTATATTTTGCCACCATTTATGCATGAATTTTTCATGACAAATATTCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGG----------TTGTACTATTATCCAACTGTCAattta ↑ 3 2 1 4 Chimp: TGTTACATTTATTTATATTGTACACATGATCTCAAAGTTTATATTTTGCCACCATTTATGCATGAATTTTTCATGACAAATATTCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTTTCAGGAAGTTGTATTATTATCCAACTGTCAattta Gorilla: -------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: TGTTACATTTATTTATATTGTACACATGATCTCAAAGTTTATATTTTGCCACCATTTATGCATGAATTTTTCATGACAAATATTCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGG----------TTGTACTATTATCCAACTGTCAattta Cluster: [ ] Orangutan: Chimp > Human ------------- chr3:75964927-75964930 Template switch process: F1: L TATTCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTT 1 F3: 4 TATTATCCAACTGTCAATTTATTTATTTATT R RF: GTACACATGATCTCAAAGTTTATATTTTGCCACCATTTATGCATGAATTTTTCATGACAAATATTCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTTTCAGGAAGTTGTATTATTATCCAACTGTCAATTTATTTATTTATT RR: CATGTGTACTAGAGTTTCAAATATAAAACGGTGGTAAATACGTACTTAAAAAGTACTGTTTATAAGGATTCATAAGGGTAATATACAAAGGGTCTTATCACCAAAGTCCTTCAACATAATAATAGGTTGACAGTTAAATAAATAAATAA F2: 3 CATG 2 Unidirectional alignment (log-probability: -25.1) TCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTT----------GTAcTATTATCCAACTGTCAATTTATTTATTTATT--------- TCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTTTCAGGAAGTTGTATTATTATCCAACTGTCAATTTATTTATTTATTTATTTTATT Template switch alignment (log-probability: -15.6) TCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTT|GTAC|TATTATCCAACTGTCAATTTATTTATTTATT TCCTAAGTATTCCCATTATATGTTTCCCAGAATAGTGGTT|GTAC|TATTATCCAACTGTCAATTTATTTATTTATT ========== Event 2454 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGATGCAATGGCCAGAAGACATGAACGTGTCACTAGAAGGATGTGGACATGG Chimp: AGATGCAATGGCCAGAAGACAGGAACGTGTCACTAGAAGGATGTGGACA--- ↓ 1 43 2 Gorilla: AGATGCAATGGCCAGAAGACATGACAGTGTCACTAGAAGGATGTGGACATGG Human: AGATGCAATGGCCAGAAGACATGAACGTGTCACTAGAAGGATGTGGACATGG Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr3:77406124-77406128 Template switch process: F1: L CACTGGATATGCAGAGTTTAAGATGCAATGGCCAGAAGACA 1 F3: 4 GTGTCACTAGAAGGATGTGGACATGGGCTCCGGGACTGTT R RF: CACTCAATATGCAGAGTTTAAGATGCAATGGCCAGAAGACAGGAACGTGTCACTAGAAGGATGTGGACATGGGCTCCGGGACTGTT RR: GTGAGTTATACGTCTCAAATTCTACGTTACCGGTCTTCTGTCCTTGCACAGTGATCTTCCTACACCTGTACCCGAGGCCCTGACAA F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -59.8) ACTggATATGCAGAGTTTAAGATGCAATGGCCAGAAGACAtGAcaGTGTCACTAGAAGGATGTGGACAtgggctccgggactgtt ACTCAATATGCAGAGTTTAAGATGCAATGGCCAGAAGACAGGAACGTGTCACTAGAAGGATGTGGACA----------------- Template switch alignment (log-probability: -27.4) ACTggATATGCAGAGTTTAAGATGCAATGGCCAGAAGACA|TGACA|GTGTCACTAGAAGGATGTGGACATGGGCTCCGGGACTGTT ACTCAATATGCAGAGTTTAAGATGCAATGGCCAGAAGACA|TGACA|GTGTCACTAGAAGGATGTGGACATGGGCTCCGGGACTGTT ========== Event 2455 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCTTTGAAAGCCAAATACCAAAAGTGA--------AACTAAGAACACCATGATATAAGGA Chimp: CCTTTGAAAGCCAAATACCAAAGTTTC----ACTTCTCTAAGAACACCATGATGTAAGGA Gorilla: CCTTTGAAAGCCAAATACCAAAGTTTCACTT----CTCGAAGAACACCATGATATAAGGA ↓ 3 2 4 ↑ 3 1 4 Human: CCTTTGAAAGCCAAATACCAAAAGTGA--------AACTAAGAACACCATGATATAAGGA Cluster: [ ] Orangutan: cctttgaaagccaaataccaaagcttgactt----ctctaagaacaccatgATATAAGGA Gorilla > Human --------------- chr3:122082640-122082648 Template switch process: F1: L CTTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA 1 F3: 4 AAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG R RF: CTTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAAGTTTCACTTCTCGAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG RR: GAAATGGGAACTCTTTAAGGGAAACTTTCGGTTTATGGTTTCAAAGTGAAGAGCTTCTTGTGGTACTATATTCCTTCCGAAAATTTCTTCAATC F2: 3 TCAAAGTGA 2 Unidirectional alignment (log-probability: -34.2) TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA-------------agtgaaactAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAAGTTTCACTTCTCG---------AAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG Template switch alignment (log-probability: -16.9) TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA|AGTGAAACT|AAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA|AGTGAAACT|AAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG Human > Gorilla --------------- chr3:123719707-123719717 Template switch process: F1: L CTTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA 1 F3: 4 CGAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG R RF: CTTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAAAGTGAAACTAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTTAG RR: GAAATGGGAACTCTTTAAGGGAAACTTTCGGTTTATGGTTTTCACTTTGATTCTTGTGGTACTATATTCCTTCCGAAAATTTCTTCAATC F2: 3 TCTTCACTTTG 2 Unidirectional alignment (log-probability: -39.8) TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA---------gtttcacttctcgAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTT TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAAAGTGAAACT-------------AAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTT Template switch alignment (log-probability: -28.2) TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA|GTTTCACTTcT|CgAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTT TTTACCCTTGAGAAATTCCCTTTGAAAGCCAAATACCAAA|GTTTCACTTTT|CTAAGAACACCATGATATAAGGAAGGCTTTTAAAGAAGTT ========== Event 2456 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATACTGTTGATTTCCTGCTTAAATGC------TTCTG------ATAGAGTTTGTGAGCTAAAGTTA Chimp: ATACTGTTGATTTCCTGCTTAAATGC---TTCTTCTG------ATAGAGTTTGTGAGCTAAAGTTA ↓ 3 2 1 4 Gorilla: ATACTGTTGATTTCCTGCTTAAATGCTTC---TTCTGAGCATTTAAGAGTTTGTGAGCTAAAGTTA Human: ATACTGTTGATTTCCTGCTTAAATGC------TTCTG------ATAGAGTTTGTGAGCTAAAGTTA Cluster: [ ] Orangutan: ATACTGTTGATTTCCTGCTTAAATGCTTC---TTCTG------ATAGAGTTTGTGAGCTAAAGTTA Chimp > Gorilla --------------- chr3:123725567-123725573 Template switch process: F1: L AAAGCCTTGTCTAATATACTGTTGATTTCCTGCTTAAATGCTTCTTCTGA 1 F3: 4 AGAGTTTGTGAGCTAAAGTTAATTATGAAGGGAATTA R RF: AAAGCCTTGTCTAATATACTGTTGATTTCCTGCTTAAATGCTTCTTCTGATAGAGTTTGTGAGCTAAAGTTAATTATGAAGGGAATTA RR: TTTCGGAACAGATTATATGACAACTAAAGGACGAATTTACGAAGAAGACTATCTCAAACACTCGATTTCAATTAATACTTCCCTTAAT F2: 3 ATTTACG 2 Unidirectional alignment (log-probability: -25.1) CTAATATACTGTTGATTTCCTGCTTAAATGCTTCTTCTGAgcatttaAGAGTTTGTGAGCTAAAGTTAATTATGAAGGGAATTA CTAATATACTGTTGATTTCCTGCTTAAATGCTTCTTCTGA------TAGAGTTTGTGAGCTAAAGTTAATTATGAAGGGAATTA Template switch alignment (log-probability: -16.8) CTAATATACTGTTGATTTCCTGCTTAAATGCTTCTTCTGA|GCATTTA|AGAGTTTGTGAGCTAAAGTTAATTATGAAGGGAATTA CTAATATACTGTTGATTTCCTGCTTAAATGCTTCTTCTGA|GCATTTA|AGAGTTTGTGAGCTAAAGTTAATTATGAAGGGAATTA ========== Event 2457 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAG--------------------AACAATGCTAAGCCCTCAGTGCCA Chimp: TTATGATGGAGAAAATTATTTTGTATTTTGAGGGGAGAG----------AAGGGGATACAACAATGCTAAGCCCTCAGTGCCA Gorilla: TTATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAGAAGGGGATAC----------AAAAATGCTAAGCCCTCAGTGCCA ↑ 3 2 14 Human: TTATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAG--------------------AACAATGCTAAGCCCTCAGTGCCA Cluster: [ ] Orangutan: TTATGATGAAGAAAATTATTTTGTGTCTCAAGGGGAGGGAAGGGGATCC----------AACAATGCTAAGCCCTCAGTGCCA Human > Gorilla --------------- chr3:123063250-123063259 Template switch process: F1: L ATTTATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAGAAG 1 F3: 4 AATGCTAAGCCCTCAGTGCCAGGAGAAAACATTCATCTTT R RF: ATTTATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAGAACAATGCTAAGCCCTCAGTGCCAGGAGAAAACATTCATCTTG RR: TAAATACTACCTCTTTTAATAAAACATAGAGCTCCCCTCTCTTGTTACGATTCGGGAGTCACGGTCCTCTTTTGTAAGTAGAAC F2: 3 AAACATAGGG 2 Unidirectional alignment (log-probability: -39) ATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAGaaggggatacAAaAATGCTAAGCCCTCAGTGCCAGGAGAAAACATTCATCTTt ATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAG----------AACAATGCTAAGCCCTCAGTGCCAGGAGAAAACATTCATCTT- Template switch alignment (log-probability: -33.6) ATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAGAAg|GgGATACAAA|AATGCTAAGCCCTCAGTGCCAGGAGAAAACATTCATCTTt ATGATGGAGAAAATTATTTTGTATCTCGAGGGGAGAGAAC|GAGATACAAA|AATGCTAAGCCCTCAGTGCCAGGAGAAAACATTCATCTTG ========== Event 2458 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATACACAAATCATTAATGTTCAATTAAAATATGTCAAATTAATG------------------------------------------------------------------------------------------------------TTGTT-TTTTCTGATTTGATCATTAACCTGCTTATTTTAAATTTTAGATTGAGGTCTATTATT Chimp: AAATACACAAATCATTAATGTTCAATTAAAATATGTCAAATTAACGTTGTTTTTTCTGATTTGATCATTAACCTACTTATTTTAAATTAGAAAAAACAACGTTAATTTGACATATTTTAATTGAACATAAAAATATGTCAAATTAACGTTGTT-TTTTCTGATTTGATCATTAACCTACTTATTTTAAATTTTAGATTGAGGTCTATTATT ↑ 3 4 2 1 Gorilla: AAATACACAAATCATTAATGTTCAATTAAAATATGTCAAATTAACG------------------------------------------------------------------------------------------------------TTGTT-TTTTCTGATTTGATCATTAACCTGCTTATTTTAAATTTTAGATTGAGGTCTATTATT Human: AAATACACAAATCATTAATGTTCAATTAAAATATGTCAAATTAATG------------------------------------------------------------------------------------------------------TTGTT-TTTTCTGATTTGATCATTAACCTGCTTATTTTAAATTTTAGATTGAGGTCTATTATT Cluster: [ ] Orangutan: AAATACACAAATCATTAATATTCAATTAAAATATGTCAAATTAATG------------------------------------------------------------------------------------------------------TTGTTTTTTTCTGATTTGATCATTAACCTGCTTATTTTAAATTTTAGTTTGAGGTCTGTTATT Gorilla > Chimp --------------- chr3:124439764-124439801 Template switch process: F1: L CACAAATCATTAATGTTCAATTAAAATATGTCAAATTAACGTTGTTTTTTCTGATTTGATCATTAACCTACTTATTTTAAATT 1 F3: 4 ATAAAAATATGTCAAATTAACGTTGTTTTTTCTGATTTGATCATTAACCTACTTATTTTAAA R RF: CACAAATCATTAATGTTCAATTAAAATATGTCAAATTAACGTTGTTTTTTCTGATTTGATCATTAACCTGCTTATTTTAAATT RR: GTGTTTAGTAATTACAAGTTAATTTTATACAGTTTAATTGCAACAAAAAAGACTAAACTAGTAATTGGACGAATAAAATTTAA F2: 3 CAAGTTAATTTTATACAGTTTAATTGCAACAAAAAAGA 2 Unidirectional alignment (log-probability: -160) GTTTTTTCTGATTTGATCATTAACCTaCTTATTTTAAAttagaaaaaacaacgttaatttgacatattttaattgaacataaaaatatgtcaaattaacgttgttttttctgatttga GTTTTTTCTGATTTGATCATTAACCTGCTTATTTTAAA-------------------------------------------------------------------------------- Template switch alignment (log-probability: -38.4) GTTTTTTCTGATTTGATCATTAACCTaCTTATTTTAAATT|AGAAAAAACAACGTTAATTTGACATATTTTAATTGAAC|ATaAAAATATGTCAAATTAACGTTGTTTTTTCTGATTTGA GTTTTTTCTGATTTGATCATTAACCTGCTTATTTTAAATT|AGAAAAAACAACGTTAATTTGACATATTTTAATTGAAC|ATTAAAATATGTCAAATTAACGTTGTTTTTTCTGATTTGA ========== Event 2459 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGAGAAAAATGTATTTATGTGTACATGTATGTATATGTATAGTAac Chimp: aaaaagaaaaaTGTATTTATGCGTACATGTATGTATATGTATAGTAac ↓ 13 24 Gorilla: AAAGAGAAAAATGTATTTATGTGTACGTGTATGTATATGTATAGTAac Human: AAAGAGAAAAATGTATTTATGTGTACATGTATGTATATGTATAGTAac Cluster: [ ] Orangutan: AAAGAGAAAAATGTATTTATGTGTACATGTATGTATATGTGTAGTAac Chimp > Gorilla --------------- chr3:123124981-123124986 Template switch process: F1: L AAGCAGGACAAGAATTTCAAAAAGAGAAAAATGTATTTATG 1 F3: 4 TGTATGTATATGTATAGTAACACACACACACACACACAC R RF: AAGCAGGACAAGAATTTCAAAAAAAGAAAAATGTATTTATGCGTACATGTATGTATATGTATAGTAACACACACACACACACACAC RR: TTCGTCCTGTTCTTAAAGTTTTTTTCTTTTTACATAAATACGCATGTACATACATATACATATCATTGTGTGTGTGTGTGTGTGTG F2: 3 GCATGT 2 Unidirectional alignment (log-probability: -34.5) AGCAGGACAAGAATTTCAAAAAgAGAAAAATGTATTTATGtGTACgTGTATGTATATGTATAGTAACACACACACACAcacacac AGCAGGACAAGAATTTCAAAAAAAGAAAAATGTATTTATGCGTACATGTATGTATATGTATAGTAACACACACACACA------- Template switch alignment (log-probability: -22) AGCAGGACAAGAATTTCAAAAAgAGAAAAATGTATTTATG|TGTACG|TGTATGTATATGTATAGTAACACACACACACACACACAC AGCAGGACAAGAATTTCAAAAAAAGAAAAATGTATTTATG|TGTACG|TGTATGTATATGTATAGTAACACACACACACACACACAC ========== Event 2460 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATAAAATTATATATTTTCAA----------------ATGAGTTTTTAAAATTATATCCAAGAAACTTaaaa-a--aaaaaagaaaaGCACTAGCCATTCTCACTTGCATCCATCCATCCCTGAGTTAAAATTCTGAGGATTATTATCTCACCTCCTATTTGGACCTGCTTTCTAGGTTACTATTTGTTTCTATAT ↓ 4 1 3 2 Chimp: AATAAAATTATATATTTTCAA--------ATCTAGGAATGAGTTTTTAAAATTATATCCAAGAAACTTaaaa--aaaaaaaaGAAAAGCACTAGCCATTCTCACTTGCATCCATCCATCCCTGAGTTAAAATTCTGAGGATTATTATCTCACCTCCTATTTGGACCTGCTTTCTAGGTTACTATTTGTTTCTATAT Gorilla: AATAAAATTATATATTTTCAAATCTAGGA--------ATAAGTTTTTAAAATTATATCCAAGAAACTTaaaa-----aaaaaGAAAAGTACTAGCCATTCTCACTTGCATCCATCCATCCCTGAGTTAAAATTCTGAGGATTATTATCTCACCTCCTATTTGGACCTGCTTTCTAGGTTACTGTTTGTTTGTATAT Human: AATAAAATTATATATTTTCAA----------------ATGAGTTTTTAAAATTATATCCAAGAAACTTaaaa-a--aaaaaagaaaaGCACTAGCCATTCTCACTTGCATCCATCCATCCCTGAGTTAAAATTCTGAGGATTATTATCTCACCTCCTATTTGGACCTGCTTTCTAGGTTACTATTTGTTTCTATAT Cluster: [ ] Orangutan: AATAAAATTATATATTTTCAAATCTAGGA--------ATGAGTTTTTAAAATTATATCCAAGAAACTTaaaaa---aaaaaaGAGAAGCACTA-GCATCCTCACTTGCATCTGTCCTTCCCTGAGTTAAAATTCTGAGGGTTGTTATCTCACCTCCTATTTGGACCTGCTTTCTAGTCTACTATTTGTTTCTATAT Human > Chimp ------------- chr3:78908829-78908832 Template switch process: F1: L TTTTTGATATCCAAATAACCAATAAAATTATATATTTTCAAAT 1 F3: 4 GAATGAGTTTTTAAAATTATATCCAAGAAACTTAAAAAAAA R RF: TTTTTGATATCCAAATAACCAATAAAATTATATATTTTCAAATGAGTTTTTAAAATTATATCCAAGAAACTTAAAAAAAAAAAGAAAAGCACTAGCCATTCTCACTTGCATCCATCCATCCCTGAGTTAAAATTCTGAGGATTATTATCTCACCTCCTATTTGGACCTGCTTTCTAG RR: AAAAACTATAGGTTTATTGGTTATTTTAATATATAAAAGTTTACTCAAAAATTTTAATATAGGTTCTTTGAATTTTTTTTTTTCTTTTCGTGATCGGTAAGAGTGAACGTAGGTAGGTAGGGACTCAATTTTAAGACTCCTAATAATAGAGTGGAGGATAAACCTGGACGAAAGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -31.1) TTGATATCCAAATAACCAATAAAATTATATATTTTCAaatctaggAATGAGTTTTTAAAATTATATCCAAGAAACTTAAAAAAA TTGATATCCAAATAACCAATAAAATTATATATTTTCA--------AATGAGTTTTTAAAATTATATCCAAGAAACTTAAAAAAA Template switch alignment (log-probability: -21.8) TTGATATCCAAATAACCAATAAAATTATATATTTTCAAAT|CTAG|gAATGAGTTTTTAAAATTATATCCAAGAAACTTAAAAAAA TTGATATCCAAATAACCAATAAAATTATATATTTTCAAAT|CTAG|AAATGAGTTTTTAAAATTATATCCAAGAAACTTAAAAAAA ========== Event 2461 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTAGAAATAAGAAATGATTCATAAG----TATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACAT Chimp: TTTAGAAATAAGAAATGATTCATAAG----TATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACAT ↓ 1 4 3 2 Gorilla: TTTAGAAATAAGAAATGATTCCTAATTTGCATTTGCTTGTGAATGCAAACCAAAAGTCAGATACCACAT ↑ 1 4 3 2 Human: TTTAGAAATAAGAAATGATTCATAAG----TATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACAT Cluster: [ ] Orangutan: TTTAGAAATAAGAAATGATTCATAAG----TATTGCTTGTGAATGCAAACCAAAAGTCAGATATCACAT Human > Gorilla --------------- chr3:78784389-78784396 Template switch process: F1: L AATTTTAAAAACAACAATATTTTAGAAATAAGAAATGATTCCTAA 1 F3: 4 TGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA R RF: AATTTTAAAAACAACAATATTTTAGAAATAAGAAATGATTCATAAGTATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA RR: TTAAAATTTTTGTTGTTATAAAATCTTTATTCTTTACTAAGTATTCATAACGAACACTTACGTTTGGTTTTCAGTCTATGGTGTACGT F2: 3 TTACGTTT 2 Unidirectional alignment (log-probability: -33.3) TAAAAACAACAATATTTTAGAAATAAGAAATGATTCcTAAtTtgcatTTGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA TAAAAACAACAATATTTTAGAAATAAGAAATGATTCATAAGT----ATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA Template switch alignment (log-probability: -22.3) TAAAAACAACAATATTTTAGAAATAAGAAATGATTCcTAA|TTTGCATT|TGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA TAAAAACAACAATATTTTAGAAATAAGAAATGATTCATAA|TTTGCATT|TGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA Chimp > Gorilla --------------- chr3:78784389-78784396 Template switch process: F1: L AATTTTAAAAACAACAATATTTTAGAAATAAGAAATGATTCCTAA 1 F3: 4 TGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA R RF: AATTTTAAAAACAACAATATTTTAGAAATAAGAAATGATTCATAAGTATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA RR: TTAAAATTTTTGTTGTTATAAAATCTTTATTCTTTACTAAGTATTCATAACGAACACTTACGTTTGGTTTTCAGTCTATGGTGTACGT F2: 3 TTACGTTT 2 Unidirectional alignment (log-probability: -33.3) TAAAAACAACAATATTTTAGAAATAAGAAATGATTCcTAAtTtgcatTTGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA TAAAAACAACAATATTTTAGAAATAAGAAATGATTCATAAGT----ATTGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA Template switch alignment (log-probability: -22.3) TAAAAACAACAATATTTTAGAAATAAGAAATGATTCcTAA|TTTGCATT|TGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA TAAAAACAACAATATTTTAGAAATAAGAAATGATTCATAA|TTTGCATT|TGCTTGTGAATGCAAACCAAAAGTCAGATACCACATGCA ========== Event 2462 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAATTGAGAATGAGGAAAACTACTACGCTGTGAAAAATACAGCGTA-------------------------GTATTTTGGCTTTGTTAGTTTTGTA Chimp: CAATTGAGAATGAGgaaaaatactacgctgtgaaaaatactatgct----------gtgaaaaatacAAGGTTCCTTTGGCTTTGTTAGTTTTGTA Gorilla: CAATTGAGAATGAGGAAAAATACTACGCTGTGAA------------AAATACAAGG---------------TTCCTTTGGCTTTGTTAGTTTTGTA ↓ 3 2 1 4 Human: CAATTGAGAATGAGGAAAACTACTACGCTGTGAAAAATACAGCGTA-------------------------GTATTTTGGCTTTGTTAGTTTTGTA Cluster: [ ] Orangutan: CAATTGAGAAAAAGGAAAAATACTATGCTGTGAA------------AAATACAAAG---------------TTCCTTTGGCTTTGTTAGTTTTGTA Gorilla > Human --------------- chr3:120725457-120725465 Template switch process: F1: L CTTTTTTCAATTGAGAATGAGGAAAACTACTACGCTGTGAAAAATACA 1 F3: 4 TTTGGCTTTGTTAGTTTTGTATCTACTCAAGGGTACTGAA R RF: CTTTTTTCAATTGAGAATGAGGAAAAATACTACGCTGTGAAAAATACAAGGTTCCTTTGGCTTTGTTAGTTTTGTACCTACTCAAGGGTACTGAA RR: GAAAAAAGTTAACTCTTACTCCTTTTTATGATGCGACACTTTTTATGTTCCAAGGAAACCGAAACAATCAAAACATGGATGAGTTCCCATGACTT F2: 3 TATGATGCG 2 Unidirectional alignment (log-probability: -45.1) AATTGAGAATGAGGAAAAcTACTACGCTGTGAAAAATACA-------gcgtagtatTTTGGCTTTGTTAGTTTTGTAtCTACTCAAGGGTACTGAA AATTGAGAATGAGGAAAAATACTACGCTGTGAAAAATACAAGGTTCC---------TTTGGCTTTGTTAGTTTTGTACCTACTCAAGGGTACTGAA Template switch alignment (log-probability: -28.1) AATTGAGAATGAGGAAAAcTACTACGCTGTGAAAAATACA|GCGTAGTAT|TTTGGCTTTGTTAGTTTTGTAtCTACTCAAGGGTACTGAA AATTGAGAATGAGGAAAAATACTACGCTGTGAAAAATACA|GCGTAGTAT|TTTGGCTTTGTTAGTTTTGTACCTACTCAAGGGTACTGAA ========== Event 2463 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATAGTATTTATAATTCAATTATGTCTT-------TGTTTATCCTTTTCAGAGCT---- ↓ 3 2 1 4 Chimp: TATAGTATTTATAATTCAATTATGTCTTTCAGACATAATTATCCTTTTCAGAGCT---- ↑ 3 2 1 4 Gorilla: TATAGTATTTATAATTCAATTATGTCTT-------TGTTTATCCTTTTCAGAGCT---- Human: TATAGTATTTATAATTCAATTATGTCTT-------TGTTTATCCTTTTCAGAGCT---- Cluster: [ ] Orangutan: TAGAGTATTTCTAATTCAATTATGTCTT-------TGTTTATCCTTTTCAGAACTTACT Human > Chimp ------------- chr3:124633455-124633462 Template switch process: F1: L GTAATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTTC 1 F3: 4 TTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA R RF: GTAATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTTGTTTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA RR: CATTAGCTGGACCATATCATAAATATTAAGTTAATACAGAAACAAATAGGAAAAGTCTCGAGACTTCTCCTTGAATGAGATATT F2: 3 AATACAGA 2 Unidirectional alignment (log-probability: -33) ATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTTcagacataaTTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA ATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTT-------GTTTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA Template switch alignment (log-probability: -22.3) ATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTTc|AGACATAA|TTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA ATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTTG|AGACATAA|TTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA Gorilla > Chimp --------------- chr3:124633455-124633462 Template switch process: F1: L GTAATCGACCTGGTATAGTATTTATAATTCAATTATGTCTTTC 1 F3: 4 TTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA R RF: GTAATTGACCTGGTATAGTATTTATAATTCAATTATGTCTTTGTTTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA RR: CATTAACTGGACCATATCATAAATATTAAGTTAATACAGAAACAAATAGGAAAAGTCTCGAGACTTCTCCTTGAATGAGATATT F2: 3 AATACAGA 2 Unidirectional alignment (log-probability: -37.5) ATcGACCTGGTATAGTATTTATAATTCAATTATGTCTTtcagacaTaaTTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA ATTGACCTGGTATAGTATTTATAATTCAATTATGTCTT-------TGTTTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA Template switch alignment (log-probability: -27.8) ATcGACCTGGTATAGTATTTATAATTCAATTATGTCTTTc|AGACATAA|TTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA ATTGACCTGGTATAGTATTTATAATTCAATTATGTCTTTG|AGACATAA|TTATCCTTTTCAGAGCTCTGAAGAGGAACTTACTCTATAA ========== Event 2464 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TACTACCCAGAGGATGAAAGAATAACCAGGATAACCTGGTTGTTTTAGAGAGTCATATTTT ↑ 13 4 2 Chimp: TACTACCCAGAGGATGAAAGA-------AGTTATCCTGGTTGTTTTAGAGAGTCATATTTT Gorilla: TACTACCCAGAGGATGAAAGA-------AGTTATCCTGGTTGTTTTAGAGAGTCATATTTT ↓ 13 4 2 Human: TACTACCCAGAGGATGAAAGAATAACCAGGATAACCTGGTTGTTTTAGAGAGTCATATTTT Cluster: [ ] Orangutan: ---AAGCCAGAGGATGAAAGA-------AGTTATCCTGGTTGTTTTAAAGAGTCATATTTT Chimp > Human ------------- chr3:118881081-118881091 Template switch process: F1: L ACAACATATGAATAAATATATACTACCCAGAGGATGAAAGAAT 1 F3: 4 CCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT R RF: ACAACATATGAATAAATATATACTACCCAGAGGATGAAAGAAGTTATCCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT RR: TGTTGTATACTTATTTATATATGATGGGTCTCCTACTTTCTTCAATAGGACCAACAAAATCTCTCAGTATAAAATTACAATTTTACA F2: 3 AATAGGACCAA 2 Unidirectional alignment (log-probability: -33) ACATATGAATAAATATATACTACCCAGAGGATGAAAGAAtaaccagGaTAaCCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT ACATATGAATAAATATATACTACCCAGAGGATGAAAGAA-------GTTATCCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT Template switch alignment (log-probability: -22.7) ACATATGAATAAATATATACTACCCAGAGGATGAAAGAAt|AACCAGGATAA|CCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT ACATATGAATAAATATATACTACCCAGAGGATGAAAGAAG|AACCAGGATAA|CCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT Gorilla > Human --------------- chr3:118881081-118881091 Template switch process: F1: L ACAACATATGAATAAATATATACTACCCAGAGGATGAAAGAAT 1 F3: 4 CCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT R RF: ACAACATATGAATAAATATATACTACCCAGAGGATGAAAGAAGTTATCCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT RR: TGTTGTATACTTATTTATATATGATGGGTCTCCTACTTTCTTCAATAGGACCAACAAAATCTCTCAGTATAAAATTACAATTTTACA F2: 3 AATAGGACCAA 2 Unidirectional alignment (log-probability: -32.1) ACATATGAATAAATATATACTACCCAGAGGATGAAAGAAtaaccagGaTAaCCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT ACATATGAATAAATATATACTACCCAGAGGATGAAAGAA-------GTTATCCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT Template switch alignment (log-probability: -22.7) ACATATGAATAAATATATACTACCCAGAGGATGAAAGAAt|AACCAGGATAA|CCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT ACATATGAATAAATATATACTACCCAGAGGATGAAAGAAG|AACCAGGATAA|CCTGGTTGTTTTAGAGAGTCATATTTTAATGTTAAAATGT ========== Event 2465 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGGAGAAGTGGGGGAGGGTG----CAATGTGCAATCAAATGAGAGCTAGAGAAAAGaaaaaaaaa------------------------------aaaaaCAACAACAGCAACCACCATTGCCACTCTCACACTGAGAGGAA Chimp: ATGGAGAAGTGGGGGAGGGTG----CAAAGTGCAATCAAATGAGAGCTAGAGAAAAGaaaaa----------------------------aaaaaaaaCAACAACAACAGCAACCACCATTGCCACTCTCACACTGAGAGGAA ↓ 1 4 3 2 Gorilla: ATGGAGAAGTGGGGGAGGGTGCAAGCAATGTGCAATCAAATGAGAGCTAGAGaaaagaaaaaaaaa---------aaaaaaaaaaaaaaa------aaaaaaaaCAACAGCAACCACCATTGCCACTCTCACACTGAGAGGAA Human: ATGGAGAAGTGGGGGAGGGTG----CAATGTGCAATCAAATGAGAGCTAGAGAAAAGaaaaaaaaa------------------------------aaaaaCAACAACAGCAACCACCATTGCCACTCTCACACTGAGAGGAA Cluster: [ ] Orangutan: ATGGAGAAGTGGGGGAGGGTG----CAACGTGCAATCAAATGAGAGCTAGagaaaagaaaagaaaacaaaacaaa---------------------aagaaaaaaaCCAGCAACCACCACTGCCACTCTCACACTGAGAGGAA Chimp > Gorilla --------------- chr3:120704052-120704056 Template switch process: F1: L GCTACAAACAGCCTCCCTCTATGGAGAAGTGGGGGAGGGTGCAA 1 F3: 4 GTGCAATCAAATGAGAGCTAGAGAAAAGAAAAAAAAAAAA R RF: GCTACAAACAGCCTCCCTCTATGGAGAAGTGGGGGAGGGTGCAAAGTGCAATCAAATGAGAGCTAGAGAAAAGAAAAAAAAAAAAACAACAACAACAGCAACCACCATTGC RR: CGATGTTTGTCGGAGGGAGATACCTCTTCACCCCCTCCCACGTTTCACGTTAGTTTACTCTCGATCTCTTTTCTTTTTTTTTTTTTGTTGTTGTTGTCGTTGGTGGTAACG F2: 3 TAACG 2 Unidirectional alignment (log-probability: -38.9) CAAACAGCCTCCCTCTATGGAGAAGTGGGGGAGGGTgcaaGCAAtGTGCAATCAAATGAGAGCTAGAGAAAAGAAAAAaaaaaaa CAAACAGCCTCCCTCTATGGAGAAGTGGGGGAGGGT----GCAAAGTGCAATCAAATGAGAGCTAGAGAAAAGAAAAA------- Template switch alignment (log-probability: -16.4) CAAACAGCCTCCCTCTATGGAGAAGTGGGGGAGGGTGCAA|GCAAT|GTGCAATCAAATGAGAGCTAGAGAAAAGAAAAAAAAAAAA CAAACAGCCTCCCTCTATGGAGAAGTGGGGGAGGGTGCAA|GCAAT|GTGCAATCAAATGAGAGCTAGAGAAAAGAAAAAAAAAAAA ========== Event 2466 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTGGAGCTAAACTTGAGAGGTACATTTAACCTACAACAAAT----------AACCTAGCaaaaaaa--------- Chimp: ACTGGAGCTAAACTTGAGAGGTACATGTAACCTACAACAAAT-----ATCGTACCCTAGCaaaaa----------- Gorilla: ACTGGAGCTAAACTTGAGAGGTACATTTAACCTACAACAAATATCGT-----ACCCTAGCaaaaaaa----aaaaa ↑ 3 2 14 Human: ACTGGAGCTAAACTTGAGAGGTACATTTAACCTACAACAAAT----------AACCTAGCaaaaaaa--------- Cluster: [ ] Orangutan: ACTGGAGCTAAACTTGAGAGGTACATTTAACCTACAACAAATATCAT-----ACCCTAGCaaaaa--aaaa----- Human > Gorilla --------------- chr3:80392484-80392488 Template switch process: F1: L CTGGAGCTAAACTTGAGAGGTACATTTAACCTACAACAAATATC 1 F3: 4 CTAGCAAAAAAAAAAAAAAAAAAAAAAAA R RF: CTGGAGCTAAACTTGAGAGGTACATTTAACCTACAACAAATAACCTAGCAAAAAAAAGAAAAAAAAAAAAAAA RR: GACCTCGATTTGAACTCTCCATGTAAATTGGATGTTGTTTATTGGATCGTTTTTTTTCTTTTTTTTTTTTTTT F2: 3 CCATG 2 Unidirectional alignment (log-probability: -40) AGCTAAACTTGAGAGGTACATTTAACCTACAACAAAtatcgTAcCCTAGCAAAAAAAAaAAAAAAAAAAAAaaa AGCTAAACTTGAGAGGTACATTTAACCTACAACAAA-----TAACCTAGCAAAAAAAAGAAAAAAAAAAAA--- Template switch alignment (log-probability: -27.2) AGCTAAACTTGAGAGGTACATTTAACCTACAACAAATAtC|GTACC|CTAGCAAAAAAAAaAAAAAAAAAAAAAAA AGCTAAACTTGAGAGGTACATTTAACCTACAACAAATAAC|GTACC|CTAGCAAAAAAAAGAAAAAAAAAAAAAAA ========== Event 2467 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTCTGAAAGTCCTTACAAATTCACCTGT-ATCTAAACACAATCA-AGGTTTTAGTTGAAA------TGTCACTGCCTAGTGTCAAG Chimp: TTTCTGAAAGTCCTTACAAATTCACCTGT-ATCTAAACACAATCA-AGGTTTTAGTTGAAA---TGTTGTCACTGCCTAGTGTCAAG ↓ 1 4 3 2 Gorilla: ----------------------AACCTTG-ATTTAAACACAATCA-AGGTTTTAGTTGAAATGT---TGTCACTGCCTAGTGTCAAG Human: TTTCTGAAAGTCCTTACAAATTCACCTGT-ATCTAAACACAATCA-AGGTTTTAGTTGAAA------TGTCACTGCCTAGTGTCAAG Cluster: [ ] Orangutan: ----------------------CACCTGTACTCTAAAGACAATCAAAGGTTTTAGCTGAAATGT---TGTCACTGCCCAGTGTCAAG Chimp > Gorilla --------------- chr3:79548494-79548501 Template switch process: F1: L AA 1 F3: 4 TAAACACAATCAAGGTTTTAGTTGAAATGTTGTCACTGCCTAGTGTCAAGTATTTTCTCCTGGGACTTTT R RF: AATTCACCTGTATCTAAACACAATCAAGGTTTTAGTTGAAATGTTGTCACTGCCTAGTGTCAAGTATTTTCTCCTGGGACTTTT RR: TTAAGTGGACATAGATTTGTGTTAGTTCCAAAATCAACTTTACAACAGTGACGGATCACAGTTCATAAAAGAGGACCCTGAAAA F2: 3 TTAGTTCC 2 Unidirectional alignment (log-probability: -27.6) A----ACCTtgATtTAAACACAATCAAGGTTTTAGTTGAAATGTTGTCACTGCC AATTCACCTGTATCTAAACACAATCAAGGTTTTAGTTGAAATGTTGTCACTGCC Template switch alignment (log-probability: -16.5) AA|CCTTGATT|TAAACACAATCAAGGTTTTAGTTGAAATGTTGTCACTGCC AA|CCTTGATT|TAAACACAATCAAGGTTTTAGTTGAAATGTTGTCACTGCC ========== Event 2468 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GAAGCAATGGAACCAGAGGAAA----------------------------------------TATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCCAGAAATGTCTGATAGACTCAGAGATATATCATTATTTTATATGAATATATCATATTACT ↓ 4 1 3 2 Chimp: GAAGCAATGGAACCAGAGGAAA--------------------TATTGTTAAAATACTGAAAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCCAGAAATGTCTGATAGACTCAGAGATATATCATTATTTTATATGAATATATCATATTACT Gorilla: GAAGCAATGGAACCAGAGGAAATATTGTTAAAATACTGAAAA--------------------TATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCCAGAAATGTCTGATAGACTCAGAGATATATCATTATTTTATATGAATATATCATATTACT ↑ 4 1 3 2 Human: GAAGCAATGGAACCAGAGGAAA----------------------------------------TATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCCAGAAATGTCTGATAGACTCAGAGATATATCATTATTTTATATGAATATATCATATTACT Cluster: [ ] Orangutan: GAAGCAATGGAGCCAGAGGAAATATTGTTaaaatactgaaaa--------------------tattgaaaatgctgCATTAAAATGAGGAAACACTGAGCTCAGAAATGTCTGATACACTCAGAGATATATCATTATTTTATATGAATATATCATATTACC Human > Chimp ------------- chr3:121495133-121495143 Template switch process: F1: L TGATCCAGTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGT 1 F3: 4 AAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCC R RF: TGATCCAGTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCCAGAAATGTCTGATAGACTCAGAGATATATCATTATTTTA RR: ACTAGGTCAACTTTCTAATCTTCGTTACCTTGGTCTCCTTTATAACTTTCACGACATAATTTTACTCCTTTGTGACTCGGGTCTTTACAGACTATCTGAGTCTCTATATAGTAATAAAAT F2: 3 AGTCATAAAAT 2 Unidirectional alignment (log-probability: -39.7) GTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGttaaaatactgaaaatattgAAAGTGCTGTATTAAAATGAGGAAACACTGAG GTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTG--------------------AAAGTGCTGTATTAAAATGAGGAAACACTGAG Template switch alignment (log-probability: -28.8) GTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGt|TAAAATAcTGA|AAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAG GTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGA|TAAAATAATGA|AAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAG Human > Gorilla --------------- chr3:120266567-120266577 Template switch process: F1: L TGATCCAGTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGT 1 F3: 4 AAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCC R RF: TGATCCAGTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAGCCCAGAAATGTCTGATAGACTCAGAGATATATCATTATTTTA RR: ACTAGGTCAACTTTCTAATCTTCGTTACCTTGGTCTCCTTTATAACTTTCACGACATAATTTTACTCCTTTGTGACTCGGGTCTTTACAGACTATCTGAGTCTCTATATAGTAATAAAAT F2: 3 AGTCATAAAAT 2 Unidirectional alignment (log-probability: -39.6) GTTGAAAGATTAGAAGCAATGGAACCAGAGGAaatattgttaaaatactgaaAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAG GTTGAAAGATTAGAAGCAATGGAACCAGAGGA--------------------AATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAG Template switch alignment (log-probability: -28.4) GTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGt|TAAAATAcTGA|AAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAG GTTGAAAGATTAGAAGCAATGGAACCAGAGGAAATATTGA|TAAAATAATGA|AAATATTGAAAGTGCTGTATTAAAATGAGGAAACACTGAG ========== Event 2469 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AACTTTTTTTGGGTACAAGGCATCATTGCTTTTAGCTCTATATTGTGTCAAGTGAAAATGGAACACAATAAAATGATAGCTGGAAATT--------AGGATGCAGTGAATTGAATTACTTAATT Chimp: AACTCTTTTTGGGTACAAGGCATCATTGCTTTTAGCTCTATATTGTGTCAAGTGAAAATGGAACACAATAAAATGATAGCTGGAAATT----AGAGAGGACGTAGTGAATTGAATTACTTAATT Gorilla: AACTCTTTTTGGGTACAAGGCATCATTGCTTTTAGCTCTATATTGTGTCAAGTGAAAATGGAACACAGTAAAATGATAGCTGGAAATTAGAG----AGGACATAGTGAATTGAATAACTTAATT ↓ 3 2 1 4 Human: AACTTTTTTTGGGTACAAGGCATCATTGCTTTTAGCTCTATATTGTGTCAAGTGAAAATGGAACACAATAAAATGATAGCTGGAAATT--------AGGATGCAGTGAATTGAATTACTTAATT Cluster: [ ] Orangutan: AACTCTTTTTGGGTACAAGGCATCATTGCTTTTAGCTCCATATTGTGTCAAGTGAAGATGAAACACAATAAAATGATAGCTGGAAATTAGAG----AGGACGTAGTGAATTGAATTACTTAATT Gorilla > Human --------------- chr3:118573230-118573234 Template switch process: F1: L TCAAGTGAAAATGGAACACAATAAAATGATAGCTGGAAATTAG 1 F3: 4 AGTGAATTGAATTACTTAATTGCAAGCTTAGATTTCTAAA R RF: GCATCATTGCTTTTAGCTCTATATTGTGTCAAGTGAAAATGGAACACAGTAAAATGATAGCTGGAAATTAGAGAGGACATAGTGAATTGAATAACTTAATTGCAAGCTTAGATTTCTAAA RR: CGTAGTAACGAAAATCGAGATATAACACAGTTCACTTTTACCTTGTGTCATTTTACTATCGACCTTTAATCTCTCCTGTATCACTTAACTTATTGAATTAACGTTCGAATCTAAAGATTT F2: 3 CGTAG 2 Unidirectional alignment (log-probability: -38.8) AGTGAAAATGGAACACAaTAAAATGATAGCTGGAAATT----AGGAtgcAGTGAATTGAATtACTTAATTGCAAGCTTAGATTTCTAAA AGTGAAAATGGAACACAGTAAAATGATAGCTGGAAATTAGAGAGGACATAGTGAATTGAATAACTTAATTGCAAGCTTAGATTTCTAAA Template switch alignment (log-probability: -27.4) AGTGAAAATGGAACACAaTAAAATGATAGCTGGAAATTAG|GATGC|AGTGAATTGAATtACTTAATTGCAAGCTTAGATTTCTAAA AGTGAAAATGGAACACAGTAAAATGATAGCTGGAAATTAG|GATGC|AGTGAATTGAATAACTTAATTGCAAGCTTAGATTTCTAAA ========== Event 2470 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TT-TTTTCCAAATAACTTTGG-----ATTCTTTATGTAAATTACTGGTGTTTTGACTGGCTCAGTTAAATTT Chimp: TT-TTTTCCAAATAACTTTGGAAAAAACTAGTAATTTACATTACTAGTGTTTTGACTGGCTCAGTTAAATTT ↑ 1 3 4 2 Gorilla: TT-TTTTCCAAATAACTTTGG-----ATTCTTTATGTAAATTACTAGTGTTTTGACTGGCTCAGTTAAATTT Human: TT-TTTTCCAAATAACTTTGG-----ATTCTTTATGTAAATTACTGGTGTTTTGACTGGCTCAGTTAAATTT Cluster: [ ] Orangutan: TTTTTTTCCAAATAACTTTGG-----ATTATTTATGTAAATTACTAGTGTTTTGACTGGCTCAGTTAAATTT Gorilla > Chimp --------------- chr3:121361942-121361958 Template switch process: F1: L TTTAAAGATTAGTTATTTATATTTTTTCCAAATAACTTTGGA 1 F3: 4 ATTACTAGTGTTTTGACTGGCTCAGTTAAATTTCAGCATT R RF: TTTAAAGATTAGTTATTTATATTTTTTCCAAATAACTTTGGATTCTTTATGTAAATTACTAGTGTTTTGACTGGCTCAGTTAAATTTCAGCATT RR: AAATTTCTAATCAATAAATATAAAAAAGGTTTATTGAAACCTAAGAAATACATTTAATGATCACAAAACTGACCGAGTCAATTTAAAGTCGTAA F2: 3 CATTTAATGATCAAAAA 2 Unidirectional alignment (log-probability: -42.7) TAAAGATTAGTTATTTATATTTTTTCCAAATAACTTTGGA----------AAaaactagtaatttacATTACTAGTGTTTTGACTGGCTCAGTTAAATTTCAGCATT TAAAGATTAGTTATTTATATTTTTTCCAAATAACTTTGGATTCTTTATGTAA---------------ATTACTAGTGTTTTGACTGGCTCAGTTAAATTTCAGCATT Template switch alignment (log-probability: -23.4) TAAAGATTAGTTATTTATATTTTTTCCAAATAACTTTGGA|AAAaACTAGTAATTTAC|ATTACTAGTGTTTTGACTGGCTCAGTTAAATTTCAGCATT TAAAGATTAGTTATTTATATTTTTTCCAAATAACTTTGGA|AAACACTAGTAATTTAC|ATTACTAGTGTTTTGACTGGCTCAGTTAAATTTCAGCATT ========== Event 2471 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GCCTCTTTATATGATCAAGTGTTAAATATTCTTGTTAAATATGTTAATATTCCAGTGTTAAATATTTTCCCCACAT ↓ 1 4 3 2 Chimp: GCCTCTTTATATGATCAAGTGAC-----------------------TGATTCCAGTGTTAAATATTTTCCCCACAT Gorilla: GCCTCTTTATATGATCAAGTGAC-----------------------TGATTCCAGTGTTAAATATTTTCCCCACAT ↑ 1 4 3 2 Human: GCCTCTTTATATGATCAAGTGTTAAATATTCTTGTTAAATATGTTAATATTCCAGTGTTAAATATTTTCCCCACAT Cluster: [ ] Orangutan: ATCTCTTCATATGATCAAGTGAC-----------------------TGATTCCAGTGTTAAATAGTTTCCCCACAT Human > Chimp ------------- chr3:119886767-119886770 Template switch process: F1: L CACTAGTATTATCTCACTTTGCCTCTTTATATGATCAAGTG 1 F3: 4 ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA R RF: CACTAGTATTTTCTCACTTTGCCTCTTTATATGATCAAGTGTTAAATATTCTTGTTAAATATGTTAATATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA RR: GTGATCATAAAAGAGTGAAACGGAGAAATATACTAGTTCACAATTTATAAGAACAATTTATACAATTATAAGGTCACAATTTATAAAAGGGGTGTACGGTCGTCGGTT F2: 3 GTCA 2 Unidirectional alignment (log-probability: -34.3) ACTAGTATTaTCTCACTTTGCCTCTTTATATGATCAAGtgacTG---------------------------ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA ACTAGTATTTTCTCACTTTGCCTCTTTATATGATCAAG----TGTTAAATATTCTTGTTAAATATGTTAATATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA Template switch alignment (log-probability: -21.8) ACTAGTATTaTCTCACTTTGCCTCTTTATATGATCAAGTG|ACTG|ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA ACTAGTATTTTCTCACTTTGCCTCTTTATATGATCAAGTG|ACTG|ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA Human > Gorilla --------------- chr3:118698854-118698857 Template switch process: F1: L CACTAGTACTATCTCACTTTGCCTCTTTATATGATCAAGTG 1 F3: 4 ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA R RF: CACTAGTATTTTCTCACTTTGCCTCTTTATATGATCAAGTGTTAAATATTCTTGTTAAATATGTTAATATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA RR: GTGATCATAAAAGAGTGAAACGGAGAAATATACTAGTTCACAATTTATAAGAACAATTTATACAATTATAAGGTCACAATTTATAAAAGGGGTGTACGGTCGTCGGTT F2: 3 GTCA 2 Unidirectional alignment (log-probability: -38.8) ACTAGTAcTaTCTCACTTTGCCTCTTTATATGATCAAGtgacTG---------------------------ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA ACTAGTATTTTCTCACTTTGCCTCTTTATATGATCAAG----TGTTAAATATTCTTGTTAAATATGTTAATATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA Template switch alignment (log-probability: -27.3) ACTAGTAcTaTCTCACTTTGCCTCTTTATATGATCAAGTG|ACTG|ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA ACTAGTATTTTCTCACTTTGCCTCTTTATATGATCAAGTG|ACTG|ATTCCAGTGTTAAATATTTTCCCCACATGCCAGCAGCCAA ========== Event 2472 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCACAAGCAGCTCATGGACTTTATG--G------------------------CAATTGCCTTTTCTAGAGCC Chimp: GTCATAAGCAGCTCATGGACTTTATGTTG-----------CCATAAAGTCCTAAACTTGCCTTTTCTAGAACC ↑ 3 1 2 4 Gorilla: GTCATAAGCAGCTCATGGACTTTATG--GCAATCCTCCTA-------------AACTTGCCTTTTCTAGAGCC Human: GTCACAAGCAGCTCATGGACTTTATG--G------------------------CAATTGCCTTTTCTAGAGCC Cluster: [ ] Orangutan: GTCACAAGCAGCTCATGGACTTGATG--GCAATCCTCCCA-------------AACTTGCCTTTTCTAGAGCC Gorilla > Chimp --------------- chr3:83177304-83177314 Template switch process: F1: L AAAGCTTTGGATGTTGTCATAAGCAGCTCATGGACTTTATG 1 F3: 4 TCCTAAACTTGCCTTTTCTAGAACCCACTTATTCACAAATTTTCT R RF: AAAGCTTTGGATGTTGTCATAAGCAGCTCATGGACTTTATGGCAATCCTCCTAAACTTGCCTTTTCTAGAGCCCACTTATTCACAAATTTTCT RR: TTTCGAAACCTACAACAGTATTCGTCGAGTACCTGAAATACCGTTAGGAGGATTTGAACGGAAAAGATCTCGGGTGAATAAGTGTTTAAAAGA F2: 3 GAAATACCGTT 2 Unidirectional alignment (log-probability: -40.9) AAGCTTTGGATGTTGTCATAAGCAGCTCATGGACTTTATGttgccataaaG------TCCTAAACTTGCCTTTTCTAGAaCCCACTTATTCACAAAT AAGCTTTGGATGTTGTCATAAGCAGCTCATGGACTTTATG----------GCAATCCTCCTAAACTTGCCTTTTCTAGAGCCCACTTATTCACAAAT Template switch alignment (log-probability: -22.8) AAGCTTTGGATGTTGTCATAAGCAGCTCATGGACTTTATG|TTGCCATAAAG|TCCTAAACTTGCCTTTTCTAGAaCCCACTTATTCACAAAT AAGCTTTGGATGTTGTCATAAGCAGCTCATGGACTTTATG|TTGCCATAAAG|TCCTAAACTTGCCTTTTCTAGAGCCCACTTATTCACAAAT ========== Event 2473 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTTTCCCCTCCCA-TTTCATGACTGCTTAGAATTGTGTCATGGTTTTATTTTCCTTATGTGAAAATTACCTACAATGCTAGATGTTT-TTTTGGTAT-CTCCTACC------------Cttttcttttt---tttttttttttttttttttttGTC-ATCGCTAGATACATGC--TATC ↓ 3 2 1 4 Chimp: CTTTTCCCCTCCCATTTTCATGACTGCTTAGAATTGGTTCATGGTTA--TTTTCCTTATGTGAAAATTACCTACAATGCTAGATGTT---TTTGGTATCCTCCTACC-------------Ctttcttttt----ttttttttttttttttttttGTCATTCGCTAGATACATGC--TATC Gorilla: CTTTTCCCCTCCCA-TTTCGTGACTGCTTAGAATTGTGTCATGGTTTTATTTTCCTTATGTGAAAATTACCTACAATGCTAGATGttt-ttttGGTAT-CTCCTACC------CCTGTCCttttttttttttt-ttttttttttttttttttttGTC-AGCGCTAGATACATGC----TC Human: CTTTTCCCCTCCCA-TTTCATGACTGCTTAGAATTGTGTCATGGTTTTATTTTCCTTATGTGAAAATTACCTACAATGCTAGATGTTT-TTTTGGTAT-CTCCTACC------------Cttttcttttt---tttttttttttttttttttttGTC-ATCGCTAGATACATGC--TATC Cluster: [] Orangutan: CTTTTCCCCTCCCA-CTTCATGACTGCTTAGAATTGTGTCATGGTTTTATTTTCCTTATGTGAAAATTATCTACAATTCTAGATGttttttttGGTAT-CTCCTACCCCTGGC------Cttttctttt------tttttttttttttttttttGTC-AGCGCTAGATACATGTTA--TC Human > Chimp ------------- chr3:118287991-118287995 Template switch process: F1: L CCTACCCTTT-CTTTTTTTTTTTTTTTTTTTTTTTTT 1 F3: 4 TCGCTAGATACATGCTATCAGGTCCTAAAAAAGAGAAAG R RF: ATGACTGCTTAGAATTGTGTCATGGTTTTATTTTCCTTATGTGAAAATTACCTACAATGCTAGATGTTTTTTTGGTATCTCCTACCCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTGTCATCGCTAGATACATGCTATCAGGTCCTAAAAAAGAGAAAA RR: TACTGACGAATCTTAACACAGTACCAAAATAAAAGGAATACACTTTTAATGGATGTTACGATCTACAAAAAAACCATAGAGGATGGGAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAACAGTAGCGATCTATGTACGATAGTCCAGGATTTTTTCTCTTTT F2: 3 TACTG 2 Unidirectional alignment (log-probability: -38.9) CCTACCCTTT--cTTTTTTTTTTTTTTTTTTTTTTTTTGTCAtTCGCTAGATACATGCTATCAGGTCCTAAAAAAGAGAAA-G CCTACCCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTGTCA-TCGCTAGATACATGCTATCAGGTCCTAAAAAAGAGAAAAG Template switch alignment (log-probability: -32) CCTACCCTTT-CTTTTTTTTTTTTTTTTTTTTTTTTT|GTCAT|TCGCTAGATACATGCTATCAGGTCCTAAAAAAGAGAAAg CCTACCCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTT|GTCAT|TCGCTAGATACATGCTATCAGGTCCTAAAAAAGAGAAAA ========== Event 2474 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGAAATCCAACTCTTGGTCTTGTC--------------------------------------------------------------------------------------TCTTTGATCTTGTGTCTTAAACT-TCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTACTGT-GCAACATATTGCAGGGTCTAAATGATGG ↓ 4 3 1 2 Chimp: CTGAAATCCAACTCTTGGTCTTGTCTCTTTGATCTTGTGTCTTAAACTTCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTATATGTTACACAGTAAAGCAGGGCTTGTCTCTTTGATCTTGTGTCTTTAACT-TCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTACTGT-GTAACATATTGCAGGGTCTAAATGATGG Gorilla: CTGAAATCCAACTCTTGGTCTTGTC--------------------------------------------------------------------------------------TGTTTGATCTTGTGTCTTAAACTTCCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTACTGTGTTAACATATTGCAGGTTCTAAATGATGG Human: CTGAAATCCAACTCTTGGTCTTGTC--------------------------------------------------------------------------------------TCTTTGATCTTGTGTCTTAAACT-TCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTACTGT-GCAACATATTGCAGGGTCTAAATGATGG Cluster: [ ] Orangutan: CTGAAATCCAACTCTTGGTCTTGTC------------------------------------------------------------------------------------------TGATCTTGTGTCTTTAACTTCCTGACTGGGTTCTTCCTAGCCAAGCACTGCTTTACTGT-GTAACATATTGCAGGGTCTAAATGATGG Human > Chimp ------------- chr3:194094800-194094821 Template switch process: F1: L CAAGGGCTTCCCACAGCTGAAATCCAACTCTTGGTCTTGTCTCTTTGATCTTGTGTCTTAAACTTCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTA 1 F3: 4 CTTGTCTCTTTGATCTTGTGTCTTTAACTTCTGACTGGGTTCTTCC R RF: CAAGGGCTTCCCACAGCTGAAATCCAACTCTTGGTCTTGTCTCTTTGATCTTGTGTCTTAAACTTCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTATAGCCAAGCCCTGCTTTACTGTGCAACATA RR: GTTCCCGAAGGGTGTCGACTTTAGGTTGAGAACCAGAACAGAGAAACTAGAACACAGAATTTGAAGACTGACCCAAGAAGGATCGGTTCGGGACGAAATATCGGTTCGGGACGAAATGACACGTTGTAT F2: 3 GGGACGAAATGACACATTGTAT 2 Unidirectional alignment (log-probability: -132) AAACTTCTGACTGGGTTCTTCCtagccaagccctgctttatatgttacacagtaaagcagggcttgtctctttgatcttgtgtctttaacttctgactgggt AAACTTCTGACTGGGTTCTTCC-------------------------------------------------------------------------------- Template switch alignment (log-probability: -31) AAACTTCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTA|TATGTTaCACAGTAAAGCAGGG|CTTGTCTCTTTGATCTTGTGTCTTtAACTTCTGACTGGGT AAACTTCTGACTGGGTTCTTCCTAGCCAAGCCCTGCTTTA|TATGTTGCACAGTAAAGCAGGG|CTTGTCTCTTTGATCTTGTGTCTTAAACTTCTGACTGGGT ========== Event 2475 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCCTTTTTTCTTTGAAAGTCA----TGTTCTACATGTAT----GCATGTAGAACAGTGCTGATTTTTCTTGAGT Chimp: CCCTTTTTTCTTTGAAAGTCA----TGTTCTACATGTAT----GCATGTAGAACAGTGCTGATCTTTCTTGAGT ↑ 1 3 4 2 Gorilla: CCCTTTTTTCTTTGAAAGTCATACATGACTTTCATGTATGCATACATGTAGAACAGTGCTGATTTTTCTTGAGT ↓ 1 3 4 2 Human: CCCTTTTTTCTTTGAAAGTCA----TGTTCTACATGTAT----GCATGTAGAACAGTGCTGATTTTTCTTGAGT Cluster: [ ] Orangutan: CCCTTTTTTATTTGAAAGTCA----TGTTCTACATGTAT----GCATATAGAACAGTGCTGATTTTTCTTGAGT Gorilla > Human --------------- chr3:189781965-189781978 Template switch process: F1: L TTTTGTATACATCCCT----CCCTTTTTTCTTTGAAAGTCAT 1 F3: 4 CATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA R RF: TTTTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCATACATGACTTTCATGTATGCATACATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA RR: AAAACATATGTAGGGAGAGAGGGAAAAAAGAAACTTTCAGTATGTACTGAAAGTACATACGTATGTACATCTTGTCACGACTAAAAAGAACTCACAAATACTGT F2: 3 GTATGTACATCTTG 2 Unidirectional alignment (log-probability: -48.3) TTTTGTATACATCCC----TCCCTTTTTTCTTTGAAAGTCAtgttcTA---------CATGTATG----CATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA TTTTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCA-----TACATGACTTTCATGTATGCATACATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA Template switch alignment (log-probability: -27.4) TTTTGTATACATCCCT----CCCTTTTTTCTTTGAAAGTCAT|GTTCTACATGTATG|CATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA TTTTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT|GTTCTACATGTATG|CATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA Gorilla > Chimp --------------- chr3:193876987-193877000 Template switch process: F1: L GTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT 1 F3: 4 CATGTAGAACAGTGCTGATCTTTCTTGAGTGTTTATGACA R RF: GTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCATACATGACTTTCATGTATGCATACATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA RR: CATATGTAGGGAGAGAGGGAAAAAAGAAACTTTCAGTATGTACTGAAAGTACATACGTATGTACATCTTGTCACGACTAAAAAGAACTCACAAATACTGT F2: 3 GTATGTACATCTTG 2 Unidirectional alignment (log-probability: -43.8) GTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAtgttcTA---------CATGTATG----CATGTAGAACAGTGCTGATcTTTCTTGAGTGTTTATGACA GTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCA-----TACATGACTTTCATGTATGCATACATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA Template switch alignment (log-probability: -23) GTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT|GTTCTACATGTATG|CATGTAGAACAGTGCTGATcTTTCTTGAGTGTTTATGACA GTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT|GTTCTACATGTATG|CATGTAGAACAGTGCTGATTTTTCTTGAGTGTTTATGACA ========== Event 2476 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTGATTTTGTATACATCCC--------TCCCTTTTTTCTTTGAAAGTCA----TGTTCTACATGTAT----GCATGTAGAACAGTGCTGATTT Chimp: CTTTGATTTTGTATACATCCC----TCTCTCCCTTTTTTCTTTGAAAGTCA----TGTTCTACATGTAT----GCATGTAGAACAGTGCTGATCT ↓ 3 1 2 4 Gorilla: CTTTGATTTTGTATACATCCCTCTC----TCCCTTTTTTCTTTGAAAGTCATACATGACTTTCATGTATGCATACATGTAGAACAGTGCTGATTT Human: CTTTGATTTTGTATACATCCC--------TCCCTTTTTTCTTTGAAAGTCA----TGTTCTACATGTAT----GCATGTAGAACAGTGCTGATTT Cluster: [ ] Orangutan: CTTTGATTTTGTATACATCCCTCTC----TCCCTTTTTTATTTGAAAGTCA----TGTTCTACATGTAT----GCATATAGAACAGTGCTGATTT Chimp > Gorilla --------------- chr3:192642170-192642179 Template switch process: F1: L TTCTTTGCCTCCTTAGCCTTCTTTGATTTTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT 1 F3: 4 CATGTAT R RF: TTCTTTGCCTCCTTAGCCTTCTTTGATTTTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCATGTTCTACATGTAT RR: AAGAAACGGAGGAATCGGAAGAAACTAAAACATATGTAGGGAGAGAGGGAAAAAAGAAACTTTCAGTACAAGATGTACATA F2: 3 TTTCAGTACA 2 Unidirectional alignment (log-probability: -33.8) TTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCA-----TAcatgactttCATGTAT TTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCATGTTCTA---------CATGTAT Template switch alignment (log-probability: -16.8) TTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT|ACATGACTTT|CATGTAT TTGTATACATCCCTCTCTCCCTTTTTTCTTTGAAAGTCAT|ACATGACTTT|CATGTAT ========== Event 2477 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAGAGTTGCAGAGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTC Chimp: ATAGAGTTGC--AGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTC ↓ 3 2 1 4 Gorilla: ATAGAGTTGCAGAGTCTAGGACCATTTGAGACACA---ATGGTCTTTTATATTCAATAGACATTC ↑ 3 2 1 4 Human: ATAGAGTTGCAGAGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTC Cluster: [ ] Orangutan: Human > Gorilla --------------- chr3:116218950-116218955 Template switch process: F1: L AGCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACA 1 F3: 4 TTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT R RF: AGCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT RR: TCGTTGTATCTCAACGTCTCAGATCCTGGTAAACTCTGTGTACCATCCACAAAATATAAGTTATCTGTAAGTAAAAGTATTTTTACTATA F2: 3 CTGGTA 2 Unidirectional alignment (log-probability: -27.7) GCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACA---atGGTcTTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT GCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT Template switch alignment (log-probability: -16.5) GCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACA|ATGGTC|TTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT GCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACA|ATGGTC|TTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT Chimp > Gorilla --------------- chr3:116218950-116218955 Template switch process: F1: L AGCAACATAGAGTTGCAGAGTCTAGGACCATTTGAGACACA 1 F3: 4 TTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT R RF: AGCAACATAGAGTTGC--AGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT RR: TCGTTGTATCTCAACG--TCAGATCCTGGTAAACTCTGTGTACCATCCACAAAATATAAGTTATCTGTAAGTAAAAGTATTTTTACTATA F2: 3 CTGGTA 2 Unidirectional alignment (log-probability: -40.3) GCAACATAGAGTTGCagAGTCTAGGACCATTTGAGACACA---atGGTcTTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT GCAACATAGAGTTGC--AGTCTAGGACCATTTGAGACACATGGTAGGTGTTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT Template switch alignment (log-probability: -29.1) GCAACATAGAGTTGCagAGTCTAGGACCATTTGAGACACA|ATGGTC|TTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT GCAACATAGAGTTGC--AGTCTAGGACCATTTGAGACACA|ATGGTC|TTTTATATTCAATAGACATTCATTTTCATAAAAATGATAT ========== Event 2478 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTTTGCATAGTGATGTTTG----TTCACGTACTTGTCACTATGGTTGCAAATTAACAGTTGCA Chimp: TTCTTTGCATAGTGATGTTTG----TTCACATACTTGTCATTATGGTTGCAAATTAACAGTTGCA Gorilla: TTCTTTGCATAGTGATGTTTGCATAGTGACATACTTGTCACTATGGTTGCAAATTAACAGTTGCA ↑ 1 4 3 2 Human: TTCTTTGCATAGTGATGTTTG----TTCACGTACTTGTCACTATGGTTGCAAATTAACAGTTGCA Cluster: [ ] Orangutan: TTCTTTGCATAGTGATGTTTG----TTCACATATTTGTCACTATGGTTGCAAATTAACAGTTGCA Human > Gorilla --------------- chr3:86279681-86279690 Template switch process: F1: L GCTTTACGTTGACAATACAATTCTTTGCATAGTGATGTTTG 1 F3: 4 TACTTGTCACTATGGTTGCAAATTAACAGTTGCAATTCGA R RF: GCTTTACGTTGACAATACAATTCTTTGCATAGTGATGTTTGTTCACGTACTTGTCACTATGGTTGCAAATTAACAGTTGCAATTCGA RR: CGAAATGCAACTGTTATGTTAAGAAACGTATCACTACAAACAAGTGCATGAACAGTGATACCAACGTTTAATTGTCAACGTTAAGCT F2: 3 ACAGTGATAC 2 Unidirectional alignment (log-probability: -33.3) CTTTACGTTGACAATACAATTCTTTGCATAGTGATGTTTGcatagTgACaTACTTGTCACTATGGTTGCAAATTAACAGTTGCAATTCGA CTTTACGTTGACAATACAATTCTTTGCATAGTGATGTTTG----TTCACGTACTTGTCACTATGGTTGCAAATTAACAGTTGCAATTCGA Template switch alignment (log-probability: -17) CTTTACGTTGACAATACAATTCTTTGCATAGTGATGTTTG|CATAGTGACA|TACTTGTCACTATGGTTGCAAATTAACAGTTGCAATTCGA CTTTACGTTGACAATACAATTCTTTGCATAGTGATGTTTG|CATAGTGACA|TACTTGTCACTATGGTTGCAAATTAACAGTTGCAATTCGA ========== Event 2479 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GTACTTTGATATTTGCTTTTCCCCAGTTATCATGACACCTTATGAAATTT----------------------------ATGGACAAATTTAGATATAAATTTAGATTTGGACaaatttagtttattcactttaactgtatataccattttattatat ↑ 1 4 3 2 Chimp: GTACTTTGATATTTGCTTTTC-CCACGTATCATGACACCTTATGAAATTtatggacaaatttagatataaatttagatatggacaaatttagatataaatttagatatggacaaatttagtttattcactttaactgtatataccattttattatat ↓ 1 4 3 2 Gorilla: GTACTTTGACATTTGCTTTTCCCCAGTTATCATGACACCTTATGAAATTt----------------------------atggacaaatgtagatataaatttagatatggacaaatttagtttattcactttaactgtatataccagtttattatgt Human: GTACTTTGATATTTGCTTTTCCCCAGTTATCATGACACCTTATGAAATTT----------------------------ATGGACAAATTTAGATATAAATTTAGATTTGGACaaatttagtttattcactttaactgtatataccattttattatat Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------------------------------------------------------N------------ Chimp > Human ------------- chr3:85762829-85762832 Template switch process: F1: L TTATATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTCCC 1 F3: 4 TATCATGACACCTTATGAAATTT R RF: TTATATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTCCCACGTATCATGACACCTTATGAAATTTATGGACAAATTTAGATATAAATTTAGATATGGACAAATTTAGATATAAATTTAGATATGGACAAATTTAGTTTATTCACTTTAACTG RR: AATATACGGTTTTATAGGGACATGAAACTATAAACGAAAAGGGTGCATAGTACTGTGGAATACTTTAAATACCTGTTTAAATCTATATTTAAATCTATACCTGTTTAAATCTATATTTAAATCTATACCTGTTTAAATCAAATAAGTGAAATTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -32.3) TATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTcCCCAgtTATCATGACACCTTATGAAATTT----------------- TATGCCAAAATATCCCTGTACTTTGATATTTGCTTTT-CCCACGTATCATGACACCTTATGAAATTTATGGACAAATTTAGATA Template switch alignment (log-probability: -15.5) TATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTCCC|CAGT|TATCATGACACCTTATGAAATTT TATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTCCC|CAGT|TATCATGACACCTTATGAAATTT Chimp > Gorilla --------------- chr3:87361171-87361174 Template switch process: F1: L TTATATGCCAAAATATCCCTGTACTTTGACATTTGCTTTTCCC 1 F3: 4 TATCATGACACCTTATGAAATTT R RF: TTATATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTCCCACGTATCATGACACCTTATGAAATTTATGGACAAATTTAGATATAAATTTAGATATGGACAAATTTAGATATAAATTTAGATATGGACAAATTTAGTTTATTCACTTTAACTG RR: AATATACGGTTTTATAGGGACATGAAACTATAAACGAAAAGGGTGCATAGTACTGTGGAATACTTTAAATACCTGTTTAAATCTATATTTAAATCTATACCTGTTTAAATCTATATTTAAATCTATACCTGTTTAAATCAAATAAGTGAAATTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -36.3) TATGCCAAAATATCCCTGTACTTTGAcATTTGCTTTTcCCCAgtTATCATGACACCTTATGAAATTT----------------- TATGCCAAAATATCCCTGTACTTTGATATTTGCTTTT-CCCACGTATCATGACACCTTATGAAATTTATGGACAAATTTAGATA Template switch alignment (log-probability: -21.3) TATGCCAAAATATCCCTGTACTTTGAcATTTGCTTTTCCC|CAGT|TATCATGACACCTTATGAAATTT TATGCCAAAATATCCCTGTACTTTGATATTTGCTTTTCCC|CAGT|TATCATGACACCTTATGAAATTT ========== Event 2480 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TCTTATTTTAGACACTCCTCTGTTAAAACAGGTGTTTTAACATGTTAAAACAGACCAGGTTTTCCTGGTCTCAAA ↑ 4 2 1 Chimp: TCTTATTTTAGACACTCCTCTGTTA----------------------AAACAGACCAGGTTTTCCTGGTCTCAAA ↓ 4 3 2 1 Gorilla: TCTTATTTTAGACACTCCTCTGTTAAAACAGACGTTTTAACGTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAA Human: TCTTATTTTAGACACTCCTCTGTTAAAACAGGTGTTTTAACATGTTAAAACAGACCAGGTTTTCCTGGTCTCAAA Cluster: [ ] Orangutan: TCTTATTTTAGGCACTTCTATGTT----------------------AAAACAGACCAGGTTTTCCTGGTCTCAAA Chimp > Human ------------- chr3:87256623-87256632 Template switch process: F1: L TAATTGAAATATGTACTCTTATTTTAGACACTCCTCTGTTAAAACAGG 1 F3: 4 TGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGACCTGTGA R RF: TAATTGAAATATCTACTCTTATTTTAGACACTCCTCTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGACCTGTGA RR: ATTAACTTTATAGATGAGAATAAAATCTGTGAGGAGACAATTTTGTCTGGTCCAAAAGGACCAGAGTTTTCTCTGGACACT F2: 3 ACAATTTTGT 2 Unidirectional alignment (log-probability: -48.5) ATATgTACTCTTATTTTAGACACTCCTCTGTTAAAACaggtgttttaacatgttaaaacAGACCAGGTTTTCCTGGTCTCAAAAGAGACC ATATCTACTCTTATTTTAGACACTCCTCTGTTAAAAC----------------------AGACCAGGTTTTCCTGGTCTCAAAAGAGACC Template switch alignment (log-probability: -28.7) ATATgTACTCTTATTTTAGACACTCCTCTGTTAAAACAGg|TGTTTTAACA|TGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGACC ATATCTACTCTTATTTTAGACACTCCTCTGTTAAAACAGA|TGTTTTAACA|TGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGACC Chimp > Gorilla --------------- chr3:88870824-88870831 Template switch process: F1: L TAATTGAAATATGTACTCTTATTTTAGACACTCCTCTGTTAAAACAGAC 1 F3: 4 GTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGACCTGTGA R RF: TAATTGAAATATCTACTCTTATTTTAGACACTCCTCTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGACCTGTGA RR: ATTAACTTTATAGATGAGAATAAAATCTGTGAGGAGACAATTTTGTCTGGTCCAAAAGGACCAGAGTTTTCTCTGGACACT F2: 3 CAATTTTG 2 Unidirectional alignment (log-probability: -48) TATgTACTCTTATTTTAGACACTCCTCtgttaaaacagacgttttaacgTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGAC TATCTACTCTTATTTTAGACACTCCTC----------------------TGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGAC Template switch alignment (log-probability: -28.1) TATgTACTCTTATTTTAGACACTCCTCTGTTAAAACAGAC|GTTTTAAC|gTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGAC TATCTACTCTTATTTTAGACACTCCTCTGTTAAAACAGAC|GTTTTAAC|CTGTTAAAACAGACCAGGTTTTCCTGGTCTCAAAAGAGAC ========== Event 2481 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AGCTGCCAGCTCGGCCCATCGAG------------CTCAGAAGCTCGCGCTCGCGACAGGCGCTTCCT ↑ 3 1 24 Chimp: AGCTGCCAGCTCGGCCCATCGAG------------CTTA------TGCGCTCGCGACAGGCGCTTCCT Gorilla: AGCCGCCAGCTCCGCCCATCGAG------------CTCAGAAGCTCGCGCTCGCGACAGGCGCTTCCT Human: AGCTGCCAGCTCGGCCCATCGAG------------CTCAGAAGCTCGCGCTCGCGACAGGCGCTTCCT Cluster: [ ] Orangutan: AGCTGCCAGCTCGGCCCGTCGAGCGCAGAAGCGAGCTCAGAAGCTCGCGCTCCCGACAGGCGCTTCCT Chimp > Human ------------- chr3:87052823-87052832 Template switch process: F1: L GGTGTAAGCACCAACCAGCTGCCAGCTCGGCCCATCGAGCT 1 F3: 4 CGCTCGCGACAGGCGCTTCCTTCCCGAGGCTGGCTCCCC R RF: GGTGTAAGCACCAACCAGCTGCCAGCTCGGCCCATCGAGCTTATGCGCTCGCGACAGGCGCTTCCTTCCCGAGGCTGGCTCCCC RR: CCACATTCGTGGTTGGTCGACGGTCGAGCCGGGTAGCTCGAATACGCGAGCGCTGTCCGCGAAGGAAGGGCTCCGACCGAGGGG F2: 3 GCTCGAAGAC 2 Unidirectional alignment (log-probability: -31.6) GTGTAAGCACCAACCAGCTGCCAGCTCGGCCCATCGAGCTcAgaagctcGCGCTCGCGACAGGCGCTTCCTTCCCGAGGCTGGCTCCCC GTGTAAGCACCAACCAGCTGCCAGCTCGGCCCATCGAGCTTA------TGCGCTCGCGACAGGCGCTTCCTTCCCGAGGCTGGCTCCCC Template switch alignment (log-probability: -22.5) GTGTAAGCACCAACCAGCTGCCAGCTCGGCCCATCGAGCT|CAgAAGCTCG|CGCTCGCGACAGGCGCTTCCTTCCCGAGGCTGGCTCCCC GTGTAAGCACCAACCAGCTGCCAGCTCGGCCCATCGAGCT|CATAAGCTCG|CGCTCGCGACAGGCGCTTCCTTCCCGAGGCTGGCTCCCC ========== Event 2482 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACACTTATCAAGACAAGGGACGTGGCCATTTCACTTTGAAATCAAAGTGAAATCAGGTAATTcctga ↑ 3 4 1 2 Chimp: ACACTTATCAAGACAAGGGACATGGCCATT-----------TCAAAGTGAAATCAGGTAATTcctga Gorilla: ACACTTATCAAGACAAGGGACGTGGCCATT-----------TCAAAGTGAAATCAGGTAATTcctga ↓ 3 4 1 2 Human: ACACTTATCAAGACAAGGGACGTGGCCATTTCACTTTGAAATCAAAGTGAAATCAGGTAATTcctga Cluster: [ ] Orangutan: acacttatcaagacaagggacgtggccatt-----------tcaaagtgaaatcaggtaattcctga Chimp > Human ------------- chr3:189486754-189486761 Template switch process: F1: L CTATAATCATCAGGGTACAGACACTTATCAAGACAAGGGACGTGGCCATTTCA 1 F3: 4 TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT R RF: CTATAATCATCAGGGTACAGACACTTATCAAGACAAGGGACATGGCCATTTCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT RR: GATATTAGTAGTCCCATGTCTGTGAATAGTTCTGTTCCCTGTACCGGTAAAGTTTCACTTTAGTCCATTAAGGACTTTCAAGGGTCTGAA F2: 3 AAAGTTTC 2 Unidirectional alignment (log-probability: -32.8) GGTACAGACACTTATCAAGACAAGGGACgTGGCCATTTCactttgaaatcAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT GGTACAGACACTTATCAAGACAAGGGACATGGCCATTTC-----------AAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT Template switch alignment (log-probability: -22.5) GGTACAGACACTTATCAAGACAAGGGACgTGGCCATTTCA|CTTTGAAA|TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT GGTACAGACACTTATCAAGACAAGGGACATGGCCATTTCA|CTTTGAAA|TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT Gorilla > Human --------------- chr3:189486754-189486761 Template switch process: F1: L TCAGGGTACAGACACTTATCAAGACAAGGGACGTGGCCATTTCA 1 F3: 4 TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT R RF: TCAGGGTACAGACACTTATCAAGACAAGGGACGTGGCCATTTCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT RR: AGTCCCATGTCTGTGAATAGTTCTGTTCCCTGCACCGGTAAAGTTTCACTTTAGTCCATTAAGGACTTTCAAGGGTCTGAA F2: 3 AAAGTTTC 2 Unidirectional alignment (log-probability: -26.7) GGTACAGACACTTATCAAGACAAGGGACGTGGCCATTtcactttgaaaTCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT GGTACAGACACTTATCAAGACAAGGGACGTGGCCATT-----------TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT Template switch alignment (log-probability: -16.8) GGTACAGACACTTATCAAGACAAGGGACGTGGCCATTTCA|CTTTGAAA|TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT GGTACAGACACTTATCAAGACAAGGGACGTGGCCATTTCA|CTTTGAAA|TCAAAGTGAAATCAGGTAATTCCTGAAAGTTCCCAGACTT ========== Event 2483 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CATATTTTGTTTAATGAAACATGACCTTTTCCAAAACACACGTATATTTTTGAAATGCACATGAAACTTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTGGTCATGATTTTAGCTGTCACAAACTCT ↑ 3 2 1 4 Chimp: CATATTTTGTTTAATGAAACATGACCTTTTCCAAAACACACGTATACTTTTGAAATGCACATGAAACTTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTGAT--TAATTTTAGCTGTCACAAGCTCT Gorilla: CATATTTTGCTTAATGAAACATGACCTTTTCCAAAACACACGTATATTTTTGAAATGCACATGAAACTTTGGCTTTAAGGATCACAGAAAATGATTAACTTATCTTGGTCATGATTTTAGCTGTCACAAACTCT Human: CATATTTTGTTTAATGAAACATGACCTTTTCCAAAACACACGTATATTTTTGAAATGCACATGAAACTTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTGGTCATGATTTTAGCTGTCACAAACTCT Cluster: [ ] Orangutan: CATATTTTGTTTAATGAAACATGACCTTTTCCAAAACACACATATATTTTTGAAACACACATGAAACTTTGGCTTTAAGGATCACAGAAAATGATTGATTTATCTTGGTCATGATTTTAGCTGTCACAAACTCT Chimp > Human ------------- chr3:109264898-109264903 Template switch process: F1: L CTTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTG 1 F3: 4 ATTTTAGCTGTCACAAACTCTCAAATGTTTTATTATACTC R RF: CATGACCTTTTCCAAAACACACGTATACTTTTGAAATGCACATGAAACTTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTGATTAATTTTAGCTGTCACAAGCTCTCAAATGTTTTATTATACTC RR: GTACTGGAAAAGGTTTTGTGTGCATATGAAAACTTTACGTGTACTTTGAAACCGAAATTCCTAGTGTCTTTTACTAATTAAATAGAACTAATTAAAATCGACAGTGTTCGAGAGTTTACAAAATAATATGAG F2: 3 GTACTG 2 Unidirectional alignment (log-probability: -31.8) TTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTGgTcaTgATTTTAGCTGTCACAAaCTCTCAAATGTTTTATTATACTC TTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTGAT--TAATTTTAGCTGTCACAAGCTCTCAAATGTTTTATTATACTC Template switch alignment (log-probability: -22) TTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTG|GTCATG|ATTTTAGCTGTCACAAaCTCTCAAATGTTTTATTATACTC TTTGGCTTTAAGGATCACAGAAAATGATTAATTTATCTTG|GTCATG|ATTTTAGCTGTCACAAGCTCTCAAATGTTTTATTATACTC ========== Event 2484 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TAATGTCCCCAAGTGACTGGCTTCTGTA-GTGCCAGTCACTACCCAAATGCC Chimp: TAATGTCCCCAAGTGACTGGCTTCTGTA-GTGCCAGTCACTACCCAAATGCC ↓ 13 24 ↑ 13 24 Gorilla: TAATGTCCCCAAGTGACTGGC-ACTACAGAAGCCAGTCACTACCCAAATGCC ↓ 13 24 ↑ 13 24 Human: TAATGTCCCCAAGTGACTGGCTTCTGTA-GTGCCAGTCACTACCCAAATGCC Cluster: [ ] Orangutan: TAATGTCCCCAAG----GTGCTTCTGTA-GTGCCAGTCACCACCAAAATGCC Gorilla > Human --------------- chr3:109144083-109144091 Template switch process: F1: L CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC 1 F3: 4 GCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC R RF: CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCACTACAGAAGCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC RR: GATTCAGTATCGAGAGTAAGATTACAGGGGTTCACTGACCGTGATGTCTTCGGTCAGTGATGGGTTTACGGTCTAGAGGACATGTCGTAG F2: 3 TGATGTCTT 2 Unidirectional alignment (log-probability: -39.5) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC---------ttctgtagtGCCAGTCACTACCCAAATGCCAGATtTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCACTACAGAA---------GCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC Template switch alignment (log-probability: -22.4) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|TTCTGTAGT|GCCAGTCACTACCCAAATGCCAGATtTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|TTCTGTAGT|GCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC Human > Gorilla --------------- chr3:110600737-110600745 Template switch process: F1: L CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC 1 F3: 4 GCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC R RF: CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCTTCTGTAGTGCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC RR: GATTCAGTATCGAGAGTAAGATTACAGGGGTTCACTGACCGAAGACATCACGGTCAGTGATGGGTTTACGGTCTAAAGGACATGTCGTAG F2: 3 AAGACATCA 2 Unidirectional alignment (log-probability: -39.5) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC---------actacagaaGCCAGTCACTACCCAAATGCCAGATcTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCTTCTGTAGT---------GCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC Template switch alignment (log-probability: -22.4) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|ACTACAGAA|GCCAGTCACTACCCAAATGCCAGATcTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|ACTACAGAA|GCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC Gorilla > Chimp --------------- chr3:111659684-111659692 Template switch process: F1: L CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC 1 F3: 4 GCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC R RF: CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCACTACAGAAGCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC RR: GATTCAGTATCGAGAGTAAGATTACAGGGGTTCACTGACCGTGATGTCTTCGGTCAGTGATGGGTTTACGGTCTAGAGGACATGTCGTAG F2: 3 TGATGTCTT 2 Unidirectional alignment (log-probability: -39.5) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC---------ttctgtagtGCCAGTCACTACCCAAATGCCAGATtTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCACTACAGAA---------GCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC Template switch alignment (log-probability: -22.4) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|TTCTGTAGT|GCCAGTCACTACCCAAATGCCAGATtTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|TTCTGTAGT|GCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC Chimp > Gorilla --------------- chr3:110600737-110600745 Template switch process: F1: L CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC 1 F3: 4 GCCAGTCACTACCCAAATGCCAGATCTCCTGTACAGCATC R RF: CTAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCTTCTGTAGTGCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC RR: GATTCAGTATCGAGAGTAAGATTACAGGGGTTCACTGACCGAAGACATCACGGTCAGTGATGGGTTTACGGTCTAAAGGACATGTCGTAG F2: 3 AAGACATCA 2 Unidirectional alignment (log-probability: -39.5) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC---------actacagaaGCCAGTCACTACCCAAATGCCAGATcTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGCTTCTGTAGT---------GCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC Template switch alignment (log-probability: -22.4) TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|ACTACAGAA|GCCAGTCACTACCCAAATGCCAGATcTCCTGTACAGCATC TAAGTCATAGCTCTCATTCTAATGTCCCCAAGTGACTGGC|ACTACAGAA|GCCAGTCACTACCCAAATGCCAGATTTCCTGTACAGCATC ========== Event 2485 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GGTCTTTTAAGGCTTCTCCAAT----------------------------ATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGTTAAATGCTGTGTTCATTTAGCCTTGAGA ↓ 4 1 3 2 Chimp: GGTCTTTTAAGGCTTCTCCAAT--------------ATCTTAGCATTAATATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGTTAAATGGTGTGTTCATTTAGCCTTGAGA Gorilla: Human: GGTCTTTTAAGGCTTCTCCAAT----------------------------ATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGTTAAATGCTGTGTTCATTTAGCCTTGAGA Cluster: [ ] Orangutan: GGTCTTTTAAGGCTTTTCCAATATCTTAGCATTAAT--------------ATCATGCGTGGGTAC-TGAAAAGTAGTCTATTACTGTTAAAGAGTGTGTTCATTTAGCCTTGAGA Human > Chimp ------------- chr3:105454688-105454693 Template switch process: F1: L TGTTTTGTAAATGTATGTCGGTCTTTTAAGGCTTCTCCAATATCTT 1 F3: 4 AATATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGTTAA R RF: TGTTTTGTAAATGTATGTTGGTCTTTTAAGGCTTCTCCAATATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGTTAAATGCT RR: ACAAAACATTTACATACAACCAGAAAATTCCGAAGAGGTTATAGAACGTACCCATGAACTTTTCATCAGATAATGACAATTTACGA F2: 3 TTACGA 2 Unidirectional alignment (log-probability: -37) GTAAATGTATGTcGGTCTTTTAAGGCTTCTCCAATATCTtagcattaatatctTGCATGGGTACTTGAAAAGTAGTCTATTACTGT GTAAATGTATGTTGGTCTTTTAAGGCTTCTCCAATATCT--------------TGCATGGGTACTTGAAAAGTAGTCTATTACTGT Template switch alignment (log-probability: -22.2) GTAAATGTATGTcGGTCTTTTAAGGCTTCTCCAATATCTT|AGCATT|AATATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGT GTAAATGTATGTTGGTCTTTTAAGGCTTCTCCAATATCTT|AGCATT|AATATCTTGCATGGGTACTTGAAAAGTAGTCTATTACTGT ========== Event 2486 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCTTCAGTACTTTCACTTTTAT------AG-TACACGTTGTACTTTTCCTAATATCTAA Chimp: ACCTTCAGTACTTTCACTTTTAT------AG-TACACGTTGTACTTTTCCTAATATCTAA ↓ 1 3 4 2 Gorilla: ACCTTCAGTACTTTCACTTTTGAACGTGTACTAACACGTTGTACTTTTCCTAATATCTAA ↑ 1 3 4 2 Human: ACCTTCAGTACTTTCACTTTTAT------AG-TACACGTTGTACTTTTCCTAATATCTAA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr3:104787277-104787287 Template switch process: F1: L ATATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTG 1 F3: 4 ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA R RF: ATATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTATAGTACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA RR: TATACGATATATAAATAGATTGGAAGTCATGAAAGTGAAAATATCATGTGCAACATGAAAAGGATTATAGATTTCTGTTTCTGTTT F2: 3 ATCATGTGCAA 2 Unidirectional alignment (log-probability: -36.7) ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTtgaacgtgtacTA----ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTT-----------TATAGTACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA Template switch alignment (log-probability: -22.7) ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTg|AACGTGTACTA|ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTA|AACGTGTACTA|ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA Chimp > Gorilla --------------- chr3:104787277-104787287 Template switch process: F1: L ATATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTG 1 F3: 4 ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA R RF: ATATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTATAGTACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA RR: TATACGATATATAAATAGATTGGAAGTCATGAAAGTGAAAATATCATGTGCAACATGAAAAGGATTATAGATTTCTGTTTCTGTTT F2: 3 ATCATGTGCAA 2 Unidirectional alignment (log-probability: -36.7) ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTtgaacgtgtacTA----ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTT-----------TATAGTACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA Template switch alignment (log-probability: -22.7) ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTg|AACGTGTACTA|ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA ATGCTATATATTTATCTAACCTTCAGTACTTTCACTTTTA|AACGTGTACTA|ACACGTTGTACTTTTCCTAATATCTAAAGACAAAGACAAA ========== Event 2487 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAATGCAGAGCAGTTGAGTCTATGGAGACATAGCATTCTTAGCATGATGCTGCC ↑ 3 1 4 Chimp: GAATGCAGAGCAGTTGAGTCTAT------GTCTCATTCTTAGCATGATGCTGCC Gorilla: GAATGCAGAGCAGTTGAGTCTAT------GTCTCATTCTTAGCATGATGCTGCC ↓ 3 1 4 Human: GAATGCAGAGCAGTTGAGTCTATGGAGACATAGCATTCTTAGCATGATGCTGCC Cluster: [ ] Orangutan: GAATGCAGAGCAGGTGAGTCTGT------GTCTCATTTTTAGCATGATGCTGCC Chimp > Human ------------- chr3:102610455-102610463 Template switch process: F1: L CTTCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATG 1 F3: 4 CATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC R RF: CTTCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATGTCTCATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC RR: GAAGAAACTACTCCTCGCCTTACGTCTCGTCAACTCAGATACAGAGTAAGAATCGTACTACGACGGTGCTACGTACGGTCAGAAG F2: 3 GATACAGAG 2 Unidirectional alignment (log-probability: -31.6) TCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATGgagacaTagCATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC TCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATG------TCTCATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC Template switch alignment (log-probability: -16.4) TCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATG|GAGACATAG|CATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC TCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATG|GAGACATAG|CATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC Gorilla > Human --------------- chr3:102610455-102610463 Template switch process: F1: L CTTCTTTGATGAGGAGCGGAATGCAGAGCAGTTGAGTCTATG 1 F3: 4 CATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC R RF: CTTCTTTGATGAGGAGCAGAATGCAGAGCAGTTGAGTCTATGTCTCATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC RR: GAAGAAACTACTCCTCGTCTTACGTCTCGTCAACTCAGATACAGAGTAAGAATCGTACTACGACGGTGCTACGTACGGTCAGAAG F2: 3 GATACAGAG 2 Unidirectional alignment (log-probability: -36.1) TCTTTGATGAGGAGCgGAATGCAGAGCAGTTGAGTCTATGgagacaTagCATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC TCTTTGATGAGGAGCAGAATGCAGAGCAGTTGAGTCTATG------TCTCATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC Template switch alignment (log-probability: -22.4) TCTTTGATGAGGAGCgGAATGCAGAGCAGTTGAGTCTATG|GAGACATAG|CATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC TCTTTGATGAGGAGCAGAATGCAGAGCAGTTGAGTCTATG|GAGACATAG|CATTCTTAGCATGATGCTGCCACGATGCATGCCAGTCTTC ========== Event 2488 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTACTCAGGACTGGTTCACA-TTAGGCTGCTTGAGCACttttttttttttttttttttttt---------ttttttGCCCTTTTCCCTGACCTGGTAAAATAGGCCTGGCTACTTAGTAAAGGCTGGTGAAT ↓ 1 4 3 2 Chimp: CTTACTCAGGACTGGTTCACATTTAGCCTGCTTGAGCACtttt-------------------tttttttttttttttGCCCTTTTCCCTGACCTGGTAAAATAGGCCTGGCTACTTAGTAAAGGCTGGTGAAT Gorilla: CTTACTCAGGACTGGTTCACATTTAGCCTGCTTGAGCACttttttttttggttttttttttt---------ttttttGCCCTTTTCCCTGACCTGGTAAAATAGGCCTGGCTACTTAGTAAAGGCTGGTGAAT Human: CTTACTCAGGACTGGTTCACA-TTAGGCTGCTTGAGCACttttttttttttttttttttttt---------ttttttGCCCTTTTCCCTGACCTGGTAAAATAGGCCTGGCTACTTAGTAAAGGCTGGTGAAT Cluster: [ ] Orangutan: CTTACTCAGGACTGGTTCACATTTAGCCTGCTTGAGCACtttttt------------ttttt---------ttttttGCCCTTTTCCCT--GCTAGTAGAATAGGCCTGGCTACCTGGTAAAGGCTGGTGAAT Human > Chimp ------------- chr4:103124063-103124066 Template switch process: F1: L CACTTAGGATCTCTCATGTGCTTACTCAGGACTGGTTCACATT 1 F3: 4 CTGCTTGAGCACTTTTTTTTT R RF: CACTTAGGATCTCTCATGTGCTTACTCAGGACTGGTTCACATTAGGCTGCTTGAGCACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCCTTTTCCCTGACCTGGTAAAATAGGCCTGGCTA RR: GTGAATCCTAGAGAGTACACGAATGAGTCCTGACCAAGTGTAATCCGACGAACTCGTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGGGAAAAGGGACTGGACCATTTTATCCGGACCGAT F2: 3 CGAT 2 Unidirectional alignment (log-probability: -26.2) TTAGGATCTCTCATGTGCTTACTCAGGACTGGTTCACAtTTAGcCTGCTTGAGCACTTTTTTTTT-------------- TTAGGATCTCTCATGTGCTTACTCAGGACTGGTTCACA-TTAGGCTGCTTGAGCACTTTTTTTTTTTTTTTTTTTTTTT Template switch alignment (log-probability: -15.4) TTAGGATCTCTCATGTGCTTACTCAGGACTGGTTCACATT|TAGC|CTGCTTGAGCACTTTTTTTTT TTAGGATCTCTCATGTGCTTACTCAGGACTGGTTCACATT|TAGC|CTGCTTGAGCACTTTTTTTTT ========== Event 2489 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGTCAACACTGGTTCACTC--------------------------------------CTCCAGGTACTCCTGGTGTAGTGAAGTGGTAAAATGTGTACGTTTACAT--CTGTGATGGCACATGCAAatatatatatatatac-------- Chimp: TGTGTCAACACTGGTTCACTC--------------------------------------CTCCAGGTACTCCTGGTGTACTGAAGTGGTAAAATGTGTATGTTTACAT--CTGTGATGGCACATGCAAatatatatatatatgt---atata ↓ 1 4 3 2 Gorilla: TGTGTCAACACTGGTTCACTC----------------------------------------------------------------------------CATATTTGCAT----TTGATGGCACATGCAAatatatatatatatatata----- Human: TGTGTCAACACTGGTTCACTC--------------------------------------CTCCAGGTACTCCTGGTGTAGTGAAGTGGTAAAATGTGTACGTTTACAT--CTGTGATGGCACATGCAAatatatatatatatac-------- Cluster: [ ] Orangutan: TGTGTCAATACTGGTTCACTCCTCCAGGTACTCCTGGTGCAGTGAAGTGGTAAAATGTG--------------------------------------TATGTTTACATCT--GTGATGGCACATGCAAatatatatatata----ta----- Chimp > Gorilla --------------- chr4:112294030-112294038 Template switch process: F1: L CCCTGGACTCCAGAGACAAGTGTGTCAACACTGGTTCACTCC 1 F3: 4 TTTGATGGCACATGCAAATATATATATATA--TATATAA R RF: CCCTGGACTCCAGAGACAAGTGTGTCAACACTGGTTCACTCCTCCAGGTACTCCTGGTGTACTGAAGTGGTAAAATGTGTATGTTTACATCTGTGATGGCACATGCAAATATATATATATATGTATATAA RR: GGGACCTGAGGTCTCTGTTCACACAGTTGTGACCAAGTGAGGAGGTCCATGAGGACCACATGACTTCACCATTTTACACATACAAATGTAGACACTACCGTGTACGTTTATATATATATATACATATATT F2: 3 ACGTTTATA 2 Unidirectional alignment (log-probability: -47.4) CTGGACTCCAGAGACAAGTGTGTCAACACTGGTTCACTCCatatttgcatT--------------------------------------------------TGATGGCACATGCAAATATATATATATA--TATATAA CTGGACTCCAGAGACAAGTGTGTCAACACTGGTTCACTCC----------TCCAGGTACTCCTGGTGTACTGAAGTGGTAAAATGTGTATGTTTACATCTGTGATGGCACATGCAAATATATATATATATGTATATAA Template switch alignment (log-probability: -32.2) CTGGACTCCAGAGACAAGTGTGTCAACACTGGTTCACTCC|ATATTTGCA|TtTGATGGCACATGCAAATATATATATATA--TATATAA CTGGACTCCAGAGACAAGTGTGTCAACACTGGTTCACTCC|ATATTTGCA|TGTGATGGCACATGCAAATATATATATATATGTATATAA ========== Event 2490 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: CCTCTGGTTCTTGAATAGACAGGATATTGAATGGACATAATATTTTAACATTCATCtattatactt ↓ 13 24 ↑ 13 24 Chimp: CCTCTGGTTCTTGAATAGACAAAATATTATGTCCATTCAATATCCTAACATTCATCtattatactt ↓ 13 24 ↑ 13 24 Gorilla: CCTCTGGTTCTTGAATAGACAGGATATTGAATGGACATAATATTTTAACATTCATCtactatactt Human: CCTCTGGTTCTTGAATAGACAGGATATTGAATGGACATAATATTTTAACATTCATCtattatactt Cluster: [ ] Orangutan: Chimp > Human ------------- chr4:179840965-179840988 Template switch process: F1: L TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA 1 F3: 4 TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT R RF: TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAAAATATTATGTCCATTCAATATCCTAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT RR: ACTTTTGGGTTGTACATAATGGAGACCAAGAACTTATCTGTTTTATAATACAGGTAAGTTATAGGATTGTAAGTAGATAATATGAAATTCGAGATCTCATGTACA F2: 3 TTTATAATACAGGTAAGTTATAGG 2 Unidirectional alignment (log-probability: -56.9) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA------------------------ggatattgaatggacataatatttTAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAAAATATTATGTCCATTCAATATCC------------------------TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT Template switch alignment (log-probability: -18.2) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|GGATATTGAATGGACATAATATTT|TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|GGATATTGAATGGACATAATATTT|TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT Human > Chimp ------------- chr4:183958188-183958211 Template switch process: F1: L TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA 1 F3: 4 TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT R RF: TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAGGATATTGAATGGACATAATATTTTAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT RR: ACTTTTGGGTTGTACATAATGGAGACCAAGAACTTATCTGTCCTATAACTTACCTGTATTATAAAATTGTAAGTAGATAATATGAAATTCGAGATCTCATGTACA F2: 3 CCTATAACTTACCTGTATTATAAA 2 Unidirectional alignment (log-probability: -56.9) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA------------------------aaatattatgtccattcaatatccTAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAGGATATTGAATGGACATAATATTT------------------------TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT Template switch alignment (log-probability: -18.2) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|AAATATTATGTCCATTCAATATCC|TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|AAATATTATGTCCATTCAATATCC|TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT Gorilla > Chimp --------------- chr4:183958188-183958211 Template switch process: F1: L TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA 1 F3: 4 TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT R RF: TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAGGATATTGAATGGACATAATATTTTAACATTCATCTACTATACTTTAAGCTCTAGAGTACATGT RR: ACTTTTGGGTTGTACATAATGGAGACCAAGAACTTATCTGTCCTATAACTTACCTGTATTATAAAATTGTAAGTAGATGATATGAAATTCGAGATCTCATGTACA F2: 3 CCTATAACTTACCTGTATTATAAA 2 Unidirectional alignment (log-probability: -60.4) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAaaATATT--------ATgtccattcAATATccTAACATTCATCTAtTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAGGATATTGAATGGACAT--------AATATTTTAACATTCATCTACTATACTTTAAGCTCTAGAGTACATGT Template switch alignment (log-probability: -24.3) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|AAATATTATGTCCATTCAATATCC|TAACATTCATCTAtTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|AAATATTATGTCCATTCAATATCC|TAACATTCATCTACTATACTTTAAGCTCTAGAGTACATGT Chimp > Gorilla --------------- chr4:193395950-193395973 Template switch process: F1: L TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA 1 F3: 4 TAACATTCATCTACTATACTTTAAGCTCTAGAGTACATGT R RF: TGAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAAAATATTATGTCCATTCAATATCCTAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT RR: ACTTTTGGGTTGTACATAATGGAGACCAAGAACTTATCTGTTTTATAATACAGGTAAGTTATAGGATTGTAAGTAGATAATATGAAATTCGAGATCTCATGTACA F2: 3 TTTATAATACAGGTAAGTTATAGG 2 Unidirectional alignment (log-probability: -60.4) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAggATATTgaatggacAT--------AATATttTAACATTCATCTAcTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACAAAATATT--------ATGTCCATTCAATATCCTAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT Template switch alignment (log-probability: -24.3) GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|GGATATTGAATGGACATAATATTT|TAACATTCATCTAcTATACTTTAAGCTCTAGAGTACATGT GAAAACCCAACATGTATTACCTCTGGTTCTTGAATAGACA|GGATATTGAATGGACATAATATTT|TAACATTCATCTATTATACTTTAAGCTCTAGAGTACATGT ========== Event 2491 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: GGACAAAGAGACTAGCCACTTAGAGTAA--CTTTAACAAAATCTTACTCAATCAAAAGTGTTAATTTAAATCA Chimp: GGACAAAGAGACTAGCCACTTAGAGTAA--CTTTAACAAAATCTTACTCAATGAAAAGTGTTAATTTAAATCA Gorilla: GGACAAAGAGACTAGCCACTTTGAGTAAGATTTTGTTAA--AGTTACTCTATGAAAAGTGTTAATTTAAATCA ↓ 13 24 ↑ 13 24 Human: GGACAAAGAGACTAGCCACTTAGAGTAA--CTTTAACAAAATCTTACTCAATCAAAAGTGTTAATTTAAATCA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr4:179838356-179838382 Template switch process: F1: L ATTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTT 1 F3: 4 ATCAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATAGAG R RF: ATTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTTTGAGTAAGATTTTGTTAAAGTTACTCTATGAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATAGAG RR: TAAGTGATGTTCTTGGGTTTCCTGTTTCTCTGATCGGTGAAACTCATTCTAAAACAATTTCAATGAGATACTTTTCACAATTAAATTTAGTTCTCTGACTACATATATCTC F2: 3 ACTCATTCTAAAACAATTTCAATGAGA 2 Unidirectional alignment (log-probability: -56.8) TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTTaGAGTAA-------------ctttaacaaaatcTTACTCaATcAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTTTGAGTAAGATTTTGTTAAAG-------------TTACTCTATGAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA Template switch alignment (log-probability: -24.8) TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTT|AGAGTAACTTTAACAAAATCTTACTCA|ATcAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTT|AGAGTAACTTTAACAAAATCTTACTCA|ATGAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA Human > Gorilla --------------- chr4:193393325-193393351 Template switch process: F1: L ATTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTT 1 F3: 4 ATGAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATAGAG R RF: ATTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTTAGAGTAACTTTAACAAAATCTTACTCAATCAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATAGAG RR: TAAGTGATGTTCTTGGGTTTCCTGTTTCTCTGATCGGTGAATCTCATTGAAATTGTTTTAGAATGAGTTAGTTTTCACAATTAAATTTAGTTCTCTGACTACATATATCTC F2: 3 TCTCATTGAAATTGTTTTAGAATGAGT 2 Unidirectional alignment (log-probability: -56.8) TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTTtGAGTAA-------------gattttgttaaagTTACTCtATgAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTTAGAGTAACTTTAACAAAATC-------------TTACTCAATCAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA Template switch alignment (log-probability: -24.8) TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTT|TGAGTAAGATTTTGTTAAAGTTACTCT|ATgAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA TTCACTACAAGAACCCAAAGGACAAAGAGACTAGCCACTT|TGAGTAAGATTTTGTTAAAGTTACTCT|ATCAAAAGTGTTAATTTAAATCAAGAGACTGATGTATATA ========== Event 2492 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TACTTAGATTGAACATATAGAGAATATTGACTTCAAATATACATTTtagatgatatttaatgccatgggaatgaatgaaattactcagagaatagagagtgagaagtggtctagattaagccccaaataagtcagacattttgaagtcagtcagatagagacaaagggc ↑ 4 1 3 2 Chimp: TACTTAGATTGAACATATAGATA-------------ATATACATTTtagatgatatttaatgccatgggaatgaatgaaattactcagagaatagagagtgagaagtggtctagattaagccccaaataagtcagacattttgaagtcagtcagatagagacaaagggc Gorilla: TACTTAGATTGAACATATAGAGAATATTGACTTGAAATATACATTTtagatgatatttaatgccatgggaatgaatgaaattactcagagaatagagagtgagaagtggtctagattaagccccaaataagtcagacattttgaagtcagtcagacagagacaaagggc Human: TACTTAGATTGAACATATAGAGAATATTGACTTCAAATATACATTTtagatgatatttaatgccatgggaatgaatgaaattactcagagaatagagagtgagaagtggtctagattaagccccaaataagtcagacattttgaagtcagtcagatagagacaaagggc Cluster: [ ] Orangutan: TACTTAGATTGAACGTATACAGAATATTGACTTGAAATATACATTTtagatgatatttaatgccatcggaatgaatgaaattactcagagaataaagagtgagacataccctagactaagccccaaataactcagacattttgaag----tcagatagagacaaagggc Chimp > Human ------------- chr4:103607663-103607670 Template switch process: F1: L TGTGTACTTAATCTATTGTATACTTAGATTGAACATATAGAGAATAT 1 F3: 4 AATATACATTTTAGATGATATTTAATGCCATGGGAATGAAT R RF: TGTGTACTTAATCTATTGTATACTTAGATTGAACATATAGATAATATACATTTTAGATGATATTTAATGCCATGGGAATGAATGAAATTACTCAGAGAATAGAGAGTGAGAAGTGGTCTAGATTAAGCCCCAAATAAGTCAGACATTTTGAAGTCA RR: ACACATGAATTAGATAACATATGAATCTAACTTGTATATCTATTATATGTAAAATCTACTATAAATTACGGTACCCTTACTTACTTTAATGAGTCTCTTATCTCTCACTCTTCACCAGATCTAATTCGGGGTTTATTCAGTCTGTAAAACTTCAGT F2: 3 ACTTCAGT 2 Unidirectional alignment (log-probability: -35.6) TTAATCTATTGTATACTTAGATTGAACATATAGAgAAtattgacttcaaaTATACATTTTAGATGATATTTAATGCCATGGGAATGAA TTAATCTATTGTATACTTAGATTGAACATATAGATAA-------------TATACATTTTAGATGATATTTAATGCCATGGGAATGAA Template switch alignment (log-probability: -22.4) TTAATCTATTGTATACTTAGATTGAACATATAGAgAATAT|TGACTTCA|AATATACATTTTAGATGATATTTAATGCCATGGGAATGAA TTAATCTATTGTATACTTAGATTGAACATATAGATAATAT|TGACTTCA|AATATACATTTTAGATGATATTTAATGCCATGGGAATGAA ========== Event 2493 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATCCCAGGGAAAAACCAGCATGTATTGGATGGTTCAAGTACCATCAAGTATTGAATGGTACTTGAACTTGTTAAATGTGCACAAA Chimp: AATCCCAGGGAAAAACCAGCATGTATTG--------------------------TATGGTACTTGAACTTGTTAAATGTGCACAAA Gorilla: AATCCCAGGGAAAAACCAGCATGTATTG--------------------------TATGGTACTTGAACTTGTTAAATGTGCACAAA ↓ 4 3 1 2 Human: AATCCCAGGGAAAAACCAGCATGTATTGGATGGTTCAAGTACCATCAAGTATTGAATGGTACTTGAACTTGTTAAATGTGCACAAA Cluster: [ ] Orangutan: AATCTCAGGGAAAAATCAGCCTGTACTG--------------------------TATGGTACTTGAACTTGTTAAATATGCACAAA Gorilla > Human --------------- chr4:85097332-85097342 Template switch process: F1: L CATATTTACTTTTAATCCCAGGGAAAAACCAGCATGTATTGGATGGT 1 F3: 4 CAAGTATTGAATGGTACTTGAACTTGTTAAATGTGCACAAAATGCTTTGT R RF: CATATTTACTTTTAATCCCAGGGAAAAACCAGCATGTATTGTATGGTACTTGAACTTGTTAAATGTGCACAAAATGCTTTGT RR: GTATAAATGAAAATTAGGGTCCCTTTTTGGTCGTACATAACATACCATGAACTTGAACAATTTACACGTGTTTTACGAAACA F2: 3 TACCATGAACT 2 Unidirectional alignment (log-probability: -53.8) ACTTTTAATCCCAGGGAAAAACCAGCATGTATtggatggttcaagtaccatcaagtatTGaATGGTACTTGAACTTGTTAAATGTGCACAA ACTTTTAATCCCAGGGAAAAACCAGCATGTAT--------------------------TGTATGGTACTTGAACTTGTTAAATGTGCACAA Template switch alignment (log-probability: -34.1) ACTTTTAATCCCAGGGAAAAACCAGCATGTATTGgATGGT|TCAAGTACCAT|CAaGTATTGaATGGTACTTGAACTTGTTAAATGTGCACAA ACTTTTAATCCCAGGGAAAAACCAGCATGTATTGTATGGT|TCAAGTACCAT|CATGTATTGTATGGTACTTGAACTTGTTAAATGTGCACAA ========== Event 2494 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGAACATTTAAGCAGCAGAATA------CTGTTTAAGTAGTAGTCTATCCACTTAGCTTGTGATTCATCAGTA---------TACCATCATTATTCAGACCTT Chimp: GAAGAACATTTAAGCAGCAGACTACTACTACTATTTAAGAAGTAGTCTATCCACTTAGCTTGTGATTCATCAGTA---------TACCATCATTATTCAGACCTT ↓ 1 4 3 2 Gorilla: GAAGAACATTTAAGCAGCAGAATA------CTGTTTAAGTAGTAGTCTATCCACTTAGCTTGTGATTCATCAGTA------------------TATTCAGACCTT Human: GAAGAACATTTAAGCAGCAGAATA------CTGTTTAAGTAGTAGTCTATCCACTTAGCTTGTGATTCATCAGTA---------TACCATCATTATTCAGACCTT Cluster: [ ] Orangutan: GAAGAACGTTTAAGCAGCAGAATA------CTGTTTAAGTAGTAGTCTGTCCACTTAGCTTGTGATTCATCAGTATGCCATCGT---------TATTCAGACCTT Chimp > Gorilla --------------- chr4:86214245-86214250 Template switch process: F1: L CTGAGCCAACTGTGTGCTTAGAAGAACATTTAAGCAGCAGA 1 F3: 4 TTTAAGTAGTAGTCTATCCACTTAGCTTGTGATTCATCAGTA R RF: CTGAGCCAACTGTGTGCTTAGAAGAACATTTAAGCAGCAGACTACTACTACTATTTAAGAAGTAGTCTATCCACTTAGCTTGTGATTCATCAGTA RR: GACTCGGTTGACACACGAATCTTCTTGTAAATTCGTCGTCTGATGATGATGATAAATTCTTCATCAGATAGGTGAATCGAACACTAAGTAGTCAT F2: 3 GTCATA 2 Unidirectional alignment (log-probability: -34.9) TGAGCCAACTGTGTGCTTAGAAGAACATTTAAGCAGCAG------AaTACTgTTTAAGtAGTAGTCTATCCACTTAGCTTGTGATTCATCAG TGAGCCAACTGTGTGCTTAGAAGAACATTTAAGCAGCAGACTACTACTACTATTTAAGAAGTAGTCTATCCACTTAGCTTGTGATTCATCAG Template switch alignment (log-probability: -22.1) TGAGCCAACTGTGTGCTTAGAAGAACATTTAAGCAGCAGA|ATACTG|TTTAAGtAGTAGTCTATCCACTTAGCTTGTGATTCATCAG TGAGCCAACTGTGTGCTTAGAAGAACATTTAAGCAGCAGA|ATACTG|TTTAAGAAGTAGTCTATCCACTTAGCTTGTGATTCATCAG ========== Event 2495 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTGCAGAAGAGGCAGTGTGTACTGATGCT-------------------CAAGCAATGGCAATTCAGGTTAAGAACA Chimp: ACTGCAGACGAGGCAGCGTGTACTTATGCT-------------------CAAGCAATGGCAATTCAGGTTAAGAACA Gorilla: ACTGCAGAAGAGGCAGTGTGTACTGATGCTCAAGCAATCAGTACATGCTCAAGCAATGGCAATTCAGGTTAAGAACA ↑ 3 24 1 Human: ACTGCAGAAGAGGCAGTGTGTACTGATGCT-------------------CAAGCAATGGCAATTCAGGTTAAGAACA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr4:86176438-86176443 Template switch process: F1: L TTTTTCAGACGACTGCAGAAGAGGCAGTGTGTACTGATGCTCAAGCAAT 1 F3: 4 ATGCTCAAGCAATGGCAATTCAGGTTAAGAACAGATGCCTGTTAT R RF: TTTTTCAAACGACTGCAGAAGAGGCAGTGTGTACTGATGCTCAAGCAATGGCAATTCAGGTTAAGAACAGATGCCTGTTAT RR: AAAAAGTTTGCTGACGTCTTCTCCGTCACACATGACTACGAGTTCGTTACCGTTAAGTCCAATTCTTGTCTACGGACAATA F2: 3 CATGAC 2 Unidirectional alignment (log-probability: -43.7) CGACTGCAGAAGAGGCAGTGTGTACTGatgctcaagcaatcagtacATGCTCAAGCAATGGCAATTCAGGTTAAGAACAGATGCCT CGACTGCAGAAGAGGCAGTGTGTACTG-------------------ATGCTCAAGCAATGGCAATTCAGGTTAAGAACAGATGCCT Template switch alignment (log-probability: -22.3) CGACTGCAGAAGAGGCAGTGTGTACTGATGCTCAAGCAAT|CAGTAC|ATGCTCAAGCAATGGCAATTCAGGTTAAGAACAGATGCCT CGACTGCAGAAGAGGCAGTGTGTACTGATGCTCAAGCAAT|CAGTAC|ATGCTCAAGCAATGGCAATTCAGGTTAAGAACAGATGCCT ========== Event 2496 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTATGCTCAAGGCCTCCATAGCAT-TGTGTCTGCATCAAGCCAGAATCTAAATCTT ↓ 1 4 3 2 Chimp: CTTATGCTCAAGGCCTCCATAATGCAGATGTCTGCATCAAGCCAGAATCTAAATCTT ↑ 1 4 3 2 Gorilla: CTTATGCTCAAGGCCTCCATAGCAT-TGTGTCTGCATCAAGCCAGAATCTAAATCTT Human: CTTATGCTCAAGGCCTCCATAGCAT-TGTGTCTGCATCAAGCCAGAATCTAAATCTT Cluster: [ ] Orangutan: CTTATGCTCAAGGCCTCCATAGCAT-TGTGTCTGCATCAAGCCCGAATCTAAATCTT Human > Chimp ------------- chr4:85598891-85598897 Template switch process: F1: L CCCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA 1 F3: 4 TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT R RF: CCCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATAGCATTGTGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT RR: GGGACCTAATTTTGGGTGTCGAATACGAGTTCCGGAGGTATCGTAACACAGACGTAGTTCGGTCTTAGATTTAGAACCTAGAGTAAA F2: 3 AGACGTA 2 Unidirectional alignment (log-probability: -31.5) CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATaatgcagA------TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCAT-------AGCATTGTGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT Template switch alignment (log-probability: -16.2) CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA|ATGCAGA|TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA|ATGCAGA|TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT Gorilla > Chimp --------------- chr4:85598891-85598897 Template switch process: F1: L CCCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA 1 F3: 4 TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT R RF: CCCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATAGCATTGTGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT RR: GGGACCTAATTTTGGGTGTCGAATACGAGTTCCGGAGGTATCGTAACACAGACGTAGTTCGGTCTTAGATTTAGAACCTAGAGTAAA F2: 3 AGACGTA 2 Unidirectional alignment (log-probability: -31) CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA------atgcagaTGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATAGCATTG-------TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT Template switch alignment (log-probability: -16.6) CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA|ATGCAGA|TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT CCTGGATTAAAACCCACAGCTTATGCTCAAGGCCTCCATA|ATGCAGA|TGTCTGCATCAAGCCAGAATCTAAATCTTGGATCTCATTT ========== Event 2497 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: aatatgagtgagCATGTTATGGAATGAAACAAGTAAGATTC----ACCATAAGTTTTATTTCCTCAACATATAT ↓ 13 24 ↑ 13 24 Chimp: aatatgagtgagCATGTTATG--GTGAATCTTACTTGTTTC--ATTCCATAAGCTTTATTTCCTCAACATATAT Gorilla: aatatgagtgagAATGTTATG--GTGAATCTTACTTGTTTCAT--TCCATAAGTTTTATTTCCTCAACATATAT Human: aatatgagtgagCATGTTATGGAATGAAACAAGTAAGATTC----ACCATAAGTTTTATTTCCTCAACATATAT Cluster: [ ] Orangutan: aatatgagtgagCATGTTTTG--GTGAATCTTACTTGTTTCAT--TCCATAAGTTTTATTTCTTCAACATATAT Chimp > Human ------------- chr4:107513721-107513740 Template switch process: F1: L GAAGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG 1 F3: 4 CCATAAGTTTTATTTCCTCAACATATATTTATAGGTCAAATTTTGTTT R RF: GAAGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGGTGAATCTTACTTGTTTCATTCCATAAGCTTTATTTCCTCAACATATATTTATAGGTCAAATTTGGTTT RR: CTTCGATTACATCAACCTCGTTATACTCACTCGTACAATACCACTTAGAATGAACAAAGTAAGGTATTCGAAATAAAGGAGTTGTATATAAATATCCAGTTTAAACCAAA F2: 3 ACTTAGAATGAACAAAGTAA 2 Unidirectional alignment (log-probability: -63) AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG--------------------aatgaaacaagtaagattcaCCATAAGtTTTATTTCCTCAACATATATTTATAGGTCAAA AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGGTGAATCTTACTTGTTTCATT--------------------CCATAAGCTTTATTTCCTCAACATATATTTATAGGTCAAA Template switch alignment (log-probability: -29.9) AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG|AATGAAACAAGTAAGATTCA|CCATAAGtTTTATTTCCTCAACATATATTTATAGGTCAAA AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG|AATGAAACAAGTAAGATTCA|CCATAAGCTTTATTTCCTCAACATATATTTATAGGTCAAA Human > Chimp ------------- chr4:110436318-110436337 Template switch process: F1: L GAAGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG 1 F3: 4 CCATAAGCTTTATTTCCTCAACATATATTTATAGGTCAAATTTGGTTT R RF: GAAGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGGAATGAAACAAGTAAGATTCACCATAAGTTTTATTTCCTCAACATATATTTATAGGTCAAATTTTGTTT RR: CTTCGATTACATCAACCTCGTTATACTCACTCGTACAATACCTTACTTTGTTCATTCTAAGTGGTATTCAAAATAAAGGAGTTGTATATAAATATCCAGTTTAAAACAAA F2: 3 TTACTTTGTTCATTCTAAGT 2 Unidirectional alignment (log-probability: -63) AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG--------------------tgaatcttacttgtttcattCCATAAGcTTTATTTCCTCAACATATATTTATAGGTCAAA AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGGAATGAAACAAGTAAGATTCA--------------------CCATAAGTTTTATTTCCTCAACATATATTTATAGGTCAAA Template switch alignment (log-probability: -29.9) AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG|TGAATCTTACTTGTTTCATT|CCATAAGcTTTATTTCCTCAACATATATTTATAGGTCAAA AGCTAATGTAGTTGGAGCAATATGAGTGAGCATGTTATGG|TGAATCTTACTTGTTTCATT|CCATAAGTTTTATTTCCTCAACATATATTTATAGGTCAAA ========== Event 2498 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CCCACAGATGCCAATGATTCAATTCAGAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG----AGGCTAAGAATTCTGGGACTCATATTGccaaccctaaggtggacacagtctagttggtgagacagaagtatatacaaatcatgctgagggcttgtgctaaaacagaa ↑ 1 4 3 2 Chimp: CCCACAGATGCCAATGATTCA-ATCACAAAGCATTAACTGACCAGTGGCATGGGCTGAC----AGTGAGGCTGAGAATTCTGGGACTCATATTGCCAACCCTAAGGTGGACACAGTCTAGTTGGTGAGACAGAAGTATATACAAATCATGCTGAGGGCTTGTGCTAAAACAGAA ↓ 1 4 3 2 Gorilla: CCCACAGATGCCAATGATTCAATTCAGAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG----AGGCTGAGAATTCTGGGACTCATATTGCCAAccttaaggtggacacagtctagttggtgagacacaagtatatacaaatcatgctgagggcttgtgctaaaacagaa Human: CCCACAGATGCCAATGATTCAATTCAGAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG----AGGCTAAGAATTCTGGGACTCATATTGccaaccctaaggtggacacagtctagttggtgagacagaagtatatacaaatcatgctgagggcttgtgctaaaacagaa Cluster: [ ] Orangutan: CCCACAGATGCCAATAATttaattcagaaagcattaactgaccactggcatgggctgacagta----aggctgagaattctgggattcacattgtcagccctaaggtggacacagtctagttggtgagacagatgtatacacaaatcatgctgagggcttgtgctgaaacagaa Chimp > Human ------------- chr4:11120100-11120103 Template switch process: F1: L TCACATCTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAT 1 F3: 4 AAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG R RF: TCACATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAATCACAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTGAGGCTGAGAATTCTGGGACTCATATTGCCAACCCTAAGGTGGACACAGTCTAGTTGGTGAGACAGAAGTATATACAAATCATGCTGA RR: AGTGTAAACCTACTCGTCAAGGGTGTCTACGGTTACTAAGTTAGTGTTTCGTAATTGACTGGTCACCGTACCCGACTGTCACTCCGACTCTTAAGACCCTGAGTATAACGGTTGGGATTCCACCTGTGTCAGATCAACCACTCTGTCTTCATATATGTTTAGTACGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -24.4) CATcTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAtTCAgAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG CATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAA-TCACAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG Template switch alignment (log-probability: -21.7) CATcTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAT|TCAG|AAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG CATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAT|TCAG|AAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG Chimp > Gorilla --------------- chr4:10462635-10462638 Template switch process: F1: L TCACATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAT 1 F3: 4 AAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG R RF: TCACATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAATCACAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTGAGGCTGAGAATTCTGGGACTCATATTGCCAACCCTAAGGTGGACACAGTCTAGTTGGTGAGACAGAAGTATATACAAATCATGCTGA RR: AGTGTAAACCTACTCGTCAAGGGTGTCTACGGTTACTAAGTTAGTGTTTCGTAATTGACTGGTCACCGTACCCGACTGTCACTCCGACTCTTAAGACCCTGAGTATAACGGTTGGGATTCCACCTGTGTCAGATCAACCACTCTGTCTTCATATATGTTTAGTACGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -17.9) CATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAtTCAgAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG CATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAA-TCACAAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG Template switch alignment (log-probability: -16.2) CATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAT|TCAG|AAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG CATTTGGATGAGCAGTTCCCACAGATGCCAATGATTCAAT|TCAG|AAAGCATTAACTGACCAGTGGCATGGGCTGACAGTG ========== Event 2499 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATCACATTTAATGACCTTCA-----ATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAA ↓ 1 3 4 2 Chimp: CATCACATTTAATGACCTTCACACCTGATATTTATCAGGTGTGATGCCAGGCTCTTTCCAA ↑ 1 3 4 2 Gorilla: CATCACATTTAATGACCTTCA-----ATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAA Human: CATCACATTTAATGACCTTCA-----ATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAA Cluster: [ ] Orangutan: CATCACATTTAATGACCTTCA-----ATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAA Human > Chimp ------------- chr4:11347146-11347156 Template switch process: F1: L ACCCATTACTAAGAGAGGAGCATCACATTTAATGACCTTCA 1 F3: 4 TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT R RF: ACCCATTACTAAGAGAAGAGCATCACATTTAATGACCTTCAATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT RR: TGGGTAATGATTCTCTTCTCGTAGTGTAAATTACTGGAAGTTAATTTATAGTCCACACTACGGTCCGAGAAAGGTTTGTAGCGACAA F2: 3 TTATAGTCCAC 2 Unidirectional alignment (log-probability: -38.8) CCCATTACTAAGAGAgGAGCATCACATTTAATGACCTTCAcacctgatATT---TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT CCCATTACTAAGAGAAGAGCATCACATTTAATGACCTTCA--------ATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT Template switch alignment (log-probability: -22.6) CCCATTACTAAGAGAgGAGCATCACATTTAATGACCTTCA|CACCTGATATT|TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT CCCATTACTAAGAGAAGAGCATCACATTTAATGACCTTCA|CACCTGATATT|TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT Gorilla > Chimp --------------- chr4:11347146-11347156 Template switch process: F1: L ACCCATTACTAAGAGAGGAGCATCACATTTAATGACCTTCA 1 F3: 4 TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT R RF: ACCCATTACTAAGAGAAGAGCATCACATTTAATGACCTTCAATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT RR: TGGGTAATGATTCTCTTCTCGTAGTGTAAATTACTGGAAGTTAATTTATAGTCCACACTACGGTCCGAGAAAGGTTTGTAGCGACAA F2: 3 TTATAGTCCAC 2 Unidirectional alignment (log-probability: -37.8) CCCATTACTAAGAGAgGAGCATCACATTTAATGACCTTCAcacctgatATT---TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT CCCATTACTAAGAGAAGAGCATCACATTTAATGACCTTCA--------ATTAAATATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT Template switch alignment (log-probability: -22.6) CCCATTACTAAGAGAgGAGCATCACATTTAATGACCTTCA|CACCTGATATT|TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT CCCATTACTAAGAGAAGAGCATCACATTTAATGACCTTCA|CACCTGATATT|TATCAGGTGTGATGCCAGGCTCTTTCCAAACATCGCTGTT ========== Event 2500 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAGGGCCAGGCACTGAGGAA--AGATC-ATCCCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT Chimp: GTAGGACCAGGCACTGAGGAA--AGATC-AGCCCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT ↓ 1 4 3 2 Gorilla: GTAGGACCAGGCACTGAGGAA----CTCATGTTCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT ↑ 1 4 3 2 Human: GTAGGGCCAGGCACTGAGGAA--AGATC-ATCCCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT Cluster: [ ] Orangutan: GTAGGACCAGGCACTGAGGAAAG--ATC-AGCCCCAGCTAATTGGAACATGAGAAGCA---------AAGCCT Human > Gorilla --------------- chr4:119498673-119498680 Template switch process: F1: L CCTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAA 1 F3: 4 CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT R RF: CCTGAATGGGTTTGCACTCTGTAGGGCCAGGCACTGAGGAAAGATCATCCCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT RR: GGACTTACCCAAACGTGAGACATCCCGGTCCGTGACTCCTTTCTAGTAGGGGTCGATTAACCTTGTACTCTTCGTTTCGTCCGTTTCGGA F2: 3 TTGTACTC 2 Unidirectional alignment (log-probability: -36.6) CTGAATGGGTTTGCACTCTGTAGGaCCAGGCACTGAGGAA--------CtcatgttCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT CTGAATGGGTTTGCACTCTGTAGGGCCAGGCACTGAGGAAAGATCATCC-------CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT Template switch alignment (log-probability: -22.3) CTGAATGGGTTTGCACTCTGTAGGaCCAGGCACTGAGGAA|CTCATGTT|CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT CTGAATGGGTTTGCACTCTGTAGGGCCAGGCACTGAGGAA|CTCATGTT|CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT Chimp > Gorilla --------------- chr4:119498673-119498680 Template switch process: F1: L CCTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAA 1 F3: 4 CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT R RF: CCTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAAAGATCAGCCCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT RR: GGACTTACCCAAACGTGAGACATCCTGGTCCGTGACTCCTTTCTAGTCGGGGTCGATTAACCTTGTACTCTTCGTTTCGTCCGTTTCGGA F2: 3 TTGTACTC 2 Unidirectional alignment (log-probability: -31.1) CTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAA--------CtcatgttCCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT CTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAAAGATCAGCC-------CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT Template switch alignment (log-probability: -16.7) CTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAA|CTCATGTT|CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT CTGAATGGGTTTGCACTCTGTAGGACCAGGCACTGAGGAA|CTCATGTT|CCAGCTAATTGGAACATGAGAAGCAAAGCAGGCAAAGCCT ========== Event 2501 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATTGACAGATGATGTTCAGGG--AGAACAGTTCCTGTAGGTCTGAACAAGAT ↓ 1 3 4 2 Chimp: CATTGACAGATGATGTTCAGGAACTGTTCTGTTCCTGTAGGTCTGAACGAGAT ↑ 1 3 4 2 Gorilla: CATTGACAGATGATGTTCAGGG--AGAACAGTTCCTGTAGGTCTGAATGAGAT Human: CATTGACAGATGATGTTCAGGG--AGAACAGTTCCTGTAGGTCTGAACAAGAT Cluster: [ ] Orangutan: CATTGACAGAACATGTTCAGGG--AGAACAGTTCCTGTAGGTCTGAATGAGAT Human > Chimp ------------- chr4:82565516-82565524 Template switch process: F1: L GGGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG 1 F3: 4 GTTCCTGTAGGTCTGAACGAGATGGGTCTCTGGAAAGTCA R RF: GGGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGGGAGAACAGTTCCTGTAGGTCTGAACAAGATGGGTCTCTGGAAAGTCA RR: CCCACCTTATTACCGAATACGTAACTGTCTACTACAAGTCCCTCTTGTCAAGGACATCCAGACTTGTTCTACCCAGAGACCTTTCAGT F2: 3 TCTTGTCAA 2 Unidirectional alignment (log-probability: -38.9) GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG------AactgttctGTTCCTGTAGGTCTGAACgAGATGGGTCTCTGGAAAGTCA GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGGGAGAACA--------GTTCCTGTAGGTCTGAACAAGATGGGTCTCTGGAAAGTCA Template switch alignment (log-probability: -22.4) GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG|AACTGTTCT|GTTCCTGTAGGTCTGAACgAGATGGGTCTCTGGAAAGTCA GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG|AACTGTTCT|GTTCCTGTAGGTCTGAACAAGATGGGTCTCTGGAAAGTCA Gorilla > Chimp --------------- chr4:82565516-82565524 Template switch process: F1: L GGGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG 1 F3: 4 GTTCCTGTAGGTCTGAACGAGATGGGTCTCTGGAAAGTCA R RF: GGGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGGGAGAACAGTTCCTGTAGGTCTGAATGAGATGGGTCTCTGGAAAGTCA RR: CCCACCTTATTACCGAATACGTAACTGTCTACTACAAGTCCCTCTTGTCAAGGACATCCAGACTTACTCTACCCAGAGACCTTTCAGT F2: 3 TCTTGTCAA 2 Unidirectional alignment (log-probability: -38) GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG------AactgttctGTTCCTGTAGGTCTGAAcGAGATGGGTCTCTGGAAAGTCA GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGGGAGAACA--------GTTCCTGTAGGTCTGAATGAGATGGGTCTCTGGAAAGTCA Template switch alignment (log-probability: -22.4) GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG|AACTGTTCT|GTTCCTGTAGGTCTGAAcGAGATGGGTCTCTGGAAAGTCA GGTGGAATAATGGCTTATGCATTGACAGATGATGTTCAGG|AACTGTTCT|GTTCCTGTAGGTCTGAATGAGATGGGTCTCTGGAAAGTCA ========== Event 2502 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCA----CCTGCATGAGTGTCACTGTTTCT ↓ 3 2 1 4 Chimp: CTGTCAGGGACAAGCATAACTAGTCTGCATAAGTGCAGACTAGTGCATGAGTGTCACTGTTTCT ↑ 3 2 1 4 Gorilla: CTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCA----CCTGCATGAGTGTCACTGTTTCC Human: CTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCA----CCTGCATGAGTGTCACTGTTTCT Cluster: [ ] Orangutan: CTGTCAGGGACAAGCATAACTAGCCTGCATAAGCTCA----CCTGCATGAGTGTCACTGTTTCT Human > Chimp ------------- chr4:82014054-82014063 Template switch process: F1: L CAATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG 1 F3: 4 TGCATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT R RF: CAATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCACCTGCATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT RR: GTTAGAATGACAGTCCCTGTTCGTATTGATCAGACGTATTCGAGTGGACGTACTCACAGTGACAAAGATAAAAAGAATGAAACAGGA F2: 3 GATCAGACGT 2 Unidirectional alignment (log-probability: -35.8) AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG------TGCagactagtgcATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCACCTGC----------ATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT Template switch alignment (log-probability: -16.5) AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG|TGCAGACTAG|TGCATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG|TGCAGACTAG|TGCATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT Gorilla > Chimp --------------- chr4:82014054-82014063 Template switch process: F1: L CAATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG 1 F3: 4 TGCATGAGTGTCACTGTTTCTATTTTTCTTACTTTGTCCT R RF: CAATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCACCTGCATGAGTGTCACTGTTTCCATTTTTCTTACTTTGTCCT RR: GTTAGAATGACAGTCCCTGTTCGTATTGATCAGACGTATTCGAGTGGACGTACTCACAGTGACAAAGGTAAAAAGAATGAAACAGGA F2: 3 GATCAGACGT 2 Unidirectional alignment (log-probability: -40.8) AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG------tgcagactagTGCATGAGTGTCACTGTTTCtATTTTTCTTACTTTGTCCT AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAGCTCACC----------TGCATGAGTGTCACTGTTTCCATTTTTCTTACTTTGTCCT Template switch alignment (log-probability: -22.5) AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG|TGCAGACTAG|TGCATGAGTGTCACTGTTTCtATTTTTCTTACTTTGTCCT AATCTTACTGTCAGGGACAAGCATAACTAGTCTGCATAAG|TGCAGACTAG|TGCATGAGTGTCACTGTTTCCATTTTTCTTACTTTGTCCT ========== Event 2503 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAGATGCTAAAATTCACATATCATAAAATTTA ↑ 3 2 1 4 Chimp: AATTTAGCTGAATATAATTTTTAGCATCTTTATGGAA----GTATGATTCACATATCATAAAATTTA Gorilla: AATTTAGCTGAATATAATTTTTAACATCTTCATGGAA----GTATGATTCACGTATCATAAAATTTA Human: AATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAGATGCTAAAATTCACATATCATAAAATTTA Cluster: [ ] Orangutan: AATTTAGCTGAATATAATTTTtaacatctttatggaa----gtatgagtcacatatcataaaattta Chimp > Human ------------- chr4:112336540-112336547 Template switch process: F1: L ATGAAATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAG 1 F3: 4 ATTCACATATCATAAAATTTAACCATTTTAAGGGTATAAT R RF: ATGAAATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAGTATGATTCACATATCATAAAATTTAACCATTTTAAGGGTATAAT RR: TACTTTAAATCGACTTATATTAAAAATCGTAGAAATACCTTCATACTAAGTGTATAGTATTTTAAATTGGTAAAATTCCCATATTA F2: 3 AAATCGTA 2 Unidirectional alignment (log-probability: -28.4) GAAATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAG-ATGctaaaATTCACATATCATAAAATTTAACCATTTTAAGGGTATAAT GAAATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAGTATG-----ATTCACATATCATAAAATTTAACCATTTTAAGGGTATAAT Template switch alignment (log-probability: -16.3) GAAATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAG|ATGCTAAA|ATTCACATATCATAAAATTTAACCATTTTAAGGGTATAAT GAAATTTAGCTGAATATAATTTTTAGCATCTTTATGGAAG|ATGCTAAA|ATTCACATATCATAAAATTTAACCATTTTAAGGGTATAAT ========== Event 2504 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAATCAGTTGTCTGAAAAGT------GC----AGTTTTAGAATATAAACTGCAAATTCCTTTCCCATGATA ↑ 1 4 3 2 Chimp: CAAATCAGTTGTCTGAAAAGT---GGCTC--AATGGTTTAGAACATAAACTGCATATTCCTTTCCCATGATA Gorilla: CAAATCAGTTGTCTGAAAAGTGGC---TCAA--TGGTTTAGAATATAAACTGCATATTCCTTTCCCATGATA ↓ 1 4 3 2 Human: CAAATCAGTTGTCTGAAAAGT------GC----AGTTTTAGAATATAAACTGCAAATTCCTTTCCCATGATA Cluster: [ ] Orangutan: CAAATCAGTTGTCTGAAAAGCGGC---TCAA--TGGTTTAGAATACAAACTGCATATTCCTTTCCCATGATA Chimp > Human ------------- chr4:75008933-75008936 Template switch process: F1: L TGACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG 1 F3: 4 TTTAGAATATAAACTGCAAATTCCTTTCCCATGATAAATCCTGACTTT R RF: TGACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTGGCTCAATGGTTTAGAACATAAACTGCATATTCCTTTCCCATGATAAATCCTGACTTT RR: ACTGTGAGGGGAGTCGAGTCGTTTAGTCAACAGACTTTTCACCGAGTTACCAAATCTTGTATTTGACGTATAAGGAAAGGGTACTATTTAGGACTGAAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -39.4) ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTGcagt---------TTTAGAAtATAAACTGCAaATTCCTTTCCCATGATAAATC ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG----GCTCAATGGTTTAGAACATAAACTGCATATTCCTTTCCCATGATAAATC Template switch alignment (log-probability: -27.9) ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG|CAGT|TTTAGAAtATAAACTGCAaATTCCTTTCCCATGATAAATC ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG|CAGT|TTTAGAACATAAACTGCATATTCCTTTCCCATGATAAATC Gorilla > Human --------------- chr4:75008933-75008936 Template switch process: F1: L TGACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG 1 F3: 4 TTTAGAATATAAACTGCAAATTCCTTTCCCATGATAAATC R RF: TGACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTGGCTCAATGGTTTAGAATATAAACTGCATATTCCTTTCCCATGATAAATC RR: ACTGTGAGGGGAGTCGAGTCGTTTAGTCAACAGACTTTTCACCGAGTTACCAAATCTTATATTTGACGTATAAGGAAAGGGTACTATTTAG F2: 3 TGAC 2 Unidirectional alignment (log-probability: -32) ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG---CA--GtTTTAGAATATAAACTGCAaATTCCTTTCCCATGATAAATC ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTGGCTCAATGGTTTAGAATATAAACTGCATATTCCTTTCCCATGATAAATC Template switch alignment (log-probability: -21.8) ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG|CAGT|TTTAGAATATAAACTGCAaATTCCTTTCCCATGATAAATC ACACTCCCCTCAGCTCAGCAAATCAGTTGTCTGAAAAGTG|CAGT|TTTAGAATATAAACTGCATATTCCTTTCCCATGATAAATC ========== Event 2505 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ccatcataaaactatggagcaaatgccaagagaatctgaggCCTCACTTTTGGCAATCTTAAACTGCTGAACC Chimp: TCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTG-GCATTTGCTTTTGGCAATCTTAAACTGCTGAACC ↑ 3 2 1 4 Gorilla: TCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTGAGGCCTCACTTTTGACAATCTTAAACTGCTGAACC Human: ccatcataaaactatggagcaaatgccaagagaatctgaggCCTCACTTTTGGCAATCTTAAACTGCTGAACC Cluster: [ ] Orangutan: tcatcataaaactatggagcaaatgccaagagaatctgaggCCTCACTTTTGGCAATCTTAAACTGCTGAACC Gorilla > Chimp --------------- chr4:76415260-76415266 Template switch process: F1: L TATTCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTG 1 F3: 4 CTTTTGGCAATCTTAAACTGCTGAACCAATACTAGCAACCACTACTC R RF: TATTCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTGAGGCCTCACTTTTGACAATCTTAAACTGCTGAACCAATACTAGCAACCACTACTC RR: ATAAGTAGTATTTTGATACCTCGTTTACGGTTCTCTTAGACTCCGGAGTGAAAACTGTTAGAATTTGACGACTTGGTTATGATCGTTGGTGATGAG F2: 3 GTTTACG 2 Unidirectional alignment (log-probability: -36.7) ATTCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTG--------gcatttgCTTTTGgCAATCTTAAACTGCTGAACCAATACTAGCAACC ATTCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTGAGGCCTCA-------CTTTTGACAATCTTAAACTGCTGAACCAATACTAGCAACC Template switch alignment (log-probability: -22.3) ATTCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTG|GCATTTG|CTTTTGgCAATCTTAAACTGCTGAACCAATACTAGCAACC ATTCATCATAAAACTATGGAGCAAATGCCAAGAGAATCTG|GCATTTG|CTTTTGACAATCTTAAACTGCTGAACCAATACTAGCAACC ========== Event 2506 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AACTGGAAGCACTGTATTTATGTCTACGTATTGCGTG-------TGTACAAAGAGATCTAAAAGGGAACA Chimp: AACTGGAAGAACTGTATTTATGTCTATGTATTACGTG-------TGTACAAAGAGATCTAAAAGGGAACA ↓ 3 2 1 4 Gorilla: AACTGGAAGCACTGTATTTATGTCTATGTATTATGTGATACATAGACATAAAGAGATCTAAAAGGGAACA Human: AACTGGAAGCACTGTATTTATGTCTACGTATTGCGTG-------TGTACAAAGAGATCTAAAAGGGAACA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr4:127785981-127785992 Template switch process: F1: L AAAATGGTAACTGGAAGCACTGTATTTATGTCTATGTATTATGTG 1 F3: 4 AAAGAGATCTAAAAGGGAACAGAGACATCTGATTACAGAA R RF: AAAATGGTAACTGGAAGAACTGTATTTATGTCTATGTATTACGTGTGTACAAAGAGATCTAAAAGGGAACAGAGACATCTGATTACAGAA RR: TTTTACCATTGACCTTCTTGACATAAATACAGATACATAATGCACACATGTTTCTCTAGATTTTCCCTTGTCTCTGTAGACTAATGTCTT F2: 3 TACAGATACATA 2 Unidirectional alignment (log-probability: -47.8) GGTAACTGGAAGcACTGTATTTATGTCTATGTATTA----TGTgatacatagacAtAAAGAGATCTAAAAGGGAACAGAGACATCTGATTACAGAA GGTAACTGGAAGAACTGTATTTATGTCTATGTATTACGTGTGT-----------ACAAAGAGATCTAAAAGGGAACAGAGACATCTGATTACAGAA Template switch alignment (log-probability: -28.4) GGTAACTGGAAGcACTGTATTTATGTCTATGTATTAtGTG|ATACATAGACAT|AAAGAGATCTAAAAGGGAACAGAGACATCTGATTACAGAA GGTAACTGGAAGAACTGTATTTATGTCTATGTATTACGTG|ATACATAGACAT|AAAGAGATCTAAAAGGGAACAGAGACATCTGATTACAGAA ========== Event 2507 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTATGAAAATATATACTTAAAA---CAGATAGCAACAGATATGTTAAAATATGATATGCATGTAAATGCATAGAAAATGCCGAACAGGTGAAAGAAGAGGGTTGAGATTTTGTATTTATGTTTGCTGACACATTTTTCTTTGTTACAGTCCTGCCCTTATCTGTTACTGACAATGTATTCATGTC Chimp: -CTATGAAAATATATACTTAAAA---CAG-AAGCTACAGATATGTTAAAATATGATATGCATGTAAATGCATAGAAAATGCCGAACAGGAGAAAGAAGAGGGTTGAGATTTTGTATTTATGTTTGCTGACACATTTTTCTTTGTTACAGTCCTGCCCTTATCTGTTAATGACAATGTATTCATGTC Gorilla: TCTATGAAAATATATACTTAATACTTAAAACAGCAACAGATATGTTAAAATATGATATGCATGTAAATGCATAGAAAATGCCGAACAGGTGAGAGAAGAGGGTTGAGATTTAGTATTTATGTTTGCTGACACATTTTTCTTTGTTACAGTCCTGCCTTTATCTGTTAATGATAATGTATTCATGTC ↓ 1 4 3 2 Human: TCTATGAAAATATATACTTAAAA---CAGATAGCAACAGATATGTTAAAATATGATATGCATGTAAATGCATAGAAAATGCCGAACAGGTGAAAGAAGAGGGTTGAGATTTTGTATTTATGTTTGCTGACACATTTTTCTTTGTTACAGTCCTGCCCTTATCTGTTACTGACAATGTATTCATGTC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr4:116038651-116038657 Template switch process: F1: L TTAGACCTATATGTTCTCTATCTATGAAAATATATACTTAA 1 F3: 4 AGCAACAGATATGTTAAAATATGATATGCATGTAAATGCA R RF: TTAGACCTATATGTTCTCTATCTATGAAAATATATACTTAATACTTAAAACAGCAACAGATATGTTAAAATATGATATGCATGTAAATGCATAGAAAATGCCGAACAGGTGAGAGAAGAGGGTTGAGATTTAGTATTTATGTTTGCTGACACATTTTTCTTTGTTACAGTCCTGCCTTTATCTGTT RR: AATCTGGATATACAAGAGATAGATACTTTTATATATGAATTATGAATTTTGTCGTTGTCTATACAATTTTATACTATACGTACATTTACGTATCTTTTACGGCTTGTCCACTCTCTTCTCCCAACTCTAAATCATAAATACAAACGACTGTGTAAAAAGAAACAATGTCAGGACGGAAATAGACAA F2: 3 TAGACAA 2 Unidirectional alignment (log-probability: -26.8) TAGACCTATATGTTCTCTATCTATGAAAATATATACT-------TAAAACagatAGCAACAGATATGTTAAAATATGATATGCATGTAAATGCA TAGACCTATATGTTCTCTATCTATGAAAATATATACTTAATACTTAAAAC----AGCAACAGATATGTTAAAATATGATATGCATGTAAATGCA Template switch alignment (log-probability: -16.6) TAGACCTATATGTTCTCTATCTATGAAAATATATACTTAA|AACAGAT|AGCAACAGATATGTTAAAATATGATATGCATGTAAATGCA TAGACCTATATGTTCTCTATCTATGAAAATATATACTTAA|AACAGAT|AGCAACAGATATGTTAAAATATGATATGCATGTAAATGCA ========== Event 2508 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGAATTTTGAGTTATCTATCCAAAGACAATGGTCTTTGTCATAATCCTGTTTTCTC ↑ 31 4 2 Chimp: ATGAATTTTGAGTTATCTATC-------CATTGTCTTTGTCATAATCCTGTTTTCTC Gorilla: ATGAATTTTGAGTTATCTATC-------CATTGTCTTTGTCATAATCCTGTTTTCTC Human: ATGAATTTTGAGTTATCTATCCAAAGACAATGGTCTTTGTCATAATCCTGTTTTCTC Cluster: [ ] Orangutan: ATGAATTTTGAGTTATCTATC-------GATTGTCTTTGTCATAATCCTGTTTTCTC Chimp > Human ------------- chr4:72914025-72914033 Template switch process: F1: L CACTGGAAAATGTCTGCAGGATGAATTTTGAGTTATCTATCCA 1 F3: 4 GTCTTTGTCATAATCCTGTTTTCTCTCAGATTTCATTCAT R RF: CACTGGAAAATGTCTGTAGGATGAATTTTGAGTTATCTATCCATTGTCTTTGTCATAATCCTGTTTTCTCTCAGATTTCATTCAT RR: GTGACCTTTTACAGACATCCTACTTAAAACTCAATAGATAGGTAACAGAAACAGTATTAGGACAAAAGAGAGTCTAAAGTAAGTA F2: 3 GTAACAGAA 2 Unidirectional alignment (log-probability: -33) TGGAAAATGTCTGcAGGATGAATTTTGAGTTATCTATCCaaagacaATgGTCTTTGTCATAATCCTGTTTTCTCTCAGATTTCATTCAT TGGAAAATGTCTGTAGGATGAATTTTGAGTTATCTATCC-------ATTGTCTTTGTCATAATCCTGTTTTCTCTCAGATTTCATTCAT Template switch alignment (log-probability: -22.4) TGGAAAATGTCTGcAGGATGAATTTTGAGTTATCTATCCA|AAGACAATG|GTCTTTGTCATAATCCTGTTTTCTCTCAGATTTCATTCAT TGGAAAATGTCTGTAGGATGAATTTTGAGTTATCTATCCA|AAGACAATG|GTCTTTGTCATAATCCTGTTTTCTCTCAGATTTCATTCAT ========== Event 2509 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: gttcCATAAGTATGTATGGAATACA-----------TATGAATACATATGTATTCATATGTATTCCATACATACTTCTGTGTAT Chimp: gttcCATAAGTATGTATGGAATACA-----------TATGAATACATATGTATTCATATGTATTCCATACATACTTCTGTGTAT ↑ 3 4 1 2 Gorilla: gttcCATAAGTATGTATGGAATACA-------------------------------TATGTATTCCATACATACTTATGTGTAT ↓ 3 4 1 2 Human: gttcCATAAGTATGTATGGAATACA-----------TATGAATACATATGTATTCATATGTATTCCATACATACTTCTGTGTAT Cluster: [ ] Orangutan: gttcCATAAGTATGTATGGAATAC-ATATCTATTCA--------------------TATGTATTCCATACATACTGATGTGTAT Gorilla > Human --------------- chr4:72953014-72953027 Template switch process: F1: L AAGTTCAATTTTGACTGTTCCATAAGTATGTATGGAATACATATG 1 F3: 4 CATATGTATTCCATACATACTTCTGTGTATGTATGGATATTA R RF: AAGTTCAATTTTGACTGTTCCATAAGTATGTATGGAATACATATGTATTCCATACATACTTATGTGTATGTATGGATATTA RR: TTCAAGTTAAAACTGACAAGGTATTCATACATACCTTATGTATACATAAGGTATGTATGAATACACATACATACCTATAAT F2: 3 TTATGTATACATAA 2 Unidirectional alignment (log-probability: -45.2) CAATTTTGACTGTTCCATAAGTATGTATGGAATAcatatgaatacatatgtattCATATGTATTCCATACATACTTcTGTGTATGTATGGATAT CAATTTTGACTGTTCCATAAGTATGTATGGAATA--------------------CATATGTATTCCATACATACTTATGTGTATGTATGGATAT Template switch alignment (log-probability: -23.2) CAATTTTGACTGTTCCATAAGTATGTATGGAATACATATG|AATACATATGTATT|CATATGTATTCCATACATACTTcTGTGTATGTATGGATAT CAATTTTGACTGTTCCATAAGTATGTATGGAATACATATG|AATACATATGTATT|CATATGTATTCCATACATACTTATGTGTATGTATGGATAT Gorilla > Chimp --------------- chr4:74158787-74158800 Template switch process: F1: L AAGTTCAATTTTGACTGTTCCATAAGTATGTATGGAATACATATG 1 F3: 4 CATATGTATTCCATACATACTTCTGTGTATGTATGGATATTA R RF: AAGTTCAATTTTGACTGTTCCATAAGTATGTATGGAATACATATGTATTCCATACATACTTATGTGTATGTATGGATATTA RR: TTCAAGTTAAAACTGACAAGGTATTCATACATACCTTATGTATACATAAGGTATGTATGAATACACATACATACCTATAAT F2: 3 TTATGTATACATAA 2 Unidirectional alignment (log-probability: -45.2) CAATTTTGACTGTTCCATAAGTATGTATGGAATAcatatgaatacatatgtattCATATGTATTCCATACATACTTcTGTGTATGTATGGATAT CAATTTTGACTGTTCCATAAGTATGTATGGAATA--------------------CATATGTATTCCATACATACTTATGTGTATGTATGGATAT Template switch alignment (log-probability: -23.2) CAATTTTGACTGTTCCATAAGTATGTATGGAATACATATG|AATACATATGTATT|CATATGTATTCCATACATACTTcTGTGTATGTATGGATAT CAATTTTGACTGTTCCATAAGTATGTATGGAATACATATG|AATACATATGTATT|CATATGTATTCCATACATACTTATGTGTATGTATGGATAT ========== Event 2510 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGCATCCAACAGATTTTTCCT--------TATGTCCTATTAACAAGAACTGCTTTAT Chimp: CAGCATCCAACAGATTTTTCTT--------TATGTCCTATTAACAAGAACTGCTTTAT Gorilla: CCGCATCCAACAGATTTTTCCATAAGGACATAAGTCCTATTAACAAGAACTGCTTTAT ↑ 3 1 4 2 Human: CAGCATCCAACAGATTTTTCCT--------TATGTCCTATTAACAAGAACTGCTTTAT Cluster: [ ] Orangutan: CCTCATCCAACAGATTTTTCCT--------TATGTCCTATTAACAAGAACTGCTTTAT Human > Gorilla --------------- chr4:74088083-74088091 Template switch process: F1: L CCAAGGGAACTCTTCCCGTACCGCATCCAACAGATTTTTCCATA 1 F3: 4 GTCCTATTAACAAGAACTGCTTTATTTGCCCAGAGAGGTG R RF: CCAAGGGAACTCTTCCCGTACAGCATCCAACAGATTTTTCCTTATGTCCTATTAACAAGAACTGCTTTATTTGCCCAGAGAGGTG RR: GGTTCCCTTGAGAAGGGCATGTCGTAGGTTGTCTAAAAAGGAATACAGGATAATTGTTCTTGACGAAATAAACGGGTCTCTCCAC F2: 3 AATACAGGA 2 Unidirectional alignment (log-probability: -39) GGGAACTCTTCCCGTACcGCATCCAACAGATTTTTCcataaggaCaTAaGTCCTATTAACAAGAACTGCTTTATTTGCCCAGAGAGGTG GGGAACTCTTCCCGTACAGCATCCAACAGATTTTTC--------CTTATGTCCTATTAACAAGAACTGCTTTATTTGCCCAGAGAGGTG Template switch alignment (log-probability: -28) GGGAACTCTTCCCGTACcGCATCCAACAGATTTTTCCaTA|AGGACATAA|GTCCTATTAACAAGAACTGCTTTATTTGCCCAGAGAGGTG GGGAACTCTTCCCGTACAGCATCCAACAGATTTTTCCTTA|AGGACATAA|GTCCTATTAACAAGAACTGCTTTATTTGCCCAGAGAGGTG ========== Event 2511 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAATGCCAAGAAGTTGAGTTTCAATGAATGCTACATATATAGCATTCA-----------------------------------GTACTTGAAACATTTATTAAT Chimp: GAATGCCAAGAAGTTGAGTTTCAATGAATGCTACATATATAGCATTCA-------------GTGAATGCTATATCTGTATCTGATACTTGAAATATTTATTAAT ↑ 4 3 2 Gorilla: GAATGCCAAGAAGTTGAGTTTCAATGAATGCT----------------ATATCTGTATCTG----------------------ATACTTGAAACATTTATTAAT ↓ 3 2 4 Human: GAATGCCAAGAAGTTGAGTTTCAATGAATGCTACATATATAGCATTCA-----------------------------------GTACTTGAAACATTTATTAAT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr4:117536522-117536533 Template switch process: F1: L TATTTATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTACAT 1 F3: 4 GTACTTGAAACATTTATTAATAAAAATAATCATCAGGGCTG R RF: TATTTATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTATATCTGTATCTGATACTTGAAACATTTATTAATAAAAATAATCATCAGGGCTG RR: ATAAATACTCTTACGGTTCTTCAACTCAAAGTTACTTACGATATAGACATAGACTATGAACTTTGTAAATAATTATTTTTATTAGTAGTCCCGAC F2: 3 ACTTACGATATA 2 Unidirectional alignment (log-probability: -43.9) ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTAcAT---------AtatagcattcagTACTTGAAACATTTATTAATAAAAATAATCATCAGGGCT ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTATATCTGTATCTGA------------TACTTGAAACATTTATTAATAAAAATAATCATCAGGGCT Template switch alignment (log-probability: -28.4) ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTAcAT|ATATAGCATTCA|gTACTTGAAACATTTATTAATAAAAATAATCATCAGGGCT ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTATAT|ATATAGCATTCA|ATACTTGAAACATTTATTAATAAAAATAATCATCAGGGCT Gorilla > Chimp --------------- chr4:120616653-120616660 Template switch process: F1: L TATTTATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTACAT 1 F3: 4 TTCAGTGAATGCTATATCTGTATCTGATACTTGAAATATTTATTAATAAAAATAATCATCAGGGCT R RF: TATTTATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTATATCTGTATCTGATACTTGAAACATTTATTAATAAAAATAATCATCAGGGCT RR: ATAAATACTCTTACGGTTCTTCAACTCAAAGTTACTTACGATATAGACATAGACTATGAACTTTGTAAATAATTATTTTTATTAGTAGTCCCGA F2: 3 ACGATATA 2 Unidirectional alignment (log-probability: -52.5) ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGctacatatatagcattcagtgaatgCTATATCTGTATCTGATACTTGAAAtATT ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATG-------------------------CTATATCTGTATCTGATACTTGAAACATT Template switch alignment (log-probability: -34) ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTAcAT|ATATAGCA|TTCAgTGAATGCTATATCTGTATCTGATACTTGAAAtATT ATGAGAATGCCAAGAAGTTGAGTTTCAATGAATGCTATAT|ATATAGCA|TTCAATGAATGCTATATCTGTATCTGATACTTGAAACATT ========== Event 2512 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTTTATGTATTCATGTAAGGCTAATGCCTTACAGTTAACAGATTTCTTT ↑ 3 1 24 Chimp: GTTTTATGTATTCATGTAAGGC--A-TTATTACAGTTAACAGATTTCTTT Gorilla: GTTTTATGTATTCATGTAAGGC--A-TTATTACAGTTAACAGATTTCTTT ↓ 3 1 24 Human: GTTTTATGTATTCATGTAAGGCTAATGCCTTACAGTTAACAGATTTCTTT Cluster: [ ] Orangutan: GTTTTATGTATTCATGTAAGGC--A-TTATTACAGTTAACAGATTTCTTT Chimp > Human ------------- chr4:117724933-117724939 Template switch process: F1: L AGCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC 1 F3: 4 TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA R RF: AGCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGCATTATTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA RR: TCGTAAAATATATCTAACACAAAATACATAAGTACATTCCGTAATAATGTCAATTGTCTAAAGAAATTCGTTCGATTGATTACAT F2: 3 CCGTAAT 2 Unidirectional alignment (log-probability: -28.4) GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC--TAatgccTTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGCATTA-----TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA Template switch alignment (log-probability: -16.2) GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC|TAATGCC|TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC|TAATGCC|TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA Gorilla > Human --------------- chr4:117724933-117724939 Template switch process: F1: L AGCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC 1 F3: 4 TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA R RF: AGCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGCATTATTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA RR: TCGTAAAATATATCTAACACAAAATACATAAGTACATTCCGTAATAATGTCAATTGTCTAAAGAAATTCGTTCGATTGATTACAT F2: 3 CCGTAAT 2 Unidirectional alignment (log-probability: -27.9) GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC--TAatgccTTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGCATTA-----TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA Template switch alignment (log-probability: -16.6) GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC|TAATGCC|TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA GCATTTTATATAGATTGTGTTTTATGTATTCATGTAAGGC|TAATGCC|TTACAGTTAACAGATTTCTTTAAGCAAGCTAACTAATGTA ========== Event 2513 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGAGAAGCATATATAAAATTGTTACCCAACAATATTCATTGTTGTTACCCAACAATGAAACGAGAGTGTTCAACTTGAA Chimp: AAGAGAAGCATATATAAAATTGTTACCC-----------------------AACAATGAAAC--GAGTGTTCAACTTGAA Gorilla: AAGAGAAGCATATATAAAATTGTTACCC-----------------------AACAATGAAACGAGAGTGTTCACCTTGAA ↓ 4 3 1 2 Human: AAGAGAAGCATATATAAAATTGTTACCCAACAATATTCATTGTTGTTACCCAACAATGAAACGAGAGTGTTCAACTTGAA Cluster: [ ] Orangutan: AAGAGAAGCATATATAAAATTGTTACCC-----------------------------AAAACGAGAGTGTTCAACTTGAA Gorilla > Human --------------- chr4:72128909-72128915 Template switch process: F1: L ACTACCTAACCCAAAGAGAAGCATATATAAAATTGTTACCCAACAATA 1 F3: 4 TTGTTACCCAACAATGAAACGAGAGTGTTCAACTTGAACAAGGGTTGGA R RF: ACTACCTAACCCAAAGAGAAGCATATATAAAATTGTTACCCAACAATGAAACGAGAGTGTTCACCTTGAACAAGGGTTGGA RR: TGATGGATTGGGTTTCTCTTCGTATATATTTTAACAATGGGTTGTTACTTTGCTCTCACAAGTGGAACTTGTTCCCAACCT F2: 3 GTTACTT 2 Unidirectional alignment (log-probability: -49.5) ACCCAAAGAGAAGCATATATAAAATTGTTACccaacaatattcattgttgttacCCAACAATGAAACGAGAGTGTTCAaCTTGAACA ACCCAAAGAGAAGCATATATAAAATTGTTAC-----------------------CCAACAATGAAACGAGAGTGTTCACCTTGAACA Template switch alignment (log-probability: -28) ACCCAAAGAGAAGCATATATAAAATTGTTACCCAACAATa|TTCATTG|TTGTTACCCAACAATGAAACGAGAGTGTTCAaCTTGAACA ACCCAAAGAGAAGCATATATAAAATTGTTACCCAACAATG|TTCATTG|TTGTTACCCAACAATGAAACGAGAGTGTTCACCTTGAACA ========== Event 2514 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGCTGCCTTCTAAGTAGGAGTCTCTAGAAAGCACCACACCTAGCAAAGTAGGCCCTGGGATCTGATTCCGGAAGCACACT----CTTAGAGAGGGCAAGAGTAACCAAAGTGAAGACTATGGAA---AAGCAAGAAGTACAGAtttcttt----ttttttttttttttcagacggagtttcgctcttgttgcccaggctggagtgcaatggcaccatctcagctcact Chimp: AGGCTGCCTTCTAAGTAGGAGTCTCTAGAAAGCACCACACCTAGCAAAGTAGGCCCTGGGATCTGATTCAGGAAGCACACT------CAGAGAGGGCAAGAGTAACCAAAGTGAAGACTATGGAA---AAGCAAGAAGTACAGatttattt-atttattttttttttttcagacagagtttcgctcttgttgtccaggctggagtgcaatggcaccatctcagctcact Gorilla: AGGCTGCCTTCTAAGTAGGAGTCTCTAGAAAGCACCACACCTAGCAAAGTAGGCCCTGGGATCTGATTCAGGAAGCACACT--CT--TAGAGAGGGCAAGAGTAACCAAAGTGACTCTTTCCAATCTGTAC--CAAAGTACAGAtttcttt----ttttctttttttttcagacggagtttcgctcttgttgcccaggctggagtgcaatggcaccatctcagctcact ↓ 3 2 1 4 Human: AGGCTGCCTTCTAAGTAGGAGTCTCTAGAAAGCACCACACCTAGCAAAGTAGGCCCTGGGATCTGATTCCGGAAGCACACT----CTTAGAGAGGGCAAGAGTAACCAAAGTGAAGACTATGGAA---AAGCAAGAAGTACAGAtttcttt----ttttttttttttttcagacggagtttcgctcttgttgcccaggctggagtgcaatggcaccatctcagctcact Cluster: [ ] Orangutan: AGGCTGCCTTTTAATTAGGAGTCTCTAGAAAGCACCACACCTAGGAAAGTAGGCCCTGGGATCTGATTCAGGAAGCACACTCT----TAGAGAGGGCAAGAGTAACCAAAGTGAAGACTATGGAA---AAGCAAGAAGCACAGAtttctttt---tttttcttttttttcagacggagtttcactcttgttgcccaggctggagtgcaatggcaccatctcagctcact Gorilla > Human --------------- chr4:71843597-71843601 Template switch process: F1: L CTAGCAAAGTAGGCCCTGGGATCTGATTCCGGAAGCACACTCTTAGAGAGGGCAAGAGTAACCAAAGTGA 1 F3: 4 ATGGAA R RF: AGTCTCTAGAAAGCACCACACCTAGCAAAGTAGGCCCTGGGATCTGATTCAGGAAGCACACTCTTAGAGAGGGCAAGAGTAACCAAAGTGACTCTTTCCAATCTGTACCAAAGTACAGATTTCTTTTTTTCTTTTTTTTTCAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAATGGCA RR: TCAGAGATCTTTCGTGGTGTGGATCGTTTCATCCGGGACCCTAGACTAAGTCCTTCGTGTGAGAATCTCTCCCGTTCTCATTGGTTTCACTGAGAAAGGTTAGACATGGTTTCATGTCTAAAGAAAAAAAGAAAAAAAAAGTCTGCCTCAAAGCGAGAACAACGGGTCCGACCTCACGTTACCGT F2: 3 TCAGA 2 Unidirectional alignment (log-probability: -39.5) GGAAGCACACTCTTAGAGAGGGCAAGAGTAACCAAAGTGA-------------agactatggaa GGAAGCACACTCTTAGAGAGGGCAAGAGTAACCAAAGTGACTCTTTCCAATCT----------- Template switch alignment (log-probability: -27.3) GGAAGCACACTCTTAGAGAGGGCAAGAGTAACCAAAGTGA|AGACT|ATGGaA GGAAGCACACTCTTAGAGAGGGCAAGAGTAACCAAAGTGA|AGACT|ATGGCA ========== Event 2515 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGTTGAGTTATGAAGGTCAGAT------------------TTTGAAATAAATGCAGATTTTGAAAGACTATGTGGGGAA-AAAATGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTACAACAGAAAAGAGTGCACTG Chimp: TAGTTGAGTTATGAAGGTCAGAT------------------TTTGAAATAAATGCAGATTTTGAAAGACTATGTGGGGaaaaaaaTGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTACAACAGAAAAGAGTGCACTG ↑ 4 1 3 2 Gorilla: TAGTTGAGTTATGAAGGTCAGAT------------------------------------TTTGAAAGACTATGTGGGGaaaaaaaTGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTACAACAGAAAAGAGTGCACTG ↓ 4 1 3 2 Human: TAGTTGAGTTATGAAGGTCAGAT------------------TTTGAAATAAATGCAGATTTTGAAAGACTATGTGGGGAA-AAAATGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTACAACAGAAAAGAGTGCACTG Cluster: [ ] Orangutan: TAGTTGAGTTATGAAGGTCAGATTTTGAAATAAATGCAGAT------------------TTTGAAAGACTATGTGGGGAAAAAAGTGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTACAACAGAAAAGAGTGCACTG Gorilla > Human --------------- chr4:118749160-118749166 Template switch process: F1: L ATACCAGCAATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAA 1 F3: 4 AGATTTTGAAAGACTATGTGGGG-AAAAAATGCTATGAGTACAA R RF: ATGCCAGCAATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTA RR: TACGGTCGTTAAGTACATATCAACTCAATACTTCCAGTCTAAAACTTTCTGATACACCCCTTTTTTTACGATACTCATGTTCTACGACACCTGTACCTTCGTAAAT F2: 3 CGTAAAT 2 Unidirectional alignment (log-probability: -52.1) AATTCATGTATAGTTGAGTTATGAAGGTcagattttgaaataaatgCAGATTTTGAAAGACTATGTGGGG-AAAAAATGCTATGAGTA AATTCATGTATAGTTGAGTTATGAAGGT------------------CAGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGTA Template switch alignment (log-probability: -32.2) AATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAA|TAAATGC|AGATTTTGAAAGACTATGTGGGG-AAAAAATGCTATGAGTA AATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAA|TAAATGC|AGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGTA Gorilla > Chimp --------------- chr4:121594344-121594350 Template switch process: F1: L ATGCCAGCAATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAA 1 F3: 4 AGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGTACAA R RF: ATGCCAGCAATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGTACAAGATGCTGTGGACATGGAAGCATTTA RR: TACGGTCGTTAAGTACATATCAACTCAATACTTCCAGTCTAAAACTTTCTGATACACCCCTTTTTTTACGATACTCATGTTCTACGACACCTGTACCTTCGTAAAT F2: 3 CGTAAAT 2 Unidirectional alignment (log-probability: -36.8) AATTCATGTATAGTTGAGTTATGAAGGTCAGattttgaaataaatgcagATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGT AATTCATGTATAGTTGAGTTATGAAGGTCAG------------------ATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGT Template switch alignment (log-probability: -16.9) AATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAA|TAAATGC|AGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGT AATTCATGTATAGTTGAGTTATGAAGGTCAGATTTTGAAA|TAAATGC|AGATTTTGAAAGACTATGTGGGGAAAAAAATGCTATGAGT ========== Event 2516 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGAAAACAACATTAGCAAAGTGAAAGCACTAAGA-----------AAAGTAGATTTATGCTATAAAA Chimp: GGGAAAACAACATTAGCAAAGTGAAAGCACTAAGa-----------a--------------------- Gorilla: GGGAAAACAACATTAGCAAAGTGAAAGCACTTCTTAGTGCTTTCACTGAGTAGATTTATGCTATAAAA ↑ 3 1 2 4 Human: GGGAAAACAACATTAGCAAAGTGAAAGCACTAAGA-----------AAAGTAGATTTATGCTATAAAA Cluster: [ ] Orangutan: GGGAAAACAACATTAGCAAAGTGAAGGCACTAAGA-----------AAAGTAGATTTATGCTATAAAA Human > Gorilla --------------- chr4:132709540-132709555 Template switch process: F1: L CATTAAAGTAGGGAAAACAACATTAGCAAAGTGAAAGCACT 1 F3: 4 GAGTAGATTTATGCTATAAAAAGCAACAAATCTAGCTAAAA R RF: CATTAAAGTAGGGAAAACAACATTAGCAAAGTGAAAGCACTAAGAAAAGTAGATTTATGCTATAAAAAGCAACAAATCTAGCTAAAA RR: GTAATTTCATCCCTTTTGTTGTAATCGTTTCACTTTCGTGATTCTTTTCATCTAAATACGATATTTTTCGTTGTTTAGATCGATTTT F2: 3 TCACTTTCGTGATTCT 2 Unidirectional alignment (log-probability: -45.4) ATTAAAGTAGGGAAAACAACATTAGCAAAGTGAAAGCACTtcttagtgctttcactg------AGTAGATTTATGCTATAAAAAGCAACAAATCTAGCTAAA ATTAAAGTAGGGAAAACAACATTAGCAAAGTGAAAGCACT-----------------AAGAAAAGTAGATTTATGCTATAAAAAGCAACAAATCTAGCTAAA Template switch alignment (log-probability: -23.3) ATTAAAGTAGGGAAAACAACATTAGCAAAGTGAAAGCACT|TCTTAGTGCTTTCACT|gAGTAGATTTATGCTATAAAAAGCAACAAATCTAGCTAAA ATTAAAGTAGGGAAAACAACATTAGCAAAGTGAAAGCACT|TCTTAGTGCTTTCACT|AAGTAGATTTATGCTATAAAAAGCAACAAATCTAGCTAAA ========== Event 2517 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGGATCCCTTATTATTTTGCCT-----CAACAGTGGATGCTGAGAAGGaaaaaaaaCATGCAGAAA ↓ 1 4 3 2 Chimp: AAGGATCCCTTATTATTTTGCTTCTCAGCATCAGTGGATGCTGAGAAGGaaaaaaaaCATGCAGAAA ↑ 1 4 3 2 Gorilla: AAGGATCCCTTATTATTTTGCCT-----CAACAGTGGATGCTGAGAAGGaaa-aaaaCATGCAGAAA Human: AAGGATCCCTTATTATTTTGCCT-----CAACAGTGGATGCTGAGAAGGaaaaaaaaCATGCAGAAA Cluster: [ ] Orangutan: ------------------------------------------------------------------- Human > Chimp ------------- chr4:124984584-124984593 Template switch process: F1: L GAGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGC 1 F3: 4 CAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA R RF: GAGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGCCTCAACAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA RR: CTCAGTGTAAATGGAACGAGTTCCTAGGGAATAATAAAACGGAGTTGTCACCTACGACTCTTCCTTTTTTTTGTACGTCTTTACGT F2: 3 TACGACTCTT 2 Unidirectional alignment (log-probability: -30.1) AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGCtTctcagCAtCAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGCCT-----CAACAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA Template switch alignment (log-probability: -16.5) AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGC|TTCTCAGCAT|CAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGC|TTCTCAGCAT|CAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA Gorilla > Chimp --------------- chr4:124984584-124984593 Template switch process: F1: L GAGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGC 1 F3: 4 CAGTGGATGCTGAGAAGGAAAAAAAACATGCAGAAATGCA R RF: GAGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGCCTCAACAGTGGATGCTGAGAAGGAAAAAAACATGCAGAAATGCA RR: CTCAGTGTAAATGGAACGAGTTCCTAGGGAATAATAAAACGGAGTTGTCACCTACGACTCTTCCTTTTTTTGTACGTCTTTACGT F2: 3 TACGACTCTT 2 Unidirectional alignment (log-probability: -40.3) AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGCtTctcagCAtCAGTGGATGCTGAGAAGGaAAAAAAACATGCAGAAATGCA AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGCCT-----CAACAGTGGATGCTGAGAAGG-AAAAAAACATGCAGAAATGCA Template switch alignment (log-probability: -28.2) AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGC|TTCTCAGCAT|CAGTGGATGCTGAGAAGGaAAAAAAACATGCAGAAATGCA AGTCACATTTACCTTGCTCAAGGATCCCTTATTATTTTGC|TTCTCAGCAT|CAGTGGATGCTGAGAAGG-AAAAAAACATGCAGAAATGCA ========== Event 2518 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCCACATGGTAAAAAGTATCTCACTGTCACA------------------TTAGTTGGgttctcattcaggtcaac ↓ 3 2 4 1 Chimp: GGCCACATGGTAAAAAGTATCTCACTGTAACATTAGTTACAGTGAGAACATTAGTTGGgttctcattcaggtcagc ↑ 3 2 4 1 Gorilla: GGCCACATGGTAAAAAGTATCTCACTGTCACA------------------TTAGTTGGgttctcattcaggtcaac Human: GGCCACATGGTAAAAAGTATCTCACTGTCACA------------------TTAGTTGGgttctcattcaggtcaac Cluster: [ ] Orangutan: GGCCACATGGTAAAAAGTATCTCACTGTCACA------------------TTAGTTGGgttctcattcaggtcaac Human > Chimp ------------- chr4:126030857-126030865 Template switch process: F1: L GTGCCATCCCTTAGGCCACATGGTAAAAAGTATCTCACTGTAACATTAGTT 1 F3: 4 ACATTAGTTGGGTTCTCATTCAGGTCAGCAAGAATTAGGAGAT R RF: GTGCCATCCCTTAGGCCACATGGTAAAAAGTATCTCACTGTCACATTAGTTGGGTTCTCATTCAGGTCAACAAGAATTAGGAGAT RR: CACGGTAGGGAATCCGGTGTACCATTTTTCATAGAGTGACAGTGTAATCAACCCAAGAGTAAGTCCAGTTGTTCTTAATCCTCTA F2: 3 AGAGTGACA 2 Unidirectional alignment (log-probability: -48.8) TAGGCCACATGGTAAAAAGTATCTCACTGTaACATTAgttacagtgagaacattaGTTGGGTTCTCATTCAGGTCAgCAAGAATTAGGA TAGGCCACATGGTAAAAAGTATCTCACTGTCACATTA------------------GTTGGGTTCTCATTCAGGTCAACAAGAATTAGGA Template switch alignment (log-probability: -28.6) TAGGCCACATGGTAAAAAGTATCTCACTGTaACATTAGTT|ACAGTGAGA|ACATTAGTTGGGTTCTCATTCAGGTCAgCAAGAATTAGGA TAGGCCACATGGTAAAAAGTATCTCACTGTCACATTAGTT|ACAGTGAGA|ACATTAGTTGGGTTCTCATTCAGGTCAACAAGAATTAGGA Gorilla > Chimp --------------- chr4:126030857-126030865 Template switch process: F1: L GTGCCATCCCTTAGGCCACATGGTAAAAAGTATCTCACTGTAACATTAGTT 1 F3: 4 ACATTAGTTGGGTTCTCATTCAGGTCAGCAAGAATTAGGAGAT R RF: GTGCCATCCCTTAGGCCACATGGTAAAAAGTATCTCACTGTCACATTAGTTGGGTTCTCATTCAGGTCAACAAGAATTAGGAGAT RR: CACGGTAGGGAATCCGGTGTACCATTTTTCATAGAGTGACAGTGTAATCAACCCAAGAGTAAGTCCAGTTGTTCTTAATCCTCTA F2: 3 AGAGTGACA 2 Unidirectional alignment (log-probability: -47.9) TAGGCCACATGGTAAAAAGTATCTCACTGTaacattagttacagtgagaACATTAGTTGGGTTCTCATTCAGGTCAgCAAGAATTAGGA TAGGCCACATGGTAAAAAGTATCTCACTGT------------------CACATTAGTTGGGTTCTCATTCAGGTCAACAAGAATTAGGA Template switch alignment (log-probability: -28.2) TAGGCCACATGGTAAAAAGTATCTCACTGTaACATTAGTT|ACAGTGAGA|ACATTAGTTGGGTTCTCATTCAGGTCAgCAAGAATTAGGA TAGGCCACATGGTAAAAAGTATCTCACTGTCACATTAGTT|ACAGTGAGA|ACATTAGTTGGGTTCTCATTCAGGTCAACAAGAATTAGGA ========== Event 2519 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGTTTTAACTTCTGGCTATA--TATATGCA----------GAATACATGAAAAATATTAAGATGC Chimp: GAGTTTTAACTTCTGGCTATATATATATGCA----------GAATACATGAAAAATATTAAGATGC ↑ 1 3 2 4 Gorilla: GAGTTTTAACTTCTGGCTATA--TATATGCTGTTCTGCATGTATTCCATGAAAAATATTAAGATGC Human: GAGTTTTAACTTCTGGCTATA--TATATGCA----------GAATACATGAAAAATATTAAGATGC Cluster: [ ] Orangutan: GAGTTTGAACTTCTGGCTATA--TATATGCA----------GAATACATGAAAAATATTAAGATGG Gorilla > Chimp --------------- chr4:126305727-126305734 Template switch process: F1: L TGAGAATGAAGTATGCTGTGGAGTTTTAACTTCTGGCTATATATAT 1 F3: 4 TACATGAAAAATATTAAGATGCTGGTCTGCTGCTTCGAGGAC R RF: TGAGAATGAAGTATGCTGTGGAGTTTTAACTTCTGGCTATATATATGCTGTTCTGCATGTATTCCATGAAAAATATTAAGATGCTGGTCTGCTGCTTCAAGGAC RR: ACTCTTACTTCATACGACACCTCAAAATTGAAGACCGATATATATACGACAAGACGTACATAAGGTACTTTTTATAATTCTACGACCAGACGACGAAGTTCCTG F2: 3 AAGACGTA 2 Unidirectional alignment (log-probability: -41.1) TGAAGTATGCTGTGGAGTTTTAACTTCTGGCTATATATAT--------------ATgcagaaTaCATGAAAAATATTAAGATGCTGGTCTGCTGCTTCgAGG TGAAGTATGCTGTGGAGTTTTAACTTCTGGCTATATATATGCTGTTCTGCATGTAT------TCCATGAAAAATATTAAGATGCTGGTCTGCTGCTTCAAGG Template switch alignment (log-probability: -28) TGAAGTATGCTGTGGAGTTTTAACTTCTGGCTATATATAT|ATGCAGAA|TaCATGAAAAATATTAAGATGCTGGTCTGCTGCTTCgAGG TGAAGTATGCTGTGGAGTTTTAACTTCTGGCTATATATAT|ATGCAGAA|TCCATGAAAAATATTAAGATGCTGGTCTGCTGCTTCAAGG ========== Event 2520 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACCAATAAACATATTTTTCTAGGTAATCAATTACTAT-----------TAACAGGGAACACATAACTGAG Chimp: CTACCAATAAACATATTTTTCTAGATAATCAATTACTAT-----------TAACAGGGAACACATAACTGAG ↓ 3 2 14 Gorilla: CTACCAATAAACATATTTTTCTAGATAATCAATTACTATTGATTATCTAGAAACAGGGAACACATAACTGAG Human: CTACCAATAAACATATTTTTCTAGGTAATCAATTACTAT-----------TAACAGGGAACACATAACTGAG Cluster: [ ] Orangutan: CTACCAATAAACGTATTTTTCTAGATAATCAATTACTAT-----------TAACAGGGAACACATAACCGAG Chimp > Gorilla --------------- chr4:138809290-138809300 Template switch process: F1: L TACTACCAATAAACATATTTTTCTAGATAATCAATTACTATT 1 F3: 4 AACAGGGAACACATAACTGAGAAGTTTAACATTTTAAGTG R RF: TACTACCAATAAACATATTTTTCTAGATAATCAATTACTATTAACAGGGAACACATAACTGAGAAGTTTAACATTTTAAGTG RR: ATGATGGTTATTTGTATAAAAAGATCTATTAGTTAATGATAATTGTCCCTTGTGTATTGACTCTTCAAATTGTAAAATTCAC F2: 3 AGATCTATTAG 2 Unidirectional alignment (log-probability: -26.7) CTACCAATAAACATATTTTTCTAGATAATCAATTACTATTgattatctagaAACAGGGAACACATAACTGAGAAGTTTAACATTTTAAGTG CTACCAATAAACATATTTTTCTAGATAATCAATTACTATT-----------AACAGGGAACACATAACTGAGAAGTTTAACATTTTAAGTG Template switch alignment (log-probability: -17.2) CTACCAATAAACATATTTTTCTAGATAATCAATTACTATT|GATTATCTAGA|AACAGGGAACACATAACTGAGAAGTTTAACATTTTAAGTG CTACCAATAAACATATTTTTCTAGATAATCAATTACTATT|GATTATCTAGA|AACAGGGAACACATAACTGAGAAGTTTAACATTTTAAGTG ========== Event 2521 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: CAAACAATTTCAGTTCTCCCGATGGGGCAAAGCACCCAAATGACACT-TAGAATAAGAAATCATTGGGAGATATACCAA------ATTGTTGGGAGATGTCAGTTGGGTGCTTTGCCCCATTGGGAGAACTGAAATTGTTTG Chimp: CAAACAATTTCAGTTCTCCCGATGGGGCAAAGCACCCAACTGACACT-TAGAATAAGAAATTATTGGGAGATATACCAA------ATTATTGGGAGATGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATTGTTTG ↓ 13 24 ↑ 1 3 4 2 Gorilla: CAAACAATTTCAGTTCTCCCAATGGGGCAAAGCACCCAACTGACATCTCCCAATA------ATTTGGTATCTCTCCCAATAATTTCTTAT-TCTAAGTGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATTGTTTG Human: CAAACAATTTCAGTTCTCCCGATGGGGCAAAGCACCCAAATGACACT-TAGAATAAGAAATCATTGGGAGATATACCAA------ATTGTTGGGAGATGTCAGTTGGGTGCTTTGCCCCATTGGGAGAACTGAAATTGTTTG Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------TCTAAGTGTCAGTTGGGTGCTTTGCCCCATTGGTAGAACTGAAATTGTTTG Gorilla > Chimp --------------- chr4:128535354-128535423 Template switch process: F1: L CAATTTCAGTTCTCCC 1 F3: 4 TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT R RF: CAATTTCAGTTCTCCCAATGGGGCAAAGCACCCAACTGACATCTCCCAATAATTTGGTATCTCTCCCAATAATTTCTTATTCTAAGTGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT RR: GTTAAAGTCAAGAGGGTTACCCCGTTTCGTGGGTTGACTGTAGAGGGTTATTAAACCATAGAGAGGGTTATTAAAGAATAAGATTCACAGTCAACCCACGAAACGGGGTAGCCCTCTTGACTTTAA F2: 3 AGAGGGTTATTAAACCATATAGAGGGTTATTAAAGAATAAGATTCACAGTCAACCCACGAAACGGGGTAG 2 Unidirectional alignment (log-probability: -91.3) CAATTTCAGTTCTCCCgATGGGGCAAAGCACCCAACTGACA----------------------------------------CTtAGaataagaaattattgggagatataccaaattattgggagaTGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT CAATTTCAGTTCTCCCAATGGGGCAAAGCACCCAACTGACATCTCCCAATAATTTGGTATCTCTCCCAATAATTTCTTATTCTAAG----------------------------------------TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT Template switch alignment (log-probability: -29.5) CAATTTCAGTTCTCCC|GATGGGGCAAAGCACCCAACTGACACTTAGAATAAGAAATTATTGGGAGAtATACCAAATTATTGGGAGA|TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT CAATTTCAGTTCTCCC|GATGGGGCAAAGCACCCAACTGACACTTAGAATAAGAAATTATTGGGAGAGATACCAAATTATTGGGAGA|TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT Chimp > Gorilla --------------- chr4:137623428-137623472 Template switch process: F1: L CAATTTCAGTTCTCCCAATGGGGCAAAGCACCCAACTGACA 1 F3: 4 TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT R RF: CAATTTCAGTTCTCCCGATGGGGCAAAGCACCCAACTGACACTTAGAATAAGAAATTATTGGGAGATATACCAAATTATTGGGAGATGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT RR: GTTAAAGTCAAGAGGGCTACCCCGTTTCGTGGGTTGACTGTGAATCTTATTCTTTAATAACCCTCTATATGGTTTAATAACCCTCTACAGTCAACCCACGAAACGGGGTAGCCCTCTTGACTTTAA F2: 3 GAATCTTATTCTTTAATAACCCTCTCTATGGTTTAATAACCCTCT 2 Unidirectional alignment (log-probability: -91.3) AATTTCAGTTCTCCCaATGGGGCAAAGCACCCAACTGACAtctcccaataatttggtatctctcccaataatttcttattCTaAG----------------------------------------TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT AATTTCAGTTCTCCCGATGGGGCAAAGCACCCAACTGACA----------------------------------------CTTAGAATAAGAAATTATTGGGAGATATACCAAATTATTGGGAGATGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT Template switch alignment (log-probability: -32.5) AATTTCAGTTCTCCCaATGGGGCAAAGCACCCAACTGACA|TCTCCCAATAATTTGGTATcTCTCCCAATAATTTCTTATTCTAAG|TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT AATTTCAGTTCTCCCGATGGGGCAAAGCACCCAACTGACA|TCTCCCAATAATTTGGTATATCTCCCAATAATTTCTTATTCTAAG|TGTCAGTTGGGTGCTTTGCCCCATCGGGAGAACTGAAATT ========== Event 2522 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATTTTTGTAAGTAACACTTTGTTCTTGCACTATTGAATATAGATGCATCAATCTATAATTTGATGCATC ↓ 13 24 ↑ 13 24 Chimp: ATTTTTGTAAGTAACACTTTGATGCATCTATATTCAATAGTGCAAGAACAATCTATAATTTGATGCATC Gorilla: ATTTTTGTAAGTAACACTTTGATGCATCTATATTCAATAGTGCAAGAACAATCTATAATTTGATGCATC ↓ 13 24 ↑ 13 24 Human: ATTTTTGTAAGTAACACTTTGTTCTTGCACTATTGAATATAGATGCATCAATCTATAATTTGATGCATC Cluster: [ ] Orangutan: ATTTTTGTAAGTAACACTTTGATGCATCTAAATTCAATAGTGCAAAAACAATCTATAATTTGATGCATC Chimp > Human ------------- chr4:127543747-127543773 Template switch process: F1: L TCACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTG 1 F3: 4 CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG R RF: TCACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTGATGCATCTATATTCAATAGTGCAAGAACAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG RR: AGTGATAAGAATTCGGAAGTTAAAAACATTCATTGTGAAACTACGTAGATATAAGTTATCACGTTCTTGTTAGATATTAAACTACGTAGATTTAAGTAAATTCATGTC F2: 3 TACGTAGATATAAGTTATCACGTTCTT 2 Unidirectional alignment (log-probability: -58.4) CACTATTCTTAAGgCTTCAATTTTTGTAAGTAACACTTTGttcttgcactattgaatatagATGCAT---------------------CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTG---------------------ATGCATCTATATTCAATAGTGCAAGAACAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Template switch alignment (log-probability: -24.6) CACTATTCTTAAGgCTTCAATTTTTGTAAGTAACACTTTG|TTCTTGCACTATTGAATATAGATGCAT|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTG|TTCTTGCACTATTGAATATAGATGCAT|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Human > Chimp ------------- chr4:130522574-130522600 Template switch process: F1: L TCACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTG 1 F3: 4 CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG R RF: TCACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTGTTCTTGCACTATTGAATATAGATGCATCAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG RR: AGTGATAAGAATTCCGAAGTTAAAAACATTCATTGTGAAACAAGAACGTGATAACTTATATCTACGTAGTTAGATATTAAACTACGTAGATTTAAGTAAATTCATGTC F2: 3 AAGAACGTGATAACTTATATCTACGTA 2 Unidirectional alignment (log-probability: -58.4) CACTATTCTTAAGcCTTCAATTTTTGTAAGTAACACTTT---------------------GATGCATctatattcaatagtgcaagaaCAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTGTTCTTGCACTATTGAATATAGATGCAT---------------------CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Template switch alignment (log-probability: -24.6) CACTATTCTTAAGcCTTCAATTTTTGTAAGTAACACTTTG|ATGCATCTATATTCAATAGTGCAAGAA|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTG|ATGCATCTATATTCAATAGTGCAAGAA|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Gorilla > Human --------------- chr4:127543747-127543773 Template switch process: F1: L TCACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTG 1 F3: 4 CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG R RF: TCACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTGATGCATCTATATTCAATAGTGCAAGAACAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG RR: AGTGATAAGAATTCGGAAGTTAAAAACATTCATTGTGAAACTACGTAGATATAAGTTATCACGTTCTTGTTAGATATTAAACTACGTAGATTTAAGTAAATTCATGTC F2: 3 TACGTAGATATAAGTTATCACGTTCTT 2 Unidirectional alignment (log-probability: -57.5) CACTATTCTTAAGgCTTCAATTTTTGTAAGTAACACTTTgttcttgcactattgaatataGATGCAT---------------------CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTT---------------------GATGCATCTATATTCAATAGTGCAAGAACAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Template switch alignment (log-probability: -24.7) CACTATTCTTAAGgCTTCAATTTTTGTAAGTAACACTTTG|TTCTTGCACTATTGAATATAGATGCAT|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTG|TTCTTGCACTATTGAATATAGATGCAT|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Human > Gorilla --------------- chr4:139579028-139579054 Template switch process: F1: L TCACTATTCTTAAGCCTTCAATTTTTGTAAGTAACACTTTG 1 F3: 4 CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG R RF: TCACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTGTTCTTGCACTATTGAATATAGATGCATCAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG RR: AGTGATAAGAATTCCGAAGTTAAAAACATTCATTGTGAAACAAGAACGTGATAACTTATATCTACGTAGTTAGATATTAAACTACGTAGATTTAAGTAAATTCATGTC F2: 3 AAGAACGTGATAACTTATATCTACGTA 2 Unidirectional alignment (log-probability: -57.5) CACTATTCTTAAGcCTTCAATTTTTGTAAGTAACACTTT---------------------GATGCATctatattcaatagtgcaagaaCAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTGTTCTTGCACTATTGAATATAGATGCAT---------------------CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG Template switch alignment (log-probability: -24.7) CACTATTCTTAAGcCTTCAATTTTTGTAAGTAACACTTTG|ATGCATCTATATTCAATAGTGCAAGAA|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG CACTATTCTTAAGGCTTCAATTTTTGTAAGTAACACTTTG|ATGCATCTATATTCAATAGTGCAAGAA|CAATCTATAATTTGATGCATCTAAATTCATTTAAGTACAG ========== Event 2523 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ttatattttaGTATTTCCGCCTGAAGCTGAGTCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTAT ↑ 1 4 3 2 Chimp: ttatattttagtatttCCGCCAG-----TCATCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTAT Gorilla: ttatattttagtatttCCGCCAG-----TCATCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTAT ↓ 1 4 3 2 Human: ttatattttaGTATTTCCGCCTGAAGCTGAGTCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTAT Cluster: [ ] Orangutan: TTATATTTTAGTATTTCCGCCAG-----TCATCTTCTAACTCAGCTTCAACACACTGTTACTAAGTTAT Chimp > Human ------------- chr4:123985340-123985349 Template switch process: F1: L AAGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC 1 F3: 4 TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA R RF: AAGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCCAGTCATCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA RR: TTCGGGACGAAAATAAATAAAATATAAAATCATAAAGGCGGTCAGTAGAAGATTGAGTCGAAGTTGTGTAACAATGATTCAATAGT F2: 3 GAGTCGAAGT 2 Unidirectional alignment (log-probability: -32.8) AGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCCtgaagctgAGTC---TTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA AGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC--------AGTCATCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA Template switch alignment (log-probability: -16.5) AGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC|TGAAGCTGAG|TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA AGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC|TGAAGCTGAG|TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA Gorilla > Human --------------- chr4:123985340-123985349 Template switch process: F1: L AAGCCCTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC 1 F3: 4 TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA R RF: AAGCCTTGCTTTTATTTATTTTATATTTTAGTATTTCCGCCAGTCATCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA RR: TTCGGAACGAAAATAAATAAAATATAAAATCATAAAGGCGGTCAGTAGAAGATTGAGTCGAAGTTGTGTAACAATGATTCAATAGT F2: 3 GAGTCGAAGT 2 Unidirectional alignment (log-probability: -37.8) AGCCcTGCTTTTATTTATTTTATATTTTAGTATTTCCGCCtgaagctgAG---TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA AGCCTTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC--------AGTCATCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA Template switch alignment (log-probability: -22.5) AGCCcTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC|TGAAGCTGAG|TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA AGCCTTGCTTTTATTTATTTTATATTTTAGTATTTCCGCC|TGAAGCTGAG|TCTTCTAACTCAGCTTCAACACATTGTTACTAAGTTATCA ========== Event 2524 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACTTGTTCTGATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTATAAACGTTATAGCTAAGGGAAAATTGAGTGTGCAAG Chimp: ACTTGTTCTGATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAACGTTATAGCTAAGGGAAAATTGAGTGTGCAAG ↑ 3 2 41 Gorilla: ACTTGTTCTGATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGT------------AAAGGGAAAATTGAGTGTGCAAG ↓ 3 2 41 Human: ACTTGTTCTGATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTATAAACGTTATAGCTAAGGGAAAATTGAGTGTGCAAG Cluster: [ ] Orangutan: ACTTGTTATGATTTTTAGTAGCTATAACGTTTACACGAAAACTTTATGTGT------------AAAGGGAAAATTGAGTGTGCAAG Gorilla > Human --------------- chr4:129094778-129094787 Template switch process: F1: L TGATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTATAAA 1 F3: 4 AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA R RF: TGATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA RR: ACTAAAAATCATCGATATTGCAAATGTGTTTTTGAAAAACACATTTCCCTTTTAACTCACACGTTCCAGGTTGAGCAAAAACTT F2: 3 TCGATATTGC 2 Unidirectional alignment (log-probability: -33.7) TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTaTAaacgttatagctAAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTA------------AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA Template switch alignment (log-probability: -22.6) TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTaTAAA|CGTTATAGCT|AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAA|CGTTATAGCT|AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA Gorilla > Chimp --------------- chr4:132143896-132143905 Template switch process: F1: L ATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAA 1 F3: 4 AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA R RF: ATTTTTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA RR: TAAAAATCATCGATATTGCAAATGTGTTTTTGAAAAACACATTTCCCTTTTAACTCACACGTTCCAGGTTGAGCAAAAACTT F2: 3 TCGATATTGC 2 Unidirectional alignment (log-probability: -28.2) TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAaacgttatagctAAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTA------------AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA Template switch alignment (log-probability: -17.1) TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAA|CGTTATAGCT|AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA TTAGTAGCTATAACGTTTACACAAAAACTTTTTGTGTAAA|CGTTATAGCT|AAGGGAAAATTGAGTGTGCAAGGTCCAACTCGTTTTTGAA ========== Event 2525 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCCAGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAATG--CATTTAGATTCAACCTAGTTTTT Chimp: CCCAGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAATG--CATTTAGATTCAACCTAGTTTTT ↑ 3 2 1 4 Gorilla: CCCAGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAACCCTAGTTTAGATTCAACCTAGTTTTT ↓ 3 2 1 4 Human: CCCAGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAATG--CATTTAGATTCAACCTAGTTTTT Cluster: [ ] Orangutan: CCCAGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAATG--CATTTAGATTCAACCTAGTTTTT Gorilla > Human --------------- chr4:129604936-129604939 Template switch process: F1: L AGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA 1 F3: 4 TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT R RF: AGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAACCCTAGTTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT RR: TCATGAGAACAGACTCACGTTCAAAGGGTTCCCGTACTTTTGGGATCAAATCTAAGTTGGATCAAAAATGTAAGGTCTTACTAAGGA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -26.7) GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA------tgcaTTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAACCCTAG----TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT Template switch alignment (log-probability: -16.2) GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA|TGCA|TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA|TGCA|TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT Gorilla > Chimp --------------- chr4:132679612-132679615 Template switch process: F1: L AGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA 1 F3: 4 TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT R RF: AGTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAACCCTAGTTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT RR: TCATGAGAACAGACTCACGTTCAAAGGGTTCCCGTACTTTTGGGATCAAATCTAAGTTGGATCAAAAATGTAAGGTCTTACTAAGGA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -26.7) GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA------tgcaTTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAACCCTAG----TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT Template switch alignment (log-probability: -16.2) GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA|TGCA|TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT GTACTCTTGTCTGAGTGCAAGTTTCCCAAGGGCATGAAAA|TGCA|TTTAGATTCAACCTAGTTTTTACATTCCAGAATGATTCCT ========== Event 2526 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATCCAGATTTTGTTCCCCATTTCAAGTGTGAGATGAATCCCATACTTGAAACCAACATTCGAGGTATTC ↑ 1 4 3 2 Chimp: ATCCAGATTTTGTTCCCCATTG--TTTGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTATTC Gorilla: ATCCAGATTTTGTTCCCCATTG--TTTGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTATTC ↓ 1 4 3 2 Human: ATCCAGATTTTGTTCCCCATTTCAAGTGTGAGATGAATCCCATACTTGAAACCAACATTCGAGGTATTC Cluster: [ ] Orangutan: ATCCCGACTTTGTTCCCCATTG--TTTGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTATTC Chimp > Human ------------- chr4:13098575-13098579 Template switch process: F1: L CAATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT 1 F3: 4 TGTGAGATGAATCCCATACTTGAAACCAACATTCGAGGTA R RF: CAATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATTGTTTGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTA RR: GTTAAAGAACGACAAAATTTTAGGTCTAAAACAAGGGGTAACAAACACTCTACTTAGGGTGTGAACTTTGGTTGTAAGCTCCAT F2: 3 GAACT 2 Unidirectional alignment (log-probability: -33) AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATTtcaaG--TGTGAGATGAATCCCAtACTTGAAACCAACATTCGAGGTA AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT----GTTTGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTA Template switch alignment (log-probability: -21.9) AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT|TCAAG|TGTGAGATGAATCCCAtACTTGAAACCAACATTCGAGGTA AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT|TCAAG|TGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTA Gorilla > Human --------------- chr4:13098575-13098579 Template switch process: F1: L CAATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT 1 F3: 4 TGTGAGATGAATCCCATACTTGAAACCAACATTCGAGGTA R RF: CAATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATTGTTTGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTA RR: GTTAAAGAACGACAAAATTTTAGGTCTAAAACAAGGGGTAACAAACACTCTACTTAGGGTGTGAACTTTGGTTGTAAGCTCCAT F2: 3 GAACT 2 Unidirectional alignment (log-probability: -32) AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCAT--TTcaagTGTGAGATGAATCCCAtACTTGAAACCAACATTCGAGGTA AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATTGTT----TGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTA Template switch alignment (log-probability: -21.9) AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT|TCAAG|TGTGAGATGAATCCCAtACTTGAAACCAACATTCGAGGTA AATTTCTTGCTGTTTTAAAATCCAGATTTTGTTCCCCATT|TCAAG|TGTGAGATGAATCCCACACTTGAAACCAACATTCGAGGTA ========== Event 2527 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AAAGAGACATTACATAAATCAAAGGTTTATAACCTTAGAATTTAGGAATTCAAACaatt Chimp: AAAGAGACATTACATAAATCAAAGGTTTA------TGTAATTTAGGAATTCAAACAATT ↓ 3 2 1 4 Gorilla: AAAGAGACATTACATAAATCAAAGGTTTATAACCTTAGAATTTAGGAATTCAAACAATT Human: AAAGAGACATTACATAAATCAAAGGTTTATAACCTTAGAATTTAGGAATTCAAACaatt Cluster: [ ] Orangutan: AAAGAGCGATTACATAAATCAAAGGTTTATAACCTTAGAATTTAGAAATTCAAACAATT Chimp > Gorilla --------------- chr4:60421976-60421983 Template switch process: F1: L GAAATACATTGAAAAGAGACATTACATAAATCAAAGGTTTAT 1 F3: 4 AATTTAGGAATTCAAACAATTAAAAAAA R RF: GAAATACGTTGAAAAGAGACATTACATAAATCAAAGGTTTATGTAATTTAGGAATTCAAACAATTAAAAAAC RR: CTTTATGCAACTTTTCTCTGTAATGTATTTAGTTTCCAAATACATTAAATCCTTAAGTTTGTTAATTTTTTG F2: 3 GATTCCAA 2 Unidirectional alignment (log-probability: -48.8) AATACaTTGAAAAGAGACATTACATAAATCAAAGGTTTAtaacctTagAATTTAGGAATTCAAACAATTAAAAAAa----------- AATACGTTGAAAAGAGACATTACATAAATCAAAGGTTTA------TGTAATTTAGGAATTCAAACAATTAAAAAACAATTGAAAAAT Template switch alignment (log-probability: -33) AATACaTTGAAAAGAGACATTACATAAATCAAAGGTTTAT|AACCTTaG|AATTTAGGAATTCAAACAATTAAAAAAa AATACGTTGAAAAGAGACATTACATAAATCAAAGGTTTAT|AACCTTTG|AATTTAGGAATTCAAACAATTAAAAAAC ========== Event 2528 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGAATATGGAGCTAGAAGAG---------ACGGTATG-------CTAATTATATGTATACCTCTCATTCAGTATACATGCTTATGTATAGTATTTAAGGAAATGGATTGCATACCCACAGTAATTCTAATTATT Chimp: TTGAATATGGAGCTAGAAGAG---------AAGGTATG-------CTAATTATATGTATACCTCTCATTCAGTATACATGCTTATGTATAGTATTTAAGGAAATGGATTGCATACCCACAGTAATTCTAATTATT ↑ 1 4 3 2 Gorilla: TTGAATATGGAGCTAGAAGAGAAGCTCTAGAAGGTATACATATACATAATTATATGTATACCTCTCATTCAGTATACATGCTTATGTATAGTATTTAAGGAAATGGATTGCATACCCACAGTAATTCTAATTATT ↓ 1 4 3 2 Human: TTGAATATGGAGCTAGAAGAG---------ACGGTATG-------CTAATTATATGTATACCTCTCATTCAGTATACATGCTTATGTATAGTATTTAAGGAAATGGATTGCATACCCACAGTAATTCTAATTATT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr4:58189811-58189816 Template switch process: F1: L TTTAGATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGACG 1 F3: 4 TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG R RF: TTTAGATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAGCTCTAGAAGGTATACATATACATAATTATATGTATACCTCTCATTCAGTATACATGCTTATGTATAGTATTTAAGGAAATGGATTGCATAC RR: AAATCTAATTGGACTCTATAAACTTATACCTCGATCTTCTCTTCGAGATCTTCCATATGTATATGTATTAATATACATATGGAGAGTAAGTCATATGTACGAATACATATCATAAATTCCTTTACCTAACGTATG F2: 3 CGTATG 2 Unidirectional alignment (log-probability: -32.6) GATTAACCTGAGATATTTGAATATGGAGCTAGAAG---------AGAcGGTATgC-------TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAGCTCTAGAAGGTATACATATACATAATTATATGTATACCTCTCATTCAGTATACATGCTTATG Template switch alignment (log-probability: -22.1) GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAcG|GTATGC|TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAG|GTATGC|TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG Gorilla > Chimp --------------- chr4:59287583-59287588 Template switch process: F1: L TTTAGATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAG 1 F3: 4 TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG R RF: TTTAGATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAGCTCTAGAAGGTATACATATACATAATTATATGTATACCTCTCATTCAGTATACATGCTTATGTATAGTATTTAAGGAAATGGATTGCATAC RR: AAATCTAATTGGACTCTATAAACTTATACCTCGATCTTCTCTTCGAGATCTTCCATATGTATATGTATTAATATACATATGGAGAGTAAGTCATATGTACGAATACATATCATAAATTCCTTTACCTAACGTATG F2: 3 CGTATG 2 Unidirectional alignment (log-probability: -27.1) GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAA---------GGTATgC-------TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAGCTCTAGAAGGTATACATATACATAATTATATGTATACCTCTCATTCAGTATACATGCTTATG Template switch alignment (log-probability: -16.6) GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAG|GTATGC|TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG GATTAACCTGAGATATTTGAATATGGAGCTAGAAGAGAAG|GTATGC|TAATTATATGTATACCTCTCATTCAGTATACATGCTTATG ========== Event 2529 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: actcaggtagctttgatttttgg---tctagagtaggaaatttttcttatgcattcct Chimp: ACTCAGGTAGCTTTGATTTTTGGTCCTCTAGACCA-AAAATTTTTCTTATGCATTCCT ↑ 3 1 2 4 Gorilla: ATTCAGGTAGCTTTGATTTTTGG---TCTAGAGTAGGAAATTTTTCTTATGCATTCCT Human: actcaggtagctttgatttttgg---tctagagtaggaaatttttcttatgcattcct Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr4:135268760-135268770 Template switch process: F1: L TTTACCGATTAGGAAGAAACTCAGGTAGCTTTGATTTTTGGTC 1 F3: 4 AAATTTTTCTTATGCATTCCTAGGCTGCAGGGCCAAATTG R RF: TTTACCGATTAAGAAGAAATTCAGGTAGCTTTGATTTTTGGTCTAGAGTAGGAAATTTTTCTTATGCATTCCTAGGCTGCAGGGCCAAATTG RR: AAATGGCTAATTCTTCTTTAAGTCCATCGAAACTAAAAACCAGATCTCATCCTTTAAAAAGAATACGTAAGGATCCGACGTCCCGGTTTAAC F2: 3 AACCAGATCTC 2 Unidirectional alignment (log-probability: -48) ACCGATTAgGAAGAAAcTCAGGTAGCTTTGATTTTTGGTCctctagaccaa---------AAATTTTTCTTATGCATTCCTAGGCTGCAGGGCCAAATTG ACCGATTAAGAAGAAATTCAGGTAGCTTTGATTTTTGGTC-----------TAGAGTAGGAAATTTTTCTTATGCATTCCTAGGCTGCAGGGCCAAATTG Template switch alignment (log-probability: -28.2) ACCGATTAgGAAGAAAcTCAGGTAGCTTTGATTTTTGGTC|CTCTAGACCAA|AAATTTTTCTTATGCATTCCTAGGCTGCAGGGCCAAATTG ACCGATTAAGAAGAAATTCAGGTAGCTTTGATTTTTGGTC|CTCTAGACCAA|AAATTTTTCTTATGCATTCCTAGGCTGCAGGGCCAAATTG ========== Event 2530 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTTATCACTTAATATTTTCTCATAAGCATTTTTTTAAGTAACTTAAAAATTATTTTACAGACTTA-AAATTGTGCAATATGCTTATTAATCATTATTTAAAGCAAT Chimp: TTTTATCACTTAATATTTTTTCATAAGCATTTTTCTAAGTAACTTAAAAATTATTTTACAGACTTAAAAATTGTGCAATATGCTTATTAATCATTATTTAAAGCAAT Gorilla: TTTTATCACTTAATATTTTCT-CTAAGCATT-TTTTAAGTAATTTAAAAATTATTTTACAGACTTAAAAATTGTGCAATATGCTTATTAATCATTATTTAAGGCAAT ↓ 1 4 3 2 ↑ 1 4 3 2 Human: TTTTATCACTTAATATTTTCTCATAAGCATTTTTTTAAGTAACTTAAAAATTATTTTACAGACTTA-AAATTGTGCAATATGCTTATTAATCATTATTTAAAGCAAT Cluster: [ ] Orangutan: TTTTATCACTTAATATTTTCTCATAAGCATTTTTTTAAGTAATTTAAAAATTATTTTACAGACTTAAAAATTGTGCAATATGCTTATTAATCATTATTTAAAGCAAT Gorilla > Human --------------- chr4:134122338-134122345 Template switch process: F1: L TCTGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC 1 F3: 4 TTTTTTAAGTAACTTAAAAATTATTTTACAGACTTAAAATT R RF: TCTGCCATCATGTACCATGATTTTATCACTTAATATTTTCTCTAAGCATTTTTTAAGTAATTTAAAAATTATTTTACAGACTTAAAAATTGTGCAATATGCTTAT RR: AGACGGTAGTACATGGTACTAAAATAGTGAATTATAAAAGAGATTCGTAAAAAATTCATTAAATTTTTAATAAAATGTCTGAATTTTTAACACGTTATACGAATA F2: 3 TACGAATA 2 Unidirectional alignment (log-probability: -38.9) TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTCaTAAGCAtTTTTTTAAGTAAcTTAAAAATTATTTTACAGACTT-AAAAT TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC-TAAGCA-TTTTTTAAGTAATTTAAAAATTATTTTACAGACTTAAAAAT Template switch alignment (log-probability: -27.8) TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC|ATAAGCAT|TTTTTTAAGTAAcTTAAAAATTATTTTACAGACTTAAAAt TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC|ATAAGCAT|TTTTTTAAGTAATTTAAAAATTATTTTACAGACTTAAAAA Human > Gorilla --------------- chr4:146187480-146187485 Template switch process: F1: L TCTGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC 1 F3: 4 TTTTTTAAGTAATTTAAAAATTATTTTACAGACTTAAAA---------------ATT R RF: TCTGCCATCATGTACCATGATTTTATCACTTAATATTTTCTCATAAGCATTTTTTTAAGTAACTTAAAAATTATTTTACAGACTTAAAATTGTGCAATATGCTTATT RR: AGACGGTAGTACATGGTACTAAAATAGTGAATTATAAAAGAGTATTCGTAAAAAAATTCATTGAATTTTTAATAAAATGTCTGAATTTTAACACGTTATACGAATAA F2: 3 ACGAAT 2 Unidirectional alignment (log-probability: -37.5) TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC-TAAGCA-TTTTTTAAGTAAtTTAAAAATTATTTTACAGACTTaAAAA TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTCATAAGCATTTTTTTAAGTAACTTAAAAATTATTTTACAGACTT-AAAA Template switch alignment (log-probability: -32.6) TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC|TAAGCA|TTTTTTAAGTAAtTTAAAAATTATTTTACAGACTTAAAA---------------A TGCCATCATGTACCATGATTTTATCACTTAATATTTTCTC|TAAGCA|TTTTTTAAGTAACTTAAAAATTATTTTACAGACTTAAAATTGTGCAATATGCTTA ========== Event 2531 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCCCACAAGACCCTTTTTCATGGAATACCTTTTTAAGATCTCACATATAGTTTTTCTATGGATTACAAT-CAAAAATGTTAAAATATAAGTT Chimp: TTCCCACAAGACGCTTTTTCATGTAATACCTTTTTAAGATCTCACATATAGTTTTTCTATGGATTACCAT-GAAAAATGTTAAAATATAAGTT ↑ 3 2 1 4 Gorilla: TTCCCACAAGACCCTTTTTCATGGAATACCTTTTTAAGATCTTACATATAGTTTTTCTATGGATTACATTCCAAAAATGTTAAAATATAAGTT Human: TTCCCACAAGACCCTTTTTCATGGAATACCTTTTTAAGATCTCACATATAGTTTTTCTATGGATTACAAT-CAAAAATGTTAAAATATAAGTT Cluster: [ ] Orangutan: TTCCCACAAGACCCTTTTTCATGGAATACCTTTTTAAGATCTCACATATAGTTTTTCTATGGATTACAATCTAAAAATGTTAAAATATAGGTT Gorilla > Chimp --------------- chr4:137683290-137683293 Template switch process: F1: L TACCTTTTTAAGATCTCACATATAGTTTTTCTATGGATTAC 1 F3: 4 AAAAATGTTAAAATATAAGTTATTTCTGAAAAATGT R RF: CATGGAATACCTTTTTAAGATCTTACATATAGTTTTTCTATGGATTACATTCCAAAAATGTTAAAATATAAGTTATTTCTGAAAAATGT RR: GTACCTTATGGAAAAATTCTAGAATGTATATCAAAAAGATACCTAATGTAAGGTTTTTACAATTTTATATTCAATAAAGACTTTTTACA F2: 3 GTAC 2 Unidirectional alignment (log-probability: -37.6) ACCTTTTTAAGATCTcACATATAGTTTTTCTATGGATTA----CCatgAAAAATGTTAAAATATAAGTTATTTCTGAAAAATGT---- ACCTTTTTAAGATCTTACATATAGTTTTTCTATGGATTACATTCC---AAAAATGTTAAAATATAAGTTATTTCTGAAAAATGTTAAA Template switch alignment (log-probability: -21.6) ACCTTTTTAAGATCTcACATATAGTTTTTCTATGGATTAC|CATG|AAAAATGTTAAAATATAAGTTATTTCTGAAAAATGT ACCTTTTTAAGATCTTACATATAGTTTTTCTATGGATTAC|CATG|AAAAATGTTAAAATATAAGTTATTTCTGAAAAATGT ========== Event 2532 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGAACAGGTCTGGTGCCAGATACTGGAGTATCTGACCACTGGGTCAGATGTGAGAGAAAGTCAGAGAAGGCAGAGATGAAAGGATCCACTGACAGCCTGAGAAAATGCCCCT Chimp: GGAACAGGTCTGGTGCCAGATGCTGGAG------TTCAG-TGGTCAGATGTGAGAGAAAGTCAAAGAAGGTAGAGATGAAAGGATCCACTGACAGCCTGAGAAAATGCCCCT Gorilla: AGAACAGGTCTGGTGCCAGATGCTGGAG------TTCAG-TGGTCAGATGTGAGAGAAAGTCAGAGAAGGTAGAGATGAAAGGATCCACTGACAGCCTGAGAAAATGCCCCT ↓ 1 3 4 2 ↑ 1 4 3 2 Human: AGAACAGGTCTGGTGCCAGATACTGGAGTATCTGACCACTGGGTCAGATGTGAGAGAAAGTCAGAGAAGGCAGAGATGAAAGGATCCACTGACAGCCTGAGAAAATGCCCCT Cluster: [ ] Orangutan: AGAACAGGTCTGGTGCCAGATCCTGGAG------TCCAG-TGGTCAGATGTGAGAGAAAGTCAGAGAAGGTAGAGATGAAAGGATCCACTGAGAGCCTGAGAAAATGCCCCT Gorilla > Human --------------- chr4:13697058-13697069 Template switch process: F1: L TAACTAGTCTTCCTTCCTTGAGAACAGGTCTGGTGCCAGATACTGGAGT 1 F3: 4 GGTCAGATGTGAGAGAAAGTCAGAGAAGGCAGAGATGAAA R RF: TAACTAGTCTTCCTTCCTTGAGAACAGGTCTGGTGCCAGATGCTGGAGTTCAGTGGTCAGATGTGAGAGAAAGTCAGAGAAGGTAGAGATGAAA RR: ATTGATCAGAAGGAAGGAACTCTTGTCCAGACCACGGTCTACGACCTCAAGTCACCAGTCTACACTCTCTTTCAGTCTCTTCCATCTCTACTTT F2: 3 GTCACCAGTCTA 2 Unidirectional alignment (log-probability: -49.3) TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATaCTGGAGTatctgaccactg-----GGTCAGATGTGAGAGAAAGTCAGAGAAGGcAGAGATGAAA TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATGCTGGAGT------------TCAGTGGTCAGATGTGAGAGAAAGTCAGAGAAGGTAGAGATGAAA Template switch alignment (log-probability: -28.5) TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATaCTGGAGT|ATCTGACCACTG|GGTCAGATGTGAGAGAAAGTCAGAGAAGGcAGAGATGAAA TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATGCTGGAGT|ATCTGACCACTG|GGTCAGATGTGAGAGAAAGTCAGAGAAGGTAGAGATGAAA Human > Gorilla --------------- chr4:13051022-13051026 Template switch process: F1: L TAACTAGTCTTCCTTCCTTGAGAACAGGTCTGGTGCCAGATGCTGGAGT 1 F3: 4 GGTCAGATGTGAGAGAAAGTCAGAGAAGGTAGAGATGAAA R RF: TAACTAGTCTTCCTTCCTTGAGAACAGGTCTGGTGCCAGATACTGGAGTATCTGACCACTGGGTCAGATGTGAGAGAAAGTCAGAGAAGGCAGAGATGAAAGGATCCACTGA RR: ATTGATCAGAAGGAAGGAACTCTTGTCCAGACCACGGTCTATGACCTCATAGACTGGTGACCCAGTCTACACTCTCTTTCAGTCTCTTCCGTCTCTACTTTCCTAGGTGACT F2: 3 TGACT 2 Unidirectional alignment (log-probability: -39.6) TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATgCTGGAGT------------tcagtGGTCAGATGTGAGAGAAAGTCAGAGAAGGtAGAGATGAAA TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATACTGGAGTATCTGACCACTG-----GGTCAGATGTGAGAGAAAGTCAGAGAAGGCAGAGATGAAA Template switch alignment (log-probability: -27.6) TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATgCTGGAGT|TCAGT|GGTCAGATGTGAGAGAAAGTCAGAGAAGGtAGAGATGAAA TTCCTTCCTTGAGAACAGGTCTGGTGCCAGATACTGGAGT|TCAGT|GGTCAGATGTGAGAGAAAGTCAGAGAAGGCAGAGATGAAA ========== Event 2533 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGCCCAGAGAAGGCCGAGAGGGCTCAGCGCAGCAC Chimp: TTGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGCCCAGAGAAGGCCGAGAGGGCTCAGCGCAGCAC ↓ 3 2 1 4 Gorilla: TTGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGCAGTAGCAAGGCTGAGAGGGCTCAGCGCAGCAC Human: TTGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGCCCAGAGAAGGCCGAGAGGGCTCAGCGCAGCAC Cluster: [ ] Orangutan: TTGGGTCCAGGAGGCAGTTACTACTGCTCCGGGGACCAAGCCCAGAGAAGGCCAAGAGGGCTCAGCGCAGCAC Chimp > Gorilla --------------- chr4:12896425-12896430 Template switch process: F1: L TTGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGC 1 F3: 4 AAGGCTGAGAGGGCTCAGCGCAGCACAGGGATGCAGGCAGTGGGTG R RF: TTGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGCCCAGAGAAGGCCGAGAGGGCTCAGCGCAGCACAGGGATGCAGGCAGTGGGTG RR: AACCCGGGTCCGCCGTCAACGATGACGAGGCCCCTGGTTCGGGTCTCTTCCGGCTCTCCCGAGTCGCGTCGTGTCCCTACGTCCGTCACCCAC F2: 3 CGATGA 2 Unidirectional alignment (log-probability: -32.2) TGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGC----AGtagcAAGGCtGAGAGGGCTCAGCGCAGCACAGGGATGCAGGCAG TGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGCCCAGAG----AAGGCCGAGAGGGCTCAGCGCAGCACAGGGATGCAGGCAG Template switch alignment (log-probability: -22.2) TGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGC|AGTAGC|AAGGCtGAGAGGGCTCAGCGCAGCACAGGGATGCAGGCAG TGGGCCCAGGCGGCAGTTGCTACTGCTCCGGGGACCAAGC|AGTAGC|AAGGCCGAGAGGGCTCAGCGCAGCACAGGGATGCAGGCAG ========== Event 2534 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAATGTCTTCCACATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAAACAT-------------TAAGACAAGATAAAAATGAGA ↓ 4 3 2 1 Chimp: AAATGTCTTCCACATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAACAAGTATAAAACAGGTAAAAGACAAGATAAAAATGAGA Gorilla: AAATGTCTTCCACATTAAAAGGTAATTATCTGTGTTTTATACTTGTTTAAAAACAT-------------CAAGACAAGATAAAAATGAGA Human: AAATGTCTTCCACATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAAACAT-------------TAAGACAAGATAAAAATGAGA Cluster: [ ] Orangutan: AAATGTCTTCCACATTAAAAGGTAATTATCTGTGTTTTATACTTGTTTAAAAACAT-------------TAAGACAAGATAAAAATGAGA Human > Chimp ------------- chr4:57515436-57515447 Template switch process: F1: L ACATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAA 1 F3: 4 AGGTAA--------------------------------AAGACAAGATAAAAATGAGACTAGCCCTCACCAAACAGAA R RF: ACATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAAACATTAAGACAAGATAAAAATGAGACTAGCCCTCACCAAACAGAA RR: TGTAATTTTCCATTAATGGACACAAAATATGAACAAATTTTTGTAATTCTGTTCTATTTTTACTCTGATCGGGAGTGGTTTGTCTT F2: 3 CAAAATATGAAC 2 Unidirectional alignment (log-probability: -45.8) CATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAacaagtataaaacaggtAA----AAGACAAGATAAAAATGAGACTAGCCCTCACCAA CATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAA-----------------AACATTAAGACAAGATAAAAATGAGACTAGCCCTCACCAA Template switch alignment (log-probability: -28.7) CATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAA|CAAGTATAAAAC|AGGTAA--------------------------------AAGACAAGATAAAAATGAGACTAGCCCTCACCAA CATTAAAAGGTAATTACCTGTGTTTTATACTTGTTTAAAA|CAAGTATAAAAC|AGGTAATTACCTGTGTTTTATACTTGTTTAAAAACATTAAGACAAGATAAAAATGAGACTAGCCCTCACCAA ========== Event 2535 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCAGCCAATGTAGGTTCAAA----------G----------------GTAAAAAGAGTTGGTAAGATGAAAGAGAAAGAATTTTAGAAGAGAAAACTCTGCCATGGGTCAAGTAAGAATTTCAAAGAGAAATGACTCCATCCATTTTCCTCAAAGGT-----AATAGTACAGGAG Chimp: TGCAGCCAATGTAGGTTCAAA-----GCTATG----------------GTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTTAGAAGAGAAAACTCTGCCATGGGTCAAGTAAGAATTTCAAAGAGAAATGACTCCCTCCATTTTCCTCAAAGGT-----AATAGTACAGGAG ↓ 4 1 3 2 Gorilla: TGCAGCCAATGTAGGTTCAAAGCTAT-----GGTAAAACTTTGAGTTGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTTAGAAGAGAAAACTCTGCAATGGGTCAAGTAAGAATTTCAAAGAGAAATGACTCCATCCATTTTCCCTAAAGGT-----AATAGTACAGGAG Human: TGCAGCCAATGTAGGTTCAAA----------G----------------GTAAAAAGAGTTGGTAAGATGAAAGAGAAAGAATTTTAGAAGAGAAAACTCTGCCATGGGTCAAGTAAGAATTTCAAAGAGAAATGACTCCATCCATTTTCCTCAAAGGT-----AATAGTACAGGAG Cluster: [ ] Orangutan: TGCAGCCAATGTAGGTTCAAAGCTAT-----G----------------GTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTTAGAAGAGAAAACTCTGCCATGGGTCAAGTAAGAATTTCAAAGAGAAATGACTCCATCCATTTTCCTCAAAGGTAATATAATAGTACAGGAG Chimp > Gorilla --------------- chr4:57088743-57088749 Template switch process: F1: L GTTTGTAGACTTTCACACAATGCAGCCAATGTAGGTTCAAAGCTATGGTAAAA 1 F3: 4 TTGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTTAGA R RF: GTTTGTAGACTTTCACACAATGCAGCCAATGTAGGTTCAAAGCTATGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTTAGAAGAGAAAACTCTGCCATGGGTCAAGTAAGAATTTCAAAGAGAAATGACTCCCTCCATTTTCCTCAAAG RR: CAAACATCTGAAAGTGTGTTACGTCGGTTACATCCAAGTTTCGATACCATTTTTCTCAACCATTCTACTTTCTCTTTGTTAAAATCTTCTCTTTTGAGACGGTACCCAGTTCATTCTTAAAGTTTCTCTTTACTGAGGGAGGTAAAAGGAGTTTC F2: 3 GAGTTTC 2 Unidirectional alignment (log-probability: -34) CACACAATGCAGCCAATGTAGGTTCAAAGCTAtggtaaaactttgagtTGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTT CACACAATGCAGCCAATGTAGGTTCAAAGCTA----------------TGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTT Template switch alignment (log-probability: -22.5) CACACAATGCAGCCAATGTAGGTTCAAAGCTATGGTAAAA|CTTTGAG|tTGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTT CACACAATGCAGCCAATGTAGGTTCAAAGCTATGGTAAAA|CTTTGAG|ATGGTAAAAAGAGTTGGTAAGATGAAAGAGAAACAATTTT ========== Event 2536 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AAAACTGTGGTTTCATGATTGCAAGCCTAGACTGGTGCCCATCATTATCACTTTTGGTAAAGGTATAGGATCTGAGTTaaaaaagaaaaaagaaaTTAAGTGTGAAATGTATCTTGCAAGAGTCAATTCTA--GATG--------------------CCTAC-TCACTAGCTGTTTT ↑ 3 2 1 4 Chimp: AAAACTGTGGTTTCATGATTGCAAGCCTAGACTGGTGCCCATCATTATCACTTTTGGTAAAGGTATAGGATCTGAGTTaaaaaagaaaaaagaaaTTAAGTGTGAAATGTATTCT----------------------GCGAGAGTCAATTCTAGATGCCTAC-TCACTAGCTATTTT Gorilla: AAAACTGTGGTTTCATGATTGCAAGCCTAGACTGGTGCCCATCATTATCACTTTTGGAAAAGGTATAGGATCTGAGTTaaaaaagaaaaaagaaaTTAAGTGTGAAATGTATCTTGCGAGAGTCAATTCTA--GATG--------------------CCTAC-TCACTAGCTATTTT Human: AAAACTGTGGTTTCATGATTGCAAGCCTAGACTGGTGCCCATCATTATCACTTTTGGTAAAGGTATAGGATCTGAGTTaaaaaagaaaaaagaaaTTAAGTGTGAAATGTATCTTGCAAGAGTCAATTCTA--GATG--------------------CCTAC-TCACTAGCTGTTTT Cluster: [ ] Orangutan: AAAACTGTGGTTTCATGATTGCAAGCCTAGACTGGTGCCCATCATTATTACTTATGGTAAAGGTATAGGATCTGAGTTAAAA-------AAGAAATTAAGTGTGAAATGTATCTTGCGAGAGTCAATTCTAGGAATG--------------------CCTACTCCACTAGCTATTTT Chimp > Human ------------- chr4:53484447-53484452 Template switch process: F1: L CTGAGTTAAAAAAGAAAAAAGAAATTAAGTGTGAAATGTAT 1 F3: 4 AGAGTCAATTCTAGATGCCTACTCACTAGCTGTTTTCTTCTCCCTTTTTTCTTGAAC R RF: TGCAAGCCTAGACTGGTGCCCATCATTATCACTTTTGGTAAAGGTATAGGATCTGAGTTAAAAAAGAAAAAAGAAATTAAGTGTGAAATGTATTCTGCGAGAGTCAATTCTAGATGCCTACTCACTAGCTATTTTCTTCTCCCTTTTTTCTTGAAC RR: ACGTTCGGATCTGACCACGGGTAGTAATAGTGAAAACCATTTCCATATCCTAGACTCAATTTTTTCTTTTTTCTTTAATTCACACTTTACATAAGACGCTCTCAGTTAAGATCTACGGATGAGTGATCGATAAAAGAAGAGGGAAAAAAGAACTTG F2: 3 ACGTTC 2 Unidirectional alignment (log-probability: -35) TGAGTTAAAAAAGAAAAAAGAAATTAAGTGTGAAATGTATctTGCaAGAGTCAATTCTAGATGCCTACTCACTAGCTgTTTTCTTC TGAGTTAAAAAAGAAAAAAGAAATTAAGTGTGAAATGTATTCTGCGAGAGTCAATTCTAGATGCCTACTCACTAGCTATTTTCTTC Template switch alignment (log-probability: -22.3) TGAGTTAAAAAAGAAAAAAGAAATTAAGTGTGAAATGTAT|CTTGCA|AGAGTCAATTCTAGATGCCTACTCACTAGCTgTTTTCTTC TGAGTTAAAAAAGAAAAAAGAAATTAAGTGTGAAATGTAT|CTTGCA|AGAGTCAATTCTAGATGCCTACTCACTAGCTATTTTCTTC ========== Event 2537 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: AGACTAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATATCTACTGTTATAGAAATAGAGTTCATTTCATAGAAC Chimp: AGACCAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATATCTACTGTTA------TAGAGTTCATTTCGTAGAAC ↓ 3 2 1 4 ↑ 3 2 1 4 Gorilla: AGACTAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAA----TACTGTTATAGAAATAGAGTTCATTTCGTAGAAC Human: AGACTAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATATCTACTGTTATAGAAATAGAGTTCATTTCATAGAAC Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr4:139921628-139921636 Template switch process: F1: L ACCAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATA 1 F3: 4 ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATTC R RF: ACTAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATACTGTTATAGAAATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATTC RR: TGATCGTTGTTATTCTAAAGATATTGTCATCTAATTATTTTATGACAATATCTTTATCTCAAGTAAAGCATCTTGAACTAATTATCTCAGGTAAG F2: 3 TTGTCATCT 2 Unidirectional alignment (log-probability: -32.3) AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAAtatcTACTGTT------ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAA----TACTGTTATAGAAATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT Template switch alignment (log-probability: -22.5) AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATA|TCTACTGTT|ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATA|TCTACTGTT|ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT Chimp > Gorilla --------------- chr4:148778857-148778867 Template switch process: F1: L ACTAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATA 1 F3: 4 ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATTC R RF: ACCAGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATATCTACTGTTATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATTC RR: TGGTCGTTGTTATTCTAAAGATATTGTCATCTAATTATTTTATAGATGACAATATCTCAAGTAAAGCATCTTGAACTAATTATCTCAGGTAAG F2: 3 AAGATATTGTC 2 Unidirectional alignment (log-probability: -35.1) AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAA----TACTGTTatagaaATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATATCTACTGTT------ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT Template switch alignment (log-probability: -22.7) AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATA|CTGTTATAGAA|ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT AGCAACAATAAGATTTCTATAACAGTAGATTAATAAAATA|CTGTTATAGAA|ATAGAGTTCATTTCGTAGAACTTGATTAATAGAGTCCATT ========== Event 2538 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGTCCCAGCTGGCTTGAGACCAGAGAGGTTGTCTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAA Chimp: GTGTCCCAGCTGGCTTGAGAC----AAAGTTATCTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAA ↑ 1 4 3 2 Gorilla: GTGTCCCAGCTGGCTTGAGACCAGAGAGGTTGCCTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAA Human: GTGTCCCAGCTGGCTTGAGACCAGAGAGGTTGTCTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAA Cluster: [ ] Orangutan: GTGTCCCAGCTGGCTTGAGACCAGAGAGGTTGTCTTTTTTGATTACTTTGCATCCTGAAACGGTGAAAA Gorilla > Chimp --------------- chr4:141616207-141616215 Template switch process: F1: L ATTCTAGTCACATCCTGGTAGTGTCCCAGCTGGCTTGAGAC 1 F3: 4 TTTTCTGATAACTTTGCATCCTGAAATGGTGAAAACGAA R RF: ATTCTAGTCACATCCTGGTAGTGTCCCAGCTGGCTTGAGACCAGAGAGGTTGCCTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAACGAA RR: TAAGATCAGTGTAGGACCATCACAGGGTCGACCGAACTCTGGTCTCTCCAACGGAAAAGACTATTGAAACGTAGGACTTTACCACTTTTGCTT F2: 3 CTATTGAAA 2 Unidirectional alignment (log-probability: -32.7) TTCTAGTCACATCCTGGTAGTGTCCCAGCTGGCTTGAGA------------CaaagttatCTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAACGAA TTCTAGTCACATCCTGGTAGTGTCCCAGCTGGCTTGAGACCAGAGAGGTTGC--------CTTTTCTGATAACTTTGCATCCTGAAATGGTGAAAACGAA Template switch alignment (log-probability: -16.8) TTCTAGTCACATCCTGGTAGTGTCCCAGCTGGCTTGAGAC|AAAGTTATC|TTTTCTGATAACTTTGCATCCTGAAATGGTGAAAACGAA TTCTAGTCACATCCTGGTAGTGTCCCAGCTGGCTTGAGAC|AAAGTTATC|TTTTCTGATAACTTTGCATCCTGAAATGGTGAAAACGAA ========== Event 2539 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GAGAAAATGTTCTGTTTTTATGCATACTAGATAGTATGCATAAAGACACTTATAATTTAGAT ↑ 3 1 2 4 Chimp: GAGAAAATGTTCTGTTTTTATGCATACTATC--------TGAAAGACACTTATAATTTAGAT Gorilla: GAGAAAATGTTCCGTTTTTATGCATATTATC--------TGAAAGACACTTATAATTTAGAT Human: GAGAAAATGTTCTGTTTTTATGCATACTAGATAGTATGCATAAAGACACTTATAATTTAGAT Cluster: [ ] Orangutan: GAGAAAATGTTCTGTTTTTATGCATACTATC--------TGAAAGACACTTATAATTTAGAT Chimp > Human ------------- chr4:137879387-137879398 Template switch process: F1: L AGAATCTACTTTGAGAAAATGTTCTGTTTTTATGCATACTA 1 F3: 4 AAAGACACTTATAATTTAGATTTTAGAGTCCCAGACAATA R RF: AGAATGTACTTTGAGAAAATGTTCTGTTTTTATGCATACTATCTGAAAGACACTTATAATTTAGATTTTAGAGTCCCAGACAATA RR: TCTTACATGAAACTCTTTTACAAGACAAAAATACGTATGATAGACTTTCTGTGAATATTAAATCTAAAATCTCAGGGTCTGTTAT F2: 3 TACGTATGATAG 2 Unidirectional alignment (log-probability: -43.1) GAATcTACTTTGAGAAAATGTTCTGTTTTTATGCATACTA---GAtagtatgcataAAGACACTTATAATTTAGATTTTAGAGTCCCAGACAATA GAATGTACTTTGAGAAAATGTTCTGTTTTTATGCATACTATCTGA-----------AAGACACTTATAATTTAGATTTTAGAGTCCCAGACAATA Template switch alignment (log-probability: -22.8) GAATcTACTTTGAGAAAATGTTCTGTTTTTATGCATACTA|GATAGTATGCAT|AAAGACACTTATAATTTAGATTTTAGAGTCCCAGACAATA GAATGTACTTTGAGAAAATGTTCTGTTTTTATGCATACTA|GATAGTATGCAT|AAAGACACTTATAATTTAGATTTTAGAGTCCCAGACAATA ========== Event 2540 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAGCATAAGCTACACAATAG-GATGAACATTGAACT-CATCCACAAACATTTATAATGGGTACATAACTCTATAATATGAACTTTAGAAACTCTTAAAGAAGCATACAGTACAGTCCATGAACCAAAAA ↓ 1 4 3 2 Chimp: TTAGCATAAGCTACACAATAGCTGTATTCATTGAACT-CATCCACAAACATTTATAATGGGTACATAACTCTATAATATGAACTTTAGAAACTCTTAGAGAAGCATATGGTACAGTCCATGAACCAAAAA Gorilla: TTAGCATAAGCTACACCATAGCTGTATTCACTGAACT-CACCCACAAACATTTATAATGGGTAGATAACTCTATAATATGAACTTTAGAAACTCTTAAAGAAGCATACGGTACAGTCCATGAACCAAAAA Human: TTAGCATAAGCTACACAATAG-GATGAACATTGAACT-CATCCACAAACATTTATAATGGGTACATAACTCTATAATATGAACTTTAGAAACTCTTAAAGAAGCATACAGTACAGTCCATGAACCAAAAA Cluster: [ ] Orangutan: TTAGCATAAGCTACACAATAGCTGTATTCATTGAACTCTATCCACAAACATTTATAATGGGTACATAACTCTATAATATGAACTTTAGAAACTCTTAAAGAAGCATACAGTACAGTCCATGAACCAAAAA Human > Chimp ------------- chr4:141293153-141293158 Template switch process: F1: L AACTTCTATAATCAGACAATTTAGCATAAGCTACACAATAG 1 F3: 4 TCATTGAACTCATCCACAAACATTTATAATGGGTACATAAC R RF: AACTTCTATAATCAGACAATTTAGCATAAGCTACACAATAGGATGAACATTGAACTCATCCACAAACATTTATAATGGGTACATAACTCTATAATATGAACTTTAGAAACTCTTAAAGAAGCATACAG RR: TTGAAGATATTAGTCTGTTAAATCGTATTCGATGTGTTATCCTACTTGTAACTTGAGTAGGTGTTTGTAAATATTACCCATGTATTGAGATATTATACTTGAAATCTTTGAGAATTTCTTCGTATGTC F2: 3 TATGTC 2 Unidirectional alignment (log-probability: -31.5) ACTTCTATAATCAGACAATTTAGCATAAGCTACACAATAGctgtatt------CATTGAACTCATCCACAAACATTTATAATGGGTACATAA ACTTCTATAATCAGACAATTTAGCATAAGCTACACAATAG-------GATGAACATTGAACTCATCCACAAACATTTATAATGGGTACATAA Template switch alignment (log-probability: -22) ACTTCTATAATCAGACAATTTAGCATAAGCTACACAATAG|CTGTAT|tCATTGAACTCATCCACAAACATTTATAATGGGTACATAA ACTTCTATAATCAGACAATTTAGCATAAGCTACACAATAG|CTGTAT|ACATTGAACTCATCCACAAACATTTATAATGGGTACATAA ========== Event 2541 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAATTTTCCAAATAAGTTAA----AAGTTTGTAATTaca---aacaaaacaaaacaaaac-aaaaca--aaaa ↑ 1 3 4 2 Chimp: TTAATTTTCCAAATAAGTTAA--AACAGTTTGTAATTaca------------aaacaaaac-aaaaca--aaac Gorilla: TTCATTTTCCAAATAAGTTAAAA--CAGTTTGTAATTacaaaa----------aacaaaaaacaaacaaacaaa Human: TTAATTTTCCAAATAAGTTAA----AAGTTTGTAATTaca---aacaaaacaaaacaaaac-aaaaca--aaaa Cluster: [ ] Orangutan: TTAATTTTCCAAATAAGTTAAAA--CAGTTTGTAATTACaaaa------------------------------- Chimp > Human ------------- chr4:50907914-50907927 Template switch process: F1: L GGCCACAATTTTCTAATGACTTAATTTTCCAAATAAGTTAAAAG 1 F3: 4 CAAAACAAAACAAAACAAAACAAA R RF: GGCCACAATTTTCTAATGACTTAATTTTCCAAATAAGTTAAAACAGTTTGTAATTACAAAACAAAACAAAACAAAACAAA RR: CCGGTGTTAAAAGATTACTGAATTAAAAGGTTTATTCAATTTTGTCAAACATTAATGTTTTGTTTTGTTTTGTTTTGTTT F2: 3 AAACATTAATGTTT 2 Unidirectional alignment (log-probability: -34.1) ACAATTTTCTAATGACTTAATTTTCCAAATAAGTTAAA--AGTTTGTAATTACAaacaaaacaAAACAAAACAAAACAAA ACAATTTTCTAATGACTTAATTTTCCAAATAAGTTAAAACAGTTTGTAATTACA---------AAACAAAACAAAACAAA Template switch alignment (log-probability: -22.7) ACAATTTTCTAATGACTTAATTTTCCAAATAAGTTAAAAg|TTTGTAATTACAAA|CAAAACAAAACAAAACAAAACAAA ACAATTTTCTAATGACTTAATTTTCCAAATAAGTTAAAAC|TTTGTAATTACAAA|CAAAACAAAACAAAACAAAACAAA ========== Event 2542 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGAGTGAGACATTCTTTGTGATGACTTCTTCCAAATa--------------ttgta-gtt--------------atacaattgtagttatacaatCTACAGGAATAGATATTTGGAAGAAGTCATCACAAAGAATGTCTC---- ↑ 1 4 3 2 Chimp: TGAGTGAGACATTCTTTGTGACAACTTCTTCCAAATA-------TCTATTCCTGTAGatt--------------gtataactacaattgtata-actac-------aatATTTGGAAGAAGTCATCACAAAGAATGTCTC---- Gorilla: TGAGTGAGACATTCTTTGTGATGACTTCTTCCAAATATCTATTC-------CTGTAGATT----------------------------GTATA-ACTAC-------AATATTTGGAAGAAGTCATCACAAAGAATGTCTC---- Human: TGAGTGAGACATTCTTTGTGATGACTTCTTCCAAATa--------------ttgta-gtt--------------atacaattgtagttatacaatCTACAGGAATAGATATTTGGAAGAAGTCATCACAAAGAATGTCTC---- Cluster: [] Orangutan: TGAGTGAGACATTCTTTGTGATGACTTCTTCCAAATATCTATTC-------CTGTAGattgtttaactacaatt--------------gtata-actac-------aatATTTGGAAGAAGTCGTCNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr4:137456981-137457005 Template switch process: F1: L AAAGGAGTCACCTGCAATCCTGAGTGAGACATTCTTTGTGA 1 F3: 4 TACAATTGT R RF: AAAGGAGTCACCTGCAATCCTGAGTGAGACATTCTTTGTGACAACTTCTTCCAAATATCTATTCCTGTAGATTGTATAACTACAATTGTATAACTACAATATTTGGAAGAAGTCA RR: TTTCCTCAGTGGACGTTAGGACTCACTCTGTAAGAAACACTGTTGAAGAAGGTTTATAGATAAGGACATCTAACATATTGATGTTAACATATTGATGTTATAAACCTTCTTCAGT F2: 3 ATTGATGTTATAAACCTTCTTCAGT 2 Unidirectional alignment (log-probability: -51) AAGGAGTCACCTGCAATCCTGAGTGAGACATTCTTTGTGAtgACTTCTTCCAAATAT-------TGTAGttatacaATTGT-------- AAGGAGTCACCTGCAATCCTGAGTGAGACATTCTTTGTGACAACTTCTTCCAAATATCTATTCCTGTAG-------ATTGTATAACTAC Template switch alignment (log-probability: -17.7) AAGGAGTCACCTGCAATCCTGAGTGAGACATTCTTTGTGA|TGACTTCTTCCAAATATTGTAGTTA|TACAATTGT AAGGAGTCACCTGCAATCCTGAGTGAGACATTCTTTGTGA|TGACTTCTTCCAAATATTGTAGTTA|TACAATTGT ========== Event 2543 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TACAATGCAAAAATACAATCTAGGTAACTA--------ATGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTG ↓ 3 2 4 1 Chimp: TACAATGCAAAAATACAATCTAGGTAACTGAAAGTTACCTAGAATCTGAAAGTTCATGCTCAAAAATAAGTTTG ↑ 3 2 4 1 Gorilla: TACAATGCAAAAATACAATCTAGGTAACTA--------ACGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTG Human: TACAATGCAAAAATACAATCTAGGTAACTA--------ATGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTG Cluster: [ ] Orangutan: TACAATGCAAAAATACGATTTAGGTAACTA--------ACGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTG Human > Chimp ------------- chr4:140817009-140817014 Template switch process: F1: L TATAACCAACAATACAATGCAAAAATACAATCTAGGTAAC----------TGAAAGTT 1 F3: 4 AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA R RF: TATAACCAACAATACAATGCAAAAATACAATCTAGGTAACTAATGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA RR: ATATTGGTTGTTATGTTACGTTTTTATGTTAGATCCATTGATTACGTTAGACTTTCAAGTACGAGTTTTTATTCAAACCAGTATCT F2: 3 GATCCA 2 Unidirectional alignment (log-probability: -40.1) ACAATACAATGCAAAAATACAATCTAGGTAACT-----gaaagttacctagAATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA ACAATACAATGCAAAAATACAATCTAGGTAACTAATGC-------------AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA Template switch alignment (log-probability: -26.9) ACAATACAATGCAAAAATACAATCTAGGTAAC----------TGAAAGTT|ACCTAG|AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA ACAATACAATGCAAAAATACAATCTAGGTAACTAATGCAATCTGAAAGTT|ACCTAG|AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA Gorilla > Chimp --------------- chr4:140817009-140817014 Template switch process: F1: L TATAACCAACAATACAATGCAAAAATACAATCTAGGTAA----------CTGAAAGTT 1 F3: 4 AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA R RF: TATAACCAACAATACAATGCAAAAATACAATCTAGGTAACTAACGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA RR: ATATTGGTTGTTATGTTACGTTTTTATGTTAGATCCATTGATTGCGTTAGACTTTCAAGTACGAGTTTTTATTCAAACCAGTATCT F2: 3 GATCCA 2 Unidirectional alignment (log-probability: -39.6) ACAATACAATGCAAAAATACAATCTAGGTAACTgaaagttacctagA-----ATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA ACAATACAATGCAAAAATACAATCTAGGTAACT-------------AACGCAATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA Template switch alignment (log-probability: -26.9) ACAATACAATGCAAAAATACAATCTAGGTAA----------CTGAAAGTT|ACCTAG|AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA ACAATACAATGCAAAAATACAATCTAGGTAACTAACGCAATCTGAAAGTT|ACCTAG|AATCTGAAAGTTCATGCTCAAAAATAAGTTTGGTCATAGA ========== Event 2544 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCAGAACAAGGGTGGAATTAAATTAGACACATCAGCAGCGTCTAAGCCTAGTGCCCTGGATcatcattccgccttccctcaccccgctctgctttttctttgttccatagcacttataactgtctaacatactatgtaatttacact ↑ 1 4 3 2 Chimp: GCAGAACAAGGGTGGAATTAA-----AGGCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATcatcattccgccttccctcaccccgctctgctttttctttgttccatagcacttataactgtctaacatactatgtaatttacact Gorilla: GCAGAACAAGGGTGGAATTAA-----AGGCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATcatcattccgccttccctcaccccgctctgctttttctttgttccatagcacttataactgtctaacatactatgtaatttacact ↓ 1 4 3 2 Human: GCAGAACAAGGGTGGAATTAAATTAGACACATCAGCAGCGTCTAAGCCTAGTGCCCTGGATcatcattccgccttccctcaccccgctctgctttttctttgttccatagcacttataactgtctaacatactatgtaatttacact Cluster: [ ] Orangutan: GCAGGACAAGGGTGGAATTAA-----AGGCATCAGCAGTGTCTAAGCCTAGTGCCCTGGATcatcattctgccttccctcaccccgctctgctttttctttgttctatagcacttacaagtgtctaacatactatgtaatttacact Chimp > Human ------------- chr4:139823594-139823600 Template switch process: F1: L TCTGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAA 1 F3: 4 CATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC R RF: TCTGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAAGGCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTCCGCCTTCCCTCACCCCGCTCTGCTTTTTCTTTGTTCCATAGCACTTATAACTGTCTAA RR: AGACGAGACCCGTCCTCCGTCGTCTTGTTCCCACCTTAATTTCCGTAGTCGTCGCAGATTCGGATCACGGGACCTAGTAGTAAGGCGGAAGGGAGTGGGGCGAGACGAAAAAGAAACAAGGTATCGTGAATATTGACAGATT F2: 3 ACAGATT 2 Unidirectional alignment (log-probability: -30.1) TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAattagAcaCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAA-----AGGCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC Template switch alignment (log-probability: -16.2) TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAA|TTAGACA|CATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAA|TTAGACA|CATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC Gorilla > Human --------------- chr4:139823594-139823600 Template switch process: F1: L TCTGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAA 1 F3: 4 CATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC R RF: TCTGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAAGGCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTCCGCCTTCCCTCACCCCGCTCTGCTTTTTCTTTGTTCCATAGCACTTATAACTGTCTAA RR: AGACGAGACCCGTCCTCCGTCGTCTTGTTCCCACCTTAATTTCCGTAGTCGTCGCAGATTCGGATCACGGGACCTAGTAGTAAGGCGGAAGGGAGTGGGGCGAGACGAAAAAGAAACAAGGTATCGTGAATATTGACAGATT F2: 3 ACAGATT 2 Unidirectional alignment (log-probability: -29.2) TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAattagAcaCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAA-----AGGCATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC Template switch alignment (log-probability: -16.6) TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAA|TTAGACA|CATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC TGCTCTGGGCAGGAGGCAGCAGAACAAGGGTGGAATTAAA|TTAGACA|CATCAGCAGCGTCTAAGCCTAGTGCCCTGGATCATCATTC ========== Event 2545 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGTACCACTTAAGCATGTTA-----TAAAATGCC-AAAGCCATTCATGGTCATTATGGTGTCCACaaatatgttcacaaattcttgacactcccttcagaagggagaa Chimp: CAGTACCACTTAAGCATGTTA-----TAAAATGTCAAAAGCCATTCATGGTCATTATGGTGTCCACaaatatgttcacaaattcttgacactcccttcagaagggagaa Gorilla: CAGTACCACTTAAGCATGTTA----------TGTCAAAAGCCATTCATGGTCATTATGGTGTCCACaaatatgttcacaaatacttgacactcccttcagaagggagaa ↑ 1 4 3 2 Human: CAGTACCACTTAAGCATGTTA-----TAAAATGCC-AAAGCCATTCATGGTCATTATGGTGTCCACaaatatgttcacaaattcttgacactcccttcagaagggagaa Cluster: [ ] Orangutan: CAGTACCACTTAAGCAAGTTATAAAA-----TGTCAAAAGCCATTCGTGGTCATTATGGTGTCCACaaatatgttcacaaattcttgacactcctttcagaagggagaa Human > Gorilla --------------- chr4:152081414-152081417 Template switch process: F1: L CATCCTAAGCTTTCCTGAGCCAGTACCACTTAAGCATGTTAT 1 F3: 4 AAAGCCATTCATGGTCATTATGGTGTCCACAAATATGTTC R RF: CATCCTAAGCTTTCCTGAGCCAGTACCACTTAAGCATGTTATAAAATGCCAAAGCCATTCATGGTCATTATGGTGTCCACAAATATGTTCACAAATTCTTGAC RR: GTAGGATTCGAAAGGACTCGGTCATGGTGAATTCGTACAATATTTTACGGTTTCGGTAAGTACCAGTAATACCACAGGTGTTTATACAAGTGTTTAAGAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -25.3) TCCTAAGCTTTCCTGAGCCAGTACCACTTAAGCATGTTATgtcA-------AAAGCCATTCATGGTCATTATGGTGTCCACAAATATGTTC TCCTAAGCTTTCCTGAGCCAGTACCACTTAAGCATGTTAT---AAAATGCCAAAGCCATTCATGGTCATTATGGTGTCCACAAATATGTTC Template switch alignment (log-probability: -16.3) TCCTAAGCTTTCCTGAGCCAGTACCACTTAAGCATGTTAT|GTCA|AAAGCCATTCATGGTCATTATGGTGTCCACAAATATGTTC TCCTAAGCTTTCCTGAGCCAGTACCACTTAAGCATGTTAT|GTCA|AAAGCCATTCATGGTCATTATGGTGTCCACAAATATGTTC ========== Event 2546 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTGATTCTTGTTTTTGCAACATGTTAATGTTGCAATGACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAAT Chimp: CTTGATTCTTGTTTTTGCAACATGTTAATGTTGCAATGACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAAT ↑ 4 13 2 Gorilla: CTTGATTCTTGTTTTTGCAACATG-------------------TTAATGTCATTGCAGGGTATCCAGTAAACTAAAT Human: CTTGATTCTTGTTTTTGCAACATGTTAATGTTGCAATGACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAAT Cluster: [ ] Orangutan: CTTGATTCTTGTTTTTGCAACATG-------------------TTAATGTCATTGCAGGGTATCCAGTAAACTAAAT Gorilla > Chimp --------------- chr4:142882476-142882482 Template switch process: F1: L TTCCTCTTTCTCTTTTGCTTGATTCTTGTTTTTGCAACATGTTAATGT 1 F3: 4 ACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAATTTAGAC R RF: TTCCTCTTTCTCTTTTGCTTGATTCTTGTTTTTGCAACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAATTTAGAC RR: AAGGAGAAAGAGAAAACGAACTAAGAACAAAAACGTTGTACAATTACAGTAACGTCCCATAGGTCATTTGATTTAAATCTG F2: 3 GTAACGT 2 Unidirectional alignment (log-probability: -38.2) TCTCTTTTGCTTGATTCTTGTTTTTGCAACAtgttaatgttgcaatgacaTGTTAATGTCATTGCAGGGTATCCAGTAAACTAAATT TCTCTTTTGCTTGATTCTTGTTTTTGCAACA-------------------TGTTAATGTCATTGCAGGGTATCCAGTAAACTAAATT Template switch alignment (log-probability: -16.9) TCTCTTTTGCTTGATTCTTGTTTTTGCAACATGTTAATGT|TGCAATG|ACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAATT TCTCTTTTGCTTGATTCTTGTTTTTGCAACATGTTAATGT|TGCAATG|ACATGTTAATGTCATTGCAGGGTATCCAGTAAACTAAATT ========== Event 2547 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACTCTTGTTGTTGAATAAAAGCAAAGTTTAAAAAATATTT--TTTTCCTCCAAATTTCGGTCTGGAATGCCACCCAGGCCTCTCAATCTAGCTTTGAACTTGAGTCTAAAGAAAATATTTGATCTTCTTTGTCTTTCAACTTGACAAAATGTTCTT---CTTTTTTGAAATCCCCCTTTATAAAACACATTGACAAGCACACTTTGTTTTAAGTGTGCTTGTCAATGTGTTTTATAAAGATAAAGCTCTTAGAAG ↑ 4 1 3 2 Chimp: AACTCTTGTTGTTGAATAAAAGCAAAGTTTAAAAAATAttt-tttttCCTCCAAATTTCAGTCTGGAATGCCACCCAGGCCTCTCAATCTAGCTTTGAACTTGAGTCTAAAGAAAATATTTGATCTTCTTTGTCTTTCAACTTGACAAAATGTT---CTTCTTTTTTGAAATCCCCCT------------------------TTTTGTTTTAAGTGAGCTTGTCAATGTGTTTTATAAAGGTAAATCTCTTAGAAG Gorilla: AACTCTTGTTGTTGAATAAAAGCAAAGTTTAAAAAATAttt-tttttCCTCCAAATTTCAGTCTGGAATGCCACCCAGGCCTCTCAATCTAGCTTTGAACTTGAGTCTAAAGAAAATATTTGAtcttttttgtctttcaactcgacaaaatgttctt---cttttttgaaatccccct------------------------ttttgttttAAGTGTGCTTGTCAATGTGTTTTATAAAGGTAAAGCTCTTAGAAA Human: AACTCTTGTTGTTGAATAAAAGCAAAGTTTAAAAAATATTT--TTTTCCTCCAAATTTCGGTCTGGAATGCCACCCAGGCCTCTCAATCTAGCTTTGAACTTGAGTCTAAAGAAAATATTTGATCTTCTTTGTCTTTCAACTTGACAAAATGTTCTT---CTTTTTTGAAATCCCCCTTTATAAAACACATTGACAAGCACACTTTGTTTTAAGTGTGCTTGTCAATGTGTTTTATAAAGATAAAGCTCTTAGAAG Cluster: [ ] Orangutan: AACTCTTGTTGTTGAATAAAAGCAAAGTTTAAAAAATAtttttttttCCTCCAAATTTCGGTCTGGAATGCCCCCCAGGCCTCTCAATCTAGCTTTGAACTTGAGTCTAAAGAAAATATTTGATCTTCTTTATCTTTCAACTTGACAAAATGTTCTT---CGTTTTTGAAATCCCCCT------------------------TTTTGTTTTAAGTGTGCTTGTCAATGTGTTTTATAAAGGTAAAGCTCTTAGAGG Chimp > Human ------------- chr4:141247217-141247231 Template switch process: F1: L AAATATTTGATCTTCTTTGTCTTTCAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCTTT 1 F3: 4 AAGCA R RF: AAATATTTGATCTTCTTTGTCTTTCAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCTTTAAGTTTAAAAAATATTTTTTTTCCTCCAAATTTCAGTCTGGAATGCCACCCAGGCCTCTCAATCTAGCTTTGAACTTGAGTCTAAAGAAAATATTTGATCTTCTTTGTCTTTCAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCTTTTTGTTTTAAGTGAGCTTGTCAATGTGTTTTAT RR: TTTATAAACTAGAAGAAACAGAAAGTTGAACTGTTTTACAAGAAGAAAAAACTTTAGGGGGAAATTCAAATTTTTTATAAAAAAAAGGAGGTTTAAAGTCAGACCTTACGGTGGGTCCGGAGAGTTAGATCGAAACTTGAACTCAGATTTCTTTTATAAACTAGAAGAAACAGAAAGTTGAACTGTTTTACAAGAAGAAAAAACTTTAGGGGGAAAAACAAAATTCACTCGAACAGTTACACAAAATA F2: 3 CAGTTACACAAAATA 2 Unidirectional alignment (log-probability: -39.4) CAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCTttataaaacacattgacaagca CAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCT---------------------- Template switch alignment (log-probability: -16.9) CAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCTTT|ATAAAACACATTGAC|AAGCA CAACTTGACAAAATGTTCTTCTTTTTTGAAATCCCCCTTT|ATAAAACACATTGAC|AAGCA ========== Event 2548 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAGTAACAACATTATATCATGGT--TACTGTCTACCAGTCTTCTTCAGGA Chimp: AGGAGTAACAACATTATATCATGGT--TACTGTCTACCAGTCTTCTTCAGGA ↓ 1 3 42 Gorilla: AGGAGTAACAACATTATATCACAGT----ATGTCTACCAGTCTTCTTCAGGA ↑ 1 3 42 Human: AGGAGTAACAACATTATATCATGGT--TACTGTCTACCAGTCTTCTTCAGGA Cluster: [ ] Orangutan: AGGAGTAACAACATTATATCATGGTTA--CTGTCTACCAGTCTTCTTCAGGA Human > Gorilla --------------- chr4:189433162-189433166 Template switch process: F1: L AACTCAAACCATGGCATAATAGGAGTAACAACATTATATCA 1 F3: 4 TGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATCC R RF: AACTCAAACCATGGCATAATAGGAGTAACAACATTATATCATGGTTACTGTCTACCAGTCTTCTTCAGGAGCTGCCTGACCCCTATCC RR: TTGAGTTTGGTACCGTATTATCCTCATTGTTGTAATATAGTACCAATGACAGATGGTCAGAAGAAGTCCTCGACGGACTGGGGATAGG F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -32.2) ACTCAAACCATGGCATAATAGGAGTAACAACATTATATC------ACagtaTGTCTACCAGTCTTCTTCAGGAGtTGCCTGACCCCTATCC ACTCAAACCATGGCATAATAGGAGTAACAACATTATATCATGGTTAC----TGTCTACCAGTCTTCTTCAGGAGCTGCCTGACCCCTATCC Template switch alignment (log-probability: -21.9) ACTCAAACCATGGCATAATAGGAGTAACAACATTATATCA|CAGTA|TGTCTACCAGTCTTCTTCAGGAGtTGCCTGACCCCTATCC ACTCAAACCATGGCATAATAGGAGTAACAACATTATATCA|CAGTA|TGTCTACCAGTCTTCTTCAGGAGCTGCCTGACCCCTATCC Chimp > Gorilla --------------- chr4:189433162-189433166 Template switch process: F1: L AACTCAAACCATGGCATAATAGGAGTAACAACATTATATCA 1 F3: 4 TGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATCC R RF: AACTTAAACCATGGCATAATAGGAGTAACAACATTATATCATGGTTACTGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATTC RR: TTGAATTTGGTACCGTATTATCCTCATTGTTGTAATATAGTACCAATGACAGATGGTCAGAAGAAGTCCTCAACGGACTGGGGATAAG F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -37.7) ACTcAAACCATGGCATAATAGGAGTAACAACATTATATC------ACagtaTGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATcC ACTTAAACCATGGCATAATAGGAGTAACAACATTATATCATGGTTAC----TGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATTC Template switch alignment (log-probability: -27.4) ACTcAAACCATGGCATAATAGGAGTAACAACATTATATCA|CAGTA|TGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATcC ACTTAAACCATGGCATAATAGGAGTAACAACATTATATCA|CAGTA|TGTCTACCAGTCTTCTTCAGGAGTTGCCTGACCCCTATTC ========== Event 2549 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACATGGATTGTGTGCCTCTTACTAC---------TTGAGGCTCCTCGCCTGGTGAGTAG Chimp: ACATGGATTGTGTGCCTCTTACTAC---------TTGAGGCTCCTCGCCTGGTGAGTAG ↓ 3 1 42 Gorilla: ACATGGATTGTGTGCCTCTTACTACTCTCAAGTAGTAAGGCTCCTCGCCTGGTGAGTAG ↑ 3 1 42 Human: ACATGGATTGTGTGCCTCTTACTAC---------TTGAGGCTCCTCGCCTGGTGAGTAG Cluster: [ ] Orangutan: ----------------------------------------------------------- Human > Gorilla --------------- chr4:48577581-48577591 Template switch process: F1: L CTGATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT 1 F3: 4 AGGCTCCTCGCCTGGTGAGTAGTCTTTTTCTGTGAGATCC R RF: CTGATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACTTGAGGCTCCTCGCCTGGTGAGTAGTCCTTTTCTGTGGGATCC RR: GACTAGGACAACCGTGTGTACCTAACACACGGAGAATGATGAACTCCGAGGAGCGGACCACTCATCAGGAAAAGACACCCTAGG F2: 3 ATGATGAACTC 2 Unidirectional alignment (log-probability: -40.4) GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACTctcaagtagTaAGGCTCCTCGCCTGGTGAGTAGTCtTTTTCTGTGaGATCC GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT---------TGAGGCTCCTCGCCTGGTGAGTAGTCCTTTTCTGTGGGATCC Template switch alignment (log-probability: -28.2) GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT|CTCAAGTAGTA|AGGCTCCTCGCCTGGTGAGTAGTCtTTTTCTGTGaGATCC GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT|CTCAAGTAGTA|AGGCTCCTCGCCTGGTGAGTAGTCCTTTTCTGTGGGATCC Chimp > Gorilla --------------- chr4:48577581-48577591 Template switch process: F1: L CTGATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT 1 F3: 4 AGGCTCCTCGCCTGGTGAGTAGTCTTTTTCTGTGAGATCC R RF: CTGATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACTTGAGGCTCCTCGCCTGGTGAGTAGTCCTTTTCTGTGGGATCC RR: GACTAGGACAACCGTGTGTACCTAACACACGGAGAATGATGAACTCCGAGGAGCGGACCACTCATCAGGAAAAGACACCCTAGG F2: 3 ATGATGAACTC 2 Unidirectional alignment (log-probability: -40.4) GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACTctcaagtagTaAGGCTCCTCGCCTGGTGAGTAGTCtTTTTCTGTGaGATCC GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT---------TGAGGCTCCTCGCCTGGTGAGTAGTCCTTTTCTGTGGGATCC Template switch alignment (log-probability: -28.2) GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT|CTCAAGTAGTA|AGGCTCCTCGCCTGGTGAGTAGTCtTTTTCTGTGaGATCC GATCCTGTTGGCACACATGGATTGTGTGCCTCTTACTACT|CTCAAGTAGTA|AGGCTCCTCGCCTGGTGAGTAGTCCTTTTCTGTGGGATCC ========== Event 2550 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGATGATGAAACTCCTCACCTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGA--------------------------------------------------------------------------------------TCTTGACTCAGATGATAAAAGCC ↓ 3 4 2 1 Chimp: GGATGATGAAACTCCTCACCTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCTACCTTCAGCCCATTGTTGACAGTCAGGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCTTGACTCAGATGATAAAAGCC ↑ 3 4 2 1 Gorilla: GGATGATGAAACTCCTCACCTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGA--------------------------------------------------------------------------------------TCTTGACTCAGATGATAAAAGCC Human: GGATGATGAAACTCCTCACCTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGA--------------------------------------------------------------------------------------TCTTGACTCAGATGATAAAAGCC Cluster: [ ] Orangutan: GGATGATGAAACTCCTCAGCTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGA--------------------------------------------------------------------------------------TCTTGACTCAGATGATAAGAGCC Human > Chimp ------------- chr4:47374332-47374357 Template switch process: F1: L CACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCT 1 F3: 4 GAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCTTGACTCAGATGATAAAAGCCTCAGTTTTGTCCTCCAT R RF: CTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCTTGACTCAGATGATAAAAGCCTCAGTTTTGTCCTCCAT RR: GACTGACAGTTGTTACCCGACTTCCATCTCTTTCCTGTGAGACTCTAGTAGTGTTTAGCCTAGGAGTTCCGGTGTCTAGAACTGAGTCTACTATTTTCGGAGTCAAAACAGGAGGTA F2: 3 GACTGACAGTTGTTACCCGACTTCCA 2 Unidirectional alignment (log-probability: -129) ctgagatcatcacaaatcggatcctcaaggccacagatctaccttcagcccattgttgacagtcaggaaggtagagaaaggaCACTCTGAGATCATCACAAATCGG ----------------------------------------------------------------------------------CACTCTGAGATCATCACAAATCGG Template switch alignment (log-probability: -19.5) CTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCT|ACCTTCAGCCCATTGTTGACAGTCAG|GAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGG CTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCT|ACCTTCAGCCCATTGTTGACAGTCAG|GAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGG Gorilla > Chimp --------------- chr4:47374332-47374357 Template switch process: F1: L CACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCT 1 F3: 4 GAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCTTGACTCAGATGATAAAAGCCTCAGTTTTGTCCTCCAT R RF: CTGACTGTCAACAATGGGCTGAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCTTGACTCAGATGATAAAAGCCTCAGTTTTGTCCTCCAT RR: GACTGACAGTTGTTACCCGACTTCCATCTCTTTCCTGTGAGACTCTAGTAGTGTTTAGCCTAGGAGTTCCGGTGTCTAGAACTGAGTCTACTATTTTCGGAGTCAAAACAGGAGGTA F2: 3 GACTGACAGTTGTTACCCGACTTCCA 2 Unidirectional alignment (log-probability: -129) ctgagatcatcacaaatcggatcctcaaggccacagatctaccttcagcccattgttgacagtcaggaaggtagagaaaggaCACTCTGAGATCATCACAAATCGG ----------------------------------------------------------------------------------CACTCTGAGATCATCACAAATCGG Template switch alignment (log-probability: -20.3) CTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCT|ACCTTCAGCCCATTGTTGACAGTCAG|GAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGG CTGAGATCATCACAAATCGGATCCTCAAGGCCACAGATCT|ACCTTCAGCCCATTGTTGACAGTCAG|GAAGGTAGAGAAAGGACACTCTGAGATCATCACAAATCGG ========== Event 2551 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ACTCAGAGCTTTGAGGTCTTGGATGCTGAATGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGG ↑ 4 1 3 2 Chimp: ACTCAGAGCTTTGAGGTCTTG-----------GATGGTGGTATTATTCAGATTAGAATGGACATCAAGGG ↓ 4 1 3 2 Gorilla: ACTCAGAGCTTTGAGGTCTTGGATGCTGAATGGATGGTGGTATTATTCAGATTAGAACGGACATCAAGGA Human: ACTCAGAGCTTTGAGGTCTTGGATGCTGAATGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGG Cluster: [ ] Orangutan: ACTCAGAGCTTTGAGGTCTTGGATGCTGAATGGATGGTGGCATTATTCAGATTAGAACGGACATCAAGGG Chimp > Human ------------- chr4:144594697-144594702 Template switch process: F1: L GAGAGGAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATG 1 F3: 4 GGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGGA R RF: GAGAGGAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGGA RR: CTCTCCTCCCTACCTCCTACTGAGTCTCGAAACTCCAGAACCTACCACCATAATAAGTCTAATCTTACCTGTAGTTCCCCT F2: 3 TAAGTC 2 Unidirectional alignment (log-probability: -26.7) GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTtggatgctgaaTGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGG GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCT-----------TGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGG Template switch alignment (log-probability: -16.1) GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATG|CTGAAT|GGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGG GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATG|CTGAAT|GGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGG Chimp > Gorilla --------------- chr4:156815529-156815534 Template switch process: F1: L GAGAGGAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATG 1 F3: 4 GGATGGTGGTATTATTCAGATTAGAACGGACATCAAGGAGA R RF: GAGAGGAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGGA RR: CTCTCCTCCCTACCTCCTACTGAGTCTCGAAACTCCAGAACCTACCACCATAATAAGTCTAATCTTACCTGTAGTTCCCCT F2: 3 TAAGTC 2 Unidirectional alignment (log-probability: -37.7) GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTtggatgctgaaTGGATGGTGGTATTATTCAGATTAGAAcGGACATCAAGGaG GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCT-----------TGGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGG Template switch alignment (log-probability: -27.6) GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATG|CTGAAT|GGATGGTGGTATTATTCAGATTAGAAcGGACATCAAGGaG GAGGGATGGAGGATGACTCAGAGCTTTGAGGTCTTGGATG|CTGAAT|GGATGGTGGTATTATTCAGATTAGAATGGACATCAAGGGG ========== Event 2552 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAGA----GGCCCAAGTCTCTCCTAGCCTCAG Chimp: ATCCAGCCACATGGAGAGGCCAGTTACTCTGAACAGA----GGCCCAAGTCTCTCCTAGCCTCAG ↓ 3 2 1 4 Gorilla: ATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAGT-AACTGGCCAAGTCTCTCCTAGCCTCAG ↑ 3 2 1 4 Human: ATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAGA----GGCCCAAGTCTCTCCTAGCCTCAG Cluster: [ ] Orangutan: GTCCAGCCACATGGAGAGGCCAGTTACTCTGAACAGAG---GGCCCAAGTTTCTCCTAGCCTCAG Human > Gorilla --------------- chr4:158296097-158296103 Template switch process: F1: L AGGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAG 1 F3: 4 CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTCAAA R RF: AGGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAGAGGCCCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTAAAA RR: TCCAATAGGTCGGTGCACCTCTCCGGTCAATGAGACTTGTCTCCGGGTTCAGAGAGGATCGGAGTCTGGGAGATCCTTTCATTTT F2: 3 GGTCAAT 2 Unidirectional alignment (log-probability: -36.4) GGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAG----taactggCCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTcAAA GGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAGAGGC-------CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTAAAA Template switch alignment (log-probability: -22.1) GGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAG|TAACTGG|CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTcAAA GGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAG|TAACTGG|CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTAAAA Chimp > Gorilla --------------- chr4:158296097-158296103 Template switch process: F1: L AGGTTATCCAGCCACGTGGAGAGGCCAGTTACTCTGAACAG 1 F3: 4 CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTCAAA R RF: AGGTTATCCAGCCACATGGAGAGGCCAGTTACTCTGAACAGAGGCCCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTAAAA RR: TCCAATAGGTCGGTGTACCTCTCCGGTCAATGAGACTTGTCTCCGGGTTCAGAGAGGATCGGAGTCTGGGAGATCCTTTCATTTT F2: 3 GGTCAAT 2 Unidirectional alignment (log-probability: -41.9) GGTTATCCAGCCACgTGGAGAGGCCAGTTACTCTGAACAG----taactggCCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTcAAA GGTTATCCAGCCACATGGAGAGGCCAGTTACTCTGAACAGAGGC-------CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTAAAA Template switch alignment (log-probability: -27.7) GGTTATCCAGCCACgTGGAGAGGCCAGTTACTCTGAACAG|TAACTGG|CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTcAAA GGTTATCCAGCCACATGGAGAGGCCAGTTACTCTGAACAG|TAACTGG|CCAAGTCTCTCCTAGCCTCAGACCCTCTAGGAAAGTAAAA ========== Event 2553 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCATTTTAAGGGGAAAATGGCAAGGGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCT---------------------------------TCTATTTCTCTCCTTTTTCCAAGTATCCAGCAAGGCCA ↓ 3 2 4 1 Chimp: TTTCATTTTAAGGGGAAAATGGCAAGGGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTTTGCCAACCATCCTCTTCTATTTCTCTCCTTTTCCCAAGTATCCAGCAAGGCCA ↑ 3 2 4 1 Gorilla: TTTCATTTTAAGGGGAAAATGGCAAGCGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCT---------------------------------TCTATTTCTCTCCTTTTTCCAAGTATCCAGCAAGGCCA Human: TTTCATTTTAAGGGGAAAATGGCAAGGGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCT---------------------------------TCTATTTCTCTCCTTTTTCCAAGTATCCAGCAAGGCCA Cluster: [ ] Orangutan: TTTCATTTTAAGGGGAAAATGGCAAGGGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCTGACCACCCTCT---------------------------------TCTATTTCTCTCCTTTTTCCAAGTATCCAGAAAGGCCA Human > Chimp ------------- chr4:45279334-45279338 Template switch process: F1: L ATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT 1 F3: 4 ACCATCCTCTTCTATTTCTCTCCTTTTCCCAAGTATCCAGCAAGGCCACC R RF: TGGCAAGGGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTTCCAAGTATCCAGCAAGGCCACC RR: ACCGTTCCCCTATCTTGTATATAAACTCTCTTTCGTTAGAGACCAGACAAGAGACCGGAAAACTATAGATCGTGGTTTCTCCGACTTTCATTTTGGTTTAATTAGTCGGACTCTAGTAATGTATTCGGCTGGTAGGAGAAGATAAAGAGAGGAAAAAGGTTCATAGGTCGTTCCGGTGG F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -58.4) TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTTtgccaaccatcctcttctatttctctccttttcCCAAGTATCCAG TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT---------------------------------CCAAGTATCCAG Template switch alignment (log-probability: -22.4) TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT|TGCCA|ACCATCCTCTTCTATTTCTCTCCTTTTcCCAAGTATCCAG TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT|TGCCA|ACCATCCTCTTCTATTTCTCTCCTTTTTCCAAGTATCCAG Gorilla > Chimp --------------- chr4:45279334-45279338 Template switch process: F1: L ATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT 1 F3: 4 ACCATCCTCTTCTATTTCTCTCCTTTTCCCAAGTATCCAGCAAGGCCACC R RF: TGGCAAGCGGATAGAACATATATTTGAGAGAAAGCAATCTCTGGTCTGTTCTCTGGCCTTTTGATATCTAGCACCAAAGAGGCTGAAAGTAAAACCAAATTAATCAGCCTGAGATCATTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTTCCAAGTATCCAGCAAGGCCACC RR: ACCGTTCGCCTATCTTGTATATAAACTCTCTTTCGTTAGAGACCAGACAAGAGACCGGAAAACTATAGATCGTGGTTTCTCCGACTTTCATTTTGGTTTAATTAGTCGGACTCTAGTAATGTATTCGGCTGGTAGGAGAAGATAAAGAGAGGAAAAAGGTTCATAGGTCGTTCCGGTGG F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -58.3) TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTTtgccaaccatcctcttctatttctctccttttcCCAAGTATCCAG TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT---------------------------------CCAAGTATCCAG Template switch alignment (log-probability: -22.6) TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT|TGCCA|ACCATCCTCTTCTATTTCTCTCCTTTTcCCAAGTATCCAG TTACATAAGCCGACCATCCTCTTCTATTTCTCTCCTTTTT|TGCCA|ACCATCCTCTTCTATTTCTCTCCTTTTTCCAAGTATCCAG ========== Event 2554 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCATCCTTCAATTCTCTGAGCTA--------------------TTCCAGTATTCTTTCAATTAAGCTCAAATT Chimp: ACCATCCTTCAATTCTCTGAGCTA--------------------TTCCAGTATTCTTTCAATTAAGCTCAAATT ↓ 4 3 1 2 Gorilla: ACCATCCTTCAATTCTCTGAGCTATTCCAGAATACTGGAAGCTATTCCAGTATTCTTTCAATTAAGCTCAAATT ↑ 4 3 1 2 Human: ACCATCCTTCAATTCTCTGAGCTA--------------------TTCCAGTATTCTTTCAATTAAGCTCAAATT Cluster: [ ] Orangutan: ACCATCCTTCAATTCTCTGAGCTA--------------------TTCCAGTATTCTTTCAATTAAGCTCAAATT Human > Gorilla --------------- chr4:45544780-45544788 Template switch process: F1: L TCCTGTAGTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAG 1 F3: 4 AGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACTGAAAC R RF: TCCTGTAGTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACTGAAAC RR: AGGACATCAAGGACTCTTGGTAGGAAGTTAAGAGACTCGATAAGGTCATAAGAAAGTTAATTCGAGTTTAAAATGACTTTG F2: 3 AGGTCATAA 2 Unidirectional alignment (log-probability: -39.6) GTTCCTGAGAACCATCCTTCAATTCTCTGAGCtattccagaatactggaagcTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT GTTCCTGAGAACCATCCTTCAATTCTCTGAGC--------------------TATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT Template switch alignment (log-probability: -17.1) GTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAG|AATACTGGA|AGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT GTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAG|AATACTGGA|AGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT Chimp > Gorilla --------------- chr4:45544780-45544788 Template switch process: F1: L TCCTGTAGTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAG 1 F3: 4 AGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACTGAAAC R RF: TCCTGTAGTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACTGAAAC RR: AGGACATCAAGGACTCTTGGTAGGAAGTTAAGAGACTCGATAAGGTCATAAGAAAGTTAATTCGAGTTTAAAATGACTTTG F2: 3 AGGTCATAA 2 Unidirectional alignment (log-probability: -39.6) GTTCCTGAGAACCATCCTTCAATTCTCTGAGCtattccagaatactggaagcTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT GTTCCTGAGAACCATCCTTCAATTCTCTGAGC--------------------TATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT Template switch alignment (log-probability: -17.1) GTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAG|AATACTGGA|AGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT GTTCCTGAGAACCATCCTTCAATTCTCTGAGCTATTCCAG|AATACTGGA|AGCTATTCCAGTATTCTTTCAATTAAGCTCAAATTTTACT ========== Event 2555 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGAAGATTAAAAACTATTTA--------GACCCTTTTCAAGTCTCCATTATGGCTA ↓ 3 4 2 Chimp: GGGAAGATTAAAAACTATTTAAAAGGGTCTACCCTTTTCAAGTCTCCATTATGGCTG ↑ 3 4 2 Gorilla: GGGAAGTTTAAAAACTATTTA--------GACCCTTTTCAAGTCTCCATTATGGCTA Human: GGGAAGATTAAAAACTATTTA--------GACCCTTTTCAAGTCTCCATTATGGCTA Cluster: [ ] Orangutan: GGGAAGATTAAAAACTATTTA--------GACCCTTTTCAAGTCTCCATTATGGCTA Human > Chimp ------------- chr4:43855473-43855481 Template switch process: F1: L CTTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTA 1 F3: 4 ACCCTTTTCAAGTCTCCATTATGGCTGAAAAACAATCCTT R RF: CTTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTAGACCCTTTTCAAGTCTCCATTATGGCTAAAAAACAATCCTT RR: GAAAGACATAATTCTTTTGTCCCTTCTAATTTTTGATAAATCTGGGAAAAGTTCAGAGGTAATACCGATTTTTTGTTAGGAA F2: 3 TCTGGGAAA 2 Unidirectional alignment (log-probability: -34.4) TTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTAaaagggtctACCCTTTTCAAGTCTCCATTATGGCTgAAAAACAATCCTT TTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTA--------GACCCTTTTCAAGTCTCCATTATGGCTAAAAAACAATCCTT Template switch alignment (log-probability: -22.4) TTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTA|AAAGGGTCT|ACCCTTTTCAAGTCTCCATTATGGCTgAAAAACAATCCTT TTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTA|AAAGGGTCT|ACCCTTTTCAAGTCTCCATTATGGCTAAAAAACAATCCTT Gorilla > Chimp --------------- chr4:43855473-43855481 Template switch process: F1: L CTTTCTGTATTAAGAAAACAGGGAAGATTAAAAACTATTTA 1 F3: 4 ACCCTTTTCAAGTCTCCATTATGGCTGAAAAACAATCCTT R RF: CTTTCTGTATTAAGAAAACAGGGAAGTTTAAAAACTATTTAGACCCTTTTCAAGTCTCCATTATGGCTAAAAAACAATCCTT RR: GAAAGACATAATTCTTTTGTCCCTTCAAATTTTTGATAAATCTGGGAAAAGTTCAGAGGTAATACCGATTTTTTGTTAGGAA F2: 3 TCTGGGAAA 2 Unidirectional alignment (log-probability: -39) TTTCTGTATTAAGAAAACAGGGAAGaTTAAAAACTATTTAaaagggtctACCCTTTTCAAGTCTCCATTATGGCTgAAAAACAATCCTT TTTCTGTATTAAGAAAACAGGGAAGTTTAAAAACTATTTA--------GACCCTTTTCAAGTCTCCATTATGGCTAAAAAACAATCCTT Template switch alignment (log-probability: -27.9) TTTCTGTATTAAGAAAACAGGGAAGaTTAAAAACTATTTA|AAAGGGTCT|ACCCTTTTCAAGTCTCCATTATGGCTgAAAAACAATCCTT TTTCTGTATTAAGAAAACAGGGAAGTTTAAAAACTATTTA|AAAGGGTCT|ACCCTTTTCAAGTCTCCATTATGGCTAAAAAACAATCCTT ========== Event 2556 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGAAAGCCATTTATACAGAAAC--GTGAGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTTCTCAGTGAATTAAAG Chimp: AGAAAGCCATTTATACAGAAAC--GTGAGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTTCTCAGTGAATTAAAG ↑ 1 4 3 2 Gorilla: AGAAAGCCATTTATACAGAAATCCTGTTGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTTCTCAGTGAATTAAAG ↓ 1 4 3 2 Human: AGAAAGCCATTTATACAGAAAC--GTGAGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTTCTCAGTGAATTAAAG Cluster: [ ] Orangutan: AGAAAGCCATTTATATAGAAAC--ATGAGCACCCTGCTGCAACTTTACCTAAACATTCTCACGAACTTCTCAGTGAATTAAAG Gorilla > Human --------------- chr4:43086188-43086192 Template switch process: F1: L ATAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA 1 F3: 4 GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT R RF: ATAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAATCCTGTTGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT RR: TATTTTAAAGACCACTATCTTCTTTCGGTAAATATGTCTTTAGGACAACGTGGGACAACGTTGAAATGGATTTGTAAGAGTGCTTGAA F2: 3 AGTGC 2 Unidirectional alignment (log-probability: -28.2) TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA-------cgtgaGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAATCCTGTT-----GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT Template switch alignment (log-probability: -16.4) TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA|CGTGA|GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA|CGTGA|GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT Gorilla > Chimp --------------- chr4:43657553-43657557 Template switch process: F1: L ATAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA 1 F3: 4 GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT R RF: ATAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAATCCTGTTGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT RR: TATTTTAAAGACCACTATCTTCTTTCGGTAAATATGTCTTTAGGACAACGTGGGACAACGTTGAAATGGATTTGTAAGAGTGCTTGAA F2: 3 AGTGC 2 Unidirectional alignment (log-probability: -28.2) TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA-------cgtgaGCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAATCCTGTT-----GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT Template switch alignment (log-probability: -16.4) TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA|CGTGA|GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT TAAAATTTCTGGTGATAGAAGAAAGCCATTTATACAGAAA|CGTGA|GCACCCTGTTGCAACTTTACCTAAACATTCTCACGAACTT ========== Event 2557 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGACATTATTTAGAGTTCCCCAGATCTTCCAGGGATACTCTTAATTTATAGGAAAATTT Chimp: AGGACATTATTTAGAGTTCCCTGGATCTTCCAGGGATACTCTTAATTTATAGGAAAATTT ↑ 3 1 2 4 Gorilla: AGGACATTATTCAGAGTTCCCTGGAAGATC-TCAGATACCCTTAATTTATAGGAAAATTT Human: AGGACATTATTTAGAGTTCCCCAGATCTTCCAGGGATACTCTTAATTTATAGGAAAATTT Cluster: [ ] Orangutan: AGAACATTATTTAGAGTCCCCTGGAAGATC-TCAGATACTCTTAATTTATAGGAAAATTG Gorilla > Chimp --------------- chr4:42170499-42170507 Template switch process: F1: L ACATAAACAACTAGAAAGGACATTATTTAGAGTTCCCTGGA 1 F3: 4 GATACTCTTAATTTATAGGAAAATTTATTACCAGATCTATTTAGAT R RF: ACATAAACAACTAGAAAGGACATTATTCAGAGTTCCCTGGAAGATCTCAGATACCCTTAATTTATAGGAAAATTTATTACCAGATCTATTTAGAT RR: TGTATTTGTTGATCTTTCCTGTAATAAGTCTCAAGGGACCTTCTAGAGTCTATGGGAATTAAATATCCTTTTAAATAATGGTCTAGATAAATCTA F2: 3 GGACCTTCT 2 Unidirectional alignment (log-probability: -45.1) CATAAACAACTAGAAAGGACATTATTtAGAGTTCCCTGG--------AtcttccaggGATACtCTTAATTTATAGGAAAATTTATTACCAGATCTAT CATAAACAACTAGAAAGGACATTATTCAGAGTTCCCTGGAAGATCTCA---------GATACCCTTAATTTATAGGAAAATTTATTACCAGATCTAT Template switch alignment (log-probability: -28.1) CATAAACAACTAGAAAGGACATTATTtAGAGTTCCCTGGA|TCTTCCAGG|GATACtCTTAATTTATAGGAAAATTTATTACCAGATCTAT CATAAACAACTAGAAAGGACATTATTCAGAGTTCCCTGGA|TCTTCCAGG|GATACCCTTAATTTATAGGAAAATTTATTACCAGATCTAT ========== Event 2558 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGATAGACTCCCTTGTTACT--TGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA Chimp: ATGATAGACTCCCTTGTTACT--TGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA ↓ 1 4 3 2 Gorilla: ATGATAGACTCCCTTGTTACT----CAGTTGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA ↑ 1 4 3 2 Human: ATGATAGACTCCCTTGTTACT--TGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA Cluster: [ ] Orangutan: ATGATAGACTCCCTTGATACTTG--A--AAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA Human > Gorilla --------------- chr4:41830109-41830113 Template switch process: F1: L TTTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACT 1 F3: 4 GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA R RF: TTTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACTTGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA RR: AAACATCGTAACTTTGAAAATACTATCTGAGGGAACAATGAACTTTCTCGAGTGTTACATCGTTTGACTCATTTAAGTAACTAGTAGT F2: 3 TTGAC 2 Unidirectional alignment (log-probability: -26.7) TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACtcagTT------GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTAC----TTGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA Template switch alignment (log-probability: -16.4) TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACT|CAGTT|GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACT|CAGTT|GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA Chimp > Gorilla --------------- chr4:41830109-41830113 Template switch process: F1: L TTTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACT 1 F3: 4 GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA R RF: TTTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACTTGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA RR: AAACATCGTAACTTTGAAAATACTATCTGAGGGAACAATGAACTTTCTCGAGTGTTACATCGTTTGACTCATTTAAGTAACTAGTAGT F2: 3 TTGAC 2 Unidirectional alignment (log-probability: -26.7) TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACtcagTT------GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTAC----TTGAAAGAGCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA Template switch alignment (log-probability: -16.4) TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACT|CAGTT|GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA TTGTAGCATTGAAACTTTTATGATAGACTCCCTTGTTACT|CAGTT|GCTCACAATGTAGCAAACTGAGTAAATTCATTGATCATCA ========== Event 2559 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGGTCTGAGGGAAGTTAAGTGAC-----TAGCTCCGTCAATTAGGGACTGAGTTGTGACTTCAGGA Chimp: CTGGCCTGAGGGAAGTTAAGTCCCTAATTGAGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGA ↑ 1 4 3 2 Gorilla: CTGGCCTGAGGGAAGTTAAGTGAC-----TAGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGA Human: CTGGTCTGAGGGAAGTTAAGTGAC-----TAGCTCCGTCAATTAGGGACTGAGTTGTGACTTCAGGA Cluster: [ ] Orangutan: CTGGCCTGAGGGAAGTTAAGTGAC-----TAGCCCCATCAATTAGGGACTGAGTTGTGACTTCAGGA Gorilla > Chimp --------------- chr4:41816857-41816865 Template switch process: F1: L TCAATTGAACAAAAGGAAAGCTGGCCTGAGGGAAGTTAAGT 1 F3: 4 AGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGATCT R RF: TCAACTGAACAAAAGGAAAGCTGGCCTGAGGGAAGTTAAGTGACTAGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGATCT RR: AGTTGACTTGTTTTCCTTTCGACCGGACTCCCTTCAATTCACTGATCGGGGCAGTTAATCCCTGACTCAACACTGAAGTCCTAGA F2: 3 GTTAATCCC 2 Unidirectional alignment (log-probability: -34.7) CAAtTGAACAAAAGGAAAGCTGGCCTGAGGGAAGTTAAGTccCTaattgAGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGATCT CAACTGAACAAAAGGAAAGCTGGCCTGAGGGAAGTTAAGTGACT-----AGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGATCT Template switch alignment (log-probability: -22.4) CAAtTGAACAAAAGGAAAGCTGGCCTGAGGGAAGTTAAGT|CCCTAATTG|AGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGATCT CAACTGAACAAAAGGAAAGCTGGCCTGAGGGAAGTTAAGT|CCCTAATTG|AGCCCCGTCAATTAGGGACTGAGTTGTGACTTCAGGATCT ========== Event 2560 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAGCTGACTTGAATCCTAGTCAAGAGCTTCA ↑ 3 2 1 4 Chimp: ACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAAC------CAATCCTAGTCAAGAGCTTCA Gorilla: ACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAAC------CAATCCTAATCAAGAGCTTCA Human: ACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAGCTGACTTGAATCCTAGTCAAGAGCTTCA Cluster: [ ] Orangutan: ACAAGGTTGGCCTTATTCCAAGTCAGCAGTGAAGAAC------CAATCCTAGTCAAGAGCTTCA Chimp > Human ------------- chr4:42047299-42047306 Template switch process: F1: L CATAGCACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGA 1 F3: 4 GAATCCTAGTCAAGAGCTTCACTGGAGTGACAGCCATGGGC R RF: CATAGCACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAACCAATCCTAGTCAAGAGCTTCACTGGAGTGACAGCCATGGGC RR: GTATCGTGTTCCAACCGGAATAAGATTCAGTCGTCACTTCTTGGTTAGGATCAGTTCTCGAAGTGACCTCACTGTCGGTACCCG F2: 3 TTCAGTCG 2 Unidirectional alignment (log-probability: -31.6) ATAGCACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAgCtgacttgAATCCTAGTCAAGAGCTTCACTGGAGTGACAGCCATGGG ATAGCACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGAAC------CAATCCTAGTCAAGAGCTTCACTGGAGTGACAGCCATGGG Template switch alignment (log-probability: -22.3) ATAGCACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGA|GCTGACTT|gAATCCTAGTCAAGAGCTTCACTGGAGTGACAGCCATGGG ATAGCACAAGGTTGGCCTTATTCTAAGTCAGCAGTGAAGA|GCTGACTT|CAATCCTAGTCAAGAGCTTCACTGGAGTGACAGCCATGGG ========== Event 2561 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: GTTTCAGTTGCTAGCTTCTTCATTTTACTCCTCTTAGCATGTGATGGCAAGGGCCTCAAAGCCTTCAGAAATGTTGGTTGAGTCTGAATTAAGGAAGCAGATGTTAAAAACCTTGTGTGTTGCACCTCTCCTTGGATTC-TACAATGAAGCTTTCATTTGATTTTTAGA Chimp: GTTTCAGTTGCTAGCTTCTTCATTTTACTCCTCTTAGCATGTGATGGCAAGGGCCTCAAAGCCTTCAGAAATGTTGGTTGAGTCTGAATTAAGGAAGCAGATGTTAAAAACCTTGTGTGTTGCATCTCTCCTTGGATTC-TACAATGAAGCTTTCATTTGATTTTTAGA Gorilla: GTTTCAGTTGCTAGCTTCTTCATTTTACTCCTCTTAGCATGTGATGGCAAGGGCCTCAAAGCCTTCAGAAATGTTGGTTGAGTCTGAATTAAGGAAGCAGATGTTAAAAACGTTGTGTGTTGCACCTCTCCTTGGATTCTTTCCAAGGAGCTTTCATTTGATTTTTAGA ↓ 3 2 1 4 ↑ 3 2 1 4 Human: GTTTCAGTTGCTAGCTTCTTCATTTTACTCCTCTTAGCATGTGATGGCAAGGGCCTCAAAGCCTTCAGAAATGTTGGTTGAGTCTGAATTAAGGAAGCAGATGTTAAAAACCTTGTGTGTTGCACCTCTCCTTGGATTC-TACAATGAAGCTTTCATTTGATTTTTAGA Cluster: [ ] Orangutan: GTTTCATTTGCTAGCTTCTTCACTTTACTCCTCTTAGCATGTGATGGCAAAGGCCTCAAAGCTTTCAGAAATGTTGGTTGAGTCTGAATTAAGGAAGCAGATGTTAAAAATCTTGTATGTTGCACCTCTCCTTGGATTC-TACATTGAAGCTTTCATTTGGTTTTTAGG Gorilla > Human --------------- chr4:41993679-41993685 Template switch process: F1: L AGATGTTAAAAACCTTGTGTGTTGCACCTCTCCTTGGATTCT 1 F3: 4 AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG R RF: TCATTTTACTCCTCTTAGCATGTGATGGCAAGGGCCTCAAAGCCTTCAGAAATGTTGGTTGAGTCTGAATTAAGGAAGCAGATGTTAAAAACGTTGTGTGTTGCACCTCTCCTTGGATTCTTTCCAAGGAGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG RR: AGTAAAATGAGGAGAATCGTACACTACCGTTCCCGGAGTTTCGGAAGTCTTTACAACCAACTCAGACTTAATTCCTTCGTCTACAATTTTTGCAACACACAACGTGGAGAGGAACCTAAGAAAGGTTCCTCGAAAGTAAACTAAAAATCTCTAACCAACTAACTGAAAC F2: 3 AGTAACA 2 Unidirectional alignment (log-probability: -36.6) ATGTTAAAAACcTTGTGTGTTGCACCTCTCCTTGGATTCT--------acaatgaAGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG ATGTTAAAAACGTTGTGTGTTGCACCTCTCCTTGGATTCTTTCCAAGG-------AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG Template switch alignment (log-probability: -27.7) ATGTTAAAAACcTTGTGTGTTGCACCTCTCCTTGGATTCT|AcAATGA|AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG ATGTTAAAAACGTTGTGTGTTGCACCTCTCCTTGGATTCT|AAAATGA|AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG Human > Gorilla --------------- chr4:42506424-42506430 Template switch process: F1: L AGATGTTAAAAACGTTGTGTGTTGCACCTCTCCTTGGATTCTT 1 F3: 4 AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG R RF: AGATGTTAAAAACCTTGTGTGTTGCACCTCTCCTTGGATTCTACAATGAAGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG RR: TCTACAATTTTTGGAACACACAACGTGGAGAGGAACCTAAGATGTTACTTCGAAAGTAAACTAAAAATCTCTAACCAACTAACTGAAAC F2: 3 GGAACCT 2 Unidirectional alignment (log-probability: -38) TGTTAAAAACgTTGTGTGTTGCACCTCTCCTTGGATTCT-------ttccaaggAGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG TGTTAAAAACCTTGTGTGTTGCACCTCTCCTTGGATTCTACAATGA--------AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG Template switch alignment (log-probability: -27.7) TGTTAAAAACgTTGTGTGTTGCACCTCTCCTTGGATTCTt|TCCAAGG|AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG TGTTAAAAACCTTGTGTGTTGCACCTCTCCTTGGATTCTA|TCCAAGG|AGCTTTCATTTGATTTTTAGAGATTGGTTGATTGACTTTG ========== Event 2562 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAACTGCAATATGGATGTAGGC----AGTTATAGAAGAGTTATAACTTGCATGTCTATGTACCAACTGCTCATTAACTTGCAAGGCAG Chimp: CAACTGCAATATGGATGTAGGA--GTCTTAATAGAAGAGTTATTACTTGCATGTCTATGAACCAACTGCTCATTAACTTGCAAGGCAG Gorilla: CAACTGCAATATGGATGTAGGAGT--CTTCATAGAAGAGTTATAACTTGCATGTCTATGAACCAACTGCTCATTAACTTGCAAGGCAG ↓ 1 4 3 2 Human: CAACTGCAATATGGATGTAGGC----AGTTATAGAAGAGTTATAACTTGCATGTCTATGTACCAACTGCTCATTAACTTGCAAGGCAG Cluster: [ ] Orangutan: CAACTGCAATATGGATGTAGGAGT--CTTAATAGAAGAGTTATAACTTGTATGTCTATGAACCAACTGCTCATTAACTTGCAAGGCAG Gorilla > Human --------------- chr4:175330610-175330614 Template switch process: F1: L TGGTTAATTTTCTGCCCTTTCAACTGCAATATGGATGTAGG 1 F3: 4 ATAGAAGAGTTATAACTTGCATGTCTATGTACCAACTGCT R RF: TGGTTAATTTTCTGCCCTTTCAACTGCAATATGGATGTAGGAGTCTTCATAGAAGAGTTATAACTTGCATGTCTATGAACCAACTGCT RR: ACCAATTAAAAGACGGGAAAGTTGACGTTATACCTACATCCTCAGAAGTATCTTCTCAATATTGAACGTACAGATACTTGGTTGACGA F2: 3 TTGAC 2 Unidirectional alignment (log-probability: -32.2) GGTTAATTTTCTGCCCTTTCAACTGCAATATGGATGTAGG------CagttATAGAAGAGTTATAACTTGCATGTCTATGtACCAACTGCT GGTTAATTTTCTGCCCTTTCAACTGCAATATGGATGTAGGAGTCTTC----ATAGAAGAGTTATAACTTGCATGTCTATGAACCAACTGCT Template switch alignment (log-probability: -21.9) GGTTAATTTTCTGCCCTTTCAACTGCAATATGGATGTAGG|CAGTT|ATAGAAGAGTTATAACTTGCATGTCTATGtACCAACTGCT GGTTAATTTTCTGCCCTTTCAACTGCAATATGGATGTAGG|CAGTT|ATAGAAGAGTTATAACTTGCATGTCTATGAACCAACTGCT ========== Event 2563 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: taattacaaCATTGTCATGTGCATGACACATGACAAGCaatataatttattaatatattaaGTCACTGGTTTTTTGTTGTTGTTCAAAATGTAGCTTTGTGGAAACCATCATGTCT-TATTTCAgacaagacc Chimp: taattacaaCATTGTCATGTGTCATGCACATGACAAGCAATATAATTTATTAATATATTAAGTCACTGGTTTTTTGTTGTTGTTCAAAATGTAGCTTTGTGGAAACCATCATGTCT-TATTTCAgacaagacc Gorilla: taattacaaCATTGTCATGTGTCGTGCACATGACAAGCAATATAATTTATTAATATATTAAGTCACTGGTTTTTTGTTGTCGTTCAAAATGTAGCTTTGTGGAAACCATCATGTCT-TATTTCAgacaagacc ↓ 1 4 3 2 Human: taattacaaCATTGTCATGTGCATGACACATGACAAGCaatataatttattaatatattaaGTCACTGGTTTTTTGTTGTTGTTCAAAATGTAGCTTTGTGGAAACCATCATGTCT-TATTTCAgacaagacc Cluster: [ ] Orangutan: taattacaaCATTGTCATGTGTCGTACACATGACAAGCAATATAATTTATTAATATATTAAGTCACTGGTTTTTTGTTGTTGTTCAAAATGTAGCTTTGTGGAAACCATCATGTCTTCATTTCAGACAAGACC Gorilla > Human --------------- chr4:149737960-149737964 Template switch process: F1: L ACTTTAATTACAATCACTTATAATTACAACATTGTCATGTG 1 F3: 4 CACATGACAAGCAATATAATTTATTAATATATTAAGTCAC R RF: ACTTTAATTACAATCACTTATAATTACAACATTGTCATGTGTCGTGCACATGACAAGCAATATAATTTATTAATATATTAAGTCACTGGTTTTTTGTTGTCGTTCAAAATGTAGCTTTGTGGAAACCATCATG RR: TGAAATTAATGTTAGTGAATATTAATGTTGTAACAGTACACAGCACGTGTACTGTTCGTTATATTAAATAATTATATAATTCAGTGACCAAAAAACAACAGCAAGTTTTACATCGAAACACCTTTGGTAGTAC F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -27.7) CTTTAATTACAATCACTTATAATTACAACATTGTCATGTG-CaTGaCACATGACAAGCAATATAATTTATTAATATATTAAGTCAC CTTTAATTACAATCACTTATAATTACAACATTGTCATGTGTCGTG-CACATGACAAGCAATATAATTTATTAATATATTAAGTCAC Template switch alignment (log-probability: -16.4) CTTTAATTACAATCACTTATAATTACAACATTGTCATGTG|CATGA|CACATGACAAGCAATATAATTTATTAATATATTAAGTCAC CTTTAATTACAATCACTTATAATTACAACATTGTCATGTG|CATGA|CACATGACAAGCAATATAATTTATTAATATATTAAGTCAC ========== Event 2564 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GACTCGCAAGAAACTTAATTATA------CTGTTTGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAATCACTGCTATGAATGTATC Chimp: GACTTGCAAGAAACTTAATTACA---GGTAAGTCTGACTCTTAAATAAGCAAAATACCACTTTTCAACAATAATCACTGCTATGAATGTATC Gorilla: GACTTGCAAGAAACTTAATTACAGGT---AAGTCTGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAATCACTGCTATGAATGTATC ↓ 1 4 3 2 Human: GACTCGCAAGAAACTTAATTATA------CTGTTTGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAATCACTGCTATGAATGTATC Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr4:40015951-40015957 Template switch process: F1: L TGACAAATTTATAGGCTTAAGACTCGCAAGAAACTTAATTA 1 F3: 4 TGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAAT R RF: TGACAAATTTATAGGCTTAAGACTTGCAAGAAACTTAATTACAGGTAAGTCTGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAAT RR: ACTGTTTAAATATCCGAATTCTGAACGTTCTTTGAATTAATGTCCATTCAGACTGAGAATTTATTCGTTTTATGATGAAAAGTTGTTATTA F2: 3 TTGTCAT 2 Unidirectional alignment (log-probability: -36.7) GACAAATTTATAGGCTTAAGACTcGCAAGAAACTTAATTA----------TactgtttGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAAT GACAAATTTATAGGCTTAAGACTTGCAAGAAACTTAATTACAGGTAAGTCT-------GACTCTTAAATAAGCAAAATACTACTTTTCAACAATAAT Template switch alignment (log-probability: -27.7) GACAAATTTATAGGCTTAAGACTcGCAAGAAACTTAATTA|TAcTGTT|TGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAAT GACAAATTTATAGGCTTAAGACTTGCAAGAAACTTAATTA|TATTGTT|TGACTCTTAAATAAGCAAAATACTACTTTTCAACAATAAT ========== Event 2565 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCACCCCGGATGTATTTCTG--------------------AGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGCCAACTTATCTTAAAGGCCATTCATTCTGAACACTGCATAAAGCAAGATCAAACACCTCAAGCTCTGACCGAAGGGTGAGTATGCAGC ↓ 4 1 3 2 Chimp: TCCACCCCGGATGTATTTCTG----------AGTGTCAGTGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGCCGACTTATCTTAAAGGCCATTCATTCTGAACACTGCATAAAGCAAGATCAAACACCTCAAGCTCTGACTGAAGGGTGAGTATGCAGC Gorilla: TCCACCCCGGATGTATTTCTGAGTGTCAGTG----------AGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGCCGACTTATCTTAAAGTCCATTCATTCTGAACACTGCAT-AAGCAAGATCAAACACCTCAAGCTCTGACTGAAGGGTGAGTATGCAGC Human: TCCACCCCGGATGTATTTCTG--------------------AGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGCCAACTTATCTTAAAGGCCATTCATTCTGAACACTGCATAAAGCAAGATCAAACACCTCAAGCTCTGACCGAAGGGTGAGTATGCAGC Cluster: [ ] Orangutan: TCCAACCTGGATGTATTTCTGAGTGTCAGTG----------AGTGAACTGGTCTAATACCTAATTCCAAGAGTGTATGCCGACTTATTTTAAAGGCCATTCATTCTGAACTCTGCAT-AAGCAAGATCAAACACCTCAAGCTCTGACTGAAGGGTGAGTATGCAGC Human > Chimp ------------- chr4:155159053-155159056 Template switch process: F1: L TGATATCACCCACCCACCCGTCCACCCCGGATGTATTTCTGAGTG 1 F3: 4 TGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGCCG R RF: TGACATCACCCACCCACCCGTCCACCCCGGATGTATTTCTGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGCCAACTTATCTTAAAGGCCATTCATTCTGAACACTGCATAAAGCAAGATCAAACACCTCAAGCTCTGA RR: ACTGTAGTGGGTGGGTGGGCAGGTGGGGCCTACATAAAGACTCACTTGACCGGATTATGGATTAAGATTCTCACATACGGTTGAATAGAATTTCCGGTAAGTAAGACTTGTGACGTATTTCGTTCTAGTTTGTGGAGTTCGAGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -37.3) TCACCCACCCACCCGTCCACCCCGGATGTATTTCtgagtgtcagTGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGC TCACCCACCCACCCGTCCACCCCGGATGTATTTC----------TGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGC Template switch alignment (log-probability: -27.9) TCACCCACCCACCCGTCCACCCCGGATGTATTTCTGAGTG|TCAG|TGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGC TCACCCACCCACCCGTCCACCCCGGATGTATTTCTGAGTG|TCAG|TGAGTGAACTGGCCTAATACCTAATTCTAAGAGTGTATGC ========== Event 2566 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAAAATAGGGGGAATAATGAT-------GCTAACATGGAAGTCAGCATTTTCCCTCCATG Chimp: caaaataGGGGGAATAATGAT-------GCTAACATGGAAGTCAGCATTTTCCCTCCATa ↓ 13 4 2 Gorilla: caaaataGGGGGAATAATGATGTTCCATGTTAGCATGGAAGTCAGCATTTTCCCTCCATa ↑ 13 4 2 Human: CAAAATAGGGGGAATAATGAT-------GCTAACATGGAAGTCAGCATTTTCCCTCCATG Cluster: [ ] Orangutan: CAAAATAGGGGGAATAATGAT-------GCTAACATGGAAGTCAGCATTTTCCCTCCATa Human > Gorilla --------------- chr4:163258552-163258562 Template switch process: F1: L ATTAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATG 1 F3: 4 CATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA R RF: ATTAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATGCTAACATGGAAGTCAGCATTTTCCCTCCATGAAAAAAGACAGGA RR: TAATTTTGTATGATATTTTCGTTTTATCCCCCTTATTACTACGATTGTACCTTCAGTCGTAAAAGGGAGGTACTTTTTTCTGTCCT F2: 3 GATTGTACCTT 2 Unidirectional alignment (log-probability: -37.6) TAAAACATACTATAAAAGCAAAATAGGGGGAATAATGatgttccATGtTAgCATGGAAGTCAGCATTTTCCCTCCATaAAAAAAGACAGGA TAAAACATACTATAAAAGCAAAATAGGGGGAATAATG-------ATGCTAACATGGAAGTCAGCATTTTCCCTCCATGAAAAAAGACAGGA Template switch alignment (log-probability: -22.7) TAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATG|TTCCATGTTAG|CATGGAAGTCAGCATTTTCCCTCCATaAAAAAAGACAGGA TAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATG|TTCCATGTTAG|CATGGAAGTCAGCATTTTCCCTCCATGAAAAAAGACAGGA Chimp > Gorilla --------------- chr4:163258552-163258562 Template switch process: F1: L ATTAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATG 1 F3: 4 CATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA R RF: ATTAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATGCTAACATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA RR: TAATTTTGTATGATATTTTCGTTTTATCCCCCTTATTACTACGATTGTACCTTCAGTCGTAAAAGGGAGGTATTTTTTTCTGTCCT F2: 3 GATTGTACCTT 2 Unidirectional alignment (log-probability: -32.1) TAAAACATACTATAAAAGCAAAATAGGGGGAATAATGatgttccATGtTAgCATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA TAAAACATACTATAAAAGCAAAATAGGGGGAATAATG-------ATGCTAACATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA Template switch alignment (log-probability: -17.2) TAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATG|TTCCATGTTAG|CATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA TAAAACATACTATAAAAGCAAAATAGGGGGAATAATGATG|TTCCATGTTAG|CATGGAAGTCAGCATTTTCCCTCCATAAAAAAAGACAGGA ========== Event 2567 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GGTTGTAATAAAAATTGACATACAGTCATTATTTATTTATCACATAACAAATACCTTCATTAAACGCAGTCACATAATCTTCACAGCTCTACTGCCTCTCAGATCTGCAAGTTTATCATGTATATTCAAATGACTGCAGTGGCAGCAACAAACAAA ↑ 1 4 3 2 Chimp: GGTTGTAATAAAAATTGACAT--AGT---CATTTATTTATCACATAACAAATACCTTCATTAAACGCAGTCACATAATCTTCACAGCTCTACTGCCTCTCAGATCTGCAAGTTTATCATGTATATTCAAATGACTGCAGTGGCAGCAACAAACAAA Gorilla: GGTTGTAATAAAAATTGACATATAGTCATTATTTATTTATCACACAACAAATACCTTCATTAAACGCAGTCACATAATCTTCACAGCTCTACTGCCTCTCAGATCTGCAAGTTTATCATGTATATTCAAATGACTGCAGTGGCAGCAACAAACAAA Human: GGTTGTAATAAAAATTGACATACAGTCATTATTTATTTATCACATAACAAATACCTTCATTAAACGCAGTCACATAATCTTCACAGCTCTACTGCCTCTCAGATCTGCAAGTTTATCATGTATATTCAAATGACTGCAGTGGCAGCAACAAACAAA Cluster: [ ] Orangutan: GGTTGTAACAAAAATTGACATATAGTCATTATTTATTTATCACATAACAAATACCTTCATTAAACGCAGTCACATAATCTTCACTGCTCTGCTGCCTCTCAGATCTGCAAGTTTATCATGTATGTTCAAATGACTGCAGTGGCAGCAACAAACAAA Chimp > Human ------------- chr4:38572589-38572596 Template switch process: F1: L TTGGTATTTATGAGTATTTGGGTTGTAATAAAAATTGACATA 1 F3: 4 ATTTATTTATCACATAACAAATACCTTCATTAAACGCAGT R RF: TTGGTATTTATGAGTATTTGGGTTGTAATAAAAATTGACATAGTCATTTATTTATCACATAACAAATACCTTCATTAAACGCAGTCACATAATCTTCACAGCTCTACTGCCTCTCAGATCTGCAAGTTTATCATGTATATTCAAATGACTG RR: AACCATAAATACTCATAAACCCAACATTATTTTTAACTGTATCAGTAAATAAATAGTGTATTGTTTATGGAAGTAATTTGCGTCAGTGTATTAGAAGTGTCGAGATGACGGAGAGTCTAGACGTTCAAATAGTACATATAAGTTTACTGAC F2: 3 TTACTGAC 2 Unidirectional alignment (log-probability: -28.4) GGTATTTATGAGTATTTGGGTTGTAATAAAAATTGACATacAGTCattATTTATTTATCACATAACAAATACCTTCATTAAACGCAGT GGTATTTATGAGTATTTGGGTTGTAATAAAAATTGACAT--AGTC---ATTTATTTATCACATAACAAATACCTTCATTAAACGCAGT Template switch alignment (log-probability: -16.3) GGTATTTATGAGTATTTGGGTTGTAATAAAAATTGACATA|CAGTCATT|ATTTATTTATCACATAACAAATACCTTCATTAAACGCAGT GGTATTTATGAGTATTTGGGTTGTAATAAAAATTGACATA|CAGTCATT|ATTTATTTATCACATAACAAATACCTTCATTAAACGCAGT ========== Event 2568 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTGGCAGGCAGTGGGGTCAGGCAGGCAGGTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTGCTGGTTCACCTGGGTTATCAGTGAGTCATCAGCCCCAGTGGGTCCAAC ↓ 1 4 3 2 Chimp: GTGGCAGGCAGTGGGGTCAGG--TGACTGTGGCACCCTCTCCAAGTTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTGCTGGTTCACCTGGGTTATCAGTGAGTCATCAGCCCCAATGGGTCCAAC Gorilla: GTGGCAGGCAGTGGGGTCAGG--TGACTGTGGCACCCTCTCCAAGTTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTTCTGGTTCACCTGGGTTATCAGTGAGTCATCAGCCCCAGTGGGTCCAAC ↑ 1 4 3 2 Human: GTGGCAGGCAGTGGGGTCAGGCAGGCAGGTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTGCTGGTTCACCTGGGTTATCAGTGAGTCATCAGCCCCAGTGGGTCCAAC Cluster: [ ] Orangutan: GTGGCAGGCAGTGGGGTCAGG--TGACTGTGGCACCCTCTCCAAGTTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTGCTGGTTCACCTGGGTTATCAGTGAGTCATCAGCCCCAGTGGGTCCAAC Human > Chimp ------------- chr4:39064282-39064286 Template switch process: F1: L ACCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG 1 F3: 4 GTGGCACCCTCTCCAAGTTAGAAGCCACCCTTCCTTGGCT R RF: ACCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGGCAGGCAGGTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTGCTGGTTCACCTGGGTTATCAGTGAGTCA RR: TGGAAGACAGTGAGTCCGTCCACCGTCCGTCACCCCAGTCCGTCCGTCCACCGTGGGAGAGGTTTAATCTTCGGTGGGAAGGAACCGAAAAGGAAACTATTGTCTCCTTTTTTGATCGATTGACGACCAAGTGGACCCAATAGTCACTCAGT F2: 3 TCAGT 2 Unidirectional alignment (log-probability: -34.7) CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGGtgact-------GTGGCACCCTCTCCAAgTTAGAAGCCACCCTTCCTTGGCT CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG-----CAGGCAGGTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCT Template switch alignment (log-probability: -21.9) CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG|TGACT|GTGGCACCCTCTCCAAgTTAGAAGCCACCCTTCCTTGGCT CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG|TGACT|GTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCT Human > Gorilla --------------- chr4:39082697-39082701 Template switch process: F1: L ACCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG 1 F3: 4 GTGGCACCCTCTCCAAGTTAGAAGCCACCCTTCCTTGGCT R RF: ACCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGGCAGGCAGGTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCTTTTCCTTTGATAACAGAGGAAAAAACTAGCTAACTGCTGGTTCACCTGGGTTATCAGTGAGTCA RR: TGGAAGACAGTGAGTCCGTCCACCGTCCGTCACCCCAGTCCGTCCGTCCACCGTGGGAGAGGTTTAATCTTCGGTGGGAAGGAACCGAAAAGGAAACTATTGTCTCCTTTTTTGATCGATTGACGACCAAGTGGACCCAATAGTCACTCAGT F2: 3 TCAGT 2 Unidirectional alignment (log-probability: -33.7) CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAG-------GtgactGTGGCACCCTCTCCAAgTTAGAAGCCACCCTTCCTTGGCT CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGGCAGGCAG-----GTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCT Template switch alignment (log-probability: -21.9) CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG|TGACT|GTGGCACCCTCTCCAAgTTAGAAGCCACCCTTCCTTGGCT CCTTCTGTCACTCAGGCAGGTGGCAGGCAGTGGGGTCAGG|TGACT|GTGGCACCCTCTCCAAATTAGAAGCCACCCTTCCTTGGCT ========== Event 2569 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAGCCATCCATCCCTTCTTCCTG-TGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCT Chimp: AGAGCCATCCATCCCTTCTTCCTG-TGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCT ↓ 1 4 3 2 Gorilla: AGAGCCATCCATCCCTTCTTCTTACAGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCT ↑ 1 4 3 2 Human: AGAGCCATCCATCCCTTCTTCCTG-TGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCT Cluster: [ ] Orangutan: AGAGTCATCCATCCCTTCTTCCTG-TGTCTGAGCACTGCAAATGCTCCTCGTGGGGAACCT Human > Gorilla --------------- chr4:165023446-165023451 Template switch process: F1: L TCAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC 1 F3: 4 TCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC R RF: TCAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTCCTGTGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC RR: AGTTGACGAGAAAGGTTGGGTCTCGGTAGGTAGGGAAGAAGGACACAGACTCGTGACATTTACGAGGAGCACCCCTTGGACGATG F2: 3 GACATT 2 Unidirectional alignment (log-probability: -26.5) CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC---TtacaGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTCCTGT----GTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC Template switch alignment (log-probability: -16.5) CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC|TTACAG|TCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC|TTACAG|TCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC Chimp > Gorilla --------------- chr4:165023446-165023451 Template switch process: F1: L TCAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC 1 F3: 4 TCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC R RF: TCAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTCCTGTGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC RR: AGTTGACGAGAAAGGTTGGGTCTCGGTAGGTAGGGAAGAAGGACACAGACTCGTGACATTTACGAGGAGCACCCCTTGGACGATG F2: 3 GACATT 2 Unidirectional alignment (log-probability: -26.5) CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC---TtacaGTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTCCTGT----GTCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC Template switch alignment (log-probability: -16.5) CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC|TTACAG|TCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC CAACTGCTCTTTCCAACCCAGAGCCATCCATCCCTTCTTC|TTACAG|TCTGAGCACTGTAAATGCTCCTCGTGGGGAACCTGCTAC ========== Event 2570 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TTCAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTAATGCCCTGTTGACTTAGtgtttctt ↑ 3 2 1 4 Chimp: TTAAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTGATGACCTGTTGACTTAGTGTTTCtt Gorilla: TTAAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTAATGCCCTGTTGACTTAGTatttctt Human: TTCAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTAATGCCCTGTTGACTTAGtgtttctt Cluster: [ ] Orangutan: TTAAAAGTTTATTCATTAAGCATTTTAGCTAAAAATACTTAGTGCCCTGTTGACTTAGTGtttctt Chimp > Human ------------- chr4:153597213-153597217 Template switch process: F1: L CTTCAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTT 1 F3: 4 CCTGTTGACTTAGTGTTTCTTTTTTTGTTTATTAATTTTT R RF: CTTAAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTGATGACCTGTTGACTTAGTGTTTCTTTTTTTGTTTATTAATTTTT RR: GAATTCTCAAATAAGTAATTCGTAAAATTGATTTTTATGAACTACTGGACAACTGAATCACAAAGAAAAAAACAAATAATTAAAAA F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -33.1) TTcAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTaATGcCCTGTTGACTTAGTGTTTCTTTTTTTGTTTATTAAttttt TTAAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTTGATGACCTGTTGACTTAGTGTTTCTTTTTTTGTTTATTAA----- Template switch alignment (log-probability: -21.9) TTcAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTT|AATGC|CCTGTTGACTTAGTGTTTCTTTTTTTGTTTATTAATTTTT TTAAGAGTTTATTCATTAAGCATTTTAACTAAAAATACTT|AATGC|CCTGTTGACTTAGTGTTTCTTTTTTTGTTTATTAATTTTT ========== Event 2571 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCCTAATACATAGAAAAATCC----------AAGTTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACTTATTTGTGGCCCTGTGTGACATGTTGGGCAGGATTTAAAACTTGTACTAATAAAATTTAAAAGA ↑ 1 4 3 2 Chimp: CCCCTAATACATAGAAAAATCT-----ACTATTATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACTTATTTGTGGCCCTGTGTGACATGTTGGGCAGGATTTAAAACTTGTACTAATAAAATTTAAAAGA Gorilla: CCCCTAATACATAGAAAAATCTACTTT-----TATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACTTATTTGTGGCCCTGTGTGACATGTTGGGCAGGATTTAAAACTTGTACTAATAAAATTTAAAAGA ↓ 1 4 3 2 Human: CCCCTAATACATAGAAAAATCC----------AAGTTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACTTATTTGTGGCCCTGTGTGACATGTTGGGCAGGATTTAAAACTTGTACTAATAAAATTTAAAAGA Cluster: [ ] Orangutan: CCCCTAATACACAGAAAAATCTACTTT-----TATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACATATTTGTGGCCCTGTGTGACATGTTGGGCAGAATTTAAAAATTGTACTAATAAAATTTAAAAGA Chimp > Human ------------- chr4:154510602-154510607 Template switch process: F1: L CTTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC 1 F3: 4 TTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT R RF: CTTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATCTACTATTATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACTTATTTGTGGCCCTGTGTGACATGTTGGGCAGGATTTAAAACTTG RR: GAACTATCAAGTAATAAAATGGGGATTATGTATCTTTTTAGATGATAATACAAACGTCTTGTTTTGAACCTCTACACTCAAGACCACCAAAGTCCGAGTGAATAAACACCGGGACACACTGTACAACCCGTCCTAAATTTTGAAC F2: 3 TTGAAC 2 Unidirectional alignment (log-probability: -27.4) TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATCcaagT---------TTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC----TACTATTATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT Template switch alignment (log-probability: -16) TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC|CAAGTT|TTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC|CAAGTT|TTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT Gorilla > Human --------------- chr4:154510602-154510607 Template switch process: F1: L CTTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC 1 F3: 4 TTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT R RF: CTTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATCTACTTTTATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTTCAGGCTCACTTATTTGTGGCCCTGTGTGACATGTTGGGCAGGATTTAAAACTTG RR: GAACTATCAAGTAATAAAATGGGGATTATGTATCTTTTTAGATGAAAATACAAACGTCTTGTTTTGAACCTCTACACTCAAGACCACCAAAGTCCGAGTGAATAAACACCGGGACACACTGTACAACCCGTCCTAAATTTTGAAC F2: 3 TTGAAC 2 Unidirectional alignment (log-probability: -26.9) TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATCcaagT---------TTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC----TACTTTTATGTTTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT Template switch alignment (log-probability: -16.5) TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC|CAAGTT|TTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT TTGATAGTTCATTATTTTACCCCTAATACATAGAAAAATC|CAAGTT|TTGCAGAACAAAACTTGGAGATGTGAGTTCTGGTGGTTT ========== Event 2572 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AATTGTCTCATTATGCAACAAAATGCATTTGGTATCTAAACATGGCTATCATTTGTAAAAAGAACTTAAAGTAAGGTATTAAA-----TAAAGATGAAACCATTTGCAAATGATGCCTCTTCAGATC ↓ 3 2 1 4 Chimp: AATTGTCTCATTATGCAACAAAATGCATTTGGTATCTAAACATGGCTATCATTTGTAAAAAGAACTTAAAGTAAGGTATTAAA-----TAAAGATGAAAGCATTTTCAAATGATGCCTCTTCAGATC Gorilla: ------------------------------------------------------------------------------------------------------------------------------- Human: AATTGTCTCATTATGCAACAAAATGCATTTGGTATCTAAACATGGCTATCATTTGTAAAAAGAACTTAAAGTAAGGTATTAAA-----TAAAGATGAAACCATTTGCAAATGATGCCTCTTCAGATC Cluster: [ ] Orangutan: AATTGTCTCATTATGCAATAAAATGCATTTGGTATCTAAATATGGCTATCATTTGTAAAAAGAATTTAAAGTAAGGTATTAAATAAAATAAAGATGAAAGCATTTTCAAATGATGCCTCTTCAGATC Human > Chimp ------------- chr4:15844063-15844069 Template switch process: F1: L TGTAAAAAGAACTTAAAGTAAGGTATTAAATAAAGATGAAA 1 F3: 4 CAAATGATGCCTCTTCAGATCAAGCCAAAAATATTGGTAC R RF: AAAATGCATTTGGTATCTAAACATGGCTATCATTTGTAAAAAGAACTTAAAGTAAGGTATTAAATAAAGATGAAACCATTTGCAAATGATGCCTCTTCAGATCAAGCCAAAAATATTGGTAA RR: TTTTACGTAAACCATAGATTTGTACCGATAGTAAACATTTTTCTTGAATTTCATTCCATAATTTATTTCTACTTTGGTAAACGTTTACTACGGAGAAGTCTAGTTCGGTTTTTATAACCATT F2: 3 TTTTACG 2 Unidirectional alignment (log-probability: -27.1) GTAAAAAGAACTTAAAGTAAGGTATTAAATAAAGATGAAAgCATTTtCAAATGATGCCTCTTCAGATCAAGCCAAAAATATTggtac GTAAAAAGAACTTAAAGTAAGGTATTAAATAAAGATGAAACCATTTGCAAATGATGCCTCTTCAGATCAAGCCAAAAATATT----- Template switch alignment (log-probability: -22.1) GTAAAAAGAACTTAAAGTAAGGTATTAAATAAAGATGAAA|GCATTTT|CAAATGATGCCTCTTCAGATCAAGCCAAAAATATTGGTAc GTAAAAAGAACTTAAAGTAAGGTATTAAATAAAGATGAAA|GCATTTT|CAAATGATGCCTCTTCAGATCAAGCCAAAAATATTGGTAA ========== Event 2573 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCATTTATCATCTCACGTTTTGCC--------------ATCCTTTGGTTGTATAGACCA Chimp: TTCATTTATCATCTCACGTTTTGCC-----------ATTATCCTTTGGTTGTATAGACCA ↓ 3 1 24 Gorilla: TTCATTTATCATCTCACGTTTTGCA---ATGGCAAA---ATCCTTTGGTTGTATAGACCA Human: TCCATTTATCATCTCACGTTTTGCC--------------ATCCTTTGGTTGTATAGACCA Cluster: [ ] Orangutan: TTCATTTATCATCTCACGTTTTGCCATT-----------ATCCTTTGGTTGAATAGACCA Chimp > Gorilla --------------- chr4:187917868-187917876 Template switch process: F1: L TACCTTGTTTGTTTTTATTCATTTATCATCTCACGTTTTGC 1 F3: 4 ATCCTTTGGTTGTATAGACCAATGATATCCAACCAAACAG R RF: TACCTTGTTTGTTTTTATTCATTTATCATCTCACGTTTTGCCATTATCCTTTGGTTGTATAGACCAAGGATATCCAACCAAACAG RR: ATGGAACAAACAAAAATAAGTAAATAGTAGAGTGCAAAACGGTAATAGGAAACCAACATATCTGGTTCCTATAGGTTGGTTTGTC F2: 3 AAACGGTAA 2 Unidirectional alignment (log-probability: -34.7) ACCTTGTTTGTTTTTATTCATTTATCATCTCACGTTTTGCaatggCAaaATCCTTTGGTTGTATAGACCAAtGATATCCAACCAAACAG ACCTTGTTTGTTTTTATTCATTTATCATCTCACGTTTTGC-----CATTATCCTTTGGTTGTATAGACCAAGGATATCCAACCAAACAG Template switch alignment (log-probability: -22.4) ACCTTGTTTGTTTTTATTCATTTATCATCTCACGTTTTGC|AATGGCAAA|ATCCTTTGGTTGTATAGACCAAtGATATCCAACCAAACAG ACCTTGTTTGTTTTTATTCATTTATCATCTCACGTTTTGC|AATGGCAAA|ATCCTTTGGTTGTATAGACCAAGGATATCCAACCAAACAG ========== Event 2574 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AAACCTCAGACTTCGTTGATTTGCATCAATATGTAGACATGGTA-TGGCAATTCTATTTCACATCCCGTGAATTTTAAGCTGATGCAAATGCAGAAGAATAAGCCAATATACTGAC Chimp: AAACCTCAGACTTCATTGATTTGCATCAATATGTAGACATGGTATTGGCAATTCTATTTCACATCCCCTGAATTTTAAGCTGATGCAAATGCAGAAGAATAAGCCAATATACTGAC Gorilla: AAACCTCAGACTTCATTGATTTGCATCAATATGTAGACATGGTATTGGCAATTCTATTTCACATCCCCTGAATTTTAAGCTGATGCAAACGT---AGAATAAGCCAATATACTGAC ↓ 3 2 1 4 Human: AAACCTCAGACTTCGTTGATTTGCATCAATATGTAGACATGGTA-TGGCAATTCTATTTCACATCCCGTGAATTTTAAGCTGATGCAAATGCAGAAGAATAAGCCAATATACTGAC Cluster: [ ] Orangutan: -------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr4:33186342-33186347 Template switch process: F1: L CAATTCTATTTCACATCCCGTGAATTTTAAGCTGATGCAAA 1 F3: 4 AGAATAAGCCAATATACTGACAAACCAAATAAACTTGGA R RF: TTTGCATCAATATGTAGACATGGTATTGGCAATTCTATTTCACATCCCCTGAATTTTAAGCTGATGCAAACGTAGAATAAGCCAATATACTGACAAACCAAATAAACTTGGG RR: AAACGTAGTTATACATCTGTACCATAACCGTTAAGATAAAGTGTAGGGGACTTAAAATTCGACTACGTTTGCATCTTATTCGGTTATATGACTGTTTGGTTTATTTGAACCC F2: 3 AGACGT 2 Unidirectional alignment (log-probability: -41.6) AATTCTATTTCACATCCCgTGAATTTTAAGCTGATGCAAAtgcaGaAGAATAAGCCAATATACTGACAAACCAAATAAACTT-GGA AATTCTATTTCACATCCCCTGAATTTTAAGCTGATGCAAAC---GTAGAATAAGCCAATATACTGACAAACCAAATAAACTTGGGA Template switch alignment (log-probability: -33) AATTCTATTTCACATCCCgTGAATTTTAAGCTGATGCAAA|TGCAgA|AGAATAAGCCAATATACTGACAAACCAAATAAACTTGGa AATTCTATTTCACATCCCCTGAATTTTAAGCTGATGCAAA|TGCAAA|AGAATAAGCCAATATACTGACAAACCAAATAAACTTGGG ========== Event 2575 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTAATAGAGAATAAAAGATGCG-TCATCACGTGATTCTCGAATGTGAGACTCCTACTGAAA Chimp: CCTTAATAGAGAATAAAAGATGCG-TCATCACGTGATTCTCGAATGTGAGACTCCTACTGAAA ↓ 1 4 3 2 Gorilla: TCTTAATAGAGAATAAAAGATTCGAGAATCACGTGATTCTCGAATGTGAGACTCCTACTGAAA ↑ 1 4 3 2 Human: CCTTAATAGAGAATAAAAGATGCG-TCATCACGTGATTCTCGAATGTGAGACTCCTACTGAAA Cluster: [ ] Orangutan: CCTTAATAGAGAATAAAAGATGTG-TCATCATGTGATTCTCGAATGTGAGACTCCTACTGAAA Human > Gorilla --------------- chr4:187724498-187724504 Template switch process: F1: L TGAGGTCTCAAGGTGAGTCTTCTTAATAGAGAATAAAAGAT 1 F3: 4 TCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA R RF: TGAGGTCTCAAGGTGAGTCTCCTTAATAGAGAATAAAAGATGCGTCATCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA RR: ACTCCAGAGTTCCACTCAGAGGAATTATCTCTTATTTTCTACGCAGTAGTGCACTAAGAGCTTACACTCTGAGGATGACTTTTCGT F2: 3 AAGAGCT 2 Unidirectional alignment (log-probability: -32.1) GAGGTCTCAAGGTGAGTCTtCTTAATAGAGAATAAAAGAT---TCgagaATCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA GAGGTCTCAAGGTGAGTCTCCTTAATAGAGAATAAAAGATGCGTC----ATCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA Template switch alignment (log-probability: -22.1) GAGGTCTCAAGGTGAGTCTtCTTAATAGAGAATAAAAGAT|TCGAGAA|TCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA GAGGTCTCAAGGTGAGTCTCCTTAATAGAGAATAAAAGAT|TCGAGAA|TCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA Chimp > Gorilla --------------- chr4:187724498-187724504 Template switch process: F1: L TGAGGTCTCAAGGTGAGTCTTCTTAATAGAGAATAAAAGAT 1 F3: 4 TCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA R RF: TGAGGTCTCAAGGTGAGTCTCCTTAATAGAGAATAAAAGATGCGTCATCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA RR: ACTCCAGAGTTCCACTCAGAGGAATTATCTCTTATTTTCTACGCAGTAGTGCACTAAGAGCTTACACTCTGAGGATGACTTTTCGT F2: 3 AAGAGCT 2 Unidirectional alignment (log-probability: -32.1) GAGGTCTCAAGGTGAGTCTtCTTAATAGAGAATAAAAGAT---TCgagaATCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA GAGGTCTCAAGGTGAGTCTCCTTAATAGAGAATAAAAGATGCGTC----ATCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA Template switch alignment (log-probability: -22.1) GAGGTCTCAAGGTGAGTCTtCTTAATAGAGAATAAAAGAT|TCGAGAA|TCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA GAGGTCTCAAGGTGAGTCTCCTTAATAGAGAATAAAAGAT|TCGAGAA|TCACGTGATTCTCGAATGTGAGACTCCTACTGAAAAGCA ========== Event 2576 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAACTTTGCAAAATGCCTAGGCACATCAGT--AGATGATGTGCCTTTAGGGCTATTG Chimp: AAACTTTGCAAAATGCCTAGGCACATCAGT--AGATGATGTGCCTTTAGGGCTATTG ↑ 1 3 4 2 Gorilla: AAACTTTACAAAATGCCTAGGTATTACCCTACTGATGATGTGCCTTTAGGGCTATTG ↓ 1 3 4 2 Human: AAACTTTGCAAAATGCCTAGGCACATCAGT--AGATGATGTGCCTTTAGGGCTATTG Cluster: [ ] Orangutan: AAACTTTGCAAAATGCCTAGATATTACCCTACTGATGATGTGACTTTAGGGCTATCG Gorilla > Human --------------- chr4:32245287-32245294 Template switch process: F1: L ATAGTGGTACCCATGTGGTTAAACTTTGCAAAATGCCTAGGCA 1 F3: 4 GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC R RF: ATAGTGGTACCCATGTGGTTAAACTTTACAAAATGCCTAGGTATTACCCTACTGATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC RR: TATCACCATGGGTACACCAATTTGAAATGTTTTACGGATCCATAATGGGATGACTACTACACGGAAATCCCGATAACTCGGTACCATTTTTTG F2: 3 ATGACTAC 2 Unidirectional alignment (log-probability: -38.2) GTGGTACCCATGTGGTTAAACTTTgCAAAATGCCTAGgcacatcaGTA----------GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC GTGGTACCCATGTGGTTAAACTTTACAAAATGCCTAG--------GTATTACCCTACTGATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC Template switch alignment (log-probability: -27.8) GTGGTACCCATGTGGTTAAACTTTgCAAAATGCCTAGGcA|CATCAGTA|GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC GTGGTACCCATGTGGTTAAACTTTACAAAATGCCTAGGTA|CATCAGTA|GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC Gorilla > Chimp --------------- chr4:32644260-32644267 Template switch process: F1: L ATAGTGGTACCCATGTGGTTAAACTTTGCAAAATGCCTAGGCA 1 F3: 4 GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC R RF: ATAGTGGTACCCATGTGGTTAAACTTTACAAAATGCCTAGGTATTACCCTACTGATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC RR: TATCACCATGGGTACACCAATTTGAAATGTTTTACGGATCCATAATGGGATGACTACTACACGGAAATCCCGATAACTCGGTACCATTTTTTG F2: 3 ATGACTAC 2 Unidirectional alignment (log-probability: -38.2) GTGGTACCCATGTGGTTAAACTTTgCAAAATGCCTAGgcacatcaGTA----------GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC GTGGTACCCATGTGGTTAAACTTTACAAAATGCCTAG--------GTATTACCCTACTGATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC Template switch alignment (log-probability: -27.8) GTGGTACCCATGTGGTTAAACTTTgCAAAATGCCTAGGcA|CATCAGTA|GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC GTGGTACCCATGTGGTTAAACTTTACAAAATGCCTAGGTA|CATCAGTA|GATGATGTGCCTTTAGGGCTATTGAGCCATGGTAAAAAAC ========== Event 2577 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGAGTTCTTCATAAACCAATTAACTAA--TTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTTTGTACTGAATGTATCTATATAAGCTACT Chimp: ATGAGTTCTTCATAAACCAATTAACTAATTTTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTTTGTACTGAATGTATCTATATAAGCTACT ↓ 1 4 3 2 Gorilla: ATGAGTTCTTCATAAACCAATAAACTAA--TTGTAGGTT----------ATCAGTTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTTTGTACTGAATGTATCTATATAAGCTACT ↑ 1 4 3 2 Human: ATGAGTTCTTCATAAACCAATTAACTAA--TTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTTTGTACTGAATGTATCTATATAAGCTACT Cluster: [ ] Orangutan: ATGAGTTCTTCATAAACCAATTAACTAA--TTGTACGTT----------ATCAGTTGGGTTATCAAAGAAGTTTCCGTTATGTGGACATAGTTTTTGTACTGAATGTATCTATATAAGCTACT Human > Gorilla --------------- chr4:32469980-32469984 Template switch process: F1: L TAAAATGAGTTCTTCATAAACCAATAAACTAATTGTAGGTTA 1 F3: 4 TGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT R RF: TAAAATGAGTTCTTCATAAACCAATTAACTAATTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTTTGTACTGA RR: ATTTTACTCAAGAAGTATTTGGTTAATTGATTAACATCCAATTAAACTATTGGGTTGACCCAATAGTTTCTTCAAAGGGAATACACCTGTATCAAAAACATGACT F2: 3 TGACT 2 Unidirectional alignment (log-probability: -33.6) AAATGAGTTCTTCATAAACCAATaAACTAATTGTAGGTTA----------tCAgtTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT AAATGAGTTCTTCATAAACCAATTAACTAATTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT Template switch alignment (log-probability: -21.9) AAATGAGTTCTTCATAAACCAATaAACTAATTGTAGGTTA|TCAGT|TGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT AAATGAGTTCTTCATAAACCAATTAACTAATTGTAGGTTA|TCAGT|TGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT Chimp > Gorilla --------------- chr4:32469980-32469984 Template switch process: F1: L GGATTTTGCATACTCTTAAAATGAGTTCTTCATAAACCAATAAACTAA--TTGTAGGTTA 1 F3: 4 TGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT R RF: GGATTTTGCATACTCTTAAAATGAGTTCTTCATAAACCAATTAACTAATTTTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTTTGTACTGA RR: CCTAAAACGTATGAGAATTTTACTCAAGAAGTATTTGGTTAATTGATTAAAACATCCAATTAAACTATTGGGTTGACCCAATAGTTTCTTCAAAGGGAATACACCTGTATCAAAAACATGACT F2: 3 TGACT 2 Unidirectional alignment (log-probability: -43.6) AAATGAGTTCTTCATAAACCAATaAACTAA--TTGTAGGTTAt----------CAgtTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT AAATGAGTTCTTCATAAACCAATTAACTAATTTTGTAGGTTAATTTGATAACCCAACTGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT Template switch alignment (log-probability: -32.1) AAATGAGTTCTTCATAAACCAATaAACTAA--TTGTAGGTTA|TCAGT|TGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT AAATGAGTTCTTCATAAACCAATTAACTAATTTTGTAGGTTA|TCAGT|TGGGTTATCAAAGAAGTTTCCCTTATGTGGACATAGTTTT ========== Event 2578 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tctcaaaaaaaaaaaaaaaGGAAGTAGGCTTTCAAGACTAGCCCTTATTGTTTGATGATATAAGGA ↓ 1 4 3 2 Chimp: tctcaaaaaaa-aaaaaaaGGAA--GGGCTAGTAAGACTAGCCCTTATTGTTTGATGATATAAGGA Gorilla: tctcaaaaaaa-aaaaaaaGGAAGTAGGCTTTCAAGACTAGCCCTTATTGTTTGATGATATAAGGA Human: tctcaaaaaaaaaaaaaaaGGAAGTAGGCTTTCAAGACTAGCCCTTATTGTTTGATGATATAAGGA Cluster: [ ] Orangutan: tgtcaaaaaaa-aaaaaaaGGAAGTAGGCTTTCAAGACTAGCCCTTATTGTTTGATGATATAAGGA Human > Chimp ------------- chr4:158280954-158280963 Template switch process: F1: L CAACAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAAGG 1 F3: 4 AAGACTAGCCCTTATTGTTTGATGATATAAGGACCCCTGC R RF: CAACAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAAAGGAAGTAGGCTTTCAAGACTAGCCCTTATTGTTTGATGATATAAGGACCCCTGC RR: GTTGTCTCGCTCTGAAGCAGAGTTTTTTTTTTTTTTTCCTTCATCCGAAAGTTCTGATCGGGAATAACAAACTACTATATTCCTGGGGACG F2: 3 TGATCGGGAA 2 Unidirectional alignment (log-probability: -39.1) CAACAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAA---------------ggaagggctagtAAGACTAGCCCTTATTGTTTGATGATATAAGGACCCCTGC CAACAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAAAGGAAGTAGGCTTTC------------AAGACTAGCCCTTATTGTTTGATGATATAAGGACCCCTGC Template switch alignment (log-probability: -22.5) CAACAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAAgG|AAGGGCTAGT|AAGACTAGCCCTTATTGTTTGATGATATAAGGACCCCTGC CAACAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAAAG|AAGGGCTAGT|AAGACTAGCCCTTATTGTTTGATGATATAAGGACCCCTGC ========== Event 2579 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGCTTTTTAAATGGCATACAGATAGTTTAGTTGTATTCTATGAACAAAAACTATTTAAGAAACAAATATTACTAGAGC Chimp: ATGCTTTTTAAATAGCATACAGATAGTTTAGTTATATTCTATGAACA-AAACTACTTAAGAAACAAATATTACTAGAGC ↓ 3 2 1 4 Gorilla: ATGCTTTTTAAATGGCATACAGATAGTTTAGTTGTATTCTATGAACAAAAACTATCTGAGAAACAAATATTACTAGAGC Human: ATGCTTTTTAAATGGCATACAGATAGTTTAGTTGTATTCTATGAACAAAAACTATTTAAGAAACAAATATTACTAGAGC Cluster: [ ] Orangutan: ATGCTTTTTAAATGGCATACAGATAGTTTAGTTGTATTCTATGAACAAAAACTATTTGAGAAACAAGTACTACTAGAGC Chimp > Gorilla --------------- chr4:31408944-31408951 Template switch process: F1: L TTTAAATGGCATACAGATAGTTTAGTTGTATTCTATGAACAAAA 1 F3: 4 AGAAACAAATATTACTAGAGCCCCAAAATGGGCTAAAATA R RF: TTTAAATAGCATACAGATAGTTTAGTTATATTCTATGAACAAAACTACTTAAGAAACAAATATTACTAGAGCCCCAAAATGGGCTAAAATA RR: AAATTTATCGTATGTCTATCAAATCAATATAAGATACTTGTTTTGATGAATTCTTTGTTTATAATGATCTCGGGGTTTTACCCGATTTTAT F2: 3 GTCTATCA 2 Unidirectional alignment (log-probability: -40.1) AATgGCATACAGATAGTTTAGTTgTATTCTATGAACaAAAACTAtcTgAGAAACAAATATTACTAGAGCCCCAAAATGGGCTAAAATA AATAGCATACAGATAGTTTAGTTATATTCTATGAAC-AAAACTACTTAAGAAACAAATATTACTAGAGCCCCAAAATGGGCTAAAATA Template switch alignment (log-probability: -27.9) AATgGCATACAGATAGTTTAGTTgTATTCTATGAACAAAA|ACTATCTG|AGAAACAAATATTACTAGAGCCCCAAAATGGGCTAAAATA AATAGCATACAGATAGTTTAGTTATATTCTATGAACAAAA|ACTATCTG|AGAAACAAATATTACTAGAGCCCCAAAATGGGCTAAAATA ========== Event 2580 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AGAATATACTATACTCACAGA----TC-------AGTCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAATGTTAGGTAAGATCCTGA----CGTTATTTTCAATAACAC ↑ 1 4 3 2 Chimp: AGAATATACTATACTCACAGACTGATCTGTGACAGATCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAATGTTAGGTAAGATCCTGA--CAGGTTATTTTCAATAACAC ↓ 1 4 3 2 Gorilla: AGAATATACTATACTCACAGA----TC-------AGTCTTGTAAAAGCCTTGGACAGTACGATTCTTGGGACAAAATGTTAGGTAAGATCCTGACA--TGTTATTTTCAATAACAC Human: AGAATATACTATACTCACAGA----TC-------AGTCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAATGTTAGGTAAGATCCTGA----CGTTATTTTCAATAACAC Cluster: [ ] Orangutan: AGAATATACTATACTCACAGA----TC-------AGTCTTGTAAAAGCCGTGGACAGTATGATTCTTGGGACAAAATGTTAGGTAAGATCCTGACA--TGTTATTTTCAATAACAC Chimp > Human ------------- chr4:30754272-30754275 Template switch process: F1: L CAAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA 1 F3: 4 TCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA R RF: CAAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGACTGATCTGTGACAGATCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAATGTTAGGTAAGATCCTGA RR: GTTTCATCCCGTAAAGACTTTCTTATATGATATGAGTGTCTGACTAGACACTGTCTAGAACATTTTCGGAACCTGTCATACTAAGAACCCTGTTTTACAATCCATTCTAGGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -27.7) AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGAtcag---------------TCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA----CTGATCTGTGACAGATCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA Template switch alignment (log-probability: -15.8) AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA|TCAG|TCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA|TCAG|TCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA Chimp > Gorilla --------------- chr4:31040349-31040352 Template switch process: F1: L CAAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA 1 F3: 4 TCTTGTAAAAGCCTTGGACAGTACGATTCTTGGGACAAAA R RF: CAAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGACTGATCTGTGACAGATCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAATGTTAGGTAAGATCCTGA RR: GTTTCATCCCGTAAAGACTTTCTTATATGATATGAGTGTCTGACTAGACACTGTCTAGAACATTTTCGGAACCTGTCATACTAAGAACCCTGTTTTACAATCCATTCTAGGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -32.3) AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA----------tCAG-TCTTGTAAAAGCCTTGGACAGTAcGATTCTTGGGACAAAA AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGACTGATCTGTGACAGATCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA Template switch alignment (log-probability: -21.7) AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA|TCAG|TCTTGTAAAAGCCTTGGACAGTAcGATTCTTGGGACAAAA AAAGTAGGGCATTTCTGAAAGAATATACTATACTCACAGA|TCAG|TCTTGTAAAAGCCTTGGACAGTATGATTCTTGGGACAAAA ========== Event 2581 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGGATAGA--TATTTGTCATTTGAATT-AATGT ↓ 3 2 1 4 Chimp: CATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGGTCATTTGAATTTGTCATTTGAATT-AATGT Gorilla: CACAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGGCTAGA--TATTTGTCATTTGAATT-AATGT Human: CATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGGATAGA--TATTTGTCATTTGAATT-AATGT Cluster: [ ] Orangutan: CACAGAAACCTAAT-AAAGTTCAAGTGAAATATGAACTTGGCTAGA--TATTTGTCATCTGAATTAAATGT Human > Chimp ------------- chr4:31319326-31319334 Template switch process: F1: L CATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGG 1 F3: 4 TTTGTCATTTGAATTAATGTAGCTTTGTAAATAAATTCT R RF: CATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGGATAGATATTTGTCATTTGAATTAATGTAGCTTTGTAAATAAATTCT RR: GTATCTTTGGATTATTTTCAAGTTCACTTTATACTTGAACCTATCTATAAACAGTAAACTTAATTACATCGAAACATTTATTTAAGA F2: 3 AAGTTTACT 2 Unidirectional alignment (log-probability: -31.5) ATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGgtcatttGA-----ATTTGTCATTTGAATTAATGTAGCTTTGTAAATAAATTCT ATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTG-------GATAGATATTTGTCATTTGAATTAATGTAGCTTTGTAAATAAATTCT Template switch alignment (log-probability: -22.4) ATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGG|TCAtTTGAA|TTTGTCATTTGAATTAATGTAGCTTTGTAAATAAATTCT ATAGAAACCTAATAAAAGTTCAAGTGAAATATGAACTTGG|TCACTTGAA|TTTGTCATTTGAATTAATGTAGCTTTGTAAATAAATTCT ========== Event 2582 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: aaagaaaCTGAATGCAAAAGTGCATGGAGATTTAGAAGTGATTACCGACTCGCACAATCACACATGTACATCCTCTCATAACTGTGA--------------------------------------------------------------------------------------------------------------CAGGGTAGTTTCTGTTATACTCAACAT ↓ 3 4 2 1 Chimp: aaagaaactgaatgcaaaagTGCATGGAGATTTAGAAGTGATTACCGACTCGCACAATCACACATGTACATCCTCTCATAACTGTGACAGGGTACATGTGTGATTGTGCGAGTCGGTAATCACTTCTAAATCTCCATGCACTTAGAAGTGATTACCGACTCGCACAATCACACATGTACATCCTCTCATAACTGTGACAGGGTAGTTTCTGTTATACTCAACAT Gorilla: aaagaaactgaatgcaaaagTGCATGGAGATTTAGAAGAGATTACCGACTCTCACAATCACACATGTACATCCTCTCATAACTGTGA--------------------------------------------------------------------------------------------------------------CAGGGTAGTTTCTGTTATATTCAACAT Human: aaagaaaCTGAATGCAAAAGTGCATGGAGATTTAGAAGTGATTACCGACTCGCACAATCACACATGTACATCCTCTCATAACTGTGA--------------------------------------------------------------------------------------------------------------CAGGGTAGTTTCTGTTATACTCAACAT Cluster: [ ] Orangutan: aaagaaaCTGAATGCAAAAGTGCATGGAGATTTAGAAGTGATTACCGACTCTCACAATCACACATGTACATCCTCTCATAACTGTGA--------------------------------------------------------------------------------------------------------------CAGGGTAGTTTCTGTTATACTCAACAT Human > Chimp ------------- chr4:30541881-30541927 Template switch process: F1: L GACTCGCACAATCACACATGTACATCCTCTCATAACTGTGACAGGGTA 1 F3: 4 TTAGAAGTGATTACCGACTCGCACAATCACACATGTACATCCTCTCATAACTGTGACAGGGTAGTTTCTGTTATACTCAACATCATTTTAAATGAT R RF: GTGCATGGAGATTTAGAAGTGATTACCGACTCGCACAATCACACATGTACATCCTCTCATAACTGTGACAGGGTAGTTTCTGTTATACTCAACATCATTTTAAATGAT RR: CACGTACCTCTAAATCTTCACTAATGGCTGAGCGTGTTAGTGTGTACATGTAGGAGAGTATTGACACTGTCCCATCAAAGACAATATGAGTTGTAGTAAAATTTACTA F2: 3 CACGTACCTCTAAATCTTCACTAATGGCTGAGCGTGTTAGTGTGTAC 2 Unidirectional alignment (log-probability: -163) caatcacacatgtacatcctctcataactgtgacagggtacatgtgtgattgtgcgagtcggtaatcacttctaaatctccatgcacttagaagtgattaccGACTCGCACAATCACACATGTACAT ------------------------------------------------------------------------------------------------------GACTCGCACAATCACACATGTACAT Template switch alignment (log-probability: -22) CAATCACACATGTACATCCTCTCATAACTGTGACAGGGTA|CATGTGTGATTGTGCGAGTCGGTAATCACTTCTAAATCTCCATGCAC|TTAGAAGTGATTACCGACTCGCACAATCACACATGTACAT CAATCACACATGTACATCCTCTCATAACTGTGACAGGGTA|CATGTGTGATTGTGCGAGTCGGTAATCACTTCTAAATCTCCATGCAC|TTAGAAGTGATTACCGACTCGCACAATCACACATGTACAT ========== Event 2583 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAAGGCTACCAGAACAATGGTTGTGCAGT--------AGGAACAATGAAAGTTTACAGGGGTGTA Chimp: AGAAGGCTACCAGAACAATGGCTGTGCAGT--------AGGAACAATGAAAGTTTACAGGGGTGTA ↓ 3 4 2 Gorilla: AGAAGGCTACCAGAACAATGGTTGTGCATTGTTCCTACTGGAACAATGAAAGTTTACAGGGGTGTA ↑ 3 4 2 Human: AGAAGGCTACCAGAACAATGGTTGTGCAGT--------AGGAACAATGAAAGTTTACAGGGGTGTA Cluster: [ ] Orangutan: AGAAGGCTACTAGAACAATGGTTGTGCAGT--------AGGAACAATGAAAGTTTACAGGGGTGTA Human > Gorilla --------------- chr4:28941059-28941069 Template switch process: F1: L AAAAAAGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCA 1 F3: 4 GGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG R RF: AAAAAGGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCAGTAGGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG RR: TTTTTCCGGGAAATCTTCCGATGGTCTTGTTACCAACACGTCATCCTTGTTACTTTCAAATGTCCCCACATTTGTCTAGACTTC F2: 3 TCATCCTTGTT 2 Unidirectional alignment (log-probability: -39) AAAAaGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCAtTgttcctactGGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG AAAAGGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCAGT--------AGGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG Template switch alignment (log-probability: -22.6) AAAAaGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCA|TTGTTCCTACT|GGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG AAAAGGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCA|TTGTTCCTACT|GGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG Chimp > Gorilla --------------- chr4:28941059-28941069 Template switch process: F1: L AGGCAGGAAAAAAGCCCTTTAGAAGGCTACCAGAACAATGGTTGTGCA 1 F3: 4 GGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG R RF: AGGCAGGAAAAAAGCCCTTTAGAAGGCTACCAGAACAATGGCTGTGCAGTAGGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG RR: TCCGTCCTTTTTTCGGGAAATCTTCCGATGGTCTTGTTACCGACACGTCATCCTTGTTACTTTCAAATGTCCCCACATTTGTCTAGACTTC F2: 3 TCATCCTTGTT 2 Unidirectional alignment (log-probability: -39.1) AAAAAGCCCTTTAGAAGGCTACCAGAACAATGGtTGTGCAtTgttcctactGGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG AAAAAGCCCTTTAGAAGGCTACCAGAACAATGGCTGTGCAGT--------AGGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG Template switch alignment (log-probability: -22.8) AAAAAGCCCTTTAGAAGGCTACCAGAACAATGGtTGTGCA|TTGTTCCTACT|GGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG AAAAAGCCCTTTAGAAGGCTACCAGAACAATGGCTGTGCA|TTGTTCCTACT|GGAACAATGAAAGTTTACAGGGGTGTAAACAGATCTGAAG ========== Event 2584 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGGAATGACATGAAGAGTTACTGAAAGGAATTAAAAATAATGTGATCGATGTAGACTTAACTGACAGCAG ↓ 1 4 3 2 Chimp: GAGGAATGACATGAAGAGTTA----CATCGATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCAG ↑ 1 4 3 2 Gorilla: GAGGAATGACATGAAGAGTTACTGAAAGGAATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCAG Human: GAGGAATGACATGAAGAGTTACTGAAAGGAATTAAAAATAATGTGATCGATGTAGACTTAACTGACAGCAG Cluster: [ ] Orangutan: GAGGAATGACACGAAGAGTTACTAAAAGGAATTTAAAATAATGTAATCGACGTAGACTTAACTGACAGCAG Human > Chimp ------------- chr4:165817604-165817607 Template switch process: F1: L CAACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC 1 F3: 4 ATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA R RF: CAACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTACTGAAAGGAATTAAAAATAATGTGATCGATGTAGACTTAACTGACAGCA RR: GTTGACCGTTTTGACACAATCTCCTTACTGTACTTCTCAATGACTTTCCTTAATTTTTATTACACTAGCTACATCTGAATTGACTGTCGT F2: 3 GCTA 2 Unidirectional alignment (log-probability: -31.8) ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC-------AtcgATTAAAAATAATGTaATCGATGTAGACTTAACTGACAGCA ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTACTGAAAGGA---ATTAAAAATAATGTGATCGATGTAGACTTAACTGACAGCA Template switch alignment (log-probability: -21.8) ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC|ATCG|ATTAAAAATAATGTaATCGATGTAGACTTAACTGACAGCA ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC|ATCG|ATTAAAAATAATGTGATCGATGTAGACTTAACTGACAGCA Gorilla > Chimp --------------- chr4:165817604-165817607 Template switch process: F1: L CAACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC 1 F3: 4 ATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA R RF: CAACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTACTGAAAGGAATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA RR: GTTGACCGTTTTGACACAATCTCCTTACTGTACTTCTCAATGACTTTCCTTAATTTTTATTACATTAGCTACATCTGAATTGACTGTCGT F2: 3 GCTA 2 Unidirectional alignment (log-probability: -25.3) ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC-------AtcgATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTACTGAAAGGA---ATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA Template switch alignment (log-probability: -16.3) ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC|ATCG|ATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA ACTGGCAAAACTGTGTTAGAGGAATGACATGAAGAGTTAC|ATCG|ATTAAAAATAATGTAATCGATGTAGACTTAACTGACAGCA ========== Event 2585 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCACATTTCCATATCATACTTTACTTTACGCTATTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTGTTTTTCTCCTTTCCTCTTTGAACAAAGTCAGGAAAAATGTGTCAGTAGGAGAAAGGAGGAGCTGAA Chimp: CTTCACATTTCCATATCATAC-----TTTACGCTATTACTTCATGGGCTCCTGGGCATTTGGTCT----GTTTTTCTCCTTTCCTCTTTGAACAAAGTCAGGAAAAATGTGTCAGTAGGAGAAAGGAGGAGCTGAA Gorilla: CTTCACATTTCCATATCATAC-----TTTACACTGTTACTTCATGGGCTCCTGGGCATTTGGTCT----GTTTTTCTCCTTTCCTCTTTGAACAAAGTCAGGAAAAATGTGTCAGTAGGAGAAAGGAGGAGCTGAA ↑ 1 4 3 2 Human: CTTCACATTTCCATATCATACTTTACTTTACGCTATTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTGTTTTTCTCCTTTCCTCTTTGAACAAAGTCAGGAAAAATGTGTCAGTAGGAGAAAGGAGGAGCTGAA Cluster: [ ] Orangutan: CTTCACATTTCCATATCATAC-----TTTACGCTCTTACTTCATGGGCTCCTGGGCATTTGGTGT----GTTTTTCTCCTTTCCTCTTTGAACAAAGTCAGGAAAAATGTGTCAGTAGGAGAAAGGAGGAGCTGAA Human > Gorilla --------------- chr4:176238519-176238522 Template switch process: F1: L AGAAATCATTCTCTTGCAAACTTCACATTTCCATATCATACTTTAC 1 F3: 4 TTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTTT R RF: GGAAATCATTCTCTTGCAAACTTCACATTTCCATATCATACTTTACTTTACGCTATTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTGTTTTTCTCCTTTCCTCTTTGAACAAAGTCAGGAAAAATGTGTCAGT RR: CCTTTAGTAAGAGAACGTTTGAAGTGTAAAGGTATAGTATGAAATGAAATGCGATAATGAAGTACCCGAGGACCCGTAAACCAGACAAACAAAAAGAGGAAAGGAGAAACTTGTTTCAGTCCTTTTTACACAGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -37.7) CATTCTCTTGCAAACTTCACATTTCCATATCA-----TACTTTACaCTgTTACTTCATGGGCTCCTGGGCATTTGGTC----TGTTTTT CATTCTCTTGCAAACTTCACATTTCCATATCATACTTTACTTTACGCTATTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTGTTTTT Template switch alignment (log-probability: -27.3) CATTCTCTTGCAAACTTCACATTTCCATATCATACTTTAC|ACTG|TTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTtT CATTCTCTTGCAAACTTCACATTTCCATATCATACTTTAC|ACTG|TTACTTCATGGGCTCCTGGGCATTTGGTCTGTTTGT ========== Event 2586 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: acttaaatcagaccAGAGTGTAGGCATCCATGGAT----TTATACATTGAACTTTCCTCATT Chimp: acttaaatcagaccAGAGTGTAGGCATCCATGGAT----TTATACATTGAACTTTCCTCATT ↓ 3 2 1 4 Gorilla: acttaaatcagaccAGAGTGTAGGCATCCATGGATGCCTACATACATTGAACTTTCTTCATT ↑ 3 2 1 4 Human: acttaaatcagaccAGAGTGTAGGCATCCATGGAT----TTATACATTGAACTTTCCTCATT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr4:26532737-26532742 Template switch process: F1: L TAAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAT 1 F3: 4 ATACATTGAACTTTCTTCATTTTCCTCCTCTTTCACTTTA R RF: TAAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGATTTATACATTGAACTTTCCTCATTTTCCTCCTCTTTCACTTTA RR: ATTTCTTGAATTTAGTCTGGTCTCACATCCGTAGGTACCTAAATATGTAACTTGAAAGGAGTAAAAGGAGGAGAAAGTGAAAT F2: 3 CATCCG 2 Unidirectional alignment (log-probability: -33.2) AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAtgccTacATACATTGAACTTTCtTCATTTTCCTCCTCTTTCACTTTA AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGA----TTTATACATTGAACTTTCCTCATTTTCCTCCTCTTTCACTTTA Template switch alignment (log-probability: -22) AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAT|GCCTAC|ATACATTGAACTTTCtTCATTTTCCTCCTCTTTCACTTTA AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAT|GCCTAC|ATACATTGAACTTTCCTCATTTTCCTCCTCTTTCACTTTA Chimp > Gorilla --------------- chr4:26532737-26532742 Template switch process: F1: L TAAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAT 1 F3: 4 ATACATTGAACTTTCTTCATTTTCCTCCTCTTTCACTTTA R RF: TAAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGATTTATACATTGAACTTTCCTCATTTTCCTCCTCTTTCACTTTA RR: ATTTCTTGAATTTAGTCTGGTCTCACATCCGTAGGTACCTAAATATGTAACTTGAAAGGAGTAAAAGGAGGAGAAAGTGAAAT F2: 3 CATCCG 2 Unidirectional alignment (log-probability: -33.2) AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAtgccTacATACATTGAACTTTCtTCATTTTCCTCCTCTTTCACTTTA AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGA----TTTATACATTGAACTTTCCTCATTTTCCTCCTCTTTCACTTTA Template switch alignment (log-probability: -22) AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAT|GCCTAC|ATACATTGAACTTTCtTCATTTTCCTCCTCTTTCACTTTA AAAGAACTTAAATCAGACCAGAGTGTAGGCATCCATGGAT|GCCTAC|ATACATTGAACTTTCCTCATTTTCCTCCTCTTTCACTTTA ========== Event 2587 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTTGAGAAGCGCGGCTAGCT--GGCTGTGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAA ↓ 1 4 3 2 Chimp: CCTTGAGAAGCGCGGCTAGCTGTAGATGCGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAA Gorilla: CCTTGAGAAGCGCAGCTAGCT--GGCTGTGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAA Human: CCTTGAGAAGCGCGGCTAGCT--GGCTGTGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAA Cluster: [ ] Orangutan: CCTTGAGAAGCGCGGCTAGCT--GGCTGTGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAT Human > Chimp ------------- chr4:168026264-168026270 Template switch process: F1: L TATTTGGAGCCAAATCTCTTCCTTGAGAAGCGCGGCTAGCTG 1 F3: 4 GTCCTTCATGCATCTACAATAATCTGCTTAGGTCAAAGGA R RF: TATTTGGAGCCAAATCTCTTCCTTGAGAAGCGCGGCTAGCTGGCTGTGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAAAGGA RR: ATAAACCTCGGTTTAGAGAAGGAACTCTTCGCGCCGATCGACCGACACAGGAAGTACGTAGATGTTATTAGACGAATCCAGTTTCCT F2: 3 CGTAGAT 2 Unidirectional alignment (log-probability: -25.8) TTTGGAGCCAAATCTCTTCCTTGAGAAGCGCGGCTAGCTGtaGaTGcGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAAAGGA TTTGGAGCCAAATCTCTTCCTTGAGAAGCGCGGCTAGCTG--GCTGTGTCCTTCATGCATCTACAATAATCTGCTTAGGTCAAAGGA Template switch alignment (log-probability: -16.2) TTTGGAGCCAAATCTCTTCCTTGAGAAGCGCGGCTAGCTG|TAGATGC|GTCCTTCATGCATCTACAATAATCTGCTTAGGTCAAAGGA TTTGGAGCCAAATCTCTTCCTTGAGAAGCGCGGCTAGCTG|TAGATGC|GTCCTTCATGCATCTACAATAATCTGCTTAGGTCAAAGGA ========== Event 2588 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AAGATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAAA----ACA-----------ATACCTGCTTTCTTGTGGAGGTCA ↓ 4 2 1 Chimp: AAGATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAACATGCACAAATTTGTGCATGTTACTGCTTTCTTGTGGAGGTCA Gorilla: Human: AAGATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAAA----ACA-----------ATACCTGCTTTCTTGTGGAGGTCA Cluster: [ ] Orangutan: Human > Chimp ------------- chr4:62416332-62416341 Template switch process: F1: L AGATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAA 1 F3: 4 TTTGTGCATGTTA------------------CTGCTTTCTTGTGGAGGTCAAAATTTGTTATCAAGTAATA R RF: AGATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAAAACAATACCTGCTTTCTTGTGGAGGTCAAAATTTGTTATCAAGTAATA RR: TCTAAACGTTTATTACAGAAACACGTACAATGTTGAAAGTTTTGTTATGGACGAAAGAACACCTCCAGTTTTAAACAATAGTTCATTAT F2: 3 AAACACGTAC 2 Unidirectional alignment (log-probability: -53.1) GATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCA-------ACatgcacaaatttgtgcatgttaCTGCTTTCTTGTGGAGGTCAAAATTTG GATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAAAACAATAC----------------------CTGCTTTCTTGTGGAGGTCAAAATTTG Template switch alignment (log-probability: -27.9) GATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAA|CATGCACAAA|TTTGTGCATGTTA------------------CTGCTTTCTTGTGGAGGTCAAAATTTG GATTTGCAAATAATGTCTTTGTGCATGTTACAACTTTCAA|CATGCACAAA|TTTGTGCATGTTACAACTTTCAAAACAATACCTGCTTTCTTGTGGAGGTCAAAATTTG ========== Event 2589 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTTGTCCACAGGCAAACCCTAAAACTGTTGGGATGTAGGATCTGTGCTTGGATTTAGAagcag-cgaaatataggtaatgaaaattaaaatggagctgaggacatcttggttctcactctagacttgaccttgggtgagtaaaggaattgcttgagtcacagtttcctcatctgtaaactgaagca ↑ 1 4 3 2 Chimp: GGTTGTCCACAGGCAAACCCTCCTTCTCTTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGCTGAAATATAGGTAATGAAAATTAAAATGGAGCTGAGGACatcttggttctcactctagacttgaccttgggtgagtaaaggaattgcttgagtcacagttttctcatctgtaaactgaagca Gorilla: GGTTGTCCACAGGCAAACCCTCCTTCTGTTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGCTGAAATATAGGTAATGAAAATTAAAATGgagctgaggagatcttggttctcactctagacttgaccttgggtgagtaaaggaattgcttgagtcacagttttctcacctgtaaactgaagca Human: GGTTGTCCACAGGCAAACCCTAAAACTGTTGGGATGTAGGATCTGTGCTTGGATTTAGAagcag-cgaaatataggtaatgaaaattaaaatggagctgaggacatcttggttctcactctagacttgaccttgggtgagtaaaggaattgcttgagtcacagtttcctcatctgtaaactgaagca Cluster: [ ] Orangutan: GGTTGTCCACAGGCAAACCCTAAAGCTGTTGGGATGTAGGATCTGTGCTTGGATTTGGAAGCAGCTGAAATATAGGTAAtgaaaattaaaatggagctgaggagatcttggttctcactctagatttgaccttgggtgagtaaaggaattgcttgagtcacagttttctcatctgtaaactgaagCA Chimp > Human ------------- chr4:25501575-25501581 Template switch process: F1: L TGGTGAATCTTCAGAAGGAGGGTTGTCCACAGGCAAACCCT 1 F3: 4 TTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGCGA R RF: TGGTGAATCTTCAGAAGGAGGGTTGTCCACAGGCAAACCCTCCTTCTCTTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGCTGAAATATAGGTAATGAAAATTAAAATGGAGCTGAGGACATCTTGGTTCTCACTCTAGACTTGACCTTGGGTGAGTAAAGGAATTGCTTGAGTCACAGTTTT RR: ACCACTTAGAAGTCTTCCTCCCAACAGGTGTCCGTTTGGGAGGAAGAGAACCCTACATCCTAGACACGAACCTAAATCTTCGTCGACTTTATATCCATTACTTTTAATTTTACCTCGACTCCTGTAGAACCAAGAGTGAGATCTGAACTGGAACCCACTCATTTCCTTAACGAACTCAGTGTCAAAA F2: 3 GTCAAAA 2 Unidirectional alignment (log-probability: -41) GGTGAATCTTCAGAAGGAGGGTTGTCCACAGGCAAACCCTaaaaCTgTTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGC-GA GGTGAATCTTCAGAAGGAGGGTTGTCCACAGGCAAACCCTCCTTCTCTTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGCTGA Template switch alignment (log-probability: -26.2) GGTGAATCTTCAGAAGGAGGGTTGTCCACAGGCAAACCCT|AAAACTG|TTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAGcga GGTGAATCTTCAGAAGGAGGGTTGTCCACAGGCAAACCCT|AAAACTG|TTGGGATGTAGGATCTGTGCTTGGATTTAGAAGCAG--C ========== Event 2590 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGGTGGGCCCTGAACTATGGTAACTATGGTTACCATGTGGTAACCATGTGGT Chimp: GTGGTGGGCCCTGAACTATGG-GCCCATAGTTACCATGTGGTAACCATGTGGT Gorilla: GTGGTGGGCCCTGAACTATGG-GCCCATAGTTACCATGTGGTAACCATGTGGT ↓ 1 3 4 2 Human: GTGGTGGGCCCTGAACTATGGTAACTATGGTTACCATGTGGTAACCATGTGGT Cluster: [ ] Orangutan: GTGGTGGGCCCTGAACTA---------------------------------CT Gorilla > Human --------------- chr4:25443635-25443642 Template switch process: F1: L TTATCAATTTCGTCTGAAATGTGGTGGGCCCTGAACTATGG 1 F3: 4 GTTACCATGTGGTAACCATGTGGTGGGCACAATCCTTTAA R RF: TTATCAATTTTGTCTGAAATGTGGTGGGCCCTGAACTATGGGCCCATAGTTACCATGTGGTAACCATGTGGTGGGCATAATCCTTTAA RR: AATAGTTAAAACAGACTTTACACCACCCGGGACTTGATACCCGGGTATCAATGGTACACCATTGGTACACCACCCGTATTAGGAAATT F2: 3 GTATCAAT 2 Unidirectional alignment (log-probability: -40.6) TATCAATTTcGTCTGAAATGTGGTGGGCCCTGAACTATGG-----TAactatgGTTACCATGTGGTAACCATGTGGTGGGCAcAATCCTTTAA TATCAATTTTGTCTGAAATGTGGTGGGCCCTGAACTATGGGCCCATA------GTTACCATGTGGTAACCATGTGGTGGGCATAATCCTTTAA Template switch alignment (log-probability: -27.8) TATCAATTTcGTCTGAAATGTGGTGGGCCCTGAACTATGG|TAACTATG|GTTACCATGTGGTAACCATGTGGTGGGCAcAATCCTTTAA TATCAATTTTGTCTGAAATGTGGTGGGCCCTGAACTATGG|TAACTATG|GTTACCATGTGGTAACCATGTGGTGGGCATAATCCTTTAA ========== Event 2591 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGACTCAACATGAAGTCTGTCTCAGAATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACTGGGGTAAGTCTTTTCCCTCCAGGAGCTAAGTTGACCTCTGGGGAACGAAGAAGGGAGGTGCTAAGCTGAGCATACCAGGGCTCTGAAATTAACTGAGCTGCCATCATAGGAAAGAA ↑ 1 4 3 2 Chimp: GGACTCAACATGAAGTCTGTCC--TAATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACTGGGGTAAGTCTTTTCCCTCCAGGAGCTAAGTTGACCTCTGGGGAAAGAAGAAGGGAGGTGCTAAGCTGAGCATACCAGGGCTCTGAAATTAACTGAGCTGCCATCATAGGAAAGAA Gorilla: GGACTCAACATGAAGTCTGTCC--TAATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACTGGGGTAAGTCGTTTCCCCCCAGGAGCTAAGTTGACCTCTGGGGAACGAAGAAGGGAGGTGCTAAGCTGAGCATACCAGGGCTCTGAAATTAACTGAGCTGCCATCATAGGAAAGAA Human: GGACTCAACATGAAGTCTGTCTCAGAATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACTGGGGTAAGTCTTTTCCCTCCAGGAGCTAAGTTGACCTCTGGGGAACGAAGAAGGGAGGTGCTAAGCTGAGCATACCAGGGCTCTGAAATTAACTGAGCTGCCATCATAGGAAAGAA Cluster: [ ] Orangutan: GGACTCAA-CTGAAGTCTGTCC--TAATTCTGAGCCTCAGAACCAGGTGTAGGCAAAGCTGCACTGGGGTAAGTCTTTTCCCCCCAGGAGCTAAGTTGACCTCTGGGAGAGGAAGAAGGGAAGTGCT-------------TAGGGCTCTGAAATTAACTGAGCTGCTATCATAGGAAAGAA Chimp > Human ------------- chr4:173531802-173531805 Template switch process: F1: L AAATGTTACCTTTGGTTGGAGGACTCAACATGAAGTCTGTC 1 F3: 4 AATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACT R RF: AAATGTTACCTTTGGTTGGAGGACTCAACATGAAGTCTGTCCTAATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACTGGGGTAAGTCTTTTCCCTCCAGGAGCTAAGTTGACCTCTGGGGAAAGAAGAAGGGAGGTGCTAAGCTGAGCATACCAGGGCTCTGAAATTAACTGA RR: TTTACAATGGAAACCAACCTCCTGAGTTGTACTTCAGACAGGATTAAGACTCGGAGTCTTGGTCCACGTCCGTTTCGACGTGACCCCATTCAGAAAAGGGAGGTCCTCGATTCAACTGGAGACCCCTTTCTTCTTCCCTCCACGATTCGACTCGTATGGTCCCGAGACTTTAATTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -25.5) AATGTTACCTTTGGTTGGAGGACTCAACATGAAGTCTGT-CTcagAATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACT AATGTTACCTTTGGTTGGAGGACTCAACATGAAGTCTGTCCT---AATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACT Template switch alignment (log-probability: -15.8) AATGTTACCTTTGGTTGGAGGACTCAACATGAAGTCTGTC|TCAG|AATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACT AATGTTACCTTTGGTTGGAGGACTCAACATGAAGTCTGTC|TCAG|AATTCTGAGCCTCAGAACCAGGTGCAGGCAAAGCTGCACT ========== Event 2592 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGGCACTACACTATGCTGATTTGAAGA-----------ATTCCTATTGAAGAATTCAATAGGAATTC-TTCGGATTACATACATTGTCCTAT Chimp: TGGGCACTACACTGTGCTGATTTGA--------------ATT-----------CTTCAATAGGAATTCAATAGGATTACATACATTGTCCTAT ↑ 1 3 2 4 Gorilla: TGGGCACTACACTGTGCTGATCTGAAGAATTCCTATTGAATTCTTATTGAAGAATTCAATAGGAATTC-TTCGGATTACATACATTGTCCTAT Human: TGGGCACTACACTATGCTGATTTGAAGA-----------ATTCCTATTGAAGAATTCAATAGGAATTC-TTCGGATTACATACATTGTCCTAT Cluster: [ ] Orangutan: TGGGCATTACACTGTGCTGATTTGAAGA-----------ATTCCTGT--------------TGAATTC-TTCAAATTACATACATTGTCCTAC Gorilla > Chimp --------------- chr4:177314414-177314439 Template switch process: F1: L ATACGGTATCTTTCTGGCCACAGGGATCAGGTGGATGGGTAGTAACGCTACCTGTCTCTTTTTTTTTTTACAGATGCAACTGGGCACTACACTGTGCTGAT 1 F3: 4 GGATTACATACATTGTCCTATACTTCATTTCTCTGACCAGGGCACCTATGATTTTTATAGTCTTATATTAATAATAATTT R RF: ATACGGTATCTTTCTGGCCACAGGGATCAGGTGGATGGGTAGTAACGCTACCTGTCTCTTTTTTTTT-TACAGATGCAACTGGGCACTACACTGTGCTGATCTGAAGAATTCCTATTGAATTCTTATTGAAGAATTCAATAGGAATTCTTCGGATTACATACATTGTCCTATACTTCATTTCTCTGACCAGGGCACCTATGATTTTTATAGTCTTATATCAATAATAATTT RR: TATGCCATAGAAAGACCGGTGTCCCTAGTCCACCTACCCATCATTGCGATGGACAGAGAAAAAAAAA-ATGTCTACGTTGACCCGTGATGTGACACGACTAGACTTCTTAAGGATAACTTAAGAATAACTTCTTAAGTTATCCTTAAGAAGCCTAATGTATGTAACAGGATATGAAGTAAAGAGACTGGTCCCGTGGATACTAAAAATATCAGAATATAGTTATTATTAAA F2: 3 ATAACTTAAGGATAACTTCTTAAGTT 2 Unidirectional alignment (log-probability: -62.6) TTTTtTTTACAGATGCAACTGGGCACTACACTGTGCTGAT--------------TTGAATTC-----------TTCAATAGGAATTCaaTaGGATTACATACATTGTCCTATACTTCATTTCTCTGACCAG TTTT-TTTACAGATGCAACTGGGCACTACACTGTGCTGATCTGAAGAATTCCTATTGAATTCTTATTGAAGAATTCAATAGGAATTC-TTCGGATTACATACATTGTCCTATACTTCATTTCTCTGACCAG Template switch alignment (log-probability: -43.3) TTTTTTtTACAGATGCAACTGGGCACTACACTGTGCTGAT|TTGAATTCTTCAATAgGAATTCAATA|GGATTACATACATTGTCCTATACTTCATTTCTCTGACCAG TTTTTT-TACAGATGCAACTGGGCACTACACTGTGCTGAT|TTGAATTCTTCAATAAGAATTCAATA|GGATTACATACATTGTCCTATACTTCATTTCTCTGACCAG ========== Event 2593 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ATGAGAAATGAAGGCAAATAAGCTAGACAAA--------------------CGTTTGGCAGAAAGGGTATAG ↓ 3 1 4 Chimp: ATGAGAAATGAAGGCAAATAAGCTAGACGTT----------TGTCTAGCTTTGTTTGGCAGAAAGGGTATAG Gorilla: ATGAGAAATGAAGGCAAATAAGCTAGACGTTTGTCTAGCTT----------TGTTTGGCAGAAAGGGTATAG ↑ 3 1 4 Human: ATGAGAAATGAAGGCAAATAAGCTAGACAAA--------------------CGTTTGGCAGAAAGGGTATAG Cluster: [ ] Orangutan: ATGAGAAATGAAGGCAAATAAGCTAGACGTTTGTCTAGCTT----------TATTTGGCAGAAAGGGTATAG Human > Chimp ------------- chr4:169557441-169557453 Template switch process: F1: L CAAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC 1 F3: 4 TGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTGG R RF: CAAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGACAAACGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTGG RR: GTTTACTTCACACTACTCTTTACTTCCGTTTATTCGATCTGTTTGCAAACCGTCTTTCCCATATCAAGTAAAGTCTAAAATGACC F2: 3 TTCGATCTGTTTG 2 Unidirectional alignment (log-probability: -41.5) AAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAG----ACGTttgtctagctttgtTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG AAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGACAAACGT--------------TTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG Template switch alignment (log-probability: -22.9) AAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC|GTTTGTCTAGCTT|tGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG AAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC|GTTTGTCTAGCTT|CGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG Human > Gorilla --------------- chr4:178231147-178231159 Template switch process: F1: L CAAATGCAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC 1 F3: 4 TGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTGG R RF: CAAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGACAAACGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTGG RR: GTTTACTTCACACTACTCTTTACTTCCGTTTATTCGATCTGTTTGCAAACCGTCTTTCCCATATCAAGTAAAGTCTAAAATGACC F2: 3 TTCGATCTGTTTG 2 Unidirectional alignment (log-probability: -46.5) AAATGcAGTGTGATGAGAAATGAAGGCAAATAAGCTAGACgtttgtctagcttt----GTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG AAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC--------------AAACGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG Template switch alignment (log-probability: -28.4) AAATGcAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC|GTTTGTCTAGCTT|tGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG AAATGAAGTGTGATGAGAAATGAAGGCAAATAAGCTAGAC|GTTTGTCTAGCTT|CGTTTGGCAGAAAGGGTATAGTTCATTTCAGATTTTACTG ========== Event 2594 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCA------------------------GTTGAGAGAGGCTTGGAAAGA Chimp: AAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAGATTGCTTTTAGAGAAAAGCAAGCCTTGAGAGAGGCTTGGAAAGA ↑ 4 3 2 1 Gorilla: AAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCA------------------------GTTGAGAGAGGCTTGGAAAGA Human: AAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCA------------------------GTTGAGAGAGGCTTGGAAAGA Cluster: [ ] Orangutan: AAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCA------------------------ATTGAGAGAGGCTTGGACAGA Gorilla > Chimp --------------- chr4:24035601-24035609 Template switch process: F1: L CTCAAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAG 1 F3: 4 AGAGAAAAGCAAGCC-----TTGAGAGAGGCTTGGAAAGACACATCTACAGATGCATATT R RF: CTCAAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAGTTGAGAGAGGCTTGGAAAGACACATCTACAGATGCATATT RR: GAGTTTTCTTTCAGACTTATCCTCTCTTTTCGTTAGGAAGTCAACTCTCTCCGAACCTTTCTGTGTAGATGTCTACGTATAA F2: 3 TTTTCGTTA 2 Unidirectional alignment (log-probability: -45.4) CAAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAGattgcttttagagaaaagcaagccTTGAGAGAGGCTTGGAAAGACACAT CAAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAG------------------------TTGAGAGAGGCTTGGAAAGACACAT Template switch alignment (log-probability: -32.8) CAAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAG|ATTGCTTTT|AGAGAAAAGCAAgCC-----TTGAGAGAGGCTTGGAAAGACACAT CAAAAGAAAGTCTGAATAGGAGAGAAAAGCAATCCTTCAG|ATTGCTTTT|AGAGAAAAGCAATCCTTCAGTTGAGAGAGGCTTGGAAAGACACAT ========== Event 2595 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGGTTGTTTAATGAGAAAAC------------------ATCAAGGACTGCAGTCCTTGAACCATATGCTAGCCAATACA Chimp: GGGGTTGTTTAGTGAGAAAAC------------------ATCAAGGACTGCAGTCCTTGAACCATATGCTAGCCAATACG Gorilla: GGGGTTGTTTAATGAGAAAAC--------AAATGACTCTATATACCACTGCAGTCCTTGAACCATATGCTAGCCAATACA ↓ 1 4 3 2 Human: GGGGTTGTTTAATGAGAAAAC------------------ATCAAGGACTGCAGTCCTTGAACCATATGCTAGCCAATACA Cluster: [ ] Orangutan: GGGGTTGTTTAATGTGAAAACAAATGACT----------ATATACCACTGCAGTCCTTGAACCATATGCTAGCCAATACA Gorilla > Human --------------- chr4:23430867-23430872 Template switch process: F1: L ATAACTTAAAAAAATTATTTGGGGTTGTTTAATGAGAAAACA 1 F3: 4 ACTGCAGTCCTTGAACCATATGCTAGCCAATACAAAAGCC R RF: ATAA-TTAAAAAAATTATTTGGGGTTGTTTAATGAGAAAACAAATGACTCTATATACCACTGCAGTCCTTGAACCATATGCTAGCCAATACAAAAGCC RR: TATT-AATTTTTTTAATAAACCCCAACAAATTACTCTTTTGTTTACTGAGATATATGGTGACGTCAGGAACTTGGTATACGATCGGTTATGTTTTCGG F2: 3 GGAACT 2 Unidirectional alignment (log-probability: -40.9) AAcTTAAAAAAATTATTTGGGGTTGTTTAATGAGAAAACAtcAAgG------------ACTGCAGTCCTTGAACCATATGCTAGCCAATACAAAAGCC AA-TTAAAAAAATTATTTGGGGTTGTTTAATGAGAAAACA--AATGACTCTATATACCACTGCAGTCCTTGAACCATATGCTAGCCAATACAAAAGCC Template switch alignment (log-probability: -27.7) AAcTTAAAAAAATTATTTGGGGTTGTTTAATGAGAAAACA|TCAAGG|ACTGCAGTCCTTGAACCATATGCTAGCCAATACAAAAGCC AA-TTAAAAAAATTATTTGGGGTTGTTTAATGAGAAAACA|TCAAGG|ACTGCAGTCCTTGAACCATATGCTAGCCAATACAAAAGCC ========== Event 2596 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ---------aaa----aaaaaTTAAACATTAAAAAGATTAACTTTTTAATGtttaatttttgtgggtacatagtag ↑ 1 4 3 2 Chimp: ------------aaaaaaaaaTTAAACATTAA-AATATTAACTTTTTAATGtttaatttttgtgggtacatagtag Gorilla: -----aaaa-------aaaaaTTAAACATTAAAAAGATTAACTTTTTAATGtttaatttttgtgggtacatagtag Human: ---------aaa----aaaaaTTAAACATTAAAAAGATTAACTTTTTAATGtttaatttttgtgggtacatagtag Cluster: [ ] Orangutan: taaat-----------aaaaattaaacattaaaaaGATTAACTTTTTACTGtttaatttttgtgggtacatagtag Chimp > Human ------------- chr4:169061038-169061052 Template switch process: F1: L GACCACGCCTGTCTCAAAAAAAAAAA 1 F3: 4 ATTAACTTTTTAATGTTTAATTTTTGTGGGTACATAGTAG R RF: GACCACGCCTGTCTCAAAAAAAAAAAATTAAACATTAAAATATTAACTTTTTAATGTTTAATTTTTGTGGGTACATAGTAG RR: CTGGTGCGGACAGAGTTTTTTTTTTTTAATTTGTAATTTTATAATTGAAAAATTACAAATTAAAAACACCCATGTATCATC F2: 3 GAAAAATTACAAATT 2 Unidirectional alignment (log-probability: -28.6) GACCACGCCTGTCTC-AAAAAAAAAAATTAAACATTaAAAAgATTAACTTTTTAATGTTTAATTTTTGTGGGTACATAGTAG GACCACGCCTGTCTCAAAAAAAAAAAATTAAACATT-AAAATATTAACTTTTTAATGTTTAATTTTTGTGGGTACATAGTAG Template switch alignment (log-probability: -16.8) GACCACGCCTGTCTCAAAAAAAAAAA|TTAAACATTAAAAAG|ATTAACTTTTTAATGTTTAATTTTTGTGGGTACATAGTAG GACCACGCCTGTCTCAAAAAAAAAAA|TTAAACATTAAAAAG|ATTAACTTTTTAATGTTTAATTTTTGTGGGTACATAGTAG ========== Event 2597 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AGGTCAACAGGATTGAGCACT---CACAAGAGGGAATGCGACAGCCTTTCTTAGAGAGCATCCCCAGGCTCTGAAAAGCTGAAGAATCTTAAGGACTTGTAGAGCCCTCACCTTTGACTCAGTTCTTGAGAGCGAGCTTATTCTTTCCC Chimp: AGGTCAACAGGATTGAGCACTCCTCAACAGGGGGAATGCGACAGCCTTTCTTAGAGAGCATCCCCAGGCTCCGAAAAGCTGAAGAATCTTAAGGACTTGTAGAGCCCTCACCTTTGACTCAGTTCTTGAGAGCGAGCTTATTCTTTCCC ↓ 1 4 3 2 Gorilla: AGGTCAACAGGATTGAGCACT---CTCAAGAGGGAATGCGACGGCCTTTCTTAGAGAGCATCCCCAGGCTCTGAAAAGCTGAAGAATCTTAAGGACTTGTAGAGCCCTCACCTTTGACTCAGTTCTTGAGAGCGAGCTTATTCTTTCCC Human: AGGTCAACAGGATTGAGCACT---CACAAGAGGGAATGCGACAGCCTTTCTTAGAGAGCATCCCCAGGCTCTGAAAAGCTGAAGAATCTTAAGGACTTGTAGAGCCCTCACCTTTGACTCAGTTCTTGAGAGCGAGCTTATTCTTTCCC Cluster: [ ] Orangutan: GGGTCAACAGGATTGAGCACT---CACAAGAGGGAATGTGACAGCCTTTCTTAGAGAGCATCCCCAGGCTCTGAAAAGCTGAAAAATCTTAAGGTCTTGTAGAGCCCTCACCTTTGACTCAGTTCTTGAGAGCGAGCTTACTCTTTCCC Chimp > Gorilla --------------- chr4:22996427-22996432 Template switch process: F1: L CTGCTCCTTGTGTCCCCTGAAGGTCAACAGGATTGAGCACTC 1 F3: 4 GGGAATGCGACGGCCTTTCTTAGAGAGCATCCCCAGGCTC R RF: CTGCTCCTTGTGTCCCCTGAAGGTCAACAGGATTGAGCACTCCTCAACAGGGGGAATGCGACAGCCTTTCTTAGAGAGCATCCCCAGGCTCCGAAAAGCTGAAGAATCTTAAGGACTTGTAGAGCCCTCACCTTTGACTCAGTTCTTGA RR: GACGAGGAACACAGGGGACTTCCAGTTGTCCTAACTCGTGAGGAGTTGTCCCCCTTACGCTGTCGGAAAGAATCTCTCGTAGGGGTCCGAGGCTTTTCGACTTCTTAGAATTCCTGAACATCTCGGGAGTGGAAACTGAGTCAAGAACT F2: 3 AGAACT 2 Unidirectional alignment (log-probability: -31.9) GCTCCTTGTGTCCCCTGAAGGTCAACAGGATTGAGCACT-CTCA--AGaGGGAATGCGACgGCCTTTCTTAGAGAGCATCCCCAGGCTC GCTCCTTGTGTCCCCTGAAGGTCAACAGGATTGAGCACTCCTCAACAGGGGGAATGCGACAGCCTTTCTTAGAGAGCATCCCCAGGCTC Template switch alignment (log-probability: -22) GCTCCTTGTGTCCCCTGAAGGTCAACAGGATTGAGCACTC|TCAAGA|GGGAATGCGACgGCCTTTCTTAGAGAGCATCCCCAGGCTC GCTCCTTGTGTCCCCTGAAGGTCAACAGGATTGAGCACTC|TCAAGA|GGGAATGCGACAGCCTTTCTTAGAGAGCATCCCCAGGCTC ========== Event 2598 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGAATACGCTTAAttttttttAGCACATAGATCATAACTT----TCCTTTTGTGATGTTAAACTAGATGATTTTTAT Chimp: GTGAATACGCTTAAttttttttAGCACATAGATCATAACTT----TCCTTTTGTGATGTTAAACTAGATGATTTTTAT ↓ 3 2 1 4 Gorilla: GTGAATACGCTTAAttttttttAGCACATAGATCATAACTT--------GTGCTAAAGTTAAACTAGATGATTTTTAC ↑ 3 2 1 4 Human: GTGAATACGCTTAAttttttttAGCACATAGATCATAACTT----TCCTTTTGTGATGTTAAACTAGATGATTTTTAT Cluster: [ ] Orangutan: GTGAATATACTTAAttttttttAGCATATAGATCATAACTTTCCT----TTTGTGATGTTAAACTAGATGATTTTTAT Human > Gorilla --------------- chr4:182400146-182400153 Template switch process: F1: L GTGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTT 1 F3: 4 GTTAAACTAGATGATTTTTACTGTATGTTTGAAAAATGTT R RF: GTGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTTTCCTTTTGTGATGTTAAACTAGATGATTTTTATTGTATGTTTGAAAAATGTT RR: CACTTATGCGAATTAAAAAAAATCGTGTATCTAGTATTGAAAGGAAAACACTACAATTTGATCTACTAAAAATAACATACAAACTTTTTACAA F2: 3 AAATCGTG 2 Unidirectional alignment (log-probability: -36.4) TGAATACGCTTAATTTTTTTTAGCACATAGATCATAAC-------TTGTGctaAaGTTAAACTAGATGATTTTTAcTGTATGTTTGAAAAATGTT TGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTTTCCTTTTGTG---ATGTTAAACTAGATGATTTTTATTGTATGTTTGAAAAATGTT Template switch alignment (log-probability: -22.3) TGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTT|GTGCTAAA|GTTAAACTAGATGATTTTTAcTGTATGTTTGAAAAATGTT TGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTT|GTGCTAAA|GTTAAACTAGATGATTTTTATTGTATGTTTGAAAAATGTT Chimp > Gorilla --------------- chr4:182400146-182400153 Template switch process: F1: L GTGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTT 1 F3: 4 GTTAAACTAGATGATTTTTACTGTATGTTTGAAAAATGTT R RF: GTGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTTTCCTTTTGTGATGTTAAACTAGATGATTTTTATTGTATGTTTGAAAAATGTT RR: CACTTATGCGAATTAAAAAAAATCGTGTATCTAGTATTGAAAGGAAAACACTACAATTTGATCTACTAAAAATAACATACAAACTTTTTACAA F2: 3 AAATCGTG 2 Unidirectional alignment (log-probability: -36.4) TGAATACGCTTAATTTTTTTTAGCACATAGATCATAAC-------TTGTGctaAaGTTAAACTAGATGATTTTTAcTGTATGTTTGAAAAATGTT TGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTTTCCTTTTGTG---ATGTTAAACTAGATGATTTTTATTGTATGTTTGAAAAATGTT Template switch alignment (log-probability: -22.3) TGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTT|GTGCTAAA|GTTAAACTAGATGATTTTTAcTGTATGTTTGAAAAATGTT TGAATACGCTTAATTTTTTTTAGCACATAGATCATAACTT|GTGCTAAA|GTTAAACTAGATGATTTTTATTGTATGTTTGAAAAATGTT ========== Event 2599 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCTTCCTCCCATCACACTGCCCTTCTGTTTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAAACTGGAGGGCTTGCTGGAGGGCTGCTTCTTC ↑ 3 2 1 4 Chimp: CTCTTCCTCCCATCACACTGCCCTCCTGTTTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAAGC------CATTGCTGGAGGGCTGCTTCTTC Gorilla: CTTTTCCTCCCATCACACTGCCCTTCTGTTTTCACTTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAAGC------CATTGCTGGAGGGCTGCTTCTTC Human: CTCTTCCTCCCATCACACTGCCCTTCTGTTTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAAACTGGAGGGCTTGCTGGAGGGCTGCTTCTTC Cluster: [ ] Orangutan: CTTTTCCTCCCATCACAATGCCCTTCTGTTTTTACCTGCTCCCATCTGCCAGCCTCCCAGTAAGCAGAAGC------CATTGCTGGAAGGCTGCTTCTTC Chimp > Human ------------- chr4:17408434-17408443 Template switch process: F1: L TTTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAA 1 F3: 4 TTGCTGGAGGGCTGCTTCTTCCAGCAAGGAGAAACGGTGA R RF: GCCCTCCTGTTTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAAGCCATTGCTGGAGGGCTGCTTCTTCCAGCAAGGAGAAACGGTGA RR: CGGGAGGACAAAAGTGGACGAGAATAGATGGTCGGAGGGTCGTTCGTCTTCGGTAACGACCTCCCGACGAAGAAGGTCGTTCCTCTTTGCCACT F2: 3 CGGGAGGTCA 2 Unidirectional alignment (log-probability: -32.8) TTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAAactggaggGC--TTGCTGGAGGGCTGCTTCTTCCAGCAAGGAGAAACGGTGA TTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAA--------GCCATTGCTGGAGGGCTGCTTCTTCCAGCAAGGAGAAACGGTGA Template switch alignment (log-probability: -22.5) TTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAA|ACtGGAGGGC|TTGCTGGAGGGCTGCTTCTTCCAGCAAGGAGAAACGGTGA TTTCACCTGCTCTTATCTACCAGCCTCCCAGCAAGCAGAA|ACAGGAGGGC|TTGCTGGAGGGCTGCTTCTTCCAGCAAGGAGAAACGGTGA ========== Event 2600 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: GGAGTTAAGTTTCTAAAAAGTCTAAAAAACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAAATACGCTAAACCAAAGATGAAATTCAAATTTTTAAAAAACTGATTTTCCTCATATGGAATAGG ↓ 1 4 3 2 Chimp: GGAGTAAAGTTTCTAAAAAGTTCA---GACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAAATACGCTAAACCAAAGATGAAATTCAAATTTTTAAAAAACTGATTTTCCTTATATGGAATAGG Gorilla: GGAGTTAAGTTTCTAAAAAGTCCA---GACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAAATACACTAAACCAAAGATGAAATTCAAATTTTTAAAAAACTGATTTTCCTTATATGGAATAGG Human: GGAGTTAAGTTTCTAAAAAGTCTAAAAAACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAAATACGCTAAACCAAAGATGAAATTCAAATTTTTAAAAAACTGATTTTCCTCATATGGAATAGG Cluster: [ ] Orangutan: GGAGTTAAGTTTCTAAAAAGTCCA---GACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAAATATACTAAACCAAAGATGAAATTCAAATTTTTAAAAAACTGATTTTCCTCATATGGAATAGA Human > Chimp ------------- chr4:17887104-17887107 Template switch process: F1: L CCAGGCACAGGTTATATTTAGGAGTAAAGTTTCTAAAAAGT 1 F3: 4 ACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAA R RF: CCAGGCACAGGTTATATTTAGGAGTTAAGTTTCTAAAAAGTCTAAAAAACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAAATACGCTAAACCAAAGATGAAATTCAAATTTTTAAAAAACTGA RR: GGTCCGTGTCCAATATAAATCCTCAATTCAAAGATTTTTCAGATTTTTTGATAAAGAAAGGTCGAAATATGAATAGATTTTTCTGGTTTATGCGATTTGGTTTCTACTTTAAGTTTAAAAATTTTTTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -33.2) CAGGCACAGGTTATATTTAGGAGTaAAGTTTCTAAAAAGT-------tcagACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAA CAGGCACAGGTTATATTTAGGAGTTAAGTTTCTAAAAAGTCTAAAAA----ACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAA Template switch alignment (log-probability: -21.8) CAGGCACAGGTTATATTTAGGAGTaAAGTTTCTAAAAAGT|TCAG|ACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAA CAGGCACAGGTTATATTTAGGAGTTAAGTTTCTAAAAAGT|TCAG|ACTATTTCTTTCCAGCTTTATACTTATCTAAAAAGACCAA ========== Event 2601 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTGGTTCTTCGCGGTGTTTA--CAGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTAAGGTGCCAATCTACCGCATCTTGAATCTGACTGTTGCAGACGAACTG ↓ 1 4 3 2 Chimp: TCCTGGTTCTTCGCGGTGTTTGATTCGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTAAGGTGCCAATCTACCGCATCTTGAATCTGACTGTTGCAGACGAACTG ↑ 1 4 3 2 Gorilla: TCCTGGTTCTTCGCGGTGTTTA--CAGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTAAGGTGCCAATCTACCGCATCTTGAATCTGACTGTTGCAGACGAACTG Human: TCCTGGTTCTTCGCGGTGTTTA--CAGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTAAGGTGCCAATCTACCGCATCTTGAATCTGACTGTTGCAGACGAACTG Cluster: [ ] Orangutan: TCCTGGTTCTTCGCGGTGTTTA--CAGTGGGTTTTGATTCGGGTGAAGAAGATCCAAATGAGGTTAAGGTGCCATTCCACCGCATCTTGAATCTGACTGTTGCAGACGAACTG Human > Chimp ------------- chr4:16779334-16779338 Template switch process: F1: L ATGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT 1 F3: 4 GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA R RF: ATGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTTACAGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTAAGGTGCCAATCTACCGCATCTTGAATC RR: TACTAATTTCGGCACTTCAAAGGACCAAGAAGCGCCACAAATGTCACCCAAAACTAAGCCCCCTTCTTCTCGGTTTTCTCCAATTCCACGGTTAGATGGCGTAGAACTTAG F2: 3 CTTAG 2 Unidirectional alignment (log-probability: -28.5) TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTTgattc---GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT-----ACAGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA Template switch alignment (log-probability: -15.9) TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT|GATTC|GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT|GATTC|GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA Gorilla > Chimp --------------- chr4:16779334-16779338 Template switch process: F1: L ATGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT 1 F3: 4 GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA R RF: ATGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTTACAGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTAAGGTGCCAATCTACCGCATCTTGAATC RR: TACTAATTTCGGCACTTCAAAGGACCAAGAAGCGCCACAAATGTCACCCAAAACTAAGCCCCCTTCTTCTCGGTTTTCTCCAATTCCACGGTTAGATGGCGTAGAACTTAG F2: 3 CTTAG 2 Unidirectional alignment (log-probability: -28) TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT---gattcGTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTTACA-----GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA Template switch alignment (log-probability: -16.4) TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT|GATTC|GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA TGATTAAAGCCGTGAAGTTTCCTGGTTCTTCGCGGTGTTT|GATTC|GTGGGTTTTGATTCGGGGGAAGAAGAGCCAAAAGAGGTTA ========== Event 2602 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 134 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCAGGGTCTCCATGGGTCAGATCCAGGTATGGCTATCCCCTGTTCTTTCTTTTGTATAGCAATGTATATAAATGGTCTTTCCTCTGGTCTGTATGGCCAGGAGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCCAGAATATCAGATAGGAAGAACTCACAgggacactccaaatgtattctgggggacactaaatgtattcacagggacactccaaatgatattctggATGGGAAGAACTCACAGGA ↑ 1 4 3 2 Chimp: CCAGGGTCTCCATGGGTCAGATCCAGGTATGGCTATCCCCTGTTCTTCCTTTTGTATAGCAATGTATATAAATGGTCTTTCCTCTGGTCTGTATGGCCAGGAGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCT--------GGATGGGAAGAACTCACAgggacactccaaatgtattctgggggacactaaatgtattcacagggacactccaaatgatattctggATGGGAAGAACTCACAGGA Gorilla: CCAGGGTCTCCATGGGTCAGATCCAGGTATGGCTATCCCCTGTTCTTTCTTTTGTATAGCAATGTATATAAATGGTCTTTCCTCTGGTCTGTATGGCCAGGAGCATAGCTTGAGTAACCAGCTGTAATGTTTTCTGATATTCT--------GGATCGGAAGAACTCACAgggacactccaaatgtattctgggggacactaaatgtattcacagggacactccgaatgatattctggATGGGAAGAACTCACAGGA ↓ 1 4 3 2 ↑ 3 2 1 4 Human: CCAGGGTCTCCATGGGTCAGATCCAGGTATGGCTATCCCCTGTTCTTTCTTTTGTATAGCAATGTATATAAATGGTCTTTCCTCTGGTCTGTATGGCCAGGAGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCCAGAATATCAGATAGGAAGAACTCACAgggacactccaaatgtattctgggggacactaaatgtattcacagggacactccaaatgatattctggATGGGAAGAACTCACAGGA Cluster: [ ] Orangutan: CCAGGGTCTCCATGGGTCAGATCCAGGTATGGCTATCCCCTGTTCTTTCTTTTGTATATCAGTGTATATAAATGTTTTTTCCTCTGGTCTGTATGGCCAGGAGCATATCTTGAGTAACCAGCTATAATGTTTTCtgatattct--------ggatgggaagaactcacagggacagtccaaatgtattctgggggacactaaatgtattcacagggacactccaaatgatattctggatgggaagaactcacagga Chimp > Human ------------- chr4:174391261-174391270 Template switch process: F1: L AGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTC 1 F3: 4 GATAGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA R RF: AGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCTGGATGGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGACACTAAATGTATTCACAGGGACACTCCAAATGATATTCTG RR: TCGTATCGAACTCATTGGTCGATATTACAAAAGACTATAAGACCTACCCTTCTTGAGTGTCCCTGTGAGGTTTACATAAGACCCCCTGTGATTTACATAAGTGTCCCTGTGAGGTTTACTATAAGAC F2: 3 ACTATAAGAC 2 Unidirectional alignment (log-probability: -40.5) GCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCcagaatatcaGATaGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG GCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTC--------TGGATGGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG Template switch alignment (log-probability: -22.6) GCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTC|CAGAATATCA|GATaGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG GCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTC|CAGAATATCA|GATGGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG Gorilla > Human --------------- chr4:174391261-174391270 Template switch process: F1: L AGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTC 1 F3: 4 GATAGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA R RF: AGCATAGCTTGAGTAACCAGCTGTAATGTTTTCTGATATTCTGGATCGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGACACTAAATGTATTCACAGGGACACTCCGAATGATATTCTG RR: TCGTATCGAACTCATTGGTCGACATTACAAAAGACTATAAGACCTAGCCTTCTTGAGTGTCCCTGTGAGGTTTACATAAGACCCCCTGTGATTTACATAAGTGTCCCTGTGAGGCTTACTATAAGAC F2: 3 ACTATAAGAC 2 Unidirectional alignment (log-probability: -44.5) GCATAGCTTGAGTAACCAGCTaTAATGTTTTCTGATATTCcagaatatcaGATaGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG GCATAGCTTGAGTAACCAGCTGTAATGTTTTCTGATATTC--------TGGATCGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG Template switch alignment (log-probability: -28.1) GCATAGCTTGAGTAACCAGCTaTAATGTTTTCTGATATTC|CAGAATATCA|GATaGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG GCATAGCTTGAGTAACCAGCTGTAATGTTTTCTGATATTC|CAGAATATCA|GATCGGAAGAACTCACAGGGACACTCCAAATGTATTCTGG Human > Gorilla --------------- chr4:187224883-187224888 Template switch process: F1: L AGCATAGCTTGAGTAACCAGCTGTAATGTTTTCTGATATTC 1 F3: 4 GGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA R RF: GATCCAGGTATGGCTATCCCCTGTTCTTTCTTTTGTATAGCAATGTATATAAATGGTCTTTCCTCTGGTCTGTATGGCCAGGAGCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCCAGAATATCAGATAGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA RR: CTAGGTCCATACCGATAGGGGACAAGAAAGAAAACATATCGTTACATATATTTACCAGAAAGGAGACCAGACATACCGGTCCTCGTATCGAACTCATTGGTCGATATTACAAAAGACTATAAGGTCTTATAGTCTATCCTTCTTGAGTGTCCCTGTGAGGTTTACATAAGACCCCCT F2: 3 CTAGGT 2 Unidirectional alignment (log-probability: -33.5) GCATAGCTTGAGTAACCAGCTgTAATGTTTTCTGATATTC--------tgGATcGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA GCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTCCAGAATATCAGATAGGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA Template switch alignment (log-probability: -22) GCATAGCTTGAGTAACCAGCTgTAATGTTTTCTGATATTC|TGGATC|GGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA GCATAGCTTGAGTAACCAGCTATAATGTTTTCTGATATTC|TGGATC|GGAAGAACTCACAGGGACACTCCAAATGTATTCTGGGGGA ========== Event 2603 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCGAAGTCTGCCTATTATTCAGATGGCAGGTATCCTATGGGAAGCACAAACTACA ↓ 1 3 24 Chimp: TTCGAAGTCTGCCTATTCTTCAGATGGG---ATACCTATGGGAAGCACAAACTACA ↑ 1 3 24 Gorilla: TTAGAAGTCTGCCTATTCTTCGGATGGCAGGTATCCTATGGGAAGCACAAACTACA Human: TTCGAAGTCTGCCTATTATTCAGATGGCAGGTATCCTATGGGAAGCACAAACTACA Cluster: [ ] Orangutan: TTCGAAGTCTGCCTGTTCTTCAGATGGG---ATACCTATGGGAAGCAGAAACTACA Human > Chimp ------------- chr4:178502455-178502459 Template switch process: F1: L GACTATTCATTGATTTCGAAGTCTGCCTATTCTTCAGATGG 1 F3: 4 CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA R RF: GACTATTCATTGATTTCGAAGTCTGCCTATTATTCAGATGGCAGGTATCCTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA RR: CTGATAAGTAACTAAAGCTTCAGACGGATAATAAGTCTACCGTCCATAGGATACCCTTCGTGTTTGATGTGTCGTACACTTGTGAGGT F2: 3 CATAG 2 Unidirectional alignment (log-probability: -33.2) ACTATTCATTGATTTCGAAGTCTGCCTATTcTTCAGATGGgataC-------CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA ACTATTCATTGATTTCGAAGTCTGCCTATTATTCAGATGG----CAGGTATCCTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA Template switch alignment (log-probability: -21.9) ACTATTCATTGATTTCGAAGTCTGCCTATTcTTCAGATGG|GATAC|CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA ACTATTCATTGATTTCGAAGTCTGCCTATTATTCAGATGG|GATAC|CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA Gorilla > Chimp --------------- chr4:178502455-178502459 Template switch process: F1: L TTTGAGGACTATTCATTGATTTCGAAGTCTGCCTATTCTTCAGATGG 1 F3: 4 CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA R RF: TTTGAGGACTATTCATTGATTTAGAAGTCTGCCTATTCTTCGGATGGCAGGTATCCTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA RR: AAACTCCTGATAAGTAACTAAATCTTCAGACGGATAAGAAGCCTACCGTCCATAGGATACCCTTCGTGTTTGATGTGTCGTACACTTGTGAGGT F2: 3 CATAG 2 Unidirectional alignment (log-probability: -37.5) ACTATTCATTGATTTcGAAGTCTGCCTATTCTTCaGATGG--GaTA-CCTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA ACTATTCATTGATTTAGAAGTCTGCCTATTCTTCGGATGGCAGGTATCCTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA Template switch alignment (log-probability: -27.5) ACTATTCATTGATTTcGAAGTCTGCCTATTCTTCaGATGG|GATAC|CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA ACTATTCATTGATTTAGAAGTCTGCCTATTCTTCGGATGG|GATAC|CTATGGGAAGCACAAACTACACAGCATGTGAACACTCCA ========== Event 2604 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATTCTGTCACAACATTAAG--GGATTTAAGAATAGCAACAACAATAAAACAAAGGATT ↓ 1 4 3 2 Chimp: ATATTCTGTCACAACATTAAGTTGCTATTAAGAATAGCAACAACAATAAAACAAAGGATT Gorilla: ATATTCTGTCGCAACATTAAG--GGATTTAAGAATAGCAACAACAATAAAACAAAGGATT Human: ATATTCTGTCACAACATTAAG--GGATTTAAGAATAGCAACAACAATAAAACAAAGGATT Cluster: [ ] Orangutan: ATATTATGTCACAACATTAAG--AGATTTAAGAATAGCAACAACAATAAAACAAAGGATT Human > Chimp ------------- chr4:178749816-178749821 Template switch process: F1: L AAATTAGGGAGCACATGGAAATATTCTGTCACAACATTAAG 1 F3: 4 TTAAGAATAGCAACAACAATAAAACAAAGGATTGTGACCA R RF: AAATTAGGGAGCACATGGAAATATTCTGTCACAACATTAAGGGATTTAAGAATAGCAACAACAATAAAACAAAGGATTGTGACCA RR: TTTAATCCCTCGTGTACCTTTATAAGACAGTGTTGTAATTCCCTAAATTCTTATCGTTGTTGTTATTTTGTTTCCTAACACTGGT F2: 3 ATCGTT 2 Unidirectional alignment (log-probability: -28.5) AATTAGGGAGCACATGGAAATATTCTGTCACAACATTAAG---TtgctaTTAAGAATAGCAACAACAATAAAACAAAGGATTGTGACCA AATTAGGGAGCACATGGAAATATTCTGTCACAACATTAAGGGAT-----TTAAGAATAGCAACAACAATAAAACAAAGGATTGTGACCA Template switch alignment (log-probability: -16) AATTAGGGAGCACATGGAAATATTCTGTCACAACATTAAG|TTGCTA|TTAAGAATAGCAACAACAATAAAACAAAGGATTGTGACCA AATTAGGGAGCACATGGAAATATTCTGTCACAACATTAAG|TTGCTA|TTAAGAATAGCAACAACAATAAAACAAAGGATTGTGACCA ========== Event 2605 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTATTGTATCAGTTCTTTTCAGC----------------------------------------------------------------------------------ATACTGTCTCTTATCTTCATTTAACTG Chimp: TCTATTGTATCAGTTCTTTTCGGC----------------------------------------------------------------------------------ATACTGTCTCTTATCTTCATTTAACTA ↑ 1 3 24 Gorilla: TCTATTGTATCAGTTCTTTTCAGC--------------------------------------------------------------AAGTATGCTGAAAAGATAAGACAGTATCTCTTATCTTCATTTAACTG ↓ 1 3 24 Human: TCTATTGTATCAGTTCTTTTCAGC----------------------------------------------------------------------------------ATACTGTCTCTTATCTTCATTTAACTG Cluster: [ ] Orangutan: tctgttgtatcagttcttttcagtatactgtctcttagctgattctaatgttatctgtattttctgttgtatcagttcttttcagt--------------------atactgtctcttagctTCATTTAACTG Gorilla > Human --------------- chr4:174573035-174573039 Template switch process: F1: L TAATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCA 1 F3: 4 TCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC R RF: TAATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCAAGTATGCTGAAAAGATAAGACAGTATCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC RR: ATTACAATAGACATAAAAGATAACATAGTCAAGAAAAGTCGTTCATACGACTTTTCTATTCTGTCATAGAGAATAGAAGTAAATTGACATGTCAAAGTAAGAAAAAG F2: 3 GTCAT 2 Unidirectional alignment (log-probability: -26.2) ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCA-----------------------TActgTCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCAAGTATGCTGAAAAGATAAGACAGTA---TCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC Template switch alignment (log-probability: -16.4) ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCA|TACTG|TCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCA|TACTG|TCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC Gorilla > Chimp --------------- chr4:178821741-178821745 Template switch process: F1: L TTCTAATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCGGCA 1 F3: 4 TCTCTTATCTTCATTTAACTATACAGTTTCATTCTTTTTC R RF: TTCTAATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCAAGTATGCTGAAAAGATAAGACAGTATCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC RR: AAGATTACAATAGACATAAAAGATAACATAGTCAAGAAAAGTCGTTCATACGACTTTTCTATTCTGTCATAGAGAATAGAAGTAAATTGACATGTCAAAGTAAGAAAAAG F2: 3 GTCAT 2 Unidirectional alignment (log-probability: -37.2) ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCgGCA-----------------------TActgTCTCTTATCTTCATTTAACTaTACAGTTTCATTCTTTTTC ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCAAGTATGCTGAAAAGATAAGACAGTA---TCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC Template switch alignment (log-probability: -27.5) ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCgGCA|TACTG|TCTCTTATCTTCATTTAACTaTACAGTTTCATTCTTTTTC ATGTTATCTGTATTTTCTATTGTATCAGTTCTTTTCAGCA|TACTG|TCTCTTATCTTCATTTAACTGTACAGTTTCATTCTTTTTC ========== Event 2606 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTGTTCCAACTAGAGCTGCACCGATATAGTACCTTCAAAAGCACAGACTCATTCACAGCTACGGAACACAGGCAAAAGAGGTTAACAGGTTCACTTTGAACATAATAAAGTAGACCGTAAGATACAATCTGCCTACAAACGaaaaaaaaaaaa-aaaaaaaaa Chimp: AGTGTTCCAACTACAGCTGCATTGATATAGTACCTTCAAAAGCACAGACTCATTCACAGCTACGGAACACAGGCCAAACAGGTTAACAGGTTCACTTTGAACATAATAAGGTAGACCGTCAGATACAATCTGCCTACCAGTGaaaaaaaaaa-----------a ↑ 3 2 1 4 Gorilla: AGTGTTCCAACTAGAGCTGCACTGATATAGTACCTTCAAAAGCACAGACTCATTCACAGCTACGGAACACAGGCAAAACAGGTTAACAGGTTCACTTTGAACATAATAAGGTAGACCATAAGATACAATCTGCCTACAAATGGaaaaaaaaaaa---------- Human: AGTGTTCCAACTAGAGCTGCACCGATATAGTACCTTCAAAAGCACAGACTCATTCACAGCTACGGAACACAGGCAAAAGAGGTTAACAGGTTCACTTTGAACATAATAAAGTAGACCGTAAGATACAATCTGCCTACAAACGaaaaaaaaaaaa-aaaaaaaaa Cluster: [ ] Orangutan: AGTGTTTCAAGTAGAGCTGCACTGATATAATACCTTCAAAAGCACAGACTCATTCACAGCTACGGAACACAGGCAAAACAGGTTAACAGGTTCACTTTGAACATAATAAGGTAGACCGTAAGATACAATCTGCCTACAAACGaaaaaaa-----a--------- Gorilla > Chimp --------------- chr4:179917510-179917514 Template switch process: F1: L AACAGGTTAACAGGTTCACTTTGAACATAATAAGGTAGACCGTCAGATACAATCTGCCTAC 1 F3: 4 AAAAAAAAAAAAAAAA R RF: CACTGATATAGTACCTTCAAAAGCACAGACTCATTCACAGCTACGGAACACAGGCAAAACAGGTTAACAGGTTCACTTTGAACATAATAAGGTAGACCATAAGATACAATCTGCCTACAAATGGAAAAAAAAAAAAAAAA RR: GTGACTATATCATGGAAGTTTTCGTGTCTGAGTAAGTGTCGATGCCTTGTGTCCGTTTTGTCCAATTGTCCAAGTGAAACTTGTATTATTCCATCTGGTATTCTATGTTAGACGGATGTTTACCTTTTTTTTTTTTTTTT F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -38.3) TGAACATAATAAGGTAGACCgTcAGATACAATCTGCCTACcAgTGaAAAAAAAAAAAAAaa TGAACATAATAAGGTAGACCATAAGATACAATCTGCCTACAAATGGAAAAAAAAAAAAA-- Template switch alignment (log-probability: -27.3) TGAACATAATAAGGTAGACCgTcAGATACAATCTGCCTAC|CAGTG|AAAAAAAAAAAAAAAA TGAACATAATAAGGTAGACCATAAGATACAATCTGCCTAC|CAGTG|AAAAAAAAAAAAAAAA ========== Event 2607 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACACCTTTCCAAATGTCTCTC----AAGAGAAAGTCTGAATCACAATTTTTCTGATGAAAAAAATGTCCTCCTCATCACATA ↑ 1 3 4 2 Chimp: ACACCTTTCCAAATGTCTCTC--AGAAGAGAAAGTCTGAATCACAAGTAT----CAGaaaaaaaTGTCCTCCTCATCACATA Gorilla: ACACCTTTCCAAATGTCTCTCAG--AAGAGAAAGTCTGAATCACAAGTAT----CAGaaaaaaaTGTCCTCCTCATCACATA ↓ 1 3 4 2 Human: ACACCTTTCCAAATGTCTCTC----AAGAGAAAGTCTGAATCACAATTTTTCTGATGAAAAAAATGTCCTCCTCATCACATA Cluster: [ ] Orangutan: ACACCTTTCCAAATGGCTCTCAG--AAGAGAAAGTCTGAATCACAAGTAT----CAGAAAAAAATGTCCTCCTCATCACACA Chimp > Human ------------- chr4:175697399-175697408 Template switch process: F1: L ACTTATGAAGCACAGTAATAACACCTTTCCAAATGTCTCTC--AAGAGAAAGTCTGAATCACAA 1 F3: 4 GAAAAAAAT R RF: ACTTATGAAGCACAGTAATAACACCTTTCCAAATGTCTCTCAGAAGAGAAAGTCTGAATCACAAGTATCAGAAAAAAAT RR: TGAATACTTCGTGTCATTATTGTGGAAAGGTTTACAGAGAGTCTTCTCTTTCAGACTTAGTGTTCATAGTCTTTTTTTA F2: 3 TAGTCTTTTT 2 Unidirectional alignment (log-probability: -46) ACCTTTCCAAATGTCTCTC--AAGAGAAAGTCTGAATCACA------AtttttctgatGAAAAAAAT ACCTTTCCAAATGTCTCTCAGAAGAGAAAGTCTGAATCACAAGTATCA----------GAAAAAAAT Template switch alignment (log-probability: -26.6) ACCTTTCCAAATGTCTCTC--AAGAGAAAGTCTGAATCACAA|TTTTTCTGAT|GAAAAAAAT ACCTTTCCAAATGTCTCTCAGAAGAGAAAGTCTGAATCACAA|TTTTTCTGAT|GAAAAAAAT Gorilla > Human --------------- chr4:175697399-175697408 Template switch process: F1: L ACTTATGAAGCACAGTAATAACACCTTTCCAAATGTCTCTC--AAGAGAAAGTCTGAATCACAA 1 F3: 4 GAAAAAAAT R RF: ACTTATGAAGCACAGTAATAACACCTTTCCAAATGTCTCTCAGAAGAGAAAGTCTGAATCACAAGTATCAGAAAAAAAT RR: TGAATACTTCGTGTCATTATTGTGGAAAGGTTTACAGAGAGTCTTCTCTTTCAGACTTAGTGTTCATAGTCTTTTTTTA F2: 3 TAGTCTTTTT 2 Unidirectional alignment (log-probability: -44.6) ACCTTTCCAAATGTCTCTC--AAGAGAAAGTCTGAATCACAAtTtttctgAT--GAAAAAAAT ACCTTTCCAAATGTCTCTCAGAAGAGAAAGTCTGAATCACAAGT------ATCAGAAAAAAAT Template switch alignment (log-probability: -26.6) ACCTTTCCAAATGTCTCTC--AAGAGAAAGTCTGAATCACAA|TTTTTCTGAT|GAAAAAAAT ACCTTTCCAAATGTCTCTCAGAAGAGAAAGTCTGAATCACAA|TTTTTCTGAT|GAAAAAAAT ========== Event 2608 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAATCTTAGATGGTAAAACAGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTT Chimp: GAAATCTTAGATGGTAAAACAGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTT ↓ 1 4 3 2 Gorilla: GAAATCTTAGATGGTAAAACACT-AGACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCCCCTT ↑ 1 4 3 2 Human: GAAATCTTAGATGGTAAAACAGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTT Cluster: [ ] Orangutan: GAAATCTTAGATGGTAAAATAGAGTTAAGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTT Human > Gorilla --------------- chr4:189023876-189023879 Template switch process: F1: L TGATTTCAGTGTCATTATATGAAATCTTAGATGGTAAAACA 1 F3: 4 ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCCCCTTCCA R RF: TGATTTCAGTGCCATTATATGAAATCTTAGATGGTAAAACAGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTTCCA RR: ACTAAAGTCACGGTAATATACTTTAGAATCTACCATTTTGTCTCAATGCAAGGATGTCAGATCACAAAAACGAAGAGGAGGAAGGT F2: 3 GATC 2 Unidirectional alignment (log-probability: -36.2) GATTTCAGTGtCATTATATGAAATCTTAGATGGTAAAACactAG----ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCcCCTTCCA GATTTCAGTGCCATTATATGAAATCTTAGATGGTAAAAC---AGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTTCCA Template switch alignment (log-probability: -27.3) GATTTCAGTGtCATTATATGAAATCTTAGATGGTAAAACA|CTAG|ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCcCCTTCCA GATTTCAGTGCCATTATATGAAATCTTAGATGGTAAAACA|CTAG|ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTTCCA Chimp > Gorilla --------------- chr4:189023876-189023879 Template switch process: F1: L TGATTTCAGTGTCATTATATGAAATCTTAGATGGTAAAACA 1 F3: 4 ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCCCCTTCCA R RF: TGATTTCAGTGCCATTATATGAAATCTTAGATGGTAAAACAGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTTCCA RR: ACTAAAGTCACGGTAATATACTTTAGAATCTACCATTTTGTCTCAATGCAAGGATGTCAGATCACAAAAACGAAGAGGAGGAAGGT F2: 3 GATC 2 Unidirectional alignment (log-probability: -36.2) GATTTCAGTGtCATTATATGAAATCTTAGATGGTAAAACactAG----ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCcCCTTCCA GATTTCAGTGCCATTATATGAAATCTTAGATGGTAAAAC---AGAGTTACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTTCCA Template switch alignment (log-probability: -27.3) GATTTCAGTGtCATTATATGAAATCTTAGATGGTAAAACA|CTAG|ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCcCCTTCCA GATTTCAGTGCCATTATATGAAATCTTAGATGGTAAAACA|CTAG|ACGTTCCTACAGTCTAGTGTTTTTGCTTCTCCTCCTTCCA ========== Event 2609 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC-GTATGCGAAGAAGTCCAGGGCTGAAGT ↓ 3 2 1 4 Chimp: CTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGACTCCATGTGAAGAAGTCCAGGGCTGAAGT ↑ 3 2 1 4 Gorilla: CTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC-GTATGCGAAGAAGTCCAGGGCTGAAGT Human: CTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC-GTATGCGAAGAAGTCCAGGGCTGAAGT Cluster: [ ] Orangutan: CTAAAAGCAGAGCCTGAGGACATGGAGCTTGGGGAT-GTATGCGAAAAAGTCCAGGGCTGAAGT Human > Chimp ------------- chr4:18449800-18449806 Template switch process: F1: L GTTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC 1 F3: 4 GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA R RF: GTTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGACGTATGCGAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA RR: CAAAGGATTTTCGTCTCGGACTCCTGTACCTCGGACCCCTGCATACGCTTCTTCAGGTCCCGACTTCAACCATACTTGTCGGTTTGT F2: 3 TGTACCT 2 Unidirectional alignment (log-probability: -28.5) TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGACtccatGT----GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC-----GTATGCGAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA Template switch alignment (log-probability: -16.2) TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC|TCCATGT|GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC|TCCATGT|GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA Gorilla > Chimp --------------- chr4:18449800-18449806 Template switch process: F1: L GTTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC 1 F3: 4 GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA R RF: GTTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGACGTATGCGAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA RR: CAAAGGATTTTCGTCTCGGACTCCTGTACCTCGGACCCCTGCATACGCTTCTTCAGGTCCCGACTTCAACCATACTTGTCGGTTTGT F2: 3 TGTACCT 2 Unidirectional alignment (log-probability: -28.1) TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGACtccatGT----GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC-----GTATGCGAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA Template switch alignment (log-probability: -16.6) TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC|TCCATGT|GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA TTTCCTAAAAGCAGAGCCTGAGGACATGGAGCCTGGGGAC|TCCATGT|GAAGAAGTCCAGGGCTGAAGTTGGTATGAACAGCCAAACA ========== Event 2610 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTGTTGGTAAAAATAGATAACGCTCTAAGGGAGGTCTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTT Chimp: ATTGTTGGTAAAAATAGATAACACTCTAAGGGAGGTCTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTT Gorilla: ATTGTTGGTAAAAATAGATAATGCTCTTAATTTA--GTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTT ↓ 1 4 3 2 Human: ATTGTTGGTAAAAATAGATAACGCTCTAAGGGAGGTCTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTT Cluster: [ ] Orangutan: ATTGTTGGTAAAAATAGATAATGCTCTTAATTTA--GTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTT Gorilla > Human --------------- chr4:17971021-17971030 Template switch process: F1: L CAAAATGACTGGAAAAACTAATTGTTGGTAAAAATAGATAACGCTCT 1 F3: 4 TCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTTC R RF: CAAAATGACTGGAAAAACTAATTGTTGGTAAAAATAGATAATGCTCTTAATTTAGTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTTC RR: GTTTTACTGACCTTTTTGATTAACAACCATTTTTATCTATTACGAGAATTAAATCAGTCGGTATCTGGAGGGAAAGGTTATGACCATTCTCAAAG F2: 3 CTGGAGGGAA 2 Unidirectional alignment (log-probability: -41) ACTGGAAAAACTAATTGTTGGTAAAAATAGATAAcGCTCT--------aagggaggtcTCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTTC ACTGGAAAAACTAATTGTTGGTAAAAATAGATAATGCTCTTAATTTAG----------TCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTTC Template switch alignment (log-probability: -22.7) ACTGGAAAAACTAATTGTTGGTAAAAATAGATAAcGCTCT|AAGGGAGGTC|TCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTTC ACTGGAAAAACTAATTGTTGGTAAAAATAGATAATGCTCT|AAGGGAGGTC|TCAGCCATAGACCTCCCTTTCCAATACTGGTAAGAGTTTC ========== Event 2611 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACATTTTAGTCATTTCCAAGTTTTCTGAAAAATTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATATGCTTCCACTGCTAGATACAAC Chimp: ACATTTTAGTCATTTCCAAGTTTTCTGAAAAATTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATATGCTTCCACTGCTAGATACAAC ↓ 1 4 3 2 Gorilla: ACATTTTAGTCATTTCCAAGTCATTTTCCAATGTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATATGCTTCCACTGCTAGATACAAC ↑ 1 4 3 2 Human: ACATTTTAGTCATTTCCAAGTTTTCTGAAAAATTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATATGCTTCCACTGCTAGATACAAC Cluster: [ ] Orangutan: ACATTTTAGTCATTTCCAAGTTTTCTGAAAAATTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATGTGCTTCCACTGCTAGATACAAC Human > Gorilla --------------- chr4:17488243-17488254 Template switch process: F1: L AATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGT 1 F3: 4 TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG R RF: AATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGTTTTCTGAAAAATTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATATG RR: TTATTGTGACGAGACCCAATTGTAAAATCAGTAAAGGTTCAAAAGACTTTTTAAAACGGTTGTAAGATAACGTTAACAAAAAGATCGTGTAACATTATAC F2: 3 GTAACCTTTTAC 2 Unidirectional alignment (log-probability: -38.5) ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAG------------TcattttccaatgTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGTTTTCTGAAAAAT------------TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG Template switch alignment (log-probability: -28.3) ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGT|CATtTTcCAATG|TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGT|CATATTACAATG|TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG Chimp > Gorilla --------------- chr4:17488243-17488254 Template switch process: F1: L AATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGT 1 F3: 4 TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG R RF: AATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGTTTTCTGAAAAATTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTGTAATATG RR: TTATTGTGACGAGACCCAATTGTAAAATCAGTAAAGGTTCAAAAGACTTTTTAAAACGGTTGTAAGATAACGTTAACAAAAAGATCGTGTAACATTATAC F2: 3 GTAACCTTTTAC 2 Unidirectional alignment (log-probability: -38.5) ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAG------------TcattttccaatgTTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGTTTTCTGAAAAAT------------TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG Template switch alignment (log-probability: -28.3) ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGT|CATtTTcCAATG|TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG ATAACACTGCTCTGGGTTAACATTTTAGTCATTTCCAAGT|CATATTACAATG|TTTGCCAACATTCTATTGCAATTGTTTTTCTAGCACATTG ========== Event 2612 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: cactgtGTAAAGTATAA----------GTGTGTAAAGTATTA-----CTTTACTTTATAAAGTAAAGATAGGTGAGATG Chimp: cactgtGTAAAGTATAA-----GTGAAGTGCGTAAAGTATTA----------CTTTATAAAGTAAAGATAGGTGAGATG Gorilla: cactgtgtaaagtataagtgaa-----gtgcataaagTATTA----------CTTTATAAAGTAAAGATAGGTGAGATG ↓ 1 3 4 2 Human: cactgtGTAAAGTATAA----------GTGTGTAAAGTATTA-----CTTTACTTTATAAAGTAAAGATAGGTGAGATG Cluster: [ ] Orangutan: cactgtgtaaagtataagtgaa-----gtgcGTAAAGTATTACTTTA-----CTTTATAAAGTAAAGATAGGTGAGATG Gorilla > Human --------------- chr4:177571913-177571927 Template switch process: F1: L CAGGCACTGTGTAAAGTATAAGTG 1 F3: 4 TACTTTATAAAGTAAAGATAGGTGAGATGTTCATCCAGCCTT R RF: CAGGCACTGTGTAAAGTATAAGTGAAGTGCATAAAGTATTACTTTATAAAGTAAAGATAGGTGAGATGTTCATCCAGCCTT RR: GTCCGTGACACATTTCATATTCACTTCACGTATTTCATAATGAAATATTTCATTTCTATCCACTCTACAAGTAGGTCGGAA F2: 3 TTCATTATGAAATGT 2 Unidirectional alignment (log-probability: -37.7) CAGGCACTGTGTAAAGTATAAGTG---TG--TAAAGTAttactTTACTTTATAAAGTAAAGATAGGTGAGATGTTCATCCAGCC CAGGCACTGTGTAAAGTATAAGTGAAGTGCATAAAGTA-----TTACTTTATAAAGTAAAGATAGGTGAGATGTTCATCCAGCC Template switch alignment (log-probability: -28.3) CAGGCACTGTGTAAAGTATAAGTG|TgTAAAGTAtTACTT|TACTTTATAAAGTAAAGATAGGTGAGATGTTCATCCAGCC CAGGCACTGTGTAAAGTATAAGTG|TATAAAGTAATACTT|TACTTTATAAAGTAAAGATAGGTGAGATGTTCATCCAGCC ========== Event 2613 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATGGTTGAATAAAATGCTGCTTATAGCAGTTCATTCATATAGAAACTA ↑ 3 1 4 Chimp: AATGGTTGAATAAAATGCTGC-T---ATAGTTCATTCATATAGAAACTA Gorilla: AATGGTTGAATAAAATGCTGC-T---ATAGTTCATTCATATAGAAACTA ↓ 3 1 4 Human: AATGGTTGAATAAAATGCTGCTTATAGCAGTTCATTCATATAGAAACTA Cluster: [ ] Orangutan: AACGGTTGCATAAAATGCTGC-T---ATAGTTCATTCATATAGAAACCA Chimp > Human ------------- chr4:179609842-179609847 Template switch process: F1: L AATATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCT 1 F3: 4 AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA R RF: AATATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCTATAGTTCATTCATATAGAAACTATATATTTTATACTATTTCA RR: TTATAAAATTAGGAGCATTTTTACCAACTTATTTTACGACGATATCAAGTAAGTATATCTTTGATATATAAAATATGATAAAGT F2: 3 CGATAT 2 Unidirectional alignment (log-probability: -26.9) TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCtTATagcAGTTCATTCATATAGAAACTATATATTTTATACTATTTCA TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGC-TAT---AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA Template switch alignment (log-probability: -16) TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCT|TATAGC|AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCT|TATAGC|AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA Gorilla > Human --------------- chr4:179609842-179609847 Template switch process: F1: L AATATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCT 1 F3: 4 AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA R RF: AATATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCTATAGTTCATTCATATAGAAACTATATATTTTATACTATTTCA RR: TTATAAAATTAGGAGCATTTTTACCAACTTATTTTACGACGATATCAAGTAAGTATATCTTTGATATATAAAATATGATAAAGT F2: 3 CGATAT 2 Unidirectional alignment (log-probability: -26.4) TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCtTATagcAGTTCATTCATATAGAAACTATATATTTTATACTATTTCA TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGC-TAT---AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA Template switch alignment (log-probability: -16.5) TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCT|TATAGC|AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA TATTTTAATCCTCGTAAAAATGGTTGAATAAAATGCTGCT|TATAGC|AGTTCATTCATATAGAAACTATATATTTTATACTATTTCA ========== Event 2614 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCTATGAGTTCAATAGGTACTTTATGAAATTTGATGGAATTTCA-CGATTGTCTTAAGTTGCAGATA Chimp: TCTATGAGTTCAATAGGTACTCTATGAAATTTGATGGAATTTCA-CGATTGTCTTAAGTTGCAGATA ↓ 3 24 ↑ 13 2 4 Gorilla: TCTATGAGTTCAATAGGTACTCTGTGAAATTCCATCAAATTTCATAGATTGTCTTAAGTTGCAGATA ↓ 13 2 4 ↑ 3 24 Human: TCTATGAGTTCAATAGGTACTTTATGAAATTTGATGGAATTTCA-CGATTGTCTTAAGTTGCAGATA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr4:180880947-180880968 Template switch process: F1: L AGGTATTTGTGGGAACTAGTTCTATGAGTTCAATAGGTACTTT 1 F3: 4 GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC R RF: AGGTATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTGTGAAATTCCATCAAATTTCATAGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC RR: TCCATAAACATCCTTGATCAAGATACTCAAGTTATCCATGAGACACTTTAAGGTAGTTTAAAGTATCTAACAGAATTCAACGTCTATGTAGAGAAAGGGTTCCTTG F2: 3 CACTTTAAGGTAGTTTAAAGTA 2 Unidirectional alignment (log-probability: -55.4) TATTTGTgGGAACTAGTTCTATGAGTTCAATAGGTACTtTaTGAAATTtgATggAATTTCA-cGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTGTGAAATTCCATCAAATTTCATAGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Template switch alignment (log-probability: -29.6) TATTTGTgGGAACTAGTTCTATGAGTTCAATAGGTACTtT|ATGAAATTTGATGGAATTTCAC|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT|ATGAAATTTGATGGAATTTCAC|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Human > Gorilla --------------- chr4:193821632-193821654 Template switch process: F1: L AGGTATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT 1 F3: 4 GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC R RF: AGGTATTTGTGGGAACTAGTTCTATGAGTTCAATAGGTACTTTATGAAATTTGATGGAATTTCACGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC RR: TCCATAAACACCCTTGATCAAGATACTCAAGTTATCCATGAAATACTTTAAACTACCTTAAAGTGCTAACAGAATTCAACGTCTATGTAGAGAAAGGGTTCCTTG F2: 3 ATACTTTAAACTACCTTAAAGTG 2 Unidirectional alignment (log-probability: -56.8) TATTTGTaGGAACTAGTTCTATGAGTTCAATAGGTACTcTgTGAAATTccATcaAATTTCAtaGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTGGGAACTAGTTCTATGAGTTCAATAGGTACTTTATGAAATTTGATGGAATTTCA-CGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Template switch alignment (log-probability: -29.7) TATTTGTaGGAACTAGTTCTATGAGTTCAATAGGTACTcT|GTGAAATTCCATCAAATTTCATA|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTGGGAACTAGTTCTATGAGTTCAATAGGTACTTT|GTGAAATTCCATCAAATTTCATA|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Gorilla > Chimp --------------- chr4:185200563-185200584 Template switch process: F1: L GTATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT 1 F3: 4 GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC R RF: GTATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTGTGAAATTCCATCAAATTTCATAGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC RR: CATAAACATCCTTGATCAAGATACTCAAGTTATCCATGAGACACTTTAAGGTAGTTTAAAGTATCTAACAGAATTCAACGTCTATGTAGAGAAAGGGTTCCTTG F2: 3 CACTTTAAGGTAGTTTAAAGTA 2 Unidirectional alignment (log-probability: -44.4) TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTaTGAAATTtgATggAATTTCA-cGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTGTGAAATTCCATCAAATTTCATAGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Template switch alignment (log-probability: -18.5) TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT|ATGAAATTTGATGGAATTTCAC|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT|ATGAAATTTGATGGAATTTCAC|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Chimp > Gorilla --------------- chr4:193821632-193821654 Template switch process: F1: L GTATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT 1 F3: 4 GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC R RF: GTATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTATGAAATTTGATGGAATTTCACGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC RR: CATAAACATCCTTGATCAAGATACTCAAGTTATCCATGAGATACTTTAAACTACCTTAAAGTGCTAACAGAATTCAACGTCTATGTAGAGAAAGGGTTCCTTG F2: 3 ATACTTTAAACTACCTTAAAGTG 2 Unidirectional alignment (log-probability: -45.7) TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTgTGAAATTccATcaAATTTCAtaGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCTATGAAATTTGATGGAATTTCA-CGATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC Template switch alignment (log-probability: -18.7) TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT|GTGAAATTCCATCAAATTTCATA|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC TATTTGTAGGAACTAGTTCTATGAGTTCAATAGGTACTCT|GTGAAATTCCATCAAATTTCATA|GATTGTCTTAAGTTGCAGATACATCTCTTTCCCAAGGAAC ========== Event 2615 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: AAATACAGAGACAAAACATATGCAGTGGACCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCCAAAAGCAGAGGTGAGGATATCTTTCCTCT ↓ 3 2 1 4 Chimp: AAATACAGAGACAAAACATATGCAGTGGACCTTCTAGAAAGTACCAGGCGGAGGCAAAAGTGACCC-AAAGCATAGGTGAGGATATCTTTCCTCT Gorilla: AAATACAGAGACAAAACATATGCAGTGGACCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCC-AAAGCATAGGTGAGGATATCTTTCCTCT Human: AAATACAGAGACAAAACATATGCAGTGGACCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCCAAAAGCAGAGGTGAGGATATCTTTCCTCT Cluster: [ ] Orangutan: AAATACAGAGACCAAACACATGCAGTGGACCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCC-AAAGCAGAGGTGAGGATATCTTTCCTCT Human > Chimp ------------- chr4:8709085-8709088 Template switch process: F1: L TGGACCTTCTAGAAAGTACCAGGCGGAGGCAAAAGTGACCCAAA 1 F3: 4 AGGTGAGGATATCTTTCCTCTTAGAAAGGGAACCTTTTTT R RF: ATGCAGTGGACCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCCAAAAGCAGAGGTGAGGATATCTTTCCTCTTAGAAAGGGAACCTTTTTT RR: TACGTCACCTGGAAGATCTTTCATGGACCGCCTCCGTTTTCACTGGGTTTTCGTCTCCACTCCTATAGAAAGGAGAATCTTTCCCTTGGAAAAAA F2: 3 TACG 2 Unidirectional alignment (log-probability: -31.7) CCTTCTAGAAAGTACCaGGCGGAGGCAAAAGTGACCC-AAAGCAtAGGTGAGGATATCTTTCCTCTTAGAAAGGGAACCTTTTTt CCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCCAAAAGCAGAGGTGAGGATATCTTTCCTCTTAGAAAGGGAACCTTTTT- Template switch alignment (log-probability: -21.8) CCTTCTAGAAAGTACCaGGCGGAGGCAAAAGTGACCCAAA|GCAT|AGGTGAGGATATCTTTCCTCTTAGAAAGGGAACCTTTTTT CCTTCTAGAAAGTACCTGGCGGAGGCAAAAGTGACCCAAA|GCAT|AGGTGAGGATATCTTTCCTCTTAGAAAGGGAACCTTTTTT ========== Event 2616 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTTGGGAATAACTGGAAGAGAACTATAGTTCTCCTTTCTTTTTAATATGAAAT ↑ 3 2 4 Chimp: ATTTGGGAATAACTGGAAGAGAACTAGAAATAACCTTTCTTTTTAATATGAAAT Gorilla: ATTTGGGAATAACTGGAAGAGAACTACAAATAACCTTTCTTTTTAATATGAAAT ↓ 3 2 4 Human: ATTTGGGAATAACTGGAAGAGAACTATAGTTCTCCTTTCTTTTTAATATGAAAT Cluster: [ ] Orangutan: ATTTGGAAATAACTGGAAGAGAACTATAAATAACCTTTCTTTTTAATATGAAAT Chimp > Human ------------- chr4:7640787-7640793 Template switch process: F1: L TAAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTA 1 F3: 4 CCTTTCTTTTTAATATGAAATCGCACAATTCAATTCTGAT R RF: TAAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTAGAAATAACCTTTCTTTTTAATATGAAATCACACAATTCAATTCTGAT RR: ATTTATTTTGTATTGTAAACCCTTATTGACCTTCTCTTGATCTTTATTGGAAAGAAAAATTATACTTTAGTGTGTTAAGTTAAGACTA F2: 3 TCTTGAT 2 Unidirectional alignment (log-probability: -36.7) AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTAtAgtTctCCTTTCTTTTTAATATGAAATCgCACAATTCAATTCTGAT AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTAGAAATAACCTTTCTTTTTAATATGAAATCACACAATTCAATTCTGAT Template switch alignment (log-probability: -22.1) AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTA|TAGTTCT|CCTTTCTTTTTAATATGAAATCgCACAATTCAATTCTGAT AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTA|TAGTTCT|CCTTTCTTTTTAATATGAAATCACACAATTCAATTCTGAT Gorilla > Human --------------- chr4:7640787-7640793 Template switch process: F1: L TAAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTA 1 F3: 4 CCTTTCTTTTTAATATGAAATCGCACAATTCAATTCTGAT R RF: TAAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTACAAATAACCTTTCTTTTTAATATGAAATCACACAATTCAAGTCTGAT RR: ATTTATTTTGTATTGTAAACCCTTATTGACCTTCTCTTGATGTTTATTGGAAAGAAAAATTATACTTTAGTGTGTTAAGTTCAGACTA F2: 3 TCTTGAT 2 Unidirectional alignment (log-probability: -39.9) AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTAtAgtTctCCTTTCTTTTTAATATGAAATCgCACAATTCAAtTCTGAT AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTACAAATAACCTTTCTTTTTAATATGAAATCACACAATTCAAGTCTGAT Template switch alignment (log-probability: -27.7) AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTA|TAGTTCT|CCTTTCTTTTTAATATGAAATCgCACAATTCAAtTCTGAT AAATAAAACATAACATTTGGGAATAACTGGAAGAGAACTA|TAGTTCT|CCTTTCTTTTTAATATGAAATCACACAATTCAAGTCTGAT ========== Event 2617 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGACAGAGCTTTGGAACAGT---AACAGTAAAAACCTCGGGGTTAATTATATCAACAACTCCCCATTGACTTGCAAGGTTGAGAGAGGGCCAGAGAACCCTTCCTCCCGTTTTTT-CAATCTTCTTCCCTTACATTCCACCAGCCCTAGTTGTCTACTGTGCCTCTCAGTTGACAATGCT Chimp: GAGACAGAGCTTTGGAACAGTAACAACAGTAAAAACCCCGGGGTTAATTATATC---AACTCCCCATTGACTTGCAAGGTTGAGAGAGGGCCAGAGACCCCTTCCTCCCGTTTTTT-CAA---TCTTCCCTTACATTCCACCAGCCCCAGTTGTCTACTGTGCCTCTCAGTTGACAATGCT ↑ 1 4 3 2 Gorilla: GAGACAGAGCTTTGGAACAGT---AACAGTA-AATCCCCGGGGTTAATTATATC---AACTCCCCATTGACTTGCAAGGTTGAGAGAGGGCCAGAGAACCCTTCCTCCCGTTTTTT-CAA---TCTTCCCTTACATTCCACCAGCCCTAGTTGTCTACTGTGCCTCTCAGTTGACAATGCT Human: GAGACAGAGCTTTGGAACAGT---AACAGTAAAAACCTCGGGGTTAATTATATCAACAACTCCCCATTGACTTGCAAGGTTGAGAGAGGGCCAGAGAACCCTTCCTCCCGTTTTTT-CAATCTTCTTCCCTTACATTCCACCAGCCCTAGTTGTCTACTGTGCCTCTCAGTTGACAATGCT Cluster: [ ] Orangutan: GAGACAGAGCTTTGGAACAGT---AACAGTAAAAACCCCGGGGTTAATTATATC---AACTCCCCATTGACTTGCAAGGTTGAGAGAGGGCCAGAGAACCCTTCGTCCTGTTTTTTCGAA---TCTTCCCTTCCATTCCACCAGCCCTAGTTGTCTACTGTGCCTCTCAGTTGACAATGCT Gorilla > Chimp --------------- chr4:7379918-7379923 Template switch process: F1: L TGTGGTCTCTTCTCCATCAAGAGACAGAGCTTTGGAACAGTAACA 1 F3: 4 AAAACCCCGGGGTTAATTATATCAACTCCCCATTGACTTGCAAG R RF: TGTGGTCTCTCCTCCATCAAGAGACAGAGCTTTGGAACAGTAACAGTAAATCCCCGGGGTTAATTATATCAACTCCCCATTGACTTGCAAGGTTGAGAGAGGGCCAGAGAACCCTTCCTCCCGTTTTTTCAATCTTCCCTTACATTCCACCAGCCCTAGTTGTCTACTGT RR: ACACCAGAGAGGAGGTAGTTCTCTGTCTCGAAACCTTGTCATTGTCATTTAGGGGCCCCAATTAATATAGTTGAGGGGTAACTGAACGTTCCAACTCTCTCCCGGTCTCTTGGGAAGGAGGGCAAAAAAGTTAGAAGGGAATGTAAGGTGGTCGGGATCAACAGATGACA F2: 3 ATGACA 2 Unidirectional alignment (log-probability: -37.6) TCTCTtCTCCATCAAGAGACAGAGCTTTGGAACAGTaacAACAGTaAAAaCCCCGGGGTTAATTATATCAACTCCCCATTGACTTG TCTCTCCTCCATCAAGAGACAGAGCTTTGGAACAGT---AACAGT-AAATCCCCGGGGTTAATTATATCAACTCCCCATTGACTTG Template switch alignment (log-probability: -27.7) TCTCTtCTCCATCAAGAGACAGAGCTTTGGAACAGTAACA|ACAGTA|AAAaCCCCGGGGTTAATTATATCAACTCCCCATTGACTTG TCTCTCCTCCATCAAGAGACAGAGCTTTGGAACAGTAACA|ACAGTA|AAATCCCCGGGGTTAATTATATCAACTCCCCATTGACTTG ========== Event 2618 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAATTCCCAACCTCCCTATGC-CCATGAGGCGTAGGGAGGTTGGGAATTATTC Chimp: ATAATTCCCAACCTCCCTATGC-CCATGAGGCGTAGGGAGGTTGGGAATTATTC ↓ 3 1 2 4 Gorilla: ATAATTCCCAACCTCCCTATGCCTCAT-GGGCATAGGGAGGTTGGGAATTATTC ↑ 3 1 2 4 Human: ATAATTCCCAACCTCCCTATGC-CCATGAGGCGTAGGGAGGTTGGGAATTATTC Cluster: [ ] Orangutan: ---------------------C-TCAT-GGGGGTAGGGACGTTGGGAATTATTC Human > Gorilla --------------- chr4:17954359-17954367 Template switch process: F1: L CCAGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC 1 F3: 4 TAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA R RF: CCAGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCCCATGAGGCGTAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA RR: GGTCTTTTCTATGATGTCTTATTAAGGGTTGGAGGGATACGGGTACTCCGCATCCCTCCAACCCTTAATAAGACATCATAGAAAAGACCAT F2: 3 ACGGGTACT 2 Unidirectional alignment (log-probability: -27.8) AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCCtCATG-GGCaTAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC-CATGAGGCGTAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA Template switch alignment (log-probability: -16.9) AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC|TCATGGGCA|TAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC|TCATGGGCA|TAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA Chimp > Gorilla --------------- chr4:17954359-17954367 Template switch process: F1: L CCAGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC 1 F3: 4 TAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA R RF: CCAGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCCCATGAGGCGTAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA RR: GGTCTTTTCTATGATGTCTTATTAAGGGTTGGAGGGATACGGGTACTCCGCATCCCTCCAACCCTTAATAAGACATCATAGAAAAGACCAT F2: 3 ACGGGTACT 2 Unidirectional alignment (log-probability: -27.8) AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCCtCATG-GGCaTAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC-CATGAGGCGTAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA Template switch alignment (log-probability: -16.9) AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC|TCATGGGCA|TAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA AGAAAAGATACTACAGAATAATTCCCAACCTCCCTATGCC|TCATGGGCA|TAGGGAGGTTGGGAATTATTCTGTAGTATCTTTTCTGGTA ========== Event 2619 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAGCTGAACTACAGCTGAATT-ATATGCAAAAGCCTTTGCATATAATTGCATATGTGTTCAATTG ↑ 1 4 3 2 Chimp: GAAGCTGAACTACAGCTGAATATCAATTATAAAGCCTTTGCATATAATTGCATATGTGTTCAATTG Gorilla: GAAGCTGAACTACAGCTGAATATCAATTATAAAGCCTTTGCATATAATTGCATATGTGTTCAATTG ↓ 1 4 3 2 Human: GAAGCTGAACTACAGCTGAATT-ATATGCAAAAGCCTTTGCATATAATTGCATATGTGTTCAATTG Cluster: [ ] Orangutan: GAAGCTGAACTACAGCTGAATATCAATTATAAAGCCTTTGC----------ATATGTGTTCAATTG Chimp > Human ------------- chr4:8270805-8270814 Template switch process: F1: L TCAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAAT 1 F3: 4 AGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC R RF: TCAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAATATCAATTATAAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC RR: AGTCGACTAGTCCGATACTACTTCGACTTGATGTCGACTTATAGTTAATATTTCGGAAACGTATATTAACGTATACACAAGTTAACGAAG F2: 3 AAACGTATAT 2 Unidirectional alignment (log-probability: -28.7) CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTG------AATTATatgcaAAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAATATCAATTAT-----AAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC Template switch alignment (log-probability: -16.5) CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAAT|TATATGCAAA|AGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAAT|TATATGCAAA|AGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC Gorilla > Human --------------- chr4:8270805-8270812 Template switch process: F1: L TCAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAAT 1 F3: 4 AAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC R RF: TCAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAATATCAATTATAAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC RR: AGTCGACTAGTCCGATACTACTTCGACTTGATGTCGACTTATAGTTAATATTTCGGAAACGTATATTAACGTATACACAAGTTAACGAAG F2: 3 ACGTATAT 2 Unidirectional alignment (log-probability: -28.2) CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTG------AATTATatgcaAAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAATATCAATTAT-----AAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC Template switch alignment (log-probability: -16.7) CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAAT|TATATGCA|AAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC CAGCTGATCAGGCTATGATGAAGCTGAACTACAGCTGAAT|TATATGCA|AAAGCCTTTGCATATAATTGCATATGTGTTCAATTGCTTC ========== Event 2620 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAATTTATTCGTAAAAATGT-------TCATTTGTCTCTTAACTGCTTTGTTAATATATAG ↓ 1 3 4 2 Chimp: AAAATTTATTCGTAAAAATGTGTAAGAGACAAATGTCTCTTAACTGCTTTGTTAATATATAG ↑ 1 3 4 2 Gorilla: AAAATTTATTCGTAAAAATGT-------TCATTTGTCTCTTAACTGCTTTGTTAATATATAG Human: AAAATTTATTCGTAAAAATGT-------TCATTTGTCTCTTAACTGCTTTGTTAATATATAG Cluster: [ ] Orangutan: AAAATTTATTCATAAAAATGT-------TCATTTGTCTCTTAACTGCTTTGTTAATATATAA Human > Chimp ------------- chr4:8460880-8460890 Template switch process: F1: L AGGACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTG 1 F3: 4 TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC R RF: AGGACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTTCATTTGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC RR: TCCTGTTAGTAAAAGGTACATTTTAAATAAGCATTTTTACAAGTAAACAGAGAATTGACGAAACAATTATATATCATGTCACCTGG F2: 3 AAACAGAGAAT 2 Unidirectional alignment (log-probability: -38.6) GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATG-----TgtaagagacaaaTGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTTCATT------------TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC Template switch alignment (log-probability: -22.7) GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTg|TAAGAGACAAA|TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTT|TAAGAGACAAA|TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC Gorilla > Chimp --------------- chr4:8460880-8460890 Template switch process: F1: L AGGACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTG 1 F3: 4 TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC R RF: AGGACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTTCATTTGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC RR: TCCTGTTAGTAAAAGGTACATTTTAAATAAGCATTTTTACAAGTAAACAGAGAATTGACGAAACAATTATATATCATGTCACCTGG F2: 3 AAACAGAGAAT 2 Unidirectional alignment (log-probability: -37.6) GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTgtaagagaCAaaTGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGT-------TCATTTGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC Template switch alignment (log-probability: -22.7) GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTg|TAAGAGACAAA|TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC GACAATCATTTTCCATGTAAAATTTATTCGTAAAAATGTT|TAAGAGACAAA|TGTCTCTTAACTGCTTTGTTAATATATAGTACAGTGGACC ========== Event 2621 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGGAGTCACAACCTACATGCTAACTGTTACCTACTAATTGGTAGGTAACAGTTGCTCGTGTGATATCCTAA ↑ 3 1 4 2 Chimp: ATGGAGTCACAACCTACATGC--------------CAATTAGTAGGTAACAGTTGCTCGTGTGATATCCTAA Gorilla: ATGGAGTCACAACCTATATGC--------------CAATTAGTAGGTGAGAGTTGCTCGTGTGATATCTTAA Human: ATGGAGTCACAACCTACATGCTAACTGTTACCTACTAATTGGTAGGTAACAGTTGCTCGTGTGATATCCTAA Cluster: [ ] Orangutan: ATGGAGTCACAACCTATATGC--------------CAACTAGTAGGTAACCGTTGCTCGTGTGATATCTTAA Chimp > Human ------------- chr4:6321713-6321729 Template switch process: F1: L TTGGACAAAGCAAGGTCTTCATGGAGTCACAACCTACATGCTAA 1 F3: 4 GTAGGTAACAGTTGCTCGTGTGATATCCTAAACTCAGACT R RF: TTGGACAAAGCAAGGTCTTCATGGAGTCACAACCTACATGCCAATTAGTAGGTAACAGTTGCTCGTGTGATATCCTAAACTCAGACT RR: AACCTGTTTCGTTCCAGAAGTACCTCAGTGTTGGATGTACGGTTAATCATCCATTGTCAACGAGCACACTATAGGATTTGAGTCTGA F2: 3 GTTAATCATCCATTGTC 2 Unidirectional alignment (log-probability: -43.1) ACAAAGCAAGGTCTTCATGGAGTCACAACCTACATGCtAActgttacctactaaTTgGTAGGTAACAGTTGCTCGTGTGATATCCTAAACTCAGACT ACAAAGCAAGGTCTTCATGGAGTCACAACCTACATGCCAA--------------TTAGTAGGTAACAGTTGCTCGTGTGATATCCTAAACTCAGACT Template switch alignment (log-probability: -23.4) ACAAAGCAAGGTCTTCATGGAGTCACAACCTACATGCtAA|CTGTTACCTACTAATTG|GTAGGTAACAGTTGCTCGTGTGATATCCTAAACTCAGACT ACAAAGCAAGGTCTTCATGGAGTCACAACCTACATGCCAA|CTGTTACCTACTAATTG|GTAGGTAACAGTTGCTCGTGTGATATCCTAAACTCAGACT ========== Event 2622 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: tgaacaaaacagGGTGAAAAA-CA--GTCTGTCtacccaaaagaattaaaagcaggaaccagaagatatttgtacaaccatgttcacaggagcactattacagtagccaaaaggtagacgtaac--------ccatcaacagatgaatagataaccaaaatgtagactatctgcacagtggagtagta Chimp: tgaacaaaacagGGTGAAAAA-CA--CTCTGTCTACCCAAAAGAATTAAAAGCAGGAACCagaagatatttgtacaaccatgttcacaggagcactgttacagtagccaaaaggtagatgtaac--------ccatcaacagatgaatagataaccaaaatgtagactatctgcacagtggagtagta Gorilla: tgaacaaaacagGGTGAAAAACCACTCTATGTCtacccaaaagaattaaaagcaggaaccagaagatatttgtacaaccatgttcacaggagcactgttacagtagccaaaaggtagacgtaac--------ccatcaacagatgaatagataaccaaaatgtagactatctgcacagtggagtagta ↓ 1 4 3 2 Human: tgaacaaaacagGGTGAAAAA-CA--GTCTGTCtacccaaaagaattaaaagcaggaaccagaagatatttgtacaaccatgttcacaggagcactattacagtagccaaaaggtagacgtaac--------ccatcaacagatgaatagataaccaaaatgtagactatctgcacagtggagtagta Cluster: [ ] Orangutan: tgaacaaaacagGGTGAAAAA-CA--CTCTGTCtacccaaaagaattaaaagcaggaaccagaaaatatttgtacaaccatgttcacaggagcactattacagtagccaaaaggttgacgtaacccaggggtccatcaacagatgaatacataaccaaaatgtagactatctgcacagtggagtagta Gorilla > Human --------------- chr4:188319267-188319270 Template switch process: F1: L AGGTGTTGGGATTATAACATTGAACAAAACAGGGTGAAAAAC 1 F3: 4 TGTCTACCCAAAAGAATTAAAAGCAGGAACCAGAAGATAT R RF: AGGTGTTGGGATTATAACATTGAACAAAACAGGGTGAAAAACCACTCTATGTCTACCCAAAAGAATTAAAAGCAGGAACCAGAAGATATTTGTACAACCATGTTCACAGGAGCACTGTTACAGTAGCCAAAAGGTAGACGTAACCCATCAACAGATGAATAGATAACCAAAATGTAGACT RR: TCCACAACCCTAATATTGTAACTTGTTTTGTCCCACTTTTTGGTGAGATACAGATGGGTTTTCTTAATTTTCGTCCTTGGTCTTCTATAAACATGTTGGTACAAGTGTCCTCGTGACAATGTCATCGGTTTTCCATCTGCATTGGGTAGTTGTCTACTTATCTATTGGTTTTACATCTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -25.3) GTGTTGGGATTATAACATTGAACAAAACAGGGTGAAAAAC------AgtcTGTCTACCCAAAAGAATTAAAAGCAGGAACCAGAAGATAT GTGTTGGGATTATAACATTGAACAAAACAGGGTGAAAAACCACTCTA---TGTCTACCCAAAAGAATTAAAAGCAGGAACCAGAAGATAT Template switch alignment (log-probability: -16.3) GTGTTGGGATTATAACATTGAACAAAACAGGGTGAAAAAC|AGTC|TGTCTACCCAAAAGAATTAAAAGCAGGAACCAGAAGATAT GTGTTGGGATTATAACATTGAACAAAACAGGGTGAAAAAC|AGTC|TGTCTACCCAAAAGAATTAAAAGCAGGAACCAGAAGATAT ========== Event 2623 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GATTTAGGATATTTATCAACTGACC--------------------CCTTCCTGGATTATCAGCCCTGGGAGCAC--TCTCTGCCTTGTGGCAAAGTTGGTTCCACACCTTTTCAGctcctcttctagcctagaagcaccttaagggcagggtgcctcatatatttttCCTCCAT Chimp: GATTTAGGATATTTATCAACTAACC----------CGGAAGGGAAGCTTCCTggattatcagccctgggattatcagccctgCCTTGCGGCAAagttggttgcacaccttttcagctcctcttctagcctagaagtaccttaagggcagggtgcctcatatatttttcttccat ↓ 1 4 3 2 Gorilla: GATTTAGGATATTTATCAACTGACCCGGAAGGGAA----------GCTTCCTGGATTATCAGCCCTGGGAGCAC--CCTCTGCCTTGCGGCAAAGTTGGTTCCACACCTTTTCAGCTCCTCTTCTAGCCTAGAAGCACCTTAAAAGCAGGTTGCCTCATATATTTTTCCTCCAT Human: GATTTAGGATATTTATCAACTGACC--------------------CCTTCCTGGATTATCAGCCCTGGGAGCAC--TCTCTGCCTTGTGGCAAAGTTGGTTCCACACCTTTTCAGctcctcttctagcctagaagcaccttaagggcagggtgcctcatatatttttCCTCCAT Cluster: [ ] Orangutan: GATTTGGGATATTTATCAACTGACCCGGAAGGGAA----------GCTTCCTGGATTATCAGCCCTGGGAGCAC--CCTCTGCCTTGAGGCAAAGTTGGTTCCACACCTTTTCAGCTCCTCTTCTAGCCTAGAGGCACCTTAAGGACAGGGTGCCTCATATATTTTTCCTCCAT Chimp > Gorilla --------------- chr4:5366167-5366173 Template switch process: F1: L GTACTTATTGCCAGGATTGAGATTTAGGATATTTATCAACTGACCCGGAAGGGAAGCTTCCTGGATTATCAGCCCTGGGA 1 F3: 4 CTGCCT R RF: GTACTTATTGCCAGGATTGAGATTTAGGATATTTATCAACTAACCCGGAAGGGAAGCTTCCTGGATTATCAGCCCTGGGATTATCAGCCCTGCCTTGCGGCAAAGTTGGTTGCACACCTTTTCAGCTCCTCTTCTAGCCTAGAAGTACCTTAAGGGCAGGGTGC RR: CATGAATAACGGTCCTAACTCTAAATCCTATAAATAGTTGATTGGGCCTTCCCTTCGAAGGACCTAATAGTCGGGACCCTAATAGTCGGGACGGAACGCCGTTTCAACCAACGTGTGGAAAAGTCGAGGAGAAGATCGGATCTTCATGGAATTCCCGTCCCACG F2: 3 TCCCACG 2 Unidirectional alignment (log-probability: -35.3) TgACCCGGAAGGGAAGCTTCCTGGATTATCAGCCCTGGGAgcacccT--------CTGCCT TAACCCGGAAGGGAAGCTTCCTGGATTATCAGCCCTGGGA------TTATCAGCCCTGCCT Template switch alignment (log-probability: -22.3) TgACCCGGAAGGGAAGCTTCCTGGATTATCAGCCCTGGGA|GCACCCT|CTGCCT TAACCCGGAAGGGAAGCTTCCTGGATTATCAGCCCTGGGA|GCACCCT|CTGCCT ========== Event 2624 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGGGAAAAGAGAAAATTTATACGAGAATTTTCTAGGGGA---------AGAAGAGCAGGAAGGAATTACAG Chimp: TTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGGAAAATTCTAGTATAAGAGCAGGAAGGAATTACAG ↑ 3 2 1 4 Gorilla: TTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGGGA---------AGAAGAGCAGGAAGGAATTACAG Human: TTGGGAAAAGAGAAAATTTATACGAGAATTTTCTAGGGGA---------AGAAGAGCAGGAAGGAATTACAG Cluster: [ ] Orangutan: TTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGGGA---------AGAAGAGCAGGAAGGAATTACAG Gorilla > Chimp --------------- chr4:4583043-4583055 Template switch process: F1: L GAGTTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGG 1 F3: 4 AAGAGCAGGAAGGAATTACAGACAGAGTCACATTTGCAAA R RF: GAGTTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGGGAAGAAGAGCAGGAAGGAATTACAGACAGAGTCACATTTGCAAA RR: CTCAACCCTTTTCTCTTTTAAATATGATCTTAAAAGATCCCCTTCTTCTCGTCCTTCCTTAATGTCTGTCTCAGTGTAAACGTTT F2: 3 TATGATCTTAAAA 2 Unidirectional alignment (log-probability: -34.9) AGTTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGGaaaattctaGtAtAAGAGCAGGAAGGAATTACAGACAGAGTCACATTTGCAAA AGTTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGG---------GAAGAAGAGCAGGAAGGAATTACAGACAGAGTCACATTTGCAAA Template switch alignment (log-probability: -17.4) AGTTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGG|AAAATTCTAGTAT|AAGAGCAGGAAGGAATTACAGACAGAGTCACATTTGCAAA AGTTGGGAAAAGAGAAAATTTATACTAGAATTTTCTAGGG|AAAATTCTAGTAT|AAGAGCAGGAAGGAATTACAGACAGAGTCACATTTGCAAA ========== Event 2625 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCCTTATTCAAACCGAAATTGTACATGATGGAACTGGTCTATTTTCTGTGACAGTGCACTTGCA Chimp: AACCTTATTCAAACCGAAATTGTACATGATGGAACTGTGTACAATTCTGTGACAGTGCACTTGCA ↑ 3 2 1 4 Gorilla: AACCTTATTCAAACCGAAATTGTACATGATGGAACTGGTCTATTTTCTGTGACAGTGCACTTGCA Human: AGCCTTATTCAAACCGAAATTGTACATGATGGAACTGGTCTATTTTCTGTGACAGTGCACTTGCA Cluster: [ ] Orangutan: AACCTTATTCAAACAGAAATTTTACATGATGGAACTGGTCCATTTTCTGTGACAGTGCACTTGCA Gorilla > Chimp --------------- chr4:192675661-192675667 Template switch process: F1: L GGAAAACCTTATTCAAACCGAAATTGTACATGATGGAACTG 1 F3: 4 TTCTGTGACAGTGCACTTGCACATTTTAGTGTCGCACTTT R RF: GGAAAACCTTATTCAAACCGAAATTGTACATGATGGAACTGGTCTATTTTCTGTGACAGTGCACTTGCACATTTTAGTATCGCACTTT RR: CCTTTTGGAATAAGTTTGGCTTTAACATGTACTACCTTGACCAGATAAAAGACACTGTCACGTGAACGTGTAAAATCATAGCGTGAAA F2: 3 AACATGT 2 Unidirectional alignment (log-probability: -35.1) GAAAACCTTATTCAAACCGAAATTGTACATGATGGAACTG------TgtacaaTTCTGTGACAGTGCACTTGCACATTTTAGTgTCGCACTTT GAAAACCTTATTCAAACCGAAATTGTACATGATGGAACTGGTCTATT------TTCTGTGACAGTGCACTTGCACATTTTAGTATCGCACTTT Template switch alignment (log-probability: -22.1) GAAAACCTTATTCAAACCGAAATTGTACATGATGGAACTG|TGTACAA|TTCTGTGACAGTGCACTTGCACATTTTAGTgTCGCACTTT GAAAACCTTATTCAAACCGAAATTGTACATGATGGAACTG|TGTACAA|TTCTGTGACAGTGCACTTGCACATTTTAGTATCGCACTTT ========== Event 2626 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TGAGCACAGGGGCCTTCTGTGCAGGCCAAGGTGCTCACCAAAGGGCTACGGGCTACATTCAGCAGAGTGTAAGGCCCTGTCAGTGGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTTGCGTGTCAAACAATAAAACTCAAA Chimp: TGAGCACAGGGGCCTTCTGTGCAGGCCAAGGTGCTCACCAAAGGGCTACGGGCTACACTCAGCAGAGTGTAAGGCCCTGTCAGTGGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTTGCATGTCAAACAATAAAACTCAAA ↑ 3 2 1 4 Gorilla: TGAGCGCGGGGGCCTTCTGTGCAGGCCAAGGTGCTCACCGAAGGGCTACGGGCTACACTCAGCAGAGTGTAAGGCCCTGTCAGTGGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTCAGGTGTCAAACAATAAAAGTCAAA Human: TGAGCACAGGGGCCTTCTGTGCAGGCCAAGGTGCTCACCAAAGGGCTACGGGCTACATTCAGCAGAGTGTAAGGCCCTGTCAGTGGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTTGCGTGTCAAACAATAAAACTCAAA Cluster: [ ] Orangutan: TGAGCGCAGGGGCCTTCTGTGCAGGCCAGGGTGCTCACCGAAGGGCTACGGGCTACGCTCAGCAGAGTGTAAGGCCCTGTCAGTGGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCGTTGCATGTCAAACAATAAAAGTCAAA Gorilla > Chimp --------------- chr4:1672439-1672442 Template switch process: F1: L GGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCT 1 F3: 4 TGTCAAACAATAAAACTCAAAGCTCCGTACACGCCTCTCT R RF: TGCAGGCCAAGGTGCTCACCGAAGGGCTACGGGCTACACTCAGCAGAGTGTAAGGCCCTGTCAGTGGCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTCAGGTGTCAAACAATAAAAGTCAAAGCTCCGTACACGCCTCTCT RR: ACGTCCGGTTCCACGAGTGGCTTCCCGATGCCCGATGTGAGTCGTCTCACATTCCGGGACAGTCACCGTGGGACTGTCCTCTGGTCTTTGTTTTCATAGTCTGGGAGTCCACAGTTTGTTATTTTCAGTTTCGAGGCATGTGCGGAGAGA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -45.5) GCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTtgcaTGTCAAACAATAAAAcTCAAAGCTCCGTACACGcctctct GCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCTCAGGTGTCAAACAATAAAAGTCAAAGCTCCGTACACG------- Template switch alignment (log-probability: -21.7) GCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCT|TGCA|TGTCAAACAATAAAAcTCAAAGCTCCGTACACGCCTCTCT GCACCCTGACAGGAGACCAGAAACAAAAGTATCAGACCCT|TGCA|TGTCAAACAATAAAAGTCAAAGCTCCGTACACGCCTCTCT ========== Event 2627 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CACCAAGGGGGATTACTCAGAAGTTTAAAGCATGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGACGTTTCAAAGCCATGAATCCCCAAGAAGTGAAGGA ↑ 4 1 3 2 Chimp: CACCAAGGGGGATTACTCAGA--------------AGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGACGTTTCAAAGCCATGAATCCCCAAGAAGTGAAGGA ↓ 4 1 3 2 Gorilla: CACCAAGGGGGATTACTCAGAAGTTTAAAGCATGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGACGTTTCAAAGCCATGAATCCCCACGAAGTGAAGGA Human: CACCAAGGGGGATTACTCAGAAGTTTAAAGCATGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGACGTTTCAAAGCCATGAATCCCCAAGAAGTGAAGGA Cluster: [ ] Orangutan: CACCAAGGGGGATTACTCAGAAGTTTAAAGCATGAGGTTTAAAGGAATGTTATCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGATGTTTCAAAGCCATGAATCCCCAAGAAGTGAAGGA Chimp > Human ------------- chr4:170974801-170974804 Template switch process: F1: L AAGGCGGACATGATTCATTTCACCAAGGGGGATTACTCAGAAGTTTAAAG 1 F3: 4 AAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAA R RF: AAGGCGGACATGATTCATTTCACCAAGGGGGATTACTCAGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGACGTTTCAAAGCCATG RR: TTCCGCCTGTACTAAGTAAAGTGGTTCCCCCTAATGAGTCTTCAATTTTCCTTACAACAGACACCTGACGAGAATTCTTTTTGTTCAGTGAGGTCCTCTCCTTTCTGACTGCAAAGTTTCGGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -31.1) TGATTCATTTCACCAAGGGGGATTACTCAgaagtttaaagcatGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA TGATTCATTTCACCAAGGGGGATTACTCA--------------GAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA Template switch alignment (log-probability: -22) TGATTCATTTCACCAAGGGGGATTACTCAGAAGTTtAAAG|CATG|AAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA TGATTCATTTCACCAAGGGGGATTACTCAGAAGTTAAAAG|CATG|AAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA Chimp > Gorilla --------------- chr4:184333776-184333779 Template switch process: F1: L AAGGCGGACATGATTCATTTCACCAAGGGGGATTACTCAGAAGTTTAAAG 1 F3: 4 AAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAA R RF: AAGGCGGACATGATTCATTTCACCAAGGGGGATTACTCAGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAAAACAAGTCACTCCAGGAGAGGAAAGACTGACGTTTCAAAGCCATG RR: TTCCGCCTGTACTAAGTAAAGTGGTTCCCCCTAATGAGTCTTCAATTTTCCTTACAACAGACACCTGACGAGAATTCTTTTTGTTCAGTGAGGTCCTCTCCTTTCTGACTGCAAAGTTTCGGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -31) TGATTCATTTCACCAAGGGGGATTACTCAgaagtttaaagcatGAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA TGATTCATTTCACCAAGGGGGATTACTCA--------------GAAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA Template switch alignment (log-probability: -22) TGATTCATTTCACCAAGGGGGATTACTCAGAAGTTtAAAG|CATG|AAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA TGATTCATTTCACCAAGGGGGATTACTCAGAAGTTAAAAG|CATG|AAGTTAAAAGGAATGTTGTCTGTGGACTGCTCTTAAGAAA ========== Event 2628 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AATAAATTTGTTGTGACACCAG--------CAGTAAAGAAGCCAGTTTACCCAAGG Chimp: AATAAATTGGTTGTGACACCAGTTTACTACTGGTAAAGAAGCCAGTTTACCCAAGG ↑ 3 1 4 2 Gorilla: AATAAATTGGTTGTGACACCAG--------TAGTAAAGAAGCCAGTTTACCCAAGG Human: AATAAATTTGTTGTGACACCAG--------CAGTAAAGAAGCCAGTTTACCCAAGG Cluster: [ ] Orangutan: -------------------------------------------------------- Gorilla > Chimp --------------- chr4:175088643-175088651 Template switch process: F1: L AGGCTGGATTTGGACTGCAAATAAATTGGTTGTGACACCAGT 1 F3: 4 GTAAAGAAGCCAGTTTACCCAAGGCAACACTGGGGGGACA R RF: AGGCTGGATTTGGACTGCAAATAAATTGGTTGTGACACCAGTAGTAAAGAAGCCAGTTTACCCAAGGCAACACTGGGGGGACA RR: TCCGACCTAAACCTGACGTTTATTTAACCAACACTGTGGTCATCATTTCTTCGGTCAAATGGGTTCCGTTGTGACCCCCCTGT F2: 3 GTCATCATT 2 Unidirectional alignment (log-probability: -27.9) GCTGGATTTGGACTGCAAATAAATTGGTTGTGACACCAGtttactacTgGTAAAGAAGCCAGTTTACCCAAGGCAACACTGGGGGGACA GCTGGATTTGGACTGCAAATAAATTGGTTGTGACACCAG--------TAGTAAAGAAGCCAGTTTACCCAAGGCAACACTGGGGGGACA Template switch alignment (log-probability: -16.9) GCTGGATTTGGACTGCAAATAAATTGGTTGTGACACCAGT|TTACTACTG|GTAAAGAAGCCAGTTTACCCAAGGCAACACTGGGGGGACA GCTGGATTTGGACTGCAAATAAATTGGTTGTGACACCAGT|TTACTACTG|GTAAAGAAGCCAGTTTACCCAAGGCAACACTGGGGGGACA ========== Event 2629 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GCATTAAATTAGAGAGGTGTA---------------TGTCCAAAGAACGAAACTTGGATTTGGCGTTTCATGATATTCCACAGAGGTCAAGG ↓ 1 4 3 2 Chimp: GCATTAAATTAGAGAGGTGTA------------------------------TCATGAAATTGGCGTTTCATGATATTCCACAGAGGTCAAGG Gorilla: Human: GCATTAAATTAGAGAGGTGTA---------------TGTCCAAAGAACGAAACTTGGATTTGGCGTTTCATGATATTCCACAGAGGTCAAGG Cluster: [ ] Orangutan: GCATTAAATTAGAGAAGTGTATGTCCAAAGAACGAA---------------ACTTGGATTTGGCGTTTCATGATATTCCGCTGATGTCAAGG Human > Chimp ------------- chr4:196681-196687 Template switch process: F1: L TTGCTGTGTCGGGCAGCCCTGCATTAAATTAGAGAGGTGTAT 1 F3: 4 TTGGCGTTTCATGATATTCCACAGAGGTCAAGGGAAAACT R RF: TTGCTGTGTCGGGCAGCCCTGCATTAAATTAGAGAGGTGTATGTCCAAAGAACGAAACTTGGATTTGGCGTTTCATGATATTCCACAGAGGTCAAGGGAAAACT RR: AACGACACAGCCCGTCGGGACGTAATTTAATCTCTCCACATACAGGTTTCTTGCTTTGAACCTAAACCGCAAAGTACTATAAGGTGTCTCCAGTTCCCTTTTGA F2: 3 AAAGTAC 2 Unidirectional alignment (log-probability: -29.7) GCTGTGTCGGGCAGCCCTGCATTAAATTAGAGAGGTGTAT---------------CaTGaAaTTGGCGTTTCATGATATTCCACAGAGGTCAAGGGAAAACT GCTGTGTCGGGCAGCCCTGCATTAAATTAGAGAGGTGTATGTCCAAAGAACGAAACTTGGATTTGGCGTTTCATGATATTCCACAGAGGTCAAGGGAAAACT Template switch alignment (log-probability: -16.2) GCTGTGTCGGGCAGCCCTGCATTAAATTAGAGAGGTGTAT|CATGAAA|TTGGCGTTTCATGATATTCCACAGAGGTCAAGGGAAAACT GCTGTGTCGGGCAGCCCTGCATTAAATTAGAGAGGTGTAT|CATGAAA|TTGGCGTTTCATGATATTCCACAGAGGTCAAGGGAAAACT ========== Event 2630 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAACGCTAGAGAGCTGAAAATGTCATTTAAAGTGCTAATACTGTTTAATATCTTGTA ↓ 1 4 3 2 Chimp: TGAACGCTAGAGAGCTGAAAA--TTAGCTAAAGTGCTAATACTGTTTAATATCTTGTA Gorilla: TGAATGCTAGAGAGCTGAAAACGTCATTTAAAGTGCTAATACTGTTTAATATCTTGTA Human: TGAACGCTAGAGAGCTGAAAATGTCATTTAAAGTGCTAATACTGTTTAATATCTTGTA Cluster: [ ] Orangutan: TGAATGCTAGAGAGCTGAAAGTGTCATTTAAAGTGCTAATATTGTTTAATATCTTGTA Human > Chimp ------------- chr4:20833651-20833654 Template switch process: F1: L TGAAAATAATGTCTACGAATTGAACGCTAGAGAGCTGAAAAT 1 F3: 4 TAAAGTGCTAATACTGTTTAATATCTTGTAAATGTCTTTA R RF: TGAAAATAATGTCTACGAATTGAACGCTAGAGAGCTGAAAATGTCATTTAAAGTGCTAATACTGTTTAATATCTTGTAAATGTCTTTA RR: ACTTTTATTACAGATGCTTAACTTGCGATCTCTCGACTTTTACAGTAAATTTCACGATTATGACAAATTATAGAACATTTACAGAAAT F2: 3 CGAT 2 Unidirectional alignment (log-probability: -25.7) AAAATAATGTCTACGAATTGAACGCTAGAGAGCTGAAA-----ATTagcTAAAGTGCTAATACTGTTTAATATCTTGTAAATGTCTTTA AAAATAATGTCTACGAATTGAACGCTAGAGAGCTGAAAATGTCATT---TAAAGTGCTAATACTGTTTAATATCTTGTAAATGTCTTTA Template switch alignment (log-probability: -15.8) AAAATAATGTCTACGAATTGAACGCTAGAGAGCTGAAAAT|TAGC|TAAAGTGCTAATACTGTTTAATATCTTGTAAATGTCTTTA AAAATAATGTCTACGAATTGAACGCTAGAGAGCTGAAAAT|TAGC|TAAAGTGCTAATACTGTTTAATATCTTGTAAATGTCTTTA ========== Event 2631 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGATTCTCTTCTCTAGAACTGAACCTATGGATTGA-----------GTTAGGTTCAAACCTATGGATTGAGTTACTGGAAAATAAATGACTGAA Chimp: AGATTCTCTTCTCTAGAACTGAACCTATGGATTGA-----------GTTAGGTTCAAACCCATGGATTGAGTTACTGGAAAATAAATGACTGAA ↑ 3 4 2 1 Gorilla: AGATTCTCTTCTCTAGAATTGAACCTATGGATTGA-----------------------------------GTTACTGGAAAATAAATGACTGAA ↓ 3 4 2 1 Human: AGATTCTCTTCTCTAGAACTGAACCTATGGATTGA-----------GTTAGGTTCAAACCTATGGATTGAGTTACTGGAAAATAAATGACTGAA Cluster: [ ] Orangutan: AGATTCTCTTCTCTAGAACTGAACCTATGGATTGAGTTAGGTTGAA------------------------CTTACTGGAAAATAAACGACTGAA Gorilla > Human --------------- chr4:20690136-20690141 Template switch process: F1: L TATAGAAGATTCTCTTCTCTAGAACTGAACCTATGGATTGAGTTA 1 F3: 4 AACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAATTTAATTAACTTATT R RF: TATAGAAGATTCTCTTCTCTAGAATTGAACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAATTTAGTTAACTTATT RR: ATATCTTCTAAGAGAAGAGATCTTAACTTGGATACCTAACTCAATGACCTTTTATTTACTGACTTTAAATCAATTGAATAA F2: 3 ACTTGG 2 Unidirectional alignment (log-probability: -56.4) AAGATTCTCTTCTCTAGAAcTGaacctatggattgagttaggttcaAACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAAT AAGATTCTCTTCTCTAGAATTG------------------------AACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAAT Template switch alignment (log-probability: -28) AAGATTCTCTTCTCTAGAAcTGAACCTATGGATTGAGTTA|GGTTCA|AACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAAT AAGATTCTCTTCTCTAGAATTGAACCTATGGATTGAGTTA|GGTTCA|AACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAAT Gorilla > Chimp --------------- chr4:21023199-21023204 Template switch process: F1: L TATAGAAGATTCTCTTCTCTAGAACTGAACCTATGGATTGAGTTA 1 F3: 4 AACCCATGGATTGAGTTACTGGAAAATAAATGACTGAAATTTAGTTAACTTATT R RF: TATAGAAGATTCTCTTCTCTAGAATTGAACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAATTTAGTTAACTTATT RR: ATATCTTCTAAGAGAAGAGATCTTAACTTGGATACCTAACTCAATGACCTTTTATTTACTGACTTTAAATCAATTGAATAA F2: 3 ACTTGG 2 Unidirectional alignment (log-probability: -50.9) AAGATTCTCTTCTCTAGAAcTGAACCTatggattgagttaggttcaaacccATGGATTGAGTTACTGGAAAATAAATGACTGAAAT AAGATTCTCTTCTCTAGAATTGAACCT------------------------ATGGATTGAGTTACTGGAAAATAAATGACTGAAAT Template switch alignment (log-probability: -28) AAGATTCTCTTCTCTAGAAcTGAACCTATGGATTGAGTTA|GGTTCA|AACCcATGGATTGAGTTACTGGAAAATAAATGACTGAAAT AAGATTCTCTTCTCTAGAATTGAACCTATGGATTGAGTTA|GGTTCA|AACCTATGGATTGAGTTACTGGAAAATAAATGACTGAAAT ========== Event 2632 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ATAACTGTT-ACTATTCATGT--A-AACAGCTTAAGTAGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACCACGGGTTTTAAATATACTATGTAGATATCTGGAGAAAGTTGTCTTTAGAGCTGTtcttagctctgacactg-gct ↑ 1 4 3 2 Chimp: ATAACTGTT-ACTATTCATGTACC-ACTAGCCTAAGTGGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACCACGGGTTTTAAATATACTATGTAGATATCTGGAGAAAGTTGTCTTTAGAGCTGTtcttagctctgacactg-gct Gorilla: ATAACTTTT-ACTATTCATGT--A-AACAGCCTAAGTAGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACCACGGGTTTTAAATATACTATGTAGATATCTGGAGAAAGTTGTCTTTAGAGCTGTtcttagctctgacactg-gct Human: ATAACTGTT-ACTATTCATGT--A-AACAGCTTAAGTAGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACCACGGGTTTTAAATATACTATGTAGATATCTGGAGAAAGTTGTCTTTAGAGCTGTtcttagctctgacactg-gct Cluster: [ ] Orangutan: ataactgttaactattCATGT--AAGACAGCCTAAGTAGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACCACGGGTTTTAAATATACTATGTAGATATCTGGAGAAAGTTGTCTTTAGAGCTGTTCTTAGCTCTGACACTGGTCT Chimp > Human ------------- chr4:21135982-21135988 Template switch process: F1: L CAAGTTAATTGGCAGTCAGTCATAACTGTTACTATTCATGTA 1 F3: 4 TAAGTAGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACC R RF: CAAGTTAATTGGCAGTCAATCATAACTGTTACTATTCATGTACCACTAGCCTAAGTGGTAGTATTTATTACATCTTCCAAAACAAAAATATTTTACCACGGGTTTTAAATATACTATGTAGATATCTGGAGAAAGTTGTCTTTAGAGCTGTT RR: GTTCAATTAACCGTCAGTTAGTATTGACAATGATAAGTACATGGTGATCGGATTCACCATCATAAATAATGTAGAAGGTTTTGTTTTTATAAAATGGTGCCCAAAATTTATATGATACATCTATAGACCTCTTTCAACAGAAATCTCGACAA F2: 3 TCGACAA 2 Unidirectional alignment (log-probability: -41.1) AGTTAATTGGCAGTCAgTCATAACTGTTACTATTCATGTA--AacAGCtTAAGTaGTAGTATTTATTACATCTTCCAAAACAAAAATAT AGTTAATTGGCAGTCAATCATAACTGTTACTATTCATGTACCACTAGCCTAAGTGGTAGTATTTATTACATCTTCCAAAACAAAAATAT Template switch alignment (log-probability: -28.3) AGTTAATTGGCAGTCAgTCATAACTGTTACTATTCATGTA|AACAGCT|TAAGTaGTAGTATTTATTACATCTTCCAAAACAAAAATAT AGTTAATTGGCAGTCAATCATAACTGTTACTATTCATGTA|AACAGCT|TAAGTGGTAGTATTTATTACATCTTCCAAAACAAAAATAT ========== Event 2633 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTCTGAATTTGGGCAGTGTCCACTGGGATTATAGACCCAGTGGATGAGAGTCAAACAATGTA Chimp: TTTCTGAATTTGGGCAGTGTCT----AAATTATAGACCCAGTGGATGAGAGTCAAACAATGTA Gorilla: TTTCTGAATTTGGGCAGTGTCT----AAATTATAGACCCAGTGGATGAGAGTCAAACAATGTA ↓ 1 4 3 2 Human: TTTCTGAATTTGGGCAGTGTCCACTGGGATTATAGACCCAGTGGATGAGAGTCAAACAATGTA Cluster: [ ] Orangutan: TTTCTGAATTTTGGCAGTGTCT----AAATTATAGACCCAGTGGATGAGAGTCAAACAATGTA Gorilla > Human --------------- chr4:20882224-20882230 Template switch process: F1: L TTTTTTCTAATCTAGTGATATTTCTGAATTTGGGCAGTGTC 1 F3: 4 ATTATAGACCCAGTGGATGAGAGTCAAACAATGTACAAGG R RF: TTTTTTCTAATCTAGTGATATTTCTGAATTTGGGCAGTGTCTAAATTATAGACCCAGTGGATGAGAGTCAAACAATGTACAAGG RR: AAAAAAGATTAGATCACTATAAAGACTTAAACCCGTCACAGATTTAATATCTGGGTCACCTACTCTCAGTTTGTTACATGTTCC F2: 3 GGGTCAC 2 Unidirectional alignment (log-probability: -27.7) TTTTTCTAATCTAGTGATATTTCTGAATTTGGGCAGTGTCcActgggATTATAGACCCAGTGGATGAGAGTCAAACAATGTACAAGG TTTTTCTAATCTAGTGATATTTCTGAATTTGGGCAGTGTCTAA----ATTATAGACCCAGTGGATGAGAGTCAAACAATGTACAAGG Template switch alignment (log-probability: -16.6) TTTTTCTAATCTAGTGATATTTCTGAATTTGGGCAGTGTC|CACTGGG|ATTATAGACCCAGTGGATGAGAGTCAAACAATGTACAAGG TTTTTCTAATCTAGTGATATTTCTGAATTTGGGCAGTGTC|CACTGGG|ATTATAGACCCAGTGGATGAGAGTCAAACAATGTACAAGG ========== Event 2634 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATATATAAAAAAGAAAAGCTGTGCAACTTTTCTTTTTTGTTGCATAAATGTGCAACAAAATGTGCTAAGTGTGCAACTAAagaaggtaagccataat--caacctaacagcagaattaataaaatataaaattattttaaaatattttttaaatataaaaatgttattttttgaagacattaataaaatagataaatctcc Chimp: TATATATAAAAAAGAAAAGCTGTGCAACtt----tttttGTTGCACAAATGTGCACCAAAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAAT--CAACCTAACAGCAGaattaataaaatataaaattattttaaaatattttttaaatataaaaatgttattttttgaagacattaataaaatggataaatCTCC ↓ 1 4 3 2 Gorilla: TATATATAAAAAAGAAAAGCT-------------------------GAATG------TCAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAAT--CAACCTAACAGCAGaattaataaaatataaaattattttaaaatattttttaaatataaaaatgttattttttgaagacattaataaaatggataaatCTCC ↑ 1 4 3 2 Human: TATATATAAAAAAGAAAAGCTGTGCAACTTTTCTTTTTTGTTGCATAAATGTGCAACAAAATGTGCTAAGTGTGCAACTAAagaaggtaagccataat--caacctaacagcagaattaataaaatataaaattattttaaaatattttttaaatataaaaatgttattttttgaagacattaataaaatagataaatctcc Cluster: [ ] Orangutan: TATATATAAAAAAGAAAAGCT-------------------------GAATG------TCAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCTTAATAATAACCTAACAGCAGaattaataaaatataaaattattttaaaatattttttaaatataaaaatgttattttttgaagacattaataaaatggataaatctcc Human > Gorilla --------------- chr4:180209049-180209054 Template switch process: F1: L AAGGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG 1 F3: 4 AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC R RF: AAGGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTGTGCAACTTTTCTTTTTTGTTGCATAAATGTGCAACAAAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATCAACCTAACAGCAGAATTAATAAAATATAAAATTATTTTAAAATATTTTTTAAATATAAAAATGTTATTTTTTGAAGACATT RR: TTCCTTTATGTGATTCACGAATATATATTTTTTCTTTTCGACACGTTGAAAAGAAAAAACAACGTATTTACACGTTGTTTTACACGATTCACACGTTGATTTCTTCCATTCGGTATTAGTTGGATTGTCGTCTTAATTATTTTATATTTTAATAAAATTTTATAAAAAATTTATATTTTTACAATAAAAAACTTCTGTAA F2: 3 CTGTAA 2 Unidirectional alignment (log-probability: -27.8) GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG-------------------------AATGTc------AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTGTGCAACTTTTCTTTTTTGTTGCATAAATGTGCAACAAAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC Template switch alignment (log-probability: -16.5) GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG|AATGTC|AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG|AATGTC|AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC Chimp > Gorilla --------------- chr4:180209049-180209054 Template switch process: F1: L AAGGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG 1 F3: 4 AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC R RF: AAGGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTGTGCAACTTTTTTTGTTGCACAAATGTGCACCAAAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATCAACCTAACAGCAGAATTAATAAAATATAAAATTATTTTAAAATATTTTTTAAATATAAAAATGTTATTTTTTGAAGACATT RR: TTCCTTTATGTGATTCACGAATATATATTTTTTCTTTTCGACACGTTGAAAAAAACAACGTGTTTACACGTGGTTTTACACGATTCACACGTTGATTTCTTCCATTCGGTATTAGTTGGATTGTCGTCTTAATTATTTTATATTTTAATAAAATTTTATAAAAAATTTATATTTTTACAATAAAAAACTTCTGTAA F2: 3 CTGTAA 2 Unidirectional alignment (log-probability: -27.6) GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG---------------------AATGTc------AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTGTGCAACTTTTTTTGTTGCACAAATGTGCACCAAAATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC Template switch alignment (log-probability: -16.5) GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG|AATGTC|AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC GGAAATACACTAAGTGCTTATATATAAAAAAGAAAAGCTG|AATGTC|AATGTGCTAAGTGTGCAACTAAAGAAGGTAAGCCATAATC ========== Event 2635 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: cactgtttgcgatcaccaaaaaatggccatGTGGCCA-TTTTTTCAACAT----AAAGCATTAAAACCATTTGTTAAA--AAGTGAAAGATGTACTTCCC ↑ 3 2 1 4 Chimp: cactgtttgtgatcaccaaaaaatggccatgt---tatattgttcaacat----aaAGCATTAAAACCATTTGTTA--AAAAGTGAAAGATGTACTTCCC Gorilla: cactgtttgtgatcaccaaaaaatggccatgt---tatattgttcaacat----aaAGCATTAAAACCATTTGTTAAA--AAGTGAAAGACGTACTTCCC Human: cactgtttgcgatcaccaaaaaatggccatGTGGCCA-TTTTTTCAACAT----AAAGCATTAAAACCATTTGTTAAA--AAGTGAAAGATGTACTTCCC Cluster: [ ] Orangutan: cactgtttgtgatcaccaaaaaatggtcatgt---tatattgttcaacataaTAAAAACATTAAAACCATTTGTTAAA--AAGT---------------- Chimp > Human ------------- chr4:166989893-166989901 Template switch process: F1: L GGTTGAACCTTATGAAATTGCCAATAATCCACTGTTTGCGATCACCAAAAAATGGCCATGT 1 F3: 4 TTCAACATAAAGCATTAAAACCATTTGTTAAAAAGTGAAAGATGTACTTCCCCAGTTTTTTTTTTTTTTTTT-------GGCCATTATGAACTCAGATAACTGAATTATTTCACTTTTTAAATAAATGAATG R RF: GGTTGAACCTTATGAAATTGCCAATAATCCACTGTTTGTGATCACCAAAAAATGGCCATGTTATATTGTTCAACATAAAGCATTAAAACCATTTGTTAAAAAGTGAAAGATGTACTTCCCCAGTTTTTTTTTTTTTTTTTTTTTTTTGGCCATTATGAACTCAGATAACTGAATTATTTCGCTTTTTAAATAAATGAATG RR: CCAACTTGGAATACTTTAACGGTTATTAGGTGACAAACACTAGTGGTTTTTTACCGGTACAATATAACAAGTTGTATTTCGTAATTTTGGTAAACAATTTTTCACTTTCTACATGAAGGGGTCAAAAAAAAAAAAAAAAAAAAAAAACCGGTAATACTTGAGTCTATTGACTTAATAAAGCGAAAAATTTATTTACTTAC F2: 3 TTTTACCGG 2 Unidirectional alignment (log-probability: -56.4) CAATAATCCACTGTTTGcGATCACCAAAAAATGGCCATG------TGgccattttTTCAACATAAAGCATTAAAACCATTTGTTAAAAAGTGAAA CAATAATCCACTGTTTGTGATCACCAAAAAATGGCCATGTTATATTG--------TTCAACATAAAGCATTAAAACCATTTGTTAAAAAGTGAAA Template switch alignment (log-probability: -40.7) CAATAATCCACTGTTTGcGATCACCAAAAAATGGCCATGT|GGCCATTTT|TTCAACATAAAGCATTAAAACCATTTGTTAAAAAGTGAAA CAATAATCCACTGTTTGTGATCACCAAAAAATGGCCATGT|GGCCATTTT|TTCAACATAAAGCATTAAAACCATTTGTTAAAAAGTGAAA ========== Event 2636 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: ctgttggccttggcaaattgtacagaca--atttgtctgtacacagagtcagtgtggaaaggaacgca Chimp: CTGTTGGCCTTGGCAAATTGTACAGACA--ATTTGTCTGTACACAGAGTCAGTGTGGAAAGGAACGCA ↑ 3 14 Gorilla: CTGTTGGCCTTGGCAAATTGTACAGACA-------------AACAGACTCAGTGTGGAAAGGAAGGCA Human: ctgttggccttggcaaattgtacagaca--atttgtctgtacacagagtcagtgtggaaaggaacgca Cluster: [ ] Orangutan: ttgttggccatagcaaattgtacagccaaa-----------cacagagtccatgtggaaaggaaggca Gorilla > Chimp --------------- chr4:170880422-170880432 Template switch process: F1: L GTTTGATTTTGTCCTGTTGGCCTTGGCAAATTGTACAGACAA 1 F3: 4 ACAGAGTCAGTGTGGAAAGGAACGCACAAAGGATGTAATCAGGTGT R RF: GTTTGATTTTGTCCTGTTGGCCTTGGCAAATTGTACAGACAAACAGACTCAGTGTGGAAAGGAAGGCACAAAGGATGTAATCAGGTGT RR: CAAACTAAAACAGGACAACCGGAACCGTTTAACATGTCTGTTTGTCTGAGTCACACCTTTCCTTCCGTGTTTCCTACATTAGTCCACA F2: 3 CATGTCTGTTT 2 Unidirectional alignment (log-probability: -37.8) TTGATTTTGTCCTGTTGGCCTTGGCAAATTGTACAGACAAtttgtctgtacACAGAgTCAGTGTGGAAAGGAAcGCACAAAGGATGTAATC TTGATTTTGTCCTGTTGGCCTTGGCAAATTGTACAGACAA-----------ACAGACTCAGTGTGGAAAGGAAGGCACAAAGGATGTAATC Template switch alignment (log-probability: -28.3) TTGATTTTGTCCTGTTGGCCTTGGCAAATTGTACAGACAA|TTTGTCTGTAC|ACAGAgTCAGTGTGGAAAGGAAcGCACAAAGGATGTAATC TTGATTTTGTCCTGTTGGCCTTGGCAAATTGTACAGACAA|TTTGTCTGTAC|ACAGACTCAGTGTGGAAAGGAAGGCACAAAGGATGTAATC ========== Event 2637 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TGGTTAAATGAATACTCTTTACT--TTGTGTTCAAGCCTTCTT--TCTAATAATCTTAAAATAACAATGTA Chimp: TGGTTAAATGAATACTCTTTACT--TTGTGTTCAAGCCTTCTT--TCTAATAATCTTAAAATAACAATGTA ↓ 13 24 ↑ 13 24 Gorilla: TGGTTAAATGAATACTCTTTATT----AGAAAGAAGGCTTGAACACAAAGTAATCTTAAAATAACAATGTA ↓ 13 24 ↑ 13 24 Human: TGGTTAAATGAATACTCTTTACT--TTGTGTTCAAGCCTTCTT--TCTAATAATCTTAAAATAACAATGTA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr4:167546658-167546682 Template switch process: F1: L AGGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA 1 F3: 4 TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG R RF: AGCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTATTAGAAAGAAGGCTTGAACACAAAGTAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG RR: TCGGATGAATTTTAATTTATACCAATTTACTTATGAGAAATAATCTTTCTTCCGAACTTGTGTTTCATTAGAATTTTATTGTTACATTCCTATTTAACTGTTTGTC F2: 3 AATCTTTCTTCCGAACTTGTGTTTC 2 Unidirectional alignment (log-probability: -63.4) GgCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA-------------------------ctttgtgttcaagccttctttctaaTAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTATTAGAAAGAAGGCTTGAACACAAAG-------------------------TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Template switch alignment (log-probability: -24.4) GgCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|CTTTGTGTTCAAGCCTTCTTTCTAA|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|CTTTGTGTTCAAGCCTTCTTTCTAA|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Human > Gorilla --------------- chr4:180849588-180849612 Template switch process: F1: L AGCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA 1 F3: 4 TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG R RF: AGGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTACTTTGTGTTCAAGCCTTCTTTCTAATAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG RR: TCCGATGAATTTTAATTTATACCAATTTACTTATGAGAAATGAAACACAAGTTCGGAAGAAAGATTATTAGAATTTTATTGTTACATTCCTATTTAACTGTTTGTC F2: 3 GAAACACAAGTTCGGAAGAAAGATT 2 Unidirectional alignment (log-probability: -63.4) GcCTACTTAAAATTAAATATGGTTAAATGAATACTCTTT-------------------------AttagaaagaaggcttgaacacaaagTAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTACTTTGTGTTCAAGCCTTCTTTCTAA-------------------------TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Template switch alignment (log-probability: -24.4) GcCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|TTAGAAAGAAGGCTTGAACACAAAG|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|TTAGAAAGAAGGCTTGAACACAAAG|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Gorilla > Chimp --------------- chr4:171440556-171440580 Template switch process: F1: L AGGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA 1 F3: 4 TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG R RF: AGCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTATTAGAAAGAAGGCTTGAACACAAAGTAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG RR: TCGGATGAATTTTAATTTATACCAATTTACTTATGAGAAATAATCTTTCTTCCGAACTTGTGTTTCATTAGAATTTTATTGTTACATTCCTATTTAACTGTTTGTC F2: 3 AATCTTTCTTCCGAACTTGTGTTTC 2 Unidirectional alignment (log-probability: -63.4) GgCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA-------------------------ctttgtgttcaagccttctttctaaTAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTATTAGAAAGAAGGCTTGAACACAAAG-------------------------TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Template switch alignment (log-probability: -24.4) GgCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|CTTTGTGTTCAAGCCTTCTTTCTAA|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|CTTTGTGTTCAAGCCTTCTTTCTAA|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Chimp > Gorilla --------------- chr4:180849588-180849612 Template switch process: F1: L AGCCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA 1 F3: 4 TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG R RF: AGGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTACTTTGTGTTCAAGCCTTCTTTCTAATAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG RR: TCCGATGAATTTTAATTTATACCAATTTACTTATGAGAAATGAAACACAAGTTCGGAAGAAAGATTATTAGAATTTTATTGTTACATTCCTATTTAACTGTTTGTC F2: 3 GAAACACAAGTTCGGAAGAAAGATT 2 Unidirectional alignment (log-probability: -63.4) GcCTACTTAAAATTAAATATGGTTAAATGAATACTCTTT-------------------------AttagaaagaaggcttgaacacaaagTAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTACTTTGTGTTCAAGCCTTCTTTCTAA-------------------------TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG Template switch alignment (log-probability: -24.4) GcCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|TTAGAAAGAAGGCTTGAACACAAAG|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG GGCTACTTAAAATTAAATATGGTTAAATGAATACTCTTTA|TTAGAAAGAAGGCTTGAACACAAAG|TAATCTTAAAATAACAATGTAAGGATAAATTGACAAACAG ========== Event 2638 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATGACAAGAGAGCACCAAAACTAAGAAATTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGTGAAGTTAGATGCTTTCTTAGCACTGCTGAGTAACCTGATA Chimp: AATGACAAGAGAGCACCAAAA------CGTTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGTGAAGTTAGATGCTTTCTTAGCACTGCTGAGTAACCTGATA Gorilla: AATGACAAGAGAGCACCAAAA------TGTTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGTGAAGTTAGATGCTTTCTTAGCACTGCTGAGTAACCTGATA ↓ 1 4 3 2 Human: AATGACAAGAGAGCACCAAAACTAAGAAATTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGTGAAGTTAGATGCTTTCTTAGCACTGCTGAGTAACCTGATA Cluster: [ ] Orangutan: AATGACAAGAGAGCACCAAAA------CATTCATCGCTAAGACTTTCAAAGCAACCGTCTTTGCCTTGTGAAGTTAGATGCTTTCTTAGCACTGCTGAGTAACCTGATA Gorilla > Human --------------- chr4:23546646-23546653 Template switch process: F1: L AAAGAGAGTGAGGAGAAGTAAATGACAAGAGAGCACCAAAA 1 F3: 4 TTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGT R RF: AAAGAAAGCGAGGAGAAGTAAATGACAAGAGAGCACCAAAATGTTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGTGAAGTTAGATGCTTTCTTAG RR: TTTCTTTCGCTCCTCTTCATTTACTGTTCTCTCGTGGTTTTACAAGTAGCGATTCTTAAAGTTTCGTTGGTAGAAACGGAACACTTCAATCTACGAAAGAATC F2: 3 AAAGAATC 2 Unidirectional alignment (log-probability: -41.6) AAGAgAGtGAGGAGAAGTAAATGACAAGAGAGCACCAAAactaagAaaTTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGT AAGAAAGCGAGGAGAAGTAAATGACAAGAGAGCACCAAA------ATGTTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGT Template switch alignment (log-probability: -27.8) AAGAgAGtGAGGAGAAGTAAATGACAAGAGAGCACCAAAA|CTAAGAAA|TTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGT AAGAAAGCGAGGAGAAGTAAATGACAAGAGAGCACCAAAA|CTAAGAAA|TTCATCGCTAAGAATTTCAAAGCAACCATCTTTGCCTTGT ========== Event 2639 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: GGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTGCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCATCT ↓ 3 1 2 4 ↑ 3 1 2 4 Chimp: GGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTCAGAACGCAGCAT------------CTGTGCCACTGATTCCCATCT ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: GGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTGCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCGTCT Human: GGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTGCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCATCT Cluster: [ ] Orangutan: GGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTGCATTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCATCT Chimp > Human ------------- chr4:2407428-2407451 Template switch process: F1: L CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT 1 F3: 4 GCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC R RF: CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTCAGAACGCAGCATCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC RR: GACACTCCAACGTCGGACAGGGGAATCCGGGGAGTCTACGAGTCTTGCGTCGTAGACACGGTGACTAAGGGTAGACCCCACACCCGAATACTTG F2: 3 TCCGGGGAGTCTACGAGTCTTGCG 2 Unidirectional alignment (log-probability: -57.6) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT------GCgttctgAGCATCTgaggggcctgctGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAA TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTCAGAACGC------AGCATCT------------GTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAA Template switch alignment (log-probability: -24.3) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|GCGTTCTGAGCATCTGAGGGGCCT|gCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAA TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|GCGTTCTGAGCATCTGAGGGGCCT|TCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAA Human > Chimp ------------- chr4:2743904-2743916 Template switch process: F1: L CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT 1 F3: 4 CTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC R RF: CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTGCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC RR: GACACTCCAACGTCGGACAGGGGAATCCGGGGAGTCTACGACGCAAGACTCGTAGACTCCCCGGACGACACGGTGACTAAGGGTAGACCCCACACCCGAATACTTG F2: 3 TACGACGCAAGAC 2 Unidirectional alignment (log-probability: -41) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTcagaacGC------AGCATCTG------------TGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT------GCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC Template switch alignment (log-probability: -16.9) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|CAGAACGCAGCAT|CTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|CAGAACGCAGCAT|CTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC Gorilla > Chimp --------------- chr4:2743904-2743916 Template switch process: F1: L CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT 1 F3: 4 CTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC R RF: CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTGCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCGTCTGGGGTGTGGGCTTATGAAC RR: GACACTCCAACGTCGGACAGGGGAATCCGGGGAGTCTACGACGCAAGACTCGTAGACTCCCCGGACGACACGGTGACTAAGGGCAGACCCCACACCCGAATACTTG F2: 3 TACGACGCAAGAC 2 Unidirectional alignment (log-probability: -45.5) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTcagaacGC------AGCAT------------CTGTGCCACTGATTCCCaTCTGGGGTGTGGGCTTATGAAC TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT------GCGTTCTGAGCATCTGAGGGGCCTGCTGTGCCACTGATTCCCGTCTGGGGTGTGGGCTTATGAAC Template switch alignment (log-probability: -22.9) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|CAGAACGCAGCAT|CTGTGCCACTGATTCCCaTCTGGGGTGTGGGCTTATGAAC TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|CAGAACGCAGCAT|CTGTGCCACTGATTCCCGTCTGGGGTGTGGGCTTATGAAC Chimp > Gorilla --------------- chr4:2375085-2375108 Template switch process: F1: L CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT 1 F3: 4 GCTGTGCCACTGATTCCCGTCTGGGGTGTGGGCTTATGAAC R RF: CTGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTCAGAACGCAGCATCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAAC RR: GACACTCCAACGTCGGACAGGGGAATCCGGGGAGTCTACGAGTCTTGCGTCGTAGACACGGTGACTAAGGGTAGACCCCACACCCGAATACTTG F2: 3 TCCGGGGAGTCTACGAGTCTTGCG 2 Unidirectional alignment (log-probability: -62.2) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT------GCgttctgAGCATctgaggggcctgCTGTGCCACTGATTCCCgTCTGGGGTGTGGGCTTATGAA TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCTCAGAACGC------AGCAT------------CTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAA Template switch alignment (log-probability: -29.8) TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|GCGTTCTGAGCATCTGAGGGGCCT|gCTGTGCCACTGATTCCCgTCTGGGGTGTGGGCTTATGAA TGTGAGGTTGCAGCCTGTCCCCTTAGGCCCCTCAGATGCT|GCGTTCTGAGCATCTGAGGGGCCT|TCTGTGCCACTGATTCCCATCTGGGGTGTGGGCTTATGAA ========== Event 2640 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ctgtaatagcaacaaaaaatggacaaagacaGTGCCCCTCCCTTAAAGGAAATGTTTCA--------------------------------GAAGTCTGAAACATTGGAAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCACT Chimp: ctgtaatagcaacaaaaaatggacaaagacaGTGCCCCTCCCTTAAAGGAAATGTTTCA--------------------------------GAAGTCTAAAACATTGGAAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCACT Gorilla: ctataatagcaacaaaaaatggacaaagacaGTGCCCCTCCCTTAAAGGAAATGTTTCA----------------------------------------------------------------GACACTGTTGCTTCCATCTCACT ↓ 4 3 2 Human: ctgtaatagcaacaaaaaatggacaaagacaGTGCCCCTCCCTTAAAGGAAATGTTTCA--------------------------------GAAGTCTGAAACATTGGAAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCACT Cluster: [ ] Orangutan: ctgtaatagcaacaaaaaatggacaaagacaGTGCCCCTCCCTTAAAGGAAATGTTTCAGAAGTCTGAAACATTGGAAAGGAAATGTTTCA--------------------------------GACACTATTGCTTCCATCTCACT Gorilla > Human --------------- chr4:165321809-165321819 Template switch process: F1: L ATGGACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTTCAGAA 1 F3: 4 TGG----------------------AAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCACTGGACAGTATTTTATATA R RF: ATGGACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCACTGGACAGTATTTTATATA RR: TACCTGTTTCTGTCACGGGGAGGGAATTTCCTTTACAAAGTCTGTGACAACGAAGGTAGAGTGACCTGTCATAAAATATAT F2: 3 TACAAAGTCTG 2 Unidirectional alignment (log-probability: -56.9) ACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTTcagaagtctgaaacattggaaaggaaatgtttCAGACACTGTTGCTTCCATCTCAC ACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTT--------------------------------CAGACACTGTTGCTTCCATCTCAC Template switch alignment (log-probability: -34) ACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTTCAGAa|GTCTGAAACAT|TGG----------------------AAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCAC ACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTTCAGAC|GTCTGAAACAT|TGGACAAAGACAGTGCCCCTCCCTTAAAGGAAATGTTTCAGACACTGTTGCTTCCATCTCAC ========== Event 2641 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: CAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCTCA-CATGTAGTCACTGCATGGGGTGTGGG ↓ 3 2 1 4 Chimp: CAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCTTGAGGGCTGGTCACTGCATGGGGTGTGGG Gorilla: CAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCTTGAGGGATGGTCACTGCATGGGGTGTGGG Human: CAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCTCA-CATGTAGTCACTGCATGGGGTGTGGG Cluster: [ ] Orangutan: CAACACCGGTAGGTACACTGCCCTCACTTGTAGGCCTTGAGGGATGGTCACTGCATGGGGTGTGGG Human > Chimp ------------- chr4:26093775-26093781 Template switch process: F1: L CCATCAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCT 1 F3: 4 TGGTCACTGCATGGGGTGTGGGGGTCCTTTAGATTCCCATCT R RF: CCATCAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCTCACATGTAGTCACTGCATGGGGTGTGGGGGTCCTTTAGATTCCCATCT RR: GGTAGTTGTGACCATCCATGTGACGGGAGTGAACATCCGGAGTGTACATCAGTGACGTACCCCACACCCCCAGGAAATCTAAGGGTAGA F2: 3 CGGGAGT 2 Unidirectional alignment (log-probability: -34.5) CATCAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCTtgagggctg--------GTCACTGCATGGGGTGTGGGGGTCCTTTAGATTCCCAT CATCAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCT---------CACATGTAGTCACTGCATGGGGTGTGGGGGTCCTTTAGATTCCCAT Template switch alignment (log-probability: -22.2) CATCAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCT|TGAGGGC|TgGTCACTGCATGGGGTGTGGGGGTCCTTTAGATTCCCAT CATCAACACTGGTAGGTACACTGCCCTCACTTGTAGGCCT|TGAGGGC|TAGTCACTGCATGGGGTGTGGGGGTCCTTTAGATTCCCAT ========== Event 2642 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAAATCTTAGCACCCTGCAGACTGTAGTCTGCACCATGTTATCTACCATGA Chimp: GGAAATCTTAGCACCCTGCAGACTGTAGTCTGCACCATGTTATCTACCATGA ↑ 3 1 2 4 Gorilla: GGAAATCTTAGCACCCTGCAGACTAC----AGCACCATGTTATCTACCATGA ↓ 3 1 2 4 Human: GGAAATCTTAGCACCCTGCAGACTGTAGTCTGCACCATGTTATCTACCATGA Cluster: [ ] Orangutan: GGAAATCTTAGCACCCTGCAGACTAC----AGCACCATGTTAGCTACCATGA Gorilla > Human --------------- chr4:25378374-25378380 Template switch process: F1: L TGGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT 1 F3: 4 GCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG R RF: TGGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACTACAGCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG RR: ACCTTTGATCCACTATTCCTTTAGAATCGTGGGACGTCTGATGTCGTGGTACAATAGATGGTACTAGGTCAGCGGTCCCATAAC F2: 3 TCTGATG 2 Unidirectional alignment (log-probability: -27.7) GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACTgtagtCtGCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT----ACAGCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG Template switch alignment (log-probability: -16.6) GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT|GTAGTCT|GCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT|GTAGTCT|GCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG Gorilla > Chimp --------------- chr4:25805123-25805129 Template switch process: F1: L TGGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT 1 F3: 4 GCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG R RF: TGGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACTACAGCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG RR: ACCTTTGATCCACTATTCCTTTAGAATCGTGGGACGTCTGATGTCGTGGTACAATAGATGGTACTAGGTCAGCGGTCCCATAAC F2: 3 TCTGATG 2 Unidirectional alignment (log-probability: -27.7) GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACTgtagtCtGCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT----ACAGCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG Template switch alignment (log-probability: -16.6) GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT|GTAGTCT|GCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG GGAAACTAGGTGATAAGGAAATCTTAGCACCCTGCAGACT|GTAGTCT|GCACCATGTTATCTACCATGATCCAGTCGCCAGGGTATTG ========== Event 2643 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTTTCCATTAGGGTACTCAATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAA ↓ 1 4 3 2 Chimp: CTCTTTCCATTAGGGTACTCAG--CCTATACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAA ↑ 1 4 3 2 Gorilla: CTCTTTCCATTAGGGTACTCAATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAA Human: CTCTTTCCATTAGGGTACTCAATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAA Cluster: [ ] Orangutan: CTCTTTCCATTAGGGTACTCAATTATTCTACTTAGATACATATAGGCTGGAGACGTATGCTGAAGAA Human > Chimp ------------- chr4:27507749-27507753 Template switch process: F1: L CTCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA 1 F3: 4 TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA R RF: CTCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCAATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA RR: GAGTGATCGTTTGTTTTATCGAGAAAGGTAATCCCATGAGTTAATAAGATGAATCTATGCATATCCGACCTCTGCATACGACTTCTTT F2: 3 ATCCG 2 Unidirectional alignment (log-probability: -27.2) TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCAgcctA------TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA----ATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA Template switch alignment (log-probability: -15.9) TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA|GCCTA|TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA|GCCTA|TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA Gorilla > Chimp --------------- chr4:27507749-27507753 Template switch process: F1: L CTCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA 1 F3: 4 TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA R RF: CTCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCAATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA RR: GAGTGATCGTTTGTTTTATCGAGAAAGGTAATCCCATGAGTTAATAAGATGAATCTATGCATATCCGACCTCTGCATACGACTTCTTT F2: 3 ATCCG 2 Unidirectional alignment (log-probability: -26.7) TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCAgcctA------TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA----ATTATTCTACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA Template switch alignment (log-probability: -16.4) TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA|GCCTA|TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA TCACTAGCAAACAAAATAGCTCTTTCCATTAGGGTACTCA|GCCTA|TACTTAGATACGTATAGGCTGGAGACGTATGCTGAAGAAA ========== Event 2644 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACACACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCACAC----------------------------------------------AGATGCCTTGGGCCACTGCTCCCCTACTTTTCTGC Chimp: ACACACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCTCAC------------------------AGTGGCCCACACCACCTGGCACACATGCCTTGGGCCACTGCTCCCCTACTTTTCTGC Gorilla: ACACACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCTCACAGTGGCCCACACCACCTGGCACAC----------------------AGATGCCTTGGGCCACTGCTCCCCTACTTTTCTGC ↑ 4 1 3 2 Human: ACACACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCACAC----------------------------------------------AGATGCCTTGGGCCACTGCTCCCCTACTTTTCTGC Cluster: [ ] Orangutan: ACACACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCTCACAGTGGCCCATACCACCTGGCACAC----------------------AGATGCCTTGGGCCACCGCTCCCCTACTCTTCTGC Human > Gorilla --------------- chr4:2694254-2694260 Template switch process: F1: L ACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCTCACAG 1 F3: 4 CACCA---------------CCTGGCACACAGATGCCTTGGGCCACTGCTCCCCTACTTTTCTGCCTAGG R RF: ACAGACCACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCACACAGATGCCTTGGGCCACTGCTCCCCTACTTTTCTGCCTAGG RR: TGTCTGGTGGTGTTCGTGGTCGTTCTACCTTCCACGGACCGTGTGTCTACGGAACCCGGTGACGAGGGGATGAAAAGACGGATCC F2: 3 ACCCGGT 2 Unidirectional alignment (log-probability: -45.4) ACCACAAGCACCAGCAAGATGGAAGGTGCCTGgctcacagtggcccacaccacctgGCACACAGATGCCTTGGGCCACTGCTCCCCT ACCACAAGCACCAGCAAGATGGAAGGTGCCTG------------------------GCACACAGATGCCTTGGGCCACTGCTCCCCT Template switch alignment (log-probability: -33.2) ACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCtCACAG|TGGCCCA|CACCA---------------CCTGGCACACAGATGCCTTGGGCCACTGCTCCCCT ACCACAAGCACCAGCAAGATGGAAGGTGCCTGGCACACAG|TGGCCCA|CACCAGCAAGATGGAAGGTGCCTGGCACACAGATGCCTTGGGCCACTGCTCCCCT ========== Event 2645 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: gatgtgactgtagcaggtcttaatggtcag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------act---ttggccttttcttactgtgaatg Chimp: AATGTGACTGTGGCAGGTCTTAATGGTCAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT---TTGGCCTTTCCTTACTATGAATG ↓ 3 12 4 Gorilla: GATGTGACTGTAGCAGGTCTTAATGGTCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCATTAAGGCCTTTCCTTACTATGAATG Human: gatgtgactgtagcaggtcttaatggtcag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------act---ttggccttttcttactgtgaatg Cluster: [ ] Orangutan: gatgtgagtgtagcaggtcttaatggtcagactttggcctttcctcactatgaatgagaaaccaTAAAAATTCTCAGGCATGATTCTTAATTTTGTTTGTATATGGCAGGGTGGCAGGTTGAATTTGTTATTGTGTTGTGTGCACATTTTAGACTAGAAGTCATACTAAAAATACCTTTAGGATTAATTAATTATTTGTGTTTCATACTCCAGGCAAATTTGTGTTTCACAAATTCTAGAAATTCTTCTAGAAATATACTAGAAGGTAGAGTCCCCAATTATACACACATATGCCTGTATGTATATAGTGTATAGTAAATATGTGTACACACATACAAGGGAGGGAAATAAATAAAAACAACCAGTCCAGTAGGCCTAATATTAATAAATATATTTCAAGACAGAAACAAAGAACCAGTAAAAATAGAGGAGAAGGAAGAAAGAATAGTCAACAAAACAGCAGAAAACAAGTCATGGTTaaaaaaaaaaagaaaaaaaaCAGGTCCATCTCTAAACCTAGCCTATGACAATCCTTATAAACTTAAAGATCACATTAGTTTGCAAAGATGTTTGCAGCTCATGACTATTCtccgtatgcttaacctttagacttctttgttctcccatcttatgctttccaagtcctttacctctcaaccaagccattcaccaatgttcatgagtctatgtacattctaaacaatggacacttctcttcccacacaaagaggatggccaggttaaccatccaaattgttgtccaatgaggtgatttcctttcactgctgtttttagggccaccttgagaaaggttggaaggcagcCAAGTCCATTTAAAAGCAAGTCACTGGTTTAACAGTGAGGGATGACATGGGTGTCCTGGCCACCAGCTAATACCCTTTTACCCTGCTCATGTGGAATCCTGAAGGTGCCACTTCAATACTGTAATGAATTACTTCTGGATACACCTGACTTTATGAAACAGTGGGCCTGGAAAAAGCCAGGTGTGAAGTTCAGTTTTATTTGTCAGCTTGACTAATTTTTCTATAAGTCCCTAGTTAGTTATTCATTCAGAGTATTTGTAGTACGTTTGAGTATAGATTTACAATCAGTTCACTTTAAGGGAATTATTATAGATAATCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGATTAGTTCCCGTCTTCTGAAGTGTATTTGTCTTCTAAGGCTTCCTACATTTTTGACACTTCTTGTTCAACTGGTCCCATTAAGGGGAGGTCATCTATCTGTGGGACTTTCCACACAGTCCTGTTCCCATTGGACTATTTGTGACAGAGCAGTAAGTAGTACTATCATAAGCCTGTGACAAAaaggtgtactgttatctgttccagatggacacttgcaagtactattcctgatctgcatttttgctaaggatggaatagtatatattttcacaatcaatggctgcagatcacatatctgatgccgtattaatacgctttagtacagatttctcattccacacaacagctacaattaacattgctacatggtggagatggcaatattggatgctatcctccagtatccatctggctttttttatgagtcagaaacatgaactgaatggagatataacgaacatcaccaccccaaggatagccctagcctctaccattctttccaggacatgatattgtttttttatgtttctattttggctggtggaaaggtgcttttggaagttgccagctgactttctcactatgatggttcttacgccacagaacaaggaggcaatgtggggcctgacatctatcaactgtgagtacatccattcaaatttatgttcgggaactaggaaaattgctactaggtgaaatggacccaccgtaagccacatttggccaggattccatttattatctggccttcataatgccttcactctaacaaagaagccttatgaggctttgggttgttagttataaatgccagtgtaggccttgtgtacgactgtctttaatatcattctgctttccccactgtatagttcctgaagtcaataactgtagtttcctttgaggaaggaatcgggggataacatccacatgcacatgtcatggtgtcacaaagtccttccttatgaaaactcaacagcttcagtacatgggttctgggtttgaaaactagatgaaatttagaaactaggcaaagggttgcaactttttttattggggtgaccattcttagattgctgatcatcaatcctaatttcttttgtttTCATAGTTTGAGAGCCACCTATCTATCTTGATCATAGGCACAGCATGCACTATTACCTAATTGCATAGCTCATCATACTTTATATAGAAACCCTATTNNNNNNNNNNTTAAAGCATGAGATGTTCTTTTTCATTATCTCCAGATATATTGTGCAATttatatcttatttgctagaatttagtcagatgatcacacagctaccagtgctggggaGAAAAGTTCAGTTCACTTTGTCTGTataaaattaaacattttcttacggataaaattaaactttttcttacggaGCAAGTCAGGGAATATATATTGAATTTGATCATTAATAGgcgatggctcacacctgtaatcccagcactttgggaggctgaggtgggcagattatttgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatacagacaaatgagcccagttggtgatatgcacctgtaatcccagctacttgggagactgaggcatgagaattgattgaatccagtaggcggaggttgcagtgagccaagatcaagccactgcattccagcctgggtgacagagtgagaccctgtctcaaaacaaacaaaacaaacaagcaaacaaaaaacGTTACTAATCCCTGCAGCACAATTTGGATGTACAAAGTGCGACAAcattattcaacaaatgtactgaagatggcttctatgcttcacttttttctaagttctggatgtgagaggggtcttagagattgaaaactgaaaaaaagacattgtctctgtactcaaagagctgatagtctagtagggaaagataaagatgcataaataTCCCTAACATGTTTTTCACTAAGATGAACTGATGTATGAGTTCAGAGGTGGAAAAGACTGCTCCCAGAAGAGTGTTGGATAGCTGCGTAAATAaagacattttaaggtacaggaaactcatgggcacagtcatggagctggaaaaattctaagtagctatagagaaaattaagtaattcagtttggctagagtgcaatatataaattggggaaattgagttaaaatctggaagagtaGAATGTGATGAGTGTAGCAGGTCTTAATGGTCAGACT---TTGGCCTTTCCTCACTATGAATG Chimp > Gorilla --------------- chr4:27157539-27157548 Template switch process: F1: L AAGGGTAGAATACGATGTGACTGTAGCAGGTCTTAATGGTC 1 F3: 4 GGCCTTTCCTTACTATGAATGAGAAACCATAAAAATTCTC R RF: AAGGGTAGAATACAATGTGACTGTGGCAGGTCTTAATGGTCAGACTTTGGCCTTTCCTTACTATGAATGAGAAACCATAAAAATTCTC RR: TTCCCATCTTATGTTACACTGACACCGTCCAGAATTACCAGTCTGAAACCGGAAAGGAATGATACTTACTCTTTGGTATTTTTAAGAG F2: 3 AATTACCAGT 2 Unidirectional alignment (log-probability: -42.9) AGGGTAGAATACgATGTGACTGTaGCAGGTCTTAATGGTCtGACcatTaaGGCCTTTCCTTACTATGAATGAGAAACCATAAAAATTCTC AGGGTAGAATACAATGTGACTGTGGCAGGTCTTAATGGTCAGAC---TTTGGCCTTTCCTTACTATGAATGAGAAACCATAAAAATTCTC Template switch alignment (log-probability: -28) AGGGTAGAATACgATGTGACTGTaGCAGGTCTTAATGGTC|TGACCATTAA|GGCCTTTCCTTACTATGAATGAGAAACCATAAAAATTCTC AGGGTAGAATACAATGTGACTGTGGCAGGTCTTAATGGTC|TGACCATTAA|GGCCTTTCCTTACTATGAATGAGAAACCATAAAAATTCTC ========== Event 2646 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAATCCTTGCTATATGACGAAG----------CCTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCTGCCCTGCAGTCATCTAGAGC Chimp: ATAATCCTTGCTATATGACGAAG----------CCTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCTGCCCTGCAGTCATCTAGAGC ↑ 1 4 3 2 Gorilla: ATAATCCTTGCTATATGACGAGGAGCTACCTCTTGTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCTGCCCTGCAGTCATCTAGAGC ↓ 1 4 3 2 Human: ATAATCCTTGCTATATGACGAAG----------CCTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCTGCCCTGCAGTCATCTAGAGC Cluster: [ ] Orangutan: ATAATCCTTGCTATATGACAAGGAGCTACGTCTTGCACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCTGCCCTGCATTCATCTAGAGC Gorilla > Human --------------- chr4:28559013-28559017 Template switch process: F1: L TTATGTCTTATTACACAGTCATAATCCTTGCTATATGACGA 1 F3: 4 ACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC R RF: TTATGTCTTATTACACAGTCATAATCCTTGCTATATGACGAGGAGCTACCTCTTGTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCT RR: AATACAGAATAATGTGTCAGTATTAGGAACGATATACTGCTCCTCGATGGAGAACATGACTTCGGATGAAAAGGGAATAGCTCCAGTGTACGGAGTGAAGTCCGA F2: 3 TCCGA 2 Unidirectional alignment (log-probability: -26.7) TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGAaG-----CC-----TACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGAGGAGCTACCTCTTGTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC Template switch alignment (log-probability: -16.3) TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGA|AGCCT|ACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGA|AGCCT|ACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC Gorilla > Chimp --------------- chr4:28955174-28955178 Template switch process: F1: L TTATGTCTTATTACACAGTCATAATCCTTGCTATATGACGA 1 F3: 4 ACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC R RF: TTATGTCTTATTACACAGTCATAATCCTTGCTATATGACGAGGAGCTACCTCTTGTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTCACTTCAGGCT RR: AATACAGAATAATGTGTCAGTATTAGGAACGATATACTGCTCCTCGATGGAGAACATGACTTCGGATGAAAAGGGAATAGCTCCAGTGTACGGAGTGAAGTCCGA F2: 3 TCCGA 2 Unidirectional alignment (log-probability: -26.7) TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGAaG-----CC-----TACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGAGGAGCTACCTCTTGTACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC Template switch alignment (log-probability: -16.3) TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGA|AGCCT|ACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC TATGTCTTATTACACAGTCATAATCCTTGCTATATGACGA|AGCCT|ACTGAAGCCTACTTTTCCCTTATCGAGGTCACATGCCTC ========== Event 2647 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TC-----CATCATAAGTGATCT-----TATGTGTTCCATCACTTATGAtggaacacaactcttgtgttcagaaccca ↑ 1 4 3 2 Chimp: TC-----CATCATAAGTGATCA-----TAA------GCTCACTTGTGATGGAACACAACTCTTGTGTTCAGAACCCA Gorilla: TC-----CATCATAAGTGATCA-----TAA------GATCACTTATGATGGAACACAACTCTTGTGTTCAGAACCCA Human: TC-----CATCATAAGTGATCT-----TATGTGTTCCATCACTTATGAtggaacacaactcttgtgttcagaaccca Cluster: [ ] Orangutan: TATAAGTGATCATAAGtgatcacttatgat------gatcacttatgatggaacacaactcttgtgttcagaaccca Chimp > Human ------------- chr4:160483261-160483269 Template switch process: F1: L AGTGAAATAATAAAGCTAGGGTCTTTCCATCATAAGTGATCTTA 1 F3: 4 TCACTTATGATGGAACACAACTCTTGTGTTCAGAACCCAACTCTGAT R RF: AGTGAAATAATAAAGCTAGGGTCTTTCCATCATAAGTGATCATAAGCTCACTTGTGATGGAACACAACTCTTGTGTTCAGAACCCAACTCTGAT RR: TCACTTTATTATTTCGATCCCAGAAAGGTAGTATTCACTAGTATTCGAGTGAACACTACCTTGTGTTGAGAACACAAGTCTTGGGTTGAGACTA F2: 3 ACCTTGTGT 2 Unidirectional alignment (log-probability: -43.3) AAATAATAAAGCTAGGGTCTTTCCATCATAAGTGATcttatgtgttcCA-----TCACTTaTGATGGAACACAACTCTTGTGTTCAGAACCCAA AAATAATAAAGCTAGGGTCTTTCCATCATAAGTGAT-----------CATAAGCTCACTTGTGATGGAACACAACTCTTGTGTTCAGAACCCAA Template switch alignment (log-probability: -28.6) AAATAATAAAGCTAGGGTCTTTCCATCATAAGTGATCtTA|TGTGTTCCA|TCACTTaTGATGGAACACAACTCTTGTGTTCAGAACCCAA AAATAATAAAGCTAGGGTCTTTCCATCATAAGTGATCATA|TGTGTTCCA|TCACTTGTGATGGAACACAACTCTTGTGTTCAGAACCCAA ========== Event 2648 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ATGATTCAGCTTATTTAAGTC-----------TTAAAAAGGATTCAGATATGAAGATATCTGAATCCAATGTGGTTATTATA ↓ 1 3 4 2 Chimp: ATGATTCAGCTTATTTAAGTC----------------------TCAGATATCTTCATATCTGAATCCAATGTGGTTATTATG Gorilla: ATGATTCAGCTTATTTAAGTC----------------------TCAGATATCTTCATATCTGAATCCAATGTGGTTATTATG ↑ 1 3 4 2 Human: ATGATTCAGCTTATTTAAGTC-----------TTAAAAAGGATTCAGATATGAAGATATCTGAATCCAATGTGGTTATTATA Cluster: [ ] Orangutan: ATGATTCAGCTTACTTAAGTCTTAAAAAGGAT-----------TCAGATATCTTCATATCTGAATCCAATGTGGTTATTATG Human > Chimp ------------- chr4:163891144-163891154 Template switch process: F1: L ACCATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCT 1 F3: 4 ATATCTGAATCCAATGTGGTTATTATGTGAAATAAGCTTA R RF: ACCATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCTTAAAAAGGATTCAGATATGAAGATATCTGAATCCAATGTGGTTATTATATGAAATAAGCTTA RR: TGGTAATGAATCAGGACATCTACTAAGTCGAATAAATTCAGAATTTTTCCTAAGTCTATACTTCTATAGACTTAGGTTACACCAATAATATACTTTATTCGAAT F2: 3 CTTCTATAGAC 2 Unidirectional alignment (log-probability: -41.5) CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTC-----------TCAGATATcttcATATCTGAATCCAATGTGGTTATTATgTGAAATAAGCTTA CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCTTAAAAAGGATTCAGATATGAAGATATCTGAATCCAATGTGGTTATTATATGAAATAAGCTTA Template switch alignment (log-probability: -22.7) CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCT|CAGATATCTTC|ATATCTGAATCCAATGTGGTTATTATgTGAAATAAGCTTA CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCT|CAGATATCTTC|ATATCTGAATCCAATGTGGTTATTATATGAAATAAGCTTA Human > Gorilla --------------- chr4:173276083-173276093 Template switch process: F1: L ACCATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCT 1 F3: 4 ATATCTGAATCCAATGTGGTTATTATGTGAAATAAGCTTA R RF: ACCATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCTTAAAAAGGATTCAGATATGAAGATATCTGAATCCAATGTGGTTATTATATGAAATAAGCTTA RR: TGGTAATGAATCAGGACATCTACTAAGTCGAATAAATTCAGAATTTTTCCTAAGTCTATACTTCTATAGACTTAGGTTACACCAATAATATACTTTATTCGAAT F2: 3 CTTCTATAGAC 2 Unidirectional alignment (log-probability: -39.2) CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTC-----------TCAGATATcttcATATCTGAATCCAATGTGGTTATTATgTGAAATAAGCTTA CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCTTAAAAAGGATTCAGATATGAAGATATCTGAATCCAATGTGGTTATTATATGAAATAAGCTTA Template switch alignment (log-probability: -22.7) CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCT|CAGATATCTTC|ATATCTGAATCCAATGTGGTTATTATgTGAAATAAGCTTA CATTACTTAGTCCTGTAGATGATTCAGCTTATTTAAGTCT|CAGATATCTTC|ATATCTGAATCCAATGTGGTTATTATATGAAATAAGCTTA ========== Event 2649 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AAAATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTT----AGTCATGAAACAAGTCAGTATAGCTATG ↑ 3 2 1 4 Chimp: AAAATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTT--AGAGTCGCAAAACAAGTCAGTATAGCTATG Gorilla: Human: AAAATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTT----AGTCATGAAACAAGTCAGTATAGCTATG Cluster: [ ] Orangutan: AAAATAACTTTTGCAAAGTCATGAGTTACCTTTAGTCATTTAG--AGTTACAAAACAAGTCAGTATAGCTGTG Chimp > Human ------------- chr4:31769135-31769139 Template switch process: F1: L AAAATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTTAG 1 F3: 4 AAACAAGTCAGTATAGCTATGAGAATAAAGTTTCCTATTT R RF: AAAATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTTAGAGTCGCAAAACAAGTCAGTATAGCTATGAGAATAAAGATTCCTATTT RR: TTTTATTGAAAACGTTTCAGTACTCAATGGAAATTAGTAAATCTCAGCGTTTTGTTCAGTCATATCGATACTCTTATTTCTAAGGATAAA F2: 3 GTACT 2 Unidirectional alignment (log-probability: -34.7) ATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTTAgtcatG-------AAACAAGTCAGTATAGCTATGAGAATAAAGtTTCCTATTT ATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTTA-----GAGTCGCAAAACAAGTCAGTATAGCTATGAGAATAAAGATTCCTATTT Template switch alignment (log-probability: -21.9) ATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTTAG|TCATG|AAACAAGTCAGTATAGCTATGAGAATAAAGtTTCCTATTT ATAACTTTTGCAAAGTCATGAGTTACCTTTAATCATTTAG|TCATG|AAACAAGTCAGTATAGCTATGAGAATAAAGATTCCTATTT ========== Event 2650 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: AATGGCATAAACCAATATTATACCAATATTTTATACCATTATAAAATATTGGTTATATAAATAACTTCAGAATA Chimp: AATGGCataaaccaatattataccaatattttataatggtataaaatattggttatataaataaCTTCAGAATA Gorilla: AATGGCATAAACCAATATTAAACCAATATTTTATAATGGTATAAAATATTGGTTATATAAATAACTTCAGAATA ↑ 1 3 4 2 Human: AATGGCATAAACCAATATTATACCAATATTTTATACCATTATAAAATATTGGTTATATAAATAACTTCAGAATA Cluster: [ ] Orangutan: AATGGTATAAACCAATATTATACCAATATTTTATAACAGTATAAAATATTGGTTATATAAATAACTTCAGAATA Human > Gorilla --------------- chr4:31848681-31848699 Template switch process: F1: L TTTTATAATGGCATAAACCAATATTA 1 F3: 4 TATAAAATATTGGTTATATAAATAACTTCAGAATAGTTTT R RF: TTTTATAATGGCATAAACCAATATTATACCAATATTTTATACCATTATAAAATATTGGTTATATAAATAACTTCAGAATAGTTTT RR: AAAATATTACCGTATTTGGTTATAATATGGTTATAAAATATGGTAATATTTTATAACCAATATATTTATTGAAGTCTTATCAAAA F2: 3 GGTAATATTTTATAACCAA 2 Unidirectional alignment (log-probability: -28.8) TTTTATAATGGCATAAACCAATATTAaACCAATATTTTATAatggTATAAAATATTGGTTATATAAATAACTTCAGAATAGTTTT TTTTATAATGGCATAAACCAATATTATACCAATATTTTATACCATTATAAAATATTGGTTATATAAATAACTTCAGAATAGTTTT Template switch alignment (log-probability: -17.8) TTTTATAATGGCATAAACCAATATTA|AACCAATATTTTATAATGG|TATAAAATATTGGTTATATAAATAACTTCAGAATAGTTTT TTTTATAATGGCATAAACCAATATTA|AACCAATATTTTATAATGG|TATAAAATATTGGTTATATAAATAACTTCAGAATAGTTTT ========== Event 2651 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TATTATCCACAAATGTGTTGTGTGTGACAACCCCAGTTGTCACCATCTTCCAGTCATAAGAAT ↑ 1 4 3 2 Chimp: TATTATCCACAAATGTGTTGT--GTTCCTACCCTAGTTGTCACCATCTTCCAGTCATAAGAAT Gorilla: TATTATCCACAAATGTGTTGTGTGTGACAACCCCAGTTGTCACCATCTTTAAGTCATAAGAAT Human: TATTATCCACAAATGTGTTGTGTGTGACAACCCCAGTTGTCACCATCTTCCAGTCATAAGAAT Cluster: [ ] Orangutan: TATGATCCACAAATGTGTTGTGTGTTCCTACCCTAGTTGTCACTGTCTTCCTGTCATAAGAAT Chimp > Human ------------- chr4:32766917-32766922 Template switch process: F1: L CTGATATGTATTCACCTGTGTATTATCCACAAATGTGTTGTGT 1 F3: 4 ACCCCAGTTGTCACCATCTTCCAGTCATAAGAATGGAGTCTTCAT R RF: CTGATATGTATTCACCTGTGTATTATCCACAAATGTGTTGTGTTCCTACCCTAGTTGTCACCATCTTCCAGTCATAAGAATGGAGTCTTCAT RR: GACTATACATAAGTGGACACATAATAGGTGTTTACACAACACAAGGATGGGATCAACAGTGGTAGAAGGTCAGTATTCTTACCTCAGAAGTA F2: 3 ACAGTG 2 Unidirectional alignment (log-probability: -36) ATATGTATTCACCTGTGTATTATCCACAAATGTGTTGTGTgtgaca----ACCCcAGTTGTCACCATCTTCCAGTCATAAGAATGGAGTC ATATGTATTCACCTGTGTATTATCCACAAATGTGTTGTGT------TCCTACCCTAGTTGTCACCATCTTCCAGTCATAAGAATGGAGTC Template switch alignment (log-probability: -22.2) ATATGTATTCACCTGTGTATTATCCACAAATGTGTTGTGT|GTGACA|ACCCcAGTTGTCACCATCTTCCAGTCATAAGAATGGAGTC ATATGTATTCACCTGTGTATTATCCACAAATGTGTTGTGT|GTGACA|ACCCTAGTTGTCACCATCTTCCAGTCATAAGAATGGAGTC ========== Event 2652 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CGTTCTTGGTGATGGGAGAATCACATTCAGTTGTACAACTGAATGTGAAAATGAAAGGTGATGGTG Chimp: CATTCTTGGTGATGGGAGAATCACATTCAGTTGTACAACTGAATGTGAAAATGAAAGGTGATGGTG ↑ 1 4 3 2 Gorilla: CATTCTTGGTGATGGGAGAAT--------CTACTACAACTGAATGTGAAAATGAAAGGTGATGGTG ↓ 1 4 3 2 Human: CGTTCTTGGTGATGGGAGAATCACATTCAGTTGTACAACTGAATGTGAAAATGAAAGGTGATGGTG Cluster: [ ] Orangutan: CATTCTTGGTGATGGGAGAAT--------CTACTACAACTGAATGTGAAAATGAAAGGTGATGGTG Gorilla > Human --------------- chr4:32693227-32693237 Template switch process: F1: L AGCATATAATCGGAAAAATTCGTTCTTGGTGATGGGAGAATC 1 F3: 4 TACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA R RF: AGCATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATCTACTACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA RR: TCGTATATTAGCCTTTTTAAGTAAGAACCACTACCCTCTTAGATGATGTTGACTTACACTTTTACTTTCCACTACCACTGTCTTT F2: 3 GTTGACTTACA 2 Unidirectional alignment (log-probability: -39) CATATAATCGGAAAAATTCgTTCTTGGTGATGGGAGAATCacattcagTtgTACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA CATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATC--------TACTACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA Template switch alignment (log-probability: -22.7) CATATAATCGGAAAAATTCgTTCTTGGTGATGGGAGAATC|ACATTCAGTTG|TACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA CATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATC|ACATTCAGTTG|TACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA Gorilla > Chimp --------------- chr4:33096635-33096645 Template switch process: F1: L AGCATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATC 1 F3: 4 TACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA R RF: AGCATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATCTACTACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA RR: TCGTATATTAGCCTTTTTAAGTAAGAACCACTACCCTCTTAGATGATGTTGACTTACACTTTTACTTTCCACTACCACTGTCTTT F2: 3 GTTGACTTACA 2 Unidirectional alignment (log-probability: -33.5) CATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATCacattcagTtgTACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA CATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATC--------TACTACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA Template switch alignment (log-probability: -17.2) CATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATC|ACATTCAGTTG|TACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA CATATAATCGGAAAAATTCATTCTTGGTGATGGGAGAATC|ACATTCAGTTG|TACAACTGAATGTGAAAATGAAAGGTGATGGTGACAGAAA ========== Event 2653 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCATATCCATAAAGCTGTGCCTCAAGTATATCCCAT--GTCACATTACATAATCCTTATACA ↓ 3 2 1 4 Chimp: TCCATATCCGTAAAGCTGTGCCTCAAGTATATCCCTTGAGGCACATTACATAATCCTTATACA Gorilla: TCCATATCCATAAAGCTGTGCCTCAAGTATATCCCAT--GTCACATTACATAATCTTTATACA Human: TCCATATCCATAAAGCTGTGCCTCAAGTATATCCCAT--GTCACATTACATAATCCTTATACA Cluster: [ ] Orangutan: TCCATATCCATAAAGCTGTGCCTCAAGTATATCCCAT--GTCACATTACATAATCCTCATACA Human > Chimp ------------- chr4:163383819-163383825 Template switch process: F1: L TAAATCTCCATATCCGTAAAGCTGTGCCTCAAGTATATCCC 1 F3: 4 ACATTACATAATCCTTATACATAGTGATATGTTGCTTTC R RF: TAAATCTCCATATCCATAAAGCTGTGCCTCAAGTATATCCCATGTCACATTACATAATCCTTATACATAGTGATATGTTGCTTTC RR: ATTTAGAGGTATAGGTATTTCGACACGGAGTTCATATAGGGTACAGTGTAATGTATTAGGAATATGTATCACTATACAACGAAAG F2: 3 CGGAGTT 2 Unidirectional alignment (log-probability: -31.8) AAATCTCCATATCCgTAAAGCTGTGCCTCAAGTATATCCCtTGaggCACATTACATAATCCTTATACATAGTGATATGTTGCTTTC AAATCTCCATATCCATAAAGCTGTGCCTCAAGTATATCCCATG--TCACATTACATAATCCTTATACATAGTGATATGTTGCTTTC Template switch alignment (log-probability: -22.1) AAATCTCCATATCCgTAAAGCTGTGCCTCAAGTATATCCC|TTGAGGC|ACATTACATAATCCTTATACATAGTGATATGTTGCTTTC AAATCTCCATATCCATAAAGCTGTGCCTCAAGTATATCCC|TTGAGGC|ACATTACATAATCCTTATACATAGTGATATGTTGCTTTC ========== Event 2654 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAAGTGGGTAAATGTCTTCCTCT---------------------------------------------------------------------CTACTACTAGGTCATGCCAATTTACA Chimp: TCAAGTGGGTAAATGTCTTCCTCT--------------------------------------------------CTACTAAGTAGAGACGTCTCTACTACTAGGTCATGCCAATTTACA Gorilla: TCAAGTGGGTAAATGTCTTCCTCTCTACTAAG-------------------------------TACAGACCTCT-------------------CTACTACTAGGTCATGCCAATTTACA ↑ 4 3 21 Human: TCAAGTGGGTAAATGTCTTCCTCT---------------------------------------------------------------------CTACTACTAGGTCATGCCAATTTACA Cluster: [ ] Orangutan: TCAAGTGGGTAAATGTCTTcctctctactaagtagaagtagagacctctctactaagtagaagtagagacctct-------------------ctactaCTAGGTCATGCCAATTTACA Human > Gorilla --------------- chr4:172640729-172640736 Template switch process: F1: L TTTAGCCTACAGTATGTTCAAGTGGGTAAATGTCTTCCTCTCTACTA 1 F3: 4 CCTCTCTACTACTAGGTCATGCCAATTTACATTTAAACATATGAT R RF: TTTAGCCTACAGTATGTTCAAGTGGGTAAATGTCTTCCTCTCTACTACTAGGTCATGCCAATTTACATTTAAACATATGAT RR: AAATCGGATGTCATACAAGTTCACCCATTTACAGAAGGAGAGATGATGATCCAGTACGGTTAAATGTAAATTTGTATACTA F2: 3 AGACATGA 2 Unidirectional alignment (log-probability: -38.2) TACAGTATGTTCAAGTGGGTAAATGTCTTCCTctctactaagtacagacctCTCTACTACTAGGTCATGCCAATTTACATTTAAACAT TACAGTATGTTCAAGTGGGTAAATGTCTTCCT-------------------CTCTACTACTAGGTCATGCCAATTTACATTTAAACAT Template switch alignment (log-probability: -22.5) TACAGTATGTTCAAGTGGGTAAATGTCTTCCTCTCTACTA|AGTAcAGA|CCTCTCTACTACTAGGTCATGCCAATTTACATTTAAACAT TACAGTATGTTCAAGTGGGTAAATGTCTTCCTCTCTACTA|AGTAGAGA|CCTCTCTACTACTAGGTCATGCCAATTTACATTTAAACAT ========== Event 2655 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTCAAAAGAATGATAAGGA----------------------------GGTTATATGTTGGGCATTGGGACCTGCAGGGGATTGACTGGGTTCCTTACAATTTTAGCATACTTTATTTCCATTCCTAGGAA Chimp: CTTTCAAAAGAATGATAAGGAGCATTGATATGCTGGGCATTGGGCATTGAATGATATGTTGGGCATTGGGACCTGCAGGGGATTGACTGGGTTCCTTACAATTTTAGCATACTTTATTTCCATTCCTAGGAA ↓ 1 4 3 2 Gorilla: CTTTCAAAAGAATGATAAGGA----------------------------GGTATTCTATTGGGCATTGAGACCTGCAGGGGATTGACTGGGTTCCTTACCATTTTAGTATACTTTATTTCCATTCATAGGAA Human: CTTTCAAAAGAATGATAAGGA----------------------------GGTTATATGTTGGGCATTGGGACCTGCAGGGGATTGACTGGGTTCCTTACAATTTTAGCATACTTTATTTCCATTCCTAGGAA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNN----------------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTTTATTTCCATTCATAGGAA Chimp > Gorilla --------------- chr4:172703091-172703098 Template switch process: F1: L GTTTCCAACTGGGAGTTAAACTTTCAAAAGAATGATAAGGAG 1 F3: 4 TTGGGCATTGAGACCTGCAGGGGATTGACTGGGTTCCTTA R RF: GTTTCCAACTGGGAGTTAAACTTTCAAAAGAATGATAAGGAGCATTGATATGCTGGGCATTGGGCATTGAATGATATGTTGGGCATTGGGACCTGCAGGGGATTGACTGGGTTCCTTACAATTTTAGCATAC RR: CAAAGGTTGACCCTCAATTTGAAAGTTTTCTTACTATTCCTCGTAACTATACGACCCGTAACCCGTAACTTACTATACAACCCGTAACCCTGGACGTCCCCTAACTGACCCAAGGAATGTTAAAATCGTATG F2: 3 ATCTTATG 2 Unidirectional alignment (log-probability: -38) TTCCAACTGGGAGTTAAACTTTCAAAAGAATGATAAGGAG-----------------------------------GtattctaTTGGGCATTGaGACCTGCAGGGGATTGACTGGGTTCCTTA TTCCAACTGGGAGTTAAACTTTCAAAAGAATGATAAGGAGCATTGATATGCTGGGCATTGGGCATTGAATGATATG-------TTGGGCATTGGGACCTGCAGGGGATTGACTGGGTTCCTTA Template switch alignment (log-probability: -27.8) TTCCAACTGGGAGTTAAACTTTCAAAAGAATGATAAGGAG|GTATtCTA|TTGGGCATTGaGACCTGCAGGGGATTGACTGGGTTCCTTA TTCCAACTGGGAGTTAAACTTTCAAAAGAATGATAAGGAG|GTATGCTA|TTGGGCATTGGGACCTGCAGGGGATTGACTGGGTTCCTTA ========== Event 2656 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAAAAGGATTTTCATAAGTTTCATTAATGCGTAATTAGCACTTCGTATTAATGAAAAGGCAGATTTAAAGGAGAA Chimp: GAAAAAGGATTTTCATAAGTC--------AGCTAATTAGCACTACGCATTAATGAAAAGGCAGATTTAAAGGAGAA Gorilla: GAAAAAGGATTTTCATAAGTC--------AGCTAATTAGCACTACGCATTAATGAAAAGGCAGATTTAAAGGAGAA ↓ 1 4 3 2 Human: GAAAAAGGATTTTCATAAGTTTCATTAATGCGTAATTAGCACTTCGTATTAATGAAAAGGCAGATTTAAAGGAGAA Cluster: [ ] Orangutan: GAAAAAGGATTTTCATAAGTC--------AGCTAATTAGCACTATGCATTAACGAAAAGGCAGATGTAAAGGAGAA Gorilla > Human --------------- chr4:33262391-33262402 Template switch process: F1: L AAAAGGATTTTCATAAGT 1 F3: 4 TAATTAGCACTTCGTATTAATGAAAAGGCAGATTTAAAGGAGAATAAGAAAATAT R RF: AAAAGGATTTTCATAAGTCAGCTAATTAGCACTACGCATTAATGAAAAGGCAGATTTAAAGGAGAATAAGAAAATAT RR: TTTTCCTAAAAGTATTCAGTCGATTAATCGTGATGCGTAATTACTTTTCCGTCTAAATTTCCTCTTATTCTTTTATA F2: 3 GCGTAATTACTT 2 Unidirectional alignment (log-probability: -49) AAAAGGATTTTCATAAGT----ttcattaatgcgTAATTAGCACTtCGtATTAATGAAAAGGCAGATTTAAAGG AAAAGGATTTTCATAAGTCAGC------------TAATTAGCACTACGCATTAATGAAAAGGCAGATTTAAAGG Template switch alignment (log-probability: -28.1) AAAAGGATTTTCATAAGT|TTCATTAATGCG|TAATTAGCACTtCGtATTAATGAAAAGGCAGATTTAAAGG AAAAGGATTTTCATAAGT|TTCATTAATGCG|TAATTAGCACTACGCATTAATGAAAAGGCAGATTTAAAGG ========== Event 2657 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAAGATTCACTTTGTACATATTCATTGTCAAGATAATGACAAT------GAATATGGAATGTCTGCAAAGAAGAAAGAATCC ↑ 3 2 1 4 Chimp: TTAAGATTCACTTTGTACATATTCATTGTCAAGATAAGAAAAAT---CTTTCAGTTGGAATGCCTGCAAAGAAGAAAGAATCC Gorilla: TTAAGATTCACTTTGTACATATTCATTGTCAAGATAAGAAAAATCTT---TCAGTTGGAATGTCTGCAAAGAAGAAAGAATCC Human: TTAAGATTCACTTTGTACATATTCATTGTCAAGATAATGACAAT------GAATATGGAATGTCTGCAAAGAAGAAAGAATCC Cluster: [ ] Orangutan: TTAAGATTCACTTTGTACATATTCATTGTCAAGATAAGAAAAATCTT---TCAGTTGGAAAGTCTGCAAAGAAGAAAGAATCC Chimp > Human ------------- chr4:159211309-159211320 Template switch process: F1: L CTACTTAAGATTCACTTTGTACATATTCATTGTCAAGATAA 1 F3: 4 TGGAATGTCTGCAAAGAAGAAAGAATCCAAAAGTTACATATTTAAATG R RF: CTACTTAAGATTCACTTTGTACATATTCATTGTCAAGATAAGAAAAATCTTTCAGTTGGAATGCCTGCAAAGAAGAAAGAATCCAAAAGTTACATATTTAAATG RR: GATGAATTCTAAGTGAAACATGTATAAGTAACAGTTCTATTCTTTTTAGAAAGTCAACCTTACGGACGTTTCTTCTTTCTTAGGTTTTCAATGTATAAATTTAC F2: 3 ATAAGTAACAGT 2 Unidirectional alignment (log-probability: -43.7) TACTTAAGATTCACTTTGTACATATTCATTGTCAAGATAA--------------TgacaatgaataTGGAATGtCTGCAAAGAAGAAAGAATCCAAAAGTTACATA TACTTAAGATTCACTTTGTACATATTCATTGTCAAGATAAGAAAAATCTTTCAGT-----------TGGAATGCCTGCAAAGAAGAAAGAATCCAAAAGTTACATA Template switch alignment (log-probability: -22.9) TACTTAAGATTCACTTTGTACATATTCATTGTCAAGATAA|TGACAATGAATA|TGGAATGtCTGCAAAGAAGAAAGAATCCAAAAGTTACATA TACTTAAGATTCACTTTGTACATATTCATTGTCAAGATAA|TGACAATGAATA|TGGAATGCCTGCAAAGAAGAAAGAATCCAAAAGTTACATA ========== Event 2658 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGGAAAGGATAAGTGGGTGTG----------------TGTGCCCGTGCACATGTGTGCACATGTGCACACACTTGACAGAATCCAATG Chimp: GGGAAAGGATAAGTGGGTGTG----------------TGTGCCCGTGCACATGTGTGCACATGTGCACACACTTGACAGAATCCAATG ↑ 4 3 2 Gorilla: GGGAAAGGATAAGTGGGTGTG--------------------------------TGTGCACATGTGCACACACTTGACAGAATCCAATG ↓ 4 3 2 Human: GGGAAAGGATAAGTGGGTGTG----------------TGTGCCCGTGCACATGTGTGCACATGTGCACACACTTGACAGAATCCAATG Cluster: [ ] Orangutan: GGGAAAGGATAAGTGGGTGTGTGTGCCCGTGCACATG----------------TGTGCACATGTGGGCACACCTGACAGAATCCAATG Gorilla > Human --------------- chr4:159331464-159331472 Template switch process: F1: L TGATTTAGAGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCCC 1 F3: 4 TGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC R RF: TGATTTAGAGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC RR: ACTAAATCTCTTTATCAGGTCCCTTTCCTATTCACCCACACACACGTGTACACGTGTGTGAACTGTCTTAGGTTACGGTTG F2: 3 GTACACGTG 2 Unidirectional alignment (log-probability: -33.9) AGAAATAGTCCAGGGAAAGGATAAGTGGGTGtgtgtgcccgtgcacaTGTGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC AGAAATAGTCCAGGGAAAGGATAAGTGGGTG----------------TGTGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC Template switch alignment (log-probability: -22.6) AGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCcC|GTGCACATG|TGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC AGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCAC|GTGCACATG|TGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC Gorilla > Chimp --------------- chr4:163205271-163205279 Template switch process: F1: L TGATTTAGAGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCCC 1 F3: 4 TGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC R RF: TGATTTAGAGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC RR: ACTAAATCTCTTTATCAGGTCCCTTTCCTATTCACCCACACACACGTGTACACGTGTGTGAACTGTCTTAGGTTACGGTTG F2: 3 GTACACGTG 2 Unidirectional alignment (log-probability: -33.9) AGAAATAGTCCAGGGAAAGGATAAGTGGGTGtgtgtgcccgtgcacaTGTGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC AGAAATAGTCCAGGGAAAGGATAAGTGGGTG----------------TGTGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC Template switch alignment (log-probability: -22.6) AGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCcC|GTGCACATG|TGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC AGAAATAGTCCAGGGAAAGGATAAGTGGGTGTGTGTGCAC|GTGCACATG|TGTGCACATGTGCACACACTTGACAGAATCCAATGCCAAC ========== Event 2659 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCCTATGACCAGTAAGGAGCCA----TCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCT Chimp: CCCCTATGACCAGTAAGGAGCCA----TCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCT ↓ 1 4 3 2 Gorilla: CCCCTATGACCAGTAAGGAGCAAATGTACAAATGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCT ↑ 1 4 3 2 Human: CCCCTATGACCAGTAAGGAGCCA----TCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCT Cluster: [ ] Orangutan: --------------------------------------------------------------------- Human > Gorilla --------------- chr4:35704612-35704622 Template switch process: F1: L CCAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC 1 F3: 4 TGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT R RF: CCAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGCCATCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT RR: GGTCTCAGTGGGACTGGTTGGGGGATACTGGTCATTCCTCGGTAGATGACGGATAAACATGTAAAATACCTACACAGTTCACGGAGTA F2: 3 AAACATGTAAA 2 Unidirectional alignment (log-probability: -36.4) CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGCaaatgtaCA---AaTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC-------CATCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT Template switch alignment (log-probability: -17.1) CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC|AAATGTACAAA|TGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC|AAATGTACAAA|TGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT Chimp > Gorilla --------------- chr4:35704612-35704622 Template switch process: F1: L CCAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC 1 F3: 4 TGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT R RF: CCAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGCCATCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT RR: GGTCTCAGTGGGACTGGTTGGGGGATACTGGTCATTCCTCGGTAGATGACGGATAAACATGTAAAATACCTACACAGTTCACGGAGTA F2: 3 AAACATGTAAA 2 Unidirectional alignment (log-probability: -36.4) CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGCaaatgtaCA---AaTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC-------CATCTACTGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT Template switch alignment (log-probability: -17.1) CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC|AAATGTACAAA|TGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT CAGAGTCACCCTGACCAACCCCCTATGACCAGTAAGGAGC|AAATGTACAAA|TGCCTATTTGTACATTTTATGGATGTGTCAAGTGCCTCAT ========== Event 2660 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTGCCTCTATCTGCTTTACCTTCA--GTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAAAGAGAGAAGGCTGTCAC Chimp: CTGCCTCTATCTGCTTTACCTTCA--GTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAATGAGAGAAGGCTGTCAC ↓ 1 4 3 2 ↑ 1 4 3 2 Gorilla: CTGCCTCTATCTGCTTTACCTATCGTTTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAATGAGAGAAGGCTGTCAC ↓ 1 4 3 2 ↑ 1 4 3 2 Human: CTGCCTCTATCTGCTTTACCTTCA--GTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAAAGAGAGAAGGCTGTCAC Cluster: [ ] Orangutan: CTGCCTCTATCTGCTTTACCTTCA--GTACAGGCCAACGATGGTGATCCACAGTGAGGTTCTGAAAATGAGAGAAGGCTGTCAC Gorilla > Human --------------- chr4:152153900-152153903 Template switch process: F1: L TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT 1 F3: 4 TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA R RF: TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCTATCGTTTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA RR: AGAAGTAGACTGTCTACTCTGACGGAGATAGACGAAATGGATAGCAAATGTCCGGTTGCTACCGCTAGGTGTCACTCCAAGACTTTT F2: 3 GACT 2 Unidirectional alignment (log-probability: -25.2) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACC-----TTcagTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCTATCGTT---TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Template switch alignment (log-probability: -16.2) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|TCAG|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|TCAG|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Human > Gorilla --------------- chr4:165308042-165308047 Template switch process: F1: L TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT 1 F3: 4 TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA R RF: TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCTTCAGTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA RR: AGAAGTAGACTGTCTACTCTGACGGAGATAGACGAAATGGAAGTCATGTCCGGTTGCTACCGCTAGGTGTCACTCCAAGACTTTT F2: 3 TTGCTA 2 Unidirectional alignment (log-probability: -28) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCtatcgTT---TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACC-----TTCAGTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Template switch alignment (log-probability: -16.5) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|ATCGTT|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|ATCGTT|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Gorilla > Chimp --------------- chr4:156056169-156056172 Template switch process: F1: L TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT 1 F3: 4 TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA R RF: TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCTATCGTTTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA RR: AGAAGTAGACTGTCTACTCTGACGGAGATAGACGAAATGGATAGCAAATGTCCGGTTGCTACCGCTAGGTGTCACTCCAAGACTTTT F2: 3 GACT 2 Unidirectional alignment (log-probability: -25.2) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACC-----TTcagTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCTATCGTT---TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Template switch alignment (log-probability: -16.2) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|TCAG|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|TCAG|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Chimp > Gorilla --------------- chr4:165308042-165308047 Template switch process: F1: L TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT 1 F3: 4 TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA R RF: TCTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCTTCAGTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA RR: AGAAGTAGACTGTCTACTCTGACGGAGATAGACGAAATGGAAGTCATGTCCGGTTGCTACCGCTAGGTGTCACTCCAAGACTTTT F2: 3 TTGCTA 2 Unidirectional alignment (log-probability: -28) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCtatcgTT---TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACC-----TTCAGTACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA Template switch alignment (log-probability: -16.5) CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|ATCGTT|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA CTTCATCTGACAGATGAGACTGCCTCTATCTGCTTTACCT|ATCGTT|TACAGGCCAACGATGGCGATCCACAGTGAGGTTCTGAAAA ========== Event 2661 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: gatatctgtatttccatgtaattggctACAAATTATATGGAAGGCTGGGTACAGACATTCAGCCTTCTTCTCATTCTTTTGTTGCTAAATATAAAATGTAGGATGACATTCTCC------------------------------TTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATATAGCC-----------------------------------------AATTATATAAAATTCTCCTTTAAGTaaccaattatatggaaatacagacatcaacat Chimp: gatatctgtatttccatgtaattggctACAAATTATATGGAAGGCTGGGTACAGACATTCAGCCTTCTTCTCATTCTTTTGTTGCTAAATATGAAATGTAGGATGACATTCTCC------------------------------TTAAAGAGAAGttctcctttaagtaaccaattatatagccaattatataaaattctcctttaagtaaccaattatatagccagttatataaaattctcctttaagtaaccaattatatggaaatacagacatcaacat Gorilla: ggtatctgtatttccatgtaattggctACAAATTATATGGAAGGCTGAGTACAGACATTCAGCCTTCTTCTCATTCTTTTGTTGCTAAATATAAAATGTAGGATGACATTCTCC----------------------------------------------------------------------------------------------------------------TTTAAGAGAAGTTCTCCTTTAAGTaaccaattatatggaaatacagacatcaacat ↓ 3 2 4 1 Human: gatatctgtatttccatgtaattggctACAAATTATATGGAAGGCTGGGTACAGACATTCAGCCTTCTTCTCATTCTTTTGTTGCTAAATATAAAATGTAGGATGACATTCTCC------------------------------TTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATATAGCC-----------------------------------------AATTATATAAAATTCTCCTTTAAGTaaccaattatatggaaatacagacatcaacat Cluster: [ ] Orangutan: gatatctgtatttccatgtaattggCTACAAATTATATGGAAGGCTGAGTACAGACATTCAGCCTTCTTCTCATTCTCTTGTTGCTAAATATAAAATGTAGGATGACATTCTCCTTTAAGAGAAGTTCTCCTTTAAGTAACCAA-----------------------------------------------------------------------------------TTATATAAAATTCTCCTTTAAGTaaccaattatatggaaatatagatatcaacat Gorilla > Human --------------- chr4:152333850-152333857 Template switch process: F1: L TTCTTTTGTTGCTAAATATAAAATGTAGGATGACATTCTCCTTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATAT 1 F3: 4 ATATAAAA-----------------------------TTCTCCTTTAAGTAACCAATTATATGGAAATACAGACATC R RF: AATTGGCTACAAATTATATGGAAGGCTGAGTACAGACATTCAGCCTTCTTCTCATTCTTTTGTTGCTAAATATAAAATGTAGGATGACATTCTCCTTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATATGGAAATACAGACATC RR: TTAACCGATGTTTAATATACCTTCCGACTCATGTCTGTAAGTCGGAAGAAGAGTAAGAAAACAACGATTTATATTTTACATCCTACTGTAAGAGGAAATTCTCTTCAAGAGGAAATTCATTGGTTAATATACCTTTATGTCTGTAG F2: 3 TTAACCGA 2 Unidirectional alignment (log-probability: -70) CTCCTTTAAGAGAAGttctcctttaagtaaccaattatatagccaattatataaaaTTCTCCTTTAAGTAACCAATTATATGGAAATA CTCCTTTAAGAGAAG-----------------------------------------TTCTCCTTTAAGTAACCAATTATATGGAAATA Template switch alignment (log-probability: -29) CTCCTTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATAT|AGCCAATT|ATATAAAA-----------------------------TTCTCCTTTAAGTAACCAATTATATGGAAATA CTCCTTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATAT|AGCCAATT|ATATAAAATGTAGGATGACATTCTCCTTTAAGAGAAGTTCTCCTTTAAGTAACCAATTATATGGAAATA ========== Event 2662 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCACATAAGTAGACCATGTCCATGTG------CTGTTGTAGTAAGTGCACCACAGAAGTCTATGAAAGGA Chimp: AGCACATAAGTAGACCATGTCCATGTG------CTGTTGTACTAAGTGCACCACAGAAGTGTATGAAAGGA ↓ 3 12 4 Gorilla: AGCACATAAGTAGACCACGTCCATGTG------------CACCACATGGACCACAGAAGTGTATGAAAGGA Human: AGCACATAAGTAGACCATGTCCATGTG------CTGTTGTAGTAAGTGCACCACAGAAGTCTATGAAAGGA Cluster: [ ] Orangutan: AGCACATAAGTAGACCATGTCCATGTGCTGTTG------TACTAAGTGCACAACAGAAGTGTATGAAAGGA Chimp > Gorilla --------------- chr4:37975284-37975293 Template switch process: F1: L TCCTGAGGGAAACAAGCACATAAGTAGACCACGTCCATGTGC 1 F3: 4 CCACAGAAGTGTATGAAAGGAGACCAGTGACTGGGACAT R RF: TCCTGAGGGAAACAAGCACATAAGTAGACCATGTCCATGTGCTGTTGTACTAAGTGCACCACAGAAGTGTATGAAAGGAGACCAGTGACTGGGACAT RR: AGGACTCCCTTTGTTCGTGTATTCATCTGGTACAGGTACACGACAACATGATTCACGTGGTGTCTTCACATACTTTCCTCTGGTCACTGACCCTGTA F2: 3 AGGTACACCA 2 Unidirectional alignment (log-probability: -38.9) CTGAGGGAAACAAGCACATAAGTAGACCAcGTCCATGTGC------ACcAcaTGgACCACAGAAGTGTATGAAAGGAGACCAGTGACTGGGACAT CTGAGGGAAACAAGCACATAAGTAGACCATGTCCATGTGCTGTTGTACTAAGTGCACCACAGAAGTGTATGAAAGGAGACCAGTGACTGGGACAT Template switch alignment (log-probability: -28) CTGAGGGAAACAAGCACATAAGTAGACCAcGTCCATGTGC|AcCACATGGA|CCACAGAAGTGTATGAAAGGAGACCAGTGACTGGGACAT CTGAGGGAAACAAGCACATAAGTAGACCATGTCCATGTGC|AGCACATGGA|CCACAGAAGTGTATGAAAGGAGACCAGTGACTGGGACAT ========== Event 2663 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GACATATATACTCCTAATGAA--------AGCAG------TTGTTGTTGCCAACAACTGAAAACATTTCTTGTTTAATA ↑ 1 4 3 2 Chimp: GACATATATACTCCTAATGAA----AGATAGCAG---GTAATATTGTTGCCAACAACTGGAAACATTTCTTGTTTAATA Gorilla: GACATATGTACTCCTAATGAA--------AGCAGCTA---ATATTGTTGCCAACAACTGAAAACATTTCTTGTTTAACA Human: GACATATATACTCCTAATGAA--------AGCAG------TTGTTGTTGCCAACAACTGAAAACATTTCTTGTTTAATA Cluster: [ ] Orangutan: GACATATATACTCCTAATGAAAGAT----AGCAGCTA---ATATTGTTGCCAACAACTGGAAACATTTCTTGTTTAATA Chimp > Human ------------- chr4:39700020-39700025 Template switch process: F1: L AAATGTATTCCAGGTTAGTTGACATATATACTCCTAATGAAAG 1 F3: 4 TTGTTGCCAACAACTGAAAACATTTCTTGTTTAATAAGGT R RF: AAATGTATTCCAGGTTAGTTGACATATATACTCCTAATGAAAGATAGCAGGTAATATTGTTGCCAACAACTGGAAACATTTCTTGTTTAATAAGGT RR: TTTACATAAGGTCCAATCAACTGTATATATGAGGATTACTTTCTATCGTCCATTATAACAACGGTTGTTGACCTTTGTAAAGAACAAATTATTCCA F2: 3 GTTGAC 2 Unidirectional alignment (log-probability: -36.4) TGTATTCCAGGTTAGTTGACATATATACTCCTAATGAAAgcagttG-------------TTGTTGCCAACAACTGaAAACATTTCTTGTTTAATAAGGT TGTATTCCAGGTTAGTTGACATATATACTCCTAATGAAA------GATAGCAGGTAATATTGTTGCCAACAACTGGAAACATTTCTTGTTTAATAAGGT Template switch alignment (log-probability: -22.1) TGTATTCCAGGTTAGTTGACATATATACTCCTAATGAAAG|CAGTTG|TTGTTGCCAACAACTGaAAACATTTCTTGTTTAATAAGGT TGTATTCCAGGTTAGTTGACATATATACTCCTAATGAAAG|CAGTTG|TTGTTGCCAACAACTGGAAACATTTCTTGTTTAATAAGGT ========== Event 2664 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAGAAAACAGGAAATGCAA----ACAGACAGgttttttgttgtt---------tttgttgtttgtttgttttgttttgttttgtttAGAACAGTACCTGTATAAATATGGAAGGAAACTT Chimp: AGAAGAAAACAGGAAATGCAA----ATAGACAGgttttttgttgtt---------tttgttgtttgttt----------gttttgtttAGAACAGTACCTGTATAAATATGGAAGGAAACTT Gorilla: AGAAGAAAACAGGAAATGCAA--------ACAGgttttttgttgtttttgttgtttttgttgtttgtttgttttgttttgttttgtttAGAACAGTACCTGTATAAATATGGAAGGAAACTT ↓ 1 4 3 2 Human: AGAAGAAAACAGGAAATGCAA----ACAGACAGgttttttgttgtt---------tttgttgtttgtttgttttgttttgttttgtttAGAACAGTACCTGTATAAATATGGAAGGAAACTT Cluster: [ ] Orangutan: AGAAGAAAACAGGAAATGCAAACAG----ACAGgttttttgttgtt---------tttgttgtttgtttgttttgttttgttttgtttAGAACAGTACTTGTATAAATATGGAAGGAAACTT Gorilla > Human --------------- chr4:39700357-39700362 Template switch process: F1: L AGCATCAAAAGTGTTTCAGAAGAAGAAAACAGGAAATGCAAACAG 1 F3: 4 TTTTTGTTGTTTTTGTTGTTTGTTT R RF: AGCATCAAAAGTGTTTCAGAAGAAGAAAACAGGAAATGCAAACAGGTTTTTTGTTGTTTTTGTTGTTTTTGTTGTTTGTTTGTTTTGTTTTGTTTTGTTTAGAACAGTACCTGT RR: TCGTAGTTTTCACAAAGTCTTCTTCTTTTGTCCTTTACGTTTGTCCAAAAAACAACAAAAACAACAAAAACAACAAACAAACAAAACAAAACAAAACAAATCTTGTCATGGACA F2: 3 TGGACA 2 Unidirectional alignment (log-probability: -26.7) CAAAAGTGTTTCAGAAGAAGAAAACAGGAAATGCAAacagACAGGT---------TTTTTGTTGTTTTTGTTGTTTGTTT CAAAAGTGTTTCAGAAGAAGAAAACAGGAAATGCAA----ACAGGTTTTTTGTTGTTTTTGTTGTTTTTGTTGTTTGTTT Template switch alignment (log-probability: -16.2) CAAAAGTGTTTCAGAAGAAGAAAACAGGAAATGCAAACAG|ACAGGT|TTTTTGTTGTTTTTGTTGTTTGTTT CAAAAGTGTTTCAGAAGAAGAAAACAGGAAATGCAAACAG|ACAGGT|TTTTTGTTGTTTTTGTTGTTTGTTT ========== Event 2665 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 346 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTTCTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCT--CATAGCAACTTGGAGAAAAACAAT Chimp: CTTGTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCT--CATAGCAACTTGGAGAAAAACAAT ↓ 3 2 1 4 Gorilla: CTTCTGTGTCTAAATGACTTATATGACTACTTGGATAGTCATAT----AAGCAACTTGGAGAAAAACAAT ↓ 3 1 42 ↑ 3 2 1 4 Human: CTTCTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCT--CATAGCAACTTGGAGAAAAACAAT Cluster: [ ] Orangutan: CTTCTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCTCA--TAGCAACTTGGAGAAAAACAAT Gorilla > Human --------------- chr4:40794113-40794119 Template switch process: F1: L TTTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT 1 F3: 4 TCAT---AGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT R RF: TTTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGATAGTCATATAAGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT RR: AAAGAGAAGACACAGATTTACTGAATATACTGATGAACCTATCAGTATATTCGTTGAACCTCTTTTTGTTATAATTTATAAAAGTTATAA F2: 3 CTATCAG 2 Unidirectional alignment (log-probability: -36.9) TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT---------gactatctcatAGCAACTTGGAGAAAAACAATATTAAATATTTTCAA TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGATAGTCATATA-----------AGCAACTTGGAGAAAAACAATATTAAATATTTTCAA Template switch alignment (log-probability: -26.6) TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT|GACTATC|TCAT---AGCAACTTGGAGAAAAACAATATTAAATATTTTCAA TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT|GACTATC|TCATATAAGCAACTTGGAGAAAAACAATATTAAATATTTTCAA Human > Gorilla --------------- chr4:40600761-40600769 Template switch process: F1: L TTTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT 1 F3: 4 AGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT R RF: TTTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCTCATAGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT RR: AAAGAGAAGACACAGATTTACTGAATATACTGATGAACCTACTGATAGAGTATCGTTGAACCTCTTTTTGTTATAATTTATAAAAGTTATAA F2: 3 ATATACTGA 2 Unidirectional alignment (log-probability: -34.1) TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGG-----------ATagtcatataAGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCTCAT---------AGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT Template switch alignment (log-probability: -16.9) TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT|AGTCATATA|AGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT TTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT|AGTCATATA|AGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT Chimp > Gorilla --------------- chr4:40600761-40600769 Template switch process: F1: L TTTCTCTTCTGTGTCTAAATGACTTATATGACTACTTGGAT 1 F3: 4 AGCAACTTGGAGAAAAACAATATTAAATATTTTCAATATT R RF: TTTCTCTTGTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCTCATAGCAACTTGGAGAAAAACAATGTTAAATATTTTCAATATT RR: AAAGAGAACACACAGATTTACTGAATATACTGATGAACCTACTGATAGAGTATCGTTGAACCTCTTTTTGTTACAATTTATAAAAGTTATAA F2: 3 ATATACTGA 2 Unidirectional alignment (log-probability: -45.2) TTCTCTTcTGTGTCTAAATGACTTATATGACTACTTGG-----------ATagtcatataAGCAACTTGGAGAAAAACAATaTTAAATATTTTCAATATT TTCTCTTGTGTGTCTAAATGACTTATATGACTACTTGGATGACTATCTCAT---------AGCAACTTGGAGAAAAACAATGTTAAATATTTTCAATATT Template switch alignment (log-probability: -27.9) TTCTCTTcTGTGTCTAAATGACTTATATGACTACTTGGAT|AGTCATATA|AGCAACTTGGAGAAAAACAATaTTAAATATTTTCAATATT TTCTCTTGTGTGTCTAAATGACTTATATGACTACTTGGAT|AGTCATATA|AGCAACTTGGAGAAAAACAATGTTAAATATTTTCAATATT ========== Event 2666 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCAGGTTTTAGCAGTGGTCAGTTGGAGTGCAGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGACTGGTGGCTGGAGATTATCTGTAGAAATGCAAAAAgtgaagcatcatagaaaagcactctcttcagatttagaaaccc Chimp: GCCAGGTTTTAGCAGTGGTCAGTTTGAGTGCAGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGACTGGTGGCTGGAGATTATCTGTAGAAATGCAAAAAgtgaagcatcatagaaaagcactctcttcagatttagaaaccc ↑ 4 1 3 2 Gorilla: GCCAGGTTTTAGCAGTGGTCA-----------GTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGACTGGTGGCTGGAGATTATCTGTAGAAATGCAAAAAgtgaagcatcatagaaaagcactctcttcagatttagaaaccc Human: GCCAGGTTTTAGCAGTGGTCAGTTGGAGTGCAGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGACTGGTGGCTGGAGATTATCTGTAGAAATGCAAAAAgtgaagcatcatagaaaagcactctcttcagatttagaaaccc Cluster: [ ] Orangutan: GCCAGGTTTTAGCAGTGGTCA-----------GTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGACTGGTGGCTGGAGATTATCTGTAGAAATGCAAAAAgtgaagcatcatagaaaagcactctcttcagatttagaaaccc Gorilla > Chimp --------------- chr4:41997873-41997877 Template switch process: F1: L AGGGAAGGATCCCGGCCAGAGCCAGGTTTTAGCAGTGGTCAGTTTG 1 F3: 4 AGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGAC R RF: AGGGAAGGATCCCGGCCAGAGCCAGGTTTTAGCAGTGGTCAGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGACTGGTGGCTGGAGATTATCTGTAGAAATGCAAAAAGTGAAGCATCATAGAAAAGCACT RR: TCCCTTCCTAGGGCCGGTCTCGGTCCAAAATCGTCACCAGTCAAACCCACGTCACCCGGACACCTAATCCTACCGTCTCTGACCACCGACCTCTAATAGACATCTTTACGTTTTTCACTTCGTAGTATCTTTTCGTGA F2: 3 CGTGA 2 Unidirectional alignment (log-probability: -26.7) GGATCCCGGCCAGAGCCAGGTTTTAGCAGTGGTcagtttgagtgCAGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGA GGATCCCGGCCAGAGCCAGGTTTTAGCAGTGGT-----------CAGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGA Template switch alignment (log-probability: -16.5) GGATCCCGGCCAGAGCCAGGTTTTAGCAGTGGTCAGTTTG|AGTGC|AGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGA GGATCCCGGCCAGAGCCAGGTTTTAGCAGTGGTCAGTTTG|AGTGC|AGTTTGGGTGCAGTGGGCCTGTGGATTAGGATGGCAGAGA ========== Event 2667 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: A---ACGACAGCATGGCGTGTGTGTGCATGCGTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCATCGAAGGTGGGAGATAATCAA ↑ 4 1 3 2 Chimp: A---ACGACAGCATGGCGTGTG------------TGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCATCGAGGGTGGGAGATAATCAA Gorilla: A------ACAGCATGGCGTGTGTGTGCATGCGCGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCATCGAGGGTGGGAGATAATCAA Human: A---ACGACAGCATGGCGTGTGTGTGCATGCGTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCATCGAAGGTGGGAGATAATCAA Cluster: [ ] Orangutan: aaca---acagcatggcgtgtgtgtgcatgcgtgtgtgcttgcgtgtggtaggtgtgGCAGGCTCCTGCATCGAGGGTGGGAGATAATCAA Chimp > Human ------------- chr4:4608255-4608258 Template switch process: F1: L AAGCGACACAGGCCCTGAGCTTAACGACAGCATGGCGTGTGTGTGC 1 F3: 4 GTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCATCGA R RF: AAGCGACACAGGCCCTGAGCTTAACGACAGCATGGCGTGTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCATCGA RR: TTCGCTGTGTCCGGGACTCGAATTGCTGTCGTACCGCACACACACGAGCGCACACCATCCACACCGTCCGAGGACGTAGCT F2: 3 CGTA 2 Unidirectional alignment (log-probability: -28.2) CACAGGCCCTGAGCTTAACGACAGCATGGCGTgtgtgtgcatgcGTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCAT CACAGGCCCTGAGCTTAACGACAGCATGGCGT------------GTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCAT Template switch alignment (log-probability: -15.9) CACAGGCCCTGAGCTTAACGACAGCATGGCGTGTGTGTGC|ATGC|GTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCAT CACAGGCCCTGAGCTTAACGACAGCATGGCGTGTGTGTGC|ATGC|GTGTGTGCTCGCGTGTGGTAGGTGTGGCAGGCTCCTGCAT ========== Event 2668 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GT-TTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTTGCCTTATAATCCTCATGAGACAGAATTAA ↑ 3 2 1 4 Chimp: GT-TTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTCC------CATCCTCATGAGACAGAATTAA Gorilla: GT-TTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTCC------CATCCTCATGAGACAGAATTAA ↓ 3 2 1 4 Human: GT-TTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTTGCCTTATAATCCTCATGAGACAGAATTAA Cluster: [ ] Orangutan: TTTTTTTCGTGTCTCTGAATATAAGGCAGCCTTGCTGCC------CATTCTCATGAGACAGAATTAA Chimp > Human ------------- chr4:147694254-147694262 Template switch process: F1: L ATGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCT 1 F3: 4 ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA R RF: ATGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTCCCATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA RR: TACTACAAAAAGGACAGAGACTTATATTCCGTCGGAACGGAGGGTAGGAGTACTCTGTCTTAATTATACATTACAGTCTTATTT F2: 3 ATATTCCGT 2 Unidirectional alignment (log-probability: -31.6) TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTtgCcttataATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTCCC------ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA Template switch alignment (log-probability: -16.4) TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCT|TGCCTTATA|ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCT|TGCCTTATA|ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA Gorilla > Human --------------- chr4:147694254-147694262 Template switch process: F1: L ATGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCT 1 F3: 4 ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA R RF: ATGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTCCCATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA RR: TACTACAAAAAGGACAGAGACTTATATTCCGTCGGAACGGAGGGTAGGAGTACTCTGTCTTAATTATACATTACAGTCTTATTT F2: 3 ATATTCCGT 2 Unidirectional alignment (log-probability: -30.6) TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTtgCcttataATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCTCCC------ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA Template switch alignment (log-probability: -16.9) TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCT|TGCCTTATA|ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA TGATGTTTTTCCTGTCTCTGAATATAAGGCAGCCTTGCCT|TGCCTTATA|ATCCTCATGAGACAGAATTAATATGTAATGTCAGAATAAA ========== Event 2669 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATAGAAGGCTTGTTTAACTGGCTATTCCAAGAGACAACGATCTCTTGGAATAGCATTATCTCTGTCCTAACCAT Chimp: AATAGAAGCCTTGTTTAACTGGCTATTCCAAGAGACAACGATCTCTTGGAATAGCATTATCTCTGTCCTAACCAT ↑ 1 4 3 2 Gorilla: AATAGAAGGCTTGTTTAACTGACT-------TAGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAACCAT ↓ 1 4 3 2 Human: AATAGAAGGCTTGTTTAACTGGCTATTCCAAGAGACAACGATCTCTTGGAATAGCATTATCTCTGTCCTAACCAT Cluster: [ ] Orangutan: AATAGAAGGCTTGTTTAGCTGACT-------TAGACAACGATCTCTTGGAACAGCATTATCTCTGTCCTAACCAT Gorilla > Human --------------- chr4:146061296-146061306 Template switch process: F1: L CATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTG 1 F3: 4 AGACAACGATCTCTTGGAATAGCATTATCTCTGTCCTAAC R RF: CATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTGACTTAGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAAC RR: GTACATGAATTAAAGTTTCTTTATCTTCCGAACAAATTGACTGAATCTGTTGCTAGAGAACCTTATCGTAACAGAGACAGGATTG F2: 3 GAACCTTATCG 2 Unidirectional alignment (log-probability: -37.6) ATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTGgCTattccaagAGACAACGATCTCTTGGAATAGCATTaTCTCTGTCCTAAC ATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTGACTT-------AGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAAC Template switch alignment (log-probability: -22.6) ATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTG|GCTATTCCAAG|AGACAACGATCTCTTGGAATAGCATTaTCTCTGTCCTAAC ATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTG|GCTATTCCAAG|AGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAAC Gorilla > Chimp --------------- chr4:149813149-149813159 Template switch process: F1: L CATGTACTTAATTTCAAAGAAATAGAAGCCTTGTTTAACTG 1 F3: 4 AGACAACGATCTCTTGGAATAGCATTATCTCTGTCCTAAC R RF: CATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTGACTTAGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAAC RR: GTACATGAATTAAAGTTTCTTTATCTTCCGAACAAATTGACTGAATCTGTTGCTAGAGAACCTTATCGTAACAGAGACAGGATTG F2: 3 GAACCTTATCG 2 Unidirectional alignment (log-probability: -43.1) ATGTACTTAATTTCAAAGAAATAGAAGcCTTGTTTAACTGgCTattccaagAGACAACGATCTCTTGGAATAGCATTaTCTCTGTCCTAAC ATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTGACT-------TAGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAAC Template switch alignment (log-probability: -28.2) ATGTACTTAATTTCAAAGAAATAGAAGcCTTGTTTAACTG|GCTATTCCAAG|AGACAACGATCTCTTGGAATAGCATTaTCTCTGTCCTAAC ATGTACTTAATTTCAAAGAAATAGAAGGCTTGTTTAACTG|GCTATTCCAAG|AGACAACGATCTCTTGGAATAGCATTGTCTCTGTCCTAAC ========== Event 2670 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTAATAAAAAGCGTGGGATTTGTAG----------ATAAACAACCATTCTGAACTTCCCTCAA Chimp: TTTAATAAAAAGCGTGGGACTTGTAG----------ATAAACAACCATTCTGAATTTCCCTCAA ↓ 3 1 4 Gorilla: TTTAATAAAAAGCGTGGGACTTGTAGACTTGTTTATCTACAAGACCATTCTGAACTTCCCTCAA Human: TTTAATAAAAAGCGTGGGATTTGTAG----------ATAAACAACCATTCTGAACTTCCCTCAA Cluster: [ ] Orangutan: TTTAATAAAAAGCGTGGGACTTGTAG----------ATAAACAACCATTCTGAACTTCCCTCAA Chimp > Gorilla --------------- chr4:158651171-158651185 Template switch process: F1: L GGGAATTCATCCCAATTTAATAAAAAGCGTGGGACTTGTAGAC 1 F3: 4 ACCATTCTGAACTTCCCTCAAAGGGGTCATTTATTGAACC R RF: GGGAATTCATCCCAATTTAATAAAAAGCGTGGGACTTGTAGATAAACAACCATTCTGAATTTCCCTCAAAGGGGTCATTTATTGAACC RR: CCCTTAAGTAGGGTTAAATTATTTTTCGCACCCTGAACATCTATTTGTTGGTAAGACTTAAAGGGAGTTTCCCCAGTAAATAACTTGG F2: 3 GAACATCTATTTGTT 2 Unidirectional alignment (log-probability: -47.4) AATTCATCCCAATTTAATAAAAAGCGTGGGACTTGTAGActtgtttatcTAcAagACCATTCTGAAcTTCCCTCAAAGGGGTCATTTATTGAACC AATTCATCCCAATTTAATAAAAAGCGTGGGACTTGTAGA----------TAAACAACCATTCTGAATTTCCCTCAAAGGGGTCATTTATTGAACC Template switch alignment (log-probability: -28.7) AATTCATCCCAATTTAATAAAAAGCGTGGGACTTGTAGAc|TTGTTTATCTACAAG|ACCATTCTGAAcTTCCCTCAAAGGGGTCATTTATTGAACC AATTCATCCCAATTTAATAAAAAGCGTGGGACTTGTAGAT|TTGTTTATCTACAAG|ACCATTCTGAATTTCCCTCAAAGGGGTCATTTATTGAACC ========== Event 2671 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGGAATTCCCTACTACAATGCCAGGTTCCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGA Chimp: CAGGAATTACCTACTACAATG-----GACCCCCTGTCAGAACCTGGTAGCAGCATCCAATCTGAGA Gorilla: CAGGAATTCCCTACTACAATG-----GACCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGA ↓ 1 4 3 2 Human: CAGGAATTCCCTACTACAATGCCAGGTTCCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGA Cluster: [ ] Orangutan: CAGGAATTCCCTACTACAATG-----GACCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGA Gorilla > Human --------------- chr4:145351198-145351204 Template switch process: F1: L CATAAGACTGCTGGTCATCCCAGGAATTCCCTACTACAATG 1 F3: 4 CCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGAAA R RF: CATAAGACTACTGGTCATCCCAGGAATTCCCTACTACAATGGACCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGAAA RR: GTATTCTGATGACCAGTAGGGTCCTTAAGGGATGATGTTACCTGGGGGACAGTCTTGGACCGTCGTCGTAGGTTAGACTCTTT F2: 3 TTGGACC 2 Unidirectional alignment (log-probability: -34.7) ATAAGACTgCTGGTCATCCCAGGAATTCCCTACTACAATgccagGttCCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGAAA ATAAGACTACTGGTCATCCCAGGAATTCCCTACTACAAT-----GGACCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGAAA Template switch alignment (log-probability: -22.1) ATAAGACTgCTGGTCATCCCAGGAATTCCCTACTACAATG|CCAGGTT|CCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGAAA ATAAGACTACTGGTCATCCCAGGAATTCCCTACTACAATG|CCAGGTT|CCCCCTGTCAGAACCTGGCAGCAGCATCCAATCTGAGAAA ========== Event 2672 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: tttctatttattattgacacagtttgggtaggttgtatgtttttagaaatttatccatttccacctgtccatctagattatccaatttgttgacgtataattattcataatagtttcttaaaatcTCACAAAATTTTGATGCCTTGTTTCTGC---------------CAACTGGTAAACATGATTTGGGGCTAG Chimp: tttctatttattattgacacagtttgggtaggttgtatgtttttagaaatttatccatttccacctgtccatctagattatccaatttgttgacatataattattcataatagtttcttaaaatcTCACAAAATTTTGATGCCTTGTTTCTGC---------------CAACTGGTAAACATGATTTGGGGCTAG ↑ 3 2 1 4 Gorilla: tttctatttattattgacacagtttgggtaggttgtatgtttttagaaatttatccatttccacctgtccatctagattatccaatttgttgacatatacttattcataatagtttcttaaaatcTCACAAAATTTTGATGCCTTGTTTCTGCCTTGTTACATGTTACAATCATGTAAACATGATTTGGGGCTAG ↓ 3 2 1 4 Human: tttctatttattattgacacagtttgggtaggttgtatgtttttagaaatttatccatttccacctgtccatctagattatccaatttgttgacgtataattattcataatagtttcttaaaatcTCACAAAATTTTGATGCCTTGTTTCTGC---------------CAACTGGTAAACATGATTTGGGGCTAG Cluster: [ ] Orangutan: tttctatttgttattgacacagtttgggtaggtcgtatgtttttagaaattcatccatttccacctgtc-ctctagattatccaatttgttggcatataattattcataatagtttcttaaaatcTCACAAAATTTTGATGCCTTGTTTCTGC---------------CAACTGGTAAACATGATTTGGGGCTAG Gorilla > Human --------------- chr4:47320036-47320040 Template switch process: F1: L GTTTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC 1 F3: 4 GTAAACATGATTTGGGGCTAGGAAGCCTGGAAATGAAATG R RF: CAGTTTGGGTAGGTTGTATGTTTTTAGAAATTTATCCATTTCCACCTGTCCATCTAGATTATCCAATTTGTTGACATATACTTATTCATAATAGTTTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCCTTGTTACATGTTACAATCATGTAAACATGATTTGGGGCTAGGAGCCTGGAAATGAAATG RR: GTCAAACCCATCCAACATACAAAAATCTTTAAATAGGTAAAGGTGGACAGGTAGATCTAATAGGTTAAACAACTGTATATGAATAAGTATTATCAAAGAATTTTAGAGTGTTTTAAAACTACGGAACAAAGACGGAACAATGTACAATGTTAGTACATTTGTACTAAACCCCGATCCTCGGACCTTTACTTTAC F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -39.5) TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC---------------AaCtgGTAAACATGATTTGGGGCTAGGaAGCCTGGAAATGAAATG TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCCTTGTTACATGTTACAATCATGTAAACATGATTTGGGGCTAGG-AGCCTGGAAATGAAATG Template switch alignment (log-probability: -27.5) TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC|AACTG|GTAAACATGATTTGGGGCTAGGaAGCCTGGAAATGAAATG TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC|AACTG|GTAAACATGATTTGGGGCTAGG-AGCCTGGAAATGAAATG Gorilla > Chimp --------------- chr4:109725107-109725111 Template switch process: F1: L GTTTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC 1 F3: 4 GTAAACATGATTTGGGGCTAGGAAGCCTGGAAATGAAATG R RF: CAGTTTGGGTAGGTTGTATGTTTTTAGAAATTTATCCATTTCCACCTGTCCATCTAGATTATCCAATTTGTTGACATATACTTATTCATAATAGTTTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCCTTGTTACATGTTACAATCATGTAAACATGATTTGGGGCTAGGAGCCTGGAAATGAAATG RR: GTCAAACCCATCCAACATACAAAAATCTTTAAATAGGTAAAGGTGGACAGGTAGATCTAATAGGTTAAACAACTGTATATGAATAAGTATTATCAAAGAATTTTAGAGTGTTTTAAAACTACGGAACAAAGACGGAACAATGTACAATGTTAGTACATTTGTACTAAACCCCGATCCTCGGACCTTTACTTTAC F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -39.5) TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC---------------AaCtgGTAAACATGATTTGGGGCTAGGaAGCCTGGAAATGAAATG TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCCTTGTTACATGTTACAATCATGTAAACATGATTTGGGGCTAGG-AGCCTGGAAATGAAATG Template switch alignment (log-probability: -27.5) TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC|AACTG|GTAAACATGATTTGGGGCTAGGaAGCCTGGAAATGAAATG TTCTTAAAATCTCACAAAATTTTGATGCCTTGTTTCTGCC|AACTG|GTAAACATGATTTGGGGCTAGG-AGCCTGGAAATGAAATG ========== Event 2673 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCgtttttttg-----ttttgttttgagacggagttttgctcttgttgcccaggctggagtgcagtggcacaatatccgctcac Chimp: AGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCGtttttttg-----ttttgttttgagacggagttttgctcttgttgcccaggctggagtgcagtggcacaatatccgctcac ↓ 1 4 3 2 Gorilla: AGTGCTTGAACATAGTAGATATGCACTGAATGTGTTTGGAGTTGTGCgtttttttgttttgttttgttttcagacggagttttgctcttgttgcccaggctggcgtgcagtggcacaatatccgctcac ↑ 1 4 3 2 Human: AGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCgtttttttg-----ttttgttttgagacggagttttgctcttgttgcccaggctggagtgcagtggcacaatatccgctcac Cluster: [ ] Orangutan: agtgcctgaacacagtagatatgcaatgaatgtgtttgaaGTTGTGGgtttttttg-----ttttgttttgagatggagtttcgctcttgttgcccaggctggagtgcagttgcacaatatcggctcac Human > Gorilla --------------- chr4:47228848-47228852 Template switch process: F1: L TTATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATA 1 F3: 4 TGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTG R RF: TTATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTGAGACGGAGTTTTGCTCTTGTTGCCCAGGCTGGAGTGCA RR: AATATTGTTTTCAAGTAATGTCACGAACTTGTATCATCTATGCGTCACTTACACAAACCTCAACACGCAAAAAAACAAAACAAAACTCTGCCTCAAAACGAGAACAACGGGTCCGACCTCACGT F2: 3 CACGT 2 Unidirectional alignment (log-probability: -26.1) TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATAtGCAcTGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGttttg TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTG----- Template switch alignment (log-probability: -16.4) TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATA|TGCAC|TGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTG TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATA|TGCAC|TGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTG Chimp > Gorilla --------------- chr4:47228848-47228852 Template switch process: F1: L TTATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATA 1 F3: 4 TGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTG R RF: TTATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTGAGACGGAGTTTTGCTCTTGTTGCCCAGGCTGGAGTGCA RR: AATATTGTTTTCAAGTAATGTCACGAACTTGTATCATCTATGCGTCACTTACACAAACCTCAACACGCAAAAAAACAAAACAAAACTCTGCCTCAAAACGAGAACAACGGGTCCGACCTCACGT F2: 3 CACGT 2 Unidirectional alignment (log-probability: -26.1) TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATAtGCAcTGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGttttg TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATACGCAGTGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTG----- Template switch alignment (log-probability: -16.4) TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATA|TGCAC|TGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTG TATAACAAAAGTTCATTACAGTGCTTGAACATAGTAGATA|TGCAC|TGAATGTGTTTGGAGTTGTGCGTTTTTTTGTTTTGTTTTG ========== Event 2674 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGTGCTTCATGGAGaaggtgactgtaagaggtctcc-----gtacaccctgggtagttgcagtttaag Chimp: GAGTGCTTCATGGAGAAGGTGACTGTAAGAGGTCTCC-----GTACACCCTGGGTAGTTGCAGTTTAAG ↓ 3 2 1 4 Gorilla: GAGTGCTTCATGGAGAAGGTGACTGTAAGAGGTAGTC----------ACCTGGGTAGTTGCAGTTTAAG Human: GAGTGCTTCATGGAGaaggtgactgtaagaggtctcc-----gtacaccctgggtagttgcagtttaag Cluster: [ ] Orangutan: GAGTGCTTCATGGAGAAGGTGACTGTAAGAGGTCTCCATACA-----Ccctgggtagttgcagtttacg Chimp > Gorilla --------------- chr4:154547202-154547206 Template switch process: F1: L TTTGTGATGAGTGCTTCATGGAGAAGGTGACTGTAAGAGGT 1 F3: 4 CCTGGGTAGTTGCAGTTTAAGTCTCTTTTCTGGCATCATT R RF: TTTGTGATGAGTGCTTCATGGAGAAGGTGACTGTAAGAGGTCTCCGTACACCCTGGGTAGTTGCAGTTTAAGTCTCTTTTCTGGCATCATT RR: AAACACTACTCACGAAGTACCTCTTCCACTGACATTCTCCAGAGGCATGTGGGACCCATCAACGTCAAATTCAGAGAAAAGACCGTAGTAA F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -28.3) TTGTGATGAGTGCTTCATGGAGAAGGTGACTGTAAGAGGT----------agtcaCCTGGGTAGTTGCAGTTTAAGTCTCTTTTCTGGCATCATT TTGTGATGAGTGCTTCATGGAGAAGGTGACTGTAAGAGGTCTCCGTACAC-----CCTGGGTAGTTGCAGTTTAAGTCTCTTTTCTGGCATCATT Template switch alignment (log-probability: -16.4) TTGTGATGAGTGCTTCATGGAGAAGGTGACTGTAAGAGGT|AGTCA|CCTGGGTAGTTGCAGTTTAAGTCTCTTTTCTGGCATCATT TTGTGATGAGTGCTTCATGGAGAAGGTGACTGTAAGAGGT|AGTCA|CCTGGGTAGTTGCAGTTTAAGTCTCTTTTCTGGCATCATT ========== Event 2675 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGTGTATTCATGTTATTCTC---------------------------AGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGCA ↓ 34 2 1 Chimp: AGGTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCAATACTGAGTATTGCCCATGTCATTGCATTTTTATTGCACTTCTTGCA ↑ 34 2 1 Gorilla: AGGTGTATTCATGTTATTCTC---------------------------AGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGCA Human: AGGTGTATTCATGTTATTCTC---------------------------AGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGCA Cluster: [ ] Orangutan: AGGTGTATTCATGTTATTCTC---------------------------AGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGCA Human > Chimp ------------- chr4:77918648-77918653 Template switch process: F1: L TTACGATGATTTGAAGCTGCAGGTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA 1 F3: 4 AGTATTGCCCATGTCATTGCATTTTTATTGCACTTCTTGC R RF: TTACGATGATTTGAAGCTGCAGGTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGC RR: AATGCTACTAAACTTCGACGTCCACATAAGTACAATAAGAGTCATAACGGGTCCAGTAACGTAAAAATAACGTGAAGAACG F2: 3 GTCATA 2 Unidirectional alignment (log-probability: -49.7) GTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCAatactgagtattgcccatgtcattgcaTTTTTATTGCACTTCTTGC GTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA---------------------------TTTTTATTGCACTTCTTGC Template switch alignment (log-probability: -22.4) GTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA|ATACTG|AGTATTGCCCAtGTCATTGCATTTTTATTGCACTTCTTGC GTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA|ATACTG|AGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGC Gorilla > Chimp --------------- chr4:77918648-77918653 Template switch process: F1: L TTACGATGATTTGAAGCTGCAGGTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA 1 F3: 4 AGTATTGCCCATGTCATTGCATTTTTATTGCACTTCTTGC R RF: TTACGATGATTTGAAGCTGCAGGTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGC RR: AATGCTACTAAACTTCGACGTCCACATAAGTACAATAAGAGTCATAACGGGTCCAGTAACGTAAAAATAACGTGAAGAACG F2: 3 GTCATA 2 Unidirectional alignment (log-probability: -49.7) GTGTATTCATGTTATTCTCAGTATTGCCCAGgtcattgcaatactgagtattgcccatGTCATTGCATTTTTATTGCACTTCTTGC GTGTATTCATGTTATTCTCAGTATTGCCCAG---------------------------GTCATTGCATTTTTATTGCACTTCTTGC Template switch alignment (log-probability: -22.5) GTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA|ATACTG|AGTATTGCCCAtGTCATTGCATTTTTATTGCACTTCTTGC GTGTATTCATGTTATTCTCAGTATTGCCCAGGTCATTGCA|ATACTG|AGTATTGCCCAGGTCATTGCATTTTTATTGCACTTCTTGC ========== Event 2676 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCACAAAGAGAACTAGAGCAAGGTAGTTTCAAAGCTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGG Chimp: CCACAAGGAGAACTAGAGCAA----------CCGCTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGG Gorilla: CCACAAAGAGAACTAGAGCAA----------CCACTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGG ↓ 4 1 3 2 Human: CCACAAAGAGAACTAGAGCAAGGTAGTTTCAAAGCTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGG Cluster: [ ] Orangutan: CCACAAGGAGAACTAGAGCAA----------CCGCTCAGGTAGGCTTTGAAAAGCTGTTGGTGGTGAGGGGG Gorilla > Human --------------- chr4:137320501-137320508 Template switch process: F1: L AAGTGGCAACAAAAAGAGGACCACAAAGAGAACTAGAGCA-------AGGTAG 1 F3: 4 CTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGGTA R RF: AAGTGGCAACAAAAAGAGGACCACAAAGAGAACTAGAGCAACCACTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGGTA RR: TTCACCGTTGTTTTTCTCCTGGTGTTTCTCTTGATCTCGTTGGTGAGTCCATCCGAAACTTTTCGACGACCACCACTCCCCCAT F2: 3 GAAACTTT 2 Unidirectional alignment (log-probability: -39.5) CAACAAAAAGAGGACCACAAAGAGAACTAGAGCAAggtagtttcaaagC---TCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGGTA CAACAAAAAGAGGACCACAAAGAGAACTAGAGCAA-------------CCACTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGGTA Template switch alignment (log-probability: -27) CAACAAAAAGAGGACCACAAAGAGAACTAGAGCA-------AGGTAG|TTTCAAAG|CTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGGTA CAACAAAAAGAGGACCACAAAGAGAACTAGAGCAACCACTCAGGTAG|TTTCAAAG|CTCAGGTAGGCTTTGAAAAGCTGCTGGTGGTGAGGGGGTA ========== Event 2677 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTTAAGAGTTTGGATCAATTTGTAGCACTGGATGTGCTACAAAATCCGGGAGGTAGTGGAT ↑ 1 3 4 2 Chimp: ATTTAAGAGTTTGGATCAATTCAAATC-----CAGTGCTACAAAATCCGGGAGGTAATGGAT Gorilla: ATTTAAGAGTTTGGATCAATTCAAATC-----CAGTGCTACAAAATCCGGGAGGTAATGGAT ↓ 1 3 4 2 Human: ATTTAAGAGTTTGGATCAATTTGTAGCACTGGATGTGCTACAAAATCCGGGAGGTAGTGGAT Cluster: [ ] Orangutan: ATTTAAGAGTTTGGATCAATTCAAATC-----CAGTGCTACAAAATCCGGGAGGTAATGGAT Chimp > Human ------------- chr4:136328143-136328155 Template switch process: F1: L TTTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT 1 F3: 4 GTGCTACAAAATCCGGGAGGTAGTGGATGCTTTCAACATA R RF: TTTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATTCAAATCCAGTGCTACAAAATCCGGGAGGTAATGGATGCTTTCAACATA RR: AAAAGAAAACCTTCTAAACTTAAATTCTCAAACCTAGTTAAGTTTAGGTCACGATGTTTTAGGCCCTCCATTACCTACGAAAGTTGTAT F2: 3 TAGGTCACGATGT 2 Unidirectional alignment (log-probability: -46.2) TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT--------tgtagcactggatGTGCTACAAAATCCGGGAGGTAgTGGATGCTTTCAACATA TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATTCAAATCCA-------------GTGCTACAAAATCCGGGAGGTAATGGATGCTTTCAACATA Template switch alignment (log-probability: -22.9) TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT|TGTAGCACTGGAT|GTGCTACAAAATCCGGGAGGTAgTGGATGCTTTCAACATA TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT|TGTAGCACTGGAT|GTGCTACAAAATCCGGGAGGTAATGGATGCTTTCAACATA Gorilla > Human --------------- chr4:136328143-136328155 Template switch process: F1: L TTTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT 1 F3: 4 GTGCTACAAAATCCGGGAGGTAGTGGATGCTTTCAACATA R RF: TTTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATTCAAATCCAGTGCTACAAAATCCGGGAGGTAATGGATGCTTTCAACATA RR: AAAAGAAAACCTTCTAAACTTAAATTCTCAAACCTAGTTAAGTTTAGGTCACGATGTTTTAGGCCCTCCATTACCTACGAAAGTTGTAT F2: 3 TAGGTCACGATGT 2 Unidirectional alignment (log-probability: -45.2) TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT--------tgtagcactggatGTGCTACAAAATCCGGGAGGTAgTGGATGCTTTCAACATA TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATTCAAATCCA-------------GTGCTACAAAATCCGGGAGGTAATGGATGCTTTCAACATA Template switch alignment (log-probability: -22.9) TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT|TGTAGCACTGGAT|GTGCTACAAAATCCGGGAGGTAgTGGATGCTTTCAACATA TTTCTTTTGGAAGATTTGAATTTAAGAGTTTGGATCAATT|TGTAGCACTGGAT|GTGCTACAAAATCCGGGAGGTAATGGATGCTTTCAACATA ========== Event 2678 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTCAATGAAGGGATGAAGTTT------------------------------AATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATCGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGACTTAACTTATATTAAGCTTCCTGGTCTGTGGACACAC ↓ 4 1 3 2 Chimp: TTCAATGAAGGGATGAAGTTT-------------------AATAGCTTATTAATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATTGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGACTTAACTTATATTAAGCTTCCTGGTCTGTGGACACAC Gorilla: TTCAATGAAGGGATGAAGTTT--------AATAGCTTATT-----------AATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATTGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGACTTAACTTATATTAAGCTTCCTGGTCTGTGGACACAC ↑ 4 1 3 2 Human: TTCAATGAAGGGATGAAGTTT------------------------------AATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATCGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGACTTAACTTATATTAAGCTTCCTGGTCTGTGGACACAC Cluster: [ ] Orangutan: TTCAACGAAGGGATGAAGTTTAATAGCTT----------------------AATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATTGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGGCTTAACTTATATTAAGCTTCCTGGTCTGTGGACACAC Human > Chimp ------------- chr4:76198953-76198957 Template switch process: F1: L AAAATACAAGTG-AAATGATTTCAATGAAGGGATGAAGTTTAATA 1 F3: 4 TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTTTA R RF: AAAATACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATCGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGACTTAACTTATATTAAGC RR: TTTTATGTTCACTTTTACTAAAGTTACTTCCCTACTTCAAATTATGTCACGTATGAAATATAAAAGTAAAATTGTGAAAATACTAGCAGTGAGGTAGTGATGTCACTGTATTATAAAACAATTTATACCAACCTGAATTGAATATAATTCG F2: 3 ATTCG 2 Unidirectional alignment (log-probability: -37) TACAAGTG-AAATGATTTCAATGAAGGGATGAAGTTTAATAgcttattaataCAGTGCATACTTTATATTTTCATTTTAACACTTT TACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATA-----------CAGTGCATACTTTATATTTTCATTTTAACACTTT Template switch alignment (log-probability: -26.3) TACAAGTG-AAATGATTTCAATGAAGGGATGAAGTTTAATA|GCTTA|TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTT TACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATA|GCTTA|TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTT Human > Gorilla --------------- chr4:74358191-74358195 Template switch process: F1: L AAAATACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATA 1 F3: 4 TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTTTA R RF: AAAATACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATACAGTGCATACTTTATATTTTCATTTTAACACTTTTATGATCGTCACTCCATCACTACAGTGACATAATATTTTGTTAAATATGGTTGGACTTAACTTATATTAAGC RR: TTTTATGTTCACTTTTACTAAAGTTACTTCCCTACTTCAAATTATGTCACGTATGAAATATAAAAGTAAAATTGTGAAAATACTAGCAGTGAGGTAGTGATGTCACTGTATTATAAAACAATTTATACCAACCTGAATTGAATATAATTCG F2: 3 ATTCG 2 Unidirectional alignment (log-probability: -26.7) ACAAGTGAAAATGATTTCAATGAAGGGATGAAGTttaatagcttaTTAATACAGTGCATACTTTATATTTTCATTTTAACACTTT ACAAGTGAAAATGATTTCAATGAAGGGATGAAGT-----------TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTT Template switch alignment (log-probability: -16.5) ACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATA|GCTTA|TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTT ACAAGTGAAAATGATTTCAATGAAGGGATGAAGTTTAATA|GCTTA|TTAATACAGTGCATACTTTATATTTTCATTTTAACACTTT ========== Event 2679 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: taacttcaagcttttaagcct---------actgaactgtcaggatgatggtacttttaatggtgatgggaaaatgggagaaATTGTATGGATGTACAGTAGCAGATTATTCACATTTGTGTTACAGGAAATCACAGTCTGAATAGAAAATGGTCAGA Chimp: TGACTTCAAGCTTTTAAGCCTGAAGTCAGGCTTAAACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAATGGGAGAAATTGTATGGATGTACAGTAGCAGATTATTCACATTTGTGTTACAGGAAATCACAGTCTGAATAGAAAATGGTCAGA ↓ 1 4 3 2 Gorilla: TGACTTCAAGCTTTTAAGCCT---------ACTGAACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAATGGGAGAAATTGTATGGATGTACAGTAGCAGATTATTCACATTTGTGTTACAGGAAATCACAGTCTGAATAGAAAATGGTCAGA Human: taacttcaagcttttaagcct---------actgaactgtcaggatgatggtacttttaatggtgatgggaaaatgggagaaATTGTATGGATGTACAGTAGCAGATTATTCACATTTGTGTTACAGGAAATCACAGTCTGAATAGAAAATGGTCAGA Cluster: [ ] Orangutan: tgacttcaagcttttaagcct---------actgaactgtcaggatgatggtacttttaatggtgatgggaaaatgggagaaATTGTATGGATGTACAGTAGCAGATTATTCACATTTGTGTTACAGGAAATCACAATCTCAATAGAAAATGGTCAGA Chimp > Gorilla --------------- chr4:127687775-127687778 Template switch process: F1: L GAGGTATTAAGACAGATGATTGACTTCAAGCTTTTAAGCCT 1 F3: 4 AACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAA R RF: GAGGTATTAAGACAGATGATTGACTTCAAGCTTTTAAGCCTGAAGTCAGGCTTAAACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAATGGGAGAAATTGTATGGATGTACAGTAGCAGATTATTCACATTTGTGTTACAGGAAATCACAGT RR: CTCCATAATTCTGTCTACTAACTGAAGTTCGAAAATTCGGACTTCAGTCCGAATTTGACAGTCCTACTACCATGAAAATTACCACTACCCTTTTACCCTCTTTAACATACCTACATGTCATCGTCTAATAAGTGTAAACACAATGTCCTTTAGTGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -25.6) AGGTATTAAGACAGATGATTGACTTCAAGCTTTTAAGCC------------TActgAACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAA AGGTATTAAGACAGATGATTGACTTCAAGCTTTTAAGCCTGAAGTCAGGCTTA---AACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAA Template switch alignment (log-probability: -16.2) AGGTATTAAGACAGATGATTGACTTCAAGCTTTTAAGCCT|ACTG|AACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAA AGGTATTAAGACAGATGATTGACTTCAAGCTTTTAAGCCT|ACTG|AACTGTCAGGATGATGGTACTTTTAATGGTGATGGGAAAA ========== Event 2680 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AAAACAGAACGCAGTGAAGATTTTAGATTGGCTTTTGGAGGCTCAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGAATCGAAAATGTATAggccgggtgcggtggc ↑ 3 2 1 4 Chimp: AAAAC--AACGCAGTGAAGATTTTAGATTGGCTTTTGGAGGCTCAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGAC------CGGTATAggccgggtgcggtggc ↓ 3 2 1 4 Gorilla: AAAACAGAAGGCAGTGAAGATTTTAGATTGGCTTTTGGAGGCTTAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGCTCTAAAGAATCGAAAATGTATAggccgggtgcggtggc Human: AAAACAGAACGCAGTGAAGATTTTAGATTGGCTTTTGGAGGCTCAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGAATCGAAAATGTATAggccgggtgcggtggc Cluster: [ ] Orangutan: AAAACAGAAGGCAGTGGAGATTTTAGATCGGCTTTTGGAGGCTCAACTTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGCTCTAAAGAACAGAAAATGTATAggccgggtgcggtggc Chimp > Human ------------- chr4:55355163-55355171 Template switch process: F1: L GGTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGA 1 F3: 4 GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC R RF: ATTTTAGATTGGCTTTTGGAGGCTCAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGACCGGTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC RR: TAAAATCTAACCGAAAACCTCCGAGTTCGACCCAGAAATTTTTGTTTGTTCTCGATACTGAACAAGATTTCTGGCCATATCCGGCCCACGCCACCGAGTGCGGACATTAGGGTCG F2: 3 TAAAAGCTA 2 Unidirectional alignment (log-probability: -34.2) GTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGAatcgaaaat---GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC GTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGA---------CCGGTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC Template switch alignment (log-probability: -22.4) GTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGA|ATCgAAAAT|GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC GTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGA|ATCTAAAAT|GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC Chimp > Gorilla --------------- chr4:129617920-129617928 Template switch process: F1: L CTTAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGCTCTAAAGA 1 F3: 4 GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC R RF: ATTTTAGATTGGCTTTTGGAGGCTCAAGCTGGGTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGACCGGTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC RR: TAAAATCTAACCGAAAACCTCCGAGTTCGACCCAGAAATTTTTGTTTGTTCTCGATACTGAACAAGATTTCTGGCCATATCCGGCCCACGCCACCGAGTGCGGACATTAGGGTCG F2: 3 TAAAAGCTA 2 Unidirectional alignment (log-probability: -44.9) GTCTTTAAAAACAAACAAGAGCTATGACTTGcTCTAAAGAatcgaaaat---GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC GTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGA---------CCGGTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC Template switch alignment (log-probability: -33.6) GTCTTTAAAAACAAACAAGAGCTATGACTTGcTCTAAAGA|ATCgAAAAT|GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC GTCTTTAAAAACAAACAAGAGCTATGACTTGTTCTAAAGA|ATCTAAAAT|GTATAGGCCGGGTGCGGTGGCTCACGCCTGTAATCCCAGC ========== Event 2681 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GGAGATGGGGCAAAAGGAGTGGCTTTAAAAAGCTTCTGggctgggcgcggtgg ↑ 1 3 4 2 Chimp: GGAGATGGGGCAAAAGGAGTG---T--TAAAGCTTCTGggctgggcgcggtgg Gorilla: GGAGATGGGGCAAAACGAATGGCTTTAAAAAGCTGCTGggctgggcgcggtgg Human: GGAGATGGGGCAAAAGGAGTGGCTTTAAAAAGCTTCTGggctgggcgcggtgg Cluster: [ ] Orangutan: GGAGATGGGGCAAAAGGAGTGGCTTTAAAAAGCTTCTGggctgggcgcggtgg Chimp > Human ------------- chr4:5781538-5781544 Template switch process: F1: L TTCTGGGTGTAAAAGTGATTGGAGATGGGGCAAAAGGAGTG 1 F3: 4 AAAGCTTCTGGGCTGGGCGCGGTGGCCCACACCTGTAATC R RF: TTCTGGGTGTAAAAGTGATTGGAGATGGGGCAAAAGGAGTGTTAAAGCTTCTGGGCTGGGCGCGGTGGCCCACACCTGTAATC RR: AAGACCCACATTTTCACTAACCTCTACCCCGTTTTCCTCACAATTTCGAAGACCCGACCCGCGCCACCGGGTGTGGACATTAG F2: 3 AATTTCG 2 Unidirectional alignment (log-probability: -28.3) TCTGGGTGTAAAAGTGATTGGAGATGGGGCAAAAGGAGTGgctTTaaAAAGCTTCTGGGCTGGGCGCGGTGGCCCACACCTGTAATC TCTGGGTGTAAAAGTGATTGGAGATGGGGCAAAAGGAGTG---TT--AAAGCTTCTGGGCTGGGCGCGGTGGCCCACACCTGTAATC Template switch alignment (log-probability: -16.2) TCTGGGTGTAAAAGTGATTGGAGATGGGGCAAAAGGAGTG|GCTTTAA|AAAGCTTCTGGGCTGGGCGCGGTGGCCCACACCTGTAATC TCTGGGTGTAAAAGTGATTGGAGATGGGGCAAAAGGAGTG|GCTTTAA|AAAGCTTCTGGGCTGGGCGCGGTGGCCCACACCTGTAATC ========== Event 2682 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGAGGTGACGAGTTACCTGTAAC----------TGGAGAGGACTGGAAAGAACAATGAGTACtgtagtggg Chimp: GTGAGGTGACGAGTTACCTGTAAC----------TGGAGAGGACTGGAAAGAACAATGAGTACtgtagtggg ↓ 1 3 42 Gorilla: GTGAGGTGACGAGTTACCTGTTCT--------------------TTCCAGGAACAATGAGTACtgtagtggg ↑ 1 3 42 Human: GTGAGGTGACGAGTTACCTGTAAC----------TGGAGAGGACTGGAAAGAACAATGAGTACtgtagtggg Cluster: [ ] Orangutan: gggaggtgacgagttacctgtaactgaagaggac----------tggaaagaacaatgagtactgtagtggg Human > Gorilla --------------- chr4:5839329-5839337 Template switch process: F1: L AGTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT 1 F3: 4 GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA R RF: AGTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGTAACTGGAGAGGACTGGAAAGAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA RR: TCATACCTCCCACGACGGGACACTCCACTGCTCAATGGACATTGACCTCTCCTGACCTTTCTTGTTACTCATGACATCACCCAAGTCTCTACTTGGGGTT F2: 3 GACCTTTCT 2 Unidirectional alignment (log-probability: -34.5) GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT-------------------tctttccagGAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGTAACTGGAGAGGACTGGAAA---------GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA Template switch alignment (log-probability: -16.9) GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT|TCTTTCCAG|GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT|TCTTTCCAG|GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA Chimp > Gorilla --------------- chr4:5839329-5839337 Template switch process: F1: L AGTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT 1 F3: 4 GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA R RF: AGTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGTAACTGGAGAGGACTGGAAAGAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA RR: TCATACCTCCCACGACGGGACACTCCACTGCTCAATGGACATTGACCTCTCCTGACCTTTCTTGTTACTCATGACATCACCCAAGTCTCTACTTGGGGTT F2: 3 GACCTTTCT 2 Unidirectional alignment (log-probability: -34.5) GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT-------------------tctttccagGAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGTAACTGGAGAGGACTGGAAA---------GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA Template switch alignment (log-probability: -16.9) GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT|TCTTTCCAG|GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA GTATGGAGGGTGCTGCCCTGTGAGGTGACGAGTTACCTGT|TCTTTCCAG|GAACAATGAGTACTGTAGTGGGTTCAGAGATGAACCCCAA ========== Event 2683 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTCTGGATTACAATGAACATA--TATTAGCTAGAATAGTAATTCTAGCTAATACATATGTCCCCGTGGCCAT Chimp: CTCTGGATTACAATGAACATA--TATTAGCTAGAATAGTAATTCTAGCTAATACATATGTCCCCGTGGCCAT ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: CTCTGGATTACAATGAACATATATATTAGCTAGAATTACTATTCTAACTAATACATATGCCCCTGTGGCCAT ↓ 1 3 4 2 ↑ 1 3 4 2 Human: CTCTGGATTACAATGAACATA--TATTAGCTAGAATAGTAATTCTAGCTAATACATATGTCCCCGTGGCCAT Cluster: [] Orangutan: CTCTGGATTACAATGAACATA--TATTAGCTAGAATAGTAATTCTAGCTAATACATATGTCCCTGTGGCCGT Gorilla > Human --------------- chr4:133770031-133770051 Template switch process: F1: L ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATAT 1 F3: 4 CTAATACATATGTCCC R RF: ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATATATTAGCTAGAATTACTATTCTAACTAATACATATGCCCC RR: TACAAATACAGTGACTGTGTGAGACCTAATGTTACTTGTATATATAATCGATCTTAATGATAAGATTGATTATGTATACGGGG F2: 3 GATCTTAATGATAAGATCGAT 2 Unidirectional alignment (log-probability: -44.1) TTATGTCACTGACACACTCTGGATTACAATGAACATATA--TTAGCTAGAATagtaATTCTAgCTAATACATATGtCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATATATTAGCTAGAATTACTATTCTAACTAATACATATGCCCC Template switch alignment (log-probability: -28.9) TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|TAGcTAGAATAGTAATTCTAG|CTAATACATATGtCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|TAGTTAGAATAGTAATTCTAG|CTAATACATATGCCCC Human > Gorilla --------------- chr4:72335081-72335096 Template switch process: F1: L ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATAT 1 F3: 4 ATTCTAACTAATACATATGCCCC R RF: ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATATTAGCTAGAATAGTAATTCTAGCTAATACATATGTCCC RR: TACAAATACAGTGACTGTGTGAGACCTAATGTTACTTGTATATAATCGATCTTATCATTAAGATCGATTATGTATACAGGG F2: 3 TCATTAAGATCGATTA 2 Unidirectional alignment (log-probability: -46.9) TTATGTCACTGACACACTCTGGATTACAATGAACATATATatTAGCTAGAATtactATTCTAaCTAATACATATGcCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATAT--TAGCTAGAATAGTAATTCTAGCTAATACATATGTCCC Template switch alignment (log-probability: -28.4) TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|ATTAGCTAGAATTACT|ATTCTAaCTAATACATATGcCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|ATTAGCTAGAATTACT|ATTCTAGCTAATACATATGTCCC Gorilla > Chimp --------------- chr4:74141367-74141387 Template switch process: F1: L ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATAT 1 F3: 4 CTAATACATATGTCCC R RF: ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATATATTAGCTAGAATTACTATTCTAACTAATACATATGCCCC RR: TACAAATACAGTGACTGTGTGAGACCTAATGTTACTTGTATATATAATCGATCTTAATGATAAGATTGATTATGTATACGGGG F2: 3 GATCTTAATGATAAGATCGAT 2 Unidirectional alignment (log-probability: -44.1) TTATGTCACTGACACACTCTGGATTACAATGAACATATA--TTAGCTAGAATagtaATTCTAgCTAATACATATGtCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATATATTAGCTAGAATTACTATTCTAACTAATACATATGCCCC Template switch alignment (log-probability: -28.9) TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|TAGcTAGAATAGTAATTCTAG|CTAATACATATGtCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|TAGTTAGAATAGTAATTCTAG|CTAATACATATGCCCC Chimp > Gorilla --------------- chr4:72335081-72335096 Template switch process: F1: L ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATAT 1 F3: 4 ATTCTAACTAATACATATGCCCC R RF: ATGTTTATGTCACTGACACACTCTGGATTACAATGAACATATATTAGCTAGAATAGTAATTCTAGCTAATACATATGTCCC RR: TACAAATACAGTGACTGTGTGAGACCTAATGTTACTTGTATATAATCGATCTTATCATTAAGATCGATTATGTATACAGGG F2: 3 TCATTAAGATCGATTA 2 Unidirectional alignment (log-probability: -46.9) TTATGTCACTGACACACTCTGGATTACAATGAACATATATatTAGCTAGAATtactATTCTAaCTAATACATATGcCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATAT--TAGCTAGAATAGTAATTCTAGCTAATACATATGTCCC Template switch alignment (log-probability: -28.4) TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|ATTAGCTAGAATTACT|ATTCTAaCTAATACATATGcCCC TTATGTCACTGACACACTCTGGATTACAATGAACATATAT|ATTAGCTAGAATTACT|ATTCTAGCTAATACATATGTCCC ========== Event 2684 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TTCCCATACTCCAATTTCTTTTCAGCAATCAATTGCTGAAATTTCTTTCACAAAATGATAAT ↑ 3 2 1 4 Chimp: TTCCCATACTCCAATTTCTTTTCAGCAATCAATT--AAAACTTTCTTTCACAAAATGATAAT Gorilla: -------------------------------------------------------------- Human: TTCCCATACTCCAATTTCTTTTCAGCAATCAATTGCTGAAATTTCTTTCACAAAATGATAAT Cluster: [ ] Orangutan: -------------------------------------------------------------- Chimp > Human ------------- chr4:57892440-57892446 Template switch process: F1: L ATTAGTTTTCCCATACTCCAATTTCTTTTCAGCAATCAATT 1 F3: 4 TTTCTTTCACAAAATGATAATAATGTCCTTTTTTCTGTCA R RF: ATTAGTTTTCCCATACTCCAATTTCTTTTCAGCAATCAATTAAAACTTTCTTTCACAAAATGATAATAATGTCCTTTTTTCTGTCA RR: TAATCAAAAGGGTATGAGGTTAAAGAAAAGTCGTTAGTTAATTTTGAAAGAAAGTGTTTTACTATTATTACAGGAAAAAAGACAGT F2: 3 AAAGTCG 2 Unidirectional alignment (log-probability: -27) TTAGTTTTCCCATACTCCAATTTCTTTTCAGCAATCAATTgctgAAA--TTTCTTTCACAAAATGATAATAATGTCCTTTTTTCTGTCA TTAGTTTTCCCATACTCCAATTTCTTTTCAGCAATCAATT----AAAACTTTCTTTCACAAAATGATAATAATGTCCTTTTTTCTGTCA Template switch alignment (log-probability: -16.2) TTAGTTTTCCCATACTCCAATTTCTTTTCAGCAATCAATT|GCTGAAA|TTTCTTTCACAAAATGATAATAATGTCCTTTTTTCTGTCA TTAGTTTTCCCATACTCCAATTTCTTTTCAGCAATCAATT|GCTGAAA|TTTCTTTCACAAAATGATAATAATGTCCTTTTTTCTGTCA ========== Event 2685 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCACCTCCCTATTCCTGGTCCTAGGGCCCGTGTCCAGGAGC-----ATAgctctgtaggaagactgtgg Chimp: GCCACCTCCCTATTCCTGGTCCTAGGGCCCGTGTCCAGGAGC-----ATAGCTCTGTAGGAAGACTGTGG ↓ 3 2 1 4 Gorilla: GCCACCTCCCTATTCCTGGTCCTAGGGCCTGTGTCCAGGAGCCCTAGGAAGCTCTGTAGGAAGACTGTGG Human: GCCACCTCCCTATTCCTGGTCCTAGGGCCCGTGTCCAGGAGC-----ATAgctctgtaggaagactgtgg Cluster: [ ] Orangutan: GCCACCTCCCTATTCCTGGTCCTAGGGCccgtgcccaggagc-----atagctctgtaggaagactgtgg Chimp > Gorilla --------------- chr4:131647051-131647057 Template switch process: F1: L CCACCTCCCTATTCCTGGTCCTAGGGCCTGTGTCCAGGAGC 1 F3: 4 AGCTCTGTAGGAAGACTGTGGGATTAGCTCACACTTCCTG R RF: CCACCTCCCTATTCCTGGTCCTAGGGCCCGTGTCCAGGAGCATAGCTCTGTAGGAAGACTGTGGGATTAGCTCACACTTCCTG RR: GGTGGAGGGATAAGGACCAGGATCCCGGGCACAGGTCCTCGTATCGAGACATCCTTCTGACACCCTAATCGAGTGTGAAGGAC F2: 3 AGGATCC 2 Unidirectional alignment (log-probability: -34.7) CACCTCCCTATTCCTGGTCCTAGGGCCtGTGTCCAGGAGCcctaggaAGCTCTGTAGGAAGACTGTGGGATTAGCTCACACTTCCTG CACCTCCCTATTCCTGGTCCTAGGGCCCGTGTCCAGGAGC-----ATAGCTCTGTAGGAAGACTGTGGGATTAGCTCACACTTCCTG Template switch alignment (log-probability: -22.1) CACCTCCCTATTCCTGGTCCTAGGGCCtGTGTCCAGGAGC|CCTAGGA|AGCTCTGTAGGAAGACTGTGGGATTAGCTCACACTTCCTG CACCTCCCTATTCCTGGTCCTAGGGCCCGTGTCCAGGAGC|CCTAGGA|AGCTCTGTAGGAAGACTGTGGGATTAGCTCACACTTCCTG ========== Event 2686 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: TTCTGGCCTGCCATATTTGCAAAGATGTTGG-------CCAACATCAGTATCAAGAGCCT ↓ 3 1 2 4 ↑ 1 3 2 4 Chimp: TTCTGGCCTGCCATATTTGCAAACATGCCAACATCTTTGCAACATCAGTATCAAGAGCCT Gorilla: TTCTGGCCTGCCATATTTGCAAAGACGTTGG-------CCAACATAAGTATCAAGAGCCT Human: TTCTGGCCTGCCATATTTGCAAAGATGTTGG-------CCAACATCAGTATCAAGAGCCT Cluster: [ ] Orangutan: Chimp > Human ------------- chr4:60038391-60038399 Template switch process: F1: L ATATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAA 1 F3: 4 CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT R RF: ATATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAACATGCCAACATCTTTGCAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT RR: TATAGAAGTAATTTCGGAAAGACCGGACGGTATAAACGTTTGTACGGTTGTAGAAACGTTGTAGTCATAGTTCTCGGAGTAGACGTTACATCGTCGA F2: 3 CGGTTGTAG 2 Unidirectional alignment (log-probability: -30.5) TATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAAgATG---------TTGgcCAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT TATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAACATGCCAACATCTTTG--CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT Template switch alignment (log-probability: -16.4) TATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAA|GATGTTGGC|CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT TATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAA|GATGTTGGC|CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT Human > Chimp ------------- chr4:124051451-124051462 Template switch process: F1: L ATATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAACATG 1 F3: 4 CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT R RF: ATATCTTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAAGATGTTGGCCAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT RR: TATAGAAGTAATTTCGGAAAGACCGGACGGTATAAACGTTTCTACAACCGGTTGTAGTCATAGTTCTCGGAGTAGACGTTACATCGTCGA F2: 3 GTTTCTACAACC 2 Unidirectional alignment (log-probability: -40.2) TTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAAcATGccaacatctTTG--CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT TTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAAGATG---------TTGGCCAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT Template switch alignment (log-probability: -22.8) TTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAAcATG|CCAACATCTTTG|CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT TTCATTAAAGCCTTTCTGGCCTGCCATATTTGCAAAGATG|CCAACATCTTTG|CAACATCAGTATCAAGAGCCTCATCTGCAATGTAGCAGCT ========== Event 2687 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGCAACTTGACTCTCTATTGCCC---CATGTA--------ATGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACTACTCTCTGCAACAGGTTCCCCAATCCA Chimp: ATGCAACTTGACTCTCTGTTGCCC---CATGTA--------ATGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACTACCCTCTGCAACAGGTTCCCCAATCCA Gorilla: ATGCAACTTGACTCTCTATTGACTCTCTATTTATGGACCATTAGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACTACTCTCTGCAATAGGTTCCCCAATCCA ↑ 3 4 2 1 Human: ATGCAACTTGACTCTCTATTGCCC---CATGTA--------ATGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACTACTCTCTGCAACAGGTTCCCCAATCCA Cluster: [ ] Orangutan: TTGCAACTTGACTCTCTATTGCCC---CATGTA--------ATGGTTCATAAATTTGTACCTGTTTATTTCCTGTCAAAAACTACTCTCTACAACAGGTTCCCCAATCCA Human > Gorilla --------------- chr4:134534582-134534596 Template switch process: F1: L TGGCTGGCTATACATTATGGATGCAACTTGACTCTCTATTG---------------------------------------------------ACTCTCT 1 F3: 4 GGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACT R RF: TGGCTGGCTATACATTATGGATGCAACTTGACTCTCTATTGCCCCATGTAATGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACTACTCTCT RR: ACCGACCGATATGTAATACCTACGTTGAACTGAGAGATAACGGGGTACATTACCAGGTATTTAAACACGGACACGTAAAGGACAGTTTTTGATGAGAGA F2: 3 ATTACCAGGTATTTA 2 Unidirectional alignment (log-probability: -52.8) TATACATTATGGATGCAACTTGACTCTCTATTGactctctatttatggaccatta-----------GGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACT TATACATTATGGATGCAACTTGACTCTCTATTG----------------------CCCCATGTAATGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACT Template switch alignment (log-probability: -30.2) TATACATTATGGATGCAACTTGACTCTCTATTG---------------------------------------------------ACTCTCT|ATTTATGGACCATTA|GGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACT TATACATTATGGATGCAACTTGACTCTCTATTGCCCCATGTAATGGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACTACTCTCT|ATTTATGGACCATTA|GGTCCATAAATTTGTGCCTGTGCATTTCCTGTCAAAAACT ========== Event 2688 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTCTTCACCATGTGGGTGTGCATGC--ACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTGAGTGTATATGCACAAATatgtatccttctgattc ↓ 1 4 3 2 Chimp: CTTCTTCACCATGTGGGTGTGTGTGCACACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTGAGTGTATATGCACAAATatttatccttctgattc Gorilla: CTTCTTCACCATGTGGGTGTGTGTGC--AGGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTGAGTGTATATGCACAAATatttatccttctgattc Human: CTTCTTCACCATGTGGGTGTGCATGC--ACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTGAGTGTATATGCACAAATatgtatccttctgattc Cluster: [ ] Orangutan: CTTCTTCACCATGCGGGTGTGTGTGC--ACGCACCTGAGTACATGTGTATGTTTTTGTTTCCATGTGAGTGTATATGCACAAATATTTATCCTTCTGATTC Human > Chimp ------------- chr4:70066093-70066098 Template switch process: F1: L ACAAAGTGGATGTTATTTTACTTCTTCACCATGTGGGTGTG 1 F3: 4 CACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTGA R RF: ACAAAGTGGATGTTATTTTACTTCTTCACCATGTGGGTGTGCATGCACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTGAGTGTATATGCACA RR: TGTTTCACCTACAATAAAATGAAGAAGTGGTACACCCACACGTACGTGCGTGGACTCATGTACACGTACAAAAACAAAGGTACACTCACATATACGTGT F2: 3 ACGTGT 2 Unidirectional alignment (log-probability: -25.8) CAAAGTGGATGTTATTTTACTTCTTCACCATGTGGGTGTGtgTGcaCACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTG CAAAGTGGATGTTATTTTACTTCTTCACCATGTGGGTGTGCATG--CACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTG Template switch alignment (log-probability: -16) CAAAGTGGATGTTATTTTACTTCTTCACCATGTGGGTGTG|TGTGCA|CACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTG CAAAGTGGATGTTATTTTACTTCTTCACCATGTGGGTGTG|TGTGCA|CACGCACCTGAGTACATGTGCATGTTTTTGTTTCCATGTG ========== Event 2689 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: ccaaataagtatgtacaacaaatcta-caagagtcacaaattcaaataaccattt Chimp: CCAAATAAGTATGTACAACAAATCTA-CAAGAGTCACAAATTCAAATAACCATTT ↓ 1 3 4 2 Gorilla: CCAAATAAGTATGTACAACAAGACTCTTGTAAGTCACAAATTCAAATAACCAT-T Human: ccaaataagtatgtacaacaaatcta-caagagtcacaaattcaaataaccattt Cluster: [ ] Orangutan: ccaaataagtatgtacaacaaatcta-tgagagtcacaaattcaaataaccattt Chimp > Gorilla --------------- chr4:135027620-135027629 Template switch process: F1: L GGAAAATGACAAATCAATAACCAAATAAGTATGTACAACAA 1 F3: 4 AGTCACAAATTCAAATAACCA-TTTTTACAGATTTTTTTT R RF: GGAAAATGACAAATCAATAACCAAATAAGTATGTACAACAAATCTACAAGAGTCACAAATTCAAATAACCATTTTTTACAGATTTTTTTT RR: CCTTTTACTGTTTAGTTATTGGTTTATTCATACATGTTGTTTAGATGTTCTCAGTGTTTAAGTTTATTGGTAAAAAATGTCTAAAAAAAA F2: 3 ATGTTCTCAG 2 Unidirectional alignment (log-probability: -43.8) GAAAATGACAAATCAATAACCAAATAAGTATGTACAA--------CAAGactcttgtaAGTCACAAATTCAAATAACCA-TTTTTACAGATTTTTTTT GAAAATGACAAATCAATAACCAAATAAGTATGTACAACAAATCTACAAG---------AGTCACAAATTCAAATAACCATTTTTTACAGATTTTTTTT Template switch alignment (log-probability: -26.8) GAAAATGACAAATCAATAACCAAATAAGTATGTACAACAA|GACTCTTGTA|AGTCACAAATTCAAATAACCA-TTTTTACAGATTTTTTTT GAAAATGACAAATCAATAACCAAATAAGTATGTACAACAA|GACTCTTGTA|AGTCACAAATTCAAATAACCATTTTTTACAGATTTTTTTT ========== Event 2690 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGATACGTAAGAAGAGAGGCC--CAAGAAAAAACTTTGGCAATTCATTGTGCAGACCAACAA Chimp: CTGATATGTAAGAAGAGAGGCTTTGCCAAAGAAACTTTGGCAATTCATTGTGCAGACCAACAA ↑ 1 4 3 2 Gorilla: CTGATATGTAAGAAGAGAGGCC--CCAGAAAAAACTTTGGCAATTCATTGTGCAGACCAACAA Human: CTGATACGTAAGAAGAGAGGCC--CAAGAAAAAACTTTGGCAATTCATTGTGCAGACCAACAA Cluster: [ ] Orangutan: CAGATATGTAAGAAGAGAGGCC--CCAGAAAAAACTTTGGCAATTCATTGTGCAGACCAACAA Gorilla > Chimp --------------- chr4:125200333-125200341 Template switch process: F1: L TAATCATATATTCTAGCTTGCTGATATGTAAGAAGAGAGGCT 1 F3: 4 AAACTTTGGCAATTCATTGTGCAGACCAACAAGAAGTGTT R RF: TAATCATATATTCTTGCTTGCTGATATGTAAGAAGAGAGGCCCCAGAAAAAACTTTGGCAATTCATTGTGCAGACCAACAAGAAGTGTT RR: ATTAGTATATAAGAACGAACGACTATACATTCTTCTCTCCGGGGTCTTTTTTGAAACCGTTAAGTAACACGTCTGGTTGTTCTTCACAA F2: 3 GAAACCGTT 2 Unidirectional alignment (log-probability: -40.9) ATCATATATTCTaGCTTGCTGATATGTAAGAAGAGAGGC--------tttgccaaagAAACTTTGGCAATTCATTGTGCAGACCAACAAGAAGTGTT ATCATATATTCTTGCTTGCTGATATGTAAGAAGAGAGGCCCCAGAAA----------AAACTTTGGCAATTCATTGTGCAGACCAACAAGAAGTGTT Template switch alignment (log-probability: -27.9) ATCATATATTCTaGCTTGCTGATATGTAAGAAGAGAGGCt|TTGCCAAAG|AAACTTTGGCAATTCATTGTGCAGACCAACAAGAAGTGTT ATCATATATTCTTGCTTGCTGATATGTAAGAAGAGAGGCC|TTGCCAAAG|AAACTTTGGCAATTCATTGTGCAGACCAACAAGAAGTGTT ========== Event 2691 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAAACTCAAAAAATGCCATTTTTATCTACAGATAAAAATGGTAAGGAGACAGCTTTTTA ↑ 3 1 2 4 Chimp: TTAAACTCAAAAAATGCCATTTTTATCTGTAG--CATATTGGTAAGGAGACAGCTTTTTA Gorilla: TTAAACTCAAAAAATGCCATTTTTATCTGTAG--TATATTGGTAAGGAGACAGCTTTTTA ↓ 3 1 2 4 Human: TTAAACTCAAAAAATGCCATTTTTATCTACAGATAAAAATGGTAAGGAGACAGCTTTTTA Cluster: [ ] Orangutan: TTAAACTCAAAAAATGCCATCTTTATCTGTAG--TATATTGGT--AGAGACAGCTTTTTA Chimp > Human ------------- chr4:128881476-128881486 Template switch process: F1: L ATGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCT 1 F3: 4 TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC R RF: ATGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCTGTAGCATATTGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC RR: TACACGAATATTGAATTTGAGTTTTTTACGGTAAAAATAGACATCGTATAACCATTCCTCTGTCGAAAAATTCAATTCTGTCCGTATGTG F2: 3 AAAAATAGACA 2 Unidirectional alignment (log-probability: -37.4) TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATC---------TacagataaaaaTGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCTGTAGCATAT-----------TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC Template switch alignment (log-probability: -16.6) TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCT|ACAGATAAAAA|TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCT|ACAGATAAAAA|TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC Gorilla > Human --------------- chr4:128881476-128881486 Template switch process: F1: L ATGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCT 1 F3: 4 TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC R RF: ATGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCTGTAGTATATTGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC RR: TACACGAATATTGAATTTGAGTTTTTTACGGTAAAAATAGACATCATATAACCATTCCTCTGTCGAAAAATTCAATTCTGTCCGTATGTG F2: 3 AAAAATAGACA 2 Unidirectional alignment (log-probability: -36.9) TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATC---------TacagataaaaaTGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCTGTAGTATAT-----------TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC Template switch alignment (log-probability: -17.1) TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCT|ACAGATAAAAA|TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC TGTGCTTATAACTTAAACTCAAAAAATGCCATTTTTATCT|ACAGATAAAAA|TGGTAAGGAGACAGCTTTTTAAGTTAAGACAGGCATACAC ========== Event 2692 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCATTATTCATAGAGTTTCTC---------CTGAAACTCTTGGTTTCAGAGTTTCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCttttcttt------ttt--ttttttCAATATTGAGGGGGTCAAATAACCTTATATTAAATAAGTA Chimp: CCATTATTCACAGAGTTTCTC----------------------------CGACTCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCTTTTCttt---------ttttttttCAATATTGACGGAGTCAAATAACCTTATATTAAATAAGTA Gorilla: CCATTATTCATAGAGTTTCTCCTGAAAATT-------------------TGACTCTGAAAACCAAGGCACCTACAGTAAGACTCAAGGATCTTTTCttt-----t-----ttttttCAATATTGAGGGGGTCAAATAACCTTATATTAAATAAGTA ↑ 1 4 3 2 Human: CCATTATTCATAGAGTTTCTC---------CTGAAACTCTTGGTTTCAGAGTTTCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCttttcttt------ttt--ttttttCAATATTGAGGGGGTCAAATAACCTTATATTAAATAAGTA Cluster: [ ] Orangutan: GCATTATTCATAGAGTTTCTCCTGAAAATT-------------------TGACTCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCttttcttttttttt-----ttttttCAATATTGAGGGAGTCAAATAACCTTATATTAAATAAGTA Human > Gorilla --------------- chr4:67296348-67296354 Template switch process: F1: L CATCATTAGTTTGGGTCCTCCCATTATTCATAGAGTTTCTCCTGAAA 1 F3: 4 TCTGAAAACCAAGGCACCTACAGTAAGACTCAAGGATCTT R RF: CATCATTAGTTTGGGTCCTCCCATTATTCATAGAGTTTCTCCTGAAACTCTTGGTTTCAGAGTTTCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCTTTTCTTTTTTTTTTTTCAATATTGAGGGGGTCAAAT RR: GTAGTAATCAAACCCAGGAGGGTAATAAGTATCTCAAAGAGGACTTTGAGAACCAAAGTCTCAAAGACTTTTGGTTCCGTGAATGTCATTCTGAGTTCCTAGAAAAGAAAAAAAAAAAAGTTATAACTCCCCCAGTTTA F2: 3 CAGTTTA 2 Unidirectional alignment (log-probability: -35.7) AGTTTGGGTCCTCCCATTATTCATAGAGTTTCTCCTGAAaatttgAC----------------TCTGAAAACCAAGGCACcTACAGTAAGACTCAAGGATCTT AGTTTGGGTCCTCCCATTATTCATAGAGTTTCTCCTGAA------ACTCTTGGTTTCAGAGTTTCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCTT Template switch alignment (log-probability: -22.3) AGTTTGGGTCCTCCCATTATTCATAGAGTTTCTCCTGAAA|ATTTGAC|TCTGAAAACCAAGGCACcTACAGTAAGACTCAAGGATCTT AGTTTGGGTCCTCCCATTATTCATAGAGTTTCTCCTGAAA|ATTTGAC|TCTGAAAACCAAGGCACTTACAGTAAGACTCAAGGATCTT ========== Event 2693 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTAATTGATATTCTGAATTTTTGTCA----GAAGAGAGAGTTTCCAGCAGCTATGT------------GTTTGTGTTTACATTAGTTGCTGATTTAAATATTTATAGGATTCATATAAATTAAATATTATTTCTGTATTTCTTCTTAATTCTAGAAAGTCCGATGAATGTACAGGCATTGGAG Chimp: CTAATTGATATTCTGAATTTTTGTCA----TAAGAGAGAGTTTCCAGCAGCTGTGT------------GTTTGTGTTTACATTAGTTGCTGATTTAAATATTTATAGGATTCATATAAATTAAATATTATTTCTGTATTTCTTCTTAATTCTAGAAAGTCTGATGAATGTACAGGCATTGGAG ↓ 1 4 3 2 Gorilla: CTAATTGATATTCTGAATTTT-TTCA--------GGAGAGTTTCCAGCAGCTGTGT------------GTTTGTGTTTACATTAGTTGCTGATTTAAATATTTATAGGATTCATATAAATTCAATATTATTTCTGTATTTCTTCTTAATTCTAGAAAGTCTGATGAATGTACAGGCATTGGAG Human: CTAATTGATATTCTGAATTTTTGTCA----GAAGAGAGAGTTTCCAGCAGCTATGT------------GTTTGTGTTTACATTAGTTGCTGATTTAAATATTTATAGGATTCATATAAATTAAATATTATTTCTGTATTTCTTCTTAATTCTAGAAAGTCCGATGAATGTACAGGCATTGGAG Cluster: [ ] Orangutan: CTAATTGATATTCTGAATTTTTGTCAGAAG----AGAGAGTTTCCAGCAGCtgtgtgtgtgcgtgtgtgtgtgtgtTTACATTAGTTGCTGATTTAAATATTTATAGGATTCATATAAATTAAATATTATTTCTGTATTTCTTCTTAATACTAGAAAGTCTGATGAATGTACAGGCATTGGAG Chimp > Gorilla --------------- chr4:67267869-67267872 Template switch process: F1: L AGTTCTTAGAAACAATGATTCTAATTGATATTCTGAATTTTT 1 F3: 4 GAGAGTTTCCAGCAGCTGTGTGTTTGTGTTTACATTAGTT R RF: AGTTCTTAGAAACAATGATTCTAATTGATATTCTGAATTTTTGTCATAAGAGAGAGTTTCCAGCAGCTGTGTGTTTGTGTTTACATTAGTTGCTGATTTAAATATTTATAGGATTCATATAAATTAAATATTATTTCTGTATTTCTTCTTAATTCTAGAAAGTCTGA RR: TCAAGAATCTTTGTTACTAAGATTAACTATAAGACTTAAAAACAGTATTCTCTCTCAAAGGTCGTCGACACACAAACACAAATGTAATCAACGACTAAATTTATAAATATCCTAAGTATATTTAATTTATAATAAAGACATAAAGAAGAATTAAGATCTTTCAGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -25.4) TTCTTAGAAACAATGATTCTAATTGATATTCTGAATTTTTtcaG--------GAGAGTTTCCAGCAGCTGTGTGTTTGTGTTTACATTAGTT TTCTTAGAAACAATGATTCTAATTGATATTCTGAATTTTT---GTCATAAGAGAGAGTTTCCAGCAGCTGTGTGTTTGTGTTTACATTAGTT Template switch alignment (log-probability: -16.3) TTCTTAGAAACAATGATTCTAATTGATATTCTGAATTTTT|TCAG|GAGAGTTTCCAGCAGCTGTGTGTTTGTGTTTACATTAGTT TTCTTAGAAACAATGATTCTAATTGATATTCTGAATTTTT|TCAG|GAGAGTTTCCAGCAGCTGTGTGTTTGTGTTTACATTAGTT ========== Event 2694 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATCTATGGTCCATCCAACCACAACATTGGTTAATTGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAACTGA Chimp: ATCTATGGTCCATCCAACCACAACATTGGTTAATTGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAACTAA Gorilla: ATCTACGGTCCATCCAACCAC-AC---------ATGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAACTAA ↓ 1 4 3 2 Human: ATCTATGGTCCATCCAACCACAACATTGGTTAATTGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAACTGA Cluster: [ ] Orangutan: ATCTATGGTCCATCCAACCAC-AC---------ATGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAACTAA Gorilla > Human --------------- chr4:128092041-128092052 Template switch process: F1: L GACTGGCTCGCTGTGTATACATCTATGGTCCATCCAACCACA 1 F3: 4 TGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAAC R RF: GACTGGCTCGCTGTGTATACATCTACGGTCCATCCAACCACACATGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAAC RR: CTGACCGAGCGACACATATGTAGATGCCAGGTAGGTTGGTGTGTACCTAAAAAATTAATTGGTTAAAGTATTTATAAGTTTTTG F2: 3 TAATTGGTTACA 2 Unidirectional alignment (log-probability: -40.6) CTGGCTCGCTGTGTATACATCTAtGGTCCATCCAACCACaACAttggttaatTGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAAC CTGGCTCGCTGTGTATACATCTACGGTCCATCCAACCAC-ACA---------TGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAAC Template switch alignment (log-probability: -28.3) CTGGCTCGCTGTGTATACATCTAtGGTCCATCCAACCACA|AcATTGGTTAAT|TGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAAC CTGGCTCGCTGTGTATACATCTACGGTCCATCCAACCACA|AAATTGGTTAAT|TGGATTTTTTAATTAACCAATTTCATAAATATTCAAAAAC ========== Event 2695 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTAGCATATGGCAGGTGTCCAAGCTCACTGAGGA---TACTATTCTTTTCCTCCAGAACTAAGA Chimp: CTTAGCATATGGCAGGTGTCCAAGCTCACTGAGGA---TACTATTCTTTTCCTCCAGAACTAAGA ↓ 4 3 12 Gorilla: CTTAGCATATGGCAGGTGTCCAAGCTCAGTGAGCTCCAAGC-TCACTTTTCCTCCAGAACTAAGA ↑ 4 3 12 Human: CTTAGCATATGGCAGGTGTCCAAGCTCACTGAGGA---TACTATTCTTTTCCTCCAGAACTAAGA Cluster: [ ] Orangutan: CTTAGCATATGGCAGGTGTCCAAGCTCACTGAGGA---TACTAT-TTTTTCCTCCAGAACTAAGA Human > Gorilla --------------- chr4:66785775-66785781 Template switch process: F1: L CTTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCA 1 F3: 4 CCAAGCTCA--------------CTTTTCCTCCAGAACTAAGAACAGAACTAGCTATTTATTA R RF: CCTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCACTGAGGATACTATTCTTTTCCTCCAGAACTAAGAACAGAACTAGCTATTTATTA RR: GGAAGAATCTAAAGAATCGTATACCGTCCACAGGTTCGAGTGACTCCTATGATAAGAAAAGGAGGTCTTGATTCTTGTCTTGATCGATAAATAAT F2: 3 TCGAGTG 2 Unidirectional alignment (log-probability: -48) tTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCAgTGAGctccaagctca---------CTTTTCCTCCAGAACTAAGAACAGAACTAGC CTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCACTGAG-----------GATACTATTCTTTTCCTCCAGAACTAAGAACAGAACTAGC Template switch alignment (log-probability: -32.8) tTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCA|GTGAGCT|CCAAGCTCA--------------CTTTTCCTCCAGAACTAAGAACAGAACTAGC CTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCA|GTGAGCT|CCAAGCTCACTGAGGATACTATTCTTTTCCTCCAGAACTAAGAACAGAACTAGC Chimp > Gorilla --------------- chr4:66785775-66785781 Template switch process: F1: L CTTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCA 1 F3: 4 CCAAGCTCA--------------CTTTTCCTCCAGAACTAAGAACAGAACTAGCTATTTATTA R RF: CCTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCACTGAGGATACTATTCTTTTCCTCCAGAACTAAGAACAGAACTAGCTATTTATTA RR: GGAAGAATCTAAAGAATCGTATACCGTCCACAGGTTCGAGTGACTCCTATGATAAGAAAAGGAGGTCTTGATTCTTGTCTTGATCGATAAATAAT F2: 3 TCGAGTG 2 Unidirectional alignment (log-probability: -48) tTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCAgTGAGctccaagctca---------CTTTTCCTCCAGAACTAAGAACAGAACTAGC CTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCACTGAG-----------GATACTATTCTTTTCCTCCAGAACTAAGAACAGAACTAGC Template switch alignment (log-probability: -32.8) tTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCA|GTGAGCT|CCAAGCTCA--------------CTTTTCCTCCAGAACTAAGAACAGAACTAGC CTTCTTAGATTTCTTAGCATATGGCAGGTGTCCAAGCTCA|GTGAGCT|CCAAGCTCACTGAGGATACTATTCTTTTCCTCCAGAACTAAGAACAGAACTAGC ========== Event 2696 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CTTCCCAAATGATTCAGCTACTCGTTAACAGCATAACGA------------------------------GTAGCCAGAGACCTAAGTTTCAT ↑ 3 2 1 4 Chimp: CTTCCCAAATGATTCAGCTACTCGTTAACAGCATAATAA---------------TAAATAAAATTTGAGCCAGCCAGAGACCTAAGTTTCAT Gorilla: Human: CTTCCCAAATGATTCAGCTACTCGTTAACAGCATAACGA------------------------------GTAGCCAGAGACCTAAGTTTCAT Cluster: [ ] Orangutan: CTTCCCAAATGATTCAGCTACTCGTTAACAGCATAATAATAAATAAAATTTGAG---------------CCAGCCAGAGATCTAAGTTtcat Chimp > Human ------------- chr4:62928330-62928334 Template switch process: F1: L AAGGTCTTCCCAAATGATTCAGCTACTCGTTAACAGCATAA 1 F3: 4 AGCCAGAGACCTAAGTTTCATTCTTGTCTTCTGCCTCATT R RF: AAGGTCTTCCCAAATGATTCAGCTACTCGTTAACAGCATAATAATAAATAAAATTTGAGCCAGCCAGAGACCTAAGTTTCATTCTTGTCTTCTGCCTCATT RR: TTCCAGAAGGGTTTACTAAGTCGATGAGCAATTGTCGTATTATTATTTATTTTAAACTCGGTCGGTCTCTGGATTCAAAGTAAGAACAGAAGACGGAGTAA F2: 3 TGAGC 2 Unidirectional alignment (log-probability: -27.9) AGGTCTTCCCAAATGATTCAGCTACTCGTTAACAGCATAAcgagT-------------------AGCCAGAGACCTAAGTTTCATTCTTGTCTTCTGCCTCATT AGGTCTTCCCAAATGATTCAGCTACTCGTTAACAGCATAA----TAATAAATAAAATTTGAGCCAGCCAGAGACCTAAGTTTCATTCTTGTCTTCTGCCTCATT Template switch alignment (log-probability: -15.9) AGGTCTTCCCAAATGATTCAGCTACTCGTTAACAGCATAA|CGAGT|AGCCAGAGACCTAAGTTTCATTCTTGTCTTCTGCCTCATT AGGTCTTCCCAAATGATTCAGCTACTCGTTAACAGCATAA|CGAGT|AGCCAGAGACCTAAGTTTCATTCTTGTCTTCTGCCTCATT ========== Event 2697 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCATCTATCTGCCCTTAAAA-AACCTAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACAACAGTCATTGAATACACAATTTAGAC ↓ 1 4 3 2 Chimp: AGCATCTATCTGCCCTTAAAAAGACTTAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACAC--AAGTCATTGAATACACAATTTAGAC Gorilla: AGCATCTATCTGCCCTTAAAAAGACTTAAAATTTCTCAATAGTTAGCATAACTCTTCTCACACAACAGTCATTGAATACACAATTTAGAC Human: AGCATCTATCTGCCCTTAAAA-AACCTAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACAACAGTCATTGAATACACAATTTAGAC Cluster: [ ] Orangutan: AGCATCTATCTGCCCTTAAAAAGACTTAAAGTTTGTCAATAGTGAGCATAACTCTTCTCACACAACAGACATTCAATACACAATTTAGAC Human > Chimp ------------- chr4:66794362-66794365 Template switch process: F1: L TATACATGTTTGAATTTATTAGCATCTATCTGCCCTTAAAAA 1 F3: 4 TAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACA R RF: TATACATGTTTGAATTTATTAGCATCTATCTGCCCTTAAAAAACCTAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACAACAGTC RR: ATATGTACAAACTTAAATAATCGTAGATAGACGGGAATTTTTTGGATTTCAAAGAGTTATCAATCGTATTGAGAAGAGTGTGTTGTCAG F2: 3 TCAG 2 Unidirectional alignment (log-probability: -25.7) TACATGTTTGAATTTATTAGCATCTATCTGCCCTTAAAAAgACtTAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACA-- TACATGTTTGAATTTATTAGCATCTATCTGCCCTTAAAAA-ACCTAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACAAC Template switch alignment (log-probability: -15.8) TACATGTTTGAATTTATTAGCATCTATCTGCCCTTAAAAA|GACT|TAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACA TACATGTTTGAATTTATTAGCATCTATCTGCCCTTAAAAA|GACT|TAAAGTTTCTCAATAGTTAGCATAACTCTTCTCACACA ========== Event 2698 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTCATAGATTTCACATTCCTAGACAATTTCATCCAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGTTT--TTTTAAATCAACTTACTGAAATTATTCTT--------------------------------------------------------AGGTAAATACTTATTCATAAGCAGAAAGGGTTGCTCCACTTTCTGTATTAAGAGGAGACAGGCACTATGAGTGAGAAAGACACGAGTCTAGCTGT Chimp: TTTCATAGATTTCACATTCCTAGGCAATTTCATCCAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGTTT-TTTCTAAATCAACTTACTGAAATTATTCTT-------------------------------------AGGTATCTAGGAAAAATTTAGGTAGATACTTATTCATAAGCAGAAAGGGTTGCTGCATTTTCTGTATTAAGAGGAGACAGGCACTGTGAGTGAGAAAGACACGAGTCTAGCTGT Gorilla: TTTCATAGATTTCACATTCCTAGGCAATTTCATCCAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGTTT-TTTCTAAATCAACTTACTGAAATTATTCTT-------------------AGGTATCTAGGAAAATTT-------------------AGGTAAATACTTATTCTTAAGCAGAAAGGGTTGCTGCATTTTCTGTATTAAGAGGAGACAGGCACTGTGAGTGAGAAAGACACGAGTCTAGCTGT ↑ 3 2 1 4 Human: TTTCATAGATTTCACATTCCTAGACAATTTCATCCAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGTTT--TTTTAAATCAACTTACTGAAATTATTCTT--------------------------------------------------------AGGTAAATACTTATTCATAAGCAGAAAGGGTTGCTCCACTTTCTGTATTAAGAGGAGACAGGCACTATGAGTGAGAAAGACACGAGTCTAGCTGT Cluster: [ ] Orangutan: TTTCATAGATTTCACATTCCTAGACAATTTCATCCAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGtttttttttAAATCAACTTACTGAAATTATTATTAAGTCTCTAGGAAAAATTT-------------------------------------AGGTAAATACTTATTCATAAGCAGAAAGGGTTGCTCCACTTTCTGTATTAAGAGGAGACAGGCACTGTGAGTGAGAAAGACATGAGTCTAGCTGT Human > Gorilla --------------- chr4:138165535-138165539 Template switch process: F1: L CAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGTTTTTTCTAAATCAACTTACTGAAATTATTCTTAGGTA 1 F3: 4 GAAA R RF: CTAGACAATTTCATCCAAAGATAGGAGGGGGTATTATAATTGTATATTTTGTGTTTTTT-TAAATCAACTTACTGAAATTATTCTTAGGTAAATACTTATTCATAAGCAGAAAGGGTTGCTCCACTTTCTGTATTAAGAGGAGACAGGCACTATGAGTGAGAAA RR: GATCTGTTAAAGTAGGTTTCTATCCTCCCCCATAATATTAACATATAAAACACAAAAAA-ATTTAGTTGAATGACTTTAATAAGAATCCATTTATGAATAAGTATTCGTCTTTCCCAACGAGGTGAAAGACATAATTCTCCTCTGTCCGTGATACTCACTCTTT F2: 3 GATCT 2 Unidirectional alignment (log-probability: -39) TGTTTTTTcTAAATCAACTTACTGAAATTATTCTTaggtatctaggaaa TGTTTTTT-TAAATCAACTTACTGAAATTATTCTT-------------- Template switch alignment (log-probability: -27.5) TGTTTTTTcTAAATCAACTTACTGAAATTATTCTTAGGTA|TCTAG|GAAA TGTTTTTT-TAAATCAACTTACTGAAATTATTCTTAGGTA|TCTAG|GAAA ========== Event 2699 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CGTAACTTGGCTTCTTGAACTCCAGG-------CATCTAGTATATATACCCATGAAGCAGAAAAGAGTTTACCAA Chimp: tgtaacttggcttcttgaactccAGG-------CATCTAGTACATATACCCACGAAGCAGAAAAGAGTTTACCAA Gorilla: TGTAACTTGGCTTCTTGAACTTCATG--------------GGTATACACCCATGAAGCAGAAAAGAGTTTACCAA ↑ 1 4 3 2 Human: CGTAACTTGGCTTCTTGAACTCCAGG-------CATCTAGTATATATACCCATGAAGCAGAAAAGAGTTTACCAA Cluster: [ ] Orangutan: tgtaacttggcttcttgaactccAGGAATCTAG-------TATATATACCCACGAGGCAGAAAAGAGTTTACCAA Human > Gorilla --------------- chr4:140911763-140911770 Template switch process: F1: L TTTGAATAGAGACTAGATGGTGTAACTTGGCTTCTTGAACT 1 F3: 4 ATACACCCATGAAGCAGAAAAGAGTTTACCAAATGTGGAGTATA R RF: TTTGAATAGAGACTAGATGGCGTAACTTGGCTTCTTGAACTCCAGGCATCTAGTATATATACCCATGAAGCAGAAAAGAGTTTACCAAATGTGGAGTATA RR: AAACTTATCTCTGATCTACCGCATTGAACCGAAGAACTTGAGGTCCGTAGATCATATATATGGGTACTTCGTCTTTTCTCAAATGGTTTACACCTCATAT F2: 3 TGGGTACT 2 Unidirectional alignment (log-probability: -40.7) TTGAATAGAGACTAGATGGtGTAACTTGGCTTCTTGAACTtCAtgGG---------TATAcACCCATGAAGCAGAAAAGAGTTTACCAAATGTGGAG TTGAATAGAGACTAGATGGCGTAACTTGGCTTCTTGAACTCCA--GGCATCTAGTATATATACCCATGAAGCAGAAAAGAGTTTACCAAATGTGGAG Template switch alignment (log-probability: -27.9) TTGAATAGAGACTAGATGGtGTAACTTGGCTTCTTGAACT|TCATGGGT|ATAcACCCATGAAGCAGAAAAGAGTTTACCAAATGTGGAG TTGAATAGAGACTAGATGGCGTAACTTGGCTTCTTGAACT|TCATGGGT|ATATACCCATGAAGCAGAAAAGAGTTTACCAAATGTGGAG ========== Event 2700 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GACTGTAACTTTTGGCTGAAGCAACT---ATTTGTTTATCAAGAAGTTTGTAAAAGTAAATT Chimp: GACTGTAACTTTTGGCTGAAGCAACT---ATTTGTTTATCAAGAAGTTTGTAAAAGTAAATT ↓ 1 4 3 2 Gorilla: GACTGTAACTTTTGGCTGAAGTTGATAAACTTTGTTTATCAAGAAGTTTGTAAAAGTAAATT Human: GACTGTAACTTTTGGCTGAAGCAACT---ATTTGTTTATCAAGAAGTTTGTAAAAGTAAATT Cluster: [ ] Orangutan: GACTGTAACTTTTGGCTGAAGCAACT---ATTTGTTTATCAATAAGTTTGTAAAAGTAAATT Chimp > Gorilla --------------- chr4:140898524-140898532 Template switch process: F1: L AGAAATCTTCCAAGTTTTCTGACTGTAACTTTTGGCTGAAG 1 F3: 4 TTTGTTTATCAAGAAGTTTGTAAAAGTAAATTTTGCGTAT R RF: AGAAATCTTCCAAGTTTTCTGACTGTAACTTTTGGCTGAAGCAACTATTTGTTTATCAAGAAGTTTGTAAAAGTAAATTTTGCGTAT RR: TCTTTAGAAGGTTCAAAAGACTGACATTGAAAACCGACTTCGTTGATAAACAAATAGTTCTTCAAACATTTTCATTTAAAACGCATA F2: 3 CAAATAGTT 2 Unidirectional alignment (log-probability: -32.4) GAAATCTTCCAAGTTTTCTGACTGTAACTTTTGGCTGAAGttgataaaC-----TTTGTTTATCAAGAAGTTTGTAAAAGTAAATTTTGCGTAT GAAATCTTCCAAGTTTTCTGACTGTAACTTTTGGCTGAAG--------CAACTATTTGTTTATCAAGAAGTTTGTAAAAGTAAATTTTGCGTAT Template switch alignment (log-probability: -16.9) GAAATCTTCCAAGTTTTCTGACTGTAACTTTTGGCTGAAG|TTGATAAAC|TTTGTTTATCAAGAAGTTTGTAAAAGTAAATTTTGCGTAT GAAATCTTCCAAGTTTTCTGACTGTAACTTTTGGCTGAAG|TTGATAAAC|TTTGTTTATCAAGAAGTTTGTAAAAGTAAATTTTGCGTAT ========== Event 2701 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGTCTTGGTAATTCCTGACCTCTCC---------TTATAGAGACAACAGGGCCcatccctcctca Chimp: GGTCTTGGTAATTCCTGACCTTATCTCTATAAGGATATAGAGACAACAGGGCCcatccctcctca ↑ 1 3 4 2 Gorilla: GGTCTTGGTAATTCCTGACCTCTCC---------TTATAGAGACAACAGGGCCcatccctcctca Human: GGTCTTGGTAATTCCTGACCTCTCC---------TTATAGAGACAACAGGGCCcatccctcctca Cluster: [ ] Orangutan: GGTCTTGGTAATTCCTGACCTCTCC---------TTATGGAGACAACAGGGCCcatccctcttca Gorilla > Chimp --------------- chr4:7166065-7166078 Template switch process: F1: L TTCCTGGGTTATCTCTGACAGGTCTTGGTAATTCCTGACCT 1 F3: 4 TATAGAGACAACAGGGCCCATCCCTCCTCAATCTTTCTCT R RF: TTCCTGGGTTATCTCTGACAGGTCTTGGTAATTCCTGACCTCTCCTTATAGAGACAACAGGGCCCATCCCTCCTCAATCTTTCTTT RR: AAGGACCCAATAGAGACTGTCCAGAACCATTAAGGACTGGAGAGGAATATCTCTGTTGTCCCGGGTAGGGAGGAGTTAGAAAGAAA F2: 3 AGGAATATCTCTAT 2 Unidirectional alignment (log-probability: -45.1) TCCTGGGTTATCTCTGACAGGTCTTGGTAATTCCTGACCT----TatctctataaggaTATAGAGACAACAGGGCCCATCCCTCCTCAATCTTTCTcT TCCTGGGTTATCTCTGACAGGTCTTGGTAATTCCTGACCTCTCCT-------------TATAGAGACAACAGGGCCCATCCCTCCTCAATCTTTCTTT Template switch alignment (log-probability: -28.5) TCCTGGGTTATCTCTGACAGGTCTTGGTAATTCCTGACCT|TaTCTCTATAAGGA|TATAGAGACAACAGGGCCCATCCCTCCTCAATCTTTCTcT TCCTGGGTTATCTCTGACAGGTCTTGGTAATTCCTGACCT|TGTCTCTATAAGGA|TATAGAGACAACAGGGCCCATCCCTCCTCAATCTTTCTTT ========== Event 2702 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTCACAATTATCCCTGTTGACAATAACCCACTGCACTTA--TACAAGATGAGATAGTTTGCACCAT Chimp: GCTCACAATTATCCCTGTTGACAGTAACCCACTGCACTTA--TACAAGATGAGATAGTTTGCACCAT Gorilla: GCTCACAATTATCCCTGTTGACAATAACCCACTGTTATTG----TCAGATGAGATAGTTTGCACCAT ↑ 3 2 1 4 Human: GCTCACAATTATCCCTGTTGACAATAACCCACTGCACTTA--TACAAGATGAGATAGTTTGCACCAT Cluster: [ ] Orangutan: GCTCACAATTATCCCTGTTGACAATAACCCACTGCACTTATA--CAAGATGAGACAGTTTGCACCAT Human > Gorilla --------------- chr4:139686576-139686583 Template switch process: F1: L ATCTCAAGCTCACAATTATCCCTGTTGACAATAACCCACTG 1 F3: 4 AGATGAGATAGTTTGCACCATTACTGCCACAATTGTTTTC R RF: ACCTCAAGCTCACAATTATCCCTGTTGACAATAACCCACTGCACTTATACAAGATGAGATAGTTTGCACCATTACTGCCACAATTGTTTTC RR: TGGAGTTCGAGTGTTAATAGGGACAACTGTTATTGGGTGACGTGAATATGTTCTACTCTATCAAACGTGGTAATGACGGTGTTAACAAAAG F2: 3 CTGTTATT 2 Unidirectional alignment (log-probability: -36.7) tCTCAAGCTCACAATTATCCCTGTTGACAATAACCCACTGttattgtC---------AGATGAGATAGTTTGCACCATTACTGCCACAATTGTTTTC CCTCAAGCTCACAATTATCCCTGTTGACAATAACCCACTG-------CACTTATACAAGATGAGATAGTTTGCACCATTACTGCCACAATTGTTTTC Template switch alignment (log-probability: -22.3) tCTCAAGCTCACAATTATCCCTGTTGACAATAACCCACTG|TTATTGTC|AGATGAGATAGTTTGCACCATTACTGCCACAATTGTTTTC CCTCAAGCTCACAATTATCCCTGTTGACAATAACCCACTG|TTATTGTC|AGATGAGATAGTTTGCACCATTACTGCCACAATTGTTTTC ========== Event 2703 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: ATACACAAATTTTGAAGATTTACAGGGATCTTCAGTTCCCTAAGGCTAACTAAATTCAATAATGCCAGCTTTAATGTCTTAGGTTCTAGGTCATTTCTCTAGAAATATCCCTGTAAAATTGACGTATATATT--TTAATT Chimp: ATACACAAATTTTGAAGATTTACAGGGATCTTCAGTTCCCTAAGGCTAACTAAATTCAATAATGCCAGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAA--------------ATGACATATATATT--TTAATT ↓ 3 2 4 1 Gorilla: ATACACAAATTCTGAAGATTTACAGGGATCTTCAGTTCCCTAAGGCTAACTAAATTCAATAATGCCAGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAATATCCCTGTAAAATTGACATATATATT--TTAATT Human: ATACACAAATTTTGAAGATTTACAGGGATCTTCAGTTCCCTAAGGCTAACTAAATTCAATAATGCCAGCTTTAATGTCTTAGGTTCTAGGTCATTTCTCTAGAAATATCCCTGTAAAATTGACGTATATATT--TTAATT Cluster: [ ] Orangutan: atacgcaaattttgaagatttacagggATCTTCAGTTCCTTAAGGCTAACTAAATTTAATAATGCCAGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAATATCCCTGTAAAATTGACATATATATTTTGTAATT Chimp > Gorilla --------------- chr4:139668480-139668489 Template switch process: F1: L GCCAGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAAT 1 F3: 4 AATTGACATATATATTTTAATTATTTCATTCATTCTCTTTTTT R RF: TTACAGGGATCTTCAGTTCCCTAAGGCTAACTAAATTCAATAATGCCAGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAATGACATATATATTTTAATTATTTCATTCATTCTCTTTTTT RR: AATGTCCCTAGAAGTCAAGGGATTCCGATTGATTTAAGTTATTACGGTCGAAATTACGGAATCCAAGATCCAGTAAAGAGATCTTTACTGTATATATAAAATTAATAAAGTAAGTAAGAGAAAAAA F2: 3 AATGTCCCTA 2 Unidirectional alignment (log-probability: -39.2) AGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAAtatccctgtaaaatTGACATATATATTTTAATTATTTCATTCATTCTCTTT AGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAA--------------TGACATATATATTTTAATTATTTCATTCATTCTCTTT Template switch alignment (log-probability: -22.6) AGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAAT|ATCCCTGTAA|AAtTGACATATATATTTTAATTATTTCATTCATTCTCTTT AGCTTTAATGCCTTAGGTTCTAGGTCATTTCTCTAGAAAT|ATCCCTGTAA|AAATGACATATATATTTTAATTATTTCATTCATTCTCTTT ========== Event 2704 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTCTAGAACTTGCCATATTGAAGCTTTAAAGTTCAAATGAAGTATTTGAACTTCATTGTCACCCAGTTTATG ↑ 4 1 3 2 Chimp: TTTCTAGAACTTGCCATATTGAAGCTTTAAG-----CAT-GTCTATTTGAACTTCATTGTCACCCAGTTTATG Gorilla: TTTCTAGAACTTGCCATATTGAAGCTTTAAA-----CAT-GTCTATTTGAACTTCATTGTCACCCAGTTTATG ↓ 4 1 3 2 Human: TTTCTAGAACTTGCCATATTGAAGCTTTAAAGTTCAAATGAAGTATTTGAACTTCATTGTCACCCAGTTTATG Cluster: [ ] Orangutan: TTTCTAGAATTTGCCATATTGAAGCTTTAAA-----CAT-GTCTACTTGAACTTCATTGTCACCCAGTTTATG Chimp > Human ------------- chr4:66760811-66760818 Template switch process: F1: L TTCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAA 1 F3: 4 TGAAG-------------TATTTGAACTTCATTGTCACCCAGTTTATGTCTTCAGTAT R RF: TTCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAGCATGTCTATTTGAACTTCATTGTCACCCAGTTTATGTCTTCAGTAT RR: AAGGTTTTGATAAAGATCTTGAACGGTATAACTTCGAAATTCGTACAGATAAACTTGAAGTAACAGTGGGTCAAATACAGAAGTCATA F2: 3 AAACTTGA 2 Unidirectional alignment (log-probability: -38.7) TCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTaaagttcaaatgAAG------TATTTGAACTTCATTGTCACCCAGTTTATGTCTTC TCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTT------------AAGCATGTCTATTTGAACTTCATTGTCACCCAGTTTATGTCTTC Template switch alignment (log-probability: -27.3) TCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAA|AGTTCAAA|TGAAG-------------TATTTGAACTTCATTGTCACCCAGTTTATGTCTTC TCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAA|AGTTCAAA|TGAAGCTTTAAGCATGTCTATTTGAACTTCATTGTCACCCAGTTTATGTCTTC Gorilla > Human --------------- chr4:66760812-66760818 Template switch process: F1: L TCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAA 1 F3: 4 TGAAG-------------TATTTGAACTTCATTGTCACCCAGTTTATGTCTTCAGTAT R RF: TCCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAACATGTCTATTTGAACTTCATTGTCACCCAGTTTATGTCTTCAGTAT RR: AGGTTTTGATAAAGATCTTGAACGGTATAACTTCGAAATTTGTACAGATAAACTTGAAGTAACAGTGGGTCAAATACAGAAGTCATA F2: 3 AAACTTG 2 Unidirectional alignment (log-probability: -38.2) CCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAA------gttcaaatgaagTATTTGAACTTCATTGTCACCCAGTTTATGTCTTC CCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAACATGTC------------TATTTGAACTTCATTGTCACCCAGTTTATGTCTTC Template switch alignment (log-probability: -27.1) CCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAA|GTTCAAA|TGAAG-------------TATTTGAACTTCATTGTCACCCAGTTTATGTCTTC CCAAAACTATTTCTAGAACTTGCCATATTGAAGCTTTAAA|GTTCAAA|TGAAGCTTTAAACATGTCTATTTGAACTTCATTGTCACCCAGTTTATGTCTTC ========== Event 2705 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACATGACAAGAGAAAAACT-----ATGATTTCTGTATGACTCACCTTG Chimp: CTACATGACAAGAGAAAAACT-----ATGATTTCTGTATGACTCACCTTG ↓ 3 1 4 2 Gorilla: CTACAGGACAAGAGAAAAACTTCATAGAGATTTCTGTATGACTCACCTTG Human: CTACATGACAAGAGAAAAACT-----ATGATTTCTGTATGACTCACCTTG Cluster: [ ] Orangutan: CTACATGACAAGAGAAAAACTTCATAGAGATTTCTGTATGACTCACCTTG Chimp > Gorilla --------------- chr4:63266275-63266280 Template switch process: F1: L AATATTGTGCAAAAAAATAACTACAGGACAAGAGAAAAACT 1 F3: 4 AGATTTCTGTATGACTCACCTTGTAGACAATATTTTTTTT R RF: AATATTGTGCAAAAAAATAACTACATGACAAGAGAAAAACTATGATTTCTGTATGACTCACCTTGTAGACAATATTTTTTTT RR: TTATAACACGTTTTTTTATTGATGTACTGTTCTCTTTTTGATACTAAAGACATACTGAGTGGAACATCTGTTATAAAAAAAA F2: 3 GATACT 2 Unidirectional alignment (log-probability: -40.1) ATATTGTGCAAAAAAATAACTACAgGACAAGAGAAAAACTtcATagaGATTTCTGTATGACTCACCTTGTAGACAATATTTTTTTT- ATATTGTGCAAAAAAATAACTACATGACAAGAGAAAAACT--AT---GATTTCTGTATGACTCACCTTGTAGACAATATTTTTTTTT Template switch alignment (log-probability: -27.5) ATATTGTGCAAAAAAATAACTACAgGACAAGAGAAAAACT|TCATAG|aGATTTCTGTATGACTCACCTTGTAGACAATATTTTTTTT ATATTGTGCAAAAAAATAACTACATGACAAGAGAAAAACT|TCATAG|TGATTTCTGTATGACTCACCTTGTAGACAATATTTTTTTT ========== Event 2706 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTAAAGATTTTATGTAAAAACGGTAGGTTGTTTTTGAtttttttttttttt---------------ttttttttttttttttttttttttagagacaggatcttgctgttgcccaggcttgggggcagtggcgtgatcatagctctctgtaacctcaaactgt ↓ 1 4 3 2 Chimp: TCTTAAAGATTTTATGTAAAAGCTATAGGTTGtttttgatttttttttttttt-------------------------------ttttttttagagacaggatcttgctgttgcccaggcttgggggcagtggcgtgatcatagctctctgtaacctcaaactgt Gorilla: TCTTAAAGATTTTATGTAAGAACTATAGGTTGtttttgattttttttttttttttttttttttttttt-----------tttttttttttttagagacaggatcttgctcttgcccaggcttgggggcagtggcgtgatcatagctctctgtaacctcaaactgt Human: TCTTAAAGATTTTATGTAAAAACGGTAGGTTGTTTTTGAtttttttttttttt---------------ttttttttttttttttttttttttagagacaggatcttgctgttgcccaggcttgggggcagtggcgtgatcatagctctctgtaacctcaaactgt Cluster: [ ] Orangutan: TCTTAAAGATTTTATGTAAAAACTATAGG----TTTTGAttttttt--------------------------------------ttttttttagagacagggtcttgctgttgcccaagcttgggtgcagtggcatgatcatagctctctgtaacctcaaactgt Human > Chimp ------------- chr4:62736765-62736769 Template switch process: F1: L AAAAACAAAAAAAAACATAGTCTTAAAGATTTTATGTAAAA 1 F3: 4 AGGTTGTTTTTGATTTTTTTTTTTTTT R RF: AAAAA-AAAAAAAAACATAGTCTTAAAGATTTTATGTAAAAACGGTAGGTTGTTTTTGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGAGACAGGATCTTGCTGTTGCCCAGGCTTGGGGGCAGTGGCGTGATCATAGC RR: TTTTT-TTTTTTTTTGTATCAGAATTTCTAAAATACATTTTTGCCATCCAACAAAAACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATCTCTGTCCTAGAACGACAACGGGTCCGAACCCCCGTCACCGCACTAGTATCG F2: 3 TATCG 2 Unidirectional alignment (log-probability: -38.1) AAAAcAAAAAAAAACATAGTCTTAAAGATTTTATGTAAAAgCtaTAGGTTGTTTTTGATTTTTTTTTTTTTT------------ AAAA-AAAAAAAAACATAGTCTTAAAGATTTTATGTAAAAACGGTAGGTTGTTTTTGATTTTTTTTTTTTTTTTTTTTTTTTTT Template switch alignment (log-probability: -27.3) AAAAcAAAAAAAAACATAGTCTTAAAGATTTTATGTAAAA|GCTAT|AGGTTGTTTTTGATTTTTTTTTTTTTT AAAA-AAAAAAAAACATAGTCTTAAAGATTTTATGTAAAA|GCTAT|AGGTTGTTTTTGATTTTTTTTTTTTTT ========== Event 2707 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: aatttcaattgtgataaatgttacaaagaaaaatgaagaagCCTCTGA-----G-GTGGAT-CATTA-ATTAAA-TAGTTC-TCTGA-CCTTG-AGCATC-TATGT-ACCCC-TCCTAT-GGCCT-ATCCAC-TAATG-ACAT-----CTGACAGTA----------ACATCACTCATAAGGAATGTTGC Chimp: aatttcaattgtgataaatgttacaaagaaaaatgaagaagCCTCTGA-----G-GTGGAT-CATTA-ATTAAA-TAGTTC-TCTGA-CCTTG-AGCATC-TATGT-ACCCC-TCCTAT-GGCAT-ATCCAC-AAATG-ACAT-----CTGACATCA-----TTTGTGGATCACTCATAAGGAATGTTGC Gorilla: aatttcaattgtgataaatgttacaaagaaaaatgaagaagCCTCTGA-----G-GTGGAT-CATTA-ATTAAA-TAGTTC-TCTGA-CCTTG-AGCATC-TATGT-ACCCC-TCCTAT-GGCAT-ATCCAC-AAATG-ACAT-----CTGACATCATTTGT-----GGATCACTCATAAGGAATGTTGC ↓ 3 2 1 4 Human: aatttcaattgtgataaatgttacaaagaaaaatgaagaagCCTCTGA-----G-GTGGAT-CATTA-ATTAAA-TAGTTC-TCTGA-CCTTG-AGCATC-TATGT-ACCCC-TCCTAT-GGCCT-ATCCAC-TAATG-ACAT-----CTGACAGTA----------ACATCACTCATAAGGAATGTTGC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-----NNNNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chr4:67837906-67837910 Template switch process: F1: L TAGTTCTCTGACCTTGAGCATCTATGTACCCCTCCTATGGCCTATCCACTAATGACATCTGACA 1 F3: 4 ATCACTCATAAGGAAT R RF: GTTACAAAGAAAAATGAAGAAGCCTCTGAGGTGGATCATTAATTAAATAGTTCTCTGACCTTGAGCATCTATGTACCCCTCCTATGGCATATCCACAAATGACATCTGACATCATTTGTGGATCACTCATAAGGAAT RR: CAATGTTTCTTTTTACTTCTTCGGAGACTCCACCTAGTAATTAATTTATCAAGAGACTGGAACTCGTAGATACATGGGGAGGATACCGTATAGGTGTTTACTGTAGACTGTAGTAAACACCTAGTGAGTATTCCTTA F2: 3 CAATG 2 Unidirectional alignment (log-probability: -37.9) TGTACCCCTCCTATGGCcTATCCACtAATGACATCTGACA---------GtaacATCACTCATAAGGAAT TGTACCCCTCCTATGGCATATCCACAAATGACATCTGACATCATTTGTGG----ATCACTCATAAGGAAT Template switch alignment (log-probability: -27.4) TGTACCCCTCCTATGGCcTATCCACtAATGACATCTGACA|GTAAC|ATCACTCATAAGGAAT TGTACCCCTCCTATGGCATATCCACAAATGACATCTGACA|GTAAC|ATCACTCATAAGGAAT ========== Event 2708 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGATTGAATAATTAACCTGTCAGTGTTTACTAAGAACATGGAAGGTATGGAAACTAGTATAAAACATAAACCCTATACTCCAGGAATTTATATCCTACTTGGGGAAAC-----------AAGTATGACACAAGTAGAAGAATATGTGATAATTAA Chimp: AGGATTGAATAATTAACCTGTCAGTGTTTACTAAGAACATGGAATGTATGGAAACTAGTATAAAACATAAACCCTATACTCCAGGAATTTATAATCTATTTGGGGAAAC-----------AAGTATGACACAAGTAGAATAATATGTAATAATTAA Gorilla: AGGATTGAATAATTAACCTGTCAGTGTTTACTAAGAACATGGAAGGTATGGAAACTAGTTTAAAACATAAACCCTATACTCCAGGAATTTATATCCTACTTGGGGAAAC----------------------AAGTAGAAGAATATGTGATAATTAA ↓ 3 2 4 1 Human: AGGATTGAATAATTAACCTGTCAGTGTTTACTAAGAACATGGAAGGTATGGAAACTAGTATAAAACATAAACCCTATACTCCAGGAATTTATATCCTACTTGGGGAAAC-----------AAGTATGACACAAGTAGAAGAATATGTGATAATTAA Cluster: [ ] Orangutan: AGGATTGAATAACTAACCTGTCAGTGTTTACTAAGAACATGAAAGGTATGGGAACTAGTATAAAACATAAACCCTATACTCCAGGAATTTATAATCTATTTGGGGAAACAAGTATGACAC-----------AAGTAGAATAATATGTAATAATTAA Gorilla > Human --------------- chr4:121964618-121964621 Template switch process: F1: L AAACCCTATACTCCAGGAATTTATATCCTACTTGGGGAAACAAGTA 1 F3: 4 ACAAGTAGAAGAATATGTGATAATTAATTCTTATGAGATACA R RF: GTCAGTGTTTACTAAGAACATGGAAGGTATGGAAACTAGTTTAAAACATAAACCCTATACTCCAGGAATTTATATCCTACTTGGGGAAACAAGTAGAAGAATATGTGATAATTAATTCTTATGAGATACA RR: CAGTCACAAATGATTCTTGTACCTTCCATACCTTTGATCAAATTTTGTATTTGGGATATGAGGTCCTTAAATATAGGATGAACCCCTTTGTTCATCTTCTTATACACTATTAATTAAGAATACTCTATGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -26.7) TATACTCCAGGAATTTATATCCTACTTGGGGAAacaagtatgacACAAGTAGAAGAATATGTGATAATTAATTCTTATGAGATA TATACTCCAGGAATTTATATCCTACTTGGGGAA-----------ACAAGTAGAAGAATATGTGATAATTAATTCTTATGAGATA Template switch alignment (log-probability: -16.4) TATACTCCAGGAATTTATATCCTACTTGGGGAAACAAGTA|TGAC|ACAAGTAGAAGAATATGTGATAATTAATTCTTATGAGATA TATACTCCAGGAATTTATATCCTACTTGGGGAAACAAGTA|TGAC|ACAAGTAGAAGAATATGTGATAATTAATTCTTATGAGATA ========== Event 2709 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTAGAAGAGTTGATTCAAAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTG-----------------------------------------------------------------------------------------AATTTTGAAGTGATACCTGTTTCCTACA ↓ 3 4 2 1 Chimp: TTCTAGAAGAGTTGATTCAAAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGATTGGAGTTGATGAATAGAGTTGCTGATGAAGCCAGTACAGTCACATTGTGATTTCTTAACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATACCTGTTTCCTACA ↑ 3 4 2 1 Gorilla: TTCTAGAAGAGTTGATTCAAAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTG-----------------------------------------------------------------------------------------AATTTTGAAGTGATACCTGTTTCCTACA Human: TTCTAGAAGAGTTGATTCAAAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTG-----------------------------------------------------------------------------------------AATTTTGAAGTGATACCTGTTTCCTACA Cluster: [ ] Orangutan: TTCTAGAAGAGTTGATTCAAAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCTGATTCTCCTGTG-----------------------------------------------------------------------------------------AATTTTGAAGTGATACCTGTTTCCTACA Human > Chimp ------------- chr4:61035437-61035493 Template switch process: F1: L CAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGA 1 F3: 4 AACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATACCTGTTTCCTACAAGAAGAGCAATA R RF: AAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATACCTGTTTCCTACAAGAAGAGCAATA RR: TTCTTTAGTGTTACACTGACATGACCGAAGTAGTCGTTGAGATAAGTAGTTGAGGTTAGGGCTAAGAGGACACTTAAAACTTCACTATGGACAAAGGATGTTCTTCTCGTTAT F2: 3 TTCTTTAGTGTTACACTGACATGACCGAAGTAGTCGTTGAGATAAGTAGTTGAGGTT 2 Unidirectional alignment (log-probability: -139) TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTgattggagttgatgaatagagttgctgatgaagccagtacagtcacattgtgatttcttaactccaatcccgattctcctgtgaattttGAAGTGATAC TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTT-----------------------------------------------------------------------------------------GAAGTGATAC Template switch alignment (log-probability: -22.7) TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGA|TTGGAGTTGATGAATAGAGTTGCTGATGAAGCCAGTACAGTCACATTGTGATTTCTT|AACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATAC TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGA|TTGGAGTTGATGAATAGAGTTGCTGATGAAGCCAGTACAGTCACATTGTGATTTCTT|AACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATAC Gorilla > Chimp --------------- chr4:61035437-61035493 Template switch process: F1: L CAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGA 1 F3: 4 AACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATACCTGTTTCCTACAAGAAGAGCAATA R RF: AAGAAATCACAATGTGACTGTACTGGCTTCATCAGCAACTCTATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATACCTGTTTCCTACAAGAAGAGCAATA RR: TTCTTTAGTGTTACACTGACATGACCGAAGTAGTCGTTGAGATAAGTAGTTGAGGTTAGGGCTAAGAGGACACTTAAAACTTCACTATGGACAAAGGATGTTCTTCTCGTTAT F2: 3 TTCTTTAGTGTTACACTGACATGACCGAAGTAGTCGTTGAGATAAGTAGTTGAGGTT 2 Unidirectional alignment (log-probability: -139) TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGattggagttgatgaatagagttgctgatgaagccagtacagtcacattgtgatttcttaactccaatcccgattctcctgtgaattttgAAGTGATAC TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTG-----------------------------------------------------------------------------------------AAGTGATAC Template switch alignment (log-probability: -23.6) TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGA|TTGGAGTTGATGAATAGAGTTGCTGATGAAGCCAGTACAGTCACATTGTGATTTCTT|AACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATAC TATTCATCAACTCCAATCCCGATTCTCCTGTGAATTTTGA|TTGGAGTTGATGAATAGAGTTGCTGATGAAGCCAGTACAGTCACATTGTGATTTCTT|AACTCCAATCCCGATTCTCCTGTGAATTTTGAAGTGATAC ========== Event 2710 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAAATAGTTTTTGTCTTTAGCATACAA-------TAATTCATGAGTTTGAAATAATG Chimp: AAAAATAGTTTATGTCTTTAGCATACTATTGTATACTATTCATGAGTTTGAAATAATG ↑ 3 1 24 Gorilla: AAAAATAGTTTATGTCTTTAGCATACAA-------TAATTCATGAGTTTGAAATAATG Human: GAAAATAGTTTTTGTCTTTAGCATACAA-------TAATTCATGAGTTTGAAATAATG Cluster: [ ] Orangutan: GAAAATAGTTTATGTCTTTAGCATACAA-------TAATTCATGAGTTTGAAATAATG Gorilla > Chimp --------------- chr4:60744177-60744187 Template switch process: F1: L TAAGGAAATGATGATAAAAATAGTTTATGTCTTTAGCATAC 1 F3: 4 ATTCATGAGTTTGAAATAATGAAAAGTATTAAAATGATGC R RF: TGAGGAAATGATGATAAAAATAGTTTATGTCTTTAGCATACAATAATTCATGAGTTTGAAATAATGAAAAGTATTAAAATGATGC RR: ACTCCTTTACTACTATTTTTATCAAATACAGAAATCGTATGTTATTAAGTACTCAAACTTTATTACTTTTCATAATTTTACTACG F2: 3 TCATATGTTAT 2 Unidirectional alignment (log-probability: -37.6) aAGGAAATGATGATAAAAATAGTTTATGTCTTTAGCATACtATtgtatactATTCATGAGTTTGAAATAATGAAAAGTATTAAAATGATGC GAGGAAATGATGATAAAAATAGTTTATGTCTTTAGCATACAAT-------AATTCATGAGTTTGAAATAATGAAAAGTATTAAAATGATGC Template switch alignment (log-probability: -28.2) aAGGAAATGATGATAAAAATAGTTTATGTCTTTAGCATAC|TATTGTATaCT|ATTCATGAGTTTGAAATAATGAAAAGTATTAAAATGATGC GAGGAAATGATGATAAAAATAGTTTATGTCTTTAGCATAC|TATTGTATGCT|ATTCATGAGTTTGAAATAATGAAAAGTATTAAAATGATGC ========== Event 2711 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTGTAGGTCGTCTAACAATGATG-ACTTATCAATAAGAAAAGTATGggccaggc ↓ 3 1 2 4 Chimp: ATTTGTAGGTCGTCTAACAATGATGAAGTCATCATTAAGAAAAGTATGggccaggc Gorilla: ATTTGTAAGTCGTCTAACAATGATG-ACTTATCAATaaaaaaaGTATGggccaggc Human: ATTTGTAGGTCGTCTAACAATGATG-ACTTATCAATAAGAAAAGTATGggccaggc Cluster: [ ] Orangutan: ATTTGTAAGTCATCTAACAATGATG-ACTTATCAATAAGAAAAGTATGggccaggc Human > Chimp ------------- chr4:134165097-134165105 Template switch process: F1: L CAATATATTTATTGCAATTTGTAGGTCGTCTAACAATGATGA 1 F3: 4 TAAGAAAAGTATGGGCCAGGCACGGTGGCTCACACCTGTA R RF: CAATATATTTATTGCAATTTGTAGGTCGTCTAACAATGATGACTTATCAATAAGAAAAGTATGGGCCAGGCACGGTGGCTCACACCTGTA RR: GTTATATAAATAACGTTAAACATCCAGCAGATTGTTACTACTGAATAGTTATTCTTTTCATACCCGGTCCGTGCCACCGAGTGTGGACAT F2: 3 TACTACTGA 2 Unidirectional alignment (log-probability: -30.4) ATATATTTATTGCAATTTGTAGGTCGTCTAACAATGATGaAgTcATCAtTAAGAAAAGTATGGGCCAGGCACGGTGGCTCACACCTGTA ATATATTTATTGCAATTTGTAGGTCGTCTAACAATGATG-ACTTATCAATAAGAAAAGTATGGGCCAGGCACGGTGGCTCACACCTGTA Template switch alignment (log-probability: -16.4) ATATATTTATTGCAATTTGTAGGTCGTCTAACAATGATGA|AGTCATCAT|TAAGAAAAGTATGGGCCAGGCACGGTGGCTCACACCTGTA ATATATTTATTGCAATTTGTAGGTCGTCTAACAATGATGA|AGTCATCAT|TAAGAAAAGTATGGGCCAGGCACGGTGGCTCACACCTGTA ========== Event 2712 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AAGATCAGAATTTAAAAACAGTATCTTTTCTCTAGGTGGTACAATTAAAAACAACTGTCTTCATGCTTTTCTGAATTTCCAAATTTTATATAGTAAA--CGTACTTAATTTAGGAGGAAAATCCCAAATTaaaaaaaaTTCTTAAGTTCAAGAGTATAAGA------------TACTAACGGTTTCCATGTGAAGGGC Chimp: aaGATCAGAATTTAAAAACAGTATCTTTTCTCTAGGTGGTACAATTAAAAACAACTCTCTTCATGCTTTTCTGAATTTCCAAATTTTATATAATAAA--CGTACTTAATTTAGGAGGAAAATCCCAAATTaaaaaaaaTTCTTAAGTTCAAGAGTATAACTTGAACTTAAACCTTCACACGGTTTCCATGTGAAGCGC ↓ 3 2 1 4 Gorilla: aaGATCAGAATTTAAAAACAGTATCTTTTCTCTAGGCGGTACAATTAAAAACAACTGTCTTCATGCTTTTCTGAATTTCCAAATTTTATATAATAAA--CGTACTTAATTTAGGAGGAAAATCCCAAATTaaaaaaaaTTCTTAAGTTCAAGAGTATAAGA------------TACTAACGGTTTCCATGTGAAGGGC Human: AAGATCAGAATTTAAAAACAGTATCTTTTCTCTAGGTGGTACAATTAAAAACAACTGTCTTCATGCTTTTCTGAATTTCCAAATTTTATATAGTAAA--CGTACTTAATTTAGGAGGAAAATCCCAAATTaaaaaaaaTTCTTAAGTTCAAGAGTATAAGA------------TACTAACGGTTTCCATGTGAAGGGC Cluster: [ ] Orangutan: AAGATCAGAATTTAAAAACAGTATCTTTTCTCTAGGTGGTACAATTAAAAACAACTGTCTTCATGCTTTTCTGAATTTCCAGATTTTATATAATAAACATGTACTTAATTTAGGAGGAAAATCCTAAATTAA-AAAAATTCTTA----AAAGAGTATAAGA------------TACTAACGGTTTACATGCGAAGGGC Chimp > Gorilla --------------- chr4:195896170-195896175 Template switch process: F1: L AAATCCCAAATTAAAAAAAATTCTTAAGTTCAAGAGTATAA 1 F3: 4 AACGGTTTCCATGTGAAGGGCATGAGTCTACCAACCCATGG R RF: AGTATCTTTTCTCTAGGTGGTACAATTAAAAACAACTCTCTTCATGCTTTTCTGAATTTCCAAATTTTATATAATAAACGTACTTAATTTAGGAGGAAAATCCCAAATTAAAAAAAATTCTTAAGTTCAAGAGTATAACTTGAACTTAAACCTTCACACGGTTTCCATGTGAAGCGCATGAGTCTACCAACCCATGG RR: TCATAGAAAAGAGATCCACCATGTTAATTTTTGTTGAGAGAAGTACGAAAAGACTTAAAGGTTTAAAATATATTATTTGCATGAATTAAATCCTCCTTTTAGGGTTTAATTTTTTTTAAGAATTCAAGTTCTCATATTGAACTTGAATTTGGAAGTGTGCCAAAGGTACACTTCGCGTACTCAGATGGTTGGGTACC F2: 3 TCATAG 2 Unidirectional alignment (log-probability: -37.2) AATCCCAAATTAAAAAAAATTCTTAAGTTCAAGAGTATAA-------------------gatactaACGGTTTCCATGTGAAGgGCATGAGTCTACCAACCCATG AATCCCAAATTAAAAAAAATTCTTAAGTTCAAGAGTATAACTTGAACTTAAACCTTCAC-------ACGGTTTCCATGTGAAGCGCATGAGTCTACCAACCCATG Template switch alignment (log-probability: -27.5) AATCCCAAATTAAAAAAAATTCTTAAGTTCAAGAGTATAA|GATACT|aACGGTTTCCATGTGAAGgGCATGAGTCTACCAACCCATG AATCCCAAATTAAAAAAAATTCTTAAGTTCAAGAGTATAA|GATACT|CACGGTTTCCATGTGAAGCGCATGAGTCTACCAACCCATG ========== Event 2713 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CACTTGTGTTTCTGCTTGGCAGATTTACTTCAGGTAAATCTGAAGTACCTGATTTAAGG Chimp: CACTTGTGTTTCTGCTTGGCAGATTTACTTCAGGTAAATCTGAAGTACCTGATTTAAGG ↑ 3 12 4 Gorilla: CACTTGTGTTTCTGCTTGGCACATTTACCTGAGCCACCTCTGAAGTACCTGATTTAAGG ↓ 3 12 4 Human: CACTTGTGTTTCTGCTTGGCAGATTTACTTCAGGTAAATCTGAAGTACCTGATTTAAGG Cluster: [ ] Orangutan: CACTTGTGTTTCTGCTTGGCAGATTTACCTGAGCCACCTCTGAAATACCTGATTTAAGG Gorilla > Human --------------- chr4:71345620-71345627 Template switch process: F1: L GGACACCACAAATGTACACCCACTTGTGTTTCTGCTTGGCAGATTTACTT 1 F3: 4 TCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA R RF: GGACACCACAAATGTACACCCACTTGTGTTTCTGCTTGGCACATTTACCTGAGCCACCTCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA RR: CCTGTGGTGTTTACATGTGGGTGAACACAAAGACGAACCGTGTAAATGGACTCGGTGGAGACTTCATGGACTAAATTCCCGTACCGGTAATTCGTGGT F2: 3 AAATGGAC 2 Unidirectional alignment (log-probability: -40) AATGTACACCCACTTGTGTTTCTGCTTGGCAgATTTACtTcAGgtAaaTCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA AATGTACACCCACTTGTGTTTCTGCTTGGCACATTTACCTGAGCCACCTCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA Template switch alignment (log-probability: -28) AATGTACACCCACTTGTGTTTCTGCTTGGCAgATTTACtT|CAGGTAAA|TCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA AATGTACACCCACTTGTGTTTCTGCTTGGCACATTTACCT|CAGGTAAA|TCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA Gorilla > Chimp --------------- chr4:135237005-135237012 Template switch process: F1: L GGACACCACAAATGTACACCCACTTGTGTTTCTGCTTGGCAGATTTACTT 1 F3: 4 TCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA R RF: GGACACCACAAATGTACACCCACTTGTGTTTCTGCTTGGCACATTTACCTGAGCCACCTCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA RR: CCTGTGGTGTTTACATGTGGGTGAACACAAAGACGAACCGTGTAAATGGACTCGGTGGAGACTTCATGGACTAAATTCCCGTACCGGTAATTCGTGGT F2: 3 AAATGGAC 2 Unidirectional alignment (log-probability: -40) AATGTACACCCACTTGTGTTTCTGCTTGGCAgATTTACtTcAGgtAaaTCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA AATGTACACCCACTTGTGTTTCTGCTTGGCACATTTACCTGAGCCACCTCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA Template switch alignment (log-probability: -28) AATGTACACCCACTTGTGTTTCTGCTTGGCAgATTTACtT|CAGGTAAA|TCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA AATGTACACCCACTTGTGTTTCTGCTTGGCACATTTACCT|CAGGTAAA|TCTGAAGTACCTGATTTAAGGGCATGGCCATTAAGCACCA ========== Event 2714 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAATATCTTTCCCTAACATGGCAATAACCACAAAGCTTT-CTGCAGTTTATGTTACTAATAA ↓ 3 2 1 4 Chimp: AAAATATCTTTCCCTAACATGGCAATAACCACAACATTGCCATGCAGTTTATGTTACTAATAA Gorilla: AAAATATCTCTCCCCAACATGACAATAACCACAAAGCTTT-CTGCAGTTTATGTTACTAATAA Human: AAAATATCTTTCCCTAACATGGCAATAACCACAAAGCTTT-CTGCAGTTTATGTTACTAATAA Cluster: [ ] Orangutan: AAAATATCTTTCCCCAGCATGACAATAAACACAAAGCTTT-CTGCAGTT--TGTTACTAATAA Human > Chimp ------------- chr4:55962047-55962053 Template switch process: F1: L TGGAACAAAAATATCTTTCCCTAACATGGCAATAACCACAAC 1 F3: 4 TGCAGTTTATGTTACTAATAACTTTTATTCTGCTTTTATC R RF: TGGAACAAAAATATCTTTCCCTAACATGGCAATAACCACAAAGCTTTCTGCAGTTTATGTTACTAATAACTTTTATTCTGCTTTTATC RR: ACCTTGTTTTTATAGAAAGGGATTGTACCGTTATTGGTGTTTCGAAAGACGTCAAATACAATGATTATTGAAAATAAGACGAAAATAG F2: 3 ACCGTTA 2 Unidirectional alignment (log-probability: -31.5) GAACAAAAATATCTTTCCCTAACATGGCAATAACCACAAcattgccA------TGCAGTTTATGTTACTAATAACTTTTATTCTGCTTTTATC GAACAAAAATATCTTTCCCTAACATGGCAATAACCACAA-------AGCTTTCTGCAGTTTATGTTACTAATAACTTTTATTCTGCTTTTATC Template switch alignment (log-probability: -22.2) GAACAAAAATATCTTTCCCTAACATGGCAATAACCACAAc|ATTGCCA|TGCAGTTTATGTTACTAATAACTTTTATTCTGCTTTTATC GAACAAAAATATCTTTCCCTAACATGGCAATAACCACAAA|ATTGCCA|TGCAGTTTATGTTACTAATAACTTTTATTCTGCTTTTATC ========== Event 2715 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: cactctggaaacagatgaCAGTGCCACGCATGCTTGGA-CTGTGAGTCGCCTCCAGGTGCACCAGGAGGGGAGGAATCCAGGCTTTAGAGCCAACGTCTCTGGAGTACACTGAGGGCACTGCCTG Chimp: cactctggaaacagatgaCAGTGCCACGCATGCTTGGA-CTGTGAGTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTTTAGAGCCAACGTCTCTGGAGTACACTGAGGGCACTGCCTG ↓ 1 4 3 2 Gorilla: cactctggaaacagatgaCAGAGCCACGCGTGCTTGGACCTCCAGGTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTTTAGAGCCAACGTCTCTGGAGTACACTGAGGGCACTGCCTG Human: cactctggaaacagatgaCAGTGCCACGCATGCTTGGA-CTGTGAGTCGCCTCCAGGTGCACCAGGAGGGGAGGAATCCAGGCTTTAGAGCCAACGTCTCTGGAGTACACTGAGGGCACTGCCTG Cluster: [ ] Orangutan: CACTCTGGAAACAGATGACGGTGCCACGCATGCTTGGA-GTGTAAGTGGACTCCAGGTGCACCAGGAGGGGAAGAACCCAGGCTTTACAGCCAACATCTCTGGAGTACACTGAGGGCTCTGCCTG Chimp > Gorilla --------------- chr4:195471105-195471110 Template switch process: F1: L GTCACTCTGACAGCAGAGGGCACTCTGGAAACAGATGACAGAGCCACGCGTGCTTGGAC 1 F3: 4 GTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTT R RF: GTCACTCTGACAGCAGAGGGCACTCTGGAAACAGATGACAGTGCCACGCATGCTTGGACTGTGAGTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTTTAGAGCCAACGTCTCTGGAG RR: CAGTGAGACTGTCGTCTCCCGTGAGACCTTTGTCTACTGTCACGGTGCGTACGAACCTGACACTCACCGGAGGTCCACGTGGTCCTCCCCTCCTTGGGTCCGAAATCTCGGTTGCAGAGACCTC F2: 3 GACCTC 2 Unidirectional alignment (log-probability: -40.8) GCACTCTGGAAACAGATGACAGaGCCACGCgTGCTTGGACctccag-----GTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTT GCACTCTGGAAACAGATGACAGTGCCACGCATGCTTGGAC------TGTGAGTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTT Template switch alignment (log-probability: -28) GCACTCTGGAAACAGATGACAGaGCCACGCgTGCTTGGAC|CTCCAG|GTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTT GCACTCTGGAAACAGATGACAGTGCCACGCATGCTTGGAC|CTCCAG|GTGGCCTCCAGGTGCACCAGGAGGGGAGGAACCCAGGCTT ========== Event 2716 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTCTAGCTTTGCAGAGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATGT--GCAAATGTCTGATGCAGTGTCTGA ↑ 3 2 1 4 Chimp: GTTCTAGCTTTGCAGAGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATTG----GAATGTCTGATGCAGTGTCTGA Gorilla: GTTCTAGCTTTGCAGAGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATTG----GAATGTCTGATGCAGTGTCTGA Human: GTTCTAGCTTTGCAGAGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATGT--GCAAATGTCTGATGCAGTGTCTGA Cluster: [ ] Orangutan: GTTCTAGCTTTGCAGAGACTGCACTGACATTCAAAG-GTAGGTGAAAGGGGGAATGTGC--AAATGTCTGATGCAGTGTCTGA Chimp > Human ------------- chr4:115239470-115239474 Template switch process: F1: L GAGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAAT 1 F3: 4 AATGTCTGATGCAGTGTCTGATGCTGCCCATATTACTTGC R RF: GAGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATTGGAATGTCTGATGCAGTGTCTGATGCTGCCCATATTACTTGC RR: CTCTGACGTGACTGTAAGTTTCCAATCCACTTTCCCCCTTAACCTTACAGACTACGTCACAGACTACGACGGGTATAATGAACG F2: 3 ACGTG 2 Unidirectional alignment (log-probability: -25.8) AGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATgtGcaAATGTCTGATGCAGTGTCTGATGCTGCCCATATTACTTGC AGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAATTGG--AATGTCTGATGCAGTGTCTGATGCTGCCCATATTACTTGC Template switch alignment (log-probability: -15.9) AGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAAT|GTGCA|AATGTCTGATGCAGTGTCTGATGCTGCCCATATTACTTGC AGACTGCACTGACATTCAAAGGTTAGGTGAAAGGGGGAAT|GTGCA|AATGTCTGATGCAGTGTCTGATGCTGCCCATATTACTTGC ========== Event 2717 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAGACAGAAAAACACAATGTGAAG-CTTCATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCCAAACC Chimp: AT----AGAAAAACACAATGTGAAG-CTTCATTTTTGGTACCGTGCTAAGCTTCTCTAAACTTTCTCCCAAACC Gorilla: ATAGACAGAAAAACACAATGTTTGGTACACATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCCAAACC ↓ 1 4 3 2 Human: ATAGACAGAAAAACACAATGTGAAG-CTTCATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCCAAACC Cluster: [ ] Orangutan: ATAGACAGAAAAACACAATGTGAAG-CTTCATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCCAAACC Gorilla > Human --------------- chr4:76431513-76431519 Template switch process: F1: L CAGAAGGAAGGAGAGAAGTAATAGACAGAAAAACACAATGT 1 F3: 4 CATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCC R RF: CAGAAGGAAGGAGAGAAGTAATAGACAGAAAAACACAATGTTTGGTACACATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCC RR: GTCTTCCTTCCTCTCTTCATTATCTGTCTTTTTGTGTTACAAACCATGTGTAAAAACCATGACACGATTCGAAGAGATTTGAAAGAGGG F2: 3 TTCGAAG 2 Unidirectional alignment (log-probability: -28.2) AGAAGGAAGGAGAGAAGTAATAGACAGAAAAACACAATGTgaagcTT------CATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCC AGAAGGAAGGAGAGAAGTAATAGACAGAAAAACACAATGT-----TTGGTACACATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCC Template switch alignment (log-probability: -16.6) AGAAGGAAGGAGAGAAGTAATAGACAGAAAAACACAATGT|GAAGCTT|CATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCC AGAAGGAAGGAGAGAAGTAATAGACAGAAAAACACAATGT|GAAGCTT|CATTTTTGGTACTGTGCTAAGCTTCTCTAAACTTTCTCCC ========== Event 2718 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AACCCAGTCAAGATGGTGGAAAGACCT------------------------------AAGTGGCAAACTTAGGCCACTGGGCCCTTCCTGGT ↑ 1 4 3 2 Chimp: AACCCAGTCAAGATGGTGGAAGGACTT---------------GGTCTTGCCTGTCCCAGTAGGCAAACTTAGGCCACTGGGCCCTTCCTGGT Gorilla: AACCCAGTCAAGATGGTGGAAGGACTTGGTCTTGCCTGTCCC---------------AGTAGGCAAACTTAGGCCACTGGGCCCTTCCTGGT ↓ 1 4 3 2 Human: AACCCAGTCAAGATGGTGGAAAGACCT------------------------------AAGTGGCAAACTTAGGCCACTGGGCCCTTCCTGGT Cluster: [ ] Orangutan: AACCCAGTCAAGATGGTGGAAGGACTTGGTCTTGCCTGTCCC---------------AGTAGGCAAACTTAGGCCACTGGGCCCTTCCTGGT Chimp > Human ------------- chr4:113191669-113191674 Template switch process: F1: L GGCTCCCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAAGAC 1 F3: 4 GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT R RF: GGCTCCCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAGGACTTGGTCTTGCCTGTCCCAGTAGGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT RR: CCGAGGGTCCCTAGGATTCCTTGGGTCAGTTCTACCACCTTCCTGAACCAGAACGGACAGGGTCATCCGTTTGAATCCGGTGACCCGGGAAGGACCACCACATCTA F2: 3 TGAATC 2 Unidirectional alignment (log-probability: -35.3) CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAA------------------------AgacctaagtGGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAGGACTTGGTCTTGCCTGTCCCAGTA---------GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT Template switch alignment (log-probability: -22.1) CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAaGAC|CTAAGT|GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAGGAC|CTAAGT|GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT Gorilla > Human --------------- chr4:113191669-113191674 Template switch process: F1: L GGCTCCCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAAGAC 1 F3: 4 GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT R RF: GGCTCCCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAGGACTTGGTCTTGCCTGTCCCAGTAGGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT RR: CCGAGGGTCCCTAGGATTCCTTGGGTCAGTTCTACCACCTTCCTGAACCAGAACGGACAGGGTCATCCGTTTGAATCCGGTGACCCGGGAAGGACCACCACATCTA F2: 3 TGAATC 2 Unidirectional alignment (log-probability: -34.4) CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAaGACctaagT--------------------GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAGGAC-----TTGGTCTTGCCTGTCCCAGTAGGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT Template switch alignment (log-probability: -22.1) CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAaGAC|CTAAGT|GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT CCAGGGATCCTAAGGAACCCAGTCAAGATGGTGGAAGGAC|CTAAGT|GGCAAACTTAGGCCACTGGGCCCTTCCTGGTGGTGTAGAT ========== Event 2719 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: CACACGGGGTCTTGCCACTTTGAAGCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGC ↓ 13 24 ↑ 13 24 Chimp: CACACGGGGTCTTGCCACTTTAAAACTGGTTGTGCCCCATGCTTCAAACTGCCATCAACAGGGGGC ↓ 13 24 ↑ 13 24 Gorilla: CACACGGGGTCTTGCCACTTTGAAGCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGC Human: CACACGGGGTCTTGCCACTTTGAAGCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGC Cluster: [ ] Orangutan: Chimp > Human ------------- chr4:113010721-113010744 Template switch process: F1: L GACTGT-TTCAGGAATTAGACACACGGGGTCTTGCCACTTT 1 F3: 4 AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC R RF: GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTAAAACTGGTTGTGCCCCATGCTTCAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC RR: CTGACACAAGTCCTTAATCTGTGTGCCCCAGAACGGTGAAATTTTGACCAACACGGGGTACGAAGTTTGACGGTAGTTGTCCCCCGCGAATCATTGGTATTTTCG F2: 3 TTTTGACCAACACGGGGTACGAAG 2 Unidirectional alignment (log-probability: -67.1) GACTGT-TTCAGGAATTAGACACACGGGGTCTTGCCACTTT------------------------gaagcatggggcacaaccagttttAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTAAAACTGGTTGTGCCCCATGCTTC------------------------AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Template switch alignment (log-probability: -28.5) GACTGT-TTCAGGAATTAGACACACGGGGTCTTGCCACTTT|GAAGCATGGGGCACAACCAGTTTT|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT|GAAGCATGGGGCACAACCAGTTTT|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Human > Chimp ------------- chr4:53289619-53289642 Template switch process: F1: L GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT 1 F3: 4 AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC R RF: GACTGT-TTCAGGAATTAGACACACGGGGTCTTGCCACTTTGAAGCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC RR: CTGACA-AAGTCCTTAATCTGTGTGCCCCAGAACGGTGAAACTTCGTACCCCGTGTTGGTCAAAATTTGACGGTAGTTGTCCCCCGCGAATCATTGGTATTTTCG F2: 3 CTTCGTACCCCGTGTTGGTCAAAA 2 Unidirectional alignment (log-probability: -68.5) ACTGTgTTCAGGAATTAGACACACGGGGTCTTGCCACTTTaaaactggttgtgccccatgcttc------------------------AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ACTGT-TTCAGGAATTAGACACACGGGGTCTTGCCACTTT------------------------GAAGCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Template switch alignment (log-probability: -29.9) ACTGTgTTCAGGAATTAGACACACGGGGTCTTGCCACTTT|AAAACTGGTTGTGCCCCATGCTTC|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ACTGT-TTCAGGAATTAGACACACGGGGTCTTGCCACTTT|AAAACTGGTTGTGCCCCATGCTTC|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Gorilla > Chimp --------------- chr4:53289619-53289642 Template switch process: F1: L GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT 1 F3: 4 AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC R RF: GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTGAAGCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC RR: CTGACACAAGTCCTTAATCTGTGTGCCCCAGAACGGTGAAACTTCGTACCCCGTGTTGGTCAAAATTTGACGGTAGTTGTCCCCCGCGAATCATTGGTATTTTCG F2: 3 CTTCGTACCCCGTGTTGGTCAAAA 2 Unidirectional alignment (log-probability: -55.6) ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTaAAactggttgtgccccatGC----------------TTcAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTGAA----------------GCATGGGGCACAACCAGTTTTAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Template switch alignment (log-probability: -18.8) ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT|AAAACTGGTTGTGCCCCATGCTTC|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT|AAAACTGGTTGTGCCCCATGCTTC|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Chimp > Gorilla --------------- chr4:114931911-114931934 Template switch process: F1: L GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT 1 F3: 4 AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC R RF: GACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTAAAACTGGTTGTGCCCCATGCTTCAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC RR: CTGACACAAGTCCTTAATCTGTGTGCCCCAGAACGGTGAAATTTTGACCAACACGGGGTACGAAGTTTGACGGTAGTTGTCCCCCGCGAATCATTGGTATTTTCG F2: 3 TTTTGACCAACACGGGGTACGAAG 2 Unidirectional alignment (log-probability: -55.6) ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTgAA----------------GCatggggcacaaccagtTTtAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTTAAAACTGGTTGTGCCCCATGC----------------TTCAAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC Template switch alignment (log-probability: -18.8) ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT|GAAGCATGGGGCACAACCAGTTTT|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ACTGTGTTCAGGAATTAGACACACGGGGTCTTGCCACTTT|GAAGCATGGGGCACAACCAGTTTT|AAACTGCCATCAACAGGGGGCGCTTAGTAACCATAAAAGC ========== Event 2720 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTCCGCGGCCCGCACTGCTGAAGCCCAGCCCGGAGCCCCAAGCCCGGTACCT---------CCCGAGGCTACGCTGCCAGACTTCTTACCAAAGAGGC-GGGCTTCACTTGCCCCTGTGTTTCTCTCC Chimp: TTTCCGCGGCCCGCACTGCGGAAGCCCAGCCCGGAGCCCCAAGCCCGGTACCT---------CCCGAGGCTACGCTGCCAGACTTCTTACCAAAGAGGC-GGGCTTCACTTGCCCCTGTGTTTCTCTCC ↑ 3 2 1 4 Gorilla: TTTCCGCGGCCCGCACTGCTGAAGCCCAGCCCGGAGCCCCAAGCCCGGTTCCT---------CCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGCCCTGTGTTTCTTGCCCCTGTGTTTCTCTCC ↓ 3 2 1 4 Human: TTTCCGCGGCCCGCACTGCTGAAGCCCAGCCCGGAGCCCCAAGCCCGGTACCT---------CCCGAGGCTACGCTGCCAGACTTCTTACCAAAGAGGC-GGGCTTCACTTGCCCCTGTGTTTCTCTCC Cluster: [ ] Orangutan: TTTCCGCGGCCCGCACTGCTGAAGCCCAGCCCGGAGCCCCAAGCCCGGTTCCTCCCGCTGCTCCCGAGGCTACGCTGCCAGACTTCTTACCAAAGAGGC-GGGCTTCACTTGCCCCTGTGTTTCTCTCC Gorilla > Human --------------- chr4:182426236-182426243 Template switch process: F1: L ACCTCCCGAGGCTACGCTGCCAGACTTCTTACCAAAGAGGC 1 F3: 4 CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG R RF: TGAAGCCCAGCCCGGAGCCCCAAGCCCGGTTCCTCCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGCCCTGTGTTTCTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG RR: ACTTCGGGTCGGGCCTCGGGGTTCGGGCCAAGGAGGGCTCCGACGCGACGGTCTGAAGAATGGTTTCTCCGGGACACAAAGAACGGGGACACAAAGAGAGGGGCCAAAAGTGAATGCGAC F2: 3 ACTTCGGG 2 Unidirectional alignment (log-probability: -43.6) CCTCCCGAGGCTaCGCTGCCAGACTTCTTACCAAAGAGGCgggcttca---------CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG CCTCCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGC--------CCTGTGTTTCTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG Template switch alignment (log-probability: -27.8) CCTCCCGAGGCTaCGCTGCCAGACTTCTTACCAAAGAGGC|GGGCTTCA|CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG CCTCCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGC|GGGCTTCA|CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG Gorilla > Chimp --------------- chr4:186217636-186217643 Template switch process: F1: L ACCTCCCGAGGCTACGCTGCCAGACTTCTTACCAAAGAGGC 1 F3: 4 CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG R RF: TGAAGCCCAGCCCGGAGCCCCAAGCCCGGTTCCTCCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGCCCTGTGTTTCTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG RR: ACTTCGGGTCGGGCCTCGGGGTTCGGGCCAAGGAGGGCTCCGACGCGACGGTCTGAAGAATGGTTTCTCCGGGACACAAAGAACGGGGACACAAAGAGAGGGGCCAAAAGTGAATGCGAC F2: 3 ACTTCGGG 2 Unidirectional alignment (log-probability: -43.6) CCTCCCGAGGCTaCGCTGCCAGACTTCTTACCAAAGAGGCgggcttca---------CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG CCTCCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGC--------CCTGTGTTTCTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG Template switch alignment (log-probability: -27.8) CCTCCCGAGGCTaCGCTGCCAGACTTCTTACCAAAGAGGC|GGGCTTCA|CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG CCTCCCGAGGCTGCGCTGCCAGACTTCTTACCAAAGAGGC|GGGCTTCA|CTTGCCCCTGTGTTTCTCTCCCCGGTTTTCACTTACGCTG ========== Event 2721 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTT-------CCTAAAGTGTGTAGTCTGAGAAACCTGAATT Chimp: TAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTT-------CCTAAAGTGCGTAGTCTGAGAAACCTGAATT ↓ 13 24 ↑ 13 24 Gorilla: TAAGCTTTCTGGCTCCCTTTA-------GGAAACTACCTTCTCCCATTTTAAAGTGCATAGTCTGAGAAACCTGAATT ↓ 13 24 ↑ 13 24 Human: TAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTT-------CCTAAAGTGTGTAGTCTGAGAAACCTGAATT Cluster: [ ] Orangutan: TAAGCTTTCCGGCTTCCTTTA-------GGAAACTACCTTCTCCCATTTTAAAGTGCATAGTCTGAGAAACCTGAATT Gorilla > Human --------------- chr4:112807344-112807364 Template switch process: F1: L TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA 1 F3: 4 TAAAGTGTGTAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC R RF: TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAGGAAACTACCTTCTCCCATTTTAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC RR: AGTAATATAAACGGAACCGTATTCGAAAGACCGAGGGAAATCCTTTGATGGAAGAGGGTAAAATTTCACGTATCAGACTCTTTGGACTTAATAAGTCAAGTGAGGTTGAAG F2: 3 CCTTTGATGGAAGAGGGTAAA 2 Unidirectional alignment (log-probability: -63.1) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA---------------------aaatgggagaaggtagtttccTAAAGTGtgTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAGGAAACTACCTTCTCCCATTT---------------------TAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCAC Template switch alignment (log-probability: -29.7) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|AAATGGGAGAAGGTAGTTTCC|TAAAGTGtgTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|AAATGGGAGAAGGTAGTTTCC|TAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCAC Human > Gorilla --------------- chr4:114725101-114725121 Template switch process: F1: L TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA 1 F3: 4 TAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC R RF: TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTTCCTAAAGTGTGTAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC RR: AGTAATATAAACGGAACCGTATTCGAAAGACCGAGGGAAATTTTACCCTCTTCCATCAAAGGATTTCACACATCAGACTCTTTGGACTTAATAAGTCAAGTGAGGTTGAAG F2: 3 TTTACCCTCTTCCATCAAAGG 2 Unidirectional alignment (log-probability: -63.1) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA---------------------ggaaactaccttctcccatttTAAAGTGcaTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTTCC---------------------TAAAGTGTGTAGTCTGAGAAACCTGAATTATTCAGTTCAC Template switch alignment (log-probability: -29.7) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|GGAAACTACCTTCTCCCATTT|TAAAGTGcaTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|GGAAACTACCTTCTCCCATTT|TAAAGTGTGTAGTCTGAGAAACCTGAATTATTCAGTTCAC Gorilla > Chimp --------------- chr4:53082992-53083012 Template switch process: F1: L TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA 1 F3: 4 TAAAGTGCGTAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC R RF: TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAGGAAACTACCTTCTCCCATTTTAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC RR: AGTAATATAAACGGAACCGTATTCGAAAGACCGAGGGAAATCCTTTGATGGAAGAGGGTAAAATTTCACGTATCAGACTCTTTGGACTTAATAAGTCAAGTGAGGTTGAAG F2: 3 CCTTTGATGGAAGAGGGTAAA 2 Unidirectional alignment (log-probability: -57.5) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA---------------------aaatgggagaaggtagtttccTAAAGTGCgTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAGGAAACTACCTTCTCCCATTT---------------------TAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCAC Template switch alignment (log-probability: -24.1) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|AAATGGGAGAAGGTAGTTTCC|TAAAGTGCgTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|AAATGGGAGAAGGTAGTTTCC|TAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCAC Chimp > Gorilla --------------- chr4:114725101-114725121 Template switch process: F1: L TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA 1 F3: 4 TAAAGTGCATAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC R RF: TCATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTTCCTAAAGTGCGTAGTCTGAGAAACCTGAATTATTCAGTTCACTCCAACTTC RR: AGTAATATAAACGGAACCGTATTCGAAAGACCGAGGGAAATTTTACCCTCTTCCATCAAAGGATTTCACGCATCAGACTCTTTGGACTTAATAAGTCAAGTGAGGTTGAAG F2: 3 TTTACCCTCTTCCATCAAAGG 2 Unidirectional alignment (log-probability: -57.5) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA---------------------ggaaactaccttctcccatttTAAAGTGCaTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTAAAATGGGAGAAGGTAGTTTCC---------------------TAAAGTGCGTAGTCTGAGAAACCTGAATTATTCAGTTCAC Template switch alignment (log-probability: -24.1) CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|GGAAACTACCTTCTCCCATTT|TAAAGTGCaTAGTCTGAGAAACCTGAATTATTCAGTTCAC CATTATATTTGCCTTGGCATAAGCTTTCTGGCTCCCTTTA|GGAAACTACCTTCTCCCATTT|TAAAGTGCGTAGTCTGAGAAACCTGAATTATTCAGTTCAC ========== Event 2722 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CAGCTGCAGGGGAGAGAGGCACGC-------------TTGATTTCAGCTTGAGCTGAAATCAAGACACATGTATGCATCTTG Chimp: CAGCTGCAGGGGAGAGAGGCATGC-------------TTGATTTCAGCTTGAGCTGAAATCAAGACACATGTATGCATCTTG ↑ 4 1 3 2 Gorilla: CAGCTGCAGGGGAGAGAGGCACGC------------------------TCGAGCTGAAATCAAGACACATGTATGCATCTTG ↓ 4 1 3 2 Human: CAGCTGCAGGGGAGAGAGGCACGC-------------TTGATTTCAGCTTGAGCTGAAATCAAGACACATGTATGCATCTTG Cluster: [ ] Orangutan: TAGCTgcaggggagagaggcaggggagagaggcaCGC-----------TCGAGCTGAAATCAAGACACATGTCTGCATCTTG Gorilla > Human --------------- chr4:182309325-182309332 Template switch process: F1: L CCTGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACGCT 1 F3: 4 GCTTGAGCTGAAATCAAGACACATGTATGCATCTTGCTCTTTCT R RF: CCTGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACGCTCGAGCTGAAATCAAGACACATGTATGCATCTTGCTCTTTCT RR: GGACCAAAGACGGACACGTCGACGTCCCCTCTCTCCGTGCGAGCTCGACTTTAGTTCTGTGTACATACGTAGAACGAGAAAGA F2: 3 ACTTTAGT 2 Unidirectional alignment (log-probability: -32.2) TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACgcttgatttcaGCTtGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCAC-----------GCTCGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT Template switch alignment (log-probability: -22.4) TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACGCT|TGATTTCA|GCTtGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACGCT|TGATTTCA|GCTCGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT Gorilla > Chimp --------------- chr4:186101445-186101452 Template switch process: F1: L GCCCCTGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCATGCT 1 F3: 4 GCTTGAGCTGAAATCAAGACACATGTATGCATCTTGCTCTTTCT R RF: GCCCCTGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACGCTCGAGCTGAAATCAAGACACATGTATGCATCTTGCTCTTTCT RR: CGGGGACCAAAGACGGACACGTCGACGTCCCCTCTCTCCGTGCGAGCTCGACTTTAGTTCTGTGTACATACGTAGAACGAGAAAGA F2: 3 ACTTTAGT 2 Unidirectional alignment (log-probability: -37.8) TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCAtgcttgatttcaGCTtGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCA-----------CGCTCGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT Template switch alignment (log-probability: -28) TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCAtGCT|TGATTTCA|GCTtGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT TGGTTTCTGCCTGTGCAGCTGCAGGGGAGAGAGGCACGCT|TGATTTCA|GCTCGAGCTGAAATCAAGACACATGTATGCATCTTGCTCT ========== Event 2723 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TACCTGTGTTAAGACAGGTATCTTAACATGCATAGATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA ↑ 4 1 3 2 Chimp: TACCTGTGTTAAGACAGGTAT----------------CTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA Gorilla: TACCTGTGTTAAGACAGGTAT----------------CTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA ↓ 4 1 3 2 Human: TACCTGTGTTAAGACAGGTATCTTAACATGCATAGATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA Cluster: [ ] Orangutan: TACCTGTGTTAAGACAGGTAT----------------CTTAAATCAATCTAGGCATGGCTACCATTATTTCAATGCA Chimp > Human ------------- chr4:111241933-111241941 Template switch process: F1: L CTTTTCCCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAA 1 F3: 4 ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA R RF: CTTTTCCCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA RR: GAAAAGGGACTACACTGATAATGGACACAATTCTGTCCATAGAATTTAGTTAGATACGTACCGATGGTAATAAAGTGACGT F2: 3 GATACGTAC 2 Unidirectional alignment (log-probability: -33.9) CCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTaacatgcatagatcttAAATCAATCTATGCATGGCTACCATTATTTCACTG CCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTT----------------AAATCAATCTATGCATGGCTACCATTATTTCACTG Template switch alignment (log-probability: -16.5) CCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAA|CATGCATAG|ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTG CCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAA|CATGCATAG|ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTG Gorilla > Human --------------- chr4:111241933-111241941 Template switch process: F1: L CTTTTCCCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAA 1 F3: 4 ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA R RF: CTTTTCCCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTGCA RR: GAAAAGGGACTACACTGATAATGGACACAATTCTGTCCATAGAATTTAGTTAGATACGTACCGATGGTAATAAAGTGACGT F2: 3 GATACGTAC 2 Unidirectional alignment (log-probability: -33.9) CCTGATGTGACTATTACCTGTGTTAAGACAGGTatcttaacatgcatagATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTG CCTGATGTGACTATTACCTGTGTTAAGACAGGT----------------ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTG Template switch alignment (log-probability: -17) CCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAA|CATGCATAG|ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTG CCTGATGTGACTATTACCTGTGTTAAGACAGGTATCTTAA|CATGCATAG|ATCTTAAATCAATCTATGCATGGCTACCATTATTTCACTG ========== Event 2724 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCAAGACATCAAGTTTGATACTGGTCTCTAGACC--AGTATCGTAACATTGTTTTTAAAG Chimp: GCAAGACATCAAGTTTGATACTGGTCTCTAGACC--AGTATCGTAACATTGTTTTTAAAG ↑ 3 2 1 4 Gorilla: GCAAGACATCAAGTTTGATACTGGTCTCTAGAGGAAAAGATCGTAACATTGTTTTTAAAG ↓ 3 2 1 4 Human: GCAAGACATCAAGTTTGATACTGGTCTCTAGACC--AGTATCGTAACATTGTTTTTAAAG Cluster: [ ] Orangutan: GCAAGACATCAAGTTTGATACTGGTCTCTAGAGGAAAAGATCGTAACATTGTTTTTAATG Gorilla > Human --------------- chr4:111179042-111179046 Template switch process: F1: L TATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA 1 F3: 4 ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA R RF: TATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGAGGAAAAGATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA RR: ATATTGAGACGTTCTGTAGTTCAAACTATGACCAGAGATCTCCTTTTCTAGCATTGTAACAAAAATTTCTTTAAACTCTATTTATTAT F2: 3 TGACC 2 Unidirectional alignment (log-probability: -28.2) ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA-------ccagtATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGAGGAAAAG-----ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA Template switch alignment (log-probability: -16.4) ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA|CCAGT|ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA|CCAGT|ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA Gorilla > Chimp --------------- chr4:51438768-51438772 Template switch process: F1: L TATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA 1 F3: 4 ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA R RF: TATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGAGGAAAAGATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA RR: ATATTGAGACGTTCTGTAGTTCAAACTATGACCAGAGATCTCCTTTTCTAGCATTGTAACAAAAATTTCTTTAAACTCTATTTATTAT F2: 3 TGACC 2 Unidirectional alignment (log-probability: -28.2) ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA-------ccagtATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGAGGAAAAG-----ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA Template switch alignment (log-probability: -16.4) ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA|CCAGT|ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA ATAACTCTGCAAGACATCAAGTTTGATACTGGTCTCTAGA|CCAGT|ATCGTAACATTGTTTTTAAAGAAATTTGAGATAAATAATA ========== Event 2725 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGAAGAATAGGAAATGAGAGGTC-TGAATCTTCCAATTCAGACATATGGATTTGATGATGCT Chimp: AGAAGAATAGGAAATGAGAGGTC-TGAATCTTCCAATTCAGAC--CTGGATTTGATGATGCT Gorilla: AGAAGAATAGGAAATGAGAGGCCTTTTATCTTCCAATTCAGACATATGGATTTGATGATGCT ↓ 1 4 3 2 Human: AGAAGAATAGGAAATGAGAGGTC-TGAATCTTCCAATTCAGACATATGGATTTGATGATGCT Cluster: [ ] Orangutan: AGAAGAATAGGAAATGAGAGGCCTTTTATCTTCCAATTCAGACATATGGATTTGATGATGCT Gorilla > Human --------------- chr4:110013740-110013745 Template switch process: F1: L TTAATAGATTTTCTTTGTAAAGAAGAATAGGAAATGAGAGG 1 F3: 4 TCTTCCAATTCAGACATATGGATTTGATGATGCTTTACT R RF: TTAATAGCTTTTCTTTGTAAAGAAGAATAGGAAATGAGAGGCCTTTTATCTTCCAATTCAGACATATGGATTTGATGATGCTTTACT RR: AATTATCGAAAAGAAACATTTCTTCTTATCCTTTACTCTCCGGAAAATAGAAGGTTAAGTCTGTATACCTAAACTACTACGAAATGA F2: 3 AAGTCT 2 Unidirectional alignment (log-probability: -32.2) TAATAGaTTTTCTTTGTAAAGAAGAATAGGAAATGAGAGG-----TctgaATCTTCCAATTCAGACATATGGATTTGATGATGCTTTACT TAATAGCTTTTCTTTGTAAAGAAGAATAGGAAATGAGAGGCCTTTT----ATCTTCCAATTCAGACATATGGATTTGATGATGCTTTACT Template switch alignment (log-probability: -22) TAATAGaTTTTCTTTGTAAAGAAGAATAGGAAATGAGAGG|TCTGAA|TCTTCCAATTCAGACATATGGATTTGATGATGCTTTACT TAATAGCTTTTCTTTGTAAAGAAGAATAGGAAATGAGAGG|TCTGAA|TCTTCCAATTCAGACATATGGATTTGATGATGCTTTACT ========== Event 2726 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTCTCAAGCGCTTCTGGAGC-------------------TTTTCGTCACCAAAGGAACTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCCACTAGGCA Chimp: TTTCTCAAGCGCCTCTGGAGC-------------------TTTTCGTCACCAAAGGAACTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCCACTAGGCA Gorilla: TTTCTCAAGCGCTTCTGGAGC--------------------------------------TTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCCACTAGGCA ↓ 4 3 1 2 Human: TTTCTCAAGCGCTTCTGGAGC-------------------TTTTCGTCACCAAAGGAACTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCCACTAGGCA Cluster: [ ] Orangutan: TCTCTCAAGCGCTTCTGGAGCTTTTCGTCACCAAAGGAAC-------------------TTTCTGGAAAAAAATTCCTTTGGTGACTCTTCACCATCCACTAGGCA Gorilla > Human --------------- chr4:80207708-80207720 Template switch process: F1: L CTCACCTCCACACTTTTCCGTTTCTCAAGCGCTTCTGGAGCTT------------TTC 1 F3: 4 CTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCCA R RF: CTCACCTCCACACTTTTCCGTTTCTCAAGCGCTTCTGGAGCTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCCA RR: GAGTGGAGGTGTGAAAAGGCAAAGAGTTCGCGAAGACCTCGAAAGACCTTTTTTCAAGGAAACCACTGAGAAGTGGTAGGT F2: 3 AAGGAAACCACTG 2 Unidirectional alignment (log-probability: -38.2) TCCACACTTTTCCGTTTCTCAAGCGCTTCTGGAGcttttcgtcaccaaaggaaCTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCC TCCACACTTTTCCGTTTCTCAAGCGCTTCTGGAG-------------------CTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCC Template switch alignment (log-probability: -27.9) TCCACACTTTTCCGTTTCTCAAGCGCTTCTGGAGCTT------------TTC|GTCACCAAAGGAA|CTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCC TCCACACTTTTCCGTTTCTCAAGCGCTTCTGGAGCTTTCTGGAAAAAAGTTC|GTCACCAAAGGAA|CTTTCTGGAAAAAAGTTCCTTTGGTGACTCTTCACCATCC ========== Event 2727 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTACAGTCCGGTCTAAGTtttatttattcagcaagc Chimp: AAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTACAGTCCAGTCTAAGTtttatttattcagcaagc ↓ 3 21 4 Gorilla: AAGAGTTTAAGTAAGAATCTATTCTAGACTT---------------AGTCTAGAAT-----AAGTCCAGTCTAGGTtttatttattcagcaagc ↑ 3 21 4 Human: AAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTACAGTCCGGTCTAAGTtttatttattcagcaagc Cluster: [ ] Orangutan: Human > Gorilla --------------- chr4:91298805-91298815 Template switch process: F1: L CTACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT 1 F3: 4 AGTCCAGTCTAGGTTTTATTTATTCAGCAAGCATTTTACAAACATTTACTAT R RF: CTACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTACAGTCCGGTCTAAGTTTTATTTATTCAGCAAGCATTTTACAAACATTTACTAT RR: GATGTGACGATTCTCAAATTCATTCTTAGATAAGATCTGAACTGGAGTCTTTGGATTCATATATTACGAATGTCAGGCCAGATTCAAAATAAATAAGTCGTTCGTAAAATGTTTGTAAATGATA F2: 3 ATAAGATCTGA 2 Unidirectional alignment (log-probability: -49.2) TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT-------------------------------agtctagaataAGTCCaGTCTAgGTTTTATTTATTCAGCAAGCATTTTACA TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTAC-----------AGTCCGGTCTAAGTTTTATTTATTCAGCAAGCATTTTACA Template switch alignment (log-probability: -28.5) TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT|AGTCTAGAATA|AGTCCaGTCTAgGTTTTATTTATTCAGCAAGCATTTTACA TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT|AGTCTAGAATA|AGTCCGGTCTAAGTTTTATTTATTCAGCAAGCATTTTACA Chimp > Gorilla --------------- chr4:91298805-91298815 Template switch process: F1: L CTACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT 1 F3: 4 AGTCCAGTCTAGGTTTTATTTATTCAGCAAGCATTTTACA R RF: CTACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTACAGTCCAGTCTAAGTTTTATTTATTCAGCAAGCATTTTACA RR: GATGTGACGATTCTCAAATTCATTCTTAGATAAGATCTGAACTGGAGTCTTTGGATTCATATATTACGAATGTCAGGTCAGATTCAAAATAAATAAGTCGTTCGTAAAATGT F2: 3 ATAAGATCTGA 2 Unidirectional alignment (log-probability: -43.5) TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT-------------------------------agtctagaataAGTCCAGTCTAgGTTTTATTTATTCAGCAAGCATTTTACA TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTTGACCTCAGAAACCTAAGTATATAATGCTTAC-----------AGTCCAGTCTAAGTTTTATTTATTCAGCAAGCATTTTACA Template switch alignment (log-probability: -22.6) TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT|AGTCTAGAATA|AGTCCAGTCTAgGTTTTATTTATTCAGCAAGCATTTTACA TACACTGCTAAGAGTTTAAGTAAGAATCTATTCTAGACTT|AGTCTAGAATA|AGTCCAGTCTAAGTTTTATTTATTCAGCAAGCATTTTACA ========== Event 2728 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGAGATAGTCTTCTCACGGA---CGTTCAGCTCATCATAAGACAATCTGAAGTTCAATCAGTTTATAGGCTTCTCTAGTAATTA-CATAGCATGGGTTAGTCTACCCTTAGGCTCTATAACCA Chimp: GAGAGATAGTCTTCTCACGGA---CGTTCAGCTCATCATAAGACAATCTGCAGTTCAATCAGTTTATAGGCTTCTCTAGTAATTACAATAGCATGGGTTAGTCTACCCTTAGGCTCTATAACCA ↓ 1 4 3 2 Gorilla: GAGAGATAGTCTTCTCACGGAAGACTATCAGCTCATCATAAGACAATCTGCAGTTCAGTCAGTTTATAGGCTTCTCTAGTAATTACAATAGCATGGGTTAGTCTACCCTTAGGCTCTATAACCA ↑ 1 4 3 2 Human: GAGAGATAGTCTTCTCACGGA---CGTTCAGCTCATCATAAGACAATCTGAAGTTCAATCAGTTTATAGGCTTCTCTAGTAATTA-CATAGCATGGGTTAGTCTACCCTTAGGCTCTATAACCA Cluster: [ ] Orangutan: GAGAGATAGTCTTCTCATGGA---CGTTCAGCTCATCATAAGACAATCTGCAGTTCAATCCATTTATAGGCTTCTCTAGTAATTACAATAGCATGGGTTAGTCTACCCTTAGGCTCTATCACCA Human > Gorilla --------------- chr4:92309857-92309862 Template switch process: F1: L TTTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGA 1 F3: 4 TCAGCTCATCATAAGACAATCTGCAGTTCAGTCAGTTTAT R RF: TTTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGACGTTCAGCTCATCATAAGACAATCTGAAGTTCAATCAGTTTATAGGCTTCTCTAGTAATTACATAGCATGGGTTAGTCT RR: AAATCATTTATATTTATAAACTCTCTATCAGAAGAGTGCCTGCAAGTCGAGTAGTATTCTGTTAGACTTCAAGTTAGTCAAATATCCGAAGAGATCATTAATGTATCGTACCCAATCAGA F2: 3 ATCAGA 2 Unidirectional alignment (log-probability: -37.3) TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGgaaGACtaTCAGCTCATCATAAGACAATCTGcAGTTCAgTCAGTTTAT TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACG---GACGTTCAGCTCATCATAAGACAATCTGAAGTTCAATCAGTTTAT Template switch alignment (log-probability: -27.5) TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGA|AGACTA|TCAGCTCATCATAAGACAATCTGcAGTTCAgTCAGTTTAT TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGA|AGACTA|TCAGCTCATCATAAGACAATCTGAAGTTCAATCAGTTTAT Chimp > Gorilla --------------- chr4:92309857-92309862 Template switch process: F1: L TTTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGA 1 F3: 4 TCAGCTCATCATAAGACAATCTGCAGTTCAGTCAGTTTAT R RF: TTTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGACGTTCAGCTCATCATAAGACAATCTGCAGTTCAATCAGTTTATAGGCTTCTCTAGTAATTACAATAGCATGGGTTAGTCT RR: AAATCATTTATATTTATAAACTCTCTATCAGAAGAGTGCCTGCAAGTCGAGTAGTATTCTGTTAGACGTCAAGTTAGTCAAATATCCGAAGAGATCATTAATGTTATCGTACCCAATCAGA F2: 3 ATCAGA 2 Unidirectional alignment (log-probability: -31.8) TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGgaaGACtaTCAGCTCATCATAAGACAATCTGCAGTTCAgTCAGTTTAT TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACG---GACGTTCAGCTCATCATAAGACAATCTGCAGTTCAATCAGTTTAT Template switch alignment (log-probability: -22) TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGA|AGACTA|TCAGCTCATCATAAGACAATCTGCAGTTCAgTCAGTTTAT TTAGTAAATATAAATATTTGAGAGATAGTCTTCTCACGGA|AGACTA|TCAGCTCATCATAAGACAATCTGCAGTTCAATCAGTTTAT ========== Event 2729 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATTGCTTGCCCTGGCACTTGTG-CCCTTCACAATGCATTGAATATTTCCATTCATTTTTC Chimp: TTATTGCTTGCCCTGGCACTTGTG-CCCTTCACAATGCATTGAATATTTCCATTCATTTTTC ↓ 1 4 3 2 Gorilla: TTATTGCTTGCCCTGGCACTTCAATGCATTCACAATGCATTGAATATTTCCATTCATTTTTC ↑ 1 4 3 2 Human: TTATTGCTTGCCCTGGCACTTGTG-CCCTTCACAATGCATTGAATATTTCCATTCATTTTTC Cluster: [ ] Orangutan: TTATTGCTTGCCCTGGCACTTGTG-CCCTTCACAATGCATTGAATATTTCTGTTCATTTTTC Human > Gorilla --------------- chr4:111103651-111103657 Template switch process: F1: L TTTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT 1 F3: 4 TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT R RF: TTTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTTGTGCCCTTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT RR: AAAGATTCTTACATTGTTTAAATAACGAACGGGACCGTGAACACGGGAAGTGTTACGTAACTTATAAAGGTAAGTAAAAAGATATCA F2: 3 ACGTAAC 2 Unidirectional alignment (log-probability: -29.5) TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT-----CaatgcaTTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTTGTGCCC------TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT Template switch alignment (log-probability: -16.6) TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT|CAATGCA|TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT|CAATGCA|TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT Chimp > Gorilla --------------- chr4:111103651-111103657 Template switch process: F1: L TTTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT 1 F3: 4 TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT R RF: TTTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTTGTGCCCTTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT RR: AAAGATTCTTACATTGTTTAAATAACGAACGGGACCGTGAACACGGGAAGTGTTACGTAACTTATAAAGGTAAGTAAAAAGATATCA F2: 3 ACGTAAC 2 Unidirectional alignment (log-probability: -29.5) TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT-----CaatgcaTTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTTGTGCCC------TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT Template switch alignment (log-probability: -16.6) TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT|CAATGCA|TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT TTCTAAGAATGTAACAAATTTATTGCTTGCCCTGGCACTT|CAATGCA|TTCACAATGCATTGAATATTTCCATTCATTTTTCTATAGT ========== Event 2730 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTCATGAACAATGATGGTA----TTGTCTTATGTGAGTACACATGAGTGTatttacacaaat Chimp: CTTTCATGAACAATGATGGTA----TTGTCTTATGTGAGTACACATGAGTGTatttacacaaat ↓ 1 4 3 2 Gorilla: CTTTCATGAACAATGATGGTATGTGTACTCTTATGTGAGTACACATGAGTGTatttacacaaat ↑ 1 4 3 2 Human: CTTTCATGAACAATGATGGTA----TTGTCTTATGTGAGTACACATGAGTGTatttacacaaat Cluster: [ ] Orangutan: CTTTCATGAACAATGATGGTA----TTGTCTTATGTGAGTACACATGAGTGTatttacataaat Human > Gorilla --------------- chr4:92484697-92484702 Template switch process: F1: L GTGTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT 1 F3: 4 TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA R RF: GTGTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTATTGTCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA RR: CACACTTGAAAAGTTAGGTGGAAAGTACTTGTTACTACCATAACAGAATACACTCATGTGTACTCACATAAATGTGTTTACAAT F2: 3 CATGTG 2 Unidirectional alignment (log-probability: -26.4) GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTATgTGtacTCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT-TG---TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA Template switch alignment (log-probability: -16.5) GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT|GTGTAC|TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT|GTGTAC|TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA Chimp > Gorilla --------------- chr4:92484697-92484702 Template switch process: F1: L GTGTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT 1 F3: 4 TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA R RF: GTGTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTATTGTCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA RR: CACACTTGAAAAGTTAGGTGGAAAGTACTTGTTACTACCATAACAGAATACACTCATGTGTACTCACATAAATGTGTTTACAAT F2: 3 CATGTG 2 Unidirectional alignment (log-probability: -26.4) GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTATgTGtacTCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT-TG---TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA Template switch alignment (log-probability: -16.5) GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT|GTGTAC|TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA GTGAACTTTTCAATCCACCTTTCATGAACAATGATGGTAT|GTGTAC|TCTTATGTGAGTACACATGAGTGTATTTACACAAATGTTA ========== Event 2731 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTCTTCCCACTGCTAGCTAGTG------------------CCTCCATCTGGCCCACCCTTAGCACCTGTCCAG-TCTTGGGGTGGGGACAGGAGGGATTTAG Chimp: TTTCTTCCCACTGCTAGCTAGTG------------------CCTCCATCTGGCCCACCCTTAGCACCTGTCTAG-TCTTGGGGTGGGGACAGGAGGGATTTAG ↓ 1 3 4 2 Gorilla: TTTCTTCCCACTGCTAGCTAGCC------------------------------------CCAAGACTAGACAGGTGCTAAGGGTGGGGACAGGAGGGATTTAG ↑ 1 3 4 2 Human: TTTCTTCCCACTGCTAGCTAGTG------------------CCTCCATCTGGCCCACCCTTAGCACCTGTCCAG-TCTTGGGGTGGGGACAGGAGGGATTTAG Cluster: [ ] Orangutan: TTTCTTCCCACTGCTAACTAGTGCCTCCATCTGGCCCACCC------------------TTAGCACCTGTCTAG-TCTTGGGGTGGGGACAGGAGGGCTTTAG Human > Gorilla --------------- chr4:92925384-92925406 Template switch process: F1: L CCAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAG 1 F3: 4 GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC R RF: CCAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAGTGCCTCCATCTGGCCCACCCTTAGCACCTGTCCAGTCTTGGGGTGGGGACAGGAGGGATTTAGTTCTAGGCTTCAGTTTC RR: GGTCCTGACGGAGTACTGAGAAAGAAGGGTGACGATCGATCACGGAGGTAGACCGGGTGGGAATCGTGGACAGGTCAGAACCCCACCCCTGTCCTCCCTAAATCAAGATCCGAAGTCAAAG F2: 3 AATCGTGGACAGATCAGAACCCC 2 Unidirectional alignment (log-probability: -61.3) CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTA----------------------------------------GccccaagactagacaggtgctaaGGGTGGGGACAGGAGGGATTTAGTTCTAGGCTcCAGTTTC CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAGTGCCTCCATCTGGCCCACCCTTAGCACCTGTCCAGTCTTG-----------------------GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTTCAGTTTC Template switch alignment (log-probability: -29.7) CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAG|CCCCAAGACTaGACAGGTGCTAA|GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTcCAGTTTC CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAG|CCCCAAGACTGGACAGGTGCTAA|GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTTCAGTTTC Chimp > Gorilla --------------- chr4:92925384-92925406 Template switch process: F1: L CCAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAG 1 F3: 4 GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC R RF: CCAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAGTGCCTCCATCTGGCCCACCCTTAGCACCTGTCTAGTCTTGGGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC RR: GGTCCTGACGGAGTACTGAGAAAGAAGGGTGACGATCGATCACGGAGGTAGACCGGGTGGGAATCGTGGACAGATCAGAACCCCACCCCTGTCCTCCCTAAATCAAGATCCGAGGTCAAAG F2: 3 AATCGTGGACAGATCAGAACCCC 2 Unidirectional alignment (log-probability: -55.7) CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTA----------------------------------------GccccaagactagacaggtgctaaGGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAGTGCCTCCATCTGGCCCACCCTTAGCACCTGTCTAGTCTTG-----------------------GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC Template switch alignment (log-probability: -18.7) CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAG|CCCCAAGACTAGACAGGTGCTAA|GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC CAGGACTGCCTCATGACTCTTTCTTCCCACTGCTAGCTAG|CCCCAAGACTAGACAGGTGCTAA|GGGTGGGGACAGGAGGGATTTAGTTCTAGGCTCCAGTTTC ========== Event 2732 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAACCTAGTTGTGTAAATCAGTCTTGTAGAAGACAAAAGTTCAGATTGAGACA ↑ 1 3 4 2 Chimp: AAACCTAGTTGTGTAAATCAGACC--TACAAGACAAAAGTTCAGATTGAGACA Gorilla: AAACCTAGTTGTGTAAATCAGACC--TACAAGACAAAAGTTCAGATTGAGACA ↓ 1 3 4 2 Human: AAACCTAGTTGTGTAAATCAGTCTTGTAGAAGACAAAAGTTCAGATTGAGACA Cluster: [ ] Orangutan: AAGTCTAGTTGTGTAAATGAGACC--TACAAGACAAAAGTTCAGATTGAGATA Chimp > Human ------------- chr4:106607941-106607948 Template switch process: F1: L GCAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAG 1 F3: 4 AAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG R RF: GCAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAGACCTACAAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG RR: CGTTAAGGAGTTCGTTGGACTTTGGATCAACACATTTAGTCTGGATGTTCTGTTTTCAAGTCTAACTCTGTGATAATCCAATAGATC F2: 3 GATGTTCT 2 Unidirectional alignment (log-probability: -31.8) CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAGtCttgTAgAAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAGAC--CTACAAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG Template switch alignment (log-probability: -16.3) CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAG|TCTTGTAG|AAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAG|TCTTGTAG|AAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG Gorilla > Human --------------- chr4:106607941-106607948 Template switch process: F1: L GCAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAG 1 F3: 4 AAGACAAAAGTTCAGATTGAGACACTATTAGGTTATCTAG R RF: GCAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAGACCTACAAGACAAAAGTTCAGATTGAGACATTATTAGGTTATCTAG RR: CGTTAAGGAGTTCGTTGGACTTTGGATCAACACATTTAGTCTGGATGTTCTGTTTTCAAGTCTAACTCTGTAATAATCCAATAGATC F2: 3 GATGTTCT 2 Unidirectional alignment (log-probability: -35.9) CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAGtCttgTAgAAGACAAAAGTTCAGATTGAGACAcTATTAGGTTATCTAG CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAGAC--CTACAAGACAAAAGTTCAGATTGAGACATTATTAGGTTATCTAG Template switch alignment (log-probability: -22.3) CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAG|TCTTGTAG|AAGACAAAAGTTCAGATTGAGACAcTATTAGGTTATCTAG CAATTCCTCAAGCAACCTGAAACCTAGTTGTGTAAATCAG|TCTTGTAG|AAGACAAAAGTTCAGATTGAGACATTATTAGGTTATCTAG ========== Event 2733 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTATTTTCTCCTTCTCTGACATGGTCTTTAAC--------------CATGTCTCTGTTGGACACATCCATA ↑ 3 2 1 4 Chimp: TTATTTTCTCCTTCTCTGACATGGTCTTTAAC-------AGCCTTCTCTTTCTCTGTTGGACACATCCATA Gorilla: TTATTTTCTCCTTCTCTGACATGGTCTTTAACAGTCTTC-------TCTTTCTCTGTTGGACACATCCATA ↓ 3 2 1 4 Human: TTATTTTCTCCTTCTCTGACATGGTCTTTAAC--------------CATGTCTCTGTTGGACACATCCATA Cluster: [ ] Orangutan: TTATTTTCTCCTTCTCTGACATGGTCTTTAACAGCCTTC-------TCTTTCTCTGTTGGACACATCCATA Chimp > Human ------------- chr4:84377114-84377117 Template switch process: F1: L CCACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC 1 F3: 4 TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA R RF: CCACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAACAGCCTTCTCTTTCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA RR: GGTGGATCAAATAAAAGAGGAAGAGACTGTACCAGAAATTGTCGGAAGAGAAAGAGACAACCTGTGTAGGTATCTTTTCTGTCTTCCAGTGT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -27.5) CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAACcatg-----------TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC----AGCCTTCTCTTTCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA Template switch alignment (log-probability: -15.8) CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC|CATG|TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC|CATG|TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA Gorilla > Human --------------- chr4:84377114-84377117 Template switch process: F1: L CCACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC 1 F3: 4 TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA R RF: CCACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAACAGTCTTCTCTTTCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA RR: GGTGGATCAAATAAAAGAGGAAGAGACTGTACCAGAAATTGTCAGAAGAGAAAGAGACAACCTGTGTAGGTATCTTTTCTGTCTTCCAGTGT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -26.9) CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC-----------catgTCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAACAGTCTTCTCTT----TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA Template switch alignment (log-probability: -16.2) CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC|CATG|TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA CACCTAGTTTATTTTCTCCTTCTCTGACATGGTCTTTAAC|CATG|TCTCTGTTGGACACATCCATAGAAAAGACAGAAGGTCACA ========== Event 2734 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGAC---CAGAGCTGGAGGCAAGGTGGCTGAT ↓ 3 2 1 4 Chimp: TGCCCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAC----AACCTGTAGATCTGGAGGCAAGGTGGCTGAT ↑ 3 2 1 4 Gorilla: TGCCCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGAC---CAGAGCTGGAGGCAAGGTGGCTGAT Human: TGCCCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGAC---CAGAGCTGGAGGCAAGGTGGCTGAT Cluster: [ ] Orangutan: TGCCCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGAC---CAGAGCTGGAGGCAAGGTGTCTGAT Human > Chimp ------------- chr4:87601999-87602006 Template switch process: F1: L CCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA 1 F3: 4 AGATCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCAGAAC R RF: CCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGACCAGAGCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCAGAAC RR: GGTCACTCCGATAGTCTGTCCAACATCTAATTCCACTAGATTTAACCTGGTCTCGACCTCCGTTCCACCGACTAAGCTGAGGAGGGTCGTCTTG F2: 3 TGTCCAAC 2 Unidirectional alignment (log-probability: -37.6) CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA--------CaacctgtAGAtCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGACC-------AGAGCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA Template switch alignment (log-probability: -22.3) CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA|CAACCTGT|AGAtCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA|CAACCTGT|AGAGCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA Gorilla > Chimp --------------- chr4:87601999-87602006 Template switch process: F1: L CCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA 1 F3: 4 AGATCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCAGAAC R RF: CCAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGACCAGAGCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCAGAAC RR: GGTCACTCCGATAGTCTGTCCAACATCTAATTCCACTAGATTTAACCTGGTCTCGACCTCCGTTCCACCGACTAAGCTGAGGAGGGTCGTCTTG F2: 3 TGTCCAAC 2 Unidirectional alignment (log-probability: -36.3) CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAcA----ACCtgtAGAtCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTAAATTGGACC---AGAGCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA Template switch alignment (log-probability: -22.4) CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA|CAACCTGT|AGAtCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA CAGTGAGGCTATCAGACAGGTTGTAGATTAAGGTGATCTA|CAACCTGT|AGAGCTGGAGGCAAGGTGGCTGATTCGACTCCTCCCAGCA ========== Event 2735 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAACCTCAGAGGAGAAGCAGG-------CATTTGAGTGTCGCCTGAACCCCGAGGTCATC Chimp: TAACCTCAGAGGAGAAGCAGG-------CATTTGAGTGTCGCCTGAACCCCGAGGTCATC ↓ 1 3 4 2 Gorilla: TAACCTCAGAGGAGAAGCAGGCGACACTCAAATGAGTGTCGCCTGAACCCCGAGGTCATC ↑ 1 3 4 2 Human: TAACCTCAGAGGAGAAGCAGG-------CATTTGAGTGTCGCCTGAACCCCGAGGTCATC Cluster: [ ] Orangutan: TAACCTCAGAGAAGAAGCAGG-------CATTTGAGTGTCGCCTGAACCCCGAGGTCATC Human > Gorilla --------------- chr4:97448243-97448252 Template switch process: F1: L AAATAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGC 1 F3: 4 TGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA R RF: AAACAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGCATTTGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA RR: TTTGTTCATTCTCTACCATTATTGGAGTCTCCTCTTCGTCCGTAAACTCACAGCGGACTTGGGGCTCCAGTAGACGTGTCGTGAT F2: 3 AAACTCACAG 2 Unidirectional alignment (log-probability: -37.6) AtAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGcgacactCAaaTGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA ACAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGG-------CATTTGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA Template switch alignment (log-probability: -22.5) AtAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGC|GACACTCAAA|TGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA ACAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGC|GACACTCAAA|TGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA Chimp > Gorilla --------------- chr4:97448243-97448252 Template switch process: F1: L AAATAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGC 1 F3: 4 TGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA R RF: AAACAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGCATTTGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA RR: TTTGTTCATTCTCTACCATTATTGGAGTCTCCTCTTCGTCCGTAAACTCACAGCGGACTTGGGGCTCCAGTAGACGTGTCGTGAT F2: 3 AAACTCACAG 2 Unidirectional alignment (log-probability: -37.6) AtAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGcgacactCAaaTGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA ACAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGG-------CATTTGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA Template switch alignment (log-probability: -22.5) AtAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGC|GACACTCAAA|TGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA ACAAGTAAGAGATGGTAATAACCTCAGAGGAGAAGCAGGC|GACACTCAAA|TGAGTGTCGCCTGAACCCCGAGGTCATCTGCACAGCACTA ========== Event 2736 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCCAACACCTGGGCTAAATGAGGAAGTATCAAAAATACTTCCTCATTTAGC--------------- Chimp: CTCCAACACCTGGGCTAAATGAGGAAGTATTTTTGATACTTCCTCATTTAGC--------------- ↑ 3 1 2 4 Gorilla: CTCCAACACCTGGGCTAAATGAGGAAGTATCAAAAATACTTCCTCGTTTAGC--------------- Human: CTCCAACACCTGGGCTAAATGAGGAAGTATCAAAAATACTTCCTCATTTAGC--------------- Cluster: [ ] Orangutan: CTCCAACACCTGGGCTAAATGAGGAAGTATTTTTGATACTTCNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr4:87906117-87906132 Template switch process: F1: L CGTAGCTATGGCTCCAACACCTGGGCTAAATGAGGAAGTAT 1 F3: 4 TTTAGCCCAGGTGTTGGAGCCATAGCTAC R RF: CGTAGCTATGGCTCCAACACCTGGGCTAAATGAGGAAGTATCAAAAATACTTCCTCGTTTAGCCCAGGTGTTGGAGCCATAGCTAC RR: GCATCGATACCGAGGTTGTGGACCCGATTTACTCCTTCATAGTTTTTATGAAGGAGCAAATCGGGTCCACAACCTCGGTATCGATG F2: 3 ACTCCTTCATAGTTTT 2 Unidirectional alignment (log-probability: -33.6) GTAGCTATGGCTCCAACACCTGGGCTAAATGAGGAAGTAT-----ttttgATACTTCCTCaTTTAGCCCAGGTGTTGGAGCCATAGCTAC GTAGCTATGGCTCCAACACCTGGGCTAAATGAGGAAGTATCAAAA-----ATACTTCCTCGTTTAGCCCAGGTGTTGGAGCCATAGCTAC Template switch alignment (log-probability: -17.5) GTAGCTATGGCTCCAACACCTGGGCTAAATGAGGAAGTAT|TTTTGATACTTCCTCA|TTTAGCCCAGGTGTTGGAGCCATAGCTAC GTAGCTATGGCTCCAACACCTGGGCTAAATGAGGAAGTAT|TTTTGATACTTCCTCA|TTTAGCCCAGGTGTTGGAGCCATAGCTAC ========== Event 2737 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG----------GCCCTCCCTCCTGGCCATTTTCT Chimp: AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG----------GCCCTCCCTCCTGGCCATTTTCT ↓ 4 3 2 1 Gorilla: AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTGCAGATATCTGCAGCTCCCTCCTGGCCATTTTCT ↑ 4 3 2 1 Human: AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG----------GCCCTCCCTCCTGGCCATTTTCT Cluster: [ ] Orangutan: AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG----------GCCCTTCCTCCTGGCCATTTTCT Human > Gorilla --------------- chr4:98893976-98893983 Template switch process: F1: L TAACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG 1 F3: 4 TGCAG-------------------CTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAGCACAG R RF: TAACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTGGCCCTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAGCACAG RR: ATTGGAACAGACTACGTTAAACGTCAGTCTATAGACACGACCGGGAGGGAGGACCGGTAAAAGAAGAATCGTTTTTGTCGTGTC F2: 3 CTATAGAC 2 Unidirectional alignment (log-probability: -38) AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTGcagatatctgcaG--CTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG------------GCCCTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG Template switch alignment (log-probability: -27.6) AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG|CAGATATC|TGCAG-------------------CTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG|CAGATATC|TGCAGTCAGATATCTGTGCTGGCCCTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG Chimp > Gorilla --------------- chr4:98893976-98893983 Template switch process: F1: L TAACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG 1 F3: 4 TGCAG-------------------CTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAGCACAG R RF: TAACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTGGCCCTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAGCACAG RR: ATTGGAACAGACTACGTTAAACGTCAGTCTATAGACACGACCGGGAGGGAGGACCGGTAAAAGAAGAATCGTTTTTGTCGTGTC F2: 3 CTATAGAC 2 Unidirectional alignment (log-probability: -38) AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTGcagatatctgcaG--CTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG------------GCCCTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG Template switch alignment (log-probability: -27.6) AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG|CAGATATC|TGCAG-------------------CTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG AACCTTGTCTGATGCAATTTGCAGTCAGATATCTGTGCTG|CAGATATC|TGCAGTCAGATATCTGTGCTGGCCCTCCCTCCTGGCCATTTTCTTCTTAGCAAAAACAG ========== Event 2738 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AAACCACTGTCAATTACATTTT----------------------AAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAATTCCTACAACTGAGAAGTTTTTTCTAGGCTCCTAGCAAACAACACATGGACTACA ↓ 4 1 3 2 Chimp: AAACCACTGTCAATTACATTTT-----------AAACCTAGTTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAATTCCTACAACTGAGAAGTTTTTTCCAGGCTCCTAGCAAACAACACATGGACTACA Gorilla: AAACCACTGTCAATTACATTTTAAACCTAGTTT-----------AAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAATTCCTACAACTGAGAAGTTTTTTCCAGGCTCCTAGCAAACAACACACGGACTACA ↑ 4 1 3 2 Human: AAACCACTGTCAATTACATTTT----------------------AAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAATTCCTACAACTGAGAAGTTTTTTCTAGGCTCCTAGCAAACAACACATGGACTACA Cluster: [ ] Orangutan: AAACCACTGTCAATTATATTTTAAACCTAGTTT-----------AAACAGGCTGCTGTGGACACATTCATACAAAGAGACAAACTTCCTACAACTGAGAAGTTTTTTCCAGGCTCCTAGAAAACAACACATGAACTACA Human > Chimp ------------- chr4:105113859-105113862 Template switch process: F1: L CAACAACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAAC 1 F3: 4 TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAA R RF: CAACAACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAATTCCTACAACTGAGAAGTTTTTTCTAGGCTCCTAG RR: GTTGTTGACGATGTTCCTCTTTGGTGACAGTTAATGTAAAATTTGTCCGACGACACCTGTGTAAGTATTTTTCTCTGTTTTAAGGATGTTGACTCTTCAAAAAAGATCCGAGGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -26.7) ACTGCTACAAGGAGAAACCACTGTCAATTACATtttaaacctagTTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA ACTGCTACAAGGAGAAACCACTGTCAATTACAT-----------TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA Template switch alignment (log-probability: -15.9) ACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAAC|CTAG|TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA ACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAAC|CTAG|TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA Human > Gorilla --------------- chr4:104953402-104953405 Template switch process: F1: L CAACAACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAAC 1 F3: 4 TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAA R RF: CAACAACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACAAAATTCCTACAACTGAGAAGTTTTTTCTAGGCTCCTAG RR: GTTGTTGACGATGTTCCTCTTTGGTGACAGTTAATGTAAAATTTGTCCGACGACACCTGTGTAAGTATTTTTCTCTGTTTTAAGGATGTTGACTCTTCAAAAAAGATCCGAGGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -26.7) ACTGCTACAAGGAGAAACCACTGTCAATTACATTttaaacctagtTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA ACTGCTACAAGGAGAAACCACTGTCAATTACATT-----------TTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA Template switch alignment (log-probability: -16.4) ACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAAC|CTAG|TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA ACTGCTACAAGGAGAAACCACTGTCAATTACATTTTAAAC|CTAG|TTTAAACAGGCTGCTGTGGACACATTCATAAAAAGAGACA ========== Event 2739 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGCAACAT-------------ATAATAAGGGTACCTCACCGAGGCAGGTCTAATCCCAGATTTC ↓ 3 2 1 4 Chimp: AGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGCTTGAT---------------------AGTAC-TAAC--CCTCAGGTCTAATCCCAGATTTC Gorilla: AGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGCAACAT--------ATAAG--------GGTACCTCAACGAGGCAGATCTAATCCCAGATTTC Human: AGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGCAACAT-------------ATAATAAGGGTACCTCACCGAGGCAGGTCTAATCCCAGATTTC Cluster: [ ] Orangutan: AGTGAACCTTCTAAAGCTGGTTAGTACTCTCAAGCAGCAACATATAATAAA-------------GGTACCTCAACGAGGCAGGTCTAACCCCAGATTTC Human > Chimp ------------- chr4:102843913-102843926 Template switch process: F1: L GACAGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGC 1 F3: 4 CCT--------CAGGTCTAATCCCAGATTTCTTCTCAGATATCTAGTACAG R RF: GACAGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGCAACATATAATAAGGGTACCTCACCGAGGCAGGTCTAATCCCAGATTTCTTCTCAGATATCTAGTACAG RR: CTGTCACTTGGAAGATTTCGACCAATCATGATAGTTCGTCGTTGTATATTATTCCCATGGAGTGGCTCCGTCCAGATTAGGGTCTAAAGAAGAGTCTATAGATCATGTC F2: 3 CAATCATGATAGTT 2 Unidirectional alignment (log-probability: -47) ACAGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGC----------------------------ttgatagtactaaccctCAGGTCTAATCCCAGATTTCTTCTCAGATATCTAGTA ACAGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGCAACATATAATAAGGGTACCTCACCGAGG-----------------CAGGTCTAATCCCAGATTTCTTCTCAGATATCTAGTA Template switch alignment (log-probability: -27.7) ACAGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGC|TTGATAGTACTAAC|CCT--------CAGGTCTAATCCCAGATTTCTTCTCAGATATCTAGTA ACAGTGAACCTTCTAAAGCTGGTTAGTACTATCAAGCAGC|TTGATAGTACTAAC|CCTCACCGAGGCAGGTCTAATCCCAGATTTCTTCTCAGATATCTAGTA ========== Event 2740 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ----------CAGCTTACCATGCTAGCTGAGAGGAGGCAGGGAGGTGAATCAGAAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGATACAGCATTTGGGAGGGATTCCTAAAAAC Chimp: -CATGGTGGGTAGCTTACCATGCTAGCTGAGAGGAGGCAGGGAGGTGAATCAGGAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACACAGCATTTGGGAGGGATTCCTAAAAAC ↑ 3 2 1 4 Gorilla: G---------TAGCTTACCATGCTAGCTGAGAGGAGGCAGGGAGGTGAATCAGGAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACAC-CCTCTTGGGAGGGATTCCTAAAAAC ↓ 3 2 1 4 Human: ----------CAGCTTACCATGCTAGCTGAGAGGAGGCAGGGAGGTGAATCAGAAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGATACAGCATTTGGGAGGGATTCCTAAAAAC Cluster: [ ] Orangutan: G---------TAGCTTACCATGCTAGCTGAGAGGAGGCAGGGAGGTGACTCAGGAGATCCAGGCGAAGCACTATCAAGGACAGACTCTTGACACAGCATTTGGGAGGGATTCCTAAAAAC Gorilla > Human --------------- chr4:100997365-100997369 Template switch process: F1: L CAGAAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGATAC 1 F3: 4 TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA R RF: ATGCTAGCTGAGAGGAGGCAGGGAGGTGAATCAGGAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACACCCTCTTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA RR: TACGATCGACTCTCCTCCGTCCCTCCACTTAGTCCTCTAGGTCCGTTTCGTGATAGTTCTTGTCCGAGAACTGTGGGAGAACCCTCCCTAAGGATTTTTGACAAATCCTTCAGAATAAT F2: 3 TACGA 2 Unidirectional alignment (log-probability: -38) AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGA-------TacagcattTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACACCCTCT--------TGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA Template switch alignment (log-probability: -27.5) AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGAtAC|AGCAT|TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACAC|AGCAT|TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA Gorilla > Chimp --------------- chr4:102894553-102894557 Template switch process: F1: L GAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACAC 1 F3: 4 TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA R RF: ATGCTAGCTGAGAGGAGGCAGGGAGGTGAATCAGGAGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACACCCTCTTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA RR: TACGATCGACTCTCCTCCGTCCCTCCACTTAGTCCTCTAGGTCCGTTTCGTGATAGTTCTTGTCCGAGAACTGTGGGAGAACCCTCCCTAAGGATTTTTGACAAATCCTTCAGAATAAT F2: 3 TACGA 2 Unidirectional alignment (log-probability: -28) AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACA----CagcatTTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACACCCTC-----TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA Template switch alignment (log-probability: -16.4) AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACAC|AGCAT|TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA AGATCCAGGCAAAGCACTATCAAGAACAGGCTCTTGACAC|AGCAT|TTGGGAGGGATTCCTAAAAACTGTTTAGGAAGTCTTATTA ========== Event 2741 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAACTGCGTGGGTGCTCTGGCGACAT-TGTTTGCACTGTTTATACAACCAGACAGCGTTTTAGACTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCT ↓ 1 4 3 2 Chimp: CAAACTGCGTGGGTGCTCTGGTGACATTAGTTTGGA-------CAC---------------GAATATAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCT ↑ 1 4 3 2 Gorilla: CAAACTGCGTGGGTGCTCTGGCGACAT-TGTTTGCACTGTTTATACAACCAGACAGCGTTTTAGACTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCT Human: CAAACTGCGTGGGTGCTCTGGCGACAT-TGTTTGCACTGTTTATACAACCAGACAGCGTTTTAGACTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCT Cluster: [ ] Orangutan: CAAACTGCGTGGGTGCTCTGGCGACAT-TGTTTGCACTGTTTATACAACCAGACAGAGTTTCAGACTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCT Human > Chimp ------------- chr4:94632363-94632377 Template switch process: F1: L ATTAAGGTTCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGTGACATT 1 F3: 4 ATAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTCC R RF: ATTCAGGTTCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGCGACATTGTTTGCACTGTTTATACAACCAGACAGCGTTTTAGACTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTCC RR: TAAGTCCAAGACTTCCTTACGTTTGACGCACCCACGAGACCGCTGTAACAAACGTGACAAATATGTTGGTCTGTCGCAAAATCTGATTTAAGCACAGGTTTGATTGTGCGTGCCCTTGTCCGAGG F2: 3 TAAGCACAGGTTTGA 2 Unidirectional alignment (log-probability: -56.4) TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGtGACATTaGTTTG-----------------------------GACacgaataTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGCGACATT-GTTTGCACTGTTTATACAACCAGACAGCGTTTTAGAC-------TAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC Template switch alignment (log-probability: -35.3) TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGtGACATT|AGTTTGGACACGAAT|aTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGCGACATT|AGTTTGGACACGAAT|CTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC Gorilla > Chimp --------------- chr4:94632363-94632377 Template switch process: F1: L ATTAAGGTTCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGTGACATT 1 F3: 4 ATAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTCC R RF: ATTCAGGTTCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGCGACATTGTTTGCACTGTTTATACAACCAGACAGCGTTTTAGACTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTCC RR: TAAGTCCAAGACTTCCTTACGTTTGACGCACCCACGAGACCGCTGTAACAAACGTGACAAATATGTTGGTCTGTCGCAAAATCTGATTTAAGCACAGGTTTGATTGTGCGTGCCCTTGTCCGAGG F2: 3 TAAGCACAGGTTTGA 2 Unidirectional alignment (log-probability: -54.6) TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGtGACATTaGTTTG-----------------------------GACacgaataTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGCGACATT-GTTTGCACTGTTTATACAACCAGACAGCGTTTTAGAC-------TAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC Template switch alignment (log-probability: -34.4) TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGtGACATT|AGTTTGGACACGAAT|aTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC TCTGAAGGAATGCAAACTGCGTGGGTGCTCTGGCGACATT|AGTTTGGACACGAAT|CTAAATTCGTGTCCAAACTAACACGCACGGGAACAGGCTC ========== Event 2742 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTCAGCACCTGCCAAGCTGCCT---ACTATCTAAAAGGAGATGTACACT Chimp: TCTCAGCACCTGCCAAGCTGCCT---ACTATCTAAAAGGAGATGTACACT ↓ 3 1 24 Gorilla: TCTCAGCACCTGCCAAGCTGCCAGTAGGCATCTAAAAGGAGATGTACACT ↑ 3 1 24 Human: TCTCAGCACCTGCCAAGCTGCCT---ACTATCTAAAAGGAGATGTACACT Cluster: [ ] Orangutan: TCTCAGCACCTGCCAAGCTGCCT---ACTATCTAAAAGGAGATGTACTCT Human > Gorilla --------------- chr4:99028534-99028540 Template switch process: F1: L GAGCAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC 1 F3: 4 ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT R RF: AAGGAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCCTACTATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT RR: TTCCTCTTTTTTATGATAAAGAGTCGTGGACGGTTCGACGGATGATAGATTTTCCTCTACATGTGAAACTGGATGTAATGACTCA F2: 3 CGGATGA 2 Unidirectional alignment (log-probability: -41.9) AGcAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCcagtaggC----ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT AGGAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGC-------CTACTATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT Template switch alignment (log-probability: -27.7) AGcAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC|AGTAGGC|ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT AGGAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC|AGTAGGC|ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT Chimp > Gorilla --------------- chr4:99028534-99028540 Template switch process: F1: L GAGCAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC 1 F3: 4 ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT R RF: GAGGAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCCTACTATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT RR: CTCCTCTTTTTTATGATAAAGAGTCGTGGACGGTTCGACGGATGATAGATTTTCCTCTACATGTGAAACTGGATGTAATGACTCA F2: 3 CGGATGA 2 Unidirectional alignment (log-probability: -36.4) AGcAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC----agtaggcATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT AGGAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCCTACT-------ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT Template switch alignment (log-probability: -22.1) AGcAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC|AGTAGGC|ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT AGGAGAAAAAATACTATTTCTCAGCACCTGCCAAGCTGCC|AGTAGGC|ATCTAAAAGGAGATGTACACTTTGACCTACATTACTGAGT ========== Event 2743 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ---TAAGTTACATGGATACAT------AGACTAACAAATGCATAAGTGTATGcacacacaca------cacacacacacacCTGTCAGTCTATCTCtatgtatcatatatagaa Chimp: ---TAAGTTACATGGATACAT------AGACTAACAAATGCATAAGTGTATGcacacacaca----------cacacacacCTGTCAGTCTATCTCTATGTATCCtatatagaa ↓ 1 4 3 2 Gorilla: ---TAAGTTACATGGATACATAGAGATAGACTGACAAATGCATAAGTGTATGcacacacaca--------cacacacacacCTGTCAGTCTATCTCtatgtatcatatatagaa ↑ 1 4 3 2 Human: ---TAAGTTACATGGATACAT------AGACTAACAAATGCATAAGTGTATGcacacacaca------cacacacacacacCTGTCAGTCTATCTCtatgtatcatatatagaa Cluster: [ ] Orangutan: ATATAAGTTACATGGATACATAGAGATAGACTGACAAATGCATAAGTGTATGcacacacacacacaca--cacacacacacCTGTCAGT------CTATGTATCatatatagaa Human > Gorilla --------------- chr4:99441306-99441314 Template switch process: F1: L ATTCATAAGTAGAAAATCATACATAAGTTACATGGATACATAGA 1 F3: 4 ACAAATGCATAAGTGTATGCACACACACACACACACAC R RF: ATTCATAAGTAGAAAATCATACATAAGTTACATGGATACATAGACTAACAAATGCATAAGTGTATGCACACACACACACACACACACACCTGTCAGTCTATC RR: TAAGTATTCATCTTTTAGTATGTATTCAATGTACCTATGTATCTGATTGTTTACGTATTCACATACGTGTGTGTGTGTGTGTGTGTGTGGACAGTCAGATAG F2: 3 GTCAGATAG 2 Unidirectional alignment (log-probability: -31.9) ATAAGTAGAAAATCATACATAAGTTACATGGATACatagagATAGACTgACAAATGCATAAGTGTATGCACACACACACACACACAC-- ATAAGTAGAAAATCATACATAAGTTACATGGATAC------ATAGACTAACAAATGCATAAGTGTATGCACACACACACACACACACAC Template switch alignment (log-probability: -16.9) ATAAGTAGAAAATCATACATAAGTTACATGGATACATAGA|GATAGACTG|ACAAATGCATAAGTGTATGCACACACACACACACACAC ATAAGTAGAAAATCATACATAAGTTACATGGATACATAGA|GATAGACTG|ACAAATGCATAAGTGTATGCACACACACACACACACAC Chimp > Gorilla --------------- chr4:99441306-99441314 Template switch process: F1: L ATTCATAAGTAGAAAATCATACATAAGTTACATGGATACATAGA 1 F3: 4 ACAAATGCATAAGTGTATGCACACACACACACACACACAC R RF: ATTCATAAGTAGAAAATCATACATAAGTTACATGGATACATAGACTAACAAATGCATAAGTGTATGCACACACACACACACACACCTGTCAGTCTATC RR: TAAGTATTCATCTTTTAGTATGTATTCAATGTACCTATGTATCTGATTGTTTACGTATTCACATACGTGTGTGTGTGTGTGTGTGGACAGTCAGATAG F2: 3 GTCAGATAG 2 Unidirectional alignment (log-probability: -34.7) ATAAGTAGAAAATCATACATAAGTTACATGGATACatagagATAGACTgACAAATGCATAAGTGTATGCACACACACACACACACACac ATAAGTAGAAAATCATACATAAGTTACATGGATAC------ATAGACTAACAAATGCATAAGTGTATGCACACACACACACACACAC-- Template switch alignment (log-probability: -26.5) ATAAGTAGAAAATCATACATAAGTTACATGGATACATAGA|GATAGACTG|ACAAATGCATAAGTGTATGCACACACACACACACACAcaC ATAAGTAGAAAATCATACATAAGTTACATGGATACATAGA|GATAGACTG|ACAAATGCATAAGTGTATGCACACACACACACACACA--C ========== Event 2744 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTTCCTTTCTGTCATGCCATGGACATTGCTCATGGAACATTGGTAAAAATAT ↑ 31 2 4 Chimp: AGTTCCTTTCTGTCATGCCATATCCCATGCTCGTGGAACATTGGTAAAAATAT Gorilla: AGTTCCCTTCTGTCATGCCATATCCCATGCTCGTGGAACATTGGTAAAAATAT Human: AGTTCCTTTCTGTCATGCCATGGACATTGCTCATGGAACATTGGTAAAAATAT Cluster: [ ] Orangutan: AGCTCCTTTCTGTCATGCCATATCCCATTCTCGTGGAACATTGGTAAAAATAT Chimp > Human ------------- chr4:96570166-96570171 Template switch process: F1: L ACGATTTTTTTTAGCGTGCCAGTTCCTTTCTGTCATGCCAT 1 F3: 4 TGCTCATGGAACATTGGTAAAAATATCATTAAGATGCAAGTTTTAG R RF: ACGATTTTTTTTAGCGTGCCAGTTCCTTTCTGTCATGCCATATCCCATGCTCGTGGAACATTGGTAAAAATATCATTAAGATGCAAGTTTTAA RR: TGCTAAAAAAAATCGCACGGTCAAGGAAAGACAGTACGGTATAGGGTACGAGCACCTTGTAACCATTTTTATAGTAATTCTACGTTCAAAATT F2: 3 TACAGG 2 Unidirectional alignment (log-probability: -53.2) CGATTTTTTTTAGCGTGCCAGTTCCTTTCTGTCATGCCATggacAT----TGCTCaTGGAACATTGGTAAAAATATCATTAAGATGCaag CGATTTTTTTTAGCGTGCCAGTTCCTTTCTGTCATGCCAT----ATCCCATGCTCGTGGAACATTGGTAAAAATATCATTAAGATGC--- Template switch alignment (log-probability: -34.1) CGATTTTTTTTAGCGTGCCAGTTCCTTTCTGTCATGCCAT|GGAcAT|TGCTCaTGGAACATTGGTAAAAATATCATTAAGATGCAAG CGATTTTTTTTAGCGTGCCAGTTCCTTTCTGTCATGCCAT|GGATAT|TGCTCGTGGAACATTGGTAAAAATATCATTAAGATGCAAG ========== Event 2745 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CACATCTTAAAATGAGCTGAA--------------------------------TGTAGGCAGGATGAATGAAGTAAAAACA Chimp: CACATCTTAAAATGAGCTGAA-----------------TGCCTACTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACA ↑ 1 4 3 2 Gorilla: CACATCTTAAAATGAGCTGAAGGGTGTCACTTTCAACA---------------AGTAGGCAGGATGAATGAAGTAAAAACA Human: CACATCTTAAAATGAGCTGAA--------------------------------TGTAGGCAGGATGAATGAAGTAAAAACA Cluster: [ ] Orangutan: CACATCTTAAAATGAGCTGAAGGGTGTCACTTTCAACA---------------AGTAGGCAGGGTGAATGAAGTAAAAACA Gorilla > Chimp --------------- chr4:98368498-98368503 Template switch process: F1: L AGACAAATGCATATAAAAGTCACATCTTAAAATGAGCTGAA 1 F3: 4 CTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACACTACCCCACATA R RF: AGACAAATGCATATAAAAGACACATCTTAAAATGAGCTGAAGGGTGTCACTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACACTACCCCACACA RR: TCTGTTTACGTATATTTTCTGTGTAGAATTTTACTCGACTTCCCACAGTGAAAGTTGTTCATCCGTCCTACTTACTTCATTTTTGTGATGGGGTGTGT F2: 3 ATCCGT 2 Unidirectional alignment (log-probability: -39) GACAAATGCATATAAAAGtCACATCTTAAAATGAGCTGAA---TGcCtACTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACACTA GACAAATGCATATAAAAGACACATCTTAAAATGAGCTGAAGGGTGTC-ACTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACACTA Template switch alignment (log-probability: -27.7) GACAAATGCATATAAAAGtCACATCTTAAAATGAGCTGAA|TGCCTA|CTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACACTA GACAAATGCATATAAAAGACACATCTTAAAATGAGCTGAA|TGCCTA|CTTTCAACAAGTAGGCAGGATGAATGAAGTAAAAACACTA ========== Event 2746 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCTATAAGTTAGAGATTTTAAAGAAGGTTTTTAACCTAGCATATTATTCAGGCTTTGGTTC Chimp: AGCTATAAGTTAGAGATTTTATGCTAGGTTTTTAACCTAGCATATTATTCAGGCTTTGGTTC ↑ 1 4 3 2 Gorilla: AGCTATAAGTTAGAGATTTTAAAGAAGATTTTTAACCTAGCAGATTATTCAGGCTTTGGTTC Human: AGCTATAAGTTAGAGATTTTAAAGAAGGTTTTTAACCTAGCATATTATTCAGGCTTTGGTTC Cluster: [ ] Orangutan: AGCTATAAGTTAGAGATTTTAAAGAAGATTTTTAACCTAGCAGATTATTCAGGCTTTGGTTC Gorilla > Chimp --------------- chr4:97551434-97551440 Template switch process: F1: L TCATTTGCATGGTATGGAGTAGCTATAAGTTAGAGATTTTA 1 F3: 4 TTTTTAACCTAGCATATTATTCAGGCTTTGGTTCATCTGA R RF: TCATTTGCATGGTATGGAGTAGCTATAAGTTAGAGATTTTAAAGAAGATTTTTAACCTAGCAGATTATTCAGGCTTTGGTTCATCTGA RR: AGTAAACGTACCATACCTCATCGATATTCAATCTCTAAAATTTCTTCTAAAAATTGGATCGTCTAATAAGTCCGAAACCAAGTAGACT F2: 3 GGATCGT 2 Unidirectional alignment (log-probability: -34.4) CATTTGCATGGTATGGAGTAGCTATAAGTTAGAGATTTTAtgctAGgTTTTTAACCTAGCAtATTATTCAGGCTTTGGTTCATCTGA CATTTGCATGGTATGGAGTAGCTATAAGTTAGAGATTTTAAAGAAGATTTTTAACCTAGCAGATTATTCAGGCTTTGGTTCATCTGA Template switch alignment (log-probability: -22.1) CATTTGCATGGTATGGAGTAGCTATAAGTTAGAGATTTTA|TGCTAGG|TTTTTAACCTAGCAtATTATTCAGGCTTTGGTTCATCTGA CATTTGCATGGTATGGAGTAGCTATAAGTTAGAGATTTTA|TGCTAGG|TTTTTAACCTAGCAGATTATTCAGGCTTTGGTTCATCTGA ========== Event 2747 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAATAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGCTTCTGGACATATACTAGAGGCATAAAGACAAAAT Chimp: AAACAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGCTTCTGGACATATACTAGAGGCATAAAGACAAAAT ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: AAACAAAGCCAGAAAATATAA----------TCCAGAGGCATTTTCTGGACATATACTAGAGGCATAAAGACAAAAT ↓ 1 3 4 2 ↑ 1 3 4 2 Human: AAATAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGCTTCTGGACATATACTAGAGGCATAAAGACAAAAT Cluster: [ ] Orangutan: AAACAAAGCCAGAAAATATAC--------------ATAAATGCTTCTGGACATATACTAGAGGAATAAAGACAAAAT Gorilla > Human --------------- chr4:94588579-94588597 Template switch process: F1: L AAGTACAGAAAGTGGCAGAAAAATAAAGCCAGAAAATATAATCT 1 F3: 4 TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT R RF: AAGTACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCCAGAGGCATTTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT RR: TTCATGTCTTTCACCGTCTTTTTGTTTCGGTCTTTTATATTAGGTCTCCGTAAAAGACCTGTATATGATCTCCGTATTTCTGTTTTAGTCACA F2: 3 CGTAAAAGACCTGTATATG 2 Unidirectional alignment (log-probability: -54) ACAGAAAGTGGCAGAAAAAtAAAGCCAGAAAATATAATCtgtatatgtccagaaaatgC---------TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT ACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC-------------------CAGAGGCATTTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Template switch alignment (log-probability: -29.3) ACAGAAAGTGGCAGAAAAAtAAAGCCAGAAAATATAATCt|GTATATGTCCAGAAAATGC|TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT ACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCC|GTATATGTCCAGAAAATGC|TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Human > Gorilla --------------- chr4:96226584-96226594 Template switch process: F1: L AAGTACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC 1 F3: 4 TCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT R RF: AAGTACAGAAAGTGGCAGAAAAATAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGCTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT RR: TTCATGTCTTTCACCGTCTTTTTATTTCGGTCTTTTATATTAGACATATACAGGTCTTTTACGAAGACCTGTATATGATCTCCGTATTTCTGTTTTAGTCACA F2: 3 TTTACGGAGAC 2 Unidirectional alignment (log-probability: -40.1) TACAGAAAGTGGCAGAAAAAcAAAGCCAGAAAATATAATC-------------------CagaggcattTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT TACAGAAAGTGGCAGAAAAATAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGC---------TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Template switch alignment (log-probability: -28.2) TACAGAAAGTGGCAGAAAAAcAAAGCCAGAAAATATAATC|CAGAgGCATTT|TCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT TACAGAAAGTGGCAGAAAAATAAAGCCAGAAAATATAATC|CAGAAGCATTT|TCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Gorilla > Chimp --------------- chr4:96307137-96307155 Template switch process: F1: L AAGTACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCT 1 F3: 4 TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT R RF: AAGTACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCCAGAGGCATTTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT RR: TTCATGTCTTTCACCGTCTTTTTGTTTCGGTCTTTTATATTAGGTCTCCGTAAAAGACCTGTATATGATCTCCGTATTTCTGTTTTAGTCACA F2: 3 CGTAAAAGACCTGTATATG 2 Unidirectional alignment (log-probability: -48.4) ACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCtgtatatgtccagaaaatgC---------TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT ACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC-------------------CAGAGGCATTTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Template switch alignment (log-probability: -23.7) ACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCt|GTATATGTCCAGAAAATGC|TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT ACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCC|GTATATGTCCAGAAAATGC|TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Chimp > Gorilla --------------- chr4:96226584-96226594 Template switch process: F1: L AAGTACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC 1 F3: 4 TCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT R RF: AAGTACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGCTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT RR: TTCATGTCTTTCACCGTCTTTTTGTTTCGGTCTTTTATATTAGACATATACAGGTCTTTTACGAAGACCTGTATATGATCTCCGTATTTCTGTTTTAGTCACA F2: 3 TTTACGGAGAC 2 Unidirectional alignment (log-probability: -34.6) TACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC-------------------CagaggcattTTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT TACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATCTGTATATGTCCAGAAAATGC---------TTCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT Template switch alignment (log-probability: -22.7) TACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC|CAGAgGCATTT|TCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT TACAGAAAGTGGCAGAAAAACAAAGCCAGAAAATATAATC|CAGAAGCATTT|TCTGGACATATACTAGAGGCATAAAGACAAAATCAGTGT ========== Event 2748 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAATTATGCCATCTAGTGACCATACTAGCCTTACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACATA- ↑ 1 4 3 2 Chimp: AAATTATGCCATCTAGTGACC--AATTGCCTCACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACATA- Gorilla: AAATTATGCCATCTAGTGACC--AGTTGCCTCACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACGTA- Human: AAATTATGCCATCTAGTGACCATACTAGCCTTACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACATA- Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTACATCAGTTTCTCACATAG Chimp > Human ------------- chr4:91521324-91521332 Template switch process: F1: L CAATATTAATACTTGGCCTCAAATTATGCCATCTAGTGACCAT 1 F3: 4 ACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACA R RF: CAATATTAATACTTGGCCTCAAATTATGCCATCTAGTGACCAATTGCCTCACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACA RR: GTTATAATTATGAACCGGAGTTTAATACGGTAGATCACTGGTTAACGGAGTGAGTCATTGTATATTCCGATCAATGTAGTCAAAGAGTGT F2: 3 TTCCGATCA 2 Unidirectional alignment (log-probability: -31.9) TATTAATACTTGGCCTCAAATTATGCCATCTAGTGACCatAcTaGCCTtACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACA TATTAATACTTGGCCTCAAATTATGCCATCTAGTGACC--AATTGCCTCACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACA Template switch alignment (log-probability: -22.4) TATTAATACTTGGCCTCAAATTATGCCATCTAGTGACCAt|ACTAGCCTT|ACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACA TATTAATACTTGGCCTCAAATTATGCCATCTAGTGACCAA|ACTAGCCTT|ACTCAGTAACATATAAGGCTAGTTACATCAGTTTCTCACA ========== Event 2749 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTACTGGAAA-AAAGATA-AATAACA-GGGAAGTGCTAGTGAATGTTATAGACAAGG ↓ 1 4 3 2 Chimp: GTACTGGAAA-AAAGATA-AAAGCAC-TGGAAGTGCTAGTGAATGTTATAGACAAGG ↑ 1 4 3 2 Gorilla: GTACTGGAAA-AAAGATA-AATAACA-GGGAAGTGCTAGTGAATGTTATAGACAAGG Human: GTACTGGAAA-AAAGATA-AATAACA-GGGAAGTGCTAGTGAATGTTATAGACAAGG Cluster: [ ] Orangutan: GTACTGGAAAAAAAGATAAAATAACAGGGGAAGTGCTAGTGAAAGTTATAGACAAGG Human > Chimp ------------- chr4:101668120-101668125 Template switch process: F1: L GCTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA 1 F3: 4 GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT R RF: GCTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAATAACAGGGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT RR: CGATAAGAACATATCTGTTCTTCATGACCTTTTTTCTATTTATTGTCCCTTCACGATCACTTACAATATCTGTTCCTTGATACAAAA F2: 3 TCACGA 2 Unidirectional alignment (log-probability: -27.1) CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA----AGcactGGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAATAACAG----GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT Template switch alignment (log-probability: -16) CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA|AGCACT|GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA|AGCACT|GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT Gorilla > Chimp --------------- chr4:101668120-101668125 Template switch process: F1: L GCTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA 1 F3: 4 GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT R RF: GCTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAATAACAGGGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT RR: CGATAAGAACATATCTGTTCTTCATGACCTTTTTTCTATTTATTGTCCCTTCACGATCACTTACAATATCTGTTCCTTGATACAAAA F2: 3 TCACGA 2 Unidirectional alignment (log-probability: -26.6) CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA----AGcactGGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAATAACAG----GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT Template switch alignment (log-probability: -16.5) CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA|AGCACT|GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT CTATTCTTGTATAGACAAGAAGTACTGGAAAAAAGATAAA|AGCACT|GGAAGTGCTAGTGAATGTTATAGACAAGGAACTATGTTTT ========== Event 2750 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGGTCCTGCTGCCAAGATCATAGCAGGGATGTTTGTCCTCGTGTATCTGCACAG ↓ 3 2 1 4 Chimp: CAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGG------------CAGA-----------ATATGTCCTCGTGTATCTGCACAG Gorilla: CAAACTCTCTCTAGCCTCATATTCTGCTATTGCTTGGTCCTGCTGCCAAGAGCATAGCAGGGATGTTTGTCCTCATGTATCTGAACAA Human: CAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGGTCCTGCTGCCAAGATCATAGCAGGGATGTTTGTCCTCGTGTATCTGCACAG Cluster: [ ] Orangutan: CAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGGTCCTGCTGCCAAGAGCATAGCAGGGATGTTTGTCCTCGTGTATCTGCATAG Human > Chimp ------------- chr4:92283552-92283558 Template switch process: F1: L CCTGCAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGG 1 F3: 4 TGTCCTCGTGTATCTGCACAGGTGCAACAGCCTCCTAATT R RF: CCTGCAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGGTCCTGCTGCCAAGATCATAGCAGGGATGTTTGTCCTCGTGTATCTGCACAGGTGCAACAGCCTCCTAATT RR: GGACGTTTGAGAGAGATCGGAGTATAAGACGGTAACGAACCAGGACGACGGTTCTAGTATCGTCCCTACAAACAGGAGCACATAGACGTGTCCACGTTGTCGGAGGATTAA F2: 3 ATAAGAC 2 Unidirectional alignment (log-probability: -32.7) CTGCAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGGcagaata------------------------------TGTCCTCGTGTATCTGCACAGGTGCAACAGCCTCCTAATT CTGCAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGG-------TCCTGCTGCCAAGATCATAGCAGGGATGTTTGTCCTCGTGTATCTGCACAGGTGCAACAGCCTCCTAATT Template switch alignment (log-probability: -16.2) CTGCAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGG|CAGAATA|TGTCCTCGTGTATCTGCACAGGTGCAACAGCCTCCTAATT CTGCAAACTCTCTCTAGCCTCATATTCTGCCATTGCTTGG|CAGAATA|TGTCCTCGTGTATCTGCACAGGTGCAACAGCCTCCTAATT ========== Event 2751 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GCAAAACTTCTCTTCATACTTCTGTCTT------------------------------------------------------------------------CATATTGCTGTCTGttttttttgttttgttttctgtttttGTTAAACATGAATGCGATGTCCTCTATGCAGGCATAAGGATGTAAGGTTTATTTTTCCCCTCTGCCTTTCCTTTCCAGCTCTCTCTTTGAGGACAGATTTCCTCATCTATCAGTGA Chimp: GCAAAACTTCTCTTCATACTTTTTGCTT------------------------------------TCCACTGGCCTTTCTCTGAATATTTGACAGCAAATAGGTATTGCTGTCTGttttttttgttttgttttttgtttttgttAAACATGAATGCGATGTCCTCTATGCAGGCATAAGGATGTAAGGTTTATTTTTCCCCTCTGCCTTTCCTTTCCAGCTCTCTCTTTGAGGACAGATTTCCTCATCTATCAGTGA ↓ 1 4 3 2 Gorilla: GCAAAACTTCTCTTCATACTTCTGTCTT------------------------------------------------------------------------CATATTGCTGTCTGttttttttgttttgttttctgtttttgttAAACATGAACGCGATGTCCTCTATGCAGGCATAAGGATGTAAGGTTTATTTTTCCCCTCTGCCTTTCCTTTCCAGCTCTCTCTTTGAGGACAGATTTCCTCATCTATCAGTGA Human: GCAAAACTTCTCTTCATACTTCTGTCTT------------------------------------------------------------------------CATATTGCTGTCTGttttttttgttttgttttctgtttttGTTAAACATGAATGCGATGTCCTCTATGCAGGCATAAGGATGTAAGGTTTATTTTTCCCCTCTGCCTTTCCTTTCCAGCTCTCTCTTTGAGGACAGATTTCCTCATCTATCAGTGA Cluster: [ ] Orangutan: GCAGAACTTCTCTTCATACTCTTTGCTTTCCACTGGACTTCCTCTGAGTGTTTGACAGCAAATA------------------------------------GGTATTGCTGTCTGttttttttG---------TTGTTGTTGTTAAACATGAGCACGATGTCCTCTATGCAGGCATAAGGATGTAAGGTTTATTTTTCCCCTCTGCCTCTCCTTTCCAGCTCTCTCTTTGAGGACAGATTTCCTCATCTATCAGTGA Chimp > Gorilla --------------- chr17:85570316-85570324 Template switch process: F1: L CCTGGAATTATCTTCATGCTGCAAAACTTCTCTTCATACTT 1 F3: 4 TATTGCTGTCTGTTTTTTTTGTTTTGTTTTCTGTTTTTGT R RF: CCTGGAATTATCTTCATGCTGCAAAACTTCTCTTCATACTTTTTGCTTTCCACTGGCCTTTCTCTGAATATTTGACAGCAAATAGGTATTGCTGTCTGTTTTTTTTGTTTTGTTTTTTGTTTTTGTTAAACATGAATGCGATGTCCTCTATGCAGGCATAAGGATGTAAGGTTTATTTTTCCCCTCTGCCTTTCCTTTCCAGCTCTCTCTTTGAGGACAG RR: GGACCTTAATAGAAGTACGACGTTTTGAAGAGAAGTATGAAAAACGAAAGGTGACCGGAAAGAGACTTATAAACTGTCGTTTATCCATAACGACAGACAAAAAAAACAAAACAAAAAACAAAAACAATTTGTACTTACGCTACAGGAGATACGTCCGTATTCCTACATTCCAAATAAAAAGGGGAGACGGAAAGGAAAGGTCGAGAGAGAAACTCCTGTC F2: 3 ACTTCTGTC 2 Unidirectional alignment (log-probability: -41.4) CTGGAATTATCTTCATGCTGCAAAACTTCTCTTCATACTT---------------------------------------------ctgtcttcaTATTGCTGTCTGTTTTTTTTGTTTTGTTTTcTGTTTTTGT CTGGAATTATCTTCATGCTGCAAAACTTCTCTTCATACTTTTTGCTTTCCACTGGCCTTTCTCTGAATATTTGACAGCAAATAGG---------TATTGCTGTCTGTTTTTTTTGTTTTGTTTTTTGTTTTTGT Template switch alignment (log-probability: -27.9) CTGGAATTATCTTCATGCTGCAAAACTTCTCTTCATACTT|CTGTCtTCA|TATTGCTGTCTGTTTTTTTTGTTTTGTTTTcTGTTTTTGT CTGGAATTATCTTCATGCTGCAAAACTTCTCTTCATACTT|CTGTCCTCA|TATTGCTGTCTGTTTTTTTTGTTTTGTTTTTTGTTTTTGT ========== Event 2752 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTA------TTTGTCACATAA----CAGTCCATACTGTCAAAATGCATTGAAGAGTATGAACATTTCGTGAAGAGCATGGGAATGAAAACAATGATGTATGTGAGGTCTAAATTGGACTCAGAAGACCTAGATGTGTTT Chimp: TTA------TTTGTCACATAACTAACTTTCCCTACTGTCAAAATGCATTGAGGAGTATGAACATTTCGTGAAGAGCATGGGAATGAAAACAACGATGTATGTGAGGTCTAAATTGGACTCAGAAGACCTAGACGTGTTT ↓ 1 4 3 2 Gorilla: TTA------TTTGTCACATAA----CAGTCCATACTGTCAAAATGCATTGAGGAGTATGAACATTTGGTGAAGAGCATGGGAATGAAAACAACGATGTACGTGAGGTCTAAATTGGACTCAGAAGACCTAGACGTGTTT Human: TTA------TTTGTCACATAA----CAGTCCATACTGTCAAAATGCATTGAAGAGTATGAACATTTCGTGAAGAGCATGGGAATGAAAACAATGATGTATGTGAGGTCTAAATTGGACTCAGAAGACCTAGATGTGTTT Cluster: [ ] Orangutan: TTATTGTATTTTGTCAGATAA----CTGTCCATACTGTCAAAATGCATTGAGGAGTATGAACATTTTGTGAAGAGCATTGGAATGAAAACAACGATGTATGTGAGGTCTAAATTGGACTCAGAAGACCTAGATGTGTTT Chimp > Gorilla --------------- chr5:83543927-83543932 Template switch process: F1: L CCTCCCTGAGCCAAGAACGAGGGGTTTTATTTGTCACATAAC 1 F3: 4 TACTGTCAAAATGCATTGAGGAGTATGAACATTTGGTGAA R RF: CCTCCCTGAGCCAAGAACGAGGGGTTTTATTTGTCACATAACTAACTTTCCCTACTGTCAAAATGCATTGAGGAGTATGAACATTTCGTGAAGAGCATGGGAATGAAAACAACGATGTATGTGAGGTCTAAATTGGACT RR: GGAGGGACTCGGTTCTTGCTCCCCAAAATAAACAGTGTATTGATTGAAAGGGATGACAGTTTTACGTAACTCCTCATACTTGTAAAGCACTTCTCGTACCCTTACTTTTGTTGCTACATACACTCCAGATTTAACCTGA F2: 3 ACCTGA 2 Unidirectional alignment (log-probability: -33.3) TCCCTGAGCCAAGAACGAGGGGTTTTATTTGTCACA----TAACagTCCaTACTGTCAAAATGCATTGAGGAGTATGAACATTTgGTGAA TCCCTGAGCCAAGAACGAGGGGTTTTATTTGTCACATAACTAACTTTCCCTACTGTCAAAATGCATTGAGGAGTATGAACATTTCGTGAA Template switch alignment (log-probability: -22) TCCCTGAGCCAAGAACGAGGGGTTTTATTTGTCACATAAC|AGTCCA|TACTGTCAAAATGCATTGAGGAGTATGAACATTTgGTGAA TCCCTGAGCCAAGAACGAGGGGTTTTATTTGTCACATAAC|AGTCCA|TACTGTCAAAATGCATTGAGGAGTATGAACATTTCGTGAA ========== Event 2753 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGATTCTGAGTATGTCACTGACCTATAAATATATTTAATCAGAGAGACCCTAATTTATGTCA Chimp: aaGATACTGAGTATGTCACTGACCTATTAATATAT-AGGTCAGAGAGACCCTAATTTATGTAA ↑ 3 2 1 4 Gorilla: AAGATACTGAGTATGTCACTGACCTATTAATATATTTAATCGGAGAGACCCTAATTTATGTAA Human: AAGATTCTGAGTATGTCACTGACCTATAAATATATTTAATCAGAGAGACCCTAATTTATGTCA Cluster: [ ] Orangutan: AAGATACTGAGTATGTCACTGACCTATTAATATATTTAATTAGAGAGACCCTAATTTATGTAA Gorilla > Chimp --------------- chr5:81469228-81469233 Template switch process: F1: L AAAAAAAAGATACTGAGTATGTCACTGACCTATTAATATAT 1 F3: 4 GAGAGACCCTAATTTATGTAAAGCTTACTAAATTATATAT R RF: AAAAGAAAGATACTGAGTATGTCACTGACCTATTAATATATTTAATCGGAGAGACCCTAATTTATGTAAAGTTTACTAAATTATATAT RR: TTTTCTTTCTATGACTCATACAGTGACTGGATAATTATATAAATTAGCCTCTCTGGGATTAAATACATTTCAAATGATTTAATATATA F2: 3 ACTGGA 2 Unidirectional alignment (log-probability: -40.3) AAAaAAAGATACTGAGTATGTCACTGACCTATTAATATAT---AggTCaGAGAGACCCTAATTTATGTAAAGcTTACTAAATTATATAT AAAGAAAGATACTGAGTATGTCACTGACCTATTAATATATTTAA--TCGGAGAGACCCTAATTTATGTAAAGTTTACTAAATTATATAT Template switch alignment (log-probability: -27.5) AAAaAAAGATACTGAGTATGTCACTGACCTATTAATATAT|AGGTCA|GAGAGACCCTAATTTATGTAAAGcTTACTAAATTATATAT AAAGAAAGATACTGAGTATGTCACTGACCTATTAATATAT|AGGTCA|GAGAGACCCTAATTTATGTAAAGTTTACTAAATTATATAT ========== Event 2754 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: TCAGGAAAAAAGTAATTTTCAAAGTAT-TCTAG------------------GTATACTTTGAATTATTTACATACTAAAATA ↓ 3 24 ↑ 3 1 2 4 Chimp: TCAGGAAAAAAGTAATTTTCAAAGTATACCTAG------------------AAAT-----AAATTATTTACATACTAAAATA Gorilla: TCAGGAAAAAAGTAATTTTCAAAGTATACCTAG------------------AAAT-----AAATTATTTACATACTAAAATA ↓ 3 1 2 4 Human: TCAGGAAAAAAGTAATTTTCAAAGTAT-TCTAG------------------GTATACTTTGAATTATTTACATACTAAAATA Cluster: [ ] Orangutan: TCAGGAAAAAATTAATTTTCAAAGTATACCTGGTATGTATGTATACCTAGTATGT-----AAATTATTTACATACTAAAATA Chimp > Human ------------- chr5:101702528-101702542 Template switch process: F1: L TAACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT 1 F3: 4 AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA R RF: TAACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTATACCTAGAAATAAATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA RR: ATTGGTCTTTTTGGAGTCCTTTTTTCATTAAAAGTTTCATATGGATCTTTATTTAATAAATGTATGATTTTATTAGAATAGATCAACTCTAT F2: 3 GTTTCATATGGATCT 2 Unidirectional alignment (log-probability: -43.3) AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT-----------tctaggtatactttgAATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTATACCTAGAAATA---------------AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA Template switch alignment (log-probability: -17.1) AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT|TCTAGGTATACTTTG|AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT|TCTAGGTATACTTTG|AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA Human > Chimp ------------- chr5:101062101-101062108 Template switch process: F1: L TAACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT 1 F3: 4 ATA-----AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA R RF: TAACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTATTCTAGGTATACTTTGAATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA RR: ATTGGTCTTTTTGGAGTCCTTTTTTCATTAAAAGTTTCATAAGATCCATATGAAACTTAATAAATGTATGATTTTATTAGAATAGATCAACTCTAT F2: 3 AAGATCCA 2 Unidirectional alignment (log-probability: -37.7) AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT---------------acctagaaataAATTATTTACATACTAAAATAATCTTATCTAGTTGAG AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTATTCTAGGTATACTTTG-----------AATTATTTACATACTAAAATAATCTTATCTAGTTGAG Template switch alignment (log-probability: -26.8) AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT|ACCTAGAA|ATA-----AATTATTTACATACTAAAATAATCTTATCTAGTTGAG AACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT|ACCTAGAA|ATACTTTGAATTATTTACATACTAAAATAATCTTATCTAGTTGAG Gorilla > Human --------------- chr5:101702528-101702542 Template switch process: F1: L TAACCAGAAAAACCTCAGGAAAAAAGTAATTTTCAAAGTAT 1 F3: 4 AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA R RF: TAACCAGAAAATCCTCAGGAAAAAAGTAATTTTCAAAGTATACCTAGAAATAAATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA RR: ATTGGTCTTTTAGGAGTCCTTTTTTCATTAAAAGTTTCATATGGATCTTTATTTAATAAATGTATGATTTTATTAGAATAGATCAACTCTAT F2: 3 GTTTCATATGGATCT 2 Unidirectional alignment (log-probability: -47.9) AACCAGAAAAaCCTCAGGAAAAAAGTAATTTTCAAAGTATtC-------TAggtatactttgAATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA AACCAGAAAATCCTCAGGAAAAAAGTAATTTTCAAAGTATACCTAGAAATA-----------AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA Template switch alignment (log-probability: -23.2) AACCAGAAAAaCCTCAGGAAAAAAGTAATTTTCAAAGTAT|TCTAGGTATACTTTG|AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA AACCAGAAAATCCTCAGGAAAAAAGTAATTTTCAAAGTAT|TCTAGGTATACTTTG|AATTATTTACATACTAAAATAATCTTATCTAGTTGAGATA ========== Event 2755 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTAAAAACATAGGTTATCTTTAGTTTTTTTGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGC ↓ 1 3 4 2 Chimp: TTTAAAAACATAGGTTATCTTC----------------------------------------TGCAAACTATATGCAGAAGATAAAAGCTGAAGATGC ↑ 1 3 4 2 Gorilla: TTTAAAAACATAGGTTATCTTTAGtttttttGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGC Human: TTTAAAAACATAGGTTATCTTTAGTTTTTTTGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGC Cluster: [ ] Orangutan: TTTAAAAACATAGGTTATCTTTAGTTTTTTTGTTGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGC Human > Chimp ------------- chr5:80516786-80516797 Template switch process: F1: L TAAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT 1 F3: 4 TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT R RF: TAAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTTTAGTTTTTTTGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT RR: ATTTTTAACCGTTGACTATAAAATTTTTGTATCCAATAGAAATCAAAAAAACTACTCCACCTTTATCGTCCTAGATATATGATCGTATATCAAACGTCTTCTATTTTCGACTTCTACGTGTTTTATCTGTAGA F2: 3 ATATCAAACGTC 2 Unidirectional alignment (log-probability: -38.1) AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTTctgcaaactaTA--------------------------------------------------TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT----------TAGTTTTTTTGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT Template switch alignment (log-probability: -16.8) AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT|CTGCAAACTATA|TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT|CTGCAAACTATA|TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT Gorilla > Chimp --------------- chr5:80516786-80516797 Template switch process: F1: L TAAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT 1 F3: 4 TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT R RF: TAAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTTTAGTTTTTTTGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT RR: ATTTTTAACCGTTGACTATAAAATTTTTGTATCCAATAGAAATCAAAAAAACTACTCCACCTTTATCGTCCTAGATATATGATCGTATATCAAACGTCTTCTATTTTCGACTTCTACGTGTTTTATCTGTAGA F2: 3 ATATCAAACGTC 2 Unidirectional alignment (log-probability: -37.6) AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTTctgcaaactaTA--------------------------------------------------TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT----------TAGTTTTTTTGATGAGGTGGAAATAGCAGGATCTATATACTAGCATATAGTTTGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT Template switch alignment (log-probability: -17.3) AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT|CTGCAAACTATA|TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT AAAAATTGGCAACTGATATTTTAAAAACATAGGTTATCTT|CTGCAAACTATA|TGCAGAAGATAAAAGCTGAAGATGCACAAAATAGACATCT ========== Event 2756 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTGTAAGAAAAGATTATTTTTCTTGATTTCTGA------AGAGATCAGC---TTCAAAAGCTGA Chimp: TCTGTAAGAAAAGATTATTTTTCTTGATTTCTGA------AGAGATCAGC---TTCAAAAGCTGA Gorilla: TCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAAATCAAGAAAATCAGC---TTCAAAAGCTGA ↑ 3 2 1 4 Human: TCTGTAAGAAAAGATTATTTTTCTTGATTTCTGA------AGAGATCAGC---TTCAAAAGCTGA Cluster: [ ] Orangutan: TCTGTGAGAAAATATTATTTTTCTTGATTTCTGA------AGAGATCAGCTAAGTCAAAAGCTGA Human > Gorilla --------------- chr5:80443797-80443805 Template switch process: F1: L TAGAGAGTCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAA 1 F3: 4 ATCAGCTTCAAAAGCTGATTTTATAAAAATAAGTATACTT R RF: TAGAGAGTCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAAGAGATCAGCTTCAAAAGCTGATTTTATAAAAATAACTATACTT RR: ATCTCTCAGACATTCTTTTCTAATAAAAAGAACTAAAGACTTCTCTAGTCGAAGTTTTCGACTAAAATATTTTTATTGATATGAA F2: 3 AAAGAACTA 2 Unidirectional alignment (log-probability: -36.1) GAGAGTCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAAatcaagaAaATCAGCTTCAAAAGCTGATTTTATAAAAATAAgTATACTT GAGAGTCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAAG------AGATCAGCTTCAAAAGCTGATTTTATAAAAATAACTATACTT Template switch alignment (log-probability: -22.4) GAGAGTCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAA|ATCAAGAAA|ATCAGCTTCAAAAGCTGATTTTATAAAAATAAgTATACTT GAGAGTCTGTAAGAAAAGATTATTTTTCTTGATTTCTGAA|ATCAAGAAA|ATCAGCTTCAAAAGCTGATTTTATAAAAATAACTATACTT ========== Event 2757 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: tgagaataactagtaAAACTATATGTGTTCATA-----------TATATACAATTATCTCCttggcaaa Chimp: tgagaataactagtaAAACTATATGTGTTCATA-----------TATATACAATTATCTCCttggcaaa ↑ 3 1 2 4 Gorilla: tgagaataactagtaAAACTATATGAACACATTAACAAAGGAAAATTACACAATTATCTCCttggcaaa ↓ 3 1 2 4 Human: tgagaataactagtaAAACTATATGTGTTCATA-----------TATATACAATTATCTCCttggcaaa Cluster: [ ] Orangutan: tgagaataactagtaAAACTATATGAACACATTAACAAAGGAAAATTATACAATTATCTCCttggcaaa Gorilla > Human --------------- chr5:78474731-78474740 Template switch process: F1: L TTTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG 1 F3: 4 TATACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGCTAA R RF: TTTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATGAACACATTAACAAAGGAAAATTACACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGCTAA RR: AAACTCCACCCATTTGACTCTTATTGATCATTTTGATATACTTGTGTAATTGTTTCCTTTTAATGTGTTAATAGAGGAACCGTTTTCAAAAGACGTTTCTCGATT F2: 3 ATATACTTGT 2 Unidirectional alignment (log-probability: -40.2) TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG--------------------TgttcatataTAtACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATGAACACATTAACAAAGGAAAAT---------TACACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC Template switch alignment (log-probability: -22.6) TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG|TGTTCATATA|TAtACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG|TGTTCATATA|TACACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC Gorilla > Chimp --------------- chr5:79470604-79470613 Template switch process: F1: L TTTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG 1 F3: 4 TATACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGCTAA R RF: TTTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATGAACACATTAACAAAGGAAAATTACACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGCTAA RR: AAACTCCACCCATTTGACTCTTATTGATCATTTTGATATACTTGTGTAATTGTTTCCTTTTAATGTGTTAATAGAGGAACCGTTTTCAAAAGACGTTTCTCGATT F2: 3 ATATACTTGT 2 Unidirectional alignment (log-probability: -40.2) TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG--------------------TgttcatataTAtACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATGAACACATTAACAAAGGAAAAT---------TACACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC Template switch alignment (log-probability: -22.6) TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG|TGTTCATATA|TAtACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC TTGAGGTGGGTAAACTGAGAATAACTAGTAAAACTATATG|TGTTCATATA|TACACAATTATCTCCTTGGCAAAAGTTTTCTGCAAAGAGC ========== Event 2758 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTATTCAGATAAATAGTCTCTTCTTA-GAGACAAAAAGAGACAACACAC ↑ 31 24 Chimp: TTTATTCAGATAAATAGTCTC---TAAGAAGACAAAAAGAGACAACACAC Gorilla: TTTATTCAGATAAATAGTCTC---TAAGAAGACAAAAAGAGACAACACAC Human: TTTATTCAGATAAATAGTCTCTTCTTA-GAGACAAAAAGAGACAACACAC Cluster: [ ] Orangutan: TTTATTCAGATAAATAGTCTC---TAAGAAGACAAAAAGAGACAATACAC Chimp > Human ------------- chr5:77483976-77483981 Template switch process: F1: L ATTGTACCTGTGTATTAAACTTTATTCAGATAAATAGTCTCT 1 F3: 4 AGACAAAAAGAGACAACACACTATGAGAATTGTATAAATA R RF: ATTGTACCTGTGTATTAAACTTTATTCAGATAAATAGTCTCTAAGAAGACAAAAAGAGACAACACACTATGAGAATTGTATAAATA RR: TAACATGGACACATAATTTGAAATAAGTCTATTTATCAGAGATTCTTCTGTTTTTCTCTGTTGTGTGATACTCTTAACATATTTAT F2: 3 GATTCT 2 Unidirectional alignment (log-probability: -30) TGTACCTGTGTATTAAACTTTATTCAGATAAATAGTCTCTtcttag----AGACAAAAAGAGACAACACACTATGAGAATTGTATAAATA TGTACCTGTGTATTAAACTTTATTCAGATAAATAGTCTCT------AAGAAGACAAAAAGAGACAACACACTATGAGAATTGTATAAATA Template switch alignment (log-probability: -16) TGTACCTGTGTATTAAACTTTATTCAGATAAATAGTCTCT|TCTTAG|AGACAAAAAGAGACAACACACTATGAGAATTGTATAAATA TGTACCTGTGTATTAAACTTTATTCAGATAAATAGTCTCT|TCTTAG|AGACAAAAAGAGACAACACACTATGAGAATTGTATAAATA ========== Event 2759 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 345 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATGGAAATCATTGGTGATCTTAGAGAGTTATATA-AGCCCAACATAATCTACCTAGCTGTATTTAAGATGCAGCAAAAATGGAGGGAAAATAC Chimp: ATGGAAATCATTGGTGATCTT----AGTTATATA-AGCCCAGCATAATCTACCTAGCTGTATTTAAGATGCAACAAAAATGGAGGGAAAATAC ↑ 1 3 4 2 Gorilla: ATGGAAATCACTGGTGATCTTAGAGAGTTAAATACAGCTAGGTAGATTATG-TTGGGCTTATATAAGATGCAGCAAAAATGGAGGGAAAATAC ↓ 13 24 ↑ 13 24 Human: ATGGAAATCATTGGTGATCTTAGAGAGTTATATA-AGCCCAACATAATCTACCTAGCTGTATTTAAGATGCAGCAAAAATGGAGGGAAAATAC Cluster: [ ] Orangutan: AAGGAAATCATTGGTGATCTTAGACAGTTATATA-AGCCCAACATAATCTACCTAGCTGTATTTAAGATGCAGCAAAAATGGAGGGAAAATAC Gorilla > Human --------------- chr5:77615225-77615256 Template switch process: F1: L GTTGAAAGTCAATGGAAATCATTGGTGATCTTAGAGAGTTA 1 F3: 4 TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA R RF: GTTGAAAGTCAATGGAAATCACTGGTGATCTTAGAGAGTTAAATACAGCTAGGTAGATTATGTTGGGCTTATATAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA RR: CAACTTTCAGTTACCTTTAGTGACCACTAGAATCTCTCAATTTATGTCGATCCATCTAATACAACCCGAATATATTCTACGTCGTTTTTACCTCCCTTTTATGAGAGTATAAT F2: 3 TTATGTCGATCCATCTAATACAACCCGAATAT 2 Unidirectional alignment (log-probability: -67.9) TTGAAAGTCAATGGAAATCAtTGGTGATCTTAGAGAGTTA----------------------------TATAagcccaacataatctacctagctgtattTAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA TTGAAAGTCAATGGAAATCACTGGTGATCTTAGAGAGTTAAATACAGCTAGGTAGATTATGTTGGGCTTATA----------------------------TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA Template switch alignment (log-probability: -25.3) TTGAAAGTCAATGGAAATCAtTGGTGATCTTAGAGAGTTA|TATAAGCCCAACATAATCTACCTAGCTGTATT|TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA TTGAAAGTCAATGGAAATCACTGGTGATCTTAGAGAGTTA|TATAAGCCCAACATAATCTACCTAGCTGTATT|TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA Human > Gorilla --------------- chr5:78512534-78512565 Template switch process: F1: L GTTGAAAGTCAATGGAAATCACTGGTGATCTTAGAGAGTTA 1 F3: 4 TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA R RF: GTTGAAAGTCAATGGAAATCATTGGTGATCTTAGAGAGTTATATAAGCCCAACATAATCTACCTAGCTGTATTTAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA RR: CAACTTTCAGTTACCTTTAGTAACCACTAGAATCTCTCAATATATTCGGGTTGTATTAGATGGATCGACATAAATTCTACGTCGTTTTTACCTCCCTTTTATGAGAGTATAAT F2: 3 ATATTCGGGTTGTATTAGATGGATCGACATAA 2 Unidirectional alignment (log-probability: -67.9) TTGAAAGTCAATGGAAATCAcTGGTGATCTTAGAGAGTTAaatacagctaggtagattatgttgggctTATA----------------------------TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA TTGAAAGTCAATGGAAATCATTGGTGATCTTAGAGAGTTA----------------------------TATAAGCCCAACATAATCTACCTAGCTGTATTTAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA Template switch alignment (log-probability: -25.3) TTGAAAGTCAATGGAAATCAcTGGTGATCTTAGAGAGTTA|AATACAGCTAGGTAGATTATGTTGGGCTTATA|TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA TTGAAAGTCAATGGAAATCATTGGTGATCTTAGAGAGTTA|AATACAGCTAGGTAGATTATGTTGGGCTTATA|TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA Gorilla > Chimp --------------- chr5:78612187-78612221 Template switch process: F1: L TTTACATAAGTTGAAAGTCAATGGAAATCATTGGTGATCTTAG 1 F3: 4 TAAGATGCAACAAAAATGGAGGGAAAATACTCTCATATTACTGTGAGATA R RF: TTTACATAAGTTGAAAGTCAATGGAAATCACTGGTGATCTTAGAGAGTTAAATACAGCTAGGTAGATTATGTTGGGCTTATATAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTACTGTGAGATC RR: AAATGTATTCAACTTTCAGTTACCTTTAGTGACCACTAGAATCTCTCAATTTATGTCGATCCATCTAATACAACCCGAATATATTCTACGTCGTTTTTACCTCCCTTTTATGAGAGTATAATGACACTCTAG F2: 3 TTATGTCGATCCATCTAATACGACCCGAATATATT 2 Unidirectional alignment (log-probability: -82.3) ACATAAGTTGAAAGTCAATGGAAATCAtTGGTGATCTTAG----------------------------------TTATAtaagcccagcataatctacctagctgtattTAAGATGCAaCAAAAATGGAGGGAAAATACTCTCATATTA ACATAAGTTGAAAGTCAATGGAAATCACTGGTGATCTTAGAGAGTTAAATACAGCTAGGTAGATTATGTTGGGCTTATA------------------------------TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA Template switch alignment (log-probability: -42.5) ACATAAGTTGAAAGTCAATGGAAATCAtTGGTGATCTTAG|TTATATAAGCCCAgCATAATCTACCTAGCTGTATT|TAAGATGCAaCAAAAATGGAGGGAAAATACTCTCATATTA ACATAAGTTGAAAGTCAATGGAAATCACTGGTGATCTTAG|TTATATAAGCCCAACATAATCTACCTAGCTGTATT|TAAGATGCAGCAAAAATGGAGGGAAAATACTCTCATATTA ========== Event 2760 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGCGGCTGTCTTCCTAGGCAC-ATCTCATAGTAAAATAAATATTACTATGACAAAATCTCATTGTGAATACAA Chimp: AAGCGGCTGTCTTCCTAGGCAT-ATCTCATAGTAAAATAAATATTACTATGACAAAATCTCATTGTGAATACAA ↓ 1 3 4 2 Gorilla: AAGCGGCTGTCTTCCTAGGCACACTGTCATAGTAATATTTATTTTACTATGACAAAATCTCATTGTGAATACAA Human: AAGCGGCTGTCTTCCTAGGCAC-ATCTCATAGTAAAATAAATATTACTATGACAAAATCTCATTGTGAATACAA Cluster: [ ] Orangutan: AAGCGGCTGTCTTCCTAGGCAC-ATCTCATAGTAAAATAAATATTACTATGACAAAATCTCATTGTGAATACAA Chimp > Gorilla --------------- chr5:78307195-78307213 Template switch process: F1: L GGGTTTTACCTTAACAGCTAAAGCGGCTGTCTTCCTAGGCACAC 1 F3: 4 TTACTATGACAAAATCTCATTGTGAATACAAGTTTCATTA R RF: GGGTTTTACCTTAACAGCTAAAGCGGCTGTCTTCCTAGGCATATCTCATAGTAAAATAAATATTACTATGACAAAATCTCATTGTGAATACAAGTTTCATTA RR: CCCAAAATGGAATTGTCGATTTCGCCGACAGAAGGATCCGTATAGAGTATCATTTTATTTATAATGATACTGTTTTAGAGTAACACTTATGTTCAAAGTAAT F2: 3 TTATTTATAATGATACTGT 2 Unidirectional alignment (log-probability: -45.7) TTTACCTTAACAGCTAAAGCGGCTGTCTTCCTAGGCAcAcTgTCATAGTAAtATttATtTTACTATGACAAAATCTCATTGTGAATACAAGTTTCATTA TTTACCTTAACAGCTAAAGCGGCTGTCTTCCTAGGCATA-TCTCATAGTAAAATAAATATTACTATGACAAAATCTCATTGTGAATACAAGTTTCATTA Template switch alignment (log-probability: -29.3) TTTACCTTAACAGCTAAAGCGGCTGTCTTCCTAGGCAcAc|TGTCATAGTAATATTTATT|TTACTATGACAAAATCTCATTGTGAATACAAGTTTCATTA TTTACCTTAACAGCTAAAGCGGCTGTCTTCCTAGGCATAT|TGTCATAGTAATATTTATT|TTACTATGACAAAATCTCATTGTGAATACAAGTTTCATTA ========== Event 2761 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTTCTTTCTCTTCCAACAATACAG----ATGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCCGAGGAGC Chimp: TTCTTCTTTCTCTTCCAACAATACAG----ATGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCCAAGGAGC Gorilla: TTCTTCTTTCTCTTCCAACAAGAGAAATTCTTGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCCAAGGAGC ↑ 1 4 3 2 Human: TTCTTCTTTCTCTTCCAACAATACAG----ATGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCCGAGGAGC Cluster: [ ] Orangutan: TTCTTCTTTCTCTTCCAACAATACAG----ATGGTATTTCCCCCAAAGACAGAATTTCTAGAAAACTTCCCAAGGAGC Human > Gorilla --------------- chr5:90397511-90397518 Template switch process: F1: L AAACAACGCTGACACATTACTTCTTCTTTCTCTTCCAACAAGA 1 F3: 4 TGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCC R RF: AAACAACGCTGACAAATTACTTCTTCTTTCTCTTCCAACAATACAGATGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCC RR: TTTGTTGCGACTGTTTAATGAAGAAGAAAGAGAAGGTTGTTATGTCTACCATAAAGGGGGGTTCTGTCTTAAAGATCTTTTGAAGGG F2: 3 TCTTAAAG 2 Unidirectional alignment (log-probability: -37.9) CAACGCTGACAcATTACTTCTTCTTTCTCTTCCAACA----AGAgaaattctTGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCC CAACGCTGACAAATTACTTCTTCTTTCTCTTCCAACAATACAGA--------TGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCC Template switch alignment (log-probability: -27.8) CAACGCTGACAcATTACTTCTTCTTTCTCTTCCAACAAgA|GAAATTCT|TGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCC CAACGCTGACAAATTACTTCTTCTTTCTCTTCCAACAATA|GAAATTCT|TGGTATTTCCCCCCAAGACAGAATTTCTAGAAAACTTCCC ========== Event 2762 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGGCTCCATGACAAAGCTG-----TGGATAGATCCCATGTACCCAGGGTCCCAGAACACC ↓ 1 3 4 2 Chimp: TCTGGCTCCATGACAAAGCTGTACATGGGATCTATCCCATGTACCCAGGGTCCCAGAACACC Gorilla: TCTGGCTCCATGACAAAGCTG-----TGGATAGATCCCATGCACCCAGGGTCCCAGAACACC Human: TCTGGCTCCATGACAAAGCTG-----TGGATAGATCCCATGTACCCAGGGTCCCAGAACACC Cluster: [ ] Orangutan: TCTGGCTGCATGACAAAGCCG-----TAGATAGATCTCATGCACCCAGGGTCCCAGAACACC Human > Chimp ------------- chr5:170748137-170748147 Template switch process: F1: L GCCAACCTCAATTCTGCTTTTCTGGCTCCATGACAAAGCTGT 1 F3: 4 ATCCCATGTACCCAGGGTCCCAGAACACCTGCACCTTGTG R RF: GCCAACCTGAATTCTGCTTTTCTGGCTCCATGACAAAGCTGTGGATAGATCCCATGTACCCAGGGTCCCAGAACACCTGCACCTTGTG RR: CGGTTGGACTTAAGACGAAAAGACCGAGGTACTGTTTCGACACCTATCTAGGGTACATGGGTCCCAGGGTCTTGTGGACGTGGAACAC F2: 3 TCTAGGGTACA 2 Unidirectional alignment (log-probability: -36.1) CAACCTcAATTCTGCTTTTCTGGCTCCATGACAAAGCTGTacatgGGATctATCCCATGTACCCAGGGTCCCAGAACACCTGCACCTTGTG CAACCTGAATTCTGCTTTTCTGGCTCCATGACAAAGCTGT-----GGATAGATCCCATGTACCCAGGGTCCCAGAACACCTGCACCTTGTG Template switch alignment (log-probability: -22.7) CAACCTcAATTCTGCTTTTCTGGCTCCATGACAAAGCTGT|ACATGGGATCT|ATCCCATGTACCCAGGGTCCCAGAACACCTGCACCTTGTG CAACCTGAATTCTGCTTTTCTGGCTCCATGACAAAGCTGT|ACATGGGATCT|ATCCCATGTACCCAGGGTCCCAGAACACCTGCACCTTGTG ========== Event 2763 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CAAACTTCTTCAATGGTTTTTGTTAAATGGCCATTTGTTAAATGGCCCCTGTCTGTACTTAAATATTAGGTAAGAGAGCTATTAGGAAGGAAAGCCAGAAGGACGGCAGGCATAAATATCTTTTTCT Chimp: CAAACTTCTTCAATGGTTTTTGTT---------------AAATGGCCCCTGTCTGTACTTAAATATTAGGTAAGAGAGCTATTAGGAAGGAAAGCCAGAAGGATGGCAGACATAAATATCTTTTTCT Gorilla: CAAACTTCTTCAATGGTTTTTGTT---------------AAATGACACCTGTCTGTGCTTAAATATTAGGTAAGAGAGCTATTAGGAAGGAAAGCCAGAAGGATGGCAGACATAAATATCTTTTTCT ↓ 4 1 3 2 Human: CAAACTTCTTCAATGGTTTTTGTTAAATGGCCATTTGTTAAATGGCCCCTGTCTGTACTTAAATATTAGGTAAGAGAGCTATTAGGAAGGAAAGCCAGAAGGACGGCAGGCATAAATATCTTTTTCT Cluster: [ ] Orangutan: CAAACTTCTTCAATGGTTTTTGTT---------------AAATGGCACCTGTCTGTGCTTAAATATTAGGTAAGAGAGCTATTAGAAAGGAAAGCCAGAAGGATGGCAGACATAAATATCTTTTTCT Gorilla > Human --------------- chr5:108714154-108714158 Template switch process: F1: L AAAGCTGATTATTCCCCCAAACTTCTTCAATGGTTTTTGTTAAATG 1 F3: 4 TTGTTAAATGGCCCCTGTCTGTACTTAAATATTAGGTAAGAGAGCTATTAGGAAGGAAAGCCA R RF: AAAGCTGATTATTCCCCCAAACTTCTTCAATGGTTTTTGTTAAATGACACCTGTCTGTGCTTAAATATTAGGTAAGAGAGCTATTAGGAAGGAAAGCCAGAAGGATGGC RR: TTTCGACTAATAAGGGGGTTTGAAGAAGTTACCAAAAACAATTTACTGTGGACAGACACGAATTTATAATCCATTCTCTCGATAATCCTTCCTTTCGGTCTTCCTACCG F2: 3 TACCG 2 Unidirectional alignment (log-probability: -49.3) GATTATTCCCCCAAACTTCTTCAATGGTTTTTGttaaatggccatttgTTAAATGgCcCCTGTCTGTaCTTAAATATTAGGTAAG GATTATTCCCCCAAACTTCTTCAATGGTTTTTG---------------TTAAATGACACCTGTCTGTGCTTAAATATTAGGTAAG Template switch alignment (log-probability: -33.6) GATTATTCCCCCAAACTTCTTCAATGGTTTTTGTTAAATG|GCCAT|TTGTTAAATGgCcCCTGTCTGTaCTTAAATATTAGGTAAG GATTATTCCCCCAAACTTCTTCAATGGTTTTTGTTAAATG|GCCAT|TTGTTAAATGACACCTGTCTGTGCTTAAATATTAGGTAAG ========== Event 2764 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AATAGTTGCCCCAATAAGGATC--ATCTGAGACCtttctttcatttctttttttgttttcCATAGat------------------------------------------------------------------------------------agatagatg Chimp: AATAGTTGCCCCAATAAGGATT--ATCTGAGACCT----TTCATTTCtttttttGTTTTCCATAGat------------------------------------------------------------------------------------agatagatg ↑ 1 4 3 2 Gorilla: AATAGTTGCCCCAATAAGGATC----ATGAGACCTTTCTTTCATTTCtttttttGTTTTCCatagat----agatagatagatagatagatagatagatagatagatacacagacagacagacagacagacagacagatagatagatagatagatagatg Human: AATAGTTGCCCCAATAAGGATC--ATCTGAGACCtttctttcatttctttttttgttttcCATAGat------------------------------------------------------------------------------------agatagatg Cluster: [ ] Orangutan: AATAGTTGCCCCAATAAGGATCAT--CTGAGACctttctttcatttctttttttgttttcCATAGATAGAG--------------------------------------------------------------------------------AGATAGATG Gorilla > Chimp --------------- chr5:73600062-73600067 Template switch process: F1: L TCAGAATAATTTGATATTGAAATAGTTGCCCCAATAAGGAT 1 F3: 4 AGAC----CTTTCATTTCTTTTTTTGTTTTCCATAGAT R RF: TCAGAATAATTTGATATTGAAATAGTTGCCCCAATAAGGATCATGAGACCTTTCTTTCATTTCTTTTTTTGTTTTCCATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATACACAGACAGACAGACAGACAGACAGACAGATA RR: AGTCTTATTAAACTATAACTTTATCAACGGGGTTATTCCTAGTACTCTGGAAAGAAAGTAAAGAAAAAAACAAAAGGTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATGTGTCTGTCTGTCTGTCTGTCTGTCTGTCTAT F2: 3 GTCTAT 2 Unidirectional alignment (log-probability: -36.6) CAGAATAATTTGATATTGAAATAGTTGCCCCAATAAGGATtAtcTGAGAC----CTTTCATTTCTTTTTTTGTTTTCCATAGAT------------ CAGAATAATTTGATATTGAAATAGTTGCCCCAATAAGGATCA--TGAGACCTTTCTTTCATTTCTTTTTTTGTTTTCCATAGATAGATAGATAGAT Template switch alignment (log-probability: -26.3) CAGAATAATTTGATATTGAAATAGTTGCCCCAATAAGGAT|TATCTG|AGAC----CTTTCATTTCTTTTTTTGTTTTCCATAGAT CAGAATAATTTGATATTGAAATAGTTGCCCCAATAAGGAT|TATCTG|AGACCTTTCTTTCATTTCTTTTTTTGTTTTCCATAGAT ========== Event 2765 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTAATACTAACGTGGCATT-CTAAC--AAGTGCTTGGAAGGAAAAACCAAG-------- Chimp: TATTAATACTAACGTGGCATT-CTAAC--AAGTGCTTGGAAGGAAAAACCAAG-------- Gorilla: TATTAATACTAACGTGGCATTCGTGGC----ATGCTTGGAAGGAAAAACCAAG-------- ↓ 1 4 3 2 Human: TATTAATACTAACGTGGCATT-CTAAC--AAGTGCTTGGAAGGAAAAACCAAG-------- Cluster: [ ] Orangutan: TATTAATACTAACGTGGCGTT-CTAACAA--GTGCTTGGAAGGAAAAACCAAGCCGGATTA Gorilla > Human --------------- chr5:10994182-10994188 Template switch process: F1: L TACACAAGTTACAAAAAACATATTAATACTAACGTGGCATTC 1 F3: 4 TGCTTGGAAGGAAAAACCAAG R RF: TACACAAGTTACAAAAAACATATTAATACTAACGTGGCATTCGTGGCATGCTTGGAAGGAAAAACCAAG RR: ATGTGTTCAATGTTTTTTGTATAATTATGATTGCACCGTAAGCACCGTACGAACCTTCCTTTTTGGTTC F2: 3 GAACAAT 2 Unidirectional alignment (log-probability: -37) CACAAGTTACAAAAAACATATTAATACTAACGTGGCATTCtaacaaG-----TGCTTGGAAGGAAAAACCAAG------------------- CACAAGTTACAAAAAACATATTAATACTAACGTGGCATTC------GTGGCATGCTTGGAAGGAAAAACCAAGCCGGATTAGGGGATAGACG Template switch alignment (log-probability: -27.2) CACAAGTTACAAAAAACATATTAATACTAACGTGGCATTC|TaaCAAG|TGCTTGGAAGGAAAAACCAAG CACAAGTTACAAAAAACATATTAATACTAACGTGGCATTC|TTCCAAG|TGCTTGGAAGGAAAAACCAAG ========== Event 2766 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGTGTTTACCATGTTCACTGCATCA---CAAAGCTGGAAGGAAGGCAGAGCTGGGC Chimp: GTGTGTTTACCATGTTCACTGCATCA---CAAAGCTGGAAGGAAGGCAGAGCTGGGC ↓ 3 12 4 Gorilla: GTGTGTTTACCATGTTCACTGCATCACTGTGATGCAGGAAGGAAGGCAGAGCTGGGC ↑ 3 12 4 Human: GTGTGTTTACCATGTTCACTGCATCA---CAAAGCTGGAAGGAAGGCAGAGCTGGGC Cluster: [ ] Orangutan: GTGTGTTTACCATGTTCACTGCATCA---CAAAGCTGGAAGGAAGGCAGAGCTGGGC Human > Gorilla --------------- chr5:94320589-94320597 Template switch process: F1: L AACAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCAC 1 F3: 4 GGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC R RF: AACAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCACAAAGCTGGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC RR: TTGTTCTGTACAGGTCACACAAATGGTACAAGTGACGTAGTGTTTCGACCTTCCTTCCGTCTCGACCCGGTCAATGTCGGAATAGAAG F2: 3 ACGTAGTGT 2 Unidirectional alignment (log-probability: -31.9) CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCACtgtgAtGCaGGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCACA---AAGCTGGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC Template switch alignment (log-probability: -16.9) CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCAC|TGTGATGCA|GGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCAC|TGTGATGCA|GGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC Chimp > Gorilla --------------- chr5:94320589-94320597 Template switch process: F1: L AACAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCAC 1 F3: 4 GGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC R RF: AACAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCACAAAGCTGGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC RR: TTGTTCTGTACAGGTCACACAAATGGTACAAGTGACGTAGTGTTTCGACCTTCCTTCCGTCTCGACCCGGTCAATGTCGGAATAGAAG F2: 3 ACGTAGTGT 2 Unidirectional alignment (log-probability: -31.9) CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCACtgtgAtGCaGGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCACA---AAGCTGGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC Template switch alignment (log-probability: -16.9) CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCAC|TGTGATGCA|GGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC CAAGACATGTCCAGTGTGTTTACCATGTTCACTGCATCAC|TGTGATGCA|GGAAGGAAGGCAGAGCTGGGCCAGTTACAGCCTTATCTTC ========== Event 2767 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAATATTAGAGCCTTTGAGTTAAGCTCACTCACAGTGAGCTTAACCACCACCAgcatgtcatttt Chimp: AAATGTTAGAGCCTTTGAGTTAAGCTCACTCACAGTG----CACCCACCACCAgcacgtcatttt Gorilla: AAATGTTAGAGCCTTTGAGTTAAGCTCACTCACAGTG----CACCCACCACCAgcacgtcatttt ↓ 3 2 1 4 Human: AAATATTAGAGCCTTTGAGTTAAGCTCACTCACAGTGAGCTTAACCACCACCAgcatgtcatttt Cluster: [ ] Orangutan: AAATGTTAGAGCCTTTGAGTTAAGCTCACTCACAGTG----CACCCACCACCAgcacgtcatttt Gorilla > Human --------------- chr5:110545225-110545231 Template switch process: F1: L GTAGAAATATTAGAGCCTTTGAGTTAAGCTCACTCACAGTG 1 F3: 4 CCACCACCAGCATGTCATTTTATTCTGTTTAAAACTCAAA R RF: GTAGAAATGTTAGAGCCTTTGAGTTAAGCTCACTCACAGTGCACCCACCACCAGCACGTCATTTTATTCTGTTTAAAACTCAAA RR: CATCTTTACAATCTCGGAAACTCAATTCGAGTGAGTGTCACGTGGGTGGTGGTCGTGCAGTAAAATAAGACAAATTTTGAGTTT F2: 3 AATTCGA 2 Unidirectional alignment (log-probability: -38.8) TAGAAATaTTAGAGCCTTTGAGTTAAGCTCACTCACAGTGagcttAaCCACCACCAGCAtGTCATTTTATTCTGTTTAAAACTCAAA TAGAAATGTTAGAGCCTTTGAGTTAAGCTCACTCACAGTGC----ACCCACCACCAGCACGTCATTTTATTCTGTTTAAAACTCAAA Template switch alignment (log-probability: -27.7) TAGAAATaTTAGAGCCTTTGAGTTAAGCTCACTCACAGTG|AGCTTAA|CCACCACCAGCAtGTCATTTTATTCTGTTTAAAACTCAAA TAGAAATGTTAGAGCCTTTGAGTTAAGCTCACTCACAGTG|AGCTTAA|CCACCACCAGCACGTCATTTTATTCTGTTTAAAACTCAAA ========== Event 2768 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cattaacaagaggatctaacaggacactattagactattata--taataattaagaagagttttgttc Chimp: CATTAACAAGAGGATCTAATAGGACACTATCAGATAATAGTGTCCTGTAATTAAGAAGAGTTTtgttt ↑ 3 2 1 4 Gorilla: CATTAACAAGAGGATCTAACAGGACACTATTAGACTATTATA--TAATAATTAAGAAGAGTTTtgttt Human: cattaacaagaggatctaacaggacactattagactattata--taataattaagaagagttttgttc Cluster: [ ] Orangutan: cattaacaagaggatctaacaggacactattagactattata--taataattaagaagagttttgttt Gorilla > Chimp --------------- chr5:110010770-110010782 Template switch process: F1: L TTTAGATCAATCATTAACAAGAGGATCTAATAGGACACTATCAGA 1 F3: 4 TAATTAAGAAGAGTTTTGTTTCATCCTGTATTGCTGCTTG R RF: TCTAGATCAATCATTAACAAGAGGATCTAACAGGACACTATTAGACTATTATATAATAATTAAGAAGAGTTTTGTTTCATCCTGTATTGCTGCTTG RR: AGATCTAGTTAGTAATTGTTCTCCTAGATTGTCCTGTGATAATCTGATAATATATTATTAATTCTTCTCAAAACAAAGTAGGACATAACGACGAAC F2: 3 GTCCTGTGATAAT 2 Unidirectional alignment (log-probability: -52.1) ATCAATCATTAACAAGAGGATCTAAtAGGACACTATcAG--------ATAAtagtgtcctgTAATTAAGAAGAGTTTTGTTTCATCCTGTATTGCTGCTTG ATCAATCATTAACAAGAGGATCTAACAGGACACTATTAGACTATTATATAA----------TAATTAAGAAGAGTTTTGTTTCATCCTGTATTGCTGCTTG Template switch alignment (log-probability: -34) ATCAATCATTAACAAGAGGATCTAAtAGGACACTATcAGA|TAATAGTGTCCTG|TAATTAAGAAGAGTTTTGTTTCATCCTGTATTGCTGCTTG ATCAATCATTAACAAGAGGATCTAACAGGACACTATTAGA|TAATAGTGTCCTG|TAATTAAGAAGAGTTTTGTTTCATCCTGTATTGCTGCTTG ========== Event 2769 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CACTGACTCAGAAACAAGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAG------------------------GAGGTTATCTCTTGATCCAGGCCA ↓ 3 2 4 1 Chimp: cactgactCAGAAACAAGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAG------------GAGGCTGAAAAGGAGGTTATCTCTTGATCCAGGCCA Gorilla: cactgactCAGAAACAAGCTTTTCAGTTGATGTTCAAATGATCTTGCAGGAGGAGGTTGAAAAG------------GAGGTTATCTCTTGATCCAGGCCA Human: CACTGACTCAGAAACAAGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAG------------------------GAGGTTATCTCTTGATCCAGGCCA Cluster: [ ] Orangutan: CACTGACTCAGAAACAAGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAGGAGGCTGAAAAG------------GAGGTTATCTCTTGATCCAGGCCA Human > Chimp ------------- chr5:110424213-110424219 Template switch process: F1: L AAACAAGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAGGAGG 1 F3: 4 GGAGGTTATCTCTTGATCCAGGCCATCCTATGGCAGTGTCT R RF: AAACAAGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAGGAGGTTATCTCTTGATCCAGGCCATCCTATGGCAGTGTCT RR: TTTGTTCGAAAAGTCTACTACAAGTTGTCTAGAACGTCCTCCTCCAATAGAGAACTAGGTCCGGTAGGATACCGTCACAGA F2: 3 AAAAGTC 2 Unidirectional alignment (log-probability: -28.2) AGCTTTTCAGATGATGTTCAACAGATCTTGCAGGaggaggctgaaaAGGAGGTTATCTCTTGATCCAGGCCATCCTATGGCAGTGTC AGCTTTTCAGATGATGTTCAACAGATCTTGCAGG------------AGGAGGTTATCTCTTGATCCAGGCCATCCTATGGCAGTGTC Template switch alignment (log-probability: -16.3) AGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAGGAGG|CTGAAAA|GGAGGTTATCTCTTGATCCAGGCCATCCTATGGCAGTGTC AGCTTTTCAGATGATGTTCAACAGATCTTGCAGGAGGAGG|CTGAAAA|GGAGGTTATCTCTTGATCCAGGCCATCCTATGGCAGTGTC ========== Event 2770 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTGGGCTGGTTCTATTATTGCTTCCAATACACAGGCATAATTTAGTAAAACTCACAACTCACAACTTTGCCTTAGGAAatatatat-acatatatatTTAAGCATTAACCACAGGCA--------------------------------------------------------------------AAAAAGACTCCAAGAAATGTGGGCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTAAACAAAAGGTGGTTGTATT Chimp: TCTGGGCTGGTTCTATTATTGCTTCCAATACACAGGCATAATTTAGTAA---------------------------------------------------------------------AACTCACAACTCACAACTTTGCCTTGGGAAatatatatacatatatatTTAAGCATTAACCACAGGCAAAAAAGACTCCAAGAAATGTGCCCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTAAACAAAAGGTGGTTGTATT ↑ 1 3 4 2 Gorilla: TCTGGGCTGGTTCTATTATTGTTTCCAATACACAGGCATAATTTAGTAAAACTCACAACTCACAACTTTGCCTTAGGAAatatatatannatatatatTTAAGCATTAACCACAGGCA--------------------------------------------------------------------AAAAAGACTCCAAGAAATGTGGGCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTAAACAAAAGATGGTTGTATT Human: GCTGGGCTGGTTCTATTATTGCTTCCAATACACAGGCATAATTTAGTAAAACTCACAACTCACAACTTTGCCTTAGGAAatatatat-acatatatatTTAAGCATTAACCACAGGCA--------------------------------------------------------------------AAAAAGACTCCAAGAAATGTGGGCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTAAACAAAAGGTGGTTGTATT Cluster: [] Orangutan: GCTGGGCTGGTTCTATTATTGCTTCCAATACGCAGACATAATTTAGTAAAACTCACAACTCACAACTTTGCCTTAGGTAATATATAC-ACATATATATTTAAGCATTAACCACAGGCA--------------------------------------------------------------------AAAAGGACTCAAAGAAATGGGCCCACATTTCTTTGAGTCTTTTTTGCCTGTGGTTAAT-GTTAAACAAAAGGTGGTTGTATT Gorilla > Chimp --------------- chr5:170349034-170349074 Template switch process: F1: L TT 1 F3: 4 CACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTA R RF: TTGTTTCCAATACACAGGCATAATTTAGTAAAACTCACAACTCACAACTTTGCCTTAGGAAATATATATANNATATATATTTAAGCATTAACCACAGGCAAAAAAGACTCCAAGAAATGTGGGCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTA RR: AACAAAGGTTATGTGTCCGTATTAAATCATTTTGAGTGTTGAGTGTTGAAACGGAATCCTTTATATATATNNTATATATAAATTCGTAATTGGTGTCCGTTTTTTCTGAGGTTCTTTACACCCGTGTAAAGAACCTCAGAAAAAACGGACACCAATTACGAAT F2: 3 CCGTGTAAAGAACCTCAGAAAAAACGGACACCAATTACGAA 2 Unidirectional alignment (log-probability: -45.1) ttaagcattaaccacaggcaAAAAAGACTCCAAGAAATGTGccCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTA --------------------AAAAAGACTCCAAGAAATGTGGGCACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTA Template switch alignment (log-probability: -20) TT|AAGCATTAACCACAGGCAAAAAAGACTCCAAGAAATGTGCC|CACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTA TT|AAGCATTAACCACAGGCAAAAAAGACTCCAAGAAATGTGCC|CACATTTCTTGGAGTCTTTTTTGCCTGTGGTTAATGCTTA ========== Event 2771 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tatactttacgtgtactaact--------catttaattctcagagcagccccctgagttagAG Chimp: TATACTTTACGTGTACTAACT--------TATTTAATTCTCAGAGCAGCCCCCTGAGTTAGAG ↓ 1 3 4 2 Gorilla: TATACTTTACGTGTACTAACTCTGAGAATTAAATAATTCTCAGAGCAGCCCCCTGAGTTAGAG Human: tatactttacgtgtactaact--------catttaattctcagagcagccccctgagttagAG Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr5:95399003-95399014 Template switch process: F1: L TAACATCTATCGGCACATATTATACTTTACGTGTACTAACT 1 F3: 4 TAATTCTCAGAGCAGCCCCCTGAGTTAGAGATAAGAATAA R RF: TAACATCTATCAGCACATATTATACTTTACGTGTACTAACTTATTTAATTCTCAGAGCAGCCCCCTGAGTTAGAGATAAGAATAA RR: ATTGTAGATAGTCGTGTATAATATGAAATGCACATGATTGAATAAATTAAGAGTCTCGTCGGGGGACTCAATCTCTATTCTTATT F2: 3 AAATTAAGAGTC 2 Unidirectional alignment (log-probability: -39) AACATCTATCgGCACATATTATACTTTACGTGTACTAACtctgagaaTTAaaTAATTCTCAGAGCAGCCCCCTGAGTTAGAGATAAGAATAA AACATCTATCAGCACATATTATACTTTACGTGTACTAAC--------TTATTTAATTCTCAGAGCAGCCCCCTGAGTTAGAGATAAGAATAA Template switch alignment (log-probability: -22.8) AACATCTATCgGCACATATTATACTTTACGTGTACTAACT|CTGAGAATTAAA|TAATTCTCAGAGCAGCCCCCTGAGTTAGAGATAAGAATAA AACATCTATCAGCACATATTATACTTTACGTGTACTAACT|CTGAGAATTAAA|TAATTCTCAGAGCAGCCCCCTGAGTTAGAGATAAGAATAA ========== Event 2772 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATATTGAGTTTTCATAATCATATCTAGTGATCATAATCTCTGATCACTAGAAAGAGAGGTTCCTCTTCCC Chimp: ACACTGAGTTTTCATAATCAT-----------ATAATCTCTGATCACTAGAAAGAGAGGCTCCTCTTCCC Gorilla: ATATTGAGTTTTCATAATCAT-----------ATAATCTCTGATCACTAGAAAGAGAGGCTCCTCTTCAC ↓ 41 3 2 Human: ATATTGAGTTTTCATAATCATATCTAGTGATCATAATCTCTGATCACTAGAAAGAGAGGTTCCTCTTCCC Cluster: [ ] Orangutan: ATATTGAGTTTTCATAATCAT-----------ATAATCTCTGATCACTAGAAAGAGAGGCTCCACTTCCC Gorilla > Human --------------- chr5:113941586-113941594 Template switch process: F1: L GAAATTCAGGCAATTTAGGAATATTGAGTTTTCATAATCATAT 1 F3: 4 ATAATCTCTGATCACTAGAAAGAGAGGTTCCTCTTCCCAA R RF: GAAATTCAGGCAATTTAGGAATATTGAGTTTTCATAATCATATAATCTCTGATCACTAGAAAGAGAGGCTCCTCTTCACAA RR: CTTTAAGTCCGTTAAATCCTTATAACTCAAAAGTATTAGTATATTAGAGACTAGTGATCTTTCTCTCCGAGGAGAAGTGTT F2: 3 CTAGTGATC 2 Unidirectional alignment (log-probability: -37.7) ATTCAGGCAATTTAGGAATATTGAGTTTTCATAATCATatctagtgatcATAATCTCTGATCACTAGAAAGAGAGGtTCCTCTTCcCAA ATTCAGGCAATTTAGGAATATTGAGTTTTCATAATCAT-----------ATAATCTCTGATCACTAGAAAGAGAGGCTCCTCTTCACAA Template switch alignment (log-probability: -28) ATTCAGGCAATTTAGGAATATTGAGTTTTCATAATCATAT|CTAGTGATC|ATAATCTCTGATCACTAGAAAGAGAGGtTCCTCTTCcCAA ATTCAGGCAATTTAGGAATATTGAGTTTTCATAATCATAT|CTAGTGATC|ATAATCTCTGATCACTAGAAAGAGAGGCTCCTCTTCACAA ========== Event 2773 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTGTAGTATAAAGACAGGTGAGCAGTAAAGCCATTCCTGAGACACCATCAAAATTAGCAATTTGTCTCCTGGTCCAGGGCTGCAAAAGAGCAAGGAAGCTACAGTTTCACAGTTTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCT---------CAAAATATTTTCAAAGTCTTTCCT Chimp: GTTGTAGTATAAAGACAGGCGAGCAGTAAAGCCATTCCTGAGACACCATCAAAATTAGCAATTTGTCTCCTGGTCCAGGGCTGCAAAAGAGCAAGGAAGCTACAATTTCACAGTTTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCTTTTTACTGCTGGAATATTTTCAAAGTCTTTCCT ↑ 3 2 1 4 Gorilla: GTTGTAGTATAAAGACAGGCGAGCAGTAAAGCCATTCCTGAGACACCATCAGAATTAGCAATTTGTCTCCTGGTCCAGGGCTGCAAAAGAGCAAGGAAGCTACAATTTCACAGTTTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCT---------CAAAATATTTTCAAAGTCTTTCCT Human: GTTGTAGTATAAAGACAGGTGAGCAGTAAAGCCATTCCTGAGACACCATCAAAATTAGCAATTTGTCTCCTGGTCCAGGGCTGCAAAAGAGCAAGGAAGCTACAGTTTCACAGTTTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCT---------CAAAATATTTTCAAAGTCTTTCCT Cluster: [ ] Orangutan: GTTGTAGTATAAAGACAGGCGAGCAGTAAAGCCATTCCTGAGACACCATCAAAATTAGCAATTTGTCTCCTGGTCCAGGGCTCCAAAAGAGCAAGGAAGCTACAATTTCACAGTTTTTGGTATTCTTTAGGGGAGAGTAAAAAGTCCTGGTCT---------CAGAATATTTTCAAAGTCTTTCCT Gorilla > Chimp --------------- chr5:67552879-67552889 Template switch process: F1: L GTTTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCTT 1 F3: 4 AATATTTTCAAAGTCTTTCCTCTTCTCTCTCTGCCTGGCT R RF: CGAGCAGTAAAGCCATTCCTGAGACACCATCAGAATTAGCAATTTGTCTCCTGGTCCAGGGCTGCAAAAGAGCAAGGAAGCTACAATTTCACAGTTTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCTCAAAATATTTTCAAAGTCTTTCCTCTTCTCTCTCTGCCTGGCT RR: GCTCGTCATTTCGGTAAGGACTCTGTGGTAGTCTTAATCGTTAAACAGAGGACCAGGTCCCGACGTTTTCTCGTTCCTTCGATGTTAAAGTGTCAAAAACCATAAGAAATCCCGTCTCATTTTTCAGGACCAGAGTTTTATAAAAGTTTCAGAAAGGAGAAGAGAGAGACGGACCGA F2: 3 GGTCGTCATTT 2 Unidirectional alignment (log-probability: -38) TTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCT---ttttactgctggAATATTTTCAAAGTCTTTCCTCTTCTCTCTCTGCCTGGCT TTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCTCAA------------AATATTTTCAAAGTCTTTCCTCTTCTCTCTCTGCCTGGCT Template switch alignment (log-probability: -28.2) TTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCTt|TTTACTGCTgG|AATATTTTCAAAGTCTTTCCTCTTCTCTCTCTGCCTGGCT TTTTGGTATTCTTTAGGGCAGAGTAAAAAGTCCTGGTCTC|TTTACTGCTCG|AATATTTTCAAAGTCTTTCCTCTTCTCTCTCTGCCTGGCT ========== Event 2774 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTAATCCCAAATTATGAAGTTACTCCT---GTAAGTTGCTCTGTGTTCATTCT Chimp: TTTAATCCCAAATTATGAAGTTACTCCT---GCAAGTTGCTCTGTGTTCATTCT Gorilla: TTTAATCCCAAATTATGAAGTTACAGGAGTAACAAGTTGCTCTGTGTTCATTCT ↑ 3 1 2 4 Human: TTTAATCCCAAATTATGAAGTTACTCCT---GTAAGTTGCTCTGTGTTCATTCT Cluster: [ ] Orangutan: TTTAATCCCAAATTATGAAGTTATTCCT---GCAAGTTGCTCCGTGTTCATTCT Human > Gorilla --------------- chr5:66614385-66614393 Template switch process: F1: L GTTGAAGTCATTAACACTTTAATCCCAAATTATGAAGTTAC 1 F3: 4 AAGTTGCTCTGTGTTCATTCTTTTCCCTCTTGTATCCCCT R RF: GTTGAAGTCATTAACACTTTAATCCCAAATTATGAAGTTACTCCTGTAAGTTGCTCTGTGTTCATTCTTTTCCCTCTTGTATCCCCT RR: CAACTTCAGTAATTGTGAAATTAGGGTTTAATACTTCAATGAGGACATTCAACGAGACACAAGTAAGAAAAGGGAGAACATAGGGGA F2: 3 CAATGAGGA 2 Unidirectional alignment (log-probability: -33.9) TTGAAGTCATTAACACTTTAATCCCAAATTATGAAGTTAC------aggagtaacAAGTTGCTCTGTGTTCATTCTTTTCCCTCTTGTATCCCCT TTGAAGTCATTAACACTTTAATCCCAAATTATGAAGTTACTCCTGT---------AAGTTGCTCTGTGTTCATTCTTTTCCCTCTTGTATCCCCT Template switch alignment (log-probability: -16.9) TTGAAGTCATTAACACTTTAATCCCAAATTATGAAGTTAC|AGGAGTAAC|AAGTTGCTCTGTGTTCATTCTTTTCCCTCTTGTATCCCCT TTGAAGTCATTAACACTTTAATCCCAAATTATGAAGTTAC|AGGAGTAAC|AAGTTGCTCTGTGTTCATTCTTTTCCCTCTTGTATCCCCT ========== Event 2775 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGCCCTGTAAAAGTTTGGATGACTGTTGCTTCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCGTCATGGATTTTCCAGCTGATGGCCT ↑ 3 2 1 4 Chimp: GTGCCCTGTAAAAGTTTGGATGACTGTTGCTTCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCATCACGGATTTTCCAGCTGATGGCCT Gorilla: GTGCCCTGTAAAAGTTTGGATGACTGTTGCTTCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCATCATGGATTTTCCGGCTGATGGCCT Human: GTGCCCTGTAAAAGTTTGGATGACTGTTGCTTCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCGTCATGGATTTTCCAGCTGATGGCCT Cluster: [ ] Orangutan: GTGCCCTGTAAA-ATGTGGATGACTGCTGCTTCTCTGAAACTTATCGACACATTTTCCCCAGTCTCTCCCCATCATGGATTTTCCAGCTGATGGCCT Chimp > Human ------------- chr5:116860503-116860507 Template switch process: F1: L TTCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCC 1 F3: 4 GGATTTTCCAGCTGATGGCCTTCAGACTTTCTCATT R RF: ATGACTGTTGCTTCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCATCACGGATTTTCCAGCTGATGGCCTTCAGACTTTCTCATT RR: TACTGACAACGAAGAGACTTTGAATAGGTGTGTAAAAGGGGTCAAAGAGGGGTAGTGCCTAAAAGGTCGACTACCGGAAGTCTGAAAGAGTAA F2: 3 TACTG 2 Unidirectional alignment (log-probability: -27.1) TCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCgTCAtGGATTTTCCAGCTGATGGCCTTCAGACTTTCtcatt TCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCCATCACGGATTTTCCAGCTGATGGCCTTCAGACTTTC----- Template switch alignment (log-probability: -15.8) TCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCC|GTCAT|GGATTTTCCAGCTGATGGCCTTCAGACTTTCTCATT TCTCTGAAACTTATCCACACATTTTCCCCAGTTTCTCCCC|GTCAT|GGATTTTCCAGCTGATGGCCTTCAGACTTTCTCATT ========== Event 2776 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG----------CTAGAATGTCAAAAGCTTTCATATG Chimp: AAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG-----ACACATTGAAATGTCAAAAGCTTT--CATG Gorilla: AAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAGACACA-----TTGAAATGTCAAAAGCTTTCATATG ↓ 3 2 1 4 Human: AAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG----------CTAGAATGTCAAAAGCTTTCATATG Cluster: [ ] Orangutan: AAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAGACACA-----TTGAAATGTCAAAAGCTTTCATATG Gorilla > Human --------------- chr5:115905691-115905694 Template switch process: F1: L ATATTTTAAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG 1 F3: 4 AATGTCAAAAGCTTTCATATGTTTCATGTCCATGTTACTT R RF: ATATTTTAAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAGACACATTGAAATGTCAAAAGCTTTCATATGTTTCACGTCCATGTTACTT RR: TATAAAATTCATACAAACTTTCCGAAGATCGAAATAAGGTCTGTGTAACTTTACAGTTTTCGAAAGTATACAAAGTGCAGGTACAATGAA F2: 3 GATC 2 Unidirectional alignment (log-probability: -32.4) TATTTTAAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG---------ctagAATGTCAAAAGCTTTCATATGTTTCAtGTCCATGTTACTT TATTTTAAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAGACACATTGA----AATGTCAAAAGCTTTCATATGTTTCACGTCCATGTTACTT Template switch alignment (log-probability: -21.7) TATTTTAAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG|CTAG|AATGTCAAAAGCTTTCATATGTTTCAtGTCCATGTTACTT TATTTTAAGTATGTTTGAAAGGCTTCTAGCTTTATTCCAG|CTAG|AATGTCAAAAGCTTTCATATGTTTCACGTCCATGTTACTT ========== Event 2777 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAGTGGAACTAGCTGGGGTG----------TGCTGGGGTGTGCAGAACCACATGAGGTGGTTCTGCAGGTGTCACTGTACC Chimp: GTAGTGGAACTAGCTGGGGTG----------TGCTG---------AACCCACCTCATGTGATTCTGCAGGTGTCACTGTACC ↓ 3 2 4 Gorilla: GTAGTGGAACTAGCTGGGGTG--------------------TGCAGAACCACATGAGGTGGTTCTGCAGGTGTCACTGTACC Human: GTAGTGGAACTAGCTGGGGTG----------TGCTGGGGTGTGCAGAACCACATGAGGTGGTTCTGCAGGTGTCACTGTACC Cluster: [ ] Orangutan: GTAGCGGAACTAGCTGGGGTGTGCTGGGGTG----------TGCAGAACCACATGAGGTGGTTCTGCAGGCGTCACTGTACC Chimp > Gorilla --------------- chr5:99565585-99565595 Template switch process: F1: L TTGCTAGTATGGGCAAGGAGGTAGTGGAACTAGCTGGGGTGTGCAGAACC 1 F3: 4 TTCTGCAGGTGTCACTGTACCAGGGCCTGCAGGAGCACCT R RF: TTGCTAGTATGGGCAAGGAGGTAGTGGAACTAGCTGGGGTGTGCTGAACCCACCTCATGTGATTCTGCAGGTGTCACTGTACCAGGGCCTGCAGGAGCACCT RR: AACGATCATACCCGTTCCTCCATCACCTTGATCGACCCCACACGACTTGGGTGGAGTACACTAAGACGTCCACAGTGACATGGTCCCGGACGTCCTCGTGGA F2: 3 GGTGGAGTACA 2 Unidirectional alignment (log-probability: -38.8) GGGCAAGGAGGTAGTGGAACTAGCTGGGGTGTGCaGAA-CCACaTgAgGTGgTTCTGCAGGTGTCACTGTACCAGGGCCTGCAGGAGCACCT GGGCAAGGAGGTAGTGGAACTAGCTGGGGTGTGCTGAACCCACCTCATGTGATTCTGCAGGTGTCACTGTACCAGGGCCTGCAGGAGCACCT Template switch alignment (log-probability: -22.9) GGGCAAGGAGGTAGTGGAACTAGCTGGGGTGTGCaGAACC|ACATGAGGTGG|TTCTGCAGGTGTCACTGTACCAGGGCCTGCAGGAGCACCT GGGCAAGGAGGTAGTGGAACTAGCTGGGGTGTGCTGAACC|ACATGAGGTGG|TTCTGCAGGTGTCACTGTACCAGGGCCTGCAGGAGCACCT ========== Event 2778 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CACCATCTCCTTTCAAAGGCATGCTTAAAACAAACATTTCATAAGCATAGAAGCaaaaaa------- Chimp: CACCATCTCCTTTCAAAGGCATGCTTAAAACAAACATTTCATAAGCATAGAAGCaaaaaa------- ↑ 1 4 3 2 Gorilla: CACCATCTCCTTTCAAAGGCACGCTTGAAACAAACATTTCATAAGCATAGAAGCaaaaaa------- ↓ 1 4 3 2 Human: CACCATCTCCTTTCAAAGGCATGCTTAAAACAAACATTTCATAAGCATAGAAGCaaaaaa------- Cluster: [ ] Orangutan: CACCATCTCCTTTCAAAGGCATGCTTAAAACAAACATTTCATAAGCGTAGAAGCaaaaaaaaaaaaa Gorilla > Human --------------- chr5:64455874-64455879 Template switch process: F1: L GAGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCA 1 F3: 4 AAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA R RF: GAGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCACGCTTGAAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA RR: CTCTGGGGTTTTCGTGTATGGTGGTAGAGGAAAGTTTCCGTGCGAACTTTGTTTGTAAAGTATTCGTATCTTCGTTTTTTTTTTTTT F2: 3 ATTCGT 2 Unidirectional alignment (log-probability: -29) AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCAtGCTTaAAACAAACATTTCATAAGCATAGAAGCAAAAAAaaaaaaa AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCACGCTTGAAACAAACATTTCATAAGCATAGAAGCAAAAAA------- Template switch alignment (log-probability: -16.5) AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCA|TGCTTA|AAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCA|TGCTTA|AAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA Gorilla > Chimp --------------- chr5:65224525-65224530 Template switch process: F1: L GAGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCA 1 F3: 4 AAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA R RF: GAGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCACGCTTGAAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA RR: CTCTGGGGTTTTCGTGTATGGTGGTAGAGGAAAGTTTCCGTGCGAACTTTGTTTGTAAAGTATTCGTATCTTCGTTTTTTTTTTTTT F2: 3 ATTCGT 2 Unidirectional alignment (log-probability: -29) AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCAtGCTTaAAACAAACATTTCATAAGCATAGAAGCAAAAAAaaaaaaa AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCACGCTTGAAACAAACATTTCATAAGCATAGAAGCAAAAAA------- Template switch alignment (log-probability: -16.5) AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCA|TGCTTA|AAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA AGACCCCAAAAGCACATACCACCATCTCCTTTCAAAGGCA|TGCTTA|AAACAAACATTTCATAAGCATAGAAGCAAAAAAAAAAAAA ========== Event 2779 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAATTCAAATAATAGCATAGCTTTTAG---GTGAGCAACAGCAGGAGGGCAC Chimp: AGGAATTCAAATAATAGCATAGCTTTTAG---GTGAGCAACAGCAGGAGGGCAC ↓ 3 1 2 4 Gorilla: AGGAATTCAAATAATAGCATAGCTTAAAAGCTATGAGCAACAGCAGGAGGGCAC ↑ 3 1 2 4 Human: AGGAATTCAAATAATAGCATAGCTTTTAG---GTGAGCAACAGCAGGAGGGCAC Cluster: [ ] Orangutan: AGGAATTCAAATAATAGCATAGCTTTTAG---GTGAGCAACAGCAGGAGGGCAC Human > Gorilla --------------- chr5:64771718-64771725 Template switch process: F1: L GATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTT 1 F3: 4 TGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT R RF: GATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTTTTAGGTGAGCAACAGCAGGAGGGCACAATATCTGCTTTCAGTGTT RR: CTATATTGATCTTCTTTCCTTAAGTTTATTATCGTATCGAAAATCCACTCGTTGTCGTCCTCCCGTGTTATAGACGAAAGTCACAA F2: 3 ATCGAAAA 2 Unidirectional alignment (log-probability: -37.3) ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTTaaAaGctaTGAGCAACAGCAGGAGGGCACAATtTCTGCTTTCAGTGTT ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTTTTAGG---TGAGCAACAGCAGGAGGGCACAATATCTGCTTTCAGTGTT Template switch alignment (log-probability: -22.3) ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTT|AAAAGCTA|TGAGCAACAGCAGGAGGGCACAATtTCTGCTTTCAGTGTT ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTT|AAAAGCTA|TGAGCAACAGCAGGAGGGCACAATATCTGCTTTCAGTGTT Chimp > Gorilla --------------- chr5:64771718-64771725 Template switch process: F1: L GATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTT 1 F3: 4 TGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT R RF: GATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTTTTAGGTGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT RR: CTATATTGATCTTCTTTCCTTAAGTTTATTATCGTATCGAAAATCCACTCGTTGTCGTCCTCCCGTGTTAAAGACGAAAGTCACAA F2: 3 ATCGAAAA 2 Unidirectional alignment (log-probability: -31.8) ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTTaaAaGctaTGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTTTTAGG---TGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT Template switch alignment (log-probability: -16.7) ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTT|AAAAGCTA|TGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT ATATAACTAGAAGAAAGGAATTCAAATAATAGCATAGCTT|AAAAGCTA|TGAGCAACAGCAGGAGGGCACAATTTCTGCTTTCAGTGTT ========== Event 2780 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTAAAAGGAGTTATGTGAGTAC------AGCATCCCACTCTAGGTAATAGCTCTTG Chimp: ATTAAAAGGAGTTATGTGAGTAC------AGCATCCCACTCTAGGTAATAGCTCTTG ↓ 13 4 2 Gorilla: ATTAAAAGGAGTTATGTGAGTGTGATGCTGTCATCACACTCTAGGTAATAGCTCTTG ↑ 13 4 2 Human: ATTAAAAGGAGTTATGTGAGTAC------AGCATCCCACTCTAGGTAATAGCTCTTG Cluster: [ ] Orangutan: ATTAAAAGGAGTTATGTGAGTAC------AGCATCTCACTATAGGTAACAGCTCTTG Human > Gorilla --------------- chr5:100668891-100668900 Template switch process: F1: L CAGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT 1 F3: 4 CATCACACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGTATTTA R RF: CAGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGTACAGCATCCCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGTATTTA RR: GTCCAACCCGTTAAACCACTTAATTTTCCTCAATACACTCATGTCGTAGGGTGAGATCCATTATCGAGAACCATCTCGGGATACATAAAT F2: 3 TGTCGTAGTG 2 Unidirectional alignment (log-probability: -39.3) AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT---GtgatgctgtCATCaCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGTACAG---------CATCCCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT Template switch alignment (log-probability: -28.2) AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT|GtGATGCTGT|CATCaCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT|GGGATGCTGT|CATCCCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT Chimp > Gorilla --------------- chr5:100668891-100668900 Template switch process: F1: L CAGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT 1 F3: 4 CATCACACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGTATTTA R RF: CAGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGTACAGCATCCCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGTATTTA RR: GTCCAACCCGTTAAACCACTTAATTTTCCTCAATACACTCATGTCGTAGGGTGAGATCCATTATCGAGAACCATCTCGGGATACATAAAT F2: 3 TGTCGTAGTG 2 Unidirectional alignment (log-probability: -39.3) AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT---GtgatgctgtCATCaCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGTACAG---------CATCCCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT Template switch alignment (log-probability: -28.2) AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT|GtGATGCTGT|CATCaCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT AGGTTGGGCAATTTGGTGAATTAAAAGGAGTTATGTGAGT|GGGATGCTGT|CATCCCACTCTAGGTAATAGCTCTTGGTAGAGCCCTATGT ========== Event 2781 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGAACTCAGACACACACTGAAC----------CAC-----TGCAAGAGCATCTCCTTCACGACTGTCTGC ↓ 1 34 2 Chimp: CTGAACTCAGACACACACTGATGCTCTTGCAGT---GGCACTGCAAGAGCATCTCCTTCACGACTGTCTGC ↑ 1 34 2 Gorilla: CTGAACTCAGACACACACTGAAC----------CAC-----TGCAAGAGCATCTCCTTCATGACTGTCTGC Human: CTGAACTCAGACACACACTGAAC----------CAC-----TGCAAGAGCATCTCCTTCACGACTGTCTGC Cluster: [ ] Orangutan: CTGAACTCAGACACACACTGAAC----------CAC-----TGCAAGAGCATCTCCTTCACAACTGTCTGC Human > Chimp ------------- chr5:12133037-12133050 Template switch process: F1: L GCTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA 1 F3: 4 CACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACACAG R RF: GCTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGAACCACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACACAG RR: CGATTACCGACCTTAGTTCGGACTTGAGTCTGTGTGTGACTTGGTGACGTTCTCGTAGAGGAAGTGCTGACAGACGATTCTGTGTC F2: 3 GGTGACGTTCTCGT 2 Unidirectional alignment (log-probability: -40.2) CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGAtgCtcttgcagtggcACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACA CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGAACC------------ACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACA Template switch alignment (log-probability: -17.1) CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA|TGCTCTTGCAGTGG|CACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACA CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA|TGCTCTTGCAGTGG|CACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACA Gorilla > Chimp --------------- chr5:12133037-12133050 Template switch process: F1: L GCTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA 1 F3: 4 CACTGCAAGAGCATCTCCTTCACGACTGTCTGCTAAGACACAG R RF: GCTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGAACCACTGCAAGAGCATCTCCTTCATGACTGTCTGCTAAGACACAG RR: CGATTACCGACCTTAGTTCGGACTTGAGTCTGTGTGTGACTTGGTGACGTTCTCGTAGAGGAAGTACTGACAGACGATTCTGTGTC F2: 3 GGTGACGTTCTCGT 2 Unidirectional alignment (log-probability: -44.8) CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGAtgctcttgcagtggCACTGCAAGAGCATCTCCTTCAcGACTGTCTGCTAAGACA CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA------------ACCACTGCAAGAGCATCTCCTTCATGACTGTCTGCTAAGACA Template switch alignment (log-probability: -23.1) CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA|TGCTCTTGCAGTGG|CACTGCAAGAGCATCTCCTTCAcGACTGTCTGCTAAGACA CTAATGGCTGGAATCAAGCCTGAACTCAGACACACACTGA|TGCTCTTGCAGTGG|CACTGCAAGAGCATCTCCTTCATGACTGTCTGCTAAGACA ========== Event 2782 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CAAGAGATAGTCACTGCCGCATAAG----------------------------------AGAATTTAAGAGTGACATATATCCCACTGAAAGCCAACTAGG Chimp: CAAGAGATAGTCACTGCCGCATAAG----------------------------------AGAATTTATGAGTGACATACATCCCACTGAAAGCCAACTAGG ↓ 4 3 2 1 Gorilla: CAAGAGATAGTCACTGCCGCATAAGAGAATTCATGAGTGACATAAATGTCACTCATAAGAGAATTTATGAGTGACATATATCCCACTGAAAGCCAACTAGG Human: CAAGAGATAGTCACTGCCGCATAAG----------------------------------AGAATTTAAGAGTGACATATATCCCACTGAAAGCCAACTAGG Cluster: [ ] Orangutan: CAAGAGGTAGTCACT---------G----------------------------------AGAATTTATGAGTGACATATATCCCACTGAAAGCCAACTACG Chimp > Gorilla --------------- chr5:64528799-64528804 Template switch process: F1: L ATAGAAAACTATGCGGCAAGAGATAGTCACTGCCGCATAAGAGAATTCATGAGTGACATAAAT 1 F3: 4 CATAAGAGAATTTATGAGTGACATATATCCCACTGAAAGCCAACTA R RF: ATAGAAAACTATGCGGCAAGAGATAGTCACTGCCGCATAAGAGAATTTATGAGTGACATACATCCCACTGAAAGCCAACTA RR: TATCTTTTGATACGCCGTTCTCTATCAGTGACGGCGTATTCTCTTAAATACTCACTGTATGTAGGGTGACTTTCGGTTGAT F2: 3 TCACTG 2 Unidirectional alignment (log-probability: -65.3) TAGTCACTGCCGCATAagagaattcatgagtgacataaatgtcactcataAGAGAATTTATGAGTGACATAtATCCCACTGAAAGC TAGTCACTGCCGCATA----------------------------------AGAGAATTTATGAGTGACATACATCCCACTGAAAGC Template switch alignment (log-probability: -33.7) TAGTCACTGCCGCATAAGAGAATTcATGAGTGACATAaAT|GTCACT|CATAAGAGAATTTATGAGTGACATAtATCCCACTGAAAGC TAGTCACTGCCGCATAAGAGAATTTATGAGTGACATACAT|GTCACT|CATAAGAGAATTTATGAGTGACATACATCCCACTGAAAGC ========== Event 2783 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAATTACTGTGCTGGATAGAAACTTAGATTTATGAAATCTAAGTTACATAAATTTTTATTTGA Chimp: TAATTATTGTGCTGGATAGAA-----AAACCATGAAATCTAAGTTACATAAATTTTTATTTGA Gorilla: TAATTATTGTGCTGGATAGAA-----AAACCATGAAATCTAAGTTACATAAATTTTTATTTGA ↓ 1 4 3 2 Human: TAATTACTGTGCTGGATAGAAACTTAGATTTATGAAATCTAAGTTACATAAATTTTTATTTGA Cluster: [ ] Orangutan: TAATTATTGTGCTGGGTAGAA-----AAACCATGAAATCTAAGTTACATAAATTTTTATTTGA Gorilla > Human --------------- chr5:63395275-63395283 Template switch process: F1: L CAGATTGAAAGTTGACATTGTAATTACTGTGCTGGATAGAAA 1 F3: 4 ATGAAATCTAAGTTACATAAATTTTTATTTGAATCTTGCC R RF: CAGATTAAAAGTTGACATTGTAATTATTGTGCTGGATAGAAAAACCATGAAATCTAAGTTACATAAATTTTTATTTGAATCTTGCC RR: GTCTAATTTTCAACTGTAACATTAATAACACGACCTATCTTTTTGGTACTTTAGATTCAATGTATTTAAAAATAAACTTAGAACGG F2: 3 TTTAGATTC 2 Unidirectional alignment (log-probability: -43.3) GATTgAAAGTTGACATTGTAATTAcTGTGCTGGATAGAAA---CttagatttATGAAATCTAAGTTACATAAATTTTTATTTGAATCTTGCC GATTAAAAGTTGACATTGTAATTATTGTGCTGGATAGAAAAACC--------ATGAAATCTAAGTTACATAAATTTTTATTTGAATCTTGCC Template switch alignment (log-probability: -27.9) GATTgAAAGTTGACATTGTAATTAcTGTGCTGGATAGAAA|CTTAGATTT|ATGAAATCTAAGTTACATAAATTTTTATTTGAATCTTGCC GATTAAAAGTTGACATTGTAATTATTGTGCTGGATAGAAA|CTTAGATTT|ATGAAATCTAAGTTACATAAATTTTTATTTGAATCTTGCC ========== Event 2784 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGTTTTCAGCATAGAGTCCCCCTCTGCCCT----GACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGAATTAT Chimp: ATGTTTTCAGCATAGAGTCCCCCTCTGCCCT----GACAGTGTTTCCATCACTGTACATTGGCGATTCCATGTAGAATTAT ↓ 1 4 3 2 Gorilla: ATGTTTTCAGCATAGAGTCCCTCTCTGCCCCAATGTACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGAATTAT ↑ 1 4 3 2 Human: ATGTTTTCAGCATAGAGTCCCCCTCTGCCCT----GACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGAATTAT Cluster: [ ] Orangutan: ATGTTTTCAGCATAGAGTCCCCCTCCGCCCT----GACAGTGTTTCCATCACTGTACATTGACAATTCCATGTAGAATTAT Human > Gorilla --------------- chr5:63558122-63558127 Template switch process: F1: L AGGAAGGATACCTGTCATGTATGTTTTCAGCATAGAGTCCCTCTCTGCCC 1 F3: 4 ACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA R RF: AGGAAGGATACCTGTCATGTATGTTTTCAGCATAGAGTCCCCCTCTGCCCTGACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA RR: TCCTTCCTATGGACAGTACATACAAAAGTCGTATCTCAGGGGGAGACGGGACTGTCACAAAGGTAGTGACATGTAACCGTTAAGGTACATCT F2: 3 TGTAAC 2 Unidirectional alignment (log-probability: -32.1) CCTGTCATGTATGTTTTCAGCATAGAGTCCCtCTCTGCCCcaaTGtACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA CCTGTCATGTATGTTTTCAGCATAGAGTCCCCCTCTGCCC---TG-ACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA Template switch alignment (log-probability: -22.2) CCTGTCATGTATGTTTTCAGCATAGAGTCCCtCTCTGCCC|CAATGT|ACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA CCTGTCATGTATGTTTTCAGCATAGAGTCCCCCTCTGCCC|CAATGT|ACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA Chimp > Gorilla --------------- chr5:63558122-63558127 Template switch process: F1: L AGGAAGGATACCTGTCATGTATGTTTTCAGCATAGAGTCCCTCTCTGCCC 1 F3: 4 ACAGTGTTTCCATCACTGTACATTGGCAATTCCATGTAGA R RF: AGGAAGGATACCTGTCATGTATGTTTTCAGCATAGAGTCCCCCTCTGCCCTGACAGTGTTTCCATCACTGTACATTGGCGATTCCATGTAGA RR: TCCTTCCTATGGACAGTACATACAAAAGTCGTATCTCAGGGGGAGACGGGACTGTCACAAAGGTAGTGACATGTAACCGCTAAGGTACATCT F2: 3 TGTAAC 2 Unidirectional alignment (log-probability: -37.6) CCTGTCATGTATGTTTTCAGCATAGAGTCCCtCTCTGCCCcaaTGtACAGTGTTTCCATCACTGTACATTGGCaATTCCATGTAGA CCTGTCATGTATGTTTTCAGCATAGAGTCCCCCTCTGCCC---TG-ACAGTGTTTCCATCACTGTACATTGGCGATTCCATGTAGA Template switch alignment (log-probability: -27.7) CCTGTCATGTATGTTTTCAGCATAGAGTCCCtCTCTGCCC|CAATGT|ACAGTGTTTCCATCACTGTACATTGGCaATTCCATGTAGA CCTGTCATGTATGTTTTCAGCATAGAGTCCCCCTCTGCCC|CAATGT|ACAGTGTTTCCATCACTGTACATTGGCGATTCCATGTAGA ========== Event 2785 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CATTACCTGTAGTGAAGCA-TCTGT-ATGCTTAATAAATACAAATTAAGCGGGGAGTAAAAAACTTATAATTT Chimp: CATTACCTGTAGTGAAGCATACAGTAGTGCTTAATAAATACAAATTAAGCAGTGAGTAAAAAACTTATAATTT Gorilla: CATTACCTGTAGTGAAGCATACAGTAGTGCTTAATAAATACAAATTAAGCAGTGAGTAAAAAACTTATAATTT ↓ 3 2 4 Human: CATTACCTGTAGTGAAGCA-TCTGT-ATGCTTAATAAATACAAATTAAGCGGGGAGTAAAAAACTTATAATTT Cluster: [ ] Orangutan: CATTACCTGTAGTGAAGTATACAGTAGTGCTTAATAAATACAAATTAAGCAGTGAGTAAAAAACTTAGAATTT Gorilla > Human --------------- chr5:60526382-60526386 Template switch process: F1: L TAGTGAAGCAT 1 F3: 4 TGCTTAATAAATACAAATTAAGCGGGGAGTAAAAAACTTATAATTTTAATTTGTTTCATGAAGTAT R RF: TAGTGAAGCATACAGTAGTGCTTAATAAATACAAATTAAGCAGTGAGTAAAAAACTTATAATTTTAATTTGTTTCATGAAGTAT RR: ATCACTTCGTATGTCATCACGAATTATTTATGTTTAATTCGTCACTCATTTTTTGAATATTAAAATTAAACAAAGTACTTCATA F2: 3 ATGTC 2 Unidirectional alignment (log-probability: -37.3) TAGTGAAGCAT-CtGTA-TGCTTAATAAATACAAATTAAGCgGgGAGTAAAAAACTTA TAGTGAAGCATACAGTAGTGCTTAATAAATACAAATTAAGCAGTGAGTAAAAAACTTA Template switch alignment (log-probability: -27.3) TAGTGAAGCAT|CTGTA|TGCTTAATAAATACAAATTAAGCgGgGAGTAAAAAACTTA TAGTGAAGCAT|CTGTA|TGCTTAATAAATACAAATTAAGCAGTGAGTAAAAAACTTA ========== Event 2786 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCATGTACTTCACATGATTTTACATA--------------------------------------------------------AATTAAAGAAATTGAGTAATCTCAGTGAATTTAAGATTATACATTTCTATTGAATGATTTCAACCATCCCATGATTATATTTG Chimp: CCATGTACTTCACATTATTTTACATA--------------------------------------------------------AATTAAAGAAATTGAGTAATCTCAGTGAATTTAAGATTATACATTTCTATTGAATGATTTCAACCATCCCATGATTATATTTG ↓ 4 1 3 2 Gorilla: CCATGTACTTCACATTATTTTGCTTGAAATCATTCAATAGAAATGTATAATCTTAAATTCACTGAGATTACTCAATTTCTTACATAAAAGAAATTGAGTAATCTCAGTGAATTTAAGATTATACATTTCTATTGAATGATTTCAAGCATCCCATGATTATATTTG Human: CCATGTACTTCACATGATTTTACATA--------------------------------------------------------AATTAAAGAAATTGAGTAATCTCAGTGAATTTAAGATTATACATTTCTATTGAATGATTTCAACCATCCCATGATTATATTTG Cluster: [ ] Orangutan: CCATGTACTTCACATTATTTTACATA--------------------------------------------------------AATTAAAGAAATGGAGTAAACTCAGTGAATTTACGATTATACATTTCTATTGAATGATCTCAACCATCCCGTGAATGTATTTG Chimp > Gorilla --------------- chr17:83371035-83371090 Template switch process: F1: L TATCATTAGAATTCCAAGGCCCATGTACTTCACATTATTTTGC 1 F3: 4 TTACATA----AAAGAAATTGAGTAATCTCAGTGAATTTAAGATTATACAT R RF: TATCATTAGAATTCCAAGGCCCATGTACTTCACATTATTTTACATAAATTAAAGAAATTGAGTAATCTCAGTGAATTTAAGATTATACATTTCTATTGAATGATTTCAA RR: ATAGTAATCTTAAGGTTCCGGGTACATGAAGTGTAATAAAATGTATTTAATTTCTTTAACTCATTAGAGTCACTTAAATTCTAATATGTAAAGATAACTTACTAAAGTT F2: 3 CTTTAACTCATTAGAGTCACTTAAATTCTAATATGTAAAGATAACTTACTAAAGTT 2 Unidirectional alignment (log-probability: -107) CATTAGAATTCCAAGGCCCATGTACTTCACATTATTttgcttgaaatcattcaatagaaatgtataatcttaaattcactgagattactcaatttcTTACATA----AAAGAAATTGAGTAATCTCAGTGAATTTAAGAT CATTAGAATTCCAAGGCCCATGTACTTCACATTATT------------------------------------------------------------TTACATAAATTAAAGAAATTGAGTAATCTCAGTGAATTTAAGAT Template switch alignment (log-probability: -38.5) CATTAGAATTCCAAGGCCCATGTACTTCACATTATTTTgC|TTGAAATCATTCAATAGAAATGTATAATCTTAAATTCACTGAGATTACTCAATTTC|TTACATA----AAAGAAATTGAGTAATCTCAGTGAATTTAAGAT CATTAGAATTCCAAGGCCCATGTACTTCACATTATTTTAC|TTGAAATCATTCAATAGAAATGTATAATCTTAAATTCACTGAGATTACTCAATTTC|TTACATAAATTAAAGAAATTGAGTAATCTCAGTGAATTTAAGAT ========== Event 2787 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CTTGATGGCTTGGGTGTGACTTCAGGTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGTG----AGAAGTCAGTTTGCTCCCTGACTCAATTACAATAAGTTAGA ↑ 1 4 3 2 Chimp: CTTGATGGCTTGGGTGTGACTATAAGTTCTGAAAATGATGTTTCAGTCATAAGTAAATT----AGTGAGAAGTCAGTTTGCTCCCTGACTCAATTATAATAAGTTAGA Gorilla: Human: CTTGATGGCTTGGGTGTGACTTCAGGTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGTG----AGAAGTCAGTTTGCTCCCTGACTCAATTACAATAAGTTAGA Cluster: [ ] Orangutan: Chimp > Human ------------- chr5:168639513-168639516 Template switch process: F1: L AACAGATACTAAATACGTACCTTGATGGCTTGGGTGTGACT 1 F3: 4 GTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGTG R RF: AAGAGATACTAAATACGTACCTTGATGGCTTGGGTGTGACTATAAGTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGTGAGAAGTCAGTTTGCTCCCTGA RR: TTCTCTATGATTTATGCATGGAACTACCGAACCCACACTGATATTCAAGACTTTTACTACAAAGTCAGTATTCATTTAATCACTCTTCAGTCAAACGAGGGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -34.8) AcAGATACTAAATACGTACCTTGATGGCTTGGGTGTGACTtcAgGTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGtg AGAGATACTAAATACGTACCTTGATGGCTTGGGTGTGACTATAAGTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAG-- Template switch alignment (log-probability: -21.7) AcAGATACTAAATACGTACCTTGATGGCTTGGGTGTGACT|TCAG|GTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGTG AGAGATACTAAATACGTACCTTGATGGCTTGGGTGTGACT|TCAG|GTTCTGAAAATGATGTTTCAGTCATAAGTAAATTAGTG ========== Event 2788 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATCCTCCTCTCTTTCCAACT--------CAGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG ↓ 1 4 3 2 Chimp: GATCCTCCTCTCTTTCCAACTCTTACAGATGGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTGCAG ↑ 1 4 3 2 Gorilla: CATCCTCCTCTCTTTCCAACT--------CAGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG Human: GATCCTCCTCTCTTTCCAACT--------CAGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG Cluster: [ ] Orangutan: GGTCCTCCTCTCTTTCCAACT--------CAGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACGG Human > Chimp ------------- chr5:122735182-122735190 Template switch process: F1: L CTTCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTC 1 F3: 4 GATATAACTTCCATCTGTAAGAGTAGGTTTATAATTGCAG R RF: CTTCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTCAGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG RR: GAAGGACTCGTGATCAAGTTCTAGGAGGAGAGAAAGGTTGAGTCTATATTGAAGGTAGACATTCTCATCCAAATATTAATGTC F2: 3 GTAGACATT 2 Unidirectional alignment (log-probability: -34.4) TCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTCttacagatgGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTgCAG TCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTC--------AGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG Template switch alignment (log-probability: -22.4) TCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTC|TTACAGATG|GATATAACTTCCATCTGTAAGAGTAGGTTTATAATTgCAG TCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTC|TTACAGATG|GATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG Gorilla > Chimp --------------- chr5:122735182-122735190 Template switch process: F1: L CTTCCTGAGCACTAGTTCAAGATCCTCCTCTCTTTCCAACTC 1 F3: 4 GATATAACTTCCATCTGTAAGAGTAGGTTTATAATTGCAG R RF: CTTCCTGAGCACTAGTTCAACATCCTCCTCTCTTTCCAACTCAGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG RR: GAAGGACTCGTGATCAAGTTGTAGGAGGAGAGAAAGGTTGAGTCTATATTGAAGGTAGACATTCTCATCCAAATATTAATGTC F2: 3 GTAGACATT 2 Unidirectional alignment (log-probability: -39) TCCTGAGCACTAGTTCAAgATCCTCCTCTCTTTCCAACTCttacagatgGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTgCAG TCCTGAGCACTAGTTCAACATCCTCCTCTCTTTCCAACTC--------AGATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG Template switch alignment (log-probability: -27.9) TCCTGAGCACTAGTTCAAgATCCTCCTCTCTTTCCAACTC|TTACAGATG|GATATAACTTCCATCTGTAAGAGTAGGTTTATAATTgCAG TCCTGAGCACTAGTTCAACATCCTCCTCTCTTTCCAACTC|TTACAGATG|GATATAACTTCCATCTGTAAGAGTAGGTTTATAATTACAG ========== Event 2789 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: GATTTCTGCTGTCTTCTGAACCCACTCAGAGAGGTAGGAAACCCAGAATCAGGCTGGGGGATACCCCATGGGAGCCtgcattcatttcctagtgatgaggtaacaaataccacaaactgagtggcttgaatagcagaaatgtat Chimp: GAGTTCTGCTGTCTTCTGAACTC---AGAAGAGGTAGGAAACCCAGAATCAGGCTGGAGGATACCCCATGGGAGCCtgcattcatttcctagtgatgaggtaacaaataccacaaactgagtggcttgaatagcagaaatgtat ↓ 1 4 3 2 Gorilla: GAGTTCTGCTGTCTTCTGAACCCACTCAGAGAGGTAGGAAACCCAGAATCAGGCTGGGAGATACCCCATGGGAGCCtgcattcatttcctagttatgaggtaacaaataccacaaactgagtggcttgaatagcagaaatgtat Human: GATTTCTGCTGTCTTCTGAACCCACTCAGAGAGGTAGGAAACCCAGAATCAGGCTGGGGGATACCCCATGGGAGCCtgcattcatttcctagtgatgaggtaacaaataccacaaactgagtggcttgaatagcagaaatgtat Cluster: [ ] Orangutan: GAGTTCTGCTGTCTTCTGAACCCACTCAGAGAGGGAGGAAACCCAGAATCAGGCTGGGGGATACCCCATGGGAGCCtgcattcatttcctagtgatgaggtaacaaataccacaaactgagtggcttgaatagcagaaatgtac Chimp > Gorilla --------------- chr5:58240284-58240291 Template switch process: F1: L TGACCAGGGGTCTTCCTCCAGAGTTCTGCTGTCTTCTGAAC 1 F3: 4 AGAGGTAGGAAACCCAGAATCAGGCTGGGAGATACCCCAT R RF: TGACCAGGGGTCTTCCTCCAGAGTTCTGCTGTCTTCTGAACTCAGAAGAGGTAGGAAACCCAGAATCAGGCTGGAGGATACCCCATGGGAGCCTGCATTCATTTCCTAGTGATGAGGTAACAAATACCACAAACTGAGTGG RR: ACTGGTCCCCAGAAGGAGGTCTCAAGACGACAGAAGACTTGAGTCTTCTCCATCCTTTGGGTCTTAGTCCGACCTCCTATGGGGTACCCTCGGACGTAAGTAAAGGATCACTACTCCATTGTTTATGGTGTTTGACTCACC F2: 3 GACTCACC 2 Unidirectional alignment (log-probability: -37.5) GACCAGGGGTCTTCCTCCAGAGTTCTGCTGTCTTCTGAacccACTCAG-AGAGGTAGGAAACCCAGAATCAGGCTGGgaGATACCCCAT GACCAGGGGTCTTCCTCCAGAGTTCTGCTGTCTTCTGA----ACTCAGAAGAGGTAGGAAACCCAGAATCAGGCTGGAGGATACCCCAT Template switch alignment (log-probability: -27.8) GACCAGGGGTCTTCCTCCAGAGTTCTGCTGTCTTCTGAAC|CCACTCAG|AGAGGTAGGAAACCCAGAATCAGGCTGGgaGATACCCCAT GACCAGGGGTCTTCCTCCAGAGTTCTGCTGTCTTCTGAAC|CCACTCAG|AGAGGTAGGAAACCCAGAATCAGGCTGGAGGATACCCCAT ========== Event 2790 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTATTGAGATATCATTTATATACAGTAAATTATTTAACTGTATATAAACTTTTAATTGTGGAATT Chimp: TTTATTGAGATATCATTTATATACAGTAAATTATAC-------ATTAAACTTTTAATTGCAGAATT Gorilla: TTTATTGAGATATCATTTATATACAGTAAATTATAC-------ATTAAACTTTTAATTGTGGAATT ↓ 3 2 1 4 Human: TTTATTGAGATATCATTTATATACAGTAAATTATTTAACTGTATATAAACTTTTAATTGTGGAATT Cluster: [ ] Orangutan: TTTATTGAGATATCATTTATATACAGTAAATTATAC-------ATTAAACTTTTAATTGTGGAATT Gorilla > Human --------------- chr5:59610030-59610040 Template switch process: F1: L AGCTTTGTTTATTGAGATATCATTTATATACAGTAAATTAT 1 F3: 4 TAAACTTTTAATTGTGGAATTATGTATCTGTTATTTGCTT R RF: AGCTTTGTTTATTGAGATATCATTTATATACAGTAAATTATACATTAAACTTTTAATTGTGGAATTATGTATCTGTTATTTGCTT RR: TCGAAACAAATAACTCTATAGTAAATATATGTCATTTAATATGTAATTTGAAAATTAACACCTTAATACATAGACAATAAACGAA F2: 3 ATATGTCAATT 2 Unidirectional alignment (log-probability: -35.2) GCTTTGTTTATTGAGATATCATTTATATACAGTAAATTAT---TtaactgtataTAAACTTTTAATTGTGGAATTATGTATCTGTTATTTGCTT GCTTTGTTTATTGAGATATCATTTATATACAGTAAATTATACAT----------TAAACTTTTAATTGTGGAATTATGTATCTGTTATTTGCTT Template switch alignment (log-probability: -22.6) GCTTTGTTTATTGAGATATCATTTATATACAGTAAATTAT|TTaACTGTATA|TAAACTTTTAATTGTGGAATTATGTATCTGTTATTTGCTT GCTTTGTTTATTGAGATATCATTTATATACAGTAAATTAT|TTTACTGTATA|TAAACTTTTAATTGTGGAATTATGTATCTGTTATTTGCTT ========== Event 2791 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GACTAAAGAATGAAGGTTTTAAACCTGAATTATATGGGTTTAAACGGGTCAGCATTTTACTAG Chimp: GACTAAAGAATGAAGGTTTTAAACCTGAATTATACAGGTTTAAACGGGTCAGCATTTTACTAG ↑ 3 2 1 4 Gorilla: GACTAAAGAATGAAGGTTTTAAACCTGAATTATA-------TAACGGGTCAGTATTTTACTAG Human: GACTAAAGAATGAAGGTTTTAAACCTGAATTATATGGGTTTAAACGGGTCAGCATTTTACTAG Cluster: [ ] Orangutan: AACTAAAGAATGAAGATTTTAAACCTGAATTATA-------TAACAGGTCAACATTTTACTAG Gorilla > Chimp --------------- chr5:56798259-56798266 Template switch process: F1: L CTAGTCTGACTAAAGAATGAAGGTTTTAAACCTGAATTATA 1 F3: 4 AACGGGTCAGCATTTTACTAGCTCTGGAGACATAGTATTT R RF: CTAGTCTGACTAAAGAATGAAGGTTTTAAACCTGAATTATATAACGGGTCAGTATTTTACTAGCTCTGGAGACATAATATTT RR: GATCAGACTGATTTCTTACTTCCAAAATTTGGACTTAATATATTGCCCAGTCATAAAATGATCGAGACCTCTGTATTATAAA F2: 3 ATTTGGAC 2 Unidirectional alignment (log-probability: -37.5) TAGTCTGACTAAAGAATGAAGGTTTTAAACCTGAATTATAcaggtttaAACGGGTCAGcATTTTACTAGCTCTGGAGACATAgTATTT TAGTCTGACTAAAGAATGAAGGTTTTAAACCTGAATTATA-------TAACGGGTCAGTATTTTACTAGCTCTGGAGACATAATATTT Template switch alignment (log-probability: -27.8) TAGTCTGACTAAAGAATGAAGGTTTTAAACCTGAATTATA|CAGGTTTA|AACGGGTCAGcATTTTACTAGCTCTGGAGACATAgTATTT TAGTCTGACTAAAGAATGAAGGTTTTAAACCTGAATTATA|CAGGTTTA|AACGGGTCAGTATTTTACTAGCTCTGGAGACATAATATTT ========== Event 2792 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTGCTCTTGATTCATTCTCAGACTTGAATTACTGGGTTTGCTTATCTAGAAGGATCAAATTAATCAAAT Chimp: AGTCCTCTTGATTCATTCCCAGACTTGAATTACTGGGTTTGCTTATCTAGAAGGATCAAATTAATCAAAT ↓ 1 4 3 2 Gorilla: AGTCCTCTTGATTCATTCCCAAACTCTAGATA-AGGGTTTGCTTATCTACAAGGATCAAATTAATCAAAT Human: AGTGCTCTTGATTCATTCTCAGACTTGAATTACTGGGTTTGCTTATCTAGAAGGATCAAATTAATCAAAT Cluster: [ ] Orangutan: ACTCCTCTTGATTCGTTCCCAGACTTGAATTACTGTGTTTGCTTATCTAGAAGGATCAAATTAATCAAGT Chimp > Gorilla --------------- chr5:56979918-56979925 Template switch process: F1: L AGGGCTGAGAAGGTGAATGCAGTCCTCTTGATTCATTCCCAAACT 1 F3: 4 GGGTTTGCTTATCTACAAGGATCAAATTAATCAAATAGTT R RF: AGGGCTGAGAAGGTGAATGCAGTCCTCTTGATTCATTCCCAGACTTGAATTACTGGGTTTGCTTATCTAGAAGGATCAAATTAATCAAATAGTT RR: TCCCGACTCTTCCACTTACGTCAGGAGAACTAAGTAAGGGTCTGAACTTAATGACCCAAACGAATAGATCTTCCTAGTTTAATTAGTTTATCAA F2: 3 AATAGATC 2 Unidirectional alignment (log-probability: -40.7) TGAGAAGGTGAATGCAGTCCTCTTGATTCATTCCCAaACT-------CTagataaGGGTTTGCTTATCTAcAAGGATCAAATTAATCAAATAGTT TGAGAAGGTGAATGCAGTCCTCTTGATTCATTCCCAGACTTGAATTACT------GGGTTTGCTTATCTAGAAGGATCAAATTAATCAAATAGTT Template switch alignment (log-probability: -27.9) TGAGAAGGTGAATGCAGTCCTCTTGATTCATTCCCAaACT|CTAGATAA|GGGTTTGCTTATCTAcAAGGATCAAATTAATCAAATAGTT TGAGAAGGTGAATGCAGTCCTCTTGATTCATTCCCAGACT|CTAGATAA|GGGTTTGCTTATCTAGAAGGATCAAATTAATCAAATAGTT ========== Event 2793 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CGTAAACTTCAACGCGTCTAAATGCTAATT-----------------------TGTGATGGGCCAAGAGTAGGCAGAGA Chimp: CATAAACTTCAATGCTTCTAAATGCTAATT-----------------------TGTGATGGGCCAAGAGTAGGCAGAGA ↓ 3 4 2 1 Gorilla: CATAAACTTCAATGCTTCTAAATGCTAATTTGTGATTTAGCATTTGGCCCATTTGTGATGGGCCAAGAGTAGGCAGAGA Human: CGTAAACTTCAACGCGTCTAAATGCTAATT-----------------------TGTGATGGGCCAAGAGTAGGCAGAGA Cluster: [ ] Orangutan: CATAAACTTCAGTGCTTCTAAATGCTAATT-----------------------TGTGATGGGCCAAGAGTAGGCAGAGA Chimp > Gorilla --------------- chr5:57250414-57250422 Template switch process: F1: L AGATATATACACATAAACTTCAATGCTTCTAAATGCTAATTTGTGAT 1 F3: 4 GGCCCATTTGTGATGGGCCAAGAGTAGGCAGAGAAGAGATGATAAAAA R RF: AGATATATACACATAAACTTCAATGCTTCTAAATGCTAATTTGTGATGGGCCAAGAGTAGGCAGAGAAGAGATGATAAAAA RR: TCTATATATGTGTATTTGAAGTTACGAAGATTTACGATTAAACACTACCCGGTTCTCATCCGTCTCTTCTCTACTATTTTT F2: 3 TTTACGATT 2 Unidirectional alignment (log-probability: -44) TACACATAAACTTCAATGCTTCTAAATGCTAAtttgtgatttagcatttggcccaTTTGTGATGGGCCAAGAGTAGGCAGAGAAGAGAT TACACATAAACTTCAATGCTTCTAAATGCTAA-----------------------TTTGTGATGGGCCAAGAGTAGGCAGAGAAGAGAT Template switch alignment (log-probability: -33.8) TACACATAAACTTCAATGCTTCTAAATGCTAATTTGTGAT|TTAGCATTT|gGCccATTTGTGATGGGCCAAGAGTAGGCAGAGAAGAGAT TACACATAAACTTCAATGCTTCTAAATGCTAATTTGTGAT|TTAGCATTT|TGCTAATTTGTGATGGGCCAAGAGTAGGCAGAGAAGAGAT ========== Event 2794 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: atgcaatgcttagcacataatagacactaaataaatatcattttcctattatCATATGGTTAATTCAAAGTGTGTGGTC---------------------------------------------------------------------------------------------------------------------------------------------ATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTAGGAAGTGGATAAAAAG- ↓ 3 4 2 1 Chimp: atgcaatgcttagcacataatagacactaaataaatatcattttcctattatCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACACTTTGAATTAACCATATGATAATAGGAAAATGATATTTATTTAGTGTCAATTAAATAAATATCATTTTCCTATTATCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTAGGAAGTGGATAAAAAG- ↑ 3 4 2 1 Gorilla: atgcaatgcttagcacataatagacactaaataaatatcattttcctattatCATATGGGTAATTCAAAGTGTGTGGTC---------------------------------------------------------------------------------------------------------------------------------------------ATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTAGGAAGTGGATAAAAAG- Human: atgcaatgcttagcacataatagacactaaataaatatcattttcctattatCATATGGTTAATTCAAAGTGTGTGGTC---------------------------------------------------------------------------------------------------------------------------------------------ATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTAGGAAGTGGATAAAAAG- Cluster: [ ] Orangutan: atgcaatgcttagcacataatagacaataaataaatatcaatttcctattatCATATGGCTAACTCAAAGTGTGTGGTC---------------------------------------------------------------------------------------------------------------------------------------------ATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTAGTAAGTGGGTAAAAAGG Human > Chimp ------------- chr5:56448142-56448193 Template switch process: F1: L CATTTTCCTATTATCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCAC 1 F3: 4 TAAATAAATATCATTTTCCTATTATCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTA R RF: ATAGACACTAAATAAATATCATTTTCCTATTATCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTA RR: TATCTGTGATTTATTTATAGTAAAAGGATAATAGTATACCAATTAAGTTTCACACACCAGTAGGACTTCTTGACCCGACCTTAGGTACGTGGTAGTGAAT F2: 3 TAACTGTGATTTATTTATAGTAAAAGGATAATAGTATACCAATTAAGTTTCA 2 Unidirectional alignment (log-probability: -208) gtcatcctgaagaactgggctggaatccatgcaccatcacactttgaattaaccatatgataataggaaaatgatatttatttagtgtcaattaaataaatatCATTTTCCTATTATCATATGGTTAATTCA -------------------------------------------------------------------------------------------------------CATTTTCCTATTATCATATGGTTAATTCA Template switch alignment (log-probability: -28.9) GTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCAC|ACTTTGAATTAACCATATGATAATAGGAAAATGATATTTATTTAGTGTCaAT|TAAATAAATATCATTTTCCTATTATCATATGGTTAATTCA GTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCAC|ACTTTGAATTAACCATATGATAATAGGAAAATGATATTTATTTAGTGTCTAT|TAAATAAATATCATTTTCCTATTATCATATGGTTAATTCA Gorilla > Chimp --------------- chr5:56448142-56448193 Template switch process: F1: L CATTTTCCTATTATCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCAC 1 F3: 4 TAAATAAATATCATTTTCCTATTATCATATGGTTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTA R RF: ATAGACACTAAATAAATATCATTTTCCTATTATCATATGGGTAATTCAAAGTGTGTGGTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCACTTA RR: TATCTGTGATTTATTTATAGTAAAAGGATAATAGTATACCCATTAAGTTTCACACACCAGTAGGACTTCTTGACCCGACCTTAGGTACGTGGTAGTGAAT F2: 3 TAACTGTGATTTATTTATAGTAAAAGGATAATAGTATACCAATTAAGTTTCA 2 Unidirectional alignment (log-probability: -214) gtcatcctgaagaactgggctggaatccatgcaccatcacactttgaattaaccatatgataataggaaaatgatatttatttagtgtcaattaaataaatatCATTTTCCTATTATCATATGGtTAATTCA -------------------------------------------------------------------------------------------------------CATTTTCCTATTATCATATGGGTAATTCA Template switch alignment (log-probability: -46.2) GTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCAC|ACTTTGAATTAaCCATATGATAATAGGAAAATGATATTTATTTAGTGTCaAT|TAAATAAATATCATTTTCCTATTATCATATGGtTAATTCA GTCATCCTGAAGAACTGGGCTGGAATCCATGCACCATCAC|ACTTTGAATTACCCATATGATAATAGGAAAATGATATTTATTTAGTGTCTAT|TAAATAAATATCATTTTCCTATTATCATATGGGTAATTCA ========== Event 2795 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTTAAAGGGAAAAAGGGCGT----GAGC------TCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGaaaaaaaaaTATGGTGAGAAGCTCGCTCCTTTCAACTTGTTTGGTACTGACAGCTGATAGAAGCTATTTTCTAATAATAAACATC Chimp: TTTTAAAGGGAAAAAGGGCGT--GGCAAC---TCTCCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGGaaaaaaaaTATGGTGAGAAGCTCGCTCCTTTCAACTTGTTTGGTACTGACAGCTGATAGAAGCTATTTTCTAATAATAAACATC Gorilla: TTTTAAAGGGAAAAAGGGCGTGG--CAACTCT---CCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGaaaaaaaaaTATGGTGAGAAGCTCGCTCCTTTCAACTTGTTTGGTACTGACAGCTGATAGAAGCTATTTTCTAATAATAAACATC ↓ 1 4 3 2 Human: TTTTAAAGGGAAAAAGGGCGT----GAGC------TCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGaaaaaaaaaTATGGTGAGAAGCTCGCTCCTTTCAACTTGTTTGGTACTGACAGCTGATAGAAGCTATTTTCTAATAATAAACATC Cluster: [ ] Orangutan: TTTTAAAGGGAAAAAGGGCGTGG--CAACTCT---CCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGaa-aaaaaaTATGGTGAGAAGCTCGCTCCTTTCAACTTGTTTGGTACTGACAGCTGATAGAAGCTATTTTCTAATAATAAACATA Gorilla > Human --------------- chr5:54668259-54668262 Template switch process: F1: L ACTTCATTTAATTATTCAGTTTTTAAAGGGAAAAAGGGCGTG 1 F3: 4 CACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGAAA R RF: ACTTCATTTAATTATTCAGTTTTTAAAGGGAAAAAGGGCGTGGCAACTCTCCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGAAAAAAAAATATGGTGAGAAGCTCGCTCCTTTCAACTTGTTTGGTACTGACAGCTGATAGAAGCT RR: TGAAGTAAATTAATAAGTCAAAAATTTCCCTTTTTCCCGCACCGTTGAGAGGTGTGTCACTCGACAAATAAATTTATAGTAATTCCTCTTTTTTTTTATACCACTCTTCGAGCGAGGAAAGTTGAACAAACCATGACTGTCGACTATCTTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -26.5) TTCATTTAATTATTCAGTTTTTAAAGGGAAAAAGGGCGTG--AgCT---CACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGAAA TTCATTTAATTATTCAGTTTTTAAAGGGAAAAAGGGCGTGGCAACTCTCCACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGAAA Template switch alignment (log-probability: -16.3) TTCATTTAATTATTCAGTTTTTAAAGGGAAAAAGGGCGTG|AGCT|CACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGAAA TTCATTTAATTATTCAGTTTTTAAAGGGAAAAAGGGCGTG|AGCT|CACACAGTGAGCTGTTTATTTAAATATCATTAAGGAGAAA ========== Event 2796 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGTGGGTCAGTGTGATCTGA-CTACCAGAAAGAGTCATGCAGACTATAAATGTGATATAttt ↓ 1 4 3 2 Chimp: TTGTGGGTCAGTGTGATCTGACCTGCATGAAAGAGTCATGCAGACTATAAATGTGATATAttt ↑ 1 4 3 2 Gorilla: TTGTGGGTCAGTGTGATCTGA-CTACCAGAAAGAGTCATGCAGACTATAAATGTGATATAttt Human: TTGTGGGTCAGTGTGATCTGA-CTACCAGAAAGAGTCATGCAGACTATAAATGTGATATAttt Cluster: [ ] Orangutan: TTGTGGGTCAGTGTGATCTGA-CTACCAGAAAGAGTCATGCAGACTATAAATGTGATATattt Human > Chimp ------------- chr5:55422810-55422815 Template switch process: F1: L CCTTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC 1 F3: 4 GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG R RF: CCTTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGACTACCAGAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG RR: GGAAAAGATTTTCGTTACGAAACACCCAGTCACACTAGACTGATGGTCTTTCTCAGTACGTCTGATATTTACACTATATAAACCTCC F2: 3 TACGTC 2 Unidirectional alignment (log-probability: -28.5) TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGACctgcaT----GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC-----TACCAGAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG Template switch alignment (log-probability: -16) TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC|CTGCAT|GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC|CTGCAT|GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG Gorilla > Chimp --------------- chr5:55422810-55422815 Template switch process: F1: L CCTTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC 1 F3: 4 GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG R RF: CCTTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGACTACCAGAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG RR: GGAAAAGATTTTCGTTACGAAACACCCAGTCACACTAGACTGATGGTCTTTCTCAGTACGTCTGATATTTACACTATATAAACCTCC F2: 3 TACGTC 2 Unidirectional alignment (log-probability: -28.1) TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGACctgcaT----GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC-----TACCAGAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG Template switch alignment (log-probability: -16.5) TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC|CTGCAT|GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG TTTTCTAAAAGCAATGCTTTGTGGGTCAGTGTGATCTGAC|CTGCAT|GAAAGAGTCATGCAGACTATAAATGTGATATATTTGGAGG ========== Event 2797 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGGAAACTGGACAAGCCCAAGAGTGTCCTTGCTCAATGGATGGGCTGTTTTGACACCTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTGAT Chimp: ATGGAAACTGGACAAGCCCAAAAGT--ACTT-----------------------GACGTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTGAT ↑ 1 4 3 2 Gorilla: ATGGAAACTGGACAAGCCCAAGAGTGTCCTTGCTCAATGGATGGGCTATTTTGACACCTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTGAT Human: ATGGAAACTGGACAAGCCCAAGAGTGTCCTTGCTCAATGGATGGGCTGTTTTGACACCTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTGAT Cluster: [ ] Orangutan: ATGGAAACTGGACAAGCCCACGAGTGTCCTTGCTCAATGGATGGGCTATTTTGACACCTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTGAT Gorilla > Chimp --------------- chr5:127528784-127528791 Template switch process: F1: L GTCCTGCCTATCACATGTGAATGGAAACTGGACAAGCCCAAAAGT 1 F3: 4 TACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTG R RF: GTCCTGTCTATCACATGTGAATGGAAACTGGACAAGCCCAAGAGTGTCCTTGCTCAATGGATGGGCTATTTTGACACCTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTG RR: CAGGACAGATAGTGTACACTTACCTTTGACCTGTTCGGGTTCTCACAGGAACGAGTTACCTACCCGATAAAACTGTGGATGAAAACTTTGGTGCAGTTCAGTGCATTGATCCAAAGAC F2: 3 GCAGTTCA 2 Unidirectional alignment (log-probability: -43.1) GcCTATCACATGTGAATGGAAACTGGACAAGCCCAAaAGT----------------------------ACttgACgTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTG GTCTATCACATGTGAATGGAAACTGGACAAGCCCAAGAGTGTCCTTGCTCAATGGATGGGCTATTTTGAC---ACCTACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTG Template switch alignment (log-probability: -27.9) GcCTATCACATGTGAATGGAAACTGGACAAGCCCAAaAGT|ACTTGACG|TACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTG GTCTATCACATGTGAATGGAAACTGGACAAGCCCAAGAGT|ACTTGACG|TACTTTTGAAACCACGTCAAGTCACGTAACTAGGTTTCTG ========== Event 2798 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gctctcaagaaactcagagtttagtggCT-----TCTTTTCCTCATTAAAGGGTTCCTTTGTTCCTTTGTTG Chimp: gctctcaagaaactcagagtttagtggCT-----TCTTTTCCTCATTAAAGAGTTCCTTTGTTCCTTCGTTG ↓ 3 1 2 4 Gorilla: gctctcaagaaactcagagtttagtAGCCACTAAACTTTTCCTCATTAAGGGGTTCCTTTGTTCCTTCGTTG Human: gctctcaagaaactcagagtttagtggCT-----TCTTTTCCTCATTAAAGGGTTCCTTTGTTCCTTTGTTG Cluster: [ ] Orangutan: gctctcaagaaactcagagtttagtggCT-----TCTTTTCCTCATTAAAGAGTTCCTTTGTTCCTTCGTTG Chimp > Gorilla --------------- chr5:110713016-110713025 Template switch process: F1: L GAAACTCAGAGTTTAGT 1 F3: 4 CTTTTCCTCATTAAGGGGTTCCTTTGTTCCTTCGTTGTTCTTGTTTTCTACTTGGAA R RF: GAAACTCAGAGTTTAGTGGCTTCTTTTCCTCATTAAAGAGTTCCTTTGTTCCTTCGTTGTTCTTGTTTTCTACTTGGAA RR: CTTTGAGTCTCAAATCACCGAAGAAAAGGAGTAATTTCTCAAGGAAACAAGGAAGCAACAAGAACAAAAGATGAACCTT F2: 3 AAATCACCGA 2 Unidirectional alignment (log-probability: -45.6) GAAACTCAGAGTTTAGTaGCcactaaaCTTTTCCTCATTAAgGgGTTCCTTTGTTCCTTCGTTGTTC GAAACTCAGAGTTTAGTGGCT-----TCTTTTCCTCATTAAAGAGTTCCTTTGTTCCTTCGTTGTTC Template switch alignment (log-probability: -27.9) GAAACTCAGAGTTTAGT|AGCCACTAAA|CTTTTCCTCATTAAgGgGTTCCTTTGTTCCTTCGTTGTTC GAAACTCAGAGTTTAGT|AGCCACTAAA|CTTTTCCTCATTAAAGAGTTCCTTTGTTCCTTCGTTGTTC ========== Event 2799 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAGAGAAACAGACATTAGTTATGTCTTTAAAAAACCTGGCCAA--------CAGACAAACCTAAGTAAAATAGCCTGAGGAA ↓ 13 24 ↑ 13 24 Chimp: AAGAGAAACAGACATTAGTTAGGTTTGTC----TGTTGGCCAG----GTTTTTTAAAGACATAAGTAAAATAGCCTGAGGAA Gorilla: AAGAGAAACAGACATTAGTTAGGTTTGTC----TGTTGGCCAGGTTT----TTTAAAGACATAAATAAAATAGCCTGAGGAA Human: AAGAGAAACAGACATTAGTTATGTCTTTAAAAAACCTGGCCAA--------CAGACAAACCTAAGTAAAATAGCCTGAGGAA Cluster: [ ] Orangutan: AAGAGAAACAGACATTAGTTAGGTTTGTC----TGGTAGCCAGGTTT----TTTAAAGACATAAGTAAAATAGCCTGAGGAA Chimp > Human ------------- chr5:128172011-128172042 Template switch process: F1: L TCAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA 1 F3: 4 TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT R RF: TCAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTAGGTTTGTCTGTTGGCCAGGTTTTTTAAAGACATAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT RR: AGTTAGGTTTCGTATTCGAATTCTCTTTGTCTGTAATCAATCCAAACAGACAACCGGTCCAAAAAATTTCTGTATTCATTTTATCGGACTCCTTTTTAAAAATTTACTGGTGA F2: 3 CCAAACAGACAACCGGTCCAAAAAATTTCTGT 2 Unidirectional alignment (log-probability: -68.5) CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA----TGTC--------------TTTAAAaaacctggccaacaGACAaaccTAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTAGGTTTGTCTGTTGGCCAGGTTTTTTAAA--------------GACA----TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT Template switch alignment (log-probability: -19.2) CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA|TGTCTTTAAAAAACCTGGCCAACAGACAAACC|TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA|TGTCTTTAAAAAACCTGGCCAACAGACAAACC|TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT Human > Chimp ------------- chr5:128060472-128060503 Template switch process: F1: L TCAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA 1 F3: 4 TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT R RF: TCAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTATGTCTTTAAAAAACCTGGCCAACAGACAAACCTAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT RR: AGTTAGGTTTCGTATTCGAATTCTCTTTGTCTGTAATCAATACAGAAATTTTTTGGACCGGTTGTCTGTTTGGATTCATTTTATCGGACTCCTTTTTAAAAATTTACTGGTGA F2: 3 ACAGAAATTTTTTGGACCGGTTGTCTGTTTGG 2 Unidirectional alignment (log-probability: -68.5) CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTAggttTGTCTgttggccaggttttTTAA--------------AGACA----TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA----TGTCT--------------TTAAAAAACCTGGCCAACAGACAAACCTAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT Template switch alignment (log-probability: -19.2) CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA|GGTTTGTCTGTTGGCCAGGTTTTTTAAAGACA|TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT CAATCCAAAGCATAAGCTTAAGAGAAACAGACATTAGTTA|GGTTTGTCTGTTGGCCAGGTTTTTTAAAGACA|TAAGTAAAATAGCCTGAGGAAAAATTTTTAAATGACCACT ========== Event 2800 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAGAATTCTTTTACAAGATAAATGTTTACAAGGATGTA---------------------------------AACTATGTAACATTTAGTTAAATATT Chimp: AAAGAATTCTTTTACAAGATAAATGTTTACAAGGATGTAAACTATATCCTTGTAACTATGTACAAGGATGTAAACTATGTAACATTTAGTTAAATATT ↑ 4 3 2 1 Gorilla: AAAGAATTCTTTTACAAGATAAATGTTTACAAGGATGTA---------------------------------AACTATGTAACATTTAGTTAAATATT Human: AAAGAATTCTTTTACAAGATAAATGTTTACAAGGATGTA---------------------------------AACTATGTAACATTTAGTTAAATATT Cluster: [ ] Orangutan: AAATAATTCTTTTACAAGATAAATGTTTACAAGGATGTA---------------------------------AACTATGTAACATTTAGTTAAATATT Gorilla > Chimp --------------- chr5:127956834-127956840 Template switch process: F1: L AAAAAGAATTCTTTTACAAGATAAATGTTTACAAGGATGTAAACTAT 1 F3: 4 TAACTATGTACAAGGATGTAAACTATGTAACATTTAGTTAAATATTTAACAAGCTGCTTC R RF: AAAAAGAATTCTTTTACAAGATAAATGTTTACAAGGATGTAAACTATGTAACATTTAGTTAAATATTTAACAAGCTGCTTC RR: TTTTTCTTAAGAAAATGTTCTATTTACAAATGTTCCTACATTTGATACATTGTAAATCAATTTATAAATTGTTCGACGAAG F2: 3 GTTCCTA 2 Unidirectional alignment (log-probability: -58.3) ATTCTTTTACAAGATAAATGTTTACAAGGATGtaaactatatccttgtaactatgtacaaggatgTAAACTATGTAACATTTAGTTA ATTCTTTTACAAGATAAATGTTTACAAGGATG---------------------------------TAAACTATGTAACATTTAGTTA Template switch alignment (log-probability: -33.8) ATTCTTTTACAAGATAAATGTTTACAAGGATGTAAACTAT|ATCCTTG|TAAcTaTgTACAAGGATGTAAACTATGTAACATTTAGTTA ATTCTTTTACAAGATAAATGTTTACAAGGATGTAAACTAT|ATCCTTG|TAAATGTTTACAAGGATGTAAACTATGTAACATTTAGTTA ========== Event 2801 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAATGTGGACACAAAATAATTACAATCCTATATTGTACAAAAAGTCTGTAATTTTAAAATTACAGACTTTTTGTACAATATAGGATTGTAATTATTCTTCAACATTTACTTTAA ↑ 3 2 1 4 Chimp: AGAAATGTGGACACAAAATAATTACAATCCTATATTGTACAAAATGTCTGTAATTTTAAAA-------------GGCAAATATCAGCCAGGGAAAATTCTTCAACATTTACTTTAA Gorilla: AGAAATGTGGACACAAAATAATTACAATCCTATATTGTACAA-AAGTCTGTAATTTTAAAA-------------GGCAAATATCAGCCAGGGAAAATTCTTCAACATTTACTTTAA Human: AGAAATGTGGACACAAAATAATTACAATCCTATATTGTACAAAAAGTCTGTAATTTTAAAATTACAGACTTTTTGTACAATATAGGATTGTAATTATTCTTCAACATTTACTTTAA Cluster: [ ] Orangutan: CGAAATGTGGACACAAAATAATTAAAATCCTATATTGTACAAAAAGTCTGTAATTTTAAAA-------------GGCAAATATCAGCCAGGGAAAATTCTTCAACATTTACTTTAA Chimp > Human ------------- chr5:129132111-129132144 Template switch process: F1: L ATTACAATCCTATATTGTACAAAAAGTCTGTAATTTTAAAA 1 F3: 4 ATTCTTCAACATTTACTTTAAAAGGACATATTCTTTTTTA R RF: AATTACAATCCTATATTGTACAAAATGTCTGTAATTTTAAAAGGCAAATATCAGCCAGGGAAAATTCTTCAACATTTACTTTAAAAGGACATATTCTTTTTTA RR: TTAATGTTAGGATATAACATGTTTTACAGACATTAAAATTTTCCGTTTATAGTCGGTCCCTTTTAAGAAGTTGTAAATGAAATTTTCCTGTATAAGAAAAAAT F2: 3 TTAATGTTAGGATATAACATGTTTTTCAGACATT 2 Unidirectional alignment (log-probability: -77.1) TTACAATCCTATATTGTACAAAAaGTCTGTAATTTTAAAAttacagactttttgtacaatataggattgtaatt---------------------ATTCTTCAACATTTACTTTAAAAGGACATATTCTTTTTTA TTACAATCCTATATTGTACAAAATGTCTGTAATTTTAAAA----------------------------------GGCAAATATCAGCCAGGGAAAATTCTTCAACATTTACTTTAAAAGGACATATTCTTTTTTA Template switch alignment (log-probability: -31.4) TTACAATCCTATATTGTACAAAAaGTCTGTAATTTTAAAA|TTACAGACtTTTTGTACAATATAGGATTGTAATT|ATTCTTCAACATTTACTTTAAAAGGACATATTCTTTTTTA TTACAATCCTATATTGTACAAAATGTCTGTAATTTTAAAA|TTACAGACATTTTGTACAATATAGGATTGTAATT|ATTCTTCAACATTTACTTTAAAAGGACATATTCTTTTTTA ========== Event 2802 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTGGAACGATTTAAAAATAGGCATTATATAATCAGATGTTATTTTCTTCACTCAATTAGAAATACC ↓ 3 2 1 4 Chimp: CTGTGGAACGATTTAAAAATAGGCATTATATAATCAATGCCTA---TATTCACTCAATTAGAAATACC Gorilla: CTGTGGAACGATTTAAAAATAGGCATTATATAATCAGATGTTATTT-TTTCACTCAATTAGAAATACC Human: CTGTGGAACGATTTAAAAATAGGCATTATATAATCAGATGTTATTTTCTTCACTCAATTAGAAATACC Cluster: [ ] Orangutan: CTGTGGAATGATTTAAAAATAGGCATTATATAATCAGATGTTATTTTCTTCTCTCAATAAGAAATATC Human > Chimp ------------- chr5:129065811-129065817 Template switch process: F1: L CAGATCTGTGGAACGATTTAAAAATAGGCATTATATAATCA 1 F3: 4 TATTCACTCAATTAGAAATACCTATGTATCATCTCTGAATTC R RF: CAGATCTGTGGAACGATTTAAAAATAGGCATTATATAATCAGATGTTATTTTCTTCACTCAATTAGAAATACCTATGTATCATCTCTGAATTC RR: GTCTAGACACCTTGCTAAATTTTTATCCGTAATATATTAGTCTACAATAAAAGAAGTGAGTTAATCTTTATGGATACATAGTAGAGACTTAAG F2: 3 ATCCGTA 2 Unidirectional alignment (log-probability: -34.7) AGATCTGTGGAACGATTTAAAAATAGGCATTATATAATCaatgcctatA------------TTCACTCAATTAGAAATACCTATGTATCATCTCTGAAT AGATCTGTGGAACGATTTAAAAATAGGCATTATATAATC---------AGATGTTATTTTCTTCACTCAATTAGAAATACCTATGTATCATCTCTGAAT Template switch alignment (log-probability: -22.2) AGATCTGTGGAACGATTTAAAAATAGGCATTATATAATCA|ATGCCTA|TaTTCACTCAATTAGAAATACCTATGTATCATCTCTGAAT AGATCTGTGGAACGATTTAAAAATAGGCATTATATAATCA|ATGCCTA|TCTTCACTCAATTAGAAATACCTATGTATCATCTCTGAAT ========== Event 2803 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATAATGAACCTCATGCTGTTGAACAGGTTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTAT-AGACATCCATAGGAAAAATTCTGCTGTAATTATAACCTTATTTTGATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGTACTTGAACACAAGTATTGTA ↑ 1 4 3 2 Chimp: ATAATGAACCTCATGCTGTTG-ACACG-TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAAGACA-TCATAGGAAAAATTCTGCTGTAATTATAACC-TATATTTATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGTACTTGAACACAAGTATTGTA ↓ 1 4 3 2 Gorilla: ATAATGAACCTCATGCTGTTGAACAGGTTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTAT-AGACATCCATAGGAAAAATTCTGCTGTAATTATAACCTTATTTTGATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGTACTTGAACACAAGTATTGTA Human: ATAATGAACCTCATGCTGTTGAACAGGTTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTAT-AGACATCCATAGGAAAAATTCTGCTGTAATTATAACCTTATTTTGATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGTACTTGAACACAAGTATTGTA Cluster: [ ] Orangutan: ATAATGAACCTCATGGTGTTGAACAGGTTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTAT-AGACATCCATAGGAAAAATTCTGCTGTAATTATAACCTTATTTTGATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGTACTTGAACACAAGTATTGTA Chimp > Human ------------- chr5:129737712-129737717 Template switch process: F1: L CCTGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA 1 F3: 4 TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAG R RF: CCTGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGACACGTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAAGACATCATAGGAAAAATTCTGCTGTAATTATAACCTATATTTATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGT RR: GGACGTCCTCTACACATTTGTATTACTTGGAGTACGACAACTGTGCAAAATCTCTTACATAATACTTAAACCAAGTCTAAATATTCTGTAGTATCCTTTTTAAGACGACATTAATATTGGATATAAATATACCTTTTCTTTTCAGTTTTATCTCTGAAACTAGTACAAGTACTTGTACA F2: 3 TGGACA 2 Unidirectional alignment (log-probability: -40.2) TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGAacaggt----TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTAT-AG TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA------CACGTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAAG Template switch alignment (log-probability: -28) TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA|ACAgGT|TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAg TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA|ACATGT|TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAA Chimp > Gorilla --------------- chr5:113164192-113164197 Template switch process: F1: L CCTGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA 1 F3: 4 TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAG R RF: CCTGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGACACGTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAAGACATCATAGGAAAAATTCTGCTGTAATTATAACCTATATTTATATGGAAAAGAAAAGTCAAAATAGAGACTTTGATCATGTTCATGAACATGT RR: GGACGTCCTCTACACATTTGTATTACTTGGAGTACGACAACTGTGCAAAATCTCTTACATAATACTTAAACCAAGTCTAAATATTCTGTAGTATCCTTTTTAAGACGACATTAATATTGGATATAAATATACCTTTTCTTTTCAGTTTTATCTCTGAAACTAGTACAAGTACTTGTACA F2: 3 TGGACA 2 Unidirectional alignment (log-probability: -38.9) TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGaACAgGtTTTTAGAGAATGTATTATGAATTTGGTTCAGATTTAT-AG TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTG-ACACG-TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAAG Template switch alignment (log-probability: -27.5) TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA|ACAgGT|TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAg TGCAGGAGATGTGTAAACATAATGAACCTCATGCTGTTGA|ACATGT|TTTTAGAGAATGTATTATGAATTTGGTTCAGATTTATAA ========== Event 2804 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCCTCAGATCCTCCCAGGCCTCCCTGGCACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCC ↑ 1 4 3 2 Chimp: ACCCTCAGATCCTCCCAGGCCAGTCAA-GACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCC Gorilla: ACCCTCAGATCCTCCCAGGCCAGTCAA-GACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCC ↓ 1 4 3 2 Human: ACCCTCAGATCCTCCCAGGCCTCCCTGGCACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCC Cluster: [ ] Orangutan: ACCCTCAGATCCTCCCAGGCCAGTCAA-GACTCCCCAGTGCCAGGAACCCAGGAATACCAAGAGGCC Chimp > Human ------------- chr5:132069569-132069577 Template switch process: F1: L CATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC 1 F3: 4 CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA R RF: CATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCCAGTCAAGACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA RR: GTACACCAACTCCCAATTGGTGGGAGTCTAGGAGGGTCCGGTCAGTTCTGAGGGGTCACGGTCCTTGGACCCTTATGGTTCTCCGGTT F2: 3 ACGGTCCCT 2 Unidirectional alignment (log-probability: -33) ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCctccctggCA-------CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGC--------CAGTCAAGACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA Template switch alignment (log-probability: -22.4) ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC|TcCCTGGCA|CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC|TTCCTGGCA|CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA Gorilla > Human --------------- chr5:132069569-132069577 Template switch process: F1: L CATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC 1 F3: 4 CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA R RF: CATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCCAGTCAAGACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA RR: GTACACCAACTCCCAATTGGTGGGAGTCTAGGAGGGTCCGGTCAGTTCTGAGGGGTCACGGTCCTTGGACCCTTATGGTTCTCCGGTT F2: 3 ACGGTCCCT 2 Unidirectional alignment (log-probability: -32.5) ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC-------tccctggcACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCCAGTCAAG--------ACTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA Template switch alignment (log-probability: -22.4) ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC|TcCCTGGCA|CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA ATGTGGTTGAGGGTTAACCACCCTCAGATCCTCCCAGGCC|TTCCTGGCA|CTCCCCAGTGCCAGGAACCTGGGAATACCAAGAGGCCAA ========== Event 2805 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CATGATTTCAAAGATTCACTTAAGAATC--AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGAGCTTCCCCCAAGATACTGTTCCTAGGGCAATGAGTGGTATAGATTCTGTAAGTGATGGACTAGGTA ↑ 1 4 3 2 Chimp: CATGATTTCAAAGATTCACTT---AATC-AAAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGAGCTTCCCCCAAGATACTGTTCCTAGGGCAATGAGTGGTATAGATTCTGTAAGTGATGGACTAGGTA Gorilla: CATGATTTCAAAGATTCACTTAAGAATCA-AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGAGCTTCCCCCAAGATACTGTTCCCAGGGCAATGAGTGGTATAGATTCTGTAAGTGATGGACTAGGTA Human: CATGATTTCAAAGATTCACTTAAGAATC--AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGAGCTTCCCCCAAGATACTGTTCCTAGGGCAATGAGTGGTATAGATTCTGTAAGTGATGGACTAGGTA Cluster: [ ] Orangutan: CATGATTTCAAATATTCACTTAGGAATCA-AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGAGCTTCCCCCAAGATACTGTTCCTACGGCAATGAGTGGTATAGATTCTGTAAGTGATGGACTAGGTA Chimp > Human ------------- chr5:48313827-48313831 Template switch process: F1: L TAGCTTCTGTGGTCCTAGGGCATGATTTCAAAGATTCACTTAA 1 F3: 4 AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGA R RF: TAGCTTCTGTGGTCCTAGGGCATGATTTCAAAGATTCACTTAATCAAAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGAGCTTCCCCCAAGATACTGTTCCTAGGGCAATGAGTGGTATAGATTC RR: ATCGAAGACACCAGGATCCCGTACTAAAGTTTCTAAGTGAATTAGTTTTCCCAGACCTCTGGACTTTCGTAAACAAGTACAGGTCTCGAAGGGGGTTCTATGACAAGGATCCCGTTACTCACCATATCTAAG F2: 3 CTAAG 2 Unidirectional alignment (log-probability: -25.5) CTTCTGTGGTCCTAGGGCATGATTTCAAAGATTCACTTaagAATC-AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGA CTTCTGTGGTCCTAGGGCATGATTTCAAAGATTCACTT---AATCAAAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGA Template switch alignment (log-probability: -15.9) CTTCTGTGGTCCTAGGGCATGATTTCAAAGATTCACTTAA|GAATC|AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGA CTTCTGTGGTCCTAGGGCATGATTTCAAAGATTCACTTAA|GAATC|AAAGGGTCTGGAGACCTGAAAGCATTTGTTCATGTCCAGA ========== Event 2806 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 124 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTTTGGAAATCTTTCACTTGG----------GCTCTGGACCCCAGAGAGGCACCCAAGAGATATTCACTCACT ↓ 13 24 ↑ 13 24 Chimp: GTTTGGAAATCTTTCACTTGG-----GTGCCTCCCTGGGGTCCAGA-----GCCCAAGAGATATTCACTCACT Gorilla: GTTTGGAAATCTTTCACTTGGGTGCC-----TCTCTGGGGTCCAGA-----GCCCAAGAGATATTCACTCACT ↑ 13 24 Human: GTTTGGAAATCTTTCACTTGG----------GCTCTGGACCCCAGAGAGGCACCCAAGAGATATTCACTCACT Cluster: [ ] Orangutan: GTTTGGAAATCTTTCACTTGGGTGCC-----TCTCTGGGGTCCAGA-----GCCCAAGAAATATTCACTCGCT Chimp > Human ------------- chr5:47633899-47633918 Template switch process: F1: L GTTCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG 1 F3: 4 CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC R RF: GTTCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGGTGCCTCCCTGGGGTCCAGAGCCCAAGAGATATTCACTCACTCTTCGCTCATTTGTTCAGC RR: CAAGAATAATAGACATCAGTCAAACCTTTAGAAAGTGAACCCACGGAGGGACCCCAGGTCTCGGGTTCTCTATAAGTGAGTGAGAAGCGAGTAAACAAGTCG F2: 3 ACGGAGAGACCCCAGGTCTC 2 Unidirectional alignment (log-probability: -56.9) TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGG--------------------GctctggaccccagagaggcaCCCAAGAGATATTCACTCACTCTTCaCTCATTTGTTCAGC TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGGTGCCTCCCTGGGGTCCAGAG--------------------CCCAAGAGATATTCACTCACTCTTCGCTCATTTGTTCAGC Template switch alignment (log-probability: -29.8) TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG|CTCTGGACCCCAGaGAGGCA|CCCAAGAGATATTCACTCACTCTTCaCTCATTTGTTCAGC TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG|CTCTGGACCCCAGGGAGGCA|CCCAAGAGATATTCACTCACTCTTCGCTCATTTGTTCAGC Human > Chimp ------------- chr5:48073609-48073628 Template switch process: F1: L GTTCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG 1 F3: 4 CCCAAGAGATATTCACTCACTCTTCGCTCATTTGTTCAGC R RF: GTTCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGGCTCTGGACCCCAGAGAGGCACCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC RR: CAAGAATAATAGACATCAGTCAAACCTTTAGAAAGTGAACCCGAGACCTGGGGTCTCTCCGTGGGTTCTCTATAAGTGAGTGAGAAGTGAGTAAACAAGTCG F2: 3 GAGACCTGGGGTCCCTCCGT 2 Unidirectional alignment (log-probability: -56.9) TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG--------------------tgcctccctggggtccagagCCCAAGAGATATTCACTCACTCTTCgCTCATTTGTTCAGC TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGGCTCTGGACCCCAGAGAGGCA--------------------CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC Template switch alignment (log-probability: -29.8) TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG|TGCCTCcCTGGGGTCCAGAG|CCCAAGAGATATTCACTCACTCTTCgCTCATTTGTTCAGC TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG|TGCCTCTCTGGGGTCCAGAG|CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC Human > Gorilla --------------- chr5:47942408-47942427 Template switch process: F1: L GTTCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG 1 F3: 4 CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC R RF: GTTCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGGCTCTGGACCCCAGAGAGGCACCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC RR: CAAGAATAATAGACATCAGTCAAACCTTTAGAAAGTGAACCCGAGACCTGGGGTCTCTCCGTGGGTTCTCTATAAGTGAGTGAGAAGTGAGTAAACAAGTCG F2: 3 GAGACCTGGGGTCTCTCCGT 2 Unidirectional alignment (log-probability: -44.9) TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGGtgcctCTCTGGggtCCAGAG-----CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG-----CTCTGGACCCCAGAGAGGCACCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC Template switch alignment (log-probability: -18.3) TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG|TGCCTCTCTGGGGTCCAGAG|CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC TCTTATTATCTGTAGTCAGTTTGGAAATCTTTCACTTGGG|TGCCTCTCTGGGGTCCAGAG|CCCAAGAGATATTCACTCACTCTTCACTCATTTGTTCAGC ========== Event 2807 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTCAACATGGAGTGGAGAAGCTGGGGCTATTTTGGGGGTGACATACTATGTATCCATTGCTCAGACAGCTCAGTGTGCTGTCTATGTGCTA Chimp: GGTCAACATGGAGTGGAGAAGCTGGGGCTATTTTGGGGGTGACATATTATGTATCCATTGCTCAGA---GGCAGTGTGCTGTCTGTGTGCTA Gorilla: GGTCAACATGGAGTGGAAAAGCTGGGGCTATTTTGGGGGTGACATATTATGTATCCATTGCTCAGA---GGCAGTGTGCTGTCTGTGTGCTA ↓ 3 2 1 4 Human: GGTCAACATGGAGTGGAGAAGCTGGGGCTATTTTGGGGGTGACATACTATGTATCCATTGCTCAGACAGCTCAGTGTGCTGTCTATGTGCTA Cluster: [ ] Orangutan: GGTCAACATGGAGTGGAGAAGCTAGGGCTATTTTGGGGGTGACATATTATGTATCCACTGCTCAGA---GGCAGTGTGCT----GTGTGCTA Gorilla > Human --------------- chr5:48048591-48048595 Template switch process: F1: L GGCTATTTTGGGGGTGACATACTATGTATCCATTGCTCAGA 1 F3: 4 CAGTGTGCTGTCTATGTGCTAAAAGGGAACTTTCCTCCAC R RF: AGCTGGGGCTATTTTGGGGGTGACATATTATGTATCCATTGCTCAGAGGCAGTGTGCTGTCTGTGTGCTAAAAGGGAACTTTCCTCCAC RR: TCGACCCCGATAAAACCCCCACTGTATAATACATAGGTAACGAGTCTCCGTCACACGACAGACACACGATTTTCCCTTGAAAGGAGGTG F2: 3 TCGAC 2 Unidirectional alignment (log-probability: -37.3) GCTATTTTGGGGGTGACATAcTATGTATCCATTGCTCAGAcagctCAGTGTGCTGTCTaTGTGCTAAAAGGGAACTTTCCTCCAC GCTATTTTGGGGGTGACATATTATGTATCCATTGCTCAGAGG---CAGTGTGCTGTCTGTGTGCTAAAAGGGAACTTTCCTCCAC Template switch alignment (log-probability: -27.4) GCTATTTTGGGGGTGACATAcTATGTATCCATTGCTCAGA|CAGCT|CAGTGTGCTGTCTaTGTGCTAAAAGGGAACTTTCCTCCAC GCTATTTTGGGGGTGACATATTATGTATCCATTGCTCAGA|CAGCT|CAGTGTGCTGTCTGTGTGCTAAAAGGGAACTTTCCTCCAC ========== Event 2808 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAGACAGGGCCTAAGAAATTCACCTGAtttttttttttttt-----ttttttttttttttttGTGGT Chimp: GGAAGGCAGGGCCTAAGAAATTCACCTGAtttttttttttttt-----tttt--ttttttttttGT--- ↓ 31 2 4 Gorilla: GGAAGGCAGGGCCTAAGAAAT-TACGTGAtttttttttttt-t-------------------ttgtggt Human: GGAAGACAGGGCCTAAGAAATTCACCTGAtttttttttttttt-----ttttttttttttttttGTGGT Cluster: [ ] Orangutan: GGAAGGCAGGGCCTAAGAAATTCGCCTGAttttttttttttttctttt--------------ttgtggt Chimp > Gorilla --------------- chr5:47946293-47946299 Template switch process: F1: L ACAGCCATGTACTCTCTTCAGGAAGGCAGGGCCTAAGAAATT 1 F3: 4 TTTTTTTTTTTTTTGTGGTGGTG R RF: ACAGCCATGTACTCTCTTCAGGAAGGCAGGGCCTAAGAAATTCACCTGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGGTGGTG RR: TGTCGGTACATGAGAGAAGTCCTTCCGTCCCGGATTCTTTAAGTGGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAACACCACCAC F2: 3 TAGTGCA 2 Unidirectional alignment (log-probability: -42) AGCCATGTACTCTCTTCAGGAAGGCAGGGCCTAAGAAATT-ACgTGA-------------TTTTTTTTTTTTTTTGTGgtggtg AGCCATGTACTCTCTTCAGGAAGGCAGGGCCTAAGAAATTCACCTGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGTG------ Template switch alignment (log-probability: -27.2) AGCCATGTACTCTCTTCAGGAAGGCAGGGCCTAAGAAATT|AcGTGAt|TTTTTTTTTTTTTTGTGGTGGTG AGCCATGTACTCTCTTCAGGAAGGCAGGGCCTAAGAAATT|AGGTGAA|TTTTTTTTTTTTTTGTGGTGGTG ========== Event 2809 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTCTGAAGAGAGAACTCCAGTTCAAATACAAGAACTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTC ↑ 1 4 3 2 Chimp: TCTCTGAAGAGAGAACTCCAG--------GAGAATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTC Gorilla: TCTCTGAAGAGAGAACTCCAG--------GACAATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTC ↓ 1 4 3 2 Human: TCTCTGAAGAGAGAACTCCAGTTCAAATACAAGAACTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTC Cluster: [ ] Orangutan: TCTCTGAAGAGAGAACTCCAG--------GAGAATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTC Chimp > Human ------------- chr5:135644955-135644966 Template switch process: F1: L TACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG 1 F3: 4 AACTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGTCT R RF: TACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAGGAGAATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGTCT RR: ATGTCACCTTCCGTCACGTCAGAGACTTCTCTCTTGAGGTCCTCTTAGAGAACATAAACTTCCGTTCCCCCTAGGCGAAAGGACAGA F2: 3 GAACATAAACTT 2 Unidirectional alignment (log-probability: -40.1) ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG-----TtcaaatacaagaaCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAGGAGAAT-------------CTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT Template switch alignment (log-probability: -22.8) ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG|TTCAAATACAAG|AaCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG|TTCAAATACAAG|ATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT Gorilla > Human --------------- chr5:135644955-135644966 Template switch process: F1: L TACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG 1 F3: 4 AACTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGTCT R RF: TACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAGGACAATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGTCT RR: ATGTCACCTTCCGTCACGTCAGAGACTTCTCTCTTGAGGTCCTGTTAGAGAACATAAACTTCCGTTCCCCCTAGGCGAAAGGACAGA F2: 3 GAACATAAACTT 2 Unidirectional alignment (log-probability: -39) ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAGttCAaatacaagAaCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAGGACA--------ATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT Template switch alignment (log-probability: -22.8) ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG|TTCAAATACAAG|AaCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT ACAGTGGAAGGCAGTGCAGTCTCTGAAGAGAGAACTCCAG|TTCAAATACAAG|ATCTCTTGTATTTGAAGGCAAGGGGGATCCGCTTTCCTGT ========== Event 2810 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTGGACGGCATCATGTCCCCTTACTCCCTTGACC-TCATCTAAATCCAGATCTCAGTCTATGACCTGGT Chimp: AGTGGACGGCATCATGTCCCCTTACTCCCTTGACC-TCATCTAAATCCAGATCTCAGTCTATGACCTGGT ↓ 1 3 4 2 Gorilla: AGTGGACGGCATCATGTCCCCCTGGA-TTTAGATCTGGATCTAAATCCAGATCTCAGTCTATGACCTGGT ↑ 1 3 4 2 Human: AGTGGACGGCATCATGTCCCCTTACTCCCTTGACC-TCATCTAAATCCAGATCTCAGTCTATGACCTGGT Cluster: [ ] Orangutan: AGTGGACGGCATCATGTCCCGTTACTCCCTTGACC-TCATCTAAATCCAGATCTCAGTCTATGACCTGTT Human > Gorilla --------------- chr5:44796467-44796482 Template switch process: F1: L ACTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC 1 F3: 4 ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG R RF: ACTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCCTTACTCCCTTGACCTCATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG RR: TGAGGTCCTGTCATCGAACCTCACCTGCCGTAGTACAGGGGAATGAGGGAACTGGAGTAGATTTAGGTCTAGAGTCAGATACTGGACCAAGGAAATC F2: 3 GGTCTAGATTTAGGTC 2 Unidirectional alignment (log-probability: -43) CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC---------------CtggatttagatctggATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCCTTACTCCCTTGACCTC---------------ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG Template switch alignment (log-probability: -28.8) CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC|CTGGATTTAGATctGG|ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC|CTGGATTTAGATGAGG|ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG Chimp > Gorilla --------------- chr5:44796467-44796482 Template switch process: F1: L ACTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC 1 F3: 4 ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG R RF: ACTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCCTTACTCCCTTGACCTCATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG RR: TGAGGTCCTGTCATCGAACCTCACCTGCCGTAGTACAGGGGAATGAGGGAACTGGAGTAGATTTAGGTCTAGAGTCAGATACTGGACCAAGGAAATC F2: 3 GGTCTAGATTTAGGTC 2 Unidirectional alignment (log-probability: -43) CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC---------------CtggatttagatctggATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCCTTACTCCCTTGACCTC---------------ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG Template switch alignment (log-probability: -28.8) CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC|CTGGATTTAGATctGG|ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG CTCCAGGACAGTAGCTTGGAGTGGACGGCATCATGTCCCC|CTGGATTTAGATGAGG|ATCTAAATCCAGATCTCAGTCTATGACCTGGTTCCTTTAG ========== Event 2811 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GGAAATGGGAGAGCCCCAGGCCTCAAGAGAGGCAGGATTAACTCTTTTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT--CTTGAGACCCTGTAGGAGGCAGTGCGGGA Chimp: GGAAATGGGAGAGCCCCAGGCCTCAAGAGAGGCAGGATTAACTCTTTTCTTGTTATCTCTGCACAAGACACCAAGAGCAGCAGCCT--CTTGAGACCCTGTAGGAGGCAGTGCGGGA Gorilla: GGAAATGGGAGAGCCTCAGGCCTCAAGAGAGGCAGGATTAACTCTTTTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT----TG-CTGCCTGTAGGAGGCAGTGCGGGA ↓ 3 2 1 4 Human: GGAAATGGGAGAGCCCCAGGCCTCAAGAGAGGCAGGATTAACTCTTTTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT--CTTGAGACCCTGTAGGAGGCAGTGCGGGA Cluster: [ ] Orangutan: GGAAATGGGAGAGCCCCAGGCCTCAAGAGAGGCAGGATTAACTCTTTTCTTGTTAC-CCTTTGCAAGACACCAAGAGCAGCAGCCTCT--TGAGACCCTGCAGGAGGCAGTGCGGGA Gorilla > Human --------------- chr5:138620343-138620350 Template switch process: F1: L TTTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT 1 F3: 4 CCTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAG R RF: GCCTCAAGAGAGGCAGGATTAACTCTTTTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCTTGCTGCCTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAG RR: CGGAGTTCTCTCCGTCCTAATTGAGAAAAGAACAATAGGGACGTGTTCTGTGGTTCTCGTCGTCGGAACGACGGACATCCTCCGTCACGCCCTTCAGGACCTGTCCTTGGTC F2: 3 CAGAGTTC 2 Unidirectional alignment (log-probability: -32.4) TTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT-----cttgagacCCTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAG TTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCTTGCTG--------CCTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAG Template switch alignment (log-probability: -22.3) TTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT|CTTGAGaC|CCTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAG TTCTTGTTATCCCTGCACAAGACACCAAGAGCAGCAGCCT|CTTGAGGC|CCTGTAGGAGGCAGTGCGGGAAGTCCTGGACAGGAACCAG ========== Event 2812 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: agccacagtgcccggccTTGAAACCTGTAGTTGTGT-----------GTTAGGTTTCTTTTCCAGTCGGAGAATTTCAACA Chimp: agccacagtgcccggccTTGAAACCTGTAGTTGTGT-----------GTTAGGTTTCTGTTCCAGTCGGAGAATTTCAACA ↑ 3 2 4 1 Gorilla: agccacagtgcccggccTTGAAACCTGTAGTTGTGT----------------------GTTCCAGTCGGAGAATTTCAACA Human: agccacagtgcccggccTTGAAACCTGTAGTTGTGT-----------GTTAGGTTTCTTTTCCAGTCGGAGAATTTCAACA Cluster: [ ] Orangutan: agccacagcgcccgaccTTGAAACCTGTAGTTGTGTGTTAGGTTTCT-----------GTTCCAGTCGGAGAATTTCAACA Gorilla > Chimp --------------- chr5:138801069-138801075 Template switch process: F1: L GCATGAGCCACAGTGCCCGGCCTTGAAACCTGTAGTTGTGTGTT 1 F3: 4 TGTTCCAGTCGGAGAATTTCAACAATGATGTAGGTTTTTGA R RF: GCATGAGCCACAGTGCCCGGCCTTGAAACCTGTAGTTGTGTGTTCCAGTCGGAGAATTTCAACAATGATGTAGGTTTTTTA RR: CGTACTCGGTGTCACGGGCCGGAACTTTGGACATCAACACACAAGGTCAGCCTCTTAAAGTTGTTACTACATCCAAAAAAT F2: 3 CTTTGGA 2 Unidirectional alignment (log-probability: -32.2) GAGCCACAGTGCCCGGCCTTGAAACCTGTAGTTGTGtgttaggtttcTGTTCCAGTCGGAGAATTTCAACAATGATGTAGGTTTTTg GAGCCACAGTGCCCGGCCTTGAAACCTGTAGTTGTG-----------TGTTCCAGTCGGAGAATTTCAACAATGATGTAGGTTTTTT Template switch alignment (log-probability: -22.2) GAGCCACAGTGCCCGGCCTTGAAACCTGTAGTTGTGTGTT|AGGTTTC|TGTTCCAGTCGGAGAATTTCAACAATGATGTAGGTTTTTg GAGCCACAGTGCCCGGCCTTGAAACCTGTAGTTGTGTGTT|AGGTTTC|TGTTCCAGTCGGAGAATTTCAACAATGATGTAGGTTTTTT ========== Event 2813 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TATTGTTAAACTCTAGCTGCAACTTTA----GATGCAGCTAGAGTTTAACAGGA Chimp: tcctgttaaactCTAGCTGCATCTAAA--GTAATGCAGCTAGAGTTTAACAGGA Gorilla: TATTGTTAAACTCTAGCTGCATCTAAAGT--AATGCAGCTAGAGTTTAACAGGA ↓ 13 2 4 Human: TATTGTTAAACTCTAGCTGCAACTTTA----GATGCAGCTAGAGTTTAACAGGA Cluster: [ ] Orangutan: ------------------acatctaaagt--aatgcagctagAGTTTAACAGGA Gorilla > Human --------------- chr5:40891508-40891515 Template switch process: F1: L ATCAAAACTTTGTTTTGCACTATTGTTAAACTCTAGCTGCA 1 F3: 4 TGCAGCTAGAGTTTAACAGGATTGAGCCTTTACATTTAT R RF: ATCAAAACTTTGTTTTGCACTATTGTTAAACTCTAGCTGCATCTAAAGTAATGCAGCTAGAGTTTAACAGGATTGAGCCTTTACATTTAT RR: TAGTTTTGAAACAAAACGTGATAACAATTTGAGATCGACGTAGATTTCATTACGTCGATCTCAAATTGTCCTAACTCGGAAATGTAAATA F2: 3 AGATTTCA 2 Unidirectional alignment (log-probability: -27.6) TCAAAACTTTGTTTTGCACTATTGTTAAACTCTAGCTGCAaCTttAG--ATGCAGCTAGAGTTTAACAGGATTGAGCCTTTACATTTAT TCAAAACTTTGTTTTGCACTATTGTTAAACTCTAGCTGCATCTAAAGTAATGCAGCTAGAGTTTAACAGGATTGAGCCTTTACATTTAT Template switch alignment (log-probability: -16.7) TCAAAACTTTGTTTTGCACTATTGTTAAACTCTAGCTGCA|ACTTTAGA|TGCAGCTAGAGTTTAACAGGATTGAGCCTTTACATTTAT TCAAAACTTTGTTTTGCACTATTGTTAAACTCTAGCTGCA|ACTTTAGA|TGCAGCTAGAGTTTAACAGGATTGAGCCTTTACATTTAT ========== Event 2814 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGCACCGAGGACAGCAAGGCTTCTGTTCCCGATCCCATGAATACACATAATATAG--------------------------ccttcttctctttctcccttacccctttcctccctcccttctttac Chimp: AAGCACCGAGGACAGCAAGGCTTCTGTTCCCGATCCCATGAATACACATAATATAG-------------CCTTGCTAttttcccttcttctctttctcccttacccctttcctccctcccttctttcc Gorilla: AAGCACCGAGGACAGCAAGGCCTCTGTTCCTGATCCCATGAATACACATAATATAGCCTTGCTAttttc-------------ccttcttctctctctcccttacccctttcctccctcccttctttcc ↑ 3 2 1 4 Human: AAGCACCGAGGACAGCAAGGCTTCTGTTCCCGATCCCATGAATACACATAATATAG--------------------------ccttcttctctttctcccttacccctttcctccctcccttctttac Cluster: [ ] Orangutan: AAGCACCGAGGACAGCGAGGCTTCTGTTCCCGATCCCATGAATACACATAATATAGCCTTGCTATTTtc-------------ccttcctctctttctcccttaccactttcctccctcccttctttcc Human > Gorilla --------------- chr5:39925936-39925939 Template switch process: F1: L TATCTTTCCAAATAGACTCTAAGCACCGAGGACAGCAAGGCCTCTGTTCCTGATCCCATGAATACACATAATATAGCCTT 1 F3: 4 TTTTCCC R RF: TATCTTTCCAAATAGACTCTAAGCACCGAGGACAGCAAGGCTTCTGTTCCCGATCCCATGAATACACATAATATAGCCTTCTTCTCTTTCTCCCTTACCCCTTTCCTCCCTCCCTTCTTTACTTCCTTTGTTCCTTCTCTTCCC RR: ATAGAAAGGTTTATCTGAGATTCGTGGCTCCTGTCGTTCCGAAGACAAGGGCTAGGGTACTTATGTGTATTATATCGGAAGAAGAGAAAGAGGGAATGGGGAAAGGAGGGAGGGAAGAAATGAAGGAAACAAGGAAGAGAAGGG F2: 3 ATCG 2 Unidirectional alignment (log-probability: -37.6) CcTCTGTTCCtGATCCCATGAATACACATAATATAGCCttgctattttccc CTTCTGTTCCCGATCCCATGAATACACATAATATAGCC------------- Template switch alignment (log-probability: -32.9) CcTCTGTTCCtGATCCCATGAATACACATAATATAGCCTT|GCTA|TtTTCCC CTTCTGTTCCCGATCCCATGAATACACATAATATAGCCTT|GCTA|TCTTCCC ========== Event 2815 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGCCACACAGGCCGGCCCCTGTGGCTCATTCCTGC--------------TGGAATGAAAACCACTACCAAGGGTAAG ↑ 1 3 4 2 Chimp: GGCCACACAGGCCGGCCCCTGG--GCAGTACCTGC-------TGACAGCAGGAATGAAAACCACTACCAAGGGTAAG Gorilla: GGCCACACAGGCCGGCCCCTGG--GCAGTACCTGCTGACAGC-------AGGAATGAAAACCACTACCAAGGGTAAG ↓ 1 3 4 2 Human: GGCCACACAGGCCGGCCCCTGTGGCTCATTCCTGC--------------TGGAATGAAAACCACTACCAAGGGTAAG Cluster: [ ] Orangutan: GGCCACACAGGCCGGCCCCTGG--GCAGTACCTGCTGACAGC-------AAGAATGAAAACCACTACCAAGGGTAAG Chimp > Human ------------- chr5:39017166-39017176 Template switch process: F1: L AGGAAAGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTGTGGC 1 F3: 4 GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA R RF: AGGAAAGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTG-GGCAGTACCTGCTGACAGCAGGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA RR: TCCTTTCCCGAATCTAGTAGCCGGTGTGTCCGGCCGGGGAC-CCGTCATGGACGACTGTCGTCCTTACTTTTGGTGATGGTTCCCATTCACGAATACCCACT F2: 3 TCGTCCTTACT 2 Unidirectional alignment (log-probability: -43.7) AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTG--------------------tggctcattcctgctGGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTGGGCAGTACCTGCTGACAGCA---------------GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA Template switch alignment (log-probability: -28.4) AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTGtGGC|TCATTCCTGCT|GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTG-GGC|TCATTCCTGCT|GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA Gorilla > Human --------------- chr5:39017166-39017176 Template switch process: F1: L AGGAAAGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTGTGGC 1 F3: 4 GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA R RF: AGGAAAGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTG-GGCAGTACCTGCTGACAGCAGGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA RR: TCCTTTCCCGAATCTAGTAGCCGGTGTGTCCGGCCGGGGAC-CCGTCATGGACGACTGTCGTCCTTACTTTTGGTGATGGTTCCCATTCACGAATACCCACT F2: 3 TCGTCCTTACT 2 Unidirectional alignment (log-probability: -43.2) AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTG--------------------tggctcattcctgctGGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTGGGCAGTACCTGCTGACAGCA---------------GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA Template switch alignment (log-probability: -28.4) AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTGtGGC|TCATTCCTGCT|GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA AGGGCTTAGATCATCGGCCACACAGGCCGGCCCCTG-GGC|TCATTCCTGCT|GGAATGAAAACCACTACCAAGGGTAAGTGCTTATGGGTGA ========== Event 2816 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAAGGCCAAACAGCATTCCTTATGGCTGCGTCAGCTC--TCTCTGGAAAGTCGAGCAAGACAGCAT-AGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC----CCCTAAGTATATCAAATCAGTGTGCCTT Chimp: AAAAGGCCAAACAGCATTCCTTATGGCTGCGTCAGCTC--TCTCTGGAAAGTCGAGCAAGACAGCATATGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC----CCCTAAGTATATCAAATCAGTGTGCCTT ↑ 3 2 1 4 Gorilla: AAAAGGCCAAACAGCATTCCTTAGGGCTGCGTCAGCTC--TCTCTGGAAAGTCGAGCAAGACAGCATATGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC--------TGATATATCAAATCAGTGTGCCTT ↓ 3 2 1 4 Human: AAAAGGCCAAACAGCATTCCTTATGGCTGCGTCAGCTC--TCTCTGGAAAGTCGAGCAAGACAGCAT-AGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC----CCCTAAGTATATCAAATCAGTGTGCCTT Cluster: [ ] Orangutan: AAAAGGCCAAACAGCGTTCCTTAAGGCTGCGTCAGCTCTCTCTCTGGAAAGTTGAGCAAGACAGCATGTGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCACCCCT----AAGTATATCAAATCAGTGTGCCTT Gorilla > Human --------------- chr5:166812094-166812100 Template switch process: F1: L GTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC 1 F3: 4 TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG R RF: CTTAGGGCTGCGTCAGCTCTCTCTGGAAAGTCGAGCAAGACAGCATATGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCACTGATATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG RR: GAATCCCGACGCAGTCGAGAGAGACCTTTCAGCTCGTTCTGTCGTATACACAATAGATTATCACAGGACGGGACACGACCGGGGAGGTGACTATATAGTTTAGTCACACGGAAGGAGTACTCCACTACACCC F2: 3 GAATCCC 2 Unidirectional alignment (log-probability: -30.8) TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC---ccctaagTATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCACTGA-------TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG Template switch alignment (log-probability: -16.6) TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC|CCCTAAG|TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC|CCCTAAG|TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG Gorilla > Chimp --------------- chr5:166886898-166886904 Template switch process: F1: L GTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC 1 F3: 4 TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG R RF: CTTAGGGCTGCGTCAGCTCTCTCTGGAAAGTCGAGCAAGACAGCATATGTGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCACTGATATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG RR: GAATCCCGACGCAGTCGAGAGAGACCTTTCAGCTCGTTCTGTCGTATACACAATAGATTATCACAGGACGGGACACGACCGGGGAGGTGACTATATAGTTTAGTCACACGGAAGGAGTACTCCACTACACCC F2: 3 GAATCCC 2 Unidirectional alignment (log-probability: -30.8) TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC---ccctaagTATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCACTGA-------TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG Template switch alignment (log-probability: -16.6) TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC|CCCTAAG|TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG TGTTATCTAATAGTGTCCTGCCCTGTGCTGGCCCCTCCAC|CCCTAAG|TATATCAAATCAGTGTGCCTTCCTCATGAGGTGATGTGGG ========== Event 2817 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTGCAATTAAGAAATGTCTATACAAAT-------AGGCCTTAGCTTTAGCAAAAAGTAG Chimp: CCTGCAATTAAGAAATATCTATACAAAT-------AGGCCTTAGCTTTAGCAAAAAGTAG ↓ 3 1 24 Gorilla: CCTGCAATTAAGAAATATCTATACAACTATTTGTATAGCTTTAGCTTTAGCAAAAAGTAG ↑ 3 1 24 Human: CCTGCAATTAAGAAATGTCTATACAAAT-------AGGCCTTAGCTTTAGCAAAAAGTAG Cluster: [ ] Orangutan: ACTGCAATTAAGAAATATCTATACAAAT-------AGGCCTTAGCTTTAGCAAAAAGTAG Human > Gorilla --------------- chr5:37771001-37771011 Template switch process: F1: L AGCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAA 1 F3: 4 GCTTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCATCAA R RF: AGCTGCCTTAATTGCCCTGCAATTAAGAAATGTCTATACAAATAGGCCTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCATCAA RR: TCGACGGAATTAACGGGACGTTAATTCTTTACAGATATGTTTATCCGGAATCGAAATCGTTTTTCATCTTCCGAAGTACTGGGTAGTT F2: 3 ATATGTTTATC 2 Unidirectional alignment (log-probability: -43.1) GCTGCCTTAATTGCCCTGCAATTAAGAAATaTCTATACAAcTAtttgtataGCtTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCAT GCTGCCTTAATTGCCCTGCAATTAAGAAATGTCTATACAAATA-------GGCCTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCAT Template switch alignment (log-probability: -28.2) GCTGCCTTAATTGCCCTGCAATTAAGAAATaTCTATACAA|CTATTTGTATA|GCtTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCAT GCTGCCTTAATTGCCCTGCAATTAAGAAATGTCTATACAA|CTATTTGTATA|GCCTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCAT Chimp > Gorilla --------------- chr5:37771001-37771011 Template switch process: F1: L AGCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAA 1 F3: 4 GCTTTAGCTTTAGCAAAAAGTAGAAGGCTTCATGACCCATCAA R RF: AGCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAAATAGGCCTTAGCTTTAGCAAAAAGTAGAAGTCTTCATGACCCATCAA RR: TCGACGGAATTAACGGGACGTTAATTCTTTATAGATATGTTTATCCGGAATCGAAATCGTTTTTCATCTTCAGAAGTACTGGGTAGTT F2: 3 ATATGTTTATC 2 Unidirectional alignment (log-probability: -43.1) GCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAAcTAtttgtataGCtTTAGCTTTAGCAAAAAGTAGAAGgCTTCATGACCCAT GCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAAATAG-------GCCTTAGCTTTAGCAAAAAGTAGAAGTCTTCATGACCCAT Template switch alignment (log-probability: -28.2) GCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAA|CTATTTGTATA|GCtTTAGCTTTAGCAAAAAGTAGAAGgCTTCATGACCCAT GCTGCCTTAATTGCCCTGCAATTAAGAAATATCTATACAA|CTATTTGTATA|GCCTTAGCTTTAGCAAAAAGTAGAAGTCTTCATGACCCAT ========== Event 2818 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTAtgatgtaggactgtgtttgcctagagaacgaggcatattttaaaaattttgcataaaagcacaaagctagtggA Chimp: ATTATGATGTAGGACTGTGTTATG------------CAAAATTTTAAAAATTTTGCATAAAAGCACAAAGCTAGTGGA ↑ 1 34 2 Gorilla: ATTATGATGTAGGACTGTGTTTGCCTAGAGAACGAGGCATATTTTTAAAATTTTGCATAAAAGCACAAAGCTAGTGGA Human: ATTAtgatgtaggactgtgtttgcctagagaacgaggcatattttaaaaattttgcataaaagcacaaagctagtggA Cluster: [ ] Orangutan: ATTAtgatgtaggactgtgtttgcctagagaacgaggcatatttttaaaattttgcataaaagcacaaagctagtggA Gorilla > Chimp --------------- chr5:37738236-37738248 Template switch process: F1: L TGCTGCCCACCACCATATCTATTATGATGTAGGACTGTGTT 1 F3: 4 AAAATTTTGCATAAAAGCACAAAGCTAGTGGAAATGCTTT R RF: TGCTGCCCACCACCATATCTATTATGATGTAGGACTGTGTTTGCCTAGAGAACGAGGCATATTTTTAAAATTTTGCATAAAAGCACAAAGCTAGTGGAAATGCTTT RR: ACGACGGGTGGTGGTATAGATAATACTACATCCTGACACAAACGGATCTCTTGCTCCGTATAAAAATTTTAAAACGTATTTTCGTGTTTCGATCACCTTTACGAAA F2: 3 ATTTTAAAACGTA 2 Unidirectional alignment (log-probability: -34.3) GCTGCCCACCACCATATCTATTATGATGTAGGACTGTGTT-----------------ATgcaaaATTTTaAAAATTTTGCATAAAAGCACAAAGCTAGTGGAAATGCTTT GCTGCCCACCACCATATCTATTATGATGTAGGACTGTGTTTGCCTAGAGAACGAGGCAT-----ATTTTTAAAATTTTGCATAAAAGCACAAAGCTAGTGGAAATGCTTT Template switch alignment (log-probability: -17.4) GCTGCCCACCACCATATCTATTATGATGTAGGACTGTGTT|ATGCAAAATTTTA|AAAATTTTGCATAAAAGCACAAAGCTAGTGGAAATGCTTT GCTGCCCACCACCATATCTATTATGATGTAGGACTGTGTT|ATGCAAAATTTTA|AAAATTTTGCATAAAAGCACAAAGCTAGTGGAAATGCTTT ========== Event 2819 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATAATAGCTTCATTAGATGGTAAGCTCCATGAAGTGTCAAATGTCCATTTCTGACATAGAGACAATTGCTTCATTGGTTTATTCCCTCTTGTATCT Chimp: ATATAATAGCTTCATTAGATGTCA--ATGAATGAAGTGTCAAATGTCCATTTCTGACATAGAGACAATTGCTTCATTGGTTTATTCCCTCTTGTATCT ↑ 1 4 3 2 Gorilla: ATATAATAGCTTCATTAGATGGTAAGCTCCATGAAGTGTCACATGTCCATTTCTGACATAGAGACAATTGCTTCATTGGTTTATTCCCTCTTGTGTCT Human: ATATAATAGCTTCATTAGATGGTAAGCTCCATGAAGTGTCAAATGTCCATTTCTGACATAGAGACAATTGCTTCATTGGTTTATTCCCTCTTGTATCT Cluster: [ ] Orangutan: ATATAATAGCTTCATTAGACGGTAAGCTCCATGAAGTATCAAATGTCCATTTCTGACACAGAGGCAGTTGCTTCATTGGTTTATTCCCTCTTGTGTCT Gorilla > Chimp --------------- chr5:36717401-36717407 Template switch process: F1: L GTGGTCCTACAGCCCTTTCCATATAATAGCTTCATTAGATGT 1 F3: 4 TGAAGTGTCAAATGTCCATTTCTGACATAGAGACAATTG R RF: GTGGTCCTACAGCCCTTTCCATATAATAGCTTCATTAGATGGTAAGCTCCATGAAGTGTCACATGTCCATTTCTGACATAGAGACAATTGCTTCATTG RR: CACCAGGATGTCGGGAAAGGTATATTATCGAAGTAATCTACCATTCGAGGTACTTCACAGTGTACAGGTAAAGACTGTATCTCTGTTAACGAAGTAAC F2: 3 AAGTAAC 2 Unidirectional alignment (log-probability: -36.7) GGTCCTACAGCCCTTTCCATATAATAGCTTCATTAGATG---------tcaatgaATGAAGTGTCAaATGTCCATTTCTGACATAGAGACAATTG GGTCCTACAGCCCTTTCCATATAATAGCTTCATTAGATGGTAAGCTCC-------ATGAAGTGTCACATGTCCATTTCTGACATAGAGACAATTG Template switch alignment (log-probability: -27.7) GGTCCTACAGCCCTTTCCATATAATAGCTTCATTAGATGt|CAATGAA|TGAAGTGTCAaATGTCCATTTCTGACATAGAGACAATTG GGTCCTACAGCCCTTTCCATATAATAGCTTCATTAGATGG|CAATGAA|TGAAGTGTCACATGTCCATTTCTGACATAGAGACAATTG ========== Event 2820 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAAACCTTCTAAGAGACCATCAGGAGATGAATAAGAGGATATGTACCAAAAAGATC---------------AAGATGAATTAACCTTTGGGTGAAGTTGAGTAACCCAACTGATGGAGCCAGAGGGGATGGAAGGAAGATGTGGCCTGATATCATGAACTAAAAAGGTAGTTTGAGTTAAATT Chimp: GGAAAACCTTCTAAGAGACCACCAGGAGATGAATAAGAGGATATGTACCAAAAAGATC---------------AAGATGAATTAACCTTTGGGTGAAGTTGAGTAACCCAACTGTTGGAGCCAGAGGGGATGGAAGGAAGATGTGGCCTGATATCATGAACTAAAAAGGTAGTTTGAGTTAAATT Gorilla: GGAAAACCTTCTAAGAGACCACCAGAAGATGAATAAGAGGATATGTACCAAaaaggtacaaaggtacaaagAGGATATGAATTAACCTTTGGGTGAAGTTGAGTAACCCAACTGATGGAGCCAGAGGGGATGGAAGGAAGATGTGGCCTGATATCATGAACTAAAATGGTAGTTTGAGTTAAATT ↑ 3 2 1 4 Human: GGAAAACCTTCTAAGAGACCATCAGGAGATGAATAAGAGGATATGTACCAAAAAGATC---------------AAGATGAATTAACCTTTGGGTGAAGTTGAGTAACCCAACTGATGGAGCCAGAGGGGATGGAAGGAAGATGTGGCCTGATATCATGAACTAAAAAGGTAGTTTGAGTTAAATT Cluster: [ ] Orangutan: GGAAAACCTTCTAAGAGACCACCAGGAGATGAATAAGAGGATATGTACCAAAAAGATC---------------AAGATGAATTAACCTTTGGGTGAAGTCGAGTAACCCAACTGATGGAGCCAGTGGGGATGGAAGGAAGATGTGGCCCAATATCATGAACTAAAAAGGTAGTTTGAGTTAAATT Human > Gorilla --------------- chr5:36408898-36408901 Template switch process: F1: L CATTTTGAAATAACTACTGTGGAAAACCTTCTAAGAGACCACCAGAAGATGAATAAGAGGATATGTACCAAAAAG 1 F3: 4 AAAGGTA R RF: CATTTTGAAATAACTACTGTGGAAAACCTTCTAAGAGACCATCAGGAGATGAATAAGAGGATATGTACCAAAAAGATCAAGATGAATTAACCTTTGGGTGAAGTTGAGTAACCCAACTGATGGAGCCAGAGGGGATGGAAGGAAGATGTGGCCTGATATCATGAACTAAAAAGGTA RR: GTAAAACTTTATTGATGACACCTTTTGGAAGATTCTCTGGTAGTCCTCTACTTATTCTCCTATACATGGTTTTTCTAGTTCTACTTAATTGGAAACCCACTTCAACTCATTGGGTTGACTACCTCGGTCTCCCCTACCTTCCTTCTACACCGGACTATAGTACTTGATTTTTCCAT F2: 3 CATG 2 Unidirectional alignment (log-probability: -41.4) AGACCAcCAGaAGATGAATAAGAGGATATGTACCAAAAAGgTacaaaggta AGACCATCAGGAGATGAATAAGAGGATATGTACCAAAAAGATC-------- Template switch alignment (log-probability: -27.3) AGACCAcCAGaAGATGAATAAGAGGATATGTACCAAAAAG|GTAC|AAAGGTA AGACCATCAGGAGATGAATAAGAGGATATGTACCAAAAAG|GTAC|AAAGGTA ========== Event 2821 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GTGTCGGCTTATGGGTGTACAGCACCAGCATCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCT ↑ 1 4 3 2 Chimp: GTGTTGGCTTATGGGTGTACA------GCAGCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCT Gorilla: GTGTCGGCTTATGGGTGTACAGCACCAGCAGCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCT Human: GTGTCGGCTTATGGGTGTACAGCACCAGCATCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCT Cluster: [ ] Orangutan: GTGTCAGCTTATGGGTGTACAGCACCAGCAGCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCT Chimp > Human ------------- chr5:34919490-34919496 Template switch process: F1: L GGTTCTGGTTTCTCTGAACTGTGTCGGCTTATGGGTGTACAGCA 1 F3: 4 CAGGAATGCTGGGAGGAAAGAGTGGCTGAGCTGGGGTTCA R RF: GGTTCTGGTTTCTCTGAACTGTGTTGGCTTATGGGTGTACAGCAGCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCTGGGGTTCA RR: CCAAGACCAAAGAGACTTGACACAACCGAATACCCACATGTCGTCGTCCTTACGACCCTCCTTTCTCACCGACTCGACCCCAAGT F2: 3 TACGACC 2 Unidirectional alignment (log-probability: -31.6) CTGGTTTCTCTGAACTGTGTcGGCTTATGGGTGTAcagcacCAGCAtCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCTGGGGTTCA CTGGTTTCTCTGAACTGTGTTGGCTTATGGGTGTA------CAGCAGCAGGAATGCTGGGAGGAAAGAGTGGCTGAGCTGGGGTTCA Template switch alignment (log-probability: -22.2) CTGGTTTCTCTGAACTGTGTcGGCTTATGGGTGTACAGCA|CCAGCAT|CAGGAATGCTGGGAGGAAAGAGTGGCTGAGCTGGGGTTCA CTGGTTTCTCTGAACTGTGTTGGCTTATGGGTGTACAGCA|CCAGCAT|CAGGAATGCTGGGAGGAAAGAGTGGCTGAGCTGGGGTTCA ========== Event 2822 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATACTAATGACATAGCTGTTA--GTTGA--------AACTAATGTGAAAATTTT--------------CTTCCTATCTAGTTCTCAACTATGA Chimp: ATACTAATAAGATAGCTGTTA--GTTGA--------AACTAATGTGAAAATTTT--------------CTTCCTATCTAGTTCTCAACTATGA ↑ 13 2 4 Gorilla: ATACTAATGAGATAGCTGTTA----GGA----------------AGAAAATTTTCACATTAGTTTCAACTATCTATCTAGTTCTCAACTATGA ↓ 13 2 4 Human: ATACTAATGACATAGCTGTTA--GTTGA--------AACTAATGTGAAAATTTT--------------CTTCCTATCTAGTTCTCAACTATGA Cluster: [ ] Orangutan: ATACTAATGAGATGGCTGTTAGT--TGAAACTACTA--------TGAAAATTTT--------------CT-TCTATCTAGTTCTCAACTATGA Gorilla > Human --------------- chr5:34935331-34935356 Template switch process: F1: L TTGGAATTTCCAAACCTCCAATACTAATGACATAGCTGTTAG 1 F3: 4 CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA R RF: TTGGAATTTCCAAGCCTCCAATACTAATGAGATAGCTGTTAGGAAGAAAATTTTCACATTAGTTTCAACTATCTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA RR: AACCTTAAAGGTTCGGAGGTTATGATTACTCTATCGACAATCCTTCTTTTAAAAGTGTAATCAAAGTTGATAGATAGATCAAGAGTTGATACTTCTATGGTTAGTCTTAGGT F2: 3 CTTCTTTTAAAAGTGTAATCAAAGTT 2 Unidirectional alignment (log-probability: -66.5) GGAATTTCCAAaCCTCCAATACTAATGAcATAGCTGTTAGttGAAactaatgtGAAAATTTTC--------TTC------CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA GGAATTTCCAAGCCTCCAATACTAATGAGATAGCTGTTAG--GAA--------GAAAATTTTCACATTAGTTTCAACTATCTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA Template switch alignment (log-probability: -30.1) GGAATTTCCAAaCCTCCAATACTAATGAcATAGCTGTTAG|TTGAAACTAATGTGAAAATTTTCTTC|CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA GGAATTTCCAAGCCTCCAATACTAATGAGATAGCTGTTAG|TTGAAACTAATGTGAAAATTTTCTTC|CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA Gorilla > Chimp --------------- chr5:35145497-35145522 Template switch process: F1: L TTGTAATTTCCAAGCCTCCAATACTAATAAGATAGCTGTTAG 1 F3: 4 CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA R RF: TTGGAATTTCCAAGCCTCCAATACTAATGAGATAGCTGTTAGGAAGAAAATTTTCACATTAGTTTCAACTATCTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA RR: AACCTTAAAGGTTCGGAGGTTATGATTACTCTATCGACAATCCTTCTTTTAAAAGTGTAATCAAAGTTGATAGATAGATCAAGAGTTGATACTTCTATGGTTAGTCTTAGGT F2: 3 CTTCTTTTAAAAGTGTAATCAAAGTT 2 Unidirectional alignment (log-probability: -66.5) GtAATTTCCAAGCCTCCAATACTAATaAGATAGCTGTTAGttGAAactaatgtGAAAATTTTC--------TTC------CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA GGAATTTCCAAGCCTCCAATACTAATGAGATAGCTGTTAG--GAA--------GAAAATTTTCACATTAGTTTCAACTATCTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA Template switch alignment (log-probability: -30.1) GtAATTTCCAAGCCTCCAATACTAATaAGATAGCTGTTAG|TTGAAACTAATGTGAAAATTTTCTTC|CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA GGAATTTCCAAGCCTCCAATACTAATGAGATAGCTGTTAG|TTGAAACTAATGTGAAAATTTTCTTC|CTATCTAGTTCTCAACTATGAAGATACCAATCAGAATCCA ========== Event 2823 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: aaaaaagacTAATCCCTACTC------------------ACAAGTAGCAAGAATTGAGATGTGAGCacagtatcaagcaatggtta ↓ 4 1 3 2 Chimp: aaaaaagacTAATCCCTACTC---------ACAGCTCACACAAGTAGCAAGAATTGAGATG------------------------- Gorilla: aaaaaagacTAATCCCTACTCACAGCTCAC---------ACAAGTAGCAAGAATTGAGATGTGAGCacagtatcaagcaatggtta Human: aaaaaagacTAATCCCTACTC------------------ACAAGTAGCAAGAATTGAGATGTGAGCacagtatcaagcaatggtta Cluster: [ ] Orangutan: aaaaaaGACTAATTCCTGCTCACAGCTCAC---------ACAAGTAGCAAGAATTGAGATGTGAGCacagtatcaagcaatggtta Human > Chimp ------------- chr5:35458999-35459003 Template switch process: F1: L AAAAAAGACAAACAAAACAAAAAAGACTAATCCCTACTCACA 1 F3: 4 CACAAGTAGCAAGAATTGAGATG R RF: AAAAAAGACAAACAAAACAAAAAAGACTAATCCCTACTCACAAGTAGCAAGAATTGAGATGTGAGC RR: TTTTTTCTGTTTGTTTTGTTTTTTCTGATTAGGGATGAGTGTTCATCGTTCTTAACTCTACACTCG F2: 3 ACTCG 2 Unidirectional alignment (log-probability: -31.8) AAAAGACAAACAAAACAAAAAAGACTAATCCCTACTcacagctcaCACAAGTAGCAAGAATTGAGATG------------------ AAAAGACAAACAAAACAAAAAAGACTAATCCCTACT---------CACAAGTAGCAAGAATTGAGATGTGAGCACAGTATCAAGCA Template switch alignment (log-probability: -15.6) AAAAGACAAACAAAACAAAAAAGACTAATCCCTACTCACA|GCTCA|CACAAGTAGCAAGAATTGAGATG AAAAGACAAACAAAACAAAAAAGACTAATCCCTACTCACA|GCTCA|CACAAGTAGCAAGAATTGAGATG ========== Event 2824 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAGTCTTGAAGAAAATGGCT-------TATGC-TTGCCCAGAGTTCCTGATCATGTTCT-CCTCCTACCCTCCACCTCCA Chimp: TTAGTCTTGAAGAAAATGGCT-------TATGC-TTGCCCAGAGTTCCTGATCATGTTCT-CCTCCTACCCTCCACCTCCA ↓ 3 4 2 1 Gorilla: TTAGTCTTGAAGAAAATGGCTTCCTGATCATGTTCTGATCA-GGAACATGATCATGTTCT-CCTCCTACCCTCCACCTCCA Human: TTAGTCTTGAAGAAAATGGCT-------TATGC-TTGCCCAGAGTTCCTGATCATGTTCT-CCTCCTACCCTCCACCTCCA Cluster: [ ] Orangutan: TTAGTCTTGAAGAAAGTGGCT-------TATGC-TTGCGCAGAATTCCTGATCATGTTCTCCCTCCTACCCTCCACCTCCA Chimp > Gorilla --------------- chr5:127832998-127833006 Template switch process: F1: L CCAACAGTCCACGTCGTTGATTAGTCTTGAAGAAAATGGC----------------TTCCTGATCATGTTCT 1 F3: 4 CATGATCATGTTCTCCTCCTACCCTCCACCTCCATGTAAGTT R RF: CCAACAGTCCACGTCGTTGATTAGTCTTGAAGAAAATGGCTTATGCTTGCCCAGAGTTCCTGATCATGTTCTCCTCCTACCCTCCACCTCCATGTAAGTT RR: GGTTGTCAGGTGCAGCAACTAATCAGAACTTCTTTTACCGAATACGAACGGGTCTCAAGGACTAGTACAAGAGGAGGATGGGAGGTGGAGGTACATTCAA F2: 3 AAGGACTAG 2 Unidirectional alignment (log-probability: -54.6) TTGATTAGTCTTGAAGAAAATGGC----------------TTCCtgatcatgttctgatcaggaacaTGATCATGTTCTCCTCCTACCCTCCACCTCCATGTAAG TTGATTAGTCTTGAAGAAAATGGCTTATGCTTGCCCAGAGTTCC-----------------------TGATCATGTTCTCCTCCTACCCTCCACCTCCATGTAAG Template switch alignment (log-probability: -33.4) TTGATTAGTCTTGAAGAAAATGGC----------------TTCCTGATCATGTTCT|GATCAGGAA|CaTGATCATGTTCTCCTCCTACCCTCCACCTCCATGTAAG TTGATTAGTCTTGAAGAAAATGGCTTATGCTTGCCCAGAGTTCCTGATCATGTTCT|GATCAGGAA|CCTGATCATGTTCTCCTCCTACCCTCCACCTCCATGTAAG ========== Event 2825 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CAGGCTGCCTTGAATTCATTGGTTTTAACAACCAAGGGGATGAAAAGGAAGG Chimp: CAGGCTGCCTTGAATTCATTGGTTTTAACAACCAAGGGGATGAAAAGGAAGG Gorilla: CAGGCTGCCTTGAATTCATTG----TTAAAACCAAGGGGATGAAAAGGAAGG ↓ 3 4 2 Human: CAGGCTGCCTTGAATTCATTGGTTTTAACAACCAAGGGGATGAAAAGGAAGG Cluster: [ ] Orangutan: CAGGCTGCCTTGAATTCATTG----TTAAAACCAAGGGGATGAAAAGGAAGG Gorilla > Human --------------- chr5:34087019-34087026 Template switch process: F1: L GGTTGTGAATTTCTTCAAACCAGGCTGCCTTGAATTCATTG 1 F3: 4 AACCAAGGGGATGAAAAGGAAGGGCATGGCAGGAGGCGGA R RF: GGTTGTGAATTTCTTAAAACCAGGCTGCCTTGAATTCATTGTTAAAACCAAGGGGATGAAAAGGAAGGGCATGGCAGGAGGCGGA RR: CCAACACTTAAAGAATTTTGGTCCGACGGAACTTAAGTAACAATTTTGGTTCCCCTACTTTTCCTTCCCGTACCGTCCTCCGCCT F2: 3 CAATTTTG 2 Unidirectional alignment (log-probability: -32) GTTGTGAATTTCTTcAAACCAGGCTGCCTTGAATTCATTGgttTTAAcAACCAAGGGGATGAAAAGGAAGGGCATGGCAGGAGGCGGA GTTGTGAATTTCTTAAAACCAGGCTGCCTTGAATTCATTG---TTAA-AACCAAGGGGATGAAAAGGAAGGGCATGGCAGGAGGCGGA Template switch alignment (log-probability: -22.3) GTTGTGAATTTCTTcAAACCAGGCTGCCTTGAATTCATTG|GTTTTAAC|AACCAAGGGGATGAAAAGGAAGGGCATGGCAGGAGGCGGA GTTGTGAATTTCTTAAAACCAGGCTGCCTTGAATTCATTG|GTTTTAAC|AACCAAGGGGATGAAAAGGAAGGGCATGGCAGGAGGCGGA ========== Event 2826 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cctatgtaaaccctaggacccagtgatttaattcttaa----gtttatattccaaaatatgtgtag------------------aaaaataagaagtacacatattttggaata---taaacttaagaattaaatcactgggtcctagggtttacatgtgta Chimp: cctatgtaaaccctaggacccagtgatttaattc----ttaagtttatattccaaaaTATGTGTAG------------------AAAAATAAGAAGTACACATATTTTGGA---ATATAAACTTAAGAATTAAATCACTGGGTCCTAGGGTTTACATGTGTa ↑ 3 1 2 4 Gorilla: cctatgtaaaccctaggacccagtgatttaattcttaa----gtttatattccaaaaTATGTGTACTTCTTATTT------------------TTCTACACATATTTTGGAATA---TAAACTTAAGAATTAAATCACTGTGTCCTAGGGTTTACATGTGTa Human: cctatgtaaaccctaggacccagtgatttaattcttaa----gtttatattccaaaatatgtgtag------------------aaaaataagaagtacacatattttggaata---taaacttaagaattaaatcactgggtcctagggtttacatgtgta Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNN---------NNNNNNNNN---------NNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr5:34441842-34441896 Template switch process: F1: L TGTA 1 F3: 4 GTCCTAGGGTTTACAT R RF: CCAGTGATTTAATTCTTAAGTTTATATTCCAAAATATGTGTACTTCTTATTTTTCTACACATATTTTGGAATATAAACTTAAGAATTAAATCACTGTGTCCTAGGGTTTACAT RR: GGTCACTAAATTAAGAATTCAAATATAAGGTTTTATACACATGAAGAATAAAAAGATGTGTATAAAACCTTATATTTGAATTCTTAATTTAGTGACACAGGATCCCAAATGTA F2: 3 GGTCACTAAATTAAGAATTCAAATATAAGGTTTTATACACATGAAGAATAAAAAG 2 Unidirectional alignment (log-probability: -45.2) TGTA-------------gaaaaataagaagTACACATATTTTGGAATATAAACTTAAGAATTAAATCACTGgGTCCTAGGGTTTACAT TGTACTTCTTATTTTTC-------------TACACATATTTTGGAATATAAACTTAAGAATTAAATCACTGTGTCCTAGGGTTTACAT Template switch alignment (log-probability: -21.2) TGTA|GAAAAATAAGAAGTACACATATTTTGGAATATAAACTTAAGAATTAAATCACTGG|GTCCTAGGGTTTACAT TGTA|GAAAAATAAGAAGTACACATATTTTGGAATATAAACTTAAGAATTAAATCACTGG|GTCCTAGGGTTTACAT ========== Event 2827 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 124 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATGAGTATCTTGTCAAGCGCTTGTCTACACTAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCACTCAGCATGGCATACTACACGTCAG ↓ 1 4 3 2 ↑ 1 4 3 2 Chimp: ATGAGTATCTTGTCAAGCGCT-----CTGAGAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCACTCAGCATGGCATACTACACGTCAG Gorilla: ATGAGTATCTTGTCAAGCGCT-----CTGAGAATTTGCATAGTTAGTGTGGAGAGAGTACATGTATATGCACTCAGCATGGCATACTACACGTCAG ↑ 1 4 3 2 Human: ATGAGTATCTTGTCAAGCGCTTGTCTACACTAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCACTCAGCATGGCATACTACACGTCAG Cluster: [ ] Orangutan: ATGAGTATCTTGTCAAGCGCT-----CTGAGAATTTGCATAGTTAGTGTGGAGAGAGTACATGTATATGCACTCAGCATGGCATACTACATGCCAG Chimp > Human ------------- chr5:33580230-33580239 Template switch process: F1: L CATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT 1 F3: 4 AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA R RF: CATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCTCTGAGAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA RR: GTAAGTCGGGTGTGTACGGTTACTCATAGAACAGTTCGCGAGACTCTTAAACGTATCAATCACATCTCTCTCATGTACATATACGT F2: 3 TCACATCTGT 2 Unidirectional alignment (log-probability: -32.8) ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCTtgtctacaCT---AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT--------CTGAGAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA Template switch alignment (log-probability: -22.5) ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT|TgTCTACACT|AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT|TCTCTACACT|AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA Human > Chimp ------------- chr5:33770645-33770649 Template switch process: F1: L CATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT 1 F3: 4 AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA R RF: CATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCTTGTCTACACTAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCACTCAG RR: GTAAGTCGGGTGTGTACGGTTACTCATAGAACAGTTCGCGAACAGATGTGATTAAACGTATCAATCACATCTCTCTCATGTACATATACGTGAGTC F2: 3 GAGTC 2 Unidirectional alignment (log-probability: -25.9) ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT--------CTgagAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCTTGTCTACACT---AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA Template switch alignment (log-probability: -15.9) ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT|CTGAG|AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT|CTGAG|AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA Human > Gorilla --------------- chr5:33733590-33733594 Template switch process: F1: L CATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT 1 F3: 4 AATTTGCATAGTTAGTGTGGAGAGAGTACATGTATATGCA R RF: CATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCTTGTCTACACTAATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCACTCAG RR: GTAAGTCGGGTGTGTACGGTTACTCATAGAACAGTTCGCGAACAGATGTGATTAAACGTATCAATCACATCTCTCTCATGTACATATACGTGAGTC F2: 3 GAGTC 2 Unidirectional alignment (log-probability: -30.9) ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT--------CTgagAATTTGCATAGTTAGTGTgGAGAGAGTACATGTATATGCA ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCTTGTCTACACT---AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA Template switch alignment (log-probability: -21.9) ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT|CTGAG|AATTTGCATAGTTAGTGTgGAGAGAGTACATGTATATGCA ATTCAGCCCACACATGCCAATGAGTATCTTGTCAAGCGCT|CTGAG|AATTTGCATAGTTAGTGTAGAGAGAGTACATGTATATGCA ========== Event 2828 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTCTCCTTGAAAGCTGGCCAAATGGTGGCCAGGAGAAGGGAAGGGATGCATATAGAGACAAGGGGaaattatttaaaaattattttaaaattCAGACAGCATTTGAGCAGAGTAGCAACAACAAAACTAAAGCCAATAAT Chimp: TCTCTCCTTGAAAGCTGGCCAAATGGTGGCCAGGAGAAGGGAAGGGATGCATATAGAGGCAAGGGGaaattatttaaaaattatttaaaaattCAGACAGCATTTAAGCAGAGTAGCAACAACAAAACTAAAGCCAATAAT ↓ 3 2 1 4 Gorilla: TCTCTCCTTGAAAGCTGGCCAAATGGTGGCCAGGAGAAGGGAAGGGATGCATATAGAGGCAAGGGGaaattatttaaaaattatttaaaaattCAGACAGCATTTGAGCAGCATTTGAACGACAAAACTAAAGCCAATAAT ↑ 3 2 1 4 Human: TCTCTCCTTGAAAGCTGGCCAAATGGTGGCCAGGAGAAGGGAAGGGATGCATATAGAGACAAGGGGaaattatttaaaaattattttaaaattCAGACAGCATTTGAGCAGAGTAGCAACAACAAAACTAAAGCCAATAAT Cluster: [ ] Orangutan: TCTCTCCTTGAAAGCTGGCCAAATGGTGGCCAGGAGAAGGGAAGGGATGCACATAGAGGCAAGGGGaaattatttaaaaattatttaaaaattCAGACAGCATTTGAGCAGAGTAGCAACAACAAAACTAAAGCCAACAAT Human > Gorilla --------------- chr5:33566792-33566797 Template switch process: F1: L TATTTAAAAATTATTTAAAAATTCAGACAGCATTTGAGCAG 1 F3: 4 AACGACAAAACTAAAGCCAATAATAAGAGTATTAAAATGAATCC R RF: CAAATGGTGGCCAGGAGAAGGGAAGGGATGCATATAGAGACAAGGGGAAATTATTTAAAAATTATTTTAAAATTCAGACAGCATTTGAGCAGAGTAGCAACAACAAAACTAAAGCCAATAATAAGAGTATTAAAATGAATCC RR: GTTTACCACCGGTCCTCTTCCCTTCCCTACGTATATCTCTGTTCCCCTTTAATAAATTTTTAATAAAATTTTAAGTCTGTCGTAAACTCGTCTCATCGTTGTTGTTTTGATTTCGGTTATTATTCTCATAATTTTACTTAGG F2: 3 GTTTAC 2 Unidirectional alignment (log-probability: -38.1) ATTTAAAAATTATTTaAAAATTCAGACAGCATTTGAGCAG--------CAtttgaacgACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA ATTTAAAAATTATTTTAAAATTCAGACAGCATTTGAGCAGAGTAGCAACA--------ACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA Template switch alignment (log-probability: -27.6) ATTTAAAAATTATTTaAAAATTCAGACAGCATTTGAGCAG|CATTTG|AACgACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA ATTTAAAAATTATTTTAAAATTCAGACAGCATTTGAGCAG|CATTTG|AACAACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA Chimp > Gorilla --------------- chr5:33566792-33566797 Template switch process: F1: L GGAAATTATTTAAAAATTATTTAAAAATTCAGACAGCATTTGAGCAG 1 F3: 4 AACGACAAAACTAAAGCCAATAATAAGAGTATTAAAATGAATCC R RF: CAAATGGTGGCCAGGAGAAGGGAAGGGATGCATATAGAGGCAAGGGGAAATTATTTAAAAATTATTTAAAAATTCAGACAGCATTTAAGCAGAGTAGCAACAACAAAACTAAAGCCAATAATAAGAGTATTAAAATGAATCC RR: GTTTACCACCGGTCCTCTTCCCTTCCCTACGTATATCTCCGTTCCCCTTTAATAAATTTTTAATAAATTTTTAAGTCTGTCGTAAATTCGTCTCATCGTTGTTGTTTTGATTTCGGTTATTATTCTCATAATTTTACTTAGG F2: 3 GTTTAC 2 Unidirectional alignment (log-probability: -38.2) ATTTAAAAATTATTTAAAAATTCAGACAGCATTTgAGCAG--------CAtttgaacgACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA ATTTAAAAATTATTTAAAAATTCAGACAGCATTTAAGCAGAGTAGCAACA--------ACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA Template switch alignment (log-probability: -27.8) ATTTAAAAATTATTTAAAAATTCAGACAGCATTTgAGCAG|CATTTG|AACgACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA ATTTAAAAATTATTTAAAAATTCAGACAGCATTTAAGCAG|CATTTG|AACAACAAAACTAAAGCCAATAATAAGAGTATTAAAATGA ========== Event 2829 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ttctaactccccgtTACCTACAGAAGT--GCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTT Chimp: TTCTAACTCCCCGTTACCTACAGAAGT--GCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTT ↓ 3 1 2 4 Gorilla: ttctaactccccgtTACCTACAGAAGT----ATGCACTTCTG-TGCATTTGAGTGAGTTCCTTTT ↑ 3 1 2 4 Human: ttctaactccccgtTACCTACAGAAGT--GCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTT Cluster: [ ] Orangutan: TTCTAACTCCCCGTTACCTACAGAATTGC--ATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTC Human > Gorilla --------------- chr5:32980303-32980314 Template switch process: F1: L CCTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT 1 F3: 4 GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC R RF: CCTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGTGCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC RR: GGAACGAACTTTCAAAGATTGAGGGGCAATGGATGTCTTCACGTATGAGGAGACACCGTAAACTCACTCAAGGAAAATCCCCTTTATGACGTACTG F2: 3 TGTCTTCACGTA 2 Unidirectional alignment (log-probability: -37.5) CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT--ATgCaCtTCTGT-GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGTGCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC Template switch alignment (log-probability: -17.3) CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT|ATGCACTTCTGT|GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT|ATGCACTTCTGT|GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC Chimp > Gorilla --------------- chr5:32980303-32980314 Template switch process: F1: L CCTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT 1 F3: 4 GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC R RF: CCTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGTGCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC RR: GGAACGAACTTTCAAAGATTGAGGGGCAATGGATGTCTTCACGTATGAGGAGACACCGTAAACTCACTCAAGGAAAATCCCCTTTATGACGTACTG F2: 3 TGTCTTCACGTA 2 Unidirectional alignment (log-probability: -37.5) CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT--ATgCaCtTCTGT-GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGTGCATACTCCTCTGTGGCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC Template switch alignment (log-probability: -17.3) CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT|ATGCACTTCTGT|GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC CTTGCTTGAAAGTTTCTAACTCCCCGTTACCTACAGAAGT|ATGCACTTCTGT|GCATTTGAGTGAGTTCCTTTTAGGGGAAATACTGCATGAC ========== Event 2830 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTT-TTTTTCTTTCCAAATGACTAAGGAAAG-----TACAGATTGTTTTCACTCACCTGTGC Chimp: CttttttttCTTTCCAAATGACTAAGGAAAG-----TACAGATTGTTTTCGCTCACCTGTGC ↓ 3 1 2 4 Gorilla: CCtttttttCTTTCCAAATGACTAAGGTACTTTCCTTAGTCATTGTTTTCGCTCACCTGTGC Human: CTT-TTTTTCTTTCCAAATGACTAAGGAAAG-----TACAGATTGTTTTCACTCACCTGTGC Cluster: [ ] Orangutan: CttttttttCTTTCCAAATGACTAAGGAAAG-----TACAGATTGTTTTCGCTCACCTGTGC Chimp > Gorilla --------------- chr5:133621747-133621760 Template switch process: F1: L TCTTTTCATGTACACCTTTTTTTCTTTCCAAATGACTAAGG 1 F3: 4 ATTGTTTTCGCTCACCTGTGCCCTAGATGGACTTTTCCC R RF: TCTTTTCATGTACACTTTTTTTTCTTTCCAAATGACTAAGGAAAGTACAGATTGTTTTCGCTCACCTGTGCCCTAGATTGACTTTTCCC RR: AGAAAAGTACATGTGAAAAAAAAGAAAGGTTTACTGATTCCTTTCATGTCTAACAAAAGCGAGTGGACACGGGATCTAACTGAAAAGGG F2: 3 CTGATTCCTTTCAT 2 Unidirectional alignment (log-probability: -59) CTTTTCATGTACACcTTTTTTTCTTTCCAAATGACTAAGGtactttccttagtc---------ATTGTTTTCGCTCACCTGTGCCCTAGATgGACTTTTCCC- CTTTTCATGTACACTTTTTTTTCTTTCCAAATGACTAAGG--------------AAAGTACAGATTGTTTTCGCTCACCTGTGCCCTAGATTGACTTTTCCCC Template switch alignment (log-probability: -28.5) CTTTTCATGTACACcTTTTTTTCTTTCCAAATGACTAAGG|TACTTTCCTTAGTC|ATTGTTTTCGCTCACCTGTGCCCTAGATgGACTTTTCCC CTTTTCATGTACACTTTTTTTTCTTTCCAAATGACTAAGG|TACTTTCCTTAGTC|ATTGTTTTCGCTCACCTGTGCCCTAGATTGACTTTTCCC ========== Event 2831 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ----------gtgtgtgtgtgtatgtACACACAAACGTGTGTA--------------------CTGCTGCTATAAATATTTTTG ↑ 1 4 3 2 Chimp: ----------gt--gtgtgtgtATGTAAACACAAACGTGTGTA----------CATACTAATAGTGCTGCTATAAAtatttttg Gorilla: ----------------gtgtgtATGTATACACAAACGTGTGTACATACTAATA----------GTGCTGCTATAAAtatttttg Human: ----------gtgtgtgtgtgtatgtACACACAAACGTGTGTA--------------------CTGCTGCTATAAATATTTTTG Cluster: [ ] Orangutan: acaaacgtgt------gtgtgtatgtatacacaaacgtgtgtaCATACTAATA----------GTGCTGCTATAAATATTTTTG Chimp > Human ------------- chr5:15137962-15137969 Template switch process: F1: L TTGTGTGTGTGTGTGTGT 1 F3: 4 ACACAAACGTGTGTAC----------TGCTGCTATAAATATTTTTGAACATTCCCTGATAAATATA R RF: TTGTGTGTGTGTGTGTGTATGTAAACACAAACGTGTGTACATACTAATAGTGCTGCTATAAATATTTTTGAACATTCCCTGATAAATATA RR: AACACACACACACACACATACATTTGTGTTTGCACACATGTATGATTATCACGACGATATTTATAAAAACTTGTAAGGGACTATTTATAT F2: 3 CATGTATG 2 Unidirectional alignment (log-probability: -40.6) TtgTGTGTGTGTGTGTGTGTATGTAcACACAAACGTGTGTAC----------TGCTGCTATAAATATTTTTGAACA T--TGTGTGTGTGTGTGTGTATGTAAACACAAACGTGTGTACATACTAATAGTGCTGCTATAAATATTTTTGAACA Template switch alignment (log-probability: -26.9) TTGTGTGTGTGTGTGTGT|GTATGTAC|ACACAAACGTGTGTAC----------TGCTGCTATAAATATTTTTGAACA TTGTGTGTGTGTGTGTGT|GTATGTAC|ACACAAACGTGTGTACATACTAATAGTGCTGCTATAAATATTTTTGAACA ========== Event 2832 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGCTTCATTCTGAGTCTTCAGAATGAAAAGACTGATGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG ↑ 4 1 3 2 Chimp: TGGCTTCATTCTGAGTCTTCATT------CCTTGGCTGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG Gorilla: TGGCTTCATTCTGAGTCTTCATT------CCTTGGATGGAGACTCAGTCTTTTCATCCATCAGATGGGGCTGCTGG Human: TGGCTTCATTCTGAGTCTTCAGAATGAAAAGACTGATGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG Cluster: [ ] Orangutan: TGGCTTCATTCTGAGTCTTCATT------CCTTGGATGGAGACTCAGTCTTTTCATCTATCAGATGGGGCTGCTGG Chimp > Human ------------- chr5:150520334-150520346 Template switch process: F1: L CCTGCTAATGAATCCTGGCTTGGCTTCATTCTGAGTCTTCA-----------GA 1 F3: 4 TGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG R RF: CCTGCTAATGAATCCTGGCTTGGCTTCATTCTGAGTCTTCATTCCTTGGCTGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG RR: GGACGATTACTTAGGACCGAACCGAAGTAAGACTCAGAAGTAAGGAACCGACCTCTGAGTCAGAAAAGTAGATAGTATACCCCGACGACC F2: 3 AGTCAGAAAAGTA 2 Unidirectional alignment (log-probability: -43.2) GCTAATGAATCCTGGCTTGGCTTCATTCTGAGTCTTCA---------gaatgaaaagactgaTGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG GCTAATGAATCCTGGCTTGGCTTCATTCTGAGTCTTCATTCCTTGGC---------------TGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG Template switch alignment (log-probability: -27.7) GCTAATGAATCCTGGCTTGGCTTCATTCTGAGTCTTCA-----------GA|ATGAAAAGACTGA|TGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG GCTAATGAATCCTGGCTTGGCTTCATTCTGAGTCTTCATTCCTTGGCTGGA|ATGAAAAGACTGA|TGGAGACTCAGTCTTTTCATCTATCATATGGGGCTGCTGG ========== Event 2833 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CACCTTGTTGCAGAACACAGAT----GACTGACTGCCCAGGGTTGGAAGGctgggcagtcagggaaggcaccattgcagaggcggcctttgcacttggctttgaaacataaataggaaacagtcaaacttcaaagagcaaaaagg Chimp: CACCTTGTCGCAGAACACAGAT----GACTGACTGCCCGGGGTTGGAAggctgggcagtcagggaaggcaccatcgcagaggcggcctttgcacttggctttgaaagataaataggaaacagtcaaacttcaaagagcaaaaagg ↑ 1 4 3 2 Gorilla: CACCTTGTTGCAGAACACAGAA--------CACTGCCCAGGGTTGGAAggctgggcagtcagggaaggcaccatcgcagaggcggcctttgcacgtggctttgaaagataaataggaaacagtcaaacttcaaagagcaaaaagg ↓ 1 4 3 2 Human: CACCTTGTTGCAGAACACAGAT----GACTGACTGCCCAGGGTTGGAAGGctgggcagtcagggaaggcaccattgcagaggcggcctttgcacttggctttgaaacataaataggaaacagtcaaacttcaaagagcaaaaagg Cluster: [ ] Orangutan: CACCTTGTTGCAGAACACAGATGACT----GACTGCCCAGGGATGGAAGGctgggcagtcagggaaggcaccattgcagaggcggcctttgcacttggctttgaaagataaataggaaacagtcaaacttcaaagagcaaaaagg Gorilla > Human --------------- chr5:150350789-150350794 Template switch process: F1: L GCCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGA 1 F3: 4 ACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC R RF: GCCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGAACACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCACCATCGCAGAGGCGGCCTTTGCACGTGGCTTTGAAAGATAAATAGGAAACAGTCA RR: CGGTCCCCACCTCCGTCCCGGTGGAACAACGTCTTGTGTCTTGTGACGGGTCCCAACCTTCCGACCCGTCAGTCCCTTCCGTGGTAGCGTCTCCGCCGGAAACGTGCACCGAAACTTTCTATTTATCCTTTGTCAGT F2: 3 GTCAGT 2 Unidirectional alignment (log-probability: -26.4) CCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGAtgACtgACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC CCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGA--AC--ACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC Template switch alignment (log-probability: -16.5) CCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGA|TGACTG|ACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC CCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGA|TGACTG|ACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC Gorilla > Chimp --------------- chr5:150549059-150549064 Template switch process: F1: L GCCAGGGGTGGAGGCAGGGCCACCTTGTCGCAGAACACAGA 1 F3: 4 ACTGCCCGGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCACCATCGCAG R RF: GCCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGAACACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCACCATCGCAGAGGCGGCCTTTGCACGTGGCTTTGAAAGATAAATAGGAAACAGTCA RR: CGGTCCCCACCTCCGTCCCGGTGGAACAACGTCTTGTGTCTTGTGACGGGTCCCAACCTTCCGACCCGTCAGTCCCTTCCGTGGTAGCGTCTCCGCCGGAAACGTGCACCGAAACTTTCTATTTATCCTTTGTCAGT F2: 3 GTCAGT 2 Unidirectional alignment (log-probability: -37.6) CCAGGGGTGGAGGCAGGGCCACCTTGTcGCAGAACACAGAtgACtgACTGCCCgGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC CCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGA--AC--ACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC Template switch alignment (log-probability: -27.7) CCAGGGGTGGAGGCAGGGCCACCTTGTcGCAGAACACAGA|TGACTG|ACTGCCCgGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC CCAGGGGTGGAGGCAGGGCCACCTTGTTGCAGAACACAGA|TGACTG|ACTGCCCAGGGTTGGAAGGCTGGGCAGTCAGGGAAGGCAC ========== Event 2834 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTTGGGTTGGAATTTGATGCA--------TTGCACTGCTTGCAATGAAGAACACTGActaatata Chimp: GGTTGGGTTGGAATTTGATGCT----TGTCTTCTACTGCTTGCAGTGAAGAACACTGACTAATATA Gorilla: GGTTGGGTTGGAATTTGATGCTTGTC----TTCTACTGCTTGCAATGAAGAACACTGActaatata ↓ 1 4 3 2 Human: GGTTGGGTTGGAATTTGATGCA--------TTGCACTGCTTGCAATGAAGAACACTGActaatata Cluster: [ ] Orangutan: GGTTGGGTTGGAATTTGATGCTTGTC----TTCTACTGCTTGCAATGAAGAACACTGActaatata Gorilla > Human --------------- chr5:151229089-151229094 Template switch process: F1: L AAAGGAATTCTAGAACGTCAGGTTGGGTTGGAATTTGATGC 1 F3: 4 CTGCTTGCAATGAAGAACACTGACTAATATAAATCTTTG R RF: AAAGGAATTCTAGAACGTCAGGTTGGGTTGGAATTTGATGCTTGTCTTCTACTGCTTGCAATGAAGAACACTGACTAATATAAATCTTTG RR: TTTCCTTAAGATCTTGCAGTCCAACCCAACCTTAAACTACGAACAGAAGATGACGAACGTTACTTCTTGTGACTGATTATATTTAGAAAC F2: 3 ACGTTA 2 Unidirectional alignment (log-probability: -27.7) AAGGAATTCTAGAACGTCAGGTTGGGTTGGAATTTGATGC----aTTgcACTGCTTGCAATGAAGAACACTGACTAATATAAATCTTTG AAGGAATTCTAGAACGTCAGGTTGGGTTGGAATTTGATGCTTGTCTTCTACTGCTTGCAATGAAGAACACTGACTAATATAAATCTTTG Template switch alignment (log-probability: -16.5) AAGGAATTCTAGAACGTCAGGTTGGGTTGGAATTTGATGC|ATTGCA|CTGCTTGCAATGAAGAACACTGACTAATATAAATCTTTG AAGGAATTCTAGAACGTCAGGTTGGGTTGGAATTTGATGC|ATTGCA|CTGCTTGCAATGAAGAACACTGACTAATATAAATCTTTG ========== Event 2835 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: AAGTTTTCCCTAAAATGCTCAGTCTGCTATCCAAATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCACTGTATATCTTCTGTTGTTAGCAGGTCT ↓ 3 2 1 4 Chimp: AAGTTTTCCCTAAAACGCTCAGTCTGCTATCCAAATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCA-CGACTGTCTTCTGTTGTTAGCAGGTCT Gorilla: AAGTTTTCCCTAAAACGCTCAGTCTGCTATCCAAATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCA-CAACTGTCTTCAGTTGTTAGCAGTTCT Human: AAGTTTTCCCTAAAATGCTCAGTCTGCTATCCAAATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCACTGTATATCTTCTGTTGTTAGCAGGTCT Cluster: [ ] Orangutan: AAGTTTTCCCTAAAATGCCCAGTCTGCTATCCAAATTTCAGCTCCCAACCTTCTAGGATATACAGTGCAAGCA-TGACTGTCTTCTATTGTTAGCAGGTCT Human > Chimp ------------- chr5:29309029-29309033 Template switch process: F1: L AAATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCAC 1 F3: 4 TCTTCTGTTGTTAGCAGGTCTCTTGTTTGAGAGAGCTATT R RF: CAGTCTGCTATCCAAATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCACTGTATATCTTCTGTTGTTAGCAGGTCTCTTGTTTGAGAGAGCTATT RR: GTCAGACGATAGGTTTAAAGTCGAGGGTTAGAAGATCCTATATGTCACGTTCGTGACATATAGAAGACAACAATCGTCCAGAGAACAAACTCTCTCGATAA F2: 3 GTCAG 2 Unidirectional alignment (log-probability: -25.7) ATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCacgACTG----TCTTCTGTTGTTAGCAGGTCTCTTGTTTGAGAGAGCTATT ATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGC---ACTGTATATCTTCTGTTGTTAGCAGGTCTCTTGTTTGAGAGAGCTATT Template switch alignment (log-probability: -15.9) ATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCAC|GACTG|TCTTCTGTTGTTAGCAGGTCTCTTGTTTGAGAGAGCTATT ATTTCAGCTCCCAATCTTCTAGGATATACAGTGCAAGCAC|GACTG|TCTTCTGTTGTTAGCAGGTCTCTTGTTTGAGAGAGCTATT ========== Event 2836 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGGCCTCAATCAAAGAAGGCT-------ATCGGATGTGGGGAGAGGAACATTGGTTCT Chimp: TTGGCCTCAATCAAAGAAGGCT-------ATCGGATGTGGGGAGAGGAACATTGGTTCT ↓ 1 3 4 2 Gorilla: TTGGCCTCAATCAAAGAAGGCCACATCCGATAGGATGTGGGGAGAGGAACATTGGTTCT ↑ 1 3 4 2 Human: TTGGCCTCAATCAAAGAAGGCT-------ATCGGATGTGGGGAGAGGAACATTGGTTCT Cluster: [ ] Orangutan: TTGGCCTCAATCAAAGAAGGCT-------ATCGGATTTGGGGAGAGGAACATTGGTTCT Human > Gorilla --------------- chr5:137236581-137236591 Template switch process: F1: L AGAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGC 1 F3: 4 GGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTCTCAA R RF: AGAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGCTATCGGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTTTCAA RR: TCTTCGTGGTATTAATGACAAACCGGAGTTAGTTTCTTCCGATAGCCTACACCCCTCTCCTTGTAACCAAGAAGAAGAGAAAGTT F2: 3 ATAGCCTACAC 2 Unidirectional alignment (log-probability: -37.6) GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGccacatcCgATaGGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTcTCAA GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGG-------CTATCGGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTTTCAA Template switch alignment (log-probability: -22.6) GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGC|CACATCCGATA|GGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTcTCAA GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGC|CACATCCGATA|GGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTTTCAA Chimp > Gorilla --------------- chr5:137236581-137236591 Template switch process: F1: L AGAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGC 1 F3: 4 GGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTCTCAA R RF: AGAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGCTATCGGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTTTCAA RR: TCTTCGTGGTATTAATGACAAACCGGAGTTAGTTTCTTCCGATAGCCTACACCCCTCTCCTTGTAACCAAGAAGAAGAGAAAGTT F2: 3 ATAGCCTACAC 2 Unidirectional alignment (log-probability: -37.6) GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGccacatcCgATaGGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTcTCAA GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGG-------CTATCGGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTTTCAA Template switch alignment (log-probability: -22.6) GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGC|CACATCCGATA|GGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTcTCAA GAAGCACCATAATTACTGTTTGGCCTCAATCAAAGAAGGC|CACATCCGATA|GGATGTGGGGAGAGGAACATTGGTTCTTCTTCTCTTTCAA ========== Event 2837 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TCTGGAAATGTAAATGTTTATAGTACTCC-------ACT-AATGAGTCATGGAACGATGTTT ↓ 3 2 4 Chimp: TCTGGAAATGTAAATGTTTATAGTACTCCATGGAGTACTATATGAGTCATGGAGCGATGTTT Gorilla: -------------------------------------------------------------- Human: TCTGGAAATGTAAATGTTTATAGTACTCC-------ACT-AATGAGTCATGGAACGATGTTT Cluster: [ ] Orangutan: -------------------------------------------------------------- Human > Chimp ------------- chr5:180212190-180212200 Template switch process: F1: L GGCAGTGGGTGGTCTGGAAATGTAAATGTTTATAGTACTCCA 1 F3: 4 ATGAGTCATGGAGCGATGTTTCCTATTGAAAATGTTTTA R RF: GGCAGTGGGTGGTCTGGAAATGTAAATGTTTATAGTACTCCACTAATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTT RR: CCGTCACCCACCAGACCTTTACATTTACAAATATCATGAGGTGATTACTCAGTACCTTGCTACAAAGGATAACTTTTACAAAAA F2: 3 TATCATGAGGT 2 Unidirectional alignment (log-probability: -51.9) CAGTGGGTGGTCTGGAAATGTAAATGTTTATAGTACTCCatggagtACTAtATGAGTCATGGAgCGATGTTTCCTATTGAAAATGTTTTa- CAGTGGGTGGTCTGGAAATGTAAATGTTTATAGTACTCC-------ACTA-ATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTTG Template switch alignment (log-probability: -28.6) CAGTGGGTGGTCTGGAAATGTAAATGTTTATAGTACTCCA|TGGAGTACTAT|ATGAGTCATGGAgCGATGTTTCCTATTGAAAATGTTTTa CAGTGGGTGGTCTGGAAATGTAAATGTTTATAGTACTCCA|TGGAGTACTAT|ATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTT ========== Event 2838 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: ACAGAAATAATaaaaaaa-aaaGAT----------------ACCAGATAGAAATAGAGATCTTTATTCTTTGTGAATAAAGATCTCTATTTCTATCTGGTATCttt----ttttttttggaagat ↓ 1 3 4 2 ↑ 1 3 4 2 Chimp: ATAGAAATAATaaa--aa-aaaGAT----------------ACCAGATAGAAATAGAGATCTTTATTCACAAAGAATAAAGAtctctatttctatctggtatctttttttttttttttggaagat Gorilla: ATAGAAATAATaaa--aaaaaaGAT--------------------------------ATTCTTTATTCACAAAGAATaaagatctctatttctatctggtatcttt----t-ttttttggaagat Human: ACAGAAATAATaaaaaaa-aaaGAT----------------ACCAGATAGAAATAGAGATCTTTATTCTTTGTGAATAAAGATCTCTATTTCTATCTGGTATCttt----ttttttttggaagat Cluster: [ ] Orangutan: ATAGAAATa---aa--aa-aaaaaTACCAGATAGAAATAGA----------------GATCTTT-----------ATAAAGATCTCTATTTCTATCTGGTATCttt----ttttttttggaagat Chimp > Human ------------- chr5:27230210-27230246 Template switch process: F1: L TAAAAAAAA 1 F3: 4 GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTT R RF: TAAAAAAAAGATACCAGATAGAAATAGAGATCTTTATTCACAAAGAATAAAGATCTCTATTTCTATCTGGTATCTTTTTT RR: ATTTTTTTTCTATGGTCTATCTTTATCTCTAGAAATAAGTGTTTCTTATTTCTAGAGATAAAGATAGACCATAGAAAAAA F2: 3 TGTTTCTTATTTCTAGAGATAAAGATAGACCATAGAA 2 Unidirectional alignment (log-probability: -49) TaaAAAAAAAAGATACCAGATAGAAATAGAGATCTTTATTC-----tttgtGAATAAAGATCTCTATTTCTATCTGGTATCTTTTTT---- T--AAAAAAAAGATACCAGATAGAAATAGAGATCTTTATTCACAAA-----GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTTTTTT Template switch alignment (log-probability: -19.1) TAAAAAAAA|AAGATACCAGATAGAAATAGAGATCTTTATTCTTTGT|GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTT TAAAAAAAA|AAGATACCAGATAGAAATAGAGATCTTTATTCTTTGT|GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTT Human > Chimp ------------- chr5:27348166-27348200 Template switch process: F1: L TAAAAAAAA 1 F3: 4 GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTTTTTT R RF: TAAAAAAAAAAGATACCAGATAGAAATAGAGATCTTTATTCTTTGTGAATAAAGATCTCTATTTCTATCTGGTATCTTTTTTTTTT RR: ATTTTTTTTTTCTATGGTCTATCTTTATCTCTAGAAATAAGAAACACTTATTTCTAGAGATAAAGATAGACCATAGAAAAAAAAAA F2: 3 AAACACTTATTTCTAGAGATAAAGATAGACCATAG 2 Unidirectional alignment (log-probability: -51.8) T--AAAAAAAAGATACCAGATAGAAATAGAGATCTTTATTC-----acaaaGAATAAAGATCTCTATTTCTATCTGGTATCTTTTTTtttt TAAAAAAAAAAGATACCAGATAGAAATAGAGATCTTTATTCTTTGT-----GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTT---- Template switch alignment (log-probability: -19) TAAAAAAAA|GATACCAGATAGAAATAGAGATCTTTATTCACAAA|GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTTTTTT TAAAAAAAA|GATACCAGATAGAAATAGAGATCTTTATTCACAAA|GAATAAAGATCTCTATTTCTATCTGGTATCTTTTTTTTTT ========== Event 2839 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTTGTAAAGTTAAAGTGGATTCCAGCCACACTAGAATCCAAGTTGAATTCAAATTTACT Chimp: TATTTGTAAAGTTAAAGTGGATTCCAGCCACACTAGAATCCAAGTTGAATTCAAATTTACT ↑ 3 1 2 4 Gorilla: TATTTGTAAAGTTAAAGTGGATTCCAGTGTGGCTGGAATTCAAGTTGAATTCAAATTTACT ↓ 3 1 2 4 Human: TATTTGTAAAGTTAAAGTGGATTCCAGCCACACTAGAATCCAAGTTGAATTCAAATTTACT Cluster: [ ] Orangutan: TATTTGTAAAGTTAAAGTGGATTCCAGTCACACTGGAATCCAAGTTGAATTCAAATTTACT Gorilla > Human --------------- chr5:27480397-27480409 Template switch process: F1: L TGCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAG 1 F3: 4 CAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG R RF: TGCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAGTGTGGCTGGAATTCAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG RR: ACGAATCCACATTTATAAACATTTCAATTTCACCTAAGGTCACACCGACCTTAAGTTCAACTTAAGTTTAAATGAGGATACGACCCCCGACACC F2: 3 CTAAGATCACACC 2 Unidirectional alignment (log-probability: -38.1) GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCA--------GccacactaGAATcCAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAGTGTGGCTG--------GAATTCAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG Template switch alignment (log-probability: -22.9) GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAG|CCACACTaGAATC|CAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAG|CCACACTGGAATC|CAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG Gorilla > Chimp --------------- chr5:27599766-27599778 Template switch process: F1: L TGCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAG 1 F3: 4 CAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG R RF: TGCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAGTGTGGCTGGAATTCAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG RR: ACGAATCCACATTTATAAACATTTCAATTTCACCTAAGGTCACACCGACCTTAAGTTCAACTTAAGTTTAAATGAGGATACGACCCCCGACACC F2: 3 CTAAGATCACACC 2 Unidirectional alignment (log-probability: -38.1) GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCA--------GccacactaGAATcCAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAGTGTGGCTG--------GAATTCAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG Template switch alignment (log-probability: -22.9) GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAG|CCACACTaGAATC|CAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG GCTTAGGTGTAAATATTTGTAAAGTTAAAGTGGATTCCAG|CCACACTGGAATC|CAAGTTGAATTCAAATTTACTCCTATGCTGGGGGCTGTGG ========== Event 2840 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGAGACTACAAAAGTATAGAATACATTGATGTTGAAGAGCACAGGGTGAGTGTCAGGGATTGAAAGGGACACAAAAGCATGAGATTGGCCTATATTAGCCATGAATAGTGAACTAGAT Chimp: CTGAGACTACAAAAGTATAGAATACATTGATGTTGAAGAGCACAGGGTGAGTGTCAGGGATTGAAAGGGACACAAAAGCATGAAATTGGCCTATATTAGCCATGAATAGTGAACTAGAT ↓ 3 2 1 4 Gorilla: CTGAGACTACAAAAGTATAGAATACATTGATGTTGAAGAACACAGGGTGAGTGTCAGGGATTGAAAGGGACACAAAAGCATGAGATTGGCCTGTATTCGCCATGAATAGTGAACTAGAT Human: CTGAGACTACAAAAGTATAGAATACATTGATGTTGAAGAGCACAGGGTGAGTGTCAGGGATTGAAAGGGACACAAAAGCATGAGATTGGCCTATATTAGCCATGAATAGTGAACTAGAT Cluster: [ ] Orangutan: CTGAGACTGCGAAAGTATAGAATACACTGATGTTGAAGAACACAGGGTGAGTATCAGGGATTGAAAGGGACACAAAAGCATGAGATTGGCCTGTATTAGCCATGAATAGTGAACTAGAT Chimp > Gorilla --------------- chr5:138625940-138625945 Template switch process: F1: L CAGGGTGAGTGTCAGGGATTGAAAGGGACACAAAAGCATGAGATTGGCCT 1 F3: 4 GCCATGAATAGTGAACTAGATAGTGTGTGTGTGTGTGTGT R RF: GAATACATTGATGTTGAAGAGCACAGGGTGAGTGTCAGGGATTGAAAGGGACACAAAAGCATGAAATTGGCCTATATTAGCCATGAATAGTGAACTAGATAGTGTGTGTGTGTGTGTGT RR: CTTATGTAACTACAACTTCTCGTGTCCCACTCACAGTCCCTAACTTTCCCTGTGTTTTCGTACTTTAACCGGATATAATCGGTACTTATCACTTGATCTATCACACACACACACACACA F2: 3 CTTATG 2 Unidirectional alignment (log-probability: -37.5) GTCAGGGATTGAAAGGGACACAAAAGCATGAgATTGGCCTgTATTcGCCATGAATAGTGAACTAGATAGTGTGTGTGtgtgtgtgt GTCAGGGATTGAAAGGGACACAAAAGCATGAAATTGGCCTATATTAGCCATGAATAGTGAACTAGATAGTGTGTGTG--------- Template switch alignment (log-probability: -22.2) GTCAGGGATTGAAAGGGACACAAAAGCATGAgATTGGCCT|GTATTC|GCCATGAATAGTGAACTAGATAGTGTGTGTGTGTGTGTGT GTCAGGGATTGAAAGGGACACAAAAGCATGAAATTGGCCT|GTATTC|GCCATGAATAGTGAACTAGATAGTGTGTGTGTGTGTGTGT ========== Event 2841 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATCAGCAAGAAATATAGAA----TGAC--CCTTACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAAAGGG Chimp: AAATCAGCAAGAAATATAGAA----TGAG--CCTTACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAAAGGG ↓ 1 4 3 2 Gorilla: AAATCAGCAAGAAATATAGAAGTTTCAAG----CAACTTCTCCAAACTGTTGCTTGAAAAAATATTGTTAGAGAAAGGG ↑ 1 4 3 2 Human: AAATCAGCAAGAAATATAGAA----TGAC--CCTTACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAAAGGG Cluster: [ ] Orangutan: AAATCAGCAAGAAATGTAGAA----TGAGCC--TTACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAAAGGG Human > Gorilla --------------- chr5:25976120-25976128 Template switch process: F1: L TTTTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAAG 1 F3: 4 ACTTCTCCAAACTGTTGCTTGAAAAAATATTGTTAGAGAA R RF: TTTTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAATGACCCTTACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAA RR: AAAATTCTCTTATTTATCTATTTAGTCGTTCTTTATATCTTACTGGGAATGAAGAGGTTCGACAACGAACTTTTTTATAACAATCTCTT F2: 3 ACGAACTTT 2 Unidirectional alignment (log-probability: -40.9) TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAA--------gtttcaagcaACTTCTCCAAaCTGTTGCTTGAAAAAATATTGTTAGAGAA TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAATGACCCTT----------ACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAA Template switch alignment (log-probability: -27.9) TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAAg|TTTCAAGCA|ACTTCTCCAAaCTGTTGCTTGAAAAAATATTGTTAGAGAA TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAAT|TTTCAAGCA|ACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAA Chimp > Gorilla --------------- chr5:25976120-25976128 Template switch process: F1: L TTTTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAAG 1 F3: 4 ACTTCTCCAAACTGTTGCTTGAAAAAATATTGTTAGAGAA R RF: TTTTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAATGAGCCTTACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAA RR: AAAATTCTCTTATTTATCTATTTAGTCGTTCTTTATATCTTACTCGGAATGAAGAGGTTCGACAACGAACTTTTTTATAACAATCTCTT F2: 3 ACGAACTTT 2 Unidirectional alignment (log-probability: -40.9) TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAA--------gtttcaagcaACTTCTCCAAaCTGTTGCTTGAAAAAATATTGTTAGAGAA TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAATGAGCCTT----------ACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAA Template switch alignment (log-probability: -27.9) TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAAg|TTTCAAGCA|ACTTCTCCAAaCTGTTGCTTGAAAAAATATTGTTAGAGAA TTAAGAGAATAAATAGATAAATCAGCAAGAAATATAGAAT|TTTCAAGCA|ACTTCTCCAAGCTGTTGCTTGAAAAAATATTGTTAGAGAA ========== Event 2842 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTTGGTGGGGTAACATCAGGCC-ATGCAT------------------TGATGTTTTTGTTTTCTGGATTCCCCT ↑ 13 2 4 Chimp: CCTTGGTGGGGTAACATCAGGTCAATGCAT---------GGCCTGAGTAGCTGTCTTTGTTTTCTGGATTCCCCT Gorilla: CCTTGGTGGGGTAACATCAGGCCAATGCATGGCCTGAGT---------AGCTGTCTTTGTTTTCTGGATTCCCCT Human: CCTTGGTGGGGTAACATCAGGCC-ATGCAT------------------TGATGTTTTTGTTTTCTGGATTCCCCT Cluster: [ ] Orangutan: CCTTGGTGGGGTAACATCAGGCCAATGCATGGCCTGAGT---------AGCTGTCTTTGTTTTCTGGATTCCCCT Chimp > Human ------------- chr5:15589739-15589749 Template switch process: F1: L GAAGCTTAAAAGAGAGGGTACCTTGGTGGGGTAACATCAGG 1 F3: 4 TGTTTTTGTTTTCTGGATTCCCCTGTTGGTTTTCCAATCCAGCC R RF: GAAGCTTAAAAGAGAGGGTACCTTGGTGGGGTAACATCAGGTCAATGCATGGCCTGAGTAGCTGTCTTTGTTTTCTGGATTCCCCTGTTGGTTTCCCAATCCAGCC RR: CTTCGAATTTTCTCTCCCATGGAACCACCCCATTGTAGTCCAGTTACGTACCGGACTCATCGACAGAAACAAAAGACCTAAGGGGACAACCAAAGGGTTAGGTCGG F2: 3 AGTTACGTACC 2 Unidirectional alignment (log-probability: -48.5) AAGCTTAAAAGAGAGGGTACCTTGGTGGGGTAACATCAGG------------------------CcatgcattgatgttTTTGTTTTCTGGATTCCCCTGTTGGTTTtCCAATCC AAGCTTAAAAGAGAGGGTACCTTGGTGGGGTAACATCAGGTCAATGCATGGCCTGAGTAGCTGTC--------------TTTGTTTTCTGGATTCCCCTGTTGGTTTCCCAATCC Template switch alignment (log-probability: -28.7) AAGCTTAAAAGAGAGGGTACCTTGGTGGGGTAACATCAGG|CCATGCATTGA|TGTtTTTGTTTTCTGGATTCCCCTGTTGGTTTtCCAATCC AAGCTTAAAAGAGAGGGTACCTTGGTGGGGTAACATCAGG|CCATGCATTGA|TGTCTTTGTTTTCTGGATTCCCCTGTTGGTTTCCCAATCC ========== Event 2843 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATATTATA----GTTAATTTAAAACTGAT-----------------------GGACCACTAGTTTTAAAACTGAGGGATTCCATCAAATATCAAAAAC Chimp: TTGTATTATA----GTTAATTTAAAACTGAT-----------------------GGACCATCAGTTTTAAAACTGAGGGATTCCATCAACTATCAAAAAC ↑ 4 3 21 Gorilla: TTGTATTATA----GTTAATTTAAAACTGAT----------------------------------------------GGATTCCATCAAATATCAAAAAC Human: TCATATTATA----GTTAATTTAAAACTGAT-----------------------GGACCACTAGTTTTAAAACTGAGGGATTCCATCAAATATCAAAAAC Cluster: [ ] Orangutan: TTGTATTATAGTTAGTTAATTTAAAACTGATGGACCACCAGTTTTAAAACTGAG-----------------------GGGTTCCATCAAATATCAAAAAC Gorilla > Chimp --------------- chr5:24242536-24242543 Template switch process: F1: L TCTTAATTTTCTTTTTGTATTATAGTTAATTTAAAACTGATGGA 1 F3: 4 TTTAAAACTGAGGGATTCCATCAACTATCAAAAACCTTAAGTGTTCCCAACT R RF: TCTTAATTTTCTTTTTGTATTATAGTTAATTTAAAACTGATGGATTCCATCAAATATCAAAAACCTTAAGTGTTCCCAACT RR: AGAATTAAAAGAAAAACATAATATCAATTAAATTTTGACTACCTAAGGTAGTTTATAGTTTTTGGAATTCACAAGGGTTGA F2: 3 TGACTACC 2 Unidirectional alignment (log-probability: -49.5) AATTTTCTTTTTGTATTATAGTTAATTTAAAACTGATggaccatcagttttaaaactgagGGATTCCATCAAcTATCAAAAACCTTAA AATTTTCTTTTTGTATTATAGTTAATTTAAAACTGAT-----------------------GGATTCCATCAAATATCAAAAACCTTAA Template switch alignment (log-probability: -28.1) AATTTTCTTTTTGTATTATAGTTAATTTAAAACTGATGGA|CCATCAGT|TTTAAAACTGAgGGATTCCATCAAcTATCAAAAACCTTAA AATTTTCTTTTTGTATTATAGTTAATTTAAAACTGATGGA|CCATCAGT|TTTAAAACTGATGGATTCCATCAAATATCAAAAACCTTAA ========== Event 2844 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTGATCCCCCCAAAAGTCTTTACCCCAGAAAATAAAAGAGTACCAGGAAATATAGTACTCTTTTATAGTACTCTTAAATAGGCACAATTCAAAAGTGGATCAGTAAAGGTCATAAATATAGTAGGCTGAGGATTAGT Chimp: TTTGATCCCCCCAAAAGTCTTTACCCCACAAAATAAAAGAGTACCAGGAAATATA--------------AGCATTTAAATAGGCACAATTCAAAAGTGGATCAGTAAAGGTcataaatatagtaggctgaggattagt Gorilla: TTTGATCCCCCCAAAAGTCTTCACCCCACAAAATAAAAGAGTACCAGGAAATATA--------------AGCATTTAAATAGGCACAATTCAAAAGTGGATCAGTAAAGGTCATAAATATAGTAGGCTGAGGATTAGT ↓ 3 2 1 4 Human: TTTGATCCCCCCAAAAGTCTTTACCCCAGAAAATAAAAGAGTACCAGGAAATATAGTACTCTTTTATAGTACTCTTAAATAGGCACAATTCAAAAGTGGATCAGTAAAGGTCATAAATATAGTAGGCTGAGGATTAGT Cluster: [ ] Orangutan: TTTGATCTCCCCAAAAGTCTTCACCCCACAAAATAAAAGAGTACCAGGAAATATA--------------AGCATTTAAATAGGCACAATTCAAAAGTGGAACAGTAAAGGTCATAAATATAGTAGGCTGAGGATTAGT Gorilla > Human --------------- chr5:22912721-22912729 Template switch process: F1: L TTCCCAAAGGTTAGCCATATTTTGATCCCCCCAAAAGTCTTTACCCCAGAAAATAAAAGAGTACCAGGAAATATA 1 F3: 4 TATAG R RF: TTCCCAAAGGTTAGCCATATTTTGATCCCCCCAAAAGTCTTCACCCCACAAAATAAAAGAGTACCAGGAAATATAAGCATTTAAATAGGCACAATTCAAAAGTGGATCAGTAAAGGTCATAAATATAG RR: AAGGGTTTCCAATCGGTATAAAACTAGGGGGGTTTTCAGAAGTGGGGTGTTTTATTTTCTCATGGTCCTTTATATTCGTAAATTTATCCGTGTTAAGTTTTCACCTAGTCATTTCCAGTATTTATATC F2: 3 TTTCTCATG 2 Unidirectional alignment (log-probability: -39) AGTCTTtACCCCAgAAAATAAAAGAGTACCAGGAAATATAgtactcttttatag AGTCTTCACCCCACAAAATAAAAGAGTACCAGGAAATATA-------------- Template switch alignment (log-probability: -27.9) AGTCTTtACCCCAgAAAATAAAAGAGTACCAGGAAATATA|GTACTCTTT|TATAG AGTCTTCACCCCACAAAATAAAAGAGTACCAGGAAATATA|GTACTCTTT|TATAG ========== Event 2845 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGCCTCAAACCACTGATGTGGGCT--------------GCCA------GGCCCACCACGTGTGAAAGATCAAATCTG ↓ 31 4 2 ↑ 1 3 4 Chimp: AGCCTCGAACCACTGATGTGGACT-------GTGGTGGGCCT---GGCAGCCCACCACGTGTGAAAGATCAAATCTG Gorilla: AGCCTCGAACCACTGATGTGGACCGTGGTGG-------GCCTGGC---AGCCCACCACCTGTGAAAGATCAAATCTG Human: AGCCTCAAACCACTGATGTGGGCT--------------GCCA------GGCCCACCACGTGTGAAAGATCAAATCTG Cluster: [ ] Orangutan: AGTCTCGAACCACTGATGTGGACCGTGGTGG-------GCCTGGC---AGCCCACCACGTGTGAAAGATCAAATCTG Chimp > Human ------------- chr5:21604497-21604505 Template switch process: F1: L AATTGGGACGTCAGTCCTGGAGCCTCAAACCACTGATGTGG 1 F3: 4 CCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT R RF: AATTGGGACGTCAGTCCTGGAGCCTCGAACCACTGATGTGGACTGTGGTGGGCCTGGCAGCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT RR: TTAACCCTGCAGTCAGGACCTCGGAGCTTGGTGACTACACCTGACACCACCCGGACCGTCGGGTGGTGCACACTTTCTAGTTTAGACAAATATGCGACA F2: 3 GGACCGTCG 2 Unidirectional alignment (log-probability: -39.6) ATTGGGACGTCAGTCCTGGAGCCTCaAACCACTGATGTGG------------------GCtgccaggcCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT ATTGGGACGTCAGTCCTGGAGCCTCGAACCACTGATGTGGACTGTGGTGGGCCTGGCAGC--------CCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT Template switch alignment (log-probability: -22.4) ATTGGGACGTCAGTCCTGGAGCCTCaAACCACTGATGTGG|GCTGCCAGG|CCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT ATTGGGACGTCAGTCCTGGAGCCTCGAACCACTGATGTGG|GCTGCCAGG|CCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT Human > Chimp ------------- chr5:21635373-21635386 Template switch process: F1: L AATTGGGACGTCAGTCCTGGAGCCTCGAACCACTGATGTGGACTG 1 F3: 4 GCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT R RF: AATTGGGACGTCAGTCCTGGAGCCTCAAACCACTGATGTGGGCTGCCAGGCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT RR: TTAACCCTGCAGTCAGGACCTCGGAGTTTGGTGACTACACCCGACGGTCCGGGTGGTGCACACTTTCTAGTTTAGACAAATATGCGACA F2: 3 ACGGTCCGGGTGGT 2 Unidirectional alignment (log-probability: -53.4) GGACGTCAGTCCTGGAGCCTCgAACCACTGATGTG--------GactgtggtgggcctggcaGCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT GGACGTCAGTCCTGGAGCCTCAAACCACTGATGTGGGCTGCCAG------------------GCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT Template switch alignment (log-probability: -29.1) GGACGTCAGTCCTGGAGCCTCgAACCACTGATGTGGaCTG|TGGTGGGCCTGGCA|GCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT GGACGTCAGTCCTGGAGCCTCAAACCACTGATGTGGGCTG|TGGTGGGCCTGGCA|GCCCACCACGTGTGAAAGATCAAATCTGTTTATACGCTGT ========== Event 2846 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTTAAACAAAATATCTAACTCAAT-TAGTTTCTGAATctagaagcatga Chimp: TCTTAAACAAAATATCTAACTAATTGAACTTTCTGAATctagaagcatga Gorilla: TCTTAAACAAAATATCTAACTAATTGAACTTTCTGAATctagaagcatga ↓ 31 2 4 Human: TCTTAAACAAAATATCTAACTCAAT-TAGTTTCTGAATctagaagcatga Cluster: [ ] Orangutan: TCTTAAACAAAATATCTAACTAATTGAACTTTCTGAATctagaagcatga Gorilla > Human --------------- chr5:21495662-21495668 Template switch process: F1: L ATCAAACAAAAATACACAACTCTTAAACAAAATATCTAACT 1 F3: 4 TTTCTGAATCTAGAAGCATGACATAGCGGAAAGAACACTG R RF: ATCAAACAAAAATACACAACTCTTAAACAAAATATCTAACTAATTGAACTTTCTGAATCTAGAAGCATGACATAGCGGAAAGAACACTG RR: TAGTTTGTTTTTATGTGTTGAGAATTTGTTTTATAGATTGATTAACTTGAAAGACTTAGATCTTCGTACTGTATCGCCTTTCTTGTGAC F2: 3 GATTAAC 2 Unidirectional alignment (log-probability: -27.8) TCAAACAAAAATACACAACTCTTAAACAAAATATCTAACTcAATT--AgTTTCTGAATCTAGAAGCATGACATAGCGGAAAGAACACTG TCAAACAAAAATACACAACTCTTAAACAAAATATCTAACT-AATTGAACTTTCTGAATCTAGAAGCATGACATAGCGGAAAGAACACTG Template switch alignment (log-probability: -16.6) TCAAACAAAAATACACAACTCTTAAACAAAATATCTAACT|CAATTAG|TTTCTGAATCTAGAAGCATGACATAGCGGAAAGAACACTG TCAAACAAAAATACACAACTCTTAAACAAAATATCTAACT|CAATTAG|TTTCTGAATCTAGAAGCATGACATAGCGGAAAGAACACTG ========== Event 2847 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATATTAGGGAAGGCAAAACTTAGAACTCAAAATTACATGTGCTTTAGAATTTGCTGG Chimp: ATATTAGGGAAGGCAAAACTTAGAACTCAAAATTACATGTGCTTTAGAATTTGCTGG ↓ 13 24 ↑ 13 24 Gorilla: ATATTAGGGAAGGCAAAACTTGTAATTTTGAGTTCTATGTGCTTTAGAATTTGCTGG ↓ 13 24 ↑ 13 24 Human: ATATTAGGGAAGGCAAAACTTAGAACTCAAAATTACATGTGCTTTAGAATTTGCTGG Cluster: [ ] Orangutan: ATATTAGGGAAGGCAAAACTTAGAACTCAAAATTACATGTGCTTTAGAATTTGCTAG Gorilla > Human --------------- chr5:20946059-20946073 Template switch process: F1: L GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT 1 F3: 4 ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA R RF: GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTGTAATTTTGAGTTCTATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA RR: CATATGTTACCAAGATAAAGTATAATCCCTTCCGTTTTGAACATTAAAACTCAAGATACACGAAATCTTAAACGACCATAGTTTATCTGATCCCGT F2: 3 CATTAAAACTCAAGA 2 Unidirectional alignment (log-probability: -48.5) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACT---------------TagaactcaaaattacATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAaGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTGTAATTTTGAGTTCT---------------ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA Template switch alignment (log-probability: -23.2) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|AGAACTCAAAATTAC|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAaGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|AGAACTCAAAATTAC|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA Human > Gorilla --------------- chr5:20886412-20886426 Template switch process: F1: L GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT 1 F3: 4 ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA R RF: GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTAGAACTCAAAATTACATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA RR: CATATGTTACCAAGATAAAGTATAATCCCTTCCGTTTTGAATCTTGAGTTTTAATGTACACGAAATCTTAAACGACCATAGTTTATCTGATTCCGT F2: 3 TCTTGAGTTTTAATG 2 Unidirectional alignment (log-probability: -48.5) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT---------------gtaattttgagttctATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAgGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTAGAACTCAAAATTAC---------------ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA Template switch alignment (log-probability: -23.2) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|GTAATTTTGAGTTCT|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAgGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|GTAATTTTGAGTTCT|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA Gorilla > Chimp --------------- chr5:20976902-20976916 Template switch process: F1: L GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT 1 F3: 4 ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA R RF: GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTGTAATTTTGAGTTCTATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA RR: CATATGTTACCAAGATAAAGTATAATCCCTTCCGTTTTGAACATTAAAACTCAAGATACACGAAATCTTAAACGACCATAGTTTATCTGATCCCGT F2: 3 CATTAAAACTCAAGA 2 Unidirectional alignment (log-probability: -48.5) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACT---------------TagaactcaaaattacATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAaGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTGTAATTTTGAGTTCT---------------ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA Template switch alignment (log-probability: -23.2) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|AGAACTCAAAATTAC|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAaGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|AGAACTCAAAATTAC|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA Chimp > Gorilla --------------- chr5:20886412-20886426 Template switch process: F1: L GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT 1 F3: 4 ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAGGGCA R RF: GTATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTAGAACTCAAAATTACATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA RR: CATATGTTACCAAGATAAAGTATAATCCCTTCCGTTTTGAATCTTGAGTTTTAATGTACACGAAATCTTAAACGACCATAGTTTATCTGATTCCGT F2: 3 TCTTGAGTTTTAATG 2 Unidirectional alignment (log-probability: -48.5) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT---------------gtaattttgagttctATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAgGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTTAGAACTCAAAATTAC---------------ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA Template switch alignment (log-probability: -23.2) TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|GTAATTTTGAGTTCT|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAgGGCA TATACAATGGTTCTATTTCATATTAGGGAAGGCAAAACTT|GTAATTTTGAGTTCT|ATGTGCTTTAGAATTTGCTGGTATCAAATAGACTAAGGCA ========== Event 2848 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: -AAAGATTATAAGATCACACATAAGGTTGTGATTGAGTAGCAGTGTCTAATGCAGTATGGGATAAGAAAGTGGTAGCCTATGCACCAGGGGTCTGCCCTACACTGAATCATGATATCTAGACTCTTTAACCTT---CTTACATTTCAGCAATCTATCGATCAT Chimp: -AAAGATTATAAGATCACACATAAGGTTGTGATTGAGTAGCAGTGTCTAATGCAGTATGGGATAAGAAAGTGGTAGCCTATGCACCAGGGGTCTGCCCTACACTGAATCATGATATCTAGACTCTTTAACCTT---CTTACATTTCAGCAATCTATCGATCAT ↓ 3 2 1 4 Gorilla: -AAAGATTATAAGATCACACATAAGGTTGTGATTGAGTAGCAGTGTCTAATACAGTATGGGATAAGAAAGTGGTAGCCTATGCACCAGGGGTCTGCCCTACACTGTATCATGATATCTAGACTCTTTAACCTTCTTCTTATGTTTCAGCAATCTATCGATCAT ↑ 3 2 1 4 Human: -AAAGATTATAAGATCACACATAAGGTTGTGATTGAGTAGCAGTGTCTAATGCAGTATGGGATAAGAAAGTGGTAGCCTATGCACCAGGGGTCTGCCCTACACTGAATCATGATATCTAGACTCTTTAACCTT---CTTACATTTCAGCAATCTATCGATCAT Cluster: [ ] Orangutan: aaaagattataagatcacacatagggttgtgattcattagcagcgtctaatacagtatgggataagaaagtggtagcCTATTCACCAGGGGTCTGCCCTACACTGTATCATGATATCTAGACTCTTGAACCTT---CTTATATTTCAGCAATCTATCGATCAT Human > Gorilla --------------- chr5:21920535-21920540 Template switch process: F1: L CTGCCCTACACTGTATCATGATATCTAGACTCTTTAACCTTCTT 1 F3: 4 TTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG R RF: CATAAGGTTGTGATTGAGTAGCAGTGTCTAATGCAGTATGGGATAAGAAAGTGGTAGCCTATGCACCAGGGGTCTGCCCTACACTGAATCATGATATCTAGACTCTTTAACCTTCTTACATTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG RR: GTATTCCAACACTAACTCATCGTCACAGATTACGTCATACCCTATTCTTTCACCATCGGATACGTGGTCCCCAGACGGGATGTGACTTAGTACTATAGATCTGAGAAATTGGAAGAATGTAAAGTCGTTAGATAGCTAGTAATACAGAATCTTCATATTC F2: 3 GTATTC 2 Unidirectional alignment (log-probability: -31.8) CCTACACTGtATCATGATATCTAGACTCTTTAACcttCTTCTTAtgTTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG CCTACACTGAATCATGATATCTAGACTCTTTAAC---CTTCTTACATTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG Template switch alignment (log-probability: -22.1) CCTACACTGtATCATGATATCTAGACTCTTTAACCTTCTT|CTTATG|TTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG CCTACACTGAATCATGATATCTAGACTCTTTAACCTTCTT|CTTATG|TTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG Chimp > Gorilla --------------- chr5:21920535-21920540 Template switch process: F1: L CTGCCCTACACTGTATCATGATATCTAGACTCTTTAACCTTCTT 1 F3: 4 TTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG R RF: CATAAGGTTGTGATTGAGTAGCAGTGTCTAATGCAGTATGGGATAAGAAAGTGGTAGCCTATGCACCAGGGGTCTGCCCTACACTGAATCATGATATCTAGACTCTTTAACCTTCTTACATTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG RR: GTATTCCAACACTAACTCATCGTCACAGATTACGTCATACCCTATTCTTTCACCATCGGATACGTGGTCCCCAGACGGGATGTGACTTAGTACTATAGATCTGAGAAATTGGAAGAATGTAAAGTCGTTAGATAGCTAGTAATACAGAATCTTCATATTC F2: 3 GTATTC 2 Unidirectional alignment (log-probability: -31.8) CCTACACTGtATCATGATATCTAGACTCTTTAACcttCTTCTTAtgTTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG CCTACACTGAATCATGATATCTAGACTCTTTAAC---CTTCTTACATTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG Template switch alignment (log-probability: -22.1) CCTACACTGtATCATGATATCTAGACTCTTTAACCTTCTT|CTTATG|TTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG CCTACACTGAATCATGATATCTAGACTCTTTAACCTTCTT|CTTATG|TTTCAGCAATCTATCGATCATTATGTCTTAGAAGTATAAG ========== Event 2849 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATATATGGCTCCTCAGAGTT-GAGACCTGAAGCCTGAGACTCCTGAA Chimp: ACATATATGGCTCCTCAGAGTT-GAGACCTGAAGCCTGAGACTCCTGAA ↑ 31 2 4 Gorilla: ACATATATGGCTCCTCAGAGTCTCAACTCTGAAGCCTGAGACTCCTGAA ↓ 31 2 4 Human: ACATATATGGCTCCTCAGAGTT-GAGACCTGAAGCCTGAGACTCCTGAA Cluster: [ ] Orangutan: ACATATATGGCTCCTCAGAGTT-GAGACCTGAAGCCTGAGACTCCTGAA Gorilla > Human --------------- chr5:161316231-161316236 Template switch process: F1: L AGGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT 1 F3: 4 CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCAGTGA R RF: AGGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGTCTCAACTCTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA RR: TCCAACTGTAAAGACTATAGTGTATATACCGAGGAGTCTCAGAGTTGAGACTTCGGACTCTGAGGACTTGGAGTCAGACGACGTGACT F2: 3 CAGAGT 2 Unidirectional alignment (log-probability: -33.7) GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT------TgagacCTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCAgTGA GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGTCTCAACT-----CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA Template switch alignment (log-probability: -22) GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT|TGAGAC|CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCAgTGA GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT|TGAGAC|CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA Gorilla > Chimp --------------- chr5:161664615-161664620 Template switch process: F1: L AGGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT 1 F3: 4 CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA R RF: AGGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGTCTCAACTCTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA RR: TCCAACTGTAAAGACTATAGTGTATATACCGAGGAGTCTCAGAGTTGAGACTTCGGACTCTGAGGACTTGGAGTCAGACGACGTGACT F2: 3 CAGAGT 2 Unidirectional alignment (log-probability: -28.1) GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT------TgagacCTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGTCTCAACT-----CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA Template switch alignment (log-probability: -16.5) GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT|TGAGAC|CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA GGTTGACATTTCTGATATCACATATATGGCTCCTCAGAGT|TGAGAC|CTGAAGCCTGAGACTCCTGAACCTCAGTCTGCTGCACTGA ========== Event 2850 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCAAGTGCTAGCAGGAATCT--AGGCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCCTAAACTATGatttttaaaaaattatttatgatataaaaatgaattaaaCACCAGGTTTCTGGTATTACTAGTAGCACTTTGAAGTTTATGAAATA ↓ 1 4 3 2 Chimp: ACCAAGTGCTAGCAGGAATCTGCTAGCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCCTAAACTATGATTTTCAAAAAATTATTTCTAATATAAAAATGAATTAAACACCAGATTTCTGGTATTACTAGTAGCACTTTGAAATTTATGAAATA Gorilla: ACCAAGTGCTAGCAGGAATCT--AGGCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCCTAAACTATGATTTTTAAAAAATTATTTATATTATAAAAATGAATTAAACACCAGGTTTCTGGTATCACTAGTAGCACTTTGAAATTTATGAAATA Human: ACCAAGTGCTAGCAGGAATCT--AGGCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCCTAAACTATGatttttaaaaaattatttatgatataaaaatgaattaaaCACCAGGTTTCTGGTATTACTAGTAGCACTTTGAAGTTTATGAAATA Cluster: [ ] Orangutan: ACCAAGTGCTAGCAGGAATCT--AGGCCGCTAGAAAGATACTAAAAAATATCAATAGTATGATCCTAAACTATGATTTTTGAAAAATTATTTATAATATAAAAATGAATTAAACACCAGGTTTCTGGTATTACTAGTAGTACTTTGAAATTTATGAAATA Human > Chimp ------------- chr5:162254369-162254372 Template switch process: F1: L CATTAGAAGCACCTGAAAGTACCAAGTGCTAGCAGGAATCT 1 F3: 4 GCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCC R RF: CATTAGAAGCACCTGAAAGTACCAAGTGCTAGCAGGAATCTAGGCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCCTAAACTATGATTTTTAAAAAATTATTTATGATATAAAAATGAATTAAACACCAGGTTTCTGGTATTACTAGTAGC RR: GTAATCTTCGTGGACTTTCATGGTTCACGATCGTCCTTAGATCCGGTGATCTTTCTATGATTTTTTACAGTTATCATACTAGGATTTGATACTAAAAATTTTTTAATAAATACTATATTTTTACTTAATTTGTGGTCCAAAGACCATAATGATCATCG F2: 3 ATCG 2 Unidirectional alignment (log-probability: -25.5) ATTAGAAGCACCTGAAAGTACCAAGTGCTAGCAGGAATctgCTA-GCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCC ATTAGAAGCACCTGAAAGTACCAAGTGCTAGCAGGAAT---CTAGGCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCC Template switch alignment (log-probability: -15.8) ATTAGAAGCACCTGAAAGTACCAAGTGCTAGCAGGAATCT|GCTA|GCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCC ATTAGAAGCACCTGAAAGTACCAAGTGCTAGCAGGAATCT|GCTA|GCCACTAGAAAGATACTAAAAAATGTCAATAGTATGATCC ========== Event 2851 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: cccaggctggagtgcagtggcatgatctcagctcactgcaacctctgctcctgggttcaaacgattcttctgcctcagcatcctgatagcCATCATATTTTAAATTCAATAACCTACCTTTGCTTAGCTTCCTTCCCTT Chimp: cccaggctggagtgcagtggcatgatctcagctcactgcaacctccgctcctgggttcaaacgattctcctgcctcagcatcctgatagcCATCATATTTTAAATTCAACA----TGCTTTGCTTAGCTTCCTTCCCtt ↑ 3 2 1 4 Gorilla: cccaggctggagtgcagtggcatgatctcagctcactgcaacctccgctcctgggttcaaacgattctcctgcctcagcatcctgatagcCATCATATTTTAAATTCAATAACCTACCTTTGCTTAGCTTCCTTCCCtt Human: cccaggctggagtgcagtggcatgatctcagctcactgcaacctctgctcctgggttcaaacgattcttctgcctcagcatcctgatagcCATCATATTTTAAATTCAATAACCTACCTTTGCTTAGCTTCCTTCCCTT Cluster: [ ] Orangutan: cccaggctggagtgcagtggcatgatctcagctcactgcaacctccgctcctgggttcaaacaattctcctgcctcagcatcctgatagcCATCATAT------------TACCTACCTTTGCTTAGCTTCCTTCCCTT Gorilla > Chimp --------------- chr5:163687705-163687709 Template switch process: F1: L CCTGCCTCAGCATCCTGATAGCCATCATATTTTAAATTCAA 1 F3: 4 TTTGCTTAGCTTCCTTCCCTTTTTTTAGCCATTAAAAA R RF: GCATGATCTCAGCTCACTGCAACCTCCGCTCCTGGGTTCAAACGATTCTCCTGCCTCAGCATCCTGATAGCCATCATATTTTAAATTCAATAACCTACCTTTGCTTAGCTTCCTTCCCTTTTTTTAGCCATTATAAA RR: CGTACTAGAGTCGAGTGACGTTGGAGGCGAGGACCCAAGTTTGCTAAGAGGACGGAGTCGTAGGACTATCGGTAGTATAAAATTTAAGTTATTGGATGGAAACGAATCGAAGGAAGGGAAAAAAATCGGTAATATTT F2: 3 CGTAC 2 Unidirectional alignment (log-probability: -35.1) CTGCCTCAGCATCCTGATAGCCATCATATTTTAAATTCA-------ACatgCTTTGCTTAGCTTCCTTCCCTTTTTTTAGCCATTA-AAAA CTGCCTCAGCATCCTGATAGCCATCATATTTTAAATTCAATAACCTAC---CTTTGCTTAGCTTCCTTCCCTTTTTTTAGCCATTATAAAA Template switch alignment (log-probability: -21.8) CTGCCTCAGCATCCTGATAGCCATCATATTTTAAATTCAA|CATGC|TTTGCTTAGCTTCCTTCCCTTTTTTTAGCCATTAaAAA CTGCCTCAGCATCCTGATAGCCATCATATTTTAAATTCAA|CATGC|TTTGCTTAGCTTCCTTCCCTTTTTTTAGCCATTATAAA ========== Event 2852 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ---GTGTGCTGTATTATACGA----ATATGCATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAAC--------AAAAATGTTCAGCCATAGGTTAAGCATATAAAGCTTTCTATTTTTGTC Chimp: ---GTGTGCTGTATTATACGA----ATATGCATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAAC----AAATAAAAATGTTCAGCCATAGGTTAAGCATATAAAGCTTTCTATTTTTGTC ↑ 1 4 3 2 Gorilla: GTGGTGTGCTGTATTATACGAAAGAAAAT-GATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAAC--------AAAAATGTTCAGCCATAGGTTAAGCATATAAAGCTTTCTATTTTTGTC ↓ 1 4 3 2 Human: ---GTGTGCTGTATTATACGA----ATATGCATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAAC--------AAAAATGTTCAGCCATAGGTTAAGCATATAAAGCTTTCTATTTTTGTC Cluster: [ ] Orangutan: ---GTGTGCTGTATTATACGA----ATATGCATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAACAAAT----AAAAATGTTCAGCCATAGGTTAAGCATATAAAGCTTTCTATTTTTGTC Gorilla > Human --------------- chr5:164625578-164625582 Template switch process: F1: L CTTGAAATTGTTCTCCATAT---GTGTGCTGTATTATACGAA 1 F3: 4 ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA R RF: CTTGAAATTGTTCTCCATATGTGGTGTGCTGTATTATACGAAAGAAAATGATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAACAAAAATGTTCAGCCATAGGTTAAGCATA RR: GAACTTTAACAAGAGGTATACACCACACGACATAATATGCTTTCTTTTACTAGAGTTTCTTTTACTATCATGTTATTTTATTATAATACTCAGGTTATTTTAATTAACGGATAAATATTACCTTAGATAAATTTAAAAAAGTAAATTGATAAAAACTTTGTTTTTACAAGTCGGTATCCAATTCGTAT F2: 3 CGTAT 2 Unidirectional alignment (log-probability: -37.7) CTTGAAATTGTTCTCCATAT---GTGTGCTGTATTATAC----GAAtATGcATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA CTTGAAATTGTTCTCCATATGTGGTGTGCTGTATTATACGAAAGAAAATG-ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA Template switch alignment (log-probability: -26.2) CTTGAAATTGTTCTCCATAT---GTGTGCTGTATTATACGAA|TATGC|ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA CTTGAAATTGTTCTCCATATGTGGTGTGCTGTATTATACGAA|TATGC|ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA Gorilla > Chimp --------------- chr5:165086677-165086681 Template switch process: F1: L CTTGAAATTGTTCTCCATAT---GTGTGCTGTATTATACGAA 1 F3: 4 ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA R RF: CTTGAAATTGTTCTCCATATGTGGTGTGCTGTATTATACGAAAGAAAATGATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGAGTCCAATAAAATTAATTGCCTATTTATAATGGAATCTATTTAAATTTTTTCATTTAACTATTTTTGAAACAAAAATGTTCAGCCATAGGTTAAGCATA RR: GAACTTTAACAAGAGGTATACACCACACGACATAATATGCTTTCTTTTACTAGAGTTTCTTTTACTATCATGTTATTTTATTATAATACTCAGGTTATTTTAATTAACGGATAAATATTACCTTAGATAAATTTAAAAAAGTAAATTGATAAAAACTTTGTTTTTACAAGTCGGTATCCAATTCGTAT F2: 3 CGTAT 2 Unidirectional alignment (log-probability: -37.7) CTTGAAATTGTTCTCCATAT---GTGTGCTGTATTATAC----GAAtATGcATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA CTTGAAATTGTTCTCCATATGTGGTGTGCTGTATTATACGAAAGAAAATG-ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA Template switch alignment (log-probability: -26.2) CTTGAAATTGTTCTCCATAT---GTGTGCTGTATTATACGAA|TATGC|ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA CTTGAAATTGTTCTCCATATGTGGTGTGCTGTATTATACGAA|TATGC|ATCTCAAAGAAAATGATAGTACAATAAAATAATATTATGA ========== Event 2853 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAGGTTCATTAAAATTGTGTGTGTGT--------GTATATATATACATATACAAGGACTATTGCTGATGGAAAAATTTAGAAATGTGGTATGGCCTTAATTTTTATGCAGTCATTTCAACTGCAACACATACATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCAACTGCAGCTTAATAAGAGAAGTTTCT Chimp: ATAGGTTCATTAAAATtgtgtgtgtgt--------gtgtATATATACATATACAAGGACTATTGCTGATGGAAAAATTTAGAAATGTGGTATGGCCTTAATTTTTATGCAGTCATTTCAACTGCAACACGTACATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCAACTGCAGCTTAATAAGAGAAGTTTCT ↑ 3 2 4 1 Gorilla: ACAGGTTCATTAAAATtgtgtatgtgtgtgtgtgtatatatatatacatataCAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCA------------------------------------------------------------------------------------ACTGCAGCTTAATAAGAGAAGTTTCT Human: ATAGGTTCATTAAAATTGTGTGTGTGT--------GTATATATATACATATACAAGGACTATTGCTGATGGAAAAATTTAGAAATGTGGTATGGCCTTAATTTTTATGCAGTCATTTCAACTGCAACACATACATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCAACTGCAGCTTAATAAGAGAAGTTTCT Cluster: [ ] Orangutan: ATAGGTTCATTAAAATTGTGT--------------GTGTATATATACATATACAAGGACTATTGCTGATGGAAAAATTTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCA------------------------------------------------------------------------------------ACTGCAACTTAATAAGAGAAGTTTCT Gorilla > Chimp --------------- chr5:15786918-15786925 Template switch process: F1: L GGAAAAATTTAGAAATGTGGTATGGCCTTAATTTTTATGCAGTCATTTCAACTGCA 1 F3: 4 ATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCAACTGCAGCTTAATAAGAGAAGTTTCTTAGGTCTGTTGGGA R RF: GTATGTGTGTGTGTGTATATATATATACATATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGGTATGGCCTTAATTTTTATGCAATCATTTCAACTGCAGCTTAATAAGAGAAGTTTCTTAGGTCTGTTGGGA RR: CATACACACACACACATATATATATATGTATATGTTCCTGATAACGACTACCTTTTTTAATCTTTACACCATACCGGAATTAAAAATACGTTAGTAAAGTTGACGTCGAATTATTCTCTTCAAAGAATCCAGACAACCCT F2: 3 CATGCACA 2 Unidirectional alignment (log-probability: -126) gtggtatggccttaatttttatgcagtcatttcaactgcaacacgtacatacaaggactattgctgatGGAAAAAATTAGAAATGTGG --------------------------------------------------------------------GGAAAAAATTAGAAATGTGG Template switch alignment (log-probability: -35.2) GTGGTATGGCCTTAATTTTTATGCAgTCATTTCAACTGCA|ACACgTAC|ATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGG GTGGTATGGCCTTAATTTTTATGCAATCATTTCAACTGCA|ACACATAC|ATACAAGGACTATTGCTGATGGAAAAAATTAGAAATGTGG ========== Event 2854 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCAAAACAACAATAATGGAAACAT--------------------------------------------------------------------------------------------------------ACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTAAGATTAATGTACCTTCAGCTTGTGCCTATTCTTATGCAC ↓ 4 3 1 2 Chimp: TCAAAACAACAATAATGGAAACATACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTAGCTGAAGGTGCATTAATCTTAATCACTGTTTATTTGTGGGTGTTTAGATGTATAACATACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTAAGATTAATGCACCTTCAGCTTGTGCCTATTCTTATGCAC Gorilla: TCAAAACAACAATAATGGAAACAT--------------------------------------------------------------------------------------------------------ACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTAAGATTAATGCACCTTCAGCTTGTGCCTATTCTTATGCAC Human: TCAAAACAACAATAATGGAAACAT--------------------------------------------------------------------------------------------------------ACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTAAGATTAATGTACCTTCAGCTTGTGCCTATTCTTATGCAC Cluster: [ ] Orangutan: TCAAAACAACAATAATGGAAACAT--------------------------------------------------------------------------------------------------------ACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTGAGATTAATGCACCTTCAGCTTGTGCTTATTCTTATGCAC Human > Chimp ------------- chr5:167671179-167671231 Template switch process: F1: L ATTTCTGCGTGTTTCATTCAAAACAACAATAATGGAAACATACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTA 1 F3: 4 AACATACCCTGCATGTAATACATCTAAACACCCACAAATAAACAG R RF: ATTTCTGCGTGTTTCATTCAAAACAACAATAATGGAAACATACCCTGCATGTAATACATCTAAACACCCACAAATAAACAGTGATTATGATTAAGATTAATGTACCTTCAGC RR: TAAAGACGCACAAAGTAAGTTTTGTTGTTATTACCTTTGTATGGGACGTACATTATGTAGATTTGTGGGTGTTTATTTGTCACTAATACTAATTCTAATTACATGGAAGTCG F2: 3 TATGTAGATTTGTGGGTGTTTATTTGTCACTAATTCTAATTACGTGGAAGTCG 2 Unidirectional alignment (log-probability: -157) CATGTAATACATCTAAACACCCACAAATAAACAGtgattagctgaaggtgcattaatcttaatcactgtttatttgtgggtgtttagatgtataacataccctgcatgtaatacatctaaacacccacaaata CATGTAATACATCTAAACACCCACAAATAAACAG--------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -28.5) CATGTAATACATCTAAACACCCACAAATAAACAGTGATTA|GCTGAAGGTgCATTAATCTTAATCACTGTTTATTTGTGGGTGTTTAGATGTAT|AACATACCCTGCATGTAATACATCTAAACACCCACAAATA CATGTAATACATCTAAACACCCACAAATAAACAGTGATTA|GCTGAAGGTACATTAATCTTAATCACTGTTTATTTGTGGGTGTTTAGATGTAT|AACATACCCTGCATGTAATACATCTAAACACCCACAAATA ========== Event 2855 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CTGAAAGAGGCAGGGAGCTCC----CAGGCAGCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA Chimp: CTGAAAGAGGCAGGGAGCTCC----CAGGCTGCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA ↑ 1 4 3 2 Gorilla: CTGAAAGAGGCAGGGAGCTCCTCTTTCAGCAGCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA Human: CTGAAAGAGGCAGGGAGCTCC----CAGGCAGCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA Cluster: [ ] Orangutan: CTAAAAGAGGCAGGGAGCTCC----CAGGCAGCAACCATATACTGAACCTGTGCCCTGTGGGAAGGGGAAA Gorilla > Chimp --------------- chr5:167712077-167712082 Template switch process: F1: L AAAATAGCTTTTACATGCAACTGAAAGAGGCAGGGAGCTCC 1 F3: 4 GCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA R RF: AAAATAGCTTTTACATGCAACTGAAAGAGGCAGGGAGCTCCTCTTTCAGCAGCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA RR: TTTTATCGAAAATGTACGTTGACTTTCTCCGTCCCTCGAGGAGAAAGTCGTCGTTGGTATATGACTCGGACACGGGACACCCTTCCCCTTT F2: 3 TCGGAC 2 Unidirectional alignment (log-probability: -26.8) AAATAGCTTTTACATGCAACTGAAAGAGGCAGGGAGCTCC--------CAggctGCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA AAATAGCTTTTACATGCAACTGAAAGAGGCAGGGAGCTCCTCTTTCAGCA----GCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA Template switch alignment (log-probability: -16.5) AAATAGCTTTTACATGCAACTGAAAGAGGCAGGGAGCTCC|CAGGCT|GCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA AAATAGCTTTTACATGCAACTGAAAGAGGCAGGGAGCTCC|CAGGCT|GCAACCATATACTGAGCCTGTGCCCTGTGGGAAGGGGAAA ========== Event 2856 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: ACTGCACAAC----CCATTAGGAATCTCTCTACTCTTTCTACCTCTACATATGTCTGGAACACTGTTCAttc--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tttttttttttttttttttttttttgtggcggggggtggggacagagtctcaccctatggcccaggctggagtgcagtgacgcaatctcggctcactg Chimp: ACTGCACAAC----CCATTAGCAAT--CTCTACTGTTTCTACCTCTACATATGTCTGGAACACTGTTCATTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tttttttttttGTGGCGGGGGGTGgggacagagtctcaccctatggcccaggctggagtgcagtgacgcaatctcggctcactg Gorilla: ACTGCACAAC----CCATTAGCAAT--CTCTACTGTTTCTACCTCTACATATGTCTGGAACACTGTTCAttc-----------------------------tttttttttttttttttttttttgagacagtcttgctctgtcacccaggctggagtgcagtggtgcgatctcggctcactgcaacctctgcctcccaggttcaagcaattctcctgcctcagcctcctgagtagctgggattacaggtgcccaccaccacAGAtataacagaatatttgggactgggaagtttataaagaaaagaggttcctctggctcatgattctgctggctggacaattcaagattcagcacctatgtctgacgagggcctcagaaggaggaaggggacttgttgtgcagagatcacatggcaagagatcttttcttttttttttttaatcaaccagctctcacaggaactaatagagcaagaattcactcacctctgaaggagggcattgatctattcatgaaggatccaccctcataatccaaactcctcccactaggtcctacctcctaacattgccatattgcgtatcaaatgtcaacatgatatttggaggggacaaacatccaaaccatagcaATCTGTAAAGACAACTTCTCTCCTTTAGACTGTCCTAGTGCTgtggtaaaagagaaggtaattttggaccctggctgccttgatttgaaccccacttctttccataaaatctagtgaccctaggcaaataacttagtctcactgtacttcaactctcttactggtaaaatgggaaaaataattaataatggctttgttaggattaaattagttagtgtatataaaaacaatgtgacacatattactcaaGTGTATGCTGTTACCACTATACTATATGGTATTTTCCACTATATGCTATTTTCTCCCCAATTCTAACCCTCATTTCCCAGAAAGaaaaaaaTACTTAAAGGGAAAATTGTTTGCATAAATTTCTGAATAATCAAAATATTCAGAATTCACTTGGCTTATGGAGATAGTAAGATACATGCACATATATTTATTTTTAtttctttcttcaacttttaggttccagggtacatgaacaggatgtgcaggtttgttacataggtaaacgtgtgccatggtggtttgctgcacagatcaacctattacccaggcattaagctcagcatccattagctattcttcctgatgctgtccctccccctgccttccccacaggccccagtgtgtgttgttttcctccatgtgtccatgACACAGACACATACTTATAAATACACATGTGTTTATATCAATTTATAAAATCAAGAATTAATTTTAGAAATAGTAACTGGCTTAGACTATGCTCCATTTTCTTTCCCCAAATTAATGCAAAATCTACATTAGAATGGCTTTCAATGTTTGAAGAAATGAAACTATTCAGAAGTTTACATAAGGAAGCAATTTGCTTGGATTGAATAAGGTAATACATAAGTATGTAAAACCCTTTCTCTGTAAATGCTGCTTTTAATTAGGAATGGAGCTCTGAAAGAAATCCTAGTTATTATATCCACAAACTGAACTCAGGCAACTATTTTAATTGGAACagaaaaaaccaaaatgcagaagatttatcaaggaaatttgaaaattagaaaaaaaaGAACACCTAGTTCATAGTAAACAACATTTTGTGTTCTTTTTCTTTACCCCAGTAAAGAGATTGGAATAATCCCCTTGTCAGAGGAGATGGATGGCGTACATTCAGGATTCTGCAGGGCATTAAATAGTTGTTGCCATGTCAGGCAACTCTCTTCGGTTATTAATACCGAATAAAATCAACATTCTTCTCCTTCTTTCTTGAGTTAAACATTTCCCCTCCATTCCATTCCTGCTGTCTGTCCTTTCAGTTCTTTGCGTTTGTCGTAGTTCTTCCTCTAGCAAGGCTTTTTCTCTTCTCTTTGGCAACATCTCTCACATTTTACACAGCAGCCAAAGAAACCTTGACTTATTTTCATCTTTTTCCTTCCTTTGGCTATTCTTTTGAGGGAAAAGACATGTTTCTGTCATTCTCTTTAGATTGCATTTATCCAGTAGAAGCAGTCTGTGTTTTTGCAATAACCAACATCTGGGCAAAAGGGAAAAGGAGAAGTGGGTTTGGCGAATGACAGCCTGCGGAGGGCTGATCGTCACCTTCAACTCAATTGAGCACCACGACCCTCAACCTGATAAGACTGCCCAACTGATTATATCAGCTTCCCTCTTCATCTGGCACTTCCAGTGTATGAGGCCCAATTAGTATATGGCAAGAATTGAGTCTTCCTACAAGCTGAAGAGTATGGTCTAATAAGTATTAAGTCAGTTGCGCATTCCTATGTCACTTGGTAACATCTGAGGTCAGTAGACCCACACTTAACAAGTGCCTAAGGAATTAAGTAAATAGTGCCTAAAATACTCTGAGCTTGTTTTGAGGTAAATTAGGCCTCGAATAGTagcagcagcagcagcagcagTGGAGGTGGTAGTAATAGTTTTTCATAGCAGTGGTTGCGGTAGTAGTAGCAGTAGTAaatgtttattgagcacttactatatgccaggcactgttttcaataccttatatttattctctcattgcatcctcataactaactgcctcatcgaaagggactattattaattaaactctacagagaagaaactgcagccaagaaaatttaataatttacctagggtcacacagctagtatatattagagcagggattcaaatactgcatgtctttctttctccacaagtgaagctgatttctgtgaatcatactgccTTGCATGGTAGTATATAAATCTCTCCAGAGTGTTGTGTAAACTCTGAGgaatcaagattctcatcactaggtctgtctgactccagagtccacatttttaactactatataatgcaatcctcctTAAAACTGAATACTTTGTATTATTGCATGGGGAGAAAATATATCCAAGAGGACATTGACAGCATCTGTGTCTACACAGCATTACACATTTGGAGGATATATCCTTCCAGTATTGCTTAGAAGGAAGACACCCAGTTCAGCTGACTCTACCATTGATAGCCTACCTAGATTTCACTTCACAATTCCTGGCTTTTTCTCACTTTACATGTTTAGTAAGCAAATTTCTGATCTTTATTTAAGGAGGCTTTTCTCTTAGAAAAGAATCGGCTCAACAGCTATTTTGAATATTGGTCCTCATGGCCATTATGTATTTTTCATTATCCATTACTTAATTGACTTGCTGGTATGAATTAATTATGGATTTGGGGTAGTTGAGAATGttttttttttAACTCGATGAACTAATCATCTCCGAATATATCGACGATTAAAAAACGCAGATCTATAGAAGCAACATAGACATCGAAAATGTTTTTAATATCACATTTGTGGCATTATAGTTATCACATTATAGTTTGCTAAGTGCTCTTACAtataatacatttatttaatatctgtctcacactaagctgttaccagcagaagagcatgaaacatgtctattcaccagtgagttcccaacaatgggcattgcacctagcacatgataggtgcttgataaatatttgttggatgcttgaaAGTtcttgcctgatcctcagcagaagtctttgatctaggtagaggtgacattgtcttcatttttcagatgagcaaacaagagcagaggaaagttaagtaacttggccatgatATGGGGTAACTGGTCAGTTACTAATTCCATGATACTTCAGTTCTCATTTATTTTTTGTACTATAATAAACAATAATGAATCttttgtgggtccacatgcatcaacaatttcagaggtattctttacaaaaaaaatacaacattacaagcacaaaatcaagtacagaggccaggcatggtggctcatgcctataataccagcactttgagaggctgaggcaggcagatcacctgaggtcaggagttcgagaccagcctggccaacatggttaaaccccatctctactaaaaatacaaaaattagccaggcatagtggcacatgtctgtaatcccagctgctcaggaggctgaagcaggagaatcacttgaacccaagaggcagaggttgcagtgagcagagatcgcatcacagcattccagcctccatctcaaaaaaaaaaaaaaaaaattaagtacagagacttgaaagggcttgaacaagtaagtggcactgaaacttaagctttatttggttcttgttttatctggctctgATTATAATAGCTTTTATTTGTTATTGTTCTAATAATCATTAAGGCTTTGACTTTAAGAAAAATGTTATTTCTTTTTCATATAAAATTCTCGCATGAATTTTCTTTTGGAATATTAGCATCTTCTTTTGTCCTAATTCACTCCCTTAAGTCAGGGCATTAGATGCAGAATAATCATCAAACCAAGATTCACGGTGGCTGGGGCCTTTCATGTGGCTCCTCTAAGCAGCTTTAACCATGAGTCTGATTTAGACAAGTGGACATGGGGAATTGGCTTGGAAGAGGGACTGCAGGTGGTGGAATCATATCAAGGAAGGTCCATGAGTAGCAGAGCATAAAGAATATACAGAGAACTGAGAAGCAGTAAAGGCTAATGTTGCAAGTGGTGGGCCAACTAGAGAGAGCTAATACAGGATGAGACTGGAAGATGGTTTGGATTTTTTGATGGCCAGCCTTAAAGACTAAGATGTCTGGACTTTACACAGTAAGACCTAAGAAGTAATAGATCTTTGAATTAGATATGATAAAAACTACATATCAAGAAGACAGACCTTAAAGCATGGCCAAGATAGAGTATGTTAGCTCTACATTTTAACCATGAAATCAAAGAACAGTAATATCTTAGAAAATCAAAAATATTTTCTTCATTGTTCCACTGAAGGTAATCACACTGAAATCATGAGCCACAATCTTGTCCCTTTTTCTGTCACAGCTATGGATACACTgctttccttctacctgccctgcagctcttaccccgcctcctgggccctcctcaaccagtcctctgtgagtcccctgaagctctgtcctgtgttgccatcttttctctgtctacactctcatctagtctcattgctttaaaatcatcaatgtgttcaggacagcccacatccgtatcgctagccttatccttttccccaagctttaaactcatttaatcaagtactctacctacatgtctaatgggactttcaaacaacatatctacagtagaactctgaatgtgtctccatgtgttccttctgcccgtaacctacccaccacctcacccagccttccctgataggtgaaatacgtctacattcactcagctcctcaggtcagaaaactaacagtcaccacgtgttattttttgttctcccacaagtcacattcaatttatcagaaattctctacttacaaaataaatcttgaatttaaaaaaaaGTTATCGTCTAagaattctagaaacatagtggcagcaggagtagaagaggtgttgaatcttatgagccaccacataaaaacagataagtaaatagagtgcaaaccccaaaatcggtggacaacactgacaataaagttaggagaaggtatctctgatctccgagatacaaTGCATGgatcgtgatcttgaaatatcttttcctactgaaataaacaaaggctttttatggggcttattttaggtctggggcaggactatacaagttgagccagggatatgttgtgattcccgatacgaaggaagttatcatactactttttgatatcatgtcaaaggagcaccatagctaatccgaagagtcattggccaaagatgggtttatttgaaacttattggaataatgactcatataataataatgtaatagaccaaaatccaacaaatgctgtttaactccttgagttgaagataatatTTTTCCAAGCAATTAACCACACTCCTTTCTCCCCTGAAAGAAGAAAAAATGGCAAAGAACACTTTATATACACTGCTCTCTCCAAAGCTAATTATTGACCCCTACCCCCATGTTGTCACTCCTAAACCTCACATTTATTTATTTAAAATGTATATAGATTAAACATCTATTTTTTGGTATACTACTGTGAATTTTGACAGATGCAtaaccactattatactcaagatacagaacagttccatcaacccaaaatatttgcttgtgactcttttccttgcccccacccctggcaaccactatctgttctccagccatataattttgccttttatagaatgttgtataaatggaatcatctaataggtagccttttgagcctgtattcttttacacagcaaaattcatttgagattgatatacattgtgtgtgtcaatagtttgttcctcattattggtaggtagaattatattttgtgggtgtaccataggttgcttatctgctcaccagttatagggcatttaggttgtttctagtttgagtgattatgaattaaaaccaatataattatccacttacaggttttattgtgaataaaattttcatttctcttgggtaaataccgagtagtgggattgctaaattgtattataagtgtagacttaactttacaagaaattgccaaagtatttttcaaagtggCTAAACAATCATATTTTTTAAACGAGtttgttatcttaggaaaataatagaaaaaaattattgccaaaactgtctattaatggtaaaaaatcaagcattggtcccagcttcacgatatgaattataccattgggtaaccaactagtagagaaagggaagtgtctatttataaaattatttctcataagaagtgaaatgaaatggtaaaatattaccaatttgcaactcctaatgcattttcctactagtatcacaaatatgttataatcagatgtaatgtgtttcctaataaaagaacacagtaccaccaatgatcttgctaaaggattaaatccaagtctgatgaagactctgggtccaattttcaggaatacagaaaaaaagaaaaacgccagcaccacgctatgcaatcagctaattccagaccaagaaaacctatgtgtcaaataccctacatcctttaacaaataaaatgtaaagaaaagaaaaagaaggacgtggaaagctttagcttaaaagaggcttcaaagatacatcaaCTATAAGAAAGAAATGAGCTTGACCCaactatgatgtctagaaatgcacactaggtgataaaattgtaaaaaataggatggagaaaaaaggacaagagtaaaaatagtgcttattttggcagagaaaaaggattttaataagtatggggcatgtggagggtttctggagtggctggccaagttctatttcttgttctgggtggtggttacaagggtatttgccttagaatatcattaagctatgtaatcattttgtctgattttccgtatctatgctttattttacaataagaaagggctgagcactgtggctcatgcctgcaatccgagcactttgggagggcaaagcaagagaatctcttgaggcaaggagttcaagaccagtctgagcaacatagtaagaccccacctctacaaaaaatagtttttaaaaatactaatgtttaaaagaaaaaCctcaccaggaccactcataccactctaaattaaatctctatctctagaaacctgccccagcctcctaattattatccctgcctcttcttctgtcccctatagtccattttccacactacagtcagagccatcatttAAGATGTACAATTGAAggctggaggcagtggctcacacctgtaatcccagcactttgggaggccaaggcgggcagatcatgaggtcaggagttcgagaccagcctgatcaacaaggtaaaaccccgaatctactaaaaaatacaaaaattagctaggcatggtggtggcacctgtaatcccagctactcaggaggctgaggcaggagaattgcttgaacctgggaggcagaggttgcagtgagccgagatcgcaccactgcactccagcctgggtgacagagcaagactgtctcaaaaaaaaaaaaaaaaaaaaaaagaaTGAACAGTGTTCCAGACATATGTAGAGGTAGAAACAGTAGAGATTGCTAATGGGTTGTGCAGTAATAGCTCACTGGGATATTGGGTAGTCTCATGGGTAGTATAGATTAGACTTATACAGACTATATATAAGTATAGATTAGACTTACATAGACTTAGACTTAATCTTTACTGGGTACTTGGGGCAACGTGGGGTGTAAGAATGGTGTATGCCAGGCATTGCTGTAGGAGTGTGACATCAGTAAGCACATTTAGTTCTGAAGTCATATTtatatgtacataatattaaaaatttactagtcctttaagccttctcccttccatcccatccagtctttgatgactgcttccaaaataaaataattttccatgctttaatctgctgtttcagggcatggagtggtatatcttctcatttctataaaacaggcacacattgtggttgtattcaagatttttcagttttagatattttctgatcactccctactttggaagaaaaggatgcacccttttcaatatccactcaaaacacacacacacacacacacacgcatacctttctaccagcctttcaatgtagttttgtcataatttttgattagattaactgaaaaattttttaacatcatatttgtcatgcaaatgctagtcataatagaaccatgctgtataatacaaatgcatttcttttttatacagattttctcttccctgaaggtaataattgtctcatttttcatgtgcccagtttcccaggtacctatcactatttcatATGGAAACACCAGAGTGACTAAGGGAGGTTCCCTTCATTTCTTTCTTGCTTTGCTGTGGCCTGGCTGATTTCTAGGACTGCTACACACCCATCTTTCTTGGAGAATTGAAGGTATCTCTCTTCAATACCATCCACTGAATTCCCATTGCCTCTCTCCTATAGTGGAGCCTCTGCTTCTCTTTCTTCATTATTTTCCTGTCTTCAGAGACTATATTTTTCAACAGTTTTGGAGATGTTGCATCAAGATCCCgcatatttgaaaatgtgtacattctacttctcactcttgtttgatactttggataggtaaaaaatactacaatgaaaataattttccttTGGTTTTATATATTTTCTGATCTACTAAATCAGTCACCTTCAATTTCCTACTTTTCAATAGTACAATTTCCTGTATTGTTATTTTTAATGTGGTTTTTCAGAATGAGGGGAATGGTAAACAAATATGCTTTtatcacttaagccaatactagttgctctgacagataaaccctcaaaacttggtggcataatgcaatatgagtttctctctaacataaattccatttggTGATGTCTTTGTGTTTGCTTTTGTAGGAAAGTTCTGCTCTTGTAGCAGCCAGGACCTAGGAGCTGTCTTTAGTACATGAATGGATGTTAATTCCCACATAAcggatggggaaacagacagagctttgtatgatggagaagtttttgtgtgtcaagtctaagtgacacgtgtcacttccaaccacatttcattagccagaactcagtcaaatggccaccactaatatcaaaagaggctaacaataatactagcgtgcatccaggcataaatggaaaTTTCTGTATCTGGTATATTGCTGTTAAAGAAAAGTCACCATAATTTGACATAACTAGCTAGGAAGTTACATCACGGAAGCATTATAGGAGATTAGGTAATATTCTATCAAATTGAAAACACACACCTGGCTACAACTTTGAAAGAAAAATTTCAACTCTATTCCATTCTCTGCCACAGTGTTCAGTTTATCATATTTATCCAGAAAACTAAATTATTTGAATTATTGTAAAAGCTGTGGCAATAATTATGATGATAATAATAGTAACaataataaggtacatttattatattctaaattagtatctgatactatggtgagttattgggccttttctattgtgatttatacaataaaacatgcatgagctgggtaatatttttatccccatttcatggatgaaccacagagaggccaagaatttgatcatagtcctatgcttaatatacactggttttgagactatgcctgtgtcactcaaaaatgtaatggtgttcccactacatcatgctgcTTTATATTATGTCATGGGATTTAAATAGAGCCATATAAAAATGTCTACGATATGATGTGTCTTCCTGATTCTCCATCATTATTATACCCTCTCCGACCCAGTCAAAAATTTGTGTTTGAGTTATAAGAAGCAAATGGTTTCAGTATTTATGAATCTTATTTTTAATAAAAAATCTTGGATACTTGCTCTTTATGGTCAAACTGCTAAAATTCATAAGTGGCATAAATAATCTGACAATAGCAAGCCCATTGTGTTTAATGTATGTTCAGTGGCATAATTCAGTCTTAAAACTTGTCCTCCCTGGTAAAGCTGCCAAGCTGAAACAATGAAGGGTTTTAGCTGCAAAGTGAAGTTTGCTGGAATTATAATATTCCTTGTGACCTCTGGGATGACTAAACACTATTTAATTCCTTCTCTTTATTCACTACAATGAAAAAGACTTGGAAACCTGCTGGAGCAGAGGTAACATTTCCTTTTGAGACCATAGCCAGACATTAATACTCTCAGGGGAgggggggATAAGGCTTTCAATTTGGTAGTGGAATACCTTATTTACTGTAATGGTACAAATGTCTTATTCCTCGTTGGTATTGTAAGAACTATGATGTAACACCAGAGTCAATTATCTCAAATTATAGTGACTGGAATAATTAGACTTTTTCTTCTCTAGCAGTGCACTAAAAATTTAGCTGTGGCTGAAATAGAACTCGTTTATAACTGGCTGAAGGTAGCTATACAAGAGCAGCATGTGGCTCCTTTTTCAAGAGCTTTAGCTTTTAGGTACTGTTACTGCTAATTACTTCAGGTGAGAAACACGATAGCTGTCAAACTTTACCATCAACTCTTGCTTTGAACCAGCTAAAATAGAAATGCTTGAATAGTTAAGAGTCCGTTTCTTTCACTCACCATTACATGGAGGTGCTAAATGCAAAGAAGCTGTAGTCGGCATCTTTGTGTTCAATCCCCTTCCCTGGCTGATTGAATAGCATTTGATCTGATGTGAAGATTTTTAACTTCCTTTCTATACATAGCCCCAGCATGATCAATACCAAAATGCATCTCCAATCCAGGCTACTTTACATCCCATTTGCCTAAAGAGTTTATGTAATGAAATTCACAGGAGGCAAAATCTATAAATGAGTTACTGACAAAGTGGGAATGGCACCCAGAGATGCTGATTCTAAAAAGGAGTAGTACCTGAAGTTGACTGATAAGGTTTTAAAACCACATGCCTGTATCATCAGCAACACAGCCAGCCCTAGGCAAGACGAAGAAGCTAGAGCAATCTCTAGCACTGCTGGGCTCCGTATTTCATGGTGGCATCTGCCAGCCCCTGTTTTCCCACTTCCTTCTTAGGTACTTCCTATGCCTACTCCCTATTCCAAAGCCTGTTCGAAAAGCTTGTTTTCTAATTCCTCAGTTACACAAATCTCACAAATAATAGATTAACAATGTGTTACTGTACTCATATGAGGAGAGGTTGCATTTTCATAATGAACTAGTCTAGGTGAAACAAAATATTGGAATTTTACATTAAACCAAAAAGCTTGAGATTGTCTTGGCACCCATAAAACTCACACAATGTAATAAGTTTCTTATTTTTCCTATGGGTAAAATAAATGCAGGTATTCAATAAAATTTAGAGCCCAGAAAGGTAGAGCTAGAGGAGTTTTCCAAGCTAGTATTTCCCTTTTAAAATGCAATATATGAAATAGCCCTATCAGATGAGCAACACGGAGGGTGCTTGTTAAACAAGCAAATACAGGAAGTCatacaaatttgggggccttagccaaatagaatagaattgcttgtagtgaagccccagaatctgcatttagacgagcacccccagatgttcttatgcTATGATCGTGGTTAtggagtccatctacctgagttcctgtactcaactcaaccattcattataggcaaattatttaggagatctgtgcttcagtttcctcatctgtaaaatagggatgataatggaacctatctcattaaattgctatggaggttaaatgagttaacaattacaaagcatttagaatagggcctggcactatatgggtgtttgctaaataatgactaCACTAGACTTTGAGAAACACAGATCTAATGATATAATGCCTTTAAAATCATTGCCACAATTTCAGATAAACAGTCTAAAAGATGATGTTGGTAAGtgcggtataaaatgaaataaatttagtcacgttcagttcctgtcacagagctcctaaaacgtttggaatttcctaagtgataggggtatcttttgttATTCACAATGAGCCCCTTTCATAGCTACCTGAAttgttgcaactgaggtgacttaacaagcgtgtggggtctctagatggcctcaggatggggaccatcaggagaaagaactcattaaaggattagatgattggaactttcagtcccacccatcgacctctgagaaagggtggggaggatggagattaggctttatgacaactcctgaacaacaaggtttgatgagcttccaggttgctgaacacatagaggtgctagaagggtggcatccagagagagcatgaaaactccttgcccctgcggtgtaccttgccctatgcctctccttacctggttgttcatctggatgctttgtaatttacaccctttaaaataaaccagtaagcatgttttcctaagttctgtgagccAtgaaactgcctttgcaaagattatgattgaaattacctttgcaaaattatgacagtgagagaaatctgacacagttcactccatcttgcttccgacctccaagctgtctttgggtgtaggccaagctgggtgtaggccaagctaacttggtgagaaatttagtttatagtttcaccttaaagcaaggatgataatagcctttcccaaaacaaaaccacctttgtaaaactaatgaaagtccacaaggttaaaattataagagggacccaaattctgctaagatgtaggtgtagttaaataacaaccaaccattgtttttcacaagattggtaacttccccaattacttctatagataacatcactattatagaccctaagattggtcttttgagatattttttcagacttcggtgtttctgactccatgagccctatggccccacccagaggttcacacagcacataaggacatttttccacacccctatgatttcacccccaaccagtcagcagcatccattacctagccttctgcccaccaaactatccttgaaaaactctcacctctgagcctttggggtgactgatttaataactctctctcctacatggccagccttgtgttaattaaactctttcattattgcaaaagcatggtctcagtgaattggttttgtctgtgcagtgggcagaaataacccgtctggcaattacatgacagtaggagaagtctagcatggctgaacatatcttgcatctagcttcacagactggctaacctctcttattcctcggcattggccaagctaaccatgggagaagtttagtttatagcttaacctactaagggtgatgataatccctccctggaactaaccccctctttgcctagggaacaaagctacctttgtaaaactaatcaaaggccagaaatgagattaggatcatgggagagacctgaattcagctaaaatgtagatacagtttctatattcccttacttctcaggagtcatgtggccagaggtcacaagatttgtgacttccccaattgctcctatagataacatcacttttgcagaacttaaaattgatcttttaagatgttttttagacttgtgcattctggtaacccaccgaccccattcagactcatgactcataatgcaacgggttctgtggctcccatcctatggcagactcagtacatgaagaccgttttccacactccaatgatttcatctccaaccagtcagcaacacccattccttaatctcctgcccaccaaattatccataaaaaccctagcctgacttagcaaggaggctgatttgagtaatagtaaactcctatccttccactttgctggccttgcagtaattaaactctttctttactgcaataatgctgtctcagtgaattggttttatctgtgcagcaggcaagacgaacccttcagacaattacagccactctagcaaaataatcagacctaaagagggagtcaggggaaccccagtttgcagctggtcagtcagaagtatagttgacaacctacaacttgagattagcccctgaagtgagggcaatcttgtgggactaggcccccaacctgtgcgatctgacaccattcccaggtagatagcctcagaactgaatggaattatagaatacccagttagtgtctgctagagaattgtttgatgggtggggaaatccactacacatctagtcacagaagtgttccttgttaagtgtgagagtaTATTACAGTAAGCATGTCTTATTAATTGAATCAACGCAATTTATaaaaaaaattgcattacatatgttaaaagaaaaaattataataaatttaaagatcttaattggttttatttataattctagaatcagataacaccttattctgtacaatagaatataaatacaaaaacagaatgagtattctgataaactgagcgattggttttatacatagaaaatggctgaggaaagaagaaacagaaaacaaaagcagattgattgtttcaaagttactttccctgtaaaggttaaacacaggggacttccttatcatgctagctaaaactggcttgtttggggatttagctattatcgttcattcttctcatttctgggaaggtcatataaacaacttagtttcaccttggtgatagcatgagtgactccattttgatttggtttgttgggcctagggtaggagctcaatccaaaccaatggcctcctataaattttatgaaacaTATACGACTAAGTAGAAGGTACTGCATTTGTGTAGAATGCATTAAAAAGGAAGAAGCATATAGGCTTGTGATAGGCATGTGATCCTGGTTTTGTAACTCTTTGTCTAGGAATTAATTTATCCAAGAATGTATTGACACGGGAAATATTTGCAAAAATGTTATGAAATATAGGTAATTTGTGAAAGCACAGAGAAGCCAGCAGGATGAAATAAACACCATAATATGCAAAGAAACTAGCTCTAGATTATGTATTAAGACACTAGTTTTATGAATGAAACGCCCATTGAATGTGTTGTATTTTGTAAAACATGGCTGGAATGATGTGTGTAAGTCATCCATGGAAACCTTATGCAATGCAATGAAAAGAGACTGGTTTGATTTTCTTTGAAGTGTTTTCTTGTAAGAAGAGATAAAAGCAGACATCTATTTTCTTTGATGTTTTTATCCTAAATTTTGTATTTGATTTTCCTATAAGCGTTATAGAAAGTTTTCTTTTCAATTCACTATACCATATTCCTATTTTCAgagaaggaaagatttataggaattggcaagtcccttgcgggcatttcaacaactaagagctgatttctcatggcagagttGCGAGTTTCACTTTTACTTTTCTAAGTTTTAATCCATTATGCAAAATAATGTTTCCACCTGAAACCAAATGTTCTGCACTTCAGTACTTTGCATGCTGTTTACTTCTCAGAAGAGAAAAGAGACGTGTGTTAAACCTCAGATAAGCAAGGCACACGTCTATGAACCACAATGATATCATTCAATGCCATGTTTATACCTAGTTAGAAATAAGGGAACATCTGCTGATTAAAAAATAGAACTGTAATAGTGGCCAGCAGGGAATAAAACACTTTATTGAGCTTTGTTATGTAGATGGAAATGTGCTTTGTAGAAAATGCTTTATTTGCAAATAAAACAACTAACTGCTGGGGCTAGAAATACATTCACAAAGTAGATTCTGAACTAATTTTGAGAAAATATTCACTTTAATGTGGGCATTAGCTAATGCTTCTGCCTTTCCCCAAATTTACGTTGTTTTTGACTATCAGAAGGAAGACTTACATAGCTCCCAACAAAATCCTGCTTAGTAGGACTCTATTTACACTGACCCAGTATTGCCATTCCTGGGGCCTTTTCCTTAATTTCTTCCAAAATGTCTTTGGTCCTTTCATTCATTCATTCATTCGATAAATAACTAAAATCCTGGTATATCTCTTTCGGTACCTAACACATCCCATCTCATTCCATCTTGGgtttttgtttgtttgtttgtttgtttgttATGGCCTGTTAAAGGAAATCTTGAAACACATTATTAACAAAATGAGATACCGTGATATCTTTATTTTCAACTTGCCTCCCCTCCCTTGGCCTGGATAGTCTCTTTAGAGGTCACTCAGGTCTTCCTAAGTTTCAATGCCAAAATCTTTTACAGTTTGATTGGCCTTTTCTTGAAACTATTTCCTGGCTGAACAACTGCAGCACTAAACATGTGTGGCTCTTCCTCCATATCTCTAAATATTCCTTCTCTAGTTCTTCTTCATTCTCCTATCTCCTAAAGAGTGATATTACAGAAGACTCTGCTCTCAGGTCACGTTTTTCACCCATCATGTGTTGGCCTTCCCTCTTCCTTGCTTCCTCATTCTGTTACTCTCTGTGGCTTGGTGCATATCTCTAACCTATGGCTTTCATCCTTCTCTTCTCCAAGCTGTAGCCACCTTAGTGTCTTGGTCCTGTAATCTTTAGTTTTAATTAGAAATAGAGAACTGTAGATTTATAAAACAAGGAGGACACAGGCATGGTTTGATAAAAATAGATGGCAATAGTTTAGCCTTCAGCAAAATAGGGGAGGCTGTGGCAATGTATATCTCAACCTTGAAAATCATCACTGTCATTCTGATGGGATAGATTGAGAAAGGGGTTCTGGAGTGCAGGCCAAGTTGTCTTGTATAGTCAGCTCTGCTGTAGCCTGAGGACACCATGGGTAGAGCTAAGACTGAATATTTATTCATTTATTTAGTCATTCACTGAATTTGtttattcatttatagacatttaaaaattggagtgcatactcaatgttaggctatttttatttttcatagtgaaatagcaattaataaggcagtctctgtgttcaggaagcttacacagttttctggtaaggagagacagagagtaacctataaaaacacattgattagcaatccatcaaaaaatttcaaatagaatataagtgccgtgaacaacaaaaaagacaggatgatgggagaaagaatgactagacagtggggaggggataactagattcttaggaaagcctctctggagatttgaagttgtggaatgaaagctgaagtgcaaagatctggagggagagggagagggagaacaagtgccaagccctgagatcaggatgaactgaacgaaggagaaatgagtagaagaagatggggttcaggacacaggtagcgacgagggacttttaaggagcttaggttttcttcttattgcaaatggcaagcgactggagggttttaaaaagctgagtgtcactcatctAcagttgactattgaacaacacagatttgaactgtgtgggtccacttacataggaatttttttcaataaaacttacactgagtgttcctgcctctcctgcctccgcttctctctcatctccctcttccacccctgatatagcagggccaacccctcctcttcgttctcctcctcaacctacttaatgtgaagacagagaggatgaagacctttatgataatccccttccacttaataaatagtaaatatattttctcttccttatgatttttcaaataactttttctttcctctaacttactttatagtaagactacagtacatgatacagaaaacatacaaactatgagttatcaactgtatgtttccagtcaacagtaggctggtaatggttaggttttgggggagtcaaaagttatacacagattttcaactgcttgggggtcagctccccaacccctacattgttcaagggtcaactgTACAtctttttcctttttctttttctttcttttttctttctttctttttttttt--------------tttttttttttgtggtggggggtggggacagagtctcaccctatggcccaggctggagtgcagtgatgcagtctcggctcactg ↑ 1 4 3 2 Human: ACTGCACAAC----CCATTAGGAATCTCTCTACTCTTTCTACCTCTACATATGTCTGGAACACTGTTCAttc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tttttttttttttttttttttttttgtggcggggggtggggacagagtctcaccctatggcccaggctggagtgcagtgacgcaatctcggctcactg Cluster: [ ] Orangutan: actgcacaatccgtccgttagcaat--ctctactgtttctacctctacatatgtctggaacactgtccattcttttttttttttttttttttttttttttc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttttttttttgtggcagggggtggggacagagtcttaccctatggcccaggctggagtgcagtgatgcaatctcggctccctg Human > Gorilla --------------- chr5:150251470-150251473 Template switch process: F1: L TACCCAATATCCCAGTGAGCTATTACTGCACAACCCATTAGCAATCTCT 1 F3: 4 TTTCTACCTCTACATATGTCTGGAACACTGTTCATTCTTT R RF: TACCCAATATCCCAGTGAGCTATTACTGCACAACCCATTAGGAATCTCTCTACTCTTTCTACCTCTACATATGTCTGGAACACTGTTCATTCTTTTTTTTTTTTTTTTTTTTTTTTTGTGGCGGGGGGTGGGGACAGAGTCTCACCCTATGGCCCAGGCTGGAGTGCAGT RR: ATGGGTTATAGGGTCACTCGATAATGACGTGTTGGGTAATCCTTAGAGAGATGAGAAAGATGGAGATGTATACAGACCTTGTGACAAGTAAGAAAAAAAAAAAAAAAAAAAAAAAAACACCGCCCCCCACCCCTGTCTCAGAGTGGGATACCGGGTCCGACCTCACGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -33.2) TCCCAGTGAGCTATTACTGCACAACCCATTAGcAA--TCTCTACTgTTTCTACCTCTACATATGTCTGGAACACTGTTCATTCttt TCCCAGTGAGCTATTACTGCACAACCCATTAGGAATCTCTCTACTCTTTCTACCTCTACATATGTCTGGAACACTGTTCATTC--- Template switch alignment (log-probability: -21.9) TCCCAGTGAGCTATTACTGCACAACCCATTAGcAATCTCT|ACTG|TTTCTACCTCTACATATGTCTGGAACACTGTTCATTCTTT TCCCAGTGAGCTATTACTGCACAACCCATTAGGAATCTCT|ACTG|TTTCTACCTCTACATATGTCTGGAACACTGTTCATTCTTT ========== Event 2857 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCCAGCTTGCTTGGGCCATCTAAAGCAGGATTTGCTTTAGAGGCCAAGTTTGATGAACA Chimp: AGCCAGTTTGCTTGGGCCATC--GGTCAAATCCTGCTTTAGAGGCCAAGTTTGATGAACA Gorilla: AGCCAGCTTGCTTGGGCCATC--GGTCAAATCCTGCTTTAGAGGCCAAGTTTGATGAACA ↓ 1 3 4 2 Human: AGCCAGCTTGCTTGGGCCATCTAAAGCAGGATTTGCTTTAGAGGCCAAGTTTGATGAACA Cluster: [ ] Orangutan: AGCCAGCTTGCTTGGGCCATT--GGTCAAATCCTGCTTTAGAGGACAAGTTTGATGAACA Gorilla > Human --------------- chr5:13755829-13755840 Template switch process: F1: L ATCTTTATAAAACAAGAGGGAGCCAGCTTGCTTGGGCCATC 1 F3: 4 TGCTTTAGAGGCCAAGTTTGATGAACAATGAGCTCTATTA R RF: ATCTTTATAAAACAAGAGGGAGCCAGCTTGCTTGGGCCATCGGTCAAATCCTGCTTTAGAGGCCAAGTTTGATGAACAATGAGCTCTATTA RR: TAGAAATATTTTGTTCTCCCTCGGTCGAACGAACCCGGTAGCCAGTTTAGGACGAAATCTCCGGTTCAAACTACTTGTTACTCGAGATAAT F2: 3 TTAGGACGAAAT 2 Unidirectional alignment (log-probability: -38.4) TCTTTATAAAACAAGAGGGAGCCAGCTTGCTTGGGCCAT----------CtaaagcaggattTGCTTTAGAGGCCAAGTTTGATGAACAATGAGCTCTATTA TCTTTATAAAACAAGAGGGAGCCAGCTTGCTTGGGCCATCGGTCAAATCC------------TGCTTTAGAGGCCAAGTTTGATGAACAATGAGCTCTATTA Template switch alignment (log-probability: -17.3) TCTTTATAAAACAAGAGGGAGCCAGCTTGCTTGGGCCATC|TAAAGCAGGATT|TGCTTTAGAGGCCAAGTTTGATGAACAATGAGCTCTATTA TCTTTATAAAACAAGAGGGAGCCAGCTTGCTTGGGCCATC|TAAAGCAGGATT|TGCTTTAGAGGCCAAGTTTGATGAACAATGAGCTCTATTA ========== Event 2858 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: aatgtaaaaaaCCAGGTACCCTGGAGAAGCCAACAGGATAACCCCTGAGCTGTCACATGAGATAGGAACAAATGCACAGAGAGCACTGTGGCTGcccccgccccccttccccAGGGCTCCCCGCTCCAGCTCCAGGACTTGTTTATGGCCTGGGGGA ↑ 3 2 1 4 Chimp: aatgtgaaaaaCCAGGTACCCTGGAGAAGCCAACAGGATAACCCCTGAGCTGTCACATGAGATAGGAACAAATGCACAGAGAGCACTGTGGCTGcccccgccccccttccccAGGGCTCCCCGC------TCCAGAACTTGTTTATGGCCTGGGGGA Gorilla: aatgtgaaaaaCCAGGTACCCTGGAGAAGCCAACAGGATAACCCCTGAGCTGTCACATGAGATAGGAACAAATGCACAGAGAGCACTGTGGCTGcccccgccccccttccccAGGGCTCCCCGC------TCCAGGACTTGTTTATGGCCTGGGGGA Human: aatgtaaaaaaCCAGGTACCCTGGAGAAGCCAACAGGATAACCCCTGAGCTGTCACATGAGATAGGAACAAATGCACAGAGAGCACTGTGGCTGcccccgccccccttccccAGGGCTCCCCGCTCCAGCTCCAGGACTTGTTTATGGCCTGGGGGA Cluster: [ ] Orangutan: aatgtgaaaaaCCAGGTACCATGGAAGAGCCAACAGGATAACCCCTGAGCTGTCACATGAGATAGGAACAAATGCACAGAGAGCACTGTGGCTGCCCCCGTCCCCCTTCCCCAGGGCTCCCCAC------TCCAGGACTTGTTTATGGCCTGGGGGA Chimp > Human ------------- chr5:169081058-169081064 Template switch process: F1: L CACTGTGGCTGCCCCCGCCCCCCTTCCCCAGGGCTCCCCGCTCCAG 1 F3: 4 ACTTGTTTATGGCCTGGGGGAACAGGGAAGGACAGGAGCC R RF: CCTGGAGAAGCCAACAGGATAACCCCTGAGCTGTCACATGAGATAGGAACAAATGCACAGAGAGCACTGTGGCTGCCCCCGCCCCCCTTCCCCAGGGCTCCCCGCTCCAGAACTTGTTTATGGCCTGGGGGAACAGGGAAGGACAGGAGCC RR: GGACCTCTTCGGTTGTCCTATTGGGGACTCGACAGTGTACTCTATCCTTGTTTACGTGTCTCTCGTGACACCGACGGGGGCGGGGGGAAGGGGTCCCGAGGGGCGAGGTCTTGAACAAATACCGGACCCCCTTGTCCCTTCCTGTCCTCGG F2: 3 GGACCTC 2 Unidirectional alignment (log-probability: -25.6) GGCTGCCCCCGCCCCCCTTCCCCAGGGCTCCCCgctccaGCTCCAGgACTTGTTTATGGCCTGGGGGAACAGGGAAGGACAGGAGCC GGCTGCCCCCGCCCCCCTTCCCCAGGGCTCCCC------GCTCCAGAACTTGTTTATGGCCTGGGGGAACAGGGAAGGACAGGAGCC Template switch alignment (log-probability: -16.3) GGCTGCCCCCGCCCCCCTTCCCCAGGGCTCCCCGCTCCAG|CTCCAGG|ACTTGTTTATGGCCTGGGGGAACAGGGAAGGACAGGAGCC GGCTGCCCCCGCCCCCCTTCCCCAGGGCTCCCCGCTCCAG|CTCCAGG|ACTTGTTTATGGCCTGGGGGAACAGGGAAGGACAGGAGCC ========== Event 2859 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGGTCCCCATCTCAGAGAATAGCTCTGAGCAAGGGCTCATGCTTCCCTCCTTTTCACTT Chimp: CTGGTCCCCATCTCAGAGAATGGCTCCT------TGCTCATGCTTCCCTCCTTTTCACTT Gorilla: CTGGTCCCCATCTCAGAGAATGGCTCCT------TGCTCATGCTTCCCTCCTTTTCACTT ↓ 3 4 2 Human: CTGGTCCCCATCTCAGAGAATAGCTCTGAGCAAGGGCTCATGCTTCCCTCCTTTTCACTT Cluster: [ ] Orangutan: CTGGTCCCCATCTCAGAGAATGGCTCCT------TGCTCATGCTTCCCTCCTTTTCACTT Gorilla > Human --------------- chr5:169214805-169214813 Template switch process: F1: L CATCTCCTTCCATCCCCAACCTGGTCCCCATCTCAGAGAATAGCTC 1 F3: 4 GCTCATGCTTCCCTCCTTTTCACTTGACACTCATGATGTG R RF: CATCTCCTTCCATCCCCAACCTGGTCCCCATCTCAGAGAATGGCTCCTTGCTCATGCTTCCCTCCTTTTCACTTGACATTCATGATGTG RR: GTAGAGGAAGGTAGGGGTTGGACCAGGGGTAGAGTCTCTTACCGAGGAACGAGTACGAAGGGAGGAAAAGTGAACTGTAAGTACTACAC F2: 3 GGAACGAGT 2 Unidirectional alignment (log-probability: -43.4) CTTCCATCCCCAACCTGGTCCCCATCTCAGAGAATaGCTC--TgagcaaggGCTCATGCTTCCCTCCTTTTCACTTGACAcTCATGATGTG CTTCCATCCCCAACCTGGTCCCCATCTCAGAGAATGGCTCCTT--------GCTCATGCTTCCCTCCTTTTCACTTGACATTCATGATGTG Template switch alignment (log-probability: -28) CTTCCATCCCCAACCTGGTCCCCATCTCAGAGAATaGCTC|TGAGCAAGG|GCTCATGCTTCCCTCCTTTTCACTTGACAcTCATGATGTG CTTCCATCCCCAACCTGGTCCCCATCTCAGAGAATGGCTC|TGAGCAAGG|GCTCATGCTTCCCTCCTTTTCACTTGACATTCATGATGTG ========== Event 2860 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTC-------CTGAGAGCTTGGAGCAAGAGGC Chimp: AATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTC-------CTGAGAGCTTGGAGCAAGAGGC ↓ 3 2 1 4 Gorilla: AATCAAACACTTTGACCCATACTTCTTGAAAGAGGGTCAAGCAGTATGAGAGCTTGGAGCAAGAGGC ↑ 3 2 1 4 Human: AATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTC-------CTGAGAGCTTGGAGCAAGAGGC Cluster: [ ] Orangutan: AATCAAACACTTTGATCCATACTGCTTGAAAGAGTGTC-------CTGGGAGCTTGGAGCAAGAGGC Human > Gorilla --------------- chr5:153229693-153229700 Template switch process: F1: L ACAAATCAAACACTTTGACCCATACTTCTTGAAAGAGGGTC 1 F3: 4 TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTTTGTG R RF: ACAAATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTCCTGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTCTGTG RR: TGTTTAGTTTGTGAAACTGGGTATGACGAACTTTCTCCCAGGACTCTCGAACCTCGTTCTCCGAGTACGGTCGTCAAGACAC F2: 3 ATGACGAA 2 Unidirectional alignment (log-probability: -37.5) CAAATCAAACACTTTGACCCATACTtCTTGAAAGAGGGTCaagcagtaTGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTtTGTG CAAATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTCC-------TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTCTGTG Template switch alignment (log-probability: -27.8) CAAATCAAACACTTTGACCCATACTtCTTGAAAGAGGGTC|AAGCAGTA|TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTtTGTG CAAATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTC|AAGCAGTA|TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTCTGTG Chimp > Gorilla --------------- chr5:153229693-153229700 Template switch process: F1: L ACAAATCAAACACTTTGACCCATACTTCTTGAAAGAGGGTC 1 F3: 4 TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTTTGTG R RF: ACAAATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTCCTGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTCTGTG RR: TGTTTAGTTTGTGAAACTGGGTATGACGAACTTTCTCCCAGGACTCTCGAACCTCGTTCTCCGAGTACGGTCGTCAAGACAC F2: 3 ATGACGAA 2 Unidirectional alignment (log-probability: -37.5) CAAATCAAACACTTTGACCCATACTtCTTGAAAGAGGGTCaagcagtaTGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTtTGTG CAAATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTCC-------TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTCTGTG Template switch alignment (log-probability: -27.8) CAAATCAAACACTTTGACCCATACTtCTTGAAAGAGGGTC|AAGCAGTA|TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTtTGTG CAAATCAAACACTTTGACCCATACTGCTTGAAAGAGGGTC|AAGCAGTA|TGAGAGCTTGGAGCAAGAGGCTCATGCCAGCAGTTCTGTG ========== Event 2861 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CATGCCCACAAACACGCATGTTTTCTTAAGGGGAT-GGATGCCCTTAAGAAAATGCAATTTGTTAACGCCGT Chimp: CATGCCCACAAACACGCATGT--GACTGAGGGGATGGGATGCCCTTAAGAAAATGCGATTTGTTAACGCCGT Gorilla: CATGCCCACAAACACGCATGT--GACTGAGGGGATGGGATGCCCTTAAGAAAATGCGATTTGTTAACGCCGT ↓ 1 4 3 2 Human: CATGCCCACAAACACGCATGTTTTCTTAAGGGGAT-GGATGCCCTTAAGAAAATGCAATTTGTTAACGCCGT Cluster: [ ] Orangutan: CATGCCCACAAACACGCATGT--GACTGAAGGGATGGGATGCCCTTAAGAAAATGCGATTTGTTAACGCTGT Gorilla > Human --------------- chr5:9776128-9776141 Template switch process: F1: L ACTTGATTAGTAATCTCCAGCATGCCCACAAACACGCATGT 1 F3: 4 GGATGCCCTTAAGAAAATGCAATTTGTTAACGCCGTACTG R RF: ACTTGATTAGTAATCTCCAGCATGCCCACAAACACGCATGTGACTGAGGGGATGGGATGCCCTTAAGAAAATGCGATTTGTTAACGCCGTACTG RR: TGAACTAATCATTAGAGGTCGTACGGGTGTTTGTGCGTACACTGACTCCCCTACCCTACGGGAATTCTTTTACGCTAAACAATTGCGGCATGAC F2: 3 TAGGGGAATTCTTT 2 Unidirectional alignment (log-probability: -46.4) CTTGATTAGTAATCTCCAGCATGCCCACAAACACGCATGT-----tttcttaAGGGGAT-GGATGCCCTTAAGAAAATGCaATTTGTTAACGCCGTACTG CTTGATTAGTAATCTCCAGCATGCCCACAAACACGCATGTGACTG-------AGGGGATGGGATGCCCTTAAGAAAATGCGATTTGTTAACGCCGTACTG Template switch alignment (log-probability: -28.5) CTTGATTAGTAATCTCCAGCATGCCCACAAACACGCATGT|TTTCTTAAGGGgAT|GGATGCCCTTAAGAAAATGCaATTTGTTAACGCCGTACTG CTTGATTAGTAATCTCCAGCATGCCCACAAACACGCATGT|TTTCTTAAGGGCAT|GGATGCCCTTAAGAAAATGCGATTTGTTAACGCCGTACTG ========== Event 2862 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGTCACTGGTGGCTGGGGATGGCTTGTCCATCAGCTAGCAGC----CAGACAATCGAATAGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACGCCATCTCCGCCAGCCCTCATTTAAT Chimp: AGGTCACTGGTGGCTGGGGATGGCTTGTCCATCAGCTAGCAGC--------CAATCGAATAGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACGCCGTCTCTGCCAGCCCTCATTTAAT Gorilla: AGGTCACTGGTGGCTGGGGATGGCTTGTCCATCAGCTAGCAGC--------CAATCGAATAGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACACTGTCTCCGCCAGCCCTCATTTAAT ↓ 3 2 1 4 Human: AGGTCACTGGTGGCTGGGGATGGCTTGTCCATCAGCTAGCAGC----CAGACAATCGAATAGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACGCCATCTCCGCCAGCCCTCATTTAAT Cluster: [ ] Orangutan: AGGTCACCGGTGGCTGGGGATGGCTTGTCCACCAGCTAGCAGCCAGA----CAATCGAATAGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACGCCGTCTCCACCAGCCTTCATTTAAT Gorilla > Human --------------- chr5:173268359-173268363 Template switch process: F1: L AGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCAC 1 F3: 4 CTCCGCCAGCCCTCATTTAATGTCTTGTTGGAGCATAAT R RF: ATGGCTTGTCCATCAGCTAGCAGCCAATCGAATAGCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACACTGTCTCCGCCAGCCCTCATTTAATGTCTTGTTGGAGCATAAC RR: TACCGAACAGGTAGTCGATCGTCGGTTAGCTTATCGCGGGATGTACCCTGTCCTCCTCGCGGACTCGAGAAGTGTGACAGAGGCGGTCGGGAGTAAATTACAGAACAACCTCGTATTG F2: 3 TACCG 2 Unidirectional alignment (log-probability: -28.8) GCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACgCcaTCTCCGCCAGCCCTCATTTAATGTCTTGTTGGAGCATaat GCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCACACTGTCTCCGCCAGCCCTCATTTAATGTCTTGTTGGAGCAT--- Template switch alignment (log-probability: -21.8) GCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCAC|GCCAT|CTCCGCCAGCCCTCATTTAATGTCTTGTTGGAGCATAAt GCGCCCTACATGGGACAGGAGGAGCGCCTGAGCTCTTCAC|GCCAT|CTCCGCCAGCCCTCATTTAATGTCTTGTTGGAGCATAAC ========== Event 2863 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTATTCTCAACAAGCTGCAAACG--CGGTCCTCAGCAGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCCTC-CCGACAGGGACCCTGGCAGCCTCATGG-GGGAGG-ATTTTGTTCATCGGTCCCCTTGCTCTCCCATTGTTTGCAAGCGAGGACTGAAGGAGAAA ↓ 1 4 3 2 Chimp: GTATTCTCAACAAGCTGCAAACG--CT--GCAAACAAGGACACACCCTGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCCTC-CGGACAGGGACCCTGGCAGCCTCACGG-GGGAGGATTTTTGTTCATCGGTCCCCTTGCTCTCCCATTGTTTGCAAGCGAGGACTAAAGGAGAAA Gorilla: GTATTCTCAACAAGCTGCAAATG--CT--GCAAACAAGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCCTC-CCGACAGGGACCCTGGCAGCCTCATGG-GGGAGG-ATTTTGTTCATCGGTCCCCTTGCTCTCCCATTGTTTGTAAGCGAGGACTAAAGGAGAAA ↑ 1 4 3 2 Human: GTATTCTCAACAAGCTGCAAACG--CGGTCCTCAGCAGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCCTC-CCGACAGGGACCCTGGCAGCCTCATGG-GGGAGG-ATTTTGTTCATCGGTCCCCTTGCTCTCCCATTGTTTGCAAGCGAGGACTGAAGGAGAAA Cluster: [ ] Orangutan: GTATTCTCAACAAGCTGCAAACGCGCT--CCTCAGCAGGGCACACCCCGCTGGAGGCCCTTGAGTCCTTAG---AAAGGGCTGTGGTCTCCTCGACAGGGACCCTGGCAGCCTCATGGGGGGAGG-ATTTTGTTCATCAGTCCCCTTGCTCTCCGATTGTTTGCAAGCGAGGACTAAAGGAGAAA Human > Chimp ------------- chr5:1840788-1840795 Template switch process: F1: L GGGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGC 1 F3: 4 AGGACACACCCTGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCC R RF: GGGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGCGGTCCTCAGCAGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCCTCCCGACAGGGACCCTGGCAGCCTCATGGGGGAGGATTTTGTTCATCGGTCCCCTTGCTCTCCCATTGTTTGCA RR: CCCTCGTGATTTTCATTCATAAGAGTTGTTCGACGTTTGCGCCAGGAGTCGTCCCGTGTGGGGCGACCTCCGGGGACTCAGGAGTCCCTCTTCCCGACACCGGAGGGCTGTCCCTGGGACCGTCGGAGTACCCCCTCCTAAAACAAGTAGCCAGGGGAACGAGAGGGTAACAAACGT F2: 3 ACAAACGT 2 Unidirectional alignment (log-probability: -45.2) GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGC--------------tgcaaacaaggaCACACCCtGCTGGAGGCCCCTGAGTCCTCAGGGAGA GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGCGGTCCTCAGCAGGG------------CACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA Template switch alignment (log-probability: -28.5) GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGC|TGCAAACA|AGGaCACACCCtGCTGGAGGCCCCTGAGTCCTCAGGGAGA GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGC|TGCAAACA|AGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA Human > Gorilla --------------- chr17:1825243-1825250 Template switch process: F1: L AAAGGGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAATGC 1 F3: 4 AGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA R RF: AAAGGGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGCGGTCCTCAGCAGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGAAGGGCTGTGGCCTCCCGACAGGGACCCTGGCAGCCTCATGGGGGAGGATTTTGTTCATCGGTCCCCTTGCTCTCCCATTGTTTGCA RR: TTTCCCTCGTGATTTTCATTCATAAGAGTTGTTCGACGTTTGCGCCAGGAGTCGTCCCGTGTGGGGCGACCTCCGGGGACTCAGGAGTCCCTCTTCCCGACACCGGAGGGCTGTCCCTGGGACCGTCGGAGTACCCCCTCCTAAAACAAGTAGCCAGGGGAACGAGAGGGTAACAAACGT F2: 3 ACAAACGT 2 Unidirectional alignment (log-probability: -37.1) GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAA-------------tgctgcaaacaAGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGCGGTCCTCAGC-----------AGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA Template switch alignment (log-probability: -22.3) GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAAtGC|TGCAAACA|AGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA GGAGCACTAAAAGTAAGTATTCTCAACAAGCTGCAAACGC|TGCAAACA|AGGGCACACCCCGCTGGAGGCCCCTGAGTCCTCAGGGAGA ========== Event 2864 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AGAGCTCTCAGCATGGCAGCACTAAGG-----------------------------------------------CCAGCTGGACCCTACTTGGGAGGATAG ↓ 3 4 2 1 Chimp: AGAGCTCTCAGCATGGCAGCACTAAGG-----------------------------CCAGCTGCCTTAGTGGGGCCAGCTGGACCCTACTTGGGAGGATAG Gorilla: AGAGCTCTCAGCATGGCAGCACTAAGG-----------CCAGCTGCCTTAGTGGGG------------------CCAGCTGGACCCTACTTGGGAGGATAG ↑ 3 4 2 1 Human: AGAGCTCTCAGCATGGCAGCACTAAGG-----------------------------------------------CCAGCTGGACCCTACTTGGGAGGATAG Cluster: [ ] Orangutan: AGAGCTCCCAGCATGGCAGCACTAAGGCTGTTTTGGGG------------------------------------CCAGCTGGACCCTACTTGGGAGGATAG Human > Chimp ------------- chr5:174338731-174338738 Template switch process: F1: L GGGATGCCCCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTG 1 F3: 4 GGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAAAGA R RF: GGGTTGCCCCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAAAGA RR: CCCAACGGGGAGGGTCTCGAGAGTCGTACCGTCGTGATTCCGGTCGACCTGGGATGAACCCTCCTATCTCTTCACCTTTCT F2: 3 GTGATTCC 2 Unidirectional alignment (log-probability: -42.8) CCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGctgccttagtggggccagCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA CCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAG------------------CTGGACCCTACTTGGGAGGATAGAGAAGTGGAA Template switch alignment (log-probability: -28.5) CCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTG|CCTTAGTG|gGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA CCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTG|CCTTAGTG|AGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA Human > Gorilla --------------- chrCABD030155455:18311-18318 Template switch process: F1: L GGGATGCCCCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTG 1 F3: 4 GGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAAAGA R RF: GGGTTGCCCCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAAAGA RR: CCCAACGGGGAGGGTCTCGAGAGTCGTACCGTCGTGATTCCGGTCGACCTGGGATGAACCCTCCTATCTCTTCACCTTTCT F2: 3 GTGATTCC 2 Unidirectional alignment (log-probability: -42.3) CCTCCCAGAGCTCTCAGCATGGCAGCACTAAggccagctgccttagtggGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA CCTCCCAGAGCTCTCAGCATGGCAGCACTAA------------------GGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA Template switch alignment (log-probability: -28) CCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTG|CCTTAGTG|gGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA CCTCCCAGAGCTCTCAGCATGGCAGCACTAAGGCCAGCTG|CCTTAGTG|AGGCCAGCTGGACCCTACTTGGGAGGATAGAGAAGTGGAA ========== Event 2865 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCTATTTTATAAAATAATG------GTTATAAATAAGAAACTCAGTCTTAATTCTCTTTAGT Chimp: ATTCTATTTTATAAAATAATG------GTTATAAATAAGAAACTCAGTCTTAATTCTCTTTAGT ↓ 1 4 3 2 Gorilla: ATTCTATTTTATAAAATAATGAGTTTCTTTATAAATAAGAAACTCAGTCTTAATTCTTTTTAG- Human: ATTCTATTTTATAAAATAATG------GTTATAAATAAGAAACTCAGTCTTAATTCTCTTTAGT Cluster: [ ] Orangutan: ATTCTGTTTTATAAAATAATG------GTTATAAATAAGAA----AGTCTTAATTCTTTTTAGT Chimp > Gorilla --------------- chr5:157969910-157969916 Template switch process: F1: L CTTTTTATCAGTATAGTAGCATTCTATTTTATAAAATAATG 1 F3: 4 TTATAAATAAGAAACTCAGTCTTAATTCTTTTTAGTTCT R RF: CTTTTTATCAGTATAGTAGCATTCTATTTTATAAAATAATGGTTATAAATAAGAAACTCAGTCTTAATTCTCTTTAGTT RR: GAAAAATAGTCATATCATCGTAAGATAAAATATTTTATTACCAATATTTATTCTTTGAGTCAGAATTAAGAGAAATCAA F2: 3 TCTTTGA 2 Unidirectional alignment (log-probability: -40.3) TTTTTATCAGTATAGTAGCATTCTATTTTATAAAATAATGagtttctTTATAAATAAGAAACTCAGTCTTAATTCTtTTTAG-TTCT TTTTTATCAGTATAGTAGCATTCTATTTTATAAAATAATG------GTTATAAATAAGAAACTCAGTCTTAATTCTCTTTAGTTTCT Template switch alignment (log-probability: -31.7) TTTTTATCAGTATAGTAGCATTCTATTTTATAAAATAATG|AGTTTCT|TTATAAATAAGAAACTCAGTCTTAATTCTtTTTAGTtcT TTTTTATCAGTATAGTAGCATTCTATTTTATAAAATAATG|AGTTTCT|TTATAAATAAGAAACTCAGTCTTAATTCTCTTTAGT--T ========== Event 2866 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTAGGGAGGAGATTTAATATTGAAATG------------------------------------------------------ACAGAAATTTACTTGTGGTCAAGAAATAG Chimp: AGTAGGGAGGAGATTTAATATTGAAATG---------------------------ACAGAAATTGTCATTTCATTGAAAATGACAGAAATTTACTTGTGATCAAGAAATAG Gorilla: GGTAGGGAGGAGATTTAATATTGAAATGACAGAAATTGTCATTTCATTGAAAATG---------------------------ACAGAAATTTACTTGTGGTCAAGAAATAG ↑ 4 3 2 1 Human: GGTAGGGAGGAGATTTAATATTGAAATG------------------------------------------------------ACAGAAATTTACTTGTGGTCAAGAAATAG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr5:5819181-5819188 Template switch process: F1: L ACCATAGCATATGGGTAGGGAGGAGATTTAATATTGAAATGACAGAAATT 1 F3: 4 ATTGAAAATGACAGAAATTTACTTGTGGTCAAGAAATAGCGCTCAATCAC R RF: ACCATAGCATATGGGTAGGGAGGAGATTTAATATTGAAATGACAGAAATTTACTTGTGGTCAAGAAATAGCTCTCAATCAC RR: TGGTATCGTATACCCATCCCTCCTCTAAATTATAACTTTACTGTCTTTAAATGAACACCAGTTCTTTATCGAGAGTTAGTG F2: 3 CTTTACTG 2 Unidirectional alignment (log-probability: -55.2) ATGGGTAGGGAGGAGATTTAATATTGAAAtgacagaaattgtcatttcattgaaaaTGACAGAAATTTACTTGTGGTCAAGAAATAGC ATGGGTAGGGAGGAGATTTAATATTGAAA---------------------------TGACAGAAATTTACTTGTGGTCAAGAAATAGC Template switch alignment (log-probability: -33.9) ATGGGTAGGGAGGAGATTTAATATTGAAATGACAGAAATT|GTCATTTC|ATTGaAAATGACAGAAATTTACTTGTGGTCAAGAAATAGC ATGGGTAGGGAGGAGATTTAATATTGAAATGACAGAAATT|GTCATTTC|ATTG-AAATGACAGAAATTTACTTGTGGTCAAGAAATAGC ========== Event 2867 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTAGTGGCCTGAAACAATT-----------------GAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCT Chimp: GTTTAGTGGCCTGAAACAATT-----------------GAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCT ↓ 4 3 2 Gorilla: GTTTAGTGGCCTGAAACAATT-----TGGGATCCCAATTAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCT ↑ 4 3 2 Human: GTTTAGTGGCCTGAAACAATT-----------------GAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCT Cluster: [ ] Orangutan: GTTTAGTGGCCTGAAACAATTGAAAG------------TTAAGCCGTTTGGGATCCCAGTTAAACTCAAGGTCCTGCT Human > Gorilla --------------- chr5:161656215-161656225 Template switch process: F1: L TTAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATT 1 F3: 4 TTAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCTT R RF: TTAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATTGAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCTT RR: AATCCTTTGTCTAGTTACACCAAATCACCGGACTTTGTTAACTTTCGGTAAACCCTAGGGTTAATTTGAGTTCCAGGACGAA F2: 3 AACCCTAGGGT 2 Unidirectional alignment (log-probability: -33.7) TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATttgggatcccaaTtAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAAT------------TGAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC Template switch alignment (log-probability: -22.7) TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATT|TGGGATCCCAA|TtAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATT|TGGGATCCCAA|TGAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC Chimp > Gorilla --------------- chr5:161656215-161656225 Template switch process: F1: L TTAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATT 1 F3: 4 TTAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCTT R RF: TTAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATTGAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGCTT RR: AATCCTTTGTCTAGTTACACCAAATCACCGGACTTTGTTAACTTTCGGTAAACCCTAGGGTTAATTTGAGTTCCAGGACGAA F2: 3 AACCCTAGGGT 2 Unidirectional alignment (log-probability: -33.7) TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATttgggatcccaaTtAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAAT------------TGAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC Template switch alignment (log-probability: -22.7) TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATT|TGGGATCCCAA|TtAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC TAGGAAACAGATCAATGTGGTTTAGTGGCCTGAAACAATT|TGGGATCCCAA|TGAAAGCCATTTGGGATCCCAATTAAACTCAAGGTCCTGC ========== Event 2868 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATAACTGCTGTTTTTAGACGGATAAAAAAATATTCAATACAAAAGAACAAACACAAAGAAGTGCTCCTTCTGTCTAGAGAACCATATGGTAAGG-AAAGTGCTCTTTCTGAATGACACGCATGTATCAGTAATAACCTAGAAAATATAA Chimp: TAATAACTGCTGTTTTTAGATGGATaaaaaaaTATTCAATACAAAAGAACAAACACAAAGAAGTGCTCCTTCTGTCTAGAGAACAATATGGTAAGGAAAAGTGCTCTTTCTGAATGACACGCATGTATCAGTAATAACCTAGAAAATATAA ↓ 1 4 3 2 Gorilla: TAATAACTGCTCTTTTTAGACTGATAA-AAAATATTCAATACAAAAGAACAAACA---CGAAGTGCTCCTTCTGTCTAGAGAACAATATGGTAAGG-AAAGTGCTCTTTCTGAATGACACGCATGTATCAGTAATAACCTAGAAAATATAA Human: TAATAACTGCTGTTTTTAGACGGATAAAAAAATATTCAATACAAAAGAACAAACACAAAGAAGTGCTCCTTCTGTCTAGAGAACCATATGGTAAGG-AAAGTGCTCTTTCTGAATGACACGCATGTATCAGTAATAACCTAGAAAATATAA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr5:721906-721910 Template switch process: F1: L TTTAGA 1 F3: 4 AAAAAATATTCAATACAAAAGAACAAACAC---GAAGTGCTCCTTCTGTCTAGAGAACAATATGGTAAGGAA R RF: TTTAGATGGATAAAAAAATATTCAATACAAAAGAACAAACACAAAGAAGTGCTCCTTCTGTCTAGAGAACAATATGGTAAGGAAAAGTGCTCTTTCTGAATGACACGCATGTATCAG RR: AAATCTACCTATTTTTTTATAAGTTATGTTTTCTTGTTTGTGTTTCTTCACGAGGAAGACAGATCTCTTGTTATACCATTCCTTTTCACGAGAAAGACTTACTGTGCGTACATAGTC F2: 3 TAGTC 2 Unidirectional alignment (log-probability: -38.7) TTTAGActGAT-AAAAAATATTCAATACAAAAGAACAAACAC---GAAGTGCTCC TTTAGATGGATAAAAAAATATTCAATACAAAAGAACAAACACAAAGAAGTGCTCC Template switch alignment (log-probability: -26.1) TTTAGA|CTGAT|AAAAAATATTCAATACAAAAGAACAAACAC---GAAGTGCTCC TTTAGA|CTGAT|AAAAAATATTCAATACAAAAGAACAAACACAAAGAAGTGCTCC ========== Event 2869 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGTCTGTGCCCTCCCTCAGTGG--TGCTGAGTCCCCAGTCCTAGTGCAGGTTCTGGACAGCCGAAC Chimp: TGTGTCTGTGCCCTCCCTCAGTGG--TGCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAAC ↓ 1 4 3 2 Gorilla: TGTGTCTGTGCCCTCCCTCAGCACTAGGCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAAC ↑ 1 4 3 2 Human: TGTGTCTGTGCCCTCCCTCAGTGG--TGCTGAGTCCCCAGTCCTAGTGCAGGTTCTGGACAGCCGAAC Cluster: [ ] Orangutan: TGTGTCTGTGCCCTCCCTCAGTGG--TGCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAAC Human > Gorilla --------------- chr5:164180244-164180249 Template switch process: F1: L GGGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG 1 F3: 4 GCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA R RF: GGGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAGTGGTGCTGAGTCCCCAGTCCTAGTGCAGGTTCTGGACAGCCGAA RR: CCCCCTAACACCCCCACCAGACACAGACACGGGAGGGAGTCACCACGACTCAGGGGTCAGGATCACGTCCAAGACCTGTCGGCTT F2: 3 GATCAC 2 Unidirectional alignment (log-probability: -40.5) GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG----cactagGCTGAGTCCCCAGTCCTAGTGCgGGTTCTGGACAGCtGAA GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAGTGGT------GCTGAGTCCCCAGTCCTAGTGCAGGTTCTGGACAGCCGAA Template switch alignment (log-probability: -27.5) GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG|CACTAG|GCTGAGTCCCCAGTCCTAGTGCgGGTTCTGGACAGCtGAA GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG|CACTAG|GCTGAGTCCCCAGTCCTAGTGCAGGTTCTGGACAGCCGAA Chimp > Gorilla --------------- chr5:164180244-164180249 Template switch process: F1: L GGGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG 1 F3: 4 GCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA R RF: GGGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAGTGGTGCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA RR: CCCCCTAACACCCCCACCAGACACAGACACGGGAGGGAGTCACCACGACTCAGGGGTCAGGATCACGCCCAAGACCTGTCGACTT F2: 3 GATCAC 2 Unidirectional alignment (log-probability: -29.5) GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG----cactagGCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAGTGGT------GCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA Template switch alignment (log-probability: -16.5) GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG|CACTAG|GCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA GGGGATTGTGGGGGTGGTCTGTGTCTGTGCCCTCCCTCAG|CACTAG|GCTGAGTCCCCAGTCCTAGTGCGGGTTCTGGACAGCTGAA ========== Event 2870 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCAACGTGGGGTTGAAATCT--GCAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGA ↓ 1 4 3 2 Chimp: GTCAATGTGGGGTTGAAATCTGGTCAGA---CCCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGA ↑ 1 4 3 2 Gorilla: GTCAACGTGGGGTTGAAATCT--GCAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGA Human: GTCAACGTGGGGTTGAAATCT--GCAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGA Cluster: [ ] Orangutan: GTCAACGTGGGATTGAAATCT--GCAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGA Human > Chimp ------------- chr5:180331922-180331929 Template switch process: F1: L TTATGTATGTGCTACCTGGGGTCAATGTGGGGTTGAAATCTG 1 F3: 4 CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC R RF: TTATGTATGTGCTACCTGGGGTCAACGTGGGGTTGAAATCTGCAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC RR: AATACATACACGATGGACCCCAGTTGCACCCCAACTTTAGACGTCCGTAAAGTCTTCGTACCCAGACTGGGTACAAAAGACGGAAGTCTGG F2: 3 CCAGACTG 2 Unidirectional alignment (log-probability: -37.6) ATGTATGTGCTACCTGGGGTCAAtGTGGGGTTGAAATCTGgtcagacC--------CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC ATGTATGTGCTACCTGGGGTCAACGTGGGGTTGAAATCTG-------CAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC Template switch alignment (log-probability: -22.3) ATGTATGTGCTACCTGGGGTCAAtGTGGGGTTGAAATCTG|GTCAGACC|CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC ATGTATGTGCTACCTGGGGTCAACGTGGGGTTGAAATCTG|GTCAGACC|CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC Gorilla > Chimp --------------- chr5:180331922-180331929 Template switch process: F1: L TTATGTATGTGCTACCTGGGGTCAATGTGGGGTTGAAATCTG 1 F3: 4 CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC R RF: TTATGTATGTGCTACCTGGGGTCAACGTGGGGTTGAAATCTGCAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC RR: AATACATACACGATGGACCCCAGTTGCACCCCAACTTTAGACGTCCGTAAAGTCTTCGTACCCAGACTGGGTACAAAAGACGGAAGTCTGG F2: 3 CCAGACTG 2 Unidirectional alignment (log-probability: -36.6) ATGTATGTGCTACCTGGGGTCAAtGTGGGGTTGAAATCTGgtcagacC--------CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC ATGTATGTGCTACCTGGGGTCAACGTGGGGTTGAAATCTG-------CAGGCATTTCAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC Template switch alignment (log-probability: -22.3) ATGTATGTGCTACCTGGGGTCAAtGTGGGGTTGAAATCTG|GTCAGACC|CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC ATGTATGTGCTACCTGGGGTCAACGTGGGGTTGAAATCTG|GTCAGACC|CAGAAGCATGGGTCTGACCCATGTTTTCTGCCTTCAGACC ========== Event 2871 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: agaaaatcctataagtAGGATATAATACTAGGGCCACATGGGA-----------------------------------------------------------------------------------TTCTAGCTCATACTCAACTCTGTG Chimp: AGAAAATCCTATAAGTAGGATATAATACTAGGGCCACATGGGA------------------------------------------------TTCTGTATTCTGTATAATACTAGGGCCACATGGGATTCTAGCTCATACTCAACTCTGTG Gorilla: AGAAAATCCTATAAGTAGGATATAATACTAGGGCCACATGGGA-------------TTCTGTATTCTGTATAATACTAGGGACACATGGGA-----------------------------------TTCTAGCTCATACTCAACTCTGTG ↑ 4 3 2 1 Human: agaaaatcctataagtAGGATATAATACTAGGGCCACATGGGA-----------------------------------------------------------------------------------TTCTAGCTCATACTCAACTCTGTG Cluster: [ ] Orangutan: AGAAAATCCTATAAGTAGGATATAATACTAGGGCCACATGGGATTCTGTATTCTTT----------------------------------------------------------------------TACTAGCTCATACTCAACTCTGTG Human > Gorilla --------------- chr17:77485923-77485929 Template switch process: F1: L AAAATCCTATAAGTAGGATATAATACTAGGGCCACATGGGATTCT 1 F3: 4 GTATAATACTAGGGACACATGGGATTCTAGCTCATACTCAACTCTGTGATTCATTAAGCTTTTT R RF: AAAATCCTATAAGTAGGATATAATACTAGGGCCACATGGGATTCTAGCTCATACTCAACTCTGTGATTCATTAAGCTTTTT RR: TTTTAGGATATTCATCCTATATTATGATCCCGGTGTACCCTAAGATCGAGTATGAGTTGAGACACTAAGTAATTCGAAAAA F2: 3 TCTTATG 2 Unidirectional alignment (log-probability: -61.2) CCTATAAGTAGGATATAATACTAGGGCCACATGGgattctgtattctgtataatactagggacacatggGATTCTAGCTCATACTCA CCTATAAGTAGGATATAATACTAGGGCCACATGG-----------------------------------GATTCTAGCTCATACTCA Template switch alignment (log-probability: -33.8) CCTATAAGTAGGATATAATACTAGGGCCACATGGGATTCT|GTATTcT|gTATAATACTAGGGaCACATGGGATTCTAGCTCATACTCA CCTATAAGTAGGATATAATACTAGGGCCACATGGGATTCT|GTATTAT|ATATAATACTAGGGCCACATGGGATTCTAGCTCATACTCA ========== Event 2872 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: Atttttt---ttttttttttttttttGACAGAGAAGACT----CTCAAAAAATGGGCCTACCTTTCACCACG Chimp: Atttt---ttt-ttttttttttttttAACAGAGAAGACT--CTGTCAAAAAATGGGCCTACCTTTCACCACG Gorilla: Atttttt---------ttttttttttAATAGAGAAGACTCT--GTCAAAAAATGGGCCTACCTTTCACCACG ↓ 1 4 3 2 Human: Atttttt---ttttttttttttttttGACAGAGAAGACT----CTCAAAAAATGGGCCTACCTTTCACCACG Cluster: [ ] Orangutan: Attttttt---------t-ttttttttACAGAGAAGACTCT--GTCAAAAAATGGGCCTACTTTTCACCACG Gorilla > Human --------------- chr5:330811-330819 Template switch process: F1: L TGTGGATTTTTTTTTTTTTTTT 1 F3: 4 AGAGAAGACTC--TCAAAAAATGGGCCTACCTTTCACCACGAACTGCGGCTCT R RF: TGTGGATTTTTTTTTTTTTTTTAATAGAGAAGACTCTGTCAAAAAATGGGCCTACCTTTCACCACGAACTGCGGCTCT RR: ACACCTAAAAAAAAAAAAAAAATTATCTCTTCTGAGACAGTTTTTTACCCGGATGGAAAGTGGTGCTTGACGCCGAGA F2: 3 CAGTTTTTT 2 Unidirectional alignment (log-probability: -40.3) TGTGGATTTTTTTTTTTTTTttttttTTgAcAGAGAAGACTC--TCAAAAAATGGGCCTACCTTTCACCACGA TGTGGATTTTTTTTTTTTTT------TTAATAGAGAAGACTCTGTCAAAAAATGGGCCTACCTTTCACCACGA Template switch alignment (log-probability: -26.5) TGTGGATTTTTTTTTTTTTTTT|TTTTTTGAC|AGAGAAGACTC--TCAAAAAATGGGCCTACCTTTCACCACGA TGTGGATTTTTTTTTTTTTTTT|TTTTTTGAC|AGAGAAGACTCTGTCAAAAAATGGGCCTACCTTTCACCACGA ========== Event 2873 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: agccagataagacagaagccatgatggagacaatacacacttattctccatgtggatagatttggtcgccac Chimp: AGCCAGATAAGACAGAAGCCA-CATG---------GACACTTATTCTCCATGTGGATAGATTTGGTCCCCAC ↑ 1 4 3 2 Gorilla: AGCCAGATAAGACAGAAGCCATGTTGGAGACAATACACACTTATTCTCCATGTGGTTAGATTTGGTCCCCAC Human: agccagataagacagaagccatgatggagacaatacacacttattctccatgtggatagatttggtcgccac Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr5:95656571-95656575 Template switch process: F1: L CTACCTCAGAAGGAAGGTCTAGCCAGATAAGACAGAAGCCA 1 F3: 4 ACACTTATTCTCCATGTGGATAGATTTGGTCCCCACAAAA R RF: CTACCTCAGAAGGAAGGTCTAGCCAGATAAGACAGAAGCCATGTTGGAGACAATACACACTTATTCTCCATGTGGTTAGATTTGGTCCCCACAAAA RR: GATGGAGTCTTCCTTCCAGATCGGTCTATTCTGTCTTCGGTACAACCTCTGTTATGTGTGAATAAGAGGTACACCAATCTAAACCAGGGGTGTTTT F2: 3 GGTAC 2 Unidirectional alignment (log-probability: -32.6) TACCTCAGAAGGAAGGTCTAGCCAGATAAGACAGAAGCC--------------ACatggACACTTATTCTCCATGTGGaTAGATTTGGTCCCCACAAAA TACCTCAGAAGGAAGGTCTAGCCAGATAAGACAGAAGCCATGTTGGAGACAATAC----ACACTTATTCTCCATGTGGTTAGATTTGGTCCCCACAAAA Template switch alignment (log-probability: -21.9) TACCTCAGAAGGAAGGTCTAGCCAGATAAGACAGAAGCCA|CATGG|ACACTTATTCTCCATGTGGaTAGATTTGGTCCCCACAAAA TACCTCAGAAGGAAGGTCTAGCCAGATAAGACAGAAGCCA|CATGG|ACACTTATTCTCCATGTGGTTAGATTTGGTCCCCACAAAA ========== Event 2874 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATGCAGGAAACTTACAATTTCAATGA---TGTT-----TCATTGAATTCACTATCAGTGTAAAATTTTTCCGATTAATCATGTGTTTTATCAGAGCATAAAAATTATGTGAACTATATGAGGTTTCATGAGTTACAGAGTATATTTAAAAcattttatccttactaaaacctgatgaggtagaaagagcaaatg Chimp: CATGCAGGAAACTTACAATTTCAATGA---TGTT-----TCACTGAATTCACTATCAGTGTAAAATTTTTCAGATTAATCATGTGTTTTATCAGAGCATAAAAATTATGTGAACTATATGAGGTTTCATGAGTTACAGAGTATATTTAAAAcattttattctcactaaaacctgatgaggtagaaagagcaaatg ↓ 4 1 3 2 Gorilla: CATGCAGGAAACTTACAATTTCAATGATTCAGTTCAATGATACTGAATTCACTATCAGTGTAAAATTTTTCAGATTAATCATGTGTTTTATCAGAGCATAAAAATTATGTGAACTACATGAGGTTTCATGAGTTACAGAGTGTATTTAAAAcattttatccttactaaaacctgatgaggtagaaagagcagatg Human: CATGCAGGAAACTTACAATTTCAATGA---TGTT-----TCATTGAATTCACTATCAGTGTAAAATTTTTCCGATTAATCATGTGTTTTATCAGAGCATAAAAATTATGTGAACTATATGAGGTTTCATGAGTTACAGAGTATATTTAAAAcattttatccttactaaaacctgatgaggtagaaagagcaaatg Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr17:76673118-76673121 Template switch process: F1: L TGCTATCTAATGACCATGCAGGAAACTTACAATTTCAATGAT 1 F3: 4 TTCAATGAT-----ACTGAATTCACTATCAGTGTAAAATTTTTCAGATTAATCA R RF: TGCTATCTAATGACCATGCAGGAAACTTACAATTTCAATGATGTTTCACTGAATTCACTATCAGTGTAAAATTTTTCAGATTAATCATGTGTTTTATCAGAGCATAAAAATTATGTGAACTATATGAGGTTTCATGAGTTACAGAGTATATTTAAAACATTTTATTCTCACTAAAACCTGA RR: ACGATAGATTACTGGTACGTCCTTTGAATGTTAAAGTTACTACAAAGTGACTTAAGTGATAGTCACATTTTAAAAAGTCTAATTAGTACACAAAATAGTCTCGTATTTTTAATACACTTGATATACTCCAAAGTACTCAATGTCTCATATAAATTTTGTAAAATAAGAGTGATTTTGGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -36.6) CTATCTAATGACCATGCAGGAAACTTACAATTTCAATGA---TTCagttcaatgatACTGAATTCACTATCAGTGTAAAATTTTTCA CTATCTAATGACCATGCAGGAAACTTACAATTTCAATGATGTTTC-----------ACTGAATTCACTATCAGTGTAAAATTTTTCA Template switch alignment (log-probability: -26.5) CTATCTAATGACCATGCAGGAAACTTACAATTTCAATGAT|TCAG|TTCAATGAT-----ACTGAATTCACTATCAGTGTAAAATTTTTCA CTATCTAATGACCATGCAGGAAACTTACAATTTCAATGAT|TCAG|TTCAATGATGTTTCACTGAATTCACTATCAGTGTAAAATTTTTCA ========== Event 2875 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTAT-AAATATGAGAAATATCAGCCAACAGCACTTTCATCTGTTTTTCCGAAGTAAAGTGACATAAAATATGGAGTTGCCTATTGATACAAATTTTAAGTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGGGCTGACCAAagatctcgtgttaagtg ↑ 3 2 1 4 Chimp: GTAT--AATATGAGAAATATCAGCCAACAGCACTTTCATCTGTTTTTCCAAAGTAAAGTGACATAAAATATGGAGTTGCCTATTGATACAAATTTTAAGTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGA-GGCTGGCCAAagatctcgtgttaagtg Gorilla: GTAT--AATATGAGAAGTATCAGCCAACAGCAGTTTCATCTGTTTTTCCCAGGTAAAGTGACATAAAATATGGAGTTGCCTATTGATACAAATTTTAAGTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGGGCTGGCCAAagatctcgtgttaagtg Human: GTAT-AAATATGAGAAATATCAGCCAACAGCACTTTCATCTGTTTTTCCGAAGTAAAGTGACATAAAATATGGAGTTGCCTATTGATACAAATTTTAAGTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGGGCTGACCAAagatctcgtgttaagtg Cluster: [ ] Orangutan: GTATA-AATATGAGAAATATCAGCCAACAGCACTTTCATCTGTTTTTCCGAAGTAAAGTGACATAAAATATGGAGTTGCCTATTGATACAAATTTTAAGTAGGTAGAAAGAAGCATCTAAACAGAAAATCAAGAGAGGGCTGGCCAAagatctcgtgttaagtg Chimp > Human ------------- chr5:162522274-162522278 Template switch process: F1: L TAAGTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGG 1 F3: 4 CCAAAGATCTCGTGTTAAGTGTTCTTACACAC R RF: TCAGCCAACAGCACTTTCATCTGTTTTTCCAAAGTAAAGTGACATAAAATATGGAGTTGCCTATTGATACAAATTTTAAGTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGGCTGGCCAAAGATCTCGTGTTAAGTGTTCTTACACAC RR: AGTCGGTTGTCGTGAAAGTAGACAAAAAGGTTTCATTTCACTGTATTTTATACCTCAACGGATAACTATGTTTAAAATTCATCCATCCTTCTTCGTAGATTTTTCTTCTAGTTCTCTCCGACCGGTTTCTAGAGCACAATTCACAAGAATGTGTG F2: 3 AGTCG 2 Unidirectional alignment (log-probability: -25.8) GTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAgGGCTGaCCAAAGATCTCGTGTTAAGTGTTCTTACACAC---- GTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGA-GGCTGGCCAAAGATCTCGTGTTAAGTGTTCTTACACACACAC Template switch alignment (log-probability: -15.8) GTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGG|GCTGA|CCAAAGATCTCGTGTTAAGTGTTCTTACACAC GTAGGTAGGAAGAAGCATCTAAAAAGAAGATCAAGAGAGG|GCTGA|CCAAAGATCTCGTGTTAAGTGTTCTTACACAC ========== Event 2876 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ----------------------TAAACagattctgtttagaatctgtttagaatctgttATTCTTTTTAAAAAGTGATCAGTCCATTTC ↑ 3 1 2 4 Chimp: GACTGATCGCTTTTAAAAAAGAATaacagattctaaacagattctaaacagaatctGTTATTCTT-TTTAAAAGTGATCAGTCCATTTC Gorilla: ----------------------ATAGcagattctaaacagattctaaacagaatctGTTATTCTTTTTTAAAAGTGATCAGTCCATTTC Human: ----------------------TAAACagattctgtttagaatctgtttagaatctgttATTCTTTTTAAAAAGTGATCAGTCCATTTC Cluster: [ ] Orangutan: Chimp > Human ------------- chr5:162100200-162100229 Template switch process: F1: L AACAGATTCT 1 F3: 4 TTTTAAAAAGTGATCAGTCCATTTCAGGATGGTTTGTACTATGGG R RF: AGAATAACAGATTCTAAACAGATTCTAAACAGAATCTGTTATTCTTTTTAAAAGTGATCAGTCCATTTCAGGATGGTTTGTACTATGGG RR: TCTTATTGTCTAAGATTTGTCTAAGATTTGTCTTAGACAATAAGAAAAATTTTCACTAGTCAGGTAAAGTCCTACCAAACATGATACCC F2: 3 TCTTATTGTCTAAGATTTGTCTAAGATTTG 2 Unidirectional alignment (log-probability: -55) AACAGATTCT---------------gtttagaatctgtttAGAATCTGTTATTCTTTTTaAAAAGTGATCAGTCCATTTCAGGATGGTTTGTACT AACAGATTCTAAACAGATTCTAAAC---------------AGAATCTGTTATTCTTTTT-AAAAGTGATCAGTCCATTTCAGGATGGTTTGTACT Template switch alignment (log-probability: -24.5) AACAGATTCT|GTTTAGAATCTGTTTAGAATCTGTTATTCT|TTTTaAAAAGTGATCAGTCCATTTCAGGATGGTTTGTACT AACAGATTCT|GTTTAGAATCTGTTTAGAATCTGTTATTCT|TTTTTAAAAGTGATCAGTCCATTTCAGGATGGTTTGTACT ========== Event 2877 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAAT-CTAAATTATTTTTGAAATAAAAATA Chimp: TTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAAT-CTAAATTATTTTTGAAATAAAAATA ↓ 1 3 4 ↑ 1 3 24 Gorilla: TTAATATGTTGAAATTAATAATT-TAGATTTGCCACATTACTTATTATTTTTGAAATAAAAATA ↓ 1 3 24 ↑ 1 3 4 Human: TTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAAT-CTAAATTATTTTTGAAATAAAAATA Cluster: [ ] Orangutan: TTAATATGTTGAAATTAATAAAAAGTAATGTGGTAAAC-CTAAATTGTTTTTGAAATAAAAATA Gorilla > Human --------------- chr5:161448403-161448422 Template switch process: F1: L GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAA 1 F3: 4 ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG R RF: GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAATTTAGATTTGCCACATTACTTATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG RR: CAATTACTAACCTTTAAAGAAATTATACAACTTTAATTATTAAATCTAAACGGTGTAATGAATAATAAAAACTTTATTTTTATTGTGTTTCATAAAGTCTTC F2: 3 AATCTAAACGGTGTAATGAA 2 Unidirectional alignment (log-probability: -51.9) TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA---------------------aaagtaatgtggcaaatctaaATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAATTTAGATTTGCCACATTACTT---------------------ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Template switch alignment (log-probability: -23.8) TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAa|AAGTAATGTGGCAAATCTAA|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAT|AAGTAATGTGGCAAATCTAA|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Human > Gorilla --------------- chr17:75349041-75349061 Template switch process: F1: L GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA 1 F3: 4 ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG R RF: GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAATCTAAATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG RR: CAATTACTAACCTTTAAAGAAATTATACAACTTTAATTATTTTTCATTACACCGTTTAGATTTAATAAAAACTTTATTTTTATTGTGTTTCATAAAGTCTTC F2: 3 TTCATTACACCGTTTAGATTT 2 Unidirectional alignment (log-probability: -51.9) TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATA---------------------AtttagatttgccacattacttATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAATCTAA---------------------ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Template switch alignment (log-probability: -18.4) TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA|TTTAGATTTGCCACATTACTT|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA|TTTAGATTTGCCACATTACTT|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Gorilla > Chimp --------------- chr5:94304716-94304735 Template switch process: F1: L GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAA 1 F3: 4 ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG R RF: GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAATTTAGATTTGCCACATTACTTATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG RR: CAATTACTAACCTTTAAAGAAATTATACAACTTTAATTATTAAATCTAAACGGTGTAATGAATAATAAAAACTTTATTTTTATTGTGTTTCATAAAGTCTTC F2: 3 AATCTAAACGGTGTAATGAA 2 Unidirectional alignment (log-probability: -51.9) TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA---------------------aaagtaatgtggcaaatctaaATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAATTTAGATTTGCCACATTACTT---------------------ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Template switch alignment (log-probability: -23.8) TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAa|AAGTAATGTGGCAAATCTAA|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAT|AAGTAATGTGGCAAATCTAA|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Chimp > Gorilla --------------- chr17:75349041-75349061 Template switch process: F1: L GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA 1 F3: 4 ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG R RF: GTTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAATCTAAATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG RR: CAATTACTAACCTTTAAAGAAATTATACAACTTTAATTATTTTTCATTACACCGTTTAGATTTAATAAAAACTTTATTTTTATTGTGTTTCATAAAGTCTTC F2: 3 TTCATTACACCGTTTAGATTT 2 Unidirectional alignment (log-probability: -51.9) TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATA---------------------AtttagatttgccacattacttATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAAAAAGTAATGTGGCAAATCTAA---------------------ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG Template switch alignment (log-probability: -18.4) TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA|TTTAGATTTGCCACATTACTT|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG TTAATGATTGGAAATTTCTTTAATATGTTGAAATTAATAA|TTTAGATTTGCCACATTACTT|ATTATTTTTGAAATAAAAATAACACAAAGTATTTCAGAAG ========== Event 2878 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGATATTTTACCCGTCATGCACGTTCGTGC-----------------TTGAAAATACTTCCAAGTAACTTGCGTCTGCTTCACAGGTGAGGAGACAGGGGCTCAGAGCCCCTGGGGGGCAGTGTCGGCCGTCCTCTCTGCATCACTGGCTCCACCATTCACAAAAC Chimp: AGATATTTTACCCGTCATGCACGTTCGTGC-----------------TTGAAAATACTTCCAAGTAACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGAGCCCCTGGGGGGCAGTGTCGGCAGTCCTCTCTGCATCACTGGCTCCACCATTCACAAAAC ↓ 1 4 3 2 Gorilla: AGATATTTTACCCGTCATGCAAG-TCATGC----------------------------------AGACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGAGCCCCTGGCGGGCAGTGTCGGCAGTCCTCTCTGAATCACTAGCTCCACCATTCACAAAAC ↑ 1 4 3 2 Human: AGATATTTTACCCGTCATGCACGTTCGTGC-----------------TTGAAAATACTTCCAAGTAACTTGCGTCTGCTTCACAGGTGAGGAGACAGGGGCTCAGAGCCCCTGGGGGGCAGTGTCGGCCGTCCTCTCTGCATCACTGGCTCCACCATTCACAAAAC Cluster: [ ] Orangutan: AGATATTTTACCAGTCATGCATGTTCATGCTTGAAAATACTTCCAAG-----------------TAACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGAGCCCCTGAGGGACAGTGTCAGCAGTCCTCTCTGAATCACTGGCTCCTCCATTCACAAAAC Human > Gorilla --------------- chr17:93750563-93750572 Template switch process: F1: L GCTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA 1 F3: 4 ACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGA R RF: GCTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCACGTTCGTGCTTGAAAATACTTCCAAGTAACTTGCGTCTGCTTCACAGGTGAGGAGACAGGGGCTCAGAGCCCCTGGGGGGCAGTGTCGGCCGTCCTCTCTGCATCACT RR: CGACGCGTCACTACGCCAGATCTATAAAATGGGCAGTACGTGCAAGCACGAACTTTTATGAAGGTTCATTGAACGCAGACGAAGTGTCCACTCCTCTGTCCCCGAGTCTCGGGGACCCCCCGTCACAGCCGGCAGGAGAGACGTAGTGA F2: 3 GACGTACTGA 2 Unidirectional alignment (log-probability: -40.5) CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA---------------------------AgtcatgcagACTTGCGTCTGCTTCACAGGTGAGGAGACAGaGGCTCAGA CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCACGTTCGTGCTTGAAAATACTTCCAAGTA---------ACTTGCGTCTGCTTCACAGGTGAGGAGACAGGGGCTCAGA Template switch alignment (log-probability: -28) CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA|AGTcATGCAG|ACTTGCGTCTGCTTCACAGGTGAGGAGACAGaGGCTCAGA CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA|AGTGATGCAG|ACTTGCGTCTGCTTCACAGGTGAGGAGACAGGGGCTCAGA Chimp > Gorilla --------------- chr17:93750563-93750572 Template switch process: F1: L GCTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA 1 F3: 4 ACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGA R RF: GCTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCACGTTCGTGCTTGAAAATACTTCCAAGTAACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGAGCCCCTGGGGGGCAGTGTCGGCAGTCCTCTCTGCATCACT RR: CGACGCGTCACTACGCCAGATCTATAAAATGGGCAGTACGTGCAAGCACGAACTTTTATGAAGGTTCATTGAACGCAGACGAAGTGTCCACTCCTCTGTCTCCGAGTCTCGGGGACCCCCCGTCACAGCCGTCAGGAGAGACGTAGTGA F2: 3 GACGTACTGA 2 Unidirectional alignment (log-probability: -35) CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA---------------------------AgtcatgcagACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGA CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCACGTTCGTGCTTGAAAATACTTCCAAGTA---------ACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGA Template switch alignment (log-probability: -22.5) CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA|AGTcATGCAG|ACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGA CTGCGCAGTGATGCGGTCTAGATATTTTACCCGTCATGCA|AGTGATGCAG|ACTTGCGTCTGCTTCACAGGTGAGGAGACAGAGGCTCAGA ========== Event 2879 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGAAATGCTTCTCTACTCTCA-----------------------------------CTGTCACCTAAAGTAATAGGGAATAAACCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGTTATGTT--CACTGACAGGCTTGCTAGCAGATAGG ↓ 3 2 1 4 Chimp: TGGAAATGCTTCTCTACTCTCA-----------------------------------CTGTCACCTAAAGTAATAGGGAATAAACCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATGACAGTGATGTCAGGCTTGCTAGCAGATAGG ↑ 1 3 4 2 Gorilla: tggaaatgcttctctactctcactgtcacttgtagtggaaatgcttctctactctcactgtcacCTAAAGTAATAGGGAATAAACCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATGTT--CACTGTCAGGCTTGCTAGCAGATAGG Human: TGGAAATGCTTCTCTACTCTCA-----------------------------------CTGTCACCTAAAGTAATAGGGAATAAACCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGTTATGTT--CACTGACAGGCTTGCTAGCAGATAGG Cluster: [ ] Orangutan: TGGAAACACTTCTCTACCCTCC-----------------------------------CTGTCACCTAAAGTAATAGGGAATAAACCCAAGAACCCTGCTTCTGCTTTCCCCCAAAACCAGTTATGTT--CACTGTCAGGCTTGCTAGCAGATAGG Human > Chimp ------------- chr5:93807780-93807786 Template switch process: F1: L ATAAACCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATG 1 F3: 4 TGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATTACT R RF: TCACTGTCACCTAAAGTAATAGGGAATAAACCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGTTATGTTCACTGACAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATTACT RR: AGTGACAGTGGATTTCATTATCCCTTATTTGGGTTTTTGGGACGAAGACGAAAGGGGGTTTTGGTCAATACAAGTGACTGTCCGAACGATCGTCTATCCCAGAGGACACCAGTTAATGA F2: 3 AGTGACA 2 Unidirectional alignment (log-probability: -40.5) CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGaTA-------TGACAGtgatgtcagGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGTTATGTTCACTGACAG---------GCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT Template switch alignment (log-probability: -28.3) CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGaTATG|ACAGTGA|TGtCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGTTATG|ACAGTGA|TGACAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT Gorilla > Chimp --------------- chr5:93807780-93807786 Template switch process: F1: L CCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATG 1 F3: 4 TGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT R RF: CCCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATGTTCACTGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT RR: GGGTTTTTGGGACGAAGACGAAAGGGGGTTTTGGTCTATACAAGTGACAGTCCGAACGATCGTCTATCCCAGAGGACACCAGTTAA F2: 3 AGTGACA 2 Unidirectional alignment (log-probability: -28) CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATG---ACagtgaTGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATGTTCAC-----TGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT Template switch alignment (log-probability: -16.6) CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATG|ACAGTGA|TGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT CCAAAAACCCTGCTTCTGCTTTCCCCCAAAACCAGATATG|ACAGTGA|TGTCAGGCTTGCTAGCAGATAGGGTCTCCTGTGGTCAATT ========== Event 2880 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGTTTGCTGCTTTCTGGGAAAG-CTGCTGGCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTG ↑ 1 4 3 2 Chimp: GTGTTTGCTGCTTTCTGGGAAGGGGTTTGGGCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTG Gorilla: GTGTCTGCTGCTTTCTGGGAAGGGGTTGGGGCCATGCTCCCAGCAGCTCAGGAAGGGCAGGAGCACTG ↓ 1 4 3 2 Human: GTGTTTGCTGCTTTCTGGGAAAG-CTGCTGGCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTG Cluster: [ ] Orangutan: Chimp > Human ------------- chr5:2163501-2163508 Template switch process: F1: L CACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAA 1 F3: 4 GCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA R RF: CACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAAGGGGTTTGGGCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA RR: GTGACGTAGAAGAGGTAGATCACAAACGACGAAAGACCCTTCCCCAAACCCGGTACGAGGGTCGTCGAATCCTTCCCGTCCTCGTGACT F2: 3 GTCGTCGA 2 Unidirectional alignment (log-probability: -31.6) ACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAAagctgct--------GGCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA ACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAA-------GGGGTTTGGGCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA Template switch alignment (log-probability: -16.3) ACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAA|AGCTGCTG|GCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA ACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAA|AGCTGCTG|GCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA Gorilla > Human --------------- chr5:2163501-2163508 Template switch process: F1: L CACTGCATCTTCTCCATCTAGTGTTTGCTGCTTTCTGGGAA 1 F3: 4 GCCATGCTCCCAGCAGCTTAGGAAGGGCAGGAGCACTGA R RF: CACTGCATCTTCTCCATCTAGTGTCTGCTGCTTTCTGGGAAGGGGTTGGGGCCATGCTCCCAGCAGCTCAGGAAGGGCAGGAGCACTGA RR: GTGACGTAGAAGAGGTAGATCACAGACGACGAAAGACCCTTCCCCAACCCCGGTACGAGGGTCGTCGAGTCCTTCCCGTCCTCGTGACT F2: 3 GTCGTCGA 2 Unidirectional alignment (log-probability: -42.1) ACTGCATCTTCTCCATCTAGTGTtTGCTGCTTTCTGGGAA--------agctgctGGCCATGCTCCCAGCAGCTtAGGAAGGGCAGGAGCACTGA ACTGCATCTTCTCCATCTAGTGTCTGCTGCTTTCTGGGAAGGGGTTGG-------GGCCATGCTCCCAGCAGCTCAGGAAGGGCAGGAGCACTGA Template switch alignment (log-probability: -27.8) ACTGCATCTTCTCCATCTAGTGTtTGCTGCTTTCTGGGAA|AGCTGCTG|GCCATGCTCCCAGCAGCTtAGGAAGGGCAGGAGCACTGA ACTGCATCTTCTCCATCTAGTGTCTGCTGCTTTCTGGGAA|AGCTGCTG|GCCATGCTCCCAGCAGCTCAGGAAGGGCAGGAGCACTGA ========== Event 2881 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAGGAGCAGATGCCAATTAAGGGGT--------GGCTTACAAGCACTGGACCCAAATCTGAATGTAA---GAAGAT ↓ 41 3 2 Chimp: TAAGGAGCAGATGCCAATTAATTTGGGTCCAGTGCAATTACAAGCACTGGACCCAAATCTGAATGTAA---GAAGAT ↑ 41 3 2 Gorilla: TAAGGAGCAGATGCCAATTAAGGGGT--------GGCTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAAGAG Human: TAAGGAGCAGATGCCAATTAAGGGGT--------GGCTTACAAGCACTGGACCCAAATCTGAATGTAA---GAAGAT Cluster: [ ] Orangutan: Human > Chimp ------------- chr5:2334906-2334919 Template switch process: F1: L AAAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA 1 F3: 4 AA--------TTACAAGCACTGGACCCAAATCTGAATGTAAGAAGATAAT R RF: AAAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAAGGGGTGGCTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGATAAT RR: TTTCGACTTTAAATTTTTTCATTCCTCGTCTACGGTTAATTCCCCACCGAATGTTCGTGACCTGGGTTTAGACTTACATTCTTCTATTA F2: 3 CGTGACCTGGGTTT 2 Unidirectional alignment (log-probability: -44.5) AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA--------tttgggtccagtgcaaTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGATA AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAAGGGGTGGC----------------TTACAAGCACTGGACCCAAATCTGAATGTAAGAAGATA Template switch alignment (log-probability: -27.7) AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA|TTTGGGTCCAGTGC|AA--------TTACAAGCACTGGACCCAAATCTGAATGTAAGAAGATA AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA|TTTGGGTCCAGTGC|AAGGGGTGGCTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGATA Gorilla > Chimp --------------- chr5:2334906-2334919 Template switch process: F1: L AAAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA 1 F3: 4 AA--------TTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAT R RF: AAAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAAGGGGTGGCTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAA RR: TTTCGACTTTAAATTTTTTCATTCCTCGTCTACGGTTAATTCCCCACCGAATGTTCGTGACCTGGGTTTAGACTTACATTCTTCTT F2: 3 CGTGACCTGGGTTT 2 Unidirectional alignment (log-probability: -56.4) AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTaatttgggtccagtgcAA--------TTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAt--- AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATT----------------AAGGGGTGGCTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAAGAG Template switch alignment (log-probability: -33.2) AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA|TTTGGGTCCAGTGC|AA--------TTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAt AAGCTGAAATTTAAAAAAGTAAGGAGCAGATGCCAATTAA|TTTGGGTCCAGTGC|AAGGGGTGGCTTACAAGCACTGGACCCAAATCTGAATGTAAGAAGAA ========== Event 2882 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tcacagccactaccctaGTCC--------ACCTCCAGGGAACAGAGAAGTTCTTCATAA Chimp: tcacagccactaccctaGTCC--------ACCTCCAGGAAACAGAGAAGTTCTTCATAA ↓ 3 1 4 2 Gorilla: tcacagccactaccctaGTCCCTGGAGGTGGCTCCAGGGAACAGAGAAGTTCTTCATAA ↑ 3 1 4 2 Human: tcacagccactaccctaGTCC--------ACCTCCAGGGAACAGAGAAGTTCTTCATAA Cluster: [ ] Orangutan: tcacagccaccaccctaGTCC--------ACCTCCAGGGAACACAGAAGTTCTTCATAA Human > Gorilla --------------- chr17:22220209-22220218 Template switch process: F1: L GTTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC 1 F3: 4 CTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCT R RF: GTTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCCACCTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCT RR: CAACTGTGGTTTCGGTAACGAGTGTCGGTGATGGGATCAGGTGGAGGTCCCTTGTCTCTTCAAGAAGTATTTTATTGATTCGA F2: 3 GGTGGAGGTC 2 Unidirectional alignment (log-probability: -33.5) TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCCctggaggtggCTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCT TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC--------ACCTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCT Template switch alignment (log-probability: -17) TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC|CTGGAGGTGG|CTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCT TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC|CTGGAGGTGG|CTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCT Chimp > Gorilla --------------- chr17:22220209-22220218 Template switch process: F1: L GTTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC 1 F3: 4 CTCCAGGGAACAGAGAAGTTCTTCATAAAATAACTAAGCTGTTTTATT R RF: GTTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCCACCTCCAGGAAACAGAGAAGTTCTTCATAAAATAACTAAGCTGTTTTATT RR: CAACTGTGGTTTCGGTAACGAGTGTCGGTGATGGGATCAGGTGGAGGTCCTTTGTCTCTTCAAGAAGTATTTTATTGATTCGACAAAATAA F2: 3 GGTGGAGGTC 2 Unidirectional alignment (log-probability: -39.1) TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCCctggaggtggCTCCAGGgAACAGAGAAGTTCTTCATAAAATAACTAAGCT TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC--------ACCTCCAGGAAACAGAGAAGTTCTTCATAAAATAACTAAGCT Template switch alignment (log-probability: -22.7) TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC|CTGGAGGTGG|CTCCAGGgAACAGAGAAGTTCTTCATAAAATAACTAAGCT TTGACACCAAAGCCATTGCTCACAGCCACTACCCTAGTCC|CTGGAGGTGG|CTCCAGGAAACAGAGAAGTTCTTCATAAAATAACTAAGCT ========== Event 2883 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTGGAAATGTAAATGTTTATAGTACTCCATGGAGTACTATATGAGTCATGGAACGATGTTT Chimp: TCTGGAAGTGTAAATGTTTATAGTACTCCA-------CT-AATGAGTCATGGAACGATGTTT ↓ 3 2 4 Gorilla: TCTGGAAATGTAAATGTTTAT-ATACTCCATGGAGTACTATATGAGTCATGGAACGATGTTT Human: TCTGGAAATGTAAATGTTTATAGTACTCCATGGAGTACTATATGAGTCATGGAACGATGTTT Cluster: [ ] Orangutan: TCTGGAAATGTAAATGTTTATAGTACTCCA-------CT-AATGAGTCATGGAACGATGTTT Chimp > Gorilla --------------- chr17:244724-244734 Template switch process: F1: L AACCACTGGGCAGTGGGTGGTCTGGAAATGTAAATGTTTATA-TACTCCA 1 F3: 4 ATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTGT R RF: AACCACTGGGCAGTGGGTGGTCTGGAAGTGTAAATGTTTATAGTACTCCACTAATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTGT RR: TTGGTGACCCGTCACCCACCAGACCTTCACATTTACAAATATCATGAGGTGATTACTCAGTACCTTGCTACAAAGGATAACTTTTACAAAACA F2: 3 TATCATGAGGT 2 Unidirectional alignment (log-probability: -47.6) GCAGTGGGTGGTCTGGAAaTGTAAATGTTTATA-TACTCCatggagtACTAtATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTGT GCAGTGGGTGGTCTGGAAGTGTAAATGTTTATAGTACTCC-------ACTA-ATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTGT Template switch alignment (log-probability: -32.6) GCAGTGGGTGGTCTGGAAaTGTAAATGTTTATA-TACTCCA|TGGAGTACTAT|ATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTGT GCAGTGGGTGGTCTGGAAGTGTAAATGTTTATAGTACTCCA|TGGAGTACTAT|ATGAGTCATGGAACGATGTTTCCTATTGAAAATGTTTTGT ========== Event 2884 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTATTTCTCGTCCTTATTACTACAT---------------GTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGAGacattgggatttgctgatttaggtgtcttagctcccaaagaagaagagctgtcaccaggggacacaaaaagtgctcacagaactggaagttgacattgccacatggacaattag Chimp: GTTATTTCTCATCCTTATTACTACAT---------------GTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGAGacattgggatttgctgatttaggtgtcttagctcccaaagaagaagagctgtcaccaggggacacaaaaagtgcccacagaactggaagttgacattgccacatggacaattag ↓ 4 1 3 2 Gorilla: GTTATTTCTCATCCTTATTACTACATGTTGGTCAACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGAGACATTGGGATTTGCTGATTTaggtgtcttagctcccaaagaagaagagctgtcacca-gggacacaaaaagtgcccacagaactggaagttgacattgccacatggacaatttg ↑ 4 1 3 2 Human: GTTATTTCTCGTCCTTATTACTACAT---------------GTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGAGacattgggatttgctgatttaggtgtcttagctcccaaagaagaagagctgtcaccaggggacacaaaaagtgctcacagaactggaagttgacattgccacatggacaattag Cluster: [ ] Orangutan: GTTATTTCTCATCCTTATTGCTACAT---------------GTTGACCAAGGCATGAGTTACTTCAGAATCACTTGCATGAGacattgggatttgctgatttaggcatcttagttcccaaagaagaagagctgtcaccaggggacacaaaaagtgcccacagaactggaagttgacacggccacatggacaatttg Human > Gorilla --------------- chr17:71181405-71181408 Template switch process: F1: L TCCTCTTTATCTGGGGTTATTTCTCATCCTTATTACTACATGTTG 1 F3: 4 ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGA R RF: TCCTCTTTATCTGGGGTTATTTCTCGTCCTTATTACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGAGACATTGGGATTTGCTGATTTAGGTGTCTTAGCTCCCAAAGAAGAAGAGCTGTCACCAGGGGACACAAAAAGTGCTCACAGAACTGGAAGTTGAC RR: AGGAGAAATAGACCCCAATAAAGAGCAGGAATAATGATGTACAACTGGTTCCGTACTCAATGAAGTCTTAGTGAACATACTCTGTAACCCTAAACGACTAAATCCACAGAATCGAGGGTTTCTTCTTCTCGACAGTGGTCCCCTGTGTTTTTCACGAGTGTCTTGACCTTCAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -38) TTTATCTGGGGTTATTTCTCaTCCTTATTactacatgttggtcaACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACT TTTATCTGGGGTTATTTCTCGTCCTTATT---------------ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACT Template switch alignment (log-probability: -22) TTTATCTGGGGTTATTTCTCaTCCTTATTACTACATGTTG|GTCA|ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACT TTTATCTGGGGTTATTTCTCGTCCTTATTACTACATGTTG|GTCA|ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACT Chimp > Gorilla --------------- chr17:71181405-71181408 Template switch process: F1: L TCCTCTTTATCTGGGGTTATTTCTCATCCTTATTACTACATGTTG 1 F3: 4 ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGA R RF: TCCTCTTTATCTGGGGTTATTTCTCATCCTTATTACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACTTGTATGAGACATTGGGATTTGCTGATTTAGGTGTCTTAGCTCCCAAAGAAGAAGAGCTGTCACCAGGGGACACAAAAAGTGCCCACAGAACTGGAAGTTGAC RR: AGGAGAAATAGACCCCAATAAAGAGTAGGAATAATGATGTACAACTGGTTCCGTACTCAATGAAGTCTTAGTGAACATACTCTGTAACCCTAAACGACTAAATCCACAGAATCGAGGGTTTCTTCTTCTCGACAGTGGTCCCCTGTGTTTTTCACGGGTGTCTTGACCTTCAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -32.5) TTTATCTGGGGTTATTTCTCATCCTTATTACTACatgttggtcaactacATGTTGACCAAGGCATGAGTTACTTCAGAATCACT TTTATCTGGGGTTATTTCTCATCCTTATTACTAC---------------ATGTTGACCAAGGCATGAGTTACTTCAGAATCACT Template switch alignment (log-probability: -16.5) TTTATCTGGGGTTATTTCTCATCCTTATTACTACATGTTG|GTCA|ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACT TTTATCTGGGGTTATTTCTCATCCTTATTACTACATGTTG|GTCA|ACTACATGTTGACCAAGGCATGAGTTACTTCAGAATCACT ========== Event 2885 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: aaaatttatCTTGAAAAAATAGTATTTTCATTGTAGTGGTCCTTCACT----CAATGAAAATACTCCATTAttttcaagcttttt ↑ 1 4 3 2 Chimp: AAAATTTATCTTGaaaaa--aaTATT----TTGTAGTGGTCCTT----CACTCAATGAAAATACTCCATTAttttcaagcttttt Gorilla: AAAATTTATCTTGaaaaa--aaTATT----TTGTAGTGGTCCTTCACT----CAGTGAAAATACTCCATTAttttcaagcttttt Human: aaaatttatCTTGAAAAAATAGTATTTTCATTGTAGTGGTCCTTCACT----CAATGAAAATACTCCATTAttttcaagcttttt Cluster: [ ] Orangutan: Chimp > Human ------------- chr5:157495238-157495247 Template switch process: F1: L ATTTATCTTGAAAAAAT 1 F3: 4 TTGTAGTGGTCCTTCACTCAATGAAAATACTCCATTATTTTCAAGCTTTTTCATTTTT R RF: ATTTATCTTGAAAAAAATATTTTGTAGTGGTCCTTCACTCAATGAAAATACTCCATTATTTTCAAGCTTTTTCATTTTT RR: TAAATAGAACTTTTTTTATAAAACATCACCAGGAAGTGAGTTACTTTTATGAGGTAATAAAAGTTCGAAAAAGTAAAAA F2: 3 ACTTTTATGA 2 Unidirectional alignment (log-probability: -35.7) ATTTATCTTGAAAAAA----TagtattttcaTTGTAGTGGTCCTTCACTCAATGAAAATACTCCATTATTT ATTTATCTTGAAAAAAATATT----------TTGTAGTGGTCCTTCACTCAATGAAAATACTCCATTATTT Template switch alignment (log-probability: -22.4) ATTTATCTTGAAAAAAt|AGTATTTTCA|TTGTAGTGGTCCTTCACTCAATGAAAATACTCCATTATTT ATTTATCTTGAAAAAAA|AGTATTTTCA|TTGTAGTGGTCCTTCACTCAATGAAAATACTCCATTATTT ========== Event 2886 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGTGGAAAGGTCTGATCCAGTAAGC--ACT------GTGTGCAATCCAGCACTGCCCTCTC-TCCTGAGC Chimp: GTGTGGAAAGGTCTGATCCAGTAAGC--ACT------GTGTGCAATCCAGCACTGCCCTCTCTTCCTGAAC Gorilla: GTGTGGAAAGGTCTGATCCAGCAAGCAAGCTGGATTGCTGTGCAATCCAGCACTGCCCTCTC-TCCTGAGC ↑ 1 4 3 2 Human: GTGTGGAAAGGTCTGATCCAGTAAGC--ACT------GTGTGCAATCCAGCACTGCCCTCTC-TCCTGAGC Cluster: [ ] Orangutan: GTGTGAAAAGGTCTGATCCAGTAAGC--ACT------GCGTGCAATCCAGCACTGCCCTCTC-TCCTGAGC Human > Gorilla --------------- chr17:70428943-70428952 Template switch process: F1: L TGACAATTTGTGGCAGGGTGGTGTGGAAAGGTCTGATCCAGCAAGCAA 1 F3: 4 TGTGCAATCCAGCACTGCCCTCTCTCCTGAGCATGGCAGA R RF: TGACAATTTGTGGCAGGGTGGTGTGGAAAGGTCTGATCCAGTAAGCACTGTGTGCAATCCAGCACTGCCCTCTCTCCTGAGCATGGCAGA RR: ACTGTTAAACACCGTCCCACCACACCTTTCCAGACTAGGTCATTCGTGACACACGTTAGGTCGTGACGGGAGAGAGGACTCGTACCGTCT F2: 3 CGTTAGGTCG 2 Unidirectional alignment (log-probability: -37.8) TGTGGCAGGGTGGTGTGGAAAGGTCTGATCCAGcAAGCAagCTGgattgcTGTGCAATCCAGCACTGCCCTCTCTCCTGAGCATGGCAGA TGTGGCAGGGTGGTGTGGAAAGGTCTGATCCAGTAAGCA--CTG------TGTGCAATCCAGCACTGCCCTCTCTCCTGAGCATGGCAGA Template switch alignment (log-probability: -28.2) TGTGGCAGGGTGGTGTGGAAAGGTCTGATCCAGcAAGCAa|GCTGGATTGC|TGTGCAATCCAGCACTGCCCTCTCTCCTGAGCATGGCAGA TGTGGCAGGGTGGTGTGGAAAGGTCTGATCCAGTAAGCAC|GCTGGATTGC|TGTGCAATCCAGCACTGCCCTCTCTCCTGAGCATGGCAGA ========== Event 2887 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTACTGAAGTCACTTTGAAACCCAAAAACATTGTAGAAAATATTGACAAAATAATAGTTTTGAACAATAGTTCAAAACCTTTATTTTTCAACTAAAAC Chimp: TTACTGAAGTCACTTTGAAACTCAAAAACATTGTAGAAAATATTGACAAAATAAT-----------ATTGTTCAAAACCTTTATTTTTCAACTAAAAC Gorilla: TTACTGAAGTCACTTTGAAACTCAAAAACACTGTAGAAAATATTGACAAAATAAT-----------ATTGTTCAAAACCTTTATATTTCAACTAAAAC ↓ 4 13 2 Human: TTACTGAAGTCACTTTGAAACCCAAAAACATTGTAGAAAATATTGACAAAATAATAGTTTTGAACAATAGTTCAAAACCTTTATTTTTCAACTAAAAC Cluster: [ ] Orangutan: TTACTGAAGTCACTTTGAAACTCAAAAACATTGTAGAAAATATTGACAAAATATT-----------ATTGTTCAAAACCTTTATTTTTCAACTAAAAC Gorilla > Human --------------- chr5:158977131-158977141 Template switch process: F1: L TGTCTCCAAATATGACAGCTTTACTGAAGTCACTTTGAAACCCAAAAACATTGTAGAAAATATTGACAAAATAATA 1 F3: 4 TAGT R RF: TGTCTCCAAATATGACAGCTTTACTGAAGTCACTTTGAAACTCAAAAACACTGTAGAAAATATTGACAAAATAATACCAATTATAACACTGTCTTATGCCATTTGAAAGTTGAATGTCTCCAAATATGACAGCTTTACTGAAGTCACTTTGAAACTCAAAAACACTGTAGAAAATATTGACAAAATAATATTGTTCAAAAC RR: ACAGAGGTTTATACTGTCGAAATGACTTCAGTGAAACTTTGAGTTTTTGTGACATCTTTTATAACTGTTTTATTATGGTTAATATTGTGACAGAATACGGTAAACTTTCAACTTACAGAGGTTTATACTGTCGAAATGACTTCAGTGAAACTTTGAGTTTTTGTGACATCTTTTATAACTGTTTTATTATAACAAGTTTTG F2: 3 AACAAGTTTTG 2 Unidirectional alignment (log-probability: -43.2) GAAACcCAAAAACAtTGTAGAAAATATTGACAAAATAATagttttgaacaATaGT GAAACTCAAAAACACTGTAGAAAATATTGACAAAATAAT-----------ATTGT Template switch alignment (log-probability: -28.1) GAAACcCAAAAACAtTGTAGAAAATATTGACAAAATAATA|GTTTTGAACAA|TAGT GAAACTCAAAAACACTGTAGAAAATATTGACAAAATAATA|GTTTTGAACAA|TAGT ========== Event 2888 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGCTACATTGAAATGCCAATATAATTCAAATAA ↑ 3 2 1 4 Chimp: ATTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGTAA------CATGCCAATATAATTCAAATAA Gorilla: ATTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGTAA------CATGCCAATATAATTCAAATAA ↓ 3 2 1 4 Human: ATTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGCTACATTGAAATGCCAATATAATTCAAATAA Cluster: [ ] Orangutan: ATTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGTAA------CATGCCAATATAATTCAAATAA Chimp > Human ------------- chr5:22664903-22664912 Template switch process: F1: L TTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG 1 F3: 4 ATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG R RF: TTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGTAACATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG RR: AAACTTAAACTTAAACTAAAGTTACATCGTTTTACAGAGACATTGTACGGTTATATTAAGTTTATTATCAAAATCCAAAACAAAC F2: 3 AAGTTACATC 2 Unidirectional alignment (log-probability: -31.6) TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGctacatTgAaATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG------TAACATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG Template switch alignment (log-probability: -16.5) TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG|CTACATTGAA|ATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG|CTACATTGAA|ATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG Gorilla > Human --------------- chr5:22664903-22664912 Template switch process: F1: L TTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG 1 F3: 4 ATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG R RF: TTTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGTAACATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG RR: AAACTTAAACTTAAACTAAAGTTACATCGTTTTACAGAGACATTGTACGGTTATATTAAGTTTATTATCAAAATCCAAAACAAAC F2: 3 AAGTTACATC 2 Unidirectional alignment (log-probability: -30.6) TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTGctacatTgAaATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG------TAACATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG Template switch alignment (log-probability: -17) TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG|CTACATTGAA|ATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG TTGAATTTGAATTTGATTTCAATGTAGCAAAATGTCTCTG|CTACATTGAA|ATGCCAATATAATTCAAATAATAGTTTTAGGTTTTGTTTG ========== Event 2889 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATTGTGGCATATAAAAATTAATTGTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA----GAATTTTTTTAATACCGTTGTTAAAATTTTTATTGTTAATGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGACACGACTACAATTCATTCCAA Chimp: TAATTGTGGCATATAAAAATTAATTGTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA--GACAAtttttttAATACCGTTGTTAAAATTTTTATTGTTAATGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGACACGACTACAATTCATTCCAA ↓ 1 4 3 2 Gorilla: TAATTGTGGCATATAAAAATTGTCAGCCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAAGA--CAAtttttttAATACCGTTGTTAAAATTTTTATTGTTAATGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGACACGACTACAATTCATTCCAA ↑ 1 4 3 2 Human: TAATTGTGGCATATAAAAATTAATTGTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA----GAATTTTTTTAATACCGTTGTTAAAATTTTTATTGTTAATGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGACACGACTACAATTCATTCCAA Cluster: [ ] Orangutan: TAATTGTGGCATATAAAAA----TTGTCAACAAAATGTAAAATGTTGAGATTTGAGTATATGAAAGA--CAATCTTTTTGATACTATTGTTAAAATGTTTATTGTTAGTGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGACACGACTACAATTCATTCCAA Human > Gorilla --------------- chr17:23165466-23165469 Template switch process: F1: L CCCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATT 1 F3: 4 GCCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAAGA R RF: CCCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATTAATTGTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAAGAATTTTTTTAATACCGTTGTTAAAATTTTTATTGTTAATGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGAC RR: GGGAGTAGTGACCACAATATATTAACACCGTATATTTTTAATTAACAGTCGTTTTACATTTTACAACTCTAAACTCATATACTTTCTTAAAAAAATTATGGCAACAATTTTAAAAATAACAATTACAAATTATATTTATCCTTAAACGGGATACACAATCCAATAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -36.2) CCTCATCACTGGTGTTATATAATTGTGGCATATAAAA----ATTGTcagcCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA CCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATTAATTGT----CAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA Template switch alignment (log-probability: -21.8) CCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATT|GTCA|GcCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA CCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATT|GTCA|GTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA Chimp > Gorilla --------------- chr17:23165466-23165469 Template switch process: F1: L CCCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATT 1 F3: 4 GCCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAAGA R RF: CTCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATTAATTGTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAAGACAATTTTTTTAATACCGTTGTTAAAATTTTTATTGTTAATGTTTAATATAAATAGGAATTTGCCCTATGTGTTAGGTTATTGAC RR: GAGAGTAGTGACCACAATATATTAACACCGTATATTTTTAATTAACAGTCGTTTTACATTTTACAACTCTAAACTCATATACTTTCTGTTAAAAAAATTATGGCAACAATTTTAAAAATAACAATTACAAATTATATTTATCCTTAAACGGGATACACAATCCAATAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -41.7) cCTCATCACTGGTGTTATATAATTGTGGCATATAAA----AATTGTcagcCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA TCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATTAATTGT----CAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA Template switch alignment (log-probability: -27.3) cCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATT|GTCA|GcCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA TCTCATCACTGGTGTTATATAATTGTGGCATATAAAAATT|GTCA|GTCAGCAAAATGTAAAATGTTGAGATTTGAGTATATGAAA ========== Event 2890 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GGCCTTCTCCTTCCCAACACTGGGGTTGGTCTTGACCAACATGCCCCAGTTGCCATCACCT Chimp: GGCCTTCTCCTTCCCAACACT----GTGGTCAAGACCAATGTGCCCCAGTTGCCATCACCT Gorilla: GGCCTTCTCCTTCCCAACACT----GTGGTCAAGACCAACGTGCCCCAGTTGCCATCACCT ↑ 1 3 4 2 Human: GGCCTTCTCCTTCCCAACACTGGGGTTGGTCTTGACCAACATGCCCCAGTTGCCATCACCT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr17:93342034-93342041 Template switch process: F1: L CCAATTACACATTTTTATAAGGCCTTCTCCTTCCCAACACTG 1 F3: 4 ACCAACGTGCCCCAGTTGCCATCACCTTGACTCACTTAGCATCCACT R RF: CCAATTACACATTTTTATAAGGCCTTCTCCTTCCCAACACTGGGGTTGGTCTTGACCAACATGCCCCAGTTGCCATCACCTTGACTCACTTAGCATCCACC RR: GGTTAATGTGTAAAAATATTCCGGAAGAGGAAGGGTTGTGACCCCAACCAGAACTGGTTGTACGGGGTCAACGGTAGTGGAACTGAGTGAATCGTAGGTGG F2: 3 GAACTGGT 2 Unidirectional alignment (log-probability: -40.3) AATTACACATTTTTATAAGGCCTTCTCCTTCCCAACACTG----TGGTCaaGACCAACgTGCCCCAGTTGCCATCACCTTGACTCACTTAGC AATTACACATTTTTATAAGGCCTTCTCCTTCCCAACACTGGGGTTGGTCTTGACCAACATGCCCCAGTTGCCATCACCTTGACTCACTTAGC Template switch alignment (log-probability: -28) AATTACACATTTTTATAAGGCCTTCTCCTTCCCAACACTG|TGGTCAAG|ACCAACgTGCCCCAGTTGCCATCACCTTGACTCACTTAGC AATTACACATTTTTATAAGGCCTTCTCCTTCCCAACACTG|TGGTCAAG|ACCAACATGCCCCAGTTGCCATCACCTTGACTCACTTAGC ========== Event 2891 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: caaagtgctgggattacaggcatgagccactgtgcccggccCCTATATCACTATTTCTATAT------------TTCTCTCACATAAAATTCCTTCCCC Chimp: caaagtgctgggattacaggcatgagccactgtgcccagccCCTATATCACTATTTCTATAT------------TTCTCTCACATAAAATTCCTTCCCC ↓ 3 2 4 1 Gorilla: caaagtgctgggattacaggcatgagccactgtgcccggccCCTATATCACTATTTCTATATTTCTCATGCTATTTCTCTCACATAAAATTCCTTCCCC ↑ 3 2 4 1 Human: caaagtgctgggattacaggcatgagccactgtgcccggccCCTATATCACTATTTCTATAT------------TTCTCTCACATAAAATTCCTTCCCC Cluster: [ ] Orangutan: caaagtgctgggattacagacctgagccactgtacccggccCCTATATCACTATTTCTATATTTCTCATGCTATTTCTCTCACATAAAATTCCTTCCCC Human > Gorilla --------------- chr17:24879199-24879202 Template switch process: F1: L ATGAGCCACTGTGCCCGGCCCCTATATCACTATTTCTATATTTCTC 1 F3: 4 TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGTTAT R RF: GCATGAGCCACTGTGCCCGGCCCCTATATCACTATTTCTATATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGTTAT RR: CGTACTCGGTGACACGGGCCGGGGATATAGTGATAAAGATATAAAGAGAGTGTATTTTAAGGAAGGGGAATAGGAGTACAATA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -28.1) CACTGTGCCCGGCCCCTATATCACTATTTCTATatttctcatgctATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT CACTGTGCCCGGCCCCTATATCACTATTTCTAT------------ATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT Template switch alignment (log-probability: -16.4) CACTGTGCCCGGCCCCTATATCACTATTTCTATATTTCTC|ATGC|TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT CACTGTGCCCGGCCCCTATATCACTATTTCTATATTTCTC|ATGC|TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT Chimp > Gorilla --------------- chr17:24879199-24879202 Template switch process: F1: L ATGAGCCACTGTGCCCGGCCCCTATATCACTATTTCTATATTTCTC 1 F3: 4 TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGTTAT R RF: GCATGAGCCACTGTGCCCAGCCCCTATATCACTATTTCTATATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGTTAT RR: CGTACTCGGTGACACGGGTCGGGGATATAGTGATAAAGATATAAAGAGAGTGTATTTTAAGGAAGGGGAATAGGAGTACAATA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -33.7) CACTGTGCCCgGCCCCTATATCACTATTTCTAtatttctcatgcTATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT CACTGTGCCCAGCCCCTATATCACTATTTCTA------------TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT Template switch alignment (log-probability: -21.9) CACTGTGCCCgGCCCCTATATCACTATTTCTATATTTCTC|ATGC|TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT CACTGTGCCCAGCCCCTATATCACTATTTCTATATTTCTC|ATGC|TATTTCTCTCACATAAAATTCCTTCCCCTTATCCTCATGT ========== Event 2892 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GATACAGTAAATAAATATGCCTGCAAAAATAGATTTAGTTTCTGAAGCTGAAAATAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGCTTTGAATACATGCTATAGGTACAATAAAACCTATAGTACCATA ↓ 3 2 1 4 Chimp: GATACAGTAAATAAATACGCCTGCAAAAATAGATTTAGTTTCTGAAGCTGAAAATAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGTT------------TACAG---GAATAAAACCTATAGTACCATA Gorilla: GATACAGTAAATAAATATGCCTGCAAAAATAGATTTAGTTTCTGAAGCTGAAAATAGTAAAAACGGTGAAAATTCACTTCAAAGCATTGACATGTT------------TACAG---GAATAAAACCTATAGTACCATA ↑ 3 2 1 4 Human: GATACAGTAAATAAATATGCCTGCAAAAATAGATTTAGTTTCTGAAGCTGAAAATAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGCTTTGAATACATGCTATAGGTACAATAAAACCTATAGTACCATA Cluster: [ ] Orangutan: GATACAGTAAATAAATATGCCTGCAAAAATAAATGTAGTTTCTGAAGCTGAAAATAGTAAAAATGGTGAAAATTCATTTCAAAGCATTGACATGTT------------TACAG---AAATAAAACCTATGGTACCATA Human > Chimp ------------- chr5:87794757-87794764 Template switch process: F1: L ATAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATG 1 F3: 4 AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT R RF: CCTGCAAAAATAGATTTAGTTTCTGAAGCTGAAAATAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGCTTTGAATACATGCTATAGGTACAATAAAACCTATAGTACCATATATGCCCCATCTCATTACT RR: GGACGTTTTTATCTAAATCAAAGACTTCGACTTTTATCATTTTTACCACTTTTAAGTGAAGTTTCGTAACTGTACGAAACTTATGTACGATATCCATGTTATTTTGGATATCATGGTATATACGGGGTAGAGTAATGA F2: 3 GGACATTT 2 Unidirectional alignment (log-probability: -32.4) TAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGtT------------------TACAggaATAAAACCTATAGTACCATATATGCCCCATCTCATTACT TAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGCTTTGAATACATGCTATAGGTACA---ATAAAACCTATAGTACCATATATGCCCCATCTCATTACT Template switch alignment (log-probability: -22.3) TAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATG|TTTaCAGG|AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT TAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATG|TTTGCAGG|AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT Human > Gorilla --------------- chr17:68867347-68867354 Template switch process: F1: L ATAGTAAAAACGGTGAAAATTCACTTCAAAGCATTGACATG 1 F3: 4 AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT R RF: CCTGCAAAAATAGATTTAGTTTCTGAAGCTGAAAATAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGCTTTGAATACATGCTATAGGTACAATAAAACCTATAGTACCATATATGCCCCATCTCATTACT RR: GGACGTTTTTATCTAAATCAAAGACTTCGACTTTTATCATTTTTACCACTTTTAAGTGAAGTTTCGTAACTGTACGAAACTTATGTACGATATCCATGTTATTTTGGATATCATGGTATATACGGGGTAGAGTAATGA F2: 3 GGACATTT 2 Unidirectional alignment (log-probability: -37) TAGTAAAAAcGGTGAAAATTCACTTCAAAGCATTGACATGtT------------------TACaggAATAAAACCTATAGTACCATATATGCCCCATCTCATTACT TAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATGCTTTGAATACATGCTATAGGTAC---AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT Template switch alignment (log-probability: -27.8) TAGTAAAAAcGGTGAAAATTCACTTCAAAGCATTGACATG|TTTaCAGG|AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT TAGTAAAAATGGTGAAAATTCACTTCAAAGCATTGACATG|TTTGCAGG|AATAAAACCTATAGTACCATATATGCCCCATCTCATTACT ========== Event 2893 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TGTCATTAAGTCAATAATACAGAGTTTATTTTGTATTTTGTATGGATATATATGTTATCTCATGATTCAaattctcataattctcataatCAAAATTCATTGAATTTGAATTATGAGATAGCATATATGCCTATACAAAATACAAAATAAACTCTATATTATTGCTTCAAATAAAAT Chimp: TGTCATTAAGTCAATAATACAGAGTTTATTTTGTATTTTGTATGGATATATATGCTATCTCATGATTCAaattctcataattctcataatCAAAATTCATTGAATTTGAATTATGAGATAGCATATATGCCTATACA-------AAATAAACTCTATATTATTGCTTCAAATAAAAT ↓ 3 2 1 4 Gorilla: TGTCATTAAGTCAATAATACAGAGTTTATTTTGTAGTTTGTATGGATATATATGCTATCTCATGATTCAaattctcataattctcataatCGAAATTCATTGAATTTGAATTATGAGATAGCATATATGCCTATACAAAATACAAAATAAACTCTGTATTATTGCTTCAAATAAAAT Human: TGTCATTAAGTCAATAATACAGAGTTTATTTTGTATTTTGTATGGATATATATGTTATCTCATGATTCAaattctcataattctcataatCAAAATTCATTGAATTTGAATTATGAGATAGCATATATGCCTATACAAAATACAAAATAAACTCTATATTATTGCTTCAAATAAAAT Cluster: [ ] Orangutan: TGTCATTAAGTCAATAATACAGAGTCTATTTTGCATTTTGTATGGATATATATGCTATCTCATGATTGAaattctcataattctcataattGAAATTCATCGAATTTAAATTATGAGATAGCATATATGCCTATACAAAATACAGAAGAAACTCTATATTATTGCTTCAAATAAAAT Chimp > Gorilla --------------- chr17:69584657-69584670 Template switch process: F1: L TCATTGAATTTGAATTATGAGATAGCATATATGCCTATACAAAATA 1 F3: 4 TATTATTGCTTCAAATAAAATGGAAATC R RF: CAGAGTTTATTTTGTATTTTGTATGGATATATATGCTATCTCATGATTCAAATTCTCATAATTCTCATAATCAAAATTCATTGAATTTGAATTATGAGATAGCATATATGCCTATACAAAATAAACTCTATATTATTGCTTCAAATAAAATGGAAAGC RR: GTCTCAAATAAAACATAAAACATACCTATATATACGATAGAGTACTAAGTTTAAGAGTATTAAGAGTATTAGTTTTAAGTAACTTAAACTTAATACTCTATCGTATATACGGATATGTTTTATTTGAGATATAATAACGAAGTTTATTTTACCTTTCG F2: 3 GTCTCAAATAAAAC 2 Unidirectional alignment (log-probability: -32) AATTTGAATTATGAGATAGCATATATGCCTATAcaaaataCAAAATAAACTCTgTATTATTGCTTCAAATAAAATGGAAAtC AATTTGAATTATGAGATAGCATATATGCCTATA-------CAAAATAAACTCTATATTATTGCTTCAAATAAAATGGAAAGC Template switch alignment (log-probability: -22.9) AATTTGAATTATGAGATAGCATATATGCCTATACAAAATA|CAAAATAAACTCTG|TATTATTGCTTCAAATAAAATGGAAAtC AATTTGAATTATGAGATAGCATATATGCCTATACAAAATA|CAAAATAAACTCTG|TATTATTGCTTCAAATAAAATGGAAAGC ========== Event 2894 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGTGTCTGACAAAGGTTTATTAACTTTGTTTATGCATTTTTACAACGTAATCATAATTTTAACTAAGGCTAGA Chimp: GTGTGTCTGACAAAGGTTTATTAACTTTGTTT--------ATACAAAGTTAATATAATTTTAACTAAGGCTAGA ↑ 3 2 1 4 Gorilla: GTGTGTCTGACAAAGGTTTATTAACTTTGTTTATGCGTTTTTACAAAGTAATCATAATTTTAACTAAGGCTAGA Human: GTGTGTCTGACAAAGGTTTATTAACTTTGTTTATGCATTTTTACAACGTAATCATAATTTTAACTAAGGCTAGA Cluster: [ ] Orangutan: GTGTGTCTGACAAAGATTTATTAATTTTGTTTATGCATTTTTACAAAGTAATCATAATTTTAACTAAGGCTAGA Gorilla > Chimp --------------- chr5:87038233-87038243 Template switch process: F1: L AATTCCAGAGTGTGTCTGACAAAGGTTTATTAACTTTGTTTAT 1 F3: 4 ATAATTTTAACTAAGGCTAGAAAAGTATGGAAAAATTTTT R RF: AATTCCAGAGTGTGTCTGACAAAGGTTTATTAACTTTGTTTATGCGTTTTTACAAAGTAATCATAATTTTAACTAAGGCTAGAAAAGTATGGAAAATTTTTT RR: TTAAGGTCTCACACAGACTGTTTCCAAATAATTGAAACAAATACGCAAAAATGTTTCATTAGTATTAAAATTGATTCCGATCTTTTCATACCTTTTAAAAAA F2: 3 TAATTGAAACA 2 Unidirectional alignment (log-probability: -33.6) TCCAGAGTGTGTCTGACAAAGGTTTATTAACTTTGTTTAT--------ACAAAGTtAatATAATTTTAACTAAGGCTAGAAAAGTATGGAAAAaTTTTT TCCAGAGTGTGTCTGACAAAGGTTTATTAACTTTGTTTATGCGTTTTTACAAAGTAATCATAATTTTAACTAAGGCTAGAAAAGTATGGAAAATTTTTT Template switch alignment (log-probability: -22.7) TCCAGAGTGTGTCTGACAAAGGTTTATTAACTTTGTTTAT|ACAAAGTTAAT|ATAATTTTAACTAAGGCTAGAAAAGTATGGAAAAaTTTTT TCCAGAGTGTGTCTGACAAAGGTTTATTAACTTTGTTTAT|ACAAAGTTAAT|ATAATTTTAACTAAGGCTAGAAAAGTATGGAAAATTTTTT ========== Event 2895 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: aataattttCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTA Chimp: aataattttCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTA ↓ 3 2 1 4 Gorilla: aataattttCATATAGGTTCAGATAAAACTAATTAGTTT-------------TATCTGTAAATCCATTGCATGGTTTTA ↑ 3 2 1 4 Human: aataattttCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTA Cluster: [ ] Orangutan: ----------------------------------------------------tatatatt------------------- Human > Gorilla --------------- chr17:69229990-69229994 Template switch process: F1: L CAAATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTT 1 F3: 4 TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG R RF: CAAATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG RR: GTTTATTAAAAGTATATCCAAGTCTATTTTGATTAATCAAAACACATAAATAATACACATATTTAGGTAACGTACCAAAATATTAAATGAAGTGTCTCTC F2: 3 GTCTA 2 Unidirectional alignment (log-probability: -26.9) AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTT-----------TTATcTG--TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG Template switch alignment (log-probability: -16.4) AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTT|ATCTG|TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTT|ATCTG|TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG Chimp > Gorilla --------------- chr17:69229990-69229994 Template switch process: F1: L CAAATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTT 1 F3: 4 TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG R RF: CAAATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG RR: GTTTATTAAAAGTATATCCAAGTCTATTTTGATTAATCAAAACACATAAATAATACACATATTTAGGTAACGTACCAAAATATTAAATGAAGTGTCTCTC F2: 3 GTCTA 2 Unidirectional alignment (log-probability: -26.9) AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTT-----------TTATcTG--TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTTGTGTATTTATTATGTGTATAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG Template switch alignment (log-probability: -16.4) AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTT|ATCTG|TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG AATAATTTTCATATAGGTTCAGATAAAACTAATTAGTTTT|ATCTG|TAAATCCATTGCATGGTTTTATAATTTACTTCACAGAGAG ========== Event 2896 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TACAAATCATGAGATGGAGTACCATTGTCTAATGCTATTAATGCATTTAATCTGCCATTTAAGCCTTT Chimp: TACAAATCATGAGATGGAGTACCATTAGACAATGCTATT---------AATCTGCCATTTAAGCCTTT ↑ 3 1 2 4 Gorilla: TACAAATCATGAGATGGAGTACCATTGTCTAATGCTATTAATGCATTTAATCTGCCATTTAAGCCTTT Human: TACAAATCATGAGATGGAGTACCATTGTCTAATGCTATTAATGCATTTAATCTGCCATTTAAGCCTTT Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr5:95123744-95123754 Template switch process: F1: L GATACGATACTCTCCTACAAATCATGAGATGGAGTACCATT 1 F3: 4 TTAATCTGCCATTTAAGCCTTTGCCAGATTTCTGTTTTGTTC R RF: GATATGATACTCTCCTACAAATCATGAGATGGAGTACCATTGTCTAATGCTATTAATGCATTTAATCTGCCATTTAAGCCTTTGCCAGATTTCTGTTTTGTTC RR: CTATACTATGAGAGGATGTTTAGTACTCTACCTCATGGTAACAGATTACGATAATTACGTAAATTAGACGGTAAATTCGGAAACGGTCTAAAGACAAAACAAG F2: 3 ATCGTAACAGA 2 Unidirectional alignment (log-probability: -39.1) ATAcGATACTCTCCTACAAATCATGAGATGGAGTACCATTagacAATGCTA---------TTAATCTGCCATTTAAGCCTTTGCCAGATTTCTGTTTTGT ATATGATACTCTCCTACAAATCATGAGATGGAGTACCATTGTCTAATGCTATTAATGCATTTAATCTGCCATTTAAGCCTTTGCCAGATTTCTGTTTTGT Template switch alignment (log-probability: -28.2) ATAcGATACTCTCCTACAAATCATGAGATGGAGTACCATT|AGACAATGcTA|TTAATCTGCCATTTAAGCCTTTGCCAGATTTCTGTTTTGT ATATGATACTCTCCTACAAATCATGAGATGGAGTACCATT|AGACAATGGTA|TTAATCTGCCATTTAAGCCTTTGCCAGATTTCTGTTTTGT ========== Event 2897 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGATTGATGATTATTTTTTATTGACGAATAGGTACTTGCCGTCTATATCATGAAGAGA ↓ 1 3 4 2 Chimp: TGATTGATGATTATTTTTTAT---CAAGTACCTACTTGCCGTCTATATCATGAAGACA ↑ 1 3 4 2 Gorilla: TGATTGATGATTATTTTTTATTGTTGAATAGGTACTTGCCGTCTATATCATGAAGAGA Human: TGATTGATGATTATTTTTTATTGACGAATAGGTACTTGCCGTCTATATCATGAAGAGA Cluster: [ ] Orangutan: TGATTGATAATTATTTTTTATTGATGAATAGGTGCTTGTTGTCTATATCATGAAGAGA Human > Chimp ------------- chr5:3149896-3149903 Template switch process: F1: L GAGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT 1 F3: 4 TACTTGCCGTCTATATCATGAAGACAGATTCCTTTTCAAC R RF: GAGTTCATATTAGTGACTACTGATTGATGATTATTTTTTATTGACGAATAGGTACTTGCCGTCTATATCATGAAGAGAGATTCCTTTTCAAC RR: CTCAAGTATAATCACTGATGACTAACTACTAATAAAAAATAACTGCTTATCCATGAACGGCAGATATAGTACTTCTCTCTAAGGAAAAGTTG F2: 3 CCATGAAC 2 Unidirectional alignment (log-probability: -39.2) AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTATcaagtacc-----------TACTTGCCGTCTATATCATGAAGAcAGATTCCTTTTCAAC AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT--------TGACGAATAGGTACTTGCCGTCTATATCATGAAGAGAGATTCCTTTTCAAC Template switch alignment (log-probability: -22.3) AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT|CAAGTACC|TACTTGCCGTCTATATCATGAAGAcAGATTCCTTTTCAAC AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT|CAAGTACC|TACTTGCCGTCTATATCATGAAGAGAGATTCCTTTTCAAC Gorilla > Chimp --------------- chr5:3149896-3149903 Template switch process: F1: L GAGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT 1 F3: 4 TACTTGCCGTCTATATCATGAAGACAGATTCCTTTTCAAC R RF: GAGTTCATATTAGTGACTACTGATTGATGATTATTTTTTATTGTTGAATAGGTACTTGCCGTCTATATCATGAAGAGAGATTCCTTTTCAAC RR: CTCAAGTATAATCACTGATGACTAACTACTAATAAAAAATAACAACTTATCCATGAACGGCAGATATAGTACTTCTCTCTAAGGAAAAGTTG F2: 3 CCATGAAC 2 Unidirectional alignment (log-probability: -38.2) AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT-----------caagtaccTACTTGCCGTCTATATCATGAAGAcAGATTCCTTTTCAAC AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTATTGTTGAATAGG--------TACTTGCCGTCTATATCATGAAGAGAGATTCCTTTTCAAC Template switch alignment (log-probability: -22.3) AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT|CAAGTACC|TACTTGCCGTCTATATCATGAAGAcAGATTCCTTTTCAAC AGTTCATATTAGTGACTACTGATTGATGATTATTTTTTAT|CAAGTACC|TACTTGCCGTCTATATCATGAAGAGAGATTCCTTTTCAAC ========== Event 2898 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATA--AAAAATGACATCATAAATAA Chimp: GGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATA--AAAAATGACATCATAAATAA ↓ 3 2 1 4 Gorilla: GGAGTAGGAGTAAAATGAAACATGCAATTTTACATTTTGCATGTAATAAAAATGACATCATAAATAA ↑ 3 2 1 4 Human: GGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATA--AAAAATGACATCATAAATAA Cluster: [ ] Orangutan: GGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATA--AAAAATGACATCATAAATAA Human > Gorilla --------------- chr17:65639400-65639407 Template switch process: F1: L CTTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT 1 F3: 4 AAT-AAAAATGACATCATAAATAACTGCAATTATGGAATCTGAG R RF: CTTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATAAAAAATGACATCATAAATAACTGCAATTATGGAATCTGAG RR: GAAAACCTCATCCTCATTTTACTTTGTACGTTAAAATGTAACTCCTTTATTTTTTACTGTAGTATTTATTGACGTTAATACCTTAGACTC F2: 3 TGTACGTT 2 Unidirectional alignment (log-probability: -36.9) TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT---------ttgcatgtaatAAAAATGACATCATAAATAACTGCAATTATGGAATCT TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATA-----------AAAAATGACATCATAAATAACTGCAATTATGGAATCT Template switch alignment (log-probability: -26.6) TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT|TTGCATGT|AAT-AAAAATGACATCATAAATAACTGCAATTATGGAATCT TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT|TTGCATGT|AATAAAAAATGACATCATAAATAACTGCAATTATGGAATCT Chimp > Gorilla --------------- chr17:65639400-65639407 Template switch process: F1: L CTTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT 1 F3: 4 AAT-AAAAATGACATCATAAATAACTGCAATTATGGAATCTGAG R RF: CTTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATAAAAAATGACATCATAAATAACTGCAATTATGGAATCTGAG RR: GAAAACCTCATCCTCATTTTACTTTGTACGTTAAAATGTAACTCCTTTATTTTTTACTGTAGTATTTATTGACGTTAATACCTTAGACTC F2: 3 TGTACGTT 2 Unidirectional alignment (log-probability: -36.9) TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT---------ttgcatgtaatAAAAATGACATCATAAATAACTGCAATTATGGAATCT TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATTGAGGAAATA-----------AAAAATGACATCATAAATAACTGCAATTATGGAATCT Template switch alignment (log-probability: -26.6) TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT|TTGCATGT|AAT-AAAAATGACATCATAAATAACTGCAATTATGGAATCT TTTTGGAGTAGGAGTAAAATGAAACATGCAATTTTACATT|TTGCATGT|AATAAAAAATGACATCATAAATAACTGCAATTATGGAATCT ========== Event 2899 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCTCCAAGGCAGCCTCCCCG------------------------------------------------------------------AGCTGCCTGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCTGAGGGTACCTGCAC Chimp: Ctctccaaggcagcctccccg-----agtctccaaggcagcctccccgagtctccaaggcagcctccccgagtctgcagcctccccgagctgcCTGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCTGAGGGTACCTGCAC Gorilla: CTCTCCAAGGCAGCCTCCCCGAGTC-----------------------------------------------------------------T-GCAGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCTGAGGGTACctgcac ↑ 1 4 3 2 Human: CTCTCCAAGGCAGCCTCCCCG------------------------------------------------------------------AGCTGCCTGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCTGAGGGTACCTGCAC Cluster: [ ] Orangutan: CTCTCCAAGGCAGCCTCCCCGAGT-C----------------------------------------------------------------TGCCTGCAAACAGGAGCCCCCATGGCAGCCATGTGCAGAGTACCTGAGGGTACCTACAC Human > Gorilla --------------- chr17:95578174-95578179 Template switch process: F1: L GTGCGTCTCCATGGAGGCCCCTCTCCAAGGCAGCCTCCCCGAG 1 F3: 4 GCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCT R RF: GTGAGTCTTCATGGAGGCCCCTCTCCAAGGCAGCCTCCCCGAGCTGCCTGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCT RR: CACTCAGAAGTACCTCCGGGGAGAGGTTCCGTCGGAGGGGCTCGACGGACGTTTGTCCTCGGGGGTACCGTCGGTGCACGTCTCATGGA F2: 3 ACGTCT 2 Unidirectional alignment (log-probability: -38.8) cGTCTcCATGGAGGCCCCTCTCCAAGGCAGCCTCCCCGAGtCTG-CaGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCT AGTCTTCATGGAGGCCCCTCTCCAAGGCAGCCTCCCCGAG-CTGCCTGCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCT Template switch alignment (log-probability: -27.6) cGTCTcCATGGAGGCCCCTCTCCAAGGCAGCCTCCCCGAG|TCTGCA|GCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCT AGTCTTCATGGAGGCCCCTCTCCAAGGCAGCCTCCCCGAG|TCTGCA|GCAAACAGGAGCCCCCATGGCAGCCACGTGCAGAGTACCT ========== Event 2900 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAGATATCTTGTAAATTCTGATTCCTTCATAGGAATCAGTTCTCGCTGTGTTCAAATTGTTTTAT ↑ 3 2 1 4 Chimp: CCAGATATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCACTGTGTTCAAATTGTTTTAT Gorilla: CCAGATATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCGCTGTGTTCAAATTGTTTTAT ↓ 3 2 1 4 Human: CCAGATATCTTGTAAATTCTGATTCCTTCATAGGAATCAGTTCTCGCTGTGTTCAAATTGTTTTAT Cluster: [ ] Orangutan: CCAGACATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCACTGTGTTCAAATTGTTTTAT Chimp > Human ------------- chr5:31583120-31583125 Template switch process: F1: L CTCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAG 1 F3: 4 GTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTGTACAGTGTG R RF: CTCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCACTGTGTTCAAATTGTTTTATATTTAGTTGTGTACAGTG RR: GAGACAGAGGTCTATAGAACATTTAAGACTAAGGAAGTATCATGAAACAAGAGTGACACAAGTTTAACAAAATATAAATCAACACATGTCAC F2: 3 ACTAAG 2 Unidirectional alignment (log-probability: -50.9) TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAGgAaTcaGTTCTCgCTGTGTTCAAATTGTTTTATATTTAGTTGTGta TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCACTGTGTTCAAATTGTTTTATATTTAGTTGTG-- Template switch alignment (log-probability: -32.2) TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAG|GAATCA|GTTCTCgCTGTGTTCAAATTGTTTTATATTTAGTTGTGTA TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAG|GAATCA|GTTCTCACTGTGTTCAAATTGTTTTATATTTAGTTGTGTA Gorilla > Human --------------- chr5:31583120-31583125 Template switch process: F1: L CTCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAG 1 F3: 4 GTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTGTA R RF: CTCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTGTA RR: GAGACAGAGGTCTATAGAACATTTAAGACTAAGGAAGTATCATGAAACAAGAGCGACACAAGTTTAACAAAATATAAATCAACACAT F2: 3 ACTAAG 2 Unidirectional alignment (log-probability: -32.9) TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAGgAaTcaGTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTGta TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAGTACTTTGTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTG-- Template switch alignment (log-probability: -16.5) TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAG|GAATCA|GTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTGTA TCTGTCTCCAGATATCTTGTAAATTCTGATTCCTTCATAG|GAATCA|GTTCTCGCTGTGTTCAAATTGTTTTATATTTAGTTGTGTA ========== Event 2901 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGTCAT-TTCTATGAAACATTTTTGTAATCACTAAGATTTTTAAAAAAACATATGTAAATAAACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAACCAGAAACATGTCAACTGACAAGCAATCT Chimp: ATGTCAT-TTCTATGGAACATTTCTGTAATCACTAAGATTTTTTAAAAAACATATGTAAATAAACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAACTAGAAACATGTCAACTGACAAGCAATCT ↓ 3 2 1 4 Gorilla: ATGTCAT-TTCTATGAAACATTTTTGTAATCACTAAGATTTTTTaaaa-aaaTATGTAAATAAACAACAGTGTATATATTGGGCTTAATCTCACTTTGAAACCAGAAATATGTCAACTGACAAGCAATCT Human: ATGTCAT-TTCTATGAAACATTTTTGTAATCACTAAGATTTTTAAAAAAACATATGTAAATAAACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAACCAGAAACATGTCAACTGACAAGCAATCT Cluster: [ ] Orangutan: ATGTCATTTTGTATGAAACATTTTTGTAATCACTAAGATTTTTTAAAAAACATATGTAAATAAACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAACCAGAAACATGTCAACTGACAAGCAATCT Chimp > Gorilla --------------- chr17:3479783-3479789 Template switch process: F1: L AAACAACAGTGTATATATTGGGCTTAATCTCACTTTGAAAC 1 F3: 4 ATGTCAACTGACAAGCAATCTTTTCCATCTCTGTTCTGAC R RF: ATTTCTGTAATCACTAAGATTTTTTAAAAAACATATGTAAATAAACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAACTAGAAACATGTCAACTGACAAGCAATCTTTTCTATCTCTGTTCTGAC RR: TAAAGACATTAGTGATTCTAAAAAATTTTTTGTATACATTTATTTGTTGTCACATGTATAACCCGAATTAGAGTGAAACTTTGATCTTTGTACAGTTGACTGTTCGTTAGAAAAGATAGAGACAAGACTG F2: 3 TAAAGAC 2 Unidirectional alignment (log-probability: -50) AACAACAGTGTAtATATTGGGCTTAATCTCACTTTGAAACcAGAAAtATGTCAACTGACAAGCAATCTTTTCcatctctgttctgac AACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAACTAGAAACATGTCAACTGACAAGCAATCTTTTCT-------------- Template switch alignment (log-probability: -27.7) AACAACAGTGTAtATATTGGGCTTAATCTCACTTTGAAAC|CAGAAAT|ATGTCAACTGACAAGCAATCTTTTCcATCTCTGTTCTGAC AACAACAGTGTACATATTGGGCTTAATCTCACTTTGAAAC|CAGAAAT|ATGTCAACTGACAAGCAATCTTTTCTATCTCTGTTCTGAC ========== Event 2902 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ATATACTTGCAAGCAAAAATAGTATTATAGTTACATTAGCCAAT-AAATAGTGAAATTACATATTAAAAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAATTAATACGAGAGGATATTAGTAAGAACAAC ↑ 3 2 1 4 Chimp: ATATACTTGCAAGCAAAAATAGTATTATAGTAACATTAGCCAAT-AAATAGTGAAATTACATATTAAAAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAAT-----ATTGAGGATATTAGTAAGAACAAC Gorilla: ATATACTTGCAAGCAAAAATAGTATTATAGTAACATTAGCCAAT-AAATAGTGAAATTACATATTAAAAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAATTAATACGAGAGGATATTAGTAACAACAAC Human: ATATACTTGCAAGCAAAAATAGTATTATAGTTACATTAGCCAAT-AAATAGTGAAATTACATATTAAAAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAATTAATACGAGAGGATATTAGTAAGAACAAC Cluster: [ ] Orangutan: ACATACCTGCAAGCAAAAATGGTATTATAGTAATATTAGCCAATAAAATAGTGAAATTACATATTAAAAATCATTGTGAATGCAGATGATTGAGGAAGGCTGTTAATTAATATGAGAGGAAATTAGTAAGAACAAC Chimp > Human ------------- chr5:32404757-32404764 Template switch process: F1: L AAAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAAT 1 F3: 4 GAGGATATTAGTAAGAACAACTGGACAGTTTTGTGAGTAG R RF: TAGTATTATAGTAACATTAGCCAATAAATAGTGAAATTACATATTAAAAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAATATTGAGGATATTAGTAAGAACAACTGGACAGTTTTGTGAGTAG RR: ATCATAATATCATTGTAATCGGTTATTTATCACTTTAATGTATAATTTTTAGTAACACTTACGTGTACTAACTCCTTCCGACAATTATAACTCCTATAATCATTCTTGTTGACCTGTCAAAACACTCATC F2: 3 AGCATAAT 2 Unidirectional alignment (log-probability: -31.3) AAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAATtaatacgA--GAGGATATTAGTAAGAACAACTGGACAGTTTTGTGAGTAG AAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAAT-------ATTGAGGATATTAGTAAGAACAACTGGACAGTTTTGTGAGTAG Template switch alignment (log-probability: -22.3) AAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAAT|TAATACgA|GAGGATATTAGTAAGAACAACTGGACAGTTTTGTGAGTAG AAATCATTGTGAATGCACATGATTGAGGAAGGCTGTTAAT|TAATACTA|GAGGATATTAGTAAGAACAACTGGACAGTTTTGTGAGTAG ========== Event 2903 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ATCAACAACACGTGGTCTCTGCATGGGACAGTGAGGTCAGGTAGAGAGATGTTAGTCACTTTAGTCAAAGTGAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCT--------CCCCATGAATCACTGTGGGTCAGAGGCTTGTGtttaaa Chimp: ATCAACAACACGTGGTCTCTGCATGGGACAGTGAGGTCAGGTAGAGAGATGTTAGTCACTTTAGTCAAAGTGAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCT--------CCCCATGAATCACTGTGCGTCAGAGGCTTGTGTTTaaa ↑ 3 2 14 Gorilla: ATCAACAACAGGTGGTCTCTACATGGGACAGTGAGGTCAGGTAGAGAGATGTTAGTCACTTTAGTCAAAGTGAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCT----------------CTCACTGTGTGTCAGAGGCTTGTGTTTaaa Human: ATCAACAACACGTGGTCTCTGCATGGGACAGTGAGGTCAGGTAGAGAGATGTTAGTCACTTTAGTCAAAGTGAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCT--------CCCCATGAATCACTGTGGGTCAGAGGCTTGTGtttaaa Cluster: [ ] Orangutan: ATCAACAACAGGTGGTCTCTACATGGAACAGTGAGGTCAGGTAGAGAGATGTTAGTCACTTCAGTCAAAGTGAAGTGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTCCCCATGA--------ATCACTGTGTGTCAGAGGCTTGTGTTTTaa Gorilla > Chimp --------------- chr5:99659467-99659474 Template switch process: F1: L GTGAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTC 1 F3: 4 TCACTGTGCGTCAGAGGCTTGTGTTTAAAAAAAAAAAAAAAAAAAA R RF: TACATGGGACAGTGAGGTCAGGTAGAGAGATGTTAGTCACTTTAGTCAAAGTGAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTCTCACTGTGTGTCAGAGGCTTGTGTTTAAAAAAAAAAAAAAAAAAAA RR: ATGTACCCTGTCACTCCAGTCCATCTCTCTACAATCAGTGAAATCAGTTTCACTTCCCTTCAATGGTCATCGTACCTCGAGAGATTCGAGAGAGTGACACACAGTCTCCGAACACAAATTTTTTTTTTTTTTTTTTTT F2: 3 AAGTACCC 2 Unidirectional alignment (log-probability: -39) GAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTCcccatgaaTCACTGTGcGTCAGAGGCTTGTGTTTAAAAAAAAAAAAAA GAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTC--------TCACTGTGTGTCAGAGGCTTGTGTTTAAAAAAAAAAAAAA Template switch alignment (log-probability: -28) GAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTC|CCCATGaA|TCACTGTGcGTCAGAGGCTTGTGTTTAAAAAAAAAAAAAA GAAGGGAAGTTACCAGTAGCATGGAGCTCTCTAAGCTCTC|CCCATGTA|TCACTGTGTGTCAGAGGCTTGTGTTTAAAAAAAAAAAAAA ========== Event 2904 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: cttggcctcccaaagtgctgggattacaagcgtgagtcaccatgcccCACCTGAAGC--------CAGACTTTTGAACTTACTCACTTCTAATCGTGTTTCTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATTTGTGAAATAACATGAAATCCTTCT---CCACgccgggcgcggtggctcacgcctgtaatccctgcattttgggaggccaaggcgggcggatcacgaggtcaggagatcgagaccatcctgtctaacacggtgaaaccccgtctctactaaaaatataaaaaattagccgggcgtg Chimp: -ttg-gctcccaaagtgctgggattacaagcgtgagtcaccatgcccCACCCGAAGC--------CAGACTTTTGAACTTACTCACTTATAATCATGTTTCTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCTTTGTGAAATAACATGAAATTCT---TCTCCACgccgggcgcggtggctcacg-ctgtaatc-ccacattttgggaggccaaggcgggcggatcacgaggtcaggagatcgagaccatcctgtctaacacggtgaaaccccgtctctactaaaaatacaa-aatttagccgggcgtg ↑ 3 2 1 4 Gorilla: cttggcctcccaaggtgctgggattacaagcgtgagtcaccatgtccCACCCGAAGC--------CAGACTTCTGAACTTACTCACTTATAATCATGTTTCTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCTTTGTGAAATAACATGAAATTCTTCT---CCACgccgggcgcggtggctcacgcctgtaatccccgcattttgggaagccaaggcaggcggatcacgaggtcaggagatcgagaccatcctgtctaacacggtgaaaccccgtctctactaaaaatacaaaaaattagccaggtgtg Human: cttggcctcccaaagtgctgggattacaagcgtgagtcaccatgcccCACCTGAAGC--------CAGACTTTTGAACTTACTCACTTCTAATCGTGTTTCTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATTTGTGAAATAACATGAAATCCTTCT---CCACgccgggcgcggtggctcacgcctgtaatccctgcattttgggaggccaaggcgggcggatcacgaggtcaggagatcgagaccatcctgtctaacacggtgaaaccccgtctctactaaaaatataaaaaattagccgggcgtg Cluster: [ ] Orangutan: cttggcctcccaaagtgctgggattacaagcgtgagccaccacgA-TGAC-------CGTTTTATATCACTTTTGTTTCTTCACGCTTAGATTACTGTTGTTGCCGTTTATTATGTTGTTGTGAGTCCCACATACACCTTCTTTCGTGGGGAAGGAGCGCATAAGTTAATTTTCTTTTCATCGCAAACACCGACACCTGTTTTCAAGTTACGGAAGTTCTAGAAACTCCCTGTCGAAATGTTCATCAAGTGCGGACTTTAAATCCCTGTCGTGGTGTTAGCTCTCATCAAAGAGATATTATAATGGTGAGGTTCTGTCTGGGTTGTATGCAGCATGTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr5:100156930-100156938 Template switch process: F1: L TAATCATGTTTCTCCCTCTTTGTGAAATAACATGAAATTCTTCTCCACGCCGGGCGCGGTGGCTCACGC 1 F3: 4 ACAT R RF: GGGATTACAAGCGTGAGTCACCATGTCCCACCCGAAGCCAGACTTCTGAACTTACTCACTTATAATCATGTTTCTCCCTCTTTGTGAAATAACATGAAATTCTTCTCCACGCCGGGCGCGGTGGCTCACGC RR: CCCTAATGTTCGCACTCAGTGGTACAGGGTGGGCTTCGGTCTGAAGACTTGAATGAGTGAATATTAGTACAAAGAGGGAGAAACACTTTATTGTACTTTAAGAAGAGGTGCGGCCCGCGCCACCGAGTGCG F2: 3 CCCTAATGT 2 Unidirectional alignment (log-probability: -26.3) ACATGAAATTCTTCTCCACGCCGGGCGCGGTGGCTCACG-CTGTAAT-CCCaCAT ACATGAAATTCTTCTCCACGCCGGGCGCGGTGGCTCACGCCTGTAATCCCCGCAT Template switch alignment (log-probability: -16.7) ACATGAAATTCTTCTCCACGCCGGGCGCGGTGGCTCACGC|TGTAATCCC|ACAT ACATGAAATTCTTCTCCACGCCGGGCGCGGTGGCTCACGC|TGTAATCCC|ACAT ========== Event 2905 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTCAAATTTGAGATCCTAGCTTTGATTTATATCA-AAGCCACTGACCTGTCTTCCAGTTT Chimp: TTTCAAATTTGAGATCCTAGCTTTGATTTATATCTGATACCACTGACCTGTCTTCCAGTTT Gorilla: TTTCAAATTTGAGATCCTAGCTTTGATTTATACCTGATACCACTGACCTGTCTTCCAGTTT ↓ 3 2 1 4 Human: TTTCAAATTTGAGATCCTAGCTTTGATTTATATCA-AAGCCACTGACCTGTCTTCCAGTTT Cluster: [ ] Orangutan: TTTCAAATATGAGATCCTAGCTTTGATTTATATCTGATACCACTGACTTGTCTTCCAGTTT Gorilla > Human --------------- chr5:147708206-147708212 Template switch process: F1: L TCTACCTCATTTCAAATTTGAGATCCTAGCTTTGATTTATA 1 F3: 4 CACTGACCTGTCTTCCAGTTTGGGCTGTCTGGCCTCCCT R RF: TCTACCTTATTTCAAATTTGAGATCCTAGCTTTGATTTATACCTGATACCACTGACCTGTCTTCCAGTTTGGGCTGTCTGGCCTCCCT RR: AGATGGAATAAAGTTTAAACTCTAGGATCGAAACTAAATATGGACTATGGTGACTGGACAGAAGGTCAAACCCGACAGACCGGAGGGA F2: 3 CGAAACT 2 Unidirectional alignment (log-probability: -35.1) CTACCTcATTTCAAATTTGAGATCCTAGCTTTGATTT-------ATAtcaaagCCACTGACCTGTCTTCCAGTTTGGGCTGTCTGGCCTCCCT CTACCTTATTTCAAATTTGAGATCCTAGCTTTGATTTATACCTGATA------CCACTGACCTGTCTTCCAGTTTGGGCTGTCTGGCCTCCCT Template switch alignment (log-probability: -22.1) CTACCTcATTTCAAATTTGAGATCCTAGCTTTGATTTATA|TCAAAGC|CACTGACCTGTCTTCCAGTTTGGGCTGTCTGGCCTCCCT CTACCTTATTTCAAATTTGAGATCCTAGCTTTGATTTATA|TCAAAGC|CACTGACCTGTCTTCCAGTTTGGGCTGTCTGGCCTCCCT ========== Event 2906 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTC------TGCTCATCAGTGAATTGTATACACTGATACTTCCCACATCTTCCAACACATGTATACAAGGAATTGCCAACATTCTTCTTATGGGGCT Chimp: TTC------TGCTCATCAGTGGGCAAT---------------------------AGCCATGTATACAAGGAATTGCCAACATTCTTCTTATGGGGCT Gorilla: TTC------TGCTCATCAGTGGGCAAT---------------------------AACCATGTATACAAGGAATTGCCAACATTCTTCTTATGGGGCT ↑ 1 4 3 2 Human: TTC------TGCTCATCAGTGAATTGTATACACTGATACTTCCCACATCTTCCAACACATGTATACAAGGAATTGCCAACATTCTTCTTATGGGGCT Cluster: [ ] Orangutan: TTACTAAGAGATACATCAGTGGGCAAT---------------------------AACCATGTATACAAGGAATTGCCAACATTCTTCTTATGGAGCG Human > Gorilla --------------- chr17:35837807-35837812 Template switch process: F1: L TGAGGATATAACTGGATACCTGTTCATTCTGCTCATCAGTG 1 F3: 4 AAC-CATGTATACAAGGAATTGCCAACATTCTTCTTATGGGGCT R RF: TGAGGATATAACTGGATACCTGTTCATTCTGCTCATCAGTGAATTGTATACACTGATACTTCCCACATCTTCCAACACATGTATACAAGGAATTGCCAACATTCTTCTTATGGGGCT RR: ACTCCTATATTGACCTATGGACAAGTAAGACGAGTAGTCACTTAACATATGTGACTATGAAGGGTGTAGAAGGTTGTGTACATATGTTCCTTAACGGTTGTAAGAAGAATACCCCGA F2: 3 TAACGG 2 Unidirectional alignment (log-probability: -35.4) GAGGATATAACTGGATACCTGTTCATTCTGCTCATCAGTG------------------------------------ggcaataacCATGTATACAAGGAATTGCCAACATTCTTCTTATGGG GAGGATATAACTGGATACCTGTTCATTCTGCTCATCAGTGAATTGTATACACTGATACTTCCCACATCTTCCAACA---------CATGTATACAAGGAATTGCCAACATTCTTCTTATGGG Template switch alignment (log-probability: -26.4) GAGGATATAACTGGATACCTGTTCATTCTGCTCATCAGTG|GGCAAT|AAC-CATGTATACAAGGAATTGCCAACATTCTTCTTATGGG GAGGATATAACTGGATACCTGTTCATTCTGCTCATCAGTG|GGCAAT|AACACATGTATACAAGGAATTGCCAACATTCTTCTTATGGG ========== Event 2907 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGACTCAGTTTTCCTAACTCCAGAAAT-------------------------GGACCTACCATTAGGGTCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCTTTTTAGCTCTTGCAAACTCAGTTCCTGGATAATCAAGCAAGGCCCAATCCAacatttgaactttagactatcatacatatgacatgcacaaattgtaagtacagtcatgtgccacat Chimp: TTGACTCAGTTTTCCTAACTCCAGAAAT-------------------------GGACCTACCATTAGGGTCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCTTTTTAGCTCTTGCAAACTCAGTTCCTGGATAATCAAGCAAGGCCCAATCCAacatttgaactttagactatcatacatatgacatgcacaaattgtaagtacagtcatgtgccacat ↑ 4 1 3 2 Gorilla: TTGACTCAGTTTTCCTAACTCCAGAAAT--------------------------------------------------GGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCTTTTTAGCTCTTGCAAACTCAGTTCCTGGATAATCAAGCAAGGCCCAATCCAacatttgaattttagactatcatacatatgacatgcacaaattgtaagtacagtcatgtgccacat Human: TTGACTCAGTTTTCCTAACTCCAGAAAT-------------------------GGACCTACCATTAGGGTCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCTTTTTAGCTCTTGCAAACTCAGTTCCTGGATAATCAAGCAAGGCCCAATCCAacatttgaactttagactatcatacatatgacatgcacaaattgtaagtacagtcatgtgccacat Cluster: [ ] Orangutan: TTGACTCAGTTTTCCTAACTCCAGAAATGGACCTACCATTAGGGTCCAGAAAT-------------------------GGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCTTTTTAGCTCTTGCAAACTCAGTTCCTGGATAATCAAGCAAGGCCCAATCCAACATTTGAATTTTAGACTATCGTACATATGACAtgcacaaattgtaagtacagtcatgtgccacat Gorilla > Chimp --------------- chr5:102632574-102632584 Template switch process: F1: L TCTACTCAGGTTTTTGACTCAGTTTTCCTAACTCCAGAAATGGACC 1 F3: 4 TCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCT R RF: TCTACTCAGGTTTTTGACTCAGTTTTCCTAACTCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTCTGAGGTTCTTTTTAGCTCTTGCAAACTCAGTTCCTGGATAATCAAGCAAGGCCCAATCCAACATTTGAATTTTAGACTATCATACATATGACATGCACAAATTGTA RR: AGATGAGTCCAAAAACTGAGTCAAAAGGATTGAGGTCTTTACCTGGGACGGTAGGGACAATCCGTCCCTAAGACTCCAAGAAAAATCGAGAACGTTTGAGTCAAGGACCTATTAGTTCGTTCCGGGTTAGGTTGTAAACTTAAAATCTGATAGTATGTATACTGTACGTGTTTAACAT F2: 3 GGGATTACCAT 2 Unidirectional alignment (log-probability: -46.8) CAGGTTTTTGACTCAGTTTTCCTAACTCCAGAAatggacctaccattagggtccagaaATGGACCCTGCCATCCCTGTTAGGCAGGGATTC CAGGTTTTTGACTCAGTTTTCCTAACTCCAGAA-------------------------ATGGACCCTGCCATCCCTGTTAGGCAGGGATTC Template switch alignment (log-probability: -34) CAGGTTTTTGACTCAGTTTTCCTAACTCCAGAAATGGACC|TACcATTaGgG|TCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTC CAGGTTTTTGACTCAGTTTTCCTAACTCCAGAAATGGACC|TACAATTTGTG|TCCAGAAATGGACCCTGCCATCCCTGTTAGGCAGGGATTC ========== Event 2908 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGGAGCCTGGGTTTTCATCTAAAAGCTGGCTTTTAGATGTCTGGTCAATGGCATGTC ↑ 3 1 2 4 Chimp: CTGGAGCCTGGGTTTTCATCTAAAAGCCAGG-CTGAAATGTCTGGTCAATGGCATGTC Gorilla: CTGGAGCCTGGGTTTTCATCTAAAAGCCAGG-CTGAAATGTCTGGTCAATGGCATGTC ↓ 3 1 2 4 Human: CTGGAGCCTGGGTTTTCATCTAAAAGCTGGCTTTTAGATGTCTGGTCAATGGCATGTC Cluster: [ ] Orangutan: CTGGAGCCTGGGTTTTCATCTAAAAGCCAGG-CTGAAATGTCTGGTCAATGGCATGTC Chimp > Human ------------- chr5:34719728-34719737 Template switch process: F1: L CTTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC 1 F3: 4 ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT R RF: CTTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGCCAGGCTGAAATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT RR: GAAGATCGAAACTTGACCTCGGACCCAAAAGTAGATTTTCGGTCCGACTTTACAGACCAGTTACCGTACAGTCATTGACTTGAGACGCGA F2: 3 GATTTTCGGT 2 Unidirectional alignment (log-probability: -36) TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC---------tggcttttagATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGCCAGGCTGAA----------ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT Template switch alignment (log-probability: -16.5) TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC|TGGCTTTTAG|ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC|TGGCTTTTAG|ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT Gorilla > Human --------------- chr5:34719728-34719737 Template switch process: F1: L CTTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC 1 F3: 4 ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT R RF: CTTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGCCAGGCTGAAATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT RR: GAAGATCGAAACTTGACCTCGGACCCAAAAGTAGATTTTCGGTCCGACTTTACAGACCAGTTACCGTACAGTCATTGACTTGAGACGCGA F2: 3 GATTTTCGGT 2 Unidirectional alignment (log-probability: -35.1) TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAA-----GCTGgcttttAgATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGCCAGGCTG------AAATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT Template switch alignment (log-probability: -17) TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC|TGGCTTTTAG|ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT TTCTAGCTTTGAACTGGAGCCTGGGTTTTCATCTAAAAGC|TGGCTTTTAG|ATGTCTGGTCAATGGCATGTCAGTAACTGAACTCTGCGCT ========== Event 2909 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GTTCTAGAAACT---CCTACTCAATAATACAATAAGTGTATTGTACTTATTACCAAACTCAATAATACAATAAGTGAAGCTCTTTTAAATAGTCTC Chimp: GTTCTAGAAACT---CCTACTCAATAATACAATAAGTGTATTGTACTTATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTAAATAGTCTC ↑ 4 3 2 1 Gorilla: GTTCTAGAAACT---CCTACTGTGTAA--------------------TATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTAAATAGTCTC Human: GTTCTAGAAACT---CCTACTCAATAATACAATAAGTGTATTGTACTTATTACCAAACTCAATAATACAATAAGTGAAGCTCTTTTAAATAGTCTC Cluster: [ ] Orangutan: GTTCTAGAAACTCCTCCTACTCTGTAA--------------------TATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTAAATAGTCTC Gorilla > Chimp --------------- chr5:104367953-104367961 Template switch process: F1: L GTGTCTTGCAATAATCTGTCCATGTTCTAGAAACTCCT------------------ACTCAATAATACAATAAGTG 1 F3: 4 TATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTA R RF: GTGTCTTGCAATAATCTGTCCATGTTCTAGAAACTCCTACTGTGTAATATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTA RR: CACAGAACGTTATTAGACAGGTACAAGATCTTTGAGGATGACACATTATAATGGTTTGAGTTATTATGTTATTCACTTAGAGAAAAT F2: 3 TCATGTTAT 2 Unidirectional alignment (log-probability: -55) TCCATGTTCTAGAAACTCCTACTcaataatacaataaGTGTAttgtactTATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTA TCCATGTTCTAGAAACTCCTACT--------------GTGTA------ATATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTA Template switch alignment (log-probability: -33.5) TCCATGTTCTAGAAACTCCT------------------ACTCAATAATACAATAAGTG|TATTGTAcT|TATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTA TCCATGTTCTAGAAACTCCTACTGTGTAATATTACCAAACTCAATAATACAATAAGTG|TATTGTATT|TATTACCAAACTCAATAATACAATAAGTGAATCTCTTTTA ========== Event 2910 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTCTATTGTAACTTGCATGTTTTACGTATCATTATGTATGATACGTAAAAACCATACACACATTACGTATA ↑ 3 2 14 Chimp: GTCTATTGTAACTTGCATGTTTTACGTATCATTATGTA-----------TACCATACACACATTACGTATA Gorilla: GTCTATTGTAACTTGCATGTTTTACATATCATTATGTA-----------TACCATACACACATTACGTATA Human: GTCTATTGTAACTTGCATGTTTTACGTATCATTATGTATGATACGTAAAAACCATACACACATTACGTATA Cluster: [ ] Orangutan: Chimp > Human ------------- chr5:145082136-145082146 Template switch process: F1: L GTGGTCTATTGTAACTTGCATGTTTTACGTATCATTATGTAT 1 F3: 4 ACCATACACACATTACGTATACTATATATTGTATTCATGC R RF: GTGGTCTATTGTAACTTGCATGTTTTACGTATCATTATGTATACCATACACACATTACGTATACTATATATTGTATTCATGC RR: CACCAGATAACATTGAACGTACAAAATGCATAGTAATACATATGGTATGTGTGTAATGCATATGATATATAACATAAGTACG F2: 3 AAAATGCATAG 2 Unidirectional alignment (log-probability: -26.8) GGTCTATTGTAACTTGCATGTTTTACGTATCATTATGTATgatacgtaaaaACCATACACACATTACGTATACTATATATTGTATTCATGC GGTCTATTGTAACTTGCATGTTTTACGTATCATTATGTAT-----------ACCATACACACATTACGTATACTATATATTGTATTCATGC Template switch alignment (log-probability: -16.7) GGTCTATTGTAACTTGCATGTTTTACGTATCATTATGTAT|GATACGTAAAA|ACCATACACACATTACGTATACTATATATTGTATTCATGC GGTCTATTGTAACTTGCATGTTTTACGTATCATTATGTAT|GATACGTAAAA|ACCATACACACATTACGTATACTATATATTGTATTCATGC ========== Event 2911 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGATGC----AGTCAACGTGCAGATTGATCTTT ↑ 3 2 1 4 Chimp: CTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACCC--ACGTTCAACGTGCAGATTGATCTTT Gorilla: CTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACCCAC--GTTCAACGTGCAGATTGATCTTT ↓ 3 2 1 4 Human: CTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGATGC----AGTCAACGTGCAGATTGATCTTT Cluster: [ ] Orangutan: CTGCAACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACTCAC--GTTCAAAGTGCAGATTGATCTTT Chimp > Human ------------- chr5:3731522-3731526 Template switch process: F1: L AGCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA 1 F3: 4 TCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA R RF: AGCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACCCACGTTCAACGTGCAGATTGATCTTTATTGATCTTTAGATATTCA RR: TCGACGCTGAGGAACCTTGAAGACGTAGGGTCAGTACCTCTGGGTGCAAGTTGCACGTCTAACTAGAAATAACTAGAAATCTATAAGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -33.2) GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA------TgcagTCAACGTGCAGATTGATCTTTATTGATCTTTAaATATTCA GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACCCACGT----TCAACGTGCAGATTGATCTTTATTGATCTTTAGATATTCA Template switch alignment (log-probability: -21.9) GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA|TGCAG|TCAACGTGCAGATTGATCTTTATTGATCTTTAaATATTCA GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA|TGCAG|TCAACGTGCAGATTGATCTTTATTGATCTTTAGATATTCA Gorilla > Human --------------- chr5:3731522-3731526 Template switch process: F1: L AGCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA 1 F3: 4 TCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA R RF: AGCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACCCACGTTCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA RR: TCGACGCTGAGGAACCTTGAAGACGTAGGGTCAGTACCTCTGGGTGCAAGTTGCACGTCTAACTAGAAATAACTAGAAATTTATAAGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -26.7) GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA------TgcagTCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGACCCACGT----TCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA Template switch alignment (log-probability: -16.4) GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA|TGCAG|TCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA GCTGCGACTCCTTGGAACTTCTGCATCCCAGTCATGGAGA|TGCAG|TCAACGTGCAGATTGATCTTTATTGATCTTTAAATATTCA ========== Event 2912 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: aaccatatcaCTCTCCCAGTGT------------------CTTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTT ↓ 4 3 12 Chimp: aaccatatcaCTCTCCCAGTGCTCTAGCAGATTCTGCTAGATTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTT ↑ 4 3 12 Gorilla: aaccatatcaCTCTCCCAGTGT------------------CTTCCTCTAGCAGAAATCCCTGGGACAGCACCCTT Human: aaccatatcaCTCTCCCAGTGT------------------CTTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTT Cluster: [ ] Orangutan: aaccatatcactctcccagtgt------------------cttcctctagcagaaatccctggggcaggaccctt Human > Chimp ------------- chr5:3926983-3926992 Template switch process: F1: L CTTGGGTTGGGTTACAGCCAAACCATATCACTCTCCCAGTG-----CTCTAGCAGA 1 F3: 4 TTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC R RF: CTTGGGTTGGGTTACAGCCAAACCATATCACTCTCCCAGTGTCTTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC RR: GAACCCAACCCAATGTCGGTTTGGTATAGTGAGAGGGTCACAGAAGGAGATCGTCTTTAGGGACCCCGTCGTGGGAACAGACG F2: 3 AGATCGTCTT 2 Unidirectional alignment (log-probability: -47) TTACAGCCAAACCATATCACTCTCCCAGTGctctagcagatTCTgctagatTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC TTACAGCCAAACCATATCACTCTCCCAGTG-----------TCT-------TCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC Template switch alignment (log-probability: -27.2) TTACAGCCAAACCATATCACTCTCCCAGTG-----CTCTAGCAGA|TTCTGCTAGA|TTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC TTACAGCCAAACCATATCACTCTCCCAGTGTCTTCCTCTAGCAGA|TTCTGCTAGA|TTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC Gorilla > Chimp --------------- chr5:3926983-3926992 Template switch process: F1: L CTTGGGTTGGGTTACAGCCAAACCATATCACTCTCCCAGTG-----CTCTAGCAGA 1 F3: 4 TTCCTCTAGCAGAAATCCCTGGGGCAGCACCCTTGTCTGC R RF: CTTGGGTTGGGTTACAGCCAAACCATATCACTCTCCCAGTGTCTTCCTCTAGCAGAAATCCCTGGGACAGCACCCTTGTCTGC RR: GAACCCAACCCAATGTCGGTTTGGTATAGTGAGAGGGTCACAGAAGGAGATCGTCTTTAGGGACCCTGTCGTGGGAACAGACG F2: 3 AGATCGTCTT 2 Unidirectional alignment (log-probability: -52.1) TTACAGCCAAACCATATCACTCTCCCAGTGctctagcagatTCtgctagaTTCCTCTAGCAGAAATCCCTGGGgCAGCACCCTTGTCTGC TTACAGCCAAACCATATCACTCTCCCAGTG-----------TC-------TTCCTCTAGCAGAAATCCCTGGGACAGCACCCTTGTCTGC Template switch alignment (log-probability: -32.8) TTACAGCCAAACCATATCACTCTCCCAGTG-----CTCTAGCAGA|TTCTGCTAGA|TTCCTCTAGCAGAAATCCCTGGGgCAGCACCCTTGTCTGC TTACAGCCAAACCATATCACTCTCCCAGTGTCTTCCTCTAGCAGA|TTCTGCTAGA|TTCCTCTAGCAGAAATCCCTGGGACAGCACCCTTGTCTGC ========== Event 2913 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGAGCCCATATGTCGCAGTCTC------------AAGATTCACTGTATGCCAATTTATTAATCAG ↓ 314 2 Chimp: AAGAGCCCATATGTCGCAGTCTCACAGTGAATCTTGGGATTCACTGTATGCCAATTTATTAATCAG ↑ 3 1 4 2 Gorilla: AAGAGCCCATATGTCGCAGTCCC------------AAGATTCACTGTATGCCAATTTATTAATCAG Human: AAGAGCCCATATGTCGCAGTCTC------------AAGATTCACTGTATGCCAATTTATTAATCAG Cluster: [ ] Orangutan: AAGATCCCATATGTTGCAGTCCC------------AAGATTCACCGTGTGCTAATTTATTAATCAG Human > Chimp ------------- chr5:76303720-76303731 Template switch process: F1: L CCTTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCA 1 F3: 4 GGATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG R RF: CCTTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCAAGATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG RR: GGAAACGTCTGAAGGGATTTCTCGGGTATACAGCGTCAGAGTTCTAAGTGACATACGGTTAAATAATTAGTCTATTGTTAGTC F2: 3 GTTCTAAGTGAC 2 Unidirectional alignment (log-probability: -34.2) TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCAcagtgaatcttggGATTCACTGTATGCCAATTTATTAATCAGATAACAATCA TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCA------------AGATTCACTGTATGCCAATTTATTAATCAGATAACAATCA Template switch alignment (log-probability: -22.8) TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCA|CAGTGAATCTTG|gGATTCACTGTATGCCAATTTATTAATCAGATAACAATCA TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCA|CAGTGAATCTTG|AGATTCACTGTATGCCAATTTATTAATCAGATAACAATCA Gorilla > Chimp --------------- chr5:76303720-76303732 Template switch process: F1: L GCCCTTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCTCA 1 F3: 4 GATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG R RF: GCCCTTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCCCAAGATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG RR: CGGGAAACGTCTGAAGGGATTTCTCGGGTATACAGCGTCAGGGTTCTAAGTGACATACGGTTAAATAATTAGTCTATTGTTAGTC F2: 3 GGTTCTAAGTGAC 2 Unidirectional alignment (log-probability: -39.2) TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCtCAcagtgaatcttggGATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCCCA------------AGATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG Template switch alignment (log-probability: -23) TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCtCA|CAGTGAATCTTGG|GATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG TTTGCAGACTTCCCTAAAGAGCCCATATGTCGCAGTCCCA|CAGTGAATCTTGG|GATTCACTGTATGCCAATTTATTAATCAGATAACAATCAG ========== Event 2914 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CAAGAAAACACAGGAAAAGCTGAATCTTCCTGTATAGACGAACTACGCAGGATATGTAAAATATTATTTATCTTACTATAGTACAGGTAAAGATGTTTTAAATATCATACTCTTTTA-----TT---CAGTCCTTTGGGGGTCTCACAACC Chimp: CAAGAAAACACAGGAAAAGCTGAATCTTCCTGTATAGACGAACTACGCAGGATATGTAAAATATTATTTATCTTACTATAGTACAGGTAAAGATGTTTTAAATATCATACTCTTTTA-----TT---TAGTCCTTTGGGGGTCTCACAACC Gorilla: CAAGAAAACACAGGAAAAGCTGAATCTTCCTGTATACACGAACTACGCAGGATATGTAAAATATTATTTATCTTGCTATAGTACCGGTAAAGATGTTTTAAATATCATACTCTTTTATGATATTTAAAAATCCTTTGGGGGTCTCACAACC ↓ 3 2 1 4 Human: CAAGAAAACACAGGAAAAGCTGAATCTTCCTGTATAGACGAACTACGCAGGATATGTAAAATATTATTTATCTTACTATAGTACAGGTAAAGATGTTTTAAATATCATACTCTTTTA-----TT---CAGTCCTTTGGGGGTCTCACAACC Cluster: [ ] Orangutan: CAAGAAAACACAGGAAAAGCTGAATCTTCCTGTATAGATGAACTACGCAGGATATGTAAAATATTATTTATCTTACTACAGTACAGGTAAAGATGTTTTAAATATCATACTCTTTTA-----TT---TAGTCCTTTGGGGGTCTCTCAACC Gorilla > Human --------------- chr5:143824196-143824199 Template switch process: F1: L TATAGTACAGGTAAAGATGTTTTAAATATCATACTCTTTTAT 1 F3: 4 TCCTTTGGGGGTCTCACAACCCATCCTCCTACAAGACCAC R RF: CTGAATCTTCCTGTATACACGAACTACGCAGGATATGTAAAATATTATTTATCTTGCTATAGTACCGGTAAAGATGTTTTAAATATCATACTCTTTTATGATATTTAAAAATCCTTTGGGGGTCTCACAACCCATCCTCATACAAGACCAC RR: GACTTAGAAGGACATATGTGCTTGATGCGTCCTATACATTTTATAATAAATAGAACGATATCATGGCCATTTCTACAAAATTTATAGTATGAGAAAATACTATAAATTTTTAGGAAACCCCCAGAGTGTTGGGTAGGAGTATGTTCTGGTG F2: 3 GACT 2 Unidirectional alignment (log-probability: -36.6) TAGTACaGGTAAAGATGTTTTAAATATCATACTCTTTTATtcaG-----------TCCTTTGGGGGTCTCACAACCCATCCTCcTACAAGACCAC TAGTACCGGTAAAGATGTTTTAAATATCATACTCTTTTAT---GATATTTAAAAATCCTTTGGGGGTCTCACAACCCATCCTCATACAAGACCAC Template switch alignment (log-probability: -27.3) TAGTACaGGTAAAGATGTTTTAAATATCATACTCTTTTAT|TCAG|TCCTTTGGGGGTCTCACAACCCATCCTCcTACAAGACCAC TAGTACCGGTAAAGATGTTTTAAATATCATACTCTTTTAT|TCAG|TCCTTTGGGGGTCTCACAACCCATCCTCATACAAGACCAC ========== Event 2915 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGATAGTAAAAAAATAATACCCAGAAACACTTCAAAGTGTTAATCAAATACTTAAAAGTCTAAATGTAAGTAATTTATAATAACACTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAA-AGTTTC--TGAGAGGAATATAGTATTTATAATA Chimp: AGGTAGTaaaaaaaTAATACCCAGAAACACTTCAAAGTGTTAATCAAATACTTAAAAGTCTAAATGTAAGTAATTTATAATAACACTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAGTAAGAGCAGATAAAA-AGTTTC--TGAGAGGAATATAGTATTTATAATA ↑ 3 2 1 4 Gorilla: AGGTAGTaaaaaaaTAATACCCAGAAACACTTCAAAGTGTTAATCAAACACTTAAAAATCTAAATGTAAGTAATTTATAATAACACTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAATGTTTT----TTAGGAATATAGTATTTATAATA ↓ 3 2 1 4 Human: AGATAGTAAAAAAATAATACCCAGAAACACTTCAAAGTGTTAATCAAATACTTAAAAGTCTAAATGTAAGTAATTTATAATAACACTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAA-AGTTTC--TGAGAGGAATATAGTATTTATAATA Cluster: [ ] Orangutan: AGGTAGTAAAAAAATAATACCCAGAAACACTTCAAAGTGTTAATCAAATACTTAAAAATCTAAATGTAAGTAATTTATAATAACATTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAA-AGTTTCTG--AAAGGAATATACTATTTATAATA Gorilla > Human --------------- chr5:37200729-37200737 Template switch process: F1: L CTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAA 1 F3: 4 AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA R RF: CCCAGAAACACTTCAAAGTGTTAATCAAACACTTAAAAATCTAAATGTAAGTAATTTATAATAACACTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAATGTTTTTTAGGAATATAGTATTTATAATATAGAACTATCAATTGAATA RR: GGGTCTTTGTGAAGTTTCACAATTAGTTTGTGAATTTTTAGATTTACATTCATTAAATATTATTGTGAAATTTAGAATTTTGGTCGATTGATATTACAATACTAAAAAATTATTCTCGTCTATTTTTACAAAAAATCCTTATATCATAAATATTATATCTTGATAGTTAACTTAT F2: 3 GAGTCTTTG 2 Unidirectional alignment (log-probability: -33.6) AACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAAg----TTTctgagAGGAATATAGTATTTATAATATAGAACTATCAATTGAATA AACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAATGTTTTTT-----AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA Template switch alignment (log-probability: -22.4) AACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAA|GTTTCTGaG|AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA AACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAA|GTTTCTGGG|AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA Gorilla > Chimp --------------- chr5:104804164-104804172 Template switch process: F1: L CTAACTATAATGTTATGATTTTTTAGTAAGAGCAGATAAAAA 1 F3: 4 AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA R RF: CCCAGAAACACTTCAAAGTGTTAATCAAACACTTAAAAATCTAAATGTAAGTAATTTATAATAACACTTTAAATCTTAAAACCAGCTAACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAATGTTTTTTAGGAATATAGTATTTATAATATAGAACTATCAATTGAATA RR: GGGTCTTTGTGAAGTTTCACAATTAGTTTGTGAATTTTTAGATTTACATTCATTAAATATTATTGTGAAATTTAGAATTTTGGTCGATTGATATTACAATACTAAAAAATTATTCTCGTCTATTTTTACAAAAAATCCTTATATCATAAATATTATATCTTGATAGTTAACTTAT F2: 3 GAGTCTTTG 2 Unidirectional alignment (log-probability: -39.1) AACTATAATGTTATGATTTTTTAgTAAGAGCAGATAAAAA----gTTTctgagAGGAATATAGTATTTATAATATAGAACTATCAATTGAATA AACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAATGTTTTTT-----AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA Template switch alignment (log-probability: -27.9) AACTATAATGTTATGATTTTTTAgTAAGAGCAGATAAAAA|GTTTCTGaG|AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA AACTATAATGTTATGATTTTTTAATAAGAGCAGATAAAAA|GTTTCTGGG|AGGAATATAGTATTTATAATATAGAACTATCAATTGAATA ========== Event 2916 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GCCTTGCCATCAGGGGAGTCCTCA-CAGTGATCTGGCGAGCACTCTGGCCTGGCTTGTC-----------ATGTGCTCATTCCTGGTTCA ↓ 3 1 2 4 ↑ 13 24 Chimp: GCCTTGCCATCAGGGGAGTCCTCGCCAGCTCAC-TGTGAGGACTCTGG-----------CCTGGCTTGTCATGTGCTCATTCCTGGTTCA Gorilla: GCCTTGCCATCAGGGGAGTCCTCGCCAGCTCAC-TGTGAGGACTCTGGCCTGGCTTGTC-----------ATGTGCTCATTCCTGGTTCA ↓ 13 24 ↑ 3 1 2 4 Human: GCCTTGCCATCAGGGGAGTCCTCA-CAGTGATCTGGCGAGCACTCTGGCCTGGCTTGTC-----------ATGTGCTCATTCCTGGTTCA Cluster: [ ] Orangutan: GCCTTGCCATCAGGGGAGTCCTCACCAGCTCGC-CGTGAGGACTCTGGCCTGGCTTGTC-----------ATGTGCTCATTCCTGGTTTA Chimp > Human ------------- chr5:143066444-143066456 Template switch process: F1: L GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC 1 F3: 4 GAGCACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGTCCTGTGGCTGGACATAGG R RF: GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCGCCAGCTCACTGTGAGGACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGTCCTGTGGCTGGACATAGG RR: CCGAGGAGGTTCGAATACCGGAACGGTAGTCCCCTCAGGAGCGGTCGAGTGACACTCCTGAGACCGGACCGAACAGTACACGAGTAAGGACCAAGTCAGGACACCGACCTGTATCC F2: 3 CGGTCTAGTGACA 2 Unidirectional alignment (log-probability: -43.6) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCacagtgatctggcgaGC---------------ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC---------------GCCAGCTCACTGTGAGGACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT Template switch alignment (log-probability: -29.3) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|ACAGTGAtCTGGC|GAGcACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|ACAGTGAGCTGGC|GAGGACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT Human > Chimp ------------- chr5:75786233-75786249 Template switch process: F1: L GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC 1 F3: 4 ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGTCCTGTGGCTGGACATAGG R RF: GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCACAGTGATCTGGCGAGCACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGTCCTGTGGCTGGACATAGG RR: CCGAGGAGGTTCGAATACCGGAACGGTAGTCCCCTCAGGAGTGTCACTAGACCGCTCGTGAGACCGGACCGAACAGTACACGAGTAAGGACCAAGTCAGGACACCGACCTGTATCC F2: 3 GGAGTGTCACTCGACCG 2 Unidirectional alignment (log-probability: -43.6) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC---------------GCcagctcactgtgaggACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCACAGTGATCTGGCGAGC---------------ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT Template switch alignment (log-probability: -23.7) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|GCCAGcTCACTGTGAGG|ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|GCCAGATCACTGTGAGG|ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT Gorilla > Human --------------- chr5:143066444-143066456 Template switch process: F1: L GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC 1 F3: 4 GAGCACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT R RF: GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCGCCAGCTCACTGTGAGGACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT RR: CCGAGGAGGTTCGAATACCGGAACGGTAGTCCCCTCAGGAGCGGTCGAGTGACACTCCTGAGACCGGACCGAACAGTACACGAGTAAGGACCAAGTCA F2: 3 CGGTCTAGTGACA 2 Unidirectional alignment (log-probability: -42.6) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCacagtgatctgGC-----------GAGcACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC-----------GCCAGCTCACTGTGAGGACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT Template switch alignment (log-probability: -28.5) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|ACAGTGAtCTGGC|GAGcACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|ACAGTGAGCTGGC|GAGGACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTT Human > Gorilla --------------- chr17:56869636-56869652 Template switch process: F1: L GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC 1 F3: 4 ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT R RF: GGCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCACAGTGATCTGGCGAGCACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT RR: CCGAGGAGGTTCGAATACCGGAACGGTAGTCCCCTCAGGAGTGTCACTAGACCGCTCGTGAGACCGGACCGAACAGTACACGAGTAAGGACCAAGTCA F2: 3 GGAGTGTCACTCGACCG 2 Unidirectional alignment (log-probability: -42.6) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC-----------GCcagctcactgtGAGgACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTCACAGTGATCTGGC-----------GAGCACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT Template switch alignment (log-probability: -23.4) GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|GCCAGcTCACTGTGAGG|ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT GCTCCTCCAAGCTTATGGCCTTGCCATCAGGGGAGTCCTC|GCCAGATCACTGTGAGG|ACTCTGGCCTGGCTTGTCATGTGCTCATTCCTGGTTCAGT ========== Event 2917 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTTGTACTTATTCATCAAGCAACCCGTGGAAGCTACAAG ↓ 3 2 1 4 Chimp: GGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTT------CATCAGCAAACAACCCGTGGAAGCTACAAG Gorilla: GGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTTGTACTTATTCATCAAGCAACCCGTGGAAGCTACAAG Human: GGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTTGTACTTATTCATCAAGCAACCCGTGGAAGCTACAAG Cluster: [ ] Orangutan: GGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTTGTGCTTATTCATCAGGCAACCCGTGGAAGCTACAAG Human > Chimp ------------- chr5:73736741-73736746 Template switch process: F1: L AGATGTGGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTT 1 F3: 4 CAAACAACCCGTGGAAGCTACAAGTGTCATGTCAGCTACAGAGC R RF: AGATGTGGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTTGTACTTATTCATCAAGCAACCCGTGGAAGCTACAAGTGTCATGTCAGCTACAGAGC RR: TCTACACCTCTTCTCGGAAATGGTAGACTACCAAACCACAACATGAATAAGTAGTTCGTTGGGCACCTTCGATGTTCACAGTACAGTCGATGTCTCG F2: 3 GACTAC 2 Unidirectional alignment (log-probability: -32) GATGTGGAGAAGAGCCTTTACCATCTGATGGTTTGGTG---------TTCATcagCAAaCAACCCGTGGAAGCTACAAGTGTCATGTCAGCTACA GATGTGGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTTGTACTTATTCAT---CAAGCAACCCGTGGAAGCTACAAGTGTCATGTCAGCTACA Template switch alignment (log-probability: -22.1) GATGTGGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTT|CATCAG|CAAaCAACCCGTGGAAGCTACAAGTGTCATGTCAGCTACA GATGTGGAGAAGAGCCTTTACCATCTGATGGTTTGGTGTT|CATCAG|CAAGCAACCCGTGGAAGCTACAAGTGTCATGTCAGCTACA ========== Event 2918 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAAGGAGGCAGAGCAGCCTCCCATGGGCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGACTCTCCATGGTTCATTTTTCCAGAGGGATC ↑ 1 4 3 2 Chimp: CCAAGGAGGCAGAGCAGCCTCTGC--TGCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGACTCTCCATGGTTCATTTTTCCAGAGGGATC Gorilla: CCAAGGAGGCAGAGCAACCTCCCATGGGCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGATACTCTCCATGGTTCATTTTTCCAGAGGGATC Human: CCAAGGAGGCAGAGCAGCCTCCCATGGGCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGACTCTCCATGGTTCATTTTTCCAGAGGGATC Cluster: [ ] Orangutan: ---CGGAGGCAGAGCAGCCTCCCATGGGCTAGACTCCGAAGTCTCGGCATGGGTCATGAATTTGGGACTCTCCGTGATTCATTTTTCCAGAGGGATC Chimp > Human ------------- chr5:4425927-4425932 Template switch process: F1: L AATCAGATGGACGGTAAACACCAAGGAGGCAGAGCAGCCTC 1 F3: 4 GCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGA R RF: AATCAGATGGACGGTAAACACCAAGGAGGCAGAGCAGCCTCTGCTGCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGACTCTCCATGG RR: TTAGTCTACCTGCCATTTGTGGTTCCTCCGTCTCGTCGGAGACGACGATCTGAGACTCCTGAGCCGTACCCAGTACTTAAACCCTGAGAGGTACC F2: 3 GGTACC 2 Unidirectional alignment (log-probability: -30) ATCAGATGGACGGTAAACACCAAGGAGGCAGAGCAGCCTCccatgg----GCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGA ATCAGATGGACGGTAAACACCAAGGAGGCAGAGCAGCCTC------TGCTGCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGA Template switch alignment (log-probability: -16) ATCAGATGGACGGTAAACACCAAGGAGGCAGAGCAGCCTC|CCATGG|GCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGA ATCAGATGGACGGTAAACACCAAGGAGGCAGAGCAGCCTC|CCATGG|GCTAGACTCTGAGGACTCGGCATGGGTCATGAATTTGGGA ========== Event 2919 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGATTATCTCATAGCCTGTTCCCTGT-------GTACTTCCAGGTGATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA Chimp: TGATTGTCCCATAGCCTGTTCCCTGT-------GTACTTCCAGGTGATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA ↓ 1 4 3 2 Gorilla: TGATTGTCCCATAGCCTGTTCTTAGA--------------G-AGGCATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA Human: TGATTATCTCATAGCCTGTTCCCTGT-------GTACTTCCAGGTGATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA Cluster: [ ] Orangutan: TGATTGTCCCATAGCCTGTTCCCTGTGTGCTTC-------CAGGTGATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA Chimp > Gorilla --------------- chr17:4360763-4360772 Template switch process: F1: L AGAAAAGTTTGGGATCATTGTGATTGTCCCATAGCCTGTTC 1 F3: 4 ATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA R RF: AGAAAAGTTTGGGATCATTGTGATTGTCCCATAGCCTGTTCCCTGTGTACTTCCAGGTGATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA RR: TCTTTTCAAACCCTAGTAACACTAACAGGGTATCGGACAAGGGACACATGAAGGTCCACTACTTATGTACGGAGAGATTCTACATAGATAACCAAGTAT F2: 3 CGGAGAGATT 2 Unidirectional alignment (log-probability: -34.5) GAAAAGTTTGGGATCATTGTGATTGTCCCATAGCCTGTTCttagagaggC-----------------ATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA GAAAAGTTTGGGATCATTGTGATTGTCCCATAGCCTGTTC---------CCTGTGTACTTCCAGGTGATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA Template switch alignment (log-probability: -17) GAAAAGTTTGGGATCATTGTGATTGTCCCATAGCCTGTTC|TTAGAGAGGC|ATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA GAAAAGTTTGGGATCATTGTGATTGTCCCATAGCCTGTTC|TTAGAGAGGC|ATGAATACATGCCTCTCTAAGATGTATCTATTGGTTCATA ========== Event 2920 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: cactagaccaactgCCTCTCCAATGTAACCATTGGAGCACCTACCTCTTTATTTGG Chimp: CACTAGACCAACTGCCTCTCCAAT-----GGTTATAGCACCTACCTCTTTATTTGG Gorilla: CACTAGACCAACTGCCTCTCCAAT-----GGTTATAGCACCTACCTCTTTATTTGG ↓ 3 1 2 4 Human: cactagaccaactgCCTCTCCAATGTAACCATTGGAGCACCTACCTCTTTATTTGG Cluster: [ ] Orangutan: cactagaccaactgCTTCTCCAAT-----GGTTATAGCACCTACCTCTTTATTTGG Gorilla > Human --------------- chr5:139879435-139879444 Template switch process: F1: L GATTTTGTGTTCCTAATCACTAGACCAACTGCCTCTCCAATG 1 F3: 4 AGCACCTACCTCTTTATTTGGGAATGGCTCAATTTATGAA R RF: GAGTTTGTGTTCCTAATCACTAGACCAACTGCCTCTCCAATGGTTATAGCACCTACCTCTTTATTTGGGAATGGCTCAATTTATGAA RR: CTCAAACACAAGGATTAGTGATCTGGTTGACGGAGAGGTTACCAATATCGTGGATGGAGAAATAAACCCTTACCGAGTTAAATACTT F2: 3 GGTTACCAAT 2 Unidirectional alignment (log-probability: -39.3) tTTTGTGTTCCTAATCACTAGACCAACTGCCTCTCCAATG----TaaccattggAGCACCTACCTCTTTATTTGGGAATGGCTCAATTTATGAA GTTTGTGTTCCTAATCACTAGACCAACTGCCTCTCCAATGGTTAT---------AGCACCTACCTCTTTATTTGGGAATGGCTCAATTTATGAA Template switch alignment (log-probability: -22.5) tTTTGTGTTCCTAATCACTAGACCAACTGCCTCTCCAATG|TAACCATTGG|AGCACCTACCTCTTTATTTGGGAATGGCTCAATTTATGAA GTTTGTGTTCCTAATCACTAGACCAACTGCCTCTCCAATG|TAACCATTGG|AGCACCTACCTCTTTATTTGGGAATGGCTCAATTTATGAA ========== Event 2921 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATTCCAAAAATGTCTCTAATTAACTGTAATTATACATACTTTGAGAAAA ↓ 13 2 4 ↑ 31 24 Chimp: ATTCCAAAAATGTCTCTAATT-ACAG-TATTATACATACTTTGAGAAAA Gorilla: ATTCCAAAAATGTCTCTAATT-ACAG-TATTATACATACTTTGAGAAAA ↓ 31 24 ↑ 13 2 4 Human: ATTCCAAAAATGTCTCTAATTAACTGTAATTATACATACTTTGAGAAAA Cluster: [ ] Orangutan: ATTCCAAAAATGTCTCTAATT-ACAG-TATTAGACATACTTTGACAAAA Chimp > Human ------------- chr5:43308974-43308979 Template switch process: F1: L TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA 1 F3: 4 ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT R RF: TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTACAGTATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT RR: ATCCGTTTCTTATGATGTTATAAGGTTTTTACAGAGATTAATGTCATAATATGTATGAAACTCTTTTATTGGATAGAAACAAGAAA F2: 3 ATGTCA 2 Unidirectional alignment (log-probability: -30) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATtaactgTA----ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAAT------TACAGTATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Template switch alignment (log-probability: -16) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|ACTGTA|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|ACTGTA|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Human > Chimp ------------- chr5:111031596-111031599 Template switch process: F1: L TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA 1 F3: 4 ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT R RF: TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTAACTGTAATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT RR: ATCCGTTTCTTATGATGTTATAAGGTTTTTACAGAGATTAATTGACATTAATATGTATGAAACTCTTTTATTGGATAGAAACAAGAAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -27.2) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTAcagt------ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA----ACTGTAATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Template switch alignment (log-probability: -15.8) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|CAGT|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|CAGT|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Gorilla > Human --------------- chr5:43308974-43308979 Template switch process: F1: L TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA 1 F3: 4 ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT R RF: TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTACAGTATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT RR: ATCCGTTTCTTATGATGTTATAAGGTTTTTACAGAGATTAATGTCATAATATGTATGAAACTCTTTTATTGGATAGAAACAAGAAA F2: 3 ATGTCA 2 Unidirectional alignment (log-probability: -29.1) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTaACtGTaATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATT-ACAGT-ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Template switch alignment (log-probability: -16.5) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|ACTGTA|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|ACTGTA|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Human > Gorilla --------------- chr17:43802675-43802678 Template switch process: F1: L TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA 1 F3: 4 ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT R RF: TAGGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTAACTGTAATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT RR: ATCCGTTTCTTATGATGTTATAAGGTTTTTACAGAGATTAATTGACATTAATATGTATGAAACTCTTTTATTGGATAGAAACAAGAAA F2: 3 TGAC 2 Unidirectional alignment (log-probability: -26.3) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATT-ACaGT-ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTAACTGTAATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT Template switch alignment (log-probability: -16.3) GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|CAGT|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT GGCAAAGAATACTACAATATTCCAAAAATGTCTCTAATTA|CAGT|ATTATACATACTTTGAGAAAATAACCTATCTTTGTTCTTT ========== Event 2922 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACCTATGTTGCTTAAACATAT------TAAATTTGA----TAAAAATCGT----TGAAAATAAAA--CTATCAGTTTTTTCAAACTGGG Chimp: ACCTATGTTGCTTAAACATAT----TATAAATTTGA----TAAAAATCGT----TGAAAATAAAA--CTATCAGTTTTTTCAAACTGGG ↓ 1 3 4 ↑ 3 1 2 4 Gorilla: ACCTATGTTGCTTAAACATATT-------AGTTTTATTTTCAACGATTTT--------TATCAAATTATATCAGTTTTTTCAAACTGGG ↓ 13 2 4 ↑ 13 4 Human: ACCTATGTTGCTTAAACATAT------TAAATTTGA----TAAAAATCGT----TGAAAATAAAA--CTATCAGTTTTTTCAAACTGGG Cluster: [ ] Orangutan: ACCTATGTTGTTTAAACATATTATA----AATTTGA----TAAAAATCGTTGAA----AATAAAA--CTATCAGTTTTTTCAAACTGGG Gorilla > Human --------------- chr5:137998983-137999011 Template switch process: F1: L TATGCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTA 1 F3: 4 TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT R RF: TATGCTGTGAGTCAGATTACACCTATGTTGCTTAAACATATTAGTTTTATTTTCAACGATTTTTATCAAATTATATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT RR: ATACGACACTCAGTCTAATGTGGATACAACGAATTTGTATAATCAAAATAAAAGTTGCTAAAAATAGTTTAATATAGTCAAAAAAGTTTGACCCTCTGAATCATACTTTTCTA F2: 3 CAAAATAAAAGTTGCTAAAAATAGTTTAA 2 Unidirectional alignment (log-probability: -67.5) GCTGTGAaTCAGATTACACCTATGTTGCTTAAACATATT-------------------------AAATTtgataaaaatcgttgaaaataaaacTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT GCTGTGAGTCAGATTACACCTATGTTGCTTAAACATATTAGTTTTATTTTCAACGATTTTTATCAAATT------------------------ATATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT Template switch alignment (log-probability: -25) GCTGTGAaTCAGATTACACCTATGTTGCTTAAACATATTA|AATTTGATAAAAATCGTTGAAAATAAAAC|TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT GCTGTGAGTCAGATTACACCTATGTTGCTTAAACATATTA|AATTTGATAAAAATCGTTGAAAATAAAAC|TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT Human > Gorilla --------------- chr17:51848208-51848236 Template switch process: F1: L TATGCTGTGAGTCAGATTACACCTATGTTGCTTAAACATATTA 1 F3: 4 ATATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT R RF: TATGCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTAAATTTGATAAAAATCGTTGAAAATAAAACTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT RR: ATACGACACTTAGTCTAATGTGGATACAACGAATTTGTATAATTTAAACTATTTTTAGCAACTTTTATTTTGATAGTCAAAAAAGTTTGACCCTCTGAATCATACTTTTCTA F2: 3 TTAAACTATTTTTAGCAACTTTTATTTTG 2 Unidirectional alignment (log-probability: -68.9) GCTGTGAgTCAGATTACACCTATGTTGCTTAAACATATTagttttattttcaacgatttttatcAAATTa------------------------TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA GCTGTGAATCAGATTACACCTATGTTGCTTAAACATATT-------------------------AAATTTGATAAAAATCGTTGAAAATAAAACTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA Template switch alignment (log-probability: -30.5) GCTGTGAgTCAGATTACACCTATGTTGCTTAAACATATTA|GTTTTATTTTCAACGATTTTTATCAAATT|aTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA GCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTA|GTTTTATTTTCAACGATTTTTATCAAATT|CTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA Gorilla > Chimp --------------- chr5:70625314-70625342 Template switch process: F1: L TATGCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTA----TA 1 F3: 4 TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT R RF: TATGCTGTGAGTCAGATTACACCTATGTTGCTTAAACATATTAGTTTTATTTTCAACGATTTTTATCAAATTATATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT RR: ATACGACACTCAGTCTAATGTGGATACAACGAATTTGTATAATCAAAATAAAAGTTGCTAAAAATAGTTTAATATAGTCAAAAAAGTTTGACCCTCTGAATCATACTTTTCTA F2: 3 CAAAATAAAAGTTGCTAAAAATAGTTTAA 2 Unidirectional alignment (log-probability: -69.3) TGTGAaTCAGATTACACCTATGTTGCTTAAACATATTA----------------------------TAaatttgataaaaatcgttgaaaataaaacTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT TGTGAGTCAGATTACACCTATGTTGCTTAAACATATTAGTTTTATTTTCAACGATTTTTATCAAATTA-----------------------------TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT Template switch alignment (log-probability: -35) TGTGAaTCAGATTACACCTATGTTGCTTAAACATATTA----TA|AATTTGATAAAAATCGTTGAAAATAAAAC|TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT TGTGAGTCAGATTACACCTATGTTGCTTAAACATATTAGTTTTA|AATTTGATAAAAATCGTTGAAAATAAAAC|TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT Chimp > Gorilla --------------- chr17:51848208-51848236 Template switch process: F1: L TATGCTGTGAGTCAGATTACACCTATGTTGCTTAAACATATTA 1 F3: 4 ATATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT R RF: TATGCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTATAAATTTGATAAAAATCGTTGAAAATAAAACTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGAT RR: ATACGACACTTAGTCTAATGTGGATACAACGAATTTGTATAATATTTAAACTATTTTTAGCAACTTTTATTTTGATAGTCAAAAAAGTTTGACCCTCTGAATCATACTTTTCTA F2: 3 TTAAACTATTTTTAGCAACTTTTATTTTG 2 Unidirectional alignment (log-probability: -67.9) GCTGTGAgTCAGATTACACCTATGTTGCTTAAACATATTAgttttattttcaacgatttttatcaaatTA-----------------------------TATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA GCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTA----------------------------TAAATTTGATAAAAATCGTTGAAAATAAAACTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA Template switch alignment (log-probability: -30.5) GCTGTGAgTCAGATTACACCTATGTTGCTTAAACATATTA|GTTTTATTTTCAACGATTTTTATCAAATT|aTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA GCTGTGAATCAGATTACACCTATGTTGCTTAAACATATTA|GTTTTATTTTCAACGATTTTTATCAAATT|CTATCAGTTTTTTCAAACTGGGAGACTTAGTATGAAAAGA ========== Event 2923 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATACTTCTGTGCAAAATATGAATTTAATTCATTAAATTCATAATGAATTAAATT----CTTATGTCTAAATTTGAAAGGT ↑ 3 2 1 4 Chimp: ATACTTCTGTGCAAAATATGAATTTAATTCATT------ATGACAATTTAATTTCAAAATTATGTCTAAATTTGAAAGGT ↓ 3 2 1 4 Gorilla: ATACTTCTGTGCAAAATATGAATTTAATTCATTAAATTCATAATGAATTAAATT----CTTATGTCTAAATTTGAAAGGT Human: ATACTTCTGTGCAAAATATGAATTTAATTCATTAAATTCATAATGAATTAAATT----CTTATGTCTAAATTTGAAAGGT Cluster: [ ] Orangutan: -----TCTGT-GAAAATATGAATTTAATTCATTAAATTCATAATGAATTAAATT----CTTATGTCTAAATTTGAAAAGT Chimp > Human ------------- chr5:45034368-45034384 Template switch process: F1: L GAATATGAATACTTCTGTGCAAAATATGAATTTAATTCATTA----AATT 1 F3: 4 TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA R RF: GAATATGAATACTTCTGTGCAAAATATGAATTTAATTCATTATGACAATTTAATTTCAAAATTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA RR: CTTATACTTATGAAGACACGTTTTATACTTAAATTAAGTAATACTGTTAAATTAAAGTTTTAATACAGATTTAAACTTTCCAAACTTTTAGAAGATTCTTT F2: 3 CTTAAATTAAGTAATAC 2 Unidirectional alignment (log-probability: -49.4) GAATACTTCTGTGCAAAATATGAATTTAATTCATT-----------------AAAttcataatgaattaaattcTTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA GAATACTTCTGTGCAAAATATGAATTTAATTCATTATGACAATTTAATTTCAAAA-------------------TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA Template switch alignment (log-probability: -27.9) GAATACTTCTGTGCAAAATATGAATTTAATTCATTA----AATT|CATAATGAATTAAATTC|TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA GAATACTTCTGTGCAAAATATGAATTTAATTCATTATGACAATT|CATAATGAATTAAATTC|TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA Chimp > Gorilla --------------- chr17:45548208-45548224 Template switch process: F1: L GAATATGAATACTTCTGTGCAAAATATGAATTTAATTCATTA----AATT 1 F3: 4 TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA R RF: GAATATGAATACTTCTGTGCAAAATATGAATTTAATTCATTATGACAATTTAATTTCAAAATTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA RR: CTTATACTTATGAAGACACGTTTTATACTTAAATTAAGTAATACTGTTAAATTAAAGTTTTAATACAGATTTAAACTTTCCAAACTTTTAGAAGATTCTTT F2: 3 CTTAAATTAAGTAATAC 2 Unidirectional alignment (log-probability: -48.9) GAATACTTCTGTGCAAAATATGAATTTAATTCATT-----------------AAAttcataatgaattaaattcTTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA GAATACTTCTGTGCAAAATATGAATTTAATTCATTATGACAATTTAATTTCAAAA-------------------TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA Template switch alignment (log-probability: -28) GAATACTTCTGTGCAAAATATGAATTTAATTCATTA----AATT|CATAATGAATTAAATTC|TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA GAATACTTCTGTGCAAAATATGAATTTAATTCATTATGACAATT|CATAATGAATTAAATTC|TTATGTCTAAATTTGAAAGGTTTGAAAATCTTCTAAGAAA ========== Event 2924 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATAATCAGTAGTATATTATAGTT-AATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAACTTACTCTTACATCTAATTGCATCTGAAAATCTTCAGAGACACTAA ↓ 1 4 3 2 Chimp: TATAATCAGTAGTATATTATACAGATATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAATTTACTCTTACATCTAATTGCATCTGAAAATCTTCAGAGCCACTAA ↑ 1 4 3 2 Gorilla: TATAATCAGTAGTATATTATAGTT-AATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAATTTACTCTTACATCTAATTGCATCTGAAAATCTTCAGAGCCACTAA Human: TATAATCAGTAGTATATTATAGTT-AATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAACTTACTCTTACATCTAATTGCATCTGAAAATCTTCAGAGACACTAA Cluster: [ ] Orangutan: TATAATCGGTAGTATATTATAGTT-AATACCCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAATTTACTCTTACATCTAATTGCATCTGAAAATCTTCAGAGCCACTAA Human > Chimp ------------- chr5:112115566-112115570 Template switch process: F1: L TTATTAAATCATTAAAATAATATAATCAGTAGTATATTATA 1 F3: 4 ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT R RF: TTATTAAATCATTAAAATAATATAATCAGTAGTATATTATAGTTAATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAACTTACTCTTACATCTAATTGCATCTG RR: AATAATTTAGTAATTTTATTATATTAGTCATCATATAATATCAATTATGAGACAATATAGAAGGGACAGAGATGTTGATAGAGTATGATTTCCTGTCAATACACCCGAAAAAATCCAGTTTATTAGTTGAATGAGAATGTAGATTAACGTAGAC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -28.5) TATTAAATCATTAAAATAATATAATCAGTAGTATATTATAcagat----ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT TATTAAATCATTAAAATAATATAATCAGTAGTATATTATA-----GTTAATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT Template switch alignment (log-probability: -15.9) TATTAAATCATTAAAATAATATAATCAGTAGTATATTATA|CAGAT|ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT TATTAAATCATTAAAATAATATAATCAGTAGTATATTATA|CAGAT|ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT Gorilla > Chimp --------------- chr5:112115566-112115570 Template switch process: F1: L TTATTAAATCATTAAAATAATATAATCAGTAGTATATTATA 1 F3: 4 ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT R RF: TTATTAAATCATTAAAATAATATAATCAGTAGTATATTATAGTTAATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCATACTAAAGGACAGTTATGTGGGCTTTTTTAGGTCAAATAATCAATTTACTCTTACATCTAATTGCATCTG RR: AATAATTTAGTAATTTTATTATATTAGTCATCATATAATATCAATTATGAGACAATATAGAAGGGACAGAGATGTTGATAGAGTATGATTTCCTGTCAATACACCCGAAAAAATCCAGTTTATTAGTTAAATGAGAATGTAGATTAACGTAGAC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -28) TATTAAATCATTAAAATAATATAATCAGTAGTATATTA----TAcagatATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT TATTAAATCATTAAAATAATATAATCAGTAGTATATTATAGTTA-----ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT Template switch alignment (log-probability: -16.4) TATTAAATCATTAAAATAATATAATCAGTAGTATATTATA|CAGAT|ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT TATTAAATCATTAAAATAATATAATCAGTAGTATATTATA|CAGAT|ATACTCTGTTATATCTTCCCTGTCTCTACAACTATCTCAT ========== Event 2925 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CGGAAGAGTATAAACCATAGAGACTCTTGAGTCATTGTGTCTCCATGAAAGCG ↑ 1 3 4 2 Chimp: CGGAAGAGTATAAACCATAGAAAC--AAGAGTCATTGTGTCTCCATGAAAGCG Gorilla: CGGAAGAGTATAAACCATAGAGAC--AAGAGTCATTGTGTCTCCATGAAAGCG Human: CGGAAGAGTATAAACCATAGAGACTCTTGAGTCATTGTGTCTCCATGAAAGCG Cluster: [ ] Orangutan: TGGAAGAGTATAAACCATAGAGAC--AAGAGTCATTGTGTCTCCATGAAAGCA Chimp > Human ------------- chr5:45198500-45198507 Template switch process: F1: L ACAAGTTATTTAGAAGTGGCCGGAAGAGTATAAACCATAGA 1 F3: 4 AGTCATTGTGTCTCCATGAAAGCGGAGCGTTAGTGCAAA R RF: ACAAGTTATTTACAAGTGGCCGGAAGAGTATAAACCATAGAAACAAGAGTCATTGTGTCTCCATGAAAGCGGAGCGTTAGTGCAAA RR: TGTTCAATAAATGTTCACCGGCCTTCTCATATTTGGTATCTTTGTTCTCAGTAACACAGAGGTACTTTCGCCTCGCAATCACGTTT F2: 3 GTTCTCAG 2 Unidirectional alignment (log-probability: -37.4) CAAGTTATTTAgAAGTGGCCGGAAGAGTATAAACCATAG-----AGactcttgAGTCATTGTGTCTCCATGAAAGCGGAGCGTTAGTGCAAA CAAGTTATTTACAAGTGGCCGGAAGAGTATAAACCATAGAAACAAG-------AGTCATTGTGTCTCCATGAAAGCGGAGCGTTAGTGCAAA Template switch alignment (log-probability: -22.2) CAAGTTATTTAgAAGTGGCCGGAAGAGTATAAACCATAGA|GACTCTTG|AGTCATTGTGTCTCCATGAAAGCGGAGCGTTAGTGCAAA CAAGTTATTTACAAGTGGCCGGAAGAGTATAAACCATAGA|GACTCTTG|AGTCATTGTGTCTCCATGAAAGCGGAGCGTTAGTGCAAA ========== Event 2926 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTGATTGATTTCTTAGTACAGT----ACTTTAATGCATTTCACATTTTGTACAATCTT Chimp: TTTGATTGATTTCTTAGTATAATGCATTCTTTAATGCATTTCACATTTTGTACAATCTT ↑ 1 4 3 2 Gorilla: TTTGATTGATTTCTTAGTATAGT----ACTTTAATGCATTTCACATTTTGTACAATCTT Human: TTTGATTGATTTCTTAGTACAGT----ACTTTAATGCATTTCACATTTTGTACAATCTT Cluster: [ ] Orangutan: TTTGATTGATTGCTTAGTATAGT----ATTTTAATGCATTTCACATTTTGTACAATCTT Gorilla > Chimp --------------- chr5:113044747-113044753 Template switch process: F1: L TAGGTGCAAATTTTTTAGTATTTGATTGATTTCTTAGTATA 1 F3: 4 CTTTAATGCATTTCACATTTTGTACAATCTTCTGAAAAAG R RF: TAGGTGCAAATTTTTTAGTATTTGATTGATTTCTTAGTATAGTACTTTAATGCATTTCACATTTTGTACAATCTTCTGAAAAAG RR: ATCCACGTTTAAAAAATCATAAACTAACTAAAGAATCATATCATGAAATTACGTAAAGTGTAAAACATGTTAGAAGACTTTTTC F2: 3 TTACGTA 2 Unidirectional alignment (log-probability: -27.7) AGGTGCAAATTTTTTAGTATTTGATTGATTTCTTAGTATAatgcaTtCTTTAATGCATTTCACATTTTGTACAATCTTCTGAAAAAG AGGTGCAAATTTTTTAGTATTTGATTGATTTCTTAGTATA----GTACTTTAATGCATTTCACATTTTGTACAATCTTCTGAAAAAG Template switch alignment (log-probability: -16.6) AGGTGCAAATTTTTTAGTATTTGATTGATTTCTTAGTATA|ATGCATT|CTTTAATGCATTTCACATTTTGTACAATCTTCTGAAAAAG AGGTGCAAATTTTTTAGTATTTGATTGATTTCTTAGTATA|ATGCATT|CTTTAATGCATTTCACATTTTGTACAATCTTCTGAAAAAG ========== Event 2927 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCTCCTTTAGATTTTTCTTAATTTTCCCCTGAGGTTTCT----------CCATTTTAAGAAAATAGCACTCATGA ↓ 13 24 ↑ 13 24 Chimp: CCTCCTTTAGATTTTTCTTAAAAT-----GGAGAAACCT-----CAGGGGAAAATTAAGAAAATAGCACTCATGA Gorilla: CCTCCTTTAGATTTTTCTTAAAAT-----GGAGAAACCTCAGGG-----GAAAATTAAGAAAATAGCACTCATGA ↓ 13 24 ↑ 13 24 Human: CCTCCTTTAGATTTTTCTTAATTTTCCCCTGAGGTTTCT----------CCATTTTAAGAAAATAGCACTCATGA Cluster: [ ] Orangutan: CCTCCTTTAGATTTTTCTTAAAGT-----GGAGAAACCTCAGGG-----AAAAATTAAGAAAATAGCACTCATGA Chimp > Human ------------- chr5:176962562-176962584 Template switch process: F1: L TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA 1 F3: 4 TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA R RF: TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAAAATGGAGAAACCTCAGGGGAAAATTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA RR: AGTTTGGTGTCCAGGAAAAAGGAGGAAATCTAAAAAGAATTTTACCTCTTTGGAGTCCCCTTTTAATTCTTTTATCGTGAGTACTGGTATGTCCGAGGACGTAT F2: 3 TTACCTCTTTGGAGTCCCCTTTT 2 Unidirectional alignment (log-probability: -55.4) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTT-----------------------AAttttcccctgaggtttctccattTTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAAAATGGAGAAACCTCAGGGGAAAA-----------------------TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Template switch alignment (log-probability: -18.1) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|TTTTCCCCTGAGGTTTCTCCATT|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|TTTTCCCCTGAGGTTTCTCCATT|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Human > Chimp ------------- chr5:177192397-177192419 Template switch process: F1: L TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA 1 F3: 4 TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA R RF: TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAATTTTCCCCTGAGGTTTCTCCATTTTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA RR: AGTTTGGTGTCCAGGAAAAAGGAGGAAATCTAAAAAGAATTAAAAGGGGACTCCAAAGAGGTAAAATTCTTTTATCGTGAGTACTGGTATGTCCGAGGACGTAT F2: 3 AAAAGGGGACTCCAAAGAGGTAA 2 Unidirectional alignment (log-probability: -55.4) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA-----------------------aatggagaaacctcaggggaaaaTTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAATTTTCCCCTGAGGTTTCTCCATT-----------------------TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Template switch alignment (log-probability: -18.1) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|AATGGAGAAACCTCAGGGGAAAA|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|AATGGAGAAACCTCAGGGGAAAA|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Gorilla > Human --------------- chr5:176962562-176962584 Template switch process: F1: L TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA 1 F3: 4 TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA R RF: TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAAAATGGAGAAACCTCAGGGGAAAATTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA RR: AGTTTGGTGTCCAGGAAAAAGGAGGAAATCTAAAAAGAATTTTACCTCTTTGGAGTCCCCTTTTAATTCTTTTATCGTGAGTACTGGTATGTCCGAGGACGTAT F2: 3 TTACCTCTTTGGAGTCCCCTTTT 2 Unidirectional alignment (log-probability: -54.9) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTA-----------------------AttttcccctgaggtttctccattTTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAAAATGGAGAAACCTCAGGGGAAAA-----------------------TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Template switch alignment (log-probability: -18.7) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|TTTTCCCCTGAGGTTTCTCCATT|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|TTTTCCCCTGAGGTTTCTCCATT|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Human > Gorilla --------------- chr17:91219865-91219887 Template switch process: F1: L TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA 1 F3: 4 TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA R RF: TCAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAATTTTCCCCTGAGGTTTCTCCATTTTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA RR: AGTTTGGTGTCCAGGAAAAAGGAGGAAATCTAAAAAGAATTAAAAGGGGACTCCAAAGAGGTAAAATTCTTTTATCGTGAGTACTGGTATGTCCGAGGACGTAT F2: 3 AAAAGGGGACTCCAAAGAGGTAA 2 Unidirectional alignment (log-probability: -54.9) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA-----------------------aatggagaaacctcaggggaaaaTTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAATTTTCCCCTGAGGTTTCTCCATT-----------------------TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA Template switch alignment (log-probability: -18.7) CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|AATGGAGAAACCTCAGGGGAAAA|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA CAAACCACAGGTCCTTTTTCCTCCTTTAGATTTTTCTTAA|AATGGAGAAACCTCAGGGGAAAA|TTAAGAAAATAGCACTCATGACCATACAGGCTCCTGCATA ========== Event 2928 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTACTCTCCATTTTTTGTGTACTGGATACATTTTTGCGAGGGCTGCCCTATTCTTAGGGACAAATT Chimp: GTACTCTCCATTCTTTGTGTACTGGATACATTTTTGCGAGGGCTGCCCTATTCTTAGGGACAAATT ↓ 3 2 1 4 Gorilla: GTACTCTCCATTCTTTGTGTACTGGATACATTTTTGTATCCAGAACCCTATTCTTAGGAACAAATT Human: GTACTCTCCATTTTTTGTGTACTGGATACATTTTTGCGAGGGCTGCCCTATTCTTAGGGACAAATT Cluster: [ ] Orangutan: GTACTCTCCATTCTTTGTGTACTGGATACATTTTTGCAAAGGCTGTTCTATTCTTAGGGACAAATT Chimp > Gorilla --------------- chr17:91065679-91065687 Template switch process: F1: L TGCTTGTACTCTCCATTCTTTGTGTACTGGATACATTTTTG 1 F3: 4 CCCTATTCTTAGGAACAAATTGATTCACAAATAGAATTTG R RF: TGCTTGTACTCTCCATTCTTTGTGTACTGGATACATTTTTGCGAGGGCTGCCCTATTCTTAGGGACAAATTGATTCACAAATAGAATTTG RR: ACGAACATGAGAGGTAAGAAACACATGACCTATGTAAAAACGCTCCCGACGGGATAAGAATCCCTGTTTAACTAAGTGTTTATCTTAAAC F2: 3 AAGACCTAT 2 Unidirectional alignment (log-probability: -39.5) GCTTGTACTCTCCATTCTTTGTGTACTGGATACATTTT---------TGtatccagaaCCCTATTCTTAGGaACAAATTGATTCACAAATAGAATTTG GCTTGTACTCTCCATTCTTTGTGTACTGGATACATTTTTGCGAGGGCTG---------CCCTATTCTTAGGGACAAATTGATTCACAAATAGAATTTG Template switch alignment (log-probability: -27.9) GCTTGTACTCTCCATTCTTTGTGTACTGGATACATTTTTG|TATCCAGaA|CCCTATTCTTAGGaACAAATTGATTCACAAATAGAATTTG GCTTGTACTCTCCATTCTTTGTGTACTGGATACATTTTTG|TATCCAGTA|CCCTATTCTTAGGGACAAATTGATTCACAAATAGAATTTG ========== Event 2929 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ttccctctcaatTTTGTGAAAAGTTAGAATTAGGCATCAATGAAatatatacgtatacagacacacag--------------acaaacacacacacatataTGGAAGTGAATGAATCTTCTATCTTTCAATGAGT ↓ 1 4 3 2 Chimp: ttccctctcaatTTTGTGAAATTGATTCATTAGGCATCAATGAAATATATACGTATacagacacacac--------------acacaaacacacacaTATATGGAAGTGAATGAATCTTCTATCTTTCAATGAGT Gorilla: Human: ttccctctcaatTTTGTGAAAAGTTAGAATTAGGCATCAATGAAatatatacgtatacagacacacag--------------acaaacacacacacatataTGGAAGTGAATGAATCTTCTATCTTTCAATGAGT Cluster: [ ] Orangutan: ttccctctcaatTTTGAGAA-AGTTAGAATTAGGCATCAATGAAATATATATGTATACAAACGCACACATGCGCGCGCGTGTGcacacacacacacaTATATGGAAGTGAATGAATCTTCTATCTTTCAATGAGT Human > Chimp ------------- chr5:64354745-64354752 Template switch process: F1: L CCATGAAGAAGATTTTAAATTTCCCTCTCAATTTTGTGAAA 1 F3: 4 TTAGGCATCAATGAAATATATACGTATACAGACACACAC R RF: CCATGAAGAAGATTTTAAATTTCCCTCTCAATTTTGTGAAAAGTTAGAATTAGGCATCAATGAAATATATACGTATACAGACACACAGACAAACACACACACATATATGGAAGTGAATGAA RR: GGTACTTCTTCTAAAATTTAAAGGGAGAGTTAAAACACTTTTCAATCTTAATCCGTAGTTACTTTATATATGCATATGTCTGTGTGTCTGTTTGTGTGTGTGTATATACCTTCACTTACTT F2: 3 ACTTAGTT 2 Unidirectional alignment (log-probability: -37.5) CATGAAGAAGATTTTAAATTTCCCTCTCAATTTTGTGAAAttgattc-------ATTAGGCATCAATGAAATATATACGTATACAGACACACAc CATGAAGAAGATTTTAAATTTCCCTCTCAATTTTGTGAAA-------AGTTAGAATTAGGCATCAATGAAATATATACGTATACAGACACACAG Template switch alignment (log-probability: -28.2) CATGAAGAAGATTTTAAATTTCCCTCTCAATTTTGTGAAA|TTgATTCA|TTAGGCATCAATGAAATATATACGTATACAGACACACAc CATGAAGAAGATTTTAAATTTCCCTCTCAATTTTGTGAAA|TTCATTCA|TTAGGCATCAATGAAATATATACGTATACAGACACACAG ========== Event 2930 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: cgtta--tatatatatgtTAGAGTACATAGAGCGTTCATAGAGCGTACTCTACCATATATATGTACatatat ↑ 3 2 1 4 Chimp: cgtta--tatatatatGTTAGAGTACATAGAGCGTTCATAGAGCATACTCCACCATATATATGTACGtata- ↓ 3 2 1 4 Gorilla: cgtta--tatatatatGTTAGAGTACATAGAGCGTTCATACAGCGTACTCTACCATATATATGTACatatat Human: cgtta--tatatatatgtTAGAGTACATAGAGCGTTCATAGAGCGTACTCTACCATATATATGTACatatat Cluster: [ ] Orangutan: cgttatgtatatatatgttaGAGTA--CAGAGTGTTCATAGAGTGTACTCTACCATATATATGTACatatat Chimp > Human ------------- chr5:130362841-130362847 Template switch process: F1: L GTTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGC 1 F3: 4 ACCATATATATGTACATATATTGATAAGCTTATATA R RF: GTTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGCATACTCCACCATATATATGTACGTATATTGATAAGCTTATATA RR: CAATATATATATACAATCTCATGTATCTCGCAAGTATCTCGTATGAGGTGGTATATATACATGCATATAACTATTCGAATATAT F2: 3 TCTCATG 2 Unidirectional alignment (log-probability: -43.1) TTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGCgTACTCtACCATATATATGTACaTATATTGAtaagcttatata TTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGCATACTCCACCATATATATGTACGTATATTGA------------ Template switch alignment (log-probability: -22.1) TTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGC|GTACTCT|ACCATATATATGTACaTATATTGATAAGCTTATATA TTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGC|GTACTCT|ACCATATATATGTACGTATATTGATAAGCTTATATA Chimp > Gorilla --------------- chr17:44877653-44877659 Template switch process: F1: L ATACGTTATATATATATGTTAGAGTACATAGAGCGTTCATACAGC 1 F3: 4 ACCATATATATGTACATATATTGATAAGCTTATATA R RF: ATACGTTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGCATACTCCACCATATATATGTACGTATATTGATAAGCTTATATA RR: TATGCAATATATATATACAATCTCATGTATCTCGCAAGTATCTCGTATGAGGTGGTATATATACATGCATATAACTATTCGAATATAT F2: 3 TCTCATG 2 Unidirectional alignment (log-probability: -47.1) TTATATATATATGTTAGAGTACATAGAGCGTTCATAcAGCgTACTCtACCATATATATGTACaTATATTGAtaagcttatata TTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGCATACTCCACCATATATATGTACGTATATTGA------------ Template switch alignment (log-probability: -27.7) TTATATATATATGTTAGAGTACATAGAGCGTTCATAcAGC|GTACTCT|ACCATATATATGTACaTATATTGATAAGCTTATATA TTATATATATATGTTAGAGTACATAGAGCGTTCATAGAGC|GTACTCT|ACCATATATATGTACGTATATTGATAAGCTTATATA ========== Event 2931 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGATAAAGAACTCAGACAAGT-------------GACATGTTAAGGAATGTACACTTTATTCTGTGAATAAT ↓ 1 3 4 2 Chimp: GGATAAAGAACTCAGACAAGTGTACATTCCTTAACATGTGTTAAGGAATGTACACTTTATTCTGTGAATAAT ↑ 1 3 4 2 Gorilla: GGATAAAGAACTCAGACAAGT-------------GACATGTTAAGGAATGTACACTTTATTCTGTGAATAAT Human: GGATAAAGAACTCAGACAAGT-------------GACATGTTAAGGAATGTACACTTTATTCTGTGAATAAT Cluster: [ ] Orangutan: AGATAAAGAACTCAGACAAGT-------------GACATGTTAAGGAATGTACACTTTATTCTGTGAATAAT Human > Chimp ------------- chr5:118257155-118257170 Template switch process: F1: L CCAGCTGCAAGAGTAGCCAAGGATAAAGAACTCAGACAAGTG 1 F3: 4 TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC R RF: CCAGCTGCAAGAGTAGCCAGGGATAAAGAACTCAGACAAGTGACATGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC RR: GGTCGACGTTCTCATCGGTCCCTATTTCTTGAGTCTGTTCACTGTACAATTCCTTACATGTGAAATAAGACACTTATTAAAGTCG F2: 3 GTACAATTCCTTACAT 2 Unidirectional alignment (log-probability: -45.9) AGCTGCAAGAGTAGCCAaGGATAAAGAACTCAGACAAGTGtACATtccttaacatgtGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC AGCTGCAAGAGTAGCCAGGGATAAAGAACTCAGACAAGTG-ACAT------------GTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC Template switch alignment (log-probability: -23.3) AGCTGCAAGAGTAGCCAaGGATAAAGAACTCAGACAAGTG|TACATTCCTTAACATG|TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC AGCTGCAAGAGTAGCCAGGGATAAAGAACTCAGACAAGTG|TACATTCCTTAACATG|TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC Gorilla > Chimp --------------- chr5:118257155-118257170 Template switch process: F1: L CCAGCTGCAAGAGTAGCCAAGGATAAAGAACTCAGACAAGTG 1 F3: 4 TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC R RF: CCAGCTGCAAGAGTAGCCAGGGATAAAGAACTCAGACAAGTGACATGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC RR: GGTCGACGTTCTCATCGGTCCCTATTTCTTGAGTCTGTTCACTGTACAATTCCTTACATGTGAAATAAGACACTTATTAAAGTCG F2: 3 GTACAATTCCTTACAT 2 Unidirectional alignment (log-probability: -44.9) AGCTGCAAGAGTAGCCAaGGATAAAGAACTCAGACAAGTGtacattccttaACAtgTGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC AGCTGCAAGAGTAGCCAGGGATAAAGAACTCAGACAAGTG-----------ACA--TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC Template switch alignment (log-probability: -23.3) AGCTGCAAGAGTAGCCAaGGATAAAGAACTCAGACAAGTG|TACATTCCTTAACATG|TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC AGCTGCAAGAGTAGCCAGGGATAAAGAACTCAGACAAGTG|TACATTCCTTAACATG|TGTTAAGGAATGTACACTTTATTCTGTGAATAATTTCAGC ========== Event 2932 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATATTTTAACGTAGAAAATGTCC----TTATCATATGTCTTACACCTGTAATGTTTCCAG Chimp: AAATATTTTAACGTAGAAAATGTCC----TTATCATATATCTTACACCTGTAATGTTTCCAG ↓ 4 1 2 Gorilla: AAATATTTTAACGTAGAAAATGTCCGATAAGGACATATGTCCTACACCTGTAATGTTTCCAG Human: AAATATTTTAACGTAGAAAATGTCC----TTATCATATGTCTTACACCTGTAATGTTTCCAG Cluster: [ ] Orangutan: AAATATTTTAATGTAGAAAATGTCC----TTATCATATGTCTTACACCTGTAATGTTTCCAG Chimp > Gorilla --------------- chr17:43746796-43746806 Template switch process: F1: L TATTTTATTAAATAGAAAATATTTTAACGTAGAAAATGTCC 1 F3: 4 ATGTCC-------------TACACCTGTAATGTTTCCAGGTAGTTTGAGTTATTGTGAA R RF: TATTTTATTAAATAGAAAATATTTTAACGTAGAAAATGTCCTTATCATATATCTTACACCTGTAATGTTTCCAGGTAGTTTGAGTTATTGTGAA RR: ATAAAATAATTTATCTTTTATAAAATTGCATCTTTTACAGGAATAGTATATAGAATGTGGACATTACAAAGGTCCATCAAACTCAATAACACTT F2: 3 TACAGGAATAG 2 Unidirectional alignment (log-probability: -43.5) ATTTTATTAAATAGAAAATATTTTAACGTAGAAAATGTCC----gataaggaCATATgTCcTACACCTGTAATGTTTCCAGGTAGTTTGAGTTAT ATTTTATTAAATAGAAAATATTTTAACGTAGAAAATGTCCTTAT--------CATATATCTTACACCTGTAATGTTTCCAGGTAGTTTGAGTTAT Template switch alignment (log-probability: -27.7) ATTTTATTAAATAGAAAATATTTTAACGTAGAAAATGTCC|GATAAGGACAT|ATGTCC-------------TACACCTGTAATGTTTCCAGGTAGTTTGAGTTAT ATTTTATTAAATAGAAAATATTTTAACGTAGAAAATGTCC|GATAAGGACAT|ATGTCCTTATCATATATCTTACACCTGTAATGTTTCCAGGTAGTTTGAGTTAT ========== Event 2933 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CTACTTACTACTCTTGCTGTAG----------TAAAAGAACCTTATGGTTCTTTTACTTTAGACTAGGTGATTATAT ↑ 1 3 4 2 Chimp: CCACTTACTACTCTTGCTGTAA----AGAGTAGTAAAGAACCATAAGGTTCTTTTACTTTAGACTAGGTGATTATAT ↓ 1 3 4 2 Gorilla: CCACTTACTACTCTTGCTGTAG----------CAAAAGAACCTTATGGTTCTTTTACTTTAGACTAGGTGATTATAT Human: CTACTTACTACTCTTGCTGTAG----------TAAAAGAACCTTATGGTTCTTTTACTTTAGACTAGGTGATTATAT Cluster: [ ] Orangutan: CCACTTATTATTCTTGCTGTAGAAAA------GAAAAGAATCATAAGGTTCTTTTACTTTAGACTAGGTGATTATAT Chimp > Human ------------- chr5:129833554-129833568 Template switch process: F1: L TAACTGAAACATTTCAGTGTCTACTTACTACTCTTGCTGTA 1 F3: 4 GGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG R RF: TAACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTAAAGAGTAGTAAAGAACCATAAGGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG RR: ATTGACTTTGTAAAGTCACAGGTGAATGATGAGAACGACATTTCTCATCATTTCTTGGTATTCCAAGAAAATGAAATCTGATCCACTAATATAATAAATTAC F2: 3 TATTCCAAGAAAATG 2 Unidirectional alignment (log-probability: -39.5) AACTGAAACATTTCAGTGTCtACTTACTACTCTTGCTGT----AGTA--AAAGAACCtTAtGGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG AACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTAAAGAGTAGTAAAGAACCATAAGGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG Template switch alignment (log-probability: -23.1) AACTGAAACATTTCAGTGTCtACTTACTACTCTTGCTGTA|GTAAAAGAACCTTAT|GGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG AACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTA|GTAAAAGAACCTTAT|GGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG Chimp > Gorilla --------------- chr17:44328226-44328240 Template switch process: F1: L TAACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTA 1 F3: 4 GGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG R RF: TAACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTAAAGAGTAGTAAAGAACCATAAGGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG RR: ATTGACTTTGTAAAGTCACAGGTGAATGATGAGAACGACATTTCTCATCATTTCTTGGTATTCCAAGAAAATGAAATCTGATCCACTAATATAATAAATTAC F2: 3 TATTCCAAGAAAACG 2 Unidirectional alignment (log-probability: -35.1) AACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTAgcA--------AAAGAACCtTAtGGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG AACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTA--AAGAGTAGTAAAGAACCATAAGGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG Template switch alignment (log-probability: -23.2) AACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTA|GcAAAAGAACCTTAT|GGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG AACTGAAACATTTCAGTGTCCACTTACTACTCTTGCTGTA|GTAAAAGAACCTTAT|GGTTCTTTTACTTTAGACTAGGTGATTATATTATTTAATG ========== Event 2934 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: aatatgtcactgtgcctgacacataagatCTCAATAAACCATGTTAAATGAAACATATCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTGATATGTTTATTGTAATTAAACTGCTTACAATAGACTTGATGCAGAAATGGTGCTAGATATTCATAAATCTGTTGGCACCA ↓ 4 3 1 2 Chimp: aatatgtcactgtgccggacacataagatCTCAATAAACCATGTTAAATGAAACATATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTGAATATCTTGCACCATTTCTGCATCAAGTCTATTGTAAGCAGTTTAATTACAATAAACATATCAGTTTGATATGTTTCACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGATATGTTTATTGTAATTAAACTGCTTACAATAGACTTGATGCAGAAATGGTGCTAGATATTCATAAATCTGTTGGCACCA ↑ 4 3 1 2 Gorilla: aatatgtcactgtgcctgacacataagatCTCAATAAACCATGTTAAATGAAACATATCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTGATATGTTTATTGTAATTAAACTGCTTACAATAGACTTGATGCAGAAATGGTGCTAGATATTCATAAATCTGTTGGCACCA Human: aatatgtcactgtgcctgacacataagatCTCAATAAACCATGTTAAATGAAACATATCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTGATATGTTTATTGTAATTAAACTGCTTACAATAGACTTGATGCAGAAATGGTGCTAGATATTCATAAATCTGTTGGCACCA Cluster: [ ] Orangutan: aatatgtcactgtgcctgacacataagatCTCAATAAACCATGTTAAATGAAACACATCAAACTGATACGTTTATTGTAATTAAACTGCTTACAATAGACTTGACGCAGAAGTGGTGCTAGATATTCATAAATCTGTTGGCACCAACGAAGAGTTGCTGCATCAATAAAGATTTGGTACAGAGAGACTTACAAAGAATATACATTAACAGCAAACCACATACACTTTATCATCTGTATGATCCTTCCCCACACGACTGATTAAGAAAAACAAATCTCACATACCTAGATGGCTCAAAAGCACTATCCTCCACTAATGGGGGGGATAATGGCAATTTCGTCTCCAGGTTGAAGCAGGAGGAGCTGATCTCCAAGCTCGACATATTCTTGACGAACAGCTAATATTATCTGATTTCTAACATCAGCCAATCTAAAGGGGAAAAAATATGACTCAAAGTATCAACGCTATGATAGACCTCAAATCGCTTCAGCTGCAATTAGAGATATCACATAGATATAATTATATAAAGCATCACTTGCAAAATTACCAATTAAATTTACACATAGTATATGGAGAAAGGACATATCCACTGAAGAACATACTTATACACCACAAAGATATGTTAAACTGCTGTCAACTCTTTATTGGATGTTGTACGCCTTGGGGAATTAAACAACAAAAAAATGCACAAAAACCACACCAGACTGGAGGCAACACTCAAACCAGGTCAAAAGAAAAGTTTCCAATCAGTACATGGCCTTTCCAGGGTCCTTCTCTCCATGTGTTCAAGCACAAGTAGAGCTGCCCACAAACTATGCCTGTACACATTATCCTACTCAAATATGGATTAAGTTGCTTAGAAAGATGAAAAGATAGCATAGGTCATAAAGCCACCTGCAATACAGCTTTATTAGCTGTTCCTTTATACCTGAACAATGGTAAGCTTTCTTTTCAGGCACAGTGAAAATGTATACAAGACCAGCTATCTTCCTCCAGGTAAAGCAGAATGGGAGACCCCACTGTGTTTCATTGATTATCAGGCCACTGTAAGAGCAACTTAAAAGATGAAATCATGAAGTGGTTTGCTTTTAAACACTTATTGTGGAGTATCTTTTACACAGAACTAGGACTTCCAGGTTAAACATCTATACAAGCTTAAGTGACACCATTAATATTCCTGAATCACCCTCAAATAAGTCACTTTTAAATTTTGTTCCAAAAAGAACTTGAAGTGGGAATGACATAACTAAAATTACAGGTTTTTCAAGAACCAGaaaaaaaaTTAAATATTACAAAAACTCAAATTCAGCAGCATCTAGGATTTGTTGTAACTCATTTTTCTTTTAATCTTAGAAATTTCTATGTTGAGCTCTCTAAAGAGAGGGGCAGAACAAAATGTTTAAAGCACACATTTTTAACAGAATTTGTAACAATTTCATTTAATGTTATAAAATTGCAGAAGTGACGTGTGCAGTGTTTTGTAAATTATCAAAGAGAATATAATCATGCCCCTCTGGGGTTCACTGTGTTTTGGGGTAAAATATCTTTAACCTTTCTTTAAAATACGGTGCACATTTAGAGTTTTTCAGTGTTCCAAAAAATACAACTAACGATTCTTTTTGACATTAAGCACGGAAATCGAAATTAACCTTATTTTTACTTTTATCATTTATGTATTTTGAAAATATTTAACTGTTACTCATATGCATTCTACAAATTTTTACTACCCACCCATGTCTAGCTTTCTATCTCCTTTCCACNNNNNNNNNNCCAGaaaaaatataatcggtcggtcataaagacacatgcacacgtctgtcactgcagcactattcacaatagcaaagacatggaatcactaaatggcccatcagtgtagactggataaagaaaatgtggtacatatacatcatggaatactatgcagccataagaaagaacaagatcaagtcctttgcagggacatggatggagctggaggccattatccttagccaactaatgcgggaacataaaaccaaataccaaatgttctcacttacaagtgggagataaatattgagtacacatggacacaaagaaggaaaccatagacactggagcctacttgagggtggagggtgggaggagggagaggatcgaaaaaataactgatgggcactagacttaatacctgggtgacaaaattatctgtacaagaaaccgcctgggtgacaaaattatctgtacaagaaaccgccatgatacaagttcccctgaacttaaaaGTTAAATAAATTCTTTTTAAGTTGGCTCTTTTACTTattagctatgtgattagctatgtgatcataggcaagttttttaagtcctctgaatttgtttttctacctgcaaaatatagatattaatatgtcactgtgcctgacacataagatCTCAATAAACCATGTTAAATGAAACACATCA--------------------------------------------------------------------------------------------------------------------------AACTGATATGTTTATTGTAATTAAACTGCTTACAATAGA--CGACGCAGAAGTGGTGCTAGATATTCATAAATCTGTTGGCACCA Human > Chimp ------------- chr5:120353952-120354026 Template switch process: F1: L CACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGA 1 F3: 4 CACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGATATGTTTATTGTAATTAAACTGCTTACAATAGAC R RF: CACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGATATGTTTATTGTAATTAAACTGCTTACAATAGACTTGATGCAGAAATGGTGCTAGATAT RR: GTGTATTCTAGAGTTATTTGGTACAATTTACTTTGTATAGTTTGACTATACAAATAACATTAATTTGACGAATGTTATCTGAACTACGTCTTTACCACGATCTATA F2: 3 TTTGTATAGTTTGACTATACAAATAACATTAATTTGACGAATGTTATCTGAACTACGTCTTTACCACGTTCTATA 2 Unidirectional alignment (log-probability: -180) gatctcaataaaccatgttaaatgaaacatatcaaactgaatatcttgcaccatttctgcatcaagtctattgtaagcagtttaattacaataaacatatcagtttgatatgtttCACATAAGATCTCAATAAACCATGTTAAATGAAACATATC -------------------------------------------------------------------------------------------------------------------CACATAAGATCTCAATAAACCATGTTAAATGAAACATATC Template switch alignment (log-probability: -31.1) GATCTCAATAAACCATGTTAAATGAAACATATCAAACTGA|ATATCTtGCACCATTTCTGCATCAAGTCTATTGTAAGCAGTTTAATTACAATAAACATATCAGTTTGATATGTTT|CACATAAGATCTCAATAAACCATGTTAAATGAAACATATC GATCTCAATAAACCATGTTAAATGAAACATATCAAACTGA|ATATCTAGCACCATTTCTGCATCAAGTCTATTGTAAGCAGTTTAATTACAATAAACATATCAGTTTGATATGTTT|CACATAAGATCTCAATAAACCATGTTAAATGAAACATATC Gorilla > Chimp --------------- chr5:120353952-120354026 Template switch process: F1: L CACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGA 1 F3: 4 CACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGATATGTTTATTGTAATTAAACTGCTTACAATAGAC R RF: CACATAAGATCTCAATAAACCATGTTAAATGAAACATATCAAACTGATATGTTTATTGTAATTAAACTGCTTACAATAGACTTGATGCAGAAATGGTGCTAGATAT RR: GTGTATTCTAGAGTTATTTGGTACAATTTACTTTGTATAGTTTGACTATACAAATAACATTAATTTGACGAATGTTATCTGAACTACGTCTTTACCACGATCTATA F2: 3 TTTGTATAGTTTGACTATACAAATAACATTAATTTGACGAATGTTATCTGAACTACGTCTTTACCACGTTCTATA 2 Unidirectional alignment (log-probability: -181) gatctcaataaaccatgttaaatgaaacatatcaaactgaatatcttgcaccatttctgcatcaagtctattgtaagcagtttaattacaataaacatatcagtttgatatgtttCACATAAGATCTCAATAAACCATGTTAAATGAAACATATC -------------------------------------------------------------------------------------------------------------------CACATAAGATCTCAATAAACCATGTTAAATGAAACATATC Template switch alignment (log-probability: -31.6) GATCTCAATAAACCATGTTAAATGAAACATATCAAACTGA|ATATCTtGCACCATTTCTGCATCAAGTCTATTGTAAGCAGTTTAATTACAATAAACATATCAGTTTGATATGTTT|CACATAAGATCTCAATAAACCATGTTAAATGAAACATATC GATCTCAATAAACCATGTTAAATGAAACATATCAAACTGA|ATATCTAGCACCATTTCTGCATCAAGTCTATTGTAAGCAGTTTAATTACAATAAACATATCAGTTTGATATGTTT|CACATAAGATCTCAATAAACCATGTTAAATGAAACATATC ========== Event 2935 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAGTAACTACGCTAACTGGT------AGTTACTGTCCCTGAGATTATTTCAGCTA ↓ 13 4 2 Chimp: TTAGTAACTACGCTAACTGGTAACAGTAACTACTGTCCCTGAGATTATTTCAGCTA ↑ 13 4 2 Gorilla: TTAGTAACTACACTAACTGGT------AGTTACTGTCCCTGAGATTATTTCAGCTA Human: TTAGTAACTACGCTAACTGGT------AGTTACTGTCCCTGAGATTATTTCAGCTA Cluster: [ ] Orangutan: TTAGTAACTACGCTAACTGGT------AGTTACTGTCCCTGAGATTATTTCAGCTA Human > Chimp ------------- chr5:120151145-120151152 Template switch process: F1: L TTTAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGTA 1 F3: 4 TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT R RF: TTTAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGTAGTTACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT RR: AAATCTGTGGGTTCGGAGTTAATCATTGATGCGATTGACCATCAATGACAGGGACTCTAATAAAGTCGATTATAAAAATCAATA F2: 3 CAATGACA 2 Unidirectional alignment (log-probability: -29.8) TAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGTaacAGTaacTACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT TAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGT---AGT---TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT Template switch alignment (log-probability: -16.3) TAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGTA|ACAGTAAC|TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT TAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGTA|ACAGTAAC|TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT Gorilla > Chimp --------------- chr5:120151145-120151152 Template switch process: F1: L TTTAGACACCCAAGCCTCAATTAGTAACTACGCTAACTGGTA 1 F3: 4 TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT R RF: TTTAGACACCCAAGCCTCAATTAGTAACTACACTAACTGGTAGTTACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT RR: AAATCTGTGGGTTCGGAGTTAATCATTGATGTGATTGACCATCAATGACAGGGACTCTAATAAAGTCGATTATAAAAATCAATA F2: 3 CAATGACA 2 Unidirectional alignment (log-probability: -34.8) TAGACACCCAAGCCTCAATTAGTAACTACgCTAACTGGTaacAGTaacTACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT TAGACACCCAAGCCTCAATTAGTAACTACACTAACTGGT---AGT---TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT Template switch alignment (log-probability: -22.3) TAGACACCCAAGCCTCAATTAGTAACTACgCTAACTGGTA|ACAGTAAC|TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT TAGACACCCAAGCCTCAATTAGTAACTACACTAACTGGTA|ACAGTAAC|TACTGTCCCTGAGATTATTTCAGCTAATATTTTTAGTTAT ========== Event 2936 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGAGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGG--------------------------CTGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGAGATAGGAAGTGCAGCAGAGGGGAGATCCGAAGAGCTCTGATTCAGACAAGGAGCATCTGCAGTGAATTTAGGTGGAGGCAGC Chimp: GAGAGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGG--------------------------CTGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGAGATAGGAAGTGCAGCAGAGGGGAGATCCGAAGAGCTCTGATTCAGACAAGGAGCATCTGCAGTGAATTTAGGTGGAGGCAGC Gorilla: GAGAGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGCCTCCAGATGACCTCCAGATGTGAGAATGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGAGATAGGAAGTGCAGCAGAGGGGAGATCCGAAGAGCTCTGATTCAGACAAGGAGCATCTGCAGTGAATTTAGTTGGAGGCAGC ↑ 4 1 3 2 Human: GAGAGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGG--------------------------CTGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGAGATAGGAAGTGCAGCAGAGGGGAGATCCGAAGAGCTCTGATTCAGACAAGGAGCATCTGCAGTGAATTTAGGTGGAGGCAGC Cluster: [ ] Orangutan: GAGAGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGG--------------------------CTGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGAGATAGGAAGTGCAGCAGAGGGGAGATCCGAAGAGCTCTGATTCAGACATGGAGCATCTGCAGTGAATTTAGGCGGAGGCAGC Human > Gorilla --------------- chr17:52364343-52364349 Template switch process: F1: L AGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGC 1 F3: 4 TGACCTCCAGATGTGAGAA-------TGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGA R RF: AGTAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGCTGGGAGGGGAACACTGGAAAGCAGTGGTGCCTTTCAGGGAGATAGGAAGTGCAGCAGAGGGGAGATCCGAAGAGCTCTGATTCAGACAAGGAGCATCTGCAG RR: TCATTACTTAGATTTAACTGGAGGTCTACACTCTTACCTCCGACCCTCCCCTTGTGACCTTTCGTCACCACGGAAAGTCCCTCTATCCTTCACGTCGTCTCCCCTCTAGGCTTCTCGAGACTAAGTCTGTTCCTCGTAGACGTC F2: 3 AGACCTC 2 Unidirectional alignment (log-probability: -48.3) TAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGCctccagatgacctccagatgtgagaaTGGGAGGGGAACACTGGAAAG TAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGC--------------------------TGGGAGGGGAACACTGGAAAG Template switch alignment (log-probability: -32.7) TAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGC|CTcCAGA|TGACCTCCAGATGTGAGAA-------TGGGAGGGGAACACTGGAAAG TAATGAATCTAAATTGACCTCCAGATGTGAGAATGGAGGC|CTGCAGA|TGACCTCCAGATGTGAGAATGGAGGCTGGGAGGGGAACACTGGAAAG ========== Event 2937 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTAGTATAAATTTCCATCCA--------------ATTAAGGAAGGG--AAACAGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGA Chimp: ATTAGTATAAGTTTCCATCCA-------ATACTTGATTAAGGAAGGG--AAACAGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGA ↓ 1 4 3 2 Gorilla: ATTAGTATAAGTTTCCATCCAATACTTG-------ATTAAGGAAAGG----CCTGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGA Human: ATTAGTATAAATTTCCATCCA--------------ATTAAGGAAGGG--AAACAGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGA Cluster: [ ] Orangutan: ATTAGTATAAGTTTCCATCTAATACTTG-------ATTAAGGAAGGGAA--ACAGAGCAAATTTCAGGCCGGCATAGGAAGCCATCTCTGA Chimp > Gorilla --------------- chr17:52723068-52723074 Template switch process: F1: L TTATAAGGAGGCTTCAGAGAATTAGTATAAGTTTCCATCCAATACTTGATTAAGGAA 1 F3: 4 AGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGAGTG R RF: TTATAAGGAGGCTTCAGAGAATTAGTATAAGTTTCCATCCAATACTTGATTAAGGAAGGGAAACAGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGAGTG RR: AATATTCCTCCGAAGTCTCTTAATCATATTCAAAGGTAGGTTATGAACTAATTCCTTCCCTTTGTCTCGTTTAGAGTCCGGACGTATCCTTCGGTAGAGACTCAC F2: 3 GTCCGGA 2 Unidirectional alignment (log-probability: -27.9) AGAATTAGTATAAGTTTCCATCCAATACTTGATTAAGGAAaGG--cCtGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGAGTG AGAATTAGTATAAGTTTCCATCCAATACTTGATTAAGGAAGGGAAACAGAGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGAGTG Template switch alignment (log-probability: -17) AGAATTAGTATAAGTTTCCATCCAATACTTGATTAAGGAA|AGGCCTG|AGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGAGTG AGAATTAGTATAAGTTTCCATCCAATACTTGATTAAGGAA|AGGCCTG|AGCAAATCTCAGGCCTGCATAGGAAGCCATCTCTGAGTG ========== Event 2938 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATGACTTAGATATTAAGAT----TAGCCTTAAAAGAAATACAGATTCAAAAT Chimp: TTATGACTTAGATATTAAGAT----TAGCCTTAAAAGAAATACAGATTCAAAAT ↓ 13 4 2 Gorilla: TTATGACTTAGATATTAAGATTTTAAGGCTTTAAAAGAAATACAGATTCAAAAT ↑ 13 4 2 Human: TTATGACTTAGATATTAAGAT----TAGCCTTAAAAGAAATACAGATTCAAAAT Cluster: [ ] Orangutan: TTATGACTTAGATATTAAGAT----TAGCCTTAAAAGAAATACAGATACAAAAT Human > Gorilla --------------- chr17:41739149-41739156 Template switch process: F1: L TTATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATT 1 F3: 4 TTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT R RF: TTATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATTAGCCTTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT RR: AATATGAAGACAGTTCAGGAAATACTGAATCTATAATTCTAATCGGAATTTTCTTTATGTCTAAGTTTTAATAACGAGATCAACCA F2: 3 TCGGAATT 2 Unidirectional alignment (log-probability: -27.7) ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATTttaagGCtTTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATTA----GCCTTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT Template switch alignment (log-probability: -16.8) ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATT|TTAAGGCT|TTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATT|TTAAGGCT|TTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT Chimp > Gorilla --------------- chr17:41739149-41739156 Template switch process: F1: L TTATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATT 1 F3: 4 TTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT R RF: TTATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATTAGCCTTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT RR: AATATGAAGACAGTTCAGGAAATACTGAATCTATAATTCTAATCGGAATTTTCTTTATGTCTAAGTTTTAATAACGAGATCAACCA F2: 3 TCGGAATT 2 Unidirectional alignment (log-probability: -27.7) ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATTttaagGCtTTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATTA----GCCTTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT Template switch alignment (log-probability: -16.8) ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATT|TTAAGGCT|TTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT ATACTTCTGTCAAGTCCTTTATGACTTAGATATTAAGATT|TTAAGGCT|TTAAAAGAAATACAGATTCAAAATTATTGCTCTAGTTGGT ========== Event 2939 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAG---------GTCAGACACAGCCTTGGCTCACTGGGCCAGA Chimp: ACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAG---------GTCAGACACAGCCTTGGCTCACTGGGCCAGA ↓ 1 3 2 4 ↑ 3 1 2 4 Gorilla: ACTCTGTACAGTCCTACAGTTTGTCTGACCTGCTGAACCAG------------------GGCCTTGGCTCACTGGGCCAGA ↓ 3 1 2 4 ↑ 1 3 2 4 Human: ACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAG---------GTCAGACACAGCCTTGGCTCACTGGGCCAGA Cluster: [ ] Orangutan: CCTCTGTACAGTCCTACAGTTTGTCTGACCTGCTTTAGCGGATCAGACAC---------AGCCTTGGCTCACTGGGCCAGA Gorilla > Human --------------- chr5:126622621-126622639 Template switch process: F1: L CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTTTGACCTG 1 F3: 4 GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT R RF: CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTCTGACCTGCTGAACCAGGGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT RR: GTATTTTTACTTTTATATGAGACATGTCAGGATGTCAAACAGACTGGACGACTTGGTCCCGGAACCGAGTGACCCGGTCTACTGCCGGTAATGTTCTTA F2: 3 ACACAGACTGGACGACTTG 2 Unidirectional alignment (log-probability: -51.7) GAAAATATACTCTGTACAGTCCTACAGTTTGTtTGACCTGgTtcAgCAGGtcagacacaGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT GAAAATATACTCTGTACAGTCCTACAGTTTGTCTGACCTGCTGAACCAGG---------GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Template switch alignment (log-probability: -29.4) GAAAATATACTCTGTACAGTCCTACAGTTTGTtTGACCTG|GTTCAGCAGGTCAGACAcA|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT GAAAATATACTCTGTACAGTCCTACAGTTTGTCTGACCTG|GTTCAGCAGGTCAGACAAA|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Human > Gorilla --------------- chr17:41059546-41059563 Template switch process: F1: L CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGT 1 F3: 4 GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT R RF: CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAGGTCAGACACAGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT RR: GTATTTTTACTTTTATATGAGACATGTCAGGATGTCAAACAAACTGGACCAAGTCGTCCAGTCTGTGTCGGAACCGAGTGACCCGGTCTACTGCCGGTAATGTTCTTA F2: 3 GGACCAAGTCGTCCAGTC 2 Unidirectional alignment (log-probability: -39.2) ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTcTGACCTGcTgaAcCAGG---------GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAGGTCAGACACAGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Template switch alignment (log-probability: -18) ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGT|CTGACCTGCTGAACCAGG|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGT|CTGACCTGCTGAACCAGG|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Gorilla > Chimp --------------- chr5:59729732-59729750 Template switch process: F1: L CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTTTGACCTG 1 F3: 4 GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT R RF: CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTCTGACCTGCTGAACCAGGGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT RR: GTATTTTTACTTTTATATGAGACATGTCAGGATGTCAAACAGACTGGACGACTTGGTCCCGGAACCGAGTGACCCGGTCTACTGCCGGTAATGTTCTTA F2: 3 ACACAGACTGGACGACTTG 2 Unidirectional alignment (log-probability: -51.7) GAAAATATACTCTGTACAGTCCTACAGTTTGTtTGACCTGgTtcAgCAGGtcagacacaGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT GAAAATATACTCTGTACAGTCCTACAGTTTGTCTGACCTGCTGAACCAGG---------GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Template switch alignment (log-probability: -29.4) GAAAATATACTCTGTACAGTCCTACAGTTTGTtTGACCTG|GTTCAGCAGGTCAGACAcA|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT GAAAATATACTCTGTACAGTCCTACAGTTTGTCTGACCTG|GTTCAGCAGGTCAGACAAA|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Chimp > Gorilla --------------- chr17:41059546-41059563 Template switch process: F1: L CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGT 1 F3: 4 GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT R RF: CATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAGGTCAGACACAGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT RR: GTATTTTTACTTTTATATGAGACATGTCAGGATGTCAAACAAACTGGACCAAGTCGTCCAGTCTGTGTCGGAACCGAGTGACCCGGTCTACTGCCGGTAATGTTCTTA F2: 3 GGACCAAGTCGTCCAGTC 2 Unidirectional alignment (log-probability: -39.2) ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTcTGACCTGcTgaAcCAGG---------GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGTTTGACCTGGTTCAGCAGGTCAGACACAGCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT Template switch alignment (log-probability: -18) ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGT|CTGACCTGCTGAACCAGG|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT ATAAAAATGAAAATATACTCTGTACAGTCCTACAGTTTGT|CTGACCTGCTGAACCAGG|GCCTTGGCTCACTGGGCCAGATGACGGCCATTACAAGAAT ========== Event 2940 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: acacaggggagagacaggcacagagaaaaggaggaggaaatgtg-------------actatggagacagagataggaatgatgcagtcacatgcctgggaaaccaccagaagttggaagaggcaaggaatggaa Chimp: ACACAGGGGAGAGACAGGCACGGAGTAAAGGAGGAGGAAATGTG-------------ACTATGGAGACAGAGATAGGAATGATGCAGTCACAtgcctgggaaaccaccagaagttggaagaggcaaggaatggaa ↑ 3 2 4 Gorilla: ACACAGGGGAGAGACAGGCACAGAGAAAAGGAGGAGGAAATGTAGTCACATTTCCTATCTCtggagacagagataggaatgatgcagtcacatgcctgggaaaccaccagaagttggaagaggcaaggaatagaa Human: acacaggggagagacaggcacagagaaaaggaggaggaaatgtg-------------actatggagacagagataggaatgatgcagtcacatgcctgggaaaccaccagaagttggaagaggcaaggaatggaa Cluster: [ ] Orangutan: acacaggggagagacaggcacagagaaaaggaggaggaaatgtg-------------actatggagacagagattggaatgatgcagtcacacgcctgggaaaccaccagaagttggaagaggcaaggaatggaa Gorilla > Chimp --------------- chr5:60045727-60045731 Template switch process: F1: L AGGCTTTCCTTATAAATGAAACACAGGGGAGAGACAGGCACGGAGTAAAGGAGGAGGAAATGT 1 F3: 4 TGGAG R RF: AGGCTTTCCTTATAAATGAAACACAGGGGAGAGACAGGCACAGAGAAAAGGAGGAGGAAATGTAGTCACATTTCCTATCTCTGGAG RR: TCCGAAAGGAATATTTACTTTGTGTCCCCTCTCTGTCCGTGTCTCTTTTCCTCCTCCTTTACATCAGTGTAAAGGATAGAGACCTC F2: 3 ATCAG 2 Unidirectional alignment (log-probability: -38.1) CAGGGGAGAGACAGGCACgGAGtAAAGGAGGAGGAAATGtgacTA-----------------TGGAG CAGGGGAGAGACAGGCACAGAGAAAAGGAGGAGGAAATG----TAGTCACATTTCCTATCTCTGGAG Template switch alignment (log-probability: -27) CAGGGGAGAGACAGGCACgGAGtAAAGGAGGAGGAAATGT|GACTA|TGGAG CAGGGGAGAGACAGGCACAGAGAAAAGGAGGAGGAAATGT|GACTA|TGGAG ========== Event 2941 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCCAAAACACTTGATTATCAGT----AGAACAGAACTTCCTGTTCTACCAGGTAAAGAACAACTTGTG ↑ 1 4 3 2 Chimp: GCCCAAAACACTTGATTATCAAT--CACGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTG Gorilla: GCCCAAAACACTTGATTATCAATCA--CGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTG ↓ 1 4 3 2 Human: GCCCAAAACACTTGATTATCAGT----AGAACAGAACTTCCTGTTCTACCAGGTAAAGAACAACTTGTG Cluster: [ ] Orangutan: GCCCAAAACACTTGATTATCAATCA--CGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTG Chimp > Human ------------- chr5:126179217-126179225 Template switch process: F1: L GTAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCA 1 F3: 4 AACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTGG R RF: GTAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCAATCACGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTGG RR: CATCTCCTTCGAGTAACGGACGGGTTTTGTGAACTAATAGTTAGTGCACGGGGTGAAGGACAAGATGGTCCATTTCTTGTTGAACACGTCACC F2: 3 GACAAGATG 2 Unidirectional alignment (log-probability: -34.6) TAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCAgtagaacagA-----------ACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG TAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCA---------ATCACGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG Template switch alignment (log-probability: -22.4) TAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCA|GTAGAACAG|aACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG TAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCA|GTAGAACAG|CACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG Gorilla > Human --------------- chr5:126179217-126179225 Template switch process: F1: L GTAGAGGAAGCTCATTGCCTGCCCAAAACACTTGATTATCA 1 F3: 4 AACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTGG R RF: GTAGAGGAAGCTCACTGCCTGCCCAAAACACTTGATTATCAATCACGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTGG RR: CATCTCCTTCGAGTGACGGACGGGTTTTGTGAACTAATAGTTAGTGCACGGGGTGAAGGACAAGATGGTCCATTTCTTGTTGAACACGTCACC F2: 3 GACAAGATG 2 Unidirectional alignment (log-probability: -39.7) TAGAGGAAGCTCAtTGCCTGCCCAAAACACTTGATTATCAgtagaacagA-----------ACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG TAGAGGAAGCTCACTGCCTGCCCAAAACACTTGATTATCA---------ATCACGTGCCCCACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG Template switch alignment (log-probability: -27.9) TAGAGGAAGCTCAtTGCCTGCCCAAAACACTTGATTATCA|GTAGAACAG|aACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG TAGAGGAAGCTCACTGCCTGCCCAAAACACTTGATTATCA|GTAGAACAG|CACTTCCTGTTCTACCAGGTAAAGAACAACTTGTGCAGTG ========== Event 2942 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCAGCAGTGCACTTTACAAC----ATAACTGGGTACAAACAACACACAACTGAGAAACAA ↓ 1 3 4 2 Chimp: GTCAGCAGTGCACTTTACAACGTTTGTACCCAGGTACAAACAACACACAACTGAGAAACAA Gorilla: gtcagcagtgcactttacagt----gtaactgggtacaaacaACACACAACTGAGAAACAA Human: GTCAGCAGTGCACTTTACAAC----ATAACTGGGTACAAACAACACACAACTGAGAAACAA Cluster: [ ] Orangutan: GTCAGCAGTGCACTTTACAAC----GTAACTGGGTACAAACAACACACAACTGATGAACAA Human > Chimp ------------- chr5:59485762-59485772 Template switch process: F1: L ATTTCTACTCATGACCCCCAGTCAGCAGTGCACTTTACAAC 1 F3: 4 GGTACAAACAACACACAACTGAGAAACAACACTTCTCCTT R RF: ATTTCTACTCATGACCCCCAGTCAGCAGTGCACTTTACAACATAACTGGGTACAAACAACACACAACTGAGAAACAACACTTCTCCTT RR: TAAAGATGAGTACTGGGGGTCAGTCGTCACGTGAAATGTTGTATTGACCCATGTTTGTTGTGTGTTGACTCTTTGTTGTGAAGAGGAA F2: 3 ACCCATGTTTG 2 Unidirectional alignment (log-probability: -35.8) TTTCTACTCATGACCCCCAGTCAGCAGTGCACTTTACAAC------GtttgtacccaGGTACAAACAACACACAACTGAGAAACAACACTTCTCCTT TTTCTACTCATGACCCCCAGTCAGCAGTGCACTTTACAACATAACTG----------GGTACAAACAACACACAACTGAGAAACAACACTTCTCCTT Template switch alignment (log-probability: -16.6) TTTCTACTCATGACCCCCAGTCAGCAGTGCACTTTACAAC|GTTTGTACCCA|GGTACAAACAACACACAACTGAGAAACAACACTTCTCCTT TTTCTACTCATGACCCCCAGTCAGCAGTGCACTTTACAAC|GTTTGTACCCA|GGTACAAACAACACACAACTGAGAAACAACACTTCTCCTT ========== Event 2943 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATACATTCATCAATTATGC---CAAGCTTTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATT Chimp: ACATACATTCATCAATTATGC---CAAGCTTTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATT ↑ 1 4 3 2 Gorilla: ACATACATTCATCAATTATGCCATCAATAATTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATT ↓ 1 4 3 2 Human: ACATACATTCATCAATTATGC---CAAGCTTTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATT Cluster: [ ] Orangutan: ACATACATTCATCAATTATGC---CAAGCTTTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATT Gorilla > Human --------------- chr5:128173147-128173150 Template switch process: F1: L TTCAGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA 1 F3: 4 TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC R RF: TTCAGGTTTAGAACAGATAAACATACATTCATCAATTATGCCATCAATAATTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC RR: AAGTCCAAATCTTGTCTATTTGTATGTAAGTAGTTAATACGGTAGTTATTAAAGATTAATAAGTTTCGATTTTTGATAAACCTCTATAAG F2: 3 TCGA 2 Unidirectional alignment (log-probability: -25.3) AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA------AgctTTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCATCAATAA---TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC Template switch alignment (log-probability: -16.3) AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA|AGCT|TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA|AGCT|TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC Gorilla > Chimp --------------- chr5:61288220-61288223 Template switch process: F1: L TTCAGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA 1 F3: 4 TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC R RF: TTCAGGTTTAGAACAGATAAACATACATTCATCAATTATGCCATCAATAATTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC RR: AAGTCCAAATCTTGTCTATTTGTATGTAAGTAGTTAATACGGTAGTTATTAAAGATTAATAAGTTTCGATTTTTGATAAACCTCTATAAG F2: 3 TCGA 2 Unidirectional alignment (log-probability: -25.3) AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA------AgctTTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCATCAATAA---TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC Template switch alignment (log-probability: -16.3) AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA|AGCT|TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC AGGTTTAGAACAGATAAACATACATTCATCAATTATGCCA|AGCT|TTTCTAATTATTCAAAGCTAAAAACTATTTGGAGATATTC ========== Event 2944 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TACTTTAACTGACCCATACCTATTGATAACCAAGTTTGGC---TCGCATGCTAAAGAGGATGTCTC Chimp: TACTTTAACTGACCCATACCTATTGATAACCAAGTTTGGC---TCGCATGCTAAAGAGGATGTCTC ↓ 3 2 1 4 Gorilla: TACTTTAACTGACCCATACCTATTGATAACCAAGGTTATCAATAGGCATGCTAAAGAGGATGTCTC ↑ 3 2 1 4 Human: TACTTTAACTGACCCATACCTATTGATAACCAAGTTTGGC---TCGCATGCTAAAGAGGATGTCTC Cluster: [ ] Orangutan: TACTTTAACTGACCCATACCTATTGATAACCAAGTTTGGC---TCGCGTGCTAAAGAGGATGTCTC Human > Gorilla --------------- chr17:56107117-56107127 Template switch process: F1: L CCCATGCTACTTTAACTGACCCATACCTATTGATAACCAAG 1 F3: 4 GCATGCTAAAGAGGATGTCTCCTACGCTCATCCAGAATGG R RF: CCCATGCTACTTTAACTGACCCATACCTATTGATAACCAAGTTTGGCTCGCATGCTAAAGAGGATGTCTCCTACGTTCATCCAGAATGG RR: GGGTACGATGAAATTGACTGGGTATGGATAACTATTGGTTCAAACCGAGCGTACGATTTCTCCTACAGAGGATGCAAGTAGGTCTTACC F2: 3 GATAACTATTG 2 Unidirectional alignment (log-probability: -42) CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAGgTTatcaataG----GCATGCTAAAGAGGATGTCTCCTACGcTCATCCAGAATGG CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAGTTT-------GGCTCGCATGCTAAAGAGGATGTCTCCTACGTTCATCCAGAATGG Template switch alignment (log-probability: -22.6) CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAG|GTTATCAATAG|GCATGCTAAAGAGGATGTCTCCTACGcTCATCCAGAATGG CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAG|GTTATCAATAG|GCATGCTAAAGAGGATGTCTCCTACGTTCATCCAGAATGG Chimp > Gorilla --------------- chr17:56107117-56107127 Template switch process: F1: L CCCATGCTACTTTAACTGACCCATACCTATTGATAACCAAG 1 F3: 4 GCATGCTAAAGAGGATGTCTCCTACGCTCATCCAGAATGG R RF: CCCATGCTACTTTAACTGACCCATACCTATTGATAACCAAGTTTGGCTCGCATGCTAAAGAGGATGTCTCCTACGTTCATCCAGAATGG RR: GGGTACGATGAAATTGACTGGGTATGGATAACTATTGGTTCAAACCGAGCGTACGATTTCTCCTACAGAGGATGCAAGTAGGTCTTACC F2: 3 GATAACTATTG 2 Unidirectional alignment (log-probability: -42) CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAGgTTatcaataG----GCATGCTAAAGAGGATGTCTCCTACGcTCATCCAGAATGG CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAGTTT-------GGCTCGCATGCTAAAGAGGATGTCTCCTACGTTCATCCAGAATGG Template switch alignment (log-probability: -22.6) CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAG|GTTATCAATAG|GCATGCTAAAGAGGATGTCTCCTACGcTCATCCAGAATGG CCATGCTACTTTAACTGACCCATACCTATTGATAACCAAG|GTTATCAATAG|GCATGCTAAAGAGGATGTCTCCTACGTTCATCCAGAATGG ========== Event 2945 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAG---AAATGGAATTTctattccatgaataggcctattccatgaatttgcctattcATGGAATAGAAATAGAAAAAAGTTTTACTCTTTTCAA Chimp: GGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAG---AAATGGAATTTCTATT-----------------CCATGAATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTACTCTTTTCAA ↑ 4 3 2 1 Gorilla: GGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAG---------------------------------------------------------------AAATAGAAAAAAGTTTTACTCTTTTCAA Human: GGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAG---AAATGGAATTTctattccatgaataggcctattccatgaatttgcctattcATGGAATAGAAATAGAAAAAAGTTTTACTCTTTTCAA Cluster: [ ] Orangutan: GGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAGAAA----------------------------------------------------------------------CTCTTTTAGTCTTTTCAA Gorilla > Chimp --------------- chr5:57958793-57958806 Template switch process: F1: L AGGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAGAAATGGAA 1 F3: 4 ATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTACTCTTTTCAAAACTCTGCTGGG R RF: AGGGGGAAAATACCACTTCCATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTACTCTTTTCAAAACTCCGCTGGG RR: TCCCCCTTTTATGGTGAAGGTAAACGGATAAGTACCTTATCTTTATCTTTTTTCAAAATGAGAAAAGTTTTGAGGCGACCC F2: 3 AGTACCTTATCTTT 2 Unidirectional alignment (log-probability: -78.2) ATACCACTTCCatttgcctattcatggaatagaaatggaatttctattccatgaATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTAC ATACCACTTCC-------------------------------------------ATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTAC Template switch alignment (log-probability: -29.2) ATACCACTTCCATTTGCCTATTCATGGAATAGAAATgGAA|TTTCTATTCCATGA|ATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTAC ATACCACTTCCATTTGCCTATTCATGGAATAGAAATAGAA|TTTCTATTCCATGA|ATTTGCCTATTCATGGAATAGAAATAGAAAAAAGTTTTAC ========== Event 2946 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCCCCTCTGGTTGATCTTCCCTCAGGTAGGAAGTAGCCCTGAGGAGGGGG Chimp: CCCCCTCTGGTTGATCTTCCCTCAGGTGGGAAGTAGCCCTGAGGAGGGGG ↓ 3 2 4 ↑ 3 24 Gorilla: CCCCCTCTGGTTGATCTTCCCACCT-GAGGAAGTAGCCCTGAGGAGGGGG ↓ 13 4 ↑ 13 2 4 Human: CCCCCTCTGGTTGATCTTCCCTCAGGTAGGAAGTAGCCCTGAGGAGGGGG Cluster: [ ] Orangutan: CCCCCTCTGGTTGATCTTCCCTCAGGTGGAAAGTAGCCCTGAGGAGGGGG Gorilla > Human --------------- chr5:6338038-6338043 Template switch process: F1: L CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC 1 F3: 4 AGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGAGTTGTG R RF: CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCACCTGAGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTG RR: GGGACCCAGGACTAGTGGTCGGGGGAGACCAACTAGAAGGGTGGACTCCTTCATCGGGACTCCTCCCCCTCGTGTCTCCCCAACAC F2: 3 TGGACT 2 Unidirectional alignment (log-probability: -34.5) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCtCagGtAGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGaGTTGTG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCACCTG-AGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTG Template switch alignment (log-probability: -22) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|TCAGGT|AGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGaGTTGTG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|TCAGGT|AGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTG Human > Gorilla --------------- chr17:6461349-6461354 Template switch process: F1: L CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC 1 F3: 4 GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTG R RF: CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCTCAGGTAGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGAGTTGTG RR: GGGACCCAGGACTAGTGGTCGGGGGAGACCAACTAGAAGGGAGTCCATCCTTCATCGGGACTCCTCCCCCTCGTGTCTCCTCAACAC F2: 3 AGTCCA 2 Unidirectional alignment (log-probability: -33.1) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCaCctG-AGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGgGTTGTG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCTCAGGTAGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGAGTTGTG Template switch alignment (log-probability: -22) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|ACCTGA|GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGgGTTGTG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|ACCTGA|GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGAGTTGTG Gorilla > Chimp --------------- chr5:6507409-6507415 Template switch process: F1: L CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC 1 F3: 4 GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG R RF: CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCACCTGAGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG RR: GGGACCCAGGACTAGTGGTCGGGGGAGACCAACTAGAAGGGTGGACTCCTTCATCGGGACTCCTCCCCCTCGTGTCTCCCCAACACC F2: 3 GTGGACT 2 Unidirectional alignment (log-probability: -31) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC------tcaggtgGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCACCTGA-------GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG Template switch alignment (log-probability: -16.6) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|TCAGGTG|GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|TCAGGTG|GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG Chimp > Gorilla --------------- chr17:6461349-6461355 Template switch process: F1: L CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC 1 F3: 4 GAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG R RF: CCCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCTCAGGTGGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG RR: GGGACCCAGGACTAGTGGTCGGGGGAGACCAACTAGAAGGGAGTCCACCCTTCATCGGGACTCCTCCCCCTCGTGTCTCCCCAACACC F2: 3 GAGTCCA 2 Unidirectional alignment (log-probability: -29.6) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC-------acctgaGGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCCTCAGGTG------GGAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG Template switch alignment (log-probability: -16.6) CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|ACCTGAG|GAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG CCTGGGTCCTGATCACCAGCCCCCTCTGGTTGATCTTCCC|ACCTGAG|GAAGTAGCCCTGAGGAGGGGGAGCACAGAGGGGTTGTGG ========== Event 2947 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGTGAAATTGCAAAAATTGAA----ATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATG Chimp: TGTGTGAAATTGCAAAAATTGAA----ATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATG ↓ 1 4 3 2 Gorilla: TGTGTGAAATTGCAAAAATTGCAAGTACCAACCTCTTTGGTACTTGGTACTTATCCAAAATGTTCTCATG ↑ 1 4 3 2 Human: TGTGTGAAATTGCAAAAATTGAA----ATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATG Cluster: [ ] Orangutan: TGTGTGAAATTGCAAAAATTGAA----ATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTTATG Human > Gorilla --------------- chr17:36013957-36013963 Template switch process: F1: L TTCCCAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGCAA 1 F3: 4 CCTCTTTGGTACTTGGTACTTATCCAAAATGTTCTCATGT R RF: TTCCCAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGAAATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATGT RR: AAGGGTTTTGTGAACCGAAAACACACTTTAACGTTTTTAACTTTATCGGAGAAACCATGAACCATGAATAAGTTTTACAAGAGTACA F2: 3 AACCATG 2 Unidirectional alignment (log-probability: -37.9) CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGcaagtaccAA----CCTCTTTGGTACTTGGTACTTATcCAAAATGTTCTCATGT CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTG--------AAATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATGT Template switch alignment (log-probability: -27.7) CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGcAA|GTACCAA|CCTCTTTGGTACTTGGTACTTATcCAAAATGTTCTCATGT CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGAAA|GTACCAA|CCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATGT Chimp > Gorilla --------------- chr17:36013957-36013963 Template switch process: F1: L TTCCCAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGCAA 1 F3: 4 CCTCTTTGGTACTTGGTACTTATCCAAAATGTTCTCATGT R RF: TTCCCAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGAAATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATGT RR: AAGGGTTTTGTGAACCGAAAACACACTTTAACGTTTTTAACTTTATCGGAGAAACCATGAACCATGAATAAGTTTTACAAGAGTACA F2: 3 AACCATG 2 Unidirectional alignment (log-probability: -37.9) CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGcaagtaccAA----CCTCTTTGGTACTTGGTACTTATcCAAAATGTTCTCATGT CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTG--------AAATAGCCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATGT Template switch alignment (log-probability: -27.7) CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGcAA|GTACCAA|CCTCTTTGGTACTTGGTACTTATcCAAAATGTTCTCATGT CAAAACACTTGGCTTTTGTGTGAAATTGCAAAAATTGAAA|GTACCAA|CCTCTTTGGTACTTGGTACTTATTCAAAATGTTCTCATGT ========== Event 2948 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TTGATATTCAAGCCAATAATTGATATTCAAGTGACATAGTTATGTCACTAATGA Chimp: TTGATATTCAAGCCAATAATTTTACT--TGGTGACATAGTTATGTCACTAATGA Gorilla: TTGATATTCAAGCCAATAATTTCACT--TGGTGACATAGTTATGTCACTAATGA ↑ 1 3 4 2 Human: TTGATATTCAAGCCAATAATTGATATTCAAGTGACATAGTTATGTCACTAATGA Cluster: [ ] Orangutan: TTGGTATTCAAGCCAATAATTTTACT--TGGTGACATAGTTATGTCACTAATGA Human > Gorilla --------------- chr17:59179299-59179305 Template switch process: F1: L TTTCTTAAAAGAGAAATGAATTGATATTCAAGCCAATAATT 1 F3: 4 GTGACATAGTTATGTCACTAATGAAGGTAACCCATCCTCA R RF: TTTCTTAATAGAGAAATGAATTGATATTCAAGCCAATAATTGATATTCAAGTGACATAGTTATGTCACTAATGAAGGTAACCCATCCTCA RR: AAAGAATTATCTCTTTACTTAACTATAAGTTCGGTTATTAACTATAAGTTCACTGTATCAATACAGTGATTACTTCCATTGGGTAGGAGT F2: 3 GTTCACT 2 Unidirectional alignment (log-probability: -35.2) TTCTTAAaAGAGAAATGAATTGATATTCAAGCCAATAAtttcacTTG--------GTGACATAGTTATGTCACTAATGAAGGTAACCCATCCTCA TTCTTAATAGAGAAATGAATTGATATTCAAGCCAATAA------TTGATATTCAAGTGACATAGTTATGTCACTAATGAAGGTAACCCATCCTCA Template switch alignment (log-probability: -22.1) TTCTTAAaAGAGAAATGAATTGATATTCAAGCCAATAATT|TCACTTG|GTGACATAGTTATGTCACTAATGAAGGTAACCCATCCTCA TTCTTAATAGAGAAATGAATTGATATTCAAGCCAATAATT|TCACTTG|GTGACATAGTTATGTCACTAATGAAGGTAACCCATCCTCA ========== Event 2949 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATGCATGGATGGATAGATAGATGTGCTACATCTGCACATCTGCAGCTGCATTGCTTCGctca ↑ 3 2 1 4 Chimp: AATGCATGGATGGATAGATAGATGTGCTACATCTTAATA---CCAGCTGCATTGCTTCGctca Gorilla: AATGCATGGATGGATAGATAGATGTGCTACATCTTAATA---CCAGCTGCATTGCTTCGctca ↓ 3 2 1 4 Human: AATGCATGGATGGATAGATAGATGTGCTACATCTGCACATCTGCAGCTGCATTGCTTCGctca Cluster: [ ] Orangutan: AATGCATGGATGGATAGATAGATGTGCTACATCTTAATA---CCAGCTGCATTGCTTCGctca Chimp > Human ------------- chr5:119784380-119784387 Template switch process: F1: L AGAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT 1 F3: 4 GCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCCA R RF: AGAGACAAATGCATGGATGGATAGATAGATGTGCTACATCTTAATACCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCCA RR: TCTCTGTTTACGTACCTACCTATCTATCTACACGATGTAGAATTATGGTCGACGTAACGAAGCGAGTCACTTAACGTAGTGAGAGGT F2: 3 TCTACACG 2 Unidirectional alignment (log-probability: -34.4) GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCTgcacatctg------CAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCC GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT---------TAATACCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCC Template switch alignment (log-probability: -22.3) GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT|GCACATCT|gCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCC GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT|GCACATCT|CCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCC Gorilla > Human --------------- chr5:119784380-119784387 Template switch process: F1: L AGAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT 1 F3: 4 GCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTCTCCA R RF: AGAGACAAATGCATGGATGGATAGATAGATGTGCTACATCTTAATACCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTATCCA RR: TCTCTGTTTACGTACCTACCTATCTATCTACACGATGTAGAATTATGGTCGACGTAACGAAGCGAGTCACTTAACGTAGTGATAGGT F2: 3 TCTACACG 2 Unidirectional alignment (log-probability: -39.4) GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT------gcacatctgCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTcTCC GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCTTAATAC---------CAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTATCC Template switch alignment (log-probability: -27.8) GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT|GCACATCT|gCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTcTCC GAGACAAATGCATGGATGGATAGATAGATGTGCTACATCT|GCACATCT|CCAGCTGCATTGCTTCGCTCAGTGAATTGCATCACTATCC ========== Event 2950 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCCTGCTCCTCTTCTTTAGCATGGATTCTCCAGCTCCTGTCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCC--------------------CACCTGATTCTCTGGAGCACAAGG ↓ 3 2 4 1 Chimp: CCCCTGCTCCTCTTCTTTAGCATGGATTCTCCAGCTCCTGTCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCC----------CACCATGCCCCACCTGATTCTCTGGAGCACAAGG Gorilla: CCCCTGCTCCTCTTCTTTAGCATGGATTCTCCAGCTCCTGTCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCCCACCATGCCC----------CACCTGATTCTCTGCAGCACAAGG Human: CCCCTGCTCCTCTTCTTTAGCATGGATTCTCCAGCTCCTGTCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCC--------------------CACCTGATTCTCTGGAGCACAAGG Cluster: [ ] Orangutan: CCCCTGCTCCTCTTTTTTAGCATGGATTCTCCAGCTCCTGTCTTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCCCACCATGCCC----------CACCTGATTCTCTGCAGCACAAGG Human > Chimp ------------- chr5:53205956-53205959 Template switch process: F1: L TCCTGTCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCCCACC 1 F3: 4 CCCACCTGATTCTCTGGAGCACAAGGGCACAGGTTCCCTGCC R RF: GCATGGATTCTCCAGCTCCTGTCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCCCACCTGATTCTCTGGAGCACAAGGGCACAGGCTCCCTGCC RR: CGTACCTAAGAGGTCGAGGACAGGAGAGAAAAAGAAAGCGGAACAAAGACTCTTAGGGTGGACTAAGAGACCTCGTGTTCCCGTGTCCGAGGGACGG F2: 3 CGTA 2 Unidirectional alignment (log-probability: -31.3) TCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATcccaccatgcCCCACCTGATTCTCTGGAGCACAAGGGCACAGGtTCCCTG TCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAAT----------CCCACCTGATTCTCTGGAGCACAAGGGCACAGGCTCCCTG Template switch alignment (log-probability: -21.9) TCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCCCACC|ATGC|CCCACCTGATTCTCTGGAGCACAAGGGCACAGGtTCCCTG TCCTCTCTTTTTCTTTCGCCTTGTTTCTGAGAATCCCACC|ATGC|CCCACCTGATTCTCTGGAGCACAAGGGCACAGGCTCCCTG ========== Event 2951 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGGCTAAAAATTTTCCATCT--------TGACCATCTGCTGACAGAGCAAAATTGTTAA Chimp: GGGGCTAAAAATTTTCCATCT--------TGACCATCTGCTGACAGAGCAAAATTGTTAA ↓ 3 4 2 Gorilla: GGGGCTAAAAATTTTCCATCTTTAGCAGATGGTCATCTGCTGACAGAGCAAAATTGTTAA ↑ 3 4 2 Human: GGGGCTAAAAATTTTCCATCT--------TGACCATCTGCTGACAGAGCAAAATTGTTAA Cluster: [ ] Orangutan: GGGGCTAAAAATTTTCCATCT--------TGACCATCTGCTGACAGAGCAAAACTGTTAA Human > Gorilla --------------- chr17:33186150-33186158 Template switch process: F1: L AATGTGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTTA 1 F3: 4 CATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTAT R RF: AATGTGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTGACCATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTTT RR: TTACACTACCTCTACTTATTCCCCGATTTTTAAAAGGTAGAACTGGTAGACGACTGTCTCGTTTTAACAATTTATTTGGTTCAAA F2: 3 TGGTAGACG 2 Unidirectional alignment (log-probability: -39) TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTttagcagaTGgtCATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTaT TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCT--------TGACCATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTTT Template switch alignment (log-probability: -28) TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTtA|GCAGATGGT|CATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTaT TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTGA|GCAGATGGT|CATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTTT Chimp > Gorilla --------------- chr17:33186150-33186158 Template switch process: F1: L AATGTGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTTA 1 F3: 4 CATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTAT R RF: AATGTGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTGACCATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTTT RR: TTACACTACCTCTACTTATTCCCCGATTTTTAAAAGGTAGAACTGGTAGACGACTGTCTCGTTTTAACAATTTATTTGGTTCAAA F2: 3 TGGTAGACG 2 Unidirectional alignment (log-probability: -39) TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTttagcagaTGgtCATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTaT TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCT--------TGACCATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTTT Template switch alignment (log-probability: -28) TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTtA|GCAGATGGT|CATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTaT TGATGGAGATGAATAAGGGGCTAAAAATTTTCCATCTTGA|GCAGATGGT|CATCTGCTGACAGAGCAAAATTGTTAAATAAACCAAGTTT ========== Event 2952 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTAG--ATTCTATTGCTGAGGCAGTGGGAAG ↓ 3 2 1 4 Chimp: AGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTGTACTTCCCATTGCTGAGGCAGTGGGAAG ↑ 3 2 1 4 Gorilla: AGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTAG--ATTCTATTGCTGAggcagtgggaag Human: AGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTAG--ATTCTATTGCTGAGGCAGTGGGAAG Cluster: [ ] Orangutan: AGGAATTCAGAAGGTTGGAGAAGTACAGACCTGCTAG--ACTGTATTGCTGAGGCAGTGGGAAG Human > Chimp ------------- chr5:51394472-51394478 Template switch process: F1: L ATGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT 1 F3: 4 CCATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGGCT R RF: ATGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTAGATTCTATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGGCT RR: TACCTCTCCTTAAGTCTTCCTACCTCTTCATGTCTGGACGATCTAAGATAACGACTCCGTCACCCTTCCCTTCATCTCCCCTCTCCGA F2: 3 CTTCATG 2 Unidirectional alignment (log-probability: -34.4) TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTgtacttcccA-------TTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT---------AGATTCTATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG Template switch alignment (log-probability: -22.2) TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT|GTACTTC|CcATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT|GTACTTC|CTATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG Gorilla > Chimp --------------- chr5:51394472-51394478 Template switch process: F1: L ATGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT 1 F3: 4 CCATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGGCT R RF: ATGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTAGATTCTATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGGCT RR: TACCTCTCCTTAAGTCTTCCTACCTCTTCATGTCTGGACGATCTAAGATAACGACTCCGTCACCCTTCCCTTCATCTCCCCTCTCCGA F2: 3 CTTCATG 2 Unidirectional alignment (log-probability: -33.9) TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTG-------CTgtacttcccATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCTAGATTCT---------ATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG Template switch alignment (log-probability: -22.2) TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT|GTACTTC|CcATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG TGGAGAGGAATTCAGAAGGATGGAGAAGTACAGACCTGCT|GTACTTC|CTATTGCTGAGGCAGTGGGAAGGGAAGTAGAGGGGAGAGG ========== Event 2953 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGCTGATGGAAGAACAGAGAAAAGCTTAAAAGG-----AAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATC ↑ 1 4 3 2 Chimp: TTGCTGATGGAAGAACAGAGAGG----AAAAAAG-----AAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATC Gorilla: TTGCTGATGGACGAACAGAGAGG----AAAAAAG-----AAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTCATC Human: TTGCTGATGGAAGAACAGAGAAAAGCTTAAAAGG-----AAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATC Cluster: [ ] Orangutan: TTGCTGATGGAAGAACAGAGAGG----AAAAAAGAAAACAAAACCTCTTAAGCATTCTCTCAATTGTCTTTTATC Chimp > Human ------------- chr5:118143201-118143211 Template switch process: F1: L TTTATCCTCCTTTTTCCTCTTTGCTGATGGAAGAACAGAGAA 1 F3: 4 GAAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATCTGC R RF: TTTATCCTCCTTTTTCCTCTTTGCTGATGGAAGAACAGAGAGGAAAAAAGAAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATCTGC RR: AAATAGGAGGAAAAAGGAGAAACGACTACCTTCTTGTCTCTCCTTTTTTCTTTTGGAAAATTCGAAGAAGAGTCAACAGAAAATAGACG F2: 3 GAAAATTCGAA 2 Unidirectional alignment (log-probability: -34.4) TATCCTCCTTTTTCCTCTTTGCTGATGGAAGAACAGAG-----AAAAgcttaaaagGAAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATCTGC TATCCTCCTTTTTCCTCTTTGCTGATGGAAGAACAGAGAGGAAAAAA---------GAAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATCTGC Template switch alignment (log-probability: -22.7) TATCCTCCTTTTTCCTCTTTGCTGATGGAAGAACAGAGAa|AAGCTTAAAAG|GAAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATCTGC TATCCTCCTTTTTCCTCTTTGCTGATGGAAGAACAGAGAG|AAGCTTAAAAG|GAAAACCTTTTAAGCTTCTTCTCAGTTGTCTTTTATCTGC ========== Event 2954 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TAACTTTAGAGGTTAGAACTT--TATTTTAAAAT-TTCAAATGACTATTTTAAAA--TATAGGGAAAGAAAATCTGT Chimp: TAACTTTAGAGGTTAGAACTT--TATTTTAAAAT-TTCAAATGACTATTTTAAAA--TATAGGGAAAGAAAATCTGT ↓ 13 2 4 ↑ 13 24 Gorilla: TAACTTTAGAGGTTAGAACTT----TTTTAAAATAGTCATTTG-AAATTTTAAAATATATAGGGAAAGAAAATCTGT ↓ 13 24 ↑ 13 2 4 Human: TAACTTTAGAGGTTAGAACTT--TATTTTAAAAT-TTCAAATGACTATTTTAAAA--TATAGGGAAAGAAAATCTGT Cluster: [ ] Orangutan: CAACTTTAGAGGCTAGAACTTTA--TTTTAAAAT-TTCTAATGACTATTTTAAAA--TATAGGGAAAGAAAATCTGT Gorilla > Human --------------- chr5:66821351-66821379 Template switch process: F1: L TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT 1 F3: 4 ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG R RF: TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTTTTAAAATAGTCATTTGAAATTTTAAAATATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG RR: ACGACAAAGAAATGGAAACAATTGAAATCTCCAATCTTGAAAAAATTTTATCAGTAAACTTTAAAATTTTATATATCCCTTTCTTTTAGACACCAAAACCATAAACAAGGAC F2: 3 AAATTTTATCAGTAAACTTTAAAATTTTA 2 Unidirectional alignment (log-probability: -49.1) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT-------------------ATTTTAAAATttcaaatgactattttaaaATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTTTTAAAATAGTCATTTGAAATTTTAAAAT-------------------ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Template switch alignment (log-probability: -19.5) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|ATTTTAAAATTTCAAATGACTATTTTAAA|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|ATTTTAAAATTTCAAATGACTATTTTAAA|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Human > Gorilla --------------- chr17:66980274-66980302 Template switch process: F1: L TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT 1 F3: 4 ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG R RF: TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTATTTTAAAATTTCAAATGACTATTTTAAAATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG RR: ACGACAAAGAAATGGAAACAATTGAAATCTCCAATCTTGAAATAAAATTTTAAAGTTTACTGATAAAATTTTATATCCCTTTCTTTTAGACACCAAAACCATAAACAAGGAC F2: 3 TAAAATTTTAAAGTTTACTGATAAAATTT 2 Unidirectional alignment (log-probability: -49.1) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTtttaaaatagtcatttgaaATTTTAAAAT-------------------ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT-------------------ATTTTAAAATTTCAAATGACTATTTTAAAATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Template switch alignment (log-probability: -19.5) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|TTTAAAATAGTCATTTGAAATTTTAAAAT|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|TTTAAAATAGTCATTTGAAATTTTAAAAT|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Gorilla > Chimp --------------- chr5:134371940-134371968 Template switch process: F1: L TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT 1 F3: 4 ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG R RF: TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTTTTAAAATAGTCATTTGAAATTTTAAAATATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG RR: ACGACAAAGAAATGGAAACAATTGAAATCTCCAATCTTGAAAAAATTTTATCAGTAAACTTTAAAATTTTATATATCCCTTTCTTTTAGACACCAAAACCATAAACAAGGAC F2: 3 AAATTTTATCAGTAAACTTTAAAATTTTA 2 Unidirectional alignment (log-probability: -49.1) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT-------------------ATTTTAAAATttcaaatgactattttaaaATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTTTTAAAATAGTCATTTGAAATTTTAAAAT-------------------ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Template switch alignment (log-probability: -19.5) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|ATTTTAAAATTTCAAATGACTATTTTAAA|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|ATTTTAAAATTTCAAATGACTATTTTAAA|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Chimp > Gorilla --------------- chr17:66980274-66980302 Template switch process: F1: L TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT 1 F3: 4 ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG R RF: TGCTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTATTTTAAAATTTCAAATGACTATTTTAAAATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCTG RR: ACGACAAAGAAATGGAAACAATTGAAATCTCCAATCTTGAAATAAAATTTTAAAGTTTACTGATAAAATTTTATATCCCTTTCTTTTAGACACCAAAACCATAAACAAGGAC F2: 3 TAAAATTTTAAAGTTTACTGATAAAATTT 2 Unidirectional alignment (log-probability: -49.1) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTTtttaaaatagtcatttgaaATTTTAAAAT-------------------ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT-------------------ATTTTAAAATTTCAAATGACTATTTTAAAATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT Template switch alignment (log-probability: -19.5) CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|TTTAAAATAGTCATTTGAAATTTTAAAAT|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT CTGTTTCTTTACCTTTGTTAACTTTAGAGGTTAGAACTTT|TTTAAAATAGTCATTTGAAATTTTAAAAT|ATATAGGGAAAGAAAATCTGTGGTTTTGGTATTTGTTCCT ========== Event 2955 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GACGTCAAACGCCATCACAGGCTAG--------------GATTGCTTGGTGGGTTTACCTAATG ↑ 1 3 4 Chimp: GACGTCAAACGCCATCACAGGACTG-------GTGCAATCCTAGCTTGGTGGGTTTACCTAATG Gorilla: GACGTCAAACGCCATCACAGGACCGGTGCAAT-------CCTAGCTTGGTGGGTTTACCTAATG ↓ 1 3 4 Human: GACGTCAAACGCCATCACAGGCTAG--------------GATTGCTTGGTGGGTTTACCTAATG Cluster: [ ] Orangutan: GACGTCAAACGCCATCACAGGACCGGTGCAAT-------CCTAGCTTGGTGGGTTTACCTAATG Chimp > Human ------------- chr5:67196648-67196655 Template switch process: F1: L ACCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG 1 F3: 4 GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA R RF: ACCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGGACTGGTGCAATCCTAGCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA RR: TGGTGGGTTTTCTTCGTCGACTGCAGTTTGCGGTAGTGTCCTGACCACGTTAGGATCGAACCACCCAAATGGATTACGAACCTCGACTCTTTACCT F2: 3 TTAGGATC 2 Unidirectional alignment (log-probability: -29) CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG------------CTAggattGCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGGACTGGTGCAATCCTA-----GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA Template switch alignment (log-probability: -16.3) CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG|CTAGGATT|GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG|CTAGGATT|GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA Gorilla > Human --------------- chr5:67196648-67196655 Template switch process: F1: L ACCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG 1 F3: 4 GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA R RF: ACCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGGACCGGTGCAATCCTAGCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA RR: TGGTGGGTTTTCTTCGTCGACTGCAGTTTGCGGTAGTGTCCTGGCCACGTTAGGATCGAACCACCCAAATGGATTACGAACCTCGACTCTTTACCT F2: 3 TTAGGATC 2 Unidirectional alignment (log-probability: -28.5) CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG------------CTAggattGCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGGACCGGTGCAATCCTA-----GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA Template switch alignment (log-probability: -16.7) CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG|CTAGGATT|GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA CCACCCAAAAGAAGCAGCTGACGTCAAACGCCATCACAGG|CTAGGATT|GCTTGGTGGGTTTACCTAATGCTTGGAGCTGAGAAATGGA ========== Event 2956 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GCCATGTCCCAGGCCATACAC---------------CTGAGCCTCTTCTGCCTTGGTTTCC ↑ 13 2 4 Chimp: GCCATGTCCCAGGCCATACACTCAGGTGTATGGAAACCAGGCCTCTTCTGCCTTGGTTTCC ↓ 13 2 4 Gorilla: GCCATGTCCCAGGCCATACAC---------------CTGAGCCTCTTCTGCCTTGGTTTCC Human: GCCATGTCCCAGGCCATACAC---------------CTGAGCCTCTTCTGCCTTGGTTTCC Cluster: [ ] Orangutan: GCCATGTCCCAGGACATACAC---------------CTGGGCCTCTTCCGCCTTGGTTTCC Chimp > Human ------------- chr5:113541008-113541011 Template switch process: F1: L CAATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC 1 F3: 4 GCCTCTTCTGCCTTGGTTTCCTGAACTGCATTTTGTTTTC R RF: CAATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACACTCAGGTGTATGGAAACCAGGCCTCTTCTGCCTTGGTTTCCTGAACAGCATTTTGTTTTC RR: GTTAGTGGACGGGAAGGGTTCGGTACAGGGTCCGGTATGTGAGTCCACATACCTTTGGTCCGGAGAAGACGGAACCAAAGGACTTGTCGTAAAACAAAAG F2: 3 AGTC 2 Unidirectional alignment (log-probability: -33.9) AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACACctga-------------------GCCTCTTCTGCCTTGGTTTCCTGAACtGCATTTTGTTTTC AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC----TCAGGTGTATGGAAACCAGGCCTCTTCTGCCTTGGTTTCCTGAACAGCATTTTGTTTTC Template switch alignment (log-probability: -21.8) AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC|CTGA|GCCTCTTCTGCCTTGGTTTCCTGAACtGCATTTTGTTTTC AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC|CTGA|GCCTCTTCTGCCTTGGTTTCCTGAACAGCATTTTGTTTTC Chimp > Gorilla --------------- chr17:27694501-27694504 Template switch process: F1: L CAATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC 1 F3: 4 GCCTCTTCTGCCTTGGTTTCCTGAACTGCATTTTGTTTTC R RF: CAATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACACTCAGGTGTATGGAAACCAGGCCTCTTCTGCCTTGGTTTCCTGAACAGCATTTTGTTTTC RR: GTTAGTGGACGGGAAGGGTTCGGTACAGGGTCCGGTATGTGAGTCCACATACCTTTGGTCCGGAGAAGACGGAACCAAAGGACTTGTCGTAAAACAAAAG F2: 3 AGTC 2 Unidirectional alignment (log-probability: -32.9) AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC-------------------ctgaGCCTCTTCTGCCTTGGTTTCCTGAACtGCATTTTGTTTTC AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACACTCAGGTGTATGGAAACCAG----GCCTCTTCTGCCTTGGTTTCCTGAACAGCATTTTGTTTTC Template switch alignment (log-probability: -21.7) AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC|CTGA|GCCTCTTCTGCCTTGGTTTCCTGAACtGCATTTTGTTTTC AATCACCTGCCCTTCCCAAGCCATGTCCCAGGCCATACAC|CTGA|GCCTCTTCTGCCTTGGTTTCCTGAACAGCATTTTGTTTTC ========== Event 2957 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTCTTCTGATACCAAGAACATATGTGAAACATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTCA Chimp: ATTCTTCGGATACCAAGAACA-------GAAATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTCA Gorilla: ATTCTTCTGATACCAAGAACA-------GAAATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTCA ↓ 1 4 3 2 Human: ATTCTTCTGATACCAAGAACATATGTGAAACATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTCA Cluster: [ ] Orangutan: ATTCTTCTGATACCAAGAACA-------GAAATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTCA Gorilla > Human --------------- chr5:113295051-113295060 Template switch process: F1: L TACATGTTCAAAAACTAACAATTCTTCTGATACCAAGAACA 1 F3: 4 ATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTC R RF: TACATGTTCAAAAACTAACAATTCTTCTGATACCAAGAACAGAAATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTC RR: ATGTACAAGTTTTTGATTGTTAAGAAGACTATGGTTCTTGTCTTTATGTTCAATACAAAGTGTATTATGTCTTCGTTTCCCGAG F2: 3 CAAAGTGTAT 2 Unidirectional alignment (log-probability: -30.7) ACATGTTCAAAAACTAACAATTCTTCTGATACCAAGAACAtatgtGAAacATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTC ACATGTTCAAAAACTAACAATTCTTCTGATACCAAGAACA-----GAA--ATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTC Template switch alignment (log-probability: -17) ACATGTTCAAAAACTAACAATTCTTCTGATACCAAGAACA|TATGTGAAAC|ATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTC ACATGTTCAAAAACTAACAATTCTTCTGATACCAAGAACA|TATGTGAAAC|ATACAAGTTATGTTTCACATAATACAGAAGCAAAGGGCTC ========== Event 2958 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCCTACTGGGCTCTGAGATGGGGGGTCAGACTCCAAGGCCCAGTATATTGGttttt------------------tttttttttttgagatggagttttgctcttgttgcccaggctggagtgcaatggggttcaatcttggctcactgcaatccccacctcccgggtt Chimp: ACCCTACTGGGCTCTGAGATGGGGGGTCAGACTCCAAGGCCCAGTATATTGGttttt---------------tgttttttttttttgagatggagttttgctcttgttgcccaggctggagtgcaatggggttcaatcttggctcactgcaatccccacctcacgggtt Gorilla: ACCCTACTGGACTCTGAGATGCAGTGTCAGACTCCAAGGCCCAGTATATTGGttttt--------------t---tttttttttttgagatggagttttgctcttgttgcccaggctggagtgcaatggggttcaatcttggctcactgcaatccccgcctcccgggtt ↑ 1 4 3 2 Human: ACCCTACTGGGCTCTGAGATGGGGGGTCAGACTCCAAGGCCCAGTATATTGGttttt------------------tttttttttttgagatggagttttgctcttgttgcccaggctggagtgcaatggggttcaatcttggctcactgcaatccccacctcccgggtt Cluster: [ ] Orangutan: ACCCTACTGGGCTCTGAGATGGGGGGTCAGACTCCAAGACCCAGTATATTGGTATTGGtttttttttttttt---tttttttttttgagatggagttttgctcttgttgcccaggctggagtgcaat--ggttcaatctcggctcactgcaatccccgcctcccgggtt Human > Gorilla --------------- chr17:27507776-27507779 Template switch process: F1: L GATAAGTAGATCTTCCCACTACCCTACTGGACTCTGAGATG 1 F3: 4 GTCAGACTCCAAGGCCCAGTATATTGGTTTTTTTTTTTTT R RF: GATAAGTAGATCTTCCCACTACCCTACTGGGCTCTGAGATGGGGGGTCAGACTCCAAGGCCCAGTATATTGGTTTTTTTTTTTTTTTTGAGATGGAGTTTTGCTCTTGTTGCCCAGGCTGGAGTGCAATGGGGTTCAATCTTGGCTCACTG RR: CTATTCATCTAGAAGGGTGATGGGATGACCCGAGACTCTACCCCCCAGTCTGAGGTTCCGGGTCATATAACCAAAAAAAAAAAAAAAACTCTACCTCAAAACGAGAACAACGGGTCCGACCTCACGTTACCCCAAGTTAGAACCGAGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -31.4) ATAAGTAGATCTTCCCACTACCCTACTGGaCTCTGAGATGcaGtGTCAGACTCCAAGGCCCAGTATATTGGTTTTTTTTTTTTt ATAAGTAGATCTTCCCACTACCCTACTGGGCTCTGAGATGGGGGGTCAGACTCCAAGGCCCAGTATATTGGTTTTTTTTTTTT- Template switch alignment (log-probability: -21.7) ATAAGTAGATCTTCCCACTACCCTACTGGaCTCTGAGATG|CAGT|GTCAGACTCCAAGGCCCAGTATATTGGTTTTTTTTTTTTT ATAAGTAGATCTTCCCACTACCCTACTGGGCTCTGAGATG|CAGT|GTCAGACTCCAAGGCCCAGTATATTGGTTTTTTTTTTTTT ========== Event 2959 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCCAGAGTGTGGAACTGAAGATTAGTATCTTAGAGGGCCAGGTGACGCTTTA ↑ 3 1 42 Chimp: GCCCAGAGTGTGGAACTGAAGA------TACTAGAGGGCCAGGTGACGCTTTA Gorilla: GCCTGGAGTGTGGAACTGAAGA------TACTAAAGGGCCAGGTGACGCTTTA Human: GCCCAGAGTGTGGAACTGAAGATTAGTATCTTAGAGGGCCAGGTGACGCTTTA Cluster: [ ] Orangutan: GCCCAGAGTGTGGAACTGAAGA------TACTAGAGGGCCAGGTGACACTTTA Chimp > Human ------------- chr5:73388583-73388590 Template switch process: F1: L ACACAGCAAAGTGACAGATGCCCAGAGTGTGGAACTGAAGAT 1 F3: 4 TAGAGGGCCAGGTGACGCTTTAAAAAGCAAGCGCATAGAT R RF: ACACAGCAAAGTGACAGATGCCCAGAGTGTGGAACTGAAGATACTAGAGGGCCAGGTGACGCTTTAAAAAGCAAGCGCACAGAT RR: TGTGTCGTTTCACTGTCTACGGGTCTCACACCTTGACTTCTATGATCTCCCGGTCCACTGCGAAATTTTTCGTTCGCGTGTCTA F2: 3 TCTATGAT 2 Unidirectional alignment (log-probability: -37.5) ACAGCAAAGTGACAGATGCCCAGAGTGTGGAACTGAAGattagtATctTAGAGGGCCAGGTGACGCTTTAAAAAGCAAGCGCAtAGAT ACAGCAAAGTGACAGATGCCCAGAGTGTGGAACTGAAG------ATACTAGAGGGCCAGGTGACGCTTTAAAAAGCAAGCGCACAGAT Template switch alignment (log-probability: -22.3) ACAGCAAAGTGACAGATGCCCAGAGTGTGGAACTGAAGAT|TAGTATCT|TAGAGGGCCAGGTGACGCTTTAAAAAGCAAGCGCAtAGAT ACAGCAAAGTGACAGATGCCCAGAGTGTGGAACTGAAGAT|TAGTATCT|TAGAGGGCCAGGTGACGCTTTAAAAAGCAAGCGCACAGAT ========== Event 2960 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAATGCCACCTGTAGGATAACTAG--------TCCCATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT ↓ 1 4 3 2 Chimp: AGAATGCCACCTGTAGGATAAGTTTTTGAGAAAAACAATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT ↑ 1 4 3 2 Gorilla: AGAATGCCACCTGTAGGATAAGTAG--------TCCCATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT Human: AGAATGCCACCTGTAGGATAACTAG--------TCCCATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT Cluster: [ ] Orangutan: AGAATGCCACCTGTAGGATAAGTAG--------TCCCATGGCTTGTTTTTCTCAA-AAAGGAAGGAAACCTACCTTT Human > Chimp ------------- chr5:139487208-139487221 Template switch process: F1: L GGAGACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGT 1 F3: 4 ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT R RF: GGAGACCACACAAGAAATGTAGAATGCCACCTGTAGGATAACTAGTCCCATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT RR: CCTCTGGTGTGTTCTTTACATCTTACGGTGGACATCCTATTGATCAGGGTACCGAACAAAAAGAGTTTTTTCCTTCCTTTGGATGGAAA F2: 3 ACAAAAAGAGTTTT 2 Unidirectional alignment (log-probability: -44.5) GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAA--------gtttttgagaaaaacaATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAACTAGTCCC----------------ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT Template switch alignment (log-probability: -23) GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAgT|TTTTGAGAAAAACA|ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAACT|TTTTGAGAAAAACA|ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT Gorilla > Chimp --------------- chr5:139487208-139487221 Template switch process: F1: L AGACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGT 1 F3: 4 ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT R RF: AGACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGTAGTCCCATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT RR: TCTGGTGTGTTCTTTACATCTTACGGTGGACATCCTATTCATCAGGGTACCGAACAAAAAGAGTTTTTTCCTTCCTTTGGATGGAAA F2: 3 ACAAAAAGAGTTTT 2 Unidirectional alignment (log-probability: -39.6) GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGTttttgagaaaaacA-----ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGT-------------AGTCCCATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT Template switch alignment (log-probability: -17.5) GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGT|TTTTGAGAAAAACA|ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT GACCACACAAGAAATGTAGAATGCCACCTGTAGGATAAGT|TTTTGAGAAAAACA|ATGGCTTGTTTTTCTCAAAAAAGGAAGGAAACCTACCTTT ========== Event 2961 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTGCTAGGTTCAGATCAGGT--------TCAGATCCTCATTCGCAGGTGATTGGTCTGAACCCtgtatcagtcagggtt ↑ 1 4 3 2 Chimp: ATTGCTAGGTTCAGATCAGGT----GACTCTCCATCCTCATTCGCAGGTGATTGGTCTGAACCCtgtatcagtcagggtt Gorilla: ATTGCTAGGTTCAGATCAGGTGACT----CTCCATCCTCATTCGCAGGTGATTGGTCTGAACCCtgtattagtcagggtt ↓ 1 4 3 2 Human: ATTGCTAGGTTCAGATCAGGT--------TCAGATCCTCATTCGCAGGTGATTGGTCTGAACCCtgtatcagtcagggtt Cluster: [ ] Orangutan: ATTGCTAGGTTCAGATCAGGTGACT----CTCCTTCCTCATTCACAGGTGATTGGTCTGAACCCT------gtcagggtt Chimp > Human ------------- chr5:74330612-74330615 Template switch process: F1: L AAGGGGTTCTTCGAGCATAAATTGCTAGGTTCAGATCAGGT 1 F3: 4 ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT R RF: AAGGGGTTCTTGGAGCATAAATTGCTAGGTTCAGATCAGGTGACTCTCCATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT RR: TTCCCCAAGAACCTCGTATTTAACGATCCAAGTCTAGTCCACTGAGAGGTAGGAGTAAGCGTCCACTAACCAGACTTGGGACATAGTCA F2: 3 GACT 2 Unidirectional alignment (log-probability: -31.8) AGGGGTTCTTcGAGCATAAATTGCTAGGTTCAGATCAGGTtcaG-------ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT AGGGGTTCTTGGAGCATAAATTGCTAGGTTCAGATCAGGT---GACTCTCCATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT Template switch alignment (log-probability: -21.8) AGGGGTTCTTcGAGCATAAATTGCTAGGTTCAGATCAGGT|TCAG|ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT AGGGGTTCTTGGAGCATAAATTGCTAGGTTCAGATCAGGT|TCAG|ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT Gorilla > Human --------------- chr5:74330612-74330615 Template switch process: F1: L AAGGGGTTCTTCGAGCATAAATTGCTAGGTTCAGATCAGGT 1 F3: 4 ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATCAGT R RF: AAGGGGTTCTTGGAGCATAAATTGCTAGGTTCAGATCAGGTGACTCTCCATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATTAGT RR: TTCCCCAAGAACCTCGTATTTAACGATCCAAGTCTAGTCCACTGAGAGGTAGGAGTAAGCGTCCACTAACCAGACTTGGGACATAATCA F2: 3 GACT 2 Unidirectional alignment (log-probability: -36.4) AGGGGTTCTTcGAGCATAAATTGCTAGGTTCAGATCAGGTtcaG-------ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATcAGT AGGGGTTCTTGGAGCATAAATTGCTAGGTTCAGATCAGGT---GACTCTCCATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATTAGT Template switch alignment (log-probability: -27.3) AGGGGTTCTTcGAGCATAAATTGCTAGGTTCAGATCAGGT|TCAG|ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATcAGT AGGGGTTCTTGGAGCATAAATTGCTAGGTTCAGATCAGGT|TCAG|ATCCTCATTCGCAGGTGATTGGTCTGAACCCTGTATTAGT ========== Event 2962 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTTTCCTCCAAAGTGTTAGATTCTCTGCTTCATCCTGGCTTTT-------GGCTAACATAATACCCTGTAATG ↓ 13 24 Chimp: CTCTTTCCTCCAAAGTGTTAG-------CCAAAAGCCAGGATGAAGCAGAGAATCTAACATAATACCCTGTAATG Gorilla: CTCTTTCCTCCAAAGTGTTAGATTCTCTGCTTCATCCTGGCTTTT-------GGCTAACATAATGCCCTGTAATG Human: CTCTTTCCTCCAAAGTGTTAGATTCTCTGCTTCATCCTGGCTTTT-------GGCTAACATAATACCCTGTAATG Cluster: [ ] Orangutan: CTCTTTCCTCCAAAGTGTTAGATTCTCTGCTTCATCCTGGT-TTT-------AGCTAACATAATACCTTGTAATG Human > Chimp ------------- chr5:140124533-140124558 Template switch process: F1: L GTCTGGTTCTGGCAAGGTAGCTCTTTCCTCCAAAGTGTTAG 1 F3: 4 CTAACATAATACCCTGTAATGCTGAATTTCATACCTTCAA R RF: GTCTGGTTCTGGCAAGGTAGCTCTTTCCTCCAAAGTGTTAGATTCTCTGCTTCATCCTGGCTTTTGGCTAACATAATACCCTGTAATGCTGAATTTCATACCTTCAA RR: CAGACCAAGACCGTTCCATCGAGAAAGGAGGTTTCACAATCTAAGAGACGAAGTAGGACCGAAAACCGATTGTATTATGGGACATTACGACTTAAAGTATGGAAGTT F2: 3 TAAGAGACGAAGTAGGACCGAAAACC 2 Unidirectional alignment (log-probability: -56.9) TCTGGTTCTGGCAAGGTAGCTCTTTCCTCCAAAGTGTTAGccaaaagccaggatgaagcagagaAT------------------------CTAACATAATACCCTGTAATGCTGAATTTCATACCTTCAA TCTGGTTCTGGCAAGGTAGCTCTTTCCTCCAAAGTGTTAG------------------------ATTCTCTGCTTCATCCTGGCTTTTGGCTAACATAATACCCTGTAATGCTGAATTTCATACCTTCAA Template switch alignment (log-probability: -18.5) TCTGGTTCTGGCAAGGTAGCTCTTTCCTCCAAAGTGTTAG|CCAAAAGCCAGGATGAAGCAGAGAAT|CTAACATAATACCCTGTAATGCTGAATTTCATACCTTCAA TCTGGTTCTGGCAAGGTAGCTCTTTCCTCCAAAGTGTTAG|CCAAAAGCCAGGATGAAGCAGAGAAT|CTAACATAATACCCTGTAATGCTGAATTTCATACCTTCAA ========== Event 2963 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGCATACAAGGTGTGTATGT--GTGTGCGCGCCAGCTAACTAAGCATACGGGgtgtgtgt Chimp: AAGCATACAAGgtgtgtatgt--gtgtgtgcgcaagctaactaagcatacggggtgtgtgt Gorilla: AAGCATACAAGGTGTGTATGT----GTGTGCACGAGCT-GCTAAGCATACAGGgtgtgtgt ↑ 1 3 2 4 Human: AAGCATACAAGGTGTGTATGT--GTGTGCGCGCCAGCTAACTAAGCATACGGGgtgtgtgt Cluster: [ ] Orangutan: AAGCATACAAGGTGTGTATGTGT--GTGTGCACGAGCT-GCTAAGCATACTCtgtgtgtgt Human > Gorilla --------------- chr17:74695061-74695065 Template switch process: F1: L AGGGCCTTGTGCCAGCTGCTAAGCATACAAGGTGTGTATGTGTGTGCACG 1 F3: 4 CTAAGCATACAGGGTGTGTGTGTGTGTGTG R RF: AGGGCCTTGTGCCAGCTGCTAAGCATACAAGGTGTGTATGTGTGTGCGCGCCAGCTAACTAAGCATACGGGGTGTGTGTGTGTGTGTG RR: TCCCGGAACACGGTCGACGATTCGTATGTTCCACACATACACACACGCGCGGTCGATTGATTCGTATGCCCCACACACACACACACAC F2: 3 GTCGA 2 Unidirectional alignment (log-probability: -43.9) GCCAGCTGCTAAGCATACAAGGTGTGTATGTGTGTGC----------AcgagctgCTAAGCATACaGGGTGTGTGTGTGTGTGTG---------- GCCAGCTGCTAAGCATACAAGGTGTGTATGTGTGTGCGCGCCAGCTAA-------CTAAGCATACGGGGTGTGTGTGTGTGTGTGTGTGTGTGTG Template switch alignment (log-probability: -27.4) GCCAGCTGCTAAGCATACAAGGTGTGTATGTGTGTGCaCG|AGCTG|CTAAGCATACaGGGTGTGTGTGTGTGTGTG GCCAGCTGCTAAGCATACAAGGTGTGTATGTGTGTGCGCG|AGCTG|CTAAGCATACGGGGTGTGTGTGTGTGTGTG ========== Event 2964 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AACACCTAGACACACTGCCATTTGAAGGTGAGTCTTTaagaaatgctttttggggccgggcgtggtgg Chimp: AACACCTAGACACACTGCCATTTGAAGGTGAGTCTTTAAGAAATGCTTTTTGGggccgggcatggtgg Gorilla: AACACCTAGACACACTGCCAT-TGA-AGCATTTCTTTAAGAAATGCTTTTTGGggccgggcgtggtgg ↑ 1 4 3 2 Human: AACACCTAGACACACTGCCATTTGAAGGTGAGTCTTTaagaaatgctttttggggccgggcgtggtgg Cluster: [ ] Orangutan: AACAACTAGACACACTGCCATTTGAAGGTGAGTCTTTAAGAAATGCTTTTTGGggccgggcgcagtgg Human > Gorilla --------------- chr17:75004820-75004826 Template switch process: F1: L GTGTAATGTCTTGAATGACAAACACCTAGACACACTGCCATTG 1 F3: 4 TCTTTAAGAAATGCTTTTTGGGGCCGGGCGTGGTGGCTCA R RF: GTGTAATGTCTTGAATGACAAACACCTAGACACACTGCCATTTGAAGGTGAGTCTTTAAGAAATGCTTTTTGGGGCCGGGCGTGGTGGCTCA RR: CACATTACAGAACTTACTGTTTGTGGATCTGTGTGACGGTAAACTTCCACTCAGAAATTCTTTACGAAAAACCCCGGCCCGCACCACCGAGT F2: 3 TTACGAA 2 Unidirectional alignment (log-probability: -31.2) TAATGTCTTGAATGACAAACACCTAGACACACTGCCATT---------GaagcattTCTTTAAGAAATGCTTTTTGGGGCCGGGCGTGGTGGCTCA TAATGTCTTGAATGACAAACACCTAGACACACTGCCATTTGAAGGTGAG-------TCTTTAAGAAATGCTTTTTGGGGCCGGGCGTGGTGGCTCA Template switch alignment (log-probability: -22.2) TAATGTCTTGAATGACAAACACCTAGACACACTGCCATTg|AAGCATT|TCTTTAAGAAATGCTTTTTGGGGCCGGGCGTGGTGGCTCA TAATGTCTTGAATGACAAACACCTAGACACACTGCCATTT|AAGCATT|TCTTTAAGAAATGCTTTTTGGGGCCGGGCGTGGTGGCTCA ========== Event 2965 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ACGCACAAAAACTGCCAGTAGAAGTCCTAGAAA-------CACAGCTGAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGTGACTACACCATCACGTATATGGCAGCTATTGTAAAAGTTTCCTGGGAAAAACAGCTGTATCCTCTGGGAACTGTTTCA ↓ 3 2 1 4 ↑ 1 4 3 2 Chimp: ACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACTTCTAGGACTTC-TAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGTGACTACACCATCACATATATGGCAGCTATTGTAAAAGTTTCCTGGGAAAAACAGCTGTATCCTCTGGGAACTGTTTCA ↓ 1 4 3 2 ↑ 3 2 1 4 Gorilla: ACGCACAAAAACTGCCAGTAGAAGTCCTAGAAA-------CACAGCTGAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGTGACTACACCATCACATATATAGCAGCTATTGTAAAAGTTTCCTGGGAAAAACAGCTGTATCCTCTGGGAACTGTTTCA Human: ACGCACAAAAACTGCCAGTAGAAGTCCTAGAAA-------CACAGCTGAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGTGACTACACCATCACGTATATGGCAGCTATTGTAAAAGTTTCCTGGGAAAAACAGCTGTATCCTCTGGGAACTGTTTCA Cluster: [ ] Orangutan: ACGCACAAAAACTGCCAGTAGAAGTCCTAGAAA-------CACAGCTGAGAGCTTCGTTAGTGTCCACA-TGGGGGCAACGGCACAGTGACTACACCATCACATATATGGCAGCTATTATAAAAGTTTCCTGGGAAAAACAGCTGTATCCTCTGAGAACTGTTTCA Chimp > Human ------------- chr5:104163099-104163105 Template switch process: F1: L TGGGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC 1 F3: 4 AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT R RF: TGGGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACTTCTAGGACTTCTAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGTGACTACACCATCACATATATGGCAGCTATTGTAAAAGTTTCCTGGGAAAAACAGCTGT RR: ACCCGCCCTGCGTGTTTTTGACGGTCATCTTCAGGATCTTTGAAGATCCTGAAGATCTCGAAGCAATCACAGGTGTAGTCCCCGTTACCGTGTCACTGATGTGGTAGTGTATATACCGTCGATAACATTTTCAAAGGACCCTTTTTGTCGACA F2: 3 GTCGACA 2 Unidirectional alignment (log-probability: -37.9) GGCaGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC-------------AcagctgaGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACTTCTAGGACTTCTA-------GAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Template switch alignment (log-probability: -22.2) GGCaGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|ACAGCTG|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|ACAGCTG|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Human > Chimp ------------- chr5:38411608-38411620 Template switch process: F1: L TGGGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC 1 F3: 4 AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT R RF: TGGGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACACAGCTGAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT RR: ACCCGTCCTGCGTGTTTTTGACGGTCATCTTCAGGATCTTTGTGTCGACTCTCGAAGCAATCACAGGTGTAGTCCCCGTTACCGTGTCA F2: 3 TCTTCAGGATCTT 2 Unidirectional alignment (log-probability: -46.2) GGCgGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC-------ttctaggacttctAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACACAGCTG-------------AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Template switch alignment (log-probability: -22.9) GGCgGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|TTCTAGGACTTCT|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|TTCTAGGACTTCT|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Gorilla > Chimp --------------- chr5:38411608-38411620 Template switch process: F1: L TGGGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC 1 F3: 4 AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT R RF: TGGGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACACAGCTGAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT RR: ACCCGTCCTGCGTGTTTTTGACGGTCATCTTCAGGATCTTTGTGTCGACTCTCGAAGCAATCACAGGTGTAGTCCCCGTTACCGTGTCA F2: 3 TCTTCAGGATCTT 2 Unidirectional alignment (log-probability: -45.2) GGCgGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACttctaggacttct-------AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC-------------ACAGCTGAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Template switch alignment (log-probability: -22.9) GGCgGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|TTCTAGGACTTCT|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|TTCTAGGACTTCT|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Chimp > Gorilla --------------- chr17:19129105-19129111 Template switch process: F1: L TGGGCAGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC 1 F3: 4 AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT R RF: TGGGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACTTCTAGGACTTCTAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGTGACTACACCATCACATATATGGCAGCTATTGTAAAAGTTTCCTGGGAAAAACAGCTGT RR: ACCCGCCCTGCGTGTTTTTGACGGTCATCTTCAGGATCTTTGAAGATCCTGAAGATCTCGAAGCAATCACAGGTGTAGTCCCCGTTACCGTGTCACTGATGTGGTAGTGTATATACCGTCGATAACATTTTCAAAGGACCCTTTTTGTCGACA F2: 3 GTCGACA 2 Unidirectional alignment (log-probability: -36.9) GGCaGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC-------------acagctgAGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAACTTCTAGGACTTCT-------AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT Template switch alignment (log-probability: -22.2) GGCaGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|ACAGCTG|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT GGCGGGACGCACAAAAACTGCCAGTAGAAGTCCTAGAAAC|ACAGCTG|AGAGCTTCGTTAGTGTCCACATCAGGGGCAATGGCACAGT ========== Event 2966 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAAAAATAGTAATATTTTACTTGAACACAAAGT--------TCAAGTGCTTAACTATGATTTAAAACT ↑ 3 2 1 4 Chimp: GAAAAAATAGTAATATTTTACTTGAACACAAAGT----TTATACATGCGCTTAACTATGATTTAAAACT Gorilla: GAAAAAATAGTAATATTTTACTTGAACACAAAGTTTAT----ACGTGGGCTTAACTATGATTTAAAACT Human: GAAAAAATAGTAATATTTTACTTGAACACAAAGT--------TCAAGTGCTTAACTATGATTTAAAACT Cluster: [ ] Orangutan: GAAAAAATAGTAATATTTTACTTGAACACAAAGTTTAT----ACATGCTCTTAACTATGATTTAAAACT Chimp > Human ------------- chr5:7891228-7891232 Template switch process: F1: L GTTGAAAGAAAAAATAGTAATATTTTACTTGAACACAAAGTT 1 F3: 4 GCTTAACTATGATTTAAAACTAGAACATGATTTGA R RF: GTTGAAAGAAAAAATAGTAATATTTTACTTGAACACAAAGTTTATACATGCGCTTAACTATGATTTAAAACTAGAACATGATTT RR: CAACTTTCTTTTTTATCATTATAAAATGAACTTGTGTTTCAAATATGTACGCGAATTGATACTAAATTTTGATCTTGTACTAAA F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -33.6) TGAAAGAAAAAATAGTAATATTTTACTTGAACACAAAGTT----CAaGtGCTTAACTATGATTTAAAACTAGAACATGATT-----TGA TGAAAGAAAAAATAGTAATATTTTACTTGAACACAAAGTTTATACATGCGCTTAACTATGATTTAAAACTAGAACATGATTTATTTTGA Template switch alignment (log-probability: -25.9) TGAAAGAAAAAATAGTAATATTTTACTTGAACACAAAGTT|CAAGT|GCTTAACTATGATTTAAAACTAGAACATGATTtga TGAAAGAAAAAATAGTAATATTTTACTTGAACACAAAGTT|CAAGT|GCTTAACTATGATTTAAAACTAGAACATGATT--T ========== Event 2967 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTAGAGATTCAAGATGGTAGGTAAATGTC-AGTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGAGGTCCAGATGTTCCCAGGATATTGACTCCAAAGGGCCGTGGTTTCA ↑ 1 4 3 2 Chimp: CTTAGAGATTCAAGATGGTAGATAAATAAAATGTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGAGGTCCAGATGTTCCCAGGACATTGACTCCAAAGGGCCGTGGTTTCA Gorilla: CTTAGAGGTTCAAGATGGTAGATAAATAAAATGTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGAGGTCCAGATGTTCCCAGGATATTGACTCCAAAGGGCCGTGGTTTCA Human: CTTAGAGATTCAAGATGGTAGGTAAATGTC-AGTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGAGGTCCAGATGTTCCCAGGATATTGACTCCAAAGGGCCGTGGTTTCA Cluster: [ ] Orangutan: CTTAGAGATTCAAGATGGTAGATAAATAAAATGTCAGTCTTCAGGAAATCTTCATTTTAATCTCATTAATGAGGTCCAGATGTTCCCAGGATATTGACTCCAAAGGGCCGTGGTTTCA Chimp > Human ------------- chr5:102764182-102764185 Template switch process: F1: L ACTGTGCCCTGCTGAGCCCTCTTAGAGATTCAAGATGGTAGGTAAAT 1 F3: 4 GTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGA R RF: ACTGTGCCCTGCTGAGCCCTCTTAGAGATTCAAGATGGTAGATAAATAAAATGTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGAGGTCCAGATGTTCCCAGGACATTGAC RR: TGACACGGGACGACTCGGGAGAATCTCTAAGTTCTACCATCTATTTATTTTACAGTCAGAAGTCCTTTAGAAGGAAAATTAGAGTAATTACTCCAGGTCTACAAGGGTCCTGTAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -31.7) CCTGCTGAGCCCTCTTAGAGATTCAAGATGGTAGgTAAATgtcA----GTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGA CCTGCTGAGCCCTCTTAGAGATTCAAGATGGTAGATAAAT---AAAATGTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGA Template switch alignment (log-probability: -21.9) CCTGCTGAGCCCTCTTAGAGATTCAAGATGGTAGgTAAAT|GTCA|GTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGA CCTGCTGAGCCCTCTTAGAGATTCAAGATGGTAGATAAAT|GTCA|GTCAGTCTTCAGGAAATCTTCCTTTTAATCTCATTAATGA ========== Event 2968 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCAGAAATTCTTTTGAAATGATAAAGATGCTTTATCTAAGCATCTTTAAAATATAATTGCATACTTTC Chimp: TTCAGAAATTCTTTTGAAATG-----TACGC-TTATCTAAGCatctttaaaatataattgcatactttc Gorilla: TTCAGAAATTCTTTTGAAATG-----TACGC-TTATCTAAGCatctttaaaatataattgcatactttc ↓ 1 4 3 2 Human: TTCAGAAATTCTTTTGAAATGATAAAGATGCTTTATCTAAGCATCTTTAAAATATAATTGCATACTTTC Cluster: [ ] Orangutan: TTCAGAAATTCTTTTGAAATG-----TACGC-TTATCTAAGCATCTTTAAAATATAATTGCATACTTTC Gorilla > Human --------------- chr5:100794002-100794011 Template switch process: F1: L GGTTACCAAAGAATAAATTATTCAGAAATTCTTTTGAAATGA 1 F3: 4 TTATCTAAGCATCTTTAAAATATAATTGCATACTTTCCTA R RF: GGTTACCTAAGAATAAATTATTCAGAAATTCTTTTGAAATGTACGCTTATCTAAGCATCTTTAAAATATAATTGCATACTTTCCTG RR: CCAATGGATTCTTATTTAATAAGTCTTTAAGAAAACTTTACATGCGAATAGATTCGTAGAAATTTTATATTAACGTATGAAAGGAC F2: 3 TCGTAGAAAT 2 Unidirectional alignment (log-probability: -46.3) TTACCaAAGAATAAATTATTCAGAAATTCTTTTGAAATGataaagatgcT----TTATCTAAGCATCTTTAAAATATAATTGCATACTTTCCTa TTACCTAAGAATAAATTATTCAGAAATTCTTTTGAAATG----------TACGCTTATCTAAGCATCTTTAAAATATAATTGCATACTTTCCTG Template switch alignment (log-probability: -33.6) TTACCaAAGAATAAATTATTCAGAAATTCTTTTGAAATGa|TAAAGATGCT|TTATCTAAGCATCTTTAAAATATAATTGCATACTTTCCTa TTACCTAAGAATAAATTATTCAGAAATTCTTTTGAAATGT|TAAAGATGCT|TTATCTAAGCATCTTTAAAATATAATTGCATACTTTCCTG ========== Event 2969 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCACCTGACTTCTTGGTGTACTTGTTACTTCTTG-----------------GTGTACTTGGTGTACTAACACCAAGG ↓ 3 2 4 1 Chimp: ACCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTACACAAGTACTTGGTGTACTTGGTGTACTAACACCAAGG ↑ 3 2 4 1 Gorilla: ACCACCTGACTTCTTGGTGTACTTGTTACTTCTTG-----------------GTGTACTTGGTGTACTAACACCAAGG Human: ACCACCTGACTTCTTGGTGTACTTGTTACTTCTTG-----------------GTGTACTTGGTGTACTAACACCAAGG Cluster: [ ] Orangutan: ACCACCTGCCTTCTTGGTGTACTTGTTAGTCC--------------------------------------------TG Human > Chimp ------------- chr5:173754982-173754988 Template switch process: F1: L TTCTTCACCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAC 1 F3: 4 CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTCGCTGT R RF: TTCTTCACCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTGGCTGT RR: AAGAAGTGGTGGACTGAAGAACCACATGAACAATGAAGAACCACATGAACCACATGATTGTGGTTCCAACCGAAACCGACA F2: 3 ATGAACA 2 Unidirectional alignment (log-probability: -41.4) CCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAcacaagtacttggtgtaCTTGGTGTACTAACACCAAGGTTGGCTTTcG CCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTA-----------------CTTGGTGTACTAACACCAAGGTTGGCTTTGG Template switch alignment (log-probability: -22.3) CCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAC|ACAAGTA|CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTcG CCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAC|ACAAGTA|CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTGG Gorilla > Chimp --------------- chr5:173754982-173754988 Template switch process: F1: L TTCTTCACCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAC 1 F3: 4 CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTCGCTGT R RF: TTCTTCACCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTGGCTGT RR: AAGAAGTGGTGGACTGAAGAACCACATGAACAATGAAGAACCACATGAACCACATGATTGTGGTTCCAACCGAAACCGACA F2: 3 ATGAACA 2 Unidirectional alignment (log-probability: -40.8) CCACCTGACTTCTTGGTGTACTTGTTACTTcttggtgtacacaagtaCTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTcG CCACCTGACTTCTTGGTGTACTTGTTACTT-----------------CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTGG Template switch alignment (log-probability: -22.4) CCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAC|ACAAGTA|CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTcG CCACCTGACTTCTTGGTGTACTTGTTACTTCTTGGTGTAC|ACAAGTA|CTTGGTGTACTTGGTGTACTAACACCAAGGTTGGCTTTGG ========== Event 2970 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 134 Detected in comparisons: 1234 Multiple sequence alignment: Human: TAAGTATCTCCTTGACCAAAA-TGTT--------ATCAGACTGGGACATATCTAATCAGCATGCTGTCTCACATTCCATA ↑ 13 24 Chimp: TAAGTATCTCCTTGACCAAAATAGAT----ATGTCCCAGTCTG----ATA-ACAATCAGTATGCTGTCTCACATTCCATA Gorilla: TAAGTATCTCCTTGACCAAAATAGATATGT----CCCAGTCTG----ATA-ACAATCAGTATGCTGTCTCACATTCCATA ↓ 13 24 ↑ 13 24 Human: TAAGTATCTCCTTGACCAAAA-TGTT--------ATCAGACTGGGACATATCTAATCAGCATGCTGTCTCACATTCCATA Cluster: [ ] Orangutan: TAAGTATCTCCTTGACCAAAATANNNNNNN----NNNNNNNNN----NNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr5:98945198-98945219 Template switch process: F1: L AAATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT 1 F3: 4 AATCAGCATGCTGTCTCACATTCCATAATATATGACACCACTCTGTA R RF: AAAGTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAATAGATATGTCCCAGTCTGATAACAATCAGTATGCTGTCTCACATTCCATAATATATGACACCACTCTGTA RR: TTTCATTCGATAAAGATTTTATTCATAGAGGAACTGGTTTTATCTATACAGGGTCAGACTATTGTTAGTCATACGACAGAGTGTAAGGTATTATATACTGTGGTGAGACAT F2: 3 TCTATACAGGGTCAGACTATTG 2 Unidirectional alignment (log-probability: -65.9) AtTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT----------------------gttatcagactgggacatatctAATCAGcATGCTGTCTCACATTCCATAATATATGACACCA AGTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAATAGATATGTCCCAGTCTGATAAC----------------------AATCAGTATGCTGTCTCACATTCCATAATATATGACACCA Template switch alignment (log-probability: -30.1) AtTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT|GTTATCAGACTGGGACATATCT|AATCAGcATGCTGTCTCACATTCCATAATATATGACACCA AGTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT|GTTATCAGACTGGGACATATCT|AATCAGTATGCTGTCTCACATTCCATAATATATGACACCA Gorilla > Human --------------- chr5:98945198-98945219 Template switch process: F1: L AAATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT 1 F3: 4 AATCAGCATGCTGTCTCACATTCCATAATATATGACACCACTCTGTA R RF: AAATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAATAGATATGTCCCAGTCTGATAACAATCAGTATGCTGTCTCACATTCCATAATATATGACACCACTCTGTA RR: TTTAATTCGATAAAGATTTTATTCATAGAGGAACTGGTTTTATCTATACAGGGTCAGACTATTGTTAGTCATACGACAGAGTGTAAGGTATTATATACTGTGGTGAGACAT F2: 3 TCTATACAGGGTCAGACTATTG 2 Unidirectional alignment (log-probability: -58.3) ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAATgttatcagactgggAcATATcT--------------AATCAGcATGCTGTCTCACATTCCATAATATATGACACCA ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT--------------AGATATGTCCCAGTCTGATAACAATCAGTATGCTGTCTCACATTCCATAATATATGACACCA Template switch alignment (log-probability: -24.2) ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT|GTTATCAGACTGGGACATATCT|AATCAGcATGCTGTCTCACATTCCATAATATATGACACCA ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT|GTTATCAGACTGGGACATATCT|AATCAGTATGCTGTCTCACATTCCATAATATATGACACCA Human > Gorilla --------------- chr5:100172211-100172232 Template switch process: F1: L AAATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT 1 F3: 4 AATCAGTATGCTGTCTCACATTCCATAATATATGACACCACTCTGTA R RF: AAATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAATGTTATCAGACTGGGACATATCTAATCAGCATGCTGTCTCACATTCCATAATATATGACACCACTCTGTA RR: TTTAATTCGATAAAGATTTTATTCATAGAGGAACTGGTTTTACAATAGTCTGACCCTGTATAGATTAGTCGTACGACAGAGTGTAAGGTATTATATACTGTGGTGAGACAT F2: 3 CAATAGTCTGACCCTGTATAGA 2 Unidirectional alignment (log-probability: -58.3) ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT--------------AgATATgTcccagtctgataacAATCAGtATGCTGTCTCACATTCCATAATATATGACACCA ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAATGTTATCAGACTGGGACATATCT--------------AATCAGCATGCTGTCTCACATTCCATAATATATGACACCA Template switch alignment (log-probability: -24.2) ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT|AGATATGTCCCAGTCTGATAAC|AATCAGtATGCTGTCTCACATTCCATAATATATGACACCA ATTAAGCTATTTCTAAAATAAGTATCTCCTTGACCAAAAT|AGATATGTCCCAGTCTGATAAC|AATCAGCATGCTGTCTCACATTCCATAATATATGACACCA ========== Event 2971 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATAACCCACGTCCTCAAGCCC------------------------------------TTCACTGCAAAAACATGGCCTTGTCCACAAAGAGGGAATGGCCCTGCATTGAGTTGGATCCTCACATCCAGCACACACTGCATTTCATCAATGGCAATGCCAAAGTCATATTCAGGTAGGCTGAGAAGAAGCaaaaaaaaaaaaa ↓ 4 1 3 2 Chimp: CATAACCCACGTCCTCAAGCCC------------------TTCTCTGCCTCAGCCCCCTTCACTGCAAAAACATGGGCTTGTCCACAAAGAGGGAATGGCCCTGCATTGAGTTGGATCCTCACATC-----------------CATCAATGGCAATGCCAAAGTCATATTCAGGTAGGCTGAGAAGAAGCaaaaaaaaaaa-- Gorilla: TATAATCCACGTCCTCAAGCCCTTCTCTGCCTCAGCCCCC------------------TTCACTGCAAAAACATGGGCTTGTCCACAAAGAGGGAATGGCCCTGCATTGAGTTGGATCCTCACATCCAGCACACGCTGCATTTCATCAATGGCAATGCCAAAGTCATATTCAGGTAGGCTGAGAAGAAGCaaaaaaaaaaa-- Human: CATAACCCACGTCCTCAAGCCC------------------------------------TTCACTGCAAAAACATGGCCTTGTCCACAAAGAGGGAATGGCCCTGCATTGAGTTGGATCCTCACATCCAGCACACACTGCATTTCATCAATGGCAATGCCAAAGTCATATTCAGGTAGGCTGAGAAGAAGCaaaaaaaaaaaaa Cluster: [ ] Orangutan: CATAACCTGCGTCCTCAAGCCCTTCTCTGCCTCAGC-CCC------------------TCCACTGCAAAAACATGGGCTTGTCCACAAAGAGGGAATGGCCCTGCATTATGTTGGATCCTCACATCCAGAGCACGCTGCATTTCATCAATGGCAATGCCAAAGTTATATTCAGGTAGGCTGAGAAGAAGCaaaaaaa------ Human > Chimp ------------- chr5:33290311-33290317 Template switch process: F1: L CCCGATAGCTTCACCAGAGCATAACCCACGTCCTCAAGCCCTTCTCTGC 1 F3: 4 CCCTTCACTGCAAAAACATGGGCTTGTCCACAAAGAGGGAATG R RF: CCCGATAGCTTCACCAGAGCATAACCCACGTCCTCAAGCCCTTCACTGCAAAAACATGGCCTTGTCCACAAAGAGGGAATGGCCCTGCATTGAGTTGGATCCTCACATCCAGCACACACTGCATTTCATCAATGGCAATGCCAAAGTCATATTCAGGTAGGCTGAG RR: GGGCTATCGAAGTGGTCTCGTATTGGGTGCAGGAGTTCGGGAAGTGACGTTTTTGTACCGGAACAGGTGTTTCTCCCTTACCGGGACGTAACTCAACCTAGGAGTGTAGGTCGTGTGTGACGTAAAGTAGTTACCGTTACGGTTTCAGTATAAGTCCATCCGACTC F2: 3 CCGACTC 2 Unidirectional alignment (log-probability: -42.8) TTCACCAGAGCATAACCCACGTCCTCAAGCCCTtctctgcctcagccccctTCACTGCAAAAACATGGgCTTGTCCACAAAGAGGGA TTCACCAGAGCATAACCCACGTCCTCAAGCCCT------------------TCACTGCAAAAACATGGCCTTGTCCACAAAGAGGGA Template switch alignment (log-probability: -28.3) TTCACCAGAGCATAACCCACGTCCTCAAGCCCTTCtCTGC|CTCAGCC|CCCTTCACTGCAAAAACATGGgCTTGTCCACAAAGAGGGA TTCACCAGAGCATAACCCACGTCCTCAAGCCCTTCACTGC|CTCAGCC|CCCTTCACTGCAAAAACATGGCCTTGTCCACAAAGAGGGA ========== Event 2972 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCGAACCTATGCTTGATTGAAGTCAGT-GTTACATGGCAATCCTTGACCATGGT Chimp: CCCGAACCTATGCTTGATTGAAGTCAGT-GTTAAATGGCAATCCTTGACCATGGT ↓ 3 12 4 Gorilla: CCCGAACCTATGCTTGATTGAAGTCACTGACTTCATGGCAATCCTTGACCATGGT Human: CCCGAACCTATGCTTGATTGAAGTCAGT-GTTACATGGCAATCCTTGACCATGGT Cluster: [ ] Orangutan: CCCGAACCTATGCTTGATTGAAGTCAGT-GTTATACGGCAATCCTTGACCATGGT Chimp > Gorilla --------------- chr5:100124254-100124261 Template switch process: F1: L TATGAAACACACCCTCCCGAACCTATGCTTGATTGAAGTCA 1 F3: 4 ATGGCAATCCTTGACCATGGTTTTTGTCAATTGTTCCTAT R RF: TATGAAACACACCCTCCCGAACCTATGCTTGATTGAAGTCAGTGTTAAATGGCAATCCTTGACCATGGTTTTTGTCAATTGTTCCTAT RR: ATACTTTGTGTGGGAGGGCTTGGATACGAACTAACTTCAGTCACAATTTACCGTTAGGAACTGGTACCAAAAACAGTTAACAAGGATA F2: 3 CTTCAGTC 2 Unidirectional alignment (log-probability: -32.1) ATGAAACACACCCTCCCGAACCTATGCTTGATTGAAGTCAcTG---ActtcATGGCAATCCTTGACCATGGTTTTTGTCAATTGTTCCTAT ATGAAACACACCCTCCCGAACCTATGCTTGATTGAAGTCAGTGTTAA----ATGGCAATCCTTGACCATGGTTTTTGTCAATTGTTCCTAT Template switch alignment (log-probability: -16.7) ATGAAACACACCCTCCCGAACCTATGCTTGATTGAAGTCA|CTGACTTC|ATGGCAATCCTTGACCATGGTTTTTGTCAATTGTTCCTAT ATGAAACACACCCTCCCGAACCTATGCTTGATTGAAGTCA|CTGACTTC|ATGGCAATCCTTGACCATGGTTTTTGTCAATTGTTCCTAT ========== Event 2973 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAAGAAAGCAGAAAGGAAAT-GTCGTGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGG-AGCGTTTATTCAACTGTGGGGCTCTTAGCCTTTGCACACAGGAGCCTCTGGGCTTGGCCTGTCTCCTGAGGGCCACACATTCTCCTGATA Chimp: TGAAGAAAGCAGAAAGGAAATGCTCGTGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGACGCGTTTATTCAACTGCGGGGCTCTTAGCCTTTGCACACAGGAGCCTCTGGGCTTGGCCTGTCTCCTGAGGGCCACACATTCTCCTGATA Gorilla: TGAAGAAAGCAGAAAGGAAATGCTCAGGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGACGCGTTTATTCAACTGCGGGGCTCTTAGCCTTTGCACACAGGAGCCTCTGGGCTTGGCCTGTCTCCTGAGAGCCACACATTCTCCTGATA ↑ 1 4 3 2 Human: TGAAGAAAGCAGAAAGGAAAT-GTCGTGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGG-AGCGTTTATTCAACTGTGGGGCTCTTAGCCTTTGCACACAGGAGCCTCTGGGCTTGGCCTGTCTCCTGAGGGCCACACATTCTCCTGATA Cluster: [ ] Orangutan: TGAAGAAAGCAGAAAGGAAATGCTCGTGAAGAAAACAAGTTCTGTCAGCAAATGGTGTTTCTGGACGCGTTTATTCAGCTGCGGGGCTCTTAGCCTTTGCACACAGGAGCCTCTGGGCTTGGCCTGTCTCCTGAGGGCCACACATTCTCCTGATA Human > Gorilla --------------- chr5:101409405-101409409 Template switch process: F1: L TAAGCAGAATACAAAGCACTTGAAGAAAGCAGAAAGGAAATG 1 F3: 4 GAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGACG R RF: TAAGCAGAATACAAAGCACTTGAAGAAAGCAGAAAGGAAATGTCGTGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGAGCGTTTATTCAACTGTGGGGCTCTTAGCCTTTGCACACAGGAGCCTCTGGGCTTGGCCTGTCTCCTGAG RR: ATTCGTCTTATGTTTCGTGAACTTCTTTCGTCTTTCCTTTACAGCACTTCTTTTGTTCGAGACAGTCGTTTACCACAAAGACCTCGCAAATAAGTTGACACCCCGAGAATCGGAAACGTGTGTCCTCGGAGACCCGAACCGGACAGAGGACTC F2: 3 GACTC 2 Unidirectional alignment (log-probability: -34.6) AGCAGAATACAAAGCACTTGAAGAAAGCAGAAAGGAAATGcTCagGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGAcG AGCAGAATACAAAGCACTTGAAGAAAGCAGAAAGGAAATG-TCGTGAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGA-G Template switch alignment (log-probability: -26) AGCAGAATACAAAGCACTTGAAGAAAGCAGAAAGGAAATG|CTCAG|GAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGGacg AGCAGAATACAAAGCACTTGAAGAAAGCAGAAAGGAAATG|CTCAG|GAAGAAAACAAGCTCTGTCAGCAAATGGTGTTTCTGG--A ========== Event 2974 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tctggccTGTTTTTGTTTTCA------------GGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAACATTTTAC ↓ 1 4 3 2 Chimp: tctggccTGTTTTTGTTTTCAGGCCTTGCATGGGGCAAAATAAATTGTTTTGCCCCATGCAAGGCAATTTGTCTAACATTGTAC ↑ 1 4 3 2 Gorilla: tctggccTGTTTTTGTTTTCA------------GGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAACATTTTAC Human: tctggccTGTTTTTGTTTTCA------------GGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAACATTTTAC Cluster: [ ] Orangutan: tctggccTGTTGTTGTTTTCA------------GGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAAC---ATAC Human > Chimp ------------- chr5:35563290-35563302 Template switch process: F1: L TACAGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCAGG 1 F3: 4 AAAATAAATTGTTTTGCCCCATGCAAGGCAATTTGTCTAA R RF: TACAGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCAGGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAA RR: ATGTCCGTACTCGGTGGTGAAGACCGGACAAAAACAAAAGTCCTTTTTATTTAATAAAACGGGGTACGTTCCGTTAAACAGATT F2: 3 CGGGGTACGTTCC 2 Unidirectional alignment (log-probability: -40.2) AGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCAggccttgcatggGGcAAAATAAATTgTTTTGCCCCATGCAAGGCAATTTGTCTAA AGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCA------------GGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAA Template switch alignment (log-probability: -22.9) AGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCAGG|CCTTGCATGGGGC|AAAATAAATTgTTTTGCCCCATGCAAGGCAATTTGTCTAA AGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCAGG|CCTTGCATGGGGC|AAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAA Gorilla > Chimp --------------- chr5:35563290-35563302 Template switch process: F1: L TACAGGCATGAGCCACCACTTCTGGCCTGTTTTTGTTTTCAGG 1 F3: 4 AAAATAAATTGTTTTGCCCCATGCAAGGCAATTTGTCTAA R RF: TACAGGCATGAGTCACCACTTCTGGCCTGTTTTTGTTTTCAGGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAA RR: ATGTCCGTACTCAGTGGTGAAGACCGGACAAAAACAAAAGTCCTTTTTATTTAATAAAACGGGGTACGTTCCGTTAAACAGATT F2: 3 CGGGGTACGTTCC 2 Unidirectional alignment (log-probability: -44.7) AGGCATGAGcCACCACTTCTGGCCTGTTTTTGTTTTCAggccttgcatggGGcAAAATAAATTgTTTTGCCCCATGCAAGGCAATTTGTCTAA AGGCATGAGTCACCACTTCTGGCCTGTTTTTGTTTTCA------------GGAAAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAA Template switch alignment (log-probability: -28.5) AGGCATGAGcCACCACTTCTGGCCTGTTTTTGTTTTCAGG|CCTTGCATGGGGC|AAAATAAATTgTTTTGCCCCATGCAAGGCAATTTGTCTAA AGGCATGAGTCACCACTTCTGGCCTGTTTTTGTTTTCAGG|CCTTGCATGGGGC|AAAATAAATTATTTTGCCCCATGCAAGGCAATTTGTCTAA ========== Event 2975 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GTAGTAAAGGCCAACCTGGTACATTTGCATGATGCAAATGTACGGATGCAGGCCTCAGCAGAA ↑ 3 2 1 4 Chimp: GTAGTAAAGGCCAACCTGGTACATTTGCATGA------TGTTCGGATGCAGGCCTCAGCAGAA Gorilla: GTAGTAAAGGCCAACCTGGTACATTTGCATGA------TGTTCGGATGCAGGCCTCAGCAGAA Human: GTAGTAAAGGCCAACCTGGTACATTTGCATGATGCAAATGTACGGATGCAGGCCTCAGCAGAA Cluster: [ ] Orangutan: Chimp > Human ------------- chr5:82778181-82778188 Template switch process: F1: L AGGTAGAATGTAGTAAAGGCCAACCTGGTACATTTGCATGATG 1 F3: 4 CGGATGCAGGCCTCAGCAGAAGTATCCATGGAAACAAACT R RF: AGGTAGAATGTAGTAAAGGCCAACCTGGTACATTTGCATGATGTTCGGATGCAGGCCTCAGCAGAAGTATCCATGGAAACAAACT RR: TCCATCTTACATCATTTCCGGTTGGACCATGTAAACGTACTACAAGCCTACGTCCGGAGTCGTCTTCATAGGTACCTTTGTTTGA F2: 3 ATGTAAAC 2 Unidirectional alignment (log-probability: -25.6) TAGAATGTAGTAAAGGCCAACCTGGTACATTTGCATGatgcaaATGTaCGGATGCAGGCCTCAGCAGAAGTATCCATGGAAACAAACT TAGAATGTAGTAAAGGCCAACCTGGTACATTTGCATG------ATGTTCGGATGCAGGCCTCAGCAGAAGTATCCATGGAAACAAACT Template switch alignment (log-probability: -16.3) TAGAATGTAGTAAAGGCCAACCTGGTACATTTGCATGATG|CAAATGTA|CGGATGCAGGCCTCAGCAGAAGTATCCATGGAAACAAACT TAGAATGTAGTAAAGGCCAACCTGGTACATTTGCATGATG|CAAATGTA|CGGATGCAGGCCTCAGCAGAAGTATCCATGGAAACAAACT ========== Event 2976 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCC---CCTTCAAAGCAAACATGCTTTGTGGC Chimp: AATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCC---CCTTCAAAGCAAACATGCTTTGTGGC ↓ 3 2 1 4 Gorilla: AATAAATGACTTAGACTTTTGGCTAGTTTCTAGATAAAACTAGC------CAAAAGCAAACATGCTTTGTGGC ↑ 3 2 1 4 Human: AATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCC---CCTTCAAAGCAAACATGCTTTGTGGC Cluster: [ ] Orangutan: AATAAATGACCTAGACTGTTGGCTAGTTTCTAGATAAAAGGTCCCCT---TCAAAGCAAACATGCTTTGTGGC Human > Gorilla --------------- chr17:8554924-8554930 Template switch process: F1: L GTAATAAATGACTTAGACTTTTGGCTAGTTTCTAGATAAAA 1 F3: 4 AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC R RF: GTAATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCCCCTTCAAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC RR: CATTATTTACTAGATCTGAAAACCGATCAAAGATCTATTTTCCAGGGGAAGTTTCGTTTGTACGAAACACCGACTTCTAAACATTTCACGG F2: 3 ACCGATC 2 Unidirectional alignment (log-probability: -40.8) TAATAAATGActTAGACTTTTGGCTAGTTTCTAGATAAAA---------CtagccaAAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC TAATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCCCCTTC------AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC Template switch alignment (log-probability: -27.7) TAATAAATGActTAGACTTTTGGCTAGTTTCTAGATAAAA|CTAGCCA|AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC TAATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAA|CTAGCCA|AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC Chimp > Gorilla --------------- chr17:8554924-8554930 Template switch process: F1: L GTAATAAATGACTTAGACTTTTGGCTAGTTTCTAGATAAAA 1 F3: 4 AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC R RF: GTAATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCCCCTTCAAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC RR: CATTATTTACTAGATCTGAAAACCGATCAAAGATCTATTTTCCAGGGGAAGTTTCGTTTGTACGAAACACCGACTTCTAAACATTTCACGG F2: 3 ACCGATC 2 Unidirectional alignment (log-probability: -40.8) TAATAAATGActTAGACTTTTGGCTAGTTTCTAGATAAAA---------CtagccaAAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC TAATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAAGGTCCCCTTC------AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC Template switch alignment (log-probability: -27.7) TAATAAATGActTAGACTTTTGGCTAGTTTCTAGATAAAA|CTAGCCA|AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC TAATAAATGATCTAGACTTTTGGCTAGTTTCTAGATAAAA|CTAGCCA|AAAGCAAACATGCTTTGTGGCTGAAGATTTGTAAAGTGCC ========== Event 2977 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GTGTCTCCCACATTCAGAAAGCCAGGTGACCTCCTGGCTATAGAGCACAAAGAGAT Chimp: GTGTCTCCCACATTCAGAAAG----CTGGTCACCTGTCTATAGAACACAAAGAGAT Gorilla: GTGTCTCCCACATTCAGAAAG----CTGGTCACCTGGCTATAGAGCACAAAGAGAT ↓ 1 3 4 2 Human: GTGTCTCCCACATTCAGAAAGCCAGGTGACCTCCTGGCTATAGAGCACAAAGAGAT Cluster: [ ] Orangutan: GTGTCTCCCACATTCAGAAAG----CTGGTCACCTGGCTATAGAGCACAAAGAGAT Gorilla > Human --------------- chr5:83424375-83424382 Template switch process: F1: L GGTAGTCACAGGCTGTAAAGGTGTCTCCCACATTCAGAAAGC 1 F3: 4 CTCCTGGCTATAGAGCACAAAGAGATCTTTGGAGTTTTATGA R RF: GGTAGTCACAGGCTGTAAAGGTGTCTCCCACATTCAGAAAGCTGGTCACCTGGCTATAGAGCACAAAGAGATCTTTGGAGTTTTATGA RR: CCATCAGTGTCCGACATTTCCACAGAGGGTGTAAGTCTTTCGACCAGTGGACCGATATCTCGTGTTTCTCTAGAAACCTCAAAATACT F2: 3 CAGTGGAC 2 Unidirectional alignment (log-probability: -32.4) TAGTCACAGGCTGTAAAGGTGTCTCCCACATTCAGAAAGC----CAggtgacctCCTGGCTATAGAGCACAAAGAGATCTTTGGAGTTTTAT TAGTCACAGGCTGTAAAGGTGTCTCCCACATTCAGAAAGCTGGTCA--------CCTGGCTATAGAGCACAAAGAGATCTTTGGAGTTTTAT Template switch alignment (log-probability: -22.3) TAGTCACAGGCTGTAAAGGTGTCTCCCACATTCAGAAAGC|CAGGTGAC|CtCCTGGCTATAGAGCACAAAGAGATCTTTGGAGTTTTAT TAGTCACAGGCTGTAAAGGTGTCTCCCACATTCAGAAAGC|CAGGTGAC|CACCTGGCTATAGAGCACAAAGAGATCTTTGGAGTTTTAT ========== Event 2978 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: cctgctccatgctcgcagGTT--------------CTAGAAGTGAGACCTTCTAGAACAGAATGCCTCACTGTAG Chimp: cctgctccatgctggcagGTT-------GTTCCCTATAGAAGGTCTCACTTCTAGAACAGAATGCCTCACTGTAG Gorilla: cctgctccatgctcgcagGTTGTTCCCT-------ATAGAAGGTCTCACTTCTAGAACAGAATGCCTCACTGTAG ↓ 1 3 4 2 Human: cctgctccatgctcgcagGTT--------------CTAGAAGTGAGACCTTCTAGAACAGAATGCCTCACTGTAG Cluster: [ ] Orangutan: cctgctccatgctggcagGTTGTTCCCT-------ATAGAAGGTCTCACTTCTAGAACAGAATGCCTCACCGTAG Gorilla > Human --------------- chr5:83790741-83790753 Template switch process: F1: L CTGTGCAGCCCAGCATTGCTCCTGCTCCATGCTCGCAGGTT 1 F3: 4 CTTCTAGAACAGAATGCCTCACTGTAGGCAGAATGAAAGT R RF: CTGTGCAGCCCAGCATTGCTCCTGCTCCATGCTCGCAGGTTGTTCCCTATAGAAGGTCTCACTTCTAGAACAGAATGCCTCACTGTAGGCAGAATGAAAGT RR: GACACGTCGGGTCGTAACGAGGACGAGGTACGAGCGTCCAACAAGGGATATCTTCCAGAGTGAAGATCTTGTCTTACGGAGTGACATCCGTCTTACTTTCA F2: 3 CAGAGTGAAGATC 2 Unidirectional alignment (log-probability: -40.3) TGTGCAGCCCAGCATTGCTCCTGCTCCATGCTCGCAGGTT--------------------ctagaagtgagacCTTCTAGAACAGAATGCCTCACTGTAGGCAGAATGAAAGT TGTGCAGCCCAGCATTGCTCCTGCTCCATGCTCGCAGGTTGTTCCCTATAGAAGGTCTCA-------------CTTCTAGAACAGAATGCCTCACTGTAGGCAGAATGAAAGT Template switch alignment (log-probability: -17.4) TGTGCAGCCCAGCATTGCTCCTGCTCCATGCTCGCAGGTT|CTAGAAGTGAGAC|CTTCTAGAACAGAATGCCTCACTGTAGGCAGAATGAAAGT TGTGCAGCCCAGCATTGCTCCTGCTCCATGCTCGCAGGTT|CTAGAAGTGAGAC|CTTCTAGAACAGAATGCCTCACTGTAGGCAGAATGAAAGT ========== Event 2979 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 36 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTCAAAATAGAATAGATTTCCCCTTCATTTCAGAAGGAATGAAGGGGAAAAACAACAGATTTATTGTGC Chimp: TTTCAAAATAGAATAGATTTCCCCTTCA-TTCAGAAGGAATGAAGCGGGAAAACGACAGATTTATTGTGC ↓ 3 1 2 4 Gorilla: TTTCAAAATAGAATAGATTTCCCCTTCA-TTCCTTCTGAATGAAGGGGAAAAACGACAGATTTATTGTGC ↓ 1 3 42 Human: TTTCAAAATAGAATAGATTTCCCCTTCATTTCAGAAGGAATGAAGGGGAAAAACAACAGATTTATTGTGC Cluster: [ ] Orangutan: TTTCAAAATAGAATAGATTTTCCCTTCA-TTCAGAAGGAATGAAAGGGAAAAACGACAGATTTATTGTGC Gorilla > Human --------------- chr5:173019897-173019903 Template switch process: F1: L ATTAGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATT 1 F3: 4 GAATGAAGGGGAAAAACAACAGATTTATTGTGCAGCATTC R RF: ATTAGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTCCTTCTGAATGAAGGGGAAAAACGACAGATTTATTGTGCAGCATTC RR: TAATCCTTCATAAAAAGTTTTATCTTATCTAAAGGGGAAGTAAGGAAGACTTACTTCCCCTTTTTGCTGTCTAAATAACACGTCGTAAG F2: 3 GAAGACT 2 Unidirectional alignment (log-probability: -35.1) AGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATT-----TcagaagGAATGAAGGGGAAAAACaACAGATTTATTGTGCAGCATTC AGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTCCTTCT------GAATGAAGGGGAAAAACGACAGATTTATTGTGCAGCATTC Template switch alignment (log-probability: -22.2) AGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATT|TCAGAAG|GAATGAAGGGGAAAAACaACAGATTTATTGTGCAGCATTC AGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATT|TCAGAAG|GAATGAAGGGGAAAAACGACAGATTTATTGTGCAGCATTC Chimp > Gorilla --------------- chr17:87175115-87175131 Template switch process: F1: L AGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTC 1 F3: 4 AAAACGACAGATTTATTGTGCAGCATTCAAAAGCTTACAC R RF: AGGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTCAGAAGGAATGAAGCGGGAAAACGACAGATTTATTGTGCAGCATTCAAAAGCTTACAC RR: TCCTTCATAAAAAGTTTTATCTTATCTAAAGGGGAAGTAAGTCTTCCTTACTTCGCCCTTTTGCTGTCTAAATAACACGTCGTAAGTTTTCGAATGTG F2: 3 AGGGGAAGTAAGTCTTC 2 Unidirectional alignment (log-probability: -53.1) GGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTC-----cttctGAATGAAGgGGaAAAACGACAGATTTATTGTGCAGCATTCAAAAGCTtacac GGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTCAGAAG-----GAATGAAGCGGGAAAACGACAGATTTATTGTGCAGCATTCAAAAGCT----- Template switch alignment (log-probability: -17.9) GGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTC|CTTCTGAATGAAGGGGA|AAAACGACAGATTTATTGTGCAGCATTCAAAAGCTTACAC GGAAGTATTTTTCAAAATAGAATAGATTTCCCCTTCATTC|CTTCTGAATGAAGGGGA|AAAACGACAGATTTATTGTGCAGCATTCAAAAGCTTACAC ========== Event 2980 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTGTCCTTTCAAAAACAACC-AGAATAAGCATTTTTTAGTGAAAGAGAAAA ↓ 1 3 4 2 Chimp: TTTGTCCTTTCAAAAACAACCATGCTTATGCATTTTTTAGTGAAAGAGAAAA ↑ 1 3 4 2 Gorilla: TTTGTCCTTTCAAAAACAACC-AGAATAAGCATTTTTTAGTGAAAGAGAAAA Human: TTTGTCCTTTCAAAAACAACC-AGAATAAGCATTTTTTAGTGAAAGAGAAAA Cluster: [ ] Orangutan: TTTGTCCTTTCAAAAACAACC-AGAATAAGCATTTTTTAGTGAAAGAGAAAA Human > Chimp ------------- chr5:150930151-150930157 Template switch process: F1: L TTATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA 1 F3: 4 GCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT R RF: TTATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCAGAATAAGCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT RR: AATACTTATTTATCGTCTGTAAACAGGAAAGTTTTTGTTGGTCTTATTCGTAAAAAATCACTTTCTCTTTTTGACTTAATGAATGTAA F2: 3 TATTCGT 2 Unidirectional alignment (log-probability: -30.4) ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCAtGctTAtGCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA-GAATAAGCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT Template switch alignment (log-probability: -16.2) ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA|TGCTTAT|GCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA|TGCTTAT|GCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT Gorilla > Chimp --------------- chr5:150930151-150930157 Template switch process: F1: L TTATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA 1 F3: 4 GCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT R RF: TTATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCAGAATAAGCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT RR: AATACTTATTTATCGTCTGTAAACAGGAAAGTTTTTGTTGGTCTTATTCGTAAAAAATCACTTTCTCTTTTTGACTTAATGAATGTAA F2: 3 TATTCGT 2 Unidirectional alignment (log-probability: -29) ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCAtGctTAtGCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA-GAATAAGCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT Template switch alignment (log-probability: -16.6) ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA|TGCTTAT|GCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT ATGAATAAATAGCAGACATTTGTCCTTTCAAAAACAACCA|TGCTTAT|GCATTTTTTAGTGAAAGAGAAAAACTGAATTACTTACATT ========== Event 2981 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CGTAAATGGAATAACATTTTGTTCTACTATAGTAGAACAATTATTAGCAGGCATAGAATT Chimp: CGTAAATGGAATAACATTTTGTGCTACTAT-ATATGATTATTATTAGCAGGCATAGAATT Gorilla: CGTAAATGGAATAACATTTTGTTCTACTAT-ATACGATTATTATTAGCAGGCATAGAATT ↓ 3 2 1 4 Human: CGTAAATGGAATAACATTTTGTTCTACTATAGTAGAACAATTATTAGCAGGCATAGAATT Cluster: [ ] Orangutan: CGTAAATGGAATAACATGTTGTTCTACTAT-ATACGATTATTATTAGCAGGCATAGAATT Gorilla > Human --------------- chr5:84674959-84674966 Template switch process: F1: L TAAGTAAAATACGTAAATGGAATAACATTTTGTTCTACTATA 1 F3: 4 ATTATTAGCAGGCATAGAATTGGGCAAAAATCTGTAGCTG R RF: TAAGTAAAATACGTAAATGGAATAACATTTTGTTCTACTATATACGATTATTATTAGCAGGCATAGAATTGGGCAAAAATCTGTAGCTG RR: ATTCATTTTATGCATTTACCTTATTGTAAAACAAGATGATATATGCTAATAATAATCGTCCGTATCTTAACCCGTTTTTAGACATCGAC F2: 3 ACAAGATG 2 Unidirectional alignment (log-probability: -32.5) AGTAAAATACGTAAATGGAATAACATTTTGTTCTACTATA-------gtagaacaATTATTAGCAGGCATAGAATTGGGCAAAAATCTGTAGCTG AGTAAAATACGTAAATGGAATAACATTTTGTTCTACTATATACGATT--------ATTATTAGCAGGCATAGAATTGGGCAAAAATCTGTAGCTG Template switch alignment (log-probability: -16.8) AGTAAAATACGTAAATGGAATAACATTTTGTTCTACTATA|GTAGAACA|ATTATTAGCAGGCATAGAATTGGGCAAAAATCTGTAGCTG AGTAAAATACGTAAATGGAATAACATTTTGTTCTACTATA|GTAGAACA|ATTATTAGCAGGCATAGAATTGGGCAAAAATCTGTAGCTG ========== Event 2982 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATGAAACGGTTTTAAAATCTAA------GAATAAAATAGCCCCAAATATATGGATTCATATATAGATAA--------GCACATTGAATAGATTCATGAATGACTAAATTATAGA Chimp: ATATGAAACTGTTTTAAAATCTAA---GAAGAATAAAATAGCCCCAAATATATGGATTCATATATAGATAA--------GCACATTGAATAGATTCATGAATGACTAAATTATAGA Gorilla: ATATGAAACGGTTTTAAAATCAAAGAA---GAATCAAATAGCCCCAAATATATGGATTCATATATAGATAAGCACATAAGCACATTGAATAGATTCATGAATTACTAAATTATAGA ↑ 1 4 3 2 Human: ATATGAAACGGTTTTAAAATCTAA------GAATAAAATAGCCCCAAATATATGGATTCATATATAGATAA--------GCACATTGAATAGATTCATGAATGACTAAATTATAGA Cluster: [ ] Orangutan: ATATAAAACGGTTTTAAAATCTAAGAA---GAATAAAATAGCCCCAAATACATGGATTCATATATAGATAA--------GCACATTGAATAGATTCATGAATGACTAAATTATAGA Human > Gorilla --------------- chr5:67310500-67310504 Template switch process: F1: L TTATTCTTGAGGAGCTGACTATATGAAACGGTTTTAAAATCAAAGAA 1 F3: 4 AAATAGCCCCAAATATATGGATTCATATATAGATAAGCAC R RF: TTATTCTTGAGGAGCTGACTATATGAAACGGTTTTAAAATCTAAGAATAAAATAGCCCCAAATATATGGATTCATATATAGATAAGCACATTGAATAGATTC RR: AATAAGAACTCCTCGACTGATATACTTTGCCAAAATTTTAGATTCTTATTTTATCGGGGTTTATATACCTAAGTATATATCTATTCGTGTAACTTATCTAAG F2: 3 CTAAG 2 Unidirectional alignment (log-probability: -38.8) TGAGGAGCTGACTATATGAAACGGTTTTAAAATCaaagAAGAATcAAATAGCCCCAAATATATGGATTCATATATAGATAAgcac TGAGGAGCTGACTATATGAAACGGTTTTAAAATC---TAAGAATAAAATAGCCCCAAATATATGGATTCATATATAGATAA---- Template switch alignment (log-probability: -22) TGAGGAGCTGACTATATGAAACGGTTTTAAAATCaAAGAA|GAATC|AAATAGCCCCAAATATATGGATTCATATATAGATAAGCAC TGAGGAGCTGACTATATGAAACGGTTTTAAAATCTAAGAA|GAATC|AAATAGCCCCAAATATATGGATTCATATATAGATAAGCAC ========== Event 2983 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: AATCTAGCATTATTGCAAACCTTAGCCCATTACCTCCCTCAAGGGTATACAGTGTTTAGTGTG Chimp: Gorilla: AATCTAGCATTATTGCAAACCC---------------TTGAGGGGTATACAGTGTTTAGTGTG ↑ 1 3 4 Human: AATCTAGCATTATTGCAAACCTTAGCCCATTACCTCCCTCAAGGGTATACAGTGTTTAGTGTG Cluster: [ ] Orangutan: --------------------------------------------------------------- Human > Gorilla --------------- chr5:97864770-97864775 Template switch process: F1: L ATATGGAATAAAAATATCTGAATCTAGCATTATTGCAAACC 1 F3: 4 GGGTATACAGTGTTTAGTGTGTTGAAATGGTCTGAGAAAA R RF: ATATGGAATAAAAATATCTGAATCTAGCATTATTGCAAACCTTAGCCCATTACCTCCCTCAAGGGTATACAGTGTTTAGTGTGTTGAAATGGTCTGAGAAAA RR: TATACCTTATTTTTATAGACTTAGATCGTAATAACGTTTGGAATCGGGTAATGGAGGGAGTTCCCATATGTCACAAATCACACAACTTTACCAGACTCTTTT F2: 3 GAGTTC 2 Unidirectional alignment (log-probability: -28.3) TATGGAATAAAAATATCTGAATCTAGCATTATTGCAAAC---------------CCtTgAgGGGTATACAGTGTTTAGTGTGTTGAAATGGTCTGAGAAAA TATGGAATAAAAATATCTGAATCTAGCATTATTGCAAACCTTAGCCCATTACCTCCCTCAAGGGTATACAGTGTTTAGTGTGTTGAAATGGTCTGAGAAAA Template switch alignment (log-probability: -16.5) TATGGAATAAAAATATCTGAATCTAGCATTATTGCAAACC|CTTGAG|GGGTATACAGTGTTTAGTGTGTTGAAATGGTCTGAGAAAA TATGGAATAAAAATATCTGAATCTAGCATTATTGCAAACC|CTTGAG|GGGTATACAGTGTTTAGTGTGTTGAAATGGTCTGAGAAAA ========== Event 2984 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGATGGGATTTATGGTAATTGCAATGGTGTTGGGACTGGGGGT---TTTTCCCATCTCTATTATAATTAGCAATGGGGTCATTATTTTCATCTGATGGATGTGTATTCTAGCTCTAAAATATTATTATTGCAAAGGCTTGCATTCTAGGCATA Chimp: AGATGGGATTTCTGGTAATTGCAATGGTGTTGGGACTGGG-GT---TTTTCCCATATCTGTTATAATTAGCAATGGGGTCATTATTTTCATCTGATGGATGTGTATTCTAGCTCTAAAATATTATTATTGCAAAGGCTTGCATTCTAGGCATA ↑ 3 2 1 4 Gorilla: AGATGGGATTTCTGGTAATTGCAATGGTGTTGGGATTGGG-tt-tttttttCCATCTCTATTATAATTAGCAATGGGGTCATTATTTTCATCTGATGGATGTGTAGTCTAGCTCTAAAATAT---TATTGC-AAGGCTTGCATTCTAGGCATA Human: AGATGGGATTTATGGTAATTGCAATGGTGTTGGGACTGGGGGT---TTTTCCCATCTCTATTATAATTAGCAATGGGGTCATTATTTTCATCTGATGGATGTGTATTCTAGCTCTAAAATATTATTATTGCAAAGGCTTGCATTCTAGGCATA Cluster: [ ] Orangutan: AGATGGGATTTCTGGTAATTGCAATGGTGTTGGGATTGGG-GTT--TTTTTCCATTTCTATTATAATTAGCAATGGGGTCATTATTTTCATCTGATGGATGTGTATTCTAGCTCTAAAATAT---TATTGCAAAGGCTTGCATTCTAGGCATA Gorilla > Chimp --------------- chr5:151342323-151342328 Template switch process: F1: L TTATTTTCATCTGATGGATGTGTATTCTAGCTCTAAAATATTATT 1 F3: 4 AAGGCTTGCATTCTAGGCATATTTCTATGTACTAAC R RF: TGCAATGGTGTTGGGATTGGGTTTTTTTTTCCATCTCTATTATAATTAGCAATGGGGTCATTATTTTCATCTGATGGATGTGTAGTCTAGCTCTAAAATATTATTGCAAGGCTTGCATTCTAGGCATATTTCTATGTACTAAC RR: ACGTTACCACAACCCTAACCCAAAAAAAAAGGTAGAGATAATATTAATCGTTACCCCAGTAATAAAAGTAGACTACCTACACATCAGATCGAGATTTTATAATAACGTTCCGAACGTAAGATCCGTATAAAGATACATGATTG F2: 3 ACGTTA 2 Unidirectional alignment (log-probability: -31.9) TTCATCTGATGGATGTGTAtTCTAGCTCTAAAAtatTATTATTGCaAAGGCTTGCATTCTAGGCATATTTCTATGTACTAAC TTCATCTGATGGATGTGTAGTCTAGCTCTAAAA---TATTATTGC-AAGGCTTGCATTCTAGGCATATTTCTATGTACTAAC Template switch alignment (log-probability: -22) TTCATCTGATGGATGTGTAtTCTAGCTCTAAAATATTATT|ATTGCA|AAGGCTTGCATTCTAGGCATATTTCTATGTACTAAC TTCATCTGATGGATGTGTAGTCTAGCTCTAAAATATTATT|ATTGCA|AAGGCTTGCATTCTAGGCATATTTCTATGTACTAAC ========== Event 2985 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tataCGTATTCACTTATTCAG--CGTTTAAT----TCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACAAAAC ↓ 1 4 3 2 Chimp: TATACGTATTCACTTATTCAG-CCGCTTAAG--TGGCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACAAAAC ↑ 1 4 3 2 Gorilla: TATACGTATTCACTTATTCAG--CGTTTAAT----TCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACAAAAC Human: tataCGTATTCACTTATTCAG--CGTTTAAT----TCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACAAAAC Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr5:30303928-30303938 Template switch process: F1: L AGATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC 1 F3: 4 CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA R RF: AGATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGCGTTTAATTCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA RR: TCTAAACAGACTAGGTTTGAATATGCATAAGTGAATAAGTCGCAAATTAAGAAAAGACAAGACGGTGAATTCCCGTAAATTCCAAGATGT F2: 3 GGTGAATTCGC 2 Unidirectional alignment (log-probability: -35.9) ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGCcgcttaagtgG-------CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC----------GTTTAATTCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA Template switch alignment (log-probability: -22.7) ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC|CgCTTAAGTGG|CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC|CCCTTAAGTGG|CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA Gorilla > Chimp --------------- chr5:30303928-30303938 Template switch process: F1: L AGATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC 1 F3: 4 CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA R RF: AGATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGCGTTTAATTCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA RR: TCTAAACAGACTAGGTTTGAATATGCATAAGTGAATAAGTCGCAAATTAAGAAAAGACAAGACGGTGAATTCCCGTAAATTCCAAGATGT F2: 3 GGTGAATTCGC 2 Unidirectional alignment (log-probability: -35.4) ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGCcgcttaagtgG-------CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC----------GTTTAATTCTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA Template switch alignment (log-probability: -22.7) ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC|CgCTTAAGTGG|CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA ATTTGTCTGATCCAAACTTATACGTATTCACTTATTCAGC|CCCTTAAGTGG|CTTTTCTGTTCTGCCACTTAAGGGCATTTAAGGTTCTACA ========== Event 2986 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAATCACCTAATACTGTCTTCATTAATTAAATTCTGAGACAAG-----------TATTGATGCAAGCAGTATGCTg Chimp: TTAATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAATTTAATTAATGCAATTGATGCAAGTAGTATGCTg ↑ 3 2 1 4 Gorilla: TTAATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAAG-----------TATTGATGCAAGTAGTATGCTg Human: TTAATCACCTAATACTGTCTTCATTAATTAAATTCTGAGACAAG-----------TATTGATGCAAGCAGTATGCTg Cluster: [ ] Orangutan: TTAATCATCTAATACTGTCTTCATTAATAAAATTCTGAGGCAAG-----------TATTGATGCAAGTAGTATGCTg Gorilla > Chimp --------------- chr5:30171091-30171103 Template switch process: F1: L AATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAA 1 F3: 4 ATTGATGCAAGTAGTATGCTGGAAAATGGTGGAAGTGAAA R RF: AATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAAGTATTGATGCAAGTAGTATGCTGGAAAATGATGGAAGTGAAA RR: TTAGTAGATTATGACAGAAGTAATTAATTTAAGACTCTGTTCATAACTACGTTCATCATACGACCTTTTACTACCTTCACTTT F2: 3 ACGTAATTAATTT 2 Unidirectional alignment (log-probability: -37.8) ATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAAtTtaattaatgcaATTGATGCAAGTAGTATGCTGGAAAATGgTGGAAGTGAAA ATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAAGT-----------ATTGATGCAAGTAGTATGCTGGAAAATGATGGAAGTGAAA Template switch alignment (log-probability: -28.4) ATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAA|TTTAATTAATGcA|ATTGATGCAAGTAGTATGCTGGAAAATGgTGGAAGTGAAA ATCATCTAATACTGTCTTCATTAATTAAATTCTGAGACAA|TTTAATTAATGAA|ATTGATGCAAGTAGTATGCTGGAAAATGATGGAAGTGAAA ========== Event 2987 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATAAGGTAATATATCTACACATACTAAAAGA----------------------TAAATATAAAAATAAATGAGCACTTA ↓ 3 4 1 2 Chimp: CATAAGGTAATATATCTACACATACTAAAAGATATATTTATCTTTTAATATGTATAAGTATAAAAATAAATGAGCACTTA Gorilla: CATAAGGTAATATATCTACACGTACTAAAAGA----------------------TAAATATAAAAATAAATGAGCACTTA Human: CATAAGGTAATATATCTACACATACTAAAAGA----------------------TAAATATAAAAATAAATGAGCACTTA Cluster: [ ] Orangutan: CATAAGGTAATATATCTACACTTACTAAAAGA----------------------TAAATATAAAAATAAATGATTGCTTA Human > Chimp ------------- chr5:173029391-173029409 Template switch process: F1: L AAATTTCTACATAAGGTAATATATCTACACATACTAAAAGATA 1 F3: 4 ATAAGTATAAAAATAAATGAGCACTTACAAATTCTTCTGAACTAA R RF: AAATTTCTACATAAGGTAATATATCTACACATACTAAAAGATAAATATAAAAATAAATGAGCACTTACAAATTCTTCTGAACTAA RR: TTTAAAGATGTATTCCATTATATAGATGTGTATGATTTTCTATTTATATTTTTATTTACTCGTGAATGTTTAAGAAGACTTGATT F2: 3 TGTATAATTTTCTATTTAT 2 Unidirectional alignment (log-probability: -48.6) TTTCTACATAAGGTAATATATCTACACATACTAAAAGATAtAtttatcttttaatatgtataagTATAAAAATAAATGAGCACTTACAAATTCTTCTGA TTTCTACATAAGGTAATATATCTACACATACTAAAAGATAAA----------------------TATAAAAATAAATGAGCACTTACAAATTCTTCTGA Template switch alignment (log-probability: -29.7) TTTCTACATAAGGTAATATATCTACACATACTAAAAGATA|TATTTATCTTTTAaTATGT|ATAAgTATAAAAATAAATGAGCACTTACAAATTCTTCTGA TTTCTACATAAGGTAATATATCTACACATACTAAAAGATA|TATTTATCTTTTAGTATGT|ATAAATATAAAAATAAATGAGCACTTACAAATTCTTCTGA ========== Event 2988 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTCTCAGGCTCTGCATGCTACCACACTCCTTTGCTCCTTGGGGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACC ↓ 1 4 3 2 Chimp: ACTCTCAGGCTCTGCATGCTA-----------A---GCT---TGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACC ↑ 1 4 3 2 Gorilla: ACTCTCAGGCTCTGCATGCTACCACCCTCCTTTGCTCCTTGGAGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACC Human: ACTCTCAGGCTCTGCATGCTACCACACTCCTTTGCTCCTTGGGGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACC Cluster: [ ] Orangutan: ACTCTCAGGCTCTGAATGCTACCACCCTCCTTTGCTCCTTGGAGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACC Human > Chimp ------------- chr5:152895485-152895489 Template switch process: F1: L TGCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA 1 F3: 4 GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT R RF: TGCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTACCACACTCCTTTGCTCCTTGGGGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT RR: ACGAAGAGGGACCATACGACTGAGAGTCCGAGACGTACGATGGTGTGAGGAAACGAGGAACCCCTCTAGAAAAGAGTTCGAAGGGAGAACTGAAGACATGGTA F2: 3 TTCGA 2 Unidirectional alignment (log-probability: -29.5) GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTAagctt----------------------GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA-----CCACACTCCTTTGCTCCTTGGGGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT Template switch alignment (log-probability: -15.9) GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA|AGCTT|GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA|AGCTT|GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT Gorilla > Chimp --------------- chr5:152895485-152895489 Template switch process: F1: L TGCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA 1 F3: 4 GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT R RF: TGCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTACCACCCTCCTTTGCTCCTTGGAGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT RR: ACGAAGAGGGACCATACGACTGAGAGTCCGAGACGTACGATGGTGGGAGGAAACGAGGAACCTCTCTAGAAAAGAGTTCGAAGGGAGAACTGAAGACATGGTA F2: 3 TTCGA 2 Unidirectional alignment (log-probability: -27.5) GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA---------------------AgcttGAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTACCACCCTCCTTTGCTCCTTGGA----GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT Template switch alignment (log-probability: -16.4) GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA|AGCTT|GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT GCTTCTCCCTGGTATGCTGACTCTCAGGCTCTGCATGCTA|AGCTT|GAGATCTTTTCTCAAGCTTCCCTCTTGACTTCTGTACCAT ========== Event 2989 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGAGTTT--------------ACTGATATCTTTCTTATTGACCAAAGTCCCATA-AAAGTATAGGGGA Chimp: GCCTTAACATACCCCTGTATTTGTAGGTAGAAAAGAGTTT--------------ACTGGTATCTTTCTTATTGACCAAAGTCCCATA-AAAGTATAGGGGA Gorilla: GCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGACC-T--------------------------ACGAATGACCAAAGCCCCATA-AAAGTATAGGGGA ↑ 3 2 1 4 Human: GCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGAGTTT--------------ACTGATATCTTTCTTATTGACCAAAGTCCCATA-AAAGTATAGGGGA Cluster: [ ] Orangutan: GCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGAGTTTGCTGATATCTTTTC------------TTTATTGACCAAAGTCCCATAAAAAGTATAGGGGA Human > Gorilla --------------- chr5:70759312-70759319 Template switch process: F1: L GAGGGGCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGA 1 F3: 4 TGACCAAAGCCCCATAAAAGTATAGGGGAGCATCATAAAAGATCACCACA R RF: GAGGGGCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGAGTTTACTGATATCTTTCTTATTGACCAAAGTCCCATAAAAGTATAGGGGAGCATCATAAAAGATCACCACA RR: CTCCCCGGAATTGTATGGGGACATAAGCATCCATCTTTTCTCAAATGACTATAGAAAGAATAACTGGTTTCAGGGTATTTTCATATCCCCTCGTAGTATTTTCTAGTGGTGT F2: 3 AAGCATCC 2 Unidirectional alignment (log-probability: -38.9) AGGGGCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGA---------------------cctacgaaTGACCAAAGcCCCATAAAAGTATAGGGGAGCATCATAAAA AGGGGCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGAGTTTACTGATATCTTTCTTAT--------TGACCAAAGTCCCATAAAAGTATAGGGGAGCATCATAAAA Template switch alignment (log-probability: -22.5) AGGGGCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGA|CCTACGAA|TGACCAAAGcCCCATAAAAGTATAGGGGAGCATCATAAAA AGGGGCCTTAACATACCCCTGTATTCGTAGGTAGAAAAGA|CCTACGAA|TGACCAAAGTCCCATAAAAGTATAGGGGAGCATCATAAAA ========== Event 2990 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAACA----CGCGAAGCCATGAGGAGTTATG ↓ 3 2 1 4 Chimp: TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAACTTCATGGCGAAGCCATGAGGAGTTATG Gorilla: TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAACA----TGCGAAGCCATTAGGAGTTATG Human: TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAACA----CGCGAAGCCATGAGGAGTTATG Cluster: [ ] Orangutan: TGGTGCATTTTCAAAGGACCATAAAGCTAACCTGATTAACA----TGAGAGGCCATGAGGAGCTATG Human > Chimp ------------- chr5:153447460-153447465 Template switch process: F1: L ATGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAAC 1 F3: 4 GCGAAGCCATGAGGAGTTATGAGAAGTCAGTGGCTATCCT R RF: ATGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAACACGCGAAGCCATGAGGAGTTATGAGAAGTCAGTGGCTATCCT RR: TACCACGTAAAAACTTCCTGGTACTTCGATTGGACTAATTGTGCGCTTCGGTACTCCTCAATACTCTTCAGTCACCGATAGGA F2: 3 GTACTT 2 Unidirectional alignment (log-probability: -28.7) TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAACttcatgGCGAAGCCATGAGGAGTTATGAGAAGTCAGTGGCTATCCT TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAAC----ACGCGAAGCCATGAGGAGTTATGAGAAGTCAGTGGCTATCCT Template switch alignment (log-probability: -16) TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAAC|TTCATG|GCGAAGCCATGAGGAGTTATGAGAAGTCAGTGGCTATCCT TGGTGCATTTTTGAAGGACCATGAAGCTAACCTGATTAAC|TTCATG|GCGAAGCCATGAGGAGTTATGAGAAGTCAGTGGCTATCCT ========== Event 2991 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGAT-TTTAAAATAAGGTTCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT-----------------ACTGTACTTTGTGTAAATATTGCAA Chimp: AGATTTTTAAAATAAGGTTCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT-----------------ACTGTACTTTGTGTAAATATTGCAA ↑ 3 2 1 4 Gorilla: AGAT-TTTAAAATAAGGTTCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATTTTGTGTAAATATTACAAATATTACTTTGTGTAAATATTGCAA ↓ 3 2 1 4 Human: AGAT-TTTAAAATAAGGTTCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT-----------------ACTGTACTTTGTGTAAATATTGCAA Cluster: [ ] Orangutan: AGAT-TTTAAAATAAGGTTCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT-----------------ACTGTACTTTGTGTAAATATTTCAA Gorilla > Human --------------- chr5:87332125-87332128 Template switch process: F1: L TCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT 1 F3: 4 TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT R RF: TCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATTTTGTGTAAATATTACAAATATTACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT RR: AGTCATCATGGTACTATGGTGTACATCATACACTTTAATAAAACACATTTATAATGTTTATAATGAAACACATTTATAACGTTCTCTAGACACTCGAGGAAA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -27.5) CAGTAGTACCATGATACCACATGTAGTATGTGAAATTAT---------------------TactgTACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT CAGTAGTACCATGATACCACATGTAGTATGTGAAATTATTTTGTGTAAATATTACAAATAT----TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT Template switch alignment (log-probability: -16.2) CAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT|ACTG|TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT CAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT|ACTG|TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT Gorilla > Chimp --------------- chr5:153573493-153573496 Template switch process: F1: L TCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT 1 F3: 4 TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT R RF: TCAGTAGTACCATGATACCACATGTAGTATGTGAAATTATTTTGTGTAAATATTACAAATATTACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT RR: AGTCATCATGGTACTATGGTGTACATCATACACTTTAATAAAACACATTTATAATGTTTATAATGAAACACATTTATAACGTTCTCTAGACACTCGAGGAAA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -27.5) CAGTAGTACCATGATACCACATGTAGTATGTGAAATTAT---------------------TactgTACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT CAGTAGTACCATGATACCACATGTAGTATGTGAAATTATTTTGTGTAAATATTACAAATAT----TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT Template switch alignment (log-probability: -16.2) CAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT|ACTG|TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT CAGTAGTACCATGATACCACATGTAGTATGTGAAATTATT|ACTG|TACTTTGTGTAAATATTGCAAGAGATCTGTGAGCTCCTTT ========== Event 2992 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TATGCCAAAAGACATCCAGCTAGCATGCCGCACACATGCTAGCACATGGAGAACGTGCTTAAAAATCCACTATG ↑ 3 2 4 1 Chimp: TATGCCAAAAGACATCCAGCTAGCATGCCGCACA----------CGTGGAGAATGTGCTTAAAAATCCACTATG Gorilla: TATGCCAAAAGACATCCAGCTAGCATGCCGCACA----------CGTGGAGAACGTGCTTAAAAATCCACTATG Human: TATGCCAAAAGACATCCAGCTAGCATGCCGCACACATGCTAGCACATGGAGAACGTGCTTAAAAATCCACTATG Cluster: [ ] Orangutan: TATGCCAAAAGACATCGAGCTAGCATGCCGCACA----------CGTGGAGAACGTGCTTAAAAATCCACTATG Chimp > Human ------------- chr5:88603122-88603128 Template switch process: F1: L TAACAATTATGCCAAAAGACATCCAGCTAGCATGCCGCACAC 1 F3: 4 CACATGGAGAACGTGCTTAAAAATCCACTATGATGGGAAACATTTCATTCTA R RF: TAACAATTATGCCAAAAGACATCCAGCTAGCATGCCGCACACGTGGAGAATGTGCTTAAAAATCCACTATGATGGGAAACATTTCATTCTA RR: ATTGTTAATACGGTTTTCTGTAGGTCGATCGTACGGCGTGTGCACCTCTTACACGAATTTTTAGGTGATACTACCCTTTGTAAAGTAAGAT F2: 3 GATCGTA 2 Unidirectional alignment (log-probability: -37.4) ACAATTATGCCAAAAGACATCCAGCTAGCATGCCGCAcacatgctagCACaTGGAGAAcGTGCTTAAAAATCCACTATGATGGGAAA ACAATTATGCCAAAAGACATCCAGCTAGCATGCCGCA----------CACGTGGAGAATGTGCTTAAAAATCCACTATGATGGGAAA Template switch alignment (log-probability: -28.4) ACAATTATGCCAAAAGACATCCAGCTAGCATGCCGCACAC|ATGCTAG|CACaTGGAGAAcGTGCTTAAAAATCCACTATGATGGGAAA ACAATTATGCCAAAAGACATCCAGCTAGCATGCCGCACAC|ATGCTAG|CACGTGGAGAATGTGCTTAAAAATCCACTATGATGGGAAA ========== Event 2993 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTCTTCCTCAAAAGAGAAGTAAT--------------------GATAACTTCTCTTTATATTCCACAACTCAAAGAGAAGTTA Chimp: CATTCTTCTTCAAAAGAGAAGTAAT--------------------GATAACTTCTCTTTATATTCCACAACTCAAAGAGAAGTTA Gorilla: CATTCTTCCTCAAAAGAGAAGGAATGGAATATAAAGAGAAGTTATCATTACTTCTCTTTATATTCCATAACTCAAAGAGAAGTTA ↑ 3 1 4 2 Human: CATTCTTCCTCAAAAGAGAAGTAAT--------------------GATAACTTCTCTTTATATTCCACAACTCAAAGAGAAGTTA Cluster: [ ] Orangutan: CATTCTTCCTCAAAAGAGAAGGAAC--------------------G---------------------GAATATAAAGAGAAGTTA Human > Gorilla --------------- chr5:70857582-70857604 Template switch process: F1: L CCTTAATCATCTTTATATTCCATTCTTCCTCAAAAGAGAAGGAATG 1 F3: 4 ACTTCTCTTTATATTCCATAACTCAAAGAGAAGTTATCAT R RF: CCTTAATCATCTTTATATTCCATTCTTCCTCAAAAGAGAAGTAATGATAACTTCTCTTTATATTCCACAACTCAAAGAGAAGTTATCAT RR: GGAATTAGTAGAAATATAAGGTAAGAAGGAGTTTTCTCTTCATTACTATTGAAGAGAAATATAAGGTGTTGAGTTTCTCTTCAATAGTA F2: 3 TTACTATTGAAGAGAAATATAAG 2 Unidirectional alignment (log-probability: -56.3) TCATCTTTATATTCCATTCTTCCTCAAAAGAGAAGgAATGgaatataaagagaagttatcATtACTTCTCTTTATATTCCAtAACTCAAAGAGAAGTTATCAT TCATCTTTATATTCCATTCTTCCTCAAAAGAGAAGTAATG--------------------ATAACTTCTCTTTATATTCCACAACTCAAAGAGAAGTTATCAT Template switch alignment (log-probability: -29.8) TCATCTTTATATTCCATTCTTCCTCAAAAGAGAAGgAATG|GAATATAAAGAGAAGTTATCATT|ACTTCTCTTTATATTCCAtAACTCAAAGAGAAGTTATCAT TCATCTTTATATTCCATTCTTCCTCAAAAGAGAAGTAATG|GAATATAAAGAGAAGTTATCATT|ACTTCTCTTTATATTCCACAACTCAAAGAGAAGTTATCAT ========== Event 2994 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTTTGATTTCTGTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGAATATATATAAACTAAGGACTTTCT ↓ 3 2 1 4 Chimp: ACTTTGATTTCTATCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGCATGTATATAAACTAAGGACTTTCT Gorilla: ACTTTGATTTCTGTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGAATGTATATAAACTAAGGACTTTCT Human: ACTTTGATTTCTGTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGAATATATATAAACTAAGGACTTTCT Cluster: [ ] Orangutan: ACTTTGATTTCTGTCAGTTCATGATTTTTCTCTTGGATTTCAAGACGGTAGAATGTACATAAACTAAGGACTTTCT Human > Chimp ------------- chr5:172710546-172710549 Template switch process: F1: L CTATCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAG 1 F3: 4 TATATAAACTAAGGACTTTCTCCTCCAAAACAACAACAAC R RF: CTGTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGAATATATATAAACTAAGGACTTTCTCCTCCAAAACAACAACAAC RR: GACAGTGAAGTACTAAAAAGAGAACCTAAAGTTCTACCATCTTATATATATTTGATTCCTGAAAGAGGAGGTTTTGTTGTTGTTG F2: 3 GTAC 2 Unidirectional alignment (log-probability: -34.5) TaTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGcATgTATATAAACTAAGGACTTTCTCCTCCAAAACAACaacaac TGTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAGAATATATATAAACTAAGGACTTTCTCCTCCAAAACAAC------ Template switch alignment (log-probability: -21.8) TaTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAG|CATG|TATATAAACTAAGGACTTTCTCCTCCAAAACAACAACAAC TGTCACTTCATGATTTTTCTCTTGGATTTCAAGATGGTAG|CATG|TATATAAACTAAGGACTTTCTCCTCCAAAACAACAACAAC ========== Event 2995 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAACTGCCAGACTGTCTCTGACC---------------TTTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCA Chimp: TAACTGCCAGACTGTCTCTGACC---------------TTTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCA ↓ 1 4 3 2 Gorilla: TAACTGCCAGACTGTCTCTGATC------------------------------TGAACTTTTATTAAAGTTCTTCTCTTGAGAAATTGTCCA ↑ 1 4 3 2 Human: TAACTGCCAGACTGTCTCTGACC---------------TTTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCA Cluster: [ ] Orangutan: TAACTGCCAGACTGTCTCTGACCTTTGACTCTAATTTA---------------GGAAGAGTTATTAAAGT---TCTCTTGAGAAATTGTCCA Human > Gorilla --------------- chr5:73314398-73314403 Template switch process: F1: L GGAAAGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGATCT 1 F3: 4 TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG R RF: GGAAAGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGACCTTTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG RR: CCTTTCTTGACAAAAGAACCATTGACGGTCTGACAGAGACTGGAAACTGAGATTAAATCCTTCTCAATAATTTCAAGAAGAGAACTCTTTAACAGGTCTCAAAAC F2: 3 TTCAAG 2 Unidirectional alignment (log-probability: -32.9) AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGAtCTgaacTT-------------------TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGACCT----TTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG Template switch alignment (log-probability: -22.1) AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGAtCT|GAACTT|TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGACCT|GAACTT|TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG Chimp > Gorilla --------------- chr5:73314398-73314403 Template switch process: F1: L GGAAAGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGATCT 1 F3: 4 TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG R RF: GGAAAGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGACCTTTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG RR: CCTTTCTTGACAAAAGAACCATTGACGGTCTGACAGAGACTGGAAACTGAGATTAAATCCTTCTCAATAATTTCAAGAAGAGAACTCTTTAACAGGTCTCAAAAC F2: 3 TTCAAG 2 Unidirectional alignment (log-probability: -32.9) AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGAtCTgaacTT-------------------TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGACCT----TTGACTCTAATTTAGGAAGAGTTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG Template switch alignment (log-probability: -22.1) AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGAtCT|GAACTT|TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG AGAACTGTTTTCTTGGTAACTGCCAGACTGTCTCTGACCT|GAACTT|TTATTAAAGTTCTTCTCTTGAGAAATTGTCCAGAGTTTTG ========== Event 2996 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: gaccaggctggtgttgaactcctgacctcgtgatccacttgtctcggcctctcaaagtgctaggattacagatgtgagccaccgcccccggccTGCCAAGCATGTTTGCAGCAAGATGCAAGGGAGTAAGTGAACAAAGGGACCATTAAAATTGGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTCCTGCAGGAGGTTAGGTGATTGTG Chimp: gaccaggctggtgttgaactcctgaccttgtgatccacttgtctcggcctctcaaagtgctaggattacagatgtgagccaccgcccccggccTGCCAAGCATGTTTGCAGCAAGATGCAAGGGAGTAAGTGAACAAAGGGACCATTAAAATTGGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTCCTGCAGGAGGTTAGGTGATTGTG Gorilla: gaccaggctggtgttgaactcctgaccttgtgatccacttgtctcggcctctcgaagtgctaggattacagatgtgagccaccgcccccggccTGCCAAGCATGTTTGCAGCAAGATGCAAGGGAGTAAGTGAACAAAGGGACGGTTAAAATTGGGCACTCCTggatcacgaggtcaggagatcgagaccatcctggctaacacggtgaaaccccgtctctactaaaaatacaaaaaattagccgggcgtggtagtgggcgcctgtagtcccagctactcgggaggctgaggcaggagaatggcgtcaacccgggaggtggagcttgcagtgagccgagatcgcgccactgcactccagcctgggcgacaaagcaagactccgtctcaaaaaaaacaaaaacaaaaacaaaaacaaaaacaaaaaaaaaaaaTTGGGCACTCCTGCAGGAGGTTAGGTGATTGTG ↑ 3 4 2 1 Human: gaccaggctggtgttgaactcctgacctcgtgatccacttgtctcggcctctcaaagtgctaggattacagatgtgagccaccgcccccggccTGCCAAGCATGTTTGCAGCAAGATGCAAGGGAGTAAGTGAACAAAGGGACCATTAAAATTGGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTCCTGCAGGAGGTTAGGTGATTGTG Cluster: [] Orangutan: gaccaggctggtgttgaactcctgaccttgtgttccacttgtctcggcctctcaaagtgctgggattacagatgtgagccaccgcccccggccCGCCAAGCATGTTTGCAGCAAGATGCCAGGGAGTAAGTGAATGAAGGGACCGTTAAAATTGGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACTCCTACAGGAGGTTAGGTGATTGTG Human > Gorilla --------------- chr17:86495871-86495886 Template switch process: F1: L TGTTTGCAGCAAGATGCAAGGGAGTAAGTGAACAAAGGGACGGTTAAAATTGGGCACTCCTG 1 F3: 4 GATCG R RF: TCCTGACCTCGTGATCCACTTGTCTCGGCCTCTCAAAGTGCTAGGATTACAGATGTGAGCCACCGCCCCCGGCCTGCCAAGCATGTTTGCAGCAAGATGCAAGGGAGTAAGTGAACAAAGGGACCATTAAAATTGGGCACTCCTGCAGGAGGTTAGGTGATTG RR: AGGACTGGAGCACTAGGTGAACAGAGCCGGAGAGTTTCACGATCCTAATGTCTACACTCGGTGGCGGGGGCCGGACGGTTCGTACAAACGTCGTTCTACGTTCCCTCATTCACTTGTTTCCCTGGTAATTTTAACCCGTGAGGACGTCCTCCAATCCACTAAC F2: 3 AGGACTGGAGCACTAG 2 Unidirectional alignment (log-probability: -60.2) AGTAAGTGAACAAAGGGACggTTAAAATTGGGcactcctggatcacgaggtcaggagatcg AGTAAGTGAACAAAGGGACCATTAAAATTGGG----------------------------- Template switch alignment (log-probability: -34) AGTAAGTGAACAAAGGGACggTTAAAATTGGGCACTCCTG|GATCACGAGGTCAGGA|GATcG AGTAAGTGAACAAAGGGACCATTAAAATTGGGCACTCCTG|GATCACGAGGTCAGGA|GATTG ========== Event 2997 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: gaatataactatttgttcacagctgaattgagccctattc-------------------------------------------------------tgct-aggtggtatgaaca-atctgtcaattctggtctcctttggcct Chimp: gaatataactATTTGTTCGCAGCTGAATTGAGCCCTATTCTGCTAGGTGCTATTGACAGATTGTTCATAGCACCCAGCTGAATTGAGCCCTATTCTGCT-AGGTGCTATGAACA-ATCTGTCAATTCTGGTCTCCTTTGGCCT ↑ 4 3 1 2 Gorilla: gaatataactatttgttCGCAGCTGAATTGAGCCCTATTC-------------------------------------------------------TGCT-AGGTGGTATGAACA-ATCTGTCAATTCTGGTCTCCTTTGGCCT Human: gaatataactatttgttcacagctgaattgagccctattc-------------------------------------------------------tgct-aggtggtatgaaca-atctgtcaattctggtctcctttggcct Cluster: [ ] Orangutan: gaatataactatttgttcgcagctgaattgagccctattc-------------------------------------------------------tgctagggtggTATGAACAATTCTGTCAATTCTGGTCTCCTTTGGCCT Gorilla > Chimp --------------- chr5:157236250-157236270 Template switch process: F1: L GGAATATAACTATTTGTTCGCAGCTGAATTGAGCCCTATTCTGCTAGGTGCTAT 1 F3: 4 CAGCTGAATTGAGCCCTATTCTGCTAGGTGCTATGAACAATCTGTCAATTCTGGTCTCCTTTGGCCTTATT R RF: GGAATATAACTATTTGTTCGCAGCTGAATTGAGCCCTATTCTGCTAGGTGGTATGAACAATCTGTCAATTCTGGTCTCCTTTGGCCTTATT RR: CCTTATATTGATAAACAAGCGTCGACTTAACTCGGGATAAGACGATCCACCATACTTGTTAGACAGTTAAGACCAGAGGAAACCGGAATAA F2: 3 CCACGATACTTGTTAGACAGT 2 Unidirectional alignment (log-probability: -95.6) TGTTCGcagctgaattgagccctattctgctaggtgctattgacagattgttcatagcaccCAGCTGAATTGAGCCCTATTCTGCTAGGTGcTATGAACAA TGTTCG-------------------------------------------------------CAGCTGAATTGAGCCCTATTCTGCTAGGTGGTATGAACAA Template switch alignment (log-probability: -35.9) TGTTCGCAGCTGAATTGAGCCCTATTCTGCTAGGTGcTAT|TGACAGATTGTTCATAgCACC|CAGCTGAATTGAGCCCTATTCTGCTAGGTGcTATGAACAA TGTTCGCAGCTGAATTGAGCCCTATTCTGCTAGGTGGTAT|TGACAGATTGTTCATACCACC|CAGCTGAATTGAGCCCTATTCTGCTAGGTGGTATGAACAA ========== Event 2998 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGAAGAAATGAGCACGACCGG----GAG-------CGGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAGCAGTCCATCTAAATCTGTCTCAGGAGCtttctttctttcttt---- ↓ 1 4 3 2 Chimp: AAGAAGAAATGAGCACGACCGC--TCCTG-------AGGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAGCAGTCCATCTAAATCTGTCTCAGGAGctttctttcttttcttttct Gorilla: AAGAAGAAATGAGCACGACCGCTC--CTGACAGGAGCGGTCCATCTAAACCGGTCCATTTAGATGAACAGGTTTTAGGAGTCCATCTAAATCTGTCTCAGGAGCtttctttttttt------- Human: AAGAAGAAATGAGCACGACCGG----GAG-------CGGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAGCAGTCCATCTAAATCTGTCTCAGGAGCtttctttctttcttt---- Cluster: [ ] Orangutan: AAGAATAAATGAGCACGACCGCTC--CTG-------A---------------------------ATACAGGTTTTAGCAGTCCATCTAAATCTGTCTCAGGATCtttctttttt--------- Human > Chimp ------------- chr5:157580281-157580287 Template switch process: F1: L CTGCAGATTGAACTCTGGGGAAGAAGAAATGAGCACGACCG 1 F3: 4 GGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAG R RF: CTGCAGATTGAACTCTGGGGAAGAAGAAATGAGCACGACCGGGAGCGGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAGCAGTCCATCTAAATCTGTCTCAGGAG RR: GACGTCTAACTTGAGACCCCTTCTTCTTTACTCGTGCTGGCCCTCGCCAGGTAGATTTGGCCAGGTAAATCTACCTGTCCAAAATCGTCAGGTAGATTTAGACAGAGTCCTC F2: 3 AGTCCTC 2 Unidirectional alignment (log-probability: -30) TGCAGATTGAACTCTGGGGAAGAAGAAATGAGCACGACC----GCtcctgaGGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAG TGCAGATTGAACTCTGGGGAAGAAGAAATGAGCACGACCGGGAGC------GGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAG Template switch alignment (log-probability: -16.2) TGCAGATTGAACTCTGGGGAAGAAGAAATGAGCACGACCG|CTCCTGA|GGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAG TGCAGATTGAACTCTGGGGAAGAAGAAATGAGCACGACCG|CTCCTGA|GGTCCATCTAAACCGGTCCATTTAGATGGACAGGTTTTAG ========== Event 2999 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACG-----TCAATAGGGCCATCttttttttCTT ↓ 3 2 1 4 Chimp: ATCTAGTGTGGAGGCAAAGTTGTATTCCTGAATAGGAATACAATAGGGCCATCttttttttCTT ↑ 3 2 1 4 Gorilla: ATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACG-----TCAGTAGGGCCATCttttttttCTT Human: ATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACG-----TCAATAGGGCCATCttttttttCTT Cluster: [ ] Orangutan: ATCTAGTGTGGAGGCAAAGTTCTATTCTTGTACA-----GGAATAGGGCCAttttttttttCTT Human > Chimp ------------- chr5:158206672-158206679 Template switch process: F1: L AAACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAAT 1 F3: 4 AATAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATG R RF: AAACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACGTCAATAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATG RR: TTTGTTAACTAGATCACACCTCCGTTTCAACATAAGGACTTGCAGTTATCCCGGTAGAAAAAAAAGAACGTAGTCATACCCTAC F2: 3 CATAAGGA 2 Unidirectional alignment (log-probability: -31.3) ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAA--TaggaataCAATAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATG ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACGT-------CAATAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATG Template switch alignment (log-probability: -22.3) ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAAt|AGGAATAC|AATAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATG ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAAC|AGGAATAC|AATAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATG Gorilla > Chimp --------------- chr5:158206672-158206681 Template switch process: F1: L AAACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAAT 1 F3: 4 TAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATGAAG R RF: AAACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACGTCAGTAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATGAAG RR: TTTGTTAACTAGATCACACCTCCGTTTCAACATAAGGACTTGCAGTCATCCCGGTAGAAAAAAAAGAACGTAGTCATACCCTACTTC F2: 3 AACATAAGGA 2 Unidirectional alignment (log-probability: -36.4) ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAA--TaggaataCAaTAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATGAAG ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAACGT-------CAGTAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATGAAG Template switch alignment (log-probability: -22.5) ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAAt|AGGAATACAA|TAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATGAAG ACAATTGATCTAGTGTGGAGGCAAAGTTGTATTCCTGAAC|AGGAATACAA|TAGGGCCATCTTTTTTTTCTTGCATCAGTATGGGATGAAG ========== Event 3000 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAAAATCTGAAACATATACCTGTATTA--------------TAACA----CGTCTCACTGTGTCCAATGA Chimp: ATAAAATCTGAAACATATACCTGTATTA--------------TAACA--CATGTCTCACTGTGTCCAATGA ↓ 3 42 1 Gorilla: ATAAAATCTGAAACATATACCTGTATTATAATACAGGTATTATAACACA--TGTCTCACTGTGTCCAGTGA Human: ATAAAATCTGAAACATATACCTGTATTA--------------TAACA----CGTCTCACTGTGTCCAATGA Cluster: [ ] Orangutan: ATAAAATCTGAAACATATACCTGTATTA--------------TAACACA--TGTCTCACTGTGTCCAGTGA Chimp > Gorilla --------------- chr5:74613816-74613821 Template switch process: F1: L CAGCTTGCCACCCATAAAATCTGAAACATATACCTGTATTATAA 1 F3: 4 TATTATAACACATGTCTCACTGTGTCCAGTGATGTTTTTAATAATTTGTAGC R RF: CAGCTTGCCACCCATAAAATCTGAAACATATACCTGTATTATAACACATGTCTCACTGTGTCCAATGATGTTTTTAATAATTTGTAGC RR: GTCGAACGGTGGGTATTTTAGACTTTGTATATGGACATAATATTGTGTACAGAGTGACACAGGTTACTACAAAAATTATTAAACATCG F2: 3 GGACAT 2 Unidirectional alignment (log-probability: -36.6) TTGCCACCCATAAAATCTGAAACATATACCTGTATtataatacaggtatTATAACACATGTCTCACTGTGTCCAgTGATGTTTTTA TTGCCACCCATAAAATCTGAAACATATACCTGTAT--------------TATAACACATGTCTCACTGTGTCCAATGATGTTTTTA Template switch alignment (log-probability: -22.4) TTGCCACCCATAAAATCTGAAACATATACCTGTATTATAA|TACAGG|TATTATAACACATGTCTCACTGTGTCCAgTGATGTTTTTA TTGCCACCCATAAAATCTGAAACATATACCTGTATTATAA|TACAGG|TATTATAACACATGTCTCACTGTGTCCAATGATGTTTTTA ========== Event 3001 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: tgcacgacatacttggGAATATGACATACTTactgtcagaattctcaatcaaaccaca ↑ 1 4 3 2 Chimp: tgcacgacatacttggGAATA---GCTACTTactgtcagaattcttaatcaaaccaca Gorilla: tgcacgacatacttggGAATA---GCTACTTactgtcagaattctcaatcaaaccaca ↓ 1 4 3 2 Human: tgcacgacatacttggGAATATGACATACTTactgtcagaattctcaatcaaaccaca Cluster: [ ] Orangutan: tgcatgacatacttggGAATA---GCTACTTactgtcacaattctcaatcaaaccaca Chimp > Human ------------- chr5:89134142-89134146 Template switch process: F1: L ATATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATA 1 F3: 4 TACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC R RF: ATATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATAGCTACTTACTGTCAGAATTCTTAATCAAACCACAATCATCCC RR: TATATCGGTCAAAGGAAGACACGTGCTGTATGAACCCTTATCGATGAATGACAGTCTTAAGAATTAGTTTGGTGTTAGTAGGG F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -33.2) TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATatgAcaTACTTACTGTCAGAATTCTcAATCAAACCACAATCATCCC TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAAT---AGCTACTTACTGTCAGAATTCTTAATCAAACCACAATCATCCC Template switch alignment (log-probability: -21.9) TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATA|TGACA|TACTTACTGTCAGAATTCTcAATCAAACCACAATCATCCC TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATA|TGACA|TACTTACTGTCAGAATTCTTAATCAAACCACAATCATCCC Gorilla > Human --------------- chr5:89134142-89134146 Template switch process: F1: L ATATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATA 1 F3: 4 TACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC R RF: ATATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATAGCTACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC RR: TATATCGGTCAAAGGAAGACACGTGCTGTATGAACCCTTATCGATGAATGACAGTCTTAAGAGTTAGTTTGGTGTTAGTAGGG F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -26.3) TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATatgAcaTACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAAT---AGCTACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC Template switch alignment (log-probability: -16.4) TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATA|TGACA|TACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC TATAGCCAGTTTCCTTCTGTGCACGACATACTTGGGAATA|TGACA|TACTTACTGTCAGAATTCTCAATCAAACCACAATCATCCC ========== Event 3002 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ggactatgtgtacctctccagactcagtgaccatgattacctttcctataacctgcagctcagccaaagtggactacttgcattgcctaagcatgctctgttcctttctCATCACATTCTGTATGAGAAATTTGTTTCTTCCCCAAATCT------------------------------------GTCCCTCATGGTCTAGCATAGCTGTCTT ↓ 3 2 4 1 Chimp: ggactatgtgtacctctccagactcagtgaccatgattacctttcctataacctgcagctcagccaaagtggactacttgcattgcctaagcatgctctgttcctttctCATCACATTCTGTATGAGAAATTTGTTTCTTCCCCAAATCT------------------GCCCCTCAGAGTCTATCTGTCCTTCATGGTCTAGCATAGCTGTCTT Gorilla: ggactatgtgtacctctccagactcagtgaccatgattacctttcctataacctgcagctcagccaaagtggactacttgcattgcctaagcatgctctgttcctttctcatcacattctgtatgagaaatttgtttcttccccaaatctgcccctcaaagtctatct------------------gtctctcatggtctagcatagctgtctt Human: ggactatgtgtacctctccagactcagtgaccatgattacctttcctataacctgcagctcagccaaagtggactacttgcattgcctaagcatgctctgttcctttctCATCACATTCTGTATGAGAAATTTGTTTCTTCCCCAAATCT------------------------------------GTCCCTCATGGTCTAGCATAGCTGTCTT Cluster: [ ] Orangutan: ggactatgtgtacctctccagactcagtgaccatgattacctttcctataacctgcagctcagccaaagtggactacttgcattgcctaagcatgctctgttcctttctcatcacattctgtatgagaaatttgtttcttccccaaatctgccgctcagagtctatct------------------gtccttcatggtctagcatagctgtctt Human > Chimp ------------- chr5:155396362-155396367 Template switch process: F1: L CATCACATTCTGTATGAGAAATTTGTTTCTTCCCCAAATCTGCCCCTCA 1 F3: 4 ATCTGTCCTTCATGGTCTAGCATAGCTGTCTTCTTTTCAATAAAGTTCT R RF: AGACTCAGTGACCATGATTACCTTTCCTATAACCTGCAGCTCAGCCAAAGTGGACTACTTGCATTGCCTAAGCATGCTCTGTTCCTTTCTCATCACATTCTGTATGAGAAATTTGTTTCTTCCCCAAATCTGTCCCTCATGGTCTAGCATAGCTGTCTTCTTTTCAATAAAGTTCT RR: TCTGAGTCACTGGTACTAATGGAAAGGATATTGGACGTCGAGTCGGTTTCACCTGATGAACGTAACGGATTCGTACGAGACAAGGAAAGAGTAGTGTAAGACATACTCTTTAAACAAAGAAGGGGTTTAGACAGGGAGTACCAGATCGTATCGACAGAAGAAAAGTTATTTCAAGA F2: 3 TCTGAG 2 Unidirectional alignment (log-probability: -42.8) CTGTATGAGAAATTTGTTTCTTCCCCAAATCTGcCCCTCagagtctatctgtccttcATGGTCTAGCATAGCTGTCTTCTTTTCAA CTGTATGAGAAATTTGTTTCTTCCCCAAATCTGTCCCTC------------------ATGGTCTAGCATAGCTGTCTTCTTTTCAA Template switch alignment (log-probability: -28.3) CTGTATGAGAAATTTGTTTCTTCCCCAAATCTGcCCCTCA|GAGTCT|ATCTGTCCtTCATGGTCTAGCATAGCTGTCTTCTTTTCAA CTGTATGAGAAATTTGTTTCTTCCCCAAATCTGTCCCTCA|GAGTCT|ATCTGTCCCTCATGGTCTAGCATAGCTGTCTTCTTTTCAA ========== Event 3003 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAGGAGTATTTTCCCACTGGTAGC--------AAATGCTACCTGGGGACAATAGTCAATAGATT Chimp: TAAGGAGTATTTTCCCACTGGTAGC--------AAATGCTGCCTGGGGACAATAGTCAATAGATT Gorilla: TAAGGAGTATTTTCCCACTGGTAGC----------------ATTAGGGACAATAGTCAATAGATT ↓ 3 1 4 Human: TAAGGAGTATTTTCCCACTGGTAGC--------AAATGCTACCTGGGGACAATAGTCAATAGATT Cluster: [ ] Orangutan: TAAGGAGTATTTTCCCACTGGTAGCAAATGCTA--------CCTGGGGACAACAGTCAATAGATT Gorilla > Human --------------- chr5:87032248-87032256 Template switch process: F1: L AATAGTAGTTAAAATATAAGGAGTATTTTCCCACTGGTAGCA 1 F3: 4 TGGGGACAATAGTCAATAGATTGATTGCTGATAGCTAAACGT R RF: AATAGTAGTTAAAATATAAGGAGTATTTTCCCACTGGTAGCATTAGGGACAATAGTCAATAGATTGATTGCTGATAGCTAAACGT RR: TTATCATCAATTTTATATTCCTCATAAAAGGGTGACCATCGTAATCCCTGTTATCAGTTATCTAACTAACGACTATCGATTTGCA F2: 3 CCATCGTAA 2 Unidirectional alignment (log-probability: -33.5) TAGTAGTTAAAATATAAGGAGTATTTTCCCACTGGTAGCAaatgctaccTgGGGACAATAGTCAATAGATTGATTGCTGATAGCTAAAC TAGTAGTTAAAATATAAGGAGTATTTTCCCACTGGTAGCAT--------TAGGGACAATAGTCAATAGATTGATTGCTGATAGCTAAAC Template switch alignment (log-probability: -22.5) TAGTAGTTAAAATATAAGGAGTATTTTCCCACTGGTAGCA|AATGCTACC|TgGGGACAATAGTCAATAGATTGATTGCTGATAGCTAAAC TAGTAGTTAAAATATAAGGAGTATTTTCCCACTGGTAGCA|AATGCTACC|TAGGGACAATAGTCAATAGATTGATTGCTGATAGCTAAAC ========== Event 3004 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ACTAGCTGAGGGATATGACCAGATCTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAGAACTTCCTATGCTAAGGTACAGGAATATGGCACAGGGGCCAGTGAGTCTTGGAGGAGCCATCTCTCCCGCAAAATGATCTTTTGGATGCTaaa------ ↑ 1 4 3 2 Chimp: ACTAGCTGAGGGATATGACCAA--GTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAGAACTTCCTATGCTAAGGTACAGGAATATGGCACAGGAGCCAGTGAGTCTTGGAGGAGCCATCTCTCCCGCAAAATGATCTTTTGGATGCTaaaa---aa Gorilla: ACTAGCTGAGGGATATGACCAGATCTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAGAACTTCCTATGCTAAGGTACAGGAATATGGCACAGGAGCCAGTGAGTCTTGGAGGAGCCATCTCTCCTGCAAAATGATCTTTTGGATGCTaaaa----- Human: ACTAGCTGAGGGATATGACCAGATCTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAGAACTTCCTATGCTAAGGTACAGGAATATGGCACAGGGGCCAGTGAGTCTTGGAGGAGCCATCTCTCCCGCAAAATGATCTTTTGGATGCTaaa------ Cluster: [ ] Orangutan: ACTAGCTGAGGGATATGACCAGATCTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAGAACTTCCTATGCTAAGGTACAGGAATATGGCACAGGAGCCAGTGAGTCTTGGAGGAGCCATCTCTCCCGCAAAATGATCTTTTGGATGCTAAAAAAG-- Chimp > Human ------------- chr5:86824902-86824905 Template switch process: F1: L ATGCTTGGCTGGAAAACATGACTAGCTGAGGGATATGACCA 1 F3: 4 TTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAG R RF: ATGCTTGGCTGGAAAACATGACTAGCTGAGGGATATGACCAAGTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAGAACTTCCTATGCTAAGGTACAGGAATATGGCACAGGAGCCAGTGAGTCTTGGAGGAGCCATCTCTCCCGCAAAATGATC RR: TACGAACCGACCTTTTGTACTGATCGACTCCCTATACTGGTTCAACCGTCACCAAGTCGGAACCCCTTTGGACCCAAAACATCTTGAAGGATACGATTCCATGTCCTTATACCGTGTCCTCGGTCACTCAGAACCTCCTCGGTAGAGAGGGCGTTTTACTAG F2: 3 CTAG 2 Unidirectional alignment (log-probability: -25.5) TGCTTGGCTGGAAAACATGACTAGCTGAGGGATATGACC-AGatcTTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAG TGCTTGGCTGGAAAACATGACTAGCTGAGGGATATGACCAAG---TTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAG Template switch alignment (log-probability: -15.8) TGCTTGGCTGGAAAACATGACTAGCTGAGGGATATGACCA|GATC|TTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAG TGCTTGGCTGGAAAACATGACTAGCTGAGGGATATGACCA|GATC|TTGGCAGTGGTTCAGCCTTGGGGAAACCTGGGTTTTGTAG ========== Event 3005 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACGAGCAGAGGGCTCGGTGGTTC----TGACCAGCAGGGTATGGACAGCAACAGGACCTGTGGCCAGGTGTCAGAATGCACCTCAGAAATGATTCAAGCCCCACTGTT ↑ 1 4 3 2 Chimp: AACGAGCAGAGGGCTCGGTGGCTC--CAGAACCAGCAGAGTATGGACAGCAACAGGACCTGTGGCCAGGTGTCAGAATGCACCTCAGAAATGATTCAAGCCCCACTGTT Gorilla: GACGAGCAGAGGGCTCGGTGGCTCCA--GAACCAGCAGAGTATGGACAGCAACAGGACCTGTGGCCAGGTGTCAGAATGCACCTCAGAAATGATTCAAGCCCCACTGTT Human: AACGAGCAGAGGGCTCGGTGGTTC----TGACCAGCAGGGTATGGACAGCAACAGGACCTGTGGCCAGGTGTCAGAATGCACCTCAGAAATGATTCAAGCCCCACTGTT Cluster: [ ] Orangutan: AACGAGCAGAGGGCTCAGTGGCTCCA--GAACCAGCAGAGTATGGACAGTAACAGGACCTGTGGGCAGGTGTCAGAACGCACCTCAGAAATGATTCAAGCCCCGCTGTT Chimp > Human ------------- chr5:171589655-171589660 Template switch process: F1: L GAGGGGAGGCAAGGGGATGTAACGAGCAGAGGGCTCGGTGG 1 F3: 4 CCAGCAGGGTATGGACAGCAACAGGACCTGTGGCCAGGTGTCAGAATG R RF: GAGGGGAGGCAAGGGGATGTAACGAGCAGAGGGCTCGGTGGCTCCAGAACCAGCAGAGTATGGACAGCAACAGGACCTGTGGCCAGGTGTCAGAATGCACCTCAGAA RR: CTCCCCTCCGTTCCCCTACATTGCTCGTCTCCCGAGCCACCGAGGTCTTGGTCGTCTCATACCTGTCGTTGTCCTGGACACCGGTCCACAGTCTTACGTGGAGTCTT F2: 3 AGTCTT 2 Unidirectional alignment (log-probability: -34.8) AGGGGAGGCAAGGGGATGTAACGAGCAGAGGGCTCGGTGgttctG-------ACCAGCAGgGTATGGACAGCAACAGGACCTGTGGCCAGGTG AGGGGAGGCAAGGGGATGTAACGAGCAGAGGGCTCGGTG-----GCTCCAGAACCAGCAGAGTATGGACAGCAACAGGACCTGTGGCCAGGTG Template switch alignment (log-probability: -22.2) AGGGGAGGCAAGGGGATGTAACGAGCAGAGGGCTCGGTGG|TTCTGA|CCAGCAGgGTATGGACAGCAACAGGACCTGTGGCCAGGTG AGGGGAGGCAAGGGGATGTAACGAGCAGAGGGCTCGGTGG|TTCTGA|CCAGCAGAGTATGGACAGCAACAGGACCTGTGGCCAGGTG ========== Event 3006 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCTGCTGTTAGCAAGCACTAAAATCCTGACTTTAACAGCATAGTAGTAAAAATGCCTCAGTGA ↓ 1 4 3 2 Chimp: ATCTGCTGTTAGCAAGCACTAC------TATGTTAACAGCATAGTAGTAAAAATGCCTCAGTGA ↑ 1 4 3 2 Gorilla: ATCTGCTGTTAGCAAGCACTAAAATCCTGATTTTAACAGCATAGTAGTAAAAATGCCTCAGTGA Human: ATCTGCTGTTAGCAAGCACTAAAATCCTGACTTTAACAGCATAGTAGTAAAAATGCCTCAGTGA Cluster: [ ] Orangutan: ATCTGCTGTTAGCAAGCACTAAAATCCTGATTTTAACAGCATAGTAGTAAAAATGCCTCAGTGA Human > Chimp ------------- chr5:19699773-19699777 Template switch process: F1: L AAGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA 1 F3: 4 TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTCAGCT R RF: AAGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTAAAATCCTGACTTTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTAAGCT RR: TTCGACGAAGAATTGAAGAGTAGACGACAATCGTTCGTGATTTTAGGACTGAAATTGTCGTATCATCATTTTTACGGAGTCACTAAATTCGA F2: 3 GTATC 2 Unidirectional alignment (log-probability: -31.9) AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACT---------ACTatgTTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTcAGCT AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTAAAATCCTGACT---TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTAAGCT Template switch alignment (log-probability: -21.9) AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA|CTATG|TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTcAGCT AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA|CTATG|TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTAAGCT Gorilla > Chimp --------------- chr5:19699773-19699777 Template switch process: F1: L AAGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA 1 F3: 4 TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTCAGCT R RF: AAGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTAAAATCCTGATTTTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTAAGCT RR: TTCGACGAAGAATTGAAGAGTAGACGACAATCGTTCGTGATTTTAGGACTAAAATTGTCGTATCATCATTTTTACGGAGTCACTAAATTCGA F2: 3 GTATC 2 Unidirectional alignment (log-probability: -32) AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA-----CT-ATgTTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTcAGCT AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTAAAATCCTGATTTTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTAAGCT Template switch alignment (log-probability: -21.9) AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA|CTATG|TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTcAGCT AGCTGCTTCTTAACTTCTCATCTGCTGTTAGCAAGCACTA|CTATG|TTAACAGCATAGTAGTAAAAATGCCTCAGTGATTTAAGCT ========== Event 3007 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACAGTCAAAGAAGAACCCAGGTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTtagggctgccagat Chimp: CACAGTCAAAGAAGAACCCAGGTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTtagggctgccagat ↓ 1 4 3 2 Gorilla: CACAGTCAAAGAAGAACCCAGAC-C-A-TACTGTGTATGGTCATAAATACACAGTATTGTCTAACTtagggctgccagat ↑ 1 4 3 2 Human: CACAGTCAAAGAAGAACCCAGGTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTtagggctgccagat Cluster: [ ] Orangutan: CACAGTCAAAGAAGAAGCCAGGTCCAGTAAGTTAGCATGGTCATAAATACACAGTATTGTCTAACTtagggctgccagat Human > Gorilla --------------- chr5:86146450-86146461 Template switch process: F1: L TGTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG 1 F3: 4 ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC R RF: TGTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAGGTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC RR: ACATTGTCTCATGAAATAAAGTGTCAGTTTCTTCTTGGGTCCAGGTCATTCAATAGTACCAGTATTTATGTGTCATAACAGATTGAATCCCGACGG F2: 3 TGTGTCATACCA 2 Unidirectional alignment (log-probability: -35.7) GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAGaccatactgtGT-------------ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG----------GTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC Template switch alignment (log-probability: -22.8) GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG|ACcATACTGTGT|ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG|ACAATACTGTGT|ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC Chimp > Gorilla --------------- chr5:86146450-86146461 Template switch process: F1: L TGTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG 1 F3: 4 ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC R RF: TGTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAGGTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC RR: ACATTGTCTCATGAAATAAAGTGTCAGTTTCTTCTTGGGTCCAGGTCATTCAATAGTACCAGTATTTATGTGTCATAACAGATTGAATCCCGACGG F2: 3 TGTGTCATACCA 2 Unidirectional alignment (log-probability: -35.7) GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAGaccatactgtGT-------------ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG----------GTCCAGTAAGTTATCATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC Template switch alignment (log-probability: -22.8) GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG|ACcATACTGTGT|ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC GTAACAGAGTACTTTATTTCACAGTCAAAGAAGAACCCAG|ACAATACTGTGT|ATGGTCATAAATACACAGTATTGTCTAACTTAGGGCTGCC ========== Event 3008 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAAGGACATATCTACAGGTG----TTA--ACATGACAAATATGAGACATGGG ↓ 3 1 4 2 Chimp: GGAAGGACATATCTACAGGTGTTTGTTAACACATGACAAATATGAGACATGGG Gorilla: GGAAGGACATATCTACAGGTG----TTA--ACATGACAAATATGAGACATGGG Human: GGAAGGACATATCTACAGGTG----TTA--ACATGACAAATATGAGACATGGG Cluster: [ ] Orangutan: GGAAGGACATATCTACAGGTG----TTA--ACATGACAAATATGAgacatggg Human > Chimp ------------- chr5:85091221-85091227 Template switch process: F1: L TACATGAGCATGAGAAAAATGGAAGGACATATCTACAGGTGTT 1 F3: 4 ACATGACAAATATGAGACATGGGGTGCTGATGTTATAAAA R RF: TACATGAGCATGAGGAAAATGGAAGGACATATCTACAGGTGTTAACATGACAAATATGAGACATGGGGTGCTGATGTTATAAAA RR: ATGTACTCGTACTCCTTTTACCTTCCTGTATAGATGTCCACAATTGTACTGTTTATACTCTGTACCCCACGACTACAATATTTT F2: 3 CAATTGT 2 Unidirectional alignment (log-probability: -31.6) ATGAGCATGAGaAAAATGGAAGGACATATCTACAGGTGTTtgttaacACATGACAAATATGAGACATGGGGTGCTGATGTTATAAAA ATGAGCATGAGGAAAATGGAAGGACATATCTACAGGTGTT------AACATGACAAATATGAGACATGGGGTGCTGATGTTATAAAA Template switch alignment (log-probability: -22.2) ATGAGCATGAGaAAAATGGAAGGACATATCTACAGGTGTT|TGTTAAC|ACATGACAAATATGAGACATGGGGTGCTGATGTTATAAAA ATGAGCATGAGGAAAATGGAAGGACATATCTACAGGTGTT|TGTTAAC|ACATGACAAATATGAGACATGGGGTGCTGATGTTATAAAA ========== Event 3009 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CATAGCTGCCCTGGTAAGATACTGCCAGTAAGCACTGGCAATTAAATTGGG ↑ 3 21 4 Chimp: CATAGCTGCCCTGGTAAGATACTG--CATGAGCACTGGCAATTAAATTGGG Gorilla: CATAGCTGTCCTGGTAAGATACTG--CATGAGCACTGGCAATTAAATTGGG Human: CATAGCTGCCCTGGTAAGATACTGCCAGTAAGCACTGGCAATTAAATTGGG Cluster: [ ] Orangutan: CATAGCTGCCCTGGTAAGATACTG--CATGAGCACTGGCAATTAAATTGGG Chimp > Human ------------- chr5:83432868-83432872 Template switch process: F1: L TTGACAGTGGGCAGAACCATAGCTGCCCTGGTAAGATACTGC 1 F3: 4 AGCACTGGCAATTAAATTGGGCAGTGCAATATGTCCCCCA R RF: TTGACAGTGGGCAGAACCATAGCTGCCCTGGTAAGATACTGCATGAGCACTGGCAATTAAATTGGGCAGTGCAATATGTCCCCCA RR: AACTGTCACCCGTCTTGGTATCGACGGGACCATTCTATGACGTACTCGTGACCGTTAATTTAACCCGTCACGTTATACAGGGGGT F2: 3 ATGAC 2 Unidirectional alignment (log-probability: -25.8) GACAGTGGGCAGAACCATAGCTGCCCTGGTAAGATACTGCcagTaAGCACTGGCAATTAAATTGGGCAGTGCAATATGTCCCCCA GACAGTGGGCAGAACCATAGCTGCCCTGGTAAGATACTGC--ATGAGCACTGGCAATTAAATTGGGCAGTGCAATATGTCCCCCA Template switch alignment (log-probability: -15.9) GACAGTGGGCAGAACCATAGCTGCCCTGGTAAGATACTGC|CAGTA|AGCACTGGCAATTAAATTGGGCAGTGCAATATGTCCCCCA GACAGTGGGCAGAACCATAGCTGCCCTGGTAAGATACTGC|CAGTA|AGCACTGGCAATTAAATTGGGCAGTGCAATATGTCCCCCA ========== Event 3010 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TTAATTATTAATTTCAAAAAAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCACACAAC------------------------ATTTTATTTATTCTTTTCTTCAG ↓ 3 2 4 1 Chimp: TTAATTATTAATTTCAAAAAAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCGCACAAC------------ATTAGTGACTTCATTTTATTTATTCTTTTCTTCAG Gorilla: TTAATTATTAATGTCAAAAAAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCACACAACATTAGTGACTTC------------ATTTTATTTATTCTTTTCTTCAG ↑ 3 2 4 1 Human: TTAATTATTAATTTCAAAAAAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCACACAAC------------------------ATTTTATTTATTCTTTTCTTCAG Cluster: [ ] Orangutan: TTAATTATTAATTTCAAAAAAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGACTGTACAGTCACATAACATTAGTGACTTC------------ATTTTATTTATTCTTTTCTTCAG Human > Chimp ------------- chr5:97944887-97944894 Template switch process: F1: L ACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCGCACAACATT 1 F3: 4 CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAATG R RF: AAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCACACAACATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAATG RR: TTCAGTGAAGTTTGTGAAGTTTTCAGTTGTATCTTCCCCCTTTTGGGGGTTATTGACTAACATGTCAGTGTGTTGTAAAATAAATAAGAAAAGAAGTCAGAACCTTTGGTTTTAC F2: 3 TTCAGTGA 2 Unidirectional alignment (log-probability: -34.2) GGAAAACCCCCAATAACTGATTGTACAGTCgCACAACATtagtgacttcatTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT GGAAAACCCCCAATAACTGATTGTACAGTCACACAACAT------------TTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT Template switch alignment (log-probability: -22.5) GGAAAACCCCCAATAACTGATTGTACAGTCgCACAACATT|AGTGACTT|CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT GGAAAACCCCCAATAACTGATTGTACAGTCACACAACATT|AGTGACTT|CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT Human > Gorilla --------------- chr5:81491292-81491299 Template switch process: F1: L AGGGGGAAAACCCCCAATAACTGATTGTACAGTCACACAACATT 1 F3: 4 CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAATG R RF: AAGTCACTTCAAACACTTCAAAAGTCAACATAGAAGGGGGAAAACCCCCAATAACTGATTGTACAGTCACACAACATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAATG RR: TTCAGTGAAGTTTGTGAAGTTTTCAGTTGTATCTTCCCCCTTTTGGGGGTTATTGACTAACATGTCAGTGTGTTGTAAAATAAATAAGAAAAGAAGTCAGAACCTTTGGTTTTAC F2: 3 TTCAGTGA 2 Unidirectional alignment (log-probability: -28.1) GGAAAACCCCCAATAACTGATTGTACAGTCACACAAcattagtgacttCATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT GGAAAACCCCCAATAACTGATTGTACAGTCACACAA------------CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT Template switch alignment (log-probability: -16.8) GGAAAACCCCCAATAACTGATTGTACAGTCACACAACATT|AGTGACTT|CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT GGAAAACCCCCAATAACTGATTGTACAGTCACACAACATT|AGTGACTT|CATTTTATTTATTCTTTTCTTCAGTCTTGGAAACCAAAAT ========== Event 3011 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 456 Detected in comparisons: 3456 Multiple sequence alignment: Human: attacaaagttattacaaagttattacGATTTCCACATAAAGCAAACAAGATCATTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTACATAAA Chimp: attacaaagttattacaaaggtattaTGATTGCCACATAAAGCAAACAAGATCGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTACATAAA ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: attacaaagttattacaaagttattaTGATTTCCACATAAAGCAAACGATCTTGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTACATAAA ↑ 31 2 4 Human: attacaaagttattacaaagttattacGATTTCCACATAAAGCAAACAAGATCATTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTACATAAA Cluster: [ ] Orangutan: attacaaagttattacaaaggtattaTGATTTCCACATAAAGCAAA-----------CCATTATGTGGAAATCATAATACCTTTGTAATAACTACATAAA Human > Gorilla --------------- chr5:83154108-83154115 Template switch process: F1: L AAGTTATTACAAAGTTATTATGATTTCCACATAAAGCAAAC 1 F3: 4 TTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTA R RF: AAGTTATTACAAAGTTATTACGATTTCCACATAAAGCAAACAAGATCATTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTA RR: TTCAATAATGTTTCAATAATGCTAAAGGTGTATTTCGTTTGTTCTAGTAAACGAAATACACCTTTAGTATTATGGAAACATTATTGAT F2: 3 TGTTCTAG 2 Unidirectional alignment (log-probability: -34.4) AGTTATTACAAAGTTATTAtGATTTCCACATAAAGCAAACgAtcTtgTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTA AGTTATTACAAAGTTATTACGATTTCCACATAAAGCAAACAAGATCATTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTA Template switch alignment (log-probability: -22.2) AGTTATTACAAAGTTATTAtGATTTCCACATAAAGCAAAC|GATCTTGT|TTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTA AGTTATTACAAAGTTATTACGATTTCCACATAAAGCAAAC|GATCTTGT|TTGCTTTATGTGGAAATCATAATACCTTTGTAATAACTA Gorilla > Chimp --------------- chr5:83282276-83282308 Template switch process: F1: L AAGTTATTACAAAG 1 F3: 4 GTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT R RF: AAGTTATTACAAAGTTATTATGATTTCCACATAAAGCAAACGATCTTGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT RR: TTCAATAATGTTTCAATAATACTAAAGGTGTATTTCGTTTGCTAGAACAAACGAAATACACCTTTAGTATTATGGAAACATTATTGA F2: 3 CTAGAACAAACGAAATACACCGTTAGTATTATG 2 Unidirectional alignment (log-probability: -34.3) AAGTTATTACAAAGgTATTATGATTgCCACATAAAGCAAACaAgaTcGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT AAGTTATTACAAAGTTATTATGATTTCCACATAAAGCAAACGATCTTGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT Template switch alignment (log-probability: -24.8) AAGTTATTACAAAG|GTATTATGATTgCCACATAAAGCAAACAAGATC|GTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT AAGTTATTACAAAG|GTATTATGATTTCCACATAAAGCAAACAAGATC|GTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT Chimp > Gorilla --------------- chr5:83154092-83154113 Template switch process: F1: L AAGTTATTACAAAGTTATTATGATT 1 F3: 4 GTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT R RF: AAGTTATTACAAAGGTATTATGATTGCCACATAAAGCAAACAAGATCGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT RR: TTCAATAATGTTTCCATAATACTAACGGTGTATTTCGTTTGTTCTAGCAAACGAAATACACCTTTAGTATTATGGAAACATTATTGA F2: 3 TTCTAGCAAACGAAATACACCT 2 Unidirectional alignment (log-probability: -34.3) AAGTTATTACAAAGtTATTATGATTtCCACATAAAGCAAACgAtcTtGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT AAGTTATTACAAAGGTATTATGATTGCCACATAAAGCAAACAAGATCGTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT Template switch alignment (log-probability: -23.7) AAGTTATTACAAAGtTATTATGATT|TCCACATAAAGCAAACGATCTT|GTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT AAGTTATTACAAAGGTATTATGATT|TCCACATAAAGCAAACGATCTT|GTTTGCTTTATGTGGAAATCATAATACCTTTGTAATAACT ========== Event 3012 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: GACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCA Chimp: GACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAACGTAGGGGAAATGCATCA ↓ 3 1 2 4 ↑ 1 3 4 2 Gorilla: GACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATATCTGCAATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCA ↓ 1 3 4 2 Human: GACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCA Cluster: [ ] Orangutan: GACTGCATTTTCCCTGCCTTCCAAAAGCTGGCAGATAT-----------------------------------CTGCAATA Gorilla > Human --------------- chr6:69563389-69563411 Template switch process: F1: L TGTGACTGCATTTTCCCTACGTT 1 F3: 4 ATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCATC R RF: TGTGACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATATCTGCAATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATC RR: ACACTGACGTAAAAGGGATGCAAAGTTTTCGATCGTCTATAGACGTTATAGACGATCGAAAACCTTGCATCCCCTTTACGTAGTAG F2: 3 GACGTTATAGACGATCGAAAACC 2 Unidirectional alignment (log-probability: -38.7) TGTGACTGCATTTTCCCTACGTTcCAAAAGCTAGCAGATAT-TGCAgATATCTGCTAGtTTTTGGAAtGTAGGGGAAATGCATCATC TGTGACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATATCTGCA-ATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATC Template switch alignment (log-probability: -29.2) TGTGACTGCATTTTCCCTACGTT|CCAAAAGCTAGCAGATATTGCAG|ATATCTGCTAGtTTTTGGAAtGTAGGGGAAATGCATCATC TGTGACTGCATTTTCCCTACGTT|CCAAAAGCTAGCAGATATTGCAG|ATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATC Gorilla > Chimp --------------- chr6:70800108-70800130 Template switch process: F1: L TGTGACTGCATTTTCCCTACGTT 1 F3: 4 ATATCTGCTAGTTTTTGGAACGTAGGGGAAATGCATCATC R RF: TGTGACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATATCTGCAATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATC RR: ACACTGACGTAAAAGGGATGCAAAGTTTTCGATCGTCTATAGACGTTATAGACGATCGAAAACCTTGCATCCCCTTTACGTAGTAG F2: 3 GACGTTATAGACGATCGAAAACC 2 Unidirectional alignment (log-probability: -33.2) TGTGACTGCATTTTCCCTACGTTcCAAAAGCTAGCAGATAT-TGCAgATATCTGCTAGtTTTTGGAACGTAGGGGAAATGCATCATC TGTGACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATATCTGCA-ATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATC Template switch alignment (log-probability: -23.7) TGTGACTGCATTTTCCCTACGTT|CCAAAAGCTAGCAGATATTGCAG|ATATCTGCTAGtTTTTGGAACGTAGGGGAAATGCATCATC TGTGACTGCATTTTCCCTACGTT|CCAAAAGCTAGCAGATATTGCAG|ATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATC Chimp > Gorilla --------------- chr6:69927364-69927380 Template switch process: F1: L TGTGACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATAT 1 F3: 4 TTTTGGAACGTAGGGGAAATGCATCATC R RF: TGTGACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAACGTAGGGGAAATGCATCATC RR: ACACTGACGTAAAAGGGATGCAAGGTTTTCGATCGTCTATAACGTCTATAGACGATCAAAAACCTTGCATCCCCTTTACGTAGTAG F2: 3 CGATCGTCTATAACGTC 2 Unidirectional alignment (log-probability: -33.2) GTGACTGCATTTTCCCTACGTTtCAAAAGCTAGCAGATATcTGCA-ATATCTGCTAGcTTTTGGAACGTAGGGGAAATGCATCATC GTGACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATAT-TGCAGATATCTGCTAGTTTTTGGAACGTAGGGGAAATGCATCATC Template switch alignment (log-probability: -23.1) GTGACTGCATTTTCCCTACGTTtCAAAAGCTAGCAGATAT|CTGCAATATCTGCTAGC|TTTTGGAACGTAGGGGAAATGCATCATC GTGACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATAT|CTGCAATATCTGCTAGC|TTTTGGAACGTAGGGGAAATGCATCATC ========== Event 3013 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCATCAC Chimp: GTGACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAACGTAGGGGAAATGCATCATCAC Gorilla: GTGACTGCATTTTCCCTACGTTTCAAAAGCTAGCAGATATCTGCAATATCTGCTAGCTTTTGGAACGTAGGGGAAATGCATCATCAC ↑ 3 1 2 4 Human: GTGACTGCATTTTCCCTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCATCAC Cluster: [ ] Orangutan: GTGACTGCATTTTCCCTGCCTTCCAAAAGCTGGCAGATAT-----------------------------------CTGCAATATCAC Human > Gorilla --------------- chr6:69927364-69927389 Template switch process: F1: L CTACGTTTCAAAAGCTAGCAGATAT 1 F3: 4 GTAGGGGAAATGCATCATCACTGCCTTTGTCTTAACCATG R RF: CTACGTTCCAAAAGCTAGCAGATATTGCAGATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCATCACTGCCTTTGTCTTAACCATG RR: GATGCAAGGTTTTCGATCGTCTATAACGTCTATAGACGATCAAAAACCTTACATCCCCTTTACGTAGTAGTGACGGAAACAGAATTGGTAC F2: 3 CAAGGTTTTCGATCGTCTATAACGTC 2 Unidirectional alignment (log-probability: -38.8) CTACGTTtCAAAAGCTAGCAGATATcTGCA-ATATCTGCTAGcTTTTGGAAcGTAGGGGAAATGCATCATCACTGCCTTTGTCTTAACCATG CTACGTTCCAAAAGCTAGCAGATAT-TGCAGATATCTGCTAGTTTTTGGAATGTAGGGGAAATGCATCATCACTGCCTTTGTCTTAACCATG Template switch alignment (log-probability: -24.2) CTACGTTtCAAAAGCTAGCAGATAT|CTGCAATATCTGCTAGCTTTTGGAAC|GTAGGGGAAATGCATCATCACTGCCTTTGTCTTAACCATG CTACGTTCCAAAAGCTAGCAGATAT|CTGCAATATCTGCTAGCTTTTGGAAC|GTAGGGGAAATGCATCATCACTGCCTTTGTCTTAACCATG ========== Event 3014 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAAAGAGTCATGTCCATATATC---TGAAAATTATGGCTGAATCTATTTATTCCTTGGCAA Chimp: AAAAGAGTCATGTCCATATATC---TGAAAATTGTGGCTGAATCTATTTATTCCTTGGCAA Gorilla: AAAAGAGTCATGTCCATATATT------CAGTTATGGCTGAATCTATTTATTCCATGGCAA ↓ 3 42 ↑ 1 4 3 2 Human: AAAAGAGTCATGTCCATATATC---TGAAAATTATGGCTGAATCTATTTATTCCTTGGCAA Cluster: [ ] Orangutan: AAAAGAGTCATGTCCATATATCTGA---AAATTATGGCTGAATCTATTTATTCCATGGCAA Gorilla > Human --------------- chr6:69173436-69173440 Template switch process: F1: L TATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT 1 F3: 4 AATTATGGCTGAATCTATTTATTCCTTGGCAAGTAGTTAAAG R RF: TATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATATTCAGTTATGGCTGAATCTATTTATTCCATGGCAAGTAGTTAAAG RR: ATATTTTAAAAACTTTAGTATTTTCTCAGTACAGGTATATAAGTCAATACCGACTTAGATAAATAAGGTACCGTTCATCAATTTC F2: 3 AAGTC 2 Unidirectional alignment (log-probability: -36.4) ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT----ctgaaaaTTATGGCTGAATCTATTTATTCCtTGGCAAGTAGTTAA ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATATTCAG-------TTATGGCTGAATCTATTTATTCCATGGCAAGTAGTTAA Template switch alignment (log-probability: -27.4) ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT|CTGAA|AaTTATGGCTGAATCTATTTATTCCtTGGCAAGTAGTTAA ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT|CTGAA|AGTTATGGCTGAATCTATTTATTCCATGGCAAGTAGTTAA Human > Gorilla --------------- chr6:69534678-69534681 Template switch process: F1: L TATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT 1 F3: 4 TTATGGCTGAATCTATTTATTCCATGGCAAGTAGTTAAAG R RF: TATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATATCTGAAAATTATGGCTGAATCTATTTATTCCTTGGCAAGTAGTTAAAG RR: ATATTTTAAAAACTTTAGTATTTTCTCAGTACAGGTATATAGACTTTTAATACCGACTTAGATAAATAAGGAACCGTTCATCAATTTC F2: 3 GACT 2 Unidirectional alignment (log-probability: -32.3) ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT-------tcagTTATGGCTGAATCTATTTATTCCaTGGCAAGTAGTTAAAG ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATATCTGAAAA----TTATGGCTGAATCTATTTATTCCTTGGCAAGTAGTTAAAG Template switch alignment (log-probability: -21.7) ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT|TCAG|TTATGGCTGAATCTATTTATTCCaTGGCAAGTAGTTAAAG ATAAAATTTTTGAAATCATAAAAGAGTCATGTCCATATAT|TCAG|TTATGGCTGAATCTATTTATTCCTTGGCAAGTAGTTAAAG ========== Event 3015 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTATATTTTTCTACTGAGTCTTAATGATTTGCAAATCATTAAG---ACTCAGTAGAAAAATATAGGAAG Chimp: TCCTATATTTTTCTACTGAGTCTTAATG--------ATCATTAAG---ACTCAGTAGAAAAATATAGGAAG ↑ 3 2 1 4 Gorilla: TCCTATATTTTTCTACTGAGTCTTAATGATTTGCAAATCATTAAGAAAAATCAGTAGAAAAATATAGGAAG Human: TCCTATATTTTTCTACTGAGTCTTAATGATTTGCAAATCATTAAG---ACTCAGTAGAAAAATATAGGAAG Cluster: [ ] Orangutan: TCCT--------------------------------------AGG---ACTCAGTAGAAAAATATAGGAAG Gorilla > Chimp --------------- chr6:106582401-106582409 Template switch process: F1: L AAATGCCATTTCTTCCTATATTTTTCTACTGAGTCTTAATGAT 1 F3: 4 TCAGTAGAAAAATATAGGAAGAAGTCGGTAACTGGATGAC R RF: AAATGCCATTTCTTCCTATATTTTTCTACTGAGTCTTAATGATTTGCAAATCATTAAGAAAAATCAGTAGAAAAATATAGGAAGAAGTCGGTAACTGGATGAC RR: TTTACGGTAAAGAAGGATATAAAAAGATGACTCAGAATTACTAAACGTTTAGTAATTCTTTTTAGTCATCTTTTTATATCCTTCTTCAGCCATTGACCTACTG F2: 3 CAGAATTAC 2 Unidirectional alignment (log-probability: -26.9) TGCCATTTCTTCCTATATTTTTCTACTGAGTCTTAATGAT--------CATTAAG---AcTCAGTAGAAAAATATAGGAAGAAGTCGGTAACTGGATGAC TGCCATTTCTTCCTATATTTTTCTACTGAGTCTTAATGATTTGCAAATCATTAAGAAAAATCAGTAGAAAAATATAGGAAGAAGTCGGTAACTGGATGAC Template switch alignment (log-probability: -16.9) TGCCATTTCTTCCTATATTTTTCTACTGAGTCTTAATGAT|CATTAAGAC|TCAGTAGAAAAATATAGGAAGAAGTCGGTAACTGGATGAC TGCCATTTCTTCCTATATTTTTCTACTGAGTCTTAATGAT|CATTAAGAC|TCAGTAGAAAAATATAGGAAGAAGTCGGTAACTGGATGAC ========== Event 3016 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ttccatagcaccctgCACTTAG-------CAAAGGATGATAGGTTAGAAAAGGCTTAAAATGTCTGTATTAGGAACT Chimp: ttccatagcaccctgCACTTAG-------CAAAGGATGATAGGTTAGAAAAGGCTTGAAATGTCTGTATTAGGAACT ↑ 1 3 42 Gorilla: TTCCATAGCACCCTGCACTTACCCTTTTCTAACCTATCATCCTT-------TGCTTAAAATGTCTGTATTAGGAACT ↓ 1 3 42 Human: ttccatagcaccctgCACTTAG-------CAAAGGATGATAGGTTAGAAAAGGCTTAAAATGTCTGTATTAGGAACT Cluster: [ ] Orangutan: ----------------------------------------------------------------------------- Gorilla > Human --------------- chr6:67130431-67130454 Template switch process: F1: L TATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA 1 F3: 4 GCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA R RF: TATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTACCCTTTTCTAACCTATCATCCTTTGCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA RR: ATATTCAGAGACTATAAACAAAGGTATCGTGGGACGTGAATGGGAAAAGATTGGATAGTAGGAAACGAATTTTACAGACATAATCCTTGAAATATCACCAAAAAT F2: 3 GAAAAGATTGGATAGTAGGAAACG 2 Unidirectional alignment (log-probability: -56.4) ATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA------------------------gcaaaggatgataggttagaaaagGCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA ATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTACCCTTTTCTAACCTATCATCCTTT------------------------GCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA Template switch alignment (log-probability: -18.8) ATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA|GCAAAGGATGATAGGTTAGAAAAG|GCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA ATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA|GCAAAGGATGATAGGTTAGAAAAG|GCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA Gorilla > Chimp --------------- chr6:68320238-68320261 Template switch process: F1: L TGTAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA 1 F3: 4 GCTTGAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTATATGT R RF: TATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTACCCTTTTCTAACCTATCATCCTTTGCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTATATGT RR: ATATTCAGAGACTATAAACAAAGGTATCGTGGGACGTGAATGGGAAAAGATTGGATAGTAGGAAACGAATTTTACAGACATAATCCTTGAAATATCACCAAAAATATACA F2: 3 GAAAAGATTGGATAGTAGGAAACG 2 Unidirectional alignment (log-probability: -67.5) gTAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA------------------------gcaaaggatgataggttagaaaagGCTTgAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA ATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTACCCTTTTCTAACCTATCATCCTTT------------------------GCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA Template switch alignment (log-probability: -29.9) gTAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA|GCAAAGGATGATAGGTTAGAAAAG|GCTTgAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA ATAAGTCTCTGATATTTGTTTCCATAGCACCCTGCACTTA|GCAAAGGATGATAGGTTAGAAAAG|GCTTAAAATGTCTGTATTAGGAACTTTATAGTGGTTTTTA ========== Event 3017 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTTCTTGACATTTTGTATCAGCT--------ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA---- Chimp: ACTTTCTTGACATTTTGTATCAGTT----ATATATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA---- Gorilla: ACTTTCTTGACATTTTGTATCTGTCATTT----ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA---- ↑ 1 4 3 2 Human: ACTTTCTTGACATTTTGTATCAGCT--------ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA---- Cluster: [ ] Orangutan: ACTTTCTTGACATTTTGTATCAGTT--------ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAATAAT Human > Gorilla --------------- chr6:67509811-67509818 Template switch process: F1: L TATGATTATATAATGAATTCACTTTCTTGACATTTTGTATC 1 F3: 4 ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA R RF: TATGATTATATAATGAATTCACTTTCTTGACATTTTGTATCAGCTATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA RR: ATACTAATATATTACTTAAGTGAAAGAACTGTAAAACATAGTCGATAAAAGAGATTCTTATTTACTGTATACAACTTCTTACTT F2: 3 TTTACTGT 2 Unidirectional alignment (log-probability: -34.5) ATGATTATATAATGAATTCACTTTCTTGACATTTTGTAtctgTCAttTATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA- ATGATTATATAATGAATTCACTTTCTTGACATTTTGTA----TCAGCTATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAAT Template switch alignment (log-probability: -16.7) ATGATTATATAATGAATTCACTTTCTTGACATTTTGTATC|TGTCATTT|ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA ATGATTATATAATGAATTCACTTTCTTGACATTTTGTATC|TGTCATTT|ATTTTCTCTAAGAATAAATGACATATGTTGAAGAATGAA ========== Event 3018 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGTCAAAGTAATGAAAGGGGTCTCCTTTTGGAA ↑ 3 2 1 4 Chimp: AAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGA------TGGGAAAGGGGTCTCCTTTTGGAA Gorilla: AAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGA------TGGGAAAGGGGTCTCCTTTTGGAA ↓ 3 2 1 4 Human: AAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGTCAAAGTAATGAAAGGGGTCTCCTTTTGGAA Cluster: [ ] Orangutan: AAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGA------TGGGAAAGGGGTTTCCTTTTGGAA Chimp > Human ------------- chr6:103981076-103981085 Template switch process: F1: L GTAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG 1 F3: 4 GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT R RF: GTAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGATGGGAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT RR: CATTTTCGATACGATTAGTACCCTAATGAAACTGACACTCCTACCCTTTCCCCAGAGGAAAACCTTTCGTATATACATGGAACCA F2: 3 TAATGAAACT 2 Unidirectional alignment (log-probability: -32.8) TAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGtcaaagtaATG--AAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT TAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG--------ATGGGAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT Template switch alignment (log-probability: -16.5) TAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG|TCAAAGTAAT|GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT TAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG|TCAAAGTAAT|GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT Gorilla > Human --------------- chr6:103981076-103981085 Template switch process: F1: L GTAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG 1 F3: 4 GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT R RF: GCAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGATGGGAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT RR: CGTTTTCGATACGATTAGTACCCTAATGAAACTGACACTCCTACCCTTTCCCCAGAGGAAAACCTTTCGTATATACATGGAACCA F2: 3 TAATGAAACT 2 Unidirectional alignment (log-probability: -37.8) tAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGGtcaaagtaAT--GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT CAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG--------ATGGGAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT Template switch alignment (log-probability: -22.5) tAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG|TCAAAGTAAT|GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT CAAAAGCTATGCTAATCATGGGATTACTTTGACTGTGAGG|TCAAAGTAAT|GAAAGGGGTCTCCTTTTGGAAAGCATATATGTACCTTGGT ========== Event 3019 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: agggatctctgactACCAGGCAAC----TCCCTTGTAATGTTAATAATCTGTTCCAGAAAATCATATGT Chimp: agggatctctgactACCAGGCAAC----TCCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATATGT ↓ 1 4 3 2 Gorilla: agggatctctgactACCAGGCGATTACTACCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATACGT Human: agggatctctgactACCAGGCAAC----TCCCTTGTAATGTTAATAATCTGTTCCAGAAAATCATATGT Cluster: [ ] Orangutan: agggatctctgactACCAGGCAAC----TCCCTTGTAATATTAGTAATCTGTTCCAGAAAATCATATGT Chimp > Gorilla --------------- chr6:66865738-66865745 Template switch process: F1: L AATATCAGCTCCACCATCGCAGGGATCTCTGACTACCAGGC 1 F3: 4 CCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATACGT R RF: AATATCAGCTCCACCATCGCAGGGATCTCTGACTACCAGGCAACTCCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATATGT RR: TTATAGTCGAGGTGGTAGCGTCCCTAGAGACTGATGGTCCGTTGAGGGAACATTACAATCATTAGACAAGGTCTTTTAGTATACA F2: 3 ATCATTAG 2 Unidirectional alignment (log-probability: -33.3) ATATCAGCTCCACCATCGCAGGGATCTCTGACTACCAGGCgAtTactaCCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATAcGT ATATCAGCTCCACCATCGCAGGGATCTCTGACTACCAGGCAACT----CCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATATGT Template switch alignment (log-probability: -22.3) ATATCAGCTCCACCATCGCAGGGATCTCTGACTACCAGGC|GATTACTA|CCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATAcGT ATATCAGCTCCACCATCGCAGGGATCTCTGACTACCAGGC|GATTACTA|CCCTTGTAATGTTAGTAATCTGTTCCAGAAAATCATATGT ========== Event 3020 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGACCCATTGTCCCCAACATGGCTCGTGATGGT-------------GAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGT Chimp: TCAGACCCATTGTCCCCAACATGGCTGGTGACGGT-------------GAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGT ↓ 3 2 1 4 Gorilla: TCAGACCCATTGTCCCCAACATGGCTCGTGACGGT--------------------------GCCATGAGGTCAGTCCTCCTGCCTAGT ↑ 3 2 1 4 Human: TCAGACCCATTGTCCCCAACATGGCTCGTGATGGT-------------GAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGT Cluster: [ ] Orangutan: TCAGACCCATTGTCCCCAACATGGCTCGTGACGGTGAAGGGCTGCTGG-------------GACAGAAGGTCAGTCCTCCTGCCTAGT Human > Gorilla --------------- chr6:172005432-172005436 Template switch process: F1: L TCTGCTTCTCTCAGACCCATTGTCCCCAACATGGCTCGTGACGGTG 1 F3: 4 AGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC R RF: TCTGCTTCTCTCAGACCCATTGTCCCCAACATGGCTCGTGATGGTGAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGTTGGCCCATTTTGCTCTTCC RR: AGACGAAGAGAGTCTGGGTAACAGGGGTTGTACCGAGCACTACCACTTCCCGACGACCCTGTCTTCCAGTCAGGAGGACGGATCAACCGGGTAAAACGAGAAGG F2: 3 GTACC 2 Unidirectional alignment (log-probability: -38.8) TCTCTCAGACCCATTGTCCCCAACATGGCTCGTGacggtgccATG---------------------AGGTCAGTCCTCCTGCCTAGTTGGCCtATTTTGCTCTTCC TCTCTCAGACCCATTGTCCCCAACATGGCTCGTG--------ATGGTGAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGTTGGCCCATTTTGCTCTTCC Template switch alignment (log-probability: -27.5) TCTCTCAGACCCATTGTCCCCAACATGGCTCGTGAcGGTG|CCATG|AGGTCAGTCCTCCTGCCTAGTTGGCCtATTTTGCTCTTCC TCTCTCAGACCCATTGTCCCCAACATGGCTCGTGATGGTG|CCATG|AGGTCAGTCCTCCTGCCTAGTTGGCCCATTTTGCTCTTCC Chimp > Gorilla --------------- chr6:172005432-172005436 Template switch process: F1: L ATTTCTCTGCTTCTCTCAGACCCATTGTCCCCAACATGGCTCGTGACGGTG 1 F3: 4 AGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC R RF: ATTTCTCTGCTTCTCTCAGACCCATTGTCCCCAACATGGCTGGTGACGGTGAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC RR: TAAAGAGACGAAGAGAGTCTGGGTAACAGGGGTTGTACCGACCACTGCCACTTCCCGACGACCCTGTCTTCCAGTCAGGAGGACGGATCAACCGGATAAAACGAGAAGG F2: 3 GTACC 2 Unidirectional alignment (log-probability: -33.8) TCTCTCAGACCCATTGTCCCCAACATGGCTcGTGACGGT-------------GcCAtgAGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC TCTCTCAGACCCATTGTCCCCAACATGGCTGGTGACGGTGAAGGGCTGCTGGGACAGAAGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC Template switch alignment (log-probability: -22.1) TCTCTCAGACCCATTGTCCCCAACATGGCTcGTGACGGTG|CCATG|AGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC TCTCTCAGACCCATTGTCCCCAACATGGCTGGTGACGGTG|CCATG|AGGTCAGTCCTCCTGCCTAGTTGGCCTATTTTGCTCTTCC ========== Event 3021 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATACAAATAGAATTGCATCTCAAGTTTACAACCTTA-------ACTTTCAAAGTCCTTTACATGT Chimp: TATACAAATAGAATTGCATCTCAAGTTTACAACCTTAAACTTGAGGTTTCAAAGTCCTTTACATG- ↑ 3 2 14 Gorilla: TATACAAATAGAATTGCATCTCAAGTTTACAACCTTA-------ACTTTCAAAGTCCTTTACATG- Human: TATACAAATAGAATTGCATCTCAAGTTTACAACCTTA-------ACTTTCAAAGTCCTTTACATGT Cluster: [ ] Orangutan: TATACAAATAGAATTGCATCTCAAGTTTACAGCCTTA-------ACTTTCAAAGTCCTTTACATG- Gorilla > Chimp --------------- chr6:174236718-174236724 Template switch process: F1: L TTCATATACAAATAGAATTGCATCTCAAGTTTACAACCTTAA 1 F3: 4 GTTTCAAAGTCCTTTACATGTAAGTTTTTTTTTTTTTTT R RF: TTCATATACAAATAGAATTGCATCTCAAGTTTACAACCTTAACTTTCAAAGTCCTTTACATGTAAGTTTTTTTTTTTTT RR: AAGTATATGTTTATCTTAACGTAGAGTTCAAATGTTGGAATTGAAAGTTTCAGGAAATGTACATTCAAAAAAAAAAAAA F2: 3 GAGTTCA 2 Unidirectional alignment (log-probability: -43.2) CATATACAAATAGAATTGCATCTCAAGTTTACAACCTTAAacttgaggTTTCAAAGTCCTTTACATGTAAGTTTTTTTTttttttt CATATACAAATAGAATTGCATCTCAAGTTTACAACCTTAAC-------TTTCAAAGTCCTTTACATGTAAGTTTTTTTT------- Template switch alignment (log-probability: -31.7) CATATACAAATAGAATTGCATCTCAAGTTTACAACCTTAA|ACTTGAG|gTTTCAAAGTCCTTTACATGTAAGTTTTTTTTTTTTttT CATATACAAATAGAATTGCATCTCAAGTTTACAACCTTAA|ACTTGAG|CTTTCAAAGTCCTTTACATGTAAGTTTTTTTTTTTT--T ========== Event 3022 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: ATGGGTTTGTTTCTCCCCAGCATCAGCTGGGCATTGCGGTAGCTCTCTGTCT ↑ 31 2 4 Chimp: ATGGGTTTGTTTCTCCCCAGCTGATGGTGGGGATTGCGGTAGCTCTCTGTCT Gorilla: atgggtttgtttctccccagcatcagctggggattgcggtagctctctgtct Human: ATGGGTTTGTTTCTCCCCAGCATCAGCTGGGCATTGCGGTAGCTCTCTGTCT Cluster: [ ] Orangutan: ATGGGTTTGTTTCTCCCCAGCATGAGCTGGGGATTGCGGTAGCTCTCTGTCT Chimp > Human ------------- chr6:65405107-65405112 Template switch process: F1: L GGTAGCCTTTGATTTCTAGGATGGGTTTGTTTCTCCCCAGC 1 F3: 4 TGGGCATTGCGGTAGCTCTCTGTCTCTTTCACTTGAGCACCTTCA R RF: GGTAGCCTTTGATTTCTAGGATGGGTTTGTTTCTCCCCAGCTGATGGTGGGGATTGCGGTAGCTCTCTGTCTCTTTCACTTGAGCACCTTCA RR: CCATCGGAAACTAAAGATCCTACCCAAACAAAGAGGGGTCGACTACCACCCCTAACGCCATCGAGAGACAGAGAAAGTGAACTCGTGGAAGT F2: 3 CGACTA 2 Unidirectional alignment (log-probability: -36.1) GTAGCCTTTGATTTCTAGGATGGGTTTGTTTCTCCCcagcatCAGC------TGGGcATTGCGGTAGCTCTCTGTCTCTTTCACTTGAGCAC GTAGCCTTTGATTTCTAGGATGGGTTTGTTTCTCCC------CAGCTGATGGTGGGGATTGCGGTAGCTCTCTGTCTCTTTCACTTGAGCAC Template switch alignment (log-probability: -22.1) GTAGCCTTTGATTTCTAGGATGGGTTTGTTTCTCCCCAGC|ATCAGC|TGGGcATTGCGGTAGCTCTCTGTCTCTTTCACTTGAGCAC GTAGCCTTTGATTTCTAGGATGGGTTTGTTTCTCCCCAGC|ATCAGC|TGGGGATTGCGGTAGCTCTCTGTCTCTTTCACTTGAGCAC ========== Event 3023 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AATAGGAGATGACCACAGGTCTC--TCTTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT Chimp: AATAGGAGATGACCACAGGTCTC--T-CTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT Gorilla: AATAGGAGATGACCACAGGTCACTGG-CTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT ↑ 1 4 3 2 Human: AATAGGAGATGACCACAGGTCTC--TCTTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT Cluster: [ ] Orangutan: AATAGGAGATGACCACAGGTCTC--T-CTCCTCAGGTTAAGAGCCAGTGTGATTGTACAGACACTGCT Human > Gorilla --------------- chr6:65551413-65551418 Template switch process: F1: L ACTTAAAGAGAAAACATTTAAATAGGAGATGACCACAGGTC 1 F3: 4 TCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT R RF: ACTTAAAGAGAAAACATTTAAATAGGAGATGACCACAGGTCTCTCTTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT RR: TGAATTTCTCTTTTGTAAATTTATCCTCTACTGGTGTCCAGAGAGAAGGAGTCCAATTCTCGGTCATTCTAGCATGTCTGTGACGA F2: 3 CGGTCA 2 Unidirectional alignment (log-probability: -29) CTTAAAGAGAAAACATTTAAATAGGAGATGACCACAGGTCaCTggcTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT CTTAAAGAGAAAACATTTAAATAGGAGATGACCACAGGTCTCT-CTTCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT Template switch alignment (log-probability: -16.5) CTTAAAGAGAAAACATTTAAATAGGAGATGACCACAGGTC|ACTGGC|TCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT CTTAAAGAGAAAACATTTAAATAGGAGATGACCACAGGTC|ACTGGC|TCCTCAGGTTAAGAGCCAGTAAGATCGTACAGACACTGCT ========== Event 3024 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGAAATACTTCCCTGTGTCTGATGAATTCTCTAACTTACAAGTTGTTTG------TAAGGTAAAGCTTACCTTCTACCATCCAAGTTGAAATTAC Chimp: CAGAAATACTTCCCTGTGTCTGATGAATTCTCTAACTTACAAGTTGTTTG---ATCAGAGGTAAAGTTCACCTTCCACCATCCAAGTTGAAATTAC Gorilla: CAGAAATACTTCCCTGTGTCTGATGAATTCTCTAACTTACAAGTTGTTTGATC---AGAGGTAAAGCTCACCTTCCACCATCCAAGTTGAAATTAC ↑ 3 2 1 4 Human: CAGAAATACTTCCCTGTGTCTGATGAATTCTCTAACTTACAAGTTGTTTG------TAAGGTAAAGCTTACCTTCTACCATCCAAGTTGAAATTAC Cluster: [ ] Orangutan: CAGAAATACTTCCCTGTGTCTGATGAATTCTCTAACTTACAAGTTGTTTGATC---AGAGGTAAAGCTGACCTTCCACCATCCAAGTTGAAATTAC Human > Gorilla --------------- chr6:65829755-65829759 Template switch process: F1: L GAATTCTCTAACTTACAAGTTGTTTG 1 F3: 4 AGGTAAAGCTCACCTTCCACCATCCAAGTTGAAATTACCAGATACCCTCAAAGCATTA R RF: CTGATGAATTCTCTAACTTACAAGTTGTTTGTAAGGTAAAGCTTACCTTCTACCATCCAAGTTGAAATTACCAGATACCCTCAAAGCATTA RR: GACTACTTAAGAGATTGAATGTTCAACAAACATTCCATTTCGAATGGAAGATGGTAGGTTCAACTTTAATGGTCTATGGGAGTTTCGTAAT F2: 3 GACTA 2 Unidirectional alignment (log-probability: -37.3) GAATTCTCTAACTTACAAGTTGTTTGatcagAGGTAAAGCTcACCTTCcACCATCCAAGTTGAAATTACCA GAATTCTCTAACTTACAAGTTGTTTG---TAAGGTAAAGCTTACCTTCTACCATCCAAGTTGAAATTACCA Template switch alignment (log-probability: -27.5) GAATTCTCTAACTTACAAGTTGTTTG|ATCAG|AGGTAAAGCTcACCTTCcACCATCCAAGTTGAAATTACCA GAATTCTCTAACTTACAAGTTGTTTG|ATCAG|AGGTAAAGCTTACCTTCTACCATCCAAGTTGAAATTACCA ========== Event 3025 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTGTAATGTTTTTCATAGAACTTCTGGT--------------------------------TCAGAAGTTCTTAACTGTTTGAATGTAACC ↑ 3 2 1 4 Chimp: CTTGTAATGTTTTTCATAGAACTTCTGGT----------------TAAGGGAGAGATTTCCTCAGAA-GACTTAACTGTTTGAATGTAACC Gorilla: CTTGTAATGTTTTTCATAGAACTTCTGGTTAAGGGAGCGATTTCC----------------TCAGAA-GACTTAACTGTTTGAATGTAACC ↓ 3 2 1 4 Human: CTTGTAATGTTTTTCATAGAACTTCTGGT--------------------------------TCAGAAGTTCTTAACTGTTTGAATGTAACC Cluster: [ ] Orangutan: CCTGTAATGTTTTTCATAGAACTTCTGGTTAAGGGAGAGATTTCC----------------TTAGAA-GACTTAACTGTTTGAATGTAACC Chimp > Human ------------- chr6:106648684-106648691 Template switch process: F1: L ATTAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTT 1 F3: 4 CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT R RF: ATTAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTTAAGGGAGAGATTTCCTCAGAAGACTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT RR: TAATCGTAAGGTGAACATTACAAAAAGTATCTTGAAGACCAATTCCCTCTCTAAAGGAGTCTTCTGAATTGACAAACTTACATTGGGAAAAGTCGACCTTCTGGA F2: 3 TTGAAGAC 2 Unidirectional alignment (log-probability: -29.5) TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGT----------------TCAGAAGttCTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTTAAGGGAGAGATTTCCTCAGAAG-ACTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT Template switch alignment (log-probability: -16.3) TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTT|CAGAAGTT|CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTT|CAGAAGTT|CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT Gorilla > Human --------------- chr6:106648684-106648691 Template switch process: F1: L ATTAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTT 1 F3: 4 CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT R RF: ATTAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTTAAGGGAGCGATTTCCTCAGAAGACTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT RR: TAATCGTAAGGTGAACATTACAAAAAGTATCTTGAAGACCAATTCCCTCGCTAAAGGAGTCTTCTGAATTGACAAACTTACATTGGGAAAAGTCGACCTTCTGGA F2: 3 TTGAAGAC 2 Unidirectional alignment (log-probability: -28.5) TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGT----------------TCAGAAGttCTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTTAAGGGAGCGATTTCCTCAGAAGA-CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT Template switch alignment (log-probability: -16.8) TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTT|CAGAAGTT|CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT TAGCATTCCACTTGTAATGTTTTTCATAGAACTTCTGGTT|CAGAAGTT|CTTAACTGTTTGAATGTAACCCTTTTCAGCTGGAAGACCT ========== Event 3026 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: AACAAATGTAAAGAGAAAGAATTGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTACCTCTAAGCATCC------------------------------------TGTGGTGTTTGAAATAAAAGAAA ↓ 3 1 2 4 ↑ 3 1 2 4 Chimp: AACAAATGTAAAGAGAAAGAATTGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTAGAGGTAAGCATCCTATTATTCAATTTGCATCTGAAAACAGTCACAATTCTGGGGTGTTTGAAATAAAAGAAA Gorilla: Human: AACAAATGTAAAGAGAAAGAATTGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTACCTCTAAGCATCC------------------------------------TGTGGTGTTTGAAATAAAAGAAA Cluster: [ ] Orangutan: AACAAATGTAAAGAGAAAGAATCGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTACCTCTAAGCATCC------------------------------------TGGGGTGTTTGAAATAAAAGAAA Chimp > Human ------------- chr6:106979854-106979865 Template switch process: F1: L TGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTA 1 F3: 4 CTGTGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAATCTCTT R RF: TGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTAGAGGTAAGCATCCTATTATTCAATTTGCATCTGAAAACAGTCACAATTCTGGGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAACCTCTT RR: ACACTGACAAAAGTCTACGTTTAACTTATTATCCTACGAATCTCCATTCGTAGGATAATAAGTTAAACGTAGACTTTTGTCAGTGTTAAGACCCCACAAACTTTATTTTCTTTCTTCGTTGAGAATTGGAGAA F2: 3 CTACGAATCTCC 2 Unidirectional alignment (log-probability: -48.9) GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTAcctcTAAGCATCCT------------------------------------GtGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAAtC GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTAGAGGTAAGCATCCTATTATTCAATTTGCATCTGAAAACAGTCACAATTCTGGGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAACC Template switch alignment (log-probability: -28.8) GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTA|CCTCTAAGCATC|CTGtGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAAtC GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTA|CCTCTAAGCATC|CTGGGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAACC Human > Chimp ------------- chr6:110427247-110427294 Template switch process: F1: L TGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTA 1 F3: 4 CTGGGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAACCTCTT R RF: AATTGTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTACCTCTAAGCATCCTGTGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAATCTCTT RR: TTAACACTGACAAAAGTCTACGTTTAACTTATTATCCTACGAATGGAGATTCGTAGGACACCACAAACTTTATTTTCTTTCTTCGTTGAGAATTAGAGAA F2: 3 TTAACACTGACAAAAGTCTACGTTTAACTTATTATCCTACGAATGGAG 2 Unidirectional alignment (log-probability: -98.8) GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTAgaggTAAGCATCctattattcaatttgcatctgaaaacagtcacaattCTGgGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAAcC GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTACCTCTAAGCATC------------------------------------CTGTGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAATC Template switch alignment (log-probability: -33.2) GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTA|GAGGTAAGCATCCTATTATTCAATTTGCATCTGAAAACAGTCACAATT|CTGgGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAAcC GTGACTGTTTTCAGATGCAAATTGAATAATAGGATGCTTA|GAGGTAAGCATCCTATTATTCAATTTGCATCTGAAAACAGTCACAATT|CTGTGGTGTTTGAAATAAAAGAAAGAAGCAACTCTTAATC ========== Event 3027 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATGTGCACTGGGTAAGTCACCCTTATCTGG-------AACAGTTTCAACTTCTTAGGCT ↓ 3 1 2 4 Chimp: TATGTGCACTGGGTAAGTCACCCTTATCCAGATAAGGATACAGTTTCAACTTCTTAGGCT ↑ 3 1 2 4 Gorilla: TATGTGCACTGGGTAAGTCACCCTTATCTGG-------AACAGTTTCAACTTCTTAGGCT Human: TATGTGCACTGGGTAAGTCACCCTTATCTGG-------AACAGTTTCAACTTCTTAGGCT Cluster: [ ] Orangutan: TATGTGCACTGGGTAAGTCACCCTTATCTGG-------AACAGTTTCAACTTCTTAGGCT Human > Chimp ------------- chr6:64661379-64661389 Template switch process: F1: L GTAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATC 1 F3: 4 ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC R RF: GTAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATCTGGAACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC RR: CATTTCTCTAACTATACACGTGACCCATTCAGTGGGAATAGACCTTGTCAAAGTTGAAGAATCCGATGAGAACGAAAAATATTAG F2: 3 TAGGAATAGAC 2 Unidirectional alignment (log-probability: -33) TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATCcaGAtaaggatACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATCTGGA-------ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC Template switch alignment (log-probability: -22.6) TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATC|CAGATAAGGaT|ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATC|CAGATAAGGGT|ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC Gorilla > Chimp --------------- chr6:64661379-64661389 Template switch process: F1: L GTAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATC 1 F3: 4 ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC R RF: GTAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATCTGGAACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC RR: CATTTCTCTAACTATACACGTGACCCATTCAGTGGGAATAGACCTTGTCAAAGTTGAAGAATCCGATGAGAACGAAAAATATTAG F2: 3 TAGGAATAGAC 2 Unidirectional alignment (log-probability: -32) TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATCcaGAtaaggatACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATCTGGA-------ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC Template switch alignment (log-probability: -22.6) TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATC|CAGATAAGGaT|ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC TAAAGAGATTGATATGTGCACTGGGTAAGTCACCCTTATC|CAGATAAGGGT|ACAGTTTCAACTTCTTAGGCTACTCTTGCTTTTTATAATC ========== Event 3028 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CATCCCACAAATGAAAGATTATGGGATCTTTAGTGATCCCATAATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCTAGACAAAT ↑ 3 24 1 Chimp: CATCCCACAAATGAAAGATTATGGGATCA------------CTATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCTAGACAAAT Gorilla: CATCCCACAAATGAAAGATTATGGGATCTTTAGTGATCCCATAATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCTAGACAAAT Human: CATCCCACAAATGAAAGATTATGGGATCTTTAGTGATCCCATAATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCTAGACAAAT Cluster: [ ] Orangutan: CATCCCACAAATGAAAGATTATGGGATCTTTAGTGATCCCATAATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCTAGACAAAT Chimp > Human ------------- chr6:63231496-63231507 Template switch process: F1: L AGTTTCATGTGCACATCCCACAAATGAAAGATTATGGGA----------------------------TCTTT 1 F3: 4 ATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCT R RF: AGTTTCATGTGCACATCCCACAAATGAAAGATTATGGGATCACTATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCT RR: TCAAAGTACACGTGTAGGGTGTTTACTTTCTAATACCCTAGTGATAGTTTCATTCTCAGTCGAGTTTAGAAAAGAGTCCGAGGA F2: 3 ATACCCTAGTGA 2 Unidirectional alignment (log-probability: -40.2) TCATGTGCACATCCCACAAATGAAAGATTATGGGATctttagtgatccCAtaATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCT TCATGTGCACATCCCACAAATGAAAGATTATGGGAT------------CACTATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCT Template switch alignment (log-probability: -28.5) TCATGTGCACATCCCACAAATGAAAGATTATGGGA----------------------------TCTTT|AGTGATCCCATA|ATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCT TCATGTGCACATCCCACAAATGAAAGATTATGGGATCACTATCAAAGTAAGAGTCAGCTCAAATCTTT|AGTGATCCCATA|ATCAAAGTAAGAGTCAGCTCAAATCTTTTCTCAGGCTCCT ========== Event 3029 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: GAGGCAGAAAGATGGATTTGATAACACTGGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATT-GTTGTTGCCTTTGAGTGTTAAAATT ↓ 3 2 1 4 Chimp: GAGGCAGAAAGATGGATTTGATAACACTGGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATGTTATCTTGCCTTTGAGTGTTAAAATT Gorilla: GAGGCAGAAAGACGGATTTGATAACACTGGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATGTTATCTTGCCTTTGAGTGTTAAAATT Human: GAGGCAGAAAGATGGATTTGATAACACTGGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATT-GTTGTTGCCTTTGAGTGTTAAAATT Cluster: [ ] Orangutan: GAGGCAGAAAGATGTACTTGATAACACTGGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATGTTATCTTGCCTTTGAGTGTTAAAATT Human > Chimp ------------- chr6:64170696-64170701 Template switch process: F1: L GGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAAT 1 F3: 4 TTGCCTTTGAGTGTTAAAATTTAAAAAGACCCAAGTATAA R RF: GATAACACTGGTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATTGTTGTTGCCTTTGAGTGTTAAAATTTAAAAAGACCCAAGTATAA RR: CTATTGTGACCACCGAGACAGTCTTCAGTACTCTACTGGTGCCCCTTTTAACAACAACGGAAACTCACAATTTTAAATTTTTCTGGGTTCATATT F2: 3 CTATTG 2 Unidirectional alignment (log-probability: -28.5) GTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAA----TGttatcTTGCCTTTGAGTGTTAAAATTTAAAAAGACCCAAGTATAA GTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAATTGTTG-----TTGCCTTTGAGTGTTAAAATTTAAAAAGACCCAAGTATAA Template switch alignment (log-probability: -16) GTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAAT|GTTATC|TTGCCTTTGAGTGTTAAAATTTAAAAAGACCCAAGTATAA GTGGCTCTGTCAGAAGTCATGAGATGACCACGGGGAAAAT|GTTATC|TTGCCTTTGAGTGTTAAAATTTAAAAAGACCCAAGTATAA ========== Event 3030 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGACAGAATATAAGCAGAGAAAGCTATAGCTGTTA-----CTTTGCAGAGAACCTAATGATT Chimp: AAGGACAGAATATAAGCGGAGAAAGCTATAGCTGTTA-----CTTTGCAGAGAACCTAATGATT ↓ 3 2 1 4 Gorilla: AAGGACAGAATATAAGCAGAGAAAGCTATAGCTATAGCTTTCTTTTGCAGAGAACCTAATGATT ↑ 3 2 1 4 Human: AAGGACAGAATATAAGCAGAGAAAGCTATAGCTGTTA-----CTTTGCAGAGAACCTAATGATT Cluster: [ ] Orangutan: AAGGACAGAATATAAGCAGAGAAAGCTATAGCTGTTC-----CTTTACAGAGAATCTAATGATT Human > Gorilla --------------- chr6:63795255-63795264 Template switch process: F1: L ACTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCT 1 F3: 4 TTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA R RF: ACTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCTGTTACTTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA RR: TGAACCAATTCCTGTCTTATATTCGTCTCTTTCGATATCGACAATGAAACGTCTCTTGGATTACTAAACAGAATAAAACTTTGATT F2: 3 TCTTTCGATA 2 Unidirectional alignment (log-probability: -34.7) CTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCTatagctTTctTTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA CTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCT-----GTTACTTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA Template switch alignment (log-probability: -17) CTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCT|ATAGCTTTCT|TTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA CTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCT|ATAGCTTTCT|TTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA Chimp > Gorilla --------------- chr6:63795255-63795264 Template switch process: F1: L ACTTGGTTAAGGACAGAATATAAGCAGAGAAAGCTATAGCT 1 F3: 4 TTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA R RF: ACTTGGTTAAGGACAGAATATAAGCGGAGAAAGCTATAGCTGTTACTTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA RR: TGAACCAATTCCTGTCTTATATTCGCCTCTTTCGATATCGACAATGAAACGTCTCTTGGATTACTAAACAGAATAAAACTTTGATT F2: 3 TCTTTCGATA 2 Unidirectional alignment (log-probability: -40.2) CTTGGTTAAGGACAGAATATAAGCaGAGAAAGCTATAGCTatagctTTctTTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA CTTGGTTAAGGACAGAATATAAGCGGAGAAAGCTATAGCTG-----TTACTTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA Template switch alignment (log-probability: -22.5) CTTGGTTAAGGACAGAATATAAGCaGAGAAAGCTATAGCT|ATAGCTTTCT|TTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA CTTGGTTAAGGACAGAATATAAGCGGAGAAAGCTATAGCT|ATAGCTTTCT|TTTGCAGAGAACCTAATGATTTGTCTTATTTTGAAACTAA ========== Event 3031 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGGCTCCACACTGCAGCCTTGACCAGGCGCGGCACG-TAAGGAGGTATGTGGCTCTTCCCAT Chimp: AGAGGCTCCACACTGCAGCCTTGACCAGGCACGGCTGGTCAAGGAGGTATGTGGCTCTTCCCAT ↑ 3 2 1 4 Gorilla: AGAGGCTCCACACTGCAGCCTTGACCAGGCACGGCACG-TAAAGAGGTATGTGGCTCTTCCCAT Human: AGAGGCTCCACACTGCAGCCTTGACCAGGCGCGGCACG-TAAGGAGGTATGTGGCTCTTCCCAT Cluster: [ ] Orangutan: AGAGGCTCCACACTGCAGCCTTGACCAGGCACAGCATG-TAAGGAGGTATGTGGCTCTTCCCAT Gorilla > Chimp --------------- chr6:64307583-64307590 Template switch process: F1: L CCTGTGAGAGGCTCCACACTGCAGCCTTGACCAGGCACGGC 1 F3: 4 GAGGTATGTGGCTCTTCCCATTCCCGTAGGAGGAAAGGCA R RF: CCTGTGAGAGGCTCCACACTGCAGCCTTGACCAGGCACGGCACGTAAAGAGGTATGTGGCTCTTCCCATTCCCGTAGGAGGAAAGGCA RR: GGACACTCTCCGAGGTGTGACGTCGGAACTGGTCCGTGCCGTGCATTTCTCCATACACCGAGAAGGGTAAGGGCATCCTCCTTTCCGT F2: 3 GAACTGGT 2 Unidirectional alignment (log-probability: -29) CTGTGAGAGGCTCCACACTGCAGCCTTGACCAGGCACGGCtgGTcAAgGAGGTATGTGGCTCTTCCCATTCCCGTAGGAGGAAAGGCA CTGTGAGAGGCTCCACACTGCAGCCTTGACCAGGCACGGCACGT-AAAGAGGTATGTGGCTCTTCCCATTCCCGTAGGAGGAAAGGCA Template switch alignment (log-probability: -16.7) CTGTGAGAGGCTCCACACTGCAGCCTTGACCAGGCACGGC|TGGTCAAG|GAGGTATGTGGCTCTTCCCATTCCCGTAGGAGGAAAGGCA CTGTGAGAGGCTCCACACTGCAGCCTTGACCAGGCACGGC|TGGTCAAG|GAGGTATGTGGCTCTTCCCATTCCCGTAGGAGGAAAGGCA ========== Event 3032 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GAACAAGGCTTAAATTGTTTGGTAAAGAGCAAAGAACCCTTTGGTTTCAGAAAAAAGAGAGGGAGACGGCAAGAGTCACAATGCTGTGAGGGGCTGGAGTCCTCTATGAAACAGGAACACTGGTAGCTATTGCCAGAAAACTTTCTCA-----------------------TGCAAAGAGTATACTTTGCCACATGCAAAGAGTGTACATTACAATTAtctttccttt Chimp: GAACAAGGCTTAAATTGTTTGGTAAAGAGCAAAGAACCCTTTGGTTTCAGAAAAAAGAGAGGGAGACGGCAAGAGTCAAAATGCTGTGAGGGGCTGGAGTCCTCTATGAAACAGGAACACTGGTAGCTATTGCCAGAAAACTTTCTCA-----------------------TGCAAAGAGTATACTTTGCCACATGCAAAGAGTGTACATTACAATCAtctttccttt ↑ 3 2 4 1 Gorilla: GAACAAGGCTTAAATTGTTTGGTAAAGAGCAAAGAACCCTTTGGTTTCAGAAAAAAGAGAAGGAGACGGCAAGAGTCAAAATGCTGTGAGGGGCTGGAGTCCTCTATGAAACAGGAACACTGGTAGCTACTGCCAGAAAACTTTCTCA----------------------------------------------TGCAAAGAGTGTACATTACAATCAtctttccttt Human: GAACAAGGCTTAAATTGTTTGGTAAAGAGCAAAGAACCCTTTGGTTTCAGAAAAAAGAGAGGGAGACGGCAAGAGTCACAATGCTGTGAGGGGCTGGAGTCCTCTATGAAACAGGAACACTGGTAGCTATTGCCAGAAAACTTTCTCA-----------------------TGCAAAGAGTATACTTTGCCACATGCAAAGAGTGTACATTACAATTAtctttccttt Cluster: [ ] Orangutan: GAACAAGGCTTAAATTGTTTGGTAAAGAGCAAAGAACCCTTTGGTTTCAGAAAAAAGAGAGGGAGACAGCAAGAGTCAAAATGCTGTGAGGGGCTGGAGTTCTCTATGAAACAGGAACACTGGTAGCTATTGCCAGAAAACTTTCTCATGCAAAGAGTGTACTTTGCCACA-----------------------TGCAAAGAGTGTACATTACAATCATctttccttt Gorilla > Chimp --------------- chr6:63167680-63167686 Template switch process: F1: L GAAACAGGAACACTGGTAGCTATTGCCAGAAAACTTTCTCATGCAAAGAGTATAC 1 F3: 4 CATGCAAAGAGTGTACATTACAATCATCTTTCCTTTCTTCCT R RF: TGGTAAAGAGCAAAGAACCCTTTGGTTTCAGAAAAAAGAGAAGGAGACGGCAAGAGTCAAAATGCTGTGAGGGGCTGGAGTCCTCTATGAAACAGGAACACTGGTAGCTACTGCCAGAAAACTTTCTCATGCAAAGAGTGTACATTACAATCATCTTTCCTTTCTTCCT RR: ACCATTTCTCGTTTCTTGGGAAACCAAAGTCTTTTTTCTCTTCCTCTGCCGTTCTCAGTTTTACGACACTCCCCGACCTCAGGAGATACTTTGTCCTTGTGACCATCGATGACGGTCTTTTGAAAGAGTACGTTTCTCACATGTAATGTTAGTAGAAAGGAAAGAAGGA F2: 3 ACCGTTT 2 Unidirectional alignment (log-probability: -49.5) GTAGCTAtTGCCAGAAAACTTTCTcatgcaaagagtatactttgccaCATGCAAAGAGTGTACATTACAATCATCTTTCCTTTCTTC GTAGCTACTGCCAGAAAACTTTCT-----------------------CATGCAAAGAGTGTACATTACAATCATCTTTCCTTTCTTC Template switch alignment (log-probability: -33.6) GTAGCTAtTGCCAGAAAACTTTCTCATGCAAAGAGTaTAC|TTTgCCA|CATGCAAAGAGTGTACATTACAATCATCTTTCCTTTCTTC GTAGCTACTGCCAGAAAACTTTCTCATGCAAAGAGTGTAC|TTTACCA|CATGCAAAGAGTGTACATTACAATCATCTTTCCTTTCTTC ========== Event 3033 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: CAAAGACTCTAATTCAGGATTAGACCCTAGTCTCCTTTCTTGAGACCTATTC ↓ 1 3 42 ↑ 1 3 4 2 Chimp: CAAAGACTCTAATTCAGGATT-AACTAGGGTCTCCTTTCTTGAGACCTATTC Gorilla: CAAAGACTCTAATTCAGGATT-AACTAGGGTCTCCTTTCTTGAGACCTATTC ↓ 1 3 4 2 ↑ 1 3 42 Human: CAAAGACTCTAATTCAGGATTAGACCCTAGTCTCCTTTCTTGAGACCTATTC Cluster: [ ] Orangutan: CAAAGACTCTAATTCAGGATT-AACTAGGGTCTCCTTTCTTGAGACCTATTC Chimp > Human ------------- chr6:59593614-59593620 Template switch process: F1: L AATTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA 1 F3: 4 GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT R RF: AATTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAACTAGGGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT RR: TTAAGAAACAATGGATATTCGTTTCTGAGATTAAGTCCTAATTGATCCCAGAGGAAAGAACTCTGGATAAGGTTTAGTCCTAGACGAA F2: 3 ATCCCAG 2 Unidirectional alignment (log-probability: -30) TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAgaccctA-----GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA------ACTAGGGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Template switch alignment (log-probability: -16.2) TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|GACCCTA|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|GACCCTA|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Human > Chimp ------------- chr6:60591204-60591209 Template switch process: F1: L AATTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA 1 F3: 4 GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT R RF: AATTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAGACCCTAGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT RR: TTAAGAAACAATGGATATTCGTTTCTGAGATTAAGTCCTAATCTGGGATCAGAGGAAAGAACTCTGGATAAGGTTTAGTCCTAGACGAA F2: 3 GGATCA 2 Unidirectional alignment (log-probability: -28.7) TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAactagG------GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA-----GACCCTAGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Template switch alignment (log-probability: -16) TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|ACTAGG|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|ACTAGG|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Gorilla > Human --------------- chr6:59593614-59593620 Template switch process: F1: L AATTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA 1 F3: 4 GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT R RF: AATTATTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAACTAGGGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT RR: TTAATAAACAATGGATATTCGTTTCTGAGATTAAGTCCTAATTGATCCCAGAGGAAAGAACTCTGGATAAGGTTTAGTCCTAGACGAA F2: 3 ATCCCAG 2 Unidirectional alignment (log-probability: -35.1) TTcTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA-----GaccctaGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTATTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAACTAGG------GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Template switch alignment (log-probability: -22.2) TTcTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|GACCCTA|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTATTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|GACCCTA|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Human > Gorilla --------------- chr6:59846068-59846073 Template switch process: F1: L AATTATTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA 1 F3: 4 GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT R RF: AATTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAGACCCTAGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT RR: TTAAGAAACAATGGATATTCGTTTCTGAGATTAAGTCCTAATCTGGGATCAGAGGAAAGAACTCTGGATAAGGTTTAGTCCTAGACGAA F2: 3 GGATCA 2 Unidirectional alignment (log-probability: -33.7) TTaTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA------ActaggGTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTAGACCCTA-----GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT Template switch alignment (log-probability: -22) TTaTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|ACTAGG|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT TTCTTTGTTACCTATAAGCAAAGACTCTAATTCAGGATTA|ACTAGG|GTCTCCTTTCTTGAGACCTATTCCAAATCAGGATCTGCTT ========== Event 3034 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGAACTGAATACTGCCATAA--AGGGCCAACGACTCTCTTCGAGACATCAGAAGGCACAGTCTACATAGCCAC Chimp: AAGAACTGAATACTGCCATAA--AGGGCCAACGACTCTCTTCGAGACATCAGAAGGCACGGTCTATATAGCCAC ↓ 1 4 3 2 Gorilla: AAGAACTGAATACTGCCATAA----TACTGATGTCTCTCTTCGAGACATCAGAAGGCACGGTCTACATAGCCAC Human: AAGAACTGAATACTGCCATAA--AGGGCCAACGACTCTCTTCGAGACATCAGAAGGCACAGTCTACATAGCCAC Cluster: [ ] Orangutan: AAGAACTGAATACCGCCATAAAG--GGCCGATGACTCTCTTCGAGACATCAGAAGGCACAGTCTGCATAGCCAC Chimp > Gorilla --------------- chr6:59343006-59343014 Template switch process: F1: L ATATGCCACCTTTCAACAGCAAGAACTGAATACTGCCATAA 1 F3: 4 CTCTCTTCGAGACATCAGAAGGCACGGTCTACATAGCCAC R RF: ATATGCCACCTTTCAACAGCAAGAACTGAATACTGCCATAAAGGGCCAACGACTCTCTTCGAGACATCAGAAGGCACGGTCTATATAGCCAC RR: TATACGGTGGAAAGTTGTCGTTCTTGACTTATGACGGTATTTCCCGGTTGCTGAGAGAAGCTCTGTAGTCTTCCGTGCCAGATATATCGGTG F2: 3 TGTAGTCAT 2 Unidirectional alignment (log-probability: -39.6) TATGCCACCTTTCAACAGCAAGAACTGAATACTGCCATA-----------AtactgatgtCTCTCTTCGAGACATCAGAAGGCACGGTCTAcATAGCCAC TATGCCACCTTTCAACAGCAAGAACTGAATACTGCCATAAAGGGCCAACGA---------CTCTCTTCGAGACATCAGAAGGCACGGTCTATATAGCCAC Template switch alignment (log-probability: -27.9) TATGCCACCTTTCAACAGCAAGAACTGAATACTGCCATAA|TaCTGATGT|CTCTCTTCGAGACATCAGAAGGCACGGTCTAcATAGCCAC TATGCCACCTTTCAACAGCAAGAACTGAATACTGCCATAA|TTCTGATGT|CTCTCTTCGAGACATCAGAAGGCACGGTCTATATAGCCAC ========== Event 3035 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGAGCCACCATATTGATTA-GTGTG-TCTCACATCTCTTTTTctttaaaggata ↓ 1 3 4 2 Chimp: AGAGAGCCACCATATTGATTAGATGTGAGACCACATCTCTTTTTctttaaaggata ↑ 1 3 4 2 Gorilla: AGAGAGCCACCATATTGATTA-GTGTG-TCTCACATCTCTTTTTctttaaaggata Human: AGAGAGCCACCATATTGATTA-GTGTG-TCTCACATCTCTTTTTctttaaaggata Cluster: [ ] Orangutan: AGAGAGCCACCATATTGATT--ATGTG-TCTCACATCTCTTTTTCTTTAAAGGAAA Human > Chimp ------------- chr6:60246735-60246743 Template switch process: F1: L GAGCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAG 1 F3: 4 CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA R RF: GAGCAAACACTGAGACTGAAAGAGAGCCACCATATTGATTAGTGTGTCTCACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA RR: CTCGTTTGTGACTCTGACTTTCTCTCGGTGGTATAACTAATCACACAGAGTGTAGAGAAAAAGAAATTTCCTATTTTCAAGAGAACTTT F2: 3 CAGAGTGTA 2 Unidirectional alignment (log-probability: -40.4) GCAAACAtTGAGACTGAAAGAGAGCCACCATATTGATTAG-------atgtgagacCACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA GCAAACACTGAGACTGAAAGAGAGCCACCATATTGATTAGTGTGTCT---------CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA Template switch alignment (log-probability: -22.4) GCAAACAtTGAGACTGAAAGAGAGCCACCATATTGATTAG|ATGTGAGAC|CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA GCAAACACTGAGACTGAAAGAGAGCCACCATATTGATTAG|ATGTGAGAC|CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA Gorilla > Chimp --------------- chr6:60246735-60246743 Template switch process: F1: L GAGCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAG 1 F3: 4 CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA R RF: GAGCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAGTGTGTCTCACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA RR: CTCGTTTGTAACTCTGACTTTCTCTCGGTGGTATAACTAATCACACAGAGTGTAGAGAAAAAGAAATTTCCTATTTTCAAGAGAACTTT F2: 3 CAGAGTGTA 2 Unidirectional alignment (log-probability: -33.9) GCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAG-------atgtgagacCACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA GCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAGTGTGTCT---------CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA Template switch alignment (log-probability: -16.9) GCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAG|ATGTGAGAC|CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA GCAAACATTGAGACTGAAAGAGAGCCACCATATTGATTAG|ATGTGAGAC|CACATCTCTTTTTCTTTAAAGGATAAAAGTTCTCTTGAAA ========== Event 3036 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: tctcTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACACACATGCTCCCCTTCTAGATTTCTAAC Chimp: tctcTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACACACATGCTCCCCTTCTAGGTTTCTAAC ↓ 3 2 1 4 Gorilla: tctcTGCAGAACCCTGACGAATTCACTGAGCAAACTCTC------AGTGAATTCACATGTTCCCCTTCTAGATTTCTAAC ↑ 3 2 1 4 Human: tctcTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACACACATGCTCCCCTTCTAGATTTCTAAC Cluster: [ ] Orangutan: -------------------------------------------------------------------------------- Human > Gorilla --------------- chr6:59449107-59449115 Template switch process: F1: L CTCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT 1 F3: 4 CACATGTTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGACTGACCC R RF: CTCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACACACATGCTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGACTGACCC RR: GAGAGAGACGTCTTGGGACTGCTTAAGTGACTCGTTTGAGATCCTAGACCGTTTGTGTGTACGAGGGGAAGATCTAAAGATTGTTCTCTCTCTTCTGACTGGG F2: 3 TTAAGTGAC 2 Unidirectional alignment (log-probability: -37) TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT-------------CAgtgaattCACATGtTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGA TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACA-------CACATGCTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGA Template switch alignment (log-probability: -22.6) TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT|CAGTGAATT|CACATGtTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGA TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT|CAGTGAATT|CACATGCTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGA Chimp > Gorilla --------------- chr6:59449107-59449115 Template switch process: F1: L CTCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT 1 F3: 4 CACATGTTCCCCTTCTAGATTTCTAACAAGAGAGAGAAGACTGACCC R RF: CTCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACACACATGCTCCCCTTCTAGGTTTCTAACAAGAGAGAGAAGACTGACCC RR: GAGAGAGACGTCTTGGGACTGCTTAAGTGACTCGTTTGAGATCCTAGACCGTTTGTGTGTACGAGGGGAAGATCCAAAGATTGTTCTCTCTCTTCTGACTGGG F2: 3 TTAAGTGAC 2 Unidirectional alignment (log-probability: -42.5) TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT-------------CAgtgaattCACATGtTCCCCTTCTAGaTTTCTAACAAGAGAGAGAAGA TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCTAGGATCTGGCAAACA-------CACATGCTCCCCTTCTAGGTTTCTAACAAGAGAGAGAAGA Template switch alignment (log-probability: -28.1) TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT|CAGTGAATT|CACATGtTCCCCTTCTAGaTTTCTAACAAGAGAGAGAAGA TCTCTCTGCAGAACCCTGACGAATTCACTGAGCAAACTCT|CAGTGAATT|CACATGCTCCCCTTCTAGGTTTCTAACAAGAGAGAGAAGA ========== Event 3037 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGCTCTCTGCCACCTATTGCCCAAT--CTAGCCAGGAGACTGTTTCCCGATTAATGTTGACAAATCATGATT Chimp: GGCTCTCTGCCACCTATTGCCCAAT--CTAGCCAGGAGACTGTTCCCCGATTAATGTTGACAAATCATGATT Gorilla: GGCTCTCTGCCACCTATTGCC-AATAGGGAAACAGGAGACTGTTTCCCGATTAATGTTGACAAATCACGATT ↑ 1 4 3 2 Human: GGCTCTCTGCCACCTATTGCCCAAT--CTAGCCAGGAGACTGTTTCCCGATTAATGTTGACAAATCATGATT Cluster: [ ] Orangutan: GGCTCTCTGCTGCCTATTGCCCAAT--CTAGCCAGGAGACTGTTTCCCGATTAATGTTGACAAATCATGATT Human > Gorilla --------------- chr6:114488375-114488385 Template switch process: F1: L CATGGGTTATCCTGATTCCAGGCTCTCTGCCACCTATTGCC 1 F3: 4 AGGAGACTGTTTCCCGATTAATGTTGACAAATCACGATT R RF: CATGGGTTATCCTGATTCCAGGCTCTCTGCCACCTATTGCCCAATCTAGCCAGGAGACTGTTTCCCGATTAATGTTGACAAATCATGATT RR: GTACCCAATAGGACTAAGGTCCGAGAGACGGTGGATAACGGGTTAGATCGGTCCTCTGACAAAGGGCTAATTACAACTGTTTAGTACTAA F2: 3 CAAAGGGATAA 2 Unidirectional alignment (log-probability: -41) ATGGGTTATCCTGATTCCAGGCTCTCTGCCACCTATTGC---------CaatagggaaaCAGGAGACTGTTTCCCGATTAATGTTGACAAATCAcGATT ATGGGTTATCCTGATTCCAGGCTCTCTGCCACCTATTGCCCAATCTAGC----------CAGGAGACTGTTTCCCGATTAATGTTGACAAATCATGATT Template switch alignment (log-probability: -28.1) ATGGGTTATCCTGATTCCAGGCTCTCTGCCACCTATTGCC|AATaGGGAAAC|AGGAGACTGTTTCCCGATTAATGTTGACAAATCAcGATT ATGGGTTATCCTGATTCCAGGCTCTCTGCCACCTATTGCC|AATCGGGAAAC|AGGAGACTGTTTCCCGATTAATGTTGACAAATCATGATT ========== Event 3038 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGATGTAAGAAGAAATCTACATATAGC----------------------CCATAATAGGGCTATATGTAGCCCATAAAACGGGCTGACTCCTTCATGAT Chimp: AGATGTAAGAAGAAATctacatatagc----------------------ccataatagggctatatgtagcccataaaacgggctGACTCCTTCATGAT Gorilla: AAATGTAAGAAGAAATCTACATATAGC--------------------------------------------CCATAAAACGGGCTGACTCCTTCATGAT ↓ 3 4 2 1 Human: AGATGTAAGAAGAAATCTACATATAGC----------------------CCATAATAGGGCTATATGTAGCCCATAAAACGGGCTGACTCCTTCATGAT Cluster: [ ] Orangutan: agatgtaagaagaaatCTACATATAGCCCATAATAGGGCTATATGTAGC----------------------CCATAAAACGGGCTGACTCCTTCGTGAT Gorilla > Human --------------- chr6:57234546-57234555 Template switch process: F1: L AGTGTTTATCAGTAAGATGTAAGAAGAAATCTACATATAGCCCATAATA 1 F3: 4 TAGCCCATAAAACGGGCTGACTCCTTCATGATGTCTGTTGCCCT R RF: AGTGTTTATCAGTAAAATGTAAGAAGAAATCTACATATAGCCCATAAAACGGGCTGACTCCTTCATGATGTCTGTTGCCCT RR: TCACAAATAGTCATTTTACATTCTTCTTTAGATGTATATCGGGTATTTTGCCCGACTGAGGAAGTACTACAGACAACGGGA F2: 3 GTATATCGGG 2 Unidirectional alignment (log-probability: -48) CAGTAAgATGTAAGAAGAAATCTACATAtagcccataatagggctatatgTAGCCCATAAAACGGGCTGACTCCTTCATGATGTCTGTTG CAGTAAAATGTAAGAAGAAATCTACATA----------------------TAGCCCATAAAACGGGCTGACTCCTTCATGATGTCTGTTG Template switch alignment (log-probability: -28.3) CAGTAAgATGTAAGAAGAAATCTACATATAGCCCATAAtA|GGGCTATATG|TAGCCCATAAAACGGGCTGACTCCTTCATGATGTCTGTTG CAGTAAAATGTAAGAAGAAATCTACATATAGCCCATAAAA|GGGCTATATG|TAGCCCATAAAACGGGCTGACTCCTTCATGATGTCTGTTG ========== Event 3039 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTGGAATCTTTGTCTTCTATCT-AGTCAGTAAGGGACTATTTGAAGTGCATGGGTATTAGCCTGTGTTTGTGTAGATGGACATTAATCTAGGGcactggttctgaactagggacaatttctccgccggggactctgggcaatgttcctagacatggctgtcacacagggc ↑ 1 4 3 2 Chimp: CTTGGAATCTTTGTCTTCTATGCATATCAGTAAGGGACTATTTGAAGTGCATGGGTATCAGCCTGTGTTTGTGTAGATGGACATTAATCTAGGGcattggttctgaactagggacaatttctctgccggggactctgggcaatgttcctagacatggctgtcacacagggc Gorilla: CTTAGAATCTTTATCTTCTATGCATATCAGTAAGGGACTATTTGAAGTGCATGGGTATCAGCCTGTGTTTGTGTAGATGGACATTAATCTAGGGcattggttctgaactagggacaatttctccgccggggactctgggcaatgttcctagacatggctgtcacacagggc Human: CTTGGAATCTTTGTCTTCTATCT-AGTCAGTAAGGGACTATTTGAAGTGCATGGGTATTAGCCTGTGTTTGTGTAGATGGACATTAATCTAGGGcactggttctgaactagggacaatttctccgccggggactctgggcaatgttcctagacatggctgtcacacagggc Cluster: [ ] Orangutan: CTTGGAATCTTTGTCTTCTATGCATATCAGTAAGGGACTATTTGAAGTGCATGGGTATCAGCCTGTGTTTGTGTAGATGGACATTAATCTAGGGcattggttctgaactaggaacaatttctcccccggggactctgggcaatgttcctagagacggctgtcacacagggc Chimp > Human ------------- chr6:114796149-114796152 Template switch process: F1: L TCATAAAGTTAATTTTACATCTTGGAATCTTTGTCTTCTAT 1 F3: 4 TCAGTAAGGGACTATTTGAAGTGCATGGGTATTAGCCTGT R RF: TCATAAAGTTAATTTTACATCTTGGAATCTTTGTCTTCTATGCATATCAGTAAGGGACTATTTGAAGTGCATGGGTATCAGCCTGTGTTTGTGTAGATGGACATTAATCTAGGGCATTGGTTCTGAACTAGGGACAATTTCTCTGCCGGGGACTCTGGGCAATGTTCCTAG RR: AGTATTTCAATTAAAATGTAGAACCTTAGAAACAGAAGATACGTATAGTCATTCCCTGATAAACTTCACGTACCCATAGTCGGACACAAACACATCTACCTGTAATTAGATCCCGTAACCAAGACTTGATCCCTGTTAAAGAGACGGCCCCTGAGACCCGTTACAAGGATC F2: 3 GATC 2 Unidirectional alignment (log-probability: -31.7) CATAAAGTTAATTTTACATCTTGGAATCTTTGTCTTCTATctaG----TCAGTAAGGGACTATTTGAAGTGCATGGGTATtAGCCTGT CATAAAGTTAATTTTACATCTTGGAATCTTTGTCTTCTAT---GCATATCAGTAAGGGACTATTTGAAGTGCATGGGTATCAGCCTGT Template switch alignment (log-probability: -21.8) CATAAAGTTAATTTTACATCTTGGAATCTTTGTCTTCTAT|CTAG|TCAGTAAGGGACTATTTGAAGTGCATGGGTATtAGCCTGT CATAAAGTTAATTTTACATCTTGGAATCTTTGTCTTCTAT|CTAG|TCAGTAAGGGACTATTTGAAGTGCATGGGTATCAGCCTGT ========== Event 3040 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGCTTCAATCAGTTTTATGTTCAT-ACACATGAAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTC Chimp: GTGCTTCAACCAGTTTTATGTTCAT-ACACATGAAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTC ↓ 1 4 3 2 Gorilla: GTGCTTCAACCAGTTTTATGTCCAGAAGACA-TAAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTG Human: GTGCTTCAATCAGTTTTATGTTCAT-ACACATGAAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTC Cluster: [ ] Orangutan: GTGCTTCAACCAGTTTTATGTCCAT-ACACATGAAAAGGTCTTCTGGTCAAATAAGAAAGTATGGTC Chimp > Gorilla --------------- chr6:116617577-116617587 Template switch process: F1: L TGGCTTTTGGAAGACATGCAGTGCTTCAACCAGTTTTATGT 1 F3: 4 AAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTGCTTCTG R RF: TGGCTTTTGGAAGACATGCAGTGCTTCAACCAGTTTTATGTTCATACACATGAAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTCCTTCTG RR: ACCGAAAACCTTCTGTACGTCACGAAGTTGGTCAAAATACAAGTATGTGTACTTTTCCAGAAGACCAGCTTATTCTTTCATACCAGGAAGAC F2: 3 TACAGAAGACC 2 Unidirectional alignment (log-probability: -41) GGCTTTTGGAAGACATGCAGTGCTTCAACCAGTTTTATGTccagaagacaT----------AAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTgCTTCTG GGCTTTTGGAAGACATGCAGTGCTTCAACCAGTTTTATGT----------TCATACACATGAAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTCCTTCTG Template switch alignment (log-probability: -28.2) GGCTTTTGGAAGACATGCAGTGCTTCAACCAGTTTTATGT|CCAGAAGACaT|AAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTgCTTCTG GGCTTTTGGAAGACATGCAGTGCTTCAACCAGTTTTATGT|CCAGAAGACCT|AAAAGGTCTTCTGGTCGAATAAGAAAGTATGGTCCTTCTG ========== Event 3041 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: aaaTATGAGGAGTTGTTATTGTCAACTAAGTGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGTGAC------AGATGGAAGAATTGCTTGGACA Chimp: -------AGGAGTTGTTATTGTCAACTAAATGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGTGAC------AGATGGAAGAATTGCTTGGACA ↑ 3 2 1 4 Gorilla: -------AGGAGTTATTATTGTCAACTAAGTGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGGAAGAATTAATGATGGAAGAATTGCTTGGACA ↓ 3 2 1 4 Human: aaaTATGAGGAGTTGTTATTGTCAACTAAGTGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGTGAC------AGATGGAAGAATTGCTTGGACA Cluster: [ ] Orangutan: -------aggtgttgttattgtCAACTAAGTGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGTGAC------AGATGGAAGAATTGCTTGGACA Gorilla > Human --------------- chr6:116430089-116430093 Template switch process: F1: L AACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG 1 F3: 4 GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT R RF: TGTCAACTAAGTGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGGAAGAATTAATGATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT RR: ACAGTTGATTCACGTTGTCAAGATCTTTCGATCGTAAAGACTCAATTTTCCAAAATATTGAACAATATCTGAATTAAAAGTCACCCCTCTAATTTTACCTTCTTAATTACTACCTTCTTAACGAACCTGTTTTAGTACATCGAGTAAAA F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -26.9) ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG----------TgacaGATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGGAAGAATTAAT----GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT Template switch alignment (log-probability: -16.4) ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG|TGACA|GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG|TGACA|GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT Gorilla > Chimp --------------- chr6:120054333-120054337 Template switch process: F1: L AACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG 1 F3: 4 GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT R RF: TGTCAACTAAGTGCAACAGTTCTAGAAAGCTAGCATTTCTGAGTTAAAAGGTTTTATAACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGGAAGAATTAATGATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT RR: ACAGTTGATTCACGTTGTCAAGATCTTTCGATCGTAAAGACTCAATTTTCCAAAATATTGAACAATATCTGAATTAAAAGTCACCCCTCTAATTTTACCTTCTTAATTACTACCTTCTTAACGAACCTGTTTTAGTACATCGAGTAAAA F2: 3 ACAGT 2 Unidirectional alignment (log-probability: -26.9) ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG----------TgacaGATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATGGAAGAATTAAT----GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT Template switch alignment (log-probability: -16.4) ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG|TGACA|GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT ACTTGTTATAGACTTAATTTTCAGTGGGGAGATTAAAATG|TGACA|GATGGAAGAATTGCTTGGACAAAATCATGTAGCTCATTTT ========== Event 3042 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TGAGAAACTGAAATATTCCCTGCCTCAATGACTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAAtttttttttAATCATTGAAATACTCAGAGCATAATAA ↑ 4 1 3 2 Chimp: TGAGAAACTGAAATATTCCCT------------GCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAAttttttttCAATCATTGAAatactcagagcataataa ↓ 4 1 3 2 Gorilla: TGAGAAACTGAAATATTCCCTGCCTCAATGACTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAAttttt-tttAATCATTGAAATACTCAGAGCATAATAA Human: TGAGAAACTGAAATATTCCCTGCCTCAATGACTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAAtttttttttAATCATTGAAATACTCAGAGCATAATAA Cluster: [ ] Orangutan: TGAGAAACTGAAATATTCCCTGCCTCAATGACTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAAttttttttAAATCACCGAAATACTCAAAGCATAATAA Chimp > Human ------------- chr6:116018689-116018694 Template switch process: F1: L TTATATACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCT 1 F3: 4 CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTAT R RF: TTATATACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAATTTTTTTTCAATCATTG RR: AATATATGTTTATACACAAAACTCTTTGACTTTATAAGGGACGGAATGATCATTCGTATAACGTTAATTTATTTTAAAATAAGGTCTTAAAATCACTATGTTTCTGTAAAGGTGGTACGAGAAACGGACCCTATTAAAAAAAAGTTAGTAAC F2: 3 AGTAAC 2 Unidirectional alignment (log-probability: -28.2) TACAAATATGTGTTTTGAGAAACTGAAATATTCCctgcctcaatgaCTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT TACAAATATGTGTTTTGAGAAACTGAAATATTCC------------CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT Template switch alignment (log-probability: -16.1) TACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCT|CAATGA|CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT TACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCT|CAATGA|CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT Chimp > Gorilla --------------- chr6:118265774-118265779 Template switch process: F1: L TTATATACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCT 1 F3: 4 CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTAT R RF: TTATATACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTTATTCCAGAATTTTAGTGATACAAAGACATTTCCACCATGCTCTTTGCCTGGGATAATTTTTTTTCAATCATTG RR: AATATATGTTTATACACAAAACTCTTTGACTTTATAAGGGACGGAATGATCATTCGTATAACGTTAATTTATTTTAAAATAAGGTCTTAAAATCACTATGTTTCTGTAAAGGTGGTACGAGAAACGGACCCTATTAAAAAAAAGTTAGTAAC F2: 3 AGTAAC 2 Unidirectional alignment (log-probability: -28.1) TACAAATATGTGTTTTGAGAAACTGAAATATTCCctgcctcaatgaCTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT TACAAATATGTGTTTTGAGAAACTGAAATATTCC------------CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT Template switch alignment (log-probability: -16.6) TACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCT|CAATGA|CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT TACAAATATGTGTTTTGAGAAACTGAAATATTCCCTGCCT|CAATGA|CTGCCTTACTAGTAAGCATATTGCAATTAAATAAAATTTT ========== Event 3043 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCTTGTTTTGTACTGTTTCATGTTTGCATCCAAACATGATTTGCTACCTGTGGGTCTCC Chimp: CTCTTGTTTTGTACTGTTTCATGTTTGGAC-GATATTCTATTTGCTACCTGTGGGTCTCC Gorilla: CTCTTGTTTTGTACTGTTTCATGTTTGGAT-GATATTCTATTTGCTACCTGTGGGTCTCC ↓ 3 1 2 4 Human: CTCTTGTTTTGTACTGTTTCATGTTTGCATCCAAACATGATTTGCTACCTGTGGGTCTCC Cluster: [ ] Orangutan: CTCTTGTTTTGTACTGTTTCATGTTTGGAT-GATATTCTATTTGCTACCTGTGGGTCT-C Gorilla > Human --------------- chr6:115848197-115848208 Template switch process: F1: L CATTTGCATGGAGACTCTTGTTTTGTACTGTTTCATGTTTG 1 F3: 4 ATTTGCTACCTGTGGGTCTCCCTGATGCACAGAAAAAAAA R RF: CATTTGCATGGAGACTCTTGTTTTGTACTGTTTCATGTTTGGATGATATTCTATTTGCTACCTGTGGGTCTCCCTGATGCACAGAAAAAAAA RR: GTAAACGTACCTCTGAGAACAAAACATGACAAAGTACAAACCTACTATAAGATAAACGATGGACACCCAGAGGGACTACGTGTCTTTTTTTT F2: 3 GTACAAACCTAC 2 Unidirectional alignment (log-probability: -45.1) ATTTGCATGGAGACTCTTGTTTTGTACTGTTTCATGTTTGcatccaaacatG----------ATTTGCTACCTGTGGGTCTCCCTGATGCACAGAAAAAAAa ATTTGCATGGAGACTCTTGTTTTGTACTGTTTCATGTTTG-----------GATGATATTCTATTTGCTACCTGTGGGTCTCCCTGATGCACAGAAAAAAA- Template switch alignment (log-probability: -17.3) ATTTGCATGGAGACTCTTGTTTTGTACTGTTTCATGTTTG|CATCCAAACATG|ATTTGCTACCTGTGGGTCTCCCTGATGCACAGAAAAAAAA ATTTGCATGGAGACTCTTGTTTTGTACTGTTTCATGTTTG|CATCCAAACATG|ATTTGCTACCTGTGGGTCTCCCTGATGCACAGAAAAAAAA ========== Event 3044 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: gctgactttccaggagatgactgactttccaggaAGGCCATAAAAAGTCAGTCTATCTTTTGGGTTGTTGGTG ↑ 3 2 1 4 Chimp: gctgactttccaggagatgactgactttccaggaAGGCCATA-------AGACTATCTTTTGGGTTGTTGGTG Gorilla: gctgactttccaggagatgactgactttccaggaAGGCCATA-------AGACTATCTTTTGGGCTGTTGGTG ↓ 3 2 1 4 Human: gctgactttccaggagatgactgactttccaggaAGGCCATAAAAAGTCAGTCTATCTTTTGGGTTGTTGGTG Cluster: [ ] Orangutan: gctgactttccaggagatgactgattttccaggaAGGCCATA-------AGACTATCTTTTGGGTTGTTGGTG Chimp > Human ------------- chr6:118139586-118139594 Template switch process: F1: L CTGACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAA 1 F3: 4 CTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA R RF: CTGACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAAGACTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA RR: GACTGAAAGGTCCTCTACTGACTGAAAGGTCCTTCCGGTATTCTGATAGAAAACCCAACAACCACCGGTACTTAGTCTAATTAT F2: 3 TGACTGAAA 2 Unidirectional alignment (log-probability: -27) GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAaaaagtcAGtCTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATA-------AGACTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA Template switch alignment (log-probability: -16.4) GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAA|AAAGTCAGT|CTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAA|AAAGTCAGT|CTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA Gorilla > Human --------------- chr6:118139586-118139594 Template switch process: F1: L CTGACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAA 1 F3: 4 CTATCTTTTGGGTTGTTGGTGGCCATGAATCAGATTAATA R RF: CTGACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAAGACTATCTTTTGGGCTGTTGGTGGCCATGAATCAGATTAATA RR: GACTGAAAGGTCCTCTACTGACTGAAAGGTCCTTCCGGTATTCTGATAGAAAACCCGACAACCACCGGTACTTAGTCTAATTAT F2: 3 TGACTGAAA 2 Unidirectional alignment (log-probability: -32) GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAaaaagtcAGtCTATCTTTTGGGtTGTTGGTGGCCATGAATCAGATTAATA GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATA-------AGACTATCTTTTGGGCTGTTGGTGGCCATGAATCAGATTAATA Template switch alignment (log-probability: -22.4) GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAA|AAAGTCAGT|CTATCTTTTGGGtTGTTGGTGGCCATGAATCAGATTAATA GACTTTCCAGGAGATGACTGACTTTCCAGGAAGGCCATAA|AAAGTCAGT|CTATCTTTTGGGCTGTTGGTGGCCATGAATCAGATTAATA ========== Event 3045 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAGATCTGTCTTTTCCATTT-------TCTTAGACAAAGAATTTTTCTTTGCAAAATTACATGAC ↓ 1 4 2 Chimp: CAAGATCTGTCTTTTCCATTTCCAAAATTCTT-TGCAAATAATTTTTCTTTGCAAAATTACATGAC Gorilla: CAAGATCTGTCTTTTCTATTT-------TCTTAGACAAAGAATTTTTCTTTGCAAAATTACATGAC Human: CAAGATCTGTCTTTTCCATTT-------TCTTAGACAAAGAATTTTTCTTTGCAAAATTACATGAC Cluster: [ ] Orangutan: CAAGATCTGTCTTTTCCATTT-------TCTTAGACAAAGAATTTTTCTTTGCAAAATTACATGAC Human > Chimp ------------- chr6:122396007-122396017 Template switch process: F1: L TCAGCCACACCTGAAGCAAACAAGATCTGTCTTTTCCATTTCC 1 F3: 4 CAAATAATTTTTCTTTGCAAAATTACATGACTTATTTTTCTTAAG R RF: TCAGCCACACCTGAAGCAAACAAGATCTGTCTTTTCCATTTTCTTAGACAAAGAATTTTTCTTTGCAAAATTACATGACTTATTTTTCTTAAG RR: AGTCGGTGTGGACTTCGTTTGTTCTAGACAGAAAAGGTAAAAGAATCTGTTTCTTAAAAAGAAACGTTTTAATGTACTGAATAAAAAGAATTC F2: 3 GTTTCTTAAAA 2 Unidirectional alignment (log-probability: -43.3) GCCACACCTGAAGCAAACAAGATCTGTCTTTTCCATTtccaaaaTTCTTtG-CAAAtAATTTTTCTTTGCAAAATTACATGACTTATTTTTC GCCACACCTGAAGCAAACAAGATCTGTCTTTTCCATT-------TTCTTAGACAAAGAATTTTTCTTTGCAAAATTACATGACTTATTTTTC Template switch alignment (log-probability: -28.8) GCCACACCTGAAGCAAACAAGATCTGTCTTTTCCATTTcC|AAAATTCTTTG|CAAAtAATTTTTCTTTGCAAAATTACATGACTTATTTTTC GCCACACCTGAAGCAAACAAGATCTGTCTTTTCCATTTTC|AAAATTCTTTG|CAAAGAATTTTTCTTTGCAAAATTACATGACTTATTTTTC ========== Event 3046 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACCTCAATCTTGGCAGTTGTT------CTGTGCAGA-----TATAAGTAATGAAAATAGTG Chimp: ACCTCAATCTTGGCAGTTGTT---CTACTGTGCAGA-----TATAAGTAATGAAAATAGTG Gorilla: ACCTCAATCTTGGCAGTTGTTCTA---CTGCGCAGATATAATATAAGTAATGAAAATAGTG ↓ 1 3 2 4 Human: ACCTCAATCTTGGCAGTTGTT------CTGTGCAGA-----TATAAGTAATGAAAATAGTG Cluster: [ ] Orangutan: ACCTCAATCTTGGCAGTTGTTCCA---CTGCGCAGA-----TATAAGTAATGAAAATAGTG Gorilla > Human --------------- chr6:118653713-118653718 Template switch process: F1: L TTATCGTTGAACCTCAATAAACCTCAATCTTGGCAGTTGTTCT 1 F3: 4 ATATAAGTAATGAAAATAGTGACTCTGTGTA R RF: TTATCGTTGAACCTCAATAAACCTCAATCTTGGCAGTTGTTCTACTGCGCAGATATAATATAAGTAATGAAAATAGTGACTCTGTGTG RR: AATAGCAACTTGGAGTTATTTGGAGTTAGAACCGTCAACAAGATGACGCGTCTATATTATATTCATTACTTTTATCACTGAGACACAC F2: 3 GACGTG 2 Unidirectional alignment (log-probability: -39.3) TCGTTGAACCTCAATAAACCTCAATCTTGGCAGTTGTTCT---GtGCAG-----ATATAAGTAATGAAAATAGTGACTCTGTGTa--------- TCGTTGAACCTCAATAAACCTCAATCTTGGCAGTTGTTCTACTGCGCAGATATAATATAAGTAATGAAAATAGTGACTCTGTGTGTGTGTGTGT Template switch alignment (log-probability: -27.3) TCGTTGAACCTCAATAAACCTCAATCTTGGCAGTTGTTCT|GtGCAG|ATATAAGTAATGAAAATAGTGACTCTGTGTa TCGTTGAACCTCAATAAACCTCAATCTTGGCAGTTGTTCT|GCGCAG|ATATAAGTAATGAAAATAGTGACTCTGTGTG ========== Event 3047 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTAGGAAACAAAATAGTCTAAAGCCTTTGA---AAAAGTGAAACTGCTACTTATTTTCACTTG Chimp: TTCTAGGAAACAAAATAGTCTAAAGCCTTTGA---AAAAGTGAAACTGCTACTTATTTTCACTTG ↓ 3 2 1 4 Gorilla: TTCTAGGAAACAAAATAGTCTAAAGCCTTTGA------CTTTAGACTGCTACTTATTTTCACTTG ↑ 3 2 1 4 Human: TTCTAGGAAACAAAATAGTCTAAAGCCTTTGA---AAAAGTGAAACTGCTACTTATTTTCACTTG Cluster: [ ] Orangutan: TTCTAGGAAACAAAATAGTCTAAAGCCTTTGAAAA---AGTGAAACTGCTACTTATTTTCACTTG Human > Gorilla --------------- chr6:161021432-161021437 Template switch process: F1: L TAAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGA 1 F3: 4 ACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG R RF: TAAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGAAAAAGTGAAACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG RR: ATTTATATAAAGATCCTTTGTTTTATCAGATTTCGGAAACTTTTTCACTTTGACGATGAATAAAAGTGAACCCCCACCTTTTAAAAATAC F2: 3 GATTTC 2 Unidirectional alignment (log-probability: -29.7) AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTG---------ActttagACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGAAAAAGTGAA------ACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG Template switch alignment (log-probability: -16.5) AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGA|CTTTAG|ACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGA|CTTTAG|ACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG Chimp > Gorilla --------------- chr6:161021432-161021437 Template switch process: F1: L TAAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGA 1 F3: 4 ACTGCTACTTATTTTCACTTGGGGGTGGAAAATTTTTATG R RF: TAAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGAAAAAGTGAAACTGCTACTTATTTTCACTTGGGGATGGAAAATTTTTATG RR: ATTTATATAAAGATCCTTTGTTTTATCAGATTTCGGAAACTTTTTCACTTTGACGATGAATAAAAGTGAACCCCTACCTTTTAAAAATAC F2: 3 GATTTC 2 Unidirectional alignment (log-probability: -35.2) AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTG---------ActttagACTGCTACTTATTTTCACTTGGGGgTGGAAAATTTTTATG AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGAAAAAGTGAA------ACTGCTACTTATTTTCACTTGGGGATGGAAAATTTTTATG Template switch alignment (log-probability: -22) AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGA|CTTTAG|ACTGCTACTTATTTTCACTTGGGGgTGGAAAATTTTTATG AAATATATTTCTAGGAAACAAAATAGTCTAAAGCCTTTGA|CTTTAG|ACTGCTACTTATTTTCACTTGGGGATGGAAAATTTTTATG ========== Event 3048 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: atagtatttcaaacggTACAAACTGTGTACAGAAGTACACAGTTATCAAAAATGCACACACTT ↑ 1 4 3 2 Chimp: atagtatttcaaaCGGTACAAT----CACCAGAAGTACACAGTTATCAAAAATGCACACACTT Gorilla: atagtatttcaaaCGGTACAAT----CACCAGAAGTACACAGTTATCAAAAATGCACACACTT ↓ 1 4 3 2 Human: atagtatttcaaacggTACAAACTGTGTACAGAAGTACACAGTTATCAAAAATGCACACACTT Cluster: [ ] Orangutan: ATAGTATTTCAAACCGTACAAT----CATCAGAAGTACACAGTTATCAAAAATGCACACACTT Chimp > Human ------------- chr6:49397124-49397131 Template switch process: F1: L TTTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA 1 F3: 4 CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG R RF: TTTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAATCACCAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG RR: AAATATTTTGAACTATTTTTTATCATAAAGTTTGCCATGTTAGTGGTCTTCATGTGTCAATAGTTTTTACGTGTGTGAAGTGAAC F2: 3 ATGTGTCA 2 Unidirectional alignment (log-probability: -29.9) TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA--ACtgtgtaCAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAATCAC------CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG Template switch alignment (log-probability: -16.3) TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA|ACTGTGTA|CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA|ACTGTGTA|CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG Gorilla > Human --------------- chr6:49397124-49397131 Template switch process: F1: L TTTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA 1 F3: 4 CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG R RF: TTTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAATCACCAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG RR: AAATATTTTGAACTATTTTTTATCATAAAGTTTGCCATGTTAGTGGTCTTCATGTGTCAATAGTTTTTACGTGTGTGAAGTGAAC F2: 3 ATGTGTCA 2 Unidirectional alignment (log-probability: -29.4) TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA--ACtgtgtaCAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAATCAC------CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG Template switch alignment (log-probability: -16.7) TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA|ACTGTGTA|CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG TTATAAAACTTGATAAAAAATAGTATTTCAAACGGTACAA|ACTGTGTA|CAGAAGTACACAGTTATCAAAAATGCACACACTTCACTTG ========== Event 3049 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTGAAAGAAAATCTAATACGTGGAGCAAGA-------ATTGAAAGCAGAAAGTAGATGGGCCAAGA Chimp: TTTGAAAGAAAATCTAATACGTTGAGCAAGA-------ATTGAAAGCAGAAAGTAGATGGGCCAAGA Gorilla: TTTGAAAGAAAATCTAATACGTGGAGCAGAAAGCTCCACGTGAAAGCAGAAAGTAGATGGGCCAAGA ↑ 3 2 4 1 Human: TTTGAAAGAAAATCTAATACGTGGAGCAAGA-------ATTGAAAGCAGAAAGTAGATGGGCCAAGA Cluster: [ ] Orangutan: ------------------------------------------------------------------- Human > Gorilla --------------- chr6:123940187-123940192 Template switch process: F1: L AGTTGAAGATGCATTTGAAAGAAAATCTAATACGTGGAGCA------GAAAGC 1 F3: 4 TGAAAGCAGAAAGTAGATGGGCCAAGAAGACAGGTGGGGG R RF: AGTTGAAGATGCATTTGAAAGAAAATCTAATACGTGGAGCAAGAATTGAAAGCAGAAAGTAGATGGGCCAAGAAGACAGGTGGGGG RR: TCAACTTCTACGTAAACTTTCTTTTAGATTATGCACCTCGTTCTTAACTTTCGTCTTTCATCTACCCGGTTCTTCTGTCCACCCCC F2: 3 GCACCT 2 Unidirectional alignment (log-probability: -37.6) GATGCATTTGAAAGAAAATCTAATACGTGGAGCAgaAAgctccacgTGAAAGCAGAAAGTAGATGGGCCAAGAAGACAGGTGGGGG GATGCATTTGAAAGAAAATCTAATACGTGGAGCAAGAA-------TTGAAAGCAGAAAGTAGATGGGCCAAGAAGACAGGTGGGGG Template switch alignment (log-probability: -26.7) GATGCATTTGAAAGAAAATCTAATACGTGGAGCA------GAAAGC|TCCACG|TGAAAGCAGAAAGTAGATGGGCCAAGAAGACAGGTGGGGG GATGCATTTGAAAGAAAATCTAATACGTGGAGCAAGAATTGAAAGC|TCCACG|TGAAAGCAGAAAGTAGATGGGCCAAGAAGACAGGTGGGGG ========== Event 3050 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: --TTTTTAGGTAATTTTTTAGGTGTGACATTTACTGATCTCTTTGAGTAAATGCAACT ↓ 1 4 3 2 Chimp: TCTTTTTAGGTAATTTTTTAGAT--CAGATTTACTGATCTCTTTGAGTAAAAGCAACT Gorilla: --TTTGTAGGTAATTTTTTAGGTGTGACATTTACTGACCTCTTTGAGTAAATGCAACT Human: --TTTTTAGGTAATTTTTTAGGTGTGACATTTACTGATCTCTTTGAGTAAATGCAACT Cluster: [ ] Orangutan: --TTTTTAGGTAATTTTTTAGGTGTAACATTTACTAATCCCTTTGAGTAAATGCAACT Human > Chimp ------------- chr6:127201046-127201050 Template switch process: F1: L AAATCTGACCACATATAATCTTTTTAGGTAATTTTTTAG 1 F3: 4 ATTTACTGATCTCTTTGAGTAAAAGCAACTTTATTCTTAT R RF: AAATCTGACCACATATAATCTTTTTAGGTAATTTTTTAGGTGTGACATTTACTGATCTCTTTGAGTAAATGCAACTTTATTCTTAT RR: TTTAGACTGGTGTATATTAGAAAAATCCATTAAAAAATCCACACTGTAAATGACTAGAGAAACTCATTTACGTTGAAATAAGAATA F2: 3 GACTA 2 Unidirectional alignment (log-probability: -33.2) AAATCTGACCACATATAATCTTTTTAGGTAATTTTTTAGatcaG------ATTTACTGATCTCTTTGAGTAAAaGCAACTTTATTCTTAT AAATCTGACCACATATAATCTTTTTAGGTAATTTTTTAG----GTGTGACATTTACTGATCTCTTTGAGTAAATGCAACTTTATTCTTAT Template switch alignment (log-probability: -21.9) AAATCTGACCACATATAATCTTTTTAGGTAATTTTTTAG|ATCAG|ATTTACTGATCTCTTTGAGTAAAaGCAACTTTATTCTTAT AAATCTGACCACATATAATCTTTTTAGGTAATTTTTTAG|ATCAG|ATTTACTGATCTCTTTGAGTAAATGCAACTTTATTCTTAT ========== Event 3051 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TAATATCAGTAATATCAAAACAGTATATTACTGTTTTACCAATACAGTAATATACTGTAATATCAAAAAGAAAAAA ↑ 1 3 4 2 Chimp: TAATATCAGTAATATCAAAACTG----------TATTGGTAAAACAGTAATATACTGTAATATCaaaaagaaaaaa Gorilla: TAATATCAGCAATATCAAAACAGTATATTACTGTTTTACCAATATAGTAATATACTGTAATATCaaaaagaaaaaa Human: TAATATCAGTAATATCAAAACAGTATATTACTGTTTTACCAATACAGTAATATACTGTAATATCAAAAAGAAAAAA Cluster: [ ] Orangutan: TAATATCAGTGATATCAAAACAGTATATTACTGTTTTACCAATACAGTAATATACTGTAATATCAAAAAGAAAAAA Chimp > Human ------------- chr6:123984475-123984496 Template switch process: F1: L TGTAGCACTGACCAATACTGTAATATCAGTAATATCAAAAC 1 F3: 4 ACAGTAATATACTGTAATATCAAAAAGAAAAAAGATATAG R RF: TATAGCACTGACCAATACTGTAATATCAGTAATATCAAAACTGTATTGGTAAAACAGTAATATACTGTAATATCAAAAAGAAAAAAGATATAG RR: ATATCGTGACTGGTTATGACATTATAGTCATTATAGTTTTGACATAACCATTTTGTCATTATATGACATTATAGTTTTTCTTTTTTCTATATC F2: 3 TAACCATTTTGTCATTATATGA 2 Unidirectional alignment (log-probability: -56.5) gTAGCACTGACCAATACTGTAATATCAGTAATATCAAAACaGTAT------AttactgttttaccaatACAGTAATATACTGTAATATCAAAAAGAAAAAAGATATAG ATAGCACTGACCAATACTGTAATATCAGTAATATCAAAACTGTATTGGTAAA----------------ACAGTAATATACTGTAATATCAAAAAGAAAAAAGATATAG Template switch alignment (log-probability: -24) gTAGCACTGACCAATACTGTAATATCAGTAATATCAAAAC|AGTATATTACTGTTTTACCAAT|ACAGTAATATACTGTAATATCAAAAAGAAAAAAGATATAG ATAGCACTGACCAATACTGTAATATCAGTAATATCAAAAC|AGTATATTACTGTTTTACCAAT|ACAGTAATATACTGTAATATCAAAAAGAAAAAAGATATAG ========== Event 3052 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: catttaggaactca-----tggacaattttaaaaaatacattaaccttttcccacagtgattgtgaagcataaaccagacatcatgctatttAACATTTAAACTGTCCAAAAGATAATATAtttttatga ↑ 3 2 1 4 Chimp: catttaggaactca-----tggacaattttAAAAAATACATTAACCTTTTCCCACAGTGATTGTGAAGCATAAACCAGACATCATGCTGTTTAACATTTAAACGGTCCGAAAGATAATATATTTTTATGA Gorilla: CATTTAGGAACTCA-----TGGACAATTTTAAAAAATACATTAACCTTTTCCCACAGTGATTGTGAAGCATAAACCAGACATCAAGCTGTTTAACATTTCAACGGTCCAAAAGATAATATATTTTTATGA Human: catttaggaactca-----tggacaattttaaaaaatacattaaccttttcccacagtgattgtgaagcataaaccagacatcatgctatttAACATTTAAACTGTCCAAAAGATAATATAtttttatga Cluster: [ ] Orangutan: CATTTAGGAACCCACATTTAGGACAATTTAAAAAAATATATT-ACCTTTTCCCACAGTGATTTTGAAGCATAAACCAGACATCATGCTATTTAACATTTAAACTGTCCGAAAGATAATATATTTTTATGA Chimp > Human ------------- chr6:125967299-125967304 Template switch process: F1: L GTGAAGCATAAACCAGACATCATGCTATTTAACATTTAAAC 1 F3: 4 AAAGATAATATATTTTTATGACTTTTTTTTTTTTTTTTTT R RF: TGGACAATTTTAAAAAATACATTAACCTTTTCCCACAGTGATTGTGAAGCATAAACCAGACATCATGCTGTTTAACATTTAAACGGTCCGAAAGATAATATATTTTTATGACTTTTTTTTTTTTTTTTTT RR: ACCTGTTAAAATTTTTTATGTAATTGGAAAAGGGTGTCACTAACACTTCGTATTTGGTCTGTAGTACGACAAATTGTAAATTTGCCAGGCTTTCTATTATATAAAAATACTGAAAAAAAAAAAAAAAAAA F2: 3 ACCTGT 2 Unidirectional alignment (log-probability: -31.7) TGAAGCATAAACCAGACATCATGCTaTTTAACATTTAAACtGTCCaAAAGATAATATATTTTTATGACTTTTTTTTTTTTTTtttt TGAAGCATAAACCAGACATCATGCTGTTTAACATTTAAACGGTCCGAAAGATAATATATTTTTATGACTTTTTTTTTTTTTT---- Template switch alignment (log-probability: -22) TGAAGCATAAACCAGACATCATGCTaTTTAACATTTAAAC|TGTCCA|AAAGATAATATATTTTTATGACTTTTTTTTTTTTTTTTTT TGAAGCATAAACCAGACATCATGCTGTTTAACATTTAAAC|TGTCCA|AAAGATAATATATTTTTATGACTTTTTTTTTTTTTTTTTT ========== Event 3053 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGAAGACTTACTTTTTGAGATGTCTTGGCAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAAC ↓ 1 4 3 2 Chimp: TTGAAGACTTACTTTTTGAGA-ATCT-TGAAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAAC ↑ 1 4 3 2 Gorilla: TTGAAGACTTACTTTTTGAGATGTCTTGGCAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAAC Human: TTGAAGACTTACTTTTTGAGATGTCTTGGCAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAAC Cluster: [ ] Orangutan: TTGAAGACTTACTTTTTGAGATGTTTTGGCAGAGTAGTCTTCCAGGTTCTCTGCAGGAAGCAAAAAC Human > Chimp ------------- chr6:129438477-129438483 Template switch process: F1: L TGAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA 1 F3: 4 AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC R RF: TGAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGATGTCTTGGCAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC RR: ACTTAAGTTACTTGTGAATCAACTTCTGAATGAAAAACTCTACAGAACCGTCTCATCAGAAGGTCTAAGAGATGTCCTTCGTTTTTGTTG F2: 3 AGTTCTA 2 Unidirectional alignment (log-probability: -31.7) GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAgaatcttGA---------AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGA-------GATGTCTTGGCAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC Template switch alignment (log-probability: -22.1) GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA|ATCTtGA|AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA|ATCTGGA|AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC Gorilla > Chimp --------------- chr6:129438477-129438483 Template switch process: F1: L TGAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA 1 F3: 4 AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC R RF: TGAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGATGTCTTGGCAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC RR: ACTTAAGTTACTTGTGAATCAACTTCTGAATGAAAAACTCTACAGAACCGTCTCATCAGAAGGTCTAAGAGATGTCCTTCGTTTTTGTTG F2: 3 AGTTCTA 2 Unidirectional alignment (log-probability: -31.2) GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA---------atcttgaAGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGATGTCTTGGC-------AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC Template switch alignment (log-probability: -22.1) GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA|ATCTtGA|AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC GAATTCAATGAACACTTAGTTGAAGACTTACTTTTTGAGA|ATCTGGA|AGAGTAGTCTTCCAGATTCTCTACAGGAAGCAAAAACAAC ========== Event 3054 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAAAATTTTgttaggaaagtatatatgtgtatacacacacacacac----acacacacaca Chimp: TTAAAATTTTGTTAGGAAAGT----ATGTGTATacacacacacacac------acacacaca ↑ 1 3 2 4 Gorilla: TTAAAATTTTGTTAGGAAAGTATATATGTGTATacacacacacacac--acacacacacaca Human: TTAAAATTTTgttaggaaagtatatatgtgtatacacacacacacac----acacacacaca Cluster: [ ] Orangutan: TTAAAATTTTGTTATGAAAGtatatatgtgtatatatatatatacacacacacatatatata Gorilla > Chimp --------------- chr6:128853133-128853140 Template switch process: F1: L ATCATGATAACTAAATGTATTTAAAATTTTGTTAGGAAAGTAT 1 F3: 4 ACACACACACACACACACACATATAT R RF: ATCATGATAACTAAATGTATTTAAAATTTTGTTAGGAAAGTATATATGTGTATACACACACACACACACACACACACACACATATAT RR: TAGTACTATTGATTTACATAAATTTTAAAACAATCCTTTCATATATACACATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATA F2: 3 CATATGTG 2 Unidirectional alignment (log-probability: -26.5) ATGATAACTAAATGTATTTAAAATTTTGTTAGGAAAGTAT----GTGTAT----ACACACACACACACACACACACAtATAT ATGATAACTAAATGTATTTAAAATTTTGTTAGGAAAGTATATATGTGTATACACACACACACACACACACACACACACATAT Template switch alignment (log-probability: -16.4) ATGATAACTAAATGTATTTAAAATTTTGTTAGGAAAGTAT|GTGTATAC|ACACACACACACACACACACATATAT ATGATAACTAAATGTATTTAAAATTTTGTTAGGAAAGTAT|GTGTATAC|ACACACACACACACACACACATATAT ========== Event 3055 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCCCACAATTATCTGGTTATTATTTGTAACCA----------------GGTAACTTGGCTAGACTTGTGGGTAGGTCAGCA Chimp: GTCCCACAATTATCTGGTTATTATTTGTAACCA----------------GGTAACTTGGCTAGACTTGTGGGTAGGTCAGCA ↓ 4 1 3 2 Gorilla: GTCCCACAATTATCTGGTTATTATTTGTAACTAGCCAAGTTACATTATTTGTAACTTGGCTAGACTTGTGGGTAGGTCAGCA ↑ 4 1 3 2 Human: GTCCCACAATTATCTGGTTATTATTTGTAACCA----------------GGTAACTTGGCTAGACTTGTGGGTAGGTCAGCA Cluster: [ ] Orangutan: GTCCCACAGTTATCTGGTTATTATTTGTAACCA----------------GGTAACTTGGCTAGACTTGTGGGTAGGTCAGCA Human > Gorilla --------------- chr6:127109011-127109022 Template switch process: F1: L CAGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAAC 1 F3: 4 ATTATTT--------GTAACTTGGCTAGACTTGTGGGTAGGTCAGCAGAGCTCAT R RF: CAGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAACCAGGTAACTTGGCTAGACTTGTGGGTAGGTCAGCAGAGCTCAT RR: GTCCTACTGTCAGGGTGTTAATAGACCAATAATAAACATTGGTCCATTGAACCGATCTGAACACCCATCCAGTCGTCTCGAGTA F2: 3 CATTGAACCGAT 2 Unidirectional alignment (log-probability: -39.5) AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAACtAGccaagttacattatttGTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAACCAG----------------GTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG Template switch alignment (log-probability: -27.6) AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAAC|TAGCCAAGTTAC|ATTATTT--------GTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAAC|TAGCCAAGTTAC|ATTATTTGTAACCAGGTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG Chimp > Gorilla --------------- chr6:127109011-127109022 Template switch process: F1: L CAGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAAC 1 F3: 4 ATTATTT--------GTAACTTGGCTAGACTTGTGGGTAGGTCAGCAGAGCTCAT R RF: CAGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAACCAGGTAACTTGGCTAGACTTGTGGGTAGGTCAGCAGAGCTCAT RR: GTCCTACTGTCAGGGTGTTAATAGACCAATAATAAACATTGGTCCATTGAACCGATCTGAACACCCATCCAGTCGTCTCGAGTA F2: 3 CATTGAACCGAT 2 Unidirectional alignment (log-probability: -39.5) AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAACtAGccaagttacattatttGTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAACCAG----------------GTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG Template switch alignment (log-probability: -27.6) AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAAC|TAGCCAAGTTAC|ATTATTT--------GTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG AGGATGACAGTCCCACAATTATCTGGTTATTATTTGTAAC|TAGCCAAGTTAC|ATTATTTGTAACCAGGTAACTTGGCTAGACTTGTGGGTAGGTCAGCAG ========== Event 3056 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAACCAAATTCCAATTGGAGTTGATTA--GTTCTGTTTTGGGCCTGATTTAGATGACATCATT Chimp: AGAACCAAATTCCCATTGGAGTTGCTTA--GTTCTGTTTTGGGCCTGATTTAGATGACATCATT Gorilla: AGAACCAAATTCCAATTGGAGTTGATGA----ACTAATCAACTCCTGATTTAGATGACATCATT ↑ 3 1 2 4 Human: AGAACCAAATTCCAATTGGAGTTGATTA--GTTCTGTTTTGGGCCTGATTTAGATGACATCATT Cluster: [ ] Orangutan: AGAACCAAATTCCAATTGGAGTTGATTAGT--TCTGTTTTGGGCCTGATTTAGATGAGATCATT Human > Gorilla --------------- chr6:44173533-44173545 Template switch process: F1: L TAAAATATTGGATTTAGAACCAAATTCCAATTGGAGTTGAT 1 F3: 4 CCTGATTTAGATGACATCATTTCATGTGTAGAAGTAGGGG R RF: TAAAAGATTGGATTTAGAACCAAATTCCAATTGGAGTTGATTAGTTCTGTTTTGGGCCTGATTTAGATGACATCATTTCATGTGTAGAAGTAGGGG RR: ATTTTCTAACCTAAATCTTGGTTTAAGGTTAACCTCAACTAATCAAGACAAAACCCGGACTAAATCTACTGTAGTAAAGTACACATCTTCATCCCC F2: 3 TCAACTAATCAAG 2 Unidirectional alignment (log-probability: -44.1) AAAAtATTGGATTTAGAACCAAATTCCAATTGGAGTTGAT--------------GaactaatcaactCCTGATTTAGATGACATCATTTCATGTGTAGAAGTAGGGG AAAAGATTGGATTTAGAACCAAATTCCAATTGGAGTTGATTAGTTCTGTTTTGGG------------CCTGATTTAGATGACATCATTTCATGTGTAGAAGTAGGGG Template switch alignment (log-probability: -22.9) AAAAtATTGGATTTAGAACCAAATTCCAATTGGAGTTGAT|GAACTAATCAACT|CCTGATTTAGATGACATCATTTCATGTGTAGAAGTAGGGG AAAAGATTGGATTTAGAACCAAATTCCAATTGGAGTTGAT|GAACTAATCAACT|CCTGATTTAGATGACATCATTTCATGTGTAGAAGTAGGGG ========== Event 3057 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTATTTTCTCATTAACTTCCTTATGACATAAAAGATG-AACTGATATTTGCCACCTGGTCTTTT Chimp: TTTCTTTTCTCATTAACTTCCTTATGACATAAAAGATC-AACTGATATTTGCCACCTGGTCTTTT Gorilla: TTTCTTTTCTCATTAACTTCCTTATGACATAAAAGATCATAAGGATATTTGCCACCTGGTCTTTT ↑ 3 2 1 4 Human: TTTATTTTCTCATTAACTTCCTTATGACATAAAAGATG-AACTGATATTTGCCACCTGGTCTTTT Cluster: [ ] Orangutan: TTTCTTTTCTCATTAACTTCATTATGAAATAAAAGATC-AACTGATATTTGCCACCTGGTCTTTT Human > Gorilla --------------- chr6:13557813-13557819 Template switch process: F1: L CTTATTTCTTTTCTCATTAACTTCCTTATGACATAAAAGAT 1 F3: 4 ATATTTGCCACCTGGTCTTTTGAAATGGAAGACCACTAG R RF: CTTATTTATTTTCTCATTAACTTCCTTATGACATAAAAGATGAACTGATATTTGCCACCTGGTCTTTTGAAATGGAAGACCACTAG RR: GAATAAATAAAAGAGTAATTGAAGGAATACTGTATTTTCTACTTGACTATAAACGGTGGACCAGAAAACTTTACCTTCTGGTGATC F2: 3 GGAATAC 2 Unidirectional alignment (log-probability: -33.6) TTATTTcTTTTCTCATTAACTTCCTTATGACATAAAAGATcataaG----GATATTTGCCACCTGGTCTTTTGAAATGGAAGACCACTAG TTATTTATTTTCTCATTAACTTCCTTATGACATAAAAGAT-----GAACTGATATTTGCCACCTGGTCTTTTGAAATGGAAGACCACTAG Template switch alignment (log-probability: -22.1) TTATTTcTTTTCTCATTAACTTCCTTATGACATAAAAGAT|CATAAGG|ATATTTGCCACCTGGTCTTTTGAAATGGAAGACCACTAG TTATTTATTTTCTCATTAACTTCCTTATGACATAAAAGAT|CATAAGG|ATATTTGCCACCTGGTCTTTTGAAATGGAAGACCACTAG ========== Event 3058 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCAGAGAAAATCATAGTCCGTGTGTATGTTCGAGTGTGAAAGTGTAACCTTCCCTTAAGCCTGAAAGTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATTACATGGTCCagaaagaa-aagaaag- Chimp: GCCAGAGAAAATCATAGTCCATGTGTATGTTTGAGTGTGAAAGTGTAACCTTCCCTTAAGCCTGAAAGTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATCACATGGTCCagaaagaa-aagaaag- ↑ 3 2 1 4 Gorilla: GCCAGAGAAAATCATAGTCCATGTGTACGTTCGAGTGTGAAAGTGTAACCTTCCCTTAAGCCTGAAAGTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATTACGAGGTCCagaaagaa-aagaaag- Human: GCCAGAGAAAATCATAGTCCGTGTGTATGTTCGAGTGTGAAAGTGTAACCTTCCCTTAAGCCTGAAAGTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATTACATGGTCCagaaagaa-aagaaag- Cluster: [ ] Orangutan: GCCAGAGAAAATCATAGTTCATGTGTATGTTCCAGTGTGAAAATATAACCTTCCCTTAAGCCTGAAAGTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATTACACGGTCCAGCAagaaagagagaga Gorilla > Chimp --------------- chr6:43757054-43757059 Template switch process: F1: L GTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTAT 1 F3: 4 GTCCAGAAAGAAAAGAAA------GAAAGAAAGAAAGAAAGAAAG R RF: CATGTGTACGTTCGAGTGTGAAAGTGTAACCTTCCCTTAAGCCTGAAAGTAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATTACGAGGTCCAGAAAGAAAAGAAAGAGAAGGAAAGAAAGAAAGAAAGAAAG RR: GTACACATGCAAGCTCACACTTTCACATTGGAAGGGAATTCGGACTTTCATCTCCCTTTGACCCATGATCACTTGTTATATTCTTGATAATGCTCCAGGTCTTTCTTTTCTTTCTCTTCCTTTCTTTCTTTCTTTCTTTC F2: 3 GTACAC 2 Unidirectional alignment (log-probability: -35.9) TAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATcACatGGTCCAGAAAGAAAAGAAAGaaAGAAaGAAAGAAAGAAAG TAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTATTACGAGGTCCAGAAAGAAAAGAAAG--AGAAGGAAAGAAAGAAAG Template switch alignment (log-probability: -26.5) TAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTAT|CACATG|GTCCAGAAAGAAAAGAAA------GAAAGAAAGAAAGAAAGAAAG TAGAGGGAAACTGGGTACTAGTGAACAATATAAGAACTAT|CACATG|GTCCAGAAAGAAAAGAAAGAGAAGGAAAGAAAGAAAGAAAGAAAG ========== Event 3059 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGGTTAGAATTACAGTATGA-------AACAGATATGTTTATCTGTTTCCACATAAACAGATACATAAT Chimp: ATGGTTAGAATTACAGTATGA-------AACAGATATGTTTATCTGTTTCCACATAAACAGATACATAAT ↓ 1 3 4 2 Gorilla: ATGGTTAGAATTACAGTATGAAACAGGAAACAGATAAACATATCTGTTTCCACATAAACAGATACATAAT ↑ 1 3 4 2 Human: ATGGTTAGAATTACAGTATGA-------AACAGATATGTTTATCTGTTTCCACATAAACAGATACATAAT Cluster: [ ] Orangutan: ATGGTTAGAATTACAGTATGAAACAGGAAACAGATAAACATATCTGTTTCCACATAAACAGATACATAAT Human > Gorilla --------------- chr6:130703665-130703678 Template switch process: F1: L AGAGTAATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG 1 F3: 4 TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG R RF: AGAGTAATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAGATATGTTTATCTGTTTCCACATAAACAGATACATAATTGTACATGTG RR: TCTCATTAATTCTTTCTGTATACCAATCTTAATGTCATACTTTGTCTATACAAATAGACAAAGGTGTATTTGTCTATGTATTAACATGTACAC F2: 3 ACAAATAGACAAAG 2 Unidirectional alignment (log-probability: -39.7) ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAGgaaacagataaacA------TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG-------------ATATGTTTATCTGTTTCCACATAAACAGATACATAATTGTACATGTG Template switch alignment (log-probability: -17.6) ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG|GAAACAGATAAACA|TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG|GAAACAGATAAACA|TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG Chimp > Gorilla --------------- chr6:130703665-130703678 Template switch process: F1: L AGAGTAATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG 1 F3: 4 TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG R RF: AGAGTAATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAGATATGTTTATCTGTTTCCACATAAACAGATACATAATTGTACATGTG RR: TCTCATTAATTCTTTCTGTATACCAATCTTAATGTCATACTTTGTCTATACAAATAGACAAAGGTGTATTTGTCTATGTATTAACATGTACAC F2: 3 ACAAATAGACAAAG 2 Unidirectional alignment (log-probability: -39.7) ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAGgaaacagataaacA------TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG-------------ATATGTTTATCTGTTTCCACATAAACAGATACATAATTGTACATGTG Template switch alignment (log-probability: -17.6) ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG|GAAACAGATAAACA|TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG ATTAAGAAAGACATATGGTTAGAATTACAGTATGAAACAG|GAAACAGATAAACA|TATCTGTTTCCACATAAACAGATACATAATTGTACATGTG ========== Event 3060 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TATAATTTATTTTTCATTCTGCAACTACCTCTAGTTGCAGATCACTGTACAGTCCAGATT ↑ 3 1 24 Chimp: TATAATTTATTTTTCATTCTGCAACTA--------GAGGGATCACTGTACAGTCCAGATT Gorilla: TATAATTTATTTTTCATTCTGCAACTA--------GAGGGATCACTGTACAGTCCAGATT ↓ 3 1 24 Human: TATAATTTATTTTTCATTCTGCAACTACCTCTAGTTGCAGATCACTGTACAGTCCAGATT Cluster: [ ] Orangutan: TATAA----CTTTTCATTCTGCAACTA--------GAGGGATCGCTGTACAGTCCAGATT Chimp > Human ------------- chr6:128352411-128352422 Template switch process: F1: L TAGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA 1 F3: 4 GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC R RF: TAGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTAGAGGGATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC RR: ATCAACGTGATAGGATATTAAATAAAAAGTAAGACGTTGATCTCCCTAGTGACATGTCAGGTCTAAACTAACGGAGAAGGAACCG F2: 3 ACGTTGATCTCC 2 Unidirectional alignment (log-probability: -38.6) AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA----cctctagttgcaGATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTAGAGG------------GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC Template switch alignment (log-probability: -16.8) AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA|CCTCTAGTTGCA|GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA|CCTCTAGTTGCA|GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC Gorilla > Human --------------- chr6:128352411-128352422 Template switch process: F1: L TAGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA 1 F3: 4 GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC R RF: TAGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTAGAGGGATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC RR: ATCAACGTGATAGGATATTAAATAAAAAGTAAGACGTTGATCTCCCTAGTGACATGTCAGGTCTAAACTAACGGAGAAGGAACCG F2: 3 ACGTTGATCTCC 2 Unidirectional alignment (log-probability: -38.1) AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA----cctctagttgcaGATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTAGAGG------------GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC Template switch alignment (log-probability: -17.3) AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA|CCTCTAGTTGCA|GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC AGTTGCACTATCCTATAATTTATTTTTCATTCTGCAACTA|CCTCTAGTTGCA|GATCACTGTACAGTCCAGATTTGATTGCCTCTTCCTTGGC ========== Event 3061 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGGCTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTAT-----------------------CTCTCTGAGTTGTCATACAAT ↓ 3 4 2 1 Chimp: TGGGCTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTGTTTAGAAGGACAATTAGAGAAATTGTCTCTGAGTTGTCATACAAT ↑ 3 4 2 1 Gorilla: TGGGCTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTAT-----------------------CTCTCTGAGTTGTCATACAAT Human: TGGGCTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTAT-----------------------CTCTCTGAGTTGTCATACAAT Cluster: [ ] Orangutan: TAGGCTTCTGTTTCCTTTTTCTCTAATTGTCCTTCTAAACTAATTAT-----------------------CTCTCTGAGTTGTCATACAAT Human > Chimp ------------- chr6:42023740-42023760 Template switch process: F1: L CTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT 1 F3: 4 AATTG-------------------TCTCTGAGTTGTCATACAATATTTTGATGAAAAATACAGA R RF: CTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTATCTCTCTGAGTTGTCATACAATATTTTGATGAAAAATACAGA RR: GAAGACAAAGAAAAAAGAGATTAACAGGAAGATTTGATTAATAGAGAGACTCAACAGTATGTTATAAAACTACTTTTTATGTCT F2: 3 AGAGATTAACAGGAAGATTTG 2 Unidirectional alignment (log-probability: -56) TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTgTttagaaggacaattagagaaattgTCTCTGAGTTGTCATACAATATTTTGATGAAAAAT TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTATC-----------------------TCTCTGAGTTGTCATACAATATTTTGATGAAAAAT Template switch alignment (log-probability: -29.2) TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT|GTTTAGAAGGACAATTAGAGA|AATTG-------------------TCTCTGAGTTGTCATACAATATTTTGATGAAAAAT TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT|GTTTAGAAGGACAATTAGAGA|AATTGTCCTTCTAAACTAATTATCTCTCTGAGTTGTCATACAATATTTTGATGAAAAAT Gorilla > Chimp --------------- chr6:42023740-42023760 Template switch process: F1: L CTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT 1 F3: 4 AATTG-------------------TCTCTGAGTTGTCATACAATATTTTGATGAAAAATACAGA R RF: CTTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTATCTCTCTGAGTTGTCATACAATATTTTGATGAAAAATACAGA RR: GAAGACAAAGAAAAAAGAGATTAACAGGAAGATTTGATTAATAGAGAGACTCAACAGTATGTTATAAAACTACTTTTTATGTCT F2: 3 AGAGATTAACAGGAAGATTTG 2 Unidirectional alignment (log-probability: -55) TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATTgtttagaaggacaattagagaaatTgTCTCTGAGTTGTCATACAATATTTTGATGAAAAAT TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT-----------------------ATCTCTCTGAGTTGTCATACAATATTTTGATGAAAAAT Template switch alignment (log-probability: -29.2) TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT|GTTTAGAAGGACAATTAGAGA|AATTG-------------------TCTCTGAGTTGTCATACAATATTTTGATGAAAAAT TTCTGTTTCTTTTTTCTCTAATTGTCCTTCTAAACTAATT|GTTTAGAAGGACAATTAGAGA|AATTGTCCTTCTAAACTAATTATCTCTCTGAGTTGTCATACAATATTTTGATGAAAAAT ========== Event 3062 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: -TAATGCCCTCATTGAAATTA--GGTCAATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAATGTCGTGAGCTCCCGGAATGGACTGCAAGCCAGGATGGTGACAGGCCCACTAGAGTGCGCCA ↑ 1 4 3 2 Chimp: -TAATGCCCTCATTGAAATTAGAAGGAGATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAATGTCATGAGCTCCCGGAATGGACTGCAAGCCAGGATGGTGACAGGCCCGCTAGAGTGCGCCA Gorilla: -TAATCCCC-TATTGAAATTA--GGTCAATGGAGAAGGGTCACCATCTCACTGAGCTCCCACAACAGTGTCATGAGCTCCCGGAATGGACTGCAAGCCAGGATGGTGACAGGCCCACTAGAGTGCGCCA Human: -TAATGCCCTCATTGAAATTA--GGTCAATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAATGTCGTGAGCTCCCGGAATGGACTGCAAGCCAGGATGGTGACAGGCCCACTAGAGTGCGCCA Cluster: [ ] Orangutan: TTAATGCCCTCATTGAAATTA--AGTCAATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAATGTCATGAGCTCCTGGAATGGACTGCAAGCCAGGATGGTGACGGGCCCACTAGAGTGCACCA Chimp > Human ------------- chr6:40082116-40082119 Template switch process: F1: L TAAATTGTGATTTTCCATTTTTAATGCCCTCATTGAAATTAG 1 F3: 4 ATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAAT R RF: TAAATTGTGATTTTCCATTTTTAATGCCCTCATTGAAATTAGAAGGAGATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAATGTCATGAGCTCCCGGAATGGACTGCAAGCCAGGATGGTGAC RR: ATTTAACACTAAAAGGTAAAAATTACGGGAGTAACTTTAATCTTCCTCTACCTCTTCCCAGTGGTAGAGTAACTCGAGGGTGTCGTTACAGTACTCGAGGGCCTTACCTGACGTTCGGTCCTACCACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -25.7) AATTGTGATTTTCCATTTTTAATGCCCTCATTGAAATTAGgtcA-----ATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAAT AATTGTGATTTTCCATTTTTAATGCCCTCATTGAAATTAG---AAGGAGATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAAT Template switch alignment (log-probability: -15.8) AATTGTGATTTTCCATTTTTAATGCCCTCATTGAAATTAG|GTCA|ATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAAT AATTGTGATTTTCCATTTTTAATGCCCTCATTGAAATTAG|GTCA|ATGGAGAAGGGTCACCATCTCATTGAGCTCCCACAGCAAT ========== Event 3063 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATCCACAGAGAAATCTCTCC-------AGCATCA---------GCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATGGTCCTTCAAGCCCAGTAGCA Chimp: AATCCACAGAGAAATCTCTCC-------AGCATCA---------GCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATGGTCCTTCAAGCCCAGTAGCA ↑ 1 4 3 2 Gorilla: AATCCACAGAGAAATCTCTCCAAATTTCTGCATTTGGCAGAAATCCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATGGTCCTTCAAGCCCAGTAGCA ↓ 1 4 3 2 Human: AATCCACAGAGAAATCTCTCC-------AGCATCA---------GCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATGGTCCTTCAAGCCCAGTAGCA Cluster: [ ] Orangutan: AATCTACAGAGAAATCTCTCC-------AGCATCA---------GCAGGTCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATGGTCCTTTAAGCCCAGTAGCA Gorilla > Human --------------- chr6:40346165-40346170 Template switch process: F1: L AGAACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAG 1 F3: 4 CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA R RF: AGAACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAAATTTCTGCATTTGGCAGAAATCCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATG RR: TCTTGACGTGCGTCTTACCTTTAGGTGTCTCTTTAGAGAGGTTTAAAGACGTAAACCGTCTTTAGGTCTAGACGGTTTACGTCACTACAAAGTCCTCACCGGAGTCTCCTCGACTAC F2: 3 GACTAC 2 Unidirectional alignment (log-probability: -31.3) ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCA-------GCAT----CAG-----CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAAATTTCTGCATTTGGCAGAAATCCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA Template switch alignment (log-probability: -22.1) ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAg|CATCAG|CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAA|CATCAG|CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA Gorilla > Chimp --------------- chr6:41019081-41019086 Template switch process: F1: L AGAACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAG 1 F3: 4 CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA R RF: AGAACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAAATTTCTGCATTTGGCAGAAATCCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCAGAGGAGCTGATG RR: TCTTGACGTGCGTCTTACCTTTAGGTGTCTCTTTAGAGAGGTTTAAAGACGTAAACCGTCTTTAGGTCTAGACGGTTTACGTCACTACAAAGTCCTCACCGGAGTCTCCTCGACTAC F2: 3 GACTAC 2 Unidirectional alignment (log-probability: -31.3) ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCA-------GCAT----CAG-----CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAAATTTCTGCATTTGGCAGAAATCCAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA Template switch alignment (log-probability: -22.1) ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAg|CATCAG|CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA ACTGCACGCAGAATGGAAATCCACAGAGAAATCTCTCCAA|CATCAG|CAGATCTGCCAAATGCAGTGATGTTTCAGGAGTGGCCTCA ========== Event 3064 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATCGAGCTGCACGTGTTTATGTACTCTTTATGTATGACTAACTGT---GATGATGAGGACAACAAACCTAAGGACTCACTGTCCTGTTGCTATAGGCCAATATCATAGTATAACAGTTAAAAAGCAAACTTGCCTCTA Chimp: AAATCGAGCTGCACGTGTTTAGGTACTCTTTATGTATG----ACTGT---GATGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGCTATAGGCCAATATCATAGTATAACAGTTAAAAAGCAAACTTGCCTCGA ↓ 1 4 3 2 Gorilla: AAATCGAGCTGCACGTGTTTATGTACTCTCTATGTATGACTAACTGT------GATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGCTATAGGCCAATATCATAGTATAACAGTTAAAAAGCAAACTTGCCTCTA Human: AAATCGAGCTGCACGTGTTTATGTACTCTTTATGTATGACTAACTGT---GATGATGAGGACAACAAACCTAAGGACTCACTGTCCTGTTGCTATAGGCCAATATCATAGTATAACAGTTAAAAAGCAAACTTGCCTCTA Cluster: [ ] Orangutan: AAATCGAGCTGCACGCGTTTATGTACTCTTTATGTATGACTAACTGTGAT---GATGAGGACAACAAACCAAAGGACTTACTGTCCTGTTACTATAGGCCAATATCATAGTATAACAGTTAAAAAGCAAACTTGCCTCTA Chimp > Gorilla --------------- chr6:40337381-40337385 Template switch process: F1: L AGCAACAGAGGCATTTAAAGAAATCGAGCTGCACGTGTTTATGTACTCTCTATGTATGACT 1 F3: 4 TGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGCT R RF: AGCAACAGAGGCATTTAAAGAAATCGAGCTGCACGTGTTTAGGTACTCTTTATGTATGACTGTGATGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGCTATAGGCCAATATCATAGTATAACAGTT RR: TCGTTGTCTCCGTAAATTTCTTTAGCTCGACGTGCACAAATCCATGAGAAATACATACTGACACTACTACTCCTGTTGTTTGGATTCCTGAATGACAGGACAACGATATCCGGTTATAGTATCATATTGTCAA F2: 3 GTCAA 2 Unidirectional alignment (log-probability: -37.9) AATCGAGCTGCACGTGTTTAtGTACTCTcTATGTATGactaACTG---TGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGC AATCGAGCTGCACGTGTTTAGGTACTCTTTATGTATG----ACTGTGATGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGC Template switch alignment (log-probability: -27.9) AATCGAGCTGCACGTGTTTAtGTACTCTcTATGTATGACT|AACTG|TGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGC AATCGAGCTGCACGTGTTTAGGTACTCTTTATGTATGACT|AACTG|TGATGAGGACAACAAACCTAAGGACTTACTGTCCTGTTGC ========== Event 3065 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: ATAACCCTAATAAAAGTCTCTACATGTTTTGGTTAGTTTT----------GAAGAAAAGACCCATCTCACCCAACC ↓ 13 24 ↑ 13 24 Chimp: ATAACCCTAATAAAAGTCTCTTCT-----TCAAAACTAAC-----CAAAACATGTAAAGACCCATCTCACCCAACC Gorilla: Human: ATAACCCTAATAAAAGTCTCTACATGTTTTGGTTAGTTTT----------GAAGAAAAGACCCATCTCACCCAACC Cluster: [ ] Orangutan: ATAACCCTAATAAAAGTCTCTTCT-----TCAAAACTAACCAAAA-----CATGTAAAGACCCATCTCACCCAACC Chimp > Human ------------- chr6:39656778-39656801 Template switch process: F1: L TAGTTATAACATTCTAAACTATAACCCTAATAAAAGTCTCT 1 F3: 4 AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT R RF: TAGTTATAATATTCTAAACTATAACCCTAATAAAAGTCTCTTCTTCAAAACTAACCAAAACATGTAAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT RR: ATCAATATTATAAGATTTGATATTGGGATTATTTTCAGAGAAGAAGTTTTGATTGGTTTTGTACATTTCTGGGTAGAGTGGGTTGGTCTGGTGTACGACGGATTA F2: 3 AGAAGTTTTGATTGGTTTTGTACA 2 Unidirectional alignment (log-probability: -54) AGTTATAAcATTCTAAACTATAACCCTAATAAAAGTCTCT------------------ACATGTtttggttagttttgaagaAAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT AGTTATAATATTCTAAACTATAACCCTAATAAAAGTCTCTTCTTCAAAACTAACCAAAACATGT------------------AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT Template switch alignment (log-probability: -24.2) AGTTATAAcATTCTAAACTATAACCCTAATAAAAGTCTCT|ACATGTTTTGGTTAGTTTTGAAGA|AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT AGTTATAATATTCTAAACTATAACCCTAATAAAAGTCTCT|ACATGTTTTGGTTAGTTTTGAAGA|AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT Human > Chimp ------------- chr6:40327544-40327567 Template switch process: F1: L TAGTTATAATATTCTAAACTATAACCCTAATAAAAGTCTCT 1 F3: 4 AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT R RF: TAGTTATAACATTCTAAACTATAACCCTAATAAAAGTCTCTACATGTTTTGGTTAGTTTTGAAGAAAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT RR: ATCAATATTGTAAGATTTGATATTGGGATTATTTTCAGAGATGTACAAAACCAATCAAAACTTCTTTTCTGGGTAGAGTGGGTTGGTCTGGTGTACGACGGATTA F2: 3 TGTACAAAACCAATCAAAACTTCT 2 Unidirectional alignment (log-probability: -54) AGTTATAAtATTCTAAACTATAACCCTAATAAAAGTCTCTtcttcaaaactaaccaaaACATGT------------------AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT AGTTATAACATTCTAAACTATAACCCTAATAAAAGTCTCT------------------ACATGTTTTGGTTAGTTTTGAAGAAAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT Template switch alignment (log-probability: -24.2) AGTTATAAtATTCTAAACTATAACCCTAATAAAAGTCTCT|TCTTCAAAACTAACCAAAACATGT|AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT AGTTATAACATTCTAAACTATAACCCTAATAAAAGTCTCT|TCTTCAAAACTAACCAAAACATGT|AAAGACCCATCTCACCCAACCAGACCACATGCTGCCTAAT ========== Event 3066 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: gtg--------tgtgtgtgtgtgtCTTGATGTTTAATTTTCTCTCATAGAGTTGGTCAGTAAAGCATATCTAGCACACAAAGGGACAAAAATGGAGGCAAATCACATCAAGGAATAAGCTTACTGTTCCCC ↑ 1 4 3 2 Chimp: gtg----tgtgtgtgtgtgtgtgtCTTG---ATTAATTTTCTCTCATAGATTTGGTCAGTAAAGCATATCTAGCACACAAAGGGACAAAAATGGAGGCAAATCACATCAAGGAATAAGCTTACTGTTCTCC Gorilla: gtgtgtg----tgggtgtgtgtgtCTTGATGTTTAATTTTCTCTCATAGATTTGGTCAGTAAAGCATATCTAGCACACAAAGGGACAAAAATGGAGGCAAATCACATCAAGGAATAAGCTTACTGTTCCCC Human: gtg--------tgtgtgtgtgtgtCTTGATGTTTAATTTTCTCTCATAGAGTTGGTCAGTAAAGCATATCTAGCACACAAAGGGACAAAAATGGAGGCAAATCACATCAAGGAATAAGCTTACTGTTCCCC Cluster: [ ] Orangutan: at--gtg----tgtgtgtgtgtgtCTTGATGTTTAATTTTCTCTCATAGATTTGGTCAGTAAAGCATATCTAGCACACAAAGGGACAAAAATGAAGGCAAATCACATCAAGGAATAAGCTTACTGTTCCCC Chimp > Human ------------- chr6:39223166-39223173 Template switch process: F1: L TATATGTGTGTGGGCATGTGTGTGTGTGTGTGT 1 F3: 4 TTAATTTTCTCTCATAGAGTTGGTCAGTAAAGCATATCTA R RF: TATATGTGTGTGGGCATGTGTGTGTGTGTGTGTGTGTCTTGATTAATTTTCTCTCATAGATTTGGTCAGTAAAGCATATCTAGCACACAAAGGGACAAAAATGGAGGCAAATCACATCAAG RR: ATATACACACACCCGTACACACACACACACACACACAGAACTAATTAAAAGAGAGTATCTAAACCAGTCATTTCGTATAGATCGTGTGTTTCCCTGTTTTTACCTCCGTTTAGTGTAGTTC F2: 3 TGTAGTTC 2 Unidirectional alignment (log-probability: -31.6) TATATGTGTGTGGGCA----TGTGTGTGTGTGTGTGTCTTGAtgtTTAATTTTCTCTCATAGAgTTGGTCAGTAAAGCATATCTA TATATGTGTGTGGGCATGTGTGTGTGTGTGTGTGTGTCTTGA---TTAATTTTCTCTCATAGATTTGGTCAGTAAAGCATATCTA Template switch alignment (log-probability: -22.1) TATATGTGTGTGGGCATGTGTGTGTGTGTGTGT|CTTGATGT|TTAATTTTCTCTCATAGAgTTGGTCAGTAAAGCATATCTA TATATGTGTGTGGGCATGTGTGTGTGTGTGTGT|CTTGATGT|TTAATTTTCTCTCATAGATTTGGTCAGTAAAGCATATCTA ========== Event 3067 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACTGTGAACTCAAATCTCTGA----------------------TAGCT--ACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATG Chimp: ACTGTGAACTCAAATCTCTGA----------------------TAGCT--ACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATG ↓ 31 4 2 ↑ 1 3 2 4 Gorilla: ACTTTTAACTCAAATCTCTGATTGATTAAAAGAAGTTGTACTGTAGCT----ATTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATG ↓ 1 3 2 4 ↑ 31 4 2 Human: ACTGTGAACTCAAATCTCTGA----------------------TAGCT--ACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATG Cluster: [ ] Orangutan: ACTGTGAACTCAAATCTCTGA----------------------TAGCTAC--AATACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATG Gorilla > Human --------------- chr6:130969686-130969693 Template switch process: F1: L CTACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGAT 1 F3: 4 TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA R RF: CTACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGATTGATTAAAAGAAGTTGTACTGTAGCTATTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA RR: GATGTCTAATAATCGATTTTTGAAAATTGAGTTTAGAGACTAACTAATTTTCTTCAACATGACATCGATAATGTTGAAGAAAATTAGTTTGTTCAATCCCACTTTTACTT F2: 3 GACATCGA 2 Unidirectional alignment (log-probability: -41.3) ACAGATTATTAGCTAAAAACTgTgAACTCAAATCTCTGA----------------------TAGCTacAgTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGATTGATTAAAAGAAGTTGTACTGTAGCT--ATTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Template switch alignment (log-probability: -27.8) ACAGATTATTAGCTAAAAACTgTgAACTCAAATCTCTGAT|AGCTACAG|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGAT|AGCTACAG|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Human > Gorilla --------------- chr6:133441016-133441043 Template switch process: F1: L CTACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGAT 1 F3: 4 TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA R RF: CTACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGATAGCTACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA RR: GATGTCTAATAATCGATTTTTGACACTTGAGTTTAGAGACTATCGATGTCATGTTGAAGAAAATTAGTTTGTTCAATCCCACTTTTACTT F2: 3 TATCGATGTCATGTTGAAGAAAATTAGT 2 Unidirectional alignment (log-probability: -69) ACAGATTATTAGCTAAAAACTtTtAACTCAAATCTCTGAttgattaaaagaagttgtactgTAGCTAt--TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGA----------------------TAGCTACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Template switch alignment (log-probability: -30.4) ACAGATTATTAGCTAAAAACTtTtAACTCAAATCTCTGAT|TGATTAAAAGAAGTTGTACTGTAGCTAT|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGAT|TGATTAAAAGAAGTTGTACTGTAGCTAT|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Gorilla > Chimp --------------- chr6:134894645-134894652 Template switch process: F1: L CTACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGAT 1 F3: 4 TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA R RF: CTACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGATTGATTAAAAGAAGTTGTACTGTAGCTATTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA RR: GATGTCTAATAATCGATTTTTGAAAATTGAGTTTAGAGACTAACTAATTTTCTTCAACATGACATCGATAATGTTGAAGAAAATTAGTTTGTTCAATCCCACTTTTACTT F2: 3 GACATCGA 2 Unidirectional alignment (log-probability: -41.3) ACAGATTATTAGCTAAAAACTgTgAACTCAAATCTCTGA----------------------TAGCTacAgTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGATTGATTAAAAGAAGTTGTACTGTAGCT--ATTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Template switch alignment (log-probability: -27.8) ACAGATTATTAGCTAAAAACTgTgAACTCAAATCTCTGAT|AGCTACAG|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGAT|AGCTACAG|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Chimp > Gorilla --------------- chr6:133441016-133441043 Template switch process: F1: L CTACAGATTATTAGCTAAAAACTTTTAACTCAAATCTCTGAT 1 F3: 4 TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA R RF: CTACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGATAGCTACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA RR: GATGTCTAATAATCGATTTTTGACACTTGAGTTTAGAGACTATCGATGTCATGTTGAAGAAAATTAGTTTGTTCAATCCCACTTTTACTT F2: 3 TATCGATGTCATGTTGAAGAAAATTAGT 2 Unidirectional alignment (log-probability: -69) ACAGATTATTAGCTAAAAACTtTtAACTCAAATCTCTGAttgattaaaagaagttgtactgTAGCTAt--TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGA----------------------TAGCTACAGTACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA Template switch alignment (log-probability: -30.4) ACAGATTATTAGCTAAAAACTtTtAACTCAAATCTCTGAT|TGATTAAAAGAAGTTGTACTGTAGCTAT|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ACAGATTATTAGCTAAAAACTGTGAACTCAAATCTCTGAT|TGATTAAAAGAAGTTGTACTGTAGCTAT|TACAACTTCTTTTAATCAAACAAGTTAGGGTGAAAATGAA ========== Event 3068 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: acacacacagTCAAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATACAAGTGGGCATGCACAAGCCTGCACATTGTCT ↑ 3 2 1 4 Chimp: acacacacaGTCAAAGCACATGCCCAGTTGTGCACACATAAATGGGCACAT---AATGTGCACGCACAAGCCTGCACATTGTCT Gorilla: ACACACACAGTCAAAGCACATGCCCAGTTGTgcacacataaatgggcacatacaaatgggcacgcacaaGCCTGCACGTTGTCT Human: acacacacagTCAAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATACAAGTGGGCATGCACAAGCCTGCACATTGTCT Cluster: [ ] Orangutan: ACACACACAGTCAAAGCACATGCCCAGTTGTgcacacacaaatgggcacatacaaatgggcacacaca--aCTGCACATTGTCT Chimp > Human ------------- chr6:38663152-38663162 Template switch process: F1: L TCAAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATA 1 F3: 4 GCACAAGCCTGCACATTGTCTAAAGGTATTTGTTATACAA R RF: TCAAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATAATGTGCACGCACAAGCCTGCACATTGTCTAAAGGTATTTGTTATACAA RR: AGTTTCGTGTACGGGTCAACACGTGTGTATTTACCCGTGTATTACACGTGCGTGTTCGGACGTGTAACAGATTTCCATAAACAATATGTT F2: 3 TACGGGTGAAC 2 Unidirectional alignment (log-probability: -33.3) AAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATacaAgTGgGCAtGCACAAGCCTGCACATTGTCTAAAGGTATTTGTTATACAA AAAGCACATGCCCAGTTGTGCACACATAAATGGGCACAT---AATGTGCACGCACAAGCCTGCACATTGTCTAAAGGTATTTGTTATACAA Template switch alignment (log-probability: -22.7) AAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATA|CAAgTGGGCAT|GCACAAGCCTGCACATTGTCTAAAGGTATTTGTTATACAA AAAGCACATGCCCAGTTGTGCACACATAAATGGGCACATA|CAACTGGGCAT|GCACAAGCCTGCACATTGTCTAAAGGTATTTGTTATACAA ========== Event 3069 ========== Phylogenetic placement: unresolved Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: CAAATGATTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTTACCAA--------------------------------------GAACAAATATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAACATACCAGCT Chimp: CAAATGATTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTTACCAA--------------------------------------GAACAAATATTCTGTAATATTATATTTTTA---------------------------- Gorilla: -------TTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTTGGTAA----------------------------------------------------------------------------GGAAGGTGAACATACCAGCT ↓ 4 3 1 2 Human: CAAATGATTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTTACCAA--------------------------------------GAACAAATATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAACATACCAGCT Cluster: [ ] Orangutan: -------TTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTTACCAAGAACAAATATTCTGTAATATTATATTTGTTCTTGGTAA--------------------------------------GGAAGGTGAACATACCAGCT Gorilla > Human --------------- chr6:38510364-38510376 Template switch process: F1: L ATGATTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTT 1 F3: 4 ATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAACATACCAGCTAGACGAGGGTAAACAGCTTT R RF: ----TTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAACATACCAGCTAGACGAGGGTAAACAGCTTT RR: ----AAAGGAGGACTCTAAGACATTATAATATAAACAAGAACCATTCCTTCCACTTGTATGGTCGATCTGCTCCCATTTGTCGAAA F2: 3 TAAACAAGAACCA 2 Unidirectional alignment (log-probability: -75.7) tgaTTTCCTCCTGAGattctgtaatattatatttgttcttaccaagaacaaatATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAA ---TTTCCTCCTGAG--------------------------------------ATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAA Template switch alignment (log-probability: -33.5) tgaTTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTT|ACCAAGAACAAAT|ATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAA ---TTTCCTCCTGAGATTCTGTAATATTATATTTGTTCTT|ACCAAGAACAAAT|ATTCTGTAATATTATATTTGTTCTTGGTAAGGAAGGTGAA ========== Event 3070 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: catctcttcttGCCATCACCTCATGTGCTTTAGCTGACAGGTCCATTCATGctgtggccccttgactgtgg Chimp: catctcttcttGCCATCACCTTATGTGCTTTAGCTGACAAGTCCATTCATGCTGTGG-------------- ↓ 1 4 3 2 Gorilla: catctcttcttGCCATCACCTCATGAGCTTTAGCTGACAGGTCCATTCATGctgtggccccttgactgtgg Human: catctcttcttGCCATCACCTCATGTGCTTTAGCTGACAGGTCCATTCATGctgtggccccttgactgtgg Cluster: [ ] Orangutan: catctcttcttGCCATCACCTCGTGCGCTTTAGCTGACAGGTCCATTCATGCTGTGG-------------- Chimp > Gorilla --------------- chr6:38459930-38459934 Template switch process: F1: L TCTTCATCTCTTTCCCACTTCATCTCTTCTTGCCATCACCT 1 F3: 4 GCTTTAGCTGACAGGTCCATTCATGCTGTGGCCCCTTGAC R RF: TCTTCATCTCTTTCCCACTTCATCTCTTCTTGCCATCACCTTATGTGCTTTAGCTGACAAGTCCATTCATGCTGTGGCCCCTTGAC RR: AGAAGTAGAGAAAGGGTGAAGTAGAGAAGAACGGTAGTGGAATACACGAAATCGACTGTTCAGGTAAGTACGACACCGGGGAACTG F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -37.3) CTTCATCTCTTTCCCACTTCATCTCTTCTTGCCATCACCTcATGaGCTTTAGCTGACAgGTCCATTCATGCTGTGGccccttgac CTTCATCTCTTTCCCACTTCATCTCTTCTTGCCATCACCTTATGTGCTTTAGCTGACAAGTCCATTCATGCTGTGG--------- Template switch alignment (log-probability: -21.9) CTTCATCTCTTTCCCACTTCATCTCTTCTTGCCATCACCT|CATGA|GCTTTAGCTGACAgGTCCATTCATGCTGTGGCCCCTTGAC CTTCATCTCTTTCCCACTTCATCTCTTCTTGCCATCACCT|CATGA|GCTTTAGCTGACAAGTCCATTCATGCTGTGGCCCCTTGAC ========== Event 3071 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCAG---GATTTGGTCAGAATCATTCCAGGA Chimp: gactggagaggcaatggATTTGAGCTCGAAAGGCAG---GATTTGGTCAGAATCATTCCAGGA ↓ 3 2 1 4 Gorilla: GACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCGAGCTCAATTGGTCAGAATCATTCCAGGA ↑ 3 2 1 4 Human: GACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCAG---GATTTGGTCAGAATCATTCCAGGA Cluster: [ ] Orangutan: GACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCAG---GATTTGGTCAGAATCATTCTAGGA Human > Gorilla --------------- chr6:38057310-38057317 Template switch process: F1: L GCAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC 1 F3: 4 TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT R RF: GCAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCAGGATTTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT RR: CGTTGTTCTGACCTCTCCGTTACCTAAACTCGAGCTTTCCGTCCTAAACCAGTCTTAGTAAGGTCCTAGTCTCGTTGTCACTAGTA F2: 3 AACTCGAG 2 Unidirectional alignment (log-probability: -30.9) CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCgagctcaA----TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC-------AGGATTTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT Template switch alignment (log-probability: -16.7) CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC|GAGCTCAA|TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC|GAGCTCAA|TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT Chimp > Gorilla --------------- chr6:38057310-38057317 Template switch process: F1: L GCAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC 1 F3: 4 TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT R RF: ACAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCAGGATTTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT RR: TGTTGTTCTGACCTCTCCGTTACCTAAACTCGAGCTTTCCGTCCTAAACCAGTCTTAGTAAGGTCCTAGTCTCGTTGTCACTAGTA F2: 3 AACTCGAG 2 Unidirectional alignment (log-probability: -36.4) CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGCgagctcaA----TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC-------AGGATTTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT Template switch alignment (log-probability: -22.3) CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC|GAGCTCAA|TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT CAACAAGACTGGAGAGGCAATGGATTTGAGCTCGAAAGGC|GAGCTCAA|TTGGTCAGAATCATTCCAGGATCAGAGCAACAGTGATCAT ========== Event 3072 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ccacacatagAAACAACGTTTCTTCCAGAGTGAGATTTCTGGAAGGTCATTTGGTAATATGCATT ↑ 1 4 3 2 Chimp: CCACACATAGAAACAACGTTTT------TGTGAGATTTCTGGAAGGTCATTTGGTAATATGCATT Gorilla: CCACACATAGAAACAACATTTT------TGTGAGAtttctggaaggtcatttggcaatatgcatt Human: ccacacatagAAACAACGTTTCTTCCAGAGTGAGATTTCTGGAAGGTCATTTGGTAATATGCATT Cluster: [ ] Orangutan: ccacacatagAAACAACGTTTT------TGTGAGAtttctggaaggtcatttggtaatatgcatt Chimp > Human ------------- chr6:133606000-133606007 Template switch process: F1: L AGGGATCCAGTTTCATTCTTCCACACATAGAAACAACGTTT 1 F3: 4 GTGAGATTTCTGGAAGGTCATTTGGTAATATGCATTAATA R RF: AGGGATCCAGTTTCATTCTTCCACACATAGAAACAACGTTTTTGTGAGATTTCTGGAAGGTCATTTGGTAATATGCATTAATA RR: TCCCTAGGTCAAAGTAAGAAGGTGTGTATCTTTGTTGCAAAAACACTCTAAAGACCTTCCAGTAAACCATTATACGTAATTAT F2: 3 AGACCTTC 2 Unidirectional alignment (log-probability: -25.6) GGGATCCAGTTTCATTCTTCCACACATAGAAACAACGTTTcTtccagaGTGAGATTTCTGGAAGGTCATTTGGTAATATGCATTAATA GGGATCCAGTTTCATTCTTCCACACATAGAAACAACGTTTTT------GTGAGATTTCTGGAAGGTCATTTGGTAATATGCATTAATA Template switch alignment (log-probability: -16.3) GGGATCCAGTTTCATTCTTCCACACATAGAAACAACGTTT|CTTCCAGA|GTGAGATTTCTGGAAGGTCATTTGGTAATATGCATTAATA GGGATCCAGTTTCATTCTTCCACACATAGAAACAACGTTT|CTTCCAGA|GTGAGATTTCTGGAAGGTCATTTGGTAATATGCATTAATA ========== Event 3073 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: AATATTTGCAGAAGGTGGCATCCC------------------------------CAAGATCTGAAGAAATGACTCATGTTAGAATGGGGGAAAGCGAGTCCTATCAGTTCCAAAAGGGGCATGAAGGAAGCAACATTTTCAGCAAGTACAGTTTTCATGGACAGACTGAATCCTGTGGCTTCCCCTAGTT ↓ 4 1 3 2 Chimp: AATATTTGCAGAAGGTGGCATCCC------------------CATTCAGATCCCCAAGATCTGAAGAACTGACTCATGTTAGAATGGGGGAAAGCGAGTCCTATCAGTTCCAAAA-GGGCATGAAGGAAGCAGCCTTTTCAGCAAGTACAGTTTTCATGGACAGACTGAATCCTGTGGCTTCCCCTAGTT Gorilla: AATATTTGCAGAAGGTGGCATCCC------CATTCAGATCCC------------CAAGATCTGAAGAACTGACTCATGTTAGAATGGGGGAAAGTGAGTCCTGTCAGTTCCAAAA-GGGCATGAAGGAAGCAACCTTTTCAGCAAGCACAGTTTTCATGGACAGACTGAATCCTGTGGCTTCCCCTAGTT ↑ 4 1 3 2 Human: AATATTTGCAGAAGGTGGCATCCC------------------------------CAAGATCTGAAGAAATGACTCATGTTAGAATGGGGGAAAGCGAGTCCTATCAGTTCCAAAAGGGGCATGAAGGAAGCAACATTTTCAGCAAGTACAGTTTTCATGGACAGACTGAATCCTGTGGCTTCCCCTAGTT Cluster: [ ] Orangutan: AATATTTGCAGAAGGTGGCATGCCCATTTT------------------------AAAG--ATGAATAACTGACTCATGTTAGAATGGGGGAAAGCGAGTCCTATCAGTTCCAAAA-GGGCATGAAGGAAGCAACATTTTCAGCAAGTACAGTTTTCATGGACAGACTGAATCCTGTGGCTTCCCCTAGTT Human > Chimp ------------- chr6:38367385-38367389 Template switch process: F1: L TGTATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCA 1 F3: 4 ATCCCCAAGATCTGAAGAACTGACTCATGTTAGAATGGGGGAAAG R RF: TGTATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCAAGATCTGAAGAAATGACTCATGTTAGAATGGGGGAAAGCGAGTCCTATCAGTTCCAAAAGGGGCATGAAGGAAGCAACATTTTCAGCAAGTACAGTTTTCATGGACAGACTGAA RR: ACATACCCAGGTGTCTGTTATAAACGTCTTCCACCGTAGGGGTTCTAGACTTCTTTACTGAGTACAATCTTACCCCCTTTCGCTCAGGATAGTCAAGGTTTTCCCCGTACTTCCTTCGTTGTAAAAGTCGTTCATGTCAAAAGTACCTGTCTGACTT F2: 3 GACTT 2 Unidirectional alignment (log-probability: -34.2) ATGGGTCCACAGACAATATTTGCAGAAGGTGGCatccccattcagATCCCCAAGATCTGAAGAAcTGACTCATGTTAGAATGGGG ATGGGTCCACAGACAATATTTGCAGAAGGTGGC------------ATCCCCAAGATCTGAAGAAATGACTCATGTTAGAATGGGG Template switch alignment (log-probability: -22) ATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCA|TTCAG|ATCCCCAAGATCTGAAGAAcTGACTCATGTTAGAATGGGG ATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCA|TTCAG|ATCCCCAAGATCTGAAGAAATGACTCATGTTAGAATGGGG Human > Gorilla --------------- chr6:37662996-37663000 Template switch process: F1: L TGTATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCA 1 F3: 4 ATCCCCAAGATCTGAAGAACTGACTCATGTTAGAATGGGGGAAAG R RF: TGTATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCAAGATCTGAAGAAATGACTCATGTTAGAATGGGGGAAAGCGAGTCCTATCAGTTCCAAAAGGGGCATGAAGGAAGCAACATTTTCAGCAAGTACAGTTTTCATGGACAGACTGAA RR: ACATACCCAGGTGTCTGTTATAAACGTCTTCCACCGTAGGGGTTCTAGACTTCTTTACTGAGTACAATCTTACCCCCTTTCGCTCAGGATAGTCAAGGTTTTCCCCGTACTTCCTTCGTTGTAAAAGTCGTTCATGTCAAAAGTACCTGTCTGACTT F2: 3 GACTT 2 Unidirectional alignment (log-probability: -33.7) ATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCcccattcagatcCCCAAGATCTGAAGAAcTGACTCATGTTAGAATGGGG ATGGGTCCACAGACAATATTTGCAGAAGGTGGCATC------------CCCAAGATCTGAAGAAATGACTCATGTTAGAATGGGG Template switch alignment (log-probability: -22.1) ATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCA|TTCAG|ATCCCCAAGATCTGAAGAAcTGACTCATGTTAGAATGGGG ATGGGTCCACAGACAATATTTGCAGAAGGTGGCATCCCCA|TTCAG|ATCCCCAAGATCTGAAGAAATGACTCATGTTAGAATGGGG ========== Event 3074 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAACTAAGGGACCTCACCCACCTGT------GAGGATGGAGCATGTGGCCTCA-AAA ↓ 3 1 2 4 Chimp: CAACTAAGGGACCTCACCCACATGT---GCTCACAGTGGAGCATGTGGCCTCA-AAA Gorilla: CAACTAAGGGACCTCACCCACCTGTGCT---CACAATGGAGCATGTGGCCTCA-AAA Human: CAACTAAGGGACCTCACCCACCTGT------GAGGATGGAGCATGTGGCCTCA-AAA Cluster: [ ] Orangutan: CAACTAAGGGACCTCACCCACATGTGCT---CACAGTGGAGGATGTGGCCTCAACAA Human > Chimp ------------- chr6:37257203-37257209 Template switch process: F1: L ATAGAATCATCAAACAATACCAACTAAGGGACCTCACCCACATGTG 1 F3: 4 TGGAGCATGTGGCCTCAAAATCAGGGCTGACCTAAACTCT R RF: ATAGAATCATCAAACAATACCAACTAAGGGACCTCACCCACCTGTGAGGATGGAGCATGTGGCCTCAAAATCAGGGCTGACCTAAACTCT RR: TATCTTAGTAGTTTGTTATGGTTGATTCCCTGGAGTGGGTGGACACTCCTACCTCGTACACCGGAGTTTTAGTCCCGACTGGATTTGAGA F2: 3 GACACTC 2 Unidirectional alignment (log-probability: -34.5) TCATCAAACAATACCAACTAAGGGACCTCACCCACaTGTGctcacAG--TGGAGCATGTGGCCTCAAAATCAGGGCTGACCTAAACTCT TCATCAAACAATACCAACTAAGGGACCTCACCCACCTGTG-----AGGATGGAGCATGTGGCCTCAAAATCAGGGCTGACCTAAACTCT Template switch alignment (log-probability: -22.2) TCATCAAACAATACCAACTAAGGGACCTCACCCACaTGTG|CTCACAG|TGGAGCATGTGGCCTCAAAATCAGGGCTGACCTAAACTCT TCATCAAACAATACCAACTAAGGGACCTCACCCACCTGTG|CTCACAG|TGGAGCATGTGGCCTCAAAATCAGGGCTGACCTAAACTCT ========== Event 3075 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGATATCCTATAAGTAGACATGATTTTATACCAGTGAATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATTTCATGTCTAGAAACATCCATCTCTGC ↑ 3 2 1 4 Chimp: TTGATATCCTATAAGTAGACATGATTTTATACCAGTGAATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTAT-TGACTTCTAGAAACATCCATCTCTGC Gorilla: TTGATATCCTATAAGTAGACATGATTTTATACCAGTGAATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCA-TAT-TGACTTCTAGAAACATTCACCTCTGC Human: TTGATATCCTATAAGTAGACATGATTTTATACCAGTGAATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATTTCATGTCTAGAAACATCCATCTCTGC Cluster: [ ] Orangutan: TTGATATCCTATAAGTAGACATGATTTTATACCAGTGAATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTAC-TGACTTCTAGAAACATACATCTCTGC Chimp > Human ------------- chr6:13439034-13439038 Template switch process: F1: L ATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATT 1 F3: 4 TCTAGAAACATCCATCTCTGCAATCAGGGTACTCAGGGAT R RF: CATGATTTTATACCAGTGAATGAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATTGACTTCTAGAAACATCCATCTCTGCAATCAGGGTACTCAGGGAT RR: GTACTAAAATATGGTCACTTACTCTTGTCTTAGTATCTTTACTTTCGGTTAAACGTAATAACTGAAGATCTTTGTAGGTAGAGACGTTAGTCCCATGAGTCCCTA F2: 3 GTACT 2 Unidirectional alignment (log-probability: -27.1) GAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATttcaTG---TCTAGAAACATCCATCTCTGCAATCAGGGTACTCAGGGAT GAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTAT----TGACTTCTAGAAACATCCATCTCTGCAATCAGGGTACTCAGGGAT Template switch alignment (log-probability: -15.9) GAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATT|TCATG|TCTAGAAACATCCATCTCTGCAATCAGGGTACTCAGGGAT GAGAACAGAATCATAGAAATGAAAGCCAATTTGCATTATT|TCATG|TCTAGAAACATCCATCTCTGCAATCAGGGTACTCAGGGAT ========== Event 3076 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGCTAAGCCAGCTATTTTAT------------AGTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACAACGGATTT ↓ 1 4 3 2 Chimp: CTGCTAAGCCAGCTATTTTAT--ACATTTGAGACATCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACAACGGATTT ↑ 1 4 3 2 Gorilla: CTGCTAAGCCAGCTATTTTATAT----------AGTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACAACAGATTT Human: CTGCTAAGCCAGCTATTTTAT------------AGTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACAACGGATTT Cluster: [ ] Orangutan: CTGCTAAGCCAGCTATTTTAT------------AGTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACAATGGATTT Human > Chimp ------------- chr6:35931840-35931850 Template switch process: F1: L ATGCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA 1 F3: 4 TCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA R RF: ATGCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATAGTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA RR: TACGTAAATGAGGTAAATCAGACGATTCGGTCGATAAAATATCAGACCACGGGGTGACCTACAGAGTTTACACACGTTTATGT F2: 3 ACAGAGTTTAC 2 Unidirectional alignment (log-probability: -31.3) GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATAcatttgagacaTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA----------GTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA Template switch alignment (log-probability: -16.7) GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA|CATTTGAGACA|TCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA|CATTTGAGACA|TCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA Gorilla > Chimp --------------- chr6:35931840-35931850 Template switch process: F1: L ATGCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA 1 F3: 4 TCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA R RF: ATGCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATATAGTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA RR: TACGTAAATGAGGTAAATCAGACGATTCGGTCGATAAAATATATCAGACCACGGGGTGACCTACAGAGTTTACACACGTTTATGT F2: 3 ACAGAGTTTAC 2 Unidirectional alignment (log-probability: -33.5) GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATAcAtttgagacaTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATATA--------GTCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA Template switch alignment (log-probability: -17.2) GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA|CATTTGAGACA|TCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA GCATTTACTCCATTTAGTCTGCTAAGCCAGCTATTTTATA|CATTTGAGACA|TCTGGTGCCCCACTGGATGTCTCAAATGTGTGCAAATACA ========== Event 3077 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAATATTGGTAGTGAATGATTG------GC------TATCA--------------------------------------------CTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAAAA ↑ 1 4 3 2 Chimp: AGAATATTGGTAGTGAATGATAA---GGAGC---TAATATTA------------------------CTCCAATTTGAATGGTTCTTGTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAAAA Gorilla: AGAATATTGGTAGTGAATGATAAGGA---GCTAA---TATTACTC----CAATTTGAATGGTTCTT--------------------GTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAAAA ↓ 1 4 3 2 Human: AGAATATTGGTAGTGAATGATTG------GC------TATCA--------------------------------------------CTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAAAA Cluster: [ ] Orangutan: AGAATATTGCTAGTGAATGATAAGGA---GCTAA---TATTACTCTGATTAATTTGAATGGTTCTT--------------------GTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAAAA Chimp > Human ------------- chr6:136910648-136910657 Template switch process: F1: L GTAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGAT 1 F3: 4 TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA R RF: GTAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGATAAGGAGCTAATATTACTCCAATTTGAATGGTTCTTGTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA RR: CATCGAACCTAAGACTAGAGTCTTATAACCATCACTTACTATTCCTCGATTATAATGAGGTTAAACTTACCAAGAACATAAGTTTTAATCACTATCGGTTCTTTAATGTAATCAGTT F2: 3 CACTATCGGT 2 Unidirectional alignment (log-probability: -34.4) TAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGA----------------------------------TTGgctatcacTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA TAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGATAAGGAGCTAATATTACTCCAATTTGAATGGTTCTTG--------TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA Template switch alignment (log-probability: -16.5) TAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGAT|TGGCTATCAC|TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA TAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGAT|TGGCTATCAC|TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA Gorilla > Human --------------- chr6:136910648-136910657 Template switch process: F1: L GTAGCTTGGATTCTGATCTCAGAATATTGGTAGTGAATGAT 1 F3: 4 TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA R RF: GTAGCTTGGATTCTGATCACAGAATATTGGTAGTGAATGATAAGGAGCTAATATTACTCCAATTTGAATGGTTCTTGTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA RR: CATCGAACCTAAGACTAGTGTCTTATAACCATCACTTACTATTCCTCGATTATAATGAGGTTAAACTTACCAAGAACATAAGTTTTAATCACTATCGGTTCTTTAATGTAATCAGTT F2: 3 CACTATCGGT 2 Unidirectional alignment (log-probability: -39.4) TAGCTTGGATTCTGATCtCAGAATATTGGTAGTGAATGA----------------------------------TTGgctatcacTATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA TAGCTTGGATTCTGATCACAGAATATTGGTAGTGAATGATAAGGAGCTAATATTACTCCAATTTGAATGGTTCTTG--------TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA Template switch alignment (log-probability: -22.5) TAGCTTGGATTCTGATCtCAGAATATTGGTAGTGAATGAT|TGGCTATCAC|TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA TAGCTTGGATTCTGATCACAGAATATTGGTAGTGAATGAT|TGGCTATCAC|TATTCAAAATTAGTGATAGCCAAGAAATTACATTAGTCAA ========== Event 3078 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CATTCTGACTCTCATTCAAAACCTGGT----------------TGTTGTTGATACTAACAGCCTCAATCCCTGGCAGCCCTC ↑ 1 3 4 2 Chimp: CATTCTGACTCTCATTCAAAAACTGGT--------TCTCGTGAGGTTGTTAGTATCAACAACCTCAATCCCTGGCAGCCCTC Gorilla: CATTCTGACTCTCATTCAAAAACTGGTTCTCGTGA--------GGTTGTTAGTATCAACAACCTCAATCCCTGGCAGCCCTC ↓ 1 3 4 2 Human: CATTCTGACTCTCATTCAAAACCTGGT----------------TGTTGTTGATACTAACAGCCTCAATCCCTGGCAGCCCTC Cluster: [ ] Orangutan: CATTCTGACTCTCATTCAAAAACTGGTTCTCGTGA--------GGTTGTCAGTATCAACAACCTCGATCCCTGGCAGCCCTC Chimp > Human ------------- chr6:32574860-32574871 Template switch process: F1: L TCAGGAATTATATTTTCAATCATTCTGACTCTCATTCAAAACCTGGTT 1 F3: 4 AACAGCCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACCCTCTG R RF: TCAGGAATTATATTTTCAATCATTCTGACTCTCATTCAAAAACTGGTTCTCGTGAGGTTGTTAGTATCAACAACCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACCCTCTG RR: AGTCCTTAATATAAAAGTTAGTAAGACTGAGAGTAAGTTTTTGACCAAGAGCACTCCAACAATCATAGTTGTTGGAGTTAGGGACCGTCGGGAGAGGAGGACTTCTGGGAGAC F2: 3 TCATAGTTGTTG 2 Unidirectional alignment (log-probability: -47.5) TATATTTTCAATCATTCTGACTCTCATTCAAAAcCTGGTT--------GTTGTTgaTActAACAgCCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC TATATTTTCAATCATTCTGACTCTCATTCAAAAACTGGTTCTCGTGAGGTTGTTAGTATCAACAACCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC Template switch alignment (log-probability: -29) TATATTTTCAATCATTCTGACTCTCATTCAAAAcCTGGTT|GTTGTTGATACT|AACAgCCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC TATATTTTCAATCATTCTGACTCTCATTCAAAAACTGGTT|GTTGTTGATACT|AACAACCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC Gorilla > Human --------------- chr6:32574860-32574871 Template switch process: F1: L TCAGGAATTATATTTTCAATCATTCTGACTCTCATTCAAAACCTGGTT 1 F3: 4 AACAGCCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACCCTCTG R RF: TCAGGAATTATATTTTCAATCATTCTGACTCTCATTCAAAAACTGGTTCTCGTGAGGTTGTTAGTATCAACAACCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACCCTCTG RR: AGTCCTTAATATAAAAGTTAGTAAGACTGAGAGTAAGTTTTTGACCAAGAGCACTCCAACAATCATAGTTGTTGGAGTTAGGGACCGTCGGGAGAGGAGGACTTCTGGGAGAC F2: 3 TCATAGTTGTTG 2 Unidirectional alignment (log-probability: -44.7) TATATTTTCAATCATTCTGACTCTCATTCAAAAcCTGGTT--------GTTGTTgaTActAACAgCCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC TATATTTTCAATCATTCTGACTCTCATTCAAAAACTGGTTCTCGTGAGGTTGTTAGTATCAACAACCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC Template switch alignment (log-probability: -28.6) TATATTTTCAATCATTCTGACTCTCATTCAAAAcCTGGTT|GTTGTTGATACT|AACAgCCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC TATATTTTCAATCATTCTGACTCTCATTCAAAAACTGGTT|GTTGTTGATACT|AACAACCTCAATCCCTGGCAGCCCTCTCCTCCTGAAGACC ========== Event 3079 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTACTCAGAGGTAAAGAGGAC-------AAG---CTCTCACCAAatctacccagaggaaaagaag Chimp: TCTACTCAGAGGTAAAGAGGAC-------AAG---CTCTCACCAAatctatccagaggaaaagaag ↓ 1 3 4 2 Gorilla: TCTACCCAGAGGTAAAGAGGATTTGGTGAGAGCTTGTCTCACCAAatctacccagaggaaaagaag ↑ 1 3 4 2 Human: TCTACTCAGAGGTAAAGAGGAC-------AAG---CTCTCACCAAatctacccagaggaaaagaag Cluster: [ ] Orangutan: TCTACCCAGAGGTAAAGAGGAC-------AAG---CTCTCACGAAatctacccaaaggaaaagaag Human > Gorilla --------------- chr6:32706566-32706580 Template switch process: F1: L ACCATCATTATCTCACCAAATCTACCCAGAGGTAAAGAGGA 1 F3: 4 TCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG R RF: ACCATCATTATCTCACCAAATCTACTCAGAGGTAAAGAGGACAAGCTCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG RR: TGGTAGTAATAGAGTGGTTTAGATGAGTCTCCATTTCTCCTGTTCGAGAGTGGTTTAGATGGGTCTCCTTTTCTTCAGCAATATAC F2: 3 GTTCGAGAGTGGTTT 2 Unidirectional alignment (log-probability: -48) CCATCATTATCTCACCAAATCTACcCAGAGGTAAAGAGGAtttggtgagagcttg-----TCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG CCATCATTATCTCACCAAATCTACTCAGAGGTAAAGAGGA---------------CAAGCTCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG Template switch alignment (log-probability: -23.2) CCATCATTATCTCACCAAATCTACcCAGAGGTAAAGAGGA|TTTGGTGAGAGCTTG|TCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG CCATCATTATCTCACCAAATCTACTCAGAGGTAAAGAGGA|TTTGGTGAGAGCTTG|TCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG Chimp > Gorilla --------------- chr6:32706566-32706580 Template switch process: F1: L ACCATCATTATCTCACCAAATCTACCCAGAGGTAAAGAGGA 1 F3: 4 TCTCACCAAATCTACCCAGAGGAAAAGAAGTCGTTATATG R RF: ACCATCATTATCTCACCAAATCTACTCAGAGGTAAAGAGGACAAGCTCTCACCAAATCTATCCAGAGGAAAAGAAGTCGTTATATG RR: TGGTAGTAATAGAGTGGTTTAGATGAGTCTCCATTTCTCCTGTTCGAGAGTGGTTTAGATAGGTCTCCTTTTCTTCAGCAATATAC F2: 3 GTTCGAGAGTGGTTT 2 Unidirectional alignment (log-probability: -53.5) CCATCATTATCTCACCAAATCTACcCAGAGGTAAAGAGGAtttggtgagagcttg-----TCTCACCAAATCTAcCCAGAGGAAAAGAAGTCGTTATATG CCATCATTATCTCACCAAATCTACTCAGAGGTAAAGAGGA---------------CAAGCTCTCACCAAATCTATCCAGAGGAAAAGAAGTCGTTATATG Template switch alignment (log-probability: -28.7) CCATCATTATCTCACCAAATCTACcCAGAGGTAAAGAGGA|TTTGGTGAGAGCTTG|TCTCACCAAATCTAcCCAGAGGAAAAGAAGTCGTTATATG CCATCATTATCTCACCAAATCTACTCAGAGGTAAAGAGGA|TTTGGTGAGAGCTTG|TCTCACCAAATCTATCCAGAGGAAAAGAAGTCGTTATATG ========== Event 3080 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCACATTTCTACTGTGCTGTCTT---AGCCAGCTTCTCGTGGGCAGGGCTGTCAAGT Chimp: GCCACATTTCTACTGTGCTGTCTT---AGCCAGCTTCTCGTGGGCAGGGCTGTCAAGT ↓ 1 4 3 2 Gorilla: GCCACATTTCTACTGTGCTGTAGAAGCTGCCAGCTTCTCGTGGGCAGGGCTGTCAAGT ↑ 1 4 3 2 Human: GCCACATTTCTACTGTGCTGTCTT---AGCCAGCTTCTCGTGGGCAGGGCTGTCAAGT Cluster: [ ] Orangutan: GCCACATCTCTACTGTGCTGTCTT---AGCCAGCTTCTCATGGGCAGGGCAGTCAAGT Human > Gorilla --------------- chr6:33016519-33016525 Template switch process: F1: L GTTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT 1 F3: 4 GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG R RF: GTTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGTCTTAGCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG RR: CAAACACGGGGTTAGAAGTCCGGTGTAAAGATGACACGACAGAATCGGTCGAAGAGCACCCGTCCCGACAGTTCAGTTGAGGGTC F2: 3 TCGAAGA 2 Unidirectional alignment (log-probability: -27.9) TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGTagaagCT--GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT-----CTTAGCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG Template switch alignment (log-probability: -16.6) TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT|AGAAGCT|GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT|AGAAGCT|GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG Chimp > Gorilla --------------- chr6:33016519-33016525 Template switch process: F1: L GTTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT 1 F3: 4 GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG R RF: GTTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGTCTTAGCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG RR: CAAACACGGGGTTAGAAGTCCGGTGTAAAGATGACACGACAGAATCGGTCGAAGAGCACCCGTCCCGACAGTTCAGTTGAGGGTC F2: 3 TCGAAGA 2 Unidirectional alignment (log-probability: -27.9) TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGTagaagCT--GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT-----CTTAGCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG Template switch alignment (log-probability: -16.6) TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT|AGAAGCT|GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG TTTGTGCCCCAATCTTCAGGCCACATTTCTACTGTGCTGT|AGAAGCT|GCCAGCTTCTCGTGGGCAGGGCTGTCAAGTCAACTCCCAG ========== Event 3081 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTCCTCATCCTCACTCCTAGTTTCTCCCCGTTGGTTG------GTTTATCCCATAGTGTGTGCTT ↓ 3 2 1 4 Chimp: TTCTCCTTATCCTCACTCCTAGTTTCTCCCCGTTGGGGAGAAACTATTTATCCCATAGTGTGTGCTT Gorilla: TTCTCCTCATCCTCACTCCTAGTTTCTCCCCGTTGGTTG------GTTTATCCCATAGTGTGTGGTT Human: TTCTCCTCATCCTCACTCCTAGTTTCTCCCCGTTGGTTG------GTTTATCCCATAGTGTGTGCTT Cluster: [ ] Orangutan: TTCTCCTCATCCTCACTCCTAGTTTTTCCCCGTTGGTTG------GTTTATCCCATAGTGTGTGCTT Human > Chimp ------------- chr6:31750033-31750042 Template switch process: F1: L CATTTTTCTCCTTATCCTCACTCCTAGTTTCTCCCCGTTGG 1 F3: 4 TTTATCCCATAGTGTGTGCTTAACTGAATTCAATTACTCT R RF: CATTTTTCTCCTCATCCTCACTCCTAGTTTCTCCCCGTTGGTTGGTTTATCCCATAGTGTGTGCTTAACTGAATTCAATTACTCT RR: GTAAAAAGAGGAGTAGGAGTGAGGATCAAAGAGGGGCAACCAACCAAATAGGGTATCACACACGAATTGACTTAAGTTAATGAGA F2: 3 ATCAAAGAGG 2 Unidirectional alignment (log-probability: -38.7) ATTTTTCTCCTtATCCTCACTCCTAGTTTCTCCCCGTTGG--GGagaaactaTTTATCCCATAGTGTGTGCTTAACTGAATTCAATTACTCT ATTTTTCTCCTCATCCTCACTCCTAGTTTCTCCCCGTTGGTTGG--------TTTATCCCATAGTGTGTGCTTAACTGAATTCAATTACTCT Template switch alignment (log-probability: -22.5) ATTTTTCTCCTtATCCTCACTCCTAGTTTCTCCCCGTTGG|GGAGAAACTA|TTTATCCCATAGTGTGTGCTTAACTGAATTCAATTACTCT ATTTTTCTCCTCATCCTCACTCCTAGTTTCTCCCCGTTGG|GGAGAAACTA|TTTATCCCATAGTGTGTGCTTAACTGAATTCAATTACTCT ========== Event 3082 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTCTGTATATGTATATACAC--ACACACAAACACGTCAAATAAGCATGCAGT----------------------------TTCTGTAGAGA Chimp: TGTCTGTATATGTATATACAC--ACACACAAACACGTCAAATAAGCACGCAGT--------------TTGCAAAATCAAGTGTCTGTAGAGA ↓ 1 43 2 Gorilla: TGTCTGTATATGTATATACAC----ACACAAACACGTCAAATAAGCATGCAATTTGCAAAATCAAGT--------------GTCTGTAGAGA Human: TGTCTGTATATGTATATACAC--ACACACAAACACGTCAAATAAGCATGCAGT----------------------------TTCTGTAGAGA Cluster: [ ] Orangutan: TGTCTGTATATGTATATACACAC--ACACAAACATGTAAAATAAGCATACAGTTTGCAAAATCAAGT--------------GTCTGTAGAGA Chimp > Gorilla --------------- chr6:31676954-31676958 Template switch process: F1: L TATTTACACATACAGATTGCTGTCTGTATATGTATAT--ACACACACAAACACGTCAAATAAGCA 1 F3: 4 TTTGCAAAATCAA R RF: TATTTACACATACAGATTGCTGTCTGTATATGTATATACACACACACAAACACGTCAAATAAGCACGCAGTTTGCAAAATCAA RR: ATAAATGTGTATGTCTAACGACAGACATATACATATATGTGTGTGTGTTTGTGCAGTTTATTCGTGCGTCAAACGTTTTAGTT F2: 3 AACGT 2 Unidirectional alignment (log-probability: -45.9) CTGTATATGTATATACACAC--ACAAACACGTCAAATAAGCAtGCAaTttgcaaaatcaa CTGTATATGTATATACACACACACAAACACGTCAAATAAGCACGCAGT------------ Template switch alignment (log-probability: -26.1) CTGTATATGTATAT--ACACACACAAACACGTCAAATAAGCA|TGCAA|TTTGCAAAATCAA CTGTATATGTATATACACACACACAAACACGTCAAATAAGCA|TGCAA|TTTGCAAAATCAA ========== Event 3083 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTCTAAAGCCAAGACACAGTGGAAAGGCTTTTCCACTGAAGCCCCACTCCACCT Chimp: tttctaaagccaagacgcagt----cagcctttccactgaagccccACTCCACCT Gorilla: TTTCTAAAGCCAAGACACAGT----CAGCCTTTCCACTGAAGCCCCACTCCACCT ↓ 1 3 4 2 Human: TTTCTAAAGCCAAGACACAGTGGAAAGGCTTTTCCACTGAAGCCCCACTCCACCT Cluster: [ ] Orangutan: TTTCTAAAGCCAAGACACAGT----CAGCCTTTCCACTGAAGCCCCACTCCACCT Gorilla > Human --------------- chr6:14407394-14407402 Template switch process: F1: L TTGTGGTGGCTCCATTTGTGTTTCTAAAGCCAAGACACAGT 1 F3: 4 TTTCCACTGAAGCCCCACTCCACCTCCAGCACCAGCCACA R RF: TTGTGGTGGCTCCATGTGTGTTTCTAAAGCCAAGACACAGTCAGCCTTTCCACTGAAGCCCCACTCCACCTCCAGCACCAGCCACA RR: AACACCACCGAGGTACACACAAAGATTTCGGTTCTGTGTCAGTCGGAAAGGTGACTTCGGGGTGAGGTGGAGGTCGTGGTCGGTGT F2: 3 TCGGAAAGG 2 Unidirectional alignment (log-probability: -38.8) TGTGGTGGCTCCATtTGTGTTTCTAAAGCCAAGACACAGTggaaagGCtTTTCCACTGAAGCCCCACTCCACCTCCAGCACCAGCCACA TGTGGTGGCTCCATGTGTGTTTCTAAAGCCAAGACACAGT----CAGCCTTTCCACTGAAGCCCCACTCCACCTCCAGCACCAGCCACA Template switch alignment (log-probability: -22.4) TGTGGTGGCTCCATtTGTGTTTCTAAAGCCAAGACACAGT|GGAAAGGCT|TTTCCACTGAAGCCCCACTCCACCTCCAGCACCAGCCACA TGTGGTGGCTCCATGTGTGTTTCTAAAGCCAAGACACAGT|GGAAAGGCT|TTTCCACTGAAGCCCCACTCCACCTCCAGCACCAGCCACA ========== Event 3084 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ATGAGGGGCCAAATAACTGCACAGATTCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAAGCTGTTGGAGCTGGGCGTGCAGACTCGAGCAGGACAAACCGTCCCACCTGGTGAGATGACATCAGGAGTC Chimp: ATGAGGGGCCAAATAACTGCACAGGTTCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAAGCTGTTGGAGCTGGGCGTGCAGACTCGAGCAGG-AAAACCAACCCACCTGGTGAGATGACATCAGGAGTC ↑ 1 4 3 2 Gorilla: ATGAGGGGCCAAATAACTGCAAAT-ATCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAAGCTGTTGGAGCTGGGCGTGCAGACTCGAGCAGG-AAAACCATCCCACCTGGTGAGATGACATCAGGAGTC Human: ATGAGGGGCCAAATAACTGCACAGATTCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAAGCTGTTGGAGCTGGGCGTGCAGACTCGAGCAGGACAAACCGTCCCACCTGGTGAGATGACATCAGGAGTC Cluster: [ ] Orangutan: ATGAGGGGCCAAACAACTGCACAGGTTCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGTGAAGCTGTTGGAGCTGGGCATGCAGAC-TGAGCAGG-AAAACCATCCCACCTGGTGAGATGACATTAAGAGT- Gorilla > Chimp --------------- chr6:14402641-14402645 Template switch process: F1: L TAATCGTGAGAGGCTTTTCAATGAGGGGCCAAATAACTGCA 1 F3: 4 TCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAA R RF: TAACCGTGAGAGGCTTTTCAATGAGGGGCCAAATAACTGCAAATATCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAAGCTGTTGGAGCTGGGCGTGCAGACTCGAGCAGGAAAACCATCCCACCTG RR: ATTGGCACTCTCCGAAAAGTTACTCCCCGGTTTATTGACGTTTATAGACCCACAACCCACTTCGGACAGGGGTTTGAACCCGCTTCGACAACCTCGACCCGCACGTCTGAGCTCGTCCTTTTGGTAGGGTGGAC F2: 3 TGGAC 2 Unidirectional alignment (log-probability: -33.5) AAtCGTGAGAGGCTTTTCAATGAGGGGCCAAATAACTGC----AcaggtTCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAA AACCGTGAGAGGCTTTTCAATGAGGGGCCAAATAACTGCAAATA-----TCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAA Template switch alignment (log-probability: -21.9) AAtCGTGAGAGGCTTTTCAATGAGGGGCCAAATAACTGCA|CAGGT|TCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAA AACCGTGAGAGGCTTTTCAATGAGGGGCCAAATAACTGCA|CAGGT|TCTGGGTGTTGGGTGAAGCCTGTCCCCAAACTTGGGCGAA ========== Event 3085 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGAAAATGAGTTTGACTCTTTTCCCCTAACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGTCATATTGATTATTTTTGGCTTTCACTGACTCTAACAAGGTAGACCAATGT Chimp: GTGAAAATGAGTTTGACTCTTTTCCCCTAACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGCCATATTGATTATTTTTGGCTTTCACTGACTCTAACAAGGTAGACCAATGT ↓ 1 4 3 2 Gorilla: GTGAAAATGAGTTTGACTCTTA----GTCACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGTCATATTGATTATTTTTGGCTTTCACTGACTCTAACAAGGTAGACCAATGT ↑ 1 4 3 2 Human: GTGAAAATGAGTTTGACTCTTTTCCCCTAACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGTCATATTGATTATTTTTGGCTTTCACTGACTCTAACAAGGTAGACCAATGT Cluster: [ ] Orangutan: GTGAAAATGAGTTTGACTCTTTTCCCCTAACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGTCATATTGATTATTTTTGGCTTTCACTGACTCTAACAAGGTAGACCAATGT Human > Gorilla --------------- chr6:144569546-144569549 Template switch process: F1: L TTTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTT 1 F3: 4 ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT R RF: TTTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTTTTCCCCTAACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGTCATATTGATTATTTTTGGCTTTCACTGACT RR: AAAAGGGTTGGTCTTTTGTACACTTTTACTCAAACTGAGAAAAGGGGATTGTAATACGTTTAAACTTTCCTTTACGTCAATAGAAAGTACAGTATAACTAATAAAAACCGAAAGTGACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -25.3) TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCT-------TAgtcACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTTTTCCCCTA---ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT Template switch alignment (log-probability: -16.2) TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTT|AGTC|ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTT|AGTC|ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT Chimp > Gorilla --------------- chr6:144569546-144569549 Template switch process: F1: L TTTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTT 1 F3: 4 ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT R RF: TTTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTTTTCCCCTAACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCATGCCATATTGATTATTTTTGGCTTTCACTGACT RR: AAAAGGGTTGGTCTTTTGTACACTTTTACTCAAACTGAGAAAAGGGGATTGTAATACGTTTAAACTTTCCTTTACGTCAATAGAAAGTACGGTATAACTAATAAAAACCGAAAGTGACTGA F2: 3 CTGA 2 Unidirectional alignment (log-probability: -25.3) TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCT-------TAgtcACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTTTTCCCCTA---ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT Template switch alignment (log-probability: -16.2) TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTT|AGTC|ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT TTTCCCAACCAGAAAACATGTGAAAATGAGTTTGACTCTT|AGTC|ACATTATGCAAATTTGAAAGGAAATGCAGTTATCTTTCAT ========== Event 3086 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTGGAATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAACTAAAATAATGGAAA-----GGTACTAGAAAG------------------------------AAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGAT------------------------------CTCCTTC-----TGTTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAG Chimp: TTTGGAATAATTTTCCTAGACGTTTGGAGAGTATCTTGTAGCTAAAATAATGGAAA-----GGTACTAGAAAG------------------------------AAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGAT------------------------------CTCCTTC-----TGTTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAG ↓ 1 3 4 2 ↑ 13 24 Gorilla: TTTGGCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAA----------CAGAAGG------------------------------------------------------------AGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTTTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAG ↓ 13 24 ↑ 1 3 4 2 Human: TTTGGAATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAACTAAAATAATGGAAA-----GGTACTAGAAAG------------------------------AAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGAT------------------------------CTCCTTC-----TGTTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAG Cluster: [ ] Orangutan: TTTGGCATAATTTTCCTACAAGTTTGGAGAGTATCTTGTAGCTAAAATAATGGAAAGGTAC-----TAGAAAGAAAATAGCCCAGAGAAGTTGGGAGCTGAGT------------------------------TGATGACAAAGCCATGTGAT------------------------------CTCCTTC-----TGTTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAG Gorilla > Human --------------- chr6:28346381-28346475 Template switch process: F1: L AGAACCATCAATGTTATTAATG----TATTTAAAATTAATGATATTTTGGAATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAACTA 1 F3: 4 TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACTCCTTTTAAACCACAGAA R RF: AGAACCATCAATGTTATTAATGTATTTATTTAAAATTAATGATATTTTGGCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTTTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACCCCTTTTAAACCACAGAA RR: TCTTGGTAGTTACAATAATTACATAAATAAATTTTAATTACTATAAAACCGTATTAAAAGGATCTTCAAACCTCTCATAGAACATCGATCGTATTACCTTTGTCTTCCTCTAGTGTACCGAAACAGTAGTTGAGTCGAGGGTCGAAGAGACCCGATAAAAGAAAGATCATGGAAAGGTAATAAAATCGATGTTCTATGAGAGGTTTGAAGATCGGAAAAATCTCTGTCAAAGATTTCTATACTCAGTCGTGATGGGGAAAATTTGGTGTCTT F2: 3 CGTATTACCTTTGTCTTCCTCTAGTGTACCGAAACAGTAGTTGAGTCGAGGGTCGAAGAGACCCGATAAAAGAAAGATCATGGAAAGGTAATAAA 2 Unidirectional alignment (log-probability: -177) GaATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAaCTAaaATAATGGAAA-----------------------------------------------------------------------ggtactagaaagaaaatagcccagagaagctgggagctgagttgatgacaaagccatgtgatctccttctgTTTCCATTATgcTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG GCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACC-----------------------------------------------------------------------TTTCCATTATTTTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Template switch alignment (log-probability: -55.9) GaATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAaCTA|AAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTGTTTCCATTATGC|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG GCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTA|AAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTGTTTCCATTATGC|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Human > Gorilla --------------- chr6:28165704-28165802 Template switch process: F1: L AGAACCATCAATGTTATTAATGTATTTATTTAAAATTAATGATATTTTGGCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTA 1 F3: 4 TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACCCCTTTTAAACCACAGAA R RF: AGAACCATCAATGTTATTAATG----TATTTAAAATTAATGATATTTTGGAATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAACTAAAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTGTTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACTCCTTTTAAACCACAGAA RR: TCTTGGTAGTTACAATAATTAC----ATAAATTTTAATTACTATAAAACCTTATTAAAAGGATCTTCAAACCTCTCATAGAACATTGATTTTATTACCTTTCCATGATCTTTCTTTTATCGGGTCTCTTCGACCCTCGACTCAACTACTGTTTCGGTACACTAGAGGAAGACAAAGGTAATACGATCGATGTTCTATGAGAGGTTTGAAGATCGGAAAAATCTCTGTCAAAGATTTCTATACTCAGTCGTGATGAGGAAAATTTGGTGTCTT F2: 3 TTTATTACCTTTCCATGATCTTTCTTTTATCGGGTCTCTTCGACCCTCGACTCAACTACTGTTTCGGTACACTAGAGGAAGACAAAGGTAATACGATCG 2 Unidirectional alignment (log-probability: -182) TTTGGcATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAgCTAgcATAATGGAAA-----------------------------------------------------------------------cagaaggagatcacatggctttgtcatcaactcagctcccagcttctctgggctattttctttctagtaccTTTCCATTATttTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG TTTGGAATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAACTAAAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTG-----------------------------------------------------------------------TTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Template switch alignment (log-probability: -56.3) TTTGGcATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTA|GCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTT|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG TTTGGAATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTA|GCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTT|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Gorilla > Chimp --------------- chr6:28952070-28952164 Template switch process: F1: L AGAACCATCAATGTTATTAATG----TATTTAAAATTAATGATATTTTGGAATAATTTTCCTAGACGTTTGGAGAGTATCTTGTAGCTA 1 F3: 4 TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACCCCTTTTAAACCACAGAA R RF: AGAACCATCAATGTTATTAATGTATTTATTTAAAATTAATGATATTTTGGCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTTTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACCCCTTTTAAACCACAGAA RR: TCTTGGTAGTTACAATAATTACATAAATAAATTTTAATTACTATAAAACCGTATTAAAAGGATCTTCAAACCTCTCATAGAACATCGATCGTATTACCTTTGTCTTCCTCTAGTGTACCGAAACAGTAGTTGAGTCGAGGGTCGAAGAGACCCGATAAAAGAAAGATCATGGAAAGGTAATAAAATCGATGTTCTATGAGAGGTTTGAAGATCGGAAAAATCTCTGTCAAAGATTTCTATACTCAGTCGTGATGGGGAAAATTTGGTGTCTT F2: 3 CGTATTACCTTTGTCTTCCTCTAGTGTACCGAAACAGTAGTTGAGTCGAGGGTCGAAGAGACCCGATAAAAGAAAGATCATGGAAAGGTAATAAA 2 Unidirectional alignment (log-probability: -171) GaATAATTTTCCTAGAcGTTTGGAGAGTATCTTGTAGCTAaaATAATGGAAA-----------------------------------------------------------------------ggtactagaaagaaaatagcccagagaagctgggagctgagttgatgacaaagccatgtgatctccttctgTTTCCATTATgcTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG GCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACC-----------------------------------------------------------------------TTTCCATTATTTTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Template switch alignment (log-probability: -50.3) GaATAATTTTCCTAGAcGTTTGGAGAGTATCTTGTAGCTA|AAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTGTTTCCATTATGC|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG GCATAATTTTCCTAGAAGTTTGGAGAGTATCTTGTAGCTA|AAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTGTTTCCATTATGC|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Chimp > Gorilla --------------- chr6:28165684-28165802 Template switch process: F1: L AGAACCATCAATGTTATTAATGTATTTATTTAAAATTAATGATATTTTGGCATAATTTTCCTAGA 1 F3: 4 TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACCCCTTTTAAACCACAGAA R RF: AGAACCATCAATGTTATTAATG----TATTTAAAATTAATGATATTTTGGAATAATTTTCCTAGACGTTTGGAGAGTATCTTGTAGCTAAAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTGTTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAGACAGTTTCTAAAGATATGAGTCAGCACTACCCCTTTTAAACCACAGAA RR: TCTTGGTAGTTACAATAATTAC----ATAAATTTTAATTACTATAAAACCTTATTAAAAGGATCTGCAAACCTCTCATAGAACATCGATTTTATTACCTTTCCATGATCTTTCTTTTATCGGGTCTCTTCGACCCTCGACTCAACTACTGTTTCGGTACACTAGAGGAAGACAAAGGTAATACGATCGATGTTCTATGAGAGGTTTGAAGATCGGAAAAATCTCTGTCAAAGATTTCTATACTCAGTCGTGATGGGGAAAATTTGGTGTCTT F2: 3 TTTATTACCTTTCCATGATCTTTCTTTTATCGGGTCTCTTCGACCCTCGACTCAACTACTGTTTCGGTACACTAGAGGAAGACAAAGGTAATACGATCGATGTTCTATGAGAGGTTTGA 2 Unidirectional alignment (log-probability: -177) ttatTTAAAATTAATGATATTTTGGcATAATTTTCCTAGAaGTTTGGAGAGTATCTTGTAGCTAgcATAATGGAAA-----------------------------------------------------------------------cagaaggagatcacatggctttgtcatcaactcagctcccagcttctctgggctattttctttctagtaccTTTCCATTATttTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG ----TTAAAATTAATGATATTTTGGAATAATTTTCCTAGACGTTTGGAGAGTATCTTGTAGCTAAAATAATGGAAAGGTACTAGAAAGAAAATAGCCCAGAGAAGCTGGGAGCTGAGTTGATGACAAAGCCATGTGATCTCCTTCTG-----------------------------------------------------------------------TTTCCATTATGCTAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG Template switch alignment (log-probability: -52.9) tTATTTAAAATTAATGATATTTTGGcATAATTTTCCTAGA|AGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTT|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG -TATTTAAAATTAATGATATTTTGGAATAATTTTCCTAGA|AGTTTGGAGAGTATCTTGTAGCTAGCATAATGGAAACAGAAGGAGATCACATGGCTTTGTCATCAACTCAGCTCCCAGCTTCTCTGGGCTATTTTCTTTCTAGTACCTTTCCATTATTT|TAGCTACAAGATACTCTCCAAACTTCTAGCCTTTTTAGAG ========== Event 3087 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGACGAAAGTG----CAAACAGTTACTGTCTA------GTCCCATTATTACTTGGAACAGAc ↓ 3 2 1 4 Chimp: AGAGACGAAAGTG----CAAACAGTTACTGTCTAGTAACTGTTCCATTATTACTTGGAACAGAC Gorilla: AGAGACGAAAGTG--------CAGTTACTGTCTA------GTCCCATTATTACTTGGAACAGAC Human: AGAGACGAAAGTG----CAAACAGTTACTGTCTA------GTCCCATTATTACTTGGAACAGAc Cluster: [ ] Orangutan: AGAGACGAAAGTGCAAA----CAGTTACTGTCTA------GTCCCATTATTACTTTGAACAGAC Human > Chimp ------------- chr6:148026321-148026327 Template switch process: F1: L TATTTTCCATAAGAGACGAAAGTGCAAACAGTTACTGTCTAGT 1 F3: 4 CCATTATTACTTGGAACAGACTTTTTCTTCTTTTCCTTGT R RF: TATTTTCCATAAGAGACGAAAGTGCAAACAGTTACTGTCTAGTCCCATTATTACTTGGAACAGACTTTTTCTTCTTTTCCTTGT RR: ATAAAAGGTATTCTCTGCTTTCACGTTTGTCAATGACAGATCAGGGTAATAATGAACCTTGTCTGAAAAAGAAGAAAAGGAACA F2: 3 TTGTCAA 2 Unidirectional alignment (log-probability: -25.6) TTTCCATAAGAGACGAAAGTGCAAACAGTTACTGTCTAgtaactGTtCCATTATTACTTGGAACAGACTTTTTCTTCTTTTCCTTGT TTTCCATAAGAGACGAAAGTGCAAACAGTTACTGTCTA------GTCCCATTATTACTTGGAACAGACTTTTTCTTCTTTTCCTTGT Template switch alignment (log-probability: -16.2) TTTCCATAAGAGACGAAAGTGCAAACAGTTACTGTCTAGT|AACTGTT|CCATTATTACTTGGAACAGACTTTTTCTTCTTTTCCTTGT TTTCCATAAGAGACGAAAGTGCAAACAGTTACTGTCTAGT|AACTGTT|CCATTATTACTTGGAACAGACTTTTTCTTCTTTTCCTTGT ========== Event 3088 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAATGATTTAACAAAGTTGAA-----GGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTG Chimp: CAATGATTTAACAAAGTTGAA-----GGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTG ↓ 1 4 3 2 Gorilla: CAATGATTTAACAAAGTTGAATCTGCCACTCCTGGAGAGTGGCAGATGAACTCGTTACAGTCACTG ↑ 1 4 3 2 Human: CAATGATTTAACAAAGTTGAA-----GGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTG Cluster: [ ] Orangutan: CAATGATTTCACAAAGTTGAA-----GGCTCCTGGAGACTGGCAGATGAACACGTTACAGTCACTG Human > Gorilla --------------- chr6:26819814-26819820 Template switch process: F1: L CTACATTTAAACTGAACAAACAATGATTTAACAAAGTTGAA 1 F3: 4 CTCCTGGAGAGTGGCAGATGAACTCGTTACAGTCACTGCT R RF: CTACATTTAAATTGAACAAACAATGATTTAACAAAGTTGAAGGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTGCT RR: GATGTAAATTTAACTTGTTTGTTACTAAATTGTTTCAACTTCCGAGGACCTCTCACCGTCTACTTGTGCAATGTCAGTGACGA F2: 3 ACCGTCT 2 Unidirectional alignment (log-probability: -40.2) TACATTTAAAcTGAACAAACAATGATTTAACAAAGTTGAAtctgccaCTCCTGGAGAGTGGCAGATGAACtCGTTACAGTCACTGCT TACATTTAAATTGAACAAACAATGATTTAACAAAGTTGAA-----GGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTGCT Template switch alignment (log-probability: -27.7) TACATTTAAAcTGAACAAACAATGATTTAACAAAGTTGAA|TCTGCCA|CTCCTGGAGAGTGGCAGATGAACtCGTTACAGTCACTGCT TACATTTAAATTGAACAAACAATGATTTAACAAAGTTGAA|TCTGCCA|CTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTGCT Chimp > Gorilla --------------- chr6:26819814-26819820 Template switch process: F1: L CTACATTTAAACTGAACAAACAATGATTTAACAAAGTTGAA 1 F3: 4 CTCCTGGAGAGTGGCAGATGAACTCGTTACAGTCACTGCT R RF: CTACATTTAAATTGAACAAACAATGATTTAACAAAGTTGAAGGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTGCT RR: GATGTAAATTTAACTTGTTTGTTACTAAATTGTTTCAACTTCCGAGGACCTCTCACCGTCTACTTGTGCAATGTCAGTGACGA F2: 3 ACCGTCT 2 Unidirectional alignment (log-probability: -40.2) TACATTTAAAcTGAACAAACAATGATTTAACAAAGTTGAAtctgccaCTCCTGGAGAGTGGCAGATGAACtCGTTACAGTCACTGCT TACATTTAAATTGAACAAACAATGATTTAACAAAGTTGAA-----GGCTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTGCT Template switch alignment (log-probability: -27.7) TACATTTAAAcTGAACAAACAATGATTTAACAAAGTTGAA|TCTGCCA|CTCCTGGAGAGTGGCAGATGAACtCGTTACAGTCACTGCT TACATTTAAATTGAACAAACAATGATTTAACAAAGTTGAA|TCTGCCA|CTCCTGGAGAGTGGCAGATGAACACGTTACAGTCACTGCT ========== Event 3089 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CGATTGCACTTTGTTTGTCCATGCATCCTCTTGAAACTTAGTGAATTT-TTTTGTGATAAGAATGATTAAAAAAACCTTTCTGGGACAAATATGTTAATCACATTTAATCACATGTAATCAAAATTTTGGTCTTTTAACCA ↑ 3 2 4 1 Chimp: AGATTGCACCTTGTTTGTCCATGCATCCTCTTGAAACTTAGTGAAttt-ttttGTGATAAGAATGATTaaaaaaaCCTTTCTGGGACAAATATTTTAATCACATTTA----------ATCAAAATTTTGGTCTTTTAACCA Gorilla: CGATCGCACTTTGTTTGTCCATGCGTCCTCTTGAAACTTAGTGAAttttttttGTGATAAGAATGATTaaaaaaaCCTTTCTGGGACAAATATTTTAATCACATTTAATCACATGTAATCAAAACTTTGGTCTTTTAACCA Human: CGATTGCACTTTGTTTGTCCATGCATCCTCTTGAAACTTAGTGAATTT-TTTTGTGATAAGAATGATTAAAAAAACCTTTCTGGGACAAATATGTTAATCACATTTAATCACATGTAATCAAAATTTTGGTCTTTTAACCA Cluster: [ ] Orangutan: TGATTGCACCTTGTTTGTCCATGCATCCTCTTGAAACTTAGTGAATAT-TTTTGTGACAAGAACGATaaaaaaaaCCTTTCTGGGACAAATATTTTAATCACATTTAATCACGTGTAATCAAAATTTTGGTCTTTTAACCA Chimp > Human ------------- chr6:145061587-145061590 Template switch process: F1: L TTAAAAAAACCTTTCTGGGACAAATATGTTAATCACATTTAATCA 1 F3: 4 TAATCAAAATTTTGGTCTTTTAACCAAAACATTTTTTATAGA R RF: CATGCATCCTCTTGAAACTTAGTGAATTTTTTTGTGATAAGAATGATTAAAAAAACCTTTCTGGGACAAATATTTTAATCACATTTAATCAAAATTTTGGTCTTTTAACCAAAACATTTTTTATAGA RR: GTACGTAGGAGAACTTTGAATCACTTAAAAAAACACTATTCTTACTAATTTTTTTGGAAAGACCCTGTTTATAAAATTAGTGTAAATTAGTTTTAAAACCAGAAAATTGGTTTTGTAAAAAATATCT F2: 3 GTAC 2 Unidirectional alignment (log-probability: -31.3) AAAACCTTTCTGGGACAAATATgttaatcacaTTTAATCACATgTAATCAAAATTTTGGTCTTTTAACCAAAACATTTTTTATA AAAACCTTTCTGGGACAAATAT----------TTTAATCACATTTAATCAAAATTTTGGTCTTTTAACCAAAACATTTTTTATA Template switch alignment (log-probability: -21.9) AAAACCTTTCTGGGACAAATATgTTAATCACATTTAATCA|CATG|TAATCAAAATTTTGGTCTTTTAACCAAAACATTTTTTATA AAAACCTTTCTGGGACAAATATTTTAATCACATTTAATCA|CATG|TAATCAAAATTTTGGTCTTTTAACCAAAACATTTTTTATA ========== Event 3090 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATTTCGGTTCATCCTATATG---------GGTACTATTAATGTATCTAATTATACATTAACAGTACTTATTAA--------TAATA Chimp: AATTTTGGTTCATCCTATATG---------Ggtactattaatgtatctaattatacattaatagtacttaataa----tacttaata Gorilla: AATTTCGGTTCATCCTATATG------------------GATGTATCtaattatacattaatagtacttaataatact----taata ↓ 14 3 2 Human: AATTTCGGTTCATCCTATATG---------GGTACTATTAATGTATCTAATTATACATTAACAGTACTTATTAA--------TAATA Cluster: [ ] Orangutan: AATTTTGGTTCATCCTATATGGGTACTATT---------AATGGATCTAATTATACATTAACAGTACTTATTAA--------TAATA Gorilla > Human --------------- chr6:24085583-24085591 Template switch process: F1: L CATAAACGTTACATGTATATAATTTCGGTTCATCCTATATGG 1 F3: 4 ATGTATCTAATTATACATTAACAGTACTTATTAATA R RF: CATAAACGTTACATGTATATAATTTCGGTTCATCCTATATGGATGTATCTAATTATACATTAATAGTACTTAATAATA RR: GTATTTGCAATGTACATATATTAAAGCCAAGTAGGATATACCTACATAGATTAATATGTAATTATCATGAATTATTAT F2: 3 ATTATCATG 2 Unidirectional alignment (log-probability: -41.8) TAAACGTTACATGTATATAATTTCGGTTCATCCTATATGGgtactattaATGTATCTAATTATACATTAAcAGTACTTAtTAATA---- TAAACGTTACATGTATATAATTTCGGTTCATCCTATATGG---------ATGTATCTAATTATACATTAATAGTACTTAATAATACTTA Template switch alignment (log-probability: -27.8) TAAACGTTACATGTATATAATTTCGGTTCATCCTATATGG|GTACTATTA|ATGTATCTAATTATACATTAAcAGTACTTAtTAATA TAAACGTTACATGTATATAATTTCGGTTCATCCTATATGG|GTACTATTA|ATGTATCTAATTATACATTAATAGTACTTAATAATA ========== Event 3091 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TCCACTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAAGCTGTT---GATACTGCAGTTTTGTCACATTTTAT ↑ 3 2 1 4 Chimp: TCCACTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAGGCTGTTTTAAAATGTGCAGTTTTGTCACATTTTAT Gorilla: TCCATTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAAGCTGTT---GATACTGCAGTTCTGTCACATTTTAT Human: TCCACTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAAGCTGTT---GATACTGCAGTTTTGTCACATTTTAT Cluster: [ ] Orangutan: CCCACTGTGGCTGCTTTTGGTATTTTAGAGACCTCCAAGCTGTT---GATACTGCAGTTTTGTCACATTTTAT Chimp > Human ------------- chr6:145249542-145249546 Template switch process: F1: L ATCCTCCACTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAAGCTGTT 1 F3: 4 TGCAGTTTTGTCACATTTTATCAGTTCCTCTAAGGTGTCT R RF: ATCCTCCACTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAGGCTGTTTTAAAATGTGCAGTTTTGTCACATTTTATCAGTTCCTCTAAGGTGTCT RR: TAGGAGGTGACACCGACGAAAACCATAGAATCTCTGGAGGTCCGACAAAATTTTACACGTCAAAACAGTGTAAAATAGTCAAGGAGATTCCACAGA F2: 3 CATAG 2 Unidirectional alignment (log-probability: -33.3) CTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAaGCTGT-------TGatacTGCAGTTTTGTCACATTTTATCAGTTCCTCTAAGGTGTCT CTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAGGCTGTTTTAAAATG----TGCAGTTTTGTCACATTTTATCAGTTCCTCTAAGGTGTCT Template switch alignment (log-probability: -22) CTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAaGCTGTT|GATAC|TGCAGTTTTGTCACATTTTATCAGTTCCTCTAAGGTGTCT CTGTGGCTGCTTTTGGTATCTTAGAGACCTCCAGGCTGTT|GATAC|TGCAGTTTTGTCACATTTTATCAGTTCCTCTAAGGTGTCT ========== Event 3092 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AACCCTTTCAGTGGGGGGAAC----CCACTGAAAACATAAGACCCCTGTTCAATGACGTGAGAGCAGGTCAGCGTAGCAGTGGAGTCATCTACAGAAGGATA Chimp: AACCCTTTCAGTGGGGGGAAC--CATCAAGAAAAACATAAGACCCCTGTTCAATGGGGTGAGAGCAGGTCAGCGTAGCAGTGGAGTCATCTACAGAAGGATA Gorilla: AACCCTTTCAGTGGGGGGAACCA--TCAAGAAAAACATAAGACCCCTGTTCAATGGGGTGAGAGCAGGTCAGCGTAGCAGTGGAGTCATCTACAGAAGGATA ↓ 1 4 3 2 Human: AACCCTTTCAGTGGGGGGAAC----CCACTGAAAACATAAGACCCCTGTTCAATGACGTGAGAGCAGGTCAGCGTAGCAGTGGAGTCATCTACAGAAGGATA Cluster: [ ] Orangutan: AGCCCTTTCAGTGGGGGGAACCA--TCAAGAAAAACATAAGACCCCTGTTCAGTGGGGTGAGAGCAGGTCAGCGCAGCAGTGGAGTCATCTACAGAAGGATA Gorilla > Human --------------- chr6:145269699-145269703 Template switch process: F1: L TACTATTTCATCCAATATGCAACCCTTTCAGTGGGGGGAACC 1 F3: 4 AAAACATAAGACCCCTGTTCAATGACGTGAGAGCAGGTCA R RF: TACTATTTCATCCAATATGCAACCCTTTCAGTGGGGGGAACCATCAAGAAAAACATAAGACCCCTGTTCAATGGGGTGAGAGCAGGTCAGCGTAGCAGTG RR: ATGATAAAGTAGGTTATACGTTGGGAAAGTCACCCCCCTTGGTAGTTCTTTTTGTATTCTGGGGACAAGTTACCCCACTCTCGTCCAGTCGCATCGTCAC F2: 3 GTCAC 2 Unidirectional alignment (log-probability: -38.7) CTATTTCATCCAATATGCAACCCTTTCAGTGGGGGGAACC--CActgAAAACATAAGACCCCTGTTCAATGacGTGAGAGCAGGTCA CTATTTCATCCAATATGCAACCCTTTCAGTGGGGGGAACCATCAAGAAAAACATAAGACCCCTGTTCAATGGGGTGAGAGCAGGTCA Template switch alignment (log-probability: -27.4) CTATTTCATCCAATATGCAACCCTTTCAGTGGGGGGAACC|CACTG|AAAACATAAGACCCCTGTTCAATGacGTGAGAGCAGGTCA CTATTTCATCCAATATGCAACCCTTTCAGTGGGGGGAACC|CACTG|AAAACATAAGACCCCTGTTCAATGGGGTGAGAGCAGGTCA ========== Event 3093 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAACCTAATGAAGCGTACAGTT----CTTACT ↑ 3 2 1 4 Chimp: ACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA---ATCCCAGCGTACAGTT----CTTACT Gorilla: ACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA---ATCCCAGCGTACAGTT--------CT Human: ACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAACCTAATGAAGCGTACAGTT----CTTACT Cluster: [ ] Orangutan: ACATTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA---ATCCCAGCGTACAGTTCTTA----CT Chimp > Human ------------- chr6:147859711-147859718 Template switch process: F1: L CAACACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA 1 F3: 4 AGCGTACAGTTCTTACTCTGTTTTTTGGGTTTTTTGTTTG R RF: CAACACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAAATCCCAGCGTACAGTTCTTACTCTGTTTTTTGGGTTTTTTGTTTG RR: GTTGTGTGAATTTTCGTAAAAGAAGTAATCCAACGTACATTTAGGGTCGCATGTCAAGAATGAGACAAAAAACCCAAAAAACAAAC F2: 3 AGTAATCC 2 Unidirectional alignment (log-probability: -29.9) AACACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA---CCtaatgaAGCGTACAGTTCTTACTCTGTTTTTTGGGTTTTTTGTTTG AACACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAAATCCC------AGCGTACAGTTCTTACTCTGTTTTTTGGGTTTTTTGTTTG Template switch alignment (log-probability: -16.3) AACACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA|CCTAATGA|AGCGTACAGTTCTTACTCTGTTTTTTGGGTTTTTTGTTTG AACACACTTAAAAGCATTTTCTTCATTAGGTTGCATGTAA|CCTAATGA|AGCGTACAGTTCTTACTCTGTTTTTTGGGTTTTTTGTTTG ========== Event 3094 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTCTCCATAAACCTCACACTTAATGGAATAAGCTCATTTCAGCTCCAGATCCCTAgtga ↓ 1 3 4 2 Chimp: GCTCTCCATAAACCTCACACTAAATGAGC---TTTCATTTCAGCTCCAGATCCCTAgtga ↑ 1 3 4 2 Gorilla: GCTCTCCATAAACCTCACACTTAATGGAATAAGCTCATTTCAGCTCCAGATCCCTAgtga Human: GCTCTCCATAAACCTCACACTTAATGGAATAAGCTCATTTCAGCTCCAGATCCCTAgtga Cluster: [ ] Orangutan: GCTCTCCATAAACCTCACACTTAATGGAATAAGCTCATTTCAGCTCCAGATCCCTAgtga Human > Chimp ------------- chr6:151707965-151707974 Template switch process: F1: L AGCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACT 1 F3: 4 TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT R RF: AGCTCAGTGTGACATACCAGGCTCTCCATAAACCTCACACTTAATGGAATAAGCTCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT RR: TCGAGTCACACTGTATGGTCCGAGAGGTATTTGGAGTGTGAATTACCTTATTCGAGTAAAGTCGAGGTCTAGGGATCACTTGAACACCTGTTCA F2: 3 TTCGAGTAAA 2 Unidirectional alignment (log-probability: -36.3) GCTCAGTGgGACATACCAGGCTCTCCATAAACCTCACACTaAATG-----AGCttTCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT GCTCAGTGTGACATACCAGGCTCTCCATAAACCTCACACTTAATGGAATAAGC--TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT Template switch alignment (log-probability: -22.5) GCTCAGTGgGACATACCAGGCTCTCCATAAACCTCACACT|AAATGAGCTT|TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT GCTCAGTGTGACATACCAGGCTCTCCATAAACCTCACACT|AAATGAGCTT|TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT Gorilla > Chimp --------------- chr6:151707965-151707974 Template switch process: F1: L AGCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACT 1 F3: 4 TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT R RF: AGCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACTTAATGGAATAAGCTCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT RR: TCGAGTCACCCTGTATGGTCCGAGAGGTATTTGGAGTGTGAATTACCTTATTCGAGTAAAGTCGAGGTCTAGGGATCACTTGAACACCTGTTCA F2: 3 TTCGAGTAAA 2 Unidirectional alignment (log-probability: -29.4) GCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACTaAATG-----AGCttTCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT GCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACTTAATGGAATAAGC--TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT Template switch alignment (log-probability: -17) GCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACT|AAATGAGCTT|TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT GCTCAGTGGGACATACCAGGCTCTCCATAAACCTCACACT|AAATGAGCTT|TCATTTCAGCTCCAGATCCCTAGTGAACTTGTGGACAAGT ========== Event 3095 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTAACTGGAATTCAGGCCATTCA-------GAAATGTATTAGGTTGTAAG--ATTTCCTCTGAA Chimp: CTAACTGGAATTCAGGCCATTCA-------GAAATGTATTAGGTTGTAAG--ATTTCCTCTGAA ↓ 3 1 2 4 Gorilla: CTAACTGGAATTCAGGCCATTCA--------------TCTGAATTGTAAG--ATTTCATCTGAA ↑ 3 1 2 4 Human: CTAACTGGAATTCAGGCCATTCA-------GAAATGTATTAGGTTGTAAG--ATTTCCTCTGAA Cluster: [ ] Orangutan: CTAACTGGAATTCAGGCCATTCAGAAATGT-------ATTAGGTTGTAAGAAGTTCCCTCTGAA Human > Gorilla --------------- chr6:150840603-150840608 Template switch process: F1: L ATAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA 1 F3: 4 TTGTAAGATTTCATCTGAAAATGTTGCCTCTTATGAATTA R RF: ATAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCAGAAATGTATTAGGTTGTAAGATTTCCTCTGAAAATGTTGCCTCTTATGAATTA RR: TATTGACCCGTTTGAACCGATTGACCTTAAGTCCGGTAAGTCTTTACATAATCCAACATTCTAAAGGAGACTTTTACAACGGAGAATACTTAAT F2: 3 AAGTCT 2 Unidirectional alignment (log-probability: -31) TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCAtctGAA----------TTGTAAGATTTCaTCTGAAAATGTTGCCTCTTATGAATTA TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA---GAAATGTATTAGGTTGTAAGATTTCCTCTGAAAATGTTGCCTCTTATGAATTA Template switch alignment (log-probability: -22) TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA|TCTGAA|TTGTAAGATTTCaTCTGAAAATGTTGCCTCTTATGAATTA TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA|TCTGAA|TTGTAAGATTTCCTCTGAAAATGTTGCCTCTTATGAATTA Chimp > Gorilla --------------- chr6:150840603-150840608 Template switch process: F1: L ATAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA 1 F3: 4 TTGTAAGATTTCATCTGAAAATGTTGCCTCTTATGAATTA R RF: ATAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCAGAAATGTATTAGGTTGTAAGATTTCCTCTGAAAATGTTGCCTCTTATGAATTA RR: TATTGACCCGTTTGAACCGATTGACCTTAAGTCCGGTAAGTCTTTACATAATCCAACATTCTAAAGGAGACTTTTACAACGGAGAATACTTAAT F2: 3 AAGTCT 2 Unidirectional alignment (log-probability: -31) TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCAtctGAA----------TTGTAAGATTTCaTCTGAAAATGTTGCCTCTTATGAATTA TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA---GAAATGTATTAGGTTGTAAGATTTCCTCTGAAAATGTTGCCTCTTATGAATTA Template switch alignment (log-probability: -22) TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA|TCTGAA|TTGTAAGATTTCaTCTGAAAATGTTGCCTCTTATGAATTA TAACTGGGCAAACTTGGCTAACTGGAATTCAGGCCATTCA|TCTGAA|TTGTAAGATTTCCTCTGAAAATGTTGCCTCTTATGAATTA ========== Event 3096 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TTATTTCTGGGACCAGCCCTCATCAAGTCCACGTCATCTGACTCGCCTTACTTCAGGAAAATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGAGCACTTGAACAGAATCTGAAAAGAATTGCATGTTTATCC Chimp: TTATTTCTGGGACCAGCCCTCATCAAGTCCATGTAATCTGACTCGCCTTACTTCAGGAAAATTGGTTTCAGAACATATTTCTGGTGAACTA-------------------GAATCTGAAAAGAATTGCATGTTTATCC ↓ 3 2 4 1 Gorilla: TTATTTCTGGGACCAGCCCTCATCAAGTCCATGTCATCTGACTTGCCTTACTTCAGGAAAATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGAGCACTTGAAGAGAATCTGAAAAGAATTGCATGTTTATCC Human: TTATTTCTGGGACCAGCCCTCATCAAGTCCACGTCATCTGACTCGCCTTACTTCAGGAAAATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGAGCACTTGAACAGAATCTGAAAAGAATTGCATGTTTATCC Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr6:22981905-22981915 Template switch process: F1: L CTTCAGGAAAATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGA 1 F3: 4 GAATCTGAAAAGAATTGCATGTTTATCCATATATATAGTT R RF: TCATCAAGTCCATGTAATCTGACTCGCCTTACTTCAGGAAAATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGAAAAGAATTGCATGTTTATCCATATATATAGTT RR: AGTAGTTCAGGTACATTAGACTGAGCGGAATGAAGTCCTTTTAACCAAAGTCTTGTATAAAGACCACTTGATCTTAGACTTTTCTTAACGTACAAATAGGTATATATATCAA F2: 3 AGAAGTTCACG 2 Unidirectional alignment (log-probability: -38.2) AATTGGTTTCAGAACATATTTCTGGTGAACTagaatctgagcacttgaagAGAATCTGAAAAGAATTGCATGTTTATCCATATATATAGTT AATTGGTTTCAGAACATATTTCTGGTGAACT-------------------AGAATCTGAAAAGAATTGCATGTTTATCCATATATATAGTT Template switch alignment (log-probability: -28.4) AATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGA|GcACTTGAaGA|GAATCTGAAAAGAATTGCATGTTTATCCATATATATAGTT AATTGGTTTCAGAACATATTTCTGGTGAACTAGAATCTGA|GGACTTGATGA|GAATCTGAAAAGAATTGCATGTTTATCCATATATATAGTT ========== Event 3097 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAA-------------------------------------------CAGACTCCTGTGATCAGAGGCAGAGCGTATGACCATTTAAAGGTATCATTCCACATAACCTGGTGGAAAAGGACATCTTCGTTTCCTGTGCTGTTAGGTGTCAGTTTGGGGGAAACGTGTTCCC Chimp: TTCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAA-------------------------------------------GAGACTCCTGTGATCAGAGGCAGAGCGTATGACCATTTAAAGGTATCATTCCACATAACCTGGTGGAAAAGGACATCTTTGTTTCCTGTGCTGTTAGGTGTCAGTTTGGGGGAAACGTGTTCCC ↓ 4 1 3 2 Gorilla: TTCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAA---------------------------CTGAAAATTATAAGAACTGACTCCTGTGATCAGAGGCAGAGCATATGACCATTTAAAGGTATCATTCCACATAACCTGGTGGGAAAGGACATCTTCGTTTCCTGTGCTGTCAGGTGTCAGTTTGGGGGAAACGTGTTCCC Human: TTCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAA-------------------------------------------CAGACTCCTGTGATCAGAGGCAGAGCGTATGACCATTTAAAGGTATCATTCCACATAACCTGGTGGAAAAGGACATCTTCGTTTCCTGTGCTGTTAGGTGTCAGTTTGGGGGAAACGTGTTCCC Cluster: [ ] Orangutan: TTCTTGTGGGAGGAAATGTAAATAATAAGAACTGATTAAAAAGACACTCCTGTGATCAGAGGCAGAGCGTATGACCATTTAAAGGTATCATCATTCCACATAACCTGGTGGAAAAGGGCATCTTCGTTTCCTGTGCTGTTAGGTGTCACTTTGGGGGAAACGTGTTCCCCAGGTTATGCACAGATGGCAGCACAGGCATGGAGTGAAGGCCTCGGGGGGTGAGCACAGCCAGTCTGCTCACGGACAGAAGGAAAAGCAGCCATCGTGAATGCTCCTCTGCCGCAGCTGCTTCAGTAGCAGGAGCAGCAGCTCATATAACAAATGTTTCATGACGAATGCAAACAAAAGCCAGCTCCAAAATTCCAGCCATGTTATGTCCAAGCCAGTTCAAAATCATATAACCACTCCATTTGAGTTTTTTCTCCTCTCTAAATACATTCCATATGAGCCGTGGTGTCAGGGTTGCTGGGATCGCCTGCGTTCACTCAGAAAACTGTTGTTAACGCCCAGACTGAAGGGAAAGTCAATCAGTGGGAAAACAAACTCAAAGAAAACACGGAGGCCCAGGTGTGGGGGAAGGAGTTTTCCCCAGCCAGGCAGGACCCCTGGAATGAGGCTGGAGGCTGGGGAACACTCTTCCAGCACAGAAGGAAGAGTGTTCTTGCCTGGGAGCAGGAATGTGTTCAGTGGGGCCCCTGTGCCTGCGGAGGCCTGGCCACAGCCAAGCACCgcgactcaaagtgtggtccacggaccggtgccagtccgcaagctgcttgctaccagcccgtgacaagataagggcagaaattaagaagcagcatttggaagctttgatgggaattttacgtggctgtggtcatttttctgacaatttatttttatcgtcgtttacaaaagtgtcaatctgaaatggattaggtagggaaaacaaTCTGAGGTTATTGGAGAAGCACCGCCATAGATTTTCCTCCCAGTGTGGGCTGCCTGGGTCAGCAAGGTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTCTTAAGCTACCTGGTTGTGGCACTGTATCATAGGAAACTAATGCAGTTAGAAGTCCTTCTTCCTCCCCATTTCAGGGAAGACCTGAGGTCTGTGATAGTAAGATCTGCTCACGTTCAAAGCAGCTACGAGGAGCAAATCCTGGATTAGGACAAAAAGCCTTCAAAGATGAACATTGTCCTCTGAACTGCCTTTCTTTGTTGTAGAAAGGAATTAGGGggaaaaaaagatgtctaatatttggggaaagctttataagtgattttacagtgatgcaatgaaatatagtgaggtggttggagttttagtttgaagaatgttaatacattggaaaatagaaaaacaatgaaaaatctgacacaatattatatttatattatacaatatttttatatatttgttgtatacacacacacacacacaatatgcttagcagaacaaactagaaggaaaaataccaagagaattgcagttgttagttgtggtggtttctgcatggttttagtttctcctgtagactttcctgtgttctctgcctttcctgtaacacacgtgcgttacAGagagccacatgtattagggaccatccgcgtccagacactatgcgctgtgatatatatacatatttctttttcttttcttttttttttttttttttttttttgttgagatggagtttcattctagttgcccaggctggagtgcactgacgtgatctcggctcaccgcaaccttcgcctcccaggttcaagagattctcctgcctcagcctcctgagtaactgggattacaggcatgcaccaccatgcccagctaattttctgtttttaatagagatggggtttctccatgttggtcaggctggtctcaaactcccgaacttaggtgatccacccgcctcggcctcccaaagtgctgggatgatacatgtgtatttctaatagtcacagcggcatggcaagttagatattagcattgctattctacaaaggacaaaacacagccagacagtctaaggaccatactcagggtctcacagctggtgcaaggcagagcctgtctggctccaaaccctgtgggcttcccaccatgctttgtagctttttctattTTTGTGATCAAACaaaaaaaaaaaaaaaaaaGAGGACAGTGAGAAGGGCCACAACTGAGCAGCGAGGAAACAAGAGGAAACTGTCGCTATGGCCCCTTAAGGGAGGGCTTGCTTGTGCTCTGTCCTCTGTCATTTGCACGAAGTAGAGGAGTCCTCTTTTTTTGGCAGTTAACTCCACAGAGGCTTCTTGAAGACAGGGGCCATAACTCGTCACTTCCTGAGACCCACAGCACCTGCCGCAAAATACTATCNNNNNNNNNNCTATGatgatcgcacccattgcactccagcccaggtgacagagcaagaccttgtttcaaaaataaaataaaataaaaataaaaatGAGAAACTGAAGCCAGCCAGAGAATTTGAGAGAATGATCCATAGTCATCCACAAAAATGTGTAAGTAAGGGGCAAGATTCACATATTTCTGAGCAGTGAATATTAATGTATTTCTGAACACTTTTTCTCAACTCTTAAAGACATGCTGTGAGCCATCAATATTTTTCTAGTCATAATTTTTAGGAGCTAAAATCTCAGTGGTGGTAAGGGCCAAAATAAATAAGCACATGAAAGACAAGGAACATGTGAATATGTGTAATAGGAACAGTCATATGAGCATCCCTCTATAAACCCTTGACTTGGCAAATAACGAGCTGTTCTGGTTCAATAGCGCCACCTAGCATCCAGACATAGAACTCTATGACTAATATTAACCTATTACCTTCTCCCTTCCTAGTGACTTGAAAACTCATGTGTCCAATCCTTTTACCTTGTGTTTGAAATACTTTCCatgactagcactacattagtattcattttcaacacgtttccgttacaaatgtaaacactggagccacagtagggaatttactagacttttgtgggctgccttgagaatacggtcaccaagtattacaaaggaaaaatatgtaacgaattccaaacgagtgacttaaatcctaactttgagaatttaagttcatttataagctgagTGCTTTGTTTGAAATATTTATACTTAGTTTTATAAACAATCACAGAGTACACATTTAAATATTATGCttttttttttttACTATGCATGAATGATAAATTAGACCTCCCATTAGAAGGATAGTAGTGTGCTCACTGATTTCATTGACGTTGCAGTTTCAATTTTGAGGATATTTGCTAGAAAATGATAACAAATAAGTAGAAGAAAACTTTTAAATAGTATGCTACAGAAATAATTCAAATTTTAATCCATCAATAAAAATATCAGCCTGAGTTCTACACTAAATAATAAAAGCTTGGCCTATTTATAATAAAGAACAGTTATTCTTTAAggaaaggacattgagttgggagttaggaggaacttctagttctttgtctgccatggttctgcccatatgacccggagcaaatcCAGTTTTCAAGTGGATGGTCTTTAAGATCTTATTATTCTAATACCAGTGTATCATGTAGAATGTTTTAAGGCTGCTTGTTCTATCTTTTGTTACTTGGCACAATTATGGGGTGCTTTTACCCCCTCAAAAATATTCTTAGGCAGTCCCCATTGCCTTAGTAATCCTCAAGTTTAGTTGTGGGGGTGGTCTCCACCTCTTGGTGTCCTCTAGGACAGGACGAAATCCTAGCTGGAGAGTTCCTCCTTCAGAATGTGTTCTTCCTTGGAGCTACTGATGCTCAAGTGATCAAGACAGGGGTCCCAACTCCAACTCTCTGGTCACGATTTCCATCCCTCTCTCTTCATACcacacacacacacacacacacCTGTGGAGAAGACAGTATGTCATAAtgcagtcaaatgctctaccactgagttatccccccATCttttttttttttttttttttttttttgaggcagagttttacttttgttgtccaggctggagtgcaatggcacgatctcggctcactgcaacctccgcctcctgggttcaggccattctcctgcctcagcttcccatgtagctgggattacaggctcccactaacatgcccacctaatttttgtatttttggtagagacgggatttcaccatgttgatcaggctggtcttgaactcctgacctcaggtgagccacctgcctcggcctcccaaagtgctgggattactggtgtgatccaccatgcccagcccagtatgtcataatgattagagcacaggctctgagatagacagcctgcatgctagaccccctcctccacttaactgcataaccagaggcaaggtatagcccctctaagcctcagtttcccatctggataagatgcataaataatcttatctacttcataggtcttgtgagtcttgcctgatcaatccatgcagagtccttagcccagccttgctatatgatgatgttcagtaaTTAGCCTGCCCACCAAGCCCATCACAGAGACACAGGCTGTCCCTGAAAGAACTGGACTGAGCTCTCTTTGTAACTTCCAGATGAAGAAGAGAAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGCTTGACACAGATGTCAATATGTCCAATTGAGGCCTTAAAATGAGATTTTGGATATGAAAGGATTCCAAGTCCAATTGATTGCAGTAGTCAAACTGCACTTATGAAAGCCAGTGGCGTCTAGGGGAAGAGGGTGGAGTTTTGCAATCAAATAAGTTTATGTGAGTTAAAAatatatatatgtatatctaaattatatatataaattatatgtaatatataatgtatatattgtatgctatatattatatataaaatatatacatttttgtatacattatattattatatacgatatatatacattatataatatatatatattatataGATACACCACTAACTCTGGCTTTAGTTTTAAAAACTGTCATTTTAGAAAGCCTGAATTAAACAAATTCTCTCTTTCATTTTTAATTTCCATTTTTATCTTCCACTTCTATTGCTTCTGTGCTACAGCAAAACTCAAAAATATTCTGGAACCTCCCAAATATACAATGATGGTTAGGAGGAATTCAGATTAGCTATTTTTAGAAAGCAATTAAGTTGTTTCTAAAAACTCAGTTATCATTGATGAAAACAGGACTCCAATTTGCTATTGGTTCATTTACCATCGATATTCTCTATAAAGAtttttttttCACCAGCCGTGTCCCAGGCTCAGATCCTAATAATGTCAGCACTGGATCTtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgCACGTGCGTGCGCACGCACCTACCCATGTTCAAACAACTAGACTCCTTATTAATATAGCACTCATACATGATGCAATCATCTTAAGATCACAAAATCAGTAGGTTTCTAAGTCATAATTacttatataacaatttgcagttataaaacactttcatatagatgatctcatttgattcttacacaaaccccctgaagttgaggaagacaactttttttttctcattttctaaacaaggaaaccaaggctcaaagaggctgaacaacttgctcacggtctcgcccaagtcctaagggatagcactgacattcaagcttctgtccccaggcccatCACAAAACATAGATTTGTGATTCTTCTAAAATCCTTCTTTATATTTTATTCATTAATTCAGAAGTTAATGAGTACTAAGCATTCATAGTATGTATTGCCATTAAACGCAAAAGCTTAAAAATAAATCCTAGGCTGGACACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCATGGCACACATgcctgtaatcccagctactcaggaggctgacgcattgagaattgcttgaacctggaaggtggaggttgcagtgagctgagatcgagccattgcactccagcctgggtgacagagcaagactccatctcaaaaaaaaaTCTAAGCTGAAGGCATGTAACTGTTTCAACTGTAGCTATTGGGCAAATAGTTCATTAAAAAAGAAAACATAATGTAAACCCCTTTAAATTAACTTCTAAACACTTGTGttttttttAGTGAACATTTTTCTGAGGGGAACTCTATAACCATAGGCTGATAACATCATTTAGTTTACAGAAACATCACCAATTCACAAGAATTCAGCCTCTAGGCTTGTTTAATTTACTTTATGAAAGCTTAAATTGCAGCATAATATATGTGCGTTTGGCCTATTTCAACTATTACTATTTGTTTTATTGGAAAAGATAATTACTTTAAGTTATATAATCTTTAAACATGTTTTACTCTTGCTTACTGATTTGTTCTTGCCTTGGGATCATCTCTCCTCCAGGAGAAAGCATTTCCAATTTTATTATGAAAGATTAACAGGAAAATAGAACTTCCTTCACAGACATTGACTTTCTAGGAATAACTTTACAAAAATATTTCTCTTCTCTGAAAACTAATATTTAAATAGGTATAATCTGAAACTACCAGAAAAATTCAACAAACACATCCAGCAAATAAATATCTGAGTGTCTGTGATGTCCCTTTCCTGGGGAAGGGCAGTATAAAGATGAAAACCATGTCTAGCTGGAAAGCTGTCACTAACAGGGCTGGGGCGCATAACCTTGTggagacatttgtgccgggctttaatgggtgcgtaggagtttgccaagtggacgtggaaggaggcattttaatcagaagaaaataacatgattggaagcgtggaggtgagaaagCATAGAAGCACCCAGAGTGAGGAGAGCTGGGGCTTGGGCCAGCCCACATCAGCCCCTGCCTGCGGGCCCAGCCTCTTGGAGCCAGGCTCACTCACCCTGCCTTTAAGACGGTCCTACCAGAGGCAGGAGAAGGATCCACAGCCTCAGCTCTCTGTGGCGCAACCTGGCACTGAGTCACTCATACCAATCTCAGCGCCAGTGGCCAAGCCGCTGCTGCCGGAGGGCCTGTGTCACCCTCCCCCCGTTTCCCTGCCCTCTTCCCATCCTCACCACCACCCAAGCTCCCTGGCTTCCTAACAGCGTGGCAGGGATCCTCCCAGGCCCCCATCCTCCTCCAGCCTGAGTTCTTCCTCCCTGCTGTCTTCCCAGTCTTCCCCGCTAAGATCCCACCACCCTTTAGACCCGGGCTCACACCAGCTCCCGTTGGCCCCCTGTGCCTCGCACTGAATACAGGAGGTCGCACACTGCATCCCCAAACACCAAGTACTGCCCTGCCTGACCACCTATGTTCCCCTGGGCCCACCAGCATGGACTGTCCTTCTGTTACCAGTCACTGCCTGATCCAGGCCTGAGCTGCCTGTGTCCCCCGACACCGTCATCCTCTGTTCTTCCTGGCCTTCTTCACTGGGAGCCATCGGGATCATCCCTCCAAAACAAGTTCTTCCAGCCCCACCTCCCTCCCACCCTGTGCACCCAGGGAAATTCATCTCTTCTGGGTCCCAACCTTGGCCTCGGGAGAGCCCCAGATGCCCCCCTCTGTGTCTACCCCAGTTACTCAGTGTGGTCAGACTTGGGGGTTGTACAGTTTTCTCTCTCATGATTCATTTCCCCAGGGAAAAAGCTGGCTAATAATATCTGGGTGTGCGGGGGAGGTACCAGTGTGTTTCTGTGTTTAGAGGTGAATTTTTTTCTACTTTAGAATTTAATCACTTCTACTTTGAGCAGTTTTTAGCTGAGCTGACAGTAATATGCTCTGCATTGAGTATTTGTAGGGGTGGAATTAGTCACCACAGATTTCAATTTTTGGACTTTCCTGATAACTCCACAAAGCTGGAAGTCTTCTAACGCTTGAGTAAAGATTGGAAACCTGACCCCAGGGGTTGATGGTTGATCTTTATAAAAACGACCTTGTGGTCTTTTTGTTCTTTTATGCTTAAATTGTCAAGGTCCCTGTCCACCCCGGGGATTAATGTGGTGATGTGGAAAGAGCACTAGACAAAGGATTTCAAAACTGTCTTCAGGCCCTTGGCTTGTGGCCTTAGCACTCTGACATTCTTTGCTTATAAAGTGTACCCCCTGCCGGGGCGAAGTACAATCCTTACCCGTTTTGCATGACTCAACATTTTATAATGGAAGCTTCTATTCTTGTCTGGTTAAATCTTTTTCAAATAAGAATATTTCTTGGTCTGTATATTTTTCTTGTCTGAGACATTTTTATCAATACATAATGTCCTAGCTTTTCACATCTTGCAAATGGCACAGAATTGTGAAAGAATACAGCAAAAAGCTAGAAATATACCTGTGCGTATAACATTGCTGGGGATTTTTATGTGTGGTTTCTTGTGGGTTCTAGTAAGCACATTCATTTCATTACCTACAAACGCATAGAAAAATCCAACATAATCCCCCACTGATGAGAAGAAGAGAGGGTTGTTTGTCAGGTGGGGTAGTTTCACTTGACTTGAAGGTCTCACCCCGCCCCTCATCTTTACCATACCATGCGCTTCTAGATGCTTCTGCTGCATTGTCAGCCAGACTCTACCAGAACTGTTTTTCAAAACATGTGTTCCTAGGATTTTACTTCCCTGCATTTTTTGCtatatctattaagtaatgcatatatacaattaaaaatcaaatagtcctataagatgcataatgaaaagcagcagtttcctattccaacccttccaaagatgaagtctgatgttgcagagccaatcactttcagcgcagccagatgtttcttcggataatcaccgcgctatctgtaactagtatgcacaggctgctatttcttgatttactggggtcatgatctcattctcttattccattacctttacttctacttccttgctcctctctgtcttcctaagatggtcatacccacatttgagatgcatggtcctgctgacgttgctatgactatatacattttgttggctgctgatctgagtagtacatcatgattttgtttcatttcttgcacaacttaattgtttttcctggaattatttattgccttcatttatttgcctagatttatttgtacctatcaaaaattttgtatgtaccaaaattttcatatgtgccattagatctgctgcattcaatattacttttggtattatttaaatattaattaccagataagtatgtcagttccatcccaacctgccctcccttcccccagaggccctctcctctttccacccagagctctttaagctccatcgcaacctgccctcccttcccccagagaccctctcttcccccagaggccctcccttcccccagaggccctctcctctttccaccaagaaagctcctgctcctagtgtatctgggctcattactctaaacacagctttactgcagcttccctttactatatttctcagttgggttccagttttcttaatctcggggatgctatttcttgatttaataactcattttacttcaagatgttcctaagttgcctcctcatgaaaggtgcatgggagggaaattttttttgagtcattgaaggtttgaaaagctcagtattccagtctaacttgatggctagtttggttctcatattcatgctcattctctctctctctctctccttggattgtctctttataccttttatgaaattttacaatatgcctcggtatgtgtgctaaatatttagtagatactttcaggcttaaaactcctgtcttctatttctgggaattcttaacattttgtttctttgatgattttaccaccactatgttctgcttcttttctggaatgcttttagtggtcagatacttgaacctctagattcatcctttctatgtgcttcgctgttttttcctccctcaattgccatcttttgaacatttttttctctggaagaattcctcaatttgtattctagccactctgttgaatcttctctttttcagcctttctttcttctttttatataacatcttgttcttgttagtggatggatgcaatattaccttaaagttctaaaaattatagagattggtttaagcgttttcatttattccctgctttatctctatttgctccgggttcctttgtactgttttggttggtttgggctctctttttcagtctgaaggctttcctctggtgacatttgtctgtttttcattttaagagtgaggcactaaagagctaattgcagccggacatggtggctcacacctgtaatcccagcactttgggaagccgaggtgggtggatcacttgagctcaggagttcaagaccagcctggacaacatagtgaaaccggtctctacaaaaaaaatacaaaaattagctgggtgtggtggtgtacactcgtagtcccagctatttgagaggctgaggtgggaggatcgcttgagccccagaggcagatgttgcagggttgcagtgagccaagattgtgccactgcgcttcagcctgggtgacagagtaagaccccatctttaaaaaagaaaagaaaagaaaagctatttgcaagtgctgtgcaatgaaggaggctcattgaccagtggacctcgctttaggataatcaaatagcagtagaggttttgctggaaaaagatttgttagtgattgtagtttttttctctctggagtttgtccagttttcccactgaaaaattatccaaacatctgctttggggatGGGAGGTGAAGTGTGGTAGGAAAGTGGAGCATGCATGCAACTGGTTGCTGGTGTGGAAACAGGCGCTGAAAGTTCTCACTGAATGCACGAGTCTCCCCAGTGCTGGGATTTTAGCCCATACCTCTCCTTCCCACTCCTCTGGGTTAGCAAATCAGTATGGAGCCTCTGCCCAAACTCTCTGGAGACTGATCCTAAGATTGCCTGCCCCTGGCTGTGGAGGGAACTGGGGTCCCAGCTGCTTCATACCTAGACTGCCAGCCTCACACCCACCTCTCCCGTCGGGGACACCCAGTGGTACTCCATCTCTGACTCTCAGCTGGGTGAGCTGACACTCCCGAGCCATGTCCCTTTTTGTCAGCGCTTCAGACTCTTCTCTTCCTCTGCTTTGCCTAATCGGATGCGTGCTTCCTACCGCATTTCATCTTCCAGAAATTGGTGGAGGCCTGCCTTCCACTGATAATCCTTCTCCAGCATTTTATCCATCTTTTAATAAAATGCCATCTTTAATAAAATTATCattccttcactgtcattttagagaagtttttcaaaggacaggcattgaaggcatgtaatcagcccacaacatttaactgggaatGTTCTAACTACCTGAACTTTGAGATTCTGCTGCCAGTTTTGTGTTTACAGTTCTTAGCTAGATCTGTCACACGTATTTTTTATGCAGTATCTGTGTAGCCATGATGTGAATCAGACTACTGTAGCACTGCCTTCAGCATCTGTGTCTTGGGATTATAGTACTGGTAAAATTTCAAAAGCAAAACTAACAAACAAAAACAAGATCCTTTAACGGTAATTGATTAATTAATCCCTTTTGGGTTTTTACTGGATGACATTACCATGATGAAGCTCCAAACTTAATACTATGATTTTAAAATTACCTAGAAGACAAATCAGGGCTGTATTGGAGTTTTCTTGTGGGAGGAAATGTAAATAATAAGAACTGATTAAAAA----------------GACACTCCTGTGATCAGAGGCAGAGCGTATGACCATTTAAAGGTATCATTCCACATAACCTGGTGGAAAAGGGCATCTTCGTGTCCTGTGCTGTTAGGTGTCAGTTTGGGGGAAACGTGTTCCC Chimp > Gorilla --------------- chr6:151790404-151790407 Template switch process: F1: L TTCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAAAAA 1 F3: 4 AAATTATAAGAACT----------GACTCCTGTGATCAGAGGCAGAGCATATGACCATTTAAAG R RF: TTCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAAAAAGAGACTCCTGTGATCAGAGGCAGAGCGTATGACCATTTAAAGGTATCATTCCACATAACCTGGTGGAAAAGGACATCTTTGTTTCCTGTGCTGTTAGGTGTCAG RR: AAGAACACCCTCCTTTACATTTAATATTCTTGACTATTTTTCTCTGAGGACACTAGTCTCCGTCTCGCATACTGGTAAATTTCCATAGTAAGGTGTATTGGACCACCTTTTCCTGTAGAAACAAAGGACACGACAATCCACAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -49.2) TCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAAAaactgaaaattatAAGAactGACTCCTGTGATCAGAGGCAGAGCaT TCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAAA-------------AAGA---GACTCCTGTGATCAGAGGCAGAGCGT Template switch alignment (log-probability: -32.3) TCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAAAAA|CTGA|AAATTATAAGAACT----------GACTCCTGTGATCAGAGGCAGAGCaT TCTTGTGGGAGGAAATGTAAATTATAAGAACTGATAAAAA|CTGA|AAATTATAAGAACTGATAAAAAGAGACTCCTGTGATCAGAGGCAGAGCGT ========== Event 3098 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ATGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAACCTTATTTAACCCATACCTTACATGATTTAAGGTATTAC ↓ 3 2 1 4 Chimp: ATGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAAGGT--------AC---ATTTACATGATTTAAGGTATTAC Gorilla: ATGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAAGGT--------AC---ATTTACATGATTTAAGGTATTAC ↑ 3 2 1 4 Human: ATGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAACCTTATTTAACCCATACCTTACATGATTTAAGGTATTAC Cluster: [ ] Orangutan: ATGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAAGGT--------AC---ATTTACATGATTTAAGGTATTAT Human > Chimp ------------- chr6:153012955-153012961 Template switch process: F1: L TGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA 1 F3: 4 TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT R RF: TGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAACCTTATTTAACCCATACCTTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT RR: ACTCAATCCACACGTTTTTACATTGTAATACCCAATTTATTGGAATAAATTGGGTATGGAATGTACTAAATTCCATAATGATTTGTACGTAGGATTCCA F2: 3 TACATGG 2 Unidirectional alignment (log-probability: -32.1) GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAAggtacat------------------TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA-------CCTTATTTAACCCATACCTTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT Template switch alignment (log-probability: -22.1) GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA|GgTACAT|TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA|GTTACAT|TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT Human > Gorilla --------------- chr6:151663830-151663836 Template switch process: F1: L TGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA 1 F3: 4 TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT R RF: TGAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAACCTTATTTAACCCATACCTTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT RR: ACTCAATCCACACGTTTTTACATTGTAATACCCAATTTATTGGAATAAATTGGGTATGGAATGTACTAAATTCCATAATGATTTGTACGTAGGATTCCA F2: 3 TACATGG 2 Unidirectional alignment (log-probability: -31.6) GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA------------------ggtacatTTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAACCTTATTTAACCCATACC-------TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT Template switch alignment (log-probability: -22.1) GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA|GgTACAT|TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT GAGTTAGGTGTGCAAAAATGTAACATTATGGGTTAAATAA|GTTACAT|TTACATGATTTAAGGTATTACTAAACATGCATCCTAAGGT ========== Event 3099 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGCAGGAGAGCCCCAAGCAGG----------------------ACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGACTCACCCCTG ↓ 4 1 3 2 Chimp: GGCAGGAGAGCCCCAAGCAGG-----------ACAGCCAGGTGACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGACTCACCCCTG Gorilla: GGCAGGAGAGCCCCAAGCAGGACAGCCAGGTG-----------ACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGACTCACCCCTG ↑ 4 1 3 2 Human: GGCAGGAGAGCCCCAAGCAGG----------------------ACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGACTCACCCCTG Cluster: [ ] Orangutan: GTCAGGAGAGCACCAAGCAGGACAGCCAGGTG-----------ACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGCCTCACCCCTG Human > Chimp ------------- chr6:154152833-154152838 Template switch process: F1: L GAGGAAGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAG 1 F3: 4 GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGA R RF: GAGGAAGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGA RR: CTCCTTCCATCTTCCTCCGACCGTCCTCTCGGGGTTCGTCCTGTCCTCCTCCCCGAAAACACGTGTGGACCCGGGAGGACT F2: 3 TGGACC 2 Unidirectional alignment (log-probability: -26.7) AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGgacagccaggtGACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAG-----------GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG Template switch alignment (log-probability: -16.1) AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAG|CCAGGT|GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAG|CCAGGT|GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG Human > Gorilla --------------- chr6:152811190-152811195 Template switch process: F1: L GAGGAAGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAG 1 F3: 4 GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGA R RF: GAGGAAGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTGA RR: CTCCTTCCATCTTCCTCCGACCGTCCTCTCGGGGTTCGTCCTGTCCTCCTCCCCGAAAACACGTGTGGACCCGGGAGGACT F2: 3 TGGACC 2 Unidirectional alignment (log-probability: -26.7) AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGgacagccaggtGACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAG-----------GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG Template switch alignment (log-probability: -16.6) AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAG|CCAGGT|GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG AGGTAGAAGGAGGCTGGCAGGAGAGCCCCAAGCAGGACAG|CCAGGT|GACAGGAGGAGGGGCTTTTGTGCACACCTGGGCCCTCCTG ========== Event 3100 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTGACATGAAAGCCTCTCTCCCTCTTTTCCTTA Chimp: GAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTGACATGAAAGCCTCTCTCCCTCTTTTCCTTA ↑ 3 2 1 4 Gorilla: GAGCTTGGATGTCAAAAGCCTTTCATGTCTTT---------TCCCTCTCTCCCTCTTTTCCTTA ↓ 3 2 1 4 Human: GAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTGACATGAAAGCCTCTCTCCCTCTTTTCCTTA Cluster: [ ] Orangutan: GAGCTTGGATGTCAAAAGCCTTTCATGTCTTT---------TCCCTCTCTCCCTCTTTTCCTTA Gorilla > Human --------------- chr6:149644254-149644263 Template switch process: F1: L GTTCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTT 1 F3: 4 CCTCTCTCCCTCTTTTCCTTAATAGTCTCCCTGGAGATCT R RF: GTTCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTCCCTCTCTCCCTCTTTTCCTTAATAGTCTTCCTGGAGATCT RR: CAAGATCTACTCGAACCTACAGTTTTCGGAAAGTACAGAAAAGGGAGAGAGGGAGAAAAGGAATTATCAGAAGGACCTCTAGA F2: 3 GAAAGTACAG 2 Unidirectional alignment (log-probability: -34.9) TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTgacatgaaagCCTCTCTCCCTCTTTTCCTTAATAGTCTcCCTGGAGATCT TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTC---------CCTCTCTCCCTCTTTTCCTTAATAGTCTTCCTGGAGATCT Template switch alignment (log-probability: -22.5) TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTT|GACATGAAAG|CCTCTCTCCCTCTTTTCCTTAATAGTCTcCCTGGAGATCT TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTT|GACATGAAAG|CCTCTCTCCCTCTTTTCCTTAATAGTCTTCCTGGAGATCT Gorilla > Chimp --------------- chr6:153746628-153746637 Template switch process: F1: L GTTCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTT 1 F3: 4 CCTCTCTCCCTCTTTTCCTTAATAGTCTCCCTGGAGATCT R RF: GTTCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTCCCTCTCTCCCTCTTTTCCTTAATAGTCTTCCTGGAGATCT RR: CAAGATCTACTCGAACCTACAGTTTTCGGAAAGTACAGAAAAGGGAGAGAGGGAGAAAAGGAATTATCAGAAGGACCTCTAGA F2: 3 GAAAGTACAG 2 Unidirectional alignment (log-probability: -34.9) TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTgacatgaaagCCTCTCTCCCTCTTTTCCTTAATAGTCTcCCTGGAGATCT TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTTC---------CCTCTCTCCCTCTTTTCCTTAATAGTCTTCCTGGAGATCT Template switch alignment (log-probability: -22.5) TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTT|GACATGAAAG|CCTCTCTCCCTCTTTTCCTTAATAGTCTcCCTGGAGATCT TCTAGATGAGCTTGGATGTCAAAAGCCTTTCATGTCTTTT|GACATGAAAG|CCTCTCTCCCTCTTTTCCTTAATAGTCTTCCTGGAGATCT ========== Event 3101 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGACATATTCTGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATT---TT----CAATGACTTCTCTATGGAGAAATAA Chimp: AGACATATTCTGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATT---TT----CAATGACTTCTCTATGGAGAAATAA ↓ 3 2 1 4 Gorilla: AGACATATTCTGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTTGTTTCTAGTCATTACTTCTCTATGGAGAAATAA ↑ 3 2 1 4 Human: AGACATATTCTGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATT---TT----CAATGACTTCTCTATGGAGAAATAA Cluster: [ ] Orangutan: AGACATATTCTGTATGTGAGAATAGAAACATGTAAGAAGCAATGCACTATT---TT----CAATGACTTCTCTATGGAGAAATAA Human > Gorilla --------------- chr6:20088049-20088058 Template switch process: F1: L TGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT 1 F3: 4 ATTACTTCTCTATGGAGAAATAAATATCAACCTAGACTGTCAG R RF: TGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTTTCAATGACTTCTCTATGGAGAAATAAATATCAACCTAGACTGTCAG RR: ACATACACTCTTATCTTTGTACATTCTTTGTTACGTGATAAAAGTTACTGAAGAGATACCTCTTTATTTATAGTTGGATCTGACAGTC F2: 3 CTGATCTTTG 2 Unidirectional alignment (log-probability: -37.8) TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTTgtttctagTC-ATtACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT--------TCAATGACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT Template switch alignment (log-probability: -28.1) TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT|GTTTCTAgTC|ATtACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT|GTTTCTATTC|ATGACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT Chimp > Gorilla --------------- chr6:20088049-20088058 Template switch process: F1: L TGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT 1 F3: 4 ATTACTTCTCTATGGAGAAATAAATATCAACCTAGACTGTCAG R RF: TGTATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTTTCAATGACTTCTCTATGGAGAAATAAATATCAACCTAGACTGTCAG RR: ACATACACTCTTATCTTTGTACATTCTTTGTTACGTGATAAAAGTTACTGAAGAGATACCTCTTTATTTATAGTTGGATCTGACAGTC F2: 3 CTGATCTTTG 2 Unidirectional alignment (log-probability: -37.8) TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTTgtttctagTC-ATtACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT--------TCAATGACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT Template switch alignment (log-probability: -28.1) TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT|GTTTCTAgTC|ATtACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT TATGTGAGAATAGAAACATGTAAGAAACAATGCACTATTT|GTTTCTATTC|ATGACTTCTCTATGGAGAAATAAATATCAACCTAGACTGT ========== Event 3102 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AACCCATTGTTCCTTGAAATTGACTTAACCAATTAAGTCCAGGACTTAACCAAACTAAATACTGTAAAATTCA ↑ 34 2 1 Chimp: AACCCATTGTTCCTTGAAATTGACT---------------------TAACCAAACTAAATACTGTAAAATTCA Gorilla: AACCCATTGTTCCTTGAAATTGACTTAACCAATTAAGTCCAGGACTTAACCAAACTAAATACTGTAAAATTCA Human: AACCCATTGTTCCTTGAAATTGACTTAACCAATTAAGTCCAGGACTTAACCAAACTAAATACTGTAAAATTCA Cluster: [ ] Orangutan: AACCCATTGTTCCTTGAAATTGACTTAACCAATTAAGTCCAGGACTTAACCAAACTAAATACTGTAAAATTCA Chimp > Human ------------- chr6:19219780-19219788 Template switch process: F1: L AATCAAGGAAGCTCCAAACCCATTGTTCCTTGAAATTGACTTAACCAA 1 F3: 4 GGACTTAACCAAACTAAATACTGTAAAATTCAGGATATTTTCAGG R RF: AATCAAGGAAGCTCCAAACCCATTGTTCCTTGAAATTGACTTAACCAAACTAAATACTGTAAAATTCAGGATATTTTCAGG RR: TTAGTTCCTTCGAGGTTTGGGTAACAAGGAACTTTAACTGAATTGGTTTGATTTATGACATTTTAAGTCCTATAAAAGTCC F2: 3 ACCTGAATT 2 Unidirectional alignment (log-probability: -41.1) AAGCTCCAAACCCATTGTTCCTTGAAATTGACTTAACCaattaagtccaggacttaaccAAACTAAATACTGTAAAATTCAGGATATTT AAGCTCCAAACCCATTGTTCCTTGAAATTGACTTAACC---------------------AAACTAAATACTGTAAAATTCAGGATATTT Template switch alignment (log-probability: -28.6) AAGCTCCAAACCCATTGTTCCTTGAAATTGACTTAACCAA|TTAAGTCcA|gGACTTAACCAAACTAAATACTGTAAAATTCAGGATATTT AAGCTCCAAACCCATTGTTCCTTGAAATTGACTTAACCAA|TTAAGTCAA|TGACTTAACCAAACTAAATACTGTAAAATTCAGGATATTT ========== Event 3103 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTCCTGGAAGGGCTTTCCAGG--------------------------------------------AC------------CTCTTCTGAGGTCCGAAGAAGCAAAGATCACCC ↑ 1 4 3 2 Chimp: ACTCCTGGAAGGGCTTTCCAGC----------------------CTTGCAGCTCCTAAATACCCTTAC------CTTACAGTGTTCTGAGGTCCGAAGAAGCAAAGATCACCC Gorilla: ACTCCTGGAAGGGCTTTCCAGCCTTGCAGCTCCTAAATACCCTT----------------------ACCTTACA------GTGTTCTGAGGTCCGAAGAAGCAAAGATCACCC ↓ 1 4 3 2 Human: ACTCCTGGAAGGGCTTTCCAGG--------------------------------------------AC------------CTCTTCTGAGGTCCGAAGAAGCAAAGATCACCC Cluster: [ ] Orangutan: ACTTCTGGAAGGGCTTTCCAGCCTTTCAGCTCCTAAATACCCTT----------------------ACCTTACA------GTGTTCTGAGGTCCGAAGAAGCAAAGATCACCC Chimp > Human ------------- chr6:15328181-15328186 Template switch process: F1: L AAGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG 1 F3: 4 TTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT R RF: AAGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAGCCTTGCAGCTCCTAAATACCCTTACCTTACAGTGTTCTGAGGTCCGAAGAAGCAAAGATCACCCCTCACAAAGT RR: TTCCCAGTCACCGAACGTTGTGAGGACCTTCCCGAAAGGTCGGAACGTCGAGGATTTATGGGAATGGAATGTCACAAGACTCCAGGCTTCTTCGTTTCTAGTGGGGAGTGTTTCA F2: 3 CTCCAG 2 Unidirectional alignment (log-probability: -36) AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAGgacctC---------------------------------TTCTGAGGTCCGAAGAAGCAAAGATCACCCCcCACAAAGT AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG-----CCTTGCAGCTCCTAAATACCCTTACCTTACAGTGTTCTGAGGTCCGAAGAAGCAAAGATCACCCCTCACAAAGT Template switch alignment (log-probability: -22) AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG|GACCTC|TTCTGAGGTCCGAAGAAGCAAAGATCACCCCcCACAAAGT AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG|GACCTC|TTCTGAGGTCCGAAGAAGCAAAGATCACCCCTCACAAAGT Gorilla > Human --------------- chr6:15328181-15328186 Template switch process: F1: L AAGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG 1 F3: 4 TTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT R RF: AAGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAGCCTTGCAGCTCCTAAATACCCTTACCTTACAGTGTTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT RR: TTCCCAGTCACCGAACGTTGTGAGGACCTTCCCGAAAGGTCGGAACGTCGAGGATTTATGGGAATGGAATGTCACAAGACTCCAGGCTTCTTCGTTTCTAGTGGGGGGTGTTTCA F2: 3 CTCCAG 2 Unidirectional alignment (log-probability: -29.5) AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG---------------------------------GacctcTTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAGCCTTGCAGCTCCTAAATACCCTTACCTTACAGTG-----TTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT Template switch alignment (log-probability: -16.5) AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG|GACCTC|TTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT AGGGTCAGTGGCTTGCAACACTCCTGGAAGGGCTTTCCAG|GACCTC|TTCTGAGGTCCGAAGAAGCAAAGATCACCCCCCACAAAGT ========== Event 3104 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCTAGGTTGCCACCTTCTGCCTCTTTATCACCAGGTTGTTATTTAAAACATTGGTGGGGGGTCTGAATTCCAACTTTAGAACAGATGTGTGTCACACTTACAATCCTGCTATGTCTATGTTATATTTGTTTTATAATATTTATTG---TAGTGGCTTTATTTCTTTTTGGAGATATGGTT Chimp: ACCTAGGTTGCCACCTTCTGCCTCTTTATCACCAGGTTGTTATTTAAAACATTGGTGGGGGGTCTGAATTCCAACTTTAGAACAGACGTGTGTCACACTTACAATCCTGCTATGTCTATGTTATATTTGTTTTATAATATTTATTG---TAGTGGCT----TTCTTTTTGGAGATATGGTT ↑ 3 2 1 4 Gorilla: ACCTAGGTTGCCACCTTCTGCCTCTTTATCACCAGGTTGTTATTTAAAACATTGGTGGGGGGTCTGAATTCCAACTTTAGAACAGATGTGTGTCACACTTACAATCCTGCTATGTCTATGTTATATTTGTTTTATAATATTTATTG------TGGCTTTATTTCTTTTTGGAGATATGGTT Human: ACCTAGGTTGCCACCTTCTGCCTCTTTATCACCAGGTTGTTATTTAAAACATTGGTGGGGGGTCTGAATTCCAACTTTAGAACAGATGTGTGTCACACTTACAATCCTGCTATGTCTATGTTATATTTGTTTTATAATATTTATTG---TAGTGGCTTTATTTCTTTTTGGAGATATGGTT Cluster: [ ] Orangutan: GCCTAGGTTGCCACCTTCTGCCTCTTTATCACCAGGTTGTTATTTAAAACGTT---GGGGGGTCTGAATTCCAACTTTAGAACAGATGTGTGTCACACTTAAAATC---CTATGTCTATGTTATATTTGTTTTACAATATTTATTGTAG---TGGCT----TTCTTTTTGGTGATATGGTT Gorilla > Chimp --------------- chr6:15521134-15521139 Template switch process: F1: L CCTGCTATGTCTATGTTATATTTGTTTTATAATATTTATTGT 1 F3: 4 TTTCTTTTTGGAGATATGGTTAAAAAAAAAGTCTTTGTGTT R RF: GCCTCTTTATCACCAGGTTGTTATTTAAAACATTGGTGGGGGGTCTGAATTCCAACTTTAGAACAGATGTGTGTCACACTTACAATCCTGCTATGTCTATGTTATATTTGTTTTATAATATTTATTGTGGCTTTATTTCTTTTTGGAGATATGGTTAAAAAAAAAGTCTTTGTGTC RR: CGGAGAAATAGTGGTCCAACAATAAATTTTGTAACCACCCCCCAGACTTAAGGTTGAAATCTTGTCTACACACAGTGTGAATGTTAGGACGATACAGATACAATATAAACAAAATATTATAAATAACACCGAAATAAAGAAAAACCTCTATACCAATTTTTTTTTCAGAAACACAG F2: 3 CGGTGA 2 Unidirectional alignment (log-probability: -33.4) TGCTATGTCTATGTTATATTTGTTTTATAATATTTATTgtaGTGGC----TTTCTTTTTGGAGATATGGTTAAAAAAAAAGTCTTTGTGT TGCTATGTCTATGTTATATTTGTTTTATAATATTTATT---GTGGCTTTATTTCTTTTTGGAGATATGGTTAAAAAAAAAGTCTTTGTGT Template switch alignment (log-probability: -27.6) TGCTATGTCTATGTTATATTTGTTTTATAATATTTATTGT|AGtGGC|TTTCTTTTTGGAGATATGGTTAAAAAAAAAGTCTTTGTGT TGCTATGTCTATGTTATATTTGTTTTATAATATTTATTGT|AGAGGC|TTTCTTTTTGGAGATATGGTTAAAAAAAAAGTCTTTGTGT ========== Event 3105 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGGCTTTTGTAAGGTATGTTGGGGAAAGG ↓ 3 2 1 4 Chimp: TAGAGAACGGCCATGCAAGTGCACTAGCATATGGTG-CACTTTTGTAAGGTATGTTGGGGAAAGG ↑ 3 2 1 4 Gorilla: TAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGGCTTTTATAAGGTATGTTGGGGGAAGG Human: TAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGGCTTTTGTAAGGTATGTTGGGGAAAGG Cluster: [ ] Orangutan: TAGAGAACGGCCATGCAAGTGCACTAGCATATGCAGTGGCTTTTGTAAGGTATGTTGGGGAAAGG Human > Chimp ------------- chr6:156865671-156865675 Template switch process: F1: L AAGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATG 1 F3: 4 CTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTC R RF: AAGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGGCTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTC RR: TTCATTTTATCTCTTGCCGGTACGTTCACGTGATCGTATACACCACCGAAAACATTCCATACAACCCCTTTCCTATCTACGTTCAAG F2: 3 ACGTG 2 Unidirectional alignment (log-probability: -27.2) AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATA-----TGGtgcaCTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTC AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGG----CTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTC Template switch alignment (log-probability: -15.9) AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATG|GTGCA|CTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTC AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATG|GTGCA|CTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTC Gorilla > Chimp --------------- chr6:156865671-156865675 Template switch process: F1: L AAGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATG 1 F3: 4 CTTTTGTAAGGTATGTTGGGGAAAGGATAGATGCAAGTTCCAAAAT R RF: AAGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGGCTTTTATAAGGTATGTTGGGGGAAGGATAGATGCAAGTTCCAAAAT RR: TTCATTTTATCTCTTGCCGGTACGTTCACGTGATCGTATACACCACCGAAAATATTCCATACAACCCCCTTCCTATCTACGTTCAAGGTTTTA F2: 3 ACGTG 2 Unidirectional alignment (log-probability: -37.8) AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATA-----TGGtgcaCTTTTgTAAGGTATGTTGGGGaAAGGATAGATGCAAGTTC AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATGTGGTGG----CTTTTATAAGGTATGTTGGGGGAAGGATAGATGCAAGTTC Template switch alignment (log-probability: -27.5) AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATG|GTGCA|CTTTTgTAAGGTATGTTGGGGaAAGGATAGATGCAAGTTC AGTAAAATAGAGAACGGCCATGCAAGTGCACTAGCATATG|GTGCA|CTTTTATAAGGTATGTTGGGGGAAGGATAGATGCAAGTTC ========== Event 3106 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATAGATTAATAAATTATAAGATGATTTTGAGAAATCAAAATCATTTTATTTACTTTTAAGTGATA ↓ 1 3 4 2 Chimp: AATAGATTAATAAATTATAAAATGATTTTGATTTCTCAAAATCATTTTATTTACTTTTAAGTGATA Gorilla: AATAGATTAATAAATTATAAAATGATTTTGAGAAATCAAAATCATTTTATTTACTTTTAAGTGATA Human: AATAGATTAATAAATTATAAGATGATTTTGAGAAATCAAAATCATTTTATTTACTTTTAAGTGATA Cluster: [ ] Orangutan: AATAGATTAATAAAGTATAAAGTGATTTTGAGAAATCAAAATCATTTTATTTACTTTTAAGTGATA Human > Chimp ------------- chr6:19278322-19278337 Template switch process: F1: L CAAGCCTTAAAATAGATTAATAAATTATAA 1 F3: 4 CAAAATCATTTTATTTACTTTTAAGTGATAGCAAAATCT R RF: CAAGCCTTAAAATAGATTAATAAATTATAAGATGATTTTGAGAAATCAAAATCATTTTATTTACTTTTAAGTGATAGCAAAATCT RR: GTTCGGAATTTTATCTAATTATTTAATATTCTACTAAAACTCTTTAGTTTTAGTAAAATAAATGAAAATTCACTATCGTTTTAGA F2: 3 TCTTTAGTTTTAGTAA 2 Unidirectional alignment (log-probability: -30.7) CAAGCCTTAAAATAGATTAATAAATTATAAaATGATTTTGAtttcTCAAAATCATTTTATTTACTTTTAAGTGATAGCAAAATCT CAAGCCTTAAAATAGATTAATAAATTATAAGATGATTTTGAGAAATCAAAATCATTTTATTTACTTTTAAGTGATAGCAAAATCT Template switch alignment (log-probability: -17) CAAGCCTTAAAATAGATTAATAAATTATAA|AATGATTTTGATTTCT|CAAAATCATTTTATTTACTTTTAAGTGATAGCAAAATCT CAAGCCTTAAAATAGATTAATAAATTATAA|AATGATTTTGATTTCT|CAAAATCATTTTATTTACTTTTAAGTGATAGCAAAATCT ========== Event 3107 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCAAAGGAGAGATTTTATCTTTGTCTTAAAGGA-CAGAGTCCAGAGAGGCTCCAG ↑ 3 1 4 2 Chimp: AGCAAAGGAGAGATTTTATCTT-------TAAGA-CAGAGTCCAGAGAGGCTCCAG Gorilla: AGCAAAGGAGAGATTTTATCTT-------TAAGA-CAGAGTCCAGAGAGGCTCCAG Human: AGCAAAGGAGAGATTTTATCTTTGTCTTAAAGGA-CAGAGTCCAGAGAGGCTCCAG Cluster: [ ] Orangutan: AGCAAAGGAAAGATTTTATCTT-------TAAGACAAGAGTCCAGAGGGGCTCCAG Chimp > Human ------------- chr6:17627406-17627414 Template switch process: F1: L ATATGCACAGGAATATGACAGCAAAGGAGAGATTTTATCTTT 1 F3: 4 GACAGAGTCCAGAGAGGCTCCAGACACAGGTTAACAAGCA R RF: ATATGCACAGGAATATGACAGCAAAGGAGAGATTTTATCTTTAAGACAGAGTCCAGAGAGGCTCCAGACACAGGTTAACAAGCA RR: TATACGTGTCCTTATACTGTCGTTTCCTCTCTAAAATAGAAATTCTGTCTCAGGTCTCTCCGAGGTCTGTGTCCAATTGTTCGT F2: 3 GAAATTCTG 2 Unidirectional alignment (log-probability: -27) ATGCACAGGAATATGACAGCAAAGGAGAGATTTTATCTTTgtcttaaAgGACAGAGTCCAGAGAGGCTCCAGACACAGGTTAACAAGCA ATGCACAGGAATATGACAGCAAAGGAGAGATTTTATCTTT-------AAGACAGAGTCCAGAGAGGCTCCAGACACAGGTTAACAAGCA Template switch alignment (log-probability: -16.4) ATGCACAGGAATATGACAGCAAAGGAGAGATTTTATCTTT|GTCTTAAAG|GACAGAGTCCAGAGAGGCTCCAGACACAGGTTAACAAGCA ATGCACAGGAATATGACAGCAAAGGAGAGATTTTATCTTT|GTCTTAAAG|GACAGAGTCCAGAGAGGCTCCAGACACAGGTTAACAAGCA ========== Event 3108 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTCCAGAAAGTTTGTGCCTGAAAAGACCACCAAAACCGGTCTTTTCAGTTTTGTGAGACTGTTAACTTT Chimp: TATTCCAGAAAGTTTGTGCCTGAAAAGACCACCAAAACCGGTCTTTTCAGTTTTGTGAGACTGTTAGCTTT ↑ 3 2 1 4 Gorilla: TATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGGGCT-----ATTTTGTGAGACTGTTAACTTT ↓ 3 2 1 4 Human: TATTCCAGAAAGTTTGTGCCTGAAAAGACCACCAAAACCGGTCTTTTCAGTTTTGTGAGACTGTTAACTTT Cluster: [ ] Orangutan: TATTCCAGAAAGTTTGTGTCTGAAAAGACCACCAAAACAGGGCT-----ATTTTGTGAGACTGTTAACTTT Gorilla > Human --------------- chr6:17871629-17871637 Template switch process: F1: L TATTCCAGAAAGTTTGTGCCTGAAAAGACCACCAAAACCGG 1 F3: 4 TTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC R RF: TATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGGGCTATTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC RR: ATAAGGTCTTTCAAACACGGACTTTTCTGGTCGTTTTGGCCCGATAAAACACTCTGACAATTGAAAACAGTGAAGATTTATGTTG F2: 3 GACTTTTCT 2 Unidirectional alignment (log-probability: -34.7) ATTCCAGAAAGTTTGTGCCTGAAAAGACCAcCAAAACCGGtCTtttcagTTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC ATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGGGCT-----ATTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC Template switch alignment (log-probability: -22.4) ATTCCAGAAAGTTTGTGCCTGAAAAGACCAcCAAAACCGG|TCTTTTCAG|TTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC ATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGG|TCTTTTCAG|TTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC Gorilla > Chimp --------------- chr6:18311360-18311368 Template switch process: F1: L TATTCCAGAAAGTTTGTGCCTGAAAAGACCACCAAAACCGG 1 F3: 4 TTTTGTGAGACTGTTAGCTTTTGTCACTTCTAAATACAAC R RF: TATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGGGCTATTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC RR: ATAAGGTCTTTCAAACACGGACTTTTCTGGTCGTTTTGGCCCGATAAAACACTCTGACAATTGAAAACAGTGAAGATTTATGTTG F2: 3 GACTTTTCT 2 Unidirectional alignment (log-probability: -40.2) ATTCCAGAAAGTTTGTGCCTGAAAAGACCAcCAAAACCGGtCTtttcagTTTTGTGAGACTGTTAgCTTTTGTCACTTCTAAATACAAC ATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGGGCT-----ATTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC Template switch alignment (log-probability: -27.9) ATTCCAGAAAGTTTGTGCCTGAAAAGACCAcCAAAACCGG|TCTTTTCAG|TTTTGTGAGACTGTTAgCTTTTGTCACTTCTAAATACAAC ATTCCAGAAAGTTTGTGCCTGAAAAGACCAGCAAAACCGG|TCTTTTCAG|TTTTGTGAGACTGTTAACTTTTGTCACTTCTAAATACAAC ========== Event 3109 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AACCAACACTGTTTCTTCAAACTTGAATTGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTTTATAttttttatttatggaattcaagcacactcactgacagaaaat ↑ 1 4 3 2 Chimp: AACCAACATTGTTTCTTCAAA---ACAATGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTTTACATTTTTTATTTATGGAATTCAAGCACACTCACTGACAGaaaat ↓ 1 4 3 2 Gorilla: AACCAACACTGTTTCTTCAAACTTGAATTGTACCACTTTGGCTAAAATCAGAGCAGTAATGGAAGTTTTATAttttttatttatggaattcaagcacactcactgacagaaaat Human: AACCAACACTGTTTCTTCAAACTTGAATTGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTTTATAttttttatttatggaattcaagcacactcactgacagaaaat Cluster: [ ] Orangutan: AACCAACATTGTTTCTTCAAACTTGAATTGTACCACTTTGGCTAAAATCAGAGTAGTAATGAAAGTTTTATAttttttatttatggaattcaagcacactcactgatagaaaat Chimp > Human ------------- chr6:153706659-153706665 Template switch process: F1: L TTCAGTATATGAAAGAAGATAACCAACACTGTTTCTTCAAA 1 F3: 4 TGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT R RF: TTCAGTATATGAAAGAAGATAACCAACATTGTTTCTTCAAAACAATGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTTTACATTTTTTATTTATGGAATTCAAG RR: AAGTCATATACTTTCTTCTATTGGTTGTAACAAAGAAGTTTTGTTACATGGTGAAACCGATTTTAGTCTCGTCATTACTTTCAAAATGTAAAAAATAAATACCTTAAGTTC F2: 3 TAAGTTC 2 Unidirectional alignment (log-probability: -37.4) TCAGTATATGAAAGAAGATAACCAACAcTGTTTCTTCA----AActtgaatTGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT TCAGTATATGAAAGAAGATAACCAACATTGTTTCTTCAAAACAA-------TGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT Template switch alignment (log-probability: -22.1) TCAGTATATGAAAGAAGATAACCAACAcTGTTTCTTCAAA|CTTGAAT|TGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT TCAGTATATGAAAGAAGATAACCAACATTGTTTCTTCAAA|CTTGAAT|TGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT Chimp > Gorilla --------------- chr6:156478452-156478458 Template switch process: F1: L TTCAGTATATGAAAGAAGATAACCAACACTGTTTCTTCAAA 1 F3: 4 TGTACCACTTTGGCTAAAATCAGAGCAGTAATGGAAGTTT R RF: TTCAGTATATGAAAGAAGATAACCAACATTGTTTCTTCAAAACAATGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTTTACATTTTTTATTTATGGAATTCAAG RR: AAGTCATATACTTTCTTCTATTGGTTGTAACAAAGAAGTTTTGTTACATGGTGAAACCGATTTTAGTCTCGTCATTACTTTCAAAATGTAAAAAATAAATACCTTAAGTTC F2: 3 TAAGTTC 2 Unidirectional alignment (log-probability: -41.9) TCAGTATATGAAAGAAGATAACCAACAcTGTTTCTTCA----AActtgaatTGTACCACTTTGGCTAAAATCAGAGCAGTAATGgAAGTTT TCAGTATATGAAAGAAGATAACCAACATTGTTTCTTCAAAACAA-------TGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT Template switch alignment (log-probability: -27.7) TCAGTATATGAAAGAAGATAACCAACAcTGTTTCTTCAAA|CTTGAAT|TGTACCACTTTGGCTAAAATCAGAGCAGTAATGgAAGTTT TCAGTATATGAAAGAAGATAACCAACATTGTTTCTTCAAA|CTTGAAT|TGTACCACTTTGGCTAAAATCAGAGCAGTAATGAAAGTTT ========== Event 3110 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GCAGTC-TTTATATAAGACTGTAATATTTCACTGTTCTCTGGGAA--------AGCAATCTAGATGTCAACAATAT ↓ 3 2 4 Chimp: GAAGTC-TTTATATAAGACTG----TTTTCCCAGTGAACAGTGAA----ATATTACAATCTAGATGTCAACAATAT Gorilla: GCAGTC-TTTATATAAGACTG----CTTTCCCAGTGAACAGTGAAATAT----TACAATCTAGATGTCAACAATAT ↓ 13 24 ↑ 13 24 Human: GCAGTC-TTTATATAAGACTGTAATATTTCACTGTTCTCTGGGAA--------AGCAATCTAGATGTCAACAATAT Cluster: [ ] Orangutan: GAAGTCTTTTATATAAGACTG----CTTTCCCGGTGAACAGTGAAATAT----TACAATCTTCATGTCAACAATAT Human > Chimp ------------- chr6:157855515-157855539 Template switch process: F1: L GAGGAAATGTGACTCTCCAAGGAAGTCTTTATATAAGACTGT 1 F3: 4 CAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT R RF: GAGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGTAATATTTCACTGTTCTCTGGGAAAGCAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT RR: CTCCTTTACACTGAGAGGTTCCGTCAGAAATATATTCTGACATTATAAAGTGACAAGAGACCCTTTCGTTAGATCTACAGTTGTTATATAGAAAGGAACTCAATGAA F2: 3 ATTATAAAGTGACAAGTGACCCTTT 2 Unidirectional alignment (log-probability: -60) GGAAATGTGACTCTCCAAGGaAGTCTTTATATAAGACTGTtttcccagtgaacagtgaAATATTa------------------CAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT GGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGT------------------AATATTTCACTGTTCTCTGGGAAAGCAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT Template switch alignment (log-probability: -30.4) GGAAATGTGACTCTCCAAGGaAGTCTTTATATAAGACTGT|TTTCCCAGtGAACAGTGAAATATTA|CAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT GGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGT|TTTCCCAGAGAACAGTGAAATATTA|CAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT Gorilla > Human --------------- chr6:153700587-153700612 Template switch process: F1: L GAGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG 1 F3: 4 CAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT R RF: GAGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGCTTTCCCAGTGAACAGTGAAATATTACAATCTAGATGTCAACAATATATTTTTCCTTGAGTTACTT RR: CTCCTTTACACTGAGAGGTTCCGTCAGAAATATATTCTGACGAAAGGGTCACTTGTCACTTTATAATGTTAGATCTACAGTTGTTATATAAAAAGGAACTCAATGAA F2: 3 GAAAGGGTCTCTTGTCACTTTATAAT 2 Unidirectional alignment (log-probability: -61.9) AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG------------------------TAatatttcactgttctctgggaaagCAATCTAGATGTCAACAATATATcTTTCCTTGAGTTACTT AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGCTTTCCCAGTGAACAGTGAAATATTA------------------------CAATCTAGATGTCAACAATATATTTTTCCTTGAGTTACTT Template switch alignment (log-probability: -30.1) AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG|TAATATTTCACTGTTCtCTGGGAAAG|CAATCTAGATGTCAACAATATATcTTTCCTTGAGTTACTT AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG|TAATATTTCACTGTTCACTGGGAAAG|CAATCTAGATGTCAACAATATATTTTTCCTTGAGTTACTT Human > Gorilla --------------- chr6:156472398-156472423 Template switch process: F1: L GAGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG 1 F3: 4 CAATCTAGATGTCAACAATATATTTTTCCTTGAGTTACTT R RF: GAGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGTAATATTTCACTGTTCTCTGGGAAAGCAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT RR: CTCCTTTACACTGAGAGGTTCCGTCAGAAATATATTCTGACATTATAAAGTGACAAGAGACCCTTTCGTTAGATCTACAGTTGTTATATAGAAAGGAACTCAATGAA F2: 3 ATTATAAAGTGACAAGTGACCCTTTC 2 Unidirectional alignment (log-probability: -61.9) AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTGctttcccagtgaacagtgaaatatTA------------------------CAATCTAGATGTCAACAATATATtTTTCCTTGAGTTACTT AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG------------------------TAATATTTCACTGTTCTCTGGGAAAGCAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT Template switch alignment (log-probability: -30.1) AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG|CTTTCCCAGtGAACAGTGAAATATTA|CAATCTAGATGTCAACAATATATtTTTCCTTGAGTTACTT AGGAAATGTGACTCTCCAAGGCAGTCTTTATATAAGACTG|CTTTCCCAGAGAACAGTGAAATATTA|CAATCTAGATGTCAACAATATATCTTTCCTTGAGTTACTT ========== Event 3111 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TATATAGTCATTTGGGTATTTTGCATAC------------------CCTAAAGGTATGCAAAACCTTAAAAGGCTTTACACATGTTATTT Chimp: TATATAGTCATTTGTGTATTTTGCATAC------------------CCTAAAGGTATGCAAAACCTTAAAAGGCTTTACACATGTTATTT Gorilla: TATATAGTCATTTGGGCATTTTGCATAC------------------------------------CTTAAAAGGCTTTACACATGTTATTT ↓ 3 4 2 1 Human: TATATAGTCATTTGGGTATTTTGCATAC------------------CCTAAAGGTATGCAAAACCTTAAAAGGCTTTACACATGTTATTT Cluster: [ ] Orangutan: TATATAGTTATTTGGGTATTTTGCATACCCTAAAGGTATGCAAAAC------------------CTTAAAAGGCTTTACAAATGTTATTT Gorilla > Human --------------- chr6:154181021-154181030 Template switch process: F1: L GAGAAGAAAAAACTATATAGTCATTTGGGTATTTTGCATACCCTAAA 1 F3: 4 ACCTTAAAAGGCTTTACACATGTTATTTAATATAGCACCTGA R RF: GAGAAGAAAAAACTATATAGTCATTTGGGCATTTTGCATACCTTAAAAGGCTTTACACATGTTATTTAATATAGCACCTGA RR: CTCTTCTTTTTTGATATATCAGTAAACCCGTAAAACGTATGGAATTTTCCGAAATGTGTACAATAAATTATATCGTGGACT F2: 3 AAACGTATGG 2 Unidirectional alignment (log-probability: -42.3) AAAAACTATATAGTCATTTGGGtATTTTGCATaccctaaaggtatgcaaaACCTTAAAAGGCTTTACACATGTTATTTAATATAGCACCT AAAAACTATATAGTCATTTGGGCATTTTGCAT------------------ACCTTAAAAGGCTTTACACATGTTATTTAATATAGCACCT Template switch alignment (log-probability: -28.2) AAAAACTATATAGTCATTTGGGtATTTTGCATACCcTAAA|GGTATGCAAA|ACCTTAAAAGGCTTTACACATGTTATTTAATATAGCACCT AAAAACTATATAGTCATTTGGGCATTTTGCATACCTTAAA|GGTATGCAAA|ACCTTAAAAGGCTTTACACATGTTATTTAATATAGCACCT ========== Event 3112 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGACACAAGTATGGCCCTCGGG------------ATGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCTAGAC Chimp: GAGACACAAGTATGGCCCTCGGG------------ATGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCTAGAC ↓ 1 4 3 2 Gorilla: GAGACACAAGTATGGCCCTCGTGTCTTTACCATAGCAGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCTAGAC ↑ 1 4 3 2 Human: GAGACACAAGTATGGCCCTCGGG------------ATGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCTAGAC Cluster: [ ] Orangutan: GAGACACAAGCATGGCCCTCGGG------------ATGACTTTTGTCTACTATGGTAACGAGCCTAGACTTAATCCTAGAC Human > Gorilla --------------- chr6:16028785-16028798 Template switch process: F1: L TGTGAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGTG 1 F3: 4 GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT R RF: TGTGAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGGGATGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT RR: ACACTCTGTGTCTCCTCCTCCTCTGTGTTCATACCGGGAGCCCTACTGAAAACAGATGATACCATTTCTCGGATCTGAATTAGGA F2: 3 ACGATACCATTTCT 2 Unidirectional alignment (log-probability: -42.4) GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCG---TgtctttaccatagcaGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGGGAT---------------GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT Template switch alignment (log-probability: -28.6) GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGtG|TCTTTACCATAGcA|GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGGG|TCTTTACCATAGTA|GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT Chimp > Gorilla --------------- chr6:16028785-16028798 Template switch process: F1: L TGTGAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGTG 1 F3: 4 GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT R RF: TGTGAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGGGATGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT RR: ACACTCTGTGTCTCCTCCTCCTCTGTGTTCATACCGGGAGCCCTACTGAAAACAGATGATACCATTTCTCGGATCTGAATTAGGA F2: 3 ACGATACCATTTCT 2 Unidirectional alignment (log-probability: -42.4) GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCG---TgtctttaccatagcaGACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGGGAT---------------GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT Template switch alignment (log-probability: -28.6) GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGtG|TCTTTACCATAGcA|GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT GAGACACAGAGGAGGAGGAGACACAAGTATGGCCCTCGGG|TCTTTACCATAGTA|GACTTTTGTCTACTATGGTAAAGAGCCTAGACTTAATCCT ========== Event 3113 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTCTAGAATTTGAATGTATCAGCCTTTAGAACTCTTCACGCTAAAAGAGTTACttttttttGCTAAAAG---TTTGAAAA---TAGCTG----ATAGGAAAATA----TAATT Chimp: TTCTCTAGAATTTGAATGTATCAGCCTTTAAAACTCTTCACGCTAAAAGAGTTACttttttttGCTAAAAG---TTTGAAAA---TAGCTGATTGATAGGAAAATA----TAATT ↑ 3 2 1 4 Gorilla: TTCTCTAGAATTTGAATGTATCAGCCTTTAGAACTCTTCACGCTAAAAGAGTTACttttttttGCTAAAAG---TTTGAAAATAATAGCTG----ATAGGAAAATA----TAATT Human: TTCTCTAGAATTTGAATGTATCAGCCTTTAGAACTCTTCACGCTAAAAGAGTTACttttttttGCTAAAAG---TTTGAAAA---TAGCTG----ATAGGAAAATA----TAATT Cluster: [ ] Orangutan: TTCTCTAGAATTTGAATTTATCAGCCTTTAGAACTCTTCATGCTAAAAGACTTACttttttttGCTAAAAGTTGTTTGAAAA---TAGCTG----ATAGGAAAATATAAATAATT Gorilla > Chimp --------------- chr6:159447769-159447774 Template switch process: F1: L CACGCTAAAAGAGTTACTTTTTTTTGCTAAAAGTTTGAAAATA 1 F3: 4 TGATAGGAAAATATAATTATTCCTCTTGTTATTTTTCAAGCA R RF: ATCAGCCTTTAGAACTCTTCACGCTAAAAGAGTTACTTTTTTTTGCTAAAAGTTTGAAAATAATAGCTGATAGGAAAATATAATTATTCCTCTTGTTATTTTTCAAGCA RR: TAGTCGGAAATCTTGAGAAGTGCGATTTTCTCAATGAAAAAAAACGATTTTCAAACTTTTATTATCGACTATCCTTTTATATTAATAAGGAGAACAATAAAAAGTTCGT F2: 3 TAGTCG 2 Unidirectional alignment (log-probability: -26.6) GCTAAAAGAGTTACTTTTTTTTGCTAAAAGTTTGAAAATA---GCtgatTGATAGGAAAATATAATTATTCCTCTTGTTATTTTTCAAG GCTAAAAGAGTTACTTTTTTTTGCTAAAAGTTTGAAAATAATAGC----TGATAGGAAAATATAATTATTCCTCTTGTTATTTTTCAAG Template switch alignment (log-probability: -16.6) GCTAAAAGAGTTACTTTTTTTTGCTAAAAGTTTGAAAATA|GCTGAT|TGATAGGAAAATATAATTATTCCTCTTGTTATTTTTCAAG GCTAAAAGAGTTACTTTTTTTTGCTAAAAGTTTGAAAATA|GCTGAT|TGATAGGAAAATATAATTATTCCTCTTGTTATTTTTCAAG ========== Event 3114 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCT-TTTGGTCCTTGAGTGCTATGGAGCTGTGAGGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGACATA---GTTGCTTTCCTGCTCGCTCCCT Chimp: GCT-TTTGGTCCTTGAGTGCTATGGAGCTGTGAGGGTCAGAGACGCACAGGGCTCCCCTGGGGACAGTTTAGACATA---GTTGCTTTCCTGCTCGCTCCCT ↑ 3 2 1 4 Gorilla: GCT-TTTGGTCCTTGAGTGCTATGGAGCTGTGAGGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGATTCAGAGTTTGCTTTCCTGCTCGCTCCCT ↓ 3 2 1 4 Human: GCT-TTTGGTCCTTGAGTGCTATGGAGCTGTGAGGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGACATA---GTTGCTTTCCTGCTCGCTCCCT Cluster: [ ] Orangutan: GCTTTTTGGTCCTTGGGTGCTATGGAGCTGTGAGGGTCAGAGGCGCCCAGTGCTCCCCTGGGGGCAGTTTAGACATA---GTTGCTTTTCTGCTCGGTCCCT Gorilla > Human --------------- chr6:14234780-14234784 Template switch process: F1: L AGGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGA 1 F3: 4 TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCTG R RF: CTATGGAGCTGTGAGGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGATTCAGAGTTTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG RR: GATACCTCGACACTCCCAGTCTCCGCGTGTCCCGAGGGGACCCCCGTCAAATCTAAGTCTCAAACGAAAGGACGAGCGAGGGAAAGGGACCAAAGAGAGGGC F2: 3 GATAC 2 Unidirectional alignment (log-probability: -31.9) GGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGA--CAtAG-TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCtG GGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGATTCAGAGTTTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG Template switch alignment (log-probability: -21.9) GGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGA|CATAG|TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCtG GGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGA|CATAG|TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG Gorilla > Chimp --------------- chr6:14632569-14632573 Template switch process: F1: L AGGGTCAGAGACGCACAGGGCTCCCCTGGGGACAGTTTAGA 1 F3: 4 TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG R RF: CTATGGAGCTGTGAGGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGATTCAGAGTTTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG RR: GATACCTCGACACTCCCAGTCTCCGCGTGTCCCGAGGGGACCCCCGTCAAATCTAAGTCTCAAACGAAAGGACGAGCGAGGGAAAGGGACCAAAGAGAGGGC F2: 3 GATAC 2 Unidirectional alignment (log-probability: -37.4) GGGTCAGAGaCGCACAGGGCTCCCCTGGGGaCAGTTTAGA--CAtAG-TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG GGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGATTCAGAGTTTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG Template switch alignment (log-probability: -27.4) GGGTCAGAGaCGCACAGGGCTCCCCTGGGGaCAGTTTAGA|CATAG|TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG GGGTCAGAGGCGCACAGGGCTCCCCTGGGGGCAGTTTAGA|CATAG|TTGCTTTCCTGCTCGCTCCCTTTCCCTGGTTTCTCTCCCG ========== Event 3115 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTCCTGGGTCCAGGGAGGAGGGGGTCGG-------------GAGTGGTACAGGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTACAGGCGCGGACTCCatcctcc Chimp: CTCCTGGGTCCAGGGAGGAGGGGGTCGG-------------GAGTGGTACAGGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTACAGGCGCGGACTCCatcctcc ↑ 4 1 3 2 Gorilla: CTCCTGGGTCCAGGGAGGAGGAGGTCGG--------------------------GAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTACAGGCGCGGACTCCatcctcc ↓ 4 1 3 2 Human: CTCCTGGGTCCAGGGAGGAGGGGGTCGG-------------GAGTGGTACAGGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTACAGGCGCGGACTCCatcctcc Cluster: [ ] Orangutan: CTCCTGGGTCCAGGGAGGAGGGGGTTGGGAGTGGTACAGGG-------------GAGTGAGGAGAGCCGATATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTACAGGCGCGGACTCCATCCTCC Gorilla > Human --------------- chr6:12779475-12779480 Template switch process: F1: L ATTGCCACAGAGCACTGGGGCTCCTGGGTCCAGGGAGGAGGGGGTCGGGAGTG 1 F3: 4 GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCA R RF: ATTGCCACAGAGCACTGGGGCTCCTGGGTCCAGGGAGGAGGAGGTCGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTAC RR: TAACGGTGTCTCGTGACCCCGAGGACCCAGGTCCCTCCTCCTCCAGCCCTCACTCCTCTCGGCCATAGACCACTCGCGTCACCTCCGTCCCCTCGACATG F2: 3 GACATG 2 Unidirectional alignment (log-probability: -35.2) ACTGGGGCTCCTGGGTCCAGGGAGGAGGgGGTCgggagtggtacagGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG ACTGGGGCTCCTGGGTCCAGGGAGGAGGAGGTC-------------GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG Template switch alignment (log-probability: -22.4) ACTGGGGCTCCTGGGTCCAGGGAGGAGGgGGTCGGGAGTG|GTACAG|GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG ACTGGGGCTCCTGGGTCCAGGGAGGAGGAGGTCGGGAGTG|GTACAG|GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG Gorilla > Chimp --------------- chr6:13076497-13076502 Template switch process: F1: L ATTGCCACAGAGCACTGGGGCTCCTGGGTCCAGGGAGGAGGGGGTCGGGAGTG 1 F3: 4 GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCA R RF: ATTGCCACAGAGCACTGGGGCTCCTGGGTCCAGGGAGGAGGAGGTCGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGGCAGGGGAGCTGTAC RR: TAACGGTGTCTCGTGACCCCGAGGACCCAGGTCCCTCCTCCTCCAGCCCTCACTCCTCTCGGCCATAGACCACTCGCGTCACCTCCGTCCCCTCGACATG F2: 3 GACATG 2 Unidirectional alignment (log-probability: -35.2) ACTGGGGCTCCTGGGTCCAGGGAGGAGGgGGTCgggagtggtacagGGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG ACTGGGGCTCCTGGGTCCAGGGAGGAGGAGGTC-------------GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG Template switch alignment (log-probability: -22.4) ACTGGGGCTCCTGGGTCCAGGGAGGAGGgGGTCGGGAGTG|GTACAG|GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG ACTGGGGCTCCTGGGTCCAGGGAGGAGGAGGTCGGGAGTG|GTACAG|GGGAGTGAGGAGAGCCGGTATCTGGTGAGCGCAGTGGAGG ========== Event 3116 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACCCCGTGCATAGTCACCGAGTGTCACTGTAG----GTCCCCTGCAATGGGAGCAAACAC ↓ 3 2 1 4 Chimp: ACCCCGTGCATAGTCACCGAGTGTCACTGTAGTGACACTCCCTGCAATGGGAGCAAACAC ↑ 3 2 1 4 Gorilla: ACCCCGTGCATAGTCACCGAGTGTCACTGTAG----GTCCCCTGCAATGGGAGCAAACAC Human: ACCCCGTGCATAGTCACCGAGTGTCACTGTAG----GTCCCCTGCAATGGGAGCAAACAC Cluster: [ ] Orangutan: ACCCCGTGCATAGTCACCGAGTGTCACTGTAG----GTCCCCTGCAATGGGAGCAAACAC Human > Chimp ------------- chr6:162815621-162815627 Template switch process: F1: L ACCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG 1 F3: 4 CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG R RF: ACCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAGGTCCCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG RR: TGGACCGACTGGGGCACGTATCAGTGGCTCACAGTGACATCCAGGGGACGTTACCCTCGTTTGTGGCGTCGACCGAAAAGCGAC F2: 3 TCACAGT 2 Unidirectional alignment (log-probability: -31.4) CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAGtgacact---CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG-------GTCCCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG Template switch alignment (log-probability: -16.2) CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG|TGACACT|CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG|TGACACT|CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG Gorilla > Chimp --------------- chr6:162815621-162815627 Template switch process: F1: L ACCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG 1 F3: 4 CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCTG R RF: ACCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAGGTCCCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCCG RR: TGGACCGACTGGGGCACGTATCAGTGGCTCACAGTGACATCCAGGGGACGTTACCCTCGTTTGTGGCGTCGACCGAAAAGCGGC F2: 3 TCACAGT 2 Unidirectional alignment (log-probability: -36.4) CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG---tgacactCCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCtG CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAGGTC-------CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCCG Template switch alignment (log-probability: -22.1) CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG|TGACACT|CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCtG CCTGGCTGACCCCGTGCATAGTCACCGAGTGTCACTGTAG|TGACACT|CCCTGCAATGGGAGCAAACACCGCAGCTGGCTTTTCGCCG ========== Event 3117 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCATCTTAGCTCCACTGAGACA---TCCCATTCTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG Chimp: ATCATCTTAGCTCCACTGAGACA---TCCCATTCTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG ↓ 1 4 3 2 Gorilla: ATCATCTTAGCTCCACTGAGATG------GAGCTTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG ↑ 1 4 3 2 Human: ATCATCTTAGCTCCACTGAGACA---TCCCATTCTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG Cluster: [ ] Orangutan: AGCATCTTAGCTCCACTGAGACATCC---CATTCTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG Human > Gorilla --------------- chr6:164064266-164064272 Template switch process: F1: L TTCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA 1 F3: 4 TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG R RF: TTCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGACATCCCATTCTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG RR: AAGCCGGACTAAAGAGACTTTAGTAGAATCGAGGTGACTCTGTAGGGTAAGAGATCCGGGGTCTTCGAGGTGAGAGACCGTGTTTAGGTCC F2: 3 TCGAGGT 2 Unidirectional alignment (log-probability: -31.2) TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA----------tggagctTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGACATCCCATTC-------TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG Template switch alignment (log-probability: -16.6) TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA|TGGAGCT|TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA|TGGAGCT|TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG Chimp > Gorilla --------------- chr6:164064266-164064272 Template switch process: F1: L TTCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA 1 F3: 4 TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG R RF: TTCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGACATCCCATTCTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG RR: AAGCCGGACTAAAGAGACTTTAGTAGAATCGAGGTGACTCTGTAGGGTAAGAGATCCGGGGTCTTCGAGGTGAGAGACCGTGTTTAGGTCC F2: 3 TCGAGGT 2 Unidirectional alignment (log-probability: -31.2) TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA----------tggagctTCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGACATCCCATTC-------TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG Template switch alignment (log-probability: -16.6) TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA|TGGAGCT|TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG TCGGCCTGATTTCTCTGAAATCATCTTAGCTCCACTGAGA|TGGAGCT|TCTAGGCCCCAGAAGCTCCACTCTCTGGCACAAATCCAGG ========== Event 3118 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGGCCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACTCTGAGAAGCGTCTCCACCTCAATACCAACC ↑ 3 2 1 4 Chimp: AAGGCCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACT--G-ATCGCTTCTCCACCTCAATACCAACC Gorilla: AAGGCCCCCATGCCTGCCCTTCTCAGAGTAGGCTGTGCTGCACT--G-ATCGCTTCTCCACCTCAATACCAACC Human: ATGGCCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACTCTGAGAAGCGTCTCCACCTCAATACCAACC Cluster: [ ] Orangutan: AAGGACCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACT--G-ATTGCTTTTCCACCTCAATACTAACA Chimp > Human ------------- chr6:169107328-169107334 Template switch process: F1: L GCCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACT 1 F3: 4 GCGTCTCCACCTCAATACCAACCCTGTAGACTTGGCTTAAAGC R RF: GCCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACTGATCGCTTCTCCACCTCAATACCAACCCTGTAGACTTGGCTTAAAGC RR: CGGGGGTACGGACGGGAAGAGTCTCACCCGACACGACGTGACTAGCGAAGAGGTGGAGTTATGGTTGGGACATCTGAACCGAATTTCG F2: 3 AAGAGTC 2 Unidirectional alignment (log-probability: -32.9) CCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACT-----CTgagaagcgTCTCCACCTCAATACCAACCCTGTAGACTTGGCTTAA CCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACTGATCGCT--------TCTCCACCTCAATACCAACCCTGTAGACTTGGCTTAA Template switch alignment (log-probability: -22.2) CCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACT|CTGAGAA|GCgTCTCCACCTCAATACCAACCCTGTAGACTTGGCTTAA CCCCCATGCCTGCCCTTCTCAGAGTGGGCTGTGCTGCACT|CTGAGAA|GCTTCTCCACCTCAATACCAACCCTGTAGACTTGGCTTAA ========== Event 3119 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGAGGAAGAGTGGATCCTCATACTGGTGGCTGC-----------------AGGCTACTAGTATCTGCAGGCTGAGGTGCCGTGCTGACCTAC Chimp: GGAGGAAGAGTGGATCCTCAtactggtggctgc-----------------aggctactagtggctgcaggctGAGGTGCCGTGCTGACCTAC Gorilla: GGAGGAAGAGTGGATCCTTATACTGGTGGCTGC----------------------------------AGGCTGAGGTGCCGTGCTGACCTAC ↓ 3 2 4 1 Human: GGAGGAAGAGTGGATCCTCATACTGGTGGCTGC-----------------AGGCTACTAGTATCTGCAGGCTGAGGTGCCGTGCTGACCTAC Cluster: [ ] Orangutan: GGAGGAAGAGTGGATCCTCAtactggtggctgcaggctactagtggctgc-----------------aggctGAGGTGCCGTGCTGACCTAG Gorilla > Human --------------- chr6:169161833-169161840 Template switch process: F1: L GGGTCCCTGGAGGAAGAGTGGATCCTCATACTGGTGGCTGCAGGCT 1 F3: 4 CTGCAGGCTGAGGTGCCGTGCTGACCTACCTCAGACCGGGGGTT R RF: GGGTCCCTGGAGGAAGAGTGGATCCTTATACTGGTGGCTGCAGGCTGAGGTGCCGTGCTGACCTACCTCAGACCGGGGGTT RR: CCCAGGGACCTCCTTCTCACCTAGGAATATGACCACCGACGTCCGACTCCACGGCACGACTGGATGGAGTCTGGCCCCCAA F2: 3 TATGATCA 2 Unidirectional alignment (log-probability: -40.8) CTGGAGGAAGAGTGGATCCTcATACTGGTGGctgcaggctactagtatCTGCAGGCTGAGGTGCCGTGCTGACCTACCTCAGACCGGG CTGGAGGAAGAGTGGATCCTTATACTGGTGG-----------------CTGCAGGCTGAGGTGCCGTGCTGACCTACCTCAGACCGGG Template switch alignment (log-probability: -28) CTGGAGGAAGAGTGGATCCTcATACTGGTGGCTGCAGGCT|ACtAGTAT|CTGCAGGCTGAGGTGCCGTGCTGACCTACCTCAGACCGGG CTGGAGGAAGAGTGGATCCTTATACTGGTGGCTGCAGGCT|ACCAGTAT|CTGCAGGCTGAGGTGCCGTGCTGACCTACCTCAGACCGGG ========== Event 3120 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTATC-TTCCAACAAATATTTTT---------------AATCCCCTGATTTTTAATCCCCAGGGGTACAGGCCATTGGCTAAATACCCCTCATATAATCAGTCCCTTTATTCACTCCTGTGCTATCACTCTCTGCCAACAGAGCTTG Chimp: TTATC-TTCCAACAAATATTTTT---------------AATCCCCTGACTTTTAATCCCCAGGGGTACAGGCCATTGGCTAAATACCCCTCATATAATCAGTCCCTTTATTCACTCCTGTGCTATCACTCTCTGCCAACAGAGCTTG ↑ 4 1 3 2 Gorilla: TTATC-TTCCAACAAATATTTTT------------------------------AATCCCCAGGGGTAGAGGCCATTGGCTAAATACCCCTCATATAATCAGTCCCTTTATTCACTCCTGTGCTGTCACTCTCTGCCAACAGAGCTTG Human: TTATC-TTCCAACAAATATTTTT---------------AATCCCCTGATTTTTAATCCCCAGGGGTACAGGCCATTGGCTAAATACCCCTCATATAATCAGTCCCTTTATTCACTCCTGTGCTATCACTCTCTGCCAACAGAGCTTG Cluster: [ ] Orangutan: TTATCTTTCCAACAAATATTTTTAATCCCCTGATTTTT---------------AATCCCCAGGGGTACAGGCCATTGGCTAAATACCCCTCATATAATCAGTACCTTTATTCACTCCTGTGCTATCACTCTCTGCCAACAGAGCTTG Gorilla > Chimp --------------- chr6:173552140-173552143 Template switch process: F1: L TCTTCTATTTATCTCTTGATTATCTTCCAACAAATATTTTTAATCCCC 1 F3: 4 TTTTAATCCCCAGGGGTACAGGCCATTGGCTAAATACCCCTCAT R RF: TCTTCTATTTATCTCTTGATTATCTTCCAACAAATATTTTTAATCCCCAGGGGTAGAGGCCATTGGCTAAATACCCCTCATATAATCAGTCCCTTTATTCACTCCTGTGCTGTCA RR: AGAAGATAAATAGAGAACTAATAGAAGGTTGTTTATAAAAATTAGGGGTCCCCATCTCCGGTAACCGATTTATGGGGAGTATATTAGTCAGGGAAATAAGTGAGGACACGACAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -38) TTATCTCTTGATTATCTTCCAACAAATATTTttaatcccctgacttTTAATCCCCAGGGGTAcAGGCCATTGGCTAAATACCCC TTATCTCTTGATTATCTTCCAACAAATATTT---------------TTAATCCCCAGGGGTAGAGGCCATTGGCTAAATACCCC Template switch alignment (log-probability: -22) TTATCTCTTGATTATCTTCCAACAAATATTTTTAATCCCC|TGAC|TTTTAATCCCCAGGGGTAcAGGCCATTGGCTAAATACCCC TTATCTCTTGATTATCTTCCAACAAATATTTTTAATCCCC|TGAC|TTTTAATCCCCAGGGGTAGAGGCCATTGGCTAAATACCCC ========== Event 3121 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGGTGTGAGCAGCAAGAATGAA----TCTTCTTCATCTCCTTGTCAACCTGT Chimp: GTGGTGTGAGCAGCAAGAATGAA----TCTTCTTCATCTCCTTGTCAACCTGT ↓ 3 1 24 Gorilla: GTGGTGTGAGCAGCAAGAATGAAGAAGATTCATTCATCTCCTTGTCAACCTGT ↑ 3 1 24 Human: GTGGTGTGAGCAGCAAGAATGAA----TCTTCTTCATCTCCTTGTCAACCTGT Cluster: [ ] Orangutan: GTGGTGTGAGCGGCAGGAATGAA----TCTTCTTCATCTCCTTGTCAATCTGT Human > Gorilla --------------- chr6:164514633-164514641 Template switch process: F1: L CATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAA 1 F3: 4 TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT R RF: CATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAATCTTCTTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT RR: GTAGACTCAAGTGCCCGTCACCACACTCGTCGTTCTTACTTAGAAGAAGTAGAGGAACAGTTGGACAATATACGAGAGAACGACGA F2: 3 ACTTAGAAG 2 Unidirectional alignment (log-probability: -33.8) ATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAA-----gaagattcaTTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT ATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAATCTTC---------TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT Template switch alignment (log-probability: -16.9) ATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAA|GAAGATTCA|TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT ATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAA|GAAGATTCA|TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT Chimp > Gorilla --------------- chr6:164514633-164514641 Template switch process: F1: L CATCTGAGTTCACGGGCAGTGGTGTGAGCAGCAAGAATGAA 1 F3: 4 TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT R RF: CATCTGAGTTCATGGGCAGTGGTGTGAGCAGCAAGAATGAATCTTCTTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT RR: GTAGACTCAAGTACCCGTCACCACACTCGTCGTTCTTACTTAGAAGAAGTAGAGGAACAGTTGGACAATATACGAGAGAACGACGA F2: 3 ACTTAGAAG 2 Unidirectional alignment (log-probability: -39.3) ATCTGAGTTCAcGGGCAGTGGTGTGAGCAGCAAGAATGAagaagattcA-----TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT ATCTGAGTTCATGGGCAGTGGTGTGAGCAGCAAGAATGA---------ATCTTCTTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT Template switch alignment (log-probability: -22.4) ATCTGAGTTCAcGGGCAGTGGTGTGAGCAGCAAGAATGAA|GAAGATTCA|TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT ATCTGAGTTCATGGGCAGTGGTGTGAGCAGCAAGAATGAA|GAAGATTCA|TTCATCTCCTTGTCAACCTGTTATATGCTCTCTTGCTGCT ========== Event 3122 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CGGTGGCCTTTGGATTAATGATCGGTGGATCCCAGATGCAGC-TCCTTTTGAAGTCTGGGGTAAAGA Chimp: CGGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCACCGATCTTTTGAAGTCTGGggtaaaga ↑ 3 2 1 4 Gorilla: CAGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCAGC-TCCTTTTGAAGTCTGGggtaaaga Human: CGGTGGCCTTTGGATTAATGATCGGTGGATCCCAGATGCAGC-TCCTTTTGAAGTCTGGGGTAAAGA Cluster: [ ] Orangutan: CAGTGGCCTTTGGGTTAGTGATCGGTGGATCCCAGATGCGGC-TCCCTTTGAGGTCTGGAgtaaaga Gorilla > Chimp --------------- chr6:8969626-8969631 Template switch process: F1: L GCGGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCA 1 F3: 4 TTTTGAAGTCTGGGGTAAAGAGCCTCCGTCAAATGGCTC R RF: GCAGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCAGCTCCTTTTGAAGTCTGGGGTAAAGAGCCTCCGTCAAATGGCTC RR: CGTCACCGGAAACCCAATTACTAGCCACCTAGGGTCTACGTCGAGGAAAACTTCAGACCCCATTTCTCGGAGGCAGTTTACCGAG F2: 3 CTAGCC 2 Unidirectional alignment (log-probability: -32.1) CgGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCA---CcgatCTTTTGAAGTCTGGGGTAAAGAGCCTCCGTCAAATGGCTC CAGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCAGCTC----CTTTTGAAGTCTGGGGTAAAGAGCCTCCGTCAAATGGCTC Template switch alignment (log-probability: -22) CgGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCA|CCGATC|TTTTGAAGTCTGGGGTAAAGAGCCTCCGTCAAATGGCTC CAGTGGCCTTTGGGTTAATGATCGGTGGATCCCAGATGCA|CCGATC|TTTTGAAGTCTGGGGTAAAGAGCCTCCGTCAAATGGCTC ========== Event 3123 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTAATAATGAACACTTATAATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCA----GAAA----ACATATCTAATAGTTTAGTAAA Chimp: TCTAATAATGAACACTTATAATGTTTACTGTGGAAAGTTTTAATGTGTAGAAACTCA----GAAA----ACATATCTAATAGTTTAGTAAA ↓ 3 2 1 4 Gorilla: TCTAATAATGAACACTTATAATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCAGACAGAAAACATTCATATCTAATAGTTTAGTAAA ↑ 3 2 1 4 Human: TCTAATAATGAACACTTATAATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCA----GAAA----ACATATCTAATAGTTTAGTAAA Cluster: [ ] Orangutan: TCTAATAATGAACCCTTATAATTTTTACTGTGGAAAGTTTTAATGTGTGAAAACTCAGACAGAAAACATTCATATCTAATAGTTTAGTAAA Human > Gorilla --------------- chr6:7949208-7949218 Template switch process: F1: L TATAATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCAGA 1 F3: 4 CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT R RF: TATAATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCAGAAAACATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT RR: ATATTACAAATGACACCTTTCAAAATTACACATTTTTGAGTCTTTTGTATAGATTATCAAATCATTTACCGTTTTATATAAAATAA F2: 3 TTACAAAAGAC 2 Unidirectional alignment (log-probability: -32.2) AATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTcagaCAGAAAAcattCATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT AATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACT----CAGAAAA----CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT Template switch alignment (log-probability: -22.7) AATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCAGA|CAGaAAACATT|CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT AATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCAGA|CAGTAAACATT|CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT Chimp > Gorilla --------------- chr6:7949208-7949218 Template switch process: F1: L TGAACACTTATAATGTTTACTGTGGAAAGTTTTAATGTGTAAAAACTCAGA 1 F3: 4 CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT R RF: TGAACACTTATAATGTTTACTGTGGAAAGTTTTAATGTGTAGAAACTCAGAAAACATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT RR: ACTTGTGAATATTACAAATGACACCTTTCAAAATTACACATCTTTGAGTCTTTTGTATAGATTATCAAATCATTTACCGTTTTATATAAAATAA F2: 3 TTACAAAAGAC 2 Unidirectional alignment (log-probability: -37.8) AATGTTTACTGTGGAAAGTTTTAATGTGTAaAAACTcagaCAGAAAAcattCATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT AATGTTTACTGTGGAAAGTTTTAATGTGTAGAAACT----CAGAAAA----CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT Template switch alignment (log-probability: -28.4) AATGTTTACTGTGGAAAGTTTTAATGTGTAaAAACTCAGA|CAGaAAACATT|CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT AATGTTTACTGTGGAAAGTTTTAATGTGTAGAAACTCAGA|CAGTAAACATT|CATATCTAATAGTTTAGTAAATGGCAAAATATATTTTATT ========== Event 3124 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGTGACCAATACCATCACA-------GCCAGCTGCCTTTGCGAAACTAAGATGCTTACaaaaaaaaaaaaaaagaaaagaaaaaTTCTAGAATCTGATTAGCAGAGCTAAGCAGTTCCTGTTGTACTGACATGTAGGATTAAGCTATGGC-TTGAAATTCACATG Chimp: AGAGTGACCAATACCATCACA-------GCCAGCTGCCTTTGCGAAACTAAGATGCTTACaaaaa----aaaaaagaaaagaaaaaTTCTAGAATCTGATTAGCAGAGCTAAGCAGTTCCTGTTGTACTGACATGTAGGATTAAGCTATGGCTATGAAATTCACATG ↑ 4 1 3 2 Gorilla: AGAGTGACCAATACCATCACA--------------GCCTTTGCGAAACTAAGATGCTTACaaaaaaaaaaaaaaagaaaagaaaaaTTCTAGAATCTGATTAGCAGAGCTAAGCAGTTCCTGTTGTACTGACATGTAGGATTAAGCTATGGCTATGAAATTCACATG Human: AGAGTGACCAATACCATCACA-------GCCAGCTGCCTTTGCGAAACTAAGATGCTTACaaaaaaaaaaaaaaagaaaagaaaaaTTCTAGAATCTGATTAGCAGAGCTAAGCAGTTCCTGTTGTACTGACATGTAGGATTAAGCTATGGC-TTGAAATTCACATG Cluster: [ ] Orangutan: AGAGTGACCAGTACCATCACAGCCAGCT-------GCCTTTGCGAAACTAAGATGCTTACaaaaa---aaaaaaagaaaagaaaaaTTCTGGAATCTGATTAGCAGAGCTAAGCAGTTCCTGTTGTACTGACATGTAGGATTAAGCTATGGCTATGAAATTCACATG Gorilla > Chimp --------------- chr6:8720757-8720760 Template switch process: F1: L TCCCATGTATATTCTTCAGCAGAGTGACCAATACCATCACAGCC 1 F3: 4 GCCTTTGCGAAACTAAGATGCTTACAAAAAAAAAAA R RF: TCCCATGTATATTCTTCAGCAGAGTGACCAATACCATCACAGCCTTTGCGAAACTAAGATGCTTACAAAAAAAAAAAAAAAGAAAAGAAAAATTCTAGAATCTGATTAGCAGAGCTAAGCAGTTCCTGTTGTACTGACATGTAGGATTAAGCT RR: AGGGTACATATAAGAAGTCGTCTCACTGGTTATGGTAGTGTCGGAAACGCTTTGATTCTACGAATGTTTTTTTTTTTTTTTCTTTTCTTTTTAAGATCTTAGACTAATCGTCTCGATTCGTCAAGGACAACATGACTGTACATCCTAATTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -27.8) ATGTATATTCTTCAGCAGAGTGACCAATACCATCACAgccagctGCCTTTGCGAAACTAAGATGCTTACAAAAAAAAAAA---- ATGTATATTCTTCAGCAGAGTGACCAATACCATCACA-------GCCTTTGCGAAACTAAGATGCTTACAAAAAAAAAAAAAAA Template switch alignment (log-probability: -16.2) ATGTATATTCTTCAGCAGAGTGACCAATACCATCACAGCC|AGCT|GCCTTTGCGAAACTAAGATGCTTACAAAAAAAAAAA ATGTATATTCTTCAGCAGAGTGACCAATACCATCACAGCC|AGCT|GCCTTTGCGAAACTAAGATGCTTACAAAAAAAAAAA ========== Event 3125 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATGTCACAGGGCTTCTTTA----------AACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCAGCTCAGCTTG Chimp: ATATGTCACAGGGCTTCTTTA----------AACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCAGCTCAGCTTG ↓ 1 4 3 2 Gorilla: GTATGTCACAGGGCTTCTTTAAGTGAAGGCCAGCAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCAGCTCAGCTTG ↑ 1 4 3 2 Human: ATATGTCACAGGGCTTCTTTA----------AACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCAGCTCAGCTTG Cluster: [ ] Orangutan: ATATGTCACAGGGCTTCTTTA----------AAGGGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCAGCTCAGCTTG Human > Gorilla --------------- chr6:166058666-166058676 Template switch process: F1: L TCTCTGTTTTGGTCCAGCCTGTATGTCACAGGGCTTCTTTAA 1 F3: 4 CAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA R RF: TCTCTGTTTTGGTCCAGCCTATATGTCACAGGGCTTCTTTAAACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA RR: AGAGACAAAACCAGGTCGGATATACAGTGTCCCGAAGAAATTTGTCACTGACCCGGAAAGACGACCGGAAGTGAATTGAGAGT F2: 3 GACCGGAAGTG 2 Unidirectional alignment (log-probability: -36.3) TCTGTTTTGGTCCAGCCTgTATGTCACAGGGCTTCTTTAagtgaaggccAgCAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA TCTGTTTTGGTCCAGCCTATATGTCACAGGGCTTCTTTA----------AACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA Template switch alignment (log-probability: -22.7) TCTGTTTTGGTCCAGCCTgTATGTCACAGGGCTTCTTTAA|GTGAAGGCCAG|CAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA TCTGTTTTGGTCCAGCCTATATGTCACAGGGCTTCTTTAA|GTGAAGGCCAG|CAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA Chimp > Gorilla --------------- chr6:166058666-166058676 Template switch process: F1: L TCTCTGTTTTGGTCCAGCCTGTATGTCACAGGGCTTCTTTAA 1 F3: 4 CAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA R RF: TCTCTGTTTTGGTCCAGCCTATATGTCACAGGGCTTCTTTAAACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA RR: AGAGACAAAACCAGGTCGGATATACAGTGTCCCGAAGAAATTTGTCACTGACCCGGAAAGACGACCGGAAGTGAATTGAGAGT F2: 3 GACCGGAAGTG 2 Unidirectional alignment (log-probability: -36.3) TCTGTTTTGGTCCAGCCTgTATGTCACAGGGCTTCTTTAagtgaaggccAgCAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA TCTGTTTTGGTCCAGCCTATATGTCACAGGGCTTCTTTA----------AACAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA Template switch alignment (log-probability: -22.7) TCTGTTTTGGTCCAGCCTgTATGTCACAGGGCTTCTTTAA|GTGAAGGCCAG|CAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA TCTGTTTTGGTCCAGCCTATATGTCACAGGGCTTCTTTAA|GTGAAGGCCAG|CAGTGACTGGGCCTTTCTGCTGGCCTTCACTTAACTCTCA ========== Event 3126 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CTGCTGTGCCATCAGTCCCCACAGGTC------GTGCCGCTCTCGACCTGCTGTCACACATGCAGAATAG ↑ 1 4 3 2 Chimp: CTGCTGTGCCATCAGTCCCCAAGAGCTGTGTGTCTGCCGCTCTCGACCTGCTGTCACCCATGCAGAATAG Gorilla: Human: CTGCTGTGCCATCAGTCCCCACAGGTC------GTGCCGCTCTCGACCTGCTGTCACACATGCAGAATAG Cluster: [ ] Orangutan: Chimp > Human ------------- chr6:3656221-3656227 Template switch process: F1: L CACTGCCCATGCCCCCTTGTCTGCTGTGCCATCAGTCCCCA 1 F3: 4 TGCCGCTCTCGACCTGCTGTCACACATGCAGAATAGAAGG R RF: CACTGCCCATGCCCCCTTGTCTGCTGTGCCATCAGTCCCCAAGAGCTGTGTGTCTGCCGCTCTCGACCTGCTGTCACCCATGCAGAATAGAAGG RR: GTGACGGGTACGGGGGAACAGACGACACGGTAGTCAGGGGTTCTCGACACACAGACGGCGAGAGCTGGACGACAGTGGGTACGTCTTATCTTCC F2: 3 GCTGGAC 2 Unidirectional alignment (log-probability: -36.4) ACTGCCCATGCCCCCTTGTCTGCTGTGCCATCAGTCCCCA------------CaggtcgTGCCGCTCTCGACCTGCTGTCACaCATGCAGAATAGAAGG ACTGCCCATGCCCCCTTGTCTGCTGTGCCATCAGTCCCCAAGAGCTGTGTGTC------TGCCGCTCTCGACCTGCTGTCACCCATGCAGAATAGAAGG Template switch alignment (log-probability: -22.1) ACTGCCCATGCCCCCTTGTCTGCTGTGCCATCAGTCCCCA|CAGGTCG|TGCCGCTCTCGACCTGCTGTCACaCATGCAGAATAGAAGG ACTGCCCATGCCCCCTTGTCTGCTGTGCCATCAGTCCCCA|CAGGTCG|TGCCGCTCTCGACCTGCTGTCACCCATGCAGAATAGAAGG ========== Event 3127 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: gaaatgtaaccgcctttg---ttagtattaaaaggtCTCATCTTTTAATACTATTACAAAGGCGGTTACATTTCAACATGtcac Chimp: gaaatgtaactgcctttg-taatagtattaaaagatgagacctttTAATACT--AACAAAGGCAGTTACATTTCAACATGtcac Gorilla: gaaatgtaactgcctttgt-aatagtattaaaagatgagacctttTAATACT--AACAAAGGCAGTTACATTTCAACATGtcac ↓ 13 24 Human: gaaatgtaaccgcctttg---ttagtattaaaaggtCTCATCTTTTAATACTATTACAAAGGCGGTTACATTTCAACATGtcac Cluster: [ ] Orangutan: gaaatgtaactgcctttgt-aataatattaaaagatgagacctttTAATACT--AACAAAGGCAGTTACATTTCAACATGTCAC Gorilla > Human --------------- chr6:164978849-164978881 Template switch process: F1: L CGCCTTTGT 1 F3: 4 ACAAAGGCGGTTACATTTCAACATGTCACACACCGGGGACTGTTGTGGG R RF: TGCCTTTGTAATAGTATTAAAAGATGAGACCTTTTAATACTAACAAAGGCAGTTACATTTCAACATGTCACACACCGGGGACTGTTGTGGG RR: ACGGAAACATTATCATAATTTTCTACTCTGGAAAATTATGATTGTTTCCGTCAATGTAAAGTTGTACAGTGTGTGGCCCCTGACAACACCC F2: 3 TTATCATAATTTTCTACTCTGGAAAATTATGAT 2 Unidirectional alignment (log-probability: -61.6) cGCCTTTGT--TAGTATTAAAAGgtctcAT-----CTTTTAATACTAttACAAAGGCgGTTACATTTCAACATGTCACACACCGGGGAC TGCCTTTGTAATAGTATTAAAAG-----ATGAGACCTTTTAATACTA--ACAAAGGCAGTTACATTTCAACATGTCACACACCGGGGAC Template switch alignment (log-probability: -30.4) cGCCTTTGT|TAGTATTAAAAGGTCTCATCTTTTAATACTATT|ACAAAGGCgGTTACATTTCAACATGTCACACACCGGGGAC TGCCTTTGT|TAGTATTAAAAGGTCTCATCTTTTAATACTATT|ACAAAGGCAGTTACATTTCAACATGTCACACACCGGGGAC ========== Event 3128 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GTCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGGTCATAAAGTCACTAGGTCACCTCCAGACG Chimp: Gorilla: ATCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGG---AAAACTCACTAGGTCACCTCCAGACG ↓ 3 2 1 4 Human: GTCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGGTCATAAAGTCACTAGGTCACCTCCAGACG Cluster: [ ] Orangutan: ATCAATGTTTTCCTTTCCTCTTTATGACCTGATTTGG---AAAACTCACTAGGTCACCTCCAGACG Gorilla > Human --------------- chr6:4992525-4992532 Template switch process: F1: L GATCGTCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGG 1 F3: 4 TCACTAGGTCACCTCCAGACGACAGTAGCAGACGGTCACG R RF: GATCATCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGGAAAACTCACTAGGTCACCTCCAGACGACAGTAGCAGACGGTCACG RR: CTAGTAGTTACAAAAAGAAAGGAGAAATACTGGACTAAACCTTTTGAGTGATCCAGTGGAGGTCTGCTGTCATCGTCTGCCAGTGC F2: 3 GAAATACT 2 Unidirectional alignment (log-probability: -31.8) ATCgTCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGGtcatAAAgTCACTAGGTCACCTCCAGACGACAGTAGCAGACGGTCACG ATCATCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGGA---AAACTCACTAGGTCACCTCCAGACGACAGTAGCAGACGGTCACG Template switch alignment (log-probability: -22.3) ATCgTCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGG|TCATAAAG|TCACTAGGTCACCTCCAGACGACAGTAGCAGACGGTCACG ATCATCAATGTTTTTCTTTCCTCTTTATGACCTGATTTGG|TCATAAAG|TCACTAGGTCACCTCCAGACGACAGTAGCAGACGGTCACG ========== Event 3129 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGACAGGGCCCTAAACAATGCGAAGACAGGCTGGGCTGCAGCAGTGCCCCCTCCTTAGTTCTGTGGCAGCCAGAGAAGGCTCCTGGCTGTGGTTGGGAGGTGACGGAACAGTCAGAGCATGTGAGTCCTTCATA Chimp: GGGACAGGGCCCTAAACAATGCCAAGACAGGCTGGGCTGCAGTAGTGCCCCCTCCTTAGTTCTGTGGCAGCCAGAGAAGGCTCCTGGCTGTGGTTGGGAGGTGACGGAACAGTCAGAGCATGTGAGTCCTTCATA ↓ 1 4 3 2 Gorilla: GGGACAGGGCCCTAAACAATG-TGACACAGGCTGGGCTGCAGCAGTGCCCCCTCCTTAGTTCTGTGGCAGCCAGAGAAGGCTCCTGGCTGTGGTTGGGAGGTGACGGAACAGTCAGAGCATGCGAGTCCTTCATA Human: GGGACAGGGCCCTAAACAATGCGAAGACAGGCTGGGCTGCAGCAGTGCCCCCTCCTTAGTTCTGTGGCAGCCAGAGAAGGCTCCTGGCTGTGGTTGGGAGGTGACGGAACAGTCAGAGCATGTGAGTCCTTCATA Cluster: [ ] Orangutan: GGGACAGGGCCCAAAACAATGCCAAGACAGGGTGGGTTGCAGTGGTGCCCCCTTCTTAGTTCTGTGGCAGCCACAGAAGGCTCCTGGTTGTGGTTGGGAGGTGACGGAACAGTCAGAGCATGTGAGTCCTTCATA Chimp > Gorilla --------------- chr6:168873328-168873331 Template switch process: F1: L CATTGGCTCACCAATATTTTGGGACAGGGCCCTAAACAATG 1 F3: 4 ACAGGCTGGGCTGCAGCAGTGCCCCCTCCTTAGTTCTGTG R RF: CATTGGCTCACAAATATTTTGGGACAGGGCCCTAAACAATGCCAAGACAGGCTGGGCTGCAGTAGTGCCCCCTCCTTAGTTCTGTGGCAGCCAGAGAAGGCTCCTGGCTGTGGTTGGGAGGTGACGGAACAGTCA RR: GTAACCGAGTGTTTATAAAACCCTGTCCCGGGATTTGTTACGGTTCTGTCCGACCCGACGTCATCACGGGGGAGGAATCAAGACACCGTCGGTCTCTTCCGAGGACCGACACCAACCCTCCACTGCCTTGTCAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -36.2) ATTGGCTCACcAATATTTTGGGACAGGGCCCTAAACAATGtgaC----ACAGGCTGGGCTGCAGcAGTGCCCCCTCCTTAGTTCTGTG ATTGGCTCACAAATATTTTGGGACAGGGCCCTAAACAATG---CCAAGACAGGCTGGGCTGCAGTAGTGCCCCCTCCTTAGTTCTGTG Template switch alignment (log-probability: -27.3) ATTGGCTCACcAATATTTTGGGACAGGGCCCTAAACAATG|TGAC|ACAGGCTGGGCTGCAGcAGTGCCCCCTCCTTAGTTCTGTG ATTGGCTCACAAATATTTTGGGACAGGGCCCTAAACAATG|TGAC|ACAGGCTGGGCTGCAGTAGTGCCCCCTCCTTAGTTCTGTG ========== Event 3130 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACGAAATATCCCTCCTCACTT-ACA----GTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTGGTGGAGAGCTGTCAGCAAGTGAACACTGACTCGGAAACTGCAGTTGTA Chimp: ACGAAATATCCCTCCTCACTT-ACAGTGAGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTGGTGGAGAGCTGTCAGCAAGTGAACACTGACTCGGAAACTGCAGTTGTA ↑ 1 4 3 2 Gorilla: ACGAAATATCCCTCCTCACTTAACA----GTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTGGTGGAGAGCTGTCAGCAAGTGAACACTGACTCGGAAACTGCAGTTGTA Human: ACGAAATATCCCTCCTCACTT-ACA----GTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTGGTGGAGAGCTGTCAGCAAGTGAACACTGACTCGGAAACTGCAGTTGTA Cluster: [ ] Orangutan: ACGAAATATCCCGCCTCACTC-ACA----GTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTGGTGGAGAGCTGTGAGCAAGTGAACACTGACTCGGAAACTGCAGTTGTA Gorilla > Chimp --------------- chr6:4169494-4169498 Template switch process: F1: L AGGATTCGGAAACTTCAGATACGAAATATCCCTCCTCACTTA 1 F3: 4 AGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTG R RF: AGGATTCGGAAACTTCCGATACGAAATATCCCTCCTCACTTAACAGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGTGGTGGAGAGCTGTCAGCAAGTGAACACTG RR: TCCTAAGCCTTTGAAGGCTATGCTTTATAGGGAGGAGTGAATTGTCACCCTCCACGACCTATCAACTGATCAGGTCATACCTCACCACCTCTCGACAGTCGTTCACTTGTGAC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -31.8) GATTCGGAAACTTCaGATACGAAATATCCCTCCTCACTTAcagtgAGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGT GATTCGGAAACTTCCGATACGAAATATCCCTCCTCACTTAAC---AGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGT Template switch alignment (log-probability: -21.9) GATTCGGAAACTTCaGATACGAAATATCCCTCCTCACTTA|CAGTG|AGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGT GATTCGGAAACTTCCGATACGAAATATCCCTCCTCACTTA|CAGTG|AGTGGGAGGTGCTGGATAGTTGACTAGTCCAGTATGGAGT ========== Event 3131 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGTGCCTCTTTTCAGGCAGCAATGCAGGCATTGCTTTGTGTTTCTGATTTTTAAA ↑ 3 1 2 4 Chimp: AGGTGCCTCTTTTCAGGCAGCAATGCCTGCA----TTTGTGTTTCTGATTTTTAAA Gorilla: AGGTGCCTCTTTTCAGGCAGCAATGCCTGCA----TTTGTGTTTCTGATTTTTAAA ↓ 3 1 2 4 Human: AGGTGCCTCTTTTCAGGCAGCAATGCAGGCATTGCTTTGTGTTTCTGATTTTTAAA Cluster: [ ] Orangutan: AGGTGCCTCTTTTCAGGCAGCAATGCCTGCA----TTTGTGTTTCTGATTTTTAAA Chimp > Human ------------- chr6:166519785-166519793 Template switch process: F1: L TGGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGC 1 F3: 4 TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA R RF: TGGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGCCTGCATTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA RR: ACCTTGGGGAGAAGTTCCACGGAGAAAAGTCCGTCGTTACGGACGTAAACACAAAGACTAAAAATTTACTAGAGGTGGTTATCTGT F2: 3 CGTTACGGA 2 Unidirectional alignment (log-probability: -28.7) GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGCagGCAttgcTTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGCCTGCA----TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA Template switch alignment (log-probability: -16.4) GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGC|AGGCATTGC|TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGC|AGGCATTGC|TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA Gorilla > Human --------------- chr6:166519785-166519793 Template switch process: F1: L TGGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGC 1 F3: 4 TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA R RF: TGGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGCCTGCATTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA RR: ACCTTGGGGAGAAGTTCCACGGAGAAAAGTCCGTCGTTACGGACGTAAACACAAAGACTAAAAATTTACTAGAGGTGGTTATCTGT F2: 3 CGTTACGGA 2 Unidirectional alignment (log-probability: -27.7) GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGCagGCAttgcTTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGCCTGCA----TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA Template switch alignment (log-probability: -16.9) GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGC|AGGCATTGC|TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA GGAACCCCTCTTCAAGGTGCCTCTTTTCAGGCAGCAATGC|AGGCATTGC|TTTGTGTTTCTGATTTTTAAATGATCTCCACCAATAGACA ========== Event 3132 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATGCAGTCAGAAGGGCCAAGCCTT--CATGC-AGCCTGACTCCCTGAATTTAACATG Chimp: TATGCAGTCAGAAGGGCCAAGCCTT--CATGC-AGCCTGACTCCCTGAATTTAACATG ↓ 3 1 2 4 Gorilla: TAGGCAGTCAGAAGGGCCAAGCCTTCGCATGAAGGCTTGACTCCCTGAATTTAACATG ↑ 3 1 2 4 Human: TATGCAGTCAGAAGGGCCAAGCCTT--CATGC-AGCCTGACTCCCTGAATTTAACATG Cluster: [ ] Orangutan: TATGCAGTCAGAAGGGCCGAGCCTT--CATGC-AACCTGAGTCCCTGAATTTAACATG Human > Gorilla --------------- chr6:171182816-171182826 Template switch process: F1: L CCAGCATTGCAAATTATAGGCAGTCAGAAGGGCCAAGCCTTC 1 F3: 4 TGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC R RF: CCAGCATTGCAAATTATATGCAGTCAGAAGGGCCAAGCCTTCATGCAGCCTGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC RR: GGTCGTAACGTTTAATATACGTCAGTCTTCCCGGTTCGGAAGTACGTCGGACTGAGGGACTTAAATTGTACTCCGTCTCCTTATCTGACG F2: 3 TCGGAAGTACG 2 Unidirectional alignment (log-probability: -39.1) AGCATTGCAAATTATAgGCAGTCAGAAGGGCCAAGCCTTC--GCAtgaagGCtTGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC AGCATTGCAAATTATATGCAGTCAGAAGGGCCAAGCCTTCATGCA-----GCCTGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC Template switch alignment (log-probability: -22.7) AGCATTGCAAATTATAgGCAGTCAGAAGGGCCAAGCCTTC|GCATGAAGGCT|TGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC AGCATTGCAAATTATATGCAGTCAGAAGGGCCAAGCCTTC|GCATGAAGGCT|TGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC Chimp > Gorilla --------------- chr6:171182816-171182826 Template switch process: F1: L CCAGCATTGCAAATTATAGGCAGTCAGAAGGGCCAAGCCTTC 1 F3: 4 TGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC R RF: CCAGCATTGCAAATTATATGCAGTCAGAAGGGCCAAGCCTTCATGCAGCCTGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC RR: GGTCGTAACGTTTAATATACGTCAGTCTTCCCGGTTCGGAAGTACGTCGGACTGAGGGACTTAAATTGTACTCCGTCTCCTTATCTGACG F2: 3 TCGGAAGTACG 2 Unidirectional alignment (log-probability: -39.1) AGCATTGCAAATTATAgGCAGTCAGAAGGGCCAAGCCTTC--GCAtgaagGCtTGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC AGCATTGCAAATTATATGCAGTCAGAAGGGCCAAGCCTTCATGCA-----GCCTGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC Template switch alignment (log-probability: -22.7) AGCATTGCAAATTATAgGCAGTCAGAAGGGCCAAGCCTTC|GCATGAAGGCT|TGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC AGCATTGCAAATTATATGCAGTCAGAAGGGCCAAGCCTTC|GCATGAAGGCT|TGACTCCCTGAATTTAACATGAGGCAGAGGAATAGACTGC ========== Event 3133 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CACAATGTATGCAGTCAATACTTGTGAGAAGTCTGGCTGC--AGAAGTAGGAGACAGAGCAACAACTGG Chimp: CACAATGTATGCAGTCAATACTTCTGAGAAGTCTGGCTGC--AGAAGTAGGAGACAGAGCAACAACTGG ↑ 3 2 1 4 Gorilla: cacaATGGATGCAGTCAATACTTCTGAGAAGTCTGGCTGTGAAAAGGGAGGAGACAGAGCAACAACTGG ↓ 3 2 1 4 Human: CACAATGTATGCAGTCAATACTTGTGAGAAGTCTGGCTGC--AGAAGTAGGAGACAGAGCAACAACTGG Cluster: [ ] Orangutan: cacaATGGATGCAGTCAATACTTCTGAGAAGTCTGGCTGCGAGAAGGGAGGAGATAGAGTAACAACTGA Gorilla > Human --------------- chr6:169076169-169076175 Template switch process: F1: L GACACAATGTATGCAGTCAATACTTGTGAGAAGTCTGGCTG 1 F3: 4 AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC R RF: GACACAATGGATGCAGTCAATACTTCTGAGAAGTCTGGCTGTGAAAAGGGAGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC RR: CTGTGTTACCTACGTCAGTTATGAAGACTCTTCAGACCGACACTTTTCCCTCCTCTGTCTCGTTGTTGACCTTACACAGGTCTTGGAGGG F2: 3 TGAAGAC 2 Unidirectional alignment (log-probability: -40.7) ACACAATGtATGCAGTCAATACTTgTGAGAAGTCTGGCTgcagaaGT--------AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC ACACAATGGATGCAGTCAATACTTCTGAGAAGTCTGGCT------GTGAAAAGGGAGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC Template switch alignment (log-probability: -27.7) ACACAATGtATGCAGTCAATACTTgTGAGAAGTCTGGCTG|CAGAAGT|AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC ACACAATGGATGCAGTCAATACTTCTGAGAAGTCTGGCTG|CAGAAGT|AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC Gorilla > Chimp --------------- chr6:173773080-173773086 Template switch process: F1: L GACACAATGTATGCAGTCAATACTTCTGAGAAGTCTGGCTG 1 F3: 4 AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC R RF: GACACAATGGATGCAGTCAATACTTCTGAGAAGTCTGGCTGTGAAAAGGGAGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC RR: CTGTGTTACCTACGTCAGTTATGAAGACTCTTCAGACCGACACTTTTCCCTCCTCTGTCTCGTTGTTGACCTTACACAGGTCTTGGAGGG F2: 3 TGAAGAC 2 Unidirectional alignment (log-probability: -35.2) ACACAATGtATGCAGTCAATACTTCTGAGAAGTCTGGCTgcagaaGT--------AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC ACACAATGGATGCAGTCAATACTTCTGAGAAGTCTGGCT------GTGAAAAGGGAGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC Template switch alignment (log-probability: -22.1) ACACAATGtATGCAGTCAATACTTCTGAGAAGTCTGGCTG|CAGAAGT|AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC ACACAATGGATGCAGTCAATACTTCTGAGAAGTCTGGCTG|CAGAAGT|AGGAGACAGAGCAACAACTGGAATGTGTCCAGAACCTCCC ========== Event 3134 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAGATGCCAAGGTCAGGCA---------------TCAGCTTTCAGAGAATGCAGCTGCGTCAGAG Chimp: AGGAGATGCCAAGGTCAGGCG---------------TCAGCTTTCAGAGAATGCAGCTGCCTCAGAG ↓ 4 31 2 Gorilla: AGGAGATGCCAAGGTCAGGCGTCAGCTCTGAAAGCGTCAGCTTTCAGAGAATGCAGCTGAGTCAGAG Human: AGGAGATGCCAAGGTCAGGCA---------------TCAGCTTTCAGAGAATGCAGCTGCGTCAGAG Cluster: [ ] Orangutan: AGGAGATGCCAATGTCAGGCG---------------TCAGCTTTCAGAGAATGCAGCTGCGTCAGAG Chimp > Gorilla --------------- chr6:1073255-1073261 Template switch process: F1: L CCTGCGCCTGAGCAGTGCTGAGGAGATGCCAAGGTCAGGCGTCAGCT 1 F3: 4 CGTCAGCTTTCAGAGAATGCAGCTGAGTCAGAGATGGAGACA R RF: CCTGCGCCTGAGCAGTGCTGAGGAGATGCCAAGGTCAGGCGTCAGCTTTCAGAGAATGCAGCTGCCTCAGAGATGGAGACA RR: GGACGCGGACTCGTCACGACTCCTCTACGGTTCCAGTCCGCAGTCGAAAGTCTCTTACGTCGACGGAGTCTCTACCTCTGT F2: 3 GAAAGTC 2 Unidirectional alignment (log-probability: -43.5) CTGAGCAGTGCTGAGGAGATGCCAAGGTCAGGcgtcagctctgaaagCGTCAGCTTTCAGAGAATGCAGCTGagTCAGAGATGGAGA CTGAGCAGTGCTGAGGAGATGCCAAGGTCAGG---------------CGTCAGCTTTCAGAGAATGCAGCTGCCTCAGAGATGGAGA Template switch alignment (log-probability: -27.9) CTGAGCAGTGCTGAGGAGATGCCAAGGTCAGGCGTCAGCT|CTGAAAG|CGTCAGCTTTCAGAGAATGCAGCTGagTCAGAGATGGAGA CTGAGCAGTGCTGAGGAGATGCCAAGGTCAGGCGTCAGCT|CTGAAAG|CGTCAGCTTTCAGAGAATGCAGCTGCCTCAGAGATGGAGA ========== Event 3135 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCTACCTCCACATCCCACACCTCTGCTGCCCAAGGGTCAGCACTGGCCAGCTGGAACTTGGAAT Chimp: CTCTACCTCCACATCCCACACCTCTGCTGCCCAAGGGTCAGCACTGGCCAGCTGGAACTCGGAAT ↓ 1 4 3 2 Gorilla: CTCTACCTCCACATCCCACAC-AGTGCTG-ACAAGGGTCAGCACTGGCCAGCTGGAACTTGGAAT ↑ 1 4 3 2 Human: CTCTACCTCCACATCCCACACCTCTGCTGCCCAAGGGTCAGCACTGGCCAGCTGGAACTTGGAAT Cluster: [ ] Orangutan: Human > Gorilla --------------- chr6:172786912-172786919 Template switch process: F1: L GAGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACAC 1 F3: 4 CAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC R RF: GAGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACACCTCTGCTGCCCAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC RR: CTCGAAGCATCTCGACGTCTGAGATGGAGGTGTAGGGTGTGGAGACGACGGGTTCCCAGTCGTGACCGGTCGACCTTGAACCTTAAGAGAG F2: 3 AGTCGTGA 2 Unidirectional alignment (log-probability: -32.6) AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACA----------CagtgctgaCAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACACCTCTGCTGCC--------CAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC Template switch alignment (log-probability: -16.7) AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACAC|AGTGCTGA|CAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACAC|AGTGCTGA|CAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC Chimp > Gorilla --------------- chr6:172786912-172786919 Template switch process: F1: L GAGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACAC 1 F3: 4 CAAGGGTCAGCACTGGCCAGCTGGAACTTGGAATTCTCTC R RF: GAGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACACCTCTGCTGCCCAAGGGTCAGCACTGGCCAGCTGGAACTCGGAATTCTCTC RR: CTCGAAGCATCTCGACGTCTGAGATGGAGGTGTAGGGTGTGGAGACGACGGGTTCCCAGTCGTGACCGGTCGACCTTGAGCCTTAAGAGAG F2: 3 AGTCGTGA 2 Unidirectional alignment (log-probability: -38.2) AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACA----------CagtgctgaCAAGGGTCAGCACTGGCCAGCTGGAACTtGGAATTCTCTC AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACACCTCTGCTGCC--------CAAGGGTCAGCACTGGCCAGCTGGAACTCGGAATTCTCTC Template switch alignment (log-probability: -22.3) AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACAC|AGTGCTGA|CAAGGGTCAGCACTGGCCAGCTGGAACTtGGAATTCTCTC AGCTTCGTAGAGCTGCAGACTCTACCTCCACATCCCACAC|AGTGCTGA|CAAGGGTCAGCACTGGCCAGCTGGAACTCGGAATTCTCTC ========== Event 3136 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: tGGTGACCCGCACTGTCTTCTCTCCTCACTCTGAGGAGAGCCTCActctgtggacaccgcaga ↓ 1 43 2 Chimp: TGGTGACCCGCACTGTCTTCTCTCCAGGC-------TGAGCCTCActctgtggacaccgcaga Gorilla: tGGTGACCCGCACTGTCTTCTTTCCAGGC-------TGAGCCTCActctgtggacactgcaga ↑ 1 43 2 Human: tGGTGACCCGCACTGTCTTCTCTCCTCACTCTGAGGAGAGCCTCActctgtggacaccgcaga Cluster: [ ] Orangutan: Human > Chimp ------------- chr6:415540-415544 Template switch process: F1: L TCTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCC 1 F3: 4 GAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT R RF: TCTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCCTCACTCTGAGGAGAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT RR: AGAGAGACCGGACCCGACCACTGGGCGTGACAGAAGAGAGGAGTGAGACTCCTCTCGGAGTGAGACACCTGTGGCGTCTGTGGACGAGTGGGA F2: 3 TCGGA 2 Unidirectional alignment (log-probability: -27.5) CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCcaggCT-----------GAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTC----CTCACTCTGAGGAGAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT Template switch alignment (log-probability: -15.9) CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCC|AGGCT|GAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCC|AGGCT|GAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT Human > Gorilla --------------- chr6:381297-381301 Template switch process: F1: L TGTCTCTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTTTCC 1 F3: 4 GAGCCTCACTCTGTGGACACTGCAGACACCTGCTCACCCT R RF: TGTCTCTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCCTCACTCTGAGGAGAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT RR: ACAGAGAGAGACCGGACCCGACCACTGGGCGTGACAGAAGAGAGGAGTGAGACTCCTCTCGGAGTGAGACACCTGTGGCGTCTGTGGACGAGTGGGA F2: 3 TCGGA 2 Unidirectional alignment (log-probability: -37) CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTttccaggCT--------------GAGCCTCACTCTGTGGACACtGCAGACACCTGCTCACCCT CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCT-------CTCCTCACTCTGAGGAGAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT Template switch alignment (log-probability: -27.5) CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTtTCC|AGGCT|GAGCCTCACTCTGTGGACACtGCAGACACCTGCTCACCCT CTCTCTGGCCTGGGCTGGTGACCCGCACTGTCTTCTCTCC|AGGCT|GAGCCTCACTCTGTGGACACCGCAGACACCTGCTCACCCT ========== Event 3137 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ctatgctattgaattgtgtcattggctaattccttaAGAAACAGTCCAATGGGGGAACAAA--------CAAACTAATGGATTAAAACACACTGTGataatgaaagctaacattaatgcttactgtgtga Chimp: TTATGCTATTGAGTTGTGTCACTGGGTAATTCCTTAAGAAACAGTCCAATGGGGGAACAAA----CAATCAAACTAATGGATTAAAACACACTGTGataatgaaagctaacattaatgcctactgtgtga ↓ 1 4 3 2 Gorilla: TTATGCTATTGAGTTGTGTCATTAGCTAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACAAT----CAAACTAATGGATTAAAACACACTGTGATAaagaaagctaacattaatgcttactgtgtga Human: ctatgctattgaattgtgtcattggctaattccttaAGAAACAGTCCAATGGGGGAACAAA--------CAAACTAATGGATTAAAACACACTGTGataatgaaagctaacattaatgcttactgtgtga Cluster: [ ] Orangutan: TTATGCTA-GGAGTTGTGTCACTCGCTAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACAAT----CAAACTAATGGATTAAAACACACTGTGATAGTGaaagctaacattaatgcttactgtgtga Chimp > Gorilla --------------- chr6:154743742-154743746 Template switch process: F1: L TTTAATCAGGTTATTTTGTTTTATGCTATTGAGTTGTGTCA 1 F3: 4 TAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACAAT R RF: TTTAATCAGGTTATTTTGTTTTATGCTATTGAGTTGTGTCACTGGGTAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACAATCAAACTAATGGATTAAAACACACTGTGATAATGAAAGCTAA RR: AAATTAGTCCAATAAAACAAAATACGATAACTCAACACAGTGACCCATTAAGGAATTCTTTGTCAGGTTACCCCCTTGTTTGTTAGTTTGATTACCTAATTTTGTGTGACACTATTACTTTCGATT F2: 3 CGATT 2 Unidirectional alignment (log-probability: -28.8) TTAATCAGGTTATTTTGTTTTATGCTATTGAGTTGTGTCAtTaGcTAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACaat TTAATCAGGTTATTTTGTTTTATGCTATTGAGTTGTGTCACTGGGTAATTCCTTAAGAAACAGTCCAATGGGGGAACAAAC--- Template switch alignment (log-probability: -16.3) TTAATCAGGTTATTTTGTTTTATGCTATTGAGTTGTGTCA|TTAGC|TAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACAAT TTAATCAGGTTATTTTGTTTTATGCTATTGAGTTGTGTCA|TTAGC|TAATTCCTTAAGAAACAGTCCAATGGGGGAACAAACAAT ========== Event 3138 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGCATGGGGATCTGTTCACCAGACA-GCTGGAGTGTTGACTCCAGCTGGAACCCACCCTGATGCCT Chimp: AGCATGGGGGTCTGTTCACCAAACAATCT--GGTGTTGACTCCAGCTGGAACCCACCCTGATGCCT Gorilla: AGCATGGGGGTCTGTTCACCAAACAATCT--GGTGTTGACTCCAGCTGGAACCCACCCTGATGCCT ↓ 1 4 3 2 Human: AGCATGGGGATCTGTTCACCAGACA-GCTGGAGTGTTGACTCCAGCTGGAACCCACCCTGATGCCT Cluster: [ ] Orangutan: ------------------------------------------------------------------ Gorilla > Human --------------- chr6:151771110-151771115 Template switch process: F1: L CTTATTTTCCTGAGCCTCACAGCATGGGGATCTGTTCACCAGACA 1 F3: 4 GTGTTGACTCCAGCTGGAACCCACCCTGATGCCTGGTAAT R RF: CTTATTTTCCTGAGCCTCACAGCATGGGGGTCTGTTCACCAAACAATCTGGTGTTGACTCCAGCTGGAACCCACCCTGATGCCTGGTAAT RR: GAATAAAAGGACTCGGAGTGTCGTACCCCCAGACAAGTGGTTTGTTAGACCACAACTGAGGTCGACCTTGGGTGGGACTACGGACCATTA F2: 3 AGGTCG 2 Unidirectional alignment (log-probability: -39.1) TTTCCTGAGCCTCACAGCATGGGGaTCTGTTCACCAgACAgctggA----GTGTTGACTCCAGCTGGAACCCACCCTGATGCCTGGTAAT TTTCCTGAGCCTCACAGCATGGGGGTCTGTTCACCAAACA-----ATCTGGTGTTGACTCCAGCTGGAACCCACCCTGATGCCTGGTAAT Template switch alignment (log-probability: -27.6) TTTCCTGAGCCTCACAGCATGGGGaTCTGTTCACCAgACA|GCTGGA|GTGTTGACTCCAGCTGGAACCCACCCTGATGCCTGGTAAT TTTCCTGAGCCTCACAGCATGGGGGTCTGTTCACCAAACA|GCTGGA|GTGTTGACTCCAGCTGGAACCCACCCTGATGCCTGGTAAT ========== Event 3139 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTAAGAATCTCTAAAAGATGTGT------TAAGAGATTCAAAACCCCAGCAGAGAACT--AT ↓ 1 4 3 2 Chimp: CTAAGAATCTCTAAAAGATGTTTTGAATCTAAGAGATTCAAAACCCCAGCAGAGAACT--AT Gorilla: CTAAGAATCTCTAAAAGATGTGT------TAAGAGATTCAAAACCCCAGCAGAGAACT---- Human: CTAAGAATCTCTAAAAGATGTGT------TAAGAGATTCAAAACCCCAGCAGAGAACT--AT Cluster: [ ] Orangutan: CTAAGAATCTCTAAAAGATGTGT------TAAGAGATTCAAAACCCCAGCAGAGAACTAT-- Human > Chimp ------------- chr6:155423570-155423577 Template switch process: F1: L TCATTTCAGAAGCTGTGAAACTAAGAATCTCTAAAAGATGT 1 F3: 4 TAAGAGATTCAAAACCCCAGCAGAGAACTATGTAACAATA R RF: TCATTTCAGAAGCTGTGAAACTAAGAATCTCTAAAAGATGTGTTAAGAGATTCAAAACCCCAGCAGAGAACTATGTAACAATA RR: AGTAAAGTCTTCGACACTTTGATTCTTAGAGATTTTCTACACAATTCTCTAAGTTTTGGGGTCGTCTCTTGATACATTGTTAT F2: 3 CTAAGTTT 2 Unidirectional alignment (log-probability: -25.6) CATTTCAGAAGCTGTGAAACTAAGAATCTCTAAAAGATGTtTtgaatcTAAGAGATTCAAAACCCCAGCAGAGAACTATGTAACAATA CATTTCAGAAGCTGTGAAACTAAGAATCTCTAAAAGATGTGT------TAAGAGATTCAAAACCCCAGCAGAGAACTATGTAACAATA Template switch alignment (log-probability: -16.3) CATTTCAGAAGCTGTGAAACTAAGAATCTCTAAAAGATGT|TTTGAATC|TAAGAGATTCAAAACCCCAGCAGAGAACTATGTAACAATA CATTTCAGAAGCTGTGAAACTAAGAATCTCTAAAAGATGT|TTTGAATC|TAAGAGATTCAAAACCCCAGCAGAGAACTATGTAACAATA ========== Event 3140 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTCAGTGGCTCCTGCAAGTTCT-----AATAAAAGCGCACTTGCCGATTTTAGGTT Chimp: ACTTTAGTGGCTCCTGCAAGTTCT-----AATAAAAGCGCACTTGCCGATTTTAGGTT Gorilla: ACTTCAGTGGCTCCTGCAAGTTCTATTTTATTAGATCGGCACTTGCCGATTTTAGGTT ↑ 3 1 2 4 Human: ACTTCAGTGGCTCCTGCAAGTTCT-----AATAAAAGCGCACTTGCCGATTTTAGGTT Cluster: [ ] Orangutan: ACTTCAGTGGCTCCTGCAAGTTCT-----AATAAAAGTGCACTTGCCAATTTTAGGTT Human > Gorilla --------------- chr6:152850884-152850895 Template switch process: F1: L AATTTTAAAGGTATCAGACTTCAGTGGCTCCTGCAAGTTCTA 1 F3: 4 GGCACTTGCCGATTTTAGGTTGTTTGTGGCGGATTAAATTT R RF: AATTTTAAAGGTATCAGACTTCAGTGGCTCCTGCAAGTTCTAATAAAAGCGCACTTGCCGATTTTAGGTTGTTTGTGGCGGATTAAATTT RR: TTAAAATTTCCATAGTCTGAAGTCACCGAGGACGTTCAAGATTATTTTCGCGTGAACGGCTAAAATCCAACAAACACCGCCTAATTTAAA F2: 3 CTAGATTATTTT 2 Unidirectional alignment (log-probability: -39.7) TTTTAAAGGTATCAGACTTCAGTGGCTCCTGCAAGTTCTA--------ttttattagatcgGCACTTGCCGATTTTAGGTTGTTTGTGGCGGATTAAATT TTTTAAAGGTATCAGACTTCAGTGGCTCCTGCAAGTTCTAATAAAAGC-------------GCACTTGCCGATTTTAGGTTGTTTGTGGCGGATTAAATT Template switch alignment (log-probability: -28.3) TTTTAAAGGTATCAGACTTCAGTGGCTCCTGCAAGTTCTA|TTTTATTAGAtC|gGCACTTGCCGATTTTAGGTTGTTTGTGGCGGATTAAATT TTTTAAAGGTATCAGACTTCAGTGGCTCCTGCAAGTTCTA|TTTTATTAGAAC|CGCACTTGCCGATTTTAGGTTGTTTGTGGCGGATTAAATT ========== Event 3141 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCACGTCTGTTCTATTAACCTATGAAGGCAAAAATTGATTTTTGCCTTCATAATATTTCTGTG----TGTTT Chimp: TTCACGTCTGTTCTATTAATCTATGAAGGCAAAAATTGATTTTTGCCTTCATAATATTTGTGTG----TGTT- ↑ 1 4 3 2 Gorilla: TTCACGTCTGTTCTATTAATCC------------ATTGATTTTTGCCTTCATAATATTTGTGTG----TGTTT Human: TTCACGTCTGTTCTATTAACCTATGAAGGCAAAAATTGATTTTTGCCTTCATAATATTTCTGTG----TGTTT Cluster: [ ] Orangutan: TTCATGTCTGTTCTATTAATTC------------ATTGATTTTTGCCTTCATAATATTtgtgtgtgtgtgttt Gorilla > Chimp --------------- chr6:21963727-21963739 Template switch process: F1: L GCACTACCACACCTGGCTTCTTCACGTCTGTTCTATTAATC 1 F3: 4 ATTGATTTTTGCCTTCATAATATTTGTGTGTGTTTGTG R RF: GCAGTACCACACCTGGCTTCTTCACGTCTGTTCTATTAATCCATTGATTTTTGCCTTCATAATATTTGTGTGTGTTTGTG RR: CGTCATGGTGTGGACCGAAGAAGTGCAGACAAGATAATTAGGTAACTAAAAACGGAAGTATTATAAACACACACAAACAC F2: 3 AAAACGGAAGTAT 2 Unidirectional alignment (log-probability: -39.2) CAcTACCACACCTGGCTTCTTCACGTCTGTTCTATTAATCtatgaaggcaaaaATTGATTTTTGCCTTCATAATATTTGTGTGTGTTTGTG CAGTACCACACCTGGCTTCTTCACGTCTGTTCTATTAATC------------CATTGATTTTTGCCTTCATAATATTTGTGTGTGTTTGTG Template switch alignment (log-probability: -22.9) CAcTACCACACCTGGCTTCTTCACGTCTGTTCTATTAATC|TATGAAGGCAAAA|ATTGATTTTTGCCTTCATAATATTTGTGTGTGTTTGTG CAGTACCACACCTGGCTTCTTCACGTCTGTTCTATTAATC|TATGAAGGCAAAA|ATTGATTTTTGCCTTCATAATATTTGTGTGTGTTTGTG ========== Event 3142 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TGGCATGTTTGTGATAATTAGCTAATATATCTTGCTTCTTTTTCCTCTTATAGCAGATAAGTTGT ↓ 13 24 ↑ 13 24 Chimp: TGGCATGTTTGTGATAATTAGGAAAAAGAAGCAAGATATATTAGCTCTTATAGCAGATAAGTTGT Gorilla: TGGCATGTTTGTGATAATTAGGAAAAAGAAGCAAGATATATTAGCTCTTATAGCAGATAAGTTGT ↓ 13 24 ↑ 13 24 Human: TGGCATGTTTGTGATAATTAGCTAATATATCTTGCTTCTTTTTCCTCTTATAGCAGATAAGTTGT Cluster: [ ] Orangutan: TGGCATGTTTGTGATAATAAGGAAAAAGAAGCAAGATATATTAGCTCTTATAGCAGATAAAGTGT Chimp > Human ------------- chr6:20824934-20824956 Template switch process: F1: L AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG 1 F3: 4 CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG R RF: AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGGAAAAAGAAGCAAGATATATTAGCTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG RR: TTTTAAGAACTGACAATTTTACCGTACAAACACTATTAATCCTTTTTCTTCGTTCTATATAATCGAGAATATCGTCTATTCAACATCAATTAACCATCAAGTAC F2: 3 CTTTTTCTTCGTTCTATATAATC 2 Unidirectional alignment (log-probability: -55.4) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATA-----------------------ATTAGctaatatatcttgcttctttttcCTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGGAAAAAGAAGCAAGATATATTAG-----------------------CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG Template switch alignment (log-probability: -18.1) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|CTAATATATCTTGCTTCTTTTTC|CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|CTAATATATCTTGCTTCTTTTTC|CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG Human > Chimp ------------- chr6:21057130-21057152 Template switch process: F1: L AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG 1 F3: 4 CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG R RF: AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGCTAATATATCTTGCTTCTTTTTCCTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG RR: TTTTAAGAACTGACAATTTTACCGTACAAACACTATTAATCGATTATATAGAACGAAGAAAAAGGAGAATATCGTCTATTCAACATCAATTAACCATCAAGTAC F2: 3 GATTATATAGAACGAAGAAAAAG 2 Unidirectional alignment (log-probability: -55.4) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG-----------------------gaaaaagaagcaagatatattagCTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGCTAATATATCTTGCTTCTTTTTC-----------------------CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG Template switch alignment (log-probability: -18.1) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|GAAAAAGAAGCAAGATATATTAG|CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|GAAAAAGAAGCAAGATATATTAG|CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG Gorilla > Human --------------- chr6:20824934-20824956 Template switch process: F1: L AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG 1 F3: 4 CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG R RF: AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGGAAAAAGAAGCAAGATATATTAGCTCTTATAGCAGATAAGTTGTAGTTAATTCGTAGTTCATG RR: TTTTAAGAACTGACAATTTTACCGTACAAACACTATTAATCCTTTTTCTTCGTTCTATATAATCGAGAATATCGTCTATTCAACATCAATTAAGCATCAAGTAC F2: 3 CTTTTTCTTCGTTCTATATAATC 2 Unidirectional alignment (log-probability: -60.4) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTA-----------------------GctaatatatcttgcttctttttcCTCTTATAGCAGATAAGTTGTAGTTAATTgGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGGAAAAAGAAGCAAGATATATTAG-----------------------CTCTTATAGCAGATAAGTTGTAGTTAATTCGTAGTTCATG Template switch alignment (log-probability: -24.2) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|CTAATATATCTTGCTTCTTTTTC|CTCTTATAGCAGATAAGTTGTAGTTAATTgGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|CTAATATATCTTGCTTCTTTTTC|CTCTTATAGCAGATAAGTTGTAGTTAATTCGTAGTTCATG Human > Gorilla --------------- chr6:21361620-21361642 Template switch process: F1: L AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG 1 F3: 4 CTCTTATAGCAGATAAGTTGTAGTTAATTCGTAGTTCATG R RF: AAAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGCTAATATATCTTGCTTCTTTTTCCTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG RR: TTTTAAGAACTGACAATTTTACCGTACAAACACTATTAATCGATTATATAGAACGAAGAAAAAGGAGAATATCGTCTATTCAACATCAATTAACCATCAAGTAC F2: 3 GATTATATAGAACGAAGAAAAAG 2 Unidirectional alignment (log-probability: -60.4) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG-----------------------gaaaaagaagcaagatatattagCTCTTATAGCAGATAAGTTGTAGTTAATTcGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAGCTAATATATCTTGCTTCTTTTTC-----------------------CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG Template switch alignment (log-probability: -24.2) AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|GAAAAAGAAGCAAGATATATTAG|CTCTTATAGCAGATAAGTTGTAGTTAATTcGTAGTTCATG AAATTCTTGACTGTTAAAATGGCATGTTTGTGATAATTAG|GAAAAAGAAGCAAGATATATTAG|CTCTTATAGCAGATAAGTTGTAGTTAATTGGTAGTTCATG ========== Event 3143 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AGGGCCTTGCCAATGAGACTGGGGACACAAATAGGATGACTCCTCAGTTGAGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAATTAGTGCACATT Chimp: AGGGCCTTGCCAATGAGACTGGGGA-----------------------------CACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAATTAGTGCACATT ↓ 4 3 2 1 Gorilla: AGGGCCTTGCCAATGAGACTGGGGACACAAATAGGATGACTCCTCAGTTGAGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAATTAGTGCACATT Human: AGGGCCTTGCCAATGAGACTGGGGACACAAATAGGATGACTCCTCAGTTGAGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAATTAGTGCACATT Cluster: [ ] Orangutan: AGGGCCTTGCCAGTGAGACTGGGGACACAAATAGGATGACTCCTCAGTTGAGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAACTAGTGCACATT Chimp > Gorilla --------------- chr6:21744775-21744779 Template switch process: F1: L ACTCTGGAGATTTTTAAGGGCCTTGCCAATGAGACTGGGGACACAAATAGGATGACT-------------CC 1 F3: 4 TGAGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAAT R RF: ACTCTGGAGATTTTTAAGGGCCTTGCCAATGAGACTGGGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACTATGAAT RR: TGAGACCTCTAAAAATTCCCGGAACGGTTACTCTGACCCCTGTGTTTATCCTACTGACTTTTCCACAAACGGTGATACTTA F2: 3 TGACT 2 Unidirectional alignment (log-probability: -52.6) GCCTTGCCAATGAGACTGGGgacacaaataggatgactcctcagttgagGACACAAATAGGATGACTGAAAAGGTGTTTGCCACT GCCTTGCCAATGAGACTGGG-----------------------------GACACAAATAGGATGACTGAAAAGGTGTTTGCCACT Template switch alignment (log-probability: -32.9) GCCTTGCCAATGAGACTGGGGACACAAATAGGATGACT-------------CC|TCAGT|TGaGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACT GCCTTGCCAATGAGACTGGGGACACAAATAGGATGACTGAAAAGGTGTTTGCC|TCAGT|TGGGGACACAAATAGGATGACTGAAAAGGTGTTTGCCACT ========== Event 3144 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TTTGTTGAAACTAGTATGGAATGACTATTCCTTTCCTTAGTGTGTGCGCC Chimp: tttGTTGAAACTAGTATGGAATGACTATTCCTTTCCTTATTGTGTGCGCC ↓ 3 2 4 ↑ 3 1 2 4 Gorilla: tttGTTGAAACCAGTATGGAATAGTC--ACCTTTCCTTAGTGTGTGCGCC ↓ 3 1 2 4 ↑ 3 2 4 Human: TTTGTTGAAACTAGTATGGAATGACTATTCCTTTCCTTAGTGTGTGCGCC Cluster: [ ] Orangutan: TTTGTTGAAACCAGTATGGAATAGTC--ATCTTTCCTTAGCGTGTGCACC Gorilla > Human --------------- chr6:22047743-22047749 Template switch process: F1: L ATTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAAT 1 F3: 4 CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG R RF: ATTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAATAGTCACCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG RR: TAACGAGAGAGTCGACAAAAAACAACTTTGGTCATACCTTATCAGTGGAAAGGAATCACACACGCGGGTACCACGTAATGTGTACC F2: 3 TTATCAG 2 Unidirectional alignment (log-probability: -36.5) TTGCTCTCTCAGCTGTTTTTTGTTGAAACtAGTATGGAAT-----gactattCCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAATAGTCA-------CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG Template switch alignment (log-probability: -22.1) TTGCTCTCTCAGCTGTTTTTTGTTGAAACtAGTATGGAAT|GACTATT|CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAAT|GACTATT|CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG Human > Gorilla --------------- chr6:22621030-22621034 Template switch process: F1: L ATTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAAT 1 F3: 4 CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG R RF: ATTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAATGACTATTCCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG RR: TAACGAGAGAGTCGACAAAAAACAACTTTGATCATACCTTACTGATAAGGAAAGGAATCACACACGCGGGTACCACGTAATGTGTACC F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -33.7) TTGCTCTCTCAGCTGTTTTTTGTTGAAACcAGTATGGAA-------TagtcaCCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAATGACTATT-----CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG Template switch alignment (log-probability: -21.9) TTGCTCTCTCAGCTGTTTTTTGTTGAAACcAGTATGGAAT|AGTCA|CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAAT|AGTCA|CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG Gorilla > Chimp --------------- chr6:22311458-22311464 Template switch process: F1: L ATTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAAT 1 F3: 4 CCTTTCCTTATTGTGTGCGCCCATGGTGCATTACACATGG R RF: ATTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAATAGTCACCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG RR: TAACGAGAGAGTCGACAAAAAACAACTTTGGTCATACCTTATCAGTGGAAAGGAATCACACACGCGGGTACCACGTAATGTGTACC F2: 3 TTATCAG 2 Unidirectional alignment (log-probability: -42) TTGCTCTCTCAGCTGTTTTTTGTTGAAACtAGTATGGAAT-----gactattCCTTTCCTTAtTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAATAGTCA-------CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG Template switch alignment (log-probability: -27.7) TTGCTCTCTCAGCTGTTTTTTGTTGAAACtAGTATGGAAT|GACTATT|CCTTTCCTTAtTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAAT|GACTATT|CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG Chimp > Gorilla --------------- chr6:22621030-22621034 Template switch process: F1: L ATTGCTCTCTCAGCTGTTTTTTGTTGAAACCAGTATGGAAT 1 F3: 4 CCTTTCCTTAGTGTGTGCGCCCATGGTGCATTACACATGG R RF: ATTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAATGACTATTCCTTTCCTTATTGTGTGCGCCCATGGTGCATTACACATGG RR: TAACGAGAGAGTCGACAAAAAACAACTTTGATCATACCTTACTGATAAGGAAAGGAATAACACACGCGGGTACCACGTAATGTGTACC F2: 3 ACTGA 2 Unidirectional alignment (log-probability: -39.2) TTGCTCTCTCAGCTGTTTTTTGTTGAAACcAGTATGGAA-------TagtcaCCTTTCCTTAgTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAATGACTATT-----CCTTTCCTTATTGTGTGCGCCCATGGTGCATTACACATGG Template switch alignment (log-probability: -27.4) TTGCTCTCTCAGCTGTTTTTTGTTGAAACcAGTATGGAAT|AGTCA|CCTTTCCTTAgTGTGTGCGCCCATGGTGCATTACACATGG TTGCTCTCTCAGCTGTTTTTTGTTGAAACTAGTATGGAAT|AGTCA|CCTTTCCTTATTGTGTGCGCCCATGGTGCATTACACATGG ========== Event 3145 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGGCTGGAGCTTGACATTAGTTTCAAGTAAATG----CAATGTTAGCATTCCCCATGAATAGTCAACT Chimp: AAAGGCTGGAGCTTGACATTAATTTCAAGTAAATG----CAATGTTAGCATTCCCCATGAATAGTCAACT ↓ 1 34 2 Gorilla: AAAGGCTGGAGCTTGACATTAGTTTCAAGT-AATG--------CTAAGCATTCCCCATGAATAGTCAACT ↑ 1 34 2 Human: AAAGGCTGGAGCTTGACATTAGTTTCAAGTAAATG----CAATGTTAGCATTCCCCATGAATAGTCAACT Cluster: [ ] Orangutan: AAAGGCTGGAGCTTGACATTAGTTTCAAGTAAATGCAAT----GTTAGCATTCCCCATGAACAGTCAACT Human > Gorilla --------------- chr6:23799894-23799898 Template switch process: F1: L TCTTATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAA 1 F3: 4 AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC R RF: TCTTATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAAATGCAATGTTAGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC RR: AGAATAGTTGATTTCCGACCTCGAACTGTAATCAAAGTTCATTTACGTTACAATCGTAAGGGGTACTTATCAGTTGAGATGACAACTCTTTCG F2: 3 ATCGT 2 Unidirectional alignment (log-probability: -26.5) TATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAA-TGC----TaAGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC TATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAAATGCAATGTTAGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC Template switch alignment (log-probability: -16.4) TATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAA|TGCTA|AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC TATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAA|TGCTA|AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC Chimp > Gorilla --------------- chr6:23799894-23799898 Template switch process: F1: L AATATTCAGTCTTATCAACTAAAGGCTGGAGCTTGACATTAGTTTCAAGTAA 1 F3: 4 AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC R RF: AATATTCAGTCTTACCAACTAAAGGCTGGAGCTTGACATTAATTTCAAGTAAATGCAATGTTAGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC RR: TTATAAGTCAGAATGGTTGATTTCCGACCTCGAACTGTAATTAAAGTTCATTTACGTTACAATCGTAAGGGGTACTTATCAGTTGAGATGACAACTCTTTCG F2: 3 ATCGT 2 Unidirectional alignment (log-probability: -37.7) TAtCAACTAAAGGCTGGAGCTTGACATTAgTTTCAAGT-AATGCtA----AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC TACCAACTAAAGGCTGGAGCTTGACATTAATTTCAAGTAAATGCAATGTTAGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC Template switch alignment (log-probability: -27.7) TAtCAACTAAAGGCTGGAGCTTGACATTAgTTTCAAGTAA|TGCTA|AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC TACCAACTAAAGGCTGGAGCTTGACATTAATTTCAAGTAA|TGCTA|AGCATTCCCCATGAATAGTCAACTCTACTGTTGAGAAAGC ========== Event 3146 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: tattcaccacTAGCAACTTATCAAGGTAAAATAATGAAATAATATCTTTAAATAAAAATGAT ↓ 13 24 ↑ 13 24 Chimp: tattcaccacTAGCAACTTATTATTTCATTATTTTACCTTGATATCTTTAAATAAAAATGAT Gorilla: tattcaccacTAGCAACTTATTATTTCATTATTTTACCTTGATATCTTTAAATAAAAATGAT ↓ 13 24 ↑ 13 24 Human: tattcaccacTAGCAACTTATCAAGGTAAAATAATGAAATAATATCTTTAAATAAAAATGAT Cluster: [ ] Orangutan: tattcaccacTAGCAACTTCTTATTTCATTATTTTACCTTGATATCTTTACATAAAaatgat Chimp > Human ------------- chr6:23418409-23418428 Template switch process: F1: L ATCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTAT 1 F3: 4 ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG R RF: ATCTGCATGGTACATCTTCATATTCACCACTAGCAACTTATTATTTCATTATTTTACCTTGATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG RR: TAGACGTACCATGTAGAAGTATAAGTGGTGATCGTTGAATAATAAAGTAATAAAATGGAACTATAGAAATTTATTTTTACTAATGAGAATAAATAATAGTC F2: 3 ATAAAGTAATAAAATGGAAC 2 Unidirectional alignment (log-probability: -53.9) TCTGCgTGGTACATCTTCATATTCACCACTAGCAACTTATcaaggtaaaataatgaaaTA------------------ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCATGGTACATCTTCATATTCACCACTAGCAACTTAT------------------TATTTCATTATTTTACCTTGATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Template switch alignment (log-probability: -23.7) TCTGCgTGGTACATCTTCATATTCACCACTAGCAACTTAT|CAAGGTAAAATAATGAAATA|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCATGGTACATCTTCATATTCACCACTAGCAACTTAT|CAAGGTAAAATAATGAAATA|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Human > Chimp ------------- chr6:23698721-23698740 Template switch process: F1: L ATCTGCATGGTACATCTTCATATTCACCACTAGCAACTTAT 1 F3: 4 ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG R RF: ATCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTATCAAGGTAAAATAATGAAATAATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG RR: TAGACGCACCATGTAGAAGTATAAGTGGTGATCGTTGAATAGTTCCATTTTATTACTTTATTATAGAAATTTATTTTTACTAATGAGAATAAATAATAGTC F2: 3 GTTCCATTTTATTACTTTAT 2 Unidirectional alignment (log-probability: -53.9) TCTGCaTGGTACATCTTCATATTCACCACTAGCAACTTAT------------------TAtttcattattttaccttgATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTATCAAGGTAAAATAATGAAATA------------------ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Template switch alignment (log-probability: -23.7) TCTGCaTGGTACATCTTCATATTCACCACTAGCAACTTAT|TATTTCATTATTTTACCTTG|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTAT|TATTTCATTATTTTACCTTG|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Gorilla > Human --------------- chr6:23418409-23418428 Template switch process: F1: L ATCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTAT 1 F3: 4 ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG R RF: ATCTGCATGGTACATCTTCATATTCACCACTAGCAACTTATTATTTCATTATTTTACCTTGATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG RR: TAGACGTACCATGTAGAAGTATAAGTGGTGATCGTTGAATAATAAAGTAATAAAATGGAACTATAGAAATTTATTTTTACTAATGAGAATAAATAATAGTC F2: 3 ATAAAGTAATAAAATGGAAC 2 Unidirectional alignment (log-probability: -53) TCTGCgTGGTACATCTTCATATTCACCACTAGCAACTTATcaaggtaaaataatgaaaTA------------------ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCATGGTACATCTTCATATTCACCACTAGCAACTTAT------------------TATTTCATTATTTTACCTTGATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Template switch alignment (log-probability: -23.8) TCTGCgTGGTACATCTTCATATTCACCACTAGCAACTTAT|CAAGGTAAAATAATGAAATA|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCATGGTACATCTTCATATTCACCACTAGCAACTTAT|CAAGGTAAAATAATGAAATA|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Human > Gorilla --------------- chr6:24049126-24049145 Template switch process: F1: L ATCTGCATGGTACATCTTCATATTCACCACTAGCAACTTAT 1 F3: 4 ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG R RF: ATCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTATCAAGGTAAAATAATGAAATAATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG RR: TAGACGCACCATGTAGAAGTATAAGTGGTGATCGTTGAATAGTTCCATTTTATTACTTTATTATAGAAATTTATTTTTACTAATGAGAATAAATAATAGTC F2: 3 GTTCCATTTTATTACTTTAT 2 Unidirectional alignment (log-probability: -53) TCTGCaTGGTACATCTTCATATTCACCACTAGCAACTTAT------------------TAtttcattattttaccttgATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTATCAAGGTAAAATAATGAAATA------------------ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG Template switch alignment (log-probability: -23.8) TCTGCaTGGTACATCTTCATATTCACCACTAGCAACTTAT|TATTTCATTATTTTACCTTG|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG TCTGCGTGGTACATCTTCATATTCACCACTAGCAACTTAT|TATTTCATTATTTTACCTTG|ATATCTTTAAATAAAAATGATTACTCTTATTTATTATCAG ========== Event 3147 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCACAAATAATGGATTAATAATAA--TAATAACCTTGGCTAGTATTGTGCCTTGATGGAAAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATTACTCTACCCAAGG Chimp: TCACAaataatgaattaataataa--taataaCCTTGGCTGTTATTGTGCCTTGATGGAAAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATTACTCTACCCAAGG ↓ 3 1 2 4 Gorilla: TCACAAATAATGGATTAATAATAA--TAATAACCTTGGCTGTTATTGTGCCTTTCCATCAAGGCACAATAACAGCCAAGGTTATTATTATTAGCACATTACTCTACCCAAGG ↑ 1 3 4 2 Human: TCACAAATAATGGATTAATAATAA--TAATAACCTTGGCTAGTATTGTGCCTTGATGGAAAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATTACTCTACCCAAGG Cluster: [ ] Orangutan: TCACAAATAGTGGATTAATAATAATATAATAACCNNNNNNNNNNNNNNNNNNNNNN-------------------------------------------------------- Human > Gorilla --------------- chr6:170683792-170683810 Template switch process: F1: L TGGATTAATAATAATAATAACCTTGGCT 1 F3: 4 AAGGCACAATAACAGCCAAGGTTATTATTATTAGCACATT R RF: TGGATTAATAATAATAATAACCTTGGCTAGTATTGTGCCTTGATGGAAAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATT RR: ACCTAATTATTATTATTATTGGAACCGATCATAACACGGAACTACCTTTCCGTGTTATTGTCGGTTCCAATAATAATACTCGTGTAA F2: 3 CTACCTTTCCGTGTTATTG 2 Unidirectional alignment (log-probability: -46.1) TGGATTAATAATAATAATAACCTTGGCTgtTATTGTGCCTTtccatc------AAGGCACAATAACAGCCAAGGTTATTATTATtAGCACATT TGGATTAATAATAATAATAACCTTGGCTAGTATTGTGCCTT------GATGGAAAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATT Template switch alignment (log-probability: -23.3) TGGATTAATAATAATAATAACCTTGGCT|GTTATTGTGCCTTTCCATC|AAGGCACAATAACAGCCAAGGTTATTATTATtAGCACATT TGGATTAATAATAATAATAACCTTGGCT|GTTATTGTGCCTTTCCATC|AAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATT Chimp > Gorilla --------------- chr6:170683805-170683842 Template switch process: F1: L TGGATTAATAATAATAATAACCTTGGCTGTTATTGTGCCTT 1 F3: 4 AGCACATT R RF: TGAATTAATAATAATAATAACCTTGGCTGTTATTGTGCCTTGATGGAAAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATT RR: ACTTAATTATTATTATTATTGGAACCGACAATAACACGGAACTACCTTTCCGTGTTATTGTCGGTTCCAATAATAATACTCGTGTAA F2: 3 TTATTATTATTGGAACCGACAATAACACGGAACTACCT 2 Unidirectional alignment (log-probability: -40.6) GgATTAATAATAATAATAACCTTGGCTGTTATTGTGCCTT------tccatcAAGGCACAATAACAGCCAAGGTTATTATTATtAGCACATT GAATTAATAATAATAATAACCTTGGCTGTTATTGTGCCTTGATGGA------AAGGCACAATAACAGCCAAGGTTATTATTATGAGCACATT Template switch alignment (log-probability: -25.3) GgATTAATAATAATAATAACCTTGGCTGTTATTGTGCCTT|TCCATCAAGGCACAATAACAGCCAAGGTTATTATTATT|AGCACATT GAATTAATAATAATAATAACCTTGGCTGTTATTGTGCCTT|TCCATCAAGGCACAATAACAGCCAAGGTTATTATTATT|AGCACATT ========== Event 3148 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAC---TTCTTATTTCCTTCGGTGATCCGAAGTACTGGCAGATTTTTCTAAGACTTCAGA--CA--TGTGGGGAGTAACTTTCATAACTCCAAAG ↑ 3 1 4 Chimp: CTAC---TTCTTATTTCCTTCG--GAT---CAGTACTGGCAGATTTTTCTAAGACTTCAGA----CATGTGGGGAATAACTTTCATAACTCCAAAG Gorilla: CTAC------TTATTTCCTTCG--GAT---CAGTACTGGCAGATTTTTCTAAGACTTCAGA------CGTGGGGAATAACTTTCATAACTCCAAAG Human: CTAC---TTCTTATTTCCTTCGGTGATCCGAAGTACTGGCAGATTTTTCTAAGACTTCAGA--CA--TGTGGGGAGTAACTTTCATAACTCCAAAG Cluster: [ ] Orangutan: CTACTTC---TTATTTCCTTCG--GAT---CAGTACTGGCAGATTTTTCTAAGACTTCAGACA----TGTGGGGAATAACCTTCATAACTTCAAAG Chimp > Human ------------- chr6:25420563-25420570 Template switch process: F1: L CGG 1 F3: 4 AGTACTGGCAGATTTTTCTAAGACTTCAGACATGTGGGGAGTAACTTTCATAACTCCAAAGAATACACTACCAGAAATGTA R RF: TCGGATCAGTACTGGCAGATTTTTCTAAGACTTCAGACATGTGGGGAATAACTTTCATAACTCCAAAGAATACACTACCAGAAATGTA RR: AGCCTAGTCATGACCGTCTAAAAAGATTCTGAAGTCTGTACACCCCTTATTGAAAGTATTGAGGTTTCTTATGTGATGGTCTTTACAT F2: 3 AGCCTAGT 2 Unidirectional alignment (log-probability: -34.4) CGgtGATCcgaAGTACTGGCAGATTTTTCTAAGACTTCAGACATGTGGGGA CG--GATC---AGTACTGGCAGATTTTTCTAAGACTTCAGACATGTGGGGA Template switch alignment (log-probability: -22.3) CGG|TGATCCGA|AGTACTGGCAGATTTTTCTAAGACTTCAGACATGTGGGGA CGG|TGATCCGA|AGTACTGGCAGATTTTTCTAAGACTTCAGACATGTGGGGA ========== Event 3149 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 234 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAAGATGAGAAATTTGTTAGGT----------AGCCGCTATGAGCTGCAAGGTTTCCTGAGGCA--GAGGTATCCG ↓ 1 3 24 Chimp: AAAGATGAGAAATTTGTTAGGA-----AATCTTGCAGCTCATAG-----CGGCTACCTGAGGCA--GAGGTATCCG Gorilla: AAAGATGAGAAATTTGTTAGGAAATCT-----TGCAGCTCACAG-----CGGCTACCTGAGGCA--GAGGTATCCG ↓ 13 24 ↑ 1 3 24 Human: AAAGATGAGAAATTTGTTAGGT----------AGCCGCTATGAGCTGCAAGGTTTCCTGAGGCA--GAGGTATCCG Cluster: [ ] Orangutan: AAAGATGAGAAATTTGTTAGGAAATCT-----TGCAGCTCATAG-----CAGCTACCTGAGGCAGAGAGGTATCTG Human > Chimp ------------- chr6:25687702-25687725 Template switch process: F1: L TGAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG 1 F3: 4 CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT R RF: TGAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGGTAGCCGCTATGAGCTGCAAGGTTTCCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT RR: ACTCATCACTAGGACCATAATTTCTACTCTTTAAACAATCCATCGGCGATACTCGACGTTCCAAAGGACTCCGTCTCCATAGGCCTTGTCTCAGTCCCTCCGGTA F2: 3 ATCGGCGATACTCGACGTTCTAAA 2 Unidirectional alignment (log-probability: -49.5) GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGGaaatcttgcagctcaTAGCgGCTA---------------CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG---------------TAGCCGCTATGAGCTGCAAGGTTTCCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT Template switch alignment (log-probability: -24.2) GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG|AAAtCTTGCAGCTCATAGCGGCTA|CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG|AAACCTTGCAGCTCATAGCGGCTA|CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT Gorilla > Human --------------- chr6:25334158-25334181 Template switch process: F1: L TGAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG 1 F3: 4 CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT R RF: TGAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGGAAATCTTGCAGCTCACAGCGGCTACCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT RR: ACTCATCACTAGGACCATAATTTCTACTCTTTAAACAATCCTTTAGAACGTCGAGTGTCGCCGATGGACTCCGTCTCCATAGGCCTTGTCTCAGTCCCTCCGGTA F2: 3 TTTGGAACGTCGAGTATCGCCGAT 2 Unidirectional alignment (log-probability: -53.4) GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG----------------------TAgccgctatgagctgcaaggtttCCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGGAAATCTTGCAGCTCACAGCGGCTA----------------------CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT Template switch alignment (log-probability: -29.8) GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG|TAGCCGCTaTGAGCTGCAAGgTTT|CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG|TAGCCGCTGTGAGCTGCAAGATTT|CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT Human > Gorilla --------------- chr6:25917787-25917810 Template switch process: F1: L TGAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG 1 F3: 4 CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT R RF: TGAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGGTAGCCGCTATGAGCTGCAAGGTTTCCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT RR: ACTCATCACTAGGACCATAATTTCTACTCTTTAAACAATCCATCGGCGATACTCGACGTTCCAAAGGACTCCGTCTCCATAGGCCTTGTCTCAGTCCCTCCGGTA F2: 3 ATCGGCGACACTCGACGTTCTAAA 2 Unidirectional alignment (log-probability: -53.4) GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGGaaatcttgcagctcacagcggcTA----------------------CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG----------------------TAGCCGCTATGAGCTGCAAGGTTTCCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT Template switch alignment (log-probability: -29.8) GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG|AAAtCTTGCAGCTCAcAGCGGCTA|CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT GAGTAGTGATCCTGGTATTAAAGATGAGAAATTTGTTAGG|AAACCTTGCAGCTCATAGCGGCTA|CCTGAGGCAGAGGTATCCGGAACAGAGTCAGGGAGGCCAT ========== Event 3150 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: TCTTGTGAATTGGAGATTCAGTGCGTGAGGAAAACAGCCTAACTATCCATAATTAAGGTAACT ↓ 1 3 24 ↑ 3 1 42 Chimp: TCTTGTGAATTGGAGATTCAG----TTAGGCTGTTTTCCTCACTATCCATAATTAAGGTAACT Gorilla: Human: TCTTGTGAATTGGAGATTCAGTGCGTGAGGAAAACAGCCTAACTATCCATAATTAAGGTAACT Cluster: [ ] Orangutan: TCTTGTGAATTGGAGATTCAGTGCATGAGGAAAACAGCATAACTATCCATAATTAAGGTAACT Chimp > Human ------------- chr6:26227136-26227152 Template switch process: F1: L GTCAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT---GC 1 F3: 4 ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA R RF: GTCAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGTTAGGCTGTTTTCCTCACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA RR: CAGTCTGTACTTCTACACCCAGAACACTTAACCTCTAAGTCAATCCGACAAAAGGAGTGATAGGTATTAATTCCATTGATGACAGTCTATAAACATT F2: 3 ATCCGACAAAAGGAGTG 2 Unidirectional alignment (log-probability: -46.3) GACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGTgcgtgaggaaaacagccTA-------------ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA GACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT-----------------TAGGCTGTTTTCCTCACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA Template switch alignment (log-probability: -27.8) GACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT---GC|GTGAGGAAAACAGCCTA|ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA GACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGTTAGGC|GTGAGGAAAACAGCCTA|ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA Human > Chimp ------------- chr6:26592056-26592070 Template switch process: F1: L GTCAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT 1 F3: 4 ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA R RF: GTCAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGTGCGTGAGGAAAACAGCCTAACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA RR: CAGTCTGTACTTCTACACCCAGAACACTTAACCTCTAAGTCACGCACTCCTTTTGTCGGATTGATAGGTATTAATTCCATTGATGACAGTCTATAAACATT F2: 3 CTCCTTTTGTCGGAT 2 Unidirectional alignment (log-probability: -40.7) CAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT-----------------TAggctgttttcctcACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA CAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGTGCGTGAGGAAAACAGCCTA-------------ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA Template switch alignment (log-probability: -17.2) CAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT|TAGGCTGTTTTCCTC|ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA CAGACATGAAGATGTGGGTCTTGTGAATTGGAGATTCAGT|TAGGCTGTTTTCCTC|ACTATCCATAATTAAGGTAACTACTGTCAGATATTTGTAA ========== Event 3151 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTCATAGAGGCAAACCATT----------------------------------AATCTTATTCAAtatttagtactggcttggtgcctggcat Chimp: TTTTCATAGAGACAAACCATT-----------------AATACTAAATATTGAATAATCTTATTCAAtatttagtattggcttggtacctggcat Gorilla: TTTTCATAGAGACAAACCATTAATACTAAATATTGAAT-----------------AATCTTATTCAAtatttagtattggcttggtgcctggcat ↑ 4 1 3 2 Human: TTTTCATAGAGGCAAACCATT----------------------------------AATCTTATTCAAtatttagtactggcttggtgcctggcat Cluster: [ ] Orangutan: TTTTCATAGAGGCAAACCATT----------------------------------AATCTTATTCAAtatttagtattggcttggtgcctgacat Human > Gorilla --------------- chr6:147176126-147176138 Template switch process: F1: L AGACTTGTCCATTTCTAGAATTTTCATAGAGACAAACCATTAAT 1 F3: 4 TAATCTTATTCAATATTTAGTATTGGCTTGGTGCCTGGCAT R RF: AGACTTGTCCATTTCTAGAATTTTCATAGAGGCAAACCATTAATCTTATTCAATATTTAGTACTGGCTTGGTGCCTGGCAT RR: TCTGAACAGGTAAAGATCTTAAAAGTATCTCCGTTTGGTAATTAGAATAAGTTATAAATCATGACCGAACCACGGACCGTA F2: 3 AAGTTATAAATCA 2 Unidirectional alignment (log-probability: -46.4) TTGTCCATTTCTAGAATTTTCATAGAGaCAAACCATtaatactaaatattgaaTAATCTTATTCAATATTTAGTAtTGGCTTGGTGCCTGGCA TTGTCCATTTCTAGAATTTTCATAGAGGCAAACCAT-----------------TAATCTTATTCAATATTTAGTACTGGCTTGGTGCCTGGCA Template switch alignment (log-probability: -28.5) TTGTCCATTTCTAGAATTTTCATAGAGaCAAACCATTAAT|ACTAAATATTGAA|TAATCTTATTCAATATTTAGTAtTGGCTTGGTGCCTGGCA TTGTCCATTTCTAGAATTTTCATAGAGGCAAACCATTAAT|ACTAAATATTGAA|TAATCTTATTCAATATTTAGTACTGGCTTGGTGCCTGGCA ========== Event 3152 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAAGTGTTCCCACTCTTCCTTAAGACT-------ACAAGATGATTGTAATACCTTGTTA ↓ 3 1 4 Chimp: GAAGTGTTCCCACTCTTCCTTAAGACTTGTAGTCTTAAGATGATTGTAATACCTTGTTA ↑ 3 1 2 4 Gorilla: GAAGTGTTCCCACTCTTCCTTAAGACT-------ACAGGATGATTGTAATACCTTGTTA Human: GAAGTGTTCCCACTCTTCCTTAAGACT-------ACAAGATGATTGTAATACCTTGTTA Cluster: [ ] Orangutan: GAAGTGTTCCCACTCTTCCTTAAGACT-------ACAAGATGATTGTAATACCTTGTTA Human > Chimp ------------- chr6:147678840-147678848 Template switch process: F1: L TTGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT 1 F3: 4 AAGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAA R RF: TTGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACTACAAGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAA RR: AACATAAAAATGAACTTCACAAGGGTGAGAAGGAATTCTGATGTTCTACTAACATTATGGAACAATAGACAAACTTCTTTATT F2: 3 TTCTGATGT 2 Unidirectional alignment (log-probability: -33) TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACTtgtagtcttAAGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAA TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT-------ACAAGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAA Template switch alignment (log-probability: -16.4) TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT|TGTAGTCTT|AAGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAA TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT|TGTAGTCTT|AAGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAA Gorilla > Chimp --------------- chr6:147678840-147678850 Template switch process: F1: L TTGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT 1 F3: 4 GATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAAGG R RF: TTGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACTACAGGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAAGG RR: AACATAAAAATGAACTTCACAAGGGTGAGAAGGAATTCTGATGTCCTACTAACATTATGGAACAATAGACAAACTTCTTTATTCC F2: 3 AATTCTGATGT 2 Unidirectional alignment (log-probability: -35.2) TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACTtgtagtcttaA---GATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAAGG TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT----------ACAGGATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAAGG Template switch alignment (log-probability: -17.1) TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT|TGTAGTCTTAA|GATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAAGG TGTATTTTTACTTGAAGTGTTCCCACTCTTCCTTAAGACT|TGTAGTCTTAA|GATGATTGTAATACCTTGTTATCTGTTTGAAGAAATAAGG ========== Event 3153 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ACTCTAACCCACTGTTATAGCC------TATTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCAttt----tttttCCCCCTATA ↓ 1 4 3 2 Chimp: ACTCTAACCCACTGTTATAGCA---TGAAACTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCAttt---ttttttCCCCCTGTA Gorilla: ACTCTAACCCACTGTTATAGCATGA---AACTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCAttt--t-tttttCCCCCTGTA ↑ 1 4 3 2 Human: ACTCTAACCCACTGTTATAGCC------TATTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCAttt----tttttCCCCCTATA Cluster: [ ] Orangutan: ACTCTAACCTACTGTTATAGCATGA---AACTGTGTAAGCCACTATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCATTCtt--ttttttCCCCCGTA Human > Chimp ------------- chr6:28046586-28046592 Template switch process: F1: L TTTCCCCATACACTTGGAGAACTCTAACCCACTGTTATAGC 1 F3: 4 TGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG R RF: TTTCCCCATGCACTTGGAGAACTCTAACCCACTGTTATAGCCTATTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCAT RR: AAAGGGGTACGTGAACCTCTTGAGATTGGGTGACAATATCGGATAACACATTCGGTTATAACCTCCACAACTACTGATATAGAACAAAAATGTTCAGTACACCTCACGTCTGACCCAAAGTA F2: 3 CAAAGTA 2 Unidirectional alignment (log-probability: -33.2) TTCCCCATaCACTTGGAGAACTCTAACCCACTGTTATAGCaTgaaAcTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG TTCCCCATGCACTTGGAGAACTCTAACCCACTGTTATAGCCT---ATTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG Template switch alignment (log-probability: -22.1) TTCCCCATaCACTTGGAGAACTCTAACCCACTGTTATAGC|ATGAAAC|TGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG TTCCCCATGCACTTGGAGAACTCTAACCCACTGTTATAGC|ATGAAAC|TGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG Human > Gorilla --------------- chr6:28403858-28403864 Template switch process: F1: L TTTCCCCATACACTTGGAGAACTCTAACCCACTGTTATAGC 1 F3: 4 TGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG R RF: TTTCCCCATGCACTTGGAGAACTCTAACCCACTGTTATAGCCTATTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTGTTTTTACAAGTCATGTGGAGTGCAGACTGGGTTTCAT RR: AAAGGGGTACGTGAACCTCTTGAGATTGGGTGACAATATCGGATAACACATTCGGTTATAACCTCCACAACTACTGATATAGAACAAAAATGTTCAGTACACCTCACGTCTGACCCAAAGTA F2: 3 CAAAGTA 2 Unidirectional alignment (log-probability: -31.8) TTCCCCATaCACTTGGAGAACTCTAACCCACTGTTATAGCaTgaaAcTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG TTCCCCATGCACTTGGAGAACTCTAACCCACTGTTATAGCCT---ATTGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG Template switch alignment (log-probability: -22.1) TTCCCCATaCACTTGGAGAACTCTAACCCACTGTTATAGC|ATGAAAC|TGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG TTCCCCATGCACTTGGAGAACTCTAACCCACTGTTATAGC|ATGAAAC|TGTGTAAGCCAATATTGGAGGTGTTGATGACTATATCTTG ========== Event 3154 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ctgagctaCATCCCCACCTCGAAAAACGTTCGTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCTCAGtt-------------ttttttttttttaaacatt--tatttattCTTTCATGAACGAACGTTAAAATTTTCATTTCCCCTT Chimp: ctgagctacatccccACCTCGAAAAACATTAGTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCTCAGGt-ttttttttttgttttttttttttttAACATT--TATTTATTCTTTCATGAACGGACGTTAAAATTTTCATTTCCCCTT Gorilla: ctgagctacatccccACCTCGGAAACCACCACTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCTCTCAGA------------ttttttattttttaacatt--tatttattctttcatgaacgaacgttaaaattttcatttcccctt ↓ 1 4 3 2 Human: ctgagctaCATCCCCACCTCGAAAAACGTTCGTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCTCAGtt-------------ttttttttttttaaacatt--tatttattCTTTCATGAACGAACGTTAAAATTTTCATTTCCCCTT Cluster: [ ] Orangutan: ctgagctacatccccACCTTGAAAAACGCTACTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTATCTC-----------------tttttttttttAAAGCATTTATATTTATTCTTTCATAAACGAACGTTAGAATTTTCATTTCCCCTT Gorilla > Human --------------- chr6:28658319-28658325 Template switch process: F1: L GCTAAGCATGCGCTCTACCACTGAGCTACATCCCCACCTCGAAAA 1 F3: 4 TCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCT R RF: GCTAAGCATGCGCTCTACCACTGAGCTACATCCCCACCTCGGAAACCACCACTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCTCTCAGATTTTTTATTTTTTAACATTTATTTATTCTTTCATGAACGAACGT RR: CGATTCGTACGCGAGATGGTGACTCGATGTAGGGGTGGAGCCTTTGGTGGTGAGAAATTTGACGAAAATACTTTCTTATATCTTTAAATGGAGAGTCTAAAAAATAAAAAATTGTAAATAAATAAGAAAGTACTTGCTTGCA F2: 3 GCTTGCA 2 Unidirectional alignment (log-probability: -33.7) GCATGCGCTCTACCACTGAGCTACATCCCCACCTCGaAAA-----ACgttcgTCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCT GCATGCGCTCTACCACTGAGCTACATCCCCACCTCGGAAACCACCAC-----TCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCT Template switch alignment (log-probability: -22.2) GCATGCGCTCTACCACTGAGCTACATCCCCACCTCGaAAA|ACGTTCG|TCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCT GCATGCGCTCTACCACTGAGCTACATCCCCACCTCGGAAA|ACGTTCG|TCTTTAAACTGCTTTTATGAAAGAATATAGAAATTTACCT ========== Event 3155 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ---CTTTAGAGATTTAACTTGGAACTATAAAAGGTCTGCTTTAAAAATCTCTAATAGATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCC---ATA-----GTTCTATTTGCTAATTATCGAT Chimp: CTAATTTAGAGATTTAACTTGAAACTATAAAAGGTCTGCTTTTAAAATCCCTAATAGATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCC---ATA-----GTTCTATTTGCTAATTATCGAT ↓ 3 2 1 4 Gorilla: ---CTTTAGAGATTTAACTTGGAACTATAAAAGGTCTGCTTTTAAAATCTCTAATAGATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCAGTTTC-----ATTCTATTTGCTAATTATCAAT Human: ---CTTTAGAGATTTAACTTGGAACTATAAAAGGTCTGCTTTAAAAATCTCTAATAGATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCC---ATA-----GTTCTATTTGCTAATTATCGAT Cluster: [ ] Orangutan: ---CTTTAGAGATTTAACTTGGAACTATAAAAGGTCTGAT-TTAAAATCTCTAATAGATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCC---ATAGTTTCGTTCTATTTGCTAATTATCGAT Chimp > Gorilla --------------- chr6:170095655-170095660 Template switch process: F1: L GATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCA 1 F3: 4 TTCTATTTGCTAATTATCAATGATTCAATAATA----TAA R RF: TGAAACTATAAAAGGTCTGCTTTTAAAATCCCTAATAGATCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCATAGTTCTATTTGCTAATTATCGATGATTCAATAATACAGTTAA RR: ACTTTGATATTTTCCAGACGAAAATTTTAGGGATTATCTAGATTCAACTGATTTAACTTTAAATTCTCCCGTAAAAGGTATCAAGATAAACGATTAATAGCTACTAAGTTATTATGTCAATT F2: 3 ACTTTG 2 Unidirectional alignment (log-probability: -41.7) TCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCAgttTcaTTCTATTTGCTAATTATCaATGATTCAATAATA----TAA TCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCA---TAGTTCTATTTGCTAATTATCGATGATTCAATAATACAGTTAA Template switch alignment (log-probability: -31.9) TCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCA|GTTTCA|TTCTATTTGCTAATTATCaATGATTCAATAATA----TAA TCTAAGTTGACTAAATTGAAATTTAAGAGGGCATTTTCCA|GTTTCA|TTCTATTTGCTAATTATCGATGATTCAATAATACAGTTAA ========== Event 3156 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAACCTTCAGTAGCACATGCTCT----GGGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAA ↓ 1 4 3 2 Chimp: AAACCTTCAGTAGCACATGCTTCAGTGTGGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAA Gorilla: AAACCTTCAGTAGCACATGCTCT----GGGCTTCCAGCTGCACAATGGTGCAGGGAGAGGGGGTGAA Human: AAACCTTCAGTAGCACATGCTCT----GGGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAA Cluster: [ ] Orangutan: AAACCTTCAGTAGCACATGCTCT----GGGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAA Human > Chimp ------------- chr6:141072541-141072546 Template switch process: F1: L GACCCTGCTGATTGTCTCCCAAACCTTCAGTAGCACATGCTT 1 F3: 4 GGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAAA R RF: GACCCTGCTGATTGTCTCCCAAACCTTCAGTAGCACATGCTCTGGGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAAA RR: CTGGGACGACTAACAGAGGGTTTGGAAGTCATCGTGTACGAGACCCGAAGGTCGACGTGTGACCACGTCCCTCTCCCCCACTTT F2: 3 TGTGAC 2 Unidirectional alignment (log-probability: -31.4) CCCTGCTGATTGTCTCCCAAACCTTCAGTAGCACATGCttcagtgT---GGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAAA CCCTGCTGATTGTCTCCCAAACCTTCAGTAGCACATGC-------TCTGGGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAAA Template switch alignment (log-probability: -22) CCCTGCTGATTGTCTCCCAAACCTTCAGTAGCACATGCTt|CAGTGT|GGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAAA CCCTGCTGATTGTCTCCCAAACCTTCAGTAGCACATGCTC|CAGTGT|GGCTTCCAGCTGCACACTGGTGCAGGGAGAGGGGGTGAAA ========== Event 3157 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ggcaacccaccccttcaGTGGTCTTTGACGTGCCCCAAAGACAC----------AGGCTGAATCCATCAATAGATCTTCCAGAGGCAGATATT ↓ 4 1 3 2 Chimp: ggcaacccaccccttcaGTGGTCTTTGACGTGCCCCAAAGACCTATTGGGTCTTTGGCTGAATCCATCAATAGATCTTCCAGAGGCAGATATT Gorilla: ggcaacccaccccttcaGTGGTCTTTGACGTGCCCCAAAGACAC----------AGGCTGAATCCATCAATAGATCTTCCAGAGGCAGATATT Human: ggcaacccaccccttcaGTGGTCTTTGACGTGCCCCAAAGACAC----------AGGCTGAATCCATCAATAGATCTTCCAGAGGCAGATATT Cluster: [ ] Orangutan: Human > Chimp ------------- chr6:140361711-140361716 Template switch process: F1: L GCAACCCACCCCTTCAGTGGTCTTTGACGTGCCCCAAAGAC 1 F3: 4 GGTCTTT-------------------GGCTGAATCCATCAATAGATCTTCCAGAGGCAGATATTAC R RF: GCAACCCACCCCTTCAGTGGTCTTTGACGTGCCCCAAAGACACAGGCTGAATCCATCAATAGATCTTCCAGAGGCAGATATTAC RR: CGTTGGGTGGGGAAGTCACCAGAAACTGCACGGGGTTTCTGTGTCCGACTTAGGTAGTTATCTAGAAGGTCTCCGTCTATAATG F2: 3 GTTATC 2 Unidirectional alignment (log-probability: -37.3) CAACCCACCCCTTCAGTGGTCTTTGACGTGCCCCAAAGACctAttgggtctttGGCTGAATCCATCAATAGATCTTCCAGAGGCAG CAACCCACCCCTTCAGTGGTCTTTGACGTGCCCCAAAGACACA----------GGCTGAATCCATCAATAGATCTTCCAGAGGCAG Template switch alignment (log-probability: -27.4) CAACCCACCCCTTCAGTGGTCTTTGACGTGCCCCAAAGAC|CTATTG|GGTCTTT-------------------GGCTGAATCCATCAATAGATCTTCCAGAGGCAG CAACCCACCCCTTCAGTGGTCTTTGACGTGCCCCAAAGAC|CTATTG|GGTCTTTGACGTGCCCCAAAGACACAGGCTGAATCCATCAATAGATCTTCCAGAGGCAG ========== Event 3158 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tatttaaatattttaataattGCTACCTCTGTTCCAG----AGCCTTCCCATCACCCTGTCCACCCT ↓ 3 2 1 4 Chimp: TATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAGGTAGCAATCCCATCACCCTGTCCACCCT ↑ 3 2 1 4 Gorilla: TATTTAAATATTTTAATAATTGCTACCTCTGTTCCAG----AGCCTTCCCATCACCCTGTCCACCCT Human: tatttaaatattttaataattGCTACCTCTGTTCCAG----AGCCTTCCCATCACCCTGTCCACCCT Cluster: [ ] Orangutan: TATTTGAATATTTTAATAATTGCTACCTCTGTTCCAG----AGCCTTCCCATCACCCTGTCCACCCT Human > Chimp ------------- chr6:138440334-138440340 Template switch process: F1: L CAACTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAG 1 F3: 4 TCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTT R RF: CAACTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAGCCTTCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTT RR: GTTGATAAATTTATAAAATTATTAACGATGGAGACAAGGTCTCGGAAGGGTAGTGGGACAGGTGGGAAATCGAAGAAGAAGAAA F2: 3 AACGATG 2 Unidirectional alignment (log-probability: -36) CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGaggtAGCaaTCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTT-- CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAG----AGCCTTCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTTTT Template switch alignment (log-probability: -16.2) CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAG|GTAGCAA|TCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTT CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAG|GTAGCAA|TCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTT Gorilla > Chimp --------------- chr6:138440334-138440340 Template switch process: F1: L CAACTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAG 1 F3: 4 TCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTCTTTTT R RF: CAACTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAGCCTTCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTTTTTTT RR: GTTGATAAATTTATAAAATTATTAACGATGGAGACAAGGTCTCGGAAGGGTAGTGGGACAGGTGGGAAATCGAAGAAGAAAAAAAA F2: 3 AACGATG 2 Unidirectional alignment (log-probability: -40.3) CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGaggtAGCaaTCCCATCACCCTGTCCACCCTTTAGCTTCTTCTtcTTTTT CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAG----AGCCTTCCCATCACCCTGTCCACCCTTTAGCTTCTTCT--TTTTT Template switch alignment (log-probability: -22.2) CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAG|GTAGCAA|TCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTcTTTTT CTATTTAAATATTTTAATAATTGCTACCTCTGTTCCAGAG|GTAGCAA|TCCCATCACCCTGTCCACCCTTTAGCTTCTTCTTTTTTTT ========== Event 3159 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCAAGAAAATTCTCAGATCT---AGTGGGTGCCTGCCACTGAGGTAGAAGTGAAGGGACT Chimp: AGCAAGAAAATTCTCAGATCT---AGTGGGTGCCAGCCACTGAGGTAGAAGTGAAGGGACT Gorilla: AGCAAGAAAATTCTCAGATCT------AAGTGCCAG-CACTGAGGTAGAAGTGAAGGGACT ↑ 1 3 4 2 Human: AGCAAGAAAATTCTCAGATCT---AGTGGGTGCCTGCCACTGAGGTAGAAGTGAAGGGACT Cluster: [ ] Orangutan: AGCAAGAAAATTCTCAGATTTAGT---GGGTGCCAGCCACTAAGGTAGAAGTAAAGGGACT Human > Gorilla --------------- chr6:135536680-135536687 Template switch process: F1: L GTGCCCTCTGAAGAGGCCACAGCAAGAAAATTCTCAGATCTA 1 F3: 4 CACTGAGGTAGAAGTGAAGGGACTATTGCAGAAAGTAAAA R RF: GTGCCCTCTGAAGAGGCCACAGCAAGAAAATTCTCAGATCTAGTGGGTGCCTGCCACTGAGGTAGAAGTGAAGGGACTATTGCAGAAAGTAAAA RR: CACGGGAGACTTCTCCGGTGTCGTTCTTTTAAGAGTCTAGATCACCCACGGACGGTGACTCCATCTTCACTTCCCTGATAACGTCTTTCATTTT F2: 3 GACCGTGA 2 Unidirectional alignment (log-probability: -31.3) GCCCTCTGAAGAGGCCACAGCAAGAAAATTCTCAGATCTaagtgccAG-----------CACTGAGGTAGAAGTGAAGGGACTATTGCAGAAAGTAAAA GCCCTCTGAAGAGGCCACAGCAAGAAAATTCTCAGATCT-------AGTGGGTGCCTGCCACTGAGGTAGAAGTGAAGGGACTATTGCAGAAAGTAAAA Template switch alignment (log-probability: -22.3) GCCCTCTGAAGAGGCCACAGCAAGAAAATTCTCAGATCTA|AGTGcCAG|CACTGAGGTAGAAGTGAAGGGACTATTGCAGAAAGTAAAA GCCCTCTGAAGAGGCCACAGCAAGAAAATTCTCAGATCTA|AGTGGCAG|CACTGAGGTAGAAGTGAAGGGACTATTGCAGAAAGTAAAA ========== Event 3160 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGGGAGCAGGAACCTGGTGCCCGAGCCG--ACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGAGTAGGCTGGGCCTACAGCGC Chimp: CAGGGAGCAGGAACCTGGTGCCCAAGCCG--ACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGAGTAGGCTGGGCCTACAGCGC ↓ 1 4 3 2 Gorilla: CAGGGAGCAGGAACCTGGTGCTCCAGCCT----GCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGAGTAGGCTGGGCGTACAGCGC ↑ 1 4 3 2 Human: CAGGGAGCAGGAACCTGGTGCCCGAGCCG--ACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGAGTAGGCTGGGCCTACAGCGC Cluster: [ ] Orangutan: CAGGGAGCAGGAACCTGGTGCCCAAGCTGAC--CCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGAGTAGGCTGGGCCTACAGCGC Human > Gorilla --------------- chr6:37866384-37866392 Template switch process: F1: L CTCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGC 1 F3: 4 CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA R RF: CTCTAGAGGTCAACTCATGGCAGGGAGCAGGAACCTGGTGCCCGAGCCGACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA RR: GAGATCTCCAGTTGAGTACCGTCCCTCGTCCTTGGACCACGGGCTCGGCTGGGACGACTCCCGTACAACTATTACCCCCTGGATTCCGACCT F2: 3 GTCCGACCT 2 Unidirectional alignment (log-probability: -38.7) TCTAGAGGTCAACTCAcGGCAGGGAGCAGGAACCTGGTGCtCcAGCCtg--CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA TCTAGAGGTCAACTCATGGCAGGGAGCAGGAACCTGGTGCCCGAGCCGACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA Template switch alignment (log-probability: -27.9) TCTAGAGGTCAACTCAcGGCAGGGAGCAGGAACCTGGTGC|TCCAGCCTg|CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA TCTAGAGGTCAACTCATGGCAGGGAGCAGGAACCTGGTGC|TCCAGCCTT|CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA Chimp > Gorilla --------------- chr6:37866384-37866392 Template switch process: F1: L CTCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGC 1 F3: 4 CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA R RF: TTCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGCCCAAGCCGACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA RR: AAGATCTCCAGTTGAGTGCCGTCCCTCGTCCTTGGACCACGGGTTCGGCTGGGACGACTCCCGTACAACTATTACCCCCTGGATTCCGACCT F2: 3 GTCCGACCT 2 Unidirectional alignment (log-probability: -38.7) TCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGCtCcAGCCtg--CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA TCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGCCCAAGCCGACCCTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA Template switch alignment (log-probability: -27.9) TCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGC|TCCAGCCTg|CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA TCTAGAGGTCAACTCACGGCAGGGAGCAGGAACCTGGTGC|TCCAGCCTT|CTGCTGAGGGCATGTTGATAATGGGGGACCTAAGGCTGGA ========== Event 3161 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAAGGGCAGCCCATTTAGAGCTGAGACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACTCAGCAAGAAGGAGGGTGACTATC ↑ 1 4 3 2 Chimp: CCAAGGGCAGCTCATTTAGAGGGTGGACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACTCAGCAAGAAGGAGGGTGACTATC Gorilla: CCAAGGGCAGCTCATTTAGAGGGTGGACCCTATCTCAGAAGACGAACTGATGTGAGATCTCAACTCAGTAAGAAGGAGGGTGACTGTC Human: CCAAGGGCAGCCCATTTAGAGCTGAGACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACTCAGCAAGAAGGAGGGTGACTATC Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------- Chimp > Human ------------- chr6:3957618-3957621 Template switch process: F1: L TCCAGGAGGAGGTGCTGGGCCCAAGGGCAGCCCATTTAGAG 1 F3: 4 GACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACT R RF: TCCAGGAGGAGGTGCTGGGCCCAAGGGCAGCTCATTTAGAGGGTGGACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACTCAG RR: AGGTCCTCCTCCACGACCCGGGTTCCCGTCGAGTAAATCTCCCACCTGGGATAGAGTCTTCTCCTTGACTACACTCTAGAGTTGAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -30.7) CCAGGAGGAGGTGCTGGGCCCAAGGGCAGCcCATTTAGAGctgaGACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACT CCAGGAGGAGGTGCTGGGCCCAAGGGCAGCTCATTTAGAGGGTGGACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACT Template switch alignment (log-probability: -21.8) CCAGGAGGAGGTGCTGGGCCCAAGGGCAGCcCATTTAGAG|CTGA|GACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACT CCAGGAGGAGGTGCTGGGCCCAAGGGCAGCTCATTTAGAG|CTGA|GACCCTATCTCAGAAGAGGAACTGATGTGAGATCTCAACT ========== Event 3162 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: acatccaacacgtagaatatcatgcagtcaCATAACTAACGTTCATGATGGACTTGGGACCTTCataaa ↑ 3 2 1 4 Chimp: ACATCCAACACGTAGAATATCATGCAGTCACATAACTAACGT-TAT-GTGGACTTGGGACCTTCATaaa ↓ 3 2 1 4 Gorilla: ACATCCAACACGTAGAATATCATGCGGTCACATAACTAACGTTCATGATGGACTTGGGACCTTCATaaa Human: acatccaacacgtagaatatcatgcagtcaCATAACTAACGTTCATGATGGACTTGGGACCTTCataaa Cluster: [ ] Orangutan: acatccaacacgtagaatatcatgcagtcacataactaatgttCATGATGGACTTGGGATCTTCAtaaa Chimp > Human ------------- chr6:38920718-38920722 Template switch process: F1: L CATCCAACACGTAGAATATCATGCAGTCACATAACTAACGTT 1 F3: 4 TGGACTTGGGACCTTCATAAAATGAAATGA R RF: CATCCAACACGTAGAATATCATGCAGTCACATAACTAACGTTATGTGGACTTGGGACCTTCATAAAATGAAATGA RR: GTAGGTTGTGCATCTTATAGTACGTCAGTGTATTGATTGCAATACACCTGAACCCTGGAAGTATTTTACTTTACT F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -31.7) TCCAACACGTAGAATATCATGCAGTCACATAACTAACGTTcATGaTGGACTTGGGACCTTCATAAAATGAAATGA---------- TCCAACACGTAGAATATCATGCAGTCACATAACTAACGTT-ATG-TGGACTTGGGACCTTCATAAAATGAAATGAAATGAAATGA Template switch alignment (log-probability: -15.7) TCCAACACGTAGAATATCATGCAGTCACATAACTAACGTT|CATGA|TGGACTTGGGACCTTCATAAAATGAAATGA TCCAACACGTAGAATATCATGCAGTCACATAACTAACGTT|CATGA|TGGACTTGGGACCTTCATAAAATGAAATGA Chimp > Gorilla --------------- chr6:39603947-39603951 Template switch process: F1: L CATCCAACACGTAGAATATCATGCGGTCACATAACTAACGTT 1 F3: 4 TGGACTTGGGACCTTCATAAAATGAAATGA R RF: CATCCAACACGTAGAATATCATGCAGTCACATAACTAACGTTATGTGGACTTGGGACCTTCATAAAATGAAATGA RR: GTAGGTTGTGCATCTTATAGTACGTCAGTGTATTGATTGCAATACACCTGAACCCTGGAAGTATTTTACTTTACT F2: 3 AGTAC 2 Unidirectional alignment (log-probability: -36.2) TCCAACACGTAGAATATCATGCgGTCACATAACTAACGTTcATGaTGGACTTGGGACCTTCATAAAATGAAATGA---------- TCCAACACGTAGAATATCATGCAGTCACATAACTAACGTT-ATG-TGGACTTGGGACCTTCATAAAATGAAATGAAATGAAATGA Template switch alignment (log-probability: -21.6) TCCAACACGTAGAATATCATGCgGTCACATAACTAACGTT|CATGA|TGGACTTGGGACCTTCATAAAATGAAATGA TCCAACACGTAGAATATCATGCAGTCACATAACTAACGTT|CATGA|TGGACTTGGGACCTTCATAAAATGAAATGA ========== Event 3163 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCCTCTCCCTTGAGCATGGAAATTCGGC----------TAAGGACCTCATGTCACTGAGGAT Chimp: GCCTCTCCCTTGAGCATGGAAATTCGGCCTTAGCCGAATTTAGACCTCATGTCACTGAGGAT ↑ 3 1 4 Gorilla: GCCTCTCCCTTGAGCATGGAAATTCGGC----------TAAGGACCTCATGTCACTGAGGAT Human: GCCTCTCCCTTGAGCATGGAAATTCGGC----------TAAGGACCTCATGTCACTGAGGAT Cluster: [ ] Orangutan: GCCTCTCCTTTGAGCATGGAAATTCGGC----------TAAGGACATCATGTCACTGAAGCT Gorilla > Chimp --------------- chr6:39841119-39841131 Template switch process: F1: L CTCCTCACTCCCAGCCTCTCCCTTGAGCATGGAAATTCGGC 1 F3: 4 AGACCTCATGTCACTGAGGATGGCCCTATATTCACAATCAA R RF: CTCCTCACTCCCAGCCTCTCCCTTGAGCATGGAAATTCGGCTAAGGACCTCATGTCACTGAGGATGGCCCTATATTCACAAGCAA RR: GAGGAGTGAGGGTCGGAGAGGGAACTCGTACCTTTAAGCCGATTCCTGGAGTACAGTGACTCCTACCGGGATATAAGTGTTCGTT F2: 3 TTTAAGCCGATTC 2 Unidirectional alignment (log-probability: -43.5) TCCTCACTCCCAGCCTCTCCCTTGAGCATGGAAATTCGGCcttagccgaattTA--GACCTCATGTCACTGAGGATGGCCCTATATTCACAAtCA TCCTCACTCCCAGCCTCTCCCTTGAGCATGGAAATTCGGC------------TAAGGACCTCATGTCACTGAGGATGGCCCTATATTCACAAGCA Template switch alignment (log-probability: -28.4) TCCTCACTCCCAGCCTCTCCCTTGAGCATGGAAATTCGGC|CTTAGCCGAATTT|aGACCTCATGTCACTGAGGATGGCCCTATATTCACAAtCA TCCTCACTCCCAGCCTCTCCCTTGAGCATGGAAATTCGGC|CTTAGCCGAATTT|GGACCTCATGTCACTGAGGATGGCCCTATATTCACAAGCA ========== Event 3164 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 125 Detected in comparisons: 1256 Multiple sequence alignment: Human: AA---GTTTATTCGTGAAGAT------AGGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATAT ↓ 13 24 ↑ 13 24 Chimp: AA---GCTTATTCGTGAAGAT---AAAAAACCAGGATGATTCTGGC---CTAAGTCTTAGCTGAGAAATAT ↑ 13 24 Gorilla: AA---GTTTATTCGTGAAGAT------AGGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATAT Human: AA---GTTTATTCGTGAAGAT------AGGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATAT Cluster: [ ] Orangutan: AAGTAGTTTATTCATGAAGATAAA---AAACCAGGATGATTCTGGC---CTAAGTCTTAGCTGAGAAATAT Chimp > Human ------------- chr6:40158126-40158147 Template switch process: F1: L ATAAGCTGCCACAGGGCCTTTGAAAGTTTATTCGTGAAGATA 1 F3: 4 TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG R RF: ATAAGCTGCCACAGAGCCTTTGAAAGCTTATTCGTGAAGATAAAAAACCAGGATGATTCTGGCCTAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG RR: TATTCGACGGTGTCTCGGAAACTTTCGAATAAGCACTTCTATTTTTTGGTCCTACTAAGACCGGATTCAGAATCGACTCTTTATACCTGGAATTCCTCAATGTC F2: 3 TTTTTGGTCCTACTAAGACCGG 2 Unidirectional alignment (log-probability: -60) AAGCTGCCACAGgGCCTTTGAAAGtTTATTCGTGAAGATA------------------GGCCagaatcatcctggtttttTAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG AAGCTGCCACAGAGCCTTTGAAAGCTTATTCGTGAAGATAAAAAACCAGGATGATTCTGGCC------------------TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG Template switch alignment (log-probability: -30) AAGCTGCCACAGgGCCTTTGAAAGtTTATTCGTGAAGATA|GGCCAGAATCATCCTGGTTTTT|TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG AAGCTGCCACAGAGCCTTTGAAAGCTTATTCGTGAAGATA|GGCCAGAATCATCCTGGTTTTT|TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG Human > Chimp ------------- chr6:40619580-40619601 Template switch process: F1: L ATAAGCTGCCACAGAGCCTTTGAAAGCTTATTCGTGAAGATA 1 F3: 4 TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG R RF: ATAAGCTGCCACAGGGCCTTTGAAAGTTTATTCGTGAAGATAGGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG RR: TATTCGACGGTGTCCCGGAAACTTTCAAATAAGCACTTCTATCCGGTCTTAGTAGGACCAAAAAATTCAGAATCGACTCTTTATACCTGGAATTCCTCAATGTC F2: 3 CCGGTCTTAGTAGGACCAAAAA 2 Unidirectional alignment (log-probability: -60) AAGCTGCCACAGaGCCTTTGAAAGcTTATTCGTGAAGATAaaaaaccaggatgattctGGCC------------------TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG AAGCTGCCACAGGGCCTTTGAAAGTTTATTCGTGAAGATA------------------GGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG Template switch alignment (log-probability: -30) AAGCTGCCACAGaGCCTTTGAAAGcTTATTCGTGAAGATA|AAAAACCAGGATGATTCTGGCC|TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG AAGCTGCCACAGGGCCTTTGAAAGTTTATTCGTGAAGATA|AAAAACCAGGATGATTCTGGCC|TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG Gorilla > Chimp --------------- chr6:40619580-40619601 Template switch process: F1: L ATAAGCTGCCACAGAGCCTTTGAAAGCTTATTCGTGAAGATA 1 F3: 4 TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG R RF: ATAAGCTGCCACAGAGCCTTTGAAAGTTTATTCGTGAAGATAGGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG RR: TATTCGACGGTGTCTCGGAAACTTTCAAATAAGCACTTCTATCCGGTCTTAGTAGGACCAAAAAATTCAGAATCGACTCTTTATACCTGGAATTCCTCAATGTC F2: 3 CCGGTCTTAGTAGGACCAAAAA 2 Unidirectional alignment (log-probability: -53) AAGCTGCCACAGAGCCTTTGAAAGcTTATTCGTGAAGATAaaaaaccaggatgattctGGCC------------------TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG AAGCTGCCACAGAGCCTTTGAAAGTTTATTCGTGAAGATA------------------GGCCAGAATCATCCTGGTTTTTTAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG Template switch alignment (log-probability: -24.1) AAGCTGCCACAGAGCCTTTGAAAGcTTATTCGTGAAGATA|AAAAACCAGGATGATTCTGGCC|TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG AAGCTGCCACAGAGCCTTTGAAAGTTTATTCGTGAAGATA|AAAAACCAGGATGATTCTGGCC|TAAGTCTTAGCTGAGAAATATGGACCTTAAGGAGTTACAG ========== Event 3165 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AACCTTATGAGGCAAACTTTAAATGTTAGATTTAGATAGAG-CTCTAAGGTACTGATACCATTAGT Chimp: AACCTTATGAGGCAAACTTTAAATGTTAGATTTAGATAGAG-CTCTAAGGTACTGATACCATTAGT Gorilla: AACCTTATGAGGCAAACTTTAG-AGCTCTATCTAAATCTAACATTTAAGGTACTGATACCATTAGT ↓ 1 3 24 Human: AACCTTATGAGGCAAACTTTAAATGTTAGATTTAGATAGAG-CTCTAAGGTACTGATACCATTAGT Cluster: [ ] Orangutan: AATCTTATGAGGCAAACTTTAAATGTTAGATTTAGATAGAG-CTCTAAGGTACTGATACCATTAGT Gorilla > Human --------------- chr6:40078368-40078390 Template switch process: F1: L AGAGATAACCTTGATATTAAAACCTTATGAGGCAAACTTTA 1 F3: 4 TAAGGTACTGATACCATTAGTGTTTACTGTATTTCTCCAT R RF: AGAGATAACCTTGATATTATAACCTTATGAGGCAAACTTTAGAGCTCTATCTAAATCTAACATTTAAGGTACTGATACCATTAGTGTTTACTGTATTTCTCTAT RR: TCTCTATTGGAACTATAATATTGGAATACTCCGTTTGAAATCTCGAGATAGATTTAGATTGTAAATTCCATGACTATGGTAATCACAAATGACATAAAGAGATA F2: 3 CTCGAGATAGATTTAGATTGTAA 2 Unidirectional alignment (log-probability: -57.1) GAGATAACCTTGATATTAaAACCTTATGAGGCAAACTTtaaatgttagatttagaTAGAGCTC-----------------TAAGGTACTGATACCATTAGTGTTTACTGTATTTCTCcAT GAGATAACCTTGATATTATAACCTTATGAGGCAAACTT-----------------TAGAGCTCTATCTAAATCTAACATTTAAGGTACTGATACCATTAGTGTTTACTGTATTTCTCTAT Template switch alignment (log-probability: -29.7) GAGATAACCTTGATATTAaAACCTTATGAGGCAAACTTTA|AATGTTAGATTTAGATAGAGCTC|TAAGGTACTGATACCATTAGTGTTTACTGTATTTCTCcAT GAGATAACCTTGATATTATAACCTTATGAGGCAAACTTTA|AATGTTAGATTTAGATAGAGCTC|TAAGGTACTGATACCATTAGTGTTTACTGTATTTCTCTAT ========== Event 3166 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCTCACAGAAATAACTCAAA------GTATGGCAG------AAGGCACCATTTCTTCCCCTGGG----C Chimp: TTCTCACAGAAATAACTCAAA------GTATGGCAG------AAGGCACCATTTCTTCCCCTGGG----C ↓ 13 24 Gorilla: TTCTCACAGAAATAACTCAAAGGTGCCTTCTGCCAT------------ACATTTCTTCCCCTGGG----- ↑ 13 24 Human: TTCTCACAGAAATAACTCAAA------GTATGGCAG------AAGGCACCATTTCTTCCCCTGGG----C Cluster: [ ] Orangutan: TTCTCACAGAAATAACTCAAA------GTATGGCAGAAGGCA------CCATTTCTTCCCCTGGGCTAC- Human > Gorilla --------------- chr6:40925838-40925852 Template switch process: F1: L GGTCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG 1 F3: 4 CATTTCTTCCCCTGGG----CTTTTAGATTGAGACTTTTA R RF: GGTCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAGTATGGCAGAAGGCACCATTTCTTCCCCTGGGCTACCTTTTAGATTGAGACTTTTA RR: CCAGACGAGAGTGGATTCCAAAGAGTGTCTTTATTGAGTTTCATACCGTCTTCCGTGGTAAAGAAGGGGACCCGATGGAAAATCTAACTCTGAAAAT F2: 3 ATACCGTCTTCCGTG 2 Unidirectional alignment (log-probability: -49.9) TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAGgtgccttctgccaTA-------------CATTTCTTCCCCTGGG----CTTTTAGATTGAGACTTTTA TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG-------------TATGGCAGAAGGCACCATTTCTTCCCCTGGGCTACCTTTTAGATTGAGACTTTTA Template switch alignment (log-probability: -27.5) TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG|GTGCCTTCTGCCATA|CATTTCTTCCCCTGGG----CTTTTAGATTGAGACTTTTA TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG|GTGCCTTCTGCCATA|CATTTCTTCCCCTGGGCTACCTTTTAGATTGAGACTTTTA Chimp > Gorilla --------------- chr6:40925838-40925852 Template switch process: F1: L GGTCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG 1 F3: 4 CATTTCTTCCCCTGGG----CTTTTAGATTGAGACTTTTA R RF: GGTCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAGTATGGCAGAAGGCACCATTTCTTCCCCTGGGCTACCTTTTAGATTGAGACTTTTA RR: CCAGACGAGAGTGGATTCCAAAGAGTGTCTTTATTGAGTTTCATACCGTCTTCCGTGGTAAAGAAGGGGACCCGATGGAAAATCTAACTCTGAAAAT F2: 3 ATACCGTCTTCCGTG 2 Unidirectional alignment (log-probability: -49.9) TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAGgtgccttctgccaTA-------------CATTTCTTCCCCTGGG----CTTTTAGATTGAGACTTTTA TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG-------------TATGGCAGAAGGCACCATTTCTTCCCCTGGGCTACCTTTTAGATTGAGACTTTTA Template switch alignment (log-probability: -27.5) TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG|GTGCCTTCTGCCATA|CATTTCTTCCCCTGGG----CTTTTAGATTGAGACTTTTA TCTGCTCTCACCTAAGGTTTCTCACAGAAATAACTCAAAG|GTGCCTTCTGCCATA|CATTTCTTCCCCTGGGCTACCTTTTAGATTGAGACTTTTA ========== Event 3167 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CGACCCCCTTGCCTTGTCCTGGGCTGGGC---TGTCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGG Chimp: TGACCCCCTTGCCTTGTCCTG--GTGGAACAAATCCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGG ↑ 1 4 3 2 Gorilla: CGACCCCCTTGCCTTGTCCTGGGCTGGGC---TGTCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGG Human: CGACCCCCTTGCCTTGTCCTGGGCTGGGC---TGTCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGG Cluster: [ ] Orangutan: CGACCCCCTTGCCTTGTCCCGGGCTGGGC---TGTCAGTCATTCGTTCCACCCCAGCATCACAGAGGTGG Gorilla > Chimp --------------- chr6:40800069-40800078 Template switch process: F1: L ATGGGGGTTTGAGGGTAAGGTGACCCCCTTGCCTTGTCCTGG 1 F3: 4 CCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGGGGCCC R RF: ATGGGGGTTTGAGGGTAAGGCGACCCCCTTGCCTTGTCCTGGGCTGGGCTGTCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGGGGCCC RR: TACCCCCAAACTCCCATTCCGCTGGGGGAACGGAACAGGACCCGACCCGACAGTCAGTAAACAAGGTGGGGTCGTAGTGTCTCCACCCCGGG F2: 3 TAAACAAGGT 2 Unidirectional alignment (log-probability: -41) GGGGGTTTGAGGGTAAGGtGACCCCCTTGCCTTGTCCTG---------GTggaacaaatcCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGGGGCC GGGGGTTTGAGGGTAAGGCGACCCCCTTGCCTTGTCCTGGGCTGGGCTGT----------CAGTCATTTGTTCCACCCCAGCATCACAGAGGTGGGGCC Template switch alignment (log-probability: -28.1) GGGGGTTTGAGGGTAAGGtGACCCCCTTGCCTTGTCCTGG|TGGAACAAAT|cCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGGGGCC GGGGGTTTGAGGGTAAGGCGACCCCCTTGCCTTGTCCTGG|TGGAACAAAT|TCAGTCATTTGTTCCACCCCAGCATCACAGAGGTGGGGCC ========== Event 3168 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTACAAAAAGCTAAGAGACACCCGTGTC------CAC----AAGGTGCCTAATTTTTCTGAATG ↓ 3 1 24 Chimp: TTACAAAAAGCTAAGAGACACCCGTGTCCTTGTGGACACGGGTGGTGCCTAATTTTTCTGAATG ↑ 3 1 24 Gorilla: TTACAAAAAGCTAAGAGACACCCGTGTC------CAC----AAGGTGCCTAATTTTTCTGAATG Human: TTACAAAAAGCTAAGAGACACCCGTGTC------CAC----AAGGTGCCTAATTTTTCTGAATG Cluster: [ ] Orangutan: TTACAAAAAGCTAAGGGACACCCGTGTC------CAC----AAGGTGCCTAATTTTTCTGAATG Human > Chimp ------------- chr6:41575944-41575957 Template switch process: F1: L ATTAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC 1 F3: 4 GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGC R RF: ATTAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCCACAAGGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGA RR: TAATTCTTTTAAAAATGTTTTTCGATTCTCTGTGGGCACAGGTGTTCCACGGATTAAAAAGACTTACAATGATGAATCCGAGACCT F2: 3 TGGGCACAGGTGTT 2 Unidirectional alignment (log-probability: -47.5) TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC----ttgtggacacgggtGGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGc TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCCACAA--------------GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGA Template switch alignment (log-probability: -23) TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC|TTGTGGACACGGGT|GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGc TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC|TTGTGGACACGGGT|GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGA Gorilla > Chimp --------------- chr6:41575944-41575957 Template switch process: F1: L ATTAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC 1 F3: 4 GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGC R RF: ATTAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCCACAAGGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGA RR: TAATTCTTTTAAAAATGTTTTTCGATTCTCTGTGGGCACAGGTGTTCCACGGATTAAAAAGACTTACAATGATGAATCCGAGACCT F2: 3 TGGGCACAGGTGTT 2 Unidirectional alignment (log-probability: -46.1) TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCCttgtggACAcgggtGGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGc TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC------ACA----AGGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGA Template switch alignment (log-probability: -23.1) TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC|TTGTGGACACGGGT|GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGc TAAGAAAATTTTTACAAAAAGCTAAGAGACACCCGTGTCC|TTGTGGACACGGGT|GGTGCCTAATTTTTCTGAATGTTACTACTTAGGCTCTGGA ========== Event 3169 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATTCCTCCAGGCAGGGCCCCTGGAATGAGGCGATACCTCATTCATCTCTTCTGAGGGGGCTAA Chimp: ATTCCTCCAGGCAGGGCCCCT----------AACGCCTCATTCATCTCTTCTGAGGGGGCTAA Gorilla: ATTCCTCCAGGCAGGGCCCCT----------ATCGCCTCATTCATCTCTTCTGAGGGGGCTAA ↓ 31 4 2 ↑ 1 3 2 4 Human: ATTCCTCCAGGCAGGGCCCCTGGAATGAGGCGATACCTCATTCATCTCTTCTGAGGGGGCTAA Cluster: [ ] Orangutan: ATTCCTCCAGCTAGGGCCCCT----------ATTGCCTCATTCATCTCTTCTGAGGGGTCTAA Gorilla > Human --------------- chr6:129333134-129333146 Template switch process: F1: L CTCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCTG 1 F3: 4 CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA R RF: CTCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCTATCGCCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA RR: GAGCCTGAGGAGGGTTGGTTTAAGGAGGTCCGTCCCGGGGATAGCGGAGTAAGTAGAGAAGACTCCCCCGATTGGGACGACAGGT F2: 3 ATAGCGGAGTAAG 2 Unidirectional alignment (log-probability: -39.5) CGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCtggaatgaggcgaTA---CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA CGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCC-------------TATCGCCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA Template switch alignment (log-probability: -22.9) CGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCTg|GAATGAGGCGATA|CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA CGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCTA|GAATGAGGCGATA|CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA Human > Gorilla --------------- chr6:131054579-131054582 Template switch process: F1: L CTCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCT 1 F3: 4 CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA R RF: CTCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCTGGAATGAGGCGATACCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA RR: GAGCCTGAGGAGGGTTGGTTTAAGGAGGTCCGTCCCGGGGACCTTACTCCGCTATGGAGTAAGTAGAGAAGACTCCCCCGATTGGGACGACAGGT F2: 3 GCTA 2 Unidirectional alignment (log-probability: -25.6) TCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCC-------------TAtcgCCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA TCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCTGGAATGAGGCGATA---CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA Template switch alignment (log-probability: -16.2) TCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCT|ATCG|CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA TCGGACTCCTCCCAACCAAATTCCTCCAGGCAGGGCCCCT|ATCG|CCTCATTCATCTCTTCTGAGGGGGCTAACCCTGCTGTCCA ========== Event 3170 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: CATCTCAAGTAGAGGACAAACTTGGGAGATTGTTCACAATCTCCCAAGTGCCCGTGGAATGGGCCCTGCAT ↑ 3 1 2 4 Chimp: CATCTCAAGTAGAGGACAAACTTGGGAGATTGTGAACAATCTC--------CCGTGGAATGGGCCCTGCAT ↓ 3 1 2 4 Gorilla: CATCTCAAGTAGAGGACAAACTTGGGAGATTGTTCACAATCTCCCAAGTGCCCGTGGAATGGGCCCTGCAT Human: CATCTCAAGTAGAGGACAAACTTGGGAGATTGTTCACAATCTCCCAAGTGCCCGTGGAATGGGCCCTGCAT Cluster: [ ] Orangutan: CATCTCAAGTAGAGGACAAACTTGGGAGATTGTTCACAATCTCCCAAGCGCCTGTGGAATGGGCCCTGCGT Chimp > Human ------------- chr6:42368118-42368133 Template switch process: F1: L CTGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGT 1 F3: 4 GCCCGTGGAATGGGCCCTGCATCCAGGCAGTATACTTGGTGG R RF: CTGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGTGAACAATCTCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGTGG RR: GACACAGAGTAGAGTTCATCTCCTGTTTGAACCCTCTAACACTTGTTAGAGGGCACCTTACCCGGGACGTAGGTCCGTCATATAAACCACC F2: 3 TGAACCCTCTAACACT 2 Unidirectional alignment (log-probability: -40.5) TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGTtcACAATCTcccaagtgCCCGTGGAATGGGCCCTGCATCCAGGCAGTATAcTTGGT TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGTGAACAATCT--------CCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGT Template switch alignment (log-probability: -29.3) TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGT|TCACAATCTCCCAAGT|gCCCGTGGAATGGGCCCTGCATCCAGGCAGTATAcTTGGT TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGT|TCACAATCTCCCAAGT|TCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGT Chimp > Gorilla --------------- chr6:43151212-43151227 Template switch process: F1: L CTGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGT 1 F3: 4 GCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGTGG R RF: CTGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGTGAACAATCTCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGTGG RR: GACACAGAGTAGAGTTCATCTCCTGTTTGAACCCTCTAACACTTGTTAGAGGGCACCTTACCCGGGACGTAGGTCCGTCATATAAACCACC F2: 3 TGAACCCTCTAACACT 2 Unidirectional alignment (log-probability: -33.6) TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGTtcACAATCTcccaagtgCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGT TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGTGAACAATCT--------CCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGT Template switch alignment (log-probability: -23.3) TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGT|TCACAATCTCCCAAGT|gCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGT TGTGTCTCATCTCAAGTAGAGGACAAACTTGGGAGATTGT|TCACAATCTCCCAAGT|TCCCGTGGAATGGGCCCTGCATCCAGGCAGTATATTTGGT ========== Event 3171 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTAAAGTATGTCACTCCTGATCTAA---AACCTTCTGAGATTCTTATTATCT ↓ 3 1 2 4 Chimp: TCTTAAAGTATGTCACTCCTGATCTTTAGATCACTTCTGAGATTCTTATTATCT Gorilla: TCTTAAAGTATGTCACTCGTGATCTAA---AAC---CTGAGATTCTTATTATCT Human: TCTTAAAGTATGTCACTCCTGATCTAA---AACCTTCTGAGATTCTTATTATCT Cluster: [ ] Orangutan: Human > Chimp ------------- chr6:132174953-132174960 Template switch process: F1: L GCTACTAAATTAGTTTTCTTAAAGTATGTCACTCCTGATCT 1 F3: 4 CTTCTGAGATTCTTATTATCTGATAGACTTCCTGGCCTGG R RF: GCTACTAAATTAGTTTTCTTAAAGTATGTCACTCCTGATCTAAAACCTTCTGAGATTCTTATTATCTGATAGACTTCCTGGCCTGG RR: CGATGATTTAATCAAAAGAATTTCATACAGTGAGGACTAGATTTTGGAAGACTCTAAGAATAATAGACTATCTGAAGGACCGGACC F2: 3 ACTAGATT 2 Unidirectional alignment (log-probability: -31.4) CTACTAAATTAGTTTTCTTAAAGTATGTCACTCCTGATCTttagatcA----CTTCTGAGATTCTTATTATCTGATAGACTTCCTGGCCTGG CTACTAAATTAGTTTTCTTAAAGTATGTCACTCCTGATCT-------AAAACCTTCTGAGATTCTTATTATCTGATAGACTTCCTGGCCTGG Template switch alignment (log-probability: -16.3) CTACTAAATTAGTTTTCTTAAAGTATGTCACTCCTGATCT|TTAGATCA|CTTCTGAGATTCTTATTATCTGATAGACTTCCTGGCCTGG CTACTAAATTAGTTTTCTTAAAGTATGTCACTCCTGATCT|TTAGATCA|CTTCTGAGATTCTTATTATCTGATAGACTTCCTGGCCTGG ========== Event 3172 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAATGCTCTGCAGCAAAAACCAAT-------ATAATGTGTAAGACTAgttctaattctgaggtatgtggattt ↓ 1 4 3 2 Chimp: ACAATGCTCTGCAGCAAAAACTAGAACTAGTCTTAATGTGTAAGACTAgttctaattctgaggtatgtggattt ↑ 1 4 3 2 Gorilla: ACAATGCTCTGCAGCAAAAACCAAT-------ATAATGTGTAAGACTAgttctaattctgaggtatgtggattt Human: ACAATGCTCTGCAGCAAAAACCAAT-------ATAATGTGTAAGACTAgttctaattctgaggtatgtggattt Cluster: [ ] Orangutan: Human > Chimp ------------- chr6:131301645-131301656 Template switch process: F1: L AGAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAAC 1 F3: 4 TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT R RF: AGAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAACCAATATAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT RR: TCTCTATTATCTTACGAAGTTGTTACGAGACGTCGTTTTTGGTTATATTACACATTCTGATCAAGATTAAGACTCCATACACCTAA F2: 3 TCTGATCAAGAT 2 Unidirectional alignment (log-probability: -35.7) GAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAAC---TAgaactagtctTAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT GAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAACCAATA----------TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT Template switch alignment (log-probability: -16.8) GAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAAC|TAGAACTAGTCT|TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT GAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAAC|TAGAACTAGTCT|TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT Gorilla > Chimp --------------- chr6:131301645-131301656 Template switch process: F1: L AGAGATAATAGAATGCTTCAACAATGCTCTGCAGCAAAAAC 1 F3: 4 TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT R RF: AGAGATAATAAAATGCTTCAACAATGCTCTGCAGCAAAAACCAATATAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT RR: TCTCTATTATTTTACGAAGTTGTTACGAGACGTCGTTTTTGGTTATATTACACATTCTGATCAAGATTAAGACTCCATACACCTAA F2: 3 TCTGATCAAGAT 2 Unidirectional alignment (log-probability: -40.7) GAGATAATAgAATGCTTCAACAATGCTCTGCAGCAAAAAC---TAgaactagtctTAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT GAGATAATAAAATGCTTCAACAATGCTCTGCAGCAAAAACCAATA----------TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT Template switch alignment (log-probability: -22.8) GAGATAATAgAATGCTTCAACAATGCTCTGCAGCAAAAAC|TAGAACTAGTCT|TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT GAGATAATAAAATGCTTCAACAATGCTCTGCAGCAAAAAC|TAGAACTAGTCT|TAATGTGTAAGACTAGTTCTAATTCTGAGGTATGTGGATT ========== Event 3173 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGCTCCGCACTCAGCACCGCCTCTCCCAGACCC-------------------------------------------------------------------TTCACTTGCATTTGTCTGTCTGTGCCACCACTCTCCAAACGTCTCTGCCAAG Chimp: CAGCTCCGCACTCAGCACTGCCTCTCCCAGACCCTTCACCTGCATTTGAGTGGTGGCACAGACAGACAAATGCAGGTGAAGGGTCTGCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGCCACCACTCTCCAAACGTCTCTGCCAAG ↑ 4 3 1 2 Gorilla: CAGCTCCACACTCAGCACCGCCTCTCCCAGACCC-------------------------------------------------------------------TTCACCTGCATTTGTCTGTCTGTGCCACCACTCTCCAAACGTCTCTGCCAAG Human: CAGCTCCGCACTCAGCACCGCCTCTCCCAGACCC-------------------------------------------------------------------TTCACTTGCATTTGTCTGTCTGTGCCACCACTCTCCAAACGTCTCTGCCAAG Cluster: [ ] Orangutan: CAGCTCCGCACTCAGCACCGCCTCTCCCAGACCC-------------------------------------------------------------------TTCACCTGCATTTGTCTGTCTGCGCCACCACTCTCCAAACGTCTCTGCCAAG Gorilla > Chimp --------------- chr6:131621710-131621747 Template switch process: F1: L CCTCTGTCAGCTCCGCACTCAGCACTGCCTCTCCCAGACCCTTCACCTGCATTTG 1 F3: 4 GCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGCCACCACTCTCCAAAC R RF: CCTCTGTCAGCTCCACACTCAGCACCGCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGCCACCACTCTCCAAAC RR: GGAGACAGTCGAGGTGTGAGTCGTGGCGGAGAGGGTCTGGGAAGTGGACGTAAACAGACAGACACGGTGGTGAGAGGTTTG F2: 3 TCTGGGAAGTGGACGTAAACAGACAGACACGGTGGTGA 2 Unidirectional alignment (log-probability: -118) CACTCAGCActgcctctcccagacccttcacctgcatttgagtggtggcacagacagacaaatgcaggtgaagggtCtGCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGC CACTCAGCA-------------------------------------------------------------------CCGCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGC Template switch alignment (log-probability: -32.2) CACTCAGCACtGCCTCTCCCAGACCCTTCACCTGCATTTG|AGTGGTGGCACAGACAGACAAATGCAGGTGAAGGGTCT|GCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGC CACTCAGCACCGCCTCTCCCAGACCCTTCACCTGCATTTG|AGTGGTGGCACAGACAGACAAATGCAGGTGAAGGGTCT|GCCTCTCCCAGACCCTTCACCTGCATTTGTCTGTCTGTGC ========== Event 3174 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTCAAATACAATGAGTGgtg------------------------------------------tgtgtgtgtgtgtgtgtgtgCGCGCGCGCGCGCACATGCTAGAGA----AAGAGTATGTCTGTGTCCTT Chimp: CCTCAAATACAATGAGTGGTG------------------------------------------------------------------TGCGCGCGCACACGCTAGAGA--AACAGAGTATGTCTGTGTCCTT ↓ 3 1 4 2 Gorilla: CCTCAAATACAATGAGTGgtg------------------------------tgtgtgtgtgCG------------------------CGCGCACACACACGCTAGAGAAA--CAGAGTATGTCTGTGTCCTT Human: CCTCAAATACAATGAGTGgtg------------------------------------------tgtgtgtgtgtgtgtgtgtgCGCGCGCGCGCGCACATGCTAGAGA----AAGAGTATGTCTGTGTCCTT Cluster: [ ] Orangutan: CCTCAAATACAATGAGTGgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtg------------------------------------tgcaCGCGCACACGCTAGAGAAA--CAGAATATGTCTGTGTCCTT Chimp > Gorilla --------------- chr6:46203343-46203356 Template switch process: F1: L GAGTGGTGTGTGTG 1 F3: 4 CACACGCTAGAGAAACAGAGTATGTCTGTGTCCTTGATCTCTCAGCATACTTCAC R RF: GAGTGGTGTGCGCGCGCACACGCTAGAGAAACAGAGTATGTCTGTGTCCTTGATCTCTCAGCATACTTCAC RR: CTCACCACACGCGCGCGTGTGCGATCTCTTTGTCTCATACAGACACAGGAACTAGAGAGTCGTATGAAGTG F2: 3 ACACGCGCGCGTGT 2 Unidirectional alignment (log-probability: -37.7) GAGTGgtgtgtgtGTGTGCGCGCGcacaCACACGCTAGAGAAACAGAGTATGTCTGTGTCCTTGATCT GAGTG--------GTGTGCGCGCG----CACACGCTAGAGAAACAGAGTATGTCTGTGTCCTTGATCT Template switch alignment (log-probability: -28.2) GAGTGGTGTGtGtG|TGTGCGCGCGCACA|CACACGCTAGAGAAACAGAGTATGTCTGTGTCCTTGATCT GAGTGGTGTGCGCG|TGTGCGCGCGCACA|CACACGCTAGAGAAACAGAGTATGTCTGTGTCCTTGATCT ========== Event 3175 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AGCAGAAGGAGTGGTTCTCAGGGATGCTGAGGAAAGACATCCAGCGGGGCTCACTGGCCTTTTGTAACCCATAGCTCTGATCATCCTTGGCCCAACCAAGTTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGCAGC-ATCCTTAGTTCTCATGTCCAAGGATTC Chimp: AGCAGAAGGAGTGGTTCTCAGGGATGCTGAGGAAAGACATCCAGCGGGGTTCACTGGCCTTTTGTAACCCATAGCTCTGATCATCCTTGGCCCAACCAAGTTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGCCATGTTTCAAAGTTCTCATGTCCAAGGATTC ↓ 3 2 1 4 Gorilla: AGCAGAAGGAGTTGTTCTCAGGGATGCTGAGGAAAGACATCCAGCGGGGCTCACTGGCCTTTTGTAACCCATAGCTCTGATCATCCTTGGCCCAACCAAGTTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGCAGC-ATCCTTAGTTCTCATGTCCAAGGATTC Human: AGCAGAAGGAGTGGTTCTCAGGGATGCTGAGGAAAGACATCCAGCGGGGCTCACTGGCCTTTTGTAACCCATAGCTCTGATCATCCTTGGCCCAACCAAGTTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGCAGC-ATCCTTAGTTCTCATGTCCAAGGATTC Cluster: [ ] Orangutan: AGTAGAAGGAGTGGTTCTCAGGGATGCTGAGGAAAGACATCCAGCGGGGCTCACTGGCCTTTTGTAACCCACAGCTCTGATCATCCTCGGCCCAACCAAGTTCTGAACTCATAAGGGTAGGAGCCATGTTTCAAAGAAGAAGC-ATCCTTAGTTCTCATGTCCAAGGATTC Chimp > Gorilla --------------- chr6:45499103-45499111 Template switch process: F1: L GTTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGC 1 F3: 4 AGTTCTCATGTCCAAGGATTCCTTTCTCACCAAGAACTTC R RF: AGGGATGCTGAGGAAAGACATCCAGCGGGGTTCACTGGCCTTTTGTAACCCATAGCTCTGATCATCCTTGGCCCAACCAAGTTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGCCATGTTTCAAAGTTCTCATGTCCAAGGATTCCTTTCTCACCAAGAACTTC RR: TCCCTACGACTCCTTTCTGTAGGTCGCCCCAAGTGACCGGAAAACATTGGGTATCGAGACTAGTAGGAACCGGGTTGGTTCAAGACTTGAGTGTTGCCATCCTCGGTACAAAGTTTCTTCGGTACAAAGTTTCAAGAGTACAGGTTCCTAAGGAAAGAGTGGTTCTTGAAG F2: 3 TTCCTACGA 2 Unidirectional alignment (log-probability: -32.6) TTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGC---------AgcatccttAGTTCTCATGTCCAAGGATTCCTTTCTCACCAAGAACTTC TTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGCCATGTTTCAA--------AGTTCTCATGTCCAAGGATTCCTTTCTCACCAAGAACTTC Template switch alignment (log-probability: -22.4) TTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGC|AGCATCCtT|AGTTCTCATGTCCAAGGATTCCTTTCTCACCAAGAACTTC TTCTGAACTCACAACGGTAGGAGCCATGTTTCAAAGAAGC|AGCATCCCT|AGTTCTCATGTCCAAGGATTCCTTTCTCACCAAGAACTTC ========== Event 3176 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTTTATTTATTCTTTCCCTACTGATGGATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACATCCAAAGGTAGGGAAAGAATAAATAAAA ↓ 13 24 ↑ 13 24 Chimp: TTTTATTTATTCTTTCCCTACCTTTGGACG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCCATCCATCAGTAGGGAAAGAATAAATAAAA Gorilla: TTTTATTTATTCTTTCCCTACCTTTGGACG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCCATCCATCAGTAGGGAAAGAATAAATAAAA ↓ 13 24 ↑ 13 24 Human: TTTTATTTATTCTTTCCCTACTGATGGATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACATCCAAAGGTAGGGAAAGAATAAATAAAA Cluster: [ ] Orangutan: TTTTGA-AAGCTTTTCCCTATCTTTGGACGTTCCAACCATTCTCAGGAATCTCAACCTTAAAACGAGGAAGGGGTACTTATACCTGCTACTACCCCTGGTGATCAAGCACGAGGGTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCATCCTTCAGTACGGAAAGAATAAATAAAA Chimp > Human ------------- chr6:44468405-44468425 Template switch process: F1: L CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC 1 F3: 4 GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG R RF: CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACCTTTGGACGTTCCATCCATCAGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG RR: GGAGAACTCTGGGAGGGTGTAAAATAAATAAGAAAGGGATGGAAACCTGCAAGGTAGGTAGTCATCCCTTTCTTATTTATTTTACACCCTCCCAGAGTTCTC F2: 3 GAAACCTACAAGGTAGGTAGT 2 Unidirectional alignment (log-probability: -52.4) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC---------------------tgatggatggaacatccaaagGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACCTTTGGACGTTCCATCCATCA---------------------GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Template switch alignment (log-probability: -23.9) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|TGATGGATGGAACaTCCAAAG|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|TGATGGATGGAACGTCCAAAG|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Human > Chimp ------------- chr6:44996078-44996098 Template switch process: F1: L CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC 1 F3: 4 GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG R RF: CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACTGATGGATGGAACATCCAAAGGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG RR: GGAGAACTCTGGGAGGGTGTAAAATAAATAAGAAAGGGATGACTACCTACCTTGTAGGTTTCCATCCCTTTCTTATTTATTTTACACCCTCCCAGAGTTCTC F2: 3 ACTACCTACCTTGCAGGTTTC 2 Unidirectional alignment (log-probability: -52.4) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC---------------------ctttggacgttccatccatcaGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACTGATGGATGGAACATCCAAAG---------------------GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Template switch alignment (log-probability: -23.9) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|CTTTGGAcGTTCCATCCATCA|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|CTTTGGATGTTCCATCCATCA|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Gorilla > Human --------------- chr6:44468405-44468425 Template switch process: F1: L CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC 1 F3: 4 GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG R RF: CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACCTTTGGACGTTCCATCCATCAGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG RR: GGAGAACTCTGGGAGGGTGTAAAATAAATAAGAAAGGGATGGAAACCTGCAAGGTAGGTAGTCATCCCTTTCTTATTTATTTTACACCCTCCCAGAGTTCTC F2: 3 GAAACCTACAAGGTAGGTAGT 2 Unidirectional alignment (log-probability: -51.9) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC---------------------tgatggatggaacatccaaagGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACCTTTGGACGTTCCATCCATCA---------------------GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Template switch alignment (log-probability: -23.9) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|TGATGGATGGAACaTCCAAAG|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|TGATGGATGGAACGTCCAAAG|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Human > Gorilla --------------- chr6:45304808-45304828 Template switch process: F1: L CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC 1 F3: 4 GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG R RF: CCTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACTGATGGATGGAACATCCAAAGGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG RR: GGAGAACTCTGGGAGGGTGTAAAATAAATAAGAAAGGGATGACTACCTACCTTGTAGGTTTCCATCCCTTTCTTATTTATTTTACACCCTCCCAGAGTTCTC F2: 3 ACTACCTACCTTGCAGGTTTC 2 Unidirectional alignment (log-probability: -51.9) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC---------------------ctttggacgttccatccatcaGTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTACTGATGGATGGAACATCCAAAG---------------------GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG Template switch alignment (log-probability: -23.9) CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|CTTTGGAcGTTCCATCCATCA|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG CTCTTGAGACCCTCCCACATTTTATTTATTCTTTCCCTAC|CTTTGGATGTTCCATCCATCA|GTAGGGAAAGAATAAATAAAATGTGGGAGGGTCTCAAGAG ========== Event 3177 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGCTGGCTGGCCTTCCAGCC---------AGGTAGCTATGAGTCAGGTCTGCATCAGGGGTGGGGACC Chimp: TTGCTGGCTGGCCTTCCAGCC---------AGGTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACC ↓ 1 4 3 2 Gorilla: TTGCTGGCTGGCCTTCCAGCCTACCTGACTCAGTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACC Human: TTGCTGGCTGGCCTTCCAGCC---------AGGTAGCTATGAGTCAGGTCTGCATCAGGGGTGGGGACC Cluster: [ ] Orangutan: CTGCTGGCTGGCCTTCCAGCC---------AGGTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACC Chimp > Gorilla --------------- chr6:45062926-45062935 Template switch process: F1: L TTTGGAATTGGGGGTTGCCATTGCTGGCTGGCCTTCCAGCCT 1 F3: 4 GTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACCCCC R RF: TTTGGAATTGGGGGTTGCCATTGCTGGCTGGCCTTCCAGCCAGGTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACCCCC RR: AAACCTTAACCCCCAACGGTAACGACCGACCGGAAGGTCGGTCCATCGATACTCAGTCCAGACGTAGTCCCCGCCCCTGGGGG F2: 3 ACTCAGTCCA 2 Unidirectional alignment (log-probability: -34.9) TGGAATTGGGGGTTGCCATTGCTGGCTGGCCTTCCAGCCtacctgactcaGTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACCCCC TGGAATTGGGGGTTGCCATTGCTGGCTGGCCTTCCAGCC---------AGGTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACCCCC Template switch alignment (log-probability: -22.5) TGGAATTGGGGGTTGCCATTGCTGGCTGGCCTTCCAGCCt|ACCTGACTCA|GTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACCCCC TGGAATTGGGGGTTGCCATTGCTGGCTGGCCTTCCAGCCA|ACCTGACTCA|GTAGCTATGAGTCAGGTCTGCATCAGGGGCGGGGACCCCC ========== Event 3178 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAGGAAACTTATTAAATAAATGTAGCCATATCCATGCATCTTCAA-----AGAATTAGGAGTTCTATATGGTACTAATATGTAAAGAGTAAATCCCTACTGACATAGgaacagtgtgaataatatgacacattttgcttataaggcggaaaataaaaatctata Chimp: TGAGGAAACTTATTAAATAAATGTAGCCATATCCATGCATCTTCAA-----AGAATTAGGAGTTCTATATGGTACTAATATGTAAAGAGTAAATCCCTATTGACATAGgaacagtgtgagtaatatgacacattttgcttataaggcggagaataaaaatctata ↓ 1 4 3 2 Gorilla: TGAGGAAACTTATTAAATAAACTT-ATAAGATCCATGCATCTTCAA-----AGAATTAGGAGTTCTATATGGTACTAATATGTAAAGAGTAAATCCCTATTGGCATAGgaacagtgtgaataatatgacacattttgcttataaggcggaaaataaaaatctata ↑ 1 4 3 2 Human: TGAGGAAACTTATTAAATAAATGTAGCCATATCCATGCATCTTCAA-----AGAATTAGGAGTTCTATATGGTACTAATATGTAAAGAGTAAATCCCTACTGACATAGgaacagtgtgaataatatgacacattttgcttataaggcggaaaataaaaatctata Cluster: [ ] Orangutan: TGAGGAAACTTATTAAATAAATGTAGCCATATCCATGCATCTTCAAAGAAAAGAACTAGGAGTTCTATACGGTAGTAATATGT-------AAATCCCTATTGACAAAGGAACAGTGTGAATAATATGACACATTTTGCTTATAAGGTGGAAAATAAAAATCTATA Human > Gorilla --------------- chr6:47622788-47622795 Template switch process: F1: L GACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA 1 F3: 4 ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC R RF: GACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAATGTAGCCATATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTACTAATATGTAAAGAGTAAATCCCTACTGACATAGGAACAGTGTGAATAATATGACACATTTTGCTTATAAG RR: CTGATGGTATACAGATAGCTACTCCTTTGAATAATTTATTTACATCGGTATAGGTACGTAGAAGTTTCTTAATCCTCAAGATATACCATGATTATACATTTCTCATTTAGGGATGACTGTATCCTTGTCACACTTATTATACTGTGTAAAACGAATATTC F2: 3 GAATATTC 2 Unidirectional alignment (log-probability: -32.6) ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA---------cttataagATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAATGTAGCCAT--------ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC Template switch alignment (log-probability: -16.7) ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA|CTTATAAG|ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA|CTTATAAG|ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC Chimp > Gorilla --------------- chr6:47622788-47622795 Template switch process: F1: L GACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA 1 F3: 4 ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC R RF: GACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAATGTAGCCATATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTACTAATATGTAAAGAGTAAATCCCTATTGACATAGGAACAGTGTGAGTAATATGACACATTTTGCTTATAAG RR: CTGATGGTATACAGATAGCTACTCCTTTGAATAATTTATTTACATCGGTATAGGTACGTAGAAGTTTCTTAATCCTCAAGATATACCATGATTATACATTTCTCATTTAGGGATAACTGTATCCTTGTCACACTCATTATACTGTGTAAAACGAATATTC F2: 3 GAATATTC 2 Unidirectional alignment (log-probability: -32.6) ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA---------cttataagATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAATGTAGCCAT--------ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC Template switch alignment (log-probability: -16.7) ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA|CTTATAAG|ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC ACTACCATATGTCTATCGATGAGGAAACTTATTAAATAAA|CTTATAAG|ATCCATGCATCTTCAAAGAATTAGGAGTTCTATATGGTAC ========== Event 3179 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATAATA-------------------------------AACTACTGGGTCCTCTTCCCTTGGGCAGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTAT Chimp: ATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATAATA-------------------------------AACTACTGGGTCCTCTTCCCTTGGGCAGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTAT ↑ 3 2 4 1 Gorilla: ATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATGATA--------------------------------------------------------------AACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTAT ↓ 3 2 4 1 Human: ATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATAATA-------------------------------AACTACTGGGTCCTCTTCCCTTGGGCAGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTAT Cluster: [ ] Orangutan: ATAAAGTGGTCCCAAGATATGGCCAGGTCCTTCATGATAAACTATTGGGTCCTCTTCCCTTGGGCAGATA-------------------------------AACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTCGGTAT Gorilla > Human --------------- chr6:123917952-123917957 Template switch process: F1: L CTTGTCATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATAATAAACTACTGGGTCCTCTTCCCT 1 F3: 4 GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTA R RF: CTTGTCATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTA RR: GAACAGTATTTCACTAGGGTTCTATACCGGTCCAGGAAGTACTATTTGATGACCCAGGAGAAGGGACACAGGAGGAGGGAACCAT F2: 3 ACGGGT 2 Unidirectional alignment (log-probability: -55.5) GGCCAGGTCCTTCATaataaactactgggtcctcttcccttgggcaGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT GGCCAGGTCCTTCAT-------------------------------GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT Template switch alignment (log-probability: -28.2) GGCCAGGTCCTTCATaATAAACTACTGGGTCCTCTTCCCT|TGGgCA|GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT GGCCAGGTCCTTCATGATAAACTACTGGGTCCTCTTCCCT|TGGCCA|GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT Gorilla > Chimp --------------- chr6:127989055-127989060 Template switch process: F1: L CTTGTCATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATAATAAACTACTGGGTCCTCTTCCCT 1 F3: 4 GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTA R RF: CTTGTCATAAAGTGATCCCAAGATATGGCCAGGTCCTTCATGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTTGGTA RR: GAACAGTATTTCACTAGGGTTCTATACCGGTCCAGGAAGTACTATTTGATGACCCAGGAGAAGGGACACAGGAGGAGGGAACCAT F2: 3 ACGGGT 2 Unidirectional alignment (log-probability: -55.5) GGCCAGGTCCTTCATaataaactactgggtcctcttcccttgggcaGATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT GGCCAGGTCCTTCAT-------------------------------GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT Template switch alignment (log-probability: -28.2) GGCCAGGTCCTTCATaATAAACTACTGGGTCCTCTTCCCT|TGGgCA|GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT GGCCAGGTCCTTCATGATAAACTACTGGGTCCTCTTCCCT|TGGCCA|GATAAACTACTGGGTCCTCTTCCCTGTGTCCTCCTCCCTT ========== Event 3180 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGTTCTAGGCCCTATAACCTAGAGTCAC-TGTGTAGTGACTCATCGATTTACTTGTCTATTT ↑ 1 3 4 2 Chimp: TGGTTCTAGGCCCTATAACCTGTGTACATGAACACAGTGACTCATCGATTTACTTGTCTAttt Gorilla: TGGTTCTAGGCCCTATAACCTGTGTACATGAACACAGTGACTCATCGATTTACTGGTCTATGT Human: TGGTTCTAGGCCCTATAACCTAGAGTCAC-TGTGTAGTGACTCATCGATTTACTTGTCTATTT Cluster: [ ] Orangutan: TGGTTCTAGGCCCTATAACCTGTGTACATGAACACAGTGACTCATCGATTTACTTGCCTATTT Chimp > Human ------------- chr6:47070654-47070665 Template switch process: F1: L TCACAATTTTCTCTTTTTATTGGTTCTAGGCCCTATAACCTA 1 F3: 4 AGTGACTCATCGATTTACTTGTCTATTTTTTTCTTTGAAG R RF: TCACAATTTTCTCTTTTTATTGGTTCTAGGCCCTATAACCTGTGTACATGAACACAGTGACTCATCGATTTACTTGTCTATTTTTTTCTTTGAAG RR: AGTGTTAAAAGAGAAAAATAACCAAGATCCGGGATATTGGACACATGTACTTGTGTCACTGAGTAGCTAAATGAACAGATAAAAAAAGAAACTTC F2: 3 TGTGTCACTGAG 2 Unidirectional alignment (log-probability: -34.6) ACAATTTTCTCTTTTTATTGGTTCTAGGCCCTATAACctagagtcaCTGTGTA----------GTGACTCATCGATTTACTTGTCTATTTTTTTCTTTGAAG ACAATTTTCTCTTTTTATTGGTTCTAGGCCCTATAAC---------CTGTGTACATGAACACAGTGACTCATCGATTTACTTGTCTATTTTTTTCTTTGAAG Template switch alignment (log-probability: -22.8) ACAATTTTCTCTTTTTATTGGTTCTAGGCCCTATAACCTa|GAGTCACTGTGT|AGTGACTCATCGATTTACTTGTCTATTTTTTTCTTTGAAG ACAATTTTCTCTTTTTATTGGTTCTAGGCCCTATAACCTG|GAGTCACTGTGT|AGTGACTCATCGATTTACTTGTCTATTTTTTTCTTTGAAG ========== Event 3181 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTTGTTACTTAACTTGGAAGATGGACACATCTCTCTCCTTTTCTTTGACC ↑ 1 3 4 2 Chimp: AGTTGTTACTTAACTTGGAAGTCATGTCCATCTCTCTCCTTTTCTTTGACC Gorilla: AGTTGTTACTTAACTTGGAAGTCATGTCCATCTCTCTCCTTTTCTTTGACC ↓ 1 3 4 2 Human: AGTTGTTACTTAACTTGGAAGATGGACACATCTCTCTCCTTTTCTTTGACC Cluster: [ ] Orangutan: AGTTGTTACTTAACTTGGAAGTTATGTCCATCTCTCTCCTTTTCTTTGACC Chimp > Human ------------- chr6:45473430-45473436 Template switch process: F1: L TTAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAG 1 F3: 4 CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA R RF: TTAATATCTAACTGATCATAAGTTGTTACTTAACTTGGAAGTCATGTCCATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA RR: AATTATAGATTGACTAGTATTCAACAATGAATTGAACCTTCAGTACAGGTAGAGAGAGGAAAAGAAACTGGGTGAGACTCTTAATTGT F2: 3 ACAGGTA 2 Unidirectional alignment (log-probability: -37.5) TAATATCTAACTGATaATAAGTTGTTACTTAACTTGGAAG-------atggacaCATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA TAATATCTAACTGATCATAAGTTGTTACTTAACTTGGAAGTCATGTC-------CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA Template switch alignment (log-probability: -22.1) TAATATCTAACTGATaATAAGTTGTTACTTAACTTGGAAG|ATGGACA|CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA TAATATCTAACTGATCATAAGTTGTTACTTAACTTGGAAG|ATGGACA|CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA Gorilla > Human --------------- chr6:45473430-45473436 Template switch process: F1: L TTAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAG 1 F3: 4 CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA R RF: TTAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAGTCATGTCCATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA RR: AATTATAGATTGACTATTATTCAACAATGAATTGAACCTTCAGTACAGGTAGAGAGAGGAAAAGAAACTGGGTGAGACTCTTAATTGT F2: 3 ACAGGTA 2 Unidirectional alignment (log-probability: -31.1) TAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAG-------atggacaCATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA TAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAGTCATGTC-------CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA Template switch alignment (log-probability: -16.6) TAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAG|ATGGACA|CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA TAATATCTAACTGATAATAAGTTGTTACTTAACTTGGAAG|ATGGACA|CATCTCTCTCCTTTTCTTTGACCCACTCTGAGAATTAACA ========== Event 3182 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGTTTTAAAGGCAGAACTTG------ATACATACAATGAAGTGACTACACAAATCC Chimp: GAAGTTTTAAAGGCAGAACTTG------ATACATACAATGAAGTGACTATACAAATCC Gorilla: GAAGTTTTAAAGGCAGAACTTGTATGTATCAAATACAGTGAAGTGACTACACAAATCC ↑ 3 1 4 2 Human: GAAGTTTTAAAGGCAGAACTTG------ATACATACAATGAAGTGACTACACAAATCC Cluster: [ ] Orangutan: GAAGTTTTAAAGGCAGAACTTG------ATACACACAATGAAGTGACTACACAAATCC Human > Gorilla --------------- chr6:168460424-168460433 Template switch process: F1: L ATTGATCCTGGAGAAAACTGAAGTTTTAAAGGCAGAACTTG 1 F3: 4 ATACAGTGAAGTGACTACACAAATCCTACTTTAATTCACTGAACTT R RF: ATTGATCCTGGAGAAAACTGAAGTTTTAAAGGCAGAACTTGATACATACAATGAAGTGACTACACAAATCCTACTTTAATTCACTGAACCT RR: TAACTAGGACCTCTTTTGACTTCAAAATTTCCGTCTTGAACTATGTATGTTACTTCACTGATGTGTTTAGGATGAAATTAAGTGACTTGGA F2: 3 AACTATGTAT 2 Unidirectional alignment (log-probability: -44.9) TTGATCCTGGAGAAAACTGAAGTTTTAAAGGCAGAACTTGtatgtatcaA---ATACAgTGAAGTGACTACACAAATCCTACTTTAATTCACT TTGATCCTGGAGAAAACTGAAGTTTTAAAGGCAGAACTTG---------ATACATACAATGAAGTGACTACACAAATCCTACTTTAATTCACT Template switch alignment (log-probability: -28.2) TTGATCCTGGAGAAAACTGAAGTTTTAAAGGCAGAACTTG|TATGTATCAA|ATACAgTGAAGTGACTACACAAATCCTACTTTAATTCACT TTGATCCTGGAGAAAACTGAAGTTTTAAAGGCAGAACTTG|TATGTATCAA|ATACAATGAAGTGACTACACAAATCCTACTTTAATTCACT ========== Event 3183 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTCTCTAAGAATGAGAGTGA-AAATCAT-CTGTTCAGATAAGTCATGATTTTGTTTTCAAA Chimp: CTTCTCTAAGAATGAGAGTGAAAAATCAT--CGTTCAGATGAGTCATGATTTTGTTTTCAAA Gorilla: CTTCTCTAAGAATGAGAGTGAAAAATCAT--TTTTCAGATGAGTCATGATTTTGTTTTCAAA ↓ 1 4 3 2 Human: CTTCTCTAAGAATGAGAGTGA-AAATCAT-CTGTTCAGATAAGTCATGATTTTGTTTTCAAA Cluster: [ ] Orangutan: CTTCTCTAAGAATGAGAGTGAAAAATCATC-TGTTCAGATGAGTCATTATTTTGTTTTCAAA Gorilla > Human --------------- chr6:122045191-122045197 Template switch process: F1: L AAGGTGTTTAAATTAAATTACTTCTCTAAGAATGAGAGTGAAAA 1 F3: 4 TTCAGATAAGTCATGATTTTGTTTTCAAAATTTTGACGAGAACTTAGA R RF: AAGGTGTTTAAATTAAATTACTTCTCTAAGAATGAGAGTGAAAAATCATTTTTCAGATGAGTCATGATTTTGTTTTCAAAATTTTGACGAGAACTTAGA RR: TTCCACAAATTTAATTTAATGAAGAGATTCTTACTCTCACTTTTTAGTAAAAAGTCTACTCAGTACTAAAACAAAAGTTTTAAAACTGCTCTTGAATCT F2: 3 GTCTACT 2 Unidirectional alignment (log-probability: -33.4) TGTTTAAATTAAATTACTTCTCTAAGAATGAGAGTGAAA-ATCATcTgTTCAGATaAGTCATGATTTTGTTTTCAAAATTTTGACGAG TGTTTAAATTAAATTACTTCTCTAAGAATGAGAGTGAAAAATCAT-TTTTCAGATGAGTCATGATTTTGTTTTCAAAATTTTGACGAG Template switch alignment (log-probability: -22.4) TGTTTAAATTAAATTACTTCTCTAAGAATGAGAGTGAAAA|TCATCTG|TTCAGATaAGTCATGATTTTGTTTTCAAAATTTTGACGAG TGTTTAAATTAAATTACTTCTCTAAGAATGAGAGTGAAAA|TCATCTG|TTCAGATGAGTCATGATTTTGTTTTCAAAATTTTGACGAG ========== Event 3184 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGGGACACAGGATTCTGTCATTGCCCTAGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCGCTC ↓ 1 4 3 2 Chimp: TGGGGACACAGGATTCTGTCAGAGACTGAGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCACTC ↑ 1 4 3 2 Gorilla: TGGGGACACAGGATTCTGTCATTGCCCTAGGGAAATTCAGTCTCTGCTTTTCCCAGGTCCACTC Human: TGGGGACACAGGATTCTGTCATTGCCCTAGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCGCTC Cluster: [ ] Orangutan: TGGGGACACAGGATTCTGTCATTGCCCTAGGGAAACTCAGTCTCTGCTTTTCCCAGATCTACGC Human > Chimp ------------- chr6:4961487-4961493 Template switch process: F1: L AGCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCA 1 F3: 4 AGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCACTCACTG R RF: AGCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCATTGCCCTAGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCGCTCACTG RR: TCGAATTCTCCCTTTTTGGGACCCCTGTGTCCTAAGACAGTAACGGGATCCCTTTGAGTCAGAGACGAAAAGGGTCCAGGCGAGTGAC F2: 3 GTCAGAG 2 Unidirectional alignment (log-probability: -36.7) GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCAgaGaCtgAGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCaCTCACTG GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCATTGCCCTAGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCGCTCACTG Template switch alignment (log-probability: -22.1) GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCA|GAGACTG|AGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCaCTCACTG GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCA|GAGACTG|AGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCGCTCACTG Gorilla > Chimp --------------- chr6:4961487-4961493 Template switch process: F1: L AGCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCA 1 F3: 4 AGGGAAACTCAGTCTCTGCTTTTCCCAGGTCCACTCACTGAGCCATCT R RF: AGCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCATTGCCCTAGGGAAATTCAGTCTCTGCTTTTCCCAGGTCCACTCACTGAGCCATCT RR: TCGAATTCTCCCTTTTTGGGACCCCTGTGTCCTAAGACAGTAACGGGATCCCTTTAAGTCAGAGACGAAAAGGGTCCAGGTGAGTGACTCGGTAGA F2: 3 GTCAGAG 2 Unidirectional alignment (log-probability: -34.5) GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCAgaGaCtgAGGGAAAcTCAGTCTCTGCTTTTCCCAGGTCCACTCACTG GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCATTGCCCTAGGGAAATTCAGTCTCTGCTTTTCCCAGGTCCACTCACTG Template switch alignment (log-probability: -22.3) GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCA|GAGACTG|AGGGAAAcTCAGTCTCTGCTTTTCCCAGGTCCACTCACTG GCTTAAGAGGGAAAAACCCTGGGGACACAGGATTCTGTCA|GAGACTG|AGGGAAATTCAGTCTCTGCTTTTCCCAGGTCCACTCACTG ========== Event 3185 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCTTTCTTTTCTTTTTCAT-------TTATTACTATGTCATTATATTTGCACATTTATGCCTTG ↓ 1 4 3 2 Chimp: TGCCTTTCTTTTCTTTTTCATTATAATGACATTACTATGTCATTATATTTGCACATTTATGCCTTG ↑ 1 4 3 2 Gorilla: TGCCTTTCTTCTCTTTTTCAT-------TTATTACTATGTCATTATATTTTCACATTTATGCCTTG Human: TGCCTTTCTTTTCTTTTTCAT-------TTATTACTATGTCATTATATTTGCACATTTATGCCTTG Cluster: [ ] Orangutan: CGCCTTTCTTTTCTTTTTCAT-------TTATTACTATGTCATTATATTTGCACATTTATGCTTTG Human > Chimp ------------- chr6:124562432-124562439 Template switch process: F1: L CTTTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATT 1 F3: 4 ATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA R RF: CTTTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATTTATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA RR: GAAAGACAGTCAACACGATTACGGAAAGAAAAGAAAAAGTAAATAATGATACAGTAATATAAACGTGTAAATACGGAACCTAT F2: 3 CAGTAATA 2 Unidirectional alignment (log-probability: -27) TTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATTataatgacATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA TTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATT-------TATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA Template switch alignment (log-probability: -16.3) TTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATT|ATAATGAC|ATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA TTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATT|ATAATGAC|ATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA Gorilla > Chimp --------------- chr6:124562432-124562439 Template switch process: F1: L CTTTCTGTCAGTTGTGCTAATGCCTTTCTTTTCTTTTTCATT 1 F3: 4 ATTACTATGTCATTATATTTGCACATTTATGCCTTGGATA R RF: CTTTCTGTCAGTTGTGCTAATGCCTTTCTTCTCTTTTTCATTTATTACTATGTCATTATATTTTCACATTTATGCCTTGGATA RR: GAAAGACAGTCAACACGATTACGGAAAGAAGAGAAAAAGTAAATAATGATACAGTAATATAAAAGTGTAAATACGGAACCTAT F2: 3 CAGTAATA 2 Unidirectional alignment (log-probability: -37.5) TTCTGTCAGTTGTGCTAATGCCTTTCTTtTCTTTTTCATTataatgacATTACTATGTCATTATATTTgCACATTTATGCCTTGGATA TTCTGTCAGTTGTGCTAATGCCTTTCTTCTCTTTTTCATTT-------ATTACTATGTCATTATATTTTCACATTTATGCCTTGGATA Template switch alignment (log-probability: -27.8) TTCTGTCAGTTGTGCTAATGCCTTTCTTtTCTTTTTCATT|ATAATGAC|ATTACTATGTCATTATATTTgCACATTTATGCCTTGGATA TTCTGTCAGTTGTGCTAATGCCTTTCTTCTCTTTTTCATT|ATAATGAC|ATTACTATGTCATTATATTTTCACATTTATGCCTTGGATA ========== Event 3186 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTAAGAATTTACTTTTAAGAGC----TAAAACTAAAGAACAGAGTCTTCAATT ↓ 31 24 Chimp: GTAAGAATTTACTTTTAAGAGG--TTTTAGCTTAAAGAACAGAGTCTTCAATT Gorilla: GTAAGAATTTACTTTTAAGAGGTT--TTAGCTTAAAGAACAGAGTCTTCAATT ↑ 31 24 Human: GTAAGAATTTACTTTTAAGAGC----TAAAACTAAAGAACAGAGTCTTCAATT Cluster: [ ] Orangutan: GTAAGAACTTACTTTTAAGAGC----TAAAAGTAAAGAACAGAGCCTTCAATT Human > Chimp ------------- chr6:50519457-50519465 Template switch process: F1: L TCTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAG 1 F3: 4 TAAAGAACAGAGTCTTCAATTGCATGCTTGCGTCACTTTG R RF: TCTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAGCTAAAACTAAAGAACAGAGTCTTCAATTGCATGGTTGCGTCACTTTG RR: AGATTATACTCCAGGATAATCATTCTTAAATGAAAATTCTCGATTTTGATTTCTTGTCTCAGAAGTTAACGTACCAACGCAGTGAAAC F2: 3 TCGATTTTG 2 Unidirectional alignment (log-probability: -37.5) CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGaggttttAGCT-----TAAAGAACAGAGTCTTCAATTGCATGcTTGCGTCACTTTG CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAG-------AGCTAAAACTAAAGAACAGAGTCTTCAATTGCATGGTTGCGTCACTTTG Template switch alignment (log-probability: -22.4) CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAG|GTTTTAGCT|TAAAGAACAGAGTCTTCAATTGCATGcTTGCGTCACTTTG CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAG|GTTTTAGCT|TAAAGAACAGAGTCTTCAATTGCATGGTTGCGTCACTTTG Human > Gorilla --------------- chr6:51057497-51057505 Template switch process: F1: L TCTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAG 1 F3: 4 TAAAGAACAGAGTCTTCAATTGCATGCTTGCATCACTTTG R RF: TCTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAGCTAAAACTAAAGAACAGAGTCTTCAATTGCATGGTTGCGTCACTTTG RR: AGATTATACTCCAGGATAATCATTCTTAAATGAAAATTCTCGATTTTGATTTCTTGTCTCAGAAGTTAACGTACCAACGCAGTGAAAC F2: 3 TCGATTTTG 2 Unidirectional alignment (log-probability: -42) CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGaggttttAGCT-----TAAAGAACAGAGTCTTCAATTGCATGcTTGCaTCACTTTG CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAG-------AGCTAAAACTAAAGAACAGAGTCTTCAATTGCATGGTTGCGTCACTTTG Template switch alignment (log-probability: -27.9) CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAG|GTTTTAGCT|TAAAGAACAGAGTCTTCAATTGCATGcTTGCaTCACTTTG CTAATATGAGGTCCTATTAGTAAGAATTTACTTTTAAGAG|GTTTTAGCT|TAAAGAACAGAGTCTTCAATTGCATGGTTGCGTCACTTTG ========== Event 3187 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGCTTGTCACTATGTCAGTGC----------------------------------CTCATGCTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGTCAGTAGAgagcagtaggtgagcaggaagggagaacggaaggcctgaggctttgtcctcagttacctcc ↑ 1 4 3 2 Chimp: TGGCTTGTCACTATGTCAGTGA-----------------CATAGTGCTTTCTTTGTGTGAAGGTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGTCAGTAGAgagcagtaggtgagcaggaagggagaacggaaggcctgaggctttgtcctcagttacctcc Gorilla: TGGCTTGTCACTATGTCAGTGACATAGTGCTTTCTTTGT-----------------GTGAAGGTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGTCAGTAGAgagcagtaggtgagcaggaagggagaacggaaggcctgaggctttgtcctcagttacctcc ↓ 1 4 3 2 Human: TGGCTTGTCACTATGTCAGTGC----------------------------------CTCATGCTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGTCAGTAGAgagcagtaggtgagcaggaagggagaacggaaggcctgaggctttgtcctcagttacctcc Cluster: [ ] Orangutan: TGGCTTGTCACTATGTCAGTGC----------------------------------CTCATGCTGGTGCTTTCTTTGTGTGAAGGGAgatgcagtgggtgggtcattagagagcactaggtgagcagg------------aaggcctgaggctttgtccttagttac---- Chimp > Human ------------- chr6:5352443-5352450 Template switch process: F1: L GCCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG 1 F3: 4 TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT R RF: GCCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTGACATAGTGCTTTCTTTGTGTGAAGGTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGTCAGTAGAGAGCAGTAGGTGAGCAGGAAGGGAGAACGGAAGGCCTGAGG RR: CGGGTGAGACGAGTCCACACACCGAACAGTGATACAGTCACTGTATCACGAAAGAAACACACTTCCACCACGAAAGAAACACACTTCCCTCTACGTCACCCACCCAGTCATCTCTCGTCATCCACTCGTCCTTCCCTCTTGCCTTCCGGACTCC F2: 3 CGTACTCC 2 Unidirectional alignment (log-probability: -33.9) CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTGcctcatgc-------------------------TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG--------ACATAGTGCTTTCTTTGTGTGAAGGTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT Template switch alignment (log-probability: -22.3) CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG|CCTCAtGC|TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG|CCTCAGGC|TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT Gorilla > Human --------------- chr6:5352443-5352450 Template switch process: F1: L GCCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG 1 F3: 4 TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT R RF: GCCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTGACATAGTGCTTTCTTTGTGTGAAGGTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGTCAGTAGAGAGCAGTAGGTGAGCAGGAAGGGAGAACGGAAGGCCTGAGG RR: CGGGTGAGACGAGTCCACACACCGAACAGTGATACAGTCACTGTATCACGAAAGAAACACACTTCCACCACGAAAGAAACACACTTCCCTCTACGTCACCCACCCAGTCATCTCTCGTCATCCACTCGTCCTTCCCTCTTGCCTTCCGGACTCC F2: 3 CGTACTCC 2 Unidirectional alignment (log-probability: -33.4) CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGT-------------------------GcctcatgcTGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTGACATAGTGCTTTCTTTGTGTGAAGG--------TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT Template switch alignment (log-probability: -22.3) CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG|CCTCAtGC|TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT CCCACTCTGCTCAGGTGTGTGGCTTGTCACTATGTCAGTG|CCTCAGGC|TGGTGCTTTCTTTGTGTGAAGGGAGATGCAGTGGGTGGGT ========== Event 3188 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TTTTTTCATAAGTAACTATTTTCATCAGTTAGCAACATTAGCTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTGATAACAATAGTTACTTATGAGG ↑ 4 3 2 Chimp: TTTTTTCATAAGTAACTATTT-------------------TCTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTGATAACAATAGTTACTTATGAGG Gorilla: Human: TTTTTTCATAAGTAACTATTTTCATCAGTTAGCAACATTAGCTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTGATAACAATAGTTACTTATGAGG Cluster: [ ] Orangutan: TTTTTTCATAAGTAACTATTTTCATCAGTTAGCAACATTTGCTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTGATAACAATAGTTACTTATGAGG Chimp > Human ------------- chr6:51177389-51177406 Template switch process: F1: L CACCCACACTATCCTACTTCTTTTTTCATAAGTAACTATTTTC 1 F3: 4 CTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTG R RF: CACCCACACTATCCTACTTCTTTTTTCATAAGTAACTATTTTCTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTGAT RR: GTGGGTGTGATAGGATGAAGAAAAAAGTATTCATTGATAAAAGATAACGTTATAGTCAATGTCATTGATTACAACGATTGACTA F2: 3 GATTACAACGATTGACTA 2 Unidirectional alignment (log-probability: -38.3) CCACACTATCCTACTTCTTTTTTCATAAGTAACTATTTTcatcagttagcaacattagCTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTG CCACACTATCCTACTTCTTTTTTCATAAGTAACTATTTT-------------------CTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTG Template switch alignment (log-probability: -17.5) CCACACTATCCTACTTCTTTTTTCATAAGTAACTATTTTC|ATCAGTTAGCAACATTAG|CTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTG CCACACTATCCTACTTCTTTTTTCATAAGTAACTATTTTC|ATCAGTTAGCAACATTAG|CTATTGCAATATCAGTTACAGTAACTAATGTTGCTAACTG ========== Event 3189 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CCCACTGAAGAAATACTTTGCTAAGAGCCCTACTCTTAGCAAATTGCTCAGGGCAGTCTCT ↑ 3 2 1 4 Chimp: CCCACGGAAGAAATACTTTGCTAAGAGCCCTA----CGGTAAATTGCTCAGGGCAGTCTC- Gorilla: Human: CCCACTGAAGAAATACTTTGCTAAGAGCCCTACTCTTAGCAAATTGCTCAGGGCAGTCTCT Cluster: [ ] Orangutan: CCTACTGAAGAAATACTTTGCTAAGAGCCCTA----CGGTGAATTGCTCAGGGCAGTCTTT Chimp > Human ------------- chr6:51195449-51195455 Template switch process: F1: L AATGTATGACCCACTGAAGAAATACTTTGCTAAGAGCCCTAC 1 F3: 4 AAATTGCTCAGGGCAGTCTCTGTGTTTGGGAGCTTCTC R RF: AATGTATGACCCACGGAAGAAATACTTTGCTAAGAGCCCTACGGTAAATTGCTCAGGGCAGTCTCTGTGTTTGGGAGCTTCTC RR: TTACATACTGGGTGCCTTCTTTATGAAACGATTCTCGGGATGCCATTTAACGAGTCCCGTCAGAGACACAAACCCTCGAAGAG F2: 3 CGATTCT 2 Unidirectional alignment (log-probability: -34.7) TGTATGACCCACtGAAGAAATACTTTGCTAAGAGCCCTACtcttaGcAAATTGCTCAGGGCAGTCTCTGTGTTTGGGAGCTTCTC TGTATGACCCACGGAAGAAATACTTTGCTAAGAGCCCTAC----GGTAAATTGCTCAGGGCAGTCTCTGTGTTTGGGAGCTTCTC Template switch alignment (log-probability: -22.1) TGTATGACCCACtGAAGAAATACTTTGCTAAGAGCCCTAC|TCTTAGC|AAATTGCTCAGGGCAGTCTCTGTGTTTGGGAGCTTCTC TGTATGACCCACGGAAGAAATACTTTGCTAAGAGCCCTAC|TCTTAGC|AAATTGCTCAGGGCAGTCTCTGTGTTTGGGAGCTTCTC ========== Event 3190 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC--------------------------------------------------------------------------AGCACTTGTCTTCTCCACTTTAACATA ↑ 3 2 1 4 Chimp: ACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC-------------------------------------CTTATACTCTCAGTCTATTGTGAAAACCCTGTTCCCTAAAAACTGTCTTCTCCACTTTAACATA Gorilla: ACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATCCTTATACTCTCAGTCTATTGTGAAAACCCTGTTCCCT-------------------------------------AAAAATTGTCTTCTCCACTTTAACATA Human: ACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC--------------------------------------------------------------------------AGCACTTGTCTTCTCCACTTTAACATA Cluster: [ ] Orangutan: ACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATCCTTATACTCTCAGTCTATTGTGAAAACCCTGTTCCCT-------------------------------------AAAAATTGTCTTCTCCACTTTAACGTA Chimp > Human ------------- chr6:119270056-119270061 Template switch process: F1: L GAGAACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC 1 F3: 4 TGTCTTCTCCACTTTAACATACTCCTATTACCATTTGATT R RF: GAGAACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATCCTTATACTCTCAGTCTATTGTGAAAACCCTGTTCCCTAAAAACTGTCTTCTCCACTTTAACATACTCCTATTACCATTTGATT RR: CTCTTGAAATTTTTTATCGGGGTTCACGACTTAATGACTAGGAATATGAGAGTCAGATAACACTTTTGGGACAAGGGATTTTTGACAGAAGAGGTGAAATTGTATGAGGATAATGGTAAACTAA F2: 3 TCACGA 2 Unidirectional alignment (log-probability: -29) AGAACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATCagcaCT-----------------------------------------TGTCTTCTCCACTTTAACATACTCCTATTACCATTTGATT AGAACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC----CTTATACTCTCAGTCTATTGTGAAAACCCTGTTCCCTAAAAACTGTCTTCTCCACTTTAACATACTCCTATTACCATTTGATT Template switch alignment (log-probability: -16) AGAACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC|AGCACT|TGTCTTCTCCACTTTAACATACTCCTATTACCATTTGATT AGAACTTTAAAAAATAGCCCCAAGTGCTGAATTACTGATC|AGCACT|TGTCTTCTCCACTTTAACATACTCCTATTACCATTTGATT ========== Event 3191 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TACTTTGAATATGTACATGAACAAAATAGCAGAAAGAAGTACAGGACAAAATCTAGG---------------------------------------------------------------------------------------------------------------------C----ATGTTCAGAATAACATGCCTAGATTTTGTCCTGTACTTCTTTCTGCTATTTTGTTCATGTTATTCTGAACATGCCTCCTATGTATGG Chimp: ---------------------------------------------------------tttttATCCCATTGTGTTGAGAAAGGCAGTCTTTCTTAAGTGGAAAGGCAGACTCGAGTTTACTTTGAATATGTACATGAACAAAATAGCAGAAAGAAGTACAGGACAAAATCCAGGC----ATGTTCAGAATAACATGCCTAGATTTTGTCCTGTACTTCGTTCTGCTATTTTGTTCATGTTATTCTGAACATGCTTCCTATGTATGG Gorilla: TACTTTGAATATGTACATGAACAAAATAGCAGAAAGAAGTACAGGACAAAATCTAGG---------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------ATGTTATTCTGAACATGGCTCCTATGTATGG ↓ 3 4 1 2 Human: TACTTTGAATATGTACATGAACAAAATAGCAGAAAGAAGTACAGGACAAAATCTAGG---------------------------------------------------------------------------------------------------------------------C----ATGTTCAGAATAACATGCCTAGATTTTGTCCTGTACTTCTTTCTGCTATTTTGTTCATGTTATTCTGAACATGCCTCCTATGTATGG Cluster: [ ] Orangutan: TACTTTGAATATGTACATGAACAAAATAGCAGAAAGAAGTATAGGACAAAATCTAGG---------------------------------------------------------------------------------------------------------------------CACAG---------------------------------------------------------GATTATTCTGAACATGCCTCCTATGTATGG Gorilla > Human --------------- chr6:119245670-119245719 Template switch process: F1: L TGAACAAAATAGCAGAAAGAAGTACAGGACAAAATCTAGGCATGTT 1 F3: 4 CATGTTATTCTGAACATGCCTCCTATGTATGGGCAACATGT R RF: TGAACAAAATAGCAGAAAGAAGTACAGGACAAAATCTAGGCATGTTATTCTGAACATGGCTCCTATGTATGGGCAACATGT RR: ACTTGTTTTATCGTCTTTCTTCATGTCCTGTTTTAGATCCGTACAATAAGACTTGTACCGAGGATACATACCCGTTGTACA F2: 3 TTGTTTTATCGTCTTTCTTCATGTCCTGTTTTAGATCCGTACAATAAGAC 2 Unidirectional alignment (log-probability: -96.9) AAATAGCAGAAAGAAGTACAGGACAAAATCTAGGcatgttcagaataacatgcctagattttgtcctgtacttctttctgctattttgttCATGTTATTCTGAACATGcCTCCTATGTATGGGCAACATG AAATAGCAGAAAGAAGTACAGGACAAAATCTAGG--------------------------------------------------------CATGTTATTCTGAACATGGCTCCTATGTATGGGCAACATG Template switch alignment (log-probability: -27.7) AAATAGCAGAAAGAAGTACAGGACAAAATCTAGGCATGTT|CAGAATAACATGCCTAGATTTTGTCCTGTACTTCTTTCTGCTATTTTGTT|CATGTTATTCTGAACATGcCTCCTATGTATGGGCAACATG AAATAGCAGAAAGAAGTACAGGACAAAATCTAGGCATGTT|CAGAATAACATGCCTAGATTTTGTCCTGTACTTCTTTCTGCTATTTTGTT|CATGTTATTCTGAACATGGCTCCTATGTATGGGCAACATG ========== Event 3192 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTT----AGTCCACTTTGGCTCTCTTCTGTGACA Chimp: AATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTT----AGTCCACTTTGGCTCTCTTCTGTGACA ↓ 3 2 1 4 Gorilla: AATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAG-GCTTG--------ATCTTTGGCTCTCTTCTGTGACA ↑ 3 2 1 4 Human: AATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTT----AGTCCACTTTGGCTCTCTTCTGTGACA Cluster: [ ] Orangutan: AGTTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTTAGTC----CACTTTGGCTCTTTTCTGTGACA Human > Gorilla --------------- chr6:120731578-120731583 Template switch process: F1: L TGTCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG 1 F3: 4 CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG R RF: TGTCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTTAGTCCACTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG RR: ACAGTTAATGTAGACCCGTCCTCTAGTTCGTGGACAGAATCCTGAAATCAGGTGAAACCGAGAGAAGACACTGTTTATCACTAAAAGAACGTC F2: 3 TAGTTC 2 Unidirectional alignment (log-probability: -29.8) TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG-----------cttgatCTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTTAGTCCA------CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG Template switch alignment (log-probability: -16.5) TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG|CTTGAT|CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG|CTTGAT|CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG Chimp > Gorilla --------------- chr6:120731578-120731583 Template switch process: F1: L TGTCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG 1 F3: 4 CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG R RF: TGTCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTTAGTCCACTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG RR: ACAGTTAATGTAGACCCGTCCTCTAGTTCGTGGACAGAATCCTGAAATCAGGTGAAACCGAGAGAAGACACTGTTTATCACTAAAAGAACGTC F2: 3 TAGTTC 2 Unidirectional alignment (log-probability: -29.8) TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG-----------cttgatCTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGGACTTTAGTCCA------CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG Template switch alignment (log-probability: -16.5) TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG|CTTGAT|CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG TCAATTACATCTGGGCAGGAGATCAAGCACCTGTCTTAGG|CTTGAT|CTTTGGCTCTCTTCTGTGACAAATAGTGATTTTCTTGCAG ========== Event 3193 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cagtttttgatctgatcagcggatttttgatc--aaatccactgatgcagaactcaggaata Chimp: cagttTTTGATCTGATCAGTGGATTTTTGATC--AAATCCACTGATGCAGAACTCAGGAATA ↑ 3 1 2 4 Gorilla: ctgttTTTGATCTGATCAGTGGAT--TTGATCAAAAATCCGCTGATGCAGAACTCAGGAATA Human: cagtttttgatctgatcagcggatttttgatc--aaatccactgatgcagaactcaggaata Cluster: [ ] Orangutan: cagt-----------------------tggtc--agatccactgatgcagaactcaggaata Gorilla > Chimp --------------- chr6:123082343-123082355 Template switch process: F1: L CACATATTTTTGATCTGCAGTTTTTGATCTGATCAGTGGATTT 1 F3: 4 CTGATGCAGAACTCAGGAATATGGAGGACCTTTGTGACTC R RF: CACATATTTTTGATCTGCTGTTTTTGATCTGATCAGTGGATTTGATCAAAAATCCGCTGATGCAGAACTCAGGAATATGGAGGACCTTTGTGACTC RR: GTGTATAAAAACTAGACGACAAAAACTAGACTAGTCACCTAAACTAGTTTTTAGGCGACTACGTCTTGAGTCCTTATACCTCCTGGAAACACTGAG F2: 3 ACCTAAACTAGTT 2 Unidirectional alignment (log-probability: -34.8) ATATTTTTGATCTGCaGTTTTTGATCTGATCAGTGGAttTTTGATC--AAATCCaCTGATGCAGAACTCAGGAATATGGAGGACCTTTGTGACTC ATATTTTTGATCTGCTGTTTTTGATCTGATCAGTGGA--TTTGATCAAAAATCCGCTGATGCAGAACTCAGGAATATGGAGGACCTTTGTGACTC Template switch alignment (log-probability: -23) ATATTTTTGATCTGCaGTTTTTGATCTGATCAGTGGATTT|TTGATCAAATCCA|CTGATGCAGAACTCAGGAATATGGAGGACCTTTGTGACTC ATATTTTTGATCTGCTGTTTTTGATCTGATCAGTGGATTT|TTGATCAAATCCA|CTGATGCAGAACTCAGGAATATGGAGGACCTTTGTGACTC ========== Event 3194 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTGTCCTTAGGGTAGAGGAA--------------------GAAAAGGCCTGGTGGATTAACAGGTAGCCATTCCTTTACTGAAGGGATATATTCTCTC---------------- Chimp: TTTTGTCCTTAGGGTAGAGGAA--------------------GAAAGGGCCTGGTGGATTAACAGGTAGCCATTCCTTTGCTGAAGGGATATATTCTCTC---------------- Gorilla: TTTTGTCCTTAGGGTAGAGGAC----------------------------------------AAGGAATATATCCCTTTACTGAAGGGATATATTCTCTC---------------- ↑ 1 4 3 2 Human: TTTTGTCCTTAGGGTAGAGGAA--------------------GAAAAGGCCTGGTGGATTAACAGGTAGCCATTCCTTTACTGAAGGGATATATTCTCTC---------------- Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--------------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr6:120991512-120991520 Template switch process: F1: L AAAGTTCCTTTCCAAAATCATTTTGTCCTTAGGGTAGAGGACAAG 1 F3: 4 CCTTTACTGAAGGGATATATTCTCTCAGACACTCATTCTG R RF: AAAGTTCCTTTCCAAAATCATTTTGTCCTTAGGGTAGAGG--AAGAAAAGGCCTGGTGGATTAACAGGTAGCCATTCCTTTACTGAAGGGATATATTCTCTCAGACACTCATTCTG RR: TTTCAAGGAAAGGTTTTAGTAAAACAGGAATCCCATCTCC--TTCTTTTCCGGACCACCTAATTGTCCATCGGTAAGGAAATGACTTCCCTATATAAGAGAGTCTGTGAGTAAGAC F2: 3 CTATATAAG 2 Unidirectional alignment (log-probability: -40.6) TCCTTTCCAAAATCATTTTGTCCTTAGGGTAGAGGA-----------------------------CaaggaatatATcCCTTTACTGAAGGGATATATTCTCTCAGACACTCATTCTG TCCTTTCCAAAATCATTTTGTCCTTAGGGTAGAGGAAGAAAAGGCCTGGTGGATTAACAGGTAGCC---------ATTCCTTTACTGAAGGGATATATTCTCTCAGACACTCATTCTG Template switch alignment (log-probability: -29.6) TCCTTTCCAAAATCATTTTGTCCTTAGGGTAGAGGacAAG|GAATATATC|CCTTTACTGAAGGGATATATTCTCTCAGACACTCATTCTG TCCTTTCCAAAATCATTTTGTCCTTAGGGTAGAGG--AAG|GAATATATC|CCTTTACTGAAGGGATATATTCTCTCAGACACTCATTCTG ========== Event 3195 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGGTCATTCCATAAAGCAGTCCAAACTCGGAAGACTGGGAAAATACAAT ↓ 3 1 2 4 Chimp: TCATGGTCATTCCATAAAGCAGTTTGGACTGGGAAGACTGGGAAAATACAAT Gorilla: TCATGGTCATTCCATAAAGCATTCCAAACTCAGAAGACTGGGAAAATACAAT Human: TCATGGTCATTCCATAAAGCAGTCCAAACTCGGAAGACTGGGAAAATACAAT Cluster: [ ] Orangutan: TCATGGTCATTCCATAAAGCATTCCAAACTCAGAAGACTGGGAAAATACAAT Human > Chimp ------------- chr6:51361753-51361760 Template switch process: F1: L GAATAGCTTGGTCTTCAATCATGGTCATTCCATAAAGCAGT 1 F3: 4 GGAAGACTGGGAAAATACAATTAATATACATTTGATACCT R RF: GAATAGCTTGGTCTTCAATCATGGTCATTCCATAAAGCAGTCCAAACTCGGAAGACTGGGAAAATACAATTAATATACTTTTGATACCT RR: CTTATCGAACCAGAAGTTAGTACCAGTAAGGTATTTCGTCAGGTTTGAGCCTTCTGACCCTTTTATGTTAATTATATGAAAACTATGGA F2: 3 GTCAGGTT 2 Unidirectional alignment (log-probability: -36.7) AATAGCTTGGTCTTCAATCATGGTCATTCCATAAAGCAGTttggACTgGGAAGACTGGGAAAATACAATTAATATACaTTTGATACCT AATAGCTTGGTCTTCAATCATGGTCATTCCATAAAGCAGTCCAAACTCGGAAGACTGGGAAAATACAATTAATATACTTTTGATACCT Template switch alignment (log-probability: -22.3) AATAGCTTGGTCTTCAATCATGGTCATTCCATAAAGCAGT|TTGGACTG|GGAAGACTGGGAAAATACAATTAATATACaTTTGATACCT AATAGCTTGGTCTTCAATCATGGTCATTCCATAAAGCAGT|TTGGACTG|GGAAGACTGGGAAAATACAATTAATATACTTTTGATACCT ========== Event 3196 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GCTCATTCTCACTCAAATTATAGATTCAATATTATTTATGGAATTTATAGCCACTTAAAAATAGAGAAGTAAAAAATGAAGTAGACTAAAGTAAAATTAGTATTAAGAGCTTTAACGGAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGATTGAATCTATTTCATTATTCTTTGACTCAA-- ↑ 3 2 41 Chimp: GCTCATTCTCACTCAAATTATAGATTCAAT---ATTTATGGAATTTATAGCCACTTAAAAATAGAGAAGTAAAAAATGAAGTAGACTAAAGTAAAATTAGT-GTAAGAGCTTTAACGGAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGA----------TTCATTATTCTTTGACTCAA-- Gorilla: GCTCACTCTCACTCAAATTATAGATTCAATATTATTTATGGAATTTATAGCCACTTAAAAATAGAGAAGTAAAAAATGAAGTAGACTAAAGTAAAATTACTGTTAAGAGCTTTAACGGAAGTATTATTTCTAGAGTTTC-TTTTCTTTTTGCTGATTGAATCTATTTCATTATTCTTTGACTCAA-- Human: GCTCATTCTCACTCAAATTATAGATTCAATATTATTTATGGAATTTATAGCCACTTAAAAATAGAGAAGTAAAAAATGAAGTAGACTAAAGTAAAATTAGTATTAAGAGCTTTAACGGAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGATTGAATCTATTTCATTATTCTTTGACTCAA-- Cluster: [ ] Orangutan: GCTCATTCTCACTCAAATTATAGATTCAAT---ATTTATGGAATTTATAGCCACTTAAAAATAGAGAAGTAAAAAATGAAGTAGACTAAAGTAAAATTAGT-CTAAGAGCTTTAACGGAAGT---ATTTCTAGAGTTTCTTTTTCTTTTTGCTGATTGAATCTATTTCATTATTCTTTGACTCAAAG Chimp > Human ------------- chr6:54161298-54161305 Template switch process: F1: L ACGGAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGATT 1 F3: 4 TTCATTATTCTTTGACTCAAAGGGAAATAAAACTGGATAT R RF: ATAGATTCAATATTTATGGAATTTATAGCCACTTAAAAATAGAGAAGTAAAAAATGAAGTAGACTAAAGTAAAATTAGTGTAAGAGCTTTAACGGAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGATTCATTATTCTTTGACTCAAAGGGAAATAAAACTGGATAT RR: TATCTAAGTTATAAATACCTTAAATATCGGTGAATTTTTATCTCTTCATTTTTTACTTCATCTGATTTCATTTTAATCACATTCTCGAAATTGCCTTCATAATAAAGATCTCAAAGAAAAAGAAAAACGACTAAGTAATAAGAAACTGAGTTTCCCTTTATTTTGACCTATA F2: 3 TATCTAAG 2 Unidirectional alignment (log-probability: -25.3) GAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGAttgaatctatTTCATTATTCTTTGACTCAAAGGGAAATAAAACTGGATAT GAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGA----------TTCATTATTCTTTGACTCAAAGGGAAATAAAACTGGATAT Template switch alignment (log-probability: -16.3) GAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGATT|GAATCTAT|TTCATTATTCTTTGACTCAAAGGGAAATAAAACTGGATAT GAAGTATTATTTCTAGAGTTTCTTTTTCTTTTTGCTGATT|GAATCTAT|TTCATTATTCTTTGACTCAAAGGGAAATAAAACTGGATAT ========== Event 3197 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AATATTTGATACATGAATGAAGA-----------GGAGACTTTAAGACTTTCAAAAGGATAAGAACCAGAggctaggcatggtggctcatacctgtaatcccggcactttgggaggccaaagcaagtggatcacttgaggccaggagttcgagaccagcctgggcaacatggtgaaacctcaccattattaa Chimp: AATATTTGATACATGAATGAAGA-----------GGAGACTTTAAGACTTTCAAAAGGATAAGAACCAGAggctaggcatggtggttcatacctgtaatcccggcactttgggaggccaaagcaagtggatcacttgaggccaggagttcgagaccagcctgggcaacatggtgaaacctcaccactattaa Gorilla: AATATTTGATACATGAATGAACC----------------------ATGTATCAAAAGGATAAGAACCAGAggctaggcatggtggctcatacctgtaatcctggcactttgggaggccaaagcaagtggatcacttgaggccaggagttcgagaccagcctgggcaacatgatgaaacctcatcactattaa ↑ 1 4 3 2 Human: AATATTTGATACATGAATGAAGA-----------GGAGACTTTAAGACTTTCAAAAGGATAAGAACCAGAggctaggcatggtggctcatacctgtaatcccggcactttgggaggccaaagcaagtggatcacttgaggccaggagttcgagaccagcctgggcaacatggtgaaacctcaccattattaa Cluster: [ ] Orangutan: AATATTTGATACATGAATGAAGAGGAGACTTTAA-----------GACTTTCAAAAGGATAAGAACCAGAggcgaggcatggtggctcatacctgtaatcccagcactttgggaggccaaagcaagtggatcacttgaggccaggagttcgagaccagcctgggcaacatggtgaaacctcatcactattaa Human > Gorilla --------------- chr6:118639450-118639454 Template switch process: F1: L TCTGGTCAAATATTTTATCAAATATTTGATACATGAATGAA 1 F3: 4 TATCAAAAGGATAAGAACCAGAGGCTAGGCATGGTGGCTCAT R RF: TCTGGTCAAATATTTCATCAAATATTTGATACATGAATGAAGAGGAGACTTTAAGACTTTCAAAAGGATAAGAACCAGAGGCTAGGCATGGTGGCTCATACCTGTAATCCCGGCACTTTGGGAGGCCAAAGCAAGTGGATCACTTGAGGCCAGGAGTTCGAGACCAGCCTGGGCAACATGG RR: AGACCAGTTTATAAAGTAGTTTATAAACTATGTACTTACTTCTCCTCTGAAATTCTGAAAGTTTTCCTATTCTTGGTCTCCGATCCGTACCACCGAGTATGGACATTAGGGCCGTGAAACCCTCCGGTTTCGTTCACCTAGTGAACTCCGGTCCTCAAGCTCTGGTCGGACCCGTTGTACC F2: 3 GTACC 2 Unidirectional alignment (log-probability: -37.1) CTGGTCAAATATTTtATCAAATATTTGATACATGAATGAA------------------ccatgtaTCAAAAGGATAAGAACCAGAGGCTAGGCATGGTGGCTC CTGGTCAAATATTTCATCAAATATTTGATACATGAATGAAGAGGAGACTTTAAGACTT-------TCAAAAGGATAAGAACCAGAGGCTAGGCATGGTGGCTC Template switch alignment (log-probability: -27.4) CTGGTCAAATATTTtATCAAATATTTGATACATGAATGAA|CCATG|TaTCAAAAGGATAAGAACCAGAGGCTAGGCATGGTGGCTC CTGGTCAAATATTTCATCAAATATTTGATACATGAATGAA|CCATG|TTTCAAAAGGATAAGAACCAGAGGCTAGGCATGGTGGCTC ========== Event 3198 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: gtcattataagaagtgatgatgctatgggcatggatgggatctccttggggaagat--tatagcagtactttagtagagaatctacagct Chimp: GTCAATATAAGAAGTGATGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGATTCTATAATCTTACATTAGTAGAGAATCTACAGCT ↓ 3 2 1 4 Gorilla: GTCACTATAAGAAGTGATGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGAT--TATAGCATTACTTTAGTAGAGAATCTACAGCT Human: gtcattataagaagtgatgatgctatgggcatggatgggatctccttggggaagat--tatagcagtactttagtagagaatctacagct Cluster: [ ] Orangutan: gtcaatataagaagtgacgatgctatggccatggatgggatctccttggggaagat--tatagcattactttagtagagaatctatagct Chimp > Gorilla --------------- chr6:116879381-116879387 Template switch process: F1: L GATGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGATT 1 F3: 4 TACTTTAGTAGAGAATCTACAGCTGAGTCTTGAAACACAAATAT R RF: GATGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGATTCTATAATCTTACATTAGTAGAGAATCTACAGCTGAGTCTTGAAACACAAATAT RR: CTACTACGATACCGGTACCTACCCTAGAGGAACCCCTTCTAAGATATTAGAATGTAATCATCTCTTAGATGTCGACTCAGAACTTTGTGTTTATA F2: 3 TACGATA 2 Unidirectional alignment (log-probability: -33.2) TGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGAT--TATAgcaTTACtTTAGTAGAGAATCTACAGCTGAGTCTTGAAACACAA TGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGATTCTATAATCTTACATTAGTAGAGAATCTACAGCTGAGTCTTGAAACACAA Template switch alignment (log-probability: -22.3) TGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGATT|ATAGCAT|TACtTTAGTAGAGAATCTACAGCTGAGTCTTGAAACACAA TGATGCTATGGCCATGGATGGGATCTCCTTGGGGAAGATT|ATAGCAT|TACATTAGTAGAGAATCTACAGCTGAGTCTTGAAACACAA ========== Event 3199 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tgcaaaacactttcaGTGCAAT---GGTGAGAAA-----------GCTCCTCCTATCTCTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCCACA Chimp: TGCAAAACACTTTCAGTGCAAT---GGTGAGAAA-----------GCTCCTCCTATCTCTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCCACA ↓ 1 4 3 2 Gorilla: TGCAAAACACTTTCAGTGCAAA------CTGAAA----------------------GTTTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCCACA Human: tgcaaaacactttcaGTGCAAT---GGTGAGAAA-----------GCTCCTCCTATCTCTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCCACA Cluster: [ ] Orangutan: TGCAAAACACTCTCAGTGCAATGGT---GAGAAAGCTCCTCCTAT-----------CTCTTGCTTTTTCTTACTTTCAGTTCTCCACGTGAACAGCCACA Chimp > Gorilla --------------- chr6:57495791-57495798 Template switch process: F1: L TTATTTGGGGCTTTTCAGTTTGCAAAACACTTTCAGTGCAA 1 F3: 4 TTTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCCAC R RF: TTATTTGGGGCTTTTCAGTTTGCAAAACACTTTCAGTGCAATGGTGAGAAAGCTCCTCCTATCTCTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCCAC RR: AATAAACCCCGAAAAGTCAAACGTTTTGTGAAAGTCACGTTACCACTCTTTCGAGGAGGATAGAGAACGAAAAAGAATGAAAGTCAAGAGGTGTACTTGTCGGTG F2: 3 GAAAGTCA 2 Unidirectional alignment (log-probability: -34.8) TATTTGGGGCTTTTCAGTTTGCAAAACACTTTCAGTGCAAactgaaagtT-----------------------TTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCC TATTTGGGGCTTTTCAGTTTGCAAAACACTTTCAGTGCAA---------TGGTGAGAAAGCTCCTCCTATCTCTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCC Template switch alignment (log-probability: -22.3) TATTTGGGGCTTTTCAGTTTGCAAAACACTTTCAGTGCAA|ACTGAAAG|TtTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCC TATTTGGGGCTTTTCAGTTTGCAAAACACTTTCAGTGCAA|ACTGAAAG|TCTTGCTTTTTCTTACTTTCAGTTCTCCACATGAACAGCC ========== Event 3200 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTCCCACAATGAATAGGTACCTTTCAAAAGA--------------------------GTATCCAGAAAGGTACTTTGGATATGTAACATA Chimp: TATTCCCACAACGAACAGGTAACTTTCAAAAGA--------------------------GTCTCCAGAAAGGTACTTTGGATATGTAACATA Gorilla: TATTCCCACAATGAATAGGTAACTTTCAAGAGAGTACCTTTCTGGATACTCTTTTGAAAGTATCCAGAAAGGTACTTTGGATATGTAACATA ↑ 3 4 1 2 Human: TATTCCCACAATGAATAGGTACCTTTCAAAAGA--------------------------GTATCCAGAAAGGTACTTTGGATATGTAACATA Cluster: [ ] Orangutan: TATTCCCACGATGAATAGGTAACTTTCAAAAGA--------------------------GTATCCAGAAAGGTACTTTGGATATGTAACATA Human > Gorilla --------------- chr6:57844687-57844708 Template switch process: F1: L AAAGACATTTTTAAAATTTCTATTCCCACAATGAATAGGTAACTTTCAAGAGAGTA 1 F3: 4 AGTATCCAGAAAGGTACTTTGGATATGTAACATACAACCCA R RF: AAAGACATTTTTAAAATTTCTATTCCCACAATGAATAGGTACCTTTCAAAAGAGTATCCAGAAAGGTACTTTGGATATGTAACATACAACCCA RR: TTTCTGTAAAAATTTTAAAGATAAGGGTGTTACTTATCCATGGAAAGTTTTCTCATAGGTCTTTCCATGAAACCTATACATTGTATGTTGGGT F2: 3 AAGTTTTCTCATAGGTCTTTCC 2 Unidirectional alignment (log-probability: -59.5) TTTCTATTCCCACAATGAATAGGTAaCTTTCAAgAGagtacctttctggatactcttttgaaAGTATCCAGAAAGGTACTTTGGATATGTAACATACAACCC TTTCTATTCCCACAATGAATAGGTACCTTTCAAAAG--------------------------AGTATCCAGAAAGGTACTTTGGATATGTAACATACAACCC Template switch alignment (log-probability: -29.9) TTTCTATTCCCACAATGAATAGGTAaCTTTCAAgAGAGTA|CCTTTCTGGATACTCTTTTGAA|AGTATCCAGAAAGGTACTTTGGATATGTAACATACAACCC TTTCTATTCCCACAATGAATAGGTACCTTTCAAAAGAGTA|CCTTTCTGGATACTCTTTTGAA|AGTATCCAGAAAGGTACTTTGGATATGTAACATACAACCC ========== Event 3201 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGAGCTGGGTTGACCTTGCCCTGATCTAGAGATcagggtttctcagccttagcact ↑ 1 3 4 2 Chimp: ATGAGCTGGGTTGACCTTGCCACATATTCTAGATcagggtttctcagccttagcact Gorilla: ATGAGCTGGGTTGACCTTGCCACATATTCT-AATcagggtttctcagccttagcact Human: ATGAGCTGGGTTGACCTTGCCCTGATCTAGAGATcagggtttctcagccttagcact Cluster: [ ] Orangutan: ATGAGCTGGGTTGACCTTGCCACATATTCTAGATcagggtttctcagccttagcact Chimp > Human ------------- chr6:56290215-56290223 Template switch process: F1: L ATTAGCAAACAGATAAAGAGATGAGCTGGGTTGACCTTGCC 1 F3: 4 AGATCAGGGTTTCTCAGCCTTAGCACTATTGATATTGTGG R RF: ATTAGCAAACAGATAAAGAGATGAGCTGGGTTGACCTTGCCACATATTCTAGATCAGGGTTTCTCAGCCTTAGCACTATTGATATTTTGG RR: TAATCGTTTGTCTATTTCTCTACTCGACCCAACTGGAACGGTGTATAAGATCTAGTCCCAAAGAGTCGGAATCGTGATAACTATAAAACC F2: 3 GATCTAGTC 2 Unidirectional alignment (log-probability: -37.6) TTAGCAAACAGATAAAGAGATGAGCTGGGTTGACCTTGCC-------CTgatctagAGATCAGGGTTTCTCAGCCTTAGCACTATTGATATTgTGG TTAGCAAACAGATAAAGAGATGAGCTGGGTTGACCTTGCCACATATTCT-------AGATCAGGGTTTCTCAGCCTTAGCACTATTGATATTTTGG Template switch alignment (log-probability: -22.4) TTAGCAAACAGATAAAGAGATGAGCTGGGTTGACCTTGCC|CTGATCTAG|AGATCAGGGTTTCTCAGCCTTAGCACTATTGATATTgTGG TTAGCAAACAGATAAAGAGATGAGCTGGGTTGACCTTGCC|CTGATCTAG|AGATCAGGGTTTCTCAGCCTTAGCACTATTGATATTTTGG ========== Event 3202 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: CTTGTATAAAAACACTTTATT------GATTGTGACCAAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAACATTGT ↓ 1 4 3 2 Chimp: CTTGTATAAAAACACTTTATTGTACTTTATAAAGTACAAGGCAATTGTACTTTATAAAATAGGGAAATAA-AAAACATTGT Gorilla: Human: CTTGTATAAAAACACTTTATT------GATTGTGACCAAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAACATTGT Cluster: [ ] Orangutan: CTTGTATAAAAACACTTTATT------GATTGTGACCAAGGCAATTGTACTTTATAGAATAGGGAAATAT-TAAACATTGT Human > Chimp ------------- chr6:59219521-59219535 Template switch process: F1: L TGGTATGTGGCAGACATGTTCTTGTATAAAAACACTTTATTG 1 F3: 4 AAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAC R RF: TGGTATGTGGCAGACATGTTCTTGTATAAAAACACTTTATTGATTGTGACCAAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAA RR: ACCATACACCGTCTGTACAAGAACATATTTTTGTGAAATAACTAACACTGGTTCCGTTAACATGAAATATTTTATCCCTTTATTTTTTT F2: 3 CATGAAATATTTCAT 2 Unidirectional alignment (log-probability: -50.5) GTATGTGGCAGACATGTTCTTGTATAAAAACACTTTATTGtactttataaagtA-------CAAGGCAATTGTACTTTATAAAATAGGGAAAT-AAAAAAC GTATGTGGCAGACATGTTCTTGTATAAAAACACTTTATTG-------------ATTGTGACCAAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAAC Template switch alignment (log-probability: -29.1) GTATGTGGCAGACATGTTCTTGTATAAAAACACTTTATTG|TAcTTTATAAAGTAC|AAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAc GTATGTGGCAGACATGTTCTTGTATAAAAACACTTTATTG|TATTTTATAAAGTAC|AAGGCAATTGTACTTTATAAAATAGGGAAATAAAAAAA ========== Event 3203 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: AGACAGTTCTTAATTTTATTCACATGGATAAGTGATAAACCAAATGCCTTTATTTAAACATTATCC----------AAATCTAGCATCAGATTGCATAACAGAGACAGCCTTATCCCATGTGGCTGAAAGGAGAGTGGCTT ↑ 1 4 3 2 Chimp: AGACAGTTCTTAATTTTATTCTCATGAATAAGTGATAAACCAAATGCCTTTATTTA----------AACATTATCCAAATCTAGCATCAGATTGTATAACAGAGACAGCCTTATCCCATGTGGCTGAAAGGAGAGTGGCTT Gorilla: Human: AGACAGTTCTTAATTTTATTCACATGGATAAGTGATAAACCAAATGCCTTTATTTAAACATTATCC----------AAATCTAGCATCAGATTGCATAACAGAGACAGCCTTATCCCATGTGGCTGAAAGGAGAGTGGCTT Cluster: [ ] Orangutan: Chimp > Human ------------- chr6:112531122-112531127 Template switch process: F1: L TAAAGTTCTTTTATCTATTAAGACAGTTCTTAATTTTATTC 1 F3: 4 ATAAGTGATAAACCAAATGCCTTTATTTAAACATTATCC R RF: TAAAGTTCTTTTATCTATTAAGACAGTTCTTAATTTTATTCTCATGAATAAGTGATAAACCAAATGCCTTTATTTAAACATTATCCAAATCTAGCATCAGATTGTATAACAGAGACAGCCTTATCCCATGT RR: ATTTCAAGAAAATAGATAATTCTGTCAAGAATTAAAATAAGAGTACTTATTCACTATTTGGTTTACGGAAATAAATTTGTAATAGGTTTAGATCGTAGTCTAACATATTGTCTCTGTCGGAATAGGGTACA F2: 3 GGTACA 2 Unidirectional alignment (log-probability: -32.8) AAAGTTCTTTTATCTATTAAGACAGTTCTTAATTTTATTCaCATGgATAAGTGATAAACCAAATGCCTTTATTTAAacattatcc AAAGTTCTTTTATCTATTAAGACAGTTCTTAATTTTATTCTCATGAATAAGTGATAAACCAAATGCCTTTATTTAA--------- Template switch alignment (log-probability: -16) AAAGTTCTTTTATCTATTAAGACAGTTCTTAATTTTATTC|ACATGG|ATAAGTGATAAACCAAATGCCTTTATTTAAACATTATCC AAAGTTCTTTTATCTATTAAGACAGTTCTTAATTTTATTC|ACATGG|ATAAGTGATAAACCAAATGCCTTTATTTAAACATTATCC ========== Event 3204 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: gggctttgtaaggccacaataaagggttcatttttCCTGCGTTTGAACCCTTTATCATGGCCTACAAAGCACTAT ↑ 3 2 4 Chimp: gggctttgtaaggccacaataaagggttcatttttCCTGCTT-----------TTCATGGCCTACAAAGCACTAT ↓ 3 2 4 Gorilla: gggctttgtaaggccacaataaagggttcatttttCCTGCTTTTGAACCCTTTATCATGGCCTACAAAGCACTAT Human: gggctttgtaaggccacaataaagggttcatttttCCTGCGTTTGAACCCTTTATCATGGCCTACAAAGCACTAT Cluster: [ ] Orangutan: gggctttgtaaggccacaataaagggttgatttttcctGCTTTTGAACCCTTTATCATGGCCTACAAAGCACTAT Chimp > Human ------------- chr6:61995101-61995110 Template switch process: F1: L AGGGCTTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCGTTT 1 F3: 4 TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG R RF: AGGGCTTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTTCATGGCCTACAAAGCACTATATTATGTATAATATATAGG RR: TCCCGAAACATTCCGGTGTTATTTCCCAAGTAAAAAGGACGAAAAGTACCGGATGTTTCGTGATATAATACATATTATATATCC F2: 3 ATTTCCCAAG 2 Unidirectional alignment (log-probability: -32.8) TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCgtttgaaccctTTaTCATGGCCTACAAAGCACTATATTATGTATAATATATAGG TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGC-----------TTTTCATGGCCTACAAAGCACTATATTATGTATAATATATAGG Template switch alignment (log-probability: -22.6) TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCgTTT|GAACCCTTTA|TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTT|GAACCCTTTA|TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG Chimp > Gorilla --------------- chr6:63676104-63676113 Template switch process: F1: L GGCTTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTT 1 F3: 4 TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG R RF: GGCTTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTTCATGGCCTACAAAGCACTATATTATGTATAATATATAGG RR: CCGAAACATTCCGGTGTTATTTCCCAAGTAAAAAGGACGAAAAGTACCGGATGTTTCGTGATATAATACATATTATATATCC F2: 3 ATTTCCCAAG 2 Unidirectional alignment (log-probability: -26.7) TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTtgaaccctttaTCATGGCCTACAAAGCACTATATTATGTATAATATATAGG TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTT-----------TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG Template switch alignment (log-probability: -17.1) TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTT|GAACCCTTTA|TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG TTTGTAAGGCCACAATAAAGGGTTCATTTTTCCTGCTTTT|GAACCCTTTA|TCATGGCCTACAAAGCACTATATTATGTATAATATATAGG ========== Event 3205 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGATACAGCTCACCAGTGAAATCATCCTGACCAA--CAGGATGGTTTCTCCAACAGGAAATATCACT Chimp: AGATACAGCTCACCAGTGAAATCATCCTGACCAA--CAGGATGGTTTCTCCAACAGGAAATATCACT Gorilla: AGATGCAGCTCACCAGTGAAATCATCCTGACCAATGCCCCATGTTCTCTCCAACAGGAAATATCACT ↓ 3 2 1 4 Human: AGATACAGCTCACCAGTGAAATCATCCTGACCAA--CAGGATGGTTTCTCCAACAGGAAATATCACT Cluster: [ ] Orangutan: AGATACAGCTCACCAGTGAAATTATCCTGACCAATGCCCCATGTTCTCTCCAACAGGAAATATCACT Gorilla > Human --------------- chr6:109214471-109214480 Template switch process: F1: L GTGCACGAGATACAGCTCACCAGTGAAATCATCCTGACCAA 1 F3: 4 TCTCCAACAGGAAATATCACTACCTCAGAAGTATTCAGAT R RF: GTGCACGAGATGCAGCTCACCAGTGAAATCATCCTGACCAATGCCCCATGTTCTCTCCAACAGGAAATATCACTACCTCAGAAGTATTCAGAT RR: CACGTGCTCTACGTCGAGTGGTCACTTTAGTAGGACTGGTTACGGGGTACAAGAGAGGTTGTCCTTTATAGTGATGGAGTCTTCATAAGTCTA F2: 3 TTGGTAGGAC 2 Unidirectional alignment (log-probability: -39.7) TGCACGAGATaCAGCTCACCAGTGAAATCATCCTGACCAA-----------CaggatggttTCTCCAACAGGAAATATCACTACCTCAGAAGTATTCAGAT TGCACGAGATGCAGCTCACCAGTGAAATCATCCTGACCAATGCCCCATGTTC---------TCTCCAACAGGAAATATCACTACCTCAGAAGTATTCAGAT Template switch alignment (log-probability: -28) TGCACGAGATaCAGCTCACCAGTGAAATCATCCTGACCAA|CAGGATGgTT|TCTCCAACAGGAAATATCACTACCTCAGAAGTATTCAGAT TGCACGAGATGCAGCTCACCAGTGAAATCATCCTGACCAA|CAGGATGATT|TCTCCAACAGGAAATATCACTACCTCAGAAGTATTCAGAT ========== Event 3206 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TAGCTTACCTGGACAAGTCACAGTATATGAGAACATTTTAGTTAAAATTTATGGTTGTCTTACTATGTTAGATATTACACTACGTCCTATACTCAGTGCTGTACTTCTTATACCCTCGTTGGGCA Chimp: TAGCTTACCTGGACAAGTCACT-AAAATGAGAACATTTTAGTTAAAATTTATGGTTGTCTTACTATGTTAGATATTACACTACATCCTATACTCAGTGCTGTACTTCTTATACCCTCGTCGGGCA ↓ 1 4 3 2 Gorilla: TAGCTTACCTGGACAAGTCACAGTACATGAGAACATTTTAGTTGAAATTTATGGTTGTCTTACTATGTTAGATATTACACTATGTCCTATACTCAGTGCTGTACTTCTTATACCCTCATTGGGCA Human: TAGCTTACCTGGACAAGTCACAGTATATGAGAACATTTTAGTTAAAATTTATGGTTGTCTTACTATGTTAGATATTACACTACGTCCTATACTCAGTGCTGTACTTCTTATACCCTCGTTGGGCA Cluster: [ ] Orangutan: TAGCCTACCTGGACAAGTCAGAGTACATCAGAACATTTTAGTTAAAATTTATAGTTGTCTTACTATGTTAGATATTATACTATGTCCTATACTCAGTGCTGTACTTCTTATACCCTCGTTGGGCA Chimp > Gorilla --------------- chr6:106530852-106530856 Template switch process: F1: L ACAGAGACTGAGAAGAAGTTTAGCTTACCTGGACAAGTCAC 1 F3: 4 ATGAGAACATTTTAGTTGAAATTTATGGTTGTCTTACTAT R RF: ACAGAGACTGAGAAGTAGTTTAGCTTACCTGGACAAGTCACTAAAATGAGAACATTTTAGTTAAAATTTATGGTTGTCTTACTATGTTAGATATTACACTACATCCTATACTCAGTGCTGTACT RR: TGTCTCTGACTCTTCATCAAATCGAATGGACCTGTTCAGTGATTTTACTCTTGTAAAATCAATTTTAAATACCAACAGAATGATACAATCTATAATGTGATGTAGGATATGAGTCACGACATGA F2: 3 CATGA 2 Unidirectional alignment (log-probability: -37.6) CAGAGACTGAGAAGaAGTTTAGCTTACCTGGACAAGTCAC---AgtacATGAGAACATTTTAGTTgAAATTTATGGTTGTCTTACTAT CAGAGACTGAGAAGTAGTTTAGCTTACCTGGACAAGTCACTAAA----ATGAGAACATTTTAGTTAAAATTTATGGTTGTCTTACTAT Template switch alignment (log-probability: -27.4) CAGAGACTGAGAAGaAGTTTAGCTTACCTGGACAAGTCAC|AGTAC|ATGAGAACATTTTAGTTgAAATTTATGGTTGTCTTACTAT CAGAGACTGAGAAGTAGTTTAGCTTACCTGGACAAGTCAC|AGTAC|ATGAGAACATTTTAGTTAAAATTTATGGTTGTCTTACTAT ========== Event 3207 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTCTAAATTGATCTGGACT------------TGACTTTAATACATTTCCAGAACATTAGAGA ↓ 314 2 Chimp: TATTCTAAATTGATCTGGACTTTATTAAAGTCAAGACTTTAATACATTTCCAGAACATTAGAGA Gorilla: TATTCTAAATTGATCTGGACT------------TGACTTTAATTCATTTCCAGAACATTAGAGA Human: TATTCTAAATTGATCTGGACT------------TGACTTTAATACATTTCCAGAACATTAGAGA Cluster: [ ] Orangutan: TATTCTAAATTGATCTGGACT------------TGACTTTAATACATTTCCAGAACATTAGAGA Human > Chimp ------------- chr6:67421612-67421623 Template switch process: F1: L TTTAATTGACTTTTGGTTAATATTCTAAATTGATCTGGACTT 1 F3: 4 GACTTTAATACATTTCCAGAACATTAGAGATGGTTGTTTG R RF: TTTAACTGACTTTTGGTTAATATTCTAAATTGATCTGGACTTGACTTTAATACATTTCCAGAACATTAGAGATGGTTGTTTG RR: AAATTGACTGAAAACCAATTATAAGATTTAACTAGACCTGAACTGAAATTATGTAAAGGTCTTGTAATCTCTACCAACAAAC F2: 3 AACTGAAATTAT 2 Unidirectional alignment (log-probability: -34.2) TAAtTGACTTTTGGTTAATATTCTAAATTGATCTGGACTTtattaaagtcaaGACTTTAATACATTTCCAGAACATTAGAGATGGTTGTTTG TAACTGACTTTTGGTTAATATTCTAAATTGATCTGGACTT------------GACTTTAATACATTTCCAGAACATTAGAGATGGTTGTTTG Template switch alignment (log-probability: -22.8) TAAtTGACTTTTGGTTAATATTCTAAATTGATCTGGACTT|TATTAAAGTCAA|GACTTTAATACATTTCCAGAACATTAGAGATGGTTGTTTG TAACTGACTTTTGGTTAATATTCTAAATTGATCTGGACTT|TATTAAAGTCAA|GACTTTAATACATTTCCAGAACATTAGAGATGGTTGTTTG ========== Event 3208 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGATCAGAAGCTGAAACAATCTGCTTGCCCCT Chimp: TATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGACCAGAAGCCGAAACAATCTGCTTGCCCCT ↓ 1 3 2 4 Gorilla: TATTATGCTGGTATGTGAAGA-------ATCTGA---AACAAGCTGAAACAATCTGCTTGCCCCT ↑ 1 3 2 4 Human: TATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGATCAGAAGCTGAAACAATCTGCTTGCCCCT Cluster: [ ] Orangutan: TATTATTCTGGTATGTGAAGAAAGCCTAGTTTTAGATCAGAAGCTGAAACAATCTGCTTGCCCCT Human > Gorilla --------------- chr6:68189736-68189743 Template switch process: F1: L GAAGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA 1 F3: 4 AAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT R RF: GAAGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGATCAGAAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT RR: CTTCGGGTATCTAGGTGGTAATAATACGACCATACACTTCTTTCGGATCAAAATCTAGTCTTCGACTTTGTTAGACGAACGGGGAGTCTTTTAATGGAAA F2: 3 CAAAGTCT 2 Unidirectional alignment (log-probability: -32.7) AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGA--------------ATCtgaaAcAAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGATC----AGAAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT Template switch alignment (log-probability: -22.3) AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA|TCTgAAAC|AAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA|TCTAAAAC|AAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT Chimp > Gorilla --------------- chr6:68189736-68189743 Template switch process: F1: L GAAGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA 1 F3: 4 AAGCTGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTTACAAA R RF: GAAGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGACCAGAAGCCGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTTACAAA RR: CTTCGGGTATCTAGGTGGTAATAATACGACCATACACTTCTTTCGGATCAAAATCTGGTCTTCGGCTTTGTTAGACGAACGGGGAGTCTTTTAATGGAAATGTTT F2: 3 CAAAGTCT 2 Unidirectional alignment (log-probability: -38.7) AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA------------------tctgaaacAAGCtGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAAAGCCTAGTTTTAGACCAG--------AAGCCGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT Template switch alignment (log-probability: -27.9) AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA|TCTgAAAC|AAGCtGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT AGCCCATAGATCCACCATTATTATGCTGGTATGTGAAGAA|TCTAAAAC|AAGCCGAAACAATCTGCTTGCCCCTCAGAAAATTACCTTT ========== Event 3209 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: AGGACATTCTCAAAGAACACTCTGGCT---GTCTTTATAAAG---GTTCTAGTTAAAGAACT------CCAGACATCATTATGGGTTG Chimp: AGGACATTCTCAAAGAACACTTTGGCT---GTCTTTATAAAG---GTTCTAGTTAAAGAACT---CTTCAAGACATCATTATGGGTTG ↓ 13 24 ↑ 1 3 4 2 Gorilla: AGGACATTCTCAAAGAACACATTAACTAGAACCTTTATAAAG------ACAGCCAAAGAACTCTT---CAAGACATCATTATGGGTTG Human: AGGACATTCTCAAAGAACACTCTGGCT---GTCTTTATAAAG---GTTCTAGTTAAAGAACT------CCAGACATCATTATGGGTTG Cluster: [ ] Orangutan: AGGACATTCTCAAAGAACACTTTGGCT---GTCTTTATAAAGGTT---CTAGTTAAAGAACTCTT---CAAGACATCATTATGGGTTG Gorilla > Chimp --------------- chr6:6624466-6624493 Template switch process: F1: L GGACATTCTCAAAGAACAC 1 F3: 4 AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAACTAGATGGGCC R RF: GGACATTCTCAAAGAACACATTAACTAGAACCTTTATAAAGACAGCCAAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAACTAGATGGGCC RR: CCTGTAAGAGTTTCTTGTGTAATTGATCTTGGAAATATTTCTGTCGGTTTCTTGAGAAGTTCTGTAGTAATACCCAACTAAAGACTTGATCTACCCGG F2: 3 TTGATCTTGGAAATATTTCTGTCGGTTT 2 Unidirectional alignment (log-probability: -62.2) GGACATTCTCAAAGAACA----------------------------CtttggctgtctttataaaggttctagttAAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA GGACATTCTCAAAGAACACATTAACTAGAACCTTTATAAAGACAGCC----------------------------AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA Template switch alignment (log-probability: -19) GGACATTCTCAAAGAACAC|TTTGGCTGTCTTTATAAAGGTTCTAGTT|AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA GGACATTCTCAAAGAACAC|TTTGGCTGTCTTTATAAAGGTTCTAGTT|AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA Chimp > Gorilla --------------- chr6:6655458-6655482 Template switch process: F1: L GGACATTCTCAAAGAACACATT 1 F3: 4 AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAACTAGATGGGCC R RF: GGACATTCTCAAAGAACACTTTGGCTGTCTTTATAAAGGTTCTAGTTAAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAACTAGATGGGCC RR: CCTGTAAGAGTTTCTTGTGAAACCGACAGAAATATTTCCAAGATCAATTTCTTGAGAAGTTCTGTAGTAATACCCAACTAAAGACTTGATCTACCCGG F2: 3 CCGACAGAAATATTTCCAAGATCAA 2 Unidirectional alignment (log-probability: -62.2) GGACATTCTCAAAGAACAC----------------------------attaactagaacctttataaagacagccAAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA GGACATTCTCAAAGAACACTTTGGCTGTCTTTATAAAGGTTCTAGTT----------------------------AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA Template switch alignment (log-probability: -24.2) GGACATTCTCAAAGAACACaTT|AACTAGAACCTTTATAAAGACAGCC|AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA GGACATTCTCAAAGAACACTTT|AACTAGAACCTTTATAAAGACAGCC|AAAGAACTCTTCAAGACATCATTATGGGTTGATTTCTGAA ========== Event 3210 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 156 Detected in comparisons: 1256 Multiple sequence alignment: Human: TGTTCATCAGAACACTTCAAC-----AG-CGACATCAGCTAGGAGAAGAAAACACAGCAAAGAG ↑ 3 1 2 4 Chimp: TGTTCATCAGAACACTTCAACTTCCTAGCTGATGTCAGCT---AGAAGAAAACACAGCAAAGAG ↓ 3 1 2 4 ↑ 1 3 4 2 Gorilla: TGTTCATCAGAACACTTCAAC-----AG-CGACATCAGCTAGGAGAAGAAAACACAGCAAAGAG Human: TGTTCATCAGAACACTTCAAC-----AG-CGACATCAGCTAGGAGAAGAAAACACAGCAAAGAG Cluster: [ ] Orangutan: -------------------------------------------NNNNNNNNNNNNNNNNNNNNN Chimp > Human ------------- chr6:6933237-6933249 Template switch process: F1: L ACGACACATTACTCTCCAACTGTTCATCAGAACACTTCAAC-----AGC 1 F3: 4 AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA R RF: ACGACACATTACTCTCCAACTGTTCATCAGAACACTTCAACTTCCTAGCTGATGTCAGCTAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA RR: TGCTGTGTAATGAGAGGTTGACAAGTAGTCTTGTGAAGTTGAAGGATCGACTACAGTCGATCTTCTTTTGTGTCGTTTCTCCCTATTTCGTTCCTCTTCT F2: 3 GGATCGACTACAG 2 Unidirectional alignment (log-probability: -45.1) CACATTACTCTCCAACTGTTCATCAGAACACTTCAAC-------------------agcgacatcagctaggAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA CACATTACTCTCCAACTGTTCATCAGAACACTTCAACTTCCTAGCTGATGTCAGCT----------------AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA Template switch alignment (log-probability: -27.4) CACATTACTCTCCAACTGTTCATCAGAACACTTCAAC-----AGC|GACATCAGCTAGG|AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA CACATTACTCTCCAACTGTTCATCAGAACACTTCAACTTCCTAGC|GACATCAGCTAGG|AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA Gorilla > Chimp --------------- chr6:6973734-6973745 Template switch process: F1: L ACGACACATTACTCTCCAACTGTTCATCAGAACACTTCAACT 1 F3: 4 TCAGCT---AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA R RF: ACGACACATTACTCTCCAACTGTTCATCAGAACACTTCAACAGCGACATCAGCTAGGAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA RR: TGCTGTGTAATGAGAGGTTGACAAGTAGTCTTGTGAAGTTGTCGCTGTAGTCGATCCTCTTCTTTTGTGTCGTTTCTCCCTATTTCGTTCCTCTTCT F2: 3 GTAGTCGATCCT 2 Unidirectional alignment (log-probability: -48.4) GACACATTACTCTCCAACTGTTCATCAGAACACTTCAActtcctagctgatgtCAGC------------tAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGG GACACATTACTCTCCAACTGTTCATCAGAACACTTCAA---------------CAGCGACATCAGCTAGGAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGG Template switch alignment (log-probability: -32.8) GACACATTACTCTCCAACTGTTCATCAGAACACTTCAACt|TCCTAGCTGATG|TCAGCT---AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGG GACACATTACTCTCCAACTGTTCATCAGAACACTTCAACA|TCCTAGCTGATG|TCAGCTAGGAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGG Chimp > Gorilla --------------- chr6:7004056-7004068 Template switch process: F1: L ACGACACATTACTCTCCAACTGTTCATCAGAACACTTCAAC-----AGC 1 F3: 4 AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA R RF: ACGACACATTACTCTCCAACTGTTCATCAGAACACTTCAACTTCCTAGCTGATGTCAGCTAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA RR: TGCTGTGTAATGAGAGGTTGACAAGTAGTCTTGTGAAGTTGAAGGATCGACTACAGTCGATCTTCTTTTGTGTCGTTTCTCCCTATTTCGTTCCTCTTCT F2: 3 GGATCGACTACAG 2 Unidirectional alignment (log-probability: -44.2) CACATTACTCTCCAACTGTTCATCAGAACACTTCAA---------------CAGCgacatcagctaggAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA CACATTACTCTCCAACTGTTCATCAGAACACTTCAACTTCCTAGCTGATGTCAGC------------TAGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA Template switch alignment (log-probability: -27.5) CACATTACTCTCCAACTGTTCATCAGAACACTTCAAC-----AGC|GACATCAGCTAGG|AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA CACATTACTCTCCAACTGTTCATCAGAACACTTCAACTTCCTAGC|GACATCAGCTAGG|AGAAGAAAACACAGCAAAGAGGGATAAAGCAAGGAGAAGA ========== Event 3211 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CTTCATTCCCACGTCACTAAGGGTGCAT-AACGTCTC----TTCGTTATGTACTCTGGCTTCCTCAAT Chimp: CTTCATTCCCACGTCACTAAGGGTGCAT-AACGTCTC----TTCGTTATGTACTCTGGCTTCCTCAAT Gorilla: CTTCATTCCCACGTCACTAAGAGTGCACAGACATGTCCAGAGACGTTATGTACTCTGGCTTCCTCAAT ↓ 1 3 4 2 Human: CTTCATTCCCACGTCACTAAGGGTGCAT-AACGTCTC----TTCGTTATGTACTCTGGCTTCCTCAAT Cluster: [ ] Orangutan: CTTCATTCCCACGTCACTAAGGGTGCAT-AACATCTC----TTCATTATGTACTCTGGCTTCCTCAAT Gorilla > Human --------------- chr6:6894201-6894210 Template switch process: F1: L GAGCAGCTGTTTAGTGATACCTTCATTCCCACGTCACTAAGGGTGCA 1 F3: 4 TCGTTATGTACTCTGGCTTCCTCAATCCCTGGAATTACTGT R RF: GAGCAGCTGTTTAGTGATACCTTCATTCCCACGTCACTAAGAGTGCACAGACATGTCCAGAGACGTTATGTACTCTGGCTTCCTCAATCCCTGGAATTACTGT RR: CTCGTCGACAAATCACTATGGAAGTAAGGGTGCAGTGATTCTCACGTGTCTGTACAGGTCTCTGCAATACATGAGACCGAAGGAGTTAGGGACCTTAATGACA F2: 3 TCTCTGCAAT 2 Unidirectional alignment (log-probability: -42.9) TGTTTAGTGATACCTTCATTCCCACGTCACTAAGgGTGC----------------AtaacgtctcttCGTTATGTACTCTGGCTTCCTCAATCCCTGGAATTACTG TGTTTAGTGATACCTTCATTCCCACGTCACTAAGAGTGCACAGACATGTCCAGAGA-----------CGTTATGTACTCTGGCTTCCTCAATCCCTGGAATTACTG Template switch alignment (log-probability: -28.2) TGTTTAGTGATACCTTCATTCCCACGTCACTAAGgGTGCA|TAACGTCTCT|tCGTTATGTACTCTGGCTTCCTCAATCCCTGGAATTACTG TGTTTAGTGATACCTTCATTCCCACGTCACTAAGAGTGCA|TAACGTCTCT|ACGTTATGTACTCTGGCTTCCTCAATCCCTGGAATTACTG ========== Event 3212 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: cataatgagcactcaacaGTCGGGCTAAA----TGCTGAAGGACAGACACTTGTAG Chimp: cataatgagcactcaacaGTTGGGCTTTAGCCCAACTGAAGGACAGACACTTGTAG ↑ 3 1 2 4 Gorilla: cataatgagcactcaacaGTTGGGCTAAA----TGCTGAAGGACAGACACTTGTAG Human: cataatgagcactcaacaGTCGGGCTAAA----TGCTGAAGGACAGACACTTGTAG Cluster: [ ] Orangutan: cataatgagcactcaacaGTTGGGCTAAA----TGCTGAAGGACAGACACTTGTAA Gorilla > Chimp --------------- chr6:70593155-70593163 Template switch process: F1: L GCATTATGCTCAACACATAATGAGCACTCAACAGTTGGGCT 1 F3: 4 CTGAAGGACAGACACTTGTAGAGCCAGGAGTGAAAGAATA R RF: GCATTATGCTCAACACATAATGAGCACTCAACAGTTGGGCTAAATGCTGAAGGACAGACACTTGTAGAGCCAGGAGTGAAAGAATA RR: CGTAATACGAGTTGTGTATTACTCGTGAGTTGTCAACCCGATTTACGACTTCCTGTCTGTGAACATCTCGGTCCTCACTTTCTTAT F2: 3 AACCCGATT 2 Unidirectional alignment (log-probability: -30.9) CATTATGCTCAACACATAATGAGCACTCAACAGTTGGGCTttagcccAA---CTGAAGGACAGACACTTGTAGAGCCAGGAGTGAAAGAATA CATTATGCTCAACACATAATGAGCACTCAACAGTTGGGCT-------AAATGCTGAAGGACAGACACTTGTAGAGCCAGGAGTGAAAGAATA Template switch alignment (log-probability: -16.9) CATTATGCTCAACACATAATGAGCACTCAACAGTTGGGCT|TTAGCCCAA|CTGAAGGACAGACACTTGTAGAGCCAGGAGTGAAAGAATA CATTATGCTCAACACATAATGAGCACTCAACAGTTGGGCT|TTAGCCCAA|CTGAAGGACAGACACTTGTAGAGCCAGGAGTGAAAGAATA ========== Event 3213 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CCATTTTAAATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCTATCCAGAGCTTTTTGTTAGCCTTTCGTAGTTACA Chimp: CCATTTTAAATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCT----------GGATGTTAGCCTTTTGTAGTTACA ↓ 4 3 1 2 Gorilla: CCATTTTAAATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCTATCCAGAGCTTTTTGTTAGCCTTTTGTAGTTACA Human: CCATTTTAAATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCTATCCAGAGCTTTTTGTTAGCCTTTCGTAGTTACA Cluster: [ ] Orangutan: CCATTTTAAATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCT----------GGATGTTAGCCTTTTGTTGTTACA Chimp > Gorilla --------------- chr6:69819340-69819349 Template switch process: F1: L ATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCT 1 F3: 4 TTT-------------------------------TGTTAGCCTTTTGTAGTTACATTCATTTTCCCTGCTAACT R RF: ATGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCTGGATGTTAGCCTTTTGTAGTTACATTCATTTTCCCTGCTAACT RR: TACTTAGTTGAAATGACGTCGTCGTCACTCTACACTCGAGACCTACAATCGGAAAACATCAATGTAAGTAAAAGGGACGATTGA F2: 3 TCGAGACCTA 2 Unidirectional alignment (log-probability: -38) TGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCT--AtccagagcttttTGTTAGCCTTTTGTAGTTACATTCATTTTCCCTGCTA TGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCTGGA------------TGTTAGCCTTTTGTAGTTACATTCATTTTCCCTGCTA Template switch alignment (log-probability: -28.4) TGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCT|ATCCAGAGCT|TTT-------------------------------TGTTAGCCTTTTGTAGTTACATTCATTTTCCCTGCTA TGAATCAACTTTACTGCAGCAGCAGTGAGATGTGAGCTCT|ATCCAGAGCT|TTTACTGCAGCAGCAGTGAGATGTGAGCTCTGGATGTTAGCCTTTTGTAGTTACATTCATTTTCCCTGCTA ========== Event 3214 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCATGCTTCTGCATGATTGAA---AGCAAA----TGCAACCCTAAAATTAATAC-AAATGGG Chimp: TCATGCTTCTGCATGATTGAA---AGCAAA----TGCAACCCTAAAATTAATAC-AAATGGG ↑ 1 3 4 Gorilla: TCATGCTTCTGCATGATTGAAATTTACAAATGGTTGCATTTGTAAAATTAATAC-AAATGGG ↓ 1 3 4 Human: TCATGCTTCTGCATGATTGAA---AGCAAA----TGCAACCCTAAAATTAATAC-AAATGGG Cluster: [ ] Orangutan: TCATGCTTCTGCACGACTGAA---AGCAAA----TGCAACCCTAAAATTAATACAAAATGGG Gorilla > Human --------------- chr6:170017295-170017305 Template switch process: F1: L GTTTTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAAG 1 F3: 4 CTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCTG R RF: GTTTTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAATTTACAAATGGTTGCATTTGTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCTG RR: CAAAACTTCCTTCATATTACAGTACGAAGACGTACTAACTTTAAATGTTTACCAACGTAAACATTTTAATTATGTTTACCCCTTTCTCTTATTTTTTAGGAC F2: 3 CCAACGTAAAC 2 Unidirectional alignment (log-probability: -38.9) TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAA-------------------GcaaatgcaacccTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAATTTACAAATGGTTGCATTTG------------TAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT Template switch alignment (log-probability: -28.2) TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAAg|CAAATGCAACC|cTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAAT|CAAATGCAACC|GTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT Gorilla > Chimp --------------- chr6:174750891-174750901 Template switch process: F1: L GTTTTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAAG 1 F3: 4 CTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCTG R RF: GTTTTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAATTTACAAATGGTTGCATTTGTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCTG RR: CAAAACTTCCTTCATATTACAGTACGAAGACGTACTAACTTTAAATGTTTACCAACGTAAACATTTTAATTATGTTTACCCCTTTCTCTTATTTTTTAGGAC F2: 3 CCAACGTAAAC 2 Unidirectional alignment (log-probability: -38.9) TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAA-------------------GcaaatgcaacccTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAATTTACAAATGGTTGCATTTG------------TAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT Template switch alignment (log-probability: -28.2) TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAAg|CAAATGCAACC|cTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT TTGAAGGAAGTATAATGTCATGCTTCTGCATGATTGAAAT|CAAATGCAACC|GTAAAATTAATACAAATGGGGAAAGAGAATAAAAAATCCT ========== Event 3215 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGACTTACTGTTTTTATCTATGCATATAGATCTAATA---AGA---GTAGTAGGGCATTGGGTACTACTGGCAATAGATTTGTGAATAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT--AATGCTGTGCTCTTGTATGAAACTCTTTT Chimp: AAGACTTACTGTTTTTATCTATGCATATAGATCTAATA---AGA---GTAGTAGGGCATTGGGTACTACTGGCAATAGATTTGTGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT--AATGCTGTGCTCTTATATGAAACTCTTTT Gorilla: AAGACTTACTGTTTTTATCTATGCATATAGATCTAATA---AGAGTAGTAGTAGGGCATTGGGTACTACTGGCAATAGATTTGTGAATAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT----AGCATAGCTCTTGTATGAAACTCTTTT ↑ 3 2 1 4 Human: AAGACTTACTGTTTTTATCTATGCATATAGATCTAATA---AGA---GTAGTAGGGCATTGGGTACTACTGGCAATAGATTTGTGAATAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT--AATGCTGTGCTCTTGTATGAAACTCTTTT Cluster: [ ] Orangutan: AAGACTTACTGTTTTTATCTATCCATACAGATCTAATAAAGAGA---GTAGTAGGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATAATGCTATGCTCTTGTATGAAACTCTTGTTTTCCTATTAAGTAGTGTATCTTCTTTGAAGTTTTTGTCTTCATTTATTTGTTGGGGGTGGGTGGAGGGGCATGAATTTGCACTGGCCTGGTTCATTTTTGACATGTCATCAATGTCCAGTGGCATCGGTTGGAAGTCCAGTCACCTTTAGACCTGCAGCCTTTCCCTGTGCAACATAGTGACAGTCCTTGTCCTCTAGAAGAGACGTGGCATGCTAACGCAGAGGGCTTTATGGTTTCCTGGGGGAATAAAGGAGACCTCTAAGTAACTCTTCCAGTTAAGATAAATCCATTGCTTGTTTATGAAAACAGCTGANNNNNNNNNNAgtggctcaatgcctgtaatcccagcactttgagaggctgaggtggaaggatagcttgagcccaggagtttgagaccagcctgggcaatatagtgagaccccttttctacaaaaaatacagaaaagttagccgagtgtgatggtacacatctgtggtcccagttactcaggaggctgaagtgggaggatcacttgagcctgcatcacctgaggctgcagtgagccgtgattgcaccactgcactccagcagcctgggtgactgagtgagaccctgtctcaaaaaaaaaaaaaaaaaaagaaTATTATTTGATATGATTTCTTCAGTCTTGTTCAGGTGATCTGTCTTTCTGGGAAAATAAAACCCTGACATCTTTTTTTCTGAAAAACTATACTTCCTAAAATACTAAGACTTACTGTTTTTATCTATCCATACAGATCTAATAAAGAGAGTATTTATTAGTATTTATTATTGTGAATAAATAA--TGCTATGCTCTTGTATGAAACTC--TT Human > Gorilla --------------- chr6:172734800-172734804 Template switch process: F1: L TAGGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATA 1 F3: 4 GCTCTTGTATGAAACTCTTTTGTTTTCCTATTAAGTAGTG R RF: TATGCATATAGATCTAATAAGAGTAGTAGGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATAATGCTGTGCTCTTGTATGAAACTCTTTTGTTTTCCTATTAAGTAGTG RR: ATACGTATATCTAGATTATTCTCATCATCCCGTAACCCATGATGACCGTTATCTAAACACTTATTTATTACGACACGAGAACATACTTTGAGAAAACAAAAGGATAATTCATCAC F2: 3 ATACG 2 Unidirectional alignment (log-probability: -26.7) GGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATAgcatA------GCTCTTGTATGAAACTCTTTTGTTTTCCTATTAAGTAGTG GGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATA----ATGCTGTGCTCTTGTATGAAACTCTTTTGTTTTCCTATTAAGTAGTG Template switch alignment (log-probability: -16.4) GGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATA|GCATA|GCTCTTGTATGAAACTCTTTTGTTTTCCTATTAAGTAGTG GGGCATTGGGTACTACTGGCAATAGATTTGTGAATAAATA|GCATA|GCTCTTGTATGAAACTCTTTTGTTTTCCTATTAAGTAGTG ========== Event 3216 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ttttcaaAACTGACCAGCATT------------------------------TTGCAGGGTGGTTAGCAAGCTGGATGATACGATACTTGAATACTCCTGAAAAAAACTA Chimp: ttttcaaAACTGACCAGCATT------------------------------TTGCAGGGTGGTTAGCAAGCTGGATGATACGATACTTGAATGCTCCTGAAAAAAGCTA ↓ 1 3 4 2 Gorilla: ttttcaaAACTGACCAGCATT------------------------------------------------------------CAAGTTTGAATGCTCCTGaaaaaaaCTA Human: ttttcaaAACTGACCAGCATT------------------------------TTGCAGGGTGGTTAGCAAGCTGGATGATACGATACTTGAATACTCCTGAAAAAAACTA Cluster: [ ] Orangutan: TTTTCAAAACTGACCAGCATTTTGCAGGGTGGTTAGAAAGCTGGATGATAT------------------------------GAC--ATGAATGCTCCTGAAAAAAACTG Chimp > Gorilla --------------- chr6:172532921-172532925 Template switch process: F1: L ATATTTTTGCTTAGAAACAGTTTTCAAAACTGACCAGCATT 1 F3: 4 TTGAATGCTCCTGAAAAAAACTAATAAAATGCAAGATTCA R RF: ATATTTTTGCTTAGAAACAGTTTTCAAAACTGACCAGCATTTTGCAGGGTGGTTAGCAAGCTGGATGATACGATACTTGAATGCTCCTGAAAAAAGCTAATAAAATGCAAGATTCA RR: TATAAAAACGAATCTTTGTCAAAAGTTTTGACTGGTCGTAAAACGTCCCACCAATCGTTCGACCTACTATGCTATGAACTTACGAGGACTTTTTTCGATTATTTTACGTTCTAAGT F2: 3 TGAAC 2 Unidirectional alignment (log-probability: -33.3) TATTTTTGCTTAGAAACAGTTTTCAAAACTGACCAGCATT---------------CAAGt---------------TTGAATGCTCCTGAAAAAAaCTAATAAAATGCAAGATTCA TATTTTTGCTTAGAAACAGTTTTCAAAACTGACCAGCATTTTGCAGGGTGGTTAGCAAGCTGGATGATACGATACTTGAATGCTCCTGAAAAAAGCTAATAAAATGCAAGATTCA Template switch alignment (log-probability: -21.9) TATTTTTGCTTAGAAACAGTTTTCAAAACTGACCAGCATT|CAAGT|TTGAATGCTCCTGAAAAAAaCTAATAAAATGCAAGATTCA TATTTTTGCTTAGAAACAGTTTTCAAAACTGACCAGCATT|CAAGT|TTGAATGCTCCTGAAAAAAGCTAATAAAATGCAAGATTCA ========== Event 3217 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TATAGTTGGGTTTAAATGCTCATG----TAGAATTCTATTATTTGCCACTCCATGGTTTAATTTC Chimp: TATAGTTGGGTTTAAATGCTCATG----TAGAATTCTATTATTTGCCACTCCATGGTTTAATTTC ↓ 3 1 2 4 Gorilla: TATAGTTGGGTTTAAATGCTCATG--------TTTCT-ACATGAGCCACTCCATGGTTTAATTTC ↑ 3 1 2 4 Human: TATAGTTGGGTTTAAATGCTCATG----TAGAATTCTATTATTTGCCACTCCATGGTTTAATTTC Cluster: [ ] Orangutan: TACATTTGGGTTTAAATGCTCAGGTAGA----ATTCTATTATTTGCCACTGCATGGTTTAATTTC Human > Gorilla --------------- chr6:101862261-101862270 Template switch process: F1: L TTAAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATGT 1 F3: 4 GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG R RF: TTAAAAGAGGTGGAAAATATAGTTGGGTTTAAATGCTCATGTAGAATTCTATTATTTGCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG RR: AATTTTCTCCACCTTTTATATCAACCCAAATTTACGAGTACATCTTAAGATAATAAACGGTGAGGTACCAAATTAAAGATTTCGACGGACGGTACAC F2: 3 AGTACATCTT 2 Unidirectional alignment (log-probability: -38.4) AAAAGgGGTGGAAAATATAGTTGGGTTTAAATGCTCATG-------------TTTctacatgaGCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG AAAAGAGGTGGAAAATATAGTTGGGTTTAAATGCTCATGTAGAATTCTATTATTT--------GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG Template switch alignment (log-probability: -22.5) AAAAGgGGTGGAAAATATAGTTGGGTTTAAATGCTCATGT|TTCTACATGA|GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG AAAAGAGGTGGAAAATATAGTTGGGTTTAAATGCTCATGT|TTCTACATGA|GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG Chimp > Gorilla --------------- chr6:101862261-101862270 Template switch process: F1: L TTAAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATGT 1 F3: 4 GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG R RF: TTAAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATGTAGAATTCTATTATTTGCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG RR: AATTTTCCCCACCTTTTATATCAACCCAAATTTACGAGTACATCTTAAGATAATAAACGGTGAGGTACCAAATTAAAGATTTCGACGGACGGTACAC F2: 3 AGTACATCTT 2 Unidirectional alignment (log-probability: -32.8) AAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATG-------------TTTctacatgaGCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG AAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATGTAGAATTCTATTATTT--------GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG Template switch alignment (log-probability: -17) AAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATGT|TTCTACATGA|GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG AAAAGGGGTGGAAAATATAGTTGGGTTTAAATGCTCATGT|TTCTACATGA|GCCACTCCATGGTTTAATTTCTAAAGCTGCCTGCCATGTG ========== Event 3218 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTTGACACAGCTGTGATGTG----------------------TGGCTCTTAGTGATTATGAGCAGGAATGTTCAGttttgtattttctttctttctttct-----ttttGGATGTGGGGTTTTGGAGGGTCTGGGTGTTTGAAAGGGGAGCTTTAAAAATAAAATTTCAGTTACTCCTTGTGCAAGAGATTAAAAACAGGCTAA ↓ 4 1 3 2 Chimp: AGTTGACACAGCTGTGATGTG-----------TGGCTTGCATGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGttttgtattttctttctttctttct-----ttttGGATGTGGGGTTTTGGAGGGTCTGGGTGTTTGAAAGGGGAGCTTTAAAAATAAAATTTCAGTTACTCCTTGTGCAAGAGATTAAAAACAGGTTAA Gorilla: AGTTGACACAGCTGTGATGTGTGGCTTGCGTG-----------TGGCTCTTAGTGATTACGAGCAGGAATGTTCAGttttgtattttctttctttctttct-----ttttGGATGTGGGGTTTTGGAGGGTCTGGGTGTTTGAAAGGGGAGCTTTAAAAATAAAATTTCAGTTACTCCTTGTGCAAGAGATTAAAAACAGGTTAA Human: AGTTGACACAGCTGTGATGTG----------------------TGGCTCTTAGTGATTATGAGCAGGAATGTTCAGttttgtattttctttctttctttct-----ttttGGATGTGGGGTTTTGGAGGGTCTGGGTGTTTGAAAGGGGAGCTTTAAAAATAAAATTTCAGTTACTCCTTGTGCAAGAGATTAAAAACAGGCTAA Cluster: [ ] Orangutan: AGTTGACGCAGCTGTGATGTGTGGCTTGTGTG-----------TGTCTCTTAGTGGTTATGAGCAGGAATGTTCAGttttgtattttctttctttctttcttttttttttGGATGTGGGGTTTTGGAGGGTCTGGTTGTTTGAAAGGGGAGCTTTAAAAATAAAATTTCAGTTACTCCTTGTGCAAGAGATTAAAAACTGGTTAA Human > Chimp ------------- chr6:72862347-72862350 Template switch process: F1: L AAGGGCTACCCTGTCACCTCAGTTGACACAGCTGTGATGTGTGGCT 1 F3: 4 TGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGTTTTGTA R RF: AAGGGCTACCCTGTCACCTCAGTTGACACAGCTGTGATGTGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGTTTTGTATTTTCTTTCTTTCTTTCTTTTTGGATGTGGGGTTTTGGAGGGTCTGGGTGTTTGAAAGGGGAGCTTTAAAAATAAAATTTCAGTTACTCCTTGTGCA RR: TTCCCGATGGGACAGTGGAGTCAACTGTGTCGACACTACACACCGAGAATCACTAATACTCGTCCTTACAAGTCAAAACATAAAAGAAAGAAAGAAAGAAAAACCTACACCCCAAAACCTCCCAGACCCACAAACTTTCCCCTCGAAATTTTTATTTTAAAGTCAATGAGGAACACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -26.7) TACCCTGTCACCTCAGTTGACACAGCTGTGATGtgtggcttgcaTGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGTTTTG TACCCTGTCACCTCAGTTGACACAGCTGTGATG-----------TGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGTTTTG Template switch alignment (log-probability: -15.9) TACCCTGTCACCTCAGTTGACACAGCTGTGATGTGTGGCT|TGCA|TGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGTTTTG TACCCTGTCACCTCAGTTGACACAGCTGTGATGTGTGGCT|TGCA|TGTGGCTCTTAGTGATTATGAGCAGGAATGTTCAGTTTTG ========== Event 3219 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATAATGATGACATATTTTCAT--------------------------GTGTTAAATGACATGAGTTTCAGGACAgtcaacaatgcaggcgctagaa ↓ 4 1 3 2 Chimp: ATAATGATGACATATTTTCAT----------------GTGACTGTATGTGTTAAATGACATGAGTTTCAGGACAgtcaacaatgcaggcgctagaa Gorilla: ATAATGATGACATATTTTCAT------GTGGCTGTAC----------GTGTTAAATGACATGAGTTTCAGGACAgtcaacaatgcaggtgctagaa Human: ATAATGATGACATATTTTCAT--------------------------GTGTTAAATGACATGAGTTTCAGGACAgtcaacaatgcaggcgctagaa Cluster: [ ] Orangutan: ATAATAATGACATATTTTCATGTGACT--------------------GTGTTAAATGACACGAGTTGCAGGACAgtcaacaatgcaggcgctagaa Human > Chimp ------------- chr6:73609092-73609096 Template switch process: F1: L AATCAGGTGCTTTACTTATTATAATGATGACATATTTTCATGTG 1 F3: 4 ATGTGTTAAATGACATGAGTTTCAGGACAGTCAACAATGCAG R RF: AATCAGGTGCTTTACTTATTATAATGATGACATATTTTCATGTGTTAAATGACATGAGTTTCAGGACAGTCAACAATGCAG RR: TTAGTCCACGAAATGAATAATATTACTACTGTATAAAAGTACACAATTTACTGTACTCAAAGTCCTGTCAGTTGTTACGTC F2: 3 TGTCA 2 Unidirectional alignment (log-probability: -25.3) AGGTGCTTTACTTATTATAATGATGACATATTTTCatgtgactgtATGTGTTAAATGACATGAGTTTCAGGACAGTCAACAATGC AGGTGCTTTACTTATTATAATGATGACATATTTTC----------ATGTGTTAAATGACATGAGTTTCAGGACAGTCAACAATGC Template switch alignment (log-probability: -16) AGGTGCTTTACTTATTATAATGATGACATATTTTCATGTG|ACTGT|ATGTGTTAAATGACATGAGTTTCAGGACAGTCAACAATGC AGGTGCTTTACTTATTATAATGATGACATATTTTCATGTG|ACTGT|ATGTGTTAAATGACATGAGTTTCAGGACAGTCAACAATGC ========== Event 3220 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: GACCATGGGAACTTCCTCTCCTCAGGGTTTCTTTCCTTAAAATGTC ↓ 13 24 ↑ 13 24 Chimp: GACCATGGAAACTTCCTCTCCCTGAGGTTTCTTTCCTTAAAATGTC Gorilla: GACCATGGAAACTTCCTCTCCCTGAGGTTTCTTTCCTTAAAATGTC Human: GACCATGGGAACTTCCTCTCCTCAGGGTTTCTTTCCTTAAAATGTC Cluster: [ ] Orangutan: GACTGTGGAAACTTCCTCTCCCTGAGGTTTCTTTCCTTAAAATGTC Chimp > Human ------------- chr6:7226736-7226739 Template switch process: F1: L TTCCATGGTCCACACAGTTAGACCATGGGAACTTCCTCTCC 1 F3: 4 GGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT R RF: TTCCATGGTCCACACAGTTAGACCATGGAAACTTCCTCTCCCTGAGGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT RR: AAGGTACCAGGTGTGTCAATCTGGTACCTTTGAAGGAGAGGGACTCCAAAGAAAGGAATTTTACAGCCAACCCGAAACAGAAAAA F2: 3 GACT 2 Unidirectional alignment (log-probability: -30.7) TCCATGGTCCACACAGTTAGACCATGGgAACTTCCTCTCCtcagGGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT TCCATGGTCCACACAGTTAGACCATGGAAACTTCCTCTCCCTGAGGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT Template switch alignment (log-probability: -21.8) TCCATGGTCCACACAGTTAGACCATGGgAACTTCCTCTCC|TCAG|GGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT TCCATGGTCCACACAGTTAGACCATGGAAACTTCCTCTCC|TCAG|GGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT Human > Chimp ------------- chr6:7267117-7267120 Template switch process: F1: L TTCCATGGTCCACACAGTTAGACCATGGAAACTTCCTCTCC 1 F3: 4 GGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT R RF: TTCCATGGTCCACACAGTTAGACCATGGGAACTTCCTCTCCTCAGGGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT RR: AAGGTACCAGGTGTGTCAATCTGGTACCCTTGAAGGAGAGGAGTCCCAAAGAAAGGAATTTTACAGCCAACCCGAAACAGAAAAA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -30.7) TCCATGGTCCACACAGTTAGACCATGGaAACTTCCTCTCCctgaGGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT TCCATGGTCCACACAGTTAGACCATGGGAACTTCCTCTCCTCAGGGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT Template switch alignment (log-probability: -21.8) TCCATGGTCCACACAGTTAGACCATGGaAACTTCCTCTCC|CTGA|GGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT TCCATGGTCCACACAGTTAGACCATGGGAACTTCCTCTCC|CTGA|GGTTTCTTTCCTTAAAATGTCGGTTGGGCTTTGTCTTTTT ========== Event 3221 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCTGGTAGCTACCATGAGACAAGCTGGCCAAATGAG ↑ 3 2 1 4 Chimp: TGAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT-----------AGAGACAAGCTGGCCAAATGAG Gorilla: TGAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT-----------AGAGACAAGCTGGCCAAATGAG ↓ 3 2 1 4 Human: TGAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCTGGTAGCTACCATGAGACAAGCTGGCCAAATGAG Cluster: [ ] Orangutan: TGA-AAAACACAAG-AGCAATGCTAGCTACCATGAGACTTCT-----------AGAGACAAGCTAGCCAAATGAG Chimp > Human ------------- chr6:163681540-163681551 Template switch process: F1: L GAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT 1 F3: 4 GAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT R RF: GAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCTAGAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT RR: CTTCTCTGTGTTCTCCGTTACGATCGATGGTACTCTGAAGATCTCTGTTCGACCGGTTTACTCGGGAAGGTTTTAAGGTGAA F2: 3 TACCATCGATGG 2 Unidirectional alignment (log-probability: -32.7) AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCTggtagctaccatGAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT-----------AGAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT Template switch alignment (log-probability: -22.8) AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT|GGTAGCTAcCAT|GAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT|GGTAGCTAGCAT|GAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT Gorilla > Human --------------- chr6:163681540-163681551 Template switch process: F1: L GAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT 1 F3: 4 GAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT R RF: GAAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCTAGAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT RR: CTTCTCTGTGTTCTCCGTTACGATCGATGGTACTCTGAAGATCTCTGTTCGACCGGTTTACTCGGGAAGGTTTTAAGGTGAA F2: 3 TACCATCGATGG 2 Unidirectional alignment (log-probability: -32.2) AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCTggtagctaccatGAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT-----------AGAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT Template switch alignment (log-probability: -22.8) AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT|GGTAGCTAcCAT|GAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT AAGAGACACAAGAGGCAATGCTAGCTACCATGAGACTTCT|GGTAGCTAGCAT|GAGACAAGCTGGCCAAATGAGCCCTTCCAAAATTCCACTT ========== Event 3222 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CACAGGTGAttttt--ttttttCTCTTGGAAAGCCACCAGCC----------TGGTGCAGTTAGAAGCATTTCCTG ↓ 3 2 1 4 Chimp: CACAGGTGAttttt-tttttttCTCTTGGAAAGCCACCAGCCTTTCCAAGAGAAATGCAGTTAGAAGCATTTCCTG ↑ 3 2 1 4 Gorilla: CACAGTTGAtttttt-ttttttCTCTTGGAAAGCCACCAGCC----------TGGTGCAGTTAGAAGCATTTCCTG Human: CACAGGTGAttttt--ttttttCTCTTGGAAAGCCACCAGCC----------TGGTGCAGTTAGAAGCATTTCCTG Cluster: [ ] Orangutan: CACAGGTGAtttttt-ttttttCTCTTGGAAAGCCACGAGCC----------TGGTGCAGTTAGAAGCATTTCCTG Human > Chimp ------------- chr6:75422552-75422563 Template switch process: F1: L CACAGGTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCT 1 F3: 4 TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC R RF: CACAGGTGATTTTTTTTTTT-CTCTTGGAAAGCCACCAGCCTGGTGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC RR: GTGTCCACTAAAAAAAAAAA-GAGAACCTTTCGGTGGTCGGACCACGTCAATCTTCGTAAAGGACTCTCACAGACTCTCTTCCG F2: 3 AAAGAGAACCTT 2 Unidirectional alignment (log-probability: -48.9) CAGGTGAtTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCTttccaagagaaaTGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC CAGGTGA-TTTTTTTTTTTCTCTTGGAAAGCCACCAGCCTGG----------TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC Template switch alignment (log-probability: -28.4) CAGGTGATTTTTTTTTTTtCTCTTGGAAAGCCACCAGCCT|TTCCAAGAGAAA|TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC CAGGTGATTTTTTTTTTT-CTCTTGGAAAGCCACCAGCCT|TTCCAAGAGAAA|TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC Gorilla > Chimp --------------- chr6:75422552-75422563 Template switch process: F1: L ACAGGTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCT 1 F3: 4 TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC R RF: ACAGTTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCTGGTGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC RR: TGTCAACTAAAAAAAAAAAAGAGAACCTTTCGGTGGTCGGACCACGTCAATCTTCGTAAAGGACTCTCACAGACTCTCTTCCG F2: 3 AAAGAGAACCTT 2 Unidirectional alignment (log-probability: -41.8) CAGgTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCTttccaagagaaaTGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC CAGTTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCT----------GGTGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC Template switch alignment (log-probability: -22.8) CAGgTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCT|TTCCAAGAGAAA|TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC CAGTTGATTTTTTTTTTTTCTCTTGGAAAGCCACCAGCCT|TTCCAAGAGAAA|TGCAGTTAGAAGCATTTCCTGAGAGTGTCTGAGAGAAGGC ========== Event 3223 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAACTGCAGAGAAATGATTC----TTCTAGAAATT------------------------TATGACTGTGAGCTAAACTGTATTGACCTGAGAGATAACTATCAAGAAGAATATAACGTGGGG Chimp: ATAACTGCAGAGAAATGATTC----TTCTAGAAATT------------------------TATGACTGTGAGCTAAACTGTATTGACCGGAGAGATAACTATCAAGAAGAATATAATGTGGGG ↓ 1 4 3 2 Gorilla: ATAACTGCAGAGAAATGATTC--------AGATAGT------------------------------------------------TATCTGAGAGATAACTATCAAGAAGAATATAATGTGGGG Human: ATAACTGCAGAGAAATGATTC----TTCTAGAAATT------------------------TATGACTGTGAGCTAAACTGTATTGACCTGAGAGATAACTATCAAGAAGAATATAACGTGGGG Cluster: [ ] Orangutan: ATAACTGCAGAGAAATGATTCTTCT----AGAAATTTATGACTGTGAGCTAAACTGTATT------------------------GACCTGAGAGATAACTATCAAGAAGAATATAATGTGGGG Chimp > Gorilla --------------- chr6:76400608-76400618 Template switch process: F1: L GAAGAGGAGGTGAAGATGGGATAACTGCAGAGAAATGATTCA 1 F3: 4 GAGAGATAACTATCAAGAAGAATATAATGTGGGGAAAATC R RF: GAAGAGGAGGTGAAGATGGGATAACTGCAGAGAAATGATTCTTCTAGAAATTTATGACTGTGAGCTAAACTGTATTGACCGGAGAGATAACTATCAAGAAGAATATAATGTGGGGAAAATC RR: CTTCTCCTCCACTTCTACCCTATTGACGTCTCTTTACTAAGAAGATCTTTAAATACTGACACTCGATTTGACATAACTGGCCTCTCTATTGATAGTTCTTCTTATATTACACCCCTTTTAG F2: 3 TCTATTGATAG 2 Unidirectional alignment (log-probability: -38.5) AGAGGAGGTGAAGATGGGATAACTGCAGAGAAATGATtcagatagttaTCT---------------------------------------GAGAGATAACTATCAAGAAGAATATAATGTGGGGAAAATC AGAGGAGGTGAAGATGGGATAACTGCAGAGAAATGAT-----------TCTTCTAGAAATTTATGACTGTGAGCTAAACTGTATTGACCGGAGAGATAACTATCAAGAAGAATATAATGTGGGGAAAATC Template switch alignment (log-probability: -22.7) AGAGGAGGTGAAGATGGGATAACTGCAGAGAAATGATTCa|GATAGTTATCT|GAGAGATAACTATCAAGAAGAATATAATGTGGGGAAAATC AGAGGAGGTGAAGATGGGATAACTGCAGAGAAATGATTCT|GATAGTTATCT|GAGAGATAACTATCAAGAAGAATATAATGTGGGGAAAATC ========== Event 3224 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCGAAACTGACATCCATTTGT---GTGGCTAGCACATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGG Chimp: TTGAAACTGACATCCATTTGT---GTGGCTAGCACATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGG ↑ 1 4 3 2 Gorilla: TTGAAACTGACATCCATTTGT------GCTAG-CCATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGG ↓ 1 4 3 2 Human: TCGAAACTGACATCCATTTGT---GTGGCTAGCACATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGG Cluster: [ ] Orangutan: TTGAAACTGACATCCATTTGTGTG---GCTAGCACATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGG Gorilla > Human --------------- chr6:94941975-94941983 Template switch process: F1: L GGCAGCAACTATCTTTGTGGTCGAAACTGACATCCATTTGTG 1 F3: 4 CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT R RF: GGCAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTGCTAGCCATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT RR: CCGTCGTGGATAGAAACACCAACTTTGACTGTAGGTAAACACGATCGGTAACAGACACGATCGGTCCGAGAAAGACCCATGTTCCTA F2: 3 ACGATCGGT 2 Unidirectional alignment (log-probability: -37.5) CAGCAaCTATCTTTGTGGTcGAAACTGACATCCATTTGTgtgGCTAGCaCATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT CAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGT---GCTAGC-CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT Template switch alignment (log-probability: -27.9) CAGCAaCTATCTTTGTGGTcGAAACTGACATCCATTTGTG|TGGCTAGCA|CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT CAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTG|TGGCTAGCA|CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT Gorilla > Chimp --------------- chr6:96801470-96801478 Template switch process: F1: L GGCAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTG 1 F3: 4 CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT R RF: GGCAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTGCTAGCCATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT RR: CCGTCGTGGATAGAAACACCAACTTTGACTGTAGGTAAACACGATCGGTAACAGACACGATCGGTCCGAGAAAGACCCATGTTCCTA F2: 3 ACGATCGGT 2 Unidirectional alignment (log-probability: -26.5) CAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTgtgGCTAGCaCATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT CAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGT---GCTAGC-CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT Template switch alignment (log-probability: -16.9) CAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTG|TGGCTAGCA|CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT CAGCACCTATCTTTGTGGTTGAAACTGACATCCATTTGTG|TGGCTAGCA|CATTGTCTGTGCTAGCCAGGCTCTTTCTGGGTACAAGGAT ========== Event 3225 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCCATGAAGACTGAAACAGG---TATTTACAAT-----GATGCCTTCTCTGTAAACGAGTCACAACTCCTAGT Chimp: CTCCATGAAGACTGAAACAGG---TATTTACAAT-----GATGCCTTCTCTGTAAACAAGTCACAACTCCTAGT ↓ 1 4 3 2 Gorilla: CTCCATGAAGACTGAAACAGG------TTACAGAGAAGGTATGCCTTCTCTGTAAACGAGTCACAACTCCTAGT ↑ 1 4 3 2 Human: CTCCATGAAGACTGAAACAGG---TATTTACAAT-----GATGCCTTCTCTGTAAACGAGTCACAACTCCTAGT Cluster: [ ] Orangutan: CTCCATGAAGACTGAAACAGGTAT---TTACAAT-----GATGCCTTCTCTGTAAACGAGTCACAACTCCTAGT Human > Gorilla --------------- chr6:95398024-95398034 Template switch process: F1: L CAAAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT 1 F3: 4 TATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTTT R RF: CAAAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGTATTTACAATGATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTTT RR: GTTTTTGTCTGACATAGTCAGAGGTACTTCTGACTTTGTCCATAAATGTTACTACGGAAGAGACATTTGCTCAGTGTTGAGGATCAGTGAAA F2: 3 GGAAGAGACAT 2 Unidirectional alignment (log-probability: -38.4) AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT----------tacagagaaggtATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTT AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGTATTTACAATG------------ATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTT Template switch alignment (log-probability: -22.7) AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT|TACAGAGAAGG|tATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTT AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT|TACAGAGAAGG|GATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTT Chimp > Gorilla --------------- chr6:95398024-95398034 Template switch process: F1: L CAAAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT 1 F3: 4 TATGCCTTCTCTGTAAACGAGTCACAACTCCTAGTCACTTT R RF: CAAAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGTATTTACAATGATGCCTTCTCTGTAAACAAGTCACAACTCCTAGTCACTTT RR: GTTTTTGTCTGACATAGTCAGAGGTACTTCTGACTTTGTCCATAAATGTTACTACGGAAGAGACATTTGTTCAGTGTTGAGGATCAGTGAAA F2: 3 GGAAGAGACAT 2 Unidirectional alignment (log-probability: -43.9) AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT----------tacagagaaggtATGCCTTCTCTGTAAACgAGTCACAACTCCTAGTCACTT AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGTATTTACAATG------------ATGCCTTCTCTGTAAACAAGTCACAACTCCTAGTCACTT Template switch alignment (log-probability: -28.2) AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT|TACAGAGAAGG|tATGCCTTCTCTGTAAACgAGTCACAACTCCTAGTCACTT AAAACAGACTGTATCAGTCTCCATGAAGACTGAAACAGGT|TACAGAGAAGG|GATGCCTTCTCTGTAAACAAGTCACAACTCCTAGTCACTT ========== Event 3226 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATCTGGAACCAGTGGTATATTTAGGAG------ACCTCTTTCCTACCAGTGAGGGAGCCATGGAA ↓ 3 4 2 Chimp: GATCTGGAACCAGTGGTATATTTAGGAAAGAGGTCTCTCTTTCCTACCAGTGAGGGAGCCATGGAA ↑ 1 3 4 2 Gorilla: GATCTGGAACCAGTGGTATATGCAGGAG------ACCTCTTTCCTACCAGTGAGGGAGCCATGGAA Human: GATCTGGAACCAGTGGTATATTTAGGAG------ACCTCTTTCCTACCAGTGAGGGAGCCATGGAA Cluster: [ ] Orangutan: GATCTGGAACCAGTGGTATATTTAGGAG------ACCTCTTTCCTACCAGTGAGGGAGCCATGGAA Human > Chimp ------------- chr6:80764684-80764692 Template switch process: F1: L TTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATTTAGGA 1 F3: 4 CTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG R RF: TTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATTTAGGAGACCTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG RR: AAAAGTCAACCGCTCTAGACCTTGGTCACCATATAAATCCTCTGGAGAAAGGATGGTCACTCCCTCGGTACCTTATCTTAAGTC F2: 3 TCTGGAGAA 2 Unidirectional alignment (log-probability: -31.6) TTTCAGTTGGCGAGATCTGGAACCAGTGGTATATTTAGGAaAgaggtctCTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG TTTCAGTTGGCGAGATCTGGAACCAGTGGTATATTTAGGAGA------CCTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG Template switch alignment (log-probability: -16.4) TTTCAGTTGGCGAGATCTGGAACCAGTGGTATATTTAGGA|AAGAGGTCT|CTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG TTTCAGTTGGCGAGATCTGGAACCAGTGGTATATTTAGGA|AAGAGGTCT|CTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG Gorilla > Chimp --------------- chr6:80764679-80764692 Template switch process: F1: L CAGAGGTTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATT 1 F3: 4 CTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG R RF: CAGAGGTTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATGCAGGAGACCTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG RR: GTCTCCAAAAGTCAACCGCTCTAGACCTTGGTCACCATATACGTCCTCTGGAGAAAGGATGGTCACTCCCTCGGTACCTTATCTTAAGTC F2: 3 TCTGGAGAAAGGAT 2 Unidirectional alignment (log-probability: -41.7) GAGGTTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATttAGGAaAgaggtctCTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG GAGGTTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATGCAGGAGA------CCTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG Template switch alignment (log-probability: -23.1) GAGGTTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATt|TAGGAAAGAGGTCT|CTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG GAGGTTTTCAGTTGGCGAGATCTGGAACCAGTGGTATATG|TAGGAAAGAGGTCT|CTCTTTCCTACCAGTGAGGGAGCCATGGAATAGAATTCAG ========== Event 3227 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: tggtggtaagggagcagagga---gagatatactataaaaaataaacaaacata Chimp: tggtggTAAGGGAGCAGAGAA---GAGATATACTATAAAAAATAaacaaacata ↑ 3 2 4 Gorilla: tggtggTAAGGGAGCAGAGAAGTATATCTATAGTATAAAAAATAaacaaacata Human: tggtggtaagggagcagagga---gagatatactataaaaaataaacaaacata Cluster: [ ] Orangutan: tggtggtaagggaacagagaa---gagatatactataaaaaataaacaaacata Gorilla > Chimp --------------- chr6:94408530-94408537 Template switch process: F1: L GAAACTTACTTATATTCCAGTGGTGGTAAGGGAGCAGAGAAG 1 F3: 4 TATAAAAAATAAACAAACATAATGAATTAGTAAAGTATAA R RF: GAAACTTACTTATATTCCAGTGGTGGTAAGGGAGCAGAGAAGTATATCTATAGTATAAAAAATAAACAAACATAATGAATTAGTAAAGTATAA RR: CTTTGAATGAATATAAGGTCACCACCATTCCCTCGTCTCTTCATATAGATATCATATTTTTTATTTGTTTGTATTACTTAATCATTTCATATT F2: 3 CATATAGA 2 Unidirectional alignment (log-probability: -27.7) AACTTACTTATATTCCAGTGGTGGTAAGGGAGCAGAGAAG---AgaTATAcTATAAAAAATAAACAAACATAATGAATTAGTAAAGTATAA AACTTACTTATATTCCAGTGGTGGTAAGGGAGCAGAGAAGTATATCTATAGTATAAAAAATAAACAAACATAATGAATTAGTAAAGTATAA Template switch alignment (log-probability: -16.8) AACTTACTTATATTCCAGTGGTGGTAAGGGAGCAGAGAAG|AGATATAC|TATAAAAAATAAACAAACATAATGAATTAGTAAAGTATAA AACTTACTTATATTCCAGTGGTGGTAAGGGAGCAGAGAAG|AGATATAC|TATAAAAAATAAACAAACATAATGAATTAGTAAAGTATAA ========== Event 3228 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGAAGGAAGGAACAACAAGCTTATTTCACATAAGAGCAGACGGAGTTGCTCTACT Chimp: GGAAGGAA-GAACAACAAGCTTATGTG------AAGCAGACAGAGTTGCTCTACT Gorilla: GGAAGGAA-GAACAACAAGCTTATGTG------AAGCAGACGGAGTTGCTCTACT ↓ 3 1 4 Human: GGAAGGAAGGAACAACAAGCTTATTTCACATAAGAGCAGACGGAGTTGCTCTACT Cluster: [ ] Orangutan: GGAAGGAA-G---AACAAGCTTATGTG------AAGCAGACGGAGTTGCTCTACT Gorilla > Human --------------- chr6:78525698-78525707 Template switch process: F1: L TCCTCCACCTGGCCCAAGGAAGGAAGGAACAACAAGCTTAT 1 F3: 4 AGCAGACGGAGTTGCTCTACTGAAAGCCAGAGTAGTGATG R RF: TCCTCCACCTGGCCCAAGGAAGGAA-GAACAACAAGCTTATGTGAAGCAGACGGAGTTGCTCTACTGAAAGCCAGAGTAGTGATG RR: AGGAGGTGGACCGGGTTCCTTCCTT-CTTGTTGTTCGAATACACTTCGTCTGCCTCAACGAGATGACTTTCGGTCTCATCACTAC F2: 3 GAATACACTT 2 Unidirectional alignment (log-probability: -41.8) CCTCCACCTGGCCCAAGGAAGGAAgGAACAACAAGCTTATtTcAcataagAGCAGACGGAGTTGCTCTACTGAAAGCCAGAGTAGTGATG CCTCCACCTGGCCCAAGGAAGGAA-GAACAACAAGCTTATGTGA------AGCAGACGGAGTTGCTCTACTGAAAGCCAGAGTAGTGATG Template switch alignment (log-probability: -28.2) CCTCCACCTGGCCCAAGGAAGGAAgGAACAACAAGCTTAT|TTCACATAAG|AGCAGACGGAGTTGCTCTACTGAAAGCCAGAGTAGTGATG CCTCCACCTGGCCCAAGGAAGGAA-GAACAACAAGCTTAT|TTCACATAAG|AGCAGACGGAGTTGCTCTACTGAAAGCCAGAGTAGTGATG ========== Event 3229 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTGGTTTCTGATTGACAGTGTATCTAT-AAGGCCTTTGTCTCAAAGTGG ↓ 3 1 2 4 Chimp: TCTGGTTTCTGATTGACAGTGTAGATACAAAGGCCTTTGTCTCAAAGTGG Gorilla: TCTGGTTTCTGATTGACAGTGTATCTAC-AAGGCCTTTGTCTCAAAGTGG Human: TCTGGTTTCTGATTGACAGTGTATCTAT-AAGGCCTTTGTCTCAAAGTGG Cluster: [ ] Orangutan: TCTGGTTTCTGATTGACAGTGTATCTAT-AAGGCCTTTGTCTTAAAGTGG Human > Chimp ------------- chr6:80488080-80488085 Template switch process: F1: L CCCATCATTATCTTGATATCTGGTTTCTGATTGACAGTGTA 1 F3: 4 AAGGCCTTTGTCTCAAAGTGGTCATAGCCCAAGCTAGTTG R RF: CCCCTCATTATCTTGATATCTGGTTTCTGATTGACAGTGTATCTATAAGGCCTTTGTCTCAAAGTGGTCATAGCCCAAGCTAGTTG RR: GGGGAGTAATAGAACTATAGACCAAAGACTAACTGTCACATAGATATTCCGGAAACAGAGTTTCACCAGTATCGGGTTCGATCAAC F2: 3 ACATAG 2 Unidirectional alignment (log-probability: -36) CCaTCATTATCTTGATATCTGGTTTCTGATTGACAGTGTA-----gatacaAAGGCCTTTGTCTCAAAGTGGTCATAGCCCAAGCTAGTTG CCCTCATTATCTTGATATCTGGTTTCTGATTGACAGTGTATCTAT------AAGGCCTTTGTCTCAAAGTGGTCATAGCCCAAGCTAGTTG Template switch alignment (log-probability: -22) CCaTCATTATCTTGATATCTGGTTTCTGATTGACAGTGTA|GATACA|AAGGCCTTTGTCTCAAAGTGGTCATAGCCCAAGCTAGTTG CCCTCATTATCTTGATATCTGGTTTCTGATTGACAGTGTA|GATACA|AAGGCCTTTGTCTCAAAGTGGTCATAGCCCAAGCTAGTTG ========== Event 3230 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTAGAATCAGAATCATAAGCCCT----TGCACTTCCCATACTTCATAATTCACA Chimp: TCTAGAATCAGAATCATAAGCCCT----TGCACTTCCCATACTTCATAATTCACA ↓ 1 3 4 2 Gorilla: TCTAGAATCAGAATCATAAGCAAGTGCAAGCACTTCCCATACTTCATAATTCACA ↑ 1 3 4 2 Human: TCTAGAATCAGAATCATAAGCCCT----TGCACTTCCCATACTTCATAATTCACA Cluster: [ ] Orangutan: TCTAGAATCAGAATCATAAGCCCT----TGCACTTCTCATACTTCATAATTCACA Human > Gorilla --------------- chr6:79426740-79426747 Template switch process: F1: L GACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC 1 F3: 4 GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA R RF: GACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGCCCTTGCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA RR: CTGACCGTAGAAGGGTTTCCAGATCTTAGTCTTAGTATTCGGGAACGTGAAGGGTATGAAGTATTAAGTGTAAAAACGAGGTATT F2: 3 AACGTGAA 2 Unidirectional alignment (log-probability: -32.3) ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC----aagtgcaaGCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGCCCTT--------GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA Template switch alignment (log-probability: -16.7) ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC|AAGTGCAA|GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC|AAGTGCAA|GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA Chimp > Gorilla --------------- chr6:79426740-79426747 Template switch process: F1: L GACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC 1 F3: 4 GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAA R RF: GACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGCCCTTGCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAC RR: CTGACCGTAGAAGGGTTTCCAGATCTTAGTCTTAGTATTCGGGAACGTGAAGGGTATGAAGTATTAAGTGTAAAAACGAGGTATG F2: 3 AACGTGAA 2 Unidirectional alignment (log-probability: -37.9) ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC----aagtgcaaGCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAa ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGCCCTT--------GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAC Template switch alignment (log-probability: -22.3) ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC|AAGTGCAA|GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAa ACTGGCATCTTCCCAAAGGTCTAGAATCAGAATCATAAGC|AAGTGCAA|GCACTTCCCATACTTCATAATTCACATTTTTGCTCCATAC ========== Event 3231 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGAGGATTTCTCAGCTGGTTCCTAAGCAAGTGCT ↑ 3 2 1 4 Chimp: GGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGT----GTGATGGCTGGTTCCTAAGCAAGTGCT Gorilla: GGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGT----GTGATGGCTGGTTCCTAAGCAAGTGCT ↓ 3 2 1 4 Human: GGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGAGGATTTCTCAGCTGGTTCCTAAGCAAGTGCT Cluster: [ ] Orangutan: GTAAAGCTTTCCTCCTCCCTGAGAAACCAGTGT----GTGATGGCTGGTTTCTAAGCAAGTGCT Chimp > Human ------------- chr6:91572400-91572408 Template switch process: F1: L GGAGGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGAG 1 F3: 4 GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA R RF: GGAGGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGTGTGATGGCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA RR: CCTCCCTTCCCTTTCCAAAGGAGGAGGGACTCTTTAGTCACACACTACCGACCAAGGATTCGTTCACGAAACGTGGGAGGGTGGCGGT F2: 3 ACTCTTTAG 2 Unidirectional alignment (log-probability: -37.3) GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAG-------TGaggatttctcaGCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGTGTGATG-----------GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA Template switch alignment (log-probability: -22.4) GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGaG|GATTTCTCA|GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGTG|GATTTCTCA|GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA Gorilla > Human --------------- chr6:91572400-91572408 Template switch process: F1: L GGAGGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGAG 1 F3: 4 GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA R RF: GGAGGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGTGTGATGGCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA RR: CCTCCCTTCCCTTTCCAAAGGAGGAGGGACTCTTTAGTCACACACTACCGACCAAGGATTCGTTCACGAAACGTGGGAGGGTGGCGGT F2: 3 ACTCTTTAG 2 Unidirectional alignment (log-probability: -36.8) GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAG-------TGaggatttctcaGCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGTGTGATG-----------GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA Template switch alignment (log-probability: -22.4) GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGaG|GATTTCTCA|GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA GGGAAGGGAAAGGTTTCCTCCTCCCTGAGAAATCAGTGTG|GATTTCTCA|GCTGGTTCCTAAGCAAGTGCTTTGCACCCTCCCACCGCCA ========== Event 3232 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GACTTTGTGAATTGTATGTCT----------------------------------------------------------------------------------------------------------------TCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCATGCACATAGGGAAGTACTCTTTGGGCTAAGGAATGTAACTTATGTCAGAAATACGAgcataccttggagatactgcaggtt Chimp: GACTTTGTGAATTGTATGTCTTCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCATGCACATATGGAAGTACTCTTTGTATGCTTGTATTTCTGACATAAGTTACATTCCTTAGCCCAAAGAGTACTTCCATATGTGCATGACTGACTGAAAGTTTATTCCAAATCATGCACATATGGAAGTACTCTTTGGGCTAAGGAATGTAACTTATGTCAGAAATAcaagcataccttggagatactgcaggtt ↑ 4 3 1 2 Gorilla: GACTTTGTGAATTGTATGTCT----------------------------------------------------------------------------------------------------------------TCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCATGCACATAGGGAAGTACTCTTTGGGCTAAGGAATGTAACTTATGTCAGAAATAcaagcataccttggagatactgcaggtt Human: GACTTTGTGAATTGTATGTCT----------------------------------------------------------------------------------------------------------------TCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCATGCACATAGGGAAGTACTCTTTGGGCTAAGGAATGTAACTTATGTCAGAAATACGAgcataccttggagatactgcaggtt Cluster: [ ] Orangutan: GACTTTGTGAATTGTATGTCT----------------------------------------------------------------------------------------------------------------TCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCGTGCACATAGGGAAGTACTCTTTGGGCTAAGGAATGTAACTTATGTCAGAAATAcaagcataccttggagatactgcaggtt Gorilla > Chimp --------------- chr6:93146921-93146982 Template switch process: F1: L TCTTTCACACCTGAAGCTATGACTTTGTGAATTGTATGTCTTCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCATGCACATATGGAAGTACTCTTTG 1 F3: 4 GACTGACTGAAAGTTTATTCCAAATCATGCACATATGGAA R RF: TCTTTCACACCTGAAGCTATGACTTTGTGAATTGTATGTCTTCAGAAATTAAAGACTGACTGAAAGTTTATTCCAAATCATGCACATAGGGAAGTACTCTTTGGTACTCTTTGGGCTAAGGAATGTAACTTATGTCAGAAATACAAGCATA RR: AGAAAGTGTGGACTTCGATACTGAAACACTTAACATACAGAAGTCTTTAATTTCTGACTGACTTTCAAATAAGGTTTAGTACGTGTATCCCTTCATGAGAAACCATGAGAAACCCGATTCCTTACATTGAATACAGTCTTTATGTTCGTAT F2: 3 TACGTGTATACCTTCATGAGAAACCCGATTCCTTACATTGAATACAGTCTTTATGTTCGTAT 2 Unidirectional alignment (log-probability: -175) AAGTTTATTCCAAATCATGCACATAtGGAAgtactctttgtatgcttgtatttctgacataagttacattccttagcccaaagagtacttccatatgtgcatgactgactgaaagtttattccaaatcatgcacatatggaa AAGTTTATTCCAAATCATGCACATAGGGAA---------------------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -41.3) AAGTTTATTCCAAATCATGCACATAtGGAAGTACTCTTTG|TATGCTTGTATTTCTGACATAAGTTACATTCCTTAGCCCAAAGAGTACTTCCaTATGTGCAT|GACTGACTGAAAGTTTATTCCAAATCATGCACATAtGGAA AAGTTTATTCCAAATCATGCACATAGGGAAGTACTCTTTG|TATGCTTGTATTTCTGACATAAGTTACATTCCTTAGCCCAAAGAGTACTTCCCTATGTGCAT|GACTGACTGAAAGTTTATTCCAAATCATGCACATAGGGAA ========== Event 3233 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTATATTCAAAGTCATACAGTAT---------------ACAGAAGGAAACATAGCTAAGCCTTC Chimp: TTATATTCAAAGTCATACAGTAT---------------ACAGAAGGAAACATAGCTAAGCCTTC ↓ 3 4 12 Gorilla: TTATATTCAAAGTCATACAGTATACACATTCTGTATACACAGAAGGAAACATAGCTAAGCCTTC ↑ 3 4 12 Human: TTATATTCAAAGTCATACAGTAT---------------ACAGAAGGAAACATAGCTAAGCCTTC Cluster: [ ] Orangutan: TTATATTCAAAGTCATACAATAT---------------ACAGAAGGAAACATAGCTAAGCCTTC Human > Gorilla --------------- chr6:91601547-91601556 Template switch process: F1: L ATGGTACTATTAAATTTGTTATATTCAAAGTCATACAGTATACACA 1 F3: 4 ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTTTTTT R RF: ATGGTACTATTAAATTTGTTATATTCAAAGTCATACAGTATACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTTTTTT RR: TACCATGATAATTTAAACAATATAAGTTTCAGTATGTCATATGTCTTCCTTTGTATCGATTCGGAAGAGTCAAACAAAAAA F2: 3 CATATGTCTT 2 Unidirectional alignment (log-probability: -32.5) CTATTAAATTTGTTATATTCAAAGTCATACAGTATacacattctgtatacACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTTTTTT CTATTAAATTTGTTATATTCAAAGTCATACAGTAT---------------ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTTTTTT Template switch alignment (log-probability: -22.6) CTATTAAATTTGTTATATTCAAAGTCATACAGTATACAcA|TTCTGTATAC|ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTTTTTT CTATTAAATTTGTTATATTCAAAGTCATACAGTATACAGA|TTCTGTATAC|ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTTTTTT Chimp > Gorilla --------------- chr6:91601547-91601556 Template switch process: F1: L ATGGTACTATTAAATTTGTTATATTCAAAGTCATACAGTATACACA 1 F3: 4 ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTT R RF: ATGGTACTATTAAATTTGTTATATTCAAAGTCATACAGTATACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTT RR: TACCATGATAATTTAAACAATATAAGTTTCAGTATGTCATATGTCTTCCTTTGTATCGATTCGGAAGAGTCAAACAA F2: 3 CATATGTCTT 2 Unidirectional alignment (log-probability: -40.6) CTATTAAATTTGTTATATTCAAAGTCATACAGTATacacattctgtatacACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTt CTATTAAATTTGTTATATTCAAAGTCATACAGTAT---------------ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGT- Template switch alignment (log-probability: -22.5) CTATTAAATTTGTTATATTCAAAGTCATACAGTATACAcA|TTCTGTATAC|ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTT CTATTAAATTTGTTATATTCAAAGTCATACAGTATACAGA|TTCTGTATAC|ACAGAAGGAAACATAGCTAAGCCTTCTCAGTTTGTT ========== Event 3234 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GATGTGTGTTACTAAAGTGTT--TAGA---CAGGGAAAATCAC------------------------------------------AAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACAT Chimp: GATGTGTGTTACTAAAGTGTT--TAGA---CGGGGAAAATCAC------------------------------------------AAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACAT ↓ 1 3 24 Gorilla: GATGTGTGTTACTAAAGTGTTACTAGAAGTCCAGTAACTTCAT------------------------------------------------------------------------------------AAACAAAGATTGATGTGAACAT ↑ 1 3 24 Human: GATGTGTGTTACTAAAGTGTT--TAGA---CAGGGAAAATCAC------------------------------------------AAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACAT Cluster: [ ] Orangutan: GATGTATGTTACTCAAGTGTT--TAGA---CAGGGAAAATCACAAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTGTAG------------------------------------------TAACAAAGATTGATGTGAACAT Human > Gorilla --------------- chr6:90091421-90091443 Template switch process: F1: L ATTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT 1 F3: 4 AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG R RF: ATTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTTTAGACAGGGAAAATCACAAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG RR: TAATGACGAACCTTAGTATTCTACACACAATGATTTCACAAATCTGTCCCTTTTAGTGTTTAACACACATCATTGTAAATACTTCAATGACCTGAAGATCATTGTTTCTAACTACACTTGTAAGTTTTGGTTTATTTCGAC F2: 3 ATACTTCAATGACCTGAAGATCA 2 Unidirectional alignment (log-probability: -53.8) TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTTactagaagtccagtaacttcaTA----------------------------------------------------------AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT---------------------TAGACAGGGAAAATCACAAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG Template switch alignment (log-probability: -18.7) TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT|ACTAGAAGTCCAGTAACTTCATA|AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT|ACTAGAAGTCCAGTAACTTCATA|AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG Chimp > Gorilla --------------- chr6:90091421-90091443 Template switch process: F1: L ATTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT 1 F3: 4 AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG R RF: ATTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTTTAGACGGGGAAAATCACAAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG RR: TAATGACGAACCTTAGTATTCTACACACAATGATTTCACAAATCTGCCCCTTTTAGTGTTTAACACACATCATTGTAAATACTTCAATGACCTGAAGATCATTGTTTCTAACTACACTTGTAAGTTTTGGTTTATTTCGAC F2: 3 ATACTTCAATGACCTGAAGATCA 2 Unidirectional alignment (log-probability: -53.8) TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTTactagaagtccagtaacttcaTA----------------------------------------------------------AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT---------------------TAGACGGGGAAAATCACAAATTGTGTGTAGTAACATTTATGAAGTTACTGGACTTCTAGTAACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG Template switch alignment (log-probability: -18.7) TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT|ACTAGAAGTCCAGTAACTTCATA|AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG TTACTGCTTGGAATCATAAGATGTGTGTTACTAAAGTGTT|ACTAGAAGTCCAGTAACTTCATA|AACAAAGATTGATGTGAACATTCAAAACCAAATAAAGCTG ========== Event 3235 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ATCACTCTCTGAATTTTAACC------------ACAGGACTTTCCACAGTCGTAAGTtgtttatgtgtg-- Chimp: ATCACTCTCTGAATTTTAACC------------ACAGGACTTTCCACAGTCTTAAGTtgtttatgtgtg-- ↑ 4 3 1 2 Gorilla: ATCACTCTCTGAATTTTAACC------------------------ACAGTCTTAAGTtgtttatgtgtg-- Human: ATCACTCTCTGAATTTTAACC------------ACAGGACTTTCCACAGTCGTAAGTtgtttatgtgtg-- Cluster: [ ] Orangutan: ATCACTCTCTGACTTTTAGCCACAGGACTTTCC------------ACAGTCTTAAGTTGTTTAtgtgtgtg Gorilla > Chimp --------------- chr6:91479021-91479026 Template switch process: F1: L CCTACTTTACATTCTCTGATATCACTCTCTGAATTTTAACCACAG 1 F3: 4 CCACAGTCTTAAGTTGTTTA--TGTGTGTGTGTGTGTCTG R RF: CCTACTTTACATTCTCTGATATCACTCTCTGAATTTTAACCACAGTCTTAAGTTGTTTATGTGTGTGTGTGTGTGTCTG RR: GGATGAAATGTAAGAGACTATAGTGAGAGACTTAAAATTGGTGTCAGAATTCAACAAATACACACACACACACACAGAC F2: 3 TTTCAG 2 Unidirectional alignment (log-probability: -37.9) TTTACATTCTCTGATATCACTCTCTGAATTTTAAccacaggactttCCACAGTCTTAAGTTGTTTA--TGTGTGTGTGTGTGTCTG TTTACATTCTCTGATATCACTCTCTGAATTTTAA------------CCACAGTCTTAAGTTGTTTATGTGTGTGTGTGTGTGTCTG Template switch alignment (log-probability: -31.9) TTTACATTCTCTGATATCACTCTCTGAATTTTAACCACAG|GACTtT|CCACAGTCTTAAGTTGTTTA--TGTGTGTGTGTGTGTCTG TTTACATTCTCTGATATCACTCTCTGAATTTTAACCACAG|GACTGT|CCACAGTCTTAAGTTGTTTATGTGTGTGTGTGTGTGTCTG ========== Event 3236 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCAATTGCGAGGCTCTATCCTATGAATAACCATTCATAGGATGGTTCCACCCTATGTAGAGTCACC Chimp: TTCAACTGAGAGGCTCTATCCTATGA---------------ATGGTTCCACCCTATGTAGAGTCACC Gorilla: TTCAATTGCGAGGCTCTATCCTATGA---------------ATGGTTCCACCCTATGTAGAGTCACC ↓ 3 41 2 Human: TTCAATTGCGAGGCTCTATCCTATGAATAACCATTCATAGGATGGTTCCACCCTATGTAGAGTCACC Cluster: [ ] Orangutan: TTCAATTGCGAGGCTCTATCCTATGA---------------ATGGTTCCACCCTATGTAGAGTCACC Gorilla > Human --------------- chr6:89726294-89726306 Template switch process: F1: L GTGAATAAAAGATGCTTCAATTGCGAGGCTCTATCCTATGAAT 1 F3: 4 ATGGTTCCACCCTATGTAGAGTCACCACAGCACAGGAGCA R RF: GTGAATAAAAGATGCTTCAATTGCGAGGCTCTATCCTATGAATGGTTCCACCCTATGTAGAGTCACCACAGCACAGGAGCA RR: CACTTATTTTCTACGAAGTTAACGCTCCGAGATAGGATACTTACCAAGGTGGGATACATCTCAGTGGTGTCGTGTCCTCGT F2: 3 GGATACTTACCAA 2 Unidirectional alignment (log-probability: -32.5) AATAAAAGATGCTTCAATTGCGAGGCTCTATCCTATGAataaccattcataggATGGTTCCACCCTATGTAGAGTCACCACAGCACAGGAGCA AATAAAAGATGCTTCAATTGCGAGGCTCTATCCTATGA---------------ATGGTTCCACCCTATGTAGAGTCACCACAGCACAGGAGCA Template switch alignment (log-probability: -17.4) AATAAAAGATGCTTCAATTGCGAGGCTCTATCCTATGAAT|AACCATTCATAGG|ATGGTTCCACCCTATGTAGAGTCACCACAGCACAGGAGCA AATAAAAGATGCTTCAATTGCGAGGCTCTATCCTATGAAT|AACCATTCATAGG|ATGGTTCCACCCTATGTAGAGTCACCACAGCACAGGAGCA ========== Event 3237 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGGCTGCTCATGGTATGTCT--CTTGGGCCTCTTCCTTATGAAGAGGATGCCAAGGTTTTCC Chimp: caggcTGCTCATGGTATGTCT--CTTGGGCCTCTTCCTTATGAAGAGGATGCCAAGGTTTTCC ↓ 1 3 4 2 Gorilla: CAGGCTGCTCATGGTATGTCTTCATAAGGAAGAGTCCTTATGAAGAGGATGCCAAGGTTTTCC ↑ 1 3 4 2 Human: CAGGCTGCTCATGGTATGTCT--CTTGGGCCTCTTCCTTATGAAGAGGATGCCAAGGTTTTCC Cluster: [ ] Orangutan: caggcTGCTTATGGTGTGTCT--CTTGGGCCTCTTCCTTATGAAGAGGATGCCAAGGTTTTCC Human > Gorilla --------------- chr6:88848196-88848208 Template switch process: F1: L CTGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT 1 F3: 4 TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG R RF: CTGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCTCTTGGGCCTCTTCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG RR: GACGTGTTCTCTCCTCCCTCGTCCGACGAGTACCATACAGAGAACCCGGAGAAGGAATACTTCTCCTACGGTTCCAAAAGGTACTTGGAGAC F2: 3 GAGAAGGAATACT 2 Unidirectional alignment (log-probability: -38.4) TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT----------TcataaggaagagTCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCTCTTGGGCCTCT------------TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG Template switch alignment (log-probability: -17.4) TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT|TCATAAGGAAGAG|TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT|TCATAAGGAAGAG|TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG Chimp > Gorilla --------------- chr6:88848196-88848208 Template switch process: F1: L CTGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT 1 F3: 4 TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTCTG R RF: CTGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCTCTTGGGCCTCTTCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTGTG RR: GACGTGTTCTCTCCTCCCTCGTCCGACGAGTACCATACAGAGAACCCGGAGAAGGAATACTTCTCCTACGGTTCCAAAAGGTACTTGGACAC F2: 3 GAGAAGGAATACT 2 Unidirectional alignment (log-probability: -43.9) TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT----------TcataaggaagagTCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTcTG TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCTCTTGGGCCTCT------------TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTGTG Template switch alignment (log-probability: -22.9) TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT|TCATAAGGAAGAG|TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTcTG TGCACAAGAGAGGAGGGAGCAGGCTGCTCATGGTATGTCT|TCATAAGGAAGAG|TCCTTATGAAGAGGATGCCAAGGTTTTCCATGAACCTGTG ========== Event 3238 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTTTATCTATCTCAAAGCCTCCCTTTATCAAAAA ↓ 3 2 1 4 Chimp: AAGATGAGAATTTGTCTTCATCAGCAAGAAGAAACTTG----CTGATAAAGCCTCCCTTTATCAAAAA ↑ 3 2 1 4 Gorilla: AAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTTTATCTATCTCAAAGCCTCCCTTTATCAAAAA Human: AAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTTTATCTATCTCAAAGCCTCCCTTTATCAAAAA Cluster: [ ] Orangutan: AAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTTTATCTATCTCAAAGCCTCCCTTTATCGAAAA Human > Chimp ------------- chr6:8804496-8804501 Template switch process: F1: L TTGCAAGATGAGAATTTGTCTTCATCAGCAAGAAGAAACTT 1 F3: 4 AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT R RF: TTGCAAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTTTATCTATCTCAAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT RR: AACGTTCTACTCTTAAACAGAACTAGTCGTTCTTCTTTGAAATAGATAGAGTTTCGGAGGGAAATAGTTTTTCAGATATAACTCATGGTTA F2: 3 TAGTCG 2 Unidirectional alignment (log-probability: -34.8) TGCAAGATGAGAATTTGTCTTcATCAGCAAGAAGAAACTTgctgaTA---------AAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT TGCAAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTT-----TATCTATCTCAAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT Template switch alignment (log-probability: -22) TGCAAGATGAGAATTTGTCTTcATCAGCAAGAAGAAACTT|GCTGAT|AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT TGCAAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTT|GCTGAT|AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT Gorilla > Chimp --------------- chr6:8804496-8804501 Template switch process: F1: L TTGCAAGATGAGAATTTGTCTTCATCAGCAAGAAGAAACTT 1 F3: 4 AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT R RF: TTGCAAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTTTATCTATCTCAAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT RR: AACGTTCTACTCTTAAACAGAACTAGTCGTTCTTCTTTGAAATAGATAGAGTTTCGGAGGGAAATAGTTTTTCAGATATAACTCATGGTTA F2: 3 TAGTCG 2 Unidirectional alignment (log-probability: -33.8) TGCAAGATGAGAATTTGTCTTcATCAGCAAGAAGAAACTTgctgaT---------AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT TGCAAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTT-----TATCTATCTCAAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT Template switch alignment (log-probability: -22) TGCAAGATGAGAATTTGTCTTcATCAGCAAGAAGAAACTT|GCTGAT|AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT TGCAAGATGAGAATTTGTCTTGATCAGCAAGAAGAAACTT|GCTGAT|AAAGCCTCCCTTTATCAAAAAGTCTATATTGAGTACCAAT ========== Event 3239 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCACCATTATGTGGAGTTTAATTCTGGTTTGAGT--------TAATAACGCAGGGAGAACTATTT ↓ 3 2 1 4 Chimp: CCACCATTATGTGGAGTTTAATTCTGGTTTGAGTAACCAGAATTATAACGCAGGGAGAACTATTT ↑ 3 2 1 4 Gorilla: CCACCATTATGTGGAGTTCAATTCTGGTTTGAGT--------TAATAACGCAGGGAGAACTATTT Human: CCACCATTATGTGGAGTTTAATTCTGGTTTGAGT--------TAATAACGCAGGGAGAACTATTT Cluster: [ ] Orangutan: CCACCATTATGTGGAGTTTAATTCTGGTTTGAGT--------TAATAACGCAGGGAGAACTGTTT Human > Chimp ------------- chr6:87751173-87751182 Template switch process: F1: L CGACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGT 1 F3: 4 ATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG R RF: CAACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGTTAATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG RR: GTTGTGCGGTGGTAATACACCTCAAATTAAGACCAAACTCAATTATTGCGTCCCTCTTGATAAAATGTGTAAACCAGAGAGAC F2: 3 TTAAGACCAA 2 Unidirectional alignment (log-probability: -34.4) gACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGTaaccagaaTtATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG AACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGT--------TAATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG Template switch alignment (log-probability: -22.5) gACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGT|AACCAGAATT|ATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG AACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGT|AACCAGAATT|ATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG Gorilla > Chimp --------------- chr6:87751173-87751182 Template switch process: F1: L CGACACGCCACCATTATGTGGAGTTTAATTCTGGTTTGAGT 1 F3: 4 ATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG R RF: CGACACGCCACCATTATGTGGAGTTCAATTCTGGTTTGAGTTAATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG RR: GCTGTGCGGTGGTAATACACCTCAAGTTAAGACCAAACTCAATTATTGCGTCCCTCTTGATAAAATGTGTAAACCAGAGAGAC F2: 3 TTAAGACCAA 2 Unidirectional alignment (log-probability: -33.5) GACACGCCACCATTATGTGGAGTTtAATTCTGGTTTGAGTaaccagaaTtATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG GACACGCCACCATTATGTGGAGTTCAATTCTGGTTTGAGT--------TAATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG Template switch alignment (log-probability: -22.5) GACACGCCACCATTATGTGGAGTTtAATTCTGGTTTGAGT|AACCAGAATT|ATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG GACACGCCACCATTATGTGGAGTTCAATTCTGGTTTGAGT|AACCAGAATT|ATAACGCAGGGAGAACTATTTTACACATTTGGTCTCTCTG ========== Event 3240 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAGTGCCTCCTCAAAGTCTATAGTTTAGGAACTATACTGTGCTATTACACTACCTAG ↑ 3 1 2 4 Chimp: CTAGTGCCTCCTCAAAGTCTATAGTT-----CCTACCCTGTGCTATTACACTACCTAG Gorilla: CTAGTGCCTCCTCAAAGTCTATAGTT-----CCTACCCTGTGCTATTACACTACCTAG ↓ 3 1 2 4 Human: CTAGTGCCTCCTCAAAGTCTATAGTTTAGGAACTATACTGTGCTATTACACTACCTAG Cluster: [ ] Orangutan: CTAGTGCCTCCTCAAAGTCTATAGTT-----CCTACCCTGTGCTATTACACTACCTAG Chimp > Human ------------- chr6:85927494-85927504 Template switch process: F1: L ATCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT 1 F3: 4 CTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT R RF: ATCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTTCCTACCCTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT RR: TAGAAGAACCCACCGGATCACGGAGGAGTTTCAGATATCAAGGATGGGACACGATAATGTGATGGATCTATTTTATTCTCTAATAGA F2: 3 ATATCAAGGAT 2 Unidirectional alignment (log-probability: -36.1) TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTTtaggaaCTAtaCTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT-----CCTACCCTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT Template switch alignment (log-probability: -16.6) TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT|TAGGAACTATA|CTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT|TAGGAACTATA|CTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT Gorilla > Human --------------- chr6:85927494-85927504 Template switch process: F1: L ATCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT 1 F3: 4 CTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT R RF: ATCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTTCCTACCCTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT RR: TAGAAGAACCCACCGGATCACGGAGGAGTTTCAGATATCAAGGATGGGACACGATAATGTGATGGATCTATTTTATTCTCTAATAGA F2: 3 ATATCAAGGAT 2 Unidirectional alignment (log-probability: -34.7) TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTTtaggaaCTAtaCTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT-----CCTACCCTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT Template switch alignment (log-probability: -17.1) TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT|TAGGAACTATA|CTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT TCTTCTTGGGTGGCCTAGTGCCTCCTCAAAGTCTATAGTT|TAGGAACTATA|CTGTGCTATTACACTACCTAGATAAAATAAGAGATTATCT ========== Event 3241 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGTCTTACCCCTAGTTAAAGTTCCATTAGGAACTTTAggtgcagagacagatatg ↑ 3 1 2 4 Chimp: TTGTCTTACCCCTAGTTAAAGTTCCTAATG---GCTTAggtgcagagacagatatg Gorilla: TTGTCTTACCCCTAGTTAAAATTCCTAATG---GCTTAggtgcagagacagatatg Human: TTGTCTTACCCCTAGTTAAAGTTCCATTAGGAACTTTAggtgcagagacagatatg Cluster: [ ] Orangutan: TTGTCTTACCCCTAGTTAAAGTTCCTAATG---GCTTAGGTGCAGAGACAGATATG Chimp > Human ------------- chr6:83976299-83976308 Template switch process: F1: L TGTAAACTTTAAGCTATTGTCTTACCCCTAGTTAAAGTTCC 1 F3: 4 TTAGGTGCAGAGACAGATATGCCCTTACAAAATGTAAATT R RF: TGTAAACTTTAAGCTATTGTCTTACCCCTAGTTAAAGTTCCTAATGGCTTAGGTGCAGAGACAGATATGCCCTTACAAAATGGAAATT RR: ACATTTGAAATTCGATAACAGAATGGGGATCAATTTCAAGGATTACCGAATCCACGTCTCTGTCTATACGGGAATGTTTTACCTTTAA F2: 3 TCAAGGATTA 2 Unidirectional alignment (log-probability: -40.4) GTAAACTTTAAGCTATTGTCTTACCCCTAGTTAAAGTTCcattaggaaCT------TTAGGTGCAGAGACAGATATGCCCTTACAAAATGtAAATT GTAAACTTTAAGCTATTGTCTTACCCCTAGTTAAAGTTC---------CTAATGGCTTAGGTGCAGAGACAGATATGCCCTTACAAAATGGAAATT Template switch alignment (log-probability: -22.5) GTAAACTTTAAGCTATTGTCTTACCCCTAGTTAAAGTTCC|ATTAGGAACT|TTAGGTGCAGAGACAGATATGCCCTTACAAAATGtAAATT GTAAACTTTAAGCTATTGTCTTACCCCTAGTTAAAGTTCC|ATTAGGAACT|TTAGGTGCAGAGACAGATATGCCCTTACAAAATGGAAATT ========== Event 3242 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CATTTTAGCCTTTAAAGTTAGAAATATGTAACTATTGATGATTGAAACATTAACATACCAT Chimp: CATTTTAGCCTTTAAAGTTAGAAATAAGTTACATATTTCTATTGAAACATTAACATATCAT ↑ 3 1 2 4 Gorilla: CATTTTAGCCTTTAAAGTTAGAAATATGTAACTGTTGATGATTGAAACATTAACATATCAT Human: CATTTTAGCCTTTAAAGTTAGAAATATGTAACTATTGATGATTGAAACATTAACATACCAT Cluster: [ ] Orangutan: CATTTTAGCCTTTAAAGTTAGAAATATGTAACTATTGATGATTGAAACATTAAAATATCAT Gorilla > Chimp --------------- chr6:88723872-88723885 Template switch process: F1: L AATTTTATTAGAATACATTTTAGCCTTTAAAGTTAGAAATA 1 F3: 4 ATTGAAACATTAACATATCATTGGACGTAAAAAGAGAAAG R RF: AATTTTATTAGAATACATTTTAGCCTTTAAAGTTAGAAATATGTAACTGTTGATGATTGAAACATTAACATATCATTGGACATAAAAAGAGAAAG RR: TTAAAATAATCTTATGTAAAATCGGAAATTTCAATCTTTATACATTGACAACTACTAACTTTGTAATTGTATAGTAACCTGTATTTTTCTCTTTC F2: 3 TCTTTATACATTGA 2 Unidirectional alignment (log-probability: -45.5) ATTTTATTAGAATACATTTTAGCCTTTAAAGTTAGAAATAagttacatatttcT-------------ATTGAAACATTAACATATCATTGGACgTAAAAAGAGAAAG ATTTTATTAGAATACATTTTAGCCTTTAAAGTTAGAAATA-------------TGTAACTGTTGATGATTGAAACATTAACATATCATTGGACATAAAAAGAGAAAG Template switch alignment (log-probability: -23) ATTTTATTAGAATACATTTTAGCCTTTAAAGTTAGAAATA|AGTTACATATTTCT|ATTGAAACATTAACATATCATTGGACgTAAAAAGAGAAAG ATTTTATTAGAATACATTTTAGCCTTTAAAGTTAGAAATA|AGTTACATATTTCT|ATTGAAACATTAACATATCATTGGACATAAAAAGAGAAAG ========== Event 3243 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ACGGACTTCCAGTATCATCCTGTCA-----TTACAGAACATCACAGAAATTGTTGTC Chimp: ACAGACTTCCAGTATCATCCTGTCA-----TTACAGAACATCACAGAAATTGTTGTC ↑ 3 1 2 4 Gorilla: ACGGACTTCCAGTATCATCCTGTAATGTTTCAATTGAACATCACAGAAATTGTTGTC ↓ 3 1 2 4 Human: ACGGACTTCCAGTATCATCCTGTCA-----TTACAGAACATCACAGAAATTGTTGTC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr6:86841247-86841254 Template switch process: F1: L TGCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGT 1 F3: 4 AACATCACAGAAATTGTTGTCCACATAGTTGAATACATA R RF: TGCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGTAATGTTTCAATTGAACATCACAGAAATTGTTGTCCACATAGTTGAATATATA RR: ACGGGAGAGATCTCGACATGCCTGAAGGTCATAGTAGGACATTACAAAGTTAACTTGTAGTGTCTTTAACAACAGGTGTATCAACTTATATAT F2: 3 GACATTAC 2 Unidirectional alignment (log-probability: -35.4) GCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGTcattacA-----------GAACATCACAGAAATTGTTGTCCACATAGTTGAATAcATA GCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGT------AATGTTTCAATTGAACATCACAGAAATTGTTGTCCACATAGTTGAATATATA Template switch alignment (log-probability: -22.2) GCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGT|CATTACAG|AACATCACAGAAATTGTTGTCCACATAGTTGAATAcATA GCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGT|CATTACAG|AACATCACAGAAATTGTTGTCCACATAGTTGAATATATA Gorilla > Chimp --------------- chr6:89917594-89917601 Template switch process: F1: L TGCCCTCTCTAGAGCTGTACAGACTTCCAGTATCATCCTGT 1 F3: 4 AACATCACAGAAATTGTTGTCCACATAGTTGAATACATA R RF: TGCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGTAATGTTTCAATTGAACATCACAGAAATTGTTGTCCACATAGTTGAATATATA RR: ACGGGAGAGATCTCGACATGCCTGAAGGTCATAGTAGGACATTACAAAGTTAACTTGTAGTGTCTTTAACAACAGGTGTATCAACTTATATAT F2: 3 GACATTAC 2 Unidirectional alignment (log-probability: -40.9) GCCCTCTCTAGAGCTGTACaGACTTCCAGTATCATCCTGTcattacA-----------GAACATCACAGAAATTGTTGTCCACATAGTTGAATAcATA GCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGT------AATGTTTCAATTGAACATCACAGAAATTGTTGTCCACATAGTTGAATATATA Template switch alignment (log-probability: -27.8) GCCCTCTCTAGAGCTGTACaGACTTCCAGTATCATCCTGT|CATTACAG|AACATCACAGAAATTGTTGTCCACATAGTTGAATAcATA GCCCTCTCTAGAGCTGTACGGACTTCCAGTATCATCCTGT|CATTACAG|AACATCACAGAAATTGTTGTCCACATAGTTGAATATATA ========== Event 3244 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTATTCCTTACTAAAAAGTCATT--TCTTTAGGATGTATTTACAGAAGTAGG Chimp: TGTATTCCTTATTAAAAAGTCATT--GCTTTAGGATGTATTTACAGAAGTAGG ↓ 1 3 42 Gorilla: TGTATTCCTTACTAAAAAGTCCTA----AAGAGGATGTATTTACAGAAGTAGG ↑ 1 3 42 Human: TGTATTCCTTACTAAAAAGTCATT--TCTTTAGGATGTATTTACAGAAGTAGG Cluster: [ ] Orangutan: TGTATTCCTTACTAAAAAGTCATCTC--TTTAGGATGTACTTACAGAAATAGG Human > Gorilla --------------- chr6:89813196-89813201 Template switch process: F1: L GACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTC 1 F3: 4 AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT R RF: GACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTCATTTCTTTAGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT RR: CTGAAATCCTTCATTTAATGACATAAGGAATGATTTTTCAGTAAAGAAATCCTACATAAATGTCTTCATCCATTTATAAAGGTTTCGTA F2: 3 GAAATC 2 Unidirectional alignment (log-probability: -29.7) ACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTC--------ctaaagAGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT ACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTCATTTCTTT------AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT Template switch alignment (log-probability: -16.5) ACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTC|CTAAAG|AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT ACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTC|CTAAAG|AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT Chimp > Gorilla --------------- chr6:89813196-89813201 Template switch process: F1: L GACTTTAGGAAGTAAATTACTGTATTCCTTACTAAAAAGTC 1 F3: 4 AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT R RF: GACTTTAGGAAGTAAATTACTGTATTCCTTATTAAAAAGTCATTGCTTTAGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT RR: CTGAAATCCTTCATTTAATGACATAAGGAATAATTTTTCAGTAACGAAATCCTACATAAATGTCTTCATCCATTTATAAAGGTTTCGTA F2: 3 GAAATC 2 Unidirectional alignment (log-probability: -35.2) ACTTTAGGAAGTAAATTACTGTATTCCTTAcTAAAAAGTC--------ctaaagAGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT ACTTTAGGAAGTAAATTACTGTATTCCTTATTAAAAAGTCATTGCTTT------AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT Template switch alignment (log-probability: -22) ACTTTAGGAAGTAAATTACTGTATTCCTTAcTAAAAAGTC|CTAAAG|AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT ACTTTAGGAAGTAAATTACTGTATTCCTTATTAAAAAGTC|CTAAAG|AGGATGTATTTACAGAAGTAGGTAAATATTTCCAAAGCAT ========== Event 3245 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TGGCTAAGTTCACTTCTAGCCCCTCCATGCCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAGAAGCAAGCTGTGGTCTCAGGCCCCAACTGCCTCCCTCCTCTCCCACATTCAGAGGCAGTACCTACCATGGACAGCGGCTTTTGTCAGCG ↑ 4 1 3 2 Chimp: TGGCTAAGTTCACTTCTAGCC----------CCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAAAAGCAAGCTGTGGTCTCAGGCCCCAACTGCCTCCCTCCTCTCCCACATTCAGAGGCAGTACCTACCATGGACAGCGGCCTTTGTCAGAG Gorilla: TGGCTAAGTTCACTTCTAGCCCCTCCATGCCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAGAAGCAAGCTGTGGTCTCAGGCCCCAACTGCCTCCCTCCTCTCCCACATTCAGAGGCAGTACCTACCATGGACAGTGGCTTTTGTCAGTG Human: TGGCTAAGTTCACTTCTAGCCCCTCCATGCCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAGAAGCAAGCTGTGGTCTCAGGCCCCAACTGCCTCCCTCCTCTCCCACATTCAGAGGCAGTACCTACCATGGACAGCGGCTTTTGTCAGCG Cluster: [ ] Orangutan: TGGCTAAGTTCACTTCTAGCCCCTCCATGCCCCTCTACCTTTGCCTCAGC-AGTCCATGACAAGGACAGAAGCAAGCTGTGGTCTCAGGCCCCAACCGCCTCCCTCCTCTCCCACATTCAGAGGCAGTACCTATCATGGACAGCGGCTTTTGTCAGAG Chimp > Human ------------- chr6:82267559-82267562 Template switch process: F1: L CCCATTTCCCCAGGTTCTGCTGGCTAAGTTCACTTCTAGCCCCTC 1 F3: 4 CCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAGAA R RF: CCCATTTCCCCAAGTTCTGCTGGCTAAGTTCACTTCTAGCCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAAAAGCAAGCTGTGGTCTCAGGCCCCAACTGCCTCCCTCCTCTCCCACATTCAGAGGCAGTACCTACCATG RR: GGGTAAAGGGGTTCAAGACGACCGATTCAAGTGAAGATCGGGGAGATGGAGACGGAGTCGTACAGGTACTGTTCCTGTTTTCGTTCGACACCAGAGTCCGGGGTTGACGGAGGGAGGAGAGGGTGTAAGTCTCCGTCATGGATGGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -37.3) TTCCCCAgGTTCTGCTGGCTAAGTTCACTTCTAgcccctccatGCCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAg TTCCCCAAGTTCTGCTGGCTAAGTTCACTTCTA----------GCCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAA Template switch alignment (log-probability: -27.9) TTCCCCAgGTTCTGCTGGCTAAGTTCACTTCTAGCCCCTC|CATG|CCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAg TTCCCCAAGTTCTGCTGGCTAAGTTCACTTCTAGCCCCTC|CATG|CCCCTCTACCTCTGCCTCAGCATGTCCATGACAAGGACAA ========== Event 3246 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: AGGCCATGTGTATCTAGATAT-----GAAATAATATTTCTGTTATTTTAAAATATAAGATCCTTGGAAGATGTC ↓ 13 24 ↑ 13 24 Chimp: AGGCCATGTGTATCTAGATATATTTTAAAATAACAGAAATATTATT-----TCATAAGATCCTCAGAAGATGTC Gorilla: AGGCCATGTGTATCTAGATAT-----GAAATAATATTTCTTTTATTTTAAAATATAAGATCCTTGGAAGATGTC Human: AGGCCATGTGTATCTAGATAT-----GAAATAATATTTCTGTTATTTTAAAATATAAGATCCTTGGAAGATGTC Cluster: [ ] Orangutan: AGGCCATGTGTATCTAGATAT-----GAAATAATATTTCTGTTATTTTAAAATATAAGGTCCTTGGAAGATGTC Chimp > Human ------------- chr6:9050536-9050562 Template switch process: F1: L TGGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAT 1 F3: 4 ATAAGATCCTTGGAAGATGTCATCTATTGGAACATGTAAC R RF: TGGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATATATTTTAAAATAACAGAAATATTATTTCATAAGATCCTCAGAAGATGTCATCTATTGGAACATGTAAC RR: ACCACTAGTATAATTAAAGATCCGGTACACATAGATCTATATAAAATTTTATTGTCTTTATAATAAAGTATTCTAGGAGTCTTCTACAGTAGATAACCTTGTACATTG F2: 3 TAAAATTTTATTGTCTTTATAATAAAG 2 Unidirectional alignment (log-probability: -58.5) GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAtgaaataatatttctgtTATTTTAAAAT-----------------ATAAGATCCTtgGAAGATGTCATCTATTGGAACATGTAAC GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATA-----------------TATTTTAAAATAACAGAAATATTATTTCATAAGATCCTCAGAAGATGTCATCTATTGGAACATGTAAC Template switch alignment (log-probability: -30.6) GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAT|GAAATAATATTTCTGTTATTTTAAAAT|ATAAGATCCTtgGAAGATGTCATCTATTGGAACATGTAAC GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAT|GAAATAATATTTCTGTTATTTTAAAAT|ATAAGATCCTCAGAAGATGTCATCTATTGGAACATGTAAC Human > Chimp ------------- chr6:9088111-9088137 Template switch process: F1: L TGGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAT 1 F3: 4 ATAAGATCCTCAGAAGATGTCATCTATTGGAACATGTAAC R RF: TGGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATATGAAATAATATTTCTGTTATTTTAAAATATAAGATCCTTGGAAGATGTCATCTATTGGAACATGTAAC RR: ACCACTAGTATAATTAAAGATCCGGTACACATAGATCTATACTTTATTATAAAGACAATAAAATTTTATATTCTAGGAACCTTCTACAGTAGATAACCTTGTACATTG F2: 3 CTTTATTATAAAGACAATAAAATTTTA 2 Unidirectional alignment (log-probability: -58.5) GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATA-----------------TATTTTAAAATAacagaaatattatttcaTAAGATCCTcaGAAGATGTCATCTATTGGAACATGTAAC GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATATGAAATAATATTTCTGTTATTTTAAAATA-----------------TAAGATCCTTGGAAGATGTCATCTATTGGAACATGTAAC Template switch alignment (log-probability: -30.6) GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAT|ATTTTAAAATAACAGAAATATTATTTC|ATAAGATCCTcaGAAGATGTCATCTATTGGAACATGTAAC GGTGATCATATTAATTTCTAGGCCATGTGTATCTAGATAT|ATTTTAAAATAACAGAAATATTATTTC|ATAAGATCCTTGGAAGATGTCATCTATTGGAACATGTAAC ========== Event 3247 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATAAAA----CAGTGTTAG----G----AATCTGATATTGACATCCAGTTTCTAAAGCCTTTCCTAA------ATTGTTAGGCAAACAAATGTTTAGTATTCAATTTACACAATGATATTCACTACCACTTATTAAACTGTTGCTTGTGTCGcccccc Chimp: ATATAAAA----CAGTGTTAG--TTT--AATAAGTGGTAGTGAATATCATTGTGTAAATTGAATACTAA---ACATTTGTTTGCCTAACA---ATTTAGGAAAGGCTTTAGAAACTGGATGTCAATATCAGA--T--TCCTGTTGCTTGTGTCGCCC--C Gorilla: ATATAAAA----CAGTGTTAGTT--TAA--TAAGTGGTAGTGAATATCATTGTGTAAGTTGAATACTAAACA---TTTGTTTGCCTAACA---ATTTAGGAAAGGCTTTAGAAACTGGATGTCAATATCAGA--T--TCCTGTTGCTTGTGTCGccc--c ↑ 1 3 24 Human: ATATAAAA----CAGTGTTAG----G----AATCTGATATTGACATCCAGTTTCTAAAGCCTTTCCTAA------ATTGTTAGGCAAACAAATGTTTAGTATTCAATTTACACAATGATATTCACTACCACTTATTAAACTGTTGCTTGTGTCGcccccc Cluster: [ ] Orangutan: ATATAAAACAGACAGTGTTAATT--TAA--TAAGTGGTAGTGAATATCATTGTGTAAATTGAATACTAAACA---TTTGTTTGCCTAACA---ATTTAGGAAAAGCTTTAGAAACTGGATGTCAATATCAGA--T--TCCTGTTGCTTGTGTCGCTC--C Human > Gorilla --------------- chr6:9162032-9162135 Template switch process: F1: L TAAGATGTCTATCATAATGATTTTATATAAAACAGTGTTAG 1 F3: 4 CTGTTGCTTGTGTCG---CCCCCCCTTGTATTATGTCACA R RF: TAAGATGTCTATCATAATGATTTTATATAAAACAGTGTTAGGAATCTGATATTGACATCCAGTTTCTAAAGCCTTTCCTAAATTGTTAGGCAAACAAATGTTTAGTATTCAATTTACACAATGATATTCACTACCACTTATTAAACTGTTGCTTGTGTCGCCCCCCCCCCTTGTATTATGTCACA RR: ATTCTACAGATAGTATTACTAAAATATATTTTGTCACAATCCTTAGACTATAACTGTAGGTCAAAGATTTCGGAAAGGATTTAACAATCCGTTTGTTTACAAATCATAAGTTAAATGTGTTACTATAAGTGATGGTGAATAATTTGACAACGAACACAGCGGGGGGGGGGAACATAATACAGTGT F2: 3 CTTAGACTATAACTGTAGGTCAAAGATTTCGGAAAGGATTTAACAATCCGTTTGTTTACAAATCATAAGTTGAATGTGTTACTATAAGTGATGGTGAATAATTT 2 Unidirectional alignment (log-probability: -183) AAGATGTCTATCATAATGATTTTATATAAAACAGTGTTAG---------------------------------------------------------------------------------------------------TTtAAtaagtggtagtgaatatcattgtgtaagttgaatactaaacatttgtttgcctaacaatttaggaaaggctttagaaactggatgtcaatatcagattcCTGTTGCTTGTGTCG---CCCCCCCTTGTATTATGTCACA AAGATGTCTATCATAATGATTTTATATAAAACAGTGTTAGGAATCTGATATTGACATCCAGTTTCTAAAGCCTTTCCTAAATTGTTAGGCAAACAAATGTTTAGTATTCAATTTACACAATGATATTCACTACCACTTATTAAA---------------------------------------------------------------------------------------------------CTGTTGCTTGTGTCGCCCCCCCCCCTTGTATTATGTCACA Template switch alignment (log-probability: -44.1) AAGATGTCTATCATAATGATTTTATATAAAACAGTGTTAG|TTTAATAAGTGGTAGTGAATATCATTGTGTAAgTTGAATACTAAACATTTGTTTGCCTAACAATTTAGGAAAGGCTTTAGAAACTGGATGTCAATATCAGATTC|CTGTTGCTTGTGTCG---CCCCCCCTTGTATTATGTCACA AAGATGTCTATCATAATGATTTTATATAAAACAGTGTTAG|TTTAATAAGTGGTAGTGAATATCATTGTGTAAATTGAATACTAAACATTTGTTTGCCTAACAATTTAGGAAAGGCTTTAGAAACTGGATGTCAATATCAGATTC|CTGTTGCTTGTGTCGCCCCCCCCCCTTGTATTATGTCACA ========== Event 3248 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GACAGTAAACACTCTTCTCTATATGCAGCCAATACATTTTTGTCAATGGGCCTATGCCTAGGGTG Chimp: GACAGTAAACACTCTTCTCTATATGCAGCCTATG-CTGCATATATATGGGCCTATGCTTAGGGTG ↑ 3 2 1 4 Gorilla: GACAGTAAACACTCTTCTCTATATGCAGCCAATACATTTTTGTCAATGGGCCTATGCTTAGGGTG Human: GACAGTAAACACTCTTCTCTATATGCAGCCAATACATTTTTGTCAATGGGCCTATGCCTAGGGTG Cluster: [ ] Orangutan: GACAGTAAACGCTCTTCTCTATATGCAGCCAATACATTTTTGTCAATGGGCCTATGCTTAGGGTG Gorilla > Chimp --------------- chr6:8918540-8918549 Template switch process: F1: L TAGCTTCCAGAGACAGTAAACACTCTTCTCTATATGCAGCCTAT 1 F3: 4 TATGGGCCTATGCTTAGGGTGGACTATCATAATATTGCATA R RF: TAGCTTCCAGAGACAGTAAACACTCTTCTCTATATGCAGCCAATACATTTTTGTCAATGGGCCTATGCTTAGGGTGGACTATCATAATATTGCATA RR: ATCGAAGGTCTCTGTCATTTGTGAGAAGAGATATACGTCGGTTATGTAAAAACAGTTACCCGGATACGAATCCCACCTGATAGTATTATAACGTAT F2: 3 ATATACGTCG 2 Unidirectional alignment (log-probability: -41.5) TTCCAGAGACAGTAAACACTCTTCTCTATATGCAGCC---------------tatgctgcatatatATGGGCCTATGCTTAGGGTGGACTATCATAATATTGCAT TTCCAGAGACAGTAAACACTCTTCTCTATATGCAGCCAATACATTTTTGTCA--------------ATGGGCCTATGCTTAGGGTGGACTATCATAATATTGCAT Template switch alignment (log-probability: -28.1) TTCCAGAGACAGTAAACACTCTTCTCTATATGCAGCCtAT|GCTGCATATA|tATGGGCCTATGCTTAGGGTGGACTATCATAATATTGCAT TTCCAGAGACAGTAAACACTCTTCTCTATATGCAGCCAAT|GCTGCATATA|AATGGGCCTATGCTTAGGGTGGACTATCATAATATTGCAT ========== Event 3249 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: GCTGGAGTGAGGGGCAGGTGG-CGCCGGTGCCAAGGCCAGCAGTGTCTGACCTCCAGAGCCATCTTGCTGTCGACACTGTCCCCAGCTTTCCCCCACCAGCTTGTCACT ↓ 1 4 3 2 Chimp: GCTGGAGTGAGGGGCAGGTGGAAGCTGGGGCCAAGGCCAGCAGTATCTGACCTCCAGAGCCATCTTGCTGTCGACACTGTCCCCAGCTTTCCCCCACCACCTTGCCACT Gorilla: Human: GCTGGAGTGAGGGGCAGGTGG-CGCCGGTGCCAAGGCCAGCAGTGTCTGACCTCCAGAGCCATCTTGCTGTCGACACTGTCCCCAGCTTTCCCCCACCAGCTTGTCACT Cluster: [ ] Orangutan: GCTGGAGTGAGGGGCAGGTGGCAGCCGGGGCCAAGGCCAGCAATGTCTGACCTCCAGAGCCATCTTGCTGTCGACACTGTCCCCAGCTTTCCCCCACCAGCTTGCCACT Human > Chimp ------------- chr6:92505147-92505154 Template switch process: F1: L CCCAAGTGAAGCTGCTTGCAGCTGGAGTGAGGGGCAGGTGG 1 F3: 4 GCCAAGGCCAGCAGTATCTGACCTCCAGAGCCATCTTGCT R RF: CCCAAGTGAAGCTGCTTGCAGCTGGAGTGAGGGGCAGGTGGCGCCGGTGCCAAGGCCAGCAGTGTCTGACCTCCAGAGCCATCTTGCTGTCGACACTGTCCCCAGCTT RR: GGGTTCACTTCGACGAACGTCGACCTCACTCCCCGTCCACCGCGGCCACGGTTCCGGTCGTCACAGACTGGAGGTCTCGGTAGAACGACAGCTGTGACAGGGGTCGAA F2: 3 GGGTCGAA 2 Unidirectional alignment (log-probability: -36.4) CCAAGTGAAGCTGCTTGCAGCTGGAGTGAGGGGCAGGTGGaaGCtGGgGCCAAGGCCAGCAGTaTCTGACCTCCAGAGCCATCTTGCT CCAAGTGAAGCTGCTTGCAGCTGGAGTGAGGGGCAGGTGG-CGCCGGTGCCAAGGCCAGCAGTGTCTGACCTCCAGAGCCATCTTGCT Template switch alignment (log-probability: -22.3) CCAAGTGAAGCTGCTTGCAGCTGGAGTGAGGGGCAGGTGG|AAGCTGGG|GCCAAGGCCAGCAGTaTCTGACCTCCAGAGCCATCTTGCT CCAAGTGAAGCTGCTTGCAGCTGGAGTGAGGGGCAGGTGG|AAGCTGGG|GCCAAGGCCAGCAGTGTCTGACCTCCAGAGCCATCTTGCT ========== Event 3250 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: TACAAGGATCCAGCTGACATC-T---GACTAGAAGGGAAAAAAAGTTCATCTTATAAAACAAGTTGTATATGCCATGCTTCTAATAAGGGATATTCTATTTCTGAAATGTCAAGATCAGGAAGGACCACAGT ↑ 1 4 3 2 Chimp: TACAAGGATCCAGCTGACATCCTGGATGTTAGAAGGGA-AAAAAGTTCATCTTATAAAACAAGTTGTATATGCCATGCTTCTAATAAGGGATATTCTATTTCTGAAATGTCAAGATCAGGAAGGACCACAGT Gorilla: TACAAGGATCCAGCTGACATC-T---GACTAGAAGGGaaaaaaaGTTCATCTTATAAAACAAGTTGTATATGCCATGCTTCTAATAAGGGATATTCTATTTCTGAAATGTCAAGATCAGGAAGGACCACAGT Human: TACAAGGATCCAGCTGACATC-T---GACTAGAAGGGAAAAAAAGTTCATCTTATAAAACAAGTTGTATATGCCATGCTTCTAATAAGGGATATTCTATTTCTGAAATGTCAAGATCAGGAAGGACCACAGT Cluster: [ ] Orangutan: TACAAGGATCCAGCTGACATC-T---GACTAGAAGGGAAAAAAAGTTCATCTTATAAAACGAGTTGTATATGCCATGCTGCTAATAAGGGATATTCTATTTCTGAAATGTCCAGATCAGGAAGGACCATAGT Chimp > Human ------------- chr6:79978013-79978016 Template switch process: F1: L AACTGTGTAATTTATGAAAATACAAGGATCCAGCTGACATC 1 F3: 4 TAGAAGGGAAAAAAAGTTCATCTTATAAAACAAGTTGTATATGCCATGCT R RF: AACTGTGTAATTTATGAAAATACAAGGATCCAGCTGACATCCTGGATGTTAGAAGGGAAAAAAGTTCATCTTATAAAACAAGTTGTATATGCCATGCTTCTAATAAGGGATATTCTATTTCTGAAATGTCA RR: TTGACACATTAAATACTTTTATGTTCCTAGGTCGACTGTAGGACCTACAATCTTCCCTTTTTTCAAGTAGAATATTTTGTTCAACATATACGGTACGAAGATTATTCCCTATAAGATAAAGACTTTACAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -37.5) ACTGTGTAATTTATGAAAATACAAGGATCCAGCTGACATCtgaC-------TAGAAGGGAAAAAaAGTTCATCTTATAAAACAAGTTGTAT ACTGTGTAATTTATGAAAATACAAGGATCCAGCTGACATC---CTGGATGTTAGAAGGGAAAAA-AGTTCATCTTATAAAACAAGTTGTAT Template switch alignment (log-probability: -27.6) ACTGTGTAATTTATGAAAATACAAGGATCCAGCTGACATC|TGAC|TAGAAGGGaAAAAAAGTTCATCTTATAAAACAAGTTGTAT ACTGTGTAATTTATGAAAATACAAGGATCCAGCTGACATC|TGAC|TAGAAGGG-AAAAAAGTTCATCTTATAAAACAAGTTGTAT ========== Event 3251 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTACCCCCTACCCATTAGGGTGCCACCTATGGCACCTATCAACGAGAAAATCCAGAGG-AA ↑ 3 2 1 4 Chimp: GTTACCCCCTACCCATTAGGGTGCCACCTA-----AATATCGACGAGAAAATCCAGAGG-AA Gorilla: GTTACCCCCTACCCATTAGGGTGCCACCTA-----AATATCAACGAGAAAATCCAGAGG-AA ↓ 3 2 1 4 Human: GTTACCCCCTACCCATTAGGGTGCCACCTATGGCACCTATCAACGAGAAAATCCAGAGG-AA Cluster: [ ] Orangutan: GTTACCCCCTACCCATTAGGGTGCCACCTA-----AATATCAACAAGAAAATCCAGAGGAAA Chimp > Human ------------- chr6:79288704-79288710 Template switch process: F1: L TATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTA 1 F3: 4 TATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGAACCAT R RF: TATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTAAATATCGACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGAACCAT RR: ATAAAGATCTACAATGGGGGATGGGTAATCCCACGGTGGATTTATAGCTGCTCTTTTAGGTCTCCTTAAGGAGGACTAAACCTTGGTA F2: 3 CCACGGT 2 Unidirectional alignment (log-probability: -36.1) ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTatggcAccTATCaACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGA ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCT-----AAATATCGACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGA Template switch alignment (log-probability: -22.2) ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTA|TGGCACC|TATCaACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGA ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTA|TGGCACC|TATCGACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGA Gorilla > Human --------------- chr6:79288704-79288710 Template switch process: F1: L TATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTA 1 F3: 4 TATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGA R RF: TATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTAAATATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGG RR: ATAAAGATCTACAATGGGGGATGGGTAATCCCACGGTGGATTTATAGTTGCTCTTTTAGGTCTCCTTAAGGAGGACTAAACCC F2: 3 CCACGGT 2 Unidirectional alignment (log-probability: -34.7) ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTatggcAccTATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGa ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCT-----AAATATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGG Template switch alignment (log-probability: -22.1) ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTA|TGGCACC|TATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGa ATTTCTAGATGTTACCCCCTACCCATTAGGGTGCCACCTA|TGGCACC|TATCAACGAGAAAATCCAGAGGAATTCCTCCTGATTTGGG ========== Event 3252 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT--------ATGATTTGACCTTCTATCTGCT ↓ 3 2 1 4 Chimp: TTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGTGGAATACATGGATTTGACCTTCTATCTGCT Gorilla: TTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT--------ATGATTTGACCTTCTATCTGCT Human: TTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT--------ATGATTTGACCTTCTATCTGCT Cluster: [ ] Orangutan: TTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT--------ATGATTTGACCTTCTATCTGCT Human > Chimp ------------- chr6:81638552-81638560 Template switch process: F1: L TTGTTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT 1 F3: 4 GGATTTGACCTTCTATCTGCTTCTTCATTCCAGTGACAAAA R RF: TTGTTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGTATGATTTGACCTTCTATCTGCTTCTTCATTCCAGTGACAAAA RR: AACAAAGTTTAAATTGTCTTTTTACATAAGGTCTAGGTACATACTAAACTGGAAGATAGACGAAGAAGTAAGGTCACTGTTTT F2: 3 TACATAAGG 2 Unidirectional alignment (log-probability: -32.7) TGTTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGTggaatacATGgATTTGACCTTCTATCTGCTTCTTCATTCCAGTGACAAA TGTTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT-------ATG-ATTTGACCTTCTATCTGCTTCTTCATTCCAGTGACAAA Template switch alignment (log-probability: -22.4) TGTTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT|GGAATACAT|gGATTTGACCTTCTATCTGCTTCTTCATTCCAGTGACAAA TGTTTCAAATTTAACAGAAAAATGTATTCCAGATCCATGT|GGAATACAT|TGATTTGACCTTCTATCTGCTTCTTCATTCCAGTGACAAA ========== Event 3253 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATACTCATGTTGGTGTTTCC----CCAGCTTTCCTAACTTGAACTCGAGTCTACATTTATTTATTCATTTGTTTG----------------tttgtttgtttaacaagctcttatatcatgttcactatgttccaggcactgt Chimp: TATACTCATGTTGGTGTTTCCAACATGAACTTTCCTAACTTGAACTCGATTCTACATTTATTTATTCAtttgtttg----tttgtttgtttgtttgtttgtttaacaagctcttatatcatgttcactatgttccaggcactgt ↑ 1 4 3 2 Gorilla: TATACTCATGTTGGTGTTTCC----CCAGCTTTCCTAACTTGAACTCGATTCTACATTTATCTATTCATTGgtttgtttg------------tttgtttgtttaacaagctcttatatcatgttcactatgttccaggcactgt Human: TATACTCATGTTGGTGTTTCC----CCAGCTTTCCTAACTTGAACTCGAGTCTACATTTATTTATTCATTTGTTTG----------------tttgtttgtttaacaagctcttatatcatgttcactatgttccaggcactgt Cluster: [ ] Orangutan: TATACTCATGTTGGTGTTTCC----CCAGCTTTCCTAACTTGAACTCGATTCTAcatttatttattcatttgtttg----------------ttcatttgtttagcaagctcttatatcatgctcactatgttccaggcactgt Gorilla > Chimp --------------- chr6:81846520-81846525 Template switch process: F1: L GGTATGAGAAGAAGGAGAAATATACTCATGTTGGTGTTTCC 1 F3: 4 AACTTTCCTAACTTGAACTCGATTCTACATTTATTTATTCAT R RF: GGTATGAGAAGAAGGAGAAATATACTCATGTTGGTGTTTCCCCAGCTTTCCTAACTTGAACTCGATTCTACATTTATCTATTCATTGGTTTGTTTGTTTGTTTGTTTAACAAGCTCTTATATCATGTT RR: CCATACTCTTCTTCCTCTTTATATGAGTACAACCACAAAGGGGTCGAAAGGATTGAACTTGAGCTAAGATGTAAATAGATAAGTAACCAAACAAACAAACAAACAAATTGTTCGAGAATATAGTACAA F2: 3 GTACAA 2 Unidirectional alignment (log-probability: -37.9) GTATGAGAAGAAGGAGAAATATACTCATGTTGGTGTTTCC----aacatgaaCTTTCCTAACTTGAACTCGATTCTACATTTATtTATTC GTATGAGAAGAAGGAGAAATATACTCATGTTGGTGTTTCCCCAG--------CTTTCCTAACTTGAACTCGATTCTACATTTATCTATTC Template switch alignment (log-probability: -27.6) GTATGAGAAGAAGGAGAAATATACTCATGTTGGTGTTTCC|AACATG|AaCTTTCCTAACTTGAACTCGATTCTACATTTATtTATTC GTATGAGAAGAAGGAGAAATATACTCATGTTGGTGTTTCC|AACATG|AGCTTTCCTAACTTGAACTCGATTCTACATTTATCTATTC ========== Event 3254 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTGGGTAGTATTACCAGATGATTCTGATACTTTCACTCATATCTAG----AATCTTTCTGACCTGAAAGAATGACATT ↓ 3 2 1 4 Chimp: ACTGGGTAGTATTACCAGATGATTCTGATACTTTCACTCATATCTAG--AGAGAATCACTGACCTGAAAGAATGACATT Gorilla: ACTGGGTAGTATTACCAGATGATTCTGATACTTTCACTCATATATATAG--AGAGTCACTGATCTGAAAGGATGACATT Human: ACTGGGTAGTATTACCAGATGATTCTGATACTTTCACTCATATCTAG----AATCTTTCTGACCTGAAAGAATGACATT Cluster: [ ] Orangutan: ACTGGGTAGTATTACCAGATGATTCTGATACTTTCACTCATATCTAGAG--AGAATCACTGACCTGAAAGAATGACATT Human > Chimp ------------- chr6:95272313-95272319 Template switch process: F1: L TAGTATTACCAGATGATTCTGATACTTTCACTCATATCTAGAG 1 F3: 4 CTGACCTGAAAGAATGACATTCATAAATTTCAGGAGGGCC R RF: TAGTATTACCAGATGATTCTGATACTTTCACTCATATCTAGAATCTTTCTGACCTGAAAGAATGACATTCATAAATTTCAGGAGGGCC RR: ATCATAATGGTCTACTAAGACTATGAAAGTGAGTATAGATCTTAGAAAGACTGGACTTTCTTACTGTAAGTATTTAAAGTCCTCCCGG F2: 3 ACTAAGA 2 Unidirectional alignment (log-probability: -31.5) TATTACCAGATGATTCTGATACTTTCACTCATATCTAGAgagaatcA-----CTGACCTGAAAGAATGACATTCATAAATTTCAGGAGGGCC TATTACCAGATGATTCTGATACTTTCACTCATATCTAGA-------ATCTTTCTGACCTGAAAGAATGACATTCATAAATTTCAGGAGGGCC Template switch alignment (log-probability: -22.2) TATTACCAGATGATTCTGATACTTTCACTCATATCTAGAg|AGAATCA|CTGACCTGAAAGAATGACATTCATAAATTTCAGGAGGGCC TATTACCAGATGATTCTGATACTTTCACTCATATCTAGAA|AGAATCA|CTGACCTGAAAGAATGACATTCATAAATTTCAGGAGGGCC ========== Event 3255 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGATGGCATTACTGATAAGGAATGAAGGCTG--------GGAACTTGATTTAATTTCATTGAAC Chimp: AGATGGCATTACTGATAAGGAATGAAGGCCCCAGCCTTCATTCCTTGATTTAATTTCATTGAAC ↑ 3 1 2 4 Gorilla: AGATGGCATTACTGATAAGGAATGAAGGCTG--------GGAACTTGATTTAATTTCATTGAAC Human: AGATGGCATTACTGATAAGGAATGAAGGCTG--------GGAACTTGATTTAATTTCATTGAAC Cluster: [ ] Orangutan: AGATGGCATTACTGATAAGGAATGAAGGCTA--------GGAACTTGATTTAATTTCATTGAAC Gorilla > Chimp --------------- chr6:95251961-95251974 Template switch process: F1: L CCATGTCACTTTAGATGGCATTACTGATAAGGAATGAAGGC 1 F3: 4 CTTGATTTAATTTCATTGAACTTACCGCTGAGAGAATTAT R RF: CCATGTCACTTTAGATGGCATTACTGATAAGGAATGAAGGCTGGGAACTTGATTTAATTTCATTGAACTTACCGCTGACAGAATTAT RR: GGTACAGTGAAATCTACCGTAATGACTATTCCTTACTTCCGACCCTTGAACTAAATTAAAGTAACTTGAATGGCGACTGTCTTAATA F2: 3 CTTACTTCCGACCC 2 Unidirectional alignment (log-probability: -46.6) CATGTCACTTTAGATGGCATTACTGATAAGGAATGAAGGccccagccttcattC------CTTGATTTAATTTCATTGAACTTACCGCTGAgAGAATTAT CATGTCACTTTAGATGGCATTACTGATAAGGAATGAAGG--------------CTGGGAACTTGATTTAATTTCATTGAACTTACCGCTGACAGAATTAT Template switch alignment (log-probability: -23) CATGTCACTTTAGATGGCATTACTGATAAGGAATGAAGGC|CCCAGCCTTCATTC|CTTGATTTAATTTCATTGAACTTACCGCTGAgAGAATTAT CATGTCACTTTAGATGGCATTACTGATAAGGAATGAAGGC|CCCAGCCTTCATTC|CTTGATTTAATTTCATTGAACTTACCGCTGACAGAATTAT ========== Event 3256 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: AAACAGGGCAATTCCTTATTATTCAATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAA-AAAATGCTAATGCACACTTTGGAATTAAATGTAGCTCTGGGTAATAGAAGATATTTAAGGAAGTGAGCAGAATTATATGCATTAAAGAAGAATTAAAGAAG Chimp: AAACAGGGCAATTCCTTATTACTCGATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAA-AAAATGCTAATGCACACTTTGGAATTAAATGTAGCTCTGGGTAACAGAAGATATTTAAGGAAGTGAGCAGAATTATATGCATTAAAGAAGAATTAAAGAAG ↓ 1 4 3 2 Gorilla: AAACAGGGCAACTCCTTATTATGCAATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGaaaaaaaTGCTAATGCACACTTTGGAATTAAATGTAGCTCTGGGTAATAGAAGATATTTAAGGAAGTGAGCAGAATTATATGCATTAAAGAAGAATTAGAGAAG Human: AAACAGGGCAATTCCTTATTATTCAATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAA-AAAATGCTAATGCACACTTTGGAATTAAATGTAGCTCTGGGTAATAGAAGATATTTAAGGAAGTGAGCAGAATTATATGCATTAAAGAAGAATTAAAGAAG Cluster: [ ] Orangutan: AAACAGGGCAATTTCTTATTTTTCAATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAA-AAAATGCTAATACACACTTTGGAATTAAATGTAGCTCTGGGTAATAGAAGATATTTAAGGAAGTGAGCAGAATTATATGCATTAAAGAAGAATTAAAGAAG Chimp > Gorilla --------------- chr6:94702453-94702456 Template switch process: F1: L TCTCGAACTCTTAAGCATAAAAACAGGGCAACTCCTTATTA 1 F3: 4 ATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAAAAA R RF: TCTCAAACTCTTAAGCATAAAAACAGGGCAATTCCTTATTACTCGATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAAAAAATGCTAATGCACACTTTGGAATTAAATGTAGCTCTGGGTAACAGAAGATATTTAAGGAAGTGAGCAGAATTATATGCA RR: AGAGTTTGAGAATTCGTATTTTTGTCCCGTTAAGGAATAATGAGCTATATTAATCTAAACATACAATTCGAAATTCTCTCTTTTTTACGATTACGTGTGAAACCTTAATTTACATCGAGACCCATTGTCTTCTATAAATTCCTTCACTCGTCTTAATATACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -37) CTCgAACTCTTAAGCATAAAAACAGGGCAAcTCCTTATTAtgCaATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAAAAa CTCAAACTCTTAAGCATAAAAACAGGGCAATTCCTTATTACTCGATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAAAA- Template switch alignment (log-probability: -27.3) CTCgAACTCTTAAGCATAAAAACAGGGCAAcTCCTTATTA|TGCA|ATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAAAAA CTCAAACTCTTAAGCATAAAAACAGGGCAATTCCTTATTA|TGCA|ATATAATTAGATTTGTATGTTAAGCTTTAAGAGAGAAAAA ========== Event 3257 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GATGTCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGGACTGATAACTACCAATGATCCTTTGT ↑ 3 2 1 4 Chimp: GATATCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGAACCAATAACTACCAATGATCCTTTGT Gorilla: GATATCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGAACTAATAACTACCAATGATCCTTTGT Human: GATGTCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGGACTGATAACTACCAATGATCCTTTGT Cluster: [ ] Orangutan: GATATCTGCTATTGTACATTCAGTCTTTGGTTAAAGAGTGGAACTAATAACTACCAATGATCCTTTGT Chimp > Human ------------- chr6:92835275-92835280 Template switch process: F1: L GATGTCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGG 1 F3: 4 TAACTACCAATGATCCTTTGTTATATATGCTTTTTT R RF: GATATCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGAACCAATAACTACCAATGATCCTTTGTTATATATGCTTTTTT RR: CTATAGACGATAACATATAAGTCAGAAACCAATTTCTCACCTTGGTTATTGATGGTTACTAGGAAACAATATATACGAAAAAA F2: 3 AGTCAG 2 Unidirectional alignment (log-probability: -32.1) ATgTCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGgACtgATAACTACCAATGATCCTTTGTTATATATGCTTTTTT--- ATATCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGGAACCAATAACTACCAATGATCCTTTGTTATATATGCTTTTTTTTT Template switch alignment (log-probability: -21.9) ATgTCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGG|GACTGA|TAACTACCAATGATCCTTTGTTATATATGCTTTTTT ATATCTGCTATTGTATATTCAGTCTTTGGTTAAAGAGTGG|GACTGA|TAACTACCAATGATCCTTTGTTATATATGCTTTTTT ========== Event 3258 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAAAAAGGCAGCACTTGGGTGCTAAAAAGCCATAATATTTTTCCTGGAAG Chimp: TTAAAAAGGCAGCACTTGGGTTT----TAGCCATAATATTTTTCCTGGAAG Gorilla: TTAAAAAGGCAGCACTTGGGTTT----TAGCCATAATATTTTTCCTGGAAG ↓ 3 4 2 Human: TTAAAAAGGCAGCACTTGGGTGCTAAAAAGCCATAATATTTTTCCTGGAAG Cluster: [ ] Orangutan: TTAAAAAGGCAGCACTTGGGTTT----TAGCCATACTATTTTTCCTGGAAG Gorilla > Human --------------- chr6:93271697-93271703 Template switch process: F1: L ATTTAGTCATTATAGGTGGATTAAAAAGGCAGCACTTGGGT 1 F3: 4 AGCCATAATATTTTTCCTGGAAGGAGAGGTGTAAATAAGT R RF: ATTTAGTCATTATAGGCGGATTAAAAAGGCAGCACTTGGGTTTTAGCCATAATATTTTTCCTGGAAGGAGAGGTGTAAATAAGT RR: TAAATCAGTAATATCCGCCTAATTTTTCCGTCGTGAACCCAAAATCGGTATTATAAAAAGGACCTTCCTCTCCACATTTATTCA F2: 3 AAAATCG 2 Unidirectional alignment (log-probability: -33.2) TTTAGTCATTATAGGtGGATTAAAAAGGCAGCACTTGGGTgcTaaaaAGCCATAATATTTTTCCTGGAAGGAGAGGTGTAAATAAGT TTTAGTCATTATAGGCGGATTAAAAAGGCAGCACTTGGGTTTT----AGCCATAATATTTTTCCTGGAAGGAGAGGTGTAAATAAGT Template switch alignment (log-probability: -22.1) TTTAGTCATTATAGGtGGATTAAAAAGGCAGCACTTGGGT|GCTAAAA|AGCCATAATATTTTTCCTGGAAGGAGAGGTGTAAATAAGT TTTAGTCATTATAGGCGGATTAAAAAGGCAGCACTTGGGT|GCTAAAA|AGCCATAATATTTTTCCTGGAAGGAGAGGTGTAAATAAGT ========== Event 3259 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTGTATAAGGCAAGTATTTTGCACATTATCATA------TGTGCATTTCCATATGATGATACTCAGCTGATTATAATCATAAA ↓ 1 4 3 2 ↑ 3 2 1 4 Chimp: TTGTATAAGGCAAGTATTTTGCACATTATCAAG---AATCATCAATTTCCATATGATGATACTCAGCTGATTATAATCATAAA Gorilla: TTGCATAAGGCAAGTATTTTGCACATTATCAAGAAT---CATCAATTTCCATATGATGATACTCAGCTGATTATAATCATAAA ↓ 3 2 1 4 ↑ 1 4 3 2 Human: TTGTATAAGGCAAGTATTTTGCACATTATCATA------TGTGCATTTCCATATGATGATACTCAGCTGATTATAATCATAAA Cluster: [ ] Orangutan: TTGTATAAGGCAAGTATTTTGCACATTATCAAGAAT---CATCAATTTCCATATGATGATACTCAGCTGATTATAATCATAAA Chimp > Human ------------- chr6:76657876-76657882 Template switch process: F1: L TAGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCAT 1 F3: 4 TTTCCATATGATGATACTCAGCTGATTATAATCATAAAG R RF: TAGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCAAGAATCATCAATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG RR: ATCCGGGGACAACATATTCCGTTCATAAAACGTGTAATAGTTCTTAGTAGTTAAAGGTATACTACTATGAGTCGACTAATATTAGTATTTC F2: 3 ACGTGTA 2 Unidirectional alignment (log-probability: -31.7) GGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCAtatgtgc----------ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG GGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCA-------AGAATCATCAATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Template switch alignment (log-probability: -22.1) GGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCAt|ATGTGCA|TTTCCATATGATGATACTCAGCTGATTATAATCATAAAG GGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCAA|ATGTGCA|TTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Human > Chimp ------------- chr6:77978190-77978199 Template switch process: F1: L TAGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCA 1 F3: 4 ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG R RF: TAGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCATATGTGCATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG RR: ATCCGGGGACAACATATTCCGTTCATAAAACGTGTAATAGTATACACGTAAAGGTATACTACTATGAGTCGACTAATATTAGTATTTC F2: 3 ACTACTAAGA 2 Unidirectional alignment (log-probability: -35.9) AGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCA-------agaatcatcaATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG AGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCATATGTGC----------ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Template switch alignment (log-probability: -22.5) AGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCA|AGaATCATCA|ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG AGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCA|AGTATCATCA|ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Gorilla > Human --------------- chr6:76657876-76657882 Template switch process: F1: L TAGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCAT 1 F3: 4 TTTCCATATGATGATACTCAGCTGATTATAATCATAAAG R RF: TAGGCCCCTGTTGCATAAGGCAAGTATTTTGCACATTATCAAGAATCATCAATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG RR: ATCCGGGGACAACGTATTCCGTTCATAAAACGTGTAATAGTTCTTAGTAGTTAAAGGTATACTACTATGAGTCGACTAATATTAGTATTTC F2: 3 ACGTGTA 2 Unidirectional alignment (log-probability: -36.7) GGCCCCTGTTGtATAAGGCAAGTATTTTGCACATT----------ATCAtatgtgcATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG GGCCCCTGTTGCATAAGGCAAGTATTTTGCACATTATCAAGAATCATCA-------ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Template switch alignment (log-probability: -27.7) GGCCCCTGTTGtATAAGGCAAGTATTTTGCACATTATCAt|ATGTGCA|TTTCCATATGATGATACTCAGCTGATTATAATCATAAAG GGCCCCTGTTGCATAAGGCAAGTATTTTGCACATTATCAA|ATGTGCA|TTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Human > Gorilla --------------- chr6:76739061-76739070 Template switch process: F1: L TAGGCCCCTGTTGCATAAGGCAAGTATTTTGCACATTATCA 1 F3: 4 ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG R RF: TAGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCATATGTGCATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG RR: ATCCGGGGACAACATATTCCGTTCATAAAACGTGTAATAGTATACACGTAAAGGTATACTACTATGAGTCGACTAATATTAGTATTTC F2: 3 ACTACTAAGA 2 Unidirectional alignment (log-probability: -40.9) AGGCCCCTGTTGcATAAGGCAAGTATTTTGCACATTATCA-------agaatcatcaATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG AGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCATATGTGC----------ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG Template switch alignment (log-probability: -28) AGGCCCCTGTTGcATAAGGCAAGTATTTTGCACATTATCA|AGaATCATCA|ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG AGGCCCCTGTTGTATAAGGCAAGTATTTTGCACATTATCA|AGTATCATCA|ATTTCCATATGATGATACTCAGCTGATTATAATCATAAAG ========== Event 3260 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGATATAGTTGCAATTTTCAG-----TGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATAC Chimp: GTGATATAGTTGCAATTTTCAG-----TGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATAC ↓ 1 4 3 2 Gorilla: GTGATATAGTTGCAATTTTCAATTATGTCTTGAGGAAAGACATAATTATTCAATGAGTGGTGATAC ↑ 1 4 3 2 Human: GTGATATAGTTGCAATTTTCAG-----TGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATAC Cluster: [ ] Orangutan: GTGATATAGTTGCAAT-TTCAG-----TGGTGAGGAAAGACATAATTATTCAATGAGTGGT----- Human > Gorilla --------------- chr6:96723639-96723647 Template switch process: F1: L CCCTCATTGGAGTTTAATGTGTGATATAGTTGCAATTTTCA 1 F3: 4 TGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA R RF: CCCTCATTGGAGTTTAGTGTGTGATATAGTTGCAATTTTCAGTGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA RR: GGGAGTAACCTCAAATCACACACTATATCAACGTTAAAAGTCACCACTCCTTTCTGTATTAATAAGTTACTCACCACTATGCTGT F2: 3 TCTGTATTA 2 Unidirectional alignment (log-probability: -34.7) CCTCATTGGAGTTTAaTGTGTGATATAGTTGCAATTTTCAattatGTctTGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA CCTCATTGGAGTTTAGTGTGTGATATAGTTGCAATTTTCA-----GTGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA Template switch alignment (log-probability: -22.4) CCTCATTGGAGTTTAaTGTGTGATATAGTTGCAATTTTCA|ATTATGTCT|TGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA CCTCATTGGAGTTTAGTGTGTGATATAGTTGCAATTTTCA|ATTATGTCT|TGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA Chimp > Gorilla --------------- chr6:96723639-96723647 Template switch process: F1: L CCCTCATTGGAGTTTAATGTGTGATATAGTTGCAATTTTCA 1 F3: 4 TGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA R RF: CCCTCATTGGAGTTTAGTGTGTGATATAGTTGCAATTTTCAGTGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA RR: GGGAGTAACCTCAAATCACACACTATATCAACGTTAAAAGTCACCACTCCTTTCTGTATTAATAAGTTACTCACCACTATGCTGT F2: 3 TCTGTATTA 2 Unidirectional alignment (log-probability: -34.7) CCTCATTGGAGTTTAaTGTGTGATATAGTTGCAATTTTCAattatGTctTGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA CCTCATTGGAGTTTAGTGTGTGATATAGTTGCAATTTTCA-----GTGGTGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA Template switch alignment (log-probability: -22.4) CCTCATTGGAGTTTAaTGTGTGATATAGTTGCAATTTTCA|ATTATGTCT|TGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA CCTCATTGGAGTTTAGTGTGTGATATAGTTGCAATTTTCA|ATTATGTCT|TGAGGAAAGACATAATTATTCAATGAGTGGTGATACGACA ========== Event 3261 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 345 Detected in comparisons: 3456 Multiple sequence alignment: Human: AATACCAAATAATAGAACTTTTATTTAGTTACCTTATTTGATTAAAGAATCAAATAAGGTAACTAAATACCAAAATAATAGAACTCATAT Chimp: AATACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTAAAGAATCAAATAAGGTAACTAAATACCAAAATAATAGAACTCGTAT ↑ 3 1 2 4 Gorilla: AATACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTCTTTAATCAAATAAGGTAGCTAAATACCAAAATAATAGAACTCGTAT ↓ 3 1 2 4 ↑ 1 3 4 2 Human: AATACCAAATAATAGAACTTTTATTTAGTTACCTTATTTGATTAAAGAATCAAATAAGGTAACTAAATACCAAAATAATAGAACTCATAT Cluster: [ ] Orangutan: -----------------------------------------------------------------------AAAATAATAGAACTTGTAT Gorilla > Human --------------- chr6:74787042-74787060 Template switch process: F1: L TACCAAATAATAGAACTTTTATTTAGTTACCTTATTTGATT 1 F3: 4 CTAAATACCAAAATAATAGAACTCA R RF: TACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTCTTTAATCAAATAAGGTAGCTAAATACCAAAATAATAGAACTCG RR: ATGGTTTATTATCTTGAACATAAATCAATGGAATAAACTAAGAAATTAGTTTATTCCATCGATTTATGGTTTTATTATCTTGAGC F2: 3 AATGGAATAAACTAAGAAA 2 Unidirectional alignment (log-probability: -39.8) ACCAAATAATAGAACTTtTATTTAGTTACCTTATTTGATTaaagAATCAAATAAGGTAaCTAAATACCAAAATAATAGAACTCa ACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTCTTTAATCAAATAAGGTAGCTAAATACCAAAATAATAGAACTCG Template switch alignment (log-probability: -28.8) ACCAAATAATAGAACTTtTATTTAGTTACCTTATTTGATT|AAAGAATCAAATAAGGTAA|CTAAATACCAAAATAATAGAACTCa ACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATT|AAAGAATCAAATAAGGTAA|CTAAATACCAAAATAATAGAACTCG Human > Gorilla --------------- chr6:75251459-75251486 Template switch process: F1: L TACCAAATAATAGAACTT 1 F3: 4 ATCAAATAAGGTAGCTAAATACCAAAATAATAGAACTCG R RF: TACCAAATAATAGAACTTTTATTTAGTTACCTTATTTGATTAAAGAATCAAATAAGGTAACTAAATACCAAAATAATAGAACTCA RR: ATGGTTTATTATCTTGAAAATAAATCAATGGAATAAACTAATTTCTTAGTTTATTCCATTGATTTATGGTTTTATTATCTTGAGT F2: 3 ATTTCTTAGTTTATTCCATTGATTTATG 2 Unidirectional alignment (log-probability: -39.8) TACCAAATAATAGAACTTgTATTTAGTTACCTTATTTGATTctttAATCAAATAAGGTAgCTAAATACCAAAATAATAGAACTCg TACCAAATAATAGAACTTTTATTTAGTTACCTTATTTGATTAAAGAATCAAATAAGGTAACTAAATACCAAAATAATAGAACTCA Template switch alignment (log-probability: -29.7) TACCAAATAATAGAACTT|GTATTTAGTTACCTTATTTGATTCTTTA|ATCAAATAAGGTAgCTAAATACCAAAATAATAGAACTCg TACCAAATAATAGAACTT|GTATTTAGTTACCTTATTTGATTCTTTA|ATCAAATAAGGTAACTAAATACCAAAATAATAGAACTCA Gorilla > Chimp --------------- chr6:76098265-76098283 Template switch process: F1: L TACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATT 1 F3: 4 CTAAATACCAAAATAATAGAACTCG R RF: TACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTCTTTAATCAAATAAGGTAGCTAAATACCAAAATAATAGAACTCG RR: ATGGTTTATTATCTTGAACATAAATCAATGGAATAAACTAAGAAATTAGTTTATTCCATCGATTTATGGTTTTATTATCTTGAGC F2: 3 AATGGAATAAACTAAGAAA 2 Unidirectional alignment (log-probability: -28.8) ACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTaaagAATCAAATAAGGTAaCTAAATACCAAAATAATAGAACTCG ACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATTCTTTAATCAAATAAGGTAGCTAAATACCAAAATAATAGAACTCG Template switch alignment (log-probability: -17.8) ACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATT|AAAGAATCAAATAAGGTAA|CTAAATACCAAAATAATAGAACTCG ACCAAATAATAGAACTTGTATTTAGTTACCTTATTTGATT|AAAGAATCAAATAAGGTAA|CTAAATACCAAAATAATAGAACTCG ========== Event 3262 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGAAAAAATAAAATCTGTACCTGCCAAAAAATCTGTACCTGCCTTCTATTTTGTGTAGAAAACTACACAAAATAA------TTTACACTTGTGTggccaggcgcggtg-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gctcatgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggaattcaagatcagcctg Chimp: TGGAAAAAATAAAATCTGTACCTGCCAAAAAATCTGTACCTGCCTTCTATTTTGTGTAGAAAACTACACAAAATAA------TTTACACTTGTGTggccaggcgcggtg-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gctcatgcctgtaatcccagcactttgggaggctgaggcgggtagatcatgaggtcaggaattcaagatcagcctg ↓ 1 3 2 4 Gorilla: ------------------------------------------TAAATTATTTTGTGTAGTTTTCTACACAAAATAGAAGGCAGGTACAGATTTTTTGGCAGGTACAGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human: TGGAAAAAATAAAATCTGTACCTGCCAAAAAATCTGTACCTGCCTTCTATTTTGTGTAGAAAACTACACAAAATAA------TTTACACTTGTGTggccaggcgcggtg-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gctcatgcctgtaatcccagcactttgggaggctgaggcgggtagatcacgaggtcaggaattcaagatcagcctg Cluster: [ ] Orangutan: ------------------------------------------TCTTCTATTTTGTGTAGAAAACTACACAAAATAA------TTTACACTTGTGTggccaggcgcggtggctcatgcctgtaattccagcactttgggaggctgaggtgggtagatcacgaggtcaggaattcaagatcagcatgggcaagatgctgatcttgccatctctactaaaaatgcaaaaaatgtgccaggcgtggtggcgggcacctgtaatcccagctactcgggaggctgaggcaggagaatggcgtgaacctggaaggcggagattgcagtgagctgcgatcacaccactgcattccagcctgggcgacagagcat---------------------------------------------------------------------------- Chimp > Gorilla --------------- chr6:75163982-75164036 Template switch process: F1: L TA 1 F3: 4 AGGT R RF: TACCTGCCAAAAAATCTGTACCTGCCTTCTATTTTGTGTAGAAAACTACACAAAATAATTTACACTTGTGTGGCCAGGCGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTAGATCATGAGGT RR: ATGGACGGTTTTTTAGACATGGACGGAAGATAAAACACATCTTTTGATGTGTTTTATTAAATGTGAACACACCGGTCCGCGCCACCGAGTACGGACATTAGGGTCGTGAAACCCTCCGACTCCGCCCATCTAGTACTCCA F2: 3 CGGTTTTTTAGACATGGACGGAAGATAAAACACATCTTTTGATGTGTTTTATTAA 2 Unidirectional alignment (log-probability: -101) T----------AAAT--------------TATTTTGTGTAGttttCTACACAAAATAgaaggcaggtacagattttttggcaggt---------------------- TACCTGCCAAAAAATCTGTACCTGCCTTCTATTTTGTGTAGAAAACTACACAAAATA----------------------------ATTTACACTTGTGTGGCCAGGC Template switch alignment (log-probability: -20.8) TA|AATTATTTTGTGTAGTTTTCTACACAAAATAGAAGGCAGGTACAGATTTTTTGGC|AGGT TA|AATTATTTTGTGTAGTTTTCTACACAAAATAGAAGGCAGGTACAGATTTTTTGGC|AGGT ========== Event 3263 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGAAGATTATTCCAACAAATTGACCTAGAGACCCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTTT Chimp: TGGAAGATTATTCCAACAAATTGACCTAGAGACCCCTTTTTCACAGCCCAAGATACTTGTAAAACTGTCCTTTT ↓ 1 4 3 2 Gorilla: TGGAAGATTATTCCAACAAAT-AATCTTG--GGCCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTTT ↑ 1 4 3 2 Human: TGGAAGATTATTCCAACAAATTGACCTAGAGACCCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTTT Cluster: [ ] Orangutan: -------------------------------------------------------------------------- Human > Gorilla --------------- chr6:10438070-10438077 Template switch process: F1: L ATCATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATA 1 F3: 4 CCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT R RF: ATCATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATTGACCTAGAGACCCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT RR: TAGTATAAACAAATTTTCTAACCTTCTAATAAGGTTGTTTAACTGGATCTCTGGGGAAAAAGTGTCGGGTTCTATGAACATTTTGAGAGGAAA F2: 3 GGGTTCTA 2 Unidirectional alignment (log-probability: -34.2) CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAAT------------aatcttgggCCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATTGACCTAGAGAC---------CCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT Template switch alignment (log-probability: -22.3) CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATa|ATCTTGGG|CCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATT|ATCTTGGG|CCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT Chimp > Gorilla --------------- chr6:10438070-10438077 Template switch process: F1: L ATCATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATA 1 F3: 4 CCCTTTTTCACAGCCCAAGATACTTGTAAAACTCTCCTTT R RF: ATCATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATTGACCTAGAGACCCCTTTTTCACAGCCCAAGATACTTGTAAAACTGTCCTTT RR: TAGTATAAACAAATTTTCTAACCTTCTAATAAGGTTGTTTAACTGGATCTCTGGGGAAAAAGTGTCGGGTTCTATGAACATTTTGACAGGAAA F2: 3 GGGTTCTA 2 Unidirectional alignment (log-probability: -39.7) CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAAT------------aatcttgggCCCTTTTTCACAGCCCAAGATACTTGTAAAACTcTCCTTT CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATTGACCTAGAGAC---------CCCTTTTTCACAGCCCAAGATACTTGTAAAACTGTCCTTT Template switch alignment (log-probability: -27.8) CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATa|ATCTTGGG|CCCTTTTTCACAGCCCAAGATACTTGTAAAACTcTCCTTT CATATTTGTTTAAAAGATTGGAAGATTATTCCAACAAATT|ATCTTGGG|CCCTTTTTCACAGCCCAAGATACTTGTAAAACTGTCCTTT ========== Event 3264 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTATTTTACATTACAGGAATA---AGTACTCACCATGATTTTGCTTATA ↓ 13 4 2 Chimp: CTATTTTACATTACAGGAATAGTACTTACTCACCATGATTTTGCTTATA ↑ 13 4 2 Gorilla: CTATTTTACATTACAGGAATA---AGTACTCACCATGATTTTGCTTATA Human: CTATTTTACATTACAGGAATA---AGTACTCACCATGATTTTGCTTATA Cluster: [ ] Orangutan: CTATTTTACATTACAGGAATA---AGTACTCACCATGATTTTGCTTATA Human > Chimp ------------- chr6:102368673-102368677 Template switch process: F1: L TGATTAAAATAGTAACTGGACTATTTTACATTACAGGAATA 1 F3: 4 TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG R RF: TGATTAAAATAGTAACTGGACTATTTTACATTACAGGAATAAGTACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG RR: ACTAATTTTATCATTGACCTGATAAAATGTAATGTCCTTATTCATGAGTGGTACTAAAACGAATATACTTCTGTCAAGGATCC F2: 3 TCATG 2 Unidirectional alignment (log-probability: -26.9) GATTAAAATAGTAACTGGACTATTTTACATTACAGGAAT-AGtactTACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG GATTAAAATAGTAACTGGACTATTTTACATTACAGGAATAAG----TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG Template switch alignment (log-probability: -15.9) GATTAAAATAGTAACTGGACTATTTTACATTACAGGAATA|GTACT|TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG GATTAAAATAGTAACTGGACTATTTTACATTACAGGAATA|GTACT|TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG Gorilla > Chimp --------------- chr6:102368673-102368677 Template switch process: F1: L TGATTAAAATAGTAACTGGACTATTTTACATTACAGGAATA 1 F3: 4 TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG R RF: TGATTAAAATAGTAACTGGACTATTTTACATTACAGGAATAAGTACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG RR: ACTAATTTTATCATTGACCTGATAAAATGTAATGTCCTTATTCATGAGTGGTACTAAAACGAATATACTTCTGTCAAGGATCC F2: 3 TCATG 2 Unidirectional alignment (log-probability: -26.3) GATTAAAATAGTAACTGGACTATTTTACATTACAGGAAtagTActTACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG GATTAAAATAGTAACTGGACTATTTTACATTACAGGAA---TAAGTACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG Template switch alignment (log-probability: -16.4) GATTAAAATAGTAACTGGACTATTTTACATTACAGGAATA|GTACT|TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG GATTAAAATAGTAACTGGACTATTTTACATTACAGGAATA|GTACT|TACTCACCATGATTTTGCTTATATGAAGACAGTTCCTAGG ========== Event 3265 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTAAAAAAATCAAATGGCTAG-GATCAAATGACAAATGATCCTAATAGCCACTTACTTTCAG Chimp: ACTaaaaaaaTCAAATGGCTATTTTTCCCATGACAAATGATCCTAATAGCCACTTACTTTCAG Gorilla: ACTaaaaaaaTCAAATGGCTATTTTTCCCATGACAAATGATCCTAATAGCCACTTACTTTCAG ↓ 1 4 3 2 Human: ACTAAAAAAATCAAATGGCTAG-GATCAAATGACAAATGATCCTAATAGCCACTTACTTTCAG Cluster: [ ] Orangutan: ACTAAAAAAATCAAATAGCTCTTTTTCCCATGACAAATGATCCTAATAGCCACTTACTTTCAG Gorilla > Human --------------- chr6:98809291-98809296 Template switch process: F1: L ACATTTGCTAATTTGACTAAACTAAAAAAATCAAATGGCTA 1 F3: 4 AATGACAAATGATCCTAATAGCCACTTACTTTCAGGAATAA R RF: ACATTTGCTAATTTGACTAAACTAAAAAAATCAAATGGCTATTTTTCCCATGACAAATGATCCTAATAGCCACTTACTTTCAGGAATAA RR: TGTAAACGATTAAACTGATTTGATTTTTTTAGTTTACCGATAAAAAGGGTACTGTTTACTAGGATTATCGGTGAATGAAAGTCCTTATT F2: 3 ACTAGG 2 Unidirectional alignment (log-probability: -31.1) CATTTGCTAATTTGACTAAACTAAAAAAATCAAATGGCTA--------ggatcaaATGACAAATGATCCTAATAGCCACTTACTTTCAGGAATA CATTTGCTAATTTGACTAAACTAAAAAAATCAAATGGCTATTTTTCCC-------ATGACAAATGATCCTAATAGCCACTTACTTTCAGGAATA Template switch alignment (log-probability: -22) CATTTGCTAATTTGACTAAACTAAAAAAATCAAATGGCTA|GGATCA|aATGACAAATGATCCTAATAGCCACTTACTTTCAGGAATA CATTTGCTAATTTGACTAAACTAAAAAAATCAAATGGCTA|GGATCA|CATGACAAATGATCCTAATAGCCACTTACTTTCAGGAATA ========== Event 3266 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TATTTATGTTCATAACAGCAAGGCTTTGCATTTGAGTCTTTTGTCTTAAGTTTGCCCATAGGTAAATTTAACACTCGAGTAACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCGAGC-----CCTGTAGCTGATGGCTGGGCTGCA Chimp: TATTTATGTTCATAACAGCAAGGCTTTGCATTTGAGTCTTTTGTCTTAAGTTTGCCCATAGGTAAATTTAACACTCGAGTAACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCAAGC-----CCTGTAGCTGATGGCTGGGCTGCA ↑ 3 2 1 4 Gorilla: TATTTATGTTCATAACAGCAAGGCTTTGCATTTGAGTCTTTTGTCTTAAGTTTGCCCATAGGTAAATTTAACACTCGAGTAACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCGAAACATCAGCGGTAGCTGATGGCTGGGCTGCA Human: TATTTATGTTCATAACAGCAAGGCTTTGCATTTGAGTCTTTTGTCTTAAGTTTGCCCATAGGTAAATTTAACACTCGAGTAACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCGAGC-----CCTGTAGCTGATGGCTGGGCTGCA Cluster: [ ] Orangutan: AATTTATGTTCATAACAGCAAGGCTTTGCATTTGAGTCTTTTGTCTTAAGTTTGCCCATAGGTAAATTTAACACTCGAGTAACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCGAGC-----CCTGTAGCTGATGACTGGGCTGCA Gorilla > Chimp --------------- chr6:102441243-102441249 Template switch process: F1: L AACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGC 1 F3: 4 GTAGCTGATGGCTGGGCTGCAAATGCTACAATACACTCCC R RF: AAGGCTTTGCATTTGAGTCTTTTGTCTTAAGTTTGCCCATAGGTAAATTTAACACTCGAGTAACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCGAAACATCAGCGGTAGCTGATGGCTGGGCTGCAAATGCTATAATACACTCCC RR: TTCCGAAACGTAAACTCAGAAAACAGAATTCAAACGGGTATCCATTTAAATTGTGAGCTCATTGGTTACGAGACAGATAACGGAACCCAACAAAAGTGATCGCTTTGTAGTCGCCATCGACTACCGACCCGACGTTTACGATATTATGTGAGGG F2: 3 TCCCGAA 2 Unidirectional alignment (log-probability: -36.8) ACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGC------------aagccctGTAGCTGATGGCTGGGCTGCAAATGCTAcAATACACTCCC ACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGCGAAACATCAGCG-------GTAGCTGATGGCTGGGCTGCAAATGCTATAATACACTCCC Template switch alignment (log-probability: -27.7) ACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGC|AAGCCcT|GTAGCTGATGGCTGGGCTGCAAATGCTAcAATACACTCCC ACCAATGCTCTGTCTATTGCCTTGGGTTGTTTTCACTAGC|AAGCCTT|GTAGCTGATGGCTGGGCTGCAAATGCTATAATACACTCCC ========== Event 3267 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGACGAGTCTCTTGTTGCAAA-------------ATGTGTGGCTCTCAGCCACACAGAACCTcggagtctcgctctgaaatccaggctg Chimp: GGACGAGTCTCTTGTTGCAAA-------------ATGTGTGGCTCTCAGCCACACAGAACCTcggagtctcgctctgaaatccaggctg ↓ 1 4 3 2 Gorilla: GGACGAGTCTCTTGTTGCAAA--------------------------AGACTCCGAGAACCTcggagtctcgctctgaaatccaggctg ↑ 1 4 3 2 Human: GGACGAGTCTCTTGTTGCAAA-------------ATGTGTGGCTCTCAGCCACACAGAACCTcggagtctcgctctgaaatccaggctg Cluster: [ ] Orangutan: GGACGAGTCTCTTGTTGCAAAATTTGTGGCTCTC-------------AGCCACACACAACCTcagagtcttgctctgaaatccaggctg Human > Gorilla --------------- chr7:76136910-76136916 Template switch process: F1: L TAAGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA 1 F3: 4 AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC R RF: TAAGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAATGTGTGGCTCTCAGCCACACAGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC RR: ATTCCTGTGGATACCTTTTCCCTGCTCAGAGAACAACGTTTTACACACCGAGAGTCGGTGTGTCTTGGAGCCTCAGAGCGAGACTTTAGGTCCGACCTCACG F2: 3 GCCTCAG 2 Unidirectional alignment (log-probability: -31.7) AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA--------------------gactccgAGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAATGTGTGGCTCTCAGCCACAC-------AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC Template switch alignment (log-probability: -16.6) AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA|GACTCCG|AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA|GACTCCG|AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC Chimp > Gorilla --------------- chr7:76136910-76136916 Template switch process: F1: L TAAGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA 1 F3: 4 AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGTGC R RF: TAAGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAATGTGTGGCTCTCAGCCACACAGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGCGC RR: ATTCCTGTGGATACCTTTTCCCTGCTCAGAGAACAACGTTTTACACACCGAGAGTCGGTGTGTCTTGGAGCCTCAGAGCGAGACTTTAGGTCCGACCTCGCG F2: 3 GCCTCAG 2 Unidirectional alignment (log-probability: -37.2) AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA--------------------gactccgAGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGtGC AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAATGTGTGGCTCTCAGCCACAC-------AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGCGC Template switch alignment (log-probability: -22.2) AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA|GACTCCG|AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGtGC AGGACACCTATGGAAAAGGGACGAGTCTCTTGTTGCAAAA|GACTCCG|AGAACCTCGGAGTCTCGCTCTGAAATCCAGGCTGGAGCGC ========== Event 3268 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTTGGTTTTCTAACTAAATAT--------------------ACTGCATAACTAT------------GTTATGCAATATATTTACAAAAAATTTTAGCATTT Chimp: TCTTGGTTTTCTAACTAAATAT--------------------ATTGCATAACTAT------------GTTATGCAATATATTTACAAAAAATTTTAGCATTT ↑ 3 2 41 Gorilla: TCTTGGTTTTCTAACTAAATAT--------------------ATTGCATAACTAT------------------------GTTTACAAAAAATTTTAGCATTT ↓ 3 2 41 Human: TCTTGGTTTTCTAACTAAATAT--------------------ACTGCATAACTAT------------GTTATGCAATATATTTACAAAAAATTTTAGCATTT Cluster: [ ] Orangutan: TCTTGGTTTTCTAACTAAATATATTATAGTTAGAAAATAGTTATTGCATAACTATGTTATGCAATAT------------ATTTACAAAAAATGTTAGCATTT Gorilla > Human --------------- chr6:96560868-96560877 Template switch process: F1: L ATGTGGTCTTGGTTTTCTAACTAAATATACTGCATAACTATGTT 1 F3: 4 TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA R RF: ATGTGGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGTTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA RR: TACACCAGAACCAAAAGATTGATTTATATAACGTATTGATACAAATGTTTTTTAAAATCGTAAAGAGACATAGTAATTATAT F2: 3 ATATAACGTA 2 Unidirectional alignment (log-probability: -33.7) GGTCTTGGTTTTCTAACTAAATATAcTGCATAACTATGttatgcaatataTTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA GGTCTTGGTTTTCTAACTAAATATATTGCATAACTATG------------TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA Template switch alignment (log-probability: -22.6) GGTCTTGGTTTTCTAACTAAATATAcTGCATAACTATGTT|ATGCAATATA|TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA GGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGTT|ATGCAATATA|TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA Gorilla > Chimp --------------- chr6:99835466-99835475 Template switch process: F1: L ATGTGGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGTT 1 F3: 4 TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA R RF: ATGTGGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGTTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA RR: TACACCAGAACCAAAAGATTGATTTATATAACGTATTGATACAAATGTTTTTTAAAATCGTAAAGAGACATAGTAATTATAT F2: 3 ATATAACGTA 2 Unidirectional alignment (log-probability: -28.2) GGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGttatgcaatataTTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA GGTCTTGGTTTTCTAACTAAATATATTGCATAACTATG------------TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA Template switch alignment (log-probability: -17.1) GGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGTT|ATGCAATATA|TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA GGTCTTGGTTTTCTAACTAAATATATTGCATAACTATGTT|ATGCAATATA|TTTACAAAAAATTTTAGCATTTCTCTGTATCATTAATATA ========== Event 3269 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: CTTCGCGAAGACGCCCAGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGC-TCTG-----------------AGAGGCCGGCAAGTGGGGCACCTGTCCCCTTCCTTGG ↓ 3 2 1 4 Chimp: CTTCGCAAAGACGCCCAGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGCACCTT------------------------------AGAGGCACCTGTCCCCTTCCTTGG Gorilla: Human: CTTCGCGAAGACGCCCAGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGC-TCTG-----------------AGAGGCCGGCAAGTGGGGCACCTGTCCCCTTCCTTGG Cluster: [ ] Orangutan: CTTCGCCAAGACGCCCAGCTCCAAGGTGGTTAAGGAGGGAGGCCGGCAAGTGGGGC---TGAGAGGTTATGGCACCTT-------------AGAGGCACCTGTCCTCTTCCTTGG Human > Chimp ------------- chr7:60652786-60652793 Template switch process: F1: L CAGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGC 1 F3: 4 GGCACCTGTCCCCTTCCTTGGAGCCCACTTGAGGTACCCC R RF: CAGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGCTCTGAGAGGCCGGCAAGTGGGGCACCTGTCCCCTTCCTTGGAGCCCACTTGAGGTACCCC RR: GTCGAGGTTCCACCCATTCCTCCCTCCGGCCGTTCACCCCGAGACTCTCCGGCCGTTCACCCCGTGGACAGGGGAAGGAACCTCGGGTGAACTCCATGGGG F2: 3 AGATTCCA 2 Unidirectional alignment (log-probability: -33.7) AGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGCaccttaga--------------------GGCACCTGTCCCCTTCCTTGGAGCCCACTTGAGGTACCCC AGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGC--------TCTGAGAGGCCGGCAAGTGGGGCACCTGTCCCCTTCCTTGGAGCCCACTTGAGGTACCCC Template switch alignment (log-probability: -22.3) AGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGC|ACCTTaGA|GGCACCTGTCCCCTTCCTTGGAGCCCACTTGAGGTACCCC AGCTCCAAGGTGGGTAAGGAGGGAGGCCGGCAAGTGGGGC|ACCTTGGA|GGCACCTGTCCCCTTCCTTGGAGCCCACTTGAGGTACCCC ========== Event 3270 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAATGGTTAGTCAGATTTACTCATGTAAATTGATTTAGAGAAGCTTCAGATAAAA ↑ 3 1 4 Chimp: AGAAATGGTTAGTCAGATTTA----CATGAATTGATTTAGAGAAGCTTCAGATAAAA Gorilla: AGAAATGGTTAGTCAGATTTA----CATGAATTGATGTAGAGAAGCTTCAGATAAAA ↓ 3 1 4 Human: AGAAATGGTTAGTCAGATTTACTCATGTAAATTGATTTAGAGAAGCTTCAGATAAAA Cluster: [ ] Orangutan: AGAAATGGTTAGTCAGATTTA----CATGAATTGATTTAGAGAAGCTTCAGATAAAA Chimp > Human ------------- chr7:148995651-148995657 Template switch process: F1: L AAACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTAC 1 F3: 4 AATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCA R RF: AAACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTACATGAATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCA RR: TTTGTTTTCTTGGTTCAAACTCTTTACCAATCAGTCTAAATGTACTTAACTAAATCTCTTCGAAGTCTATTTTGAAGGTTGGGGT F2: 3 ATGTACT 2 Unidirectional alignment (log-probability: -26.9) ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTActCATGtaAATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCA ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTA--CATG--AATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCA Template switch alignment (log-probability: -16.2) ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTAC|TCATGTA|AATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCA ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTAC|TCATGTA|AATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCA Gorilla > Human --------------- chr7:148995651-148995657 Template switch process: F1: L AAACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTAC 1 F3: 4 AATTGATTTAGAGAAGCTTCAGATAAAACTTCCAACCCCATAAGGTTT R RF: AAACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTACATGAATTGATGTAGAGAAGCTTCAGATAAAACTTCCAACCCCATAAGGTTT RR: TTTGTTTTCTTGGTTCAAACTCTTTACCAATCAGTCTAAATGTACTTAACTACATCTCTTCGAAGTCTATTTTGAAGGTTGGGGTATTCCAAA F2: 3 ATGTACT 2 Unidirectional alignment (log-probability: -32.1) ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTActCATGtaAATTGATtTAGAGAAGCTTCAGATAAAACTTCCAACCCCA ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTA--CATG--AATTGATGTAGAGAAGCTTCAGATAAAACTTCCAACCCCA Template switch alignment (log-probability: -22.4) ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTAC|TCATGTA|AATTGATtTAGAGAAGCTTCAGATAAAACTTCCAACCCCA ACAAAAGAACCAAGTTTGAGAAATGGTTAGTCAGATTTAC|TCATGTA|AATTGATGTAGAGAAGCTTCAGATAAAACTTCCAACCCCA ========== Event 3271 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGACAGTATATCTTCTTTCCAAGTGGGATGCCATGTAACTTGAAAACAACCAAAAGTAATAAA ↓ 3 1 2 4 Chimp: TAGACAGTATATCTTCTTTCCAAGC----CCACTTGGAACTTGGAAACAACCAAAAGTAATAAA Gorilla: TAGACAGTATATCTTCTTTCCAGGTGGGATGCCATGTAACTTGAAAACAACCAAAAGTAATAAA Human: TAGACAGTATATCTTCTTTCCAAGTGGGATGCCATGTAACTTGAAAACAACCAAAAGTAATAAA Cluster: [ ] Orangutan: TAGACAGTATATCTTCTTTCCAAGTGGGATGCCATGTAACTTGAAAACAACCAAAAGTAATAAA Human > Chimp ------------- chr7:108910413-108910421 Template switch process: F1: L GGTACTGCATTATTTCCTAGACAGTATATCTTCTTTCCAAG 1 F3: 4 AACTTGGAAACAACCAAAAGTAATAAAAGTTTTAGAGTCCAGATACA R RF: GGTACTGCATTATTTCCTAGACAGTATATCTTCTTTCCAAGTGGGATGCCATGTAACTTGAAAACAACCAAAAGTAATAAAAGTTTTAGAGTCCAGATACA RR: CCATGACGTAATAAAGGATCTGTCATATAGAAGAAAGGTTCACCCTACGGTACATTGAACTTTTGTTGGTTTTCATTATTTTCAAAATCTCAGGTCTATGT F2: 3 GGTTCACCC 2 Unidirectional alignment (log-probability: -36.4) GTACTGCATTATTTCCTAGACAGTATATCTTCTTTCCAAGcccactTGG----------AACTTGgAAACAACCAAAAGTAATAAAAGTTTTAGAGTCC GTACTGCATTATTTCCTAGACAGTATATCTTCTTTCCAAG------TGGGATGCCATGTAACTTGAAAACAACCAAAAGTAATAAAAGTTTTAGAGTCC Template switch alignment (log-probability: -22.5) GTACTGCATTATTTCCTAGACAGTATATCTTCTTTCCAAG|CCCACTTGG|AACTTGgAAACAACCAAAAGTAATAAAAGTTTTAGAGTCC GTACTGCATTATTTCCTAGACAGTATATCTTCTTTCCAAG|CCCACTTGG|AACTTGAAAACAACCAAAAGTAATAAAAGTTTTAGAGTCC ========== Event 3272 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGAAGAGGGAGAGGTGGCATGATACGTTCACATTACAGCCGTGCCTGGGATTTAAGTAACAG Chimp: TGAAGAGGGAAAGGTGGCATGATACATTCACATTACAGCCGTGCCTGGGATTTAAGTAACAG ↓ 3 2 1 4 Gorilla: TGAAGAGGGAAAGGTGGCATGATACATTCACCTTTGTATCATGCCTGGGATTTAAGTAACAG Human: TGAAGAGGGAGAGGTGGCATGATACGTTCACATTACAGCCGTGCCTGGGATTTAAGTAACAG Cluster: [ ] Orangutan: TGAACAGGGAAAGGTAGCATGATATGTTCACATTATGGCCGTGCCTGGGATTTAAGTAACAG Chimp > Gorilla --------------- chr7:103594831-103594837 Template switch process: F1: L CCATCTCGGCTGAAGAGGGAAAGGTGGCATGATACATTCACCTT 1 F3: 4 TGCCTGGGATTTAAGTAACAGTATTTGACTCTCAACCTAC R RF: CCATCTCAGCTGAAGAGGGAAAGGTGGCATGATACATTCACATTACAGCCGTGCCTGGGATTTAAGTAACAGTATTTGACTCTCAACCTAC RR: GGTAGAGTCGACTTCTCCCTTTCCACCGTACTATGTAAGTGTAATGTCGGCACGGACCCTAAATTCATTGTCATAAACTGAGAGTTGGATG F2: 3 ACTATGT 2 Unidirectional alignment (log-probability: -39.6) CTCgGCTGAAGAGGGAAAGGTGGCATGATACATTCAcctttgtatCA---------TGCCTGGGATTTAAGTAACAGTATTTGACTCTCAACCTAC CTCAGCTGAAGAGGGAAAGGTGGCATGATACATTCA---------CATTACAGCCGTGCCTGGGATTTAAGTAACAGTATTTGACTCTCAACCTAC Template switch alignment (log-probability: -27.7) CTCgGCTGAAGAGGGAAAGGTGGCATGATACATTCACcTT|TGTATCA|TGCCTGGGATTTAAGTAACAGTATTTGACTCTCAACCTAC CTCAGCTGAAGAGGGAAAGGTGGCATGATACATTCACATT|TGTATCA|TGCCTGGGATTTAAGTAACAGTATTTGACTCTCAACCTAC ========== Event 3273 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAAACGATTTGTTACCAAAATCCACTCCTACAATTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAG ↓ 1 4 3 2 Chimp: CAAAACGATTTGTTACCAAAAACCA---GAATGCTTAAGCCTTCTGGTTTCATGGCTGGGGGTGGGAG ↑ 1 4 3 2 Gorilla: CAAAACGATTTGTTACCAAAATCCACTCCTACAATTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAG Human: CAAAACGATTTGTTACCAAAATCCACTCCTACAATTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAG Cluster: [ ] Orangutan: CAAAGTGATTTCTCACCAAAATCCACTCCTACAATTAAACATTCTGGTTTCATGGCTGGGGGTGGGAG Human > Chimp ------------- chr7:108597664-108597673 Template switch process: F1: L AATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAA 1 F3: 4 TTAAGCCTTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTTACATGTT R RF: AATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAATCCACTCCTACAATTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTTACATGTT RR: TTAAGACACTAGTATACCAAGTTTTGCTAAACAATGGTTTTAGGTGAGGATGTTAATTCGTAAGACCAAAGTACCGACCCCCACCCTCCGTCAATGTACAA F2: 3 CGTAAGACCA 2 Unidirectional alignment (log-probability: -40.8) ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAA------------AAccagaatgcTTAAGCcTTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAATCCACTCCTACAA---------TTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT Template switch alignment (log-probability: -22.6) ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAA|ACCAGAATGC|TTAAGCcTTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAA|ACCAGAATGC|TTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT Gorilla > Chimp --------------- chr7:108597664-108597673 Template switch process: F1: L AATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAA 1 F3: 4 TTAAGCCTTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTTACATGTT R RF: AATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAATCCACTCCTACAATTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTTACATGTT RR: TTAAGACACTAGTATACCAAGTTTTGCTAAACAATGGTTTTAGGTGAGGATGTTAATTCGTAAGACCAAAGTACCGACCCCCACCCTCCGTCAATGTACAA F2: 3 CGTAAGACCA 2 Unidirectional alignment (log-probability: -39.4) ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAAaCCAgaatgC--------TTAAGCcTTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAATCCA-----CTCCTACAATTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT Template switch alignment (log-probability: -22.7) ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAA|ACCAGAATGC|TTAAGCcTTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT ATTCTGTGATCATATGGTTCAAAACGATTTGTTACCAAAA|ACCAGAATGC|TTAAGCATTCTGGTTTCATGGCTGGGGGTGGGAGGCAGTT ========== Event 3274 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTTTCATCCTGTAAAGTTATGGTTGTGAATTCTTGCGCTTAACCCTGAGCCCTCCCAGTCAT Chimp: ATTTTCATCCTGTAAAGTTATGGTTGTGAATTCTTGAGCTTAACCCTGAGCCCTCCCAGTCAT ↓ 1 34 2 Gorilla: ATTTTCATCCTGTAAAGTTAT----GTTAAGCTCAGGGCTTAACCCTGAGCCCTCCCAGTCAT Human: ATTTTCATCCTGTAAAGTTATGGTTGTGAATTCTTGCGCTTAACCCTGAGCCCTCCCAGTCAT Cluster: [ ] Orangutan: ATTTTCATCCTGTAAAGTTATGGTTGTGAATTCTTACGCTTAACCCTGAGCCCTCCCAGTCAT Chimp > Gorilla --------------- chr7:104248374-104248382 Template switch process: F1: L GCTCCTGGCAGTGCCTGACTATTTTCATCCTGTAAAGTTATG 1 F3: 4 GGGCTTAACCCTGAGCCCTCCCAGTCATGAAAATCCATTTTC R RF: GCTCCTGGCAGTGCCTGACTATTTTCATCCTGTAAAGTTATGGTTGTGAATTCTTGAGCTTAACCCTGAGCCCTCCCAGTCATGAAAATCCATTTTC RR: CGAGGACCGTCACGGACTGATAAAAGTAGGACATTTCAATACCAACACTTAAGAACTCGAATTGGGACTCGGGAGGGTCAGTACTTTTAGGTAAAAG F2: 3 ACTCGAATT 2 Unidirectional alignment (log-probability: -35.8) TCCTGGCAGTGCCTGACTATTTTCATCCTGTAAAGTTATgttaagctcaGG--------------GCTTAACCCTGAGCCCTCCCAGTCATGAAAATCCATTT TCCTGGCAGTGCCTGACTATTTTCATCCTGTAAAGTTAT----------GGTTGTGAATTCTTGAGCTTAACCCTGAGCCCTCCCAGTCATGAAAATCCATTT Template switch alignment (log-probability: -22.5) TCCTGGCAGTGCCTGACTATTTTCATCCTGTAAAGTTATG|TTAAGCTCA|GgGCTTAACCCTGAGCCCTCCCAGTCATGAAAATCCATTT TCCTGGCAGTGCCTGACTATTTTCATCCTGTAAAGTTATG|TTAAGCTCA|GAGCTTAACCCTGAGCCCTCCCAGTCATGAAAATCCATTT ========== Event 3275 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGATATCATGAGAAAAGTCATTACTGTGTTACCACAGTAATGAATAGCTTTGTCCTAGTT Chimp: TTGATATCATGAGAAAAGTCATTACTGTGTTACCACAGTAATGAATAGCTTTGTCCTAGTT Gorilla: TTGATATCATGAGAAAAGTCA-----GATGTAACACAGTAATGAATAGGTTTGTCCTAGTT ↓ 1 3 4 2 Human: TTGATATCATGAGAAAAGTCATTACTGTGTTACCACAGTAATGAATAGCTTTGTCCTAGTT Cluster: [ ] Orangutan: TTGGTGTCATGAGAACAGTCA-----GATGTAACACAGTAATGAATAGCTTTGTCCTAGTT Gorilla > Human --------------- chr7:107197285-107197296 Template switch process: F1: L AAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCA 1 F3: 4 CACAGTAATGAATAGCTTTGTCCTAGTTCCTTTAGACACA R RF: AAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCAGATGTAACACAGTAATGAATAGGTTTGTCCTAGTTCCTTTAGACACA RR: TTTGATGGTAAACGAAATAGAACTATAGTACTCTTTTCAGTCTACATTGTGTCATTACTTATCCAAACAGGATCAAGGAAATCTGTGT F2: 3 CATTGTGTCATT 2 Unidirectional alignment (log-probability: -43.8) AACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTC-------AttactgtgttacCACAGTAATGAATAGcTTTGTCCTAGTTCCTTTAGACACA AACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCAGATGTAA------------CACAGTAATGAATAGGTTTGTCCTAGTTCCTTTAGACACA Template switch alignment (log-probability: -22.8) AACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCA|TTACTGTGTTAC|CACAGTAATGAATAGcTTTGTCCTAGTTCCTTTAGACACA AACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCA|TTACTGTGTTAC|CACAGTAATGAATAGGTTTGTCCTAGTTCCTTTAGACACA ========== Event 3276 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCTTTAGATGTTTTGT--TTTCTGAT-CTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTA Chimp: ATCTTTAGATGTTTTGT--TTTCTGAT-CTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTA ↓ 1 4 3 2 Gorilla: ATCTTTAGATGTTTTGT--TTAGAGATCCTTTTTATAGGATGTCTAAATCAGGTTATACCCTTTA ↑ 1 4 3 2 Human: ATCTTTAGATGTTTTGT--TTTCTGAT-CTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTA Cluster: [ ] Orangutan: ATCCTTACATGTTTTGTTTTTTCTGAT-CTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTA Human > Gorilla --------------- chr7:106035681-106035687 Template switch process: F1: L TAAGGAGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT 1 F3: 4 CTTTTTATAGGATGTCTAAATCAGGTTATACCCTTTATTG R RF: TAAGGGGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTTTCTGATCTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTATTG RR: ATTCCCCACATTTAGAGTAAAATAGAAATCTACAAAACAAAAGACTAGAAAAATATCCTAGAGATTTAGTCCAATATGGGAAATAAC F2: 3 CTAGAGA 2 Unidirectional alignment (log-probability: -39.1) AAGGaGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTTagagaTC----CTTTTTATAGGATgTCTAAATCAGGTTATACCCTTTATTG AAGGGGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT-----TCTGATCTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTATTG Template switch alignment (log-probability: -27.7) AAGGaGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT|AGAGATC|CTTTTTATAGGATgTCTAAATCAGGTTATACCCTTTATTG AAGGGGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT|AGAGATC|CTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTATTG Chimp > Gorilla --------------- chr7:106035681-106035687 Template switch process: F1: L TAAGGAGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT 1 F3: 4 CTTTTTATAGGATGTCTAAATCAGGTTATACCCTTTATTG R RF: TAAGGGGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTTTCTGATCTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTATTG RR: ATTCCCCACATTTAGAGTAAAATAGAAATCTACAAAACAAAAGACTAGAAAAATATCCTAGAGATTTAGTCCAATATGGGAAATAAC F2: 3 CTAGAGA 2 Unidirectional alignment (log-probability: -39.1) AAGGaGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTTagagaTC----CTTTTTATAGGATgTCTAAATCAGGTTATACCCTTTATTG AAGGGGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT-----TCTGATCTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTATTG Template switch alignment (log-probability: -27.7) AAGGaGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT|AGAGATC|CTTTTTATAGGATgTCTAAATCAGGTTATACCCTTTATTG AAGGGGTGTAAATCTCATTTTATCTTTAGATGTTTTGTTT|AGAGATC|CTTTTTATAGGATCTCTAAATCAGGTTATACCCTTTATTG ========== Event 3277 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTACCCTGAGGATCAAAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCATTACTGTGTTACCACAGTAATGAATAGCTTTGTCCTAGTT Chimp: GTACCCTGAGGATCAAAACTAC-------CTTATCTTGATATCATGAGAAAAGTCATTACTGTGTTACCACAGTAATGAATAGCTTTGTCCTAGTT ↑ 4 1 3 2 Gorilla: GTACCCTGAGGATCAAAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCA-----GATGTAACACAGTAATGAATAGGTTTGTCCTAGTT Human: GTACCCTGAGGATCAAAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCATTACTGTGTTACCACAGTAATGAATAGCTTTGTCCTAGTT Cluster: [ ] Orangutan: GTACCCTGAGGATCAAAACTACCATTTGCTTTATCTTGGTGTCATGAGAACAGTCA-----GATGTAACACAGTAATGAATAGCTTTGTCCTAGTT Gorilla > Chimp --------------- chr7:111471329-111471337 Template switch process: F1: L CTGTCTTCTTCCAGTCTTTGTACCCTGAGGATCAAAACTACC-------TTATCTTGATATCATGAGAAAAGTCA 1 F3: 4 TACCA R RF: CTGTCTTCTTCCAGTCTTTGTACCCTGAGGATCAAAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCATTTGCTTTATCTTGATATCATGAGAAAAGTCAGATGTAACACAGTAA RR: GACAGAAGAAGGTCAGAAACATGGGACTCCTAGTTTTGATGGTAAACGAAATAGAACTATAGTACTCTTTTCAGTAAACGAAATAGAACTATAGTACTCTTTTCAGTCTACATTGTGTCATT F2: 3 TGTGTCATT 2 Unidirectional alignment (log-probability: -48.1) GGATCAAAACTACC-------TTATCTTGATATCATGAGAAAAGTcattactgtgttacCA--------- GGATCAAAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGT--------------CAGATGTAACA Template switch alignment (log-probability: -26.8) GGATCAAAACTACC-------TTATCTTGATATCATGAGAAAAGTCA|TTACTGTGT|TACCA GGATCAAAACTACCATTTGCTTTATCTTGATATCATGAGAAAAGTCA|TTACTGTGT|TACCA ========== Event 3278 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGAGTAAGTAGTTAATGAGCCAGAGGAATTACTCATAAAGCTGAAAAAATATTGTGAGTTAACAGCAAAGATTTCCTGGCA ↓ 13 24 ↑ 13 24 Chimp: AGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCTTTATGAGTAAACAGCAAAGATTTCCTGGCA Gorilla: AGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCTTTATGAGTAAACAGCAAAGATTTCCTGGCA ↓ 13 24 ↑ 13 24 Human: AGAGTAAGTAGTTAATGAGCCAGAGGAATTACTCATAAAGCTGAAAAAATATTGTGAGTTAACAGCAAAGATTTCCTGGCA Cluster: [ ] Orangutan: AGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCTTTATGAGTAAACAGCAAAGATTTCCTGGCA Chimp > Human ------------- chr7:51406012-51406042 Template switch process: F1: L GGGAATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAAT 1 F3: 4 AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG R RF: GGGTATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCTTTATGAGTAAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG RR: CCCATAGAGAAACTCCTTCGTCTCATTCATCAATTACTCGGCCTCCTTATTGAGTGTTATAAAAAAGTCGAAATACTCATTTGTCGTTTCTAAAGGACCGTACCACGAAGGTAGTCCTCC F2: 3 TTGAGTGTTATAAAAAAGTCGAAATACTCAT 2 Unidirectional alignment (log-probability: -70.6) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCaGAGGAATtACTCA-----------------TAaagctgaaaaaatattgTGAGTtAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCTTTA-----------------TGAGTAAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Template switch alignment (log-probability: -31.2) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCaGAGGAAT|TACTCATAAAGCTGAAAAAATATTGTGAGTT|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAAT|TACTCATAAAGCTGAAAAAATATTGTGAGTT|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Human > Chimp ------------- chr7:53994892-53994922 Template switch process: F1: L GGGTATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAAT 1 F3: 4 AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG R RF: GGGAATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAATTACTCATAAAGCTGAAAAAATATTGTGAGTTAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG RR: CCCTTAGAGAAACTCCTTCGTCTCATTCATCAATTACTCGGTCTCCTTAATGAGTATTTCGACTTTTTTATAACACTCAATTGTCGTTTCTAAAGGACCGTACCACGAAGGTAGTCCTCC F2: 3 ATGAGTATTTCGACTTTTTTATAACACTCAA 2 Unidirectional alignment (log-probability: -70.6) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCgGAGGAATaACTCAcaatattttttcagcttTA-----------------TGAGTaAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAATTACTCA-----------------TAAAGCTGAAAAAATATTGTGAGTTAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Template switch alignment (log-probability: -31.2) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCgGAGGAAT|AACTCACAATATTTTTTCAGCTTTATGAGTA|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAAT|AACTCACAATATTTTTTCAGCTTTATGAGTA|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Gorilla > Human --------------- chr7:51406012-51406042 Template switch process: F1: L GGGAATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAAT 1 F3: 4 AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG R RF: GGGAATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCTTTATGAGTAAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG RR: CCCTTAGAGAAACTCCTTCGTCTCATTCATCAATTACTCGGCCTCCTTATTGAGTGTTATAAAAAAGTCGAAATACTCATTTGTCGTTTCTAAAGGACCGTACCACGAAGGTAGTCCTCC F2: 3 TTGAGTGTTATAAAAAAGTCGAAATACTCAT 2 Unidirectional alignment (log-probability: -62) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCaGAGGAATtACTCAtAA---------AGCTgaaaaaataTTgTGAGTtAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAATAACTCACAATATTTTTTCAGCT---------TTATGAGTAAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Template switch alignment (log-probability: -25.4) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCaGAGGAAT|TACTCATAAAGCTGAAAAAATATTGTGAGTT|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAAT|TACTCATAAAGCTGAAAAAATATTGTGAGTT|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Human > Gorilla --------------- chr7:52289772-52289802 Template switch process: F1: L GGGAATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCGGAGGAAT 1 F3: 4 AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG R RF: GGGAATCTCTTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAATTACTCATAAAGCTGAAAAAATATTGTGAGTTAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG RR: CCCTTAGAGAAACTCCTTCGTCTCATTCATCAATTACTCGGTCTCCTTAATGAGTATTTCGACTTTTTTATAACACTCAATTGTCGTTTCTAAAGGACCGTACCACGAAGGTAGTCCTCC F2: 3 ATGAGTATTTCGACTTTTTTATAACACTCAA 2 Unidirectional alignment (log-probability: -62) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCgGAGGAATaACTCAcAAtattttttcAGCT---------TTaTGAGTaAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAATTACTCATAA---------AGCTGAAAAAATATTGTGAGTTAACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG Template switch alignment (log-probability: -25.4) TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCgGAGGAAT|AACTCACAATATTTTTTCAGCTTTATGAGTA|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG TTTGAGGAAGCAGAGTAAGTAGTTAATGAGCCAGAGGAAT|AACTCACAATATTTTTTCAGCTTTATGAGTA|AACAGCAAAGATTTCCTGGCATGGTGCTTCCATCAGGAGG ========== Event 3279 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ttttttCAGTCATCAAAAAGTAAAGAACACTGAAGAAGATTAATTTCCTGCTACTATATGATATAACAGTATCTGGTTTCCTTGGACAATACAGGAGATATAGTAACCCACATTTTCCAATAATCTT------------------------------------------TCATTTTTCTTGACTTTCATTTTTAGTTTATATCTTGTAATTTC ↑ 3 2 4 1 Chimp: ttttttCAGTCATCAAAAAGTAAAGAACACTGAAGAAGATTAATTTCCTGCTACTATATGATATAACAGTATCTGGTTTCCTTGGACAATACAGGAGATATAGTAACCCACATTTTCCAATAATCTT----------------------------------------------------------TCATTTTTAGTTTATATCTTGTAATTTC Gorilla: ttttttCAGTCATCAAAAAGTAAAGAACACTGAAGAAGATTAATTTACTGCTACTATATGATATAACAGTATCTGGTTTCCTTGGACAATACAGGAGATATAGTAACCCACATTTTCCAATA-ACTT----------------TCATTCTTATTGACTTTCATTTTTAG----------------TCATTTTTAGTTTATATCTTGTAATTTC Human: ttttttCAGTCATCAAAAAGTAAAGAACACTGAAGAAGATTAATTTCCTGCTACTATATGATATAACAGTATCTGGTTTCCTTGGACAATACAGGAGATATAGTAACCCACATTTTCCAATAATCTT------------------------------------------TCATTTTTCTTGACTTTCATTTTTAGTTTATATCTTGTAATTTC Cluster: [ ] Orangutan: ttttttCAGTCATCAAAAAGTAAAAAACACTGAAGAAGATCAATTTCCTACTACTATATGATATAACAGTATCTGGTTTCCTTGGACAATACAGGAGATATAGTAATCCACATTTTCCAATAATCTTTCATTTTTCTTGACTT------------------------------------------TCATTTTTAGTTTATATCTTGTAATTTC Chimp > Human ------------- chr7:109046507-109046512 Template switch process: F1: L CAATACAGGAGATATAGTAACCCACATTTTCCAATAATCTTTCATTTTT 1 F3: 4 TTTCATTTTTAGTTTATATCTTGTAATTTCTGAAGTTTTGTG R RF: GTAAAGAACACTGAAGAAGATTAATTTCCTGCTACTATATGATATAACAGTATCTGGTTTCCTTGGACAATACAGGAGATATAGTAACCCACATTTTCCAATAATCTTTCATTTTTAGTTTATATCTTGTAATTTCTGAAGTTTTGTG RR: CATTTCTTGTGACTTCTTCTAATTAAAGGACGATGATATACTATATTGTCATAGACCAAAGGAACCTGTTATGTCCTCTATATCATTGGGTGTAAAAGGTTATTAGAAAGTAAAAATCAAATATAGAACATTAAAGACTTCAAAACAC F2: 3 CAGTTC 2 Unidirectional alignment (log-probability: -33.9) AGATATAGTAACCCACATTTTCCAATAATCTTTCATTTTtcttgactttcattttTAGTTTATATCTTGTAATTTCTGAAGTTTTG AGATATAGTAACCCACATTTTCCAATAATCTTTCATTTT----------------TAGTTTATATCTTGTAATTTCTGAAGTTTTG Template switch alignment (log-probability: -22.2) AGATATAGTAACCCACATTTTCCAATAATCTTTCATTTTT|CTTgAC|TTTCATTTTTAGTTTATATCTTGTAATTTCTGAAGTTTTG AGATATAGTAACCCACATTTTCCAATAATCTTTCATTTTT|CTTTAC|TTTCATTTTTAGTTTATATCTTGTAATTTCTGAAGTTTTG ========== Event 3280 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCC----------ACCATGTTAAGTAAACTACCCT ↓ 3 2 4 1 Chimp: tatttcctttttttCTTCCACATGGATAGTCAATTACATTGCCTATCCATGTTTACATGTTAAGTAAACTACCCT Gorilla: tatttcctttatttCTTCCACATGGATAGTCAATTACATTGCC----------ACCATGTTAAGTAAACTACCCT Human: TATTTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCC----------ACCATGTTAAGTAAACTACCCT Cluster: [ ] Orangutan: tatttc--ttttttCTTCCACGTGGATAATCAATTATATTGCC----------ACCATGTTAAGTAAACTACCCT Human > Chimp ------------- chr7:52381119-52381127 Template switch process: F1: L TTTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCC 1 F3: 4 TTA---------CATGTTAAGTAAACTACCCTTTCCTTATCCATTTTAAGCA R RF: TTTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCCACCATGTTAAGTAAACTACCCTTTCCTTATCCATTTTAAGCA RR: AAAGGAAAAAAAGAAGGTGTACCTATCAGTTAATGTAACGGTGGTACAATTCATTTGATGGGAAAGGAATAGGTAAAATTCGT F2: 3 TGTACCTAT 2 Unidirectional alignment (log-probability: -37) TTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCCtatccatgtttAC-ATGTTAAGTAAACTACCCTTTCCTTATCCATTTTAA TTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCC-----------ACCATGTTAAGTAAACTACCCTTTCCTTATCCATTTTAA Template switch alignment (log-probability: -27.1) TTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCC|TATCCATGT|TTA---------CATGTTAAGTAAACTACCCTTTCCTTATCCATTTTAA TTCCTTTTTTTCTTCCACATGGATAGTCAATTACATTGCC|TATCCATGT|TTACATTGCCACCATGTTAAGTAAACTACCCTTTCCTTATCCATTTTAA ========== Event 3281 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: atctatgatatgtgatcattttacatgtttgttatccttcaataaa----TCAATATTT----TAAAGAGAAGTTGATTGAGGATGTAGAT Chimp: CTCTATGATATGTGATCATTTTACATGTTTGTTATCCTTCAATAAA----TAAATATTT----TAAAGAGAAGTTGATTGAGGATGTAGAT ↓ 3 2 1 4 Gorilla: atctatgatatgtGATCATTTTACATGTTTGTTATCCTTCAATCAA--------CATGT--------AAAAAGTTGATTGAGGATGTAGAT Human: atctatgatatgtgatcattttacatgtttgttatccttcaataaa----TCAATATTT----TAAAGAGAAGTTGATTGAGGATGTAGAT Cluster: [ ] Orangutan: atctgtgatatgtgatcattttacatgtttgttatccttcaataaataat----tATTTTAAA----GAGAAGTTGATTGAGGATGTAGAT Chimp > Gorilla --------------- chr7:147816201-147816208 Template switch process: F1: L CTATGATATGTGATCATTTTACATGTTTGTTATCCTTCAATCAA 1 F3: 4 AAGTTGATTGAGGATGTAGATCAGAGGAAATAGTGAGCAT R RF: CTATGATATGTGATCATTTTACATGTTTGTTATCCTTCAATAAATAAATATTTTAAAGAGAAGTTGATTGAGGATGTAGATCAGAGGAAATAGTGAGCAT RR: GATACTATACACTAGTAAAATGTACAAACAATAGGAAGTTATTTATTTATAAAATTTCTCTTCAACTAACTCCTACATCTAGTCTCCTTTATCACTCGTA F2: 3 AAATGTAC 2 Unidirectional alignment (log-probability: -32.6) GATATGTGATCATTTTACATGTTTGTTATCCTTCAATcAAcatgTAAA------------AAGTTGATTGAGGATGTAGATCAGAGGAAATAGTGAGCAT GATATGTGATCATTTTACATGTTTGTTATCCTTCAATAAA----TAAATATTTTAAAGAGAAGTTGATTGAGGATGTAGATCAGAGGAAATAGTGAGCAT Template switch alignment (log-probability: -22.3) GATATGTGATCATTTTACATGTTTGTTATCCTTCAATcAA|CATGTAAA|AAGTTGATTGAGGATGTAGATCAGAGGAAATAGTGAGCAT GATATGTGATCATTTTACATGTTTGTTATCCTTCAATAAA|CATGTAAA|AAGTTGATTGAGGATGTAGATCAGAGGAAATAGTGAGCAT ========== Event 3282 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATATACCTGAATTTGGAGATATCTCTGAAGG-TTATCCACTATTGAGATACTAATTGTC Chimp: ATATACCTGAATTCGGAGATACCTCTGAAGG-TTATCCACTATTGAGATACTAATTGTC ↓ 3 2 4 Gorilla: ATATACCTGAATTCGGAGATATCTCTGAATTCAGAGATACTATTGAGATACTAATTGTC ↑ 3 2 4 Human: ATATACCTGAATTTGGAGATATCTCTGAAGG-TTATCCACTATTGAGATACTAATTGTC Cluster: [ ] Orangutan: ATATACCTGAATTCGGAGATATCTCTGAAGG-TTATCCACTATTGAGATACTAATTATC Human > Gorilla --------------- chr7:114275720-114275728 Template switch process: F1: L ACTAGTAAAGAAATATACCTGAATTCGGAGATATCTCTGAA 1 F3: 4 ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA R RF: ACTAGTAAAGAAATATACCTGAATTTGGAGATATCTCTGAAGGTTATCCACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA RR: TGATCATTTCTTTATATGGACTTAAACCTCTATAGAGACTTCCAATAGGTGATAACTCTATGATTAACAGTAACGTAAACGTATCCTGT F2: 3 TAGAGACTT 2 Unidirectional alignment (log-probability: -39.5) CTAGTAAAGAAATATACCTGAATTcGGAGATATCTCTGAA--------ttcagagatACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA CTAGTAAAGAAATATACCTGAATTTGGAGATATCTCTGAAGGTTATCC---------ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA Template switch alignment (log-probability: -22.4) CTAGTAAAGAAATATACCTGAATTcGGAGATATCTCTGAA|TTCAGAGAT|ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA CTAGTAAAGAAATATACCTGAATTTGGAGATATCTCTGAA|TTCAGAGAT|ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA Chimp > Gorilla --------------- chr7:114275720-114275728 Template switch process: F1: L AATACTCAACTAGTAAAGAAATATACCTGAATTCGGAGATATCTCTGAA 1 F3: 4 ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA R RF: AATACTCAACTAGTAAAGAAATATACCTGAATTCGGAGATACCTCTGAAGGTTATCCACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA RR: TTATGAGTTGATCATTTCTTTATATGGACTTAAGCCTCTATGGAGACTTCCAATAGGTGATAACTCTATGATTAACAGTAACGTAAACGTATCCTGT F2: 3 TAGAGACTT 2 Unidirectional alignment (log-probability: -39.6) CTAGTAAAGAAATATACCTGAATTCGGAGATAtCTCTGAA--------ttcagagatACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA CTAGTAAAGAAATATACCTGAATTCGGAGATACCTCTGAAGGTTATCC---------ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA Template switch alignment (log-probability: -28.1) CTAGTAAAGAAATATACCTGAATTCGGAGATAtCTCTGAA|TTCAGAGaT|ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA CTAGTAAAGAAATATACCTGAATTCGGAGATACCTCTGAA|TTCAGAGGT|ACTATTGAGATACTAATTGTCATTGCATTTGCATAGGACA ========== Event 3283 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGATAATTACAATCTAGA---------AGTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTC ↓ 1 4 3 2 Chimp: TCATGATAATTACAATCTAGAATCTTATTGAATTAAAATTCAATAAGAGTAAATTATGGGTTGACTTC Gorilla: TCATGATAATTACAATCTAGA---------AGTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTC Human: TCATGATAATTACAATCTAGA---------AGTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTC Cluster: [ ] Orangutan: TCATGATAATTACAATCTAGA---------AGTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTC Human > Chimp ------------- chr7:47556143-47556152 Template switch process: F1: L CAATAAATATTGTTAAGTAATCATGATAATTACAATCTAGAA 1 F3: 4 TTAAAATTCAATAAGAGTAAATTATGGGTTGACTTCTACT R RF: CAATAAATATTGTTAAGTAATCATGATAATTACAATCTAGAAGTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTCTACT RR: GTTATTTATAACAATTCATTAGTACTATTAATGTTAGATCTTCAATTTTAAGTTATTCTCATTTAATACCCAACTGAAGATGA F2: 3 AAGTTATTCT 2 Unidirectional alignment (log-probability: -29.9) ATAAATATTGTTAAGTAATCATGATAATTACAATCTAGAAtcttattgaaTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTCTACT ATAAATATTGTTAAGTAATCATGATAATTACAATCTAGAA---------GTTAAAATTCAATAAGAGTAAATTATGGGTTGACTTCTACT Template switch alignment (log-probability: -16.5) ATAAATATTGTTAAGTAATCATGATAATTACAATCTAGAA|TCTTATTGAA|TTAAAATTCAATAAGAGTAAATTATGGGTTGACTTCTACT ATAAATATTGTTAAGTAATCATGATAATTACAATCTAGAA|TCTTATTGAA|TTAAAATTCAATAAGAGTAAATTATGGGTTGACTTCTACT ========== Event 3284 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAACAGAGAACTGGAACAAGTCAAG---AGATGCCAGTTTGaaaaaaaaT Chimp: AGGAACAGAGAATTGGAACAAGTTAAG---AGATGCCAGTTTGaaa-aaaaT Gorilla: AGGAACAGAGAACTGGAACAAGTCTTGACTTGATGCCAGTTTGaaa-aaaaT ↑ 3 1 2 4 Human: AGGAACAGAGAACTGGAACAAGTCAAG---AGATGCCAGTTTGaaaaaaaaT Cluster: [ ] Orangutan: AGGAACAGAGAACTCGAACAAGTCAAC---AGATGCCAGTTTGAAA-AAAAT Human > Gorilla --------------- chr7:45540387-45540393 Template switch process: F1: L TTCAAAAACAGTAGTGTAGGAACAGAGAACTGGAACAAGTC 1 F3: 4 GATGCCAGTTTG-AAAAAAATATGAATATGTGAGATTGAC R RF: TTCAAAAACAGTAGTGTAGGAACAGAGAACTGGAACAAGTCAAGAGATGCCAGTTTGAAAAAAAATATGAATATGTGAGATTGAC RR: AAGTTTTTGTCATCACATCCTTGTCTCTTGACCTTGTTCAGTTCTCTACGGTCAAACTTTTTTTTATACTTATACACTCTAACTG F2: 3 TTCAGTT 2 Unidirectional alignment (log-probability: -36.1) TCAAAAACAGTAGTGTAGGAACAGAGAACTGGAACAAGTCttGActtGATGCCAGTTTG-AAAAAAATATGAATATGTGAGATTGAC TCAAAAACAGTAGTGTAGGAACAGAGAACTGGAACAAGTCAAGA---GATGCCAGTTTGAAAAAAAATATGAATATGTGAGATTGAC Template switch alignment (log-probability: -26.4) TCAAAAACAGTAGTGTAGGAACAGAGAACTGGAACAAGTC|TTGACTT|GATGCCAGTTTG-AAAAAAATATGAATATGTGAGATTGAC TCAAAAACAGTAGTGTAGGAACAGAGAACTGGAACAAGTC|TTGACTT|GATGCCAGTTTGAAAAAAAATATGAATATGTGAGATTGAC ========== Event 3285 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACAGTTTCGTACAAATGTATTTCAGAAAATGAAAT----ACGCAAGGaaaaaaaaCTTT Chimp: ACAGTTTTGTACAAATGTATTTCATTTTCTGAAAT----ACACAAGGaaaaaaaaCTTT ↑ 3 1 2 4 Gorilla: ACAGTTTTGTACAAATGTATTTCAGAAAACGAAATACTTACACAAGGaaaaaaaaCTTT Human: ACAGTTTCGTACAAATGTATTTCAGAAAATGAAAT----ACGCAAGGaaaaaaaaCTTT Cluster: [ ] Orangutan: ACAGTTTTGTACAAATGTATTTCAGAAAATGAAAT----ACAC-AGGaaaaaaaaCTTT Gorilla > Chimp --------------- chr7:47612666-47612675 Template switch process: F1: L TACAATAACCCTTTAGTACAGTTTTGTACAAATGTATTTCA 1 F3: 4 TACACAAGGAAAAAAAACTTTGGAACTTAAAAATTTTTTTC R RF: TACAATAACCCTTTAGTACAGTTTTGTACAAATGTATTTCAGAAAACGAAATACTTACACAAGGAAAAAAAACTTTGGAACTTAAAAATTTTTTTC RR: ATGTTATTGGGAAATCATGTCAAAACATGTTTACATAAAGTCTTTTGCTTTATGAATGTGTTCCTTTTTTTTGAAACCTTGAATTTTTAAAAAAAG F2: 3 AAAGTCTTTT 2 Unidirectional alignment (log-probability: -29.8) ACAATAACCCTTTAGTACAGTTTTGTACAAATGTATTTCAttttctGAAA----------TACACAAGGAAAAAAAACTTTGGAACTTAAAAATTTTTTT ACAATAACCCTTTAGTACAGTTTTGTACAAATGTATTTCA------GAAAACGAAATACTTACACAAGGAAAAAAAACTTTGGAACTTAAAAATTTTTTT Template switch alignment (log-probability: -17) ACAATAACCCTTTAGTACAGTTTTGTACAAATGTATTTCA|TTTTCTGAAA|TACACAAGGAAAAAAAACTTTGGAACTTAAAAATTTTTTT ACAATAACCCTTTAGTACAGTTTTGTACAAATGTATTTCA|TTTTCTGAAA|TACACAAGGAAAAAAAACTTTGGAACTTAAAAATTTTTTT ========== Event 3286 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CGTTAAAAAGAAACTTAAAATGAC---------CATTACATCGCACAAATAAGAAGGT Chimp: CGTTAAAAAGAAACTTAAAATGAC---------CATTACATCGCACAAATAAGAAGGT ↓ 3 1 4 2 Gorilla: CGTTAAAAAGAAACTTAAAATGACCTAATGGTCATTTACATCGCACAAATAAGAAGGT Human: CGTTAAAAAGAAACTTAAAATGAC---------CATTACATCGCACAAATAAGAAGGT Cluster: [ ] Orangutan: CGTTAAAAACAAACTTAAAATGAC---------CATTACATCGCACAAGTAAGAAGGT Chimp > Gorilla --------------- chr7:45515155-45515164 Template switch process: F1: L GCAATCCTTCAACTTGTCGTTAAAAAGAAACTTAAAATGACC 1 F3: 4 TTACATCGCACAAATAAGAAGGTAAGTTAAATGTGTTTTT R RF: GCAATCCTTCAACTTGTCGTTAAAAAGAAACTTAAAATGACCATTACATCGCACAAATAAGAAGGTAAGTTAAATGTGTTTTT RR: CGTTAGGAAGTTGAACAGCAATTTTTCTTTGAATTTTACTGGTAATGTAGCGTGTTTATTCTTCCATTCAATTTACACAAAAA F2: 3 TACTGGTAAT 2 Unidirectional alignment (log-probability: -29.4) AATCCTTCAACTTGTCGTTAAAAAGAAACTTAAAATGACCtaatggtcatTTACATCGCACAAATAAGAAGGTAAGTTAAATGTGTTTTT AATCCTTCAACTTGTCGTTAAAAAGAAACTTAAAATGACCA---------TTACATCGCACAAATAAGAAGGTAAGTTAAATGTGTTTTT Template switch alignment (log-probability: -17) AATCCTTCAACTTGTCGTTAAAAAGAAACTTAAAATGACC|TAATGGTCAT|TTACATCGCACAAATAAGAAGGTAAGTTAAATGTGTTTTT AATCCTTCAACTTGTCGTTAAAAAGAAACTTAAAATGACC|TAATGGTCAT|TTACATCGCACAAATAAGAAGGTAAGTTAAATGTGTTTTT ========== Event 3287 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGACAAATGGC------AGATGGTTTTGTCACAAAAAAGAT Chimp: ATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC--TTTGC---TTATGGTGGTTTTGTCACAAAAAAGAT Gorilla: ATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC--TTTGCTTA---TGACGGTTTTGTCACAAAAAAGAT ↓ 3 2 1 4 Human: ATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGACAAATGGC------AGATGGTTTTGTCACAAAAAAGAT Cluster: [ ] Orangutan: ATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC--TTTGCTTA---TGATGGTTTTGTCACAAAAAAGAT Gorilla > Human --------------- chr7:116192551-116192558 Template switch process: F1: L GAATATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC 1 F3: 4 GATGGTTTTGTCACAAAAAAGATTGTTTAATGTAATCAGTTTT R RF: GAATATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGACTTTGCTTATGACGGTTTTGTCACAAAAAAGATTGTTTAATGTAATCAGTTTT RR: CTTATAATAAAAGGGGAGACCAAACGGTAAACAGAAGACTGAAACGAATACTGCCAAAACAGTGTTTTTTCTAACAAATTACATTAGTCAAAA F2: 3 ACGGTAAA 2 Unidirectional alignment (log-probability: -35.6) AATATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGACaaatggcagaT-----------GGTTTTGTCACAAAAAAGATTGTTTAATGTAATCAGT AATATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC----------TTTGCTTATGACGGTTTTGTCACAAAAAAGATTGTTTAATGTAATCAGT Template switch alignment (log-probability: -22.3) AATATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC|AAATGGCA|GAtGGTTTTGTCACAAAAAAGATTGTTTAATGTAATCAGT AATATTATTTTCCCCTCTGGTTTGCCATTTGTCTTCTGAC|AAATGGCA|GACGGTTTTGTCACAAAAAAGATTGTTTAATGTAATCAGT ========== Event 3288 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCAAACCATGTTGATTGATTGT-----------------------AAGCCACCTTGGGAGTAGATGAGAACGGCAAAGACCTGTGTGTGGGTGG ↓ 1 3 24 ↑ 1 3 24 Chimp: CCAAACCATGTTGATTGATTGC-----------------CGTTCTCATCTACTCCCAAGGTGGCT------TACAAAGACCTGTGTGTGGGTGG Gorilla: CCAAACCATGTTTATTGATTGCCATTCACATCTTGTTCT------CATCTACTCCCAAGGTGGCT------TACAAAGACCTGTGTGTGGGTGG Human: CCAAACCATGTTGATTGATTGT-----------------------AAGCCACCTTGGGAGTAGATGAGAACGGCAAAGACCTGTGTGTGGGTGG Cluster: [ ] Orangutan: CCAAACCATGTTGATTGATTGCCATTCACATCCTGTTCT------CATCTACTCCCAAGGTGGCT------TACAAAGACGTGTGTGTGGGTGG Chimp > Human ------------- chr7:41628963-41628991 Template switch process: F1: L TGTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG 1 F3: 4 CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG R RF: TGTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTGCCGTTCTCATCTACTCCCAAGGTGGCTTACAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG RR: ACATTATATACCAAACAAGTGGTTTGGTACAACTAACTAACGGCAAGAGTAGATGAGGGTTCCACCGAATGTTTCTGGACACACACCCACCCTTCCACCCCGCGTCTCTC F2: 3 GGCAAGAGTAGATGAGGGTTCCACCGAAT 2 Unidirectional alignment (log-probability: -61.4) GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG---------------------------TAagccaccttgggagtagatgagaacggCAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTGCCGTTCTCATCTACTCCCAAGGTGGCTTA---------------------------CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG Template switch alignment (log-probability: -18.9) GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG|TAAGCCACCTTGGGAGTAGATGAGAACGG|CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG|TAAGCCACCTTGGGAGTAGATGAGAACGG|CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG Human > Chimp ------------- chr7:44010383-44010411 Template switch process: F1: L TGTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG 1 F3: 4 CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG R RF: TGTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTGTAAGCCACCTTGGGAGTAGATGAGAACGGCAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG RR: ACATTATATACCAAACAAGTGGTTTGGTACAACTAACTAACATTCGGTGGAACCCTCATCTACTCTTGCCGTTTCTGGACACACACCCACCCTTCCACCCCGCGTCTCTC F2: 3 ATTCGGTGGAACCCTCATCTACTCTTGCC 2 Unidirectional alignment (log-probability: -61.4) GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTGccgttctcatctactcccaaggtggctTA---------------------------CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG---------------------------TAAGCCACCTTGGGAGTAGATGAGAACGGCAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG Template switch alignment (log-probability: -18.9) GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG|CCGTTCTCATCTACTCCCAAGGTGGCTTA|CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG GTAATATATGGTTTGTTCACCAAACCATGTTGATTGATTG|CCGTTCTCATCTACTCCCAAGGTGGCTTA|CAAAGACCTGTGTGTGGGTGGGAAGGTGGGGCGCAGAGAG ========== Event 3289 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: atgatttccacaacaactcATCATAGGAAGCTCAAAGATGTTACATTACTGAGATAGGTAATACAATTAGCAAACAT Chimp: ATGATTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTA----CCTATGA-TGGTAATACAATTAGCAAACAT ↑ 3 2 1 4 Gorilla: ATGATTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTACATTACTGAGATAGGTAATACAATTAGCAAACAT Human: atgatttccacaacaactcATCATAGGAAGCTCAAAGATGTTACATTACTGAGATAGGTAATACAATTAGCAAACAT Cluster: [ ] Orangutan: ATGATTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTACATTGCTGAGATAGGTAATACAATTAGCAAACAT Gorilla > Chimp --------------- chr7:43934080-43934086 Template switch process: F1: L GATTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTAC 1 F3: 4 GGTAATACAATTAGCAAACATGGGGGCTTAGAATTTAACT R RF: GATTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTACATTACTGAGATAGGTAATACAATTAGCAAACATGGGGGCTTAGAATTTAACT RR: CTAAAGGTGTTGTTGAGTAGTATCCTTCGAGTTTCTTCAATGTAATGACTCTATCCATTATGTTAATCGTTTGTACCCCCGAATCTTAAATTGA F2: 3 TAGTATC 2 Unidirectional alignment (log-probability: -28.4) TTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTACctatgAT----------GGTAATACAATTAGCAAACATGGGGGCTTAGAATTTAACT TTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTAC-----ATTACTGAGATAGGTAATACAATTAGCAAACATGGGGGCTTAGAATTTAACT Template switch alignment (log-probability: -16.6) TTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTAC|CTATGAT|GGTAATACAATTAGCAAACATGGGGGCTTAGAATTTAACT TTTCCACAACAACTCATCATAGGAAGCTCAAAGAAGTTAC|CTATGAT|GGTAATACAATTAGCAAACATGGGGGCTTAGAATTTAACT ========== Event 3290 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGTCCACTATTTATGATGGGATTTTCCTCATCCATAGTGAATATCCGCAC-----ACGGGGGATAT-----TTGTGGGGATATTCACTACGGATGAGGAAAATCCCATCATAAatagtggacta Chimp: TAGTCCACTATTTATGATGGGATTTTCCTCATCCATAGTGAATATCCGCAC-----ACGGGGGATAT-----TTGTGGGGATATTCACTACGGATGAGGAAAATCCCATCATAAatagtggacta ↑ 1 3 4 2 Gorilla: TAGTCCACTATTTATGATGGAATTTTCCTCATCCGTAGTGAATATCCCCAC----------AAATATCCCCCATGTGCGGATATTCACTATGGATGAGGAAAATCCCATCATAAatagtggacta ↓ 1 3 4 2 Human: TAGTCCACTATTTATGATGGGATTTTCCTCATCCATAGTGAATATCCGCAC-----ACGGGGGATAT-----TTGTGGGGATATTCACTACGGATGAGGAAAATCCCATCATAAatagtggacta Cluster: [ ] Orangutan: TAGTCCACTATTTATGATGGGATTTTCCTCATCTGTAGTGAATATCCACACACAGG-----GGATAT-----TTGTGGGGATATTCTCTATGGATGAGGAAAATCCCATCATAAatagtggacta Gorilla > Human --------------- chr7:117162469-117162529 Template switch process: F1: L ACTATTTATGATGG 1 F3: 4 GGATGAGGAAAATCCCATCATAAATAG R RF: ACTATTTATGATGGAATTTTCCTCATCCGTAGTGAATATCCCCACAAATATCCCCCATGTGCGGATATTCACTATGGATGAGGAAAATCCCATCATAAATAG RR: TGATAAATACTACCTTAAAAGGAGTAGGCATCACTTATAGGGGTGTTTATAGGGGGTACACGCCTATAAGTGATACCTACTCCTTTTAGGGTAGTATTTATC F2: 3 CATCACTTATAGGGGTGTTTATAGGGGGCACACGCCTATAAGTGATACCTACTCCTTTTAG 2 Unidirectional alignment (log-probability: -64.7) ACTATTTATGATGGgATTTTCCTCATCCaTAGTGAATATCCgCACAcgggggatatt-----------TGTGgGGATATTCACTAcGGATGAGGAAAATCCCATCATAAATAG ACTATTTATGATGGAATTTTCCTCATCCGTAGTGAATATCCCCACA-----------AATATCCCCCATGTGCGGATATTCACTATGGATGAGGAAAATCCCATCATAAATAG Template switch alignment (log-probability: -28) ACTATTTATGATGG|GATTTTCCTCATCCATAGTGAATATCCGCACAcGGGGGATATTTGTGGGGATATTCACTAC|GGATGAGGAAAATCCCATCATAAATAG ACTATTTATGATGG|GATTTTCCTCATCCATAGTGAATATCCGCACATGGGGGATATTTGTGGGGATATTCACTAC|GGATGAGGAAAATCCCATCATAAATAG Gorilla > Chimp --------------- chr7:121651584-121651644 Template switch process: F1: L ACTATTTATGATGG 1 F3: 4 GGATGAGGAAAATCCCATCATAAATAG R RF: ACTATTTATGATGGAATTTTCCTCATCCGTAGTGAATATCCCCACAAATATCCCCCATGTGCGGATATTCACTATGGATGAGGAAAATCCCATCATAAATAG RR: TGATAAATACTACCTTAAAAGGAGTAGGCATCACTTATAGGGGTGTTTATAGGGGGTACACGCCTATAAGTGATACCTACTCCTTTTAGGGTAGTATTTATC F2: 3 CATCACTTATAGGGGTGTTTATAGGGGGCACACGCCTATAAGTGATACCTACTCCTTTTAG 2 Unidirectional alignment (log-probability: -64.7) ACTATTTATGATGGgATTTTCCTCATCCaTAGTGAATATCCgCACAcgggggatatt-----------TGTGgGGATATTCACTAcGGATGAGGAAAATCCCATCATAAATAG ACTATTTATGATGGAATTTTCCTCATCCGTAGTGAATATCCCCACA-----------AATATCCCCCATGTGCGGATATTCACTATGGATGAGGAAAATCCCATCATAAATAG Template switch alignment (log-probability: -28) ACTATTTATGATGG|GATTTTCCTCATCCATAGTGAATATCCGCACAcGGGGGATATTTGTGGGGATATTCACTAC|GGATGAGGAAAATCCCATCATAAATAG ACTATTTATGATGG|GATTTTCCTCATCCATAGTGAATATCCGCACATGGGGGATATTTGTGGGGATATTCACTAC|GGATGAGGAAAATCCCATCATAAATAG ========== Event 3291 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTGAAAACTGAGGGTTTAT------TTATATCATATGAACTTGAACAGATACTTAATTACAGCAACCCAG Chimp: CTTTGAAAACTGAGGGTTTAT------TTATATCATATGAACTTGAACAGATACTTAATTACAGCAACCCAG ↓ 1 4 3 2 Gorilla: CTTTGAAAGCTGAGGGTTTATTATCTGTTCAAGAATATGAACTTGAACAGATACTTAATTACAGCAACCCAG ↑ 1 4 3 2 Human: CTTTGAAAACTGAGGGTTTAT------TTATATCATATGAACTTGAACAGATACTTAATTACAGCAACCCAG Cluster: [ ] Orangutan: CTTGGAAAACTGAGGGTTTAT------TTATATCATATGAACTTGAACAGATACTTAATTACAGCAACCCAG Human > Gorilla --------------- chr7:116342333-116342343 Template switch process: F1: L AGCATTCAAATTTATAGCCACTTTGAAAGCTGAGGGTTTATT 1 F3: 4 AATATGAACTTGAACAGATACTTAATTACAGCAACCCAGCA R RF: AGCATTCAAATTTATAGCCACTTTGAAAACTGAGGGTTTATTTATATCATATGAACTTGAACAGATACTTAATTACAGCAACCCAGCA RR: TCGTAAGTTTAAATATCGGTGAAACTTTTGACTCCCAAATAAATATAGTATACTTGAACTTGTCTATGAATTAATGTCGTTGGGTCGT F2: 3 GAACTTGTCTA 2 Unidirectional alignment (log-probability: -39.3) CATTCAAATTTATAGCCACTTTGAAAgCTGAGGGTTTAT---TATCtgttcaagaATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC CATTCAAATTTATAGCCACTTTGAAAACTGAGGGTTTATTTATATC---------ATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC Template switch alignment (log-probability: -28.2) CATTCAAATTTATAGCCACTTTGAAAgCTGAGGGTTTATT|ATCTGTTCAAG|aATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC CATTCAAATTTATAGCCACTTTGAAAACTGAGGGTTTATT|ATCTGTTCAAG|CATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC Chimp > Gorilla --------------- chr7:116342333-116342343 Template switch process: F1: L AGCATTCAAATTTATAGCCACTTTGAAAGCTGAGGGTTTATT 1 F3: 4 AATATGAACTTGAACAGATACTTAATTACAGCAACCCAGCA R RF: AGCATTCAAATTTATAGCCACTTTGAAAACTGAGGGTTTATTTATATCATATGAACTTGAACAGATACTTAATTACAGCAACCCAGCA RR: TCGTAAGTTTAAATATCGGTGAAACTTTTGACTCCCAAATAAATATAGTATACTTGAACTTGTCTATGAATTAATGTCGTTGGGTCGT F2: 3 GAACTTGTCTA 2 Unidirectional alignment (log-probability: -39.3) CATTCAAATTTATAGCCACTTTGAAAgCTGAGGGTTTAT---TATCtgttcaagaATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC CATTCAAATTTATAGCCACTTTGAAAACTGAGGGTTTATTTATATC---------ATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC Template switch alignment (log-probability: -28.2) CATTCAAATTTATAGCCACTTTGAAAgCTGAGGGTTTATT|ATCTGTTCAAG|aATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC CATTCAAATTTATAGCCACTTTGAAAACTGAGGGTTTATT|ATCTGTTCAAG|CATATGAACTTGAACAGATACTTAATTACAGCAACCCAGC ========== Event 3292 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTCTCTGAATGTTCTGCCTCAGGTGCTGCCAGTTGGGTTAAACAATCATCT Chimp: GCTCTCTGAATGTTCTGCCTCTGGTGCTGCCAGTTGGGTTAAACAATCATCT Gorilla: GCTCTCTGAATATTCTGCCTCTGGCAGCACCAGTTGGGTTAAACAATCATCT ↑ 1 3 4 2 Human: GCTCTCTGAATGTTCTGCCTCAGGTGCTGCCAGTTGGGTTAAACAATCATCT Cluster: [ ] Orangutan: GCTCTCTGAATGTTCTGCCTCTGGTGCTGCCAGTTGGGTTAAACAATCAT-C Human > Gorilla --------------- chr7:117452414-117452421 Template switch process: F1: L GCAGGAAATCGAAAGGCCAAGCTCTCTGAATATTCTGCCTC 1 F3: 4 CCAGTTGGGTTAAACAATCATCTCTAAATAAGCATTACTC R RF: GCAGGAAATCGAAAGGCCAAGCTCTCTGAATGTTCTGCCTCAGGTGCTGCCAGTTGGGTTAAACAATCATCTCTAAATAAACATTACTC RR: CGTCCTTTAGCTTTCCGGTTCGAGAGACTTACAAGACGGAGTCCACGACGGTCAACCCAATTTGTTAGTAGAGATTTATTTGTAATGAG F2: 3 ACGACGGT 2 Unidirectional alignment (log-probability: -40.6) CAGGAAATCGAAAGGCCAAGCTCTCTGAATaTTCTGCCT------CTGgcagcaCCAGTTGGGTTAAACAATCATCTCTAAATAAgCATTACTC CAGGAAATCGAAAGGCCAAGCTCTCTGAATGTTCTGCCTCAGGTGCTG------CCAGTTGGGTTAAACAATCATCTCTAAATAAACATTACTC Template switch alignment (log-probability: -27.8) CAGGAAATCGAAAGGCCAAGCTCTCTGAATaTTCTGCCTC|TGGCAGCA|CCAGTTGGGTTAAACAATCATCTCTAAATAAgCATTACTC CAGGAAATCGAAAGGCCAAGCTCTCTGAATGTTCTGCCTC|TGGCAGCA|CCAGTTGGGTTAAACAATCATCTCTAAATAAACATTACTC ========== Event 3293 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCTCAGGAAGAGGTATATCTCAGTCTCATGAGGAGACTGAGTCTTATGAGAGGAGATAAAAT ↑ 3 2 1 4 Chimp: GCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG-------TACTTATGAGAGGAGATAAAAT Gorilla: GCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG-------TACTTATGAGAGGAGATAAAAT ↓ 3 2 1 4 Human: GCCTCAGGAAGAGGTATATCTCAGTCTCATGAGGAGACTGAGTCTTATGAGAGGAGATAAAAT Cluster: [ ] Orangutan: GCCTCAGGAAGAGGTATATCTCAGTCTCATGAAG-------AACTTATGAGAGGAGATAAAAT Chimp > Human ------------- chr7:40533632-40533639 Template switch process: F1: L TAATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG 1 F3: 4 TCTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAGT R RF: TAATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGGTACTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAGT RR: ATTAAAACGGAGTCCTTCTCCATATAGAGTCAGAGTACTCCATGAATACTCTCCTCTATTTTAACTCCACTCAAATATTCTCA F2: 3 GAGTCAGA 2 Unidirectional alignment (log-probability: -32.7) AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGgagactgaGT-CTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAG--------GTACTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG Template switch alignment (log-probability: -22.3) AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG|AGACTGAG|tCTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG|AGACTGAG|ACTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG Gorilla > Human --------------- chr7:40533632-40533639 Template switch process: F1: L TAATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG 1 F3: 4 TCTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAGT R RF: TAATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGGTACTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAGT RR: ATTAAAACGGAGTCCTTCTCCATATAGAGTCAGAGTACTCCATGAATACTCTCCTCTATTTTAACTCCACTCAAATATTCTCA F2: 3 GAGTCAGA 2 Unidirectional alignment (log-probability: -32) AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGGagactgagtCTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG-------TACTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG Template switch alignment (log-probability: -22.3) AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG|AGACTGAG|tCTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG AATTTTGCCTCAGGAAGAGGTATATCTCAGTCTCATGAGG|AGACTGAG|ACTTATGAGAGGAGATAAAATTGAGGTGAGTTTATAAGAG ========== Event 3294 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTTAGCTGGTTTGTTTCTTTCCATTAGAC--------TACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCTGCCATGAAGATAAGGGACATGTGATGGAATGATTAATTGCAGGAATTATTGTATCTTGGC Chimp: TCTTAGCTGGTTTGTTTCTTTTCATTAGAC----GATTAACATTTTGCAGTCTTTTATATTGTTCATTTTCCTTTGCCTGCCATGAAGATAAGGGACATGTGATGGAATGATTAATTGCAGGAATTATTGTATCTTGGC Gorilla: TCTTAGCTGGTTTGTTTCTTTTCATTAGGCAATT----AACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCTGCCATGAAGATAAGGGACATGTGATGGAATGATTAATTGCAGGAATTATTGTATCTTGGC ↑ 1 4 3 2 Human: TCTTAGCTGGTTTGTTTCTTTCCATTAGAC--------TACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCTGCCATGAAGATAAGGGACATGTGATGGAATGATTAATTGCAGGAATTATTGTATCTTGGC Cluster: [ ] Orangutan: tcttagctggtttgtttcttttcattagacgatt----aacattttgtagtcttttatattgttcattttcctttgcctgccatgaagataagggacatgtgatggaatgattaattgcaggaattatTGAATCTTGGC Human > Gorilla --------------- chr7:39665043-39665049 Template switch process: F1: L TAGTAGAAATAAAGCATTTATCTTAGCTGGTTTGTTTCTTTTCATTAG 1 F3: 4 ACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCT R RF: TAGTAGAAATAAAGGATTTATCTTAGCTGGTTTGTTTCTTTCCATTAGACTACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCTGCCATGAAGATAAGGGACATGTGATGGAATGATTAATTGC RR: ATCATCTTTATTTCCTAAATAGAATCGACCAAACAAAGAAAGGTAATCTGATGTAAAACATCAGAAAATATAACAAGTAAAAGGAAACGGACGGTACTTCTATTCCCTGTACACTACCTTACTAATTAACG F2: 3 ATTAACG 2 Unidirectional alignment (log-probability: -38.9) ATAAAGcATTTATCTTAGCTGGTTTGTTTCTTTtCATTAGgCaattaACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCT ATAAAGGATTTATCTTAGCTGGTTTGTTTCTTTCCATTAGAC----TACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCT Template switch alignment (log-probability: -27.8) ATAAAGcATTTATCTTAGCTGGTTTGTTTCTTTtCATTAG|GCAATTA|ACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCT ATAAAGGATTTATCTTAGCTGGTTTGTTTCTTTCCATTAG|GCAATTA|ACATTTTGTAGTCTTTTATATTGTTCATTTTCCTTTGCCT ========== Event 3295 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGAATTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAG---CTTTTCTAAGTTCCAGTAAGAC Chimp: AGAATTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAG---CTTTTCTAAGTTCCAGTAAGAC ↓ 3 2 1 4 Gorilla: AGAATTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTGTTGGCTTTTGTTTTTCATAGTTCCAGTTTTCTAAGTTCCAGTAAGAC ↑ 3 2 1 4 Human: AGAATTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAG---CTTTTCTAAGTTCCAGTAAGAC Cluster: [ ] Orangutan: AGAATTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGTTACCTGTTGATTTTTGTTCTTCATAGAG---CTTTTTTAAGTTCCAGTAAGAC Human > Gorilla --------------- chr7:118355292-118355297 Template switch process: F1: L TTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTGTTGGCTTTTGTTTTTCATAG 1 F3: 4 TTTTCTAAGTTCCAGTAAG R RF: TTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAGCTTTTCTAAGTTCCAGTAAG RR: AAAATGTCATCTTTCGACCTTTTAACGAAAATAACTATGGATAACCAAAAACAAAAAGTATCTCGAAAAGATTCAAGGTCATTC F2: 3 GACCTT 2 Unidirectional alignment (log-probability: -37.3) ATTGCTTTTATTGATACCTgTTGGcTTTTGTTTTTCATAGttCcagTTTTCTAAGTTCCAGTAAG ATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAGC---TTTTCTAAGTTCCAGTAAG Template switch alignment (log-probability: -27.5) ATTGCTTTTATTGATACCTgTTGGcTTTTGTTTTTCATAG|TTCCAG|TTTTCTAAGTTCCAGTAAG ATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAG|TTCCAG|TTTTCTAAGTTCCAGTAAG Chimp > Gorilla --------------- chr7:118355292-118355297 Template switch process: F1: L TTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTGTTGGCTTTTGTTTTTCATAG 1 F3: 4 TTTTCTAAGTTCCAGTAAG R RF: TTTTACAGTAGAAAGCTGGAAAATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAGCTTTTCTAAGTTCCAGTAAG RR: AAAATGTCATCTTTCGACCTTTTAACGAAAATAACTATGGATAACCAAAAACAAAAAGTATCTCGAAAAGATTCAAGGTCATTC F2: 3 GACCTT 2 Unidirectional alignment (log-probability: -37.3) ATTGCTTTTATTGATACCTgTTGGcTTTTGTTTTTCATAGttCcagTTTTCTAAGTTCCAGTAAG ATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAGAGC---TTTTCTAAGTTCCAGTAAG Template switch alignment (log-probability: -27.5) ATTGCTTTTATTGATACCTgTTGGcTTTTGTTTTTCATAG|TTCCAG|TTTTCTAAGTTCCAGTAAG ATTGCTTTTATTGATACCTATTGGTTTTTGTTTTTCATAG|TTCCAG|TTTTCTAAGTTCCAGTAAG ========== Event 3296 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAAAATCTCTGGCTGAGGAT------------ACACT----TGATTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT Chimp: TAAAAATCTCTGGCTGAGGAT------------ACACT----TGATTGTTGTAAAAAATCAAGTGTTTCCtttttttaaaaaaaT ↑ 1 4 3 2 Gorilla: TAAAAATCTCTGGCTGAGGATATGAGGCAAAGCTCATTTAAAAGTTTGTTGTAAAAAATCAAGTGTTTCCtttttttaaaaaaaT ↓ 1 4 3 2 Human: TAAAAATCTCTGGCTGAGGAT------------ACACT----TGATTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT Cluster: [ ] Orangutan: TAAAAATCTCTGGTTGAGGATATGAGGCAAAGCtcatttaaaagtttgttgtaaaaaattaattgtttccttttttaaaaaaaaT Gorilla > Human --------------- chr7:122348487-122348493 Template switch process: F1: L TCCACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA 1 F3: 4 TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT R RF: TCCACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATATGAGGCAAAGCTCATTTAAAAGTTTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT RR: AGGTGTTGAAAGATTCCTTTATTTTTAGAGACCGACTCCTATACTCCGTTTCGAGTAAATTTTCAAACAACATTTTTTAGTTCACAAAGGAAAAAAATTTTTTTA F2: 3 AGTTCAC 2 Unidirectional alignment (log-probability: -27.5) CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATAcactTGA--------------------TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA----TGAGGCAAAGCTCATTTAAAAGTTTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT Template switch alignment (log-probability: -16.6) CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA|CACTTGA|TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA|CACTTGA|TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT Gorilla > Chimp --------------- chr7:126868763-126868769 Template switch process: F1: L TCCACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA 1 F3: 4 TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT R RF: TCCACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATATGAGGCAAAGCTCATTTAAAAGTTTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT RR: AGGTGTTGAAAGATTCCTTTATTTTTAGAGACCGACTCCTATACTCCGTTTCGAGTAAATTTTCAAACAACATTTTTTAGTTCACAAAGGAAAAAAATTTTTTTA F2: 3 AGTTCAC 2 Unidirectional alignment (log-probability: -27.5) CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATAcactTGA--------------------TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA----TGAGGCAAAGCTCATTTAAAAGTTTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT Template switch alignment (log-probability: -16.6) CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA|CACTTGA|TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT CACAACTTTCTAAGGAAATAAAAATCTCTGGCTGAGGATA|CACTTGA|TTGTTGTAAAAAATCAAGTGTTTCCTTTTTTTAAAAAAAT ========== Event 3297 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTGAAAGTCATCATGATTCAAGTGACTATATCG---------TGAGTTTCAAAGTTAGaatataa Chimp: CTTTGAAAGTCATCATGCTTCAAGTGAATATATCG---------TGAGTTTCAAAGTTAGaatataa ↓ 3 2 1 4 Gorilla: CTTTGAAAGTCATCATGCTTCAAGTGAATATATCG-TTTCACTTGAAGTTTCAAAGTTAGaatataa Human: CTTTGAAAGTCATCATGATTCAAGTGACTATATCG---------TGAGTTTCAAAGTTAGaatataa Cluster: [ ] Orangutan: CTTTGAAAGTCATCATGCTTCAAGTGAATATATCGT--------TGAGTTTCAAAGTTAGAATATAA Chimp > Gorilla --------------- chr7:122509645-122509653 Template switch process: F1: L TTCTCACTTTGAAAGTCATCATGCTTCAAGTGAATATATCGT 1 F3: 4 AGTTTCAAAGTTAGAATATAAAATATTTTCTAGAGAAATC R RF: TTCTCACTTTGAAAGTCATCATGCTTCAAGTGAATATATCGTGAGTTTCAAAGTTAGAATATAAAATATTTTCTAGAGAAATC RR: AAGAGTGAAACTTTCAGTAGTACGAAGTTCACTTATATAGCACTCAAAGTTTCAATCTTATATTTTATAAAAGATCTCTTTAG F2: 3 AGTTCACTT 2 Unidirectional alignment (log-probability: -27.9) CTCACTTTGAAAGTCATCATGCTTCAAGTGAATATATCGTttcacttgaAGTTTCAAAGTTAGAATATAAAATATTTTCTAGAGAAATC CTCACTTTGAAAGTCATCATGCTTCAAGTGAATATATCGTG--------AGTTTCAAAGTTAGAATATAAAATATTTTCTAGAGAAATC Template switch alignment (log-probability: -16.9) CTCACTTTGAAAGTCATCATGCTTCAAGTGAATATATCGT|TTCACTTGA|AGTTTCAAAGTTAGAATATAAAATATTTTCTAGAGAAATC CTCACTTTGAAAGTCATCATGCTTCAAGTGAATATATCGT|TTCACTTGA|AGTTTCAAAGTTAGAATATAAAATATTTTCTAGAGAAATC ========== Event 3298 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tacaagaaggtagttggatttgtgaCAGAAAGGTCAACCCAGA--TGATTTTATACATTAACAGGTTG ↓ 3 2 1 4 Chimp: tacaagaaggtagttggatttgtgaCAGAAAGGTCTGTCAC----AAATTTTATACATTAACAGGTTG ↑ 3 2 1 4 Gorilla: tacaagaaggcagttggatttgtgaCAGAAAGGTCAACCCAGATGTGATTTTATACATTAACAGGTTG Human: tacaagaaggtagttggatttgtgaCAGAAAGGTCAACCCAGA--TGATTTTATACATTAACAGGTTG Cluster: [ ] Orangutan: tacaagaaggcagttggatttgtgaCAGAAAGGTCAACCCAGATGTGATTTTATACATTAACAGGTTG Human > Chimp ------------- chr7:37997685-37997692 Template switch process: F1: L GAAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGTC 1 F3: 4 ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT R RF: GAAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGTCAACCCAGATGATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT RR: CTTCTCATGTTCTTCCATCAACCTAAACACTGTCTTTCCAGTTGGGTCTACTAAAATATGTAATTGTCCAACTTTAAACAGTGTATCTATA F2: 3 AACACTGT 2 Unidirectional alignment (log-probability: -30.2) AAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGTctgtcaCAA--------ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT AAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGT------CAACCCAGATGATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT Template switch alignment (log-probability: -16.3) AAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGTC|TGTCACAA|ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT AAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGTC|TGTCACAA|ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT Gorilla > Chimp --------------- chr7:37997685-37997692 Template switch process: F1: L GAAGAGTACAAGAAGGTAGTTGGATTTGTGACAGAAAGGTC 1 F3: 4 ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT R RF: GAAGAGTACAAGAAGGCAGTTGGATTTGTGACAGAAAGGTCAACCCAGATGTGATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT RR: CTTCTCATGTTCTTCCGTCAACCTAAACACTGTCTTTCCAGTTGGGTCTACACTAAAATATGTAATTGTCCAACTTTAAACAGTGTATCTATA F2: 3 AACACTGT 2 Unidirectional alignment (log-probability: -35.3) AAGAGTACAAGAAGGtAGTTGGATTTGTGACAGAAAGGTC----------TGtcacaaATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT AAGAGTACAAGAAGGCAGTTGGATTTGTGACAGAAAGGTCAACCCAGATGTG------ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT Template switch alignment (log-probability: -22.3) AAGAGTACAAGAAGGtAGTTGGATTTGTGACAGAAAGGTC|TGTCACAA|ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT AAGAGTACAAGAAGGCAGTTGGATTTGTGACAGAAAGGTC|TGTCACAA|ATTTTATACATTAACAGGTTGAAATTTGTCACATAGATAT ========== Event 3299 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GTCTCAGATTTTATCACTGTA-AAAC----AGTTAGGCATAAGGGTAAAATATTTAGAGACAACTGTCTAGCAAATACTTCAAATT Chimp: GTCTCAGATTTTATCACTGTAAAAAC----AGTTAGGCATAAGGGTAAAATATTTAGAGACAACTGTCTAGCAAATACTTCAAATT Gorilla: GTCTCAGATTTTATCACTGTAAAAAC--------AGGCATAAGGGCAAAATATTTAGAGACAACTGTCTAGCAAATACTTCAAATT ↓ 1 4 3 2 Human: GTCTCAGATTTTATCACTGTA-AAAC----AGTTAGGCATAAGGGTAAAATATTTAGAGACAACTGTCTAGCAAATACTTCAAATT Cluster: [ ] Orangutan: GTCTCAGATTTTATCACTGTAAAAACAGTT----AGGTATAAGGGCAAAATATTTAGAGACAACTGTCTAGCAAATACTTCAAATT Gorilla > Human --------------- chr7:35552627-35552631 Template switch process: F1: L CATGACCCAGACAACTTTGGGTCTCAGATTTTATCACTGTAAAA 1 F3: 4 AGGCATAAGGGTAAAATATTTAGAGACAACTGTCTAGCAA R RF: CATGACCCAGACAACTTTGGGTCTCAGATTTTATCACTGTAAAAACAGGCATAAGGGCAAAATATTTAGAGACAACTGTCTAGCAA RR: GTACTGGGTCTGTTGAAACCCAGAGTCTAAAATAGTGACATTTTTGTCCGTATTCCCGTTTTATAAATCTCTGTTGACAGATCGTT F2: 3 TTGAC 2 Unidirectional alignment (log-probability: -31.8) ACCCAGACAACTTTGGGTCTCAGATTTTATCACTGTAAAAcagttAGGCATAAGGGtAAAATATTTAGAGACAACTGTCTAGCAA ACCCAGACAACTTTGGGTCTCAGATTTTATCACTGTAAAA---ACAGGCATAAGGGCAAAATATTTAGAGACAACTGTCTAGCAA Template switch alignment (log-probability: -22) ACCCAGACAACTTTGGGTCTCAGATTTTATCACTGTAAAA|CAGTT|AGGCATAAGGGtAAAATATTTAGAGACAACTGTCTAGCAA ACCCAGACAACTTTGGGTCTCAGATTTTATCACTGTAAAA|CAGTT|AGGCATAAGGGCAAAATATTTAGAGACAACTGTCTAGCAA ========== Event 3300 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCATCTAACTATTGTTAATTCT-ATCATTTGGAAATAATATATTCTTAGCTGAAACTCACAAAACTACTTTCTTCCTCTCAAAGTATTTATAACAAGGTCTATATTTATCTGATGGACTTTACATCATTATAGTTCATCACAGAGTATTTTTTATTTTGTAAGCAT Chimp: CCATGTAACTATTGTTAATTCG-ATCATTTGAAAATAATATATTCTTAGCTGAAACTCACAAAACTACTTTGTTCCTCTCAAAGTATTTAGAACAAGGTGTATACTTATCTGATGGACTTTACATCATTATAGTTCATCACAGAGTATTTTTTATTTTGTAAGCAT ↑ 1 4 3 2 Gorilla: CCATGTAACTATTGTTAATTCTAAATATTCGAAAATAATATATTCTTAGCTGAAACTCACAAAACTACTTTGTTCCTCTTGAAGTATTTAGAACAAGGTCTATATTTATCTGATGGACTTTACATCAGTATAGTTCATCACAGATCATTTTTTATTTTGTAAGCAT Human: CCATCTAACTATTGTTAATTCT-ATCATTTGGAAATAATATATTCTTAGCTGAAACTCACAAAACTACTTTCTTCCTCTCAAAGTATTTATAACAAGGTCTATATTTATCTGATGGACTTTACATCATTATAGTTCATCACAGAGTATTTTTTATTTTGTAAGCAT Cluster: [ ] Orangutan: CCATGTAACTATTGTTAATTCT-ATCATTTGAAAATAATATATTCTTAGCTGAAACTCACAAAACTACTTTGTTCCTCTCGAAGTATTTAGAACAAGATCTATATTTATCTGATGGACTTTACGTCATTATAGTTCATTACAGAGTATT-TTTATTTTGTAAGCAT Gorilla > Chimp --------------- chr7:129994470-129994473 Template switch process: F1: L TTAAAGATTCATCCTATATACCATGTAACTATTGTTAATTC 1 F3: 4 ATTTGAAAATAATATATTCTTAGCTGAAACTCACAAAACTACTT R RF: TTAAAGATTCATCCTATATACCATGTAACTATTGTTAATTCTAAATATTCGAAAATAATATATTCTTAGCTGAAACTCACAAAACTACTTTGTTCCTCTTGAAGTATTTAGAACAAGGTCTATATTTATCTGATGGACTTTACATCAGTATAGTTCATCACAGATC RR: AATTTCTAAGTAGGATATATGGTACATTGATAACAATTAAGATTTATAAGCTTTTATTATATAAGAATCGACTTTGAGTGTTTTGATGAAACAAGGAGAACTTCATAAATCTTGTTCCAGATATAAATAGACTACCTGAAATGTAGTCATATCAAGTAGTGTCTAG F2: 3 CTAG 2 Unidirectional alignment (log-probability: -31.1) TAAAGATTCATCCTATATACCATGTAACTATTGTTAATTCgatcattT--------GAAAATAATATATTCTTAGCTGAAACTCACAAAACT TAAAGATTCATCCTATATACCATGTAACTATTGTTAATTC-------TAAATATTCGAAAATAATATATTCTTAGCTGAAACTCACAAAACT Template switch alignment (log-probability: -21.8) TAAAGATTCATCCTATATACCATGTAACTATTGTTAATTC|GATC|ATTtGAAAATAATATATTCTTAGCTGAAACTCACAAAACT TAAAGATTCATCCTATATACCATGTAACTATTGTTAATTC|GATC|ATTCGAAAATAATATATTCTTAGCTGAAACTCACAAAACT ========== Event 3301 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: ATCCTTTGATGTCATCCTGCTGTTTTCTGACTTCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATACTTTCTTCCCC ↑ 4 1 3 2 Chimp: ATCCTTTGATGTCATCCTGCTGT--------------TTTCACAAAATCTCCACCTTTTAAGTCATAATGCATAATTTCTTCCCC ↓ 4 1 3 2 Gorilla: ATCCTTTGATGTCATCCTGCTGTTTTCTGACTTCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATAATTTTTTCCCA Human: ATCCTTTGATGTCATCCTGCTGTTTTCTGACTTCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATACTTTCTTCCCC Cluster: [ ] Orangutan: ATCCTTTGATGTCATCCTGCTGTTTTCTAACTTCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATAATTTCTTCCCA Chimp > Human ------------- chr7:125925560-125925565 Template switch process: F1: L GGGTTTATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTC 1 F3: 4 CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATACTT R RF: GGGTTTATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATAATT RR: CCCAAATATAGTGAAAGGTAGGAAACTACAGTAGGACGACAAAAGTGTTTTAGAGGTGGAAAATTCAGTATTACGTATTAA F2: 3 TTCAGT 2 Unidirectional alignment (log-probability: -37) TATATCACTTTCCATCCTTTGATGTCATCCTGctgttttctgacttCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT TATATCACTTTCCATCCTTTGATGTCATCCTG--------------CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT Template switch alignment (log-probability: -22.2) TATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTC|TGACTT|CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT TATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTC|TGACTT|CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT Chimp > Gorilla --------------- chr7:125243890-125243895 Template switch process: F1: L GGGTTTATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTC 1 F3: 4 CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATAATT R RF: GGGTTTATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCATAATT RR: CCCAAATATAGTGAAAGGTAGGAAACTACAGTAGGACGACAAAAGTGTTTTAGAGGTGGAAAATTCAGTATTACGTATTAA F2: 3 TTCAGT 2 Unidirectional alignment (log-probability: -31) TATATCACTTTCCATCCTTTGATGTCATCCTGCTgttttctgacttctGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT TATATCACTTTCCATCCTTTGATGTCATCCTGCT--------------GTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT Template switch alignment (log-probability: -16.7) TATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTC|TGACTT|CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT TATATCACTTTCCATCCTTTGATGTCATCCTGCTGTTTTC|TGACTT|CTGTTTTCACAAAATCTCCACCTTTTAAGTCATAATGCAT ========== Event 3302 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTCCCACTTTTACCCACATAGTAAATTTTCTGCAAGAAAATCCTATGTGGGTAAAACCAATAATAA ↓ 1 3 4 2 Chimp: GTCCCACTTTTACCCACATAG--GATTTTCTTGCA-GAAATCCTATGTGGGTAAAACCAATAATAA Gorilla: GTCCCACTTTTACCCACATAG--GATTTTCTTGCA-GAAATCCTACGTGGGTAAAACCAATAATAA ↑ 1 3 4 2 Human: GTCCCACTTTTACCCACATAGTAAATTTTCTGCAAGAAAATCCTATGTGGGTAAAACCAATAATAA Cluster: [ ] Orangutan: GTCCCACTTTTACCCACATCG--GATTTTCTTGCA-GAAATCCGATGTGGGTAAAACCAATAATAA Human > Chimp ------------- chr7:35383616-35383628 Template switch process: F1: L ATTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG 1 F3: 4 AAATCCTATGTGGGTAAAACCAATAATAAAAATAAAAGTG R RF: ATTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAGTAAATTTTCTGCAAGAAAATCCTATGTGGGTAAAACCAATAATAAAAATGAAAGTG RR: TAATATGACACCACTAATGACAGGGTGAAAATGGGTGTATCATTTAAAAGACGTTCTTTTAGGATACACCCATTTTGGTTATTATTTTTACTTTCAC F2: 3 GACGTTCTTTTAG 2 Unidirectional alignment (log-probability: -43.7) TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG--------------GAttttcttgcagAAATCCTATGTGGGTAAAACCAATAATAAAAATaAAAGTG TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAGTAAATTTTCTGCAAGA-----------AAATCCTATGTGGGTAAAACCAATAATAAAAATGAAAGTG Template switch alignment (log-probability: -22.9) TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG|GATTTTCTTGCAG|AAATCCTATGTGGGTAAAACCAATAATAAAAATaAAAGTG TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG|GATTTTCTTGCAG|AAATCCTATGTGGGTAAAACCAATAATAAAAATGAAAGTG Human > Gorilla --------------- chr7:33476716-33476728 Template switch process: F1: L ATTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG 1 F3: 4 AAATCCTACGTGGGTAAAACCAATAATAAAAATAAAAGTGAATCTCATT R RF: ATTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAGTAAATTTTCTGCAAGAAAATCCTATGTGGGTAAAACCAATAATAAAAATGAAAGTGAATCTCATT RR: TAATATGACACCACTAATGACAGGGTGAAAATGGGTGTATCATTTAAAAGACGTTCTTTTAGGATACACCCATTTTGGTTATTATTTTTACTTTCACTTAGAGTAA F2: 3 GACGTTCTTTTAG 2 Unidirectional alignment (log-probability: -48.4) TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG--------------GAttttcttgcagAAATCCTAcGTGGGTAAAACCAATAATAAAAATaAAAGTG TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAGTAAATTTTCTGCAAGA-----------AAATCCTATGTGGGTAAAACCAATAATAAAAATGAAAGTG Template switch alignment (log-probability: -28.6) TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG|GATTTTCTTGCAG|AAATCCTAcGTGGGTAAAACCAATAATAAAAATaAAAGTG TTATACTGTGGTGATTACTGTCCCACTTTTACCCACATAG|GATTTTCTTGCAG|AAATCCTATGTGGGTAAAACCAATAATAAAAATGAAAGTG ========== Event 3303 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCCTCTTCCACCCTCCTCCAGCATCCTCAGACTGGTCTTGGGGTACAGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCAT---TTGCCCAAGTGTCCTTACAGCCCATTCCATCCCC Chimp: TTCCTCTTCCACCCTCCTCCAGCATCCTCAGACTGGTCTTGGGGAACAGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCAT---TTGCCCAAGCGTCCTTACAGCCCATTCCATCCCC ↓ 1 4 3 2 Gorilla: TTCCTCTTCCACCCTCCTCCAGCATCCTCAGACTGGTCTTGGGGTACAGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGAGGACGC------TGCAAGCGTCCTTACAGCCCATTCCATCCCC ↑ 3 2 1 4 Human: TTCCTCTTCCACCCTCCTCCAGCATCCTCAGACTGGTCTTGGGGTACAGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCAT---TTGCCCAAGTGTCCTTACAGCCCATTCCATCCCC Cluster: [ ] Orangutan: TTCCTCTTCCACCCTCCTCCAGCATCCTCAGGCTGGTCTTGGGGTACAGGGGAGACTGCAGAGGGTGATTTCAGGACTTGGGGCAGGATAGCATTTG---CCCAAGCGTCCTTATAGCCCATTCCATCCCC Human > Gorilla --------------- chr7:127041679-127041686 Template switch process: F1: L AGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA 1 F3: 4 CAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGGGGACT R RF: CAGCATCCTCAGACTGGTCTTGGGGTACAGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCATTTGCCCAAGTGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGGGGACT RR: GTCGTAGGAGTCTGACCAGAACCCCATGTCCCCTCTGACGTCTCCCACTAAAGTCCTGGAGCCCGTCCTATCGTAAACGGGTTCACAGGAATGTCGGGTAAGGTAGGGGCCCCGTCGACCCCTGA F2: 3 GTCGCAGG 2 Unidirectional alignment (log-probability: -38.3) GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA-----------ggacgctgCAAGcGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGG GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCATTTGCC--------CAAGTGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGG Template switch alignment (log-probability: -27.9) GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA|GGAcGCTG|CAAGcGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGG GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA|GGATGCTG|CAAGTGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGG Chimp > Gorilla --------------- chr7:127041679-127041685 Template switch process: F1: L AGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA 1 F3: 4 GCAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGG R RF: AGGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCATTTGCCCAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTGG RR: TCCCCTCTGACGTCTCCCACTAAAGTCCTGGAGCCCGTCCTATCGTAAACGGGTTCGCAGGAATGTCGGGTAAGGTAGGGGCCCCGTCGACC F2: 3 TCGCAGG 2 Unidirectional alignment (log-probability: -32.7) GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA-----------ggacgctgCAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTG GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGATAGCATTTGCC--------CAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTG Template switch alignment (log-probability: -22.2) GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA|GGACGCT|gCAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTG GGGGAGACTGCAGAGGGTGATTTCAGGACCTCGGGCAGGA|GGACGCT|CCAAGCGTCCTTACAGCCCATTCCATCCCCGGGGCAGCTG ========== Event 3304 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tgagctatatgagctagcacatgcaaaacagctagaacagtggctggcatacaaaataaattgctcagtgttggttaGAAATTAACCAAGGGATCGGCAGTCCTACAGAA---GAGGAAAACCTCTTTTGGGAGGA Chimp: tgagctatatgagctagcacatgcaaaacagctagaacagtggctggcatacaAAATAAATTTCTCAGTGTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTGCAAAA---GAGGAAAACCTCTTTTGGGAGGA ↓ 3 2 1 4 Gorilla: tgagctatatgagctagcacatgcaaaacagctagaacagtggctggcatacaaaataaattgctcagtgtgggttaGAAATTAACCAAGGGATCGGCAGTCCTACAAATGCATGGGAAAACCTCTTTCGGGAGGA Human: tgagctatatgagctagcacatgcaaaacagctagaacagtggctggcatacaaaataaattgctcagtgttggttaGAAATTAACCAAGGGATCGGCAGTCCTACAGAA---GAGGAAAACCTCTTTTGGGAGGA Cluster: [ ] Orangutan: tgagctatatgagcttgcacatgtaaaacagctagaactgtggctggcatacaaaataaattgctcagtGTGGATTAGAAATTAACCAAGGGATAGGCAGTCCTACAAATGCATGGGAAAACCTCTCTTGGGAGGA Chimp > Gorilla --------------- chr7:126342532-126342537 Template switch process: F1: L CTCAGTGTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTACAAA 1 F3: 4 GGAAAACCTCTTTCGGGAGGACACACTGCTCTGGTCTTGC R RF: CATGCAAAACAGCTAGAACAGTGGCTGGCATACAAAATAAATTTCTCAGTGTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTGCAAAAGAGGAAAACCTCTTTTGGGAGGACACACTGCTCTGGTCTTGC RR: GTACGTTTTGTCGATCTTGTCACCGACCGTATGTTTTATTTAAAGAGTCACACCCAATCTTTAATTGGTTCCCTAGCCGTCAGGACGTTTTCTCCTTTTGGAGAAAACCCTCCTGTGTGACGAGACCAGAACG F2: 3 GTACGT 2 Unidirectional alignment (log-probability: -37.4) GTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTaCAAAtgcAtgGGAAAACCTCTTTcGGGAGGACACACTGCTCTGGTCTTGC GTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTGCAAA---AGAGGAAAACCTCTTTTGGGAGGACACACTGCTCTGGTCTTGC Template switch alignment (log-probability: -27.6) GTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTaCAAA|TGCATG|GGAAAACCTCTTTcGGGAGGACACACTGCTCTGGTCTTGC GTGGGTTAGAAATTAACCAAGGGATCGGCAGTCCTGCAAA|TGCATG|GGAAAACCTCTTTTGGGAGGACACACTGCTCTGGTCTTGC ========== Event 3305 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGCCCTGCTAGTGCCCACCC----CGACCCCCTGCCTGCCCGTCTCTCTGCAGATGCGGACAGGCATGGTGTACCCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGGCGCCCAGGAGCCGCCTCCTCAGGGCTGGCTCATTTGATG----TCCCAGGCTGAGCTGCACACTAGGGGGATGAGGTGACCGGTGGGCACCCATCTCAGACACCCGGCTTCCCA----- ↓ 1 4 3 2 Chimp: CTGCCCTGCTAGTGCCCACCC--CCTGACCC-----------------------------------------------CCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGGCGCCCGGGAGCCGCCTCCTCAGGGCTGGCTCATTCGGTG----TCCCAGGCTGAGCTGCACACCAGGGGGATGAGGTGACCGGTGGGCACCCATCTCGGACACCCGGCTTCCCA----- Gorilla: CTGCCCTGCTAGTGCCCACCCCC--TGACCCCCTGCCTGCCCGTCTCTCTGCAGATGCGGACAGGCATGGTGTACC-CCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGGTGCCCGGGAGCCGCCTCCTCAGGGCTGGCTCATTTGGTGTGCAGCTCAGGCAGAGCTGCACACCAGGGGGATGAGGTGATTGGTGGGCACCCATCTCGGACACCTGGCTTCCCA----- Human: CTGCCCTGCTAGTGCCCACCC----CGACCCCCTGCCTGCCCGTCTCTCTGCAGATGCGGACAGGCATGGTGTACCCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGGCGCCCAGGAGCCGCCTCCTCAGGGCTGGCTCATTTGATG----TCCCAGGCTGAGCTGCACACTAGGGGGATGAGGTGACCGGTGGGCACCCATCTCAGACACCCGGCTTCCCA----- Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr7:661464-661467 Template switch process: F1: L GTTGCCTGGTTCCAGGCCGGCTGCCCTGCTAGTGCCCACCCC 1 F3: 4 CCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGGCGC R RF: GTTGCCTGGTTCCAGGCCGGCTGCCCTGCTAGTGCCCACCCCGACCCCCTGCCTGCCCGTCTCTCTGCAGATGCGGACAGGCATGGTGTACCCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGGCGCCCAGGAGCCGCCTCCTCAGGGCTGGCTCATTTGATGTCCCAGGCTGAGCTGCACACTAGGGGGATGAGGTGACCGGTGGGCACCCATCTCAG RR: CAACGGACCAAGGTCCGGCCGACGGGACGATCACGGGTGGGGCTGGGGGACGGACGGGCAGAGAGACGTCTACGCCTGTCCGTACCACATGGGGGGACGGACGGAGGAAGTGACGACCCACCTTGAGCCCCGCGGGTCCTCGGCGGAGGAGTCCCGACCGAGTAAACTACAGGGTCCGACTCGACGTGTGATCCCCCTACTCCACTGGCCACCCGTGGGTAGAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -26.5) TGCCTGGTTCCAGGCCGGCTGCCCTGCTAGTGCCCACCCCctGA-----------------------------------------------CCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGG TGCCTGGTTCCAGGCCGGCTGCCCTGCTAGTGCCCACCCC--GACCCCCTGCCTGCCCGTCTCTCTGCAGATGCGGACAGGCATGGTGTACCCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGG Template switch alignment (log-probability: -15.9) TGCCTGGTTCCAGGCCGGCTGCCCTGCTAGTGCCCACCCC|CTGA|CCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGG TGCCTGGTTCCAGGCCGGCTGCCCTGCTAGTGCCCACCCC|CTGA|CCCCCTGCCTGCCTCCTTCACTGCTGGGTGGAACTCGGGG ========== Event 3306 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTTGGTGATGGTCATGTGGCAATTTATTTTGTAATACTGGTTGGTCTCAATGTTCTAATTTTCCACAAT Chimp: TTCTTGGTGATGGTCATGTAGCAATTTATTTTGTAATA--AATTG---CTAATGTTCTAATTTTCCACAAT ↑ 3 2 1 4 Gorilla: TTCCTGGTGATGGTCATGTAGCAATTTATTTTGTAATACTGGTTGGTCTCAATGTTCTAATTTTCCACAAT Human: TTCTTGGTGATGGTCATGTGGCAATTTATTTTGTAATACTGGTTGGTCTCAATGTTCTAATTTTCCACAAT Cluster: [ ] Orangutan: ----------------------------------------------------------------------- Gorilla > Chimp --------------- chr7:135005020-135005026 Template switch process: F1: L AATTTCTTGGTGATGGTCATGTAGCAATTTATTTTGTAATA 1 F3: 4 AATGTTCTAATTTTCCACAATATCCATGTAATATGTCTAC R RF: AATTTCCTGGTGATGGTCATGTAGCAATTTATTTTGTAATACTGGTTGGTCTCAATGTTCTAATTTTCCACAATATCCATGTAATATGTCTGC RR: TTAAAGGACCACTACCAGTACATCGTTAAATAAAACATTATGACCAACCAGAGTTACAAGATTAAAAGGTGTTATAGGTACATTATACAGACG F2: 3 TCGTTAA 2 Unidirectional alignment (log-probability: -39.4) ATTTCtTGGTGATGGTCATGTAGCAATTTATTTTGTAATAaattgCT----------AATGTTCTAATTTTCCACAATATCCATGTAATATGTCTaC ATTTCCTGGTGATGGTCATGTAGCAATTTATTTTGTAATA-----CTGGTTGGTCTCAATGTTCTAATTTTCCACAATATCCATGTAATATGTCTGC Template switch alignment (log-probability: -27.7) ATTTCtTGGTGATGGTCATGTAGCAATTTATTTTGTAATA|AATTGCT|AATGTTCTAATTTTCCACAATATCCATGTAATATGTCTaC ATTTCCTGGTGATGGTCATGTAGCAATTTATTTTGTAATA|AATTGCT|AATGTTCTAATTTTCCACAATATCCATGTAATATGTCTGC ========== Event 3307 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTATGGCTGTGAGTTTCAGCACTATGGAGCTCT------------AAGATGATGAAGATAgtggtgg ↓ 3 2 41 Chimp: CTATGGCTGTGAGTTTCAGCACTATGGAGCTCTAACTCCATAGTGAAGATGATGAAGATAgtggtgg Gorilla: CTATAGCTGTGAGTTTCAGCACTATGGAGCTCT------------AAGATGATGAAGATAgtggtgg Human: CTATGGCTGTGAGTTTCAGCACTATGGAGCTCT------------AAGATGATGAAGATAgtggtgg Cluster: [ ] Orangutan: CTATGGCTGTGAGTTTTAGTACTATGGAGCTCT------------AAGATGATGAAGATagtggtgg Human > Chimp ------------- chr7:29540615-29540624 Template switch process: F1: L ATCAGCCACTATGGCTGTGAGTTTCAGCACTATGGAGCTCTAA 1 F3: 4 AAGATGATGAAGATAGTGGTGGCAGTGGT-GTGGTGGTGG R RF: ATCAGCCACTATGGCTGTGAGTTTCAGCACTATGGAGCTCTAAGATGATGAAGATAGTGGTGGCAGTGGTGGTGGTGGTGG RR: TAGTCGGTGATACCGACACTCAAAGTCGTGATACCTCGAGATTCTACTACTTCTATCACCACCGTCACCACCACCACCACC F2: 3 GTGATACCTC 2 Unidirectional alignment (log-probability: -38.4) AGCCACTATGGCTGTGAGTTTCAGCACTATGGAGCTCTaactccatagtgAAGATGATGAAGATAGTGGTGGCAGTGGT-GTGGTGGTGG AGCCACTATGGCTGTGAGTTTCAGCACTATGGAGCTCT------------AAGATGATGAAGATAGTGGTGGCAGTGGTGGTGGTGGTGG Template switch alignment (log-probability: -26.8) AGCCACTATGGCTGTGAGTTTCAGCACTATGGAGCTCTAA|CTCCATAGTG|AAGATGATGAAGATAGTGGTGGCAGTGGT-GTGGTGGTGG AGCCACTATGGCTGTGAGTTTCAGCACTATGGAGCTCTAA|CTCCATAGTG|AAGATGATGAAGATAGTGGTGGCAGTGGTGGTGGTGGTGG ========== Event 3308 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GGTGACTCTGTGCTACTCTTG-CTGGCACTTCCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAGGAGGTGTTTCCTAGCTCCAGGCACTGGGCTTGACTCACTGGGCAGTGGGAGGCAGATGCCAGGCGAAAGGGCTTGTCTGAGA ↑ 1 4 3 2 Chimp: GGTGACTCTGTGCTACTCTTGTGCTACTCTTACTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAGGAGGTGTTTCCTAGCTCCAGGCACTGGGCTTGACTCACTGGGCAGTGGGAGGCAGATGCCAGGTGAAAGGGCTTGTCTGAGA Gorilla: GGTGACTCTGTGCTACTCTTG-CTGGCACTTCCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAGGAGGTGTTTCCTAGCTCCAGGCACTGGGCTTGACTTACTGGGCAGTGGGAGGCAGATGCCAGGCGAAAGGGCTTGTCTGAGA Human: GGTGACTCTGTGCTACTCTTG-CTGGCACTTCCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAGGAGGTGTTTCCTAGCTCCAGGCACTGGGCTTGACTCACTGGGCAGTGGGAGGCAGATGCCAGGCGAAAGGGCTTGTCTGAGA Cluster: [ ] Orangutan: GGTGACTCTGTGCTACTCCTG-CTGGCACTTCCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAGGAGGTGTTTCCTAGCTCCAGGCACTGGGCTTGACTCACTGGGCAGTGGGAGGCGGATGCCAGGCAAAAGGGCTTGTCTGAGA Chimp > Human ------------- chr7:131619633-131619638 Template switch process: F1: L ACAGGACAGGGGGGCAGGTGGGTGACTCTGTGCTACTCTTG 1 F3: 4 CTTCCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAG R RF: ACAGGACAGGGGGGCAGGTGGGTGACTCTGTGCTACTCTTGTGCTACTCTTACTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCACTGAGGAGGTGTTTCCTAGCTCCAGGCACTGGGCTTGACTCACTGGGCAGTGGGAGGCAGATGCCAG RR: TGTCCTGTCCCCCCGTCCACCCACTGAGACACGATGAGAACACGATGAGAATGAGGGGACCGTGACGACTCCGTCCAGACAGTCCGTGACTCCTCCACAAAGGATCGAGGTCCGTGACCCGAACTGAGTGACCCGTCACCCTCCGTCTACGGTC F2: 3 ACGGTC 2 Unidirectional alignment (log-probability: -33.2) CAGGACAGGGGGGCAGGTGGGTGACTCTGTGCTACTCTTG-----CTggcaCTTcCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCAC CAGGACAGGGGGGCAGGTGGGTGACTCTGTGCTACTCTTGTGCTACT----CTTACTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCAC Template switch alignment (log-probability: -22.1) CAGGACAGGGGGGCAGGTGGGTGACTCTGTGCTACTCTTG|CTGGCA|CTTcCTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCAC CAGGACAGGGGGGCAGGTGGGTGACTCTGTGCTACTCTTG|CTGGCA|CTTACTCCCCTGGCACTGCTGAGGCAGGTCTGTCAGGCAC ========== Event 3309 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAAACATTTCCACTATTTGG-------CATGGGCTCTGTGATCTATGCTCATGAGAAAGGA Chimp: ATAAACATTTCCACTCTTTGG-------CATGGGCTCTGTGATCTATGCTTATGAGAAAGGA Gorilla: ATAAACATTTCCACTATTTGGCTCACAGAGTGAGCTCTGTGATCTATGCTCATGAGAAAGGA ↑ 1 4 3 2 Human: ATAAACATTTCCACTATTTGG-------CATGGGCTCTGTGATCTATGCTCATGAGAAAGGA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr7:27134851-27134858 Template switch process: F1: L ACCCCCATGTGACCTCTGGCATAAACATTTCCACTATTTGGC 1 F3: 4 TGAGCTCTGTGATCTATGCTCATGAGAAAGGATCACCTTTCTC R RF: ACCCCCATGTGACCTCTGGCATAAACATTTCCACTATTTGGCATGGGCTCTGTGATCTATGCTCATGAGAAAGGATCACCTTTCTC RR: TGGGGGTACACTGGAGACCGTATTTGTAAAGGTGATAAACCGTACCCGAGACACTAGATACGAGTACTCTTTCCTAGTGGAAAGAG F2: 3 GAGACACT 2 Unidirectional alignment (log-probability: -32.1) CCCCATGTGACCTCTGGCATAAACATTTCCACTATTTGGCtcacagagTGaGCTCTGTGATCTATGCTCATGAGAAAGGATCACCTTT CCCCATGTGACCTCTGGCATAAACATTTCCACTATTTGGCA-------TGGGCTCTGTGATCTATGCTCATGAGAAAGGATCACCTTT Template switch alignment (log-probability: -22.4) CCCCATGTGACCTCTGGCATAAACATTTCCACTATTTGGC|TCACAGAG|TGaGCTCTGTGATCTATGCTCATGAGAAAGGATCACCTTT CCCCATGTGACCTCTGGCATAAACATTTCCACTATTTGGC|TCACAGAG|TGGGCTCTGTGATCTATGCTCATGAGAAAGGATCACCTTT ========== Event 3310 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTCATGACCAAATCGGAACC----ATTCAGG---------GCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCA Chimp: GCTCATGACCAAATCGGAACC----GTTCAGG---------GCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCA ↓ 1 4 3 2 Gorilla: GCTCATGACCAAATCGGAACCATTTGTTCAGGAACTGAACAACCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCA ↑ 1 4 3 2 Human: GCTCATGACCAAATCGGAACC----ATTCAGG---------GCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNN----NNNNNNN---------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr7:27074542-27074551 Template switch process: F1: L GGCAAAGGCTTTATCCATTAGCTCATGACCAAATCGGAACCATTTGTTCAGG 1 F3: 4 CCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA R RF: GGCAAAGGCTTTATCCATTAGCTCATGACCAAATCGGAACCATT----CAGGGCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA RR: CCGTTTCCGAAATAGGTAATCGAGTACTGGTTTAGCCTTGGTAA----GTCCCGGACTCGAACAAGTCAACATTTTACCCGAGTTTAAGTCTT F2: 3 AACAAGTCAA 2 Unidirectional alignment (log-probability: -44.9) ATCCATTAGCTCATGACCAAATCGGAACCAtttgTTCAGGaactgaacaaCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA ATCCATTAGCTCATGACCAAATCGGAACCA----TTCAGG---------GCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA Template switch alignment (log-probability: -32.7) ATCCATTAGCTCATGACCAAATCGGAACCATTtgttCAGG|AACTGAACAA|CCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA ATCCATTAGCTCATGACCAAATCGGAACCATT----CAGG|AACTGAACAA|CCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA Chimp > Gorilla --------------- chr7:27074542-27074551 Template switch process: F1: L GGCAAAGGCTTTATCCATTAGCTCATGACCAAATCGGAACCATTTGTTCAGG 1 F3: 4 CCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA R RF: GGCAAAGGCTTTATCCATTAGCTCATGACCAAATCGGAACC----GTTCAGGGCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA RR: CCGTTTCCGAAATAGGTAATCGAGTACTGGTTTAGCCTTGG----CAAGTCCCGGACTCGAACAAGTCAACATTTTACCCGAGTTTAAGTCTT F2: 3 AACAAGTCAA 2 Unidirectional alignment (log-probability: -44.9) ATCCATTAGCTCATGACCAAATCGGAACCatttGTTCAGGaactgaacaaCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA ATCCATTAGCTCATGACCAAATCGGAACC----GTTCAGG---------GCCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA Template switch alignment (log-probability: -32.7) ATCCATTAGCTCATGACCAAATCGGAACCatttGTTCAGG|AACTGAACAA|CCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA ATCCATTAGCTCATGACCAAATCGGAACC----GTTCAGG|AACTGAACAA|CCTGAGCTTGTTCAGTTGTAAAATGGGCTCAAATTCAGAA ========== Event 3311 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCCTTTTCCCCAAAGCAGGAC------TTTAACTGACAGAGCTCCTGTGTGTCTAAAAAAGCAATGAATG Chimp: GCCTTTTCCCCAAAGCAGGAC------TTTAACTGACAGAGCTCCTGTGTGTCTAAAAAAGCAATGAATG ↓ 1 3 4 2 Gorilla: GCCTTTTCCCCAAAGCAGGAC------------ACACAGGAGCTCTGTGTGTCTAAAAAAGCAATGAATG ↑ 1 3 4 2 Human: GCCTTTTCCCCAAAGCAGGAC------TTTAACTGACAGAGCTCCTGTGTGTCTAAAAAAGCAATGAATG Cluster: [ ] Orangutan: GCCTTTTCCCCAAAGCAGGACTTTAAT------TGACAGAGCTCCTGTGTGTCTAAAAAAGTAACGAATG Human > Gorilla --------------- chr7:25935007-25935017 Template switch process: F1: L TAATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC 1 F3: 4 CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT R RF: TAATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGACTTTAACTGACAGAGCTCCTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT RR: ATTACTTGACCGACGTACGACGGAAAAGGGGTTTCGTCCTGAAATTGACTGTCTCGAGGACACACAGATTTTTTCGTTACTTACTCTTTACATGTCGA F2: 3 TCGAGGACACA 2 Unidirectional alignment (log-probability: -35.3) AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC--------ACAcagGAGCT-CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGACTTTAACTGACA---GAGCTCCTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT Template switch alignment (log-probability: -17.1) AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC|ACACAGGAGCT|CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC|ACACAGGAGCT|CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT Chimp > Gorilla --------------- chr7:25935007-25935017 Template switch process: F1: L TAATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC 1 F3: 4 CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT R RF: TAATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGACTTTAACTGACAGAGCTCCTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT RR: ATTACTTGACCGACGTACGACGGAAAAGGGGTTTCGTCCTGAAATTGACTGTCTCGAGGACACACAGATTTTTTCGTTACTTACTCTTTACATGTCGA F2: 3 TCGAGGACACA 2 Unidirectional alignment (log-probability: -35.3) AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC--------ACAcagGAGCT-CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGACTTTAACTGACA---GAGCTCCTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT Template switch alignment (log-probability: -17.1) AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC|ACACAGGAGCT|CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT AATGAACTGGCTGCATGCTGCCTTTTCCCCAAAGCAGGAC|ACACAGGAGCT|CTGTGTGTCTAAAAAAGCAATGAATGAGAAATGTACAGCT ========== Event 3312 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTGGGGGTAGTTTTAAAGCAGTCAAGA------TTTGACTGCTATCTCTGGATTTATCCACC ↑ 3 2 1 4 Chimp: TTTGGGGGTAGTTTTAAAGCAGTCAAGA---GGCCATGCATACTATCTCTGGATTTATCCACC Gorilla: TTTGGGGGTAGTTTTAAAGCAGTCAAGAGGC---CATGCATACTATCTCTGGATTTATCCACC ↓ 3 2 1 4 Human: TTTGGGGGTAGTTTTAAAGCAGTCAAGA------TTTGACTGCTATCTCTGGATTTATCCACC Cluster: [ ] Orangutan: TTTGGGGGTAGTTTTAAAGCAGTCAAGATGC---CATGCATACTATCTCTGGATTTATCCACC Chimp > Human ------------- chr7:134631368-134631374 Template switch process: F1: L TATGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAT 1 F3: 4 CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG R RF: TATGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAGGCCATGCATACTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG RR: ATACAAAACGACTAAACCCCCATCAAAATTTCGTCAGTTCTCCGGTACGTATGATAGAGACCTAAATAGGTGGAGGGAAGTCTCACCCGGAC F2: 3 GTCAGTT 2 Unidirectional alignment (log-probability: -31.7) TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAtttgactG----------CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGA-------GGCCATGCATACTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG Template switch alignment (log-probability: -22.2) TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAt|TTGACTG|CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAG|TTGACTG|CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG Gorilla > Human --------------- chr7:134631368-134631374 Template switch process: F1: L TATGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAT 1 F3: 4 CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTG R RF: TATGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAGGCCATGCATACTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTA RR: ATACAAAACGACTAAACCCCCATCAAAATTTCGTCAGTTCTCCGGTACGTATGATAGAGACCTAAATAGGTGGAGGGAAGTCTCACCCGGAT F2: 3 GTCAGTT 2 Unidirectional alignment (log-probability: -36.7) TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAtttgactG----------CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTg TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGA-------GGCCATGCATACTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTA Template switch alignment (log-probability: -27.7) TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAt|TTGACTG|CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTg TGTTTTGCTGATTTGGGGGTAGTTTTAAAGCAGTCAAGAG|TTGACTG|CTATCTCTGGATTTATCCACCTCCCTTCAGAGTGGGCCTA ========== Event 3313 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTAAAAAACTTAGAATTCCTGGGTT------TCTACTATAGTAGAACAGTTTCTACTGTTCTACTGCTGGTTTCTACTGCTATAGTAGAACAGTTT Chimp: ATTAAAAAACTTAGAATTCCTGGGTT------TTTACTATAGTAGAACAGTTTCTACTGTTCTACTGCTGGTTTCTACTGCTATAGTAGAACAGTTT ↓ 31 2 4 Gorilla: ATTAAAAAACTTAGAATTCCTAGGTTTACTGTTCTACTATAGCAAA-----------------------------AACTGCTATAGTAGAACAGTTT Human: ATTAAAAAACTTAGAATTCCTGGGTT------TCTACTATAGTAGAACAGTTTCTACTGTTCTACTGCTGGTTTCTACTGCTATAGTAGAACAGTTT Cluster: [ ] Orangutan: ATTAAAAAACTTAGAATTCCTGGGT------------------------------------------------------------------------ Chimp > Gorilla --------------- chr7:134086067-134086086 Template switch process: F1: L TTTTGTTTCAGCCTTTGTGGATTAAAAAACTTAGAATTCCTAGGTTT 1 F3: 4 ACTGCTATAGTAGAACAGTTTACTGGGTTTACTGTTCTAC R RF: TTTTGTTTCAGCCTTTGTGGATTAAAAAACTTAGAATTCCTGGGTTTTTACTATAGTAGAACAGTTTCTACTGTTCTACTGCTGGTTTCTACTGCTATAGTAGAACAGTTTACTGGGTTTACTGTTCTAC RR: AAAACAAAGTCGGAAACACCTAATTTTTTGAATCTTAAGGACCCAAAAATGATATCATCTTGTCAAAGATGACAAGATGACGACCAAAGATGACGATATCATCTTGTCAAATGACCCAAATGACAAGATG F2: 3 AAAACGATATCATCTTGTCA 2 Unidirectional alignment (log-probability: -50.7) TCAGCCTTTGTGGATTAAAAAACTTAGAATTCCTaGGTT----------------------TACTGTTCTACTatagcaaaa----------ACTGCTATAGTAGAACAGTTTACTGGGTTTACTGTTCTAC TCAGCCTTTGTGGATTAAAAAACTTAGAATTCCTGGGTTTTTACTATAGTAGAACAGTTTCTACTGTTCTACT---------GCTGGTTTCTACTGCTATAGTAGAACAGTTTACTGGGTTTACTGTTCTAC Template switch alignment (log-probability: -29.5) TCAGCCTTTGTGGATTAAAAAACTTAGAATTCCTaGGTTT|ACTGTTCTACTATAGcAAAA|ACTGCTATAGTAGAACAGTTTACTGGGTTTACTGTTCTAC TCAGCCTTTGTGGATTAAAAAACTTAGAATTCCTGGGTTT|ACTGTTCTACTATAGTAAAA|ACTGCTATAGTAGAACAGTTTACTGGGTTTACTGTTCTAC ========== Event 3314 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGTAATCATCTATCACTTTCTTCGCAAAAGCT-GGGCTTGGATAACAAATTGCAGTTT ↓ 3 1 2 4 Chimp: GGAGTAATCATCTATCACTTTCTTCGCTTTTGCGAAGAATTGGATAACAAATTGCAGTTT ↑ 3 1 2 4 Gorilla: GGAGTAATCATCTATCACTTTCTTCGCAAAAGCT-GGGCTTGGATAACAAATTGCAGTTT Human: GGAGTAATCATCTATCACTTTCTTCGCAAAAGCT-GGGCTTGGATAACAAATTGCAGTTT Cluster: [ ] Orangutan: Human > Chimp ------------- chr7:140065472-140065483 Template switch process: F1: L TTGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC 1 F3: 4 TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA R RF: TTGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGCAAAAGCTGGGCTTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA RR: AACTCCGACAATAACCTCATTAGTAGATAGTGAAAGAAGCGTTTTCGACCCGAACCTATTGTTTAACGTCAAATGATAGTTTCTGTTTATCT F2: 3 AAGAAGCGTTTT 2 Unidirectional alignment (log-probability: -36) TGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGCttttgcgaagAA---------TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA TGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC----------AAAAGCTGGGCTTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA Template switch alignment (log-probability: -16.8) TGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC|TTTTGCGAAGAA|TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA TGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC|TTTTGCGAAGAA|TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA Gorilla > Chimp --------------- chr7:140065472-140065483 Template switch process: F1: L TTGAGGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC 1 F3: 4 TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA R RF: TTGAAGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGCAAAAGCTGGGCTTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA RR: AACTTCGACAATAACCTCATTAGTAGATAGTGAAAGAAGCGTTTTCGACCCGAACCTATTGTTTAACGTCAAATGATAGTTTCTGTTTATCT F2: 3 AAGAAGCGTTTT 2 Unidirectional alignment (log-probability: -41) TGAgGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGCttttgcgaagAA---------TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA TGAAGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC----------AAAAGCTGGGCTTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA Template switch alignment (log-probability: -22.8) TGAgGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC|TTTTGCGAAGAA|TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA TGAAGCTGTTATTGGAGTAATCATCTATCACTTTCTTCGC|TTTTGCGAAGAA|TTGGATAACAAATTGCAGTTTACTATCAAAGACAAATAGA ========== Event 3315 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAA---TCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAA Chimp: GTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAA---TCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAA ↓ 4 1 3 2 Gorilla: GTATTGTAAGTAAAAACAGACTAAAGTACACAGTGAC------TAAAGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAA ↑ 4 1 3 2 Human: GTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAA---TCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAA Cluster: [ ] Orangutan: GTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAATCT---CACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTGAA Human > Gorilla --------------- chr7:134971100-134971104 Template switch process: F1: L TTTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACA 1 F3: 4 ACTAAA-------------------GTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAAGTG R RF: TTTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAATCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAAGTG RR: AAATTTACTCTCATAACATTCATTTTTGTCTGATTTCATGTCTCTCTTAGAGTGACAGTGACACAAAGTGACGTCCCAGAAAACATCCATTTCAC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -36.4) TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACAcAG------TgACTaaaGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAATCTCACT---GTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT Template switch alignment (log-probability: -27.2) TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACA|CAGTG|ACTAAA-------------------GTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACA|CAGTG|ACTAAAGTACAGAGAGAATCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT Chimp > Gorilla --------------- chr7:134971100-134971104 Template switch process: F1: L TTTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACA 1 F3: 4 ACTAAA-------------------GTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAAGTG R RF: TTTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAATCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGTAAAGTG RR: AAATTTACTCTCATAACATTCATTTTTGTCTGATTTCATGTCTCTCTTAGAGTGACAGTGACACAAAGTGACGTCCCAGAAAACATCCATTTCAC F2: 3 GTGAC 2 Unidirectional alignment (log-probability: -36.4) TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACAcAG------TgACTaaaGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACAGAGAGAATCTCACT---GTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT Template switch alignment (log-probability: -27.2) TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACA|CAGTG|ACTAAA-------------------GTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT TTAAATGAGAGTATTGTAAGTAAAAACAGACTAAAGTACA|CAGTG|ACTAAAGTACAGAGAGAATCTCACTGTCACTGTGTTTCACTGCAGGGTCTTTTGTAGGT ========== Event 3316 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCTAAGGGATCTATTTCTCTCTGGG------TTAATTCTAAGGAAAATCATGTCA ↓ 3 1 24 Chimp: TTCTAAGGGATCTATTTCTCTCTGGTAACCCAGAGATTCTAAGGAAAATCATGTCA ↑ 3 1 24 Gorilla: TTCTAAGGGATCTATTTCTCTCTGGG------TTAATTCTAAGGAAAATCATGTCA Human: TTCTAAGGGATCTATTTCTCTCTGGG------TTAATTCTAAGGAAAATCATGTCA Cluster: [ ] Orangutan: TTCTAAGGGATCTATTTCTCTCTGGG------TTAATTCTAAGGAAAATCATGTCA Human > Chimp ------------- chr7:25571336-25571345 Template switch process: F1: L GGTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG 1 F3: 4 ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT R RF: GGTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGGGTTAATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT RR: CCATTTTACCATGTCGAAGATTCCCTAGATAAAGAGAGACCCAATTAAGATTCCTTTTAGTACAGTCGGACATAGGTCTTAGAGA F2: 3 GAGACCCAAT 2 Unidirectional alignment (log-probability: -32.8) GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG--TAacccagagATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGGGTTA--------ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT Template switch alignment (log-probability: -16.5) GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG|TAACCCAGAG|ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG|TAACCCAGAG|ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT Gorilla > Chimp --------------- chr7:25571336-25571345 Template switch process: F1: L GGTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG 1 F3: 4 ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT R RF: GGTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGGGTTAATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT RR: CCATTTTACCATGTCGAAGATTCCCTAGATAAAGAGAGACCCAATTAAGATTCCTTTTAGTACAGTCGGACATAGGTCTTAGAGA F2: 3 GAGACCCAAT 2 Unidirectional alignment (log-probability: -32.3) GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG--TAacccagagATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGGGTTA--------ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT Template switch alignment (log-probability: -17) GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG|TAACCCAGAG|ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT GTAAAATGGTACAGCTTCTAAGGGATCTATTTCTCTCTGG|TAACCCAGAG|ATTCTAAGGAAAATCATGTCAGCCTGTATCCAGAATCTCT ========== Event 3317 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: ctgacttcatgctcatcaccatgtttaaccttcgtaa----cagccaaaaaagttggtgttaca Chimp: CTGACTTCATGCTCATCACCATGTTTAACCTTCGTTAAACATGGCCAAAAAAGTTGGTGTTACA ↑ 3 2 1 4 Gorilla: CTGACTTCATGCTCATCACCATGTTTAACCTTCGTAA----CAGCCAAAAAAGTTGGTGTTACA Human: ctgacttcatgctcatcaccatgtttaaccttcgtaa----cagccaaaaaagttggtgttaca Cluster: [ ] Orangutan: ctgacttcatgctcatcaccatgtttaacattcgtaa----cagccaaaaaagttggtgttaca Gorilla > Chimp --------------- chr7:22334516-22334523 Template switch process: F1: L ATGTGTCTGACTTCATGCTCATCACCATGTTTAACCTTCGT 1 F3: 4 GCCAAAAAAGTTGGTGTTACAGTCCCTATCTTATAAATAA R RF: ATGTGTCTGACTTCATGCTCATCACCATGTTTAACCTTCGTAACAGCCAAAAAAGTTGGTGTTACAGTCCCTATCTTATAAATAA RR: TACACAGACTGAAGTACGAGTAGTGGTACAAATTGGAAGCATTGTCGGTTTTTTCAACCACAATGTCAGGGATAGAATATTTATT F2: 3 GTACAAAT 2 Unidirectional alignment (log-probability: -26.4) TGTGTCTGACTTCATGCTCATCACCATGTTTAACCTTCGTtaAACAtgGCCAAAAAAGTTGGTGTTACAGTCCCTATCTTATAAATAA TGTGTCTGACTTCATGCTCATCACCATGTTTAACCTTCGT--AACA--GCCAAAAAAGTTGGTGTTACAGTCCCTATCTTATAAATAA Template switch alignment (log-probability: -16.7) TGTGTCTGACTTCATGCTCATCACCATGTTTAACCTTCGT|TAAACATG|GCCAAAAAAGTTGGTGTTACAGTCCCTATCTTATAAATAA TGTGTCTGACTTCATGCTCATCACCATGTTTAACCTTCGT|TAAACATG|GCCAAAAAAGTTGGTGTTACAGTCCCTATCTTATAAATAA ========== Event 3318 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTATCACTATCAATATGTATTGAGTC-----CTGTCATCCATTCACTCACCCA ↓ 3 1 2 4 Chimp: CTTATCACTATCAATATGTATTGAGGACTCAATTGTCATCCATTCACTTACCCA ↑ 3 1 2 4 Gorilla: CTTATCACTATCAATATGTATTGAGTC-----CTGTCATCCATTCACTTACCCA Human: CTTATCACTATCAATATGTATTGAGTC-----CTGTCATCCATTCACTCACCCA Cluster: [ ] Orangutan: CTCATCACTATCAATATGTATTGAGTC-----CTGTCATCCATTCACTTACCCA Human > Chimp ------------- chr7:144481553-144481560 Template switch process: F1: L TGGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAG 1 F3: 4 TGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT R RF: TGGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAGTCCTGTCATCCATTCACTCACCCATTTCCCCCAAACCCCATAT RR: ACCGTTCTTAGGTAGAGAATAGTGATAGTTATACATAACTCAGGACAGTAGGTAAGTGAGTGGGTAAAGGGGGTTTGGGGTATA F2: 3 TAACTCAG 2 Unidirectional alignment (log-probability: -36.1) GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAGgaCtcaatTGTCATCCATTCACTtACCCATTTCCCCCAAACCCCATAT GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAGTCC-----TGTCATCCATTCACTCACCCATTTCCCCCAAACCCCATAT Template switch alignment (log-probability: -22.3) GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAG|GACTCAAT|TGTCATCCATTCACTtACCCATTTCCCCCAAACCCCATAT GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAG|GACTCAAT|TGTCATCCATTCACTCACCCATTTCCCCCAAACCCCATAT Gorilla > Chimp --------------- chr7:144481553-144481560 Template switch process: F1: L TGGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAG 1 F3: 4 TGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT R RF: TGGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAGTCCTGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT RR: ACCGTTCTTAGGTAGAGAATAGTGATAGTTATACATAACTCAGGACAGTAGGTAAGTGAATGGGTAAAGGGGGTTTGGGGTATA F2: 3 TAACTCAG 2 Unidirectional alignment (log-probability: -29.2) GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAGgaCtcaatTGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAGTCC-----TGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT Template switch alignment (log-probability: -16.7) GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAG|GACTCAAT|TGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT GGCAAGAATCCATCTCTTATCACTATCAATATGTATTGAG|GACTCAAT|TGTCATCCATTCACTTACCCATTTCCCCCAAACCCCATAT ========== Event 3319 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAAGACCAGAAATCACAGTACAGCATATTGTCAACAAC--CTCTCTATAGCGACCAAAGGAGT Chimp: GAAAGACCAGAAATCACAGTACAGCATATTGTCAACAAC--CTCTCTATAGCGACCAAAGGAGT ↓ 3 2 1 4 Gorilla: GAAAGACCAGAAATCACAGTACAGCATATTGTCATATGCTGTACTCTATAGCGACCAAAGGAGT ↑ 3 2 1 4 Human: GAAAGACCAGAAATCACAGTACAGCATATTGTCAACAAC--CTCTCTATAGCGACCAAAGGAGT Cluster: [ ] Orangutan: GAAAGACCAGAAATCACAGTACAGCATATTGTCAACAAC--CTCTCTATAGTGACCAAAGGAGT Human > Gorilla --------------- chr7:14146518-14146526 Template switch process: F1: L AAATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA 1 F3: 4 CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT R RF: AAATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCAACAACCTCTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT RR: TTTATTCCTTTCTGGTCTTTAGTGTCATGTCGTATAACAGTTGTTGGAGAGATATCGCTGGTTTCCTCAAGTCCCGGACGTTCAGTGA F2: 3 ATGTCGTAT 2 Unidirectional alignment (log-probability: -32.5) AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA------TatgctgtaCTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCAACAACCT--------CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT Template switch alignment (log-probability: -16.9) AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA|TATGCTGTA|CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA|TATGCTGTA|CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT Chimp > Gorilla --------------- chr7:14146518-14146526 Template switch process: F1: L AAATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA 1 F3: 4 CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT R RF: AAATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCAACAACCTCTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT RR: TTTATTCCTTTCTGGTCTTTAGTGTCATGTCGTATAACAGTTGTTGGAGAGATATCGCTGGTTTCCTCAAGTCCCGGACGTTCAGTGA F2: 3 ATGTCGTAT 2 Unidirectional alignment (log-probability: -32.5) AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA------TatgctgtaCTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCAACAACCT--------CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT Template switch alignment (log-probability: -16.9) AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA|TATGCTGTA|CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT AATAAGGAAAGACCAGAAATCACAGTACAGCATATTGTCA|TATGCTGTA|CTCTATAGCGACCAAAGGAGTTCAGGGCCTGCAAGTCACT ========== Event 3320 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTATTTCTAATATTTGGTAATGTCAATATATGATTGACAAAGAAATATACCTTCCCCAT ↑ 1 4 3 2 Chimp: TTTATTTCTAATATTTGGTAACTG----CTATGATTGACAAAGAAATATACCTTCCCCAT Gorilla: TTTATTTCTAATATTTGGTAACTG----CTATGATTGACAAAGAAATATACCTTCCCCAT ↓ 1 4 3 2 Human: TTTATTTCTAATATTTGGTAATGTCAATATATGATTGACAAAGAAATATACCTTCCCCAT Cluster: [ ] Orangutan: TTTATTTCTAATATTTGGTAACTA----CTATGACTGACAAAGAAATATACCTTCCCCAT Chimp > Human ------------- chr7:142282021-142282027 Template switch process: F1: L TTTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA 1 F3: 4 ATATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTCA R RF: TTTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAACTGCTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTCA RR: AAAGATACCACACTTCTGTGAAATAAAGATTATAAACCATTGACGATACTAACTGTTTCTTTATATGGAAGGGGTAGGACGGAGT F2: 3 TAACTGT 2 Unidirectional alignment (log-probability: -32.8) TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAatgtcaatA----TATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTA--------ACTGCTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC Template switch alignment (log-probability: -22.2) TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA|TGTCAAT|aTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA|TGTCAAT|CTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC Gorilla > Human --------------- chr7:142282021-142282027 Template switch process: F1: L TTTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA 1 F3: 4 ATATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTCA R RF: TTTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAACTGCTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTCA RR: AAAGATACCACACTTCTGTGAAATAAAGATTATAAACCATTGACGATACTAACTGTTTCTTTATATGGAAGGGGTAGGACGGAGT F2: 3 TAACTGT 2 Unidirectional alignment (log-probability: -32.3) TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA----tgtcaataTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAACTGC--------TATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC Template switch alignment (log-probability: -22.2) TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA|TGTCAAT|aTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC TTCTATGGTGTGAAGACACTTTATTTCTAATATTTGGTAA|TGTCAAT|CTATGATTGACAAAGAAATATACCTTCCCCATCCTGCCTC ========== Event 3321 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TGCGGAAACATCGGGGGCACAGGAGCTCTTTGGAGCTCCTGTGCCTCCAGCTCAGGACTGTG Chimp: TGCGGAAACATCGGGGGCACAGGAGCTCCAAAGAGCTCCTGTGCCTCCAGCTCAGGACTGTG Gorilla: TGCGGAAACATCAGGGGCACAGGAGCTCCAAAGAGCTCCTTTGCCTCCAGCTCAGGACTGTG ↓ 3 1 2 4 Human: TGCGGAAACATCGGGGGCACAGGAGCTCTTTGGAGCTCCTGTGCCTCCAGCTCAGGACTGTG Cluster: [ ] Orangutan: -------------------------------------------------------------- Gorilla > Human --------------- chr7:16456691-16456703 Template switch process: F1: L ATTGTGCCCCAAATGCGGAAACATCGGGGGCACAGGAGCTC 1 F3: 4 TGCCTCCAGCTCAGGACTGTGTAACTGTGACCTCTCTGCC R RF: ATTGTGCCCCAAATGCGGAAACATCAGGGGCACAGGAGCTCCAAAGAGCTCCTTTGCCTCCAGCTCAGGACTGTGTAACTGTGACCTCTCTGCC RR: TAACACGGGGTTTACGCCTTTGTAGTCCCCGTGTCCTCGAGGTTTCTCGAGGAAACGGAGGTCGAGTCCTGACACATTGACACTGGAGAGACGG F2: 3 GTCCTCGAGGTTT 2 Unidirectional alignment (log-probability: -34.4) TTGTGCCCCAAATGCGGAAACATCgGGGGCACAGGAGCTCtttgGAGCTCCTgTGCCTCCAGCTCAGGACTGTGTAACTGTGACCTCTCTGCC TTGTGCCCCAAATGCGGAAACATCAGGGGCACAGGAGCTCCAAAGAGCTCCTTTGCCTCCAGCTCAGGACTGTGTAACTGTGACCTCTCTGCC Template switch alignment (log-probability: -22.9) TTGTGCCCCAAATGCGGAAACATCgGGGGCACAGGAGCTC|TTTGGAGCTCCTG|TGCCTCCAGCTCAGGACTGTGTAACTGTGACCTCTCTGCC TTGTGCCCCAAATGCGGAAACATCAGGGGCACAGGAGCTC|TTTGGAGCTCCTG|TGCCTCCAGCTCAGGACTGTGTAACTGTGACCTCTCTGCC ========== Event 3322 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCATGCACACACTTCTTAAGTGCATGCAGTTCTTCCTTGTGTGACTCC ↑ 1 4 2 Chimp: TCCATGCACATACTTCTTAAGAAAGTGCAGTTCTTCCTTGTGTGACTCC Gorilla: TCCATGCACACACTTCTTAAGAAAGTGCAGTTCTT-CTTGTGTGACTGC Human: TCCATGCACACACTTCTTAAGTGCATGCAGTTCTTCCTTGTGTGACTCC Cluster: [ ] Orangutan: TCCATGCACACACTTCTTAAGAAAGTGCAGTTCTTCCTCGTGTGACTCC Chimp > Human ------------- chr7:141321080-141321083 Template switch process: F1: L GGCCACTGGTGGGATTTTGTTCCATGCACACACTTCTTAAG 1 F3: 4 TGCAGTTCTTCCTTGTGTGACTCCCCTCTATTGAGAAGTT R RF: GGCCACTGGTGGGATTTTGTTCCATGCACATACTTCTTAAGAAAGTGCAGTTCTTCCTTGTGTGACTCCCCTCTATTGAGAAGTT RR: CCGGTGACCACCCTAAAACAAGGTACGTGTATGAAGAATTCTTTCACGTCAAGAAGGAACACACTGAGGGGAGATAACTCTTCAA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -30.7) GCCACTGGTGGGATTTTGTTCCATGCACAcACTTCTTAAGtgcaTGCAGTTCTTCCTTGTGTGACTCCCCTCTATTGAGAAGTT GCCACTGGTGGGATTTTGTTCCATGCACATACTTCTTAAGAAAGTGCAGTTCTTCCTTGTGTGACTCCCCTCTATTGAGAAGTT Template switch alignment (log-probability: -21.8) GCCACTGGTGGGATTTTGTTCCATGCACAcACTTCTTAAG|TGCA|TGCAGTTCTTCCTTGTGTGACTCCCCTCTATTGAGAAGTT GCCACTGGTGGGATTTTGTTCCATGCACATACTTCTTAAG|TGCA|TGCAGTTCTTCCTTGTGTGACTCCCCTCTATTGAGAAGTT ========== Event 3323 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACAAGATTTATCCATTACTAGAGACACTAAGCAGCACATGGGGATGGAGAGCTAATGTTCAAA Chimp: CTACAAGATTTATCCATTACTAGAGACACTAAGCAGCATATGGGAATGTAGAGCTAATGTTCAAA ↓ 3 2 1 4 Gorilla: CTACAAGATTTATCCATTACTAGAGACACTAAGTCTCTAGTGGGGATGTAGAGCTAATGTTCAAA Human: CTACAAGATTTATCCATTACTAGAGACACTAAGCAGCACATGGGGATGGAGAGCTAATGTTCAAA Cluster: [ ] Orangutan: CTACAAGCTTTATCCATTACTAGAGACACTAAGCAGCACATGGGGATGGAGAGCTAATGTTCAAA Chimp > Gorilla --------------- chr7:140820625-140820631 Template switch process: F1: L TGTTTCCCCTACAAGATTTATCCATTACTAGAGACACTAAG 1 F3: 4 TGGGGATGTAGAGCTAATGTTCAAAGAGGATTCCCGTGTGCTGGC R RF: TGTTTCCCCTACAAGATTTATCCATTACTAGAGACACTAAGCAGCATATGGGAATGTAGAGCTAATGTTCAAAGAGGATTCCCATGTGCTGGC RR: ACAAAGGGGATGTTCTAAATAGGTAATGATCTCTGTGATTCGTCGTATACCCTTACATCTCGATTACAAGTTTCTCCTAAGGGTACACGACCG F2: 3 GATCTCT 2 Unidirectional alignment (log-probability: -42.2) GTTTCCCCTACAAGATTTATCCATTACTAGAGACACTAAG-------tctctagTGGGgATGTAGAGCTAATGTTCAAAGAGGATTCCCgTGTG GTTTCCCCTACAAGATTTATCCATTACTAGAGACACTAAGCAGCATA-------TGGGAATGTAGAGCTAATGTTCAAAGAGGATTCCCATGTG Template switch alignment (log-probability: -27.8) GTTTCCCCTACAAGATTTATCCATTACTAGAGACACTAAG|TCTCTAG|TGGGgATGTAGAGCTAATGTTCAAAGAGGATTCCCgTGTG GTTTCCCCTACAAGATTTATCCATTACTAGAGACACTAAG|TCTCTAG|TGGGAATGTAGAGCTAATGTTCAAAGAGGATTCCCATGTG ========== Event 3324 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATAGTCATAGGGTAGATTGATAATTTTATCATATTCTATATGAT-------AAAATTATTTGGTTATTCTAATAAAATAT Chimp: TAATAGTCATAGGGTAGATTGATAATTTTATCATATTCTATATGAT-------AAAATTATTTGGTTATTCTAATAAAA--T Gorilla: TAATAGTCATAGGGTAGATTAATAATTTTATCATATAGAATATGAT--------------ATTGGTTATTCTAATAAAATAT ↑ 1 3 4 Human: TAATAGTCATAGGGTAGATTGATAATTTTATCATATTCTATATGAT-------AAAATTATTTGGTTATTCTAATAAAATAT Cluster: [ ] Orangutan: TAATAGTCATAGGGTAGATTGATAAT----------TCTATATGATAAAATTA-------TTTGGTTATTCTAATAAAATAT Human > Gorilla --------------- chr7:14929109-14929135 Template switch process: F1: L TATTTTAATAGTCATAGGGTAGATT 1 F3: 4 TTGGTTATTCTAATAAAATATGTTAATACTCATAAGGTAG R RF: TATTTTAATAGTCATAGGGTAGATTGATAATTTTATCATATTCTATATGATAAAATTATTTGGTTATTCTAATAAAATATGTAATACTCATAAGGTAG RR: ATAAAATTATCAGTATCCCATCTAACTATTAAAATAGTATAAGATATACTATTTTAATAAACCAATAAGATTATTTTATACATTATGAGTATTCCATC F2: 3 ATAGTATAAGATATACTATTTTAATAA 2 Unidirectional alignment (log-probability: -44.6) TATTTTAATAGTCATAGGGTAGATTaATAATTTTATCATATagaATATGATA-------TTGGTTATTCTAATAAAATATGtTAATACTCATAAGGTAG TATTTTAATAGTCATAGGGTAGATTGATAATTTTATCATATTCTATATGATAAAATTATTTGGTTATTCTAATAAAATATG-TAATACTCATAAGGTAG Template switch alignment (log-probability: -29.9) TATTTTAATAGTCATAGGGTAGATT|AATAATTTTATCATATAGAATATGATA|TTGGTTATTCTAATAAAATATGtTAATACTCATAAGGTAG TATTTTAATAGTCATAGGGTAGATT|AATAATTTTATCATATAGAATATGATA|TTGGTTATTCTAATAAAATATG-TAATACTCATAAGGTAG ========== Event 3325 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CATTAATTGAACCCAAATGTAAAATGCCCTAttttctttttcttttc-----ttgtt--ttttttt------------------------tttttttttgagacggagtctcgctctgttgcagtggcctgatcttggctcactgcaacc Chimp: CATTAATTGAACCCAAATGTAAAACGTCCTAttttctttttcttttc-----ttctttcttttttt-------------------ttttctttgtttttgagacggagtctcgctctgttgcagtggcctgatcttggctcactgcaacc Gorilla: CATTAATTGAACCCAAATGTA-AACGTCCTAttttctttttcttttc-----ttgtt--ttttttt------------------t-----tttttttttgagacggagtctcgctctgttgcagtggcatgatcttggcttactgcaacc ↓ 1 4 3 2 Human: CATTAATTGAACCCAAATGTAAAATGCCCTAttttctttttcttttc-----ttgtt--ttttttt------------------------tttttttttgagacggagtctcgctctgttgcagtggcctgatcttggctcactgcaacc Cluster: [ ] Orangutan: CATTAATTGAGCCCAAATGTAAAATGTCCTAttttctttttcttttcttttcttgtt--ttgtttttgttttttttgtgtgtgt------gttttttttgagacagagtctcgctctgttgcagtggtgtgatcttggctcactgcaacc Gorilla > Human --------------- chr7:14054317-14054320 Template switch process: F1: L CCATTTTATCCACTCCACACCATTAATTGAACCCAAATGTAAA 1 F3: 4 CCTATTTTCTTTTTCTTTTCTTGTTTTTTTTTTTTTTTT R RF: CCATTTTATCCACTCCACACCATTAATTGAACCCAAATGTAAACGTCCTATTTTCTTTTTCTTTTCTTGTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTTGCAGTGGCAT RR: GGTAAAATAGGTGAGGTGTGGTAATTAACTTGGGTTTACATTTGCAGGATAAAAGAAAAAGAAAAGAACAAAAAAAAAAAAAAAAAAACTCTGCCTCAGAGCGAGACAACGTCACCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -30.2) TTTTATCCACTCCACACCATTAATTGAACCCAAATGTAAAatGcCCTATTTTCTTTTTCTTTTCTTGTTTTTTTTTTTTTTTT- TTTTATCCACTCCACACCATTAATTGAACCCAAATGTAAAC-GTCCTATTTTCTTTTTCTTTTCTTGTTTTTTTTTTTTTTTTT Template switch alignment (log-probability: -16.3) TTTTATCCACTCCACACCATTAATTGAACCCAAATGTAAA|ATGC|CCTATTTTCTTTTTCTTTTCTTGTTTTTTTTTTTTTTTT TTTTATCCACTCCACACCATTAATTGAACCCAAATGTAAA|ATGC|CCTATTTTCTTTTTCTTTTCTTGTTTTTTTTTTTTTTTT ========== Event 3326 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCCTTTTTCTTCACACACATTA--------------------------------------GTATGGGTACAGACTATTAGTATGGGTATGAAGAAAAA---ATAATATGTACGATTATATACATACAATTATGACA----TTTGTATATATTAAGCCCTATCTTTACATTCAAATTACTCCTATCACATACATAAATAATCAAGAGGGCCAGTATGACCTCAAGCTGGATATATTT Chimp: ATCTTATTTCTTCATACACATTA---------------------------------------------------------GTATGGGTATGAAGAAAAA---ATAATATGTACGATTATATACATACAATTATGACA------CGTATCTATTAAGCCCTATCTTTACATTCAAATTACTCCTATCACATACATAAATAATCAAGGGGGCCAGTATGACCTCAAGCTGGATATATTT ↓ 4 1 3 2 Gorilla: ATCTTTTTTCTTCATACACATTA-------------------GTATGGGTACAGACTATTA-------------------GTATGGGTATGAAGAAAAA---ATAATATGTACGATTATATACATACAATTATGACA--CT--TGTATATATTAAGCCCTATCTTTACATTCAAATTACTCCTATCACATACTTAAATAATCAAGAGGGCCAGTATGACCTCAAGCTGGATATATTT Human: ATCCTTTTTCTTCACACACATTA--------------------------------------GTATGGGTACAGACTATTAGTATGGGTATGAAGAAAAA---ATAATATGTACGATTATATACATACAATTATGACA----TTTGTATATATTAAGCCCTATCTTTACATTCAAATTACTCCTATCACATACATAAATAATCAAGAGGGCCAGTATGACCTCAAGCTGGATATATTT Cluster: [ ] Orangutan: ATCTTTTTTCTTCATACACATTAGTATGGGTATAAACTATTA--------------------------------------GTATGGGTATGAAGAAAAAAGATTAATATGTACGAATATATACATACAATTATGGCAAT----TGTATATATTAAGCCCTATCTTTACACTCAAATTACTCGTATCACATACATAAATAATCGAGACGGCCAGTATGACCTTGAGCTGGATATATTT Chimp > Gorilla --------------- chr7:14111285-14111290 Template switch process: F1: L GACCATTACACATTATTAATCTTTTTTCTTCATACACATTAGTATGGGTA 1 F3: 4 ATTAGTATGGGTATGAAGAAAAAATAATATGTACGATTATATAC R RF: GACCATTACACATTATTAATCTTATTTCTTCATACACATTAGTATGGGTATGAAGAAAAAATAATATGTACGATTATATACATACAATTATGACACGTATCTATTAAGCCCTATCTTTACATTCAAATTACTCCTATCACATACATAAATAATCAAGGGGGCCAGTATG RR: CTGGTAATGTGTAATAATTAGAATAAAGAAGTATGTGTAATCATACCCATACTTCTTTTTTATTATACATGCTAATATATGTATGTTAATACTGTGCATAGATAATTCGGGATAGAAATGTAAGTTTAATGAGGATAGTGTATGTATTTATTAGTTCCCCCGGTCATAC F2: 3 TCAGAC 2 Unidirectional alignment (log-probability: -43.7) CATTATTAATCTTtTTTCTTCATACACattagtatgggtacagactATTAGTATGGGTATGAAGAAAAAATAATATGTACGATTAT CATTATTAATCTTATTTCTTCATACAC-------------------ATTAGTATGGGTATGAAGAAAAAATAATATGTACGATTAT Template switch alignment (log-probability: -27.8) CATTATTAATCTTtTTTCTTCATACACATTAGTATGGGTA|CAgACT|ATTAGTATGGGTATGAAGAAAAAATAATATGTACGATTAT CATTATTAATCTTATTTCTTCATACACATTAGTATGGGTA|CATACT|ATTAGTATGGGTATGAAGAAAAAATAATATGTACGATTAT ========== Event 3327 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGACCCTGGTATACATATTTTAACAGCTTGGACCCATAAAACCAGAATGTCAATAATGCGt--tttttttttCTGTTCCAAGAAATTTTTTTTCAATCATTT Chimp: TAAGACCCTGGTATACATATTTTAACAGCTTGGACCCATAAAACCAGAATGTCAATAATGCAt--tttttttttCTGTTCCATGAAAttttttttCACTCATTT ↓ 3 2 1 4 Gorilla: TGAGACCCTGGTATACATATTTTAACAGCTTGGACCCATGAAACCAGAATGTCAATAATGCAt--t-tttttttCTGTTAAAAGAAAttttttttCACTCATTT Human: TAAGACCCTGGTATACATATTTTAACAGCTTGGACCCATAAAACCAGAATGTCAATAATGCGt--tttttttttCTGTTCCAAGAAATTTTTTTTCAATCATTT Cluster: [ ] Orangutan: TGAGACCCTGGTATACATATTTTAACAGCTTGGACCCATAAAACCAGAATGTCAATAACGCATTAtttttttttctgttccaagaaattttttttCACTTATTT Chimp > Gorilla --------------- chr7:12659536-12659544 Template switch process: F1: L CATGAAACCAGAATGTCAATAATGCATTTTTTTTT 1 F3: 4 GAAATTTTTTTTCACTCATTTGATAAATACTTTAAATGAA R RF: TTTTAACAGCTTGGACCCATAAAACCAGAATGTCAATAATGCATTTTTTTTTTCTGTTCCATGAAATTTTTTTTCACTCATTTGATAAATACTTTAAATGAA RR: AAAATTGTCGAACCTGGGTATTTTGGTCTTACAGTTATTACGTAAAAAAAAAAGACAAGGTACTTTAAAAAAAAGTGAGTAAACTATTTATGAAATTTACTT F2: 3 AAAATTGTC 2 Unidirectional alignment (log-probability: -33.1) CATgAAACCAGAATGTCAATAATGCA-TTTTTTTTTCTGTTaaAaGAAATTTTTTTTCACTCATTTGATAAATACTTTAAATGAA CATAAAACCAGAATGTCAATAATGCATTTTTTTTTTCTGTTCCATGAAATTTTTTTTCACTCATTTGATAAATACTTTAAATGAA Template switch alignment (log-probability: -22.2) CATgAAACCAGAATGTCAATAATGCATTTTTTTTT|CTGTTAAAA|GAAATTTTTTTTCACTCATTTGATAAATACTTTAAATGAA CATAAAACCAGAATGTCAATAATGCATTTTTTTTT|CTGTTAAAA|GAAATTTTTTTTCACTCATTTGATAAATACTTTAAATGAA ========== Event 3328 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: AAAGAAGGGATGCTGATAGGTTTTTGACAAAACGCTTGGGCATCAAGAGAATGA ↓ 1 3 2 4 ↑ 13 4 2 Chimp: AAAGAAGGGATGCTGATAGGTGT---CAAAAACACTTGGGCATCAAGAGAATGA Gorilla: Human: AAAGAAGGGATGCTGATAGGTTTTTGACAAAACGCTTGGGCATCAAGAGAATGA Cluster: [ ] Orangutan: Chimp > Human ------------- chr7:147257060-147257066 Template switch process: F1: L CTAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT 1 F3: 4 AAAACGCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTGGGGGA R RF: CTAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGTGTCAAAAACACTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTGGGGGA RR: GATTCACTCTCTTAAAATACTTTCTTCCCTACGACTATCCACAGTTTTTGTGAACCCGTAGTTCTCTTACTTTTCCGAAACCAAACCCCCT F2: 3 CAGTTTT 2 Unidirectional alignment (log-probability: -37.4) TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGTttttgac----AAAACgCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTT TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT-------GTCAAAAACACTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTT Template switch alignment (log-probability: -22.3) TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT|TTTTGAC|AAAACgCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTT TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT|TTTTGAC|AAAACACTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTT Human > Chimp ------------- chr7:151769794-151769798 Template switch process: F1: L CTAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT 1 F3: 4 AAACACTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTGGGGGA R RF: CTAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGTTTTTGACAAAACGCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTGGGGGA RR: GATTCACTCTCTTAAAATACTTTCTTCCCTACGACTATCCAAAAACTGTTTTGCGAACCCGTAGTTCTCTTACTTTTCCGAAACCAAACCCCCT F2: 3 AACTG 2 Unidirectional alignment (log-probability: -33.3) TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGTgtca-------AAAACaCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTG TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT----TTTTGACAAAACGCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTG Template switch alignment (log-probability: -22) TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT|GTCAA|AAACaCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTG TAAGTGAGAGAATTTTATGAAAGAAGGGATGCTGATAGGT|GTCAA|AAACGCTTGGGCATCAAGAGAATGAAAAGGCTTTGGTTTG ========== Event 3329 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGATAGAAGCCTTCATCAATT---CTTCCAGGGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAAAGGGGC ↑ 1 4 3 2 Chimp: TGATAGAAACCTTCATCAATTGTGATTCCGGAGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAAAGGGGC Gorilla: TGATAGAAGCCTTCATCAATT---CCTCTGGAGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAAAGGGGC Human: TGATAGAAGCCTTCATCAATT---CTTCCAGGGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAAAGGGGC Cluster: [ ] Orangutan: TGATAGAAGCCTTCATCAATT---CCTCCGGAGTATCTGTGAATCACAAACCTGGAAGAACTCCTGGCTCAAAGGGAC Chimp > Human ------------- chr7:11970030-11970037 Template switch process: F1: L CTTCACATTTCTAGGGGAGATGATAGAAGCCTTCATCAATT 1 F3: 4 GTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAA R RF: CTTCACATTTCTAGGGGAGATGATAGAAACCTTCATCAATTGTGATTCCGGAGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAA RR: GAAGTGTAAAGATCCCCTCTACTATCTTTGGAAGTAGTTAACACTAAGGCCTCATAGACACTTAGTGTTTGGACCTTCTTGACGACCGAGTT F2: 3 GGACCTTC 2 Unidirectional alignment (log-probability: -35.1) TTCACATTTCTAGGGGAGATGATAGAAgCCTTCATCAATT---cTTCCaGgGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAA TTCACATTTCTAGGGGAGATGATAGAAACCTTCATCAATTGTGATTCCGGAGTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAA Template switch alignment (log-probability: -22.3) TTCACATTTCTAGGGGAGATGATAGAAgCCTTCATCAATT|CTTCCAGG|GTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAA TTCACATTTCTAGGGGAGATGATAGAAACCTTCATCAATT|CTTCCAGG|GTATCTGTGAATCACAAACCTGGAAGAACTGCTGGCTCAA ========== Event 3330 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATTAAAGAAAGACATGAAACTGGAGTACAAAATAGATGG----TGTCTCCCAAAAGTACAACT ↓ 3 2 1 4 Chimp: AATTAAAGAAAGACATGAAACTGGAGTACAAAATAGACAG--TGTGTCTCCCAAAAGTACAACT Gorilla: AATTAAAGAAAGACATGAAACTGGAGTACAAAATAGACGGTG--TATCTCCCAAAAGTACAACT Human: AATTAAAGAAAGACATGAAACTGGAGTACAAAATAGATGG----TGTCTCCCAAAAGTACAACT Cluster: [ ] Orangutan: AATTAAAGAAAGACGTGAAACTGGAGTACAAAATAGATGGTG--TGTCTCCCAAAAGTACAACT Human > Chimp ------------- chr7:149566403-149566406 Template switch process: F1: L CTCTAATTAAAGAAAGACATGAAACTGGAGTACAAAATAGA 1 F3: 4 GTGTCTCCCAAAAGTACAACTTTGAAAGAAAAAAAAAAATT R RF: CTCTAATTAAAGAAAGACATGAAACTGGAGTACAAAATAGATGGTGTCTCCCAAAAGTACAACTTTGAAAGAAAAAAAAAA RR: GAGATTAATTTCTTTCTGTACTTTGACCTCATGTTTTATCTACCACAGAGGGTTTTCATGTTGAAACTTTCTTTTTTTTTT F2: 3 TGAC 2 Unidirectional alignment (log-probability: -37.2) TCTAATTAAAGAAAGACATGAAACTGGAGTACAAAATAGAcagT-GTGTCTCCCAAAAGTACAACTTTGAAAGAAAAAAAAAaAT TCTAATTAAAGAAAGACATGAAACTGGAGTACAAAATAGA---TGGTGTCTCCCAAAAGTACAACTTTGAAAGAAAAAAAAA-AT Template switch alignment (log-probability: -27.3) TCTAATTAAAGAAAGACATGAAACTGGAGTACAAAATAGA|CAGT|GTGTCTCCCAAAAGTACAACTTTGAAAGAAAAAAAAAaat TCTAATTAAAGAAAGACATGAAACTGGAGTACAAAATAGA|CAGT|GTGTCTCCCAAAAGTACAACTTTGAAAGAAAAAAAAA--- ========== Event 3331 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTGAAGTATGTTTGCCTTGTACTGATTGCTAATTAAACAGAACTGTCATAGTAT----------------GATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA Chimp: CTTGAAGTATGTTTGCCTTGTACTGATTGCTAATTAAATAGAACTGTCGTAGTAT----------------GATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA ↓ 3 2 4 1 Gorilla: CTTGAAGTATGTTTGCCTTGTACTGATTGCTAATTAAATAGAACTGTCCTAGTACATAATTTCTTCTAGTACATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA Human: CTTGAAGTATGTTTGCCTTGTACTGATTGCTAATTAAACAGAACTGTCATAGTAT----------------GATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA Cluster: [ ] Orangutan: CTTGAAGTATGTTTGCCTTGTACTAATTGCTAATTAAATAGAACTGTCCTAGTAT----------------GATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA Chimp > Gorilla --------------- chr7:14521314-14521318 Template switch process: F1: L TATGTTTGCCTTGTACTGATTGCTAATTAAATAGAACTGTCCTAG---------TACATAATTTCTTCT 1 F3: 4 ATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA R RF: TATGTTTGCCTTGTACTGATTGCTAATTAAATAGAACTGTCGTAGTATGATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA RR: ATACAAACGGAACATGACTAACGATTAATTTATCTTGACAGCATCATACTATCAATGTATTAAAGAAGAGTACAAGTCAAAAGTCTTTT F2: 3 CATGA 2 Unidirectional alignment (log-probability: -50.6) TGCTAATTAAATAGAACTGTCcTAGTAcataatttcttctagtacATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA TGCTAATTAAATAGAACTGTCGTAGTA----------------TGATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA Template switch alignment (log-probability: -32.5) TGCTAATTAAATAGAACTGTCcTAG---------TACATAATTTCTTCT|AGTAC|ATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA TGCTAATTAAATAGAACTGTCGTAGTATGATAGTTACATAATTTCTTCT|AGTAC|ATAGTTACATAATTTCTTCTCATGTTCAGTTTTCAGAAAA ========== Event 3332 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGATTCTTATTCTACAGGACA--------GGGGATCTATATTGTTTACAAGATCTTAGTGGAATCATAGGGAAATTGA Chimp: AGATTCTTATTCTACAGGACA--------GGGGATCTATATTGTTTACAAGATCTTAGTGGAATCATAGGGAAATTGA ↓ 1 4 3 2 Gorilla: AGATTCTTATTCTACAGGACA----------------CTAAGATTTACAAGATCTTAGTGGAATCATAGGGAAATTGA ↑ 1 4 3 2 Human: AGATTCTTATTCTACAGGACA--------GGGGATCTATATTGTTTACAAGATCTTAGTGGAATCATAGGGAAATTGA Cluster: [ ] Orangutan: AGATTCTTACTCTACAGGACAGGGGATCT--------ATATTGTTTACAAGATCTTAGTGGAATCATAGGGAAATTTA Human > Gorilla --------------- chr7:147485295-147485300 Template switch process: F1: L AGTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA 1 F3: 4 TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC R RF: AGTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACAGGGGATCTATATTGTTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC RR: TCAGAGTTTGAGAAGGAGACTCTAAGAATAAGATGTCCTGTCCCCTAGATATAACAAATGTTCTAGAATCACCTTAGTATCCCTTTAACTTTTGG F2: 3 AGAATC 2 Unidirectional alignment (log-probability: -30) GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA--------------ctaagaTTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACAGGGGATCTATATTG------TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC Template switch alignment (log-probability: -16.5) GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA|CTAAGA|TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA|CTAAGA|TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC Chimp > Gorilla --------------- chr7:147485295-147485300 Template switch process: F1: L AGTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA 1 F3: 4 TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC R RF: AGTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACAGGGGATCTATATTGTTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC RR: TCAGAGTTTGAGAAGGAGACTCTAAGAATAAGATGTCCTGTCCCCTAGATATAACAAATGTTCTAGAATCACCTTAGTATCCCTTTAACTTTTGG F2: 3 AGAATC 2 Unidirectional alignment (log-probability: -30) GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA--------------ctaagaTTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACAGGGGATCTATATTG------TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC Template switch alignment (log-probability: -16.5) GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA|CTAAGA|TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC GTCTCAAACTCTTCCTCTGAGATTCTTATTCTACAGGACA|CTAAGA|TTTACAAGATCTTAGTGGAATCATAGGGAAATTGAAAACC ========== Event 3333 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: TAAAATACTGTTTTAATGTTCAA---CTGCCTTAAACAAATGTGGAATTTGAAGGAGAATTCAGG Chimp: TAAAATACTGTTTTAATGTTCAA---CTGCCTTAAACAAATGTGGAATTTGAAGGAGAATTCAGG ↓ 1 3 4 2 ↑ 3 1 2 4 Gorilla: TAAAATACTGTTTTAATGTTCCACATTTGTTTAAGGC---AGTAGAATTTGAAGGAGAATTCAGG Human: TAAAATACTGTTTTAATGTTCAA---CTGCCTTAAACAAATGTGGAATTTGAAGGAGAATTCAGG Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr7:12337882-12337898 Template switch process: F1: L GATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCAAC 1 F3: 4 GAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTCTCAC R RF: GATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCCACATTTGTTTAAGGCAGTAGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTGTCAC RR: CTATATACTCCGTTTTTTCGATTTTATGACAAAATTACAAGGTGTAAACAAATTCCGTCATCTTAAACTTCCTCTTAAGTCCCTCCAGTAGAACCACAGTG F2: 3 GTGTAAACAAATTCCGT 2 Unidirectional alignment (log-probability: -54.4) TATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTC-------------------AactgccttaaacaaatgtgGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTcTCAC TATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCCACATTTGTTTAAGGCAGTA-------------------GAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTGTCAC Template switch alignment (log-probability: -29) TATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCaAC|TGCCTTAAACAAATGTG|GAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTcTCAC TATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCCAC|TGCCTTAAACAAATGTG|GAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTGTCAC Chimp > Gorilla --------------- chr7:10158165-10158181 Template switch process: F1: L GATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTC 1 F3: 4 GTAGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTGTCAC R RF: GATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCAACTGCCTTAAACAAATGTGGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTCTCAC RR: CTATATACTCCGTTTTTTCGATTTTATGACAAAATTACAAGTTGACGGAATTTGTTTACACCTTAAACTTCCTCTTAAGTCCCTCCAGTAGAACCAGAGTG F2: 3 ACGGAATTTGTTTACAC 2 Unidirectional alignment (log-probability: -54.4) ATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTCcacatttgtttaaggcagtA-------------------GAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTgT ATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTC-------------------AACTGCCTTAAACAAATGTGGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTCT Template switch alignment (log-probability: -29) ATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTC|CACATTTGTTTAAGGCA|GTaGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTgT ATATATGAGGCAAAAAAGCTAAAATACTGTTTTAATGTTC|CACATTTGTTTAAGGCA|GTGGAATTTGAAGGAGAATTCAGGGAGGTCATCTTGGTCT ========== Event 3334 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TCCTCTAGCCTCTTTCTACACCACACATTCTCTGATCACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACGACTT ↑ 4 1 3 2 Chimp: TCCTCTAGCCTCTTTCTACACCAC------------------ACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACAACTT Gorilla: Human: TCCTCTAGCCTCTTTCTACACCACACATTCTCTGATCACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACGACTT Cluster: [ ] Orangutan: TCCTCCAGCCTCTTTCTACACCACACATTCTCTGATCACCACACATTCTCCTCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACAACTT Chimp > Human ------------- chr7:149906888-149906892 Template switch process: F1: L CAGCCCCTCGCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTC 1 F3: 4 ACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCC R RF: CAGCCCCTCGCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCC RR: GTCGGGGAGCGACGAGGAGGAGATCGGAGAAAGATGTGGTGTGTAAGAGGCGGACTTCGACGCCGTCCTGGTGGTTATAGG F2: 3 CTAGT 2 Unidirectional alignment (log-probability: -36.8) GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTctctgatcaccacacattCTCCGCCTGAAGCTGCGGCAGGACCACCAA GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATT------------------CTCCGCCTGAAGCTGCGGCAGGACCACCAA Template switch alignment (log-probability: -22.1) GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTC|TGaTC|ACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAA GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTC|TGGTC|ACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAA ========== Event 3335 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAAAGGACGCGAGTGCACAGCGTGG--CACAGAGACTCTACCATTGCTCTTTGGGCCTCCCC-ACCGAGTAGGACCTGGCTGAAGACCACCTCTCGCAGAGCGC Chimp: GGAAAGGACGCGAGTGCACAGCGTGG--CACAGAGACTCTACCATTGCTCTTTGGGCCTCCCC-ACCGAGTAGGACCTGGCTGCAGACCACCTCTCGCAGAGCGC ↓ 1 4 3 2 Gorilla: GGAAAGGACGCGAGTGCACAGTGCAG----CAGAGACTCTACCATTGCTCTTTGGGCCTCCCC-GCCGAGTAGGACCTGGCTGCAGACCACCTCTCGTAGAGCGC Human: GGAAAGGACGCGAGTGCACAGCGTGG--CACAGAGACTCTACCATTGCTCTTTGGGCCTCCCC-ACCGAGTAGGACCTGGCTGAAGACCACCTCTCGCAGAGCGC Cluster: [ ] Orangutan: GTAAAAGATGCGAGTGCACAGCGCAGCA--CAGAGACTCTACCATTCCTCTTTGGGCCTCCCCCCTCAAGTAGGACCTGGCTGCAGACCACCTCTCGCAGAGCGC Chimp > Gorilla --------------- chr7:150012702-150012707 Template switch process: F1: L AGAAGCAAACAAGTAGATATGGAAAGGACGCGAGTGCACAG 1 F3: 4 AGAGACTCTACCATTGCTCTTTGGGCCTCCCCGCCGAGT R RF: AGAAGCAAACAAGTAGATATGGAAAGGACGCGAGTGCACAGCGTGGCACAGAGACTCTACCATTGCTCTTTGGGCCTCCCCACCGAGTAGGACCTGGCTGCA RR: TCTTCGTTTGTTCATCTATACCTTTCCTGCGCTCACGTGTCGCACCGTGTCTCTGAGATGGTAACGAGAAACCCGGAGGGGTGGCTCATCCTGGACCGACGT F2: 3 CGACGT 2 Unidirectional alignment (log-probability: -33.1) GAAGCAAACAAGTAGATATGGAAAGGACGCGAGTGCACA--GTGcagCAGAGACTCTACCATTGCTCTTTGGGCCTCCCCgCCGAGT GAAGCAAACAAGTAGATATGGAAAGGACGCGAGTGCACAGCGTGGCACAGAGACTCTACCATTGCTCTTTGGGCCTCCCCACCGAGT Template switch alignment (log-probability: -22) GAAGCAAACAAGTAGATATGGAAAGGACGCGAGTGCACAG|TGCAGC|AGAGACTCTACCATTGCTCTTTGGGCCTCCCCgCCGAGT GAAGCAAACAAGTAGATATGGAAAGGACGCGAGTGCACAG|TGCAGC|AGAGACTCTACCATTGCTCTTTGGGCCTCCCCACCGAGT ========== Event 3336 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAATATGAGTGTTTTAGTGCTATTCTGAGAGTGTAGGTACCATGACCAGCCTACCCAGCTCCTGTGCAAACTGCACACACCCATCTGTTGACAACAATTCCTGGGTTTCCATTGTGTACAGGGCCTGTGGAGGACAATGAGAATAACCAGGGGGTGATGCTTCCTGGG Chimp: TAAATATGAGTGTTTTAGTGTTATTCTGAGAGTGTAGGTACCATGACCAGCCTACCCAGCTCCTGTGCAAACTGCACACACCCATCTGTTGACAACAATTCCTGGGTTTCCATTGTGTGCAGAGCCTGTGGAGGACAATGGGAATAACCAGGGGGTGATGCTTCCTGGG Gorilla: TAAATATGAGTGTTTTAGTGTTATTCTGAGAGTGTAGGTACCATGACCAGCCTACCCAGCTCCTGTGCAAACTGCACACACCCATCTGTTGACAACAATTCCTGGGTTTCCATTGTGTGCAGGGCCTGTGGAGGACAATG-------GCAGGGGGTGATGCTTCCTGGG ↓ 3 2 1 4 Human: TAAATATGAGTGTTTTAGTGCTATTCTGAGAGTGTAGGTACCATGACCAGCCTACCCAGCTCCTGTGCAAACTGCACACACCCATCTGTTGACAACAATTCCTGGGTTTCCATTGTGTACAGGGCCTGTGGAGGACAATGAGAATAACCAGGGGGTGATGCTTCCTGGG Cluster: [ ] Orangutan: TAAATATGAGTGTTTTAGTGTTATTCTGAGGGTGTAGGTACCATGACCAGCCTACCCAGCTCCTGTGCAAACTGCACACACCCATCTATTGACAACAATTCCTGGGTTCCCATTGTGTGCAGGGCCTGTGGAGGACAATGGGAATAACCACGGGGTGATGCTTCCTGGG Gorilla > Human --------------- chr7:8543275-8543282 Template switch process: F1: L TCCTGGGTTTCCATTGTGTACAGGGCCTGTGGAGGACAATG 1 F3: 4 CAGGGGGTGATGCTTCCTGGGGGACCACATACTATCTGGA R RF: GTTATTCTGAGAGTGTAGGTACCATGACCAGCCTACCCAGCTCCTGTGCAAACTGCACACACCCATCTGTTGACAACAATTCCTGGGTTTCCATTGTGTGCAGGGCCTGTGGAGGACAATGGCAGGGGGTGATGCTTCCTGGGGGACCACATACTATCTGGA RR: CAATAAGACTCTCACATCCATGGTACTGGTCGGATGGGTCGAGGACACGTTTGACGTGTGTGGGTAGACAACTGTTGTTAAGGACCCAAAGGTAACACACGTCCCGGACACCTCCTGTTACCGTCCCCCACTACGAAGGACCCCCTGGTGTATGATAGACCT F2: 3 CAATAAGA 2 Unidirectional alignment (log-probability: -32) CCTGGGTTTCCATTGTGTaCAGGGCCTGTGGAGGACAATGagaataacCAGGGGGTGATGCTTCCTGGGGGACCACATACTATCTGGA CCTGGGTTTCCATTGTGTGCAGGGCCTGTGGAGGACAATGG-------CAGGGGGTGATGCTTCCTGGGGGACCACATACTATCTGGA Template switch alignment (log-probability: -22.3) CCTGGGTTTCCATTGTGTaCAGGGCCTGTGGAGGACAATG|AGAATAAC|CAGGGGGTGATGCTTCCTGGGGGACCACATACTATCTGGA CCTGGGTTTCCATTGTGTGCAGGGCCTGTGGAGGACAATG|AGAATAAC|CAGGGGGTGATGCTTCCTGGGGGACCACATACTATCTGGA ========== Event 3337 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGAAGTATTTGTTCCCCCATAGGTGCTAAGTGAGACAATTGACTTTCTCCATTTTGCAATGGGCTTTTCTTCCCTTTACTGCTAACTCCCAAGACCGCCACGTCTGCTTTTCTGGTGA--------------------------------GCACCTATTGCTTTTCTGCTTCTCACCT--------- Chimp: CTGAAGTATTTGTTCCCCCATAGGTGCTAAGTGAGACAATTGACTTTCTCCATTTTGCAGTGGGCTTTTCTTCCCTTTACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTGG------------------------------------------------AGCTTCTCACCT--------- ↓ 3 2 4 1 Gorilla: CTAAAGTATTTGTTCCCCCATAGGTGCTAAGTGAGACAATTGACTTTCTCCATTTTGCAATGGGCTTTTCTTCCCTTTACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTGA----------------GCACCTATTGCTTTTC----------------TGCTTCTCACCtcctccagtg Human: CTGAAGTATTTGTTCCCCCATAGGTGCTAAGTGAGACAATTGACTTTCTCCATTTTGCAATGGGCTTTTCTTCCCTTTACTGCTAACTCCCAAGACCGCCACGTCTGCTTTTCTGGTGA--------------------------------GCACCTATTGCTTTTCTGCTTCTCACCT--------- Cluster: [ ] Orangutan: CTGAAATATTTGTTCCCCCATAGGTGCTAGGTGAGACAATTGACTTTCTCCATTTTGCAATGGGCTTTTCTTCCCTTTACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTGAGCACCTATTGCTTTTC--------------------------------TGCTTCTCACCT--------- Chimp > Gorilla --------------- chr7:8279064-8279072 Template switch process: F1: L TACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTG 1 F3: 4 TGCTTTTCT------GCTTCTCACCTCCTCCAGTGGTCTTCCTCCCTGTCAGCCA R RF: ATAGGTGCTAAGTGAGACAATTGACTTTCTCCATTTTGCAGTGGGCTTTTCTTCCCTTTACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTGGAGCTTCTCACCTCCTCCAGTGGTCTTCCTCCCTGTCAGCCT RR: TATCCACGATTCACTCTGTTAACTGAAAGAGGTAAAACGTCACCCGAAAAGAAGGGAAATGACGATTGAGGGTTCTGGGGGTGCAGACGAAAAGACCACCTCGAAGAGTGGAGGAGGTCACCAGAAGGAGGGACAGTCGGA F2: 3 TATCCACGA 2 Unidirectional alignment (log-probability: -93) ACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTGagcacctattgcttttctGCTTCTCACCTcctccagtggtcttcctccc ACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTG----------------GAGCTTCTCACCT-------------------- Template switch alignment (log-probability: -32.7) ACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTG|AGCACCTAT|TGCTTTTCT------GCTTCTCACCTCCTCCAGTGGTCTTCCTCCC ACTGCTAACTCCCAAGACCCCCACGTCTGCTTTTCTGGTG|AGCACCTAT|TGCTTTTCTGGTGGAGCTTCTCACCTCCTCCAGTGGTCTTCCTCCC ========== Event 3338 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATCTAAATCATACTGTATACATTGTCATAAGACAATGTATAGGAACATCAGATAT----T Chimp: ACATCTAAATCATACTGTATACATTGTCATAAGACAATGTATAGGAACATCAGATAT----- Gorilla: ACATCTAAACCATACTGTATACATTGTCTTA-------TCTTAGGAACATCAGATATTACT- ↓ 3 1 2 4 Human: ACATCTAAATCATACTGTATACATTGTCATAAGACAATGTATAGGAACATCAGATAT----T Cluster: [ ] Orangutan: Gorilla > Human --------------- chr7:7198645-7198657 Template switch process: F1: L GAAGGCAGGAATGACATCTAAATCATACTGTATACATTGTC 1 F3: 4 TAGGAACATCAGATATTACGTAAGTTTAGAGATGGA R RF: GAAGGCAGGAATGACATCTAAACCATACTGTATACATTGTCTTATCTTAGGAACATCAGATATTACTTAAGTTTAGAGATGGA RR: CTTCCGTCCTTACTGTAGATTTGGTATGACATATGTAACAGAATAGAATCCTTGTAGTCTATAATGAATTCAAATCTCTACCT F2: 3 ATGTAACAGAATA 2 Unidirectional alignment (log-probability: -50.6) AAGGCAGGAATGACATCTAAAtCATACTGTATACATTGTCataagacaatgta------TAGGAACATCAGATATTACgTAAGTTTAGAGATGGA AAGGCAGGAATGACATCTAAACCATACTGTATACATTGTC-------------TTATCTTAGGAACATCAGATATTACTTAAGTTTAGAGATGGA Template switch alignment (log-probability: -28.3) AAGGCAGGAATGACATCTAAAtCATACTGTATACATTGTC|ATAAGACAATGTA|TAGGAACATCAGATATTACgTAAGTTTAGAGATGGA AAGGCAGGAATGACATCTAAACCATACTGTATACATTGTC|ATAAGACAATGTA|TAGGAACATCAGATATTACTTAAGTTTAGAGATGGA ========== Event 3339 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TCCTCTAGCCTCTTTCTACACCACACATTCTCTGATCACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACGACTT ↑ 4 1 3 2 Chimp: TCCTCTAGCCTCTTTCTACACCAC------------------ACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACAACTT Gorilla: Human: TCCTCTAGCCTCTTTCTACACCACACATTCTCTGATCACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACGACTT Cluster: [ ] Orangutan: TCCTCCAGCCTCTTTCTACACCACACATTCTCTGATCACCACACATTCTCCTCCTGAAGCTGCGGCAGGACCACCAATATCCTCCAACAACTT Chimp > Human ------------- chr7:6559860-6559864 Template switch process: F1: L CAGCCCCTCGCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTC 1 F3: 4 ACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCC R RF: CAGCCCCTCGCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAATATCC RR: GTCGGGGAGCGACGAGGAGGAGATCGGAGAAAGATGTGGTGTGTAAGAGGCGGACTTCGACGCCGTCCTGGTGGTTATAGG F2: 3 CTAGT 2 Unidirectional alignment (log-probability: -36.8) GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTctctgatcaccacacattCTCCGCCTGAAGCTGCGGCAGGACCACCAA GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATT------------------CTCCGCCTGAAGCTGCGGCAGGACCACCAA Template switch alignment (log-probability: -22.1) GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTC|TGaTC|ACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAA GCTGCTCCTCCTCTAGCCTCTTTCTACACCACACATTCTC|TGGTC|ACCACACATTCTCCGCCTGAAGCTGCGGCAGGACCACCAA ========== Event 3340 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTCTCTCCATATACATGTGAAAAAACAGCATGC----atatatat-----------------------------atatatatatGCATGCCAATTTCCTATGGTAGTAAAt Chimp: TCTCTCTCCATATACATGTGAAAAAACGGCATGC----atatatat-----------------atatatatatatatatatatatGCATGCCAATTTCCTATGGTAGTAAAt ↑ 1 4 2 Gorilla: TCTCTCTCCATATACATGTGACAAAACAGCATGC----atatata-------------------------------tatatatatGCATGCCAATTTCCTATGGTAGTAAAt Human: TCTCTCTCCATATACATGTGAAAAAACAGCATGC----atatatat-----------------------------atatatatatGCATGCCAATTTCCTATGGTAGTAAAt Cluster: [ ] Orangutan: TCTCTCTCCATATACATGTGAAAAAACAGCATGTGTGtatatatatatatatatattatatat------------atatatatatGCATGCCAATTTCCTATAGTAGTAAAt Gorilla > Chimp --------------- chr7:9044887-9044908 Template switch process: F1: L TGAGTAAATCTCTGTCACTCTCTCTCTCCATATACATGTGAAAAAAC 1 F3: 4 TATATATATATATATGCAT R RF: TGAGTAAATCTCTGTCACTCTCTCTCTCCATATACATGTGACAAAACAGCATGCATATATATATATATATGCATGCC RR: ACTCATTTAGAGACAGTGAGAGAGAGAGGTATATGTACACTGTTTTGTCGTACGTATATATATATATATACGTACGG F2: 3 ATATATATATATATACGTACGG 2 Unidirectional alignment (log-probability: -42) ATCTCTGTCACTCTCTCTCTCCATATACATGTGAaAAAACgGCATGCatatatatatatatATATATATATATATATGCAT ATCTCTGTCACTCTCTCTCTCCATATACATGTGACAAAACAGCATGC--------------ATATATATATATATATGCAT Template switch alignment (log-probability: -23.7) ATCTCTGTCACTCTCTCTCTCCATATACATGTGAaAAAAC|GGCATGCATATATATATATATA|TATATATATATATATGCAT ATCTCTGTCACTCTCTCTCTCCATATACATGTGACAAAAC|GGCATGCATATATATATATATA|TATATATATATATATGCAT ========== Event 3341 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCACTTCACCTTCTCATCTTAG---CTGCCACTGGACCATAAGCATTTCAGGTTGC Chimp: TCACTTCACCTTCTCATCTCATCCAGTGGCACTGGACCATAGGCATTTCAGGTTGC ↑ 1 34 2 Gorilla: TCACTTCACCTTCTCATCTCAG---CTGCCACTGGACCATAGGCATTTCAGTTTGC Human: CCACTTCACCTTCTCATCTTAG---CTGCCACTGGACCATAAGCATTTCAGGTTGC Cluster: [ ] Orangutan: TCACTTCACCTTCTCATCTCAG---CTGCCACTGGACCGTAAGCATTTCAGGTGGC Gorilla > Chimp --------------- chr7:158695095-158695102 Template switch process: F1: L TCAAGGTTTCCTGGCTCCTGTCACTTCACCTTCTCATCTCA 1 F3: 4 CACTGGACCATAGGCATTTCAGGTTGCTCAGATCTCTCCC R RF: TCAAGGTTTCCTGGCTCCTGTCACTTCACCTTCTCATCTCAGCTGCCACTGGACCATAGGCATTTCAGTTTGCCCAGATCTCTCCC RR: AGTTCCAAAGGACCGAGGACAGTGAAGTGGAAGAGTAGAGTCGACGGTGACCTGGTATCCGTAAAGTCAAACGGGTCTAGAGAGGG F2: 3 GGTGACCT 2 Unidirectional alignment (log-probability: -37.3) CAAGGTTTCCTGGCTCCTGTCACTTCACCTTCTCATCTCAtCcagTGgCACTGGACCATAGGCATTTCAGgTTGCtCAGATCTCTCCC CAAGGTTTCCTGGCTCCTGTCACTTCACCTTCTCATCTCAGC---TGCCACTGGACCATAGGCATTTCAGTTTGCCCAGATCTCTCCC Template switch alignment (log-probability: -27.8) CAAGGTTTCCTGGCTCCTGTCACTTCACCTTCTCATCTCA|TCCAGTGG|CACTGGACCATAGGCATTTCAGgTTGCtCAGATCTCTCCC CAAGGTTTCCTGGCTCCTGTCACTTCACCTTCTCATCTCA|TCCAGTGG|CACTGGACCATAGGCATTTCAGTTTGCCCAGATCTCTCCC ========== Event 3342 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTTGTATCACAGGTAGCGCCCACCAAGTGTCTGAAGCTTTATGGGTCAGCCCACCTGGTCATCCCCATTGCTTGCAGGTAGTGACATCTCCCACCTTACAGATAGCTGAGAATGGAAGTCGCTACCCTCAGGACACACACCCAGCAGGTGGCCATGGCGAGGTGCCACCC Chimp: TTTTGTATCGCAGGTAGCGCCCACC-TGCGTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCATTGCTTGCAGGTAGTGACATCTCCCACCTTACAGATAGCTGAGAATGGAAGTCCCTACCCTCAGGACACACACCCAGCAGGTGGCCATGGCGAGGTGCCACCC ↑ 1 4 3 2 Gorilla: TTTTGTATCGCAGGTAGCGCCAACCAAGTGTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCATTGCTTGCAGGTAGTGACATCTCCCACCTTACAGATAGCTGAGAACGGAAGTCCCTGCCCTCAGGACACACACCCAGCAGGTGGCCATGGCGAGGTGCCACCC Human: TTTTGTATCACAGGTAGCGCCCACCAAGTGTCTGAAGCTTTATGGGTCAGCCCACCTGGTCATCCCCATTGCTTGCAGGTAGTGACATCTCCCACCTTACAGATAGCTGAGAATGGAAGTCGCTACCCTCAGGACACACACCCAGCAGGTGGCCATGGCGAGGTGCCACCC Cluster: [ ] Orangutan: TTTTGTATTGCAGGTAGCTCCCACCAAGTGTCTGGAGCTTTATGGGTCAGCCCACCTGCTCATCCCCATTGCTTGCAGGTAGTGACATCTCCCACCTTACAGATAGCTGAGAACGGAAGTCCCTACCCTCAGGACACACACCCAGCAGGTGGCCATGGCGAGATGCCACCC Gorilla > Chimp --------------- chr7:158953418-158953424 Template switch process: F1: L CCAAAAAGAAAAGCAGGTGATTTTGTATCGCAGGTAGCGCC 1 F3: 4 GTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCAT R RF: CCAAAAAGAAAAGCAGGTGATTTTGTATCGCAGGTAGCGCCAACCAAGTGTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCATTGCTTGCAGGTAGTGACATCTCCCACCTTACAGATAGCTGAGAACGGAAGTCCCTGCCCTCAGGACACACACCCAGCAGGTG RR: GGTTTTTCTTTTCGTCCACTAAAACATAGCGTCCATCGCGGTTGGTTCACAGACCTCGAAATACCCAGTCGGGTGGACCAGTAGGGGTAACGAACGTCCATCACTGTAGAGGGTGGAATGTCTATCGACTCTTGCCTTCAGGGACGGGAGTCCTGTGTGTGGGTCGTCCAC F2: 3 CGTCCAC 2 Unidirectional alignment (log-probability: -27.6) CAAAAAGAAAAGCAGGTGATTTTGTATCGCAGGTAGCGCCcACCt-GcGTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCAT CAAAAAGAAAAGCAGGTGATTTTGTATCGCAGGTAGCGCCAACCAAGTGTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCAT Template switch alignment (log-probability: -16.6) CAAAAAGAAAAGCAGGTGATTTTGTATCGCAGGTAGCGCC|CACCTGC|GTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCAT CAAAAAGAAAAGCAGGTGATTTTGTATCGCAGGTAGCGCC|CACCTGC|GTCTGGAGCTTTATGGGTCAGCCCACCTGGTCATCCCCAT ========== Event 3343 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGCTGGGCTGATGCTGTTACTCCTCTCATAGCCCACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATTGATCACGCTGTGCTGGTCTATTCTGCAGGACACTTGTCTCATCTCAGTGAAACTGGGTGCACAATGGTTCGAGGGGCTGTGACACACTTGTCCACTCTGTC Chimp: AGAGCTGGGCTGATGCTGTCACTCCTCTCATAGCCCACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATGGATCACTCTGTGCTGGTCTATTCTGTAGGACACTTGTTTCATCTCAATGAAACTGGGGGCACAATGGTTCGAGGGACTGTGACACACTTGTCCACTCTGTC ↑ 4 1 3 2 Gorilla: AGAGCTGGGCTGATGCTGTCAC----------------TCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATTGATCACTCTGTGCTGGTCTATTCTGTAGGACACTTGTCTCATCTCAGTGAAACTGGGGGCGCAATGGTTCGAGGGACTATGACACGCTTGTCCACTCTGTC Human: AGAGCTGGGCTGATGCTGTTACTCCTCTCATAGCCCACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATTGATCACGCTGTGCTGGTCTATTCTGCAGGACACTTGTCTCATCTCAGTGAAACTGGGTGCACAATGGTTCGAGGGGCTGTGACACACTTGTCCACTCTGTC Cluster: [ ] Orangutan: AGAGCTGGGCTGTTGCTGTTACTCCTCTTATAGCCCACTCCTCTGCAGGGTGACCAGGGATCACTCAAAGTATTGATCACTCTGTGCTGGTCTATTCTGTAGGACACTTGTCTCATCTCAATGAAACTGGGGGCACAATGGTTTGAGGGACTATGACACACTTGTCCACTCTGTC Gorilla > Chimp --------------- chr7:160144631-160144637 Template switch process: F1: L AAGATCCCCCACCTCATCCAGAGCTGGGCTGATGCTGTCACTCCTCT 1 F3: 4 CACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATGGATC R RF: AAGATCCCCCACCTCATCCAGAGCTGGGCTGATGCTGTCACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATTGATCACTCTGTGCTGGTCTATTCTGTAGGACACTTGTCTCATCTCAGTGAAACTGGGGGCGCAATGGTTCGAGGGACTATG RR: TTCTAGGGGGTGGAGTAGGTCTCGACCCGACTACGACAGTGAGGAGACGTCCCACTGGACCCTAGTGAGTTTCATAACTAGTGAGACACGACCAGATAAGACATCCTGTGAACAGAGTAGAGTCACTTTGACCCCCGCGTTACCAAGCTCCCTGATAC F2: 3 CCGATAC 2 Unidirectional alignment (log-probability: -39.4) CCCACCTCATCCAGAGCTGGGCTGATGCTGTCactcctctcatagcccACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATgG CCCACCTCATCCAGAGCTGGGCTGATGCTGTC----------------ACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATTG Template switch alignment (log-probability: -27.9) CCCACCTCATCCAGAGCTGGGCTGATGCTGTCACTCCTCT|CATAGcC|CACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATgG CCCACCTCATCCAGAGCTGGGCTGATGCTGTCACTCCTCT|CATAGTC|CACTCCTCTGCAGGGTGACCTGGGATCACTCAAAGTATTG ========== Event 3344 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACAGATTCAGATAA-----AG------ACTATCCTACTGGATAG--------------------TCTACATATGGAACTTCTAATCACAGTATTTTATAAAGATTTTCTTATAGCACATGAAAAAGTCAAAGTTTTGTTCTACAAACC ↑ 1 4 3 2 Chimp: AACAGATTCAGATAA-----AA---TTATGCATCCTACTGGATAG--------------------TCTACATATGGAACTTCTAATCACAGTATTTTATAAAGATTTTCTTATAGCACATGAAAAAGTCAAAGTTTTGTTCTACAAACC Gorilla: AATAGATTCAGATAAAACAAAATTA---TGCATCCTACTGGATAG----------------------------------------TCACAGTATTTTATAAAGATTTTCTTATAGCACATGAAAAAGTCAAAGTTTTGTTCTACAAACC Human: AACAGATTCAGATAA-----AG------ACTATCCTACTGGATAG--------------------TCTACATATGGAACTTCTAATCACAGTATTTTATAAAGATTTTCTTATAGCACATGAAAAAGTCAAAGTTTTGTTCTACAAACC Cluster: [ ] Orangutan: AACAGATTCAGATAAAACGAAATTA---TGCATCCTACTGGATAGTCTACATATGGAACTTCTAA--------------------TCACAGTATTTTATAAAAATTTTCTTATAGCACATGAAAAAGTTAAAGTTTTGTTCTACAAACC Chimp > Human ------------- chr7:3598841-3598844 Template switch process: F1: L TAATTACAACGAATAGATGTGAGAAAACAGATTCAGATAAA 1 F3: 4 ATCCTACTGGATAGTCTACATATGGAACTTCTAATCACAG R RF: TAATTACAATGAATAGATGTGAGAAAACAGATTCAGATAAAATTATGCATCCTACTGGATAGTCTACATATGGAACTTCTAATCACAGTATTTTATAAAGATTTTCTTATAGCACATGAAAAAGTC RR: ATTAATGTTACTTATCTACACTCTTTTGTCTAAGTCTATTTTAATACGTAGGATGACCTATCAGATGTATACCTTGAAGATTAGTGTCATAAAATATTTCTAAAAGAATATCGTGTACTTTTTCAG F2: 3 TCAG 2 Unidirectional alignment (log-probability: -33.2) AATTACAAcGAATAGATGTGAGAAAACAGATTCAGATAAAgactA-------TCCTACTGGATAGTCTACATATGGAACTTCTAATCACAG AATTACAATGAATAGATGTGAGAAAACAGATTCAGATAAA----ATTATGCATCCTACTGGATAGTCTACATATGGAACTTCTAATCACAG Template switch alignment (log-probability: -21.8) AATTACAAcGAATAGATGTGAGAAAACAGATTCAGATAAA|GACT|ATCCTACTGGATAGTCTACATATGGAACTTCTAATCACAG AATTACAATGAATAGATGTGAGAAAACAGATTCAGATAAA|GACT|ATCCTACTGGATAGTCTACATATGGAACTTCTAATCACAG ========== Event 3345 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTACTCCTTTTCTTACTGGGC--TTAGAACTGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA ↓ 1 4 3 2 Chimp: TTACTCCTTTTCTTACTGGGCTCTAAGAAATGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA Gorilla: TTACTGCTTTTCTTACTGGGC--TTAGAACTGAAAAACTCCATTTCTTAGACAATTCTGTAGTTCTTCTA Human: TTACTCCTTTTCTTACTGGGC--TTAGAACTGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA Cluster: [ ] Orangutan: TTACTGCTTTTCTTACTGGGC--TTAGAACTGAAAAACTCCATCTCGTAGAAAATTCTGCAGTTCTTCTA Human > Chimp ------------- chr7:6310567-6310574 Template switch process: F1: L AGGTGAAGCCCTAATATTTATTACTCCTTTTCTTACTGGGCT 1 F3: 4 TGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA R RF: AGGTGAAGCCCTAATATTTATTACTCCTTTTCTTACTGGGCTTAGAACTGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA RR: TCCACTTCGGGATTATAAATAATGAGGAAAAGAATGACCCGAATCTTGACTTTTTGAGGTAAAGAATCTTTTAAGACATCAAGAAGAT F2: 3 AAAGAATC 2 Unidirectional alignment (log-probability: -25.8) GTGAAGCCCTAATATTTATTACTCCTTTTCTTACTGGGctCTaAGAAaTGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA GTGAAGCCCTAATATTTATTACTCCTTTTCTTACTGGG--CTTAGAACTGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA Template switch alignment (log-probability: -16.3) GTGAAGCCCTAATATTTATTACTCCTTTTCTTACTGGGCT|CTAAGAAA|TGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA GTGAAGCCCTAATATTTATTACTCCTTTTCTTACTGGGCT|CTAAGAAA|TGAAAAACTCCATTTCTTAGAAAATTCTGTAGTTCTTCTA ========== Event 3346 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATACTAATAATTTACCAATTGTATGGGATAT------------TGTCTGCACTGTTAAAAATCCTAA Chimp: CATACTAATAATTTACCAATTGTATGGGATAT------------TGTCTGCACTGTTAAAAATCCTAA ↓ 3 1 24 Gorilla: CATACTAATAATTTACCAATTGTATGGGATAACAATATCCCAGACAACTGCACTGTTAAAAATCCTAA ↑ 3 1 24 Human: CATACTAATAATTTACCAATTGTATGGGATAT------------TGTCTGCACTGTTAAAAATCCTAA Cluster: [ ] Orangutan: aaTACTAATGATTTAACAATTGTATGGGATAT------------TGTCTGCACTGCTAAAAAACCTAA Human > Gorilla --------------- chr7:156535890-156535905 Template switch process: F1: L AAGAAAAAACCATACTAATAATTTACCAATTGTATGGGATA 1 F3: 4 CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT R RF: AAGAAAAAACCATACTAATAATTTACCAATTGTATGGGATATTGTCTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT RR: TTCTTTTTTGGTATGATTATTAAATGGTTAACATACCCTATAACAGACGTGACAATTTTTAGGATTTTAACTAAATTAAGATCAA F2: 3 AACAGACCCTATAACA 2 Unidirectional alignment (log-probability: -43.8) AGAAAAAACCATACTAATAATTTACCAATTGTATGGGATaacaatatcccagacaA----CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT AGAAAAAACCATACTAATAATTTACCAATTGTATGGGAT----------------ATTGTCTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT Template switch alignment (log-probability: -23.3) AGAAAAAACCATACTAATAATTTACCAATTGTATGGGATA|ACAATATCCCAgACAA|CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT AGAAAAAACCATACTAATAATTTACCAATTGTATGGGATA|ACAATATCCCATACAA|CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT Chimp > Gorilla --------------- chr7:156535890-156535905 Template switch process: F1: L AAGAAAAAACCATACTAATAATTTACCAATTGTATGGGATA 1 F3: 4 CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT R RF: AAGAAAAAACCATACTAATAATTTACCAATTGTATGGGATATTGTCTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT RR: TTCTTTTTTGGTATGATTATTAAATGGTTAACATACCCTATAACAGACGTGACAATTTTTAGGATTTTAACTAAATTAAGATCAA F2: 3 AACAGACCCTATAACA 2 Unidirectional alignment (log-probability: -43.8) AGAAAAAACCATACTAATAATTTACCAATTGTATGGGATaacaatatcccagacaA----CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT AGAAAAAACCATACTAATAATTTACCAATTGTATGGGAT----------------ATTGTCTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT Template switch alignment (log-probability: -23.3) AGAAAAAACCATACTAATAATTTACCAATTGTATGGGATA|ACAATATCCCAgACAA|CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT AGAAAAAACCATACTAATAATTTACCAATTGTATGGGATA|ACAATATCCCATACAA|CTGCACTGTTAAAAATCCTAAAATTGATTTAATTCTAGTT ========== Event 3347 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GTTGAGCCTGCTTGATTCTACACGTGCACACGTGTGCACATACGTGCTCACGTCACACACATGCGTGCAGTCTCATGCACACACACATGGTCTTTACTGAGCTGGAGGGCTTCCCACCCCCATGCTGGGGTGCACCCCTGAGGCCTGGTATCCAT ↑ 4 1 3 2 Chimp: GTTGAGCCTGCTTGATTCTACACG--------------------TGCTCACGTCACACACATGCGTGCAGTCTCATGCACACACACATGGTCTTTACTGAGCTGGAGGGCTTCCCACCCCCATGCTGGGGTGCACCCTTGAGGCCGGGTATCCAT Gorilla: GTTGAGCCTGCTTGATTCTacacgtgcacacgtgtgcacatatgtgctcacgtcacacacatgcgtgcagtctcatgcacacacacatgGTCTTTACTGAGCTGGAGGGCTTCCCACCCCCATGCTGGGGTGCACCCCTGAGGCCTGGTATCCAT Human: GTTGAGCCTGCTTGATTCTACACGTGCACACGTGTGCACATACGTGCTCACGTCACACACATGCGTGCAGTCTCATGCACACACACATGGTCTTTACTGAGCTGGAGGGCTTCCCACCCCCATGCTGGGGTGCACCCCTGAGGCCTGGTATCCAT Cluster: [ ] Orangutan: GTTGAGCCTGCTTGATTCTACACGTGCACACGTGTGCACATACGTCCTCACGTCACGCACATGCGTGCAGTCTCGTGCACACACACATGGTCTTTACCAAGCTGGAGGGCTTCCCACCCCTGTGCTGGGGTGCACCCCTGGGGCCTGGTATCCAT Chimp > Human ------------- chr7:1772727-1772732 Template switch process: F1: L CACCATTTGGTCTGATAGTTGAGCCTGCTTGATTCTACACGTGCACACGT 1 F3: 4 ATACGTGCTCACGTCACACACATGCGTGCAGTCTCATGCACACAC R RF: CACCATTTGGTCTGATAGTTGAGCCTGCTTGATTCTACACGTGCTCACGTCACACACATGCGTGCAGTCTCATGCACACACACATGGTCTTTACTGAGCTGGAGGGCTTCCCACCCCCATGCTGGGGTGCAC RR: GTGGTAAACCAGACTATCAACTCGGACGAACTAAGATGTGCACGAGTGCAGTGTGTGTACGCACGTCAGAGTACGTGTGTGTGTACCAGAAATGACTCGACCTCCCGAAGGGTGGGGGTACGACCCCACGTG F2: 3 CACGTG 2 Unidirectional alignment (log-probability: -39.7) TCTGATAGTTGAGCCTGCTTGATTCTACACGTgcacacgtgtgcacatacgtGCTCACGTCACACACATGCGTGCAGTCTCATGCA TCTGATAGTTGAGCCTGCTTGATTCTACACGT--------------------GCTCACGTCACACACATGCGTGCAGTCTCATGCA Template switch alignment (log-probability: -28.3) TCTGATAGTTGAGCCTGCTTGATTCTACACGTGCaCACGT|GTGCAC|AtACGTGCTCACGTCACACACATGCGTGCAGTCTCATGCA TCTGATAGTTGAGCCTGCTTGATTCTACACGTGCTCACGT|GTGCAC|ACACGTGCTCACGTCACACACATGCGTGCAGTCTCATGCA ========== Event 3348 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: ACACTTGTGCATGCACTGCAC--GTG-TTGCACTCACAGTCACATGTGCACACC------------------------------------------------GTGTGTGGGTGTAC------ACACAGCTGTACCTACtgcacatgtacatgtgtacac--atatgagcacacacatgcacactgtaca--cacacgtgcacatccacattcatccacaatgcacaaacacatgcacacacaca Chimp: Gorilla: acactcaTGCATGCACTGCAC----G-TTGCATTCACAGTCACATGTGcacacc------------------------------------------------gtgtgtgggtgtacac--acacacagctgtacctactgcacatgtacatgtgtacacat--atgagcacacacatgcacactgtaca----cacgtgcacatccacattcatccacactgcacaaacacatgcacacacaca ↑ 1 4 3 2 Human: ACACTTGTGCATGCACTGCAC--GTG-TTGCACTCACAGTCACATGTGCACACC------------------------------------------------GTGTGTGGGTGTAC------ACACAGCTGTACCTACtgcacatgtacatgtgtacac--atatgagcacacacatgcacactgtaca--cacacgtgcacatccacattcatccacaatgcacaaacacatgcacacacaca Cluster: [ ] Orangutan: ACACTCATGCAtgcactgcacgt--gtttgcactcacattcacatgtgcacaccatctgtgcactgcacatgtttgcactcacattcacatgtgcacaccatctgtgTGGGTGTACACACACACACAGCTGTACCTACTGCACATGTGCATgtgtacacat--atgagcacacacatgcacactgtacaca--catgtgcacatccacattcatccacactgcacatacacatgcacacacaca Human > Gorilla --------------- chr7:158047070-158047074 Template switch process: F1: L TACTGTATGCATGCATTTACACACTCATGCATGCACTGCACGT 1 F3: 4 TCACAGTCACATGTGCACACCGTGTGTGGGTGTACACACA R RF: TACTGTATGCATGCATTTACACACTTGTGCATGCACTGCACGTGTTGCACTCACAGTCACATGTGCACACCGTGTGTGGGTGTACACACAGCTGTACCTACTGCACATGTACATGTGTACACATATGAGCACACACATGCACACTGTACACACACGTGCACATCCACATTCATCCACAATGCA RR: ATGACATACGTACGTAAATGTGTGAACACGTACGTGACGTGCACAACGTGAGTGTCAGTGTACACGTGTGGCACACACCCACATGTGTGTCGACATGGATGACGTGTACATGTACACATGTGTATACTCGTGTGTGTACGTGTGACATGTGTGTGCACGTGTAGGTGTAAGTAGGTGTTACGT F2: 3 TACGT 2 Unidirectional alignment (log-probability: -40.1) TGTATGCATGCATTTACACACTcaTGCATGCACTGCAC--GTTGCAtTCACAGTCACATGTGCACACCGTGTGTGGGTGTACAcaca TGTATGCATGCATTTACACACTTGTGCATGCACTGCACGTGTTGCACTCACAGTCACATGTGCACACCGTGTGTGGGTGTACA---- Template switch alignment (log-probability: -27.4) TGTATGCATGCATTTACACACTcaTGCATGCACTGCACGT|TGCAT|TCACAGTCACATGTGCACACCGTGTGTGGGTGTACACACA TGTATGCATGCATTTACACACTTGTGCATGCACTGCACGT|TGCAT|TCACAGTCACATGTGCACACCGTGTGTGGGTGTACACACA ========== Event 3349 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGATGCTGAAACCACCCAAAAGC--CTCCATGACTGGAAGCTTGATATCTGACCCGGCTTTAAAGAAAGTTGGTGGCTTTGGGACAGCAGTCATGTGGCGCACAGCAGCCCATTCTTTGTTTCCAGCAGGCAGCAACAAATCCGTGAGGCTGAGCTAGCCCCTCTGTCGGG Chimp: TTGATGCTGAAACCACCCAAAAGC--CTCCATGACTGGAGGCTTGATATCTGACCCGGCTTTACAGAAAGTTGGTGGCTTTGGGACAGCAGTCATGTGGCGCACGGCAGCCCATTCTTTGTTTCCAGCAGGCAGCAAGGAATCCGTGAGGCTGAGCTAGCCCCTCTGTCGGG ↑ 1 4 3 2 Gorilla: TTGATGCTGAAACCACCCAAACGTTAAAGCATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAAGTTGGTGGCTTTGGGACAGCAGTCATGTGGCGCACAGCAGCCCGTTCTTTGTTTCCAGCAGGCAGCAACGAATCCGTGAGGCTGAGCTAGCCCCTCTGTCGGG ↓ 1 4 3 2 Human: TTGATGCTGAAACCACCCAAAAGC--CTCCATGACTGGAAGCTTGATATCTGACCCGGCTTTAAAGAAAGTTGGTGGCTTTGGGACAGCAGTCATGTGGCGCACAGCAGCCCATTCTTTGTTTCCAGCAGGCAGCAACAAATCCGTGAGGCTGAGCTAGCCCCTCTGTCGGG Cluster: [ ] Orangutan: TTGATGCTGAAACCACCCAAAGGTTAAAGCATGGCTGGAAGCTTGAGATCTGACCCGGCTTTAAAGAAAGTTGGTGGCTTTGGGAAAGCAGTCACGTGGCGCAGGGCAGCCCGTTCTTTGTTTCCAGCAGGCAGCAATGAATCCTTGAGGCTGAGCTAGCTCCTCTGTCGGG Gorilla > Human --------------- chr7:158045137-158045142 Template switch process: F1: L ACCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAA 1 F3: 4 CATGACTGGAAGCTTGATATCTGACCCGGCTTTAAAGAAA R RF: ACCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAACGTTAAAGCATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAAGTTGGTGGCTTTGGGACAGCAGTCATGTGGCGCACAGCAGCCCGTTCTTTGTTTCCAGCAGGCAGCAACGAATCCGTGAGGCT RR: TGGGGACTTAACTAGTCTCTAACTACGACTTTGGTGGGTTTGCAATTTCGTACTGACCTCCGAACTATAGACTGGGCCGAAATTTCTTTCAACCACCGAAACCCTGTCGTCAGTACACCGCGTGTCGTCGGGCAAGAAACAAAGGTCGTCCGTCGTTGCTTAGGCACTCCGA F2: 3 CTCCGA 2 Unidirectional alignment (log-probability: -32.2) CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCA------AAAGcctcCATGACTGGAaGCTTGATATCTGACCCGGCTTTAAAGAAA CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAACGTTAAAG----CATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAA Template switch alignment (log-probability: -22) CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAA|AGCCTC|CATGACTGGAaGCTTGATATCTGACCCGGCTTTAAAGAAA CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAA|AGCCTC|CATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAA Gorilla > Chimp --------------- chrKV420970:31299-31304 Template switch process: F1: L ACCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAA 1 F3: 4 CATGACTGGAGGCTTGATATCTGACCCGGCTTTACAGAAA R RF: ACCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAACGTTAAAGCATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAAGTTGGTGGCTTTGGGACAGCAGTCATGTGGCGCACAGCAGCCCGTTCTTTGTTTCCAGCAGGCAGCAACGAATCCGTGAGGCT RR: TGGGGACTTAACTAGTCTCTAACTACGACTTTGGTGGGTTTGCAATTTCGTACTGACCTCCGAACTATAGACTGGGCCGAAATTTCTTTCAACCACCGAAACCCTGTCGTCAGTACACCGCGTGTCGTCGGGCAAGAAACAAAGGTCGTCCGTCGTTGCTTAGGCACTCCGA F2: 3 CTCCGA 2 Unidirectional alignment (log-probability: -32.2) CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCA------AAAGcctcCATGACTGGAGGCTTGATATCTGACCCGGCTTTAcAGAAA CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAACGTTAAAG----CATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAA Template switch alignment (log-probability: -22) CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAA|AGCCTC|CATGACTGGAGGCTTGATATCTGACCCGGCTTTAcAGAAA CCCCTGAATTGATCAGAGATTGATGCTGAAACCACCCAAA|AGCCTC|CATGACTGGAGGCTTGATATCTGACCCGGCTTTAAAGAAA ========== Event 3350 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTTTCCTGATGCCCACATGCGTTTAC------ATG----------------------CCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGAAGAGACTCCCACCTCTGAGGCATTTGCAATGATGCCTTCTCTTTAGGCAGAGATGGCTGGTCAGGGATCCCAACCACATGTATTGGACTGACTCAGGCTCAATTTGGAGCATACTTGGATGTTTGGGTTGTT Chimp: ATTTTCCTGATGCCCACATGCATTTAC------ATG----------------------CCAAAGCTGAAGGCCCCGAGGACCCTGCAGGTGTGGGAGAGACTCCCACCTCTGAGGCATTTGCAATGATGCCTTCTCTTTAGGCAGAGATGGCTGGTCAGGGATCCCAACCACATGTATTGGACTGACTCAGGCTCAATTTGGAGCATACTTGGATGTTTGGGTTGTT ↑ 1 4 3 2 Gorilla: ATTTTCCTGATGCCCACATGCGTTTAC---TCAGTG-----------CCCCTGTCAGTGCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAGACTCCCACCTCTGAGGCATTTGCAATGATGCCTTCTCTTTAGGCAGAGATGGCTGGTCAGGGATCCCAACCACATGTATTGGACTGACTCAGGCTCAATTTGGAGCATACTTGGATGTTTGGGTTGTA ↓ 1 4 3 2 Human: ATTTTCCTGATGCCCACATGCGTTTAC------ATG----------------------CCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGAAGAGACTCCCACCTCTGAGGCATTTGCAATGATGCCTTCTCTTTAGGCAGAGATGGCTGGTCAGGGATCCCAACCACATGTATTGGACTGACTCAGGCTCAATTTGGAGCATACTTGGATGTTTGGGTTGTT Cluster: [ ] Orangutan: ATTTTCCTGATGCCCACATGCATTTACTCA---GTGTCCCTGTCAGT-----------GCAAAGCTGAGGGCCCTGAGGACCCTGTAGGTGTGGGAGAGACTCCCACCTCTGAGGCATTTGCAGTGATTCCTTCTCTTTAGGCAGAGATGGCTGGTCA-GGATCCCAACCACATGTATTGGACTGACTCAGGCTCAATTTGGAGCATACTTGGATGTTTGGGTTGTA Gorilla > Human --------------- chr7:218307-218310 Template switch process: F1: L ATTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTAC 1 F3: 4 CAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGAAGAG R RF: ATTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTACTCAGTGCCCCTGTCAGTGCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAGACTCCCACCTCTGAGGCAT RR: TAATCGTGTGTAGGTAAAAGGACTACGGGTGTACGCAAATGAGTCACGGGGACAGTCACGTTTCGACTCCCGGGGCTCCTGGGACGTCCACACCCTCTCTGAGGGTGGAGACTCCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -32.4) TTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTAC---aTGC-----------CAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGaAGAG TTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTACTCAGTGCCCCTGTCAGTGCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAG Template switch alignment (log-probability: -21.7) TTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTAC|ATGC|CAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGaAGAG TTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTAC|ATGC|CAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAG Gorilla > Chimp --------------- chr7:3342240-3342243 Template switch process: F1: L AGACGAATTAGCACACATCCATTTTCCTGATGCCCACATGCATTTAC 1 F3: 4 CAAAGCTGAAGGCCCCGAGGACCCTGCAGGTGTGGGAGAGACTCCCACCT R RF: AGACAAATTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTACTCAGTGCCCCTGTCAGTGCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAGACTCCCACCTCTGAGGCATTTGCAATGATGCCTTCTCTTTAGGCAGAGATGGCTGGTCAGGGATCCCAACCACATGTATTGGACTGACTCAGGCTCAATTTGGAGCAT RR: TCTGTTTAATCGTGTGTAGGTAAAAGGACTACGGGTGTACGCAAATGAGTCACGGGGACAGTCACGTTTCGACTCCCGGGGCTCCTGGGACGTCCACACCCTCTCTGAGGGTGGAGACTCCGTAAACGTTACTACGGAAGAGAAATCCGTCTCTACCGACCAGTCCCTAGGGTTGGTGTACATAACCTGACTGAGTCCGAGTTAAACCTCGTA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -43.7) TTAGCACACATCCATTTTCCTGATGCCCACATGCaTTTAC---aTGC-----------CAAAGCTGAaGGCCCCGAGGACCCTGCAGGTGTGGGAGAG TTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTACTCAGTGCCCCTGTCAGTGCAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAG Template switch alignment (log-probability: -33.2) TTAGCACACATCCATTTTCCTGATGCCCACATGCaTTTAC|ATGC|CAAAGCTGAaGGCCCCGAGGACCCTGCAGGTGTGGGAGAG TTAGCACACATCCATTTTCCTGATGCCCACATGCGTTTAC|ATGC|CAAAGCTGAGGGCCCCGAGGACCCTGCAGGTGTGGGAGAG ========== Event 3351 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTTTGCTGGCCGGCAGGACCACTGCGGGGGTTCCCGTGTTGAAGCAGGTCAGAGAAGGGGAAGTGGAGTAGCCGAGGGG-------------AGGAGCTGAGAACGGGAGGGCCAGGGAGCTGTGCGGCCTGTCTAGGACCCTCCAGC-------------------------AGTGAGTGCGCTCACCTCAGGCA ↑ 1 4 3 2 Chimp: TCTTTGCTGGCCGGCAGGACCGCTGTGGGGGTTCCTGTGTTGAAGCAGGTCAGAGAAGGGGAAGTGG-------------AGTAGCCGAGGGGAGGAGCTGAGAACGGGAGGGCCGGGGAGCTGTGCGGCCTGTCTAGGACCCTCCAGC-------------------------AGTGAGTGCGCTCATCTCAGGGA Gorilla: TCTTTGCTGGCCGGCAGGACCACTGCGGGGGTTCCTGTGTTGAAGCAGGTCAGAGAAGGGGAAGTGGAGTAGCCGAGGGG-------------AGGAGCTGAGAACGGGAGGGCCGGGGAGCTGTGCGGCCTGTCTAGGACCCTCCAGCAGTGAGTGCGCTCCTGGCCTGCAACAGTGAGTACGCTCATCTCAGGGA Human: TCTTTGCTGGCCGGCAGGACCACTGCGGGGGTTCCCGTGTTGAAGCAGGTCAGAGAAGGGGAAGTGGAGTAGCCGAGGGG-------------AGGAGCTGAGAACGGGAGGGCCAGGGAGCTGTGCGGCCTGTCTAGGACCCTCCAGC-------------------------AGTGAGTGCGCTCACCTCAGGCA Cluster: [ ] Orangutan: TCTTCGCTGGCCGGCAGGACCACTGCAGGGGTTCCTGTGGTGAAGCCGGTCAGAGAAGCGGAAGTAGAGGAGCCGAGGGG-------------AGGGGCTGAGAACGGGAGGGCCAGGGAGCTGTGCGGCCTGTCTAGGACCCTCCATCAGTGAGTGCGCTCCTGGCCCGCAACAGTGAGTAAGCTCATCTCAGGGA Chimp > Human ------------- chr7:308685-308689 Template switch process: F1: L CTCCTGCCGGCTCTTCTGGTTCTTTGCTGGCCGGCAGGACC 1 F3: 4 GGGGGTTCCCGTGTTGAAGCAGGTCAGAGAAGGGGAAGTGGAGTAGCCGA R RF: CTCCTGCCGGCTCTTCTGGTTCTTTGCTGGCCGGCAGGACCGCTGTGGGGGTTCCTGTGTTGAAGCAGGTCAGAGAAGGGGAAGTGGAGTAGCCGAGGGGAGGAGCTGAGAACGGGAGGGCCGGGGAGCTGTGCGGCCTGTCTAGGACCCTCCAGCAGT RR: GAGGACGGCCGAGAAGACCAAGAAACGACCGGCCGTCCTGGCGACACCCCCAAGGACACAACTTCGTCCAGTCTCTTCCCCTTCACCTCATCGGCTCCCCTCCTCGACTCTTGCCCTCCCGGCCCCTCGACACGCCGGACAGATCCTGGGAGGTCGTCA F2: 3 CGTCA 2 Unidirectional alignment (log-probability: -38.9) TCCTGCCGGCTCTTCTGGTTCTTTGCTGGCCGGCAGGACCaCTGcGGGGGTTCCcGTGTTGAAGCAGGTCAGAGAAGGGGAAGTG TCCTGCCGGCTCTTCTGGTTCTTTGCTGGCCGGCAGGACCGCTGTGGGGGTTCCTGTGTTGAAGCAGGTCAGAGAAGGGGAAGTG Template switch alignment (log-probability: -22.1) TCCTGCCGGCTCTTCTGGTTCTTTGCTGGCCGGCAGGACC|ACTGC|GGGGGTTCCcGTGTTGAAGCAGGTCAGAGAAGGGGAAGTG TCCTGCCGGCTCTTCTGGTTCTTTGCTGGCCGGCAGGACC|ACTGC|GGGGGTTCCTGTGTTGAAGCAGGTCAGAGAAGGGGAAGTG ========== Event 3352 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATTCTGTCTCCCCCTCAGACATGGCCATGTGTCCATGGCCGTGTGTCTACTGCCA ↓ 1 3 4 Chimp: AATTCTGTCTCCCCCTCAGAC---CACAT-GGTCCGTGGCCGTGTGTCTACTGCCA Gorilla: AATTCTGTCTCCCCCTCAGAC---CACTT-GGTCCATGGCCGTGTGTCTACTGCCA Human: AATTCTGTCTCCCCCTCAGACATGGCCATGTGTCCATGGCCGTGTGTCTACTGCCA Cluster: [ ] Orangutan: AATTCTGTCCCCCCCTCAGAG---CACAT-AGCCCATGGCCGTGTGTCTACTGCCG Human > Chimp ------------- chr7:3435372-3435377 Template switch process: F1: L GTATTTTTTATTTTACATTTAATTCTGTCTCCCCCTCAGAC 1 F3: 4 GTCCGTGGCCGTGTGTCTACTGCCAGCCCTAATACCAGGCCTTGT R RF: GTATTTTTTATTTTACATTTAATTCTGTCTCCCCCTCAGACATGGCCATGTGTCCATGGCCGTGTGTCTACTGCCAGCCCTAATACCAGGCCTTGT RR: CATAAAAAATAAAATGTAAATTAAGACAGAGGGGGAGTCTGTACCGGTACACAGGTACCGGCACACAGATGACGGTCGGGATTATGGTCCGGAACA F2: 3 GTACAC 2 Unidirectional alignment (log-probability: -31.9) TATTTTTTATTTTACATTTAATTCTGTCTCCCCCTCAGaccACATG-------GTCCgTGGCCGTGTGTCTACTGCCAGCCCTAATACCAGGC TATTTTTTATTTTACATTTAATTCTGTCTCCCCCTCAG---ACATGGCCATGTGTCCATGGCCGTGTGTCTACTGCCAGCCCTAATACCAGGC Template switch alignment (log-probability: -22.1) TATTTTTTATTTTACATTTAATTCTGTCTCCCCCTCAGAC|CACATG|GTCCgTGGCCGTGTGTCTACTGCCAGCCCTAATACCAGGC TATTTTTTATTTTACATTTAATTCTGTCTCCCCCTCAGAC|CACATG|GTCCATGGCCGTGTGTCTACTGCCAGCCCTAATACCAGGC ========== Event 3353 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGGAGTAAAACAATTATAGGCATATATAACAAT-----TATAGTCAATAAACCCTTCAACTAATGACA Chimp: CTGGAGTAAAACAATTATAGGCATATATAACAAT-----TATAGTCAACAAACCCTTCAACTAATGACA ↓ 3 2 1 4 Gorilla: CTGGAGTAAAACAATTATAGACATATATAACAATATATGCCTAGTCAATAAACCCTTCAACTAATGACA ↑ 3 2 1 4 Human: CTGGAGTAAAACAATTATAGGCATATATAACAAT-----TATAGTCAATAAACCCTTCAACTAATGACA Cluster: [ ] Orangutan: CTGGAGTAAAACAATTATAGGCATATGTAACAAT-----TGTAGTCAATAAAGCCTTCAACTAATGACA Human > Gorilla --------------- chr7:437748-437754 Template switch process: F1: L AAAATATCTGGAGTAAAACAATTATAGACATATATAACAAT 1 F3: 4 TAGTCAATAAACCCTTCAACTAATGACAAACATCTTCCAT R RF: AAAATATCTGGAGTAAAACAATTATAGGCATATATAACAATTATAGTCAATAAACCCTTCAACTAATGACAAACATCTTTCAT RR: TTTTATAGACCTCATTTTGTTAATATCCGTATATATTGTTAATATCAGTTATTTGGGAAGTTGATTACTGTTTGTAGAAAGTA F2: 3 CCGTATA 2 Unidirectional alignment (log-probability: -38.9) AAATATCTGGAGTAAAACAATTATAGaCATATATAACAATaTAtgccTAGTCAATAAACCCTTCAACTAATGACAAACATCTTcCAT AAATATCTGGAGTAAAACAATTATAGGCATATATAACAAT-TA----TAGTCAATAAACCCTTCAACTAATGACAAACATCTTTCAT Template switch alignment (log-probability: -27.7) AAATATCTGGAGTAAAACAATTATAGaCATATATAACAAT|ATATGCC|TAGTCAATAAACCCTTCAACTAATGACAAACATCTTcCAT AAATATCTGGAGTAAAACAATTATAGGCATATATAACAAT|ATATGCC|TAGTCAATAAACCCTTCAACTAATGACAAACATCTTTCAT Chimp > Gorilla --------------- chr7:437748-437754 Template switch process: F1: L AAAATATCTGGAGTAAAACAATTATAGACATATATAACAAT 1 F3: 4 TAGTCAATAAACCCTTCAACTAATGACAAACATCTTCCATAAGCATTT R RF: AAAATATCTGGAGTAAAACAATTATAGGCATATATAACAATTATAGTCAACAAACCCTTCAACTAATGACAAACATCTTCCATAAGCATTT RR: TTTTATAGACCTCATTTTGTTAATATCCGTATATATTGTTAATATCAGTTGTTTGGGAAGTTGATTACTGTTTGTAGAAGGTATTCGTAAA F2: 3 CCGTATA 2 Unidirectional alignment (log-probability: -39) AAATATCTGGAGTAAAACAATTATAGaCATATATAACAATaTAtgccTAGTCAAtAAACCCTTCAACTAATGACAAACATCTTCCAT AAATATCTGGAGTAAAACAATTATAGGCATATATAACAAT-TA----TAGTCAACAAACCCTTCAACTAATGACAAACATCTTCCAT Template switch alignment (log-probability: -27.9) AAATATCTGGAGTAAAACAATTATAGaCATATATAACAAT|ATATGCC|TAGTCAAtAAACCCTTCAACTAATGACAAACATCTTCCAT AAATATCTGGAGTAAAACAATTATAGGCATATATAACAAT|ATATGCC|TAGTCAACAAACCCTTCAACTAATGACAAACATCTTCCAT ========== Event 3354 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTTGTCTAGATAATATTTCTTATCTAGACAATTGTCACATTTGCAGT ↑ 4 3 2 1 Chimp: AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATT-------------------TTGAAAACAATTGTCACATTTGCAGT Gorilla: AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATT-------------------TTGAAAACAATTTTCACATTTGCAGT Human: AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTTGTCTAGATAATATTTCTTATCTAGACAATTGTCACATTTGCAGT Cluster: [ ] Orangutan: AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATT-------------------TTGAGAACAATTGTCACATTTGCAGT Chimp > Human ------------- chr7:143077776-143077782 Template switch process: F1: L AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTT 1 F3: 4 TAATATTTCTTATCTAG-----------ACAATTGTCACATTTGCAGTACAATATCAATCATGTCATT R RF: AGGTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTTTGAAAACAATTGTCACATTTGCAGTACAATATCAATCATGTCATT RR: TCCAACAACTCTTGGAAAAATTATAAAGAATAGATCTGTAAAACTTTTGTTAACAGTGTAAACGTCATGTTATAGTTAGTACAGTAA F2: 3 AGATCTG 2 Unidirectional alignment (log-probability: -55.9) GTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTT-----gtctagataatatttcttatctagACAATTGTCACATTTGCAGTACA GTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTTTGAAA------------------------ACAATTGTCACATTTGCAGTACA Template switch alignment (log-probability: -27.3) GTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTT|GTCTAGA|TAATATTTCTTATCTAG-----------ACAATTGTCACATTTGCAGTACA GTTGTTGAGAACCTTTTTAATATTTCTTATCTAGACATTT|GTCTAGA|TAATATTTCTTATCTAGACATTTTGAAAACAATTGTCACATTTGCAGTACA ========== Event 3355 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATAAACTTTAGAAACACCGAAGTTTTCTGTCCTGGACAAAGTCCAGGACAAATTATCCAGaa Chimp: AAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTGGACAAAGTCCAGGACAAATTATCCAGaa ↓ 3 2 1 4 Gorilla: AAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTGAACTTTGTCCAGGACAAATTATCCAGaa Human: AAATAAACTTTAGAAACACCGAAGTTTTCTGTCCTGGACAAAGTCCAGGACAAATTATCCAGaa Cluster: [ ] Orangutan: AAATAAACTTTAGAAACACCGAAGTTTTCTGTCCTGGACAAAGTC-----CAAATTATCCAGaa Chimp > Gorilla --------------- chr7:140902330-140902336 Template switch process: F1: L CGACTAAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTG 1 F3: 4 TCCAGGACAAATTATCCAGAAAAAAAAAAAACAAAAC R RF: TGACTAAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTGGACAAAGTCCAGGACAAATTATCCAGAAAAAAAAAAAAAAAAC RR: ACTGATTTATTTGAAATCTTTGTGGTTTCAAAAGACAGGACCTGTTTCAGGTCCTGTTTAATAGGTCTTTTTTTTTTTTTTTTG F2: 3 GTTTCAA 2 Unidirectional alignment (log-probability: -45.5) GACTAAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTGaACtttGTCCAGGACAAATTATCCAGAAAAAAAAAAAacaaaac GACTAAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTGGACAAAGTCCAGGACAAATTATCCAGAAAAAAAAAAA------- Template switch alignment (log-probability: -33.2) GACTAAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTG|AACTTTG|TCCAGGACAAATTATCCAGAAAAAAAAAAAAcAAAAC GACTAAATAAACTTTAGAAACACCAAAGTTTTCTGTCCTG|AACTTTG|TCCAGGACAAATTATCCAGAAAAAAAAAAAA-AAAAC ========== Event 3356 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCACTTTTAAGATACCTAGGACTTTAATGGCAGATGGACATCTGCCCATGTGTGAATGATATTAG Chimp: TCACATTTAAGATACCTAGGAATTTAATGT-------CCATCTGCCCATGTGTGAATGATATTAG Gorilla: TCACTTTTAAGATACCTAGGAATTTAACGT-------CCATCTGCCCATGTGTGAATGATATTAG ↓ 1 3 4 2 Human: TCACTTTTAAGATACCTAGGACTTTAATGGCAGATGGACATCTGCCCATGTGTGAATGATATTAG Cluster: [ ] Orangutan: TCACTTTTAAGATACCTAGGAATTTAATGT-------CCATCAGCCCATGTGTGAATGATATTAG Gorilla > Human --------------- chr7:18751666-18751674 Template switch process: F1: L TAAAACTGCTAAAAATTAATTCACTTTTAAGATACCTAGGACTTTAATG 1 F3: 4 CATCTGCCCATGTGTGAATGATATTAGAAAAATTCAAAAT R RF: TAAAACTGCTAAAAATTAATTCACTTTTAAGATACCTAGGAATTTAACGTCCATCTGCCCATGTGTGAATGATATTAGAAAAATTCAAAAT RR: ATTTTGACGATTTTTAATTAAGTGAAAATTCTATGGATCCTTAAATTGCAGGTAGACGGGTACACACTTACTATAATCTTTTTAAGTTTTA F2: 3 AGGTAGACG 2 Unidirectional alignment (log-probability: -37.6) TAAAAATTAATTCACTTTTAAGATACCTAGGAcTTTAAtGgCagatggaCATCTGCCCATGTGTGAATGATATTAGAAAAATTCAAAAT TAAAAATTAATTCACTTTTAAGATACCTAGGAATTTAACGTC-------CATCTGCCCATGTGTGAATGATATTAGAAAAATTCAAAAT Template switch alignment (log-probability: -28.1) TAAAAATTAATTCACTTTTAAGATACCTAGGAcTTTAAtG|GCAGATGGA|CATCTGCCCATGTGTGAATGATATTAGAAAAATTCAAAAT TAAAAATTAATTCACTTTTAAGATACCTAGGAATTTAACG|GCAGATGGA|CATCTGCCCATGTGTGAATGATATTAGAAAAATTCAAAAT ========== Event 3357 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TTAAAAGAAGCTAAGTTCAACCTTGATTCCTCTGTGTTCTAGGCCTATAGTTTACAGTTATTCAGTGACCTATAGGGAGGCATTTATAAAAAGTTTGATAACTC-CTCACAAATTTTACTCAAAATATTTCAAGAAATGATTATGAAATGACAA Chimp: TTaaaaaaaGCTAAGTTCAACAC-AGTTCCTCTGTGTTCTAGGCCTATAGTTTATAGCTATTCAGTGACCTATAGGGAAGCATTTATAAAAAGTTTGATAACTC-CTCACAAATTTTACTCAAAATATTTCAAGAAATGATTATGAAATGACAA ↓ 1 4 3 2 Gorilla: TTAAAAGAAGCTAAGTTCAACCTTGATTCCTCTGTGTTCTAGGCCTATAGTTTATAGTTATTCAGTGACCTATAGGGAGGCATTTATAAAAAGTTTGATAACTC-CTCACAAATTTTACTCAAAATATTTCAAGAAATGATTATGAAATGACAA Human: TTAAAAGAAGCTAAGTTCAACCTTGATTCCTCTGTGTTCTAGGCCTATAGTTTACAGTTATTCAGTGACCTATAGGGAGGCATTTATAAAAAGTTTGATAACTC-CTCACAAATTTTACTCAAAATATTTCAAGAAATGATTATGAAATGACAA Cluster: [ ] Orangutan: TTAAAAGAAGCTAAGTTCAACCTTGATTCCTCTGTGTTCTAGGCCTATAGTTTATAGTTATTCAGTGACCTATAGGGAGGTATTTATAAAAAGTTTGATAACTCCTTCACAAATTTTACTCAAAATATTTCAAGAAATGATTATGAAATGACAA Chimp > Gorilla --------------- chr7:19102537-19102541 Template switch process: F1: L TTTAAAAACTCAATTGAGGATTAAAAGAAGCTAAGTTCAAC 1 F3: 4 TTCCTCTGTGTTCTAGGCCTATAGTTTATAGTTATTCAGT R RF: TTTAAAAACTCAATTGAGGATTAAAAAAAGCTAAGTTCAACACAGTTCCTCTGTGTTCTAGGCCTATAGTTTATAGCTATTCAGTGACCTATAGGGAAGCATTTATAAAAAGTTTGATAACTCCTCACAAATTTTACTCAAAATATTTCAAG RR: AAATTTTTGAGTTAACTCCTAATTTTTTTCGATTCAAGTTGTGTCAAGGAGACACAAGATCCGGATATCAAATATCGATAAGTCACTGGATATCCCTTCGTAAATATTTTTCAAACTATTGAGGAGTGTTTAAAATGAGTTTTATAAAGTTC F2: 3 AGTTC 2 Unidirectional alignment (log-probability: -37.6) TTAAAAACTCAATTGAGGATTAAAAgAAGCTAAGTTCAACcttgA---TTCCTCTGTGTTCTAGGCCTATAGTTTATAGtTATTCAGT TTAAAAACTCAATTGAGGATTAAAAAAAGCTAAGTTCAAC----ACAGTTCCTCTGTGTTCTAGGCCTATAGTTTATAGCTATTCAGT Template switch alignment (log-probability: -27.4) TTAAAAACTCAATTGAGGATTAAAAgAAGCTAAGTTCAAC|CTTGA|TTCCTCTGTGTTCTAGGCCTATAGTTTATAGtTATTCAGT TTAAAAACTCAATTGAGGATTAAAAAAAGCTAAGTTCAAC|CTTGA|TTCCTCTGTGTTCTAGGCCTATAGTTTATAGCTATTCAGT ========== Event 3358 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCAATAATATGCTGACAGATAGAACTATATTGGATTGGAATAAA-ATGTAAGTATGATGATCAGAGAAA ↓ 13 24 ↑ 1 3 24 Chimp: CCAATAATATGCTGACAGATAC-ATTTTATTCCAATCCAATATAGTTCTAAGTATGATGATCAGAGAAA Gorilla: CCAATAATATGCTGACAGATAC-ATTTTATTCCAATCCAATAGAGTTCTAAGTAAGATGATCAGAGAAA Human: CCAATAATATGCTGACAGATAGAACTATATTGGATTGGAATAAA-ATGTAAGTATGATGATCAGAGAAA Cluster: [ ] Orangutan: ACAATAATATGCTGACAGATAC-ATTTTATTCCAATCCAATATAGTTCTAAGTATGATGATCAGAGAAA Chimp > Human ------------- chr7:139812004-139812029 Template switch process: F1: L TTAGTGCATGATTTTACATACCAATAATATGCTGACAGATA 1 F3: 4 TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGGAAA R RF: TTAGTGCATGATTTTACATACCAATAATATGCTGACAGATACATTTTATTCCAATCCAATATAGTTCTAAGTATGATGATCAGAGAAAAATGATGGTATTAGGTAAA RR: AATCACGTACTAAAATGTATGGTTATTATACGACTGTCTATGTAAAATAAGGTTAGGTTATATCAAGATTCATACTACTAGTCTCTTTTTACTACCATAATCCATTT F2: 3 GTAAAATAAGGTTAGGTTATATCAAG 2 Unidirectional alignment (log-probability: -65.8) TAGTGCATGATTTTACATACCAATAATATGCTGACAGATA--------------------------gaactatattggattggaataaaatgTAAGTATGATGATCAGAGAAAAATGATGGTATTAGGgAAA TAGTGCATGATTTTACATACCAATAATATGCTGACAGATACATTTTATTCCAATCCAATATAGTTC--------------------------TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGTAAA Template switch alignment (log-probability: -24.5) TAGTGCATGATTTTACATACCAATAATATGCTGACAGATA|GAACTATATTGGATTGGAATAAAATG|TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGgAAA TAGTGCATGATTTTACATACCAATAATATGCTGACAGATA|GAACTATATTGGATTGGAATAAAATG|TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGTAAA Human > Chimp ------------- chr7:147577383-147577408 Template switch process: F1: L TTAGTGCATGATTTTACATACCAATAATATGCTGACAGATA 1 F3: 4 TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGTAAA R RF: TTAGTGCATGATTTTACATACCAATAATATGCTGACAGATAGAACTATATTGGATTGGAATAAAATGTAAGTATGATGATCAGAGAAAAATGATGGTATTAGGGAAA RR: AATCACGTACTAAAATGTATGGTTATTATACGACTGTCTATCTTGATATAACCTAACCTTATTTTACATTCATACTACTAGTCTCTTTTTACTACCATAATCCCTTT F2: 3 CTTGATATAACCTAACCTTATTTTAC 2 Unidirectional alignment (log-probability: -65.8) TAGTGCATGATTTTACATACCAATAATATGCTGACAGATA--------------------------cattttattccaatccaatatagttcTAAGTATGATGATCAGAGAAAAATGATGGTATTAGGtAAA TAGTGCATGATTTTACATACCAATAATATGCTGACAGATAGAACTATATTGGATTGGAATAAAATG--------------------------TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGGAAA Template switch alignment (log-probability: -24.5) TAGTGCATGATTTTACATACCAATAATATGCTGACAGATA|CATTTTATTCCAATCCAATATAGTTC|TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGtAAA TAGTGCATGATTTTACATACCAATAATATGCTGACAGATA|CATTTTATTCCAATCCAATATAGTTC|TAAGTATGATGATCAGAGAAAAATGATGGTATTAGGGAAA ========== Event 3359 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACAGTATGTACCAATCAGGAGGCCTCTGG----GTTCTGTGAAGAAAATATTTGGTA Chimp: AACAGTATGTACCAATCAGGAAGCCTCTGG----GTTCTGTGAAGAAAATATTTGGTA ↓ 3 1 2 4 Gorilla: AACAGTATGTACCAATCAGGAGGCCTCCAGAGGCCTCCTGTGAAGAAAATATTTGGTA ↑ 3 1 2 4 Human: AACAGTATGTACCAATCAGGAGGCCTCTGG----GTTCTGTGAAGAAAATATTTGGTA Cluster: [ ] Orangutan: AACAGTATGTACCAATCAGGAGGCCTCTGG----GTTCTATGAAGAAAATATTTGATA Human > Gorilla --------------- chr7:19310185-19310194 Template switch process: F1: L TGTCCACCTAGGAAAACAGTATGTACCAATCAGGAGGCCTC 1 F3: 4 CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC R RF: TGTCCTCCTAGGAAAACAGTATGTACCAATCAGGAGGCCTCTGGGTTCTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC RR: ACAGGAGGATCCTTTTGTCATACATGGTTAGTCCTCCGGAGACCCAAGACACTTCTTTTATAAACCATTAATTAGTACGGAACGTTG F2: 3 CTCCGGAGAC 2 Unidirectional alignment (log-probability: -40.8) GTCCaCCTAGGAAAACAGTATGTACCAATCAGgaggcctccaGAGGCCTC------CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC GTCCTCCTAGGAAAACAGTATGTACCAATCAG----------GAGGCCTCTGGGTTCTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC Template switch alignment (log-probability: -22.5) GTCCaCCTAGGAAAACAGTATGTACCAATCAGGAGGCCTC|CAGAGGCCTC|CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC GTCCTCCTAGGAAAACAGTATGTACCAATCAGGAGGCCTC|CAGAGGCCTC|CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC Chimp > Gorilla --------------- chr7:19310185-19310194 Template switch process: F1: L AAGGAATGTCCACCTAGGAAAACAGTATGTACCAATCAGGAGGCCTC 1 F3: 4 CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC R RF: AAGGAATGTCCACCTAGGAAAACAGTATGTACCAATCAGGAAGCCTCTGGGTTCTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC RR: TTCCTTACAGGTGGATCCTTTTGTCATACATGGTTAGTCCTTCGGAGACCCAAGACACTTCTTTTATAAACCATTAATTAGTACGGAACGTTG F2: 3 CTCCGGAGAC 2 Unidirectional alignment (log-probability: -40.9) GTCCACCTAGGAAAACAGTATGTACCAATCAGgaggcctccaGAgGCCTC------CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC GTCCACCTAGGAAAACAGTATGTACCAATCAG----------GAAGCCTCTGGGTTCTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC Template switch alignment (log-probability: -28.2) GTCCACCTAGGAAAACAGTATGTACCAATCAGGAgGCCTC|CAGAGGCcTC|CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC GTCCACCTAGGAAAACAGTATGTACCAATCAGGAAGCCTC|CAGAGGCTTC|CTGTGAAGAAAATATTTGGTAATTAATCATGCCTTGCAAC ========== Event 3360 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAACTGATCAAACAATGAATTGGTCAATAAAAATCCTCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAAGTCAAAAGATGTGCTTGTGTATACTTTGTAATGATGCCATGAACTGGTTAAAGAGTAAAATGCTCATAGGTGAC Chimp: TTAACTGATCAAACAATGAATTCTTTG---------ATCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAAGTCAAAAGATGTGCTTGTGTATACTTTGTAATGATGCCATGAACTGGTTAAAGAGTAAAATGCTCATAGGTGCC ↑ 1 4 3 2 Gorilla: TTAACTGATCAAACAATGAATCGGTGAATAAAAATCCTCCCATATCCTTATGTATCAACaaaaaatgagagagaaaagtcaaaaaaTGTGCTTGTGTATACTTTGTAATGATGCCATGAACTGATTAAAGAGTAAAATGCTCATAGGTGCC Human: TTAACTGATCAAACAATGAATTGGTCAATAAAAATCCTCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAAGTCAAAAGATGTGCTTGTGTATACTTTGTAATGATGCCATGAACTGGTTAAAGAGTAAAATGCTCATAGGTGAC Cluster: [ ] Orangutan: TTAACTGATCAAACAATGAATTGGTGAATAAAAATCCTCCCATATCCTTATATATCAACAAAAAATGAGAGAGAAAAGTCAAAAGATGTGCTTGTGTATACTTTGTAATAATACCATGAACTGATTAAAGAGTAAAATGCTCATAGGTGCC Gorilla > Chimp --------------- chr7:18743431-18743437 Template switch process: F1: L AGCATAACCTAATCCCTCTGTTAACTGATCAAACAATGAAT 1 F3: 4 TCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAA R RF: AGCATAACCTAATCCCTTTGTTAACTGATCAAACAATGAATCGGTGAATAAAAATCCTCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAAGTCAAAAAATGTGCTTGTGTATACTTTGTAATGATGCCATGAACTGATTAAAGA RR: TCGTATTGGATTAGGGAAACAATTGACTAGTTTGTTACTTAGCCACTTATTTTTAGGAGGGTATAGGAATACATAGTTGTTTTTTACTCTCTCTTTTCAGTTTTTTACACGAACACATATGAAACATTACTACGGTACTTGACTAATTTCT F2: 3 AGTTTCT 2 Unidirectional alignment (log-probability: -37) GCATAACCTAATCCCTcTGTTAACTGATCAAACAATGAAT----------------tctttgaTCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAA GCATAACCTAATCCCTTTGTTAACTGATCAAACAATGAATCGGTGAATAAAAATCC-------TCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAA Template switch alignment (log-probability: -27.7) GCATAACCTAATCCCTcTGTTAACTGATCAAACAATGAAT|TCTTTgA|TCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAA GCATAACCTAATCCCTTTGTTAACTGATCAAACAATGAAT|TCTTTAA|TCCCATATCCTTATGTATCAACAAAAAATGAGAGAGAAAA ========== Event 3361 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGAATTCCTTTTCCTGAAAAATGTTA------ATAACA--TTTCAATACAAAATTATAGAA ↓ 3 1 2 4 Chimp: TGAATTCCTTTTCCTGAAAAATGTTAATGTTATTAACATTTTTCAATACAAAATTATAGAA Gorilla: TGAATTCCTTTTCCTGAAAAATGTTAATGTTATTAACATTTTTCAATACAAAATTATAGAA ↑ 3 1 2 4 Human: TGAATTCCTTTTCCTGAAAAATGTTA------ATAACA--TTTCAATACAAAATTATAGAA Cluster: [ ] Orangutan: TGAATTCCTTTTCCTGAAAAATGTTAATGTTATTAACATTTTTCAATACAAAGTTATAGAA Human > Chimp ------------- chr7:146939186-146939197 Template switch process: F1: L TCAATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAT 1 F3: 4 TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA R RF: TCAATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAATAACATTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA RR: AGTTACAAGTAAAATACTTAAGGAAAAGGACTTTTTACAATTATTGTAAAGTTATGTTTTAATATCTTAATAGATTATTTAATTACT F2: 3 TTACAATTATTG 2 Unidirectional alignment (log-probability: -32.7) ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAtgttatTAACATTTttCAATACAAAATTATAGAATTATCTAATAAATTAATGA ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAA------TAACATTT--CAATACAAAATTATAGAATTATCTAATAAATTAATGA Template switch alignment (log-probability: -16.8) ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAT|GTTATTAACATT|TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAT|GTTATTAACATT|TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA Human > Gorilla --------------- chr7:138938100-138938111 Template switch process: F1: L TCAATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAT 1 F3: 4 TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA R RF: TCAATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAATAACATTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA RR: AGTTACAAGTAAAATACTTAAGGAAAAGGACTTTTTACAATTATTGTAAAGTTATGTTTTAATATCTTAATAGATTATTTAATTACT F2: 3 TTACAATTATTG 2 Unidirectional alignment (log-probability: -32.2) ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAtgttatTAACAttTTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAA------TAACA--TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA Template switch alignment (log-probability: -17.3) ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAT|GTTATTAACATT|TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA ATGTTCATTTTATGAATTCCTTTTCCTGAAAAATGTTAAT|GTTATTAACATT|TTTCAATACAAAATTATAGAATTATCTAATAAATTAATGA ========== Event 3362 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTTCTGCTTAATTTTGTGGAATTGCTTACAGAAACTAAGCAATTTACATTGTTTTAAACACAT ↑ 1 4 3 2 Chimp: TTTTCTGCTTAATTTTGTGGAT---GTTACAGAAACTAAGCAATTTACATTGTTTTAAACACAT Gorilla: TTTTCTGCTTAATTTTGTGGAT---GTTACAGAAACTAAGCAATTTACAtttttttAAACACAT Human: TTTTCTGCTTAATTTTGTGGAATTGCTTACAGAAACTAAGCAATTTACATTGTTTTAAACACAT Cluster: [ ] Orangutan: TTTTCTGCTTAATTTTGTGGAT---GTTACAGAAACTAAGCAATTTACATTTTTTTAAACACAT Chimp > Human ------------- chr7:20960991-20960995 Template switch process: F1: L AGAAAATTCTTCCTTCTTAATTTTCTGCTTAATTTTGTGGA 1 F3: 4 TTACAGAAACTAAGCAATTTACATTGTTTTAAACACATGC R RF: AGAAAATTCTTCCTTCTTAATTTTCTGCTTAATTTTGTGGATGTTACAGAAACTAAGCAATTTACATTGTTTTAAACACATGC RR: TCTTTTAAGAAGGAAGAATTAAAAGACGAATTAAAACACCTACAATGTCTTTGATTCGTTAAATGTAACAAAATTTGTGTACG F2: 3 CGTTA 2 Unidirectional alignment (log-probability: -25.5) GAAAATTCTTCCTTCTTAATTTTCTGCTTAATTTTGTGGAatTGcTTACAGAAACTAAGCAATTTACATTGTTTTAAACACATGC GAAAATTCTTCCTTCTTAATTTTCTGCTTAATTTTGTGGA--TG-TTACAGAAACTAAGCAATTTACATTGTTTTAAACACATGC Template switch alignment (log-probability: -15.9) GAAAATTCTTCCTTCTTAATTTTCTGCTTAATTTTGTGGA|ATTGC|TTACAGAAACTAAGCAATTTACATTGTTTTAAACACATGC GAAAATTCTTCCTTCTTAATTTTCTGCTTAATTTTGTGGA|ATTGC|TTACAGAAACTAAGCAATTTACATTGTTTTAAACACATGC ========== Event 3363 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAAAGAAAATTATTTGGAGCAGTC--------------------------------------------------------TGAGAGACCTCCCTGAAATCATTGATCAACACATTTGATCATATTATAATATTTACATCTA ↓ 4 1 3 2 Chimp: AGAAAGAAAATTATTTGGAGCAGTC-------------------------------TGAGAGACCTCCTGAGCAAGCAGTCTGAGAGACCTCCCTGAAATCATTGATCAACACATTTGATCATATTATAATATTTACATCTA Gorilla: AGAAAGAAAATTATTTGgagcagtc----------tgagagacctcctgagcagtc-------------------------tgagagacctccCTGAAATCATTTATCAACACATTTGATCATATTATGATATTTACATCTA Human: AGAAAGAAAATTATTTGGAGCAGTC--------------------------------------------------------TGAGAGACCTCCCTGAAATCATTGATCAACACATTTGATCATATTATAATATTTACATCTA Cluster: [ ] Orangutan: AGAAAGAAAATTGTTTGGAGCAGTCTGAGAGACCT---------------------------------------------------------CCTGAAATCATTGATCAACACATTTGATCATATTATAATATTTACATCTA Human > Chimp ------------- chr7:20086921-20086927 Template switch process: F1: L CAGAATTTCCGTCTTAAGAAAGAAAATTATTTGGAGCAGTCTGAGAGACCTCC 1 F3: 4 GCAGTCTGAGAGACCTCCCTGAAATCATTGATCAACACATTTGATC R RF: CAGAATTTCCATCTTAAGAAAGAAAATTATTTGGAGCAGTCTGAGAGACCTCCCTGAAATCATTGATCAACACATTTGATC RR: GTCTTAAAGGTAGAATTCTTTCTTTTAATAAACCTCGTCAGACTCTCTGGAGGGACTTTAGTAACTAGTTGTGTAAACTAG F2: 3 AACGAGT 2 Unidirectional alignment (log-probability: -52.9) TTAAGAAAGAAAATTATTTGGAGCAGTCTGAGAGACCTCCtgagcaagcagtctgagagacctccCTGAAATCATTGATCAACACAT TTAAGAAAGAAAATTATTTGGAGCAGTCTGAGAGACCTCC-------------------------CTGAAATCATTGATCAACACAT Template switch alignment (log-probability: -28.5) TTAAGAAAGAAAATTATTTGGAGCAGTCTGAGAGACCTCC|TGAgCAA|GCAGTCTGAGAGACCTCCCTGAAATCATTGATCAACACAT TTAAGAAAGAAAATTATTTGGAGCAGTCTGAGAGACCTCC|TGATCAA|GCAGTCTGAGAGACCTCCCTGAAATCATTGATCAACACAT ========== Event 3364 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGAGCTCAGATCAGGGACAAACTGTACAAATTCCAAAGCACTCCTTCCTATAAACTTTAAGAGAATGTTGCCTTTCATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTT-ACAG------TTGTGGCTGACATAGCTGGT ↓ 3 2 1 4 Chimp: AGAGCTCAGATCAGGGACAAACTGTACAAATTCCAAAGCACTCCTTCCTATAAACTTTAAGAGAATGTTGCCTTTCATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTTAACAG---TTGTTGTGGCTGACATAGCTGGT Gorilla: AGAGCTCAGATCAGGGACAAACTGTACAAATTCCAGAGCACTCCTTCCTATAAACTTTAAGAGAATGTTGCCTTTCATTTAGACCAACTCAATCATTCCTGTTCACTTAGATCTTAACAGTTG---TTGTGGCTGACATAGCTGGT Human: AGAGCTCAGATCAGGGACAAACTGTACAAATTCCAAAGCACTCCTTCCTATAAACTTTAAGAGAATGTTGCCTTTCATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTT-ACAG------TTGTGGCTGACATAGCTGGT Cluster: [ ] Orangutan: AGAGCTCAGATCAGGGACAAACTGTACAAATTCCAAAGCACTCCTTCCTACAGACGTTAAGAGAATGTTGCCTTTCATTTAGACCTACTCAATCATTCCTATTCACTTAGATCTT-ACAGTTG---TTGTGGCTGACATAGCTGGT Human > Chimp ------------- chr7:20750250-20750255 Template switch process: F1: L TCATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTTA 1 F3: 4 GTTGTGGCTGACATAGCTGGTCACTCCTAGAGTTGACTGTA R RF: AACTGTACAAATTCCAAAGCACTCCTTCCTATAAACTTTAAGAGAATGTTGCCTTTCATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTTACAGTTGTGGCTGACATAGCTGGTCACTCCTAGAGTTGAGTGTA RR: TTGACATGTTTAAGGTTTCGTGAGGAAGGATATTTGAAATTCTCTTACAACGGAAAGTAAATCTGGTTGAGTTAGTAAGGATAAGTGAATCTAGAATGTCAACACCGACTGTATCGACCAGTGAGGATCTCAACTCACAT F2: 3 TTGACA 2 Unidirectional alignment (log-probability: -32.9) ATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTTaACAgttGTTGTGGCTGACATAGCTGGTCACTCCTAGAGTTGAcTGT ATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTT-ACA---GTTGTGGCTGACATAGCTGGTCACTCCTAGAGTTGAGTGT Template switch alignment (log-probability: -22.1) ATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTTA|ACAGTT|GTTGTGGCTGACATAGCTGGTCACTCCTAGAGTTGAcTGT ATTTAGACCAACTCAATCATTCCTATTCACTTAGATCTTA|ACAGTT|GTTGTGGCTGACATAGCTGGTCACTCCTAGAGTTGAGTGT ========== Event 3365 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: cacctggccCAAGGAAGAATATTGCTTATT-----------TAGTGGAGAGGATCCTCTGAAAT Chimp: cacctggccCAAGGAAGAATATTGCTTATT-----------TAATGGAGAGGATCCTCTGAAAT ↓ 3 2 41 Gorilla: cacctggccCAAGGAAGAATATTGCTTATTTATAAGCAATATAGTGGAGAGGATCCTCTGAAAT ↑ 3 2 41 Human: cacctggccCAAGGAAGAATATTGCTTATT-----------TAGTGGAGAGGATCCTCTGAAAT Cluster: [ ] Orangutan: cacctggccCAAGGAAGAATATTTCTTATT-----------TAGTGGAGAGGATCCTCTGAAAT Human > Gorilla --------------- chr7:21892371-21892379 Template switch process: F1: L GTAAGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTA 1 F3: 4 TAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA R RF: GTGAGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA RR: CACTCGGTGGCGTGGACCGGGTTCCTTCTTATAACGAATAAATCACCTCTCCTAGGAGACTTTATAATTCTGACTTGAACT F2: 3 ATAACGAAT 2 Unidirectional alignment (log-probability: -32.2) AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTtataagcaataTAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATT-----------TAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA Template switch alignment (log-probability: -22.4) AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTA|TAAGCAATA|TAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTA|TAAGCAATA|TAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA Chimp > Gorilla --------------- chr7:21892371-21892379 Template switch process: F1: L GTAAGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTA 1 F3: 4 TAGTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGATGT R RF: GTGAGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTAATGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGATGT RR: CACTCGGTGGCGTGGACCGGGTTCCTTCTTATAACGAATAAATTACCTCTCCTAGGAGACTTTATAATTCTGACTTGAACTACA F2: 3 ATAACGAAT 2 Unidirectional alignment (log-probability: -37.8) AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTtataagcaataTAgTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATT-----------TAATGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA Template switch alignment (log-probability: -28) AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTA|TAAGCAATA|TAgTGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA AGCCACCGCACCTGGCCCAAGGAAGAATATTGCTTATTTA|TAAGCAATA|TAATGGAGAGGATCCTCTGAAATATTAAGACTGAACTTGA ========== Event 3366 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 34 Detected in comparisons: 34 Multiple sequence alignment: Human: TGGAAACAATATAACTACATA--GT---ATTAAAGACTAGTTTATCAAAATAATCTAATTATTTATTAAATACAG Chimp: Gorilla: TGGAAACAATATAACTACATAGATTATTTTGATAAACTAGTCTTTAAT-----ACTAATTATTTATTAAATACAG ↓ 13 24 ↑ 1 3 24 Human: TGGAAACAATATAACTACATA--GT---ATTAAAGACTAGTTTATCAAAATAATCTAATTATTTATTAAATACAG Cluster: [ ] Orangutan: TGGAAACAATATAACTACATAGATTATTTTGATAAACTAGTCTTTAAT-----ACTAATTAT---TCAAATACAG Gorilla > Human --------------- chr7:23383127-23383153 Template switch process: F1: L CACCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG 1 F3: 4 CTAATTATTTATTAAATACAGGGAATAGTGATGGAAGTGT R RF: CACCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAGATTATTTTGATAAACTAGTCTTTAATACTAATTATTTATTAAATACAGTGAATAGTGATGGAAGTGT RR: GTGGATTCGTTTCGGTACACACCTTTGTTATATTGATGTATCTAATAAAACTATTTGATCAGAAATTATGATTAATAAATAATTTATGTCACTTATCACTACCTTCACA F2: 3 TAATAAAACTATTTGATCAGAAATTAT 2 Unidirectional alignment (log-probability: -63.4) CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG-------------------------TAttaaagactagtttatcaaaataatCTAATTATTTATTAAATACAGgGAATAGTGATGGAAGTGT CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAGATTATTTTGATAAACTAGTCTTTAATA-------------------------CTAATTATTTATTAAATACAGTGAATAGTGATGGAAGTGT Template switch alignment (log-probability: -24.7) CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG|TATTAAAGACTAGTTTATCAAAATAAT|CTAATTATTTATTAAATACAGgGAATAGTGATGGAAGTGT CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG|TATTAAAGACTAGTTTATCAAAATAAT|CTAATTATTTATTAAATACAGTGAATAGTGATGGAAGTGT Human > Gorilla --------------- chr7:23434501-23434527 Template switch process: F1: L CACCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG 1 F3: 4 CTAATTATTTATTAAATACAGTGAATAGTGATGGAAGTGT R RF: CACCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAGTATTAAAGACTAGTTTATCAAAATAATCTAATTATTTATTAAATACAGGGAATAGTGATGGAAGTGT RR: GTGGATTCGTTTCGGTACACACCTTTGTTATATTGATGTATCATAATTTCTGATCAAATAGTTTTATTAGATTAATAAATAATTTATGTCCCTTATCACTACCTTCACA F2: 3 ATAATTTCTGATCAAATAGTTTTATTA 2 Unidirectional alignment (log-probability: -63.4) CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG-------------------------ATtattttgataaactagtctttaataCTAATTATTTATTAAATACAGtGAATAGTGATGGAAGTGT CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAGTATTAAAGACTAGTTTATCAAAATAAT-------------------------CTAATTATTTATTAAATACAGGGAATAGTGATGGAAGTGT Template switch alignment (log-probability: -24.7) CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG|ATTATTTTGATAAACTAGTCTTTAATA|CTAATTATTTATTAAATACAGtGAATAGTGATGGAAGTGT CCTAAGCAAAGCCATGTGTGGAAACAATATAACTACATAG|ATTATTTTGATAAACTAGTCTTTAATA|CTAATTATTTATTAAATACAGGGAATAGTGATGGAAGTGT ========== Event 3367 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTGGGAGGCTGATGGGAAACCCCCCTTCGGTCTCGAGTC----------TGTGCCTTTCCATCCAGCACAAGC ↓ 13 24 ↑ 13 24 Chimp: GTGGGAGGCTGATGGGAAACC-----ACAGACTCGAGAC-----CGAAGGGGGCCTTTCCATCCAGCACAAGC Gorilla: GTGGGAGGCTGATGGGAAACC-----ACAGACTCAAGACCGAAG-----GGGGCCTTTCCATCCAGGACAAGC ↓ 13 24 Human: GTGGGAGGCTGATGGGAAACCCCCCTTCGGTCTCGAGTC----------TGTGCCTTTCCATCCAGCACAAGC Cluster: [ ] Orangutan: GTGGGAGGCTGATGGGAAACC-----ACAGACTCGAGACTGAAG-----GAGGCCTTTCCATCCAGCACAAGC Chimp > Human ------------- chr7:134639958-134639978 Template switch process: F1: L TGGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC 1 F3: 4 GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG R RF: TGGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACCACAGACTCGAGACCGAAGGGGGCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG RR: ACCATGTCCCTCCCATTCTCCACCCTCCGACTACCCTTTGGTGTCTGAGCTCTGGCTTCCCCCGGAAAGGTAGGTCGTGTTCGGAGGGATGAGAGGGCCTCC F2: 3 TGTCTGAGCTCTGGCTTCCCC 2 Unidirectional alignment (log-probability: -52.4) GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC---------------------ccccttcggtctcgagtctgtGCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACCACAGACTCGAGACCGAAGGGG---------------------GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG Template switch alignment (log-probability: -17.9) GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC|CCCCTTCGGTCTCGAGTCTGT|GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC|CCCCTTCGGTCTCGAGTCTGT|GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG Human > Chimp ------------- chr7:142313128-142313148 Template switch process: F1: L TGGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC 1 F3: 4 GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG R RF: TGGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACCCCCCTTCGGTCTCGAGTCTGTGCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG RR: ACCATGTCCCTCCCATTCTCCACCCTCCGACTACCCTTTGGGGGGAAGCCAGAGCTCAGACACGGAAAGGTAGGTCGTGTTCGGAGGGATGAGAGGGCCTCC F2: 3 GGGGAAGCCAGAGCTCAGACA 2 Unidirectional alignment (log-probability: -52.4) GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC---------------------acagactcgagaccgaaggggGCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACCCCCCTTCGGTCTCGAGTCTGT---------------------GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG Template switch alignment (log-probability: -17.9) GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC|ACAGACTCGAGACCGAAGGGG|GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC|ACAGACTCGAGACCGAAGGGG|GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG Gorilla > Human --------------- chr7:134639958-134639978 Template switch process: F1: L TGGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC 1 F3: 4 GCCTTTCCATCCAGCACAAGCCTCCCTACTCTCCCGGAGG R RF: TGGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACCACAGACTCAAGACCGAAGGGGGCCTTTCCATCCAGGACAAGCCTCCCTACTCTCCCGGAGG RR: ACCATGTCCCTCCCATTCTCCACCCTCCGACTACCCTTTGGTGTCTGAGTTCTGGCTTCCCCCGGAAAGGTAGGTCCTGTTCGGAGGGATGAGAGGGCCTCC F2: 3 TGTCTGAGCTCTGGCTTCCCC 2 Unidirectional alignment (log-probability: -57.4) GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC---------------------ccccttcggtctcgagtctgtGCCTTTCCATCCAGcACAAGCCTCCCTACTCTCCCGGAGG GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACCACAGACTCAAGACCGAAGGGG---------------------GCCTTTCCATCCAGGACAAGCCTCCCTACTCTCCCGGAGG Template switch alignment (log-probability: -29.4) GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC|CCCCTTCGGTCTcGAGTCTGT|GCCTTTCCATCCAGcACAAGCCTCCCTACTCTCCCGGAGG GGTACAGGGAGGGTAAGAGGTGGGAGGCTGATGGGAAACC|CCCCTTCGGTCTTGAGTCTGT|GCCTTTCCATCCAGGACAAGCCTCCCTACTCTCCCGGAGG ========== Event 3368 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTGAAAGCAATTCTTGCCTA------------------TTAGCAATCTGATTTGTTaaaaaaaaaa--aaaaa-----aaaaaaCCCTGTTAACAataacggagtatgccatacagatggaacaggaataaagattctctctctggctatagagtggtctctaggatat Chimp: CTTGAAAGCAATTCTTGCCTA---------TTATAGCCATTAGCAATCTGATTTGTTaaaaaaaaaa----aaa-----aaCAAACCCTGTTAACAATAACGGAGTATGCCATACAGATGAAACAGGAATAAAGATTCTCTCTCTGGCTATAGAGTGGTCTCTAGGATAT Gorilla: CTTGAAAGCAATTCTTGCCTATTATAGCCA---------TTAGCAATCTGATTTGTTaaaaaaaaaa------a-----aaaaaaCCCTGTTAACAataacggagtatgccatacagatggaacaggaataaagattctctctctggctatagagtggtctctaggatat ↑ 4 1 3 2 Human: CTTGAAAGCAATTCTTGCCTA------------------TTAGCAATCTGATTTGTTaaaaaaaaaa--aaaaa-----aaaaaaCCCTGTTAACAataacggagtatgccatacagatggaacaggaataaagattctctctctggctatagagtggtctctaggatat Cluster: [ ] Orangutan: CTTGAAAGCAATTCTTGCCTATTATAGCCA---------TTAGCAATCTGATTTGCTaaaaaaacaaac----aaacaaaaaaacaCCTGTTAACAATAACGGAGTATGCCATACAGATGGAACAG-GATAAAGATTCTCTCTCTGGCTGTAGAGTGGTCTCTAGGATAT Human > Gorilla --------------- chr7:134421755-134421759 Template switch process: F1: L GTAAACAGGCCACAATTCAACTTGAAAGCAATTCTTGCCTATTA 1 F3: 4 ATTAGCAATCTGATTTGTTAAAAAAAAAAAAAAAAAC R RF: GTAAACAGGCCACATTTCAACTTGAAAGCAATTCTTGCCTATTAGCAATCTGATTTGTTAAAAAAAAAAAAAAAAAAAAACCCTGTTAACAATAACGGAGTATGCCATACAGATGGAACAGGAATAAAGATTCTCTCTCTGGCTA RR: CATTTGTCCGGTGTAAAGTTGAACTTTCGTTAAGAACGGATAATCGTTAGACTAAACAATTTTTTTTTTTTTTTTTTTTTGGGACAATTGTTATTGCCTCATACGGTATGTCTACCTTGTCCTTATTTCTAAGAGAGAGACCGAT F2: 3 CCGAT 2 Unidirectional alignment (log-probability: -39.2) ACAGGCCACAaTTCAACTTGAAAGCAATTCTTGCCTattatagccATTAGCAATCTGATTTGTT----AAAAAAAAAAAAAAAAAC ACAGGCCACATTTCAACTTGAAAGCAATTCTTGCCT---------ATTAGCAATCTGATTTGTTAAAAAAAAAAAAAAAAAAAAAC Template switch alignment (log-probability: -27.4) ACAGGCCACAaTTCAACTTGAAAGCAATTCTTGCCTATTA|TAGCC|ATTAGCAATCTGATTTGTTAAAAAAAAAAAAAAAAAc ACAGGCCACATTTCAACTTGAAAGCAATTCTTGCCTATTA|TAGCC|ATTAGCAATCTGATTTGTTAAAAAAAAAAAAAAAAAA ========== Event 3369 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAACCAAAAGAGAGATTGCCTC---TGAG-AACACACACTGCTGGAACATTTT Chimp: CCAACCAAAAGAGAGATTGCCTC---TGAG-AACACACACTGCTGGAACATTTT ↓ 3 1 2 4 Gorilla: CCAACCAAAAGAGAGATTGCCTCTTCTCAGAGGCACACACTGCTGGAACATTTT ↑ 3 1 2 4 Human: CCAACCAAAAGAGAGATTGCCTC---TGAG-AACACACACTGCTGGAACATTTT Cluster: [ ] Orangutan: CCAACCAAAAGGGAGACTGCTGC---TGAG-AACACACACTGCTGGAACGTTTT Human > Gorilla --------------- chr7:25591608-25591616 Template switch process: F1: L GGGGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT 1 F3: 4 CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA R RF: GGGGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCTGAGAACACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA RR: CCCCTCTTTTTCAACCCTGGTTGGTTTTCTCTCTAACGGAGACTCTTGTGTGTGACGACCTTGTAAAAACGAAGGAACCTAGAGACT F2: 3 GGAGACTCT 2 Unidirectional alignment (log-probability: -32.4) GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCTtctcagagG----CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT--------GAGAACACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA Template switch alignment (log-probability: -16.9) GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT|TCTCAGAGG|CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT|TCTCAGAGG|CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA Chimp > Gorilla --------------- chr7:25591608-25591616 Template switch process: F1: L GGGGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT 1 F3: 4 CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA R RF: GGGGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCTGAGAACACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA RR: CCCCTCTTTTTCAACCCTGGTTGGTTTTCTCTCTAACGGAGACTCTTGTGTGTGACGACCTTGTAAAAACGAAGGAACCTAGAGACT F2: 3 GGAGACTCT 2 Unidirectional alignment (log-probability: -32.4) GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCTtctcagagG----CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT--------GAGAACACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA Template switch alignment (log-probability: -16.9) GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT|TCTCAGAGG|CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA GGAGAAAAAGTTGGGACCAACCAAAAGAGAGATTGCCTCT|TCTCAGAGG|CACACACTGCTGGAACATTTTTGCTTCCTTGGATCTCTGA ========== Event 3370 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGGTCCTGGAGAGTAGATTGCTGAAAGAGCCCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGC-TTTCTGGATTCTGCTGCCTTCC ↓ 3 1 2 4 Chimp: GGGGTCCTGGAGAGTAGATTGCTGAAAGAG------------------------------------CATGGTGGGCTCTTCTGGATTCTGCTGCCTTCC ↑ 3 1 2 4 Gorilla: GGGGTCCTGGAGAGTAGATTGTTGAAAGAGCCCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGC-TTTCTGGATTCTGCCGCCTTCC Human: GGGGTCCTGGAGAGTAGATTGCTGAAAGAGCCCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGC-TTTCTGGATTCTGCTGCCTTCC Cluster: [ ] Orangutan: Human > Chimp ------------- chr7:25806015-25806025 Template switch process: F1: L TTGTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGC 1 F3: 4 TTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC R RF: TTGTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGCCCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGCTTTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC RR: AACAATGTAAACCCCAGGACCTCTCATCTAACGACTTTCTCGGGTGGTACGGTGAGACCCAGGAGTAAGGTCTTCCGGTGACAGTCGAAAGACCTAAGACGACGGAAGGAGACACTTCTCGACCCGTG F2: 3 CTCGGGTGGTA 2 Unidirectional alignment (log-probability: -37.8) GTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGCatggtgggctC---------------------------------------------TTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC GTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGC----------CCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGCTTTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC Template switch alignment (log-probability: -16.7) GTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGC|ATGGTGGGCTC|TTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC GTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGC|ATGGTGGGCTC|TTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC Gorilla > Chimp --------------- chr7:25806015-25806025 Template switch process: F1: L ATGCACACATTGTTACATTTGGGGTCCTGGAGAGTAGATTGCTGAAAGAGC 1 F3: 4 TTCTGGATTCTGCTGCCTTCCTCTGTGAAGAGCTGGGCAC R RF: ATGCACACATTGTTACATTTGGGGTCCTGGAGAGTAGATTGTTGAAAGAGCCCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGCTTTCTGGATTCTGCCGCCTTCCTCTGTGAAGAGCTGGGCAC RR: TACGTGTGTAACAATGTAAACCCCAGGACCTCTCATCTAACAACTTTCTCGGGTGGTACGGTGAGACCCAGGAGTAAGGTCTTCCGGTGACAGTCGAAAGACCTAAGACGGCGGAAGGAGACACTTCTCGACCCGTG F2: 3 CTCGGGTGGTA 2 Unidirectional alignment (log-probability: -48.5) GTTACATTTGGGGTCCTGGAGAGTAGATTGcTGAAAGAGCatggtgggctC---------------------------------------------TTCTGGATTCTGCtGCCTTCCTCTGTGAAGAGCTGGGCAC GTTACATTTGGGGTCCTGGAGAGTAGATTGTTGAAAGAGC----------CCACCATGCCACTCTGGGTCCTCATTCCAGAAGGCCACTGTCAGCTTTCTGGATTCTGCCGCCTTCCTCTGTGAAGAGCTGGGCAC Template switch alignment (log-probability: -28.4) GTTACATTTGGGGTCCTGGAGAGTAGATTGcTGAAAGAGC|ATGGTGGGCTC|TTCTGGATTCTGCtGCCTTCCTCTGTGAAGAGCTGGGCAC GTTACATTTGGGGTCCTGGAGAGTAGATTGTTGAAAGAGC|ATGGTGGGCTC|TTCTGGATTCTGCCGCCTTCCTCTGTGAAGAGCTGGGCAC ========== Event 3371 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GATTCTGCTTGTTTCTGTGATACTCTGAGAATCCAG--AG----TATCTTTAATTTGGGTTGAAACAG ↑ 3 2 1 4 Chimp: GATTCTGCTTGTTTCTGTGATACTCTGAGAATCTAGGAAGTTTAGAACTTTAATTTGGGTTGAAACAG Gorilla: GATTCTGCTTGTTTCTGTAATACTCTGAGAATCCAGGAAGTTTAGAACTTTAATTTGGGTTGAAACAG Human: GATTCTGCTTGTTTCTGTGATACTCTGAGAATCCAG--AG----TATCTTTAATTTGGGTTGAAACAG Cluster: [ ] Orangutan: GATTCTGCTTGTTTCTGTGATACTCTGAGAATCCAGGAAGTTTAGAAGTTTAATTTGGGTTGAAACAG Chimp > Human ------------- chr7:26960452-26960459 Template switch process: F1: L GTCAATTAGATTCTGCTTGTTTCTGTGATACTCTGAGAATC 1 F3: 4 CTTTAATTTGGGTTGAAACAGCAGATATCAGACTACTATT R RF: GTCAATTAGATTCTGCTTGTTTCTGTGATACTCTGAGAATCTAGGAAGTTTAGAACTTTAATTTGGGTTGAAACAGCAGATATCAGACTACTATT RR: CAGTTAATCTAAGACGAACAAAGACACTATGAGACTCTTAGATCCTTCAAATCTTGAAATTAAACCCAACTTTGTCGTCTATAGTCTGATGATAA F2: 3 TATGAGAC 2 Unidirectional alignment (log-probability: -31.9) TCAATTAGATTCTGCTTGTTTCTGTGATACTCTGAGAATCcagagtaT-------------CTTTAATTTGGGTTGAAACAGCAGATATCAGACTACTATT TCAATTAGATTCTGCTTGTTTCTGTGATACTCTGAGAATC-------TAGGAAGTTTAGAACTTTAATTTGGGTTGAAACAGCAGATATCAGACTACTATT Template switch alignment (log-probability: -16.3) TCAATTAGATTCTGCTTGTTTCTGTGATACTCTGAGAATC|CAGAGTAT|CTTTAATTTGGGTTGAAACAGCAGATATCAGACTACTATT TCAATTAGATTCTGCTTGTTTCTGTGATACTCTGAGAATC|CAGAGTAT|CTTTAATTTGGGTTGAAACAGCAGATATCAGACTACTATT ========== Event 3372 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATGAAAAGAGCATCGGCACTTCACGTTCATTAAAACGTGAAGAGATGACCAACTAATGCT Chimp: AATGAAAAGAGCATCGGCACTTCACGTTCATTAAAACGTGAAGAGATGACCAACTAATGCT ↑ 1 4 3 2 Gorilla: AATGAAAAGAGCATCGGCACTG--CTGTAATTAAAACGTGAAGAGATGACCAACTAATGCT ↓ 1 4 3 2 Human: AATGAAAAGAGCATCGGCACTTCACGTTCATTAAAACGTGAAGAGATGACCAACTAATGCT Cluster: [ ] Orangutan: AATGAAAAGGGGATCGGCACTG--CTGTAATTAAAA--------CATGACCAACTAATGCT Gorilla > Human --------------- chr7:2761775-2761780 Template switch process: F1: L GACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT 1 F3: 4 TCATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTCAT R RF: GACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACTGCTGTAATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTCAT RR: CTGTTCTACCCGGTGACCTTTTACTTTTCTCGTAGCCGTGACGACATTAATTTTGCACTTCTCTACTGGTTGATTACGACGAAAGTA F2: 3 TGCACT 2 Unidirectional alignment (log-probability: -32.4) ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT------tcacgttcATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACTGCTGTA--------ATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC Template switch alignment (log-probability: -22.1) ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT|TCACGT|TcATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT|TCACGT|TAATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC Gorilla > Chimp --------------- chr7:1890144-1890149 Template switch process: F1: L GACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT 1 F3: 4 TCATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTCAT R RF: GACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACTGCTGTAATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTCAT RR: CTGTTCTACCCGGTGACCTTTTACTTTTCTCGTAGCCGTGACGACATTAATTTTGCACTTCTCTACTGGTTGATTACGACGAAAGTA F2: 3 TGCACT 2 Unidirectional alignment (log-probability: -32.4) ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT------tcacgttcATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACTGCTGTA--------ATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC Template switch alignment (log-probability: -22.1) ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT|TCACGT|TcATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC ACAAGATGGGCCACTGGAAAATGAAAAGAGCATCGGCACT|TCACGT|TAATTAAAACGTGAAGAGATGACCAACTAATGCTGCTTTC ========== Event 3373 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCGGAATCCCTTCGGAGTGACGAG---GGCGGGGTCACAGCTCGCGCACCCTCATCTGGAGAGAGGCAAGAA Chimp: GCGGAATCCCTTCGGATTGACGAG---GACGGGGTCACAGCTCGCACACCCTCATCTGGAGAGAGGCAAGCA Gorilla: GCGGAATCCCTTCGGAGTGACAGGGCGCGCGAGCTGTGACCCCG---CCCTTCATCTGGAGAGAGGCAAGAA ↑ 1 3 4 Human: GCGGAATCCCTTCGGAGTGACGAG---GGCGGGGTCACAGCTCGCGCACCCTCATCTGGAGAGAGGCAAGAA Cluster: [ ] Orangutan: GCGGAATCCCCTCGGAGTGACG-------------------------------------------------- Human > Gorilla --------------- chr7:2635195-2635221 Template switch process: F1: L AGAGACTTCCGGTTCTGACAGCGGAATCCCTTCGGAGTGAC 1 F3: 4 TCATCTGGAGAGAGGCAAGAACAGGGCAGCTTGGACCATT R RF: AGAGACTTCCGGTTCTGACAGCGGAATCCCTTCGGAGTGACGAGGGCGGGGTCACAGCTCGCGCACCCTCATCTGGAGAGAGGCAAGAACAGGGCAGCTTGGACCTTT RR: TCTCTGAAGGCCAAGACTGTCGCCTTAGGGAAGCCTCACTGCTCCCGCCCCAGTGTCGAGCGCGTGGGAGTAGACCTCTCTCCGTTCTTGTCCCGTCGAACCTGGAAA F2: 3 TCCCGCCCCAGTGTCGAGCGCGCGGGA 2 Unidirectional alignment (log-probability: -65.8) GAGACTTCCGGTTCTGACAGCGGAATCCCTTCGGAGTGAC-AGGGCG-------------------CgcgagctgtgaccccgccctTCATCTGGAGAGAGGCAAGAACAGGGCAGCTTGGACCaTT GAGACTTCCGGTTCTGACAGCGGAATCCCTTCGGAGTGACGAGGGCGGGGTCACAGCTCGCGCACCC--------------------TCATCTGGAGAGAGGCAAGAACAGGGCAGCTTGGACCTTT Template switch alignment (log-probability: -30.2) GAGACTTCCGGTTCTGACAGCGGAATCCCTTCGGAGTGAC|AGGGcGCGCGAGCTGTGACCCCGCCCT|TCATCTGGAGAGAGGCAAGAACAGGGCAGCTTGGACCaTT GAGACTTCCGGTTCTGACAGCGGAATCCCTTCGGAGTGAC|AGGGTGCGCGAGCTGTGACCCCGCCCT|TCATCTGGAGAGAGGCAAGAACAGGGCAGCTTGGACCTTT ========== Event 3374 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGAAATGAGATTTAAATATA----------TAGGCCTAACACTCATCTGCAATTCAGCGGCATTCCTTGCACATAGAAGGTG Chimp: AGGAAATGAGATTTAAATATG-----CAGATGAGGCCTAACACTCATCTGCAAGTCAGTGGTGTTCCTTGCACATAGAAGGTG Gorilla: AGGAAATGAGATTTAAATATGCAGAT-----GAGGCCTAACACTCATCTGCAAGTCAGCGGCGTTCCTTGCACATAGAAGGTG ↑ 1 4 3 2 Human: AGGAAATGAGATTTAAATATA----------TAGGCCTAACACTCATCTGCAATTCAGCGGCATTCCTTGCACATAGAAGGTG Cluster: [ ] Orangutan: AGGAAATGAGAGTTAAATATA----------TAGGCCTAACACTCATCTGCAAGTCAGCGGCATTCCTTGCACATAGAAGGTG Human > Gorilla --------------- chr7:28419081-28419087 Template switch process: F1: L GAGATTTAAATAT 1 F3: 4 AGGCCTAACACTCATCTGCAAGTCAGCGGCGTTCCTTGCACATAGAAGGTGTTTGATAAAAAATGATTATT R RF: GAGATTTAAATATATAGGCCTAACACTCATCTGCAATTCAGCGGCATTCCTTGCACATAGAAGGTGTTTGATAAAAAATGATTATT RR: CTCTAAATTTATATATCCGGATTGTGAGTAGACGTTAAGTCGCCGTAAGGAACGTGTATCTTCCACAAACTATTTTTTACTAATAA F2: 3 GTAGACG 2 Unidirectional alignment (log-probability: -38.9) GAGATTTAAATATgcagATgAGGCCTAACACTCATCTGCAAgTCAGCGGCgTTCCTTGCA GAGATTTAAATAT----AT-AGGCCTAACACTCATCTGCAATTCAGCGGCATTCCTTGCA Template switch alignment (log-probability: -27.7) GAGATTTAAATAT|GCAGATG|AGGCCTAACACTCATCTGCAAgTCAGCGGCgTTCCTTGCA GAGATTTAAATAT|GCAGATG|AGGCCTAACACTCATCTGCAATTCAGCGGCATTCCTTGCA ========== Event 3375 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGCCAAGATGTCAGGAACAGAAACACAGTAACCATCTGAATATTGATTGTATAC-----------------------------------------AATCTTTATATTGACTGTATATTGACCACCTG----T ↑ 4 1 3 2 Chimp: CAGCCAAGATGTCAGGAACAG---------AACCATCTGAATATTGATTGTATAC-----------------------AATCTGTATACAATATACAATCTTTATATTGACTGTATATTGACCATCTG--TAT Gorilla: CAGCCAAGATGTCAGGAACAGAAACACAGTAACCATCTGAATATTGATTGTATAC-----AATCTGTATACAATATAC------------------AATCTTTATATTGACTGTATATTGACCATCTGTA--T Human: CAGCCAAGATGTCAGGAACAGAAACACAGTAACCATCTGAATATTGATTGTATAC-----------------------------------------AATCTTTATATTGACTGTATATTGACCACCTG----T Cluster: [ ] Orangutan: CAGCCAAGATGTCAGGAACAGAAACACAGTGACCATCTGAATATTGATTGTATACAATCT-----------------------------------------GTATATTGACTGTATATTGACCATCTGTA--T Chimp > Human ------------- chr7:27948649-27948652 Template switch process: F1: L CAGGCATGCGGGAGCACTTACAGCCAAGATGTCAGGAACAGAAACA 1 F3: 4 AACCATCTGAATATTGATTGTATAC R RF: CAGGCATGCGGGAGCACTTACAGCCAAGATGTCAGGAACAGAACCATCTGAATATTGATTGTATACAATCTGTATACAATATACAATCTTTATATTGACTG RR: GTCCGTACGCCCTCGTGAATGTCGGTTCTACAGTCCTTGTCTTGGTAGACTTATAACTAACATATGTTAGACATATGTTATATGTTAGAAATATAACTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -31.7) TGCGGGAGCACTTACAGCCAAGATGTCAGGAACAGaaacacagtAACCATCTGAATATTGATTGTATAC--------------- TGCGGGAGCACTTACAGCCAAGATGTCAGGAACAG---------AACCATCTGAATATTGATTGTATACAATCTGTATACAATA Template switch alignment (log-probability: -21.6) TGCGGGAGCACTTACAGCCAAGATGTCAGGAACAGAAaCA|CAGT|AACCATCTGAATATTGATTGTATAC TGCGGGAGCACTTACAGCCAAGATGTCAGGAACAGAACCA|CAGT|AACCATCTGAATATTGATTGTATAC ========== Event 3376 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTAGCACCATGGATCAGGGAGTA--------------ATCTAGATgcataactcagagatactgctggtctggttccagaccattgcaatagcaaatatcacaataaagcaagtcacactaattttttgatttcccagtgca-cata-------aagttatatttacactatactgtagtctataaagtgtgcaat Chimp: CTAGCACCATGGATCAGGGAGTA--------------ATCTAGaggcataactcagagatactgctggtctggttccagaccattgcaatagcaaatatcacaataaagcaagtcacactaattttttgatttcccagtgca-cata-------aagttatatttacactatactgtagtctataaagtgtgcaat ↓ 4 1 3 2 Gorilla: CTAGCACCAGGGATCAGGGAGGCATAACTCAGAGATCAGTTAGaggcataactcagagatactgctggtctggttccagaccattgcaatagcaaatatcacaataaagcaagtcacactaattttttgatttcccagtgcactata--------------gattacactatactgtagtctataaagtgtgcaat Human: CTAGCACCATGGATCAGGGAGTA--------------ATCTAGATgcataactcagagatactgctggtctggttccagaccattgcaatagcaaatatcacaataaagcaagtcacactaattttttgatttcccagtgca-cata-------aagttatatttacactatactgtagtctataaagtgtgcaat Cluster: [ ] Orangutan: CTAGCACCATGGATCAGGGAGTA--------------ATCTAGaggcataactcagagatactgctcgtctggttccagaccactgcaatagcaaatatcacaataaagcaagtcacgctaattttttgatttcccagtgca-cataaagttac-------atttacactacactgtagtctataaagtgtgcaat Chimp > Gorilla --------------- chr7:28156355-28156358 Template switch process: F1: L GAACCCTGCTGATTGTTCAGCTAGCACCAGGGATCAGG----------GAGGCATAACTCAGAGAT 1 F3: 4 TAGAGGCATAACTCAGAGATACTGCTGGTCTGGTTCCAGA R RF: GAACCCTGCTGATTGTTCAGCTAGCACCATGGATCAGGGAGTAATCTAGAGGCATAACTCAGAGATACTGCTGGTCTGGTTCCAGACCATTGCAATAGCAAATATCACAATAAAGCAAGTCACACTAATTTTTTGATTTCCCAGTGCACATAAAGTTATATTTACACTATACTG RR: CTTGGGACGACTAACAAGTCGATCGTGGTACCTAGTCCCTCATTAGATCTCCGTATTGAGTCTCTATGACGACCAGACCAAGGTCTGGTAACGTTATCGTTTATAGTGTTATTTCGTTCAGTGTGATTAAAAAACTAAAGGGTCACGTGTATTTCAATATAAATGTGATATGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -52.2) TCAGCTAGCACCAgGGATCAGGGaggcataactcagagatcAGT----TAGAGGCATAACTCAGAGATACTGCTGGTCTGGTTCCAGA TCAGCTAGCACCATGGATCAGGG------------------AGTAATCTAGAGGCATAACTCAGAGATACTGCTGGTCTGGTTCCAGA Template switch alignment (log-probability: -32.4) TCAGCTAGCACCAgGGATCAGG----------GAGGCATAACTCAGAGAT|CAGT|TAGAGGCATAACTCAGAGATACTGCTGGTCTGGTTCCAGA TCAGCTAGCACCATGGATCAGGGAGTAATCTAGAGGCATAACTCAGAGAT|CAGT|TAGAGGCATAACTCAGAGATACTGCTGGTCTGGTTCCAGA ========== Event 3377 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGAAGGGGATGTTTGACTCCCCTTCAGACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCA ↑ 1 4 3 2 Chimp: GGAAGGGGATGTTTGACTCCCTTC--TACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCA Gorilla: GGAAGGGGATGTTTGACTCCCTTC--TACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCA ↓ 1 4 3 2 Human: GGAAGGGGATGTTTGACTCCCCTTCAGACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCA Cluster: [ ] Orangutan: GGAAGGGGATGTTTGACTCCCTTC--TACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCA Chimp > Human ------------- chr7:29079234-29079240 Template switch process: F1: L AGAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC 1 F3: 4 CACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA R RF: AGAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCCTTCTACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA RR: TCTCTAAGTCGTATTTTATACCTTCCCCTACAAACTGAGGGAAGATGTGTTTCACTTAGACTTCGTCCAGGATCTCTGTCACGTT F2: 3 AGACTTC 2 Unidirectional alignment (log-probability: -27) GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC--CTtcagACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCCTTCT----ACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA Template switch alignment (log-probability: -16.1) GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC|CTTCAGA|CACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC|CTTCAGA|CACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA Gorilla > Human --------------- chr7:29079234-29079240 Template switch process: F1: L AGAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC 1 F3: 4 CACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA R RF: AGAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCCTTCTACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA RR: TCTCTAAGTCGTATTTTATACCTTCCCCTACAAACTGAGGGAAGATGTGTTTCACTTAGACTTCGTCCAGGATCTCTGTCACGTT F2: 3 AGACTTC 2 Unidirectional alignment (log-probability: -26.5) GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC--CTtcagACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCCTTCT----ACACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA Template switch alignment (log-probability: -16.6) GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC|CTTCAGA|CACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA GAGATTCAGCATAAAATATGGAAGGGGATGTTTGACTCCC|CTTCAGA|CACAAAGTGAATCTGAAGCAGGTCCTAGAGACAGTGCAA ========== Event 3378 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTGTGCCAGGGAGGGAGAGAAAGGTGGA------------A----------TGCTTGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACTT ↑ 1 4 3 2 Chimp: cctgtgccagggagggagagaaaggTGGA------GATAAAA-----GGGTTGGAATGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACTT Gorilla: CCTGTGCCAGGGAGGGAGAGATAGGTGGAGATAAA------AGGGTT-----GGAATGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACTT ↓ 1 4 3 2 Human: CCTGTGCCAGGGAGGGAGAGAAAGGTGGA------------A----------TGCTTGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACTT Cluster: [ ] Orangutan: CCTGTGCCAGGGAGGGAGAGAAAGGTGGAGGTGAA------AGGGTT-----GGAATGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGAAGACTT Chimp > Human ------------- chr7:130009120-130009124 Template switch process: F1: L AGTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGGTGGA 1 F3: 4 TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT R RF: AGTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGGTGGAGATAAAAGGGTTGGAATGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT RR: TCAAACGGTCCGGGACACGGTCCCTCCCTCTCTTTCCACCTCTATTTTCCCAACCTTACAACAAAAGTGAAGTTCGTAAGACTCTTCGTTCCTCTGA F2: 3 TCGTA 2 Unidirectional alignment (log-probability: -27.7) GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGG---------------TGGAAtgctTGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGGTGGAGATAAAAGGGTTGGAA----TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT Template switch alignment (log-probability: -15.9) GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGGTGGA|ATGCT|TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGGTGGA|ATGCT|TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT Gorilla > Human --------------- chr7:130009120-130009124 Template switch process: F1: L TGAGTAGGAGTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAAAGGTGGA 1 F3: 4 TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT R RF: TGAGTAGGAGTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGATAGGTGGAGATAAAAGGGTTGGAATGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT RR: ACTCATCCTCAAACGGTCCGGGACACGGTCCCTCCCTCTCTATCCACCTCTATTTTCCCAACCTTACAACAAAAGTGAAGTTCGTAAGACTCTTCGTTCCTCTGA F2: 3 TCGTA 2 Unidirectional alignment (log-probability: -32.8) GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAaAGG---------------TGGAAtgctTGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGATAGGTGGAGATAAAAGGGTTGGAA----TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT Template switch alignment (log-probability: -22.1) GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGAaAGGTGGA|ATGCT|TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT GTTTGCCAGGCCCTGTGCCAGGGAGGGAGAGATAGGTGGA|ATGCT|TGTTGTTTTCACTTCAAGCATTCTGAGAAGCAAGGAGACT ========== Event 3379 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TTGAATCCAATAGCTATCAAATAGCCCATGACACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCACAGGCATGGCTTAGCTGAATGTTTTGACCTTTTAAAAATAATACTTGTAAGATGGATATCTGAAAATGGGCTAGGAACAATGGTACCCATTC Chimp: TTGAATCCAATAGCTATCAAA-TGTTGGGGACACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCACAGGCATGGCTTAGCTGAATGTTTTGACCTTTTAAAAATAATACTTGTAAGATGGATATCTGAAAATGGGCTAGGAACAATGGTACCCATTC ↓ 1 4 3 2 Gorilla: TTGAATCCAATAGCTATCAAATAGCCCATGATACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCACAGGCATGGCTTAGCTGAATGTTTTGACCTTTTAAAAATAATACTTGTAAGATGGATATCTGAAAATGGGCTAGGAACAATGGTACCCATTC Human: TTGAATCCAATAGCTATCAAATAGCCCATGACACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCACAGGCATGGCTTAGCTGAATGTTTTGACCTTTTAAAAATAATACTTGTAAGATGGATATCTGAAAATGGGCTAGGAACAATGGTACCCATTC Cluster: [ ] Orangutan: TTGAATCCAATAGCTATCAAATAGCCCATGACACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCACAGGCATGGCATAGCTGAATGTTTTGACCTTTTAAAAATAATACTTGTAAGATGGATATCTGAAAATGGGCTAGGAACAATGGTACCCATTC Chimp > Gorilla --------------- chr7:129560626-129560632 Template switch process: F1: L CCCAGGGAGAAATGCATTGTTTGAATCCAATAGCTATCAAAT 1 F3: 4 GATACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCAC R RF: TCCAGGGAGAAATGCATTGTTTGAATCCAATAGCTATCAAATGTTGGGGACACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCACCACAGGCATGGCTTAGCTGAATGTTTTGACCTTTTAAAAATAATACTTGTAAGATGGATATCTGAAAATGGGCT RR: AGGTCCCTCTTTACGTAACAAACTTAGGTTATCGATAGTTTACAACCCCTGTGGGGAGGGGTTGGAGACCACGGACGGTGAACAAGTGGTGTCCGTACCGAATCGACTTACAAAACTGGAAAATTTTTATTATGAACATTCTACCTATAGACTTTTACCCGA F2: 3 TACCCGA 2 Unidirectional alignment (log-probability: -41) CAGGGAGAAATGCATTGTTTGAATCCAATAGCTATCAAAT---------agcccatgatACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCAC CAGGGAGAAATGCATTGTTTGAATCCAATAGCTATCAAATGTTGGGGAC----------ACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCAC Template switch alignment (log-probability: -27.8) CAGGGAGAAATGCATTGTTTGAATCCAATAGCTATCAAAT|AGCCCAT|GAtACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCAC CAGGGAGAAATGCATTGTTTGAATCCAATAGCTATCAAAT|AGCCCAT|GACACCCCTCCCCAACCTCTGGTGCCTGCCACTTGTTCAC ========== Event 3380 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTTAAGTGGGTGCTGTCCTCAGCCTGCCTGCCAGGGATGTGGGAGAGGCAGATGGTGAAACTGTGATTGGCTCTGGAAGCTAAAACTAATACAACACTCCCTGCCCACCCCACCAGCTGAGGTGCGGCACCAAGGAACTCAC--TCTGGGGGGATGTCCTAAACCAAACC Chimp: A-TTAAGTGGGTGCTGTCCTCAGCCTGCCTGCCAGGGGTGTGGGAGAGGCAGATGGTGAAACTATGATTGGCTCTGGAAGCTAAAACTAATACAACACTCCCTGCCCACCCCGCCAGCCGAGGTGCGGCACCAAGGAACTCAC--TCTGGGGGGATGTCCTAAACCAAACC ↓ 3 2 1 4 Gorilla: A-TTAAGTGGGTGCTGTCCTCAGCCTGCCTGCCAGGGATGTGGGAGAGGCAGATGGTGAAACTGTGATTGGCTCTGGAAGCTAAAACTAATACAACACTCCCTGCCCACCCCGCCAGCCGAGGTGCAGCACCAAGGAACTCACTCTCTGAGGGGATGTCCTAAACCAAACC Human: ATTTAAGTGGGTGCTGTCCTCAGCCTGCCTGCCAGGGATGTGGGAGAGGCAGATGGTGAAACTGTGATTGGCTCTGGAAGCTAAAACTAATACAACACTCCCTGCCCACCCCACCAGCTGAGGTGCGGCACCAAGGAACTCAC--TCTGGGGGGATGTCCTAAACCAAACC Cluster: [ ] Orangutan: A-TTAAGTGGATGCTGTCCTCAGCCTGCCTGCCAGGGATGTGGGAGAGGCAGATGGTGAAACTGTGGTCGGCTCTGGAAGCTAAAACTAATACAACACTCCCTGCCCATCCCACCAGCCGAGGTGCAGCACCAAGGAACTCACTCTCTGGGGGGATGTCCTAAACCAAACC Chimp > Gorilla --------------- chr7:3008090-3008093 Template switch process: F1: L TGCCCACCCCGCCAGCCGAGGTGCAGCACCAAGGAACTCACTCT 1 F3: 4 GGGGATGTCCTAAACCAAACCCTGGTTTGGTTTATAGCTT R RF: TCAGCCTGCCTGCCAGGGGTGTGGGAGAGGCAGATGGTGAAACTATGATTGGCTCTGGAAGCTAAAACTAATACAACACTCCCTGCCCACCCCGCCAGCCGAGGTGCGGCACCAAGGAACTCACTCTGGGGGGATGTCCTAAACCAAACCCTGGTTTGGTTTATAACTT RR: AGTCGGACGGACGGTCCCCACACCCTCTCCGTCTACCACTTTGATACTAACCGAGACCTTCGATTTTGATTATGTTGTGAGGGACGGGTGGGGCGGTCGGCTCCACGCCGTGGTTCCTTGAGTGAGACCCCCCTACAGGATTTGGTTTGGGACCAAACCAAATATTGAA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -38.6) CACCCCGCCAGCCGAGGTGCaGCACCAAGGAACTCActCTCTGaGGGGATGTCCTAAACCAAACCCTGGTTTGGTTTATAgCTt CACCCCGCCAGCCGAGGTGCGGCACCAAGGAACTCA--CTCTGGGGGGATGTCCTAAACCAAACCCTGGTTTGGTTTATAACT- Template switch alignment (log-probability: -27.3) CACCCCGCCAGCCGAGGTGCaGCACCAAGGAACTCACTCT|CTGA|GGGGATGTCCTAAACCAAACCCTGGTTTGGTTTATAgCTT CACCCCGCCAGCCGAGGTGCGGCACCAAGGAACTCACTCT|CTGA|GGGGATGTCCTAAACCAAACCCTGGTTTGGTTTATAACTT ========== Event 3381 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCAGATTTAAATAAAAATATAAAAGACAACATATTATGTTAAATAATATGTTGTCTTTTATATTTGCCCAGTGAGCAGAAGC ↑ 3 1 2 4 Chimp: TCCAGATTTAAATAAAAATATAAAAGACAACATATTATTTA--AC----------------AATTTGCCCAGTGAGCAGAAGC Gorilla: TCCAGATTTAAATAAAAATATAAAAGACAACATATTATTTA--AC----------------AATTTGCCCAGTGAGCAGAAGC ↓ 3 1 2 4 Human: TCCAGATTTAAATAAAAATATAAAAGACAACATATTATGTTAAATAATATGTTGTCTTTTATATTTGCCCAGTGAGCAGAAGC Cluster: [ ] Orangutan: TCCAGATTTAAATAAAAATATAAAAGAAAACATATTATTTA--AC----------------AATTTGCCCGGTGAGCAGAAGC Chimp > Human ------------- chr7:129183969-129183992 Template switch process: F1: L TAATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT 1 F3: 4 ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG R RF: TAATCCAGATTTAAATAAAAATATAAAAGACAACATATTATTTAACAATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG RR: ATTAGGTCTAAATTTATTTTTATATTTTCTGTTGTATAATAAATTGTTAAACGGGTCACTCGTCTTCGATATCTATAAAATGGTACC F2: 3 TATTTTCTGTTGTATAATAAATTG 2 Unidirectional alignment (log-probability: -54.5) AATCCAGATTTAAATAAAAATATAAAAGACAACATATTATgttaaataatatgttgtcttttaT-----ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG AATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT-----------------------TTAACAATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG Template switch alignment (log-probability: -18.2) AATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT|GTTAAATAATATGTTGTCTTTTAT|ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG AATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT|GTTAAATAATATGTTGTCTTTTAT|ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG Gorilla > Human --------------- chr7:129183969-129183992 Template switch process: F1: L TAATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT 1 F3: 4 ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG R RF: TAATCCAGATTTAAATAAAAATATAAAAGACAACATATTATTTAACAATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG RR: ATTAGGTCTAAATTTATTTTTATATTTTCTGTTGTATAATAAATTGTTAAACGGGTCACTCGTCTTCGATATCTATAAAATGGTACC F2: 3 TATTTTCTGTTGTATAATAAATTG 2 Unidirectional alignment (log-probability: -53.4) AATCCAGATTTAAATAAAAATATAAAAGACAACATATTATgTtAaAtaatatgttgtcttttatATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG AATCCAGATTTAAATAAAAATATAAAAGACAACATATTATTTAACA------------------ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG Template switch alignment (log-probability: -18.8) AATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT|GTTAAATAATATGTTGTCTTTTAT|ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG AATCCAGATTTAAATAAAAATATAAAAGACAACATATTAT|GTTAAATAATATGTTGTCTTTTAT|ATTTGCCCAGTGAGCAGAAGCTATAGATATTTTACCATGG ========== Event 3382 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tttttttGTAAATTATGACATACACATTCACATTTGGAAATATAAAAAGTACAGGAAagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACCGGAAAGCACATAATTCCATGTCCCCTGAAGGAAATTATATACATTAGGC Chimp: -ttttttGTAAATTATGAAATACACATTCACATTTGGAAATTTAAAAAGTACAGG---------------------------------------------------------------------------------------------------AAAGCACATAATTCCATGTCCCCTGAAGGAAACTATATACATTAGGC ↓ 1 4 3 2 Gorilla: -ttttttGCAAATTATGAAATTTCAGGTCACATTTGGAAATTTAAAAAGTTCAGG---------------------------------------------------------------------------------------------------AAAGCACATAATTCCATGTCCCCTGAAGGAAACTATATACATTAGGC Human: tttttttGTAAATTATGACATACACATTCACATTTGGAAATATAAAAAGTACAGGAAagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTACCGGAAAGCACATAATTCCATGTCCCCTGAAGGAAATTATATACATTAGGC Cluster: [ ] Orangutan: -ttttttGTAAATTATGAAATACACATTCACATTTGGAAATTTAAAAAGTACAGG---------------------------------------------------------------------------------------------------AAAGCACATAATTCCATGTCCCCTGAAGGAAACTATATACATTTGGC Chimp > Gorilla --------------- chr7:3191634-3191639 Template switch process: F1: L AGCTTTATTAGTGTTTTGGTTTTTTTTGCAAATTATGAAAT 1 F3: 4 TCACATTTGGAAATTTAAAAAGTTCAGGAAAGCACATAAT R RF: AGCTTTATTAGTGTTTTGGTTTTTTTTGTAAATTATGAAATACACATTCACATTTGGAAATTTAAAAAGTACAGGAAAGCACATAATTCCATGTCCCCTGAA RR: TCGAAATAATCACAAAACCAAAAAAAACATTTAATACTTTATGTGTAAGTGTAAACCTTTAAATTTTTCATGTCCTTTCGTGTATTAAGGTACAGGGGACTT F2: 3 GGACTT 2 Unidirectional alignment (log-probability: -39.1) GCTTTATTAGTGTTTTGGTTTTTTTTGcAAATTATGAAAT-----TtcaggTCACATTTGGAAATTTAAAAAGTtCAGGAAAGCACATAAT GCTTTATTAGTGTTTTGGTTTTTTTTGTAAATTATGAAATACACAT-----TCACATTTGGAAATTTAAAAAGTACAGGAAAGCACATAAT Template switch alignment (log-probability: -27.5) GCTTTATTAGTGTTTTGGTTTTTTTTGcAAATTATGAAAT|TTCAGG|TCACATTTGGAAATTTAAAAAGTtCAGGAAAGCACATAAT GCTTTATTAGTGTTTTGGTTTTTTTTGTAAATTATGAAAT|TTCAGG|TCACATTTGGAAATTTAAAAAGTACAGGAAAGCACATAAT ========== Event 3383 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTGGCCACAAAAGAAGTACC-----ATGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAG Chimp: TCTGGCCACAAAAGAAGTACC-----ATGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAG ↓ 1 34 2 Gorilla: TCTGGCCACAAAAGAAGTACCAGATTCTTGACAGACTGTCAAGAATCCCTTTGAAGGGAAACATCAG ↑ 1 34 2 Human: TCTGGCCACAAAAGAAGTACC-----ATGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAG Cluster: [ ] Orangutan: TCTGGCCACAAAAGAAGTACC-----ATGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAG Human > Gorilla --------------- chr7:32590855-32590867 Template switch process: F1: L ATAAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA 1 F3: 4 CTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA R RF: ATAAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCATGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA RR: TATTTTACAGAAGGTCGAGGAGACCGGTGTTTTCTTCATGGTACCTGTCAGACAGTTCTTAGGGAAACTTCCCTTTGTAGTCGGAGGAGT F2: 3 AGACAGTTCTTAG 2 Unidirectional alignment (log-probability: -29.2) AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCAgattcTtGACAGaCTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA-----TGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA Template switch alignment (log-probability: -17.4) AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA|GATTCTTGACAGA|CTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA|GATTCTTGACAGA|CTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA Chimp > Gorilla --------------- chr7:32590855-32590867 Template switch process: F1: L ATAAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA 1 F3: 4 CTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA R RF: ATAAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCATGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA RR: TATTTTACAGAAGGTCGAGGAGACCGGTGTTTTCTTCATGGTACCTGTCAGACAGTTCTTAGGGAAACTTCCCTTTGTAGTCGGAGGAGT F2: 3 AGACAGTTCTTAG 2 Unidirectional alignment (log-probability: -29.2) AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCAgattcTtGACAGaCTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA-----TGGACAGTCTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA Template switch alignment (log-probability: -17.4) AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA|GATTCTTGACAGA|CTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA AAAATGTCTTCCAGCTCCTCTGGCCACAAAAGAAGTACCA|GATTCTTGACAGA|CTGTCAAGAATCCCTTTGAAGGGAAACATCAGCCTCCTCA ========== Event 3384 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTGCCCTTTTGATATATCTCATTGTGTTCAGACAAACACTTCCTTTCAAACACAAAAA Chimp: CTGCCCTTTTGATATATCTCATTGTGTTCAGACAAACACTTCCTTTCAAACACAAAAA ↑ 1 3 4 2 Gorilla: CTGCCCTTTTGATATATCTCACTGGTGTCT---GAACACTTCCTTTCAAACACAAAAA ↓ 1 3 4 2 Human: CTGCCCTTTTGATATATCTCATTGTGTTCAGACAAACACTTCCTTTCAAACACAAAAA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr7:126700151-126700160 Template switch process: F1: L TATGATTTTGGCACTCTTTTCTGCCCTTTTGATATATCTCATTG 1 F3: 4 AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT R RF: TATGATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCACTGGTGTCTGAACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT RR: ATACTAAAACCGTGATAAAAGACGGGAAAACTATATAGAGTGACCACAGACTTGTGAAGGAAAGTTTGTGTTTTTCCAAGGTCTTTGTTTA F2: 3 ACAGACTTGT 2 Unidirectional alignment (log-probability: -43.5) ATTTTGGCACTcTTTTCTGCCCTTTTGATATATCTCAtTG-----TGttcagacaAACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT ATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCACTGGTGTCTG--------AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT Template switch alignment (log-probability: -28.1) ATTTTGGCACTcTTTTCTGCCCTTTTGATATATCTCAtTG|TGTTCAGACA|AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT ATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCACTG|TGTTCAGACA|AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT Gorilla > Chimp --------------- chr7:134414582-134414591 Template switch process: F1: L TATGATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCATTG 1 F3: 4 AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT R RF: TATGATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCACTGGTGTCTGAACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT RR: ATACTAAAACCGTGATAAAAGACGGGAAAACTATATAGAGTGACCACAGACTTGTGAAGGAAAGTTTGTGTTTTTCCAAGGTCTTTGTTTA F2: 3 ACAGACTTGT 2 Unidirectional alignment (log-probability: -38) ATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCAtTG-----TGttcagacaAACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT ATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCACTGGTGTCTG--------AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT Template switch alignment (log-probability: -22.6) ATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCAtTG|TGTTCAGACA|AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT ATTTTGGCACTATTTTCTGCCCTTTTGATATATCTCACTG|TGTTCAGACA|AACACTTCCTTTCAAACACAAAAAGGTTCCAGAAACAAAT ========== Event 3385 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTTCTGTTTCATAAACCTTCTCATAAATCTGAAACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTC ↑ 1 4 3 2 Chimp: TGTTCTGTTTCATAAACCTTCCC----ATCTTTGACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTC Gorilla: TGTTCTGTTTCATAAACCTTCCC----ATCTTTGACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTC ↓ 1 4 3 2 Human: TGTTCTGTTTCATAAACCTTCTCATAAATCTGAAACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTC Cluster: [ ] Orangutan: TGTTCTGTTTCATAAACCTTCCC----ATCTTTGACTTTGGACTTTCAGATTTACCCCAGGAAGAAGTATTTC Chimp > Human ------------- chr7:34563553-34563561 Template switch process: F1: L ATGGTTTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCTCAT 1 F3: 4 ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA R RF: ATGGTTTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCCCATCTTTGACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA RR: TACCAAAAACGAAAACATAAACAAGACAAAGTATTTGGAAGGGTAGAAACTGAAATCTGAAAGTCTAAATGGGGTCCTTCTTCATAAAGT F2: 3 AAGTCTAAA 2 Unidirectional alignment (log-probability: -40.3) TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTC---------tcataaatctgaaACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCCCATCTTTG-------------ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA Template switch alignment (log-probability: -22.5) TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCtCAT|AAATCTGAA|ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCCCAT|AAATCTGAA|ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA Gorilla > Human --------------- chr7:34563553-34563561 Template switch process: F1: L ATGGTTTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCTCAT 1 F3: 4 ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA R RF: ATGGTTTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCCCATCTTTGACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA RR: TACCAAAAACGAAAACATAAACAAGACAAAGTATTTGGAAGGGTAGAAACTGAAATCTGAAAGTCTAAATGGGGTCCTTCTTCATAAAGT F2: 3 AAGTCTAAA 2 Unidirectional alignment (log-probability: -38.8) TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCtCataaATCTgaaACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCCC----ATCTTTGACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA Template switch alignment (log-probability: -22.5) TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCtCAT|AAATCTGAA|ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA TTTTGCTTTTGTATTTGTTCTGTTTCATAAACCTTCCCAT|AAATCTGAA|ACTTTAGACTTTCAGATTTACCCCAGGAAGAAGTATTTCA ========== Event 3386 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTCAAAGTTGATGACAAGCTAACCTACGTTATC--CAATCTCCCCCACCCTTAAGCCAG Chimp: TCTCAAAGTTGATGACAAGCTGACCT--ATTAACATAGGTCTCCCCCACCCTTAAGCCAG ↑ 3 1 2 4 Gorilla: TCTCAAAGTTGATGACAAGCTAACCTATGTTATC--CAATCTCCCCCACCCTTAAGCCAG Human: TCTCAAAGTTGATGACAAGCTAACCTACGTTATC--CAATCTCCCCCACCCTTAAGCCAG Cluster: [ ] Orangutan: TCTCAAAGTTGATGACAAGCTAACCTATGTTATC--CAATCTCCCCCACCCTTAAGCCAG Gorilla > Chimp --------------- chr7:132635315-132635323 Template switch process: F1: L AAAAGTTCAAATGGAGATTTTCTCAAAGTTGATGACAAGCTGACCTAT 1 F3: 4 TCTCCCCCACCCTTAAGCCAGGTTTTCTGAACATGGTTCT R RF: AAAAGTTCAAATGGAGATTTTCTCAAAGTTGATGACAAGCTAACCTATGTTATCCAATCTCCCCCACCCTTAAGCCAGGTTTTCTGAACATGGCTCT RR: TTTTCAAGTTTACCTCTAAAAGAGTTTCAACTACTGTTCGATTGGATACAATAGGTTAGAGGGGGTGGGAATTCGGTCCAAAAGACTTGTACCGAGA F2: 3 GGATACAAT 2 Unidirectional alignment (log-probability: -43.7) AAATGGAGATTTTCTCAAAGTTGATGACAAGCTgACCTATtaacatagG--------TCTCCCCCACCCTTAAGCCAGGTTTTCTGAACATGGtTCT AAATGGAGATTTTCTCAAAGTTGATGACAAGCTAACCTAT--------GTTATCCAATCTCCCCCACCCTTAAGCCAGGTTTTCTGAACATGGCTCT Template switch alignment (log-probability: -28.1) AAATGGAGATTTTCTCAAAGTTGATGACAAGCTgACCTAT|TAACATAGG|TCTCCCCCACCCTTAAGCCAGGTTTTCTGAACATGGtTCT AAATGGAGATTTTCTCAAAGTTGATGACAAGCTAACCTAT|TAACATAGG|TCTCCCCCACCCTTAAGCCAGGTTTTCTGAACATGGCTCT ========== Event 3387 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAAAGGAGGAGGAGTCCTTGACCAGAGTAC-TTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTC ↑ 1 4 3 2 Chimp: TAAAGGAGGAGGAGTCCTTGA---CAGTGCTTTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTC Gorilla: TAAAGGAGGAGGAGTCCTTGA---CAGTGCTTTCCAGGTAGTACTGTGAATTTACAACAGGGCTATTC Human: TAAAGGAGGAGGAGTCCTTGACCAGAGTAC-TTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTC Cluster: [ ] Orangutan: TAAATGAGGAGGAGTCCTTGA---CAGTGCTTTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTC Chimp > Human ------------- chr7:35902929-35902936 Template switch process: F1: L GCCTTTTGGGTGGCAGGTCCTAAAGGAGGAGGAGTCCTTGAC 1 F3: 4 TTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTCAAA R RF: GCCTTTTGGGTGGCAGGTCCTAAAGGAGGAGGAGTCCTTGACAGTGCTTTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTCAAA RR: CGGAAAACCCACCGTCCAGGATTTCCTCCTCCTCAGGAACTGTCACGAAAGGTCCATCATGAGACTTAAATGTTGTCCCGATAAGTTT F2: 3 CATGAGAC 2 Unidirectional alignment (log-probability: -31.5) CTTTTGGGTGGCAGGTCCTAAAGGAGGAGGAGTCCTTGACcagAGTaC-TTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTCAAA CTTTTGGGTGGCAGGTCCTAAAGGAGGAGGAGTCCTTGAC---AGTGCTTTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTCAAA Template switch alignment (log-probability: -16.3) CTTTTGGGTGGCAGGTCCTAAAGGAGGAGGAGTCCTTGAC|CAGAGTAC|TTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTCAAA CTTTTGGGTGGCAGGTCCTAAAGGAGGAGGAGTCCTTGAC|CAGAGTAC|TTCCAGGTAGTACTCTGAATTTACAACAGGGCTATTCAAA ========== Event 3388 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAATATCTTGAATGTGAGATAAGCATT------ATTTCAAGATGTTCTTGCCTAACTAATCACAAAGCAACTA Chimp: AAATACCTTGAATGTGAGATAGGCAAG---AACACCTTGAAA---TAATGCTTAACTAATCACAAAGCAACTA Gorilla: AAATATCTTGAATGTGAGATAGGCAAGAAC---ACCTTGAAA---TAATGCTTAACTAATCACAAAGCAACTA ↓ 13 24 ↑ 13 24 Human: AAATATCTTGAATGTGAGATAAGCATT------ATTTCAAGATGTTCTTGCCTAACTAATCACAAAGCAACTA Cluster: [ ] Orangutan: AAATATCTTGAATGTGAGATAGGCAAGAAC---ACCTTGAAA---TAATGCTTAACTAATCACAAAGCAACTA Gorilla > Human --------------- chr7:155703292-155703316 Template switch process: F1: L AAACCTGTCGGGCATTAGATAAATATCTTGAATGTGAGATA 1 F3: 4 TAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA R RF: AAACCTGTCTGGCATTAGATAAATATCTTGAATGTGAGATAGGCAAGAACACCTTGAAATAATGCTTAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA RR: TTTGGACAGACCGTAATCTATTTATAGAACTTACACTCTATCCGTTCTTGTGGAACTTTATTACGAATTGATTAGTGTTTCGTTGATAAGACGTTATCTACCCACT F2: 3 CCGTTCTTGTAGAACTTTATTACGA 2 Unidirectional alignment (log-probability: -61.5) AACCTGTCgGGCATTAGATAAATATCTTGAATGTGAG--------------------ATAAgcattatttcaagatgttctTGCcTAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA AACCTGTCTGGCATTAGATAAATATCTTGAATGTGAGATAGGCAAGAACACCTTGAAATAA--------------------TGCTTAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA Template switch alignment (log-probability: -29.9) AACCTGTCgGGCATTAGATAAATATCTTGAATGTGAGATA|AGCATTATTTCAAGaTGTTCTTGCC|TAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA AACCTGTCTGGCATTAGATAAATATCTTGAATGTGAGATA|AGCATTATTTCAAGGTGTTCTTGCC|TAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA Human > Gorilla --------------- chr7:155588084-155588108 Template switch process: F1: L AAACCTGTCTGGCATTAGATAAATATCTTGAATGTGAGATA 1 F3: 4 TAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA R RF: AAACCTGTCGGGCATTAGATAAATATCTTGAATGTGAGATAAGCATTATTTCAAGATGTTCTTGCCTAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA RR: TTTGGACAGCCCGTAATCTATTTATAGAACTTACACTCTATTCGTAATAAAGTTCTACAAGAACGGATTGATTAGTGTTTCGTTGATAAGACGTTATCTACCCACT F2: 3 TCGTAATAAAGTTCCACAAGAACGG 2 Unidirectional alignment (log-probability: -61.5) AACCTGTCtGGCATTAGATAAATATCTTGAATGTGAGataggcaagaacaccttgaaATAA--------------------TGCtTAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA AACCTGTCGGGCATTAGATAAATATCTTGAATGTGAG--------------------ATAAGCATTATTTCAAGATGTTCTTGCCTAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA Template switch alignment (log-probability: -29.9) AACCTGTCtGGCATTAGATAAATATCTTGAATGTGAGATA|GGCAAGAACAcCTTGAAATAATGCT|TAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA AACCTGTCGGGCATTAGATAAATATCTTGAATGTGAGATA|GGCAAGAACATCTTGAAATAATGCT|TAACTAATCACAAAGCAACTATTCTGCAATAGATGGGTGA ========== Event 3389 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTAAATGGATACATATTGCTGTACTG----CAATGTTCTTAATTCAAGCACATTTCCATAGAAGGCTTTCTGT ↑ 1 3 4 2 Chimp: CTTAAATGGATACATATTGCTATACTG--CATAATGTGCTTGATTTAAGAACATTTCCATAGAAGGCTTTCTGT Gorilla: CTTAAATGGATACATATTGCTGTACTGCA--TAATGTGCTTGATTTAAGAACATTTCCATAGAAGGCTTTCTGT ↓ 1 3 4 2 Human: CTTAAATGGATACATATTGCTGTACTG----CAATGTTCTTAATTCAAGCACATTTCCATAGAAGGCTTTCTGT Cluster: [ ] Orangutan: CTTAAATGGATACATATTGCTGTACTGCA--TAATGTGCTTGATTTAAGAACATTTCCACAGAAGGCTTTCTGT Chimp > Human ------------- chr7:37579413-37579429 Template switch process: F1: L TTGGTTATATCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCA 1 F3: 4 ACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT R RF: TTGGTTATATCTGAAGTCTACTTAAATGGATACATATTGCTATACTGCATAATGTGCTTGATTTAAGAACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT RR: AACCAATATAGACTTCAGATGAATTTACCTATGTATAACGATATGACGTATTACACGAACTAAATTCTTGTAAAGGTATCTTCCGAAAGACATACCTGGATAAGAAAA F2: 3 CGAACTTAATTCTTGTA 2 Unidirectional alignment (log-probability: -41.2) TCTGAAGTCTACTTAAATGGATACATATTGCTgTACTGC--AATGTtCTTaATTcAAGcACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT TCTGAAGTCTACTTAAATGGATACATATTGCTATACTGCATAATGTGCTTGATTTAAGAACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT Template switch alignment (log-probability: -29.5) TCTGAAGTCTACTTAAATGGATACATATTGCTgTACTGCA|ATGTTCTTAAtTCAAGC|ACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT TCTGAAGTCTACTTAAATGGATACATATTGCTATACTGCA|ATGTTCTTAAATCAAGC|ACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT Gorilla > Human --------------- chr7:37579413-37579429 Template switch process: F1: L ATATCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCA 1 F3: 4 ACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT R RF: ATATCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCATAATGTGCTTGATTTAAGAACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT RR: TATAGACTTCAGATGAATTTACCTATGTATAACGACATGACGTATTACACGAACTAAATTCTTGTAAAGGTATCTTCCGAAAGACATACCTGGATAAGAAAA F2: 3 CGAACTTAATTCTTGTA 2 Unidirectional alignment (log-probability: -33.3) TCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCA--ATGTtCTTaATTcAAGcACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT TCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCATAATGTGCTTGATTTAAGAACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT Template switch alignment (log-probability: -23.5) TCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCA|ATGTTCTTAAtTCAAGC|ACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT TCTGAAGTCTACTTAAATGGATACATATTGCTGTACTGCA|ATGTTCTTAAATCAAGC|ACATTTCCATAGAAGGCTTTCTGTATGGACCTATTCTTTT ========== Event 3390 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCAGTTTTGACAGTGCCATTGCAATACCT---GCTACACCATCTCTCCTTCTGGAATTAAAATTC Chimp: TCAGTTTTGACAGTGCCATTGCAATACCT---GCTACACCATCTCTCCTTCTGGAATTAAAATTC ↓ 3 2 1 4 Gorilla: TCAGTTTTGACAGTGCCATTGCAATACCA------TTGCAATCTTTCCTTCTGGAATTAAAATTC ↑ 3 2 1 4 Human: TCAGTTTTGACAGTGCCATTGCAATACCT---GCTACACCATCTCTCCTTCTGGAATTAAAATTC Cluster: [ ] Orangutan: TCAGTTTTGACAGTGCCATTGCAATACCTGCT---ACACCATCTCTCCTTCTGGAATTAAAATTC Human > Gorilla --------------- chr7:37198927-37198932 Template switch process: F1: L AACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC 1 F3: 4 ATCTTTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAGAAAGA R RF: AACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACCTGCTACACCATCTCTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAGAAAGA RR: TTGAACTCCTACCAGTCAAAACTGTCACGGTAACGTTATGGACGATGTGGTAGAGAGGAAGACCTTAATTTTAAGGGACCTGTCTCTCTCTTTCT F2: 3 ACGTTA 2 Unidirectional alignment (log-probability: -34.9) ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACCatTG-----CaATCTtTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAG ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC--TGCTACACCATCTCTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAG Template switch alignment (log-probability: -22.1) ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC|ATTGCA|ATCTtTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAG ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC|ATTGCA|ATCTCTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAG Chimp > Gorilla --------------- chr7:37198927-37198932 Template switch process: F1: L AACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC 1 F3: 4 ATCTTTCCTTCTGGAATTAAAATTCCCTGGACAGAGAGAGAAAGA R RF: AACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACCTGCTACACCATCTCTCCTTCTGGAATTAAAATTCCCTGGACAGAGACAGAAAGA RR: TTGAACTCCTACCAGTCAAAACTGTCACGGTAACGTTATGGACGATGTGGTAGAGAGGAAGACCTTAATTTTAAGGGACCTGTCTCTGTCTTTCT F2: 3 ACGTTA 2 Unidirectional alignment (log-probability: -40.4) ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACCatTG-----CaATCTtTCCTTCTGGAATTAAAATTCCCTGGACAGAGAgAG ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC--TGCTACACCATCTCTCCTTCTGGAATTAAAATTCCCTGGACAGAGACAG Template switch alignment (log-probability: -27.6) ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC|ATTGCA|ATCTtTCCTTCTGGAATTAAAATTCCCTGGACAGAGAgAG ACTTGAGGATGGTCAGTTTTGACAGTGCCATTGCAATACC|ATTGCA|ATCTCTCCTTCTGGAATTAAAATTCCCTGGACAGAGACAG ========== Event 3391 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGCTATAAAGGGAGTGACATGGAAGCA----------------AAACTAATGAAAGAGGAGCCTAAAGGGTGAGGTTCTGCAGGATTAAT Chimp: gtgctataaagggagtgacatggAAGCA----------------AAACTAATGAAAGAGGAGCCTAAAGGGTGAGGTTCTGCAGGATTAAT ↓ 3 1 2 4 Gorilla: gtgctataaagggagtgacatggAAGTT--------------------------------TGCT-TCCATGTGAGGTTCTGCAGGATTAAT ↑ 3 1 2 4 Human: GTGCTATAAAGGGAGTGACATGGAAGCA----------------AAACTAATGAAAGAGGAGCCTAAAGGGTGAGGTTCTGCAGGATTAAT Cluster: [ ] Orangutan: CCGCTATAAAGGGAGTGACATGGAAGCAAAACTAATGAAAGAGG----------------AGCCTAAAGGGAGAGGTTCTGCAGGATTAAT Human > Gorilla --------------- chr7:37544349-37544359 Template switch process: F1: L ATAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAG 1 F3: 4 GTGAGGTTCTGCAGGATTAATCCGGGGATAAGTGGGCAAG R RF: ATAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAGCAAAACTAATGAAAGAGGAGCCTAAAGGGTGAGGTTCTGCAGGATTAATCCAGGGATAAGTGGGCAAG RR: TATTAAGGTTTGATTCACGATATTTCCCTCACTGTACCTTCGTTTTGATTACTTTCTCCTCGGATTTCCCACTCCAAGACGTCCTAATTAGGTCCCTATTCACCCGTTC F2: 3 TACCTTCGTTT 2 Unidirectional alignment (log-probability: -43.4) TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAA----------------------------GtttgcttccatGTGAGGTTCTGCAGGATTAATCCgGGGATAAGTGGGCAAG TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAGCAAAACTAATGAAAGAGGAGCCTAAAGG-----------GTGAGGTTCTGCAGGATTAATCCAGGGATAAGTGGGCAAG Template switch alignment (log-probability: -22.6) TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAG|TTTGCTTCCAT|GTGAGGTTCTGCAGGATTAATCCgGGGATAAGTGGGCAAG TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAG|TTTGCTTCCAT|GTGAGGTTCTGCAGGATTAATCCAGGGATAAGTGGGCAAG Chimp > Gorilla --------------- chr7:37544349-37544359 Template switch process: F1: L ATAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAG 1 F3: 4 GTGAGGTTCTGCAGGATTAATCCGGGGATAAGTGGGCAAG R RF: ATAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAGCAAAACTAATGAAAGAGGAGCCTAAAGGGTGAGGTTCTGCAGGATTAATCCAGGGATAAGTGGGCAAG RR: TATTAAGGTTTGATTCACGATATTTCCCTCACTGTACCTTCGTTTTGATTACTTTCTCCTCGGATTTCCCACTCCAAGACGTCCTAATTAGGTCCCTATTCACCCGTTC F2: 3 TACCTTCGTTT 2 Unidirectional alignment (log-probability: -43.4) TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAA----------------------------GtttgcttccatGTGAGGTTCTGCAGGATTAATCCgGGGATAAGTGGGCAAG TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAGCAAAACTAATGAAAGAGGAGCCTAAAGG-----------GTGAGGTTCTGCAGGATTAATCCAGGGATAAGTGGGCAAG Template switch alignment (log-probability: -22.6) TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAG|TTTGCTTCCAT|GTGAGGTTCTGCAGGATTAATCCgGGGATAAGTGGGCAAG TAATTCCAAACTAAGTGCTATAAAGGGAGTGACATGGAAG|TTTGCTTCCAT|GTGAGGTTCTGCAGGATTAATCCAGGGATAAGTGGGCAAG ========== Event 3392 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTTTAACACTGATGTCATACAAAAGAAGCATGTCAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAATGAAATGGACTAATATCCTTGGCATAGTTGAGGTTTTGCATCTCAGTTCATCTTGCTGTGCACCAGCCTGTCAAATTGAAGTGATCTCAAAAATGGTGTGAAAAATACTGTCTGG ↑ 4 1 3 2 Chimp: TTTTAACACTGATGTCATACAA--------------AAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAATGAAATGGACTAATATCCTTGGCATAGTTGAGGTTTTGCATCTCAGTTCATCTTGCTGTGCGCCAGCCTGTCAAATTGAAGTGATCTCAAAAATGGTGTGAAAAATACTGTCTGG ↓ 4 1 3 2 Gorilla: TTTTAACACTGATGTCATACAAAAGAAGCATGTCAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAAGGAAATGGACTAATATCCTTGGCATAGTTGAGGTTTTGCATCTCAGTTCATCTTGCTGTGCACCAGCCTGTCAAACTGAAGTGATCTCAAAAATGGTGTGAAAAATACTGTCTGG Human: TTTTAACACTGATGTCATACAAAAGAAGCATGTCAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAATGAAATGGACTAATATCCTTGGCATAGTTGAGGTTTTGCATCTCAGTTCATCTTGCTGTGCACCAGCCTGTCAAATTGAAGTGATCTCAAAAATGGTGTGAAAAATACTGTCTGG Cluster: [ ] Orangutan: Chimp > Human ------------- chr7:121685781-121685785 Template switch process: F1: L AGAATACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAG 1 F3: 4 CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAA R RF: AGAATACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAATGAAATGGACTAATATCCTTGGCATAGTTGAGGTTTTGCATCTCAGTTCATCTTGCTGTGCGCCAGCCTGTCAAATTGAAGTGATCTCAAAAATG RR: TCTTATGTCATTCTTCAAAATTGTGACTACAGTATGTTTTCTTCAGTAAATATTCATGTCTCCACCACATGAGACTTTACTTTACCTGATTATAGGAACCGTATCAACTCCAAAACGTAGAGTCAAGTAGAACGACACGCGGTCGGACAGTTTAACTTCACTAGAGTTTTTAC F2: 3 TGTAC 2 Unidirectional alignment (log-probability: -31) TACAGTAAGAAGTTTTAACACTGATGTCATAcaaaagaagcatgtCAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG TACAGTAAGAAGTTTTAACACTGATGTCATA--------------CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG Template switch alignment (log-probability: -22) TACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAG|CATgT|CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG TACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAG|CATTT|CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG Chimp > Gorilla --------------- chr7:121007273-121007277 Template switch process: F1: L AGAATACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAG 1 F3: 4 CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAA R RF: AGAATACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTGAAATGAAATGGACTAATATCCTTGGCATAGTTGAGGTTTTGCATCTCAGTTCATCTTGCTGTGCGCCAGCCTGTCAAATTGAAGTGATCTCAAAAATG RR: TCTTATGTCATTCTTCAAAATTGTGACTACAGTATGTTTTCTTCAGTAAATATTCATGTCTCCACCACATGAGACTTTACTTTACCTGATTATAGGAACCGTATCAACTCCAAAACGTAGAGTCAAGTAGAACGACACGCGGTCGGACAGTTTAACTTCACTAGAGTTTTTAC F2: 3 TGTAC 2 Unidirectional alignment (log-probability: -31) TACAGTAAGAAGTTTTAACACTGATGTCATACAAAagaagcatgtcaaaAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG TACAGTAAGAAGTTTTAACACTGATGTCATACAAA--------------AGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG Template switch alignment (log-probability: -22) TACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAG|CATgT|CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG TACAGTAAGAAGTTTTAACACTGATGTCATACAAAAGAAG|CATTT|CAAAAGAAGTCATTTATAAGTACAGAGGTGGTGTACTCTG ========== Event 3393 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: AGGGGGCAACTCACAAACCCA---------------GAGGGAGAAGAAGAT--------------------AACAGCTACTACCAGTGGCATGCTT ↓ 1 3 4 2 Chimp: AGGGGGCAACTCACAAACCCA------------------------------GAGGGAGAAGCTGTTATCTTAACAGCTACTACCAGTGGCATGCTT Gorilla: ------------------------------------------------------------------------------------------------ Human: AGGGGGCAACTCACAAACCCA---------------GAGGGAGAAGAAGAT--------------------AACAGCTACTACCAGTGGCATGCTT Cluster: [ ] Orangutan: AGGGGGCAACTCACAAGCCCAGAGGGAGAAGAAGAT-----------------------------------AACAGCTACTACCAGTGGCATGCTT Human > Chimp ------------- chr7:37513501-37513509 Template switch process: F1: L TTCTGTAGACTGAAATGATTAGGGGGCAACTCACAAACCCAGAGGGAGAAG 1 F3: 4 TAACAGCTACTACCAGTGGCATGCTTTCTGCCAGTCTGGTT R RF: TTCTGTAGACTGAAATGATTAGGGGGCAACTCACAAACCCAGAGGGAGAAGAAGATAACAGCTACTACCAGTGGCATGCTTTCTGCCAGTCTGGTT RR: AAGACATCTGACTTTACTAATCCCCCGTTGAGTGTTTGGGTCTCCCTCTTCTTCTATTGTCGATGATGGTCACCGTACGAAAGACGGTCAGACCAA F2: 3 TCTATTGTC 2 Unidirectional alignment (log-probability: -34.4) GAAATGATTAGGGGGCAACTCACAAACCCAGAGGGAGAAGctgttatct----TAACAGCTACTACCAGTGGCATGCTTTCTGCCAGTCTGGT GAAATGATTAGGGGGCAACTCACAAACCCAGAGGGAGAAG---------AAGATAACAGCTACTACCAGTGGCATGCTTTCTGCCAGTCTGGT Template switch alignment (log-probability: -16.6) GAAATGATTAGGGGGCAACTCACAAACCCAGAGGGAGAAG|CTGTTATCT|TAACAGCTACTACCAGTGGCATGCTTTCTGCCAGTCTGGT GAAATGATTAGGGGGCAACTCACAAACCCAGAGGGAGAAG|CTGTTATCT|TAACAGCTACTACCAGTGGCATGCTTTCTGCCAGTCTGGT ========== Event 3394 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTATCTTAACACTTTGGAAGCATCCCAGAGCATG-GA--TACATTCAATCAAGAGTGAGACA ↓ 3 2 1 4 Chimp: TGTATCTTAACACTTTGGAAGCATCCCAGAGCATGGGATGCTCATTCAATCAAGAGTGAGACA ↑ 3 2 1 4 Gorilla: TGTATCTTAACACTTTGGAAGCATCCCAGAGCATG-GA--TACATTCAATCAAGAGTGAGACA Human: TGTATCTTAACACTTTGGAAGCATCCCAGAGCATG-GA--TACATTCAATCAAGAGTGAGACA Cluster: [ ] Orangutan: TATATCTTAACACTTTGGAAGCATCCCAGAGCATG-GA--TACATTCAATCAAGAGTGAGACA Human > Chimp ------------- chr7:37010662-37010667 Template switch process: F1: L GCACTATGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG 1 F3: 4 CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC R RF: GCACTGTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGGATACATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC RR: CGTGACACATAGAATTGTGAAACCTTCGTAGGGTCTCGTACCTATGTAAGTTAGTTCTCACTCTGTCTCACTCTGTACGTGTATG F2: 3 TCGTAG 2 Unidirectional alignment (log-probability: -35.9) ACTaTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG---gatgctCATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC ACTGTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGGATA------CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC Template switch alignment (log-probability: -22) ACTaTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG|GATGCT|CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC ACTGTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG|GATGCT|CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC Gorilla > Chimp --------------- chr7:37010662-37010667 Template switch process: F1: L GCACTATGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG 1 F3: 4 CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC R RF: GCACTGTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGGATACATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC RR: CGTGACACATAGAATTGTGAAACCTTCGTAGGGTCTCGTACCTATGTAAGTTAGTTCTCACTCTGTCTCACTCTGTACGTGTATG F2: 3 TCGTAG 2 Unidirectional alignment (log-probability: -34.9) ACTaTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG---gatgctCATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC ACTGTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGGATA------CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC Template switch alignment (log-probability: -22) ACTaTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG|GATGCT|CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC ACTGTGTATCTTAACACTTTGGAAGCATCCCAGAGCATGG|GATGCT|CATTCAATCAAGAGTGAGACAGAGTGAGACATGCACATAC ========== Event 3395 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGTCATAGTCATCATCTGAAATTTGTTCattt ↑ 3 2 1 4 Chimp: TGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGCC----ACCTCATCTGAAAATTGTTCattt Gorilla: TGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGCC----ACCTCAACTGAAAATTGTTCattt Human: TGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGTCATAGTCATCATCTGAAATTTGTTCattt Cluster: [ ] Orangutan: TGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGCC----ACCTCATCTGAAAATTGTTCattt Chimp > Human ------------- chr7:120159787-120159795 Template switch process: F1: L CTGGTCTGAGTTCCAAGTTCACTACTGACTATGAGCTCTAG 1 F3: 4 TCATCTGAAATTTGTTCATTTGTTCATTCAACATGATATT R RF: CTGGTCTGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGCCACCTCATCTGAAAATTGTTCATTTGTTCATTCAACATGATATT RR: GACCAGACTCAAGGTTCAAGTGATGACTGATACTCGAGATCGGTGGAGTAGACTTTTAACAAGTAAACAAGTAAGTTGTACTATAA F2: 3 ACTGATACT 2 Unidirectional alignment (log-probability: -34.7) TGGTCTGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGtCAtagtCaTCATCTGAAAtTTGTTCATTTGTTCATTCAACATGATATT TGGTCTGAGTTCCAAGTTCACTACTGACTATGAGCTCTAGCCA----CCTCATCTGAAAATTGTTCATTTGTTCATTCAACATGATATT Template switch alignment (log-probability: -22.4) TGGTCTGAGTTCCAAGTTCACTACTGACTATGAGCTCTAG|TCATAGTCA|TCATCTGAAAtTTGTTCATTTGTTCATTCAACATGATATT TGGTCTGAGTTCCAAGTTCACTACTGACTATGAGCTCTAG|TCATAGTCA|TCATCTGAAAATTGTTCATTTGTTCATTCAACATGATATT ========== Event 3396 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTAATGTGAATTCCTGCCTT-CTTCAAT--GCTATAAAAATGGCATTGACATCTACTTTTCAACCCTA Chimp: TCTAATGTGAATTCCTGC-CT-CTTCAAT--GCTATAAAAATGCCATTGACATCTACTTTTCAACCCTA Gorilla: TCTAATGTGAATTCCTGCCTTCTTTCAGTGTCCTATAAAAATGGCATTGACATCTACTTTTCAACCCTA ↓ 1 4 3 2 Human: TCTAATGTGAATTCCTGCCTT-CTTCAAT--GCTATAAAAATGGCATTGACATCTACTTTTCAACCCTA Cluster: [ ] Orangutan: TCTAATGTGAATTCCTGCCTT-CTTCAGTGTCCTATAAAAATGGCATTGACATGTACTTTTCAACCCTA Gorilla > Human --------------- chr7:120206014-120206018 Template switch process: F1: L CTATTAGTCTCCTGACTGTCTCTAATGTGAATTCCTGCCTTCTT 1 F3: 4 CTATAAAAATGGCATTGACATCTACTTTTCAACCCTAGTC R RF: CTATTAGTCTCCTGACTGTCTCTAATGTGAATTCCTGCCTTCTTTCAGTGTCCTATAAAAATGGCATTGACATCTACTTTTCAACCCTA RR: GATAATCAGAGGACTGACAGAGATTACACTTAAGGACGGAAGAAAGTCACAGGATATTTTTACCGTAACTGTAGATGAAAAGTTGGGAT F2: 3 GTAAC 2 Unidirectional alignment (log-probability: -37.5) TAGTCTCCTGACTGTCTCTAATGTGAATTCCTGCCTTCT-TCAaTG--CTATAAAAATGGCATTGACATCTACTTTTCAACCCTAgTc TAGTCTCCTGACTGTCTCTAATGTGAATTCCTGCCTTCTTTCAGTGTCCTATAAAAATGGCATTGACATCTACTTTTCAACCCTACTT Template switch alignment (log-probability: -27.4) TAGTCTCCTGACTGTCTCTAATGTGAATTCCTGCCTTCTT|CAATG|CTATAAAAATGGCATTGACATCTACTTTTCAACCCTagtc TAGTCTCCTGACTGTCTCTAATGTGAATTCCTGCCTTCTT|CAATG|CTATAAAAATGGCATTGACATCTACTTTTCAACCCT---A ========== Event 3397 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TATACACACATATATAGACACAT--------------------ATTTTTATGTGTATTTACA--AGAGTATTTTTAAACAA ↓ 1 3 4 2 Chimp: TATACACACATATATAGACACGT----------AAATACACATAAAAATATGTGTATTTACA--AGAGTATTTTTAAACAA Gorilla: TATACACACATATATAGACACGTAAATACACAT----------AAAAATATGTGTATTTACA--AGAGTATTTTTAAACAA ↑ 1 3 4 2 Human: TATACACACATATATAGACACAT--------------------ATTTTTATGTGTATTTACA--AGAGTATTTTTAAACAA Cluster: [ ] Orangutan: TATACACACATATATAGACACGCAAATACACAT----------AAAAATATGTGTATTTACAATAGAGTATTTTTAAACAA Human > Chimp ------------- chr7:42852344-42852360 Template switch process: F1: L TATGCATGTATTTTAGTGTGTATACACACATATATAGACAC 1 F3: 4 TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA R RF: TATGCATGTATTTTAGTGTGTATACACACATATATAGACACATATTTTTATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA RR: ATACGTACATAAAATCACACATATGTGTGTATATATCTGTGTATAAAAATACACATAAATGTTCTCATAAAAATTTGTTATGGGGTTT F2: 3 AAAAATACACATAAATG 2 Unidirectional alignment (log-probability: -44.5) ATGCATGTATTTTAGTGTGTATACACACATATATAGACACgtaaatacacataaaaA------TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA ATGCATGTATTTTAGTGTGTATACACACATATATAGACAC----------------ATATTTTTATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA Template switch alignment (log-probability: -17.4) ATGCATGTATTTTAGTGTGTATACACACATATATAGACAC|GTAAATACACATAAAAA|TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA ATGCATGTATTTTAGTGTGTATACACACATATATAGACAC|GTAAATACACATAAAAA|TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA Human > Gorilla --------------- chr7:118533190-118533206 Template switch process: F1: L TATGCATGTATTTTAGTGTGTATACACACATATATAGACAC 1 F3: 4 TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA R RF: TATGCATGTATTTTAGTGTGTATACACACATATATAGACACATATTTTTATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA RR: ATACGTACATAAAATCACACATATGTGTGTATATATCTGTGTATAAAAATACACATAAATGTTCTCATAAAAATTTGTTATGGGGTTT F2: 3 AAAAATACACATAAATG 2 Unidirectional alignment (log-probability: -44) ATGCATGTATTTTAGTGTGTATACACACATATATAGACACgtaaatacacataaaaA------TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA ATGCATGTATTTTAGTGTGTATACACACATATATAGACAC----------------ATATTTTTATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA Template switch alignment (log-probability: -17.9) ATGCATGTATTTTAGTGTGTATACACACATATATAGACAC|GTAAATACACATAAAAA|TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA ATGCATGTATTTTAGTGTGTATACACACATATATAGACAC|GTAAATACACATAAAAA|TATGTGTATTTACAAGAGTATTTTTAAACAATACCCCAAA ========== Event 3398 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ccgtacagtaggAAACAGATGCGGTAACTACTTACTA-------GGTTGATGTGTAACTTAATTAAG Chimp: ccgtacagtaggAAACAGATGCAGTAACTACTTACTA-------GGTTGATGTGTAACTTAATTAAG Gorilla: ccgtacagtaggAAACAGATGCGGTAACTACTTACTAGTTACCGCATTGATGTGTAACTTAATTAAG ↑ 3 2 1 4 Human: ccgtacagtaggAAACAGATGCGGTAACTACTTACTA-------GGTTGATGTGTAACTTAATTAAG Cluster: [ ] Orangutan: ccgtacagtaggAAACAGATGCGGTAACTACTTACTA-------GGTTGATGTGTAACTTAATTAAG Human > Gorilla --------------- chr7:118357582-118357589 Template switch process: F1: L CCCACCGTACAGTAGGAAACAGATGCGGTAACTACTTACTAG 1 F3: 4 TTGATGTGTAACTTAATTAAGGAATGAAAGATGTGTCCAT R RF: CCCACCGTACAGTAGGAAACAGATGCGGTAACTACTTACTAGGTTGATGTGTAACTTAATTAAGGAATGAAAGATGTGTCCAT RR: GGGTGGCATGTCATCCTTTGTCTACGCCATTGATGAATGATCCAACTACACATTGAATTAATTCCTTACTTTCTACACAGGTA F2: 3 ACGCCATT 2 Unidirectional alignment (log-probability: -26.5) CACCGTACAGTAGGAAACAGATGCGGTAACTACTTACTAGttaccgcaTTGATGTGTAACTTAATTAAGGAATGAAAGATGTGTCCAT CACCGTACAGTAGGAAACAGATGCGGTAACTACTTACTAGG-------TTGATGTGTAACTTAATTAAGGAATGAAAGATGTGTCCAT Template switch alignment (log-probability: -16.8) CACCGTACAGTAGGAAACAGATGCGGTAACTACTTACTAG|TTACCGCA|TTGATGTGTAACTTAATTAAGGAATGAAAGATGTGTCCAT CACCGTACAGTAGGAAACAGATGCGGTAACTACTTACTAG|TTACCGCA|TTGATGTGTAACTTAATTAAGGAATGAAAGATGTGTCCAT ========== Event 3399 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTGAGGCAATAACCAGTTGCAAGTTTTTCTAAACTTCCTGTAAGTCTACAAGTGCATTC Chimp: TTGAGGCAATAACCAGTTGCAAGTTTTTCTAAACTTCCTGTAAGTCTACAAGTGCATTC ↑ 1 3 4 2 Gorilla: TTGAGGCAATAACCAGTTGCATCTTTAGAAAAACTTCTGGTAAGTCTACAAGTGCATTC ↓ 1 3 4 2 Human: TTGAGGCAATAACCAGTTGCAAGTTTTTCTAAACTTCCTGTAAGTCTACAAGTGCATTC Cluster: [ ] Orangutan: TTGAGGCAATAACCACTTGCATCTTTAGAAAAACTTCCTGTAAGTCTACAAGTGCATTC Gorilla > Human --------------- chr7:40875632-40875640 Template switch process: F1: L GTTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA 1 F3: 4 AAACTTCCTGTAAGTCTACAAGTGCATTCCTAATGTAGACAATAATGCT R RF: GTTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCATCTTTAGAAAAACTTCTGGTAAGTCTACAAGTGCATTCCTAATGTAGACAATAATGCT RR: CAAAACAGTAAAGTTCTGGAAACTCCGTTATTGGTCAACGTAGAAATCTTTTTGAAGACCATTCAGATGTTCACGTAAGGATTACATCTGTTATTACGA F2: 3 TCTTTTTGA 2 Unidirectional alignment (log-probability: -40.8) TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCAagttttTCT------AAACTTCctGTAAGTCTACAAGTGCATTCCTAATGTAGAC TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA------TCTTTAGAAAAACTTCTGGTAAGTCTACAAGTGCATTCCTAATGTAGAC Template switch alignment (log-probability: -28.1) TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA|AGTTTTTCT|AAACTTCctGTAAGTCTACAAGTGCATTCCTAATGTAGAC TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA|AGTTTTTCT|AAACTTCTGGTAAGTCTACAAGTGCATTCCTAATGTAGAC Gorilla > Chimp --------------- chr7:124165473-124165481 Template switch process: F1: L GTTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA 1 F3: 4 AAACTTCCTGTAAGTCTACAAGTGCATTCCTAATGTAGACAATAATGCT R RF: GTTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCATCTTTAGAAAAACTTCTGGTAAGTCTACAAGTGCATTCCTAATGTAGACAATAATGCT RR: CAAAACAGTAAAGTTCTGGAAACTCCGTTATTGGTCAACGTAGAAATCTTTTTGAAGACCATTCAGATGTTCACGTAAGGATTACATCTGTTATTACGA F2: 3 TCTTTTTGA 2 Unidirectional alignment (log-probability: -40.8) TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCAagttttTCT------AAACTTCctGTAAGTCTACAAGTGCATTCCTAATGTAGAC TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA------TCTTTAGAAAAACTTCTGGTAAGTCTACAAGTGCATTCCTAATGTAGAC Template switch alignment (log-probability: -28.1) TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA|AGTTTTTCT|AAACTTCctGTAAGTCTACAAGTGCATTCCTAATGTAGAC TTTTGTCATTTCAAGACCTTTGAGGCAATAACCAGTTGCA|AGTTTTTCT|AAACTTCTGGTAAGTCTACAAGTGCATTCCTAATGTAGAC ========== Event 3400 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCTACTGAAAACAACAACAGGGGGACTGTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGATCCGGGGCATTTCCGAGGACTCTGGGGTGG ↓ 1 4 3 2 Chimp: TTTCTATTGAAAACAACAACAAT---GCCGTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGATCCGGGGCATTTCCGAGGACTCTGGGGTGG ↑ 1 4 3 2 Gorilla: TTTCTATTGAAAACAACAACAGGGGAACTGTCTCTTTGCATGGCATTGTAGTACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGATCCGGGGCATTTCCAAGGACTCTGGGGTGG Human: TTTCTACTGAAAACAACAACAGGGGGACTGTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGATCCGGGGCATTTCCGAGGACTCTGGGGTGG Cluster: [ ] Orangutan: TTTCTATTGAAAACAACAACAGGGGGACTGTCTCTTTGCATGGCATCGTAGCACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGGTCCGGGGCATTTCTGAGGACTCTGGGATGG Human > Chimp ------------- chr7:162930319-162930323 Template switch process: F1: L ATCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACA 1 F3: 4 GTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGG R RF: ATCTAGCAAGTTAATTAATTTTTCTACTGAAAACAACAACAGGGGGACTGTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGATCCGGGGCAT RR: TAGATCGTTCAATTAATTAAAAAGATGACTTTTGTTGTTGTCCCCCTGACAGAGAAACGTGCCGTAACATCATGTCCCTGTCTTCGTCCCTCCGAGACCCAACGTCTCTCCCGTCTAGGCCCCGTA F2: 3 CCGTA 2 Unidirectional alignment (log-probability: -34.7) TCTAGCAAGTTAATTAATTTTTCTAtTGAAAACAACAACAatgccG--------TCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGG TCTAGCAAGTTAATTAATTTTTCTACTGAAAACAACAACA-----GGGGGACTGTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGG Template switch alignment (log-probability: -21.9) TCTAGCAAGTTAATTAATTTTTCTAtTGAAAACAACAACA|ATGCC|GTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGG TCTAGCAAGTTAATTAATTTTTCTACTGAAAACAACAACA|ATGCC|GTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGG Gorilla > Chimp --------------- chr7:162930319-162930323 Template switch process: F1: L ATCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACA 1 F3: 4 GTCTCTTTGCACGGCATTGTAGTACAGGGACAGAAGCAGG R RF: ATCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACAGGGGAACTGTCTCTTTGCATGGCATTGTAGTACAGGGACAGAAGCAGGGAGGCTCTGGGTTGCAGAGAGGGCAGATCCGGGGCAT RR: TAGATCGTTCAATTAATTAAAAAGATAACTTTTGTTGTTGTCCCCTTGACAGAGAAACGTACCGTAACATCATGTCCCTGTCTTCGTCCCTCCGAGACCCAACGTCTCTCCCGTCTAGGCCCCGTA F2: 3 CCGTA 2 Unidirectional alignment (log-probability: -33.2) TCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACAatG---CcGTCTCTTTGCAcGGCATTGTAGTACAGGGACAGAAGCAGG TCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACAGGGGAACTGTCTCTTTGCATGGCATTGTAGTACAGGGACAGAAGCAGG Template switch alignment (log-probability: -21.9) TCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACA|ATGCC|GTCTCTTTGCAcGGCATTGTAGTACAGGGACAGAAGCAGG TCTAGCAAGTTAATTAATTTTTCTATTGAAAACAACAACA|ATGCC|GTCTCTTTGCATGGCATTGTAGTACAGGGACAGAAGCAGG ========== Event 3401 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGCTAGCTTATGAAGAAGGC-AGAATAGACACTTGTCCATAATTGTGTGCACT ↓ 1 3 4 2 Chimp: GGGCTAGCTTATGAAGAAGGCAAGTGTCTACACTTGTCCATAATTGTGTGCACT ↑ 1 3 4 2 Gorilla: GGGCTAGCTTATGAAGAAGGC-AGAATAGACACTTGTCCATAATTGTGTGTACT Human: GGGCTAGCTTATGAAGAAGGC-AGAATAGACACTTGTCCATAATTGTGTGCACT Cluster: [ ] Orangutan: GGGCTAGCTTATGAAGAAGGC-AAAATAGACACTTGTCCATAATTGTGTGCACT Human > Chimp ------------- chr7:41286488-41286494 Template switch process: F1: L CCACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCA 1 F3: 4 ACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA R RF: CCACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCAGAATAGACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA RR: GGTGAACTGACGCCGTGGGTCCCGATCGAATACTTCTTCCGTCTTATCTGTGAACAGGTATTAACACACGTGAATCTTTTAGTCAAAT F2: 3 TCTGTGA 2 Unidirectional alignment (log-probability: -28.6) ACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCA----AGtgtctACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA ACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCAGAATAG-----ACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA Template switch alignment (log-probability: -16.2) ACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCA|AGTGTCT|ACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA ACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCA|AGTGTCT|ACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA Gorilla > Chimp --------------- chr7:41286488-41286494 Template switch process: F1: L CCACTTGACTGCGGCACCCAGGGCTAGCTTATGAAGAAGGCA 1 F3: 4 ACACTTGTCCATAATTGTGTGCACTTAGAAAATCAGTTTA R RF: CCACTTGACTGCAGCACCCAGGGCTAGCTTATGAAGAAGGCAGAATAGACACTTGTCCATAATTGTGTGTACTTAGAAAATCAGTTTA RR: GGTGAACTGACGTCGTGGGTCCCGATCGAATACTTCTTCCGTCTTATCTGTGAACAGGTATTAACACACATGAATCTTTTAGTCAAAT F2: 3 TCTGTGA 2 Unidirectional alignment (log-probability: -39.1) ACTTGACTGCgGCACCCAGGGCTAGCTTATGAAGAAGGCA----AGtgtctACACTTGTCCATAATTGTGTGcACTTAGAAAATCAGTTTA ACTTGACTGCAGCACCCAGGGCTAGCTTATGAAGAAGGCAGAATAG-----ACACTTGTCCATAATTGTGTGTACTTAGAAAATCAGTTTA Template switch alignment (log-probability: -27.7) ACTTGACTGCgGCACCCAGGGCTAGCTTATGAAGAAGGCA|AGTGTCT|ACACTTGTCCATAATTGTGTGcACTTAGAAAATCAGTTTA ACTTGACTGCAGCACCCAGGGCTAGCTTATGAAGAAGGCA|AGTGTCT|ACACTTGTCCATAATTGTGTGTACTTAGAAAATCAGTTTA ========== Event 3402 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGACCGGATGTTTATTCAAATATTCAATACCTACCATTATTTGAGTAAACATCCAGTCA----------------------------------------CTGAAAAAGGATGCCTTTTTGGCATCCTTGTTCTATTGGCAATAGAACAAAATA ↑ 3 2 1 4 Chimp: AGTGACCGGATGTTTATTCAA----------------------------------------ATATTCAATACCTACCATTATTTGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGG-A--TGTGTGTTATTGGCAATAGAACAAAATA Gorilla: AGTGACCGGATGTTTATTCAAATATTCAATACCTACCATTATTTGAGTAAACATCCAGTCA----------------------------------------CTGAAAAAGGGTGCCTTTTTGG-A--TGTGTGTTATTGGCAATAGAACAAAATA Human: AGTGACCGGATGTTTATTCAAATATTCAATACCTACCATTATTTGAGTAAACATCCAGTCA----------------------------------------CTGAAAAAGGATGCCTTTTTGGCATCCTTGTTCTATTGGCAATAGAACAAAATA Cluster: [ ] Orangutan: AGTGACTGGATGTTTATTCAAATATTCAGTACCTACCATTATTTGAGTAAACATCCAGTCA----------------------------------------CTGAAAAAGGATGCCTTTTTGG-A--TGTGTGTTATTGGCAATAGAACAAAATA Chimp > Human ------------- chr7:43100201-43100211 Template switch process: F1: L CCAAAAAGGCATCTTTTTTCAGTGACCGGATGTTTATTCAAATATTCAATACCTACCATTATTTGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGG 1 F3: 4 TATTGGC R RF: CCAAAAAGGCATCTTTTTTCAGTGACCGGATGTTTATTCAAATATTCAATACCTACCATTATTTGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGGATGTGTGTTATTGGC RR: GGTTTTTCCGTAGAAAAAAGTCACTGGCCTACAAATAAGTTTATAAGTTATGGATGGTAATAAACTCATTTGTAGGTCAGTGACTTTTTCCTACGGAAAAACCTACACACAATAACCG F2: 3 CTTGTTCCTAC 2 Unidirectional alignment (log-probability: -37.6) TGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGG--------catccttgttcTATTGGC TGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGGATGTGTGT-----------TATTGGC Template switch alignment (log-probability: -23.2) TGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGG|CATCCTTgTTC|TATTGGC TGAGTAAACATCCAGTCACTGAAAAAGGATGCCTTTTTGG|CATCCTTTTTC|TATTGGC ========== Event 3403 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 346 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCCAGGTGAGATTAGACTGGCCTAGTAACTCACTTATAGCCGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTG Chimp: TCCAGGTGAGATTAGACTGGCCTAGTAACTCACTTATAGCTGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTG ↓ 3 1 2 4 Gorilla: TCCAGGTGAGATTAGACTGGCCTAGCCTATCACTTATGGCTTATTCTGTCGGCTATAAGTGAGTTACTAGGCAGAAAAAGTTCTTCCTCCTTG ↓ 13 24 ↑ 3 1 2 4 Human: TCCAGGTGAGATTAGACTGGCCTAGTAACTCACTTATAGCCGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTG Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr7:4340609-4340649 Template switch process: F1: L TTGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG 1 F3: 4 CTAGGTAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA R RF: TTGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAGCCTATCACTTATGGCTTATTCTGTCGGCTATAAGTGAGTTACTAGGCAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA RR: AACTGAGAGGTAGAGGAGGTCCACTCTAATCTGACCGGATCGGATAGTGAATACCGAATAAGACAGCCGATATTCACTCAATGATCCGTCTTTTTCAAGAAGGAGGAACCTGTGAACGGGACTTTCGT F2: 3 GGATAGTGAATACCGAATAAGATAGCCGATATTCACTCAAT 2 Unidirectional alignment (log-probability: -84.3) TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG---------------------------------------TAactcacttatagccgatagaataagccataagtgataggCTAGGtAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTG TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAGCCTATCACTTATGGCTTATTCTGTCGGCTATAAGTGAGTTA---------------------------------------CTAGGCAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTG Template switch alignment (log-probability: -32.1) TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG|TAACTCACTTATAGCCGAtAGAATAAGCCATAAGTGATAGG|CTAGGtAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTG TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG|TAACTCACTTATAGCCGACAGAATAAGCCATAAGTGATAGG|CTAGGCAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTG Human > Gorilla --------------- chr7:4217610-4217656 Template switch process: F1: L TTGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG 1 F3: 4 AGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA R RF: TTGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAGTAACTCACTTATAGCCGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA RR: AACTGAGAGGTAGAGGAGGTCCACTCTAATCTGACCGGATCATTGAGTGAATATCGGCTATCTTATTCGGTATTCACTATCCGATCCATCTTTTTCAAGAAGGAGGAACCTGTGAACGGGACTTTCGT F2: 3 CGGATCATTGAGTGAATATCGGCTGTCTTATTCGGTATTCACTATCC 2 Unidirectional alignment (log-probability: -84.3) TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAGcctatcacttatggcttattctgtcggctataagtgagtTA---------------------------------------CTAGGcAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG---------------------------------------TAACTCACTTATAGCCGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA Template switch alignment (log-probability: -27.2) TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG|CCTATCACTTATGGCTTATTCTgTCGGCTATAAGTGAGTTACTAGGC|AGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG|CCTATCACTTATGGCTTATTCTATCGGCTATAAGTGAGTTACTAGGC|AGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA Chimp > Gorilla --------------- chr7:4217610-4217656 Template switch process: F1: L TTGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG 1 F3: 4 AGAAAAAGTTCTTCCTCCTTGGACACTTGCCCTGAAAGCA R RF: TTGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAGTAACTCACTTATAGCTGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTGGACCCTTGCCCTGAAAGCA RR: AACTGAGAGGTAGAGGAGGTCCACTCTAATCTGACCGGATCATTGAGTGAATATCGACTATCTTATTCGGTATTCACTATCCGATCCATCTTTTTCAAGAAGGAGGAACCTGGGAACGGGACTTTCGT F2: 3 CGGATCATTGAGTGAATATCGGCTGTCTTATTCGGTATTCACTATCC 2 Unidirectional alignment (log-probability: -89.8) TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAGcctatcacttatggcttattctgtcggctataagtgagtTA---------------------------------------CTAGGcAGAAAAAGTTCTTCCTCCTTGGACaCTTGCCCTGAAAGCA TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG---------------------------------------TAACTCACTTATAGCTGATAGAATAAGCCATAAGTGATAGGCTAGGTAGAAAAAGTTCTTCCTCCTTGGACCCTTGCCCTGAAAGCA Template switch alignment (log-probability: -38.2) TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG|CCTATCACTTATGGCTTATTCTgTCgGCTATAAGTGAGTTACTAGGC|AGAAAAAGTTCTTCCTCCTTGGACaCTTGCCCTGAAAGCA TGACTCTCCATCTCCTCCAGGTGAGATTAGACTGGCCTAG|CCTATCACTTATGGCTTATTCTATCAGCTATAAGTGAGTTACTAGGC|AGAAAAAGTTCTTCCTCCTTGGACCCTTGCCCTGAAAGCA ========== Event 3404 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GCCTTATAAATAAGGTAAACATGAATTTCCATAACTTGTTTCTGTGTTCCTCTTCTCTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATAAAATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTCTTCATGAAATTTTGCACTTTTGTGAAA ↑ 3 2 1 4 Chimp: GCCTTATAAATAAGGTAAACATGAATTTCCATAACTTGTTTCTGTGTTCCTCTTCTCTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATA-AATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATT---TCACAAAATTTTGCACTTTTGTGAAA ↓ 3 2 1 4 Gorilla: GCCTTATAAATAAGGTAAACATGAATTTCCATAACTTGTTTCTGTGTTCCTCTTCTCTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATAAAATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTCTTCATGAAATTTTGCACTTTTGTGAAA Human: GCCTTATAAATAAGGTAAACATGAATTTCCATAACTTGTTTCTGTGTTCCTCTTCTCTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATAAAATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTCTTCATGAAATTTTGCACTTTTGTGAAA Cluster: [ ] Orangutan: GCCTTATAAATAAGGTAAACATGAATGTCCATAACTTGTTTCTGTGTTCCTCTTCTTTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATAAAATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTCTTCATGAAATTTTGCACTTTTGTGAAA Chimp > Human ------------- chr7:115781386-115781391 Template switch process: F1: L ACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTC 1 F3: 4 AAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT R RF: CATGAATTTCCATAACTTGTTTCTGTGTTCCTCTTCTCTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATAAATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTCACAAAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT RR: GTACTTAAAGGTATTGAACAAAGACACAAGGAGAAGAGAAACAAAAAGAAGGAATTCCTAAGATACGTTCCAACGTTATTTATAATGTTCGAAGTAGAAGAAAGTCCACTGGCACTGTAGTCGTAAAGTGTTTTAAAACGTGAAAACACTTTCTTACAAGGACAATACGAA F2: 3 GTACTT 2 Unidirectional alignment (log-probability: -27.3) AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATttcTTCAtgAAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCAT---TTCACAAAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT Template switch alignment (log-probability: -16.1) AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTC|TTCATG|AAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTC|TTCATG|AAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT Chimp > Gorilla --------------- chr7:114964117-114964122 Template switch process: F1: L ACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTC 1 F3: 4 AAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT R RF: CATGAATTTCCATAACTTGTTTCTGTGTTCCTCTTCTCTTTGTTTTTCTTCCTTAAGGATTCTATGCAAGGTTGCAATAAATATTACAAGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTCACAAAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT RR: GTACTTAAAGGTATTGAACAAAGACACAAGGAGAAGAGAAACAAAAAGAAGGAATTCCTAAGATACGTTCCAACGTTATTTATAATGTTCGAAGTAGAAGAAAGTCCACTGGCACTGTAGTCGTAAAGTGTTTTAAAACGTGAAAACACTTTCTTACAAGGACAATACGAA F2: 3 GTACTT 2 Unidirectional alignment (log-probability: -26.3) AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATttcTTCAtgAAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCAT---TTCACAAAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT Template switch alignment (log-probability: -16.5) AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTC|TTCATG|AAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT AGCTTCATCTTCTTTCAGGTGACCGTGACATCAGCATTTC|TTCATG|AAATTTTGCACTTTTGTGAAAGAATGTTCCTGTTATGCTT ========== Event 3405 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTCTTCACACTCAGGTGATGATGGTGACAGTGATGGTCACAGAACTGTGGtttacctagtgctcactgtctcagagcaccacaaaggtta ↑ 4 1 3 2 Chimp: TTCTTCACACTCAGGTGATGA------------TGGTCACAGAACTGTGGtttacctagtgctcactgtctcagagcaccacaaaggtta ↓ 4 1 3 2 Gorilla: TTCTTCACACTCAGGTGATGATGGTGACAGTGATGGTCacagagctgtggtttacctagtgctcactgtctcagagcaccacaaaggtta Human: TTCTTCACACTCAGGTGATGATGGTGACAGTGATGGTCACAGAACTGTGGtttacctagtgctcactgtctcagagcaccacaaaggtta Cluster: [ ] Orangutan: TTCTTCACACTCAGGTGATGA-TGTGACAGTGACGGTCACAGAGCTGTGgtttacctagtgctgactgtctcagagcaccacagaggtta Chimp > Human ------------- chr7:115085291-115085296 Template switch process: F1: L TGAGTGTTGGTCACCTGGGATTCTTCACACTCAGGTGATGATGGT 1 F3: 4 GATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCTCA R RF: TGAGTGTTGGTCACCTGGGATTCTTCACACTCAGGTGATGATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCTCA RR: ACTCACAACCAGTGGACCCTAAGAAGTGTGAGTCCACTACTACCAGTGTCTTGACACCAAATGGATCACGAGTGACAGAGT F2: 3 TGACAG 2 Unidirectional alignment (log-probability: -28.2) GTTGGTCACCTGGGATTCTTCACACTCAGGTGAtgatggtgacagTGATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCT GTTGGTCACCTGGGATTCTTCACACTCAGGTGA------------TGATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCT Template switch alignment (log-probability: -16.1) GTTGGTCACCTGGGATTCTTCACACTCAGGTGATGATGGT|GACAGT|GATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCT GTTGGTCACCTGGGATTCTTCACACTCAGGTGATGATGGT|GACAGT|GATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCT Chimp > Gorilla --------------- chr7:114219742-114219747 Template switch process: F1: L TGAGTGTTGGTCACGTGGGATTCTTCACACTCAGGTGATGATGGT 1 F3: 4 GATGGTCACAGAGCTGTGGTTTACCTAGTGCTCACTGTCTCA R RF: TGAGTGTTGGTCACCTGGGATTCTTCACACTCAGGTGATGATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCTCA RR: ACTCACAACCAGTGGACCCTAAGAAGTGTGAGTCCACTACTACCAGTGTCTTGACACCAAATGGATCACGAGTGACAGAGT F2: 3 TGACAG 2 Unidirectional alignment (log-probability: -39.2) GTTGGTCACgTGGGATTCTTCACACTCAGGTGAtgatggtgacagTGATGGTCACAGAgCTGTGGTTTACCTAGTGCTCACTGTCT GTTGGTCACCTGGGATTCTTCACACTCAGGTGA------------TGATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCT Template switch alignment (log-probability: -27.7) GTTGGTCACgTGGGATTCTTCACACTCAGGTGATGATGGT|GACAGT|GATGGTCACAGAgCTGTGGTTTACCTAGTGCTCACTGTCT GTTGGTCACCTGGGATTCTTCACACTCAGGTGATGATGGT|GACAGT|GATGGTCACAGAACTGTGGTTTACCTAGTGCTCACTGTCT ========== Event 3406 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGACTCAGACCCCAAGAAAC------------------------AGGCCTGCTTCCTAGGGCTGTGACAGGGGC---TAGTCTCCAGTCCTGGGCAAGCCACACTGTCTCC ↓ 1 4 3 2 Chimp: CAGACTCAGACCCCAAGAAAC------------------------------------------------AAGGAC---TGGTCTCCAGTCCTGGGCAAGCCACACTGTCTCC Gorilla: CAGACTCAGACCCCAAGAA-AAGGCCTGCTTCCTAGGGCTGTGAC------------------------AGGGGCTGCAGGTCTCCAGTCCTGGGCAAGCCACACTGTCTCC Human: CAGACTCAGACCCCAAGAAAC------------------------AGGCCTGCTTCCTAGGGCTGTGACAGGGGC---TAGTCTCCAGTCCTGGGCAAGCCACACTGTCTCC Cluster: [ ] Orangutan: CAGACTCAGACCCCAAGAAACAGGCCTGCTTCCTAGGGCTGTGAC------------------------AGGGGCTGCAGCTCTCCAGTCCTGGGCAAGCCATACTGTCTCC Human > Chimp ------------- chr7:122067836-122067842 Template switch process: F1: L GCAAGTGCTTCCTTTGAAGTCAGACTCAGACCCCAAGAAACA 1 F3: 4 GTCTCCAGTCCTGGGCAAGCCACACTGTCTCCTTCCCCCA R RF: GCAAGTGCTTCCTTTGAAGTCAGACTCAGACCCCAAGAAACAGGCCTGCTTCCTAGGGCTGTGACAGGGGCTAGTCTCCAGTCCTGGGCAAGCCACACTGTCTCCTTCCCCCA RR: CGTTCACGAAGGAAACTTCAGTCTGAGTCTGGGGTTCTTTGTCCGGACGAAGGATCCCGACACTGTCCCCGATCAGAGGTCAGGACCCGTTCGGTGTGACAGAGGAAGGGGGT F2: 3 GTCAGGA 2 Unidirectional alignment (log-probability: -28.4) AAGTGCTTCCTTTGAAGTCAGACTCAGACCCCAAGAAACA------------AGGaCTG------------GTCTCCAGTCCTGGGCAAGCCACACTGTCTCCTTCCCCCA AAGTGCTTCCTTTGAAGTCAGACTCAGACCCCAAGAAACAGGCCTGCTTCCTAGGGCTGTGACAGGGGCTAGTCTCCAGTCCTGGGCAAGCCACACTGTCTCCTTCCCCCA Template switch alignment (log-probability: -16.2) AAGTGCTTCCTTTGAAGTCAGACTCAGACCCCAAGAAACA|AGGACTG|GTCTCCAGTCCTGGGCAAGCCACACTGTCTCCTTCCCCCA AAGTGCTTCCTTTGAAGTCAGACTCAGACCCCAAGAAACA|AGGACTG|GTCTCCAGTCCTGGGCAAGCCACACTGTCTCCTTCCCCCA ========== Event 3407 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTAGAGACACCTCAACAGCTAGGTCCATGGAC------AAACCCTCATCTTCCCTGACCTGCTTCTCCCAC Chimp: ATTAGAGACACCTCAACAGCTAGGTCCATGGAC------AAACCCTCATCTTCCCTGAGCTGCTTCTCCCAC Gorilla: ATTAGAGACACCTCAACAGCTAGGTCCATGGAC------------CTAGCTCCCCTGACCTGCTTCTCCCAC ↑ 3 2 1 4 Human: ATTAGAGACACCTCAACAGCTAGGTCCATGGAC------AAACCCTCATCTTCCCTGACCTGCTTCTCCCAC Cluster: [ ] Orangutan: ATTAGAGACACCTCAACAGCTAGGTCCATGGACAAATCC------TCATCTCCCCTGACCTGCTTCTCCCAC Human > Gorilla --------------- chr7:113305375-113305378 Template switch process: F1: L GCCCAGGCATTAGAGACACCTCAACAGCTAGGTCCATGGAC 1 F3: 4 CTCCCCTGACCTGCTTCTCCCACAGAGCCTCAGATTCAGTAGC R RF: GCCCAGGCATTAGAGACACCTCAACAGCTAGGTCCATGGACAAACCCTCATCTTCCCTGACCTGCTTCTCCCACAGGGCCTCAGATTCAGTAGC RR: CGGGTCCGTAATCTCTGTGGAGTTGTCGATCCAGGTACCTGTTTGGGAGTAGAAGGGACTGGACGAAGAGGGTGTCCCGGAGTCTAAGTCATCG F2: 3 GATC 2 Unidirectional alignment (log-probability: -36.9) CCCAGGCATTAGAGACACCTCAACAGCTAGGTCCATGGAC-------------ctagctcCCCTGACCTGCTTCTCCCACAGaGCCTCAGATTCAGT CCCAGGCATTAGAGACACCTCAACAGCTAGGTCCATGGACAAACCCTCATCTT-------CCCTGACCTGCTTCTCCCACAGGGCCTCAGATTCAGT Template switch alignment (log-probability: -27.3) CCCAGGCATTAGAGACACCTCAACAGCTAGGTCCATGGAC|CTAG|CTcCCCTGACCTGCTTCTCCCACAGaGCCTCAGATTCAGT CCCAGGCATTAGAGACACCTCAACAGCTAGGTCCATGGAC|CTAG|CTTCCCTGACCTGCTTCTCCCACAGGGCCTCAGATTCAGT ========== Event 3408 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: ttacttcagcttatatttatgaaatagtatcaatatgagatcttaattccaatttcttttttct------------------------ttttttttgacggagtctcgctctgttgcccaggctggagtgcagcggcgggctctgggctcactgcaagcttcgcctcccaggttcacgccattctcctgcctcagcctc Chimp: TTACTTCAGCTTATATTTATGTAATTGTATC-GCATGAGATCTTAATTCCAAtttcttttttct---------------tttctttttttttttttaacggagtctcgctctgttgcccaggctggagtgcagcggccggctctcggctcactgcaagctccgcctcccaggttcacgccattctcctgcctcagcctc ↑ 1 4 3 2 Gorilla: TTACTTCAGCTTATATTTATGAAATAGTATC--AACGAGATCTTAATTCCAAtttcttttttct----ttctttctttt---------ttttttttgacggagtctcgctctgttgcccaggctggagtgcagcggcgggctctcggctcactgcaagctccgcctcccaggttcatgccattctcctgcctcagcctc Human: ttacttcagcttatatttatgaaatagtatcaatatgagatcttaattccaatttcttttttct------------------------ttttttttgacggagtctcgctctgttgcccaggctggagtgcagcggcgggctctgggctcactgcaagcttcgcctcccaggttcacgccattctcctgcctcagcctc Cluster: [ ] Orangutan: ttacttcagcttatatttatgaaagagtatc-acatgagatcttaattccaacttcttttttcttttt--------------------ttttttttgatggagtcttgctctgtcgcccagactggagtgcagcggcgggatcgcggctcactgcaagctgcgcctaccgggttcacgccattctcctgcctcagcctc Gorilla > Chimp --------------- chr7:45781285-45781288 Template switch process: F1: L TTTTCTTTTGTAGAAGTTTTTTACTTCAGCTTATATTTATGTAATTGTATC 1 F3: 4 GAGATCTTAATTCCAATTTCTTTTTTCTT R RF: TTTTCTTTTGTAGAAGTTTTTTACTTCAGCTTATATTTATGAAATAGTATCAACGAGATCTTAATTCCAATTTCTTTTTTCTTTCTTTCTTTTTTTTTTTTGACGGAGTCTCGCTCTGTTGCCCAGGCTGGAGTGCAGCGGCGGGCTCTCGGCTCACTGCAAGCTCCGCCTCCCAGGTTCATGC RR: AAAAGAAAACATCTTCAAAAAATGAAGTCGAATATAAATACTTTATCATAGTTGCTCTAGAATTAAGGTTAAAGAAAAAAGAAAGAAAGAAAAAAAAAAAACTGCCTCAGAGCGAGACAACGGGTCCGACCTCACGTCGCCGCCCGAGAGCCGAGTGACGTTCGAGGCGGAGGGTCCAAGTACG F2: 3 TACG 2 Unidirectional alignment (log-probability: -41.7) AGAAGTTTTTTACTTCAGCTTATATTTATGtAATtGTATCgcAtGAGATCTTAATTCCAATTTCTTTTTTCTT---------- AGAAGTTTTTTACTTCAGCTTATATTTATGAAATAGTATCA-ACGAGATCTTAATTCCAATTTCTTTTTTCTTTCTTTCTTTT Template switch alignment (log-probability: -27.2) AGAAGTTTTTTACTTCAGCTTATATTTATGtAATtGTATC|GCAT|GAGATCTTAATTCCAATTTCTTTTTTCTT AGAAGTTTTTTACTTCAGCTTATATTTATGAAATAGTATC|GCAT|GAGATCTTAATTCCAATTTCTTTTTTCTT ========== Event 3409 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AAATGGTAATTAATTTCAGAA------ACTGGATATCCAGGAGATTAATGGACTGTGTAA ↑ 1 4 2 Chimp: aaATGGTAATTAATTTCAGAAAAATGAAATGGTAATCCAGGAGATTAATGGACTGTGTAA Gorilla: aaGTGGTAATTAATTTCAGAC------ACTGGATATCCAGGAGATTAACGGACTGTGTAA Human: AAATGGTAATTAATTTCAGAA------ACTGGATATCCAGGAGATTAATGGACTGTGTAA Cluster: [ ] Orangutan: aaATGGTAATTAATTTCAGAA------ACTGGATAGCCAGGAGATTAATGGACTGTGTAA Chimp > Human ------------- chr7:46720856-46720861 Template switch process: F1: L TCATAGACATTTATGGAATGAAATGGTAATTAATTTCAGAAA 1 F3: 4 ATCCAGGAGATTAATGGACTGTGTAAGAGTTAGTCAAACC R RF: TCATAGACATTTATTGAATGAAATGGTAATTAATTTCAGAAAAATGAAATGGTAATCCAGGAGATTAATGGACTGTGTAAGAGTTAGTCAAACC RR: AGTATCTGTAAATAACTTACTTTACCATTAATTAAAGTCTTTTTACTTTACCATTAGGTCCTCTAATTACCTGACACATTCTCAATCAGTTTGG F2: 3 TAGGTC 2 Unidirectional alignment (log-probability: -35.3) ATAGACATTTATgGAATGAAATGGTAATTAATTTCAGA------AAcTGGatATCCAGGAGATTAATGGACTGTGTAAGAGTTAGTCAAACC ATAGACATTTATTGAATGAAATGGTAATTAATTTCAGAAAAATGAAATGGTAATCCAGGAGATTAATGGACTGTGTAAGAGTTAGTCAAACC Template switch alignment (log-probability: -22) ATAGACATTTATgGAATGAAATGGTAATTAATTTCAGAAA|CTGGAT|ATCCAGGAGATTAATGGACTGTGTAAGAGTTAGTCAAACC ATAGACATTTATTGAATGAAATGGTAATTAATTTCAGAAA|CTGGAT|ATCCAGGAGATTAATGGACTGTGTAAGAGTTAGTCAAACC ========== Event 3410 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 256 Detected in comparisons: 1256 Multiple sequence alignment: Human: TTTCTTGGGGAAGCTTGAAACGTGCATAAGCCGAGTTCACCAGATGAGCTCTCCTGGGGACGTAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCAC----TGTGGCCAGGCTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGAACATTGCAGGAGAGAGGAATTCCTT ↓ 3 1 2 4 Chimp: TTTCTTGGGGAAGCTTGAAACGTGCATCAGCCGAGTTCACCAGATGAGCTCTCCTGGGGACATAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGATGTGCTCAGATACAGATGCTTTTACATTTCTTTATCCAC--AGTCTGGCC--ACAGTGGATAAAGAAATGCAAAAGCATCTGTATCTGAGCACATCACAGGAGAGAGGAATTCCTT ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: TTTCTTGGGGAAGCTTGAAATGTGCATAAGCCGAGTTCACCAGATGAGCTCTCCTGGGGACGTAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCAC----TGTGGCCAGACTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGCACATCGCAGGAGAGAGGAATTCCTT Human: TTTCTTGGGGAAGCTTGAAACGTGCATAAGCCGAGTTCACCAGATGAGCTCTCCTGGGGACGTAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCAC----TGTGGCCAGGCTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGAACATTGCAGGAGAGAGGAATTCCTT Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Human > Chimp ------------- chr7:119767535-119767603 Template switch process: F1: L GACATAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTT 1 F3: 4 ACAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATGCAGTCTCGTCCTATATTA R RF: GACGTAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCACTGTGGCCAGGCTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGAACATTGCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATTCAGTCTCGTCCTATATTA RR: CTGCATTCCCTGTTCTGACATCCCGGTGATCGACCAACCCTTCCTTAAGGAGAGAGGACGCTACACGAGTCTATGTCTACGAAAACGTAAAGAAATAGGTGACACCGGTCCGACACCTATTTCTTTACATTTTCGTAGACATAGACTCTTGTAACGTCCTCTCTCCTTAAGGAAGGGTTGGTCGGTCACCGGTAAGTCAGAGCAGGATATAAT F2: 3 CTACACGAGTCTATGTCTACGAAAACGTAAAGAAATAGGTGACACCGGTCTGACACCTATTTCTTTACA 2 Unidirectional alignment (log-probability: -79.2) ATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTTaCATTTCTTTATCCACagTcTGGCCA--CaGTGGATAAAGAAATGcAAAAGCATCTGTATCTGAGcACATcaCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCAT ATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCAC--TGTGGCCAGGCTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGAACATTGCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCAT Template switch alignment (log-probability: -48.5) ATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTT|ACATTTCTTTATCCACAGtCTGGCCACAGTGGATAAAGAAATGCAAAAGCATCTGTATCTGAGCACATC|aCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCAT ATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTT|ACATTTCTTTATCCACAGCCTGGCCACAGTGGATAAAGAAATGCAAAAGCATCTGTATCTGAGCACATC|GCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCAT Gorilla > Chimp --------------- chr7:119767510-119767578 Template switch process: F1: L GACATAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGC 1 F3: 4 AAAAGCATCTGTATCTGAGCACATCACAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATGCAGTCTCGTCCTATATTA R RF: GACGTAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCAATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCACTGTGGCCAGACTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGCACATCGCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATGCAGTCTCGTCCTATATTA RR: CTGCATTCCCTGTTCTGACATCCCGGTGATCGACCAACCCTTCCTTAAGGAGAGAGGACGTTACACGAGTCTATGTCTACGAAAACGTAAAGAAATAGGTGACACCGGTCTGACACCTATTTCTTTACATTTTCGTAGACATAGACTCGTGTAGCGTCCTCTCTCCTTAAGGAAGGGTTGGTCGGTCACCGGTACGTCAGAGCAGGATATAAT F2: 3 CGTAAAGAAATAGGTGACACCGGTCTGACACCTATTTCTTTACATTTTCGTAGACATAGACTCGTGTAG 2 Unidirectional alignment (log-probability: -64.1) AGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCgATGTGCTCAGATACAGATGCTTTTaCATTTCTTTATCCACagTcTGGCC--ACaGTGGATAAAGAAATGcAAAAGCATCTGTATCTGAGCACATCaCAGGAGAGAGGAAT AGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCAATGTGCTCAGATACAGATGCTTTTGCATTTCTTTATCCAC--TGTGGCCAGACTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGCACATCGCAGGAGAGAGGAAT Template switch alignment (log-probability: -36.7) AGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGC|GATGTGCTCAGATACAGATGCTTTTACATTTCTTTATCCACAGTCTGGCCACAGTGGATAAAGAAATGC|AAAAGCATCTGTATCTGAGCACATCaCAGGAGAGAGGAAT AGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGC|GATGTGCTCAGATACAGATGCTTTTACATTTCTTTATCCACAGTCTGGCCACAGTGGATAAAGAAATGC|AAAAGCATCTGTATCTGAGCACATCGCAGGAGAGAGGAAT Chimp > Gorilla --------------- chr7:111409702-111409771 Template switch process: F1: L GACGTAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCAATGTGCTCAGATACAGATGCTTTT 1 F3: 4 CAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATGCAGTCTCGTCCTATATTA R RF: GACATAAGGGACAAGACTGTAGGGCCACTAGCTGGTTGGGAAGGAATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTTACATTTCTTTATCCACAGTCTGGCCACAGTGGATAAAGAAATGCAAAAGCATCTGTATCTGAGCACATCACAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATGCAGTCTCGTCCTATATTA RR: CTGTATTCCCTGTTCTGACATCCCGGTGATCGACCAACCCTTCCTTAAGGAGAGAGGACGCTACACGAGTCTATGTCTACGAAAATGTAAAGAAATAGGTGTCAGACCGGTGTCACCTATTTCTTTACGTTTTCGTAGACATAGACTCGTGTAGTGTCCTCTCTCCTTAAGGAAGGGTTGGTCGGTCACCGGTACGTCAGAGCAGGATATAAT F2: 3 GCTACACGAGTCTATGTCTACGAAAATGTAAAGAAATAGGTGTCAGACCGGTGTCACCTATTTCTTTACG 2 Unidirectional alignment (log-probability: -64.1) ATTCCTCTCTCCTGCaATGTGCTCAGATACAGATGCTTTTgCATTTCTTTATCCAC--TgTGGCCagACtGTGGATAAAGAAATGtAAAAGCATCTGTATCTGAGCACATCgCAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATG ATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTTACATTTCTTTATCCACAGTCTGGCC--ACAGTGGATAAAGAAATGCAAAAGCATCTGTATCTGAGCACATCACAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATG Template switch alignment (log-probability: -36.8) ATTCCTCTCTCCTGCaATGTGCTCAGATACAGATGCTTTT|GCATTTCTTTATCCACTGTGGCCAGACTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGCACATCG|CAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATG ATTCCTCTCTCCTGCGATGTGCTCAGATACAGATGCTTTT|GCATTTCTTTATCCACTGTGGCCAGACTGTGGATAAAGAAATGTAAAAGCATCTGTATCTGAGCACATCG|CAGGAGAGAGGAATTCCTTCCCAACCAGCCAGTGGCCATG ========== Event 3411 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GATCCCGAGACCCGCGCACTG------------------------GCACGCACGCCTTggtatg--cacagttgtacacgtgcgctgct--gtttccacgtggaaacacaaacacagtgctGCCGACGGAAGCGCCTGCCAGCGCCAGCCTTTCCTGCGGCCCCGG ↑ 3 2 4 1 Chimp: GATCCCAAGACCCGCGCACTG------------GCATGCACGTGTGCACGCACGCCTTGGTATG--CACAGTTCTACACGTGCGCTGCT--GTTTCCACGTGGAAACACAAACACAGTGCTGCCGACGGAAG----------CGCCAGCCTTTCCTGCGGCCCCGG Gorilla: GATCCCGAGACCCGCGCACTGGCATGCACGTGT------------GCACGCACGCCTTGGTATG----CAGTTCTACACGTGCGCTGCT--GTTTCCACGTGGAAACACAAACACAGTGCTGCCGACAGAAGCGCCTGCCAGCGCCAGCCTTTCCTGCGGCCCCGG Human: GATCCCGAGACCCGCGCACTG------------------------GCACGCACGCCTTggtatg--cacagttgtacacgtgcgctgct--gtttccacgtggaaacacaaacacagtgctGCCGACGGAAGCGCCTGCCAGCGCCAGCCTTTCCTGCGGCCCCGG Cluster: [ ] Orangutan: GATCCCGAGACCCGTGCACATGCAGGCACGTGT------------GCACGCACGCCTTGGTATGCA--CAGTTCTACACGTGCGGTGCTGTGTTTCCACGTGAAAACACAAACACAGTGCTGCAGACGGAAGCACCTCCCAGCGCCAGCCTTTCCTGCGGCCCCGG Chimp > Human ------------- chr7:154553258-154553262 Template switch process: F1: L GTTTCCACGTGGAAACACAAACACAGTGCTGCCGACGGAAGCGCC 1 F3: 4 GCGCCAGCCTTTCCTGCGGCCCCGGCTCAGCGGCCCTGGGC R RF: TGGCATGCACGTGTGCACGCACGCCTTGGTATGCACAGTTCTACACGTGCGCTGCTGTTTCCACGTGGAAACACAAACACAGTGCTGCCGACGGAAGCGCCAGCCTTTCCTGCGGCCCCGGCTCAGCGGCCCTGGGC RR: ACCGTACGTGCACACGTGCGTGCGGAACCATACGTGTCAAGATGTGCACGCGACGACAAAGGTGCACCTTTGTGTTTGTGTCACGACGGCTGCCTTCGCGGTCGGAAAGGACGCCGGGGCCGAGTCGCCGGGACCCG F2: 3 ACCGT 2 Unidirectional alignment (log-probability: -25.3) CACGTGGAAACACAAACACAGTGCTGCCGACGGAagcgcctgccAGCGCCAGCCTTTCCTGCGGCCCCGGCTCAGCGGCCCTGGG CACGTGGAAACACAAACACAGTGCTGCCGACGGA----------AGCGCCAGCCTTTCCTGCGGCCCCGGCTCAGCGGCCCTGGG Template switch alignment (log-probability: -16) CACGTGGAAACACAAACACAGTGCTGCCGACGGAAGCGCC|TGCCA|GCGCCAGCCTTTCCTGCGGCCCCGGCTCAGCGGCCCTGGG CACGTGGAAACACAAACACAGTGCTGCCGACGGAAGCGCC|TGCCA|GCGCCAGCCTTTCCTGCGGCCCCGGCTCAGCGGCCCTGGG ========== Event 3412 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GGGCCGCACGCCCAGACACCTCCCCTTCGCGCGAATCCAGTGTTCTGAGCTCCACTCAG------------ Chimp: GGGCAGCACGCTCAAACACCTCCCCTTCGCGCGAATCCAGTGTTCTGAGCTCCACTCAG---------GTG Gorilla: GGGCCGCACGCCCAGACACCTAGCTTTCGCGCGAATCCAGTATTCTGAGCTCCACTCAGGTGGCGCAG--- ↑ 1 4 3 2 Human: GGGCCGCACGCCCAGACACCTCCCCTTCGCGCGAATCCAGTGTTCTGAGCTCCACTCAG------------ Cluster: [ ] Orangutan: GGGCCGCGGCCGCAA-AAC-------CAGCGGGAATCCAGTGCTCTGAGCTCCAC---------------- Human > Gorilla --------------- chr7:154441037-154441040 Template switch process: F1: L CCAGGAAGGTGGCGGGGCTGGGGCCGCACGCCCAGACACCT 1 F3: 4 TTCGCGCGAATCCAGTATTCTGAGCTCCACTCAGGTGGCG R RF: CCAGGAAGGTGGCGGGGCTGGGGCCGCACGCCCAGACACCTCCCCTTCGCGCGAATCCAGTGTTCTGAGCTCCACTCAGGTGGCT RR: GGTCCTTCCACCGCCCCGACCCCGGCGTGCGGGTCTGTGGAGGGGAAGCGCGCTTAGGTCACAAGACTCGAGGTGAGTCCACCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -38.6) CAGGAAGGTGGCGGGGCTGGGGCCGCACGCCCAGACACCTagCtTTCGCGCGAATCCAGTaTTCTGAGCTCCACTCAGgtggcg CAGGAAGGTGGCGGGGCTGGGGCCGCACGCCCAGACACCTCCCCTTCGCGCGAATCCAGTGTTCTGAGCTCCACTCAG------ Template switch alignment (log-probability: -27.3) CAGGAAGGTGGCGGGGCTGGGGCCGCACGCCCAGACACCT|AGCT|TTCGCGCGAATCCAGTaTTCTGAGCTCCACTCAGGTGGCg CAGGAAGGTGGCGGGGCTGGGGCCGCACGCCCAGACACCT|AGCT|TTCGCGCGAATCCAGTGTTCTGAGCTCCACTCAGGTGGCT ========== Event 3413 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACAGGCCATAGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGACTGGGTTAGAGTCCTCACTATGCCACTTCCTCTCC ↑ 3 2 1 4 Chimp: ACAGGCCATAGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAAC---CAAGCCCCATCACTATGCCACTTCCTCTCC Gorilla: ACAGGCCATAGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAAC---CAAGCCCCCTCACTATGCCACTTCCTCTCC ↓ 3 2 1 4 Human: ACAGGCCATAGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGACTGGGTTAGAGTCCTCACTATGCCACTTCCTCTCC Cluster: [ ] Orangutan: ACAGGCCATAGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAAC---CAAGCCCCCTCACTATGCCACTTCCTCTCC Chimp > Human ------------- chr7:47225963-47225976 Template switch process: F1: L AGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA 1 F3: 4 TCACTATGCCACTTCCTCTCCCACTAGGCCATGTCCTCAG R RF: AGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAACCAAGCCCCATCACTATGCCACTTCCTCTCCCACTAGGACATGTCCTCAG RR: TCGTCTTGAACCTGAGATTGGGTCAGTAAGAGTACAGTTCTTGGTTCGGGGTAGTGATACGGTGAAGGAGAGGGTGATCCTGTACAGGAGTC F2: 3 CCTGAGATTGGGTC 2 Unidirectional alignment (log-probability: -47.8) GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAG-----------ActgggttagagtccTCACTATGCCACTTCCTCTCCCACTAGGcCATGTCCTCAG GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAACCAAGCCCCA--------------TCACTATGCCACTTCCTCTCCCACTAGGACATGTCCTCAG Template switch alignment (log-probability: -23) GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA|CTGGGTTAGAGTCC|TCACTATGCCACTTCCTCTCCCACTAGGcCATGTCCTCAG GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA|CTGGGTTAGAGTCC|TCACTATGCCACTTCCTCTCCCACTAGGACATGTCCTCAG Gorilla > Human --------------- chr7:47225963-47225974 Template switch process: F1: L AGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA 1 F3: 4 CCTCACTATGCCACTTCCTCTCCCACTAGGCCATGTCCTC R RF: AGCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAACCAAGCCCCCTCACTATGCCACTTCCTCTCCCACTAGGCCCTGTCCTC RR: TCGTCTTGAACCTGAGATTGGGTCAGTAAGAGTACAGTTCTTGGTTCGGGGGAGTGATACGGTGAAGGAGAGGGTGATCCGGGACAGGAG F2: 3 TGAGATTGGGTC 2 Unidirectional alignment (log-probability: -42.4) GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA--------CtgggttagagtCCTCACTATGCCACTTCCTCTCCCACTAGGCCaTGTCCTC GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGAACCAAGCCC-----------CCTCACTATGCCACTTCCTCTCCCACTAGGCCCTGTCCTC Template switch alignment (log-probability: -22.8) GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA|CTGGGTTAGAGT|CCTCACTATGCCACTTCCTCTCCCACTAGGCCaTGTCCTC GCAGAACTTGGACTCTAACCCAGTCATTCTCATGTCAAGA|CTGGGTTAGAGT|CCTCACTATGCCACTTCCTCTCCCACTAGGCCCTGTCCTC ========== Event 3414 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCTCTCTGAGCTGGCAGTGC--AGAGGTACGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCTAGCAAATGAACCGCCTGAGGAAATGTCCCCAAGCTGTGGCCTCTCATAGGTCACC Chimp: AGCTCTCTGAGCTGGCAGTGC--AGAGGTACGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCTAGCAAATGAACCGCCTGAGGAAATGTCCCCAAGCAGTGGCCTCTCATAGGTCACC ↓ 1 4 3 2 Gorilla: AGCCCTCTGAGCTGGCAGTGC----AAGCTCGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCTAGCAAATGAACCGCCTGAGGAAATGTCCCCAAGCTGTGGCCTCTCATAGGTCACC ↑ 1 4 3 2 Human: AGCTCTCTGAGCTGGCAGTGC--AGAGGTACGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCTAGCAAATGAACCGCCTGAGGAAATGTCCCCAAGCTGTGGCCTCTCATAGGTCACC Cluster: [ ] Orangutan: AGCTCTCTGAGCTGGCAGTGCAG--AGGTACGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCTAGCAAATGAACCGCCTGAGGAAATGTCCCCAAGCTGTGGCCTCTCATAGGTCACC Human > Gorilla --------------- chr7:111071085-111071088 Template switch process: F1: L TCCTCAGAAAGCAATCCAAGAGCCCTCTGAGCTGGCAGTGCA 1 F3: 4 CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA R RF: TCCTCAGAAAGCAATCCAAGAGCTCTCTGAGCTGGCAGTGCAGAGGTACGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCTAGCAAATGAACCGCCTGAGGAAATGTCCCCAAGCT RR: AGGAGTCTTTCGTTAGGTTCTCGAGAGACTCGACCGTCACGTCTCCATGCCTCGAACGACAAATACGTCTGGAAGAGACCTCTCCACTCGTAACTAGGACCATCCGTCGCATGGTCTCGATCGTTTACTTGGCGGACTCCTTTACAGGGGTTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -30.7) CTCAGAAAGCAATCCAAGAGCcCTCTGAGCTGGCAGTGCA-----AgctCGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA CTCAGAAAGCAATCCAAGAGCTCTCTGAGCTGGCAGTGCAGAGGTA---CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA Template switch alignment (log-probability: -21.8) CTCAGAAAGCAATCCAAGAGCcCTCTGAGCTGGCAGTGCA|AGCT|CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA CTCAGAAAGCAATCCAAGAGCTCTCTGAGCTGGCAGTGCA|AGCT|CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA Chimp > Gorilla --------------- chr7:111071085-111071088 Template switch process: F1: L TCCTCAGAAAGCAATCCAAGAGCCCTCTGAGCTGGCAGTGCA 1 F3: 4 CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA R RF: TCCTCAGAAAGCAATCCAAGAGCTCTCTGAGCTGGCAGTGCAGAGGTACGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGAGCATTGATCCTGGTAGGCAGCGTACCAGAGCT RR: AGGAGTCTTTCGTTAGGTTCTCGAGAGACTCGACCGTCACGTCTCCATGCCTCGAACGACAAATACGTCTGGAAGAGACCTCTCCACTCGTAACTAGGACCATCCGTCGCATGGTCTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -30.7) CTCAGAAAGCAATCCAAGAGCcCTCTGAGCTGGCAGTGCA-----AgctCGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA CTCAGAAAGCAATCCAAGAGCTCTCTGAGCTGGCAGTGCAGAGGTA---CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA Template switch alignment (log-probability: -21.8) CTCAGAAAGCAATCCAAGAGCcCTCTGAGCTGGCAGTGCA|AGCT|CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA CTCAGAAAGCAATCCAAGAGCTCTCTGAGCTGGCAGTGCA|AGCT|CGGAGCTTGCTGTTTATGCAGACCTTCTCTGGAGAGGTGA ========== Event 3415 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCATCAGCCGCAGCCAGGACATGGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGC----------------AGCAGGCGATGAGGGCAGCAGGGGGTTCCGCTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTTAAAAAGAGCAGCAAGCCTATCACAAAGTTCTCTCTCCCTCAAGCAGCCAGCTGGAGAGCGGGGAAAGGCTCCTGGCTTGGCAAGTGCCCAGACGTAGCACCGGGACAGTGGAAGAAGATGCT Chimp: GCATCAGCCGCAGCCAGGACATGGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGC----------------AGCAGGCGATGAGGGCAGCAGGGGGTTCCACTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTTAAAAAGAGCAGCAAGCCTATCACAAAGTTCTCTCTCCCTCAAGCAGCCAGCTGGAGAGCGGGGAAAGGCTCCTGGCTTGGCAAGTGCCCAGACGTAGCACCGGGACAGTGGAAGAAGGTGCT ↑ 4 1 3 2 Gorilla: GCATCAGCCGTAGCCAGGACATGGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGC--------------------------------AGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTTAAAAAGAGCAGCAAGCCTATCACGAAGTTCTCTCTCCCTCAAGCAGCCAGCTGGAGAGCGGGGAAAGGCTCCTGGCTTGGCAAGTGCCCAGACGTAGCACCGGGACAGTGGAAGAAGATGCT ↓ 3 2 4 1 Human: GCATCAGCCGCAGCCAGGACATGGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGC----------------AGCAGGCGATGAGGGCAGCAGGGGGTTCCGCTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTTAAAAAGAGCAGCAAGCCTATCACAAAGTTCTCTCTCCCTCAAGCAGCCAGCTGGAGAGCGGGGAAAGGCTCCTGGCTTGGCAAGTGCCCAGACGTAGCACCGGGACAGTGGAAGAAGATGCT Cluster: [ ] Orangutan: GTATCAGCCGCAGCCAGGACATGGGGATCCCTGATAGGAGAGCCCAGCAAAGGCCCCTAGGGCAGCAGGCAATGGGGGC----------------AGCAGGAGGTTCCGCTGACTTCCCCAGGACCTCCTGTAGCCTCAGCTTAAAAAGAGCAGCAAGCCTATCACAAAGTTC--TCTCCCTCAAGCAGCCAGCTGGAGAGCGGGGAAAGGCTCCTGGCTTGGCAACTGCCCAGACGGAGCACAGGGACAGCGGAAGAAGACGCT Gorilla > Human --------------- chr7:47502580-47502584 Template switch process: F1: L GGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGG 1 F3: 4 AGGGCAGCAGGGGGTTCCGCTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTT R RF: CATGGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTT RR: GTACCCCTAGGGACTACCCTCTCGGGTCGTTTCCGGGGGTCCCGTCGTCCCTCAAGGCGACTGAAGGGGTCCTGGAGGACATCAGAGTCGAA F2: 3 GTAGC 2 Unidirectional alignment (log-probability: -39.5) CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGgcagcaggcgatgaggGCAGCAGGGgGTTCCGCTGACTTCCCCAGGACCTCCT CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGG----------------GCAGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCT Template switch alignment (log-probability: -27.9) CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGG|CgATG|AGGGCAGCAGGGgGTTCCGCTGACTTCCCCAGGACCTCCT CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGG|CCATG|AGGGCAGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCT Gorilla > Chimp --------------- chr7:46921250-46921254 Template switch process: F1: L GGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGG 1 F3: 4 AGGGCAGCAGGGGGTTCCACTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTTAAAAAG R RF: GGGGATCCCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCTGTAGTCTCAGCTTAAAAAGAGCAGCAAGCCTATCACGAAGTTCTCTCTCCCTCAAGCAGCCAGCTGGAGAGCGGGGAAAGGCTCCTGGCTTGGCAAGTGCCCAGACGTAGCACCG RR: CCCCTAGGGACTACCCTCTCGGGTCGTTTCCGGGGGTCCCGTCGTCCCTCAAGGCGACTGAAGGGGTCCTGGAGGACATCAGAGTCGAATTTTTCTCGTCGTTCGGATAGTGCTTCAAGAGAGAGGGAGTTCGTCGGTCGACCTCTCGCCCCTTTCCGAGGACCGAACCGTTCACGGGTCTGCATCGTGGC F2: 3 GTAGC 2 Unidirectional alignment (log-probability: -45.1) CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGgcagcaggcgatgaggGCAGCAGGGgGTTCCaCTGACTTCCCCAGGACCTCCT CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGG----------------GCAGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCT Template switch alignment (log-probability: -33.5) CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGG|CGaTG|AGGGCAGCAGGGgGTTCCaCTGACTTCCCCAGGACCTCCT CCTGATGGGAGAGCCCAGCAAAGGCCCCCAGGGCAGCAGG|CGGTG|AGGGCAGCAGGGAGTTCCGCTGACTTCCCCAGGACCTCCT ========== Event 3416 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGTGAAACATGTGGTTCTAGATTTCAAACTTCCAACTAACTATCAGGGTTTGTGAAGTTtct Chimp: AAGTGAAACGTGTGGTTCTAGT-----TACTTGGAAGTAACTGTCAGGGTTTGTGAAGTTtct ↑ 1 3 4 2 Gorilla: AAGTGAAACGTGTGGTTCTAGATTTCAAACTTCCAAGTAACTATCAGGGTTTGTGAAGTTtct Human: AAGTGAAACATGTGGTTCTAGATTTCAAACTTCCAACTAACTATCAGGGTTTGTGAAGTTtct Cluster: [ ] Orangutan: AAGTGAAACATGTGGTTCTAGATTTCAAACTTCCAAGTAACTGTCAGGGTTTGTGAAGTTtct Gorilla > Chimp --------------- chr7:48079110-48079117 Template switch process: F1: L GACTCTCAGTAGGAAGAGGAAAGTGAAACGTGTGGTTCTAG 1 F3: 4 AAGTAACTGTCAGGGTTTGTGAAGTTTCTGGGATTTTTATTCTAATTGC R RF: GACTCTCAGTAGGAAGAGGAAAGTGAAACGTGTGGTTCTAGATTTCAAACTTCCAAGTAACTATCAGGGTTTGTGAAGTTTCTGGGATTTTTATTCTAATTGC RR: CTGAGAGTCATCCTTCTCCTTTCACTTTGCACACCAAGATCTAAAGTTTGAAGGTTCATTGATAGTCCCAAACACTTCAAAGACCCTAAAAATAAGATTAACG F2: 3 GGTTCATT 2 Unidirectional alignment (log-probability: -33.5) ACTCTCAGTAGGAAGAGGAAAGTGAAACGTGTGGTTCTAGtT-----ACTTggAAGTAACTgTCAGGGTTTGTGAAGTTTCTGGGATTTTTAT ACTCTCAGTAGGAAGAGGAAAGTGAAACGTGTGGTTCTAGATTTCAAACTTCCAAGTAACTATCAGGGTTTGTGAAGTTTCTGGGATTTTTAT Template switch alignment (log-probability: -22.5) ACTCTCAGTAGGAAGAGGAAAGTGAAACGTGTGGTTCTAG|TTACTTGG|AAGTAACTgTCAGGGTTTGTGAAGTTTCTGGGATTTTTAT ACTCTCAGTAGGAAGAGGAAAGTGAAACGTGTGGTTCTAG|TTACTTGG|AAGTAACTATCAGGGTTTGTGAAGTTTCTGGGATTTTTAT ========== Event 3417 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: TTCTGATATCCCTGGGGTGCTGGCCACCTACAGTGGCCAAGATGAAGTCAGAGTGTGA ↑ 13 4 2 Chimp: TTCTGATATCCCTGGGGTGCTTGT------AGGTGGCCAAGATGAAGTCAGAGTGTGA Gorilla: Human: TTCTGATATCCCTGGGGTGCTGGCCACCTACAGTGGCCAAGATGAAGTCAGAGTGTGA Cluster: [ ] Orangutan: Chimp > Human ------------- chr7:108489365-108489375 Template switch process: F1: L CCCTCTCCAGCTGCAGTTGTTTCTGATATCCCTGGGGTGCT 1 F3: 4 GTGGCCAAGATGAAGTCAGAGTGTGAGGTGCCTGAACTGG R RF: CCCTCTCCAGCTGCAGTTGTTTCTGATATCCCTGGGGTGCTTGTAGGTGGCCAAGATGAAGTCAGAGTGTGAGGTGCCTGAACTGG RR: GGGAGAGGTCGACGTCAACAAAGACTATAGGGACCCCACGAACATCCACCGGTTCTACTTCAGTCTCACACTCCACGGACTTGACC F2: 3 ACATCCACCGG 2 Unidirectional alignment (log-probability: -35.7) CCTCTCCAGCTGCAGTTGTTTCTGATATCCCTGGGGTGCT----GGccacctacagTGGCCAAGATGAAGTCAGAGTGTGAGGTGCCTGAACTGG CCTCTCCAGCTGCAGTTGTTTCTGATATCCCTGGGGTGCTTGTAGG----------TGGCCAAGATGAAGTCAGAGTGTGAGGTGCCTGAACTGG Template switch alignment (log-probability: -16.6) CCTCTCCAGCTGCAGTTGTTTCTGATATCCCTGGGGTGCT|GGCCACCTACA|GTGGCCAAGATGAAGTCAGAGTGTGAGGTGCCTGAACTGG CCTCTCCAGCTGCAGTTGTTTCTGATATCCCTGGGGTGCT|GGCCACCTACA|GTGGCCAAGATGAAGTCAGAGTGTGAGGTGCCTGAACTGG ========== Event 3418 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: AGTGGTCAAAGGAGGAAATTGGTTCTATACTTTTAGAAATAGTCATATATTATAGGTGACATCAA Chimp: Gorilla: AGTGGTCAAAGGAGGAAATTGGTTCTATAATTTTATAG-AACCAATATATTATAGGTGACATCAA ↑ 3 2 1 4 Human: AGTGGTCAAAGGAGGAAATTGGTTCTATACTTTTAGAAATAGTCATATATTATAGGTGACATCAA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr7:53896325-53896332 Template switch process: F1: L ATAGTTTTGTTAAGTGGTCAAAGGAGGAAATTGGTTCTATAATTTTA 1 F3: 4 ATATATTATAGGTGACATCAATTTTCAGCATATACAAATA R RF: ATAGTTTTGTTAAGTGGTCAAAGGAGGAAATTGGTTCTATACTTTTAGAAATAGTCATATATTATAGGTGACATCAATTTTCAGCATATACAAATA RR: TATCAAAACAATTCACCAGTTTCCTCCTTTAACCAAGATATGAAAATCTTTATCAGTATATAATATCCACTGTAGTTAAAAGTCGTATATGTTTAT F2: 3 ACCAAGAT 2 Unidirectional alignment (log-probability: -38.2) TGTTAAGTGGTCAAAGGAGGAAATTGGTTCTATAaTTTTA---------tagaaccaATATATTATAGGTGACATCAATTTTCAGCATATACAAATA TGTTAAGTGGTCAAAGGAGGAAATTGGTTCTATACTTTTAGAAATAGTC--------ATATATTATAGGTGACATCAATTTTCAGCATATACAAATA Template switch alignment (log-probability: -22.4) TGTTAAGTGGTCAAAGGAGGAAATTGGTTCTATAaTTTTA|TAGAACCA|ATATATTATAGGTGACATCAATTTTCAGCATATACAAATA TGTTAAGTGGTCAAAGGAGGAAATTGGTTCTATACTTTTA|TAGAACCA|ATATATTATAGGTGACATCAATTTTCAGCATATACAAATA ========== Event 3419 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTGTTCAAGGAAGGAGGGCTTAGTT----CTGCGAGTTTCTGGGGTTTAATTTGAT ↓ 1 3 4 2 Chimp: GTGTTCAAGGAAGGAGGGCTTCCTCGCAGAAGCGAGTTTCTGGGGTTTAATTTGAT Gorilla: GTGTTCAAGGAAGGAGGGCTTAGTT----CTGTGAGTTTCTGGGGTTTAATTTGAT Human: GTGTTCAAGGAAGGAGGGCTTAGTT----CTGCGAGTTTCTGGGGTTTAATTTGAT Cluster: [ ] Orangutan: GTGTTCAAGGAGGGAGGGCTTAGTT----CTGCGAGTTTCTGGGGTTTTATTTGAT Human > Chimp ------------- chr7:51178021-51178029 Template switch process: F1: L TGGTGTTTCCATTGCTCATTGTGTTCAAGGAAGGAGGGCTTC 1 F3: 4 GCGAGTTTCTGGGGTTTAATTTGATGAATTCATCTGCTCA R RF: TGGTGTTTCCATTGCTCATTGTGTTCAAGGAAGGAGGGCTTAGTTCTGCGAGTTTCTGGGGTTTAATTTGATGAATTCATCTGCTCA RR: ACCACAAAGGTAACGAGTAACACAAGTTCCTTCCTCCCGAATCAAGACGCTCAAAGACCCCAAATTAAACTACTTAAGTAGACGAGT F2: 3 AAGACGCTC 2 Unidirectional alignment (log-probability: -34.3) GTGTTTCCATTGCTCATTGTGTTCAAGGAAGGAGGGCTTcctcgcagaA-----GCGAGTTTCTGGGGTTTAATTTGATGAATTCATCTGCTCA GTGTTTCCATTGCTCATTGTGTTCAAGGAAGGAGGGCTT---------AGTTCTGCGAGTTTCTGGGGTTTAATTTGATGAATTCATCTGCTCA Template switch alignment (log-probability: -22.4) GTGTTTCCATTGCTCATTGTGTTCAAGGAAGGAGGGCTTc|CTCGCAGAA|GCGAGTTTCTGGGGTTTAATTTGATGAATTCATCTGCTCA GTGTTTCCATTGCTCATTGTGTTCAAGGAAGGAGGGCTTA|CTCGCAGAA|GCGAGTTTCTGGGGTTTAATTTGATGAATTCATCTGCTCA ========== Event 3420 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTAATAATATACAATAATG--CTTATCACAAGATGGCCTGATACT ↓ 3 4 Chimp: GTTTAATAATATACAATAATGTAAGCATCACAAGATGGCCTGATACT ↑ 3 4 Gorilla: GTTTAATAATATACAATAATG--CTTATCACAAGATGGCCTGATACT Human: GTTTAATAATATACAATAATG--CTTATCACAAGATGGCCTGATACT Cluster: [ ] Orangutan: GTTTAATGATATACAATAATG--CTTATCACAAGATGGCTTGATACT Human > Chimp ------------- chr7:51598445-51598449 Template switch process: F1: L AAAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATG 1 F3: 4 ATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG R RF: AAAGAAAGATGCTCTAAAAAGTTTAATAATATACAATAATGCTTATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG RR: TTTCTTTCTACGAGATTTTTCAAATTATTATATGTTATTACGAATAGTGTTCTACCGGACTATGAAACGTCACGGCGTTAGAAC F2: 3 CGAAT 2 Unidirectional alignment (log-probability: -33) AAGAAAGATGCTCTAAAgAGTTTAATAATATACAATAATG--TaagcATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG AAGAAAGATGCTCTAAAAAGTTTAATAATATACAATAATGCTT----ATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG Template switch alignment (log-probability: -21.9) AAGAAAGATGCTCTAAAgAGTTTAATAATATACAATAATG|TAAGC|ATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG AAGAAAGATGCTCTAAAAAGTTTAATAATATACAATAATG|TAAGC|ATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG Gorilla > Chimp --------------- chr7:51598445-51598449 Template switch process: F1: L AAAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATG 1 F3: 4 ATCACAAGATGGCCTGATACTTTGCAGTGCCGCAATCTTG R RF: AAAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATGCTTATCACAAGATGGCCTGATACTTTGCAGTGCTGCAATCTTG RR: TTTCTTTCTACGAGATTTCTCAAATTATTATATGTTATTACGAATAGTGTTCTACCGGACTATGAAACGTCACGACGTTAGAAC F2: 3 CGAAT 2 Unidirectional alignment (log-probability: -32) AAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATG--TaagcATCACAAGATGGCCTGATACTTTGCAGTGCcGCAATCTTG AAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATGCTT----ATCACAAGATGGCCTGATACTTTGCAGTGCTGCAATCTTG Template switch alignment (log-probability: -21.9) AAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATG|TAAGC|ATCACAAGATGGCCTGATACTTTGCAGTGCcGCAATCTTG AAGAAAGATGCTCTAAAGAGTTTAATAATATACAATAATG|TAAGC|ATCACAAGATGGCCTGATACTTTGCAGTGCTGCAATCTTG ========== Event 3421 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ACAGCATTCTCCTCAACAGACTGTTGAGGAGTACCCAGACACCTGACCTCAACAGCTCCAGAACAGCCCTAAAACAGCTCCTCCCTAACCACCACTCAAG ↓ 1 4 3 2 Chimp: ACAGCATTCTCCTCAACAGACGAGCTGTGAGTACCCAGACACCCGACCTCAACAGCTCCAGAACAGCCCTAAAACAGCTCCTCCCTAACCACCACTCAAG Gorilla: Human: ACAGCATTCTCCTCAACAGACTGTTGAGGAGTACCCAGACACCTGACCTCAACAGCTCCAGAACAGCCCTAAAACAGCTCCTCCCTAACCACCACTCAAG Cluster: [ ] Orangutan: Human > Chimp ------------- chr7:55851200-55851206 Template switch process: F1: L CCAAAGGCAGTACAATGAGAACAGCATTCTCCTCAACAGAC 1 F3: 4 GAGTACCCAGACACCCGACCTCAACAGCTCCAGAACAGCC R RF: CCAAAGGCAGTACAATGAGAACAGCATTCTCCTCAACAGACTGTTGAGGAGTACCCAGACACCTGACCTCAACAGCTCCAGAACAGCCCTAAAACAGCTC RR: GGTTTCCGTCATGTTACTCTTGTCGTAAGAGGAGTTGTCTGACAACTCCTCATGGGTCTGTGGACTGGAGTTGTCGAGGTCTTGTCGGGATTTTGTCGAG F2: 3 TGTCGAG 2 Unidirectional alignment (log-probability: -33.1) CAAAGGCAGTACAATGAGAACAGCATTCTCCTCAACAGAcgagCTGT----GAGTACCCAGACACCcGACCTCAACAGCTCCAGAACAGCC CAAAGGCAGTACAATGAGAACAGCATTCTCCTCAACAGA----CTGTTGAGGAGTACCCAGACACCTGACCTCAACAGCTCCAGAACAGCC Template switch alignment (log-probability: -22.1) CAAAGGCAGTACAATGAGAACAGCATTCTCCTCAACAGAC|GAGCTGT|GAGTACCCAGACACCcGACCTCAACAGCTCCAGAACAGCC CAAAGGCAGTACAATGAGAACAGCATTCTCCTCAACAGAC|GAGCTGT|GAGTACCCAGACACCTGACCTCAACAGCTCCAGAACAGCC ========== Event 3422 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: --------GAAGTAAGGAAAG------AGCTCAGGAAGCTCCATGCCCTGGTCAAGGAGA Chimp: --------GAAGTAAGGAAAG---GGCAGCTTCCTGAGCTCCATGCCCTGGTCAAGGAGA Gorilla: --------GAAGTAAGGAAAGGGC---AGCTTCCTGAGCTCCATGCCCTGGTCAAGGAGA ↓ 1 3 4 2 ↑ 1 3 4 2 Human: --------GAAGTAAGGAAAG------AGCTCAGGAAGCTCCATGCCCTGGTCAAGGAGA Cluster: [ ] Orangutan: acatccctgaagtaaggAAAGGGC------------AGCTCCATGCCCTGGTCAAGGAGA Gorilla > Human --------------- chr7:110139530-110139538 Template switch process: F1: L TCTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAG 1 F3: 4 AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT R RF: TCTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGGGCAGCTTCCTGAGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT RR: AGAGACGTCCTTAAGAGTCGTGTAGGGACTTCATTCCTTTCCCGTCGAAGGACTCGAGGTACGGGACCAGTTCCTCTGACCGTCACATTCTCA F2: 3 AGGACTCGA 2 Unidirectional alignment (log-probability: -33.8) CTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGaGCtcaggA--------AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT CTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGGGC-----AGCTTCCTGAGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT Template switch alignment (log-probability: -16.9) CTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAG|AGCTCAGGA|AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT CTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAG|AGCTCAGGA|AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT Human > Gorilla --------------- chr7:109263529-109263537 Template switch process: F1: L TCTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGGGC 1 F3: 4 AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT R RF: TCTCTGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGAGCTCAGGAAGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT RR: AGAGACGTCCTTAAGAGTCGTGTAGGGACTTCATTCCTTTCTCGAGTCCTTCGAGGTACGGGACCAGTTCCTCTGACCGTCACATTCTCA F2: 3 GTCCTTCGA 2 Unidirectional alignment (log-probability: -38) TGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGgGC-----AgcttcctgAGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT TGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGAGCTCAGGA--------AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT Template switch alignment (log-probability: -22.5) TGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGgGC|AGCTTCCTG|AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT TGCAGGAATTCTCAGCACATCCCTGAAGTAAGGAAAGAGC|AGCTTCCTG|AGCTCCATGCCCTGGTCAAGGAGACTGGCAGTGTAAGAGT ========== Event 3423 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAATTCTCAGGCACCAAGGG--------------------CAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGGTACATATCCTCATAATTTTTATGAAACCCAAATAAAGCAAGCTCTAAGAGGAGTACTGGAATCTGTTAAACCCAATTTGGATGTG ↓ 4 1 3 2 Chimp: CCAATTCTCAGGCACCAAGGG----------CAGCAGATGGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGGTACATATCCTCATAATTTTTAAGAAACCCAAATAAAGCAAGCTCTAAGGGGAGTACTGGAATCTGTTAAACCCAATTTGGCTGTG Gorilla: CCAATTCTCAGGCACCAAGGGCAGCAGATGG----------CAAACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGGTACATATCCTCATAATTTTTATGAAACCCAAATAAAGTAAGCTCTAAGAGAAGTACTGGAATCTGTTAAGCCCAATTTGGATGTG Human: CCAATTCTCAGGCACCAAGGG--------------------CAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGGTACATATCCTCATAATTTTTATGAAACCCAAATAAAGCAAGCTCTAAGAGGAGTACTGGAATCTGTTAAACCCAATTTGGATGTG Cluster: [ ] Orangutan: CCAATTCTCAGGCACCAAGGGCAGCAGATGG----------CAAACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGGTACATATCCTCATAATTTTAATGAAACCCAAATAAAGCAAGCTCTAAGAGGAGTACTGGAATCTGTTAAACCCAATTTGGATGTG Human > Chimp ------------- chr7:54356388-54356392 Template switch process: F1: L GTTCCATTAGTAAGAATCTACCAATTCTCAGGCACCAAGGGCAG 1 F3: 4 GGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGG R RF: ATTCCATTAGTAAGAATCTACCAATTCTCAGGCACCAAGGGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCTGGTACATATCCTCATAATTTTTATGAAACCCAAATAAAGCAAGCTCTAAGAGGAGTACTGGAATCTG RR: TAAGGTAATCATTCTTAGATGGTTAAGAGTCCGTGGTTCCCGTCTGTTCAATGTTACAGGAAAACATCTACATGGACGACCATGTATAGGAGTATTAAAAATACTTTGGGTTTATTTCGTTCGAGATTCTCCTCATGACCTTAGAC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -31.3) CATTAGTAAGAATCTACCAATTCTCAGGCACCAAGggcagcagatGGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCT CATTAGTAAGAATCTACCAATTCTCAGGCACCAAG----------GGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCT Template switch alignment (log-probability: -22) CATTAGTAAGAATCTACCAATTCTCAGGCACCAAGGGCAG|CAGAT|GGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCT CATTAGTAAGAATCTACCAATTCTCAGGCACCAAGGGCAG|CAGAT|GGCAGACAAGTTACAATGTCCTTTTGTAGATGTACCTGCT ========== Event 3424 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACT---CGAGTCAGGTCAGCTCTGCCAC ↓ 3 2 1 4 Chimp: TCTTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACCTGCAGAGTCAGGTCAGCTCTGCCAC ↑ 3 2 1 4 Gorilla: TCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACT---CGAGTCAGGTCAGCTCTGCCAC Human: TCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACT---CGAGTCAGGTCAGCTCTGCCAC Cluster: [ ] Orangutan: TCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACT---TGAGTCAGGTCAGCTCTGCCAC Human > Chimp ------------- chr7:161575602-161575606 Template switch process: F1: L TTTTCTTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC 1 F3: 4 GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC R RF: TTTTCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACTCGAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC RR: AAAAGGAGCAGGGGTAGGAGGGACGTCTGCGACGGCCAGTGAGCTCAGTCCAGTCGAGACGGTGGCAGGACCCACGGCACGGG F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -32.9) TTTCtTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC-CtgcaGAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC TTTCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACTC----GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC Template switch alignment (log-probability: -21.9) TTTCtTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC|CTGCA|GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC TTTCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC|CTGCA|GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC Gorilla > Chimp --------------- chr7:161575602-161575606 Template switch process: F1: L TTTTCTTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC 1 F3: 4 GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCC R RF: TTTTCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACTCGAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCT RR: AAAAGGAGCAGGGGTAGGAGGGACGTCTGCGACGGCCAGTGAGCTCAGTCCAGTCGAGACGGTGGCAGGACCCACGGCACGGA F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -37.3) TTTCtTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACctgcaGAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCc TTTCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCACTC---GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCT Template switch alignment (log-probability: -27.4) TTTCtTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC|CTGCA|GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCc TTTCCTCGTCCCCATCCTCCCTGCAGACGCTGCCGGTCAC|CTGCA|GAGTCAGGTCAGCTCTGCCACCGTCCTGGGTGCCGTGCCT ========== Event 3425 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AATATAACTTTCTCTTGGGTCAGATTCATCTGACCTTCAGCAAGGCATCCAGCT Chimp: AATATAACTTTCTCTTGGGTCAGATTCATCTGACCTTCAGCAAGGCATCCAGCT ↑ 3 1 2 4 Gorilla: AATATAACTTTCTCTTGGGTCAGATGA----AGCCTTCAGCAAGGCATCCAGCT ↓ 3 1 2 4 Human: AATATAACTTTCTCTTGGGTCAGATTCATCTGACCTTCAGCAAGGCATCCAGCT Cluster: [ ] Orangutan: AATATAACTTTCTCTTGGGTCAGGTGA----AGCCTTCAGCAAGGCATCCAGCT Gorilla > Human --------------- chr7:55335531-55335538 Template switch process: F1: L ACCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAT 1 F3: 4 CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC R RF: ACCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGATGAAGCCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC RR: TGGGTAAAATTGGTTGTTATATTGAAAGAGAACCCAGTCTACTTCGGAAGTCGTTCCGTAGGTCGATCCCTACCCTGGGGTTTTG F2: 3 AGTCTACT 2 Unidirectional alignment (log-probability: -29.4) CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAttcatcTGA--CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGA------TGAAGCCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC Template switch alignment (log-probability: -16.7) CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAT|TCATCTGA|CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAT|TCATCTGA|CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC Gorilla > Chimp --------------- chr7:54762307-54762314 Template switch process: F1: L ACCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAT 1 F3: 4 CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC R RF: ACCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGATGAAGCCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC RR: TGGGTAAAATTGGTTGTTATATTGAAAGAGAACCCAGTCTACTTCGGAAGTCGTTCCGTAGGTCGATCCCTACCCTGGGGTTTTG F2: 3 AGTCTACT 2 Unidirectional alignment (log-probability: -29.4) CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAttcatcTGA--CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGA------TGAAGCCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC Template switch alignment (log-probability: -16.7) CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAT|TCATCTGA|CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC CCCATTTTAACCAACAATATAACTTTCTCTTGGGTCAGAT|TCATCTGA|CCTTCAGCAAGGCATCCAGCTAGGGATGGGACCCCAAAAC ========== Event 3426 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTGACTGAATGAGGAGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGG-GCATTGAGCACAGAGTCAAGACCAGTTAGAACCTCT Chimp: CTGACTGAATGAGGAGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGG-GCATTGAGCACAGAATCAAGACCAGTTAGAACCTCT Gorilla: CTGACTGAATGAGGAGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGACTCTGTGAGCACACCGTCAAGACCAGTTAGAACCTCT ↓ 3 2 1 4 ↑ 1 4 3 2 Human: CTGACTGAATGAGGAGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGG-GCATTGAGCACAGAGTCAAGACCAGTTAGAACCTCT Cluster: [ ] Orangutan: CTGACTGCATAAGGAGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGG-GCATTGAGCACAGAGTCAAGACCAATTAGAACCTCT Gorilla > Human --------------- chr7:104995376-104995380 Template switch process: F1: L AGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG 1 F3: 4 TGAGCACAGAGTCAAGACCAGTTAGAACCTCTATTTGCAATGAAATGAGC R RF: AGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGACTCTGTGAGCACACCGTCAAGACCAGTTAGAACCTCTATTTGCAATGAAATGAGC RR: TCAACTACGGACACGTGTCTTCTCACGTCTTACCGAAACACTGAGACACTCGTGTGGCAGTTCTGGTCAATCTTGGAGATAAACGTTACTTTACTCG F2: 3 TACGG 2 Unidirectional alignment (log-probability: -37.8) GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG-----GgcatTGAGCACAgaGTCAAGACCAGTTAGAACCTCTATTTGCAA GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGACTCTG----TGAGCACACCGTCAAGACCAGTTAGAACCTCTATTTGCAA Template switch alignment (log-probability: -27.6) GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG|GGCAT|TGAGCACAgaGTCAAGACCAGTTAGAACCTCTATTTGCAA GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG|GGCAT|TGAGCACACCGTCAAGACCAGTTAGAACCTCTATTTGCAA Human > Gorilla --------------- chr7:104048673-104048678 Template switch process: F1: L AGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG 1 F3: 4 TGAGCACACCGTCAAGACCAGTTAGAACCTCTATTTGCAATGAAATGAGC R RF: AGTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGGGCATTGAGCACAGAGTCAAGACCAGTTAGAACCTCTATTTGCAATGAAATGAGC RR: TCAACTACGGACACGTGTCTTCTCACGTCTTACCGAAACACCCGTAACTCGTGTCTCAGTTCTGGTCAATCTTGGAGATAAACGTTACTTTACTCG F2: 3 GTCTCA 2 Unidirectional alignment (log-probability: -39.2) GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTGactctG----TGAGCACAccGTCAAGACCAGTTAGAACCTCTATTTGCAA GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG-----GGCATTGAGCACAGAGTCAAGACCAGTTAGAACCTCTATTTGCAA Template switch alignment (log-probability: -27.8) GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG|ACTCTG|TGAGCACAccGTCAAGACCAGTTAGAACCTCTATTTGCAA GTTGATGCCTGTGCACAGAAGAGTGCAGAATGGCTTTGTG|ACTCTG|TGAGCACAGAGTCAAGACCAGTTAGAACCTCTATTTGCAA ========== Event 3427 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: caatgtgctgggattataggcatgagcctccgttcccagccAAAAGTGAAAATATTTAAAAGCTGAAAGCCAACAGTTTTAACAAAATTCCAATTACAACCAGAAAGATTCCTAAATAAAGATGCAAATAAAGTGGAATTATTATCTTGTTAT Chimp: caatgtgctgggattataggcatgagcctccgtgcccagccAAAAGTGAAAATATTTAAAAGCTGAAAGCCAACAGTTTTAACAAAATTCCAATTACAACCAGAAAGATTCCTAAATAAAGATGCAAATAAAGTGGAATTATTATCTTGTTAT ↑ 3 2 4 1 Gorilla: caatgtgctgggattataggcatgagcctccgtgcccagccAAAAGTGAAAATATTTAAAAGCTGAAAGCCAACAGTTTTAACAAAATTCCAATTACAGCCAGAAAGATTCCTAAA------------TAAAGTGGAATTATTATCTTGTTAT ↓ 3 2 4 1 Human: caatgtgctgggattataggcatgagcctccgttcccagccAAAAGTGAAAATATTTAAAAGCTGAAAGCCAACAGTTTTAACAAAATTCCAATTACAACCAGAAAGATTCCTAAATAAAGATGCAAATAAAGTGGAATTATTATCTTGTTAT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr7:56103674-56103677 Template switch process: F1: L GTTTTAACAAAATTCCAATTACAACCAGAAAGATTCCTAAATAAAG 1 F3: 4 AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATGGTT R RF: GCATGAGCCTCCGTGCCCAGCCAAAAGTGAAAATATTTAAAAGCTGAAAGCCAACAGTTTTAACAAAATTCCAATTACAGCCAGAAAGATTCCTAAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATGGTT RR: CGTACTCGGAGGCACGGGTCGGTTTTCACTTTTATAAATTTTCGACTTTCGGTTGTCAAAATTGTTTTAAGGTTAATGTCGGTCTTTCTAAGGATTTATTTCACCTTAATAATAGAACAATAGTTCTGATTTACCAA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -33.7) ACAAAATTCCAATTACAaCCAGAAAGATTCCTaaataaagatgcAAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG ACAAAATTCCAATTACAGCCAGAAAGATTCCT------------AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG Template switch alignment (log-probability: -21.9) ACAAAATTCCAATTACAaCCAGAAAGATTCCTAAATAAAG|ATGC|AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG ACAAAATTCCAATTACAGCCAGAAAGATTCCTAAATAAAG|ATGC|AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG Gorilla > Chimp --------------- chr7:55545439-55545442 Template switch process: F1: L GTTTTAACAAAATTCCAATTACAACCAGAAAGATTCCTAAATAAAG 1 F3: 4 AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATGGTT R RF: GCATGAGCCTCCGTGCCCAGCCAAAAGTGAAAATATTTAAAAGCTGAAAGCCAACAGTTTTAACAAAATTCCAATTACAGCCAGAAAGATTCCTAAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATGGTT RR: CGTACTCGGAGGCACGGGTCGGTTTTCACTTTTATAAATTTTCGACTTTCGGTTGTCAAAATTGTTTTAAGGTTAATGTCGGTCTTTCTAAGGATTTATTTCACCTTAATAATAGAACAATAGTTCTGATTTACCAA F2: 3 CGTA 2 Unidirectional alignment (log-probability: -33.7) ACAAAATTCCAATTACAaCCAGAAAGATTCCTaaataaagatgcAAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG ACAAAATTCCAATTACAGCCAGAAAGATTCCT------------AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG Template switch alignment (log-probability: -21.9) ACAAAATTCCAATTACAaCCAGAAAGATTCCTAAATAAAG|ATGC|AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG ACAAAATTCCAATTACAGCCAGAAAGATTCCTAAATAAAG|ATGC|AAATAAAGTGGAATTATTATCTTGTTATCAAGACTAAATG ========== Event 3428 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: ATAAGCCACAGTCCACTTACAGA----AAAGCTGGTCTTGCAGAGTCTCTTCAGA Chimp: ATAAGCCACAGTCCACTTACAGCTTTTCTAGCCACTCTTGCAGAGTCTCTTCAGA ↓ 3 1 2 4 Gorilla: ATAAGCCACAGTCCACTTACAGA----AAAGCTGGTCTTGCAGAGTCTCTTCAGA Human: ATAAGCCACAGTCCACTTACAGA----AAAGCTGGTCTTGCAGAGTCTCTTCAGA Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr7:57004019-57004026 Template switch process: F1: L ACGTGCAGAATGACTATAAATAAGCCACAGTCCACTTACAG 1 F3: 4 GTCTTGCAGAGTCTCTTCAGAGCATGCTTTATCACCCAGAG R RF: ACGTGCAGAATGACTATAAATAAGCCACAGTCCACTTACAGCTTTTCTAGCCACTCTTGCAGAGTCTCTTCAGAGCGTGCTTTATCACCCAGAG RR: TGCACGTCTTACTGATATTTATTCGGTGTCAGGTGAATGTCGAAAAGATCGGTGAGAACGTCTCAGAGAAGTCTCGCACGAAATAGTGGGTCTC F2: 3 GTCGAAAA 2 Unidirectional alignment (log-probability: -39.8) CGTGCAGAATGACTATAAATAAGCCACAGTCCACTTACAG-------------aaaagctggTCTTGCAGAGTCTCTTCAGAGCaTGCTTTATCACCCAGA CGTGCAGAATGACTATAAATAAGCCACAGTCCACTTACAGCTTTTCTAGCCAC---------TCTTGCAGAGTCTCTTCAGAGCGTGCTTTATCACCCAGA Template switch alignment (log-probability: -27.8) CGTGCAGAATGACTATAAATAAGCCACAGTCCACTTACAG|AAAAGCTG|gTCTTGCAGAGTCTCTTCAGAGCaTGCTTTATCACCCAGA CGTGCAGAATGACTATAAATAAGCCACAGTCCACTTACAG|AAAAGCTG|CTCTTGCAGAGTCTCTTCAGAGCGTGCTTTATCACCCAGA ========== Event 3429 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGCTCAAGACTCAGGTGAGTTCTGCCTCAGATGAGGCAGAACTTTCTCAATGAAGAGCTA ↑ 1 4 3 2 Chimp: AAGCTCAAGACTCAGGTGAGTGGT----AGGATGAGGCAGAACTTTCTCAATGAAGAGCTA Gorilla: AAGCTCAAGACTCAGGTGAGTGGT----GGGATGAGGCAGAACTTTCTCAATGAAGAGCTA ↓ 1 4 3 2 Human: AAGCTCAAGACTCAGGTGAGTTCTGCCTCAGATGAGGCAGAACTTTCTCAATGAAGAGCTA Cluster: [ ] Orangutan: Chimp > Human ------------- chr7:56554110-56554118 Template switch process: F1: L GTCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT 1 F3: 4 GATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG R RF: GTCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGTGGTAGGATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG RR: CAGTCGTAATAATTGTCACTTTCGAGTTCTGAGTCCACTCACCATCCTACTCCGTCTTGAAAGAGTTACTTCTCGATCCTAGTAAC F2: 3 ACTCCGTCT 2 Unidirectional alignment (log-probability: -34.3) TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGTtctgcctcaG-----ATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT---------GGTAGGATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG Template switch alignment (log-probability: -16.4) TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT|TCTGCCTCA|GATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT|TCTGCCTCA|GATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG Gorilla > Human --------------- chr7:56554110-56554118 Template switch process: F1: L GTCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT 1 F3: 4 GATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG R RF: GTCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGTGGTGGGATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG RR: CAGTCGTAATAATTGTCACTTTCGAGTTCTGAGTCCACTCACCACCCTACTCCGTCTTGAAAGAGTTACTTCTCGATCCTAGTAAC F2: 3 ACTCCGTCT 2 Unidirectional alignment (log-probability: -33.3) TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGTtcTGcctcaGATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGTGGTG----GGATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG Template switch alignment (log-probability: -16.9) TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT|TCTGCCTCA|GATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG TCAGCATTATTAACAGTGAAAGCTCAAGACTCAGGTGAGT|TCTGCCTCA|GATGAGGCAGAACTTTCTCAATGAAGAGCTAGGATCATTG ========== Event 3430 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCATGTTGGAAGGCTCA-ATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCAC ↓ 1 4 3 2 Chimp: CCATGTTGGAAGGCTCA-ATCCTCT-AAGGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCAC ↑ 1 4 3 2 Gorilla: CCATGTTGGAAGGCTCA-ATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCAC Human: TCATGTTGGAAGGCTCA-ATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCAC Cluster: [ ] Orangutan: CCATGTTGGAAGGCTTGACTTATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGCCAC Human > Chimp ------------- chr7:160527805-160527811 Template switch process: F1: L CTGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATC 1 F3: 4 GCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC R RF: CTGCCTCTCCTGGCATTTATATCATGTTGGAAGGCTCAATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC RR: GACGGAGAGGACCGTAAATATAGTACAACCTTCCGAGTTAGTAAATGTACGAATATTCGGAATCTCCTCTCCCTGAGAGAACAGTGACG F2: 3 GAATCTC 2 Unidirectional alignment (log-probability: -35) TGCCTCTCCTGGCATTTATAcCATGTTGGAAGGCTCAATCcTcTA-AgGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC TGCCTCTCCTGGCATTTATATCATGTTGGAAGGCTCAATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC Template switch alignment (log-probability: -22.1) TGCCTCTCCTGGCATTTATAcCATGTTGGAAGGCTCAATC|CTCTAAG|GCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC TGCCTCTCCTGGCATTTATATCATGTTGGAAGGCTCAATC|CTCTAAG|GCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC Gorilla > Chimp --------------- chr7:160527805-160527811 Template switch process: F1: L CTGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATC 1 F3: 4 GCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC R RF: CTGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC RR: GACGGAGAGGACCGTAAATATGGTACAACCTTCCGAGTTAGTAAATGTACGAATATTCGGAATCTCCTCTCCCTGAGAGAACAGTGACG F2: 3 GAATCTC 2 Unidirectional alignment (log-probability: -27.6) TGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATCcTcTA-AgGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC TGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATCATTTACATGCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC Template switch alignment (log-probability: -16.6) TGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATC|CTCTAAG|GCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC TGCCTCTCCTGGCATTTATACCATGTTGGAAGGCTCAATC|CTCTAAG|GCTTATAAGCCTTAGAGGAGAGGGACTCTCTTGTCACTGC ========== Event 3431 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTAAAGGCTGTCAGGGCTGG----GCTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCCAACCACAAAAATTGATTGATTTAATCACATTAATTGAAttttttttttgagatggagtttcactcttgttgcccaggctggagtgcaatggctctatgtc Chimp: CTTAAAGGCTGTCAGGGCTGG----GCTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCCAACCACAAAAATTGATTGATTTAATCACATTAATTGAAttttttttttgagatggagtttcactcttgttgcccaggctggagtgcaatggctctatgtc ↓ 1 4 3 2 Gorilla: CTTAAAGGCTGTCAGGGCTGGCAGCCTTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCCAACCACAAAAATTGATTGATTTAATCACATTAATTGAAttt-ttttttgagatggagtttcactcttgttgcccaggctggagtgcaatggctctatgtc ↑ 1 4 3 2 Human: CTTAAAGGCTGTCAGGGCTGG----GCTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCCAACCACAAAAATTGATTGATTTAATCACATTAATTGAAttttttttttgagatggagtttcactcttgttgcccaggctggagtgcaatggctctatgtc Cluster: [ ] Orangutan: Human > Gorilla --------------- chr7:96646856-96646861 Template switch process: F1: L TGTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGG 1 F3: 4 TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC R RF: TGTATATACTTATTGGCACTCTTAAAGGCTGTCAGGGCTGGGCTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCCAACCACAAAAATTGATTGATTTAATCACATTAATTGAATTTTTTTTTTGAGATGGAGTTTCACTCTTGTTGCCCAGGCTG RR: ACATATATGAATAACCGTGAGAATTTCCGACAGTCCCGACCCGAACTAGATTCGTGTTTTACTGAGTTAGTGTCTTGGCTGGGTTGGTGTTTTTAACTAACTAAATTAGTGTAATTAACTTAAAAAAAAAACTCTACCTCAAAGTGAGAACAACGGGTCCGAC F2: 3 TCCGAC 2 Unidirectional alignment (log-probability: -31.9) GTATATACTTAcTGGCACTCTTAAAGGCTGTCAGGGCTGGcaGCctTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC GTATATACTTATTGGCACTCTTAAAGGCTGTCAGGGCTGG--GC--TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC Template switch alignment (log-probability: -22) GTATATACTTAcTGGCACTCTTAAAGGCTGTCAGGGCTGG|CAGCCT|TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC GTATATACTTATTGGCACTCTTAAAGGCTGTCAGGGCTGG|CAGCCT|TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC Chimp > Gorilla --------------- chr7:96646856-96646861 Template switch process: F1: L TGTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGG 1 F3: 4 TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC R RF: TGTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGGGCTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCCAACCACAAAAATTGATTGATTTAATCACATTAATTGAATTTTTTTTTTGAGATGGAGTTTCACTCTTGTTGCCCAGGCTG RR: ACATATATGAATGACCGTGAGAATTTCCGACAGTCCCGACCCGAACTAGATTCGTGTTTTACTGAGTTAGTGTCTTGGCTGGGTTGGTGTTTTTAACTAACTAAATTAGTGTAATTAACTTAAAAAAAAAACTCTACCTCAAAGTGAGAACAACGGGTCCGAC F2: 3 TCCGAC 2 Unidirectional alignment (log-probability: -26.4) GTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGGcaGCctTTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC GTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGG--GC--TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC Template switch alignment (log-probability: -16.5) GTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGG|CAGCCT|TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC GTATATACTTACTGGCACTCTTAAAGGCTGTCAGGGCTGG|CAGCCT|TTGATCTAAGCACAAAATGACTCAATCACAGAACCGACCC ========== Event 3432 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: AATTGCACGTAGACGGTATGTATCTTCGCTGCTCCGGGTTAAGCCACTCAGTTCTTGACAGCTCGTGTGTGGCAGTGGCATGGAAATGTACTAGTTTCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAAACAGCAGAGAAGTCATTGGAGTGTT Chimp: AATTGCACGTAGACGGTATGTATCTTCGCTGCTCCGGGTTAAGCCACTCAGTTCTTGACAGCTCGTGTGTGGCAGCGGCATGGAAATGTACTAGTTTCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAGACACCAGAGAAGTCACTGGAGTGTT Gorilla: AATTGCACATAGACGGTATGTATCTTCGCTGCTCCGGGTTAAGCCACTCAGTTCTTGACAGCTCATGTGTGGCAGCGGCATGGAAATGTACTAGTTTCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAGATACCAGAGAAGTCATTGGAGTGTT ↑ 3 2 1 4 Human: AATTGCACGTAGACGGTATGTATCTTCGCTGCTCCGGGTTAAGCCACTCAGTTCTTGACAGCTCGTGTGTGGCAGTGGCATGGAAATGTACTAGTTTCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAAACAGCAGAGAAGTCATTGGAGTGTT Cluster: [ ] Orangutan: AAGTGCACATAGATGGTATGTATTTTCACTGCTCCGAGTTAAGCCACTCAGTTCTTGACAGTTCGTGTGTGGCAGCGGCATGGAAATGTACTAGTTTCAGACATCTAGATAGGAAATGCTGGCTCATTTCAGCAAAGACACCAGAGAAGTCATTGGAGTGTT Human > Gorilla --------------- chr7:152852554-152852558 Template switch process: F1: L TTCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAA 1 F3: 4 CAGAGAAGTCATTGGAGTGTTTTTTACTGTTAACTTCCCC R RF: GTATCTTCGCTGCTCCGGGTTAAGCCACTCAGTTCTTGACAGCTCGTGTGTGGCAGTGGCATGGAAATGTACTAGTTTCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAAACAGCAGAGAAGTCATTGGAGTGTTTTTTACTGTTAACTTCCCC RR: CATAGAAGCGACGAGGCCCAATTCGGTGAGTCAAGAACTGTCGAGCACACACCGTCACCGTACCTTTACATGATCAAAGTCCGTAGATCTATCCTTCGCGGCCGAGTAAAGTCGTTTTTGTCGTCTCTTCAGTAACCTCACAAAAAATGACAATTGAAGGGG F2: 3 CATAG 2 Unidirectional alignment (log-probability: -25.9) TCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAgAtAcCAGAGAAGTCATTGGAGTGTTTTTTACTGTTAACTTCCCc TCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAAAACAGCAGAGAAGTCATTGGAGTGTTTTTTACTGTTAACTTCCC- Template switch alignment (log-probability: -16.4) TCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAA|GATAC|CAGAGAAGTCATTGGAGTGTTTTTTACTGTTAACTTCCCC TCAGGCATCTAGATAGGAAGCGCCGGCTCATTTCAGCAAA|GATAC|CAGAGAAGTCATTGGAGTGTTTTTTACTGTTAACTTCCCC ========== Event 3433 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: CCGGAGCTGTGGGCCTCCCCAGTGTACACTCCTGGGGAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAAAGAGATGACTCAggccagacgtggtggcttatacgtataatcccagtattttgggaggccaagatgggaaaatcacttgagcccaggagtttgagaccagcctgggaaac Chimp: Gorilla: CTGGAGCTGTGGGCCTCCCCAATGTACGG----TGAGAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAAAGAGATGACTCAggccagacatggtggcttatacgtataatcccagtattttgggaggccaagatgggaaaatcacttgagcccaggagtttgagaccagcctgggaaac ↓ 1 4 3 2 Human: CCGGAGCTGTGGGCCTCCCCAGTGTACACTCCTGGGGAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAAAGAGATGACTCAggccagacgtggtggcttatacgtataatcccagtattttgggaggccaagatgggaaaatcacttgagcccaggagtttgagaccagcctgggaaac Cluster: [ ] Orangutan: Gorilla > Human --------------- chr7:66527583-66527591 Template switch process: F1: L TGCAAGAGCCCCACTGCACCCCGGAGCTGTGGGCCTCCCCAGTGTAC 1 F3: 4 GAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAA R RF: TGCAAGAGCCCCACTGCACCCTGGAGCTGTGGGCCTCCCCAATGTACGGTGAGAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAAAGAGATGACTCAGGCCAGACATGGTGGCTTATACGTATAATCCCAGTATTTTGGGAGGCCAAGATGGGAAAATCACTTGAGCCCAGGAGT RR: ACGTTCTCGGGGTGACGTGGGACCTCGACACCCGGAGGGGTTACATGCCACTCTCATGTCGGTGAGGACCTGACCAAAACAAGACCCAGTTTTCTCTACTGAGTCCGGTCTGTACCACCGAATATGCATATTAGGGTCATAAAACCCTCCGGTTCTACCCTTTTAGTGAACTCGGGTCCTCA F2: 3 GGGTCCTCA 2 Unidirectional alignment (log-probability: -42) GCCCCACTGCACCCcGGAGCTGTGGGCCTCCCCAgTGTACactcctgGG---GAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAA GCCCCACTGCACCCTGGAGCTGTGGGCCTCCCCAATGTAC-------GGTGAGAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAA Template switch alignment (log-probability: -28.1) GCCCCACTGCACCCcGGAGCTGTGGGCCTCCCCAgTGTAC|ACTCCTGGG|GAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAA GCCCCACTGCACCCTGGAGCTGTGGGCCTCCCCAATGTAC|ACTCCTGGG|GAGTACAGCCACTCCTGGACTGGTTTTGTTCTGGGTCAAA ========== Event 3434 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ACTAAAACTTATTGAAAGGCGG-----------CATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGT-TTAAGGATTTCTCTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCA ↓ 3 1 4 2 ↑ 1 4 3 2 Chimp: ACTAAAACTTATTGAAAGGCGATAGATGTGTGCAATGGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGT-TTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCA ↓ 1 4 3 2 ↑ 3 1 4 2 Gorilla: ACTAAAACTTATTGAAAGGCGG-----------CATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGT-TTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCA Human: ACTAAAACTTATTGAAAGGCGG-----------CATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGT-TTAAGGATTTCTCTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCA Cluster: [ ] Orangutan: ACTAAAACTTATTGAAAGGCGG-----------CATCGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCGGGCCCCTTCACAGTTTTAAGTATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCA Chimp > Human ------------- chr7:67496581-67496585 Template switch process: F1: L TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG 1 F3: 4 GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------G R RF: TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGATAGATGTGTGCAATGGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC RR: AGGATCTCTTCTTACGTGATTTTGAATAACTTTCCGCTATCTACACACGTTACCGTGTGTAGAACTTATATCCGTGGTCTCTTACAGGACTTCGGTCCGTCCGGGGAAGTGTCAAATTCCTAAAGAAACAAAAAGAAGTAGCGAGCGTTAGTTTACGTCGTGACTTCGACAATCCGTAAACCGACACCGGTAG F2: 3 TTACG 2 Unidirectional alignment (log-probability: -27.6) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG---------------GcattGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGATAGATGTGTGCAATG----GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG Template switch alignment (log-probability: -15.8) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG|GCATT|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------g TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG|GCATT|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC Human > Chimp ------------- chr7:68124484-68124497 Template switch process: F1: L TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG--AT 1 F3: 4 GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------G R RF: TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGGCATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTCTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC RR: AGGATCTCTTCTTACGTGATTTTGAATAACTTTCCGCCGTAACGTGTGTAGAACTTATATCCGTGGTCTCTTACAGGACTTCGGTCCGTCCGGGGAAGTGTCAAATTCCTAAAGAGACAAAAAGAAGTAGCGAGCGTTAGTTTACGTCGTGACTTCGACAATCCGTAAACCGACACCGGTAG F2: 3 GTAACGTGTGTAGA 2 Unidirectional alignment (log-probability: -42.9) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGatagatgtgtgcaatG----GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG---------------GCATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG Template switch alignment (log-probability: -27.3) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG--AT|AGATGTGTGCAATG|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------g TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGGCAT|AGATGTGTGCAATG|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTCTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC Gorilla > Chimp --------------- chr7:68124484-68124497 Template switch process: F1: L TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG--AT 1 F3: 4 GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------G R RF: TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGGCATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC RR: AGGATCTCTTCTTACGTGATTTTGAATAACTTTCCGCCGTAACGTGTGTAGAACTTATATCCGTGGTCTCTTACAGGACTTCGGTCCGTCCGGGGAAGTGTCAAATTCCTAAAGAAACAAAAAGAAGTAGCGAGCGTTAGTTTACGTCGTGACTTCGACAATCCGTAAACCGACACCGGTAG F2: 3 GTAACGTGTGTAGA 2 Unidirectional alignment (log-probability: -42) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGatagatgtgtGCaATgGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG----------GC-ATTGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG Template switch alignment (log-probability: -27.3) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG--AT|AGATGTGTGCAATG|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------g TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGGCAT|AGATGTGTGCAATG|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC Chimp > Gorilla --------------- chr7:66377614-66377618 Template switch process: F1: L TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG 1 F3: 4 GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------G R RF: TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGATAGATGTGTGCAATGGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC RR: AGGATCTCTTCTTACGTGATTTTGAATAACTTTCCGCTATCTACACACGTTACCGTGTGTAGAACTTATATCCGTGGTCTCTTACAGGACTTCGGTCCGTCCGGGGAAGTGTCAAATTCCTAAAGAAACAAAAAGAAGTAGCGAGCGTTAGTTTACGTCGTGACTTCGACAATCCGTAAACCGACACCGGTAG F2: 3 TTACG 2 Unidirectional alignment (log-probability: -26.7) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG----------GC-ATtGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCGATAGATGTGTGCAATGGCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAG Template switch alignment (log-probability: -16.3) TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG|GCATT|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAA----------------------------------------------------------------------------------------------------g TCCTAGAGAAGAATGCACTAAAACTTATTGAAAGGCG|GCATT|GCACACATCTTGAATATAGGCACCAGAGAATGTCCTGAAGCCAGGCAGGCCCCTTCACAGTTTAAGGATTTCTTTGTTTTTCTTCATCGCTCGCAATCAAATGCAGCACTGAAGCTGTTAGGCATTTGGCTGTGGCCATC ========== Event 3435 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TTTTTATTTTAACTGAAAACAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTT------------------------ATAAGCACACAGAACTCCCTGCTAA ↓ 3 4 2 1 Chimp: TTTTTATTTTAACTGAAAACAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAGTCAAGAAGCCTGTTGACTTATAAGCACACAGAACTCCCTGCTAA Gorilla: Human: TTTTTATTTTAACTGAAAACAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTT------------------------ATAAGCACACAGAACTCCCTGCTAA Cluster: [ ] Orangutan: Human > Chimp ------------- chr7:90127792-90127803 Template switch process: F1: L TGAAAACAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAG 1 F3: 4 TTGAC--------------------TTATAAGCACACAGAACTCCCTGCTAATACAAGCTCTCAGAA R RF: TGAAAACAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAGCACACAGAACTCCCTGCTAATACAAGCTCTCAGAA RR: ACTTTTGTCCGAAGAACTGAACTTTTCCATGACTAACCAAATATTCGTGTGTCTTGAGGGACGATTATGTTCGAGAGTCTT F2: 3 GTCCGAAGAACT 2 Unidirectional alignment (log-probability: -45.4) CAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAGtcaagaagcctgttgacttataagCACACAGAACTCCCTGCTAATACAAGCT CAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAG------------------------CACACAGAACTCCCTGCTAATACAAGCT Template switch alignment (log-probability: -28.2) CAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAG|TCAAGAAGCCTG|TTGAC--------------------TTATAAGCACACAGAACTCCCTGCTAATACAAGCT CAGGCTTCTTGACTTGAAAAGGTACTGATTGGTTTATAAG|TCAAGAAGCCTG|TTGACTTGAAAAGGTACTGATTGGTTTATAAGCACACAGAACTCCCTGCTAATACAAGCT ========== Event 3436 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: gggcatcaagagcaaaactcagtctcaaaaaaaaaaaaa---------aaaaaaaaCATCCTGAGCTCGGCACAACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGACCTCTACTTGTCTTTTTCTGCTGTT ↓ 3 2 1 4 Chimp: gggcatcaagagcaaaactcagtctcaaaaaaaaaaaaa----------------aaaTCCTGACCTCGGCACAACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGAACTGTACTTGTCTTTTTCTGCTGTT Gorilla: gggcatcaagagcaaaactcagtctcaaaaaaaaaaaaaaaaaaaaaa-------aaaTCCTGAGCTCGGCACAACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGACCTGTACTTGTCTTTTTCTGCTGTT Human: gggcatcaagagcaaaactcagtctcaaaaaaaaaaaaa---------aaaaaaaaCATCCTGAGCTCGGCACAACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGACCTCTACTTGTCTTTTTCTGCTGTT Cluster: [ ] Orangutan: gggcatcaagagcaaaactcggtctcaaaaaaaaaaaaa----------------aaaTCCTGAGCTCGGTACAACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGACCTGTACTTCTCTTTTTCTGCTGTT Human > Chimp ------------- chr7:70143124-70143127 Template switch process: F1: L ACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGA 1 F3: 4 TACTTGTCTTTTTCTGCTGTTGGAAAATACACACACACAC R RF: CAGTCTCAAAAAAAAAAAAAAAAAAAAACATCCTGAGCTCGGCACAACTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGACCTCTACTTGTCTTTTTCTGCTGTTGGAAAATACACACACACAG RR: GTCAGAGTTTTTTTTTTTTTTTTTTTTTGTAGGACTCGAGCCGTGTTGACTCGTAAAACGATCTGGGTCGACGATCCCTTTGTAACTGGAGATGAACAGAAAAAGACGACAACCTTTTATGTGTGTGTGTC F2: 3 GTCA 2 Unidirectional alignment (log-probability: -28.5) CTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGAaCTgTACTTGTCTTTTTCTGCTGTTGGAAAATACACACacacac CTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGACCTCTACTTGTCTTTTTCTGCTGTTGGAAAATACACAC------ Template switch alignment (log-probability: -21.8) CTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGA|ACTG|TACTTGTCTTTTTCTGCTGTTGGAAAATACACACACACAc CTGAGCATTTTGCTAGACCCAGCTGCTAGGGAAACATTGA|ACTG|TACTTGTCTTTTTCTGCTGTTGGAAAATACACACACACAG ========== Event 3437 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CCAGGACTGGCTCTGACTGGCCAGGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGA-------------------------------ATCACTTGGCTGGAGAGGAGAGGAGTAGGGT Chimp: CCAGGACTGGCTCTGACTGGCCAGGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGA-------------------------------ATCACATGGCTGGAGAGGAGAGGAGCAGGGT Gorilla: CCAGGACTGGCTCTGACTGGCCAGGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGAACATTCACAGAGGAGAATTCATTCCCGAACATTCACAG---AGGAGAGGAGAGGAGTAGGGT ↓ 3 2 1 4 Human: CCAGGACTGGCTCTGACTGGCCAGGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGA-------------------------------ATCACTTGGCTGGAGAGGAGAGGAGTAGGGT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr7:88438112-88438120 Template switch process: F1: L CAGGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGAA 1 F3: 4 TGGAGAGGAGAGGAGTAGGGTGCACTTTCCCATTGGAAAGG R RF: GCCAGGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGAACATTCACAGAGGAGAATTCATTCCCGAACATTCACAGAGGAGAGGAGAGGAGTAGGGTGCACTTTCCCATTGGAAAGG RR: CGGTCCACTCGTCTCGTGATATGGACACTTACAAGGGAGGGCTTGTAAGTGTCTCCTCTTAAGTAAGGGCTTGTAAGTGTCTCCTCTCCTCTCCTCATCCCACGTGAAAGGGTAACCTTTCC F2: 3 CGGTTCACT 2 Unidirectional alignment (log-probability: -37) GGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGA--------------------------------------AtcacttggctGGAGAGGAGAGGAGTAGGGTGCACTTTCCCATTGGAAAG GGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGAACATTCACAGAGGAGAATTCATTCCCGAACATTCACAGA----------GGAGAGGAGAGGAGTAGGGTGCACTTTCCCATTGGAAAG Template switch alignment (log-probability: -28) GGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGAA|TCACtTGGC|tGGAGAGGAGAGGAGTAGGGTGCACTTTCCCATTGGAAAG GGTGAGCAGAGCACTATACCTGTGAATGTTCCCTCCCGAA|TCACCTGGC|AGGAGAGGAGAGGAGTAGGGTGCACTTTCCCATTGGAAAG ========== Event 3438 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATTGATGTATCTGATTGAAGAATGTT-GAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTT ↓ 1 4 3 2 Chimp: GATTGATGTATCTGATTGAAGTTGGCTGAAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTT ↑ 1 4 3 2 Gorilla: GATTGATGTATCTGATTGAAGAATGTT-GAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTT Human: GATTGATGTATCTGATTGAAGAATGTT-GAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTT Cluster: [ ] Orangutan: GATTGATGTATCTGATTGAAGAATGTT-GAGTTCAGCCAAGACTTAAGGTTAAGGTCCTT Human > Chimp ------------- chr7:71353801-71353808 Template switch process: F1: L TTAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAG 1 F3: 4 AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT R RF: TTAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAGAATGTTGAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT RR: AATCGTGTAAACGGACGTCCCTAACTACATAGACTAACTTCTTACAACTCAAGTCGGTTCTCAATTCCAATTCCAGGAAGATAAACAA F2: 3 AGTCGGTT 2 Unidirectional alignment (log-probability: -28.6) TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAA----GTTGgctgaAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAGAATGTTG-----AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT Template switch alignment (log-probability: -16.3) TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAG|TTGGCTGA|AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAG|TTGGCTGA|AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT Gorilla > Chimp --------------- chr7:71353801-71353808 Template switch process: F1: L TTAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAG 1 F3: 4 AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT R RF: TTAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAGAATGTTGAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT RR: AATCGTGTAAACGGACGTCCCTAACTACATAGACTAACTTCTTACAACTCAAGTCGGTTCTCAATTCCAATTCCAGGAAGATAAACAA F2: 3 AGTCGGTT 2 Unidirectional alignment (log-probability: -28.1) TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAA----GTTGgctgaAGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAGAATGTTG-----AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT Template switch alignment (log-probability: -16.7) TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAG|TTGGCTGA|AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT TAGCACATTTGCCTGCAGGGATTGATGTATCTGATTGAAG|TTGGCTGA|AGTTCAGCCAAGAGTTAAGGTTAAGGTCCTTCTATTTGTT ========== Event 3439 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGGTGCTAGATTATAATAAC---AAAAATGAAAA-ACGGCAGATCAGAGAGGATAAACTCTAAGTCATCATCTCCCTGGAATTTTCCAGAGGCCTTTAATGGAGTGAAAAGCATAAAGAAAAGTGTGCTTTATGCCTGAAACATTCTATTTTTAGG ↓ 1 4 3 2 Chimp: TAGGTGCTAGATTATAATAAC-GGCATAATGAAAA-ACGGCAGATCAGAGAGGATAACCTCTAAGTCATCATCTCCCTGGAATTTTCCAGAGGCCTTTAATGGAGTGAAAAGCATAAAGAAAAGTGTGCTTTATGCCTGAAACATTCTATTTTTAGG Gorilla: TAGGTGCTAGATTATAATAAC---AAAAATGAAAA-ATGGCAGATCAGAGAGGATAACCTCTAAGTCATCATCTCCCTGGAATTTTCCAGAGGCCTTTAATGGAGTGAAAAGCATAAAGAAAAGTGTGCTTTATGCCTGAAACATTCTATTTTTAGG Human: TAGGTGCTAGATTATAATAAC---AAAAATGAAAA-ACGGCAGATCAGAGAGGATAAACTCTAAGTCATCATCTCCCTGGAATTTTCCAGAGGCCTTTAATGGAGTGAAAAGCATAAAGAAAAGTGTGCTTTATGCCTGAAACATTCTATTTTTAGG Cluster: [ ] Orangutan: TAGGTGCTGGATTATAATAACA--AAAAATGAAAAACCGGCAGATCAGAGAGGATAACCTCTAAGTCATCATCTCGCTGGAATTTTCCAGAGGCCTTTAATGGAGTGAAAAGCATAAAGAAAAGTGTGCTTTATGCCTGAAACATTCTATTTTTAGG Human > Chimp ------------- chr7:89057119-89057123 Template switch process: F1: L GGAAAAAGAATATTCATAACTAGGTGCTAGATTATAATAAC 1 F3: 4 AATGAAAAACGGCAGATCAGAGAGGATAACCTCTAAGTCA R RF: GGAAAAAGAATATTCATAACTAGGTGCTAGATTATAATAACAAAAATGAAAAACGGCAGATCAGAGAGGATAAACTCTAAGTCATCATCTCCCTGGAATTTTCCAGAGGCCTTTAATGGAGTGAAAAGCATAAAGAAAAGTGTGCTTTATGCC RR: CCTTTTTCTTATAAGTATTGATCCACGATCTAATATTATTGTTTTTACTTTTTGCCGTCTAGTCTCTCCTATTTGAGATTCAGTAGTAGAGGGACCTTAAAAGGTCTCCGGAAATTACCTCACTTTTCGTATTTCTTTTCACACGAAATACGG F2: 3 TACGG 2 Unidirectional alignment (log-probability: -31.8) GAAAAAGAATATTCATAACTAGGTGCTAGATTATAATAACggcAtAATGAAAAACGGCAGATCAGAGAGGATAAcCTCTAAGTCA GAAAAAGAATATTCATAACTAGGTGCTAGATTATAATAAC--AAAAATGAAAAACGGCAGATCAGAGAGGATAAACTCTAAGTCA Template switch alignment (log-probability: -21.9) GAAAAAGAATATTCATAACTAGGTGCTAGATTATAATAAC|GGCAT|AATGAAAAACGGCAGATCAGAGAGGATAAcCTCTAAGTCA GAAAAAGAATATTCATAACTAGGTGCTAGATTATAATAAC|GGCAT|AATGAAAAACGGCAGATCAGAGAGGATAAACTCTAAGTCA ========== Event 3440 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TTCTCTACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTGTAGCTCAGTGCTCTTGGTTACTGAA Chimp: ----------------------------------------------------------------------- Gorilla: TTCTCTACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTATGTCTCAGTGCTCTTGGTTACTGAA ↑ 3 2 1 4 Human: TTCTCTACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTGTAGCTCAGTGCTCTTGGTTACTGAA Cluster: [ ] Orangutan: TTCTCTACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTGTATCTCAGTGCTCTTGGTTACTGAA Human > Gorilla --------------- chr7:7076844-7076848 Template switch process: F1: L CTACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGT 1 F3: 4 TCAGTGCTCTTGGTTACTGAAGCAACAAGTGATCTCTGA R RF: CTACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTGTAGCTCAGTGCTCTTGGTTACTGAAGCAACAAGTGATCTCTGA RR: GATGTCACTGGTAATCTGTAAGGTTTCGTGACAGTGAACCACATCGAGTCACGAGAACCAATGACTTCGTTGTTCACTAGAGACT F2: 3 CTGTA 2 Unidirectional alignment (log-probability: -38.7) TACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTaTgtCTCAGTGCTCTTGGTTACTGAAGCAACAAGtgatctctga TACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGTGTAGCTCAGTGCTCTTGGTTACTGAAGCAACAAG---------- Template switch alignment (log-probability: -16.3) TACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGT|ATGTC|TCAGTGCTCTTGGTTACTGAAGCAACAAGTGATCTCTGA TACAGTGACCATTAGACATTCCAAAGCACTGTCACTTGGT|ATGTC|TCAGTGCTCTTGGTTACTGAAGCAACAAGTGATCTCTGA ========== Event 3441 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGGCATTCGAGATACTACCTAAT----------------------------------AACAATGGCAATGGCCTAGATGCAGCAGTGCTAATATCAGTAGACAAGG ↓ 4 1 3 2 Chimp: TGGCATTCGAGATACTACCTAAT-----------------AACAATGACTGCTTAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATATCAGCAGACAAGG Gorilla: TGGCATTCGAGATACTACCTAATAACAATGACTGCTTAAT-----------------AACAATGGCAATGGCCTAGATGCAGCAGTGCTAGTATCAGTAGACAAGG ↑ 4 1 3 2 Human: TGGCATTCGAGATACTACCTAAT----------------------------------AACAATGGCAATGGCCTAGATGCAGCAGTGCTAATATCAGTAGACAAGG Cluster: [ ] Orangutan: Human > Chimp ------------- chr7:89587734-89587739 Template switch process: F1: L GATAATGCATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATG 1 F3: 4 TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATATCAG R RF: GATAATGCATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATATCAG RR: CTATTACGTAGGTCGAGAACCGTAAGCTCTATGATGGATTATTGTTACCGTTACCGGATCTACGTCGTCACGATTATAGTC F2: 3 TCGTCA 2 Unidirectional alignment (log-probability: -35.4) ATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAAtgactgcttaataacaaTGGCAATGGCCTAGATGCAGCAGTGCTAATA ATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAA-----------------TGGCAATGGCCTAGATGCAGCAGTGCTAATA Template switch alignment (log-probability: -16.2) ATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATG|ACTGCT|TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATA ATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATG|ACTGCT|TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATA Human > Gorilla --------------- chr7:71250811-71250816 Template switch process: F1: L GATAATGCATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATG 1 F3: 4 TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAGTATCAG R RF: GATAATGCATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATATCAG RR: CTATTACGTAGGTCGAGAACCGTAAGCTCTATGATGGATTATTGTTACCGTTACCGGATCTACGTCGTCACGATTATAGTC F2: 3 TCGTCA 2 Unidirectional alignment (log-probability: -40.8) ATCCAGCTCTTGGCATTCGAGATACTACCtaataacaatgactgctTAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAgTA ATCCAGCTCTTGGCATTCGAGATACTACC-----------------TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATA Template switch alignment (log-probability: -22.3) ATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATG|ACTGCT|TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAgTA ATCCAGCTCTTGGCATTCGAGATACTACCTAATAACAATG|ACTGCT|TAATAACAATGGCAATGGCCTAGATGCAGCAGTGCTAATA ========== Event 3442 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAAT-----------GTAAACAGCAAAATCTTCCTAA ↓ 13 24 ↑ 13 24 Chimp: ATCAACATATAATAAAAGTTT-----------ACATTTAAATACAGGAATATACTAAACAGCAAAATCTTCCTAA ↓ 13 24 ↑ 13 24 Gorilla: ATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAAT-----------GTAAACAGCAAAATCTTCCTAA Human: ATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAAT-----------GTAAACAGCAAAATCTTCCTAA Cluster: [ ] Orangutan: ATCAACATGTAATAAAAGTTTAGTATATTCCTGTATTTAAAT-----------GTGAACAGCAAAATCTTTCTAA Chimp > Human ------------- chr7:72239549-72239569 Template switch process: F1: L ACATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA 1 F3: 4 TAAACAGCAAAATCTTCCTAAATTATCTGGGTATAACTTT R RF: ACATCTGACACAGCATAAATATCAACATATAATAAAAGTTTACATTTAAATACAGGAATATACTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT RR: TGTAGACTGTGTCGTATTTATAGTTGTATATTATTTTCAAATGTAAATTTATGTCCTTATATGATTTGTCGTTTTAGAAGGATTTAAGAGACCCATATTGAAA F2: 3 GTAAATTTATGTCCTTATATG 2 Unidirectional alignment (log-probability: -55.6) ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTAgtatattcctgtATTTAAATg-----------TAAACAGCAAAATCTTCCTAAATTaTCTGGGTATAACTTT ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA-----------CATTTAAATACAGGAATATACTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT Template switch alignment (log-probability: -23.9) ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA|GTATATTCCTGTATTTAAATG|TAAACAGCAAAATCTTCCTAAATTaTCTGGGTATAACTTT ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA|GTATATTCCTGTATTTAAATG|TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT Human > Chimp ------------- chr7:89517052-89517072 Template switch process: F1: L ACATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA 1 F3: 4 TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT R RF: ACATCTGACACAGCATAAATATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAATGTAAACAGCAAAATCTTCCTAAATTATCTGGGTATAACTTT RR: TGTAGACTGTGTCGTATTTATAGTTGTATATTATTTTCAAATCATATAAGGACATAAATTTACATTTGTCGTTTTAGAAGGATTTAATAGACCCATATTGAAA F2: 3 CATATAAGGACATAAATTTAC 2 Unidirectional alignment (log-probability: -55.6) ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTAc-----------ATTTAAATacaggaatatacTAAACAGCAAAATCTTCCTAAATTcTCTGGGTATAACTTT ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAATG-----------TAAACAGCAAAATCTTCCTAAATTATCTGGGTATAACTTT Template switch alignment (log-probability: -23.9) ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA|CATTTAAATACAGGAATATAC|TAAACAGCAAAATCTTCCTAAATTcTCTGGGTATAACTTT ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA|CATTTAAATACAGGAATATAC|TAAACAGCAAAATCTTCCTAAATTATCTGGGTATAACTTT Gorilla > Chimp --------------- chr7:89517052-89517072 Template switch process: F1: L ACATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA 1 F3: 4 TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT R RF: ACATGTGACACAGCAGAAATATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAATGTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT RR: TGTACACTGTGTCGTCTTTATAGTTGTATATTATTTTCAAATCATATAAGGACATAAATTTACATTTGTCGTTTTAGAAGGATTTAAGAGACCCATATTGAAA F2: 3 CATATAAGGACATAAATTTAC 2 Unidirectional alignment (log-probability: -59.2) ATcTGACACAGCAtAAATATCAACATATAATAAAAGTTTA-----------cATTTAAATacaggaatatacTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT ATGTGACACAGCAGAAATATCAACATATAATAAAAGTTTAGTATATTCCTGTATTTAAAT-----------GTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT Template switch alignment (log-probability: -29.5) ATcTGACACAGCAtAAATATCAACATATAATAAAAGTTTA|CATTTAAATACAGGAATATAC|TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT ATGTGACACAGCAGAAATATCAACATATAATAAAAGTTTA|CATTTAAATACAGGAATATAC|TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT Chimp > Gorilla --------------- chr7:71181892-71181912 Template switch process: F1: L ACATGTGACACAGCAGAAATATCAACATATAATAAAAGTTTA 1 F3: 4 TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT R RF: ACATCTGACACAGCATAAATATCAACATATAATAAAAGTTTACATTTAAATACAGGAATATACTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT RR: TGTAGACTGTGTCGTATTTATAGTTGTATATTATTTTCAAATGTAAATTTATGTCCTTATATGATTTGTCGTTTTAGAAGGATTTAAGAGACCCATATTGAAA F2: 3 GTAAATTTATGTCCTTATATG 2 Unidirectional alignment (log-probability: -59.2) ATgTGACACAGCAgAAATATCAACATATAATAAAAGTTTAgtatattcctgtATTTAAAT-----------gTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA-----------CATTTAAATACAGGAATATACTAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT Template switch alignment (log-probability: -29.5) ATgTGACACAGCAgAAATATCAACATATAATAAAAGTTTA|GTATATTCCTGTATTTAAATG|TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT ATCTGACACAGCATAAATATCAACATATAATAAAAGTTTA|GTATATTCCTGTATTTAAATG|TAAACAGCAAAATCTTCCTAAATTCTCTGGGTATAACTTT ========== Event 3443 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGTAATCCGACCTCAGTGAAACTCAAGCCTAGATCAAACTCACGTATTGATCTAGAGATGGTAAGTGCCCCTGG Chimp: GGGTAATCCGACCTCAGTGAAACTCAAGCCG-----CAAAGCACGTATTGATCTAGAGACGGTAAGTGCCCCTGG Gorilla: GGGTAATCCGACCTCAGTGAAACTCAAGCCG-----CGAAGCGCGTATTGATCTAGAGATGGTAAGTGCCCCTGG ↓ 4 1 3 2 Human: GGGTAATCCGACCTCAGTGAAACTCAAGCCTAGATCAAACTCACGTATTGATCTAGAGATGGTAAGTGCCCCTGG Cluster: [ ] Orangutan: GGGTAATCCCACCTCAGTGAAACTCAAGCCG-----CAAAGCACGTATTGATCT----------AGTGCCCCTGG Gorilla > Human --------------- chr7:84305317-84305322 Template switch process: F1: L GCAGTGAAGCAGGGTAATCCGACCTCAGTGAAACTCAAGCC 1 F3: 4 AAACTCA------------CGTATTGATCTAGAGATGGTAAGTGCCCCTGGAGGTCAGA R RF: GCAGTGAAGCAGGGTAATCCGACCTCAGTGAAACTCAAGCCGCGAAGCGCGTATTGATCTAGAGATGGTAAGTGCCCCTGGAGGTCAGA RR: CGTCACTTCGTCCCATTAGGCTGGAGTCACTTTGAGTTCGGCGCTTCGCGCATAACTAGATCTCTACCATTCACGGGGACCTCCAGTCT F2: 3 CTAGAT 2 Unidirectional alignment (log-probability: -39.7) CAGTGAAGCAGGGTAATCCGACCTCAGTGAAACTCAAGCC--------tagatcaaactcaCGTATTGATCTAGAGATGGTAAGTGCCCCTGGA CAGTGAAGCAGGGTAATCCGACCTCAGTGAAACTCAAGCCGCGAAGCG-------------CGTATTGATCTAGAGATGGTAAGTGCCCCTGGA Template switch alignment (log-probability: -27) CAGTGAAGCAGGGTAATCCGACCTCAGTGAAACTCAAGCC|TAGATC|AAACTCA------------CGTATTGATCTAGAGATGGTAAGTGCCCCTGGA CAGTGAAGCAGGGTAATCCGACCTCAGTGAAACTCAAGCC|TAGATC|AAACTCAAGCCGCGAAGCGCGTATTGATCTAGAGATGGTAAGTGCCCCTGGA ========== Event 3444 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: ATACTATGGTTCACTAAACCTGGG--CAGACTGATACTATGCTTTTAGGTTTTAAATATTTCAT ↓ 1 4 3 2 Chimp: ATACTATGGTTCACTAAACCTAAGCATAGACTGATACTATGCTTTTAGGTTTTAAATATTTCAT Gorilla: Human: ATACTATGGTTCACTAAACCTGGG--CAGACTGATACTATGCTTTTAGGTTTTAAATATTTCAT Cluster: [ ] Orangutan: ATACTATGGTTCGCTAAACCTGGG--CACACTGATACTATGCTTTTAAGTTTTAAATATTTCAT Human > Chimp ------------- chr7:74557015-74557020 Template switch process: F1: L AGGGAGGAGAGAAGAGACGAATACTATGGTTCACTAAACCT 1 F3: 4 AGACTGATACTATGCTTTTAGGTTTTAAATATTTCATTTT R RF: AGGGAGGAGAGAAGAGACAAATACTATGGTTCACTAAACCTGGGCAGACTGATACTATGCTTTTAGGTTTTAAATATTTCATTTT RR: TCCCTCCTCTCTTCTCTGTTTATGATACCAAGTGATTTGGACCCGTCTGACTATGATACGAAAATCCAAAATTTATAAAGTAAAA F2: 3 TACGAA 2 Unidirectional alignment (log-probability: -31.8) GGGAGGAGAGAAGAGACgAATACTATGGTTCACTAAACCTaaGCatAGACTGATACTATGCTTTTAGGTTTTAAATATTTCATTTT GGGAGGAGAGAAGAGACAAATACTATGGTTCACTAAACCTGGGC--AGACTGATACTATGCTTTTAGGTTTTAAATATTTCATTTT Template switch alignment (log-probability: -22) GGGAGGAGAGAAGAGACgAATACTATGGTTCACTAAACCT|AAGCAT|AGACTGATACTATGCTTTTAGGTTTTAAATATTTCATTTT GGGAGGAGAGAAGAGACAAATACTATGGTTCACTAAACCT|AAGCAT|AGACTGATACTATGCTTTTAGGTTTTAAATATTTCATTTT ========== Event 3445 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAAAGACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTCCAAGAGGGGTT--------------- Chimp: CCAAAGACTTCCTTTGTGGCCTGAGCT--------GATGAACAGAAGCTGATTCTCAGGGGGGTT--------GGGTGGC ↑ 3 2 1 4 Gorilla: CCAAAGACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTCCCAGAGGGGTT--------------- Human: CCAAAGACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTCCAAGAGGGGTT--------------- Cluster: [ ] Orangutan: CCAAAGACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTCCCAGGGGGGTTGGGTGGCT------- Gorilla > Chimp --------------- chr7:78074372-78074376 Template switch process: F1: L ACTATCCAGCTTGTCCAAAGACTTCCTTTGTGGCCTGAGCTG--------ATGAACAGAAGCTGATTC 1 F3: 4 GGGGTTGGGTGGCT R RF: ACTATCCAGCTTGTCCAAAGACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTCCCAGAGGGGTTGGGTGGCT RR: TGATAGGTCGAACAGGTTTCTGAAGGAAACACCGGACTCGACGACTCGATTACTTGTCTTCGACTAAGGGTCTCCCCAACCCACCGA F2: 3 GGACT 2 Unidirectional alignment (log-probability: -36.2) ACTTCCTTTGTGGCCTGAGCTG--------ATGAACAGAAGCTGATTCtCAGgGGGGTTGGGtggct ACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTCCCAGAGGGGTTGGG----- Template switch alignment (log-probability: -26.3) ACTTCCTTTGTGGCCTGAGCTG--------ATGAACAGAAGCTGATTC|TCAGG|GGGGTTGGGTGGCT ACTTCCTTTGTGGCCTGAGCTGCTGAGCTAATGAACAGAAGCTGATTC|TCAGG|GGGGTTGGGTGGCT ========== Event 3446 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTCTGTAAACTCTGAGATATATGTATTGTATGACATCATACAATACATAT----ATCTCAGAGTTTGCAGAAAAGAAG Chimp: GTTTCTGTAAACTCTGAGATATATGTATCGTATGATGTCATACAATACATAT------ATCAGAGTTTGCAGAAAAGAAG ↑ 3 1 2 4 Gorilla: GTTTCTGTAAACTCTGAGATATATGTATTGTATGACATCATATAATACATAT--AT--CTCAGAGTTTGCAGAAAAGAAG Human: GTTTCTGTAAACTCTGAGATATATGTATTGTATGACATCATACAATACATAT----ATCTCAGAGTTTGCAGAAAAGAAG Cluster: [ ] Orangutan: GTTTCTGTAAACTCTGAGATATATGTATTGTATGACATCATACAATACACATAT----CTCAGAGTTTGCAGAAAAGAAG Gorilla > Chimp --------------- chr7:87962197-87962214 Template switch process: F1: L TAACGAGCTGGCAGTTTCTGTAAACTCTGAGATATATGTATCGTATGA 1 F3: 4 TCAGAGTTTGCAGAAAAGAAGATTAACTTAGGCTGAGCAC R RF: TAACGAGCTGGCAGTTTCTGTAAACTCTGAGATATATGTATTGTATGACATCATATAATACATATATCTCAGAGTTTGCAGAAAAGAAGATTAACTTAGGCTGAGCAC RR: ATTGCTCGACCGTCAAAGACATTTGAGACTCTATATACATAACATACTGTAGTATATTATGTATATAGAGTCTCAAACGTCTTTTCTTCTAATTGAATCCGACTCGTG F2: 3 ATATACATAACATACTGT 2 Unidirectional alignment (log-probability: -33.4) TGGCAGTTTCTGTAAACTCTGAGATATATGTATcGTATGAtgTCATAcAATACATATA--TCAGAGTTTGCAGAAAAGAAGATTAACTTAGGCTGAGCAC TGGCAGTTTCTGTAAACTCTGAGATATATGTATTGTATGACATCATATAATACATATATCTCAGAGTTTGCAGAAAAGAAGATTAACTTAGGCTGAGCAC Template switch alignment (log-probability: -23.7) TGGCAGTTTCTGTAAACTCTGAGATATATGTATcGTATGA|TGTCATACAATACATATA|TCAGAGTTTGCAGAAAAGAAGATTAACTTAGGCTGAGCAC TGGCAGTTTCTGTAAACTCTGAGATATATGTATTGTATGA|TGTCATACAATACATATA|TCAGAGTTTGCAGAAAAGAAGATTAACTTAGGCTGAGCAC ========== Event 3447 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGGGGAAAATCAATAAAGATGAGGCTTTCATC----CAAAGCCTCATCTCATCCAATTCAGAACT ↑ 1 4 3 2 Chimp: ATGGGGAAAATCAATAAAGATAAC-ATAAAATC--CTGAAAGCCTCATCTCATCCAATTCAGAACT Gorilla: ACGGGGAAAATCAATAAAGATAAC-ATAAAACCCT--GAAAGCCTCATCTTGTCCAATTCAGAACT Human: ATGGGGAAAATCAATAAAGATGAGGCTTTCATC----CAAAGCCTCATCTCATCCAATTCAGAACT Cluster: [ ] Orangutan: ATGGGGAAAACCAATAAAGATAAC-ATAAAACCCT--GAAAGCCTCATCTCATCCAATTCAGAACT Chimp > Human ------------- chr7:8212898-8212906 Template switch process: F1: L TTTGCTATTTACCAAGTTCCATGGGGAAAATCAATAAAGAT 1 F3: 4 ATCC--AAAGCCTCATCTCATCCAATTCAGAACTGGAAGCATGGGT R RF: TTTGCTATTTACCAAGTTCCATGGGGAAAATCAATAAAGATAACATAAAATCCTGAAAGCCTCATCTCATCCAATTCAGAACTGGAAGCATGGGT RR: AAACGATAAATGGTTCAAGGTACCCCTTTTAGTTATTTCTATTGTATTTTAGGACTTTCGGAGTAGAGTAGGTTAAGTCTTGACCTTCGTACCCA F2: 3 CTTTCGGAG 2 Unidirectional alignment (log-probability: -39.1) TTGCTATTTACCAAGTTCCATGGGGAAAATCAATAAAGA-------------TGaggctttcatccAAAGCCTCATCTCATCCAATTCAGAACTGGAAGCAT TTGCTATTTACCAAGTTCCATGGGGAAAATCAATAAAGATAACATAAAATCCTG------------AAAGCCTCATCTCATCCAATTCAGAACTGGAAGCAT Template switch alignment (log-probability: -26.8) TTGCTATTTACCAAGTTCCATGGGGAAAATCAATAAAGAT|GAGGCTTTC|ATCC--AAAGCCTCATCTCATCCAATTCAGAACTGGAAGCAT TTGCTATTTACCAAGTTCCATGGGGAAAATCAATAAAGAT|GAGGCTTTC|ATCCTGAAAGCCTCATCTCATCCAATTCAGAACTGGAAGCAT ========== Event 3448 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCATATCGGTGCTGCTCAGCTCA----------GATTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCATCTCCTTT-T Chimp: CCATATCGGTGCTGCTCAGCTAA-----ATTGATGTTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCGGCATCTCCttttt Gorilla: CCATATCGGTGCTGCTCAGCTAAATTGA-----TGTTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCATCTCCTTT-- ↓ 1 4 3 2 Human: CCATATCGGTGCTGCTCAGCTCA----------GATTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCATCTCCTTT-T Cluster: [ ] Orangutan: CCATATCGGTGCTACTCAGCTAAATTGA-----TGTTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCATCTCCCtt-t Gorilla > Human --------------- chr7:79381144-79381148 Template switch process: F1: L AAGGACTCAATGCCATATTACCATATCGGTGCTGCTCAGCT 1 F3: 4 TAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCA R RF: AAGAACTCAATGCCATATTGCCATATCGGTGCTGCTCAGCTAAATTGATGTTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCA RR: TTCTTGAGTTACGGTATAACGGTATAGCCACGACGAGTCGATTTAACTACAATTTGACATTAGAAGACCGTCAATTAGACGTAGAGACGT F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -36.4) AGgACTCAATGCCATATTaCCATATCGGTGCTGCTCAGCTcagA--------TTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCA AGAACTCAATGCCATATTGCCATATCGGTGCTGCTCAGCT---AAATTGATGTTAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCA Template switch alignment (log-probability: -27.4) AGgACTCAATGCCATATTaCCATATCGGTGCTGCTCAGCT|CAGAT|TAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCA AGAACTCAATGCCATATTGCCATATCGGTGCTGCTCAGCT|CAGAT|TAAACTGTAATCTTCTGGCAGTTAATCTGCATCTCTGCA ========== Event 3449 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AGCACTGCTGTCTACAAACTGGGGTCAGGAACTCAGCACTGGTGGATGTGGTTGCTTGAGGAAGG--AGAGTTCCTCAACCTGAGAGCCAGAAATTGACACCTTGTGGATTCACCCACT Chimp: AGCACTGCTGTCTACAAACTG------GGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGG--AGAGTTCCTCAACCTGAGAGCCAGAAATTGACACCTTGTGGATTCACCCACT ↓ 41 3 2 Gorilla: AGCACTGCTGTCTACAAACTGGGGTCAGGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGGAGAGAGTTCCTCAACCTGAGAGCCAGAAATTGACACCTTGTGGATTCACCCACT Human: AGCACTGCTGTCTACAAACTGGGGTCAGGAACTCAGCACTGGTGGATGTGGTTGCTTGAGGAAGG--AGAGTTCCTCAACCTGAGAGCCAGAAATTGACACCTTGTGGATTCACCCACT Cluster: [ ] Orangutan: AGCACTGCTGTCTACAAACTGGGGTCAGGAACTCAGCGCTGGTGGGTGTGGTTGCTTGAGGAAGG--AGAGTTCCTCAACCTGAGAGCCAGAAATTGACACCTCGTGGATTCACCCATT Chimp > Gorilla --------------- chr7:99620192-99620195 Template switch process: F1: L ACACAGGTGTTCGTCAGTACAGCACTGCTGTCTACAAACTGGG 1 F3: 4 GGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGGAG R RF: ACACAGGTGTTCGTCAGTACAGCACTGCTGTCTACAAACTGGGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGGAGAGTTCCTCAACCTGAGAGCCAGAAATTGAC RR: TGTGTCCACAAGCAGTCATGTCGTGACGACAGATGTTTGACCCTTGAGTCGTGACCACCCACACCAACGAACTCCTTCCTCTCAAGGAGTTGGACTCTCGGTCTTTAACTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -29.1) CAGGTGTTCGTCAGTACAGCACTGCTGTCTACAAACTGgggtcaGGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGGag CAGGTGTTCGTCAGTACAGCACTGCTGTCTACAAACTG------GGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGG-- Template switch alignment (log-probability: -16.3) CAGGTGTTCGTCAGTACAGCACTGCTGTCTACAAACTGGG|GTCA|GGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGGAG CAGGTGTTCGTCAGTACAGCACTGCTGTCTACAAACTGGG|GTCA|GGAACTCAGCACTGGTGGGTGTGGTTGCTTGAGGAAGGAG ========== Event 3450 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAATGTACTACCTTATATATCTGGCTTCTATATAT--------------------TTCTTTGCATGTATGCATTATGTAAATTCCAATCTG ↓ 4 1 3 2 Chimp: CCAATGTACTACCTTATATATTTGGCTTCTGTATAT----------TTCTGCATACTTCTTTGCATGTATGCATTATGTAAATTCCAATCTG Gorilla: CCAATGTACTACCTTATATATCTGGCTTCTGTATATTTCTGCATAC----------TTCTTTGCATGTATGCATTATGTAAATTCCAATCTG Human: CCAATGTACTACCTTATATATCTGGCTTCTATATAT--------------------TTCTTTGCATGTATGCATTATGTAAATTCCAATCTG Cluster: [ ] Orangutan: CCAATGTGCTACCTTATATATCTGGCTTCTGTATATTTCTGCATAC----------TTCTTTGCATGTATGCATTATGTAAATTCCAATCTG Human > Chimp ------------- chr7:84797521-84797526 Template switch process: F1: L GTCTATATATATGAAGCCTGCCAATGTACTACCTTATATATTTGGCTTCTGTATATTTCT 1 F3: 4 TTCTTTGCATGTATGCATTATGTAAATTCCAATCTGACCA R RF: GTCTATATATATGAAGCCTGCCAATGTACTACCTTATATATCTGGCTTCTATATATTTCTTTGCATGTATGCATTATGTAAATTCCAATCTGACCA RR: CAGATATATATACTTCGGACGGTTACATGATGGAATATATAGACCGAAGATATATAAAGAAACGTACATACGTAATACATTTAAGGTTAGACTGGT F2: 3 CATACG 2 Unidirectional alignment (log-probability: -37.4) CCAATGTACTACCTTATATATtTGGCTTCTgTATATTTCTgcatacttctTTGCATGTATGCATTATGTAAATTCCAATCTGACCA CCAATGTACTACCTTATATATCTGGCTTCTATATATTTCT----------TTGCATGTATGCATTATGTAAATTCCAATCTGACCA Template switch alignment (log-probability: -28.4) CCAATGTACTACCTTATATATtTGGCTTCTgTATATTTCT|GCATAC|TTCTTTGCATGTATGCATTATGTAAATTCCAATCTGACCA CCAATGTACTACCTTATATATCTGGCTTCTATATATTTCT|GCATAC|TTCTTTGCATGTATGCATTATGTAAATTCCAATCTGACCA ========== Event 3451 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTAACTGAAAATTCCTCTTAA-----GTATGA------CAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATA Chimp: TTTAACTGAAAATTCCTCTTAA-----GTATGA------CAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATA ↓ 1 4 3 2 Gorilla: TTTGACTGAAAATTCCTCTTAT----------A------------CCGATTTATGTCAATCGGTAACAAATGTCTTCCTGTCATA ↑ 1 4 3 2 Human: TTTAACTGAAAATTCCTCTTAA-----GTATGA------CAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATA Cluster: [ ] Orangutan: TTTAACTGAAAATTCCTCTTAAGTATG-----ACAGGAA------GACATTTATATCAATCGGTAACAAATGTCTTCCTGTCATA Human > Gorilla --------------- chr7:61970918-61970923 Template switch process: F1: L ACCATCCAAAACTGAAAGTTTTTGACTGAAAATTCCTCTTA 1 F3: 4 TTTATGTCAATCGGTAACAAATGTCTTCCTGTCATACTTAAAAGGA R RF: ACCATCCAAAACTGAAAGTTTTTAACTGAAAATTCCTCTTAAGTATGACAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATACTTAAAAGGA RR: TGGTAGGTTTTGACTTTCAAAAATTGACTTTTAAGGAGAATTCATACTGTCCTTCTGCAAATATAGTTAGCCATTGTTTACAGAAGGACAGTATGAATTTTCCT F2: 3 AGCCAT 2 Unidirectional alignment (log-probability: -39.8) CCATCCAAAACTGAAAGTTTTTgACTGAAAATTCCTCTTAtaccgA----------------TTTATgTCAATCGGTAACAAATGTCTTCCTGTCATACTTA CCATCCAAAACTGAAAGTTTTTAACTGAAAATTCCTCTTA-----AGTATGACAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATACTTA Template switch alignment (log-probability: -27.7) CCATCCAAAACTGAAAGTTTTTgACTGAAAATTCCTCTTA|TACCGA|TTTATgTCAATCGGTAACAAATGTCTTCCTGTCATACTTA CCATCCAAAACTGAAAGTTTTTAACTGAAAATTCCTCTTA|TACCGA|TTTATATCAATCGGTAACAAATGTCTTCCTGTCATACTTA Chimp > Gorilla --------------- chr7:61970918-61970923 Template switch process: F1: L ACCATCCAAAACTGAAAGTTTTTGACTGAAAATTCCTCTTA 1 F3: 4 TTTATGTCAATCGGTAACAAATGTCTTCCTGTCATACTTAAAAGGA R RF: ACCATCCAAAACTGAAAGTTTTTAACTGAAAATTCCTCTTAAGTATGACAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATACTTAAAAGGA RR: TGGTAGGTTTTGACTTTCAAAAATTGACTTTTAAGGAGAATTCATACTGTCCTTCTGCAAATATAGTTAGCCATTGTTTACAGAAGGACAGTATGAATTTTCCT F2: 3 AGCCAT 2 Unidirectional alignment (log-probability: -39.8) CCATCCAAAACTGAAAGTTTTTgACTGAAAATTCCTCTTAtaccgA----------------TTTATgTCAATCGGTAACAAATGTCTTCCTGTCATACTTA CCATCCAAAACTGAAAGTTTTTAACTGAAAATTCCTCTTA-----AGTATGACAGGAAGACGTTTATATCAATCGGTAACAAATGTCTTCCTGTCATACTTA Template switch alignment (log-probability: -27.7) CCATCCAAAACTGAAAGTTTTTgACTGAAAATTCCTCTTA|TACCGA|TTTATgTCAATCGGTAACAAATGTCTTCCTGTCATACTTA CCATCCAAAACTGAAAGTTTTTAACTGAAAATTCCTCTTA|TACCGA|TTTATATCAATCGGTAACAAATGTCTTCCTGTCATACTTA ========== Event 3452 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACGAAGGATCAAGTCAAATAATGCAAAT-------TTATGAGTTCAAAAATACTATTCCAGGGCTAA Chimp: ACGAAGGATCAAGTCAAATAATGCAAAT-------TTGAGAGTTCAAAAATACTATTCCAGGGCTAA ↓ 3 21 4 Gorilla: ACGAAGGATCAAGTCAAATAATGCAAATTATTTGCATTTGAGTTCA-AAATACTATTCCAGGGCTAA ↑ 3 21 4 Human: ACGAAGGATCAAGTCAAATAATGCAAAT-------TTATGAGTTCAAAAATACTATTCCAGGGCTAA Cluster: [ ] Orangutan: ACGAAGGATCAAGTCAAATAATGCAAAT-------TTAAGAGTTCAAAAATACTATTCCAGGGCTAA Human > Gorilla --------------- chr7:61681157-61681165 Template switch process: F1: L GCATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT 1 F3: 4 TGAGTTC-AAAATACTATTCCAGGGCTAATATTATCTCCAAACGTCAAA R RF: GCATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATTTATGAGTTCAAAAATACTATTCCAGGGCTAATATTATCTCCAAACGTCAAA RR: CGTATCAGTTCCTTGCTTCCTAGTTCAGTTTATTACGTTTAAATACTCAAGTTTTTATGATAAGGTCCCGATTATAATAGAGGTTTGCAGTTT F2: 3 TTACGTTTA 2 Unidirectional alignment (log-probability: -36.4) ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATTatttgcaTtTGAGTTC-AAAATACTATTCCAGGGCTAATATTATCTCCAA ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT-------TATGAGTTCAAAAATACTATTCCAGGGCTAATATTATCTCCAA Template switch alignment (log-probability: -26.9) ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT|ATTTGCATT|TGAGTTC-AAAATACTATTCCAGGGCTAATATTATCTCCAA ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT|ATTTGCATT|TGAGTTCAAAAATACTATTCCAGGGCTAATATTATCTCCAA Chimp > Gorilla --------------- chr7:61681157-61681165 Template switch process: F1: L GCATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT 1 F3: 4 TGAGTTC-AAAATACTATTCCAGGGCTAATATTATCTCCAAACGTCAAA R RF: GCATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATTTGAGAGTTCAAAAATACTATTCCAGGGCTAATATTATCTCCAAACGTCAAA RR: CGTATCAGTTCCTTGCTTCCTAGTTCAGTTTATTACGTTTAAACTCTCAAGTTTTTATGATAAGGTCCCGATTATAATAGAGGTTTGCAGTTT F2: 3 TTACGTTTA 2 Unidirectional alignment (log-probability: -41.9) ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATTatttgcaTttGAGTTC-AAAATACTATTCCAGGGCTAATATTATCTCCAA ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT-------TGAGAGTTCAAAAATACTATTCCAGGGCTAATATTATCTCCAA Template switch alignment (log-probability: -32.4) ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT|ATTTGCATT|tGAGTTC-AAAATACTATTCCAGGGCTAATATTATCTCCAA ATAGTCAAGGAACGAAGGATCAAGTCAAATAATGCAAATT|ATTTGCATT|AGAGTTCAAAAATACTATTCCAGGGCTAATATTATCTCCAA ========== Event 3453 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGATGGTAATTTCCTGTTCC---AGGTATATACCTAAGGATACCTGCTCATGGTCTCACAGCAGCA ↓ 1 4 3 2 Chimp: TTGATGGTAATTTCCTGTTCCAGCAGGTA---TCCTAAGGATACCTGCTCATGGTCTCACAGCAGCA Gorilla: TTGATGGTAATTTCCCGTTCC---AGGTATATACCTAAGGATACCTGCTCATGGTCTCACAGCAGCA Human: TTGATGGTAATTTCCTGTTCC---AGGTATATACCTAAGGATACCTGCTCATGGTCTCACAGCAGCA Cluster: [ ] Orangutan: TTGATGGTAATTTCCTGTTCC---AGGTATATACCTAAGGATACCTGCTCATGGTCTCACAGCAGCA Human > Chimp ------------- chr7:84878664-84878670 Template switch process: F1: L ATCTCAGAGCTGTTTTAAGATTGATGGTAATTTCCTGTTCCAG 1 F3: 4 CCTAAGGATACCTGCTCATGGTCTCACAGCAGCATGGCCT R RF: ATCTCAGAGCTGTTTTAAGATTGATGGTAATTTCCTGTTCCAGGTATATACCTAAGGATACCTGCTCATGGTCTCACAGCAGCATGGCCT RR: TAGAGTCTCGACAAAATTCTAACTACCATTAAAGGACAAGGTCCATATATGGATTCCTATGGACGAGTACCAGAGTGTCGTCGTACCGGA F2: 3 TATGGAC 2 Unidirectional alignment (log-probability: -25.7) TCAGAGCTGTTTTAAGATTGATGGTAATTTCCTGTTCcagCAGGTAT---CCTAAGGATACCTGCTCATGGTCTCACAGCAGCATGGCCT TCAGAGCTGTTTTAAGATTGATGGTAATTTCCTGTTC---CAGGTATATACCTAAGGATACCTGCTCATGGTCTCACAGCAGCATGGCCT Template switch alignment (log-probability: -16.2) TCAGAGCTGTTTTAAGATTGATGGTAATTTCCTGTTCCAG|CAGGTAT|CCTAAGGATACCTGCTCATGGTCTCACAGCAGCATGGCCT TCAGAGCTGTTTTAAGATTGATGGTAATTTCCTGTTCCAG|CAGGTAT|CCTAAGGATACCTGCTCATGGTCTCACAGCAGCATGGCCT ========== Event 3454 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: TGGAAGCTAAGCTGTTTAATAACAAAGGATGAGCATAATTTTAGCTAACTTGAGTTCAATCACTTA ↓ 13 24 ↑ 13 24 Chimp: TGGAAGCTAAGCTGTTTAATAGCTAAAATTATGCTCATCCTTTGTTAACTTGAGTTCAACCACTTA Gorilla: TGGAAGCTAAGCTGTTTAATAGCTAAATTTATGCTCATCCTTTGTTAACTTAAGTTCAACCACTTA Human: TGGAAGCTAAGCTGTTTAATAACAAAGGATGAGCATAATTTTAGCTAACTTGAGTTCAATCACTTA Cluster: [ ] Orangutan: TGGAAGTTAAGCTGTTTAATAGCTAAATTTATGCTCATCCTTTGTTAACTTGAGTTCAGCCACTTA Chimp > Human ------------- chr7:8746482-8746505 Template switch process: F1: L GGCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATA 1 F3: 4 TAACTTGAGTTCAATCACTTACTTTATTTGCCATATATTT R RF: GGCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATAGCTAAAATTATGCTCATCCTTTGTTAACTTGAGTTCAACCACTTACTTTATTTGCCATATATTT RR: CCGTTTATTAAGTAACGTAAACCTTCGATTCGACAAATTATCGATTTTAATACGAGTAGGAAACAATTGAACTCAAGTTGGTGAATGAAATAAACGGTATATAAA F2: 3 CGATTTTAATACGAGTAGGAAACA 2 Unidirectional alignment (log-probability: -59.9) GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATaacaaaggatgagcataattttAGC----------------------TAACTTGAGTTCAAtCACTTACTTTATTTGCCATATATTT GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAAT----------------------AGCTAAAATTATGCTCATCCTTTGTTAACTTGAGTTCAACCACTTACTTTATTTGCCATATATTT Template switch alignment (log-probability: -24.2) GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATA|ACAAAGGATGAGCATAATTTTAGC|TAACTTGAGTTCAAtCACTTACTTTATTTGCCATATATTT GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATA|ACAAAGGATGAGCATAATTTTAGC|TAACTTGAGTTCAACCACTTACTTTATTTGCCATATATTT Human > Chimp ------------- chr7:7768581-7768604 Template switch process: F1: L GGCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATA 1 F3: 4 TAACTTGAGTTCAACCACTTACTTTATTTGCCATATATTT R RF: GGCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATAACAAAGGATGAGCATAATTTTAGCTAACTTGAGTTCAATCACTTACTTTATTTGCCATATATTT RR: CCGTTTATTAAGTAACGTAAACCTTCGATTCGACAAATTATTGTTTCCTACTCGTATTAAAATCGATTGAACTCAAGTTAGTGAATGAAATAAACGGTATATAAA F2: 3 TGTTTCCTACTCGTATTAAAATCG 2 Unidirectional alignment (log-probability: -59.9) GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAA----------------------TAGCTAAaattatgctcatcctttgttaaCTTGAGTTCAAcCACTTACTTTATTTGCCATATATTT GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATAACAAAGGATGAGCATAATTTTAGCTAA----------------------CTTGAGTTCAATCACTTACTTTATTTGCCATATATTT Template switch alignment (log-probability: -24.2) GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATA|GCTAAAATTATGCTCATCCTTTGT|TAACTTGAGTTCAAcCACTTACTTTATTTGCCATATATTT GCAAATAATTCATTGCATTTGGAAGCTAAGCTGTTTAATA|GCTAAAATTATGCTCATCCTTTGT|TAACTTGAGTTCAATCACTTACTTTATTTGCCATATATTT ========== Event 3455 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCCAAGAATAGAACGCATAC--TCTCCAG-AAGAGGAGAGTGGATGCCTCACTGaaaaaaaaaaaaaaaaaa---- ↑ 1 4 3 2 Chimp: TTCCAAGAATAGAACGCATAC----TCCAGAAAGAGGAGAGTGGATGCCTCACTGgaaaaaaaaaa-------aaaa Gorilla: TTCCAAGAATAGAATGCATAC----TCCAGAAAGAGGAGAGTGGATGCCTCACTGaaaaaaaaaaaaaaaaa----- Human: TTCCAAGAATAGAACGCATAC--TCTCCAG-AAGAGGAGAGTGGATGCCTCACTGaaaaaaaaaaaaaaaaaa---- Cluster: [ ] Orangutan: TTCCAAGAATAGAATGCATTCTC--TCCAG-AAGAGGAGAGTGGATGCCTCACTGaaaaaaaaaaaaaaaaaa---- Chimp > Human ------------- chr7:83831868-83831872 Template switch process: F1: L TTTGAATCAAATTTTGCATTTTCCAAGAATAGAACGCATACTC 1 F3: 4 AAGAGGAGAGTGGATGCCTCACTGAAAAAAAAAAAAAAAA R RF: TTTGAATCAAATTTTGCATTTTCCAAGAATAGAACGCATACTCCAGAAAGAGGAGAGTGGATGCCTCACTGGAAAAAAAAAAAAAAA RR: AAACTTAGTTTAAAACGTAAAAGGTTCTTATCTTGCGTATGAGGTCTTTCTCCTCTCACCTACGGAGTGACCTTTTTTTTTTTTTTT F2: 3 GACCT 2 Unidirectional alignment (log-probability: -44.5) GAATCAAATTTTGCATTTTCCAAGAATAGAACGCATActCTCCAG-AAGAGGAGAGTGGATGCCTCACTGaAAAAAAAAAAaaaaa GAATCAAATTTTGCATTTTCCAAGAATAGAACGCATA--CTCCAGAAAGAGGAGAGTGGATGCCTCACTGGAAAAAAAAAA----- Template switch alignment (log-probability: -21.9) GAATCAAATTTTGCATTTTCCAAGAATAGAACGCATACTC|TCCAG|AAGAGGAGAGTGGATGCCTCACTGaAAAAAAAAAAAAAAA GAATCAAATTTTGCATTTTCCAAGAATAGAACGCATACTC|TCCAG|AAGAGGAGAGTGGATGCCTCACTGGAAAAAAAAAAAAAAA ========== Event 3456 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAATAGTATACAGGCAATAACT---ATACA-GGGTGAAACTACTGGCTTCAGC Chimp: CAATAGTATACAGGCAATAACT---ATACA-GGGTGAAACTACTGGCTTCAGC ↓ 3 1 24 Gorilla: CAATAGTATACAGGCAATAACTACTGTATAGTAGTGAAACTACTGGCTTCAGC ↑ 3 1 24 Human: CAATAGTATACAGGCAATAACT---ATACA-GGGTGAAACTACTGGCTTCAGC Cluster: [ ] Orangutan: -AATAGTATACAGGCAATAACT---CTACA-GGGTGAAACTACTGGCTTCAGC Human > Gorilla --------------- chr7:64912515-64912523 Template switch process: F1: L TTGCACATACTTGAATTAACAATAGTATACAGGCAATAACTA 1 F3: 4 AGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAGA R RF: TTGCACATACTTGAATTAACAATAGTATACAGGCAATAACTATACAGGGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAGA RR: AACGTGTATGAACTTAATTGTTATCATATGTCCGTTATTGATATGTCCCACTTTGATGACCGAAGTCGTTTATTTCTCACATTATTCT F2: 3 TGATATGTC 2 Unidirectional alignment (log-probability: -32.4) GCACATACTTGAATTAACAATAGTATACAGGCAATAACTActgtatagTA----GTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG GCACATACTTGAATTAACAATAGTATACAGGCAATAACTA--------TACAGGGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG Template switch alignment (log-probability: -22.4) GCACATACTTGAATTAACAATAGTATACAGGCAATAACTA|CTGTATAGT|aGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG GCACATACTTGAATTAACAATAGTATACAGGCAATAACTA|CTGTATAGT|GGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG Chimp > Gorilla --------------- chr7:64912515-64912523 Template switch process: F1: L TTGCACATACTTGAATTAACAATAGTATACAGGCAATAACTA 1 F3: 4 AGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAGA R RF: TTACACATACTTGAATTAACAATAGTATACAGGCAATAACTATACAGGGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAGA RR: AATGTGTATGAACTTAATTGTTATCATATGTCCGTTATTGATATGTCCCACTTTGATGACCGAAGTCGTTTATTTCTCACATTATTCT F2: 3 TGATATGTC 2 Unidirectional alignment (log-probability: -37.9) gCACATACTTGAATTAACAATAGTATACAGGCAATAACTActgtatagTA----GTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG ACACATACTTGAATTAACAATAGTATACAGGCAATAACTA--------TACAGGGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG Template switch alignment (log-probability: -28) gCACATACTTGAATTAACAATAGTATACAGGCAATAACTA|CTGTATAGT|aGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG ACACATACTTGAATTAACAATAGTATACAGGCAATAACTA|CTGTATAGT|GGTGAAACTACTGGCTTCAGCAAATAAAGAGTGTAATAAG ========== Event 3457 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACTGTAATGAGTATGCGTAATTGAACTCTTGCAG------CCTTTGAACGAGAGTCTCTTCCAC Chimp: ACTGTAATGAGTATGCGTAATTGAACTCTTGCATGAGTTCAATTTGAATGAGAGTCTCTTCCAC ↑ 3 2 1 4 Gorilla: ACTGTAATGAGTATGCGTAATTGAACTCTTGCAG------CCTTTGAATGAGAGCCTCTTCCAC Human: ACTGTAATGAGTATGCGTAATTGAACTCTTGCAG------CCTTTGAACGAGAGTCTCTTCCAC Cluster: [ ] Orangutan: ACTGTAATGAGTATGCATAATTGAACC-CTGCAA------CCTTTGAATGAGAGTCTTTTCCAC Gorilla > Chimp --------------- chr7:87007325-87007333 Template switch process: F1: L TCTTTTTTACTGTAATGAGTATGCGTAATTGAACTCTTGCAT 1 F3: 4 TTGAATGAGAGTCTCTTCCACCTGTCTGGAATCATATAT R RF: TCTTTTTTACTGTAATGAGTATGCGTAATTGAACTCTTGCAGCCTTTGAATGAGAGCCTCTTCCACCTGTCTGGAATCATATAT RR: AGAAAAAATGACATTACTCATACGCATTAACTTGAGAACGTCGGAAACTTACTCTCGGAGAAGGTGGACAGACCTTAGTATATA F2: 3 TAACTTGAG 2 Unidirectional alignment (log-probability: -39.2) TTTTTTACTGTAATGAGTATGCGTAATTGAACTCTTGCA---tgagttcaaTTTGAATGAGAGtCTCTTCCACCTGTCTGGAATCATATAT TTTTTTACTGTAATGAGTATGCGTAATTGAACTCTTGCAGCC---------TTTGAATGAGAGCCTCTTCCACCTGTCTGGAATCATATAT Template switch alignment (log-probability: -27.9) TTTTTTACTGTAATGAGTATGCGTAATTGAACTCTTGCAt|GAGTTCAAT|TTGAATGAGAGtCTCTTCCACCTGTCTGGAATCATATAT TTTTTTACTGTAATGAGTATGCGTAATTGAACTCTTGCAG|GAGTTCAAT|TTGAATGAGAGCCTCTTCCACCTGTCTGGAATCATATAT ========== Event 3458 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCAAGAATTCAACAAATATTTG-----GGGTAACTACTTTTATGAGGCTAGGCATGATTTATATAA Chimp: ATCAAGAATTCAACAAATATTTG-----GGGTAACTACTTTTATGAGACTAGGCATGATTTATATAA ↓ 1 4 3 2 Gorilla: ATCAAGAATTCAACAAATATTCTGATAAAAGTAACTACTTTTATGAGACTAGGCATGATTTATATAA ↑ 1 4 3 2 Human: ATCAAGAATTCAACAAATATTTG-----GGGTAACTACTTTTATGAGGCTAGGCATGATTTATATAA Cluster: [ ] Orangutan: ATCAAGAATTCAACAAATATTTG-----GGGTAACTCCTTTTATGAGACTAGGCATGATTTATATAA Human > Gorilla --------------- chr7:65345832-65345841 Template switch process: F1: L TTGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT 1 F3: 4 TAACTACTTTTATGAGACTAGGCATGATTTATATAATTT R RF: TTGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATTTGGGGTAACTACTTTTATGAGGCTAGGCATGATTTATATAATTT RR: AACGGTCAACCCATACTTATTAGTTCTTAAGTTGTTTATAAACCCCATTGATGAAAATACTCCGATCCGTACTAAATATATTAAA F2: 3 GAAAATAGTC 2 Unidirectional alignment (log-probability: -39.3) TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT----ctgataaaaGTAACTACTTTTATGAGaCTAGGCATGATTTATATAATTT TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATTTGGG---------GTAACTACTTTTATGAGGCTAGGCATGATTTATATAATTT Template switch alignment (log-probability: -28) TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT|CTgATAAAAG|TAACTACTTTTATGAGaCTAGGCATGATTTATATAATTT TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT|CTCATAAAAG|TAACTACTTTTATGAGGCTAGGCATGATTTATATAATTT Chimp > Gorilla --------------- chr7:65345832-65345841 Template switch process: F1: L TTGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT 1 F3: 4 TAACTACTTTTATGAGACTAGGCATGATTTATATAATTT R RF: TTGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATTTGGGGTAACTACTTTTATGAGACTAGGCATGATTTATATAATTT RR: AACGGTCAACCCATACTTATTAGTTCTTAAGTTGTTTATAAACCCCATTGATGAAAATACTCTGATCCGTACTAAATATATTAAA F2: 3 GAAAATAGTC 2 Unidirectional alignment (log-probability: -33.8) TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT----ctgataaaaGTAACTACTTTTATGAGACTAGGCATGATTTATATAATTT TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATTTGGG---------GTAACTACTTTTATGAGACTAGGCATGATTTATATAATTT Template switch alignment (log-probability: -22.5) TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT|CTgATAAAAG|TAACTACTTTTATGAGACTAGGCATGATTTATATAATTT TGCCAGTTGGGTATGAATAATCAAGAATTCAACAAATATT|CTCATAAAAG|TAACTACTTTTATGAGACTAGGCATGATTTATATAATTT ========== Event 3459 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATACTAGAAAAAAATATGGCAACATGATA---TTTTTCTGAATGCTTCTGAACAATTCATTC Chimp: ATACTAGaaaaaaaTATGGCAACATGATA---TTTTTCTGAATGCTTCTGAACAATTCATTC ↓ 1 3 4 2 Gorilla: ATACTAGaaaaaaaTATGGCATTCAGAAA------AACTGAATGCTTCTGAACAATTCATTC ↑ 1 3 4 2 Human: ATACTAGAAAAAAATATGGCAACATGATA---TTTTTCTGAATGCTTCTGAACAATTCATTC Cluster: [ ] Orangutan: ATACTAGAAAAAAATATGGCAAAGTGATATTT---TTCTGAATGCTTCTGAACGATTCATTC Human > Gorilla --------------- chr7:92764747-92764756 Template switch process: F1: L GAATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA 1 F3: 4 CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG R RF: GAATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCAACATGATATTTTTCTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG RR: CTTATCTCATAGGTGGAAAATATGATCTTTTTTTATACCGTTGTACTATAAAAAGACTTACGAAGACTTGTTAAGTAAGTCAAGGGTACTTCTC F2: 3 AAAAAGACTT 2 Unidirectional alignment (log-probability: -32.7) AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA-----------TTcagaaaaaCTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCAACATGATATTTTT--------CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG Template switch alignment (log-probability: -17) AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA|TTCAGAAAAA|CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA|TTCAGAAAAA|CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG Chimp > Gorilla --------------- chr7:92764747-92764756 Template switch process: F1: L GAATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA 1 F3: 4 CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG R RF: GAATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCAACATGATATTTTTCTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG RR: CTTATCTCATAGGTGGAAAATATGATCTTTTTTTATACCGTTGTACTATAAAAAGACTTACGAAGACTTGTTAAGTAAGTCAAGGGTACTTCTC F2: 3 AAAAAGACTT 2 Unidirectional alignment (log-probability: -32.7) AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA-----------TTcagaaaaaCTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCAACATGATATTTTT--------CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG Template switch alignment (log-probability: -17) AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA|TTCAGAAAAA|CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG AATAGAGTATCCACCTTTTATACTAGAAAAAAATATGGCA|TTCAGAAAAA|CTGAATGCTTCTGAACAATTCATTCAGTTCCCATGAAGAG ========== Event 3460 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGAAAGTAAAGGATATTAGC-TCAGTCAAATGTGAACATATCCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGC ↓ 1 4 3 2 Chimp: CAGAAAGTAAAGGATATTAGCTTTAGT--------------CCCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGC ↑ 1 4 3 2 Gorilla: CAGAAAGTAAAGGATATTAGC-TCAGTCAAATGTGAACATATCCCTGCTGGGACTAAAGGGTTCACCAGCTCTGTGC Human: CAGAAAGTAAAGGATATTAGC-TCAGTCAAATGTGAACATATCCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGC Cluster: [ ] Orangutan: CAGAAAGTAAAGGATATTAGC-TCAGTCAAATGTGAACATATCCCGGCTGGGACTAAAGGGTTCACCAGCTCTGTGC Human > Chimp ------------- chr7:88728208-88728213 Template switch process: F1: L TTTTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCT 1 F3: 4 CCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT R RF: TTTTCCCATTTGTGAGCTTACAGAAAGTAAAGGATATTAGCTCAGTCAAATGTGAACATATCCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT RR: AAAAGGGTAAACACTCGAATGTCTTTCATTTCCTATAATCGAGTCAGTTTACACTTGTATAGGGACGACCCTGATTTCCCAAGTGGACGAGACACGTGGAA F2: 3 CTGATT 2 Unidirectional alignment (log-probability: -35.3) TTCCCATTTtTGAGCTTACAGAAAGTAAAGGATATTAGCT------------------TtagtcCCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT TTCCCATTTGTGAGCTTACAGAAAGTAAAGGATATTAGCTCAGTCAAATGTGAACATAT-----CCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT Template switch alignment (log-probability: -22) TTCCCATTTtTGAGCTTACAGAAAGTAAAGGATATTAGCT|TTAGTC|CCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT TTCCCATTTGTGAGCTTACAGAAAGTAAAGGATATTAGCT|TTAGTC|CCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT Gorilla > Chimp --------------- chr7:88728208-88728213 Template switch process: F1: L TTTTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCT 1 F3: 4 CCCTGCTGGGACTAAAGGGTTCACCTGCTCTGTGCACCTT R RF: TTTTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCTCAGTCAAATGTGAACATATCCCTGCTGGGACTAAAGGGTTCACCAGCTCTGTGCACCTT RR: AAAAGGGTAAAAACTCGAATGTCTTTCATTTCCTATAATCGAGTCAGTTTACACTTGTATAGGGACGACCCTGATTTCCCAAGTGGTCGAGACACGTGGAA F2: 3 CTGATT 2 Unidirectional alignment (log-probability: -33.9) TTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCTttAGTC--------------CCCTGCTGGGACTAAAGGGTTCACCtGCTCTGTGCACCTT TTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCTC-AGTCAAATGTGAACATATCCCTGCTGGGACTAAAGGGTTCACCAGCTCTGTGCACCTT Template switch alignment (log-probability: -22) TTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCT|TTAGTC|CCCTGCTGGGACTAAAGGGTTCACCtGCTCTGTGCACCTT TTCCCATTTTTGAGCTTACAGAAAGTAAAGGATATTAGCT|TTAGTC|CCCTGCTGGGACTAAAGGGTTCACCAGCTCTGTGCACCTT ========== Event 3461 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AACCATTTGTGTCTGGAATAGATAAACCAAATTGCATACCATTACtttaataacatttattataattaagaaaaaacatatatatttaCATCTGTTTATCTATCTGAAACCTTACCTGTTAT Chimp: AACCATTTGTGTCTGGAATAGATAAACCAAATTGCATACCATTACTTTAATAACATTTATTATAATTAAGAAAAACCATATATATTTACATCTATTTATCTATCTGAAACCTTACCTGTTAT Gorilla: AACCATTTGTGTCTGGAATAGATAAACCAACTTGCATACCATTACTTTATTAACATTTATTATAATTAAGAAAAAACATATATATTTACATCTATTTA----TCTGAAACCTTACCTGTTAT ↓ 3 2 1 4 Human: AACCATTTGTGTCTGGAATAGATAAACCAAATTGCATACCATTACtttaataacatttattataattaagaaaaaacatatatatttaCATCTGTTTATCTATCTGAAACCTTACCTGTTAT Cluster: [ ] Orangutan: AACCATTTGTGTCTGGAATAGATAAACCAAATTGCATACCATTACTTTAATAACATTTATTATAATTAAGAAAAAACATATATATCTACATTTATTTA----TCTAAAACCTTACCTGttat Gorilla > Human --------------- chr7:85715828-85715835 Template switch process: F1: L ACATTTATTATAATTAAGAAAAAACATATATATTTACATCT 1 F3: 4 ATCTGAAACCTTACCTGTTATTCATAAATAAAAATA-----------TAAT R RF: AGATAAACCAACTTGCATACCATTACTTTATTAACATTTATTATAATTAAGAAAAAACATATATATTTACATCTATTTATCTGAAACCTTACCTGTTATTCATAAATAAAAATATCTTTTTTACTTAAT RR: TCTATTTGGTTGAACGTATGGTAATGAAATAATTGTAAATAATATTAATTCTTTTTTGTATATATAAATGTAGATAAATAGACTTTGGAATGGACAATAAGTATTTATTTTTATAGAAAAAATGAATTA F2: 3 TCTATTTG 2 Unidirectional alignment (log-probability: -40) CATTTATTATAATTAAGAAAAAACATATATATTTACATCtgttTATcTATCTGAAACCTTACCTGTTATTCATAAATAAAAATATaaT- CATTTATTATAATTAAGAAAAAACATATATATTTACATC----TATTTATCTGAAACCTTACCTGTTATTCATAAATAAAAATATCTTT Template switch alignment (log-probability: -27) CATTTATTATAATTAAGAAAAAACATATATATTTACATCT|GTTTATCT|ATCTGAAACCTTACCTGTTATTCATAAATAAAAATA-----------TAAT CATTTATTATAATTAAGAAAAAACATATATATTTACATCT|GTTTATCT|ATCTGAAACCTTACCTGTTATTCATAAATAAAAATATCTTTTTTACTTAAT ========== Event 3462 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGAAATGAGAAAATTTGGCCCAACTGTATCATAAAATTTAATTGTGATACAGTTGGTTGTGTCCTCCAAAAGTA Chimp: TTGCAATGAGAAAATTTGGCC---------TTTAAAG----TTTGTGATACAGTTGGTTGTGTCCTCCAAAAGTA Gorilla: TTGAAATGAGAAAATTTGGCC---------CTTAAAG----TTTGTGATACAGTTGGTTGTGTCCTCCAAAAGTA ↓ 13 4 2 Human: TTGAAATGAGAAAATTTGGCCCAACTGTATCATAAAATTTAATTGTGATACAGTTGGTTGTGTCCTCCAAAAGTA Cluster: [ ] Orangutan: TTGAAATGAGAAAATTTGGCC---------TTTAAAG----TTTGTGATACAGTTGCTTGTGTCCTCCGAAAGTA Gorilla > Human --------------- chr7:86624602-86624621 Template switch process: F1: L CAGCACACATTGATAGTCAGTTGAAATGAGAAAATTTGGCCC 1 F3: 4 TTGTGATACAGTTGGTTGTGTCCTCCAAAAGTATATGGAT R RF: CAGCACACATTGATAGTCAGTTGAAATGAGAAAATTTGGCCCTTAAAGTTTGTGATACAGTTGGTTGTGTCCTCCAAAAGTATATGGAT RR: GTCGTGTGTAACTATCAGTCAACTTTACTCTTTTAAACCGGGAATTTCAAACACTATGTCAACCAACACAGGAGGTTTTCATATACCTA F2: 3 AATTTAAAATACTATGTCAA 2 Unidirectional alignment (log-probability: -43.9) GCACACATTGATAGTCAGTTGAAATGAGAAAATTTGGCCCaactgtatcataaaatTTAA---TTGTGATACAGTTGGTTGTGTCCTCCAAAAGTATATGGAT GCACACATTGATAGTCAGTTGAAATGAGAAAATTTGGCCC----------------TTAAAGTTTGTGATACAGTTGGTTGTGTCCTCCAAAAGTATATGGAT Template switch alignment (log-probability: -29.3) GCACACATTGATAGTCAGTTGAAATGAGAAAATTTGGCCC|AACTGTATCAtAAAaTTTAA|TTGTGATACAGTTGGTTGTGTCCTCCAAAAGTATATGGAT GCACACATTGATAGTCAGTTGAAATGAGAAAATTTGGCCC|AACTGTATCACAAACTTTAA|TTGTGATACAGTTGGTTGTGTCCTCCAAAAGTATATGGAT ========== Event 3463 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTTGGTTGGGGAGGACAATGCCA-GGTTAACAGACACTTAATATACATCTCTGTAGAGAAT Chimp: GTTTTGGTTGGGGAGGACAATGCCA-GGTTAACAGACACTTAAAATACATCTCTGTAGAGAAT ↓ 1 4 3 2 Gorilla: GTTTTGGTTGGGGAGGACAATTTAAGTGTCTACAGACACTTAAAATACATCTCTGTAGAGAAT ↑ 1 4 3 2 Human: GTTTTGGTTGGGGAGGACAATGCCA-GGTTAACAGACACTTAATATACATCTCTGTAGAGAAT Cluster: [ ] Orangutan: GTTTCGGTTGGGGAAGACAATCCCA-GGTTAACAGACACTTAAAATACTTCTCTGTAGAGAAT Human > Gorilla --------------- chr7:68527038-68527047 Template switch process: F1: L TAAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT 1 F3: 4 ACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT R RF: TAAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAATGCCAGGTTAACAGACACTTAATATACATCTCTGTAGAGAATGTGTTCCT RR: ATTCGGATAGTTATCTTTATCAAAACCAACCCCTCCTGTTACGGTCCAATTGTCTGTGAATTATATGTAGAGACATCTCTTACACAAGGA F2: 3 TCTGTGAATT 2 Unidirectional alignment (log-probability: -36.6) AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT------TTAagtgtctACAGACACTTAAaATACATCTCTGTAGAGAATGTGTTCCT AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAATGCCAGGTTA-------ACAGACACTTAATATACATCTCTGTAGAGAATGTGTTCCT Template switch alignment (log-probability: -22.5) AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT|TTAAGTGTCT|ACAGACACTTAAaATACATCTCTGTAGAGAATGTGTTCCT AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT|TTAAGTGTCT|ACAGACACTTAATATACATCTCTGTAGAGAATGTGTTCCT Chimp > Gorilla --------------- chr7:68527038-68527047 Template switch process: F1: L TAAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT 1 F3: 4 ACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT R RF: TAAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAATGCCAGGTTAACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT RR: ATTCGGATAGTTATCTTTATCAAAACCAACCCCTCCTGTTACGGTCCAATTGTCTGTGAATTTTATGTAGAGACATCTCTTACACAAGGA F2: 3 TCTGTGAATT 2 Unidirectional alignment (log-probability: -31) AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT------TTAagtgtctACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAATGCCAGGTTA-------ACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT Template switch alignment (log-probability: -17) AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT|TTAAGTGTCT|ACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT AAGCCTATCAATAGAAATAGTTTTGGTTGGGGAGGACAAT|TTAAGTGTCT|ACAGACACTTAAAATACATCTCTGTAGAGAATGTGTTCCT ========== Event 3464 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTTCCCTATTTGCTTCCTCCACTATTAAGATGTGTCCAACTACACATCTTAATAGTTTGTTCAGGGTCTTAGTCC ↑ 14 3 2 Chimp: GGTTCCCTATTTGCTTCCTCC-----------ATGTCCAACTATACATCTTAATAGTTTGTTCAGGGTCTTAGTCC Gorilla: GGTTCCCTATTTGCTTCCTCC-----------ATGTCCAACTACACATCTTAATAGTTTGCTCAGGGTCTTAGTCC ↓ 14 3 2 Human: GGTTCCCTATTTGCTTCCTCCACTATTAAGATGTGTCCAACTACACATCTTAATAGTTTGTTCAGGGTCTTAGTCC Cluster: [ ] Orangutan: GGTTCCCTATTTGCTTCCTCC-----------ATGTCCAACTACACATCTTAATAGTTTGTTCAGGGTCTTAGTCC Chimp > Human ------------- chr7:87427600-87427610 Template switch process: F1: L CTGGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA 1 F3: 4 TGTCCAACTACACATCTTAATAGTTTGTTCAGGGTCTTAG R RF: CTGGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCATGTCCAACTATACATCTTAATAGTTTGTTCAGGGTCTTAG RR: GACCTCAACCTGAAACCTGACCAAGGGATAAACGAAGGAGGTACAGGTTGATATGTAGAATTATCAAACAAGTCCCAGAATC F2: 3 GTAGAATTATC 2 Unidirectional alignment (log-probability: -32.7) GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCActattaagatgTGTCCAACTAcACATCTTAATAGTTTGTTCAGGGTCTTAG GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA-----------TGTCCAACTATACATCTTAATAGTTTGTTCAGGGTCTTAG Template switch alignment (log-probability: -22.7) GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA|CTATTAAGATG|TGTCCAACTAcACATCTTAATAGTTTGTTCAGGGTCTTAG GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA|CTATTAAGATG|TGTCCAACTATACATCTTAATAGTTTGTTCAGGGTCTTAG Gorilla > Human --------------- chr7:87427600-87427610 Template switch process: F1: L CTGGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA 1 F3: 4 TGTCCAACTACACATCTTAATAGTTTGTTCAGGGTCTTAG R RF: CTGGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCATGTCCAACTACACATCTTAATAGTTTGCTCAGGGTCTTAG RR: GACCTCAACCTGAAACCTGACCAAGGGATAAACGAAGGAGGTACAGGTTGATGTGTAGAATTATCAAACGAGTCCCAGAATC F2: 3 GTAGAATTATC 2 Unidirectional alignment (log-probability: -32.2) GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCActattaagatgTGTCCAACTACACATCTTAATAGTTTGtTCAGGGTCTTAG GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA-----------TGTCCAACTACACATCTTAATAGTTTGCTCAGGGTCTTAG Template switch alignment (log-probability: -22.7) GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA|CTATTAAGATG|TGTCCAACTACACATCTTAATAGTTTGtTCAGGGTCTTAG GGAGTTGGACTTTGGACTGGTTCCCTATTTGCTTCCTCCA|CTATTAAGATG|TGTCCAACTACACATCTTAATAGTTTGCTCAGGGTCTTAG ========== Event 3465 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGTAATTAGTAAAATACACTGCAAATCATTCTTAATACACATTTGACGCAGATCCTACC----TGTGTTTTCCCATATATGTTTAGCT ↓ 3 2 1 4 Chimp: AGTAATTAGTAAAATACACTGCAAATCATTCTTAATACACATTTGACACAGATCCTACCTATTTGCATTTTCCCATATATGTTTAGCT Gorilla: AGTAATTAGTAAAATACACTGCAAATCATTCTTAATACACATTTGACACAGATCCTATCTATTTGTGTTTTCCCATATATGTTTAGCT Human: AGTAATTAGTAAAATACACTGCAAATCATTCTTAATACACATTTGACGCAGATCCTACC----TGTGTTTTCCCATATATGTTTAGCT Cluster: [ ] Orangutan: AGTAATTAGTAAAATACACTGCAAATCATTCTTAATACACATTTGACACAGATCCTATCTATTTGCATTTTCTTATATATGTTTAGCT Human > Chimp ------------- chr7:7891420-7891426 Template switch process: F1: L CTGCAAATCATTCTTAATACACATTTGACACAGATCCTACCT 1 F3: 4 TTTTCCCATATATGTTTAGCTATACTTTTCTTATGAAAAA R RF: CTGCAAATCATTCTTAATACACATTTGACGCAGATCCTACCTGTGTTTTCCCATATATGTTTAGCTATACTTTTCTTATGAAAAA RR: GACGTTTAGTAAGAATTATGTGTAAACTGCGTCTAGGATGGACACAAAAGGGTATATACAAATCGATATGAAAAGAATACTTTTT F2: 3 ACGTTTA 2 Unidirectional alignment (log-probability: -34.7) GCAAATCATTCTTAATACACATTTGACaCAGATCCTACCtattTGcaTTTTCCCATATATGTTTAGCTATACTTTTCTTATGAAAAA GCAAATCATTCTTAATACACATTTGACGCAGATCCTACC----TGTGTTTTCCCATATATGTTTAGCTATACTTTTCTTATGAAAAA Template switch alignment (log-probability: -22.2) GCAAATCATTCTTAATACACATTTGACaCAGATCCTACCT|ATTTGCA|TTTTCCCATATATGTTTAGCTATACTTTTCTTATGAAAAA GCAAATCATTCTTAATACACATTTGACGCAGATCCTACCT|ATTTGCA|TTTTCCCATATATGTTTAGCTATACTTTTCTTATGAAAAA ========== Event 3466 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ttgtttcctactaggggtctgactACTAGAGGT-----------------ACCTATTTTCTTATCTCTTCAACTTTTCTTTCTT ↓ 3 2 4 1 Chimp: TTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTAGTAGTCAGAGGTACCTAGTTTCTTATCTCTTCAACTTTTCTTTCTC ↑ 3 2 4 1 Gorilla: ttgtttcctactaggggtctgactACTAGAGGT-----------------ACCTATTTTCTTACCTCTTCAACTTTTCTTTCTC Human: ttgtttcctactaggggtctgactACTAGAGGT-----------------ACCTATTTTCTTATCTCTTCAACTTTTCTTTCTT Cluster: [ ] Orangutan: ttgtctcctactaggggtctgactACTAGAGGT-----------------ACCTATTTTCTTACCTCTTCAACTTTTCTTTCTC Human > Chimp ------------- chr7:91274970-91274976 Template switch process: F1: L GTGCCATTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTA 1 F3: 4 GAGGTACCTAGTTTCTTATCTCTTCAACTTTTCTTTCTCCATCTATTTTT R RF: GTGCCATTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTATTTTCTTATCTCTTCAACTTTTCTTTCTTCATCTATTTTT RR: CACGGTAAAACAAAGGATGATCCCCAGACTGATGATCTCCATGGATAAAAGAATAGAGAAGTTGAAAAGAAAGAAGTAGATAAAAA F2: 3 ACTGATG 2 Unidirectional alignment (log-probability: -54.7) TTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTAgTagtcagaggtacctagtTTCTTATCTCTTCAACTTTTCTTTCTcC TTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTATT-----------------TTCTTATCTCTTCAACTTTTCTTTCTTC Template switch alignment (log-probability: -28.4) TTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTA|GTAGTCA|GAGGTACCTAgTTTCTTATCTCTTCAACTTTTCTTTCTcC TTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTA|GTAGTCA|GAGGTACCTATTTTCTTATCTCTTCAACTTTTCTTTCTTC Gorilla > Chimp --------------- chr7:91274970-91274976 Template switch process: F1: L GTGCCATTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTA 1 F3: 4 GAGGTACCTAGTTTCTTATCTCTTCAACTTTTCTTTCTCCATCTATTTTTTCCAGTGCA R RF: GTGCCATTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTATTTTCTTACCTCTTCAACTTTTCTTTCTCCATCTATTTTTTCCAGTGCA RR: CACGGTAAAACAAAGGATGATCCCCAGACTGATGATCTCCATGGATAAAAGAATGGAGAAGTTGAAAAGAAAGAGGTAGATAAAAAAGGTCACGT F2: 3 ACTGATG 2 Unidirectional alignment (log-probability: -46.6) TTTTGTTTCCTACTAGGGGTCTGACTACTagaggtacctagtagtcAGAGGTACCTAgTTTCTTAtCTCTTCAACTTTTCTTTCTCC TTTTGTTTCCTACTAGGGGTCTGACTACT-----------------AGAGGTACCTATTTTCTTACCTCTTCAACTTTTCTTTCTCC Template switch alignment (log-probability: -28.2) TTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTA|GTAGTCA|GAGGTACCTAgTTTCTTAtCTCTTCAACTTTTCTTTCTCC TTTTGTTTCCTACTAGGGGTCTGACTACTAGAGGTACCTA|GTAGTCA|GAGGTACCTATTTTCTTACCTCTTCAACTTTTCTTTCTCC ========== Event 3467 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTCTTGGAGTAAAAAGATAGTA-CT-----------------------------------------------GTTTTTGCTTTTCTTTCTCTTTTAGTCCCCACTATCATTCAAGAAGTAGTC ↓ 1 3 24 ↑ 1 3 24 Chimp: TTCTTGCAGTAAAAAGATAGTG-GG----------------------------GACTAAAAGAGAAAGAAAAGCAAAAACA-------------------GTACTATCATTCAAGAAGTAGTC Gorilla: TTCTTGGAGTAAAAAGACAGTG-GG-------------GACTAAAAGAGAAAA-------------------GCAAAAACA-------------------GTACTATCATTCAAGAAGTAGTC Human: TTCTTGGAGTAAAAAGATAGTA-CT-----------------------------------------------GTTTTTGCTTTTCTTTCTCTTTTAGTCCCCACTATCATTCAAGAAGTAGTC Cluster: [ ] Orangutan: TTCTTGGAGTACAAAGATAGTGGGGGACTAAAAGAAAA----------------------------------GCAAAAACA-------------------GTACTATCATTCAAGAAGTAGTC Chimp > Human ------------- chr7:9035052-9035084 Template switch process: F1: L AAGGAGGGCTTCTTGTTACTTTCTTGGAGTAAAAAGATAGT 1 F3: 4 ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC R RF: AAGGAGGGCTTCTTGTTACTTTCTTGCAGTAAAAAGATAGTGGGGACTAAAAGAGAAAGAAAAGCAAAAACAGTACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC RR: TTCCTCCCGAAGAACAATGAAAGAACGTCATTTTTCTATCACCCCTGATTTTCTCTTTCTTTTCGTTTTTGTCATGATAGTAAGTTCTTCATCAGTTCGTCAAACAGTACCTCG F2: 3 CCCCTGATTTTCTCTTTCTTTTCGTTTTTGTCA 2 Unidirectional alignment (log-probability: -74.8) AGGAGGGCTTCTTGTTACTTTCTTGgAGTAAAAAGATAGT----------------------------ACtGTttttgcttttctttctcttttagtccccACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC AGGAGGGCTTCTTGTTACTTTCTTGCAGTAAAAAGATAGTGGGGACTAAAAGAGAAAGAAAAGCAAAAACAGT----------------------------ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC Template switch alignment (log-probability: -25.3) AGGAGGGCTTCTTGTTACTTTCTTGgAGTAAAAAGATAGT|ACTGTTTTTGCTTTTCTTTCTCTTTTAGTCCCC|ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC AGGAGGGCTTCTTGTTACTTTCTTGCAGTAAAAAGATAGT|ACTGTTTTTGCTTTTCTTTCTCTTTTAGTCCCC|ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC Human > Chimp ------------- chr7:8014808-8014840 Template switch process: F1: L AAGGAGGGCTTCTTGTTACTTTCTTGCAGTAAAAAGATAGT 1 F3: 4 ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC R RF: AAGGAGGGCTTCTTGTTACTTTCTTGGAGTAAAAAGATAGTACTGTTTTTGCTTTTCTTTCTCTTTTAGTCCCCACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC RR: TTCCTCCCGAAGAACAATGAAAGAACCTCATTTTTCTATCATGACAAAAACGAAAAGAAAGAGAAAATCAGGGGTGATAGTAAGTTCTTCATCAGTTCGTCAAACAGTACCTCG F2: 3 TGACAAAAACGAAAAGAAAGAGAAAATCAGGGG 2 Unidirectional alignment (log-probability: -74.8) AGGAGGGCTTCTTGTTACTTTCTTGcAGTAAAAAGATAGTggggactaaaagagaaagaaaagcaaaaACaGT----------------------------ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC AGGAGGGCTTCTTGTTACTTTCTTGGAGTAAAAAGATAGT----------------------------ACTGTTTTTGCTTTTCTTTCTCTTTTAGTCCCCACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC Template switch alignment (log-probability: -25.3) AGGAGGGCTTCTTGTTACTTTCTTGcAGTAAAAAGATAGT|GGGGACTAAAAGAGAAAGAAAAGCAAAAACAGT|ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC AGGAGGGCTTCTTGTTACTTTCTTGGAGTAAAAAGATAGT|GGGGACTAAAAGAGAAAGAAAAGCAAAAACAGT|ACTATCATTCAAGAAGTAGTCAAGCAGTTTGTCATGGAGC ========== Event 3468 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAGCAATTACGTTTCTGTTAACACAAATTCCATTGTTTGAAATTTA---ATTAAGGTTTTTCTGGAGGCAA Chimp: TAGCAATTACGTTTCTGTTAACACAAATTCCGTTGTTTGAAATTTA---ATTAAGGTTTTTCTGGAGGCAA Gorilla: TAGCAATTACGTTTCTGTTAAT-TAAATTTCAAACAATGGAATTTGAGTGTTAAGGTTTTTCTGGAGGCAA ↓ 1 3 2 4 Human: TAGCAATTACGTTTCTGTTAACACAAATTCCATTGTTTGAAATTTA---ATTAAGGTTTTTCTGGAGGCAA Cluster: [ ] Orangutan: TAGCAATTAAGTTTCTGTTAACACAAATTCCATTGTTTGAAATTTA---GTTAAGGTTTTTCTGGAGGCAA Gorilla > Human --------------- chr7:9030086-9030111 Template switch process: F1: L TGCTGAATGGGAGCAATTATTAGCAATTACGTTTCTGTTAA 1 F3: 4 TTAAGGTTTTTCTGGAGGCAATAGAATTGTATTTGAACCA R RF: TGCTGAATGGGAGCAATTATTAGCAATTACGTTTCTGTTAATTAAATTTCAAACAATGGAATTTGAGTGTTAAGGTTTTTCTGGAGGCAATACAATTGTATTTGAACCA RR: ACGACTTACCCTCGTTAATAATCGTTAATGCAAAGACAATTAATTTAAAGTTTGTTACCTTAAACTCACAATTCCAAAAAGACCTCCGTTATGTTAACATAAACTTGGT F2: 3 AATTTAAAGTTTGTTACCTTAAACAC 2 Unidirectional alignment (log-probability: -59.1) GCTGAATGGGAGCAATTATTAGCAATTACGTTTCTGTTAAcacaaattccattgtttgaaatTTAA------------------------TTAAGGTTTTTCTGGAGGCAATAgAATTGTATTTGAACCA GCTGAATGGGAGCAATTATTAGCAATTACGTTTCTGTTAA----------------------TTAAATTTCAAACAATGGAATTTGAGTGTTAAGGTTTTTCTGGAGGCAATACAATTGTATTTGAACCA Template switch alignment (log-probability: -30.1) GCTGAATGGGAGCAATTATTAGCAATTACGTTTCTGTTAA|CaCAAATTCCATTGTTTGAAATTTAA|TTAAGGTTTTTCTGGAGGCAATAgAATTGTATTTGAACCA GCTGAATGGGAGCAATTATTAGCAATTACGTTTCTGTTAA|CTCAAATTCCATTGTTTGAAATTTAA|TTAAGGTTTTTCTGGAGGCAATACAATTGTATTTGAACCA ========== Event 3469 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGCACACTGGCAAAAGACAGAGCTAACACTGGAACAAAGAACTATTGATCCGGAATG Chimp: TTGCACACTGGCAGAAGACAGAGCTGACACTGGAACTAAGAACTATTGATCCGGAATG Gorilla: TTGCACACTGGCAAAAGACAGTTCCAGTGTCAGCTCTAAGAACTATTGATGCGGAATG ↑ 31 2 4 Human: TTGCACACTGGCAAAAGACAGAGCTAACACTGGAACAAAGAACTATTGATCCGGAATG Cluster: [ ] Orangutan: TTGCACACTGGCAAAAGACAGAGCTGACTCTGGAACTAAGAACTATTGCTCCGGAATG Human > Gorilla --------------- chr7:8883014-8883029 Template switch process: F1: L GTATCTAACATCCCAGAGACTTGCACACTGGCAAAAGACAG 1 F3: 4 AAGAACTATTGATGCGGAATGCATGCTCCTTTCGAATCAT R RF: GTATCTAACATCCCAGAGACTTGCACACTGGCAAAAGACAGAGCTAACACTGGAACAAAGAACTATTGATCCGGAATGCATGCTCCTTTCGAATCAT RR: CATAGATTGTAGGGTCTCTGAACGTGTGACCGTTTTCTGTCTCGATTGTGACCTTGTTTCTTGATAACTAGGCCTTACGTACGAGGAAAGCTTAGTA F2: 3 TCTCGACTGTGACCTT 2 Unidirectional alignment (log-probability: -46.6) TATCTAACATCCCAGAGACTTGCACACTGGCAAAAGACAGttccagtgtcAGCT----------CtAAGAACTATTGATgCGGAATGCATGCTCCTTTCGAATCAT TATCTAACATCCCAGAGACTTGCACACTGGCAAAAGACAG----------AGCTAACACTGGAACAAAGAACTATTGATCCGGAATGCATGCTCCTTTCGAATCAT Template switch alignment (log-probability: -28.8) TATCTAACATCCCAGAGACTTGCACACTGGCAAAAGACAG|TTCCAGTGTcAGCTCT|AAGAACTATTGATgCGGAATGCATGCTCCTTTCGAATCAT TATCTAACATCCCAGAGACTTGCACACTGGCAAAAGACAG|TTCCAGTGTTAGCTCT|AAGAACTATTGATCCGGAATGCATGCTCCTTTCGAATCAT ========== Event 3470 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAAGAAGCCATTTACATTTAA------ATTTTCAAAGGCTGTGGAAAGAAAACATTATTTATTCTACTTTTAGAA Chimp: AAAGAAGCCATTTACACTTAATGTTTTCTTTCCACAGCCTTTGAAA------ATTTATTTCTTCTACTTTTAGAA ↓ 13 24 ↑ 13 24 Gorilla: AAAGAAGCCATTTACACTTAA------ATTTTCAAAGGCTGTGGAAAGAAAACATTATTTCTTCTACTTTTAGAA Human: AAAGAAGCCATTTACATTTAA------ATTTTCAAAGGCTGTGGAAAGAAAACATTATTTATTCTACTTTTAGAA Cluster: [ ] Orangutan: AAAGAAGCCATTTACACTTAA------ATTTTCAAAGGCTGTGGAAAGAAAACATTATTTATTCTACTTTTAGAA Gorilla > Chimp --------------- chr7:8022629-8022655 Template switch process: F1: L ACATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAA 1 F3: 4 TTATTTCTTCTACTTTTAGAATACCTTGCCACCATATAGT R RF: ACATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAAATTTTCAAAGGCTGTGGAAAGAAAACATTATTTCTTCTACTTTTAGAAGACCTTGCCACCATATAGT RR: TGTAATATTCATAAACTTAATTTCTTCGGTAAATGTGAATTTAAAAGTTTCCGACACCTTTCTTTTGTAATAAAGAAGATGAAAATCTTCTGGAACGGTGGTATATCA F2: 3 TAAAAGTTTCCGACACCTTTCTTTTGT 2 Unidirectional alignment (log-probability: -63.4) CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTaatgttttctttccacagcctttgaAAAT-------------------------TTATTTCTTCTACTTTTAGAAtACCTTGCCACCATATAGT CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTT-------------------------AAATTTTCAAAGGCTGTGGAAAGAAAACATTATTTCTTCTACTTTTAGAAGACCTTGCCACCATATAGT Template switch alignment (log-probability: -24.7) CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAA|TGTTTTCTTTCCACAGCCTTTGAAAAT|TTATTTCTTCTACTTTTAGAAtACCTTGCCACCATATAGT CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAA|TGTTTTCTTTCCACAGCCTTTGAAAAT|TTATTTCTTCTACTTTTAGAAGACCTTGCCACCATATAGT Chimp > Gorilla --------------- chr7:8905983-8906009 Template switch process: F1: L ACATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAA 1 F3: 4 TTATTTCTTCTACTTTTAGAAGACCTTGCCACCATATAGT R RF: ACATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAATGTTTTCTTTCCACAGCCTTTGAAAATTTATTTCTTCTACTTTTAGAATACCTTGCCACCATATAGT RR: TGTAATATTCATAAACTTAATTTCTTCGGTAAATGTGAATTACAAAAGAAAGGTGTCGGAAACTTTTAAATAAAGAAGATGAAAATCTTATGGAACGGTGGTATATCA F2: 3 ACAAAAGAAAGGTGTCGGAAACTTTTA 2 Unidirectional alignment (log-probability: -63.4) CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTA-------------------------AATtttcaaaggctgtggaaagaaaacaTTATTTCTTCTACTTTTAGAAgACCTTGCCACCATATAGT CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAATGTTTTCTTTCCACAGCCTTTGAAAAT-------------------------TTATTTCTTCTACTTTTAGAATACCTTGCCACCATATAGT Template switch alignment (log-probability: -24.7) CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAA|ATTTTCAAAGGCTGTGGAAAGAAAACA|TTATTTCTTCTACTTTTAGAAgACCTTGCCACCATATAGT CATTATAAGTATTTGAATTAAAGAAGCCATTTACACTTAA|ATTTTCAAAGGCTGTGGAAAGAAAACA|TTATTTCTTCTACTTTTAGAATACCTTGCCACCATATAGT ========== Event 3471 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGATTTCCTCTGGGGTGTAGGTGCAGGGTGAGCCTGCACCCAATATGACTAAATGCGAAG ↑ 1 4 3 2 Chimp: AGTGATTTCCTCTGGGGTGTAAATGTA-TATGAGCCTGCACCCAATATGACTAAATGCGAAG Gorilla: AGTGATTTCCTCTGGGGTGTAAATGTA-TATGAGACTGCACCCAATATGACTAAATGCGAAG Human: AGTGATTTCCTCTGGGGTGTAGGTGCAGGGTGAGCCTGCACCCAATATGACTAAATGCGAAG Cluster: [ ] Orangutan: AGTGATTTCCTCTGGGGTGTAAATGTA-TATGAGCCTGCACCCAATATGACTAAATGTGAAG Chimp > Human ------------- chr7:89317411-89317418 Template switch process: F1: L AAAAGAGCAGAAAAATTGAGAGTGATTTCCTCTGGGGTGTA 1 F3: 4 GTGAGCCTGCACCCAATATGACTAAATGCGAAGCAAAGAAC R RF: AAAAGAGCAGAAAAATTGAGAGTGATTTCCTCTGGGGTGTAAATGTATATGAGCCTGCACCCAATATGACTAAATGCGAAGCAAAGAAC RR: TTTTCTCGTCTTTTTAACTCTCACTAAAGGAGACCCCACATTTACATATACTCGGACGTGGGTTATACTGATTTACGCTTCGTTTCTTG F2: 3 GGACGTGG 2 Unidirectional alignment (log-probability: -34.5) AAAGAGCAGAAAAATTGAGAGTGATTTCCTCTGGGGTGTAggtgcaggg--------TGAGCCTGCACCCAATATGACTAAATGCGAAGCAAAGAA AAAGAGCAGAAAAATTGAGAGTGATTTCCTCTGGGGTGTA---------AATGTATATGAGCCTGCACCCAATATGACTAAATGCGAAGCAAAGAA Template switch alignment (log-probability: -22.3) AAAGAGCAGAAAAATTGAGAGTGATTTCCTCTGGGGTGTA|GGTGCAGG|gTGAGCCTGCACCCAATATGACTAAATGCGAAGCAAAGAA AAAGAGCAGAAAAATTGAGAGTGATTTCCTCTGGGGTGTA|GGTGCAGG|ATGAGCCTGCACCCAATATGACTAAATGCGAAGCAAAGAA ========== Event 3472 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: agcatttccatcattgcagaaatctgtactggaaagACTGATATAGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATGTCATCTtttattccttttagtaaacatttgttgaacaactacttcctgcaagtca Chimp: agcatttccatcattgcagaaatctgtactggaaagACTGATATAGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTAC------------------------------------------------------TATGTCATCTTTTATTCCTTTTAGTAAACATTTGTTGAATGTTTACTAAACAAACATTTTTCTGTACTGGAAAGACTAATATAGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTACTATGTCATCTtttattccttttagtaaacatttgttgaacaactacttcctgcaagtca ↑ 4 3 2 1 Gorilla: agcatttccatcattgcagaaatctgtactggaaagACTGATATAGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTAC----------------------------------------------------TA-----------------------------------------------------------------------------------------------------------------------------TGTCATCTtttattccttttagtaaacatttgttgaacaactacttcctgcaagtca Human: agcatttccatcattgcagaaatctgtactggaaagACTGATATAGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATGTCATCTtttattccttttagtaaacatttgttgaacaactacttcctgcaagtca Cluster: [ ] Orangutan: agcatttccatcattgcagaaagctgtactggaaa--------------------------------------------------gACTGATATAGCTAACACAGGAAAAAACATCTGAATTCTTCAAATCCTGCTA-------------------------------------------------------------------------------------------------------------------------------TGTCATCTtttattccttttagtaaacatttgttgaacaactacttcctgcaagtca Gorilla > Chimp --------------- chr7:94655777-94655784 Template switch process: F1: L AGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTACTATGTCATCTTTTATTCCTTTTAGTAAACATTTGTTGAA 1 F3: 4 AAACAAACATTTTTCTGTACTGGAAAGACTAATATAGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTACTATGTCATCTTTTATTCCTTTTAGTAAACATTTGTTGAACAA R RF: AGCTAACACAGGAAAATACATTTTAATTCTTCAAATCCTACTATGTCATCTTTTATTCCTTTTAGTAAACATTTGTTGAACAA RR: TCGATTGTGTCCTTTTATGTAAAATTAAGAAGTTTAGGATGATACAGTAGAAAATAAGGAAAATCATTTGTAAACAACTTGTT F2: 3 TCATTTGT 2 Unidirectional alignment (log-probability: -182) ctatgtcatcttttattccttttagtaaacatttgttgaatgtttactaaacaaacatttttctgtactggaaagactaatatAGCTA -----------------------------------------------------------------------------------AGCTA Template switch alignment (log-probability: -48.7) CTATGTCATCTTTTATTCCTTTTAGTAAACATTTGTTGAA|TGTTTACT|AAAcaaacattttTCTGTACTGGAAAGACTaATATAGCTA CTATGTCATCTTTTATTCCTTTTAGTAAACATTTGTTGAA|TGTTTACT|AAA----------TCTGTACTGGAAAGACTGATATAGCTA ========== Event 3473 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAATAGAA-AT-TTTTTTCCT----------------CTGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTTCACTAGTCTTAT ↓ 4 3 2 Chimp: CAATAGAA-At-ttttttCCTCACTTATATAACACTAGTGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTTCACTAGTCTTAT Gorilla: CAATAGAA-AttttttttCCT----------------CTGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTTCACTAGTCTTAT Human: CAATAGAA-AT-TTTTTTCCT----------------CTGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTTCACTAGTCTTAT Cluster: [ ] Orangutan: CAATAGAAAAT-TTTTTTCCT----------------CAAACTACATAACTCTCACTAGTGTTACATAAGAAATTTTTCACTAGTGTTAT Human > Chimp ------------- chr7:69232079-69232093 Template switch process: F1: L ATTACGTGGAACTTCTGGTTTCCAATAGAAATTTTTTTCCTCA 1 F3: 4 TGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTT R RF: ATTACTTGGAACTTCTGGTTTCCAATAGAAATTTTTTTCCTCTGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTT RR: TAATGAACCTTGAAGACCAAAGGTTATCTTTAAAAAAAGGAGACTGATGTATTGAAAGTGATCACAATATATTCTTTAAAAA F2: 3 GATCACAATATATTC 2 Unidirectional alignment (log-probability: -39.9) ACgTGGAACTTCTGGTTTCCAATAGAAATTTTTTTCCTCacttatataacactagTGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTT ACTTGGAACTTCTGGTTTCCAATAGAAATTTTTTTCCTC----------------TGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTT Template switch alignment (log-probability: -29.2) ACgTGGAACTTCTGGTTTCCAATAGAAATTTTTTTCCTCa|CTTATATAACACTAG|TGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTT ACTTGGAACTTCTGGTTTCCAATAGAAATTTTTTTCCTCT|CTTATATAACACTAG|TGACTACATAACTTTCACTAGTGTTATATAAGAAATTTTT ========== Event 3474 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AGAAGATATGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCA---ATCAGTATTGTTGACTCCATTTTCCATAGGACTTTTTTTGC--------------- Chimp: AGAAGATATGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGAA---ATCAGTATTGTTGACTCCATTTTCCATAGGACtttttttGC--------------- ↓ 13 24 ↑ 13 24 Gorilla: AGAAGATATGACAGGCaaaaaaaGTCCTATGGAAAATGGAGTCAACAATACTG---ATTGCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTATTTTGCCTGTCATATCTTCTC ↓ 13 24 ↑ 13 24 Human: AGAAGATATGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCA---ATCAGTATTGTTGACTCCATTTTCCATAGGACTTTTTTTGC--------------- Cluster: [ ] Orangutan: ------------------------------------------------------------------------------AC---TTTCTTCTTACTGATTTATTTGC--------------- Gorilla > Human --------------- chr7:65169093-65169169 Template switch process: F1: L TGACAGGCAAAA 1 F3: 4 TTTTGC R RF: TGACAGGCAAAAAAAGTCCTATGGAAAATGGAGTCAACAATACTGATTGCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTATTTTGC RR: ACTGTCCGTTTTTTTCAGGATACCTTTTACCTCAGTTGTTATGACTAACGTTGACATTTTTAACAACTGAGGTAAAAGGTATCCTGAATAAAACG F2: 3 TTTCAGGATACCTTTTACCTCAGTTGTTATGACTAACGTTGACATTTTTAACAACTGAGGTAAAAGGTATCCTGAAT 2 Unidirectional alignment (log-probability: -66.9) TGACAGGCAAAAtAAGTCCTATGGAAAATGGAGTCAACAAT-------------------ttttacagttgcaatcagtATTGTTGACTCCATTTTCCATAGGACTTtTTTTGC----- TGACAGGCAAAAAAAGTCCTATGGAAAATGGAGTCAACAATACTGATTGCAACTGTAAAA-------------------ATTGTTGACTCCATTTTCCATAGGACTTATTTTGCCTGTC Template switch alignment (log-probability: -24) TGACAGGCAAAA|TAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCAATCAGTATTGTTGACTCCATTTTCCATAGGACTTT|TTTTGC TGACAGGCAAAA|TAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCAATCAGTATTGTTGACTCCATTTTCCATAGGACTTT|TTTTGC Human > Gorilla --------------- chr7:83983402-83983478 Template switch process: F1: L TGACAGGCAAAA 1 F3: 4 TTTTGCCTGTC R RF: TGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCAATCAGTATTGTTGACTCCATTTTCCATAGGACTTTTTTTGCCTGTC RR: ACTGTCCGTTTTATTCAGGATACCTTTTACCTCAGTTGTTAAAAATGTCAACGTTAGTCATAACAACTGAGGTAAAAGGTATCCTGAAAAAAACGGACAG F2: 3 ATTCAGGATACCTTTTACCTCAGTTGTTAAAAATGTCAACGTTAGTCATAACAACTGAGGTAAAAGGTATCCTGAAA 2 Unidirectional alignment (log-probability: -73.8) TGACAGGCAAAAaAAGTCCTATGGAAAATGGAGTCAACAA-------------------TactgattgcaactgtaaaaATTGTTGACTCCATTTTCCATAGGACTTaTTTTGCctgtc TGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCAATCAGT-------------------ATTGTTGACTCCATTTTCCATAGGACTTTTTTTGC----- Template switch alignment (log-probability: -24.1) TGACAGGCAAAA|AAAGTCCTATGGAAAATGGAGTCAACAATACTGATTGCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTA|TTTTGCCTGTC TGACAGGCAAAA|AAAGTCCTATGGAAAATGGAGTCAACAATACTGATTGCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTA|TTTTGCCTGTC Gorilla > Chimp --------------- chr7:69154691-69154767 Template switch process: F1: L TGACAGGCAAAA 1 F3: 4 TTTTGC R RF: TGACAGGCAAAAAAAGTCCTATGGAAAATGGAGTCAACAATACTGATTGCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTATTTTGC RR: ACTGTCCGTTTTTTTCAGGATACCTTTTACCTCAGTTGTTATGACTAACGTTGACATTTTTAACAACTGAGGTAAAAGGTATCCTGAATAAAACG F2: 3 TTTCAGGATACCTTTTACCTCAGTTGTTATGACTAAAGTTGACATTTTTAACAACTGAGGTAAAAGGTATCCTGAAT 2 Unidirectional alignment (log-probability: -66.9) TGACAGGCAAAAtAAGTCCTATGGAAAATGGAGTCAACAAT-------------------ttttacagttgaaatcagtATTGTTGACTCCATTTTCCATAGGACTTtTTTTGC----- TGACAGGCAAAAAAAGTCCTATGGAAAATGGAGTCAACAATACTGATTGCAACTGTAAAA-------------------ATTGTTGACTCCATTTTCCATAGGACTTATTTTGCCTGTC Template switch alignment (log-probability: -29.5) TGACAGGCAAAA|TAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGaAATCAGTATTGTTGACTCCATTTTCCATAGGACTTT|TTTTGC TGACAGGCAAAA|TAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGCAATCAGTATTGTTGACTCCATTTTCCATAGGACTTT|TTTTGC Chimp > Gorilla --------------- chr7:83983402-83983478 Template switch process: F1: L TGACAGGCAAAA 1 F3: 4 TTTTGCCTGTC R RF: TGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGAAATCAGTATTGTTGACTCCATTTTCCATAGGACTTTTTTTGCCTGTC RR: ACTGTCCGTTTTATTCAGGATACCTTTTACCTCAGTTGTTAAAAATGTCAACTTTAGTCATAACAACTGAGGTAAAAGGTATCCTGAAAAAAACGGACAG F2: 3 ATTCAGGATACCTTTTACCTCAGTTGTTAAAAATGTCAACGTTAGTCATAACAACTGAGGTAAAAGGTATCCTGAAA 2 Unidirectional alignment (log-probability: -73.8) TGACAGGCAAAAaAAGTCCTATGGAAAATGGAGTCAACAA-------------------TactgattgcaactgtaaaaATTGTTGACTCCATTTTCCATAGGACTTaTTTTGCctgtc TGACAGGCAAAATAAGTCCTATGGAAAATGGAGTCAACAATTTTTACAGTTGAAATCAGT-------------------ATTGTTGACTCCATTTTCCATAGGACTTTTTTTGC----- Template switch alignment (log-probability: -29.6) TGACAGGCAAAA|AAAGTCCTATGGAAAATGGAGTCAACAATACTGATTgCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTA|TTTTGCCTGTC TGACAGGCAAAA|AAAGTCCTATGGAAAATGGAGTCAACAATACTGATTTCAACTGTAAAAATTGTTGACTCCATTTTCCATAGGACTTA|TTTTGCCTGTC ========== Event 3475 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCTCTCTTACAAAAGGAAACCATT Chimp: GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCTCTCTTACAAAAGGAAACCATT ↓ 3 2 1 4 ↑ 3 1 2 4 Gorilla: GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAACT-----GACTCTTACAAAAGGAAACCATT ↓ 3 1 2 4 ↑ 3 2 1 4 Human: GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCTCTCTTACAAAAGGAAACCATT Cluster: [ ] Orangutan: GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAACT-----GACTCTTACAAAAGGAAACCATT Gorilla > Human --------------- chr7:64757647-64757656 Template switch process: F1: L GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA 1 F3: 4 CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT R RF: GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAACTGACTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT RR: CCTACGTAGGTCCTAAACAGAGTCATTCACTCGTCGAACTTTGACTGAGAATGTTTTCCTTTGGTAACACTGATTAGTGACTCCGA F2: 3 TCGAACTTTG 2 Unidirectional alignment (log-probability: -35.3) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGA-----AgtttcaagctCTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAACTGA----------CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Template switch alignment (log-probability: -17) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|GTTTCAAGCT|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|GTTTCAAGCT|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Human > Gorilla --------------- chr7:83566366-83566370 Template switch process: F1: L GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA 1 F3: 4 CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT R RF: GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCTCTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT RR: CCTACGTAGGTCCTAAACAGAGTCATTCACTCGTCGAACTTCAAAGTTCGAGAGAATGTTTTCCTTTGGTAACACTGATTAGTGACTCCGA F2: 3 AGTCA 2 Unidirectional alignment (log-probability: -28.3) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA----------actgaCTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCT-----CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Template switch alignment (log-probability: -16.4) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|ACTGA|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|ACTGA|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Gorilla > Chimp --------------- chr7:68748145-68748154 Template switch process: F1: L GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA 1 F3: 4 CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT R RF: GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAACTGACTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT RR: CCTACGTAGGTCCTAAACAGAGTCATTCACTCGTCGAACTTTGACTGAGAATGTTTTCCTTTGGTAACACTGATTAGTGACTCCGA F2: 3 TCGAACTTTG 2 Unidirectional alignment (log-probability: -35.3) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGA-----AgtttcaagctCTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAACTGA----------CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Template switch alignment (log-probability: -17) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|GTTTCAAGCT|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|GTTTCAAGCT|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Chimp > Gorilla --------------- chr7:83566366-83566370 Template switch process: F1: L GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA 1 F3: 4 CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT R RF: GGATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCTCTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT RR: CCTACGTAGGTCCTAAACAGAGTCATTCACTCGTCGAACTTCAAAGTTCGAGAGAATGTTTTCCTTTGGTAACACTGATTAGTGACTCCGA F2: 3 AGTCA 2 Unidirectional alignment (log-probability: -28.3) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA----------actgaCTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAAGTTTCAAGCT-----CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT Template switch alignment (log-probability: -16.4) GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|ACTGA|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT GATGCATCCAGGATTTGTCTCAGTAAGTGAGCAGCTTGAA|ACTGA|CTCTTACAAAAGGAAACCATTGTGACTAATCACTGAGGCT ========== Event 3476 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTCGCTGCTTCACCATCAAAG---TCTCT-GATATCTCTCAGCCAGGAAAACCTCT Chimp: GTCGCTGCTTCACCATCAAAGTGATATCAGAATATCTCTCAGCCAGGAAAACCTCT ↑ 1 3 4 2 Gorilla: GTCGCTGCTTCACCATCAAAG---TCTCT-GATATCTCTCAGCCAGGAAAACCTCT Human: GTCGCTGCTTCACCATCAAAG---TCTCT-GATATCTCTCAGCCAGGAAAACCTCT Cluster: [ ] Orangutan: GTCGCTGCTTCACCGTCAAAG---TCTCT-GATATCTCTCAACCAGGAAAACCTCT Gorilla > Chimp --------------- chr7:98177570-98177578 Template switch process: F1: L ACCCATCATTTTGTTCCCCTGTCGCTGCTTCACCATCAAAGT 1 F3: 4 ATATCTCTCAGCCAGGAAAACCTCTGTGACAAATCCATTA R RF: GCCCGTCATTTTGTTCCCCTGTCGCTGCTTCACCATCAAAGTCTCTGATATCTCTCAGCCAGGAAAACCTCTGTGACAAATCCATTA RR: CGGGCAGTAAAACAAGGGGACAGCGACGAAGTGGTAGTTTCAGAGACTATAGAGAGTCGGTCCTTTTGGAGACACTGTTTAGGTAAT F2: 3 AGACTATAG 2 Unidirectional alignment (log-probability: -43.4) CCaTCATTTTGTTCCCCTGTCGCTGCTTCACCATCAAAG----TGatatcagaATATCTCTCAGCCAGGAAAACCTCTGTGACAAATCCATTA CCGTCATTTTGTTCCCCTGTCGCTGCTTCACCATCAAAGTCTCTG--------ATATCTCTCAGCCAGGAAAACCTCTGTGACAAATCCATTA Template switch alignment (log-probability: -27.9) CCaTCATTTTGTTCCCCTGTCGCTGCTTCACCATCAAAGT|GATATCAGA|ATATCTCTCAGCCAGGAAAACCTCTGTGACAAATCCATTA CCGTCATTTTGTTCCCCTGTCGCTGCTTCACCATCAAAGT|GATATCAGA|ATATCTCTCAGCCAGGAAAACCTCTGTGACAAATCCATTA ========== Event 3477 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCA ↓ 3 1 2 4 Chimp: GGCATGAGATGGGCTATGAAACCTTCACCTTGTGAAGGTTAATGAAGATGTTCCCAGCCCA ↑ 3 1 2 4 Gorilla: GGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCA Human: GGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCA Cluster: [ ] Orangutan: GGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCA Human > Chimp ------------- chr7:99035318-99035329 Template switch process: F1: L GACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCAC 1 F3: 4 AATGAAGATGTTCCCAGCCCACAACAGAGCTTACTGAATC R RF: GACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCACAACACAGCTTACTGAATC RR: CTGGGAGTCTCTTCCGTACTCTACCCGATACTTTGGAAGTGTTCCACTTCCCGTTACTTCTACAAGGGTCGGGTGTTGTGTCGAATGACTTAG F2: 3 TTGGAAGTGTTC 2 Unidirectional alignment (log-probability: -36.8) ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCACcttGTGAAGGttAATGAAGATGTTCCCAGCCCACAACAgAGCTTACTGAATC ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCACAACACAGCTTACTGAATC Template switch alignment (log-probability: -22.8) ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCAC|CTTGTGAAGGTT|AATGAAGATGTTCCCAGCCCACAACAgAGCTTACTGAATC ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCAC|CTTGTGAAGGTT|AATGAAGATGTTCCCAGCCCACAACACAGCTTACTGAATC Gorilla > Chimp --------------- chr7:99035318-99035329 Template switch process: F1: L GACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCAC 1 F3: 4 AATGAAGATGTTCCCAGCCCACAACAGAGCTTACTGAATC R RF: GACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCACAACACAGCTTACTGAATC RR: CTGGGAGTCTCTTCCGTACTCTACCCGATACTTTGGAAGTGTTCCACTTCCCGTTACTTCTACAAGGGTCGGGTGTTGTGTCGAATGACTTAG F2: 3 TTGGAAGTGTTC 2 Unidirectional alignment (log-probability: -34.4) ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCACcttGTGAAGGttAATGAAGATGTTCCCAGCCCACAACAgAGCTTACTGAATC ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCACAAGGTGAAGGGCAATGAAGATGTTCCCAGCCCACAACACAGCTTACTGAATC Template switch alignment (log-probability: -22.8) ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCAC|CTTGTGAAGGTT|AATGAAGATGTTCCCAGCCCACAACAgAGCTTACTGAATC ACCCTCAGAGAAGGCATGAGATGGGCTATGAAACCTTCAC|CTTGTGAAGGTT|AATGAAGATGTTCCCAGCCCACAACACAGCTTACTGAATC ========== Event 3478 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGCACAAACTGAACTAATCTCT--------GAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA ↓ 1 4 3 2 Chimp: AAGCACAAACTGAACTAATCTTAGAGGATACTAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA ↑ 1 4 3 2 Gorilla: AAGCACAAACTGAACTAATCTCT--------GAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA Human: AAGCACAAACTGAACTAATCTCT--------GAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA Cluster: [ ] Orangutan: AAGCACAAACTGAACTAATCTCT--------GAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA Human > Chimp ------------- chr7:99650085-99650094 Template switch process: F1: L TACATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTT 1 F3: 4 AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA R RF: TACATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTCTGAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA RR: ATGTAAGAGTTAGTTTTACGTTCGTGTTTGACTTGATTAGAGACTTCGGTAACATCATAGGAGAAGAGACGATCTACAGGTAGT F2: 3 TCATAGGAGA 2 Unidirectional alignment (log-probability: -34.1) CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTtagaggataCT-AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCT---------CTGAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA Template switch alignment (log-probability: -22.5) CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTt|AGAGGATACT|AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTC|AGAGGATACT|AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA Gorilla > Chimp --------------- chr7:99650085-99650094 Template switch process: F1: L TACATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTT 1 F3: 4 AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA R RF: TACATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTCTGAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA RR: ATGTAAGAGTTAGTTTTACGTTCGTGTTTGACTTGATTAGAGACTTCGGTAACATCATAGGAGAAGAGACGATCTACAGGTAGT F2: 3 TCATAGGAGA 2 Unidirectional alignment (log-probability: -33.5) CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTtaGaggatactAAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTCTG--------AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA Template switch alignment (log-probability: -22.5) CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTt|AGAGGATACT|AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA CATTCTCAATCAAAATGCAAGCACAAACTGAACTAATCTC|AGAGGATACT|AAGCCATTGTAGTATCCTCTTCTCTGCTAGATGTCCATCA ========== Event 3479 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAATCTCTAAGACCAGGGCTGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAATATTCTGTTGCTGTTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACACCTGCCCCAAGTGGGTGGATATCTGCCTTC ↑ 3 2 1 4 Chimp: GAATCTCTAAGACCAGGGCTGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAAGATTCTGTTGCTGTTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGAC-------ACGAGTGGGTGGATATCTGCCTTC Gorilla: GGATCTCTAAGACCAGGGCTGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAAGATTCTGTTGCTATTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGAC-------ACGAGTGGGTGGATATCTGCATTC ↓ 3 2 1 4 Human: GAATCTCTAAGACCAGGGCTGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAATATTCTGTTGCTGTTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACACCTGCCCCAAGTGGGTGGATATCTGCCTTC Cluster: [ ] Orangutan: GAATCTCTAAGACCAGGGCTGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAAGATTCTGTTGCTGTTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGAC-------ACAAGTGGGTGGATATCTGCCTTC Chimp > Human ------------- chr7:98628869-98628876 Template switch process: F1: L TGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAC 1 F3: 4 AGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG R RF: TGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAAGATTCTGTTGCTGTTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACACGAGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG RR: ACCCCGTCACAGACAGTGACCGAACAAACAAGGGATGGTTCTAAGACAACGACAAACTTCATCACGGTCCCAGGGGACCCTTCTACGGGGGTTCTGTGCTCACCCACCTATAGACGGAAGGACGACGTTCACCTCCGTC F2: 3 ACCCCGTC 2 Unidirectional alignment (log-probability: -27) AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAcctgcccCaAGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACA-------CGAGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG Template switch alignment (log-probability: -16.3) AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAC|CTGCCCCA|AGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAC|CTGCCCCA|AGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG Gorilla > Human --------------- chr7:98628869-98628876 Template switch process: F1: L TGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAC 1 F3: 4 AGTGGGTGGATATCTGCCTTCCTGCTGCAAGTGGAGGCAG R RF: TGGGGCAGTGTCTGTCACTGGCTTGTTTGTTCCCTACCAAGATTCTGTTGCTATTTGAAGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACACGAGTGGGTGGATATCTGCATTCCTGCTGCAAGTGGAGGCAG RR: ACCCCGTCACAGACAGTGACCGAACAAACAAGGGATGGTTCTAAGACAACGATAAACTTCATCACGGTCCCAGGGGACCCTTCTACGGGGGTTCTGTGCTCACCCACCTATAGACGTAAGGACGACGTTCACCTCCGTC F2: 3 ACCCCGTC 2 Unidirectional alignment (log-probability: -32) AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAcctgcccCaAGTGGGTGGATATCTGCcTTCCTGCTGCAAGTGGAGGCAG AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACA-------CGAGTGGGTGGATATCTGCATTCCTGCTGCAAGTGGAGGCAG Template switch alignment (log-probability: -22.3) AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAC|CTGCCCCA|AGTGGGTGGATATCTGCcTTCCTGCTGCAAGTGGAGGCAG AGTAGTGCCAGGGTCCCCTGGGAAGATGCCCCCAAGACAC|CTGCCCCA|AGTGGGTGGATATCTGCATTCCTGCTGCAAGTGGAGGCAG ========== Event 3480 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: CGTTTTCATCCAGCATCCACCT----------------GGACTTAACGTTGACGGTGCCTTTGCG ↓ 43 2 1 Chimp: CGTTTTCATCCAGCATCCACCTGGACTGAGTCCAGCCTGGACTTAACGTTGACGGTGCCTTTGCG Gorilla: ----------------------------------------------------------------- Human: CGTTTTCATCCAGCATCCACCT----------------GGACTTAACGTTGACGGTGCCTTTGCG Cluster: [ ] Orangutan: ----------------------------------------------------------------- Human > Chimp ------------- chr7:101865974-101865979 Template switch process: F1: L GGAGGAGTTTGCATCCAGACGTTTTCATCCAGCATCCACCTGGACTGA 1 F3: 4 CCTGGACTTAACGTTGACGGTGCCTTTGCGCTTAGTGGCAGAG R RF: GGAGGAGTTTGCATCCAGACGTTTTCATCCAGCATCCACCTGGACTTAACGTTGACGGTGCCTTTGCGCTTAGTGGCAGAG RR: CCTCCTCAAACGTAGGTCTGCAAAAGTAGGTCGTAGGTGGACCTGAATTGCAACTGCCACGGAAACGCGAATCACCGTCTC F2: 3 GACCTG 2 Unidirectional alignment (log-probability: -33.9) TTGCATCCAGACGTTTTCATCCAGCATCCACCTGGActgagtccagcctggaCTTAACGTTGACGGTGCCTTTGCGCTTAGTGGCA TTGCATCCAGACGTTTTCATCCAGCATCCACCTGGA----------------CTTAACGTTGACGGTGCCTTTGCGCTTAGTGGCA Template switch alignment (log-probability: -22.2) TTGCATCCAGACGTTTTCATCCAGCATCCACCTGGACTgA|GTCCAG|CCTGGACTTAACGTTGACGGTGCCTTTGCGCTTAGTGGCA TTGCATCCAGACGTTTTCATCCAGCATCCACCTGGACTTA|GTCCAG|CCTGGACTTAACGTTGACGGTGCCTTTGCGCTTAGTGGCA ========== Event 3481 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG-----CGGCGTGTTGTCACATCTGCATC Chimp: GGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG-----CGGCGTGTTGTCACATCTGCATC ↓ 3 2 1 4 Gorilla: GGAACTCTTGTGCGCCCTCACCTGGACTCACCAGGTCCAGGTGCGTGTTGTCACATCTGCATC ↑ 3 2 1 4 Human: GGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG-----CGGCGTGTTGTCACATCTGCATC Cluster: [ ] Orangutan: GGAACCCTTGTGCGCCCTCACCTGGACTCACCAGG-----TGGCGTGTTGTCACATCTGCATT Human > Gorilla --------------- chr7:79985568-79985574 Template switch process: F1: L GCTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG 1 F3: 4 GCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG R RF: TCTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGGCGGCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG RR: AGAGTCCCTTGAGAACACGCGGGAGTGGACCTGAGTGGTCCGCCGCACAACAGTGTAGACGTAGGAGGATTTTGTGTATGTGC F2: 3 TGGACCT 2 Unidirectional alignment (log-probability: -34.7) CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGgtccaGgtGCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAG-----GCGGCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG Template switch alignment (log-probability: -22.1) CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG|TCCAGGT|GCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG|TCCAGGT|GCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG Chimp > Gorilla --------------- chr7:79985568-79985574 Template switch process: F1: L GCTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG 1 F3: 4 GCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG R RF: GCTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGGCGGCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG RR: CGAGTCCCTTGAGAACACGCGGGAGTGGACCTGAGTGGTCCGCCGCACAACAGTGTAGACGTAGGAGGATTTTGTGTATGTGC F2: 3 TGGACCT 2 Unidirectional alignment (log-probability: -29.1) CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGgtccaGgtGCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAG-----GCGGCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG Template switch alignment (log-probability: -16.6) CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG|TCCAGGT|GCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG CTCAGGGAACTCTTGTGCGCCCTCACCTGGACTCACCAGG|TCCAGGT|GCGTGTTGTCACATCTGCATCCTCCTAAAACACATACACG ========== Event 3482 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GGCCATGGCCACGGTGGGAGA--------ACTGTAGGGATAAAGAAGGAGATCGGTCTGCTCTACAGGAAGGCTTTATCCCATCCTTAGGGAAGGTGAATGATCCTTAAAACAAGGCAGTCAGAGCTAGTAAGAAGGAAG ↑ 1 4 3 2 Chimp: GGCCATGGCCACGGTGGGAGATAAAGAAGGAGATAGGGATAAAGAAGGAGATCGCTCTGCTCTACAGGAAGGCTTTATCCCATCCTTAGGGAAGGTGAATGATCCTTAAAACAAGGCAGTCAGAGCTAGTAAGAAGGAAG Gorilla: GGCCATGGCCACGGTGGGAGA--------ACTGT-AGGATAAAGAAGGAGATTGGTCTGCTCTACAGGAAGGCTTTATCCCATCCTTAGGGAAGGTGAATGATCTTTAAAACAAGGCAGTCAGAGCTAGTAAGAAGGAAG Human: GGCCATGGCCACGGTGGGAGA--------ACTGTAGGGATAAAGAAGGAGATCGGTCTGCTCTACAGGAAGGCTTTATCCCATCCTTAGGGAAGGTGAATGATCCTTAAAACAAGGCAGTCAGAGCTAGTAAGAAGGAAG Cluster: [ ] Orangutan: ----------------------------------TGGGATAA---AGGAGATCAGTCTGCTCTACAGGAAGGCTTTATCCCATCCTTAGGGAAGGTGAATGATCCTTAAAACAAGGCAGTCAGAGCTAGTAAGGAGGAAG Chimp > Human ------------- chr8:44642075-44642078 Template switch process: F1: L AGAGTCAGAACAGCCCCCAAGGCCATGGCCACGGTGGGAGA 1 F3: 4 TAGGGATAAAGAAGGAGATCGGTCTGCTCTACAGGAAGGC R RF: AGAGTCAGAACAGCCCCCAAGGCCATGGCCACGGTGGGAGATAAAGAAGGAGATAGGGATAAAGAAGGAGATCGCTCTGCTCTACAGGAAGGCTTTATCCCATCCTTAGGGAAGGTGAATGATCCTTAAAACAAGGCAGT RR: TCTCAGTCTTGTCGGGGGTTCCGGTACCGGTGCCACCCTCTATTTCTTCCTCTATCCCTATTTCTTCCTCTAGCGAGACGAGATGTCCTTCCGAAATAGGGTAGGAATCCCTTCCACTTACTAGGAATTTTGTTCCGTCA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -32) GAGTCAGAACAGCCCCCAAGGCCATGGCCACGGTGGGAGA-----------ActgTAGGGATAAAGAAGGAGATCGgTCTGCTCTACAGGAAGGC GAGTCAGAACAGCCCCCAAGGCCATGGCCACGGTGGGAGATAAAGAAGGAGA---TAGGGATAAAGAAGGAGATCGCTCTGCTCTACAGGAAGGC Template switch alignment (log-probability: -21.8) GAGTCAGAACAGCCCCCAAGGCCATGGCCACGGTGGGAGA|ACTG|TAGGGATAAAGAAGGAGATCGgTCTGCTCTACAGGAAGGC GAGTCAGAACAGCCCCCAAGGCCATGGCCACGGTGGGAGA|ACTG|TAGGGATAAAGAAGGAGATCGCTCTGCTCTACAGGAAGGC ========== Event 3483 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCCTGATATGTAATATCCTTCTAAG------------------CAAGGTGCTTAGTCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTGCC--- Chimp: TCCTGATATGTAATATCCTTCTAAG------------------CAAGGTGCTTAGTCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGATGCTGCC--- Gorilla: TCCTGATATGTAATATCCTTCTAAG------------------------------------CAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTGCCAAA ↓ 4 1 3 2 Human: TCCTGATATGTAATATCCTTCTAAG------------------CAAGGTGCTTAGTCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTGCC--- Cluster: [ ] Orangutan: TCCTGATATGTAATATCATTCTAAGCAAGATGCTTAGTCTAAG------------------CAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTGCC--- Gorilla > Human --------------- chr8:43436787-43436791 Template switch process: F1: L TTTCATTCTTCTCCTTTCCTGATATGTAATATCCTTCTAAGCAAGGTG 1 F3: 4 TCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTGCC R RF: TTTCATTCTTCTCCTTTCCTGATATGTAATATCCTTCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTGCC RR: AAAGTAAGAAGAGGAAAGGACTATACATTATAGGAAGATTCGTTCCACTCTTTCAGATTCCTGTTGGTCCACGACGG F2: 3 GATTC 2 Unidirectional alignment (log-probability: -43.7) TTCTCCTTTCCTGATATGTAATATCCTTCTAagcaaggtgcttagtctaAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTG TTCTCCTTTCCTGATATGTAATATCCTTCTA------------------AGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTG Template switch alignment (log-probability: -16.6) TTCTCCTTTCCTGATATGTAATATCCTTCTAAGCAAGGTG|CTTAG|TCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTG TTCTCCTTTCCTGATATGTAATATCCTTCTAAGCAAGGTG|CTTAG|TCTAAGCAAGGTGAGAAAGTCTAAGGACAACCAGGTGCTG ========== Event 3484 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: cacatcagcacaataggaaaa--cacagagaaacacta----------acagacaaaaaagtacctttattttatactt Chimp: CACATCAGCACAGTAGGAAAA--CACAGAGAAACACTTTTTTGTCTGTTAGGACAAAAAAGTACCTTTATTTTATACTT ↑ 31 4 2 Gorilla: CACATCAGCACAGTAGGAAAA----CAGAGAAACACTA----------ACAGACAAAAAAGTACCTTTATTTTATACTT Human: cacatcagcacaataggaaaa--cacagagaaacacta----------acagacaaaaaagtacctttattttatactt Cluster: [ ] Orangutan: cacatcagcacagtaggaaaaca--cagagaaacacta----------acagacaaa-aaatacctttattttatcctt Gorilla > Chimp --------------- chr8:44521556-44521569 Template switch process: F1: L TTACAAAAGCAGTGCAAGCTCACATCAGCACAGTAGGAAAACACAGAGAAACACT 1 F3: 4 GACAAAAAAGTACC R RF: TTACAAAAGCAGTGCAAGCTCACATCAGCACAGTAGGAAA--ACAGAGAAACACTAACAGACAAAAAAGTACC RR: AATGTTTTCGTCACGTTCGAGTGTAGTCGTGTCATCCTTT--TGTCTCTTTGTGATTGTCTGTTTTTTCATGG F2: 3 GATTGTCTGTTTTT 2 Unidirectional alignment (log-probability: -53.4) AAGCTCACATCAGCACAGTAGGAAAacACAGAGAAACACTtttttgtctgttag----GACAAAAAAGTACC AAGCTCACATCAGCACAGTAGGAAA--ACAGAGAAACACT--------------AACAGACAAAAAAGTACC Template switch alignment (log-probability: -29.8) AAGCTCACATCAGCACAGTAGGAAAacACAGAGAAACACT|TTTTTGTCTGTTAG|GACAAAAAAGTACC AAGCTCACATCAGCACAGTAGGAAA--ACAGAGAAACACT|TTTTTGTCTGTTAG|GACAAAAAAGTACC ========== Event 3485 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACAGTTACAAGTTGTCATGC--------------AATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAAAGGGTGTGGCTAATTTTGCAGTAGTGTGGGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGACATGGCCTCTGAGCACACTGGCCAAGC Chimp: AACAGTTACAAGTTGTCATGC--------------AATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAAAGGGTGTGGCTAATTTTGCAGTAGTGTGGGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGACATGGCCTCTGAGCACACTggccaagc ↓ 4 1 3 2 Gorilla: AACAGTTACAAGTTGTCATGCAATATGGCCATGGCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAAAGGGTGTGGCTAATTTTGCAGTAGTGTGGGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGGCATGGCCTCTGAGCACAATggccaagc ↑ 4 1 3 2 Human: AACAGTTACAAGTTGTCATGC--------------AATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAAAGGGTGTGGCTAATTTTGCAGTAGTGTGGGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGACATGGCCTCTGAGCACACTGGCCAAGC Cluster: [ ] Orangutan: AACAGTTACAAGTTGTCATGCAATATGGCCATGGCAATAACAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAGAGGGTGTGGCTAATTTTGCAGTAGTGTGCGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGACATGGCCTCCGAGCACACTGGCCAAGC Human > Gorilla --------------- chr8:44750966-44750972 Template switch process: F1: L TGTGATTAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATAT 1 F3: 4 GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAA R RF: TGTGGTTAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAAAGGGTGTGGCTAATTTTGCAGTAGTGTGGGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGACATGGCC RR: ACACCAATCACCTCATTCACTTGTCAATGTTCAACAGTACGTTATAGTCTTCGTATAAGTTTGAGGTCGCCATCGGGTCTTTCCCACACCGATTAAAACGTCATCACACCCCACGACTCAGTCCCCTGAGGTCTTTCTAGTAAAATTTATCCTGTACCGG F2: 3 GTACCGG 2 Unidirectional alignment (log-probability: -36.5) TAGTGGAGTAAGTGAACAGTTACAAGTTGTCATgcaatatggccatgGCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG TAGTGGAGTAAGTGAACAGTTACAAGTTGTCAT--------------GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG Template switch alignment (log-probability: -22.3) TAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATAT|GGCCATG|GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG TAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATAT|GGCCATG|GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG Chimp > Gorilla --------------- chr8:44750966-44750972 Template switch process: F1: L TGTGATTAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATAT 1 F3: 4 GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAA R RF: TGTGGTTAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAGAAAGGGTGTGGCTAATTTTGCAGTAGTGTGGGGTGCTGAGTCAGGGGACTCCAGAAAGATCATTTTAAATAGGACATGGCC RR: ACACCAATCACCTCATTCACTTGTCAATGTTCAACAGTACGTTATAGTCTTCGTATAAGTTTGAGGTCGCCATCGGGTCTTTCCCACACCGATTAAAACGTCATCACACCCCACGACTCAGTCCCCTGAGGTCTTTCTAGTAAAATTTATCCTGTACCGG F2: 3 GTACCGG 2 Unidirectional alignment (log-probability: -36.5) TAGTGGAGTAAGTGAACAGTTACAAGTTGTCATgcaatatggccatgGCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG TAGTGGAGTAAGTGAACAGTTACAAGTTGTCAT--------------GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG Template switch alignment (log-probability: -22.3) TAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATAT|GGCCATG|GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG TAGTGGAGTAAGTGAACAGTTACAAGTTGTCATGCAATAT|GGCCATG|GCAATATCAGAAGCATATTCAAACTCCAGCGGTAGCCCAG ========== Event 3486 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTTCCCTAGCCTGGAACAATGTCCGGCCTGGCTTTGTCCTCA-----GCCATATTGCCTGCTCTCTTTATATC Chimp: TGTTCCCTAGCCTGGAACAATGTCCGGCCTGGCTTTGTCCTCAGGCCGGACATATTGCCTGCTCTCTTTATATC ↑ 3 2 1 4 Gorilla: TGTTCCCTAGCCTCGAACAATGTCCGGCCTGGCTTTGTCCTCA-----GCCACATTGCCTGCTCTCTTTATATC Human: TGTTCCCTAGCCTGGAACAATGTCCGGCCTGGCTTTGTCCTCA-----GCCATATTGCCTGCTCTCTTTATATC Cluster: [ ] Orangutan: TGTTCCCTAGCCTGGAACATTGTCTGGCCTGGCTTTGTCCTCA-----GCCATATTGCCTGCTTTCTTTATATC Gorilla > Chimp --------------- chr8:44006527-44006535 Template switch process: F1: L TTCCCTAGCCTGGAACAATGTCCGGCCTGGCTTTGTCCTCAG 1 F3: 4 ATTGCCTGCTCTCTTTATATCACAAAATATTAAGTTAAAA R RF: TTCCCTAGCCTCGAACAATGTCCGGCCTGGCTTTGTCCTCAGCCACATTGCCTGCTCTCTTTATATCACAAAATGTTAAGTTAAAA RR: AAGGGATCGGAGCTTGTTACAGGCCGGACCGAAACAGGAGTCGGTGTAACGGACGAGAGAAATATAGTGTTTTACAATTCAATTTT F2: 3 TACAGGCCG 2 Unidirectional alignment (log-probability: -40.2) CCCTAGCCTgGAACAATGTCCGGCCTGGCTTTGTCCTCAggccgGaCAtATTGCCTGCTCTCTTTATATCACAAAATaTTAAGTTAAAA CCCTAGCCTCGAACAATGTCCGGCCTGGCTTTGTCCTCA-----GCCACATTGCCTGCTCTCTTTATATCACAAAATGTTAAGTTAAAA Template switch alignment (log-probability: -27.9) CCCTAGCCTgGAACAATGTCCGGCCTGGCTTTGTCCTCAG|GCCGGACAT|ATTGCCTGCTCTCTTTATATCACAAAATaTTAAGTTAAAA CCCTAGCCTCGAACAATGTCCGGCCTGGCTTTGTCCTCAG|GCCGGACAT|ATTGCCTGCTCTCTTTATATCACAAAATGTTAAGTTAAAA ========== Event 3487 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTAACATTTTAATTAACACTAAAGTGGAAAGTAAAGACTTTCCACTTTAGTATAGACTAAAAAATTATTCT Chimp: ATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGACTTTCCACTTTAGTATAGACTAAAAAATTATTCT ↑ 3 2 14 Gorilla: ATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAG-------------ATATAGACTAAAAAATTATTCT ↓ 3 2 14 Human: ATTAACATTTTAATTAACACTAAAGTGGAAAGTAAAGACTTTCCACTTTAGTATAGACTAAAAAATTATTCT Cluster: [ ] Orangutan: TTTAAAATTTTAGTTAACACTAAAGTGGAAAGTAAAG-------------ATATAGACTAAAAAATTATTCT Gorilla > Human --------------- chr8:103821785-103821797 Template switch process: F1: L AGGTATTAACATTTTAATTAACACTAAAGTGGAAAGTAAAGA 1 F3: 4 TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA R RF: AGGTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGATATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA RR: TCCATAATTGTAAAATCAATTGTGATTTCACCTTTCATTTCTATATCTGATTTTTTAATAAGAACTTCTTTTTTTAGTACCT F2: 3 GATTTCACCTTTC 2 Unidirectional alignment (log-probability: -35.1) GTATTAACATTTTAaTTAACACTAAAGTGGAAAGTAAAGActttccactttagTATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA GTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGA-------------TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA Template switch alignment (log-probability: -22.9) GTATTAACATTTTAaTTAACACTAAAGTGGAAAGTAAAGA|CTTTCCACTTTAG|TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA GTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGA|CTTTCCACTTTAG|TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA Gorilla > Chimp --------------- chr8:105771087-105771099 Template switch process: F1: L AGGTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGA 1 F3: 4 TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA R RF: AGGTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGATATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA RR: TCCATAATTGTAAAATCAATTGTGATTTCACCTTTCATTTCTATATCTGATTTTTTAATAAGAACTTCTTTTTTTAGTACCT F2: 3 GATTTCACCTTTC 2 Unidirectional alignment (log-probability: -29.6) GTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGActttccactttagTATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA GTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGA-------------TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA Template switch alignment (log-probability: -17.4) GTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGA|CTTTCCACTTTAG|TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA GTATTAACATTTTAGTTAACACTAAAGTGGAAAGTAAAGA|CTTTCCACTTTAG|TATAGACTAAAAAATTATTCTTGAAGAAAAAAATCATGGA ========== Event 3488 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GACCATTTAAACATGATTGAATTTAGAAAGTATTTCCTGATAATGTCATTATTAGGAAATACTTTAATGTAGCCAT Chimp: GACCATTTAAACATGATTGAA------------TTCCTAATAATGACATTATTAGGAAATACTTTAATGTAGCCAT ↑ 1 34 2 Gorilla: AACCATTTAAACATGATTGAATTTAGAAAGCATTTCCTAATA-AGTCATTATTAGGAAATACTTTAATGTAGCCAT Human: GACCATTTAAACATGATTGAATTTAGAAAGTATTTCCTGATAATGTCATTATTAGGAAATACTTTAATGTAGCCAT Cluster: [ ] Orangutan: GACCATTTAAACATGATTGAATTTAGA--------------------------------------AATGTAGCCAT Gorilla > Chimp --------------- chr8:108457607-108457617 Template switch process: F1: L GTGGGGGACAGGGTGGATATGACCATTTAAACATGATTGAATT 1 F3: 4 CATTATTAGGAAATACTTTAATGTAGCCATTAAAACCATC R RF: GTGGGGGACAGGGTGGATATAACCATTTAAACATGATTGAATTTAGAAAGCATTTCCTAATAAGTCATTATTAGGAAATACTTTAATGTAGCCATTAAAACCATC RR: CACCCCCTGTCCCACCTATATTGGTAAATTTGTACTAACTTAAATCTTTCGTAAAGGATTATTCAGTAATAATCCTTTATGAAATTACATCGGTAATTTTGGTAG F2: 3 AGTAATAATCC 2 Unidirectional alignment (log-probability: -33.9) GGGGACAGGGTGGATATgACCATTTAAACATGATTGAA------------TTCCTAATAAtGaCATTATTAGGAAATACTTTAATGTAGCCATTAAAACCATC GGGGACAGGGTGGATATAACCATTTAAACATGATTGAATTTAGAAAGCATTTCCTAATAA-GTCATTATTAGGAAATACTTTAATGTAGCCATTAAAACCATC Template switch alignment (log-probability: -22.7) GGGGACAGGGTGGATATgACCATTTAAACATGATTGAATT|CCTAATAATGA|CATTATTAGGAAATACTTTAATGTAGCCATTAAAACCATC GGGGACAGGGTGGATATAACCATTTAAACATGATTGAATT|CCTAATAATGA|CATTATTAGGAAATACTTTAATGTAGCCATTAAAACCATC ========== Event 3489 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGAAGCTGTCTTATAAAAAT------AACTAGGATATTTCAGGATATGAAATGTTTAGTTGAGA ↓ 1 4 3 2 Chimp: AGGAAGCTGTCTTATAAAAATATCCTGAAATAGGATATTTCAGGATATGAAATGTTTAGTTGAGA Gorilla: AGGAAGCTGTCTTATAAAAAT------AACTAGGCTATTTCAGGATATGAAATGTTTAGTTGAGA Human: AGGAAGCTGTCTTATAAAAAT------AACTAGGATATTTCAGGATATGAAATGTTTAGTTGAGA Cluster: [ ] Orangutan: AGGAAGCTGTCTTATAAAAAT------AACTAGGATATTTCAGGATATGAAATGCTTAGTTGAGA Human > Chimp ------------- chr8:39128218-39128225 Template switch process: F1: L AAATCTCTTGGAGAAAAGCAAGGAAGCTGTCTTATAAAAATA 1 F3: 4 TAGGATATTTCAGGATATGAAATGTTTAGTTGAGAAGTAA R RF: AAATCTCTTGGAGAAAAGCAAGGAAGCTGTCTTATAAAAATAACTAGGATATTTCAGGATATGAAATGTTTAGTTGAGAAGTAA RR: TTTAGAGAACCTCTTTTCGTTCCTTCGACAGAATATTTTTATTGATCCTATAAAGTCCTATACTTTACAAATCAACTCTTCATT F2: 3 AAAGTCCT 2 Unidirectional alignment (log-probability: -25.6) ATCTCTTGGAGAAAAGCAAGGAAGCTGTCTTATAAAAATatcctgAAaTAGGATATTTCAGGATATGAAATGTTTAGTTGAGAAGTAA ATCTCTTGGAGAAAAGCAAGGAAGCTGTCTTATAAAAAT------AACTAGGATATTTCAGGATATGAAATGTTTAGTTGAGAAGTAA Template switch alignment (log-probability: -16.3) ATCTCTTGGAGAAAAGCAAGGAAGCTGTCTTATAAAAATA|TCCTGAAA|TAGGATATTTCAGGATATGAAATGTTTAGTTGAGAAGTAA ATCTCTTGGAGAAAAGCAAGGAAGCTGTCTTATAAAAATA|TCCTGAAA|TAGGATATTTCAGGATATGAAATGTTTAGTTGAGAAGTAA ========== Event 3490 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGCATGAATTGCATATAAAATTCATATATGCC-------AATAGCTACCAGAACTGTGTGAGGC Chimp: CAGCATGAATTGCATATAAAATTCATATATGCCAATAGCCAATAGCTACCAGAACTGTGTGAGGC ↓ 1 3 4 Gorilla: CAGCATGAATTGCATATAAAACCT----------------ATTGGCTACCAGAACTGTGTGAGGC ↑ 1 3 4 Human: CAGCATGAATTGCATATAAAATTCATATATGCC-------AATAGCTACCAGAACTGTGTGAGGC Cluster: [ ] Orangutan: CAGCATGAATTGCGTACAAAACCT----------------ATTGGCTACCAGAACCGTGTGAGGC Human > Gorilla --------------- chr8:108069368-108069373 Template switch process: F1: L CTGCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAAC 1 F3: 4 GCTACCAGAACTGTGTGAGGCGGCCAGGACAGGACCCCTG R RF: CTGCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAATTCATATATGCCAATAGCTACCAGAACTGTGTGAGGCAGCCAGGACAGGACCCCTG RR: GACGTCTGACTGACTCCCCTGTCGTACTTAACGTATATTTTAAGTATATACGGTTATCGATGGTCTTGACACACTCCGTCGGTCCTGTCCTGGGGAC F2: 3 GTTATC 2 Unidirectional alignment (log-probability: -37) GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAA----------------AcctattgGCTACCAGAACTGTGTGAGGCgGCCAGGACAGGACCCCTG GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAATTCATATATGCCAATA-------GCTACCAGAACTGTGTGAGGCAGCCAGGACAGGACCCCTG Template switch alignment (log-probability: -27.5) GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAAc|CTATTG|GCTACCAGAACTGTGTGAGGCgGCCAGGACAGGACCCCTG GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAAT|CTATTG|GCTACCAGAACTGTGTGAGGCAGCCAGGACAGGACCCCTG Chimp > Gorilla --------------- chr8:108069368-108069373 Template switch process: F1: L CTGCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAAC 1 F3: 4 GCTACCAGAACTGTGTGAGGCGGCCAGGACAGGACCCCTG R RF: CTGCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAATTCATATATGCCAATAGCCAATAGCTACCAGAACTGTGTGAGGCAGCCAGGACAGGACCCCTG RR: GACGTCTGACTGACTCCCCTGTCGTACTTAACGTATATTTTAAGTATATACGGTTATCGGTTATCGATGGTCTTGACACACTCCGTCGGTCCTGTCCTGGGGAC F2: 3 GTTATC 2 Unidirectional alignment (log-probability: -37.4) GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAA-----------------------AcctattgGCTACCAGAACTGTGTGAGGCgGCCAGGACAGGACCCCTG GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAATTCATATATGCCAATAGCCAATA-------GCTACCAGAACTGTGTGAGGCAGCCAGGACAGGACCCCTG Template switch alignment (log-probability: -27.5) GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAAc|CTATTG|GCTACCAGAACTGTGTGAGGCgGCCAGGACAGGACCCCTG GCAGACTGACTGAGGGGACAGCATGAATTGCATATAAAAT|CTATTG|GCTACCAGAACTGTGTGAGGCAGCCAGGACAGGACCCCTG ========== Event 3491 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ATTTAACCAAGGATGAGAGTCCAGATATCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTAGATAAACTAGTGATAAACTCTAGGCCTAGAGTTTCCTTC ↓ 3 2 1 4 Chimp: ATTTAACCAAGGATGAGAGTCCAGATATCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTT------CT-------GGATCTAGGCCTAGAGTTTCCTTC Gorilla: ATTTAACCAAGGATGAGAGTCCAGATATCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTT------CT-------GGATCTAGGCCTAGAGTTTCCTTC ↑ 3 2 1 4 Human: ATTTAACCAAGGATGAGAGTCCAGATATCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTAGATAAACTAGTGATAAACTCTAGGCCTAGAGTTTCCTTC Cluster: [ ] Orangutan: ATTCAACAAAGGATGAGAGTTCAGATACCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTT------CT-------GGATCTAGGCCTAGAGTTTCCTTC Human > Chimp ------------- chr8:109924992-109924997 Template switch process: F1: L AGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT 1 F3: 4 TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC R RF: TCCAGATATCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTAGATAAACTAGTGATAAACTCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC RR: AGGTCTATAGATGGACGGTCCGGAGAGAGGTTTGGGACTCTTTTAGATCAAAATAGTGATCTATTTGATCACTATTTGAGATCCGGATCTCAAAGGAAGAGAAGATGTTCGGGGTACG F2: 3 AGGTCT 2 Unidirectional alignment (log-probability: -29.3) GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTtctggA------------------TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT-----AGATAAACTAGTGATAAACTCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC Template switch alignment (log-probability: -16) GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT|TCTGGA|TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT|TCTGGA|TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC Human > Gorilla --------------- chr8:108999601-108999606 Template switch process: F1: L AGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT 1 F3: 4 TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC R RF: TCCAGATATCTACCTGCCAGGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTAGATAAACTAGTGATAAACTCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC RR: AGGTCTATAGATGGACGGTCCGGAGAGAGGTTTGGGACTCTTTTAGATCAAAATAGTGATCTATTTGATCACTATTTGAGATCCGGATCTCAAAGGAAGAGAAGATGTTCGGGGTACG F2: 3 AGGTCT 2 Unidirectional alignment (log-probability: -28.8) GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACTtctggA------------------TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT-----AGATAAACTAGTGATAAACTCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC Template switch alignment (log-probability: -16.5) GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT|TCTGGA|TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC GGCCTCTCTCCAAACCCTGAGAAAATCTAGTTTTATCACT|TCTGGA|TCTAGGCCTAGAGTTTCCTTCTCTTCTACAAGCCCCATGC ========== Event 3492 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGAAGAGTGGATAAGTACTTC-------------CAGCACAGGGAAAGGTTTGTGAGAGGGTtgt Chimp: AAGGAAGAGTGGATAAGTACTTC-------------CAGCACAGGGAAAGGTTTGTGAGAGGGTTGT ↓ 3 1 4 2 Gorilla: AAGGAAGAGTGGATAAGTACTTTCCCTGTGCTGGAAGAGCACAGGGAAAGGTTTGTGAGAGGGTTGT Human: AAGGAAGAGTGGATAAGTACTTC-------------CAGCACAGGGAAAGGTTTGTGAGAGGGTtgt Cluster: [ ] Orangutan: AAGGAAGAGTGGATAAGTACTTC-------------CAGCACAAGGAAAGGTTtgtgagagggttgt Chimp > Gorilla --------------- chr8:108933274-108933288 Template switch process: F1: L GACTGAGTTGCTCAAGTCCAAGGAAGAGTGGATAAGTACTT 1 F3: 4 AGCACAGGGAAAGGTTTGTGAGAGGGTTGTATATGTGTGC R RF: GACTGAGTTGCTCAAGTCCAAGGAAGAGTGGATAAGTACTTCCAGCACAGGGAAAGGTTTGTGAGAGGGTTGTATATGTGTGC RR: CTGACTCAACGAGTTCAGGTTCCTTCTCACCTATTCATGAAGGTCGTGTCCCTTTCCAAACACTCTCCCAACATATACACACG F2: 3 GAAGGTCGTGTCCCT 2 Unidirectional alignment (log-probability: -35.1) ACTGAGTTGCTCAAGTCCAAGGAAGAGTGGATAAGTACTTtCcctgtgctggaagAGCACAGGGAAAGGTTTGTGAGAGGGTTGTATATGTGTGC ACTGAGTTGCTCAAGTCCAAGGAAGAGTGGATAAGTACTTCC-------------AGCACAGGGAAAGGTTTGTGAGAGGGTTGTATATGTGTGC Template switch alignment (log-probability: -17.6) ACTGAGTTGCTCAAGTCCAAGGAAGAGTGGATAAGTACTT|TCCCTGTGCTGGAAG|AGCACAGGGAAAGGTTTGTGAGAGGGTTGTATATGTGTGC ACTGAGTTGCTCAAGTCCAAGGAAGAGTGGATAAGTACTT|TCCCTGTGCTGGAAG|AGCACAGGGAAAGGTTTGTGAGAGGGTTGTATATGTGTGC ========== Event 3493 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 125 Detected in comparisons: 1256 Multiple sequence alignment: Human: caggttatgtggctgctgtctgcccagCACTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATATGGGCAGGCCCTGGAGCAGCTACtgcagtgacctata ↓ 3 2 1 4 ↑ 3 2 1 4 Chimp: caggttatgtggctgctgtctgcccagCACTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGCTAC-----TGCCCTGGAGAAGCTACtgcagtgacctata ↑ 3 2 1 4 Gorilla: caggttatgtggctgctgtctgcccagCACTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATGTGGGCAGGCCCTGGAGCAGCTACtgcagtgacctata Human: caggttatgtggctgctgtctgcccagCACTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATATGGGCAGGCCCTGGAGCAGCTACtgcagtgacctata Cluster: [ ] Orangutan: caggttatgtggctgctgtctgtccagCACTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATATGGGCAGGCCCTGGAGCAGCTACtgcagtgacctata Chimp > Human ------------- chr8:108906582-108906588 Template switch process: F1: L CTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATA 1 F3: 4 GCCCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACACAATGTGGCA R RF: CTGCCCAGCACTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGCTACTGCCCTGGAGAAGCTACTGCAGTGACCTATACAGCCTTACACAATGTGGCA RR: GACGGGTCGTGAGTGTCGTCATCCCTTCGTCACGTACCTGGACCACTCTTCGATGACGGGACCTCTTCGATGACGTCACTGGATATGTCGGAATGTGTTACACCGT F2: 3 GACGGGT 2 Unidirectional alignment (log-probability: -41.8) CAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG-----atatgggcagGCCCTGGAGcAGCTACTGCAGTGACCTATACAGCCTTACA CAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGCTACT----------GCCCTGGAGAAGCTACTGCAGTGACCTATACAGCCTTACA Template switch alignment (log-probability: -28.4) CAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGaTA|TGGGCAG|GCCCTGGAGcAGCTACTGCAGTGACCTATACAGCCTTACA CAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGCTA|TGGGCAG|GCCCTGGAGAAGCTACTGCAGTGACCTATACAGCCTTACA Human > Chimp ------------- chr8:110923162-110923167 Template switch process: F1: L CTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG 1 F3: 4 CCCTGGAGAAGCTACTGCAGTGACCTATACAGCCTTACACAATGTGGCA R RF: CTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATATGGGCAGGCCCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACACAATGTGGCA RR: GAGTGTCGTCATCCCTTCGTCACGTACCTGGACCACTCTTCTATACCCGTCCGGGACCTCGTCGATGACGTCACTGGATATGTCGGAATGTGTTACACCGT F2: 3 GTCATC 2 Unidirectional alignment (log-probability: -34.9) TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGctact----------GCCCTGGAGaAGCTACTGCAGTGACCTATACAGCCTTACAC TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG-----ATATGGGCAGGCCCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACAC Template switch alignment (log-probability: -22.2) TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG|CTACTG|CCCTGGAGaAGCTACTGCAGTGACCTATACAGCCTTACAC TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG|CTACTG|CCCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACAC Gorilla > Chimp --------------- chr8:110923162-110923168 Template switch process: F1: L CTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG 1 F3: 4 CCTGGAGAAGCTACTGCAGTGACCTATACAGCCTTACACAATGTGGCA R RF: CTCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATGTGGGCAGGCCCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACACAATGTGGCA RR: GAGTGTCGTCATCCCTTCGTCACGTACCTGGACCACTCTTCTACACCCGTCCGGGACCTCGTCGATGACGTCACTGGATATGTCGGAATGTGTTACACCGT F2: 3 CGTCATC 2 Unidirectional alignment (log-probability: -34) TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGA----------AGctactGCCCTGGAGaAGCTACTGCAGTGACCTATACAGCCTTACACA TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAGATGTGGGCAG-----GCCCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACACA Template switch alignment (log-probability: -22.3) TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG|CTACTGC|CCTGGAGaAGCTACTGCAGTGACCTATACAGCCTTACACA TCACAGCAGTAGGGAAGCAGTGCATGGACCTGGTGAGAAG|CTACTGC|CCTGGAGCAGCTACTGCAGTGACCTATACAGCCTTACACA ========== Event 3494 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 156 Detected in comparisons: 1256 Multiple sequence alignment: Human: TGAAGAAAACTGGTTAACTCTAAATTGTTACT--AAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGCTAATTGTAATAACAATTA ↑ 1 3 4 2 Chimp: TGAAGAAACCTGGTTAACTCTGAATTG-TAGTAACAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGCTAATTGTAATAACAATTA ↓ 1 3 4 2 ↑ 1 4 3 2 Gorilla: TGAAGAAACCTGGTTAACTCTAAATTGTTACT--AAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGCTAATTGTAATAACAATTA Human: TGAAGAAAACTGGTTAACTCTAAATTGTTACT--AAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGCTAATTGTAATAACAATTA Cluster: [ ] Orangutan: TGAAGAAACCTGGTTAACTCTAAATTGTTACT--AAATTTTGAATCTTCCTGTATTTAGCAATAAC-ATTACTGCTAATTGTAATAACAATTA Chimp > Human ------------- chr8:109536743-109536754 Template switch process: F1: L ATTTCTAACCAGGCCCCTTCTGAAGAAAACTGGTTAACTCT 1 F3: 4 AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC R RF: ATTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTGAATTGTAGTAACAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC RR: TAAAGATTGGTCCGGGGAAGACTTCTTTGGACCAATTGAGACTTAACATCATTGTTAAAACTTAGAAGGACATAAATCGTTATTTTCAATGACG F2: 3 ATCATTGTTAAA 2 Unidirectional alignment (log-probability: -39.2) TTTCTAACCAGGCCCCTTCTGAAGAAAaCTGGTTAACTCTaAATTGttacTA-----AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC TTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTGAATTG----TAGTAACAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC Template switch alignment (log-probability: -22.8) TTTCTAACCAGGCCCCTTCTGAAGAAAaCTGGTTAACTCT|AAATTGTTACTA|AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC TTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCT|AAATTGTTACTA|AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC Gorilla > Chimp --------------- chr8:111573892-111573897 Template switch process: F1: L ATTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTGAATTGT 1 F3: 4 AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC R RF: ATTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTAAATTGTTACTAAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC RR: TAAAGATTGGTCCGGGGAAGACTTCTTTGGACCAATTGAGATTTAACAATGATTTAAAACTTAGAAGGACATAAATCGTTATTTTCAATGACG F2: 3 CAATGA 2 Unidirectional alignment (log-probability: -33.7) CCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTgAATTG----TAgtaacAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC CCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTAAATTGTTACTA-----AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC Template switch alignment (log-probability: -22.2) CCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTgAATTGT|AGTAAC|AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC CCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTAAATTGT|AGTAAC|AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC Chimp > Gorilla --------------- chr8:110596865-110596876 Template switch process: F1: L ATTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCT 1 F3: 4 AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC R RF: ATTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTGAATTGTAGTAACAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC RR: TAAAGATTGGTCCGGGGAAGACTTCTTTGGACCAATTGAGACTTAACATCATTGTTAAAACTTAGAAGGACATAAATCGTTATTTTCAATGACG F2: 3 ATCATTGTTAAA 2 Unidirectional alignment (log-probability: -32.3) TTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTaAATTGttacTA-----AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC TTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCTGAATTG----TAGTAACAATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC Template switch alignment (log-probability: -17.3) TTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCT|AAATTGTTACTA|AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC TTTCTAACCAGGCCCCTTCTGAAGAAACCTGGTTAACTCT|AAATTGTTACTA|AATTTTGAATCTTCCTGTATTTAGCAATAAAAGTTACTGC ========== Event 3495 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: CCAGAATTTATGAGCACACTCTCATAACATTTATAACCAGGCATGTTATAAATACtaatct---ta Chimp: ccagaatttatgagcacactc----taca-----tgccaggcatgttataaatactaatct---ta Gorilla: CCAGAATTTATGAGCACACTC----TACA-----TGCCACGCATGTTATAAATACtaatct---ta ↑ 1 4 3 2 Human: CCAGAATTTATGAGCACACTCTCATAACATTTATAACCAGGCATGTTATAAATACtaatct---ta Cluster: [ ] Orangutan: ccagaatttatgagcacactc----taca-----tgccaggcatgtgataaatactaatcttctca Human > Gorilla --------------- chr8:110322479-110322483 Template switch process: F1: L TACCAAGAACAATGACACTACCAGAATTTATGAGCACACTCT 1 F3: 4 CCACGCATGTTATAAATACTAATCTTAACAACACGCAAGGCTAT R RF: TACCAAGAACAATGACACTACCAGAATTTATGAGCACACTCTCATAACATTTATAACCAGGCATGTTATAAATACTAATCTTAACAACTCGCAAGGCTAT RR: ATGGTTCTTGTTACTGTGATGGTCTTAAATACTCGTGTGAGAGTATTGTAAATATTGGTCCGTACAATATTTATGATTAGAATTGTTGAGCGTTCCGATA F2: 3 GTACA 2 Unidirectional alignment (log-probability: -37.8) CCAAGAACAATGACACTACCAGAATTTATGAGCACACTCT----ACAT-----gCCAcGCATGTTATAAATACTAATCTTAACAACaCGCAAGG CCAAGAACAATGACACTACCAGAATTTATGAGCACACTCTCATAACATTTATAACCAGGCATGTTATAAATACTAATCTTAACAACTCGCAAGG Template switch alignment (log-probability: -27.5) CCAAGAACAATGACACTACCAGAATTTATGAGCACACTCT|ACATG|CCAcGCATGTTATAAATACTAATCTTAACAACaCGCAAGG CCAAGAACAATGACACTACCAGAATTTATGAGCACACTCT|ACATG|CCAGGCATGTTATAAATACTAATCTTAACAACTCGCAAGG ========== Event 3496 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: taaaattgatggtAAAACTCTAGATAGTATTTCTGACTACAAGAGGGTGCAGAACA Chimp: taaaattgatggtaaaactctagaTAGTATTTCTGACTACAAGAGGGTGCAGAACA ↓ 3 2 1 4 Gorilla: taaaattgatggtaaaactctagaTAGTATC-TAGACTACAAGAGGGTGCAGAACA Human: taaaattgatggtAAAACTCTAGATAGTATTTCTGACTACAAGAGGGTGCAGAACA Cluster: [ ] Orangutan: taaaattgatggtAAAACTCTAGATAGTATTTCTGACTACAGGGGGGTGCAGAACA Chimp > Gorilla --------------- chr8:35043930-35043933 Template switch process: F1: L AGTATAAGAAATAAAATTGATGGTAAAACTCTAGATAGTAT 1 F3: 4 ACTACAAGAGGGTGCAGAACAGAAATATTTCAGAGGTGG R RF: AGTATAAGAAATAAAATTGATGGTAAAACTCTAGATAGTATTTCTGACTACAAGAGGGTGCAGAACAGAAATATTTCAGAGGTGG RR: TCATATTCTTTATTTTAACTACCATTTTGAGATCTATCATAAAGACTGATGTTCTCCCACGTCTTGTCTTTATAAAGTCTCCACC F2: 3 GATC 2 Unidirectional alignment (log-probability: -45.8) GTATAAGAAATAAAATTGATGGTAAAACTCTAGATAGTATcTa-GACTACAAGAGGGTGCAGAACAGAAATAtttcagaggtgg GTATAAGAAATAAAATTGATGGTAAAACTCTAGATAGTATTTCTGACTACAAGAGGGTGCAGAACAGAAATA------------ Template switch alignment (log-probability: -16.2) GTATAAGAAATAAAATTGATGGTAAAACTCTAGATAGTAT|CTAG|ACTACAAGAGGGTGCAGAACAGAAATATTTCAGAGGTGG GTATAAGAAATAAAATTGATGGTAAAACTCTAGATAGTAT|CTAG|ACTACAAGAGGGTGCAGAACAGAAATATTTCAGAGGTGG ========== Event 3497 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTACTTTGGCAATTTATCATGCCATTTAT--------------------TATGTCATGTGACAAATTTGGCTGGATGGGTAGAGA ↑ 1 4 3 2 Chimp: TTACTTTGGCAATTTATCATGCCATTTAT----------TAAAGCACTTTATATTTTGTGACAAATTTGGCTGGATGGGTAGAGA Gorilla: TTACTTTGGCAATTTATCATGTCATTTATTAAAGCACTT----------TATATTTTGTGACAAGTTTGGCTGGATGGGTAGAGA ↓ 1 4 3 2 Human: TTACTTTGGCAATTTATCATGCCATTTAT--------------------TATGTCATGTGACAAATTTGGCTGGATGGGTAGAGA Cluster: [ ] Orangutan: TTACTTTGGCAATTTATCATGCCATTTATTAAAGCACTT----------TATATTTTGTGACAAATTTGGCTGGATGTATAGAGA Chimp > Human ------------- chr8:34028109-34028113 Template switch process: F1: L AATAGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTA 1 F3: 4 TGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCT R RF: AATAGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTAAAGCACTTTATATTTTGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCT RR: TTATCGTTCAACAATGAAACCGTTAAATAGTACGGTAAATAATTTCGTGAAATATAAAACACTGTTTAAACCGACCTACCCATCTCTACTCGAAAAGA F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -27.6) AGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTAtgtcA--------------TGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCT AGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTA----AAGCACTTTATATTTTGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCT Template switch alignment (log-probability: -15.9) AGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTA|TGTCA|TGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCT AGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTA|TGTCA|TGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCT Gorilla > Human --------------- chr8:34028109-34028113 Template switch process: F1: L TTAAATAAAATAGCAAGTTGTTACTTTGGCAATTTATCATGCCATTTATTA 1 F3: 4 TGTGACAAATTTGGCTGGATGGGTAGAGATGAGCTTTTCTTACTTAGAT R RF: TTAAATAAAATAGCAAGTTGTTACTTTGGCAATTTATCATGTCATTTATTAAAGCACTTTATATTTTGTGACAAGTTTGGCTGGATGGGTAGAGATGAGCTTTTCTTACTTAGAT RR: AATTTATTTTATCGTTCAACAATGAAACCGTTAAATAGTACAGTAAATAATTTCGTGAAATATAAAACACTGTTCAAACCGACCTACCCATCTCTACTCGAAAAGAATGAATCTA F2: 3 ACTGT 2 Unidirectional alignment (log-probability: -38.4) AGCAAGTTGTTACTTTGGCAATTTATCATGcCATTTATTA--------------TgtcaTGTGACAAaTTTGGCTGGATGGGTAGAGATGAGCTTTTCT AGCAAGTTGTTACTTTGGCAATTTATCATGTCATTTATTAAAGCACTTTATATTT----TGTGACAAGTTTGGCTGGATGGGTAGAGATGAGCTTTTCT Template switch alignment (log-probability: -27.9) AGCAAGTTGTTACTTTGGCAATTTATCATGcCATTTATTA|TGTCA|TGTGACAAaTTTGGCTGGATGGGTAGAGATGAGCTTTTCT AGCAAGTTGTTACTTTGGCAATTTATCATGTCATTTATTA|TGTCA|TGTGACAAGTTTGGCTGGATGGGTAGAGATGAGCTTTTCT ========== Event 3498 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: TATCACCCTCTGCAATACATCAAAAATGAACAGTGGTTCATTTCTCCTTTATGTCAGCAATCACA Chimp: gatcaccctctgcaatacatccttagagca--c-tgttcatttctgctttatgtcagcaatcaca Gorilla: TATCACCCTCTGCAATACATCCTTAGAGCA--C-TGTTCATTTCTCCTTTATGTCAGCAATCACA ↓ 1 3 4 2 Human: TATCACCCTCTGCAATACATCAAAAATGAACAGTGGTTCATTTCTCCTTTATGTCAGCAATCACA Cluster: [ ] Orangutan: TATCACCCTCTGCAATACATCCTTAGAGCA--C-TGTTCATTTCTCCTTTATGTCAGCAATCACA Gorilla > Human --------------- chr8:33522404-33522417 Template switch process: F1: L CACACTGTCACCAAGTTGTTTATCACCCTCTGCAATACATC 1 F3: 4 GTTCATTTCTCCTTTATGTCAGCAATCACAAATGTAATAA R RF: CACACTGTCACCAAGTTGGTTATCACCCTCTGCAATACATCCTTAGAGCACTGTTCATTTCTCCTTTATGTCAGCAATCACAAATGTAATAA RR: GTGTGACAGTGGTTCAACCAATAGTGGGAGACGTTATGTAGGAATCTCGTGACAAGTAAAGAGGAAATACAGTCGTTAGTGTTTACATTATT F2: 3 GTGACAAGTAAAAA 2 Unidirectional alignment (log-probability: -46.8) ACACTGTCACCAAGTTGtTTATCACCCTCTGCAATACATCaaaaatgaacagtg-----------GTTCATTTCTCCTTTATGTCAGCAATCACAAATGTAATAA ACACTGTCACCAAGTTGGTTATCACCCTCTGCAATACATC--------------CTTAGAGCACTGTTCATTTCTCCTTTATGTCAGCAATCACAAATGTAATAA Template switch alignment (log-probability: -28.5) ACACTGTCACCAAGTTGtTTATCACCCTCTGCAATACATC|AaAAATGAACAGTG|GTTCATTTCTCCTTTATGTCAGCAATCACAAATGTAATAA ACACTGTCACCAAGTTGGTTATCACCCTCTGCAATACATC|AGAAATGAACAGTG|GTTCATTTCTCCTTTATGTCAGCAATCACAAATGTAATAA ========== Event 3499 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAA---------------------TGTCATGGCCAATGGTCAGTtgggaataaaagaattaacagctggtctgtaacttgttttcttctctgaag Chimp: TAATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAA---------------------TGTCATGGCCAATGGTCAGTtgggaataaaagaattaacagctggtctgtaacttgttttcttctctgaag ↓ 4 1 3 2 Gorilla: TAATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAATTACTGAACTATCTCTTTGCATTTCATGGCCAATGGTCAGTtgggaataaaagaattaacagctggtctgtaacttgttttcttctctgaag ↑ 4 1 3 2 Human: TAATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAA---------------------TGTCATGGCCAATGGTCAGTtgggaataaaagaattaacagctggtctgtaacttgttttcttctctgaag Cluster: [ ] Orangutan: Human > Gorilla --------------- chr8:34388931-34388935 Template switch process: F1: L ATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAAT 1 F3: 4 AACTATCTCTTTGCATT---------TCATGGCCAATGGTCAGTTGGGAATAAAAGAATTAACAGC R RF: ATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAATGTCATGGCCAATGGTCAGTTGGGAATAAAAGAATTAACAGCTGGTCTGTA RR: TAATATAGATTTTCGTTTTGATAGAGAAACGTAATGACTTTACAGTACCGGTTACCAGTCAACCCTTATTTTCTTAATTGTCGACCAGACAT F2: 3 GTCAT 2 Unidirectional alignment (log-probability: -46.6) TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAattactgaactatctctttgcATtTCATGGCCAATGGTCAGTTGGGA TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAA---------------------ATGTCATGGCCAATGGTCAGTTGGGA Template switch alignment (log-probability: -32.5) TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAAT|TACtG|AACTATCTCTTTGCATT---------TCATGGCCAATGGTCAGTTGGGA TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAAT|TACAG|AACTATCTCTTTGCATTACTGAAATGTCATGGCCAATGGTCAGTTGGGA Chimp > Gorilla --------------- chr8:34388931-34388935 Template switch process: F1: L ATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAAT 1 F3: 4 AACTATCTCTTTGCATT---------TCATGGCCAATGGTCAGTTGGGAATAAAAGAATTAACAGC R RF: ATTATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAATGTCATGGCCAATGGTCAGTTGGGAATAAAAGAATTAACAGCTGGTCTGTA RR: TAATATAGATTTTCGTTTTGATAGAGAAACGTAATGACTTTACAGTACCGGTTACCAGTCAACCCTTATTTTCTTAATTGTCGACCAGACAT F2: 3 GTCAT 2 Unidirectional alignment (log-probability: -46.6) TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAattactgaactatctctttgcATtTCATGGCCAATGGTCAGTTGGGA TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAA---------------------ATGTCATGGCCAATGGTCAGTTGGGA Template switch alignment (log-probability: -32.5) TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAAT|TACtG|AACTATCTCTTTGCATT---------TCATGGCCAATGGTCAGTTGGGA TATATCTAAAAGCAAAACTATCTCTTTGCATTACTGAAAT|TACAG|AACTATCTCTTTGCATTACTGAAATGTCATGGCCAATGGTCAGTTGGGA ========== Event 3500 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 26 Detected in comparisons: 1256 Multiple sequence alignment: Human: agctggagttaTATGAAAATAGAAAAAACTTTGTTTTCTCTATTTACACCATCATACATTTATTCTA ↓ 1 3 2 4 Chimp: agctggagttaTATGAAAATAGAGAAAACAGAGTTT---------TCACCATCATACATTTATTCTA ↓ 3 1 2 4 Gorilla: agctggagttaTATGAAAATAGAGAAAACTCTGTTTTCTCTATTTACACCATCATACATTTATTCTA Human: agctggagttaTATGAAAATAGAAAAAACTTTGTTTTCTCTATTTACACCATCATACATTTATTCTA Cluster: [ ] Orangutan: agctggagtcaTATGAAAACAGAGAAAACTCTATTTTCTCTATTTACACCATCATACATTTATTCTA Human > Chimp ------------- chr8:114234784-114234797 Template switch process: F1: L GATTACATAGATATTAGGAGCTGGAGTTATATGAAAATAGA 1 F3: 4 CACCATCATACATTTATTCTAGCAAAACAAACAAACATCT R RF: GATTACATAGATATTAGGAGCTGGAGTTATATGAAAATAGAAAAAACTTTGTTTTCTCTATTTACACCATCATACATTTATTCTAGCAAAACAAACAAACATCT RR: CTAATGTATCTATAATCCTCGACCTCAATATACTTTTATCTTTTTTGAAACAAAAGAGATAAATGTGGTAGTATGTAAATAAGATCGTTTTGTTTGTTTGTAGA F2: 3 TTTTGAGACAAAAG 2 Unidirectional alignment (log-probability: -35.1) ATTACATAGATATTAGGAGCTGGAGTTATATGAAAATAGAgAAAACagagtTTT--------------CACCATCATACATTTATTCTAGCAAAACAAACAAACATCT ATTACATAGATATTAGGAGCTGGAGTTATATGAAAATAGAAAAAAC-----TTTGTTTTCTCTATTTACACCATCATACATTTATTCTAGCAAAACAAACAAACATCT Template switch alignment (log-probability: -23) ATTACATAGATATTAGGAGCTGGAGTTATATGAAAATAGA|GAAAACAgAGTTTT|CACCATCATACATTTATTCTAGCAAAACAAACAAACATCT ATTACATAGATATTAGGAGCTGGAGTTATATGAAAATAGA|GAAAACAAAGTTTT|CACCATCATACATTTATTCTAGCAAAACAAACAAACATCT Chimp > Gorilla --------------- chr8:113330487-113330499 Template switch process: F1: L ATAGATATTAGGAGCTGGAGTTATATGAAAATAGAGAAAAC 1 F3: 4 TTTACACCATCATACATTTATTCTAGCAAAACAAACAAACATCT R RF: ATAGATATTAGGAGCTGGAGTTATATGAAAATAGAGAAAACAGAGTTTTCACCATCATACATTTATTCTAGCAAAACAAACAAACATCT RR: TATCTATAATCCTCGACCTCAATATACTTTTATCTCTTTTGTCTCAAAAGTGGTAGTATGTAAATAAGATCGTTTTGTTTGTTTGTAGA F2: 3 ATCTCTTTTGTCT 2 Unidirectional alignment (log-probability: -40.5) TAGATATTAGGAGCTGGAGTTATATGAAAATAGAGAAAACtctGTTTTctctatttaCACCATCATACATTTATTCTAGCAAAACAAACAAAC TAGATATTAGGAGCTGGAGTTATATGAAAATAGAGAAAACAGAGTTTT---------CACCATCATACATTTATTCTAGCAAAACAAACAAAC Template switch alignment (log-probability: -23) TAGATATTAGGAGCTGGAGTTATATGAAAATAGAGAAAAC|TCTGTTTTCTCTA|TTTaCACCATCATACATTTATTCTAGCAAAACAAACAAAC TAGATATTAGGAGCTGGAGTTATATGAAAATAGAGAAAAC|TCTGTTTTCTCTA|TTTTCACCATCATACATTTATTCTAGCAAAACAAACAAAC ========== Event 3501 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGAATATTTTCTAAAGCC-CCTGAGTGGTATATGTTTTTATACACTTTTCTTCGCAACATTTCAAAATTCTGTTAGCA ↓ 3 1 2 4 Chimp: CTGAATATTTTCTAAAGCC-CCTGAGTGGTACATA--------TACCACTC-AGGGTATATTTCAAAATTCTGTTAGCA ↑ 3 1 2 4 Gorilla: CTGAATATTTTCTAAAGCC-CCTGAGTGGTATATGTTTTTATACATTTTTCTTCTCAACATTTCAAAATTCTGTTAGCA Human: CTGAATATTTTCTAAAGCC-CCTGAGTGGTATATGTTTTTATACACTTTTCTTCGCAACATTTCAAAATTCTGTTAGCA Cluster: [ ] Orangutan: CTGAATATTTTCTAAAGCCAAATGAGCGGTATATGTTTTTATACACTTTTCTTCTCAACATTTCAAAATTCTGTTGGCA Human > Chimp ------------- chr8:115086117-115086132 Template switch process: F1: L TTGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA 1 F3: 4 TAT-----------------ATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATTTTA R RF: TTGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTATATGTTTTTATACACTTTTCTTCGCAACATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATTTTA RR: AACCTTTTGAAGACTTATAAAAGATTTCGGGGACTCACCATATACAAAAATATGTGAAAAGAAGCGTTGTAAAGTTTTAAGACAATCGTTACAAATGAATCTATAAAAT F2: 3 GGGACTCACCATATAC 2 Unidirectional alignment (log-probability: -45.4) TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTAcatataccactcagggTAT-------------------------ATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA----------------TATGTTTTTATACACTTTTCTTCGCAACATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT Template switch alignment (log-probability: -28.4) TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA|CATATACCACTCAGGG|TAT-----------------ATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA|CATATACCACTCAGGG|TATACACTTTTCTTCGCAACATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT Gorilla > Chimp --------------- chr8:115086117-115086132 Template switch process: F1: L TTGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA 1 F3: 4 TAT-----------------ATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATTTTA R RF: TTGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTATATGTTTTTATACATTTTTCTTCTCAACATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATTTTA RR: AACCTTTTGAAGACTTATAAAAGATTTCGGGGACTCACCATATACAAAAATATGTAAAAAGAAGAGTTGTAAAGTTTTAAGACAATCGTTACAAATGAATCTATAAAAT F2: 3 GGGACTCACCATATAC 2 Unidirectional alignment (log-probability: -45) TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTAcatataccactcagggTAT-------------------------ATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA----------------TATGTTTTTATACATTTTTCTTCTCAACATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT Template switch alignment (log-probability: -28.5) TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA|CATATACCACTCAGGG|TAT-----------------ATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT TGGAAAACTTCTGAATATTTTCTAAAGCCCCTGAGTGGTA|CATATACCACTCAGGG|TATACATTTTTCTTCTCAACATTTCAAAATTCTGTTAGCAATGTTTACTTAGATATT ========== Event 3502 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAAATTTCAGGACAAGATTTGAGACAACATGATGT--------------TGTCTCAAATGTTGATTCTTCTTTCCTAC Chimp: ATAAATTTCAGGACAAGATTTGAGACAACATGATGT--------------TGTCTCAAATGTTGATTCTTCTTTCCTAC ↑ 3 2 1 4 Gorilla: ATAAATTTCAGGACAAGATTTGAGACAACATGATGT--------GTTATATCTCT-CGATGTTGATTCTTCTTTCCTAC ↓ 3 2 1 4 Human: ATAAATTTCAGGACAAGATTTGAGACAACATGATGT--------------TGTCTCAAATGTTGATTCTTCTTTCCTAC Cluster: [ ] Orangutan: ATAAATTTCAGGACAAGATTTGAGATAACATGATGTGTTATAGC------TCTCT-TGATGTTGATTCTTCTTTCCTAC Gorilla > Human --------------- chr8:113278502-113278509 Template switch process: F1: L ACAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT 1 F3: 4 ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT R RF: ACAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGTGTTATATCTCTCGATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT RR: TGTTCTATTTAAAGTCCTGTTCTAAACTCTGTTGTACTACACAATATAGAGAGCTACAACTAAGAAGAAAGGATGAACTTTTTAAAACAATCTA F2: 3 AACTCTGT 2 Unidirectional alignment (log-probability: -32.8) CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT-------------tgtctcaaATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGTGTTATATCTCTCG--------ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT Template switch alignment (log-probability: -16.7) CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT|TGTCTCAA|ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT|TGTCTCAA|ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT Gorilla > Chimp --------------- chr8:115383096-115383103 Template switch process: F1: L ACAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT 1 F3: 4 ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT R RF: ACAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGTGTTATATCTCTCGATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT RR: TGTTCTATTTAAAGTCCTGTTCTAAACTCTGTTGTACTACACAATATAGAGAGCTACAACTAAGAAGAAAGGATGAACTTTTTAAAACAATCTA F2: 3 AACTCTGT 2 Unidirectional alignment (log-probability: -32.8) CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT-------------tgtctcaaATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGTGTTATATCTCTCG--------ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT Template switch alignment (log-probability: -16.7) CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT|TGTCTCAA|ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT CAAGATAAATTTCAGGACAAGATTTGAGACAACATGATGT|TGTCTCAA|ATGTTGATTCTTCTTTCCTACTTGAAAAATTTTGTTAGAT ========== Event 3503 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTACTTTTGCAGATATACTGATT-TTTTCATACACATGTGCACACACATATATGAAACAGTTGTGTTGTCTTATTGCACAACaaaaa-tcatgaaaaaaaat--caaagaagagtattcatttaaaaattt Chimp: TTACTTTTGCAGATATACTGAtttttttCATACACATATGCACACACATATATGAAACAGTTATGTTGTCTTATTGCACAACAAAAA-TCATGaaa-aaaaT-------CAGAGTATTCATTTAAAAATTT ↑ 3 2 1 4 Gorilla: TTACTTTTGCAGATATACTGAtttttttCATACACATATGCACACACATATATGAAACAGTTGTGTTGTATTATTGCACAACAAAAA-TCATAAAATCAAAG-------AAGAGTATTCATTTAAAAATTT Human: TTACTTTTGCAGATATACTGATT-TTTTCATACACATGTGCACACACATATATGAAACAGTTGTGTTGTCTTATTGCACAACaaaaa-tcatgaaaaaaaat--caaagaagagtattcatttaaaaattt Cluster: [ ] Orangutan: TTGCTTTTGCAGATATACTGATTTTTTTCATACACATATGCACACATATATATGAAATAGTTTTGTTGTCTTATTGCaaaataaaaattcacgaaaaaaaatca-----aagagtattaatttaaaaattt Gorilla > Chimp --------------- chr8:31371635-31371644 Template switch process: F1: L TTTTTTTCATACACATATGCACACACATATATGAAACAGTTATGTTGTCTTATTGCACAACAAAAATCAT 1 F3: 4 AGAGTATT R RF: GATTTTTTTCATACACATATGCACACACATATATGAAACAGTTGTGTTGTATTATTGCACAACAAAAATCATAAAATCAAAGAAGAGTATT RR: CTAAAAAAAGTATGTGTATACGTGTGTGTATATACTTTGTCAACACAACATAATAACGTGTTGTTTTTAGTATTTTAGTTTCTTCTCATAA F2: 3 CTAAAAAAAG 2 Unidirectional alignment (log-probability: -37.7) ATGAAACAGTTaTGTTGTcTTATTGCACAACAAAAATCATgaaaAAAATC-----AGAGTATT ATGAAACAGTTGTGTTGTATTATTGCACAACAAAAATCAT----AAAATCAAAGAAGAGTATT Template switch alignment (log-probability: -28) ATGAAACAGTTaTGTTGTcTTATTGCACAACAAAAATCAT|GAAAAAAATC|AGAGTATT ATGAAACAGTTGTGTTGTATTATTGCACAACAAAAATCAT|GAAAAAAATC|AGAGTATT ========== Event 3504 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTTCCTCTGATCAGAAAGATCTGGGGGTGCTGGCACACCC-----AGACGACTAGTAACTCCCAAAGGGA Chimp: GTTTCTTCTGATCAGAAAGATCTgggggggCTGGCACACCC-----AGATGACTGGTAACTCCCAAAGGGA ↑ 3 2 1 4 Gorilla: GTTTCTTCTGATCAGAAAGATCTGGGGGTGCTGGCACAGGAGGGATTGACGACTGGTAACTCCCAAAGGGA Human: GTTTCCTCTGATCAGAAAGATCTGGGGGTGCTGGCACACCC-----AGACGACTAGTAACTCCCAAAGGGA Cluster: [ ] Orangutan: GCTTCTTCAGATCAGAAAGANNNNNNNNNNNNNNNNNNNNN-----NNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr8:10888150-10888156 Template switch process: F1: L CTGGTTTCTTCTGATCAGAAAGATCTGGGGGGGCTGGCACA 1 F3: 4 GACTGGTAACTCCCAAAGGGAGAGGTGCAGCTTTGTCACT R RF: CTGGTTTCTTCTGATCAGAAAGATCTGGGGGTGCTGGCACAGGAGGGATTGACGACTGGTAACTCCCAAAGGGAGAGGTGCAGCTTTGTC RR: GACCAAAGAAGACTAGTCTTTCTAGACCCCCACGACCGTGTCCTCCCTAACTGCTGACCATTGAGGGTTTCCCTCTCCACGTCGAAACAG F2: 3 TAGACCC 2 Unidirectional alignment (log-probability: -46.4) TGGTTTCTTCTGATCAGAAAGATCTGGGGGgGCTGGCAC-----------ACccagatGACTGGTAACTCCCAAAGGGAGAGGTGCAGCTTTGTCaCt TGGTTTCTTCTGATCAGAAAGATCTGGGGGTGCTGGCACAGGAGGGATTGAC------GACTGGTAACTCCCAAAGGGAGAGGTGCAGCTTTGTCTCC Template switch alignment (log-probability: -33.1) TGGTTTCTTCTGATCAGAAAGATCTGGGGGgGCTGGCACA|CCCAGAT|GACTGGTAACTCCCAAAGGGAGAGGTGCAGCTTTGTcact TGGTTTCTTCTGATCAGAAAGATCTGGGGGTGCTGGCACA|CCCAGAT|GACTGGTAACTCCCAAAGGGAGAGGTGCAGCTTTGT---C ========== Event 3505 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AATGTACTTATATTCTGTTAT---ATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATG Chimp: AATGTACTTATATTCTGTTAT---ATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATG ↓ 1 3 4 2 ↑ 1 3 4 2 Gorilla: AATGTACTTATATTCTGTTAT------AAGCTCTTTCAACAAAGAGCTCTATATTTCAAAATAATTCTATG ↓ 1 3 4 2 ↑ 1 3 4 2 Human: AATGTACTTATATTCTGTTAT---ATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATG Cluster: [ ] Orangutan: AATGTACTTATATTCTGTTATATA---GAGCTCTTTGTTGAAAGAGCTCTATATTTCAAA----ATCTATG Gorilla > Human --------------- chr8:29683908-29683922 Template switch process: F1: L TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA 1 F3: 4 AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG R RF: TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATAAGCTCTTTCAACAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG RR: AAACCTTTCGTCCTAGAAAATTACATGAATATAAGACAATATTCGAGAAAGTTGTTTCTCGAGATATAAAGTTTTATTAAGATACTTAAAGTAC F2: 3 GTTGTTTCTCGAGAT 2 Unidirectional alignment (log-probability: -37.5) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATAtagAGCTCTTTgttgAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA---AGCTCTTTCAACAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG Template switch alignment (log-probability: -17.7) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|TAGAGCTCTTTGTTG|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|TAGAGCTCTTTGTTG|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG Human > Gorilla --------------- chr8:30105060-30105071 Template switch process: F1: L TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA 1 F3: 4 AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG R RF: TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG RR: AAACCTTTCGTCCTAGAAAATTACATGAATATAAGACAATATATCTCGAGAAACAACTTTCTCGAGATATAAAGTTTTATTAAGATACTTAAAGTAC F2: 3 CAACTTTCTCGA 2 Unidirectional alignment (log-probability: -33.3) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA---AGCTCTTTcaacAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG Template switch alignment (log-probability: -17.3) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|AGCTCTTTCAAC|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|AGCTCTTTCAAC|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG Gorilla > Chimp --------------- chr8:30266173-30266187 Template switch process: F1: L TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA 1 F3: 4 AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTAATG R RF: TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATAAGCTCTTTCAACAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG RR: AAACCTTTCGTCCTAGAAAATTACATGAATATAAGACAATATTCGAGAAAGTTGTTTCTCGAGATATAAAGTTTTATTAAGATACTTAAAGTAC F2: 3 GTTGTTTCTCGAGAT 2 Unidirectional alignment (log-probability: -43) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATAtagAGCTCTTTgttgAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTaATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA---AGCTCTTTCAACAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG Template switch alignment (log-probability: -23.2) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|TAGAGCTCTTTGTTG|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTaATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|TAGAGCTCTTTGTTG|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG Chimp > Gorilla --------------- chr8:30105060-30105071 Template switch process: F1: L TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA 1 F3: 4 AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTCATG R RF: TTTGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTAATG RR: AAACCTTTCGTCCTAGAAAATTACATGAATATAAGACAATATATCTCGAGAAACAACTTTCTCGAGATATAAAGTTTTATTAAGATACTTAAATTAC F2: 3 CAACTTTCTCGA 2 Unidirectional alignment (log-probability: -38.8) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA---AGCTCTTTcaacAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTcATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATATAGAGCTCTTTGTTGAAAGAGCTCTATATTTCAAAATAATTCTATGAATTTAATG Template switch alignment (log-probability: -22.8) TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|AGCTCTTTCAAC|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTcATG TGGAAAGCAGGATCTTTTAATGTACTTATATTCTGTTATA|AGCTCTTTCAAC|AAAGAGCTCTATATTTCAAAATAATTCTATGAATTTAATG ========== Event 3506 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CACTAATAAACTACACTATTGCACTAGTGCAATACAATCTATTTCTCAAAAA ↑ 3 2 1 4 Chimp: CACTAATAAACTACACTATTGCACTAGAA-TATACAATCTATTTCTCAAAAA Gorilla: CACTAATAAACTACACTATTGCACTAGAA-TATACAATCTATTCCTCAAAAA Human: CACTAATAAACTACACTATTGCACTAGTGCAATACAATCTATTTCTCAAAAA Cluster: [ ] Orangutan: CACTAATAAATGACAATATTGCACTAGAA-TATACAATCTATTTCTCAAAAA Chimp > Human ------------- chr8:27880535-27880538 Template switch process: F1: L TTAAACTCCCTGCACACTAATAAACTACACTATTGCACTAG 1 F3: 4 ATACAATCTATTTCTCAAAAATTGTCTGTTAGTTGAATGT R RF: TTAAACTCCCTGCACACTAATAAACTACACTATTGCACTAGAATATACAATCTATTTCTCAAAAATTGTCTGTTAGTTGAATGT RR: AATTTGAGGGACGTGTGATTATTTGATGTGATAACGTGATCTTATATGTTAGATAAAGAGTTTTTAACAGACAATCAACTTACA F2: 3 ACGT 2 Unidirectional alignment (log-probability: -25.6) TAAACTCCCTGCACACTAATAAACTACACTATTGCACTAGtgcA--ATACAATCTATTTCTCAAAAATTGTCTGTTAGTTGAATGT TAAACTCCCTGCACACTAATAAACTACACTATTGCACTAG---AATATACAATCTATTTCTCAAAAATTGTCTGTTAGTTGAATGT Template switch alignment (log-probability: -15.8) TAAACTCCCTGCACACTAATAAACTACACTATTGCACTAG|TGCA|ATACAATCTATTTCTCAAAAATTGTCTGTTAGTTGAATGT TAAACTCCCTGCACACTAATAAACTACACTATTGCACTAG|TGCA|ATACAATCTATTTCTCAAAAATTGTCTGTTAGTTGAATGT ========== Event 3507 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAATTTGTTTGTTTTTCAACTTGGCATCATAATGAAGCAGAGATGTCAGCATAGCATTTCTTAGTGCTG ↓ 3 2 1 4 Chimp: CAAATTTGTTTGTTTTTCAACTTGGCATCATAATG---CCAA-----GTGCATAGCATTTCTTAGTGCTG ↑ 3 2 1 4 Gorilla: CAAATTTGTTTGTTTTTCAACTTGGCATCATAATGAAGCACAGATGTCAGCATAGCATTTCTTAGTGCTG Human: CAAATTTGTTTGTTTTTCAACTTGGCATCATAATGAAGCAGAGATGTCAGCATAGCATTTCTTAGTGCTG Cluster: [ ] Orangutan: CAAA--TGTTTGTTTTTCAACTTGGCATCATCATGAAGCAGAGATGTCAGGATAGCATTTCTTAGTGCTG Human > Chimp ------------- chr8:27314158-27314163 Template switch process: F1: L AGAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG 1 F3: 4 GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT R RF: AGAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATGAAGCAGAGATGTCAGCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT RR: TCTTTAGTTTAAACAAACAAAAAGTTGAACCGTAGTATTACTTCGTCTCTACAGTCGTATCGTAAAGAATCACGACGGTTATAGAACTCATTAGA F2: 3 TGAACC 2 Unidirectional alignment (log-probability: -30.5) GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATGccaagt--------------GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG------AAGCAGAGATGTCAGCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT Template switch alignment (log-probability: -16) GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG|CCAAGT|GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG|CCAAGT|GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT Gorilla > Chimp --------------- chr8:27314158-27314163 Template switch process: F1: L AGAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG 1 F3: 4 GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT R RF: AGAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATGAAGCACAGATGTCAGCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT RR: TCTTTAGTTTAAACAAACAAAAAGTTGAACCGTAGTATTACTTCGTGTCTACAGTCGTATCGTAAAGAATCACGACGGTTATAGAACTCATTAGA F2: 3 TGAACC 2 Unidirectional alignment (log-probability: -29.6) GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATGccAAG----------tGCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG--AAGCACAGATGTCAGCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT Template switch alignment (log-probability: -16.5) GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG|CCAAGT|GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT GAAATCAAATTTGTTTGTTTTTCAACTTGGCATCATAATG|CCAAGT|GCATAGCATTTCTTAGTGCTGCCAATATCTTGAGTAATCT ========== Event 3508 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTATAAATAAAAATACTCTGATCTGATGCAGATATTACAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTAGTAAATTT Chimp: CTATAAATAAAAATACTCTGATCTGATGCAGATATTACAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTAGTAAATTT ↑ 1 4 3 2 Gorilla: CTATAAATAAAAATACTCTGACC-------------TCAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTAGTAAATTT ↓ 1 4 3 2 Human: CTATAAATAAAAATACTCTGATCTGATGCAGATATTACAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTAGTAAATTT Cluster: [ ] Orangutan: CTATAAATAAAAATACTCTGACC-------------TCAGAGCATTCTGTAATAGCTGCATCAGAAGTGCCTAATTAGTAAATTT Gorilla > Human --------------- chr8:24870225-24870240 Template switch process: F1: L GGAATAATATCCATACTCAGCTATAAATAAAAATACTCTGA 1 F3: 4 CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA R RF: GGAATAATATCCATACTCAGCTATAAATAAAAATACTCTGACCTCAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA RR: CCTTATTATAGGTATGAGTCGATATTTATTTTTATGAGACTGGAGTCTCGTAAGACATTATAGACGTAGTCTTCACGGATTAAT F2: 3 ATTATAGACGTAGTCT 2 Unidirectional alignment (log-probability: -35.1) GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGAtCTgatgcagatattaCAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGACCT-------------CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA Template switch alignment (log-probability: -17.8) GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGA|TCTGATGCAGATATTA|CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGA|TCTGATGCAGATATTA|CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA Gorilla > Chimp --------------- chr8:25387481-25387496 Template switch process: F1: L GGAATAATATCCATACTCAGCTATAAATAAAAATACTCTGA 1 F3: 4 CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA R RF: GGAATAATATCCATACTCAGCTATAAATAAAAATACTCTGACCTCAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA RR: CCTTATTATAGGTATGAGTCGATATTTATTTTTATGAGACTGGAGTCTCGTAAGACATTATAGACGTAGTCTTCACGGATTAAT F2: 3 ATTATAGACGTAGTCT 2 Unidirectional alignment (log-probability: -35.1) GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGAtCTgatgcagatattaCAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGACCT-------------CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA Template switch alignment (log-probability: -17.8) GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGA|TCTGATGCAGATATTA|CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA GAATAATATCCATACTCAGCTATAAATAAAAATACTCTGA|TCTGATGCAGATATTA|CAGAGCATTCTGTAATATCTGCATCAGAAGTGCCTAATTA ========== Event 3509 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTCTCATGACGACCTAGGCTATGCTCACTGTATAACAGTAGAATTTGTTTCTAC---------------- Chimp: TCTCTCATGACGACCTAGGCTATGCTTACTGTATAACAGTAGAATTTGTTTCTAC---------------- ↑ 3 4 2 1 Gorilla: TCTCTCATGACGACCTAGGCTGTGCTCACTGTATAACAGTAGAATTTGTTTTTCT---------------- Human: TCTCTCATGACGACCTAGGCTATGCTCACTGTATAACAGTAGAATTTGTTTCTAC---------------- Cluster: [ ] Orangutan: TCTCTCAAGATGATTTAGGCTATGCTCACTGTATAACAGGAGAATTTGTTTCTACTGTTAGAATTTATTTT Gorilla > Chimp --------------- chr8:25775038-25775044 Template switch process: F1: L GCGTCAAGGCCTGCTAATCCTCTCTCATGACGACCTAGGCTATGCTTACTGTATAACAGTAGAATTTGTTT 1 F3: 4 TAGAATTTA R RF: GTGTCAAGGCCTGCTAATCCTCTCTCATGACGACCTAGGCTGTGCTCACTGTATAACAGTAGAATTTGTTT RR: CACAGTTCCGGACGATTAGGAGAGAGTACTGCTGGATCCGACACGAGTGACATATTGTCATCTTAAACAAA F2: 3 TGTCATC 2 Unidirectional alignment (log-probability: -54.3) GACCTAGGCTaTGCTtACTGTATAACAGTAGAATTTG--TTTCTactgttagaattta GACCTAGGCTGTGCTCACTGTATAACAGTAGAATTTGTTTTTCT-------------- Template switch alignment (log-probability: -38.7) GACCTAGGCTaTGCTtACTGTATAACAGTAGAATTTGTTT|CTACTGT|TAGAATTTa GACCTAGGCTGTGCTCACTGTATAACAGTAGAATTTGTTT|CTACTGT|TAGAATTTG ========== Event 3510 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: aa--aaaaaa----------gaaaagTTAAATG--------------------------------GCAAGttcattgggattgcattaa Chimp: ----------gaaaaaaaaagaaaagTTAAATG--------------------------------GCAAGttcattgggattgcattaa ↑ 1 3 2 4 Gorilla: aaaaaaaaaa----------gaaaaGTTAAATGTTGCCATTTAACTTTTTTAAGTTAAATGCCATTTAAGttcattgggattgcattaa ↓ 1 3 2 4 Human: aa--aaaaaa----------gaaaagTTAAATG--------------------------------GCAAGttcattgggattgcattaa Cluster: [ ] Orangutan: agaaaaaaag----------gaaaGGTTAAATG--------------------------------GCAAGttcattggggttgcattaa Gorilla > Human --------------- chr8:24531263-24531276 Template switch process: F1: L GACACAAAAAAGAAAAGAAAAAAAAAGA 1 F3: 4 AGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG R RF: GACACAAAAAAGAAAAGAAAAAAAAAAAGAAAAGTTAAATGTTGCCATTTAACTTTTTTAAGTTAAATGCCATTTAAGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG RR: CTGTGTTTTTTCTTTTCTTTTTTTTTTTCTTTTCAATTTACAACGGTAAATTGAAAAAATTCAATTTACGGTAAATTCAAGTAACCCTAACGTAATTTAAATATCTAATTACATC F2: 3 ACGGTAAATTGAAA 2 Unidirectional alignment (log-probability: -32.1) GACACAAAAAAGAAAAGAAAAAAA--AAGAAAAGTTAAATG---------------------------GC-----AAGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG GACACAAAAAAGAAAAGAAAAAAAAAAAGAAAAGTTAAATGTTGCCATTTAACTTTTTTAAGTTAAATGCCATTTAAGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG Template switch alignment (log-probability: -22.7) GACACAAAAAAGAAAAGAAAAAAAAAgA|AAAGTTAAATGGCA|AGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG GACACAAAAAAGAAAAGAAAAAAAAAAA|AAAGTTAAATGGCA|AGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG Gorilla > Chimp --------------- chr8:25052393-25052406 Template switch process: F1: L AGAAAAGAAAAAAAAAGA 1 F3: 4 AGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG R RF: AGAAAAGAAAAAAAAAAAGAAAAGTTAAATGTTGCCATTTAACTTTTTTAAGTTAAATGCCATTTAAGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG RR: TCTTTTCTTTTTTTTTTTCTTTTCAATTTACAACGGTAAATTGAAAAAATTCAATTTACGGTAAATTCAAGTAACCCTAACGTAATTTAAATATCTAATTACATC F2: 3 ACGGTAAATTGAAA 2 Unidirectional alignment (log-probability: -32) AGAAAAGAAAAAAAA--AGAAAAGTTAAATG---------------------------GC-----AAGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG AGAAAAGAAAAAAAAAAAGAAAAGTTAAATGTTGCCATTTAACTTTTTTAAGTTAAATGCCATTTAAGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG Template switch alignment (log-probability: -22.4) AGAAAAGAAAAAAAAAgA|AAAGTTAAATGGCA|AGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG AGAAAAGAAAAAAAAAAA|AAAGTTAAATGGCA|AGTTCATTGGGATTGCATTAAATTTATAGATTAATGTAG ========== Event 3511 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGACACTTAAAAGTAGGATTAAAAGCA-------GTAGGAGGCGTGGCCTTTGAAATAT Chimp: GTGACACTTAAAAGTAGGATTAAAAGCA-------GTAGGAGGCGTGGCCTTTGAAATAT ↓ 3 1 2 4 Gorilla: GTGACACTTAAAAGTAGGATTAAAAGCTACTGCTTTTCAAAGGCGTGGCCTTTGAAATAT Human: GTGACACTTAAAAGTAGGATTAAAAGCA-------GTAGGAGGCGTGGCCTTTGAAATAT Cluster: [ ] Orangutan: GTGACTCTTAAAAGTAGGATTAAAAGCA-------GTAAGAGGCGTGGCCTTTGAAATAT Chimp > Gorilla --------------- chr8:24022945-24022956 Template switch process: F1: L ATTTTGAGAAGTTTGTGACACTTAAAAGTAGGATTAAAAGC 1 F3: 4 AAGGCGTGGCCTTTGAAATATTTGAAACTGTTGACAGCTAT R RF: ATTTTGAGAAGTTTGTGACACTTAAAAGTAGGATTAAAAGCAGTAGGAGGCGTGGCCTTTGAAATATTTGAAACTGTTGACAGCTAT RR: TAAAACTCTTCAAACACTGTGAATTTTCATCCTAATTTTCGTCATCCTCCGCACCGGAAACTTTATAAACTTTGACAACTGTCGATA F2: 3 ACTTTTCGTCAT 2 Unidirectional alignment (log-probability: -38.2) TTTTGAGAAGTTTGTGACACTTAAAAGTAGGATTAAAAGCtactgcttttcaA-----AGGCGTGGCCTTTGAAATATTTGAAACTGTTGACAGCTA TTTTGAGAAGTTTGTGACACTTAAAAGTAGGATTAAAAGC------------AGTAGGAGGCGTGGCCTTTGAAATATTTGAAACTGTTGACAGCTA Template switch alignment (log-probability: -28.3) TTTTGAGAAGTTTGTGACACTTAAAAGTAGGATTAAAAGC|TACTGCTTTTcA|aAGGCGTGGCCTTTGAAATATTTGAAACTGTTGACAGCTA TTTTGAGAAGTTTGTGACACTTAAAAGTAGGATTAAAAGC|TACTGCTTTTAA|GAGGCGTGGCCTTTGAAATATTTGAAACTGTTGACAGCTA ========== Event 3512 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTTGGACTGTCTGTGGCACCAATGTAGCTCTGGACCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGG ↑ 1 4 3 2 Chimp: CTTGGACTGTCTGTGGCACCATTGTAGC----ATCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGG Gorilla: CTTGGACTGTCTGTGGCACCATTGTAGC----ATCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGG ↓ 1 4 3 2 Human: CTTGGACTGTCTGTGGCACCAATGTAGCTCTGGACCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGG Cluster: [ ] Orangutan: CTTGGACTGTCTGTAGCACCGTTGTAGC----ATCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGG Chimp > Human ------------- chr8:21927816-21927821 Template switch process: F1: L CAGGGAGGACTGACTGTGCCCTTGGACTGTCTGTGGCACCAATGTAGC 1 F3: 4 CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT R RF: CAGGGAGGACTGACTGTGCCCTTGGACTGTCTGTGGCACCATTGTAGCATCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT RR: GTCCCTCCTGACTGACACGGGAACCTGACAGACACCGTGGTAACATCGTAGGACACCCAGGTCTCTCTATGGAAACCAGAGACCCGAGAA F2: 3 AGGTCT 2 Unidirectional alignment (log-probability: -34.4) ACTGACTGTGCCCTTGGACTGTCTGTGGCACCAaTGTAGC-TctggaCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT ACTGACTGTGCCCTTGGACTGTCTGTGGCACCATTGTAGCAT-----CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT Template switch alignment (log-probability: -22.2) ACTGACTGTGCCCTTGGACTGTCTGTGGCACCAaTGTAGC|TCTGGA|CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT ACTGACTGTGCCCTTGGACTGTCTGTGGCACCATTGTAGC|TCTGGA|CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT Gorilla > Human --------------- chr8:21927816-21927821 Template switch process: F1: L CAGGGAGGACTGACTGTGCCCTTGGACTGTCTGTGGCACCAATGTAGC 1 F3: 4 CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT R RF: CAGAGAGGACTGACTGTGCCCTTGGACTGTCTGTGGCACCATTGTAGCATCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT RR: GTCTCTCCTGACTGACACGGGAACCTGACAGACACCGTGGTAACATCGTAGGACACCCAGGTCTCTCTATGGAAACCAGAGACCCGAGAA F2: 3 AGGTCT 2 Unidirectional alignment (log-probability: -38.8) ACTGACTGTGCCCTTGGACTGTCTGTGGCACCAaTGTAGCtctggaCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT ACTGACTGTGCCCTTGGACTGTCTGTGGCACCATTGTAGC----ATCCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT Template switch alignment (log-probability: -27.7) ACTGACTGTGCCCTTGGACTGTCTGTGGCACCAaTGTAGC|TCTGGA|CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT ACTGACTGTGCCCTTGGACTGTCTGTGGCACCATTGTAGC|TCTGGA|CCTGTGGGTCCAGAGAGATACCTTTGGTCTCTGGGCTCTT ========== Event 3513 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGACAGATGAAGTAATGAATGGGCACAGTCCTGCCTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACTGTCTCAGTTTCCGGAGGGGAggctgctgattcaatgac----cacaaacttgatagc Chimp: AAGACAGATGAAGTAATGAATGGGCACAGTCCTGCCTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACtgtctcagtttccggaggggaggctgctgattcaatgac----cacaaacttgatagc Gorilla: AAGACAGATGAAGTAATGAATGGGCACAGTCCTGCCTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACTGTCTCGGTTTCCAGAGGGGAGGCTGCTGATTCAATGAT--------Gacttgatggc ↑ 4 3 2 1 Human: AAGACAGATGAAGTAATGAATGGGCACAGTCCTGCCTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACTGTCTCAGTTTCCGGAGGGGAggctgctgattcaatgac----cacaaacttgatagc Cluster: [ ] Orangutan: AAGACAGATGAAGTAATGAATGGGCACAGTCCTGCCTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACTGTCTCAGTTTCCGGAGGGGAggctgctgattcaatgaccaca----aacttgatggc Human > Gorilla --------------- chr8:125085145-125085146 Template switch process: F1: L CTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACTGTCTCGGTTTCCAGAGGGGAGGCTGCTGATTCAATGA 1 F3: 4 ACTTGATGGC R RF: CTGCCTGAGCAAGTCACTGCTTCCCACTTGTTCACTGTCTCAGTTTCCGGAGGGGAGGCTGCTGATTCAATGACCACAAACTTGATAGCTTAAAACAACAGCAGTCTATTCCTGCACAGCTCTGGAGGGTGGAAGTCTGAAATCCTGGTGTCGGCAGGCCCACAGTCCCTCCAGCAGCCCCGGGGCA RR: GACGGACTCGTTCAGTGACGAAGGGTGAACAAGTGACAGAGTCAAAGGCCTCCCCTCCGACGACTAAGTTACTGGTGTTTGAACTATCGAATTTTGTTGTCGTCAGATAAGGACGTGTCGAGACCTCCCACCTTCAGACTTTAGGACCACAGCCGTCCGGGTGTCAGGGAGGTCGTCGGGGCCCCGT F2: 3 GT 2 Unidirectional alignment (log-probability: -38.7) ACTGTCTCgGTTTCCaGAGGGGAGGCTGCTGATTCAATGA----tgACTTGATgGC ACTGTCTCAGTTTCCGGAGGGGAGGCTGCTGATTCAATGACCACAAACTTGATAGC Template switch alignment (log-probability: -32.6) ACTGTCTCgGTTTCCaGAGGGGAGGCTGCTGATTCAATGA|TG|ACTTGATgGC ACTGTCTCAGTTTCCGGAGGGGAGGCTGCTGATTCAATGA|TG|ACTTGATAGC ========== Event 3514 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: taaagggaatgCCAGAGTGAT-TTTCAGAAA---------------ACTTATACCAATTTCTATTATCAGCTG Chimp: taaagggaatgCCAGAGTGAT-TATCAGAGTGATTTTCAGTGATTTTCTGAAACCAATTTCTATTATCAGCTG ↓ 1 3 4 2 Gorilla: taaagggaatgCCAGAGTGATTTTTCAGAAA---------------ACTTATACCAATTTCTATTATCAGCTG Human: taaagggaatgCCAGAGTGAT-TTTCAGAAA---------------ACTTATACCAATTTCTATTATCAGCTG Cluster: [ ] Orangutan: taaagggaatgCCAGAGTGAT-TTTCAGAAA---------------ACTTATACCAATTTCTATTATCAGCTG Chimp > Gorilla --------------- chr8:124971612-124971621 Template switch process: F1: L TTGAAGTGGAATTATTGGGTTAAAGGGAATGCCAGAGTGATT 1 F3: 4 CTTATACCAATTTCTATTATCAGCTGGTTTTTATAAAGCATGGGA R RF: TTGAAGTGGAATTATTGGGTTAAAGGGAATGCCAGAGTGATTATCAGAGTGATTTTCAGTGATTTTCTGAAACCAATTTCTATTATCAGCTGGTTTTTATAAAGCATGGGA RR: AACTTCACCTTAATAACCCAATTTCCCTTACGGTCTCACTAATAGTCTCACTAAAAGTCACTAAAAGACTTTGGTTAAAGATAATAGTCGACCAAAAATATTTCGTACCCT F2: 3 AAAAGACTTT 2 Unidirectional alignment (log-probability: -37.4) GAAGTGGAATTATTGGGTTAAAGGGAATGCCAGAGTGAT---------------------TTTTCaGAAaacttatACCAATTTCTATTATCAGCTGGTTTTTATAAAGCA GAAGTGGAATTATTGGGTTAAAGGGAATGCCAGAGTGATTATCAGAGTGATTTTCAGTGATTTTCTGAA-------ACCAATTTCTATTATCAGCTGGTTTTTATAAAGCA Template switch alignment (log-probability: -28.2) GAAGTGGAATTATTGGGTTAAAGGGAATGCCAGAGTGATT|TTTCAGAAAA|CTtAtACCAATTTCTATTATCAGCTGGTTTTTATAAAGCA GAAGTGGAATTATTGGGTTAAAGGGAATGCCAGAGTGATT|TTTCAGAAAA|CTGAAACCAATTTCTATTATCAGCTGGTTTTTATAAAGCA ========== Event 3515 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGCCAAGTTTTCTATTTCTGTCGTTATTGATTACTACTAAATAAAGACAGAAGTAGTAATGTTAAGCTTTTTACAGCATAAT Chimp: ATGCCAAGTTTTCTATTTCTGTCTTTATTGATTACTACTAAATAAAGACAGAAGTAGTAATCTTAAGCTTTTTACAGCATAAT Gorilla: ATGCCAAGTTTTCTATTTCTGCCTTTATT----------------------TAGTAGTAATCTTAAGCTTTTTACAGCATAAT ↑ 1 3 2 4 Human: ATGCCAAGTTTTCTATTTCTGTCGTTATTGATTACTACTAAATAAAGACAGAAGTAGTAATGTTAAGCTTTTTACAGCATAAT Cluster: [ ] Orangutan: ATGCCAAGTTTTCTATTTCTGTCTTTATT----------------------TAGTAGTAGTCTTAAGCTTTTTACAGCATAAT Human > Gorilla --------------- chr8:21223915-21223931 Template switch process: F1: L TAATTGCAGTCATCTGCTAGATGCCAAGTTTTCTATTTCTGCC 1 F3: 4 TTAAGCTTTTTACAGCATAATTATCAACTAAATAGCAATT R RF: TAATTGCAGTCATCTGCTAGATGCCAAGTTTTCTATTTCTGTCGTTATTGATTACTACTAAATAAAGACAGAAGTAGTAATGTTAAGCTTTTTACAGCATAATTATCAACTAAATAGCAATT RR: ATTAACGTCAGTAGACGATCTACGGTTCAAAAGATAAAGACAGCAATAACTAATGATGATTTATTTCTGTCTTCATCATTACAATTCGAAAAATGTCGTATTAATAGTTGATTTATCGTTAA F2: 3 CTAATGATGATTTATTT 2 Unidirectional alignment (log-probability: -34.4) TTGCAGTCATCTGCTAGATGCCAAGTTTTCTATTTCTGcCtTTATT----------------------tAGTAGTAATcTTAAGCTTTTTACAGCATAATTATCAACTAAATAGCAATT TTGCAGTCATCTGCTAGATGCCAAGTTTTCTATTTCTGTCGTTATTGATTACTACTAAATAAAGACAGAAGTAGTAATGTTAAGCTTTTTACAGCATAATTATCAACTAAATAGCAATT Template switch alignment (log-probability: -23.5) TTGCAGTCATCTGCTAGATGCCAAGTTTTCTATTTCTGcC|TTTATTTAGTAGTAATC|TTAAGCTTTTTACAGCATAATTATCAACTAAATAGCAATT TTGCAGTCATCTGCTAGATGCCAAGTTTTCTATTTCTGTC|TTTATTTAGTAGTAATC|TTAAGCTTTTTACAGCATAATTATCAACTAAATAGCAATT ========== Event 3516 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGACTGGAGTGGAGGCGAGGCACTCACACATCTTGGGTTG---------TTAGCCCACCCTGCAATGAATTT Chimp: AGACTGGAGTGGAGGCCTGGCACTCACACATCTTGGGTTGTGTGTGAGTGCAGCCCACCCTGCACTGAATTT ↑ 3 2 1 4 Gorilla: AGACTGGAGTGGAGGCGGGGCACTCACACATCTTGGGTTG---------TTAGCCCACCCTGCACTGAATTT Human: AGACTGGAGTGGAGGCGAGGCACTCACACATCTTGGGTTG---------TTAGCCCACCCTGCAATGAATTT Cluster: [ ] Orangutan: AGACTGGAGTGGAGGCCTGGCA-------------------------------------------------- Gorilla > Chimp --------------- chr8:20961705-20961714 Template switch process: F1: L AAGACTGGAGTGGAGGCCTGGCACTCACACATCTTGGGTTGT 1 F3: 4 AGCCCACCCTGCACTGAATTTAGGTTATTAAAATCTACAC R RF: AAGACTGGAGTGGAGGCGGGGCACTCACACATCTTGGGTTGTTAGCCCACCCTGCACTGAATTTAGGTTATTAAAATCTACAC RR: TTCTGACCTCACCTCCGCCCCGTGAGTGTGTAGAACCCAACAATCGGGTGGGACGTGACTTAAATCCAATAATTTTAGATGTG F2: 3 CGTGAGTGTG 2 Unidirectional alignment (log-probability: -40.4) GACTGGAGTGGAGGCctGGCACTCACACATCTTGGGTTGTgtgtgagtgcAGCCCACCCTGCACTGAATTTAGGTTATTAAAATCTACAC GACTGGAGTGGAGGCGGGGCACTCACACATCTTGGGTTGT---------TAGCCCACCCTGCACTGAATTTAGGTTATTAAAATCTACAC Template switch alignment (log-probability: -28.1) GACTGGAGTGGAGGCctGGCACTCACACATCTTGGGTTGT|GTGTGAGTGC|AGCCCACCCTGCACTGAATTTAGGTTATTAAAATCTACAC GACTGGAGTGGAGGCGGGGCACTCACACATCTTGGGTTGT|GTGTGAGTGC|AGCCCACCCTGCACTGAATTTAGGTTATTAAAATCTACAC ========== Event 3517 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ccagcagataagggggactactATGCTTTTTAAAAAGC----------------------------------------------------------------ATAGTAGTATAACcattcattcaaca ↑ 3 2 1 4 Chimp: ccagcagataagggggactactATGCTTTTTAAAATTC--------------------------------TGTATTTGATTTAACGTATTTATTTCTCCTTTCAAGCAGTATAACCATTCATTCAACA Gorilla: ccagcagataaaggggactactATGCTTTTTAAAATTCTGTATTTGATTTAACGTATTTATTTCTCCTTT--------------------------------CAAGCAGTATAACCATTCATTCAACA ↓ 3 2 1 4 Human: ccagcagataagggggactactATGCTTTTTAAAAAGC----------------------------------------------------------------ATAGTAGTATAACcattcattcaaca Cluster: [ ] Orangutan: ccagcagataagggggactactgTGCTTCTTAAAATTCTGTATTTGATTTAATGTATTTATTTCTTCTTT--------------------------------CAAGCAGTATAACcattcattcaaca Chimp > Human ------------- chr8:124982784-124982791 Template switch process: F1: L GTGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAAA 1 F3: 4 AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA R RF: GTGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAAATTCTGTATTTGATTTAACGTATTTATTTCTCCTTTCAAGCAGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA RR: CACAGGGGTCGTCTATTCCCCCTGATGATACGAAAAATTTTAAGACATAAACTAAATTGCATAAATAAAGAGGAAAGTTCGTCATATTGGTAAGTAAGTTGTTTTTAAATAAACTACGGAT F2: 3 TGATACGA 2 Unidirectional alignment (log-probability: -30.2) TGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAA-------------------------------------AAGCatagtAGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA TGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAAATTCTGTATTTGATTTAACGTATTTATTTCTCCTTTCAAGC-----AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA Template switch alignment (log-probability: -16.3) TGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAAA|AGCATAGT|AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA TGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAAA|AGCATAGT|AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA Gorilla > Human --------------- chr8:124982784-124982791 Template switch process: F1: L GTGTCCCCAGCAGATAAGGGGGACTACTATGCTTTTTAAAA 1 F3: 4 AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA R RF: GTGTCCCCAGCAGATAAAGGGGACTACTATGCTTTTTAAAATTCTGTATTTGATTTAACGTATTTATTTCTCCTTTCAAGCAGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA RR: CACAGGGGTCGTCTATTTCCCCTGATGATACGAAAAATTTTAAGACATAAACTAAATTGCATAAATAAAGAGGAAAGTTCGTCATATTGGTAAGTAAGTTGTTTTTAAATAAACTACGGAT F2: 3 TGATACGA 2 Unidirectional alignment (log-probability: -35.3) TGTCCCCAGCAGATAAgGGGGACTACTATGCTTTTTAAA-------------------------------------AAGCatagtAGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA TGTCCCCAGCAGATAAAGGGGACTACTATGCTTTTTAAAATTCTGTATTTGATTTAACGTATTTATTTCTCCTTTCAAGC-----AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA Template switch alignment (log-probability: -22.3) TGTCCCCAGCAGATAAgGGGGACTACTATGCTTTTTAAAA|AGCATAGT|AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA TGTCCCCAGCAGATAAAGGGGACTACTATGCTTTTTAAAA|AGCATAGT|AGTATAACCATTCATTCAACAAAAATTTATTTGATGCCTA ========== Event 3518 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCATTTTTGTGACTGAATGGATCAAG---------------TTTTGTAACCCTTAAGCCTAACACAGAGTCTGGCATATG Chimp: TCCATTTTTGTGACTGAATGGATCAAGCCTTAAGCCTTGATCCTTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATG ↑ 3 2 4 1 Gorilla: TCCATTTTTGTGACTGAATGGATCAAG---------------TTTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATG Human: TCCATTTTTGTGACTGAATGGATCAAG---------------TTTTGTAACCCTTAAGCCTAACACAGAGTCTGGCATATG Cluster: [ ] Orangutan: TCCATTTTTGTGACTGAATGGATCAAG---------------TTTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATG Gorilla > Chimp --------------- chr8:127408130-127408135 Template switch process: F1: L TTCCAGGATATGGATCCATTTTTGTGACTGAATGGATCAAG---------CCTTAAGCCT 1 F3: 4 TTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATGAA R RF: TTCCAGGATATGGATCCATTTTTGTGACTGAATGGATCAAGTTTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATGAA RR: AAGGTCCTATACCTAGGTAAAAACACTGACTTACCTAGTTCAAAACATTGGGAATTCGGATTGTGTCTCGGACCGTATACTT F2: 3 CCTAGT 2 Unidirectional alignment (log-probability: -38) GGATCCATTTTTGTGACTGAATGGATCAAGccttaagccttgatccTTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATGAA GGATCCATTTTTGTGACTGAATGGATCAAG---------------TTTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATGAA Template switch alignment (log-probability: -26.9) GGATCCATTTTTGTGACTGAATGGATCAAG---------CCTTAAGCCT|TGATCC|TTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATGAA GGATCCATTTTTGTGACTGAATGGATCAAGTTTTGTAACCCTTAAGCCT|TGATCC|TTTGTAACCCTTAAGCCTAACACAGAGCCTGGCATATGAA ========== Event 3519 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: CAAGCGTGCACTTAAGTGCTGATACTGGCTGCCTTAGTATCAGCCTTCTACAAGTCTTTCATCTACT Chimp: ------------------------------------------------------------------- Gorilla: CAAGCGTGCACTTAAGTGCTGATACTGGCTG------------CCTTCTACAAGTCTTTCATCTACT ↓ 3 2 4 1 Human: CAAGCGTGCACTTAAGTGCTGATACTGGCTGCCTTAGTATCAGCCTTCTACAAGTCTTTCATCTACT Cluster: [ ] Orangutan: CAAGCGTGCACTTAAGTGCTGATACTGGCTG------------CCTTCTACAAGTCTTTCATCTACT Gorilla > Human --------------- chr8:20030219-20030225 Template switch process: F1: L GACCCAATAGCAAGCGTGCACTTAAGTGCTGATACTGGCTGCCTT 1 F3: 4 GCCTTCTACAAGTCTTTCATCTACTGTTACAGGCTGATCTA R RF: GACCCAATAGCAAGCGTGCACTTAAGTGCTGATACTGGCTGCCTTCTACAAGTCTTTCATCTACTGTTACAGGCTGATCTA RR: CTGGGTTATCGTTCGCACGTGAATTCACGACTATGACCGACGGAAGATGTTCAGAAAGTAGATGACAATGTCCGACTAGAT F2: 3 ACTATGA 2 Unidirectional alignment (log-probability: -28.1) AATAGCAAGCGTGCACTTAAGTGCTGATACTGGCTgccttagtatcaGCCTTCTACAAGTCTTTCATCTACTGTTACAGGCTGATCT AATAGCAAGCGTGCACTTAAGTGCTGATACTGGCT------------GCCTTCTACAAGTCTTTCATCTACTGTTACAGGCTGATCT Template switch alignment (log-probability: -16.7) AATAGCAAGCGTGCACTTAAGTGCTGATACTGGCTGCCTT|AGTATCA|GCCTTCTACAAGTCTTTCATCTACTGTTACAGGCTGATCT AATAGCAAGCGTGCACTTAAGTGCTGATACTGGCTGCCTT|AGTATCA|GCCTTCTACAAGTCTTTCATCTACTGTTACAGGCTGATCT ========== Event 3520 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTTGGGACTGCCCTCCTTCTTAGCAATTCTATCGATTGCTAAGTCTAGATCATTCTATAGC ↑ 1 4 3 2 Chimp: TCTTGGGACTGCCCTCCTTCTCT--GATTCTATCGATTGCTAAGTCTAGATCATTCTATAGC Gorilla: TCTTGGGACTGCCCTCCTTCTCT--GATTCTATCGATCGCTAAGTCTAGATCATTCTATAGC Human: TCTTGGGACTGCCCTCCTTCTTAGCAATTCTATCGATTGCTAAGTCTAGATCATTCTATAGC Cluster: [ ] Orangutan: TCTTGGGACTGCCCTCCTTCTCT--GATTCTATCGATTACTAAGTCCAGATCATTCTATAGC Chimp > Human ------------- chr8:126499441-126499445 Template switch process: F1: L ATATCCAAAATTTGGAAGCATCTTGGGACTGCCCTCCTTCT 1 F3: 4 ATTCTATCGATTGCTAAGTCTAGATCATTCTATAGCCTAA R RF: ATATCCAAAATTTGGAAGCATCTTGGGACTGCCCTCCTTCTCTGATTCTATCGATTGCTAAGTCTAGATCATTCTATAGCCTAA RR: TATAGGTTTTAAACCTTCGTAGAACCCTGACGGGAGGAAGAGACTAAGATAGCTAACGATTCAGATCTAGTAAGATATCGGATT F2: 3 ACGAT 2 Unidirectional alignment (log-probability: -25.8) TATCCAAAATTTGGAAGCATCTTGGGACTGCCCTCCTTCTtaGcaATTCTATCGATTGCTAAGTCTAGATCATTCTATAGCCTAA TATCCAAAATTTGGAAGCATCTTGGGACTGCCCTCCTTCTCTG--ATTCTATCGATTGCTAAGTCTAGATCATTCTATAGCCTAA Template switch alignment (log-probability: -15.9) TATCCAAAATTTGGAAGCATCTTGGGACTGCCCTCCTTCT|TAGCA|ATTCTATCGATTGCTAAGTCTAGATCATTCTATAGCCTAA TATCCAAAATTTGGAAGCATCTTGGGACTGCCCTCCTTCT|TAGCA|ATTCTATCGATTGCTAAGTCTAGATCATTCTATAGCCTAA ========== Event 3521 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAAAGCACTAATGTGAGATCAAAATCATGTG Chimp: GTTACCTTTGTTCCTTGCTCTGAAACTGCCCTCTGCAAAGCACTAATGTGAGATCAATATCATGTG Gorilla: GGTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAA-TTTCAGATGTGAGATCAAAATCATGTG ↑ 3 2 1 4 Human: GTTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAAAGCACTAATGTGAGATCAAAATCATGTG Cluster: [ ] Orangutan: GGTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAAAGCACTAATGTGAGATCAAAATCATGTG Human > Gorilla --------------- chr8:16314767-16314772 Template switch process: F1: L AAAGGTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAA 1 F3: 4 ATGTGAGATCAAAATCATGTGCATGGAGGATCTGGAAGCA R RF: AAAGTTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAAAGCACTAATGTGAGATCAAAATCATGTGCATGGAGGATCTGGAAGCA RR: TTTCAATGGAAACAAGGAACGAGACTTTAACGGGAGACGTTTCGTGATTACACTCTAGTTTTAGTACACGTACCTCCTAGACCTTCGT F2: 3 GACTTT 2 Unidirectional alignment (log-probability: -32.2) AAGgTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAAtttcAG-----ATGTGAGATCAAAATCATGTGCATGGAGGATCTGGAAGCA AAGTTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAA----AGCACTAATGTGAGATCAAAATCATGTGCATGGAGGATCTGGAAGCA Template switch alignment (log-probability: -22) AAGgTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAA|TTTCAG|ATGTGAGATCAAAATCATGTGCATGGAGGATCTGGAAGCA AAGTTACCTTTGTTCCTTGCTCTGAAATTGCCCTCTGCAA|TTTCAG|ATGTGAGATCAAAATCATGTGCATGGAGGATCTGGAAGCA ========== Event 3522 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: gcaatgaCTAAAAAGCAAACAGACCAAAGCAATTTATAAGAGGAAAATACCTCtgtag Chimp: gcaatgaCTAAAAAGCAAATAGACCAAAGCAATTTATAAGAGGAAAATACCTCtgtag ↓ 3 2 1 4 Gorilla: gcaatgaCTAAAAAGCAAATAGACCAAAGCAGGTCTACAGAGGAAAATACCTCtgtag Human: gcaatgaCTAAAAAGCAAACAGACCAAAGCAATTTATAAGAGGAAAATACCTCtgtag Cluster: [ ] Orangutan: gcaatgaCTAAAAAACAAATAGACCAAAGCAATTTATAAGAGGAAAATACCTCtgtag Chimp > Gorilla --------------- chr8:16185244-16185249 Template switch process: F1: L CTGCATGCCAGCAATGACTAAAAAGCAAATAGACCAAAGCA 1 F3: 4 CAGAGGAAAATACCTCTGTAGTTGATTGAATCATGATTCCC R RF: CTGCATGCCAGCAATGACTAAAAAGCAAATAGACCAAAGCAATTTATAAGAGGAAAATACCTCTGTAGTTGATTGAATCATGATTCCC RR: GACGTACGGTCGTTACTGATTTTTCGTTTATCTGGTTTCGTTAAATATTCTCCTTTTATGGAGACATCAACTAACTTAGTACTAAGGG F2: 3 ATCTGG 2 Unidirectional alignment (log-probability: -31.1) TGCATGCCAGCAATGACTAAAAAGCAAATAGACCAAAGC-------AggtctacAGAGGAAAATACCTCTGTAGTTGATTGAATCATGATTCC TGCATGCCAGCAATGACTAAAAAGCAAATAGACCAAAGCAATTTATA-------AGAGGAAAATACCTCTGTAGTTGATTGAATCATGATTCC Template switch alignment (log-probability: -22) TGCATGCCAGCAATGACTAAAAAGCAAATAGACCAAAGCA|GGTCTA|cAGAGGAAAATACCTCTGTAGTTGATTGAATCATGATTCC TGCATGCCAGCAATGACTAAAAAGCAAATAGACCAAAGCA|GGTCTA|AAGAGGAAAATACCTCTGTAGTTGATTGAATCATGATTCC ========== Event 3523 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AATTAAGTTACAAATTTATCTGAGACTTCAGCTCAGCTTCAGACCCATGATATGTGTCTTGG ↑ 3 2 4 1 Chimp: AATTAAGTTACAAATTTATCTGAGAC-----------TTCAGACCCATGATATGTGTCTTGG ↓ 3 2 4 1 Gorilla: AATTAAGTTACAAATTTATCTGAGACTTCAGCTCAGCTTCAGACCCATGATATGTGTCTTGG Human: AATTAAGTTACAAATTTATCTGAGACTTCAGCTCAGCTTCAGACCCATGATATGTGTCTTGG Cluster: [ ] Orangutan: AATTAAGTTACAAATTTATCTCAGACTTCAGCTCAGCTTCAGACCCATGATATGTGTCTTGG Chimp > Human ------------- chr8:16629074-16629078 Template switch process: F1: L GGATGCTATTTGTTCAATTAAGTTACAAATTTATCTGAGACTTCAG 1 F3: 4 CTTCAGACCCATGATATGTGTCTTGGTCATGAACTACACCA R RF: GGATGCTATTTCTTCAATTAAGTTACAAATTTATCTGAGACTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACCA RR: CCTACGATAAAGAAGTTAATTCAATGTTTAAATAGACTCTGAAGTCTGGGTACTATACACAGAACCAGTACTTGCTGTGGT F2: 3 GACTC 2 Unidirectional alignment (log-probability: -38.7) TATTTgTTCAATTAAGTTACAAATTTATCTGAGACTTCAgctcagcttcaGACCCATGATATGTGTCTTGGTCATGAACtACACC TATTTCTTCAATTAAGTTACAAATTTATCTGAGACTTCA-----------GACCCATGATATGTGTCTTGGTCATGAACGACACC Template switch alignment (log-probability: -28) TATTTgTTCAATTAAGTTACAAATTTATCTGAGACTTCAG|CTCAG|CTTCAGACCCATGATATGTGTCTTGGTCATGAACtACACC TATTTCTTCAATTAAGTTACAAATTTATCTGAGACTTCAG|CTCAG|CTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACC Chimp > Gorilla --------------- chr8:16823020-16823024 Template switch process: F1: L GGATGCTATTTGTTCAATTAAGTTACAAATTTATCTGAGACTTCAG 1 F3: 4 CTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACCA R RF: GGATGCTATTTCTTCAATTAAGTTACAAATTTATCTGAGACTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACCA RR: CCTACGATAAAGAAGTTAATTCAATGTTTAAATAGACTCTGAAGTCTGGGTACTATACACAGAACCAGTACTTGCTGTGGT F2: 3 GACTC 2 Unidirectional alignment (log-probability: -32.2) TATTTgTTCAATTAAGTTACAAATTTATCTGAGActtcagctcagCTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACC TATTTCTTCAATTAAGTTACAAATTTATCTGAGA-----------CTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACC Template switch alignment (log-probability: -22) TATTTgTTCAATTAAGTTACAAATTTATCTGAGACTTCAG|CTCAG|CTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACC TATTTCTTCAATTAAGTTACAAATTTATCTGAGACTTCAG|CTCAG|CTTCAGACCCATGATATGTGTCTTGGTCATGAACGACACC ========== Event 3524 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GTTGGTTAGAAGGCTCTACTTTAGATAAATATTTCT-CAATGGGGAAAAGAACAAtgaa Chimp: gttggttagaaggctctactt-tgagaaATATTTATCTAATGGGGAAAAGAACAAtgaa Gorilla: GTTGGTTAGAAGGCTCTACTT-TGAGAAATATTTATCTAATGGGGAAAAGAACAAtgaa ↓ 13 24 ↑ 13 24 Human: GTTGGTTAGAAGGCTCTACTTTAGATAAATATTTCT-CAATGGGGAAAAGAACAAtgaa Cluster: [ ] Orangutan: gttggttagaaggctctactt-tgagaaATATTTATCTAATGGGGAAAAGAACAATGAA Gorilla > Human --------------- chr8:16424375-16424389 Template switch process: F1: L AGGTGATATTGATGCAGGCAGTTGGTTAGAAGGCTCTACTTT 1 F3: 4 AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC R RF: AGGTGATATTGATTCAGGCAGTTGGTTAGAAGGCTCTACTTTGAGAAATATTTATCTAATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC RR: TCCACTATAACTAAGTCCGTCAACCAATCTTCCGAGATGAAACTCTTTATAAATAGATTACCCCTTTTCTTGTTACTTATAGACGATGAACGGTTTG F2: 3 CTCTTTATAAATAGA 2 Unidirectional alignment (log-probability: -38.9) GTGATATTGATgCAGGCAGTTGGTTAGAAGGCTCTACTTTaGAtAAATATTTcTC-AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC GTGATATTGATTCAGGCAGTTGGTTAGAAGGCTCTACTTT-GAGAAATATTTATCTAATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC Template switch alignment (log-probability: -23.2) GTGATATTGATgCAGGCAGTTGGTTAGAAGGCTCTACTTT|AGATAAATATTTCTC|AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC GTGATATTGATTCAGGCAGTTGGTTAGAAGGCTCTACTTT|AGATAAATATTTCTC|AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC Human > Gorilla --------------- chr8:16614431-16614445 Template switch process: F1: L AGGTGATATTGATTCAGGCAGTTGGTTAGAAGGCTCTACTTT 1 F3: 4 AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC R RF: AGGTGATATTGATGCAGGCAGTTGGTTAGAAGGCTCTACTTTAGATAAATATTTCTCAATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC RR: TCCACTATAACTACGTCCGTCAACCAATCTTCCGAGATGAAATCTATTTATAAAGAGTTACCCCTTTTCTTGTTACTTATAGACGATGAACGGTTTG F2: 3 TCTATTTATAAAGAG 2 Unidirectional alignment (log-probability: -38.9) GTGATATTGATtCAGGCAGTTGGTTAGAAGGCTCTACTTT-GAgAAATATTTaTCtAATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC GTGATATTGATGCAGGCAGTTGGTTAGAAGGCTCTACTTTAGATAAATATTTCTC-AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC Template switch alignment (log-probability: -23.2) GTGATATTGATtCAGGCAGTTGGTTAGAAGGCTCTACTTT|GAGAAATATTTATCT|AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC GTGATATTGATGCAGGCAGTTGGTTAGAAGGCTCTACTTT|GAGAAATATTTATCT|AATGGGGAAAAGAACAATGAATATCTGCTACTTGCCAAAC ========== Event 3525 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ataatagaaaaaaagaaTGTATAGTCTCCTGGGTCAAAGAGA---------------------------TCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTAT Chimp: ataatagaaaaaaagaaTGTATAGTCTCCTGGGTCAAAGAGA---------------------------TCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTAT ↓ 3 2 1 4 Gorilla: ataatagaaaaaaagaaTATATAGTCTCCTGGGTCAAGGAGA------------------------------------------------------CTATATATTCATTTCAAAATACTTAT ↑ 3 2 1 4 Human: ataatagaaaaaaagaaTGTATAGTCTCCTGGGTCAAAGAGA---------------------------TCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTAT Cluster: [ ] Orangutan: ataatagaaaaaaagaaTTTATAGTCTCCTGGGTCAAAGAGATCTGAATTTGGATTTTGCCTAGATACA---------------------------TCATTAATTCATTTCAAAATACTTAT Human > Gorilla --------------- chr8:128693729-128693738 Template switch process: F1: L AATAATAATAGAAAAAAAGAATATATAGTCTCCTGGGTCAA 1 F3: 4 TATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTTC R RF: AATAATAATAGAAAAAAAGAATGTATAGTCTCCTGGGTCAAAGAGATCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTTC RR: TTATTATTATCTTTTTTTCTTACATATCAGAGGACCCAGTTTCTCTAGACTTAAACCTAAAACGGATCTATGTAGTAATTAAGTAAAGTTTTATGAATAGTTCATCCATAAGAAAGAAG F2: 3 ATATCAGAGG 2 Unidirectional alignment (log-probability: -38.7) ATAATAATAGAAAAAAAGAATaTATAGTCTCCTGGGTCAAgGAGA------------------CTAtAT---------ATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT ATAATAATAGAAAAAAAGAATGTATAGTCTCCTGGGTCAAAGAGATCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT Template switch alignment (log-probability: -28.1) ATAATAATAGAAAAAAAGAATaTATAGTCTCCTGGGTCAA|GGAGACTATA|tATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT ATAATAATAGAAAAAAAGAATGTATAGTCTCCTGGGTCAA|GGAGACTATA|AATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT Chimp > Gorilla --------------- chr8:128693729-128693738 Template switch process: F1: L AATAATAATAGAAAAAAAGAATATATAGTCTCCTGGGTCAA 1 F3: 4 TATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTTC R RF: AATAATAATAGAAAAAAAGAATGTATAGTCTCCTGGGTCAAAGAGATCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTTC RR: TTATTATTATCTTTTTTTCTTACATATCAGAGGACCCAGTTTCTCTAGACTTAAACCTAAAACGGATCTATGTAGTAATTAAGTAAAGTTTTATGAATAGTTCATCCATAAGAAAGAAG F2: 3 ATATCAGAGG 2 Unidirectional alignment (log-probability: -38.7) ATAATAATAGAAAAAAAGAATaTATAGTCTCCTGGGTCAAgGAGA------------------CTAtAT---------ATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT ATAATAATAGAAAAAAAGAATGTATAGTCTCCTGGGTCAAAGAGATCTGAATTTGGATTTTGCCTAGATACATCATTAATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT Template switch alignment (log-probability: -28.1) ATAATAATAGAAAAAAAGAATaTATAGTCTCCTGGGTCAA|GGAGACTATA|tATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT ATAATAATAGAAAAAAAGAATGTATAGTCTCCTGGGTCAA|GGAGACTATA|AATTCATTTCAAAATACTTATCAAGTAGGTATTCTTTCTT ========== Event 3526 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTAACCAAAATCTTATGCTCAC-------GTGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTTAGGA ↓ 1 4 3 2 Chimp: GTAACCAAAATCTTATGCTCATAAGCATAAGGTGTCCCTTATGCTTAGGTCAAAGTCCT-TTTAGGA ↑ 1 4 3 2 Gorilla: GTAACCAAAATCTTATGCTCAC-------GGGTGTCCCTTATGCTTAGGTCAAAGTCCT-TTTAGGA Human: GTAACCAAAATCTTATGCTCAC-------GTGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTTAGGA Cluster: [ ] Orangutan: ATAACCAAAATCTTATGCTCAT-------GGGTGTCCCTTATGCTTAGGTCAAAGTCCT-TTTAGGA Human > Chimp ------------- chr8:132535649-132535658 Template switch process: F1: L AGACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA 1 F3: 4 GTGTCCCTTATGCTTAGGTCAAAGTCC-TTTTAGGATGGC R RF: AGACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCACGTGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTTAGGATGGC RR: TCTGGTTGACTAAGATGATTCATTGGTTTTAGAATACGAGTGCACACAGGGAATACGAATCCAGTTTCAGGAAAAATCCTACCG F2: 3 GAATACGAAT 2 Unidirectional alignment (log-probability: -44.4) GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA--TaagcataagGTGTCCCTTATGCTTAGGTCAAAGTCC-TTTTAGGATGGC GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCACGT---------GTGTCCCTTATGCTTAGGTCAAAGTCCTTTTTAGGATGGC Template switch alignment (log-probability: -26.8) GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA|TAAGCATAAG|GTGTCCCTTATGCTTAGGTCAAAGTCC-TTTTAGGATGGC GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA|TAAGCATAAG|GTGTCCCTTATGCTTAGGTCAAAGTCCTTTTTAGGATGGC Gorilla > Chimp --------------- chr8:132535649-132535657 Template switch process: F1: L AGACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA 1 F3: 4 GGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTAGGATGGC R RF: AGACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCACGGGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTAGGATGGC RR: TCTGGTTGACTAAGATGATTCATTGGTTTTAGAATACGAGTGCCCACAGGGAATACGAATCCAGTTTCAGGAAAATCCTACCG F2: 3 AATACGAAT 2 Unidirectional alignment (log-probability: -32) GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCAtaagcataaGGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTAGGATGGC GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA-------CGGGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTAGGATGGC Template switch alignment (log-probability: -16.9) GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA|TAAGCATAA|GGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTAGGATGGC GACCAACTGATTCTACTAAGTAACCAAAATCTTATGCTCA|TAAGCATAA|GGTGTCCCTTATGCTTAGGTCAAAGTCCTTTTAGGATGGC ========== Event 3527 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AGGTAATGATTCTGGGTGACAGGTCTCAGTTGTCTATTTTGGTGACTTCACTATCTAC ↓ 3 2 1 4 Chimp: AGGTAATGATTCTGGGTGACAGGTCTCAGTTACCTG-TTTGGTGACTTCACTATCTAC Gorilla: AGGTAATGATTCTGGGTGACAGGTCTCAGTTATCTATTTTGGTGACTTCACTATCTAC Human: AGGTAATGATTCTGGGTGACAGGTCTCAGTTGTCTATTTTGGTGACTTCACTATCTAC Cluster: [ ] Orangutan: AGGTAATGATTCTGGGTGACAGGTCTCAGTTATCTATTTTGGTGACTTCACTATCTAC Human > Chimp ------------- chr8:14870611-14870615 Template switch process: F1: L ATATCCTCTCAGGTAATGATTCTGGGTGACAGGTCTCAGTT 1 F3: 4 TTTGGTGACTTCACTATCTACCATTAAGATTTTGGGGGG R RF: ATATCCTCTCAGGTAATGATTCTGGGTGACAGGTCTCAGTTGTCTATTTTGGTGACTTCACTATCTACCATTAAGATTTTCGGGGG RR: TATAGGAGAGTCCATTACTAAGACCCACTGTCCAGAGTCAACAGATAAAACCACTGAAGTGATAGATGGTAATTCTAAAAGCCCCC F2: 3 GTCCA 2 Unidirectional alignment (log-probability: -37.4) TATCCTCTCAGGTAATGATTCTGGGTGACAGGTCTCAGTtaccTG-----TTTGGTGACTTCACTATCTACCATTAAGATTTT-GGGGGG TATCCTCTCAGGTAATGATTCTGGGTGACAGGTCTCAGT----TGTCTATTTTGGTGACTTCACTATCTACCATTAAGATTTTCGGGGGG Template switch alignment (log-probability: -21.9) TATCCTCTCAGGTAATGATTCTGGGTGACAGGTCTCAGTT|ACCTG|TTTGGTGACTTCACTATCTACCATTAAGATTTTgGGGGG TATCCTCTCAGGTAATGATTCTGGGTGACAGGTCTCAGTT|ACCTG|TTTGGTGACTTCACTATCTACCATTAAGATTTTCGGGGG ========== Event 3528 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAAG-TTTCTCATGCTTCACTCTCCTTCCTA Chimp: CTTGTGCTGGACAGGATGGCCCAGTATTGTCAACACAAG-TTTCTCATGCTTCACTCTCCTTCCTA Gorilla: CTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAATACTGGACATGCTTCACTCTCCTTCCTA ↑ 3 2 1 4 Human: CTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAAG-TTTCTCATGCTTCACTCTCCTTCCTA Cluster: [ ] Orangutan: CTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAAG-TTTCTCATGCTTCACTCTCCTTCCTA Human > Gorilla --------------- chr8:134752552-134752558 Template switch process: F1: L AGCCTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAA 1 F3: 4 CATGCTTCACTCTCCTTCCTAGCAACAGGAAGACGGAAAT R RF: AGCCTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAAGTTTCTCATGCTTCACTCTCCTTCCTAGCAACAGGAAGACGGAAAT RR: TCGGAACACGACCTGTCCTACCAGGTCATAACAGTTGTGTTCAAAGAGTACGAAGTGAGAGGAAGGATCGTTGTCCTTCTGCCTTTA F2: 3 AGGTCAT 2 Unidirectional alignment (log-probability: -29.5) GCCTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAA-----TactggaCATGCTTCACTCTCCTTCCTAGCAACAGGAAGACGGAAAT GCCTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAAGTTTCT------CATGCTTCACTCTCCTTCCTAGCAACAGGAAGACGGAAAT Template switch alignment (log-probability: -16.6) GCCTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAA|TACTGGA|CATGCTTCACTCTCCTTCCTAGCAACAGGAAGACGGAAAT GCCTTGTGCTGGACAGGATGGTCCAGTATTGTCAACACAA|TACTGGA|CATGCTTCACTCTCCTTCCTAGCAACAGGAAGACGGAAAT ========== Event 3529 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTAAGGGAGAGCCCAGAGCTGCAGCA------------CTGTTCCAAGATAAAATTATTACCAGACATGCTATATAGACCCAGACCTCTCTCTCATCTTCATATGTGTGcacgcgcacacacacac----------------acacacacacacacacacacacacaTTGTCTGTTTGCATGTGGTGCTG Chimp: GTTAAGGGAGAGCCCAGAGCTGCAGCA------------ATGTTCCAAGATAAAATTATTACCAGACATGCTACATAGACCTAGACCTCTCTCTCATCTTCATATGTGTGCATGcacacacacacac------------------acacatacagacacacacacacaTTGTCTGTTTGCATGTGGTGCTG ↑ 1 4 3 2 Gorilla: GTTAAGGGAGAGCCCAGAGCTCCAGAGCTTGGAATAATTTTATTCCAAGATAAAATTATTACCAGACATGCTACATAGACCCAGACCTCTCTCTCATCTTCATATGTGTGCATGcacacacacacacacacacacacacacac--acacacacacacacacacacacaTTGTCTGTTTGCATGTGGTGCTG Human: GTTAAGGGAGAGCCCAGAGCTGCAGCA------------CTGTTCCAAGATAAAATTATTACCAGACATGCTATATAGACCCAGACCTCTCTCTCATCTTCATATGTGTGcacgcgcacacacacac----------------acacacacacacacacacacacacaTTGTCTGTTTGCATGTGGTGCTG Cluster: [ ] Orangutan: GTTAAAGGAGAGCCCAGGGCTGCAGCA------------GTGTTCCAAGAGAAAATTATTACCAGACATGCTACATAGACCCAGACCTGTCTCTCATCTTCATATGTGTGCATGcacacatacacac----------------------acacagacacacacacacaTTGTCTGTTTGCATGTGGTGCTG Gorilla > Chimp --------------- chr8:133642412-133642416 Template switch process: F1: L AAAACAAATGGCCAGAGCAGGTTAAGGGAGAGCCCAGAGCTGCAG 1 F3: 4 TTCCAAGATAAAATTATTACCAGACATGCTACATAGACCT R RF: AAAACAAATGGCCAGAGCAGGTTAAGGGAGAGCCCAGAGCTCCAGAGCTTGGAATAATTTTATTCCAAGATAAAATTATTACCAGACATGCTACATAGACCCAGACCTCTCTCTCATCTTCATATGTGTGCATGCACACACACACACACACACACACACACACACACACACACACACACACACACATTG RR: TTTTGTTTACCGGTCTCGTCCAATTCCCTCTCGGGTCTCGAGGTCTCGAACCTTATTAAAATAAGGTTCTATTTTAATAATGGTCTGTACGATGTATCTGGGTCTGGAGAGAGAGTAGAAGTATACACACGTACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAC F2: 3 GTAAC 2 Unidirectional alignment (log-probability: -39.8) AAATGGCCAGAGCAGGTTAAGGGAGAGCCCAGAGCTgCAG-----------------caatgTTCCAAGATAAAATTATTACCAGACATGCTACATAGACCt AAATGGCCAGAGCAGGTTAAGGGAGAGCCCAGAGCTCCAGAGCTTGGAATAATTTTA-----TTCCAAGATAAAATTATTACCAGACATGCTACATAGACCC Template switch alignment (log-probability: -27.5) AAATGGCCAGAGCAGGTTAAGGGAGAGCCCAGAGCTgCAG|CAATG|TTCCAAGATAAAATTATTACCAGACATGCTACATAGACCt AAATGGCCAGAGCAGGTTAAGGGAGAGCCCAGAGCTCCAG|CAATG|TTCCAAGATAAAATTATTACCAGACATGCTACATAGACCC ========== Event 3530 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTGATTTTTATTAGAAAAGAATAAATCATTCTGCAATTTACTGCTACAAA-AAGAGAAACTCTCCTTACTGTAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------GGAACATATTACATATTATAAAAACCAAGTTTAGATACCAATTAAGCAaa Chimp: TTGATTTTTATTAGAAAAGAATAAATCATTCTGCAATTTACTGCTACAAAATAGA----------------------------------------GAAACTCTCCTTACTGTAGTGGAACATATTACATATTATAAAAACCAAGTAAGGAGAGTTTCTCTATTTTGTAGCAGTAAATTGCAGAATGATTTATTCAATTTACTGCTACAAAATAGAGAAACTCTCCTTACTGTAGTGGAACATATTACATATTATAAAAACCAAGTTTAGATACCAATTAAGCAaa ↑ 3 4 2 1 Gorilla: TTGATTTTTATTAGAAAAGAATAAATCATTCTGCAATTTACTGCTACAAAATAGA--------------------GAAACTCTCCTTACTGTAGT--------------------------------------------------------------------------------------------------------------------------------------------GGAACATATTACATATTATAAAAACCAAGTTTAGATACCAATTAAGCAaa Human: TTGATTTTTATTAGAAAAGAATAAATCATTCTGCAATTTACTGCTACAAA-AAGAGAAACTCTCCTTACTGTAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------GGAACATATTACATATTATAAAAACCAAGTTTAGATACCAATTAAGCAaa Cluster: [ ] Orangutan: TTGATTTTTATTAGAAAAGAATAAATCATTCTGCAA-TTACTGCTACAAAATAGA--------------------GAAACTCTCCTTACTGTACT--------------------------------------------------------------------------------------------------------------------------------------------GGAACATATTACATATTATAAAAACCAAGTTTAGATACTAATTAAGCAaa Gorilla > Chimp --------------- chr8:12331286-12331333 Template switch process: F1: L AAAAGAATAAATCATTCTGCAATTTACTGCTACAAAATAGAGAAACTCTCCTTACTGTAGTGGAACATATTACATATTATAAAAACCAAGT 1 F3: 4 CAATTTACTGCTACAAAATAGAGAAACTCTCCTTACTGTAGTGGAACATATTACATATTATAAAAACCAAGTTTAGATACCA R RF: AAAAGAATAAATCATTCTGCAATTTACTGCTACAAAATAGAGAAACTCTCCTTACTGTAGTGGAACATATTACATATTATAAAAACCAAGTTTAGATACCA RR: TTTTCTTATTTAGTAAGACGTTAAATGACGATGTTTTATCTCTTTGAGAGGAATGACATCACCTTGTATAATGTATAATATTTTTGGTTCAAATCTATGGT F2: 3 TTATTTAGTAAGACGTTAAATGACGATGTTTTATCTCTTTGAGAGGAA 2 Unidirectional alignment (log-probability: -184) TTACTGTAGTGGAACATATTACATATTATAAAAACCAAGtaaggagagtttctctattttgtagcagtaaattgcagaatgatttattcaatttactgctacaaaatagagaaactctccttactgta TTACTGTAGTGGAACATATTACATATTATAAAAACCAAG----------------------------------------------------------------------------------------- Template switch alignment (log-probability: -23.7) TTACTGTAGTGGAACATATTACATATTATAAAAACCAAGT|AAGGAGAGTTTCTCTATTTTGTAGCAGTAAATTGCAGAATGATTTATT|CAATTTACTGCTACAAAATAGAGAAACTCTCCTTACTGTA TTACTGTAGTGGAACATATTACATATTATAAAAACCAAGT|AAGGAGAGTTTCTCTATTTTGTAGCAGTAAATTGCAGAATGATTTATT|CAATTTACTGCTACAAAATAGAGAAACTCTCCTTACTGTA ========== Event 3531 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GCTTGAAGGGCCAGAGGGGCAC--------------ACTAGAAGGCAGTTGAATTAATGGGGTCCA ↓ 3 4 12 Chimp: GCTTGAAGGGCCAGAGGGGCAGAAGGGCCTTCTAGTGTTAGAAGGCAGTTGAATTAATGGGGTCCA Gorilla: GCTTGAAGGGCCGGAGGGGCAC--------------ACCAGAAGGCAGTTGAATTAATGGGGTCCA Human: GCTTGAAGGGCCAGAGGGGCAC--------------ACTAGAAGGCAGTTGAATTAATGGGGTCCA Cluster: [ ] Orangutan: GCTTGAAGGGCCAGTGGGGCAC--------------ACCAGAAGGCAGTTGAATTAATGGGGTTCA Human > Chimp ------------- chr8:12561438-12561449 Template switch process: F1: L CTGGTTCTCAGACAGGTTGAGCTTGAAGGGCCAGAGGGGC-----AGAAGG 1 F3: 4 TAGAAGGCAGTTGAATTAATGGGGTCCAGAGAGGTTGGTC R RF: CTGGTTCTCAGACAGGTTGAGCTTGAAGGGCCAGAGGGGCACACTAGAAGGCAGTTGAATTAATGGGGTCCAGAGAGGTTGGTC RR: GACCAAGAGTCTGTCCAACTCGAACTTCCCGGTCTCCCCGTGTGATCTTCCGTCAACTTAATTACCCCAGGTCTCTCCAACCAG F2: 3 TGTGATCTTCCG 2 Unidirectional alignment (log-probability: -43.1) CTCAGACAGGTTGAGCTTGAAGGGCCAGAGGGGCAgAagggccttctagtgtTAGAAGGCAGTTGAATTAATGGGGTCCAGAGAGGTTGGTC CTCAGACAGGTTGAGCTTGAAGGGCCAGAGGGGCACAC--------------TAGAAGGCAGTTGAATTAATGGGGTCCAGAGAGGTTGGTC Template switch alignment (log-probability: -27.3) CTCAGACAGGTTGAGCTTGAAGGGCCAGAGGGGC-----AGAAGG|GCCTTCTAGTGT|TAGAAGGCAGTTGAATTAATGGGGTCCAGAGAGGTTGGTC CTCAGACAGGTTGAGCTTGAAGGGCCAGAGGGGCACACTAGAAGG|GCCTTCTAGTGT|TAGAAGGCAGTTGAATTAATGGGGTCCAGAGAGGTTGGTC ========== Event 3532 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: gaggaaaagacagtcatggacagaACTAACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCTGAGTGCACCGCGTTGTGTGACACTTGG Chimp: GAGGAAAAGGCAGTCATGGACTGCAT-TACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCTGAGTGCACCACGTTGTGTGACACTTGG ↑ 1 4 3 2 Gorilla: GAGGAAAAGACAGTCATGGACAGAACTAACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCTTAATGCACCGCGTTGTGTGACACTTGG Human: gaggaaaagacagtcatggacagaACTAACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCTGAGTGCACCGCGTTGTGTGACACTTGG Cluster: [ ] Orangutan: GAGGAAAAGACAGTCATGGACAGAACTAACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCTGAGTGCGCCGCGTTGTGTGACACTTGG Gorilla > Chimp --------------- chr8:12195295-12195300 Template switch process: F1: L AAAGTGCTCTATACACCTCGGAGGAAAAGGCAGTCATGGAC 1 F3: 4 ACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCT R RF: AAAGTGCTCTATACACCTAGGAGGAAAAGACAGTCATGGACAGAACTAACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCTTAATGCA RR: TTTCACGAGATATGTGGATCCTCCTTTTCTGTCAGTACCTGTCTTGATTGACCCAAAGGTGGTCATTACTACCACAGAAAAACACCGAATTACGT F2: 3 TTACGT 2 Unidirectional alignment (log-probability: -38.6) AAGTGCTCTATACACCTcGGAGGAAAAGgCAGTCATGGACtGcAtT-ACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCT AAGTGCTCTATACACCTAGGAGGAAAAGACAGTCATGGACAGAACTAACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCT Template switch alignment (log-probability: -27.5) AAGTGCTCTATACACCTcGGAGGAAAAGgCAGTCATGGAC|TGCATT|ACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCT AAGTGCTCTATACACCTAGGAGGAAAAGACAGTCATGGAC|TGCATT|ACTGGGTTTCCACCAGTAATGATGGTGTCTTTTTGTGGCT ========== Event 3533 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCATATTTGAATTCCACGTGA------------------------AGTGCTGGGGACCATCCATTCTTTTTGAACAGC ↑ 1 3 2 4 Chimp: CCATATTTGAATTCCACGTGA------------ATGTCCCCAGCACTTGGTGGGGATCATCCATTCTTTTTGAACAAC Gorilla: CCATATTTGAATTCCACGTGAATGTCCCCAGCA------------CTTGGTGGGgatcatccattctttttgaacaac Human: CCATATTTGAATTCCACGTGA------------------------AGTGCTGGGGACCATCCATTCTTTTTGAACAGC Cluster: [ ] Orangutan: CCATATTTGAATTCCACGTGGATGTCCCCAGCA------------CTTGGTGGGGATCATCCATTCTTTTTGAACAAC Chimp > Human ------------- chr8:12779959-12779969 Template switch process: F1: L TGAAGACCCCCTGATATTGCCCATATTTGAATTCCACGTGAA 1 F3: 4 CATCCATTCTTTTTGAACAGCCCCAGTCATGGTGGCAAGC R RF: TGAAGACCCCCTGATATTGCCCATATTTGAATTCCACGTGAATGTCCCCAGCACTTGGTGGGGATCATCCATTCTTTTTGAACAACCCCAGTCATGGTGGCAAGC RR: ACTTCTGGGGGACTATAACGGGTATAAACTTAAGGTGCACTTACAGGGGTCGTGAACCACCCCTAGTAGGTAAGAAAAACTTGTTGGGGTCAGTACCACCGTTCG F2: 3 CAGGGGTCGTG 2 Unidirectional alignment (log-probability: -35.6) AAGACCCCCTGATATTGCCCATATTTGAATTCCACGTGAAg------------TGcTGGGGAcCATCCATTCTTTTTGAACAgCCCCAGTCATGGTGGCAAGC AAGACCCCCTGATATTGCCCATATTTGAATTCCACGTGAATGTCCCCAGCACTTGGTGGGGATCATCCATTCTTTTTGAACAACCCCAGTCATGGTGGCAAGC Template switch alignment (log-probability: -22.7) AAGACCCCCTGATATTGCCCATATTTGAATTCCACGTGAA|GTGCTGGGGAC|CATCCATTCTTTTTGAACAgCCCCAGTCATGGTGGCAAGC AAGACCCCCTGATATTGCCCATATTTGAATTCCACGTGAA|GTGCTGGGGAC|CATCCATTCTTTTTGAACAACCCCAGTCATGGTGGCAAGC ========== Event 3534 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAGTCTACTAGGTGCCAGTCAGTGTCCAGGTTTTGGTAACTCCCCCTTCACTTTTCAAATCTTCACCTGATGGGACTTACTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAGGAACTCAGATGTACACTGTGTTGCTCCCTGTTTACAACC Chimp: GAGTCTACTAGGTGCCAGTCAGTGTCCAGGTTTTGGTAACTCCCCCTTCGCTTTTCAAACCTTCACCTGATGGGACTTACTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTACACTGTGTTGCTCCCTGTTTACAACC ↑ 3 2 1 4 Gorilla: GAGTCTACTAGGTGCCAGGCAGTGTCCAGGTTTTGGTAACTCCCCCTTCACTTTTCAAATCTTCACCTGATGGGACTTACTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTTTGCGTTGTTGCTCCCTGTTTACAACC ↓ 3 2 1 4 Human: GAGTCTACTAGGTGCCAGTCAGTGTCCAGGTTTTGGTAACTCCCCCTTCACTTTTCAAATCTTCACCTGATGGGACTTACTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAGGAACTCAGATGTACACTGTGTTGCTCCCTGTTTACAACC Cluster: [ ] Orangutan: GAGTCTACTAGGTGCCAGGTGGGGTCCAGGTTTTGGTAACTCCCCCTTCACTTTTCAGACCTTCACCTGATGGGACTTCCTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTGAGATGTACGCTGTGTTGCTCCCTGTTTACAGCC Gorilla > Human --------------- chr8:12775716-12775721 Template switch process: F1: L CTCTTGCCTCTCCTTCCCTCTAGCCTTAGGAACTCAGATGT 1 F3: 4 TGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT R RF: CAGTGTCCAGGTTTTGGTAACTCCCCCTTCACTTTTCAAATCTTCACCTGATGGGACTTACTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTTTGCGTTGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT RR: GTCACAGGTCCAAAACCATTGAGGGGGAAGTGAAAAGTTTAGAAGTGGACTACCCTGAATGATGGAGAACGGAGAGGAAGGGAGATCGGAATTCTTGAGTCTACAAACGCAACAACGAGGGACAAATGTTGGGTGCGGCGGGAGCGGGGTA F2: 3 GTCACA 2 Unidirectional alignment (log-probability: -34.3) TCTTGCCTCTCCTTCCCTCTAGCCTTAgGAACTCAGATGTacaCtgTGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT TCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTTTGCGTTGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT Template switch alignment (log-probability: -22) TCTTGCCTCTCCTTCCCTCTAGCCTTAgGAACTCAGATGT|ACACTG|TGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT TCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGT|ACACTG|TGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT Gorilla > Chimp --------------- chr8:13082433-13082438 Template switch process: F1: L CTCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGT 1 F3: 4 TGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT R RF: CAGTGTCCAGGTTTTGGTAACTCCCCCTTCACTTTTCAAATCTTCACCTGATGGGACTTACTACCTCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTTTGCGTTGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT RR: GTCACAGGTCCAAAACCATTGAGGGGGAAGTGAAAAGTTTAGAAGTGGACTACCCTGAATGATGGAGAACGGAGAGGAAGGGAGATCGGAATTCTTGAGTCTACAAACGCAACAACGAGGGACAAATGTTGGGTGCGGCGGGAGCGGGGTA F2: 3 GTCACA 2 Unidirectional alignment (log-probability: -28.8) TCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTacaCtgTGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT TCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGTTTGCGTTGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT Template switch alignment (log-probability: -16.5) TCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGT|ACACTG|TGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT TCTTGCCTCTCCTTCCCTCTAGCCTTAAGAACTCAGATGT|ACACTG|TGTTGCTCCCTGTTTACAACCCACGCCGCCCTCGCCCCAT ========== Event 3535 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAGACAGAGTCACTTCCCTTT-ATAAGGTGCCTTACCACATTATTAAAGCTGGAGATTTGAGGAG Chimp: AAGACAGAGTGACTTCCCTTTAATAATGTGGTAAGGCACCTT-ATAAAGCTGGAGATTTGAGGAG ↓ 13 24 ↑ 13 24 Gorilla: AAGACAGAGTGACTTCCCTTT-ATAAGGTGCCTTACCACATTATTAAAGCTGGAGATTTGAGGAG Human: AAGACAGAGTCACTTCCCTTT-ATAAGGTGCCTTACCACATTATTAAAGCTGGAGATTTGAGGAG Cluster: [ ] Orangutan: AAGACAGAGTGACTTCCCTTT-ATAAGGTGCCTAACCACATTATTAAAGCTGGAGATTTGAGGAG Gorilla > Chimp --------------- chr8:11231424-11231444 Template switch process: F1: L TCTTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA 1 F3: 4 TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT R RF: TCTTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTATAAGGTGCCTTACCACATTATTAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT RR: AGAAGGGAGAGGTACAGGTGTTCTGTCTCACTGAAGGGAAATATTCCACGGAATGGTGTAATAATTTCGACCTCTAAACTCCTCTTGTGTCGACTGGACGGAA F2: 3 ATTCCACGGAATGGTGTAATA 2 Unidirectional alignment (log-probability: -45.2) TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTAataatgtggTAAGGcaCCTTA---------TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA---------TAAGGTGCCTTACCACATTATTAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT Template switch alignment (log-probability: -18.4) TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA|ATAATGTGGTAAGGCACCTTA|TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA|ATAATGTGGTAAGGCACCTTA|TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT Chimp > Gorilla --------------- chr8:11030913-11030933 Template switch process: F1: L TCTTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA 1 F3: 4 TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT R RF: TCTTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTAATAATGTGGTAAGGCACCTTATAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT RR: AGAAGGGAGAGGTACAGGTGTTCTGTCTCACTGAAGGGAAATTATTACACCATTCCGTGGAATATTTCGACCTCTAAACTCCTCTTGTGTCGACTGGACGGAA F2: 3 TATTACACCATTCCGTGGAAT 2 Unidirectional alignment (log-probability: -45.2) TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA---------TAAGGtgCCTTAccacattatTAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTAATAATGTGGTAAGGCACCTTA---------TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT Template switch alignment (log-probability: -18.4) TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA|TAAGGTGCCTTACCACATTAT|TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT TTCCCTCTCCATGTCCACAAGACAGAGTGACTTCCCTTTA|TAAGGTGCCTTACCACATTAT|TAAAGCTGGAGATTTGAGGAGAACACAGCTGACCTGCCTT ========== Event 3536 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GTGATACCAAAAGGTACCAAT----GCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGACGGTGGTGCAAGGAATTAAACTAGCCTTGTTTAACCATTGTGATTATTATTAGTCTGTGATCC Chimp: GTGATACCAAAAGGTACCAAT----GCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGACGATGGTGCAAGGAATTAAACTAGCCTTGTTTAACCATTGTGATTATTATTAGTCTGTGATCC ↑ 4 3 2 1 Gorilla: GTGATACTAAAAGGTACCAAT-----------------------------------------------GCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGATTACTATTAGTCTGTGATCT Human: GTGATACCAAAAGGTACCAAT----GCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGACGGTGGTGCAAGGAATTAAACTAGCCTTGTTTAACCATTGTGATTATTATTAGTCTGTGATCC Cluster: [ ] Orangutan: GTGATACCAAAAGGTACCAA-TGGT-------------------------------------------GCAAGGAATTAAACTAGCCTTGTTTAAACATTGTGATTATTATTAGTCTGTGATCT Gorilla > Chimp --------------- chr8:139009021-139009027 Template switch process: F1: L ACAAAAATTTTTAAAAAGTAGTGATACCAAAAGGTACCAATGCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGA 1 F3: 4 GCAAGGAATTAAACTAGCCTTGTTTAACCATTGTGATTAT R RF: ACAAAAATTTTTAAAAAGTAGTGATACTAAAAGGTACCAATGCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGATTAC RR: TGTTTTTAAAAATTTTTCATCACTATGATTTTCCATGGTTACGTTCCTTAATTTGATCGGGACAAATTGGTAACACTAATG F2: 3 TGGTAGC 2 Unidirectional alignment (log-probability: -83.7) CAATGCAAGGAATTAAACTAGCCCtgtttaaccattgtgacgatggtgcaaggaattaaactagcctTGTTTAACCATTGTGATTAt CAATGCAAGGAATTAAACTAGCCC-------------------------------------------TGTTTAACCATTGTGATTAC Template switch alignment (log-probability: -39.5) CAATGCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGA|CgATGGT|GCAAGGAATTAAACTAGCCtTGTTTAACCATTGTGATTAt CAATGCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGA|CAATGGT|GCAAGGAATTAAACTAGCCCTGTTTAACCATTGTGATTAC ========== Event 3537 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: CCAAAAATGCTTACATTTTTATAACGTAAAAATGTAAGCATTCTGTT ↓ 13 24 ↑ 13 24 Chimp: CCAGAAATGCTTACATTTTTACGTTATAAAAATGTAAGCATTCTGTT Gorilla: Human: CCAAAAATGCTTACATTTTTATAACGTAAAAATGTAAGCATTCTGTT Cluster: [ ] Orangutan: CCAAAAATGCTTATATTTTTAAGTTATAAAAATGTAAGCATTCTGTT Chimp > Human ------------- chr8:8321560-8321564 Template switch process: F1: L GTAAATGTAACCTTTCCTTTCCAAAAATGCTTACATTTTTA 1 F3: 4 TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA R RF: GTAAATGTAACCTTTCCTTTCCAGAAATGCTTACATTTTTACGTTATAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA RR: CATTTACATTGGAAAGGAAAGGTCTTTACGAATGTAAAAATGCAATATTTTTACATTCGTAAGACAATCTTACTGTCCTCTCTTTT F2: 3 GCAAT 2 Unidirectional alignment (log-probability: -31.6) TAAATGTAACCTTTCCTTTCCAaAAATGCTTACATTTTTataACG---TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA TAAATGTAACCTTTCCTTTCCAGAAATGCTTACATTTTT---ACGTTATAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA Template switch alignment (log-probability: -21.9) TAAATGTAACCTTTCCTTTCCAaAAATGCTTACATTTTTA|TAACG|TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA TAAATGTAACCTTTCCTTTCCAGAAATGCTTACATTTTTA|TAACG|TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA Human > Chimp ------------- chr8:8601461-8601465 Template switch process: F1: L GTAAATGTAACCTTTCCTTTCCAGAAATGCTTACATTTTTA 1 F3: 4 TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA R RF: GTAAATGTAACCTTTCCTTTCCAAAAATGCTTACATTTTTATAACGTAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA RR: CATTTACATTGGAAAGGAAAGGTTTTTACGAATGTAAAAATATTGCATTTTTACATTCGTAAGACAATCTTACTGTCCTCTCTTTT F2: 3 ATTGC 2 Unidirectional alignment (log-probability: -31.6) TAAATGTAACCTTTCCTTTCCAgAAATGCTTACATTTTT---ACGttaTAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA TAAATGTAACCTTTCCTTTCCAAAAATGCTTACATTTTTATAACG---TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA Template switch alignment (log-probability: -21.9) TAAATGTAACCTTTCCTTTCCAgAAATGCTTACATTTTTA|CGTTA|TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA TAAATGTAACCTTTCCTTTCCAAAAATGCTTACATTTTTA|CGTTA|TAAAAATGTAAGCATTCTGTTAGAATGACAGGAGAGAAAA ========== Event 3538 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: tgtctagaaatgTTCAAAATTTCC----------------------------------------------AAGAATCAAAGCACCAACAGCAAATGATGCTTATGGAATTTGTTAAGCCAATACC Chimp: tgtctagaaatgTTCAAAATTTCCAAGAAACCATAAGCATCATTTGCTGTTGGTGCTTTGATTCTTCCCCAAGAATCAAAGCACCAACAGCAAATGATGCTTATGGAATTTGTTAAGCCAATACC ↑ 4 3 1 2 Gorilla: tgtctagaaatgTTCAAAATTTCC----------------------------------------------AAGAATCAAAGCACCAACAGCAAATGATGCTTATGGAATTTGTTAAGCCAGTACC Human: tgtctagaaatgTTCAAAATTTCC----------------------------------------------AAGAATCAAAGCACCAACAGCAAATGATGCTTATGGAATTTGTTAAGCCAATACC Cluster: [ ] Orangutan: tgtctagaaatgttcaaaatttcc----------------------------------------------aagaatcaaagcaccaacagcaaatgatgctcatggaatttgttaagccaatacc Gorilla > Chimp --------------- chr8:139386816-139386849 Template switch process: F1: L TTAACATATTTTTGCTTTGTCTAGAAATGTTCAAAATTTCCAAGAAAC 1 F3: 4 TCCCCAAGAATCAAAGCACCAACAGCAAATGATGCTTATGGAATT R RF: TTAACATATTTTTGCTTTGTCTAGAAATGTTCAAAATTTCCAAGAATCAAAGCACCAACAGCAAATGATGCTTATGGAATT RR: AATTGTATAAAAACGAAACAGATCTTTACAAGTTTTAAAGGTTCTTAGTTTCGTGGTTGTCGTTTACTACGAATACCTTAA F2: 3 TCTTAGTTTCGTGGTTGTCGTTTACTACGAATAC 2 Unidirectional alignment (log-probability: -77) TTTTTGCTTTGTCTAGAAATGTTCAAAATTTccaagaaaccataagcatcatttgctgttggtgctttgattcttccCCAAGAATCAAAGCACCAACAGCAAATGATGCTTATG TTTTTGCTTTGTCTAGAAATGTTCAAAATTT----------------------------------------------CCAAGAATCAAAGCACCAACAGCAAATGATGCTTATG Template switch alignment (log-probability: -36.9) TTTTTGCTTTGTCTAGAAATGTTCAAAATTTCCAAGAAaC|CATAAGCATCATTTGCTGTTGGTGCTTTGATTCT|TccCCAAGAATCAAAGCACCAACAGCAAATGATGCTTATG TTTTTGCTTTGTCTAGAAATGTTCAAAATTTCCAAGAATC|CATAAGCATCATTTGCTGTTGGTGCTTTGATTCT|TTTCCAAGAATCAAAGCACCAACAGCAAATGATGCTTATG ========== Event 3539 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: gcaaaactgagaagCCATTTATTTGTTGTGAAGC---TATTACATGGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTATAAGCCCACGAGACAGC Chimp: gcaaaactgagaagCCATTTATTTGTTGTGAAGC---TATTACATCGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTATAAGCTCACGAGACAGC Gorilla: gcaaaactgagaAGCCATTTACTTGCTGTGAAGCTTCAAACACATCGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTATAAGCTCACGAGACAGC ↓ 1 4 3 2 Human: gcaaaactgagaagCCATTTATTTGTTGTGAAGC---TATTACATGGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTATAAGCCCACGAGACAGC Cluster: [ ] Orangutan: gcaaaactgagaggCCATTTATTTGTTGTGAAGT---TATTACGTGGACTTCCCTAAAACAACATATTCTAACACATGTAATGTATAAGCCCACAAGACAGC Gorilla > Human --------------- chr8:137233838-137233845 Template switch process: F1: L GGGTCTCAGCTCCCTCAGGTGCAAAACTGAGAAGCCATTTATTTGTTGTGAAGCT 1 F3: 4 GACTTCCCTAAAACAACATATTCTAACCCATGTAATGTAT R RF: GGGTCTCAGCTCCCTCAGGTGCAAAACTGAGAAGCCATTTACTTGCTGTGAAGCTTCAAACACATCGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTAT RR: CCCAGAGTCGAGGGAGTCCACGTTTTGACTCTTCGGTAAATGAACGACACTTCGAAGTTTGTGTAGCTGAAGGGATTTTGTTGTATAAGATTGGGTACATTACATA F2: 3 GTACATTA 2 Unidirectional alignment (log-probability: -38.9) CAGGTGCAAAACTGAGAAGCCATTTAtTTGtTGTGAAGCT---AttACATgGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTAT CAGGTGCAAAACTGAGAAGCCATTTACTTGCTGTGAAGCTTCAAACACATCGACTTCCCTAAAACAACATATTCTAACCCATGTAATGTAT Template switch alignment (log-probability: -28.1) CAGGTGCAAAACTGAGAAGCCATTTAtTTGtTGTGAAGCT|ATTACATG|GACTTCCCTAAAACAACATATTCTAACCCATGTAATGTAT CAGGTGCAAAACTGAGAAGCCATTTACTTGCTGTGAAGCT|ATTACATG|GACTTCCCTAAAACAACATATTCTAACCCATGTAATGTAT ========== Event 3540 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCACAACCCATAGCCCCTTAGTGCTCACTCTCTG----AGCACTAAGTCCATGTGGTTACAGTGGA ↑ 3 2 1 4 Chimp: CCCACAACCCATAGCCCCTTAGTGCTCACTCTCTG--ACAGCCCCCAGTCCATGTGGTTACAGTGGA Gorilla: CCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGAC--AGCCCCCAGTCCATGTGGTTACAGTGGA ↓ 3 2 1 4 Human: CCCACAACCCATAGCCCCTTAGTGCTCACTCTCTG----AGCACTAAGTCCATGTGGTTACAGTGGA Cluster: [ ] Orangutan: CCCACACCCCATAGCCCCTTAGTGCTCACTCTCTGAC--AGCCCGCAGTCCATGTGGTTACAGTGGA Chimp > Human ------------- chr8:137869045-137869050 Template switch process: F1: L GGCTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGA 1 F3: 4 AGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT R RF: GGCTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGACAGCCCCCAGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT RR: CCGACGGGGTGTTGGGTATCGGGGAATCACGAGTGAGAGACTGTCGGGGGTCAGGTACACCAATGTCACCTTTTTCGGTACCTTTTTGTA F2: 3 ATCACG 2 Unidirectional alignment (log-probability: -29.1) CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTG--AGCaCtaAGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGACAGCCCCCAGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT Template switch alignment (log-probability: -16) CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGA|GCACTA|AGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGA|GCACTA|AGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT Gorilla > Human --------------- chr8:137869045-137869050 Template switch process: F1: L GGCTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGA 1 F3: 4 AGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT R RF: GGCTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGACAGCCCCCAGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT RR: CCGACGGGGTGTTGGGTATCGGGGAATCACGAGTGAGAGACTGTCGGGGGTCAGGTACACCAATGTCACCTTTTTCGGTACCTTTTTGTA F2: 3 ATCACG 2 Unidirectional alignment (log-probability: -27.6) CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTG--AGCaCtaAGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGACAGCCCCCAGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT Template switch alignment (log-probability: -16.5) CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGA|GCACTA|AGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT CTGCCCCACAACCCATAGCCCCTTAGTGCTCACTCTCTGA|GCACTA|AGTCCATGTGGTTACAGTGGAAAAAGCCATGGAAAAACAT ========== Event 3541 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: aaaagtacacagcattgcatagacatagaatacatatttatagaataaCTCGTCTACCTTCAAAAGTGGAGCCCGAC Chimp: aaaagtacacagcattgcatagacatagaatatatatttataggataaCTCATCTGCCTTCAAAAGTGGAGCTCGAC Gorilla: aaaagtatgcagcattgcatagacatagaatacatatttatagaataaCTCATCTGCCTTCAAAAGTGGAGCCCGAC ↓ 3 2 1 4 Human: aaaagtacacagcattgcatagacatagaatacatatttatagaataaCTCGTCTACCTTCAAAAGTGGAGCCCGAC Cluster: [ ] Orangutan: gaaagtacacagcattgcatagacatagaatacatatttatggaataaCTTGTCTGCCCTCAAAAGTGGGGCCAGAC Gorilla > Human --------------- chr8:7031948-7031952 Template switch process: F1: L AGCATTGCATAGACATAGAATACATATTTATAGAATAACTC 1 F3: 4 CCTTCAAAAGTGGAGCCCGACTTTTTTTTTTTTTTTT R RF: AGCATTGCATAGACATAGAATACATATTTATAGAATAACTCATCTGCCTTCAAAAGTGGAGCCCGACTTTTTTTTTTTTTTTG RR: TCGTAACGTATCTGTATCTTATGTATAAATATCTTATTGAGTAGACGGAAGTTTTCACCTCGGGCTGAAAAAAAAAAAAAAAC F2: 3 ATCTG 2 Unidirectional alignment (log-probability: -26.1) GCATTGCATAGACATAGAATACATATTTATAGAATAACTCgTCTaCCTTCAAAAGTGGAGCCCGACTTTTTTTTTTTttttt GCATTGCATAGACATAGAATACATATTTATAGAATAACTCATCTGCCTTCAAAAGTGGAGCCCGACTTTTTTTTTTT----- Template switch alignment (log-probability: -21.8) GCATTGCATAGACATAGAATACATATTTATAGAATAACTC|GTCTA|CCTTCAAAAGTGGAGCCCGACTTTTTTTTTTTTTTTt GCATTGCATAGACATAGAATACATATTTATAGAATAACTC|GTCTA|CCTTCAAAAGTGGAGCCCGACTTTTTTTTTTTTTTTG ========== Event 3542 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: ATGATATGTCTAGATATCTTGTGCTGCCATATTGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAACAATTAAAC Chimp: ATGATATGTCTAGATATCTTG-----------TGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAACAATTTAAC ↓ 4 1 3 2 Gorilla: ATGATATGTCTAGATATCTTGTGCTGCCATATTGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAAC----AAAC Human: ATGATATGTCTAGATATCTTGTGCTGCCATATTGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAACAATTAAAC Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr8:12901554-12901561 Template switch process: F1: L TCTCAAATCAGTAATGTGTGATGATATGTCTAGATATCTTGTGC 1 F3: 4 TGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAAC R RF: TCTCAAATCAGTAATGTGTGATGATATGTCTAGATATCTTGTGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAAC RR: AGAGTTTAGTCATTACACACTACTATACAGATCTATAGAACACGGGTAGAGTTTTACTAAACCGTTCGACTCTTTTG F2: 3 TATACCGT 2 Unidirectional alignment (log-probability: -33.6) AAATCAGTAATGTGTGATGATATGTCTAGATATCTTGtgctgccatatTGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAAC---- AAATCAGTAATGTGTGATGATATGTCTAGATATCTTG-----------TGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAACAATT Template switch alignment (log-probability: -22.2) AAATCAGTAATGTGTGATGATATGTCTAGATATCTTGTGC|TGCCAtAT|TGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAAC AAATCAGTAATGTGTGATGATATGTCTAGATATCTTGTGC|TGCCAAAT|TGCCCATCTCAAAATGATTTGGCAAGCTGAGAAAAC ========== Event 3543 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCATTTACATGCTGAGTACACACGTGCATCAATAC----ATATCATGGCAGGTTTCAGATG ↓ 3 2 1 4 Chimp: CTCATTTACATGCTGAGTACACACGTGCATCAACACGTGTGTATCATGGCAGGTTTCAGATG Gorilla: CTCATTTACATGCTGAGTACACACGTGCATCAACAC----ATATCATGGCAGGTTTCAGATG Human: CTCATTTACATGCTGAGTACACACGTGCATCAATAC----ATATCATGGCAGGTTTCAGATG Cluster: [ ] Orangutan: CTCATTTACATGCTGAGTACACGTGTGCATCAACAC----ATATCATGGCAGGTTTCAGATG Human > Chimp ------------- chr8:142582647-142582654 Template switch process: F1: L ACAACAGCCTCATTTACATGCTGAGTACACACGTGCATCAA 1 F3: 4 TATCATGGCAGGTTTCAGATGGTCATTTCGGTGAAACCTC R RF: ACAACAGCCTCATTTACATGCTGAGTACACACGTGCATCAATACATATCATGGCAGGTTTCAGATGGTCATTTCGGTGCAACCTC RR: TGTTGTCGGAGTAAATGTACGACTCATGTGTGCACGTAGTTATGTATAGTACCGTCCAAAGTCTACCAGTAAAGCCACGTTGGAG F2: 3 GTGTGCAC 2 Unidirectional alignment (log-probability: -34.7) CAACAGCCTCATTTACATGCTGAGTACACACGTGCATCAAcACgtgtgTATCATGGCAGGTTTCAGATGGTCATTTCGGTGaAACCTC CAACAGCCTCATTTACATGCTGAGTACACACGTGCATCAATAC----ATATCATGGCAGGTTTCAGATGGTCATTTCGGTGCAACCTC Template switch alignment (log-probability: -22.3) CAACAGCCTCATTTACATGCTGAGTACACACGTGCATCAA|CACGTGTG|TATCATGGCAGGTTTCAGATGGTCATTTCGGTGaAACCTC CAACAGCCTCATTTACATGCTGAGTACACACGTGCATCAA|CACGTGTG|TATCATGGCAGGTTTCAGATGGTCATTTCGGTGCAACCTC ========== Event 3544 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTGGCCTGCATATTAAGTATCATGTAGCAAGGTTTAATTTTTCATAGA Chimp: AGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTGGCCTGCACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA ↓ 1 3 4 2 Gorilla: GGAGGTGTCTCTCATTAAAGGCTACATGATATTTAATGTGCAGGCCACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA ↑ 3 1 2 4 Human: GGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTGGCCTGCATATTAAGTATCATGTAGCAAGGTTTAATTTTTCATAGA Cluster: [ ] Orangutan: GGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTGGCCTGCGCATTAAATATCATGTAGCGAGGTTTAATTTTCCATAGA Human > Gorilla --------------- chr8:141553332-141553345 Template switch process: F1: L CGGAGGTGTCTCTCATTAAAGGCTACATGATATTTAATGTG 1 F3: 4 TATCATGTAGCAAGGTTTAATTTTTCATAGACCTTTGGAT R RF: CGGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTGGCCTGCATATTAAGTATCATGTAGCAAGGTTTAATTTTTCATAGACCTTTGGAT RR: GCCTCCACAGAGAGTAATTTCTGATGTACTATAAATTACACCGGACGTATAATTCATAGTACATCGTTCCAAATTAAAAAGTATCTGGAAACCTA F2: 3 AAATTACACCGGAC 2 Unidirectional alignment (log-probability: -41.8) GGAGGTGTCTCTCATTAAAGgCTACATGATATTTAATGTgcaGGC---CAcATTAAaTATCATGTAGCAAGGTTTAATTTTTCATAGACCTTTGGAT GGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGT---GGCCTGCATATTAAGTATCATGTAGCAAGGTTTAATTTTTCATAGACCTTTGGAT Template switch alignment (log-probability: -23) GGAGGTGTCTCTCATTAAAGgCTACATGATATTTAATGTG|CAGGCCACATTAAA|TATCATGTAGCAAGGTTTAATTTTTCATAGACCTTTGGAT GGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTG|CAGGCCACATTAAA|TATCATGTAGCAAGGTTTAATTTTTCATAGACCTTTGGAT Chimp > Gorilla --------------- chr8:141553312-141553336 Template switch process: F1: L CGGAGGTGTCTCTCATTAAAG 1 F3: 4 CACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA R RF: CAGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGTGGCCTGCACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA RR: GTCTCCACAGAGAGTAATTTCTGATGTACTATAAATTACACCGGACGTGTAATTTATAGTACATCGTTCCAAATTAAAAAGTATCT F2: 3 CGGACGTGTAATTTATAGTACATCG 2 Unidirectional alignment (log-probability: -36.2) CgGAGGTGTCTCTCATTAAAGgCTACATGATATTTAATGTgcaGGC---CACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA CAGAGGTGTCTCTCATTAAAGACTACATGATATTTAATGT---GGCCTGCACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA Template switch alignment (log-probability: -23.9) CgGAGGTGTCTCTCATTAAAG|GCTACATGATATTTAATGTGCAGGC|CACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA CAGAGGTGTCTCTCATTAAAG|GCTACATGATATTTAATGTGCAGGC|CACATTAAATATCATGTAGCAAGGTTTAATTTTTCATAGA ========== Event 3545 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CCCCAAATCAGTGAAGAGATTTCCTATGTGCCTGAATATTGTCAAACAGTACGTGCAGAGAACA ↓ 13 24 ↑ 13 24 Chimp: CCCCAAATCAGTGAAGAGATTGACAATATTCAGGCACATAGGAAAACAGTACGTGCAGAGAACA Gorilla: CCCCAAATCAGTGAAGAGATTGACAATATTCAGGCACCTAGGAAAACAGTACGTGCGGAGAACA Human: CCCCAAATCAGTGAAGAGATTTCCTATGTGCCTGAATATTGTCAAACAGTACGTGCAGAGAACA Cluster: [ ] Orangutan: CCCCAGATCAGTGAAGAGATTGACAATATTCAGGCACATAGGAAAACAGCAGGTGCAGAGAACA Chimp > Human ------------- chr8:6027441-6027462 Template switch process: F1: L GAAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT 1 F3: 4 AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA R RF: GGAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATTGACAATATTCAGGCACATAGGAAAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA RR: CCTTCAGATATAGGTCGTTGGGGGTTTAGTCACTTCTCTAACTGTTATAAGTCCGTGTATCCTTTTGTCATGCACGTCTCTTGTGGTCGGTACCCATACCTGT F2: 3 CTGTTATAAGTCCGTGTATCCT 2 Unidirectional alignment (log-probability: -59.9) aAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT----------------------tcctatgtgcctgaatattgtcAAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA GAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATTGACAATATTCAGGCACATAGGA----------------------AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA Template switch alignment (log-probability: -24) aAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT|TCCTATGTGCCTGAATATTGTC|AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA GAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT|TCCTATGTGCCTGAATATTGTC|AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA Human > Chimp ------------- chr8:6228990-6229011 Template switch process: F1: L GGAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT 1 F3: 4 AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA R RF: GAAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATTTCCTATGTGCCTGAATATTGTCAAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA RR: CTTTCAGATATAGGTCGTTGGGGGTTTAGTCACTTCTCTAAAGGATACACGGACTTATAACAGTTTGTCATGCACGTCTCTTGTGGTCGGTACCCATACCTGT F2: 3 AGGATACACGGACTTATAACAG 2 Unidirectional alignment (log-probability: -59.9) gAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT----------------------gacaatattcaggcacataggaAAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA AAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATTTCCTATGTGCCTGAATATTGTC----------------------AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA Template switch alignment (log-probability: -24) gAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT|GACAATATTCAGGCACATAGGA|AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA AAAGTCTATATCCAGCAACCCCCAAATCAGTGAAGAGATT|GACAATATTCAGGCACATAGGA|AAACAGTACGTGCAGAGAACACCAGCCATGGGTATGGACA ========== Event 3546 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 346 Detected in comparisons: 3456 Multiple sequence alignment: Human: AGCATCTCAGAAGCCTGAGATAG---GTTGGTCCAACCACTG-GGAAGGCTT---ATCTCCTACGTCTCATGCCATGGGCCGTGATCCCCACATTTGATGTA Chimp: AGCATCTCAGAAGCCTGAGATAG---GTTGGTCCAACCACTG-GGAAGGCTT---ATCTCCTACGTCTCATACCATGGGCTGTGATCCCCACATTTGATGTA ↓ 3 1 2 4 Gorilla: AGCATCTCAGAAGCCTGAGATAGGAGATAAGCCTTCCCAGTG-GTTGGACCA------ACCTATGTCTCATGCCATGGGCCATGATCCCCACATTTGATGTA ↓ 13 24 ↑ 3 1 2 4 Human: AGCATCTCAGAAGCCTGAGATAG---GTTGGTCCAACCACTG-GGAAGGCTT---ATCTCCTACGTCTCATGCCATGGGCCGTGATCCCCACATTTGATGTA Cluster: [ ] Orangutan: AGCATCTCAGAAGCCTGAGATAG---GTTGGTCCAACCACTGGGGAAGGCTTATC---TCCTACCTCTCATGCCATGGGCTATGATCCCCATATTTGATGTA Gorilla > Human --------------- chr8:6033943-6033970 Template switch process: F1: L CATGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG 1 F3: 4 CCTACGTCTCATGCCATGGGCCGTGATCCCCACATTTGATGTAAA R RF: CATGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGGAGATAAGCCTTCCCAGTGGTTGGACCAACCTATGTCTCATGCCATGGGCCATGATCCCCACATTTGATGTAAA RR: GTACCTGGAGGGACGGAGTCGTAGAGTCTTCGGACTCTATCCTCTATTCGGAAGGGTCACCAACCTGGTTGGATACAGAGTACGGTACCCGGTACTAGGGGTGTAAACTACATTT F2: 3 TCTATTCGGAAGGGTCACCAACCTGGTT 2 Unidirectional alignment (log-probability: -65.7) TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATA-------------------GGTTGGtCCAAccactgggaaggcttatctCCTAcGTCTCATGCCATGGGCCgTGATCCCCACATTTGAT TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGGAGATAAGCCTTCCCAGTGGTTGGACCAA-------------------CCTATGTCTCATGCCATGGGCCATGATCCCCACATTTGAT Template switch alignment (log-probability: -30.5) TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG|TTGGTCCAACCACTGGGAAGGCTTATCT|CCTAcGTCTCATGCCATGGGCCgTGATCCCCACATTTGAT TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG|TTGGTCCAACCACTGGGAAGGCTTATCT|CCTATGTCTCATGCCATGGGCCATGATCCCCACATTTGAT Human > Gorilla --------------- chr8:6091272-6091304 Template switch process: F1: L CATGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG 1 F3: 4 GTCTCATGCCATGGGCCATGATCCCCACATTTGATGTAAA R RF: CATGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGGTTGGTCCAACCACTGGGAAGGCTTATCTCCTACGTCTCATGCCATGGGCCGTGATCCCCACATTTGATGTAAA RR: GTACCTGGAGGGACGGAGTCGTAGAGTCTTCGGACTCTATCCAACCAGGTTGGTGACCCTTCCGAATAGAGGATGCAGAGTACGGTACCCGGCACTAGGGGTGTAAACTACATTT F2: 3 TATCCAACCAGGTTGGTGACCCTTCCGAATAGA 2 Unidirectional alignment (log-probability: -65.7) TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAggagataagccttcccagtGGTTGGaCCAA-------------------CCTAtGTCTCATGCCATGGGCCaTGATCCCCACATTTGATGTAAA TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATA-------------------GGTTGGTCCAACCACTGGGAAGGCTTATCTCCTACGTCTCATGCCATGGGCCGTGATCCCCACATTTGATGTAAA Template switch alignment (log-probability: -25.5) TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG|AGATAAGCCTTCCCAGTGGTTGGACCAACCTAT|GTCTCATGCCATGGGCCaTGATCCCCACATTTGATGTAAA TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG|AGATAAGCCTTCCCAGTGGTTGGACCAACCTAT|GTCTCATGCCATGGGCCGTGATCCCCACATTTGATGTAAA Chimp > Gorilla --------------- chr8:6091272-6091304 Template switch process: F1: L CATGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG 1 F3: 4 GTCTCATGCCATGGGCCATGATCCCCACATTTGATGTAAATTCTCGGGCTGTGTGATG R RF: CATGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGGTTGGTCCAACCACTGGGAAGGCTTATCTCCTACGTCTCATACCATGGGCTGTGATCCCCACATTTGATGTAAATTCTCGGGCTGTGTGATG RR: GTACCTGGAGGGACGGAGTCGTAGAGTCTTCGGACTCTATCCAACCAGGTTGGTGACCCTTCCGAATAGAGGATGCAGAGTATGGTACCCGACACTAGGGGTGTAAACTACATTTAAGAGCCCGACACACTAC F2: 3 TATCCAACCAGGTTGGTGACCCTTCCGAATAGA 2 Unidirectional alignment (log-probability: -77) TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAggagataagccttcccagtGGTTGGaCCAA-------------------CCTAtGTCTCATgCCATGGGCcaTGATCCCCACATTTGATGTAAA TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATA-------------------GGTTGGTCCAACCACTGGGAAGGCTTATCTCCTACGTCTCATACCATGGGCTGTGATCCCCACATTTGATGTAAA Template switch alignment (log-probability: -36.9) TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG|AGATAAGCCTTCCCAGTGGTTGGACCAACCTAT|GTCTCATgCCATGGGCcaTGATCCCCACATTTGATGTAAA TGGACCTCCCTGCCTCAGCATCTCAGAAGCCTGAGATAGG|AGATAAGCCTTCCCAGTGGTTGGACCAACCTAT|GTCTCATACCATGGGCTGTGATCCCCACATTTGATGTAAA ========== Event 3547 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGATCTGTTGACTCTTGTTTTCAA--CAGTTTA-ATGTTGAGAACATACCATAAGGCTTC Chimp: AGATCTGTTGACTCTTGTTTTCAA--CAGTTTA-ATGTTGAGAACATACCATAAGGCTTC ↑ 1 3 4 2 Gorilla: AGATCTGTTGACTCTTGTTTTTAA--CACAGAAACTGTTGAGAACATACCATAAGGCTTC Human: AGATCTGTTGACTCTTGTTTTCAA--CAGTTTA-ATGTTGAGAACATACCATAAGGCTTC Cluster: [ ] Orangutan: AGATCTGTTGGCTCTTGTTTTCAACACAGTTTA-ATGTTGAGAACATACCATAAGGCTTC Gorilla > Chimp --------------- chr8:6199268-6199276 Template switch process: F1: L AACTACTAGGTGTTATCCCCAGATCTGTTGACTCTTGTTTT 1 F3: 4 AATGTTGAGAACATACCATAAGGCTTCCTTGCAAAAAATCCT R RF: AACTACTAGGTGCTATCCCCAGATCTGTTGACTCTTGTTTTTAACACAGAAACTGTTGAGAACATACCATAAGGCTTCCTTGCAAAAAATCCT RR: TTGATGATCCACGATAGGGGTCTAGACAACTGAGAACAAAAATTGTGTCTTTGACAACTCTTGTATGGTATTCCGAAGGAACGTTTTTTAGGA F2: 3 TTTGACAAC 2 Unidirectional alignment (log-probability: -38.2) ACTACTAGGTGtTATCCCCAGATCTGTTGACTCTTGTTttcaacagTTTAA---------TGTTGAGAACATACCATAAGGCTTCCTTGCAAAAAATC ACTACTAGGTGCTATCCCCAGATCTGTTGACTCTTGTT--------TTTAACACAGAAACTGTTGAGAACATACCATAAGGCTTCCTTGCAAAAAATC Template switch alignment (log-probability: -28) ACTACTAGGTGtTATCCCCAGATCTGTTGACTCTTGTTTT|CAACAGTTT|AaTGTTGAGAACATACCATAAGGCTTCCTTGCAAAAAATC ACTACTAGGTGCTATCCCCAGATCTGTTGACTCTTGTTTT|CAACAGTTT|ACTGTTGAGAACATACCATAAGGCTTCCTTGCAAAAAATC ========== Event 3548 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTGTTCTTATTCTCAGATAAATAAAAA-CGTATAGCCAACAAAATCAGT-----TTTTAAGTCCTCTATAAGTGGGCT ↓ 1 3 4 ↑ 3 4 2 Chimp: TTGTTCTTATTCTCAGATAAAAACTGATTTTGTTGGCTAT-----ACGT------TTTAAGTCCTCTATAAGTGGGCT Gorilla: TTGTTCTTATTCTCAGATAAAAACTGATTTTGTTGGCTAT-----ACGTTTTTA-TTTAAGTCCTCTGTAAGTGGGCT Human: TTGTTCTTATTCTCAGATAAATAAAAA-CGTATAGCCAACAAAATCAGT-----TTTTAAGTCCTCTATAAGTGGGCT Cluster: [ ] Orangutan: TTGTTCTTATTCTCAGATAAAAACTGATTTTGTTGGCTAT-----ACATTTTTA-TTTAAGTCCTCTATAAGTGGGCT Chimp > Human ------------- chr8:5599503-5599527 Template switch process: F1: L GTTTTATCACCTTACTGGGGTTGTTCTTATTCTCAGATAAATA 1 F3: 4 TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTTT R RF: GTTTTATCACCTTATTGGGGTTGTTCTTATTCTCAGATAAAAACTGATTTTGTTGGCTATACGTTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTTT RR: CAAAATAGTGGAATAACCCCAACAAGAATAAGAGTCTATTTTTGACTAAAACAACCGATATGCAAAATTCAGGAGATATTCACCCGAATAGGTGATCGGTGAAA F2: 3 TGACTAAAACAACCGATATGCAAAA 2 Unidirectional alignment (log-probability: -67.1) TTATCACCTTAcTGGGGTTGTTCTTATTCTCAGATAAA----------------------taaaaacgtatagccaacaaaatcagtTTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT TTATCACCTTATTGGGGTTGTTCTTATTCTCAGATAAAAACTGATTTTGTTGGCTATACG---------------------------TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT Template switch alignment (log-probability: -30.4) TTATCACCTTAcTGGGGTTGTTCTTATTCTCAGATAAAtA|AAAACGTATAGCCAACAAAATCAGT|TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT TTATCACCTTATTGGGGTTGTTCTTATTCTCAGATAAAAA|AAAACGTATAGCCAACAAAATCAGT|TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT Human > Chimp ------------- chr8:5786022-5786043 Template switch process: F1: L GTTTTATCACCTTATTGGGGTTGTTCTTATTCTCAGATAAA 1 F3: 4 TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTTT R RF: GTTTTATCACCTTACTGGGGTTGTTCTTATTCTCAGATAAATAAAAACGTATAGCCAACAAAATCAGTTTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTTT RR: CAAAATAGTGGAATGACCCCAACAAGAATAAGAGTCTATTTATTTTTGCATATCGGTTGTTTTAGTCAAAAATTCAGGAGATATTCACCCGAATAGGTGATCGGTGAAA F2: 3 GCATATCGGTTGTTTTAGTCAA 2 Unidirectional alignment (log-probability: -60.1) TTTTATCACCTTAtTGGGGTTGTTCTTATTCTCAGATAAA---------------------------aactgattttgttggctatacgTTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT TTTTATCACCTTACTGGGGTTGTTCTTATTCTCAGATAAATAAAAACGTATAGCCAACAAAATCAGT----------------------TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT Template switch alignment (log-probability: -24) TTTTATCACCTTAtTGGGGTTGTTCTTATTCTCAGATAAA|AACTGATTTTGTTGGCTATACG|TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT TTTTATCACCTTACTGGGGTTGTTCTTATTCTCAGATAAA|AACTGATTTTGTTGGCTATACG|TTTTAAGTCCTCTATAAGTGGGCTTATCCACTAGCCACTT ========== Event 3549 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAATACACAGCAAGAAGGACAAATAGGTTCATGGGCTGCTCAGCTCTCAAGCAGTCCGAAGTTG Chimp: AAATACACAGCAAGAAGGACAGATAGGTTCATGGGCTTCTCAGCTCTCAAGCAGTCCGAAGTTG ↓ 13 24 ↑ 13 24 Gorilla: AAATACACAGCAAGAAGGACAGATAGCTGAGCAGCCCATGAACCTCTCAAGCAGTCCGAAGTTG ↓ 13 24 Human: AAATACACAGCAAGAAGGACAAATAGGTTCATGGGCTGCTCAGCTCTCAAGCAGTCCGAAGTTG Cluster: [ ] Orangutan: AAATACACAGCAAGAAGGACAGATAGGTTCACAGGCTGCTCAGCTCTCAAGCAGTCTGAAGTTG Gorilla > Human --------------- chr8:5610710-5610726 Template switch process: F1: L TCTAACTTCACTCCTAAGTGAAATACACAGCAAGAAGGACAAATAG 1 F3: 4 CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC R RF: TCTAACTTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATAGCTGAGCAGCCCATGAACCTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC RR: AGATTGAAGTGAGGATTTACTTTATGTGTCGTTCTTCCTGTCTATCGACTCGTCGGGTACTTGGAGAGTTCGTCAGGCTTCAACCGTTCAGACGGAGTAGAGG F2: 3 GACTCGTCGGGTACTTG 2 Unidirectional alignment (log-probability: -55.2) TTCACTCCTAAgTGAAATACACAGCAAGAAGGACAaATAggttcatgggctGCTcAG------------CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC TTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATA------------GCTGAGCAGCCCATGAACCTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC Template switch alignment (log-probability: -29.1) TTCACTCCTAAgTGAAATACACAGCAAGAAGGACAaATAG|GTTCATGGGCTGCTCAG|CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC TTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATAG|GTTCATGGGCTGCTCAG|CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC Gorilla > Chimp --------------- chr8:5797196-5797212 Template switch process: F1: L CTTCACTCCTAAGTGAAATACACAGCAAGAAGGACAGATAG 1 F3: 4 CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC R RF: CTTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATAGCTGAGCAGCCCATGAACCTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC RR: GAAGTGAGGATTTACTTTATGTGTCGTTCTTCCTGTCTATCGACTCGTCGGGTACTTGGAGAGTTCGTCAGGCTTCAACCGTTCAGACGGAGTAGAGG F2: 3 GACTCTTCGGGTACTTG 2 Unidirectional alignment (log-probability: -49.6) TTCACTCCTAAgTGAAATACACAGCAAGAAGGACAGATAGgttcatgggcttCTcAG------------CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC TTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATAG------------CTGAGCAGCCCATGAACCTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC Template switch alignment (log-probability: -28.9) TTCACTCCTAAgTGAAATACACAGCAAGAAGGACAGATAG|GTTCATGGGCTtCTCAG|CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC TTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATAG|GTTCATGGGCTGCTCAG|CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC Chimp > Gorilla --------------- chr8:5651755-5651771 Template switch process: F1: L CTTCACTCCTAAATGAAATACACAGCAAGAAGGACAGATAG 1 F3: 4 CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC R RF: CTTCACTCCTAAGTGAAATACACAGCAAGAAGGACAGATAGGTTCATGGGCTTCTCAGCTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC RR: GAAGTGAGGATTCACTTTATGTGTCGTTCTTCCTGTCTATCCAAGTACCCGAAGAGTCGAGAGTTCGTCAGGCTTCAACCGTTCAGACGGAGTAGAGG F2: 3 CAAGTACCCGACGAGTC 2 Unidirectional alignment (log-probability: -49.6) TTCACTCCTAAaTGAAATACACAGCAAGAAGGACAGATAG------------CTgAGcagcccatgaacCTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC TTCACTCCTAAGTGAAATACACAGCAAGAAGGACAGATAGGTTCATGGGCTTCTCAG------------CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC Template switch alignment (log-probability: -28.9) TTCACTCCTAAaTGAAATACACAGCAAGAAGGACAGATAG|CTGAGcAGCCCATGAAC|CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC TTCACTCCTAAGTGAAATACACAGCAAGAAGGACAGATAG|CTGAGAAGCCCATGAAC|CTCTCAAGCAGTCCGAAGTTGGCAAGTCTGCCTCATCTCC ========== Event 3550 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGGGCTTCATAGCTATCAGAGG-AT--GCCAAGATAATCGTTTTCCAACA Chimp: TAGGGCTTCATAGCTATCAGAGG-AT--GCCAAGATAATCGTTTTCCAACA Gorilla: TAGGGCTTCATAGCTATCAGAGGAATGCTCCAAGATAATCGTTTTCCAACA ↑ 3 1 2 4 Human: TAGGGCTTCATAGCTATCAGAGG-AT--GCCAAGATAATCGTTTTCCAACA Cluster: [ ] Orangutan: TAGGGCTTCATAGCTATCAGAGG-AT--GCCAAGATAATCGTTTTCCAACA Human > Gorilla --------------- chr8:5679146-5679151 Template switch process: F1: L ATTAGCAGTCTTGGGGTTTAGGGCTTCATAGCTATCAGAGGA 1 F3: 4 CAAGATAATCGTTTTCCAACACAGGAT R RF: ATTAGCAGTCTTGGGGTTTAGGGCTTCATAGCTATCAGAGGATGCCAAGATAATCGTTTTCCAACACAAGAT RR: TAATCGTCAGAACCCCAAATCCCGAAGTATCGATAGTCTCCTACGGTTCTATTAGCAAAAGGTTGTGTTCTA F2: 3 CTCGTA 2 Unidirectional alignment (log-probability: -37.7) TAGCAGTCTTGGGGTTTAGGGCTTCATAGCTATCAGAGGaATGctCCAAGATAATCGTTTTCCAACACAgGAT------------ TAGCAGTCTTGGGGTTTAGGGCTTCATAGCTATCAGAGG-ATG--CCAAGATAATCGTTTTCCAACACAAGATCCTGGATTCTAC Template switch alignment (log-probability: -27.2) TAGCAGTCTTGGGGTTTAGGGCTTCATAGCTATCAGAGGA|ATgCTC|CAAGATAATCGTTTTCCAACACAgGAT TAGCAGTCTTGGGGTTTAGGGCTTCATAGCTATCAGAGGA|ATCCTC|CAAGATAATCGTTTTCCAACACAAGAT ========== Event 3551 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CACAGTATTCTGTGTCTGCTCACCGGTCTG-TCTTGAGAGGACCCATTTTATGTTTTAC ↓ 31 2 4 Chimp: CACAGTATTCTGTGTCTGCTCCCCGGTCTGTTCAAGACAGGACCCATTTTATGTTTTAC Gorilla: CACAGTATTCTGTGTCTGCTCACCGGTCTGTTCAAGACAGGACCCATTTTATGTTTTAC ↑ 31 2 4 Human: CACAGTATTCTGTGTCTGCTCACCGGTCTG-TCTTGAGAGGACCCATTTTATGTTTTAC Cluster: [ ] Orangutan: CACAGTATTCTGTGTCTGCTCACCGGTCTG-TCTTGAGAGGACCTATTTTATGTTTTAC Human > Chimp ------------- chr8:5287840-5287846 Template switch process: F1: L TGTCTCCTAGCGAATGATCTCACAGTATTCTGTGTCTGCTCCCCGGTCTGT 1 F3: 4 AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA R RF: TGTCTCCTAGCGAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGTCTTGAGAGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA RR: ACAGAGGATCGCTTACTAGAGTGTCATAAGACACAGACGAGTGGCCAGACAGAACTCTCCTGGGTAAAATACAAAATGACTACGTATAATGATAATT F2: 3 CAGAACT 2 Unidirectional alignment (log-probability: -36.1) GAATGATCTCACAGTATTCTGTGTCTGCTCcCCGGTCTGTtcaagaC-----AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA GAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGT------CTTGAGAGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA Template switch alignment (log-probability: -22.3) GAATGATCTCACAGTATTCTGTGTCTGCTCcCCGGTCTGT|TCAAGAC|AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA GAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGT|TCAAGAC|AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA Human > Gorilla --------------- chr8:5156285-5156291 Template switch process: F1: L GCGAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGT 1 F3: 4 AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA R RF: GCGAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGTCTTGAGAGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA RR: CGCTTACTAGAGTGTCATAAGACACAGACGAGTGGCCAGACAGAACTCTCCTGGGTAAAATACAAAATGACTACGTATAATGATAATT F2: 3 CAGAACT 2 Unidirectional alignment (log-probability: -29) GAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGtTCaaGAcAGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA GAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTG-TCTTGAGAGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA Template switch alignment (log-probability: -16.6) GAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGT|TCAAGAC|AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA GAATGATCTCACAGTATTCTGTGTCTGCTCACCGGTCTGT|TCAAGAC|AGGACCCATTTTATGTTTTACTGATGCATATTACTATTAA ========== Event 3552 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGGAGGTGGTCCTGGGAGGATGGACTGGCTGAGTCCAT----------------------------------------------------------------------------------------------TGTGTGGGTAAGGACTAAAAC ↑ 3 2 1 4 Chimp: TGGAGGTGGTCCTGGGAGGATGGACTGGCTGCTTCCAT-----------------------------------------------TgcctgacatgttgcagttgctccctaaatgcttgttaaatgaaCAATGTGTGGGTAAGGACTAAAAC Gorilla: TGGAGGTGGTCCTGGGAGGATGGACTGGCTGCGTccattgcctgacatgttgcagttgctccctaaatgcttgttaagtgaacaa-----------------------------------------------TGTGTGGGTAAGGACTAAAAC Human: TGGAGGTGGTCCTGGGAGGATGGACTGGCTGAGTCCAT----------------------------------------------------------------------------------------------TGTGTGGGTAAGGACTAAAAC Cluster: [ ] Orangutan: TGGAGGTGGTCCTGGGAGGATGGACTGGCTGTGTCCATTgcctgacatgttgcagatgctccctaaatgcttgttaagtgaacaa-----------------------------------------------TGTGTGAGTAAGgactaaaac Chimp > Human ------------- chr8:4700832-4700838 Template switch process: F1: L CTGCGCCTCCTGGAGGTGGTCCTGGGAGGATGGACTGGCTG 1 F3: 4 TGTGTGGGTAAGGACTAAAACAGGGTTCTTTCGTTGAGGT R RF: CTGCGCCTCCTGGAGGTGGTCCTGGGAGGATGGACTGGCTGCTTCCATTGCCTGACATGTTGCAGTTGCTCCCTAAATGCTTGTTAAATGAACAATGTGTGGGTAAGGACTAAAACAGGGTTCTTTCGTTGAGGT RR: GACGCGGAGGACCTCCACCAGGACCCTCCTACCTGACCGACGAAGGTAACGGACTGTACAACGTCAACGAGGGATTTACGAACAATTTACTTGTTACACACCCATTCCTGATTTTGTCCCAAGAAAGCAACTCCA F2: 3 TACCTGA 2 Unidirectional alignment (log-probability: -25.4) TGCGCCTCCTGGAGGTGGTCCTGGGAGGATGGACTGGCTGagTCCAT-----------------------------------------------TGTGTGGGTAAGGACTAAAACAGGGTTCTTTCGTTGAGGT TGCGCCTCCTGGAGGTGGTCCTGGGAGGATGGACTGGCTGCTTCCATTGCCTGACATGTTGCAGTTGCTCCCTAAATGCTTGTTAAATGAACAATGTGTGGGTAAGGACTAAAACAGGGTTCTTTCGTTGAGGT Template switch alignment (log-probability: -16.2) TGCGCCTCCTGGAGGTGGTCCTGGGAGGATGGACTGGCTG|AGTCCAT|TGTGTGGGTAAGGACTAAAACAGGGTTCTTTCGTTGAGGT TGCGCCTCCTGGAGGTGGTCCTGGGAGGATGGACTGGCTG|AGTCCAT|TGTGTGGGTAAGGACTAAAACAGGGTTCTTTCGTTGAGGT ========== Event 3553 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: gtCCCCTGGGAGGCCTGCAGGGGGCTGGCGTGTG-ATAGGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGT Chimp: gtcccctgggaggcctgcagggggCTGGCGTGTG-ATAGGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGT Gorilla: gtcccctgggAGGCCTGCAGGAGGCTGGTGTGCAGCGTGGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGT ↑ 1 4 3 2 Human: gtCCCCTGGGAGGCCTGCAGGGGGCTGGCGTGTG-ATAGGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGT Cluster: [ ] Orangutan: GTCCCCTGGGAGGCCTGCAGGGGGCTGGCATGTG-ATAGGAGGGACTCCATGCCATGTGGATAGAGGCAGGGGGT Human > Gorilla --------------- chr8:143081525-143081530 Template switch process: F1: L GGTGTTGGGGGATCAACGGGGTCCCCTGGGAGGCCTGCAGGAGGCTGGTGTG 1 F3: 4 GGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGTGAG R RF: GGTGTTGGGGGATCAACGGGGTCCCCTGGGAGGCCTGCAGGGGGCTGGCGTGTGATAGGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGTGAG RR: CCACAACCCCCTAGTTGCCCCAGGGGACCCTCCGGACGTCCCCCGACCGCACACTATCCTCCCTGAGGTGCGACACACCTATCTCCGTCCCCCACTC F2: 3 TGCGAC 2 Unidirectional alignment (log-probability: -36.7) TCAACGGGGTCCCCTGGGAGGCCTGCAGGaGGCTGgtgtgcaGCGT------GGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGTGAG TCAACGGGGTCCCCTGGGAGGCCTGCAGGGGGCTG-------GCGTGTGATAGGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGTGAG Template switch alignment (log-probability: -27.8) TCAACGGGGTCCCCTGGGAGGCCTGCAGGaGGCTGGtGTG|CAGCGT|GGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGTGAG TCAACGGGGTCCCCTGGGAGGCCTGCAGGGGGCTGGCGTG|CAGCGT|GGAGGGACTCCACGCTGTGTGGATAGAGGCAGGGGGTGAG ========== Event 3554 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCTGCGGAGATGGGCAGGGGACTGAGCGGGGGCTCAGGACTGGACACATCAAGTGAC Chimp: GCTGCGGAGATGGGCAGGGGACTGAGCGGGGGCTCAGGACTGGACACATCAAGTGAC ↑ 1 3 4 2 Gorilla: GCTGCGGAGATGGGCAGGGGATACC----CCGCTCAGGACTGGACACATCAAGTGAC ↓ 1 3 4 2 Human: GCTGCGGAGATGGGCAGGGGACTGAGCGGGGGCTCAGGACTGGACACATCAAGTGAC Cluster: [ ] Orangutan: GCTGCGGAGATGGGCAGGGGATACC----CCGCTCAGGGCTGGACACATCAAGTGAC Gorilla > Human --------------- chr8:3564308-3564317 Template switch process: F1: L CCCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA 1 F3: 4 GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCG R RF: CCCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGATACCCCGCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCA RR: GGGTCCAGTGGTGTCTGTCTCGACGCCTCTACCCGTCCCCTATGGGGCGAGTCCTGACCTGTGTAGTTCACTGGGTTCCTGAGTGGT F2: 3 GGGGCGAGTC 2 Unidirectional alignment (log-probability: -39.4) CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA-----CtgagcggggGCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCg CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGATACCCC---------GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCA Template switch alignment (log-probability: -22.5) CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA|CTGAGCGGGG|GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCg CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA|CTGAGCGGGG|GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCA Gorilla > Chimp --------------- chr8:3663574-3663583 Template switch process: F1: L CCCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA 1 F3: 4 GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACTG R RF: CCCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGATACCCCGCTCAGGACTGGACACATCAAGTGACCCAAGGACTCAC RR: GGGTCCAGTGGTGTCTGTCTCGACGCCTCTACCCGTCCCCTATGGGGCGAGTCCTGACCTGTGTAGTTCACTGGGTTCCTGAGTG F2: 3 GGGGCGAGTC 2 Unidirectional alignment (log-probability: -44.9) CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA-----CtgagcggggGCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACtg CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGATACCCC---------GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCACCA Template switch alignment (log-probability: -26.6) CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA|CTGAGCGGGG|GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCActg CCAGGTCACCACAGACAGAGCTGCGGAGATGGGCAGGGGA|CTGAGCGGGG|GCTCAGGACTGGACACATCAAGTGACCCAAGGACTCA--C ========== Event 3555 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: aggccccgtgtttgctgtTTTTTTC-TAGTGTCACCACTGGCCACAGCCACACTAGACCTCAGG-CAAGCTCGG-GC Chimp: ----------tttgctgtTTT--TT-CAGCGTCACCACTGGCCACAGCCACACTAGACCTCAGG-CAAGCTCGG-GC Gorilla: ----------tttgctgtTTT--TT-CAGCGTCACCACTGGCCACAGCCACACTAGACCTCAGG-CAAGCTCGG-GC ↓ 1 4 3 2 Human: aggccccgtgtttgctgtTTTTTTC-TAGTGTCACCACTGGCCACAGCCACACTAGACCTCAGG-CAAGCTCGG-GC Cluster: [ ] Orangutan: ----------TTTGCTGTTTT--TTCTAGCATCACCACTGGCCACAGCCACACTAGACCTCAGGCCAAGCTCGGGCC Gorilla > Human --------------- chr8:3209598-3209603 Template switch process: F1: L ----------------------------------------------------------------------GCCCAGTTTGGTGCATGCCGAGGCCCCGTGTTTGCTGTTTTTT 1 F3: 4 GTCACCACTGGCCACAGCCACACTAGACCTCAGGCAAGCT R RF: CAGGTTGGTGCATGGTGAGGCCTCATGTTTGCAGTGCGGGTTCCAGAGCTCATGGCTGCGGTGGGTTCTGGCCCAGTTTGGTGCATGCCGAGGCCCCGTGTTTGCTGTTTTTTCAGCGTCACCACTGGCCACAGCCACACTAGACCTCAGGCAAGCT RR: GTCCAACCACGTACCACTCCGGAGTACAAACGTCACGCCCAAGGTCTCGAGTACCGACGCCACCCAAGACCGGGTCAAACCACGTACGGCTCCGGGGCACAAACGACAAAAAAGTCGCAGTGGTGACCGGTGTCGGTGTGATCTGGAGTCCGTTCGA F2: 3 TGATCT 2 Unidirectional alignment (log-probability: -72) cagtttggtgcatgccgaggccccgtgTTTGCTGTTTTTTtctAGtGTCACCACTGGCCACAGCCACACTAGACCTCAGGCAAGCT ---------------------------TTTGCTGTTTTTT--CAGCGTCACCACTGGCCACAGCCACACTAGACCTCAGGCAAGCT Template switch alignment (log-probability: -29.9) CAGTTTGGTGCATGCCGAGGCCCCGTGTTTGCTGTTTTTT|TCTAGT|GTCACCACTGGCCACAGCCACACTAGACCTCAGGCAAGCT CAGTTTGGTGCATGCCGAGGCCCCGTGTTTGCTGTTTTTT|TCTAGT|GTCACCACTGGCCACAGCCACACTAGACCTCAGGCAAGCT ========== Event 3556 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGCATCGGGCTCTGGGTGTGTCGGGTCTCA--------GGCGATCCTGGCGTGGCAGCCGGTGGGTGTGGGCTCTCCTGAGAACCTCATCCTAGACCACCTG Chimp: GGCATCGGGCTCTGGGTGTGTTGGGTCTCA--------GGCGATCCTGGCGCGGCAGCCGGCGGGTGTGGGTTCTCCTGAGAACCTCATCCTAGACCACCTG ↑ 1 4 3 2 Gorilla: GGCATCGGGCTCTGGGTGTGTCGG-GCTCTGGGTGCGCCGCGATCCTGGCACGGCAGCCGGCGGGTGTGGGTTCTCCTGAGAACCTCATCCTAGACCACCTG Human: AGCATCGGGCTCTGGGTGTGTCGGGTCTCA--------GGCGATCCTGGCGTGGCAGCCGGTGGGTGTGGGCTCTCCTGAGAACCTCATCCTAGACCACCTG Cluster: [ ] Orangutan: GGCATCGAGCTCTGGGGGTGTTGGGTCTCA--------GGCGATCCTGGCTCGGCAGCCGGCGGGTGTGGTTTCTCCTGAGAACCTCGTCCTAGACCACCCG Gorilla > Chimp --------------- chr8:3466023-3466028 Template switch process: F1: L TTCTGGGCCCCTGCAGACCCGGCATCGGGCTCTGGGTGTGTTGGG 1 F3: 4 GCGATCCTGGCGCGGCAGCCGGCGGGTGTGGGTTCTCCTG R RF: TTCTGGGCCCCTGCAGACCCGGCATCGGGCTCTGGGTGTGTCGGGCTCTGGGTGCGCCGCGATCCTGGCACGGCAGCCGGCGGGTGTGGGTTCTCCTGAGA RR: AAGACCCGGGGACGTCTGGGCCGTAGCCCGAGACCCACACAGCCCGAGACCCACGCGGCGCTAGGACCGTGCCGTCGGCCGCCCACACCCAAGAGGACTCT F2: 3 GACTCT 2 Unidirectional alignment (log-probability: -39.2) GGCCCCTGCAGACCCGGCATCGGGCTCTGGGTGTGTtGGGtCTCaG--------GCGATCCTGGCgCGGCAGCCGGCGGGTGTGGGTTCTCCTG GGCCCCTGCAGACCCGGCATCGGGCTCTGGGTGTGTCGGG-CTCTGGGTGCGCCGCGATCCTGGCACGGCAGCCGGCGGGTGTGGGTTCTCCTG Template switch alignment (log-probability: -27.6) GGCCCCTGCAGACCCGGCATCGGGCTCTGGGTGTGTtGGG|TCTCAG|GCGATCCTGGCgCGGCAGCCGGCGGGTGTGGGTTCTCCTG GGCCCCTGCAGACCCGGCATCGGGCTCTGGGTGTGTCGGG|TCTCAG|GCGATCCTGGCACGGCAGCCGGCGGGTGTGGGTTCTCCTG ========== Event 3557 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTGAGCACCAGCCCAGGAATGCTGGTGGGCATGTGCCCCTCTTCCCTCCCACCCATGTGTGCA----CACATTTGTGCCATATACTACCGTTCCCATGTTTGCGCCTGGGCACACACTTGTGCCAGCATACACACACTTGTGCACTTGCACCTGGTGTCCAGG ↑ 3 2 4 1 Chimp: CCTGAGCACCAGCCCAGGAATGCTGGTGGGCATGTGCCCCTCTTCCCTCCCACCCATGTGTGCA--CACACATTTGTGCCATATACTACCGTTCCCATGTTCGCGCCTGGGCACACAC--------------------TTGTGCACTTGCACCTGGTGTCCAGG Gorilla: TCTGAGCACCAGCCCAGGAATGCTGGTGGGCATGTGCCTCTCTTCCCTCCCACCCATGTGTGCACA--CACATTTGTGCCATATACTACCGTTCCCATGTTCGTGCCTGGGCACACACTTGTGCCAGCATACACACACTTGTGCACTTGCACCTGGTGTCCAGG Human: CCTGAGCACCAGCCCAGGAATGCTGGTGGGCATGTGCCCCTCTTCCCTCCCACCCATGTGTGCA----CACATTTGTGCCATATACTACCGTTCCCATGTTTGCGCCTGGGCACACACTTGTGCCAGCATACACACACTTGTGCACTTGCACCTGGTGTCCAGG Cluster: [ ] Orangutan: CCTGAGC------ACAGGAACGCTGGTGGGCATGTGCCCCTCTTCCATCCCACCCATGTGTGCACA--CACATTTGTGCCATATACTACCGTTCCCATGCTCGCGGCTGGGCACACACTTGTGCCAGCATACACACACTTGTGCACTTGCACCTGGTGTCCAGG Chimp > Human ------------- chr8:2734238-2734243 Template switch process: F1: L GCCATATACTACCGTTCCCATGTTTGCGCCTGGGCACACACTTGTGC 1 F3: 4 ACACACACTTGTGCACTTGCACCTGGTGTCCAGGAACACTCCCTCAGC R RF: ATGCTGGTGGGCATGTGCCCCTCTTCCCTCCCACCCATGTGTGCACACACATTTGTGCCATATACTACCGTTCCCATGTTCGCGCCTGGGCACACACTTGTGCACTTGCACCTGGTGTCCAGGAACACTCCCTCAGC RR: TACGACCACCCGTACACGGGGAGAAGGGAGGGTGGGTACACACGTGTGTGTAAACACGGTATATGATGGCAAGGGTACAAGCGCGGACCCGTGTGTGAACACGTGAACGTGGACCACAGGTCCTTGTGAGGGAGTCG F2: 3 TACGAC 2 Unidirectional alignment (log-probability: -45.7) ACTACCGTTCCCATGTTtGCGCCTGGGCACACACTTGtgccagcatacacacacttgTGCACTTGCACCTGGTGTCCAGGAACACT ACTACCGTTCCCATGTTCGCGCCTGGGCACACACTTG--------------------TGCACTTGCACCTGGTGTCCAGGAACACT Template switch alignment (log-probability: -28.3) ACTACCGTTCCCATGTTtGCGCCTGGGCACACACTTGTGC|CAGCAT|aCACACACTTGTGCACTTGCACCTGGTGTCCAGGAACACT ACTACCGTTCCCATGTTCGCGCCTGGGCACACACTTGTGC|CAGCAT|GCACACACTTGTGCACTTGCACCTGGTGTCCAGGAACACT ========== Event 3558 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCCGGGTCCTTGCACAGGGATAGCTGATCCACCGATCAGGCCCCTCCTCCCGCTGAC Chimp: CTCCGGGTCCTTGCACTGGGAGAGCTGATCGGTG--GCAGGCCCCTCCTCCCGCTGAC Gorilla: CTCCGGGTCCTTGCACAGGGAGAGCTGATCGGTG--GCAGGCCCCTCCTCCCGCTGAC ↓ 3 1 2 4 Human: CTCCGGGTCCTTGCACAGGGATAGCTGATCCACCGATCAGGCCCCTCCTCCCGCTGAC Cluster: [ ] Orangutan: Gorilla > Human --------------- chr8:2115215-2115221 Template switch process: F1: L CTGCAGGCTGCTCTGATGGGCTCCGGGTCCTTGCACAGGGATAGCTGATC 1 F3: 4 CAGGCCCCTCCTCCCGCTGACCTCTTCCAGGCCCTCTCGC R RF: CTGCAGGCTGCTCTGATGGGCTCCGGGTCCTTGCACAGGGAGAGCTGATCGGTGGCAGGCCCCTCCTCCCGCTGACCTCTTCCAGGCCCTCTCGC RR: GACGTCCGACGAGACTACCCGAGGCCCAGGAACGTGTCCCTCTCGACTAGCCACCGTCCGGGGAGGAGGGCGACTGGAGAAGGTCCGGGAGAGCG F2: 3 TAGCCAC 2 Unidirectional alignment (log-probability: -36.6) CTCTGATGGGCTCCGGGTCCTTGCACAGGGAtAGCTGATC-----caccgatCAGGCCCCTCCTCCCGCTGACCTCTTCCAGGCCCTCTCGC CTCTGATGGGCTCCGGGTCCTTGCACAGGGAGAGCTGATCGGTGG-------CAGGCCCCTCCTCCCGCTGACCTCTTCCAGGCCCTCTCGC Template switch alignment (log-probability: -22.4) CTCTGATGGGCTCCGGGTCCTTGCACAGGGAtAGCTGATC|CACCGAT|CAGGCCCCTCCTCCCGCTGACCTCTTCCAGGCCCTCTCGC CTCTGATGGGCTCCGGGTCCTTGCACAGGGAGAGCTGATC|CACCGAT|CAGGCCCCTCCTCCCGCTGACCTCTTCCAGGCCCTCTCGC ========== Event 3559 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAAATACTTGTCCAACACCTGT------------------------GTAGGCACAAACCTGCGTGTGTGTGCTCCTCATCG Chimp: CAAATACTTGTCCAACACCTGT------------GTAGGTTTGTGTGTAGGCACAAACCTGCGTGTGTGTGCTCCTCATCG Gorilla: CAAATACTTGTCCAACACCTGTGCAGGTTTGTGT------------GTAGGCACAAAACTGCGTGTGTGTGCTCCTCATCA ↑ 4 1 3 2 Human: CAAATACTTGTCCAACACCTGT------------------------GTAGGCACAAACCTGCGTGTGTGTGCTCCTCATCG Cluster: [ ] Orangutan: CAAATACTTGTCCAACACCTGTGTAGGTTTGTGT------------GTAGGCACAAACCTGCGTGTGTGTGCTCCTCGTCC Human > Gorilla --------------- chr8:145327286-145327293 Template switch process: F1: L TCTTTTTAGGTTGACACAACAAATACTTGTCCAACACCTGTG 1 F3: 4 TGTGTAGGCACAAAACTGCGTGTGTGTGCTCCTCATCATGTGG R RF: TCTTTTTAGGTTGACACAACAAATACTTGTCCAACACCTGTGTAGGCACAAACCTGCGTGTGTGTGCTCCTCATCGTGTGG RR: AGAAAAATCCAACTGTGTTGTTTATGAACAGGTTGTGGACACATCCGTGTTTGGACGCACACACACGAGGAGTAGCACACC F2: 3 GTTTGGAC 2 Unidirectional alignment (log-probability: -39.2) TTTTTAGGTTGACACAACAAATACTTGTCCAACACCTgtgcaggtttgtGTGTAGGCACAAAaCTGCGTGTGTGTGCTCCTCATCaTG TTTTTAGGTTGACACAACAAATACTTGTCCAACACCT------------GTGTAGGCACAAACCTGCGTGTGTGTGCTCCTCATCGTG Template switch alignment (log-probability: -27.9) TTTTTAGGTTGACACAACAAATACTTGTCCAACACCTGTG|CAGGTTTG|TGTGTAGGCACAAAaCTGCGTGTGTGTGCTCCTCATCaTG TTTTTAGGTTGACACAACAAATACTTGTCCAACACCTGTG|CAGGTTTG|TGTGTAGGCACAAACCTGCGTGTGTGTGCTCCTCATCGTG ========== Event 3560 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CTGAAAATATCAGAGATGAAATAAAGCGTTAAGTCAGAATGCTTTATTCTGTCATCATGGAAATCATATTGT Chimp: CTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAATGCTTTATTCTGACATCATGGAAATCATATTGT ↑ 3 2 1 4 Gorilla: CTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAAAAACAT-ACCTGTCATCATGGAAATCATATTGT ↓ 3 2 1 4 Human: CTGAAAATATCAGAGATGAAATAAAGCGTTAAGTCAGAATGCTTTATTCTGTCATCATGGAAATCATATTGT Cluster: [ ] Orangutan: ------------------------------------------------------------------------ Gorilla > Human --------------- chr8:14415519-14415527 Template switch process: F1: L TCCTGAAAATATCAGAGATGAAATAAAGCGTTAAGTCAGAA 1 F3: 4 CTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC R RF: TCCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAAAAACATACCTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC RR: AGGACTTTTATAGTCTCTACTTTATTTCGTAATTCAGTCTTTTTGTATGGACAGTAGTACCTTTAGTATAACAAGATGATTTGTTCTTG F2: 3 TTATTTCGT 2 Unidirectional alignment (log-probability: -39.5) CCTGAAAATATCAGAGATGAAATAAAGCgTTAAGTCAGAA--------tgctttattCTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC CCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAAAAACATAC---------CTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC Template switch alignment (log-probability: -22.4) CCTGAAAATATCAGAGATGAAATAAAGCgTTAAGTCAGAA|TGCTTTATT|CTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC CCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAA|TGCTTTATT|CTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC Gorilla > Chimp --------------- chr8:13474966-13474974 Template switch process: F1: L TCCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAA 1 F3: 4 CTGACATCATGGAAATCATATTGTTCTACTAAACAAGAACATTA R RF: TCCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAAAAACATACCTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAACATTA RR: AGGACTTTTATAGTCTCTACTTTATTTCGTAATTCAGTCTTTTTGTATGGACAGTAGTACCTTTAGTATAACAAGATGATTTGTTCTTGTAAT F2: 3 TTATTTCGT 2 Unidirectional alignment (log-probability: -38.5) CCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAA-----------TgctttattctgaCATCATGGAAATCATATTGTTCTACTAAACAAGAAC CCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAAAAACATACCTGT------------CATCATGGAAATCATATTGTTCTACTAAACAAGAAC Template switch alignment (log-probability: -22.5) CCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAA|TGCTTTATT|CTGaCATCATGGAAATCATATTGTTCTACTAAACAAGAAC CCTGAAAATATCAGAGATGAAATAAAGCATTAAGTCAGAA|TGCTTTATT|CTGTCATCATGGAAATCATATTGTTCTACTAAACAAGAAC ========== Event 3561 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGCCCACGACCCGGCCCCTCGGAGGCGCAGACGCCTCCCTTCTTCCCACTGCCGTCCAGGGCCC Chimp: CAGCCCACGACCCGGCCCCTCAGAGGCGCAGACGCCTCCCTTCTTCCCACTGCCGTCCAGGGCCC ↓ 1 3 2 4 Gorilla: CAGCCCACGACCCGGCCCCTCGGAGGCGTCTGCGCC--------TCCCACTGCCGTCCAGGGCCC Human: CAGCCCACGACCCGGCCCCTCGGAGGCGCAGACGCCTCCCTTCTTCCCACTGCCGTCCAGGGCCC Cluster: [ ] Orangutan: CAGCCCACGACCCGGCCCCTTGGAGGCGCAGACACCTCCCTTCTTCCCACTGCCGTCCAGGGCCC Chimp > Gorilla --------------- chr8:903784-903798 Template switch process: F1: L CTGAACTCCCTGGGGGGCGACAGCCCACGACCCGGCCCCTC 1 F3: 4 TCCCACTGCCGTCCAGGGCCCAGGCCAGGGAAGGAGCCCT R RF: CTGAACTCCCTGGGGGGCGACAGCCCACGACCCGGCCCCTCAGAGGCGCAGACGCCTCCCTTCTTCCCACTGCCGTCCAGGGCCCAGGCCAGGGAAGGAGCCCT RR: GACTTGAGGGACCCCCCGCTGTCGGGTGCTGGGCCGGGGAGTCTCCGCGTCTGCGGAGGGAAGAAGGGTGACGGCAGGTCCCGGGTCCGGTCCCTTCCTCGGGA F2: 3 CCGCGTCTGCGGAGG 2 Unidirectional alignment (log-probability: -34.1) TGAACTCCCTGGGGGGCGACAGCCCACGACCCGGCCCCTCgGAGGCG-------------TCTgcgccTCCCACTGCCGTCCAGGGCCCAGGCCAGGGAAGGAGCCCT TGAACTCCCTGGGGGGCGACAGCCCACGACCCGGCCCCTCAGAGGCGCAGACGCCTCCCTTCT-----TCCCACTGCCGTCCAGGGCCCAGGCCAGGGAAGGAGCCCT Template switch alignment (log-probability: -17.6) TGAACTCCCTGGGGGGCGACAGCCCACGACCCGGCCCCTC|GGAGGCGTCTGCGCC|TCCCACTGCCGTCCAGGGCCCAGGCCAGGGAAGGAGCCCT TGAACTCCCTGGGGGGCGACAGCCCACGACCCGGCCCCTC|GGAGGCGTCTGCGCC|TCCCACTGCCGTCCAGGGCCCAGGCCAGGGAAGGAGCCCT ========== Event 3562 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAAGAGCCCCCATTGCAGGCAGGGGCT-----------GGGGGTGTGGAGGCC-GGCCCTGCTCACCATCTCCTGCCATGTGTCTGGGCAGCACGACCTGCCAGGGCCCGTGGCCTGTGGCGAGGGTGGCGGCAGCAGGACGGGTGGCTGAGAGCAGGGCCCGGCAGCCTGTCCGGACATGCCCGTGGCTT Chimp: ACAAGAGCCCCCATTGCAGGCAGGGGCT-----------GGGGGTGTGGAGGCC-GGCCCTGCTCACCATCTCCTGCCATGTGTCTGGGCAGCACGACCTGCCAGGACCCGTGGCCTGTGGCGAGGGTGGCGGCAGCAGGAGGGGTGGCTGAGAGCAGGGCCGAGCAGCCTGTCCGGACATGCCCGTGGCTT ↓ 4 1 3 2 Gorilla: ACAAGAGCCCCCATTGCAGGCGGGGGCTGGGCAGGCTCTGGGGGTGTGGAGGCC-GGCCCTGTTCACCATCTCCTGCCATGTGTCTGGGCAGCACAACCTGCCAGGACCCATGGCCTGTGGCGAGGGTGGTGGCAGCAGGAGGGGTGGCTGACAGCAGGGCCCAGCAGCCTGTCCGGACATGCCCGTGGCTT ↑ 4 1 3 2 Human: ACAAGAGCCCCCATTGCAGGCAGGGGCT-----------GGGGGTGTGGAGGCC-GGCCCTGCTCACCATCTCCTGCCATGTGTCTGGGCAGCACGACCTGCCAGGGCCCGTGGCCTGTGGCGAGGGTGGCGGCAGCAGGACGGGTGGCTGAGAGCAGGGCCCGGCAGCCTGTCCGGACATGCCCGTGGCTT Cluster: [ ] Orangutan: ACAAGAGCCCCCATTGCAGGCGGGGGCTGGGCAGGGTCTGGGAGTGTGGAGGCCGGGCCCTGCTCACCATCTCCTGCCATGTGTCTGGGCAGCATGACCTGCCAGGACCCGTGGCCTGTGGCAAGGGTGGTGGCATCAGGAGGGGTGGCTGAGAGCAGGGCCCAGCAGCCTGTCCGGACACGCCCTTGGCTT Human > Gorilla --------------- chr8:778136-778141 Template switch process: F1: L CCAAACTGCAAGATACAAAAACAAGAGCCCCCATTGCAGGCGGGGGCTGGG 1 F3: 4 CTGGGGGTGTGGAGGCCGGCCCTGTTCACCATCTCCTGCCAT R RF: CCAAACTGCAAGATACAAAAACAAGAGCCCCCATTGCAGGCAGGGGCTGGGGGTGTGGAGGCCGGCCCTGCTCACCATCTCCTGCCATGTGTCTGGGCAGCACGACCTGCCAGGGCCCGTGGCCTGTGGCGAGGGTGGCGGCAGCAGGACGGGTGGCTGAGAGCAGGGCCCGGCAGCCTG RR: GGTTTGACGTTCTATGTTTTTGTTCTCGGGGGTAACGTCCGTCCCCGACCCCCACACCTCCGGCCGGGACGAGTGGTAGAGGACGGTACACAGACCCGTCGTGCTGGACGGTCCCGGGCACCGGACACCGCTCCCACCGCCGTCGTCCTGCCCACCGACTCTCGTCCCGGGCCGTCGGAC F2: 3 TCGGAC 2 Unidirectional alignment (log-probability: -37.8) GATACAAAAACAAGAGCCCCCATTGCAGGCgGGGGctgggcaggctCTGGGGGTGTGGAGGCCGGCCCTGtTCACCATCTCCTGCC GATACAAAAACAAGAGCCCCCATTGCAGGCAGGGG-----------CTGGGGGTGTGGAGGCCGGCCCTGCTCACCATCTCCTGCC Template switch alignment (log-probability: -27.8) GATACAAAAACAAGAGCCCCCATTGCAGGCgGGGGCTGGG|CAGGCT|CTGGGGGTGTGGAGGCCGGCCCTGtTCACCATCTCCTGCC GATACAAAAACAAGAGCCCCCATTGCAGGCAGGGGCTGGG|CAGGCT|CTGGGGGTGTGGAGGCCGGCCCTGCTCACCATCTCCTGCC Chimp > Gorilla --------------- chr8:778136-778141 Template switch process: F1: L CCAAACTGCAAGATACAAAAACAAGAGCCCCCATTGCAGGCGGGGGCTGGG 1 F3: 4 CTGGGGGTGTGGAGGCCGGCCCTGTTCACCATCTCCTGCCAT R RF: CCAAACTGCAAGATACAAAAACAAGAGCCCCCATTGCAGGCAGGGGCTGGGGGTGTGGAGGCCGGCCCTGCTCACCATCTCCTGCCATGTGTCTGGGCAGCACGACCTGCCAGGACCCGTGGCCTGTGGCGAGGGTGGCGGCAGCAGGAGGGGTGGCTGAGAGCAGGGCCGAGCAGCCTG RR: GGTTTGACGTTCTATGTTTTTGTTCTCGGGGGTAACGTCCGTCCCCGACCCCCACACCTCCGGCCGGGACGAGTGGTAGAGGACGGTACACAGACCCGTCGTGCTGGACGGTCCTGGGCACCGGACACCGCTCCCACCGCCGTCGTCCTCCCCACCGACTCTCGTCCCGGCTCGTCGGAC F2: 3 TCGGAC 2 Unidirectional alignment (log-probability: -37.8) GATACAAAAACAAGAGCCCCCATTGCAGGCgGGGGctgggcaggctCTGGGGGTGTGGAGGCCGGCCCTGtTCACCATCTCCTGCC GATACAAAAACAAGAGCCCCCATTGCAGGCAGGGG-----------CTGGGGGTGTGGAGGCCGGCCCTGCTCACCATCTCCTGCC Template switch alignment (log-probability: -27.8) GATACAAAAACAAGAGCCCCCATTGCAGGCgGGGGCTGGG|CAGGCT|CTGGGGGTGTGGAGGCCGGCCCTGtTCACCATCTCCTGCC GATACAAAAACAAGAGCCCCCATTGCAGGCAGGGGCTGGG|CAGGCT|CTGGGGGTGTGGAGGCCGGCCCTGCTCACCATCTCCTGCC ========== Event 3563 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AGTGTGCTGAACTGATAGT------TTTAAAATATAATATTCAG------GAAGGTATACTAACATTTGACTTTTGTACTTCTTTTTTTGTGTGTGTCTT Chimp: AGTGTGTTGAACTGATAGT------TTTAAAATATAATATTCAG------GAAGGTATACTAACATTTGACTTTCGTACTTCtttttttGTGTGTGTCTT ↑ 3 12 4 Gorilla: AGTGTGTTGAACTGATAGTATACCTTCCTGAATATTATATTTTA------------AAACTAACATTTGACTTTTGTACATCtttttttGTGTGTGTCTT Human: AGTGTGCTGAACTGATAGT------TTTAAAATATAATATTCAG------GAAGGTATACTAACATTTGACTTTTGTACTTCTTTTTTTGTGTGTGTCTT Cluster: [ ] Orangutan: AGTGTGTTGAACTGATAGT------TTTAAAAGATAATATTCAGGAAGGT------ATACTAACATTTGACTTTTGTACATCTTTTTGTGTGTGTGTCTT Gorilla > Chimp --------------- chr8:133104834-133104858 Template switch process: F1: L 1 F3: 4 ACTAACATTTGACTTTCGTACTTCTTTTTTTGTGTGTGTCTTCAAAATCACATCAAAACCAG R RF: ATACCTTCCTGAATATTATATTTTAAACTAACATTTGACTTTTGTACATCTTTTTTTGTGTGTGTCTTCAAAATCACATCAAAACCAG RR: TATGGAAGGACTTATAATATAAAATTTGATTGTAAACTGAAAACATGTAGAAAAAAACACACACAGAAGTTTTAGTGTAGTTTTGGTC F2: 3 TATGGAAGGACTTATAATATAAAAT 2 Unidirectional alignment (log-probability: -57.1) TAAAatataatattcaggaaggtatACTAACATTTGACTTTcGTACtTCTTTTTTTGTGTGTGTC TAAA---------------------ACTAACATTTGACTTTTGTACATCTTTTTTTGTGTGTGTC Template switch alignment (log-probability: -29.5) |TAAAATATAATATTCAGGAAGGTAT|ACTAACATTTGACTTTcGTACtTCTTTTTTTGTGTGTGTC |TAAAATATAATATTCAGGAAGGTAT|ACTAACATTTGACTTTTGTACATCTTTTTTTGTGTGTGTC ========== Event 3564 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AAAGGACAAAGTAGTTAATATGTTTTGGAACTTTGAAGATGCTATCTGATGTTCATATCTGAAGCCACAA ↓ 1 4 3 2 Chimp: AAAGGACAAAGTAGTTAATATA---------TCAGAAGATGCTATCTGATGTTCATGTCTGAAGCCACAA Gorilla: AAAGGGCAAAGTAGTTAATATGTTTTGGAACTTTGAAGATGCTATCTGATGTTTATATCTGAAGCCACAA Human: AAAGGACAAAGTAGTTAATATGTTTTGGAACTTTGAAGATGCTATCTGATGTTCATATCTGAAGCCACAA Cluster: [ ] Orangutan: AAAGGAAAAAGTAGTTAATATATTTTGGAACTTTGAAGATGCTATCTGATGTTCATATCTGAAGCCACAA Human > Chimp ------------- chr8:133801064-133801068 Template switch process: F1: L ATGAGGAATGTTGATTTGTTAAAGGACAAAGTAGTTAATAT 1 F3: 4 AAGATGCTATCTGATGTTCATGTCTGAAGCCACAATTTT R RF: ATGAGGAATGTTGATTTGTTAAAGGACAAAGTAGTTAATATGTTTTGGAACTTTGAAGATGCTATCTGATGTTCATATCTGAAGCCACAATTTT RR: TACTCCTTACAACTAAACAATTTCCTGTTTCATCAATTATACAAAACCTTGAAACTTCTACGATAGACTACAAGTATAGACTTCGGTGTTAAAA F2: 3 GACTA 2 Unidirectional alignment (log-probability: -33.5) TGAGGAATGTTGATTTGTTAAAGGACAAAGTAGTTAATATatca-------------GAAGATGCTATCTGATGTTCATgTCTGAAGCCACAATTTT TGAGGAATGTTGATTTGTTAAAGGACAAAGTAGTTAATAT----GTTTTGGAACTTTGAAGATGCTATCTGATGTTCATATCTGAAGCCACAATTTT Template switch alignment (log-probability: -21.9) TGAGGAATGTTGATTTGTTAAAGGACAAAGTAGTTAATAT|ATCAG|AAGATGCTATCTGATGTTCATgTCTGAAGCCACAATTTT TGAGGAATGTTGATTTGTTAAAGGACAAAGTAGTTAATAT|ATCAG|AAGATGCTATCTGATGTTCATATCTGAAGCCACAATTTT ========== Event 3565 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCCTT------TGATAAATAAAAGACAGTAGCTC ↓ 3 2 1 4 Chimp: GAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCCAGTCTAAGAAATAAATAAAAGACAGTAGCTC ↑ 3 2 1 4 Gorilla: GAACACATATTTCTTTATTTTCTTAGACTGGTAGTTCCTT------TGATAAATAAAAGACAGTAGCTC Human: GAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCCTT------TGATAAATAAAAGACAGTAGCTC Cluster: [ ] Orangutan: GAACACATTTTTCTTTATTTTCTTAGACTGATAGCTCCTT------TGACAAATAAAAGACAGTAGCTC Human > Chimp ------------- chr8:131914946-131914955 Template switch process: F1: L GGAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCC 1 F3: 4 ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAC R RF: GGAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCCTTTGATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAT RR: CCTCTTGTGTAAAAAGAAATAAAAGAATCTGACCATCAAGGAAACTATTTATTTTCTGTCATCGAGTTTTAGATCACCATCTTTA F2: 3 AAGAATCTGA 2 Unidirectional alignment (log-probability: -41.7) GAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCC----agtctaagaaATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAc GAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCCTTTG----------ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAT Template switch alignment (log-probability: -22.5) GAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCC|AGTCTAAGAA|ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAc GAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCC|AGTCTAAGAA|ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAT Gorilla > Chimp --------------- chr8:131914946-131914955 Template switch process: F1: L GGAGAACACATTTTTCTTTATTTTCTTAGACTGGTAGTTCC 1 F3: 4 ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAC R RF: GGAGAACACATATTTCTTTATTTTCTTAGACTGGTAGTTCCTTTGATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAT RR: CCTCTTGTGTATAAAGAAATAAAAGAATCTGACCATCAAGGAAACTATTTATTTTCTGTCATCGAGTTTTAGATCACCATCTTTA F2: 3 AAGAATCTGA 2 Unidirectional alignment (log-probability: -46.2) GAGAACACATtTTTCTTTATTTTCTTAGACTGGTAGTTCCagtctaagaa----ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAc GAGAACACATATTTCTTTATTTTCTTAGACTGGTAGTTCC----------TTTGATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAT Template switch alignment (log-probability: -28) GAGAACACATtTTTCTTTATTTTCTTAGACTGGTAGTTCC|AGTCTAAGAA|ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAc GAGAACACATATTTCTTTATTTTCTTAGACTGGTAGTTCC|AGTCTAAGAA|ATAAATAAAAGACAGTAGCTCAAAATCTAGTGGTAGAAAT ========== Event 3566 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAGTCCACCTAAATTTTTGAGCAATAGAAATCATTCTATTGCTCCTCGGCGCACTTCTGGAAATA Chimp: TTCGTCCATCTAAATTTTTGAGCAATAGAA------TGATAACTGCTCGGCGCACTTCTGGAAATA Gorilla: TTAGTCCACCTAAATTTTTGAGCAATAGAA------TGATAACTGCTCGGCGCACTTCTGGAAATG ↓ 3 1 2 4 Human: TTAGTCCACCTAAATTTTTGAGCAATAGAAATCATTCTATTGCTCCTCGGCGCACTTCTGGAAATA Cluster: [ ] Orangutan: TTAGTCCACCTAAATTTTTGAGCAATAGAG------TGATAACTCCTCAGCGTACTTCTGGAAATA Gorilla > Human --------------- chr8:128550426-128550440 Template switch process: F1: L AATAGTTTCTATTAGTCCACCTAAATTTTTGAGCAATAGAA 1 F3: 4 CTCGGCGCACTTCTGGAAATAGTCTAAAAACACCTAATTT R RF: AATAGTTTCTATTAGTCCACCTAAATTTTTGAGCAATAGAATGATAACTGCTCGGCGCACTTCTGGAAATGTTCTAAAAACACCTAATTT RR: TTATCAAAGATAATCAGGTGGATTTAAAAACTCGTTATCTTACTATTGACGAGCCGCGTGAAGACCTTTACAAGATTTTTGTGGATTAAA F2: 3 CTCGTTATCTTACTA 2 Unidirectional alignment (log-probability: -51.8) ATAGTTTCTATTAGTCCACCTAAATTTTTGAGCAATAGAAatcattctatTG----CTcCTCGGCGCACTTCTGGAAATagTCTAAAAACACCTAATTT ATAGTTTCTATTAGTCCACCTAAATTTTTGAGCAATAGAA----------TGATAACTGCTCGGCGCACTTCTGGAAATGTTCTAAAAACACCTAATTT Template switch alignment (log-probability: -28.7) ATAGTTTCTATTAGTCCACCTAAATTTTTGAGCAATAGAA|ATCATTCTATTGCTC|CTCGGCGCACTTCTGGAAATagTCTAAAAACACCTAATTT ATAGTTTCTATTAGTCCACCTAAATTTTTGAGCAATAGAA|ATCATTCTATTGCTC|CTCGGCGCACTTCTGGAAATGTTCTAAAAACACCTAATTT ========== Event 3567 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTAAACATTTCCAGGGCACATTTTGACGTTGTTCTCCAACTGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGC----------------------CTGCTATTAGAATAATAGGTAAAAGT Chimp: GTAAACATTTCCAGGGCACATTTTGACGTTGTTCTCCAACTGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGC----------------------CTGCTATTAGAATAATAGGTAAAAGT ↓ 3 2 4 1 Gorilla: GTAAACATTTCCAGGGCACATTTTGACGTTGTTCTCCAACTGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTAGTCACAATAGTGCTGCCTGCTATTAGAATAATAGGTAAAAGT ↑ 3 2 4 1 Human: GTAAACATTTCCAGGGCACATTTTGACGTTGTTCTCCAACTGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGC----------------------CTGCTATTAGAATAATAGGTAAAAGT Cluster: [ ] Orangutan: GTAAACATTTCCAGGGCACATTTTGACGTTGTTCTCCAAATGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGtagtgctgcctgctagttacaatagtgctgcctgctattagaataATAGGTAAAAGT Human > Gorilla --------------- chr8:130575328-130575335 Template switch process: F1: L TGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTA 1 F3: 4 AGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTTTAAACACT R RF: ATTTTGACGTTGTTCTCCAACTGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTGTAAACACT RR: TAAAACTGCAACAAGAGGTTGACCTTACATTTTAAGTGAGTCTGAATGAAAGTGACCCATCACGACGGACGATAATCTTATTATCCATTTTCATAAAACATTTGTGA F2: 3 TAACACTG 2 Unidirectional alignment (log-probability: -48) TTCACTCAGACTTACTTTCACTGGGTAGTGCTgcctgctagtcacaatagtgctGCCTGCTATTAGAATAATAGGTAAAAGTATTTTt TTCACTCAGACTTACTTTCACTGGGTAGTGCT----------------------GCCTGCTATTAGAATAATAGGTAAAAGTATTTTG Template switch alignment (log-probability: -28.1) TTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTA|GTCAcAAT|AGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTt TTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTA|GTCAAAAT|AGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTG Chimp > Gorilla --------------- chr8:130575328-130575335 Template switch process: F1: L TGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTA 1 F3: 4 AGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTTTAAACACT R RF: ATTTTGACGTTGTTCTCCAACTGGAATGTAAAATTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTTTAAACACT RR: TAAAACTGCAACAAGAGGTTGACCTTACATTTTAAGTGAGTCTGAATGAAAGTGACCCATCACGACGGACGATAATCTTATTATCCATTTTCATAAAAAATTTGTGA F2: 3 TAACACTG 2 Unidirectional alignment (log-probability: -42.5) TTCACTCAGACTTACTTTCACTGGGTAGTGCTgcctgctagtcacaatagtgctGCCTGCTATTAGAATAATAGGTAAAAGTATTTTT TTCACTCAGACTTACTTTCACTGGGTAGTGCT----------------------GCCTGCTATTAGAATAATAGGTAAAAGTATTTTT Template switch alignment (log-probability: -22.6) TTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTA|GTCAcAAT|AGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTT TTCACTCAGACTTACTTTCACTGGGTAGTGCTGCCTGCTA|GTCAAAAT|AGTGCTGCCTGCTATTAGAATAATAGGTAAAAGTATTTTT ========== Event 3568 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTATCA----GGCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGATCTTGAAGAAGGAGGGATTTCTGGACAGTTAGATATTGAAG ↓ 1 4 3 2 Chimp: TCCTAGAAATTTGGCCTAGTACGTGAACTATGGCTTATGA--AATCCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGATCTTGAAGAAGGAGGGATTTCTGGACAGTTAGATATTGAAG Gorilla: TCCTAGAAATGTGGCCTAGTATGTGAACTATGGCTTATGAAA--TCCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGATCTTGAAGAAGGAGGGATTTCTGGACAGTTAGATATTGAAG ↑ 1 4 3 2 Human: TCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTATCA----GGCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGATCTTGAAGAAGGAGGGATTTCTGGACAGTTAGATATTGAAG Cluster: [ ] Orangutan: TCCTAGAAATGTGGCCTGGTACGTGAACTATGGCTTAGCAAA--TCCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGACCTTGAAGAAAGAGGGATTCCTGTACAGTTAGATATTGAAG Human > Chimp ------------- chr8:130419015-130419020 Template switch process: F1: L GACATTCTGCCTCAAAGTTCTCCTAGAAATTTGGCCTAGTACGTGAACTATGGCTTAT 1 F3: 4 CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT R RF: GACGTTCTGCCTCAAAGTTCTCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTATCAGGCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGATCTTGAAGAAGGAGGGATTTC RR: CTGCAAGACGGAGTTTCAAGAGGATCTTTAAACCGGATCATACACTTGATCCCGAATAGTCCGATCGGACTATCCGGTCCTTGTGACAGTTTGAGACCTCTAGAACTTCTTCCTCCCTAAAG F2: 3 CTAAAG 2 Unidirectional alignment (log-probability: -46.6) TCTCCTAGAAATTTGGCCTAGTAcGTGAACTAtGGCTTAT---GaaatcCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT TCTCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTATCAGG-----CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT Template switch alignment (log-probability: -34.3) TCTCCTAGAAATTTGGCCTAGTAcGTGAACTAtGGCTTAT|GAAATC|CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT TCTCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTAT|GAAATC|CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT Human > Gorilla --------------- chr8:129388959-129388964 Template switch process: F1: L CCTCAAAGTTCTCCTAGAAATGTGGCCTAGTATGTGAACTATGGCTTAT 1 F3: 4 CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT R RF: CCTCAAAGTTCTCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTATCAGGCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGATCTTGAAGAAGGAGGGATTTC RR: GGAGTTTCAAGAGGATCTTTAAACCGGATCATACACTTGATCCCGAATAGTCCGATCGGACTATCCGGTCCTTGTGACAGTTTGAGACCTCTAGAACTTCTTCCTCCCTAAAG F2: 3 CTAAAG 2 Unidirectional alignment (log-probability: -39.1) TCTCCTAGAAATgTGGCCTAGTATGTGAACTAtGGCTTatgaaATC---CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT TCTCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTT-----ATCAGGCTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT Template switch alignment (log-probability: -27.7) TCTCCTAGAAATgTGGCCTAGTATGTGAACTAtGGCTTAT|GAAATC|CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT TCTCCTAGAAATTTGGCCTAGTATGTGAACTAGGGCTTAT|GAAATC|CTAGCCTGATAGGCCAGGAACACTGTCAAACTCTGGAGAT ========== Event 3569 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AGCTCCCAGGTCCCAGGAGATGCCGCACGGGCAGTGCCGTCTGC----- Chimp: AGCTCCCAGGTCCCAGGAGATGCCGCATGGGCAGTGCCGTctgcaggtt ↑ 3 21 4 Gorilla: AGCTCCCAGGTCCCAGGAGATGCCTCACGGGCAGTGCCGTCTGC----- Human: AGCTCCCAGGTCCCAGGAGATGCCGCACGGGCAGTGCCGTCTGC----- Cluster: [ ] Orangutan: AGCTCCCAGGTCCCAGGGGAGGCCGCATGGGCAGTGCCGTCTGC----- Gorilla > Chimp --------------- chr8:146365320-146365323 Template switch process: F1: L CATACGCGTGGCGTGAAAGCTCCCAGGTCCCAGGAGATGCC 1 F3: 4 GGGCAGTGCCGTCTGCAGGTTCCCAGCCTGGGTGTGACCC R RF: CATACGTGTGGTGTGAAAGCTCCCAGGTCCCAGGAGATGCCTCACGGGCAGTGCCGTCTGCAGGTTCCCAGCCTGGGTGTGACCC RR: GTATGCACACCACACTTTCGAGGGTCCAGGGTCCTCTACGGAGTGCCCGTCACGGCAGACGTCCAAGGGTCGGACCCACACTGGG F2: 3 TACG 2 Unidirectional alignment (log-probability: -64.2) ATACGcGTGGcGTGAAAGCTCCCAGGTCCCAGGAGATGCCgCAtGGGCAGTGCCGTCTGCaggttcccagcctgggtgtgaccc ATACGTGTGGTGTGAAAGCTCCCAGGTCCCAGGAGATGCCTCACGGGCAGTGCCGTCTGC------------------------ Template switch alignment (log-probability: -27.3) ATACGcGTGGcGTGAAAGCTCCCAGGTCCCAGGAGATGCC|GCAT|GGGCAGTGCCGTCTGCAGGTTCCCAGCCTGGGTGTGACCC ATACGTGTGGTGTGAAAGCTCCCAGGTCCCAGGAGATGCC|GCAT|GGGCAGTGCCGTCTGCAGGTTCCCAGCCTGGGTGTGACCC ========== Event 3570 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGAAACTTGAAAGGTCACCTGAACCAAAGTTCAGGTCAAGACCCTCCAGCTCCT Chimp: TGAAACTTGAAAGGTCACCTGAACCAAAGTTCAGGTCAAGACCCTCCAGCTCCT ↑ 3 1 24 Gorilla: TGAAACTTGAAAGGTCACCTGAA-----CTTTGGGTCAAGACCCTCCAGCTCCT ↓ 3 1 24 Human: TGAAACTTGAAAGGTCACCTGAACCAAAGTTCAGGTCAAGACCCTCCAGCTCCT Cluster: [ ] Orangutan: TGAAACGTGAAAAGTCACCTGAA-----CTTTGAGGCAAGACCCTCCAGCTCCT Gorilla > Human --------------- chr8:19888773-19888781 Template switch process: F1: L GTATTTTTACATTTCATGTGAAACTTGAAAGGTCACCTGAAC 1 F3: 4 GGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA R RF: GTATTTTTACACTTCATGTGAAACTTGAAAGGTCACCTGAACTTTGGGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA RR: CATAAAAATGTGAAGTACACTTTGAACTTTCCAGTGGACTTGAAACCCAGTTCTGGGAGGTCGAGGAGAGGTGGGTGTCGAAAGGT F2: 3 ACTTGAAAC 2 Unidirectional alignment (log-probability: -34.7) ATTTTTACAtTTCATGTGAAACTTGAAAGGTCACCTGAACcaaagTTcaGGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA ATTTTTACACTTCATGTGAAACTTGAAAGGTCACCTGAAC-----TTTGGGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA Template switch alignment (log-probability: -22.4) ATTTTTACAtTTCATGTGAAACTTGAAAGGTCACCTGAAC|CAAAGTTCA|GGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA ATTTTTACACTTCATGTGAAACTTGAAAGGTCACCTGAAC|CAAAGTTCA|GGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA Gorilla > Chimp --------------- chr8:19147739-19147747 Template switch process: F1: L GTATTTTTACATTTCATGTGAAACTTGAAAGGTCACCTGAAC 1 F3: 4 GGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA R RF: GTATTTTTACACTTCATGTGAAACTTGAAAGGTCACCTGAACTTTGGGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA RR: CATAAAAATGTGAAGTACACTTTGAACTTTCCAGTGGACTTGAAACCCAGTTCTGGGAGGTCGAGGAGAGGTGGGTGTCGAAAGGT F2: 3 ACTTGAAAC 2 Unidirectional alignment (log-probability: -34.7) ATTTTTACAtTTCATGTGAAACTTGAAAGGTCACCTGAACcaaagTTcaGGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA ATTTTTACACTTCATGTGAAACTTGAAAGGTCACCTGAAC-----TTTGGGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA Template switch alignment (log-probability: -22.4) ATTTTTACAtTTCATGTGAAACTTGAAAGGTCACCTGAAC|CAAAGTTCA|GGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA ATTTTTACACTTCATGTGAAACTTGAAAGGTCACCTGAAC|CAAAGTTCA|GGTCAAGACCCTCCAGCTCCTCTCCACCCACAGCTTTCCA ========== Event 3571 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TAGTTTGATCCAGGGCTGAGC---ATTCCTACAGG-------------------------TGCTCCCCAGCGTTCCTCATTTCAGGCCTAGTCAGGACCTCTAGAGCCCATCTGCTGTGAGCAA Chimp: TAGTTTGATCCAGGGCTGAGC---ATTCCTACAGG-------------------------TGCTCCCCAGCGTTCCTCATTTCAGGCCTCTTCAGGAACTCTAGAGCCCATCTGCTGTGAGCAA Gorilla: TAGTTTGATCCAGGGCTGAGC------ACTAGAGG--------------------------------------------------TCCTCGTCAGGACCTCTAGATCCCATCTGCTGTGAGCAA ↑ 1 4 3 2 Human: TAGTTTGATCCAGGGCTGAGC---ATTCCTACAGG-------------------------TGCTCCCCAGCGTTCCTCATTTCAGGCCTAGTCAGGACCTCTAGAGCCCATCTGCTGTGAGCAA Cluster: [ ] Orangutan: TAGTTTGATCTAGGGCTGAGCATT---CCTACAGGTGCTCCCCAGCATTCCTCATTTCAG-------------------------GCCTTGTCAGGACCTCTAGAGCCCATCTGCTGTGAGCAA Human > Gorilla --------------- chr8:19303737-19303744 Template switch process: F1: L CTGTCCCTTACAGCATGCTGTAGTTTGATCCAGGGCTGAGCA 1 F3: 4 CCTCGTCAGGACCTCTAGATCCCATCTGCTGTGAGCAAAAGAGG R RF: CTGTCCCTTACAGCATGCTGTAGTTTGATCCAGGGCTGAGCATTCCTACAGGTGCTCCCCAGCGTTCCTCATTTCAGGCCTAGTCAGGACCTCTAGAGCCCATCTGCTGTGAGCAAAAGAGG RR: GACAGGGAATGTCGTACGACATCAAACTAGGTCCCGACTCGTAAGGATGTCCACGAGGGGTCGCAAGGAGTAAAGTCCGGATCAGTCCTGGAGATCTCGGGTAGACGACACTCGTTTTCTCC F2: 3 TGGAGATC 2 Unidirectional alignment (log-probability: -38.8) GTCCCTTACAGCATGCTGTAGTTTGATCCAGGGCTGAGCA---CTAgAGGT-------------------------CCTcGTCAGGACCTCTAGAtCCCATCTGCTGTGAGCAAAA GTCCCTTACAGCATGCTGTAGTTTGATCCAGGGCTGAGCATTCCTACAGGTGCTCCCCAGCGTTCCTCATTTCAGGCCTAGTCAGGACCTCTAGAGCCCATCTGCTGTGAGCAAAA Template switch alignment (log-probability: -27.9) GTCCCTTACAGCATGCTGTAGTTTGATCCAGGGCTGAGCA|CTAGAGGT|CCTcGTCAGGACCTCTAGAtCCCATCTGCTGTGAGCAAAA GTCCCTTACAGCATGCTGTAGTTTGATCCAGGGCTGAGCA|CTAGAGGT|CCTAGTCAGGACCTCTAGAGCCCATCTGCTGTGAGCAAAA ========== Event 3572 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: tggagtcaagaGCACATTCAGCTAACTCTCT--GAACCAGCTCCTGCCTGTCACTGTGT ↓ 3 2 1 4 Chimp: tggagtcaagaGCACATTCAGCTAACTCTCTGTTAGCTAGCTCCTGCCTGTCACTGTGT Gorilla: tggagtcaagagcacattcagctaactctct--gagccagCTCCTGCCTGTCACTGTGT Human: tggagtcaagaGCACATTCAGCTAACTCTCT--GAACCAGCTCCTGCCTGTCACTGTGT Cluster: [ ] Orangutan: tggagtcaagaGCACATTCAGCTAAC--TCT--GAGCCAGCTCCTGCCTGTCACTGTGT Human > Chimp ------------- chr8:127751867-127751872 Template switch process: F1: L AATGTGAACGTGGAGTCAAGAGCACATTCAGCTAACTCTCTG 1 F3: 4 AGCTCCTGCCTGTCACTGTGTCGCGTGGCCCTAATGGCAC R RF: AATGTGAACGTGGAGTCAAGAGCACATTCAGCTAACTCTCTGAACCAGCTCCTGCCTGTCACTGTGTCGCGTGGCCCTAATGGCAC RR: TTACACTTGCACCTCAGTTCTCGTGTAAGTCGATTGAGAGACTTGGTCGAGGACGGACAGTGACACAGCGCACCGGGATTACCGTG F2: 3 TCGATT 2 Unidirectional alignment (log-probability: -25.8) TGTGAACGTGGAGTCAAGAGCACATTCAGCTAACTCTCTGttAgCtAGCTCCTGCCTGTCACTGTGTCGCGTGGCCCTAATGGCAC TGTGAACGTGGAGTCAAGAGCACATTCAGCTAACTCTCTG--AACCAGCTCCTGCCTGTCACTGTGTCGCGTGGCCCTAATGGCAC Template switch alignment (log-probability: -16) TGTGAACGTGGAGTCAAGAGCACATTCAGCTAACTCTCTG|TTAGCT|AGCTCCTGCCTGTCACTGTGTCGCGTGGCCCTAATGGCAC TGTGAACGTGGAGTCAAGAGCACATTCAGCTAACTCTCTG|TTAGCT|AGCTCCTGCCTGTCACTGTGTCGCGTGGCCCTAATGGCAC ========== Event 3573 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GACAAGGCAGGAAGAACACAT-----------GCCATGTCCAGACCATTTACCATCATTG Chimp: GACAAGGCAGGAATAACACAT-----------ACCATGTCCAGACCATTTACCATCATTG ↓ 43 1 2 Gorilla: GACAAGGCAGGAATAACACATGCCATGGACATGCCATGTCCAGACCATTTATCATCATTG Human: GACAAGGCAGGAAGAACACAT-----------GCCATGTCCAGACCATTTACCATCATTG Cluster: [ ] Orangutan: GACGAGGCAGGAATAACACAT-----------GCCATGTCCAGACCATTTACCACCATTG Chimp > Gorilla --------------- chr8:20175805-20175810 Template switch process: F1: L CTTTTTCCTGTCTACTCTGTGACAAGGCAGGAATAACACATGCCATG 1 F3: 4 CCATGTCCAGACCATTTATCATCATTGCCCCTGGCACCTC R RF: CTTTTTCCTGTCTACTCTGTGACAAGGCAGGAATAACACATACCATGTCCAGACCATTTACCATCATTGCCCCTGGCACCTC RR: GAAAAAGGACAGATGAGACACTGTTCCGTCCTTATTGTGTATGGTACAGGTCTGGTAAATGGTAGTAACGGGGACCGTGGAG F2: 3 GTACAG 2 Unidirectional alignment (log-probability: -37.8) CTGTCTACTCTGTGACAAGGCAGGAATAACACatgccatggacATgCCATGTCCAGACCATTTAtCATCATTGCCCCTGGCACCTC CTGTCTACTCTGTGACAAGGCAGGAATAACAC-----------ATACCATGTCCAGACCATTTACCATCATTGCCCCTGGCACCTC Template switch alignment (log-probability: -27.7) CTGTCTACTCTGTGACAAGGCAGGAATAACACATgCCATG|GACATG|CCATGTCCAGACCATTTAtCATCATTGCCCCTGGCACCTC CTGTCTACTCTGTGACAAGGCAGGAATAACACATACCATG|GACATG|CCATGTCCAGACCATTTACCATCATTGCCCCTGGCACCTC ========== Event 3574 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGTGGCAGGAAGACACTGGAAAGGATGGAAGATC-AGGTTGTCCACAGTGAGCCCTGGAGG ↓ 1 3 4 2 Chimp: TGGTGGCGGGAAGACACTGGAAAGGA--CAACCTGATGGTTGTCCACAGTGAGCCCTGGAGG ↑ 1 3 4 2 Gorilla: TGGTGGCGGGAAGACACTGGAGAGGATGGAAGATC-AGGTTGTCCACAGTGAGCCCTGGAGG Human: TGGTGGCAGGAAGACACTGGAAAGGATGGAAGATC-AGGTTGTCCACAGTGAGCCCTGGAGG Cluster: [ ] Orangutan: TGGTGGCGGGAGGACACAGGACAGGATGGAAGATC-AGGTTGTCCACAGTGAGCCCTGGAGG Human > Chimp ------------- chr8:126903299-126903307 Template switch process: F1: L ACTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAAAGGA 1 F3: 4 GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC R RF: ACTTCATGAAACCAGTGGTGGCAGGAAGACACTGGAAAGGATGGAAGATCAGGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC RR: TGAAGTACTTTGGTCACCACCGTCCTTCTGTGACCTTTCCTACCTTCTAGTCCAACAGGTGTCACTCGGGACCTCCACACCCTTTCGTCGG F2: 3 TAGTCCAAC 2 Unidirectional alignment (log-probability: -37.6) CTTCATGAAACCAGTGGTGGCgGGAAGACACTGGAAAGGA--------CAacctgatGGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC CTTCATGAAACCAGTGGTGGCAGGAAGACACTGGAAAGGATGGAAGATCA-------GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC Template switch alignment (log-probability: -22.4) CTTCATGAAACCAGTGGTGGCgGGAAGACACTGGAAAGGA|CAACCTGAT|GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC CTTCATGAAACCAGTGGTGGCAGGAAGACACTGGAAAGGA|CAACCTGAT|GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC Gorilla > Chimp --------------- chr8:126903299-126903307 Template switch process: F1: L CCTTGACTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAAAGGA 1 F3: 4 GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC R RF: CCTTGACTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAGAGGATGGAAGATCAGGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC RR: GGAACTGAAGTACTTTGGTCACCACCGCCCTTCTGTGACCTCTCCTACCTTCTAGTCCAACAGGTGTCACTCGGGACCTCCACACCCTTTCGTCGG F2: 3 TAGTCCAAC 2 Unidirectional alignment (log-probability: -36.7) CTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAaAGGA--------CAacctgatGGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC CTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAGAGGATGGAAGATCA-------GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC Template switch alignment (log-probability: -22.5) CTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAaAGGA|CAACCTGAT|GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC CTTCATGAAACCAGTGGTGGCGGGAAGACACTGGAGAGGA|CAACCTGAT|GGTTGTCCACAGTGAGCCCTGGAGGTGTGGGAAAGCAGCC ========== Event 3575 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CATAGCCCATCTGCTATGGCT----------TCATGCCAAAGGGGCTtgtgtgtgtgtgtgtgtgtgcgtgtg----tgtgtgtgtgtgtgcgtgtgtg----tgtgtgtgcgcacacacccatggcttcacttctgccaaaggggctttgtgtgaat--------gtgtttgtgtgcatgcaccgatggcttcacttcatgc Chimp: CATAGCCCATCTGCTATGGCT-----TCACTTCATGCCAAAGGGGCTtgtgtgtgtgtgtgcgtgt------g--------------------------tgtgtgtgtgtgcgcacacacccatggcttcacttctgccaaaggggctttgtgtgaat----------------gtgcatgcaccgatggcttcacttcatgc ↓ 1 4 3 2 Gorilla: CATAGCCCATCTGCTATGGCTTCACT-----TCATGCCAAAGGGGCTtgtgtgtgtgtgtgtgcat------gtgtg--------------------------tgtgtgtgcgcacacacccatggcttcacttctgccaaaggggctttgtgtgaatg----tgt--------gtgcatgcaccgatggcttcacttcatgc Human: CATAGCCCATCTGCTATGGCT----------TCATGCCAAAGGGGCTtgtgtgtgtgtgtgtgtgtgcgtgtg----tgtgtgtgtgtgtgcgtgtgtg----tgtgtgtgcgcacacacccatggcttcacttctgccaaaggggctttgtgtgaat--------gtgtttgtgtgcatgcaccgatggcttcacttcatgc Cluster: [ ] Orangutan: CATAGCCCATCTGCTATggcttcact-----tcatgccaaaggggcttgtgtgtgtgtg------------------------------------------------tgcgcgcacacacccacggcttcacttctgccaaaggggctttgtgtgaatgtgtgtgt--------gtgcatgcaccgatggcttcacttcatac Chimp > Gorilla --------------- chr8:125910145-125910148 Template switch process: F1: L GTTCCTGCCTCTGAGGGTCTCATAGCCCATCTGCTATGGCTTCACTTCATGCCAAAGGGGCTTGTGTGTGTGTGTG 1 F3: 4 TGTGTG R RF: GTTCCTGCCTCTGAGGGTCTCATAGCCCATCTGCTATGGCTTCACTTCATGCCAAAGGGGCTTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTGCGCACACACCCATGGCTTCACTTCTGCCAAAGGGGCTTTGTGTGAATGTGCATGCA RR: CAAGGACGGAGACTCCCAGAGTATCGGGTAGACGATACCGAAGTGAAGTACGGTTTCCCCGAACACACACACACACGCACACACACACACACACGCGTGTGTGGGTACCGAAGTGAAGACGGTTTCCCCGAAACACACTTACACGTACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -22.2) TGGCTTCACTTCATGCCAAAGGGGCTTGTGTGTGTGTGTGtgcatGTGTG TGGCTTCACTTCATGCCAAAGGGGCTTGTGTGTGTGTGTG----CGTGTG Template switch alignment (log-probability: -16.3) TGGCTTCACTTCATGCCAAAGGGGCTTGTGTGTGTGTGTG|TGCA|TGTGTG TGGCTTCACTTCATGCCAAAGGGGCTTGTGTGTGTGTGTG|TGCA|TGTGTG ========== Event 3576 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCTTGTTGGTGAAATCTTAGGGAAGTTCCAGGCAGAACTTCCCTATGCAGAAACATGAGGTTTA Chimp: TCTTGTTGGTGAAATCTTAGGGAAGTTCCAGGC-------TTGTATGCAGAAACATGAGGTTTA Gorilla: TCTTGTTGGCGAAATCTTAGGGAAGTTCCAGGC-------TTGTATGCAGAAACATGAGGTTTA ↓ 3 2 1 4 Human: TCTTGTTGGTGAAATCTTAGGGAAGTTCCAGGCAGAACTTCCCTATGCAGAAACATGAGGTTTA Cluster: [ ] Orangutan: TCTTGTTGGTGAAATCATAGGGAAGTTCCAGGC-------TTCTATGCAGAAACATGAGGTTTA Gorilla > Human --------------- chr8:120740039-120740047 Template switch process: F1: L TTTTAACTTCTTGTTGGTGAAATCTTAGGGAAGTTCCAGGCA 1 F3: 4 TATGCAGAAACATGAGGTTTACATGACTAATGTCTTACCA R RF: TTTTAACTTCTTGTTGGCGAAATCTTAGGGAAGTTCCAGGCTTGTATGCAGAAACATGAGGTTTACATGACTAATGTCTTACCA RR: AAAATTGAAGAACAACCGCTTTAGAATCCCTTCAAGGTCCGAACATACGTCTTTGTACTCCAAATGTACTGATTACAGAATGGT F2: 3 CCCTTCAAG 2 Unidirectional alignment (log-probability: -40.7) TTAACTTCTTGTTGGtGAAATCTTAGGGAAGTTCCAGGcagaacttccC---TATGCAGAAACATGAGGTTTACATGACTAATGTCTTACCA TTAACTTCTTGTTGGCGAAATCTTAGGGAAGTTCCAGG----------CTTGTATGCAGAAACATGAGGTTTACATGACTAATGTCTTACCA Template switch alignment (log-probability: -27.9) TTAACTTCTTGTTGGtGAAATCTTAGGGAAGTTCCAGGCa|GAACTTCCC|TATGCAGAAACATGAGGTTTACATGACTAATGTCTTACCA TTAACTTCTTGTTGGCGAAATCTTAGGGAAGTTCCAGGCT|GAACTTCCC|TATGCAGAAACATGAGGTTTACATGACTAATGTCTTACCA ========== Event 3577 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCCTCTGATAGTCAACACTGCCCACCGAGAGTCACCAAAAAAGACAATGGCTACATTGGCTATGCATG ↓ 3 2 1 4 Chimp: TGCCCTCTGATAGTCAACACTGCCCACCGAGAGT--------TGGGCAGTGGCTACATTGGCTATGCATG ↑ 3 2 1 4 Gorilla: TGCCCTCTGATAGTCAACACTGCCCACCAAGAGTCACCAAAAAAGACAATGGCTACATTGGCCATGCATG Human: TGCCCTCTGATAGTCAACACTGCCCACCGAGAGTCACCAAAAAAGACAATGGCTACATTGGCTATGCATG Cluster: [ ] Orangutan: TGCCCTCTGATAGTCAACACTGCCCACCGACAGTCAGCAAAAAAGACAATGGCTACATTGGCTATGCATG Human > Chimp ------------- chr8:123799498-123799504 Template switch process: F1: L GAAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGT 1 F3: 4 TGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT R RF: GAAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGTCACCAAAAAAGACAATGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT RR: CTTTACGACGGGAGACTATCAGTTGTGACGGGTGGCTCTCAGTGGTTTTTTCTGTTACCGATGTAACCGATACGTACCGGAACACCAACCCGAGGA F2: 3 GACGGGT 2 Unidirectional alignment (log-probability: -32) AAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGTtgggcag---------------TGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT AAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGT-------CACCAAAAAAGACAATGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT Template switch alignment (log-probability: -16.2) AAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGT|TGGGCAG|TGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT AAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGT|TGGGCAG|TGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT Gorilla > Chimp --------------- chr8:123799498-123799504 Template switch process: F1: L GTCCTGGAAATGCTGCCCTCTGATAGTCAACACTGCCCACCGAGAGT 1 F3: 4 TGGCTACATTGGCTATGCATGGCCTTGTGGTTGGGCTCCT R RF: GTCCTGGAAATGCTGCCCTCTGATAGTCAACACTGCCCACCAAGAGTCACCAAAAAAGACAATGGCTACATTGGCCATGCATGGCCTTGTGGTTGGGCTCCT RR: CAGGACCTTTACGACGGGAGACTATCAGTTGTGACGGGTGGTTCTCAGTGGTTTTTTCTGTTACCGATGTAACCGGTACGTACCGGAACACCAACCCGAGGA F2: 3 GACGGGT 2 Unidirectional alignment (log-probability: -42.6) AAATGCTGCCCTCTGATAGTCAACACTGCCCACCgAGAGT---------------tgggcagTGGCTACATTGGCtATGCATGGCCTTGTGGTTGGGCTCCT AAATGCTGCCCTCTGATAGTCAACACTGCCCACCAAGAGTCACCAAAAAAGACAA-------TGGCTACATTGGCCATGCATGGCCTTGTGGTTGGGCTCCT Template switch alignment (log-probability: -27.8) AAATGCTGCCCTCTGATAGTCAACACTGCCCACCgAGAGT|TGGGCAG|TGGCTACATTGGCtATGCATGGCCTTGTGGTTGGGCTCCT AAATGCTGCCCTCTGATAGTCAACACTGCCCACCAAGAGT|TGGGCAG|TGGCTACATTGGCCATGCATGGCCTTGTGGTTGGGCTCCT ========== Event 3578 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACTTTTCCCCCTTCCTGGAGT-------ATCAACCAGCTCTAACTGACAGATTGAATGAG Chimp: ACTTTTCCCCCTTCCTGGAGT-------ATCAACCAGCTCTAACTGACAGATTGAATGAG ↓ 1 3 4 2 Gorilla: ACTTTTCCCCCTTCCTGGAGTAGAGCTGGTTGACCAGCTCTAACTGACAGATTGAATGAG ↑ 1 3 4 2 Human: ACTTTTCCCCCTTCCTGGAGT-------ATCAACCAGCTCTAACTGACAGATTGAATGAG Cluster: [ ] Orangutan: ACTTCTCCCCCTTCCTGGAGT-------ATCAACCAGCTCTAACTGACAGATTGAATGAG Human > Gorilla --------------- chr8:25195459-25195468 Template switch process: F1: L CTTAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA 1 F3: 4 ACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT R RF: CTTAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTATCAACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT RR: GAATTTTACATTCTCTTCCTTGAAAAGGGGGAAGGACCTCATAGTTGGTCGAGATTGACTGTCTAACTTACTCTTGAAGGGAAAA F2: 3 GTTGGTCGAG 2 Unidirectional alignment (log-probability: -32) TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTAgagctggTtgACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA-------TCAACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT Template switch alignment (log-probability: -17) TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA|GAGCTGGTTG|ACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA|GAGCTGGTTG|ACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT Chimp > Gorilla --------------- chr8:25195459-25195468 Template switch process: F1: L CTTAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA 1 F3: 4 ACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT R RF: CTTAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTATCAACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT RR: GAATTTTACATTCTCTTCCTTGAAAAGGGGGAAGGACCTCATAGTTGGTCGAGATTGACTGTCTAACTTACTCTTGAAGGGAAAA F2: 3 GTTGGTCGAG 2 Unidirectional alignment (log-probability: -32) TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTAgagctggTtgACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA-------TCAACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT Template switch alignment (log-probability: -17) TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA|GAGCTGGTTG|ACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT TAAAATGTAAGAGAAGGAACTTTTCCCCCTTCCTGGAGTA|GAGCTGGTTG|ACCAGCTCTAACTGACAGATTGAATGAGAACTTCCCTTTT ========== Event 3579 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCCAGAGCCATAGGAAGTTAC----------TGAACACCTAATTCTTTTTTGTGCATCTTCCCAT Chimp: CTCCAGAGCCATAGGAAGATATGAATTAGGTGTTCACACCTAATTCTTTTTTGTGCATCTTCCCAT ↑ 1 3 4 2 Gorilla: CTCCAGAGCCATAGGAAGATAC----------TGAACACCTAATTCTTTTTTGTGCATCTTCCCAT Human: CTCCAGAGCCATAGGAAGTTAC----------TGAACACCTAATTCTTTTTTGTGCATCTTCCCAT Cluster: [ ] Orangutan: CTCCAGAGCCATAGGAAGATAC----------TGAACACCTAATTCTTTTTTGTGCATCTTCCCAT Gorilla > Chimp --------------- chr8:122780859-122780871 Template switch process: F1: L GGAGTCTCCCCATTAAAAACCTCCAGAGCCATAGGAAGATAT 1 F3: 4 ACACCTAATTCTTTTTTGTGCATCTTCCCATTGGACCCTC R RF: GGAGTCTCCCCATTAAAAACCTCCAGAGCCATAGGAAGATACTGAACACCTAATTCTTTTTTGTGCATCTTCCCATTGGACCCTC RR: CCTCAGAGGGGTAATTTTTGGAGGTCTCGGTATCCTTCTATGACTTGTGGATTAAGAAAAAACACGTAGAAGGGTAACCTGGGAG F2: 3 CTTGTGGATTAAG 2 Unidirectional alignment (log-probability: -36.5) AGTCTCCCCATTAAAAACCTCCAGAGCCATAGGAAGATA-TGAattaggtgttcACACCTAATTCTTTTTTGTGCATCTTCCCATTGGACCCTC AGTCTCCCCATTAAAAACCTCCAGAGCCATAGGAAGATACTGA-----------ACACCTAATTCTTTTTTGTGCATCTTCCCATTGGACCCTC Template switch alignment (log-probability: -22.9) AGTCTCCCCATTAAAAACCTCCAGAGCCATAGGAAGATAt|GAATTAGGTGTTC|ACACCTAATTCTTTTTTGTGCATCTTCCCATTGGACCCTC AGTCTCCCCATTAAAAACCTCCAGAGCCATAGGAAGATAC|GAATTAGGTGTTC|ACACCTAATTCTTTTTTGTGCATCTTCCCATTGGACCCTC ========== Event 3580 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: cataaaatattaatgttagaa-------agaaccctacagatcccattcaactccttcgtt Chimp: CATAAAATATTAATGTTAGAA-------AGAACCCTACAGATCCCATTCAACTCCTTTGTT ↓ 1 3 4 2 Gorilla: CATGAAATATTAATGTTAGAAATCTGTAGGGTTTCTACAGATCCCATTCAACTCCTTTGTT Human: cataaaatattaatgttagaa-------agaaccctacagatcccattcaactccttcgtt Cluster: [ ] Orangutan: cataaaatattaatgttagaa-------agaatcctagagatcccattcaactcctttgtt Chimp > Gorilla --------------- chr8:121693189-121693199 Template switch process: F1: L TGTACATTTTTCTTTGCAGTCATGAAATATTAATGTTAGAAA 1 F3: 4 TCTACAGATCCCATTCAACTCCTTTGTTAAGAGAGAATGAA R RF: TGTACATTTTTCTTTGCAGTCATAAAATATTAATGTTAGAAAGAACCCTACAGATCCCATTCAACTCCTTTGTTAAGAGAGAATGAA RR: ACATGTAAAAAGAAACGTCAGTATTTTATAATTACAATCTTTCTTGGGATGTCTAGGGTAAGTTGAGGAAACAATTCTCTCTTACTT F2: 3 TTGGGATGTCT 2 Unidirectional alignment (log-probability: -43.7) TACATTTTTCTTTGCAGTCATgAAATATTAATGTTAGAAAtctgtagggttt-----CTACAGATCCCATTCAACTCCTTTGTTAAGAGAGAATGA TACATTTTTCTTTGCAGTCATAAAATATTAATGTTAGAAA------------GAACCCTACAGATCCCATTCAACTCCTTTGTTAAGAGAGAATGA Template switch alignment (log-probability: -28.2) TACATTTTTCTTTGCAGTCATgAAATATTAATGTTAGAAA|TCTGTAGGGTT|tCTACAGATCCCATTCAACTCCTTTGTTAAGAGAGAATGA TACATTTTTCTTTGCAGTCATAAAATATTAATGTTAGAAA|TCTGTAGGGTT|CCTACAGATCCCATTCAACTCCTTTGTTAAGAGAGAATGA ========== Event 3581 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTTAGACTC---TCCTCTACTAGCCCAGGTGCT Chimp: GTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTTAGACTC---TCCTCTACTAGCCCAGGTGCT ↓ 3 2 1 4 Gorilla: GTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTCAGATAATCTACCTCTACTAGCCCAGGTGCT ↑ 3 2 1 4 Human: GTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTTAGACTC---TCCTCTACTAGCCCAGGTGCT Cluster: [ ] Orangutan: GTTTGCCTCTCCCTGGGTCAGACTATCTGCTGAGTCAGACTC---TCCTCTACTAGCCCAGGTACT Human > Gorilla --------------- chr8:25325425-25325434 Template switch process: F1: L AACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT 1 F3: 4 ACCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCAG R RF: AACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTTAGACTCTCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCAG RR: TTGTTACAAACGGAGAGGGACCCAGTCTAATAGACGACTCAATCTGAGAGGAGATGATCGGGTCCACGAAACGAACATGACACCCCGTC F2: 3 TCTAATAGAC 2 Unidirectional alignment (log-probability: -33.9) ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTcagataatcTA------CCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT---------TAGACTCTCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA Template switch alignment (log-probability: -22.5) ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT|CAGATAATCT|aCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT|CAGATAATCT|TCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA Chimp > Gorilla --------------- chr8:25325425-25325434 Template switch process: F1: L AACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT 1 F3: 4 ACCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCAG R RF: AACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTTAGACTCTCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCAG RR: TTGTTACAAACGGAGAGGGACCCAGTCTAATAGACGACTCAATCTGAGAGGAGATGATCGGGTCCACGAAACGAACATGACACCCCGTC F2: 3 TCTAATAGAC 2 Unidirectional alignment (log-probability: -33.9) ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGTcagataatcTA------CCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT---------TAGACTCTCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA Template switch alignment (log-probability: -22.5) ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT|CAGATAATCT|aCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA ACAATGTTTGCCTCTCCCTGGGTCAGATTATCTGCTGAGT|CAGATAATCT|TCCTCTACTAGCCCAGGTGCTTTGCTTGTACTGTGGGGCA ========== Event 3582 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTCACACATATGCAATTCTCTTAGGCAGTTCTCAAGCAGAATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA----TGGGGATGCATGATGATATTTTATTTA ↓ 3 2 1 4 Chimp: GTCACACGTATGCAATTCTCTTAGGCAGTCCTCAAGCAGAATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA----CTA-AGTGCATGATGATATTTTGTTTA Gorilla: GTCACACGTATGCAATTCTCTTAGGCAGTCCTCAAGCAGAATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA----CTA-AGTGCATGATGATATTTTATCTA ↑ 3 2 1 4 Human: GTCACACATATGCAATTCTCTTAGGCAGTTCTCAAGCAGAATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA----TGGGGATGCATGATGATATTTTATTTA Cluster: [ ] Orangutan: GTCACACGTATGCAATTCTCTTAGGCAGTCCTCAAGCAGGATTAAAATCTGCCTGAAAATGTTCACGTTCCCCGAAATAACTGACTA-AGTGCATGATGATATTTTATTTA Human > Chimp ------------- chr8:121746980-121746984 Template switch process: F1: L AATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA 1 F3: 4 TGCATGATGATATTTTGTTTATTTCAAGCTACCACCCTAA R RF: CTTAGGCAGTTCTCAAGCAGAATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAATGGGGATGCATGATGATATTTTATTTATTTCAAGCTACCACCCTAA RR: GAATCCGTCAAGAGTTCGTCTTAATTTTAGACGGACTTTTACAAGTGCAAGGGGTTTTATTACCCCTACGTACTACTATAAAATAAATAAAGTTCGATGGTGGGATT F2: 3 GAATC 2 Unidirectional alignment (log-probability: -34.6) ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAActaag------TGCATGATGATATTTTgTTTATTTCAAGCTACCACCCTAA ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA-----TGGGGATGCATGATGATATTTTATTTATTTCAAGCTACCACCCTAA Template switch alignment (log-probability: -21.9) ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA|CTAAG|TGCATGATGATATTTTgTTTATTTCAAGCTACCACCCTAA ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA|CTAAG|TGCATGATGATATTTTATTTATTTCAAGCTACCACCCTAA Human > Gorilla --------------- chr8:120903533-120903537 Template switch process: F1: L AATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA 1 F3: 4 TGCATGATGATATTTTATCTATTTCAAGCTACCACCCTAA R RF: CTTAGGCAGTTCTCAAGCAGAATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAATGGGGATGCATGATGATATTTTATTTATTTCAAGCTACCACCCTAA RR: GAATCCGTCAAGAGTTCGTCTTAATTTTAGACGGACTTTTACAAGTGCAAGGGGTTTTATTACCCCTACGTACTACTATAAAATAAATAAAGTTCGATGGTGGGATT F2: 3 GAATC 2 Unidirectional alignment (log-probability: -33.6) ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATA------ActaagTGCATGATGATATTTTATcTATTTCAAGCTACCACCCTAA ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAATGGGGA-----TGCATGATGATATTTTATTTATTTCAAGCTACCACCCTAA Template switch alignment (log-probability: -21.9) ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA|CTAAG|TGCATGATGATATTTTATcTATTTCAAGCTACCACCCTAA ATTAAAATCTGCCTGAAAATGTTCACGTTCCCCAAAATAA|CTAAG|TGCATGATGATATTTTATTTATTTCAAGCTACCACCCTAA ========== Event 3583 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAAAGATTCTGTCTACCAAA--CTCTGCATATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA----- Chimp: TAAAAGATTCTGTCTACCAGA--CTCTGCATATCATGTGATATCCGGTGCAGGGTTACCTTGGAAAA----A Gorilla: TAAAAGATTCTGTCTACCAAA----CTGCGTATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAAACTT- ↓ 1 4 3 2 Human: TAAAAGATTCTGTCTACCAAA--CTCTGCATATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA----- Cluster: [ ] Orangutan: TAAAAGATTCTGTCTACCAAACT--CTGCATATCATGTGATATCCGGTGCAGGGTTACCTTGGAAAAACTT- Gorilla > Human --------------- chr8:118510241-118510245 Template switch process: F1: L GAATCTTCCCTCCATAATTTTAAAAGATTCTGTCTACCAAACT 1 F3: 4 TATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA R RF: GAATCTTCCCCCCATAATTTTAAAAGATTCTGTCTACCAAACTGCGTATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA RR: CTTAGAAGGGGGGTATTAAAATTTTCTAAGACAGATGGTTTGACGCATAGTACACTATAGGACACGTCCCAATGGAACCTTTT F2: 3 ACGTC 2 Unidirectional alignment (log-probability: -31.7) TCTTCCCtCCATAATTTTAAAAGATTCTGTCTACCAAActCTGCaTATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA--- TCTTCCCCCCATAATTTTAAAAGATTCTGTCTACCAAA--CTGCGTATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAAACT Template switch alignment (log-probability: -21.8) TCTTCCCtCCATAATTTTAAAAGATTCTGTCTACCAAACT|CTGCA|TATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA TCTTCCCCCCATAATTTTAAAAGATTCTGTCTACCAAACT|CTGCA|TATCATGTGATATCCTGTGCAGGGTTACCTTGGAAAA ========== Event 3584 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TGCCTGCCTAGGCCCTGAGGGAGGGTTGC-------------TCCTCCAGCAAGCCTCCGGTTGATCCTCCAGATGTTTCCTTTCTAATTTTT Chimp: TGCCTGCCCAGGCCCTGAGGGAGGGTTGC-------------TCCTCCAGCAAGCCTCCGGTTGATCCTCCAGATTTTTCCTTTCTAATTTTT ↑ 3 4 2 1 Gorilla: TGCCTGCCCAGGCCCTGAGGGAGGGTTGC------------------------------------TCCTCCAGATTTTTCCTTTCTAATTTTT Human: TGCCTGCCTAGGCCCTGAGGGAGGGTTGC-------------TCCTCCAGCAAGCCTCCGGTTGATCCTCCAGATGTTTCCTTTCTAATTTTT Cluster: [ ] Orangutan: TGCCTGCCCAGGCCCTGAGGGAGGGTTGCTTCGGGCTGGTGA-----------------------TCCTCCAGATTTTTCCTTTCTAATTTTT Gorilla > Chimp --------------- chr8:144862320-144862328 Template switch process: F1: L CCTACCCTCCCTTGCCTGCCCAGGCCCTGAGGGAGGGTTGCTCCTCCAG 1 F3: 4 GGTTGATCCTCCAGATTTTTCCTTTCTAATTTTTCATATTAGCTGA R RF: CCTACCTTCCCTTGCCTGCCCAGGCCCTGAGGGAGGGTTGCTCCTCCAGATTTTTCCTTTCTAATTTTTCATATTAGCTGA RR: GGATGGAAGGGAACGGACGGGTCCGGGACTCCCTCCCAACGAGGAGGTCTAAAAAGGAAAGATTAAAAAGTATAATCGACT F2: 3 CCTCCGAAC 2 Unidirectional alignment (log-probability: -49.5) CCTTGCCTGCCCAGGCCCTGAGGGAGGGTTGCtcctccagcaagcctccggttgaTCCTCCAGATTTTTCCTTTCTAATTTTTCATATT CCTTGCCTGCCCAGGCCCTGAGGGAGGGTTGC-----------------------TCCTCCAGATTTTTCCTTTCTAATTTTTCATATT Template switch alignment (log-probability: -33.8) CCTTGCCTGCCCAGGCCCTGAGGGAGGGTTGCTCCTCCAG|CAAgCCTCC|GGTTGaTCCTCCAGATTTTTCCTTTCTAATTTTTCATATT CCTTGCCTGCCCAGGCCCTGAGGGAGGGTTGCTCCTCCAG|CAACCCTCC|GGTTGCTCCTCCAGATTTTTCCTTTCTAATTTTTCATATT ========== Event 3585 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: gctacctcagtttgcttacctggaaaataggaatgctcatgatagccatgcatgtgagggacttagaagagtgtatacagttagtgcccaataagtgtttatgatggttTTGCTTATAAGACAAGCCCTTTTCCAGAGCCCACACTTGGTGCTGACTTAGA ↑ 3 2 4 1 Chimp: gctacctcagtttgcttacctggaaaataggaatgctcatgatagccatgcatgtgagggacttacaagagtgtatacagttagtgcccaataagtgttTATGATGGTTTTGCTTATAAGACAA-------------GCCCACACTTGGTGCTGACTTAGA ↓ 3 2 4 1 Gorilla: gctacctcagtttgcttacctggaaaataggaatgctcatgatagccatgcatgtgagggacttagaagagtgtatacagttagtgcccaataagtgtttatgatggttTTGCTTATAAGACAAGCCCTTTTCCAGAGCCCACACTTGGTGCTGACTTAGA Human: gctacctcagtttgcttacctggaaaataggaatgctcatgatagccatgcatgtgagggacttagaagagtgtatacagttagtgcccaataagtgtttatgatggttTTGCTTATAAGACAAGCCCTTTTCCAGAGCCCACACTTGGTGCTGACTTAGA Cluster: [ ] Orangutan: gctacctcagtttgcttacctggaaaataggaatgctcatgatagccatgcatgtgagggacttagaagagtgtatgcagttagtgcccaataagtgtttgtgatggttTTGCTTATAAGACAAGGCCTTTTCCAGAGCCCACACTTGGTGCTGACTTAGA Chimp > Human ------------- chr8:27566641-27566648 Template switch process: F1: L GTGCCCAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCC 1 F3: 4 AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCCA R RF: CTGGAAAATAGGAATGCTCATGATAGCCATGCATGTGAGGGACTTACAAGAGTGTATACAGTTAGTGCCCAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCCA RR: GACCTTTTATCCTTACGAGTACTATCGGTACGTACACTCCCTGAATGTTCTCACATATGTCAATCACGGGTTATTCACAAATACTACCAAAACGAATATTCTGTTCGGGTGTGAACCACGACTGAATCTTCGAAGTCGTAACGGT F2: 3 GACCTTTT 2 Unidirectional alignment (log-probability: -29.6) CAATAAGTGTTTATGATGGTTTTGCTTATAAGACAagcccttttccagAGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC CAATAAGTGTTTATGATGGTTTTGCTTATAAGACA-------------AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC Template switch alignment (log-probability: -16.4) CAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCC|TTTTCCAG|AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC CAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCC|TTTTCCAG|AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC Chimp > Gorilla --------------- chr8:26663137-26663144 Template switch process: F1: L GTGCCCAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCC 1 F3: 4 AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCCA R RF: CTGGAAAATAGGAATGCTCATGATAGCCATGCATGTGAGGGACTTACAAGAGTGTATACAGTTAGTGCCCAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCCA RR: GACCTTTTATCCTTACGAGTACTATCGGTACGTACACTCCCTGAATGTTCTCACATATGTCAATCACGGGTTATTCACAAATACTACCAAAACGAATATTCTGTTCGGGTGTGAACCACGACTGAATCTTCGAAGTCGTAACGGT F2: 3 GACCTTTT 2 Unidirectional alignment (log-probability: -29.6) CAATAAGTGTTTATGATGGTTTTGCTTATAAGACAagcccttttccagAGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC CAATAAGTGTTTATGATGGTTTTGCTTATAAGACA-------------AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC Template switch alignment (log-probability: -16.9) CAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCC|TTTTCCAG|AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC CAATAAGTGTTTATGATGGTTTTGCTTATAAGACAAGCCC|TTTTCCAG|AGCCCACACTTGGTGCTGACTTAGAAGCTTCAGCATTGCC ========== Event 3586 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAGGGGAGTTTTTAAGATAATGTTTTGCTTCTCTGGATAGCCTCAATTTTTCTCCCTATTCTCA Chimp: AAGGGGAGTTTTTAAGATAATTTTTTGCTTCTCTGGATAGCCTCAATTTTTCTCCCTATTCTCA ↓ 13 24 ↑ 13 24 Gorilla: AAGGGGAGTTTTTAAGATAATTTTTTGAGGCTATCCAGAGAAGCAATTTTTCTCCCTATTCTCA ↓ 13 24 ↑ 13 24 Human: AAGGGGAGTTTTTAAGATAATGTTTTGCTTCTCTGGATAGCCTCAATTTTTCTCCCTATTCTCA Cluster: [ ] Orangutan: AAAGGGAGTTTTTAAGATAATTTTTTGCTTCTCTGGATAGCCTCAATTTTTCTCCCTAT-TTCA Gorilla > Human --------------- chr8:27810777-27810792 Template switch process: F1: L AATCAATCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATGTTTTG 1 F3: 4 CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT R RF: ----AATCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTGAGGCTATCCAGAGAAGCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT RR: ----TTAGTAAAAGAGTCCTTTCCCCTCAAAAATTCTATTAAAAAACTCCGATAGGTCTCTTCGTTAAAAAGAGGGATAAGAGTTAGATACAGAGTAAACACA F2: 3 TCCGATAGGTCTCTTC 2 Unidirectional alignment (log-probability: -58.3) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATgTTTTGcttctctggatAGcCT-----------CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG-----------AGGCTATCCAGAGAAGCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Template switch alignment (log-probability: -38.9) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATgTTTTG|CTTCTCTGGATAGCCT|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG|CTTCTCTGGATAGCCT|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Human > Gorilla --------------- chr8:26910107-26910122 Template switch process: F1: L ----AATCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG 1 F3: 4 CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT R RF: AATCAATCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATGTTTTGCTTCTCTGGATAGCCTCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT RR: TTAGTTAGTAAAAGAGTCCTTTCCCCTCAAAAATTCTATTACAAAACGAAGAGACCTATCGGAGTTAAAAAGAGGGATAAGAGTTAGATACAGAGTAAACACA F2: 3 GAAGAGACCTATCGGA 2 Unidirectional alignment (log-probability: -52.7) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATtTTTTG-----------AGgCTatccagagaagCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATGTTTTGCTTCTCTGGATAGCCT-----------CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Template switch alignment (log-probability: -33.3) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATtTTTTG|AGGCTATCCAGAGAAG|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATGTTTTG|AGGCTATCCAGAGAAG|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Gorilla > Chimp --------------- chr8:27271091-27271106 Template switch process: F1: L TCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG 1 F3: 4 CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT R RF: TCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTGAGGCTATCCAGAGAAGCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT RR: AGTAAAAGAGTCCTTTCCCCTCAAAAATTCTATTAAAAAACTCCGATAGGTCTCTTCGTTAAAAAGAGGGATAAGAGTTAGATACAGAGTAAACACA F2: 3 TCCGATAGGTCTCTTC 2 Unidirectional alignment (log-probability: -42.6) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTGcttctctggatAGcCT-----------CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG-----------AGGCTATCCAGAGAAGCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Template switch alignment (log-probability: -17.8) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG|CTTCTCTGGATAGCCT|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG|CTTCTCTGGATAGCCT|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Chimp > Gorilla --------------- chr8:26910107-26910122 Template switch process: F1: L TCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG 1 F3: 4 CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT R RF: TCATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTGCTTCTCTGGATAGCCTCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT RR: AGTAAAAGAGTCCTTTCCCCTCAAAAATTCTATTAAAAAACGAAGAGACCTATCGGAGTTAAAAAGAGGGATAAGAGTTAGATACAGAGTAAACACA F2: 3 GAAGAGACCTATCGGA 2 Unidirectional alignment (log-probability: -42.6) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG-----------AGgCTatccagagaagCAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTGCTTCTCTGGATAGCCT-----------CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT Template switch alignment (log-probability: -17.8) CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG|AGGCTATCCAGAGAAG|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT CATTTTCTCAGGAAAGGGGAGTTTTTAAGATAATTTTTTG|AGGCTATCCAGAGAAG|CAATTTTTCTCCCTATTCTCAATCTATGTCTCATTTGTGT ========== Event 3587 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATCTGAGCTAGCTTACTCATGAGA-CAT------------TATGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCT Chimp: ATCTGAGCTAGCTTACTCATGAGCCCAC------TGTTCCATTGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGT-- Gorilla: ATCTGAGCTAGCTTACTCATGTGCCCACTGTTCC------ATTGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCT ↓ 1 4 3 2 Human: ATCTGAGCTAGCTTACTCATGAGA-CAT------------TATGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCT Cluster: [ ] Orangutan: ATCTGAGCTAGCTTACTCATGTGCCCACTGTTCC------ACTGGGGAAAACATAATGTCTCTTTAGGCATCTCCCTGTCT Gorilla > Human --------------- chr8:28902543-28902550 Template switch process: F1: L TTGCTTCAGTAATTTCAGTCATCTGAGCTAGCTTACTCATG 1 F3: 4 TGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCTC R RF: TTGCTTCAGTAATTTCAGTCATCTGAGCTAGCTTACTCATGTGCCCACTGTTCCATTGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCTC RR: AACGAAGTCATTAAAGTCAGTAGACTCGATCGAATGAGTACACGGGTGACAAGGTAACCCCTTTTGTATTACAGAGGAATCCGTAGAGGGACAGAG F2: 3 ATTACAGA 2 Unidirectional alignment (log-probability: -32.9) TGCTTCAGTAATTTCAGTCATCTGAGCTAGCTTACTCATG---------------agacattaTGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCTC TGCTTCAGTAATTTCAGTCATCTGAGCTAGCTTACTCATGTGCCCACTGTTCCAT--------TGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCTC Template switch alignment (log-probability: -16.7) TGCTTCAGTAATTTCAGTCATCTGAGCTAGCTTACTCATG|AGACATTA|TGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCTC TGCTTCAGTAATTTCAGTCATCTGAGCTAGCTTACTCATG|AGACATTA|TGGGGAAAACATAATGTCTCCTTAGGCATCTCCCTGTCTC ========== Event 3588 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: aaaagaaaGGCTTAACAATTCTAGAGAGAGGC-----------------------TATCAAAATCTGCCTTTACTGCT------------------------------------------------------------------------------------------------------TATTTTCATGATCTCATGCATATTCCTCATCGTCCA----GTATTATTTTAT ↓ 4 3 2 1 Chimp: aaaaGAAAGGCTTAACAATTCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCT-----------------------TATTTTCGTGATCTCATGCATATTCCTCATTGAAAATAAGCAGTAAAGGCAGATTTTGATAGCCTCTCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATTGTCCA----GTATTATTTTAT ↑ 4 3 2 1 Gorilla: aaaaGAAAGGCTTAACAATTCTAGAGAGAGGC-----------------------TATCAAAATCTGCCTTTACTGCT------------------------------------------------------------------------------------------------------TATTTTCGTGATCTCATGCATATTCCTCATCGTCCA----GTATTATTTTAT Human: aaaagaaaGGCTTAACAATTCTAGAGAGAGGC-----------------------TATCAAAATCTGCCTTTACTGCT------------------------------------------------------------------------------------------------------TATTTTCATGATCTCATGCATATTCCTCATCGTCCA----GTATTATTTTAT Cluster: [ ] Orangutan: aaaagaaaGGCTTAACAATTCTAGATGGAGGC-----------------------TATCAAAATCTGCCTTTACTGCT------------------------------------------------------------------------------------------------------TATTTTCATGATTTCATGCATATTCCTCATCGTCCAGTGAATATTATTTTAT Human > Chimp ------------- chr8:29344037-29344072 Template switch process: F1: L AAAGAAAAAAAAAGAAAGGCTTAACAATTCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCGTGATCTCATGCATATTCCTCAT 1 F3: 4 TCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATTGTCCAGTATTATTTTAT R RF: AAAGAAAAAAAAAGAAAGGCTTAACAATTCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCATGATCTCATGCATATTCCTCATCGTCCAGTATTATTTTAT RR: TTTCTTTTTTTTTCTTTCCGAATTGTTAAGATCTCTCTCCGATAGTTTTAGACGGAAATGACGAATAAAAGTACTAGAGTACGTATAAGGAGTAGCAGGTCATAATAAAATA F2: 3 CTCCGATAGTTTTAGACGGAAATGACGAATAAAAGT 2 Unidirectional alignment (log-probability: -170) CTTTACTGCTTATTTTCgTGATCTCATGCATATTCCTCATtgaaaataagcagtaaaggcagattttgatagcctctctagagagaggctatcaaaatctgcctttactgcttatt CTTTACTGCTTATTTTCATGATCTCATGCATATTCCTCATC--------------------------------------------------------------------------- Template switch alignment (log-probability: -39.1) CTTTACTGCTTATTTTCgTGATCTCATGCATATTCCTCAT|TGAAAATAAGCAGTAAAGGCAGATTTTGATAGCCTC|TCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATT CTTTACTGCTTATTTTCATGATCTCATGCATATTCCTCAT|TGAAAATAAGCAGTAAAGGCAGATTTTGATAGCCTC|TCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATT Gorilla > Chimp --------------- chr8:29344039-29344072 Template switch process: F1: L AAGAAAAAAAAA-GAAAGGCTTAACAATTCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATTG 1 F3: 4 TCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATTGTCCAGTAT R RF: AAGAAAAAAAAAAGAAAGGCTTAACAATTCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATCGTCCAGTAT RR: TTCTTTTTTTTTTCTTTCCGAATTGTTAAGATCTCTCTCCGATAGTTTTAGACGGAAATGACGAATAAAAGCACTAGAGTACGTATAAGGAGTAGCAGGTCATA F2: 3 CTCCGATAGTTTTAGACGGAAATGACGAATAAAA 2 Unidirectional alignment (log-probability: -173) TTACTGCTTATTTTCGTGATCTCATGCATATTCCTCAttgaaaataagcagtaaaggcagattttgatagcctctctagagagaggctatcaaaatctgcctttactgcttatt TTACTGCTTATTTTCGTGATCTCATGCATATTCCTCA----------------------------------------------------------------------------- Template switch alignment (log-probability: -42.7) TTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATtG|AAAATAAGCAGTAAAGGCAGATTTTGATAGCCTC|TCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATT TTACTGCTTATTTTCGTGATCTCATGCATATTCCTCATCG|AAAATAAGCAGTAAAGGCAGATTTTGATAGCCTC|TCTAGAGAGAGGCTATCAAAATCTGCCTTTACTGCTTATT ========== Event 3589 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CATTCTGAGTCTATGAGATCATG---------------GGTGAGGGTGGGGCAGGGGACATGAGA Chimp: CATTCTGAGTCTATGAGATCATG---------------GGTGAGGGTGGGGCAGGGGACATGAGA ↓ 3 4 1 2 Gorilla: CATTCTGAGTCTATGAGATCATGGGTCCTCACCCATGGGGTGAGGGTGGGGCAGGGGACATGAGA ↑ 3 4 1 2 Human: CATTCTGAGTCTATGAGATCATG---------------GGTGAGGGTGGGGCAGGGGACATGAGA Cluster: [ ] Orangutan: AATTCTGAGTCTATGAGATCATG---------------GGTGAGGGTGGGGCAGGGGACATGAGA Human > Gorilla --------------- chr8:28969996-28970006 Template switch process: F1: L AGACCTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGT 1 F3: 4 GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAAG R RF: AGACCTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAAG RR: TCTGGAAGAGTCAACATGGTAAGACTCAGATACTCTAGTACCCACTCCCACCCCGTCCCCTGTACTCTTAGTGTCGTCTTC F2: 3 GTACCCACTCC 2 Unidirectional alignment (log-probability: -32.5) CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATgggtcctcacccatgGGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCAT---------------GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA Template switch alignment (log-probability: -17.2) CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGT|CCTCACCCATG|GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGT|CCTCACCCATG|GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA Chimp > Gorilla --------------- chr8:28969996-28970006 Template switch process: F1: L AGACCTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGT 1 F3: 4 GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAAG R RF: AGACCTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAAG RR: TCTGGAAGAGTCAACATGGTAAGACTCAGATACTCTAGTACCCACTCCCACCCCGTCCCCTGTACTCTTAGTGTCGTCTTC F2: 3 GTACCCACTCC 2 Unidirectional alignment (log-probability: -32.5) CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATgggtcctcacccatgGGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCAT---------------GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA Template switch alignment (log-probability: -17.2) CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGT|CCTCACCCATG|GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA CTTCTCAGTTGTACCATTCTGAGTCTATGAGATCATGGGT|CCTCACCCATG|GGGTGAGGGTGGGGCAGGGGACATGAGAATCACAGCAGAA ========== Event 3590 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACACTGCATTATCTTCTCTGCAAATCAAGTTAA Chimp: TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACACTGCATTATTTTCTCTGCAAATCAAGTTAA ↑ 3 2 1 4 Gorilla: TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACA---CATATTTTTCTCTGCAAATCAAGTTAA ↓ 3 2 1 4 Human: TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACACTGCATTATCTTCTCTGCAAATCAAGTTAA Cluster: [ ] Orangutan: TATCTTCTTCACTCTCTAATAATGCAGTTGTTGCTGACA---CACATTTTTCTCTGCAAATCAAGTTAA Gorilla > Human --------------- chr8:30847374-30847380 Template switch process: F1: L GGTATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACAC 1 F3: 4 TCTTCTCTGCAAATCAAGTTAAATTTAGTAGAAAATTCTTCA R RF: GGTATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACACATATTTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTTCA RR: CCATAGAAGAAGTGAGAGATTATTACGTCAACGACGACTGTGTATAAAAAGAGACGTTTAGTTCAATTTACATCATCTTTTAAGAAGT F2: 3 ATTACGT 2 Unidirectional alignment (log-probability: -37.4) TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACActgCATtaTcTTCTCTGCAAATCAAGTTAAATtTAGTAGAAAATTCTT TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACA---CATATTTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT Template switch alignment (log-probability: -27.7) TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACAC|TGCATTA|TcTTCTCTGCAAATCAAGTTAAATtTAGTAGAAAATTCTT TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACAC|TGCATTA|TTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT Gorilla > Chimp --------------- chr8:30415072-30415078 Template switch process: F1: L GGTATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACAC 1 F3: 4 TTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT R RF: GGTATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACACATATTTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT RR: CCATAGAAGAAGTGAGAGATTATTACGTCAACGACGACTGTGTATAAAAAGAGACGTTTAGTTCAATTTACATCATCTTTTAAGAA F2: 3 ATTACGT 2 Unidirectional alignment (log-probability: -26.3) TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACActgCATtaTTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACA---CATATTTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT Template switch alignment (log-probability: -16.6) TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACAC|TGCATTA|TTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT TATCTTCTTCACTCTCTAATAATGCAGTTGCTGCTGACAC|TGCATTA|TTTTCTCTGCAAATCAAGTTAAATGTAGTAGAAAATTCTT ========== Event 3591 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: TGCTGATGGATGGTGTTGAGTTTAGTGATGCAGACACAGCCTGTG----------------GCCAGAGTTTTGCTGATGGTTCAGC ↓ 1 3 42 ↑ 1 3 24 Chimp: TGCTGATGGATGGTGTTGAGTCTG--------GCCACAGGCTGTG--------TCTGCATCACTAGAGTTTTGCTGATGGTTCAGC Gorilla: TGCTGATGGATGGTGTTGAGTCTG--------GCCACAGGCTGTGTCTGCATC--------ACTAGAGTTTTGCTGATGGTTCAGC ↓ 1 3 24 Human: TGCTGATGGATGGTGTTGAGTTTAGTGATGCAGACACAGCCTGTG----------------GCCAGAGTTTTGCTGATGGTTCAGC Cluster: [ ] Orangutan: TGCTGATGGATGGTGTTGAGTCTG--------GCCACAGGCTGTGTCTGCATC--------ACTAGAGTTTTGCTGATGGTCCAGC Chimp > Human ------------- chr8:30563257-30563281 Template switch process: F1: L TTTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTTT 1 F3: 4 AGAGTTTTGCTGATGGTTCAGCCATGTGCTAGAGAGCCCA R RF: TTTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTCTGGCCACAGGCTGTGTCTGCATCACTAGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA RR: AAAATTAAACGAGGCGGAGAACGACTACCTACCACAACTCAGACCGGTGTCCGACACAGACGTAGTGATCTCAAAACGACTACCAAGTCGGTACACGGTCTCTCGGGT F2: 3 CCGGTGTCCGACACAGACGTAGTGA 2 Unidirectional alignment (log-probability: -64.4) TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTttagtgatgcagacacagcctgTGGCC---------------------AGAGTTTTGCTGATGGTTCAGCCATGTGCtAGAGAGCCCA TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTC---------------------TGGCCACAGGCTGTGTCTGCATCACTAGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA Template switch alignment (log-probability: -30.4) TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTtT|AGTGATGCAGACACAGCCTGTGGCC|AGAGTTTTGCTGATGGTTCAGCCATGTGCtAGAGAGCCCA TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTCT|AGTGATGCAGACACAGCCTGTGGCC|AGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA Human > Chimp ------------- chr8:30117822-30117848 Template switch process: F1: L TTTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGT 1 F3: 4 AGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA R RF: TTTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTTTAGTGATGCAGACACAGCCTGTGGCCAGAGTTTTGCTGATGGTTCAGCCATGTGCTAGAGAGCCCA RR: AAAATTAAACGAGGCGGAGAACGACTACCTACCACAACTCAAATCACTACGTCTGTGTCGGACACCGGTCTCAAAACGACTACCAAGTCGGTACACGATCTCTCGGGT F2: 3 TCACTACGTCTGTGTCGGACACCGGTC 2 Unidirectional alignment (log-probability: -64.4) TTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTc---------------------TGGCCAcaggctgtgtctgcatcactaGAGTTTTGCTGATGGTTCAGCCATGTGCcAGAGAGCCCA TTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTTTAGTGATGCAGACACAGCCTGTGGCCA---------------------GAGTTTTGCTGATGGTTCAGCCATGTGCTAGAGAGCCCA Template switch alignment (log-probability: -24.6) TTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGT|CTGGCCACAGGCTGTGTCTGCATCACT|AGAGTTTTGCTGATGGTTCAGCCATGTGCcAGAGAGCCCA TTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGT|CTGGCCACAGGCTGTGTCTGCATCACT|AGAGTTTTGCTGATGGTTCAGCCATGTGCTAGAGAGCCCA Gorilla > Human --------------- chr8:30563257-30563281 Template switch process: F1: L TTTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTTT 1 F3: 4 AGAGTTTTGCTGATGGTTCAGCCATGTGCTAGAGAGCCCA R RF: TTTTAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTCTGGCCACAGGCTGTGTCTGCATCACTAGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA RR: AAAATTAAACGAGGCGGAGAACGACTACCTACCACAACTCAGACCGGTGTCCGACACAGACGTAGTGATCTCAAAACGACTACCAAGTCGGTACACGGTCTCTCGGGT F2: 3 CCGGTGTCCGACACAGACGTAGTGA 2 Unidirectional alignment (log-probability: -63) TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGtttagtgatgcagacacagccTgTGGCC---------------------AGAGTTTTGCTGATGGTTCAGCCATGTGCtAGAGAGCCCA TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAG---------------------TCTGGCCACAGGCTGTGTCTGCATCACTAGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA Template switch alignment (log-probability: -30) TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTtT|AGTGATGCAGACACAGCCTGTGGCC|AGAGTTTTGCTGATGGTTCAGCCATGTGCtAGAGAGCCCA TAATTTGCTCCGCCTCTTGCTGATGGATGGTGTTGAGTCT|AGTGATGCAGACACAGCCTGTGGCC|AGAGTTTTGCTGATGGTTCAGCCATGTGCCAGAGAGCCCA ========== Event 3592 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCGGGGAACGGTTCGCGTGCTGGGTGTTTCGC----TTCGAGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGCTCAG Chimp: CCGGGGAACGGTTCGCGTGCTGGGTGTTTCGC----TTCGAGAACGGCGGTCCCAGCTTCCCGTGAGCTGGAGGTCACGCTCAG ↓ 1 4 3 2 Gorilla: CCGGGGAACGGTTCGCGTGCTAGGTGTTTCACGGGAAGCTAGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGCTCAG ↑ 1 4 3 2 Human: CCGGGGAACGGTTCGCGTGCTGGGTGTTTCGC----TTCGAGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGCTCAG Cluster: [ ] Orangutan: CCGGGGAACGGTTCGCGTGCTGGGTGTTTCGC----TTCGAGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGCTCAG Human > Gorilla --------------- chr8:61033181-61033190 Template switch process: F1: L TCTGGCCTAAAGACAATGCTCCGGGGAACGGTTCGCGTGCTAGGTGTTTC 1 F3: 4 AGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC R RF: TCTGGCCTAAAGACAATGCTCCGGGGAACGGTTCGCGTGCTGGGTGTTTCGCTTCGAGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC RR: AGACCGGATTTCTGTTACGAGGCCCCTTGCCAAGCGCACGACCCACAAAGCGAAGCTCTTGCCGCCAGGGTCGAAGGGCACTCCACCTCCAGTGCG F2: 3 TCGAAGGGCA 2 Unidirectional alignment (log-probability: -36.5) AGACAATGCTCCGGGGAACGGTTCGCGTGCTaGGTGTTTCacgggaaGCT---AGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC AGACAATGCTCCGGGGAACGGTTCGCGTGCTGGGTGTTTC-------GCTTCGAGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC Template switch alignment (log-probability: -22.7) AGACAATGCTCCGGGGAACGGTTCGCGTGCTaGGTGTTTC|ACGGGAAGCT|AGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC AGACAATGCTCCGGGGAACGGTTCGCGTGCTGGGTGTTTC|ACGGGAAGCT|AGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC Chimp > Gorilla --------------- chr8:61033181-61033190 Template switch process: F1: L TCTGGCCTAAAGACAATGCTCCGGGGAACGGTTCGCGTGCTAGGTGTTTC 1 F3: 4 AGAACGGCGGTCCCAGCTTCCCGTGAGGTGGAGGTCACGC R RF: TCTGGCCTAAAGACAATGCTCCGGGGAACGGTTCGCGTGCTGGGTGTTTCGCTTCGAGAACGGCGGTCCCAGCTTCCCGTGAGCTGGAGGTCACGC RR: AGACCGGATTTCTGTTACGAGGCCCCTTGCCAAGCGCACGACCCACAAAGCGAAGCTCTTGCCGCCAGGGTCGAAGGGCACTCGACCTCCAGTGCG F2: 3 TCGAAGGGCA 2 Unidirectional alignment (log-probability: -42.1) AGACAATGCTCCGGGGAACGGTTCGCGTGCTaGGTGTTTCacgggaaGCT---AGAACGGCGGTCCCAGCTTCCCGTGAGgTGGAGGTCACGC AGACAATGCTCCGGGGAACGGTTCGCGTGCTGGGTGTTTC-------GCTTCGAGAACGGCGGTCCCAGCTTCCCGTGAGCTGGAGGTCACGC Template switch alignment (log-probability: -28.3) AGACAATGCTCCGGGGAACGGTTCGCGTGCTaGGTGTTTC|ACGGGAAGCT|AGAACGGCGGTCCCAGCTTCCCGTGAGgTGGAGGTCACGC AGACAATGCTCCGGGGAACGGTTCGCGTGCTGGGTGTTTC|ACGGGAAGCT|AGAACGGCGGTCCCAGCTTCCCGTGAGCTGGAGGTCACGC ========== Event 3593 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTCTTAATGTGCATGTAACTGGAAA------ATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTA Chimp: ATTCTTAATGTGCATGTAACTGGAAA------ATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTA ↓ 1 4 3 2 Gorilla: ATTCTTAATGTGCATGTAACTTGCAAGCCACTCTTAAGAGTGGCTTCCAAGGGATTTACTACAAAAGTA ↑ 1 4 3 2 Human: ATTCTTAATGTGCATGTAACTGGAAA------ATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTA Cluster: [ ] Orangutan: ATTCTTAATGTGCATGTAACTGGAAA------ATTAAGAGTGGCTTACAAGGGATCTACTACAAAAGTA Human > Gorilla --------------- chr8:61564556-61564567 Template switch process: F1: L TTGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACT 1 F3: 4 TTAAGAGTGGCTTCCAAGGGATTTACTACAAAAGTAAGGG R RF: TTGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACTGGAAAATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTAAGGT RR: AACTAATTAAAATAAGGGGGTAAGAATTACACGTACATTGACCTTTTAATTCTCACCGAAGGTTCCCTAGATGATGTTTTCATTCCA F2: 3 CTCACCGAACGT 2 Unidirectional alignment (log-probability: -47.2) TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACTtGcAAgccactcTTAAGAGTGGCTTCCAAGGGATtTACTACAAAAGTAAGGg TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACTGGAAA------ATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTAAGGT Template switch alignment (log-probability: -33.8) TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACT|TGcAAGCCACTC|TTAAGAGTGGCTTCCAAGGGATtTACTACAAAAGTAAGGg TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACT|TGGAAGCCACTC|TTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTAAGGT Chimp > Gorilla --------------- chr8:61564556-61564567 Template switch process: F1: L TTGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACT 1 F3: 4 TTAAGAGTGGCTTCCAAGGGATTTACTACAAAAGTAAGGG R RF: TTGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACTGGAAAATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTAAGGG RR: AACTAATTAAAATAAGGGGGTAAGAATTACACGTACATTGACCTTTTAATTCTCACCGAAGGTTCCCTAGATGATGTTTTCATTCCC F2: 3 CTCACCGAACGT 2 Unidirectional alignment (log-probability: -41.7) TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACTtGcAAgccactcTTAAGAGTGGCTTCCAAGGGATtTACTACAAAAGTAAGGG TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACTGGAAA------ATTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTAAGGG Template switch alignment (log-probability: -28.3) TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACT|TGcAAGCCACTC|TTAAGAGTGGCTTCCAAGGGATtTACTACAAAAGTAAGGG TGATTAATTTTATTCCCCCATTCTTAATGTGCATGTAACT|TGGAAGCCACTC|TTAAGAGTGGCTTCCAAGGGATCTACTACAAAAGTAAGGG ========== Event 3594 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GCACCACAAATGTACATGATACAAGTAAACTTGAAGAAACCAATTACATTGGGGGATAGTCTTGTTTTCTGTTAT Chimp: GCACCACAAATGTACATGATACAAGTAAACTTGAAGA--------ATACTTGAAGATAGTCTTGTTTTCTGTTCT ↑ 3 2 1 4 Gorilla: GCACCACAAATGTACATGATACAAGTAAATTTGAAGAAACCAATTACATTGGGGGATAGTCTTGTTTTCTGTTCT Human: GCACCACAAATGTACATGATACAAGTAAACTTGAAGAAACCAATTACATTGGGGGATAGTCTTGTTTTCTGTTAT Cluster: [ ] Orangutan: GCACCACAAATGTACATGATGCAAGTAAAGTTGAAGAAATCAATGACATTGGGGGATAGTCTTGTTTTCTGTTCT Gorilla > Chimp --------------- chr8:31663871-31663878 Template switch process: F1: L TTGACTTGGAAAGCACCACAAATGTACATGATACAAGTAAACTTGAAGAA 1 F3: 4 GATAGTCTTGTTTTCTGTTCTTCTGTGGACTTGCTTTATT R RF: TTGACTTGGAAAGCACCACAAATGTACATGATACAAGTAAATTTGAAGAAACCAATTACATTGGGGGATAGTCTTGTTTTCTGTTCTTCTGTGGACTTGCTTTATT RR: AACTGAACCTTTCGTGGTGTTTACATGTACTATGTTCATTTAAACTTCTTTGGTTAATGTAACCCCCTATCAGAACAAAAGACAAGAAGACACCTGAACGAAATAA F2: 3 AAGTTCAT 2 Unidirectional alignment (log-probability: -37.1) AAGCACCACAAATGTACATGATACAAGTAAAcTTGAAGAatacttgAA---------------GATAGTCTTGTTTTCTGTTCTTCTGTGGACTTGCTTTATT AAGCACCACAAATGTACATGATACAAGTAAATTTGAAGA-------AACCAATTACATTGGGGGATAGTCTTGTTTTCTGTTCTTCTGTGGACTTGCTTTATT Template switch alignment (log-probability: -28) AAGCACCACAAATGTACATGATACAAGTAAAcTTGAAGAA|TACTTGaA|GATAGTCTTGTTTTCTGTTCTTCTGTGGACTTGCTTTATT AAGCACCACAAATGTACATGATACAAGTAAATTTGAAGAA|TACTTGTA|GATAGTCTTGTTTTCTGTTCTTCTGTGGACTTGCTTTATT ========== Event 3595 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: CTATCAGTTCTACTGATAAGT------ACATGTAAGTTAAATGAGCCAGTTATCACAGTGCAAGAATTCC ↓ 3 1 2 4 ↑ 13 24 Chimp: CTATCAGTTCTACTGATAAGT---GGCTCATTTAACTTATATG---TACTTATCACAGTGCAAGAATTCC Gorilla: CTATCAGTTCTACTGATAAGTGGC---TCCTTTAACTTATATG---TACTTATCACAATGCAAGAATTCC Human: CTATCAGTTCTACTGATAAGT------ACATGTAAGTTAAATGAGCCAGTTATCACAGTGCAAGAATTCC Cluster: [ ] Orangutan: CTATCAGTTCTACTGATAAGTGGC---TCATTGAACTTATATG---CACTTATCACAATGCAAGAATTCC Chimp > Human ------------- chr8:33014544-33014563 Template switch process: F1: L AGGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGT 1 F3: 4 AGTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC R RF: AGGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGTGGCTCATTTAACTTATATGTACTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC RR: TCCAGTGGGATCGGTAATAGGATAGTCAAGATGACTATTCACCGAGTAAATTGAATATACATGAATAGTGTCACGTTCTTAAGGAGACTGACCAGAACGATAG F2: 3 CCGAGTAAATTGAATGTACA 2 Unidirectional alignment (log-probability: -50.9) GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAA--------------------GTACatgtaagttaaatgagccagTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTA GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGTGGCTCATTTAACTTATATGTAC--------------------TTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTA Template switch alignment (log-probability: -29.8) GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGT|ACATgTAAGTTAAATGAGCC|AgTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTA GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGT|ACATATAAGTTAAATGAGCC|ACTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTA Human > Chimp ------------- chr8:32608803-32608824 Template switch process: F1: L AGGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGT 1 F3: 4 TTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC R RF: AGGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGTACATGTAAGTTAAATGAGCCAGTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC RR: TCCAGTGGGATCGGTAATAGGATAGTCAAGATGACTATTCATGTACATTCAATTTACTCGGTCAATAGTGTCACGTTCTTAAGGAGACTGACCAGAACGATAG F2: 3 CATGTATATTCAATTTACTCGG 2 Unidirectional alignment (log-probability: -50.9) GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGtggctcatttaacttatatgTAC--------------------TTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAG--------------------TACATGTAAGTTAAATGAGCCAGTTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC Template switch alignment (log-probability: -24) GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGT|GGCTCATTTAACTTAtATGTAC|TTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC GGTCACCCTAGCCATTATCCTATCAGTTCTACTGATAAGT|GGCTCATTTAACTTACATGTAC|TTATCACAGTGCAAGAATTCCTCTGACTGGTCTTGCTATC ========== Event 3596 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTCTGTGTCACAGGTTTGAAGAGAGTCAGAAGTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAACTTCCTTTAGCATCTCTTCTTGTTCAGACTTCTGGAGAGTCTCCTCTTTGGAAAGGTGAGTTTGCTTCTCTTGTAAAAGGACAGAGAGGATGTTCCTAGGAAAACCTGGAATGAGGAC ↓ 1 4 3 2 Chimp: GTTCTGTGTCACAGGTTTGAA--GAGTAGGAACTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAACTTCCTTTAGCATCTCTTCTTGTTCAGACTTCTGGAGAGTCTCCTCTTTGGAAAGGTGAGTTTGCTTCTCTTGTAAAAGGACAGAGAGGATGTTCCTAGGAAAACCTGGAATGAGGAC Gorilla: GTTCTGTGTCACAGGTTTGAAGAGAGTCGGAAGTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAACTTCCTTTAGCATCTCTTCTTGTTCAGACTTCTGGAGAGTCTCCTCTTTGGAAAGGTGAGTTTGCTTCTGTTGTAAAAGGACAGAGAGGATGTTCCTAGGAAAACCTGGAATGAGGAC Human: GTTCTGTGTCACAGGTTTGAAGAGAGTCAGAAGTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAACTTCCTTTAGCATCTCTTCTTGTTCAGACTTCTGGAGAGTCTCCTCTTTGGAAAGGTGAGTTTGCTTCTCTTGTAAAAGGACAGAGAGGATGTTCCTAGGAAAACCTGGAATGAGGAC Cluster: [ ] Orangutan: GTTCTGTGTCACAGGTTTGAAGAGAGTCAGAAGTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAACTTCCTTTAGCATCCCTTCATGTTCAGACCTCTGGAGAGTCTCCTCTTTGGAAAGACAAGTTTGCTTCTCTTGTAAAAGGACAGAGAGGATGTTCCTAGGAAAACCTGGAATGAGGAC Human > Chimp ------------- chr8:115004360-115004366 Template switch process: F1: L AGTGAACTATTCTTTCAGGGGTTCTGTGTCACAGGTTTGAAGAG 1 F3: 4 TCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAAC R RF: AGTGAACTATTCTTTCAGGGGTTCTGTGTCACAGGTTTGAAGAGAGTCAGAAGTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAACTTCCTTTAGCATCTCTTCTTGTTCAGACTTCTGGAGAGTCTCCTCTTTGGAAAGGTGAGTTTGCTTCTCTTGTAAAAGGACAGAGAGGATGTTCCTA RR: TCACTTGATAAGAAAGTCCCCAAGACACAGTGTCCAAACTTCTCTCAGTCTTCAGTACACCACTTTTCGTTGTAAGACTTCAGTGTCCAATTGAAGGAAATCGTAGAGAAGAACAAGTCTGAAGACCTCTCAGAGGAGAAACCTTTCCACTCAAACGAAGAGAACATTTTCCTGTCTCTCCTACAAGGAT F2: 3 CAAGGAT 2 Unidirectional alignment (log-probability: -28.8) AACTATTCTTTCAGGGGTTCTGTGTCACAGGTTTGAAGAGtAG---GAAcTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAAC AACTATTCTTTCAGGGGTTCTGTGTCACAGGTTTGAAGAG-AGTCAGAAGTCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAAC Template switch alignment (log-probability: -16.2) AACTATTCTTTCAGGGGTTCTGTGTCACAGGTTTGAAGAG|TAGGAAC|TCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAAC AACTATTCTTTCAGGGGTTCTGTGTCACAGGTTTGAAGAG|TAGGAAC|TCATGTGGTGAAAAGCAACATTCTGAAGTCACAGGTTAAC ========== Event 3597 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTCTTATTCAGTTGCAGGCAGGGGATATTGCTCACTGTTGCTCACAGGGGATATCCCAGCACTATATTGAAACCTTG Chimp: ACTCTTATTCAGTTGCAGGCA-------GTTTTCACTGTTGCTCACAGGGGATATCCCAGCACTATATTGAAACCTTG Gorilla: ACTCTTATTCAGTTGCAGGCA-------GTTTTCACTGTTGCTCACAGGGAATATCCCAGCACTATATTGAAACCTTG ↓ 1 4 3 2 Human: ACTCTTATTCAGTTGCAGGCAGGGGATATTGCTCACTGTTGCTCACAGGGGATATCCCAGCACTATATTGAAACCTTG Cluster: [ ] Orangutan: ACTCTCATTCAGTTGCAGGCA-------GTTTTCACTGTTGCTCACAGGGGATATCCCAGCACTATATTGAAACCTTG Gorilla > Human --------------- chr8:112045320-112045329 Template switch process: F1: L TTTCACTTGTTTTTTTCTTTACTCTTATTCAGTTGCAGGCAG 1 F3: 4 TCACTGTTGCTCACAGGGGATATCCCAGCACTATATTGAA R RF: TTTCACTTGTTTTTTTCTTTACTCTTATTCAGTTGCAGGCAGTTTTCACTGTTGCTCACAGGGAATATCCCAGCACTATATTGAA RR: AAAGTGAACAAAAAAAGAAATGAGAATAAGTCAACGTCCGTCAAAAGTGACAACGAGTGTCCCTTATAGGGTCGTGATATAACTT F2: 3 CGTTATAGGG 2 Unidirectional alignment (log-probability: -37.6) TCACTTGTTTTTTTCTTTACTCTTATTCAGTTGCAGGCAGgggatatTgcTCACTGTTGCTCACAGGGgATATCCCAGCACTATATTGAA TCACTTGTTTTTTTCTTTACTCTTATTCAGTTGCAGGCAG-------TTTTCACTGTTGCTCACAGGGAATATCCCAGCACTATATTGAA Template switch alignment (log-probability: -28.1) TCACTTGTTTTTTTCTTTACTCTTATTCAGTTGCAGGCAG|GGGATATTgC|TCACTGTTGCTCACAGGGgATATCCCAGCACTATATTGAA TCACTTGTTTTTTTCTTTACTCTTATTCAGTTGCAGGCAG|GGGATATTCC|TCACTGTTGCTCACAGGGAATATCCCAGCACTATATTGAA ========== Event 3598 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TATGCCCATGGAGAATTTTATCATTGCTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTTGTGCTTTGTGCAGAAGTCTTCAGCGTGTGACTGGATTCAATGCTGCTACTCTTTTGGTCTGA ↑ 1 4 3 2 Chimp: TATGCCCATGGAGAATTTTATGATTACTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTT-------TGTGCAGAAGTCTTCAGCGTGTGACTGGATTCAATGCTGCTACTCTTTTAGTCTGA Gorilla: TATGCCCATGGAGAATTTTATGATTACACAAGGAGAGGTGTGATTTTTTAAAAGTGCGTT-------TGTGCAGAAGTCTTCAGCGTGTGACTGGATTCAATGCTGCTACTCTTTTGGTCTGA Human: TATGCCCATGGAGAATTTTATCATTGCTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTTGTGCTTTGTGCAGAAGTCTTCAGCGTGTGACTGGATTCAATGCTGCTACTCTTTTGGTCTGA Cluster: [ ] Orangutan: TATGCCCATGGAGAATTTTATGATTGCTGAAGGAGATGTGTGATTTTTTAAAAGTGCG-T-------TGTGCAGAAGTCTTCAGCGTGTGACTGGATTCAATGCTGCTACTCTTTTGGTCTGA Chimp > Human ------------- chr8:35336453-35336457 Template switch process: F1: L GGGTGGAAATCATTGTTAATTATGCCCATGGAGAATTTTAT 1 F3: 4 CTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTTGTGCT R RF: GGGTGGAAATCATTGTTAATTATGCCCATGGAGAATTTTATGATTACTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTTGTGCAGAAGTCTTCAGCGTGTGACTGGATTCAATG RR: CCCACCTTTAGTAACAATTAATACGGGTACCTCTTAAAATACTAATGAGTTCCTCTCCACACTAAAAAATTTTCACGCAAACACGTCTTCAGAAGTCGCACACTGACCTAAGTTAC F2: 3 GTTAC 2 Unidirectional alignment (log-probability: -28.5) GGTGGAAATCATTGTTAATTATGCCCATGGAGAATTTTATcATTgCTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTtgtgct GGTGGAAATCATTGTTAATTATGCCCATGGAGAATTTTATGATTACTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTT------ Template switch alignment (log-probability: -21.9) GGTGGAAATCATTGTTAATTATGCCCATGGAGAATTTTAT|CATTG|CTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTTGTGCt GGTGGAAATCATTGTTAATTATGCCCATGGAGAATTTTAT|CATTG|CTCAAGGAGAGGTGTGATTTTTTAAAAGTGCGTTTGTGCA ========== Event 3599 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTACTCTACAGCTAATAATCAC---TAAGCT------CTGAGGGAGAGCTTAGTGATTTATTTCTCTTATCTTT Chimp: ACTACTCTACAGCTAATAATCAC---TAAGCT------CTGAGGGAGAGCTTAGTGATTTATTTCTCTTATCTTT ↑ 1 3 4 2 Gorilla: ATTACTCTACAGCTAATAATCTC------CCT------------CAGAGCTTAGTGATTTATTTCTCTTATCTTG ↓ 1 3 4 2 Human: ATTACTCTACAGCTAATAATCAC---TAAGCT------CTGAGGGAGAGCTTAGTGATTTATTTCTCTTATCTTT Cluster: [ ] Orangutan: ATTACTCTATAGCTAATAATCACTAA---GCTCTGAGG------GAGAGCTTAGTGATTTCTTTCTCTTATCTTT Gorilla > Human --------------- chr8:35492238-35492252 Template switch process: F1: L ATGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATC 1 F3: 4 AGAGCTTAGTGATTTATTTCTCTTATCTTTCATCTGTTTT R RF: ATGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATCTCCCTCAGAGCTTAGTGATTTATTTCTCTTATCTTGCATCTGTTTT RR: TACGTTGTCTATCGATACAATAATGAGATGTCGATTATTAGAGGGAGTCTCGAATCACTAAATAAAGAGAATAGAACGTAGACAAAA F2: 3 GGGAGTCTCGAATCA 2 Unidirectional alignment (log-probability: -48) TGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATCactaagctctgaggg------AGAGCTTAGTGATTTATTTCTCTTATCTTtCATCTGTTTT TGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATC---------------TCCCTCAGAGCTTAGTGATTTATTTCTCTTATCTTGCATCTGTTTT Template switch alignment (log-probability: -23.2) TGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATC|ACTAAGCTCTGAGGG|AGAGCTTAGTGATTTATTTCTCTTATCTTtCATCTGTTTT TGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATC|ACTAAGCTCTGAGGG|AGAGCTTAGTGATTTATTTCTCTTATCTTGCATCTGTTTT Gorilla > Chimp --------------- chr8:35185470-35185484 Template switch process: F1: L ATGCAACAGATAGCTATGTTACTACTCTACAGCTAATAATC 1 F3: 4 AGAGCTTAGTGATTTATTTCTCTTATCTTTCATCTGTTTT R RF: ATGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATCTCCCTCAGAGCTTAGTGATTTATTTCTCTTATCTTGCATCTGTTTT RR: TACGTTGTCTATCGATACAATAATGAGATGTCGATTATTAGAGGGAGTCTCGAATCACTAAATAAAGAGAATAGAACGTAGACAAAA F2: 3 GGGAGTCTCGAATCA 2 Unidirectional alignment (log-probability: -53.5) TGCAACAGATAGCTATGTTAcTACTCTACAGCTAATAATCactaagctctgaggg------AGAGCTTAGTGATTTATTTCTCTTATCTTtCATCTGTTTT TGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATC---------------TCCCTCAGAGCTTAGTGATTTATTTCTCTTATCTTGCATCTGTTTT Template switch alignment (log-probability: -28.7) TGCAACAGATAGCTATGTTAcTACTCTACAGCTAATAATC|ACTAAGCTCTGAGGG|AGAGCTTAGTGATTTATTTCTCTTATCTTtCATCTGTTTT TGCAACAGATAGCTATGTTATTACTCTACAGCTAATAATC|ACTAAGCTCTGAGGG|AGAGCTTAGTGATTTATTTCTCTTATCTTGCATCTGTTTT ========== Event 3600 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CATAAAACAGAGCAGGCAAGA-----------------------------------------GGAGTGAATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCT Chimp: CATAAAACAGAGCAGGCAAGA--------------------------------------------------------------ATCTTTGGGTTGCTGGAGCCT Gorilla: CATAAAACAGAGCAGGCAAGA---------------------ACTGTCATTTATAATGACAG---------------------TTCTTTGGGTTGCTGGAGCCT ↑ 1 4 3 2 Human: CATAAAACAGAGCAGGCAAGA-----------------------------------------GGAGTGAATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCT Cluster: [ ] Orangutan: CATAAAACAGAGCAGGCAAGAGGAGTGAATTTATAATGACAG-----------------------------------------TTCTTTGGGTTGCTGGAGCCT Human > Gorilla --------------- chr8:65878658-65878663 Template switch process: F1: L TGGCATTAGTCAGGGACATACATAAAACAGAGCAGGCAAGA 1 F3: 4 ATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCTCGGAGTTTGCTTCTACTGG R RF: TGGCATTAGTCAGGGACATACATAAAACAGAGCAGGCAAGAGGAGTGAATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCTTGGAGTTTGCTTCTACTTG RR: ACCGTAATCAGTCCCTGTATGTATTTTGTCTCGTCCGTTCTCCTCACTTAAATATTACTGTCAAGAAACCCAACGACCTCGGAACCTCAAACGAAGATGAAC F2: 3 CTGTCA 2 Unidirectional alignment (log-probability: -39.4) GGCATTAGTCAGGGACATACATAAAACAGAGCAGGCAAGA------ActgtcATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCTcGGAG GGCATTAGTCAGGGACATACATAAAACAGAGCAGGCAAGAGGAGTGA-----ATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCTTGGAG Template switch alignment (log-probability: -27.9) GGCATTAGTCAGGGACATACATAAAACAGAGCAGGCAAGA|ACTGTC|ATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCTcGGAG GGCATTAGTCAGGGACATACATAAAACAGAGCAGGCAAGA|ACTGTC|ATTTATAATGACAGTTCTTTGGGTTGCTGGAGCCTTGGAG ========== Event 3601 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTTGAATAGGAAATAGATCATATTGGCCAATCT-------------------ATTGGCCCAATAGTGACTAAGGA Chimp: CTTTGAATAGGAAATAGATCATATTGGCCAATCT-------------------ATTGGCCCAATAGTGACTAAGGA ↓ 3 42 1 Gorilla: CTTTGAATAGGAAATAGATCATATTGGCCAATCTATATTGGCCAATATGATCTATCGGCCCAATAGTGACTAAGGA ↑ 3 42 1 Human: CTTTGAATAGGAAATAGATCATATTGGCCAATCT-------------------ATTGGCCCAATAGTGACTAAGGA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr8:66803435-66803447 Template switch process: F1: L TTTGTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTAT 1 F3: 4 ATCTATCGGCCCAATAGTGACTAAGGAAGCCACATCCCTCGTTGCTT R RF: TTTGTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTATTGGCCCAATAGTGACTAAGGAAGCCACATCCCTCGTTGCTT RR: AAACACGGAAACTTATCCTTTATCTAGTATAACCGGTTAGATAACCGGGTTATCACTGATTCCTTCGGTGTAGGGAGCAACGAA F2: 3 GTATAACCGGTTA 2 Unidirectional alignment (log-probability: -43.8) GTGCCTTTGAATAGGAAATAGATCATATTGGCCAATctatattggccaatatgatCTATcGGCCCAATAGTGACTAAGGAAGCCACATCCCTC GTGCCTTTGAATAGGAAATAGATCATATTGGCCAAT-------------------CTATTGGCCCAATAGTGACTAAGGAAGCCACATCCCTC Template switch alignment (log-probability: -23.1) GTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTAT|ATTGGCCAATATG|ATCTATcGGCCCAATAGTGACTAAGGAAGCCACATCCCTC GTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTAT|ATTGGCCAATATG|ATCTATTGGCCCAATAGTGACTAAGGAAGCCACATCCCTC Chimp > Gorilla --------------- chr8:66803435-66803447 Template switch process: F1: L TTTGTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTAT 1 F3: 4 ATCTATCGGCCCAATAGTGACTAAGGAAGCCACATCCCTCGTTGCTT R RF: TTTGTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTATTGGCCCAATAGTGACTAAGGAAGCCACATCCCTCGTTGCTT RR: AAACACGGAAACTTATCCTTTATCTAGTATAACCGGTTAGATAACCGGGTTATCACTGATTCCTTCGGTGTAGGGAGCAACGAA F2: 3 GTATAACCGGTTA 2 Unidirectional alignment (log-probability: -43.8) GTGCCTTTGAATAGGAAATAGATCATATTGGCCAATctatattggccaatatgatCTATcGGCCCAATAGTGACTAAGGAAGCCACATCCCTC GTGCCTTTGAATAGGAAATAGATCATATTGGCCAAT-------------------CTATTGGCCCAATAGTGACTAAGGAAGCCACATCCCTC Template switch alignment (log-probability: -23.1) GTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTAT|ATTGGCCAATATG|ATCTATcGGCCCAATAGTGACTAAGGAAGCCACATCCCTC GTGCCTTTGAATAGGAAATAGATCATATTGGCCAATCTAT|ATTGGCCAATATG|ATCTATTGGCCCAATAGTGACTAAGGAAGCCACATCCCTC ========== Event 3602 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGACTTGGTTTTTTATGAGTTCA-------------------------------CACTCAG--AATCTAGAAGAATGGTATAGTT Chimp: AGACTTGGTTTTTTATGAGTTCA-------------------------------CACTCAG--AATCTAGAAGAATGGTATAGTT ↑ 1 3 2 4 Gorilla: AGACTTGGTTTTTTATGAGTTTATGACTATGGTTTTATGAGTGTGAACTCATAAAACTCATACCATCTAGAAGAATGGTATAGTT ↓ 1 3 2 4 Human: AGACTTGGTTTTTTATGAGTTCA-------------------------------CACTCAG--AATCTAGAAGAATGGTATAGTT Cluster: [ ] Orangutan: AGACTTGGTTTTTTATGAGTTCA-------------------------------CACTCAG--AATCTAGAAGAATGGTATAGTT Gorilla > Human --------------- chr8:39231695-39231704 Template switch process: F1: L AATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT 1 F3: 4 ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA R RF: AATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTTTATGACTATGGTTTTATGAGTGTGAACTCATAAAACTCATACCATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA RR: TTAAAAGAACTAAAACAATATCTGAACCAAAAAATACTCAAATACTGATACCAAAATACTCACACTTGAGTATTTTGAGTATGGTAGATCTTCTTACCATATCAAAAGAACCAAATATAGAGAT F2: 3 AGACTCACAC 2 Unidirectional alignment (log-probability: -35.7) ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT------------------------------------------CacactcagaATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTTTATGACTATGGTTTTATGAGTGTGAACTCATAAAACTCATACC---------ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA Template switch alignment (log-probability: -22.5) ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT|CACACTCAgA|ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT|CACACTCATA|ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA Gorilla > Chimp --------------- chr8:39011718-39011727 Template switch process: F1: L AATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT 1 F3: 4 ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA R RF: AATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTTTATGACTATGGTTTTATGAGTGTGAACTCATAAAACTCATACCATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA RR: TTAAAAGAACTAAAACAATATCTGAACCAAAAAATACTCAAATACTGATACCAAAATACTCACACTTGAGTATTTTGAGTATGGTAGATCTTCTTACCATATCAAAAGAACCAAATATAGAGAT F2: 3 AGACTCACAC 2 Unidirectional alignment (log-probability: -35.7) ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT------------------------------------------CacactcagaATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTTTATGACTATGGTTTTATGAGTGTGAACTCATAAAACTCATACC---------ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA Template switch alignment (log-probability: -22.5) ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT|CACACTCAgA|ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA ATTTTCTTGATTTTGTTATAGACTTGGTTTTTTATGAGTT|CACACTCATA|ATCTAGAAGAATGGTATAGTTTTCTTGGTTTATATCTCTA ========== Event 3603 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: AGGCACACAATCAAGGCAATTGAACTAAGATTAAAATCTTAGTTCATTACTTGGCTCATTAGGGA Chimp: aggcacacaatcaaggcaatt------------taatcttagttcattacttggctcattaggga Gorilla: AGGCACACAATCAAGGCAATT------------TAATCTTAGTTCATTACTTGGCTCATTAGGGA ↓ 3 4 2 Human: AGGCACACAATCAAGGCAATTGAACTAAGATTAAAATCTTAGTTCATTACTTGGCTCATTAGGGA Cluster: [ ] Orangutan: aggcacacgatcaaggcaatt------------taaccttagttcattacttggctcattaggga Gorilla > Human --------------- chr8:105498969-105498981 Template switch process: F1: L TAAATTTAGGAAGAACAAAAAGGCACACAATCAAGGCAATT 1 F3: 4 AATCTTAGTTCATTACTTGGCTCATTAGGGAATAAGACAC R RF: TAAACTTAGGAAGAACAAAAAGGCACACAATCAAGGCAATTTAATCTTAGTTCATTACTTGGCTCATTAGGGAATAAGACAC RR: ATTTGAATCCTTCTTGTTTTTCCGTGTGTTAGTTCCGTTAAATTAGAATCAAGTAATGAACCGAGTAATCCCTTATTCTGTG F2: 3 AATTAGAATCAAG 2 Unidirectional alignment (log-probability: -39.2) AAAtTTAGGAAGAACAAAAAGGCACACAATCAAGGCAATTgaactaagattaaAATCTTAGTTCATTACTTGGCTCATTAGGGAATAAGACAC AAACTTAGGAAGAACAAAAAGGCACACAATCAAGGCAATT------------TAATCTTAGTTCATTACTTGGCTCATTAGGGAATAAGACAC Template switch alignment (log-probability: -22.9) AAAtTTAGGAAGAACAAAAAGGCACACAATCAAGGCAATT|GAACTAAGATTAA|AATCTTAGTTCATTACTTGGCTCATTAGGGAATAAGACAC AAACTTAGGAAGAACAAAAAGGCACACAATCAAGGCAATT|GAACTAAGATTAA|AATCTTAGTTCATTACTTGGCTCATTAGGGAATAAGACAC ========== Event 3604 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTTTGGGGGCCTGTTAACAA--------GTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAG ↓ 1 4 3 2 Chimp: TGTTTGGGGGCCTGTTAACAACTTCTGCATTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAG ↑ 1 4 3 2 Gorilla: TGTTTGGGGGCCTGTTAACAA--------GTTGCTGAAATGCAGAAGCCTTTGGATTTGTTGAGCAG Human: TGTTTGGGGGCCTGTTAACAA--------GTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAG Cluster: [ ] Orangutan: TGTCTGGGGGCCTGTTAACAA--------GTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAG Human > Chimp ------------- chr8:40421661-40421669 Template switch process: F1: L TCTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAA 1 F3: 4 TTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA R RF: TCTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAAGTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA RR: AGATGTCTTAATTGATCTCAACAAACCCCCGGACAATTGTTCAACGACTTTACGTCTTCGAAAACCTAAACAACTCGTCAGT F2: 3 TACGTCTTC 2 Unidirectional alignment (log-probability: -28.4) CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAacttctgcAtTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACA--------AGTTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA Template switch alignment (log-probability: -16.4) CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAA|CTTCTGCAT|TTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAA|CTTCTGCAT|TTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA Gorilla > Chimp --------------- chr8:40421661-40421669 Template switch process: F1: L TCTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAA 1 F3: 4 TTGCTGAAATGCAGAAGCTTTTGGATTTGTTGAGCAGTCA R RF: TCTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAAGTTGCTGAAATGCAGAAGCCTTTGGATTTGTTGAGCAGTCA RR: AGATGTCTTAATTGATCTCAACAAACCCCCGGACAATTGTTCAACGACTTTACGTCTTCGGAAACCTAAACAACTCGTCAGT F2: 3 TACGTCTTC 2 Unidirectional alignment (log-probability: -33.4) CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAacttctgcAtTTGCTGAAATGCAGAAGCtTTTGGATTTGTTGAGCAGTCA CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACA--------AGTTGCTGAAATGCAGAAGCCTTTGGATTTGTTGAGCAGTCA Template switch alignment (log-probability: -22.4) CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAA|CTTCTGCAT|TTGCTGAAATGCAGAAGCtTTTGGATTTGTTGAGCAGTCA CTACAGAATTAACTAGAGTTGTTTGGGGGCCTGTTAACAA|CTTCTGCAT|TTGCTGAAATGCAGAAGCCTTTGGATTTGTTGAGCAGTCA ========== Event 3605 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: attttttggttacaGGGTCCTGATGATGCCCAAAGCCTAGCACTTTGCAGACCCCTTGCTCTGCCTCAGCTGTAGCCAGAACCCCCAAAGTAGAAGGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGATGTTGTGGATCTCAGGAATGAGGAGGAT Chimp: attttttggttacaCGGTCCTGAGGATGCCCAAAGCCTAGCACTTTGCAGACCCCTTGCTCTGCCTCAGCTGTAGCCAGAACCCCCAAAGTAGAAGGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGATGTTGTGGATCTCAGGAATGAGGAGGAT ↓ 3 2 1 4 Gorilla: attttttggttacaGGGTTCTGATGATGCTCAAAGCCTAGCACTTTGCAGACCCCTTGCTCTGCCTCAGCTGTAGCCAGAACCCCCAAAGTAGAAGGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGATCT-CAGGATCTCAGGAATGAGGAGGAT Human: attttttggttacaGGGTCCTGATGATGCCCAAAGCCTAGCACTTTGCAGACCCCTTGCTCTGCCTCAGCTGTAGCCAGAACCCCCAAAGTAGAAGGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGATGTTGTGGATCTCAGGAATGAGGAGGAT Cluster: [ ] Orangutan: attttttggttacaGGGTCCTGATGATGCTCAAAGCCTAGCACTTTGCAGACCCCTTGCTCTGCCTCAGCTGTAGCCAGAACCCCCAAAGTAGAAGGGAATGGAGTCACACAAATAATGGAGGTCAGGTTGTGATGTTGTGGATCTCAGGAATGAGGAGGAT Chimp > Gorilla --------------- chr8:75784341-75784345 Template switch process: F1: L AGGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGAT 1 F3: 4 GATCTCAGGAATGAGGAGGATGTGTGTGTATTAGGAGTT R RF: CTGAGGATGCCCAAAGCCTAGCACTTTGCAGACCCCTTGCTCTGCCTCAGCTGTAGCCAGAACCCCCAAAGTAGAAGGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGATGTTGTGGATCTCAGGAATGAGGAGGATGTGTGTGTATTAGGAGTT RR: GACTCCTACGGGTTTCGGATCGTGAAACGTCTGGGGAACGAGACGGAGTCGACATCGGTCTTGGGGGTTTCATCTTCCCTTACCTCAGTGGGTTTATTACCTCCAGTCCAACACTACAACACCTAGAGTCCTTACTCCTCCTACACACACATAATCCTCAA F2: 3 GACTC 2 Unidirectional alignment (log-probability: -26.6) GGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGA-----TctcaGGATCTCAGGAATGAGGAGGATGTGTGTGTATTAGGAGTT GGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGATGTTGT----GGATCTCAGGAATGAGGAGGATGTGTGTGTATTAGGAGTT Template switch alignment (log-probability: -16.3) GGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGAT|CTCAG|GATCTCAGGAATGAGGAGGATGTGTGTGTATTAGGAGTT GGGAATGGAGTCACCCAAATAATGGAGGTCAGGTTGTGAT|CTCAG|GATCTCAGGAATGAGGAGGATGTGTGTGTATTAGGAGTT ========== Event 3606 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ----AATACAAACTCTCATACTTCAGTAATAGTTGAACTATTACTGAAAGAAACTAATTTTTAGCTCA ↑ 1 4 3 2 Chimp: ----AATACAAACTCTCATACGC---AATTGGTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCA Gorilla: ----AATACAAACTCTCATACGC---AATTGGTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCA ↓ 1 4 3 2 Human: ----AATACAAACTCTCATACTTCAGTAATAGTTGAACTATTACTGAAAGAAACTAATTTTTAGCTCA Cluster: [ ] Orangutan: GATCCATACGAACTCTCATACAC---AATTGGTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCA Chimp > Human ------------- chr8:102485309-102485318 Template switch process: F1: L ACTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC 1 F3: 4 GTTGAACTATTACTGAAAGAAACTAATTTTTAGCTCAGCTTTCTTT R RF: ACTCATGGATCTTACATAAATGTAAATACAAACTCTCATACGCAATTGGTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCAGCTTTCTTT RR: TGAGTACCTAGAATGTATTTACATTTATGTTTGAGAGTATGCGTTAACCAACTCGATAATGACTTTCTTTGATTAAAAACCGAGTCGAAAGAAA F2: 3 ATAATGACTT 2 Unidirectional alignment (log-probability: -47.9) CTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC-------ttcagtaataGTTGAaCTATTACTGAAAGAAACTAATTTTTaGCTCAGCT CTCATGGATCTTACATAAATGTAAATACAAACTCTCATACGCAATTG----------GTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCAGCT Template switch alignment (log-probability: -28.6) CTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC|TTCAGTAATA|GTTGAaCTATTACTGAAAGAAACTAATTTTTaGCTCAGCT CTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC|TTCAGTAATA|GTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCAGCT Gorilla > Human --------------- chr8:102485309-102485318 Template switch process: F1: L ACTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC 1 F3: 4 GTTGAACTATTACTGAAAGAAACTAATTTTTAGCTCAGCTTTCTTT R RF: ACTCATGGATCTTACATAAATGTAAATACAAACTCTCATACGCAATTGGTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCAGCTTTCTTT RR: TGAGTACCTAGAATGTATTTACATTTATGTTTGAGAGTATGCGTTAACCAACTCGATAATGACTTTCTTTGATTAAAAACCGAGTCGAAAGAAA F2: 3 ATAATGACTT 2 Unidirectional alignment (log-probability: -46.5) CTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC-------ttcagtaataGTTGAaCTATTACTGAAAGAAACTAATTTTTaGCTCAGCT CTCATGGATCTTACATAAATGTAAATACAAACTCTCATACGCAATTG----------GTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCAGCT Template switch alignment (log-probability: -28.2) CTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC|TTCAGTAATA|GTTGAaCTATTACTGAAAGAAACTAATTTTTaGCTCAGCT CTCATGGATCTTACATAAATGTAAATACAAACTCTCATAC|TTCAGTAATA|GTTGAGCTATTACTGAAAGAAACTAATTTTTGGCTCAGCT ========== Event 3607 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGACCATGGGAGTCTACAAATTACTTTCTCGTTGGGAGCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCT------------------------GATTGTTTTAGACCAACAATTTTC Chimp: TGGACCATGGGAGTCTACAGATTACTTTCTCGTTGGGAGCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCT------------------------GATTGTTTTAGACCAACAATTTTC ↓ 4 3 2 1 Gorilla: TGGACCATGGGAGTCTATAAATTACTTTCTCGTTGGGAGCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATTAGACATCTGATTAGATGTCTGATTGTTTTAGACCAACAATTTTC ↑ 43 2 1 Human: TGGACCATGGGAGTCTACAAATTACTTTCTCGTTGGGAGCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCT------------------------GATTGTTTTAGACCAACAATTTTC Cluster: [ ] Orangutan: TGGACCATGGAAGTCTATAAATTACTTTCTCTTTGGGAGCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGCTGTCTGATTAGACATCTGATTAGATGTCTAATTGTTTTAGACCAACAATTTTC Human > Gorilla --------------- chr8:67744714-67744721 Template switch process: F1: L GCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATT 1 F3: 4 GATTAGATGTCTGATTGTTTTAGACCAACAATTTTCAAATCAATTGGTGCAG R RF: GCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATTGTTTTAGACCAACAATTTTCAAATCAATTGGTGCAG RR: CGTGTAGTTAGATCACTTCCTTTCTCACAGGGTTCTACAGACTAACAAAATCTGGTTGTTAAAAGTTTAGTTAACCACGTC F2: 3 TCTACAGA 2 Unidirectional alignment (log-probability: -45.4) TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTctgattagacatctgattagatgtCTGATTGTTTTAGACCAACAATTTTCAAAT TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGT------------------------CTGATTGTTTTAGACCAACAATTTTCAAAT Template switch alignment (log-probability: -32.6) TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATT|AGACATCT|gattAGATGTCTGATTGTTTTAGACCAACAATTTTCAAAT TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATT|AGACATCT|A---AGATGTCTGATTGTTTTAGACCAACAATTTTCAAAT Chimp > Gorilla --------------- chr8:67744714-67744721 Template switch process: F1: L GCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATT 1 F3: 4 GATT------------------------------------------------AGATGTCTGATTGTTTTAGACCAACAATTTTCAAATCAATTGGTGCAG R RF: GCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATTGTTTTAGACCAACAATTTTCAAATCAATTGGTGCAG RR: CGTGTAGTTAGATCACTTCCTTTCTCACAGGGTTCTACAGACTAACAAAATCTGGTTGTTAAAAGTTTAGTTAACCACGTC F2: 3 TCTACAGA 2 Unidirectional alignment (log-probability: -45.4) TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTctgattagacatctgattagatgtCTGATTGTTTTAGACCAACAATTTTCAAAT TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGT------------------------CTGATTGTTTTAGACCAACAATTTTCAAAT Template switch alignment (log-probability: -29.3) TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATT|AGACATCT|GATT------------------------------------------------AGATGTCTGATTGTTTTAGACCAACAATTTTCAAAT TCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATT|AGACATCT|GATTACTTTCTCGTTGGGAGCACATCAATCTAGTGAAGGAAAGAGTGTCCCAAGATGTCTGATTGTTTTAGACCAACAATTTTCAAAT ========== Event 3608 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TAATGTCTCCATACAACGCAGTTGATAAC------TGCAGCAGAGACTGATAGGAGA ↑ 3 1 2 4 Chimp: TAATGTCTCCATACAACGCAGTTATCAAC---TCAAGCAGCAGAGACTGATAGGAGA Gorilla: TAATGTCTCCATACAACGCAGTTATCAACTCA---AGCAGCAGAGACTGATAGGAGA ↓ 3 1 2 4 Human: TAATGTCTCCATACAACGCAGTTGATAAC------TGCAGCAGAGACTGATAGGAGA Cluster: [ ] Orangutan: TAATGTCTCCGTACAATGCAGTTATCAACTCA---AGCAGCAGAGACTGATAGGAGA Chimp > Human ------------- chr8:48509444-48509450 Template switch process: F1: L TAAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTT 1 F3: 4 GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA R RF: TAAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTTATCAACTCAAGCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA RR: ATTTGCGAAAAGGGATGTATTACAGAGGTATGTTGCGTCAATAGTTGAGTTCGTCGTCTCTGACTATCCTCTACATCGTTTTCTTTCGTTT F2: 3 TCAATAG 2 Unidirectional alignment (log-probability: -29.1) AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTTgatAACT---GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTTATCAACTCAAGCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA Template switch alignment (log-probability: -16.2) AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTT|GATAACT|GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTT|GATAACT|GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA Gorilla > Human --------------- chr8:48509444-48509450 Template switch process: F1: L TAAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTT 1 F3: 4 GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA R RF: TAAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTTATCAACTCAAGCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA RR: ATTTGCGAAAAGGGATGTATTACAGAGGTATGTTGCGTCAATAGTTGAGTTCGTCGTCTCTGACTATCCTCTACATCGTTTTCTTTCGTTT F2: 3 TCAATAG 2 Unidirectional alignment (log-probability: -27.7) AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTTgatAACT---GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTTATCAACTCAAGCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA Template switch alignment (log-probability: -16.6) AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTT|GATAACT|GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA AAACGCTTTTCCCTACATAATGTCTCCATACAACGCAGTT|GATAACT|GCAGCAGAGACTGATAGGAGATGTAGCAAAAGAAAGCAAA ========== Event 3609 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GCACCTATGAAGAACCTAAGCACA---CTCCAAGATGGGCACACATGTCA ↓ 3 1 24 Chimp: GCACCTATGAAGAACCTAAGCAAGTGTGCCCAAGATGGGCACACATATCA ↑ 3 1 24 Gorilla: GCACCTATGAAGAACCTAAGCACA---CTCCAAGATGGGCACACATGTCA Human: GCACCTATGAAGAACCTAAGCACA---CTCCAAGATGGGCACACATGTCA Cluster: [ ] Orangutan: GCACCTATGAAGAACCTAAGCACA---CTCCAAGATGGGCACACATGTCA Human > Chimp ------------- chr8:49580560-49580566 Template switch process: F1: L ACTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA 1 F3: 4 CCAAGATGGGCACACATATCACTGTCCTGACACACCTACC R RF: ACTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCACACTCCAAGATGGGCACACATGTCACTGTCCTGACACACCTACC RR: TGAATTAGTAATGTGTACTCGTGGATACTTCTTGGATTCGTGTGAGGTTCTACCCGTGTGTACAGTGACAGGACTGTGTGGATGG F2: 3 CGTGTGA 2 Unidirectional alignment (log-probability: -35.9) CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCAagtgtgC---CCAAGATGGGCACACATaTCACTGTCCTGACACACCTACC CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA------CACTCCAAGATGGGCACACATGTCACTGTCCTGACACACCTACC Template switch alignment (log-probability: -22.1) CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA|AGTGTGC|CCAAGATGGGCACACATaTCACTGTCCTGACACACCTACC CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA|AGTGTGC|CCAAGATGGGCACACATGTCACTGTCCTGACACACCTACC Gorilla > Chimp --------------- chr8:49580560-49580566 Template switch process: F1: L ACTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA 1 F3: 4 CCAAGATGGGCACACATATCACTGTCCTGACACACCTACC R RF: ACTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCACACTCCAAGATGGGCACACATGTCACTGTCCTGACACACCTACC RR: TGAATTAGTAATGTGTACTCGTGGATACTTCTTGGATTCGTGTGAGGTTCTACCCGTGTGTACAGTGACAGGACTGTGTGGATGG F2: 3 CGTGTGA 2 Unidirectional alignment (log-probability: -34.9) CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCAagtgtgC---CCAAGATGGGCACACATaTCACTGTCCTGACACACCTACC CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA------CACTCCAAGATGGGCACACATGTCACTGTCCTGACACACCTACC Template switch alignment (log-probability: -22.1) CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA|AGTGTGC|CCAAGATGGGCACACATaTCACTGTCCTGACACACCTACC CTTAATCATTACACATGAGCACCTATGAAGAACCTAAGCA|AGTGTGC|CCAAGATGGGCACACATGTCACTGTCCTGACACACCTACC ========== Event 3610 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 256 Detected in comparisons: 1256 Multiple sequence alignment: Human: tgataagtacattaataattttatgtagtattaaaAAATGCAACTGATGCTCCAAAAAAAGTTATATGGCTATTATGATCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATTACAGAAATGCATCT----TTCTTACACT ↓ 3 2 1 4 Chimp: tgataagtacattaataattttatgtagtattaaaAAATGCAACTGATGCTCCAAAACAAGTTATATGGCTATTATGATCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATC--CATGATGCATCT----TTCTTACACT ↓ 3 2 1 4 ↑ 3 2 1 4 Gorilla: TGATAAGTACATTAATAATTTTATGTAGTATTAAAAAATGCAACTGATGCTCCaaaaaaaGTTATATGGCTATTATGATCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATTACAGAAATGCATCT----TTCTTACACT Human: tgataagtacattaataattttatgtagtattaaaAAATGCAACTGATGCTCCAAAAAAAGTTATATGGCTATTATGATCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATTACAGAAATGCATCT----TTCTTACACT Cluster: [ ] Orangutan: tgataagtacattaataattttatgtagtattaaaAAATGCAACTGATGCTCCAAAAAAAGTTATATGGTTATTATGATCCAATAGAAATTCATATATCTTTTATTATCATGGAGTCATTACAGAAATGCATCTTTCTTTCTTACACT Human > Chimp ------------- chr8:97506639-97506643 Template switch process: F1: L TCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT 1 F3: 4 ATGCATCTTTCTTACACTCACATTATATATATA R RF: TCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATTACAGAAATGCATCTTTCTTACACTCACATTATATATATA RR: AGGTTATCTTTAAGTATGTAGAAAATAATAGTACCTCAGTAATGTCTTTACGTAGAAAGAATGTGAGTGTAATATATATAT F2: 3 GTACC 2 Unidirectional alignment (log-probability: -36.2) CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATccatg-------ATGCATCTTTCTTACACTCACATTATATATATA------- CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT-----TACAGAAATGCATCTTTCTTACACTCACATTATATATATATTAATAT Template switch alignment (log-probability: -15.8) CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT|CCATG|ATGCATCTTTCTTACACTCACATTATATATATA CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT|CCATG|ATGCATCTTTCTTACACTCACATTATATATATA Gorilla > Chimp --------------- chr8:97506639-97506643 Template switch process: F1: L TCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT 1 F3: 4 ATGCATCTTTCTTACACTCACATTATATATATA R RF: TCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATTACAGAAATGCATCTTTCTTACACTCACATTATATATATA RR: AGGTTATCTTTAAGTATGTAGAAAATAATAGTACCTCAGTAATGTCTTTACGTAGAAAGAATGTGAGTGTAATATATATAT F2: 3 GTACC 2 Unidirectional alignment (log-probability: -35.2) CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT-------ccatgATGCATCTTTCTTACACTCACATTATATATATA------- CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATTACAGAA-----ATGCATCTTTCTTACACTCACATTATATATATATAAATAT Template switch alignment (log-probability: -16.2) CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT|CCATG|ATGCATCTTTCTTACACTCACATTATATATATA CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT|CCATG|ATGCATCTTTCTTACACTCACATTATATATATA Chimp > Gorilla --------------- chr8:66355910-66355917 Template switch process: F1: L TCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT 1 F3: 4 TGCATCTTTCTTACACTCACATTATATATATATAAATAT R RF: TTTATGTAGTATTAAAAAATGCAACTGATGCTCCAAAACAAGTTATATGGCTATTATGATCCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATCCATGATGCATCTTTCTTACACTCACATTATATATATATATATAT RR: AAATACATCATAATTTTTTACGTTGACTACGAGGTTTTGTTCAATATACCGATAATACTAGGTTATCTTTAAGTATGTAGAAAATAATAGTACCTCAGTAGGTACTACGTAGAAAGAATGTGAGTGTAATATATATATATATATA F2: 3 AAAGACAT 2 Unidirectional alignment (log-probability: -47.7) CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT-----tacagaaATGCATCTTTCTTACACTCACATTATATATATAtaaatat CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCATCCATG-------ATGCATCTTTCTTACACTCACATTATATATATA------- Template switch alignment (log-probability: -27.8) CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT|TACAgAAA|TGCATCTTTCTTACACTCACATTATATATATATAaATAT CCAATAGAAATTCATACATCTTTTATTATCATGGAGTCAT|TACATAAA|TGCATCTTTCTTACACTCACATTATATATATATATATAT ========== Event 3611 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAATCTATTACAGTTTTAAGCTTTTGTCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGTAAGGAG---ATAACAGACACATACTTACTGA Chimp: ACAATCTATTACAGTTTTAAGCTTTTGTCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGTAAGGAA---ATAACAGACACATACTTACTGA ↓ 3 2 1 4 Gorilla: ACAATCTATTACAGTTTTAAGCTTTTGTCT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAACAAAAGCTTAACAGACACATACTTACTGA ↑ 3 2 1 4 Human: ACAATCTATTACAGTTTTAAGCTTTTGTCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGTAAGGAG---ATAACAGACACATACTTACTGA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNN---NNNNNNNNNNNNNNNNNNNNNN Human > Gorilla --------------- chr8:66545589-66545597 Template switch process: F1: L ACAATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTA 1 F3: 4 TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT R RF: ACAATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTCTGTAAGGAGATAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT RR: TGTTACACTTTTGTTAGATAATGTCAAAATTCGAAAACAGAAGACATTCCTCTATTGTCTGTGTATGAATGACTTAAAAGAATTAAAAACCGA F2: 3 TCGAAAACA 2 Unidirectional alignment (log-probability: -32.6) ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTaacaaaagCT---------TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTT--------CTGTAAGGAGATAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT Template switch alignment (log-probability: -22.4) ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTa|ACAAAAGCT|TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTC|ACAAAAGCT|TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT Chimp > Gorilla --------------- chr8:66545589-66545597 Template switch process: F1: L ACAATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTA 1 F3: 4 TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT R RF: ACAATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTCTGTAAGGAAATAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT RR: TGTTACACTTTTGTTAGATAATGTCAAAATTCGAAAACAGAAGACATTCCTTTATTGTCTGTGTATGAATGACTTAAAAGAATTAAAAACCGA F2: 3 TCGAAAACA 2 Unidirectional alignment (log-probability: -32.6) ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTT---------AAcaaaagctTAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTCTGTAAGGAAA--------TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT Template switch alignment (log-probability: -22.4) ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTa|ACAAAAGCT|TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT ATGTGAAAACAATCTATTACAGTTTTAAGCTTTTGTCTTC|ACAAAAGCT|TAACAGACACATACTTACTGAATTTTCTTAATTTTTGGCT ========== Event 3612 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCATTAAACACTATTGAAAATGCAGTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACACCTTTAGTTGCACTGATGGTTTTGTAAGACTA ↑ 1 4 3 2 Chimp: TCCATTAAACACTATTGAAAAATTTGTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACACCTTTAGTTGCACTGATGGTTTTGTAAGATTA Gorilla: TACATTAAACACTATTGAAAAATTTGTTTTGGATACAGTCTGCAGAACCTGGAAAGTCTAACACACCTTTAGTTGCACTGATGATTTTGTAAGACTA Human: TCCATTAAACACTATTGAAAATGCAGTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACACCTTTAGTTGCACTGATGGTTTTGTAAGACTA Cluster: [ ] Orangutan: TCCATTAAACACTATTGAAAAATTTGTTTTAGATACAGTCTGTAGAACCTGGGAAGTCTAATACACCTTTAGTTGCACTGATGGTTTGGTAAGATTA Chimp > Human ------------- chr8:5017364-5017367 Template switch process: F1: L CTTGGGCATGTTATTGAGCTTCCATTAAACACTATTGAAAA 1 F3: 4 GTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACA R RF: CTTGGGCACGTTATTGAGCTTCCATTAAACACTATTGAAAAATTTGTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACACCTTTAGTTGCA RR: GAACCCGTGCAATAACTCGAAGGTAATTTGTGATAACTTTTTAAACAAAACCTATGTCAGACATCTTGGACCTTTCAGATTATGTGGAAATCAACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -30.7) TTGGGCAtGTTATTGAGCTTCCATTAAACACTATTGAAAAtgcaGTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACA TTGGGCACGTTATTGAGCTTCCATTAAACACTATTGAAAAATTTGTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACA Template switch alignment (log-probability: -21.8) TTGGGCAtGTTATTGAGCTTCCATTAAACACTATTGAAAA|TGCA|GTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACA TTGGGCACGTTATTGAGCTTCCATTAAACACTATTGAAAA|TGCA|GTTTTGGATACAGTCTGTAGAACCTGGAAAGTCTAATACA ========== Event 3613 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCTGGCTGTTATGAAATCTATGCAGCTAACCACTAACAACATTTATCATATCCTGTTATAT ↓ 3 2 1 4 Chimp: CCTGGCTGTTATGAAATCTATGCAGCTAACCACT--GCATATTTATCATATCCTGTTATAT ↑ 3 2 1 4 Gorilla: CCTGGCTGTTATGAAATCTATGCAGCTAACCACTAACAACATTTATCATATCCTGTTATAT Human: CCTGGCTGTTATGAAATCTATGCAGCTAACCACTAACAACATTTATCATATCCTGTTATAT Cluster: [ ] Orangutan: CCTGGCTGTTATGAAATCTATGCAGCTAACCACTAACAACATTTATCATATCCTGTTATAT Human > Chimp ------------- chr8:5540111-5540114 Template switch process: F1: L GTTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACT 1 F3: 4 ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC R RF: GTTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACTAACAACATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC RR: CAAAGACGGACCGACAATACTTTAGATACGTCGATTGGTGATTGTTGTAAATAGTATAGGACAATATATCTTTTCACTCTTCTTTTG F2: 3 TACG 2 Unidirectional alignment (log-probability: -27.2) TTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACtgcaT------ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC TTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCAC----TAACAACATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC Template switch alignment (log-probability: -15.8) TTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACT|GCAT|ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC TTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACT|GCAT|ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC Gorilla > Chimp --------------- chr8:5540111-5540114 Template switch process: F1: L GTTTCTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACT 1 F3: 4 ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC R RF: CTTTGTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACTAACAACATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC RR: GAAACACGGACCGACAATACTTTAGATACGTCGATTGGTGATTGTTGTAAATAGTATAGGACAATATATCTTTTCACTCTTCTTTTG F2: 3 TACG 2 Unidirectional alignment (log-probability: -37.7) TTTcTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACtgcaT------ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC TTTGTGCCTGGCTGTTATGAAATCTATGCAGCTAACCAC----TAACAACATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC Template switch alignment (log-probability: -27.3) TTTcTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACT|GCAT|ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC TTTGTGCCTGGCTGTTATGAAATCTATGCAGCTAACCACT|GCAT|ATTTATCATATCCTGTTATATAGAAAAGTGAGAAGAAAAC ========== Event 3614 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AACATTAATTGAATGACTTCCATAGGTGTGAAAAACATCAAACTAAACGAGTTGAACTTCT Chimp: AACATTAATTGAATGACTTCCATAGCTGTGAAAAACATCAAACTAAACGAGTTGAACTTCT ↓ 3 2 1 4 Gorilla: AACATTAATTGAATGACTTCCATAGGTGTGAA-ACTATGGAACTAAACGAGTTGAACTTCT ↑ 3 2 1 4 Human: AACATTAATTGAATGACTTCCATAGGTGTGAAAAACATCAAACTAAACGAGTTGAACTTCT Cluster: [ ] Orangutan: AA---CAATTGAATGACTTCCACAGGTGTAAA-AAAATCAAACTACATGAGTTGAACTTCT Human > Gorilla --------------- chr8:65070461-65070466 Template switch process: F1: L GTAATCAATAACATTAATTGAATGACTTCCATAGGTGTGAAA 1 F3: 4 AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA R RF: GTAATCAATAACATTAATTGAATGACTTCCATAGGTGTGAAAAACATCAAACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA RR: CATTAGTTATTGTAATTAACTTACTGAAGGTATCCACACTTTTTGTAGTTTGATTTGCTCAACTTGAAGAAAATTTGATTTTAAACGGT F2: 3 GGTATC 2 Unidirectional alignment (log-probability: -29.6) AATCAATAACATTAATTGAATGACTTCCATAGGTGTGAA-------ActatggAACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA AATCAATAACATTAATTGAATGACTTCCATAGGTGTGAAAAACATCA------AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA Template switch alignment (log-probability: -16.5) AATCAATAACATTAATTGAATGACTTCCATAGGTGTGAAA|CTATGG|AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA AATCAATAACATTAATTGAATGACTTCCATAGGTGTGAAA|CTATGG|AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA Chimp > Gorilla --------------- chr8:65070461-65070466 Template switch process: F1: L AAATTCTGTAATCAATAACATTAATTGAATGACTTCCATAGGTGTGAAA 1 F3: 4 AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA R RF: AAATTCTGTAATCAATAACATTAATTGAATGACTTCCATAGCTGTGAAAAACATCAAACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA RR: TTTAAGACATTAGTTATTGTAATTAACTTACTGAAGGTATCGACACTTTTTGTAGTTTGATTTGCTCAACTTGAAGAAAATTTGATTTTAAACGGT F2: 3 GGTATC 2 Unidirectional alignment (log-probability: -35.2) AATCAATAACATTAATTGAATGACTTCCATAGgTGTGAA-------ActatggAACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA AATCAATAACATTAATTGAATGACTTCCATAGCTGTGAAAAACATCA------AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA Template switch alignment (log-probability: -22.2) AATCAATAACATTAATTGAATGACTTCCATAGgTGTGAAA|CTATGG|AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA AATCAATAACATTAATTGAATGACTTCCATAGCTGTGAAA|CTATGG|AACTAAACGAGTTGAACTTCTTTTAAACTAAAATTTGCCA ========== Event 3615 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACACTGTTAATAAAGGTAATTTTA--------CACTGTTTGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAATA--ATTCTTTATG-ATTTTAAAGGTCTTTAGTTTTATGAATTTATTATAACCAAGTTGAAAGTAATTTTTAAACAGTTTATTGAAAATACAGTAACC ↑ 1 4 3 2 Chimp: ACACTGTTAATAAAGGTAATTCTA----CTCACA----CTGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAATA--ATTCTTTATG-ATTTTAAAGGTCTTTAGTTTTATGAATTTATTATAACCAAGTTGAAAGTAATTTTTAAACAGTTTATTGAAAATACAGTAACC Gorilla: ACACTGTTAATAAAGGTAATTTTACTCA----CACTGTTTGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAATA--ATTCTTTATG-ATTTTAAAGGTCTTTAGTTTTATGAATTTATTATAACCAAGTTGAAAGTAATTTTTAAACAGTTTATTGAAAATACAGTAACC Human: ACACTGTTAATAAAGGTAATTTTA--------CACTGTTTGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAATA--ATTCTTTATG-ATTTTAAAGGTCTTTAGTTTTATGAATTTATTATAACCAAGTTGAAAGTAATTTTTAAACAGTTTATTGAAAATACAGTAACC Cluster: [ ] Orangutan: ACACTGTTAATAAAGGTAATTTTACTCA----CGCTGTTTGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAATAAATTTCTTTACGAATTTTAAAGGTCTTTAGTTTTATGAATTTATTATAACCAAGTTGAAAGTAATTTTTAAACAGTTTATTGAAAATACAGTAACC Chimp > Human ------------- chr8:93264014-93264019 Template switch process: F1: L TATGAAGTGTATTTTGAAATACACTGTTAATAAAGGTAATTTTAC 1 F3: 4 TGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAAT R RF: TATGAAGTGTATTTTGAAATACACTGTTAATAAAGGTAATTCTACTCACACTGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAATAATTCTTTATGATTTTAAAGGTCTTTAGTTTTATGAATTTATTATAACCAAGTTGAAAGTAATTTTTAAACAGT RR: ATACTTCACATAAAACTTTATGTGACAATTATTTCCATTAAGATGAGTGTGACCGACGATAAATGTCAAACTTCTGGTTAATTATACTTTATTAAGAAATACTAAAATTTCCAGAAATCAAAATACTTAAATAATATTGGTTCAACTTTCATTAAAAATTTGTCA F2: 3 TTGTCA 2 Unidirectional alignment (log-probability: -33.1) AGTGTATTTTGAAATACACTGTTAATAAAGGTAATTtT----ACACTgtttGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAAT AGTGTATTTTGAAATACACTGTTAATAAAGGTAATTCTACTCACACT----GGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAAT Template switch alignment (log-probability: -22.1) AGTGTATTTTGAAATACACTGTTAATAAAGGTAATTtTAC|ACTGTT|TGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAAT AGTGTATTTTGAAATACACTGTTAATAAAGGTAATTCTAC|ACTGTT|TGGCTGCTATTTACAGTTTGAAGACCAATTAATATGAAAT ========== Event 3616 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTAGATGTAAATATAGATGCTATCATATTTGTAAT-AT------TCTTGTCTAATGGGATGGGATTAGGATG ↓ 3 2 1 4 Chimp: CTGTAGATGTAAATATAGATGCTATCATATTTGTAAT-ATGATAGCAATTGTCAAATGGGATGGGATTAGGATG Gorilla: CTGTAGATGTAAATATAGATGCTATCATATTTGTAAT-AT------TCTTGTCAAATGGGATGGGATTAGGATG Human: CTGTAGATGTAAATATAGATGCTATCATATTTGTAAT-AT------TCTTGTCTAATGGGATGGGATTAGGATG Cluster: [ ] Orangutan: CTGTAGATGTAAATATAGATGCTGTCATATTTGTAATAAT------TCTTGTCAAATGGGATGGGATTAGGATG Human > Chimp ------------- chr8:95111117-95111123 Template switch process: F1: L GTCTGTAGATGTAAATATAGATGCTATCATATTTGTAATAT 1 F3: 4 ATTGTCAAATGGGATGGGATTAGGATGACAGTCTGGCAAATTGAGGC R RF: GTCTGTAGATGTAAATATAGATGCTATCATATTTGTAATATTCTTGTCTAATGGGATGGGATTAGGATGACAGTCTGGCAAATTGAGGC RR: CAGACATCTACATTTATATCTACGATAGTATAAACATTATAAGAACAGATTACCCTACCCTAATCCTACTGTCAGACCGTTTAACTCCG F2: 3 ACGATAG 2 Unidirectional alignment (log-probability: -37.6) TCTGTAGATGTAAATATAGATGCTATCATATTTGTAATATgatagcaaTTGTCaAATGGGATGGGATTAGGATGACAGTCTGGCAAA TCTGTAGATGTAAATATAGATGCTATCATATTTGTAATAT------TCTTGTCTAATGGGATGGGATTAGGATGACAGTCTGGCAAA Template switch alignment (log-probability: -28.3) TCTGTAGATGTAAATATAGATGCTATCATATTTGTAATAT|GATAGCA|aTTGTCaAATGGGATGGGATTAGGATGACAGTCTGGCAAA TCTGTAGATGTAAATATAGATGCTATCATATTTGTAATAT|GATAGCA|CTTGTCTAATGGGATGGGATTAGGATGACAGTCTGGCAAA ========== Event 3617 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCTTGTTATTCTGAGAAAAATCTTGTATTT------AGGTATCTTGATGTTATAGAGCA Chimp: ATCTTGTTATTCTGAGAAAAATCTTGTATTT------AGGTATCTTGATGTTATAGAGCA ↓ 3 1 2 4 Gorilla: ATCTTGTTATTCTGAGAAAAATCTTGTAAATACAAGATTGTATCTTGATGTTATAGAGCA ↑ 3 1 2 4 Human: ATCTTGTTATTCTGAGAAAAATCTTGTATTT------AGGTATCTTGATGTTATAGAGCA Cluster: [ ] Orangutan: ATCTTGTTATTCTGAGAAAAATCTTGTATTT------AGGTATCTTGATGTTATAGAGCA Human > Gorilla --------------- chr8:84933700-84933710 Template switch process: F1: L TTTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTA 1 F3: 4 GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT R RF: TTTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTATTTAGGTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT RR: AAATTTATTTTAATAGAACAATAAGACTCTTTTTAGAACATAAATCCATAGAACTACAATATCTCGTCGTCGTAGTGTCTACACTA F2: 3 TTAGAACATAA 2 Unidirectional alignment (log-probability: -33.8) TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTaaatacaagATT---GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGT---------ATTTAGGTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT Template switch alignment (log-probability: -17.1) TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTA|AATACAAGATT|GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTA|AATACAAGATT|GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT Chimp > Gorilla --------------- chr8:84933700-84933710 Template switch process: F1: L TTTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTA 1 F3: 4 GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT R RF: TTTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTATTTAGGTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT RR: AAATTTATTTTAATAGAACAATAAGACTCTTTTTAGAACATAAATCCATAGAACTACAATATCTCGTCGTCGTAGTGTCTACACTA F2: 3 TTAGAACATAA 2 Unidirectional alignment (log-probability: -33.8) TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTaaatacaagATT---GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGT---------ATTTAGGTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT Template switch alignment (log-probability: -17.1) TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTA|AATACAAGATT|GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT TTAAATAAAATTATCTTGTTATTCTGAGAAAAATCTTGTA|AATACAAGATT|GTATCTTGATGTTATAGAGCAGCAGCATCACAGATGTGAT ========== Event 3618 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ATTCTATCCTCCTTATATACCATGCGGAAAATGGGCGACAGTGCATT Chimp: ATTCTATCCTCCTTATATACCATGTGGAAAATGGGCGACAGTGCATT Gorilla: ATTCTATCCTCCTTATATACCGCATAGAAAATGGGCAACAGTGCATT ↓ 3 2 4 Human: ATTCTATCCTCCTTATATACCATGCGGAAAATGGGCGACAGTGCATT Cluster: [ ] Orangutan: ATTCTATCCTCCTGATATACCATGTGGAAGATGGGTGACGGTGCATT Gorilla > Human --------------- chr8:55550394-55550398 Template switch process: F1: L TCCATGTGCCCAGCAACATCATTCTATCCTCCTTATATACC 1 F3: 4 GAAAATGGGCGACAGTGCATTGCAGTGAACAGTGCTCCAA R RF: TCCATGTGCCCAGCAACATCATTCTATCCTCCTTATATACCGCATAGAAAATGGGCAACAGTGCATTGCAGTGAATAGTGCTCCAA RR: AGGTACACGGGTCGTTGTAGTAAGATAGGAGGAATATATGGCGTATCTTTTACCCGTTGTCACGTAACGTCACTTATCACGAGGTT F2: 3 GCGTA 2 Unidirectional alignment (log-probability: -37.6) CCATGTGCCCAGCAACATCATTCTATCCTCCTTATATACC----AtgcgGAAAATGGGCgACAGTGCATTGCAGTGAAcAGTGCTCCAA CCATGTGCCCAGCAACATCATTCTATCCTCCTTATATACCGCATA----GAAAATGGGCAACAGTGCATTGCAGTGAATAGTGCTCCAA Template switch alignment (log-probability: -27.4) CCATGTGCCCAGCAACATCATTCTATCCTCCTTATATACC|ATGCG|GAAAATGGGCgACAGTGCATTGCAGTGAAcAGTGCTCCAA CCATGTGCCCAGCAACATCATTCTATCCTCCTTATATACC|ATGCG|GAAAATGGGCAACAGTGCATTGCAGTGAATAGTGCTCCAA ========== Event 3619 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TATTAAGGCTTTTTGGCTGTGAGCTTAATGATAAGCTCACAATCTTCCCCAGGAAAAAGC ↑ 3 1 2 4 Chimp: TATTAAGGCTTTTTGGCTGTGAGCTT----ATCATATTGCAATCTTCCCCAGGAAAAAGC Gorilla: TATTAAAGCTTTTTGGCTGTGAGCTT----ATCATATTGCAATCTTCCCCAGGAAAAAGC ↓ 3 1 2 4 Human: TATTAAGGCTTTTTGGCTGTGAGCTTAATGATAAGCTCACAATCTTCCCCAGGAAAAAGC Cluster: [ ] Orangutan: CATTAAGGCTTTTTGGCTGTGAGCTT----ATCATATTGCAATCTTCTCCAGGAAAAAGC Chimp > Human ------------- chr8:56565768-56565779 Template switch process: F1: L CCATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTA 1 F3: 4 CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG R RF: CCATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTATCATATTGCAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG RR: GGTAAGGTAAACTACATAATTCCGAAAAACCGACACTCGAATAGTATAACGTTAGAAGGGGTCCTTTTTCGTTAAACTTTCACCAACACC F2: 3 ACTCGAATAGTA 2 Unidirectional alignment (log-probability: -34.4) ATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTAatgataagcTCA-----CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG ATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTA---------TCATATTGCAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG Template switch alignment (log-probability: -16.8) ATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTA|ATGATAAGCTCA|CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG ATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTA|ATGATAAGCTCA|CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG Gorilla > Human --------------- chr8:56565768-56565779 Template switch process: F1: L CCATTCCATTTGATGTATTAAGGCTTTTTGGCTGTGAGCTTA 1 F3: 4 CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG R RF: CCATGCCATTTGATGTATTAAAGCTTTTTGGCTGTGAGCTTATCATATTGCAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG RR: GGTACGGTAAACTACATAATTTCGAAAAACCGACACTCGAATAGTATAACGTTAGAAGGGGTCCTTTTTCGTTAAACTTTCACCAACACC F2: 3 ACTCGAATAGTA 2 Unidirectional alignment (log-probability: -44.9) ATtCCATTTGATGTATTAAgGCTTTTTGGCTGTGAGCTTAatgataagcTCA-----CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG ATGCCATTTGATGTATTAAAGCTTTTTGGCTGTGAGCTTA---------TCATATTGCAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG Template switch alignment (log-probability: -28.3) ATtCCATTTGATGTATTAAgGCTTTTTGGCTGTGAGCTTA|ATGATAAGCTCA|CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG ATGCCATTTGATGTATTAAAGCTTTTTGGCTGTGAGCTTA|ATGATAAGCTCA|CAATCTTCCCCAGGAAAAAGCAATTTGAAAGTGGTTGTGG ========== Event 3620 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TACTGTGTTTTTCTTAAAACTT-----------------------------AAAACTGTGTCTTTCTTAAAATTTGCTA Chimp: aactgtgtttttcttaaaactt---------------aaaacagttttcttaaaactGTGTCTTTCTTAAAATTTGCTA Gorilla: AACTGTGTTTTTCTTAAAACTTAAAAACAGTTTTCTT--------------AAAACTGTGTCTTTCTTAAAATTTGCTA ↑ 4 3 1 2 Human: TACTGTGTTTTTCTTAAAACTT-----------------------------AAAACTGTGTCTTTCTTAAAATTTGCTA Cluster: [ ] Orangutan: aactgtgtttttcttaa--------aacagttttctt--------------aaaactgtgtttttcttaaaaTTTGTTA Human > Gorilla --------------- chr8:59036411-59036418 Template switch process: F1: L TGCTTGGAAAATGGTTCTTAACTGTGTTTTTCTTAAAACTTAAAA 1 F3: 4 CTTAAAACTGTGTCTTTCTTAAAATTTGCTACTAGTGATATAT R RF: TGCTTGGAAAATGGTTCTTTACTGTGTTTTTCTTAAAACTTAAAACTGTGTCTTTCTTAAAATTTGCTACAAGTGATATAT RR: ACGAACCTTTTACCAAGAAATGACACAAAAAGAATTTTGAATTTTGACACAGAAAGAATTTTAAACGATGTTCACTATATA F2: 3 TTTTGACA 2 Unidirectional alignment (log-probability: -43.5) GGAAAATGGTTCTTaACTGTGTTTTTCTTAAAActtaaaaacagttttCTTAAAACTGTGTCTTTCTTAAAATTTGCTACtAGTGATA GGAAAATGGTTCTTTACTGTGTTTTTCTTAAAA---------------CTTAAAACTGTGTCTTTCTTAAAATTTGCTACAAGTGATA Template switch alignment (log-probability: -28) GGAAAATGGTTCTTaACTGTGTTTTTCTTAAAACTTAAAA|ACAGTTTT|CTTAAAACTGTGTCTTTCTTAAAATTTGCTACtAGTGATA GGAAAATGGTTCTTTACTGTGTTTTTCTTAAAACTTAAAA|ACAGTTTT|CTTAAAACTGTGTCTTTCTTAAAATTTGCTACAAGTGATA ========== Event 3621 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: TAAATGATAAATCATGATCAACCTGTAGTTCCATGTGCTTAAGGAGCT ↓ 1 3 24 ↑ 13 4 Chimp: TAAATGATAAATCATGATCAATA-CAGGTTCCATGTGCTTAAGGAGCT Gorilla: TAAATGATAAATCATGATCAATA-CAGGTTCCATGTGCTTAAGGAGCT ↓ 13 4 Human: TAAATGATAAATCATGATCAACCTGTAGTTCCATGTGCTTAAGGAGCT Cluster: [ ] Orangutan: TAAATGATAAATCATGATCAATA-CAGGTTCCATGTGCTTAAGGAGCT Chimp > Human ------------- chr8:88960555-88960560 Template switch process: F1: L AGAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA 1 F3: 4 GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA R RF: AGAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAATACAGGTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA RR: TCTTGAAGTGACCGATAAAGATTTACTATTTAGTACTAGTTATGTCCAAGGTACACGAATTCCTCGATACCTTGTCCTGTAAATTT F2: 3 ATGTCC 2 Unidirectional alignment (log-probability: -27.1) GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAAcctgTA---GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA----TACAGGTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA Template switch alignment (log-probability: -16) GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA|CCTGTA|GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA|CCTGTA|GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA Human > Chimp ------------- chr8:90724218-90724222 Template switch process: F1: L AGAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA 1 F3: 4 GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA R RF: AGAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAACCTGTAGTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA RR: TCTTGAAGTGACCGATAAAGATTTACTATTTAGTACTAGTTGGACATCAAGGTACACGAATTCCTCGATACCTTGTCCTGTAAATTT F2: 3 GACAT 2 Unidirectional alignment (log-probability: -25.7) GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA----TAcagGTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAACCTGTA---GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA Template switch alignment (log-probability: -15.9) GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA|TACAG|GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA|TACAG|GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA Gorilla > Human --------------- chr8:88960555-88960560 Template switch process: F1: L AGAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA 1 F3: 4 GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA R RF: AGAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAATACAGGTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA RR: TCTTGAAGTGACCGATAAAGATTTACTATTTAGTACTAGTTATGTCCAAGGTACACGAATTCCTCGATACCTTGTCCTGTAAATTT F2: 3 ATGTCC 2 Unidirectional alignment (log-probability: -26.6) GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAAcctgTA---GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA----TACAGGTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA Template switch alignment (log-probability: -16.5) GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA|CCTGTA|GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA GAACTTCACTGGCTATTTCTAAATGATAAATCATGATCAA|CCTGTA|GTTCCATGTGCTTAAGGAGCTATGGAACAGGACATTTAAA ========== Event 3622 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TACTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCCC----------CATCCTTATAAACCCACCATTTCC Chimp: TACTTACGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCCC----------CATCCTTATAAACCCACCATTTCC Gorilla: TACTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCCTTCCCCTGAATAATGCTTATAAACCCACCATTTCC ↑ 3 2 1 4 Human: TACTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCCC----------CATCCTTATAAACCCACCATTTCC Cluster: [ ] Orangutan: TACTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCCC----------TATCCTTATAAACCCACCATTTCC Human > Gorilla --------------- chr8:59472289-59472299 Template switch process: F1: L ACTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCC 1 F3: 4 AATGCTTATAAACCCACCATTTCCACTTTTTATTCTGGATAGAA R RF: ACTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCCCCATCCTTATAAACCCACCATTTCCACTTTTTATTCTGGATAGAA RR: TGAATACACGAGGAGACTTAAGTCCCCTTCCTTTAATGAGGGGTAGGAATATTTGGGTGGTAAAGGTGAAAAATAAGACCTATCTT F2: 3 TAAGTCCCCTT 2 Unidirectional alignment (log-probability: -40.6) CTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTccttCCCCtgaataATgCTTATAAACCCACCATTTCCACTTTTTATTCTGGAT CTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACT----CCCC------ATCCTTATAAACCCACCATTTCCACTTTTTATTCTGGAT Template switch alignment (log-probability: -28.3) CTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCC|TTCCCCTGAAT|aATgCTTATAAACCCACCATTTCCACTTTTTATTCTGGAT CTTATGTGCTCCTCTGAATTCAGGGGAAGGAAATTACTCC|TTCCCCTGAAT|CATCCTTATAAACCCACCATTTCCACTTTTTATTCTGGAT ========== Event 3623 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGACTGGAAGAGGAAACTCAT-----TTCCTGCAGAGTGCCTGTAATGTGTCCAGTCCCTGTTTGTCTCCCTGCTGGTTGGCCGAGGCAGGCGAGTCCACCCTGGAGCACCACAGGCCTGTTCCAGGGGCCAAGAAGGCCTTTGTCTCCAGCTTCACTTTCTTACTCTTTG Chimp: TGACTGGAAGAGGAAACTCAT-----TTCCTGCAGAGTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTGGTTGGCCGAGGCAGGCGAGTCCACCCTGGAGCACCACAGGCCTGTTCCAGGGGCCAAGAAGGCCTTTGTCTCCAGCTTCACTTTCTTACTCTTTG ↑ 1 4 3 2 Gorilla: TGACTGGAAGAGGAAACTCATTTCTCTTCCAGTAATGTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTGGTTGGCTGAGGCAGGCGAGTCCACCCTGGAGCACCACAGGCCTGTTCCAGGGGCCAAGAAGGCCTTTGTCTCCAGCTTCACTTTCTTACTCTTTG Human: TGACTGGAAGAGGAAACTCAT-----TTCCTGCAGAGTGCCTGTAATGTGTCCAGTCCCTGTTTGTCTCCCTGCTGGTTGGCCGAGGCAGGCGAGTCCACCCTGGAGCACCACAGGCCTGTTCCAGGGGCCAAGAAGGCCTTTGTCTCCAGCTTCACTTTCTTACTCTTTG Cluster: [ ] Orangutan: TGACTGGAAGAGGAAACTCAT-----TTCCTACAGAGTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTGGTTGGCCGAGGTAGACAAGTCCACCCTGGAGCACCACAGGCCTGTACCAGGGGCCAAGGAGGCCTTTGTCTCCAGCTTCACTTTCTTATTCTTTG Gorilla > Chimp --------------- chr8:59055080-59055086 Template switch process: F1: L CTCTTCGATCAGCCTTAATTTGACTGGAAGAGGAAACTCATTTC 1 F3: 4 GTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTG R RF: CTCTTAGATCAGCCTTAATTTGACTGGAAGAGGAAACTCATTTCTCTTCCAGTAATGTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTGGTTGGCTGAGGCAGGCGAGTCCACCCTGGAGCACCACAGGCCTGTTCCAGGGGCCAAGAAGGCCTTTGTCTCCAG RR: GAGAATCTAGTCGGAATTAAACTGACCTTCTCCTTTGAGTAAAGAGAAGGTCATTACACGGACATTACACAGGTCAGGGACAAACCGAGGAACGACCAACCGACTCCGTCCGCTCAGGTGGGACCTCGTGGTGTCCGGACAAGGTCCCCGGTTCTTCCGGAAACAGAGGTC F2: 3 AGACGTC 2 Unidirectional alignment (log-probability: -36.9) TcGATCAGCCTTAATTTGACTGGAAGAGGAAACTCATTTC------------ctgcagaGTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTG TAGATCAGCCTTAATTTGACTGGAAGAGGAAACTCATTTCTCTTCCAGTAAT-------GTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTG Template switch alignment (log-probability: -27.7) TcGATCAGCCTTAATTTGACTGGAAGAGGAAACTCATTTC|CTGcAGA|GTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTG TAGATCAGCCTTAATTTGACTGGAAGAGGAAACTCATTTC|CTGGAGA|GTGCCTGTAATGTGTCCAGTCCCTGTTTGGCTCCTTGCTG ========== Event 3624 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAAGTGAAAAGGAATAAAAGATAGGCATCTGTAGTACAGAATTAGTACTCAG Chimp: ATAAGTGAAAAGGAATAAAAGATAGGCATCTGTAGTACAGAATTAGTACTTAG ↑ 3 1 42 Gorilla: ATAAGTGAAAAGGAATAAAAGAT------GCCTAGTACAGAATTAGTACTTAG ↓ 3 1 42 Human: ATAAGTGAAAAGGAATAAAAGATAGGCATCTGTAGTACAGAATTAGTACTCAG Cluster: [ ] Orangutan: ATAAGTGAAAAGGAATAAAAGAT------GCCTAGTACAGAATTAGTACTTAG Gorilla > Human --------------- chr8:86710027-86710034 Template switch process: F1: L CAAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAT 1 F3: 4 GTAGTACAGAATTAGTACTCAGCTGGGCCTTAAAAGGATTT R RF: CAAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGATGCCTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATTT RR: GTTTGATTGAATAATTTATATTCACTTTTCCTTATTTTCTACGGATCATGTCTTAATCATGAATCGACCCGGAATTTTCCTAAA F2: 3 TCTACGGA 2 Unidirectional alignment (log-probability: -37.8) AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAtaggcatcTG--TAGTACAGAATTAGTACTcAGCTGGGCCTTAAAAGGATT AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGA--------TGCCTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATT Template switch alignment (log-probability: -27.8) AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAT|AGGCATCT|gTAGTACAGAATTAGTACTcAGCTGGGCCTTAAAAGGATT AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAT|AGGCATCT|CTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATT Gorilla > Chimp --------------- chr8:88458475-88458482 Template switch process: F1: L CAAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAT 1 F3: 4 GTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATTT R RF: CAAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGATGCCTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATTT RR: GTTTGATTGAATAATTTATATTCACTTTTCCTTATTTTCTACGGATCATGTCTTAATCATGAATCGACCCGGAATTTTCCTAAA F2: 3 TCTACGGA 2 Unidirectional alignment (log-probability: -32.2) AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAtaggcatcTG--TAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATT AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGA--------TGCCTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATT Template switch alignment (log-probability: -22.3) AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAT|AGGCATCT|gTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATT AAACTAACTTATTAAATATAAGTGAAAAGGAATAAAAGAT|AGGCATCT|CTAGTACAGAATTAGTACTTAGCTGGGCCTTAAAAGGATT ========== Event 3625 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TACAAAGTCACTGCTCCTGGAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCT------------------------------------------------------------------------------------------------------------GCAATGCTGAAAATAACACCAATAATGAGTGAAACTGACCTGAGCGTCCAGCTTCCTCCACTGTC ↓ 4 3 1 2 Chimp: TACAAAGTCACTGCTCCTGGAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGCGCTCAGGTCAGTTTCACTCATGATTGGTGTTATTTTCAGCATTGCAGGGAACTGAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGCTGAAAATAACACCAATCATGAGTGAAACTGACCTGAGCGCCCAGCTTCCTCCACTGTC ↑ 4 3 1 2 Gorilla: TACAAAGTCACTGCTCCTGGAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCT------------------------------------------------------------------------------------------------------------GCAATGCTGAAAATAACACCAATAATGAGTGAAACTGACCCGAGCGCCCAGCTTCCTCCACTGTC Human: TACAAAGTCACTGCTCCTGGAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCT------------------------------------------------------------------------------------------------------------GCAATGCTGAAAATAACACCAATAATGAGTGAAACTGACCTGAGCGTCCAGCTTCCTCCACTGTC Cluster: [ ] Orangutan: TACAAAGTCACTGTTCCTGGAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCT------------------------------------------------------------------------------------------------------------GCAATGCTGAAAATAACACCGATAATGAGTGAAACTGACCCGAGTGCCCAGCTTCCTCCACTGTC Human > Chimp ------------- chr8:59246722-59246774 Template switch process: F1: L ACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGC 1 F3: 4 GAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGCTGAAAATAACACCAATCATGAGTGAAACTGACC R RF: ACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGCTGAAAATAACACCAATAATGAGTGAAACTGACCTGAGC RR: TGAATAGGACCTCGAGTCTCTCCCGGTACCAAGTCAAGGGACGTTACGACTTTTATTGTGGTTATTACTCACTTTGACTGGACTCG F2: 3 TCAAGGGACGTTACGACTTTTATTGTGGTTAGTACTCACTTTGACTGGACTCG 2 Unidirectional alignment (log-probability: -166) tggagctcagagagggccatggttcagttccctgcaatgcgctcaggtcagtttcactcatgattggtgttattttcagcattgcagggaactgaacaaaACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC ----------------------------------------------------------------------------------------------------ACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC Template switch alignment (log-probability: -34.6) TGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGC|GCTCAGGTCAGTTTCACTCATgATTGGTGTTATTTTCAGCATTGCAGGGAACT|GAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC TGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGC|GCTCAGGTCAGTTTCACTCATTATTGGTGTTATTTTCAGCATTGCAGGGAACT|GAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC Gorilla > Chimp --------------- chr8:59246722-59246774 Template switch process: F1: L ACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGC 1 F3: 4 GAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGCTGAAAATAACACCAATCATGAGTGAAACTGACC R RF: ACTTATCCTGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGCTGAAAATAACACCAATAATGAGTGAAACTGACCCGAGC RR: TGAATAGGACCTCGAGTCTCTCCCGGTACCAAGTCAAGGGACGTTACGACTTTTATTGTGGTTATTACTCACTTTGACTGGGCTCG F2: 3 TCAAGGGACGTTACGACTTTTATTGTGGTTAGTACTCACTTTGACTGGACTCG 2 Unidirectional alignment (log-probability: -166) tggagctcagagagggccatggttcagttccctgcaatgcgctcaggtcagtttcactcatgattggtgttattttcagcattgcagggaactgaacaaaACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC ----------------------------------------------------------------------------------------------------ACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC Template switch alignment (log-probability: -40.1) TGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGC|GCTCaGGTCAGTTTCACTCATgATTGGTGTTATTTTCAGCATTGCAGGGAACT|GAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC TGGAGCTCAGAGAGGGCCATGGTTCAGTTCCCTGCAATGC|GCTCGGGTCAGTTTCACTCATTATTGGTGTTATTTTCAGCATTGCAGGGAACT|GAACAAAACTTATCCTGGAGCTCAGAGAGGGCCATGGTTC ========== Event 3626 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: aat--------aatttactaaatttttttaCTA--------------AATGTTTTGATAATGTCCAAGTCAG Chimp: ACT----CTCCATATCTCGGCATTGTTTTGATG-------ATGTCATCAAGTGTAGAAAAtgtccaagtcag ↓ 3 2 1 4 Gorilla: ACTCTCC----ATATCTCGACATTGTTTTGATAATGCCAT-------CAAGCGTAGAAAAtgtccaagtcag Human: aat--------aatttactaaatttttttaCTA--------------AATGTTTTGATAATGTCCAAGTCAG Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr8:5679047-5679051 Template switch process: F1: L TTAGTAAATACTCTCCATATCTCGACATTGTTTTGAT 1 F3: 4 CATCAAGCGTAGAAAATGTCCAAGTCAGCCTGGGCTGCTATTACAAAA R RF: TTAGTAAATACTCTCCATATCTCGGCATTGTTTTGATGATGTCATCAAGTGTAGAAAATGTCCAAGTCAGCCTGGGCTGCTATTACAAAA RR: AATCATTTATGAGAGGTATAGAGCCGTAACAAAACTACTACAGTAGTTCACATCTTTTACAGGTTCAGTCGGACCCGACGATAATGTTTT F2: 3 CGTAA 2 Unidirectional alignment (log-probability: -38.6) TTAGTAAATACTCTCCATATCTCGaCATTGTTTTGATaATGcCATCAAGcGTAGAAAATGTCCAAGTCAGCCTGGGCTGCTA TTAGTAAATACTCTCCATATCTCGGCATTGTTTTGATGATGTCATCAAGTGTAGAAAATGTCCAAGTCAGCCTGGGCTGCTA Template switch alignment (log-probability: -27.5) TTAGTAAATACTCTCCATATCTCGaCATTGTTTTGAT|AATGC|CATCAAGcGTAGAAAATGTCCAAGTCAGCCTGGGCTGCTA TTAGTAAATACTCTCCATATCTCGGCATTGTTTTGAT|AATGC|CATCAAGTGTAGAAAATGTCCAAGTCAGCCTGGGCTGCTA ========== Event 3627 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCCCTAGTGTCTAGTTCGATGCTG--GGCGAAGGACAGGAGAAAACTCTTGAGAG ↓ 3 1 2 4 Chimp: TTCCCTAGTGTCTAGTTCGATGCCAGCATCGAAGGGCAGGAGAAAACTCTTGAGAG ↑ 3 1 2 4 Gorilla: TTCCCTAGTGTCTAGTTCGATGCTG--GGCGAAGGGCAGGAGAAAACTCTTGAGAG Human: TTCCCTAGTGTCTAGTTCGATGCTG--GGCGAAGGACAGGAGAAAACTCTTGAGAG Cluster: [ ] Orangutan: TTCCCTAGTGTCTAGTTCGATGCTG--GGCGAAGGGCAGGAGAAAACTCTTGAGAG Human > Chimp ------------- chr8:59820506-59820511 Template switch process: F1: L AAATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC 1 F3: 4 CGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTGGCTTCCT R RF: AAATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGCTGGGCGAAGGACAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTGGCTTCCT RR: TTTATAGAAGGTTTTATAAAGGGATCACAGATCAAGCTACGACCCGCTTCCTGTCCTCTTTTGAGAACTCTCCTCGGAACAGAACCGAAGGA F2: 3 TACGAC 2 Unidirectional alignment (log-probability: -34.5) AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGCcagcaT---CGAAGGgCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC-----TGGGCGAAGGACAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG Template switch alignment (log-probability: -22.2) AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC|CAGCAT|CGAAGGgCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC|CAGCAT|CGAAGGACAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG Gorilla > Chimp --------------- chr8:59820506-59820511 Template switch process: F1: L AAATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC 1 F3: 4 CGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG R RF: AAATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGCTGGGCGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG RR: TTTATAGAAGGTTTTATAAAGGGATCACAGATCAAGCTACGACCCGCTTCCCGTCCTCTTTTGAGAACTCTCCTCGGAACAGAAC F2: 3 TACGAC 2 Unidirectional alignment (log-probability: -28) AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGCcagcaT---CGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC-----TGGGCGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG Template switch alignment (log-probability: -16.5) AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC|CAGCAT|CGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG AATATCTTCCAAAATATTTCCCTAGTGTCTAGTTCGATGC|CAGCAT|CGAAGGGCAGGAGAAAACTCTTGAGAGGAGCCTTGTCTTG ========== Event 3628 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGTGCCCTATTGGCCAGCATTTTCTGA-----GATGTGAACTAAAGGACAGTTCAGAAGATGCATG Chimp: CAGTGCCCTATTGGCCAGCATTTTCTGA-----GATGTGAACTAAAGGACAGTTCAGAAGATGCATG ↓ 3 1 2 4 Gorilla: CAATGCCCTATTGGCCAGCATTTTCTGAGTTCACATCTCAGAAAATGGACAGTTCAGAAGATGCATG ↑ 3 1 2 4 Human: CAGTGCCCTATTGGCCAGCATTTTCTGA-----GATGTGAACTAAAGGACAGTTCAGAAGATGCATG Cluster: [ ] Orangutan: CAGTGCCCTATTGGCCAGCATTTTCTGA-----GATGTGAACTAAAGGACAGTTCAGAAGATGCATA Human > Gorilla --------------- chr8:54881808-54881824 Template switch process: F1: L TCAAGTTTCTACTCAATGCCCTATTGGCCAGCATTTTCTGAG 1 F3: 4 GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAAGG R RF: TCAAGTTTCTACTCAGTGCCCTATTGGCCAGCATTTTCTGAGATGTGAACTAAAGGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAGGG RR: AGTTCAAAGATGAGTCACGGGATAACCGGTCGTAAAAGACTCTACACTTGATTTCCTGTCAAGTCTTCTACGTACACAAACCCCCACTCCTCCC F2: 3 TAAAAGACTCTACACTT 2 Unidirectional alignment (log-probability: -53.8) AAGTTTCTACTCAaTGCCCTATTGGCCAGCATTTTCTGAGttcacatctcagaaaAT----------GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAaGG AAGTTTCTACTCAGTGCCCTATTGGCCAGCATTTTCTGAG---------------ATGTGAACTAAAGGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAGGG Template switch alignment (log-probability: -29) AAGTTTCTACTCAaTGCCCTATTGGCCAGCATTTTCTGAG|TTCACATCTCAGAAAAT|GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAaGG AAGTTTCTACTCAGTGCCCTATTGGCCAGCATTTTCTGAG|TTCACATCTCAGAAAAT|GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAGGG Chimp > Gorilla --------------- chr8:54881808-54881824 Template switch process: F1: L TCAAGTTTCTACTCAATGCCCTATTGGCCAGCATTTTCTGAG 1 F3: 4 GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAAGG R RF: TCAAGTTTCTACTCAGTGCCCTATTGGCCAGCATTTTCTGAGATGTGAACTAAAGGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAGGG RR: AGTTCAAAGATGAGTCACGGGATAACCGGTCGTAAAAGACTCTACACTTGATTTCCTGTCAAGTCTTCTACGTACACAAACCCCCACTCCTCCC F2: 3 TAAAAGACTCTACACTT 2 Unidirectional alignment (log-probability: -53.8) AAGTTTCTACTCAaTGCCCTATTGGCCAGCATTTTCTGAGttcacatctcagaaaAT----------GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAaGG AAGTTTCTACTCAGTGCCCTATTGGCCAGCATTTTCTGAG---------------ATGTGAACTAAAGGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAGGG Template switch alignment (log-probability: -29) AAGTTTCTACTCAaTGCCCTATTGGCCAGCATTTTCTGAG|TTCACATCTCAGAAAAT|GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAaGG AAGTTTCTACTCAGTGCCCTATTGGCCAGCATTTTCTGAG|TTCACATCTCAGAAAAT|GGACAGTTCAGAAGATGCATGTGTTTGGGGGTGAGGAGGG ========== Event 3629 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGTACGAGGATATTGCCAACCAAAGACGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGAGCTGCAGAGTCTGGCTGGGAAGCACG ↓ 1 4 3 2 Chimp: CAGTACGAGGATATTGCCAACTGCAGCTGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGAGCTGCAGAGCCTGGCTGGGAAGCACG Gorilla: CAGTACGAGGATATTGCCAACCGCAGCCGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGAGCTGCAGAGCCTGGCTGGGAAGCACG Human: CAGTACGAGGATATTGCCAACCAAAGACGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGAGCTGCAGAGTCTGGCTGGGAAGCACG Cluster: [ ] Orangutan: ---------------------------------------------------------------------------------------------- Human > Chimp ------------- chr8:62641207-62641213 Template switch process: F1: L TCATTGCTGAGGTCAAGGCACAGTACGAGGATATTGCCAAC 1 F3: 4 GGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGA R RF: TCATTGCTGAGGTCAAGGCACAGTACGAGGATATTGCCAACCAAAGACGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGAGCTGCA RR: AGTAACGACTCCAGTTCCGTGTCATGCTCCTATAACGGTTGGTTTCTGCCCGACTCCGACTCTCGTACATGGTCTAGTTCATACTCCTCGACGT F2: 3 TCGACGT 2 Unidirectional alignment (log-probability: -30.7) CATTGCTGAGGTCAAGGCACAGTACGAGGATATTGCCAACtgcAGctGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGA CATTGCTGAGGTCAAGGCACAGTACGAGGATATTGCCAACCAAAGACGGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGA Template switch alignment (log-probability: -16.2) CATTGCTGAGGTCAAGGCACAGTACGAGGATATTGCCAAC|TGCAGCT|GGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGA CATTGCTGAGGTCAAGGCACAGTACGAGGATATTGCCAAC|TGCAGCT|GGGCTGAGGCTGAGAGCATGTACCAGATCAAGTATGAGGA ========== Event 3630 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TATAAGTGTGAAAATAGGTTTTATAATTGTA----------------------------------------------------TAAACTAGAGTTTATTGATGTGTTGATT Chimp: TATAAGTGTGAAAATAGGTtttataattgta-----------------------------taaacaactagtttataattgtataaactagagtttatTGATGTGTTGATT Gorilla: TATAAGTGTGAAAATAGGTTTTATAATTGTA------TAAACAACTAGTTTGTAATTGTA-----------------------TAAACTAGAGTTTATTGATGTGTTGATT ↑ 4 3 12 Human: TATAAGTGTGAAAATAGGTTTTATAATTGTA----------------------------------------------------TAAACTAGAGTTTATTGATGTGTTGATT Cluster: [ ] Orangutan: TATAAGTGTGAAAATAGGTTTTATAATTGTATAAACA-------------------------------------------------GCTAGAGTTTATCGATGTGTTGATT Human > Gorilla --------------- chr8:54206099-54206102 Template switch process: F1: L ACGTCATTTTTATAAGTGTGAAAATAGGTTTTATAATTGTATAAACAA 1 F3: 4 TTTGTAATTGTATAAACTAGAGTTTATTGATGTGTTGATTTAGCAAATCCTA R RF: ATGTCATTTTTATAAGTGTGAAAATAGGTTTTATAATTGTATAAACTAGAGTTTATTGATGTGTTGATTTAGCAAATCCTA RR: TACAGTAAAAATATTCACACTTTTATCCAAAATATTAACATATTTGATCTCAAATAACTACACAACTAAATCGTTTAGGAT F2: 3 GATC 2 Unidirectional alignment (log-probability: -49.5) TTTATAAGTGTGAAAATAGGTTTTAtaattgtataaacaactagtttgTAATTGTATAAACTAGAGTTTATTGATGTGTTGATT TTTATAAGTGTGAAAATAGGTTTTA-----------------------TAATTGTATAAACTAGAGTTTATTGATGTGTTGATT Template switch alignment (log-probability: -33.3) TTTATAAGTGTGAAAATAGGTTTTATAATTGTATAAACaA|CTAG|TTTgTAATTGTATAAACTAGAGTTTATTGATGTGTTGATT TTTATAAGTGTGAAAATAGGTTTTATAATTGTATAAACTA|CTAG|TTTATAATTGTATAAACTAGAGTTTATTGATGTGTTGATT ========== Event 3631 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTATAGGATTTTTTGTCCAGCTCCCAGATATTCACTCTTAAAAACCTAGGGATG Chimp: TTTATAGGATTTTTTGTCCAGCTCCCAGATATTCACTCTTAAAAACCTAGGGATG ↓ 1 3 4 2 Gorilla: TTTATAGGATTTTTTGTCCAGTGAATATCTATTCACTCTTAAAAACCTAGGGATG ↑ 1 3 4 2 Human: TTTATAGGATTTTTTGTCCAGCTCCCAGATATTCACTCTTAAAAACCTAGGGATG Cluster: [ ] Orangutan: TTTATAGGATTTTTTGTCCAGCTCCCAGATATTCACTCTTAAAAACCTAGGGATG Human > Gorilla --------------- chr8:54462590-54462597 Template switch process: F1: L AAGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG 1 F3: 4 TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA R RF: AAGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAGCTCCCAGATATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA RR: TTCTTCTTTCACCACAGACTAAATATCCTAAAAAACAGGTCGAGGGTCTATAAGTGAGAATTTTTGGATCCCTACATCGATTTTTACCT F2: 3 CTATAAGT 2 Unidirectional alignment (log-probability: -31.1) AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAGtgaatatC-------TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG-------CTCCCAGATATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA Template switch alignment (log-probability: -16.7) AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG|TGAATATC|TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG|TGAATATC|TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA Chimp > Gorilla --------------- chr8:54462590-54462597 Template switch process: F1: L AAGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG 1 F3: 4 TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA R RF: AAGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAGCTCCCAGATATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA RR: TTCTTCTTTCACCACAGACTAAATATCCTAAAAAACAGGTCGAGGGTCTATAAGTGAGAATTTTTGGATCCCTACATCGATTTTTACCT F2: 3 CTATAAGT 2 Unidirectional alignment (log-probability: -31.1) AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAGtgaatatC-------TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG-------CTCCCAGATATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA Template switch alignment (log-probability: -16.7) AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG|TGAATATC|TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA AGAAGAAAGTGGTGTCTGATTTATAGGATTTTTTGTCCAG|TGAATATC|TATTCACTCTTAAAAACCTAGGGATGTAGCTAAAAATGGA ========== Event 3632 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: aatatatTCTACCTGCATGCGCATATGCTTGTGGACACACAT--ATGCGCAAACACCCACACATgctaca Chimp: aatatatTCTACCTGCATGCGCATATGCTTGTGGACACACAT--ATGCGCAAACACCCACACATgctaca ↑ 3 2 1 4 Gorilla: aatatatgCTGCCTGCATGCGCATATGCTTGTGGACACACATGAGTACTCAAACACCCACACATGCTACA ↓ 3 2 1 4 Human: aatatatTCTACCTGCATGCGCATATGCTTGTGGACACACAT--ATGCGCAAACACCCACACATgctaca Cluster: [ ] Orangutan: Gorilla > Human --------------- chr8:62044393-62044397 Template switch process: F1: L ATATATTCTACCTGCATGCGCATATGCTTGTGGACACACAT 1 F3: 4 CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT R RF: ATATATGCTGCCTGCATGCGCATATGCTTGTGGACACACATGAGTACTCAAACACCCACACATGCTACATACAGATGCGTCTCGACTT RR: TATATACGACGGACGTACGCGTATACGAACACCTGTGTGTACTCATGAGTTTGTGGGTGTGTACGATGTATGTCTACGCAGAGCTGAA F2: 3 GCGTA 2 Unidirectional alignment (log-probability: -37.7) TATATtCTaCCTGCATGCGCATATGCTTGTGGACACACATatgcG------CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT TATATGCTGCCTGCATGCGCATATGCTTGTGGACACACAT----GAGTACTCAAACACCCACACATGCTACATACAGATGCGTCTCGACTT Template switch alignment (log-probability: -27.4) TATATtCTaCCTGCATGCGCATATGCTTGTGGACACACAT|ATGCG|CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT TATATGCTGCCTGCATGCGCATATGCTTGTGGACACACAT|ATGCG|CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT Gorilla > Chimp --------------- chr8:63098060-63098064 Template switch process: F1: L ATATATTCTACCTGCATGCGCATATGCTTGTGGACACACAT 1 F3: 4 CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT R RF: ATATATGCTGCCTGCATGCGCATATGCTTGTGGACACACATGAGTACTCAAACACCCACACATGCTACATACAGATGCGTCTCGACTT RR: TATATACGACGGACGTACGCGTATACGAACACCTGTGTGTACTCATGAGTTTGTGGGTGTGTACGATGTATGTCTACGCAGAGCTGAA F2: 3 GCGTA 2 Unidirectional alignment (log-probability: -37.7) TATATtCTaCCTGCATGCGCATATGCTTGTGGACACACATatgcG------CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT TATATGCTGCCTGCATGCGCATATGCTTGTGGACACACAT----GAGTACTCAAACACCCACACATGCTACATACAGATGCGTCTCGACTT Template switch alignment (log-probability: -27.4) TATATtCTaCCTGCATGCGCATATGCTTGTGGACACACAT|ATGCG|CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT TATATGCTGCCTGCATGCGCATATGCTTGTGGACACACAT|ATGCG|CAAACACCCACACATGCTACATACAGATGCGTCTCGACTT ========== Event 3633 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGTAATTTGTCAAGACAAGTGGACCCCTTGCTAGAACACAAATCCAAACCTGAAA ↓ 1 4 3 2 Chimp: CAGTAATTTGTCAAGACAAGTTCTAGCCTTGCTAGAACACAAATCCAAACCTGAAA ↑ 1 4 3 2 Gorilla: CAGTAATTTGTCAAGACAAGTGGACCCCTTGCTAGAACACAAATCCAAACCTGAAA Human: CAGTAATTTGTCAAGACAAGTGGACCCCTTGCTAGAACACAAATCCAAACCTGAAA Cluster: [ ] Orangutan: CAGTAATTTGTCAAGACAAGTGGACCCCTTGCTAGAACACAAATCCAAACCTGAAA Human > Chimp ------------- chr8:84503416-84503420 Template switch process: F1: L CACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGT 1 F3: 4 CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA R RF: CACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGTGGACCCCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA RR: GTGTACTTTAATTTGCATTTGTCATTAAACAGTTCTGTTCACCTGGGGAACGATCTTGTGTTTAGGTTTGGACTTTCCTCATTCTT F2: 3 GATCT 2 Unidirectional alignment (log-probability: -27.1) ACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGTtctaG----CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA ACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGT----GGACCCCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA Template switch alignment (log-probability: -15.9) ACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGT|TCTAG|CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA ACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGT|TCTAG|CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA Gorilla > Chimp --------------- chr8:84503416-84503420 Template switch process: F1: L CACATGAAATTAAACGTAAACAGTAATTTGTCAAGACAAGT 1 F3: 4 CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA R RF: CACATGAAATTAAACATAAACAGTAATTTGTCAAGACAAGTGGACCCCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA RR: GTGTACTTTAATTTGTATTTGTCATTAAACAGTTCTGTTCACCTGGGGAACGATCTTGTGTTTAGGTTTGGACTTTCCTCATTCTT F2: 3 GATCT 2 Unidirectional alignment (log-probability: -32.1) ACATGAAATTAAACgTAAACAGTAATTTGTCAAGACAAGTtctaG----CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA ACATGAAATTAAACATAAACAGTAATTTGTCAAGACAAGT----GGACCCCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA Template switch alignment (log-probability: -21.9) ACATGAAATTAAACgTAAACAGTAATTTGTCAAGACAAGT|TCTAG|CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA ACATGAAATTAAACATAAACAGTAATTTGTCAAGACAAGT|TCTAG|CCTTGCTAGAACACAAATCCAAACCTGAAAGGAGTAAGAA ========== Event 3634 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CTAAACTGTGATAGGTTTACA-CCTGAGCAGCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCG ↑ 1 4 3 2 Chimp: CTAAACTGTGATAGGTTTACACTCTAA--GGCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCG Gorilla: CTAAATTGTGATAGGTTTACACTCTAA--GGCTTCTTGCTGCTCAGGTCAGGCTATAATGATTTCG Human: CTAAACTGTGATAGGTTTACA-CCTGAGCAGCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCG Cluster: [ ] Orangutan: CTAAATTGTGATAAGTTTACACTCTAA--GGCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCG Chimp > Human ------------- chr8:62609073-62609079 Template switch process: F1: L CAGGAAATTAATCTCTAAGTCTAAACTGTGATAGGTTTACAC 1 F3: 4 GCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCGACTT R RF: CAGGAAATTAATCTCTAAGTCTAAACTGTGATAGGTTTACACTCTAAGGCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCGACTT RR: GTCCTTTAATTAGAGATTCAGATTTGACACTATCCAAATGTGAGATTCCGGAGAACGACGAGTCCAGTCCGATATTACTAAAGCTGAA F2: 3 ACGAGTC 2 Unidirectional alignment (log-probability: -30.1) GGAAATTAATCTCTAAGTCTAAACTGTGATAGGTTTACAC-CTgAGcaGCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCGACTT GGAAATTAATCTCTAAGTCTAAACTGTGATAGGTTTACACTCTAAG--GCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCGACTT Template switch alignment (log-probability: -16.2) GGAAATTAATCTCTAAGTCTAAACTGTGATAGGTTTACAC|CTGAGCA|GCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCGACTT GGAAATTAATCTCTAAGTCTAAACTGTGATAGGTTTACAC|CTGAGCA|GCCTCTTGCTGCTCAGGTCAGGCTATAATGATTTCGACTT ========== Event 3635 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGAGTGTGGCTTTGATCTAGGTG----TCCAGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGT ↓ 1 4 3 2 Chimp: TGAGTGTGGCTTTGATCTAGGCTTGCACCAAGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGT ↑ 1 4 3 2 Gorilla: TGAGTGTGGCTTTGATCTAGGTG----TCCAGCCTTTCTTGGTGCAACTCATTCTGGGGAGAATGGT Human: TGAGTGTGGCTTTGATCTAGGTG----TCCAGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGT Cluster: [ ] Orangutan: TGAGTGTGGCTTTGATCTAGGTG----TCCAGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGT Human > Chimp ------------- chr8:82837676-82837683 Template switch process: F1: L GTTAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGC 1 F3: 4 AGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG R RF: GTTAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGTGTCCAGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG RR: CAATCGGTCTAAGGGTTCCGACTCACACCGAAACTAGATCCACAGGTCGGAAAGAACCACGTTTAGTAAGACCCCTCTTACCATCC F2: 3 ACCACGTT 2 Unidirectional alignment (log-probability: -32.9) TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGG----CttgcaccaAGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGTGTCC--------AGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG Template switch alignment (log-probability: -22.3) TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGc|TTGCACCA|AGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGT|TTGCACCA|AGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG Gorilla > Chimp --------------- chr8:82837676-82837683 Template switch process: F1: L GTTAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGC 1 F3: 4 AGCCTTTCTTGGTGCAAATCATTCTGGGGAGAATGGTAGG R RF: GTTAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGTGTCCAGCCTTTCTTGGTGCAACTCATTCTGGGGAGAATGGTAGG RR: CAATCGGTCTAAGGGTTCCGACTCACACCGAAACTAGATCCACAGGTCGGAAAGAACCACGTTGAGTAAGACCCCTCTTACCATCC F2: 3 ACCACGTT 2 Unidirectional alignment (log-probability: -37.9) TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGG----CttgcaccaAGCCTTTCTTGGTGCAAaTCATTCTGGGGAGAATGGTAGG TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGTGTCC--------AGCCTTTCTTGGTGCAACTCATTCTGGGGAGAATGGTAGG Template switch alignment (log-probability: -27.8) TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGc|TTGCACCA|AGCCTTTCTTGGTGCAAaTCATTCTGGGGAGAATGGTAGG TAGCCAGATTCCCAAGGCTGAGTGTGGCTTTGATCTAGGT|TTGCACCA|AGCCTTTCTTGGTGCAACTCATTCTGGGGAGAATGGTAGG ========== Event 3636 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: AAGCACTCCTTGttttttcattttttaagcatttatttatttGAAGACAGGG----TGTCATCCAAGATAACAGAGACCCTGTCTTCaaataaataaatattttaaaaatGAAAAAACAAGGAGTGCTTAG Chimp: AAGCGTTCCTTGttttttcatttttaaaatatttatttatttGAAGACAGGGTCTCTGTCATCCTGGATGA----CACCCTGTCTTCAAATAAATAAATACTTaaaaaaagaaaaaaCAAGGAGTGCTTGG ↓ 3 1 2 4 ↑ 13 24 Gorilla: AAGCACTCCTTGttttttcattttttaagtatttatttatttGAAGACAGGG----TGTCATCCAGGATGACAGAGACCCTGTCTTCaaataaataaatattttaaaaatgaaaaaaCAAGGAGTGCTTAG Human: AAGCACTCCTTGttttttcattttttaagcatttatttatttGAAGACAGGG----TGTCATCCAAGATAACAGAGACCCTGTCTTCaaataaataaatattttaaaaatGAAAAAACAAGGAGTGCTTAG Cluster: [ ] Orangutan: AAGCACTCCTTAttttttcattttttaagtatttatttatttGAAGACAGGG----TGTCATCCAGGATGACAGAGACCCTATCTTCAAGTAAATAAATATTTTAAAAATGAAAAAACAAGCAGGGCTTAG Gorilla > Chimp --------------- chr8:6729189-6729263 Template switch process: F1: L GTTTTTTCATTTTT 1 F3: 4 AAAAAAGAAAAA R RF: GTTTTTTCATTTTTTAAGTATTTATTTATTTGAAGACAGGGTGTCATCCAGGATGACAGAGACCCTGTCTTCAAATAAATAAATATTTTAAAAATGAAAAA RR: CAAAAAAGTAAAAAATTCATAAATAAATAAACTTCTGTCCCACAGTAGGTCCTACTGTCTCTGGGACAGAAGTTTATTTATTTATAAAATTTTTACTTTTT F2: 3 ATTCATAAATAAATAAACTTCTGTCCCACAGTAGGTCCTACTGTCTCTGGGACAGAAGTTTATTTATTTATAAAA 2 Unidirectional alignment (log-probability: -59.9) GTTTTTTCATTTTTaAAaTATTTATTTATTTGAAGACAGGGtctcTGTCATCCtGGATGAC----ACCCTGTCTTCAAATAAATAAATAcTTaAAAAAaGAAAAA GTTTTTTCATTTTTTAAGTATTTATTTATTTGAAGACAGGG----TGTCATCCAGGATGACAGAGACCCTGTCTTCAAATAAATAAATATTTTAAAAATGAAAAA Template switch alignment (log-probability: -29.5) GTTTTTTCATTTTT|AAAATATTTATTTATTTGAAGACAGGGTCTCTGTCATCCTGGATGACACCCTGTCTTCAAATAAATAAATACTTA|AAAAAaGAAAAA GTTTTTTCATTTTT|AAAATATTTATTTATTTGAAGACAGGGTCTCTGTCATCCTGGATGACACCCTGTCTTCAAATAAATAAATACTTA|AAAAATGAAAAA Chimp > Gorilla --------------- chr8:6174540-6174620 Template switch process: F1: L GTTTTTTCATTTTT 1 F3: 4 GAAAAA R RF: GTTTTTTCATTTTTAAAATATTTATTTATTTGAAGACAGGGTCTCTGTCATCCTGGATGACACCCTGTCTTCAAATAAATAAATACTTAAAAAAAGAAAAA RR: CAAAAAAGTAAAAATTTTATAAATAAATAAACTTCTGTCCCAGAGACAGTAGGACCTACTGTGGGACAGAAGTTTATTTATTTATGAATTTTTTTCTTTTT F2: 3 TAAAAATTTTATAAATAAATAAACTTCTGTCCCAGAGACAGTAGGACCTACTGTGGGACAGAAGTTTATTTATTTATGAAT 2 Unidirectional alignment (log-probability: -59.9) GTTTTTTCATTTTTtAAgTATTTATTTATTTGAAGACAGGG----TGTCATCCaGGATGACagagACCCTGTCTTCAAATAAATAAATAtTTtAAAAAtGAAAAA GTTTTTTCATTTTTAAAATATTTATTTATTTGAAGACAGGGTCTCTGTCATCCTGGATGAC----ACCCTGTCTTCAAATAAATAAATACTTAAAAAAAGAAAAA Template switch alignment (log-probability: -24.6) GTTTTTTCATTTTT|TAAGTATTTATTTATTTGAAGACAGGGTGTCATCCAGGATGACAGAGACCCTGTCTTCAAATAAATAAATATTTTAAAAAT|GAAAAA GTTTTTTCATTTTT|TAAGTATTTATTTATTTGAAGACAGGGTGTCATCCAGGATGACAGAGACCCTGTCTTCAAATAAATAAATATTTTAAAAAT|GAAAAA ========== Event 3637 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: aaaaaaaaGCTTTAAAAATTATAGGCCCTTCCAAAATTGATTGAATTTGTAGAAAAAATGTGTATCTTTTTATTGCCTCTGAACTCAAGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT--------GCCTATATTAAACAGCTATGTGAAATAGTGCTGAT Chimp: aaaaaaaaGCTTTAAAAATTATAGGCCCTTCCAAAATTGATTGAATTTGTAGA-AAAATGTGTATCTTTTTATTGCCTCTGAACTCAAGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT----AGCAGTCTA-TTTAA---ACTATGTGAAATAGTGCTGAT Gorilla: aaaaaaaaGCTTTAAAAATTATAGGCCCTTCCAAAATTGATTGAATTTGTAGA-AAAATGTGTATCTTTTTATTGCCTCTGAACTCAAGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAATAGCA----GTCTA-TTTAA---ACTATGTGAAATAGTGCTGAT ↓ 3 2 1 4 Human: aaaaaaaaGCTTTAAAAATTATAGGCCCTTCCAAAATTGATTGAATTTGTAGAAAAAATGTGTATCTTTTTATTGCCTCTGAACTCAAGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT--------GCCTATATTAAACAGCTATGTGAAATAGTGCTGAT Cluster: [ ] Orangutan: AA-AAATAGCTTTAAAAATTATAGGCCCTTCCAAAATTGATTGAATTTGTAGA-AAAATGTGTATCTTTTTATTGCCTCTGAACTCAAGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAATAGCA----GTCTA-TTTAA---ACTGTGTGAAATAGTGCTGAT Gorilla > Human --------------- chr8:81844814-81844820 Template switch process: F1: L AGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT 1 F3: 4 TTAAACAGCTATGTGAAATAGTGCTGATTTTCATGGCTCTTAACTAAA R RF: TATAGGCCCTTCCAAAATTGATTGAATTTGTAGAAAAATGTGTATCTTTTTATTGCCTCTGAACTCAAGGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAATAGCAGTCTATTTAAACTATGTGAAATAGTGCTGATTTTCATGGCTCTTAACTAAA RR: ATATCCGGGAAGGTTTTAACTAACTTAAACATCTTTTTACACATAGAAAAATAACGGAGACTTGAGTTCCTTTGACTTGACTTACTTACGGATATAACTTGGTTCTTATCGTCAGATAAATTTGATACACTTTATCACGACTAAAAGTACCGAGAATTGATTT F2: 3 ATATCCG 2 Unidirectional alignment (log-probability: -40) GGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAATgcctatattaaacAG-------------CTATGTGAAATAGTGCTGATTTTCATGGCTCT GGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT-------------AGCAGTCTATTTAAACTATGTGAAATAGTGCTGATTTTCATGGCTCT Template switch alignment (log-probability: -30.8) GGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT|GCCTATA|TTAAAcagCTATGTGAAATAGTGCTGATTTTCATGGCTCT GGAAACTGAACTGAATGAATGCCTATATTGAACCAAGAAT|GCCTATA|TTAAA---CTATGTGAAATAGTGCTGATTTTCATGGCTCT ========== Event 3638 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GCAAAAGAAGGAGTGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTTATTCTTGAATTAGTATTTATCCAACATAAGCTGAATTTAACTTAAAGAGACCAATATACCAAAAGATAGCTAAATATCTTGAGTGAACAAATTTAATTTCCTTATTCCACCACA Chimp: GCAAAAGAAGGAGTGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTAATTCTTGAATTAGTATTTATCCAACATAAGCTGAATTTAACTTAAAGAGACCAATATACCAAAAGATAGCTAAATATCTTGAGTGAACAAATTTAATTTCCTTATTCCACCACA ↓ 3 1 2 4 ↑ 3 1 2 4 Gorilla: GCAAAAGAAGGAGTGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTAATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTGATTCTTGAATTAGTATTTATCCAACATAAGCTGAATTTAACTTAAAGAGACCAATATACCAAAAGATAGCTAAATATCTTGAGTGAACAAATTTAATTTCCTTATTCCACCACA ↓ 3 1 2 4 ↑ 3 1 2 4 Human: GCAAAAGAAGGAGTGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTTATTCTTGAATTAGTATTTATCCAACATAAGCTGAATTTAACTTAAAGAGACCAATATACCAAAAGATAGCTAAATATCTTGAGTGAACAAATTTAATTTCCTTATTCCACCACA Cluster: [ ] Orangutan: GCAAAAGAAGGAGTGGGGTAGAGGCAGGGAATCCAGGACTAATTACAATTAATTTT-----------------------------------------------CTTGAGTTAGTATTTATCCAACATAAGCTGAATTTAACTTAAAGAGACCAATATACCAAAAGATAGCTAAATATCTTGAGTGAACAAATTTAATTTCCTTATTCCACCACA Gorilla > Human --------------- chr8:64438625-64438634 Template switch process: F1: L TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT 1 F3: 4 AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTTATTC R RF: TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTAATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTGATTC RR: ACCCCATCTCCGTCCCTTAGGTCCTGATTGATGTGAATTAATTAAGTTCTTTTAATTCACATCAATCAGGACCTAAGGGACGGAGACTAAG F2: 3 TTAAGTTCTT 2 Unidirectional alignment (log-probability: -35.1) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTttcttgAATT------AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTtATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT------AATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTGATTC Template switch alignment (log-probability: -22.5) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|TTCTTGAATT|AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTtATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|TTCTTGAATT|AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTGATTC Human > Gorilla --------------- chr8:95655463-95655507 Template switch process: F1: L TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT 1 F3: 4 GATTC R RF: TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTC RR: ACCCCATCTCCGTCCCTTAGGTCCTGATTGATGTGAATTAAAAGAACTTAATTAATTCACATCAATCAGGACCTAAG F2: 3 TCTCCGTCCCTTAGGTCCTGATTGATGTGAATTAAAAGAACTTAA 2 Unidirectional alignment (log-probability: -35.1) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT------AATTcaagaaAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTgATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATT------AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTTATTC Template switch alignment (log-probability: -20.6) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|AATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCT|GATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|AATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCT|GATTC Gorilla > Chimp --------------- chr8:65529488-65529531 Template switch process: F1: L TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT 1 F3: 4 TAATTC R RF: TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTAATTCAAGAA RR: ACCCCATCTCCGTCCCTTAGGTCCTGATTGATGTGAATTAATTAAGTTCTT F2: 3 CTCCGTCCCTTAGGTCCTGATTGATGTGAATTAATTAAGTTCTT 2 Unidirectional alignment (log-probability: -35.1) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTttcttgAATT------AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTaATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT------AATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTGATTC Template switch alignment (log-probability: -20.5) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|TTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTC|TAATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|TTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTC|TAATTC Chimp > Gorilla --------------- chr8:95655463-95655507 Template switch process: F1: L TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT 1 F3: 4 GATTC R RF: TGGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATTAATTAAGTGTAGTTAGTCCTGGATTC RR: ACCCCATCTCCGTCCCTTAGGTCCTGATTGATGTGAATTAAAAGAACTTAATTAATTCACATCAATCAGGACCTAAG F2: 3 TCTCCGTCCCTTAGGTCCTGATTGATGTGAATTAAAAGAACTTAA 2 Unidirectional alignment (log-probability: -35.1) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT------AATTcaagaaAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTgATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATTTTCTTGAATT------AATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCTAATTC Template switch alignment (log-probability: -20.6) GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|AATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCT|GATTC GGGGTAGAGGCAGGGAATCCAGGACTAACTACACTTAATT|AATTCAAGAAAATTAAGTGTAGTTAGTCCTGGATTCCCTGCCTCT|GATTC ========== Event 3639 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GATATTTGTCAAAATATTATTTTCAAACTCT---------------------------------------------------------------GAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTATTTTGTTTACAAGACTTGTG ↓ 4 3 1 2 Chimp: GATATTTGTCAAAATATTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTATAAGAAAACAGAATTACATTGTTATTTTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTATTTTGTTTACAAGACTTGTG ↑ 4 3 1 2 Gorilla: GATATTTGTCAAAATATTATTTTCAAACTCT---------------------------------------------------------------GAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTATTTTGTTTACAAGACTTGTG Human: GATATTTGTCAAAATATTATTTTCAAACTCT---------------------------------------------------------------GAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTATTTTGTTTACAAGACTTGTG Cluster: [ ] Orangutan: GATATTTGTCAAAAGATTATTTTCAAACTCT---------------------------------------------------------------GAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTCATTTTGTTTACAAGACTTGTG Human > Chimp ------------- chr8:81809684-81809709 Template switch process: F1: L TTTTCAAGGAGATATTTGTCAAAATATTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTA 1 F3: 4 TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTAT R RF: TTTTCAAGGAGATATTTGTCAAAATATTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTAT RR: AAAAGTTCCTCTATAAACAGTTTTATAATAAAAGTTTGAGACTTCTATAATTTCTTATTGTTACATTAAGACAAAAGAATA F2: 3 TTATTGTTACATTAAGACAAAAGAAT 2 Unidirectional alignment (log-probability: -101) TTAttttcaaactctgaagatattaaagaataacaatgtataagaaaacagaattacattgttattTTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT TTA---------------------------------------------------------------TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT Template switch alignment (log-probability: -19.1) TTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTA|TAAGAAAACAGAATTACATTGTTATT|TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT TTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTA|TAAGAAAACAGAATTACATTGTTATT|TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT Gorilla > Chimp --------------- chr8:81809684-81809709 Template switch process: F1: L TTTTCAAGGAGATATTTGTCAAAATATTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTA 1 F3: 4 TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTAT R RF: TTTTCAAGGAGATATTTGTCAAAATATTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATTCTGTTTTCTTAT RR: AAAAGTTCCTCTATAAACAGTTTTATAATAAAAGTTTGAGACTTCTATAATTTCTTATTGTTACATTAAGACAAAAGAATA F2: 3 TTATTGTTACATTAAGACAAAAGAAT 2 Unidirectional alignment (log-probability: -101) TTAttttcaaactctgaagatattaaagaataacaatgtataagaaaacagaattacattgttattTTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT TTA---------------------------------------------------------------TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT Template switch alignment (log-probability: -19.9) TTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTA|TAAGAAAACAGAATTACATTGTTATT|TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT TTATTTTCAAACTCTGAAGATATTAAAGAATAACAATGTA|TAAGAAAACAGAATTACATTGTTATT|TTTTCAAACTCTGAAGATATTAAAGAATAACAATGTAATT ========== Event 3640 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ACACATTATCTTAGATGAGATTATCA----------------------------------------------GTTATCAGGATGTCAATGCTTCTGTTAGTTa Chimp: ACACATTATCTTAGATGAGATTATCA-----------------------GTTATATTGATAACTGATCATCAGTTATCAGGATGTCAATGCTTCTATTAGTTA Gorilla: ACACATTATCTTAGATGAGATTATCAGTTATATTGATAACTGATCATCA-----------------------GTTATCAGGATGTCAATGCTTCTGTTAGTTa ↑ 4 3 2 1 Human: ACACATTATCTTAGATGAGATTATCA----------------------------------------------GTTATCAGGATGTCAATGCTTCTGTTAGTTa Cluster: [ ] Orangutan: ACACATTATCTTAGATGAGATTATCAGTTATATTGATAACTGATCATCA-----------------------GTTATCAGGATGTCAATGCTTCTGTTAATTa Human > Gorilla --------------- chr8:49831197-49831205 Template switch process: F1: L CTACTATGAAAGAGAACACATTATCTTAGATGAGATTATCAGTTAT----AT 1 F3: 4 ATCATCAGTTATCAGGATGTCAATGCTTCTGTTAGTTAAAAAGGAAA R RF: CTACTATGAAAGAGAACACATTATCTTAGATGAGATTATCAGTTATCAGGATGTCAATGCTTCTGTTAGTTAAAAAGGAAA RR: GATGATACTTTCTCTTGTGTAATAGAATCTACTCTAATAGTCAATAGTCCTACAGTTACGAAGACAATCAATTTTTCCTTT F2: 3 GTCAATAGT 2 Unidirectional alignment (log-probability: -44) AAAGAGAACACATTATCTTAGATGAGATTATcagttatattgataactgatcatCAGTTATCAGGATGTCAATGCTTCTGTTAGTTAAA AAAGAGAACACATTATCTTAGATGAGATTAT-----------------------CAGTTATCAGGATGTCAATGCTTCTGTTAGTTAAA Template switch alignment (log-probability: -32.7) AAAGAGAACACATTATCTTAGATGAGATTATCAGTTAT----AT|TGATAACTG|ATcATCAGTTATCAGGATGTCAATGCTTCTGTTAGTTAAA AAAGAGAACACATTATCTTAGATGAGATTATCAGTTATCAGGAT|TGATAACTG|ATTATCAGTTATCAGGATGTCAATGCTTCTGTTAGTTAAA ========== Event 3641 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTGCTGTATAATTTTAATGTTTCTGTTT---TTACTTTCCTAAGCAGATAAGCGTAAAA Chimp: TTTTGCTGTATAATTTTAATGTTTCTGTTT---TTACTTTCCTAAGCAGATAAGTGTAAAA ↓ 3 1 2 4 Gorilla: TTTTGCTGTATAATTTTAATGTTTCTGTTAAACAGATACACCTAAGCAGATAAGTGTAAAA ↑ 3 1 2 4 Human: TTTTGCTGTATAATTTTAATGTTTCTGTTT---TTACTTTCCTAAGCAGATAAGCGTAAAA Cluster: [ ] Orangutan: TTTTGCTGTATAATTTTAATGTTTCTGTTT---TTACTTTCCTAAGCAGATAAGTGTAAAA Human > Gorilla --------------- chr8:6525411-6525421 Template switch process: F1: L CAAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTT 1 F3: 4 CCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC R RF: CAAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTTTTTACTTTCCTAAGCAGATAAGCGTAAAAACTTAGACTAATTGATTAC RR: GTTCGATCCTCAAAAACGACATATTAAAATTACAAAGACAAAAATGAAAGGATTCGTCTATTCGCATTTTTGAATCTGATTAACTAATG F2: 3 ACATAGACAAA 2 Unidirectional alignment (log-probability: -42.4) AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTG--------TTaaacagatacaCCTAAGCAGATAAGtGTAAAAACTTAGACTAATTGATTAC AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTTTTTACTTT-----------CCTAAGCAGATAAGCGTAAAAACTTAGACTAATTGATTAC Template switch alignment (log-probability: -28.2) AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTT|AAACAGAtACA|CCTAAGCAGATAAGtGTAAAAACTTAGACTAATTGATTAC AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTT|AAACAGAAACA|CCTAAGCAGATAAGCGTAAAAACTTAGACTAATTGATTAC Chimp > Gorilla --------------- chr8:6525411-6525421 Template switch process: F1: L CAAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTT 1 F3: 4 CCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC R RF: CAAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTTTTTACTTTCCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC RR: GTTCGATCCTCAAAAACGACATATTAAAATTACAAAGACAAAAATGAAAGGATTCGTCTATTCACATTTTTGAATCTGATTAACTAATG F2: 3 ACATAGACAAA 2 Unidirectional alignment (log-probability: -36.9) AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTG--------TTaaacagatacaCCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTTTTTACTTT-----------CCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC Template switch alignment (log-probability: -22.6) AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTT|AAACAGAtACA|CCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC AAGCTAGGAGTTTTTGCTGTATAATTTTAATGTTTCTGTT|AAACAGAAACA|CCTAAGCAGATAAGTGTAAAAACTTAGACTAATTGATTAC ========== Event 3642 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCCAGCACTATCCTGCTTGGTAGCTTAATTGCATGATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCA----------------------------------------------------------------------------------------------------------------------------CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGTCTTCTTAAGCTTTGTACAAA ↓ 3 4 2 1 Chimp: TCCAGCACTATCCTGCTTGGTAGCTTAATTGCATGATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCACAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGTAGCAACTTTGAGACTTGTGATTTAAATCAAAGGTACTACTGAAGAATGATTATGAATCATGCAATTAAGCTACCAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGTCTTCTTAAGCTTTGTACAAA ↑ 3 4 2 1 Gorilla: TCCAGCACTATCCTGCTTGGTAGCTTAATTGCATGATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCA----------------------------------------------------------------------------------------------------------------------------CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGTCTTCTTAAGCTTTGTACAAA Human: TCCAGCACTATCCTGCTTGGTAGCTTAATTGCATGATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCA----------------------------------------------------------------------------------------------------------------------------CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGTCTTCTTAAGCTTTGTACAAA Cluster: [ ] Orangutan: TCCACCAGTATCCTGCTTGGTAGCTTAATTGCATGATTCATAATCATTCTTCA---GTACCTTTGATTTAAATCA----------------------------------------------------------------------------------------------------------------------------CAAGTCTCAAAGTTACTACATTAATTATTGCTTTGAGAACAAGATGATTGTCTTCTTAAGCTTTGTACAAA Human > Chimp ------------- chr8:67884615-67884687 Template switch process: F1: L GATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCACAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT 1 F3: 4 CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAAC R RF: GTAGCTTAATTGCATGATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCACAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT RR: CATCGAATTAACGTACTAAGTATTAGTAAGAAGTCATCATGGAAACTAAATTTAGTGTTCAGAGTTTCAACGATGTAATTAATAACGAAACTCTTGTTCTACTAACA F2: 3 CATCGAATTAACGTACTAAGTATTAGTAAGAAGTCATCATGGAAACTAAATTTAGTGTTCAGAGTTTCAACGA 2 Unidirectional alignment (log-probability: -186) GTTGCTACATTAATTATTGCTTTGAGAACaagatgattgtagcaactttgagacttgtgatttaaatcaaaggtactactgaagaatgattatgaatcatgcaattaagctaccaagtctcaaagttgctacattaattattgctttgagaac GTTGCTACATTAATTATTGCTTTGAGAAC---------------------------------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -24.9) GTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT|AGCAACTTTGAGACTTGTGATTTAAATCAAAGGTACTACTGAAGAATGATTATGAATCATGCAATTAAGCTAC|CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAAC GTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT|AGCAACTTTGAGACTTGTGATTTAAATCAAAGGTACTACTGAAGAATGATTATGAATCATGCAATTAAGCTAC|CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAAC Gorilla > Chimp --------------- chr8:67884615-67884687 Template switch process: F1: L GATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCACAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT 1 F3: 4 CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAAC R RF: GTAGCTTAATTGCATGATTCATAATCATTCTTCAGTAGTACCTTTGATTTAAATCACAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT RR: CATCGAATTAACGTACTAAGTATTAGTAAGAAGTCATCATGGAAACTAAATTTAGTGTTCAGAGTTTCAACGATGTAATTAATAACGAAACTCTTGTTCTACTAACA F2: 3 CATCGAATTAACGTACTAAGTATTAGTAAGAAGTCATCATGGAAACTAAATTTAGTGTTCAGAGTTTCAACGA 2 Unidirectional alignment (log-probability: -186) GTTGCTACATTAATTATTGCTTTGAGAACaagatgattgtagcaactttgagacttgtgatttaaatcaaaggtactactgaagaatgattatgaatcatgcaattaagctaccaagtctcaaagttgctacattaattattgctttgagaac GTTGCTACATTAATTATTGCTTTGAGAAC---------------------------------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -25.9) GTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT|AGCAACTTTGAGACTTGTGATTTAAATCAAAGGTACTACTGAAGAATGATTATGAATCATGCAATTAAGCTAC|CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAAC GTTGCTACATTAATTATTGCTTTGAGAACAAGATGATTGT|AGCAACTTTGAGACTTGTGATTTAAATCAAAGGTACTACTGAAGAATGATTATGAATCATGCAATTAAGCTAC|CAAGTCTCAAAGTTGCTACATTAATTATTGCTTTGAGAAC ========== Event 3643 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGGGATAGGATAGCAAGTGT--------GCTGCTGTGGTGAGACCTCCGTTTCCTCCTGGAGATGGCAGCTGAGCTAGGCCTTCACCTGGGATGCC Chimp: GGAGGGATAGGATAGCAAGTGAGACCTCAGTTAGCTGTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAGCTAGGCCTTCACCTGGGATGCC ↑ 4 1 3 2 Gorilla: GGAGGGATAGGATAGCAAGTGT--------GCTGCAGTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAGCTAGGCCTTCACCTGCGATGCC Human: GGAGGGATAGGATAGCAAGTGT--------GCTGCTGTGGTGAGACCTCCGTTTCCTCCTGGAGATGGCAGCTGAGCTAGGCCTTCACCTGGGATGCC Cluster: [ ] Orangutan: GGAGGGATGGGATAGCAGGCGT--------GTTGCTGTGGGGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAGCTAGGCCTTCACCTGGGATGGC Gorilla > Chimp --------------- chr8:7263227-7263230 Template switch process: F1: L CAGTTGTGCTGCTGCGTCTTGGAGGGATAGGATAGCAA-------------GTGAGACCTCAGTT 1 F3: 4 GTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAG R RF: CAGTTGCGCTGCTGCGTCTTGGAGGGATAGGATAGCAAGTGTGCTGCAGTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAGCT RR: GTCAACGCGACGACGCAGAACCTCCCTATCCTATCGTTCACACGACGTCACCACTCTGGAGTCAAAGGAGGACCTCTACCGTCGACTCGA F2: 3 TCGA 2 Unidirectional alignment (log-probability: -46.6) TGCGTCTTGGAGGGATAGGATAGCAAGTGagacctcagttagcT------GTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAG TGCGTCTTGGAGGGATAGGATAGCAAGTG--------------TGCTGCAGTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAG Template switch alignment (log-probability: -32.4) TGCGTCTTGGAGGGATAGGATAGCAA-------------GTGAGACCTCAGTT|AGCT|GTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAG TGCGTCTTGGAGGGATAGGATAGCAAGTGTGCTGCAGTGGTGAGACCTCAGTT|AGCT|GTGGTGAGACCTCAGTTTCCTCCTGGAGATGGCAGCTGAG ========== Event 3644 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTGTCAACAAATTATTAgtg----tatgtgtgtgtgaatatata----------tatgtatata----------tatattcacatatatatgtgtatatatatgtgtgtatatatatgtatatatatatacacacatatatgaatatatatgtgta--tatatatTCACACACACATATCTCCTTCTTATCTTATGA Chimp: TTTGTCAACAAATTATTAGTG----TACGTGTGTGTGAatatata--------------------tacatatatata----------------------------------------------------------------------------cata--tatatatTCACACACACATATCTCCTTCTTATCTTATGA ↑ 1 4 3 2 Gorilla: TTTGTCAACAAATTATTAGTG--------TGTGTGTGAatatata------------------------------ta----------------------------------------------------------------------------tgta--tatatatTCACACACACATATCTCCTTCTTATCTTATGA Human: TTTGTCAACAAATTATTAgtg----tatgtgtgtgtgaatatata----------tatgtatata----------tatattcacatatatatgtgtatatatatgtgtgtatatatatgtatatatatatacacacatatatgaatatatatgtgta--tatatatTCACACACACATATCTCCTTCTTATCTTATGA Cluster: [ ] Orangutan: TTTGTCAACAAATTATTAgtgtatg----tgtgtgtgtatatatatatatacata--------------------ca----------------------------------------------------------------------------catatatatatacacacacacacatatCTCCTTCTTATCTTATGA Gorilla > Chimp --------------- chr8:69335125-69335146 Template switch process: F1: L ATTATAATTCAAAAGCTTTATTTGTCAACAAATTATTAGTGT 1 F3: 4 ATATATATACATATATATATT R RF: ATTATAATTCAAAAGCTTTATTTGTCAACAAATTATTAGTGTGTGTGTGAATATATATATGTATATATATTCACACACACAT RR: TAATATTAAGTTTTCGAAATAAACAGTTGTTTAATAATCACACACACACTTATATATATACATATATATAAGTGTGTGTGTA F2: 3 CATATATATAAGTGTGTGTGCA 2 Unidirectional alignment (log-probability: -51.6) TATAATTCAAAAGCTTTATTTGTCAACAAATTATTAGTgtacGTGTGTGTGAatatatatacATATATATAcaTATATATATT TATAATTCAAAAGCTTTATTTGTCAACAAATTATTAGT----GTGTGTGTGA----------ATATATATATGTATATATATT Template switch alignment (log-probability: -34.6) TATAATTCAAAAGCTTTATTTGTCAACAAATTATTAGTGT|AcGTGTGTGTGAATATATATAC|ATATATATAcaTATATATATT TATAATTCAAAAGCTTTATTTGTCAACAAATTATTAGTGT|ATGTGTGTGTGAATATATATAC|ATATATATATGTATATATATT ========== Event 3645 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTAGCAGAATAATTTGTAAGGGACATCTTTTA------AGTAGAAAGCTAAACAATTAATT ↓ 3 2 1 4 Chimp: GTTAGCAGAATAATTTGTAAGGGACATCTTTTGATGTCCCTTAGAAAGCTAAACAATTAATT Gorilla: GTTAGCAGAATAATTTGTAAGGGACATCTTTTG------AGTAGAAAGCTAAACAATTAATT Human: GTTAGCAGAATAATTTGTAAGGGACATCTTTTA------AGTAGAAAGCTAAACAATTAATT Cluster: [ ] Orangutan: ATTAGCAGAATAATTTGTAAGGGACATCTTTTG------AGTAGAAAGCTGAACAATTAATT Human > Chimp ------------- chr8:77406960-77406968 Template switch process: F1: L GCACTTAATGTTAGCAGAATAATTTGTAAGGGACATCTTTT 1 F3: 4 TAGAAAGCTAAACAATTAATTCTTCATGCGGTGACTACGG R RF: GCACTTAATGTTAGCAGAATAATTTGTAAGGGACATCTTTTAAGTAGAAAGCTAAACAATTAATTCTTCATGCGGTGACTACGG RR: CGTGAATTACAATCGTCTTATTAAACATTCCCTGTAGAAAATTCATCTTTCGATTTGTTAATTAAGAAGTACGCCACTGATGCC F2: 3 TCCCTGTAG 2 Unidirectional alignment (log-probability: -31.6) CACTTAATGTTAGCAGAATAATTTGTAAGGGACATCTTTTgAtgtccctTAGAAAGCTAAACAATTAATTCTTCATGCGGTGACTACGG CACTTAATGTTAGCAGAATAATTTGTAAGGGACATCTTTTAA------GTAGAAAGCTAAACAATTAATTCTTCATGCGGTGACTACGG Template switch alignment (log-probability: -16.4) CACTTAATGTTAGCAGAATAATTTGTAAGGGACATCTTTT|GATGTCCCT|TAGAAAGCTAAACAATTAATTCTTCATGCGGTGACTACGG CACTTAATGTTAGCAGAATAATTTGTAAGGGACATCTTTT|GATGTCCCT|TAGAAAGCTAAACAATTAATTCTTCATGCGGTGACTACGG ========== Event 3646 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GAACTCCACAATCCTGCTGCATTGAACAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAAAGAATAGAAGTAGATGCATT ↑ 1 4 3 2 Chimp: GAACTCCACAATCCTGCTGCAATG-TGAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAAAGAATAGAAGTAGATGCATT ↓ 1 4 3 2 Gorilla: GAACTCCACAATCCTGCTGCATTGAACAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAAAGAATAGAAGTAGATGCATT Human: GAACTCCACAATCCTGCTGCATTGAACAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAAAGAATAGAAGTAGATGCATT Cluster: [ ] Orangutan: GAACTCCACAATCCTGCTGCATTGAACAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAAAGAATAGAAGTAAATGCATT Chimp > Human ------------- chr8:76564881-76564887 Template switch process: F1: L CTAAACAACATCCAAGATATGAACTCCACAATCCTGCTGCA 1 F3: 4 ATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG R RF: CTAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCAATGTGAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAA RR: GATTTGTTATAGGTTCTATACTTGAGGTGTTAGGACGACGTTACACTTAAGGTCCCCTTAAGTGTAACAACATAAGATACACCTTCGTACGGGAATCTATAACATTTTTACACCAATACGTTATGGTCGGGATACACAAGTT F2: 3 ACAAGTT 2 Unidirectional alignment (log-probability: -36) TAAACAAcATCCAAGATATGAACTCCACAATCCTGCTGCA-----ttgaacAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG TAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCAATGTG------AATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG Template switch alignment (log-probability: -22.1) TAAACAAcATCCAAGATATGAACTCCACAATCCTGCTGCA|TTGAACA|ATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG TAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCA|TTGAACA|ATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG Chimp > Gorilla --------------- chr8:46851034-46851040 Template switch process: F1: L CTAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCA 1 F3: 4 ATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG R RF: CTAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCAATGTGAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAGCATGCCCTTAGATATTGTAAAAATGTGGTTATGCAATACCAGCCCTATGTGTTCAA RR: GATTTGTTATAGGTTCTATACTTGAGGTGTTAGGACGACGTTACACTTAAGGTCCCCTTAAGTGTAACAACATAAGATACACCTTCGTACGGGAATCTATAACATTTTTACACCAATACGTTATGGTCGGGATACACAAGTT F2: 3 ACAAGTT 2 Unidirectional alignment (log-probability: -29) TAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCAtTGaacAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG TAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCAATG-TGAATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG Template switch alignment (log-probability: -16.6) TAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCA|TTGAACA|ATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG TAAACAATATCCAAGATATGAACTCCACAATCCTGCTGCA|TTGAACA|ATTCCAGGGGAATTCACATTGTTGTATTCTATGTGGAAG ========== Event 3647 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTCTAAGCAAAACACCTTTGGAAGT--------ATCAAGTAATGGGTATTTAACATT ↓ 3 1 4 Chimp: GTTCTAAGCAAAACACCTTTGGAAGTTGATACTTCCAAAGTAATGGGCATTTAACATT ↑ 3 1 4 Gorilla: GTTCTAAGCAAAACACCTTTGGAAGT--------ATCAAGTAATGGGCATTTAACATT Human: GTTCTAAGCAAAACACCTTTGGAAGT--------ATCAAGTAATGGGTATTTAACATT Cluster: [ ] Orangutan: GTTCTAAGCAAAACACTTTTGGAAGT--------ATCAAGTAATGGGCATTTAACATT Human > Chimp ------------- chr8:77898588-77898598 Template switch process: F1: L CCTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT 1 F3: 4 AAGTAATGGGCATTTAACATTTTTCGGTATTAAAATTTAG R RF: CCTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGTATCAAGTAATGGGTATTTAACATTTTTCGGTATTAAAATTTAG RR: GGAAGTGTCTCCTACCAAGATTCGTTTTGTGGAAACCTTCATAGTTCATTACCCATAAATTGTAAAAAGCCATAATTTTAAATC F2: 3 ACCTTCATAGT 2 Unidirectional alignment (log-probability: -41.6) CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGTtgatacttccA--AAGTAATGGGcATTTAACATTTTTCGGTATTAAAATTTAG CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT----------ATCAAGTAATGGGTATTTAACATTTTTCGGTATTAAAATTTAG Template switch alignment (log-probability: -22.6) CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT|TGATACTTCCA|AAGTAATGGGcATTTAACATTTTTCGGTATTAAAATTTAG CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT|TGATACTTCCA|AAGTAATGGGTATTTAACATTTTTCGGTATTAAAATTTAG Gorilla > Chimp --------------- chr8:77898588-77898598 Template switch process: F1: L CCTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT 1 F3: 4 AAGTAATGGGCATTTAACATTTTTCGGTATTAAAATTTAG R RF: CCTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGTATCAAGTAATGGGCATTTAACATTTTTCAGTATTAAAATTTAG RR: GGAAGTGTCTCCTACCAAGATTCGTTTTGTGGAAACCTTCATAGTTCATTACCCGTAAATTGTAAAAAGTCATAATTTTAAATC F2: 3 ACCTTCATAGT 2 Unidirectional alignment (log-probability: -40.6) CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGTtgatacttccA--AAGTAATGGGCATTTAACATTTTTCgGTATTAAAATTTAG CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT----------ATCAAGTAATGGGCATTTAACATTTTTCAGTATTAAAATTTAG Template switch alignment (log-probability: -22.6) CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT|TGATACTTCCA|AAGTAATGGGCATTTAACATTTTTCgGTATTAAAATTTAG CTTCACAGAGGATGGTTCTAAGCAAAACACCTTTGGAAGT|TGATACTTCCA|AAGTAATGGGCATTTAACATTTTTCAGTATTAAAATTTAG ========== Event 3648 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTAAGATAGTCAGCTTGTTAA-----TGGCTAAGAATTTAAGGATTGAAA ↓ 31 4 2 Chimp: TTTAAGACAGTCAGCTTGTTAGCCATTAGGCTAAGAATTTAAGGATTGAAA ↑ 31 4 2 Gorilla: TTTAAGATAGTCAGCTTGTTAA-----TGGCTAAGAATTTAAGGATTGAAA Human: TTTAAGATAGTCAGCTTGTTAA-----TGGCTAAGAATTTAAGGATTGAAA Cluster: [ ] Orangutan: Human > Chimp ------------- chr8:72966587-72966593 Template switch process: F1: L GTTCTTTGACTGGTTTAGCTTTTAAGACAGTCAGCTTGTTA 1 F3: 4 GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA R RF: GTTCTTTGACTGGTTTAGCTTTTAAGATAGTCAGCTTGTTAATGGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA RR: CAAGAAACTGACCAAATCGAAAATTCTATCAGTCGAACAATTACCGATTCTTAAATTCCTAACTTTTACTTACATTCTTTTAT F2: 3 ATTACCG 2 Unidirectional alignment (log-probability: -34.3) TTCTTTGACTGGTTTAGCTTTTAAGAcAGTCAGCTTGTTAgccATtaGGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA TTCTTTGACTGGTTTAGCTTTTAAGATAGTCAGCTTGTTA---AT--GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA Template switch alignment (log-probability: -22.1) TTCTTTGACTGGTTTAGCTTTTAAGAcAGTCAGCTTGTTA|GCCATTA|GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA TTCTTTGACTGGTTTAGCTTTTAAGATAGTCAGCTTGTTA|GCCATTA|GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA Gorilla > Chimp --------------- chr8:72966587-72966593 Template switch process: F1: L GTTCTTTGACTGGTTTAGCTTTTAAGACAGTCAGCTTGTTA 1 F3: 4 GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA R RF: GTTCTTTGACTGGTTTAGCTTTTAAGATAGTCAGCTTGTTAATGGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA RR: CAAGAAACTGACCAAATCGAAAATTCTATCAGTCGAACAATTACCGATTCTTAAATTCCTAACTTTTACTTACATTCTTTTAT F2: 3 ATTACCG 2 Unidirectional alignment (log-probability: -33.4) TTCTTTGACTGGTTTAGCTTTTAAGAcAGTCAGCTTGTTAgccATtaGGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA TTCTTTGACTGGTTTAGCTTTTAAGATAGTCAGCTTGTTA---AT--GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA Template switch alignment (log-probability: -22.1) TTCTTTGACTGGTTTAGCTTTTAAGAcAGTCAGCTTGTTA|GCCATTA|GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA TTCTTTGACTGGTTTAGCTTTTAAGATAGTCAGCTTGTTA|GCCATTA|GGCTAAGAATTTAAGGATTGAAAATGAATGTAAGAAAATA ========== Event 3649 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ---tgagcccaggagttcaaggctgcagtgagctatgatcgtgccactgtactccaggctgggcggagagcaagaccttgtctccaaaaaagataaaaTTGTAATAAACACATATCACAAAGAA----------------------------ACTGACTAGACCCCATGGCCCTGGT ↓ 3 2 4 1 Chimp: ---tgagcccaggagttcaaggctgcagtgagctatgatcgtgccactgtactccaggctgggcggagagcaagcccttgtctccaaaaaagataaaaTTGTAATAAACACATATCATAAAGAA--------------ACTGAGCAGCCTAAACTGACTAGACCCCATGGCCCTGGT Gorilla: ---tgagcccaggagttcaaggctgcagtgagctatgatcgtgccactgtactccaggctgggcggagagcaagaccttgtctccaaaaaagataaaaTTGTAATAAACACATATCATAAAGAAACTGAGCAGCCTAA--------------ACTGACTAGACCCCATGGCCCTGGT ↑ 3 2 4 1 Human: ---tgagcccaggagttcaaggctgcagtgagctatgatcgtgccactgtactccaggctgggcggagagcaagaccttgtctccaaaaaagataaaaTTGTAATAAACACATATCACAAAGAA----------------------------ACTGACTAGACCCCATGGCCCTGGT Cluster: [ ] Orangutan: tgctgagctcaggagttcaaggctgcagtgagctatgatcgtgccactgtactccaggctgggtggagagcaagaccttgtctccaagaaagataaaaTTGTAATAAACACATATCATA----AACTGAGCAGCCTAA--------------ACTGACTAGACCCCATGGCCCTGGT Human > Chimp ------------- chr8:76530062-76530068 Template switch process: F1: L CTTGTCTCCAAAAAAGATAAAATTGTAATAAACACATATCATAAAGAAACTGA 1 F3: 4 AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATGAA R RF: AGGCTGCAGTGAGCTATGATCGTGCCACTGTACTCCAGGCTGGGCGGAGAGCAAGACCTTGTCTCCAAAAAAGATAAAATTGTAATAAACACATATCACAAAGAAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATGAA RR: TCCGACGTCACTCGATACTAGCACGGTGACATGAGGTCCGACCCGCCTCTCGTTCTGGAACAGAGGTTTTTTCTATTTTAACATTATTTGTGTATAGTGTTTCTTTGACTGATCTGGGGTACCGGGACCAGGGTCCATACTACTT F2: 3 TCCGACG 2 Unidirectional alignment (log-probability: -37.1) AAGATAAAATTGTAATAAACACATATCAtAAAGAAACTGagcagcctaaactgACTAGACCCCATGGCCCTGGTCCCAGGTATGATG AAGATAAAATTGTAATAAACACATATCACAAAGAAACTG--------------ACTAGACCCCATGGCCCTGGTCCCAGGTATGATG Template switch alignment (log-probability: -22.4) AAGATAAAATTGTAATAAACACATATCAtAAAGAAACTGA|GCAGCCT|AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATG AAGATAAAATTGTAATAAACACATATCACAAAGAAACTGA|GCAGCCT|AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATG Human > Gorilla --------------- chr8:45239639-45239645 Template switch process: F1: L CTTGTCTCCAAAAAAGATAAAATTGTAATAAACACATATCATAAAGAAACTGA 1 F3: 4 AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATGAA R RF: AGGCTGCAGTGAGCTATGATCGTGCCACTGTACTCCAGGCTGGGCGGAGAGCAAGACCTTGTCTCCAAAAAAGATAAAATTGTAATAAACACATATCACAAAGAAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATGAA RR: TCCGACGTCACTCGATACTAGCACGGTGACATGAGGTCCGACCCGCCTCTCGTTCTGGAACAGAGGTTTTTTCTATTTTAACATTATTTGTGTATAGTGTTTCTTTGACTGATCTGGGGTACCGGGACCAGGGTCCATACTACTT F2: 3 TCCGACG 2 Unidirectional alignment (log-probability: -36.6) AAGATAAAATTGTAATAAACACATATCAtAAAGaaactgagcagcctAAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATG AAGATAAAATTGTAATAAACACATATCACAAAG--------------AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATG Template switch alignment (log-probability: -22.5) AAGATAAAATTGTAATAAACACATATCAtAAAGAAACTGA|GCAGCCT|AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATG AAGATAAAATTGTAATAAACACATATCACAAAGAAACTGA|GCAGCCT|AAACTGACTAGACCCCATGGCCCTGGTCCCAGGTATGATG ========== Event 3650 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTGGAATCCTATCTCTGATCAGAAGAGGTATAAAATGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGGACAGCTAGAATCATCCTCCAGCAGAA Chimp: ATTGGAATCCTATCTCTGATCAGAAGAGGTATAAAATGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGGACAGCTAGAATCATTCTCCAGCAGAA ↓ 1 4 3 2 Gorilla: ATTGGAATCCTATCTCTGATC----AAGC-----TGTGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGGACAGCTAGAATCATTCTCCAGCAGAA Human: ATTGGAATCCTATCTCTGATCAGAAGAGGTATAAAATGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGGACAGCTAGAATCATCCTCCAGCAGAA Cluster: [ ] Orangutan: ATTGGAATCCTATCTCTGATC----AAGC-----TGTGGCTCAGAAGAGGTATAAAAGAGTCATTCCTACCACAGGACAGTTAGAATCATTCTCCAGCAGAA Chimp > Gorilla --------------- chr8:44957994-44957998 Template switch process: F1: L AAGATAATGAAATGTGAGACATTGGAATCCTATCTCTGATCA 1 F3: 4 TGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGG R RF: AAGATAATGAAATGTGAGACATTGGAATCCTATCTCTGATCAGAAGAGGTATAAAATGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGGACAGCT RR: TTCTATTACTTTACACTCTGTAACCTTAGGATAGAGACTAGTCTTCTCCATATTTTACCGAGTCTTCTCCATATTTTCTCGGTAAGGATGGTGTCCTGTCGA F2: 3 GTCGA 2 Unidirectional alignment (log-probability: -27.1) GATAATGAAATGTGAGACATTGGAATCCTATCTCTGATC-------------AAgctgTGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGG GATAATGAAATGTGAGACATTGGAATCCTATCTCTGATCAGAAGAGGTATAAAA----TGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGG Template switch alignment (log-probability: -16.4) GATAATGAAATGTGAGACATTGGAATCCTATCTCTGATCA|AGCTG|TGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGG GATAATGAAATGTGAGACATTGGAATCCTATCTCTGATCA|AGCTG|TGGCTCAGAAGAGGTATAAAAGAGCCATTCCTACCACAGG ========== Event 3651 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCGTAGCTACCCTGGCCTCAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCT Chimp: ATCGTAGCTACCCTGGCCTCAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCT ↓ 3 2 1 4 Gorilla: ATCGTAGCTACCCTGGCCTCAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGACTGGGAGTTCAATTACCTACTTCC ↑ 3 2 1 4 Human: ATCGTAGCTACCCTGGCCTCAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCT Cluster: [ ] Orangutan: ATCGTAGCTACCCTGGCCTCAATCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAGTTACTTACTTCT Human > Gorilla --------------- chr8:44118370-44118373 Template switch process: F1: L CAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCG 1 F3: 4 GGAGTTCAATTACCTACTTCCGTTTAGGGAGAGTAGTCTT R RF: CAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCTGTTTAGGGAGAGTAGTCTT RR: GTCAGGTTACAGTAACATGTACACCACTCTCGAAGGAGAGCCGATCCTCAAGTTAATGGATGAAGACAAATCCCTCTCATCAGAA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -35.9) AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGaCTgGGAGTTCAATTACCTACTTCcGTTTAGGGAGAgtagtctt AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCTGTTTAGGGAGA-------- Template switch alignment (log-probability: -21.7) AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCG|ACTG|GGAGTTCAATTACCTACTTCcGTTTAGGGAGAGTAGTCTT AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCG|ACTG|GGAGTTCAATTACCTACTTCTGTTTAGGGAGAGTAGTCTT Chimp > Gorilla --------------- chr8:44118370-44118373 Template switch process: F1: L CAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCG 1 F3: 4 GGAGTTCAATTACCTACTTCCGTTTAGGGAGAGTAGTCTT R RF: CAGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCTGTTTAGGGAGAGTAGTCTT RR: GTCAGGTTACAGTAACATGTACACCACTCTCGAAGGAGAGCCGATCCTCAAGTTAATGGATGAAGACAAATCCCTCTCATCAGAA F2: 3 GTCA 2 Unidirectional alignment (log-probability: -35.9) AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGaCTgGGAGTTCAATTACCTACTTCcGTTTAGGGAGAgtagtctt AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCGGCTAGGAGTTCAATTACCTACTTCTGTTTAGGGAGA-------- Template switch alignment (log-probability: -21.7) AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCG|ACTG|GGAGTTCAATTACCTACTTCcGTTTAGGGAGAGTAGTCTT AGTCCAATGTCATTGTACATGTGGTGAGAGCTTCCTCTCG|ACTG|GGAGTTCAATTACCTACTTCTGTTTAGGGAGAGTAGTCTT ========== Event 3652 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AAAACTGCTTCTGATTGTAGTTTACATTCATGGTGTTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTGCCGAGGATTTGAGATCAGCCTTGCCTATAAAATAAACTATACCATGAATTTCTTTTCAGAATACTTTAT ↑ 4 1 3 2 Chimp: AAAACTGCTTCTGATTGTAGT---------------TTATTTCCAGGCATTAATACTAATAGACAGTTTTACTGCCGAGGATTTGAGATCAGCCTTGCCTATAAAATATACTATACCATGAATTTCTTTTCAGAATACTTTAT Gorilla: AAAACTGCTTCTGATTGTAGTTTACATTCATGGTGTTTATTTCCAGGCATTAATATTAATAGACAGTTTTACTGCCGAGGATTTGAGATCAGCCTTGCCTATAAAATATACTATACCATGAATTTCTTTTCAGAATACTTTAT Human: AAAACTGCTTCTGATTGTAGTTTACATTCATGGTGTTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTGCCGAGGATTTGAGATCAGCCTTGCCTATAAAATAAACTATACCATGAATTTCTTTTCAGAATACTTTAT Cluster: [ ] Orangutan: AAAACTGCTTCTGATTGTAGTTTACATTCATGGTGTATATTTCCAGGCATTAATACTAATAGACAGTTTTACTGCAGAGTATTTGAGATCAGCCTTGCCTGTAAAATATACTATACCATGAATTTCTTTTCAGAATACTTTAA Chimp > Human ------------- chr8:71647557-71647565 Template switch process: F1: L ATTCAACATTTACATGTGTTAAAACTGCTTCTGATTGTAGTTTAC 1 F3: 4 GTTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTGCC R RF: ATCCAACATTTACATGTGTTAAAACTGCTTCTGATTGTAGTTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTGCCGAGGATTTGAGATCAGCCTTGCCTATAAAATATACTATACCATGAAT RR: TAGGTTGTAAATGTACACAATTTTGACGAAGACTAACATCAAATAAAGGTCCGTAATTATGATTATCTGTCAAAATGACGGCTCCTAAACTCTAGTCGGAACGGATATTTTATATGATATGGTACTTA F2: 3 TGGTACTTA 2 Unidirectional alignment (log-probability: -38.5) ACATTTACATGTGTTAAAACTGCTTCTGATTGTAGTttacattcatggtgtTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTG ACATTTACATGTGTTAAAACTGCTTCTGATTGTAGT---------------TTATTTCCAGGCATTAATACTAATAGACAGTTTTACTG Template switch alignment (log-probability: -28.5) ACATTTACATGTGTTAAAACTGCTTCTGATTGTAGTTTAc|ATTCATGGT|GTTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTG ACATTTACATGTGTTAAAACTGCTTCTGATTGTAGTTTAT|ATTCATGGT|GTTTATTTCCAGGCATTAATACTAATAGACAGTTTTACTG ========== Event 3653 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTAAATGCTTTAAAAATATATTGAAT----------------GGCAGCCACATGTTTTGCATGATATTATTTCTATTCTACTAAC Chimp: TTAAATGCTTTAAAAATATATTGAATATCATGCAAAACATTGAACAGCCACATGTTTTGCATGATATTATTTCCATTCTACTAAC ↑ 4 1 3 2 Gorilla: TTAAATGCTTTAAAAATATATTGAAT----------------GGCAGCCACATGTTTTGCATGATATTATTTCTATTCTACTAAC Human: TTAAATGCTTTAAAAATATATTGAAT----------------GGCAGCCACATGTTTTGCATGATATTATTTCTATTCTACTAAC Cluster: [ ] Orangutan: TTAGATGCTTTAAAAATATATTGAAT----------------GGCAGCCACATGTTTTGCATGATATTATTTCTATTCTACTAAC Gorilla > Chimp --------------- chr8:75708636-75708647 Template switch process: F1: L TAACTGATCCTAAAATTAAATGCTTTAAAAATATATTGAAT 1 F3: 4 ATTGAA---CAGCCACATGTTTTGCATGATATTATTTCCATTCTACTAA R RF: TAACTGATCCTAAAATTAAATGCTTTAAAAATATATTGAATGGCAGCCACATGTTTTGCATGATATTATTTCTATTCTACTAA RR: ATTGACTAGGATTTTAATTTACGAAATTTTTATATAACTTACCGTCGGTGTACAAAACGTACTATAATAAAGATAAGATGATT F2: 3 CAAAACGTACTA 2 Unidirectional alignment (log-probability: -50.5) AACTGATCCTAAAATTAAATGCTTTAAAAATATATTGAATatcatgcaaaacattgaaCAGCCACATGTTTTGCATGATATTATTTCcATTC AACTGATCCTAAAATTAAATGCTTTAAAAATATATTGAAT----------------GGCAGCCACATGTTTTGCATGATATTATTTCTATTC Template switch alignment (log-probability: -32.8) AACTGATCCTAAAATTAAATGCTTTAAAAATATATTGAAT|ATCATGCAAAAC|ATTGAA---CAGCCACATGTTTTGCATGATATTATTTCcATTC AACTGATCCTAAAATTAAATGCTTTAAAAATATATTGAAT|ATCATGCAAAAC|ATTGAATGGCAGCCACATGTTTTGCATGATATTATTTCTATTC ========== Event 3654 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTACACTTATGTTCTGAAGGAGG-----------CATTATGGTGGGACAAATATTAACAAAGCATGatt Chimp: TTACACTTATGTTCTGAAGGAGG-----------CATTATGGTGGGACAAATATTAACAAAGCATGATT Gorilla: TTACACTTATGTTCTGAAGGACACATTTGTCCCACATTATGGTGGGACAAATATTAACAAAGCATGATT ↑ 4 1 3 2 Human: TTACACTTATGTTCTGAAGGAGG-----------CATTATGGTGGGACAAATATTAACAAAGCATGatt Cluster: [ ] Orangutan: TTACACTTATGTTCTGAAGGAGG-----------CATTATGGTGGGACAAATATTAACAAAGCATGATT Human > Gorilla --------------- chr8:49298833-49298839 Template switch process: F1: L ATTTAAGAGTTCATATAAAGTTACACTTATGTTCTGAAGGACACATT 1 F3: 4 CATTATGGTGGGACAAATATTAACAAAGCATGATTTAAAT R RF: ATTTAAGAGTTCATATAAAGTTACACTTATGTTCTGAAGGAGGCATTATGGTGGGACAAATATTAACAAAGCATGATTTAAAT RR: TAAATTCTCAAGTATATTTCAATGTGAATACAAGACTTCCTCCGTAATACCACCCTGTTTATAATTGTTTCGTACTAAATTTA F2: 3 ACCCTGT 2 Unidirectional alignment (log-probability: -37.8) AGTTCATATAAAGTTACACTTATGTTCTGAAGGAcacatttgtcccaCATTATGGTGGGACAAATATTAACAAAGCATGATTTAAAT AGTTCATATAAAGTTACACTTATGTTCTGAAGGA-----------GGCATTATGGTGGGACAAATATTAACAAAGCATGATTTAAAT Template switch alignment (log-probability: -27.8) AGTTCATATAAAGTTACACTTATGTTCTGAAGGAcaCATT|TGTCCCA|CATTATGGTGGGACAAATATTAACAAAGCATGATTTAAAT AGTTCATATAAAGTTACACTTATGTTCTGAAGGAGGCATT|TGTCCCA|CATTATGGTGGGACAAATATTAACAAAGCATGATTTAAAT ========== Event 3655 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: taaagtatccagcatgcagatactcacaataaatagttaataTACTTGGTTAGAGGTTAG--------------------------------------------------------------------------------------GTAGACTAGAAGATGCTAAATTGGAAACGGGACAGACCAT ↓ 4 3 1 2 Chimp: taaagtatccagcatgcagatactcacaataaatagttaataTACTTGGTTAGAGGTTAGGTAGACTATTTAGCATCTTCTAGTCTACCTAACCTCTAACCAAGTATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTAGAAGATGCTAAATTGGAAACGGGACAGACCAT ↑ 4 3 1 2 Gorilla: taaagcatccagcatgcagatactcacaataaatagttaataTACTTGGTTAGAGGTTAG--------------------------------------------------------------------------------------GTAGACTAGAAGATGCTAAATTGGAAATGGGACAGACCAT Human: taaagtatccagcatgcagatactcacaataaatagttaataTACTTGGTTAGAGGTTAG--------------------------------------------------------------------------------------GTAGACTAGAAGATGCTAAATTGGAAACGGGACAGACCAT Cluster: [ ] Orangutan: taaagtatccagcatgcagatactcacaataaatagttaataTACTTGGTTAGAGGTTAG--------------------------------------------------------------------------------------GTAGACTAGAAGATGCTAAATTGGAAATGGGACAGACCAT Human > Chimp ------------- chr8:70820803-70820839 Template switch process: F1: L ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTA 1 F3: 4 ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTAGAAGATGCTAAATTGGAAACGGGACAGACCAT R RF: ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTAGAAGATGCTAAATTGGAAACGGGACAGACCAT RR: TATGAGTGTTATTTATCAATTATATGAACCAATCTCCAATCCATCTGATCTTCTACGATTTAACCTTTGCCCTGTCTGGTA F2: 3 TGAACCAATCTCCAATCCATCTGATCTTCTACGATTT 2 Unidirectional alignment (log-probability: -129) ataaatagttaatatacttggttagaggttaggtagactatttagcatcttctagtctacctaacctctaaccaagtATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA -----------------------------------------------------------------------------ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA Template switch alignment (log-probability: -20.6) ATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTA|TTTAGCATCTTCTAGTCTACCTAACCTCTAACCAAGT|ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA ATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTA|TTTAGCATCTTCTAGTCTACCTAACCTCTAACCAAGT|ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA Gorilla > Chimp --------------- chr8:70820803-70820839 Template switch process: F1: L ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTA 1 F3: 4 ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTAGAAGATGCTAAATTGGAAACGGGACAGACCAT R RF: ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTAGAAGATGCTAAATTGGAAATGGGACAGACCAT RR: TATGAGTGTTATTTATCAATTATATGAACCAATCTCCAATCCATCTGATCTTCTACGATTTAACCTTTACCCTGTCTGGTA F2: 3 TGAACCAATCTCCAATCCATCTGATCTTCTACGATTT 2 Unidirectional alignment (log-probability: -135) ataaatagttaatatacttggttagaggttaggtagactatttagcatcttctagtctacctaacctctaaccaagtATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA -----------------------------------------------------------------------------ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA Template switch alignment (log-probability: -27) ATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTA|TTTAGCATCTTCTAGTCTACCTAACCTCTAACCAAGT|ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA ATAAATAGTTAATATACTTGGTTAGAGGTTAGGTAGACTA|TTTAGCATCTTCTAGTCTACCTAACCTCTAACCAAGT|ATACTCACAATAAATAGTTAATATACTTGGTTAGAGGTTA ========== Event 3656 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAGTTTCTCAGCCC-CCAAAAAGAGAAAAGGGTCATTGACAGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAACTGGAGAAAATGTAGAAGTGAGGTTTTTATTGTGGGAAATTAAGGGAA-AAAATGTATTCTACTTTTCTTATGTCTTTAGTTAAAATTATTTTTATT ↓ 1 4 3 2 Chimp: CCAGTTTCTCAGCCC-CCAAAGAGAGAAAAAAGACA----TAGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAACTGGAGAAAATGTGGAAGTGACGT-TTTATCGTGGGAAATTAAGGGAA-AAAATGTATTCTACTTTTCTTATGTCTTTAGTTAAAATTATTTTTATT Gorilla: CCAGTTTCTCAGCCC-CCAAAAAGAGAAAAGGGTCATTGACAGGTATCATTACATTTCCTATGTCACTGTTTCTTGAAAACTGGAGAAAATGTAGAAGTGAGGTTTTTATTGTGGGAAATTAAGGGA--AAAATGTATTCTACTTTTCTCATGTCTTTAGTT-GAATTATTTTTATT Human: CCAGTTTCTCAGCCC-CCAAAAAGAGAAAAGGGTCATTGACAGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAACTGGAGAAAATGTAGAAGTGAGGTTTTTATTGTGGGAAATTAAGGGAA-AAAATGTATTCTACTTTTCTTATGTCTTTAGTTAAAATTATTTTTATT Cluster: [ ] Orangutan: CCAGTTTCTCAGCCCCCCAGGAAGAGAAAAGGGTCATTGACAGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAACTGGAGAAAATGTGGAAGTGAGGTTTTTATTGTGGGAAATTAAGGGAAAAAAATGTATTCTACT-TTCTTGTATCTTTAATTAAAATTATTTTTATT Human > Chimp ------------- chr8:69476884-69476890 Template switch process: F1: L ATGTTCTTCAGCAATAATGAGCCAGTTTCTCAGCCCCCAAAGAGAGAAAA 1 F3: 4 AGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAAC R RF: ATGTTCTTCAGCAATAATGAGCCAGTTTCTCAGCCCCCAAAAAGAGAAAAGGGTCATTGACAGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAACTGGAGAAAATGTAGAAGTGAGGTTTTTATTGTGGGAAATTAAGGGAAAAAATGTATTCTACTTTTCTTATGTCTT RR: TACAAGAAGTCGTTATTACTCGGTCAAAGAGTCGGGGGTTTTTCTCTTTTCCCAGTAACTGTCCATAGTAATCTAAAGGATACAGTGACAAAGAACTTTTGACCTCTTTTACATCTTCACTCCAAAAATAACACCCTTTAATTCCCTTTTTTACATAAGATGAAAAGAATACAGAA F2: 3 TACAGAA 2 Unidirectional alignment (log-probability: -35.2) GCAATAATGAGCCAGTTTCTCAGCCCCCAAAgAGAGAAAAaaGaCAT----AGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAAC GCAATAATGAGCCAGTTTCTCAGCCCCCAAAAAGAGAAAAGGGTCATTGACAGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAAC Template switch alignment (log-probability: -22.3) GCAATAATGAGCCAGTTTCTCAGCCCCCAAAgAGAGAAAA|AAGACAT|AGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAAC GCAATAATGAGCCAGTTTCTCAGCCCCCAAAAAGAGAAAA|AAGACAT|AGGTATCATTAGATTTCCTATGTCACTGTTTCTTGAAAAC ========== Event 3657 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: tacaAATCATACAATTGTAATGTACAAAAT-----------------------------------------------------------------------------------------------------------------ACATATTTTGTACATTACAATTTCCTGACAGTGATGCTA Chimp: tacaaattatacaattgtaATGTACAAAAT-----------------------------------------------------------------------------------------------------------------ACATATTTTGTACATTACAATTTCCTGACAGTGATGCTA ↑ 3 42 1 Gorilla: tacaaattATACAATTGTAATGTACAAAAT---------------------------------------------------------------------------------------------------------------------------------ACAATTTCCTGACAGTGATGCTA ↓ 3 42 1 Human: tacaAATCATACAATTGTAATGTACAAAAT-----------------------------------------------------------------------------------------------------------------ACATATTTTGTACATTACAATTTCCTGACAGTGATGCTA Cluster: [ ] Orangutan: tacaaattgtacaaTTATAATGTACAAAATACATATTTTGTATCCTGGAAAACTACACCAGTCATTCCTTTGAAAAACTATCCCTGAGCTGCATAAATCTATTTTATGTTAAAATATGCTGCAAAATACATATTTTTTACATT----------------ACAATTTCCTGACAGTGATGCTA Gorilla > Human --------------- chr8:67993877-67993888 Template switch process: F1: L GTACATAATTGTACAAATCATACAATTGTAATGTACAAAATACA 1 F3: 4 TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTGG R RF: GTACATAATTGTACAAATTATACAATTGTAATGTACAAAATACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTGG RR: CATGTATTAACATGTTTAATATGTTAACATTACATGTTTTATGTTAAAGGACTGTCACTACGATTGTATTAAAAGAAAACC F2: 3 TACATGTTTTAT 2 Unidirectional alignment (log-probability: -39.4) ATAATTGTACAAATcATACAATTGTAATGTACAAAAtacatattttgtacatTACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG ATAATTGTACAAATTATACAATTGTAATGTACAAAA----------------TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG Template switch alignment (log-probability: -22.9) ATAATTGTACAAATcATACAATTGTAATGTACAAAATACA|TATTTTGTACAT|TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG ATAATTGTACAAATTATACAATTGTAATGTACAAAATACA|TATTTTGTACAT|TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG Gorilla > Chimp --------------- chr8:69484469-69484480 Template switch process: F1: L GTACATAATTGTACAAATTATACAATTGTAATGTACAAAATACA 1 F3: 4 TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTGG R RF: GTACATAATTGTACAAATTATACAATTGTAATGTACAAAATACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTGG RR: CATGTATTAACATGTTTAATATGTTAACATTACATGTTTTATGTTAAAGGACTGTCACTACGATTGTATTAAAAGAAAACC F2: 3 TACATGTTTTAT 2 Unidirectional alignment (log-probability: -33.9) ATAATTGTACAAATTATACAATTGTAATGTACAAAAtacatattttgtacatTACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG ATAATTGTACAAATTATACAATTGTAATGTACAAAA----------------TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG Template switch alignment (log-probability: -17.4) ATAATTGTACAAATTATACAATTGTAATGTACAAAATACA|TATTTTGTACAT|TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG ATAATTGTACAAATTATACAATTGTAATGTACAAAATACA|TATTTTGTACAT|TACAATTTCCTGACAGTGATGCTAACATAATTTTCTTTTG ========== Event 3658 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGTGGTTGCGGGCATTGTGGGC---------------TATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGACCGTCTTCAC Chimp: TGGTGGTCGTGGGCATTGTGGGC---------------TATGTGGGAACCCCTCGAGACCTCTGGACCTTCAAGACCGTCTTCAC Gorilla: TGGTGGTTGCGGGCATTGTGGAC------------------------------ATAGCCCTCTGAACCTTCAAGACCGTCTTCAC ↑ 13 2 4 Human: TGGTGGTTGCGGGCATTGTGGGC---------------TATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGACCGTCTTCAC Cluster: [ ] Orangutan: TGGTGGTTGCGGGCATTGTGGGCTATGTGGGAACCCCT---------------CGAGGCCTCTGGACCTTCAAGACCGCCTTCAC Human > Gorilla --------------- chr8:35569648-35569654 Template switch process: F1: L GACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGG 1 F3: 4 CCTCTGAACCTTCAAGACCGTCTTCACTGAGCACATCAGTGATGAGT R RF: GACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGGGCTATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGACCGTCTTCACTGAGCACATCAGTGATGAGT RR: CTGGTAACACCTCTATTGGTACCACCAACGCCCGTAACACCCGATACACCCTTGGGGAGCTCCGGAGACCTGGAAGTTCTGGCAGAAGTGACTCGTGTAGTCACTACTCA F2: 3 CGATACA 2 Unidirectional alignment (log-probability: -34.5) ACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGGacataGC--------------------CCTCTGaACCTTCAAGACCGTCTTCACTGAGCACATCAGT ACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGG-----GCTATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGACCGTCTTCACTGAGCACATCAGT Template switch alignment (log-probability: -22.3) ACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGG|ACATAGC|CCTCTGaACCTTCAAGACCGTCTTCACTGAGCACATCAGT ACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGG|ACATAGC|CCTCTGGACCTTCAAGACCGTCTTCACTGAGCACATCAGT ========== Event 3659 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGGAGATAACCATGGTGGTTGCGGGCATTGTGGGC---------------TATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGACCGT Chimp: TGTGGAGATAACCATGGTGGTCGTGGGCATTGTGGGC---------------TATGTGGGAACCCCTCGAGACCTCTGGACCTTCAAGACCGT ↓ 13 2 4 Gorilla: TGTGGAGATAACCATGGTGGTTGCGGGCATTGTGGAC------------------------------ATAGCCCTCTGAACCTTCAAGACCGT Human: TGTGGAGATAACCATGGTGGTTGCGGGCATTGTGGGC---------------TATGTGGGAACCCCTCGAGGCCTCTGGACCTTCAAGACCGT Cluster: [ ] Orangutan: TGTGGAGACAACCATGGTGGTTGCGGGCATTGTGGGCTATGTGGGAACCCCT---------------CGAGGCCTCTGGACCTTCAAGACCGC Chimp > Gorilla --------------- chr8:35569648-35569654 Template switch process: F1: L GTGGTAGAGGCTGTGACCATTGTGGAGATAACCATGGTGGTTGCGGGCATTGTGG 1 F3: 4 CCTCTGA R RF: GTGGTAGAGGCTGTGACCATTGTGGAGATAACCATGGTGGTCGTGGGCATTGTGGGCTATGTGGGAACCCCTCGAGACCTCTGG RR: CACCATCTCCGACACTGGTAACACCTCTATTGGTACCACCAGCACCCGTAACACCCGATACACCCTTGGGGAGCTCTGGAGACC F2: 3 CGATACA 2 Unidirectional alignment (log-probability: -45.2) ACCATTGTGGAGATAACCATGGTGGTtGcGGGCATTGTGGacataGC--------------------CCTCTGa ACCATTGTGGAGATAACCATGGTGGTCGTGGGCATTGTGG-----GCTATGTGGGAACCCCTCGAGACCTCTGG Template switch alignment (log-probability: -32.7) ACCATTGTGGAGATAACCATGGTGGTtGcGGGCATTGTGG|ACATAGC|CCTCTGa ACCATTGTGGAGATAACCATGGTGGTCGTGGGCATTGTGG|ACATAGC|CCTCTGG ========== Event 3660 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TCTGGAGTTCCTCCCTGTGGACTTCCTGTGAACACCTCCACACTGATGGAGCCCCCATAAGTCACTTCAGCTCACAGGGGCCAT Chimp: TCTGGAGTTCCTCCCTGTGGACTTCCTGTGAACACCTCCACACTGATGGAGCCCCCATAAGTCACTTCAGCTCACAGGGGCCAT ↑ 3 2 1 4 Gorilla: TCTGGAGTTCCTCCCTGTGGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCATGGGTTACTTCAGCTCACAGGGGCCAT ↓ 3 2 1 4 Human: TCTGGAGTTCCTCCCTGTGGACTTCCTGTGAACACCTCCACACTGATGGAGCCCCCATAAGTCACTTCAGCTCACAGGGGCCAT Cluster: [ ] Orangutan: TCTGGAGTTCCTCCCTGTGGACTTCCTGTGAACACTTCCACACTGATGGAGCCCCCATGGGTCACTTCAGCTCACAGGGGCCAT Gorilla > Human --------------- chr8:144170250-144170254 Template switch process: F1: L TGGACTTCCTGTGAACACCTCCACACTGATGGAGCCCCCAT 1 F3: 4 ACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC R RF: TGGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCATGGGTTACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC RR: ACCTGAAGGACACTTATGGAGGTGTGACTACCTCGGGGGTACCCAATGAAGTCGAGTGTCCCCGGTACGAAGGGTAAGGATGACTG F2: 3 CTGAA 2 Unidirectional alignment (log-probability: -32.9) GGACTTCCTGTGAAcACCTCCACACTGATGGAGCCCCCATaaGTcACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGac GGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCATGGGTTACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTG-- Template switch alignment (log-probability: -21.9) GGACTTCCTGTGAAcACCTCCACACTGATGGAGCCCCCAT|AAGTC|ACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC GGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCAT|AAGTC|ACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC Gorilla > Chimp --------------- chr8:146987383-146987387 Template switch process: F1: L TGGACTTCCTGTGAACACCTCCACACTGATGGAGCCCCCAT 1 F3: 4 ACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC R RF: TGGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCATGGGTTACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC RR: ACCTGAAGGACACTTATGGAGGTGTGACTACCTCGGGGGTACCCAATGAAGTCGAGTGTCCCCGGTACGAAGGGTAAGGATGACTG F2: 3 CTGAA 2 Unidirectional alignment (log-probability: -32.9) GGACTTCCTGTGAAcACCTCCACACTGATGGAGCCCCCATaaGTcACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGac GGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCATGGGTTACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTG-- Template switch alignment (log-probability: -21.9) GGACTTCCTGTGAAcACCTCCACACTGATGGAGCCCCCAT|AAGTC|ACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC GGACTTCCTGTGAATACCTCCACACTGATGGAGCCCCCAT|AAGTC|ACTTCAGCTCACAGGGGCCATGCTTCCCATTCCTACTGAC ========== Event 3661 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCA---GCTGTACTATTAGATGGATGATT Chimp: GAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCA---GCTGTACTATTAGATGGATGATT ↓ 3 2 1 4 Gorilla: GAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCGTACTTTGTACTATTAGATGGATGATT ↑ 3 2 1 4 Human: GAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCA---GCTGTACTATTAGATGGATGATT Cluster: [ ] Orangutan: GAAAGTCTATTAACTCACAAAGTATGGACACAGCTACCG---GCTGTACTATTAGATGGATGATT Human > Gorilla --------------- chr8:35908755-35908760 Template switch process: F1: L TTTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACC 1 F3: 4 TGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT R RF: TTTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCAGCTGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT RR: AAACTTTCAGATAATTGAGTGTTTCATGCCTGTGTCGATGGTCGACATGATAATCTACCTACTAATGAATTTGAGTCAGACTGA F2: 3 TTCATG 2 Unidirectional alignment (log-probability: -29.4) TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTAC---CgtacttTGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCAGC------TGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT Template switch alignment (log-probability: -16.5) TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACC|GTACTT|TGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACC|GTACTT|TGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT Chimp > Gorilla --------------- chr8:35908755-35908760 Template switch process: F1: L TTTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACC 1 F3: 4 TGTACTATTAGATGGATGATTACTTAAACTCAGTCTGACT R RF: TTTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCAGCTGTACTATTAGATGGATGATTACTTAAACTCAGGCTGACT RR: AAACTTTCAGATAATTGAGTGTTTCATGCCTGTGTCGATGGTCGACATGATAATCTACCTACTAATGAATTTGAGTCCGACTGA F2: 3 TTCATG 2 Unidirectional alignment (log-probability: -34.9) TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTAC---CgtacttTGTACTATTAGATGGATGATTACTTAAACTCAGtCTGACT TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACCAGC------TGTACTATTAGATGGATGATTACTTAAACTCAGGCTGACT Template switch alignment (log-probability: -22) TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACC|GTACTT|TGTACTATTAGATGGATGATTACTTAAACTCAGtCTGACT TTGAAAGTCTATTAACTCACAAAGTACGGACACAGCTACC|GTACTT|TGTACTATTAGATGGATGATTACTTAAACTCAGGCTGACT ========== Event 3662 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGCTCTATGGCAaaatgacgatgttcattcccagcacaaaggagagtacaggaatgcagcaggtgagcagctttccctttcttcccaaactacaccttccggtatggcttcagtattttgctttttgttacaaattcAATAAG--------------------------------------------------GAAGGTCAAACCAAGTGTAAAGGATTATTGAGCATC ↓ 3 2 4 1 Chimp: CAGCTCTATGGCAaaatgacgacgttcattcccagcacaaaggagagtacaggaatgcagcaggtgagcagctttccctttcttcccaaactacaccttccagtatggctttagtattttgctttttgttacaaattcAATAAG-------------------------GAAGGTCAAACCAAGTATCGATAAGGAAGGTCAAACCAAGTATAAAGGATTATTGAGCATC Gorilla: CAGCTCTATGGCAaaatgacgatgttcattcccagcacaaaggagagtacaggaatgcagcaggtgagcagctttccctttcttcccaaactacaccttccagtatggctttagtattttgctttttgttacaaattcgataaggaaggtcaaaccaagtatcgataag-------------------------gaaggtcaaaccaagtatAAAGGATTATTGAGCATC Human: CAGCTCTATGGCAaaatgacgatgttcattcccagcacaaaggagagtacaggaatgcagcaggtgagcagctttccctttcttcccaaactacaccttccggtatggcttcagtattttgctttttgttacaaattcAATAAG--------------------------------------------------GAAGGTCAAACCAAGTGTAAAGGATTATTGAGCATC Cluster: [ ] Orangutan: Human > Chimp ------------- chr8:66237407-66237410 Template switch process: F1: L TATGGCTTTAGTATTTTGCTTTTTGTTACAAATTCAATAAGGAAGGTCAAACCAAGT 1 F3: 4 ATAAGGAAGGTCAAACCAAGTATAAAGGATTATTGAGCATCACAC R RF: CGATGTTCATTCCCAGCACAAAGGAGAGTACAGGAATGCAGCAGGTGAGCAGCTTTCCCTTTCTTCCCAAACTACACCTTCCGGTATGGCTTCAGTATTTTGCTTTTTGTTACAAATTCAATAAGGAAGGTCAAACCAAGTGTAAAGGATTATTGAGCATCACAC RR: GCTACAAGTAAGGGTCGTGTTTCCTCTCATGTCCTTACGTCGTCCACTCGTCGAAAGGGAAAGAAGGGTTTGATGTGGAAGGCCATACCGAAGTCATAAAACGAAAAACAATGTTTAAGTTATTCCTTCCAGTTTGGTTCACATTTCCTAATAACTCGTAGTGTG F2: 3 GCTA 2 Unidirectional alignment (log-probability: -58.8) GCTTTTTGTTACAAATTCAATAAGGAAGGTCAAACCAAGTatcgataaggaaggtcaaaccaagtaTAAAGGATTATTGAGCAT GCTTTTTGTTACAAATTCAATAAGGAAGGTCAAACCAAGTG-------------------------TAAAGGATTATTGAGCAT Template switch alignment (log-probability: -28.2) GCTTTTTGTTACAAATTCAATAAGGAAGGTCAAACCAAGT|ATCG|ATAAGGAAGGTCAAACCAAGTaTAAAGGATTATTGAGCAT GCTTTTTGTTACAAATTCAATAAGGAAGGTCAAACCAAGT|ATCG|ATAAGGAAGGTCAAACCAAGTGTAAAGGATTATTGAGCAT ========== Event 3663 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: tagataggatttctcttttgt------ta---ttatttttttgagtc-agggtctcgctcggccaccccagct Chimp: tagataggatttctCTTTTGT---TGTAA---TTAtttttttgagtc-agggtctcgctcggccaccccagct ↓ 3 1 2 4 Gorilla: tagataggatttctCTTTTGTTGT---AATTATTAtttttttgagtcctgactctcgctcggccaccccagct Human: tagataggatttctcttttgt------ta---ttatttttttgagtc-agggtctcgctcggccaccccagct Cluster: [ ] Orangutan: tagataggatttctcttttgttgt---agttgttatttttttgagtc-agggtcttgctcggccaccctagct Chimp > Gorilla --------------- chr8:34284437-34284441 Template switch process: F1: L TTGCATCCCCACTGTACCTGTAGATAGGATTTCTCTTTTGTTGTAATTATTATTTTTTTGAGTC 1 F3: 4 TCTCGCTCGGCCACCCCAGC R RF: TTGCATCCCCACTGTACCTGTAGATAGGATTTCTCTTTTGTTGTAATTATT---TTTTTGAGTCAGGGTCTCGCTCGGCCACCCCAGC RR: AACGTAGGGGTGACATGGACATCTATCCTAAAGAGAAAACAACATTAATAA---AAAAACTCAGTCCCAGAGCGAGCCGGTGGGGTCG F2: 3 CAGTC 2 Unidirectional alignment (log-probability: -42.1) TAGGATTTCTCTTTTGTTGTAATTAttaTTTTTTTGAGTcctgaC----TCTCGCTCGGCCACCCCAGC TAGGATTTCTCTTTTGTTGTAATTA---TTTTTTTGAGT-----CAGGGTCTCGCTCGGCCACCCCAGC Template switch alignment (log-probability: -30.4) TAGGATTTCTCTTTTGTTGTAATTATTattTTTTTGAGTC|CTGAC|TCTCGCTCGGCCACCCCAGC TAGGATTTCTCTTTTGTTGTAATTATT---TTTTTGAGTC|CTGAC|TCTCGCTCGGCCACCCCAGC ========== Event 3664 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ca---------------------cacacacacGTATACGTGTGTGTGTGTATATACTTGGCTCTGACACA ↓ 13 4 2 Chimp: ca---------cacacacacacacacacacacGTATA--CGTGTGTGTGTATATACTTGGCTCTGACACA Gorilla: ca---------------------cacacacacaTATA--CGTGTGTGTGTATATACTTGGCTCTGACACA Human: ca---------------------cacacacacGTATACGTGTGTGTGTGTATATACTTGGCTCTGACACA Cluster: [ ] Orangutan: --ccacacaca------------cacacaTACGTATA--TGTGTGTGTATATATACTTGGCTCTGAAACA Human > Chimp ------------- chr8:65573724-65573741 Template switch process: F1: L ACACACACACACACACACACACAC 1 F3: 4 GTGTGTGTGTATATACTTGGCTCTGACACAACTCTGGTGC R RF: ACACACACACACACACACACACACGTATACGTGTGTGTGTGTATATACTTGGCTCTGACACAACTCTGGTGC RR: TGTGTGTGTGTGTGTGTGTGTGTGCATATGCACACACACACATATATGAACCGAGACTGTGTTGAGACCACG F2: 3 CATATGCACACACACACA 2 Unidirectional alignment (log-probability: -32.6) acacacacacacACACACACACACACACACACACACGTATACGTGTGTGTG--TATATACTTGGCTCTGACACAACTCTGGTGC ------------ACACACACACACACACACACACACGTATACGTGTGTGTGTGTATATACTTGGCTCTGACACAACTCTGGTGC Template switch alignment (log-probability: -17.2) ACACACACACACACACACACACAC|ACACACACACACGTATAC|GTGTGTGTGTATATACTTGGCTCTGACACAACTCTGGTGC ACACACACACACACACACACACAC|ACACACACACACGTATAC|GTGTGTGTGTATATACTTGGCTCTGACACAACTCTGGTGC ========== Event 3665 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CAGAGCTCATGGCCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAA----------CATAGTCTATGTTAATAATACAAA Chimp: CAGAGCTCATGGCCACATTCTTATTTCTACTGTGCGAACACTTGAGAAATAA----------CATTGTCTATGTTAATAATACAAA Gorilla: CAGAGCTCATGGCCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAAGTGTTTGCACTTATGTCTATGTTAATAATACAAA ↑ 4 3 2 1 Human: CAGAGCTCATGGCCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAA----------CATAGTCTATGTTAATAATACAAA Cluster: [ ] Orangutan: CAGAGCTCATTGCCACATTCTTATTTCTACTGTGCGAACACTTGAGG---------------TTCTTTCTATGTTAATAATACAAA Human > Gorilla --------------- chr8:33800180-33800188 Template switch process: F1: L GCCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAA 1 F3: 4 CTTAT--------------------------------GTCTATGTTAATAATACAAAGACTCTAGTCTTGTGAAGAA R RF: GCCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAACATAGTCTATGTTAATAATACAAAGACTCTAGTCTTGTGAAGAA RR: CGGTGTAAGAATAAAGATGACACGTTTGTGAACTCTTTATTGTATCAGATACAATTATTATGTTTCTGAGATCAGAACACTTCTT F2: 3 ACGTTTGTG 2 Unidirectional alignment (log-probability: -40.6) CCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAagtgtttgcACtTAtGTCTATGTTAATAATACAAAGACTCTAGTCTTGTG CCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATA---------ACATA-GTCTATGTTAATAATACAAAGACTCTAGTCTTGTG Template switch alignment (log-probability: -28.4) CCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAA|GTGTTTGCA|CTTAT--------------------------------GTCTATGTTAATAATACAAAGACTCTAGTCTTGTG CCACATTCTTATTTCTACTGTGCAAACACTTGAGAAATAA|GTGTTTGCA|CTTATTTCTACTGTGCAAACACTTGAGAAATAACATAGTCTATGTTAATAATACAAAGACTCTAGTCTTGTG ========== Event 3666 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGCCTCAAGATTTGGAGAAGAGGCAGAGTTTACTCAGAGAGTAAACTCACTTGAGGACAATTTCACAG Chimp: ATGCCTCAAGGTTTGGAGAACAGGCAGAGTTTACTCAGAGAGTAAACTCACTTGAGGACAATTTCACAG ↓ 1 3 4 2 Gorilla: ATGCCTCAAGGTTTGGAGA------AGAGTTTACTCTCTGAGTAAACTCACTTGAGGACAATTTCACAG Human: ATGCCTCAAGATTTGGAGAAGAGGCAGAGTTTACTCAGAGAGTAAACTCACTTGAGGACAATTTCACAG Cluster: [ ] Orangutan: --------------------------------------------------------------------- Chimp > Gorilla --------------- chr8:33581125-33581137 Template switch process: F1: L CAAAAATGCCTCAAGGTTTGGAGAA 1 F3: 4 GAGTAAACTCACTTGAGGACAATTTCACAGAGGGGATGGA R RF: CAAAAATGCCTCAAGGTTTGGAGAACAGGCAGAGTTTACTCAGAGAGTAAACTCACTTGAGGACAATTTCACAGAGGGGATGGA RR: GTTTTTACGGAGTTCCAAACCTCTTGTCCGTCTCAAATGAGTCTCTCATTTGAGTGAACTCCTGTTAAAGTGTCTCCCCTACCT F2: 3 TCTCTCATTTGAG 2 Unidirectional alignment (log-probability: -27.7) CAAAAATGCCTCAAGGTTTGGAGA------AGAGTTTACTCtctGAGTAAACTCACTTGAGGACAATTTCACAGAGGGGATGGA CAAAAATGCCTCAAGGTTTGGAGAACAGGCAGAGTTTACTCAGAGAGTAAACTCACTTGAGGACAATTTCACAGAGGGGATGGA Template switch alignment (log-probability: -17) CAAAAATGCCTCAAGGTTTGGAGAA|GAGTTTACTCTCT|GAGTAAACTCACTTGAGGACAATTTCACAGAGGGGATGGA CAAAAATGCCTCAAGGTTTGGAGAA|GAGTTTACTCTCT|GAGTAAACTCACTTGAGGACAATTTCACAGAGGGGATGGA ========== Event 3667 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAGGCATTACCTGTGCATACCTG------------------------------------GCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCCTGTGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCAGGCTGTGTAGCCTCCCGGGGGTGGGCCGGGGGCTGGGGCTCCCCCGTC ↓ 4 1 3 2 Chimp: CAGGCATTACCTGTGCATACCTG------------------GCCTTGGCCTGGACCCTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCCTGTGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCAGGCTGTGTAGCCTCCCGGGGGTGGGCCGGGGGCTGGGGCTCCCCCGTC ↑ 4 1 3 2 Gorilla: CAGGCATTACCTGTGCATACCTG------------------------------------GCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCCTGAGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCAGGCTGTGTAGCCTCCCGGGGGTGGGCCAGGGGCTGGGGCTCCCCCGTC Human: CAGGCATTACCTGTGCATACCTG------------------------------------GCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCCTGTGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCAGGCTGTGTAGCCTCCCGGGGGTGGGCCGGGGGCTGGGGCTCCCCCGTC Cluster: [ ] Orangutan: CAGGCATTACCTGTACATACCtggccctggccttgaccctg------------------gccttggccctgCGCAGCCGCTGCATGTTCTGTCTTGGCCTGTGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCAGGCTGTGGAGCCTCCCGGGGGTGGGCCGGGGGCTGGGGCTCCCCCGTC Human > Chimp ------------- chr8:7695462-7695467 Template switch process: F1: L GATGCTGTTTTCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCC 1 F3: 4 CTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCC R RF: GATGCTGCTTTCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCCTGTGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCA RR: CTACGACGAAAGACCCGGGTCCGTAATGGACACGTATGGACCGGAACCGGGACCCGTCGTCGACGTACAAGATAGAACCGGACACTGAACCTTCCGTGGCCTCGACGGAAGAAGGAGAACCACGAGAGTCGTATCTACCCAAGT F2: 3 CCAGGT 2 Unidirectional alignment (log-probability: -42.8) TCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCctggaccctggccttggcCCTGGGCAGCAGCTGCATGTTCTATCTTG TCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGC------------------CCTGGGCAGCAGCTGCATGTTCTATCTTG Template switch alignment (log-probability: -28.2) TCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCC|TGgACC|CTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTG TCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCC|TGAACC|CTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTG Gorilla > Chimp --------------- chr8:7695462-7695466 Template switch process: F1: L GATGCTGTTTTCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCC 1 F3: 4 CCTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCC R RF: GATGCTGTTTTCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTTGGCCTGAGACTTGGAAGGCACCGGAGCTGCCTTCTTCCTCTTGGTGCTCTCAGCATAGATGGGTTCAGGCTGTGTAGCCTCCCGGGGGTGGGCCA RR: CTACGACAAAAGACCCGGGTCCGTAATGGACACGTATGGACCGGAACCGGGACCCGTCGTCGACGTACAAGATAGAACCGGACTCTGAACCTTCCGTGGCCTCGACGGAAGAAGGAGAACCACGAGAGTCGTATCTACCCAAGTCCGACACATCGGAGGGCCCCCACCCGGT F2: 3 CAGGT 2 Unidirectional alignment (log-probability: -36.8) TCTGGGCCCAGGCATTACCTGTGCATACCtggccttggcctggacccTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTT TCTGGGCCCAGGCATTACCTGTGCATACC------------------TGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTT Template switch alignment (log-probability: -22.2) TCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCC|TGGaC|CCTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTT TCTGGGCCCAGGCATTACCTGTGCATACCTGGCCTTGGCC|TGGCC|CCTGGCCTTGGCCCTGGGCAGCAGCTGCATGTTCTATCTT ========== Event 3668 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAGTCTTCTACCTTTCAGTCTAATCCAGAGATTAGACTCTGGATTCCTATTACTTTTCACT ↑ 3 4 2 Chimp: AATGTCTTCTACCTTTCAGTCTAAT------------CTCTGGATTCCTATTACTTTTCACT Gorilla: AAAGTCTTCTACCTTTCAGTCTAAT------------CTCTGGATTCCTATTACTTTTCACT ↓ 3 4 2 Human: AAAGTCTTCTACCTTTCAGTCTAATCCAGAGATTAGACTCTGGATTCCTATTACTTTTCACT Cluster: [ ] Orangutan: AAAGTCTTCTACCTTTCAGTCTAAT------------CTCTGGATTCTTATTACCTTCAACT Chimp > Human ------------- chr8:61935838-61935848 Template switch process: F1: L AGAGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAATC 1 F3: 4 CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA R RF: AGAGTGGGAACATCCCAATGTCTTCTACCTTTCAGTCTAATCTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA RR: TCTCACCCTTGTAGGGTTACAGAAGATGGAAAGTCAGATTAGAGACCTAAGGATAATGAAAAGTGACTGACCCAAGGTTTT F2: 3 AGATTAGAGAC 2 Unidirectional alignment (log-probability: -34.2) AGTGGGAACATCCCAAaGTCTTCTACCTTTCAGTCTAATccagagattagaCTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA AGTGGGAACATCCCAATGTCTTCTACCTTTCAGTCTAAT------------CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA Template switch alignment (log-probability: -22.7) AGTGGGAACATCCCAAaGTCTTCTACCTTTCAGTCTAATC|CAGAGATTAGA|CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA AGTGGGAACATCCCAATGTCTTCTACCTTTCAGTCTAATC|CAGAGATTAGA|CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA Gorilla > Human --------------- chr8:61935838-61935848 Template switch process: F1: L AGAGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAATC 1 F3: 4 CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA R RF: AGAGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAATCTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA RR: TCTCACCCTTGTAGGGTTTCAGAAGATGGAAAGTCAGATTAGAGACCTAAGGATAATGAAAAGTGACTGACCCAAGGTTTT F2: 3 AGATTAGAGAC 2 Unidirectional alignment (log-probability: -28.1) AGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAATccagagattagaCTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA AGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAAT------------CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA Template switch alignment (log-probability: -17.2) AGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAATC|CAGAGATTAGA|CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA AGTGGGAACATCCCAAAGTCTTCTACCTTTCAGTCTAATC|CAGAGATTAGA|CTCTGGATTCCTATTACTTTTCACTGACTGGGTTCCAAAA ========== Event 3669 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTGGGAGCATAATCACTGAGT-GACACTAAATTAAAGTGTCAATATATTGGTCAATATGTT Chimp: TTGGGAGCATAATCACTGAGTTAATTTTAAATTAAAGTGTCAATATGTTGGTCAATATGTT Gorilla: TTGGGAGCATAATCACTGAGTTAATTTTAAATTAAAGTGTCAATATGTTGGTCAATATGTT ↓ 1 4 3 2 Human: TTGGGAGCATAATCACTGAGT-GACACTAAATTAAAGTGTCAATATATTGGTCAATATGTT Cluster: [ ] Orangutan: Gorilla > Human --------------- chr8:61618922-61618927 Template switch process: F1: L TGAATTTAAATTTGGCAGTATTGGGAGCATAATCACTGAGT 1 F3: 4 AAATTAAAGTGTCAATATATTGGTCAATATGTTATCTCT R RF: TGAATTTAAATTTGGCAGTATTGGGAGCATAATCACTGAGTTAATTTTAAATTAAAGTGTCAATATGTTGGTCAATATGTTATCTCT RR: ACTTAAATTTAAACCGTCATAACCCTCGTATTAGTGACTCAATTAAAATTTAATTTCACAGTTATACAACCAGTTATACAATAGAGA F2: 3 TCACAG 2 Unidirectional alignment (log-probability: -33.6) GAATTTAAATTTGGCAGTATTGGGAGCATAATCACTGAG------TgacacTAAATTAAAGTGTCAATATaTTGGTCAATATGTTATCTCT GAATTTAAATTTGGCAGTATTGGGAGCATAATCACTGAGTTAATTT-----TAAATTAAAGTGTCAATATGTTGGTCAATATGTTATCTCT Template switch alignment (log-probability: -22) GAATTTAAATTTGGCAGTATTGGGAGCATAATCACTGAGT|GACACT|AAATTAAAGTGTCAATATaTTGGTCAATATGTTATCTCT GAATTTAAATTTGGCAGTATTGGGAGCATAATCACTGAGT|GACACT|AAATTAAAGTGTCAATATGTTGGTCAATATGTTATCTCT ========== Event 3670 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTAAAAGTAGAAATCAGGAGATAGAACTAACTTGTTTTAAG-CCTTTTTATTTTTGCTATCTACTCGAAG Chimp: TTAAAAGTAGAAATCAGGAGACAGAACTAGCTTGTTTTAAG-CCTTTTTATTTTTGCTATCTCCTCGAAG ↓ 1 3 42 Gorilla: TTAAAAGTAGAAATCAGGAGATAAAA-AGGCTTAAAACAAGCTAGTTCTATTTTTGCTATCTACTCGAAG ↑ 13 24 Human: TTAAAAGTAGAAATCAGGAGATAGAACTAACTTGTTTTAAG-CCTTTTTATTTTTGCTATCTACTCGAAG Cluster: [ ] Orangutan: Human > Gorilla --------------- chr8:31618671-31618694 Template switch process: F1: L AGTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGATA 1 F3: 4 TATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG R RF: AGTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGATAGAACTAACTTGTTTTAAGCCTTTTTATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG RR: TCACTACAACAGTAAATGAATTTTCATCTTTAGTCCTCTATCTTGATTGAACAAAATTCGGAAAAATAAAAACGATAGATGAGCTTCGGATACGTTATAATACAC F2: 3 CTTGATCGAACAAAATTCGGAAAA 2 Unidirectional alignment (log-probability: -56) GTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGAtaaaaaggcttaaaacaagcTAG--------------------TTcTATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG GTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGA--------------------TAGAACTAACTTGTTTTAAGCCTTTTTATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG Template switch alignment (log-probability: -24.3) GTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGATA|AAAAGGCTTAAAACAAGcTAGTTC|TATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG GTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGATA|AAAAGGCTTAAAACAAGTTAGTTC|TATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG Chimp > Gorilla --------------- chr8:31618669-31618694 Template switch process: F1: L ATAGTGATGTTGTCATTTACTTAAAAGTAGAAATCAGGAGA 1 F3: 4 TATTTTTGCTATCTACTCGAAGCCTATGCAATATTATGTG R RF: ATAGTGATGTTGACATTTACTTAAAAGTAGAAATCAGGAGACAGAACTAGCTTGTTTTAAGCCTTTTTATTTTTGCTATCTCCTCGAAGCCTATGCAATATTATGTG RR: TATCACTACAACTGTAAATGAATTTTCATCTTTAGTCCTCTGTCTTGATCGAACAAAATTCGGAAAAATAAAAACGATAGAGGAGCTTCGGATACGTTATAATACAC F2: 3 CTTGATCGAACAAAATTCGGAAAAAT 2 Unidirectional alignment (log-probability: -68.9) TAGTGATGTTGtCATTTACTTAAAAGTAGAAATCAGGAGA-------------------------TaaaaaggcttaaaacaagctagttcTATTTTTGCTATCTaCTCGAAGCCTATGCAATATTATGTG TAGTGATGTTGACATTTACTTAAAAGTAGAAATCAGGAGACAGAACTAGCTTGTTTTAAGCCTTTT-------------------------TATTTTTGCTATCTCCTCGAAGCCTATGCAATATTATGTG Template switch alignment (log-probability: -30.1) TAGTGATGTTGtCATTTACTTAAAAGTAGAAATCAGGAGA|TAAAAAGGCTTAAAACAAGCTAGTTC|TATTTTTGCTATCTaCTCGAAGCCTATGCAATATTATGTG TAGTGATGTTGACATTTACTTAAAAGTAGAAATCAGGAGA|TAAAAAGGCTTAAAACAAGCTAGTTC|TATTTTTGCTATCTCCTCGAAGCCTATGCAATATTATGTG ========== Event 3671 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: AAATTTAGATAATTGATAGATTTCAAGTTTCTTGCTATACTGATGCCTATGTTTCAGTTTCCCAATATAGTGATATTTGTACCTGACTAGAATAAAATTTCAATTATTTATCAATTAGAGAAACAACTACAGCAGTTTCACCTTGAATTAAGACAAATTATCACATA Chimp: AAATTTAGATAATTGATAGATTTCAAGTTTCTTGCTATACTGATGCCTATGTTTCAGTTTCCCAATATAGTGATATTTGTACCTGACTAGAATAAAATTTCAATTATTTATCAATTAGAGAAACAACTACAGCAGTTTCACCTTGAATTAAGATGTATTATCACATA ↑ 1 4 3 2 Gorilla: AAATTTAGATAATTGATAGAT-AAAAATTTCTTGCTATACTGATGCCTATGTCTCAGTTTCCCAATATAGTGATATTTGTACCTGACTAGAATAAAATTTCAATTATTTATCAATTAGAGAAACAACTACAGCAGTTTCACCTTGAATTAAGACAAATTATCACATA Human: AAATTTAGATAATTGATAGATTTCAAGTTTCTTGCTATACTGATGCCTATGTTTCAGTTTCCCAATATAGTGATATTTGTACCTGACTAGAATAAAATTTCAATTATTTATCAATTAGAGAAACAACTACAGCAGTTTCACCTTGAATTAAGACAAATTATCACATA Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr8:62933210-62933215 Template switch process: F1: L ACTATCCTAGAAAAGTATCTAAATTTAGATAATTGATAGAT 1 F3: 4 TTTCTTGCTATACTGATGCCTATGTTTCAGTTTCCCAATA R RF: ACTATCCTAGAAAAGTATCTAAATTTAGATAATTGATAGATAAAAATTTCTTGCTATACTGATGCCTATGTCTCAGTTTCCCAATATAGTGATATTTGTACCTGACTAGAATAAAATTTCAATTATTTATCAATTAGAGAAACAACTACAGCAGTTTCACCTTGAA RR: TGATAGGATCTTTTCATAGATTTAAATCTATTAACTATCTATTTTTAAAGAACGATATGACTACGGATACAGAGTCAAAGGGTTATATCACTATAAACATGGACTGATCTTATTTTAAAGTTAATAAATAGTTAATCTCTTTGTTGATGTCGTCAAAGTGGAACTT F2: 3 GAACTT 2 Unidirectional alignment (log-probability: -34.5) CTATCCTAGAAAAGTATCTAAATTTAGATAATTGATAGAtTtcAAgTTTCTTGCTATACTGATGCCTATGTtTCAGTTTCCCAATA CTATCCTAGAAAAGTATCTAAATTTAGATAATTGATAGA-TAAAAATTTCTTGCTATACTGATGCCTATGTCTCAGTTTCCCAATA Template switch alignment (log-probability: -22) CTATCCTAGAAAAGTATCTAAATTTAGATAATTGATAGAT|TTCAAG|TTTCTTGCTATACTGATGCCTATGTtTCAGTTTCCCAATA CTATCCTAGAAAAGTATCTAAATTTAGATAATTGATAGAT|TTCAAG|TTTCTTGCTATACTGATGCCTATGTCTCAGTTTCCCAATA ========== Event 3672 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGGATAAGAACCTAAATAGTATAATAACATTTTACCAAGCATCTACAT------AACTGTATGTATATTTTCTGATAGGAAGG Chimp: TAAGGATAAGAACCTAAATAGTATAATAACATTTTACCAAGCATCTACAT------AACTGTATGTATATTTTCTGATAGGAAGG ↓ 13 4 2 Gorilla: TAAGGATAAGAACCTAAATAGGATAATAACGTTTTACCAAGCATCTACATACATACAGTTGTATGTATATTTTCTGATAGGAAGG ↑ 13 4 2 Human: TAAGGATAAGAACCTAAATAGTATAATAACATTTTACCAAGCATCTACAT------AACTGTATGTATATTTTCTGATAGGAAGG Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------- Human > Gorilla --------------- chr8:30480611-30480618 Template switch process: F1: L CTCACAGAATTTTGGAACATTAAGGATAAGAACCTAAATAGGATAATAACGTTTTACCAAGCATCTACATA 1 F3: 4 TGTATGTATATT R RF: CTCACAGAATTTTGGAACATTAAGGATAAGAACCTAAATAGTATAATAACATTTTACCAAGCATCTACATAACTGTATGTATATT RR: GAGTGTCTTAAAACCTTGTAATTCCTATTCTTGGATTTATCATATTATTGTAAAATGGTTCGTAGATGTATTGACATACATATAA F2: 3 TGACATAC 2 Unidirectional alignment (log-probability: -40.3) ACCTAAATAGgATAATAACgTTTTACCAAGCATCTACATAcatACagtTGTATGTATATT ACCTAAATAGTATAATAACATTTTACCAAGCATCTACATA---AC---TGTATGTATATT Template switch alignment (log-probability: -27.8) ACCTAAATAGgATAATAACgTTTTACCAAGCATCTACATA|CATACAGT|TGTATGTATATT ACCTAAATAGTATAATAACATTTTACCAAGCATCTACATA|CATACAGT|TGTATGTATATT Chimp > Gorilla --------------- chr8:30480611-30480618 Template switch process: F1: L CTCACAGAATTTTGGAACATTAAGGATAAGAACCTAAATAGGATAATAACGTTTTACCAAGCATCTACATA 1 F3: 4 TGTATGTATATT R RF: CTCACAGAATTTTGGAACATTAAGGATAAGAACCTAAATAGTATAATAACATTTTACCAAGCATCTACATAACTGTATGTATATT RR: GAGTGTCTTAAAACCTTGTAATTCCTATTCTTGGATTTATCATATTATTGTAAAATGGTTCGTAGATGTATTGACATACATATAA F2: 3 TGACATAC 2 Unidirectional alignment (log-probability: -40.3) ACCTAAATAGgATAATAACgTTTTACCAAGCATCTACATAcatACagtTGTATGTATATT ACCTAAATAGTATAATAACATTTTACCAAGCATCTACATA---AC---TGTATGTATATT Template switch alignment (log-probability: -27.8) ACCTAAATAGgATAATAACgTTTTACCAAGCATCTACATA|CATACAGT|TGTATGTATATT ACCTAAATAGTATAATAACATTTTACCAAGCATCTACATA|CATACAGT|TGTATGTATATT ========== Event 3673 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATTGGTTATCTCAGATTCTTAGTATGGTTTT---------AGTTAG--------TTAGTTTTACCACTTGGTAG Chimp: AAATTGGTTATCTCAGATTCTTAGTATGGTTTT---------AGTTAG--------TTAGTTTTACCACTTGGTAG ↓ 3 2 4 1 Gorilla: AAATTGGTTATCTCAGATTCTTAGTATGGTTTTACCATACTAAGTTAGTTAGATTCTTAGTTTTACCACTTGGTAG Human: AAATTGGTTATCTCAGATTCTTAGTATGGTTTT---------AGTTAG--------TTAGTTTTACCACTTGGTAG Cluster: [ ] Orangutan: AAATTGGTTATCTCAGATTCTTAGTATGATTTT---------AGTTAG--------TTAGTTTTACCACTTGGTAG Chimp > Gorilla --------------- chr8:117026930-117026939 Template switch process: F1: L CATTTAGAAAATTGGTTATCTCAGATTCTTAGTATGGTTTTA 1 F3: 4 TTAGTTAGATTCTTAGTTTTACCACTTGGTAGAATTAATGATTTGACAAATG R RF: CATTTAGAAAATTGGTTATCTCAGATTCTTAGTATGGTTTTAGTTAGTTAGTTTTACCACTTGGTAGAATTAATGATTTGACAAATG RR: GTAAATCTTTTAACCAATAGAGTCTAAGAATCATACCAAAATCAATCAATCAAAATGGTGAACCATCTTAATTACTAAACTGTTTAC F2: 3 GAATCATACC 2 Unidirectional alignment (log-probability: -45.2) TTTAGAAAATTGGTTATCTCAGATTCTTAGTATGGTTttaccatactaagTTAGTTAGattcTTAGTTTTACCACTTGGTAGAATTAATG TTTAGAAAATTGGTTATCTCAGATTCTTAGTATGGTT-------------TTAGTTAG----TTAGTTTTACCACTTGGTAGAATTAATG Template switch alignment (log-probability: -32.8) TTTAGAAAATTGGTTATCTCAGATTCTTAGTATGGTTTTA|CCATACTAAG|TTAGTTAGattcTTAGTTTTACCACTTGGTAGAATTAATG TTTAGAAAATTGGTTATCTCAGATTCTTAGTATGGTTTTA|CCATACTAAG|TTAGTTAG----TTAGTTTTACCACTTGGTAGAATTAATG ========== Event 3674 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GAGCAGGTGAAAGCTACAGAGCAGCTCCAGTAGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGATGAGTTTGGGAAATGCAGACTCTGCCTTTCTCGTGCACTCATATGAAAAGTCACCTGGGGAGCACTGGATTCTAGGTAAGTTGTTCAAA ↑ 4 1 3 2 Chimp: GAGCAGGTGAAAGCTACAGAGC------------AGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGATGAGTTTGGGAAATGCAGACTCTGACTTTCTCATGAACTCATATGAAAAATCACCTGGGGAGCACTGGATTCTAGGTAAGTTGTTCAAA ↓ 4 1 3 2 Gorilla: GAGCAGGTGAAAGCTACAGAGCAGCTCCAGTAGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGACGAGTTTGGGAAATGCAGACTCTGCCTTTCTCATGAACTCATATGAAAAATCACCTGGGGAGCACTGGATTCTAGGTAAGTTGTTCAAA Human: GAGCAGGTGAAAGCTACAGAGCAGCTCCAGTAGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGATGAGTTTGGGAAATGCAGACTCTGCCTTTCTCGTGCACTCATATGAAAAGTCACCTGGGGAGCACTGGATTCTAGGTAAGTTGTTCAAA Cluster: [ ] Orangutan: GAGCAGGTGAAAGCTACAGAGCAGCTCCGGTAGCAACATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGATGAGTTTGGGAAATGCAGACTCTGCCTTTCTCATGCACTCATATGAAAAGTCACCT-GGGAGCACTGGATTCTAGGTAAGTTGTTTAAA Chimp > Human ------------- chr8:59157583-59157588 Template switch process: F1: L TACAGCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGC 1 F3: 4 AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGA R RF: TACAGCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGATGAGTTTGGGAAATGCAGACTCTGACTTTCTCATGAACTCATATGAAAAATCACCTGGGGAGCACTGGA RR: ATGTCGTCACGTGTAATTACTCGTCCACTTTCGATGTCTCGTCGTACTGTCACACTTTAACATTCACCACTACAGACTTCTACTCAAACCCTTTACGTCTGAGACTGAAAGAGTACTTGAGTATACTTTTTAGTGGACCCCTCGTGACCT F2: 3 TGACCT 2 Unidirectional alignment (log-probability: -28.2) GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGagcagctccagtAGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA GCAGTGCACATTAATGAGCAGGTGAAAGCTACAG------------AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA Template switch alignment (log-probability: -16.1) GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGC|TCCAGT|AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGC|TCCAGT|AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA Chimp > Gorilla --------------- chr8:60247673-60247678 Template switch process: F1: L TACAGCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGC 1 F3: 4 AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGA R RF: TACAGCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGAAGATGAGTTTGGGAAATGCAGACTCTGACTTTCTCATGAACTCATATGAAAAATCACCTGGGGAGCACTGGA RR: ATGTCGTCACGTGTAATTACTCGTCCACTTTCGATGTCTCGTCGTACTGTCACACTTTAACATTCACCACTACAGACTTCTACTCAAACCCTTTACGTCTGAGACTGAAAGAGTACTTGAGTATACTTTTTAGTGGACCCCTCGTGACCT F2: 3 TGACCT 2 Unidirectional alignment (log-probability: -28.1) GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAgcagctccagtaGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGA------------GCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA Template switch alignment (log-probability: -16.6) GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGC|TCCAGT|AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA GCAGTGCACATTAATGAGCAGGTGAAAGCTACAGAGCAGC|TCCAGT|AGCAGCATGACAGTGTGAAATTGTAAGTGGTGATGTCTGA ========== Event 3675 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ttt------------ttttaatttttctttctttcttactttttaGAGGAAAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTT-TTTGAAA--CATAGAATCATTCATAAAATATTTCTATT Chimp: ttt------tatttttatttatttttctttctttcttactttttaGAGGAAAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTTTGAAA--CATAGAATCATTCATAAAATATTTCTATT Gorilla: ttttatttt------tatttatttttctttctttcttactttttaGAGGAAAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTTTGAAA----CAGAATTATTCATAAAATATTTCTATT ↓ 3 2 1 4 Human: ttt------------ttttaatttttctttctttcttactttttaGAGGAAAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTT-TTTGAAA--CATAGAATCATTCATAAAATATTTCTATT Cluster: [ ] Orangutan: ttttatttt------tatttatttttctttctttcttactttttaGAGGAAAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTCTTGAAACA--TAGAATCATTCATAAAATATTTCTATT Gorilla > Human --------------- chr8:59241227-59241234 Template switch process: F1: L AAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTT 1 F3: 4 GAATCATTCATAAAATATTTCTATTGCTTTA R RF: TATTTTTCTTTCTTTCTTACTTTTTAGAGGAAAATATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTTTGAAACAGAATTATTCATAAAATATTTCTATTGCTTTA RR: ATAAAAAGAAAGAAAGAATGAAAAATCTCCTTTTATATCATTATTCACTTATATAATAAGATATCTTCTCAAAAAACTTTGTCTTAATAAGTATTTTATAAAGATAACGAAAT F2: 3 ATACAAAG 2 Unidirectional alignment (log-probability: -36.5) ATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTT-TGAAACatAGAATcATTCATAAAATATTTCTATTGCTTTA-------------- ATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTTTGAAAC--AGAATTATTCATAAAATATTTCTATTGCTTTAGGTTTAATAAAACA Template switch alignment (log-probability: -27.6) ATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTT|GAAAcATA|GAATcATTCATAAAATATTTCTATTGCTTTA ATAGTAATAAGTGAATATATTATTCTATAGAAGAGTTTTT|GAAAAATA|GAATTATTCATAAAATATTTCTATTGCTTTA ========== Event 3676 ========== Phylogenetic placement: ILS consistent Significant comparisons: 2 Detected in comparisons: 24 Multiple sequence alignment: Human: GATTATTTAACCAATTGCTGACAGTTATACTACTGCATTGCTGCCAGGAAACAAATTTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTGT-GCTGGTCTCAATGTTATCCTGAAAC ↓ 3 2 1 4 Chimp: GATTATTTAACCAATTGCTGACAGTTATACTACTGCATTGCTGCCAGGAAACAAATTTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTGACTGTCGTCTCAATGTTATCCTGAAAC Gorilla: GATTATTTAACCAATTGCTGACAGTTATACTACTGCATTGCTGCCAGGAAACAAATTTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTGACTGTGGTCTCAATGTTATCCTGAAAC Human: GATTATTTAACCAATTGCTGACAGTTATACTACTGCATTGCTGCCAGGAAACAAATTTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTGT-GCTGGTCTCAATGTTATCCTGAAAC Cluster: [ ] Orangutan: GATTATTTAACCAATTGCTGACAGTTACACTACTGCATTGCTGCCAGGAAACAAATTTCTTCTATTAGCTGCATTCCTCTCTGAAAAATGACTCTGACTGTGGCCTCAATTTTATCCCGAAAC Human > Chimp ------------- chr8:59925825-59925830 Template switch process: F1: L TTTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTG 1 F3: 4 GTCTCAATGTTATCCTGAAACCCGTTATGGCTGAATGGCA R RF: GACAGTTATACTACTGCATTGCTGCCAGGAAACAAATTTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTGTGCTGGTCTCAATGTTATCCTGAAACCCATTATGGCTGAATGGCA RR: CTGTCAATATGATGACGTAACGACGGTCCTTTGTTTAAAGAAGATAATCGTCGTAAGGAGAGACTTTTTACTGAGACACGACCAGAGTTACAATAGGACTTTGGGTAATACCGACTTACCGT F2: 3 CTGTCA 2 Unidirectional alignment (log-probability: -36) TTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTGactgtc-----GTCTCAATGTTATCCTGAAACCCgTTATGGCTGAATGGCA TTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTG------TGCTGGTCTCAATGTTATCCTGAAACCCATTATGGCTGAATGGCA Template switch alignment (log-probability: -22) TTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTG|ACTGTC|GTCTCAATGTTATCCTGAAACCCgTTATGGCTGAATGGCA TTCTTCTATTAGCAGCATTCCTCTCTGAAAAATGACTCTG|ACTGTC|GTCTCAATGTTATCCTGAAACCCATTATGGCTGAATGGCA ========== Event 3677 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AATCTACCCCCTTGAGTCGCTCAGTCGAAGAGACTGAGACTTTCCCTTCTTCATGTTGG Chimp: AATCTACCCCCTTGAGTCGCTCAGT--------CTCTTCCTTTCCCTTCTTCATGTTGG Gorilla: AATCTACCCCCTTGAGTCGCTCAGT--------CTCTTCCTTTCCCTTCTTCATGTTGG ↓ 3 1 4 Human: AATCTACCCCCTTGAGTCGCTCAGTCGAAGAGACTGAGACTTTCCCTTCTTCATGTTGG Cluster: [ ] Orangutan: AATCTACCCCCTTGAGTCGCTCAGT--------CTCTTCCTTTCCCTTCTTCATGTTGG Gorilla > Human --------------- chr8:58629497-58629508 Template switch process: F1: L TCTGGACTCTCTCTTGAATCTACCCCCTTGAGTCGCTCAGTC 1 F3: 4 ACTTTCCCTTCTTCATGTTGGGCAACATAATTCTTCCAATT R RF: TCTGGACTCTCTCTTGAATCTACCCCCTTGAGTCGCTCAGTCTCTTCCTTTCCCTTCTTCATGTTGGGCAACATAATTCTTCCAATT RR: AGACCTGAGAGAGAACTTAGATGGGGGAACTCAGCGAGTCAGAGAAGGAAAGGGAAGAAGTACAACCCGTTGTATTAAGAAGGTTAA F2: 3 GAGTCAGAGAAG 2 Unidirectional alignment (log-probability: -39.6) TGGACTCTCTCTTGAATCTACCCCCTTGAGTCGCTCAG-----TCgaagagactgagaCTTTCCCTTCTTCATGTTGGGCAACATAATTCTTCCAAT TGGACTCTCTCTTGAATCTACCCCCTTGAGTCGCTCAGTCTCTTC-------------CTTTCCCTTCTTCATGTTGGGCAACATAATTCTTCCAAT Template switch alignment (log-probability: -22.8) TGGACTCTCTCTTGAATCTACCCCCTTGAGTCGCTCAGTC|GAAGAGACTGAG|aCTTTCCCTTCTTCATGTTGGGCAACATAATTCTTCCAAT TGGACTCTCTCTTGAATCTACCCCCTTGAGTCGCTCAGTC|GAAGAGACTGAG|CCTTTCCCTTCTTCATGTTGGGCAACATAATTCTTCCAAT ========== Event 3678 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGCTTGACAGAGTGAAAGCATGAACT---------------TCTATTTCCTTGCCCTCTCCTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGTGACATTCAGGAGCTTCTAAAAGTTCCTGCCAATAAAGGGCTGTAG Chimp: GGCTTGACAGAGTGAAAGCATGAACT---------------TCTATTTCCTTGCCCTCTCTTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGTGACATTCAGGAGCTTCTAAAAGTTCCTGCCAATAAAAGGCTGTAG ↑ 1 4 3 2 Gorilla: GGCTTGACAGAGTGAAAGCATTCACTCTGTGACAGAAGTTCACTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGTGACGTTCAGGAGCTTCTAAAAGTTCCTGCCAACAAAGGGCTGTAG ↓ 1 4 3 2 Human: GGCTTGACAGAGTGAAAGCATGAACT---------------TCTATTTCCTTGCCCTCTCCTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGTGACATTCAGGAGCTTCTAAAAGTTCCTGCCAATAAAGGGCTGTAG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr8:87499324-87499329 Template switch process: F1: L CTTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT 1 F3: 4 CTATTTCCTTGCCCTCTCCTCAGACAGCTGCAAGAGGTCATTGTTCTCAG R RF: CTTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCATTCACTCTGTGACAGAAGTTCACTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGTGACGTTCAGGAGCTTCTAAAAGTTC RR: GAAAATCGAAGTTGTAAGGACCGAACTGTCTCACTTTCGTAAGTGAGACACTGTCTTCAAGTGATAAAGGAGCGGGAGAGGAGTCTGTCGACGTTCTCCAGTAACAAGAGTCCTTAATTCACTGCAAGTCCTCGAAGATTTTCAAG F2: 3 TTCAAG 2 Unidirectional alignment (log-probability: -32.7) TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT-------------GAAcTT--CTATTTCCTtGCCCTCTCCTCAGACAGCTGCAAGAGGTCA TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCATTCACTCTGTGACAGAAGTTCACTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCA Template switch alignment (log-probability: -22.3) TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT|GAACTT|CTATTTCCTtGCCCTCTCCTCAGACAGCTGCAAGAGGTCA TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT|GAACTT|CTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCA Gorilla > Chimp --------------- chr8:89051697-89051702 Template switch process: F1: L CTTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT 1 F3: 4 CTATTTCCTTGCCCTCTCTTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGT R RF: CTTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCATTCACTCTGTGACAGAAGTTCACTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCATTGTTCTCAGGAATTAAGTGACGTTCAGGAGCTTCTAAAAGTTC RR: GAAAATCGAAGTTGTAAGGACCGAACTGTCTCACTTTCGTAAGTGAGACACTGTCTTCAAGTGATAAAGGAGCGGGAGAGGAGTCTGTCGACGTTCTCCAGTAACAAGAGTCCTTAATTCACTGCAAGTCCTCGAAGATTTTCAAG F2: 3 TTCAAG 2 Unidirectional alignment (log-probability: -38.3) TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT-------------GAAcTT--CTATTTCCTtGCCCTCTCtTCAGACAGCTGCAAGAGGTCA TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCATTCACTCTGTGACAGAAGTTCACTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCA Template switch alignment (log-probability: -28) TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT|GAACTT|CTATTTCCTtGCCCTCTCtTCAGACAGCTGCAAGAGGTCA TTTTAGCTTCAACATTCCTGGCTTGACAGAGTGAAAGCAT|GAACTT|CTATTTCCTCGCCCTCTCCTCAGACAGCTGCAAGAGGTCA ========== Event 3679 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAATTGACAAACCTTGTCCCTGTA--G---TCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACT ↓ 4 1 3 2 Chimp: CAAATTGACAAACCTTGTCCCTGTCAATTCTGATGACCAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACT ↑ 4 1 3 2 Gorilla: CAAATTGACAAACCTTGTCCCTGTA--G---TCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACT Human: CAAATTGACAAACCTTGTCCCTGTA--G---TCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACT Cluster: [ ] Orangutan: Human > Chimp ------------- chr8:89379600-89379611 Template switch process: F1: L TTCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGT 1 F3: 4 CC------------AATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTTAA R RF: TTCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGTAGTCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTTAA RR: AAGACTGGAGGTGCTAAGTTTAACTGTTTGGAACAGGGACATCAGTCATATTAAGAGTAGTCTTAACCAGAAAAGATCGGGTATTGAATT F2: 3 AGTAGTCTTAAC 2 Unidirectional alignment (log-probability: -41.7) TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTG---------TcaattctgatgaccAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGTAGTCAGTAT--------------AATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT Template switch alignment (log-probability: -27.6) TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGT|CAATTCTGATGA|CC------------AATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGT|CAATTCTGATGA|CCTGTAGTCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT Gorilla > Chimp --------------- chr8:89379600-89379611 Template switch process: F1: L TTCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGT 1 F3: 4 CC------------AATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTTAA R RF: TTCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGTAGTCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTTAA RR: AAGACTGGAGGTGCTAAGTTTAACTGTTTGGAACAGGGACATCAGTCATATTAAGAGTAGTCTTAACCAGAAAAGATCGGGTATTGAATT F2: 3 AGTAGTCTTAAC 2 Unidirectional alignment (log-probability: -41.2) TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTG---------TcaattctgatgaccAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGTAGTCAGTAT--------------AATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT Template switch alignment (log-probability: -27.7) TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGT|CAATTCTGATGA|CC------------AATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT TCTGACCTCCACGATTCAAATTGACAAACCTTGTCCCTGT|CAATTCTGATGA|CCTGTAGTCAGTATAATTCTCATCAGAATTGGTCTTTTCTAGCCCATAACTT ========== Event 3680 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGATGCCTAATTACAAAGATGTAATGTAGCCATTGCTGTAAACTTTAAAAAGTT ↑ 3 4 2 Chimp: TGATGCCTAATTACAAAGATG-----GCTACATTGCTGTAAACTTTAAAAAGTT Gorilla: TGATGCCTAATTACAAAGATG-----GCTACATTGCTGTAAACTTTAAAAAGTT Human: TGATGCCTAATTACAAAGATGTAATGTAGCCATTGCTGTAAACTTTAAAAAGTT Cluster: [ ] Orangutan: TGATGCCTAATTACAAAGATG-----GCTACATTGCTGTAAACTTTAAAAAGTT Chimp > Human ------------- chr8:87590393-87590400 Template switch process: F1: L TTGAAAAATGTTTTCTCCCATGATGCCTAATTACAAAGATGT 1 F3: 4 CATTGCTGTAAACTTTAAAAAGTTTTATGGAAGTATGTGG R RF: TTGAAAAATGTTTTCTCCCATGATGCCTAATTACAAAGATGGCTACATTGCTGTAAACTTTAAAAAGTTTTATGGAAGTATGTGG RR: AACTTTTTACAAAAGAGGGTACTACGGATTAATGTTTCTACCGATGTAACGACATTTGAAATTTTTCAAAATACCTTCATACACC F2: 3 CGATGTAA 2 Unidirectional alignment (log-probability: -31.3) GAAAAATGTTTTCTCCCATGATGCCTAATTACAAAGATGtaatgtaGC--CATTGCTGTAAACTTTAAAAAGTTTTATGGAAGTATGTGG GAAAAATGTTTTCTCCCATGATGCCTAATTACAAAGATG-------GCTACATTGCTGTAAACTTTAAAAAGTTTTATGGAAGTATGTGG Template switch alignment (log-probability: -22.3) GAAAAATGTTTTCTCCCATGATGCCTAATTACAAAGATGt|AATGTAGC|CATTGCTGTAAACTTTAAAAAGTTTTATGGAAGTATGTGG GAAAAATGTTTTCTCCCATGATGCCTAATTACAAAGATGG|AATGTAGC|CATTGCTGTAAACTTTAAAAAGTTTTATGGAAGTATGTGG ========== Event 3681 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTAGGCTAATTTAA--AAAAAGAATTCTTCTTGTAATTTTATAGAAGTTGAA-- Chimp: GCTAGGCTAATTTTaa-aaaaaTAATT---CTTTTAATTTTATAGAAGTTGAA-- Gorilla: GCTAGGCTAATTTaaaaaaaaaGAATT---CTTTTAATTTTATAGAAGTTGAA-- ↑ 3 1 2 4 Human: GCTAGGCTAATTTAA--AAAAAGAATTCTTCTTGTAATTTTATAGAAGTTGAA-- Cluster: [ ] Orangutan: GCTAGGCTAATTTaaa-aaaaaGAATT---CTTTTAATTTTATAGAAGTTGAAAT Human > Gorilla --------------- chr8:89427163-89427173 Template switch process: F1: L GATACAAACACACAGCTAGGCTAATTTAAAAAAA 1 F3: 4 TAATTTTATAGAAGTTGAAATGACAGATCTCAACTTGCAG R RF: GATAAAAACACACAGCTAGGCTAATTTAAAAAAAGAATTCTTCTTGTAATTTTATAGAAGTTGAAATGACAGATCTCAACTTGCAG RR: CTATTTTTGTGTGTCGATCCGATTAAATTTTTTTCTTAAGAAGAACATTAAAATATCTTCAACTTTACTGTCTAGAGTTGAACGTC F2: 3 TTTCTTAAGAA 2 Unidirectional alignment (log-probability: -34.7) GATAcAAACACACAGCTAGGCTAATTTaaAAAAAAAGAA---TTCTTtTAATTTTATAGAAGTTGAAATGACAGATCTCAACTTGCAG GATAAAAACACACAGCTAGGCTAATTT--AAAAAAAGAATTCTTCTTGTAATTTTATAGAAGTTGAAATGACAGATCTCAACTTGCAG Template switch alignment (log-probability: -22.5) GATAcAAACACACAGCTAGGCTAATTTAAAAAAA|AAGAATTCTTT|TAATTTTATAGAAGTTGAAATGACAGATCTCAACTTGCAG GATAAAAACACACAGCTAGGCTAATTTAAAAAAA|AAGAATTCTTT|TAATTTTATAGAAGTTGAAATGACAGATCTCAACTTGCAG ========== Event 3682 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CAAATTGCTGGAAGAGTGTTTC--CTCTAAGTCGTGAATCTAAAATACCTATTGATTAAAA ↓ 1 4 3 2 Chimp: CAAATTGCTGGAAGAGTGTTTAGATTCATAGTCGTGAATCTAAAATACCTATTGATTAAAA Gorilla: CAAATTGCTGGAAAAGTGTTTC--CTCTAAGTCGTGAATCTAAAATACCTATTGATTAAAA Human: CAAATTGCTGGAAGAGTGTTTC--CTCTAAGTCGTGAATCTAAAATACCTATTGATTAAAA Cluster: [ ] Orangutan: CAAATTGCTGGAAGAGTGTTTC--CTTTAAGTCGTGAATCTAAAATACCTATTGATTAAAA Human > Chimp ------------- chr8:89670685-89670691 Template switch process: F1: L CTTCTAATGAAATATTTTGACAAATTGCTGGAAGAGTGTTT 1 F3: 4 TAGTCGTGAATCTAAAATACCTATTGATTAAAATATCACCA R RF: CTTCTAATGAAATATTTTGACAAATTGCTGGAAGAGTGTTTCCTCTAAGTCGTGAATCTAAAATACCTATTGATTAAAATATCACCA RR: GAAGATTACTTTATAAAACTGTTTAACGACCTTCTCACAAAGGAGATTCAGCACTTAGATTTTATGGATAACTAATTTTATAGTGGT F2: 3 ACTTAGA 2 Unidirectional alignment (log-probability: -31.5) TTCTAATGAAATATTTTGACAAATTGCTGGAAGAGTGTT-----TAgattcatAGTCGTGAATCTAAAATACCTATTGATTAAAATATCACC TTCTAATGAAATATTTTGACAAATTGCTGGAAGAGTGTTTCCTCTA-------AGTCGTGAATCTAAAATACCTATTGATTAAAATATCACC Template switch alignment (log-probability: -22.2) TTCTAATGAAATATTTTGACAAATTGCTGGAAGAGTGTTT|AGATTCA|tAGTCGTGAATCTAAAATACCTATTGATTAAAATATCACC TTCTAATGAAATATTTTGACAAATTGCTGGAAGAGTGTTT|AGATTCA|AAGTCGTGAATCTAAAATACCTATTGATTAAAATATCACC ========== Event 3683 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTATTTTGGGGAAACTGGTC----TGGGTTACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTATTGCTATTACTGATTTATACAATCCTTT ↓ 1 4 3 2 Chimp: GTTATTTTGGGGAAACTGGTCTAATAGCAATACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTATTGCTATTACTGATTTATACAATCCTTT ↑ 1 4 3 2 Gorilla: GTTATTTTGGGGAAACTGGTC----TGGGTTACCTTTTATTGCTATTAGAGCATAAGAAAAGGAAAAGTATTGCTATTACTGATTTATACAATCCTTT Human: GTTATTTTGGGGAAACTGGTC----TGGGTTACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTATTGCTATTACTGATTTATACAATCCTTT Cluster: [ ] Orangutan: GTTATTTTGGGGAAACTGGTC----TGGGTTACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTATTGCTATTACTGATTTATACAATCCTTT Human > Chimp ------------- chr8:57057860-57057867 Template switch process: F1: L GACAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCT 1 F3: 4 TACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTA R RF: GACAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCTGGGTTACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTATTGCTATT RR: CTGTCCATCAGTCAGATTTCCAATAAAACCCCTTTGACCAGACCCAATGGAAAATAACGATAATCTCGTCTTCTTTTCCTTTTCATAACGATAA F2: 3 AACGATAA 2 Unidirectional alignment (log-probability: -32.9) CAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCTaatagcaa----TACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTA CAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCT--------GGGTTACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTA Template switch alignment (log-probability: -16.3) CAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCT|AATAGCAA|TACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTA CAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCT|AATAGCAA|TACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTA Gorilla > Chimp --------------- chr8:57057860-57057867 Template switch process: F1: L GACAGGTAGTCAGTCTAAAGGTTATTTTGGGGAAACTGGTCT 1 F3: 4 TACCTTTTATTGCTATTAGAGCAGAAGAAAAGGAAAAGTA R RF: GACAGGTAGTCACTCTAAAGGTTATTTTGGGGAAACTGGTCTGGGTTACCTTTTATTGCTATTAGAGCATAAGAAAAGGAAAAGTATTGCTATT RR: CTGTCCATCAGTGAGATTTCCAATAAAACCCCTTTGACCAGACCCAATGGAAAATAACGATAATCTCGTATTCTTTTCCTTTTCATAACGATAA F2: 3 AACGATAA 2 Unidirectional alignment (log-probability: -43.4) CAGGTAGTCAgTCTAAAGGTTATTTTGGGGAAACTGGTC----TaatagcaaTACCTTTTATTGCTATTAGAGCAgAAGAAAAGGAAAAGTA CAGGTAGTCACTCTAAAGGTTATTTTGGGGAAACTGGTCTGGGT--------TACCTTTTATTGCTATTAGAGCATAAGAAAAGGAAAAGTA Template switch alignment (log-probability: -27.8) CAGGTAGTCAgTCTAAAGGTTATTTTGGGGAAACTGGTCT|AATAGCAA|TACCTTTTATTGCTATTAGAGCAgAAGAAAAGGAAAAGTA CAGGTAGTCACTCTAAAGGTTATTTTGGGGAAACTGGTCT|AATAGCAA|TACCTTTTATTGCTATTAGAGCATAAGAAAAGGAAAAGTA ========== Event 3684 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGGGATATCCTGAATCCCCTGAATCACTCCTTGATTGAGGGGATAGGGAGGATGTACTCC Chimp: AGGGGATATCCTGAATCCCCTGAATCACTCCTTGATTGAGGGGTTAGGGAGGATGTACTCC Gorilla: AGGGGATATCCTGAATCCCCTGAATCAAGGAGTGATTCAAGGGATAGGGAGGATGTACTCC ↓ 3 1 2 4 Human: AGGGGATATCCTGAATCCCCTGAATCACTCCTTGATTGAGGGGATAGGGAGGATGTACTCC Cluster: [ ] Orangutan: AGGGGATATCCTTAATCCCCTGAATCACTCCTTGATTCAGGGGATAGGGAGGATGTGCTCC Gorilla > Human --------------- chr8:54516747-54516759 Template switch process: F1: L TGTAGGGTGGATTCAGGGGATATCCTGAATCCCCTGAATCA 1 F3: 4 GGGATAGGGAGGATGTACTCCTAAAAATGAGAATGTTGAT R RF: TGTAGGATGGATTCAGGGGATATCCTGAATCCCCTGAATCAAGGAGTGATTCAAGGGATAGGGAGGATGTACTCCTAAAAATGAGAATGTTGAT RR: ACATCCTACCTAAGTCCCCTATAGGACTTAGGGGACTTAGTTCCTCACTAAGTTCCCTATCCCTCCTACATGAGGATTTTTACTCTTACAACTA F2: 3 GAGTTAGTTCCTC 2 Unidirectional alignment (log-probability: -42.6) GTAGGgTGGATTCAGGGGATATCCTGAATCCCCTGAATCActccttgattgAG-----------GGGATAGGGAGGATGTACTCCTAAAAATGAGAATGTTGAT GTAGGATGGATTCAGGGGATATCCTGAATCCCCTGAATCA-----------AGGAGTGATTCAAGGGATAGGGAGGATGTACTCCTAAAAATGAGAATGTTGAT Template switch alignment (log-probability: -28.4) GTAGGgTGGATTCAGGGGATATCCTGAATCCCCTGAATCA|CTCCTTGATTgAG|GGGATAGGGAGGATGTACTCCTAAAAATGAGAATGTTGAT GTAGGATGGATTCAGGGGATATCCTGAATCCCCTGAATCA|CTCCTTGATTCAG|GGGATAGGGAGGATGTACTCCTAAAAATGAGAATGTTGAT ========== Event 3685 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AGTTGAGATTTGTCTAATAGATATACA----TACATATATATGT----ATAttataaaaacagatttatt Chimp: AGTTGAGATTTGTCTAATAGatataca----tacatatatatgt----atattataaaaacagatttatt Gorilla: AGTTGAGATTTGTCTAATAGATATACA--------TATGTATAT----CTATTAtaaaaccagatttatt ↑ 3 2 1 4 Human: AGTTGAGATTTGTCTAATAGATATACA----TACATATATATGT----ATAttataaaaacagatttatt Cluster: [ ] Orangutan: AGTTGAGATTTGTCTAATAGATATACATACA----GATATATGTATATCTAttataaaaacagatttatt Human > Gorilla --------------- chr8:55575663-55575670 Template switch process: F1: L GAAAAAACAATGAAAGTTGAGATTTGTCTAATAGATATACATA 1 F3: 4 TATTATAAAACCAGATTTATTGAGATACAATTCACATACC R RF: GAAAAAACAATGAAAGTTGAGATTTGTCTAATAGATATACATACATATATATGTATATTATAAAAACAGATTTATTGAGATACAATTCACATACC RR: CTTTTTTGTTACTTTCAACTCTAAACAGATTATCTATATGTATGTATATATACATATAATATTTTTGTCTAAATAACTCTATGTTAAGTGTATGG F2: 3 CTATATGT 2 Unidirectional alignment (log-probability: -32.4) AAAACAATGAAAGTTGAGATTTGTCTAATAGATATACATA--------TGTAtatcTATTATAAAAcCAGATTTATTGAGATACAATTCACATACC AAAACAATGAAAGTTGAGATTTGTCTAATAGATATACATACATATATATGTA----TATTATAAAAACAGATTTATTGAGATACAATTCACATACC Template switch alignment (log-probability: -22.3) AAAACAATGAAAGTTGAGATTTGTCTAATAGATATACATA|TGTATATC|TATTATAAAAcCAGATTTATTGAGATACAATTCACATACC AAAACAATGAAAGTTGAGATTTGTCTAATAGATATACATA|TGTATATC|TATTATAAAAACAGATTTATTGAGATACAATTCACATACC ========== Event 3686 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCTG--TGAAGCC-----CGGGGATAGAACTCTGGACTT Chimp: AATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCTG--TGAAGCC-----CGGGGATAGAACTCTGGACTT ↓ 3 4 2 1 Gorilla: AATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCTA----TAGCCTCTATAGGGGATAGAACTCTGGACTT Human: AATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCTG--TGAAGCC-----CGGGGATAGAACTCTGGACTT Cluster: [ ] Orangutan: AATCTTAGAAAATAGGCAGCAGCTATAGGATGAAAATCTGTG--AAGCC-----CGGGGATAGAACTCTGTACTT Chimp > Gorilla --------------- chr8:55340073-55340079 Template switch process: F1: L AAAATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCT 1 F3: 4 CTATA---------------------GGGGATAGAACTCTGGACTTAATTAGGTAGAGAGTTAGAG R RF: AAAATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCTGTGAAGCCCGGGGATAGAACTCTGGACTTAATTAGGTAGAGAGTTAGAG RR: TTTTAGAGTCTTTTATCCGTCTCCGATATCCTACTTTTAGACACTTCGGGCCCCTATCTTGAGACCTGAATTAATCCATCTCTCAATCTC F2: 3 TCCGATA 2 Unidirectional alignment (log-probability: -38.3) AAATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCT---------atagcctctataGGGGATAGAACTCTGGACTTAATTAGGTAGAGAGT AAATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCTGTGAAGCCC------------GGGGATAGAACTCTGGACTTAATTAGGTAGAGAGT Template switch alignment (log-probability: -27.6) AAATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCT|ATAGCCT|CTATA---------------------GGGGATAGAACTCTGGACTTAATTAGGTAGAGAGT AAATCTCAGAAAATAGGCAGAGGCTATAGGATGAAAATCT|ATAGCCT|CTATAGGATGAAAATCTGTGAAGCCCGGGGATAGAACTCTGGACTTAATTAGGTAGAGAGT ========== Event 3687 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 134 Detected in comparisons: 1234 Multiple sequence alignment: Human: CAGTAAAAGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCTATTGGTCAGTTGGCTTCTTAAGATGGTTCTT ↑ 3 1 2 4 Chimp: CAGTAAAAGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAAT----ATGTTGGCTTCTTAAGATGGTTCTT Gorilla: CAGTAAAAGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAAC----ATGGTGGCTTCTTAAGATGGTTCTT ↓ 3 2 4 ↑ 3 2 1 4 Human: CAGTAAAAGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCTATTGGTCAGTTGGCTTCTTAAGATGGTTCTT Cluster: [ ] Orangutan: CAGTAAAAGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAAT----ATGTTGGCTTCTTAAGATGGTTCTT Chimp > Human ------------- chr8:92473008-92473016 Template switch process: F1: L AGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC 1 F3: 4 GTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTG R RF: AGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAATATGTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTG RR: TCTTTTTCTTCAGATACAAAACTAACCGGTAAATTGACTGGTTATACAACCGAAGAATTCTACCAAGAAAAAGTCAGTAGGATGAC F2: 3 ACTGGTTAT 2 Unidirectional alignment (log-probability: -29.9) GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC--TATtggtcaGTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTG GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAATAT------GTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTG Template switch alignment (log-probability: -16.4) GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC|TATTGGTCA|GTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTG GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC|TATTGGTCA|GTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTG Gorilla > Human --------------- chr8:92473010-92473018 Template switch process: F1: L AGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCTA 1 F3: 4 TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA R RF: AGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAACATGGTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA RR: TCTTTTTCTTCAGATACAAAACTAACCGGTAAATTGACTGGTTGTACCACCGAAGAATTCTACCAAGAAAAAGTCAGTAGGATGACTT F2: 3 TGACTGGTT 2 Unidirectional alignment (log-probability: -36.8) AAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC-------tattggtcagtTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA AAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAACATGG-----------TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA Template switch alignment (log-probability: -22.4) AAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCtA|TTGGTCAGT|TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA AAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCAA|TTGGTCAGT|TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA Human > Gorilla --------------- chr8:93149704-93149710 Template switch process: F1: L AGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC 1 F3: 4 TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA R RF: AGAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCTATTGGTCAGTTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA RR: TCTTTTTCTTCAGATACAAAACTAACCGGTAAATTGACTGGATAACCAGTCAACCGAAGAATTCTACCAAGAAAAAGTCAGTAGGATGACTT F2: 3 GGTACAA 2 Unidirectional alignment (log-probability: -31.3) GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC-----------aacatggTGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACCTATTGGTCAGT-------TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA Template switch alignment (log-probability: -22.1) GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC|AACATgG|TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA GAAAAAGAAGTCTATGTTTTGATTGGCCATTTAACTGACC|AACATAG|TGGCTTCTTAAGATGGTTCTTTTTCAGTCATCCTACTGAA ========== Event 3688 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGACTCTCTGCAAAAGAGAGAAAGTATCTGTTGGCCAGTCAGATATT-----------------------------------------------------------------------------------------------CCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATCAAGTGGGAAAGCAGAC ↓ 3 4 2 1 Chimp: TGACTCTCTGCAAAAGAGAGAACGTATCTGTTGGCCAGTCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACAATGACAGCCCTTCTCCACTGGAATATCTGACTGGCCAACAGATACGTTCTCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATCAAGTGGGAAAGCAGAC ↑ 3 4 2 1 Gorilla: TGACTCTCTGCAAAAGAGAGAACATATCTGTTGGCCAGTCAGATATT-----------------------------------------------------------------------------------------------CCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATCAAGTGGGAAAGCAGAC Human: TGACTCTCTGCAAAAGAGAGAAAGTATCTGTTGGCCAGTCAGATATT-----------------------------------------------------------------------------------------------CCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATCAAGTGGGAAAGCAGAC Cluster: [ ] Orangutan: TGACTCTCTGCAAAAGAGAGAACATATCTGTTGGCCAGTCAGATATT-----------------------------------------------------------------------------------------------CCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATCAAGTGGGAAAGCAGAC Human > Chimp ------------- chr8:94040096-94040145 Template switch process: F1: L TCTGCAAAAGAGAGAACGTATCTGTTGGCCAGTCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC 1 F3: 4 TCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATC R RF: TCTGCAAAAGAGAGAAAGTATCTGTTGGCCAGTCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATC RR: AGACGTTTTCTCTCTTTCATAGACAACCGGTCAGTCTATAAGGTCACCTCTTCCCGACAGTAATTTTAGAACGTATGATAG F2: 3 CTTGCATAGACAACCGGTCAGTCTATAAGGTCACCTCTTCCCGACAGTAA 2 Unidirectional alignment (log-probability: -153) TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACaatgacagcccttctccactggaatatctgactggccaacagatacgttctcagatattccagtggagaagggctgtcattaaaatcttg TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC------------------------------------------------------------------------------------------ Template switch alignment (log-probability: -34.1) TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC|AATGACAGCCCTTCTCCACTGGAATATCTGACTGGCCAACAGATACgTTC|TCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTG TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC|AATGACAGCCCTTCTCCACTGGAATATCTGACTGGCCAACAGATACTTTC|TCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTG Gorilla > Chimp --------------- chr8:94040096-94040145 Template switch process: F1: L TCTGCAAAAGAGAGAACGTATCTGTTGGCCAGTCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC 1 F3: 4 TCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATC R RF: TCTGCAAAAGAGAGAACATATCTGTTGGCCAGTCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACTATC RR: AGACGTTTTCTCTCTTGTATAGACAACCGGTCAGTCTATAAGGTCACCTCTTCCCGACAGTAATTTTAGAACGTATGATAG F2: 3 CTTGCATAGACAACCGGTCAGTCTATAAGGTCACCTCTTCCCGACAGTAA 2 Unidirectional alignment (log-probability: -153) TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATACaatgacagcccttctccactggaatatctgactggccaacagatacgttctcagatattccagtggagaagggctgtcattaaaatcttg TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC------------------------------------------------------------------------------------------ Template switch alignment (log-probability: -34) TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC|AATGACAGCCCTTCTCCACTGGAATATCTGACTGGCCAACAGATAcGTTC|TCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTG TATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTGCATAC|AATGACAGCCCTTCTCCACTGGAATATCTGACTGGCCAACAGATATGTTC|TCAGATATTCCAGTGGAGAAGGGCTGTCATTAAAATCTTG ========== Event 3689 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTGTTAGTGGGAGGCAGAAGAACTTGACACTCATACACACAGGTTTGAAATAAGAC Chimp: TATTGTTAGTGGGAGGCAGAAGAACTTGACACTCATACACACAGGTTTGAAATAAGAC Gorilla: TATTGTTAGTGGGAGGCAGAAGAACAAGTTCTTCTCATACACAGGTTTGAAATAAGAC ↑ 3 1 2 4 Human: TATTGTTAGTGGGAGGCAGAAGAACTTGACACTCATACACACAGGTTTGAAATAAGAC Cluster: [ ] Orangutan: TATTGTTAGTCGGAGGCAGAAGAACTTGACACTCATACACACAGGTTTGAAATAAGAC Human > Gorilla --------------- chr8:93233895-93233902 Template switch process: F1: L TCCTTTACTTGTACTCTATTGTTAGTGGGAGGCAGAAGAAC 1 F3: 4 CTCAT--ACACAGGTTTGAAATAAGACAGGTGTGGCTGTTATTACAA R RF: TCCTTTACTTGTACTCTATTGTTAGTGGGAGGCAGAAGAACTTGACACTCATACACACAGGTTTGAAATAAGACAGGTGTGGCTGTTATTACAA RR: AGGAAATGAACATGAGATAACAATCACCCTCCGTCTTCTTGAACTGTGAGTATGTGTGTCCAAACTTTATTCTGTCCACACCGACAATAATGTT F2: 3 TTCTTGAA 2 Unidirectional alignment (log-probability: -38.5) CCTTTACTTGTACTCTATTGTTAGTGGGAGGCAGAAGAACaagttcttctcaT------------ACACAGGTTTGAAATAAGACAGGTGTGGCTGTTAT CCTTTACTTGTACTCTATTGTTAGTGGGAGGCAGAAGAAC------------TTGACACTCATACACACAGGTTTGAAATAAGACAGGTGTGGCTGTTAT Template switch alignment (log-probability: -26.7) CCTTTACTTGTACTCTATTGTTAGTGGGAGGCAGAAGAAC|AAGTTCTT|CTCAT--ACACAGGTTTGAAATAAGACAGGTGTGGCTGTTAT CCTTTACTTGTACTCTATTGTTAGTGGGAGGCAGAAGAAC|AAGTTCTT|CTCATACACACAGGTTTGAAATAAGACAGGTGTGGCTGTTAT ========== Event 3690 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGAGACCCTGTTTCTCTCAC------TTGCAACTTTCAGGTTGCAAGATTTGAAAAATGCTTGTC ↑ 1 4 3 2 Chimp: ATGAGACTCTGTTTCTCTCAC---TATATCTGGTTTTCAGGTTGCAAGATTTGAAAAATGCTTGTC Gorilla: ATGAGACCCTGTTTCTCTCACTAT---ATCTGGTTTTCAGGTTGCAAGATTTGAAAAATGCTTGTC ↓ 1 4 3 2 Human: ATGAGACCCTGTTTCTCTCAC------TTGCAACTTTCAGGTTGCAAGATTTGAAAAATGCTTGTC Cluster: [ ] Orangutan: ATGAGACCCTGTTTCTCTCACTAT---ATCTGGTTTTCAGGTTGCAAGATTTGAAAAATGCTTGTC Chimp > Human ------------- chr8:93655985-93655990 Template switch process: F1: L GAGCAATTTCTGTTTGCTCCATGAGACCCTGTTTCTCTCACT 1 F3: 4 TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG R RF: GAGCAATTTCTGTTTGCTCCATGAGACTCTGTTTCTCTCACTATATCTGGTTTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG RR: CTCGTTAAAGACAAACGAGGTACTCTGAGACAAAGAGAGTGATATAGACCAAAAGTCCAACGTTCTAAACTTTTTACGAACAGTTTTGAAC F2: 3 CAACGT 2 Unidirectional alignment (log-probability: -34.7) GCAATTTCTGTTTGCTCCATGAGACcCTGTTTCTCTCACT--------TgcaacTTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG GCAATTTCTGTTTGCTCCATGAGACTCTGTTTCTCTCACTATATCTGGT-----TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG Template switch alignment (log-probability: -22) GCAATTTCTGTTTGCTCCATGAGACcCTGTTTCTCTCACT|TGCAAC|TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG GCAATTTCTGTTTGCTCCATGAGACTCTGTTTCTCTCACT|TGCAAC|TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG Gorilla > Human --------------- chr8:93655985-93655990 Template switch process: F1: L GAGCAATTTCTGTTTGCTCCATGAGACCCTGTTTCTCTCACT 1 F3: 4 TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG R RF: GAGCAATTTCAGTTTGCTCCATGAGACCCTGTTTCTCTCACTATATCTGGTTTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG RR: CTCGTTAAAGTCAAACGAGGTACTCTGGGACAAAGAGAGTGATATAGACCAAAAGTCCAACGTTCTAAACTTTTTACGAACAGTTTTGAAC F2: 3 CAACGT 2 Unidirectional alignment (log-probability: -33.8) GCAATTTCtGTTTGCTCCATGAGACCCTGTTTCTCTCACT--------TgcaacTTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG GCAATTTCAGTTTGCTCCATGAGACCCTGTTTCTCTCACTATATCTGGT-----TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG Template switch alignment (log-probability: -22) GCAATTTCtGTTTGCTCCATGAGACCCTGTTTCTCTCACT|TGCAAC|TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG GCAATTTCAGTTTGCTCCATGAGACCCTGTTTCTCTCACT|TGCAAC|TTTCAGGTTGCAAGATTTGAAAAATGCTTGTCAAAACTTG ========== Event 3691 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTTGATAAAACGTACATTTTC------------ATAAGACTGTGTGAGTCTATTAAAG-------------------------------AGAAGCGTTCTGTGTTTTATTTTACCCTT Chimp: CTTGATAAAACGTACATTTTC------ATGTCTATAAGACTGTGTGAGTCTATTAAAGACTCACACAGTCTGTGAGTCTTTAATAAATAAAACACGTTCTGTGTTTTATTTTACCCTT ↑ 3 2 1 4 Gorilla: CTTGATAAAACATACATTTTCATGTCT------ATAAGACTGTGTGAGTCTATTAAAG-------------------------------AGAAGCGTTCTGTGTTTTATTTTACCGTT Human: CTTGATAAAACGTACATTTTC------------ATAAGACTGTGTGAGTCTATTAAAG-------------------------------AGAAGCGTTCTGTGTTTTATTTTACCCTT Cluster: [ ] Orangutan: CTTGATAAAACGTACATTTTCATGTCT------GTAAGACTGTGTGAGTCTATTAAAG-------------------------------AGAAGCGTTCTGTGTTTTATTTTACCGTT Gorilla > Chimp --------------- chr8:95320076-95320084 Template switch process: F1: L ACTGCAGAGGTGGATGCAAACTTGATAAAACGTACATTTTCATGTCTATAAGACTGTGTGAGTCTATTAAAGA 1 F3: 4 TCTGT R RF: ACTGCAGAGGTGGATGCAAACTTGATAAAACATACATTTTCATGTCTATAAGACTGTGTGAGTCTATTAAAGAGAAGCGTTCTGT RR: TGACGTCTCCACCTACGTTTGAACTATTTTGTATGTAAAAGTACAGATATTCTGACACACTCAGATAATTTCTCTTCGCAAGACA F2: 3 GACACACTC 2 Unidirectional alignment (log-probability: -34.8) ACATTTTCATGTCTATAAGACTGTGTGAGTCTATTAAAGactcacacagtctgt ACATTTTCATGTCTATAAGACTGTGTGAGTCTATTAAAG--------------- Template switch alignment (log-probability: -22.3) ACATTTTCATGTCTATAAGACTGTGTGAGTCTATTAAAGA|CTCACACAG|TCTGT ACATTTTCATGTCTATAAGACTGTGTGAGTCTATTAAAGA|CTCACACAG|TCTGT ========== Event 3692 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CAATATTATCCCTAGAAAATACAAATGTCCATAAATAAGT----AATTAATTTATGGACATTT----GTAAGAAAGTCTAGATAGCCT ↑ 1 4 3 2 Chimp: CAATATTATCCCTAGAAAATA------------TATAAGT----AATTAATTTATGGACATTT----GTAAGAAAGTCTAGATAGCCT Gorilla: CAATATTATCCCTAGAAAATA------------CATAAGT--------AATTTATGGACATTT----GTAAGAAAGTCTAGATAGCCT Human: CAATATTATCCCTAGAAAATACAAATGTCCATAAATAAGT----AATTAATTTATGGACATTT----GTAAGAAAGTCTAGATAGCCT Cluster: [ ] Orangutan: CAATATTATCCCTAGAAAATA------------CATAAGTAATT----AATTTACAGACATTTGTTAGTAAGAAAGTCTAGATAGCCT Chimp > Human ------------- chr8:94211170-94211182 Template switch process: F1: L TAATGTTTTAAGCATTCCTCCAATATTATCCCTAGAAAATA 1 F3: 4 ATAAGTAATTAATTTATGGACATTTGTAAGAAAGTCTAGA R RF: TAATGTTTTAAGCATTCCTCCAATATTATCCCTAGAAAATATATAAGTAATTAATTTATGGACATTTGTAAGAAAGTCTAGA RR: ATTACAAAATTCGTAAGGAGGTTATAATAGGGATCTTTTATATATTCATTAATTAAATACCTGTAAACATTCTTTCAGATCT F2: 3 AATACCTGTAAAC 2 Unidirectional alignment (log-probability: -34.2) AATGTTTTAAGCATTCCTCCAATATTATCCCTAGAAAatacaaatgtccATAaATAAGTAATTAATTTATGGACATTTGTAAGAAAGTCTAGA AATGTTTTAAGCATTCCTCCAATATTATCCCTAGAAA------------ATATATAAGTAATTAATTTATGGACATTTGTAAGAAAGTCTAGA Template switch alignment (log-probability: -16.9) AATGTTTTAAGCATTCCTCCAATATTATCCCTAGAAAATA|CAAATGTCCATAA|ATAAGTAATTAATTTATGGACATTTGTAAGAAAGTCTAGA AATGTTTTAAGCATTCCTCCAATATTATCCCTAGAAAATA|CAAATGTCCATAA|ATAAGTAATTAATTTATGGACATTTGTAAGAAAGTCTAGA ========== Event 3693 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GAGAGGAAGAGAGAAAAGGAACCATGTTTTCCATGATCAGCCTTCTGCAAACTCCCCACTGGGGACAGGAGCAGCCTGAGGAGGGACAACAGGAGGGCACAGTGAGCCCACATGCTTGTGAGCCCAAGTAGGAGAAACTGGGGCTT ↑ 3 2 4 1 Chimp: GAGAGGAAGAGAGAAAAGGAACCATGTTTTCCATGATCAGCCTTCTGCAAACTCCCCACTGGGGACAGGAGCAGCCTGAGGAGGGACAACGGGAGGGCACAGTGA----------------GCCCAAGTAGGAGAAACTGGGGCTT Gorilla: GAGAGCAAGAGAGAAAAGGAACCATGTTTTCCATGATCAGCCTTCTGCAAACTCCCCACTGGGGACAGGAGCAGCCTGAGGAGGGACAACGGGAGGGCACAGTGAGCCCACGTGCTTGTGAGCCCAAGTAGGAGAAACTGGGGCTT Human: GAGAGGAAGAGAGAAAAGGAACCATGTTTTCCATGATCAGCCTTCTGCAAACTCCCCACTGGGGACAGGAGCAGCCTGAGGAGGGACAACAGGAGGGCACAGTGAGCCCACATGCTTGTGAGCCCAAGTAGGAGAAACTGGGGCTT Cluster: [ ] Orangutan: GAGAGGAAGAGAGAAAAGGAACCATGTTTTCCATGATCAGCCTTCTGCAAACTCCCCACTGGGGACAGGAGCAGTCTGAGGAGGGACAACGGGAGGGCACAGTGAGCCCATGTGCTTGTGAGCCCAAGTAGGAGAAACTGGGGCTT Chimp > Human ------------- chr8:51260795-51260801 Template switch process: F1: L ACAGGAGCAGCCTGAGGAGGGACAACAGGAGGGCACAGTGAGCCCA 1 F3: 4 GTGAGCCCAAGTAGGAGAAACTGGGGCTTCAGTAACTTAAGAGA R RF: AACCATGTTTTCCATGATCAGCCTTCTGCAAACTCCCCACTGGGGACAGGAGCAGCCTGAGGAGGGACAACGGGAGGGCACAGTGAGCCCAAGTAGGAGAAACTGGGGCTTCAGTAACTTAAGAGA RR: TTGGTACAAAAGGTACTAGTCGGAAGACGTTTGAGGGGTGACCCCTGTCCTCGTCGGACTCCTCCCTGTTGCCCTCCCGTGTCACTCGGGTTCATCCTCTTTGACCCCGAAGTCATTGAATTCTCT F2: 3 TTCGTAC 2 Unidirectional alignment (log-probability: -39.9) GCAGCCTGAGGAGGGACAACaGGAGGGCACAGTGAGCCcacatgcttgtgagccCAAGTAGGAGAAACTGGGGCTTCAGTAACTTAA GCAGCCTGAGGAGGGACAACGGGAGGGCACAGTGAGCC----------------CAAGTAGGAGAAACTGGGGCTTCAGTAACTTAA Template switch alignment (log-probability: -28.3) GCAGCCTGAGGAGGGACAACaGGAGGGCACAGTGAGCCCA|CATGcTT|GTGAGCCCAAGTAGGAGAAACTGGGGCTTCAGTAACTTAA GCAGCCTGAGGAGGGACAACGGGAGGGCACAGTGAGCCCA|CATGGTT|GTGAGCCCAAGTAGGAGAAACTGGGGCTTCAGTAACTTAA ========== Event 3694 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATCTTTCAATTACAGCAACGATGCT---------------TTTAA---------CTAGGAGAATAATTAATGGCTTACTTC Chimp: ATCTTTCAATTACAGCAACGACGCT---------------TTTAA---------CTAGGAGAATAATTAATGGCTTACTCC ↓ 3 1 42 Gorilla: ATCTTTCAGTTACAGCAACGATGCT---------------TTTAACTCTCCTAGTTAAAAGAATAATTAATGGCTTACTCC ↑ 3 1 42 Human: ATCTTTCAATTACAGCAACGATGCT---------------TTTAA---------CTAGGAGAATAATTAATGGCTTACTTC Cluster: [ ] Orangutan: ATCTTTCAATCACAGCAACGATGCTGCCTCTTTCAATATAATTAA---------CGAGGAGAATAATTAATGGCTTACTCC Human > Gorilla --------------- chr8:96120109-96120120 Template switch process: F1: L CAGACAGTCACATCTTTCAGTTACAGCAACGATGCTTTTAACT 1 F3: 4 AGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC R RF: CAGACAGTCACATCTTTCAATTACAGCAACGATGCTTTTAACTAGGAGAATAATTAATGGCTTACTTCCAAAGTAGCCAGTATCAC RR: GTCTGTCAGTGTAGAAAGTTAATGTCGTTGCTACGAAAATTGATCCTCTTATTAATTACCGAATGAAGGTTTCATCGGTCATAGTG F2: 3 AAATTGATCCTC 2 Unidirectional alignment (log-probability: -46) ACAGTCACATCTTTCAgTTACAGCAACGATGCTTTTAACtctcctagtTAaaAGAATAATTAATGGCTTACTcCCAAAGTAGCCAGTATCAC ACAGTCACATCTTTCAATTACAGCAACGATGCTTTTAAC---------TAGGAGAATAATTAATGGCTTACTTCCAAAGTAGCCAGTATCAC Template switch alignment (log-probability: -28.3) ACAGTCACATCTTTCAgTTACAGCAACGATGCTTTTAACT|CTCCTAGTTAAA|AGAATAATTAATGGCTTACTcCCAAAGTAGCCAGTATCAC ACAGTCACATCTTTCAATTACAGCAACGATGCTTTTAACT|CTCCTAGTTAAA|AGAATAATTAATGGCTTACTTCCAAAGTAGCCAGTATCAC Chimp > Gorilla --------------- chr8:96120109-96120120 Template switch process: F1: L GATGACGTTCAGACAGTCACATCTTTCAGTTACAGCAACGATGCTTTTAACT 1 F3: 4 AGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC R RF: GATGACATTCAGACAGTCACATCTTTCAATTACAGCAACGACGCTTTTAACTAGGAGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC RR: CTACTGTAAGTCTGTCAGTGTAGAAAGTTAATGTCGTTGCTGCGAAAATTGATCCTCTTATTAATTACCGAATGAGGGTTTCATCGGTCATAGTG F2: 3 AAATTGATCCTC 2 Unidirectional alignment (log-probability: -51.6) ACAGTCACATCTTTCAgTTACAGCAACGAtGCTTTTAACtctcctagtTAaaAGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC ACAGTCACATCTTTCAATTACAGCAACGACGCTTTTAAC---------TAGGAGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC Template switch alignment (log-probability: -34.1) ACAGTCACATCTTTCAgTTACAGCAACGAtGCTTTTAACT|CTCCTAGTTAAA|AGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC ACAGTCACATCTTTCAATTACAGCAACGACGCTTTTAACT|CTCCTAGTTAAA|AGAATAATTAATGGCTTACTCCCAAAGTAGCCAGTATCAC ========== Event 3695 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTTTAAAAGTCACATTTAATTTC----CAGATTATTTCATGGATTGCCAGTGG ↓ 1 3 4 2 Chimp: ATTTTAAAAGTCACATTTAATAATCTGGAAGATTATTTCATGGATTGCCAGTGG ↑ 1 3 4 2 Gorilla: ATTTTAAAAGTCACATTTAATTTC----CAGATTATTTCATGGATTGCCAGTGG Human: ATTTTAAAAGTCACATTTAATTTC----CAGATTATTTCATGGATTGCCAGTGG Cluster: [ ] Orangutan: ATTTTAAAAGTCACATTTAATTTC----CAGATTATTTCATGGATTGCCATTGG Human > Chimp ------------- chr8:98236344-98236351 Template switch process: F1: L AAAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT 1 F3: 4 AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT R RF: AAAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAATTTCCAGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT RR: TTTTAGAATTACGTTTATAATAAAATTTTCAGTGTAAATTAAAGGTCTAATAAAGTACCTAACGGTCACCTCCTCGACCGAATAA F2: 3 AGGTCTAA 2 Unidirectional alignment (log-probability: -32.8) AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAATaatctgga----AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT--------TTCCAGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT Template switch alignment (log-probability: -16.3) AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT|AATCTGGA|AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT|AATCTGGA|AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT Gorilla > Chimp --------------- chr8:98236344-98236351 Template switch process: F1: L AAAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT 1 F3: 4 AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT R RF: AAAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAATTTCCAGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT RR: TTTTAGAATTACGTTTATAATAAAATTTTCAGTGTAAATTAAAGGTCTAATAAAGTACCTAACGGTCACCTCCTCGACCGAATAA F2: 3 AGGTCTAA 2 Unidirectional alignment (log-probability: -32.3) AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT----aatctggaAGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAATTTCC--------AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT Template switch alignment (log-probability: -16.7) AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT|AATCTGGA|AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT AAATCTTAATGCAAATATTATTTTAAAAGTCACATTTAAT|AATCTGGA|AGATTATTTCATGGATTGCCAGTGGAGGAGCTGGCTTATT ========== Event 3696 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TATTTTGTTAGAGTAGATACTAGTTAGTCGTTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTttaaa---catactatactagaaacagtttgt Chimp: TATTTTGTTAGAGTAGATACTAGTTAGTCGTTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAA---CATACTATACTAGAAACAGTTTGT ↓ 3 2 1 4 Gorilla: TATTTTGTTAGAGTAGATACTAGTTAGTCGTTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAAAACTAGACTATACTAGAAACAGTTTGT Human: TATTTTGTTAGAGTAGATACTAGTTAGTCGTTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTttaaa---catactatactagaaacagtttgt Cluster: [ ] Orangutan: TATTTTGTTAGAGTAGATACTAGTTAGTCATTATTGTTTTG-GGGTAATCCCACAGTAAATGCTTTTAAAAACTAGACTATATTAGAAACAGTTTGT Chimp > Gorilla --------------- chr8:97191640-97191645 Template switch process: F1: L GTTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAA 1 F3: 4 ACTATACTAGAAACAGTTTGTCCCTGAAGGAGGAATTAGA R RF: CTAGTTAGTCGTTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAACATACTATACTAGAAACAGTTTGTCCCTGAAGGAGGAATTAGA RR: GATCAATCAGCAATAACAAAACCCCCATTAGGGTGTCATTTACGAAAATTTGTATGATATGATCTTTGTCAAACAGGGACTTCCTCCTTAATCT F2: 3 GATCAA 2 Unidirectional alignment (log-probability: -26.3) TTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAAaactAgACTATACTAGAAACAGTTTGTCCCTGAAGGAGGAATTAGA TTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAA---CATACTATACTAGAAACAGTTTGTCCCTGAAGGAGGAATTAGA Template switch alignment (log-probability: -16.5) TTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAA|AACTAG|ACTATACTAGAAACAGTTTGTCCCTGAAGGAGGAATTAGA TTATTGTTTTGGGGGTAATCCCACAGTAAATGCTTTTAAA|AACTAG|ACTATACTAGAAACAGTTTGTCCCTGAAGGAGGAATTAGA ========== Event 3697 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCCACACAGACATTCACTGAGCCTCTGCCCAGCGTTCTGACACAGACTTC ↓ 3 1 2 4 Chimp: CCCACACAGACATTCACTGAGCAGAGGCTCAGCGTTCTGACACAGACTTC ↑ 3 1 2 4 Gorilla: CCCACACAGACATTCACTGAGCCTCTGCCCAGCGTTCTGACACAGACTTC Human: CCCACACAGACATTCACTGAGCCTCTGCCCAGCGTTCTGACACAGACTTC Cluster: [ ] Orangutan: CCTACACAGACATTCACTGAGCCTCTGCCCAGCGTTCTGA--CAGACTTC Human > Chimp ------------- chr8:9461682-9461688 Template switch process: F1: L TTGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC 1 F3: 4 CAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA R RF: TTGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGCCTCTGCCCAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA RR: AACGTCGGTGTCAAGTACGGGGTGTGTCTGTAAGTGACTCGGAGACGGGTCGCAAGACTGTGTCTGAAGGTGTTCCGGGTGTAGACCT F2: 3 TCGGAGA 2 Unidirectional alignment (log-probability: -28.6) TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGCagaggCT-----CAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC-----CTCTGCCCAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA Template switch alignment (log-probability: -16.2) TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC|AGAGGCT|CAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC|AGAGGCT|CAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA Gorilla > Chimp --------------- chr8:9461682-9461688 Template switch process: F1: L TTGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC 1 F3: 4 CAGCGTTCTGACACAGACTTCCACAAGGCCCACATCTGGA R RF: TTGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGCCTCTGCCCAGCGTTCTGACACAGACTTCCACGAGGCTCACATCTGGA RR: AACGTCGGTGTCAAGTACGGGGTGTGTCTGTAAGTGACTCGGAGACGGGTCGCAAGACTGTGTCTGAAGGTGCTCCGAGTGTAGACCT F2: 3 TCGGAGA 2 Unidirectional alignment (log-probability: -39.1) TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGCagaggCT-----CAGCGTTCTGACACAGACTTCCACaAGGCcCACATCTGGA TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC-----CTCTGCCCAGCGTTCTGACACAGACTTCCACGAGGCTCACATCTGGA Template switch alignment (log-probability: -27.7) TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC|AGAGGCT|CAGCGTTCTGACACAGACTTCCACaAGGCcCACATCTGGA TGCAGCCACAGTTCATGCCCCACACAGACATTCACTGAGC|AGAGGCT|CAGCGTTCTGACACAGACTTCCACGAGGCTCACATCTGGA ========== Event 3698 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CCCACTGAGAAATTATGTTTCTTGAAATGTGAAAGACAGCAAATCTAAAGAGCATTCTCCTGGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCTT--------CAAGAAAGCACAATGCTTTCTCTGGG Chimp: CCCACTGAGAAATTATGTTTTTTGAAATGTGAAAGACAGCAAATCTAAAGAGCATTCTCCTGGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCTT----GTGAACAGTAAGCACAATGCTTTCTCTGGG Gorilla: CCCACTGAGAAATTATGTTTCTTGAAATGTGAAAGACAGCAAATCTAAAGAGCATTCTCCTGGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCTCGTGA----ACAGTAAGCACAATGCTTTCTCTGGG ↓ 3 2 1 4 Human: CCCACTGAGAAATTATGTTTCTTGAAATGTGAAAGACAGCAAATCTAAAGAGCATTCTCCTGGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCTT--------CAAGAAAGCACAATGCTTTCTCTGGG Cluster: [ ] Orangutan: CCCACTGAGAAATTATGTTTCTTGAAATGTGAAAGACAGCAAATCTAAAGAGCATTCTCCTGGCCATATGACTTGGCTCCTTCTGCCAGCTCTTCAAGTTTCATGA----ACAGTAAGCACAATGCTTTCTCTGGG Gorilla > Human --------------- chr8:10327045-10327050 Template switch process: F1: L TGGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCT 1 F3: 4 AAGCACAATGCTTTCTCTGGGTATTTCTCTCGCGAAAAAG R RF: TCTTGAAATGTGAAAGACAGCAAATCTAAAGAGCATTCTCCTGGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCTCGTGAACAGTAAGCACAATGCTTTCTCTGGGTATTTCTCTCGTGAAAAAG RR: AGAACTTTACACTTTCTGTCGTTTAGATTTCTCGTAAGAGGACCGGTATACTGGACCGAGGAAGACGGTCGAGAAGTTCAGAGCACTTGTCATTCGTGTTACGAAAGAGACCCATAAAGAGAGCACTTTTTC F2: 3 AGAACT 2 Unidirectional alignment (log-probability: -33.8) GGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCT---------TcaagaAAGCACAATGCTTTCTCTGGGTATTTCTCTCGcGAAAAAG GGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCTCGTGAACAGT-----AAGCACAATGCTTTCTCTGGGTATTTCTCTCGTGAAAAAG Template switch alignment (log-probability: -22) GGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCT|TCAAGA|AAGCACAATGCTTTCTCTGGGTATTTCTCTCGcGAAAAAG GGCCATATGACCTGGCTCCTTCTGCCAGCTCTTCAAGTCT|TCAAGA|AAGCACAATGCTTTCTCTGGGTATTTCTCTCGTGAAAAAG ========== Event 3699 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTG---GACTTTAGTCTAAGTCTACTTAGTGGACTTAGTATTAAGTCTTTAATACT Chimp: GTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTT---CACTTTAGTCTAAGTCCACTTAGTGGACTTAGTATTAAGTCTTTAATACT ↑ 3 4 2 Gorilla: GTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTG----------------------------GACTTAGTATTAAGTCTTTAATACT ↓ 4 2 1 Human: GTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTG---GACTTTAGTCTAAGTCTACTTAGTGGACTTAGTATTAAGTCTTTAATACT Cluster: [ ] Orangutan: TTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTGGAC-------------------------------------------------- Gorilla > Human --------------- chr8:46654485-46654495 Template switch process: F1: L TCCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTGGACTT 1 F3: 4 TACTT-------AGTGGACTTAGTATTAAGTCTTTAATACTTAAAGACTTAGTATT R RF: TCCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTGGACTTAGTATTAAGTCTTTAATACTTAAAGACTTAGTATT RR: AGGACCAGAAAGACTTTTTAACACCCTGAATCTGATTTCACCTGAATCATAATTCAGAAATTATGAATTTCTGAATCATAA F2: 3 CTGAATCTGAT 2 Unidirectional alignment (log-probability: -46.8) TCTTTCTGAAAAATTGTGGGACTTAGACTAAAGtggactttagtctaagtctacttagTGGACTTAGTATTAAGTCTTTAATACTTAAAGA TCTTTCTGAAAAATTGTGGGACTTAGACTAAAG-------------------------TGGACTTAGTATTAAGTCTTTAATACTTAAAGA Template switch alignment (log-probability: -33.1) TCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTGGACTT|TAGTCTAAGTC|tACTT-------AGTGGACTTAGTATTAAGTCTTTAATACTTAAAGA TCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTGGACTT|TAGTCTAAGTC|GACTTAGACTAAAGTGGACTTAGTATTAAGTCTTTAATACTTAAAGA Gorilla > Chimp --------------- chr8:47631078-47631094 Template switch process: F1: L CTCCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTT 1 F3: 4 ACTT-------AGTGGACTTAGTATTAAGTCTTTAATACTTAAAGACTTAGTATT R RF: CTCCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTGGACTTAGTATTAAGTCTTTAATACTTAAAGACTTAGTATT RR: GAGGACCAGAAAGACTTTTTAACACCCTGAATCTGATTTCACCTGAATCATAATTCAGAAATTATGAATTTCTGAATCATAA F2: 3 CCTGAATCTGATTTCAC 2 Unidirectional alignment (log-probability: -46.8) CCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAgttcactttagtctaagtccacttaGTGGACTTAGTATTAAGTCTTTAATACTTAAAGAC CCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAA-------------------------GTGGACTTAGTATTAAGTCTTTAATACTTAAAGAC Template switch alignment (log-probability: -33.7) CCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTt|CACTTTAGTCTAAGTCC|ACTT-------AGTGGACTTAGTATTAAGTCTTTAATACTTAAAGAC CCTGGTCTTTCTGAAAAATTGTGGGACTTAGACTAAAGTG|CACTTTAGTCTAAGTCC|ACTTAGACTAAAGTGGACTTAGTATTAAGTCTTTAATACTTAAAGAC ========== Event 3700 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ACCCGAAATTTTGTGCTATACTA-gttaaaagttcgtcttcaattttgttatgct Chimp: ACCTGAAATTTTGTGCTATACTA-GTTAAAAGTTCGTCTTCAATTTTGTTATGCT ↓ 1 3 4 2 Gorilla: ACCTGAAATTTTGTGCTATACGAACTTTTAAGTTCGTCTTCAATTTTGTTATGCT Human: ACCCGAAATTTTGTGCTATACTA-gttaaaagttcgtcttcaattttgttatgct Cluster: [ ] Orangutan: acctgaaattttctgctatacta-gttaaaagttcgtcttcaattttgttatgct Chimp > Gorilla --------------- chr8:46027911-46027918 Template switch process: F1: L TTTCTGAAATTGTTGAATAAACCTGAAATTTTGTGCTATAC 1 F3: 4 AAGTTCGTCTTCAATTTTGTTATGCTATTAATTTTTTATG R RF: TTTCTGAAATTGTTGAATAAACCTGAAATTTTGTGCTATACTAGTTAAAAGTTCGTCTTCAATTTTGTTATGCTATTAATTTTTTATG RR: AAAGACTTTAACAACTTATTTGGACTTTAAAACACGATATGATCAATTTTCAAGCAGAAGTTAAAACAATACGATAATTAAAAAATAC F2: 3 TTTTCAAG 2 Unidirectional alignment (log-probability: -31) TTCTGAAATTGTTGAATAAACCTGAAATTTTGTGCTATACgaactttT------AAGTTCGTCTTCAATTTTGTTATGCTATTAATTTTTTATG TTCTGAAATTGTTGAATAAACCTGAAATTTTGTGCTATAC-------TAGTTAAAAGTTCGTCTTCAATTTTGTTATGCTATTAATTTTTTATG Template switch alignment (log-probability: -16.7) TTCTGAAATTGTTGAATAAACCTGAAATTTTGTGCTATAC|GAACTTTT|AAGTTCGTCTTCAATTTTGTTATGCTATTAATTTTTTATG TTCTGAAATTGTTGAATAAACCTGAAATTTTGTGCTATAC|GAACTTTT|AAGTTCGTCTTCAATTTTGTTATGCTATTAATTTTTTATG ========== Event 3701 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: gatatCCCCTATTAGCTTGTGAT---TT----TATAGTACCTTAGTGCATGCACCTACAT Chimp: gatatCGCCTATTAGCTTGTGAT---TT----TATAGTACCTTAGTGCATGCACCTACAT Gorilla: gatatCCCCTATTAGCTTGTGTGTACTATAAAAATAGTACCTTAGTACATGCACCTACAT ↑ 1 3 4 2 Human: gatatCCCCTATTAGCTTGTGAT---TT----TATAGTACCTTAGTGCATGCACCTACAT Cluster: [ ] Orangutan: GATATCCCCTATTAGCTTGTGAT---TT----TATAGTACCTTAATGCATGCACCTATAT Human > Gorilla --------------- chr8:46572259-46572269 Template switch process: F1: L ATATATACATATATAAAACAGATATCCCCTATTAGCTTGTGT 1 F3: 4 ATAGTACCTTAGTACATGCACCTACATTCATGACAAAACT R RF: ATATATACATATATAAAACAGATATCCCCTATTAGCTTGTGATTTTATAGTACCTTAGTGCATGCACCTACATTCATGACAAAACT RR: TATATATGTATATATTTTGTCTATAGGGGATAATCGAACACTAAAATATCATGGAATCACGTACGTGGATGTAAGTACTGTTTTGA F2: 3 AAAATATCATG 2 Unidirectional alignment (log-probability: -42.2) ATATACATATATAAAACAGATATCCCCTATTAGCTTGTG----TgtactataaaaATAGTACCTTAGTaCATGCACCTACATTCATGACAAAACT ATATACATATATAAAACAGATATCCCCTATTAGCTTGTGATTTT-----------ATAGTACCTTAGTGCATGCACCTACATTCATGACAAAACT Template switch alignment (log-probability: -28.2) ATATACATATATAAAACAGATATCCCCTATTAGCTTGTGt|GTACTATAAAA|ATAGTACCTTAGTaCATGCACCTACATTCATGACAAAACT ATATACATATATAAAACAGATATCCCCTATTAGCTTGTGA|GTACTATAAAA|ATAGTACCTTAGTGCATGCACCTACATTCATGACAAAACT ========== Event 3702 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAAATTTTGTCATGTTACATCTATAAT----GTTTTG----TGTGTGCTTATTGATTGCCAAT Chimp: TAAAATTTTGTCATGTTACGTCTATAAT----GCTTTG----TGTGTGCTTATTGATTGCCAAT ↓ 3 1 2 4 Gorilla: TAAAATTTTGTCATGTTACGTCTATAATGAAAGCATTATAGACGTGTGCTTATTGATTGCCAAT Human: TAAAATTTTGTCATGTTACATCTATAAT----GTTTTG----TGTGTGCTTATTGATTGCCAAT Cluster: [ ] Orangutan: TAAAATTTTGTCATGTTACGTCTATAAT----GCTTTG----TGTGTGCTTATTGATTGCCAAT Chimp > Gorilla --------------- chr9:37178152-37178165 Template switch process: F1: L CTTGAGCAAAAAGTAAAATTTTGTCATGTTACGTCTATAATG 1 F3: 4 GTGTGCTTATTGATTGCCAATGTACAATCTAAACTTATCT R RF: CTTGAGCAAAAAGTAAAATTTTGTCATGTTACGTCTATAATGCTTTGTGTGTGCTTATTGATTGCCAATGTACAATCTAAACTTATCT RR: GAACTCGTTTTTCATTTTAAAACAGTACAATGCAGATATTACGAAACACACACGAATAACTAACGGTTACATGTTAGATTTGAATAGA F2: 3 CAGATATTACGAAA 2 Unidirectional alignment (log-probability: -39.6) TGAGCAAAAAGTAAAATTTTGTCATGTTACGTCTATAATGaaagcattatagaC-----GTGTGCTTATTGATTGCCAATGTACAATCTAAACTTATCT TGAGCAAAAAGTAAAATTTTGTCATGTTACGTCTATAATG-------------CTTTGTGTGTGCTTATTGATTGCCAATGTACAATCTAAACTTATCT Template switch alignment (log-probability: -17.5) TGAGCAAAAAGTAAAATTTTGTCATGTTACGTCTATAATG|AAAGCATTATAGAC|GTGTGCTTATTGATTGCCAATGTACAATCTAAACTTATCT TGAGCAAAAAGTAAAATTTTGTCATGTTACGTCTATAATG|AAAGCATTATAGAC|GTGTGCTTATTGATTGCCAATGTACAATCTAAACTTATCT ========== Event 3703 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CCCAAGATATTAACAATGTTAAT---GCAAGTATATTCATATTGTAGATGACATACATATTGGCTTGCTTGt Chimp: CCCAAGATATTAACAATGTTAAT---GTAAGTATATTCATATTGAAG--AACATACATATTGGCTTGCTTGt ↓ 3 2 1 4 Gorilla: CCCAATATATTAACAATGTTAAT---GTAAGTATATTCATATTGTACATGACATACATATTGGCTTGCTTGt Human: CCCAAGATATTAACAATGTTAAT---GCAAGTATATTCATATTGTAGATGACATACATATTGGCTTGCTTGt Cluster: [ ] Orangutan: CCTAAGATATTAACAATGTTAATGTTTTAAGTATATTCATATTGTAGATGACACACATATTGGCTTGGTTGt Chimp > Gorilla --------------- chr9:84796030-84796036 Template switch process: F1: L CCCAATATATTAACAATGTTAATGTAAGTATATTCATATTG 1 F3: 4 CATACATATTGGCTTGCTTGTTTAGTTTACTTTTATCTT R RF: CCCAAGATATTAACAATGTTAATGTAAGTATATTCATATTGAAGAACATACATATTGGCTTGCTTGTTTAGTTTACTTTTATCTT RR: GGGTTCTATAATTGTTACAATTACATTCATATAAGTATAACTTCTTGTATGTATAACCGAACGAACAAATCAAATGAAAATAGAA F2: 3 AGTACAT 2 Unidirectional alignment (log-probability: -40) CCAAtATATTAACAATGTTAATGTAAGTATATTCATATTGtAcAtgACATACATATTGGCTTGCTTGTTTAGTTTACTTTTATCtt CCAAGATATTAACAATGTTAATGTAAGTATATTCATATTGAAGA--ACATACATATTGGCTTGCTTGTTTAGTTTACTTTTATC-- Template switch alignment (log-probability: -27.6) CCAAtATATTAACAATGTTAATGTAAGTATATTCATATTG|TACATgA|CATACATATTGGCTTGCTTGTTTAGTTTACTTTTATCTT CCAAGATATTAACAATGTTAATGTAAGTATATTCATATTG|TACATTA|CATACATATTGGCTTGCTTGTTTAGTTTACTTTTATCTT ========== Event 3704 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: TAAACATAATGCTAAAACTTAGAT-TGATTTTTTAAAAATCTAATGTATCACATCAATTGAAAGTGT Chimp: TAAACATAACGCTAAAACTTAGAT-TGATTTTTAAAAAATCTAATGTATCACATCAATTGAAAGTGT ↓ 13 24 ↑ 13 24 Gorilla: TAAACATAACGCTAAAACTTACATTAGATTTTTAAAAAAT-CAATCTATCACATCAATTGAAAGTGT ↓ 13 24 ↑ 13 24 Human: TAAACATAATGCTAAAACTTAGAT-TGATTTTTTAAAAATCTAATGTATCACATCAATTGAAAGTGT Cluster: [ ] Orangutan: TAAACATAACGCTAAAACTTAGAT-TGATTTTTTAAAAATCTAATGTATCACATCAATTGAAAGTGT Gorilla > Human --------------- chr9:34579424-34579447 Template switch process: F1: L GGCTACAATGGGAAATTTAATAAACATAATGCTAAAACTTA 1 F3: 4 TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT R RF: GGCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTACATTAGATTTTTAAAAAATCAATCTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT RR: CCGATGTTACCCTTTAAATTATTTGTATTGCGATTTTGAATGTAATCTAAAAATTTTTTAGTTAGATAGTGTAGTTAACTTTCACATGTTTGTTAAACGATATAA F2: 3 GTAATCTAAAAATTTTTTAGTTAG 2 Unidirectional alignment (log-probability: -44.5) GCTACAATGGGAAATTTAATAAACATAAtGCTAAAACTTAgATT-GATTTTTtAAAAATCtAATgTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT GCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTACATTAGATTTTTAAAAAATC-AATCTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT Template switch alignment (log-probability: -24.3) GCTACAATGGGAAATTTAATAAACATAAtGCTAAAACTTA|GATTGATTTTTTAAAAATCTAATG|TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT GCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTA|GATTGATTTTTTAAAAATCTAATG|TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT Human > Gorilla --------------- chr9:35642463-35642486 Template switch process: F1: L GGCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTA 1 F3: 4 TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT R RF: GGCTACAATGGGAAATTTAATAAACATAATGCTAAAACTTAGATTGATTTTTTAAAAATCTAATGTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT RR: CCGATGTTACCCTTTAAATTATTTGTATTACGATTTTGAATCTAACTAAAAAATTTTTAGATTACATAGTGTAGTTAACTTTCACATGTTTGTTAAACGATATAA F2: 3 CTAACTAAAAAATTTTTAGATTAC 2 Unidirectional alignment (log-probability: -44.5) GCTACAATGGGAAATTTAATAAACATAAcGCTAAAACTTAcATTaGATTTTTaAAAAATC-AATcTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT GCTACAATGGGAAATTTAATAAACATAATGCTAAAACTTAGATT-GATTTTTTAAAAATCTAATGTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT Template switch alignment (log-probability: -24.3) GCTACAATGGGAAATTTAATAAACATAAcGCTAAAACTTA|CATTAGATTTTTAAAAAATCAATC|TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT GCTACAATGGGAAATTTAATAAACATAATGCTAAAACTTA|CATTAGATTTTTAAAAAATCAATC|TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT Gorilla > Chimp --------------- chr9:35130442-35130465 Template switch process: F1: L ATAAACATAACGCTAAAACTTA 1 F3: 4 TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT R RF: ATAAACATAACGCTAAAACTTACATTAGATTTTTAAAAAATCAATCTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT RR: TATTTGTATTGCGATTTTGAATGTAATCTAAAAATTTTTTAGTTAGATAGTGTAGTTAACTTTCACATGTTTGTTAAACGATATAA F2: 3 GTAATCTAAAAAATTTTTAGTTAG 2 Unidirectional alignment (log-probability: -33.2) ATAAACATAACGCTAAAACTTAgATT-GATTTTTAAAAAATCtAATgTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT ATAAACATAACGCTAAAACTTACATTAGATTTTTAAAAAATC-AATCTATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT Template switch alignment (log-probability: -23.8) ATAAACATAACGCTAAAACTTA|GATTGATTTTTaAAAAATCTAATG|TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT ATAAACATAACGCTAAAACTTA|GATTGATTTTTTAAAAATCTAATG|TATCACATCAATTGAAAGTGTACAAACAATTTGCTATATT Chimp > Gorilla --------------- chr9:35642463-35642486 Template switch process: F1: L GGCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTA 1 F3: 4 TATCACATCAATTGAAAGTG R RF: GGCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTAGATTGATTTTTAAAAAATCTAATGTATCACATCAATTGAAAGTG RR: CCGATGTTACCCTTTAAATTATTTGTATTGCGATTTTGAATCTAACTAAAAATTTTTTAGATTACATAGTGTAGTTAACTTTCAC F2: 3 CTAACTAAAAAATTTTTAGATTAC 2 Unidirectional alignment (log-probability: -33.2) GCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTAcATTaGATTTTTAAAAAATC-AATcTATCACATCAATTGAAAGTG GCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTAGATT-GATTTTTAAAAAATCTAATGTATCACATCAATTGAAAGTG Template switch alignment (log-probability: -23.8) GCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTA|CATTAGATTTTTaAAAAATCAATC|TATCACATCAATTGAAAGTG GCTACAATGGGAAATTTAATAAACATAACGCTAAAACTTA|CATTAGATTTTTTAAAAATCAATC|TATCACATCAATTGAAAGTG ========== Event 3705 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTATCATGGTGTAATAGATGACATAGAAGAAATT-GATCAAAACAACTAAAAAGAAATGA ↓ 3 2 1 4 Chimp: GTATCATGGTGTAATAGATGACATAGAAGAAACTATGTCAAAACAACTAAAAAGAAATGA ↑ 3 2 1 4 Gorilla: TTATCATGGTGTAATAGATGACATAGAAGAAATT-GATCAAAACAACTAAAAAGAAATGA Human: TTATCATGGTGTAATAGATGACATAGAAGAAATT-GATCAAAACAACTAAAAAGAAATGA Cluster: [ ] Orangutan: TTATCGTGGTGTAATAGATGACATAGAAGAAATT-GATCAAAACAACCAAAAAGAAATGA Human > Chimp ------------- chr9:35113788-35113794 Template switch process: F1: L TTCTGAGAAGTATCATGGTGTAATAGATGACATAGAAGAAA 1 F3: 4 AAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA R RF: TTCTGAGAATTATCATGGTGTAATAGATGACATAGAAGAAATTGATCAAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA RR: AAGACTCTTAATAGTACCACATTATCTACTGTATCTTCTTTAACTAGTTTTGTTGATTTTTCTTTACTCTCGTCCTTTTTATGTT F2: 3 CTGTATC 2 Unidirectional alignment (log-probability: -34.5) TCTGAGAAgTATCATGGTGTAATAGATGACATAGAAGAAActatgT----CAAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA TCTGAGAATTATCATGGTGTAATAGATGACATAGAAGAAA-----TTGATCAAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA Template switch alignment (log-probability: -22.1) TCTGAGAAgTATCATGGTGTAATAGATGACATAGAAGAAA|CTATGTC|AAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA TCTGAGAATTATCATGGTGTAATAGATGACATAGAAGAAA|CTATGTC|AAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA Gorilla > Chimp --------------- chr9:35113788-35113794 Template switch process: F1: L TTCTGAGAAGTATCATGGTGTAATAGATGACATAGAAGAAA 1 F3: 4 AAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA R RF: TTCTGAGAATTATCATGGTGTAATAGATGACATAGAAGAAATTGATCAAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA RR: AAGACTCTTAATAGTACCACATTATCTACTGTATCTTCTTTAACTAGTTTTGTTGATTTTTCTTTACTCTCGTCCTTTTTATGTT F2: 3 CTGTATC 2 Unidirectional alignment (log-probability: -33.5) TCTGAGAAgTATCATGGTGTAATAGATGACATAGAAGAA----ActatgTCAAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA TCTGAGAATTATCATGGTGTAATAGATGACATAGAAGAAATTGA-----TCAAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA Template switch alignment (log-probability: -22.1) TCTGAGAAgTATCATGGTGTAATAGATGACATAGAAGAAA|CTATGTC|AAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA TCTGAGAATTATCATGGTGTAATAGATGACATAGAAGAAA|CTATGTC|AAAACAACTAAAAAGAAATGAGAGCAGGAAAAATACAA ========== Event 3706 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTCACTGGGGGTGCACAATAA------GACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGA ↓ 1 4 3 2 Chimp: TTCACTGGGGGTGCACAATAAGCATTTGGGAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGA ↑ 1 4 3 2 Gorilla: TTCACTGGGGGTGCACAATAA------GACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGA Human: TTCACTGGGGGTGCACAATAA------GACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGA Cluster: [ ] Orangutan: TTCACTGGGGGTGCACAATAA------GACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGA Human > Chimp ------------- chr9:82777320-82777327 Template switch process: F1: L TGAAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG 1 F3: 4 AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA R RF: TGAAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAGACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA RR: ACTTTTTGTGAATGGTGGGGAAGTGACCCCCACGTGTTATTCTGTTTTCGTAAGGGTTTACTTAGAAGTTACACACCCTCTCTT F2: 3 GGGTTTAC 2 Unidirectional alignment (log-probability: -31.3) AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG-CatttgggAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAGAC-------AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA Template switch alignment (log-probability: -16.3) AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG|CATTTGGG|AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG|CATTTGGG|AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA Gorilla > Chimp --------------- chr9:82777320-82777327 Template switch process: F1: L TGAAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG 1 F3: 4 AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA R RF: TGAAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAGACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA RR: ACTTTTTGTGAATGGTGGGGAAGTGACCCCCACGTGTTATTCTGTTTTCGTAAGGGTTTACTTAGAAGTTACACACCCTCTCTT F2: 3 GGGTTTAC 2 Unidirectional alignment (log-probability: -30.6) AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAgcatttGggAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAA------GACAAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA Template switch alignment (log-probability: -16.8) AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG|CATTTGGG|AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA AAAAACACTTACCACCCCTTCACTGGGGGTGCACAATAAG|CATTTGGG|AAAAGCATTCCCAAATGAATCTTCAATGTGTGGGAGAGAA ========== Event 3707 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTATGACTCAATATTTTCAGATCA------------------------------------------TAACTGTAATGTCATTACAGGAAGAATGCAC Chimp: TGTATGactcaatattttcagatca---------------------taactcattacagttagatcataactGTAATGTCATTACAGGAAGAATGCAC Gorilla: TGTATGACTCAATATTTTCAGATCATAATTCATTACAGTTAGATCA---------------------TAACTGTAATGTCATTACAGGAAGAATGCAC ↑ 4 3 1 2 Human: TGTATGACTCAATATTTTCAGATCA------------------------------------------TAACTGTAATGTCATTACAGGAAGAATGCAC Cluster: [ ] Orangutan: TGTATGACTCAATATTTTCAGATCATAACTCATTACAGTTAGATCG---------------------TAACTGTAATGTCATTACAAGAAGTATGCAC Human > Gorilla --------------- chr9:87046927-87046936 Template switch process: F1: L AGATAACAGGAATTCATGTATGACTCAATATTTTCAGATCATAATT 1 F3: 4 AGATCATAACTGTAATGTCATTACAGGAAGAATGCACAAATGCTTA R RF: AGATAACAGGAATTCATGTATGACTCAATATTTTCAGATCATAACTGTAATGTCATTACAGGAAGAATGCACAAATGCTTA RR: TCTATTGTCCTTAAGTACATACTGAGTTATAAAAGTCTAGTATTGACATTACAGTAATGTCCTTCTTACGTGTTTACGAAT F2: 3 TTGACATTAC 2 Unidirectional alignment (log-probability: -41.1) CAGGAATTCATGTATGACTCAATATTTTCAGATcataattcattacagttagatCATAACTGTAATGTCATTACAGGAAGAATGCACAAA CAGGAATTCATGTATGACTCAATATTTTCAGAT---------------------CATAACTGTAATGTCATTACAGGAAGAATGCACAAA Template switch alignment (log-probability: -22.8) CAGGAATTCATGTATGACTCAATATTTTCAGATCATAAtT|CATTACAGTT|AGATCATAACTGTAATGTCATTACAGGAAGAATGCACAAA CAGGAATTCATGTATGACTCAATATTTTCAGATCATAACT|CATTACAGTT|AGATCATAACTGTAATGTCATTACAGGAAGAATGCACAAA ========== Event 3708 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: CTATTAGCAACAGGAAATAAAAGTTGACCTGAAGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAGGTctttgggtaattccaatactgttgcagtactcagtttttgcataatggagaaaa ↑ 4 1 3 2 Chimp: CTATTAGCAACAGGAAATAAA-----------AGTTGACAtttttttCCTGAAATAATTGAATTGAAAGAAGGTctttgggtaattccaatactgttgcagtactcagtttttgcataatggagaaaa Gorilla: CTATTAGCAACAGGAAATAAAAGTTAACCTGAAGTTGACAtttttttCCTGAAATAATTGAATTGAAAAAAGGTCTTTGGGTAATTCCAATACTGTTGCAGTACTCAGTTTTTGCGTAATGGAGAAAA Human: CTATTAGCAACAGGAAATAAAAGTTGACCTGAAGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAGGTctttgggtaattccaatactgttgcagtactcagtttttgcataatggagaaaa Cluster: [ ] Orangutan: CTATTAACAACAGGAAATAAAAGTTGACCTGAAGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAGGTctttgggtaattccaatactgttgcagtactcagtttttgcataatggagaaaa Chimp > Human ------------- chr9:127764228-127764231 Template switch process: F1: L GGGAGAAGACAATTCAAGTACTATTAGCAACAGGAAATAAAAGTTGAC 1 F3: 4 AGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAG R RF: GGGAGAAGACAATTCAAGTACTATTAGCAACAGGAAATAAAAGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAGGTCTTTGGGTAATTCCAATACTGTTGCAGTACTCAG RR: CCCTCTTCTGTTAAGTTCATGATAATCGTTGTCCTTTATTTTCAACTGTAAAAAAAGGACTTTATTAACTTAACTTTCTTCCAGAAACCCATTAAGGTTATGACAACGTCATGAGTC F2: 3 AGTC 2 Unidirectional alignment (log-probability: -26.7) ACAATTCAAGTACTATTAGCAACAGGAAATAAaagttgacctgAAGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAG ACAATTCAAGTACTATTAGCAACAGGAAATAA-----------AAGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAG Template switch alignment (log-probability: -15.9) ACAATTCAAGTACTATTAGCAACAGGAAATAAAAGTTGAC|CTGA|AGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAG ACAATTCAAGTACTATTAGCAACAGGAAATAAAAGTTGAC|CTGA|AGTTGACATTTTTTTCCTGAAATAATTGAATTGAAAGAAG ========== Event 3709 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: aggatttaatggaaggatATA-------TATCTTATGTGTGTATacacacaca--------------cac Chimp: AGGATTTAATGGAAGGATATA-------TATCTTATGTGTGTatacacacaca----------------- ↓ 1 3 4 2 Gorilla: aggatttaatggaaggatATA--------------TGTGTGTATacacacacacacacacacacaca--- ↑ 1 3 4 2 Human: aggatttaatggaaggatATA-------TATCTTATGTGTGTATacacacaca--------------cac Cluster: [ ] Orangutan: aggatttaatggaaggatatatatCTTA-------TGTGTGTatacacaca------------------- Human > Gorilla --------------- chr9:39223647-39223658 Template switch process: F1: L TGATAATAAAAATAGTCGCAAGGATTTAATGGAAGGATATAT 1 F3: 4 ACACACACACACACACACACA R RF: TGATAATAAAAATAGTCACAAGGATTTAATGGAAGGATATATATCTTATGTGTGTATACACACACACACACACACACA RR: ACTATTATTTTTATCAGTGTTCCTAAATTACCTTCCTATATATAGAATACACACATATGTGTGTGTGTGTGTGTGTGT F2: 3 CACATATGTGTG 2 Unidirectional alignment (log-probability: -34.8) ATAATAAAAATAGTCgCAAGGATTTAATGGAAGGATA-------TATGTGTGTATACACACACACACACACAcacacaca ATAATAAAAATAGTCACAAGGATTTAATGGAAGGATATATATCTTATGTGTGTATACACACACACACACACA-------- Template switch alignment (log-probability: -22.3) ATAATAAAAATAGTCgCAAGGATTTAATGGAAGGATATAT|GTGTGTATACAC|ACACACACACACACACACACA ATAATAAAAATAGTCACAAGGATTTAATGGAAGGATATAT|GTGTGTATACAC|ACACACACACACACACACACA Chimp > Gorilla --------------- chr9:39223647-39223660 Template switch process: F1: L TGATAATAAAAATAGTCGCAAGGATTTAATGGAAGGATATAT 1 F3: 4 ACACACACACACACACACACACATA R RF: TGATAATAAAAATAGTCACAAGGATTTAATGGAAGGATATATATCTTATGTGTGTATACACACACACACACATACACACATA RR: ACTATTATTTTTATCAGTGTTCCTAAATTACCTTCCTATATATAGAATACACACATATGTGTGTGTGTGTGTATGTGTGTAT F2: 3 CACACATATGTGTG 2 Unidirectional alignment (log-probability: -46.4) ATAATAAAAATAGTCgCAAGGATTTAATGGAAGGATA-------TATGTGTGTATacacacacacacacACACACACACACACATA ATAATAAAAATAGTCACAAGGATTTAATGGAAGGATATATATCTTATGTGTGTAT--------------ACACACACACACACATA Template switch alignment (log-probability: -28.2) ATAATAAAAATAGTCgCAAGGATTTAATGGAAGGATATAT|GTGTGTATACACAC|ACACACACACACACAcACACACATA ATAATAAAAATAGTCACAAGGATTTAATGGAAGGATATAT|GTGTGTATACACAC|ACACACACACACACATACACACATA ========== Event 3710 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: AAATGCATTCAACCATCTTAT-CCTAGTGGATACCACCTAGAGTCAGGTTAAGCTGTTACA ↑ 1 4 3 2 Chimp: AAATGCATTCAACCATCTTATCACGTGTGAATACCA-CTAGAGTCAGGTTAAGCTGTTACA Gorilla: AAATGCATTCAACCGTCTTAT-CCTAGTGGATACCACCTAGAGTCAGGTTAAGCTGTTACA Human: AAATGCATTCAACCATCTTAT-CCTAGTGGATACCACCTAGAGTCAGGTTAAGCTGTTACA Cluster: [ ] Orangutan: AAATGCATTCAACCATCTTAT-CCTGGTGGATACCACCTAGAGTCAGGTTAAGCTGTTACA Chimp > Human ------------- chr9:107307936-107307942 Template switch process: F1: L TCTTTCCCATGTACAACTAGAAATGCATTCAACCATCTTATC 1 F3: 4 ATACCACCTAGAGTCAGGTTAAGCTGTTACATCAAAGGGCTGTTGAT R RF: TCTTTCCCATGTACAACTAGAAATGCATTCAACCATCTTATCACGTGTGAATACCACTAGAGTCAGGTTAAGCTGTTACATCAAAGGGCTGTTGAT RR: AGAAAGGGTACATGTTGATCTTTACGTAAGTTGGTAGAATAGTGCACACTTATGGTGATCTCAGTCCAATTCGACAATGTAGTTTCCCGACAACTA F2: 3 GGTGATC 2 Unidirectional alignment (log-probability: -39) TTTCCCATGTACAACTAGAAATGCATTCAACCATCTTATcctagtggatacCAC------------CTAGAGTCAGGTTAAGCTGTTACATCAAAGGGC TTTCCCATGTACAACTAGAAATGCATTCAACCATCTTAT------------CACGTGTGAATACCACTAGAGTCAGGTTAAGCTGTTACATCAAAGGGC Template switch alignment (log-probability: -27.9) TTTCCCATGTACAACTAGAAATGCATTCAACCATCTTATC|CTAGTGG|ATACCAcCTAGAGTCAGGTTAAGCTGTTACATCAAAGGGC TTTCCCATGTACAACTAGAAATGCATTCAACCATCTTATC|CTAGTGG|ATACCA-CTAGAGTCAGGTTAAGCTGTTACATCAAAGGGC ========== Event 3711 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TATCTTTTTCTTCTTTGGTTTCTTGAATTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAG Chimp: TATCTTTTTCTTCTTTGGTTTCTTGAATTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAG ↑ 1 4 3 2 Gorilla: TATCTTTTTCTTCTTTGGTTTA-GCATTTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAG ↓ 1 4 3 2 Human: TATCTTTTTCTTCTTTGGTTTCTTGAATTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAG Cluster: [ ] Orangutan: TATCTTTTTCTTCTTTGGTTTA-GCATTTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAG Gorilla > Human --------------- chr9:107323425-107323430 Template switch process: F1: L ACCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT 1 F3: 4 TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT R RF: ACCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTTAGCATTTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT RR: TGGACTGGAGTCTGAAATTTATAGAAAAAGAAGAAACCAAATCGTAAAGGATCCTTAAGTTCGAGTCTAACACAAGAAAATCCCCA F2: 3 AAGTTC 2 Unidirectional alignment (log-probability: -28) CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTTcttgaA----TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT-----AGCATTTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT Template switch alignment (log-probability: -16.5) CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT|CTTGAA|TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT|CTTGAA|TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT Gorilla > Chimp --------------- chr9:85166220-85166225 Template switch process: F1: L ACCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT 1 F3: 4 TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT R RF: ACCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTTAGCATTTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT RR: TGGACTGGAGTCTGAAATTTATAGAAAAAGAAGAAACCAAATCGTAAAGGATCCTTAAGTTCGAGTCTAACACAAGAAAATCCCCA F2: 3 AAGTTC 2 Unidirectional alignment (log-probability: -28) CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTTcttgaA----TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT-----AGCATTTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT Template switch alignment (log-probability: -16.5) CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT|CTTGAA|TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT CCTGACCTCAGACTTTAAATATCTTTTTCTTCTTTGGTTT|CTTGAA|TTCCTAGGAATTCAAGCTCAGATTGTGTTCTTTTAGGGGT ========== Event 3712 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTATGACAGGATTTAACATTTAAAC ↓ 3 2 1 4 Chimp: CCAAATATATTTTTCTTTCTACGAAGTGTAGCTTCGT------AGACAGGATTTAACATTTAAAC ↑ 3 2 1 4 Gorilla: CCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTATGACAGGATTTAACATTTAAAC Human: CCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTATGACAGGATTTAACATTTAAAC Cluster: [ ] Orangutan: CCAAATATATTTTTCCTTCTATGAAGTGTAGCTGAAAAGTTTATGAC-AGATTTAACATTTAAAC Human > Chimp ------------- chr9:86224619-86224623 Template switch process: F1: L ATTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT 1 F3: 4 GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT R RF: ATTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTATGACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT RR: TAACAAGTGGTTTATATAAAAAGAAAGATGCTTCACATCGACTTGTCAAATACTGTCCTAAATTGTAAATTTGGACATTGTATTTCTAGAGA F2: 3 ATGCT 2 Unidirectional alignment (log-probability: -27.4) TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT----------TcgtaGACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTAT----GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT Template switch alignment (log-probability: -15.9) TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT|TCGTA|GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT|TCGTA|GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT Gorilla > Chimp --------------- chr9:86224619-86224623 Template switch process: F1: L ATTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT 1 F3: 4 GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT R RF: ATTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTATGACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT RR: TAACAAGTGGTTTATATAAAAAGAAAGATGCTTCACATCGACTTGTCAAATACTGTCCTAAATTGTAAATTTGGACATTGTATTTCTAGAGA F2: 3 ATGCT 2 Unidirectional alignment (log-probability: -26.9) TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT----------TcgtaGACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCTGAACAGTTTAT----GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT Template switch alignment (log-probability: -16.4) TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT|TCGTA|GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT TTGTTCACCAAATATATTTTTCTTTCTACGAAGTGTAGCT|TCGTA|GACAGGATTTAACATTTAAACCTGTAACATAAAGATCTCT ========== Event 3713 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTCCCACAATCCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTAT---GTTTACATGTTACTTATGTCATACGTACATGCTCA Chimp: CTCCCACAATCCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTAT---GTTTACATGTTACATATGTCATACGTACATGCTCA ↓ 3 2 1 4 Gorilla: CTCCCACAATCCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTAAAAACATGACATGTTACACATGTCATACGTACATGCTCA ↑ 3 2 1 4 Human: CTCCCACAATCCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTAT---GTTTACATGTTACTTATGTCATACGTACATGCTCA Cluster: [ ] Orangutan: CTCCCACAATCCCATCAACCATGTTTT----TGTTTTTACAAATAAAAGTAT---GTTTACATGTTACGTATGTCATACGCACATGCTCA Human > Gorilla --------------- chr9:90624517-90624524 Template switch process: F1: L CCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTA 1 F3: 4 ACATGTTACACATGTCATACGTACATGCTCAATTTTAGAATGCTCATAATC R RF: CCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTATGTTTACATGTTACTTATGTCATACGTACATGCTCAATTTTAGAATGCTCATAATA RR: GGGTAGTTGGTACAAAAACAAACAAAAATGTTTATTTTCATACAAATGTACAATGAATACAGTATGCATGTACGAGTTAAAATCTTACGAGTATTAT F2: 3 GTACAAAA 2 Unidirectional alignment (log-probability: -46.1) CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTaaaaacATG---ACATGTTACacATGTCATACGTACATGCTCAATTTTAGAA CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGT------ATGTTTACATGTTACTTATGTCATACGTACATGCTCAATTTTAGAA Template switch alignment (log-probability: -33.6) CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTA|AAAACATG|ACATGTTACacATGTCATACGTACATGCTCAATTTTAGAA CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTA|AAAACATG|ACATGTTACTTATGTCATACGTACATGCTCAATTTTAGAA Chimp > Gorilla --------------- chr9:90624517-90624524 Template switch process: F1: L CCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTA 1 F3: 4 ACATGTTACACATGTCATACGTACATGCTCAATTTTAGAA R RF: CCCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTATGTTTACATGTTACATATGTCATACGTACATGCTCAATTTTAGAA RR: GGGTAGTTGGTACAAAAACAAACAAAAATGTTTATTTTCATACAAATGTACAATGTATACAGTATGCATGTACGAGTTAAAATCTT F2: 3 GTACAAAA 2 Unidirectional alignment (log-probability: -35) CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTaaaaacATG---ACATGTTACAcATGTCATACGTACATGCTCAATTTTAGAA CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGT------ATGTTTACATGTTACATATGTCATACGTACATGCTCAATTTTAGAA Template switch alignment (log-probability: -22.3) CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTA|AAAACATG|ACATGTTACAcATGTCATACGTACATGCTCAATTTTAGAA CCATCAACCATGTTTTTGTTTGTTTTTACAAATAAAAGTA|AAAACATG|ACATGTTACATATGTCATACGTACATGCTCAATTTTAGAA ========== Event 3714 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAGGAAGTTCAAAGAAACAT-TTATGG-----CGTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTATTTATGTTTTTAGATCCAACCTCTTTTTAGGATCATTACAAACACCGTGAGAGGGGTTTCTCCCCACATTGCAGAAAAGGATTTGAGTAAGGTAGGCATGTTTGACCTCTTCTGGAATA ↑ 1 4 3 2 Chimp: CCAGGAAGTTCAAAGAAACATTTTATGGGGTAGGGTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTATTTATGTTTTTAGATCCAACCTCTTTTTAGGATCATTACAAACACCGTGAGAGGGGTTTCTCCCCACATTGCAGAAAAGGATTTGAGTAAGGTAGCCATGTGTGACCTCTTCTGGAATA Gorilla: TCAGGAAGTTCAAAGAAACAT-TTATGG-----GGTAGCAGGCCTTCAGGTTTTAAAGGTAATTGTATTGTTATTTATGTTTTTAGATCCAACCTCTTTTTAGGATCATTACAAACACCATGAGAGGGGTTTCTCCCCACATTGCAGAAAAGGATTTGAGTCAGGTAGCCATGTTTGACCTCTTCTGGAATA Human: CCAGGAAGTTCAAAGAAACAT-TTATGG-----CGTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTATTTATGTTTTTAGATCCAACCTCTTTTTAGGATCATTACAAACACCGTGAGAGGGGTTTCTCCCCACATTGCAGAAAAGGATTTGAGTAAGGTAGGCATGTTTGACCTCTTCTGGAATA Cluster: [ ] Orangutan: CCAGGAAGTTCAA-----------------------AGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTATTTATGTTTTTAGATCCAACCTCTTTTTAGGATCATTACAAACACCGTGAGAGGGGTTTCTCCCCACATTGCAGAAAAGGATTTGAGTAAGGTAGCCATGTTTGACCTCTTCTGGAATA Chimp > Human ------------- chr9:29579854-29579858 Template switch process: F1: L ATTCTTCTTTCCATTTGGAGCCAGGAAGTTCAAAGAAACATTT 1 F3: 4 GTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTAT R RF: A---TTCTTTCCATTTGGAGCCAGGAAGTTCAAAGAAACATTTTATGGGGTAGGGTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTATTTATGTTTTTAGATCCAACCTCTTTTTAGGATCATTACAAACACCGTGAGAGGGGTTTCTCCCCACATTGCAGAAAAGGATTTGAGTAAGGTAGCCAT RR: T---AAGAAAGGTAAACCTCGGTCCTTCAAGTTTCTTTGTAAAATACCCCATCCCATCGTCCAGAAGTCCAAAATTTCCATTAACATAACAATAAATACAAAAATCTAGGTTGGAGAAAAATCCTAGTAATGTTTGTGGCACTCTCCCCAAAGAGGGGTGTAACGTCTTTTCCTAAACTCATTCCATCGGTA F2: 3 CGGTA 2 Unidirectional alignment (log-probability: -42) cTTCTTTCCATTTGGAGCCAGGAAGTTCAAAGAAACA-TTTATGGcGTA-----GCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTAT -TTCTTTCCATTTGGAGCCAGGAAGTTCAAAGAAACATTTTATGGGGTAGGGTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTAT Template switch alignment (log-probability: -30.4) cTTCTTTCCATTTGGAGCCAGGAAGTTCAAAGAAACATTT|ATGGC|GTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTAT -TTCTTTCCATTTGGAGCCAGGAAGTTCAAAGAAACATTT|ATGGC|GTAGCAGGTCTTCAGGTTTTAAAGGTAATTGTATTGTTAT ========== Event 3715 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: ATTGATATACTAATAAATATATCAGTTGTACTCAGTTGTCAATGAGTACATTGACAAACTAATTAGAAAGTATacta Chimp: ATTGATATACTAATAAATATATCAGTTGTACTCAGTTGTCAATGAGTACATTGAC-AACTAATTAGAAAGTATACTA ↓ 1 3 2 4 Gorilla: ATTGATATACTAATAAATATA-------------------------CTCATTGACAAACTAATTAGAAAGTATACTA Human: ATTGATATACTAATAAATATATCAGTTGTACTCAGTTGTCAATGAGTACATTGACAAACTAATTAGAAAGTATacta Cluster: [ ] Orangutan: attgatatactaataaatata-------------------------ctcattgacaaactaattAGAAGGTATACTA Chimp > Gorilla --------------- chr9:28561903-28561912 Template switch process: F1: L CACTTTAGAAGCATATATCAATTGATATACTAATAAATATA 1 F3: 4 AACTAATTAGAAAGTATACTAAGTATAATTTGAGTTAAGA R RF: CACTTTAGAAGCATATATCAATTGATATACTAATAAATATATCAGTTGTACTCAGTTGTCAATGAGTACATTGACAACTAATTAGAAAGTATACTAAGTATAATTTGAGTTAAGA RR: GTGAAATCTTCGTATATAGTTAACTATATGATTATTTATATAGTCAACATGAGTCAACAGTTACTCATGTAACTGTTGATTAATCTTTCATATGATTCATATTAAACTCAATTCT F2: 3 ACAGTTACTC 2 Unidirectional alignment (log-probability: -33.2) ACTTTAGAAGCATATATCAATTGATATACTAATAAATA---------TACT----------------CATTGACaAACTAATTAGAAAGTATACTAAGTATAATTTGAGTTAAGA ACTTTAGAAGCATATATCAATTGATATACTAATAAATATATCAGTTGTACTCAGTTGTCAATGAGTACATTGAC-AACTAATTAGAAAGTATACTAAGTATAATTTGAGTTAAGA Template switch alignment (log-probability: -17) ACTTTAGAAGCATATATCAATTGATATACTAATAAATATA|CTCATTGACA|AACTAATTAGAAAGTATACTAAGTATAATTTGAGTTAAGA ACTTTAGAAGCATATATCAATTGATATACTAATAAATATA|CTCATTGACA|AACTAATTAGAAAGTATACTAAGTATAATTTGAGTTAAGA ========== Event 3716 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: ATTTTGAAGCAATTTGATAAATAAATACAGTT----TAAGGAGTAGATTTAGACTTTCAAA----AATGTTTTTAACATGTTTATTTAGCAT ↓ 13 24 ↑ 13 24 Chimp: ATTTTGAAGCAATTTGATAAA----AACATTT--TTGAAAGTCTAAATCTACTCCTTAAAC--TGTATTTATTTAACATGTTTATTTAGCAT Gorilla: ATTTTGAAGCAATTTGATAAA----AACATTTTT--GAAAGTCTAAATCTACTCCTTAAACTG--TATTTATTTAACATGTTTATTTAGCAT ↓ 13 24 ↑ 13 24 Human: ATTTTGAAGCAATTTGATAAATAAATACAGTT----TAAGGAGTAGATTTAGACTTTCAAA----AATGTTTTTAACATGTTTATTTAGCAT Cluster: [ ] Orangutan: ATTTTGAAGCAATTTGATAAA----AACATTTTT--GAAAGTCTAAATCTACTCCTTAAACTG--TATTTATTTAACATGTTTATTTAGCAT Chimp > Human ------------- chr9:28004961-28005002 Template switch process: F1: L ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA 1 F3: 4 TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA R RF: ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAAAACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTATTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA RR: TGGCCAGACGGTCTCACACTTAAAACTTCGTTAAACTATTTTTGTAAAAACTTTCAGATTTAGATGAGGAATTTGACATAAATAAATTGTACAAATAAATCGTAAGGTCACGACTCGCTAAGT F2: 3 TTGTAAAAACTTTCAGATTTAGATGAGGAATTTGACATAAAT 2 Unidirectional alignment (log-probability: -80.7) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA----------------------------------------TAaatacagtttaaggagtagatttagactttcaaaaatgttTTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAAAACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTA----------------------------------------TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA Template switch alignment (log-probability: -20.4) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|TAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTT|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|TAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTT|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA Human > Chimp ------------- chr9:28463399-28463440 Template switch process: F1: L ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA 1 F3: 4 TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA R RF: ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAATAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTTTTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA RR: TGGCCAGACGGTCTCACACTTAAAACTTCGTTAAACTATTTATTTATGTCAAATTCCTCATCTAAATCTGAAAGTTTTTACAAAAATTGTACAAATAAATCGTAAGGTCACGACTCGCTAAGT F2: 3 ATTTATGTCAAATTCCTCATCTAAATCTGAAAGTTTTTACAA 2 Unidirectional alignment (log-probability: -80.7) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAAaacatttttgaaagtctaaatctactccttaaactgtattTA----------------------------------------TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA----------------------------------------TAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTTTTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA Template switch alignment (log-probability: -20.4) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|AACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTA|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|AACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTA|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA Gorilla > Human --------------- chr9:28004961-28005002 Template switch process: F1: L ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA 1 F3: 4 TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA R RF: ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAAAACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTATTTAACATGTTTATTTAGCATTCCAGTGCTGAGCAATTCG RR: TGGCCAGACGGTCTCACACTTAAAACTTCGTTAAACTATTTTTGTAAAAACTTTCAGATTTAGATGAGGAATTTGACATAAATAAATTGTACAAATAAATCGTAAGGTCACGACTCGTTAAGC F2: 3 TTGTAAAAACTTTCAGATTTAGATGAGGAATTTGACATAAAT 2 Unidirectional alignment (log-probability: -91.2) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA----------------------------------------TAaatacagtttaaggagtagatttagactttcaaaaatgttTTTAACATGTTTATTTAGCATTCCAGTGCTGAGCgATTCa CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAAAACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTA----------------------------------------TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCAATTCG Template switch alignment (log-probability: -32.1) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|TAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTT|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCgATTCa CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|TAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTT|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCAATTCG Human > Gorilla --------------- chr9:28821175-28821216 Template switch process: F1: L ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA 1 F3: 4 TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCAATTCG R RF: ACCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAATAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTTTTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA RR: TGGCCAGACGGTCTCACACTTAAAACTTCGTTAAACTATTTATTTATGTCAAATTCCTCATCTAAATCTGAAAGTTTTTACAAAAATTGTACAAATAAATCGTAAGGTCACGACTCGCTAAGT F2: 3 ATTTATGTCAAATTCCTCATCTAAATCTGAAAGTTTTTACAA 2 Unidirectional alignment (log-probability: -91.2) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAAaacatttttgaaagtctaaatctactccttaaactgtattTA----------------------------------------TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCaATTCg CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA----------------------------------------TAAATACAGTTTAAGGAGTAGATTTAGACTTTCAAAAATGTTTTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA Template switch alignment (log-probability: -32.1) CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|AACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTA|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCaATTCg CCGGTCTGCCAGAGTGTGAATTTTGAAGCAATTTGATAAA|AACATTTTTGAAAGTCTAAATCTACTCCTTAAACTGTATTTA|TTTAACATGTTTATTTAGCATTCCAGTGCTGAGCGATTCA ========== Event 3717 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTTACCTGGATTTATAACCAGATGCATCCATCTGGTGGCGCTTAGGAGGAACTTT ↑ 3 1 2 4 Chimp: ACTTACCTGGATTTATAACCAGATGGAT-----GAGTGGCGCTTAGGAGGAACTTT Gorilla: ACTTACCTGGATTTATAACCAGATGGAT-----GAGTGGCGCTTAGGAGGAACTTT ↓ 3 1 2 4 Human: ACTTACCTGGATTTATAACCAGATGCATCCATCTGGTGGCGCTTAGGAGGAACTTT Cluster: [ ] Orangutan: ACTTACCTGGATTTATAACCAGATGGAT-----GAGTGGCGCTTAGGAGGAACTTT Chimp > Human ------------- chr9:111613861-111613870 Template switch process: F1: L CCTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG 1 F3: 4 GTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG R RF: CCTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATGGATGAGTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG RR: GGACGACTAAACCTAATGAATGGACCTAAATATTGGTCTACCTACTCACCGCGAATCCTCCTTGAAAAATCGTTGAGAGTCACCAC F2: 3 GTCTACCTAC 2 Unidirectional alignment (log-probability: -34.3) CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATGcatccatctG----GTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG---------GATGAGTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG Template switch alignment (log-probability: -16.5) CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG|CATCCATCTG|GTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG|CATCCATCTG|GTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG Gorilla > Human --------------- chr9:111613861-111613870 Template switch process: F1: L CCTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG 1 F3: 4 GTGGCGCTTAGGAGGAACTTTTTAGCAACTCTCAGTGGTG R RF: CCTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATGGATGAGTGGCGCTTAGGAGGAACTTTTTAGCAGCTCTCAGTGGTG RR: GGACGACTAAACCTAATGAATGGACCTAAATATTGGTCTACCTACTCACCGCGAATCCTCCTTGAAAAATCGTCGAGAGTCACCAC F2: 3 GTCTACCTAC 2 Unidirectional alignment (log-probability: -39.3) CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATGcatccatctG----GTGGCGCTTAGGAGGAACTTTTTAGCAaCTCTCAGTGGTG CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG---------GATGAGTGGCGCTTAGGAGGAACTTTTTAGCAGCTCTCAGTGGTG Template switch alignment (log-probability: -22.5) CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG|CATCCATCTG|GTGGCGCTTAGGAGGAACTTTTTAGCAaCTCTCAGTGGTG CTGCTGATTTGGATTACTTACCTGGATTTATAACCAGATG|CATCCATCTG|GTGGCGCTTAGGAGGAACTTTTTAGCAGCTCTCAGTGGTG ========== Event 3718 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTGTATATGCTTTACAAGTA------TTGTTA----ACAAACAAAGAGGGAGCTGGTGCACT Chimp: ATTGTATATGCTTTACAAGTA---TTACTGTTA----ACAAACAAAGAGGGAGCTGGTGCACT Gorilla: ATTGTATATGCTTTACAAGTATTA---TTGTTA--------ACAAAGAGGGAGCTGGTGTACT ↓ 1 3 42 Human: ATTGTATATGCTTTACAAGTA------TTGTTA----ACAAACAAAGAGGGAGCTGGTGCACT Cluster: [ ] Orangutan: ATTGTATATGCTTTACAAGTATT------ATTAACAA----ACAAAGAGGGGGCTGGTGTACT Gorilla > Human --------------- chr9:25383229-25383236 Template switch process: F1: L TTGTGAATGCACTTCGAAAAATTGTATATGCTTTACAAGTATT 1 F3: 4 ACAAAGAGGGAGCTGGTGCACTCGGTGCCACCCATCATGG R RF: TTGTGAATGCACTTCGAAAAATTGTATATGCTTTACAAGTATTATTGTTAACAAAGAGGGAGCTGGTGTACTCGGTGCCACCCATCATGG RR: AACACTTACGTGAAGCTTTTTAACATATACGAAATGTTCATAATAACAATTGTTTCTCCCTCGACCACATGAGCCACGGTGGGTAGTACC F2: 3 AACAATTG 2 Unidirectional alignment (log-probability: -32.1) TGAATGCACTTCGAAAAATTGTATATGCTTTACAAGTATT---GTTaacaAACAAAGAGGGAGCTGGTGcACTCGGTGCCACCCATCATGG TGAATGCACTTCGAAAAATTGTATATGCTTTACAAGTATTATTGTT----AACAAAGAGGGAGCTGGTGTACTCGGTGCCACCCATCATGG Template switch alignment (log-probability: -22.3) TGAATGCACTTCGAAAAATTGTATATGCTTTACAAGTATT|GTTAACAA|ACAAAGAGGGAGCTGGTGcACTCGGTGCCACCCATCATGG TGAATGCACTTCGAAAAATTGTATATGCTTTACAAGTATT|GTTAACAA|ACAAAGAGGGAGCTGGTGTACTCGGTGCCACCCATCATGG ========== Event 3719 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CTGGCTTAGTGCTCTCTCTCTTGGCTTGGCCAAGAGAGAGAGAGACCAAAGCTTAGGT Chimp: CTGGCTTAGTGCTCTCTCTCTTGGCTTGGCCAGGAG--AGAGAGACCAAAGCTTAGGT Gorilla: CTGGCTTAGTGCTCTCTCTCTTGGCCAAGCCAAGAG--AGAGAGACCAAAGCTTAGGT ↓ 3 1 2 4 Human: CTGGCTTAGTGCTCTCTCTCTTGGCTTGGCCAAGAGAGAGAGAGACCAAAGCTTAGGT Cluster: [ ] Orangutan: CTGGCTTAGTGCTCTCTCTCTCAGCTTGGCCAAGAG--AGAGAGACCAAAGCTTAGGT Gorilla > Human --------------- chr9:113532372-113532380 Template switch process: F1: L GCCTCCCTGGAGGGAGCTGGCTTAGTGCTCTCTCTCTTGGC 1 F3: 4 AGAGAGAGAGACCAAAGCTTAGGTCTCCCGAAAATGTTTGCCCA R RF: GCCTCCCTGGAGGGAGCTGGCTTAGTGCTCTCTCTCTTGGCCAAGCCAAGAGAGAGAGACCAAAGCTTAGGTCTCCCGAAAATGTTTGCCCA RR: CGGAGGGACCTCCCTCGACCGAATCACGAGAGAGAGAACCGGTTCGGTTCTCTCTCTCTGGTTTCGAATCCAGAGGGCTTTTACAAACGGGT F2: 3 GAACCGGTT 2 Unidirectional alignment (log-probability: -28.1) CCTCCCTGGAGGGAGCTGGCTTAGTGCTCTCTCTCTTGgcttgGCCAAG---AGAGAGAGAGACCAAAGCTTAGGTCTCCCGAAAATGTTTG CCTCCCTGGAGGGAGCTGGCTTAGTGCTCTCTCTCTTG-----GCCAAGCCAAGAGAGAGAGACCAAAGCTTAGGTCTCCCGAAAATGTTTG Template switch alignment (log-probability: -17) CCTCCCTGGAGGGAGCTGGCTTAGTGCTCTCTCTCTTGGC|TTGGCCAAG|AGAGAGAGAGACCAAAGCTTAGGTCTCCCGAAAATGTTTG CCTCCCTGGAGGGAGCTGGCTTAGTGCTCTCTCTCTTGGC|TTGGCCAAG|AGAGAGAGAGACCAAAGCTTAGGTCTCCCGAAAATGTTTG ========== Event 3720 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGAGGAAGAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTGTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAG ↓ 1 4 3 2 Chimp: GGAGGAAGAAGGAAGAAGAGGTTC----------------------------------------AAGATGTTCTTGAACCTGAATGATTCAGGCCAAG ↑ 1 4 3 2 Gorilla: GGAGGAATAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTCTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAG Human: GGAGGAAGAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTGTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAG Cluster: [ ] Orangutan: GGAGGAAGAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTCTGGGAAGCTTGCCTCAGAGAGAACCCAAATGTTCTTGAACCTGAATGATTTAGGCCAAG Human > Chimp ------------- chr9:23910714-23910719 Template switch process: F1: L GGGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGG 1 F3: 4 ATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC R RF: GGGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTGTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC RR: CCCTGGCCCCGACCCTTCTACCTCCTTCTTCCTTCTTCTCCGGGTCGACAACGGACGACACCCTTCGAACGGAGTCTCTTTTGGGTTTACAAGAACTTGGACTTACTAAGTCCGGTTCCCAAACGTG F2: 3 GAACTT 2 Unidirectional alignment (log-probability: -31) GGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGGttCA----------------------------------------AgATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC GGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTGTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC Template switch alignment (log-probability: -16) GGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGG|TTCAAG|ATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC GGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGG|TTCAAG|ATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC Gorilla > Chimp --------------- chr9:23910714-23910719 Template switch process: F1: L GGGACCGGGGCTGGGAAGATGGAGGAAGAAGGAAGAAGAGG 1 F3: 4 ATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC R RF: GGGACCGGGGCTGGGAAGATGGAGGAATAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTCTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC RR: CCCTGGCCCCGACCCTTCTACCTCCTTATTCCTTCTTCTCCGGGTCGACAACGGACGAGACCCTTCGAACGGAGTCTCTTTTGGGTTTACAAGAACTTGGACTTACTAAGTCCGGTTCCCAAACGTG F2: 3 GAACTT 2 Unidirectional alignment (log-probability: -35.1) GGACCGGGGCTGGGAAGATGGAGGAAgAAGGAAGAAGAGGttCA----------------------------------------AgATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC GGACCGGGGCTGGGAAGATGGAGGAATAAGGAAGAAGAGGCCCAGCTGTTGCCTGCTCTGGGAAGCTTGCCTCAGAGAAAACCCAAATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC Template switch alignment (log-probability: -22) GGACCGGGGCTGGGAAGATGGAGGAAgAAGGAAGAAGAGG|TTCAAG|ATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC GGACCGGGGCTGGGAAGATGGAGGAATAAGGAAGAAGAGG|TTCAAG|ATGTTCTTGAACCTGAATGATTCAGGCCAAGGGTTTGCAC ========== Event 3721 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAGAAATGAGGAAAATGAACCT---TATATATGTGGCCTTTCTGAGCCAtcacaatagacctgggaggtaagaattattgtctgcttttattgacgaggaaacagttccattgaggtcaagtgacatgccacaatcagagcaccaggaaataatggagc Chimp: AAAGAAATGAGGAAAATGAACCT---TATATATGTGGCCTTTCTGAGCCAtcacaatagacctgggaggtaagaattattgtctgcttttattgacgaggaaacagttccattgaggtcaagtgacatgccacaatcagagcaccaagaaataatggagc ↓ 1 4 3 2 Gorilla: AAAGAAATGACGAAAATGAACAT------TTCT-GAGCCTTTCTGAGCCAtcacaatagacctgggaggtaagaattattgtctgcttttattgacgaggaaacagttccattgaggtcaagtgacatgccacaatcagagcaccaggaaataatggagc ↑ 1 4 3 2 Human: AAAGAAATGAGGAAAATGAACCT---TATATATGTGGCCTTTCTGAGCCAtcacaatagacctgggaggtaagaattattgtctgcttttattgacgaggaaacagttccattgaggtcaagtgacatgccacaatcagagcaccaggaaataatggagc Cluster: [ ] Orangutan: AAAGAAATAAGGAAAATGAACCTTat---gta-ttggcctttctaagccatcacaatagacctgggaggtaagaattattgtctgcttttattgacgaggaaacagttccattgaggtcaagtgacatgtcacaatcagagcaccaggaaataatggagc Human > Gorilla --------------- chr9:24261234-24261238 Template switch process: F1: L TACAATCATATATTGAGCCCAAAGAAATGACGAAAATGAACATT 1 F3: 4 GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT R RF: TACAATCATATATTGAGCCCAAAGAAATGAGGAAAATGAACCTTATATATGTGGCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAATTATTGTCTGCTTTTATTGACGAGGAAACAGTTCCATTGAGGTCAAGTGACATGCCACAATCAGA RR: ATGTTAGTATATAACTCGGGTTTCTTTACTCCTTTTACTTGGAATATATACACCGGAAAGACTCGGTAGTGTTATCTGGACCCTCCATTCTTAATAACAGACGAAAATAACTGCTCCTTTGTCAAGGTAACTCCAGTTCACTGTACGGTGTTAGTCT F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -37.9) ATCATATATTGAGCCCAAAGAAATGAcGAAAATGAACatttCTgA--------GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT ATCATATATTGAGCCCAAAGAAATGAGGAAAATGAAC----CTTATATATGTGGCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT Template switch alignment (log-probability: -27.5) ATCATATATTGAGCCCAAAGAAATGAcGAAAATGAACaTT|TCTGA|GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT ATCATATATTGAGCCCAAAGAAATGAGGAAAATGAACCTT|TCTGA|GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT Chimp > Gorilla --------------- chr9:24261234-24261238 Template switch process: F1: L TACAATCATATATTGAGCCCAAAGAAATGACGAAAATGAACATT 1 F3: 4 GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT R RF: TACAATCATATATTGAGCCCAAAGAAATGAGGAAAATGAACCTTATATATGTGGCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAATTATTGTCTGCTTTTATTGACGAGGAAACAGTTCCATTGAGGTCAAGTGACATGCCACAATCAGA RR: ATGTTAGTATATAACTCGGGTTTCTTTACTCCTTTTACTTGGAATATATACACCGGAAAGACTCGGTAGTGTTATCTGGACCCTCCATTCTTAATAACAGACGAAAATAACTGCTCCTTTGTCAAGGTAACTCCAGTTCACTGTACGGTGTTAGTCT F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -37.9) ATCATATATTGAGCCCAAAGAAATGAcGAAAATGAACatttCTgA--------GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT ATCATATATTGAGCCCAAAGAAATGAGGAAAATGAAC----CTTATATATGTGGCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT Template switch alignment (log-probability: -27.5) ATCATATATTGAGCCCAAAGAAATGAcGAAAATGAACaTT|TCTGA|GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT ATCATATATTGAGCCCAAAGAAATGAGGAAAATGAACCTT|TCTGA|GCCTTTCTGAGCCATCACAATAGACCTGGGAGGTAAGAAT ========== Event 3722 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: catagtaggtgctcggaaaatAACACGTCGTAGTCACCTGAAGGGGCCTATCAGTGAATGAGCTGTCC Chimp: catagtaggtgctcggaaaatAACACGTCGTAGTCACGTGT--TATCATATCAGTGAATGAGCTGTCC ↑ 3 2 1 4 Gorilla: catagtaggtgctcggaaaatAACACGTCGTAGTCATCTGAAGGGGCCTATCAGTGAATGAGCTGTCC Human: catagtaggtgctcggaaaatAACACGTCGTAGTCACCTGAAGGGGCCTATCAGTGAATGAGCTGTCC Cluster: [ ] Orangutan: catagtaggtgctcggaaaatAACACGTTGTAGTCACCTGAAGGGGCCTATCAGCGAATGAGCTGTCC Gorilla > Chimp --------------- chr9:91963718-91963725 Template switch process: F1: L TGGTACATAGTAGGTGCTCGGAAAATAACACGTCGTAGTCA 1 F3: 4 CATATCAGTGAATGAGCTGTCCAGGGCAGCCACAGGCAGACT R RF: TGGTACATAGTAGGTGCTCGGAAAATAACACGTCGTAGTCATCTGAAGGGGCCTATCAGTGAATGAGCTGTCCAGGGCAGCCACAGGCAGACT RR: ACCATGTATCATCCACGAGCCTTTTATTGTGCAGCATCAGTAGACTTCCCCGGATAGTCACTTACTCGACAGGTCCCGTCGGTGTCCGTCTGA F2: 3 TATTGTGC 2 Unidirectional alignment (log-probability: -34.1) GGTACATAGTAGGTGCTCGGAAAATAACACGTCGTAGTCA-----------CgtgttatcaTATCAGTGAATGAGCTGTCCAGGGCAGCCACAGGCAGA GGTACATAGTAGGTGCTCGGAAAATAACACGTCGTAGTCATCTGAAGGGGCC---------TATCAGTGAATGAGCTGTCCAGGGCAGCCACAGGCAGA Template switch alignment (log-probability: -22.3) GGTACATAGTAGGTGCTCGGAAAATAACACGTCGTAGTCA|CGTGTTAT|CaTATCAGTGAATGAGCTGTCCAGGGCAGCCACAGGCAGA GGTACATAGTAGGTGCTCGGAAAATAACACGTCGTAGTCA|CGTGTTAT|CCTATCAGTGAATGAGCTGTCCAGGGCAGCCACAGGCAGA ========== Event 3723 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CCATCTGTTGCCATTCTTGTCC-----TTAGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGAAAA ↓ 1 4 3 2 Chimp: CCATCTGTTGCCATTCTTGTCTAACGGGAAGTAGCAGCTTCCCGTTAGAGATGCCAAGAGAAGAAAA ↑ 1 4 3 2 Gorilla: CCATCTGTTGCCATTCTTGTCC-----TTAGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGGAAA Human: CCATCTGTTGCCATTCTTGTCC-----TTAGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGAAAA Cluster: [ ] Orangutan: CCATCTGTTGCCATTCTTGTCC-----TTAGTAGCAGCTTCCCATTAGAGATGCCAAGAGAAGAAAA Human > Chimp ------------- chr9:22145387-22145394 Template switch process: F1: L ATCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC 1 F3: 4 AGTAGCAGCTTCCCGTTAGAGATGCCAAGAGAAGAAAATC R RF: ATCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTCCTTAGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGAAAATC RR: TAGAAAGAGGGAGGGACAGTGGTAGACAACGGTAAGAACAGGAATCATCGTCGAAGGGCAATCTCTGCGGTTCTCTTCTTTTAG F2: 3 AGGGCAAT 2 Unidirectional alignment (log-probability: -37.3) TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC--TaacgggaAGTAGCAGCTTCCCGTTAGAGAtGCCAAGAGAAGAAAATC TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTCCTT-------AGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGAAAATC Template switch alignment (log-probability: -22.3) TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC|TAACGGGA|AGTAGCAGCTTCCCGTTAGAGAtGCCAAGAGAAGAAAATC TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC|TAACGGGA|AGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGAAAATC Gorilla > Chimp --------------- chr9:22145387-22145394 Template switch process: F1: L ATCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC 1 F3: 4 AGTAGCAGCTTCCCGTTAGAGATGCCAAGAGAAGAAAATC R RF: ATCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTCCTTAGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGGAAATC RR: TAGAAAGAGGGAGGGACAGTGGTAGACAACGGTAAGAACAGGAATCATCGTCGAAGGGCAATCTCTGCGGTTCTCTTCCTTTAG F2: 3 AGGGCAAT 2 Unidirectional alignment (log-probability: -41.8) TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC--TaacgggaAGTAGCAGCTTCCCGTTAGAGAtGCCAAGAGAAGaAAATC TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTCCTT-------AGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGGAAATC Template switch alignment (log-probability: -27.8) TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC|TAACGGGA|AGTAGCAGCTTCCCGTTAGAGAtGCCAAGAGAAGaAAATC TCTTTCTCCCTCCCTGTCACCATCTGTTGCCATTCTTGTC|TAACGGGA|AGTAGCAGCTTCCCGTTAGAGACGCCAAGAGAAGGAAATC ========== Event 3724 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGGAGTGTGGAGGGAAAAGGGTAATGCATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAAAAGAAGGCTAAAAGCAATTATGCCACAATACTAATAGCCATTAATTCCAAAGAGAGAAATATG Chimp: AGGAGTGTGGAGGGAAAAGGGTAATGCATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAAAAGAAGGCTAAAAGCAATTATGCCACAATACTAATAGCCATTAATTCCAAAGAGAGAAATATG ↑ 1 4 3 2 Gorilla: AGGACTGTGGAGGGAAAAGGGCAAC-AATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAAAAGAAGTCTAAAAGCAATTATGCCACAATACTAATA-GCATTAATTCCAAAGAGAGAAATATG ↓ 1 4 3 2 Human: AGGAGTGTGGAGGGAAAAGGGTAATGCATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAAAAGAAGGCTAAAAGCAATTATGCCACAATACTAATAGCCATTAATTCCAAAGAGAGAAATATG Cluster: [ ] Orangutan: AGGACTGTGGAGGGAAAAGGGCAATGCATTCATACGCTGTGAATGGCTGATTGTAGAACGGATAAAAAAGAAGGCTAAAAGCAATTATGCCACAATACTAATAGCCATTAATTCCAAAGAGAGAAACATG Gorilla > Human --------------- chr9:117097245-117097250 Template switch process: F1: L TGCTTCAGAGACAAACTCAGAGGAGTGTGGAGGGAAAAGGG 1 F3: 4 ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA R RF: TGCTTCAGAGACAAACTCAGAGGACTGTGGAGGGAAAAGGGCAACAATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAAAAGAAGTCTAAAAGCAATTATGCCACAATACTAATAGCATTA RR: ACGAAGTCTCTGTTTGAGTCTCCTGACACCTCCCTTTTCCCGTTGTTAAGTATACGACACTTGTCGACTAACATCTTTCCTATTTTTTCTTCAGATTTTCGTTAATACGGTGTTATGATTATCGTAAT F2: 3 CGTAAT 2 Unidirectional alignment (log-probability: -33.6) GCTTCAGAGACAAACTCAGAGGAgTGTGGAGGGAAAAGGgtaatGC----ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA GCTTCAGAGACAAACTCAGAGGACTGTGGAGGGAAAAGG-----GCAACAATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA Template switch alignment (log-probability: -22) GCTTCAGAGACAAACTCAGAGGAgTGTGGAGGGAAAAGGG|TAATGC|ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA GCTTCAGAGACAAACTCAGAGGACTGTGGAGGGAAAAGGG|TAATGC|ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA Gorilla > Chimp --------------- chr9:95109600-95109605 Template switch process: F1: L TGCTTCAGAGACAAACTCAGAGGAGTGTGGAGGGAAAAGGG 1 F3: 4 ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA R RF: TGCTTCAGAGACAAACTCAGAGGACTGTGGAGGGAAAAGGGCAACAATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAAAAGAAGTCTAAAAGCAATTATGCCACAATACTAATAGCATTA RR: ACGAAGTCTCTGTTTGAGTCTCCTGACACCTCCCTTTTCCCGTTGTTAAGTATACGACACTTGTCGACTAACATCTTTCCTATTTTTTCTTCAGATTTTCGTTAATACGGTGTTATGATTATCGTAAT F2: 3 CGTAAT 2 Unidirectional alignment (log-probability: -33.6) GCTTCAGAGACAAACTCAGAGGAgTGTGGAGGGAAAAGGgtaatGC----ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA GCTTCAGAGACAAACTCAGAGGACTGTGGAGGGAAAAGG-----GCAACAATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA Template switch alignment (log-probability: -22) GCTTCAGAGACAAACTCAGAGGAgTGTGGAGGGAAAAGGG|TAATGC|ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA GCTTCAGAGACAAACTCAGAGGACTGTGGAGGGAAAAGGG|TAATGC|ATTCATATGCTGTGAACAGCTGATTGTAGAAAGGATAAAA ========== Event 3725 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTGAATAAATACTTTAACTCATTAGTGACATATGGCATAGTAAATGGTGATGCTTAAT Chimp: TTTTGAATAAATACTTTAACTCATTAGTGACATATGGCATAATAAATGGTGATGCTTAAT Gorilla: TTTTGAATAAATACTTTAACTATGCCATGACATATGGCATAGTAAATGGTGATGCTTAAT ↑ 1 4 3 2 Human: TTTTGAATAAATACTTTAACTCATTAGTGACATATGGCATAGTAAATGGTGATGCTTAAT Cluster: [ ] Orangutan: CTTTGAATAAATACTTCAACTCATTAGTGATATATGGCATAGTAAATGGTGATGTTTAAT Human > Gorilla --------------- chr9:100281463-100281468 Template switch process: F1: L ATACAACACTCAAATGATATTTTTGAATAAATACTTTAACT 1 F3: 4 TGACATATGGCATAGTAAATGGTGATGCTTAATAAAACTT R RF: ATACAACACTCAAATGATATTTTTGAATAAATACTTTAACTCATTAGTGACATATGGCATAGTAAATGGTGATGCTTAATAAAACTT RR: TATGTTGTGAGTTTACTATAAAAACTTATTTATGAAATTGAGTAATCACTGTATACCGTATCATTTACCACTACGAATTATTTTGAA F2: 3 ACCGTA 2 Unidirectional alignment (log-probability: -26.6) TACAACACTCAAATGATATTTTTGAATAAATACTTTAACTatgcCA----TGACATATGGCATAGTAAATGGTGATGCTTAATAAAACTT TACAACACTCAAATGATATTTTTGAATAAATACTTTAACT----CATTAGTGACATATGGCATAGTAAATGGTGATGCTTAATAAAACTT Template switch alignment (log-probability: -16.5) TACAACACTCAAATGATATTTTTGAATAAATACTTTAACT|ATGCCA|TGACATATGGCATAGTAAATGGTGATGCTTAATAAAACTT TACAACACTCAAATGATATTTTTGAATAAATACTTTAACT|ATGCCA|TGACATATGGCATAGTAAATGGTGATGCTTAATAAAACTT ========== Event 3726 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGGACTTGAATCGAATACAATACTATATAGACTTTGAGTTTCTTGGAGTTTACTCACATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGATA------------TAGTACTCAATAAATGTCTCTTGAAAAA Chimp: ATGGACTTGAATCAAATACAATACTATATAGACTTTGAGTTTCTTGGAGTTTACTCACATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGATA------------TAGTACTCAATAAATGTCTCTTGAAAAA ↑ 3 2 1 4 Gorilla: ACAGACTTGAATCAAATACAATACTATATGGACTTTGAGTTTCTTGGATTTTACTCACATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGAAATGTCTCTTGAAAAAGAAGACAATAAATGTCTCTTGAAAAA Human: ATGGACTTGAATCGAATACAATACTATATAGACTTTGAGTTTCTTGGAGTTTACTCACATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGATA------------TAGTACTCAATAAATGTCTCTTGAAAAA Cluster: [ ] Orangutan: ATGGACTTGAATCAAATACAATACTATATAGACTTTGAGTTTCTTGGAGTTTACTCACATTTGCATTCCTCTTCTTCTCTTACCTTATATCTCTAGATA------------TAGTACTCAATAAATGTCTCTTGAAAAA Gorilla > Chimp --------------- chr9:95571314-95571322 Template switch process: F1: L ACATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGA 1 F3: 4 CAATAAATGTCTCTTGAAAAAGAAGAATGAACGACTGAAT R RF: AATACTATATGGACTTTGAGTTTCTTGGATTTTACTCACATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGAAATGTCTCTTGAAAAAGAAGACAATAAATGTCTCTTGAAAAAGAAGAATGAACGACTGAAT RR: TTATGATATACCTGAAACTCAAAGAACCTAAAATGAGTGTAAACGTAAGGAGAAGAAGAGAATAGAATATAGAGATCTTTACAGAGAACTTTTTCTTCTGTTATTTACAGAGAACTTTTTCTTCTTACTTGCTGACTTA F2: 3 TCATGATAT 2 Unidirectional alignment (log-probability: -33.7) CATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGAtAT------------AGtActCAATAAATGTCTCTTGAAAAAGAAGAATGAACGACTGAAT CATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGAAATGTCTCTTGAAAAAGAAGACAATAAATGTCTCTTGAAAAAGAAGAATGAACGACTGAAT Template switch alignment (log-probability: -22.4) CATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGA|TATAGTAcT|CAATAAATGTCTCTTGAAAAAGAAGAATGAACGACTGAAT CATTTGCATTCCTCTTCTTCTCTTATCTTATATCTCTAGA|TATAGTATT|CAATAAATGTCTCTTGAAAAAGAAGAATGAACGACTGAAT ========== Event 3727 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AACCCACTAATGTACAATTTATGGACACAATTTATGAGAACAATATATGTTCTCATAAATTAAACAGCAGAACAAATTGG ↑ 4 3 2 Chimp: aacccactaatgtaCAATTTACGGACA--------------CATATATGTTCTCATAAATTACACAGCAGAACAAATTGG Gorilla: aacccactaatgtaCAATTTACGGACA--------------CATATATGTTCTCATAAATTAAACAGCAGAACAAATTGG ↓ 4 3 2 Human: AACCCACTAATGTACAATTTATGGACACAATTTATGAGAACAATATATGTTCTCATAAATTAAACAGCAGAACAAATTGG Cluster: [ ] Orangutan: AACCCACTAATGTACAATTTACGGACA--------------CATATATGTTCTCATAAATTAAACGGCAGAACAAATTGG Chimp > Human ------------- chr9:117781892-117781904 Template switch process: F1: L ATAATCTTTGCCTTCAGAGAAACCCACTAATGTACAATTTATGGACACA 1 F3: 4 ATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA R RF: ATAATCTTTGCCTTCAGAGAAACCCACTAATGTACAATTTACGGACACATATATGTTCTCATAAATTACACAGCAGAACAAATTGGAA RR: TATTAGAAACGGAAGTCTCTTTGGGTGATTACATGTTAAATGCCTGTGTATATACAAGAGTATTTAATGTGTCGTCTTGTTTAACCTT F2: 3 ACAAGAGTATTTA 2 Unidirectional alignment (log-probability: -43.1) GCCTTCAGAGAAACCCACTAATGTACAATTTAtGGACACaatttatgagaacaATATATGTTCTCATAAATTAaACAGCAGAACAAATTGGAA GCCTTCAGAGAAACCCACTAATGTACAATTTACGGACAC--------------ATATATGTTCTCATAAATTACACAGCAGAACAAATTGGAA Template switch alignment (log-probability: -29) GCCTTCAGAGAAACCCACTAATGTACAATTTAtGGACACA|ATTTATGAGAACA|ATATATGTTCTCATAAATTAaACAGCAGAACAAATTGGAA GCCTTCAGAGAAACCCACTAATGTACAATTTACGGACACA|ATTTATGAGAACA|ATATATGTTCTCATAAATTACACAGCAGAACAAATTGGAA Gorilla > Human --------------- chr9:117781892-117781904 Template switch process: F1: L ATAATCTTTGCCTTCAGAGAAACCCACTAATGTACAATTTATGGACACA 1 F3: 4 ATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA R RF: ATAATCTTTGCCTTCAGAGAAACCCACTAATGTACAATTTACGGACACATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA RR: TATTAGAAACGGAAGTCTCTTTGGGTGATTACATGTTAAATGCCTGTGTATATACAAGAGTATTTAATTTGTCGTCTTGTTTAACCTT F2: 3 ACAAGAGTATTTA 2 Unidirectional alignment (log-probability: -36.6) GCCTTCAGAGAAACCCACTAATGTACAATTTAtGGACACaatttatgagaacaATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA GCCTTCAGAGAAACCCACTAATGTACAATTTACGGACAC--------------ATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA Template switch alignment (log-probability: -23.1) GCCTTCAGAGAAACCCACTAATGTACAATTTAtGGACACA|ATTTATGAGAACA|ATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA GCCTTCAGAGAAACCCACTAATGTACAATTTACGGACACA|ATTTATGAGAACA|ATATATGTTCTCATAAATTAAACAGCAGAACAAATTGGAA ========== Event 3728 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GTTCACAAGGGGCCTCCCAGGTGAATACTTTCTATTGAAAGTA------------TTTCTATCCAAGATCAGTGAC ↓ 3 1 2 4 Chimp: GTTCACAAGGGGCCTCCCAGGTGAATACTTTCAATAGAAAGTA------TTCACCTTTCTATCCAAGATCCGTGAC Gorilla: GTTCACAAGGGGCCTCCCAGGTGAATACTTTCAATAGAAAGTATTCACC------TTTCTATCCAAGATCAGTGAC ↑ 3 1 2 4 Human: GTTCACAAGGGGCCTCCCAGGTGAATACTTTCTATTGAAAGTA------------TTTCTATCCAAGATCAGTGAC Cluster: [ ] Orangutan: GTTCCCAAGCGGTCTCCCAGGTGAGTACTTTCAATAGATA--------------------CTCTAAGATCAGTGAC Human > Chimp ------------- chr9:97954774-97954790 Template switch process: F1: L AAGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTC 1 F3: 4 TTTCTATCCAAGATCCGTGACTGATGCCAGCCCAGGCCCC R RF: AAGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTCTATTGAAAGTATTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGCCCC RR: TTCTGGACTCAAGTGTTCCCCGGAGGGTCCACTTATGAAAGATAACTTTCATAAAGATAGGTTCTAGTCACTGACTACGGTCGGGTCCGGGG F2: 3 CCACTTATGAAAGATAA 2 Unidirectional alignment (log-probability: -37.6) AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTCaATaGAAAGTAttcaccTTTCTATCCAAGATCcGTGACTGATGCCAGCCCAGGCCCC AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTCTATTGAAAGTA------TTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGCCCC Template switch alignment (log-probability: -23.4) AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTC|AATAGAAAGTATTCACC|TTTCTATCCAAGATCcGTGACTGATGCCAGCCCAGGCCCC AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTC|AATAGAAAGTATTCACC|TTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGCCCC Human > Gorilla --------------- chr9:102697237-102697253 Template switch process: F1: L AAGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTC 1 F3: 4 TTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGTCCC R RF: AAGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTCTATTGAAAGTATTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGCCCC RR: TTCTGGACTCAAGTGTTCCCCGGAGGGTCCACTTATGAAAGATAACTTTCATAAAGATAGGTTCTAGTCACTGACTACGGTCGGGTCCGGGG F2: 3 CCACTTATGAAAGATAA 2 Unidirectional alignment (log-probability: -36.2) AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTCaATaGAAAGTAttcaccTTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGtCCC AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTCTATTGAAAGTA------TTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGCCCC Template switch alignment (log-probability: -23.4) AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTC|AATAGAAAGTATTCACC|TTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGtCCC AGACCTGAGTTCACAAGGGGCCTCCCAGGTGAATACTTTC|AATAGAAAGTATTCACC|TTTCTATCCAAGATCAGTGACTGATGCCAGCCCAGGCCCC ========== Event 3729 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AAAAGAGCAAACACTCAAAGA-----AATCAAGTCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGATTTTAATTCTAAAAGTTTCTT Chimp: AAAAGAGCAAACACTCAAAGA-----AATCAAGTCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGATTTTAATTCTAAAAGTTTCTT ↑ 1 4 3 2 Gorilla: AAAAGAGCAAACACTCAAAGA---------ACATCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGATTTTAATTCTGAAAGTTCCTT ↓ 1 4 3 2 Human: AAAAGAGCAAACACTCAAAGA-----AATCAAGTCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGATTTTAATTCTAAAAGTTTCTT Cluster: [ ] Orangutan: AAAAGAGCAAACACTCAAAGAACATC----AAGTCATAAATGGTGCATAAGAAAAGTGCTCATCTATCCTTGATTT-----------------T Gorilla > Human --------------- chr9:123174783-123174788 Template switch process: F1: L TTCCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA 1 F3: 4 TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA R RF: TTCCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAACATCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA RR: AAGGTTTAGGTCCTCATCGATTTTCTCGTTTGTGAGTTTCTTGTAGTATTTACCACGTATTCTTTCCACGAGTAGATAGGAACT F2: 3 GAACTA 2 Unidirectional alignment (log-probability: -26.4) CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAAatCAagTCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA--CA--TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA Template switch alignment (log-probability: -16.5) CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA|ATCAAG|TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA|ATCAAG|TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA Gorilla > Chimp --------------- chr9:101248033-101248038 Template switch process: F1: L TTCCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA 1 F3: 4 TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA R RF: TTCCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAACATCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA RR: AAGGTTTAGGTCCTCATCGATTTTCTCGTTTGTGAGTTTCTTGTAGTATTTACCACGTATTCTTTCCACGAGTAGATAGGAACT F2: 3 GAACTA 2 Unidirectional alignment (log-probability: -26.4) CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAAatCAagTCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA--CA--TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA Template switch alignment (log-probability: -16.5) CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA|ATCAAG|TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA CCAAATCCAGGAGTAGCTAAAAGAGCAAACACTCAAAGAA|ATCAAG|TCATAAATGGTGCATAAGAAAGGTGCTCATCTATCCTTGA ========== Event 3730 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ----AGTTTGTCCTTTCTACCTGGCCCTGGAG-------AAGGGGC-TCAGGGCC-AC-TGCCTCGTTCC ↓ 3 1 2 4 Chimp: ----AGTTTGTCCTTTCTACCTGGCCCTGGAGCCTTCTCCAGGGCCTGGAGGGCC-AC-TGCCTCGTTCC Gorilla: AGTAAGTTTGTCCTTTCTACCTGGCCCTGGAG-------AAGGGGC-TCAGGGCC-AC-TGCCTTGTTCC Human: ----AGTTTGTCCTTTCTACCTGGCCCTGGAG-------AAGGGGC-TCAGGGCC-AC-TGCCTCGTTCC Cluster: [ ] Orangutan: ----AGTTTGT-CTTTCTAACCGGCCTTGAAG-------AAGGGGC-TCAGGACCAACTGGCTTCGTTCC Human > Chimp ------------- chr9:101457897-101457913 Template switch process: F1: L GAGGCAGAGACCAAGTTTGTCCTTTCTACCTGGCCCTGGAG 1 F3: 4 AGGGCCACTGCCTCGTTCCAACCCAGGAAGGCCAGCTGCC R RF: GAGGCAGAGACCAAGTTTGTCCTTTCTACCTGGCCCTGGAGAAGGGGCTCAGGGCCACTGCCTCGTTCCAACCCAGGAAGGCCAGCTGCC RR: CTCCGTCTCTGGTTCAAACAGGAAAGATGGACCGGGACCTCTTCCCCGAGTCCCGGTGACGGAGCAAGGTTGGGTCCTTCCGGTCGACGG F2: 3 GGTCCGGGACCTCTTCC 2 Unidirectional alignment (log-probability: -44.6) AGGCAGAGACCAAGTTTGTCCTTTCTACCTGGCCCTGGAG--------CcttctccagggcctggAGGGCCACTGCCTCGTTCCAACCCAGGAAGGCCAGCTGCC AGGCAGAGACCAAGTTTGTCCTTTCTACCTGGCCCTGGAGAAGGGGCTC----------------AGGGCCACTGCCTCGTTCCAACCCAGGAAGGCCAGCTGCC Template switch alignment (log-probability: -23.4) AGGCAGAGACCAAGTTTGTCCTTTCTACCTGGCCCTGGAG|CCTTCTCCAGGGCCtGG|AGGGCCACTGCCTCGTTCCAACCCAGGAAGGCCAGCTGCC AGGCAGAGACCAAGTTTGTCCTTTCTACCTGGCCCTGGAG|CCTTCTCCAGGGCCAGG|AGGGCCACTGCCTCGTTCCAACCCAGGAAGGCCAGCTGCC ========== Event 3731 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCTCACTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCC------------TGTGTCCAGCCCTGTGCTATTCTATGATCAGCTTCA Chimp: GCCTCACTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCC------------TGTGTCCAGCCCTGTGCTATTCTACAATCAGCTTCA Gorilla: GCCTCACTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCC------------------------TGTGCTATTCTATGATCAACTTCA ↓ 3 2 4 1 Human: GCCTCACTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCC------------TGTGTCCAGCCCTGTGCTATTCTATGATCAGCTTCA Cluster: [ ] Orangutan: GCCTCACTGGGGCATGCCGGCTGGATGAAGAGGAACACAGCCTGTGTCCAGCCC------------TGTGCTATTCTATGAT------CA Gorilla > Human --------------- chr9:123424325-123424330 Template switch process: F1: L CCTCACTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCCTGTG 1 F3: 4 CCTGTGCTATTCTATGATCAGCTTCAACAGTTCCCACGCAGG R RF: CCTCACTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCCTGTGCTATTCTATGATCAACTTCAACAGTTCCCACGCAGG RR: GGAGTGACCCCGTACGACCGACCTACTTCTCCTTGTGTCGGACACGATAAGATACTAGTTGAAGTTGTCAAGGGTGCGTCC F2: 3 CGACCT 2 Unidirectional alignment (log-probability: -33.7) CTGGGGCATGCTGGCTGGATGAAGAGGAACACAGcctgtgtccagcCCTGTGCTATTCTATGATCAgCTTCAACAGTTCCCACGCA CTGGGGCATGCTGGCTGGATGAAGAGGAACACAG------------CCTGTGCTATTCTATGATCAACTTCAACAGTTCCCACGCA Template switch alignment (log-probability: -22.2) CTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCCTGTG|TCCAGC|CCTGTGCTATTCTATGATCAgCTTCAACAGTTCCCACGCA CTGGGGCATGCTGGCTGGATGAAGAGGAACACAGCCTGTG|TCCAGC|CCTGTGCTATTCTATGATCAACTTCAACAGTTCCCACGCA ========== Event 3732 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGCTCATAATGATGCTAACCAAAAGGGA----ATGTGAC---TCCTTGACACTAACCAGGGGCTAC Chimp: TTGCTCATAATGATGCTAACCAAAAGGGA----ATGTGAC---TCCTTGACACTAACCAGGGGCTAC ↓ 3 2 1 4 Gorilla: TTGCTCATAATGATGCTAACCAAAAGGGA--------CACTTTTGGTTGACACTAACCAGGGGCTAC ↑ 3 2 1 4 Human: TTGCTCATAATGATGCTAACCAAAAGGGA----ATGTGAC---TCCTTGACACTAACCAGGGGCTAC Cluster: [ ] Orangutan: TTGCTCATAATGATGCTAACCAAAAGGGAATGT----GAC---TCCTTGACACTAACCAGGGGCTAC Human > Gorilla --------------- chr9:107113778-107113786 Template switch process: F1: L GGATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA 1 F3: 4 TTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT R RF: GGATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGAATGTGACTCCTTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT RR: CCTAATAAGTGTAACGAGTATTACTACGATTGGTTTTCCCTTACACTGAGGAACTGTGATTGGTCCCCGATGACTCAGAACTTTTTTGTAA F2: 3 GGTTTTCAC 2 Unidirectional alignment (log-probability: -32.6) GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA---------CacttttggTTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGAATGTGACTCC--------TTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT Template switch alignment (log-probability: -22.4) GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA|CaCTTTTGG|TTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA|CCCTTTTGG|TTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT Chimp > Gorilla --------------- chr9:107113778-107113786 Template switch process: F1: L GGATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA 1 F3: 4 TTGACACTAACCAGGGGCTACTGAGTCTTGAAAAAACATT R RF: GGATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGAATGTGACTCCTTGACACTAACCAGGGGCTACCGAGTCTTGAAAAAACATT RR: CCTAATAAGTGTAACGAGTATTACTACGATTGGTTTTCCCTTACACTGAGGAACTGTGATTGGTCCCCGATGGCTCAGAACTTTTTTGTAA F2: 3 GGTTTTCAC 2 Unidirectional alignment (log-probability: -38.1) GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA---------CacttttggTTGACACTAACCAGGGGCTACtGAGTCTTGAAAAAACATT GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGAATGTGACTCC--------TTGACACTAACCAGGGGCTACCGAGTCTTGAAAAAACATT Template switch alignment (log-probability: -27.9) GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA|CaCTTTTGG|TTGACACTAACCAGGGGCTACtGAGTCTTGAAAAAACATT GATTATTCACATTGCTCATAATGATGCTAACCAAAAGGGA|CCCTTTTGG|TTGACACTAACCAGGGGCTACCGAGTCTTGAAAAAACATT ========== Event 3733 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CATTTCTAGATGTTCTAAACCAGCTCATCCAGGAAGGAACGAGttcatggagtccccactatatatcagacactctgctgaa--------------------------------------------------------------------------------------------------------------------------------------taatttgtacactctctctctctcgcaaccctttg Chimp: TATTTCTAGATGTTCTAAACCAGCTCATCCAGGAAGGAACGAGTTCATGGAGTCCCCACTATATATCAGACACTCTGCTGAATAATTTGAGTGTGTACAAATTATTCAGCAGAGTGTCTGATTTATAGTGGGGACTCCATGAACTCGTTCCTTCCAGCTCATCCAGGAAGGAACGAGTTCATGGAGTCCCCACTATATATCAGACACTCTGCTGAATAATTTGTACACACTCTCTCTCTCGcaaccctttg ↑ 4 3 1 2 Gorilla: CATTTCTAGATGTTCTAAACCAGCTCATCCAGGAAGGAACGAGTTCATGGAGTCCCCACTATATATCAGACACTCTGCCGAA--------------------------------------------------------------------------------------------------------------------------------------TAATTTGTACACACTCTGTCTCTCGcaaccctttg Human: CATTTCTAGATGTTCTAAACCAGCTCATCCAGGAAGGAACGAGttcatggagtccccactatatatcagacactctgctgaa--------------------------------------------------------------------------------------------------------------------------------------taatttgtacactctctctctctcgcaaccctttg Cluster: [ ] Orangutan: CATTTCTAGATGTTCTAAACCAGCTCATCCAGGGAGGAATGAGttcatagagtccccactatatatcagacactccgctgaa--------------------------------------------------------------------------------------------------------------------------------------taatttgtacacactctctctctctcaaccctttc Gorilla > Chimp --------------- chr9:101811796-101811859 Template switch process: F1: L AACGAGTTCATGGAGTCCCCACTATATATCAGACACTCTGCTGAATAATTTG 1 F3: 4 CCAGCTCATCCAGGAAGGAACGAGTTCATGGAGTCCCCACTATATATCAGACACTCTGCTGAATAATTTGTACACACTCTCTCTCTCGCAACCCTTTGAGGTG R RF: AAGGAACGAGTTCATGGAGTCCCCACTATATATCAGACACTCTGCCGAATAATTTGTACACACTCTGTCTCTCGCAACCCTTTGAGGTG RR: TTCCTTGCTCAAGTACCTCAGGGGTGATATATAGTCTGTGAGACGGCTTATTAAACATGTGTGAGACAGAGAGCGTTGGGAAACTCCAC F2: 3 TTCCTTGCTCAAGTACCTCAGGGGTGATATTTAGTCTGTGAGACGACTTATTAAACATGTGTGA 2 Unidirectional alignment (log-probability: -209) gagtccccactatatatcagacactctgctgaataatttgagtgtgtacaaattattcagcagagtgtctgatttatagtggggactccatgaactcgttccttccagctcatccaggaaggAACGAGTTCATGGAGTCCCCAC --------------------------------------------------------------------------------------------------------------------------AACGAGTTCATGGAGTCCCCAC Template switch alignment (log-probability: -52.9) GAGTCCCCACTATATATCAGACACTCTGCtGAATAATTTG|AGTGTGTACAAATTATTCaGCAGAGTGTCTGATtTATAGTGGGGACTCCATGAACTCGTTCCTT|CCAGCTCATCCAGGAAGGAACGAGTTCATGGAGTCCCCAC GAGTCCCCACTATATATCAGACACTCTGCCGAATAATTTG|AGTGTGTACAAATTATTCGGCAGAGTGTCTGATATATAGTGGGGACTCCATGAACTCGTTCCTT|CCAGCTCATCCAGGAAGGAACGAGTTCATGGAGTCCCCAC ========== Event 3734 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTCTCAGGCTTACATTAGAG----CTTACAGAGCTGCAATCCCTTGGAAGTGGGG ↓ 1 3 4 2 Chimp: TTTCTCAGGCTTACATTAGAGCAGCTCTGTAGAGCTGCAATCCCTTGGAAGTGGGG Gorilla: TTTCTCAGGCTTACATTAGAG----CTTATAGAGCTGCAATCCCTTGGAACTGGGG Human: TTTCTCAGGCTTACATTAGAG----CTTACAGAGCTGCAATCCCTTGGAAGTGGGG Cluster: [ ] Orangutan: TTTCTCAGGCTTACACTAGAG----CTTACAGAGCTGCAATCCCTTGGAACTGGGG Human > Chimp ------------- chr9:13426900-13426907 Template switch process: F1: L CAGCAAACAGTAAAATTTCTTTTCTCAGGCTTACATTAGAGC 1 F3: 4 AGAGCTGCAATCCCTTGGAAGTGGGGAGGTGCCTTAATAC R RF: CAGCAAACAGTAAAATTTCTTTTCTCAGGCTTACATTAGAGCTTACAGAGCTGCAATCCCTTGGAAGTGGGGAGGTGCCTTAATAC RR: GTCGTTTGTCATTTTAAAGAAAAGAGTCCGAATGTAATCTCGAATGTCTCGACGTTAGGGAACCTTCACCCCTCCACGGAATTATG F2: 3 TGTCTCGA 2 Unidirectional alignment (log-probability: -31.4) GCAAACAGTAAAATTTCTTTTCTCAGGCTTACATTAGAGCagctctgT---AGAGCTGCAATCCCTTGGAAGTGGGGAGGTGCCTTAATAC GCAAACAGTAAAATTTCTTTTCTCAGGCTTACATTAGAGC-------TTACAGAGCTGCAATCCCTTGGAAGTGGGGAGGTGCCTTAATAC Template switch alignment (log-probability: -16.3) GCAAACAGTAAAATTTCTTTTCTCAGGCTTACATTAGAGC|AGCTCTGT|AGAGCTGCAATCCCTTGGAAGTGGGGAGGTGCCTTAATAC GCAAACAGTAAAATTTCTTTTCTCAGGCTTACATTAGAGC|AGCTCTGT|AGAGCTGCAATCCCTTGGAAGTGGGGAGGTGCCTTAATAC ========== Event 3735 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGCCTTACCTCCAAGATTCACCTGTAG------------AAATCCCCCTCCAACACTTCAAG Chimp: CTGCCTTACCTCCAAGATTCACCTGTAG------------AAATCCCCCTCCAACACTTCAAG ↓ 3 142 Gorilla: CTGCCTTACCTCCAAGATTCACCTGTAGATTTCTACAGGTGAATCCCCCTCCAACACTTCAAG ↑ 3 142 Human: CTGCCTTACCTCCAAGATTCACCTGTAG------------AAATCCCCCTCCAACACTTCAAG Cluster: [ ] Orangutan: CTGCCTTACCTCCAAGATTCACCTGTAG------------AAATTCCCCTCCAACACTTCAAG Human > Gorilla --------------- chr9:10430876-10430887 Template switch process: F1: L CTGCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA 1 F3: 4 AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG R RF: CTGCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGAAATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG RR: GACGTCAATGGACGACGGAATGGAGGTTCTAAGTGGACATCTTTAGGGGGAGGTTGTGAAGTTCTTGTCAAACCACGGGAAC F2: 3 GTGGACATCTTT 2 Unidirectional alignment (log-probability: -28.2) GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGAtttctacaggtgAATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA------------AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG Template switch alignment (log-probability: -17.3) GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA|TTTCTACAGGTG|AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA|TTTCTACAGGTG|AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG Chimp > Gorilla --------------- chr9:10430876-10430887 Template switch process: F1: L CTGCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA 1 F3: 4 AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG R RF: CTGCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGAAATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG RR: GACGTCAATGGACGACGGAATGGAGGTTCTAAGTGGACATCTTTAGGGGGAGGTTGTGAAGTTCTTGTCAAACCACGGGAAC F2: 3 GTGGACATCTTT 2 Unidirectional alignment (log-probability: -28.2) GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGAtttctacaggtgAATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA------------AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG Template switch alignment (log-probability: -17.3) GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA|TTTCTACAGGTG|AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG GCAGTTACCTGCTGCCTTACCTCCAAGATTCACCTGTAGA|TTTCTACAGGTG|AATCCCCCTCCAACACTTCAAGAACAGTTTGGTGCCCTTG ========== Event 3736 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AttttttttGTTATAAAGAAAT----GGACAAAATATTGACAAGGCACTGTTTTTCCACACATATCACCAAT Chimp: Att-tttttGTTATAAAGAAAAACAGTGCCAAAATATTGACGAGGCACTGTTTTTCCACACATATCACCAAT ↑ 1 4 3 2 Gorilla: Att-tttttGTTATAAAGAAAT----GGCCAAAATATTGACAAGGCACTGTTTTTCCACACATATCACCAAT Human: AttttttttGTTATAAAGAAAT----GGACAAAATATTGACAAGGCACTGTTTTTCCACACATATCACCAAT Cluster: [ ] Orangutan: ATT-TTTTTGTTATAAAGAAAT----GGCCAAAATATTGACAAGGCACTGTTTTTCCACACATATCACCAAT Gorilla > Chimp --------------- chr9:11039044-11039049 Template switch process: F1: L AAGCCACAGCAATCCTTACACATTTTTTTGTTATAAAGAAA 1 F3: 4 GCCAAAATATTGACGAGGCACTGTTTTTCCACACATATCA R RF: AAGCCACAGCAATCCTTACACATTTTTTTGTTATAAAGAAATGGCCAAAATATTGACAAGGCACTGTTTTTCCACACATATCA RR: TTCGGTGTCGTTAGGAATGTGTAAAAAAACAATATTTCTTTACCGGTTTTATAACTGTTCCGTGACAAAAAGGTGTGTATAGT F2: 3 TGACAA 2 Unidirectional alignment (log-probability: -33.2) AGCCACAGCAATCCTTACACATTTTTTTGTTATAAAGAAaaacAgtGCCAAAATATTGACgAGGCACTGTTTTTCCACACATATCA AGCCACAGCAATCCTTACACATTTTTTTGTTATAAAGAA----ATGGCCAAAATATTGACAAGGCACTGTTTTTCCACACATATCA Template switch alignment (log-probability: -22) AGCCACAGCAATCCTTACACATTTTTTTGTTATAAAGAAA|AACAGT|GCCAAAATATTGACgAGGCACTGTTTTTCCACACATATCA AGCCACAGCAATCCTTACACATTTTTTTGTTATAAAGAAA|AACAGT|GCCAAAATATTGACAAGGCACTGTTTTTCCACACATATCA ========== Event 3737 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: GCCTGGGATCTCAGGTGTCTGCGAGGAAATCCAGAGCCACTTGAGCCGTGTGGTCCGGTGGGC-CCCCTCGCAGGGgcactgctcacgcacgac Chimp: GCCTGGGATCTCAGGTGTCTGCAAGGAAATCCGGAGCCACTTGAGCCGTGTGGTCCGGTGGGCCCCCCTCGCAGGGGCACTGCTCACGCACGAC Gorilla: GCCTGGGATCTCAGGTGTCTGCGAGGAAATCCAGAGCCACTTGAGCCGTGTGGTCCGCTGGGTCCTCCTTGCGGGGgcactgctcacgcacgac ↓ 3 2 1 4 Human: GCCTGGGATCTCAGGTGTCTGCGAGGAAATCCAGAGCCACTTGAGCCGTGTGGTCCGGTGGGC-CCCCTCGCAGGGgcactgctcacgcacgac Cluster: [ ] Orangutan: GCCTGGGATCTCAGGTGTCTGCAAGGAAATCCAGAGCCACTTGAGCCGTGTGGTCCGGTGGGTCCTCCTCGCAGGGgcactgcccacgcacgac Gorilla > Human --------------- chr9:128114734-128114740 Template switch process: F1: L GTCTGCGAGGAAATCCAGAGCCACTTGAGCCGTGTGGTCCGGTGGGCCC 1 F3: 4 GGGGCACTGCTCACGCACGACTTCACTTAGCTC R RF: GTCTGCGAGGAAATCCAGAGCCACTTGAGCCGTGTGGTCCGCTGGGTCCTCCTTGCGGGGGCACTGCTCACGCACGACTTCACTTAGCTC RR: CAGACGCTCCTTTAGGTCTCGGTGAACTCGGCACACCAGGCGACCCAGGAGGAACGCCCCCGTGACGAGTGCGTGCTGAAGTGAATCGAG F2: 3 ACGCTCC 2 Unidirectional alignment (log-probability: -40) GAAATCCAGAGCCACTTGAGCCGTGTGGTCCGgTGGGcCC-CCTcGCaGGGGCACTGCTCACGCACGACTTCACTTAGCTC-- GAAATCCAGAGCCACTTGAGCCGTGTGGTCCGCTGGGTCCTCCTTGCGGGGGCACTGCTCACGCACGACTTCACTTAGCTCTC Template switch alignment (log-probability: -27.7) GAAATCCAGAGCCACTTGAGCCGTGTGGTCCGgTGGGcCC|CCTCGCA|GGGGCACTGCTCACGCACGACTTCACTTAGCTC GAAATCCAGAGCCACTTGAGCCGTGTGGTCCGCTGGGTCC|CCTCGCA|GGGGCACTGCTCACGCACGACTTCACTTAGCTC ========== Event 3738 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCATGATCCCTGCCCCATGCATGGGATCATGCCCCATGCATGCCACCTGCCTGGGGGTGCCCAGCTGCT--------------TCCCACCAGAGGGGCCCCGG ↑ 3 2 4 1 Chimp: CCATGATCCCTGCCCCATGCATGGGA---------CTTCATGCCACCTGCCTGGG--------------GGTGCCCAGCTGCTTCCCACCAGAGGGGCCCCGG Gorilla: CCATGATCCCTGCCCCATGCATGGGA---------CTTCATGCCACCTGCCTGGGGGTGCCCAGCTGCT--------------TCCCACCAGAGGGGCCCCGG Human: CCATGATCCCTGCCCCATGCATGGGATCATGCCCCATGCATGCCACCTGCCTGGGGGTGCCCAGCTGCT--------------TCCCACCAGAGGGGCCCCGG Cluster: [ ] Orangutan: CCATGATCCCTGCCCCATGCATGGGA---------CTTCATGCCACCTGCCTGGGGGTGCCCAGCTGCT--------------TCCCACCAGAGGGGCCCCGG Chimp > Human ------------- chr9:10433424-10433428 Template switch process: F1: L CCATGCATGGGA--TCATGCC 1 F3: 4 CATGCCACCTGCCTGGGGGTGCCCAGCTGCTTCCCACCAGAGGGGCCCCGGGGCTGAGGGGGAGGCAGTGT R RF: CCATGCATGGGACTTCATGCCACCTGCCTGGGGGTGCCCAGCTGCTTCCCACCAGAGGGGCCCCGGGGCTGAGGGGGAGGCAGTGT RR: GGTACGTACCCTGAAGTACGGTGGACGGACCCCCACGGGTCGACGAAGGGTGGTCTCCCCGGGGCCCCGACTCCCCCTCCGTCACA F2: 3 GTACC 2 Unidirectional alignment (log-probability: -35.9) CCATGCATGGGAtcatgccccaTgCATGCCACCTGCCTGGGGGTGCCCAGCTGCTTCCCACCAG CCATGCATGGGA---------CTTCATGCCACCTGCCTGGGGGTGCCCAGCTGCTTCCCACCAG Template switch alignment (log-probability: -26.4) CCATGCATGGGA--TCATGCC|CCATG|CATGCCACCTGCCTGGGGGTGCCCAGCTGCTTCCCACCAG CCATGCATGGGACTTCATGCC|CCATG|CATGCCACCTGCCTGGGGGTGCCCAGCTGCTTCCCACCAG ========== Event 3739 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AGAAAGATATGTTAACTCCTTGCACACAGAGTGT--------------------------GCACAGGTAAACATATACATG Chimp: AGAAAGATATGTTAACTCCTTGCACACTCTGTGT-------------GCAAGGTGTGCACGCACAGGTAAAAATATACATG Gorilla: AGAAAGATATGTTAACTCCTTACATACTCTGTGTGCAAGGTGTGCAC-------------GCACAGGTAAACATATACATG ↓ 1 3 2 4 Human: AGAAAGATATGTTAACTCCTTGCACACAGAGTGT--------------------------GCACAGGTAAACATATACATG Cluster: [ ] Orangutan: Gorilla > Human --------------- chr9:9014909-9014921 Template switch process: F1: L GGGGGAGAGCAAAACGTGAGAGAAAGATATGTTAACTCCTT 1 F3: 4 GCACAGGTAAACATATACATGCACACGCTGGCATATAAAA R RF: GGGGGAGAGCAAAACGTGAGAGAAAGATATGTTAACTCCTTACATACTCTGTGTGCAAGGTGTGCACGCACAGGTAAACATATACATGCACACGCTGGCATATAAAA RR: CCCCCTCTCGTTTTGCACTCTCTTTCTATACAATTGAGGAATGTATGAGACACACGTTCCACACGTGCGTGTCCATTTGTATATGTACGTGTGCGACCGTATATTTT F2: 3 TGTGAGACACACG 2 Unidirectional alignment (log-probability: -34.8) GGGGAGAGCAAAACGTGAGAGAAAGATATGTTAACTCCT----------------------TGCACacagagtgtGCACAGGTAAACATATACATGCACACGCTGGCATATAAAA GGGGAGAGCAAAACGTGAGAGAAAGATATGTTAACTCCTTACATACTCTGTGTGCAAGGTGTGCAC---------GCACAGGTAAACATATACATGCACACGCTGGCATATAAAA Template switch alignment (log-probability: -22.9) GGGGAGAGCAAAACGTGAGAGAAAGATATGTTAACTCCTT|GCACACAGAGTgT|GCACAGGTAAACATATACATGCACACGCTGGCATATAAAA GGGGAGAGCAAAACGTGAGAGAAAGATATGTTAACTCCTT|GCACACAGAGTAT|GCACAGGTAAACATATACATGCACACGCTGGCATATAAAA ========== Event 3740 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GAATAAACTCAGGTTTCTGGATTGCTTACCAAATAAAGTGCTTTGGCCCACTACCTGAATAAAGGCAAACCTGCAATTGAGTGGAGCCCTGATCTTTTG Chimp: GAATAAACTCAGGTTTCTGGATTGCTTACCAAATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCTACAATTGAGTGGAGCCCTGATCTTTTG ↓ 3 2 1 4 Gorilla: GAATAAACTCAGGTTTCTGGATTGCTTACCAAATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCTGCAATCGAGTGGAGCCCTGATCTTTTG Human: GAATAAACTCAGGTTTCTGGATTGCTTACCAAATAAAGTGCTTTGGCCCACTACCTGAATAAAGGCAAACCTGCAATTGAGTGGAGCCCTGATCTTTTG Cluster: [ ] Orangutan: AAATAAACTCAGGTTTCTGGAATGCTTACCAAATAAAGTGCTTTGGCCCACTGTCTGGATAAAGGCAAACCTGCAATTGAATGGAGCCCTCATCTTTTG Chimp > Gorilla --------------- chr9:10742275-10742280 Template switch process: F1: L AATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCT 1 F3: 4 GAGTGGAGCCCTGATCTTTTGATGCTTACAGAAAGAAGGT R RF: GATTGCTTACCAAATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCTACAATTGAGTGGAGCCCTGATCTTTTGATGCTTACAGAAAGAAGGT RR: CTAACGAATGGTTTATTTCACGAAACCGGGTGATAGACTTATTTCCGTTTGGATGTTAACTCACCTCGGGACTAGAAAACTACGAATGTCTTTCTTCCA F2: 3 CTAACG 2 Unidirectional alignment (log-probability: -43.2) ATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCTgCAATcGAGTGGAGCCCTGATCTTTTGATgcttacagaaagaaggt ATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCTACAATTGAGTGGAGCCCTGATCTTTTGAT----------------- Template switch alignment (log-probability: -16.5) ATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCT|GCAATC|GAGTGGAGCCCTGATCTTTTGATGCTTACAGAAAGAAGGT ATAAAGTGCTTTGGCCCACTATCTGAATAAAGGCAAACCT|GCAATC|GAGTGGAGCCCTGATCTTTTGATGCTTACAGAAAGAAGGT ========== Event 3741 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: acccccaacCAAACACATTTATGCATATG-CATAAAGCAGACGAGGAAAGATTCT Chimp: acccccaacCAAACACATTTATGCATATGCCGCAAAGCAGACGAGGAAAGATTCT Gorilla: acccccaacCAAACACATTTATGCATCTGCTGCAAAGCAGACGAGGAAAGATTCT ↓ 3 2 4 Human: acccccaacCAAACACATTTATGCATATG-CATAAAGCAGACGAGGAAAGATTCT Cluster: [ ] Orangutan: ACCCCCAACCAAACACATTTATGCATCTGCTGCAAAGCAGACGAGGAAAGATTCT Gorilla > Human --------------- chr9:129504515-129504521 Template switch process: F1: L CACATATTTCCTAACACCCCCAACCAAACACATTTATGCAT 1 F3: 4 AAGCAGACGAGGAAAGATTCTAAATAGGCTCTGAATCTC R RF: CACATATTTCCTAACACCCCCAACCAAACACATTTATGCATCTGCTGCAAAGCAGACGAGGAAAGATTCTAAATAGGCTCTGAATCTT RR: GTGTATAAAGGATTGTGGGGGTTGGTTTGTGTAAATACGTAGACGACGTTTCGTCTGCTCCTTTCTAAGATTTATCCGAGACTTAGAA F2: 3 ATACGTA 2 Unidirectional alignment (log-probability: -33.1) ACATATTTCCTAACACCCCCAACCAAACACATTTATGCATaTGC-atAAAGCAGACGAGGAAAGATTCTAAATAGGCTCTGAATCTc ACATATTTCCTAACACCCCCAACCAAACACATTTATGCATCTGCTGCAAAGCAGACGAGGAAAGATTCTAAATAGGCTCTGAATCTT Template switch alignment (log-probability: -22.1) ACATATTTCCTAACACCCCCAACCAAACACATTTATGCAT|ATGCATA|AAGCAGACGAGGAAAGATTCTAAATAGGCTCTGAATCTc ACATATTTCCTAACACCCCCAACCAAACACATTTATGCAT|ATGCATA|AAGCAGACGAGGAAAGATTCTAAATAGGCTCTGAATCTT ========== Event 3742 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TGTTCATGGAAGAAGGCCGCTGCTCAGAGGCCGCGAAGCAGCCTCCGAGCCTTCTTGGACCCGCACAGAA Chimp: TGTTCATGGAAGAAGGCCGCTGCTCAGAGGCCGCGAAGCAGCCTCCGAGCCTTCTTGGACCCGCACAGAA ↑ 3 4 2 Gorilla: TGTTCATGGAAGAAGGCCGCTT--------------CGCGGCCTCTGAGCCTTCTTGGACCCGCACAGAA ↓ 3 4 2 Human: TGTTCATGGAAGAAGGCCGCTGCTCAGAGGCCGCGAAGCAGCCTCCGAGCCTTCTTGGACCCGCACAGAA Cluster: [ ] Orangutan: Gorilla > Human --------------- chr9:8781552-8781567 Template switch process: F1: L TGAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCT 1 F3: 4 GCAGCCTCCGAGCCTTCTTGGACCCGCACAGAAACCTGGAGCAGGTGGG R RF: TGAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTTCGCGGCCTCTGAGCCTTCTTGGACCCGCACAGAAACCTGGAGCAGGTGGG RR: ACTTGTCGTCGGACGGGAAGACAAGTACCTTCTTCCGGCGAAGCGCCGGAGACTCGGAAGAACCTGGGCGTGTCTTTGGACCTCGTCCACCC F2: 3 AAGCGCCGGAGACTCG 2 Unidirectional alignment (log-probability: -47.7) GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTgCtcagaggccgcgaaGCaGCCTCcGAGCCTTCTTGGACCCGCACAGAAACCTGGA GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTTC--------------GCGGCCTCTGAGCCTTCTTGGACCCGCACAGAAACCTGGA Template switch alignment (log-probability: -29) GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCT|GCTCAGAGGCCGCGAA|GCaGCCTCcGAGCCTTCTTGGACCCGCACAGAAACCTGGA GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCT|GCTCAGAGGCCGCGAA|GCGGCCTCTGAGCCTTCTTGGACCCGCACAGAAACCTGGA Gorilla > Chimp --------------- chr9:8959616-8959631 Template switch process: F1: L TGAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCT 1 F3: 4 GCAGCCTCCGAGCCTTCTTGGACCCGCACAGAAACCTGGAGCAGGTGGG R RF: TGAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTTCGCGGCCTCTGAGCCTTCTTGGACCCGCACAGAAACCTGGAGCAGGTGGG RR: ACTTGTCGTCGGACGGGAAGACAAGTACCTTCTTCCGGCGAAGCGCCGGAGACTCGGAAGAACCTGGGCGTGTCTTTGGACCTCGTCCACCC F2: 3 AAGCGCCGGAGACTCG 2 Unidirectional alignment (log-probability: -47.7) GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTgCtcagaggccgcgaaGCaGCCTCcGAGCCTTCTTGGACCCGCACAGAAACCTGGA GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCTTC--------------GCGGCCTCTGAGCCTTCTTGGACCCGCACAGAAACCTGGA Template switch alignment (log-probability: -29) GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCT|GCTCAGAGGCCGCGAA|GCaGCCTCcGAGCCTTCTTGGACCCGCACAGAAACCTGGA GAACAGCAGCCTGCCCTTCTGTTCATGGAAGAAGGCCGCT|GCTCAGAGGCCGCGAA|GCGGCCTCTGAGCCTTCTTGGACCCGCACAGAAACCTGGA ========== Event 3743 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GAATATATTTTCTGCCACAGATCTAGCAC--TTATACCCTGTTCTCAATGTAGGC ↓ 3 2 1 4 Chimp: GAATATATTTTCTGCCACAGATCTAGCACAGATCTACCCTGTTCTCAATGTAGGC Gorilla: GAATATGTTTTCTGCCACAGATCTAGCAC--TTATACCCTGTTCTCAACGTAGGC Human: GAATATATTTTCTGCCACAGATCTAGCAC--TTATACCCTGTTCTCAATGTAGGC Cluster: [ ] Orangutan: GAATATATTTTCTGCCACAGATCTAGCAC--TTATACCCTGTTCTCAATGTAGGC Human > Chimp ------------- chr9:13478719-13478723 Template switch process: F1: L CTTAACACCTCAGAATATATTTTCTGCCACAGATCTAGCAC 1 F3: 4 TACCCTGTTCTCAATGTAGGCAGCACTATAGAGAGCTTGG R RF: CTTAACACCTCAGAATATATTTTCTGCCACAGATCTAGCACTTATACCCTGTTCTCAATGTAGGCAGCACTATAGAGAGCTTGG RR: GAATTGTGGAGTCTTATATAAAAGACGGTGTCTAGATCGTGAATATGGGACAAGAGTTACATCCGTCGTGATATCTCTCGAACC F2: 3 CTAGA 2 Unidirectional alignment (log-probability: -25.8) TTAACACCTCAGAATATATTTTCTGCCACAGATCTAGCACagaTcTACCCTGTTCTCAATGTAGGCAGCACTATAGAGAGCTTGG TTAACACCTCAGAATATATTTTCTGCCACAGATCTAGCAC--TTATACCCTGTTCTCAATGTAGGCAGCACTATAGAGAGCTTGG Template switch alignment (log-probability: -15.9) TTAACACCTCAGAATATATTTTCTGCCACAGATCTAGCAC|AGATC|TACCCTGTTCTCAATGTAGGCAGCACTATAGAGAGCTTGG TTAACACCTCAGAATATATTTTCTGCCACAGATCTAGCAC|AGATC|TACCCTGTTCTCAATGTAGGCAGCACTATAGAGAGCTTGG ========== Event 3744 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: aaaaacatttatgaatgattgaaAAAATTTTTAAAAATTCAATGTATAGATTCTTTTTACAATATTATGCTATATAATTGTACTGCTGGGAGC Chimp: aaaaacatttatgaatgattgaaAAAATTTTTAAAAATTCAATGTATAGATTCTTTTTACAATATTATGCTATATAATTGTACTGCTGGGAGC Gorilla: aaaaacatttacgaatgattacattgaattttaaaaaattttttcatagattctttttaCAATACTATGCTACATAATTGTACTGCTGGGAGC ↓ 3 2 1 4 Human: aaaaacatttatgaatgattgaaAAAATTTTTAAAAATTCAATGTATAGATTCTTTTTACAATATTATGCTATATAATTGTACTGCTGGGAGC Cluster: [ ] Orangutan: aaaaacgtttatgaatgattgaaAAAATTTTTAAAAATTCAATGTATAGATTCTTTTTACAATATTATGCTATCTAATTATACTGCTGGGAAC Gorilla > Human --------------- chr9:13386989-13387010 Template switch process: F1: L 1 F3: 4 ATAGATTCTTTTTACAATATTATGCTATATAATTGTACTGCTGGGAGCTCCTCCATAGAGTCAGGGGC R RF: ACATTGAATTTTAAAAAATTTTTCATAGATTCTTTTTACAATACTATGCTACATAATTGTACTGCTGGGAGCTCCTCCATAGAGTCAGGGGC RR: TGTAACTTAAAATTTTTTAAAAAGTATCTAAGAAAAATGTTATGATACGATGTATTAACATGACGACCCTCGAGGAGGTATCTCAGTCCCCG F2: 3 TGTAACTTAAAAATTTTTAAAA 2 Unidirectional alignment (log-probability: -52.4) AAAATTTTtaaaaaTTCaatgtATAGATTCTTTTTACAATAtTATGCTAtATAATTGTACTG AAAATTTT------TTC-----ATAGATTCTTTTTACAATACTATGCTACATAATTGTACTG Template switch alignment (log-probability: -34.8) |AAAATTTTTaAAAATTCAATGT|ATAGATTCTTTTTACAATAtTATGCTAtATAATTGTACTG |AAAATTTTTTAAAATTCAATGT|ATAGATTCTTTTTACAATACTATGCTACATAATTGTACTG ========== Event 3745 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: TGGGACAGAACCACTGGCCCTTTGGTTTATGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAGTCCCAGACTCAGTCATAAACCAAAGGGAAGTGGAGGC Chimp: TGGGACAGTACCACTGGCCCTTTGGT-TATGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C----GTGGGACTCAGTCATAAACCAAAGGGAAGTGGAGGC ↓ 1 3 4 2 Gorilla: TGGGACAGTACCACTGGCCCTCTGGTTTATGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAGTCCCAGACTCAGTCATAAACCAAAGGGAAGTGGAGGC Human: TGGGACAGAACCACTGGCCCTTTGGTTTATGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAGTCCCAGACTCAGTCATAAACCAAAGGGAAGTGGAGGC Cluster: [ ] Orangutan: TGGGACAGTACCACTTGCCCTTTGGTTTATGActactgactatactaaaattaactgggcgtggttgcacgcacccccagctactcactcatgaggctgaggcaggagaatcgcttgaacccagcacgcacaggttgcagtgagctgacattgcgccactgcgctccagtcctggctgacagagagagacttcgtctctaacaaaTACATAAATAATAATTTAAAAATGCTGTAAAAGACCACAAGTTCTTCACCGCAAGAATTCAGAAGTCTTTGATGATTTAGCACCCATATTTAGGACTGTAATACTTCACTGATGTTATCCAAAAATGCCCAACGGGCTCCTTTGCTGTCGCTTTTCTAGTTAAGCCCCACTCCTATGGAGTCCAAGGACC--------------------------- Chimp > Gorilla --------------- chr9:85160693-85160707 Template switch process: F1: L CTCGTTTTCCCTGGGACATTTGGGACAGTACCACTGGCCCTCTGGTT 1 F3: 4 GACTCAGTCATAAACCAAAGGGAAGTGGAGGCCACTCCCT R RF: CTCGTTTTCCCTGGGACATTTGGGACAGTACCACTGGCCCTTTGGTTATGAGCGTGGGACTCAGTCATAAACCAAAGGGAAGTGGAGGCCACTCCCT RR: GAGCAAAAGGGACCCTGTAAACCCTGTCATGGTGACCGGGAAACCAATACTCGCACCCTGAGTCAGTATTTGGTTTCCCTTCACCTCCGGTGAGGGA F2: 3 ACCCTGAGTCAGTAT 2 Unidirectional alignment (log-probability: -46.8) TCCCTGGGACATTTGGGACAGTACCACTGGCCCTcTGGTTtatgactgagtcccA---------GACTCAGTCATAAACCAAAGGGAAGTGGAGGCCACTCCCT TCCCTGGGACATTTGGGACAGTACCACTGGCCCTTTGGTT--------------ATGAGCGTGGGACTCAGTCATAAACCAAAGGGAAGTGGAGGCCACTCCCT Template switch alignment (log-probability: -23.3) TCCCTGGGACATTTGGGACAGTACCACTGGCCCTcTGGTT|TATGACTGAGTCCCA|GACTCAGTCATAAACCAAAGGGAAGTGGAGGCCACTCCCT TCCCTGGGACATTTGGGACAGTACCACTGGCCCTTTGGTT|TATGACTGAGTCCCA|GACTCAGTCATAAACCAAAGGGAAGTGGAGGCCACTCCCT ========== Event 3746 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAGGGAGCTAAGGAAGCGCGGCGCGCC--C Chimp: CTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAA--TGCTAAGGAAGCGCGGCGCGCC--C ↑ 3 2 1 4 Gorilla: CTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAGGGAGCCAAGGAAGCGCGGCGCGCC--C Human: CTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAGGGAGCTAAGGAAGCGCGGCGCGCC--C Cluster: [ ] Orangutan: CTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAGGGAGCCAAGGAAGCGCGGCGCGCCCCT Gorilla > Chimp --------------- chr9:108458588-108458592 Template switch process: F1: L AGTCACCCTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAA 1 F3: 4 AAGGAAGCGCGGCGCGCCCCCTGGTGGTGGTAAGCCGCCA R RF: AGTCACCCTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAGGGAGCCAAGGAAGCGCGGCGCGCCCCCTGGTGGTGGTAAGCCGCCA RR: TCAGTGGGACAAGGGTCGCGCCAAAGTCGTAAATTAAAATTCCCTCGGTTCCTTCGCGCCGCGCGGGGGACCACCACCATTCGGCGGT F2: 3 TCGTA 2 Unidirectional alignment (log-probability: -27.6) GTCACCCTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAA--atGCtAAGGAAGCGCGGCGCGCCCCCTGGTGGTGGTAAGCCGCCA GTCACCCTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAAGGGAGCCAAGGAAGCGCGGCGCGCCCCCTGGTGGTGGTAAGCCGCCA Template switch alignment (log-probability: -16.4) GTCACCCTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAA|ATGCT|AAGGAAGCGCGGCGCGCCCCCTGGTGGTGGTAAGCCGCCA GTCACCCTGTTCCCAGCGCGGTTTCAGCATTTAATTTTAA|ATGCT|AAGGAAGCGCGGCGCGCCCCCTGGTGGTGGTAAGCCGCCA ========== Event 3747 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CGCAGGCAGGGCCCGGGGAAGCCCGGATCAGACCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGAC ↑ 41 3 2 Chimp: CGCAGGCAGGGCCCGGGGAAG-----------CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGAC Gorilla: CGCAGGCAGGGCCCGGGGAAG-----------CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGAC ↓ 41 3 2 Human: CGCAGGCAGGGCCCGGGGAAGCCCGGATCAGACCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGAC Cluster: [ ] Orangutan: CGCAGGCAGGGCCAGGGGAAG-----------CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGAC Chimp > Human ------------- chr9:130433943-130433951 Template switch process: F1: L GGCCCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCC 1 F3: 4 CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG R RF: GGCCCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG RR: CCGGGAACCCACCGGTCAGGGCGTCCGTCCCGGGCCCCTTCGGAGGTCCAGACTAGGCGGGGAGTCACCCTCGCCCTGTCC F2: 3 AGACTAGGC 2 Unidirectional alignment (log-probability: -26.7) CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGcccggatcagaCCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAG-----------CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG Template switch alignment (log-probability: -16.4) CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCC|CGGATCAGA|CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCC|CGGATCAGA|CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG Gorilla > Human --------------- chr9:130433943-130433951 Template switch process: F1: L GGCCCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCC 1 F3: 4 CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG R RF: GGTCCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG RR: CCAGGAACCCACCGGTCAGGGCGTCCGTCCCGGGCCCCTTCGGAGGTCCAGACTAGGCGGGGAGTCACCCTCGCCCTGTCC F2: 3 AGACTAGGC 2 Unidirectional alignment (log-probability: -32.2) CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGcccggatcagaCCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAG-----------CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG Template switch alignment (log-probability: -22.4) CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCC|CGGATCAGA|CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG CCTTGGGTGGCCAGTCCCGCAGGCAGGGCCCGGGGAAGCC|CGGATCAGA|CCTCCAGGTCTGATCCGCCCCTCAGTGGGAGCGGGACAGG ========== Event 3748 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: attcaacattcTGGGGGGACACAGTGCACACAGCACTCACTGTGCTA-GCATCAAGGGAGCAGAG ↑ 3 2 1 4 Chimp: attcaacattcTGGGGGGACACAGTGCACACTGC----ACTGCACTA-GCATCAAGGGAGCAGAG Gorilla: attcaacatttt-gggggacacagtgcacactgc----actgcgctaggcatcaagggagcagag Human: attcaacattcTGGGGGGACACAGTGCACACAGCACTCACTGTGCTA-GCATCAAGGGAGCAGAG Cluster: [ ] Orangutan: attcaACATTCTGGGGGGACACAGTGCACACTGC----ACTGTGCTAGGCATCAAGGGAGCAGAG Chimp > Human ------------- chr9:7285562-7285568 Template switch process: F1: L TCATTCACTCATTCAACATTCTGGGGGGACACAGTGCACACAGCACT 1 F3: 4 CTAGCATCAAGGGAGCAGAGGAGACCATGGTGAATATGAC R RF: TCATTCACTCATTCAACATTCTGGGGGGACACAGTGCACACTGCACTGCACTAGCATCAAGGGAGCAGAGGAGACCATGGTGAATATGAC RR: AGTAAGTGAGTAAGTTGTAAGACCCCCCTGTGTCACGTGTGACGTGACGTGATCGTAGTTCCCTCGTCTCCTCTGGTACCACTTATACTG F2: 3 GTGTCAC 2 Unidirectional alignment (log-probability: -34.4) CTCATTCAACATTCTGGGGGGACACAGTGCACACaGCACT-CACtgtgcTAGCATCAAGGGAGCAGAGGAGACCATGGTGAATATGAC CTCATTCAACATTCTGGGGGGACACAGTGCACACTGCACTGCAC-----TAGCATCAAGGGAGCAGAGGAGACCATGGTGAATATGAC Template switch alignment (log-probability: -22.3) CTCATTCAACATTCTGGGGGGACACAGTGCACACaGCACT|CACTGTG|CTAGCATCAAGGGAGCAGAGGAGACCATGGTGAATATGAC CTCATTCAACATTCTGGGGGGACACAGTGCACACTGCACT|CACTGTG|CTAGCATCAAGGGAGCAGAGGAGACCATGGTGAATATGAC ========== Event 3749 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GGAGCTAAACTCACGAAAGCA------------GGAACTGATCTCACCAGGATGGCCAATTCCTTGGCTT ↓ 1 4 3 2 Chimp: GGAGCTAAACTCACGAAAGCA------GCTGGTGAGACTGATCTCACCAGGATGGCCAATTCCTTGGCTT Gorilla: GGAGCTGAACTCACGAAAGCAGCTGGT------GAGACTGATCTCACCAGGATGGCCAATTCCTTGGCTT ↑ 1 4 3 2 Human: GGAGCTAAACTCACGAAAGCA------------GGAACTGATCTCACCAGGATGGCCAATTCCTTGGCTT Cluster: [ ] Orangutan: GGAGCTAAACTCACGAAAGCAGCTGCT------GAGACTGATCTCACCACGATGGCCAATTCCTTGGCTT Human > Chimp ------------- chr9:1287182-1287189 Template switch process: F1: L AGTCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAG 1 F3: 4 ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC R RF: AGTCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAGGAACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC RR: TCAGTTAAGTAAACCGACCACCTCGATTTGAGTGCTTTCGTCCTTGACTAGAGTGGTCCTACCGGTTAAGGAACCGAAAAGAAG F2: 3 GAGTGGTC 2 Unidirectional alignment (log-probability: -29.8) TCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAGctggtGAgACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC TCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAG-----GA-ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC Template switch alignment (log-probability: -16.3) TCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAG|CTGGTGAG|ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC TCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAG|CTGGTGAG|ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC Human > Gorilla --------------- chr9:73001248-73001255 Template switch process: F1: L AGTCAATTCATTTGGCTGGTGGAGCTGAACTCACGAAAGCAG 1 F3: 4 ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC R RF: AGTCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAGGAACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC RR: TCAGTTAAGTAAACCGACCACCTCGATTTGAGTGCTTTCGTCCTTGACTAGAGTGGTCCTACCGGTTAAGGAACCGAAAAGAAG F2: 3 GAGTGGTC 2 Unidirectional alignment (log-probability: -34.8) TCAATTCATTTGGCTGGTGGAGCTgAACTCACGAAAGCAGctggtGAgACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC TCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAG-----GA-ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC Template switch alignment (log-probability: -22.3) TCAATTCATTTGGCTGGTGGAGCTgAACTCACGAAAGCAG|CTGGTGAG|ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC TCAATTCATTTGGCTGGTGGAGCTAAACTCACGAAAGCAG|CTGGTGAG|ACTGATCTCACCAGGATGGCCAATTCCTTGGCTTTTCTTC ========== Event 3750 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGTGTTTAGTTTCATTGGTGC---------CTTACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCATGAACTA Chimp: AAGTGTTTAGTTTCATTGGTGC---------CTTACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCATGAACTA ↓ 1 4 3 2 Gorilla: AAGTGTTTAGTTTCATTGGTGATACTTTTAAGATACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCATGAACTA Human: AAGTGTTTAGTTTCATTGGTGC---------CTTACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCATGAACTA Cluster: [ ] Orangutan: AAGTGTTTAGTTTCATTGGTGC---------CTTACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCATGAACTA Chimp > Gorilla --------------- chr9:73002381-73002393 Template switch process: F1: L TGAACTACAACATTTTGTTAAAGTGTTTAGTTTCATTGGTG 1 F3: 4 ACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCA R RF: TGAACTACAACATTTTGTTAAAGTGTTTAGTTTCATTGGTGCCTTACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCA RR: ACTTGATGTTGTAAAACAATTTCACAAATCAAAGTAACCACGGAATGAAATTTCTCCATAGAATTTACAAATTTACCTCGACGT F2: 3 TAGAATTTTCATA 2 Unidirectional alignment (log-probability: -38) GAACTACAACATTTTGTTAAAGTGTTTAGTTTCATTGGTG---atacttttaagaTACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCA GAACTACAACATTTTGTTAAAGTGTTTAGTTTCATTGGTGCCT------------TACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCA Template switch alignment (log-probability: -28.4) GAACTACAACATTTTGTTAAAGTGTTTAGTTTCATTGGTG|AtACtTTTAAGAT|ACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCA GAACTACAACATTTTGTTAAAGTGTTTAGTTTCATTGGTG|AAACATTTAAGAT|ACTTTAAAGAGGTATCTTAAATGTTTAAATGGAGCTGCA ========== Event 3751 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGCCCCTG-GGGGTCATCCGGGCTACCACCCATTGGTGGTAGCCCTTGTCTGTTGCCAGTGATACC ↑ 3 1 2 4 Chimp: GGCCCCTG-GGGGTCATCCGGGCTACCACCAAT------GATCCCTTGTCTGTTGCCAGTGATACC Gorilla: GGCCCCTG-GGGGTCATCCGGGCTACCACCAAT------GATCCATTGTCTGTTGCCAGTGATACC ↓ 3 1 2 4 Human: GGCCCCTG-GGGGTCATCCGGGCTACCACCCATTGGTGGTAGCCCTTGTCTGTTGCCAGTGATACC Cluster: [ ] Orangutan: GGCCCCTGGAGGGTCACCCGGGCTACCACCAAT------GATCCCTTGTCTGTTGCCAGTGATACC Chimp > Human ------------- chr9:133561546-133561557 Template switch process: F1: L TGGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACC 1 F3: 4 CCCTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCA R RF: TGGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACCAATGATCCCTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCA RR: ACCAGTCCAGGTCCGGGGACCCCCAGTAGGCCCGATGGTGGTTACTAGGGAACAGACAACGGTCACTATGGTACAAAACAATCCCGT F2: 3 GATGGTGGTTAC 2 Unidirectional alignment (log-probability: -37.6) GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACCcATtggtggtAgCCCTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCA GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACCAAT------GATCCCTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCA Template switch alignment (log-probability: -16.8) GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACC|CATTGGTGGTAG|CCCTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCA GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACC|CATTGGTGGTAG|CCCTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCA Gorilla > Human --------------- chr9:133561546-133561560 Template switch process: F1: L TGGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACC 1 F3: 4 TTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCAAAC R RF: TGGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACCAATGATCCATTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCAAAC RR: ACCAGTCCAGGTCCGGGGACCCCCAGTAGGCCCGATGGTGGTTACTAGGTAACAGACAACGGTCACTATGGTACAAAACAATCCCGTTTG F2: 3 CCCGATGGTGGTTAC 2 Unidirectional alignment (log-probability: -39.7) GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCAC-------CCAttggtggtagcccTTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCAAAC GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACCAATGATCCA-------------TTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCAAAC Template switch alignment (log-probability: -17.6) GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACC|CATTGGTGGTAGCCC|TTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCAAAC GGTCAGGTCCAGGCCCCTGGGGGTCATCCGGGCTACCACC|CATTGGTGGTAGCCC|TTGTCTGTTGCCAGTGATACCATGTTTTGTTAGGGCAAAC ========== Event 3752 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GCTCACCCCAGCCCTCTCCCGGCAG-----GAGAGGAGGCTCAGGAGCCTCCTGCCGCACCCAGCCTCAGATGGCTTC Chimp: GCTCACCCCAGCCCTCTCCCGGCAG-----GAGAGGAGGCTCAGGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTC ↑ 1 3 4 2 Gorilla: GCTCACCCCAGCCCTCTCCCGGCAG----------GAGGCTCCTGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTC ↓ 3 1 2 4 Human: GCTCACCCCAGCCCTCTCCCGGCAG-----GAGAGGAGGCTCAGGAGCCTCCTGCCGCACCCAGCCTCAGATGGCTTC Cluster: [ ] Orangutan: GCTCACCCCAGCCCTCTCTCGGCAGGAGAG-----GAGGCTCAGGAGCCTCCTGCCGCACCCAGCCTCAGATGGCTTC Gorilla > Human --------------- chr9:133515727-133515750 Template switch process: F1: L AGCTGGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAG 1 F3: 4 CACCCAGCCTCAGATGGCTTCTGCTGG R RF: AGCTGGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAGGCTCCTGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG RR: TCGACCGGGACGTGTCCGAGTGGGGTCGGGAGAGGGCCGTCCTCCGAGGACTCGGAGGACGGTGTGGGTCGGAGTCTACCGAAGACGACC F2: 3 GCCGTCCTCCGAGGACTCGGAGGA 2 Unidirectional alignment (log-probability: -34.8) GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCaggagAGGAGGCTCagGAGCCTCCTGCCgCACCCAGCCTCAGATGGCTTCTGCTGG GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGC-----AGGAGGCTCCTGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG Template switch alignment (log-probability: -18.5) GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAG|AGGAGGCTCAGGAGCCTCCTGCCG|CACCCAGCCTCAGATGGCTTCTGCTGG GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAG|AGGAGGCTCAGGAGCCTCCTGCCG|CACCCAGCCTCAGATGGCTTCTGCTGG Gorilla > Chimp --------------- chr9:111814995-111815005 Template switch process: F1: L AGCTGGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAG 1 F3: 4 GAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG R RF: AGCTGGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAGGCTCCTGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG RR: TCGACCGGGACGTGTCCGAGTGGGGTCGGGAGAGGGCCGTCCTCCGAGGACTCGGAGGACGGTGTGGGTCGGAGTCTACCGAAGACGACC F2: 3 GACTCGGAGGA 2 Unidirectional alignment (log-probability: -29.2) GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCaggagAGGAGGCTCagGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGC-----AGGAGGCTCCTGAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG Template switch alignment (log-probability: -17.2) GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAG|AGGAGGCTCAG|GAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG GGCCCTGCACAGGCTCACCCCAGCCCTCTCCCGGCAGGAG|AGGAGGCTCAG|GAGCCTCCTGCCACACCCAGCCTCAGATGGCTTCTGCTGG ========== Event 3753 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTAGGATCAACAGTTGCTGTGGTAA----TTAAGTGCATGAACAAGGCCTACAACATTTCATGATCTTCA Chimp: TTTAGGATCAACAGTTGCTGTGGTAA----TTAAGTGCATGAACAAGGCCTACAACATTTCATGATCTTCA ↓ 1 4 3 2 Gorilla: TTTAGGATCAACAGTTGCTGTAGGCC--------TTGCATGAACAAGGCCTACAACATTTCATGATCTTCA ↑ 1 4 3 2 Human: CTTAGGATCAACAGTTGCTGTGGTAA----TTAAGTGCATGAACAAGGCCTACAACATTTCATGATCTTCA Cluster: [ ] Orangutan: TTTAGGATCAACAGTTGCTGTGGTAATTAA----GTGCATGAACAAGGCCTACAACATTTCATGGTCTTCA Human > Gorilla --------------- chr9:115427377-115427383 Template switch process: F1: L ACTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGT 1 F3: 4 GCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA R RF: ACTTTTTAATAATCACATTGCTTAGGATCAACAGTTGCTGTGGTAATTAAGTGCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA RR: TGAAAAATTATTAGTGTAACGAATCCTAGTTGTCAACGACACCATTAATTCACGTACTTGTTCCGGATGTTGTAAAGTACTAGAAGTTGTT F2: 3 TTCCGGA 2 Unidirectional alignment (log-probability: -32.3) CTTTTTAATAATCACATTGtTTAGGATCAACAGTTGCTGT--------AGgcctTGCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA CTTTTTAATAATCACATTGCTTAGGATCAACAGTTGCTGTGGTAATTAAG----TGCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA Template switch alignment (log-probability: -22.1) CTTTTTAATAATCACATTGtTTAGGATCAACAGTTGCTGT|AGGCCTT|GCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA CTTTTTAATAATCACATTGCTTAGGATCAACAGTTGCTGT|AGGCCTT|GCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA Chimp > Gorilla --------------- chr9:115427377-115427383 Template switch process: F1: L ACTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGT 1 F3: 4 GCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA R RF: ACTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGTGGTAATTAAGTGCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA RR: TGAAAAATTATTAGTGTAACAAATCCTAGTTGTCAACGACACCATTAATTCACGTACTTGTTCCGGATGTTGTAAAGTACTAGAAGTTGTT F2: 3 TTCCGGA 2 Unidirectional alignment (log-probability: -26.8) CTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGT--------AGgcctTGCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA CTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGTGGTAATTAAG----TGCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA Template switch alignment (log-probability: -16.6) CTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGT|AGGCCTT|GCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA CTTTTTAATAATCACATTGTTTAGGATCAACAGTTGCTGT|AGGCCTT|GCATGAACAAGGCCTACAACATTTCATGATCTTCAACAA ========== Event 3754 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CACCAGGGACTAGTTTCACCTGGTG------CTCTCCTGCCCGCACCCTCTGACCC Chimp: CACCAGGGACTAGTTTCGCCTGATG------CTCTCCTGCCCGCACCCTCTGACCC ↓ 3 1 24 Gorilla: CACCAGGGACTAGTTTCGCCTGATGAGAGCATCAGCCTGCCCGCAGCCTCTGACCC Human: CACCAGGGACTAGTTTCACCTGGTG------CTCTCCTGCCCGCACCCTCTGACCC Cluster: [ ] Orangutan: CACCAGGGACTAGTTTCGCCTGATG------CTCTCCTGCCCGCACCCTCGGACCC Chimp > Gorilla --------------- chr9:118243761-118243770 Template switch process: F1: L TCAGTCGTGGGGTTCCCACCAGGGACTAGTTTCGCCTGATG 1 F3: 4 CCTGCCCGCAGCCTCTGACCCTGTGATATCATAAAAACAG R RF: TCAGTCTTGGGGTTCCCACCAGGGACTAGTTTCGCCTGATGCTCTCCTGCCCGCACCCTCTGACCCTGTGATATCATAAAAACAG RR: AGTCAGAACCCCAAGGGTGGTCCCTGATCAAAGCGGACTACGAGAGGACGGGCGTGGGAGACTGGGACACTATAGTATTTTTGTC F2: 3 GACTACGAGA 2 Unidirectional alignment (log-probability: -46.2) CAGTCgTGGGGTTCCCACCAGGGACTAGTTTCGCCTGATgagagcatcaG----CCTGCCCGCAgCCTCTGACCCTGTGATATCATAAAAACAG CAGTCTTGGGGTTCCCACCAGGGACTAGTTTCGCCTGAT----------GCTCTCCTGCCCGCACCCTCTGACCCTGTGATATCATAAAAACAG Template switch alignment (log-probability: -28) CAGTCgTGGGGTTCCCACCAGGGACTAGTTTCGCCTGATG|AGAGCATCAG|CCTGCCCGCAgCCTCTGACCCTGTGATATCATAAAAACAG CAGTCTTGGGGTTCCCACCAGGGACTAGTTTCGCCTGATG|AGAGCATCAG|CCTGCCCGCACCCTCTGACCCTGTGATATCATAAAAACAG ========== Event 3755 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCCTCCTGAGCTCCAGCCACCCTGCCAATCAGGGACCAGGAGGCAGGTGTGGGAGCCCCAGAGAGAAGGAAGGGGAAAGTCTTCCCAGGCCCTGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGC-AGGAGCTGGAGACCTGGAAGGATTA ↓ 3 2 1 4 Chimp: CGCCTCCTGAGCTCCAGCCACCCTGCCAATCAGGGACCAGGAGGCAGGTGTGGGAGCCCCAGAGAGAAAGAAGGGGAAAGTCTTCCCAGGCCCTGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCGTGCAG--------ACAGGGTGCTGGAGACCTGGAAGGATTA ↑ 3 2 1 4 Gorilla: CGCCTCCTGAGCTGCAGCCACCCTGCCAATCAGGGACCAAGAGGCAGGTGTGGGAGCCCCAGAGAGAAGGAAGGGGAAAGTCTTCCCAGGCCCTGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGC-AGGAGCTGGAGACCTGGAAGGATTA Human: TGCCTCCTGAGCTCCAGCCACCCTGCCAATCAGGGACCAGGAGGCAGGTGTGGGAGCCCCAGAGAGAAGGAAGGGGAAAGTCTTCCCAGGCCCTGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGC-AGGAGCTGGAGACCTGGAAGGATTA Cluster: [ ] Orangutan: TGCCTCCTGAGCTCCAGCCACCCTGCCAATCAGGGGGCAGGAGGCAGGTGTGGGAGCCCCAGAGAGAAGGAAGGGGAAAGTCTTCCCAGGCCCCGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGTGTGCAG--------AC-AGGAGCTGGAGACCTGGAAGGATTA Human > Chimp ------------- chr9:113757563-113757568 Template switch process: F1: L CTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCGTGCAGA 1 F3: 4 GCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC R RF: ACCCTGCCAATCAGGGACCAGGAGGCAGGTGTGGGAGCCCCAGAGAGAAGGAAGGGGAAAGTCTTCCCAGGCCCTGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGCAGGAGCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC RR: TGGGACGGTTAGTCCCTGGTCCTCCGTCCACACCCTCGGGGTCTCTCTTCCTTCCCCTTTCAGAAGGGTCCGGGACCCCGGAACGTTAAACATGGATGAAGGAAGAGTGACAGTAATGACGTACGTCTTACTGTACGTCCTCGACCTCTGGACCTTCCTAATCCGGGTCGGACCTGAGAGG F2: 3 TGGGAC 2 Unidirectional alignment (log-probability: -35.1) TTGTACCTACTTCCTTCTCACTGTCATTACTGCgTGCAGA--------CAgGGtGCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC TTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGCA-GGAGCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC Template switch alignment (log-probability: -22.2) TTGTACCTACTTCCTTCTCACTGTCATTACTGCgTGCAGA|CAGGGT|GCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC TTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGA|CAGGGT|GCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC Gorilla > Chimp --------------- chr9:113757563-113757568 Template switch process: F1: L CTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCGTGCAGA 1 F3: 4 GCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC R RF: ACCCTGCCAATCAGGGACCAAGAGGCAGGTGTGGGAGCCCCAGAGAGAAGGAAGGGGAAAGTCTTCCCAGGCCCTGGGGCCTTGCAATTTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGCAGGAGCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC RR: TGGGACGGTTAGTCCCTGGTTCTCCGTCCACACCCTCGGGGTCTCTCTTCCTTCCCCTTTCAGAAGGGTCCGGGACCCCGGAACGTTAAACATGGATGAAGGAAGAGTGACAGTAATGACGTACGTCTTACTGTACGTCCTCGACCTCTGGACCTTCCTAATCCGGGTCGGACCTGAGAGG F2: 3 TGGGAC 2 Unidirectional alignment (log-probability: -33.5) TTGTACCTACTTCCTTCTCACTGTCATTACTGCgTGCAGAcaG-------GGtGCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC TTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGAATGACATGCAGGAGCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC Template switch alignment (log-probability: -22.2) TTGTACCTACTTCCTTCTCACTGTCATTACTGCgTGCAGA|CAGGGT|GCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC TTGTACCTACTTCCTTCTCACTGTCATTACTGCATGCAGA|CAGGGT|GCTGGAGACCTGGAAGGATTAGGCCCAGCCTGGACTCTCC ========== Event 3756 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: tttaataattatatttctatttttaatatttaaatatcactgtgTGATATTTA--------------AAACCACACAGTGAACTCTTTTG Chimp: tttaataattatatttctatttttaatatttaaatatcacacagtgatattta-------aatCTTAAAACCACACAGTGAACTCTTTTG Gorilla: tttaataattatatttctatgtttaatatttaaatatCACACAGTGATATTTAAATATTA-------AAACCACACAGTGAACTCTTTTG ↓ 1 3 4 2 ↑ 3 1 2 4 Human: tttaataattatatttctatttttaatatttaaatatcactgtgTGATATTTA--------------AAACCACACAGTGAACTCTTTTG Cluster: [ ] Orangutan: ---------tatat-------tttaataattatatttctatttttaatatttaaatatc------------accacagtgaactcttttg Gorilla > Human --------------- chr9:13567582-13567611 Template switch process: F1: L ATTTCTAT 1 F3: 4 TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATTACT R RF: ATTTCTATGTTTAATATTTAAATATCACACAGTGATATTTAAATATTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATTACT RR: TAAAGATACAAATTATAAATTTATAGTGTGTCACTATAAATTTATAATTTTGGTGTGTCACTTGAGAAAACATACATTTATATAATGA F2: 3 TATAGTGTGTCACTATAAATTTATAATTTT 2 Unidirectional alignment (log-probability: -33.3) ATTTCTATtTTTAATATTTAAATATCACtgtGTGATAT-------TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT ATTTCTATGTTTAATATTTAAATATCACACAGTGATATTTAAATATTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT Template switch alignment (log-probability: -18.8) ATTTCTAT|TTTTAATATTTAAATATCACTGTGTGATAT|TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT ATTTCTAT|TTTTAATATTTAAATATCACTGTGTGATAT|TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT Human > Gorilla --------------- chr9:85415262-85415278 Template switch process: F1: L ATTTCTATGTTTAATATTTAAATATCAC 1 F3: 4 TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATTACT R RF: ATTTCTATTTTTAATATTTAAATATCACTGTGTGATATTTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATTACT RR: TAAAGATAAAAATTATAAATTTATAGTGACACACTATAAATTTTGGTGTGTCACTTGAGAAAACATACATTTATATAATGA F2: 3 ATAAATTTATAGTGACA 2 Unidirectional alignment (log-probability: -43) ATTTCTATgTTTAATATTTAAATATCACacaGTGATATttaaataTTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT ATTTCTATTTTTAATATTTAAATATCACTGTGTGATAT-------TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT Template switch alignment (log-probability: -23.2) ATTTCTATgTTTAATATTTAAATATCAC|ACAGTGATATTTAAATA|TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT ATTTCTATTTTTAATATTTAAATATCAC|ACAGTGATATTTAAATA|TTAAAACCACACAGTGAACTCTTTTGTATGTAAATATATT ========== Event 3757 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CCTGGCCCCAACGGCAGGGACCCCC-CAGTCTATGCCACCCCCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT ↑ 1 4 3 2 Chimp: CCTGGCCCCAACGGCAGGGAC-CCC-CAGTCCG--GCAG-ACCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Gorilla: CCTGACCCCAACTGCAGGGACCCCC-CAGTCCG--GCAG-ACCCTTGGGTGGCATAGTCTCCCTGCTTCCAAGGAT Human: CCTGGCCCCAACGGCAGGGACCCCC-CAGTCTATGCCACCCCCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Cluster: [ ] Orangutan: CCTGGCCCCAACTGCAGGGACCCCCCGAGTCTG--GCAG-ACCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Chimp > Human ------------- chr9:136258313-136258322 Template switch process: F1: L CTGTCCTGAGGTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCCCAGTC 1 F3: 4 CCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGATGGACA R RF: CTGTCCTGAGGTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCC-AGTCCGGCAGACCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGATGGACA RR: GACAGGACTCCAAACGAGAGGGACCGGGGTTGCCGTCCCTGGGGG-TCAGGCCGTCTGGGAACCCACCGTATCAGAGGGACGAAGGCTCCTACCTGT F2: 3 CCCACCGTAT 2 Unidirectional alignment (log-probability: -43.3) GTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCC-----------cagtctatgccacccCCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGATGGACA GTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCCAGTCCGGCAGA---------------CCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGATGGACA Template switch alignment (log-probability: -28.3) GTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCCcAGTC|TATGCCACCC|CCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGATGGACA GTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCC-AGTC|TATGCCACCC|CCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGATGGACA ========== Event 3758 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTGAGGTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCC-CAGTCTATGCCACCCCCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Chimp: TCCTGAGGTTTGCTCTCCCTGGCCCCAACGGCAGGGAC-CCC-CAGTCCG--GCAG-ACCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Gorilla: TCCTGAGGTTTGCTCTCCCTGACCCCAACTGCAGGGACCCCC-CAGTCCG--GCAG-ACCCTTGGGTGGCATAGTCTCCCTGCTTCCAAGGAT ↓ 1 4 3 2 Human: TCCTGAGGTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCC-CAGTCTATGCCACCCCCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Cluster: [ ] Orangutan: TCCTGAGGTTTGCTCTCCCTGGCCCCAACTGCAGGGACCCCCCGAGTCTG--GCAG-ACCCTTGGGTGGCATAGTCTCCCTGCTTCCGAGGAT Gorilla > Human --------------- chr9:136258313-136258322 Template switch process: F1: L TTTCCGTCTCAACCCATCTGTCCTGAGGTTTGCTCTCCCTGGCCCCAACGGCAGGGACCCCCCAGTC 1 F3: 4 CCCTTGGGTGGCA R RF: TTTCCGTCTCAACCCATCTGTCCTGAGGTTTGCTCTCCCTGACCCCAACTGCAGGGACCCCCCAGTCCGGCAGACCCTTGGGTGGCATA RR: AAAGGCAGAGTTGGGTAGACAGGACTCCAAACGAGAGGGACTGGGGTTGACGTCCCTGGGGGGTCAGGCCGTCTGGGAACCCACCGTAT F2: 3 CCCACCGTAT 2 Unidirectional alignment (log-probability: -44.9) GTTTGCTCTCCCTGgCCCCAACgGCAGGGACCCCCCAGTctatgccacCC------CCCTTGGGTGGCA GTTTGCTCTCCCTGACCCCAACTGCAGGGACCCCCCAGT---------CCGGCAGACCCTTGGGTGGCA Template switch alignment (log-probability: -28) GTTTGCTCTCCCTGgCCCCAACgGCAGGGACCCCCCAGTC|TATGCCACCC|CCCTTGGGTGGCA GTTTGCTCTCCCTGACCCCAACTGCAGGGACCCCCCAGTC|TATGCCACCC|CCCTTGGGTGGCA ========== Event 3759 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATC-------AGAGACGCAAACTCAACTCACA ↓ 3 2 1 4 Chimp: ATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATGACTGACTCAAGACGCAAACTCAACTCACA ↑ 3 2 1 4 Gorilla: ATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATC-------AGAGACGCAAACTCAACTCACA Human: ATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATC-------AGAGACGCAAACTCAACTCACA Cluster: [ ] Orangutan: ATTCAAACGTAACTGCAAAGAGTCAATCACTTCGTATC-------AGAGACCCAAACTCAACTCACA Human > Chimp ------------- chr9:15526974-15526982 Template switch process: F1: L CCCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAT 1 F3: 4 AAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAAA R RF: CCCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATCAGAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAAA RR: GGGGTAAGTTTACATTGACGTTTCTCAGTCAGTGAAGCATAGTCTCTGCGTTTGAGTTGAGTGTTCCCCTTTACTTGTAAATTT F2: 3 CTCAGTCAG 2 Unidirectional alignment (log-probability: -32.7) CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAtgactgacTCA-AGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTA--------TCAGAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA Template switch alignment (log-probability: -22.4) CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAT|GACTGACTC|aAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAT|GACTGACTC|GAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA Gorilla > Chimp --------------- chr9:15526974-15526982 Template switch process: F1: L CCCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAT 1 F3: 4 AAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAAA R RF: CCCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATCAGAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAAA RR: GGGGTAAGTTTACATTGACGTTTCTCAGTCAGTGAAGCATAGTCTCTGCGTTTGAGTTGAGTGTTCCCCTTTACTTGTAAATTT F2: 3 CTCAGTCAG 2 Unidirectional alignment (log-probability: -32) CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATgActgactcaAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTATCAG-------AGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA Template switch alignment (log-probability: -22.4) CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAT|GACTGACTC|aAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA CCCATTCAAATGTAACTGCAAAGAGTCAGTCACTTCGTAT|GACTGACTC|GAGACGCAAACTCAACTCACAAGGGGAAATGAACATTTAA ========== Event 3760 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CATCTTTCAATAATTCCTTTA---------CCTGAACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACTATTTCTCAGGGCCTCTAGCTCACCCCCAAC Chimp: CATCTTTCAATAATTCCTTTATTGAAAGGGTCAGTACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACTATttctcagggcctctagctcacccccaac ↓ 1 4 3 2 Gorilla: CATCTTTCAATAATTCCTTTA---------CCTGAACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACTATTTCTCAGGGTCTCTAGCTCAGCCCCAAC Human: CATCTTTCAATAATTCCTTTA---------CCTGAACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACTATTTCTCAGGGCCTCTAGCTCACCCCCAAC Cluster: [ ] Orangutan: CATTTTTCAATCATTCCTTTA---------CCTGAACATGGTCAGCTCCCCTCCTACTTAGCAGAAAATTTCACTATTTCTCAGGGCCTCTAGCTCACCCCCAAC Chimp > Gorilla --------------- chr9:34383776-34383780 Template switch process: F1: L TCTTCCATTTTAACTGTATTCATCTTTCAATAATTCCTTTA 1 F3: 4 ACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACT R RF: TCTTCCGTTTTAACTGTACTCATCTTTCAATAATTCCTTTATTGAAAGGGTCAGTACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACTATTTCTCAGG RR: AGAAGGCAAAATTGACATGAGTAGAAAGTTATTAAGGAAATAACTTTCCCAGTCATGTACCAGTCGAGGGGAGGATAAATCGTCTTTTAAAGTGATAAAGAGTCC F2: 3 AGTCC 2 Unidirectional alignment (log-probability: -39) CTTCCaTTTTAACTGTAtTCATCTTTCAATAATTCCTTTAc---------CtGaACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACT CTTCCGTTTTAACTGTACTCATCTTTCAATAATTCCTTTATTGAAAGGGTCAGTACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACT Template switch alignment (log-probability: -27.4) CTTCCaTTTTAACTGTAtTCATCTTTCAATAATTCCTTTA|CCTGA|ACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACT CTTCCGTTTTAACTGTACTCATCTTTCAATAATTCCTTTA|CCTGA|ACATGGTCAGCTCCCCTCCTATTTAGCAGAAAATTTCACT ========== Event 3761 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTGAAATTTACAAAGGAAAGGTACTAGCTTAGAAAGAATCAtttttt Chimp: TTTGAAATTTACAAAGGAAAGCTACTAGCTTAGAAAGAATCAtttttt Gorilla: TTTGAAATTTACAAAGGAAAGCTAGTAGCTTAGAAAGAATCAtttttt ↑ 1 34 2 Human: TTTGAAATTTACAAAGGAAAGGTACTAGCTTAGAAAGAATCAtttttt Cluster: [ ] Orangutan: Human > Gorilla --------------- chr9:34483036-34483039 Template switch process: F1: L TAATTGTATAGCTAATTATATTTGAAATTTACAAAGGAAAG 1 F3: 4 TAGCTTAGAAAGAATCATTTTTTTATGTTTTTTTTTTTTT R RF: TAATTGTATAGCTAATTATATTTGAAATTTACAAAGGAAAGGTACTAGCTTAGAAAGAATCATTTTTTTATGTTTTTTTTTTTTT RR: ATTAACATATCGATTAATATAAACTTTAAATGTTTCCTTTCCATGATCGAATCTTTCTTAGTAAAAAAATACAAAAAAAAAAAAA F2: 3 GATC 2 Unidirectional alignment (log-probability: -31.8) AATTGTATAGCTAATTATATTTGAAATTTACAAAGGAAAGcTAgTAGCTTAGAAAGAATCATTTTTTTATGTTTTttttttttt AATTGTATAGCTAATTATATTTGAAATTTACAAAGGAAAGGTACTAGCTTAGAAAGAATCATTTTTTTATGTTTT--------- Template switch alignment (log-probability: -16.2) AATTGTATAGCTAATTATATTTGAAATTTACAAAGGAAAG|CTAG|TAGCTTAGAAAGAATCATTTTTTTATGTTTTTTTTTTTTT AATTGTATAGCTAATTATATTTGAAATTTACAAAGGAAAG|CTAG|TAGCTTAGAAAGAATCATTTTTTTATGTTTTTTTTTTTTT ========== Event 3762 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GCCGCTTGTTTAGAAAGACTATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAGAATTTTATTCTCCAAGTATACTGCTGTATGGCCAAGTATTAATAGTTTCATAACGTCTTTTCAGCTCTACCTAA ↑ 3 2 14 Chimp: GCCGCTTGTTTAGAAAGACTATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAA--------------------------------------------GGTTTCATAACGTCTTTTCAGCTCTACCTAA Gorilla: GCCGCTTGTTTAGAAAGGCTATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAA--------------------------------------------GGTTTCATAATGTCTTTTCAGCTCTACCTAA ↓ 3 2 14 Human: GCCGCTTGTTTAGAAAGACTATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAGAATTTTATTCTCCAAGTATACTGCTGTATGGCCAAGTATTAATAGTTTCATAACGTCTTTTCAGCTCTACCTAA Cluster: [ ] Orangutan: GCCACTTGTTTAGAAAGGCTATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTACTCAA--------------------------------------------GGTTTCATAATGTCTTTTCAGCTCTACCTAA Chimp > Human ------------- chr9:15721612-15721655 Template switch process: F1: L GGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG 1 F3: 4 GTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATC R RF: TATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAGGTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATC RR: ATAATTATGAACCGGTATGTCGTCATATGAACCTCTTATTTTAAGATAAGTTCCAAAGTATTGCAGAAAAGTCGAGATGGATTAACATCATAG F2: 3 ATAATTATGAACCGGTATGTCGTCATATGAACCTCTTATTTTAA 2 Unidirectional alignment (log-probability: -74.2) CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAGaattttattctccaagtatactgctgtatggccaagtattaataGTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATC CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG--------------------------------------------GTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATC Template switch alignment (log-probability: -20.7) CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG|AATTTTATTCTCCAAGTATACTGCTGTATGGCCAAGTATTAATA|GTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATC CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG|AATTTTATTCTCCAAGTATACTGCTGTATGGCCAAGTATTAATA|GTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATC Gorilla > Human --------------- chr9:15721612-15721655 Template switch process: F1: L GGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG 1 F3: 4 GTTTCATAACGTCTTTTCAGCTCTACCTAATTGTAGTATCTCTGTTACTA R RF: TATTAATACTTGGCCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAGGTTTCATAATGTCTTTTCAGCTCTACCTAATTGTAGTATCTCTGTTACTA RR: ATAATTATGAACCGGTATGTCGTCATATGAACCTCTTATTTTAAGATAAGTTCCAAAGTATTACAGAAAAGTCGAGATGGATTAACATCATAGAGACAATGAT F2: 3 ATAATTATGAACCGGTATGTCGTCATATGAACCTCTTATTTTAA 2 Unidirectional alignment (log-probability: -79.8) CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAGaattttattctccaagtatactgctgtatggccaagtattaataGTTTCATAAcGTCTTTTCAGCTCTACCTAATTGTAGTATC CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG--------------------------------------------GTTTCATAATGTCTTTTCAGCTCTACCTAATTGTAGTATC Template switch alignment (log-probability: -27.1) CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG|AATTTTATTCTCCAAGTATACTGCTGTATGGCCAAGTATTAATA|GTTTCATAAcGTCTTTTCAGCTCTACCTAATTGTAGTATC CCATACAGCAGTATACTTGGAGAATAAAATTCTATTCAAG|AATTTTATTCTCCAAGTATACTGCTGTATGGCCAAGTATTAATA|GTTTCATAATGTCTTTTCAGCTCTACCTAATTGTAGTATC ========== Event 3763 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AGACATGATGAAAACCGTGTCCTGGGAAGGTCTGT------CTGGCAGCGAGATACAGGCAGGTCCAAGAGTGAT ↓ 3 2 1 4 Chimp: AGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTCCTTCCCAGGAAGCGAGATGCAGGCAGGTCCAAGAGTGAT ↑ 3 2 1 4 Gorilla: AGACATGATGAAAACCGTGTCCTGGGAAGGTCTGT------CTGGCAGCGAGATACAGGCAGGTCCAAGAGTGAT Human: AGACATGATGAAAACCGTGTCCTGGGAAGGTCTGT------CTGGCAGCGAGATACAGGCAGGTCCAAGAGTGAT Cluster: [ ] Orangutan: AGACATGATGAAAACCGTGTCCTGGGAAGGTCTGT------CTGGCAGCGAGATACAGGCAGGGCCAAGAGTGAT Human > Chimp ------------- chr9:98627884-98627893 Template switch process: F1: L TCACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC 1 F3: 4 AGCGAGATGCAGGCAGGTCCAAGAGTGATGTTTTTAATAGTCCCCTGCT R RF: TCACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTCTGGCAGCGAGATACAGGCAGGTCCAAGAGTGATGTTTTTAATAGTCCCCTGCT RR: AGTGTCTCTGTACTACTTTTGGCACAGGACCCTTCCAGACAGACCGTCGCTCTATGTCCGTCCAGGTTCTCACTACAAAAATTATCAGGGGACGA F2: 3 AGGACCCTTC 2 Unidirectional alignment (log-probability: -37.6) ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTCcttcccaGGaAGCGAGATgCAGGCAGGTCCAAGAGTGATGTTTTTAATAG ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC------TGGCAGCGAGATACAGGCAGGTCCAAGAGTGATGTTTTTAATAG Template switch alignment (log-probability: -22.7) ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC|CTTCCCAGGA|AGCGAGATgCAGGCAGGTCCAAGAGTGATGTTTTTAATAG ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC|CTTCCCAGGA|AGCGAGATACAGGCAGGTCCAAGAGTGATGTTTTTAATAG Gorilla > Chimp --------------- chr9:98627884-98627893 Template switch process: F1: L TCACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC 1 F3: 4 AGCGAGATGCAGGCAGGTCCAAGAGTGATGTTTTTAATAGTCCCCTGCT R RF: TCACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTCTGGCAGCGAGATACAGGCAGGTCCAAGAGTGATGTTTTTAATAGTCCCCTGCT RR: AGTGTCTCTGTACTACTTTTGGCACAGGACCCTTCCAGACAGACCGTCGCTCTATGTCCGTCCAGGTTCTCACTACAAAAATTATCAGGGGACGA F2: 3 AGGACCCTTC 2 Unidirectional alignment (log-probability: -36.3) ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTccttccCaGGaAGCGAGATgCAGGCAGGTCCAAGAGTGATGTTTTTAATAG ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGT------CTGGCAGCGAGATACAGGCAGGTCCAAGAGTGATGTTTTTAATAG Template switch alignment (log-probability: -22.8) ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC|CTTCCCAGGA|AGCGAGATgCAGGCAGGTCCAAGAGTGATGTTTTTAATAG ACAGAGACATGATGAAAACCGTGTCCTGGGAAGGTCTGTC|CTTCCCAGGA|AGCGAGATACAGGCAGGTCCAAGAGTGATGTTTTTAATAG ========== Event 3764 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACAACGGGGTCAAATCATCAATCCATTGGCTTTA Chimp: CCCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACAATGGGGTCAAGTCATCAATCCATTGGCTTTA Gorilla: CCCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACACTGAGGTCAAGTCATCAATCCATTGGCTTTA ↑ 3 2 1 4 Human: CCCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACAACGGGGTCAAATCATCAATCCATTGGCTTTA Cluster: [ ] Orangutan: CCCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACACTGAGGTCAAATCATCAATCCATTGGCTTTA Human > Gorilla --------------- chr9:31951193-31951196 Template switch process: F1: L CCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACA 1 F3: 4 GGTCAAGTCATCAATCCATTGGCTTTAACTATTTGGGGTGTGTGTGT R RF: CCACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACAACGGGGTCAAATCATCAATCCATTGGCTTTAACTATTTGGGGTGTGTGTGT RR: GGTGACCGGTAATCATTAAGTCTTGATCAGAACTATTGTGTTGCCCCAGTTTAGTAGTTAGGTAACCGAAATTGATAAACCCCACACACACA F2: 3 AGTC 2 Unidirectional alignment (log-probability: -41.5) CACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACActGaGGTCAAgTCATCAATCCATTGGCTTTAACTATTTGGGGTg CACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACAACGGGGTCAAATCATCAATCCATTGGCTTTAACTATTTGGGGT- Template switch alignment (log-probability: -21.9) CACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACA|CTGA|GGTCAAgTCATCAATCCATTGGCTTTAACTATTTGGGGTG CACTGGCCATTAGTAATTCAGAACTAGTCTTGATAACACA|CTGA|GGTCAAATCATCAATCCATTGGCTTTAACTATTTGGGGTG ========== Event 3765 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAAATTTTTCATGCCAATGTG------ACA--------------TTAAAAATACCTTGTAATAATGATTACTTTATTGTTT Chimp: AAAATTTTTCATGCCAATGTG---ACTACA--------------TTAAAAATACCTTGTAATAATGATTACTTTATTGTTT ↓ 4 1 3 2 Gorilla: AAAATTTTTCATGCCAATGTGACT---ACATTAATTACAAGGTATTAAAAATACCTTGTAATAATGATTACTTTATTGTTT Human: AAAATTTTTCATGCCAATGTG------ACA--------------TTAAAAATACCTTGTAATAATGATTACTTTATTGTTT Cluster: [ ] Orangutan: AAAATTTTTCATGCCTATGTGACT---ACA--------------TTAAAAATACCTTGTAATAATGATTACTTTATTATCT Chimp > Gorilla --------------- chr9:32077243-32077251 Template switch process: F1: L GAAATTATACTCTCAGAATTAAAATTTTTCATGCCAATGTGACTACATTAA 1 F3: 4 ATTAAAAATACCTTGTAATAATGATTACTTTATTGTTTGTG R RF: GAAATTATACTCTCAGAATTAAAATTTTTCATGCCAATGTGACTACATTAAAAATACCTTGTAATAATGATTACTTTATTGTTTGTG RR: CTTTAATATGAGAGTCTTAATTTTAAAAAGTACGGTTACACTGATGTAATTTTTATGGAACATTATTACTAATGAAATAACAAACAC F2: 3 TGGAACATT 2 Unidirectional alignment (log-probability: -31.1) CTCAGAATTAAAATTTTTCATGCCAATGTGACTACATTaattacaaggtattAAAAATACCTTGTAATAATGATTACTTTATTGTTTGT CTCAGAATTAAAATTTTTCATGCCAATGTGACTACATT--------------AAAAATACCTTGTAATAATGATTACTTTATTGTTTGT Template switch alignment (log-probability: -17.1) CTCAGAATTAAAATTTTTCATGCCAATGTGACTACATTAA|TTACAAGGT|ATTAAAAATACCTTGTAATAATGATTACTTTATTGTTTGT CTCAGAATTAAAATTTTTCATGCCAATGTGACTACATTAA|TTACAAGGT|ATTAAAAATACCTTGTAATAATGATTACTTTATTGTTTGT ========== Event 3766 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 34 Detected in comparisons: 1234 Multiple sequence alignment: Human: GGCTCTGTGTTCCAGAATATGTACATGTGTTAGCATC------------------AT--GTACATGTAAACACATACATGCACACAGGCATACTCACATGAGA Chimp: GACTCTGTGTTCCAGAATATGTACATGTGTTAGCATC---------AGTGCATGTGT--GTATGTGTAAACACATACATGCACACAGGCATACTCACATGAGA Gorilla: GGCTCTGTGTTCCAGAATATGTACATGTGTTAGCGTCAGTGCATGT---------GT----GTGTGTAAACACATACATGCACACAGGCATACTCACATGAGA ↓ 3 2 1 4 ↑ 1 4 3 2 Human: GGCTCTGTGTTCCAGAATATGTACATGTGTTAGCATC------------------AT--GTACATGTAAACACATACATGCACACAGGCATACTCACATGAGA Cluster: [ ] Orangutan: GGCTCTGTGTTCCAGAATACGTACATGTGTTAGCATCAGTGCACGT---------GTGT--ATGTGTAAACACATACATGCACACAGGCATACTCACATGAGA Gorilla > Human --------------- chr9:120908985-120908990 Template switch process: F1: L ACATGGTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCATCA 1 F3: 4 TGTAAACACATACATGCACACAGGCATACTCACATGAGAC R RF: ACATGGTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCGTCAGTGCATGTGTGTGTGTAAACACATACATGCACACAGGCATACTCACATGAGAC RR: TGTACCACCGAGACACAAGGTCTTATACATGTACACAATCGCAGTCACGTACACACACACATTTGTGTATGTACGTGTGTCCGTATGAGTGTACTCTG F2: 3 ACATGT 2 Unidirectional alignment (log-probability: -32.5) GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCaTCA-----------TGtacaTGTAAACACATACATGCACACAGGCATACTCACATGAGAC GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCGTCAGTGCATGTGTGTG----TGTAAACACATACATGCACACAGGCATACTCACATGAGAC Template switch alignment (log-probability: -22.1) GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCaTCA|TGTACA|TGTAAACACATACATGCACACAGGCATACTCACATGAGAC GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCGTCA|TGTACA|TGTAAACACATACATGCACACAGGCATACTCACATGAGAC Human > Gorilla --------------- chr9:32217859-32217871 Template switch process: F1: L ACATGGTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCGTCA 1 F3: 4 TGTAAACACATACATGCACACAGGCATACTCACATGAGAC R RF: ACATGGTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCATCATGTACATGTAAACACATACATGCACACAGGCATACTCACATGAGAC RR: TGTACCACCGAGACACAAGGTCTTATACATGTACACAATCGTAGTACATGTACATTTGTGTATGTACGTGTGTCCGTATGAGTGTACTCTG F2: 3 GTGTGTGTACGTG 2 Unidirectional alignment (log-probability: -42.3) GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCgTCAgtgcatgtgtgTG----TGTAAACACATACATGCACACAGGCATACTCACATGAGAC GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCATCA-----------TGTACATGTAAACACATACATGCACACAGGCATACTCACATGAGAC Template switch alignment (log-probability: -28.5) GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCgTCA|GTGCATGTgTGTG|TGTAAACACATACATGCACACAGGCATACTCACATGAGAC GTGGCTCTGTGTTCCAGAATATGTACATGTGTTAGCATCA|GTGCATGTATGTG|TGTAAACACATACATGCACACAGGCATACTCACATGAGAC ========== Event 3767 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ATATTTTCAGGGACTGGGACAAGTT------------------------------------------------------------------------------------------------------------------TTCTCCTTTTTTCTCCTTTGGAGTTCCT ↓ 3 4 2 1 Chimp: ATATTTTCAGGGACTGGGACATGTT--------------------------------------------------------------------------------------------TTCTCCTTGGAGAAAACTTGTTTTCTCCTTTTTTCTCCCTTGGAGTTCCT Gorilla: ATATTTTCAGGGACTGGGACAAGtt------ttctccaaggagaaaacttgttttctccttttttctccaaagagaaaacttgttttctccttttttctccaaggagaaaacttgtt----------------------ttctccttttttctcctttGGAGTTCCT Human: ATATTTTCAGGGACTGGGACAAGTT------------------------------------------------------------------------------------------------------------------TTCTCCTTTTTTCTCCTTTGGAGTTCCT Cluster: [ ] Orangutan: ATATTTTCAGGGACTGGGACAAGA-GCCTAG-------------------------------------------------------------------------------------------------------------GGTCCTGTTTTCTCCTTTGGAGTTCCT Human > Chimp ------------- chr9:97750515-97750525 Template switch process: F1: L CCTAAGGTGCTGGGAAAGACATATTTTCAGGGACTGGGACATGTTTTCTCCTT 1 F3: 4 GTTTTCTCCTTTTTTCTCCCTTGGAGTTCCTGCCCATATGAAT R RF: CCTAAGGTGCTGGGAAAGACATATTTTCAGGGACTGGGACAAGTTTTCTCCTTTTTTCTCCTTTGGAGTTCCTGCCCATATGAAT RR: GGATTCCACGACCCTTTCTGTATAAAAGTCCCTGACCCTGTTCAAAAGAGGAAAAAAGAGGAAACCTCAAGGACGGGTATACTTA F2: 3 TTCAAAAGAGG 2 Unidirectional alignment (log-probability: -54.6) GAAAGACATATTTTCAGGGACTGGGACAtGTTTTCTCCTtggagaaaacttgttttctcctTTTTTCTCCcTTGGAGTTCCTGCCCATATG GAAAGACATATTTTCAGGGACTGGGACAAGTTTTCTCCT----------------------TTTTTCTCCTTTGGAGTTCCTGCCCATATG Template switch alignment (log-probability: -28.9) GAAAGACATATTTTCAGGGACTGGGACAtGTTTTCTCCTT|GGAGAAAACTT|GTTTTCTCCTTTTTTCTCCcTTGGAGTTCCTGCCCATATG GAAAGACATATTTTCAGGGACTGGGACAAGTTTTCTCCTT|GGAGAAAACTT|GTTTTCTCCTTTTTTCTCCTTTGGAGTTCCTGCCCATATG ========== Event 3768 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GTTACAATGCTTTTCAAATACGGTATAATTTACAAATTATACCGTATTTGCTCTCAAATCTGTCAT Chimp: GTTACAATGCTTTTCAAATATGGTATAATTTA------------CATTTGCTCTCAAATCTGTCAT Gorilla: GTTACAATGCTTTTCAAATACGGTATAATTTA------------CATTTGCTCTCAAATCTGTCAT ↓ 3 2 4 Human: GTTACAATGCTTTTCAAATACGGTATAATTTACAAATTATACCGTATTTGCTCTCAAATCTGTCAT Cluster: [ ] Orangutan: GTCACAGTGCTTTTCAAATACGGTATAATTTA------------CATTTGCTCTCAAATCTGTCAT Gorilla > Human --------------- chr9:119818587-119818597 Template switch process: F1: L TACGTATAAGTTACAATGCTTTTCAAATACGGTATAATTTACA 1 F3: 4 ATTTGCTCTCAAATCTGTCATACTCATAAGAATATAAGTT R RF: TACGTATAAGTTACAATGCTTTTCAAATACGGTATAATTTACATTTGCTCTCAAATCTGTCATACTCATAAGAATCTAAGTT RR: ATGCATATTCAATGTTACGAAAAGTTTATGCCATATTAAATGTAAACGAGAGTTTAGACAGTATGAGTATTCTTAGATTCAA F2: 3 TGCCATATTAA 2 Unidirectional alignment (log-probability: -33.7) GTATAAGTTACAATGCTTTTCAAATACGGTATAATTTACaaattataccgtATTTGCTCTCAAATCTGTCATACTCATAAGAATaTAAGTT GTATAAGTTACAATGCTTTTCAAATACGGTATAATTTAC------------ATTTGCTCTCAAATCTGTCATACTCATAAGAATCTAAGTT Template switch alignment (log-probability: -22.7) GTATAAGTTACAATGCTTTTCAAATACGGTATAATTTACA|AATTATACCGT|ATTTGCTCTCAAATCTGTCATACTCATAAGAATaTAAGTT GTATAAGTTACAATGCTTTTCAAATACGGTATAATTTACA|AATTATACCGT|ATTTGCTCTCAAATCTGTCATACTCATAAGAATCTAAGTT ========== Event 3769 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: CAGCTGAGTGAGCCAGCATGCCTTGGGCC------CCAGTGAGCTTGCAGACTGTTGCTTCC ↓ 1 3 4 2 Chimp: CAGCTGAGTGAGCCAGCATGCGTTGGGCT---CACTGGGTGAGCTTGCAGACTGTTGCTTCC Gorilla: CAGCTGAGTGAGCCAGCATGCGTTGGGCTCAC---TGGGTGAGCTTGCAGACTGTTGCTTCC ↑ 1 3 4 2 Human: CAGCTGAGTGAGCCAGCATGCCTTGGGCC------CCAGTGAGCTTGCAGACTGTTGCTTCC Cluster: [ ] Orangutan: CAGCTAAGTGAGCCAGTGTGCGTTGGGCC------CCAGTGAGCTTGCAGACTGTTGCTTCC Human > Chimp ------------- chr9:1824283-1824289 Template switch process: F1: L TGGGTGGAAAGGATCATGGTCAGCTGAGTGAGCCAGCATGCGTTGGGC 1 F3: 4 GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC R RF: TGGGTGGAAAGGATCATGGTCAGCTGAGTGAGCCAGCATGCCTTGGGCCCCAGTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC RR: ACCCACCTTTCCTAGTACCAGTCGACTCACTCGGTCGTACGGAACCCGGGGTCACTCGAACGTCTGACAACGAAGGTGACGTGAGAGACAAG F2: 3 GGTCACT 2 Unidirectional alignment (log-probability: -37.5) AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCgTTGGGC----tcactggGTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCCTTGGGCCCCA-------GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC Template switch alignment (log-probability: -22.3) AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCgTTGGGC|TCACTGG|GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCCTTGGGC|TCACTGG|GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC Human > Gorilla --------------- chr9:73502225-73502231 Template switch process: F1: L TAGGTGGAAAGGATCATGGTCAGCTGAGTGAGCCAGCATGCGTTGGGC 1 F3: 4 GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC R RF: TGGGTGGAAAGGATCATGGTCAGCTGAGTGAGCCAGCATGCCTTGGGCCCCAGTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC RR: ACCCACCTTTCCTAGTACCAGTCGACTCACTCGGTCGTACGGAACCCGGGGTCACTCGAACGTCTGACAACGAAGGTGACGTGAGAGACAAG F2: 3 GGTCACT 2 Unidirectional alignment (log-probability: -42) AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCgTTGGGCtcactgg----GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCCTTGGGC-------CCCAGTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC Template switch alignment (log-probability: -27.8) AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCgTTGGGC|TCACTGG|GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC AAGGATCATGGTCAGCTGAGTGAGCCAGCATGCCTTGGGC|TCACTGG|GTGAGCTTGCAGACTGTTGCTTCCACTGCACTCTCTGTTC ========== Event 3770 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTCTCAGCATGAAAAGCAAACGAGACT--ATAGCAAGAGTCCCTTGCAGAAACAAAATTGT---TAttcttttt-----tttttttttttttttttttgagacagagtctcactctgtcacccaggctaga Chimp: TTCTCAGCATGAAAAGCAAACGAGACT--ATAGCAAGAGTCCCTTGTAGAAACAAAATTGT-------Cttttt-----tttttttttttttttttttgagacagagtctcactctgtcacccaggctaga Gorilla: TTCTCAGCATGAAAAGCAAACCAGACTATATAGCAAGAGTCCCTTGCAGAAACAAAATTGT-------TAttct----------tttttttttttttagagagagagtctcactctgtcacccaggctaga ↓ 1 4 3 2 Human: TTCTCAGCATGAAAAGCAAACGAGACT--ATAGCAAGAGTCCCTTGCAGAAACAAAATTGT---TAttcttttt-----tttttttttttttttttttgagacagagtctcactctgtcacccaggctaga Cluster: [ ] Orangutan: TTCTCAGCATGAAAAGCAAATGAGACT--ATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTAA----ATTGTTAttct-----ttttttttttttttgagacagagtctcactctgtcacccaggctaga Gorilla > Human --------------- chr9:1894797-1894802 Template switch process: F1: L CAGCATGGAAAAAAAATAAATTCTCAGCATGAAAAGCAAAC 1 F3: 4 ATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTATTCTTT R RF: CAGCATGGAAAAAAAATAAATTCTCAGCATGAAAAGCAAACCAGACTATATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTATTCTTTTTTTTTTTTTTAGAGAGAGAGTCTC RR: GTCGTACCTTTTTTTTATTTAAGAGTCGTACTTTTCGTTTGGTCTGATATATCGTTCTCAGGGAACGTCTTTGTTTTAACAATAAGAAAAAAAAAAAAAATCTCTCTCTCAGAG F2: 3 TCAGAG 2 Unidirectional alignment (log-probability: -29) AGCATGGAAAAAAAATAAATTCTCAGCATGAAAAGCAAACgAGAC--TATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTATTcttt AGCATGGAAAAAAAATAAATTCTCAGCATGAAAAGCAAACCAGACTATATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTATT---- Template switch alignment (log-probability: -16.5) AGCATGGAAAAAAAATAAATTCTCAGCATGAAAAGCAAAC|GAGACT|ATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTATTCTTT AGCATGGAAAAAAAATAAATTCTCAGCATGAAAAGCAAAC|GAGACT|ATAGCAAGAGTCCCTTGCAGAAACAAAATTGTTATTCTTT ========== Event 3771 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTTCTCTTTCCCATAGAAATATCA-TATACCCATTCCTTTGTCATggcccagtg Chimp: TCTTCTCTTTCCCATAGAAGTATTATGATA---CTTCCTTTGTCATggcccagtg ↑ 3 1 2 4 Gorilla: TCTTCTCTTTCCCATAGAAGTATCA-TATACCCATTCCTTTGTCATGGCCCAGTG Human: TCTTCTCTTTCCCATAGAAATATCA-TATACCCATTCCTTTGTCATggcccagtg Cluster: [ ] Orangutan: TCTTCTCTTTCCCATAGAAGTATCA-TATACCGATTCCTTTGTCATggcccagtg Gorilla > Chimp --------------- chr9:1830200-1830207 Template switch process: F1: L TGAATTACTGGTTCCAAGTCTTCTCTTTCCCATAGAAGTAT 1 F3: 4 TTCCTTTGTCATGGCCCAGTGATAGGAGGCATGTACTTCC R RF: TGAATTACTGGTTCCAAGTCTTCTCTTTCCCATAGAAGTATCATATACCCATTCCTTTGTCATGGCCCAGTGATAGGAGGCATGTACTTCC RR: ACTTAATGACCAAGGTTCAGAAGAGAAAGGGTATCTTCATAGTATATGGGTAAGGAAACAGTACCGGGTCACTATCCTCCGTACATGAAGG F2: 3 CATAGTAT 2 Unidirectional alignment (log-probability: -27.8) GAATTACTGGTTCCAAGTCTTCTCTTTCCCATAGAAGTATtATgATAC---TTCCTTTGTCATGGCCCAGTGATAGGAGGCATGTACTTCC GAATTACTGGTTCCAAGTCTTCTCTTTCCCATAGAAGTATCAT-ATACCCATTCCTTTGTCATGGCCCAGTGATAGGAGGCATGTACTTCC Template switch alignment (log-probability: -16.7) GAATTACTGGTTCCAAGTCTTCTCTTTCCCATAGAAGTAT|TATGATAC|TTCCTTTGTCATGGCCCAGTGATAGGAGGCATGTACTTCC GAATTACTGGTTCCAAGTCTTCTCTTTCCCATAGAAGTAT|TATGATAC|TTCCTTTGTCATGGCCCAGTGATAGGAGGCATGTACTTCC ========== Event 3772 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTGTGTT-TGTTGAATACAATGAAAATAAAT Chimp: AAGTCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTGTATT-TGTTGAATACAATGAAAATAAAT ↓ 3 2 1 4 Gorilla: AAGGCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTAAGTTTCATTGAATACAATGAAAATAAAT Human: AAGGCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTGTGTT-TGTTGAATACAATGAAAATAAAT Cluster: [ ] Orangutan: AAGGCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTGTATT-TGTTGAATACAATGAAAACAAAT Chimp > Gorilla --------------- chr9:31545514-31545521 Template switch process: F1: L GCAAGGCCAAGAACAAGTATCTTAAACTTAGGATGTCTACT 1 F3: 4 TTGAATACAATGAAAATAAATTTGGCACATCTAGTTCATC R RF: GCAAGTCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTGTATTTGTTGAATACAATGAAAATAAATTTGGCACATCTAGTTCATC RR: CGTTCAGGTTCTTGTTCATAGAATTTGAATCCTACAGATGACATAAACAACTTATGTTACTTTTATTTAAACCGTGTAGATCAAGTAG F2: 3 ACTTTGAA 2 Unidirectional alignment (log-probability: -38) CAAGgCCAAGAACAAGTATCTTAAACTTAGGATGTCTACT-------aagtttcaTTGAATACAATGAAAATAAATTTGGCACATCTAGTTCATC CAAGTCCAAGAACAAGTATCTTAAACTTAGGATGTCTACTGTATTTG--------TTGAATACAATGAAAATAAATTTGGCACATCTAGTTCATC Template switch alignment (log-probability: -27.8) CAAGgCCAAGAACAAGTATCTTAAACTTAGGATGTCTACT|AAGTTTcA|TTGAATACAATGAAAATAAATTTGGCACATCTAGTTCATC CAAGTCCAAGAACAAGTATCTTAAACTTAGGATGTCTACT|AAGTTTAA|TTGAATACAATGAAAATAAATTTGGCACATCTAGTTCATC ========== Event 3773 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGCCCGATTTTTACTCTGTGTATCTTGCAAAAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTAC----TTAAGATACAACATTGTGATTACTGAGGTTTGCCTC ↑ 3 2 1 4 Chimp: TGCCTGCTTTTTACTCTGCGTATCTTGCAAAAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTAC--TTTTAAGATAGAACATTCTGATTACTGAGGTTTGCCTC Gorilla: TGCCCGATTTTTACTCTGTGTATCTTGCAAAAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTT--TTAAGATACAACATTCTCATTACTGAGGTTTGCCTC Human: TGCCCGATTTTTACTCTGTGTATCTTGCAAAAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTAC----TTAAGATACAACATTGTGATTACTGAGGTTTGCCTC Cluster: [ ] Orangutan: TGCCTGATTTTTACTCTGTGTATCTTGCAAAAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTT--TTAAGATACAACATTCTGATTACTGAGGTTTTCCTC Chimp > Human ------------- chr9:19158218-19158224 Template switch process: F1: L AAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTT 1 F3: 4 AACATTGTGATTACTGAGGTTTGCCTCAAAGCAATTTTCCTTTTTTC R RF: GTATCTTGCAAAAGGCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTTTTAAGATAGAACATTCTGATTACTGAGGTTTGCCTCAAAGCAATTTTCCTTTTTTC RR: CATAGAACGTTTTCCGGATGTCTTTATACGAAAGTGTTAACAATTAATAATGAAAATTCTATCTTGTAAGACTAATGACTCCAAACGGAGTTTCGTTAAAAGGAAAAAAG F2: 3 CATAGAA 2 Unidirectional alignment (log-probability: -34.7) GCCTACAGAAATATGCTTTCACAATTGTTAATTATTAC--TTAAGATAcAACATTgTGATTACTGAGGTTTGCCTCAAAGCAATTTTCC GCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTTTTAAGATAGAACATTCTGATTACTGAGGTTTGCCTCAAAGCAATTTTCC Template switch alignment (log-probability: -22.3) GCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTT|AAGATAC|AACATTgTGATTACTGAGGTTTGCCTCAAAGCAATTTTCC GCCTACAGAAATATGCTTTCACAATTGTTAATTATTACTT|AAGATAC|AACATTCTGATTACTGAGGTTTGCCTCAAAGCAATTTTCC ========== Event 3774 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGTGGTTTTCTGGATTAGCTAACCATGTAACTTTTTGGCCAAACTGGAAttttt-------ttttttt----ttttttttttttttttacatacaggatttctctacgttgccagggctgtagtgcagtagctattcacaggcacataataacatgctatggtcttgaactcctag ↑ 4 1 3 2 Chimp: AAGTGGTTTTCTGGATTAGCT--------AACTTTTTGGCCAAACTGGAAttttt-------ttttt--ttttttttttttttttttttagatacaggatttctctacgttgccagggctgtagtgcagtagctattcacaggcacgtaataacatgctatggccttgaactcctag Gorilla: AAGTGGTTTTCTGGATTAGCTAACCGTGTAACTTTTTGGCCAAACTGGAAttttt-------------------------tttttttttagatacaggatttctctacattgccagggctgcagtgcagtagctattcacaggcacgtaataacatgctatggccttgaactcctag Human: AAGTGGTTTTCTGGATTAGCTAACCATGTAACTTTTTGGCCAAACTGGAAttttt-------ttttttt----ttttttttttttttttacatacaggatttctctacgttgccagggctgtagtgcagtagctattcacaggcacataataacatgctatggtcttgaactcctag Cluster: [ ] Orangutan: AAGTGGTTTTCTGGATTAGCTAACCGTGTAACTTTTTGGCCAAACTGGAAtttttttgttgt------------------tgttgttttagatacaggatttccctgtgttgcgagggctgtagtgcagtagctattcacaggcacgtcataacatggtatggccttgaactcctag Chimp > Human ------------- chr9:118055933-118055936 Template switch process: F1: L ACGGCTATTACTATCTCTAGAAGTGGTTTTCTGGATTAGCTAAC 1 F3: 4 TAACTTTTTGGCCAAACTGGAATTTTTTTTTTTTTTT R RF: ACAGCTATTACTATCTCTAGAAGTGGTTTTCTGGATTAGCTAACTTTTTGGCCAAACTGGAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGATACAGGATTTCTCTACGTTGCCAGGGCTGTAGTGCAGTAGCTATTCACAGGCACGTAATAACATG RR: TGTCGATAATGATAGAGATCTTCACCAAAAGACCTAATCGATTGAAAAACCGGTTTGACCTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATCTATGTCCTAAAGAGATGCAACGGTCCCGACATCACGTCATCGATAAGTGTCCGTGCATTATTGTAC F2: 3 GTAC 2 Unidirectional alignment (log-probability: -35.7) CTATTACTATCTCTAGAAGTGGTTTTCTGGATTAGCtaaccatgTAACTTTTTGGCCAAACTGGAATTTTTTTTTTTTTTT-- CTATTACTATCTCTAGAAGTGGTTTTCTGGATTAGC--------TAACTTTTTGGCCAAACTGGAATTTTTTTTTTTTTTTTT Template switch alignment (log-probability: -21.8) CTATTACTATCTCTAGAAGTGGTTTTCTGGATTAGCTAAC|CATG|TAACTTTTTGGCCAAACTGGAATTTTTTTTTTTTTTT CTATTACTATCTCTAGAAGTGGTTTTCTGGATTAGCTAAC|CATG|TAACTTTTTGGCCAAACTGGAATTTTTTTTTTTTTTT ========== Event 3775 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: ccatGAAGAAATACAA-AAACCATGAAGAAATACAAGA------------ATG--GTTCTAGAAACAATTCTTGTATTTCTTCATGGTACTATGAAAAAATACAAAACC ↑ 3 1 2 4 Chimp: ccatGAAGAAATATAA-AAACCATGAAGAAATACAAGA------------ATT-GTTTCTAG-AACCATTCTTGTATTTCTTCATGGAACTATGAAAAAATACAAAACC Gorilla: CCATGAAGAAATACAAAAAACCATGAAGAAATACAAGA------------ATG--GTTCTAGAAACAATTCTTGTATTTCTTCATGGAACTATGAAAAAATACAAAACC Human: ccatGAAGAAATACAA-AAACCATGAAGAAATACAAGA------------ATG--GTTCTAGAAACAATTCTTGTATTTCTTCATGGTACTATGAAAAAATACAAAACC Cluster: [ ] Orangutan: ccatgaagaaatacaa-aaaccatgaagaaatacaagaaacAATTCTTGTATTT-CTTCTAG-AACCATTCTTGTATTTCTTCATGGAACTATGAAAAAATACAAAACC Chimp > Human ------------- chr9:21386855-21386888 Template switch process: F1: L TTCCATGAAGAAATACAAAAACCATGAAGAAATACAAGAAT 1 F3: 4 ACTATGAAAAAATACAAAA R RF: TTCCATGAAGAAATATAAAAACCATGAAGAAATACAAGAATTGTTTCTAGAACCATTCTTGTATTTCTTCATGGAACTATGAAAAAATACAAAA RR: AAGGTACTTCTTTATATTTTTGGTACTTCTTTATGTTCTTAACAAAGATCTTGGTAAGAACATAAAGAAGTACCTTGATACTTTTTTATGTTTT F2: 3 TGGTACTTCTTTATGTTCTTAACAAAGATCTTGG 2 Unidirectional alignment (log-probability: -46.7) TCCATGAAGAAATAcAAAAACCATGAAGAAATACAAGAA-TGgTTCTAGAAaCaATTCTTGTATTTCTTCATGGtACTATGAAAAAATACAAAA TCCATGAAGAAATATAAAAACCATGAAGAAATACAAGAATTGTTTCTAGAA-CCATTCTTGTATTTCTTCATGGAACTATGAAAAAATACAAAA Template switch alignment (log-probability: -25.1) TCCATGAAGAAATAcAAAAACCATGAAGAAATACAAGAAT|GGTTCTAGAAACAATTCTTGTATTTCTTCATGGT|ACTATGAAAAAATACAAAA TCCATGAAGAAATATAAAAACCATGAAGAAATACAAGAAT|GGTTCTAGAAACAATTCTTGTATTTCTTCATGGT|ACTATGAAAAAATACAAAA ========== Event 3776 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GCAATAAGCAGCTCAGAAAAAGTGAACATGCTCTCAAACAGTACTAATGATTtgat ↓ 1 3 2 4 ↑ 3 4 2 Chimp: GCAATAAGCAGCTCAGAAAAA--GAGCATG--TTCAAACAGTACTAATGATTtgat Gorilla: GCAATAAGAAGCTCAGAAAAA--GAGCATG--TTCAAACAGTACTAATGATTTGAT ↓ 3 4 2 ↑ 1 3 2 4 Human: GCAATAAGCAGCTCAGAAAAAGTGAACATGCTCTCAAACAGTACTAATGATTtgat Cluster: [ ] Orangutan: GCAATAAGAAGCTCAGAAAAA--GAGCATG--TTCAAAGAGTACTAATGATTtgat Chimp > Human ------------- chr9:16469195-16469205 Template switch process: F1: L AAAACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG 1 F3: 4 TCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC R RF: AAAACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAGAGCATGTTCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC RR: TTTTGAACGAAAGTGGATGTCGTTATTCGTCGAGTCTTTTTCTCGTACAAGTTTGTCATGATTACTAAACTATACCAAACCGAGACAGG F2: 3 CTCGTACAAGT 2 Unidirectional alignment (log-probability: -35.8) AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAA------GTgaacatgctcTCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAGAGCATGT----------TCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC Template switch alignment (log-probability: -16.7) AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG|TGAACATGCTC|TCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG|TGAACATGCTC|TCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC Human > Chimp ------------- chr9:16831608-16831615 Template switch process: F1: L AAAACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG 1 F3: 4 CAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC R RF: AAAACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAGTGAACATGCTCTCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC RR: TTTTGAACGAAAGTGGATGTCGTTATTCGTCGAGTCTTTTTCACTTGTACGAGAGTTTGTCATGATTACTAAACTATACCAAACCGAGACAGG F2: 3 TTGTACGA 2 Unidirectional alignment (log-probability: -30.3) AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAgagcatGT----------TCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAA------GTGAACATGCTCTCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC Template switch alignment (log-probability: -16.3) AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG|AGCATGTT|CAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG|AGCATGTT|CAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC Gorilla > Human --------------- chr9:16469195-16469205 Template switch process: F1: L AAAACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG 1 F3: 4 TCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC R RF: AAAACTTGCTTTCACCTACAGCAATAAGAAGCTCAGAAAAAGAGCATGTTCAAACAGTACTAATGATTTGATATGGTTTGGCTGTGTCC RR: TTTTGAACGAAAGTGGATGTCGTTATTCTTCGAGTCTTTTTCTCGTACAAGTTTGTCATGATTACTAAACTATACCAAACCGACACAGG F2: 3 CTCGTACAAGT 2 Unidirectional alignment (log-probability: -46.4) AACTTGCTTTCACCTACAGCAATAAGcAGCTCAGAAAAA------GTgaacatgctcTCAAACAGTACTAATGATTTGATATGGTTTGGCTcTGTCC AACTTGCTTTCACCTACAGCAATAAGAAGCTCAGAAAAAGAGCATGT----------TCAAACAGTACTAATGATTTGATATGGTTTGGCTGTGTCC Template switch alignment (log-probability: -28.2) AACTTGCTTTCACCTACAGCAATAAGcAGCTCAGAAAAAG|TGAACATGCTC|TCAAACAGTACTAATGATTTGATATGGTTTGGCTcTGTCC AACTTGCTTTCACCTACAGCAATAAGAAGCTCAGAAAAAG|TGAACATGCTC|TCAAACAGTACTAATGATTTGATATGGTTTGGCTGTGTCC Human > Gorilla --------------- chr9:88401658-88401665 Template switch process: F1: L AAAACTTGCTTTCACCTACAGCAATAAGAAGCTCAGAAAAAG 1 F3: 4 CAAACAGTACTAATGATTTGATATGGTTTGGCTGTGTCC R RF: AAAACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAGTGAACATGCTCTCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC RR: TTTTGAACGAAAGTGGATGTCGTTATTCGTCGAGTCTTTTTCACTTGTACGAGAGTTTGTCATGATTACTAAACTATACCAAACCGAGACAGG F2: 3 TTGTACGA 2 Unidirectional alignment (log-probability: -40.8) AACTTGCTTTCACCTACAGCAATAAGaAGCTCAGAAAAAgagcatGT----------TCAAACAGTACTAATGATTTGATATGGTTTGGCTgTGTCC AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAA------GTGAACATGCTCTCAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC Template switch alignment (log-probability: -27.8) AACTTGCTTTCACCTACAGCAATAAGaAGCTCAGAAAAAG|AGCATGTT|CAAACAGTACTAATGATTTGATATGGTTTGGCTgTGTCC AACTTGCTTTCACCTACAGCAATAAGCAGCTCAGAAAAAG|AGCATGTT|CAAACAGTACTAATGATTTGATATGGTTTGGCTCTGTCC ========== Event 3777 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCTACTGTGCCAAAAGCGAGCGTAGTGGCCGCCG-CTTCCCCCACAAAATTCCGTCAC Chimp: GCTACTGTGCCAAAAGCGAGCGTAGTGGCCGCCG-CTTCCCCCACAAAATTCCGTCAC ↓ 3 2 1 4 Gorilla: GCTACTGTGCCAAAAGCGAGCGTAGTGGCCACTACGCTCCCCCACAAAATTCCGTCAC ↑ 3 2 1 4 Human: GCTACTGTGCCAAAAGCGAGCGTAGTGGCCGCCG-CTTCCCCCACAAAATTCCGTCAC Cluster: [ ] Orangutan: GCTACTGTGCCAAAAGCG--AGTAGTGGCCGCCG-CTTCCCCCACAGAATTCCGTCAC Human > Gorilla --------------- chr9:28108212-28108218 Template switch process: F1: L ACCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCC 1 F3: 4 TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT R RF: ACCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCCGCCGCTTCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT RR: TGGGCGTTTCCCGATGACACGGTTTTCGCTCGCATCACCGGCGGCGAAGGGGGTGTTTTAAGGCAGTGAGCCCTCGACGCAACGTCA F2: 3 CGCATCA 2 Unidirectional alignment (log-probability: -28.1) CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCcactaCGC----TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGC-----CGCCGCTTCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT Template switch alignment (log-probability: -16.6) CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCC|ACTACGC|TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCC|ACTACGC|TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT Chimp > Gorilla --------------- chr9:28108212-28108218 Template switch process: F1: L ACCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCC 1 F3: 4 TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT R RF: ACCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCCGCCGCTTCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT RR: TGGGCGTTTCCCGATGACACGGTTTTCGCTCGCATCACCGGCGGCGAAGGGGGTGTTTTAAGGCAGTGAGCCCTCGACGCAACGTCA F2: 3 CGCATCA 2 Unidirectional alignment (log-probability: -28.1) CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCcactaCGC----TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGC-----CGCCGCTTCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT Template switch alignment (log-probability: -16.6) CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCC|ACTACGC|TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT CCCGCAAAGGGCTACTGTGCCAAAAGCGAGCGTAGTGGCC|ACTACGC|TCCCCCACAAAATTCCGTCACTCGGGAGCTGCGTTGCAGT ========== Event 3778 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATAAGAAAATAAAGGATTATCTGAAAGATTCC--TATGCAATCCAACACAGCTAAAACAAAGATTAGCA ↓ 3 2 1 4 Chimp: TATAAGAAAATAAAGGATTATCTGAAAGATTCCTTCAGATAATCCAACACAGCTAAAACAAAGATTAGCA ↑ 3 2 1 4 Gorilla: TATAAGAAAATAAAGGATTATCTGAAAGATTCC--TATGCAATCCAACATAGCTAAAACAAAGATTAGCA Human: TATAAGAAAATAAAGGATTATCTGAAAGATTCC--TATGCAATCCAACACAGCTAAAACAAAGATTAGCA Cluster: [ ] Orangutan: TATAAGAAAATAA-AGATTATCTGAAATATTTC--TATGTAATCCAACATAGCTAAAACAAAGATTAGCA Human > Chimp ------------- chr9:2797208-2797213 Template switch process: F1: L GCATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT 1 F3: 4 AATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTT R RF: GCATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCTATGCAATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTT RR: CGTAAATTATATTCTTTTATTTCCTAATAGACTTTCTAAGGATACGTTAGGTTGTGTCGATTTTGTTTCTAATCGTAGGTCACAAA F2: 3 TAGACT 2 Unidirectional alignment (log-probability: -27) ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCTtcagAT--AATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTT ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT----ATGCAATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTT Template switch alignment (log-probability: -16) ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT|TCAGAT|AATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTT ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT|TCAGAT|AATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTT Gorilla > Chimp --------------- chr9:2797208-2797213 Template switch process: F1: L GCATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT 1 F3: 4 AATCCAACACAGCTAAAACAAAGATTAGCATCCAGTGTTTAATTTGTGAT R RF: GCATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCTATGCAATCCAACATAGCTAAAACAAAGATTAGCATCCAGTGTTTAATTTGTGAT RR: CGTAAATTATATTCTTTTATTTCCTAATAGACTTTCTAAGGATACGTTAGGTTGTATCGATTTTGTTTCTAATCGTAGGTCACAAATTAAACACTA F2: 3 TAGACT 2 Unidirectional alignment (log-probability: -32.2) ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCTtcagAT--AATCCAACAcAGCTAAAACAAAGATTAGCATCCAGTGTTT ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT----ATGCAATCCAACATAGCTAAAACAAAGATTAGCATCCAGTGTTT Template switch alignment (log-probability: -22.3) ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT|TCAGAT|AATCCAACAcAGCTAAAACAAAGATTAGCATCCAGTGTTT ATTTAATATAAGAAAATAAAGGATTATCTGAAAGATTCCT|TCAGAT|AATCCAACATAGCTAAAACAAAGATTAGCATCCAGTGTTT ========== Event 3779 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTAATAAATATTCCTGAAGTC-ATGGCAATCCTTAGAGGTTGAACTGCCATGAGTTTCCttttttttttCTggctactgaggcttgtgcattcgtcacgtagtcctcgtgccatggttttcagctccatcaggt Chimp: CTAATAAATATTCCTGAAGTC-CTGGTAATCCTTAGAGGTTGAACTGCCATGAGTTTGCtttt--ttttCTggctactgaggcttgtgcattcgtcacttagtcctcgtgccatggttttcagctccatcaggt ↓ 1 4 3 2 Gorilla: CTAATAAATATTCCTGAAGTCCATGGC-----ATAGAGGTTGAACTGCCATGAGTTTCCtttt--ttttCTggctactgaggcttatgcattcgtcacgtagtcctcgtgccatggttttcagctccatcaggt Human: CTAATAAATATTCCTGAAGTC-ATGGCAATCCTTAGAGGTTGAACTGCCATGAGTTTCCttttttttttCTggctactgaggcttgtgcattcgtcacgtagtcctcgtgccatggttttcagctccatcaggt Cluster: [ ] Orangutan: CTGATAAATATTCCTGAAGTC-CTGGCAATCCTTAGAGGTTGAACTGCCATGAGTTTCCtttt--ttttCTggctactgaggcttgtgcattcgtcacgtagtcttcatgccatggttttcagctccatcaggt Chimp > Gorilla --------------- chr9:23816385-23816390 Template switch process: F1: L TTAATTATCCAAAGAAGCCTCTAATAAATATTCCTGAAGTCC 1 F3: 4 TAGAGGTTGAACTGCCATGAGTTTCCTTTTTTTTCTGGCT R RF: TTAATTATCCAAAGAAGCCTCTAATAAATATTCCTGAAGTCCTGGTAATCCTTAGAGGTTGAACTGCCATGAGTTTGCTTTTTTTTCTGGCTACTGAGGCTTGTGCATTCGTCACTTAGTCCTCGTGCCAT RR: AATTAATAGGTTTCTTCGGAGATTATTTATAAGGACTTCAGGACCATTAGGAATCTCCAACTTGACGGTACTCAAACGAAAAAAAAGACCGATGACTCCGAACACGTAAGCAGTGAATCAGGAGCACGGTA F2: 3 ACGGTA 2 Unidirectional alignment (log-probability: -33.4) AATTATCCAAAGAAGCCTCTAATAAATATTCCTGAAGTCCaTGG-----CaTAGAGGTTGAACTGCCATGAGTTTcCTTTTTTTTCTGGCT AATTATCCAAAGAAGCCTCTAATAAATATTCCTGAAGTCC-TGGTAATCCTTAGAGGTTGAACTGCCATGAGTTTGCTTTTTTTTCTGGCT Template switch alignment (log-probability: -22) AATTATCCAAAGAAGCCTCTAATAAATATTCCTGAAGTCC|ATGGCA|TAGAGGTTGAACTGCCATGAGTTTcCTTTTTTTTCTGGCT AATTATCCAAAGAAGCCTCTAATAAATATTCCTGAAGTCC|ATGGCA|TAGAGGTTGAACTGCCATGAGTTTGCTTTTTTTTCTGGCT ========== Event 3780 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CACTTTCATTAATCTGCTGATATTGAATGCTGAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA ↑ 1 4 3 2 Chimp: CACTTTCATTAATCTGCTGAT----AAGTCAAAATGAATCCAAGCATTCAAGACTTGaaaaaaaTCTTCAA Gorilla: CACTTTCATTAATCTGCTGAT----AAGTCAAAATGAATCCAAGCATTCAAGACTTGaaaaaaaTCTTCAA ↓ 1 4 3 2 Human: CACTTTCATTAATCTGCTGATATTGAATGCTGAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA Cluster: [ ] Orangutan: Chimp > Human ------------- chr9:113429207-113429215 Template switch process: F1: L AATGAACATGCATAATCTATCACTTTCATTAATCTGCTGATA 1 F3: 4 GAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAAA R RF: AATGAACATGCATAATCTATCACTTTCATTAATCTGCTGATAAGTCAAAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAAA RR: TTACTTGTACGTATTAGATAGTGAAAGTAATTAGACGACTATTCAGTTTTACTTAGGTTCGTAAGTTCTGAACTTTTTTTAGAAGTTT F2: 3 TCGTAAGTT 2 Unidirectional alignment (log-probability: -35.8) TGAACATGCATAATCTATCACTTTCATTAATCTGCTGAT------AttgaatgctgAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA TGAACATGCATAATCTATCACTTTCATTAATCTGCTGATAAGTCAA----------AATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA Template switch alignment (log-probability: -22.4) TGAACATGCATAATCTATCACTTTCATTAATCTGCTGATA|TTGAATGCT|gAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA TGAACATGCATAATCTATCACTTTCATTAATCTGCTGATA|TTGAATGCT|AAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA Gorilla > Human --------------- chr9:113429207-113429215 Template switch process: F1: L AATGAACATGCATAATCTATCACTTTCATTAATCTGCTGATA 1 F3: 4 GAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAAA R RF: AATGAACATGCATAATCTATCACTTTCATTAATCTGCTGATAAGTCAAAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAAA RR: TTACTTGTACGTATTAGATAGTGAAAGTAATTAGACGACTATTCAGTTTTACTTAGGTTCGTAAGTTCTGAACTTTTTTTAGAAGTTT F2: 3 TCGTAAGTT 2 Unidirectional alignment (log-probability: -35.3) TGAACATGCATAATCTATCACTTTCATTAATCTGCTGAT------AttgaatgctgAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA TGAACATGCATAATCTATCACTTTCATTAATCTGCTGATAAGTCAA----------AATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA Template switch alignment (log-probability: -22.4) TGAACATGCATAATCTATCACTTTCATTAATCTGCTGATA|TTGAATGCT|gAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA TGAACATGCATAATCTATCACTTTCATTAATCTGCTGATA|TTGAATGCT|AAATGAATCCAAGCATTCAAGACTTGAAAAAAATCTTCAA ========== Event 3781 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATTTCCAGTGAAGAT--TTAGTCTGGTTT-----------------------AAATTAGATAGCCTAATGAGCACTATGTATAGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACTACACTTTTTT--TATTTGTTTGGAAAGTATAAGAGAATGTAACTACTTTGGAAATGTATGCTGGCAATTCTAACAGTAATAGATTC Chimp: TATTTCCAGTGAAGAT----TGTCTGGTTT-----------------------AAATTACATAGCCTAATGAGCACTATGTATAGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACTACACtttttt--tATTTGTTTGGAAAGTATAAGAGAATGTAACTACTTTGGAAATGTATGCTGGCAATTCTAACAGTAATAGATTC ↑ 4 3 2 1 Gorilla: TATTTCCAGTGAAGAT----TGTCTGGTTT---------------------------------------------------------------AAATTACATAGCCTAATGATAGTATAACTACACtttttt--tATTTGTTTGGAAAGTATAAGAGAATGTAACTACTTTGGAAATGTATGCTGGCAATTCTAACAGTAATAGATTC Human: TATTTCCAGTGAAGAT--TTAGTCTGGTTT-----------------------AAATTAGATAGCCTAATGAGCACTATGTATAGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACTACACTTTTTT--TATTTGTTTGGAAAGTATAAGAGAATGTAACTACTTTGGAAATGTATGCTGGCAATTCTAACAGTAATAGATTC Cluster: [ ] Orangutan: TATTTCCAGTGAAGATTT--AGTCTGGTTTAAATTACATAGCCTAATGAGCAC---------------------------------------------------------TATAGTATAACTACACTTTTTTAAAATTTATTTGGAAAGTGTAAGAGAATGTAACTACTTTGGAAAAGTATGCTGGCAACTCTAACAGTAATAGATTC Gorilla > Chimp --------------- chr9:91103419-91103425 Template switch process: F1: L TGCCTTCCCCTGGATTATTTCCAGTGAAGATTGTCTGGTTTAAATTACATAGCCTAATGA-----------------------------------------------------------------------GCA 1 F3: 4 TAGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACTACACTTTTTTT R RF: TGCCTTCCCCTGGATTATTTCCAGTGAAGATTGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACTACACTTTTTTTATTTGTTTGGAAAGTATAAGAGAATGTAACTACTTTGGAAATGTATGCTGGCA RR: ACGGAAGGGGACCTAATAAAGGTCACTTCTAACAGACCAAATTTAATGTATCGGATTACTATCATATTGATGTGAAAAAAATAAACAAACCTTTCATATTCTCTTACATTGATGAAACCTTTACATACGACCGT F2: 3 ATGTATC 2 Unidirectional alignment (log-probability: -68.4) GTGAAGATTgtctggtttaaattacatagcctaatgagcactatgtataGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACT GTGAAGATT----------------------------------------GTCTGGTTTAAATTACATAGCCTAATGATAGTATAACT Template switch alignment (log-probability: -36.3) GTGAAGATTGTCTGGTTTAAATTACATAGCCTAATGA-----------------------------------------------------------------------GCA|CTATGTA|TaGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACT GTGAAGATTGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACTACACTTTTTTTATTTGTTTGGAAAGTATAAGAGAATGTAACTACTTTGGAAATGTATGCTGGCA|CTATGTA|TTGTCTGGTTTAAATTACATAGCCTAATGATAGTATAACT ========== Event 3782 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AATCAGGGTCACGTAACTTTAGTAGCAGCCCCTACACAGTGT--A-TGGCAGAG--GAAAACTGAAGAGACAATCAAAAGTATGA Chimp: AATCAGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGTTGCTGTGTAGGGGCTGCTACTAAAGAGACAACCAAAAGTATGA ↑ 3 2 1 4 Gorilla: AATCAGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGT--A-TGGCAGAG--GAAAACTGAAGAGACAACCAAAAGCATGA Human: AATCAGGGTCACGTAACTTTAGTAGCAGCCCCTACACAGTGT--A-TGGCAGAG--GAAAACTGAAGAGACAATCAAAAGTATGA Cluster: [ ] Orangutan: AATCAGGGTTACATAACTTTAGTAGCAGCCCCTACACAGGGT--A-TGGCAGAG--GAAAACTGAAGAGACAACCAAAAGTATGA Gorilla > Chimp --------------- chr9:26819240-26819259 Template switch process: F1: L ATCAGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGT-TG 1 F3: 4 AAGAGACAACCAAAAGTATGATACTTGCATCTGTTACTAC R RF: ATCAGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGTATGGCAGAGGAAAACTGAAGAGACAACCAAAAGCATGATACTTGCATCTGTTACTAC RR: TAGTCCCAGTGTATTGAAATCATCGTCGGGGATGTGTCCCATACCGTCTCCTTTTGACTTCTCTGTTGGTTTTCGTACTATGAACGTAGACAATGATG F2: 3 ATCATCGTCGGGGATGTGTC 2 Unidirectional alignment (log-probability: -55.7) AGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGT---------------TGctgtgtaggggctgctactaAAGAGACAACCAAAAGtATGATACTTGCATCTGTTACTAC AGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGTATGGCAGAGGAAAACTG--------------------AAGAGACAACCAAAAGCATGATACTTGCATCTGTTACTAC Template switch alignment (log-probability: -33.6) AGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGT-TG|CTGTGTAGGGGCTGCTACTA|AAGAGACAACCAAAAGtATGATACTTGCATCTGTTACTAC AGGGTCACATAACTTTAGTAGCAGCCCCTACACAGGGTATG|CTGTGTAGGGGCTGCTACTA|AAGAGACAACCAAAAGCATGATACTTGCATCTGTTACTAC ========== Event 3783 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tagcTCCAAACAGCCTCTTTTAA-----------CGGCCACATTTTGTTCTTTGATTCCAGG ↓ 3 1 4 2 Chimp: tagcTCCAAACAGCCTCTTTTAATGTGGCCATTAAGGCCACATTTTGTTCTTTGATTCCAGG ↑ 3 4 2 Gorilla: tagcTCCAGACAGCCTCTTTTAA-----------TGGCCACATTTTGTTCTTTGATTCCAGG Human: tagcTCCAAACAGCCTCTTTTAA-----------CGGCCACATTTTGTTCTTTGATTCCAGG Cluster: [ ] Orangutan: tagctCCAAACAGCCTCTTTTAA-----------CGGCCACATTTTGTTCTTTGATTCCAGG Human > Chimp ------------- chr9:90970189-90970200 Template switch process: F1: L GGCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTAA 1 F3: 4 GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA R RF: GGCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTAACGGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA RR: CCGGACTCGGTCACACGGATCGAGGTTTGTCGGAGAAAATTGCCGGTGTAAAACAAGAAACTAAGGTCCTTCCACTTTTCCT F2: 3 AATTACCGGTGT 2 Unidirectional alignment (log-probability: -32.7) GCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTAatgtggccattAaGGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA GCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTA-----------ACGGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA Template switch alignment (log-probability: -22.8) GCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTAA|TGTGGCCaTTAA|GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA GCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTAA|TGTGGCCGTTAA|GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA Gorilla > Chimp --------------- chr9:90970191-90970200 Template switch process: F1: L GGCCTGAGCCAGTGTGCCTAGCTCCAAACAGCCTCTTTTAATG 1 F3: 4 GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA R RF: GGCCTGAGCCAGTGTGCCTAGCTCCAGACAGCCTCTTTTAATGGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA RR: CCGGACTCGGTCACACGGATCGAGGTCTGTCGGAGAAAATTACCGGTGTAAAACAAGAAACTAAGGTCCTTCCACTTTTCCT F2: 3 AATTACCGGT 2 Unidirectional alignment (log-probability: -32.2) CTGAGCCAGTGTGCCTAGCTCCAaACAGCCTCTTTTAATgtggccattaaGGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA CTGAGCCAGTGTGCCTAGCTCCAGACAGCCTCTTTTAAT-----------GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA Template switch alignment (log-probability: -22.6) CTGAGCCAGTGTGCCTAGCTCCAaACAGCCTCTTTTAATG|TGGCCATTAA|GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA CTGAGCCAGTGTGCCTAGCTCCAGACAGCCTCTTTTAATG|TGGCCATTAA|GGCCACATTTTGTTCTTTGATTCCAGGAAGGTGAAAAGGA ========== Event 3784 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGAAATGgtatagcatagtggtca ↓ 3 2 1 4 Chimp: CTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCGTCATAGGGAATGgtatagcatagtggtca ↑ 3 2 1 4 Gorilla: CTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGAAATGgtatagcatagtggtca Human: CTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGAAATGgtatagcatagtggtca Cluster: [ ] Orangutan: CTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGAAATGgtatagcatagtgctca Human > Chimp ------------- chr9:27652591-27652597 Template switch process: F1: L ACTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCGT 1 F3: 4 AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC R RF: ACTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGAAATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC RR: TGACATATTATATGTAAGAAGGGATACTCCTACATATGAAGTAAGACTCTTTACCATATCGTATCACCAGTTACAATCCCGAGATTTCAG F2: 3 GGGATAC 2 Unidirectional alignment (log-probability: -34.5) GTATAATATACATTCTTCCCTATGAGGATGTATACTTCgtcatagggA---------ATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC GTATAATATACATTCTTCCCTATGAGGATGTATACTTC---------ATTCTGAGAAATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC Template switch alignment (log-probability: -22.2) GTATAATATACATTCTTCCCTATGAGGATGTATACTTCgT|CATAGGG|AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC GTATAATATACATTCTTCCCTATGAGGATGTATACTTCAT|CATAGGG|AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC Gorilla > Chimp --------------- chr9:27652591-27652597 Template switch process: F1: L ACTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCGT 1 F3: 4 AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC R RF: ACTGTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGAAATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC RR: TGACATATTATATGTAAGAAGGGATACTCCTACATATGAAGTAAGACTCTTTACCATATCGTATCACCAGTTACAATCCCGAGATTTCAG F2: 3 GGGATAC 2 Unidirectional alignment (log-probability: -34) GTATAATATACATTCTTCCCTATGAGGATGTATACTTC---------gtcatagggAATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC GTATAATATACATTCTTCCCTATGAGGATGTATACTTCATTCTGAGA---------AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC Template switch alignment (log-probability: -22.2) GTATAATATACATTCTTCCCTATGAGGATGTATACTTCgT|CATAGGG|AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC GTATAATATACATTCTTCCCTATGAGGATGTATACTTCAT|CATAGGG|AATGGTATAGCATAGTGGTCAATGTTAGGGCTCTAAAGTC ========== Event 3785 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: AAGTGTCTATTCATATCTTAG---GTATTTAACTGAAAACCTGTTAGAC---ATAGTCTAAGAGTTAGTGGCCAAGAT Chimp: AAGTGTCTATTCATATCTTAG---GTATTTAACTGAAAACCTGTTAGAC---ATTGTCTAAGAGTTAGTGGCCAAGAT Gorilla: AAGTGTCTATTCATATCTTAGACTATGTCTAACAGGTTTTCAGTTAAAT------ACCTAAGAGTTAGTGGACAAGAT ↓ 13 24 ↑ 13 24 Human: AAGTGTCTATTCATATCTTAG---GTATTTAACTGAAAACCTGTTAGAC---ATAGTCTAAGAGTTAGTGGCCAAGAT Cluster: [ ] Orangutan: AAGTGTCTATTCATATCTTAG---GTATTTAACTGAAAACCTGTTAGACATA---GTCTAAGAGTTACTGGCCAAGAT Gorilla > Human --------------- chr9:110466000-110466029 Template switch process: F1: L CATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG 1 F3: 4 CTAAGAGTTAGTGGCCAAGATAAATACATTTGAACTTGCC R RF: CATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAGACTATGTCTAACAGGTTTTCAGTTAAATACCTAAGAGTTAGTGGACAAGATAAATGCATTTGAACTTGCC RR: GTACGATAAGAAAAAATCGATTCACAGATAAGTATAGAATCTGATACAGATTGTCCAAAAGTCAATTTATGGATTCTCAATCACCTGTTCTATTTACGTAAACTTGAACGG F2: 3 TGATACAGATTGTCCAAAAGTCAATTTATG 2 Unidirectional alignment (log-probability: -76.3) ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG------------------------------gtatttaactgaaaacctgttagacatagtCTAAGAGTTAGTGGcCAAGATAAATaCATTTGAACTTGCC ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAGACTATGTCTAACAGGTTTTCAGTTAAATAC------------------------------CTAAGAGTTAGTGGACAAGATAAATGCATTTGAACTTGCC Template switch alignment (log-probability: -30.6) ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG|GTATTTAACTGAAAACCTGTTAGACATAGT|CTAAGAGTTAGTGGcCAAGATAAATaCATTTGAACTTGCC ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG|GTATTTAACTGAAAACCTGTTAGACATAGT|CTAAGAGTTAGTGGACAAGATAAATGCATTTGAACTTGCC Human > Gorilla --------------- chr9:21653513-21653542 Template switch process: F1: L CATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG 1 F3: 4 CTAAGAGTTAGTGGACAAGATAAATGCATTTGAACTTGCC R RF: CATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAGGTATTTAACTGAAAACCTGTTAGACATAGTCTAAGAGTTAGTGGCCAAGATAAATACATTTGAACTTGCC RR: GTACGATAAGAAAAAATCGATTCACAGATAAGTATAGAATCCATAAATTGACTTTTGGACAATCTGTATCAGATTCTCAATCACCGGTTCTATTTATGTAAACTTGAACGG F2: 3 CATAAATTGACTTTTGGACAATCTGTATCA 2 Unidirectional alignment (log-probability: -76.3) ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG------------------------------actatgtctaacaggttttcagttaaatacCTAAGAGTTAGTGGaCAAGATAAATgCATTTGAACTTGCC ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAGGTATTTAACTGAAAACCTGTTAGACATAGT------------------------------CTAAGAGTTAGTGGCCAAGATAAATACATTTGAACTTGCC Template switch alignment (log-probability: -30.6) ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG|ACTATGTCTAACAGGTTTTCAGTTAAATAC|CTAAGAGTTAGTGGaCAAGATAAATgCATTTGAACTTGCC ATGCTATTCTTTTTTAGCTAAGTGTCTATTCATATCTTAG|ACTATGTCTAACAGGTTTTCAGTTAAATAC|CTAAGAGTTAGTGGCCAAGATAAATACATTTGAACTTGCC ========== Event 3786 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 56 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCTCCATTGAATCATGGACTTATGAGTCAACTCAGGTTAGGTTGCACCAATCTTTGGGCTAAAGTCTTGT Chimp: CCTCCATTGAATCATGGACTTATGAGTCAACTCAGGTTAGGTTGCACCAATCTTTGGGCTAAAGTCTTGT ↓ 1 3 4 2 ↑ 13 24 Gorilla: CCTCCATTGAATCATGGACTTTGGTGCAACCTAACCTGAGTTGACTCCTATCTTTGGGCTAAAGTCTTGT Human: CCTCCATTGAATCATGGACTTATGAGTCAACTCAGGTTAGGTTGCACCAATCTTTGGGCTAAAGTCTTGT Cluster: [ ] Orangutan: CCTCCATTGAATCATGGACTTATGAGTCAACTCAGGTTAGGTTGCACCAATCTTTGGGCTAAAGTCTTGT Gorilla > Chimp --------------- chr9:88130003-88130030 Template switch process: F1: L TACTAAAAATGAACTACTGTCCTCCATTGAATCATGGACTT 1 F3: 4 ATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA R RF: TACTAAAAATGAACTACGGTCCTCCATTGAATCATGGACTTTGGTGCAACCTAACCTGAGTTGACTCCTATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA RR: ATGATTTTTACTTGATGCCAGGAGGTAACTTAGTACCTGAAACCACGTTGGATTGGACTCAACTGAGGATAGAAACCCGATTTCAGAACAGGGAAACAGTAAGAAGTGT F2: 3 ACCACGTTGGATTGGACTCAACTGAGTA 2 Unidirectional alignment (log-probability: -67.8) ACTAAAAATGAACTACtGTCCTCCATTGAATCATGGACTTatgagtcaactcaggttaggttgcacca----------------------------ATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA ACTAAAAATGAACTACGGTCCTCCATTGAATCATGGACTT----------------------------TGGTGCAACCTAACCTGAGTTGACTCCTATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA Template switch alignment (log-probability: -30.3) ACTAAAAATGAACTACtGTCCTCCATTGAATCATGGACTT|AtGAGTCAACTCAGGTTAGGTTGCACCA|ATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA ACTAAAAATGAACTACGGTCCTCCATTGAATCATGGACTT|AGGAGTCAACTCAGGTTAGGTTGCACCA|ATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA Chimp > Gorilla --------------- chr9:21545664-21545688 Template switch process: F1: L TACTAAAAATGAACTACGGTCCTCCATTGAATCATGGACTT 1 F3: 4 CCTATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA R RF: TACTAAAAATGAACTACTGTCCTCCATTGAATCATGGACTTATGAGTCAACTCAGGTTAGGTTGCACCAATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTCACA RR: ATGATTTTTACTTGATGACAGGAGGTAACTTAGTACCTGAATACTCAGTTGAGTCCAATCCAACGTGGTTAGAAACCCGATTTCAGAACAGGGAAACAGTAAGAAGTGT F2: 3 TCAGTTGAGTCCAATCCAACGTGGT 2 Unidirectional alignment (log-probability: -67.8) ACTAAAAATGAACTACgGTCCTCCATTGAATCATGGACTttggtgcaacctaacctgagttgactccT----------------------------ATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTC ACTAAAAATGAACTACTGTCCTCCATTGAATCATGGACT----------------------------TATGAGTCAACTCAGGTTAGGTTGCACCAATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTC Template switch alignment (log-probability: -30) ACTAAAAATGAACTACgGTCCTCCATTGAATCATGGACTT|TGGTGCAACCTAACCTGAGTTGACT|CCtATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTC ACTAAAAATGAACTACTGTCCTCCATTGAATCATGGACTT|TGGTGCAACCTAACCTGAGTTGACT|CCAATCTTTGGGCTAAAGTCTTGTCCCTTTGTCATTCTTC ========== Event 3787 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: taggcagcagaaagagTTTAAAGCTACCCATTTTAGGGGTA-GTCAAGTATATGAAACCCATGGTCAAGTATATG Chimp: taggcagcagaaagagTTTAAAGCTACCCATTTTAGGGGTA-GTCAAGTATATAAAACCCATGGTCAAGTATATG ↓ 3 1 2 4 Gorilla: AAGGCAGCAGAAAGAGTTTAAAGCTACC-CTAAAATGGGTA--------ACTTTAAACCCATGGTCAAGTATATG Human: taggcagcagaaagagTTTAAAGCTACCCATTTTAGGGGTA-GTCAAGTATATGAAACCCATGGTCAAGTATATG Cluster: [ ] Orangutan: taggcagcagaaagagTTTAAAGCTACC-CTAAAACGGGTAG--------CTTTAAACCCATGGTCAAGTATATG Chimp > Gorilla --------------- chr9:20636530-20636545 Template switch process: F1: L GAATAAGTATTTTAAGGCAGCAGAAAGAGTTTAAAGCTACCC 1 F3: 4 AAACCCATGGTCAAGTATATGAAAAAGTGAGGCAGCTGAA R RF: GAATAAGTATTTTTAGGCAGCAGAAAGAGTTTAAAGCTACCCATTTTAGGGGTAGTCAAGTATATAAAACCCATGGTCAAGTATATGAAAAAGTGAGGCAGCTGAA RR: CTTATTCATAAAAATCCGTCGTCTTTCTCAAATTTCGATGGGTAAAATCCCCATCAGTTCATATATTTTGGGTACCAGTTCATATACTTTTTCACTCCGTCGACTT F2: 3 TTTCAATGGGTAAAAT 2 Unidirectional alignment (log-probability: -47.4) ATAAGTATTTTaAGGCAGCAGAAAGAGTTTAAAGCTACCC----------------------TAaaatgggtaactttAAACCCATGGTCAAGTATATGAAAAAGTGAGGCAGCTGAA ATAAGTATTTTTAGGCAGCAGAAAGAGTTTAAAGCTACCCATTTTAGGGGTAGTCAAGTATATA--------------AAACCCATGGTCAAGTATATGAAAAAGTGAGGCAGCTGAA Template switch alignment (log-probability: -28.8) ATAAGTATTTTaAGGCAGCAGAAAGAGTTTAAAGCTACCC|TAAAATGGGTAaCTTT|AAACCCATGGTCAAGTATATGAAAAAGTGAGGCAGCTGAA ATAAGTATTTTTAGGCAGCAGAAAGAGTTTAAAGCTACCC|TAAAATGGGTAGCTTT|AAACCCATGGTCAAGTATATGAAAAAGTGAGGCAGCTGAA ========== Event 3788 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: ACAGATTTCATTTCTTACTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAGCAATCCATCAGAGAAAATAAAGT----GAATGAAGACAGCGTTTCAAAAGA ↓ 3 2 1 4 Chimp: ACAGATTTCATTTCTTACTCTTTATTTTCTGTGATGGGTTGTTCACAATAGAAACTGAACAACCCATCAAAGAAAATAAAGT--------GAAGACAGCGTTTCAAAAGA Gorilla: ACAGATTTCATTTCTTACTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAACAACCCATCAAAGAAAATAAAGT--------GAAGACAGCGTTTCAAAAGA ↑ 3 2 1 4 Human: ACAGATTTCATTTCTTACTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAGCAATCCATCAGAGAAAATAAAGT----GAATGAAGACAGCGTTTCAAAAGA Cluster: [ ] Orangutan: ACAGATTTCATTTCTTACTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAAAAATCCATCAAAGAAAATAAAGTGAAT----GAAGACAGCGTTTCAAAAGA Human > Chimp ------------- chr9:86209726-86209748 Template switch process: F1: L CTCTTTATTTTCTGTGATGGGTTGTTCACAATAGAAACTGA 1 F3: 4 TGAAGACAGCGTTTCAAAAGAAGAA R RF: CTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAGCAATCCATCAGAGAAAATAAAGTGAATGAAGACAGCGTTTCAAAAGAAGAA RR: GAGAAATAAAAGAAACTACCCAACAAGTGTTATCTTTGACTCGTTAGGTAGTCTCTTTTATTTCACTTACTTCTGTCGCAAAGTTTTCTTCTT F2: 3 GAAATAAAAGAAACTACCCAACA 2 Unidirectional alignment (log-probability: -35.2) TCTTTATTTTCTgTGATGGGTTGTTCACAATAGAAACTGAaCAAcCCATCAaAGAAAATAAAGTGAA----GACAGCGTTTCAAAAGAAGAA TCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAGCAATCCATCAGAGAAAATAAAGTGAATGAAGACAGCGTTTCAAAAGAAGAA Template switch alignment (log-probability: -23.8) TCTTTATTTTCTgTGATGGGTTGTTCACAATAGAAACTGA|ACAACCCATCAAAGAAAATAAAG|TGAAGACAGCGTTTCAAAAGAAGAA TCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGA|ACAACCCATCAAAGAAAATAAAG|TGAAGACAGCGTTTCAAAAGAAGAA Human > Gorilla --------------- chr9:19572494-19572516 Template switch process: F1: L CTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGA 1 F3: 4 TGAAGACAGCGTTTCAAAAGAAGAA R RF: CTCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAGCAATCCATCAGAGAAAATAAAGTGAATGAAGACAGCGTTTCAAAAGAAGAA RR: GAGAAATAAAAGAAACTACCCAACAAGTGTTATCTTTGACTCGTTAGGTAGTCTCTTTTATTTCACTTACTTCTGTCGCAAAGTTTTCTTCTT F2: 3 GAAATAAAAGAAACTACCCAACA 2 Unidirectional alignment (log-probability: -27.8) TCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAaCAAcCCATCAaAGAAAATAAAG----TGAAGACAGCGTTTCAAAAGAAGAA TCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGAGCAATCCATCAGAGAAAATAAAGTGAATGAAGACAGCGTTTCAAAAGAAGAA Template switch alignment (log-probability: -18.3) TCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGA|ACAACCCATCAAAGAAAATAAAG|TGAAGACAGCGTTTCAAAAGAAGAA TCTTTATTTTCTTTGATGGGTTGTTCACAATAGAAACTGA|ACAACCCATCAAAGAAAATAAAG|TGAAGACAGCGTTTCAAAAGAAGAA ========== Event 3789 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: AAAATTCAGTTTTTGAAAATTGGCAAGAATAAGAATTTTTAAAATTAATATTGT ↓ 13 24 ↑ 13 24 Chimp: AAAATTCAGTTTTTGAAAATTCTTAGTCTTGCCAATTTTTAAAATTAATATTGT Gorilla: AAAATTCAGTTTTTGAAAATTCTTAGTCTTGCCAATTTTTAAAATTAATATTGT Human: AAAATTCAGTTTTTGAAAATTGGCAAGAATAAGAATTTTTAAAATTAATATTGT Cluster: [ ] Orangutan: AAAATTCAGTTTTTGAAAATTCTTAGTCTTGCCAATTTTTAAAATTAATATTGT Chimp > Human ------------- chr9:29698707-29698718 Template switch process: F1: L CATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT 1 F3: 4 AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA R RF: CATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATTCTTAGTCTTGCCAATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA RR: GTATTTTCTTATTGAACCCTTTTTAAGTCAAAAACTTTTAAGAATCAGAACGGTTAAAAATTTTAATTATAACATTATTTGGTAAACAAAGAT F2: 3 GAATAAGAACGG 2 Unidirectional alignment (log-probability: -39) ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT------------ggcaagaataagAATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATTCTTAGTCTTGCC------------AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA Template switch alignment (log-probability: -22.8) ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT|GGCAAGAaTAAG|AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT|GGCAAGACTAAG|AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA Human > Chimp ------------- chr9:30290865-30290876 Template switch process: F1: L CATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT 1 F3: 4 AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA R RF: CATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATTGGCAAGAATAAGAATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA RR: GTATTTTCTTATTGAACCCTTTTTAAGTCAAAAACTTTTAACCGTTCTTATTCTTAAAAATTTTAATTATAACATTATTTGGTAAACAAAGAT F2: 3 CCGTTCTGATTC 2 Unidirectional alignment (log-probability: -39) ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT------------cttagtcttgccAATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATTGGCAAGAATAAG------------AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA Template switch alignment (log-probability: -22.8) ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT|CTTAgTCTTGCC|AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA ATAAAAGAATAACTTGGGAAAAATTCAGTTTTTGAAAATT|CTTATTCTTGCC|AATTTTTAAAATTAATATTGTAATAAACCATTTGTTTCTA ========== Event 3790 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: CTACAAGATGATTATAAGTTATATCAGGTACTTATTTAACTTTTAGAAAATCAATTA Chimp: CTACAAGATGATTATAAGTTATATCAGGCACTTATTTAACTTTTAGAAAATCAATTA ↓ 13 24 ↑ 13 24 Gorilla: CTACAAGATGATTATAAGTTAAATAAGTACCTGATATAACTTTTAGAAAATCAATTA ↓ 13 24 ↑ 13 24 Human: CTACAAGATGATTATAAGTTATATCAGGTACTTATTTAACTTTTAGAAAATCAATTA Cluster: [ ] Orangutan: CTACAAGATGATTGCAAGTTATATCAGGTACTTATTTAACTTTTAGAAAATCAATTA Gorilla > Human --------------- chr9:29772271-29772285 Template switch process: F1: L CACTAAATTGGGTGATAACTCTACAAGATGATTATAAGTTA 1 F3: 4 TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA R RF: CACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTAAATAAGTACCTGATATAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA RR: GTGATTTAACCCACTATGGAGATGTTCTACTAATATTCAATTTATTCATGGACTATATTGAAAATCTTTTAGTTAATTTTACACACAGAAAAGTTT F2: 3 TTATTCATGGACTAT 2 Unidirectional alignment (log-probability: -45.5) ACTAAATTGGGTGATAaCTCTACAAGATGATTATAAGTTAtATcAGgtaCTtATtTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTAAATAAGTACCTGATATAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Template switch alignment (log-probability: -23.2) ACTAAATTGGGTGATAaCTCTACAAGATGATTATAAGTTA|TATCAGGTACTTATT|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA|TATCAGGTACTTATT|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Human > Gorilla --------------- chr9:101873262-101873276 Template switch process: F1: L CACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA 1 F3: 4 TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA R RF: CACTAAATTGGGTGATAACTCTACAAGATGATTATAAGTTATATCAGGTACTTATTTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA RR: GTGATTTAACCCACTATTGAGATGTTCTACTAATATTCAATATAGTCCATGAATAAATTGAAAATCTTTTAGTTAATTTTACACACAGAAAAGTTT F2: 3 ATAGTCCATGAATAA 2 Unidirectional alignment (log-probability: -45.5) ACTAAATTGGGTGATAcCTCTACAAGATGATTATAAGTTAaATaAGtacCTgATaTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATAACTCTACAAGATGATTATAAGTTATATCAGGTACTTATTTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Template switch alignment (log-probability: -23.2) ACTAAATTGGGTGATAcCTCTACAAGATGATTATAAGTTA|AATAAGTACCTGATA|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATAACTCTACAAGATGATTATAAGTTA|AATAAGTACCTGATA|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Gorilla > Chimp --------------- chr9:30364038-30364052 Template switch process: F1: L CACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA 1 F3: 4 TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA R RF: CACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTAAATAAGTACCTGATATAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA RR: GTGATTTAACCCACTATGGAGATGTTCTACTAATATTCAATTTATTCATGGACTATATTGAAAATCTTTTAGTTAATTTTACACACAGAAAAGTTT F2: 3 TTATTCACGGACTAT 2 Unidirectional alignment (log-probability: -40) ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTAtATcAGgcaCTtATtTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTAAATAAGTACCTGATATAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Template switch alignment (log-probability: -23.2) ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA|TATCAGGcACTTATT|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA|TATCAGGTACTTATT|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Chimp > Gorilla --------------- chr9:101873262-101873276 Template switch process: F1: L CACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA 1 F3: 4 TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA R RF: CACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTATATCAGGCACTTATTTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA RR: GTGATTTAACCCACTATGGAGATGTTCTACTAATATTCAATATAGTCCGTGAATAAATTGAAAATCTTTTAGTTAATTTTACACACAGAAAAGTTT F2: 3 ATAGTCCATGAATAA 2 Unidirectional alignment (log-probability: -40) ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTAaATaAGtacCTgATaTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTATATCAGGCACTTATTTAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA Template switch alignment (log-probability: -23.2) ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA|AATAAGTaCCTGATA|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ACTAAATTGGGTGATACCTCTACAAGATGATTATAAGTTA|AATAAGTGCCTGATA|TAACTTTTAGAAAATCAATTAAAATGTGTGTCTTTTCAAA ========== Event 3791 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TCCTGATCCATAGAGGCAGACACAGGTCTGAGATCTGAGCATTCATGG ↑ 31 2 4 Chimp: TCCTGATCCATAGAGGCAGACCTGTGCCTGAGATCTGAGCATTCATGG Gorilla: TCCTGATCCACAGAGGCAGACCTGTGCCTGAGATCTGAGCATTCATGG ↓ 31 2 4 Human: TCCTGATCCATAGAGGCAGACACAGGTCTGAGATCTGAGCATTCATGG Cluster: [ ] Orangutan: TCCTGATCCATAGAGGCAGACCTGTGCCTGAGATCTGACCATTCATGG Chimp > Human ------------- chr9:31850174-31850179 Template switch process: F1: L GCCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGAC 1 F3: 4 CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT R RF: GCCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGACCTGTGCCTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT RR: CGGTTACTGTCGTGGGGTAGAGGACTAGGTATCTCCGTCTGGACACGGACTCTAGACTCGTAAGTACCCTGATGGCGGGAACGAAAA F2: 3 TGGACA 2 Unidirectional alignment (log-probability: -30.1) CCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGACacaggt------CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT CCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGAC------CTGTGCCTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT Template switch alignment (log-probability: -16) CCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGAC|ACAGGT|CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT CCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGAC|ACAGGT|CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT Gorilla > Human --------------- chr9:31850174-31850179 Template switch process: F1: L GCCAATGACAGCACCCCATCTCCTGATCCATAGAGGCAGAC 1 F3: 4 CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT R RF: GCCAATGACAGCACCCCATCTCCTGATCCACAGAGGCAGACCTGTGCCTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT RR: CGGTTACTGTCGTGGGGTAGAGGACTAGGTGTCTCCGTCTGGACACGGACTCTAGACTCGTAAGTACCCTGATGGCGGGAACGAAAA F2: 3 TGGACA 2 Unidirectional alignment (log-probability: -34.3) CCAATGACAGCACCCCATCTCCTGATCCAtAGAGGCAGACacagGtCTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT CCAATGACAGCACCCCATCTCCTGATCCACAGAGGCAGACCTGTGCCTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT Template switch alignment (log-probability: -22) CCAATGACAGCACCCCATCTCCTGATCCAtAGAGGCAGAC|ACAGGT|CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT CCAATGACAGCACCCCATCTCCTGATCCACAGAGGCAGAC|ACAGGT|CTGAGATCTGAGCATTCATGGGACTACCGCCCTTGCTTTT ========== Event 3792 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GTAAGAGATGCAAGCAAAGCACCTTTTCAAAGGAAAGTCTTTAACTTTCCTTGAAGACTAAGGAAAAGGT ↑ 1 3 4 2 Chimp: GTAAGAGATGCAAGCAAAGCACCTTTTCA----AAAGTCAAAGACTTTCCTTGAAGACTAAGGAAAAGGT ↓ 1 3 4 2 Gorilla: GTAAGAGATGCAAGCAAAGCAACTTTTCAAAGGAAAGTCTTTAACTTTCCTTGAAGACTAAGGAAAAGGT Human: GTAAGAGATGCAAGCAAAGCACCTTTTCAAAGGAAAGTCTTTAACTTTCCTTGAAGACTAAGGAAAAGGT Cluster: [ ] Orangutan: GTAAGAGATGCAAGCAAAGCACCTTTTCAAAGGAAAGTCTTTAACTTTCCT-TAAGACTAAGGAAAAGGT Chimp > Human ------------- chr9:32140662-32140672 Template switch process: F1: L GAAAGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAA 1 F3: 4 AACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAACCTTAAC R RF: GAAAGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAAAGTCAAAGACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAAC RR: CTTTCACGAAGACATTCTCTACGTTCGTTTCGTGGAAAAGTTTTCAGTTTCTGAAAGGAACTTCTGATTCCTTTTCCACGAATCGGAATTG F2: 3 TTTCTGAAAGG 2 Unidirectional alignment (log-probability: -41.9) AGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAAgG--AAAGtctttaACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAaCCTTAA AGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAAAGTCAAAG------ACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAA Template switch alignment (log-probability: -28.7) AGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAA|GGAAAGTCTTT|aACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAaCCTTAA AGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAA|GGAAAGTCTTT|GACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAA Chimp > Gorilla --------------- chr9:104292125-104292135 Template switch process: F1: L TGTGTTATGAAAGTGCTTCTGTAAGAGATGCAAGCAAAGCAACTTTTCAAA 1 F3: 4 AACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAAC R RF: TGTGTTATGAAAGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAAAGTCAAAGACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAAC RR: ACACAATACTTTCACGAAGACATTCTCTACGTTCGTTTCGTGGAAAAGTTTTCAGTTTCTGAAAGGAACTTCTGATTCCTTTTCCACGAATCGGAATTG F2: 3 TTTCTGAAAGG 2 Unidirectional alignment (log-probability: -40.6) AGTGCTTCTGTAAGAGATGCAAGCAAAGCAaCTTTTCAAAgG--AAAGtctttaACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAA AGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAAAGTCAAAG------ACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAA Template switch alignment (log-probability: -28.4) AGTGCTTCTGTAAGAGATGCAAGCAAAGCAaCTTTTCAAA|GGAAAGTCTTT|aACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAA AGTGCTTCTGTAAGAGATGCAAGCAAAGCACCTTTTCAAA|GGAAAGTCTTT|GACTTTCCTTGAAGACTAAGGAAAAGGTGCTTAGCCTTAA ========== Event 3793 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATGCTTTTACGATAAC--TTTTGAAATTTCAAGTTCAACTGTTATTTGTTGATGTGAA Chimp: ATGCTTTTACGATAAC--TTTTGAAATTTCAAGTTCAACTGTTATTTGTTGATGTGAA ↑ 3 1 2 4 Gorilla: ATGCTTTTACAATAAC----TTGAAATTTCAAATTCAGCTGTTATTTGTTGATGTGAA ↓ 3 1 2 4 Human: ATGCTTTTACGATAAC--TTTTGAAATTTCAAGTTCAACTGTTATTTGTTGATGTGAA Cluster: [ ] Orangutan: ----TTTTACAATAACTT--TTGAAATTTCAAATTCAACTGTTATTTATTGATGTGAA Gorilla > Human --------------- chr9:32142543-32142555 Template switch process: F1: L GTCAATGGTATATGCTTTTACGATAACTT 1 F3: 4 TTCAACTGTTATTTGTTGATGTGAATACTGATGTAATACTCAT R RF: GTCAATGGTATATGCTTTTACAATAACTTGAAATTTCAAATTCAGCTGTTATTTGTTGATGTGAATACTGATGTAATACTCAT RR: CAGTTACCATATACGAAAATGTTATTGAACTTTAAAGTTTAAGTCGACAATAAACAACTACACTTATGACTACATTATGAGTA F2: 3 GAACTTTAAAGTT 2 Unidirectional alignment (log-probability: -37.2) GTCAATGGTATATGCTTTTACgATAACttTTGAAATTTCAAgTTCAaCTGTTATTTGTTGATGTGAATACTGATGTAATACT GTCAATGGTATATGCTTTTACAATAAC--TTGAAATTTCAAATTCAGCTGTTATTTGTTGATGTGAATACTGATGTAATACT Template switch alignment (log-probability: -28.2) GTCAATGGTATATGCTTTTACgATAACTT|TTGAAATTTCAAG|TTCAaCTGTTATTTGTTGATGTGAATACTGATGTAATACT GTCAATGGTATATGCTTTTACAATAACTT|TTGAAATTTCAAG|TTCAGCTGTTATTTGTTGATGTGAATACTGATGTAATACT Gorilla > Chimp --------------- chr9:32847648-32847660 Template switch process: F1: L GTCAATGGTATATGCTTTTACGATAACTT 1 F3: 4 TTCAACTGTTATTTGTTGATGTGAATACTGATGTAATACTCAT R RF: GTCAATGGTATATGCTTTTACAATAACTTGAAATTTCAAATTCAGCTGTTATTTGTTGATGTGAATACTGATGTAATACTCAT RR: CAGTTACCATATACGAAAATGTTATTGAACTTTAAAGTTTAAGTCGACAATAAACAACTACACTTATGACTACATTATGAGTA F2: 3 GAACTTTAAAGTT 2 Unidirectional alignment (log-probability: -37.2) GTCAATGGTATATGCTTTTACgATAACttTTGAAATTTCAAgTTCAaCTGTTATTTGTTGATGTGAATACTGATGTAATACT GTCAATGGTATATGCTTTTACAATAAC--TTGAAATTTCAAATTCAGCTGTTATTTGTTGATGTGAATACTGATGTAATACT Template switch alignment (log-probability: -28.2) GTCAATGGTATATGCTTTTACgATAACTT|TTGAAATTTCAAG|TTCAaCTGTTATTTGTTGATGTGAATACTGATGTAATACT GTCAATGGTATATGCTTTTACAATAACTT|TTGAAATTTCAAG|TTCAGCTGTTATTTGTTGATGTGAATACTGATGTAATACT ========== Event 3794 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AGGGAAGAAGATCCTCAGGCCTCC-------------------CTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTTGAAGCTCAGTCCCTTATAAG Chimp: AGGGAAGAAGATCCTCAGGCCTCC-------------------CTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTTGAAGCTCAGTCCCTTATAAA ↓ 4 1 3 2 Gorilla: AGGGAAGAAGATCCTCAGGCCTCCCTCTCTGAAGCCCTGCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTTGAAGCTCAGTCCCTTATAAG ↑ 4 1 3 2 Human: AGGGAAGAAGATCCTCAGGCCTCC-------------------CTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTTGAAGCTCAGTCCCTTATAAG Cluster: [ ] Orangutan: AGGGAAGAAGATCCTCAGGGCTCCCTCTCTGCAGCCCTGCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTTGAAGCTCAGTCCCTTGTAAG Human > Gorilla --------------- chr9:105322257-105322263 Template switch process: F1: L AGCAGACCCTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTG 1 F3: 4 GCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCC R RF: AGCAGACCCTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTT RR: TCGTCTGGGAGACCCCGTCCCTTCTTCTAGGAGTCCGGAGGGAGAGACCAGTACGTGGAGGGAGGACCTCCCTGTCTCCGGAA F2: 3 TCCCGAA 2 Unidirectional alignment (log-probability: -38.2) CTCTGGGGCAGGGAAGAAGATCCTCAGGCCTccctctctgaagccctgctCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG CTCTGGGGCAGGGAAGAAGATCCTCAGGCCT-------------------CCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG Template switch alignment (log-probability: -27.9) CTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTG|AAGcCCT|gCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG CTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTG|AAGGCCT|CCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG Chimp > Gorilla --------------- chr9:105322257-105322263 Template switch process: F1: L AGCAGACCCTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTG 1 F3: 4 GCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCC R RF: AGCAGACCCTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAGAGGCCTT RR: TCGTCTGGGAGACCCCGTCCCTTCTTCTAGGAGTCCGGAGGGAGAGACCAGTACGTGGAGGGAGGACCTCCCTGTCTCCGGAA F2: 3 TCCCGAA 2 Unidirectional alignment (log-probability: -38.2) CTCTGGGGCAGGGAAGAAGATCCTCAGGCCTccctctctgaagccctgctCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG CTCTGGGGCAGGGAAGAAGATCCTCAGGCCT-------------------CCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG Template switch alignment (log-probability: -27.9) CTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTG|AAGcCCT|gCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG CTCTGGGGCAGGGAAGAAGATCCTCAGGCCTCCCTCTCTG|AAGGCCT|CCTCCCTCTCTGGTCATGCACCTCCCTCCTGGAGGGACAG ========== Event 3795 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 234 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTCAAGCCACAAGCACCTATAGGGAACTTTGACCCCTAAGTTCAACCACAGTAGTTTATTTT ↓ 1 3 24 Chimp: TTCAAGCCACAAGCACCTATAAGGG--------GTCAAAGTTCAACCACAGTACTTTATTTT Gorilla: TTCAAGCCAAAAGCACCTATAAGGG--------GTCAAAGTTCAACCACAGTAGTTTATTTT ↓ 3 1 4 2 ↑ 1 3 24 Human: TTCAAGCCACAAGCACCTATAGGGAACTTTGACCCCTAAGTTCAACCACAGTAGTTTATTTT Cluster: [ ] Orangutan: TTCAAGCCAAAAGCACCTATAAGGG--------GTCAAAGTTCAAC--CAGTAGTTTATTTT Human > Chimp ------------- chr9:34548289-34548296 Template switch process: F1: L CCTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATA 1 F3: 4 AAGTTCAACCACAGTACTTTATTTTACAAATGGCGAAGGC R RF: CCTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATAGGGAACTTTGACCCCTAAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC RR: GGAGTCAAGGTCCCACCTGTAAGTTCGGTGTTCGTGGATATCCCTTGAAACTGGGGATTCAAGTTGGTGTCATCAAATAAAATGTTTACCGCTTCCG F2: 3 ACTGGGGA 2 Unidirectional alignment (log-probability: -39.4) CTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATaaggggtcA----------------AAGTTCAACCACAGTAcTTTATTTTACAAATGGCGAAGGC CTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTAT--------AGGGAACTTTGACCCCTAAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC Template switch alignment (log-probability: -22.3) CTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATA|AGGGGTCA|AAGTTCAACCACAGTAcTTTATTTTACAAATGGCGAAGGC CTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATA|AGGGGTCA|AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC Gorilla > Human --------------- chr9:33816374-33816386 Template switch process: F1: L CCTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATAGGG 1 F3: 4 AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC R RF: CCTCAGTTCCAGGGTGGACATTCAAGCCAAAAGCACCTATAAGGGGTCAAAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC RR: GGAGTCAAGGTCCCACCTGTAAGTTCGGTTTTCGTGGATATTCCCCAGTTTCAAGTTGGTGTCATCAAATAAAATGTTTACCGCTTCCG F2: 3 TCCCCAGTTTCAA 2 Unidirectional alignment (log-probability: -49.2) AGTTCCAGGGTGGACATTCAAGCCAcAAGCACCTATAgGG----AactttgacccctAAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC AGTTCCAGGGTGGACATTCAAGCCAAAAGCACCTATAAGGGGTCA------------AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC Template switch alignment (log-probability: -28.5) AGTTCCAGGGTGGACATTCAAGCCAcAAGCACCTATAgGG|AACTTTGACCCCT|AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC AGTTCCAGGGTGGACATTCAAGCCAAAAGCACCTATAAGG|AACTTTGACCCCT|AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC Human > Gorilla --------------- chr9:106006379-106006386 Template switch process: F1: L CCTCAGTTCCAGGGTGGACATTCAAGCCAAAAGCACCTATA 1 F3: 4 AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC R RF: CCTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATAGGGAACTTTGACCCCTAAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC RR: GGAGTCAAGGTCCCACCTGTAAGTTCGGTGTTCGTGGATATCCCTTGAAACTGGGGATTCAAGTTGGTGTCATCAAATAAAATGTTTACCGCTTCCG F2: 3 ACTGGGGA 2 Unidirectional alignment (log-probability: -38.1) CTCAGTTCCAGGGTGGACATTCAAGCCAaAAGCACCTATAaGGggtcA------------AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC CTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATAGGG----AACTTTGACCCCTAAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC Template switch alignment (log-probability: -22.3) CTCAGTTCCAGGGTGGACATTCAAGCCAaAAGCACCTATA|AGGGGTCA|AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC CTCAGTTCCAGGGTGGACATTCAAGCCACAAGCACCTATA|AGGGGTCA|AAGTTCAACCACAGTAGTTTATTTTACAAATGGCGAAGGC ========== Event 3796 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ctcagcacatggtaattaCAAAGCATGGTGCCATAAGAAGTTGCTGGGGAGGCAGACATG Chimp: ctcagcacatggtaattaCAACTTCTTATGGCA-CAGAAGTTGCTGGGGAGGCAGACATG ↑ 1 3 4 2 Gorilla: ctcagcacatggtaattaCAAAGCATGGTGCCATAAGAAGTTGCTGGGGAGGCAGACATG Human: ctcagcacatggtaattaCAAAGCATGGTGCCATAAGAAGTTGCTGGGGAGGCAGACATG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr9:34467477-34467489 Template switch process: F1: L TATCTGTCGCTTAGTAGCCACTCAGCACATGGTAATTACAA 1 F3: 4 AGAAGTTGCTGGGGAGGCAGACATGTAAATGAATGCAGAA R RF: TATCTGTCACTTAGTAGCCACTCAGCACATGGTAATTACAAAGCATGGTGCCATAAGAAGTTGCTGGGGAGGCAGACATGTAAATGAATGCAGAA RR: ATAGACAGTGAATCATCGGTGAGTCGTGTACCATTAATGTTTCGTACCACGGTATTCTTCAACGACCCCTCCGTCTGTACATTTACTTACGTCTT F2: 3 CACGGTATTCTTC 2 Unidirectional alignment (log-probability: -45.6) ATCTGTCgCTTAGTAGCCACTCAGCACATGGTAATTACA--------------ActtcttatggcacAGAAGTTGCTGGGGAGGCAGACATGTAAATGAATGCAGAA ATCTGTCACTTAGTAGCCACTCAGCACATGGTAATTACAAAGCATGGTGCCATA-------------AGAAGTTGCTGGGGAGGCAGACATGTAAATGAATGCAGAA Template switch alignment (log-probability: -22.9) ATCTGTCgCTTAGTAGCCACTCAGCACATGGTAATTACAA|CTTCTTATGGCAC|AGAAGTTGCTGGGGAGGCAGACATGTAAATGAATGCAGAA ATCTGTCACTTAGTAGCCACTCAGCACATGGTAATTACAA|CTTCTTATGGCAC|AGAAGTTGCTGGGGAGGCAGACATGTAAATGAATGCAGAA ========== Event 3797 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: -------------------gTGGCAGCACCAAAAGTGCTGCCAACACCCCCTAGGCTGACTGGTC Chimp: -------------------GTGGCAGCACTTTTGGTGCTGCCAACACCCCCTAGGCTGACTGGTC ↓ 3 1 2 4 Gorilla: -------------------gTGGCAGCACCAAAAGTGCTGCCACCACCCCCTAGGCTGACTGGTC Human: -------------------gTGGCAGCACCAAAAGTGCTGCCAACACCCCCTAGGCTGACTGGTC Cluster: [ ] Orangutan: caggtttgcctACCCATTAATTACTGCACCAAAAGTGCTGCCACCACCCCCTAGGCTGACTGGTC Chimp > Gorilla --------------- chr9:105633170-105633184 Template switch process: F1: L TCACCCAGCTAGAGAATCCTTGCTGGGCCAGGTGGCAGCAC 1 F3: 4 CACCCCCTAGGCTGACTGGTCAGGGTCAGCAGCAGGATTT R RF: TCACCCAGCTAGAGAATCCTTGATGGGCCAGGTGGCAGCACTTTTGGTGCTGCCAACACCCCCTAGGCTGACTGGTCAGGGTCAGCAGCAGGATTT RR: AGTGGGTCGATCTCTTAGGAACTACCCGGTCCACCGTCGTGAAAACCACGACGGTTGTGGGGGATCCGACTGACCAGTCCCAGTCGTCGTCCTAAA F2: 3 CACCGTCGTGAAAAC 2 Unidirectional alignment (log-probability: -39.3) CACCCAGCTAGAGAATCCTTGcTGGGCCAGGTGGCAGCAC-----caaaaGTGCTGCCAcCACCCCCTAGGCTGACTGGTCAGGGTCAGCAGCAGGATTT CACCCAGCTAGAGAATCCTTGATGGGCCAGGTGGCAGCACTTTTG-----GTGCTGCCAACACCCCCTAGGCTGACTGGTCAGGGTCAGCAGCAGGATTT Template switch alignment (log-probability: -23.2) CACCCAGCTAGAGAATCCTTGcTGGGCCAGGTGGCAGCAC|CAAAAGTGCTGCCAC|CACCCCCTAGGCTGACTGGTCAGGGTCAGCAGCAGGATTT CACCCAGCTAGAGAATCCTTGATGGGCCAGGTGGCAGCAC|CAAAAGTGCTGCCAC|CACCCCCTAGGCTGACTGGTCAGGGTCAGCAGCAGGATTT ========== Event 3798 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCAATAAAGAGATTTAAAAA----AACAT---TATTATTACTAttttgagacagagtttcactctttcgcccaggctgg--agtgcagtggcacaatctcgggtcactgcaacctctgccttctggttt ↓ 1 4 3 2 Chimp: GGCAATAAAGAGATTTAAAAA--ACAGTAT---TATTATTACTAttttgagacagagtttcactctttcgcccaggctgg--agtgcagtggcacaatctcgggtcactgcaacctctgccttctggttt Gorilla: GGCAATAAAGAGATTTAAAAAAC--AGTAT---TATTATTACTAttttgagacagagtttcactctttcgcccaggctgg----agcagtggcacaatctcgggtcactgcaacctctgccttctggttt Human: GGCAATAAAGAGATTTAAAAA----AACAT---TATTATTACTAttttgagacagagtttcactctttcgcccaggctgg--agtgcagtggcacaatctcgggtcactgcaacctctgccttctggttt Cluster: [ ] Orangutan: ggcaataaagagatTTCAAAAAC--AGTATTATTATTATTACTAttttgagacagagtttcactctttcgcccaggctggag--tgcagtggtgcaatctcgggtcactgcaacctctgccttctggttt Human > Chimp ------------- chr9:81529286-81529289 Template switch process: F1: L AAGTGTTCATCTCTGTACCAGGCAATAAAGAGATTTAAAAAA 1 F3: 4 ATTATTATTACTATTTTGAGACAGAGTTTCACTCTTTCGC R RF: AAGTGTTCATCTCTGTACCAGGCAATAAAGAGATTTAAAAAAACATTATTATTACTATTTTGAGACAGAGTTTCACTCTTTCGCCCAGGCTGGAGTGCAGTGGCACAATCTCGGGTCACTG RR: TTCACAAGTAGAGACATGGTCCGTTATTTCTCTAAATTTTTTTGTAATAATAATGATAAAACTCTGTCTCAAAGTGAGAAAGCGGGTCCGACCTCACGTCACCGTGTTAGAGCCCAGTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -25.5) GTGTTCATCTCTGTACCAGGCAATAAAGAGATTT-AAAAAACagtATTATTATTACTATTTTGAGACAGAGTTTCACTCTTTCGC GTGTTCATCTCTGTACCAGGCAATAAAGAGATTTAAAAAAAC---ATTATTATTACTATTTTGAGACAGAGTTTCACTCTTTCGC Template switch alignment (log-probability: -15.8) GTGTTCATCTCTGTACCAGGCAATAAAGAGATTTAAAAAA|CAGT|ATTATTATTACTATTTTGAGACAGAGTTTCACTCTTTCGC GTGTTCATCTCTGTACCAGGCAATAAAGAGATTTAAAAAA|CAGT|ATTATTATTACTATTTTGAGACAGAGTTTCACTCTTTCGC ========== Event 3799 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATAAGTTTCCCTCCTGACTGTTCACATGTACAGGCAGCATTAGCATTTCCTGCCTGTACATGTGAACGttcctatgctctacccc ↑ 1 4 3 2 Chimp: AATAAGTTTCCCTCCTGACTG------TGTGTTTTCAGCATTAGCATTTCCTGCCTGTACATGTGAACGttcctatgctctacccc Gorilla: AATAAGTTTCCCTCCTGACTG------TGTGTTTTCAGCATTAGCATTTCCTGCCTGTACATGTGAACGttcctatgctctacccc ↓ 1 4 3 2 Human: AATAAGTTTCCCTCCTGACTGTTCACATGTACAGGCAGCATTAGCATTTCCTGCCTGTACATGTGAACGttcctatgctctacccc Cluster: [ ] Orangutan: AATAAGTTTCCCTCGTGACTG------TG-TTTTTCAGCATTAGCATTTCTTGCCTGTACATGTGAACgt---tgtgctctacccc Chimp > Human ------------- chr9:103298611-103298623 Template switch process: F1: L AGAGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGT 1 F3: 4 CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA R RF: AGAGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGTGTGTTTTCAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA RR: TCTCGGACTGATGGTTAACCTTATTCAAAGGGAGGACTGACACACAAAAGTCGTAATCGTAAAGGACGGACATGTACACTTGCAAGGAT F2: 3 GGACATGTACACT 2 Unidirectional alignment (log-probability: -38.7) AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTG------TTCacatgtacaggcAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGTGTGTTTTC------------AGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA Template switch alignment (log-probability: -16.9) AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGT|TCACATGTACAGG|CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGT|TCACATGTACAGG|CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA Gorilla > Human --------------- chr9:103298611-103298623 Template switch process: F1: L AGAGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGT 1 F3: 4 CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA R RF: AGAGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGTGTGTTTTCAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA RR: TCTCGGACTGATGGTTAACCTTATTCAAAGGGAGGACTGACACACAAAAGTCGTAATCGTAAAGGACGGACATGTACACTTGCAAGGAT F2: 3 GGACATGTACACT 2 Unidirectional alignment (log-probability: -38.2) AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTG------TTcacatgtacaggCAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGTGTGTTTT------------CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA Template switch alignment (log-probability: -17.4) AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGT|TCACATGTACAGG|CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA AGCCTGACTACCAATTGGAATAAGTTTCCCTCCTGACTGT|TCACATGTACAGG|CAGCATTAGCATTTCCTGCCTGTACATGTGAACGTTCCTA ========== Event 3800 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TAAATTAAGTGCATTTAAAACCATCTTGTCTCAAGATGGTTGCCATTCAGAAAAGCAAAA Chimp: TAAATTAAGTGCATTTAAAACGATCTTGTCTCAAGATGGTTGCCATTCAGAAAAGCAAAA ↑ 3 1 2 4 Gorilla: CAAATTAAGTGCATTTAAAACCATCTT----GAGAAGGCTTGCCATTCAGAAAAGCAAAA ↓ 3 1 2 4 Human: TAAATTAAGTGCATTTAAAACCATCTTGTCTCAAGATGGTTGCCATTCAGAAAAGCAAAA Cluster: [ ] Orangutan: CAAATTAAGTGCATTTAAGACCATCTT----GAAAAGGCTTGCCATTCAGAAAAGCAAAA Gorilla > Human --------------- chr9:134724331-134724341 Template switch process: F1: L AAAGAAAACAGGACTAAATTAAGTGCATTTAAAACCATCTTG 1 F3: 4 TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG R RF: AAAGAAAACAGGACCAAATTAAGTGCATTTAAAACCATCTTGAGAAGGCTTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG RR: TTTCTTTTGTCCTGGTTTAATTCACGTAAATTTTGGTAGAACTCTTCCGAACGGTAAGTCTTTTCGTTTTATTCATTTTGGGATTCGTC F2: 3 GGTAGAACTCT 2 Unidirectional alignment (log-probability: -39) AGAAAACAGGACtAAATTAAGTGCATTTAAAACCATCTTGtctcaAGAtGG-TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG AGAAAACAGGACCAAATTAAGTGCATTTAAAACCATCTTG-----AGAAGGCTTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG Template switch alignment (log-probability: -22.7) AGAAAACAGGACtAAATTAAGTGCATTTAAAACCATCTTG|TCTCAAGATGG|TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG AGAAAACAGGACCAAATTAAGTGCATTTAAAACCATCTTG|TCTCAAGATGG|TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG Gorilla > Chimp --------------- chr9:113125405-113125415 Template switch process: F1: L CCCAGAAAAGAAAACAGGACTAAATTAAGTGCATTTAAAACGATCTTG 1 F3: 4 TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG R RF: CCCAGAAAAGAAAACAGGACCAAATTAAGTGCATTTAAAACCATCTTGAGAAGGCTTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG RR: GGGTCTTTTCTTTTGTCCTGGTTTAATTCACGTAAATTTTGGTAGAACTCTTCCGAACGGTAAGTCTTTTCGTTTTATTCATTTTGGGATTCGTC F2: 3 GGTAGAACTCT 2 Unidirectional alignment (log-probability: -44.6) AGAAAACAGGACtAAATTAAGTGCATTTAAAACgATCTTGtctcaAGAtGG-TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG AGAAAACAGGACCAAATTAAGTGCATTTAAAACCATCTTG-----AGAAGGCTTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG Template switch alignment (log-probability: -28.3) AGAAAACAGGACtAAATTAAGTGCATTTAAAACgATCTTG|TCTCAAGATGG|TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG AGAAAACAGGACCAAATTAAGTGCATTTAAAACCATCTTG|TCTCAAGATGG|TTGCCATTCAGAAAAGCAAAATAAGTAAAACCCTAAGCAG ========== Event 3801 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CATAGTGGATTATGGGCATCT----GAAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGC ↓ 1 4 3 2 Chimp: CATAGTGGATTATGGGCATCTGCCATGGGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGC ↑ 1 4 3 2 Gorilla: CATAGTGGATTATGGGCATCT----GAAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGC Human: CATAGTGGATTATGGGCATCT----GAAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGC Cluster: [ ] Orangutan: CATAGTGGATTATGGGCATCT----GAAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGC Human > Chimp ------------- chr9:38511326-38511331 Template switch process: F1: L GTTCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG 1 F3: 4 GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC R RF: GTTCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTGAAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC RR: CAAGTTTCTTCATTATGAAAGTATCACCTAATACCCGTAGACTTCGTCCGTTTACGGTACCCTCTAAAGGAATCTTCCTCGAGG F2: 3 GGTACC 2 Unidirectional alignment (log-probability: -28.7) TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTGccatggGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG----AAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC Template switch alignment (log-probability: -16) TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG|CCATGG|GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG|CCATGG|GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC Gorilla > Chimp --------------- chr9:38511326-38511331 Template switch process: F1: L GTTCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG 1 F3: 4 GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC R RF: GTTCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTGAAGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC RR: CAAGTTTCTTCATTATGAAAGTATCACCTAATACCCGTAGACTTCGTCCGTTTACGGTACCCTCTAAAGGAATCTTCCTCGAGG F2: 3 GGTACC 2 Unidirectional alignment (log-probability: -27.7) TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTGccatggGCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTGAA----GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC Template switch alignment (log-probability: -16.5) TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG|CCATGG|GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC TCAAAGAAGTAATACTTTCATAGTGGATTATGGGCATCTG|CCATGG|GCAGGCAAATGCCATGGGAGATTTCCTTAGAAGGAGCTCC ========== Event 3802 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGTAGTCAGAGCTGCCCTAGACTACATGCTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGC ↑ 1 4 3 2 Chimp: TGTAGTCAGAGCTGCCCTAGA--AAAAACTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGC Gorilla: TGTAGTCAGAGCTGCCCTAGA--AAAAACTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGC Human: TGTAGTCAGAGCTGCCCTAGACTACATGCTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGC Cluster: [ ] Orangutan: TGTAGTCAGAGCTGCCCTAGA---AAAACTGCTGAGCACGTGGGT-GGTGGTGGCAGCGAGGC Chimp > Human ------------- chr9:38705906-38705912 Template switch process: F1: L TCCAATCACCTGCTTATTTCTGTAGTCAGAGCTGCCCTAGA 1 F3: 4 CTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGCAGGTC R RF: TCCAATCACCTGCTTATTTCTGTAGTCAGAGCTGCCCTAGAAAAAACTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGCAGGTC RR: AGGTTAGTGGACGAATAAAGACATCAGTCTCGACGGGATCTTTTTTGACGACTCGTACACCCACCCACCACCGTCGCTCCGTCCAG F2: 3 GTACATC 2 Unidirectional alignment (log-probability: -31.5) CCAATCACCTGCTTATTTCTGTAGTCAGAGCTGCCCTAGActacatg-----CTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGCAGGTC CCAATCACCTGCTTATTTCTGTAGTCAGAGCTGCCCTAGA-------AAAAACTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGCAGGTC Template switch alignment (log-probability: -22.1) CCAATCACCTGCTTATTTCTGTAGTCAGAGCTGCCCTAGA|CtACATG|CTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGCAGGTC CCAATCACCTGCTTATTTCTGTAGTCAGAGCTGCCCTAGA|CCACATG|CTGCTGAGCATGTGGGTGGGTGGTGGCAGCGAGGCAGGTC ========== Event 3803 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1234 Detected in comparisons: 1234 Multiple sequence alignment: Human: GGAATAAAAGTTTTGTAACTTAGAGATTACTGGTGAAATCAGGTTCCATCATTGTTGGCCTGACCTATGA ↓ 13 24 ↑ 13 24 Chimp: GGAATAAAAGTTTTGTAACTTTGATTTCACCAGTAATCTCTGGTTCCATCATTGTTGGCCTGACCTATGA Gorilla: GGAATAAAAGTTTTGTAACTTTGATTTCACCAGCAATCTCTGGTTCCATTATTGTTGGCCTGACCTATGA ↓ 13 24 ↑ 13 24 Human: GGAATAAAAGTTTTGTAACTTAGAGATTACTGGTGAAATCAGGTTCCATCATTGTTGGCCTGACCTATGA Cluster: [ ] Orangutan: GGAATAAAAGTTTTGTATCTTTGATTTCACCAGCAATGTCTGGTTCCATCATTGTTGGCCTGACCTATGA Chimp > Human ------------- chr9:134516179-134516198 Template switch process: F1: L AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT 1 F3: 4 GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA R RF: AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTTGATTTCACCAGTAATCTCTGGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA RR: TTACCCAACTTATCCGTCGTCCTTATTTTCAAAACATTGAAACTAAAGTGGTCATTAGAGACCAAGGTAGTAACAACCGGACTGGATACTCAAACCATTAT F2: 3 ACTAAAGTGGTCATTAGAGA 2 Unidirectional alignment (log-probability: -50.9) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACT--------------------TagagattactggtgaaatcaGGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTTGATTTCACCAGTAATCTCT--------------------GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA Template switch alignment (log-probability: -17.8) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|AGAGATTACTGGTGAAATCA|GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|AGAGATTACTGGTGAAATCA|GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA Human > Chimp ------------- chr9:112885505-112885524 Template switch process: F1: L AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT 1 F3: 4 GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA R RF: AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTAGAGATTACTGGTGAAATCAGGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA RR: TTACCCAACTTATCCGTCGTCCTTATTTTCAAAACATTGAATCTCTAATGACCACTTTAGTCCAAGGTAGTAACAACCGGACTGGATACTCAAACCATTAT F2: 3 TCTCTAATGACCACTTTAGT 2 Unidirectional alignment (log-probability: -50.9) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT--------------------tgatttcaccagtaatctctGGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTAGAGATTACTGGTGAAATCA--------------------GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA Template switch alignment (log-probability: -17.8) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|TGATTTCACCAGTAATCTCT|GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|TGATTTCACCAGTAATCTCT|GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA Gorilla > Human --------------- chr9:134516179-134516198 Template switch process: F1: L AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT 1 F3: 4 GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATATGTGGTTTT R RF: AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTTGATTTCACCAGCAATCTCTGGTTCCATTATTGTTGGCCTGACCTATGAGTTTGGTAATATGTGGTTTT RR: TTACCCAACTTATCCGTCGTCCTTATTTTCAAAACATTGAAACTAAAGTGGTCGTTAGAGACCAAGGTAATAACAACCGGACTGGATACTCAAACCATTATACACCAAAA F2: 3 ACTAAAGTGGTCATTAGAGA 2 Unidirectional alignment (log-probability: -55.3) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTagagattactggTGAaaTCA------------GGTTCCATcATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT------------TGATTTCACCAGCAATCTCTGGTTCCATTATTGTTGGCCTGACCTATGAGTTTGGTAATA Template switch alignment (log-probability: -29.5) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|AGAGATTaCTGGTGAAATCA|GGTTCCATcATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|AGAGATTGCTGGTGAAATCA|GGTTCCATTATTGTTGGCCTGACCTATGAGTTTGGTAATA Human > Gorilla --------------- chr9:46143768-46143787 Template switch process: F1: L AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT 1 F3: 4 GGTTCCATTATTGTTGGCCTGACCTATGAGTTTGGTAATATGTGGTTTT R RF: AATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTAGAGATTACTGGTGAAATCAGGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATATGTGGTTTT RR: TTACCCAACTTATCCGTCGTCCTTATTTTCAAAACATTGAATCTCTAATGACCACTTTAGTCCAAGGTAGTAACAACCGGACTGGATACTCAAACCATTATACACCAAAA F2: 3 TCTCTAACGACCACTTTAGT 2 Unidirectional alignment (log-probability: -55.3) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT------------TGAttTCAccagcaatctctGGTTCCATtATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTTAGAGATTACTGGTGAAATCA------------GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA Template switch alignment (log-probability: -29.5) ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|TGATTTCACCAGcAATCTCT|GGTTCCATtATTGTTGGCCTGACCTATGAGTTTGGTAATA ATGGGTTGAATAGGCAGCAGGAATAAAAGTTTTGTAACTT|TGATTTCACCAGTAATCTCT|GGTTCCATCATTGTTGGCCTGACCTATGAGTTTGGTAATA ========== Event 3804 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TGATGTACCTAGCACATGAGTTTCAAAGTTTTCACTCTCCAAGAATTTTCATAAGGTCAGTTTAATTATTAATAGCATGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAAC--AATGTGAAACTATAGAATTGTATG ↓ 3 2 1 4 Chimp: TGATGTACCTAGCACATGAGTTTCAAAGTTTTCACTCTCCAAGAATTTTCATAAGGTCAGTTTAATTATTAATAGCATGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAATGAAACGTGAAACTATAGAATTGTATG Gorilla: Human: TGATGTACCTAGCACATGAGTTTCAAAGTTTTCACTCTCCAAGAATTTTCATAAGGTCAGTTTAATTATTAATAGCATGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAAC--AATGTGAAACTATAGAATTGTATG Cluster: [ ] Orangutan: Human > Chimp ------------- chr9:40918990-40918995 Template switch process: F1: L ATGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAA 1 F3: 4 GTGAAACTATAGAATTGTATGAAATAAAAAATAAGAATAT R RF: GTTTCAAAGTTTTCACTCTCCAAGAATTTTCATAAGGTCAGTTTAATTATTAATAGCATGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAACAATGTGAAACTATAGAATTGTATGAAATAAAAAATAAGAATAT RR: CAAAGTTTCAAAAGTGAGAGGTTCTTAAAAGTATTCCAGTCAAATTAATAATTATCGTACAAAATGTCAATATCTTAATTACGTATTTATGTCATTTTGTTACACTTTGATATCTTAACATACTTTATTTTTTATTCTTATA F2: 3 CAAAGT 2 Unidirectional alignment (log-probability: -25.8) TGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAAtgaAAcGTGAAACTATAGAATTGTATGAAATAAAAAATAAGAATAT TGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAA--CAATGTGAAACTATAGAATTGTATGAAATAAAAAATAAGAATAT Template switch alignment (log-probability: -16) TGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAA|TGAAAC|GTGAAACTATAGAATTGTATGAAATAAAAAATAAGAATAT TGTTTTACAGTTATAGAATTAATGCATAAATACAGTAAAA|TGAAAC|GTGAAACTATAGAATTGTATGAAATAAAAAATAAGAATAT ========== Event 3805 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: CACGGGATGTGCTTCTTGGTCCTGAGACCAGTGTACCCCTTGGCCAGC Chimp: CACGGGATGTGCTTCTTGGTCCTGAGACCAATGTACCCCTTGGCCAGC ↑ 31 2 4 Gorilla: CACGGGATGTGCTTCTTGGTCTCAGGGCCAATGTACCCCTTGGCCAGC Human: CACGGGATGTGCTTCTTGGTCCTGAGACCAGTGTACCCCTTGGCCAGC Cluster: [ ] Orangutan: CACGGGATGTGCTTCTTGGTCTCAGGGCCAATATACCCCTTGGCCAGC Gorilla > Chimp --------------- chr9:111683309-111683314 Template switch process: F1: L TCAAGCTCTTGTGCTGGCGGCACGGGATGTGCTTCTTGGTC 1 F3: 4 CCAATGTACCCCTTGGCCAGCCCGAAGTCGATGATGTGGA R RF: TCAAGCTCTTGTGCTGGCGGCACGGGATGTGCTTCTTGGTCTCAGGGCCAATGTACCCCTTGGCCAGCCCGAAGTCGATGATGTGGA RR: AGTTCGAGAACACGACCGCCGTGCCCTACACGAAGAACCAGAGTCCCGGTTACATGGGGAACCGGTCGGGCTTCAGCTACTACACCT F2: 3 AGAGTC 2 Unidirectional alignment (log-probability: -28.8) CAAGCTCTTGTGCTGGCGGCACGGGATGTGCTTCTTGGTCctgaGaCCAATGTACCCCTTGGCCAGCCCGAAGTCGATGATGTGGA CAAGCTCTTGTGCTGGCGGCACGGGATGTGCTTCTTGGTCTCAGGGCCAATGTACCCCTTGGCCAGCCCGAAGTCGATGATGTGGA Template switch alignment (log-probability: -16.5) CAAGCTCTTGTGCTGGCGGCACGGGATGTGCTTCTTGGTC|CTGAGA|CCAATGTACCCCTTGGCCAGCCCGAAGTCGATGATGTGGA CAAGCTCTTGTGCTGGCGGCACGGGATGTGCTTCTTGGTC|CTGAGA|CCAATGTACCCCTTGGCCAGCCCGAAGTCGATGATGTGGA ========== Event 3806 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATAGATTTGGAGAGAGCAACTCCAACCTGAATTTCAGGGTTATGCCTGAAAATCCCAGA-------AAGTCCTGGTGGTGAGTACTAGTCTACAAAGAGGGATGCAGTTCTGAGCTGAAAAGTCCATTGCACTGAGCTGGGTTCTATAATAGCCT Chimp: ATAGATTTGGGGAGAGCAACTTCAACCTGAATTTCAGGGTTATGCCTGAAAATCCCAGA------------------------------------------------------------------------------------------------ Gorilla: ATAGATTTGGGGAGAGCAACTTCAGCCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAAAGTCCT----------------------------------------------------------------------------------------- ↑ 1 4 3 2 Human: ATAGATTTGGAGAGAGCAACTCCAACCTGAATTTCAGGGTTATGCCTGAAAATCCCAGA-------AAGTCCTGGTGGTGAGTACTAGTCTACAAAGAGGGATGCAGTTCTGAGCTGAAAAGTCCATTGCACTGAGCTGGGTTCTATAATAGCCT Cluster: [ ] Orangutan: ATAGATTTGGGGAGAGCAACTTCAACCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAAAGTCCT----------------------------------------------------------------------------------------- Human > Gorilla --------------- chr9:44052840-44052843 Template switch process: F1: L GATATAAGCCCCTTGTGTCAATAGATTTGGGGAGAGCAACT 1 F3: 4 CCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAAAGTCC R RF: GATATAAGCCCCTTGTGTCAATAGATTTGGAGAGAGCAACTCCAACCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAAAGTCCTGGTGGTGAGTACTAGTCTACAAAGAGGGATGCAGTTCTGAGCTGAAAAGTCCATTGCACTGA RR: CTATATTCGGGGAACACAGTTATCTAAACCTCTCTCGTTGAGGTTGGACTTAAAGTCCCAATACGGACTTTTAGGGTCTTTCAGGACCACCACTCATGATCAGATGTTTCTCCCTACGTCAAGACTCGACTTTTCAGGTAACGTGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -33) ATATAAGCCCCTTGTGTCAATAGATTTGGgGAGAGCAACTtCAgCCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAaagtcc ATATAAGCCCCTTGTGTCAATAGATTTGGAGAGAGCAACTCCAACCTGAATTTCAGGGTTATGCCTGAAAATCCCAGA------ Template switch alignment (log-probability: -21.7) ATATAAGCCCCTTGTGTCAATAGATTTGGgGAGAGCAACT|TCAG|CCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAAAGTCC ATATAAGCCCCTTGTGTCAATAGATTTGGAGAGAGCAACT|TCAG|CCTGAATTTCAGGGTTATGCCTGAAAATCCCAGAAAGTCC ========== Event 3807 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATGG-GGGCAAATAGGATCCCA--------------------------------------------ATTATTGAAGTcagaggttggcaaactat ↓ 43 1 2 Chimp: AATGG-GGGCAAATAGGATCCCA----------------------ATTATTTTCAAAAATTTGCCCAATTATTGAAGTcagaggttggcaaactat Gorilla: AATGG-GGGCAAATAGGATCCCAATTATTTTCAAAAATTTGCCCA----------------------ATTATTGAAGTcagaggttggcaaactat Human: AATGG-GGGCAAATAGGATCCCA--------------------------------------------ATTATTGAAGTcagaggttggcaaactat Cluster: [ ] Orangutan: AATGGGGGGCAAATAGGATCCCAATTATTTTCAAAAATTTGCCCA----------------------ATTATTGAAGTcagaggttggcaaactat Human > Chimp ------------- chr9:7354161-7354172 Template switch process: F1: L CCTCTAAGGGACCCAAATGAATGGGGGCAAATAGGATCCCAATTATT 1 F3: 4 CCCAATTATTGAAGTCAGAGGTTGGCAAACTATGGCCTTTGGGC R RF: CCTCTAAGGGACCCAAATGAATGGGGGCAAATAGGATCCCAATTATTGAAGTCAGAGGTTGGCAAACTATGGCCTTTGGGC RR: GGAGATTCCCTGGGTTTACTTACCCCCGTTTATCCTAGGGTTAATAACTTCAGTCTCCAACCGTTTGATACCGGAAACCCG F2: 3 GTTTAAAAACTT 2 Unidirectional alignment (log-probability: -42.6) GGGACCCAAATGAATGGGGGCAAATAGGATCCCAATTATtttcaaaaatttgcccaattatTGAAGTCAGAGGTTGGCAAACTATGGCCTTT GGGACCCAAATGAATGGGGGCAAATAGGATCCCAATTAT----------------------TGAAGTCAGAGGTTGGCAAACTATGGCCTTT Template switch alignment (log-probability: -28.9) GGGACCCAAATGAATGGGGGCAAATAGGATCCCAATTATT|TTCAAaAATTtG|CCCAATTATTGAAGTCAGAGGTTGGCAAACTATGGCCTTT GGGACCCAAATGAATGGGGGCAAATAGGATCCCAATTATT|TTCAATAATTGG|CCCAATTATTGAAGTCAGAGGTTGGCAAACTATGGCCTTT ========== Event 3808 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTCTCATCACACTATAAC----CCT-TAGACCAGGCTGCAAGTGGCCACACTAGACCCTGTAACTTTTCCTATTTTGTTC Chimp: TGTCTCATCACACTGTAACCTGGTCTAAGGACCAGGCTGCAAGTGGCCACACTAGACCCTGTAACTTTTCCTATTTTGTTC ↑ 13 4 2 Gorilla: TGTCTCATCACACTATAAC----CCT-TAGACCAGGCTGCAAGTGGCCACACTAGAACCTATAACTTTTCCTATTTTGTTC Human: TGTCTCATCACACTATAAC----CCT-TAGACCAGGCTGCAAGTGGCCACACTAGACCCTGTAACTTTTCCTATTTTGTTC Cluster: [ ] Orangutan: TGTCTCATCACACTATAAC----CCT-TAGACCAGGCTGCACATGGCCACACTAGACCCTATAACTTTTCCTATTTTGTTC Gorilla > Chimp --------------- chr9:7287047-7287055 Template switch process: F1: L TAACC 1 F3: 4 GACCAGGCTGCAAGTGGCCACACTAGACCCTGTAACTTTTCCTATTTTGTTCCCTACATGAATTTTGAAATA R RF: TAACCCTTAGACCAGGCTGCAAGTGGCCACACTAGAACCTATAACTTTTCCTATTTTGTTCCCTACATGAATTTTGAAATA RR: ATTGGGAATCTGGTCCGACGTTCACCGGTGTGATCTTGGATATTGAAAAGGATAAAACAAGGGATGTACTTAAAACTTTAT F2: 3 GAATCTGGT 2 Unidirectional alignment (log-probability: -43.8) TAacctggtctaagGACCAGGCTGCAAGTGGCCACACTAGAcCCTgTAACTTTT TA------------GACCAGGCTGCAAGTGGCCACACTAGAACCTATAACTTTT Template switch alignment (log-probability: -27.8) TAACC|TGGTCTAAG|GACCAGGCTGCAAGTGGCCACACTAGAcCCTgTAACTTTT TAACC|TGGTCTAAG|GACCAGGCTGCAAGTGGCCACACTAGAACCTATAACTTTT ========== Event 3809 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CACTAAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCT------TTTCTTACAGTGTATTGGTGGG Chimp: CACTAAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCT------TTTCTTACAGTGTATTGGTGGG ↓ 3 2 1 4 Gorilla: CACTAAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAAAAGAATTACCAAATTCTTACAGTGTATTGGTGGG ↑ 3 2 1 4 Human: CACTAAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCT------TTTCTTACAGTGTATTGGTGGG Cluster: [ ] Orangutan: CACTAAGCTTTATTAACTCTTTGGTAATTCTTTTACATCACGTA-ACTGCT------TTTCTTACAGTGTATTGGTGGG Human > Gorilla --------------- chr9:50760066-50760078 Template switch process: F1: L AAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA 1 F3: 4 TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT R RF: AAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCTTTTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT RR: TTTGAAATAATTGAGAAACCATTAAGAAAATGTAGTGCATTAGACGAAAAGAATGTCACATAACCACCCCGTAGACTCATCGTTTATA F2: 3 AAACCATTAAGAA 2 Unidirectional alignment (log-probability: -39.7) AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA-------aagaattaccaaaTTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCTT-------------TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT Template switch alignment (log-probability: -17.4) AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA|AAGAATTACCAAA|TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA|AAGAATTACCAAA|TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT Chimp > Gorilla --------------- chr9:50760066-50760078 Template switch process: F1: L AAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA 1 F3: 4 TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT R RF: AAACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCTTTTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT RR: TTTGAAATAATTGAGAAACCATTAAGAAAATGTAGTGCATTAGACGAAAAGAATGTCACATAACCACCCCGTAGACTCATCGTTTATA F2: 3 AAACCATTAAGAA 2 Unidirectional alignment (log-probability: -39.7) AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA-------aagaattaccaaaTTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAATCTGCTT-------------TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT Template switch alignment (log-probability: -17.4) AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA|AAGAATTACCAAA|TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT AACTTTATTAACTCTTTGGTAATTCTTTTACATCACGTAA|AAGAATTACCAAA|TTCTTACAGTGTATTGGTGGGGCATCTGAGTAGCAAATAT ========== Event 3810 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: GCTCTCCCTAGTGGCCAGTGGGAGACATATCCAAGCATGA----GCCAGTCTCCCA---ACAACGt ↓ 13 24 ↑ 13 24 Chimp: GCTCTCCCTAGTGGCCAGTGG----CTCATGCTTGGATGTGTCTCCCAGTCTCCCA---ACAACGt ↓ 13 24 ↑ 13 24 Gorilla: GCTCTCCCTAGTGGCCAGTGGGAGACACATCCAAGCATGA----GCCAGTCTCCCA---ACAACGt Human: GCTCTCCCTAGTGGCCAGTGGGAGACATATCCAAGCATGA----GCCAGTCTCCCA---ACAACGt Cluster: [ ] Orangutan: GCTCCCTCTAGTGGCCAGTGGTAGACACATCCAAGCATGA----GCCAGCCTCCCAATAACAATGt Chimp > Human ------------- chr9:757746-757765 Template switch process: F1: L CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG 1 F3: 4 CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT R RF: CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGCTCATGCTTGGATGTGTCTCCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT RR: GAGGAGTCGGACTGGATAGTCGAGAGGGATCACCGGTCACCGAGTACGAACCTACACAGAGGGTCAGAGGGTTGTTGCAAATTAAAATAAATAAATAAATA F2: 3 GAGTACGAACCTATACAGAG 2 Unidirectional alignment (log-probability: -50.9) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG--------------------gagacatatccaagcatgagCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGCTCATGCTTGGATGTGTCTC--------------------CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Template switch alignment (log-probability: -23.7) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|GAGACAtATCCAAGCATGAG|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|GAGACACATCCAAGCATGAG|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Human > Chimp ------------- chr9:649867-649886 Template switch process: F1: L CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG 1 F3: 4 CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT R RF: CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGGAGACATATCCAAGCATGAGCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT RR: GAGGAGTCGGACTGGATAGTCGAGAGGGATCACCGGTCACCCTCTGTATAGGTTCGTACTCGGTCAGAGGGTTGTTGCAAATTAAAATAAATAAATAAATA F2: 3 CTCTGTGTAGGTTCGTACTC 2 Unidirectional alignment (log-probability: -50.9) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTG--------------------GCtcatgcttggatgtgtctccCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGGAGACATATCCAAGCATGAGC--------------------CAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Template switch alignment (log-probability: -23.7) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|CTCATGCTTGGATgTGTCTC|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|CTCATGCTTGGATATGTCTC|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Gorilla > Chimp --------------- chr9:649867-649886 Template switch process: F1: L CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG 1 F3: 4 CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT R RF: CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGGAGACACATCCAAGCATGAGCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT RR: GAGGAGTCGGACTGGATAGTCGAGAGGGATCACCGGTCACCCTCTGTGTAGGTTCGTACTCGGTCAGAGGGTTGTTGCAAATTAAAATAAATAAATAAATA F2: 3 CTCTGTGTAGGTTCGTACTC 2 Unidirectional alignment (log-probability: -50.4) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTG--------------------GctcatgcttggatgtgtctcCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGGAGACACATCCAAGCATGAG--------------------CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Template switch alignment (log-probability: -18.3) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|CTCATGCTTGGATGTGTCTC|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|CTCATGCTTGGATGTGTCTC|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Chimp > Gorilla --------------- chr9:72357997-72358016 Template switch process: F1: L CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG 1 F3: 4 CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT R RF: CTCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGCTCATGCTTGGATGTGTCTCCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT RR: GAGGAGTCGGACTGGATAGTCGAGAGGGATCACCGGTCACCGAGTACGAACCTACACAGAGGGTCAGAGGGTTGTTGCAAATTAAAATAAATAAATAAATA F2: 3 GAGTACGAACCTACACAGAG 2 Unidirectional alignment (log-probability: -50.4) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG--------------------gagacacatccaagcatgagCCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGGCTCATGCTTGGATGTGTCTC--------------------CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT Template switch alignment (log-probability: -18.3) TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|GAGACACATCCAAGCATGAG|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT TCCTCAGCCTGACCTATCAGCTCTCCCTAGTGGCCAGTGG|GAGACACATCCAAGCATGAG|CCAGTCTCCCAACAACGTTTAATTTTATTTATTTATTTAT ========== Event 3811 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: TTTATGTCTAATACATGACAGC--------------------------------TGAAATTAATTTGTCTTGATTTGCTCTACTATG--------GGGAATAGTACTATAC-TTACTGTTTTTAGGGAATAGTATTATACTTATT ↓ 1 4 3 2 ↑ 1 3 2 4 Chimp: TTTATGTCTAATACATGACAGTTAGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTT----------------------------------------------CAGCTGTTTTTAGGGAATAGTATTATATTTATT ↓ 1 3 2 4 ↑ 1 4 3 2 Gorilla: TTTATGTCGAATACATGACAGC--------------------------------TGAAATTAATTTGTCTTGATTTGCTCTACTATG--------GGGAATAGTACTATAC-TTACTGTTTTTAGGGAATAGTATTATACTTATT Human: TTTATGTCTAATACATGACAGC--------------------------------TGAAATTAATTTGTCTTGATTTGCTCTACTATG--------GGGAATAGTACTATAC-TTACTGTTTTTAGGGAATAGTATTATACTTATT Cluster: [ ] Orangutan: TTTATGTCTAATACATGACAGC--------------------------------TGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTAC--------TATACTTAACTGTTTTTAGGGAATAGTATTATACTTACT Chimp > Human ------------- chr9:71920250-71920296 Template switch process: F1: L TAAAGCATGTTTCTTAATGTTGAGGCCTGATATAATATAATTTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCTAATACATGACAG 1 F3: 4 TACTTACTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAATTATGACATT R RF: TAAAGCATGTTTCTTAATGTTGAGGCCTG-----ATATAAATTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCTAATACATGACAGTTAGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAGCTGTTTTTAGGGAATAGTATTATATTTATTGTTGGATTAATTATGACATT RR: ATTTCGTACAAAGAATTACAACTCCGGAC-----TATATTTAAAAAACACACGTAATTAGTATATAAAATCCATGAAGTAAAATACAGATTATGTACTGTCAATCATGATAAGGGGTATCATCTCGTTTAGTTCTGTTTAATTAAAGTCGACAAAAATCCCTTATCATAATATAAATAACAACCTAATTAATACTGTAA F2: 3 ATCATGATAAGGGGTATCATCTCGTTTAGTTCTGTTTAATTAAAGTC 2 Unidirectional alignment (log-probability: -125) TATATTTTAGGTACTTCATTTTATGTCTAATACATGACAGctgaaattaatttgtcttgatttgctctactatggggaatagtactatacTTA---------------------------------------------CTGTTTTTAGGGAATAGTATTATAcTTATTGTTG TATATTTTAGGTACTTCATTTTATGTCTAATACATGACAG--------------------------------------------------TTAGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAGCTGTTTTTAGGGAATAGTATTATATTTATTGTTG Template switch alignment (log-probability: -70.3) TATATTTTAGGTACTTCATTTTATGTCTAATACATGACAG|CTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTA|tacttaCTGTTTTTAGGGAATAGTATTATAcTTATTGTTG TATATTTTAGGTACTTCATTTTATGTCTAATACATGACAG|CTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTA|G-----CTGTTTTTAGGGAATAGTATTATATTTATTGTTG Human > Chimp ------------- chr9:49107667-49107712 Template switch process: F1: L TAAAGCATGTTTCTTAATGTTGAGGCCTGATAT-----AAATTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCTAATACATGACAGTT 1 F3: 4 CTGTTTTTAGGGAATAGTATTATATTTATTGTTGGATTAATTATGACATT R RF: TAAAGCATGTTTCTTAATGTTGAGGCCTGATATAATATAATTTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCTAATACATGACAGCTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTATACTTACTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAATTATGACATT RR: ATTTCGTACAAAGAATTACAACTCCGGACTATATTATATTAAAAAAACACACGTAATTAGTATATAAAATCCATGAAGTAAAATACAGATTATGTACTGTCGACTTTAATTAAACAGAACTAAACGAGATGATACCCCTTATCATGATATGAATGACAAAAATCCCTTATCATAATATGAATAACAACCTAATTAATACTGTAA F2: 3 GACTTTAATTAAACAGAACTAAACGAGATGATACCCCTTATCATGA 2 Unidirectional alignment (log-probability: -111) TATTTTAGGTACTTCATTTTATGTCTAATACATGACAG--------------------------------------------------TTAgtactattccccatagtagagcaaatcaagacaaattaatttcagCTGTTTTTAGGGAATAGTATTATAtTTATTGTTGGATTAA TATTTTAGGTACTTCATTTTATGTCTAATACATGACAGCTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTATACTTA---------------------------------------------CTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAA Template switch alignment (log-probability: -50.4) TATTTTAGGTACTTCATTTTATGTCTAATACATGACAGtT|AGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAG|CTGTTTTTAGGGAATAGTATTATAtTTATTGTTGGATTAA TATTTTAGGTACTTCATTTTATGTCTAATACATGACAGCT|AGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAG|CTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAA Gorilla > Chimp --------------- chr9:49107667-49107712 Template switch process: F1: L TAAAGCATGTTTCTTAATGTTGAGGCCTGATATAAA-----TTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCTAATACATGACAGTT 1 F3: 4 CTGTTTTTAGGGAATAGTATTATATTTATTGTTGGATTAATTATGACATT R RF: TAAAGCATGTTTCTTAATGTTGAGGCCTGATATAATATAATTTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCGAATACATGACAGCTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTATACTTACTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAATTATGACATT RR: ATTTCGTACAAAGAATTACAACTCCGGACTATATTATATTAAAAAAACACACGTAATTAGTATATAAAATCCATGAAGTAAAATACAGCTTATGTACTGTCGACTTTAATTAAACAGAACTAAACGAGATGATACCCCTTATCATGATATGAATGACAAAAATCCCTTATCATAATATGAATAACAACCTAATTAATACTGTAA F2: 3 GACTTTAATTAAACAGAACTAAACGAGATGATACCCCTTATCATGA 2 Unidirectional alignment (log-probability: -115) TATTTTAGGTACTTCATTTTATGTCtAATACATGACAG--------------------------------------------------TTAgtactattccccatagtagagcaaatcaagacaaattaatttcagCTGTTTTTAGGGAATAGTATTATAtTTATTGTTGGATTAA TATTTTAGGTACTTCATTTTATGTCGAATACATGACAGCTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTATACTTA---------------------------------------------CTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAA Template switch alignment (log-probability: -55) TATTTTAGGTACTTCATTTTATGTCtAATACATGACAGtT|AGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAG|CTGTTTTTAGGGAATAGTATTATAtTTATTGTTGGATTAA TATTTTAGGTACTTCATTTTATGTCGAATACATGACAGCT|AGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAG|CTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAA Chimp > Gorilla --------------- chr9:53670794-53670840 Template switch process: F1: L TAAAGCATGTTTCTTAATGTTGAGGCCTGATATAATATAATTTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCGAATACATGACAG 1 F3: 4 TACTTACTGTTTTTAGGGAATAGTATTATACTTATTGTTGGATTAATTATGACATT R RF: TAAAGCATGTTTCTTAATGTTGAGGCCTGATATA-----AATTTTTTGTGTGCATTAATCATATATTTTAGGTACTTCATTTTATGTCTAATACATGACAGTTAGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAGCTGTTTTTAGGGAATAGTATTATATTTATTGTTGGATTAATTATGACATT RR: ATTTCGTACAAAGAATTACAACTCCGGACTATAT-----TTAAAAAACACACGTAATTAGTATATAAAATCCATGAAGTAAAATACAGATTATGTACTGTCAATCATGATAAGGGGTATCATCTCGTTTAGTTCTGTTTAATTAAAGTCGACAAAAATCCCTTATCATAATATAAATAACAACCTAATTAATACTGTAA F2: 3 ATCATGATAAGGGGTATCATCTCGTTTAGTTCTGTTTAATTAAAGTC 2 Unidirectional alignment (log-probability: -129) TATATTTTAGGTACTTCATTTTATGTCgAATACATGACAGctgaaattaatttgtcttgatttgctctactatggggaatagtactatacTTA---------------------------------------------CTGTTTTTAGGGAATAGTATTATAcTTATTGTTG TATATTTTAGGTACTTCATTTTATGTCTAATACATGACAG--------------------------------------------------TTAGTACTATTCCCCATAGTAGAGCAAATCAAGACAAATTAATTTCAGCTGTTTTTAGGGAATAGTATTATATTTATTGTTG Template switch alignment (log-probability: -74.9) TATATTTTAGGTACTTCATTTTATGTCgAATACATGACAG|CTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTA|tacttaCTGTTTTTAGGGAATAGTATTATAcTTATTGTTG TATATTTTAGGTACTTCATTTTATGTCTAATACATGACAG|CTGAAATTAATTTGTCTTGATTTGCTCTACTATGGGGAATAGTACTA|G-----CTGTTTTTAGGGAATAGTATTATATTTATTGTTG ========== Event 3812 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACGACAAAGACTATAATTCCTTTCTTTACTGTTAGCTTACTCTTGCCT ↓ 3 2 1 4 Chimp: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAAC-GCAT--GGTA----TACTTTCTTTACTGTTAGCTTACTCTTGCCT ↑ 3 2 1 4 Gorilla: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACGACAAAGACTATAATTCCTTTCTTTGCTGTTAGCTTACTCTTGCCT Human: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACGACAAAGACTATAATTCCTTTCTTTACTGTTAGCTTACTCTTGCCT Cluster: [ ] Orangutan: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACCACAAAGACTATAATTCCTTTCTTTACTGTTAGCTTACTCTTGCCT Human > Chimp ------------- chr9:69113739-69113747 Template switch process: F1: L CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACG 1 F3: 4 CTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTTGTAT R RF: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACGACAAAGACTATAATTCCTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTCGTAT RR: GATGAATAGTAATGGGTTTATATGGTACGTTAAGATAATTGCTGTTTCTGATATTAAGGAAAGAAATGACAATCGAATGAGAACGGAGTTGAAGCATA F2: 3 ATATGGTAC 2 Unidirectional alignment (log-probability: -39.4) ACTTATCATTACCCAAATATACCATGCAATTCTATTAACGcatggtatA---------------CTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTtGTAT ACTTATCATTACCCAAATATACCATGCAATTCTATTAACG--------ACAAAGACTATAATTCCTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTCGTAT Template switch alignment (log-probability: -22.4) ACTTATCATTACCCAAATATACCATGCAATTCTATTAACG|CATGGTATA|CTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTtGTAT ACTTATCATTACCCAAATATACCATGCAATTCTATTAACG|CATGGTATA|CTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTCGTAT Gorilla > Chimp --------------- chr9:69113739-69113747 Template switch process: F1: L CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACG 1 F3: 4 CTTTCTTTACTGTTAGCTTACTCTTGCCTCAACTTTGTATCAGAATCCT R RF: CTACTTATCATTACCCAAATATACCATGCAATTCTATTAACGACAAAGACTATAATTCCTTTCTTTGCTGTTAGCTTACTCTTGCCTCAACTTCGTATCAGAATCCT RR: GATGAATAGTAATGGGTTTATATGGTACGTTAAGATAATTGCTGTTTCTGATATTAAGGAAAGAAACGACAATCGAATGAGAACGGAGTTGAAGCATAGTCTTAGGA F2: 3 ATATGGTAC 2 Unidirectional alignment (log-probability: -44.1) ACTTATCATTACCCAAATATACCATGCAATTCTATTAACG---------------CatggtataCTTTCTTTaCTGTTAGCTTACTCTTGCCTCAACTTtGTAT ACTTATCATTACCCAAATATACCATGCAATTCTATTAACGACAAAGACTATAATTC--------CTTTCTTTGCTGTTAGCTTACTCTTGCCTCAACTTCGTAT Template switch alignment (log-probability: -28.2) ACTTATCATTACCCAAATATACCATGCAATTCTATTAACG|CATGGTATA|CTTTCTTTaCTGTTAGCTTACTCTTGCCTCAACTTtGTAT ACTTATCATTACCCAAATATACCATGCAATTCTATTAACG|CATGGTATA|CTTTCTTTGCTGTTAGCTTACTCTTGCCTCAACTTCGTAT ========== Event 3813 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCTTTGGTTCATCCTGAGTACGTTATAGAACACAC-----TGAAT-GTCTAGCTCATTCCTCTCTAGT Chimp: CCTTTGGTTCATCCTGAGTACGTTATAGAACACAC-----TGAAT-GTCTAGCTCATTCCTCTCTAGT ↓ 3 2 1 4 Gorilla: CCTTTGGTTCATCCTGAGTACGTTATAGAACACATGTTCTATAACGTTCTAGCTCATTCCTCTCTAGT ↑ 3 2 1 4 Human: CCTTTGGTTCATCCTGAGTACGTTATAGAACACAC-----TGAAT-GTCTAGCTCATTCCTCTCTAGT Cluster: [ ] Orangutan: CCTTTGGTTTATCCTGAGTACGTTATAGAACACAC-----TGAATGTTTTAGCTCATTCCTCTCTAGT Human > Gorilla --------------- chr9:53269206-53269218 Template switch process: F1: L TATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACA 1 F3: 4 TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT R RF: TATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACACTGAATGTCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT RR: ATAAACGGGAAACCAAGTAGGACTCATGCAATATCTTGTGTGACTTACAGATCGAGTAAGGAGAGATCATCGAAGTTCGAAAAGAAAA F2: 3 TGCAATATCTTGT 2 Unidirectional alignment (log-probability: -36.7) ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACAC-----ATGttctataacgtTCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACACTGAATG-----------TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT Template switch alignment (log-probability: -17.4) ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACA|TGTTCTATAACGT|TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACA|TGTTCTATAACGT|TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT Chimp > Gorilla --------------- chr9:53269206-53269218 Template switch process: F1: L TATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACA 1 F3: 4 TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT R RF: TATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACACTGAATGTCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT RR: ATAAACGGGAAACCAAGTAGGACTCATGCAATATCTTGTGTGACTTACAGATCGAGTAAGGAGAGATCATCGAAGTTCGAAAAGAAAA F2: 3 TGCAATATCTTGT 2 Unidirectional alignment (log-probability: -36.7) ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACAC-----ATGttctataacgtTCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACACTGAATG-----------TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT Template switch alignment (log-probability: -17.4) ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACA|TGTTCTATAACGT|TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT ATTTGCCCTTTGGTTCATCCTGAGTACGTTATAGAACACA|TGTTCTATAACGT|TCTAGCTCATTCCTCTCTAGTAGCTTCAAGCTTTTCTTTT ========== Event 3814 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTAAGAGATAAACAAAAAGCAAACTCTCTAGGTGGCTGTGATTCAGAGACCC Chimp: TTTAAGAGATAAACAAAAAGCAAACTCTCTAGGTGGCTGTGATTCAGAGACCC ↓ 1 3 4 2 Gorilla: TTTAAGAGATAAACAAAAAGC-ACCTAGAGAGGTGGCTGTGATTCAGAGACCC ↑ 1 3 4 2 Human: TTTAAGAGATAAACAAAAAGCAAACTCTCTAGGTGGCTGTGATTCAGAGACCC Cluster: [ ] Orangutan: TTTAAGAGATAAACAAAAAGCAAACTCTCTAGGTGGCTGTGATTCAGAGACCC Human > Gorilla --------------- chr9:69892361-69892367 Template switch process: F1: L TTTGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA 1 F3: 4 AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC R RF: TTTGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCAAACTCTCTAGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC RR: AAACTTAATCAGAATCCCTTAAATTCTCTATTTGTTTTTCGTTTGAGAGATCCACCGACACTAAGTCTCTGGGTCTTTTGTCTTTTATTG F2: 3 GAGATCC 2 Unidirectional alignment (log-probability: -31.1) TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA--------cctagagAGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCAAACTCTCT-------AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC Template switch alignment (log-probability: -16.6) TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA|CCTAGAG|AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA|CCTAGAG|AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC Chimp > Gorilla --------------- chr9:69892361-69892367 Template switch process: F1: L TTTGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA 1 F3: 4 AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC R RF: TTTGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCAAACTCTCTAGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC RR: AAACTTAATCAGAATCCCTTAAATTCTCTATTTGTTTTTCGTTTGAGAGATCCACCGACACTAAGTCTCTGGGTCTTTTGTCTTTTATTG F2: 3 GAGATCC 2 Unidirectional alignment (log-probability: -31.1) TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA--------cctagagAGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCAAACTCTCT-------AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC Template switch alignment (log-probability: -16.6) TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA|CCTAGAG|AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC TGAATTAGTCTTAGGGAATTTAAGAGATAAACAAAAAGCA|CCTAGAG|AGGTGGCTGTGATTCAGAGACCCAGAAAACAGAAAATAAC ========== Event 3815 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: CCTAAGTAAATAATTAAAGTACT------TAGAAAATAGAAAACGCTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAAATTTTCTAA Chimp: CCTAAGTAAATAATTAAAGTACT------TAGAAAATAGAAAACGCTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAAATTTTCTAA ↑ 1 4 3 2 Gorilla: CCTAAGTAAATAATTAAAGTATT------------TTATTAAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAAATTTTCTAA ↓ 1 4 3 2 Human: CCTAAGTAAATAATTAAAGTACT------TAGAAAATAGAAAACGCTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAAATTTTCTAA Cluster: [ ] Orangutan: CCTAAGTAAATAATCAAAGTACTTAGAAA------ACAGAAAACGCTCTATTATATAGTTTTCTATTTTCTAAGTACTTTAGAAAATTTTCTAA Gorilla > Human --------------- chr9:66185762-66185774 Template switch process: F1: L ATCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTA 1 F3: 4 AAACGCTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAA R RF: ATCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTATTTTATTAAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAA RR: TAGTAAGACATTGGTTTTTAGGATTCATTTATTAATTTCATAAAATAATTTGTGAGATAATATATCCAAAGATAAAAGATTCATGAAATCTTT F2: 3 AGATAAAAGATTC 2 Unidirectional alignment (log-probability: -41.8) TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTAcTTagaaaaTAgaAAACgCTCTATTATATAGGTTTCTATTTTCTAAGTACTTT TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTATTT------TATTAAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTT Template switch alignment (log-probability: -23) TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTA|CTTAGAAAATAGA|AAACgCTCTATTATATAGGTTTCTATTTTCTAAGTACTTT TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTA|CTTAGAAAATAGA|AAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTT Gorilla > Chimp --------------- chr9:67365737-67365749 Template switch process: F1: L ATCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTA 1 F3: 4 AAACGCTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAA R RF: ATCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTATTTTATTAAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTTAGAAA RR: TAGTAAGACATTGGTTTTTAGGATTCATTTATTAATTTCATAAAATAATTTGTGAGATAATATATCCAAAGATAAAAGATTCATGAAATCTTT F2: 3 AGATAAAAGATTC 2 Unidirectional alignment (log-probability: -41.8) TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTAcTTagaaaaTAgaAAACgCTCTATTATATAGGTTTCTATTTTCTAAGTACTTT TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTATTT------TATTAAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTT Template switch alignment (log-probability: -23) TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTA|CTTAGAAAATAGA|AAACgCTCTATTATATAGGTTTCTATTTTCTAAGTACTTT TCATTCTGTAACCAAAAATCCTAAGTAAATAATTAAAGTA|CTTAGAAAATAGA|AAACACTCTATTATATAGGTTTCTATTTTCTAAGTACTTT ========== Event 3816 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTAAGGGGAAAGGGGTCTGGGGA---------ACAGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATA Chimp: TTTTAAGGGGAAAGGGGTCTGGGGA---------ACAGaaaaaaaGCTGAACTTCTAAAACCTGCATCAGAATA ↓ 1 4 3 2 Gorilla: TTTTAAGGGGAAAGGGGTCTGAACTTCAGCTTTTTTAGaaaaaaaGCTGAACTTCTAAAACTTGCATCAGAATA ↑ 1 4 3 2 Human: TTTTAAGGGGAAAGGGGTCTGGGGA---------ACAGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATA Cluster: [ ] Orangutan: TTTTAAGGGGAAAGGGGTCTGGGGA---------ACAGA-AAAAAGCTGAACTTCTTAAACTTGCATCAGAATA Human > Gorilla --------------- chr9:67705117-67705131 Template switch process: F1: L GCTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTG 1 F3: 4 AGAAAAAAAGCTGAACTTCTAAAACTTGCATCAGAATATG R RF: GCTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTGGGGAACAGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATATG RR: CGAGGGAAAAGTCTCCTGTGAAAATTCCCCTTTCCCCAGACCCCTTGTCTTTTTTTCGACTTGAAGATTTTGGACGTAGTCTTATAC F2: 3 TTTTTTCGACTTCAA 2 Unidirectional alignment (log-probability: -43.6) CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCT---GAACttcagcttttttAGAAAAAAAGCTGAACTTCTAAAACtTGCATCAGAATATG CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTGGGGAAC------------AGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATATG Template switch alignment (log-probability: -28.7) CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTG|AAcTTCAGCTTTTTT|AGAAAAAAAGCTGAACTTCTAAAACtTGCATCAGAATATG CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTG|AAGTTCAGCTTTTTT|AGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATATG Chimp > Gorilla --------------- chr9:67705117-67705131 Template switch process: F1: L GCTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTG 1 F3: 4 AGAAAAAAAGCTGAACTTCTAAAACTTGCATCAGAATATG R RF: GCTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTGGGGAACAGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATATG RR: CGAGGGAAAAGTCTCCTGTGAAAATTCCCCTTTCCCCAGACCCCTTGTCTTTTTTTCGACTTGAAGATTTTGGACGTAGTCTTATAC F2: 3 TTTTTTCGACTTCAA 2 Unidirectional alignment (log-probability: -43.6) CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCT---GAACttcagcttttttAGAAAAAAAGCTGAACTTCTAAAACtTGCATCAGAATATG CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTGGGGAAC------------AGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATATG Template switch alignment (log-probability: -28.7) CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTG|AAcTTCAGCTTTTTT|AGAAAAAAAGCTGAACTTCTAAAACtTGCATCAGAATATG CTCCCTTTTCAGAGGACACTTTTAAGGGGAAAGGGGTCTG|AAGTTCAGCTTTTTT|AGAAAAAAAGCTGAACTTCTAAAACCTGCATCAGAATATG ========== Event 3817 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGATGAGGGCGGTTTTCAGC-----ACCTCTTGAAAAGCAGTATT--AATGTCCATTACACCTCCAGCAATCCACAGCTA Chimp: TGGATGAGGGCGGTTTTCAGC-----ACCTCTTGAAAAGCAGTATT--AACGTCCATTACACCTCCAGCAATCCACAGCTA ↓ 1 3 4 2 Gorilla: TGGATGAGGGCGGTTTTCAGC----------ATGTAAAGGA-CGTT----AGTCCATTACACCTCCAGCAATCCACAGCTA ↑ 1 3 4 2 Human: TGGATGAGGGCGGTTTTCAGC-----ACCTCTTGAAAAGCAGTATT--AATGTCCATTACACCTCCAGCAATCCACAGCTA Cluster: [ ] Orangutan: TGGATGAGGGCAGTTTTCAGCACCTC-----TTGTAAAGCAGTATTAA--CGTCCATTACACCTCCAGCAATCCACAGCTA Human > Gorilla --------------- chr9:67458436-67458449 Template switch process: F1: L TTCCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA 1 F3: 4 GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA R RF: TTCCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCACCTCTTGAAAAGCAGTATTAATGTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA RR: AAGGTGTACGATCCGGTGGTACCTACTCCCGCCAAAAGTCGTGGAGAACTTTTCGTCATAATTACAGGTAATGTGGAGGTCGTTAGGTGTCGATACCGCCACCT F2: 3 ATTGCAGGAAATGT 2 Unidirectional alignment (log-probability: -40.4) CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGC---------------------ATgtaaaggacgttaGTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCACCTCTTGAAAAGCAGTATTAAT-------------GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA Template switch alignment (log-probability: -28.6) CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA|TGTAAaGGACgTTA|GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA|TGTAATGGACATTA|GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA Chimp > Gorilla --------------- chr9:67458436-67458449 Template switch process: F1: L TTCCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA 1 F3: 4 GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA R RF: TTCCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCACCTCTTGAAAAGCAGTATTAACGTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA RR: AAGGTGTACGATCCGGTGGTACCTACTCCCGCCAAAAGTCGTGGAGAACTTTTCGTCATAATTGCAGGTAATGTGGAGGTCGTTAGGTGTCGATACCGCCACCT F2: 3 ATTGCAGGAAATGT 2 Unidirectional alignment (log-probability: -41.9) CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA----------------------tgtaaaggacgttaGTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCACCTCTTGAAAAGCAGTATTAAC--------------GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA Template switch alignment (log-probability: -23.1) CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA|TGTAAaGGACGTTA|GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA CCACATGCTAGGCCACCATGGATGAGGGCGGTTTTCAGCA|TGTAATGGACGTTA|GTCCATTACACCTCCAGCAATCCACAGCTATGGCGGTGGA ========== Event 3818 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTAGCATGACGGCTGGCTGCAATTTCTGGCAGTCACCCCAAATTCATCTCTGCCCAAATGCAGACAGGAAGCCAAACACAAAGGTTTGGTGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTTTGTCCAACTCTCAT-GAACATAAA----TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAAACATT ↓ 3 2 4 1 Chimp: TTTAGCATGACTGCTGGCTGCAATTTCTGGCAGTCACCCCAAATTCATCTCTGCCCAAATGCAGACAGGAAGCCAAACACAAAGGCTTGGTGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTTTGTTGAAA-TTAATGTAGCATTAATTGCTTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAAACATT ↑ 3 2 4 1 Gorilla: TTTAGCATGACTGCTGGCTGCAATTTCTGGCAGTCACCCCAAATTCATCTCTGCCCAAATGCAGACAGGAAGCCAAACACAAAAGCTTGGTGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTTTGTCCAACTCTCAC-GAACATAAA----TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAAACATT Human: TTTAGCATGACGGCTGGCTGCAATTTCTGGCAGTCACCCCAAATTCATCTCTGCCCAAATGCAGACAGGAAGCCAAACACAAAGGTTTGGTGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTTTGTCCAACTCTCAT-GAACATAAA----TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAAACATT Cluster: [ ] Orangutan: TTTAGCATGACTGCTGGCTGCAATTTCTGGCAGTCACCCGAAATTCATCTCTGCCCAAATGCGGACAGGAAGCCAAACGCAAAGGCTTGGTCTCAAACAGTTACCTTGGGATCACATTTTTGCTTCTTTGTCCAACTCTCAT-GAACATAAA----TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAAACATT Human > Chimp ------------- chr9:66648066-66648071 Template switch process: F1: L TGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTT---------------------------TGTTGAAATTAATGTAGCATT 1 F3: 4 TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA R RF: GCAATTTCTGGCAGTCACCCCAAATTCATCTCTGCCCAAATGCAGACAGGAAGCCAAACACAAAGGTTTGGTGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTTTGTCCAACTCTCATGAACATAAATTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA RR: CGTTAAAGACCGTCAGTGGGGTTTAAGTAGAGACGGGTTTACGTCTGTCCTTCGGTTTGTGTTTCCAAACCACAGTTTGTCAGTTGAACCCTAGTGTAAAAACGAAGAAACAGGTTGAGAGTACTTGTATTTAAGTACAACTTTAATTACATCGTAAGAAAGTTTACAACTT F2: 3 CGTTAA 2 Unidirectional alignment (log-probability: -55.2) GATCACATTTTTGCTTCTTTGTtgaaattaatgtagcattaattgC-------------------TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA GATCACATTTTTGCTTCTTTGT-----------------------CCAACTCTCATGAACATAAATTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA Template switch alignment (log-probability: -28) GATCACATTTTTGCTTCTT---------------------------TGTTGAAATTAATGTAGCATT|AATTGC|TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA GATCACATTTTTGCTTCTTTGTCCAACTCTCATGAACATAAATTCATGTTGAAATTAATGTAGCATT|AATTGC|TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA Gorilla > Chimp --------------- chr9:66648066-66648071 Template switch process: F1: L TGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTT---------------------------TGTTGAAATTAATGTAGCATT 1 F3: 4 TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA R RF: GCAATTTCTGGCAGTCACCCCAAATTCATCTCTGCCCAAATGCAGACAGGAAGCCAAACACAAAAGCTTGGTGTCAAACAGTCAACTTGGGATCACATTTTTGCTTCTTTGTCCAACTCTCACGAACATAAATTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA RR: CGTTAAAGACCGTCAGTGGGGTTTAAGTAGAGACGGGTTTACGTCTGTCCTTCGGTTTGTGTTTTCGAACCACAGTTTGTCAGTTGAACCCTAGTGTAAAAACGAAGAAACAGGTTGAGAGTGCTTGTATTTAAGTACAACTTTAATTACATCGTAAGAAAGTTTACAACTT F2: 3 CGTTAA 2 Unidirectional alignment (log-probability: -54.7) GATCACATTTTTGCTTCTTTGTtgaaattaatgtagcattaattgC-------------------TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA GATCACATTTTTGCTTCTTTGT-----------------------CCAACTCTCACGAACATAAATTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA Template switch alignment (log-probability: -28.1) GATCACATTTTTGCTTCTT---------------------------TGTTGAAATTAATGTAGCATT|AATTGC|TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA GATCACATTTTTGCTTCTTTGTCCAACTCTCACGAACATAAATTCATGTTGAAATTAATGTAGCATT|AATTGC|TTCATGTTGAAATTAATGTAGCATTCTTTCAAATGTTGAA ========== Event 3819 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: ATTGGGCACTAAAAGAACACAATG-ATTAGCTACATGCCTATCATATAAACGGCACTGTGATTAGCATCAAGGATa Chimp: ATTGGGCACTAAAAGAACACAGTG--CCGTTTATATGCCTATCATATAAATGGCACTGTGATTAGCATCAGGGATa Gorilla: ATTGGGCACTAAAAGAACACAGTG--CCGTTTATATGCCTATCATATAAATGGCACTGTGATTAGCATCAAGGATa ↑ 1 4 3 2 Human: ATTGGGCACTAAAAGAACACAATG-ATTAGCTACATGCCTATCATATAAACGGCACTGTGATTAGCATCAAGGATa Cluster: [ ] Orangutan: ATTGGGCACTGTAAGAACACAGTGA-TTAGCTACATGCCTATCATATAAACGGCACTGTCATTAGCATCAAGGATa Human > Gorilla --------------- chr9:54976301-54976311 Template switch process: F1: L CCTGAATGAATTGTAGTGTGATTGGGCACTAAAAGAACACA 1 F3: 4 ATGCCTATCATATAAATGGCACTGTGATTAGCATCAAGGA R RF: CCTGAATGAATTGTATTGTGATTGGGCACTAAAAGAACACAATGATTAGCTACATGCCTATCATATAAACGGCACTGTGATTAGCATCAAGGA RR: GGACTTACTTAACATAACACTAACCCGTGATTTTCTTGTGTTACTAATCGATGTACGGATAGTATATTTGCCGTGACACTAATCGTAGTTCCT F2: 3 TATTTGCCGTG 2 Unidirectional alignment (log-probability: -45.1) CTGAATGAATTGTAgTGTGATTGGGCACTAAAAGAACACAgtgccgtttAT----------ATGCCTATCATATAAAtGGCACTGTGATTAGCATCAAGGA CTGAATGAATTGTATTGTGATTGGGCACTAAAAGAACACA---------ATGATTAGCTACATGCCTATCATATAAACGGCACTGTGATTAGCATCAAGGA Template switch alignment (log-probability: -28.2) CTGAATGAATTGTAgTGTGATTGGGCACTAAAAGAACACA|GTGCCGTTTAT|ATGCCTATCATATAAAtGGCACTGTGATTAGCATCAAGGA CTGAATGAATTGTATTGTGATTGGGCACTAAAAGAACACA|GTGCCGTTTAT|ATGCCTATCATATAAACGGCACTGTGATTAGCATCAAGGA ========== Event 3820 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGTTAACTGTCTCCCCCTCTGTGGGTATGGCTCAGTTCCAACAAAATAGCTT ↓ 1 3 4 2 Chimp: TGTTAACTGTCTCCCCCTCTG-AGCCATAGCTCAGTTCCAACAAAATAGCTT Gorilla: TGTTAACTGTCTCCCCCTCTGTGGGTATGGCTCAGTTCCAACAAAATAGCTT Human: TGTTAACTGTCTCCCCCTCTGTGGGTATGGCTCAGTTCCAACAAAATAGCTT Cluster: [ ] Orangutan: TGTTAACTGTCTCCCCCTCTGTGGGTATGGCTCAGTTCCAACAAAATAGCTT Human > Chimp ------------- chr9:64947510-64947516 Template switch process: F1: L GTGCTACATAAGTCAAGAATTGTTAACTGTCTCCCCCTCTG 1 F3: 4 GCTCAGTTCCAACAAAATAGCTTAGGGTCATAACAGTCTG R RF: GTGCTACATAACTCAAGAATTGTTAACTGTCTCCCCCTCTGTGGGTATGGCTCAGTTCCAACAAAATAGCTTAGGGTCATAACAGTCTG RR: CACGATGTATTGAGTTCTTAACAATTGACAGAGGGGGAGACACCCATACCGAGTCAAGGTTGTTTTATCGAATCCCAGTATTGTCAGAC F2: 3 ATACCGA 2 Unidirectional alignment (log-probability: -37.6) TGCTACATAAgTCAAGAATTGTTAACTGTCTCCCCCTC--------TGagccataGCTCAGTTCCAACAAAATAGCTTAGGGTCATAACAGTCTG TGCTACATAACTCAAGAATTGTTAACTGTCTCCCCCTCTGTGGGTATG-------GCTCAGTTCCAACAAAATAGCTTAGGGTCATAACAGTCTG Template switch alignment (log-probability: -22.1) TGCTACATAAgTCAAGAATTGTTAACTGTCTCCCCCTCTG|AGCCATA|GCTCAGTTCCAACAAAATAGCTTAGGGTCATAACAGTCTG TGCTACATAACTCAAGAATTGTTAACTGTCTCCCCCTCTG|AGCCATA|GCTCAGTTCCAACAAAATAGCTTAGGGTCATAACAGTCTG ========== Event 3821 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGCAATCATTAATTTGATCTGCAAGG----TAATCGTGTACCAGGCATTAATG Chimp: TTGCAATCATTAATTTGATCTGCAAGG----TAATCGTGTACCAGGCATTAATG ↓ 3 1 2 4 Gorilla: TTGCAATCATTAATTTGATCTGCAACCTTGCAGATCGTGTACCAGGCATTAATG ↑ 3 1 2 4 Human: TTGCAATCATTAATTTGATCTGCAAGG----TAATCGTGTACCAGGCATTAATG Cluster: [ ] Orangutan: ------------------------------------------------------ Human > Gorilla --------------- chr9:65870847-65870854 Template switch process: F1: L TAATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAA 1 F3: 4 ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT R RF: TAATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAAGGTAATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT RR: ATTAAAGTGTGACTTTAACGTTAGTAATTAAACTAGACGTTCCATTAGCACATGGTCCGTAATTACAGTCGTCTATTGTCTCGTA F2: 3 GACGTTCC 2 Unidirectional alignment (log-probability: -30.9) AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAaccttgcAG---ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCA-------AGGTAATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT Template switch alignment (log-probability: -16.7) AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAA|CCTTGCAG|ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAA|CCTTGCAG|ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT Chimp > Gorilla --------------- chr9:65870847-65870854 Template switch process: F1: L TAATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAA 1 F3: 4 ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT R RF: TAATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAAGGTAATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT RR: ATTAAAGTGTGACTTTAACGTTAGTAATTAAACTAGACGTTCCATTAGCACATGGTCCGTAATTACAGTCGTCTATTGTCTCGTA F2: 3 GACGTTCC 2 Unidirectional alignment (log-probability: -30.9) AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAaccttgcAG---ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCA-------AGGTAATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT Template switch alignment (log-probability: -16.7) AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAA|CCTTGCAG|ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT AATTTCACACTGAAATTGCAATCATTAATTTGATCTGCAA|CCTTGCAG|ATCGTGTACCAGGCATTAATGTCAGCAGATAACAGAGCAT ========== Event 3822 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ACTAAACTGTCCTGCCCTTGAATCAATCCTTTATTGATTGATTCAAGGGAGGGGTGAAATGCATAAAAAACCATT ↑ 3 2 1 4 Chimp: ACTAAACTGTCCTGCCCTTGAATCAATCCTTTAT------TTTTAAGGGAAGGGGGAAATGCATAAAAAACCATT Gorilla: ACTAAACTGTCCTGCCCTTGAATCAATTCTTTAT------TTTTAAGGGAGGGGGGAAATGCATAAAAAACCATT Human: ACTAAACTGTCCTGCCCTTGAATCAATCCTTTATTGATTGATTCAAGGGAGGGGTGAAATGCATAAAAAACCATT Cluster: [ ] Orangutan: ACTAAACTGTCCTGCCCTTGAATCAATCCTTTAT------TTTTAAGGGAGGGAGGAAATGCATAAAAAACCATT Chimp > Human ------------- chr9:75691459-75691467 Template switch process: F1: L ATTGGTTACTAAACTGTCCTGCCCTTGAATCAATCCTTTATT 1 F3: 4 AAGGGAGGGGTGAAATGCATAAAAAACCATTCCCAACTGAGTGAAGGATGC R RF: ATTGGTTACTAAACTGTCCTGCCCTTGAATCAATCCTTTATTTTTAAGGGAAGGGGGAAATGCATAAAAAACCATTCCCAACTGAGTGAAGGATGC RR: TAACCAATGATTTGACAGGACGGGAACTTAGTTAGGAAATAAAAATTCCCTTCCCCCTTTACGTATTTTTTGGTAAGGGTTGACTCACTTCCTACG F2: 3 CTTAGTTAG 2 Unidirectional alignment (log-probability: -37.7) TGGTTACTAAACTGTCCTGCCCTTGAATCAATCCTTTATTgattgaTTcAAGGGAgGGGtGAAATGCATAAAAAACCATTCCCAACTGA TGGTTACTAAACTGTCCTGCCCTTGAATCAATCCTTTATT------TTTAAGGGAAGGGGGAAATGCATAAAAAACCATTCCCAACTGA Template switch alignment (log-probability: -28.6) TGGTTACTAAACTGTCCTGCCCTTGAATCAATCCTTTATT|GATTGATTC|AAGGGAgGGGtGAAATGCATAAAAAACCATTCCCAACTGA TGGTTACTAAACTGTCCTGCCCTTGAATCAATCCTTTATT|GATTGATTC|AAGGGAAGGGGGAAATGCATAAAAAACCATTCCCAACTGA ========== Event 3823 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: AGAGTTGTTTAATGGAGGATATGG----ACTTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACACAATCCACAGACCCCCTCCGTGCTTTGAGTGTACTCACAACTGAGACTGGTCCAGGATAAAAACAGGGGATAGC Chimp: AGAGTTGTTTAATGGAGGATATGG----ACTTTGAGGGTAGCTATAGGAAGTGATGGAGGCAGAAAACACAATCCACAGACCCCCTCCGTGCTTTGAGTGTACTCACAACTGAGACTGGTCCAGGATAAAAACAGGGGATAGC ↑ 1 4 3 2 Gorilla: AGAGTTGTTTAATGGAGGATAAACAACTTGTTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACACAATCCACAGACCCCGTCCGTGCTTTGAGTGTACTCACAACTGAGACTGGTCCAGGATAAAAACAGGGGATAGC ↓ 1 4 3 2 Human: AGAGTTGTTTAATGGAGGATATGG----ACTTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACACAATCCACAGACCCCCTCCGTGCTTTGAGTGTACTCACAACTGAGACTGGTCCAGGATAAAAACAGGGGATAGC Cluster: [ ] Orangutan: ----------------------------------------------------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chr9:75491371-75491375 Template switch process: F1: L GACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA 1 F3: 4 TTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC R RF: GACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATAAACAACTTGTTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACACAATCCACAGACCCCGTCCGTGCTTTGAGTGTACTCACAACTGAGACTGGTCCA RR: CTGTAAGTAAACATCCTAGATCTCAACAAATTACCTCCTATTTGTTGAACAAACTCCCATCGATATCCTACACTACCCCCGTCTTTTGTGTTAGGTGTCTGGGGCAGGCACGAAACTCACATGAGTGTTGACTCTGACCAGGT F2: 3 CAGGT 2 Unidirectional alignment (log-probability: -25.3) ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA-------TGgacTTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATAAACAACTTG---TTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC Template switch alignment (log-probability: -16.4) ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA|TGGAC|TTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA|TGGAC|TTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC Gorilla > Chimp --------------- chr9:52727191-52727195 Template switch process: F1: L GACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA 1 F3: 4 TTTGAGGGTAGCTATAGGAAGTGATGGAGGCAGAAAACAC R RF: GACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATAAACAACTTGTTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACACAATCCACAGACCCCGTCCGTGCTTTGAGTGTACTCACAACTGAGACTGGTCCA RR: CTGTAAGTAAACATCCTAGATCTCAACAAATTACCTCCTATTTGTTGAACAAACTCCCATCGATATCCTACACTACCCCCGTCTTTTGTGTTAGGTGTCTGGGGCAGGCACGAAACTCACATGAGTGTTGACTCTGACCAGGT F2: 3 CAGGT 2 Unidirectional alignment (log-probability: -36.4) ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA-------TGgacTTTGAGGGTAGCTATAGGAaGTGATGGaGGCAGAAAACAC ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATAAACAACTTG---TTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC Template switch alignment (log-probability: -27.4) ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA|TGGAC|TTTGAGGGTAGCTATAGGAaGTGATGGaGGCAGAAAACAC ACATTCATTTGTAGGATCTAGAGTTGTTTAATGGAGGATA|TGGAC|TTTGAGGGTAGCTATAGGATGTGATGGGGGCAGAAAACAC ========== Event 3824 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCATCCCAGGCTTCTTATGTGGGAACAGAAA-------CCTTCGAAGATGTCAGAAGTGAG Chimp: TTCATCCCAGGCTTCTTATGTGAGAACAGAAA-------CCTTCGAAGATGTCAGAAGTGAG ↓ 3 2 1 4 Gorilla: TTCATCCCAGGCTTCTTATGTGAGAACAGAGATGTTCTCACTTCGAAGATGTCAGAAGTGAG Human: TTCATCCCAGGCTTCTTATGTGGGAACAGAAA-------CCTTCGAAGATGTCAGAAGTGAG Cluster: [ ] Orangutan: TTCATCCCAGGCTTCTTATGTGAGAACAGAAA-------CCTTTGAAGATGTCAGAAGTGAG Chimp > Gorilla --------------- chr9:63028535-63028543 Template switch process: F1: L CCATGTGGTCTTTCATCCCAGGCTTCTTATGTGAGAACAGAGA 1 F3: 4 TTCGAAGATGTCAGAAGTGAGAACTTTGGGGGCTGAGAC R RF: CCATGTGGTCTTTCATCCCAGGCTTCTTATGTGAGAACAGAAACCTTCGAAGATGTCAGAAGTGAGAACTTTGGGGGCTGAGAC RR: GGTACACCAGAAAGTAGGGTCCGAAGAATACACTCTTGTCTTTGGAAGCTTCTACAGTCTTCACTCTTGAAACCCCCGACTCTG F2: 3 CACTCTTGT 2 Unidirectional alignment (log-probability: -32) TGTGGTCTTTCATCCCAGGCTTCTTATGTGAGAACAGAgAtgttctcaCTTCGAAGATGTCAGAAGTGAGAACTTTGGGGGCTGAGAC TGTGGTCTTTCATCCCAGGCTTCTTATGTGAGAACAGAAAC-------CTTCGAAGATGTCAGAAGTGAGAACTTTGGGGGCTGAGAC Template switch alignment (log-probability: -22.4) TGTGGTCTTTCATCCCAGGCTTCTTATGTGAGAACAGAgA|TGTTCTCAC|TTCGAAGATGTCAGAAGTGAGAACTTTGGGGGCTGAGAC TGTGGTCTTTCATCCCAGGCTTCTTATGTGAGAACAGAAA|TGTTCTCAC|TTCGAAGATGTCAGAAGTGAGAACTTTGGGGGCTGAGAC ========== Event 3825 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: ATCCCATGAAACACGAGGGTTTAAATAGATGTTG---------------------------------------------------------------TCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCTCTTGGACCCCTTTCTGCT ↓ 4 3 1 2 Chimp: ATCCCATGAAACACGAGGGTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTGAAACATAAGGCCAGCATGCATTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCTCTTGGACCCCTTTCTGCT ↑ 4 3 1 2 Gorilla: ATCCCATGAAACACGAGGGTTTAAATAGATGTTG---------------------------------------------------------------TCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCTCTTGGACCCCTTTCTGCT Human: ATCCCATGAAACACGAGGGTTTAAATAGATGTTG---------------------------------------------------------------TCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCTCTTGGACCCCTTTCTGCT Cluster: [ ] Orangutan: ATCCCATGAAACACGAGGGTTTAAATAGATGTTG---------------------------------------------------------------TCATTCCTGGCTTTAAAATGCCTGCTGGCCTTATGTTTCTCTTGGACCCCTTTCTGCT Human > Chimp ------------- chr9:70143742-70143762 Template switch process: F1: L GTGATCAATCCCATGAAACACGAGGGTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTG 1 F3: 4 TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCT R RF: ATGATCAATCCCATGAAACACGAGGGTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCT RR: TACTAGTTAGGGTACTTTGTGCTCCCAAATTTATCTACAACAGTAAGGACCGAAATTTTACGTACGACCGGAATACAAAGA F2: 3 TACGTACGACCGGAATACAAA 2 Unidirectional alignment (log-probability: -107) taaatagatgttgtcattcctggctttaaaatgcatgctgaaacataaggccagcatgcatTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC -------------------------------------------------------------TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC Template switch alignment (log-probability: -24.6) TAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTG|AAACATAAGGCCAGCATGCAT|TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC TAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTG|AAACATAAGGCCAGCATGCAT|TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC Gorilla > Chimp --------------- chr9:70143742-70143762 Template switch process: F1: L GTGATCAATCCCATGAAACACGAGGGTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTG 1 F3: 4 TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCT R RF: ATGATCAATCCCATGAAACACGAGGGTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTGGCCTTATGTTTCT RR: TACTAGTTAGGGTACTTTGTGCTCCCAAATTTATCTACAACAGTAAGGACCGAAATTTTACGTACGACCGGAATACAAAGA F2: 3 TACGTACGACCGGAATACAAA 2 Unidirectional alignment (log-probability: -107) taaatagatgttgtcattcctggctttaaaatgcatgctgaaacataaggccagcatgcatTTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC -------------------------------------------------------------TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC Template switch alignment (log-probability: -24.9) TAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTG|AAACATAAGGCCAGCATGCAT|TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC TAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGCTG|AAACATAAGGCCAGCATGCAT|TTTAAATAGATGTTGTCATTCCTGGCTTTAAAATGCATGC ========== Event 3826 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GTGTTGAGTGACCTTGAGTGAT--------CTACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTG Chimp: GTGTTGAGTGACCTTGAGTGAT--------CTACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTG ↓ 1 4 3 2 Gorilla: GTGTTGAGTGACCTTGAGTGACTCAATTAGTGACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTG ↑ 1 4 3 2 Human: GTGTTGAGTGACCTTGAGTGAT--------CTACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTG Cluster: [ ] Orangutan: GTGTTGAGTGACCTTAAGTGAT--------CTACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTG Human > Gorilla --------------- chr9:59581754-59581763 Template switch process: F1: L GTCTCAGGGAGACACAGAGGGTGTTGAGTGACCTTGAGTGAC 1 F3: 4 ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT R RF: GTCTCAGGGAGACACAGAAGGTGTTGAGTGACCTTGAGTGATCTACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT RR: CAGAGTCCCTCTGTGTCTTCCACAACTCACTGGAACTCACTAGATGTCTGAGTGATTAACTACGGTCCTCGGTCAGTCCACTGA F2: 3 GTGATTAACT 2 Unidirectional alignment (log-probability: -39.2) CTCAGGGAGACACAGAgGGTGTTGAGTGACCTTGAGTGA-CTcaattagtgACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT CTCAGGGAGACACAGAAGGTGTTGAGTGACCTTGAGTGATCT---------ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT Template switch alignment (log-probability: -28.1) CTCAGGGAGACACAGAgGGTGTTGAGTGACCTTGAGTGAc|TCAATTAGTG|ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT CTCAGGGAGACACAGAAGGTGTTGAGTGACCTTGAGTGAT|TCAATTAGTG|ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT Chimp > Gorilla --------------- chr9:59581754-59581763 Template switch process: F1: L GTCTCAGGGAGACACAGAGGGTGTTGAGTGACCTTGAGTGAC 1 F3: 4 ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT R RF: GTCTCAGGGAGACACAGAAGGTGTTGAGTGACCTTGAGTGATCTACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT RR: CAGAGTCCCTCTGTGTCTTCCACAACTCACTGGAACTCACTAGATGTCTGAGTGATTAACTACGGTCCTCGGTCAGTCCACTGA F2: 3 GTGATTAACT 2 Unidirectional alignment (log-probability: -39.2) CTCAGGGAGACACAGAgGGTGTTGAGTGACCTTGAGTGA-CTcaattagtgACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT CTCAGGGAGACACAGAAGGTGTTGAGTGACCTTGAGTGATCT---------ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT Template switch alignment (log-probability: -28.1) CTCAGGGAGACACAGAgGGTGTTGAGTGACCTTGAGTGAc|TCAATTAGTG|ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT CTCAGGGAGACACAGAAGGTGTTGAGTGACCTTGAGTGAT|TCAATTAGTG|ACAGACTCACTAATTGATGCCAGGAGCCAGTCAGGTGACT ========== Event 3827 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGGAGGTGCCAGGCAGGCAGTTGGCAT----TCCTAGGCCCACTTTACTCCTGGCCCAGGG Chimp: TGGAGGTGCCAGGCAGGCAGTTGGCAT----TCCTAGGCCCACTTTACTCCTGGCCCAGGG ↓ 1 3 4 2 Gorilla: TGGAGGTGCCAGGCAGGCAGTGGGCCTAGGAATCTAGGCCCACTTTACTCCTGGCCCAGGG ↑ 1 3 4 2 Human: TGGAGGTGCCAGGCAGGCAGTTGGCAT----TCCTAGGCCCACTTTACTCCTGGCCCAGGG Cluster: [ ] Orangutan: TGGAGGTGCCAGGCAGGCAGTTGGCAT----TCCTAGGCCCACTTTACTCCTGGCCCAGGG Human > Gorilla --------------- chr9:61789508-61789519 Template switch process: F1: L TAAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGT 1 F3: 4 CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT R RF: TAAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGTTGGCATTCCTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT RR: ATTCTTTTCGAATTAAGGTGACCTCCACGGTCCGTCCGTCAACCGTAAGGATCCGGGTGAAATGAGGACCGGGTCCCGGAAGAGGAGTA F2: 3 TAAGGATCCGGG 2 Unidirectional alignment (log-probability: -35) AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGTgGGCctaggaAT--CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGTTGGC------ATTCCTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT Template switch alignment (log-probability: -17.3) AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGT|GGGCCTAGGAAT|CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGT|GGGCCTAGGAAT|CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT Chimp > Gorilla --------------- chr9:61789508-61789519 Template switch process: F1: L TAAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGT 1 F3: 4 CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT R RF: TAAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGTTGGCATTCCTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT RR: ATTCTTTTCGAATTAAGGTGACCTCCACGGTCCGTCCGTCAACCGTAAGGATCCGGGTGAAATGAGGACCGGGTCCCGGAAGAGGAGTA F2: 3 TAAGGATCCGGG 2 Unidirectional alignment (log-probability: -35) AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGTgGGCctaggaAT--CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGTTGGC------ATTCCTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT Template switch alignment (log-probability: -17.3) AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGT|GGGCCTAGGAAT|CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT AAGAAAAGCTTAATTCCACTGGAGGTGCCAGGCAGGCAGT|GGGCCTAGGAAT|CTAGGCCCACTTTACTCCTGGCCCAGGGCCTTCTCCTCAT ========== Event 3828 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GGCAAACTCTTTCAACACCTCTTGCATTCTTGACAACAAGAATT---CTTGCATT---------------------CTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAG Chimp: GGCAAACTCTTTCAACACCTCTTGCATTCTTGACAACAAGAATT---CTTGCATT---------------------CTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAA ↑ 4 3 1 2 Gorilla: GGCAAACTCTTTCAACACCTCTTGCATTCTTGTTGTCAAGAATG------CCCTT------------------------------------------CTTCCCAATATCCAATTCAA ↓ 4 3 1 2 Human: GGCAAACTCTTTCAACACCTCTTGCATTCTTGACAACAAGAATT---CTTGCATT---------------------CTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAG Cluster: [ ] Orangutan: GGCAAACTCTTTCAACACCtcttgcattcttgacaacaagaattctt---gcattcttgttatcaagaatGCCCTT---------------------CTTCCCAATATCCAATTCAA Gorilla > Human --------------- chr9:8093395-8093405 Template switch process: F1: L TTCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTG 1 F3: 4 TCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAGCTACTACATGATAAAGGGAG R RF: TTCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAACTACTACATGATAAAAGAAG RR: AAGGTTTTACCGTTTGAGAAAGTTGTGGAGAACGTAAGAACAACAGTTCTTACGGGAAGAAGGGTTATAGGTTAAGTTGATGATGTACTATTTTCTTC F2: 3 TAAGAACAACA 2 Unidirectional alignment (log-probability: -62.2) TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTtgacaacaagaattcttgcattctTGTTGTCAAGAATGCCCTTCTTCCCAATA TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCT------------------------TGTTGTCAAGAATGCCCTTCTTCCCAATA Template switch alignment (log-probability: -34.4) TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTG|ACAACAAGAAT|TCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATA TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTG|ACAACAAGAAT|TCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATA Gorilla > Chimp --------------- chr9:8235362-8235372 Template switch process: F1: L TTCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTG 1 F3: 4 TCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAACTACTACATGATAAAGGGAG R RF: TTCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATATCCAATTCAACTACTACATGATAAAAGAAG RR: AAGGTTTTACCGTTTGAGAAAGTTGTGGAGAACGTAAGAACAACAGTTCTTACGGGAAGAAGGGTTATAGGTTAAGTTGATGATGTACTATTTTCTTC F2: 3 TAAGAACAACA 2 Unidirectional alignment (log-probability: -56.7) TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTtgacaacaagaattcttgcattctTGTTGTCAAGAATGCCCTTCTTCCCAATA TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCT------------------------TGTTGTCAAGAATGCCCTTCTTCCCAATA Template switch alignment (log-probability: -28.9) TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTG|ACAACAAGAAT|TCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATA TCCAAAATGGCAAACTCTTTCAACACCTCTTGCATTCTTG|ACAACAAGAAT|TCTTGCATTCTTGTTGTCAAGAATGCCCTTCTTCCCAATA ========== Event 3829 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: ATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTATCCTATCTAAAATTCTT-GGAATA ↓ 13 24 ↑ 13 24 Chimp: ATAACAGTATGTCAGTAGTGAGGATAATTCTCTTTTCTCATATCTAAAATTCTT-GCAATA ↓ 13 24 ↑ 13 24 Gorilla: ATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTATCCTATCTAAAATTCTT-GGAATA Human: ATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTATCCTATCTAAAATTCTT-GGAATA Cluster: [ ] Orangutan: ATAACAGTATGTCAGTAGTGATGAAAAAAGAGAACCATCCTATCTAAAATCCTTGGGAATA Chimp > Human ------------- chr9:59180383-59180401 Template switch process: F1: L AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA 1 F3: 4 TATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA R RF: AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGAGGATAATTCTCTTTTCTCATATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA RR: TTGGTTAGATCTTACAATTTTATTGTCATACAGTCATCACTCCTATTAAGAGAAAAGAGTATAGATTTTAAGAACGTTATTACGGATTCCTCTTTTGGGT F2: 3 CCTATTAAGAGAAAAGAGT 2 Unidirectional alignment (log-probability: -55.4) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTG-------------------AtgagaaaagagaattatccTATCTAAAATTCTTGgAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGAGGATAATTCTCTTTTCTCA-------------------TATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA Template switch alignment (log-probability: -23.6) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|TGAGAAAAGAGAATTATCC|TATCTAAAATTCTTGgAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|TGAGAAAAGAGAATTATCC|TATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA Human > Chimp ------------- chr9:60257406-60257424 Template switch process: F1: L AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA 1 F3: 4 TATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA R RF: AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTATCCTATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA RR: TTGGTTAGATCTTACAATTTTATTGTCATACAGTCATCACTACTCTTTTCTCTTAATAGGATAGATTTTAAGAACCTTATTACGGATTCCTCTTTTGGGT F2: 3 ACTCTTTTCTCTTAATAGG 2 Unidirectional alignment (log-probability: -55.4) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA-------------------ggataattctcttttctcaTATCTAAAATTCTTGcAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTATCC-------------------TATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA Template switch alignment (log-probability: -23.6) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|GGATAATTCTCTTTTCTCA|TATCTAAAATTCTTGcAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|GGATAATTCTCTTTTCTCA|TATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA Gorilla > Chimp --------------- chr9:60257406-60257424 Template switch process: F1: L AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA 1 F3: 4 TATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA R RF: AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTATCCTATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA RR: TTGGTTAGATCTTACAATTTTATTGTCATACAGTCATCACTACTCTTTTCTCTTAATAGGATAGATTTTAAGAACCTTATTACGGATTCCTCTTTTGGGT F2: 3 ACTCTTTTCTCTTAATAGG 2 Unidirectional alignment (log-probability: -53.7) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGAgGA-----------TAattctcttttcTCaTATCTAAAATTCTTGcAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGATGAGAAAAGAGAATTA-----------TCCTATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA Template switch alignment (log-probability: -23.7) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|GGATAATTCTCTTTTCTCA|TATCTAAAATTCTTGcAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|GGATAATTCTCTTTTCTCA|TATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA Chimp > Gorilla --------------- chr9:60548341-60548359 Template switch process: F1: L AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA 1 F3: 4 TATCTAAAATTCTTGGAATAATGCCTAAGGAGAAAACCCA R RF: AACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGAGGATAATTCTCTTTTCTCATATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA RR: TTGGTTAGATCTTACAATTTTATTGTCATACAGTCATCACTCCTATTAAGAGAAAAGAGTATAGATTTTAAGAACGTTATTACGGATTCCTCTTTTGGGT F2: 3 CCTATTAAGAGAAAAGAGT 2 Unidirectional alignment (log-probability: -53.7) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGAtGAgaaaagagaatTA-----------TCcTATCTAAAATTCTTGgAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGAGGA-----------TAATTCTCTTTTCTCATATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA Template switch alignment (log-probability: -23.7) ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|TGAGAAAAGAGAATTATCC|TATCTAAAATTCTTGgAATAATGCCTAAGGAGAAAACCCA ACCAATCTAGAATGTTAAAATAACAGTATGTCAGTAGTGA|TGAGAAAAGAGAATTATCC|TATCTAAAATTCTTGCAATAATGCCTAAGGAGAAAACCCA ========== Event 3830 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TGACTCTTTCCTCCTTCACTC--------------ACCAGATAAGCATGTACTATTGTGCCTCCCCTGACaaaaaaaaa-aaaaaaagaaaaCTGTACTAGGTATGACAAATGTCTTCAGATCAGATCTGCATTAAAATTACCCACATAT ↑ 1 4 3 2 Chimp: TGACTCTTTCCTCCTTCACTCCACTTAGTACATGCTTCACAAAAGCATGTACTATTGTGCCTCCCCTGACaaaaaaaaaaaaaGAAAGAAAACTGTACTAGGTATGACAAATGTCTTCAGATCAGATCTGCATTAAAATTACCCACATAT Gorilla: TGACTCTTTCCTCCTTCACTC--------------ACCAGATAAGCATGTATTATTGTGCCTCCCTCGCCaaaaaaaaa-aaaaaaaaaaaaCTGTACTAGGTATGACAAATGTCTTCAGATCAGATCTGCATTAAAATTACCCACATAT Human: TGACTCTTTCCTCCTTCACTC--------------ACCAGATAAGCATGTACTATTGTGCCTCCCCTGACaaaaaaaaa-aaaaaaagaaaaCTGTACTAGGTATGACAAATGTCTTCAGATCAGATCTGCATTAAAATTACCCACATAT Cluster: [ ] Orangutan: CGACTCTTTTCTCCTTCACTC--------------ACCAGATAAGCATGTATTATTGTGCCTCCCCTGCCaaaacaaaa-aaaaaaaaaCCACTGTACTAGGTATGACAAATGTCTTCAGATCAGATCTGCATTAAAATTACCCACATAT Chimp > Human ------------- chr9:59782478-59782482 Template switch process: F1: L CATATAAAAAACATTTTTAGTGACTCTTTCCTCCTTCACT-CAC 1 F3: 4 AAGCATGTACTATTGTGCCTCCCCTGACAAAAAAAAAAA R RF: CATATAAAAAACATTTTTAGTGACTCTTTCCTCCTTCACTCCACTTAGTACATGCTTCACAAAAGCATGTACTATTGTGCCTCCCCTGACAAAAAAAAAAAAAGAAAGAAAACTGTACTAGGTATGACAAATGTCTTCAGATCAGATCTG RR: GTATATTTTTTGTAAAAATCACTGAGAAAGGAGGAAGTGAGGTGAATCATGTACGAAGTGTTTTCGTACATGATAACACGGAGGGGACTGTTTTTTTTTTTTTCTTTCTTTTGACATGATCCATACTGTTTACAGAAGTCTAGTCTAGAC F2: 3 TAGAC 2 Unidirectional alignment (log-probability: -38.1) ATAAAAAACATTTTTAGTGACTCTTTCCTCCTTCACTC--------------------AccagatAAGCATGTACTATTGTGCCTCCCCTGACAAAAAAAAAAA- ATAAAAAACATTTTTAGTGACTCTTTCCTCCTTCACTCCACTTAGTACATGCTTCACAA------AAGCATGTACTATTGTGCCTCCCCTGACAAAAAAAAAAAA Template switch alignment (log-probability: -26.2) ATAAAAAACATTTTTAGTGACTCTTTCCTCCTTCACT-CAC|CAGAT|AAGCATGTACTATTGTGCCTCCCCTGACAAAAAAAAAAA ATAAAAAACATTTTTAGTGACTCTTTCCTCCTTCACTCCAC|CAGAT|AAGCATGTACTATTGTGCCTCCCCTGACAAAAAAAAAAA ========== Event 3831 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCTTGGTCATATGGAACGTGGGAACAGGGGTCTAGGTTTTGACAAGGATGGCCAGACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAGTATCAGTTTTCACAACTAGGCCACAGAATCCACTACTTCTGATATTTT---ATGTTTGCTAGTTTCCCTGTTATCACC Chimp: CTCTTGGTCATATGGAACGTGGGAACAGGGGTCTAGGTTTTGACAAGGATGGCCAGACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAG--AACCTGTTTCC---------------------------------------------AGCTAGTTTCCCTGTTATCACC ↑ 3 2 1 4 Gorilla: CTCTTGGTCATATGGAATGTGGGAACAGGGGTCTAGGTTTTGACAAGGATGGCCAGACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAGTATCAGTTTTCACAACTAGGCCACAGAATCCACTACTTCTGATATTTTATGATGTTTGCTAGTTTCCCTGTTATCACC Human: CTCTTGGTCATATGGAACGTGGGAACAGGGGTCTAGGTTTTGACAAGGATGGCCAGACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAGTATCAGTTTTCACAACTAGGCCACAGAATCCACTACTTCTGATATTTT---ATGTTTGCTAGTTTCCCTGTTATCACC Cluster: [ ] Orangutan: CTCTTGGTCATATGGAACATGGGAACAGGGGTCTAGGTTTTGACAAGGATGGCCAGACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAGTATCAGTTTTCACAACTAGGCCACAGAATCCACTACTTCTGATATTTT---ATGTTTGCTAGTTTCCCTGTTATCACC Gorilla > Chimp --------------- chr9:58466844-58466853 Template switch process: F1: L ACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAA 1 F3: 4 GCTAGTTTCCCTGTTATCACCCAGAATTCATATATTTTCA R RF: TGGGAACAGGGGTCTAGGTTTTGACAAGGATGGCCAGACACTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAGTATCAGTTTTCACAACTAGGCCACAGAATCCACTACTTCTGATATTTTATGATGTTTGCTAGTTTCCCTGTTATCACCCAGAATTCATATATTTTCA RR: ACCCTTGTCCCCAGATCCAAAACTGTTCCTACCGGTCTGTGAATCACTGGGTGTATCGTATTTCCAAGTGTGTAGGTCTCATAGTCAAAAGTGTTGATCCGGTGTCTTAGGTGATGAAGACTATAAAATACTACAAACGATCAAAGGGACAATAGTGGGTCTTAAGTATATAAAAGT F2: 3 ACCTTTGTCC 2 Unidirectional alignment (log-probability: -39.4) CTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGA----------------------------------------------------------acctgtttccaGCTAGTTTCCCTGTTATCACCCAGAATTCATATATTTTCA CTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAGTATCAGTTTTCACAACTAGGCCACAGAATCCACTACTTCTGATATTTTATGATGTTT-----------GCTAGTTTCCCTGTTATCACCCAGAATTCATATATTTTCA Template switch alignment (log-probability: -28.1) CTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAa|CCTGTTtCCA|GCTAGTTTCCCTGTTATCACCCAGAATTCATATATTTTCA CTTAGTGACCCACATAGCATAAAGGTTCACACATCCAGAG|CCTGTTCCCA|GCTAGTTTCCCTGTTATCACCCAGAATTCATATATTTTCA ========== Event 3832 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CTATGGAAAACAGGCACATCACGCCACCTTT-----------TCCTTTGATATGAAGAAATTAGACCTTTTCAACCTT ↓ 1 3 4 2 Chimp: CTATGGAAAACAGGCACATCACGCCATCTTCATATCAAAGGAAACTTTGATATGAAGAAATTAGACCTTTTCAACCTT ↑ 1 3 4 2 Gorilla: CTATGGAAAACAGGCACATCATGCCACCTTT-----------TCCTTTGATATGAAGAAATTAGACCTTTTCAACCTT Human: CTATGGAAAACAGGCACATCACGCCACCTTT-----------TCCTTTGATATGAAGAAATTAGACCTTTTCAACCTT Cluster: [ ] Orangutan: CTACAGAAAACAGGCACATCACGCCACCTTT-----------TCCTCTGATATGAAGAAATTAGACCTTTTCAACCTT Human > Chimp ------------- chr9:58068560-58068577 Template switch process: F1: L AAGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCA 1 F3: 4 CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG R RF: AAGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCACCTTTTCCTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG RR: TTCTTACCTTGTACAGATACCTTTTGTCCGTGTAGTGCGGTGGAAAAGGAAACTATACTTCTTTAATCTGGAAAAGTTGGAAAAAACC F2: 3 AAAGGAAACTATACTTCT 2 Unidirectional alignment (log-probability: -44.4) AGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCA-----TCttcatatcaaaggaaaCTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG AGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCACCTTTTC----------------CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG Template switch alignment (log-probability: -17.5) AGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCA|TCTTCATATCAAAGGAAA|CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG AGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCA|TCTTCATATCAAAGGAAA|CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG Gorilla > Chimp --------------- chr9:58068560-58068577 Template switch process: F1: L CATTCAAGAATGGAACATGTCTATGGAAAACAGGCACATCACGCCA 1 F3: 4 CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG R RF: CATTCAAGAATGGAACATGTCTATGGAAAACAGGCACATCATGCCACCTTTTCCTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG RR: GTAAGTTCTTACCTTGTACAGATACCTTTTGTCCGTGTAGTACGGTGGAAAAGGAAACTATACTTCTTTAATCTGGAAAAGTTGGAAAAAACC F2: 3 AAAGGAAACTATACTTCT 2 Unidirectional alignment (log-probability: -49.5) AGAATGGAACATGTCTATGGAAAACAGGCACATCAcGCCA-----TCttcatatcaaaggaaaCTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG AGAATGGAACATGTCTATGGAAAACAGGCACATCATGCCACCTTTTC----------------CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG Template switch alignment (log-probability: -23.7) AGAATGGAACATGTCTATGGAAAACAGGCACATCAcGCCA|TCTTCATATCAAAGGAAA|CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG AGAATGGAACATGTCTATGGAAAACAGGCACATCATGCCA|TCTTCATATCAAAGGAAA|CTTTGATATGAAGAAATTAGACCTTTTCAACCTTTTTTGG ========== Event 3833 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GAAGTCAGGCCTCAACATCCA--GGACCTTC------TGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGTTA Chimp: GAAGTCAGGCCTCAACATCCA--GGACCTTC------TGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGTTA Gorilla: GAAGTCAGGCCTCAACATCCA----TCATTCTAGGAAAGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGTTA ↑ 1 4 3 2 Human: GAAGTCAGGCCTCAACATCCA--GGACCTTC------TGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGTTA Cluster: [ ] Orangutan: GAAGTCAGGCCTCAACACCCAGG--ACCTTC------TGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGTTA Human > Gorilla --------------- chr9:58068429-58068438 Template switch process: F1: L AGGGCATGGGTGGTGACTGGGAAGTCAGGCCTCAACATCCATCA 1 F3: 4 GAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGT R RF: AGGGCATGGGTGGTGACTGGGAAGTCAGGCCTCAACATCCAGGACCTTCTGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGT RR: TCCCGTACCCACCACTGACCCTTCAGTCCGGAGTTGTAGGTCCTGGAAGACTTGACCGCAGAAAAGGATCTTTATTGGTTTAAGTTTACA F2: 3 AAAGGATCTT 2 Unidirectional alignment (log-probability: -38.3) CATGGGTGGTGACTGGGAAGTCAGGCCTCAACATCCA--------TcattctaggaaaGAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGT CATGGGTGGTGACTGGGAAGTCAGGCCTCAACATCCAGGACCTTCT------------GAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGT Template switch alignment (log-probability: -28.1) CATGGGTGGTGACTGGGAAGTCAGGCCTCAACATCCAtcA|TTCTAGGAAA|GAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGT CATGGGTGGTGACTGGGAAGTCAGGCCTCAACATCCAGGA|TTCTAGGAAA|GAACTGGCGTCTTTTCCTAGAAATAACCAAATTCAAATGT ========== Event 3834 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ttttattttcaacatttttttcttttGCAAAAGAAAGACCAACAGAAAATTGTTGTGG ↑ 13 4 2 Chimp: ttttattttcaacatt-ttttcttttGCAAA----AGACCAACAGAAAATTGTTGTGG Gorilla: ttttatttacaacatt-ttttattttGCAAA----AGACCAACAGAAAATTGTTATGG Human: ttttattttcaacatttttttcttttGCAAAAGAAAGACCAACAGAAAATTGTTGTGG Cluster: [ ] Orangutan: TTTTATTTTCAACATT-TTTTCTTTTGCAAA----AGACCAACAGAAAATTGTTATGG Chimp > Human ------------- chr9:80873320-80873332 Template switch process: F1: L TGTATTGGAATTTTATTTTCAACATTTTTT 1 F3: 4 AAAGACCAACAGAAAATTGTTGTGGTTAATAAAATAGGATTC R RF: TGTATTGGAATTTTATTTTCAACATTTTTTCTTTTGCAAAAGACCAACAGAAAATTGTTGTGGTTAATAAAATAGGATTC RR: ACATAACCTTAAAATAAAAGTTGTAAAAAAGAAAACGTTTTCTGGTTGTCTTTTAACAACACCAATTATTTTATCCTAAG F2: 3 GAAAACGTTTTCT 2 Unidirectional alignment (log-probability: -28.3) TGTATTGGAATTTTATTTTCAACAtTTTTTTCTTTTGCAaaagAAAGACCAACAGAAAATTGTTGTGGTTAATAAAATAGGAT TGTATTGGAATTTTATTTTCAACA-TTTTTTCTTTTGCA----AAAGACCAACAGAAAATTGTTGTGGTTAATAAAATAGGAT Template switch alignment (log-probability: -16.7) TGTATTGGAATTTTATTTTCAACATTTTTT|TCTTTTGCAAAAG|AAAGACCAACAGAAAATTGTTGTGGTTAATAAAATAGGAT TGTATTGGAATTTTATTTTCAACATTTTTT|TCTTTTGCAAAAG|AAAGACCAACAGAAAATTGTTGTGGTTAATAAAATAGGAT ========== Event 3835 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 34 Detected in comparisons: 3456 Multiple sequence alignment: Human: TCCAAACAGATTTTAAGATTATTAAAACATGAC----TTTGTACATAC-AAGTTATTT---TTCTTAAATATAGAAGTATCTGTGT Chimp: TC----CAGATTTTAAGATTATTAAAGCATGAC----TTTGTACATAC-AAGTTATTT---TACTTAAATATAGAAGTATCTGTGT Gorilla: tccaaacagattttaagATTAAGAAA-AATAAC-----TTGTATGTACAAAGTCATTT--TTTAATAAATATAGAAGTATCTGTGT ↓ 13 24 ↑ 13 24 Human: TCCAAACAGATTTTAAGATTATTAAAACATGAC----TTTGTACATAC-AAGTTATTT---TTCTTAAATATAGAAGTATCTGTGT Cluster: [ ] Orangutan: TCCAAACAGATTTTAAGATTAAGAAA-AATCACTTGT-ATGTATGTACAAAGTCATTTTT-TTAATAAATATAGAAGTATCTGTGT Gorilla > Human --------------- chr9:80884464-80884499 Template switch process: F1: L AGGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA 1 F3: 4 TAAATATAGAAGTATCTGTGTGTATGTATTCCTCTTCTGA R RF: AGGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTAAGAAAAATAACTTGTATGTACAAAGTCATTTTTTAATAAATATAGAAGTATCTGTGTGTATATATTCCTCTTCTGA RR: TCCTCAGAAAAAGATCAAAGAGGTTTGTCTAAAATTCTAATTCTTTTTATTGAACATACATGTTTCAGTAAAAAATTATTTATATCTTCATAGACACACATATATAAGGAGAAGACT F2: 3 TCTTTTTATTGAACATACATGTTTCAGTACAAAATT 2 Unidirectional alignment (log-probability: -73.8) GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA--------------------------------TTAAaacatgactttgtacatacaagttatttttctTAAATATAGAAGTATCTGTGTGTATgTATTCCTCTTCTGA GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTAAGAAAAATAACTTGTATGTACAAAGTCATTTTTTAA--------------------------------TAAATATAGAAGTATCTGTGTGTATATATTCCTCTTCTGA Template switch alignment (log-probability: -31.3) GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA|TTAAAAcATGACTTTGTACATACAAGTTATTTTTCT|TAAATATAGAAGTATCTGTGTGTATgTATTCCTCTTCTGA GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA|TTAAAAAATGACTTTGTACATACAAGTTATTTTTCT|TAAATATAGAAGTATCTGTGTGTATATATTCCTCTTCTGA Human > Gorilla --------------- chr9:62865138-62865173 Template switch process: F1: L AGGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA 1 F3: 4 TAAATATAGAAGTATCTGTGTGTATATATTCCTCTTCTGA R RF: AGGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTATTAAAACATGACTTTGTACATACAAGTTATTTTTCTTAAATATAGAAGTATCTGTGTGTATGTATTCCTCTTCTGA RR: TCCTCAGAAAAAGATCAAAGAGGTTTGTCTAAAATTCTAATAATTTTGTACTGAAACATGTATGTTCAATAAAAAGAATTTATATCTTCATAGACACACATACATAAGGAGAAGACT F2: 3 AATTTTTTACTGAAACATGTATGTTCAATAAAAAGA 2 Unidirectional alignment (log-probability: -73.8) GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTAagaaaaataacttgtatgtacaaagtcattttTTAA--------------------------------TAAATATAGAAGTATCTGTGTGTATaTATTCCTCTTCTGA GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA--------------------------------TTAAAACATGACTTTGTACATACAAGTTATTTTTCTTAAATATAGAAGTATCTGTGTGTATGTATTCCTCTTCTGA Template switch alignment (log-probability: -31.3) GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA|AGAAAAATAACTTGTATGTACAAAGTCATtTTTTAA|TAAATATAGAAGTATCTGTGTGTATaTATTCCTCTTCTGA GGAGTCTTTTTCTAGTTTCTCCAAACAGATTTTAAGATTA|AGAAAAATAACTTGTATGTACAAAGTCATGTTTTAA|TAAATATAGAAGTATCTGTGTGTATGTATTCCTCTTCTGA ========== Event 3836 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AACAGACAtttt---ttttttCAGGCCCGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGAGGGTTCTTTTAGAGCCTCTTCTCCAGCTACTCGGGTGGCCAAAGGTGGGGAAGAGGGGGCAGGAAGGGTCAGGGCATATGGGCCCTGAGAATCTTTTGGTTTCTGGCT ↑ 1 4 3 2 Chimp: AACAGACAttt----ttttttCAGACCTGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGA-GGTTCTTTTAGAGCCTCTTCTCCAGCTACCTGGGTGGCCAAAGGTGGGGAAGAGGGGGCAGGAAGGGTCAGGGCATATGGGCCCTGAGAATCGTTTGGTTTCTGGCT Gorilla: AACAGACAtttt---ttttttCAGACCCTCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGAGGGTTCTTTTAGAGCCTCTTCTCCAGCTACCCGGGTGGCCAAAGGTGGGGAAGAGGGGGCAGGAAGGGTCAGGGCATATGGGCCCTGAGAATCTTTTGGTTTCTGGCT Human: AACAGACAtttt---ttttttCAGGCCCGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGAGGGTTCTTTTAGAGCCTCTTCTCCAGCTACTCGGGTGGCCAAAGGTGGGGAAGAGGGGGCAGGAAGGGTCAGGGCATATGGGCCCTGAGAATCTTTTGGTTTCTGGCT Cluster: [ ] Orangutan: AACAGACAtttttttttttttCAGACCTGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGAGGGTTCTTTTAGAGCCTCTTCTCCAGCTACCCGGGTGGCCAAAGGTGGGGAAGAGGGGACAGGAAGGGTCAGGGCATATGGGCCCTGAGAATCTTTTGGTTTCTGGCT Chimp > Human ------------- chr9:81763369-81763373 Template switch process: F1: L AATTTTTAAAATGTACCTTTAACAGACATTTTTTTTT 1 F3: 4 CCCGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGAGG R RF: AATTTTTAAAATGTACCTTTAACAGACATTTTTTTTTCAGACCTGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTGAGGTTCTTTTAGAGCCTCTTCTCCAGCTACCTGGGTGGCCAAAGGTGGGGAAGAGGGGGCAGGAAGGGTCAGGGCATATGGGCCCTGA RR: TTAAAAATTTTACATGGAAATTGTCTGTAAAAAAAAAGTCTGGACGTAAGAACACTACTATTTTCCCCGGTCTTGGTTAACTCCAAGAAAATCTCGGAGAAGAGGTCGATGGACCCACCGGTTTCCACCCCTTCTCCCCCGTCCTTCCCAGTCCCGTATACCCGGGACT F2: 3 GGACT 2 Unidirectional alignment (log-probability: -33) AATTTTTAAAATGTACCTTTAACAGACAtTTTTTTTTTCAGgCCcGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTG AATTTTTAAAATGTACCTTTAACAGACA-TTTTTTTTTCAGACCTGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTG Template switch alignment (log-probability: -21.9) AATTTTTAAAATGTACCTTTAACAGACATTTTTTTTT|TCAGG|CCcGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTG AATTTTTAAAATGTACCTTTAACAGACATTTTTTTTT|TCAGG|CCTGCATTCTTGTGATGATAAAAGGGGCCAGAACCAATTG ========== Event 3837 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTTTATTTGCTGATTCTGAGTCAGGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTGCAGCTTTGTTGTTGTGCTATGGTTGTTTTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTCCTTTG----------------------ACCCCAGCCTGCTCCAGAAAATGACTTA ↑ 3 2 1 4 Chimp: TTGTATTTGCTGATTCTGAGTCAAGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTGCAGCTTTGTTGTTGTGCTACGGTTGTTTTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTTGT-----------CCCTTCAAATCTACCCAGCCTGCTCCAGAAAATGACTTA Gorilla: TTGTATTTGCTGATTCTGAGTCAAGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTGCAGCTTTGTTGTTGTGCTATGGTTGTTTTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTTGTCCCTTCAAATC-----------TACCCAGGCTGCTCCAGAAAATGACTTA ↓ 3 2 1 4 Human: TTTTATTTGCTGATTCTGAGTCAGGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTGCAGCTTTGTTGTTGTGCTATGGTTGTTTTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTCCTTTG----------------------ACCCCAGCCTGCTCCAGAAAATGACTTA Cluster: [ ] Orangutan: TTGTATTTGCTGATTCTGAGTCAAGTCTCTGAATCATCTTCCCCATACTGAATGAGAAATATGGGCTTATACTCTCACTTGTGTCTGCAGCCCCGCAGgtggtcaagagctcagtcgtgctgtcttgcagtggggttccaaccatcctttagctacttactgaatcaccttcaagtaagttattgacttctatgtgtctcagatggaatgtgtagaatggaatatgaatagtatcatactcaaagattattataaggattaaataacaccataagtaaaggacttagcatagctcttgactcattataagttccccataaatattAACTGATAATTATAGATTTGTAAAACTAAATTGTTTTGGCATAttaattgtcattctctctctaaactacactaagcagtttgagatcaggaagtgatgtgttgtctttatttctcgtacactgagcagatattaggtgcttcataaatatgtattaaatgagtgaGAATTAATCATTATAAAGGTGATAAGTGAATGGACAAGATCCTCATGCATAAATGTAGCAATTGTTTAATTATTACATTAAACAGGCTTAGGGTTTAAAACTCTCCTAAGGACTGTTCACCTGCTGGAAGTTTGACTTGCTGCACTAAGTATGGGCACATTCATAACATGTAAGCGTGAAGTGTCCTCTTTATTAAACACTGTAAATCCATTAGTCATGGAAGCAGAGGACAGCTTCAAGATTAGAGCCTCTAGGTGGAAAGAGATCGTACAAGCTTGGTCCTCAACTCTTTCCCTCTCTTCATTGTTCCATGTGAGATGGTTTCTGCTGCCACCAACCAGCATGCAGGGCACCAGAAAAGACTCCACTCCCTCTTGTTAAAACTCTGCCTCAGATGTGAACTAAAATCCCATTCCTTGCACACACCTACGATAGCTGTCCTAAACTTTCAAGAACACAAAAATGACCACGTTTCTCAAGTACAAGTTTATGGCAGTGAAACTAAGAAGCTCTAATATCCTGGTACCCCTTCATCCACACGTGAAAGCTATGGTCGATTGGTCCATTCCTTCAACAACTGCtctaggttctgtctgtactacagaagttagaaagataccaactacatttcccaaatgttcttgcagctgggttacagatgtgacttgggttctccaatgacttgcactGAATTAAGTGGCGAGAGAGTGAAGTGAGAGCAAGAGAATGGGGCAGCATCCATTGTGCCAGTGGGGTTCTCATGAGCATGTGTGTCCTCCCTCAATCGTGGACTGCACGTGGAGTGCTGCTGTCCTAGAGTCAGCACTGGGGTCAGTGGTGTTGTGAGTCCCAGGCTCTCATGACAGCAGAGGCAGCTACCACTCATCTATGCTATTTCTGTGACGTGGTGTTTAATTACTAGAACACCCAGTCTGAAGCCCACTtcctccagcataaccacaattttgcaagcacctaaatcctggtattaaatttttttctgcttaaaatagctggattagtattttgCAGTCCCCTTTCCAGTCCTTCTTTGCAGCTTTGTTGTTGTGCTATGGTTGTTTTTTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTTGTCCCTTCAAATC-----------TACCCAGCCTGCTCCAGAAAATGACTTA Chimp > Human ------------- chr9:82733132-82733135 Template switch process: F1: L TTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTCCTT 1 F3: 4 CCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT R RF: GTCAAGTCTTTGCAGCTTTGTTGTTGTGCTACGGTTGTTTTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTTGTCCCTTCAAATCTACCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT RR: CAGTTCAGAAACGTCGAAACAACAACACGATGCCAACAAAACAAGAGATCGGTTATAGAGGGGAGAAGAACCGAGGGGAAAGAACAGGGAAGTTTAGATGGGTCGGACGAGGTCTTTTACTGAATTGTTACAACGAAAA F2: 3 CAGT 2 Unidirectional alignment (log-probability: -33.6) CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTcctttgac-------------------CCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTT--------TCTTGTCCCTTCAAATCTACCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT Template switch alignment (log-probability: -21.8) CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTcCTT|TGAC|CCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTT|TGAC|CCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT Gorilla > Human --------------- chr9:82733132-82733135 Template switch process: F1: L TTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTCCTT 1 F3: 4 CCCAGCCTGCTCCAGAAAATGACTTAACAATGTTGCTTTTCTCCAC R RF: GTCAAGTCTTTGCAGCTTTGTTGTTGTGCTATGGTTGTTTTGTTCTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTTGTCCCTTCAAATCTACCCAGGCTGCTCCAGAAAATGACTTAACAATGTTGCTTTTCTCCAC RR: CAGTTCAGAAACGTCGAAACAACAACACGATACCAACAAAACAAGAGATCGGTTATAGAGGGGAGAAGAACCGAGGGGAAAGAACAGGGAAGTTTAGATGGGTCCGACGAGGTCTTTTACTGAATTGTTACAACGAAAAGAGGTG F2: 3 CAGT 2 Unidirectional alignment (log-probability: -38.3) CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTcCTT---------------tgacCCCAGcCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTTGTCCCTTCAAATCTA----CCCAGGCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT Template switch alignment (log-probability: -27.5) CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTcCTT|TGAC|CCCAGcCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT CTCTAGCCAATATCTCCCCTCTTCTTGGCTCCCCTTTCTT|TGAC|CCCAGGCTGCTCCAGAAAATGACTTAACAATGTTGCTTTT ========== Event 3838 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AAATTATGATAGTCAACATTA-------ACAatataggtatgggtatacacatagacatacatgtagatatctgtacagatatcaatactaacat Chimp: AAATTATGATAGTCAACATTA-------GCAATATAGGTATGGGTATACACATAGACATACATGTAGATATCTGTACAGATATCAATACTAACAT ↓ 1 4 3 2 Gorilla: AAATTATGATAGTCAACATTAACAGATATCAATATAGGTATGGGTATACACATAGACATACATGTAGATATCCGTACAGATATGAATATTAACAT Human: AAATTATGATAGTCAACATTA-------ACAatataggtatgggtatacacatagacatacatgtagatatctgtacagatatcaatactaacat Cluster: [ ] Orangutan: AAATTATGATAGTCAACATTAACAGATATCAATATAGGTATGGGTATACACATAGACATACATGTAGATATCTGTACAGATATCAATATTAACAT Chimp > Gorilla --------------- chr9:65148773-65148781 Template switch process: F1: L TCAGGATTCTGCACTAGTCCAAATTATGATAGTCAACATTA 1 F3: 4 AATATAGGTATGGGTATACACATAGACATACATGTAGAT R RF: TCAGGATTCTGCACTAGTCCAAATTATGATAGTCAACATTAGCAATATAGGTATGGGTATACACATAGACATACATGTAGATATCTGT RR: AGTCCTAAGACGTGATCAGGTTTAATACTATCAGTTGTAATCGTTATATCCATACCCATATGTGTATCTGTATGTACATCTATAGACA F2: 3 CTATAGACA 2 Unidirectional alignment (log-probability: -26.5) CAGGATTCTGCACTAGTCCAAATTATGATAGTCAACATtaacagaTAtCAATATAGGTATGGGTATACACATAGACATACATGTAGAT CAGGATTCTGCACTAGTCCAAATTATGATAGTCAACAT-------TAGCAATATAGGTATGGGTATACACATAGACATACATGTAGAT Template switch alignment (log-probability: -16.8) CAGGATTCTGCACTAGTCCAAATTATGATAGTCAACATTA|ACAGATATC|AATATAGGTATGGGTATACACATAGACATACATGTAGAT CAGGATTCTGCACTAGTCCAAATTATGATAGTCAACATTA|ACAGATATC|AATATAGGTATGGGTATACACATAGACATACATGTAGAT ========== Event 3839 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: TCATTCTAACATGCATTTGCTGGACACAAAGCTATAGCTGGACACAAGGTCAGTAACCACTGAAGCC Chimp: TCATTCTAACATGCATTTGCTGGACACAAGGCTATAGCTGGACACAAGGTCAGTAACCACTGAAGCC Gorilla: TCATTCTAACATGCATTTGCTGGACACAAGGCTATAGCTTGG-GGGTGGTCAGTAACCACTGAAGCC ↓ 4 1 3 2 Human: TCATTCTAACATGCATTTGCTGGACACAAAGCTATAGCTGGACACAAGGTCAGTAACCACTGAAGCC Cluster: [ ] Orangutan: TCATTCTAACATGCATTTGCTGGACATAAGGCTATAGCTTCA-GGGTGGTCAGTAACCACTGAAGCC Gorilla > Human --------------- chr9:83458272-83458279 Template switch process: F1: L CTTCATTCTAACATGCATTTGCTGGACACAA 1 F3: 4 CTGGACACAA-----------------GGTCAGTAACCACTGAAGCCAAAGAACAGAGATTTCTACA R RF: CTTCATTCTAACATGCATTTGCTGGACACAAGGCTATAGCTTGGGGGTGGTCAGTAACCACTGAAGCCAAAGAACAGAGATTTCTACA RR: GAAGTAAGATTGTACGTAAACGACCTGTGTTCCGATATCGAACCCCCACCAGTCATTGGTGACTTCGGTTTCTTGTCTCTAAAGATGT F2: 3 GATATCGA 2 Unidirectional alignment (log-probability: -38) CTTCATTCTAACATGCATTTGCTGGACACAAaGCTATAGC-------TggacacaaGGTCAGTAACCACTGAAGCCAAAGAACAGA CTTCATTCTAACATGCATTTGCTGGACACAAGGCTATAGCTTGGGGGT--------GGTCAGTAACCACTGAAGCCAAAGAACAGA Template switch alignment (log-probability: -27.4) CTTCATTCTAACATGCATTTGCTGGACACAA|AGCTATAG|CTGGACACAA-----------------GGTCAGTAACCACTGAAGCCAAAGAACAGA CTTCATTCTAACATGCATTTGCTGGACACAA|AGCTATAG|CTGGACACAAGGCTATAGCTTGGGGGTGGTCAGTAACCACTGAAGCCAAAGAACAGA ========== Event 3840 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TTCGTCAGCAATGTCCACTGCTAGAGACACAAGTGGGCAATGCAGTGGGAAATAAATGGAATGGTTGCGGGACTAAAGGACTAGAAG--------------------------------------------TCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAA Chimp: TTGGTCAGCAATGTCCAGTGCTAGAGACACAAGTGGGCAATGCAGTGGGAAATAAATGGAATGGTTGCGGAACTAAAGGActagaag----------------------tcccatttcccatttctagcagtcccatttcccatttcAGGATGTGCGGAATGGAGAA Gorilla: TTCGTCAGCAAAGTCCAGTGCTAGAGACACAAGTGGGCAATGCAGTGGGAAATAAATGGAATGGTTGCGGGACTAAAGGACTAAAAGTCCCATTTCCCATTTCTAGCAG----------------------TCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAA ↑ 3 2 4 1 Human: TTCGTCAGCAATGTCCACTGCTAGAGACACAAGTGGGCAATGCAGTGGGAAATAAATGGAATGGTTGCGGGACTAAAGGACTAGAAG--------------------------------------------TCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAA Cluster: [ ] Orangutan: ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Human > Gorilla --------------- chr9:72854901-72854904 Template switch process: F1: L CAGTGGGAAATAAATGGAATGGTTGCGGGACTAAAGGACTAAAAGTCCCATTTCCCATTTC 1 F3: 4 AGTCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAAACAG R RF: GCTAGAGACACAAGTGGGCAATGCAGTGGGAAATAAATGGAATGGTTGCGGGACTAAAGGACTAGAAGTCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAAACAG RR: CGATCTCTGTGTTCACCCGTTACGTCACCCTTTATTTACCTTACCAACGCCCTGATTTCCTGATCTTCAGGGTAAAGGGTAAAGTCCTACACGTCTTACCTCTTTGTC F2: 3 CGAT 2 Unidirectional alignment (log-probability: -48.1) GTTGCGGGACTAAAGGACtaaaagtcccatttcccatttcTAGcAGTCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAAAC GTTGCGGGACTAAAGGAC----------------------TAGAAGTCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAAAC Template switch alignment (log-probability: -22.3) GTTGCGGGACTAAAGGACTAaAAGTCCCATTTCCCATTTC|TAGC|AGTCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAAAC GTTGCGGGACTAAAGGACTAGAAGTCCCATTTCCCATTTC|TAGC|AGTCCCATTTCCCATTTCAGGATGTGCAGAATGGAGAAAC ========== Event 3841 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCTTAGGTTTCCATTATGCAAGTCTGTACACAGCAGATCCATCTTTTCAAACATGCTGGTTTTCTGGTAATATCTGAGTTAGTGTCTCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAA---------------TAAATCAGACTAGAATAAATATGTACTATTGAGCAATTTG Chimp: TTCTTAGGTTTCCATTATGCAAGTCTGTACACAGCAGATCCATCTTTTCAAACATGCTGGTTTTCTGGTAATATCTGAGTTAGTGTCTCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAA---------------TAAATCAGACTAGAATAAATATGTACTATTGAGCAATTTG ↑ 3 2 4 1 Gorilla: TTCTTAGGTTTCCATTATGCAAGTCTGTACACAGCAGATCCATCTTTTCAAACATGCTGGTTTTCTGGTAATACCTGAGTTAGTGTCTCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAA------------------------------TAAATATGTACTATTGAGCAATTTG ↓ 3 2 4 1 Human: TTCTTAGGTTTCCATTATGCAAGTCTGTACACAGCAGATCCATCTTTTCAAACATGCTGGTTTTCTGGTAATATCTGAGTTAGTGTCTCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAA---------------TAAATCAGACTAGAATAAATATGTACTATTGAGCAATTTG Cluster: [ ] Orangutan: TTCTTAGGTTTCCATTATGCAAGTCTGTACACAGCAGATCCATCTTTTCAAA-CTGCTGGTTTTCTGGTAATATCTGAGTTACTGTCCCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGAGAAATAAATCAGACTAGAA---------------TAAATATGTATTATTGAGCAATTTG Gorilla > Human --------------- chr9:53626834-53626841 Template switch process: F1: L TCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAAT 1 F3: 4 AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAGCT R RF: CAAGTCTGTACACAGCAGATCCATCTTTTCAAACATGCTGGTTTTCTGGTAATACCTGAGTTAGTGTCTCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAGCT RR: GTTCAGACATGTGTCGTCTAGGTAGAAAAGTTTGTACGACCAAAAGACCATTATGGACTCAATCACAGAGACTCAAACGATTGGGTATTCGTAAAATCCACTACCCTTTATTTATACATGATAACTCGTTAAACATTTCTCTTTCTCGA F2: 3 GATCAGAC 2 Unidirectional alignment (log-probability: -32.5) TTTGCTAACCCATAAGCATTTTAGGTGATGGGAaataaatcagactagAATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAG TTTGCTAACCCATAAGCATTTTAGGTGATGGGA---------------AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAG Template switch alignment (log-probability: -22.4) TTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAAT|CAGACTaG|AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAG TTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAAT|CAGACTTG|AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAG Gorilla > Chimp --------------- chr9:54663692-54663699 Template switch process: F1: L TCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAAT 1 F3: 4 AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGCGCT R RF: CAAGTCTGTACACAGCAGATCCATCTTTTCAAACATGCTGGTTTTCTGGTAATACCTGAGTTAGTGTCTCTGAGTTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAGCT RR: GTTCAGACATGTGTCGTCTAGGTAGAAAAGTTTGTACGACCAAAAGACCATTATGGACTCAATCACAGAGACTCAAACGATTGGGTATTCGTAAAATCCACTACCCTTTATTTATACATGATAACTCGTTAAACATTTCTCTTTCTCGA F2: 3 GATCAGAC 2 Unidirectional alignment (log-probability: -38) TTTGCTAACCCATAAGCATTTTAGGTGATGGGAaataaatcagactagAATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGcG TTTGCTAACCCATAAGCATTTTAGGTGATGGGA---------------AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAG Template switch alignment (log-probability: -28) TTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAAT|CAGACTaG|AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGcG TTTGCTAACCCATAAGCATTTTAGGTGATGGGAAATAAAT|CAGACTTG|AATAAATATGTACTATTGAGCAATTTGTAAAGAGAAAGAG ========== Event 3842 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAAGCCAATTATTTTCCTGTT--GTTGTTGTTTGGTTCCATTTTGACTAACTCCTCTTAGTCTAACTC Chimp: CAAGCCAATTATTTTCCTGTT--GTTGTTTTTTGGTTTCATTTTGACTAACTCCTCTTAGTCTAACTC ↓ 1 4 3 2 Gorilla: CAAGCCAATTATTTTCCTGTT----AGTCAAAAGGTTCCATTTTGACTAACTCCTCTTAGTCTAACTC ↑ 1 4 3 2 Human: TAAGCCAATTATTTTCCTGTT--GTTGTTGTTTGGTTCCATTTTGACTAACTCCTCTTAGTCTAACTC Cluster: [ ] Orangutan: CAAGCCAATTATTTTCCTGTTGT--TGTATTTTGGTTCCATTTTGAGTAACTCCTCTTAGTCTAATTC Human > Gorilla --------------- chr9:55043799-55043806 Template switch process: F1: L GAATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTGTT 1 F3: 4 GGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC R RF: GAATTATTGGACCTCTATTTTAAGCCAATTATTTTCCTGTTGTTGTTGTTTGGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC RR: CTTAATAACCTGGAGATAAAATTCGGTTAATAAAAGGACAACAACAACAAACCAAGGTAAAACTGATTGAGGAGAATCAGATTGAGGAGTG F2: 3 AAAACTGA 2 Unidirectional alignment (log-probability: -38.2) AATTATTGGACCTCTATTTcAAGCCAATTATTTTCCTG----------TTagtcaaaaGGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC AATTATTGGACCTCTATTTTAAGCCAATTATTTTCCTGTTGTTGTTGTTT--------GGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC Template switch alignment (log-probability: -22.3) AATTATTGGACCTCTATTTcAAGCCAATTATTTTCCTGTT|AGTCAAAA|GGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC AATTATTGGACCTCTATTTTAAGCCAATTATTTTCCTGTT|AGTCAAAA|GGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC Chimp > Gorilla --------------- chr9:55043799-55043806 Template switch process: F1: L GAATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTGTT 1 F3: 4 GGTTCCATTTTGACTAACTCCTCTTAGTCTAACTCCTCACCTTAC R RF: GAATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTGTTGTTGTTTTTTGGTTTCATTTTGACTAACTCCTCTTAGTCTAACTCCTCACCTTAC RR: CTTAATAACCTGGAGATAAAGTTCGGTTAATAAAAGGACAACAACAAAAAACCAAAGTAAAACTGATTGAGGAGAATCAGATTGAGGAGTGGAATG F2: 3 AAAACTGA 2 Unidirectional alignment (log-probability: -38.2) AATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTG----------TTagtcaaaaGGTTcCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC AATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTGTTGTTGTTTTTT--------GGTTTCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC Template switch alignment (log-probability: -22.4) AATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTGTT|AGTCAAAA|GGTTcCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC AATTATTGGACCTCTATTTCAAGCCAATTATTTTCCTGTT|AGTCAAAA|GGTTTCATTTTGACTAACTCCTCTTAGTCTAACTCCTCAC ========== Event 3843 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCCTTGCCTTGCCTTTTTCTGAAGACCCCAC----ATCCCACAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATG Chimp: TCCTTGCCTTGCCTTTTTCTGAACACCCCAT----ATCCCACAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATG ↓ 1 4 3 2 Gorilla: TCCTTGCCTTGCCTTTTTCTGGCAACTGAGA--------AGCAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATG ↑ 1 4 3 2 Human: TCCTTGCCTTGCCTTTTTCTGAAGACCCCAC----ATCCCACAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATG Cluster: [ ] Orangutan: TCCTTGCCTTGCCTTTTTCTGAAGACCCCACATCC----CACAAAACTTCTCAGCTGAAGCTGTCCATCTTTTCATG Human > Gorilla --------------- chr9:54669471-54669481 Template switch process: F1: L TTATAGTCAACATCTTCTCTTCCTTGCCTTGCCTTTTTCTGG 1 F3: 4 CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT R RF: TTATAGTCAACATTTTCTCTTCCTTGCCTTGCCTTTTTCTGAAGACCCCACATCCCACAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT RR: AATATCAGTTGTAAAAGAGAAGGAACGGAACGGAAAAAGACTTCTGGGGTGTAGGGTGTTTTGAAGAGTCAACTTCGACAGGTAGAAAAGTACTGGA F2: 3 GAAGAGTCAAC 2 Unidirectional alignment (log-probability: -39.8) ATAGTCAACATcTTCTCTTCCTTGCCTTGCCTTTTTCTggcaactgaGAAG-------------CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT ATAGTCAACATTTTCTCTTCCTTGCCTTGCCTTTTTCT---------GAAGACCCCACATCCCACAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT Template switch alignment (log-probability: -28.2) ATAGTCAACATcTTCTCTTCCTTGCCTTGCCTTTTTCTGg|CAACTGAGAAG|CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT ATAGTCAACATTTTCTCTTCCTTGCCTTGCCTTTTTCTGA|CAACTGAGAAG|CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT Chimp > Gorilla --------------- chr9:54669471-54669481 Template switch process: F1: L TTATAGTCAACATCTTCTCTTCCTTGCCTTGCCTTTTTCTGG 1 F3: 4 CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT R RF: TTATAGTCAACATTTTCTCTTCCTTGCCTTGCCTTTTTCTGAACACCCCATATCCCACAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT RR: AATATCAGTTGTAAAAGAGAAGGAACGGAACGGAAAAAGACTTGTGGGGTATAGGGTGTTTTGAAGAGTCAACTTCGACAGGTAGAAAAGTACTGGA F2: 3 GAAGAGTCAAC 2 Unidirectional alignment (log-probability: -44.2) ATAGTCAACATcTTCTCTTCCTTGCCTTGCCTTTTTCTG----------------gcaactgagaagCAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT ATAGTCAACATTTTCTCTTCCTTGCCTTGCCTTTTTCTGAACACCCCATATCCCA------------CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT Template switch alignment (log-probability: -28.2) ATAGTCAACATcTTCTCTTCCTTGCCTTGCCTTTTTCTGg|CAACTGAGAAG|CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT ATAGTCAACATTTTCTCTTCCTTGCCTTGCCTTTTTCTGA|CAACTGAGAAG|CAAAACTTCTCAGTTGAAGCTGTCCATCTTTTCATGACCT ========== Event 3844 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GGTACTACTAGTGTACTGATTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA---------CCGTGGGATGTAGAATTAAACAA Chimp: GGTACTACTAGTGTACTGATTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA---------CCGTGGGATGTAGAATTAAACAA ↓ 4 3 2 1 Gorilla: GGTACTACTAGTATACTGATTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACATAAGCTTATGTATGGGATGTAGAATTAAACAA ↑ 4 3 2 1 Human: GGTACTACTAGTGTACTGATTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA---------CCGTGGGATGTAGAATTAAACAA Cluster: [ ] Orangutan: GGTACTACTAGTGTACTGATTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA---------CCGTGGGATGTAGAATTAAACAA Human > Gorilla --------------- chr9:53307879-53307883 Template switch process: F1: L ATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA 1 F3: 4 TTATGTA---------------------------------------------------TGGGATGTAGAATTAAACAAGGTTTTAAGAACTAGAGGGC R RF: ATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACACCGTGGGATGTAGAATTAAACAAGGTTTTAAGAACTAGAGGGC RR: TATAATGGAGAAAAGACATCCTCGTTCGAATAAAAGTATGTGGCACCCTACATCTTAATTTGTTCCAAAATTCTTGATCTCCCG F2: 3 CGAAT 2 Unidirectional alignment (log-probability: -38) TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA---taagcttatgtaTGGGATGTAGAATTAAACAAGGTTTTAAGAACT TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACACCG------------TGGGATGTAGAATTAAACAAGGTTTTAAGAACT Template switch alignment (log-probability: -28.9) TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA|TAAGC|TTATGTA---------------------------------------------------TGGGATGTAGAATTAAACAAGGTTTTAAGAACT TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA|TAAGC|TTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACACCGTGGGATGTAGAATTAAACAAGGTTTTAAGAACT Chimp > Gorilla --------------- chr9:53307879-53307883 Template switch process: F1: L ATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA 1 F3: 4 TTATGTA---------------------------------------------------TGGGATGTAGAATTAAACAAGGTTTTAAGAACTAGAGGGC R RF: ATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACACCGTGGGATGTAGAATTAAACAAGGTTTTAAGAACTAGAGGGC RR: TATAATGGAGAAAAGACATCCTCGTTCGAATAAAAGTATGTGGCACCCTACATCTTAATTTGTTCCAAAATTCTTGATCTCCCG F2: 3 CGAAT 2 Unidirectional alignment (log-probability: -38) TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA---taagcttatgtaTGGGATGTAGAATTAAACAAGGTTTTAAGAACT TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACACCG------------TGGGATGTAGAATTAAACAAGGTTTTAAGAACT Template switch alignment (log-probability: -28.9) TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA|TAAGC|TTATGTA---------------------------------------------------TGGGATGTAGAATTAAACAAGGTTTTAAGAACT TATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACA|TAAGC|TTATGTATCATTCTATATTACCTCTTTTCTGTAGGAGCAAGCTTATTTTCATACACCGTGGGATGTAGAATTAAACAAGGTTTTAAGAACT ========== Event 3845 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CTTCTCGCTCCAGGAGCTCGCTGGAGAACAT--------ATCGAGGCCTGTGTGGCTCCTCA Chimp: CTTCTCGCTCCAGGAGCTCGCTGGAGAACAT----TCCCGCCGAGGCCTGTGTGGCTCCTCA Gorilla: CTTCTCGCTCCAGGAGCTCGCTGGAGAACATTCCA----GCCGAGGCCTGTGTGGCTCCTCA ↑ 3 2 1 4 Human: CTTCTCGCTCCAGGAGCTCGCTGGAGAACAT--------ATCGAGGCCTGTGTGGCTCCTCA Cluster: [ ] Orangutan: CTTCTCACTCCAGGAGCTTGCTGGAGAACATTCCA----GCAGAGGCCTGTGTGGCTCCTCA Human > Gorilla --------------- chr9:69666632-69666637 Template switch process: F1: L GGCCGTGGTACTTCTCGCTCCAGGAGCTCGCTGGAGAACAT 1 F3: 4 CGAGGCCTGTGTGGCTCCTCAGCCCATACCCTCAGGAGAA R RF: GGCTGTGGTACTTCTCGCTCCAGGAGCTCGCTGGAGAACATATCGAGGCCTGTGTGGCTCCTCAGCCCATACCCTCAGGAGAA RR: CCGACACCATGAAGAGCGAGGTCCTCGAGCGACCTCTTGTATAGCTCCGGACACACCGAGGAGTCGGGTATGGGAGTCCTCTT F2: 3 CGACCT 2 Unidirectional alignment (log-probability: -33.2) GCcGTGGTACTTCTCGCTCCAGGAGCTCGCTGGAGAACATtccagcCGAGGCCTGTGTGGCTCCTCAGCCCATACCCTCAGGAGAA GCTGTGGTACTTCTCGCTCCAGGAGCTCGCTGGAGAACAT----ATCGAGGCCTGTGTGGCTCCTCAGCCCATACCCTCAGGAGAA Template switch alignment (log-probability: -22) GCcGTGGTACTTCTCGCTCCAGGAGCTCGCTGGAGAACAT|TCCAGC|CGAGGCCTGTGTGGCTCCTCAGCCCATACCCTCAGGAGAA GCTGTGGTACTTCTCGCTCCAGGAGCTCGCTGGAGAACAT|TCCAGC|CGAGGCCTGTGTGGCTCCTCAGCCCATACCCTCAGGAGAA ========== Event 3846 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATGACAAACATAATATGTACGAGGTCCACacagcaatggggctcagtacctggagctttggaggc Chimp: TATGACAAACATAATATGTACTGAGCCC--ACAGCAATGGGGCTCAGTACCTGgagctttggaggc ↑ 1 4 3 2 Gorilla: TATGACAAACATAATATGTACGAGGTCCACACAGCAATGGGGCTCAGTACCTGgagctttggaggc Human: TATGACAAACATAATATGTACGAGGTCCACacagcaatggggctcagtacctggagctttggaggc Cluster: [ ] Orangutan: TATGACAAACATAATATGTACAAGGTCCACacagcaatggggctcagtacctggagctttggaggc Gorilla > Chimp --------------- chr9:65279569-65279574 Template switch process: F1: L CTTCACAGTGAGATGTCTTGTATGACAAACATAATATGTAC 1 F3: 4 CACAGCAATGGGGCTCAGTACCTGGAGCTTTGGAGGCGAAT R RF: CTTCACAGTGAGATGTCTTGTATGACAAACATAATATGTACGAGGTCCACACAGCAATGGGGCTCAGTACCTGGAGCTTTGGAGGCGAAT RR: GAAGTGTCACTCTACAGAACATACTGTTTGTATTATACATGCTCCAGGTGTGTCGTTACCCCGAGTCATGGACCTCGAAACCTCCGCTTA F2: 3 CCGAGT 2 Unidirectional alignment (log-probability: -27.8) TTCACAGTGAGATGTCTTGTATGACAAACATAATATGTACtGAG---CcCACAGCAATGGGGCTCAGTACCTGGAGCTTTGGAGGCGAA TTCACAGTGAGATGTCTTGTATGACAAACATAATATGTAC-GAGGTCCACACAGCAATGGGGCTCAGTACCTGGAGCTTTGGAGGCGAA Template switch alignment (log-probability: -16.5) TTCACAGTGAGATGTCTTGTATGACAAACATAATATGTAC|TGAGCC|CACAGCAATGGGGCTCAGTACCTGGAGCTTTGGAGGCGAA TTCACAGTGAGATGTCTTGTATGACAAACATAATATGTAC|TGAGCC|CACAGCAATGGGGCTCAGTACCTGGAGCTTTGGAGGCGAA ========== Event 3847 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: GGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGT-TACACAAACACATTTCACAAAGT Chimp: GGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGT-TACACAAACACATTTCACAAAGT ↓ 13 24 ↑ 13 24 Gorilla: GGCAGCCTCTTCAACTTTGTG-TAACCCTACGTTTCCCACAAACACATTTCACAAAGT ↓ 13 24 ↑ 13 24 Human: GGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGT-TACACAAACACATTTCACAAAGT Cluster: [ ] Orangutan: GGCAGCCTCTTCAACTTTGTG-TAACCCTACGTTTCCCACAAACACATTTCACAAAGT Gorilla > Human --------------- chr9:86051782-86051796 Template switch process: F1: L AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG 1 F3: 4 CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA R RF: AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGTAACCCTACGTTTCCCACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA RR: TTGAGGGTGGGGGCGTCGGTCCGTCGGAGAAGTTGAAACACATTGGGATGCAAAGGGTGTTTGTGTAAAGTGTTTCACTGGGGAAAAGTGTATTCT F2: 3 ATTGGGATGCAAAGG 2 Unidirectional alignment (log-probability: -40) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGggaaacgtagggtTA-------------CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG-------------TAACCCTACGTTTCCCACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Template switch alignment (log-probability: -17.6) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|GGAAACGTAGGGTTA|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|GGAAACGTAGGGTTA|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Human > Gorilla --------------- chr9:68115755-68115769 Template switch process: F1: L AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG 1 F3: 4 CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA R RF: AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGTTACACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA RR: TTGAGGGTGGGGGCGTCGGTCCGTCGGAGAAGTTGAAACACCCTTTGCATCCCAATGTGTTTGTGTAAAGTGTTTCACTGGGGAAAAGTGTATTCT F2: 3 CCTTTGCATCCCAAT 2 Unidirectional alignment (log-probability: -40) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG-------------TAaccctacgtttccCACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGTTA-------------CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Template switch alignment (log-probability: -17.6) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|TAACCCTACGTTTCC|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|TAACCCTACGTTTCC|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Gorilla > Chimp --------------- chr9:63338999-63339013 Template switch process: F1: L AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG 1 F3: 4 CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA R RF: AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGTAACCCTACGTTTCCCACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA RR: TTGAGGGTGGGGGCGTCGGTCCGTCGGAGAAGTTGAAACACATTGGGATGCAAAGGGTGTTTGTGTAAAGTGTTTCACTGGGGAAAAGTGTATTCT F2: 3 ATTGGGATGCAAAGG 2 Unidirectional alignment (log-probability: -40) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGggaaacgtagggtTA-------------CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG-------------TAACCCTACGTTTCCCACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Template switch alignment (log-probability: -17.6) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|GGAAACGTAGGGTTA|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|GGAAACGTAGGGTTA|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Chimp > Gorilla --------------- chr9:68115755-68115769 Template switch process: F1: L AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG 1 F3: 4 CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA R RF: AACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGTTACACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA RR: TTGAGGGTGGGGGCGTCGGTCCGTCGGAGAAGTTGAAACACCCTTTGCATCCCAATGTGTTTGTGTAAAGTGTTTCACTGGGGAAAAGTGTATTCT F2: 3 CCTTTGCATCCCAAT 2 Unidirectional alignment (log-probability: -40) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG-------------TAaccctacgtttccCACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTGGGAAACGTAGGGTTA-------------CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA Template switch alignment (log-probability: -17.6) ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|TAACCCTACGTTTCC|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ACTCCCACCCCCGCAGCCAGGCAGCCTCTTCAACTTTGTG|TAACCCTACGTTTCC|CACAAACACATTTCACAAAGTGACCCCTTTTCACATAAGA ========== Event 3848 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GATGGGACGGTCCTGAGAAGG--CCCTGGGACACCCTAGGGGTGTCATAGTGGGAACTATGCCTTTGCAG Chimp: GATGGGACGGTCCTGAGAAGG--CCCTGGGACACCCCAGGGGTGTCATAGTGGGAACTATGCCTTTGCAG ↑ 3 1 2 4 Gorilla: GATGGGACGGTCCTGAGAAGGGAGGTTATGACACCCCTGGGGTGTCATGGTGGGAACTATGCCTTTGCAG Human: GATGGGACGGTCCTGAGAAGG--CCCTGGGACACCCTAGGGGTGTCATAGTGGGAACTATGCCTTTGCAG Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Gorilla > Chimp --------------- chr9:49739452-49739470 Template switch process: F1: L CAGCCTTGTCCCTGGGGCAGGATGGGACGGTCCTGAGAAGG-------------CCCTGGG 1 F3: 4 GTGGGAACTATGCCTTTGCAGTGCCCAGG R RF: CAGCCTTGTCCCTGGGGCAGGATGGGACGGTCCTGAGAAGGGAGGTTATGACACCCCTGGGGTGTCATGGTGGGAACTATGCCTTTGCAGTGCCCAGG RR: GTCGGAACAGGGACCCCGTCCTACCCTGCCAGGACTCTTCCCTCCAATACTGTGGGGACCCCACAGTACCACCCTTGATACGGAAACGTCACGGGTCC F2: 3 ATACTGTGGGGACCCCACA 2 Unidirectional alignment (log-probability: -39.4) TCCCTGGGGCAGGATGGGACGGTCCTGAGAAGgccctGG-------GACACCCCaGGGGTGTCATaGTGGGAACTATGCCTTTGCAGTGCCCAGG TCCCTGGGGCAGGATGGGACGGTCCTGAGAAG-----GGAGGTTATGACACCCCTGGGGTGTCATGGTGGGAACTATGCCTTTGCAGTGCCCAGG Template switch alignment (log-probability: -28.5) TCCCTGGGGCAGGATGGGACGGTCCTGAGAAGG-------------CCCTGGG|ACACCCCAGGGGTGTCATA|GTGGGAACTATGCCTTTGCAGTGCCCAGG TCCCTGGGGCAGGATGGGACGGTCCTGAGAAGGGAGGTTATGACACCCCTGGG|ACACCCCAGGGGTGTCATA|GTGGGAACTATGCCTTTGCAGTGCCCAGG ========== Event 3849 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCTTTTGCAAGCTTAGATTCCTGGTGTCTCTAGTCTGTGGGTATTAATGAGGTCAGAA ↓ 1 3 4 2 Chimp: TGCTTTTGCAAGCTTAGATTCACAGACTAGAGAGTCTGTGGGTATTAATGAGGTCAGAA Gorilla: TGCTTTtgcaagcttagattcctggtgtctctagtctgtgggtattaatgaggtcagaa Human: TGCTTTTGCAAGCTTAGATTCCTGGTGTCTCTAGTCTGTGGGTATTAATGAGGTCAGAA Cluster: [ ] Orangutan: TGCTTTTGCAAGCTTAGATTCCTGGTGTCTCTAGTCTGTGGGTATTAATGAGGTCAGAA Human > Chimp ------------- chr9:66288193-66288203 Template switch process: F1: L ACAACCCTTATGTTCCCTTATGCTTTTGCAAGCTTAGATTC 1 F3: 4 AGTCTGTGGGTATTAATGAGGTCAGAATTCTCATGACAGT R RF: ACAACCCTTATGTTCCCTTATGCTTTTGCAAGCTTAGATTCCTGGTGTCTCTAGTCTGTGGGTATTAATGAGGTCAGAATTCTCATGACAGT RR: TGTTGGGAATACAAGGGAATACGAAAACGTTCGAATCTAAGGACCACAGAGATCAGACACCCATAATTACTCCAGTCTTAAGAGTACTGTCA F2: 3 GAGATCAGACA 2 Unidirectional alignment (log-probability: -37.5) CAACCCTTATGTTCCCTTATGCTTTTGCAAGCTTAGATTC-----------acagactagagAGTCTGTGGGTATTAATGAGGTCAGAATTCTCATGACAGT CAACCCTTATGTTCCCTTATGCTTTTGCAAGCTTAGATTCCTGGTGTCTCT-----------AGTCTGTGGGTATTAATGAGGTCAGAATTCTCATGACAGT Template switch alignment (log-probability: -16.6) CAACCCTTATGTTCCCTTATGCTTTTGCAAGCTTAGATTC|ACAGACTAGAG|AGTCTGTGGGTATTAATGAGGTCAGAATTCTCATGACAGT CAACCCTTATGTTCCCTTATGCTTTTGCAAGCTTAGATTC|ACAGACTAGAG|AGTCTGTGGGTATTAATGAGGTCAGAATTCTCATGACAGT ========== Event 3850 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AATGCCTCAGAGAATGAGAGATTCCATAGACATA-TATTTTCTAGGCAATTAAACCTCCA ↓ 3 2 1 4 Chimp: AATGCCTCAGACAATGAGAGATTCCATAGACATGGAATCTTCTAGGCAATTAAACCTCCA ↑ 3 2 1 4 Gorilla: AATGCCTCAGAGAATGAGAGATTCCATAGACATA-TATTTTCTAGGCAATTAAACCTCCA Human: AATGCCTCAGAGAATGAGAGATTCCATAGACATA-TATTTTCTAGGCAATTAAACCTCCA Cluster: [ ] Orangutan: AATGCCTCAGAGAATGAGAGATTCCATAGACATA-AATTTTCTAGGCAATTAAACCTCCA Human > Chimp ------------- chr9:9332673-9332678 Template switch process: F1: L GAATTGCAAATGCCTCAGACAATGAGAGATTCCATAGACAT 1 F3: 4 TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG R RF: GAATTGCAAATGCCTCAGAGAATGAGAGATTCCATAGACATATATTTTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG RR: CTTAACGTTTACGGAGTCTCTTACTCTCTAAGGTATCTGTATATAAAAGATCCGTTAATTTGGAGGTACTATTACTCCCTCAATTC F2: 3 CTAAGG 2 Unidirectional alignment (log-probability: -36) AATTGCAAATGCCTCAGAcAATGAGAGATTCCATAGACA-----TggaatcTTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG AATTGCAAATGCCTCAGAGAATGAGAGATTCCATAGACATATATT------TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG Template switch alignment (log-probability: -22) AATTGCAAATGCCTCAGAcAATGAGAGATTCCATAGACAT|GGAATC|TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG AATTGCAAATGCCTCAGAGAATGAGAGATTCCATAGACAT|GGAATC|TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG Gorilla > Chimp --------------- chr9:9332673-9332678 Template switch process: F1: L GAATTGCAAATGCCTCAGACAATGAGAGATTCCATAGACAT 1 F3: 4 TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG R RF: GAATTGCAAATGCCTCAGAGAATGAGAGATTCCATAGACATATATTTTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG RR: CTTAACGTTTACGGAGTCTCTTACTCTCTAAGGTATCTGTATATAAAAGATCCGTTAATTTGGAGGTACTATTACTCCCTCAATTC F2: 3 CTAAGG 2 Unidirectional alignment (log-probability: -34.5) AATTGCAAATGCCTCAGAcAATGAGAGATTCCATAGACATggaATcTTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG AATTGCAAATGCCTCAGAGAATGAGAGATTCCATAGACAT-ATATTTTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG Template switch alignment (log-probability: -22) AATTGCAAATGCCTCAGAcAATGAGAGATTCCATAGACAT|GGAATC|TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG AATTGCAAATGCCTCAGAGAATGAGAGATTCCATAGACAT|GGAATC|TTCTAGGCAATTAAACCTCCATGATAATGAGGGAGTTAAG ========== Event 3851 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCACCTTGGCTTGTGCCAGGC---------ACAAGTATAACCTACATAGCCTTGGACGGCAATACTGCTTTGGAGGGA Chimp: CCACCTTGGCTTGTGCCAGGC---------ACAAGTATAACCTACATAGCCTTAGATGGCAATACTGCTTTGGAGGGA ↓ 3 4 2 Gorilla: CCACCTTGGcttgtgccaggtatacttgtgccaagtataACCTACATAGCCTTAGACAGCAATACTGCTTTGGAGGGA ↑ 3 4 2 Human: CCACCTTGGCTTGTGCCAGGC---------ACAAGTATAACCTACATAGCCTTGGACGGCAATACTGCTTTGGAGGGA Cluster: [ ] Orangutan: CCACCTTGGCTTGTGCCAGGC---------ACAAGTATAACCTACATAGCCTTAGATGGCAATACTGCTTTGGAGGGA Human > Gorilla --------------- chr9:80784416-80784426 Template switch process: F1: L GTGCCAGG 1 F3: 4 CAAGTATAACCTACATAGCCTTAGACAGCAATACTGCTTTGGAGGGAGAGACACAAGGAACAATGGA R RF: GTGCCAGGCACAAGTATAACCTACATAGCCTTGGACGGCAATACTGCTTTGGAGGGAGAGACACAAGGAACAATGGA RR: CACGGTCCGTGTTCATATTGGATGTATCGGAACCTGCCGTTATGACGAAACCTCCCTCTCTGTGTTCCTTGTTACCT F2: 3 CGTGTTCATAT 2 Unidirectional alignment (log-probability: -40.3) GTGCCAGGtAtacttgtgcCAAGTATAACCTACATAGCCTTaGACaGCAATACTGCTTT GTGCCAGGCA---------CAAGTATAACCTACATAGCCTTGGACGGCAATACTGCTTT Template switch alignment (log-probability: -28) GTGCCAGG|TATACTTGTGC|CAAGTATAACCTACATAGCCTTaGACaGCAATACTGCTTT GTGCCAGG|TATACTTGTGC|CAAGTATAACCTACATAGCCTTGGACGGCAATACTGCTTT Chimp > Gorilla --------------- chr9:80784416-80784426 Template switch process: F1: L CCAGG 1 F3: 4 CAAGTATAACCTACATAGCCTTAGACAGCAATACTGCTTTGGAGGGAGAGACACAAGGAACAATGGA R RF: CCAGGCACAAGTATAACCTACATAGCCTTAGATGGCAATACTGCTTTGGAGGGAGAGACACAAGGAACAATGGA RR: GGTCCGTGTTCATATTGGATGTATCGGAATCTACCGTTATGACGAAACCTCCCTCTCTGTGTTCCTTGTTACCT F2: 3 CGTGTTCATAT 2 Unidirectional alignment (log-probability: -40.3) CCAGGtAtacttgtgcCAAGTATAACCTACATAGCCTTAGAcaGCAATACTGCTTT CCAGGCA---------CAAGTATAACCTACATAGCCTTAGATGGCAATACTGCTTT Template switch alignment (log-probability: -27.9) CCAGG|TATACTTGTGC|CAAGTATAACCTACATAGCCTTAGAcaGCAATACTGCTTT CCAGG|TATACTTGTGC|CAAGTATAACCTACATAGCCTTAGATGGCAATACTGCTTT ========== Event 3852 ========== Phylogenetic placement: ILS consistent Significant comparisons: 1 Detected in comparisons: 16 Multiple sequence alignment: Human: GTTTGTATGTGGCAGCTACAATATCTTTATACTGTATATATCTTTATCATTGTAATATGAGGGTTGCCTTATTTGTTTTTCCACAAAACTTAGAGAGACAAGGGTGCAGATGACAGGGCCAACTTCTGTACAGTAATCCTATCCAAGACAAACA ↑ 4 1 3 2 Chimp: GTTTGTATGTGGCAGCTACAATATCT-----------------TTATTATTGTAATATGAGGGTTGCCTTATTTGTTTTTCCACAAAACGTAGAGAGACAAGGGTGCAGATGACAGGGCCAACTTCTGTACAGTAATCCTATCCAAGACAAACA Gorilla: GTTTGTATGTGGCAGCTACaatatctttatattgtatatatctttatcattgtaatatGAGGGTTGCCTTATTTGTTTTTCCACAAAACTTAGAGAGACAAGGGTGCAGATGACAGGGCCAACTTCTGTACAGTAATCCTATCCAAGACCAACA Human: GTTTGTATGTGGCAGCTACAATATCTTTATACTGTATATATCTTTATCATTGTAATATGAGGGTTGCCTTATTTGTTTTTCCACAAAACTTAGAGAGACAAGGGTGCAGATGACAGGGCCAACTTCTGTACAGTAATCCTATCCAAGACAAACA Cluster: [ ] Orangutan: GTTTGTATGTGGCAGCTAtaatatctttatattgtatatatctttatcattgtaatatGAGGGTTGCCTTATTTGTTTTTCCACAAAACTTAGAGAGACAAAGGTGCAGATGACAGGGCCAACTTCTGTACAGTAATCCTATCCAAGACCAACA Chimp > Human ------------- chr9:48149234-48149239 Template switch process: F1: L ACTGTGACTTCAGGTGTTTGTATGTGGCAGCTACAATATCTTTAT 1 F3: 4 TATATCTTTATCATTGTAATATGAGGGTTGCCTTATTTGTTTTTCCACAAAA R RF: ACTGTGACTTCAGGTGTTTGTATGTGGCAGCTACAATATCTTTATTATTGTAATATGAGGGTTGCCTTATTTGTTTTTCCACAAAACGTAGAGAGACAAGGGTGCAGATGACAGGGCCAACTTCTGTACAGT RR: TGACACTGAAGTCCACAAACATACACCGTCGATGTTATAGAAATAATAACATTATACTCCCAACGGAATAAACAAAAAGGTGTTTTGCATCTCTCTGTTCCCACGTCTACTGTCCCGGTTGAAGACATGTCA F2: 3 ATGTCA 2 Unidirectional alignment (log-probability: -41.4) GACTTCAGGTGTTTGTATGTGGCAGCTACAATATCTTTATactgtatatatctttatcATTGTAATATGAGGGTTGCCTTATTTGT GACTTCAGGTGTTTGTATGTGGCAGCTACAATATCTTTATT-----------------ATTGTAATATGAGGGTTGCCTTATTTGT Template switch alignment (log-probability: -28.3) GACTTCAGGTGTTTGTATGTGGCAGCTACAATATCTTTAT|ACTGTA|tATATCTTTATcATTGTAATATGAGGGTTGCCTTATTTGT GACTTCAGGTGTTTGTATGTGGCAGCTACAATATCTTTAT|ACTGTA|AATATCTTTATTATTGTAATATGAGGGTTGCCTTATTTGT ========== Event 3853 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACAAATTGTTAGCAACTATCTTGAC------TTATATCATCAATTTTTATTGTA Chimp: ACAAATTGTTAGCAACTATCTTGAC------TTATATCATCAATTTTTATTGTA ↓ 3 1 4 Gorilla: ACAAATTGTTAGCAACTATCTTGATAAGTCAAGATATCATCAATTTTTATTGTA ↑ 3 1 4 Human: ACAAATTGTTAGCAACTATCTTGAC------TTATATCATCAATTTTTATTGTA Cluster: [ ] Orangutan: ACAAATTGTTAGCAACTATCTTGAC------TTATATCATCAATTTTTATTGTA Human > Gorilla --------------- chr9:49518226-49518234 Template switch process: F1: L TAATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA 1 F3: 4 ATATCATCAATTTTTATTGTAAATTGAATTTAAAAAACAT R RF: TAATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGACTTATATCATCAATTTTTATTGTAAATTGAATTAAAAAAACAT RR: ATTATTACATACGTCACTGTTTAACAATCGTTGATAGAACTGAATATAGTAGTTAAAAATAACATTTAACTTAATTTTTTTGTA F2: 3 GAACTGAAT 2 Unidirectional alignment (log-probability: -37.8) AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA--TaagtcaagATATCATCAATTTTTATTGTAAATTGAATTtAAAAAACAT AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGACTT--------ATATCATCAATTTTTATTGTAAATTGAATTAAAAAAACAT Template switch alignment (log-probability: -22.4) AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA|TAAGTCAAG|ATATCATCAATTTTTATTGTAAATTGAATTtAAAAAACAT AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA|TAAGTCAAG|ATATCATCAATTTTTATTGTAAATTGAATTAAAAAAACAT Chimp > Gorilla --------------- chr9:49518226-49518234 Template switch process: F1: L TAATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA 1 F3: 4 ATATCATCAATTTTTATTGTAAATTGAATTTAAAAAACAT R RF: TAATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGACTTATATCATCAATTTTTATTGTAAATTGAATTAAAAAAACAT RR: ATTATTACATACGTCACTGTTTAACAATCGTTGATAGAACTGAATATAGTAGTTAAAAATAACATTTAACTTAATTTTTTTGTA F2: 3 GAACTGAAT 2 Unidirectional alignment (log-probability: -37.8) AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA--TaagtcaagATATCATCAATTTTTATTGTAAATTGAATTtAAAAAACAT AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGACTT--------ATATCATCAATTTTTATTGTAAATTGAATTAAAAAAACAT Template switch alignment (log-probability: -22.4) AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA|TAAGTCAAG|ATATCATCAATTTTTATTGTAAATTGAATTtAAAAAACAT AATAATGTATGCAGTGACAAATTGTTAGCAACTATCTTGA|TAAGTCAAG|ATATCATCAATTTTTATTGTAAATTGAATTAAAAAAACAT ========== Event 3854 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTATGAAGATGAAAATCCAA----GCTCTCTT-AGATCATTCCCTTCTCTACACTGCTGAAAG Chimp: TTTATGAAGATAAAAATCCAAGGGAATGATCTAAGGATCATTCCCTTCTCTACACTGCTTAAAG ↑ 1 3 4 2 Gorilla: TTTATGAAGATAAAAATCCAA----GCTCTCTT-AGATCATTCCCTTCTCTACACTGCTTAAAG Human: TTTATGAAGATGAAAATCCAA----GCTCTCTT-AGATCATTCCCTTCTCTACACTGCTGAAAG Cluster: [ ] Orangutan: TTTATGAAGATAAAAATCCAA----GCTCTCTT-AGATCACTCCCTTCTCTACACTGCTTAAAG Gorilla > Chimp --------------- chr9:48284922-48284934 Template switch process: F1: L TGGCCCAAGAGCTCCATCCATTTATGAAGATAAAAATCCAAG 1 F3: 4 GATCATTCCCTTCTCTACACTGCTTAAAGTCAACCCCTTG R RF: TGGCCCAAGAGCTCCATCCATTTATGAAGATAAAAATCCAAGCTCTCTTAGATCATTCCCTTCTCTACACTGCTTAAAGTCAACCCCTTG RR: ACCGGGTTCTCGAGGTAGGTAAATACTTCTATTTTTAGGTTCGAGAGAATCTAGTAAGGGAAGAGATGTGACGAATTTCAGTTGGGGAAC F2: 3 GAATCTAGTAAGG 2 Unidirectional alignment (log-probability: -39.7) GCCCAAGAGCTCCATCCATTTATGAAGATAAAAATCCAAG--------ggaatgatctaagGATCATTCCCTTCTCTACACTGCTTAAAGTCAACCCCTTG GCCCAAGAGCTCCATCCATTTATGAAGATAAAAATCCAAGCTCTCTTA-------------GATCATTCCCTTCTCTACACTGCTTAAAGTCAACCCCTTG Template switch alignment (log-probability: -17.4) GCCCAAGAGCTCCATCCATTTATGAAGATAAAAATCCAAG|GGAATGATCTAAG|GATCATTCCCTTCTCTACACTGCTTAAAGTCAACCCCTTG GCCCAAGAGCTCCATCCATTTATGAAGATAAAAATCCAAG|GGAATGATCTAAG|GATCATTCCCTTCTCTACACTGCTTAAAGTCAACCCCTTG ========== Event 3855 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 256 Detected in comparisons: 1256 Multiple sequence alignment: Human: GGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCACCCCCAGCTCTCTGTGGGGCTG ↓ 1 3 24 Chimp: GGTTGGTGCTAACTGCGTGGGGTGCAGCAGT---GCCCCAGCTCTCTGTGGGGCTG ↓ 3 1 2 4 ↑ 1 3 24 Gorilla: GGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCACCCCCAGCTCTCTGTGGGGCTG Human: GGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCACCCCCAGCTCTCTGTGGGGCTG Cluster: [ ] Orangutan: GGTTGGTGCTAACTGCGTGGGCTGCACTGCTCCACCCCCAGCTCTCTGTGGGGCTG Human > Chimp ------------- chr9:47289069-47289079 Template switch process: F1: L CTTTGGCCCTGGACCTGCCTGGTTGGTGCTAACTGCGTGGG 1 F3: 4 CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA R RF: CTTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCACCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA RR: GAAACCGGGACCTGGACGGGCCAACCACGATTGACGCACCCGACGTGACGACGTGGGGGTCGAGAGACACCCCGACTCCCCAGTCACCGAATAAT F2: 3 GTGACGACGTG 2 Unidirectional alignment (log-probability: -42.2) TTTGGCCCTGGACCTGCCtGGTTGGTGCTAACTGCGTGGGgTGCA---------gcagtgCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA TTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCAC------CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA Template switch alignment (log-probability: -22.6) TTTGGCCCTGGACCTGCCtGGTTGGTGCTAACTGCGTGGG|GTGCAGCAGTG|CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA TTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGG|GTGCAGCAGTG|CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA Gorilla > Chimp --------------- chr9:47289069-47289079 Template switch process: F1: L CTTTGGCCCTGGACCTGCCTGGTTGGTGCTAACTGCGTGGG 1 F3: 4 CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA R RF: CTTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCACCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA RR: GAAACCGGGACCTGGACGGGCCAACCACGATTGACGCACCCGACGTGACGACGTGGGGGTCGAGAGACACCCCGACTCCCCAGTCACCGAATAAT F2: 3 GTGACGACGTG 2 Unidirectional alignment (log-probability: -40.4) TTTGGCCCTGGACCTGCCtGGTTGGTGCTAACTGCGTGGGgTGCA-----GCAgtgCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA TTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGGCTGCACTGCTGCA--CCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA Template switch alignment (log-probability: -22.6) TTTGGCCCTGGACCTGCCtGGTTGGTGCTAACTGCGTGGG|GTGCAGCAGTG|CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA TTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGG|GTGCAGCAGTG|CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA Chimp > Gorilla --------------- chr9:47924550-47924558 Template switch process: F1: L CTTTGGCCCTGGACCTGCCCGGTTGGTGCTAACTGCGTGGGCTGCA 1 F3: 4 CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA R RF: CTTTGGCCCTGGACCTGCCTGGTTGGTGCTAACTGCGTGGGGTGCAGCAGTGCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA RR: GAAACCGGGACCTGGACGGACCAACCACGATTGACGCACCCCACGTCGTCACGGGGTCGAGAGACACCCCGACTCCCCAGTCACCGAATAAT F2: 3 CACGTCGTC 2 Unidirectional alignment (log-probability: -44.6) CCCTGGACCTGCCcGGTTGGTGCTAACTGCGTGGGcTGCActgctGCA--cCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA CCCTGGACCTGCCTGGTTGGTGCTAACTGCGTGGGGTGCA-----GCAGTGCCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA Template switch alignment (log-probability: -28) CCCTGGACCTGCCcGGTTGGTGCTAACTGCGTGGGcTGCA|CTGCTGCAC|CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA CCCTGGACCTGCCTGGTTGGTGCTAACTGCGTGGGGTGCA|CTGCTGCAC|CCCCAGCTCTCTGTGGGGCTGAGGGGTCAGTGGCTTATTA ========== Event 3856 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: CTATTTCTCAAAAGTCTATATTATTACCTTAGAACTGGCCCTACGATCATGGAACTTAGATACAGGGA Chimp: Gorilla: CTATTTCTCAAAAGTCTATATGA---------------TCGTAGGATCATGGAACTTAGATACAGGGA ↑ 1 3 4 2 Human: CTATTTCTCAAAAGTCTATATTATTACCTTAGAACTGGCCCTACGATCATGGAACTTAGATACAGGGA Cluster: [ ] Orangutan: Human > Gorilla --------------- chr9:46823754-46823761 Template switch process: F1: L GGTCTGAAATTGCTCTTTGCCTATTTCTCAAAAGTCTATAT 1 F3: 4 GATCATGGAACTTAGATACAGGGACCCAGGTCTAGATAGC R RF: GGTCTGAAATTGCTCTTTGCCTATTTCTCAAAAGTCTATATTATTACCTTAGAACTGGCCCTACGATCATGGAACTTAGATACAGGGACCCAGGTCTAGATAGC RR: CCAGACTTTAACGAGAAACGGATAAAGAGTTTTCAGATATAATAATGGAATCTTGACCGGGATGCTAGTACCTTGAATCTATGTCCCTGGGTCCAGATCTATCG F2: 3 GATGCTAG 2 Unidirectional alignment (log-probability: -28.3) GTCTGAAATTGCTCTTTGCCTATTTCTCAAAAGTCTATATgAT---------------CgTAgGATCATGGAACTTAGATACAGGGACCCAGGTCTAGATAGC GTCTGAAATTGCTCTTTGCCTATTTCTCAAAAGTCTATATTATTACCTTAGAACTGGCCCTACGATCATGGAACTTAGATACAGGGACCCAGGTCTAGATAGC Template switch alignment (log-probability: -16.7) GTCTGAAATTGCTCTTTGCCTATTTCTCAAAAGTCTATAT|GATCGTAG|GATCATGGAACTTAGATACAGGGACCCAGGTCTAGATAGC GTCTGAAATTGCTCTTTGCCTATTTCTCAAAAGTCTATAT|GATCGTAG|GATCATGGAACTTAGATACAGGGACCCAGGTCTAGATAGC ========== Event 3857 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCCATGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCC Chimp: TCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCCGTGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCC ↓ 3 2 1 4 Gorilla: TCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCTGTGGTAAT----------------GGACTCCCCAGACTCTGTGCTGCCCC ↑ 3 2 1 4 Human: TCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCCATGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCC Cluster: [ ] Orangutan: TCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCTGTGGTGAT----------------GGACTCCCCAGACTCTGTGCTGCCCC Human > Gorilla --------------- chr9:46614581-46614585 Template switch process: F1: L GAGCCTCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACC---------------TGTGGTAAT 1 F3: 4 CCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC R RF: GAGCCTCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCCATGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC RR: CTCGGAGCCTTCCCGGGGGTCGGGTCAGGGAGGGACTGTGGGTACCATTAGGGTCCACACCATTAGGGTGTGGGGTCTGAGACACGACGGGGTAAGCTGCAAGAAGTCCGG F2: 3 TCAGG 2 Unidirectional alignment (log-probability: -38.2) AGGGCCCCCAGCCCAGTCCCTCCCTGACACC---------------TGTGGTAAT-ggACtCCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC AGGGCCCCCAGCCCAGTCCCTCCCTGACACCCATGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC Template switch alignment (log-probability: -27.1) AGGGCCCCCAGCCCAGTCCCTCCCTGACACC---------------TGTGGTAAT|GGACT|CCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC AGGGCCCCCAGCCCAGTCCCTCCCTGACACCCATGGTAATCCCAGGTGTGGTAAT|GGACT|CCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC Chimp > Gorilla --------------- chr9:46614581-46614585 Template switch process: F1: L GAGCCTCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCTGTGGTAAT 1 F3: 4 CCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC R RF: GAGCCTCGGAAGGGCCCCCAGCCCAGTCCCTCCCTGACACCCGTGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC RR: CTCGGAGCCTTCCCGGGGGTCGGGTCAGGGAGGGACTGTGGGCACCATTAGGGTCCACACCATTAGGGTGTGGGGTCTGAGACACGACGGGGTAAGCTGCAAGAAGTCCGG F2: 3 TCAGG 2 Unidirectional alignment (log-probability: -32.7) AGGGCCCCCAGCCCAGTCCCTCCCTGACACCtGTGGTAA---------TGG-------ACtCCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC AGGGCCCCCAGCCCAGTCCCTCCCTGACACCCGTGGTAATCCCAGGTGTGGTAATCCCACACCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC Template switch alignment (log-probability: -22.1) AGGGCCCCCAGCCCAGTCCCTCCCTGACACCtGTGGTAAT|GGACT|CCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC AGGGCCCCCAGCCCAGTCCCTCCCTGACACCCGTGGTAAT|GGACT|CCCCAGACTCTGTGCTGCCCCATTCGACGTTCTTCAGGCC ========== Event 3858 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: aacactcacacccACTTGCCCCTTGTATCTATAT-AATACAAGGGACTTCCAGATTAAAAGAA ↑ 1 3 4 2 Chimp: AACACTCACACCCACTTGCCCGTTGTA-TTATATAGATACAAGGGACTTCCAGATTAAAAGAA Gorilla: AACACTCACACCCACTTGCCCGTTGTA-TTATATAGATACAAGGGACTTCCAGATTAAAAGAA Human: aacactcacacccACTTGCCCCTTGTATCTATAT-AATACAAGGGACTTCCAGATTAAAAGAA Cluster: [ ] Orangutan: AACACTCACACCAACTTGCCCCTTGTA-TTATATAGATACAGGGGACTTCCAGATTaaaagaa Chimp > Human ------------- chr9:44678179-44678192 Template switch process: F1: L CAGGGCCAAAGGGAAAGCTAAACACTCACACCCACTTGCCC 1 F3: 4 ATACAAGGGACTTCCAGATTAAAAGAAGAAAAAAAGGAAG R RF: CAGGGTCAAAGGGAAAGCTAAACACTCACACCCACTTGCCCGTTGTATTATATAGATACAAGGGACTTCCAGATTAAAAGAAGAAAAAAAGGAAG RR: GTCCCAGTTTCCCTTTCGATTTGTGAGTGTGGGTGAACGGGCAACATAATATATCTATGTTCCCTGAAGGTCTAATTTTCTTCTTTTTTTCCTTC F2: 3 ATATATCTATGTTC 2 Unidirectional alignment (log-probability: -34.7) AGGGcCAAAGGGAAAGCTAAACACTCACACCCACTTGCCCcTTGTATcTATATA-ATACAAGGGACTTCCAGATTAAAAGAAGAAAAAAAGGAAG AGGGTCAAAGGGAAAGCTAAACACTCACACCCACTTGCCCGTTGTAT-TATATAGATACAAGGGACTTCCAGATTAAAAGAAGAAAAAAAGGAAG Template switch alignment (log-probability: -23) AGGGcCAAAGGGAAAGCTAAACACTCACACCCACTTGCCC|CTTGTATCTATATA|ATACAAGGGACTTCCAGATTAAAAGAAGAAAAAAAGGAAG AGGGTCAAAGGGAAAGCTAAACACTCACACCCACTTGCCC|CTTGTATCTATATA|ATACAAGGGACTTCCAGATTAAAAGAAGAAAAAAAGGAAG ========== Event 3859 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: GCCCTGCCCTTCAGATGGTCTCCTGTGC---------------------------------------CCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGCTGCCT ↓ 4 1 3 2 Chimp: GCCCTGCCCTTCAGATGGTCTCCTGTGC--------------------CCACCTGTACCTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGCTGCCT Gorilla: GCCCTGCCCTTCAGATGGTCTCCTGTGCCCACCTGTACCTCCTGTG-C-------------------CCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGCTGCCT ↑ 4 1 3 2 Human: GCCCTGCCCTTCAGATGGTCTCCTGTGC---------------------------------------CCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGCTGCCT Cluster: [ ] Orangutan: GCCCTGCCCTTCAGATGGTCTCCTGTGCCCACCTGTACCTCCTGTGCT-------------------CCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGCTGCCT Human > Chimp ------------- chr9:45444329-45444333 Template switch process: F1: L CACCCACCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC 1 F3: 4 CTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGC R RF: CACCCACCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGC RR: GTGGGTGGAGGGTCGGGACGGGAAGTCTACCAGAGGACACGGGTGGTCTATGTAAGGAAAACAAGTTTCGGGAAGGTACCG F2: 3 CATGT 2 Unidirectional alignment (log-probability: -38.2) CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACCtgtacctcctgtgcccaccAGATACATTCCTTTTGTTCAAAGCCC CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC-------------------AGATACATTCCTTTTGTTCAAAGCCC Template switch alignment (log-probability: -22.2) CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC|TGtAC|CTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCC CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC|TGAAC|CTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCC Human > Gorilla --------------- chr9:46075441-46075445 Template switch process: F1: L CACCCACCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC 1 F3: 4 CTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGC R RF: CACCCACCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCCTTCCATGGC RR: GTGGGTGGAGGGTCGGGACGGGAAGTCTACCAGAGGACACGGGTGGTCTATGTAAGGAAAACAAGTTTCGGGAAGGTACCG F2: 3 CATGT 2 Unidirectional alignment (log-probability: -38.2) CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTgcccacctgtacctcctgtGCCCACCAGATACATTCCTTTTGTTCAAAGCCC CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGT-------------------GCCCACCAGATACATTCCTTTTGTTCAAAGCCC Template switch alignment (log-probability: -22.2) CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC|TGtAC|CTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCC CCTCCCAGCCCTGCCCTTCAGATGGTCTCCTGTGCCCACC|TGAAC|CTCCTGTGCCCACCAGATACATTCCTTTTGTTCAAAGCCC ========== Event 3860 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TTCCTCTTTGTCTCAAAGGGCC---A--GTCTACTAGACTGGCCCACTGTGGGGTCTGCTGTGTGTTCCAACCCTGGAGGTGACACAGTCCCTGCGATAAGAAGGCCAGACTGACGGCCCTACCATCGTTGCT Chimp: TTCCTCTTTGTCTCAAAGGGCC---A--GTCTACTAGACTGGCCCACTGTGGGGTCTGCTGTGTGTTCCAACCCTGGAGGTGACACAGTCCCTGCGATGAGAAGGCCAGACTGACGGCCCTACCATCGTTGCT ↑ 1 4 3 2 Gorilla: TTCCTCTTTGTCTCAAAGGGCTCTGAGCTACTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCAACCCTGGAGGTGACACAGTCCCTGCAATGAGAAGGCCAGACTGACGGCCCTACCATCGTTGCT ↓ 1 4 3 2 Human: TTCCTCTTTGTCTCAAAGGGCC---A--GTCTACTAGACTGGCCCACTGTGGGGTCTGCTGTGTGTTCCAACCCTGGAGGTGACACAGTCCCTGCGATAAGAAGGCCAGACTGACGGCCCTACCATCGTTGCT Cluster: [ ] Orangutan: TTCCTCTTTGTCTCAAAGGGCCCTGAGCTACTACTAGACTGGCCCACTGTGGGGTCTGCTGTGTGTTCCAACCCTGGAGGTGACACAGTCCCTGCGATGAGAAGGCCAGACTGACAGCCCTACCATCGTTGCT Gorilla > Human --------------- chr9:44911956-44911959 Template switch process: F1: L CAAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC 1 F3: 4 CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGTGTTCCA R RF: CAAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGCTCTGAGCTACTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCAACCCTGGAGGTGACACAGTCCCTGCAATGAGAAGGCCAGACTG RR: GTTCTCTCTCCTGACAAGTCAAGGAGAAACAGAGTTTCCCGAGACTCGATGATGATCTGACCGGGTGACACCCCAGACGACACGTAAGGTTGGGACCTCCACTGTGTCAGGGACGTTACTCTTCCGGTCTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -36.4) AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGCcagT--------CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGtgTTCCA AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC---TCTGAGCTACTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCA Template switch alignment (log-probability: -27.3) AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC|CAGT|CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGtgTTCCA AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC|CAGT|CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCA Gorilla > Chimp --------------- chr9:45550518-45550521 Template switch process: F1: L CAAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC 1 F3: 4 CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGTGTTCCA R RF: CAAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGCTCTGAGCTACTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCAACCCTGGAGGTGACACAGTCCCTGCAATGAGAAGGCCAGACTG RR: GTTCTCTCTCCTGACAAGTCAAGGAGAAACAGAGTTTCCCGAGACTCGATGATGATCTGACCGGGTGACACCCCAGACGACACGTAAGGTTGGGACCTCCACTGTGTCAGGGACGTTACTCTTCCGGTCTGAC F2: 3 TGAC 2 Unidirectional alignment (log-probability: -36.4) AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGCcagT--------CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGtgTTCCA AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC---TCTGAGCTACTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCA Template switch alignment (log-probability: -27.3) AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC|CAGT|CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGtgTTCCA AAGAGAGAGGACTGTTCAGTTCCTCTTTGTCTCAAAGGGC|CAGT|CTACTAGACTGGCCCACTGTGGGGTCTGCTGTGCATTCCA ========== Event 3861 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TTGATTGTTACAGACTTAAAAG--------TATTTTGCCTATCTGATATTTATTGGTACTGAAGTTT Chimp: TTGATTGTTACAGACTTAAAAG--------TATTTTGCCTATCTGATATTTATTGGTACTGAAGTTT ↓ 1 4 3 2 Gorilla: TTGATTGTTACAGACTTAAAAATCAGATAGACTTTTGCCTATCTGATATTTATTGGTACTGAAGTTT ↑ 1 4 3 2 Human: TTGATTGTTACAGACTTAAAAG--------TATTTTGCCTATCTGATATTTATTGGTACTGAAGTTT Cluster: [ ] Orangutan: TTGATTGTTACAGACTTAAAAG--------TATTTTGCCTATCTGATATTTATTGGTACTGAAGTTT Human > Gorilla --------------- chr9:76911789-76911799 Template switch process: F1: L TTCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAA 1 F3: 4 TTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA R RF: TTCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAAGTATTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA RR: AAGACGTTGGAGAATAGTTGAACTAACAATGTCTGAATTTTCATAAAACGGATAGACTATAAATAACCATGACTTCAAACCAAT F2: 3 CAGATAGACTA 2 Unidirectional alignment (log-probability: -33.5) TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAaatcagatAGacTTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAA--------AGTATTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA Template switch alignment (log-probability: -22.6) TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAA|ATCAGATAGaC|TTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAA|ATCAGATAGGC|TTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA Chimp > Gorilla --------------- chr9:76911789-76911799 Template switch process: F1: L TTCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAA 1 F3: 4 TTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA R RF: TTCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAAGTATTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA RR: AAGACGTTGGAGAATAGTTGAACTAACAATGTCTGAATTTTCATAAAACGGATAGACTATAAATAACCATGACTTCAAACCAAT F2: 3 CAGATAGACTA 2 Unidirectional alignment (log-probability: -33.5) TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAaatcagatAGacTTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAA--------AGTATTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA Template switch alignment (log-probability: -22.6) TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAA|ATCAGATAGaC|TTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA TCTGCAACCTCTTATCAACTTGATTGTTACAGACTTAAAA|ATCAGATAGGC|TTTTGCCTATCTGATATTTATTGGTACTGAAGTTTGGTTA ========== Event 3862 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGATCTGTTGGGAGATGCTGTCCAG-CTGCAGGCTGTTTTGCCTGTCTGTTTTGGCACG ↓ 3 1 2 4 Chimp: TGATCTGTTGGGAGATGCTGTCCAGCCTGCAGCTGGACTTGCCTGTCTGTTTTGGCACA Gorilla: TGATCTGTTGGGAGATGCTGTCCAGCCTGCAGCTGGACTTGCCTGTCTGTTTTGGCACA ↑ 3 1 2 4 Human: TGATCTGTTGGGAGATGCTGTCCAG-CTGCAGGCTGTTTTGCCTGTCTGTTTTGGCACG Cluster: [ ] Orangutan: TGATCTGTTGGGAGATGCTGTCCAGCCTGCAGCTGGACTTGCCTGTCTGTTTTGGCACA Human > Chimp ------------- chr9:44469812-44469823 Template switch process: F1: L TTGAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC 1 F3: 4 TTGCCTGTCTGTTTTGGCACACTTGCCCTGAGGCAGAGAA R RF: TTGAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGCTGCAGGCTGTTTTGCCTGTCTGTTTTGGCACGCTTGCCCTGAGGCAGAGAA RR: AACTCTACAATCTCCCACTAGACAACCCTCTACGACAGGTCGACGTCCGACAAAACGGACAGACAAAACCGTGCGAACGGGACTCCGTCTCTT F2: 3 CAGGTCGACGTC 2 Unidirectional alignment (log-probability: -45) GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC-----------ctgcagctggacTTGCCTGTCTGTTTTGGCACaCTTGCCCTGAGGCAGAGAA GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGCTGCAGGCTGTT------------TTGCCTGTCTGTTTTGGCACGCTTGCCCTGAGGCAGAGAA Template switch alignment (log-probability: -22.8) GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC|CTGCAGCTGGAC|TTGCCTGTCTGTTTTGGCACaCTTGCCCTGAGGCAGAGAA GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC|CTGCAGCTGGAC|TTGCCTGTCTGTTTTGGCACGCTTGCCCTGAGGCAGAGAA Human > Gorilla --------------- chr9:44986770-44986781 Template switch process: F1: L TTGAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC 1 F3: 4 TTGCCTGTCTGTTTTGGCACACTTGCCCTGAGGCAGAGAA R RF: TTGAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGCTGCAGGCTGTTTTGCCTGTCTGTTTTGGCACGCTTGCCCTGAGGCAGAGAA RR: AACTCTACAATCTCCCACTAGACAACCCTCTACGACAGGTCGACGTCCGACAAAACGGACAGACAAAACCGTGCGAACGGGACTCCGTCTCTT F2: 3 CAGGTCGACGTC 2 Unidirectional alignment (log-probability: -44) GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC-----------ctgcagctggacTTGCCTGTCTGTTTTGGCACaCTTGCCCTGAGGCAGAGAA GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGCTGCAGGCTGTT------------TTGCCTGTCTGTTTTGGCACGCTTGCCCTGAGGCAGAGAA Template switch alignment (log-probability: -22.8) GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC|CTGCAGCTGGAC|TTGCCTGTCTGTTTTGGCACaCTTGCCCTGAGGCAGAGAA GAGATGTTAGAGGGTGATCTGTTGGGAGATGCTGTCCAGC|CTGCAGCTGGAC|TTGCCTGTCTGTTTTGGCACGCTTGCCCTGAGGCAGAGAA ========== Event 3863 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: attagtatcctcctgacttgacaATAGTACCACAGACTATTGTCTGTGGTGGGGTCATGATGGCT Chimp: attagtatcctcctgacttgacaATAGTACCACAGAC---AGTAAGTGGTGGGGTCATGATGGCT Gorilla: attagtatcctcCTGACTTGACAATAGTACCACAGAC---AGTAAGTGGTGGGGTCATGATGGCT ↓ 3 2 1 4 Human: attagtatcctcctgacttgacaATAGTACCACAGACTATTGTCTGTGGTGGGGTCATGATGGCT Cluster: [ ] Orangutan: attagtatcctcCTGACTTGATAATAGTACCACAGAC---AGTAAGTGGTGGGGTCATGATGGCT Gorilla > Human --------------- chr9:9872048-9872054 Template switch process: F1: L AAGCATTAGTATCCTCCTGACTTGACAATAGTACCACAGAC 1 F3: 4 TGTGGTGGGGTCATGATGGCTCCCCTCTATAATTGTTCACA R RF: AAGCATTAGTATCCTCCTGACTTGACAATAGTACCACAGACAGTAAGTGGTGGGGTCATGATGGCTCCCCTCTATAATTGTTCACA RR: TTCGTAATCATAGGAGGACTGAACTGTTATCATGGTGTCTGTCATTCACCACCCCAGTACTACCGAGGGGAGATATTAACAAGTGT F2: 3 CTGTTAT 2 Unidirectional alignment (log-probability: -31.8) AGCATTAGTATCCTCCTGACTTGACAATAGTACCACAGACtattGTctGTGGTGGGGTCATGATGGCTCCCCTCTATAATTGTTCAC AGCATTAGTATCCTCCTGACTTGACAATAGTACCACAGAC---AGTAAGTGGTGGGGTCATGATGGCTCCCCTCTATAATTGTTCAC Template switch alignment (log-probability: -22.2) AGCATTAGTATCCTCCTGACTTGACAATAGTACCACAGAC|TATTGTC|tGTGGTGGGGTCATGATGGCTCCCCTCTATAATTGTTCAC AGCATTAGTATCCTCCTGACTTGACAATAGTACCACAGAC|TATTGTC|AGTGGTGGGGTCATGATGGCTCCCCTCTATAATTGTTCAC ========== Event 3864 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CTGAAACACCACATATACATGAGCTTAAGC--AACATTTTCTGGAGTCATGTGATG Chimp: CTGAAACACCACATATACATGAGCTTAAGC--AACATTTTCTGGAGTCATGTGATG ↓ 3 2 4 Gorilla: CTGAAACACCACATATACATG-ACTTAAGC----TGTTTTCTGGAGTCATGTGATG ↑ 3 2 4 Human: CTGAAACACCACATATACATGAGCTTAAGC--AACATTTTCTGGAGTCATGTGATG Cluster: [ ] Orangutan: CTGAAACACCACATATGCATGAGCTTAAGCAA--CATTTTCTGGAGT--CGTGATG Human > Gorilla --------------- chr9:81667337-81667344 Template switch process: F1: L TTAACTGATTGGATAGATGACTGAAACACCACATATACATGA 1 F3: 4 GTTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAAC R RF: TTAACTGATTGGATAGATGACTGAAACACCACATATACATGAGCTTAAGCAACATTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAAC RR: AATTGACTAACCTATCTACTGACTTTGTGGTGTATATGTACTCGAATTCGTTGTAAAAGACCTCAGTACACTACTTAAAGTCTATTAAGTATTG F2: 3 TCGAATTC 2 Unidirectional alignment (log-probability: -32) AACTGATTGGATAGATGACTGAAACACCACATATACATGA-CTTAAGCtg--TTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA AACTGATTGGATAGATGACTGAAACACCACATATACATGAGCTTAAGCAACATTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA Template switch alignment (log-probability: -22.3) AACTGATTGGATAGATGACTGAAACACCACATATACATGA|CTTAAGCT|gTTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA AACTGATTGGATAGATGACTGAAACACCACATATACATGA|CTTAAGCT|ATTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA Chimp > Gorilla --------------- chr9:81667337-81667344 Template switch process: F1: L TTAACTGATTGGATAGATGACTGAAACACCACATATACATGA 1 F3: 4 GTTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAAC R RF: TTAACTGATTGGATAGATGACTGAAACACCACATATACATGAGCTTAAGCAACATTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAAC RR: AATTGACTAACCTATCTACTGACTTTGTGGTGTATATGTACTCGAATTCGTTGTAAAAGACCTCAGTACACTACTTAAAGTCTATTAAGTATTG F2: 3 TCGAATTC 2 Unidirectional alignment (log-probability: -32) AACTGATTGGATAGATGACTGAAACACCACATATACATGA-CTTAAGCtg--TTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA AACTGATTGGATAGATGACTGAAACACCACATATACATGAGCTTAAGCAACATTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA Template switch alignment (log-probability: -22.3) AACTGATTGGATAGATGACTGAAACACCACATATACATGA|CTTAAGCT|gTTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA AACTGATTGGATAGATGACTGAAACACCACATATACATGA|CTTAAGCT|ATTTTCTGGAGTCATGTGATGAATTTCAGATAATTCATAA ========== Event 3865 ========== Phylogenetic placement: ILS consistent Significant comparisons: 24 Detected in comparisons: 24 Multiple sequence alignment: Human: TGAACAATACCTACTATGCAGG-----------------------------------------AAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCATAGAACTTTTTTTAAAAAAACAT ↓ 4 1 3 2 Chimp: TGAACAATACCTACTATGCAGG--------------------------AAGTGCTATGGAAGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCATATAACTTTTTTaaaaaaaaCAT Gorilla: TGAACAATACCTACTATGCAGG-----------AAGTGCTATGGAAGG---------------AAGTGTTGGCAGTTACCATTTCTATATGTATTTGCTTCCATAGAACtttttttaaaaaaaaaT ↑ 4 1 3 2 Human: TGAACAATACCTACTATGCAGG-----------------------------------------AAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCATAGAACTTTTTTTAAAAAAACAT Cluster: [ ] Orangutan: taaacaATACCTACTATGCAAGAAGTGCTATGG------------------------------AAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCATAGAACTTTTTTTAAAAAAACAT Human > Chimp ------------- chr9:75036110-75036116 Template switch process: F1: L CATGAAGACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG 1 F3: 4 AGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCA R RF: CATGAAGACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCATAG RR: GTACTTCTGATCGACTCAAACTTGTTATGGATGATACGTCCTTCACAACCGTCAATAGTAAAGATATACATAAACGAAGGTATC F2: 3 AGGTATC 2 Unidirectional alignment (log-probability: -32.5) GACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTGctatggaaggaagtgTTGGCAGTTATCATTTCTATATGTATTTGCTT GACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG---------------TTGGCAGTTATCATTTCTATATGTATTTGCTT Template switch alignment (log-probability: -16.3) GACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG|CTATGGA|AGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTT GACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG|CTATGGA|AGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTT Human > Gorilla --------------- chr9:79378030-79378036 Template switch process: F1: L CATGAAGACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG 1 F3: 4 AGGAAGTGTTGGCAGTTACCATTTCTATATGTATTTGCTTCCA R RF: CATGAAGACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTTCCATAG RR: GTACTTCTGATCGACTCAAACTTGTTATGGATGATACGTCCTTCACAACCGTCAATAGTAAAGATATACATAAACGAAGGTATC F2: 3 AGGTATC 2 Unidirectional alignment (log-probability: -38) GACTAGCTGAGTTTGAACAATACCTACTATGCAggaagtgctatggaaGGAAGTGTTGGCAGTTAcCATTTCTATATGTATTTGCTT GACTAGCTGAGTTTGAACAATACCTACTATGCA---------------GGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTT Template switch alignment (log-probability: -22.3) GACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG|CTATGGA|AGGAAGTGTTGGCAGTTAcCATTTCTATATGTATTTGCTT GACTAGCTGAGTTTGAACAATACCTACTATGCAGGAAGTG|CTATGGA|AGGAAGTGTTGGCAGTTATCATTTCTATATGTATTTGCTT ========== Event 3866 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CA--CTTTCTTTACAAAACTGT----------GCCCAATCCCAGAGGGCTGAATTACATAA ↓ 31 4 2 Chimp: CA--CTTTCTTTACAAAACTGGGATTGGGCACACCCAATCCCAGAGGGCTGAATTACATAA ↑ 31 4 2 Gorilla: CA--CTTTCTTTACAAAACTGT----------GCCCAATCCCAGAGGGCAGAATTACATAA Human: CA--CTTTCTTTACAAAACTGT----------GCCCAATCCCAGAGGGCTGAATTACATAA Cluster: [ ] Orangutan: cactgtttctttacaaaactgt----------gcccaatcccagagggctgaattacataa Human > Chimp ------------- chr9:74219041-74219052 Template switch process: F1: L GAGCCACCTCGCCTGGCCTGAACACTTTCTTTACAAAACTG 1 F3: 4 CCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC R RF: GAGCCACCGCGCCTGGCCTGAACACTTTCTTTACAAAACTGTGCCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC RR: CTCGGTGGCGCGGACCGGACTTGTGAAAGAAATGTTTTGACACGGGTTAGGGTCTCCCGACTTAATGTATTGAAACCCTCGAG F2: 3 ACACGGGTTAGG 2 Unidirectional alignment (log-probability: -37.3) AGCCACCtCGCCTGGCCTGAACACTTTCTTTACAAAACTGgGattgggcacaCCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC AGCCACCGCGCCTGGCCTGAACACTTTCTTTACAAAACTGTG----------CCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC Template switch alignment (log-probability: -22.8) AGCCACCtCGCCTGGCCTGAACACTTTCTTTACAAAACTG|GGATTGGGCACA|CCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC AGCCACCGCGCCTGGCCTGAACACTTTCTTTACAAAACTG|GGATTGGGCACA|CCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC Gorilla > Chimp --------------- chr9:74219041-74219052 Template switch process: F1: L GAGCCACCTCGCCTGGCCTGAACACTTTCTTTACAAAACTG 1 F3: 4 CCCAATCCCAGAGGGCTGAATTACATAACTTTGGGAGCTC R RF: GAGCCACCGCGCCTGGCCTGAACACTTTCTTTACAAAACTGTGCCCAATCCCAGAGGGCAGAATTACATAACTTTGGGAGCTC RR: CTCGGTGGCGCGGACCGGACTTGTGAAAGAAATGTTTTGACACGGGTTAGGGTCTCCCGTCTTAATGTATTGAAACCCTCGAG F2: 3 ACACGGGTTAGG 2 Unidirectional alignment (log-probability: -41.8) AGCCACCtCGCCTGGCCTGAACACTTTCTTTACAAAACTGgGattgggcacaCCCAATCCCAGAGGGCtGAATTACATAACTTTGGGAGCTC AGCCACCGCGCCTGGCCTGAACACTTTCTTTACAAAACTGTG----------CCCAATCCCAGAGGGCAGAATTACATAACTTTGGGAGCTC Template switch alignment (log-probability: -28.3) AGCCACCtCGCCTGGCCTGAACACTTTCTTTACAAAACTG|GGATTGGGCACA|CCCAATCCCAGAGGGCtGAATTACATAACTTTGGGAGCTC AGCCACCGCGCCTGGCCTGAACACTTTCTTTACAAAACTG|GGATTGGGCACA|CCCAATCCCAGAGGGCAGAATTACATAACTTTGGGAGCTC ========== Event 3867 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 346 Detected in comparisons: 3456 Multiple sequence alignment: Human: ATCAGTTTACTTTGTTCTGGACACCTGAA-----GAGGCAGAAGCACTAGAATACC Chimp: ATCAGTTTACTTTGTTCTGGACACCTGAA-----GAGGCAGAAGCACTAGAATACC ↓ 3 1 24 Gorilla: ATCAGTTTACTTTGTTCTGGACACTTCAGGTGTCTAGGCAGAAGCACTAGAATACC ↓ 3 2 4 ↑ 3 1 24 Human: ATCAGTTTACTTTGTTCTGGACACCTGAA-----GAGGCAGAAGCACTAGAATACC Cluster: [ ] Orangutan: ATCAGTTTACTTTGTTCTGGACACCTGAG-----GAGGCAGAAGCACTAGAATACC Gorilla > Human --------------- chr9:96486727-96486732 Template switch process: F1: L AGCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC 1 F3: 4 AGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG R RF: AGCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACACTTCAGGTGTCTAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG RR: TCGGTCTAGAACCCAAGTAGTCAAATGAAACAAGACCTGTGAAGTCCACAGATCCGTCTTCGTGATCTTATGGATCGTTTCAAGTCTGGATC F2: 3 GAAGTC 2 Unidirectional alignment (log-probability: -26.9) GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC---------CTgaagAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACACTTCAGGTGTCT----AGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG Template switch alignment (log-probability: -16.5) GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC|CTGAAG|AGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC|CTGAAG|AGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG Human > Gorilla --------------- chr9:78551015-78551024 Template switch process: F1: L AGCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC 1 F3: 4 TAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG R RF: AGCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACACCTGAAGAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG RR: TCGGTCTAGAACCCAAGTAGTCAAATGAAACAAGACCTGTGGACTTCTCCGTCTTCGTGATCTTATGGATCGTTTCAAGTCTGGATC F2: 3 CTGTGGACTT 2 Unidirectional alignment (log-probability: -33.8) GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACACttcaggtgtCT----AGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTA GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC---------CTGAAGAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTA Template switch alignment (log-probability: -22.5) GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC|TTCAGGTGTC|tAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTA GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC|TTCAGGTGTC|GAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTA Chimp > Gorilla --------------- chr9:78551015-78551024 Template switch process: F1: L AGCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC 1 F3: 4 TAGGCAGAAGCACTAGAATACCTAGCAAAGTTCAGACCTAG R RF: AGCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACACCTGAAGAGGCAGAAGCACTAGAATACCTAGTAAAGTTCAGACCTAG RR: TCGGTCTAGAACCCAAGTAGTCAAATGAAACAAGACCTGTGGACTTCTCCGTCTTCGTGATCTTATGGATCATTTCAAGTCTGGATC F2: 3 CTGTGGACTT 2 Unidirectional alignment (log-probability: -39.3) GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACACttcaggtgtCT----AGGCAGAAGCACTAGAATACCTAGcAAAGTTCAGACCTA GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC---------CTGAAGAGGCAGAAGCACTAGAATACCTAGTAAAGTTCAGACCTA Template switch alignment (log-probability: -28.1) GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC|TTCAGGTGTC|tAGGCAGAAGCACTAGAATACCTAGcAAAGTTCAGACCTA GCCAGATCTTGGGTTCATCAGTTTACTTTGTTCTGGACAC|TTCAGGTGTC|GAGGCAGAAGCACTAGAATACCTAGTAAAGTTCAGACCTA ========== Event 3868 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: ACATGCTCCAATGACACCCATGGCTGCTTCCTCATAGGGCACCCTCTGCCTCTCTGGAGCCTGCCGCTGGCTCTATCGAAAGGGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGAGCAGCCAGAGGGAGTGACATGAGCTGAGAGTTGTGA Chimp: ACATGCTCCAATGACACCCATGGCTGCTTCCTCATAGGGCACCCTCTGCCTCTCTGGAGCCTGCCGCTGGCCCTATCGAAAGGGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGAGCAGCCA-----TGTGACATGAGCTGAGAGTTGTGA ↑ 3 2 1 4 Gorilla: ACATGCTCCAATGACACCCATGGCTGCTTCCTCATAGGGCACCCTCTGCCTCTCTGGAGCCTGCTGCTGGCCCTATCGAAAGGGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGGACAGCCAGAGGGAGTTACATGAGCTGAGAGTTGTGA Human: ACATGCTCCAATGACACCCATGGCTGCTTCCTCATAGGGCACCCTCTGCCTCTCTGGAGCCTGCCGCTGGCTCTATCGAAAGGGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGAGCAGCCAGAGGGAGTGACATGAGCTGAGAGTTGTGA Cluster: [ ] Orangutan: ACATGCTCCAATGACACCCATGGCTGCTTCCTCACAGGGCACCCTCTGCCTCTCTGGAGCCTGCCTCTGGCCCTATCAAAAGGGGCCAGTGGGAAATAATCATGGGGTCCTACTCTGATCTGAGCAGCCAGAGGGAGTTACATGAGCTGAGAGCTGTGA Gorilla > Chimp --------------- chr9:75481463-75481471 Template switch process: F1: L GGGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTG 1 F3: 4 GTGACATGAGCTGAGAGTTGTGAATAAACCCCTGTACTTTGTA R RF: ATGGCTGCTTCCTCATAGGGCACCCTCTGCCTCTCTGGAGCCTGCTGCTGGCCCTATCGAAAGGGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGGACAGCCAGAGGGAGTTACATGAGCTGAGAGTTGTGAATAAACCCCTGTACTTTGTA RR: TACCGACGAAGGAGTATCCCGTGGGAGACGGAGAGACCTCGGACGACGACCGGGATAGCTTTCCCCGGTCACCCTTTATCAGTACCCCAGGATGAGACTAGACCTGTCGGTCTCCCTCAATGTACTCGACTCTCAACACTTATTTGGGGACATGAAACAT F2: 3 TACCGACGA 2 Unidirectional alignment (log-probability: -33.4) GGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGagCAGCCA-----tGTgACATGAGCTGAGAGTTGTGAATAAACCCCTGTACTTT GGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTGGACAGCCAGAGGGAGTTACATGAGCTGAGAGTTGTGAATAAACCCCTGTACTTT Template switch alignment (log-probability: -22.5) GGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTG|AGCAGCCAT|GTgACATGAGCTGAGAGTTGTGAATAAACCCCTGTACTTT GGGCCAGTGGGAAATAGTCATGGGGTCCTACTCTGATCTG|AGCAGCCAT|GTTACATGAGCTGAGAGTTGTGAATAAACCCCTGTACTTT ========== Event 3869 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 134 Detected in comparisons: 1234 Multiple sequence alignment: Human: AGACACAAACACAGCCAAGGAGGCTGTTACGTAGAACAGAGAATATTTTTCCGCAGAACCTTTTAAGGAGGAAATTTTATTTTCTGTGTCATTTGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAATGGTTCTGATTAATGCCAATTTGTGCACTACTTTA ↑ 3 1 2 4 Chimp: AGACACAAACACAGCCAAGGAGGCTGTTACGTAGAACAGAGAATATTTTTCCGCAGAACCTTTTAAGGAGGAAATTTTATTTTCTGTGTCATTTGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCC--TTTAATGCCAATTTGTGCACTACTTTA Gorilla: AGACACAAACACAGCCAAGGAGGCTGTTACGTAGAACAGAGAATATTTTTCCGCAGAACCTTTTAAGGAGGAAATTTTATTTTCTGTGTCATTTGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCC--TCTAATACCAATTTGTGCACTACTTTA ↓ 3 1 2 4 ↑ 3 2 1 4 Human: AGACACAAACACAGCCAAGGAGGCTGTTACGTAGAACAGAGAATATTTTTCCGCAGAACCTTTTAAGGAGGAAATTTTATTTTCTGTGTCATTTGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAATGGTTCTGATTAATGCCAATTTGTGCACTACTTTA Cluster: [ ] Orangutan: AGACACAAACACAGCCAAGGAGGCTGTTACGTAGAACAGAGAATATTTTTCCGCAGAACCTTTTAAGGAGGAAATTTTATTTTCTGTGTCATTTGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCT--TCTAATGCCAATTTGTGCACTACTTTA Chimp > Human ------------- chr9:39290813-39290821 Template switch process: F1: L TGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA 1 F3: 4 TTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGTGA R RF: TGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCCTTTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGCGA RR: ACTCGAATCTTAATTTATTTGGAACTATCGTCCTTAGTCTTGGTCGGAAATTACGGTTAAACACGTGATGAAATCTCAGTGACCCGCT F2: 3 AGTCTTGGT 2 Unidirectional alignment (log-probability: -38.9) GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA------TggttctgaTTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGtGA GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCCT--------TTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGCGA Template switch alignment (log-probability: -22.4) GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA|TGGTTCTGA|TTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGtGA GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA|TGGTTCTGA|TTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGCGA Gorilla > Human --------------- chr9:39290813-39290822 Template switch process: F1: L TGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA 1 F3: 4 TAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAGCATTT R RF: TGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCCTCTAATACCAATTTGTGCACTACTTTAGAGTCACTGGGTGAGCATTT RR: ACTCGAATCTTAATTTATTTGGAACTATCGTCCTTAGTCTTGGTCGGAGATTATGGTTAAACACGTGATGAAATCTCAGTGACCCACTCGTAAA F2: 3 TAGTCTTGGT 2 Unidirectional alignment (log-probability: -41) GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA--------tggttctgatTAATgCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAACCAGCCTC----------TAATACCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG Template switch alignment (log-probability: -22.6) GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA|TGGTTCTGAT|TAATgCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG GAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA|TGGTTCTGAT|TAATACCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG Human > Gorilla --------------- chr9:40456819-40456825 Template switch process: F1: L TGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAAC 1 F3: 4 TAATACCAATTTGTGCACTACTTTAGAGTCACTGGGTGAGCATTT R RF: GAGGCTGTTACGTAGAACAGAGAATATTTTTCCGCAGAACCTTTTAAGGAGGAAATTTTATTTTCTGTGTCATTTGAGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAATGGTTCTGATTAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAGCATTT RR: CTCCGACAATGCATCTTGTCTCTTATAAAAAGGCGTCTTGGAAAATTCCTCCTTTAAAATAAAAGACACAGTAAACTCGAATCTTAATTTATTTGGAACTATCGTCCTTAGTCTTACCAAGACTAATTACGGTTAAACACGTGATGAAATCTCAGTGACCCACTCGTAAA F2: 3 CTCCGAC 2 Unidirectional alignment (log-probability: -38.2) AGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAA----------ccagcctcTAATaCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG AGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAATGGTTCTGAT--------TAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG Template switch alignment (log-probability: -27.8) AGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAAc|CAGCCTC|TAATaCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG AGCTTAGAATTAAATAAACCTTGATAGCAGGAATCAGAAT|CAGCCTC|TAATGCCAATTTGTGCACTACTTTAGAGTCACTGGGTGAG ========== Event 3870 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGGGAACCTGGAAGCAAAGGTGTAGGACCCTTGAATTCTGCCCCTTGG ↓ 1 3 42 Chimp: GAGGGAACCTGGAAGCAAAGGGTCCTAACCCTTGAATTCTGCCCCTTGG ↑ 1 3 42 Gorilla: GAGGGAACCTGGAAGCAAAGGTGTAGGACCCTTGAATTCTGCCCCTTGG Human: GAGGGAACCTGGAAGCAAAGGTGTAGGACCCTTGAATTCTGCCCCTTGG Cluster: [ ] Orangutan: GAGGGAACCTGGAAGCAAAGGTGTAGGAACCTTGAATTCTGCCCCTTGG Human > Chimp ------------- chr9:39840604-39840609 Template switch process: F1: L CTTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGG 1 F3: 4 ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGGAAGCT R RF: CTTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGGTGTAGGACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGAAAGCT RR: GAATGTTACTTCTGGTGTTACTCCCTTGGACCTTCGTTTCCACATCCTGGGAACTTAAGACGGGGAACCCTCATTAGAGTCTTTCGA F2: 3 ATCCTG 2 Unidirectional alignment (log-probability: -34.6) TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAG-----GGtcctaACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGgAAGCT TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGGTGTAGG-----ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGAAAGCT Template switch alignment (log-probability: -22) TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGG|GTCCTA|ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGgAAGCT TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGG|GTCCTA|ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGAAAGCT Gorilla > Chimp --------------- chr9:39840604-39840609 Template switch process: F1: L CTTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGG 1 F3: 4 ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGGAAGCT R RF: CTTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGGTGTAGGACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGAAAGCT RR: GAATGTTACTTCTGGTGTTACTCCCTTGGACCTTCGTTTCCACATCCTGGGAACTTAAGACGGGGAACCCTCATTAGAGTCTTTCGA F2: 3 ATCCTG 2 Unidirectional alignment (log-probability: -33.6) TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAG-----GGtcctaACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGgAAGCT TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGGTGTAGG-----ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGAAAGCT Template switch alignment (log-probability: -22) TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGG|GTCCTA|ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGgAAGCT TTACAATGAAGACCACAATGAGGGAACCTGGAAGCAAAGG|GTCCTA|ACCCTTGAATTCTGCCCCTTGGGAGTAATCTCAGAAAGCT ========== Event 3871 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CTACTTCTTGCTCAAATAAGC----TTCTAGTGGTCCCATGGGCCACCTTCATCTCCACCC Chimp: CTACTTCTTGCTCAAATAAGC----TTCTAGTGGTCCCATGGGCCACCTTCATCTCCACCC ↓ 1 3 4 2 Gorilla: CTACTTCTTGCTCAAATAAGC--------CATGGGACCATGGGCCACCTTCATCTCCACCC Human: CTACTTCTTGCTCAAATAAGC----TTCTAGTGGTCCCATGGGCCACCTTCATCTCCACCC Cluster: [ ] Orangutan: CTACTTCTTGCTCAAATAAGCTTCT----AGTGGTCCCATGGGCCACCTTCATCTCCACCC Chimp > Gorilla --------------- chr9:40221552-40221558 Template switch process: F1: L GCAAGAGGGTGCACCTTGACCTACTTCTTGCTCAAATAAGC 1 F3: 4 CCATGGGCCACCTTCATCTCCACCCATGCACAAGTGAGCA R RF: GCAAGAGGGTGCACCTTGACCTACTTCTTGCTCAAATAAGCTTCTAGTGGTCCCATGGGCCACCTTCATCTCCACCCATGCACAAGTGAGCA RR: CGTTCTCCCACGTGGAACTGGATGAAGAACGAGTTTATTCGAAGATCACCAGGGTACCCGGTGGAAGTAGAGGTGGGTACGTGTTCACTCGT F2: 3 AGGGTAC 2 Unidirectional alignment (log-probability: -29.8) CAAGAGGGTGCACCTTGACCTACTTCTTGCTCAAATAAGC----------CatgggaCCATGGGCCACCTTCATCTCCACCCATGCACAAGTGAGCA CAAGAGGGTGCACCTTGACCTACTTCTTGCTCAAATAAGCTTCTAGTGGTC------CCATGGGCCACCTTCATCTCCACCCATGCACAAGTGAGCA Template switch alignment (log-probability: -16.6) CAAGAGGGTGCACCTTGACCTACTTCTTGCTCAAATAAGC|CATGGGA|CCATGGGCCACCTTCATCTCCACCCATGCACAAGTGAGCA CAAGAGGGTGCACCTTGACCTACTTCTTGCTCAAATAAGC|CATGGGA|CCATGGGCCACCTTCATCTCCACCCATGCACAAGTGAGCA ========== Event 3872 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GCAGCTGACTGTGACTCTGGT---AATGATACCCAAGAGAAGGTACATGAtt- Chimp: GCAGCTGACTGTGACTCTGGT---AATGATACCCAAGAGAAGGTACATGA--- ↓ 1 3 4 2 Gorilla: GCAGCTGACTGTGACTCTGGTGGTATCATTACCCAAGAGAAGGTACATGAttt ↑ 1 3 4 2 Human: GCAGCTGACTGTGACTCTGGT---AATGATACCCAAGAGAAGGTACATGAtt- Cluster: [ ] Orangutan: Human > Gorilla --------------- chr9:80089501-80089508 Template switch process: F1: L TTCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT 1 F3: 4 TACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTAACTT R RF: TTCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGTAATGATACCCAAGAGAAGGTACATGATTTTTTTTTTTTTAACTT RR: AAGAGTCCAAGGACTAAACTCGTCGACTGACACTGAGACCATTACTATGGGTTCTCTTCCATGTACTAAAAAAAAAAAAATTGAA F2: 3 TACTATGG 2 Unidirectional alignment (log-probability: -43.5) TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT-----ggtatcatTACCCAAGAGAAGGTACATGAtTTTTTTTTTTTTTAACTT TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGTAATGA--------TACCCAAGAGAAGGTACATGA-TTTTTTTTTTTTTAACTT Template switch alignment (log-probability: -27.9) TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT|GGTATCAT|TACCCAAGAGAAGGTACATGAtTTTTTTTTTTTTTAACTT TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT|GGTATCAT|TACCCAAGAGAAGGTACATGA-TTTTTTTTTTTTTAACTT Chimp > Gorilla --------------- chr9:80089501-80089508 Template switch process: F1: L TTCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT 1 F3: 4 TACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTAA R RF: TTCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGTAATGATACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTGA RR: AAGAGTCCAAGGACTAAACTCGTCGACTGACACTGAGACCATTACTATGGGTTCTCTTCCATGTACTAAAAAAAAAAAAAACT F2: 3 TACTATGG 2 Unidirectional alignment (log-probability: -37.9) TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT-----ggtatcatTACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTaA TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGTAATGA--------TACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTGA Template switch alignment (log-probability: -22.2) TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT|GGTATCAT|TACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTaA TCTCAGGTTCCTGATTTGAGCAGCTGACTGTGACTCTGGT|GGTATCAT|TACCCAAGAGAAGGTACATGATTTTTTTTTTTTTTGA ========== Event 3873 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: GAATAATCAGCCTCTGAACACAGA---------------------GCCCAGGCAGGTCAGGGCAGAGCCCAGGCCTTCTATCCACACCTGGcctgggttcagctctcagccccg Chimp: GAATAATCAGCCTCTGAACACAGA---------------------GCCCAGGCAGGTCAGGGCAGAGCCCAGGCCTTCTATCCACACCTGGcctgggttcagctctcagccccg ↑ 4 1 3 2 Gorilla: GAATAATCAGCCTCTGAACACAGA------------------------------------------GCCCAGGCCTTCTATCCACACCTGGcctgggttcagctctcagccccg ↓ 4 1 3 2 Human: GAATAATCAGCCTCTGAACACAGA---------------------GCCCAGGCAGGTCAGGGCAGAGCCCAGGCCTTCTATCCACACCTGGcctgggttcagctctcagccccg Cluster: [ ] Orangutan: GAATAATCAGCCTCTGAATACAGAGCCCAGGCAGGTCAGGGCAGA---------------------GCCCAGGCCTTCTATCCAcaccaggcctgggttctgctctcagcctca Gorilla > Human --------------- chr9:40002686-40002693 Template switch process: F1: L CCCACTACCAAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGC 1 F3: 4 GCAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCAGCTCT R RF: CCCACTACCAAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCAGCTCT RR: GGGTGATGGTTCTGGCACTTATTAGTCGGAGACTTGTGTCTCGGGTCCGGAAGATAGGTGTGGACCGGACCCAAGTCGAGA F2: 3 GGACTGGA 2 Unidirectional alignment (log-probability: -41.1) AAGACCGTGAATAATCAGCCTCTGAACACAgagcccaggcaggtcagggcaGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA AAGACCGTGAATAATCAGCCTCTGAACACA---------------------GAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA Template switch alignment (log-probability: -28.1) AAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGC|AGGtCAGG|gCAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA AAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGC|AGGCCAGG|ACAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA Gorilla > Chimp --------------- chr9:40638763-40638770 Template switch process: F1: L CCCACTACCAAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGC 1 F3: 4 GCAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCAGCTCT R RF: CCCACTACCAAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCAGCTCT RR: GGGTGATGGTTCTGGCACTTATTAGTCGGAGACTTGTGTCTCGGGTCCGGAAGATAGGTGTGGACCGGACCCAAGTCGAGA F2: 3 GGACTGGA 2 Unidirectional alignment (log-probability: -41.1) AAGACCGTGAATAATCAGCCTCTGAACACAgagcccaggcaggtcagggcaGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA AAGACCGTGAATAATCAGCCTCTGAACACA---------------------GAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA Template switch alignment (log-probability: -28.1) AAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGC|AGGtCAGG|gCAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA AAGACCGTGAATAATCAGCCTCTGAACACAGAGCCCAGGC|AGGCCAGG|ACAGAGCCCAGGCCTTCTATCCACACCTGGCCTGGGTTCA ========== Event 3874 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ATACTGTTTCATGCAAACGCTTCATAAA---CTCAATATTC---AATGGTTTAAGTCCATGTCCTGAAG Chimp: ATACTGTTTCATGCAAACGCTTCATAAA---CTCAATATTC---AATGGTTTAAGTCCATGTCCTGAAG ↓ 13 24 Gorilla: ATACTGTTTCATGCAAACGCTCCATAAACCATTGAATATTG------AGTTTAAGTCCATGTCCTGAAG ↑ 13 24 Human: ATACTGTTTCATGCAAACGCTTCATAAA---CTCAATATTC---AATGGTTTAAGTCCATGTCCTGAAG Cluster: [ ] Orangutan: ATACTCTTTCATGCAAACGCTTCATAAA---CTCAATATTCAAT---GGTTTAAGTCCATGTCCTGAAG Human > Gorilla --------------- chr9:40964116-40964128 Template switch process: F1: L CTGTGGCAATAAGTGAGATGATACTGTTTCATGCAAACGCTCCATAAAC 1 F3: 4 GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA R RF: CTGTGGCAATAAGTGAGATGATACTGTTTCATGCAAACGCTTCATAAACTCAATATTCAATGGTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA RR: GACACCGTTATTCACTCTACTATGACAAAGTACGTTTGCGAAGTATTTGAGTTATAAGTTACCAAATTCAGGTACAGGACTTCCTCGTTACTTCATATTTGT F2: 3 AGTTATAAGTTAC 2 Unidirectional alignment (log-probability: -41.9) TAAGTGAGATGATACTGTTTCATGCAAACGCTcCATAAACcatTgAATATTgA---GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA TAAGTGAGATGATACTGTTTCATGCAAACGCTTCATAAAC---TCAATATTCAATGGTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA Template switch alignment (log-probability: -23.1) TAAGTGAGATGATACTGTTTCATGCAAACGCTcCATAAAC|CATTGAATATTGA|GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA TAAGTGAGATGATACTGTTTCATGCAAACGCTTCATAAAC|CATTGAATATTGA|GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA Chimp > Gorilla --------------- chr9:40964116-40964128 Template switch process: F1: L CTGTGGCAATAAGTGAGATGATACTGTTTCATGCAAACGCTCCATAAAC 1 F3: 4 GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA R RF: CTGTGGCAATAAGTGAGATGATACTGTTTCATGCAAACGCTTCATAAACTCAATATTCAATGGTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA RR: GACACCGTTATTCACTCTACTATGACAAAGTACGTTTGCGAAGTATTTGAGTTATAAGTTACCAAATTCAGGTACAGGACTTCCTCGTTACTTCATATTTGT F2: 3 AGTTATAAGTTAC 2 Unidirectional alignment (log-probability: -41.9) TAAGTGAGATGATACTGTTTCATGCAAACGCTcCATAAACcatTgAATATTgA---GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA TAAGTGAGATGATACTGTTTCATGCAAACGCTTCATAAAC---TCAATATTCAATGGTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA Template switch alignment (log-probability: -23.1) TAAGTGAGATGATACTGTTTCATGCAAACGCTcCATAAAC|CATTGAATATTGA|GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA TAAGTGAGATGATACTGTTTCATGCAAACGCTTCATAAAC|CATTGAATATTGA|GTTTAAGTCCATGTCCTGAAGGAGCAATGAAGTATAAACA ========== Event 3875 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TAGGTGGACTGAGACAGATTG---TTA---TAAGTAGATATCTACTATaggttgttaaggagt ↓ 1 43 2 Chimp: TAGGTGGACTGAGACAGATTGTAGATATCTACAGTAGATATCTACTATAGGTTGTTaaggagt Gorilla: TAGGTGGACTGAGATGGATTA---TTA---TAAGTAGATATCTACTATACGTTGTTaaggagt Human: TAGGTGGACTGAGACAGATTG---TTA---TAAGTAGATATCTACTATaggttgttaaggagt Cluster: [ ] Orangutan: TAGGTGGACTGAGACAGATTA---TTA---TAAGCAGATATCTACTATAGGttgttaaggaat Human > Chimp ------------- chr9:106661103-106661112 Template switch process: F1: L ATACCTTACTACTCCTCAAATAGGTGGACTGAGACAGATTGT 1 F3: 4 AGTAGATATCTACTATAGGTTGTTAAGGAGTTTTGTAGTG R RF: ATACCTTACTACTCCTCAAATAGGTGGACTGAGACAGATTGTTATAAGTAGATATCTACTATAGGTTGTTAAGGAGTTTTGTAGTG RR: TATGGAATGATGAGGAGTTTATCCACCTGACTCTGTCTAACAATATTCATCTATAGATGATATCCAACAATTCCTCAAAACATCAC F2: 3 CATCTATAGA 2 Unidirectional alignment (log-probability: -34.2) ACCTTACTACTCCTCAAATAGGTGGACTGAGACAGATTG---TAgatatctacAGTAGATATCTACTATAGGTTGTTAAGGAGTTTTGTAGTG ACCTTACTACTCCTCAAATAGGTGGACTGAGACAGATTGTTATA---------AGTAGATATCTACTATAGGTTGTTAAGGAGTTTTGTAGTG Template switch alignment (log-probability: -16.5) ACCTTACTACTCCTCAAATAGGTGGACTGAGACAGATTGT|AGATATCTAC|AGTAGATATCTACTATAGGTTGTTAAGGAGTTTTGTAGTG ACCTTACTACTCCTCAAATAGGTGGACTGAGACAGATTGT|AGATATCTAC|AGTAGATATCTACTATAGGTTGTTAAGGAGTTTTGTAGTG ========== Event 3876 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TGTGTCCTGAAAACAGAAGCAA----------GCCTGGGGGAGAGGTCAGAGCTCA ↓ 3 1 42 Chimp: TGTGTCCTGAAAACAGAAGCAA-----AGGCTTGCTGGGGGAGAGGTCAGAGCTCA Gorilla: Human: TGTGTCCTGAAAACAGAAGCAA----------GCCTGGGGGAGAGGTCAGAGCTCA Cluster: [ ] Orangutan: TGTGCCCTGAAAACAGAAGCAAAGGCT-----TGCTGGGGGAGAGGTCAGAGTTCA Human > Chimp ------------- chrX:106582218-106582224 Template switch process: F1: L AGAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAA 1 F3: 4 CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT R RF: AGAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAAGCCTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT RR: TCTCGGTTCACCCGTTTCAACACAGGACTTTTGTCTTCGTTCGGACCCCCTCTCCAGTCTCGAGTGGGACACATGGACGGTCA F2: 3 GTTCGGA 2 Unidirectional alignment (log-probability: -28.3) GAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAAagGCttgCTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT GAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAA--GC---CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT Template switch alignment (log-probability: -16.2) GAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAA|AGGCTTG|CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT GAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAA|AGGCTTG|CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT ========== Event 3877 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAAACACTTCGCCTGAATACGTTGCCAAACGTAGTGGCAATGCATTTTAATGT Chimp: AAAAACACTTCGCCTGAATACATTGCC--ATTAAGTGGCAATGCATTTTAATGT Gorilla: AAAAACACTTCGCCTGAATACGTTGCC--ATTAAGTGGCAATGCATTTTAATGT ↓ 3 2 1 4 Human: AAAAACACTTCGCCTGAATACGTTGCCAAACGTAGTGGCAATGCATTTTAATGT Cluster: [ ] Orangutan: AAAAACACTTAACCTGAATACGTTGCC--ATTAAGTGGCAATGCATTTTAATGT Gorilla > Human --------------- chrX:48798777-48798781 Template switch process: F1: L CCATGTGGGGTAGGAAAAACACTTCGCCTGAATACGTTGCCA 1 F3: 4 AGTGGCAATGCATTTTAATGTAGACTGTAATATTTGGCAT R RF: CCATGTGGGGTAGGAAAAACACTTCGCCTGAATACGTTGCCATTAAGTGGCAATGCATTTTAATGTAGACTGTAATATTTGGCAT RR: GGTACACCCCATCCTTTTTGTGAAGCGGACTTATGCAACGGTAATTCACCGTTACGTAAAATTACATCTGACATTATAAACCGTA F2: 3 TGCAA 2 Unidirectional alignment (log-probability: -26.5) ATGTGGGGTAGGAAAAACACTTCGCCTGAATACGTTGCCA--AacgtAGTGGCAATGCATTTTAATGTAGACTGTAATATTTGGCAT ATGTGGGGTAGGAAAAACACTTCGCCTGAATACGTTGCCATTA----AGTGGCAATGCATTTTAATGTAGACTGTAATATTTGGCAT Template switch alignment (log-probability: -16.4) ATGTGGGGTAGGAAAAACACTTCGCCTGAATACGTTGCCA|AACGT|AGTGGCAATGCATTTTAATGTAGACTGTAATATTTGGCAT ATGTGGGGTAGGAAAAACACTTCGCCTGAATACGTTGCCA|AACGT|AGTGGCAATGCATTTTAATGTAGACTGTAATATTTGGCAT ========== Event 3878 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTGTCCTGAAAACAGAAGCAA----------GCCTGGGGGAGAGGTCAGAGCTCA Chimp: TGTGCCCTGAAAACAGAAGCAA-----AGGCTTGCTGGGGGAGAGGTCAGAGCTCA Gorilla: TGTGTCCTGAAAACAGAAGCAAAGGCT-----TGCTGGGGGAGAGGTCAGAGCTCA ↑ 3 1 42 Human: TGTGTCCTGAAAACAGAAGCAA----------GCCTGGGGGAGAGGTCAGAGCTCA Cluster: [ ] Orangutan: TGTGCCCTGAAAACAGAAGCAAAGGCT-----TGCTGGGGTAGAGGTCAGAGCTCA Human > Gorilla --------------- chrX:107301554-107301560 Template switch process: F1: L AGAGCCAAGTGGGCAAAGGTGTGTCCTGAAAACAGAAGCAA 1 F3: 4 CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT R RF: AGAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAAGCCTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT RR: TCTCGGTTCACCCGTTTCAACACAGGACTTTTGTCTTCGTTCGGACCCCCTCTCCAGTCTCGAGTGGGACACATGGACGGTCA F2: 3 GTTCGGA 2 Unidirectional alignment (log-probability: -33.4) GAGCCAAGTGGGCAAAGgTGTGTCCTGAAAACAGAAGCAAagGCttgCTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT GAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAA--GC---CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT Template switch alignment (log-probability: -22.1) GAGCCAAGTGGGCAAAGgTGTGTCCTGAAAACAGAAGCAA|AGGCTTG|CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT GAGCCAAGTGGGCAAAGTTGTGTCCTGAAAACAGAAGCAA|AGGCTTG|CTGGGGGAGAGGTCAGAGCTCACCCTGTGTACCTGCCAGT ========== Event 3879 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGTCTTTATTGAGCTTTCAGGT--------------------------------------------------TTTGCCCAAGTACACGTTTTGAAATGAgaaagataatagtgaaaatagcctgaatatcttt-atattt Chimp: TGTCTTTATTGAGCTTTCAGGT--------------------------------------------------TTTGCCCAAGTACACGTTTTGAAATGAgaaagataatagtgaaaatagcctgaataccttt-atattt ↓ 31 4 2 Gorilla: TGTCTTTATTGAGCTTTCAGGCTATTTTCACTATTATCTTTCTCATTTCAAAACGTGTACTTGGGCAAAACCCTTGCCCAAGTACACGTTTTGAAATGAgaaagataatagtgaaaatagcctgaataccttt-atattt ↑ 31 4 2 Human: TGTCTTTATTGAGCTTTCAGGT--------------------------------------------------TTTGCCCAAGTACACGTTTTGAAATGAgaaagataatagtgaaaatagcctgaatatcttt-atattt Cluster: [ ] Orangutan: CGTATTTATTGAGCTTTCAGGC--------------------------------------------------TATTTTC------------------------------------------ACTATTATCTTTCTCATTT Human > Gorilla --------------- chrX:48034909-48034959 Template switch process: F1: L AACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGG 1 F3: 4 CTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGTG R RF: AACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGGTTTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGTGAAAATAG RR: TTGTCGTATCTGTATCCCGTACAGAAATAACTCGAAAGTCCAAAACGGGTTCATGTGCAAAACTTTACTCTTTCTATTATCACTTTTATC F2: 3 CCAAAACGGGTTCATGTGCAAAACTTTACTCTTTCTATTATCACTTTTATC 2 Unidirectional alignment (log-probability: -88.3) ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGGcTattttcactattatctttctcatttcaaaacgtgtacttgggcaaaacccTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGGTT--------------------------------------------------TTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT Template switch alignment (log-probability: -27.7) ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGG|CTATTTTCACTATTATCTTTCTCATTTCAAAACGTGTACTTGGGCAAAACC|cTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGG|CTATTTTCACTATTATCTTTCTCATTTCAAAACGTGTACTTGGGCAAAACC|TTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT Chimp > Gorilla --------------- chrX:48034909-48034959 Template switch process: F1: L AACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGG 1 F3: 4 CTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGTG R RF: AACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGGTTTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGTGAAAATAG RR: TTGTCGTATCTGTATCCCGTACAGAAATAACTCGAAAGTCCAAAACGGGTTCATGTGCAAAACTTTACTCTTTCTATTATCACTTTTATC F2: 3 CCAAAACGGGTTCATGTGCAAAACTTTACTCTTTCTATTATCACTTTTATC 2 Unidirectional alignment (log-probability: -88.3) ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGGcTattttcactattatctttctcatttcaaaacgtgtacttgggcaaaacccTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGGTT--------------------------------------------------TTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT Template switch alignment (log-probability: -27.7) ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGG|CTATTTTCACTATTATCTTTCTCATTTCAAAACGTGTACTTGGGCAAAACC|cTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT ACAGCATAGACATAGGGCATGTCTTTATTGAGCTTTCAGG|CTATTTTCACTATTATCTTTCTCATTTCAAAACGTGTACTTGGGCAAAACC|TTTGCCCAAGTACACGTTTTGAAATGAGAAAGATAATAGT ========== Event 3880 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GGGGCTGGCAGAAATTGCTCAGTCA---------------------------------------------------------------------------------------TGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGGAGTGAAAAGCCTATATGCCA ↓ 4 3 1 2 Chimp: GGGGCTGGCAGAAATTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACTCCCTTTTAAAGATGTCACTGTTAGAGGAAAGTACAACAGATATGGTTTGTTACAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGGAGTGAAAAGCCTATATGCCA ↑ 4 3 1 2 Gorilla: GGGGCTGGCAGAAATTGCTCAGTCA---------------------------------------------------------------------------------------TGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGGAGTGAAAAGCCTATATGCCA Human: GGGGCTGGCAGAAATTGCTCAGTCA---------------------------------------------------------------------------------------TGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGGAGTGAAAAGCCTATATGCCA Cluster: [ ] Orangutan: GGGACTGGCAGAAATTGCTCAGTCA---------------------------------------------------------------------------------------TGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGGAGTGAAAAGCCTATATGCCA Human > Chimp ------------- chrX:109853017-109853068 Template switch process: F1: L AAGTCAAGGGGTCTAAGGGGCTGGCAGAAATTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT 1 F3: 4 CAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACA R RF: AAGTCAAGGGGTCTAAGGGGCTGGCAGAAATTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGG RR: TTCAGTTCCCCAGATTCCCCGACCGTCTTTAACGAGTCAGTACTGACATTGTTTGGTATAGACAACATGAAAGGAGATTGTCACTGTAGAAATTTTCCC F2: 3 ATTGTTTGGTATAGACAACATGAAAGGAGATTGTCACTGTAGAAATTTTCCC 2 Unidirectional alignment (log-probability: -136) TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACTcccttttaaagatgtcactgttagaggaaagtacaacagatatggtttgttacagtcatgactgtaacaaaccatatctgttgtactTTCCT TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT---------------------------------------------------------------------------------------TTCCT Template switch alignment (log-probability: -22.2) TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT|CCCTTTTAAAGATGTCACTGTTAGAGGAAAGTACAACAGATATGGTTTGTTA|CAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCT TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT|CCCTTTTAAAGATGTCACTGTTAGAGGAAAGTACAACAGATATGGTTTGTTA|CAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCT Gorilla > Chimp --------------- chrX:109853017-109853068 Template switch process: F1: L AAGTCAAGGGGTCTAAGGGGCTGGCAGAAATTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT 1 F3: 4 CAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACA R RF: AAGTCAAGGGGTCTAAGGGGCTGGCAGAAATTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCTCTAACAGTGACATCTTTAAAAGGG RR: TTCAGTTCCCCAGATTCCCCGACCGTCTTTAACGAGTCAGTACTGACATTGTTTGGTATAGACAACATGAAAGGAGATTGTCACTGTAGAAATTTTCCC F2: 3 ATTGTTTGGTATAGACAACATGAAAGGAGATTGTCACTGTAGAAATTTTCCC 2 Unidirectional alignment (log-probability: -136) TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTActcccttttaaagatgtcactgttagaggaaagtacaacagatatggtttgttacagtcatgactgtaacaaaccatatctgttgtaCTTTCCT TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTA---------------------------------------------------------------------------------------CTTTCCT Template switch alignment (log-probability: -23) TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT|CCCTTTTAAAGATGTCACTGTTAGAGGAAAGTACAACAGATATGGTTTGTTA|CAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCT TTGCTCAGTCATGACTGTAACAAACCATATCTGTTGTACT|CCCTTTTAAAGATGTCACTGTTAGAGGAAAGTACAACAGATATGGTTTGTTA|CAGTCATGACTGTAACAAACCATATCTGTTGTACTTTCCT ========== Event 3881 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAGTACCCAATGTCAATTCTGCTTGATCAAATGATCAAGCTCTGAACTGAAATTTACTG ↑ 1 3 4 2 Chimp: GAAGTACCCAATGTCAATTCT--GTATTCATTTGATCAAGCTCTGAACTGAAATTTACTG Gorilla: GAAGTACCCAATGTCAATTCT--GTATTCATTTGATCAAGCTCTGAACTGAAATTTACTG ↓ 1 3 4 2 Human: GAAGTACCCAATGTCAATTCTGCTTGATCAAATGATCAAGCTCTGAACTGAAATTTACTG Cluster: [ ] Orangutan: GAAGTACCCAATGTCAATTCT--GTGTTCATTTGATCAAGCTCTGAACTGAAATTTCCTG Chimp > Human ------------- chrX:144854743-144854752 Template switch process: F1: L TTATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG 1 F3: 4 TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA R RF: TTATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTGTATTCATTTGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA RR: AATAAGTTCGTAGTAAGTGACTTCATGGGTTACAGTTAAGACATAAGTAAACTAGTTCGAGACTTGACTTTAAATGACACACTTTCACAT F2: 3 AAACTAGTTC 2 Unidirectional alignment (log-probability: -35.9) ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG--------cttgatcaaaTGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTGTATTCATT----------TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA Template switch alignment (log-probability: -16.5) ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG|CTTGATCAAA|TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG|CTTGATCAAA|TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA Gorilla > Human --------------- chrX:144854743-144854752 Template switch process: F1: L TTATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG 1 F3: 4 TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA R RF: TTATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTGTATTCATTTGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA RR: AATAAGTTCGTAGTAAGTGACTTCATGGGTTACAGTTAAGACATAAGTAAACTAGTTCGAGACTTGACTTTAAATGACACACTTTCACAT F2: 3 AAACTAGTTC 2 Unidirectional alignment (log-probability: -35.4) ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG--------cttgatcaaaTGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTGTATTCATT----------TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA Template switch alignment (log-probability: -17) ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG|CTTGATCAAA|TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA ATTCAAGCATCATTCACTGAAGTACCCAATGTCAATTCTG|CTTGATCAAA|TGATCAAGCTCTGAACTGAAATTTACTGTGTGAAAGTGTA ========== Event 3882 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCTGTTTATCACATGTAAATTT-CA-AGTTACACTAAGCCAGTAGCTACT------------------------TTTGGAA----ATACGTGTTAGGAAGGGGAATGCTGCTA------------GTTTAACTACCTGTAACATCCA Chimp: GATCTTAAAATGGTAGCAACTAGCAGCATTCCCCTTCCT------AACACGT--ATTTCCA-------------AAAGTAGCTACT------------GGCTTAGTGTAACT-TGAA--ATTTACATGTGAT------AAATTTCCCTA------GCAAATCTTTAACTACCTGTAACATCCA Gorilla: GGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCT------AACACGT--ATTTCCA-------------AAAGTAGCTACTGGCTTAGTGTAA------------CT-TGAAAT--TTACATGTGAT------AAACTTCCCTAGCAAAT------CTTTAACTACCTGTAACATCCA ↓ 3 1 2 4 Human: GGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCTGTTTATCACATGTAAATTT-CA-AGTTACACTAAGCCAGTAGCTACT------------------------TTTGGAA----ATACGTGTTAGGAAGGGGAATGCTGCTA------------GTTTAACTACCTGTAACATCCA Cluster: [ ] Orangutan: GGTCCTAAAGTGATAGCAACTAGCAGCATTCCCCTTCCT------AACACAT--ATTTCCAA------------AAAGTAGCTACTGGCTTAGTGTAA------------CT-TGAAAT--TTACATGTGAT------AAATTTCCCTAGCAAAT------CTTTAACTACCTGTAACATCCA Gorilla > Human --------------- chrX:43997394-43997474 Template switch process: F1: L GTAAGTTTTCACGCTAGGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCT 1 F3: 4 TTTAACTACCTGTAACATCCACACAGTGGCTTCTGCCACAGATAGGCTCCTTTTTTCAAGGCTAAGAGATACAAACATACAGCTCACACCAACACAGCAA R RF: GTAAGTTTTCACGCTAGGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCTAACACGTATTTCCAAAAGTAGCTACTGGCTTAGTGTAACTTGAAATTTACATGTGATAAACTTCCCTAGCAAATCTTTAACTACCTGTAACATCCACACAGTGGCTTCTGCCACAGATAGGCTCCTTTTTTCAGGGCTAAGAGATACAAACATACAGCTCACACCAACACAGCAA RR: CATTCAAAAGTGCGATCCAGAATTTTACTATCGTTGATCGTCGTAAGGGGAAGGATTGTGCATAAAGGTTTTCATCGATGACCGAATCACATTGAACTTTAAATGTACACTATTTGAAGGGATCGTTTAGAAATTGATGGACATTGTAGGTGTGTCACCGAAGACGGTGTCTATCCGAGGAAAAAAGTCCCGATTCTCTATGTTTGTATGTCGAGTGTGGTTGTGTCGTT F2: 3 GATCGTCGTAAGGGGAAGGATTGTGCATAAAGGTTTTCATCGATGACCGAATCACATTGAACTTTAAATGTACACTATTTG 2 Unidirectional alignment (log-probability: -147) AGGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCT---------------------------------------------------------------------------gtttatcacatgtaaatttcaagttacactaagccagtagctacttttggaaatacgtgttaggaaggggaatgctgctagTTTAACTACCTGTAACATCCACACAGTGGCTTCTGCCACA AGGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCTAACACGTATTTCCAAAAGTAGCTACTGGCTTAGTGTAACTTGAAATTTACATGTGATAAACTTCCCTAGCAAATC---------------------------------------------------------------------------------TTTAACTACCTGTAACATCCACACAGTGGCTTCTGCCACA Template switch alignment (log-probability: -32.9) AGGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCT|GTTTATCACATGTAAATTTCAAGTTACACTAAGCCAGTAGCTACTTTTGGAAATACGTGTTAGGAAGGGGAATGCTGCTAG|TTTAACTACCTGTAACATCCACACAGTGGCTTCTGCCACA AGGTCTTAAAATGATAGCAACTAGCAGCATTCCCCTTCCT|GTTTATCACATGTAAATTTCAAGTTACACTAAGCCAGTAGCTACTTTTGGAAATACGTGTTAGGAAGGGGAATGCTGCTAG|TTTAACTACCTGTAACATCCACACAGTGGCTTCTGCCACA ========== Event 3883 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG-----GGTGGTCT---CTTTCCAGTAGAACCTGACATTTTTC Chimp: AATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG-----GGTGGTCT---CTCTCCAGTAGAACCTGACATTTTTC ↓ 3 2 1 4 Gorilla: AATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG----------TTCCAGAAAACCAGTAGAACCTGACATTTTTC ↑ 3 2 1 4 Human: AATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG-----GGTGGTCT---CTTTCCAGTAGAACCTGACATTTTTC Cluster: [ ] Orangutan: AATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGGAGTGG-----TCT---CTTTCCAGTAGAACCTGACATTATTC Human > Gorilla --------------- chrX:44412381-44412391 Template switch process: F1: L GCAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG 1 F3: 4 CAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT R RF: GCAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGGGGTGGTCTCTTTCCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT RR: CGTCACTTTAGTTTCGATAAAACGATCAAAAGACCGTCTCCCCACCAGAGAAAGGTCATCTTGGACTGTAAAAAGGATAGTTCTTTATAAGGA F2: 3 CAAAAGACCTT 2 Unidirectional alignment (log-probability: -32.7) CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG----------TTccagaaaaCCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGGGGTGGTCTCTTT--------CCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT Template switch alignment (log-probability: -22.6) CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG|TtCCAGAAAAC|CAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG|TGCCAGAAAAC|CAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT Chimp > Gorilla --------------- chrX:44412381-44412390 Template switch process: F1: L GCAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG 1 F3: 4 CCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT R RF: GCAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGGGGTGGTCTCTCTCCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT RR: CGTCACTTTAGTTTCGATAAAACGATCAAAAGACCGTCTCCCCACCAGAGAGAGGTCATCTTGGACTGTAAAAAGGATAGTTCTTTATAAGGA F2: 3 AAAAGACCTT 2 Unidirectional alignment (log-probability: -34.1) CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG-----------TtccagaaaaCCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGGGGTGGTCTCTCT---------CCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT Template switch alignment (log-probability: -22.5) CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG|TtCCAGAAAA|CCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT CAGTGAAATCAAAGCTATTTTGCTAGTTTTCTGGCAGAGG|TGCCAGAAAA|CCAGTAGAACCTGACATTTTTCCTATCAAGAAATATTCCT ========== Event 3884 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TCACTTGAACTGATAGGCCAT-------GTATTAATAGTTATTATgagttcttaagtagggaagtgtcttgatt ↓ 1 4 3 2 Chimp: TCACTTGAACTGATAGGCCATTAAGAACTCATTAATAGTTATTATgagttcttaagtagggaagtgtcttgatt ↑ 1 4 3 2 Gorilla: TCACTTGAACTGATAGGCCAT-------GTATTAATAGTTATTATgagttcttaagtagggaagtgtcttgatt Human: TCACTTGAACTGATAGGCCAT-------GTATTAATAGTTATTATgagttcttaagtagggaagtgtcttgatt Cluster: [ ] Orangutan: TCACTTGAACTGATAGGCCAT-------GTATTAATAGTTATTATgagttcttaagtagggaagtgtcttgatt Human > Chimp ------------- chrX:43783550-43783558 Template switch process: F1: L GAGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT 1 F3: 4 ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT R RF: GAGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCATGTATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT RR: CTCTCCCGACCCTCCAAGGTAGTGAACTTGACTATCCGGTACATAATTATCAATAATACTCAAGAATTCATCCCTTCACAGAA F2: 3 CTCAAGAAT 2 Unidirectional alignment (log-probability: -32.7) AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT-TaagaactcATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCATGT--------ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT Template switch alignment (log-probability: -16.4) AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT|TAAGAACTC|ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT|TAAGAACTC|ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT Gorilla > Chimp --------------- chrX:43783550-43783558 Template switch process: F1: L GAGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT 1 F3: 4 ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT R RF: GAGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCATGTATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT RR: CTCTCCCGACCCTCCAAGGTAGTGAACTTGACTATCCGGTACATAATTATCAATAATACTCAAGAATTCATCCCTTCACAGAA F2: 3 CTCAAGAAT 2 Unidirectional alignment (log-probability: -32) AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCATtaagaactcATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT-------GTATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT Template switch alignment (log-probability: -16.9) AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT|TAAGAACTC|ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT AGAGGGCTGGGAGGTTCCATCACTTGAACTGATAGGCCAT|TAAGAACTC|ATTAATAGTTATTATGAGTTCTTAAGTAGGGAAGTGTCTT ========== Event 3885 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AATCACTTTAAAGGCATTAGTGAGCATGGCTAAATGCTCACTAATTATCTCCAAGTTTATGT ↑ 3 2 1 4 Chimp: AATCACTTTAAAGGCATTAGTGAGCATGGCTAAATTAAGTTTAATTATCTCCAAGTTTATGT Gorilla: AATCACTTTAAAGGCATTAGTGAGCATGGCTAAATTAAGTTTAATTATCTCCAAGTTTATGT ↓ 3 2 1 4 Human: AATCACTTTAAAGGCATTAGTGAGCATGGCTAAATGCTCACTAATTATCTCCAAGTTTATGT Cluster: [ ] Orangutan: AATCACTTTAAAGGCATTAGTGAGCATGGCTAAATTAAGTTTAATTATCTCCAAGTTTATGT Chimp > Human ------------- chrX:113857456-113857461 Template switch process: F1: L TATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT 1 F3: 4 TAATTATCTCCAAGTTTATGTGATACTTGTTCTACATAAA R RF: TATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAATTAAGTTTAATTATCTCCAAGTTTATGTCATACTTGTTCTACATAAA RR: ATACATTTAGTGAAATTTCCGTAATCACTCGTACCGATTTAATTCAAATTAATAGAGGTTCAAATACAGTATGAACAAGATGTATTT F2: 3 CACTCG 2 Unidirectional alignment (log-probability: -36.1) ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAATgctcac------TAATTATCTCCAAGTTTATGTgATACTTGTTCTACATAAA ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT------TAAGTTTAATTATCTCCAAGTTTATGTCATACTTGTTCTACATAAA Template switch alignment (log-probability: -22) ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT|GCTCAC|TAATTATCTCCAAGTTTATGTgATACTTGTTCTACATAAA ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT|GCTCAC|TAATTATCTCCAAGTTTATGTCATACTTGTTCTACATAAA Gorilla > Human --------------- chrX:113857456-113857461 Template switch process: F1: L TATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT 1 F3: 4 TAATTATCTCCAAGTTTATGTGATACTTGTTCTACATAAA R RF: TATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAATTAAGTTTAATTATCTCCAAGTTTATGTCATACTTGTTCTACATAAA RR: ATACATTTAGTGAAATTTCCGTAATCACTCGTACCGATTTAATTCAAATTAATAGAGGTTCAAATACAGTATGAACAAGATGTATTT F2: 3 CACTCG 2 Unidirectional alignment (log-probability: -35.1) ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAA------TgctcacTAATTATCTCCAAGTTTATGTgATACTTGTTCTACATAAA ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAATTAAGTT------TAATTATCTCCAAGTTTATGTCATACTTGTTCTACATAAA Template switch alignment (log-probability: -22) ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT|GCTCAC|TAATTATCTCCAAGTTTATGTgATACTTGTTCTACATAAA ATGTAAATCACTTTAAAGGCATTAGTGAGCATGGCTAAAT|GCTCAC|TAATTATCTCCAAGTTTATGTCATACTTGTTCTACATAAA ========== Event 3886 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAGTGCAAATTTGGAGTTAACTAGAACCTAAGTTCTAGTCTGTTATAAGCCTCTATGT ↑ 1 4 3 2 Chimp: ATAGTGCAAATTTGGAGTTAAA--TGACCTAAGTTCTAGTCTGTTATAAGCCTCTATGT Gorilla: ATAGTGCAAATTTGGAGTTAAA--TGACCTAAGTTCTAGTCTGTTATAAGCCTCTATGT Human: ATAGTGCAAATTTGGAGTTAACTAGAACCTAAGTTCTAGTCTGTTATAAGCCTCTATGT Cluster: [ ] Orangutan: ATAGTGCAAATTTGGAGTTAAA--TGACCTAAGTTCTAGTcttttataagcctctatgt Chimp > Human ------------- chrX:114593692-114593697 Template switch process: F1: L GCACTGTGGGAAAGGTATTTATAGTGCAAATTTGGAGTTAA 1 F3: 4 CCTAAGTTCTAGTCTGTTATAAGCCTCTATGTCCTCCTC R RF: GCACTGTGGGAAAGGTATTTATAGTGCAAATTTGGAGTTAAATGACCTAAGTTCTAGTCTGTTATAAGCCTCTATGTCCTCCTC RR: CGTGACACCCTTTCCATAAATATCACGTTTAAACCTCAATTTACTGGATTCAAGATCAGACAATATTCGGAGATACAGGAGGAG F2: 3 AAGATC 2 Unidirectional alignment (log-probability: -25.8) CACTGTGGGAAAGGTATTTATAGTGCAAATTTGGAGTTAActAgaACCTAAGTTCTAGTCTGTTATAAGCCTCTATGTCCTCCTC CACTGTGGGAAAGGTATTTATAGTGCAAATTTGGAGTTAA--ATGACCTAAGTTCTAGTCTGTTATAAGCCTCTATGTCCTCCTC Template switch alignment (log-probability: -16) CACTGTGGGAAAGGTATTTATAGTGCAAATTTGGAGTTAA|CTAGAA|CCTAAGTTCTAGTCTGTTATAAGCCTCTATGTCCTCCTC CACTGTGGGAAAGGTATTTATAGTGCAAATTTGGAGTTAA|CTAGAA|CCTAAGTTCTAGTCTGTTATAAGCCTCTATGTCCTCCTC ========== Event 3887 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: GATCCTGCTCTGC-AAGCAAGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG---GACTGTGTTTAATGACATTTGTTCT ↑ 3 2 1 4 Chimp: GATCCTGCTCTGC-AAGCAAGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATGTTTCCCAGTGTTTAATGACATTTGTTCT ↓ 3 2 1 4 Gorilla: GATCCTGCTCTGC-AAGCAAGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG---GACTGTGTTTAATGACATTTGTTCT Human: GATCCTGCTCTGC-AAGCAAGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG---GACTGTGTTTAATGACATTTGTTCT Cluster: [ ] Orangutan: GATGCAGCTCTGCAAAGCAAGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG---GACTGTGTTTAATGACATTTGTTCT Chimp > Human ------------- chrX:38893335-38893338 Template switch process: F1: L CAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG 1 F3: 4 GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG R RF: AGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATGTTTCCCAGTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG RR: TCAGTCTGTCTTCGTCGTCATTGTTTCGTCTTAACGGTCACACTAGAGGGTTACAAAGGGTCACAAATTACTGTAAACAAGACAAACAGACTTTATATTAC F2: 3 TCAG 2 Unidirectional alignment (log-probability: -25.8) AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATGgacT------GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG---TTTCCCAGTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG Template switch alignment (log-probability: -15.8) AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG|GACT|GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG|GACT|GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG Chimp > Gorilla --------------- chrX:39314451-39314454 Template switch process: F1: L CAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG 1 F3: 4 GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG R RF: AGTCAGACAGAAGCAGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATGTTTCCCAGTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG RR: TCAGTCTGTCTTCGTCGTCATTGTTTCGTCTTAACGGTCACACTAGAGGGTTACAAAGGGTCACAAATTACTGTAAACAAGACAAACAGACTTTATATTAC F2: 3 TCAG 2 Unidirectional alignment (log-probability: -25.3) AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATGgacT------GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG---TTTCCCAGTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG Template switch alignment (log-probability: -16.2) AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG|GACT|GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG AGCAGTAACAAAGCAGAATTGCCAGTGTGATCTCCCAATG|GACT|GTGTTTAATGACATTTGTTCTGTTTGTCTGAAATATAATG ========== Event 3888 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: AAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAACAAAGTCATCAATCTCAATAGGGATGCTATGG ↑ 3 2 1 4 Chimp: AAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAA----CT----CATCTCAATAGGGATGCTATGG ↓ 3 2 1 4 Gorilla: AAATTGAAAACATCTTCTCTGGTGAGTTTTGGGAAACAAAGTCATCAATCTCAATAGGGATGCTATGG Human: AAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAACAAAGTCATCAATCTCAATAGGGATGCTATGG Cluster: [ ] Orangutan: AAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAACAAAGTCATCAATCTCAATAGGGATGCTATGG Chimp > Human ------------- chrX:38321661-38321670 Template switch process: F1: L CACTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAAC 1 F3: 4 ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC R RF: CACTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAACTCATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC RR: GTGACTTTAACTTTTGTAGAAGAGACTACTCAAAACCCTTTGAGTAGAGTTATCCCTACGATACCTAAACCAGTGAAAACTACG F2: 3 ACTACTGAAA 2 Unidirectional alignment (log-probability: -32.7) CTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAACaaagTCATCaatcTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC CTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAAC----TCATC----TCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC Template switch alignment (log-probability: -22.5) CTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAAC|AAAgTCATCA|ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC CTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAAC|AAACTCATCA|ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC Chimp > Gorilla --------------- chrX:38741100-38741109 Template switch process: F1: L CACTGAAATTGAAAACATCTTCTCTGGTGAGTTTTGGGAAAC 1 F3: 4 ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC R RF: CACTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAACTCATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC RR: GTGACTTTAACTTTTGTAGAAGAGACTACTCAAAACCCTTTGAGTAGAGTTATCCCTACGATACCTAAACCAGTGAAAACTACG F2: 3 ACTACTGAAA 2 Unidirectional alignment (log-probability: -37.7) CTGAAATTGAAAACATCTTCTCTGgTGAGTTTTGGGAAACaaagtcaTCaATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC CTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAAC-------TC-ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC Template switch alignment (log-probability: -28.1) CTGAAATTGAAAACATCTTCTCTGgTGAGTTTTGGGAAAC|AAAgTCATCA|ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC CTGAAATTGAAAACATCTTCTCTGATGAGTTTTGGGAAAC|AAACTCATCA|ATCTCAATAGGGATGCTATGGATTTGGTCACTTTTGATGC ========== Event 3889 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TAAGTCTAAAAGTTGGCTTAACTAGAATGAAGCAACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAA-------------------------------------------------------------------------------------------------TTTTGATGTTT-------ACAGATAA Chimp: TAAGTCTAAAAGTTGGCTTAACTAGAATGAAGCAACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGAATTTGGTTGCCATCCAATATATTTATGGTTGCTTCATTCTAGTTAAGCAACCATAAATATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGATGTTTACAATCTACAGATAA ↑ 3 4 2 1 Gorilla: TAAGTCTAAAAGTTGGCTTAACTAGAATGAAGCAACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAA-------------------------------------------------------------------------------------------------TTTTGATGTTTACAATCTACAGATAA Human: TAAGTCTAAAAGTTGGCTTAACTAGAATGAAGCAACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAA-------------------------------------------------------------------------------------------------TTTTGATGTTT-------ACAGATAA Cluster: [ ] Orangutan: TAAGTCTAAAAGTTGGCTTAACTGGAATGAAGCAACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAA-------------------------------------------------------------------------------------------------TTTTGATGTTTACAATCTACAGATAA Gorilla > Chimp --------------- chrKV421434:16892-16935 Template switch process: F1: L AACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGA 1 F3: 4 AAGCAACCATAAATATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGATGTTTACAATCTACAGATAAATGTTTGAGTTGAT R RF: AACTAGAATGAAGCAACCATAAATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGATGTTTACAATCTACAGATAAATGTTTGAGTTGAT RR: TTGATCTTACTTCGTTGGTATTTATATAACCTACCGTTGGTTTAAGTTTAAATTTAAAACTACAAATGTTAGATGTCTATTTACAAACTCAACTA F2: 3 TTGATCTTACTTCGTTGGTATTTATATAACCTACCGTTGGTTTA 2 Unidirectional alignment (log-probability: -150) AATATATTGGATGGCAACCAAATTCAAATTTAAATTTtgaatttggttgccatccaatatatttatggttgcttcattctagttaagcaaccataaatatatattggatggcaaccaaattcaa AATATATTGGATGGCAACCAAATTCAAATTTAAATTT--------------------------------------------------------------------------------------- Template switch alignment (log-probability: -35) AATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGA|ATTTGGTTGCCATCCAATATATTTATGGTTGCTTCATTCTAGTT|AAGCAACCATAAatATATATTGGATGGCAACCAAATTCAA AATATATTGGATGGCAACCAAATTCAAATTTAAATTTTGA|ATTTGGTTGCCATCCAATATATTTATGGTTGCTTCATTCTAGTT|AAGCAACCATAA--ATATATTGGATGGCAACCAAATTCAA ========== Event 3890 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGCATATTGTATCTTACCACATGTAT---------AGAGGACCTAACACTTGGTTTTTT ↓ 3 1 4 Chimp: TGGCATATTGTATCTTACCACATGTATCTCTATACATGTGGACCTAACACTTGGTTTTTT ↑ 3 1 4 Gorilla: TGGCATGTTGTATCTTACCACATGTAT---------AGAGGACCTAACACTTGGTTTTTT Human: TGGCATATTGTATCTTACCACATGTAT---------AGAGGACCTAACACTTGGTTTTTT Cluster: [ ] Orangutan: TGGCATATTGTATCTTACCACATGTAT---------AGAGGACCTAACACTTGATTTTTT Human > Chimp ------------- chrX:118174881-118174892 Template switch process: F1: L TATTTTATGCATGTTGGCATATTGTATCTTACCACATGTAT 1 F3: 4 GGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC R RF: TATTTTATGCATGTTGGCATATTGTATCTTACCACATGTATAGAGGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC RR: ATAAAATACGTACAACCGTATAACATAGAATGGTGTACATATCTCCTGGATTGTGAACCAAAAAAGGGACACACGATCCTGATG F2: 3 TGTACATATCTC 2 Unidirectional alignment (log-probability: -35.9) ATTTTATGCATGTTGGCATATTGTATCTTACCACATGTATctctatacatGtGGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC ATTTTATGCATGTTGGCATATTGTATCTTACCACATGTAT---------AGAGGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC Template switch alignment (log-probability: -16.8) ATTTTATGCATGTTGGCATATTGTATCTTACCACATGTAT|CTCTATACATGT|GGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC ATTTTATGCATGTTGGCATATTGTATCTTACCACATGTAT|CTCTATACATGT|GGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC Gorilla > Chimp --------------- chrX:118174881-118174892 Template switch process: F1: L TATTTTATGCATGTTGGCATATTGTATCTTACCACATGTAT 1 F3: 4 GGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC R RF: TATTTTATGCATGTTGGCATGTTGTATCTTACCACATGTATAGAGGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC RR: ATAAAATACGTACAACCGTACAACATAGAATGGTGTACATATCTCCTGGATTGTGAACCAAAAAAGGGACACACGATCCTGATG F2: 3 TGTACATATCTC 2 Unidirectional alignment (log-probability: -40.4) ATTTTATGCATGTTGGCATaTTGTATCTTACCACATGTATctctatacatGtGGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC ATTTTATGCATGTTGGCATGTTGTATCTTACCACATGTAT---------AGAGGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC Template switch alignment (log-probability: -22.8) ATTTTATGCATGTTGGCATaTTGTATCTTACCACATGTAT|CTCTATACATGT|GGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC ATTTTATGCATGTTGGCATGTTGTATCTTACCACATGTAT|CTCTATACATGT|GGACCTAACACTTGGTTTTTTCCCTGTGTGCTAGGACTAC ========== Event 3891 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CTATTTCGTGTGAGGATGCCAATTCAGGGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATA ↑ 1 4 3 2 Chimp: CTATTTCGTGTGAGGATGCCA--ACGTGGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATA Gorilla: Human: CTATTTCGTGTGAGGATGCCAATTCAGGGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATA Cluster: [ ] Orangutan: Chimp > Human ------------- chrX:46757671-46757675 Template switch process: F1: L ACAATCATGAAGTGGCTCGTCTATTTCGTGTGAGGATGCCAA 1 F3: 4 GGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATAC R RF: ACAATCATGAAGTGGCTCGTCTATTTCGTGTGAGGATGCCAACGTGGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATAC RR: TGTTAGTACTTCACCGAGCAGATAAAGCACACTCCTACGGTTGCACCCGAAATTGTGGTGACTTAATGTAAGTTTTTCTCTTATG F2: 3 GACTT 2 Unidirectional alignment (log-probability: -25.8) AATCATGAAGTGGCTCGTCTATTTCGTGTGAGGATGCCAAttCagGGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATAC AATCATGAAGTGGCTCGTCTATTTCGTGTGAGGATGCCAA--CGTGGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATAC Template switch alignment (log-probability: -15.9) AATCATGAAGTGGCTCGTCTATTTCGTGTGAGGATGCCAA|TTCAG|GGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATAC AATCATGAAGTGGCTCGTCTATTTCGTGTGAGGATGCCAA|TTCAG|GGGCTTTAACACCACTGAATTACATTCAAAAAGAGAATAC ========== Event 3892 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: AATATATACCTTATGGCTTTG---TTGCACCTTT--AATGTCTATTCAGAGACGcagcataacag Chimp: AATATATACCTTATGGCTTTG---TTGCACCTTT--AATGTCTATTCAGAGACGcagcataacag ↓ 3 41 2 Gorilla: AATATATACCTTATGGCTTTGTATATAGACATTAAAGATGTCTATTCAGAGACGcagcataacag ↑ 3 41 2 Human: AATATATACCTTATGGCTTTG---TTGCACCTTT--AATGTCTATTCAGAGACGcagcataacag Cluster: [ ] Orangutan: AATATATACCTTATGGCTTTG---TTGCACCCTT--AATATCTATTCAGAGATGCTgcataacag Human > Gorilla --------------- chrX:123181185-123181197 Template switch process: F1: L AAGAGATCCTCCACCACAGTAATATATACCTTATGGCTTTGT----------AT 1 F3: 4 ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA R RF: AAGAGATCCTCCACCACAGTAATATATACCTTATGGCTTTGTTGCACCTTTAATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA RR: TTCTCTAGGAGGTGGTGTCATTATATATGGAATACCGAAACAACGTGGAAATTACAGATAAGTCTCTGCGTCGTATTGTCGCAAAGTCTCGT F2: 3 GAAATTACAGATA 2 Unidirectional alignment (log-probability: -41.2) GATCCTCCACCACAGTAATATATACCTTATGGCTTTG---------TAtatagacattaaagATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA GATCCTCCACCACAGTAATATATACCTTATGGCTTTGTTGCACCTTTA--------------ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA Template switch alignment (log-probability: -27.7) GATCCTCCACCACAGTAATATATACCTTATGGCTTTGT----------AT|ATAGACATTAAAG|ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA GATCCTCCACCACAGTAATATATACCTTATGGCTTTGTTGCACCTTTAAT|ATAGACATTAAAG|ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA Chimp > Gorilla --------------- chrX:123181185-123181197 Template switch process: F1: L AAGAGATCCTCCACCACAGTAATATATACCTTATGGCTTTGT----------AT 1 F3: 4 ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA R RF: AAGAGATCCTCCACCACAGTAATATATACCTTATGGCTTTGTTGCACCTTTAATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA RR: TTCTCTAGGAGGTGGTGTCATTATATATGGAATACCGAAACAACGTGGAAATTACAGATAAGTCTCTGCGTCGTATTGTCGCAAAGTCTCGT F2: 3 GAAATTACAGATA 2 Unidirectional alignment (log-probability: -41.2) GATCCTCCACCACAGTAATATATACCTTATGGCTTTG---------TAtatagacattaaagATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA GATCCTCCACCACAGTAATATATACCTTATGGCTTTGTTGCACCTTTA--------------ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA Template switch alignment (log-probability: -27.7) GATCCTCCACCACAGTAATATATACCTTATGGCTTTGT----------AT|ATAGACATTAAAG|ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA GATCCTCCACCACAGTAATATATACCTTATGGCTTTGTTGCACCTTTAAT|ATAGACATTAAAG|ATGTCTATTCAGAGACGCAGCATAACAGCGTTTCAGAGCA ========== Event 3893 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: aaatttttacataaattgccaaattgcctaccaTATCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCAAAAAAATAATCTCACTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT-----GCACACTTTGCCCAATTTCAACTG ↓ 3 2 1 4 Chimp: aaatttttacataaatggccaaattgcctaccaTATCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCaaaaaaaTAATCTCACTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATTCAATTTGAAACTTTGCCCAATTTCAACTG ↑ 3 2 1 4 Gorilla: aaatttttacataaattgccaaattgcctaccaTATCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCaaaaaaaTAATCTCACTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT-----GCACACTTTGCCCAATTTCAACTG Human: aaatttttacataaattgccaaattgcctaccaTATCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCAAAAAAATAATCTCACTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT-----GCACACTTTGCCCAATTTCAACTG Cluster: [ ] Orangutan: aaatttttacataaattgccaaattgcctaccataTCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCAAAAAAATAATCTCACTTGTACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT-----GCACACTTTGCTCAATTTCAACTG Human > Chimp ------------- chrX:31849843-31849849 Template switch process: F1: L CTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT 1 F3: 4 AAACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAACTA R RF: CAAATTGCCTACCATATCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCAAAAAAATAATCTCACTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATTGCACACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAACTA RR: GTTTAACGGATGGTATAGATATAAAGGAGGTATGGAATCTATCGATATCCAAAACGGTTAGAACTGTCAAACTTTCGTTTTTTTATTAGAGTGAATATGAAAGAACATAAAGATGAAAATATTTAACGGATAACGTGTGAAACGGGTTAAAGTTGACGATGGAATAAAACGATTGAT F2: 3 GTTTAAC 2 Unidirectional alignment (log-probability: -32.8) TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT---CaatttgaaACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATTGCAC--------ACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC Template switch alignment (log-probability: -22.2) TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT|CAATTTG|AaACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT|CAATTTG|ACACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC Gorilla > Chimp --------------- chrX:31849843-31849849 Template switch process: F1: L CTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT 1 F3: 4 AAACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAACTA R RF: CAAATTGCCTACCATATCTATATTTCCTCCATACCTTAGATAGCTATAGGTTTTGCCAATCTTGACAGTTTGAAAGCAAAAAAATAATCTCACTTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATTGCACACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAACTA RR: GTTTAACGGATGGTATAGATATAAAGGAGGTATGGAATCTATCGATATCCAAAACGGTTAGAACTGTCAAACTTTCGTTTTTTTATTAGAGTGAATATGAAAGAACATAAAGATGAAAATATTTAACGGATAACGTGTGAAACGGGTTAAAGTTGACGATGGAATAAAACGATTGAT F2: 3 GTTTAAC 2 Unidirectional alignment (log-probability: -32.3) TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT---CaatttgaaACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATTGCAC--------ACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC Template switch alignment (log-probability: -22.2) TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT|CAATTTG|AaACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC TTATACTTTCTTGTATTTCTACTTTTATAAATTGCCTATT|CAATTTG|ACACTTTGCCCAATTTCAACTGCTACCTTATTTTGCTAAC ========== Event 3894 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: TATCTAGATATTTGCTAAAGGTAAGTCTTATTACTCCAGTTAT--ATCTATATCTTCAGTAGTTAAGCCTAAAAGATTA Chimp: TATCTAGATATTTGCTAAAGGTAAGTCTTATTACTCCAGTTAT--ATCTGCATCTTCAGTAGTTAAGCCTAAAAGATTA Gorilla: TATCTAGATATTTGCTAAAGG----------TACTGAAGATATAGATATATATCTTCAGTACTTAAGCCTAAAAGATTA ↑ 1 3 4 2 Human: TATCTAGATATTTGCTAAAGGTAAGTCTTATTACTCCAGTTAT--ATCTATATCTTCAGTAGTTAAGCCTAAAAGATTA Cluster: [ ] Orangutan: TATCTAGATATTTGCTAAAGATAAGTCTTATTACTCCAGTTAT--ATTTCTATCTTCAGTAGTTAAGCCTAAAAGATTA Human > Gorilla --------------- chrX:125891704-125891718 Template switch process: F1: L ACATGTAGCTGGCTGCATAATATCTAGATATTTGCTAAAGGTA 1 F3: 4 TATATCTTCAGTACTTAAGCCTAAAAGATTATTTCCATGG R RF: ACATGTAGCTGGCTGCATAATATCTAGATATTTGCTAAAGGTAAGTCTTATTACTCCAGTTATATCTATATCTTCAGTAGTTAAGCCTAAAAGATTATTTCCATGG RR: TGTACATCGACCGACGTATTATAGATCTATAAACGATTTCCATTCAGAATAATGAGGTCAATATAGATATAGAAGTCATCAATTCGGATTTTCTAATAAAGGTACC F2: 3 ATAGATATAGAAGTC 2 Unidirectional alignment (log-probability: -47.1) TGTAGCTGGCTGCATAATATCTAGATATTTGCTAAAGGTActgaagatatAG------------------ATaTATATCTTCAGTAcTTAAGCCTAAAAGATTATTTCCATGG TGTAGCTGGCTGCATAATATCTAGATATTTGCTAAAGGTA----------AGTCTTATTACTCCAGTTATATCTATATCTTCAGTAGTTAAGCCTAAAAGATTATTTCCATGG Template switch alignment (log-probability: -23.2) TGTAGCTGGCTGCATAATATCTAGATATTTGCTAAAGGTA|CTGAAGATATAGATA|TATATCTTCAGTAcTTAAGCCTAAAAGATTATTTCCATGG TGTAGCTGGCTGCATAATATCTAGATATTTGCTAAAGGTA|CTGAAGATATAGATA|TATATCTTCAGTAGTTAAGCCTAAAAGATTATTTCCATGG ========== Event 3895 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGAC---------------------------------------------------------------------------------------------------TACTTTTAATCTCAAAAGCTAAACTCAATGCAGAAATGAAACAGGAAAATACATAAAGACAATAAGAGTACTTTTCTAAAGGTGGTTTATG ↓ 4 3 1 2 Chimp: TCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGACTAGTACTCTTATTGTCTTTATGTATTTTCCTGTTTCATTTCTGCATTGGGTTTAGCTTTTGAGATTAAAAGTAGTCTCTTTCAAAAAGATGAAAGAGACTACTTTTAATCTCAAAAGCTAAACCCAATGCAGAAATGAAACAGGAAAATACATAAAGACAATAAGAGTACTTTTCTAAAGGTGGTTTACG Gorilla: TCTACTTAGGAAGGGATGACAAAAAGATGAAAGGGAC---------------------------------------------------------------------------------------------------TACTTTTAATCTCAAAAGCTAAACTCAATGCAGAAATGAAACAGGAAAATACATAAAGATAATAAGAGTACTTTTCTAAAGGTGGTTTACA Human: TCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGAC---------------------------------------------------------------------------------------------------TACTTTTAATCTCAAAAGCTAAACTCAATGCAGAAATGAAACAGGAAAATACATAAAGACAATAAGAGTACTTTTCTAAAGGTGGTTTATG Cluster: [ ] Orangutan: TCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGAC---------------------------------------------------------------------------------------------------TACCTTTAATTTCAAAAGCTAAACTCAATGCAGAAATGAAACAGGAAAATACATAAAGACAATGAGAGTACTTTTCTAAAGGTGGTTTACG Human > Chimp ------------- chrX:126623147-126623225 Template switch process: F1: L CTTCTCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGACTA 1 F3: 4 CAAAAAGATGAAAGAGACTACTTTTAATCTCAAAAGCTAAACCCAATGCAGAAATGAA R RF: CTTCTCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGACTACTTTTAATCTCAAAAGCTAAACTCAATGCAGAAATGAAACAGGAAAATACATAAAGACAATAAGAGTAC RR: GAAGAGATGAATCCTTCCCTACTGTTTTTCTACTTTCTCTGATGAAAATTAGAGTTTTCGATTTGAGTTACGTCTTTACTTTGTCCTTTTATGTATTTCTGTTATTCTCATG F2: 3 TTTCTCTGATGAAAATTAGAGTTTTCGATTTGGGTTACGTCTTTACTTTGTCCTTTTATGTATTTCTGTTATTCTCATG 2 Unidirectional alignment (log-probability: -159) CTCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGACtagtactcttattgtctttatgtattttcctgtttcatttctgcattgggtttagcttttgagattaaaagtagtctctttcaaaaagatgaaagagacTACTTTTAATCTCAAAAGCTAA CTCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGAC---------------------------------------------------------------------------------------------------TACTTTTAATCTCAAAAGCTAA Template switch alignment (log-probability: -37.1) CTCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGACTA|GTACTCTTATTGTCTTTATGTATTTTCCTGTTTCATTTCTGCATTGgGTTTAGCTTTTGAGATTAAAAGTAGTCTCTTT|CAAAAAGATGAAAGAGACTACTTTTAATCTCAAAAGCTAA CTCTACTTAGGAAGGGATGACAAAAAGATGAAAGAGACTA|GTACTCTTATTGTCTTTATGTATTTTCCTGTTTCATTTCTGCATTGAGTTTAGCTTTTGAGATTAAAAGTAGTCTCTTT|CAAAAAGATGAAAGAGACTACTTTTAATCTCAAAAGCTAA ========== Event 3896 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: aagattgtttgggaattcatttgttgggtttattGGATCCGAGGATCCTCAGATCCAATAAACCCAACAAATCATCAGGAAACAGTTGTC Chimp: AAGATTGTTTGGGAATTCATGTGTTGGGTTTAT-TGATCCGAGGATCCTCAGATCCAATAAACCCAACAAATCATCAGGAAACAGTTGTC ↓ 1 3 4 2 Gorilla: AAGATTGTCTGGGAATTCATTTGTTGGGTTTACTGGATCTGAGGATCCTCGGATCCAATAAACCCAACAAATCATCAGGAAACAGTTGTC Human: aagattgtttgggaattcatttgttgggtttattGGATCCGAGGATCCTCAGATCCAATAAACCCAACAAATCATCAGGAAACAGTTGTC Cluster: [ ] Orangutan: aagattgtttgggAATTCATTTGTTGAGAATATTGGATCCGAGGATCCTCAGATCCAATAAACCCAACAAATCATCAGGAAACAGTTGTC Chimp > Gorilla --------------- chrX:12571035-12571065 Template switch process: F1: L AGTTTTGTTAAGATTGTCTGGGAATTCAT 1 F3: 4 GATCCAATAAACCCAACAAATCATCAGGA R RF: AGTTTTGTTAAGATTGTTTGGGAATTCATGTGTTGGGTTTATTGATCCGAGGATCCTCAGATCCAATAAACCCAACAAATCATCAGGA RR: TCAAAACAATTCTAACAAACCCTTAAGTACACAACCCAAATAACTAGGCTCCTAGGAGTCTAGGTTATTTGGGTTGTTTAGTAGTCCT F2: 3 GCTCCTAGGAGTCTAGGTCATTTGGGTTGTT 2 Unidirectional alignment (log-probability: -40) AGTTTTGTTAAGATTGTcTGGGAATTCATtTGTTGGGTTTAcTgGATCtGAGGATCCTCgGATCCAATAAACCCAACAAATCATCAGGA AGTTTTGTTAAGATTGTTTGGGAATTCATGTGTTGGGTTTA-TTGATCCGAGGATCCTCAGATCCAATAAACCCAACAAATCATCAGGA Template switch alignment (log-probability: -30.2) AGTTTTGTTAAGATTGTcTGGGAATTCAT|TTGTTGGGTTTAcTGGATCTGAGGATCCTCG|GATCCAATAAACCCAACAAATCATCAGGA AGTTTTGTTAAGATTGTTTGGGAATTCAT|TTGTTGGGTTTATTGGATCTGAGGATCCTCG|GATCCAATAAACCCAACAAATCATCAGGA ========== Event 3897 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: tgtgctaatttgtaacaatttgatgcatagtttcccataaaaataatttctaa-----------------------------------------------------------------------------tataataatcaatgtattcattttctcccaacttgccattaa Chimp: TGTGCTAATTTGTAACAATTTGATGCATAGTTTCTCATAAAAATAATTTCTAATATAATAATCAATGTATTCATTATTATATTAGAAATTATTTTTATGAGAAACTATGCATCAAAATAATTATTTCTAATATAATAATCAATGTATTCATTTTCTCCCAACTTGCCATTAA ↑ 3 4 2 1 Gorilla: TGTGCTAATTTGTAACAATTTGATGCATAGTTTCTCATAAAAATAATTTCTAA-----------------------------------------------------------------------------TATAATAATCAATGTATTCATTTTCTCCCAACTTGCCATTAA Human: tgtgctaatttgtaacaatttgatgcatagtttcccataaaaataatttctaa-----------------------------------------------------------------------------tataataatcaatgtattcattttctcccaacttgccattaa Cluster: [ ] Orangutan: TGTGCAAATTTGTAACAATTTGATGCATAGTTTCTCATAAAAATAATTTCTCA-----------------------------------------------------------------------------TATAATAATCAATGTATTCATTTTCTCCCAACTTGCCATTAA Gorilla > Chimp --------------- chrX:127731333-127731372 Template switch process: F1: L TAACAATTTGATGCATAGTTTCTCATAAAAATAATTTCTAATATAATAATCAATGTATTCATT 1 F3: 4 AATAATTATTTCTAATATAATAATCAATGTATTCATTTTCTCCCAACTTGCCATT R RF: TAACAATTTGATGCATAGTTTCTCATAAAAATAATTTCTAATATAATAATCAATGTATTCATTTTCTCCCAACTTGCCATT RR: ATTGTTAAACTACGTATCAAAGAGTATTTTTATTAAAGATTATATTATTAGTTACATAAGTAAAAGAGGGTTGAACGGTAA F2: 3 AACTACGTATCAAAGAGTATTTTTATTAAAGATTATATTA 2 Unidirectional alignment (log-probability: -122) CATAAAAATAatttctaatataataatcaatgtattcattattatattagaaattatttttatgagaaactatgcatcaaaataattATTTCTAATATAATAATCAATGTATTCATTTTC CATAAAAATA-----------------------------------------------------------------------------ATTTCTAATATAATAATCAATGTATTCATTTTC Template switch alignment (log-probability: -32.6) CATAAAAATAATTTCTAATATAATAATCAATGTATTCATT|ATTATATTAGAAATTATTTTTATGAGAAACTATGCATCAA|AAtAATtATTTCTAATATAATAATCAATGTATTCATTTTC CATAAAAATAATTTCTAATATAATAATCAATGTATTCATT|ATTATATTAGAAATTATTTTTATGAGAAACTATGCATCAA|AAAAATAATTTCTAATATAATAATCAATGTATTCATTTTC ========== Event 3898 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GAGCTGCCTGGGAGGTGTGCCCAGCCT--------GCCATCCCAGGAAGTGGGCAGGA ↓ 3 1 4 Chimp: GAGCTGCCTGGGAGGTGTGCCCAGCCGGTAGGCTGGGCATCCCAGGAAGTGGGCAGGA ↑ 3 1 4 Gorilla: GAGCTGCCTGGGAGGTGTGCCCAGCCT--------GCCATCCCAGGAAGTGGGCAGGA Human: GAGCTGCCTGGGAGGTGTGCCCAGCCT--------GCCATCCCAGGAAGTGGGCAGGA Cluster: [ ] Orangutan: GAGCTGCCTGGGAGGTGTGCCCAGCCT--------GCCATCCAAAGAAGTGGGCAGGA Human > Chimp ------------- chrX:129747773-129747783 Template switch process: F1: L CCAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC 1 F3: 4 CATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA R RF: CCAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCCTGCCATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA RR: GGTTTCCTACCTCGACTCGACGGACCCTCCACACGGGTCGGACGGTAGGGTCCTTCACCCGTCCTTCCCTGTCCCAGAGAGGGT F2: 3 GGGTCGGATGG 2 Unidirectional alignment (log-probability: -34.4) CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCCggtaggctgGgCATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC--------TGCCATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA Template switch alignment (log-probability: -22.6) CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC|GGtAGGCTGGG|CATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC|GGCAGGCTGGG|CATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA Gorilla > Chimp --------------- chrX:129747773-129747783 Template switch process: F1: L CCAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC 1 F3: 4 CATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA R RF: CCAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCCTGCCATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA RR: GGTTTCCTACCTCGACTCGACGGACCCTCCACACGGGTCGGACGGTAGGGTCCTTCACCCGTCCTTCCCTGTCCCAGAGAGGGT F2: 3 GGGTCGGATGG 2 Unidirectional alignment (log-probability: -33.5) CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCCggtaggctgGgCATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC--------TGCCATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA Template switch alignment (log-probability: -22.6) CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC|GGtAGGCTGGG|CATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA CAAAGGATGGAGCTGAGCTGCCTGGGAGGTGTGCCCAGCC|GGCAGGCTGGG|CATCCCAGGAAGTGGGCAGGAAGGGACAGGGTCTCTCCCA ========== Event 3899 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 3456 Detected in comparisons: 3456 Multiple sequence alignment: Human: ACTGCCTACTTGAGAACGGAAGCATT--AGCTTTTAAGAGCTGGACCCAGAGG Chimp: ACTGCCTACTTGAGAACGGAAGCATT--AGCTTTTAAGAGCTGGACCCAGAGG ↓ 1 3 4 2 ↑ 1 3 42 Gorilla: ACTGCCTACTTGAGAACGGAAAAGCTAATGCTTTTAAGAGCTGGACCCAGAGG ↓ 1 3 42 ↑ 1 3 4 2 Human: ACTGCCTACTTGAGAACGGAAGCATT--AGCTTTTAAGAGCTGGACCCAGAGG Cluster: [ ] Orangutan: ACTGCCTACTTGAGAACAGAAGCATT--AGCTTTTAAGAGGTGGACCCAGAGG Gorilla > Human --------------- chrX:24452042-24452047 Template switch process: F1: L TCTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAA 1 F3: 4 GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC R RF: TCTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAAAAGCTAATGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC RR: AGACTCTTTTGTTACCGAGGTGACGGATGAACTCTTGCCTTTTCGATTACGAAAATTCTCGACCTGGGTCTCCATGGAGTCACATAACG F2: 3 ATTACG 2 Unidirectional alignment (log-probability: -33.7) CTGAGAAAACAgTGGCTCCACTGCCTACTTGAGAACGGAAgcattA-------GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAA-----AAGCTAATGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Template switch alignment (log-probability: -22) CTGAGAAAACAgTGGCTCCACTGCCTACTTGAGAACGGAA|GCATTA|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAA|GCATTA|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Human > Gorilla --------------- chrX:24755838-24755845 Template switch process: F1: L TCTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAA 1 F3: 4 GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC R RF: TCTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAAGCATTAGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC RR: AGACTCTTTTGTCACCGAGGTGACGGATGAACTCTTGCCTTCGTAATCGAAAATTCTCGACCTGGGTCTCCATGGAGTCACATAACG F2: 3 TAATCGAA 2 Unidirectional alignment (log-probability: -36.5) CTGAGAAAACAaTGGCTCCACTGCCTACTTGAGAACGGAA-----AagctaatGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAAGCATTA-------GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Template switch alignment (log-probability: -22.3) CTGAGAAAACAaTGGCTCCACTGCCTACTTGAGAACGGAA|AAGCTAAT|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAA|AAGCTAAT|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Gorilla > Chimp --------------- chrKV421425:36063-36068 Template switch process: F1: L TCTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAA 1 F3: 4 GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC R RF: TCTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAAAAGCTAATGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC RR: AGACTCTTTTGTTACCGAGGTGACGGATGAACTCTTGCCTTTTCGATTACGAAAATTCTCGACCTGGGTCTCCATGGAGTCACATAACG F2: 3 ATTACG 2 Unidirectional alignment (log-probability: -33.7) CTGAGAAAACAgTGGCTCCACTGCCTACTTGAGAACGGAAgcattA-------GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAA-----AAGCTAATGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Template switch alignment (log-probability: -22) CTGAGAAAACAgTGGCTCCACTGCCTACTTGAGAACGGAA|GCATTA|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAA|GCATTA|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Chimp > Gorilla --------------- chrX:24755838-24755845 Template switch process: F1: L TCTGAGAAAACAATGGCTCCACTGCCTACTTGAGAACGGAA 1 F3: 4 GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC R RF: TCTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAAGCATTAGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC RR: AGACTCTTTTGTCACCGAGGTGACGGATGAACTCTTGCCTTCGTAATCGAAAATTCTCGACCTGGGTCTCCATGGAGTCACATAACG F2: 3 TAATCGAA 2 Unidirectional alignment (log-probability: -36.5) CTGAGAAAACAaTGGCTCCACTGCCTACTTGAGAACGGAA-----AagctaatGCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAAGCATTA-------GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC Template switch alignment (log-probability: -22.3) CTGAGAAAACAaTGGCTCCACTGCCTACTTGAGAACGGAA|AAGCTAAT|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC CTGAGAAAACAGTGGCTCCACTGCCTACTTGAGAACGGAA|AAGCTAAT|GCTTTTAAGAGCTGGACCCAGAGGTACCTCAGTGTATTGC ========== Event 3900 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: ATGTTCTGACCAAAATGGGGTTTGGTGGTTTGGTTTTAATGGGTGGGCAGGTGACATACtttctt--------------------tctttcttttttttttttttttttgagacagagtcttgttctgtcacccaggc-tggagtgcagtggcgcaatctcggctcactgcaagctcctcctcccaggttca Chimp: ATGTTCTGACCAAAATGGGGTTTGGTGGTTTGGTTGCAATGGGTGGGCAGGTGACATACtttctt----------------------------tttt-tttttttttttgagacagagtcttgttctgtcacccaggc-tggagtgcagtggcgcgatctcggctcactgcaagctcctcctcccaggttca Gorilla: ATGTTCTGACCAAAATGGGGT--------TTGGTTGCAATGGGTGGGCAGGTGACATACtttctt---------tcttttttttt--------ttttttttttttttttgaaacacagccttgttctgtcacccatgcgaggactgcataggcactattacagatccccggaagctcctcctcccaggctcc ↑ 1 4 3 2 Human: ATGTTCTGACCAAAATGGGGTTTGGTGGTTTGGTTTTAATGGGTGGGCAGGTGACATACtttctt--------------------tctttcttttttttttttttttttgagacagagtcttgttctgtcacccaggc-tggagtgcagtggcgcaatctcggctcactgcaagctcctcctcccaggttca Cluster: [ ] Orangutan: ATGCTCTGACCAAAATGGGGT--------TTGGTTGCAATGGGTGGGCAGGTGACATACtttctttctttcttt-------------------ttttttttttttttttgagatggagtcttgttctgtcacccaggc-tggagtgcagtggcgcgatctcgactcactgcaagctcctcctcccaggttca Human > Gorilla --------------- chrX:132243198-132243201 Template switch process: F1: L GGATATACAGGCATTTGTACATGTTCTGACCAAAATGGGGTTTGGT 1 F3: 4 ATGGGTGGGCAGGTGACATACTTTCTTTCTTTTTTTTT R RF: GGATATACAGGCATTTGTACATGTTCTGACCAAAATGGGGTTTGGTGGTTTGGTTTTAATGGGTGGGCAGGTGACATACTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGTTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCA RR: CCTATATGTCCGTAAACATGTACAAGACTGGTTTTACCCCAAACCACCAAACCAAAATTACCCACCCGTCCACTGTATGAAAGAAAGAAAGAAAAAAAAAAAAAAAAAACTCTGTCTCAGAACAAGACAGTGGGTCCGACCTCACGTCACCGCGTTAGAGCCGAGTGACGT F2: 3 ACGT 2 Unidirectional alignment (log-probability: -43.4) ACAGGCATTTGTACATGTTCTGACCAAAATGGGGTTT--------GGTTgcAATGGGTGGGCAGGTGACATACTTTCTTTcttttttttt ACAGGCATTTGTACATGTTCTGACCAAAATGGGGTTTGGTGGTTTGGTTTTAATGGGTGGGCAGGTGACATACTTTCTTT---------- Template switch alignment (log-probability: -21.8) ACAGGCATTTGTACATGTTCTGACCAAAATGGGGTTTGGT|TGCA|ATGGGTGGGCAGGTGACATACTTTCTTTCTTTtTTTTT ACAGGCATTTGTACATGTTCTGACCAAAATGGGGTTTGGT|TGCA|ATGGGTGGGCAGGTGACATACTTTCTTTCTTTCTTTTT ========== Event 3901 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAATCTCAAGTTTCTCCTGAAACTTGAGAGGCTATGTACCCAAAAGATTTTCCTGTCTTGGACTTATTCTGTGTGCATCTTTAATCTCC Chimp: CCAATCTCAAGTTTCTCCTGAAACTTGAGAGGCTATGTACCCAAAAGATTTTCCTGTCTTGGACTTATTCTGTGTGCATCTTTAATCTCC ↓ 1 3 4 2 Gorilla: CCAATCTCAAGTTTCTCCTGAGAA---------TAAG--TCCAAGAC--AGGAAAATCTTGGACTTATTCTGTGTGCATCTTTAATCTCC Human: CCAATCTCAAGTTTCTCCTGAAACTTGAGAGGCTATGTACCCAAAAGATTTTCCTGTCTTGGACTTATTCTGTGTGCATCTTTAATCTCC Cluster: [ ] Orangutan: CCAATCTCAAGTTTCTCCTGAAACTTGAGAGGCTATGTACCCAAAAGATTTTCCTGTCTTGGACTTATTCTGTGTGCATCTTTAATCTCC Chimp > Gorilla --------------- chrX:131930184-131930205 Template switch process: F1: L ATATAAAGCAAATGAATATGCCAATCTCAAGTTTCTCCTGA 1 F3: 4 TCTTGGACTTATTCTGTGTGCATCTTTAATCTCCATCTAC R RF: ATATAAAGCAAATGAATATGCCAATCTCAAGTTTCTCCTGAAACTTGAGAGGCTATGTACCCAAAAGATTTTCCTGTCTTGGACTTATTCTGTGTGCATCTTTAATCTCCATCTAC RR: TATATTTCGTTTACTTATACGGTTAGAGTTCAAAGAGGACTTTGAACTCTCCGATACATGGGTTTTCTAAAAGGACAGAACCTGAATAAGACACACGTAGAAATTAGAGGTAGATG F2: 3 AAAAGGACAGAACCTGAATAAG 2 Unidirectional alignment (log-probability: -51.1) TATAAAGCAAATGAATATGCCAATCTCAAGTTTCTCCTGagaataagtccaagacaggaAAA---------------------------------TCTTGGACTTATTCTGTGTGCATCTTTAATCTCCATCTAC TATAAAGCAAATGAATATGCCAATCTCAAGTTTCTCCTG--------------------AAACTTGAGAGGCTATGTACCCAAAAGATTTTCCTGTCTTGGACTTATTCTGTGTGCATCTTTAATCTCCATCTAC Template switch alignment (log-probability: -18.5) TATAAAGCAAATGAATATGCCAATCTCAAGTTTCTCCTGA|GAATAAGTCCAAGACAGGAAAA|TCTTGGACTTATTCTGTGTGCATCTTTAATCTCCATCTAC TATAAAGCAAATGAATATGCCAATCTCAAGTTTCTCCTGA|GAATAAGTCCAAGACAGGAAAA|TCTTGGACTTATTCTGTGTGCATCTTTAATCTCCATCTAC ========== Event 3902 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TTCAGCCATTTATTTTCTGGGAC--------TAGTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATTGCTA ↑ 1 4 3 2 Chimp: TTCAGCCATTTATTTTCTGGGTTAATTTCTGAATTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATTGCTA ↓ 1 4 3 2 Gorilla: TTCAGCCATTTATTTTCTGGGAC--------TAGTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATTGCTA Human: TTCAGCCATTTATTTTCTGGGAC--------TAGTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATTGCTA Cluster: [ ] Orangutan: TTCAGCCATTTATTTTCTGGGAC--------TAGTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATTGCTA Chimp > Human ------------- chrX:22173556-22173560 Template switch process: F1: L AAAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG 1 F3: 4 TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT R RF: AAAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGGTTAATTTCTGAATTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT RR: TTTTAACAATAGTTAAGAAGAAGTCGGTAAATAAAAGACCCAATTAAAGACTTAATTGGGTTATTAAGTTACAGATCAAGTCACTTCTCAGTAA F2: 3 GATCA 2 Unidirectional alignment (log-probability: -29) AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGgactaG-------------TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGG-----GTTAATTTCTGAATTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT Template switch alignment (log-probability: -15.9) AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG|ACTAG|TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG|ACTAG|TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT Chimp > Gorilla --------------- chrX:22447830-22447834 Template switch process: F1: L AAAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG 1 F3: 4 TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT R RF: AAAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGGTTAATTTCTGAATTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT RR: TTTTAACAATAGTTAAGAAGAAGTCGGTAAATAAAAGACCCAATTAAAGACTTAATTGGGTTATTAAGTTACAGATCAAGTCACTTCTCAGTAA F2: 3 GATCA 2 Unidirectional alignment (log-probability: -28.5) AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG-------------actagTAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGGTTAATTTCTGAAT-----TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT Template switch alignment (log-probability: -16.4) AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG|ACTAG|TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT AAATTGTTATCAATTCTTCTTCAGCCATTTATTTTCTGGG|ACTAG|TAACCCAATAATTCAATGTCTAGTTCAGTGAAGAGTCATT ========== Event 3903 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GATTTCCTCAAAGCTGTACAATTGTTGGCAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTCAGAGTCTTCTTGTACTCCAGCATGTACTTTTCACTTTTCATAATGAGTTGGAGCCTACAGCTGATTGACTCCGGTGAttttt Chimp: GATTTCCTCAAAGCTGTACAATTGTTGGCAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTCAGAGTCTTCTTGTACTCCAGCATGTACTTTTCACTTTTCATAATGAGTTGGAGCCTACAGTTGATTGACTCCGGTGAttttt Gorilla: GATTTCCTCAAAGCTGTACAAAGCTGTACAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTCAGAGTCtttttttACTCCAGCATGTACTTTTCACTTTTCATAATGAGTTGGAGCCTACAGTTGATTGACTCCGGTGAttttt ↑ 1 4 3 2 Human: GATTTCCTCAAAGCTGTACAATTGTTGGCAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTCAGAGTCTTCTTGTACTCCAGCATGTACTTTTCACTTTTCATAATGAGTTGGAGCCTACAGCTGATTGACTCCGGTGAttttt Cluster: [ ] Orangutan: GATTTCCTCAAAGCTGTACAATTGTTGGCAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTCAGAGTCTTCTTGTACTCCAGCCTGTACTTTTCACTTTTCATAATGAGTTGGAGCCTACAGTTGATTGACTCCAGTAAtttt- Human > Gorilla --------------- chrX:142950954-142950960 Template switch process: F1: L GCTGTAATAATGCTATTTCAGATTTCCTCAAAGCTGTACAA 1 F3: 4 CAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTC R RF: GCTGTAATAATGCTATTTCAGATTTCCTCAAAGCTGTACAATTGTTGGCAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTCAGAGTCTTCTTGTACTCCAGCATGTACTTTTCACTTTTCATAATGAGTTGGAGCCTACAGCT RR: CGACATTATTACGATAAAGTCTAAAGGAGTTTCGACATGTTAACAACCGTTCCTACTGTCAAAGTGAAACGGAACAGACTAGTAGAAGTCTCAGAAGAACATGAGGTCGTACATGAAAAGTGAAAAGTATTACTCAACCTCGGATGTCGA F2: 3 ATGTCGA 2 Unidirectional alignment (log-probability: -31.1) CTGTAATAATGCTATTTCAGATTTCCTCAAAGCTGTACAA-------agctgtaCAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTC CTGTAATAATGCTATTTCAGATTTCCTCAAAGCTGTACAATTGTTGG-------CAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTC Template switch alignment (log-probability: -16.6) CTGTAATAATGCTATTTCAGATTTCCTCAAAGCTGTACAA|AGCTGTA|CAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTC CTGTAATAATGCTATTTCAGATTTCCTCAAAGCTGTACAA|AGCTGTA|CAAGGATGACAGTTTCACTTTGCCTTGTCTGATCATCTTC ========== Event 3904 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 123 Detected in comparisons: 1234 Multiple sequence alignment: Human: TTAAAATTTATTAATCTAGTGATCTTTTTTGTT---------------------------------GTTAATTAACAACAAAAAAGTTCATTTTTTGTTGT----TAAACTTAGTTTAATTTAACCA- ↓ 13 24 ↑ 13 24 Chimp: TTAAAATTTATTAATCTAGTGATCTTTTTTGTT---------------------------------GTTAATTAACAACAAAAAATGAACTTTTTTGTTGT----TAAACTTAGTttaatttaaccaa Gorilla: TTAAAATTTATTAATCTAGTGATCTTTTTTGTT------------------------------------------------------------------GT----TAAACTTAGTTTAATTTAACCA- ↓ 3 4 2 Human: TTAAAATTTATTAATCTAGTGATCTTTTTTGTT---------------------------------GTTAATTAACAACAAAAAAGTTCATTTTTTGTTGT----TAAACTTAGTTTAATTTAACCA- Cluster: [ ] Orangutan: TTAAAATTTATTCCTCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAATTAACTTTTTTGTT---------------------------------GTTAATTAAACTTAGTTTAATTTAACCA- Chimp > Human ------------- chrX:20667565-20667569 Template switch process: F1: L TAATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA 1 F3: 4 TTTTTTGTTGTTAAACTTAGTTTAATTTAACCA R RF: TAATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAATGAACTTTTTTGTTGTTAAACTTAGTTTAATTTAACCA RR: ATTAGATCACTAGAAAAAACAACAATTAATTGTTGTTTTTTACTTGAAAAAACAACAATTTGAATCAAATTAAATTGGT F2: 3 ACTTG 2 Unidirectional alignment (log-probability: -36.1) AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAagttcA-----TTTTTTGTTGTTAAACTTAGTTTAATTTAACCA------- AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAA-----ATGAACTTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT Template switch alignment (log-probability: -15.8) AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA|GTTCA|TTTTTTGTTGTTAAACTTAGTTTAATTTAACCA AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA|GTTCA|TTTTTTGTTGTTAAACTTAGTTTAATTTAACCA Human > Chimp ------------- chrX:20332030-20332034 Template switch process: F1: L TAATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA 1 F3: 4 TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT R RF: TAATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAAGTTCATTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT RR: ATTAGATCACTAGAAAAAACAACAATTAATTGTTGTTTTTTCAAGTAAAAAACAACAATTTGAATCAAATTAAATTGGTTTGACAA F2: 3 CAAGT 2 Unidirectional alignment (log-probability: -45.8) AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAAtgaac-----TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAaactgtt AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA-----GTTCATTTTTTGTTGTTAAACTTAGTTTAATTTAACCA------- Template switch alignment (log-probability: -15.9) AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA|TGAAC|TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT AATCTAGTGATCTTTTTTGTTGTTAATTAACAACAAAAAA|TGAAC|TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT Gorilla > Human --------------- chrX:20667551-20667569 Template switch process: F1: L TACTGAACTTAAAATTTATTAATCTAGTGATCTTTTTTGTTGTTAA 1 F3: 4 TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTTAATTTAAAT R RF: TACTGAACTTAAAATTTATTAATCTAGTGATCTTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTTAATTTAAAT RR: ATGACTTGAATTTTAAATAATTAGATCACTAGAAAAAACAACAATTTGAATCAAATTAAATTGGTTTGACAATTAAATTTA F2: 3 ACTTGAAAAAACAACAATT 2 Unidirectional alignment (log-probability: -58.3) ACTTAAAATTTATTAATCTAGTGATCTTTTTTGttgttaattaacaacaaaaaagttcattttttgTTGTTAAACTTAGTTTAATTTAACCAAACTGTT ACTTAAAATTTATTAATCTAGTGATCTTTTTTG---------------------------------TTGTTAAACTTAGTTTAATTTAACCAAACTGTT Template switch alignment (log-probability: -24) ACTTAAAATTTATTAATCTAGTGATCTTTTTTGTTGTTAA|TTAACAACAAAAAAGtTCA|TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT ACTTAAAATTTATTAATCTAGTGATCTTTTTTGTTGTTAA|TTAACAACAAAAAAGATCA|TTTTTTGTTGTTAAACTTAGTTTAATTTAACCAAACTGTT ========== Event 3905 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA----------AAAGTCTTTCCTGCTATTTATTTTTCCGCG ↑ 3 2 1 4 Chimp: CTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA-----GTCATATGTTCTGTCCTGCTATTTATTTTTCCGCG Gorilla: CTCTTTTTATTTATTCGAAAAGACTTTTCACTACGAAGAGTCAT-----ATGTTCTGTTCTGCTATTTATTTTTCCGCG ↓ 3 2 1 4 Human: CTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA----------AAAGTCTTTCCTGCTATTTATTTTTCCGCG Cluster: [ ] Orangutan: CTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGAGTCAT-----ATGTTCTGTCCTTCTATTTATTTTTCCGCG Chimp > Human ------------- chrX:137429847-137429854 Template switch process: F1: L GCCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA 1 F3: 4 TCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT R RF: GCCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGAGTCATATGTTCTGTCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT RR: CGGAGAAAAATAAATAAGCTTTTCTGAAAAGTGATGCCTCTCAGTATACAAGACAGGACGATAAATAAAAAGGCGCAAGTGCCACGTGAACATA F2: 3 TTCTGAAA 2 Unidirectional alignment (log-probability: -31.9) CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGaaaAG--------TCTtTCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAG---AGTCATATGTTCTGTCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT Template switch alignment (log-probability: -16.3) CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA|AAAGTCTT|TCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA|AAAGTCTT|TCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT Gorilla > Human --------------- chrX:137429847-137429854 Template switch process: F1: L CTCAGCCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGGAGA 1 F3: 4 TCCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTATTA R RF: CTCAGCCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGAAGAGTCATATGTTCTGTTCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTATTA RR: GAGTCGGAGAAAAATAAATAAGCTTTTCTGAAAAGTGATGCTTCTCAGTATACAAGACAAGACGATAAATAAAAAGGCGCAAGTGCCACGTGAACATAAT F2: 3 TTCTGAAA 2 Unidirectional alignment (log-probability: -39.5) CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGgagaaAAG----------TCTtTcCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACG-----AAGAGTCATATGTTCTGTTCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT Template switch alignment (log-probability: -27.9) CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGgAGA|AAAGTCTT|TcCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT CCTCTTTTTATTTATTCGAAAAGACTTTTCACTACGAAGA|AAAGTCTT|TTCTGCTATTTATTTTTCCGCGTTCACGGTGCACTTGTAT ========== Event 3906 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGGTGAACTATACAAATAATATCAAGTGAGAATTATCATCTTGCTGCCTATCAAGGGCAGCAAGATGATACAAAATGACGAATACAAAA ↑ 4 1 3 2 Chimp: AGGTGAACTATACAAATAATATCAAGTGAGAATTGT-------------CTAAAGGGCAGCAAGATGATACAAAATGACGAATACAAAA Gorilla: AGGTGAACTATACAAATAATATCAAGTGAGAATTGT-------------CTAAAGGGCAGCAAGATGATACAAAATGACGAATACAAAA ↓ 4 1 3 2 Human: AGGTGAACTATACAAATAATATCAAGTGAGAATTATCATCTTGCTGCCTATCAAGGGCAGCAAGATGATACAAAATGACGAATACAAAA Cluster: [ ] Orangutan: Chimp > Human ------------- chrX:135903774-135903787 Template switch process: F1: L CATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATT 1 F3: 4 TATC----------------AAGGGCAGCAAGATGATACAAAATGACGAATACAAAAACC R RF: CATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATTGTCTAAAGGGCAGCAAGATGATACAAAATGACGAATACAAAAACT RR: GTAAATATCCACTTGATATGTTTATTATAGTTCACTCTTAACAGATTTCCCGTCGTTCTACTATGTTTTACTGCTTATGTTTTTGA F2: 3 CCGTCGTTCTACTA 2 Unidirectional alignment (log-probability: -47.6) ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATTaTCatcttgctgcctaTcAAGGGCAGCAAGATGATACAAAATGACGAATACAAA ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATTGTC-------------TAAAGGGCAGCAAGATGATACAAAATGACGAATACAAA Template switch alignment (log-probability: -34.1) ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATT|ATCATCTTGCTGCC|TATC----------------AAGGGCAGCAAGATGATACAAAATGACGAATACAAA ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATT|ATCATCTTGCTGCC|TATCAAGTGAGAATTGTCTAAAGGGCAGCAAGATGATACAAAATGACGAATACAAA Gorilla > Human --------------- chrX:135903774-135903787 Template switch process: F1: L CATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATT 1 F3: 4 TATC----------------AAGGGCAGCAAGATGATACAAAATGACGAATACAAAAACC R RF: CATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATTGTCTAAAGGGCAGCAAGATGATACAAAATGACGAATACAAAAACC RR: GTAAATATCCACTTGATATGTTTATTATAGTTCACTCTTAACAGATTTCCCGTCGTTCTACTATGTTTTACTGCTTATGTTTTTGG F2: 3 CCGTCGTTCTACTA 2 Unidirectional alignment (log-probability: -40.7) ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATTaTCatcttgctgcctaTcAAGGGCAGCAAGATGATACAAAATGACGAATACAAA ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATTGTC-------------TAAAGGGCAGCAAGATGATACAAAATGACGAATACAAA Template switch alignment (log-probability: -28.2) ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATT|ATCATCTTGCTGCC|TATC----------------AAGGGCAGCAAGATGATACAAAATGACGAATACAAA ATTTATAGGTGAACTATACAAATAATATCAAGTGAGAATT|ATCATCTTGCTGCC|TATCAAGTGAGAATTGTCTAAAGGGCAGCAAGATGATACAAAATGACGAATACAAA ========== Event 3907 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: GTTCTCTCTCTTGCCCTTCCAAGAGACAGAGCTAAGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACAAACCACCCATCAACCTCTTGCCTGGAAACTCTATTCAAAAGTTTCCTGTTCAGTGTCCCCATTTTTCAAGATCCCACTTTCAGCTAGAGTTCA Chimp: GTTCTCTCTCTTGCCCTTCCAAA------TCTTATGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACAAACCACCCATCAACCTCTTCCCTGGAAACCCTATTCAAAAGTTTCCTGTTCAGTGTCCCCATTTTTCAAGATCCCACTTTCAGCTAGAGTTCA Gorilla: GTTCTCTCTCTTGCCCTTCCAGA------TCTTATGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACAAACCACCCATCAACCTCTTCCCTGGAAACCCTATTCAAAAGTTTCCTGTTCAGTGTCCCCATTTTTCAAGATCCCACTTTCAGCTAGAGTTCA ↑ 1 4 3 2 Human: GTTCTCTCTCTTGCCCTTCCAAGAGACAGAGCTAAGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACAAACCACCCATCAACCTCTTGCCTGGAAACTCTATTCAAAAGTTTCCTGTTCAGTGTCCCCATTTTTCAAGATCCCACTTTCAGCTAGAGTTCA Cluster: [ ] Orangutan: GTTCTCTCTCTTGCCCTTCCAAA------TCTTATGCTGTCTCCTAGCTGTCCAGGTTGCACTGGTTCTACAAACCACCCGTGAACCTCTTCCCTGGAAACCCTATTCAAAAGTTTCCTGTTCAGTGTCCCCATTTTTCAAGATCCCACTTTCAGCTAGAGTTCA Human > Gorilla --------------- chrX:137915775-137915779 Template switch process: F1: L TTCATTCTCATCTTGAAGCAGTTCTCTCTCTTGCCCTTCCA 1 F3: 4 TATGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACAAAC R RF: TTCATTCTCATCTTGAAGCAGTTCTCTCTCTTGCCCTTCCAAGAGACAGAGCTAAGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACAAACCACCCATCAACCTCTTGCCTGGAAACTCTATTCAAAAGTTTCCTGTTCAGTGTCCCCATTTTTCAAGATC RR: AAGTAAGAGTAGAACTTCGTCAAGAGAGAGAACGGGAAGGTTCTCTGTCTCGATTCGACAGAGGATCGAGAGGTCCAACGTGACCAAGATGTTTGGTGGGTAGTTGGAGAACGGACCTTTGAGATAAGTTTTCAAAGGACAAGTCACAGGGGTAAAAAGTTCTAG F2: 3 TCTAG 2 Unidirectional alignment (log-probability: -32.8) TCATTCTCATCTTGAAGCAGTTCTCTCTCTTGCCCTTCC--------------AgatcttatGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACA TCATTCTCATCTTGAAGCAGTTCTCTCTCTTGCCCTTCCAAGAGACAGAGCTAA--------GCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACA Template switch alignment (log-probability: -22) TCATTCTCATCTTGAAGCAGTTCTCTCTCTTGCCCTTCCA|GATCT|TAtGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACA TCATTCTCATCTTGAAGCAGTTCTCTCTCTTGCCCTTCCA|GATCT|TAAGCTGTCTCCTAGCTCTCCAGGTTGCACTGGTTCTACA ========== Event 3908 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACATTGGTAAGCATGGATATTGACATATTT------------ATGTCAAAAAGACAGTTTGGAAGAATTA Chimp: ACATTGGTAAGCATGGATATTGACATATTT------------ATGTCA-AAAGACAGTTTGGAAGAATTA Gorilla: ACATTGATAAGCATGGATATTGACATATCCATATTTGACAAACTGTCA-AAAGACAGTTTGGAAGAATTA ↓ 3 2 1 4 Human: ACATTGGTAAGCATGGATATTGACATATTT------------ATGTCAAAAAGACAGTTTGGAAGAATTA Cluster: [ ] Orangutan: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN------------NNNNNN-NNNNNNNNNNNNNNNNNNNNN Gorilla > Human --------------- chrX:15258017-15258024 Template switch process: F1: L TGGATATTGGGAGACATTGGTAAGCATGGATATTGACATATT 1 F3: 4 AAAGACAGTTTGGAAGAATTAAATTTTAAAGATGCTGGAT R RF: TGGATATTGGGAGACATTGATAAGCATGGATATTGACATATCCATATTTGACAAACTGTCAAAAGACAGTTTGGAAGAATTAAATTTTAAAGATGCTGGAT RR: ACCTATAACCCTCTGTAACTATTCGTACCTATAACTGTATAGGTATAAACTGTTTGACAGTTTTCTGTCAAACCTTCTTAATTTAAAATTTCTACGACCTA F2: 3 AACTGTAT 2 Unidirectional alignment (log-probability: -38.6) GATATTGGGAGACATTGgTAAGCATGGATATTGACATAT-------------------ttatgtcaAAAAGACAGTTTGGAAGAATTAAATTTTAAAGATGCTGGAT GATATTGGGAGACATTGATAAGCATGGATATTGACATATCCATATTTGACAAACTGTC--------AAAAGACAGTTTGGAAGAATTAAATTTTAAAGATGCTGGAT Template switch alignment (log-probability: -27.8) GATATTGGGAGACATTGgTAAGCATGGATATTGACATATt|TATGTCAA|AAAGACAGTTTGGAAGAATTAAATTTTAAAGATGCTGGAT GATATTGGGAGACATTGATAAGCATGGATATTGACATATC|TATGTCAA|AAAGACAGTTTGGAAGAATTAAATTTTAAAGATGCTGGAT ========== Event 3909 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: CAATATTCTCAACTGAAACTCGGAACAG--AGTTCCGAGTCTTCCAGGAGCGTCTCCCGAGAGCG Chimp: CAATATTCTCAACTGAAACTCGGAACAG--AGTTTCGAGTCTTCCAGGAGCGTCTCCCGAGAGCG Gorilla: CAATATTCTCAACTGAAACTCGGAACAGAAAGCGGCTTGTCTTCTAGGAGCGTCTCCCGAGAGCG ↓ 3 2 1 4 Human: CAATATTCTCAACTGAAACTCGGAACAG--AGTTCCGAGTCTTCCAGGAGCGTCTCCCGAGAGCG Cluster: [ ] Orangutan: CAATATTCTCAACTGAAACTCGGAACAGAAAGCGGCTTGTCTTCTAGGAGCGTCTCCCGAGAGCG Gorilla > Human --------------- chrX:15538119-15538125 Template switch process: F1: L ATACACCAGCTTCCAATATTCTCAACTGAAACTCGGAACAGA 1 F3: 4 GTCTTCCAGGAGCGTCTCCCGAGAGCGGGCACACAGTAGTAGCTAAT R RF: ATACACCAGCTTCCAATATTCTCAACTGAAACTCGGAACAGAAAGCGGCTTGTCTTCTAGGAGCGTCTCCCGAGAGCGGGCACACAGTAGTAGCTAAT RR: TATGTGGTCGAAGGTTATAAGAGTTGACTTTGAGCCTTGTCTTTCGCCGAACAGAAGATCCTCGCAGAGGGCTCTCGCCCGTGTGTCATCATCGATTA F2: 3 AGCCTTG 2 Unidirectional alignment (log-probability: -35.3) ACACCAGCTTCCAATATTCTCAACTGAAACTCGGAACAGAgttccgA--------GTCTTCcAGGAGCGTCTCCCGAGAGCGGGCACACAGTAGT ACACCAGCTTCCAATATTCTCAACTGAAACTCGGAACAGA------AAGCGGCTTGTCTTCTAGGAGCGTCTCCCGAGAGCGGGCACACAGTAGT Template switch alignment (log-probability: -22.3) ACACCAGCTTCCAATATTCTCAACTGAAACTCGGAACAGA|GTTCCGA|GTCTTCcAGGAGCGTCTCCCGAGAGCGGGCACACAGTAGT ACACCAGCTTCCAATATTCTCAACTGAAACTCGGAACAGA|GTTCCGA|GTCTTCTAGGAGCGTCTCCCGAGAGCGGGCACACAGTAGT ========== Event 3910 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: CTGAGGACACTACTGCATTTTAGC--------------------------TGGGTATAAATACA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAAAAGTATCCTTGAGAATCTGAAATGAAGAAGTG Chimp: Gorilla: CTGAGGACACTACTGCATTTTAGCTGGGTATAAATACTCGAGTATTTAGCTGGGTATAAATACATTTTTAAAAGTATCCTTGAGAATCTGAAATGAAGAAGTGTAGGAGTGACAATTTCTTTTTCatat-------------------------------------------------------------------------gtgtgtgtgtgtgtatatacatatatatatattatatatatatataatatatatatatattttatatatatatatatataCACACACACnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntctgtcacccaggctggagtgcagtgtcaacatctcggctcactgcaacctccgcctcccaggttcaagcaattctcgtgcctccgcctccctagctggaattacaga------------------------------------------------------------------------------------------tgtgcgccaccacacctggctattttttgtgtgtgtgtttttagtagagacgaggtttcactatgttggccgggctggtctctaactcctaacctcaagtgatccacccacctcagcctcccaaagtgttgggattaaagatgtgagccaccgtgcctggccTCCATATAATTTTATGTAGATTTATACTGGTGGA-------CAATATTATACACCTATAGTTTAAAAGGAATTCACAAGAAAACCACAAGTGAAGATCAGCAAGAAATAAATAAATGATAATTTCAggccgggctcagtggcttacgcctgtaatcccagtgttttgggaggccaaagtggttggatcacctgagatcaggagaccggcctggctaacatggtgaaaccctgtctctactaaaaatacaaaaattagctgggcttggtggcaggcacctgtaatcccagctactcagg--------------------------------------- ↑ 4 1 3 2 Human: CTGAGGACACTACTGCATTTTAGC--------------------------TGGGTATAAATACA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAAAAGTATCCTTGAGAATCTGAAATGAAGAAGTG Cluster: [ ] Orangutan: CTGAGGACACTACTGCATTTTAGCTGGGTATAAATACTCGAGTATTTAGCTGGCTATAAATACATTTTTAAAAGTATCCTTGAGAATCTGAAATGAAGAAGTGTAGGAATAACAATTTCTTTTTCATATGTATGTGTGTGTGTGtatatatacatatatattatatatatatattttttttttttgaattggagtttcactc-----------------------------------------------------------------------------------------------------------------------------------------tgtcacccaggctggagtgcagtgtcaacatctcggctcactgcaacctccgcctcccaggttcaagcaattctcgtgcctccacctccctagctggaattacagatgtgtgccaccacacctggcttttttttttttttttttttttttttgtatttttagtagagacgaggtttcaccctgttggccaggctgg------------------------------------------------------------------------------tctctaactcctgacctcaagtgatccacccacctcagcctctcaaagtgttgggattaaagatgtgagccaccgtgcctggccTCCATATTATTTTATGTAGATTTATACTGGTGGACAATGGACAATATTATACACCTATAGTTTAAAAGGAATTCACAAGAAAACCACAAGTGAAGATCAGCACGAAATAAATAAATGATAATTTCAggccgggctcagtggcttacacctgtaatcccagtgttttgggaggccgaggtggttggatcacctgagatcaggagaccagcctggccaacatggtgaaaccccgtctctactaaaaatacaaaaattagctgggcttggtggcaggcacctgtaatcccagctactcagg--------------------------------------- Human > Gorilla --------------- chrX:153751152-153751159 Template switch process: F1: L CAATGTTTCAATAGTATCTGAGGACACTACTGCATTTTAGCTGGGTATAAATAC 1 F3: 4 TTAGCTGGGTATAAATACATTTTTAAAAGTATCCTTGAGAATCTG R RF: CAATGTTTCAATAGTATCTGAGGACACTACTGCATTTTAGCTGGGTATAAATACATTTTTAAAAGTATCCTTGAGAATCTG RR: GTTACAAAGTTATCATAGACTCCTGTGATGACGTAAAATCGACCCATATTTATGTAAAAATTTTCATAGGAACTCTTAGAC F2: 3 TATGAGCT 2 Unidirectional alignment (log-probability: -87.8) TATCTGAGGACACTACTGCATTTTAGCTGGGTATAAATACtcgagtatttagctgggtataaatacatttttaaaagtatccttgaga TATCTGAGGACACTACTGCATTTTAGCTGGGTATAAATACA----------------------------------------------- Template switch alignment (log-probability: -28.2) TATCTGAGGACACTACTGCATTTTAGCTGGGTATAAATAC|TCgAGtAT|TTAGCTGGGTATAAATACATTTTTAAAAGTATCCTTGAGA TATCTGAGGACACTACTGCATTTTAGCTGGGTATAAATAC|TCAAGGAT|TTAGCTGGGTATAAATACATTTTTAAAAGTATCCTTGAGA ========== Event 3911 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTCAGGATATAGTTTAATA-----------AACATTAGATTAAGAGGCCCTAATTAATCTAATGACAGCTACATGACTGACAAA Chimp: TTTTCAGGATGCAGTTTAACA-----------AACATTAGATTAAGAGGCCCTAATTAATCTAATGACAGCTACATGACTGACAAA ↑ 41 3 2 Gorilla: TTTTCAGGATACAGTTTAACA----------------------AAGAGACCCTAATTAATCTAATGACAGCTACATGACTGACAAA Human: TTTTCAGGATATAGTTTAATA-----------AACATTAGATTAAGAGGCCCTAATTAATCTAATGACAGCTACATGACTGACAAA Cluster: [ ] Orangutan: TTTTCAGGATACAGTTTAATAAGCATTATATT-----------AAGAGGCCCTAACTAATCTAATGACAGCTACATGACTGACAAA Gorilla > Chimp --------------- chrX:139169180-139169188 Template switch process: F1: L TGGTGGTTTGGGGTGGGGAGTTTTCAGGATGCAGTTTAACAAA 1 F3: 4 AAGAGGCCCTAATTAATCTAATGACAGCTACATGACTGACAAAATG R RF: TGGTGGTTTGGGGTGGGGAGTTTTCAGGATACAGTTTAACAAAGAGACCCTAATTAATCTAATGACAGCTACATGACTGACAAAATG RR: ACCACCAAACCCCACCCCTCAAAAGTCCTATGTCAAATTGTTTCTCTGGGATTAATTAGATTACTGTCGATGTACTGACTGTTTTAC F2: 3 TTAGATTAC 2 Unidirectional alignment (log-probability: -37.8) TGGTTTGGGGTGGGGAGTTTTCAGGATgCAGTTTAACAaacattagattAAGAGgCCCTAATTAATCTAATGACAGCTACATGACTGAC TGGTTTGGGGTGGGGAGTTTTCAGGATACAGTTTAACA-----------AAGAGACCCTAATTAATCTAATGACAGCTACATGACTGAC Template switch alignment (log-probability: -28.1) TGGTTTGGGGTGGGGAGTTTTCAGGATgCAGTTTAACAAA|CATTAGATT|AAGAGgCCCTAATTAATCTAATGACAGCTACATGACTGAC TGGTTTGGGGTGGGGAGTTTTCAGGATACAGTTTAACAAA|CATTAGATT|AAGAGACCCTAATTAATCTAATGACAGCTACATGACTGAC ========== Event 3912 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGAAAATAGAGCAGAAAAATAC----------------------CGTTAAGTCTTAACTTCTGTCTCTGGTGCCACCGTCCCTG ↑ 1 3 42 Chimp: CAGAAAATAGAGCAGAAAAATGT-----------CATCTGACAGAAGTTAAGACTTAA---CGGTCTCTGGTGCCACCGTCCCTG Gorilla: CAGAAAATAGAGCAGAAAAATGTCATCTGACAGA-----------AGTTAAGACTTAA---CGGTCTCTGGTGCCACCGTCCCTG ↓ 1 3 42 Human: CAGAAAATAGAGCAGAAAAATAC----------------------CGTTAAGTCTTAACTTCTGTCTCTGGTGCCACCGTCCCTG Cluster: [ ] Orangutan: CAGAAAATAGAGCAGAAAAATGTCATCTGACAGA-----------AGTTAAGACTTAA---CGGTCTCTGGTGCCACCGTCCCTG Chimp > Human ------------- chrX:11467309-11467328 Template switch process: F1: L CGAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAAT 1 F3: 4 GTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG R RF: CGAAACATCTGCATTAATATCAGAAAATAGAGCAGAAAAATGTCATCTGACAGAAGTTAAGACTTAACGGTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG RR: GCTTTGTAGACGTAATTATAGTCTTTTATCTCGTCTTTTTACAGTAGACTGTCTTCAATTCTGAATTGCCAGAGACCACGGTGGCAGGGACATAAAAATCCGTCAAATC F2: 3 TCTTCAATTCTGAATTGCCA 2 Unidirectional alignment (log-probability: -56.1) GAAACATCTaCATTAATATCAGAAAATAGAGCAGAAAAATacC-----------GTTAAGtCTTAActtCtGTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG GAAACATCTGCATTAATATCAGAAAATAGAGCAGAAAAATGTCATCTGACAGAAGTTAAGACTTAA---CGGTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG Template switch alignment (log-probability: -23.7) GAAACATCTaCATTAATATCAGAAAATAGAGCAGAAAAAT|ACCGTTAAGTCTTAACTTCT|GTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG GAAACATCTGCATTAATATCAGAAAATAGAGCAGAAAAAT|ACCGTTAAGTCTTAACTTCT|GTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG Gorilla > Human --------------- chrX:11467309-11467328 Template switch process: F1: L CGAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAAT 1 F3: 4 GTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG R RF: TGAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAATGTCATCTGACAGAAGTTAAGACTTAACGGTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG RR: ACTTTGTAGATGTAATTATAGTCTTTTATCTCGTCTTTTTACAGTAGACTGTCTTCAATTCTGAATTGCCAGAGACCACGGTGGCAGGGACATAAAAATCCGTCAAATC F2: 3 TCTTCAATTCTGAATTGCCA 2 Unidirectional alignment (log-probability: -53.3) GAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAATacC-----------GTTAAGtCTTAActtCtGTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG GAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAATGTCATCTGACAGAAGTTAAGACTTAA---CGGTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG Template switch alignment (log-probability: -23.8) GAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAAT|ACCGTTAAGTCTTAACTTCT|GTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG GAAACATCTACATTAATATCAGAAAATAGAGCAGAAAAAT|ACCGTTAAGTCTTAACTTCT|GTCTCTGGTGCCACCGTCCCTGTATTTTTAGGCAGTTTAG ========== Event 3913 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ttattttgtaGGCTTTCCTAAGCAAAGTCAGTGACCCTGTCTAGAGTAGGCATGTTTATACTAAGGGAACGGAAGGGGAGTATGTGAGTG ↓ 31 2 4 Chimp: ttattttgtaGGCTTTCCTAA----GGTCACTGACTTTGC-----------------------TGGGAAGGGAAGGGGAGTATGTGAGTG Gorilla: ttattttgtaggctttcctaagcaaagtcagtgaccctgtctacagtaggcATGTTTATACTAAGGGAAGGGAAGGGGAGTATGTGAGTG Human: ttattttgtaGGCTTTCCTAAGCAAAGTCAGTGACCCTGTCTAGAGTAGGCATGTTTATACTAAGGGAACGGAAGGGGAGTATGTGAGTG Cluster: [ ] Orangutan: ttattttgtaGGCTTTCCTAAGCAAAGTCAGTGACCCTGTCTAGAGTAGGCATGTTTATACTAAGGGAAGGGAAGGGGAGTATGTGAGTG Human > Chimp ------------- chrX:11256636-11256650 Template switch process: F1: L AGAGCAAGTGCTGTGCATTATTATTTTGTAGGCTTTCCTAAG 1 F3: 4 GGGAAGGGAAGGGGAGTATGTGAGTGGGTGGCATGAAGGGACTGTG R RF: AGAGCAAGTGCTGTGCATTATTATTTTGTAGGCTTTCCTAAGCAAAGTCAGTGACCCTGTCTAGAGTAGGCATGTTTATACTAAGGGAACGGAAGGGGAGTATGTGAGTGGGTGGCATGAAGGGACTGTG RR: TCTCGTTCACGACACGTAATAATAAAACATCCGAAAGGATTCGTTTCAGTCACTGGGACAGATCTCATCCGTACAAATATGATTCCCTTGCCTTCCCCTCATACACTCACCCACCGTACTTCCCTGACAC F2: 3 TCGTTTCAGTCACTG 2 Unidirectional alignment (log-probability: -50.9) AGCAAGTGCTGTGCATTATTATTTTGTAGGCTTTCCTAAG------------------------------------------gtcactgactttgctGGGAAgGGAAGGGGAGTATGTGAGTGGGTGGCATGAAGGG AGCAAGTGCTGTGCATTATTATTTTGTAGGCTTTCCTAAGCAAAGTCAGTGACCCTGTCTAGAGTAGGCATGTTTATACTAA---------------GGGAACGGAAGGGGAGTATGTGAGTGGGTGGCATGAAGGG Template switch alignment (log-probability: -23.3) AGCAAGTGCTGTGCATTATTATTTTGTAGGCTTTCCTAAG|GTCACTGACTTTGCT|GGGAAgGGAAGGGGAGTATGTGAGTGGGTGGCATGAAGGG AGCAAGTGCTGTGCATTATTATTTTGTAGGCTTTCCTAAG|GTCACTGACTTTGCT|GGGAACGGAAGGGGAGTATGTGAGTGGGTGGCATGAAGGG ========== Event 3914 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: CATTCACAAATTATTTTTTTACATGGATGCCGTCCATGTAAAAATTAGCTAAATATCACTAAAAT ↑ 3 2 1 4 Chimp: CATTCACAAATTGtttttttACATGGATGCCGTC---TTTAAAACTAGCTAAATATCACTAAAAT Gorilla: CATTCACAAATTAtttttttACATAGATGCCGTC---TTTAAAACTAGCTAAATATCACTAAAAT Human: CATTCACAAATTATTTTTTTACATGGATGCCGTCCATGTAAAAATTAGCTAAATATCACTAAAAT Cluster: [ ] Orangutan: ----------------------------------------------------------------- Chimp > Human ------------- chrX:145434615-145434620 Template switch process: F1: L ACATTTTCATTCACAAATTATTTTTTTACATGGATGCCGTC 1 F3: 4 AAAATTAGCTAAATATCACTAAAATATCACTATATTGAATGATCT R RF: ACATTTTCATTCACAAATTGTTTTTTTACATGGATGCCGTCTTTAAAACTAGCTAAATATCACTAAAATATCACTATATTGAATGATCT RR: TGTAAAAGTAAGTGTTTAACAAAAAAATGTACCTACGGCAGAAATTTTGATCGATTTATAGTGATTTTATAGTGATATAACTTACTAGA F2: 3 ATGTAC 2 Unidirectional alignment (log-probability: -39.3) CATTTTCATTCACAAATTaTTTTTTTACATGGATGCCGTCcatgTaAAAAtTAGCTAAATATCACTAAAATATCACTATATTGAAT CATTTTCATTCACAAATTGTTTTTTTACATGGATGCCGTC---TTTAAAACTAGCTAAATATCACTAAAATATCACTATATTGAAT Template switch alignment (log-probability: -28.1) CATTTTCATTCACAAATTaTTTTTTTACATGGATGCCGTC|CATGTA|AAAAtTAGCTAAATATCACTAAAATATCACTATATTGAAT CATTTTCATTCACAAATTGTTTTTTTACATGGATGCCGTC|CATGTA|AAAACTAGCTAAATATCACTAAAATATCACTATATTGAAT ========== Event 3915 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAAAGTTATGGAATAACTTGTATTTTTATTGCAATAAA------AAAGGAAAAGGACACTTCCTG Chimp: AAAAGTTATGGAATAACTTGTATTTTTATTGCAATAAA---AGTAAAGGAAAAGGACACTTCCTG Gorilla: AAAAGTTATGGAATAACTTGTGT-TTTATTGCAATaaaaat---aaaggaaaaggaaacttcccg ↓ 1 3 24 Human: AAAAGTTATGGAATAACTTGTATTTTTATTGCAATAAA------AAAGGAAAAGGACACTTCCTG Cluster: [ ] Orangutan: AAAAGTTATGGAATAACTTGTATTTTTATTGCAATAAAAAT---AAAGGAAAAGGACCGTTCCTG Gorilla > Human --------------- chrX:147295337-147295353 Template switch process: F1: L ACAAAATAATACAGCATGGTAAAAGTTATGGAATAACTTGT 1 F3: 4 AAAGGAAAAGGACACTTCCTGAA R RF: ACAAAATAATACAGCATGGTAAAAGTTATGGAATAACTTGTGTTTTATTGCAATAAAAATAAAGGAAAAGGAAACTTCCCGAA RR: TGTTTTATTATGTCGTACCATTTTCAATACCTTATTGAACACAAAATAACGTTATTTTTATTTCCTTTTCCTTTGAAGGGCTT F2: 3 AAATAACGTTATTTTTA 2 Unidirectional alignment (log-probability: -38.8) CAAAATAATACAGCATGGTAAAAGTTATGGAATAACTTGTatTTTTATTGCAATAAA---AAAGGAAAAGGAcACTTCCtGAA CAAAATAATACAGCATGGTAAAAGTTATGGAATAACTTGT-GTTTTATTGCAATAAAAATAAAGGAAAAGGAAACTTCCCGAA Template switch alignment (log-probability: -28.5) CAAAATAATACAGCATGGTAAAAGTTATGGAATAACTTGT|ATTTTTATTGCAATAAA|AAAGGAAAAGGAcACTTCCtGAA CAAAATAATACAGCATGGTAAAAGTTATGGAATAACTTGT|ATTTTTATTGCAATAAA|AAAGGAAAAGGAAACTTCCCGAA ========== Event 3916 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: AATGAGAATTTATAGATGAAT----TTATACAGCACCTACATACCAACAAACGCACTACTGCTACATCAAATTTGTAAATCTTCCTTTTAAAACTGAAAGGTGTTAGTTGATCTGCAATGGTGTAACTTTAAAA ↓ 1 4 3 2 Chimp: AATGAGAATTTATAGATGAAT--AGATCTACAGCACCTACATACCAACAAACGCACTACTGCTACATCAAATTTGCAAATCTTCCTTTTAAAACTGAAAGGTGTTAGTTGATCTGCAATGGTGTAACTTTTAAA Gorilla: AATGAGAATTTATAGATGAATAG--ATCTACAGCACCTACATACCAACAAACGCACTACTGCTACATCAAATTTGTAAATCTTCCTTTTAAAACTGAAAGGTGTTAGTTGATCTGCAATGGTGTAACTTTAAAA Human: AATGAGAATTTATAGATGAAT----TTATACAGCACCTACATACCAACAAACGCACTACTGCTACATCAAATTTGTAAATCTTCCTTTTAAAACTGAAAGGTGTTAGTTGATCTGCAATGGTGTAACTTTAAAA Cluster: [ ] Orangutan: Human > Chimp ------------- chrX:7911527-7911531 Template switch process: F1: L GTTATAGACATTCAAAAGGAAATGAGAATTTATAGATGAAT 1 F3: 4 TACAGCACCTACATACCAACAAACGCACTACTGCTACATC R RF: GTTATAGACATTCAAAAGGAAATGAGAATTTATAGATGAATTTATACAGCACCTACATACCAACAAACGCACTACTGCTACATCAAATTTGTAAATCTTCCTTTTAAAACTGAAAGGTGTTAGTTGATCT RR: CAATATCTGTAAGTTTTCCTTTACTCTTAAATATCTACTTAAATATGTCGTGGATGTATGGTTGTTTGCGTGATGACGATGTAGTTTAAACATTTAGAAGGAAAATTTTGACTTTCCACAATCAACTAGA F2: 3 CTAGA 2 Unidirectional alignment (log-probability: -25.8) TTATAGACATTCAAAAGGAAATGAGAATTTATAGATGAATagaTcTACAGCACCTACATACCAACAAACGCACTACTGCTACATC TTATAGACATTCAAAAGGAAATGAGAATTTATAGATGAAT--TTATACAGCACCTACATACCAACAAACGCACTACTGCTACATC Template switch alignment (log-probability: -15.9) TTATAGACATTCAAAAGGAAATGAGAATTTATAGATGAAT|AGATC|TACAGCACCTACATACCAACAAACGCACTACTGCTACATC TTATAGACATTCAAAAGGAAATGAGAATTTATAGATGAAT|AGATC|TACAGCACCTACATACCAACAAACGCACTACTGCTACATC ========== Event 3917 ========== Phylogenetic placement: ambiguous, species tree consistent Significant comparisons: 356 Detected in comparisons: 3456 Multiple sequence alignment: Human: CCTTCAGCTGCAATCCCTATGGCTTCTCCCAGTATGGCTGG-GGAAGCCTTGCTCATTGCCTGGGAGGAGGATATGTGCGTGGAATCAAGGGCAGGAAAGAGAAGAGGG Chimp: CCTTCAGCTGCAATCCCTATGGCTTCTCCCAGTATGGCTGG-GGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGGAATCAAGGGCAGGAAAGAGAAGAGGG ↓ 3 4 2 1 ↑ 1 3 4 2 Gorilla: CCTTCAGCTGCAATCCCTATGCAATTCCCCAGCCATACTGGGAGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGGAATCAAGGGCAGGAAAGAGAAGAGGG ↓ 1 3 4 2 Human: CCTTCAGCTGCAATCCCTATGGCTTCTCCCAGTATGGCTGG-GGAAGCCTTGCTCATTGCCTGGGAGGAGGATATGTGCGTGGAATCAAGGGCAGGAAAGAGAAGAGGG Cluster: [ ] Orangutan: CCTTCAGCTGCAATCCCTATGGCTTCTCCCAGTATGGCTGG-GGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGGAATCAAGGGCAGGAAAGAGAAGAGGG Gorilla > Human --------------- chrX:5888240-5888260 Template switch process: F1: L TCAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG 1 F3: 4 GAAGCCTTGCTCATTGCCTGGGAGGAGGATATGTGCGTGG R RF: TCAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGCAATTCCCCAGCCATACTGGGAGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG RR: AGTCTAAGTCAGAAACCACTGGAAGTCGACGTTAGGGATACGTTAAGGGGTCGGTATGACCCTCTTCGGAACGAGTAACGGACCCTCCCCCTATACACGTACC F2: 3 GGGTCGGTATGACCCTCTTCG 2 Unidirectional alignment (log-probability: -62.6) CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG------------------GcttctcccagtatggctGGgGAAGCCTTGCTCATTGCCTGGGAGGaGGATATGTGCgTGG CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGCAATTCCCCAGCCATACTG-----------------GGAGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG Template switch alignment (log-probability: -29.4) CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG|GCTTCTCCCAGTATGGCTGGG|GAAGCCTTGCTCATTGCCTGGGAGGaGGATATGTGCgTGG CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG|GCTTCTCCCAGTATGGCTGGG|GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG Gorilla > Chimp --------------- chrX:5671043-5671063 Template switch process: F1: L TCAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG 1 F3: 4 GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG R RF: TCAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGCAATTCCCCAGCCATACTGGGAGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG RR: AGTCTAAGTCAGAAACCACTGGAAGTCGACGTTAGGGATACGTTAAGGGGTCGGTATGACCCTCTTCGGAACGAGTAACGGACCCTCCCCCTATACACGTACC F2: 3 GGGTCGGTATGACCCTCTTCG 2 Unidirectional alignment (log-probability: -51.6) CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG------------------GcttctcccagtatggctGGgGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGCAATTCCCCAGCCATACTG-----------------GGAGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG Template switch alignment (log-probability: -18.4) CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG|GCTTCTCCCAGTATGGCTGGG|GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG CAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG|GCTTCTCCCAGTATGGCTGGG|GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG Chimp > Gorilla --------------- chrX:5970230-5970248 Template switch process: F1: L TCAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG----------------------------------------------------------------CAA 1 F3: 4 GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG R RF: TCAGATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGGCTTCTCCCAGTATGGCTGGGGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGGAATCAA RR: AGTCTAAGTCAGAAACCACTGGAAGTCGACGTTAGGGATACCGAAGAGGGTCATACCGACCCCTTCGGAACGAGTAACGGACCCTCCCCCTATACACGTACCTTAGTT F2: 3 AGGGTCATACCGACCCCTT 2 Unidirectional alignment (log-probability: -53) ATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGcaattccccagccatactG-----------------GGaGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG ATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG------------------GCTTCTCCCAGTATGGCTGGGGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG Template switch alignment (log-probability: -31.2) ATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATG----------------------------------------------------------------CAA|TTCCCCAGCCATACTGGGA|GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG ATTCAGTCTTTGGTGACCTTCAGCTGCAATCCCTATGGCTTCTCCCAGTATGGCTGGGGAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGGAATCAA|TTCCCCAGCCATACTGGGA|GAAGCCTTGCTCATTGCCTGGGAGGGGGATATGTGCATGG ========== Event 3918 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGGGGGAAGAGGGAGCTGGGC------------------------------------------------------------CAATGCCCAGGGTGCCTGGTAGAGAGAT ↑ 3 1 2 4 Chimp: ATGGGGGAAGAGGGAGCTGGGC------------------------------ATTGACTCAAGGGGCTGTTGTCTGAAGAAGGGAGGCTCAGGGTGCCTGGTAGAGAGAT Gorilla: ATGGGGGAAGAGGGAGCTGGGCATTGACTCAAGGGGCTGTTGTCTGAAGAAG------------------------------GGAGGCCCAGGGTGCCTGGTAGAGAGAT Human: ATGGGGGAAGAGGGAGCTGGGC------------------------------------------------------------CAATGCCCAGGGTGCCTGGTAGAGAGAT Cluster: [ ] Orangutan: ATGAGGGAAGAGGGAGCTGGGCGTTGACTCAAGGGGCTGTTGTCTGAAGAAG------------------------------GGAGGCCCAGGGTGCCTGTTAGAGAGAT Chimp > Human ------------- chrX:5552695-5552701 Template switch process: F1: L ATCAACAACCCAAATGGGCATGGGGGAAGAGGGAGCTGGGC 1 F3: 4 CAGGGTGCCTGGTAGAGAGATACCTTGGGCACTGGAAGGC R RF: ATCAACAACCCAAATGGGCATGGGGGAAGAGGGAGCTGGGCATTGACTCAAGGGGCTGTTGTCTGAAGAAGGGAGGCTCAGGGTGCCTGGTAGAGAGATACCTTGGGCACTGGAAGGC RR: TAGTTGTTGGGTTTACCCGTACCCCCTTCTCCCTCGACCCGTAACTGAGTTCCCCGACAACAGACTTCTTCCCTCCGAGTCCCACGGACCATCTCTCTATGGAACCCGTGACCTTCCG F2: 3 CCGTAAC 2 Unidirectional alignment (log-probability: -31.7) TCAACAACCCAAATGGGCATGGGGGAAGAGGGAGCTGGGCcaAT--------------------------------GCcCAGGGTGCCTGGTAGAGAGATACCTTGGGCACTGGAAGGC TCAACAACCCAAATGGGCATGGGGGAAGAGGGAGCTGGGC--ATTGACTCAAGGGGCTGTTGTCTGAAGAAGGGAGGCTCAGGGTGCCTGGTAGAGAGATACCTTGGGCACTGGAAGGC Template switch alignment (log-probability: -16.2) TCAACAACCCAAATGGGCATGGGGGAAGAGGGAGCTGGGC|CAATGCC|CAGGGTGCCTGGTAGAGAGATACCTTGGGCACTGGAAGGC TCAACAACCCAAATGGGCATGGGGGAAGAGGGAGCTGGGC|CAATGCC|CAGGGTGCCTGGTAGAGAGATACCTTGGGCACTGGAAGGC ========== Event 3919 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: CAGGTCTGAGACGAAAAAGGTAACTCTCTTTTCTGGGTCCTGGCCCAGTTGTGTCTCTCTCCACCTCATTCTCTGAGATGCCTGTCTCCCCTTTTTTGTCCCATCAGGAGGCAAGAGCTATCACTGGGCCAGACTCCACCAGAAGCCAAGCCAGCTTGTTACCCAGCTTCTCAAGGAGCAAAGAACAGC Chimp: CAGGTCTGAGACGAAAAAGGTAACTCTCTTTTCTGGGTCCTGGCCCAGTTGTGTCTCTCTCCACCTCATTCTCTGAGATGCCTGTCTCCCCTTTTTTGTCCCATCAGGAGGCAAGAGCTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCC------------AGCTTCTCAAGGAGCAAAGAACAGC ↓ 3 2 4 1 Gorilla: CAGGTTTGAGACGAAAAAGGTAACTCTCTTTTCTGGGTCCTGGCCCAGTTGTGTCTCTCTCCACCTCATTCTCTAAGATGCCTGTCTCCCCTTTTTTGTCCCATCAGGAGGCAAGAGCTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCCAGCTTGTTACCCAGCTTCTCAAGGAGCAAAGAACAGC Human: CAGGTCTGAGACGAAAAAGGTAACTCTCTTTTCTGGGTCCTGGCCCAGTTGTGTCTCTCTCCACCTCATTCTCTGAGATGCCTGTCTCCCCTTTTTTGTCCCATCAGGAGGCAAGAGCTATCACTGGGCCAGACTCCACCAGAAGCCAAGCCAGCTTGTTACCCAGCTTCTCAAGGAGCAAAGAACAGC Cluster: [ ] Orangutan: CAGGTCTGAGACGAAAAAGGTAACTCTCTTTTCTGGGTCCTGGCCCAGTTGTGTCTCTCTCCATCTCATTCTCTGAGATGTCTGTCTCTCCTTTTTTGTCCCATCAGGAGGCAAGAGCTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCCACCTTGTTACCCAGCTTCTCAAGCAGCAAAGAACAGC Chimp > Gorilla --------------- chrX:5610352-5610356 Template switch process: F1: L CAAGAGCTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCCAGCTT 1 F3: 4 CCAGCTTCTCAAGGAGCAAAGAACAGCCTTGTTTCTTTCTTA R RF: GTAACTCTCTTTTCTGGGTCCTGGCCCAGTTGTGTCTCTCTCCACCTCATTCTCTGAGATGCCTGTCTCCCCTTTTTTGTCCCATCAGGAGGCAAGAGCTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCCAGCTTCTCAAGGAGCAAAGAACAGCCTTGTTTCTATCTTA RR: CATTGAGAGAAAAGACCCAGGACCGGGTCAACACAGAGAGAGGTGGAGTAAGAGACTCTACGGACAGAGGGGAAAAAACAGGGTAGTCCTCCGTTCTCGATAGTGACCCGGTCTGAGGCGGTCTTCGGTTCGGTCGAAGAGTTCCTCGTTTCTTGTCGGAACAAAGATAGAAT F2: 3 CATTG 2 Unidirectional alignment (log-probability: -33.7) CTATCACTGGGCCAGACTCCGCCAGAAGCCAAGccagcttgttacCCAGCTTCTCAAGGAGCAAAGAACAGCCTTGTTTCTtTCT CTATCACTGGGCCAGACTCCGCCAGAAGCCAAG------------CCAGCTTCTCAAGGAGCAAAGAACAGCCTTGTTTCTATCT Template switch alignment (log-probability: -22.1) CTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCCAGCTT|GTTAC|CCAGCTTCTCAAGGAGCAAAGAACAGCCTTGTTTCTtTCT CTATCACTGGGCCAGACTCCGCCAGAAGCCAAGCCAGCTT|GTTAC|CCAGCTTCTCAAGGAGCAAAGAACAGCCTTGTTTCTATCT ========== Event 3920 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: AAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATCATGGGACTGTGAAAGAGAAGACACG ↓ 3 1 2 4 Chimp: AAGCCCAGCCAACTTCTCGCAGTTGAGACTCATCTCAACAGATGGGACTGTGAAAGAGAAGACACG ↑ 3 1 2 4 Gorilla: AAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATCATGGCACTGTGAAAGAGAAGACACG Human: AAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATCATGGGACTGTGAAAGAGAAGACACG Cluster: [ ] Orangutan: AAGCCCAGCCAACTTCTCACAGTTGAGATGAGTAACAGATCATGGGACTGTGAAAGAGAAGACACG Human > Chimp ------------- chrKV421457:290468-290480 Template switch process: F1: L TGGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA 1 F3: 4 ATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT R RF: TGGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATCATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT RR: ACCCGTGTCCCCTTTCGGGTCGGTTGAAGAGCGTCAACTCTACTCATTGTCTAGTACCCTGACACTTTCTCTTCTGTGCTTTCGTTCAGAAATA F2: 3 GACAACTCTACTC 2 Unidirectional alignment (log-probability: -39) GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA------------CtcatctcaacagATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATC------------ATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT Template switch alignment (log-probability: -22.9) GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA|CTCATCTCAACaG|ATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA|CTCATCTCAACTG|ATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT Gorilla > Chimp --------------- chrKV421457:290468-290480 Template switch process: F1: L TGGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA 1 F3: 4 ATGGGACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTATCTAGG R RF: TGGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATCATGGCACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTATCTAGG RR: ACCCGTGTCCCCTTTCGGGTCGGTTGAAGAGCGTCAACTCTACTCATTGTCTAGTACCGTGACACTTTCTCTTCTGTGCTTTCGTTCAGAAATAGATCC F2: 3 GACAACTCTACTC 2 Unidirectional alignment (log-probability: -44.1) GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA------------CtcatctcaacagATGGgACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGATGAGTAACAGATC------------ATGGCACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT Template switch alignment (log-probability: -28.5) GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA|CTCATCTCAACaG|ATGGgACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT GGGCACAGGGGAAAGCCCAGCCAACTTCTCGCAGTTGAGA|CTCATCTCAACTG|ATGGCACTGTGAAAGAGAAGACACGAAAGCAAGTCTTTAT ========== Event 3921 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: tataAGTCTAGAGCTGAGGGAGAGGCAGTGCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCCCACTCCCTCCTCTGGCACCAGGGTCACCAGGGCCACATGGTAGTTTCTGGTTTCACCAA Chimp: tataAGTCTAGAGCTGAGGGACACGTGGCGCTTGGAGCCCCAGGGAGTGGCTGTCCCCTCCCCCAACCCCACTCCCTCCTCTGGCACCAGGATCACCAGGGCCACATGGTAGTTTCTGGTTTCACCAA Gorilla: tataAGTCTAGAGCTGAGGGACATGTGGCGCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCCCACTCCCTCCTCTGGCACCAGGGTCACCAGGGCCACATGGTAGTTTCTGGTTTCACCAA ↑ 1 4 3 2 Human: tataAGTCTAGAGCTGAGGGAGAGGCAGTGCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCCCACTCCCTCCTCTGGCACCAGGGTCACCAGGGCCACATGGTAGTTTCTGGTTTCACCAA Cluster: [ ] Orangutan: TATAAGTCTAGAGCTGAGGGAGACGTGGCGCTTGGAGCCCCAGGGAGTGGCAGTCTCCTC-CTTAACCCCACTCCTTCCTCTGGCACCAGGGTCACCAGGGCCACATGGTAGTTTCTGATTTCACCAA Human > Gorilla --------------- chrX:150425177-150425184 Template switch process: F1: L TACATATATATAGTTGTTTATATAAGTCTAGAGCTGAGGGA 1 F3: 4 GCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCC R RF: TACATATATATAGTTGTTTATATAAGTCTAGAGCTGAGGGAGAGGCAGTGCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCCCACTCCCTCCTCTGGCACCAGGGTCACCAGGGCCACATG RR: ATGTATATATATCAACAAATATATTCAGATCTCGACTCCCTCTCCGTCACGAACCTCGGGGTCCCTCACCGTCAGGGGAGGGGGTTGGGGTGAGGGAGGAGACCGTGGTCCCAGTGGTCCCGGTGTAC F2: 3 CGGTGTAC 2 Unidirectional alignment (log-probability: -28.9) ACATATATATAGTTGTTTATATAAGTCTAGAGCTGAGGGAcAtGtgGcGCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCC ACATATATATAGTTGTTTATATAAGTCTAGAGCTGAGGGAGAGGCAGTGCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCC Template switch alignment (log-probability: -16.7) ACATATATATAGTTGTTTATATAAGTCTAGAGCTGAGGGA|CATGTGGC|GCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCC ACATATATATAGTTGTTTATATAAGTCTAGAGCTGAGGGA|CATGTGGC|GCTTGGAGCCCCAGGGAGTGGCAGTCCCCTCCCCCAACCC ========== Event 3922 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: tgaaaggaGATGTTGAAAATATAGGAAAATAAGTGGTAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAA------------------------------------------------------------------------------------------------------------ATGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATCaataa ↓ 3 4 2 1 Chimp: tgaaaggaGATGTTGAAAATATAGGAAAATAAGTGGTAGGCGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTTACTAAGTTGTAAATACATCGCCTACCACTTATTTTCCTATATAGGCGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATTaataa ↑ 3 4 2 1 Gorilla: tgaaaggaGATGTTGAAAATATAGGAAAATAAGTGGTAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAA------------------------------------------------------------------------------------------------------------AAGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATCaataa Human: tgaaaggaGATGTTGAAAATATAGGAAAATAAGTGGTAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAA------------------------------------------------------------------------------------------------------------ATGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATCaataa Cluster: [ ] Orangutan: TGCAAGGAGATGTTGAAAATATAGGAAAATAAATGGTAGGTGATGTACTTACAACTTAGTAAGTCTGCATAGAAACAGAAAA------------------------------------------------------------------------------------------------------------AAGCAAGTAGAGAGGAGAATTTCACCAAACCAAATCAATGg Human > Chimp ------------- chrKV421455:1956-1996 Template switch process: F1: L GATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTT 1 F3: 4 TAGGCGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATTAATA R RF: TATAGGAAAATAAGTGGTAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATCAATA RR: ATATCCTTTTATTCACCATCCACTACATAAATGTTGAATCATTCAGACGTATCTTTGTCTTTTTACGTTCATCTCTCCTCTCAAAGTGGTTTGGTTTAGTTAT F2: 3 ATATCCTTTTATTCACCATCCGCTACATAAATGTTGAATCA 2 Unidirectional alignment (log-probability: -166) tctgcatagaaacagaaaaatgcaagtagagaggagagttactaagttgtaaatacatcgcctaccacttattttcctatataggcGATGTATTTACAACTTAGTAAGTCTGCATAGAAAC --------------------------------------------------------------------------------------GATGTATTTACAACTTAGTAAGTCTGCATAGAAAC Template switch alignment (log-probability: -39.3) TCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTT|ACTAAGTTGTAAATACATCgCCTACCACTTATTTTCCTATA|TAGGcGATGTATTTACAACTTAGTAAGTCTGCATAGAAAC TCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTT|ACTAAGTTGTAAATACATCACCTACCACTTATTTTCCTATA|TAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAAC Gorilla > Chimp --------------- chrKV421455:1956-1996 Template switch process: F1: L GATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTT 1 F3: 4 TAGGCGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAATGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATTAATAAG R RF: TATAGGAAAATAAGTGGTAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAACAGAAAAAAGCAAGTAGAGAGGAGAGTTTCACCAAACCAAATCAATAAC RR: ATATCCTTTTATTCACCATCCACTACATAAATGTTGAATCATTCAGACGTATCTTTGTCTTTTTTCGTTCATCTCTCCTCTCAAAGTGGTTTGGTTTAGTTATTG F2: 3 ATATCCTTTTATTCACCATCCGCTACATAAATGTTGAATCA 2 Unidirectional alignment (log-probability: -177) tctgcatagaaacagaaaaatgcaagtagagaggagagttactaagttgtaaatacatcgcctaccacttattttcctatataggcGATGTATTTACAACTTAGTAAGTCTGCATAGAAAC --------------------------------------------------------------------------------------GATGTATTTACAACTTAGTAAGTCTGCATAGAAAC Template switch alignment (log-probability: -55.5) TCTGCATAGAAACAGAAAAAtGCAAGTAGAGAGGAGAGTT|ACTAAGTTGTAAATACATCgCCTACCACTTATTTTCCTATA|TAGGcGATGTATTTACAACTTAGTAAGTCTGCATAGAAAC TCTGCATAGAAACAGAAAAAAGCAAGTAGAGAGGAGAGTT|ACTAAGTTGTAAATACATCACCTACCACTTATTTTCCTATA|TAGGTGATGTATTTACAACTTAGTAAGTCTGCATAGAAAC ========== Event 3923 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: TAGGCCACGTGAGCGCCCTTATAAA------CGAGTCATAGCCCTCGTT---------------------- ↑ 1 4 3 2 Chimp: TAGGCCACGTGAGCGCCCTTACTAC---CTGACAGTCATAGCCCTCGTTTAtttatttattttttttttga Gorilla: TAGGCCACGTGAGCGCCCTTATTACCTG---ACAGTCATAGCCCTCGTT---------------------- Human: TAGGCCACGTGAGCGCCCTTATAAA------CGAGTCATAGCCCTCGTT---------------------- Cluster: [ ] Orangutan: Chimp > Human ------------- chrX:152994426-152994431 Template switch process: F1: L AAATCACCCAGTGCAACGTATAGGCCACGTGAGCGCCCTTA 1 F3: 4 AGTCATAGCCCTCGTT R RF: AAATCACCCAGTGCAACGTATAGGCCACGTGAGCGCCCTTACTACCTGACAGTCATAGCCCTCGTTTA RR: TTTAGTGGGTCACGTTGCATATCCGGTGCACTCGCGGGAATGATGGACTGTCAGTATCGGGAGCAAAT F2: 3 GCAAAT 2 Unidirectional alignment (log-probability: -38.5) AATCACCCAGTGCAACGTATAGGCCACGTGAGCGCCCTTAtaaacg---------AGTCATAGCCCTCGTT------------------------ AATCACCCAGTGCAACGTATAGGCCACGTGAGCGCCCTTA------CTACCTGACAGTCATAGCCCTCGTTTATTTATTTATTTTTTTTTTGAGA Template switch alignment (log-probability: -15.5) AATCACCCAGTGCAACGTATAGGCCACGTGAGCGCCCTTA|TAAACG|AGTCATAGCCCTCGTT AATCACCCAGTGCAACGTATAGGCCACGTGAGCGCCCTTA|TAAACG|AGTCATAGCCCTCGTT ========== Event 3924 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: GGCCCTTGGTGAAGCTGCAGGAG-----------TGAGAACACCACAGGTGGCCGCTGTGCTTATTT Chimp: GGCCCTTGGTGAAGCTGCAGGTGTTCTGTTCTCACTAGAACACCACAGGTGGCCGCTGTGCTTATTT ↑ 13 4 2 Gorilla: GGCCCTTGGTGAAGCTGCAGGAG-----------TGAGAACACCACAGGTGGCCGCTGTGCTTATTT Human: GGCCCTTGGTGAAGCTGCAGGAG-----------TGAGAACACCACAGGTGGCCGCTGTGCTTATTT Cluster: [ ] Orangutan: GGCCCTTGGTGAAGCTGCAGGAG-----------TGAGACCACCACAGGTGGCCGCTGTGCTTATTT Gorilla > Chimp --------------- chrX:153084600-153084614 Template switch process: F1: L CAGAAGGTCTGATGGTGAGGGGCCCTTGGTGAAGCTGCAGG 1 F3: 4 AGAACACCACAGGTGGCCGCTGTGCTTATTTCACAAGAAA R RF: CAGAAGGTCTGATGGTGAGGGGCCCTTGGTGAAGCTGCAGGAGTGAGAACACCACAGGTGGCCGCTGTGCTTATTTCACAAGAAA RR: GTCTTCCAGACTACCACTCCCCGGGAACCACTTCGACGTCCTCACTCTTGTGGTGTCCACCGGCGACACGAATAAAGTGTTCTTT F2: 3 TCACTCTTGTCTTGT 2 Unidirectional alignment (log-probability: -37.8) AGAAGGTCTGATGGTGAGGGGCCCTTGGTGAAGCTGCAGGtGTtctgttctcactAGAACACCACAGGTGGCCGCTGTGCTTATTTCACAAGAAA AGAAGGTCTGATGGTGAGGGGCCCTTGGTGAAGCTGCAGGAGT-----------GAGAACACCACAGGTGGCCGCTGTGCTTATTTCACAAGAAA Template switch alignment (log-probability: -28.7) AGAAGGTCTGATGGTGAGGGGCCCTTGGTGAAGCTGCAGG|TGTtcTGTTCTCACT|AGAACACCACAGGTGGCCGCTGTGCTTATTTCACAAGAAA AGAAGGTCTGATGGTGAGGGGCCCTTGGTGAAGCTGCAGG|TGTGGTGTTCTCACT|AGAACACCACAGGTGGCCGCTGTGCTTATTTCACAAGAAA ========== Event 3925 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGACAGGGCAGCGCTGGGAATGACAGGGCCCGGGGCCTGCGGGGCTGCGGAGAAGGCGGGAGACGCGGTGCGGCTGGGCCAGTCACCGCCCCGCAGGCGGTGC-------------------------------------------------------------------GC ↑ 1 4 3 2 Chimp: AAGACAGGGCAGCGCTGGGAACGAGAGGGCCCGGGGC-------------------------------------------------------------------CTGCGGGGCTGCGGAGACGGCGGGAGACGCGGTGCGGCTGGGCCAGTCACCGCCCCGCAGGCGGTGCGC Gorilla: AAGACAGGGCAGCGCTGGCAATGAGAGGGCCCGGGGCCTGCGGGGCTGCGGAGACGGCGGGAGACGCGGTGCGGCTGGGCCAGTCACCGCCCCGCAGGCGGTGC-------------------------------------------------------------------GC Human: AAGACAGGGCAGCGCTGGGAATGACAGGGCCCGGGGCCTGCGGGGCTGCGGAGAAGGCGGGAGACGCGGTGCGGCTGGGCCAGTCACCGCCCCGCAGGCGGTGC-------------------------------------------------------------------GC Cluster: [ ] Orangutan: AAGACAGGGCAGCGCTGGGAATGAGAGGGCCCGGGGCCTGCGGAGCTGCACAGACGGCGGGAGACGCGGTGCGGCTGGGCCAGTCACCGCCCCGCAGGCGGTGC-------------------------------------------------------------------GC Chimp > Human ------------- chrX:154805422-154805425 Template switch process: F1: L AAGCTGGAACACTGGAACGCAAGACAGGGCAGCGCTGGGAA 1 F3: 4 AGGGCCCGGGGCCTGCGGGGCTGCGGAGAAGGCGGGAGAC R RF: AAGCTGGAACACTGGAACGCAAGACAGGGCAGCGCTGGGAACGAGAGGGCCCGGGGCCTGCGGGGCTGCGGAGACGGCGGGAGACGCGGTGCGGCTGGGCCAGTCA RR: TTCGACCTTGTGACCTTGCGTTCTGTCCCGTCGCGACCCTTGCTCTCCCGGGCCCCGGACGCCCCGACGCCTCTGCCGCCCTCTGCGCCACGCCGACCCGGTCAGT F2: 3 CAGT 2 Unidirectional alignment (log-probability: -59.9) AGCTGGAACACTGGAACGCAAGACAGGGCAGCGCTGGGAAtGAcAGGGCCCGGGGCctgcggggctgcggagaaggcgggagac AGCTGGAACACTGGAACGCAAGACAGGGCAGCGCTGGGAACGAGAGGGCCCGGGGC---------------------------- Template switch alignment (log-probability: -21.8) AGCTGGAACACTGGAACGCAAGACAGGGCAGCGCTGGGAA|TGAC|AGGGCCCGGGGCCTGCGGGGCTGCGGAGAaGGCGGGAGAC AGCTGGAACACTGGAACGCAAGACAGGGCAGCGCTGGGAA|TGAC|AGGGCCCGGGGCCTGCGGGGCTGCGGAGACGGCGGGAGAC ========== Event 3926 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ttgccttcccctaGTTGAGAAGGGATT-----------TC------ACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATTTTCAGACCACACAAAAggta Chimp: TTGCCTTCCCCTAGTTGAGAAGGGATT-----------TC------ACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATTTTCAGACCACACAAAAggta ↓ 1 4 3 2 Gorilla: TTGCCTTCCCCTAGTTGAGAAAATACTTTTTGTGGAGTTGACAGGACCTCTAGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATTTTCAGACCACatgaaaggta ↑ 1 4 3 2 Human: ttgccttcccctaGTTGAGAAGGGATT-----------TC------ACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATTTTCAGACCACACAAAAggta Cluster: [ ] Orangutan: ttgccttcccctaGTTGAGAAGGGATT-----------TC------ACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGTTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATTTTCAGACCACACAAAAggta Human > Gorilla --------------- chrX:155921435-155921465 Template switch process: F1: L TGGGGCTGAAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAA 1 F3: 4 GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA R RF: TGGGGCTGGAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAAGGGATTTCACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATT RR: ACCCCGACCTCGTCCGACTCAACGGAAGGGGATCAACTCTTCCCTAAAGTGATAACGGGAGACAATAAAAACAGAAAGAGGGTTGAACATCCGATTAGAATTTTTATTTACCGATCTCCAGGACAGTTGAGGTGTTTTTCATAA F2: 3 ATCTCCAGGACAGTTGAGGTGTTTTTCATAA 2 Unidirectional alignment (log-probability: -71.4) GGGGCTGaAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAaaatactttttgtggagttgacaggacctctA--------------GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA GGGGCTGGAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGA-------------------------------AGGGATTTCACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA Template switch alignment (log-probability: -25.2) GGGGCTGaAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAA|AATACTTTTTGTGGAGTTGACAGGACCTCTA|GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA GGGGCTGGAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAA|AATACTTTTTGTGGAGTTGACAGGACCTCTA|GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA Chimp > Gorilla --------------- chrX:155921435-155921465 Template switch process: F1: L TGGGGCTGAAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAA 1 F3: 4 GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA R RF: TGGGGCTGGAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAAGGGATTTCACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTAATCTTAAAAATAAATGGCTAGAGGTCCTGTCAACTCCACAAAAAGTATT RR: ACCCCGACCTCGTCCGACTCAACGGAAGGGGATCAACTCTTCCCTAAAGTGATAACGGGAGACAATAAAAACAGAAAGAGGGTTGAACATCCGATTAGAATTTTTATTTACCGATCTCCAGGACAGTTGAGGTGTTTTTCATAA F2: 3 ATCTCCAGGACAGTTGAGGTGTTTTTCATAA 2 Unidirectional alignment (log-probability: -71.4) GGGGCTGaAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAaaatactttttgtggagttgacaggacctctA--------------GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA GGGGCTGGAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGA-------------------------------AGGGATTTCACTATTGCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA Template switch alignment (log-probability: -25.2) GGGGCTGaAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAA|AATACTTTTTGTGGAGTTGACAGGACCTCTA|GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA GGGGCTGGAGCAGGCTGAGTTGCCTTCCCCTAGTTGAGAA|AATACTTTTTGTGGAGTTGACAGGACCTCTA|GCCCTCTGTTATTTTTGTCTTTCTCCCAACTTGTAGGCTA ========== Event 3927 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GCATCTCTAGATCCTGTTATC------------------------------CTCTAAACGATTTAGA-GCAAGCCCTCGTTGCTTCTCAACCAGGAAGTG ↑ 1 3 2 4 Chimp: GCATCTCTAGATCCTGTTATC---------------CTGAGCAAACTGTTGCTCTAAATCGTTTAGGGCCAAGCCCTGGATGCTTCTCAACCAGGAAGTG Gorilla: Human: GCATCTCTAGATCCTGTTATC------------------------------CTCTAAACGATTTAGA-GCAAGCCCTCGTTGCTTCTCAACCAGGAAGTG Cluster: [ ] Orangutan: GCATCTCTAGATCCTGTTATCCTGAGCAAGTTGTTG---------------CTCTAAATCGTTTAGGGGCAAGCCCTTGATTCTTCTCAACCAGGAAGTG Chimp > Human ------------- chrX:153158955-153158969 Template switch process: F1: L CTTTTGTTGTCAAGCAGAGAGCATCTCTAGATCCTGTTATCCT 1 F3: 4 CAAGCCCTCGTTGCTTCTCAACCAGGAAGTGAATCGGTTTAGATCCTCTAA R RF: CTTTTGTTGTCAAGCAGAGAGCATCTCTAGATCCTGTTATCCTGAGCAAACTGTTGCTCTAAATCGTTTAGGGCCAAGCCCTGGATGCTTCTCAACCAGGAAGTGAATCGGTTTAGATCCTCTAA RR: GAAAACAACAGTTCGTCTCTCGTAGAGATCTAGGACAATAGGACTCGTTTGACAACGAGATTTAGCAAATCCCGGTTCGGGACCTACGAAGAGTTGGTCCTTCACTTAGCCAAATCTAGGAGATT F2: 3 GAGATTTAGCAAATC 2 Unidirectional alignment (log-probability: -51.9) TTGTTGTCAAGCAGAGAGCATCTCTAGATCCTGTTATCCTctaaacgatttaGAGCAA----------------------------GCCCTcGtTGCTTCTCAACCAGGAAGTGAATCGGTTT TTGTTGTCAAGCAGAGAGCATCTCTAGATCCTGTTATCCT------------GAGCAAACTGTTGCTCTAAATCGTTTAGGGCCAAGCCCTGGATGCTTCTCAACCAGGAAGTGAATCGGTTT Template switch alignment (log-probability: -29.4) TTGTTGTCAAGCAGAGAGCATCTCTAGATCCTGTTATCCT|CTAAACGATTTAGAG|CAAGCCCTcGtTGCTTCTCAACCAGGAAGTGAATCGGTTT TTGTTGTCAAGCAGAGAGCATCTCTAGATCCTGTTATCCT|CTAAACGATTTAGAG|CAAGCCCTGGATGCTTCTCAACCAGGAAGTGAATCGGTTT ========== Event 3928 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAACACTTGGTATTCTTAACCCTGC Chimp: TGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAACACTTGGTATTCTTAACCCTGC ↓ 3 2 1 4 Gorilla: TGCATGTTACATACATCTTTCTAGAAATAT--TGTATTTCT-------------AGAACTTGGTATTCTTAACCCTGC ↑ 3 2 1 4 Human: TGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAACACTTGGTATTCTTAACCCTGC Cluster: [ ] Orangutan: Human > Gorilla --------------- chrX:140084829-140084837 Template switch process: F1: L ATGGTTTGTATTGCATGTTACATACATCTTTCTAGAAATATTGT 1 F3: 4 ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC R RF: ATGGTTTGTATTGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAACACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC RR: TACCAAACATAACGTACAATGTATGTAGAAAGATCTTTATAAAACGTAAACATAATTTGTTTACGTTGTGAACCATAAGAATTGGGACGGATCCTGAGAAATAAAAGG F2: 3 AGATCTTTA 2 Unidirectional alignment (log-probability: -37.8) TTTGTATTGCATGTTACATACATCTTTCTAGAAATATT--------------------------gtatttctagaACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC TTTGTATTGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAAC-----------ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC Template switch alignment (log-probability: -22.5) TTTGTATTGCATGTTACATACATCTTTCTAGAAATATTgT|ATTTCTAGA|ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC TTTGTATTGCATGTTACATACATCTTTCTAGAAATATTTT|ATTTCTAGA|ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC Chimp > Gorilla --------------- chrX:140084829-140084837 Template switch process: F1: L ATGGTTTGTATTGCATGTTACATACATCTTTCTAGAAATATTGT 1 F3: 4 ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC R RF: ATGGTTTGTATTGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAACACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC RR: TACCAAACATAACGTACAATGTATGTAGAAAGATCTTTATAAAACGTAAACATAATTTGTTTACGTTGTGAACCATAAGAATTGGGACGGATCCTGAGAAATAAAAGG F2: 3 AGATCTTTA 2 Unidirectional alignment (log-probability: -37.8) TTTGTATTGCATGTTACATACATCTTTCTAGAAATATT--------------------------gtatttctagaACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC TTTGTATTGCATGTTACATACATCTTTCTAGAAATATTTTGCATTTGTATTAAACAAATGCAAC-----------ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC Template switch alignment (log-probability: -22.5) TTTGTATTGCATGTTACATACATCTTTCTAGAAATATTgT|ATTTCTAGA|ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC TTTGTATTGCATGTTACATACATCTTTCTAGAAATATTTT|ATTTCTAGA|ACTTGGTATTCTTAACCCTGCCTAGGACTCTTTATTTTCC ========== Event 3929 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: atacttaaaCAGTTCTAGTGGAATCAG------------TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATT ↑ 1 4 3 2 Chimp: atacttaaaCAGTTCTAGTGGTAGCTG------TGTGGATGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATT Gorilla: atacttaaaCAGTTCTAGTGGTAGCTGTGTGGA------TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATT ↓ 1 4 3 2 Human: atacttaaaCAGTTCTAGTGGAATCAG------------TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATT Cluster: [ ] Orangutan: atacttaaaCAGTTCTAATGGTAGCTGTGTGGA------TGTTGGCATGTCTGAATCTATCTGGGGTAGAGTTATT Chimp > Human ------------- chrX:21870625-21870628 Template switch process: F1: L ACTTCTTAAAAATTCCCTTAATACTTAAACAGTTCTAGTGGAA 1 F3: 4 TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA R RF: ACTTCTTAAAAATTCCCTTAATACTTAAACAGTTCTAGTGGTAGCTGTGTGGATGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTATGTATTTTATGTGGCAGCCATCCTAAAGAAGTTGTCTTGGCTTCCAAAAATACCATGTGAAGTCAGATATGTTGCTCTGTGCAGCAGATGACAGAGCTGA RR: TGAAGAATTTTTAAGGGAATTATGAATTTGTCAAGATCACCATCGACACACCTACAACCGTACAGACTAAGATAGACCCCATCTCAATAAAATACATAAAATACACCGTCGGTAGGATTTCTTCAACAGAACCGAAGGTTTTTATGGTACACTTCAGTCTATACAACGAGACACGTCGTCTACTGTCTCGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -28.9) TCTTAAAAATTCCCTTAATACTTAAACAGTTCTA-----------GTGGAatcagTGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA TCTTAAAAATTCCCTTAATACTTAAACAGTTCTAGTGGTAGCTGTGTGGA-----TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA Template switch alignment (log-probability: -21.8) TCTTAAAAATTCCCTTAATACTTAAACAGTTCTAGTGGaA|TCAG|TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA TCTTAAAAATTCCCTTAATACTTAAACAGTTCTAGTGGTA|TCAG|TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA Gorilla > Human --------------- chrX:21870625-21870628 Template switch process: F1: L ACTTCTTAAAAATTCCCTTAATACTTAAACAGTTCTAGTGGAA 1 F3: 4 TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA R RF: ACTTCTTAAAAATTCCGTTAATACTTAAACAGTTCTAGTGGTAGCTGTGTGGATGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTATGTATTTTATGTGGCAGCCATCCTAAAGAAGTTGTCTTGGCTTCCAAAAATACCATGTGAAGTCAGATATGTTGCTCTGTGCAGCAGATGACAGAGCTGA RR: TGAAGAATTTTTAAGGCAATTATGAATTTGTCAAGATCACCATCGACACACCTACAACCGTACAGACTAAGATAGACCCCATCTCAATAAAATACATAAAATACACCGTCGGTAGGATTTCTTCAACAGAACCGAAGGTTTTTATGGTACACTTCAGTCTATACAACGAGACACGTCGTCTACTGTCTCGACT F2: 3 GACT 2 Unidirectional alignment (log-probability: -33.4) TCTTAAAAATTCCcTTAATACTTAAACAGTTCTAGTGGaAtCaG------TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA TCTTAAAAATTCCGTTAATACTTAAACAGTTCTAGTGGTAGCTGTGTGGATGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA Template switch alignment (log-probability: -27.3) TCTTAAAAATTCCcTTAATACTTAAACAGTTCTAGTGGaA|TCAG|TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA TCTTAAAAATTCCGTTAATACTTAAACAGTTCTAGTGGTA|TCAG|TGTTGGCATGTCTGATTCTATCTGGGGTAGAGTTATTTTA ========== Event 3930 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TTTTTCCTGTTCTGTTTGCTGCTCAGAGTTATCTTCT-------TACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTAAGTTTTTATGTTCACTTATCCTGCTATAGAGATGAGCAATAGAGAGCAACTGAAAGTTTCCCTAC Chimp: tttttCCTGTTCTGTTTGCTGCTCAGAGTTATCTTCT-------TACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTAAGTTTTTATGTTCACTTATCCTGCTATA-------------GAGAGCAACTGAAAATTTCCCTAC ↓ 3 2 4 1 Gorilla: tttttCCTGTTCTGTTTGCTGCTCAGAGTTATCTTCTTACATCTTACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTGAGTTTATATGTTCACTTATCCTGCTATAGAGATGAGCAATAGAGAGCAACTGAAAGTTTCCCTAC Human: TTTTTCCTGTTCTGTTTGCTGCTCAGAGTTATCTTCT-------TACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTAAGTTTTTATGTTCACTTATCCTGCTATAGAGATGAGCAATAGAGAGCAACTGAAAGTTTCCCTAC Cluster: [ ] Orangutan: TTTTTCCTGTTCTGTTTGCTGCTCACAGTTATCTTCT-------TACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTAAGTTTTTATGTTCACTTATCCTGCTATAGAAATGAGCAATAGAGAGCAACTGAAAGTTTCCCTAC Chimp > Gorilla --------------- chrX:21677638-21677643 Template switch process: F1: L TTACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTGAGTTTATATGTTCACTTATCCTGCTATAGAGA 1 F3: 4 ATAGAGAG R RF: -TACATGGGGGTGGGCTACTCTTGAAGGATCTACCAAAAGTAAGTTTTTATGTTCACTTATCCTGCTATAGAGAG RR: -ATGTACCCCCACCCGATGAGAACTTCCTAGATGGTTTTCATTCAAAAATACAAGTGAATAGGACGATATCTCTC F2: 3 ACGAGT 2 Unidirectional alignment (log-probability: -46.3) CAAAAGTgAGTTTaTATGTTCACTTATCCTGCTatagagatgagcaATAGAGAG CAAAAGTAAGTTTTTATGTTCACTTATCCTGCT-------------ATAGAGAG Template switch alignment (log-probability: -38.7) CAAAAGTgAGTTTaTATGTTCACTTATCCTGCTATAGAGA|TGAGCA|ATAGAGAG CAAAAGTAAGTTTTTATGTTCACTTATCCTGCTATAGAGA|TGAGCA|ATAGAGAG ========== Event 3931 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CTCCCTGTCTTTCTAGAAGTC------TGCTCATCAAGGCTGTACAAGTCTCAGTA ↓ 3 4 2 Chimp: CTCCTTGTCTTTCTAGAAGTCTTGATGAGCACATCAAGGCTGTACAAGTCTCAGTA Gorilla: CTCCCTGTCTTTCTAGAAGTC------TGCTCATCAAGGCTGTACAAGTCTCAGTA Human: CTCCCTGTCTTTCTAGAAGTC------TGCTCATCAAGGCTGTACAAGTCTCAGTA Cluster: [ ] Orangutan: CTCCCTGTCTTTCTAGAAGTC------TGCTCATCAAGGCTGTACAAGTCTCAGTA Human > Chimp ------------- chrX:22200503-22200511 Template switch process: F1: L ATTCAGGCAGATAAATTCCACTCCTTGTCTTTCTAGAAGTCT 1 F3: 4 CATCAAGGCTGTACAAGTCTCAGTACTCAATGCCCTTATC R RF: ATTCAGGCAGATAAATTCCACTCCCTGTCTTTCTAGAAGTCTGCTCATCAAGGCTGTACAAGTCTCAGTACTCAATGCCCTTATC RR: TAAGTCCGTCTATTTAAGGTGAGGGACAGAAAGATCTTCAGACGAGTAGTTCCGACATGTTCAGAGTCATGAGTTACGGGAATAG F2: 3 ACGAGTAGT 2 Unidirectional alignment (log-probability: -31.6) TCAGGCAGATAAATTCCACTCCtTGTCTTTCTAGAAGTCTtgatgaGCaCATCAAGGCTGTACAAGTCTCAGTACTCAATGCCCTTATC TCAGGCAGATAAATTCCACTCCCTGTCTTTCTAGAAGTCT------GCTCATCAAGGCTGTACAAGTCTCAGTACTCAATGCCCTTATC Template switch alignment (log-probability: -22.4) TCAGGCAGATAAATTCCACTCCtTGTCTTTCTAGAAGTCT|TGATGAGCA|CATCAAGGCTGTACAAGTCTCAGTACTCAATGCCCTTATC TCAGGCAGATAAATTCCACTCCCTGTCTTTCTAGAAGTCT|TGATGAGCA|CATCAAGGCTGTACAAGTCTCAGTACTCAATGCCCTTATC ========== Event 3932 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCAGGCTTATTGGGGTGGAACTACCCCAACTGTG ↑ 3 2 1 4 Chimp: ATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACC------AATGAAGTGGAACTACCCCAACTGTG Gorilla: ATATGAGCATGCGGATGATCCAATAAGCCTGTAAAACC------AATGAGGTGGAACTACCCCAACTGTG ↓ 3 2 1 4 Human: ATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCAGGCTTATTGGGGTGGAACTACCCCAACTGTG Cluster: [ ] Orangutan: ATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACC------AATGAGGTGGAACTACCTCAACTGTG Chimp > Human ------------- chrX:25595128-25595137 Template switch process: F1: L CTCATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCA 1 F3: 4 GGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACAA R RF: CTCATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCAATGAAGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACAA RR: GAGTATACTCGTACGTCTACTAGGTTATTCGGACATTTTGGTTACTTCACCTTGATGGGGTTGACACTGTTACTTAGTTTACCTGTT F2: 3 GGTTATTCGG 2 Unidirectional alignment (log-probability: -37.2) CATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACC-----AggcttattgggGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA CATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCAATGAA-----------GTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA Template switch alignment (log-probability: -22.6) CATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCA|GGCTTATTGG|gGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA CATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCA|GGCTTATTGG|AGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA Gorilla > Human --------------- chrX:25595128-25595137 Template switch process: F1: L CTCATATGAGCATGCAGATGATCCAATAAGCCTGTAAAACCA 1 F3: 4 GGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA R RF: CTCATATGAGCATGCGGATGATCCAATAAGCCTGTAAAACCAATGAGGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA RR: GAGTATACTCGTACGCCTACTAGGTTATTCGGACATTTTGGTTACTCCACCTTGATGGGGTTGACACTGTTACTTAGTTTACCTGT F2: 3 GGTTATTCGG 2 Unidirectional alignment (log-probability: -36.1) CATATGAGCATGCaGATGATCCAATAAGCCTGTAAAACCaggcttAtTGgGGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA CATATGAGCATGCGGATGATCCAATAAGCCTGTAAAACC------AATGAGGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA Template switch alignment (log-probability: -22.5) CATATGAGCATGCaGATGATCCAATAAGCCTGTAAAACCA|GGCTTATTGG|GGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA CATATGAGCATGCGGATGATCCAATAAGCCTGTAAAACCA|GGCTTATTGG|GGTGGAACTACCCCAACTGTGACAATGAATCAAATGGACA ========== Event 3933 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: tttggattacaggaagcttcagtgatatataaagtgCACATGTAGTAGGAACTTCTACTTTAATAATTGTTACTCACCAGCATTTCTGCACCATATTATT Chimp: tttggattacaggaagcttcagtgatatataaagtgCACATGTAGTAGGAACTTTTACTTTAATAATTGTT----ACCAGCATTTCTGCACCATATTATT ↓ 3 2 1 4 Gorilla: tttggattacaggaagcttcagtgatatataaagtgCACATGTAGTAGGAACTTTTACTTTAATAATTGTTACTCACTGGCATTTCTGCGCCATATTATT Human: tttggattacaggaagcttcagtgatatataaagtgCACATGTAGTAGGAACTTCTACTTTAATAATTGTTACTCACCAGCATTTCTGCACCATATTATT Cluster: [ ] Orangutan: TTTGGATTACAGGAAGCTTCAGTGATATATAAAGTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTT----ACCAGCATTTCTGCAGAATATTATT Chimp > Gorilla --------------- chrX:25718841-25718846 Template switch process: F1: L AAAGTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTTAC 1 F3: 4 GCATTTCTGCGCCATATTATTTCTAAGCAACTAAATTTAA R RF: CAGTGATATATAAAGTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTTACCAGCATTTCTGCACCATATTATTTCTAAGCAACTAAATTTAA RR: GTCACTATATATTTCACGTGTACATCATCCTTGAAAATGAAATTATTAACAATGGTCGTAAAGACGTGGTATAATAAAGATTCGTTGATTTAAATT F2: 3 GTCACT 2 Unidirectional alignment (log-probability: -32) GTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTTACtCActgGCATTTCTGCgCCATATTATTTCTAAGCAACTAAATTTAA GTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTTAC-CA---GCATTTCTGCACCATATTATTTCTAAGCAACTAAATTTAA Template switch alignment (log-probability: -22.1) GTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTTAC|TCACTG|GCATTTCTGCgCCATATTATTTCTAAGCAACTAAATTTAA GTGCACATGTAGTAGGAACTTTTACTTTAATAATTGTTAC|TCACTG|GCATTTCTGCACCATATTATTTCTAAGCAACTAAATTTAA ========== Event 3934 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATGTCAACATAGTTGGTGAAAC---------------AACATTGT-TTTGCTTGACCAAATGCTAAAC ↑ 1 3 24 Chimp: ATGTCAACATAGTTGGTGAAAT----AATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAAC Gorilla: ATGTCAACATAGTTGGTGAAAT----AATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAAC ↓ 1 3 24 Human: ATGTCAACATAGTTGGTGAAAC---------------AACATTGT-TTTGCTTGACCAAATGCTAAAC Cluster: [ ] Orangutan: ATGTCAACATAGTTGGTGAAATAAAGAATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAAC Chimp > Human ------------- chrX:25892166-25892175 Template switch process: F1: L AATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAA 1 F3: 4 TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT R RF: AATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAATAATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT RR: TTAGATTTATTGTCTTATTATACAGTTGTATCAACCACTTTATTATGCTCGTTTTGTTACAACAACGAACTGGTTTACGATTTGATTTTCCAAGTCTGTCTAA F2: 3 TTGTTACAAC 2 Unidirectional alignment (log-probability: -33.8) ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAAc-----------AACAtTGTT-TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAATAATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT Template switch alignment (log-probability: -16.5) ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAA|CAACATTGTT|TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAA|CAACATTGTT|TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT Gorilla > Human --------------- chrX:25892166-25892175 Template switch process: F1: L AATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAA 1 F3: 4 TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT R RF: AATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAATAATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT RR: TTAGATTTATTGTCTTATTATACAGTTGTATCAACCACTTTATTATGCTCGTTTTGTTACAACAACGAACTGGTTTACGATTTGATTTTCCAAGTCTGTCTAA F2: 3 TTGTTACAAC 2 Unidirectional alignment (log-probability: -32.4) ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAA-----------AcAACAtTGTT-TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAATAATACGAGCAAAACAATGTTGTTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT Template switch alignment (log-probability: -17) ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAA|CAACATTGTT|TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT ATCTAAATAACAGAATAATATGTCAACATAGTTGGTGAAA|CAACATTGTT|TTGCTTGACCAAATGCTAAACTAAAAGGTTCAGACAGATT ========== Event 3935 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTACTCAAAATATTTCTGTTTAAACCAAGTGACAATGGTATCAGATTCTGATTATCAGAAGTACTGATTCAG ↓ 13 24 Chimp: TTACTCAAAATATTTCTGTTTGATACCATTGTCACTTGGTTTAGATTCTGAGTATCAGAAGTACTGATTCAG Gorilla: TTATTCAAAATATTTCTGTTTAAACCAAGTGACAATG--------------GTATCAGAACTACTGATTCAG Human: TTACTCAAAATATTTCTGTTTAAACCAAGTGACAATGGTATCAGATTCTGATTATCAGAAGTACTGATTCAG Cluster: [ ] Orangutan: TTACTCAAAATATTTCTGTTTAAACCAAGTGACAATGGTATCAGATTCTGATTATCAGAAGTACTGATTCAG Human > Chimp ------------- chrKV421382:48926-48946 Template switch process: F1: L ATGGTTGAATTGTTATTGAATTACTCAAAATATTTCTGTTT 1 F3: 4 AGATTCTGAGTATCAGAAGTACTGATTCAGTGAAAAAAGTTATGTATGTT R RF: GTGGTTGAATTGTTATTGAATTACTCAAAATATTTCTGTTTAAACCAAGTGACAATGGTATCAGATTCTGATTATCAGAAGTACTGATTCAGTGAAAAAAGTTATGTATGTT RR: CACCAACTTAACAATAACTTAATGAGTTTTATAAAGACAAATTTGGTTCACTGTTACCATAGTCTAAGACTAATAGTCTTCATGACTAAGTCACTTTTTTCAATACATACAA F2: 3 TTTGGTTCACTGTTACCATAG 2 Unidirectional alignment (log-probability: -64.5) TGGTTGAATTGTTATTGAATTACTCAAAATATTTCTGTTT---------------------gataccattgtcacttggtttAGATTCTGAgTATCAGAAGTACTGATTCAGTGAAAAAAGT TGGTTGAATTGTTATTGAATTACTCAAAATATTTCTGTTTAAACCAAGTGACAATGGTATC---------------------AGATTCTGATTATCAGAAGTACTGATTCAGTGAAAAAAGT Template switch alignment (log-probability: -30) TGGTTGAATTGTTATTGAATTACTCAAAATATTTCTGTTT|GATACCATTGTCACTTGGTTT|AGATTCTGAgTATCAGAAGTACTGATTCAGTGAAAAAAGT TGGTTGAATTGTTATTGAATTACTCAAAATATTTCTGTTT|GATACCATTGTCACTTGGTTT|AGATTCTGATTATCAGAAGTACTGATTCAGTGAAAAAAGT ========== Event 3936 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: AATGCTACTGCTCCTGGGACTGATGCATGATTACTATCAACACAGCTATATTTAGGTATGATACTTTAAAATCATCATGAAATTCCTTGGGCGGGTATTAAGAACTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATA-------TTTCAGCTTAGTCACTCACTCCAAATAAT Chimp: AATGCTACTGCTCCTGGGACTGATGCATGATTACTATCAACACAGC--TATTTAGGTATGATACTTTAAAATCATCATGAAATTCCTTGGGCGGGTATTAGGAATTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATA-------TTTCAGCTTAGTCAGTCACTCCAAATAAT ↑ 3 2 4 1 Gorilla: AATGCTACTGCTCCTGGGACTGATGCATGATTACTATCAACACAGC--TATTTAGGTATGATACTTTAAAATCATCATGAAATTCCTTGGGCGGGTATTAGGAACTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATA--------------TTAGTCAGTCACTCCAAATAAT Human: AATGCTACTGCTCCTGGGACTGATGCATGATTACTATCAACACAGCTATATTTAGGTATGATACTTTAAAATCATCATGAAATTCCTTGGGCGGGTATTAAGAACTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATA-------TTTCAGCTTAGTCACTCACTCCAAATAAT Cluster: [ ] Orangutan: AATGCTACTGCTTCTGGGACTGATGCATGATTACTATCAACACAGC--TATTTAGGTATGATACTTTAAAATCATCATGAAATTCCTTGGGCAGGTATTAGGAACTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATATTTCAGC-------TTAGTCAGTCACTCCAAATAAT Gorilla > Chimp --------------- chrX:127719616-127719619 Template switch process: F1: L AATTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATATT 1 F3: 4 CTTAGTCAGTCACTCCAAATAATATTTATTTTGCCCTATTG R RF: CTGATGCATGATTACTATCAACACAGCTATTTAGGTATGATACTTTAAAATCATCATGAAATTCCTTGGGCGGGTATTAGGAACTACTCATTATAAATGTTGATAGTTTCATTGAGAAGATATTAGTCAGTCACTCCAAATAATATTTATTTTGCCCTATTA RR: GACTACGTACTAATGATAGTTGTGTCGATAAATCCATACTATGAAATTTTAGTAGTACTTTAAGGAACCCGCCCATAATCCTTGATGAGTAATATTTACAACTATCAAAGTAACTCTTCTATAATCAGTCAGTGAGGTTTATTATAAATAAAACGGGATAAT F2: 3 GACT 2 Unidirectional alignment (log-probability: -38.9) TACTCATTATAAATGTTGATAGTTTCATTGAGAAGATAtttcagcTTAGTCAGTCACTCCAAATAATATTTATTTTGCCCTatt TACTCATTATAAATGTTGATAGTTTCATTGAGAAGATA-------TTAGTCAGTCACTCCAAATAATATTTATTTTGCCCT--- Template switch alignment (log-probability: -32.9) TACTCATTATAAATGTTGATAGTTTCATTGAGAAGATATT|TCAG|cTTAGTCAGTCACTCCAAATAATATTTATTTTGCCCTATT TACTCATTATAAATGTTGATAGTTTCATTGAGAAGATATT|TCAG|ATTAGTCAGTCACTCCAAATAATATTTATTTTGCCCTATT ========== Event 3937 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GCaaaaaaa-aaa--agtgtatatctgtaaacacacaaaaaagaagttcaaaaaaaTGTTTAAAGTCTTTTATATAAAAATTACAGATACATATTATTTTAATAACCTCATTATC Chimp: GCaaaaaa--aaa----agtatatctgtaaacacacaaaaaagaagttcaa-aaaatgtttaaagtcttttata--taaaTTACAGATATGTATTATTTTAATAACCTCATTATC Gorilla: gccaaaaaa-aag----tgtatatctgtaaacacacaaaaaagaagttcaa-aaaatgtttaaagTCTTTTATA--TAAATTACAGATATAT---ATTTTAATAACCTCATTATC ↑ 3 2 1 4 Human: GCaaaaaaa-aaa--agtgtatatctgtaaacacacaaaaaagaagttcaaaaaaaTGTTTAAAGTCTTTTATATAAAAATTACAGATACATATTATTTTAATAACCTCATTATC Cluster: [ ] Orangutan: gcaaaaaaaaaaaaG--TGTATATCTGTAAACACACAAAA---ACGTTCAA-AAAATGTTTAAAGTCTTTTATA--TAAATTACAGATATATATTATTTTAATAACCTCATTATC Human > Gorilla --------------- chrX:126231065-126231075 Template switch process: F1: L CACAAAAAAGAAGTTC-AAAAAATGTTTAAAGTCTTTTATATAAA 1 F3: 4 TATTTTAATAACCTCATTATCTG R RF: TATATCTGTAAACACACAAAAAAGAAGTTCAAAAAAATGTTTAAAGTCTTTTATATAAAAATTACAGATACATATTATTTTAATAACCTCATTATCTG RR: ATATAGACATTTGTGTGTTTTTTCTTCAAGTTTTTTTACAAATTTCAGAAAATATATTTTTAATGTCTATGTATAATAAAATTATTGGAGTAATAGAC F2: 3 ATATAGACATT 2 Unidirectional alignment (log-probability: -36.2) AAAAAGAAGTTCAAA-AAATGTTTAAAGTCTTTTATAT--AAATTACAGATAtA---TATTTTAATAACCTCATTATCTG AAAAAGAAGTTCAAAAAAATGTTTAAAGTCTTTTATATAAAAATTACAGATACATATTATTTTAATAACCTCATTATCTG Template switch alignment (log-probability: -26.6) AAAAAGAAGTTC-AAAAAATGTTTAAAGTCTTTTATATAAA|TTACAGATATA|TATTTTAATAACCTCATTATCTG AAAAAGAAGTTCAAAAAAATGTTTAAAGTCTTTTATATAAA|TTACAGATATA|TATTTTAATAACCTCATTATCTG ========== Event 3938 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 56 Detected in comparisons: 1256 Multiple sequence alignment: Human: CCATCTTGCTGGTTTATCTTAGTTTATTTTCCTTTTT-GTTATTTTTTAAA--A--------------------------------------ACATAAGTCTAATGTGCAGTTTAGG Chimp: CCATCTTGCTGGTTTATCTTAGTTTATTTTCCTTTTTGGTCATTTTTTAAA--A--------------------------------------ACACAAGTCTAATGTGCAGTTTAGG ↓ 3 2 4 ↑ 1 3 24 Gorilla: CCATCTTGCTGGTTTATCTTAT-------------------G-TTTTTAAA-AA-------------------ATGACCAAAAAGGAAAATAAACTAAGTCTAATGTGCAGTTTAGG Human: CCATCTTGCTGGTTTATCTTAGTTTATTTTCCTTTTT-GTTATTTTTTAAA--A--------------------------------------ACATAAGTCTAATGTGCAGTTTAGG Cluster: [ ] Orangutan: CCATATTGCTGG-TTATCTTAT-------------------G-TTTTTAAAA-AATGACCAAAAAGGAAAATA-------------------AACTAAGTCTAATGTGCAGTTTAGG Gorilla > Chimp --------------- chrKV421380:62885-62918 Template switch process: F1: L TGTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA 1 F3: 4 CAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT R RF: TGTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTATGTTTTTAAAAAATGACCAAAAAGGAAAATAAACTAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT RR: ACAGTCAAACGTATACGAAGGGTAGAACGACCAAATAGAATACAAAAATTTTTTACTGGTTTTTCCTTTTATTTGATTCAGATTACACGTCAAATCCCTCGACTTAAAATTCCTGA F2: 3 ACAAAAATTTTTTACTGGTTTTTCCTTTTATTTG 2 Unidirectional alignment (log-probability: -72.7) GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTAgtttattttcctttttggtcattttttaaaaacac-----------------------------------AAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGAC GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA-----------------------------------TGTTTTTAAAAAATGACCAAAAAGGAAAATAAACTAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGAC Template switch alignment (log-probability: -25.6) GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA|GTTTATTTTCCTTTTTGGTCATTTTTTAAAAACA|cAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGAC GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA|GTTTATTTTCCTTTTTGGTCATTTTTTAAAAACA|TAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGAC Chimp > Gorilla --------------- chrX:126110106-126110140 Template switch process: F1: L TGTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA 1 F3: 4 AAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT R RF: TGTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTAGTTTATTTTCCTTTTTGGTCATTTTTTAAAAACACAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT RR: ACAGTCAAACGTATACGAAGGGTAGAACGACCAAATAGAATCAAATAAAAGGAAAAACCAGTAAAAAATTTTTGTGTTCAGATTACACGTCAAATCCCTCGACTTAAAATTCCTGA F2: 3 TCAAATAAAAGGAAAAACCAGTAAAAAATTTTTGT 2 Unidirectional alignment (log-probability: -72.7) GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTAtgtttttaaaaaatgaccaaaaaggaaaataaact-----------------------------------AAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA-----------------------------------GTTTATTTTCCTTTTTGGTCATTTTTTAAAAACACAAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT Template switch alignment (log-probability: -20.2) GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA|TGTTTTTAAAAAATGACCAAAAAGGAAAATAAACT|AAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT GTCAGTTTGCATATGCTTCCCATCTTGCTGGTTTATCTTA|TGTTTTTAAAAAATGACCAAAAAGGAAAATAAACT|AAGTCTAATGTGCAGTTTAGGGAGCTGAATTTTAAGGACT ========== Event 3939 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTGTGTGTGTGCAACTTGACTGGGCAGTCAAGGAGTAGAACTCTCTTTGTATATATTC ↑ 3 1 24 Chimp: ACTGTGTGTGTGCAACTTGACTG----CCCAAGGAGTACAACTCTCTTTGTATATATTC Gorilla: ACTGTGTGTGTGCAACTTGACTG----CCCAAGGAGTACAACTCTCTTTGTATATATTC ↓ 3 1 24 Human: AGTGTGTGTGTGCAACTTGACTGGGCAGTCAAGGAGTAGAACTCTCTTTGTATATATTC Cluster: [ ] Orangutan: AGTGTGTGTGTGCAACTTGACTG----CCCAAGGAGTACAACTCTCTTTGTATATATTC Chimp > Human ------------- chrX:126582431-126582436 Template switch process: F1: L CCAAGGACCCATCTGAACAGTGTGTGTGTGCAACTTGACTG 1 F3: 4 CAAGGAGTAGAACTCTCTTTGTATATATTCTTGTATCCATTTGGCAGTAG R RF: CCAAGGACCCATCTGAACACTGTGTGTGTGCAACTTGACTGCCCAAGGAGTACAACTCTCTTTGTATATATTCTTGTATCCATTTGGCAGTAG RR: GGTTCCTGGGTAGACTTGTGACACACACACGTTGAACTGACGGGTTCCTCATGTTGAGAGAAACATATATAAGAACATAGGTAAACCGTCATC F2: 3 TGACGG 2 Unidirectional alignment (log-probability: -40.7) CAAGGACCCATCTGAACAgTGTGTGTGTGCAACTTGACTGggCagtcAAGGAGTAgAACTCTCTTTGTATATATTCTTGTATCCAT CAAGGACCCATCTGAACACTGTGTGTGTGCAACTTGACTGCCC----AAGGAGTACAACTCTCTTTGTATATATTCTTGTATCCAT Template switch alignment (log-probability: -28.2) CAAGGACCCATCTGAACAgTGTGTGTGTGCAACTTGACTG|GGCAGT|CAAGGAGTAgAACTCTCTTTGTATATATTCTTGTATCCAT CAAGGACCCATCTGAACACTGTGTGTGTGCAACTTGACTG|GGCAGT|CAAGGAGTACAACTCTCTTTGTATATATTCTTGTATCCAT Gorilla > Human --------------- chrX:126582431-126582436 Template switch process: F1: L CCAAGGACCCATCTGAACAGTGTGTGTGTGCAACTTGACTG 1 F3: 4 CAAGGAGTAGAACTCTCTTTGTATATATTCTTGTATCCATTTGGCAGTAG R RF: CCAAGGACCCATCTGAACACTGTGTGTGTGCAACTTGACTGCCCAAGGAGTACAACTCTCTTTGTATATATTCTTGTATCCATTTGGCAGTAG RR: GGTTCCTGGGTAGACTTGTGACACACACACGTTGAACTGACGGGTTCCTCATGTTGAGAGAAACATATATAAGAACATAGGTAAACCGTCATC F2: 3 TGACGG 2 Unidirectional alignment (log-probability: -38.9) CAAGGACCCATCTGAACAgTGTGTGTGTGCAACTTGACTGggcagtCAAGGAGTAgAACTCTCTTTGTATATATTCTTGTATCCAT CAAGGACCCATCTGAACACTGTGTGTGTGCAACTTGACTG----CCCAAGGAGTACAACTCTCTTTGTATATATTCTTGTATCCAT Template switch alignment (log-probability: -27.8) CAAGGACCCATCTGAACAgTGTGTGTGTGCAACTTGACTG|GGCAGT|CAAGGAGTAgAACTCTCTTTGTATATATTCTTGTATCCAT CAAGGACCCATCTGAACACTGTGTGTGTGCAACTTGACTG|GGCAGT|CAAGGAGTACAACTCTCTTTGTATATATTCTTGTATCCAT ========== Event 3940 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCCCAAAAGTAAATATTGATATTGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGACAAGAAGTGGTCATCGAACATT Chimp: CCCCAAAAGTAAATATTGATATTGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGACAAGAAGTGGTCATCGAACATT ↓ 3 2 1 4 Gorilla: CCCCAAAAGTAAATATTGATATTGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGCTGTTAATAAAGAAGTGGTCATCGAACATT ↑ 3 2 1 4 Human: CCCCAAAAGTAAATATTGATATTGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGACAAGAAGTGGTCATCGAACATT Cluster: [ ] Orangutan: CCCCAAAAGTAAGTATTGATATCGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGACAAGAAGTGGTCATCGAACATT Human > Gorilla --------------- chrX:126592051-126592059 Template switch process: F1: L TTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG 1 F3: 4 AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC R RF: TATTGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGACAAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC RR: ATAACTGTCATGATTTACCTCAAAATACCAGTCTTTATATATCTTGTCGTTATTTCGGTAACTTAAACCTGTTCTTCACCAGTAGCTTGTAAACAATCCCTAACTCCCTTG F2: 3 ATAATTGTC 2 Unidirectional alignment (log-probability: -32.6) TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG--------CtgttaataAAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGAC--------AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC Template switch alignment (log-probability: -22.4) TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG|CTGTtAATA|AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG|CTGTCAATA|AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC Chimp > Gorilla --------------- chrX:126592051-126592059 Template switch process: F1: L TTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG 1 F3: 4 AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC R RF: TATTGACAGTACTAAATGGAGTTTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGACAAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC RR: ATAACTGTCATGATTTACCTCAAAATACCAGTCTTTATATATCTTGTCGTTATTTCGGTAACTTAAACCTGTTCTTCACCAGTAGCTTGTAAACAATCCCTAACTCCCTTG F2: 3 ATAATTGTC 2 Unidirectional alignment (log-probability: -32.6) TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG--------CtgttaataAAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTGAATTTGGAC--------AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC Template switch alignment (log-probability: -22.4) TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG|CTGTtAATA|AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC TTTATGGTCAGAAATATATAGAACAGCAATAAAGCCATTG|CTGTCAATA|AAGAAGTGGTCATCGAACATTTGTTAGGGATTGAGGGAAC ========== Event 3941 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: ATAGTTTAGCACAGATTGGCCTGCTATTGCAGGCCACTCAAATACAAAAAGAAA Chimp: ATAGTTTAGCACAGATTGGCCTGCTATTGCAGGCCACTCAAATACaaaaagaaa ↑ 3 1 24 Gorilla: ATAGTTTAGCACAGATTGGCCTGCAA-----TACCACTCAAATACaaaaagaaa ↓ 3 1 24 Human: ATAGTTTAGCACAGATTGGCCTGCTATTGCAGGCCACTCAAATACAAAAAGAAA Cluster: [ ] Orangutan: ACAGTTTAGCACAGATTGGCCTGCAA-----TACCACTCAAATACAAAAAGAAA Gorilla > Human --------------- chrX:125204919-125204927 Template switch process: F1: L GTTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGC 1 F3: 4 CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC R RF: GTTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGCAATACCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC RR: CAAAAGATTTTCATGTATATCAAATCGTGTCTAACCGGACGTTATGGTGAGTTTATGTTTTTCTTTTTTCTATTTGGTCATTTTG F2: 3 GGACGTTAT 2 Unidirectional alignment (log-probability: -29.2) TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGCtATtgcaggCCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGCAATA-----CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC Template switch alignment (log-probability: -16.9) TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGC|TATTGCAGG|CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGC|TATTGCAGG|CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC Gorilla > Chimp --------------- chrX:124525468-124525476 Template switch process: F1: L GTTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGC 1 F3: 4 CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC R RF: GTTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGCAATACCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC RR: CAAAAGATTTTCATGTATATCAAATCGTGTCTAACCGGACGTTATGGTGAGTTTATGTTTTTCTTTTTTCTATTTGGTCATTTTG F2: 3 GGACGTTAT 2 Unidirectional alignment (log-probability: -29.2) TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGCtATtgcaggCCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGCAATA-----CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC Template switch alignment (log-probability: -16.9) TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGC|TATTGCAGG|CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC TTTTCTAAAAGTACATATAGTTTAGCACAGATTGGCCTGC|TATTGCAGG|CCACTCAAATACAAAAAGAAAAAAGATAAACCAGTAAAAC ========== Event 3942 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: ACATGTCAAGATTAGCAAGCTTCA------------------GATTGTGTGATAAAAGTGCAAAGAGTTCGCTAGAGCCATACTGAATAATTTGT Chimp: ACATGTCAAGATTAGCAAGCTTCA------------------AATTGTGTGATAAAAGTTCAAAGAGTTCGCTAGAGCCATATTGAATAATTTGT ↓ 1 4 3 2 Gorilla: ACATGTCAAGATTAGCAAGCTCTA------------------------------------GCAAGAGTTCGCTAGAGCCATATTGAATAATTTGT ↑ 1 4 3 2 Human: ACATGTCAAGATTAGCAAGCTTCA------------------GATTGTGTGATAAAAGTGCAAAGAGTTCGCTAGAGCCATACTGAATAATTTGT Cluster: [ ] Orangutan: ACATGTCAAGATTAGCAAGCTTCAGATTGTGCGATAAAAGTG------------------CAAAGAGTTCGCTAGAGCCATATTGGATAATTTGT Human > Gorilla --------------- chrX:31957885-31957889 Template switch process: F1: L AGCAATCCAACAACATTGAGACATGTCAAGATTAGCAAGCT 1 F3: 4 AAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC R RF: AGCAATCCAACAACATTAAGACATGTCAAGATTAGCAAGCTTCAGATTGTGTGATAAAAGTGCAAAGAGTTCGCTAGAGCCATACTGAATAATTTGTCTTTCTC RR: TCGTTAGGTTGTTGTAATTCTGTACAGTTCTAATCGTTCGAAGTCTAACACACTATTTTCACGTTTCTCAAGCGATCTCGGTATGACTTATTAAACAGAAAGAG F2: 3 CGATC 2 Unidirectional alignment (log-probability: -39.5) GCAATCCAACAACATTgAGACATGTCAAGATTAGCAAGCTctAG------------------cAAGAGTTCGCTAGAGCCATAtTGAATAATTTGTCTTTCTC GCAATCCAACAACATTAAGACATGTCAAGATTAGCAAGCTTCAGATTGTGTGATAAAAGTGCAAAGAGTTCGCTAGAGCCATACTGAATAATTTGTCTTTCTC Template switch alignment (log-probability: -27.4) GCAATCCAACAACATTgAGACATGTCAAGATTAGCAAGCT|CTAGC|AAGAGTTCGCTAGAGCCATAtTGAATAATTTGTCTTTCTC GCAATCCAACAACATTAAGACATGTCAAGATTAGCAAGCT|CTAGC|AAGAGTTCGCTAGAGCCATACTGAATAATTTGTCTTTCTC Chimp > Gorilla --------------- chrX:31957885-31957889 Template switch process: F1: L AGCAATCCAACAACATTGAGACATGTCAAGATTAGCAAGCT 1 F3: 4 AAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC R RF: AGCAATCCAACAACATTAAGACATGTCAAGATTAGCAAGCTTCAAATTGTGTGATAAAAGTTCAAAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC RR: TCGTTAGGTTGTTGTAATTCTGTACAGTTCTAATCGTTCGAAGTTTAACACACTATTTTCAAGTTTCTCAAGCGATCTCGGTATAACTTATTAAACAGAAAGAG F2: 3 CGATC 2 Unidirectional alignment (log-probability: -34.5) GCAATCCAACAACATTgAGACATGTCAAGATTAGCAAGCT-----------------------ctagcAAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC GCAATCCAACAACATTAAGACATGTCAAGATTAGCAAGCTTCAAATTGTGTGATAAAAGTTCA-----AAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC Template switch alignment (log-probability: -21.9) GCAATCCAACAACATTgAGACATGTCAAGATTAGCAAGCT|CTAGC|AAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC GCAATCCAACAACATTAAGACATGTCAAGATTAGCAAGCT|CTAGC|AAGAGTTCGCTAGAGCCATATTGAATAATTTGTCTTTCTC ========== Event 3943 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1234 Multiple sequence alignment: Human: ACTAGGAGACTGAAAACTTCTTC----------------TACATGTTCACTTGTCACCCGTCTGCAGAACAGAATTGGAGAACATC ↓ 13 24 ↑ 13 24 Chimp: ACTAGGAGACTGAAAACTTCTGC--------AGACAGGTGACAAGTGAACATG--------TAGAAGAACAGAATTGGAGAACATC Gorilla: ACTAGGAGACTGAAAACTTCTGCAGACAGGT--------GACAAGTGAACATG--------TAGAAGAACAGAATTGGAAAACATC Human: ACTAGGAGACTGAAAACTTCTTC----------------TACATGTTCACTTGTCACCCGTCTGCAGAACAGAATTGGAGAACATC Cluster: [ ] Orangutan: ACTAGGAGACTGAAAACTTCTGCAGACAAGT--------GAC----AAACATG--------TAGAAGAACAGAATTGGAAAACATC Chimp > Human ------------- chrX:32738673-32738700 Template switch process: F1: L GTTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCT 1 F3: 4 AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG R RF: GTTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCTGCAGACAGGTGACAAGTGAACATGTAGAAGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG RR: CAATTAACTTACCTCCATTTTGATCCTCTGACTTTTGAAGACGTCTGTCCACTGTTCACTTGTACATCTTCTTGTCTTAACCTCTTGTAGGTATTATTGTGTTCCTTTC F2: 3 CGTCTGCCCACTGTTCACTTGTACATCT 2 Unidirectional alignment (log-probability: -59.9) TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCttctacatgttcacttgtcacccgtcTGC--------------------------AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTC--------------------------TGCAGACAGGTGACAAGTGAACATGTAGAAGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG Template switch alignment (log-probability: -24.7) TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCT|TCTACATGTTCACTTGTCACCcGTCTGC|AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCT|TCTACATGTTCACTTGTCACCTGTCTGC|AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG Human > Chimp ------------- chrX:32950153-32950180 Template switch process: F1: L GTTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCT 1 F3: 4 AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG R RF: GTTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCTTCTACATGTTCACTTGTCACCCGTCTGCAGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG RR: CAATTAACTTACCTCCATTTTGATCCTCTGACTTTTGAAGAAGATGTACAAGTGAACAGTGGGCAGACGTCTTGTCTTAACCTCTTGTAGGTATTATTGTGTTCCTTTC F2: 3 AGATGTACAAGTGAACAGTGGACAGACG 2 Unidirectional alignment (log-probability: -59.9) TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACT--------------------------TCTGCAgacaggtgacaagtgaacatgtagaaGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCTTCTACATGTTCACTTGTCACCCGTCTGCA--------------------------GAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG Template switch alignment (log-probability: -24.7) TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCT|GCAGACaGGTGACAAGTGAACATGTAGA|AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG TTAATTGAATGGAGGTAAAACTAGGAGACTGAAAACTTCT|GCAGACGGGTGACAAGTGAACATGTAGA|AGAACAGAATTGGAGAACATCCATAATAACACAAGGAAAG ========== Event 3944 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: cgcctagccCAGAAATCTTAGTCTTTT-TAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGT ↓ 13 24 ↑ 13 24 Chimp: cgcccagccCAGAAATCTTAGAATCTCAAAACTGAGT-TAAAAAGACTGCCATATACCTGGCACTGT ↓ 13 24 ↑ 13 24 Gorilla: cgcccagccCAGAAATCTTAGTCTTTT-TAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGC Human: cgcctagccCAGAAATCTTAGTCTTTT-TAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGT Cluster: [ ] Orangutan: cgcccagcACAGAAATCTTAGTCTGTT-TAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGT Chimp > Human ------------- chrX:123160246-123160269 Template switch process: F1: L ATTACAGGCGTGAGCCACTGCGCCTAGCCCAGAAATCTTAG 1 F3: 4 CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA R RF: ATTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAGAATCTCAAAACTGAGTTAAAAAGACTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA RR: TAATGTCCGTACTCGGTGACGCGGGTCGGGTCTTTAGAATCTTAGAGTTTTGACTCAATTTTTCTGACGGTATATGGACCGTGACATCAATTCTCTACCGTATAT F2: 3 TTAGAGTTTTGACTCAATTTTTCT 2 Unidirectional alignment (log-probability: -68.8) TTACAGGCgTGAGCCACTGCGCCtAGCCCAGAAATCTTAGtctttttaactcagttttgagatt------------------------CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA TTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAG------------------------AATCTCAAAACTGAGTTAAAAAGACTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA Template switch alignment (log-probability: -30.2) TTACAGGCgTGAGCCACTGCGCCtAGCCCAGAAATCTTAG|TCTTTTTAACTCAGTTTTGAGATT|CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA TTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAG|TCTTTTTAACTCAGTTTTGAGATT|CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA Human > Chimp ------------- chrX:122457563-122457586 Template switch process: F1: L ATTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAG 1 F3: 4 CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA R RF: ATTACAGGCGTGAGCCACTGCGCCTAGCCCAGAAATCTTAGTCTTTTTAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA RR: TAATGTCCGCACTCGGTGACGCGGATCGGGTCTTTAGAATCAGAAAAATTGAGTCAAAACTCTAAGACGGTATATGGACCGTGACATCAATTCTCTACCGTATAT F2: 3 AGAAAAATTGAGTCAAAACTCTAA 2 Unidirectional alignment (log-probability: -68.8) TTACAGGCaTGAGCCACTGCGCCcAGCCCAGAAATCTTAGaatctcaaaactgagttaaaaaga------------------------CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA TTACAGGCGTGAGCCACTGCGCCTAGCCCAGAAATCTTAG------------------------TCTTTTTAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA Template switch alignment (log-probability: -30.2) TTACAGGCaTGAGCCACTGCGCCcAGCCCAGAAATCTTAG|AATCTCAAAACTGAGTTAAAAAGA|CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA TTACAGGCGTGAGCCACTGCGCCTAGCCCAGAAATCTTAG|AATCTCAAAACTGAGTTAAAAAGA|CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA Gorilla > Chimp --------------- chrX:122457563-122457586 Template switch process: F1: L ATTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAG 1 F3: 4 CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA R RF: ATTACAGGCTTGAGCCACTGCGCCCAGCCCAGAAATCTTAGTCTTTTTAACTCAGTTTTGAGATTCTGCCATATACCTGGCACTGCAGTTAAGAGATGGCATATA RR: TAATGTCCGAACTCGGTGACGCGGGTCGGGTCTTTAGAATCAGAAAAATTGAGTCAAAACTCTAAGACGGTATATGGACCGTGACGTCAATTCTCTACCGTATAT F2: 3 AGAAAAATTGAGTCAAAACTCTAA 2 Unidirectional alignment (log-probability: -67.4) TTACAGGCaTGAGCCACTGCGCCCAGCCCAGAAATCTTAG------------------------aatctcaaaactgagttaaaaagaCTGCCATATACCTGGCACTGtAGTTAAGAGATGGCATATA TTACAGGCTTGAGCCACTGCGCCCAGCCCAGAAATCTTAGTCTTTTTAACTCAGTTTTGAGATT------------------------CTGCCATATACCTGGCACTGCAGTTAAGAGATGGCATATA Template switch alignment (log-probability: -29.8) TTACAGGCaTGAGCCACTGCGCCCAGCCCAGAAATCTTAG|AATCTCAAAACTGAGTTAAAAAGA|CTGCCATATACCTGGCACTGtAGTTAAGAGATGGCATATA TTACAGGCTTGAGCCACTGCGCCCAGCCCAGAAATCTTAG|AATCTCAAAACTGAGTTAAAAAGA|CTGCCATATACCTGGCACTGCAGTTAAGAGATGGCATATA Chimp > Gorilla --------------- chrX:123029345-123029368 Template switch process: F1: L ATTACAGGCTTGAGCCACTGCGCCCAGCCCAGAAATCTTAG 1 F3: 4 CTGCCATATACCTGGCACTGCAGTTAAGAGATGGCATATA R RF: ATTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAGAATCTCAAAACTGAGTTAAAAAGACTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA RR: TAATGTCCGTACTCGGTGACGCGGGTCGGGTCTTTAGAATCTTAGAGTTTTGACTCAATTTTTCTGACGGTATATGGACCGTGACATCAATTCTCTACCGTATAT F2: 3 TTAGAGTTTTGACTCAATTTTTCT 2 Unidirectional alignment (log-probability: -67.4) TTACAGGCtTGAGCCACTGCGCCCAGCCCAGAAATCTTAG------------------------tctttttaactcagttttgagattCTGCCATATACCTGGCACTGcAGTTAAGAGATGGCATATA TTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAGAATCTCAAAACTGAGTTAAAAAGA------------------------CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA Template switch alignment (log-probability: -29.8) TTACAGGCtTGAGCCACTGCGCCCAGCCCAGAAATCTTAG|TCTTTTTAACTCAGTTTTGAGATT|CTGCCATATACCTGGCACTGcAGTTAAGAGATGGCATATA TTACAGGCATGAGCCACTGCGCCCAGCCCAGAAATCTTAG|TCTTTTTAACTCAGTTTTGAGATT|CTGCCATATACCTGGCACTGTAGTTAAGAGATGGCATATA ========== Event 3945 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: CACAGGGCATAAGAATGTATACTT-GATACTTAAAAGGATTTCTAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTTTTACACAGTAACTGTTGCCATCCTTAAGATAGCTCTTTCCTTAAGTATGCAAAAACAGTTGGGCTGTTTCAAA Chimp: CACAGGGCATAAGAATGTATACTTGCATACTTAAAAGGATTTCTAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATCTTTACACAGTAACTGTTGCCATCCTTAAGATAGCTCTTTACTTAAGTATGCAAAAACAGTTGGGCTGTTTCAAA Gorilla: CACAGGGCATAAGAATGTATATTTGCATACTTAAAAGGATTTCTAAAATTTTTACACAGTAACTGTTGCCATCCTTAAGATAGCTCTTTCCTTAAGTACGCAAAAACAGTTGGGCTGTTTCAAATGCTTATGGAAGCATCTGAAATTTCCTTGGAGAAGAATGTCTTTGTTTTAAATTTACATGTCTAAATACCAATTGTAAAGGTAAAGATTTTCTCAATAGAAAGGAGTAATCTGTTAAAAGTTaaaaaaaaTACCAATTTCTTTTGGAAAACTGCTAAGTCCTGAATTCGGAGGTCTTATTCTTGTTTATTCTAATCACCCCACCTGAAGGAAGCATAATTTTCCCCAATGACTGAAATAATAATAGTAAGAATGAGAATACATGGAAAATGATATTAAATTCTTACCATAAACAATCTTAAAATTTTCGCTTTGAGTTTAAGTTTTCTGAGATATTCCATACTTACTTAAAATGTGTTTTTACAAAGTAATAACTGCCATTATTATTTACAnnnnnnnnnnAAGTCTCaaaaagaaaaaagagaaaaaaaaaaaGATAGTATTACCTCAACATGTCTATATCATGTTCTGCAGGCATCTGACTCTGTGTTAGAGTTTCTCATTATTCTTATCACTATGTTAAGTTACATGTTTATTTGTTTGAGTGCTTGTTTTATAAACATCGACATAAAGCAGATCTATTATATGTTGTGTCTTTGCCTCTTTCTATCATCACTGGCTCTCTAGAATCTGTATTGTGCCTGGCCTATGTAGTTGCTCGTTAAATGAATGTGCTTATGTGCATGTGTATATAATTATGTGCATGCACACATGGATGTGCTCACACTGCTGGACATCCAAAATTGAGCAAGGATGTGCACAGGGCATAAGAATGTATATTTGCATACTTAAAAGGATTTCTAAAATTTTTACACAGTAACTGTTGCCATCCTTAAGATAGCTCTTTCCTTAAGTATGCAAAAACAGTTGGGCTGTTTCAAA ↑ 1 4 3 2 Human: CACAGGGCATAAGAATGTATACTT-GATACTTAAAAGGATTTCTAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTTTTACACAGTAACTGTTGCCATCCTTAAGATAGCTCTTTCCTTAAGTATGCAAAAACAGTTGGGCTGTTTCAAA Cluster: [ ] Orangutan: CACAGGGCATAAGAATGTATACTTGCATACTTAAAAGGATTTCTAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATCTTTACACGGTAACGGTTCCCATCCTTATGATAGCTCTTTACTTAAGTATGCA-AAACAGTTGGGCTGTTTCAAA Human > Gorilla --------------- chrX:123131741-123131746 Template switch process: F1: L CAAAATTGAGCAAGGATGTGCACAGGGCATAAGAATGTATA 1 F3: 4 TACTTAAAAGGATTTCTAAAATTTTTACACAGTAACTGT R RF: CAAAATTGAGCAGCGATGTGCACAGGGCATAAGAATGTATACTTGATACTTAAAAGGATTTCTAAAATTTTTACACAGTAACTGTTGCCATCCTTAAGATAGCTCTTTCCTTAAGTATGCAAA RR: GTTTTAACTCGTCGCTACACGTGTCCCGTATTCTTACATATGAACTATGAATTTTCCTAAAGATTTTAAAAATGTGTCATTGACAACGGTAGGAATTCTATCGAGAAAGGAATTCATACGTTT F2: 3 ACGTTT 2 Unidirectional alignment (log-probability: -64.1) AAAATTGAGCAagGATGTGCACAGGGCATAAGAATGTATAtTTGcATACTTAAAAGGATTTCTAAaatttttacacagtaactgt AAAATTGAGCAGCGATGTGCACAGGGCATAAGAATGTATACTTG-ATACTTAAAAGGATTTCTAA-------------------- Template switch alignment (log-probability: -27.5) AAAATTGAGCAagGATGTGCACAGGGCATAAGAATGTATA|TTTGCA|TACTTAAAAGGATTTCTAAAATTTTTACACAGTAACTGT AAAATTGAGCAGCGATGTGCACAGGGCATAAGAATGTATA|TTTGCA|TACTTAAAAGGATTTCTAAAATTTTTACACAGTAACTGT ========== Event 3946 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TATACTTGTTACTGTGCCTCTGCAAAATCAATTTGGGAAAATATTTTAAATGTCCTAGATTTTCAAATATTGACATATTTA Chimp: TATACTTGTTGCTGTGCCTCTTTAAAACCAATTTGGGAAAATATTTTAAATGTCCTAGATTTTCAAATATTGACCTATTTA ↑ 31 2 4 Gorilla: TATACTTGTTGCTGTGCCTCTGTAAAATCAATTTGGGAAAATCTAGGACATTTAAAATACTTTCAAATATTGACCTATTTA Human: TATACTTGTTACTGTGCCTCTGCAAAATCAATTTGGGAAAATATTTTAAATGTCCTAGATTTTCAAATATTGACATATTTA Cluster: [ ] Orangutan: TGTACTTGTTGCTGTGCCTCTGTAAAATTAATTTGGGAAAATATTTTAAATATCCTAGATTTTCAAATATTGACCGATTTA Gorilla > Chimp --------------- chrX:122851422-122851439 Template switch process: F1: L CTCCCTCTAGTGGATTTCAGTATACTTGTTGCTGTGCCTCTTTAAAACCAATTTGGGAAAAT 1 F3: 4 TTTCAAAT R RF: CTCCCTCTAGTGGATTTCAGTATACTTGTTGCTGTGCCTCTGTAAAATCAATTTGGGAAAATCTAGGACATTTAAAATACTTTCAAAT RR: GAGGGAGATCACCTAAAGTCATATGAACAACGACACGGAGACATTTTAGTTAAACCCTTTTAGATCCTGTAAATTTTATGAAAGTTTA F2: 3 TAGATCCTGTAAATTTTA 2 Unidirectional alignment (log-probability: -53.1) TACTTGTTGCTGTGCCTCTtTAAAAcCAATTTGGGAAAAT-------ATTTtAAATgtcctagAtTTTCAAAT TACTTGTTGCTGTGCCTCTGTAAAATCAATTTGGGAAAATCTAGGACATTTAAAAT-------ACTTTCAAAT Template switch alignment (log-probability: -28.8) TACTTGTTGCTGTGCCTCTtTAAAAcCAATTTGGGAAAAT|ATTTTAAATGTCCTAGAT|TTTCAAAT TACTTGTTGCTGTGCCTCTGTAAAATCAATTTGGGAAAAT|ATTTTAAATGTCCTAGAT|TTTCAAAT ========== Event 3947 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: TATAGATTATATCCACAAGAAACT---------------------------------------------------------------------------------------TATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCATATTTTGATAGGCCTATGGAAATCCCTGATTTATTTTTTCTGCTAAAA ↓ 4 3 1 2 Chimp: TATAGATTATATCCACAAGAAACTTATACACAAATTTTATTAGATCATTATCAGGGATTTCCATAGGCCTATCAAAATATGGTGCAACTTTCTATAATGATCTAATAAACTTATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCATATTTTGATAGGCCTATGGAAATCCCTGATTTATTTTTTCTGCTAAAA ↑ 4 3 1 2 Gorilla: TGTAGATTATATCCACAAGAAACT---------------------------------------------------------------------------------------TATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCGTATTTTGATAGGCCTATGGAAATCCCTGATTTATTTTTTCTGCTAAAA Human: TATAGATTATATCCACAAGAAACT---------------------------------------------------------------------------------------TATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCATATTTTGATAGGCCTATGGAAATCCCTGATTTATTTTTTCTGCTAAAA Cluster: [ ] Orangutan: TATAGATTGTATCCACAAAAAACT---------------------------------------------------------------------------------------TATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCATATTTTGATAGGCCTATGGAAATCCCTGATTTATTTTTTCTGGTAAAA Human > Chimp ------------- chrX:121820228-121820282 Template switch process: F1: L TGAGGATGTTGAATAGATATAGATTATATCCACAAGAAACTTATACACAAATTTTATTAGATCATTAT 1 F3: 4 AAACTTATACACAAATTTTATTAGATCATTATAGAAAGTTGCACC R RF: TGAGAATGTTGAATAGATATAGATTATATCCACAAGAAACTTATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCATATTTTGATAGGCCTATGGAAATCCCTG RR: ACTCTTACAACTTATCTATATCTAATATAGGTGTTCTTTGAATATGTGTTTAAAATAATCTAGTAATATCTTTCAACGTGGTATAAAACTATCCGGATACCTTTAGGGAC F2: 3 TAATCTAGTAATATCTTTCAACGTGGTATAAAACTATCCGGATACCTTTAGGGAC 2 Unidirectional alignment (log-probability: -142) TCCACAAGAAACTTATACACAAATTTTATTAGATCATTAtcagggatttccataggcctatcaaaatatggtgcaactttctataatgatctaataaacttatacacaaattttattagatcattaTAGAAAGTT TCCACAAGAAACTTATACACAAATTTTATTAGATCATTA---------------------------------------------------------------------------------------TAGAAAGTT Template switch alignment (log-probability: -28.5) TCCACAAGAAACTTATACACAAATTTTATTAGATCATTAT|CAGGGATTTCCATAGGCCTATCAAAATATGGTGCAACTTTCTATAATGATCTAAT|AAACTTATACACAAATTTTATTAGATCATTATAGAAAGTT TCCACAAGAAACTTATACACAAATTTTATTAGATCATTAT|CAGGGATTTCCATAGGCCTATCAAAATATGGTGCAACTTTCTATAATGATCTAAT|AAACTTATACACAAATTTTATTAGATCATTATAGAAAGTT Gorilla > Chimp --------------- chrX:121820228-121820282 Template switch process: F1: L TGAGGATGTTGAATAGATATAGATTATATCCACAAGAAACTTATACACAAATTTTATTAGATCATTAT 1 F3: 4 AAACTTATACACAAATTTTATTAGATCATTATAGAAAGTTGCACC R RF: TGAGGATGTTGAATAGATGTAGATTATATCCACAAGAAACTTATACACAAATTTTATTAGATCATTATAGAAAGTTGCACCGTATTTTGATAGGCCTATGGAAATCCCTG RR: ACTCCTACAACTTATCTACATCTAATATAGGTGTTCTTTGAATATGTGTTTAAAATAATCTAGTAATATCTTTCAACGTGGCATAAAACTATCCGGATACCTTTAGGGAC F2: 3 TAATCTAGTAATATCTTTCAACGTGGTATAAAACTATCCGGATACCTTTAGGGAC 2 Unidirectional alignment (log-probability: -141) TCCACAAGAAACTTATACACAAATTTTATTAGATCATtatcagggatttccataggcctatcaaaatatggtgcaactttctataatgatctaataaacttatacacaaattttattagatcatTATAGAAAGTT TCCACAAGAAACTTATACACAAATTTTATTAGATCAT---------------------------------------------------------------------------------------TATAGAAAGTT Template switch alignment (log-probability: -34.4) TCCACAAGAAACTTATACACAAATTTTATTAGATCATTAT|CAGGGATTTCCATAGGCCTATCAAAATAtGGTGCAACTTTCTATAATGATCTAAT|AAACTTATACACAAATTTTATTAGATCATTATAGAAAGTT TCCACAAGAAACTTATACACAAATTTTATTAGATCATTAT|CAGGGATTTCCATAGGCCTATCAAAATACGGTGCAACTTTCTATAATGATCTAAT|AAACTTATACACAAATTTTATTAGATCATTATAGAAAGTT ========== Event 3948 ========== Phylogenetic placement: ILS consistent Significant comparisons: 4 Detected in comparisons: 24 Multiple sequence alignment: Human: TAGCAAAATATTGGATTAATATGAATACCAATCAGTAGCGATGGATACAATAACTTACTGTTTATTTATGATGAATAATAACGTAGATCTGTGTTGACATAAGAGATATCCATTATACAGTATTAAATTTTAAAATTGACCAAACAATAA-GAAATTGTGACACCTGTATCTTTTT Chimp: TAGCAAAATATTGGATTAATATGAATACCAATCAGTAGCGATGGATACAATAACTTACTGTTTATTTATGATGAATAATAACGTAGATCTGTGTTGACATAAGAGATATCCATTATACGGTATTAAATTTTAAAATTGACCAAACAGTATGCATATTGTGACACCTGTATCTTTTT Gorilla: TAGCAAAATATTGGATTCATATGAATACCAATCAGTAGCGATGGATACAATAACTTACTGTTTATTTATGATGAATAATAACGTAGATCTGTGTTGACATAAGAGATATCCATTATACAGTATTAAATTTTAACATTGACCAAACAGTATGCATATTGTGACACCTGTATCTTTTT ↑ 3 2 1 4 Human: TAGCAAAATATTGGATTAATATGAATACCAATCAGTAGCGATGGATACAATAACTTACTGTTTATTTATGATGAATAATAACGTAGATCTGTGTTGACATAAGAGATATCCATTATACAGTATTAAATTTTAAAATTGACCAAACAATAA-GAAATTGTGACACCTGTATCTTTTT Cluster: [ ] Orangutan: TAGCAAAATATTGGATTAATATGAATACCAATCAGTAGCGATGGATACAATAACTTACTGTTTATTTATGATGAATAATAACGTAGATCTGTGTTGACATAAGAGCTATCCATTATACAGTATTAAATTTTAAAATTGACCAAACAGTATGCATATTGTGACACCTGTATCTTTTT Human > Gorilla --------------- chrX:119893414-119893422 Template switch process: F1: L ATATCCATTATACAGTATTAAATTTTAACATTGACCAAACA 1 F3: 4 TTGTGACACCTGTATCTTTTTAAATGCACACACACACAC R RF: TATGAATACCAATCAGTAGCGATGGATACAATAACTTACTGTTTATTTATGATGAATAATAACGTAGATCTGTGTTGACATAAGAGATATCCATTATACAGTATTAAATTTTAAAATTGACCAAACAATAAGAAATTGTGACACCTGTATCTTTTTAAATGCACACACACACAC RR: ATACTTATGGTTAGTCATCGCTACCTATGTTATTGAATGACAAATAAATACTACTTATTATTGCATCTAGACACAACTGTATTCTCTATAGGTAATATGTCATAATTTAAAATTTTAACTGGTTTGTTATTCTTTAACACTGTGGACATAGAAAAATTTACGTGTGTGTGTGTG F2: 3 ATACGTATG 2 Unidirectional alignment (log-probability: -49.8) TATCCATTATACAGTATTAAATTTTAAcATTGACCAAACAgTAtGcAtATTGTGACACCTGTATCTTTTTAAATGCACACACacacac TATCCATTATACAGTATTAAATTTTAAAATTGACCAAACAATAAG-AAATTGTGACACCTGTATCTTTTTAAATGCACACAC------ Template switch alignment (log-probability: -27.9) TATCCATTATACAGTATTAAATTTTAAcATTGACCAAACA|GTATgCATA|TTGTGACACCTGTATCTTTTTAAATGCACACACACACAC TATCCATTATACAGTATTAAATTTTAAAATTGACCAAACA|GTATTCATA|TTGTGACACCTGTATCTTTTTAAATGCACACACACACAC ========== Event 3949 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: CACTCTTCATGCTAGTTGCTAGAAGCAATCTTCAATATGTTATTcacagggac Chimp: CACTCTTCATGCTAGTTGCTAT-----TGCTTCAATATGTTATTCACAGGGAC Gorilla: CACTCTTCATGCTAGTTGCTAT-----TGCTTCAATATGTTATTCACAGGGac ↓ 3 4 2 Human: CACTCTTCATGCTAGTTGCTAGAAGCAATCTTCAATATGTTATTcacagggac Cluster: [ ] Orangutan: Gorilla > Human --------------- chrX:36805410-36805417 Template switch process: F1: L ATCTGAATTCTAAGCACTCGCACTCTTCATGCTAGTTGCTA 1 F3: 4 CTTCAATATGTTATTCACAGGGACACACACAGACACACAC R RF: ATCTGAATTCTAAGCACTCGCACTCTTCATGCTAGTTGCTATTGCTTCAATATGTTATTCACAGGGACACACACACACACACAC RR: TAGACTTAAGATTCGTGAGCGTGAGAAGTACGATCAACGATAACGAAGTTATACAATAAGTGTCCCTGTGTGTGTGTGTGTGTG F2: 3 TAACGAAG 2 Unidirectional alignment (log-probability: -36.3) TCTGAATTCTAAGCACTCGCACTCTTCATGCTAGTTGCTA--GaagcaatCTTCAATATGTTATTCACAGGGACACACACAgACACACAC TCTGAATTCTAAGCACTCGCACTCTTCATGCTAGTTGCTATTG-------CTTCAATATGTTATTCACAGGGACACACACACACACACAC Template switch alignment (log-probability: -22.3) TCTGAATTCTAAGCACTCGCACTCTTCATGCTAGTTGCTA|GAAGCAAT|CTTCAATATGTTATTCACAGGGACACACACAgACACACAC TCTGAATTCTAAGCACTCGCACTCTTCATGCTAGTTGCTA|GAAGCAAT|CTTCAATATGTTATTCACAGGGACACACACACACACACAC ========== Event 3950 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: GGAGATATTGGGCACAGTTGTGTAAGCATTT------TACTAGGATTTCAGTAGAAGGAAGAAAATGAAGGGCTGTC Chimp: GGAGATCTTGGGCACAGTTGTATAAGCATTT------TACTAGGATTTCAGTAGAAGGAAGAAAATGAAGGGCTGTC ↓ 1 4 3 2 Gorilla: GGAGATCTTGGGCACAGTTGTTT----CTTCTACTGAAACTAGGGTTTCAGTAGAAGGAAGAAAATGAAGGGCTGTC Human: GGAGATATTGGGCACAGTTGTGTAAGCATTT------TACTAGGATTTCAGTAGAAGGAAGAAAATGAAGGGCTGTC Cluster: [ ] Orangutan: GGAGATCTTAGGCACAGTTGTGTAAGCATTT------TACTAGGGTTTCAGTAGAAGGAAGAAAATGAAGGGCTGTC Chimp > Gorilla --------------- chrX:38820345-38820355 Template switch process: F1: L ATCAAATTGCTGACTATGATGGAGATCTTGGGCACAGTTGTTT 1 F3: 4 ACTAGGGTTTCAGTAGAAGGAAGAAAATGAAGGGCTGTCTAGAAACT R RF: ATCAAATTGCTGACTATGATGGAGATCTTGGGCACAGTTGTATAAGCATTTTACTAGGATTTCAGTAGAAGGAAGAAAATGAAGGGCTGTCTAGAAACT RR: TAGTTTAACGACTGATACTACCTCTAGAACCCGTGTCAACATATTCGTAAAATGATCCTAAAGTCATCTTCCTTCTTTTACTTCCCGACAGATCTTTGA F2: 3 AAGTCATCTTC 2 Unidirectional alignment (log-probability: -42.5) AAATTGCTGACTATGATGGAGATCTTGGGCACAGTTG---------TTTcttctactgaaACTAGGgTTTCAGTAGAAGGAAGAAAATGAAGGGCTGTCT AAATTGCTGACTATGATGGAGATCTTGGGCACAGTTGTATAAGCATTTT-----------ACTAGGATTTCAGTAGAAGGAAGAAAATGAAGGGCTGTCT Template switch alignment (log-probability: -28.4) AAATTGCTGACTATGATGGAGATCTTGGGCACAGTTGTtT|CTTCTACTGAA|ACTAGGgTTTCAGTAGAAGGAAGAAAATGAAGGGCTGTCT AAATTGCTGACTATGATGGAGATCTTGGGCACAGTTGTAT|CTTCTACTGAA|ACTAGGATTTCAGTAGAAGGAAGAAAATGAAGGGCTGTCT ========== Event 3951 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: TTACAGAATAAGGTCTTAGCATGTACATCTGTA-CATGTACATCTAAAACCAAGTAAATAG Chimp: TTACAGAATAAGGTCTTAGCATGTACAGA--TACTAGCTGAATCTAAAACCAAGTAAATAG Gorilla: TTACAGAATAAGGTCTTAGCATGTACAGA--TACTAGCTGAATCTAAAACCAAGTAAATAG ↓ 4 3 1 2 Human: TTACAGAATAAGGTCTTAGCATGTACATCTGTA-CATGTACATCTAAAACCAAGTAAATAG Cluster: [ ] Orangutan: TTACAGAATAAGGTCTTAGCATGTACAGA--TACTGGCTGAATCTAAAACCAAGTAAATAG Gorilla > Human --------------- chrX:117033766-117033771 Template switch process: F1: L GGGAAGCAGGTGAATTACAGAATAAGGTCTTAGCATGTACA 1 F3: 4 CATGTAC-------------ATCTAAAACCAAGTAAATAGTGTGGCCTGATGAATGGCCT R RF: GGGAAGCAGGTGAATTACAGAATAAGGTCTTAGCATGTACAGATACTAGCTGAATCTAAAACCAAGTAAATAGTGTGGCCTGATGAATGGCCT RR: CCCTTCGTCCACTTAATGTCTTATTCCAGAATCGTACATGTCTATGATCGACTTAGATTTTGGTTCATTTATCACACCGGACTACTTACCGGA F2: 3 ATGTCT 2 Unidirectional alignment (log-probability: -39.9) GGAAGCAGGTGAATTACAGAATAAGGTCTTAGCATGTAC------------AtctgtacatgtacATCTAAAACCAAGTAAATAGTGTGGCCTGATGA GGAAGCAGGTGAATTACAGAATAAGGTCTTAGCATGTACAGATACTAGCTGA-------------ATCTAAAACCAAGTAAATAGTGTGGCCTGATGA Template switch alignment (log-probability: -27.1) GGAAGCAGGTGAATTACAGAATAAGGTCTTAGCATGTACA|TCTGTA|CATGTAC-------------ATCTAAAACCAAGTAAATAGTGTGGCCTGATGA GGAAGCAGGTGAATTACAGAATAAGGTCTTAGCATGTACA|TCTGTA|CATGTACAGATACTAGCTGAATCTAAAACCAAGTAAATAGTGTGGCCTGATGA ========== Event 3952 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: GAAGGGATGTCTACCTCCACACTCCAGTATGGTTATACTGGAAAATGGGGAAGCAATCCCCC ↑ 3 4 2 Chimp: GAAGGGATGTCTACCTCCACAAAC---------CATACTGGAAAATGGGGAAGCAATCCCCC Gorilla: GAAGGGAGGTCTGCCTCCACAAAC---------CATACTGGAAAATGGGGAAGCAATCCCCC Human: GAAGGGATGTCTACCTCCACACTCCAGTATGGTTATACTGGAAAATGGGGAAGCAATCCCCC Cluster: [ ] Orangutan: GAGGGGAAGTCTACCTCCACAAAC---------CATACTGGAAAATGGGAAAGCAATCCCCC Chimp > Human ------------- chrX:116615988-116615999 Template switch process: F1: L TGACCCCAACCCTGAGTGTGGAAGGGATGTCTACCTCCACAC 1 F3: 4 ATACTGGAAAATGGGGAAGCAATCCCCCAAGGGAAAAATC R RF: TGACCCCAACCCTGAGTGTGGAAGGGATGTCTACCTCCACAAACCATACTGGAAAATGGGGAAGCAATCCCCCAAGGGAAAAATC RR: ACTGGGGTTGGGACTCACACCTTCCCTACAGATGGAGGTGTTTGGTATGACCTTTTACCCCTTCGTTAGGGGGTTCCCTTTTTAG F2: 3 TTGGTATGACCT 2 Unidirectional alignment (log-probability: -35.9) ACCCCAACCCTGAGTGTGGAAGGGATGTCTACCTCCACActCCagtatggttATACTGGAAAATGGGGAAGCAATCCCCCAAGGGAAAAATC ACCCCAACCCTGAGTGTGGAAGGGATGTCTACCTCCACAAACC---------ATACTGGAAAATGGGGAAGCAATCCCCCAAGGGAAAAATC Template switch alignment (log-probability: -22.8) ACCCCAACCCTGAGTGTGGAAGGGATGTCTACCTCCACAc|TCCAGTATGGTT|ATACTGGAAAATGGGGAAGCAATCCCCCAAGGGAAAAATC ACCCCAACCCTGAGTGTGGAAGGGATGTCTACCTCCACAA|TCCAGTATGGTT|ATACTGGAAAATGGGGAAGCAATCCCCCAAGGGAAAAATC ========== Event 3953 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: ATATATAATACAGTTTTTAAAGTAACAAATTATCACTTGTTACTTTAAAGTAAACTAACTTAGTAG Chimp: Gorilla: atatataataCAGTTTCTAAAGTAACAAGTTATCACTGAAATACATAAAGTAAACTAACTTAGTAG ↓ 3 2 1 4 Human: ATATATAATACAGTTTTTAAAGTAACAAATTATCACTTGTTACTTTAAAGTAAACTAACTTAGTAG Cluster: [ ] Orangutan: ATATGTAATACAGTTTTTAAAGTAACAAGTTATCATTGAAATACATAAAGTACACTAACTTAGTAC Gorilla > Human --------------- chrX:41059246-41059253 Template switch process: F1: L TGGTATTTGAAATATATATAATACAGTTTTTAAAGTAACAAATTATCACT 1 F3: 4 TAAAGTAAACTAACTTAGTAGTAAGAATGATGTGAAAATA R RF: TGGTATTTGAAATATATATAATACAGTTTCTAAAGTAACAAGTTATCACTGAAATACATAAAGTAAACTAACTTAGTAGTAAGAATGATGTGAAAATA RR: ACCATAAACTTTATATATATTATGTCAAAGATTTCATTGTTCAATAGTGACTTTATGTATTTCATTTGATTGAATCATCATTCTTACTACACTTTTAT F2: 3 TTCATTGT 2 Unidirectional alignment (log-probability: -43.7) AATATATATAATACAGTTTtTAAAGTAACAAaTTATCACttgttactT--------TAAAGTAAACTAACTTAGTAGTAAGAATGATGTGAAAATA AATATATATAATACAGTTTCTAAAGTAACAAGTTATCAC--------TGAAATACATAAAGTAAACTAACTTAGTAGTAAGAATGATGTGAAAATA Template switch alignment (log-probability: -28) AATATATATAATACAGTTTtTAAAGTAACAAaTTATCACT|TGTTACTT|TAAAGTAAACTAACTTAGTAGTAAGAATGATGTGAAAATA AATATATATAATACAGTTTCTAAAGTAACAAGTTATCACT|TGTTACTT|TAAAGTAAACTAACTTAGTAGTAAGAATGATGTGAAAATA ========== Event 3954 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AAGCCCTAAGGAAAATATTTATGAACAGTCTAAAAGAATAATAATGCTAATTTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT--GT----------TC------AAACTATATGTTATGGTTAGAGTGTC Chimp: AAGCCCTAAGGAAAACATTTATGAACAGTCTAAAAGAATAATAATGCTAATTTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT--GT----------TC------AAACTACATGTTATGGTTAGAGTGTC Gorilla: AAGCCCTAAGGAAAATATTTATGAACAGTCTAAAAGAAGAATAATGCTAATTTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTATATGTTCCTTTATAGTCAAAGGTATACTGTATGTTATGGTTAGAGTGTC ↓ 3 2 1 4 Human: AAGCCCTAAGGAAAATATTTATGAACAGTCTAAAAGAATAATAATGCTAATTTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT--GT----------TC------AAACTATATGTTATGGTTAGAGTGTC Cluster: [ ] Orangutan: AAGCCCTAAGGAAAATATTTATGAACAGTCTAAAAGAAGAATAATGCTAATTTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT--GT----------TC------AAACTATATGTTATGGTTAGAGTGTC Gorilla > Human --------------- chrX:42323944-42323950 Template switch process: F1: L TTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT 1 F3: 4 CTATATGTTATGGTTAGAGTGTCCCTGAAGCTTAGAAGAAAAA R RF: TATGAACAGTCTAAAAGAAGAATAATGCTAATTTATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTATATGTTCCTTTATAGTCAAAGGTATACTGTATGTTATGGTTAGAGTGTCCCTGAAGCTTAGAAGAAAAA RR: ATACTTGTCAGATTTTCTTCTTATTACGATTAAATATTCCATTTAACCCTTTACTCTCAGTTTCCTTATAATATACAAGGAAATATCAGTTTCCATATGACATACAATACCAATCTCACAGGGACTTCGAATCTTCTTTTT F2: 3 AAACTTG 2 Unidirectional alignment (log-probability: -42.3) TATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTATgT------------TCAA------ACTaTATGTTATGGTTAGAGTGTCCCTGAAGCTTAGAAGAA TATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTATATGTTCCTTTATAGTCAAAGGTATACTGTATGTTATGGTTAGAGTGTCCCTGAAGCTTAGAAGAA Template switch alignment (log-probability: -27.7) TATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT|GTTCAaA|CTaTATGTTATGGTTAGAGTGTCCCTGAAGCTTAGAAGAA TATAAGGTAAATTGGGAAATGAGAGTCAAAGGAATATTAT|GTTCATA|CTGTATGTTATGGTTAGAGTGTCCCTGAAGCTTAGAAGAA ========== Event 3955 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: GAGTAGGAGGACAATTTACAAACTG---CCTGTCCATAGGACATTCTCTGCT Chimp: GAGTAGGAGGACAATTTACAAACTG---CCTGTCCATAGGGCATTCTCTGGT ↓ 3 1 2 4 Gorilla: GAGTAGGAGGACAATTTACAAACGGCAGTTTGTCCATAGGACATTCTCTGCT ↑ 3 1 2 4 Human: GAGTAGGAGGACAATTTACAAACTG---CCTGTCCATAGGACATTCTCTGCT Cluster: [ ] Orangutan: GAGTAGGAGGACAATTTACAAACTG---CCTGTCCATAGGACATTCTCTGCT Human > Gorilla --------------- chrX:42455221-42455228 Template switch process: F1: L TAAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAAC 1 F3: 4 GTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC R RF: TAAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAACTGCCTGTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC RR: ATTTTTGATAACTTTCTCCTCATCCTCCTGTTAAATGTTTGACGGACAGGTATCCTGTAAGAGACGATCCCCTCTTAATATACTG F2: 3 TTTGACGG 2 Unidirectional alignment (log-probability: -26.3) AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAACgGCagttTGTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAACTGCC---TGTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC Template switch alignment (log-probability: -16.7) AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAAC|GGCAGTTT|GTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAAC|GGCAGTTT|GTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC Chimp > Gorilla --------------- chrX:42455221-42455228 Template switch process: F1: L TAAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAAC 1 F3: 4 GTCCATAGGACATTCTCTGCTAGGGGAGAATTATATGAC R RF: TAAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAACTGCCTGTCCATAGGGCATTCTCTGGTAGGGGAGAATTATATGAC RR: ATTTTTGATAACTTTCTCCTCATCCTCCTGTTAAATGTTTGACGGACAGGTATCCCGTAAGAGACCATCCCCTCTTAATATACTG F2: 3 TTTGACGG 2 Unidirectional alignment (log-probability: -37.3) AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAACgGCagttTGTCCATAGGaCATTCTCTGcTAGGGGAGAATTATATGAC AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAACTGCC---TGTCCATAGGGCATTCTCTGGTAGGGGAGAATTATATGAC Template switch alignment (log-probability: -27.8) AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAAC|GGCAGTTT|GTCCATAGGaCATTCTCTGcTAGGGGAGAATTATATGAC AAAAACTATTGAAAGAGGAGTAGGAGGACAATTTACAAAC|GGCAGTTT|GTCCATAGGGCATTCTCTGGTAGGGGAGAATTATATGAC ========== Event 3956 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: AAGGAAAGTAGAGCCACCTTCGCAAGCATTTA----CAGTGGGTAAGTACTTATGTATT Chimp: AAGGAAAGTAGAGCCACCTTCGCAAGCATTTA----CAGTGGGTAAGTACTTATGTATT Gorilla: AAGGAAAGTAGAGCCACCTTCACAAGCATTAAATGCTTGTGGGTAAGTATTTATGTATT ↑ 3 12 4 Human: AAGGAAAGTAGAGCCACCTTCGCAAGCATTTA----CAGTGGGTAAGTACTTATGTATT Cluster: [ ] Orangutan: AAGGAAAGTAGAGCCACCTTCACAAGCATTTA----CAGTGGGTAAGTACTTATGTATT Human > Gorilla --------------- chrX:113236152-113236159 Template switch process: F1: L AAGAAAACATTTGTACTGAGAAGGAAAGTAGAGCCACCTTCACAAGCATT 1 F3: 4 GTGGGTAAGTATTTATGTATTTGTGATTTATTTGCTTATA R RF: AAGAAAACATTTGTACTGAGAAGGAAAGTAGAGCCACCTTCGCAAGCATTTACAGTGGGTAAGTACTTATGTATTTGTGATTTATTTGCTTATA RR: TTCTTTTGTAAACATGACTCTTCCTTTCATCTCGGTGGAAGCGTTCGTAAATGTCACCCATTCATGAATACATAAACACTAAATAAACGAATAT F2: 3 TTCGTAAA 2 Unidirectional alignment (log-probability: -42) TTGTACTGAGAAGGAAAGTAGAGCCACCTTCaCAAGCATT---AaatgcttGTGGGTAAGTAtTTATGTATTTGTGATTTATTTGCTTATA TTGTACTGAGAAGGAAAGTAGAGCCACCTTCGCAAGCATTTACA-------GTGGGTAAGTACTTATGTATTTGTGATTTATTTGCTTATA Template switch alignment (log-probability: -28) TTGTACTGAGAAGGAAAGTAGAGCCACCTTCaCAAGCATT|AAATGCTT|GTGGGTAAGTAtTTATGTATTTGTGATTTATTTGCTTATA TTGTACTGAGAAGGAAAGTAGAGCCACCTTCGCAAGCATT|AAATGCTT|GTGGGTAAGTACTTATGTATTTGTGATTTATTTGCTTATA ========== Event 3957 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: CATGTAAAGCTTACCTGCAAACCATGAGA--------------------------------------TTCAAATAAACAAATCCGTGTGCAC ↓ 3 4 1 2 Chimp: CATGTAAAGCTTACCTGCAAACCATGAGA-------------------TTGTTGAATCTCATGGTTGTTCAAATAAACAAATCCGTGTGCAC Gorilla: CATGTAAAGCTTACCTGCAAACCATGAGATTGTTGAATCTCATGGTTG-------------------TTCAAATAAACAAATCTGTGTGCAC Human: CATGTAAAGCTTACCTGCAAACCATGAGA--------------------------------------TTCAAATAAACAAATCCGTGTGCAC Cluster: [ ] Orangutan: CATGTAAAGCTTACCTGCAAACCATGAGATTGTTGAATCTCATGGTTG-------------------TTCAAATAAACAAATCCGTGTGCAC Human > Chimp ------------- chrX:111613907-111613921 Template switch process: F1: L GGGAGTTTCTTCCATGTAAAGCTTACCTGCAAACCATGAGATTG 1 F3: 4 GTTCAAATAAACAAATCCGTGTGCACATGTAGGAACTCATT R RF: GGGAGTTTCTTCCATGTAAAGCTTACCTGCAAACCATGAGATTCAAATAAACAAATCCGTGTGCACATGTAGGAACTCATT RR: CCCTCAAAGAAGGTACATTTCGAATGGACGTTTGGTACTCTAAGTTTATTTGTTTAGGCACACGTGTACATCCTTGAGTAA F2: 3 TTGGTACTCTAAGTT 2 Unidirectional alignment (log-probability: -38.2) GTTTCTTCCATGTAAAGCTTACCTGCAAACCATGAGATtgttgaatctcatggttgtTCAAATAAACAAATCCGTGTGCACATGTAGGAACTCAT GTTTCTTCCATGTAAAGCTTACCTGCAAACCATGAGAT-------------------TCAAATAAACAAATCCGTGTGCACATGTAGGAACTCAT Template switch alignment (log-probability: -29.2) GTTTCTTCCATGTAAAGCTTACCTGCAAACCATGAGATTg|TTGAATCTCATGGTT|gTTCAAATAAACAAATCCGTGTGCACATGTAGGAACTCAT GTTTCTTCCATGTAAAGCTTACCTGCAAACCATGAGATTC|TTGAATCTCATGGTT|ATTCAAATAAACAAATCCGTGTGCACATGTAGGAACTCAT ========== Event 3958 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TTTATTTCCCATGTGAATGCACATGCCCACTGCATGTGcacac--acac----acacacacacgc Chimp: tttatttcccatgtgaatgcacatgcccactgcatgtgcacac--ac--acacacacacacacgc Gorilla: TTTATTTCCCATGTGAATGCACATGCAGTGGGCATGTGcacac----------acacacacacgc ↑ 3 1 2 4 Human: TTTATTTCCCATGTGAATGCACATGCCCACTGCATGTGcacac--acac----acacacacacgc Cluster: [ ] Orangutan: TTTATTTCCCATTTGAATGCACATGCCGGCTGTATGTGcacacac--------acacacacac-- Human > Gorilla --------------- chrX:111159947-111159958 Template switch process: F1: L TCATCCTTTGCGTGATTTATTTCCCATGTGAATGCACATGC 1 F3: 4 CACACACACACACACGCACACGCCTGCTG R RF: TCATCCTTTGCATGATTTATTTCCCATGTGAATGCACATGCCCACTGCATGTGCACACACACACACACACACGCACACGCGTGCTG RR: AGTAGGAAACGTACTAAATAAAGGGTACACTTACGTGTACGGGTGACGTACACGTGTGTGTGTGTGTGTGTGCGTGTGCGCACGAC F2: 3 GTGTACGGGTGA 2 Unidirectional alignment (log-probability: -48.1) CATCCTTTGCgTGATTTATTTCCCATGTGAATGCACATG---------------CAgtgggcatgtgCACACACACACACACGCACACGCcTGCTG CATCCTTTGCATGATTTATTTCCCATGTGAATGCACATGCCCACTGCATGTGCACA-----------CACACACACACACACGCACACGCGTGCTG Template switch alignment (log-probability: -28) CATCCTTTGCgTGATTTATTTCCCATGTGAATGCACATGC|AGTGGGCATGTG|CACACACACACACACGCACACGCcTGCTG CATCCTTTGCATGATTTATTTCCCATGTGAATGCACATGC|AGTGGGCATGTG|CACACACACACACACGCACACGCGTGCTG ========== Event 3959 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: GGG---GG--TGGGGGATCCCAAATACTTACAGGGGTAAGTAACTGAGTGATTGGTACTTTTGCA Chimp: GGG---GG--TGGGGGATCCC------------CTGTAAGTAACTGAGTGATTGGTACTTTTGCA Gorilla: GGG---GG--TGGGGGATCCC------------CTGTAAGTAACTGAGTGATTGGTACTTTTGCA ↓ 3 1 4 2 Human: GGG---GG--TGGGGGATCCCAAATACTTACAGGGGTAAGTAACTGAGTGATTGGTACTTTTGCA Cluster: [ ] Orangutan: GGGGTGGGTTGGGGGGATCCC------------CTGTAAGTAACTGAGTGATTGGTACTTTTGCA Gorilla > Human --------------- chrX:47092257-47092270 Template switch process: F1: L GTGATATGGCTATTTCTTTTATTTTGGGGGTGGGGGATCCC 1 F3: 4 GTAAGTAACTGAGTGATTGGTACTTTTGCATACTTCCAAA R RF: GTGATATGGCTATTTCTTTTATTTTGGGGGTGGGGGATCCCCTGTAAGTAACTGAGTGATTGGTACTTTTGCATACTTCCAAA RR: CACTATACCGATAAAGAAAATAAAACCCCCACCCCCTAGGGGACATTCATTGACTCACTAACCATGAAAACGTATGAAGGTTT F2: 3 GGGACATTCATAAA 2 Unidirectional alignment (log-probability: -37.9) TGATATGGCTATTTCTTTTATTTTGGGGGTGGGGGATCCCaaataCTtacagggGTAAGTAACTGAGTGATTGGTACTTTTGCATACTTCCAAA TGATATGGCTATTTCTTTTATTTTGGGGGTGGGGGATCCC-----CT-------GTAAGTAACTGAGTGATTGGTACTTTTGCATACTTCCAAA Template switch alignment (log-probability: -28.5) TGATATGGCTATTTCTTTTATTTTGGGGGTGGGGGATCCC|AaaTACTTACAGGG|GTAAGTAACTGAGTGATTGGTACTTTTGCATACTTCCAAA TGATATGGCTATTTCTTTTATTTTGGGGGTGGGGGATCCC|AGTTACTTACAGGG|GTAAGTAACTGAGTGATTGGTACTTTTGCATACTTCCAAA ========== Event 3960 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: GGGGTTCATTAGAGCCTACCCTTCATTTTCATGAAGGGTACAACATGGTTTCAGATGATCC ↑ 3 1 24 Chimp: GGGGTTCATTAGAGCCTACCCTTC------ATGA-AAGTATAACATGGTTTCAGATGATCC Gorilla: GGGGTTCATTAGAGCCTACCCTTC------ATGA-AAGTACAACATGGTTTCAGATGATCC ↓ 3 1 24 Human: GGGGTTCATTAGAGCCTACCCTTCATTTTCATGAAGGGTACAACATGGTTTCAGATGATCC Cluster: [ ] Orangutan: Chimp > Human ------------- chrX:47420589-47420599 Template switch process: F1: L GCCCTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT 1 F3: 4 GTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGTACAG R RF: GCCCTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCATGAAAGTATAACATGGTTTCAGATGATCCTGTATTAGCTACCGGTACAG RR: CGGGACCGTATTACGGACCCCAAGTAATCTCGGATGGGAAGTACTTTCATATTGTACCAAAGTCTACTAGGACATAATCGATGGCCATGTC F2: 3 GGAAGTACTTT 2 Unidirectional alignment (log-probability: -41.6) CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT-------TttcatgaagggtacAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCATGAAAGTAT--------------AACATGGTTTCAGATGATCCTGTATTAGCTACCGGT Template switch alignment (log-probability: -22.8) CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT|TTTCATGAAGG|GTAcAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT|TTTCATGAAGG|GTATAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT Gorilla > Human --------------- chrX:47420589-47420599 Template switch process: F1: L GCCCTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT 1 F3: 4 GTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT R RF: GCCCTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCATGAAAGTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT RR: CGGGACCGTATTACGGACCCCAAGTAATCTCGGATGGGAAGTACTTTCATGTTGTACCAAAGTCTACTAGGACATAATCGATGGCCA F2: 3 GGAAGTACTTT 2 Unidirectional alignment (log-probability: -35.2) CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCATtttcatgaagG---GTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT----------GAAAGTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT Template switch alignment (log-probability: -17.2) CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT|TTTCATGAAGG|GTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT CTGGCATAATGCCTGGGGTTCATTAGAGCCTACCCTTCAT|TTTCATGAAGG|GTACAACATGGTTTCAGATGATCCTGTATTAGCTACCGGT ========== Event 3961 ========== Phylogenetic placement: ILS consistent Significant comparisons: 6 Detected in comparisons: 16 Multiple sequence alignment: Human: acactctactcaaagatcagtcaatcTACTGATTGACAATCTACTCAAAGATCAGACTAAGACCA Chimp: ACACTCTACTCAAAGATCAGTCAAT---------------CTACTCAAAGATCAGACTAAGACCA ↓ 3 4 2 1 Gorilla: ATACTCTACTCAAAGATCAGTCAATCTACTGATTGACAGTCTACTCAAAGATCAGACTAAGACCA Human: acactctactcaaagatcagtcaatcTACTGATTGACAATCTACTCAAAGATCAGACTAAGACCA Cluster: [ ] Orangutan: acactctactcaaagatcagt--------------------------------------tgaccA Chimp > Gorilla --------------- chrX:106840701-106840707 Template switch process: F1: L CCATTGTATATTCTTGATACTCTACTCAAAGATCAGTCAATCTACT 1 F3: 4 AGTCTACTCAAAGATCAGACTAAGACCATATGTCTTAGTCTGT R RF: CCATTGTATATTCTTGACACTCTACTCAAAGATCAGTCAATCTACTCAAAGATCAGACTAAGACCATATGTCTTAGTCTGT RR: GGTAACATATAAGAACTGTGAGATGAGTTTCTAGTCAGTTAGATGAGTTTCTAGTCTGATTCTGGTATACAGAATCAGACA F2: 3 CAGTTAG 2 Unidirectional alignment (log-probability: -38) TATATTCTTGAtACTCTACTCAAAGATCAGTCAAtctactgattgacagTCTACTCAAAGATCAGACTAAGACCATATGTCTTAGTC TATATTCTTGACACTCTACTCAAAGATCAGTCAA---------------TCTACTCAAAGATCAGACTAAGACCATATGTCTTAGTC Template switch alignment (log-probability: -27.9) TATATTCTTGAtACTCTACTCAAAGATCAGTCAATCTACT|GATTGAC|AgTCTACTCAAAGATCAGACTAAGACCATATGTCTTAGTC TATATTCTTGACACTCTACTCAAAGATCAGTCAATCTACT|GATTGAC|AATCTACTCAAAGATCAGACTAAGACCATATGTCTTAGTC ========== Event 3962 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: ATTTTAATTCAAACAAGTATTTCAGATTAATTCAACAAGAATGCCACTCGAATTCATTC-TAATTTAACATTAATCAAGATTaaa-a Chimp: ATTTTAATTCAAACAAGTATTCCAGATAAAT-TAGAATGAATTCGAGTGGCATTCTTGTTGAATTAAACATTAATCAAGATTaaaaa Gorilla: ATTTTAATTCAAACAAGTATTCCAGATAAAT-TAGAATGAATTCGAGTGGCATTCTTGTTGAATTAAACATTAATCAAGATTTaaaa ↓ 13 24 Human: ATTTTAATTCAAACAAGTATTTCAGATTAATTCAACAAGAATGCCACTCGAATTCATTC-TAATTTAACATTAATCAAGATTaaa-a Cluster: [ ] Orangutan: --------------------------------------------------------------------------------------- Gorilla > Human --------------- chrX:106098713-106098750 Template switch process: F1: L AGATATGAATTTGAAAGGACATTTTAATTCAAACAAGTATTTCAGAT 1 F3: 4 AACATTAATCAAGA-TTAAAAAAAAGAATAAATGGTGTTC R RF: AGATATGAATTTGAAAGGACATTTTAATTCAAACAAGTATTCCAGATAAATTAGAATGAATTCGAGTGGCATTCTTGTTGAATTAAACATTAATCAAGATTTAAAAAAAAGAATAAATGGTGTTC RR: TCTATACTTAAACTTTCCTGTAAAATTAAGTTTGTTCATAAGGTCTATTTAATCTTACTTAAGCTCACCGTAAGAACAACTTAATTTGTAATTAGTTCTAAATTTTTTTTCTTATTTACCACAAG F2: 3 TTTAATCTTACTTAAGCTCACCGTAAGAACAACTTAAT 2 Unidirectional alignment (log-probability: -84.8) AATTTGAAAGGACATTTTAATTCAAACAAGTATTtCAGATtAATTcaacaAGAATgccactcGAATT-------CATTCT-----AATTtAACATTAATCAAGA-TTAAAAAAAAGAATAAATGGTGTTC AATTTGAAAGGACATTTTAATTCAAACAAGTATTCCAGATAAATT-----AGAAT-------GAATTCGAGTGGCATTCTTGTTGAATTAAACATTAATCAAGATTTAAAAAAAAGAATAAATGGTGTTC Template switch alignment (log-probability: -36) AATTTGAAAGGACATTTTAATTCAAACAAGTATTtCAGAT|TAATTCAACAAGAATGCCACTCGAATTCATTCTAATTT|AACATTAATCAAGA-TTAAAAAAAAGAATAAATGGTGTTC AATTTGAAAGGACATTTTAATTCAAACAAGTATTCCAGAT|TAATTCAACAAGAATGCCACTCGAATTCATTCTAATTT|AACATTAATCAAGATTTAAAAAAAAGAATAAATGGTGTTC ========== Event 3963 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CTCCACTCCTCCTTACAGTAAGTATCAAGTAAAGATACTTGACAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTT ↑ 4 3 1 2 Chimp: CTCCACTCCTCCTTACAGTAAGTA-----------------------TCAAGTATCTTTCTAGTTCTCCATTGCTGTT Gorilla: CTCCACGCCTCCTTACAGTAAGTA-----------------------TCAAGTATCTTTCTAGTTCTCCATTGCTGTT ↓ 4 3 1 2 Human: CTCCACTCCTCCTTACAGTAAGTATCAAGTAAAGATACTTGACAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTT Cluster: [ ] Orangutan: TTCCACTCCTCCTTACAGTAAGTA-----------------------TCAAGTATCTTTCTAGTTCTCCACTGTTGCT Chimp > Human ------------- chrX:105524885-105524895 Template switch process: F1: L TGGATCTCATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAAGTA 1 F3: 4 CAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAAAAAAA R RF: CGGATCTCATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAAAAAAA RR: GCCTAGAGTAGATTCTTGAGGTGAGGAGGAATGTCATTCATAGTTCATAGAAAGATCAAGAGGTAACGACAAAGTTTTTTT F2: 3 AGTTCATAGAA 2 Unidirectional alignment (log-probability: -58.6) ATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAAgtaaagatacttgacagtatcaaGTATCTTTCTAGTTCTCCATTGCTGTTTCAA ATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAA-----------------------GTATCTTTCTAGTTCTCCATTGCTGTTTCAA Template switch alignment (log-probability: -28.9) ATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAAGTA|AAGATACTTGA|cAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAA ATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAAGTA|AAGATACTTGA|AAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAA Gorilla > Human --------------- chrX:105524885-105524895 Template switch process: F1: L TGGATCTCATCTAAGAACTCCACTCCTCCTTACAGTAAGTATCAAGTA 1 F3: 4 CAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAAAA R RF: TGGATCTCATCTAAGAACTCCACGCCTCCTTACAGTAAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAAAA RR: ACCTAGAGTAGATTCTTGAGGTGCGGAGGAATGTCATTCATAGTTCATAGAAAGATCAAGAGGTAACGACAAAGTTTT F2: 3 AGTTCATAGAA 2 Unidirectional alignment (log-probability: -56.3) ATCTAAGAACTCCACtCCTCCTTACAGTAagtatcaagtaaagatacttgacAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAA ATCTAAGAACTCCACGCCTCCTTACAGTA-----------------------AGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAA Template switch alignment (log-probability: -28.4) ATCTAAGAACTCCACtCCTCCTTACAGTAAGTATCAAGTA|AAGATACTTGA|cAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAA ATCTAAGAACTCCACGCCTCCTTACAGTAAGTATCAAGTA|AAGATACTTGA|AAGTATCAAGTATCTTTCTAGTTCTCCATTGCTGTTTCAA ========== Event 3964 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: CCAGCTCTCACCTGGGAAAGC----TGTCCCTG-----GGATCCTCAGACATACGAATTCCTTTTTTCTCTTTATCCCCCTCTACATGAAAtccttcctctgctcttattcctcttccatcacctgctgtttctgctccttctcct Chimp: CCAGCTCTCACCTGGGAAAGC----TGTCCCTG-----GGATCCTCAGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACATGAAATCCTTCCTCTGCTCTTATTCCTCTTCCATCACCTGCTGTTTCTGCTCCTTCTCCT ↓ 1 4 3 2 Gorilla: CCAGCTCTCACCTGGGAAAGC--------TCAG----------GTGAGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACATGAAATCCTTCCTCTGCTCTTATTCCTCTTCCATCACCTGCTGTTTCTGCTCCTTCTCCT ↑ 1 4 3 2 Human: CCAGCTCTCACCTGGGAAAGC----TGTCCCTG-----GGATCCTCAGACATACGAATTCCTTTTTTCTCTTTATCCCCCTCTACATGAAAtccttcctctgctcttattcctcttccatcacctgctgtttctgctccttctcct Cluster: [ ] Orangutan: CCAGCTCTCACCTGGGAAAGCAGTC----CCTGGAATC-----CTCAGACATACAAATTCCTTTCTTCTCTTTATTCCCCTCTACATGAAATCCTTCCTCTGCTCTTATTCCTCTTCCATCACCTGCTCTTTCTGCTCCTTCTCCT Human > Gorilla --------------- chrX:51674750-51674755 Template switch process: F1: L GAAACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCT 1 F3: 4 AGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACATGAAATCCTTCCTCTGCTC R RF: GAAACACAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCTGTCCCTGGGATCCTCAGACATACGAATTCCTTTTTTCTCTTTATCCCCCTCTACATGAAATCCTTCCTCTGCTCTTATTCCTCTTCCATCACCTG RR: CTTTGTGTCTTATCAACTTGGGTCGAGAGTGGACCCTTTCGACAGGGACCCTAGGAGTCTGTATGCTTAAGGAAAAAAGAGAAATAGGGGGAGATGTACTTTAGGAAGGAGACGAGAATAAGGAGAAGGTAGTGGAC F2: 3 GTGGAC 2 Unidirectional alignment (log-probability: -45.4) AACAgAGAATAGTTGAACCCAGCTCTCACCTGGGAAAG--------------CTCaggtgAGACATACaAATTCCTTTcTTCTCTTTATCCCCCTCTACA AACACAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCTGTCCCTGGGATCCTC-----AGACATACGAATTCCTTTTTTCTCTTTATCCCCCTCTACA Template switch alignment (log-probability: -33.5) AACAgAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCT|CAGGTG|AGACATACaAATTCCTTTcTTCTCTTTATCCCCCTCTACA AACACAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCT|CAGGTG|AGACATACGAATTCCTTTTTTCTCTTTATCCCCCTCTACA Chimp > Gorilla --------------- chrX:51674750-51674755 Template switch process: F1: L GAAACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCT 1 F3: 4 AGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACA R RF: GAAACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCTGTCCCTGGGATCCTCAGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACATGAAATCCTTCCTCTGCTCTTATTCCTCTTCCATCACCTG RR: CTTTGTCTCTTATCAACTTGGGTCGAGAGTGGACCCTTTCGACAGGGACCCTAGGAGTCTGTATGTTTAAGGAAAGAAGAGAAATAGGGGGAGATGTACTTTAGGAAGGAGACGAGAATAAGGAGAAGGTAGTGGAC F2: 3 GTGGAC 2 Unidirectional alignment (log-probability: -28.6) AACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAG--------------CTCaggtgAGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACA AACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCTGTCCCTGGGATCCTC-----AGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACA Template switch alignment (log-probability: -16.5) AACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCT|CAGGTG|AGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACA AACAGAGAATAGTTGAACCCAGCTCTCACCTGGGAAAGCT|CAGGTG|AGACATACAAATTCCTTTCTTCTCTTTATCCCCCTCTACA ========== Event 3965 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: CACTTGATATTTGTGGAATGATACAGACTTTTCTGTATC----------ATTCCACAGAATTGTTCAATTAGTTAAACAT ↓ 3 1 2 4 Chimp: CATTTGATATTTGTGGAATGATACAGAAAAGTCTGTATC--------------------ATTGTTCAATTAGTTAAACAT ↑ 3 1 2 4 Gorilla: CACTTGATATTTGTGGAATGATACAGACTTTTCTGTATCATTCCACAGA----------ATTGTTCAATTAGTTAAACAT Human: CACTTGATATTTGTGGAATGATACAGACTTTTCTGTATC----------ATTCCACAGAATTGTTCAATTAGTTAAACAT Cluster: [ ] Orangutan: Human > Chimp ------------- chrKV421461:47729-47740 Template switch process: F1: L AGTGTATGGGACAACATTTGATATTTGTGGAATGATACAGA 1 F3: 4 ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT R RF: AGTGTATGGGACAACACTTGATATTTGTGGAATGATACAGACTTTTCTGTATCATTCCACAGAATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT RR: TCACATACCCTGTTGTGAACTATAAACACCTTACTATGTCTGAAAAGACATAGTAAGGTGTCTTAACAAGTTAATCAATTTGTATTGAATAATCAAGACTTTA F2: 3 CTATGTCTGAAA 2 Unidirectional alignment (log-probability: -41.5) GTGTATGGGACAACAtTTGATATTTGTGGAATGATACAGAaaagTCTGTATCATT----------GTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT GTGTATGGGACAACACTTGATATTTGTGGAATGATACAGACTTTTCTGTATCATTCCACAGAATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT Template switch alignment (log-probability: -22.8) GTGTATGGGACAACAtTTGATATTTGTGGAATGATACAGA|AAAGTCTGTATC|ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT GTGTATGGGACAACACTTGATATTTGTGGAATGATACAGA|AAAGTCTGTATC|ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT Gorilla > Chimp --------------- chrKV421461:47729-47740 Template switch process: F1: L AGTGTATGGGACAACATTTGATATTTGTGGAATGATACAGA 1 F3: 4 ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT R RF: AGTATATGGGACAACACTTGATATTTGTGGAATGATACAGACTTTTCTGTATCATTCCACAGAATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT RR: TCATATACCCTGTTGTGAACTATAAACACCTTACTATGTCTGAAAAGACATAGTAAGGTGTCTTAACAAGTTAATCAATTTGTATTGAATAATCAAGACTTTA F2: 3 CTATGTCTGAAA 2 Unidirectional alignment (log-probability: -44.7) GTgTATGGGACAACAtTTGATATTTGTGGAATGATACAGAaaagTCTGTATC----------ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT GTATATGGGACAACACTTGATATTTGTGGAATGATACAGACTTTTCTGTATCATTCCACAGAATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT Template switch alignment (log-probability: -28.3) GTgTATGGGACAACAtTTGATATTTGTGGAATGATACAGA|AAAGTCTGTATC|ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT GTATATGGGACAACACTTGATATTTGTGGAATGATACAGA|AAAGTCTGTATC|ATTGTTCAATTAGTTAAACATAACTTATTAGTTCTGAAAT ========== Event 3966 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: ACAGAGATAGCTAGGACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGTGTCAGATAAGCTAGAATGCTTATAC ↑ 3 2 1 4 Chimp: ACAGAGATAGCTAGGACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGG--TTGGATAAGCTAGAATGCTTATAC Gorilla: Human: ACAGAGATAGCTAGGACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGTGTCAGATAAGCTAGAATGCTTATAC Cluster: [ ] Orangutan: ACAGAGATAGCTAGGACTATGACTGATTATTCACGTTACCCCTGCCCTTGTTGGTGTCAGATAAGCTAGAATGCTTATAC Chimp > Human ------------- chrX:55555880-55555883 Template switch process: F1: L GGACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGT 1 F3: 4 GATAAGCTAGAATGCTTATACTCTGGTCTTTCTGTTGAAC R RF: GGACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGTTGGATAAGCTAGAATGCTTATACTCTGGTCTTTCTGTTGAAC RR: CCTGATACTGACTAATAAGTGCAATGGTGACGGGAACAACCAACCTATTCGATCTTACGAATATGAGACCAGAAAGACAACTTG F2: 3 ACTG 2 Unidirectional alignment (log-probability: -25.5) ACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGG-TGtcaGATAAGCTAGAATGCTTATACTCTGGTCTTTCTGTTGAAC ACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGTTG---GATAAGCTAGAATGCTTATACTCTGGTCTTTCTGTTGAAC Template switch alignment (log-probability: -15.8) ACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGT|GTCA|GATAAGCTAGAATGCTTATACTCTGGTCTTTCTGTTGAAC ACTATGACTGATTATTCACGTTACCACTGCCCTTGTTGGT|GTCA|GATAAGCTAGAATGCTTATACTCTGGTCTTTCTGTTGAAC ========== Event 3967 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: AGCAATTGTTAGACTCACACAC-----------------------------------ATTGCCTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGAAATGTTTCTCTTTTCATGTTAGGAATTTCCCTTATAGGTGGAGAGTAAGATCTTTAAACCTTCTATGGGTAATGTCAAACACAGAGACCTAACT Chimp: AGCAATTGTTAGACTCACACAC-----------------------------------GTTGCCTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGAAATGTTTCTCTTTTCATGTTAGGAATTTCCCTTATAGGTGGAGAGTAAGATCTTTAAACCTTCTATGGGTAATGTCAAGCACAGAGACCTAACT Gorilla: AGCAATTGTTAGACTCACACAAGAACAGAATGGTAATTTAAAATTAACATTTTAATTCTGTTCTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGAAATGTTTCTCTTTTCATGTTAGGAATTTCCCTTATAGGTGGAGAGTAAGATCTTTAAACCTTCTATGGGTAATGTCAAACACAGAGACCTAACT ↓ 1 4 3 2 Human: AGCAATTGTTAGACTCACACAC-----------------------------------ATTGCCTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGAAATGTTTCTCTTTTCATGTTAGGAATTTCCCTTATAGGTGGAGAGTAAGATCTTTAAACCTTCTATGGGTAATGTCAAACACAGAGACCTAACT Cluster: [ ] Orangutan: AGCAATTGTTAGACTCACACAC-----------------------------------GTTGCCTCTTCAAGAACAGAATGTTAATTAAAAATTTGTGTATGAAATGTTTCTCTTTTCATGTTAGGAATTTCCCTTATAGGTGGAGAGTAAGATCTTTAAAACTTCTATGGGTAATGTCAAACACAGAGACCTAACT Gorilla > Human --------------- chrX:100674249-100674255 Template switch process: F1: L CCTGACCTTAAACTGCATTCAGCAATTGTTAGACTCACACA 1 F3: 4 TCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGA R RF: CCTGACCTTAAACTGCATTCAGCAATTGTTAGACTCACACAAGAACAGAATGGTAATTTAAAATTAACATTTTAATTCTGTTCTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGAAATGTTTCTCTTTTCATGTTAGGAATTTCCCTTATAGGTGGAGAGTAAGATCTTTAAACCTTCTATGGGTAATG RR: GGACTGGAATTTGACGTAAGTCGTTAACAATCTGAGTGTGTTCTTGTCTTACCATTAAATTTTAATTGTAAAATTAAGACAAGAGAAGTTCTTGTCTTACAATTAAATTTTAAACACATACTTTACAAAGAGAAAAGTACAATCCTTAAAGGGAATATCCACCTCTCATTCTAGAAATTTGGAAGATACCCATTAC F2: 3 CCGTTAC 2 Unidirectional alignment (log-probability: -31.4) CTGACCTTAAACTGCATTCAGCAATTGTTAGACTCACACA-----------------------------------------cattgcCTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGA CTGACCTTAAACTGCATTCAGCAATTGTTAGACTCACACAAGAACAGAATGGTAATTTAAAATTAACATTTTAATTCTGTT------CTCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGA Template switch alignment (log-probability: -22.1) CTGACCTTAAACTGCATTCAGCAATTGTTAGACTCACACA|CATTgCC|TCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGA CTGACCTTAAACTGCATTCAGCAATTGTTAGACTCACACA|CATTACC|TCTTCAAGAACAGAATGTTAATTTAAAATTTGTGTATGA ========== Event 3968 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TAGGTCTCCGTGACTTCAGGG--TGCAGCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG ↑ 1 4 3 2 Chimp: TAGGTCTCCGTGACTTCAGGGCGTGATTCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGATGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG ↓ 1 4 3 2 Gorilla: TAGGTCTCCGTGACTTCAGGG--TGCAGCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTTATTTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG Human: TAGGTCTCCGTGACTTCAGGG--TGCAGCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG Cluster: [ ] Orangutan: TAGGTCTCCGTGACTTCAGGG--TACAGCCAGGTTGGACCAGATAGACTGGGGTCCCCCGTGTGGCCAGGTGACCTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG Chimp > Human ------------- chrX:155422911-155422915 Template switch process: F1: L GGGACATGTTTTGGGGTCTCTAGGTCTCCGTGACTTCAGGG 1 F3: 4 CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA R RF: GGGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATTCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGATGAGAGGTTCTTCTGCA RR: CCCTGTACAAAACCCCAGAAATCCAGAGGCACTGAAGTCCCGCACTAAGGTCCAACCTGGTCTTTCTGACCCCAGGGGGCACACCGGTCCACTAAACCCCTGAGACCCAGAGGTTCCTACTCTCCAAGAAGACGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -33.2) GGACATGTTTTGGGGTCTcTAGGTCTCCGTGACTTCAGGG------TgcagCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATT----CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA Template switch alignment (log-probability: -21.9) GGACATGTTTTGGGGTCTcTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA Chimp > Gorilla --------------- chrX:155860686-155860690 Template switch process: F1: L GGGACATGTTTTGGGGTCCCTAGGTCTCCGTGACTTCAGGG 1 F3: 4 CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA R RF: GGGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATTCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGATGAGAGGTTCTTCTGCA RR: CCCTGTACAAAACCCCAGAAATCCAGAGGCACTGAAGTCCCGCACTAAGGTCCAACCTGGTCTTTCTGACCCCAGGGGGCACACCGGTCCACTAAACCCCTGAGACCCAGAGGTTCCTACTCTCCAAGAAGACGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -37.7) GGACATGTTTTGGGGTCccTAGGTCTCCGTGACTTCAGGG------TgcagCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATT----CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA Template switch alignment (log-probability: -27.4) GGACATGTTTTGGGGTCccTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA ========== Event 3969 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GCGAATTTTTTCTCCTTCTCACTGTCCCCAGGGACAGTGTCCCAGGGAAGGGACAGCCCT Chimp: Gorilla: GCGAATTTTTTCTCCTTCTCAGTGTCCCCAG----CATTTCCCAGGGAAGGGACAGCCCT ↓ 3 2 1 4 Human: GCGAATTTTTTCTCCTTCTCACTGTCCCCAGGGACAGTGTCCCAGGGAAGGGACAGCCCT Cluster: [ ] Orangutan: GTGAATTTTTTCTCCTTCTCACTGTCCCCAG----CATTTCCCAGGGAGGGGACAGCCCT Gorilla > Human --------------- chrX:804732-804739 Template switch process: F1: L TTTCACAACTGCGAATTTTTTCTCCTTCTCACTGTCCCCAG 1 F3: 4 TCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT R RF: TTTCACAACTGCGAATTTTTTCTCCTTCTCAGTGTCCCCAGCATTTCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT RR: AAAGTGTTGACGCTTAAAAAAGAGGAAGAGTCACAGGGGTCGTAAAGGGTCCCTTCCCTGTCGGGAAGGGTTAAGCTAGAGGGAA F2: 3 GTGACAGG 2 Unidirectional alignment (log-probability: -37.5) TTCACAACTGCGAATTTTTTCTCCTTCTCAcTGTCCCCAGggaCAgTgTCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT TTCACAACTGCGAATTTTTTCTCCTTCTCAGTGTCCCCAG---CA-TTTCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT Template switch alignment (log-probability: -27.8) TTCACAACTGCGAATTTTTTCTCCTTCTCAcTGTCCCCAG|GGACAgTG|TCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT TTCACAACTGCGAATTTTTTCTCCTTCTCAGTGTCCCCAG|GGACACTG|TCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT ========== Event 3970 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TTTATTCTTCTAAATAACAAGAAC-------------------------------------------------------------------------------------------------------ATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAACATGGTAACTGAAAGTAAACCAGTTTGACATTTTGACTGAAAT ↓ 4 3 1 2 Chimp: TTTATTCTTGTAAATAACAAGAACATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAACATGGTACTGGTTTACTTTCAGTTACCATGTTGTTACTATGGTTCTTCAGTTGTAGTTAGAACATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAACATGGTAACTGAAAGTAAACCAGTTTGACATTTCGACTGAAAT Gorilla: TTTATTCTTCTAAATAACAAGAAC-------------------------------------------------------------------------------------------------------ATAATTTGTTACAATTACACCTGAAGAACCATAGTAACAACATGGTAACTGAAAGTAAACCAGTTTGACATTTTGACTGAAAT Human: TTTATTCTTCTAAATAACAAGAAC-------------------------------------------------------------------------------------------------------ATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAACATGGTAACTGAAAGTAAACCAGTTTGACATTTTGACTGAAAT Cluster: [ ] Orangutan: Human > Chimp ------------- chrX:93538893-93538943 Template switch process: F1: L TCTAAAAAATCAAGTTTTTTATTCTTGTAAATAACAAGAACATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAACATGGTA 1 F3: 4 AGAACATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAA R RF: TCTAAAACATCAAGTTTTTTATTCTTCTAAATAACAAGAACATAATTTGTTACAACTACAACTGAAGAACCATAGTAACAACATGGTACATGGTAACTGAAAGTAAACCAG RR: AGATTTTGTAGTTCAAAAAATAAGAAGATTTATTGTTCTTGTATTAAACAATGTTGATGTTGACTTCTTGGTATCATTGTTGTACCATGTACCATTGACTTTCATTTGGTC F2: 3 TTGATGTTGACTTCTTGGTATCATTGTTGTACCATTGACTTTCATTTGGTC 2 Unidirectional alignment (log-probability: -168) GTTACAACTACAACTGAAGAACCATAGTAACAAcatggtactggtttactttcagttaccatgttgttactatggttcttcagttgtagttagaacataatttgttacaactacaactgaagaaccatagt GTTACAACTACAACTGAAGAACCATAGTAACAA-------------------------------------------------------------------------------------------------- Template switch alignment (log-probability: -34.3) GTTACAACTACAACTGAAGAACCATAGTAACAACATGGTA|CTGGTTTACTTTCAGTTACCATGTTGTTACTATGGTTCTTCAGTTGTAGTT|AGAACATAATTTGTTACAACTACAACTGAAGAACCATAGT GTTACAACTACAACTGAAGAACCATAGTAACAACATGGTA|CTGGTTTACTTTCAGTTACCATGTTGTTACTATGGTTCTTCAGTTGTAGTT|AGAACATAATTTGTTACAACTACAACTGAAGAACCATAGT ========== Event 3971 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: ACCACACCCTTGCATGCATCT--------------TGGTG--GCCATAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCC ↑ 1 4 3 2 Chimp: ACCACACCCTTGCATGCATCTTCCCGTCGGGAGCCTGGTCGCACTGTAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCC Gorilla: Human: ACCACACCCTTGCATGCATCT--------------TGGTG--GCCATAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCC Cluster: [ ] Orangutan: Chimp > Human ------------- chrX:65873695-65873702 Template switch process: F1: L CTCCCTCAGCCCTATCTCCCACCACACCCTTGCATGCATCTT 1 F3: 4 TAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCCAA R RF: CTCCCTCAGCCCTATCTCCCACCACACCCTTGCATGCATCTTCCCGTCGGGAGCCTGGTCGCACTGTAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCCAA RR: GAGGGAGTCGGGATAGAGGGTGGTGTGGGAACGTACGTAGAAGGGCAGCCCTCGGACCAGCGTGACATCTCGCGTTACCGGTGGACAAGGAAAGGATGCCGGGGTT F2: 3 ACCGGTGG 2 Unidirectional alignment (log-probability: -32.4) CCCTCAGCCCTATCTCCCACCACACCCTTGCATGCATCT-----------------------TGgtggccaTAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCCAA CCCTCAGCCCTATCTCCCACCACACCCTTGCATGCATCTTCCCGTCGGGAGCCTGGTCGCACTG-------TAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCCAA Template switch alignment (log-probability: -16.3) CCCTCAGCCCTATCTCCCACCACACCCTTGCATGCATCTT|GGTGGCCA|TAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCCAA CCCTCAGCCCTATCTCCCACCACACCCTTGCATGCATCTT|GGTGGCCA|TAGAGCGCAATGGCCACCTGTTCCTTTCCTACGGCCCCAA ========== Event 3972 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 4 Detected in comparisons: 4 Multiple sequence alignment: Human: TCTGTTCTATTCTCCACAATACCTGGTA------T------AGTAGTAGGCATTCATTAGAAGCT Chimp: tctgttctattctccacaatacctggta------t------agtagtaggcattcattagaagct Gorilla: TCTGTTCTATTCTCCACAATACCTGGTATTACTATAGCAGGTATAGTAGGCATTCATTAGAAGCT ↑ 3 1 42 Human: TCTGTTCTATTCTCCACAATACCTGGTA------T------AGTAGTAGGCATTCATTAGAAGCT Cluster: [ ] Orangutan: TCTGTTCTATTCTCCACAATACCTGGTA------T------AGTAGTAGGCATTCATTAGAAGCT Human > Gorilla --------------- chrX:91516558-91516571 Template switch process: F1: L GTAAATTGCTGTTTCTGTTCTATTCTCCACAATACCTGGTAT 1 F3: 4 TAGTAGGCATTCATTAGAAGCTAGAAAATAAAAACTTGTT R RF: GTAAATTGCTGTTTCTGTTCTATTCTCCACAATACCTGGTATAGTAGTAGGCATTCATTAGAAGCTAGAAAATAAAAACTTGTT RR: CATTTAACGACAAAGACAAGATAAGAGGTGTTATGGACCATATCATCATCCGTAAGTAATCTTCGATCTTTTATTTTTGAACAA F2: 3 ATGGACGATATCAT 2 Unidirectional alignment (log-probability: -37.9) AAATTGCTGTTTCTGTTCTATTCTCCACAATACCTGGTATtactatagcAGgtaTAGTAGGCATTCATTAGAAGCTAGAAAATAAAAACTTGTT AAATTGCTGTTTCTGTTCTATTCTCCACAATACCTGGTAT---------AG---TAGTAGGCATTCATTAGAAGCTAGAAAATAAAAACTTGTT Template switch alignment (log-probability: -23.1) AAATTGCTGTTTCTGTTCTATTCTCCACAATACCTGGTAT|TACTATAgCAGGTA|TAGTAGGCATTCATTAGAAGCTAGAAAATAAAAACTTGTT AAATTGCTGTTTCTGTTCTATTCTCCACAATACCTGGTAT|TACTATACCAGGTA|TAGTAGGCATTCATTAGAAGCTAGAAAATAAAAACTTGTT ========== Event 3973 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: TGCATGTTTTGATAGAGACTTAG--GGATGCCTACTTAGACAGCTGCCCTTCCCGCCACTTA ↓ 1 4 3 2 Chimp: TGCATGTTTTGATAGAGACTTTGTCTAAGACCTACTTAGACAGCTGCCCTTCCCGCCACTTA Gorilla: TGCATGTTTTGATAGAGACTTAG--GGATGCCTACTTAGACAGCTGCCCTTCCTGCCACTTA Human: TGCATGTTTTGATAGAGACTTAG--GGATGCCTACTTAGACAGCTGCCCTTCCCGCCACTTA Cluster: [ ] Orangutan: TGCATGTTTTGATAGAGACTTAG--GGATGCCTACTTAGACAGCTGCCCTTCCCGCCACTTC Human > Chimp ------------- chrX:91055713-91055720 Template switch process: F1: L TTGTTATTGTGTTTGGTAAATGCATGTTTTGATAGAGACTT 1 F3: 4 ACCTACTTAGACAGCTGCCCTTCCCGCCACTTATAGCAATT R RF: TTGTTATTGTGTTTGGTAAATGCATGTTTTGATAGAGACTTAGGGATGCCTACTTAGACAGCTGCCCTTCCCGCCACTTATAGCAATT RR: AACAATAACACAAACCATTTACGTACAAAACTATCTCTGAATCCCTACGGATGAATCTGTCGACGGGAAGGGCGGTGAATATCGTTAA F2: 3 GAATCTGT 2 Unidirectional alignment (log-probability: -31.5) TGTTATTGTGTTTGGTAAATGCATGTTTTGATAGAGACTT-----TGtctaagaCCTACTTAGACAGCTGCCCTTCCCGCCACTTATAGCAAT TGTTATTGTGTTTGGTAAATGCATGTTTTGATAGAGACTTAGGGATG-------CCTACTTAGACAGCTGCCCTTCCCGCCACTTATAGCAAT Template switch alignment (log-probability: -22.3) TGTTATTGTGTTTGGTAAATGCATGTTTTGATAGAGACTT|TGTCTAAG|aCCTACTTAGACAGCTGCCCTTCCCGCCACTTATAGCAAT TGTTATTGTGTTTGGTAAATGCATGTTTTGATAGAGACTT|TGTCTAAG|GCCTACTTAGACAGCTGCCCTTCCCGCCACTTATAGCAAT ========== Event 3974 ========== Phylogenetic placement: species tree consistent Significant comparisons: 4 Detected in comparisons: 46 Multiple sequence alignment: Human: GTCTTACTTAGAATTACCT-----TTCCAGTACTCAAGATTCAATGGGTACTCATGCAAGATGTTGGCTAAATGA Chimp: GTCTTACTTAGAATTACCG-----TTCCAGTACTCAAGATTCAATGGGTACTCATGCAAGACGTTGGCTAAATGA Gorilla: GTCTTACTTAGAATTACCTTGAATCTTGAGTACTCAAGATTCAATGGATACTCACGCAAGATGTTGGCTAAATGA ↑ 1 4 3 2 Human: GTCTTACTTAGAATTACCT-----TTCCAGTACTCAAGATTCAATGGGTACTCATGCAAGATGTTGGCTAAATGA Cluster: [ ] Orangutan: GTCTTACTTAGAATTACCT-----TTCCAGTACTCAAGATTCAATGGGTACTCACGCAAGATGTTGGCTAAATGA Human > Gorilla --------------- chrX:90848073-90848080 Template switch process: F1: L CTTAGAATTACCTT 1 F3: 4 AGTACTCAAGATTCAATGGATACTCACGCAAGATGTTGGCTAAATGAATGGGTACCAAACAAGGGAT R RF: CTTAGAATTACCTTTCCAGTACTCAAGATTCAATGGGTACTCATGCAAGATGTTGGCTAAATGAATGGGTACCAAACAAGGGAT RR: GAATCTTAATGGAAAGGTCATGAGTTCTAAGTTACCCATGAGTACGTTCTACAACCGATTTACTTACCCATGGTTTGTTCCCTA F2: 3 GTTCTAAG 2 Unidirectional alignment (log-probability: -40.2) CTTAGAATTACCTTgaatcTtgAGTACTCAAGATTCAATGGaTACTCAcGCAAGATGTTGGC CTTAGAATTACCTT-----TCCAGTACTCAAGATTCAATGGGTACTCATGCAAGATGTTGGC Template switch alignment (log-probability: -27.8) CTTAGAATTACCTT|GAATCTTG|AGTACTCAAGATTCAATGGaTACTCAcGCAAGATGTTGGC CTTAGAATTACCTT|GAATCTTG|AGTACTCAAGATTCAATGGGTACTCATGCAAGATGTTGGC ========== Event 3975 ========== Phylogenetic placement: species tree consistent Significant comparisons: 25 Detected in comparisons: 25 Multiple sequence alignment: Human: GTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGCAGCTTCATTGCCATTAAGGGAACTGAGAG ↓ 3 2 1 4 Chimp: GTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTACTT-GGTACTGCCATTAAGGGAACTGAGAG ↑ 3 2 1 4 Gorilla: GTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGCAGCTTCATTGCCATTAAGGGAACTGAGAG Human: GTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGCAGCTTCATTGCCATTAAGGGAACTGAGAG Cluster: [ ] Orangutan: GTTAGAACTCCAGCCAAGAGTACGAAGGTTCAGTGCAGCTTCATTGCCATTAAGGGAACTGAGAG Human > Chimp ------------- chrX:89836915-89836921 Template switch process: F1: L GCAAAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTAC 1 F3: 4 TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA R RF: GCAAAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGCAGCTTCATTGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA RR: CGTTTCTCAATCTTGAGGTCGGTTCTCATGGTTCCAAGTCACGTCGAAGTAACGGTAATTCCCTTGACTCTCAATCCGTCCCTGTGACTTT F2: 3 CATGGTT 2 Unidirectional alignment (log-probability: -34.6) AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTacttggtac----------TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGT---------GCAGCTTCATTGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA Template switch alignment (log-probability: -22.2) AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTaC|TTGGTAC|TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGC|TTGGTAC|TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA Gorilla > Chimp --------------- chrX:89836915-89836921 Template switch process: F1: L GCAAAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTAC 1 F3: 4 TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA R RF: GCAAAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGCAGCTTCATTGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA RR: CGTTTCTCAATCTTGAGGTCGGTTCTCATGGTTCCAAGTCACGTCGAAGTAACGGTAATTCCCTTGACTCTCAATCCGTCCCTGTGACTTT F2: 3 CATGGTT 2 Unidirectional alignment (log-probability: -34.1) AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAG----------TacttggtacTGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGCAGCTTCAT---------TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA Template switch alignment (log-probability: -22.2) AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTaC|TTGGTAC|TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA AAGAGTTAGAACTCCAGCCAAGAGTACCAAGGTTCAGTGC|TTGGTAC|TGCCATTAAGGGAACTGAGAGTTAGGCAGGGACACTGAAA ========== Event 3976 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CAGGTTCTTCCATAGTAGGGATATCT-TTATGATATCATAAAGAACATTTCTGTTGAACTAAA ↑ 1 4 3 2 Chimp: CAGGTTCTTCCATAGTAGGGAGATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAA Gorilla: CAGGTTCTTCCATAGTAGGGAGATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAA ↓ 1 4 3 2 Human: CAGGTTCTTCCATAGTAGGGATATCT-TTATGATATCATAAAGAACATTTCTGTTGAACTAAA Cluster: [ ] Orangutan: CAGGTTCTTCCACAGTAGGGAGATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAA Chimp > Human ------------- chrX:69572598-69572604 Template switch process: F1: L GCATATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGATAT 1 F3: 4 ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA R RF: GCATATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAGATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA RR: CGTATAAATTAACTGGGTGTGTCCAAGAAGGTATCATCCCTCTACAGTAAGGTATAGTATTTCTTGTAAAGACAACTTGATTTCTAAATGTT F2: 3 GTATTTC 2 Unidirectional alignment (log-probability: -34.6) ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAtatctttatGA----------TATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGA---------GATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA Template switch alignment (log-probability: -22.2) ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAtAT|CTTTATG|ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAGAT|CTTTATG|ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA Gorilla > Human --------------- chrX:69572598-69572604 Template switch process: F1: L GCATATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGATAT 1 F3: 4 ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA R RF: GCATATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAGATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA RR: CGTATAAATTAACTGGGTGTGTCCAAGAAGGTATCATCCCTCTACAGTAAGGTATAGTATTTCTTGTAAAGACAACTTGATTTCTAAATGTT F2: 3 GTATTTC 2 Unidirectional alignment (log-probability: -34.1) ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAtatctttatG----------ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGA---------GATGTCATTCCATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA Template switch alignment (log-probability: -22.2) ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAtAT|CTTTATG|ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA ATTTAATTGACCCACACAGGTTCTTCCATAGTAGGGAGAT|CTTTATG|ATATCATAAAGAACATTTCTGTTGAACTAAAGATTTACAA ========== Event 3977 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 13 Multiple sequence alignment: Human: AAGCATTTCAGAAATGATTCCCAATGTCAGGGTCCACTGGGAGGGGTCAGGTGAGGAGAAGCAGTCCCGGAAGTAGTGTATGAGCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTG------------CCTCATTGGGTGCCTTCCCTTTctctgaggttggtt Chimp: AAGCATTTCAGAAATGATTCCCAATGTCAGGGTCCATTGGCAGGGGTCAGGTGAGGAGAAGCAGTCCCGGAAGTAGTGTATGAGCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTG------------CCTCGTTGGGTGCCTTCCCTTTCTCTGAGGTTGGTT Gorilla: AAGCATTTCAGAAATGATTCCCAATGTCAGGGTCCATTGGCAGGGGTCAGGTGAGGAGAAGCAGTCCCGGAAGTAGTGTATGAGCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTG------------------------CCTGCCCTTTCTCTGAGGTTGGTT ↓ 3 2 4 1 Human: AAGCATTTCAGAAATGATTCCCAATGTCAGGGTCCACTGGGAGGGGTCAGGTGAGGAGAAGCAGTCCCGGAAGTAGTGTATGAGCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTG------------CCTCATTGGGTGCCTTCCCTTTctctgaggttggtt Cluster: [ ] Orangutan: AAGCATTTCAGAAATGATTCCCAATGTCAGGGTCCATTGGCAGGGGTCAGGTGAGGAGAAGCAGTACTGGAAGTAGTGTATGAGCCTGACTGTCCCTTGGTTCTGTAACATACTTCCCTGCCTCGTTGGGTG------------CCTGCCCTTTCTCTGAGGTTGGTT Gorilla > Human --------------- chrX:86844650-86844656 Template switch process: F1: L ATGAGCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTGCCT 1 F3: 4 TGCCTTCCCTTTCTCTGAGGTTGGTTCTCCCCCTTCCCCAACAAGA R RF: CCCAATGTCAGGGTCCATTGGCAGGGGTCAGGTGAGGAGAAGCAGTCCCGGAAGTAGTGTATGAGCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTGCCTGCCCTTTCTCTGAGGTTGGTTCTCCCCCTTCCCCAACAAGA RR: GGGTTACAGTCCCAGGTAACCGTCCCCAGTCCACTCCTCTTCGTCAGGGCCTTCATCACATACTCGAACTGACAGGGAACCAAGACATTGTATGAAGGGACGGACGGGAAAGAGACTCCAACCAAGAGGGGGAAGGGGTTGTTCT F2: 3 GGGTTAC 2 Unidirectional alignment (log-probability: -33.7) GCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCtgcctcattgggTGCCTtCCCTTTCTCTGAGGTTGGTTCTCCCCCTTCCCCA GCTTGACTGTCCCTTGGTTCTGTAACATACTTCCC------------TGCCTGCCCTTTCTCTGAGGTTGGTTCTCCCCCTTCCCCA Template switch alignment (log-probability: -22.4) GCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTGCCT|CATTGGG|TGCCTtCCCTTTCTCTGAGGTTGGTTCTCCCCCTTCCCCA GCTTGACTGTCCCTTGGTTCTGTAACATACTTCCCTGCCT|CATTGGG|TGCCTGCCCTTTCTCTGAGGTTGGTTCTCCCCCTTCCCCA ========== Event 3978 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: TTGGCTGCAGGAGGGGCATGGCTAGGAACCCTTTCCTAGCCGGGGAAGCAGACTTGGCTTAG Chimp: -------------------------------------------------------------- Gorilla: TTGGCTGCAGGAGGGGCATGGCTAGGAAAGGGTTCCTAGCTGGGGAAGCAGACTTGGCTTAG ↓ 3 1 2 4 Human: TTGGCTGCAGGAGGGGCATGGCTAGGAACCCTTTCCTAGCCGGGGAAGCAGACTTGGCTTAG Cluster: [ ] Orangutan: TTGGCTGCAGGAGAGGCATGGCTAGGAAACGGTTCCTAGCTGGGTAAGTGGACTTGGCTTAG Gorilla > Human --------------- chrX:70067133-70067145 Template switch process: F1: L GGGTGAGGAGAGCTTGGCTGCAGGAGGGGCATGGCTAGGAA 1 F3: 4 GGGGAAGCAGACTTGGCTTAGCACGGGGCACATGTGGGTG R RF: GGGTGAGGAGAGCTTGGCTGCAGGAGGGGCATGGCTAGGAAAGGGTTCCTAGCTGGGGAAGCAGACTTGGCTTAGCATGGGGCACATGTGGGTG RR: CCCACTCCTCTCGAACCGACGTCCTCCCCGTACCGATCCTTTCCCAAGGATCGACCCCTTCGTCTGAACCGAATCGTACCCCGTGTACACCCAC F2: 3 CCGATCCTTTCCC 2 Unidirectional alignment (log-probability: -34.4) GGTGAGGAGAGCTTGGCTGCAGGAGGGGCATGGCTAGGAAccctTTCCTAGCcGGGGAAGCAGACTTGGCTTAGCAcGGGGCACATGTGGGTG GGTGAGGAGAGCTTGGCTGCAGGAGGGGCATGGCTAGGAAAGGGTTCCTAGCTGGGGAAGCAGACTTGGCTTAGCATGGGGCACATGTGGGTG Template switch alignment (log-probability: -22.9) GGTGAGGAGAGCTTGGCTGCAGGAGGGGCATGGCTAGGAA|CCCTTTCCTAGCC|GGGGAAGCAGACTTGGCTTAGCAcGGGGCACATGTGGGTG GGTGAGGAGAGCTTGGCTGCAGGAGGGGCATGGCTAGGAA|CCCTTTCCTAGCC|GGGGAAGCAGACTTGGCTTAGCATGGGGCACATGTGGGTG ========== Event 3979 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: AACACACCCAATGGTTTCCTACCTGTCCACCACCCAGAAAAAGCAGGCAAGCAAGTAAACTGTCTTAAATGAGGAAAGAGGGGAAACAGGCCAGAGGGTGACCTCTTATTTATGCAACAGCTACTGCCTATCAGGTA---GGAGGACTGGCTGTTTCTACCCTT Chimp: AACACACCCAATGGTTTCCTACCTGTCCACCACCCAGAAAAAGCAGGCAAGCAAGTAAACTGTCTTAAATGAGGAAAGAGGGGAAACAGGCCACAGGGTGACCTCTTATTTATGCAACAGCTACTGCCTATTAGGTA---GGAGGACTGGCTGTTTCTACCCTT ↓ 3 2 1 4 Gorilla: AACACACCCAATGGTTTCCTACCTGTCCACCACCCAGAAAAAGCAGGCAAGCAAGTAAACTGTCTTAAATGAGGAAAGAGGGGAAACAGGCCACAGGGCGACCTCTTATTTATGCAACAGCTACTGCCTATCAGGTA------GGACTGGCTGTTTCTACCCTT Human: AACACACCCAATGGTTTCCTACCTGTCCACCACCCAGAAAAAGCAGGCAAGCAAGTAAACTGTCTTAAATGAGGAAAGAGGGGAAACAGGCCAGAGGGTGACCTCTTATTTATGCAACAGCTACTGCCTATCAGGTA---GGAGGACTGGCTGTTTCTACCCTT Cluster: [ ] Orangutan: AACACACCCAGTGGTTTCCTACCTGTCTACCACCCAGAAAAAGCAGGCAAGCAAGTAAACTGCCTTAAATGAGGAAAAGGGGGAAACAGGCCACAGGGTGACCTCTTACTTATGCGACAGCTACTGCCTATCAGGTAGGA---GGACGGGCTGTTTCTACCCCT Chimp > Gorilla --------------- chrX:71012454-71012459 Template switch process: F1: L CCACAGGGCGACCTCTTATTTATGCAACAGCTACTGCCTAT 1 F3: 4 GGACTGGCTGTTTCTACCCTTTCTGCACACAGGAACGG R RF: TACCTGTCCACCACCCAGAAAAAGCAGGCAAGCAAGTAAACTGTCTTAAATGAGGAAAGAGGGGAAACAGGCCACAGGGTGACCTCTTATTTATGCAACAGCTACTGCCTATTAGGTAGGAGGACTGGCTGTTTCTACCCTTTCTGCACACAGGAACGG RR: ATGGACAGGTGGTGGGTCTTTTTCGTCCGTTCGTTCATTTGACAGAATTTACTCCTTTCTCCCCTTTGTCCGGTGTCCCACTGGAGAATAAATACGTTGTCGATGACGGATAATCCATCCTCCTGACCGACAAAGATGGGAAAGACGTGTGTCCTTGCC F2: 3 ATGGAC 2 Unidirectional alignment (log-probability: -30.3) CACAGGGcGACCTCTTATTTATGCAACAGCTACTGCCTATcAGGT---AGGACTGGCTGTTTCTACCCTTTCTGCACACAGGAACGg CACAGGGTGACCTCTTATTTATGCAACAGCTACTGCCTATTAGGTAGGAGGACTGGCTGTTTCTACCCTTTCTGCACACAGGAACG- Template switch alignment (log-probability: -22) CACAGGGcGACCTCTTATTTATGCAACAGCTACTGCCTAT|CAGGTA|GGACTGGCTGTTTCTACCCTTTCTGCACACAGGAACGG CACAGGGTGACCTCTTATTTATGCAACAGCTACTGCCTAT|CAGGTA|GGACTGGCTGTTTCTACCCTTTCTGCACACAGGAACGG ========== Event 3980 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: tgtaacatatacaagtgactaaat-------------------gtttgtacctaaaatatgtaaagaatttctaaa Chimp: TGTAACATATACAAGTGACTACATGTTTGTAGTTTAGGTACATGTTTGTACCTAAAATATGTAAAGAATTTCTA-- ↑ 4 3 1 2 Gorilla: TGTAACATATACAAGTGACTAAAT-------------------GTttgtacctaaaatatgtaaagaatttctaaa Human: tgtaacatatacaagtgactaaat-------------------gtttgtacctaaaatatgtaaagaatttctaaa Cluster: [ ] Orangutan: tgtaacatatacaagtgactaaat-------------------gtttgtacctaaaatatgtaaagaatttctaaa Gorilla > Chimp --------------- chrX:7387934-7387942 Template switch process: F1: L GGACTGGGAATGTTTATATTTGTAACATATACAAGTGACTACATGTTTGTAG 1 F3: 4 ATGTTTGTACCTAAAATATGTAAAGAATTTCTA R RF: GGACTGGGAATGTTTATATTTGTAACATATACAAGTGACTAAATGTTTGTACCTAAAATATGTAAAGAATTTCTA RR: CCTGACCCTTACAAATATAAACATTGTATATGTTCACTGATTTACAAACATGGATTTTATACATTTCTTAAAGAT F2: 3 CATGGATTT 2 Unidirectional alignment (log-probability: -50.8) TTTATATTTGTAACATATACAAGTGACtacatgtttgtagtttaggTAcATGTTTGTACCTAAAATATGTAAAGAATTTCTA--------- TTTATATTTGTAACATATACAAGTGAC-------------------TAAATGTTTGTACCTAAAATATGTAAAGAATTTCTAAAAGTCAAT Template switch alignment (log-probability: -28) TTTATATTTGTAACATATACAAGTGACTAcATGTTTGTAg|TTTAGGTAC|ATGTTTGTACCTAAAATATGTAAAGAATTTCTA TTTATATTTGTAACATATACAAGTGACTAAATGTTTGTAC|TTTAGGTAC|ATGTTTGTACCTAAAATATGTAAAGAATTTCTA ========== Event 3981 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: ATAGCATTGAACTTAGCCAAGAAATCAGGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA ↑ 1 4 3 2 Chimp: ATAGCATTGAACTTAGCCAAGGGG-TATGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA Gorilla: ATAGCATTGAACTTAGCCAAGGGG-TATGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA ↓ 1 4 3 2 Human: ATAGCATTGAACTTAGCCAAGAAATCAGGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA Cluster: [ ] Orangutan: Chimp > Human ------------- chrX:76652295-76652301 Template switch process: F1: L GGTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAG 1 F3: 4 GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA R RF: GGTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAGGGGTATGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA RR: CCACTGTCAAAGGAATTGTATATCGTAACTTGAATCGGTTCCCCATACTAATTACTCCAGGACTAAAGATGATCTTTGTACTTTATT F2: 3 GACTAAA 2 Unidirectional alignment (log-probability: -30) GTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAGaaatcaG-----GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA GTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAG------GGGTATGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA Template switch alignment (log-probability: -16.2) GTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAG|AAATCAG|GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA GTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAG|AAATCAG|GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA Gorilla > Human --------------- chrX:76652295-76652301 Template switch process: F1: L GGTGACAGTTTCCTTAACATATAGCATTGAACTTAGCCAAG 1 F3: 4 GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA R RF: GGTGACACTTTCCTTAACATATAGCATTGAACTTAGCCAAGGGGTATGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA RR: CCACTGTGAAAGGAATTGTATATCGTAACTTGAATCGGTTCCCCATACTAATTACTCCAGGACTAAAGATGATCTTTGTACTTTATT F2: 3 GACTAAA 2 Unidirectional alignment (log-probability: -35) GTGACAgTTTCCTTAACATATAGCATTGAACTTAGCCAAGaaatcaG-----GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA GTGACACTTTCCTTAACATATAGCATTGAACTTAGCCAAG------GGGTATGATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA Template switch alignment (log-probability: -22.1) GTGACAgTTTCCTTAACATATAGCATTGAACTTAGCCAAG|AAATCAG|GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA GTGACACTTTCCTTAACATATAGCATTGAACTTAGCCAAG|AAATCAG|GATTAATGAGGTCCTGATTTCTACTAGAAACATGAAATAA ========== Event 3982 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 1256 Detected in comparisons: 1256 Multiple sequence alignment: Human: TTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGT-TTGGCTGTGCAGATCACAATAGAGATAAGTTATAGGGTGATG ↓ 3 1 2 4 ↑ 13 24 Chimp: TTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACAGCC-AAACCTAAGGTTCTGGCAGTGCAGATCACAATTGAGATAAGTTATAGGGTGATG ↓ 13 24 ↑ 13 24 Gorilla: TTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGT-TTGGCTGTGCAGATCACAATTGAGATAAGTTATAGGGTGATG Human: TTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGT-TTGGCTGTGCAGATCACAATAGAGATAAGTTATAGGGTGATG Cluster: [ ] Orangutan: TTTCTTAGTAAAGGTTCTTAATTGTGATCTGCACTGCCAGAAACTTAGGT-TTGGCTGTGCAGATCACAATTGAGATAAGTTATAGGGTGATG Chimp > Human ------------- chrX:75317309-75317330 Template switch process: F1: L AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC 1 F3: 4 GTGCAGATCACAATAGAGATAAGTTATAGGGTGATGAAGA R RF: AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACAGCCAAACCTAAGGTTCTGGCAGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA RR: TCAACAGAAAGAATCATTTCCAAGAGTTAACACTAGACGTGTCGGTTTGGATTCCAAGACCGTCACGTCTAGTGTTAACTCTATTCAATATCCCACTACTTCT F2: 3 TCGGTTTGGATTCCAAGACCGT 2 Unidirectional alignment (log-probability: -46.8) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACtGCCAgAACCTtAGGTT-TGGCtGTGCAGATCACAATaGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACAGCCA-AACCTAAGGTTCTGGCAGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA Template switch alignment (log-probability: -24) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|TGCCAGAACCTTAGGTTTGGCT|GTGCAGATCACAATaGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|TGCCAGAACCTTAGGTTTGGCT|GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA Human > Chimp ------------- chrX:75379082-75379118 Template switch process: F1: L AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC 1 F3: 4 GAGATAAGTTATAGGGTGATGAAGA R RF: AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGTTTGGCTGTGCAGATCACAATAGAGATAAGTTATAGGGTGATGAAGA RR: TCAACAGAAAGAATCATTTCCAAGAGTTAACACTAGACGTGACGGTCTTGGAATCCAAACCGACACGTCTAGTGTTATCTCTATTCAATATCCCACTACTTCT F2: 3 TTAACACTAGACGTGACGGTCTTGGAATCCAAACCGA 2 Unidirectional alignment (log-probability: -46.8) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACaGCCA-AACCTaAGGTTcTGGCaGTGCAGATCACAATtGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGTT-TGGCTGTGCAGATCACAATAGAGATAAGTTATAGGGTGATGAAGA Template switch alignment (log-probability: -19.6) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|AGCCAAACCTAAGGTTCTGGCAGTGCAGATCACAATT|GAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|AGCCAAACCTAAGGTTCTGGCAGTGCAGATCACAATT|GAGATAAGTTATAGGGTGATGAAGA Gorilla > Chimp --------------- chrX:75379082-75379103 Template switch process: F1: L AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC 1 F3: 4 GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA R RF: AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGTTTGGCTGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA RR: TCAACAGAAAGAATCATTTCCAAGAGTTAACACTAGACGTGACGGTCTTGGAATCCAAACCGACACGTCTAGTGTTAACTCTATTCAATATCCCACTACTTCT F2: 3 ACGGTCTTGGAATCCAAACCGA 2 Unidirectional alignment (log-probability: -39) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACaGCCA-AACCTaAGGTTcTGGCaGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACTGCCAGAACCTTAGGTT-TGGCTGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA Template switch alignment (log-probability: -18.5) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|AGCCAAACCTAAGGTTCTGGCA|GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|AGCCAAACCTAAGGTTCTGGCA|GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA Chimp > Gorilla --------------- chrX:75997358-75997379 Template switch process: F1: L AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC 1 F3: 4 GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA R RF: AGTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACAGCCAAACCTAAGGTTCTGGCAGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA RR: TCAACAGAAAGAATCATTTCCAAGAGTTAACACTAGACGTGTCGGTTTGGATTCCAAGACCGTCACGTCTAGTGTTAACTCTATTCAATATCCCACTACTTCT F2: 3 TCGGTTTGGATTCCAAGACCGT 2 Unidirectional alignment (log-probability: -39) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACtGCCAgAACCTtAGGTT-TGGCtGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCACAGCCA-AACCTAAGGTTCTGGCAGTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA Template switch alignment (log-probability: -18.5) GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|TGCCAGAACCTTAGGTTTGGCT|GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA GTTGTCTTTCTTAGTAAAGGTTCTCAATTGTGATCTGCAC|TGCCAGAACCTTAGGTTTGGCT|GTGCAGATCACAATTGAGATAAGTTATAGGGTGATGAAGA ========== Event 3983 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: TTTTTCTCAAGTCAAGGACAAACA-------CAGGTGCTTTATGGGGAATGATTCTGAAAAA Chimp: TTTTTCTCAAGTCAAGGACAAACA-------TAGGTGCTTTATGGGGAATGATTCTGAAAAA ↑ 3 1 42 Gorilla: TTTTTCTCAAGTCAAGGACAAACA--------------CCTATGGGGAATGATTCTGAAAAA Human: TTTTTCTCAAGTCAAGGACAAACA-------CAGGTGCTTTATGGGGAATGATTCTGAAAAA Cluster: [ ] Orangutan: TTTTTCTCAAGTCAAGGACAAACACAGGTGC-------TTTATGGGGAATGATTCTGAAAAA Gorilla > Chimp --------------- chrX:73359094-73359102 Template switch process: F1: L AGCAATTCAAAATGGTATTTTTCTCAAGTCAAGGACAAACA 1 F3: 4 TATGGGGAATGATTCTGAAAAATCTGTTGTTTGATAGAGT R RF: AGCAATTCAAAATGGTATTTTTCTCAAGTCAAGGACAAACACCTATGGGGAATGATTCTGAAAAATCTGTTGTTTGATAGAGT RR: TCGTTAAGTTTTACCATAAAAAGAGTTCAGTTCCTGTTTGTGGATACCCCTTACTAAGACTTTTTAGACAACAAACTATCTCA F2: 3 TTCGTGGAT 2 Unidirectional alignment (log-probability: -32) GCAATTCAAAATGGTATTTTTCTCAAGTCAAGGACAAACAtaggtgcttTATGGGGAATGATTCTGAAAAATCTGTTGTTTGATAGAGT GCAATTCAAAATGGTATTTTTCTCAAGTCAAGGACAAACA-------CCTATGGGGAATGATTCTGAAAAATCTGTTGTTTGATAGAGT Template switch alignment (log-probability: -22.4) GCAATTCAAAATGGTATTTTTCTCAAGTCAAGGACAAACA|TAGGTGcTT|TATGGGGAATGATTCTGAAAAATCTGTTGTTTGATAGAGT GCAATTCAAAATGGTATTTTTCTCAAGTCAAGGACAAACA|TAGGTGTTT|TATGGGGAATGATTCTGAAAAATCTGTTGTTTGATAGAGT ========== Event 3984 ========== Phylogenetic placement: species tree consistent Significant comparisons: 6 Detected in comparisons: 46 Multiple sequence alignment: Human: TCTTTGCACCACTAGAATGAGGTACCTTTTGCTGTAAATTTTAAAACTAGCATTCTTGCATATACATCAATCATTCTGAGAATAGTTAACGTGAGCGTATTCTTAAAAAACTATTACCTCTTGAAATAGGAACAAAAAATAGGTGTACCTTATATTTGGCACAAGAAGTTA Chimp: TCTTTGCACCACTAGAATGAGGTACCTTTTGCTGTAAATTTTAAAACTAGCATTCTTGCATATACATCAATCATTCTGAGAATAGTTAACGTGAGCGTATTCTTAAAAAACTATTACCTCTAGAAATAGGAACAAAAAATGGG---TTCCTATATTTGGCACAAGAAGTTA ↓ 3 2 1 4 Gorilla: TCTTTGCACCACTAGAATGAGGTACCTTTTGCTGTAAATTTTAAAACTAGCATTCTTGAGTATACATCAATCATTCTGAGAATAGTTAACGTGAGTGTATTCTTAAAAAACTATTACCTCTTGAAATAGGAACAAAAAATGGGTGTACCTTATATTTGGCACAAGAAGTTA Human: TCTTTGCACCACTAGAATGAGGTACCTTTTGCTGTAAATTTTAAAACTAGCATTCTTGCATATACATCAATCATTCTGAGAATAGTTAACGTGAGCGTATTCTTAAAAAACTATTACCTCTTGAAATAGGAACAAAAAATAGGTGTACCTTATATTTGGCACAAGAAGTTA Cluster: [ ] Orangutan: TCTTTGCACCACTAGAATGAGGTACCTTCTGCTATAAATTTTAAAACTGGAATTCTTGCATATACA----TCATTCTGAGAACAGTTAATGTGAGTGCATTCTTAAAAAACTATTGCCTGTTGAAATAGGAACAA-AAATGGGTGTACCTTATATTTGACACAAGAAGTTA Chimp > Gorilla --------------- chrX:73658772-73658777 Template switch process: F1: L TTAAAAAACTATTACCTCTTGAAATAGGAACAAAAAATGGGT 1 F3: 4 TATATTTGGCACAAGAAGTTAAACAACTATAACAAATAAA R RF: AGGTACCTTTTGCTGTAAATTTTAAAACTAGCATTCTTGCATATACATCAATCATTCTGAGAATAGTTAACGTGAGCGTATTCTTAAAAAACTATTACCTCTAGAAATAGGAACAAAAAATGGGTTCCTATATTTGGCACAAGAAGTTAAACAACTATAACAAATAAA RR: TCCATGGAAAACGACATTTAAAATTTTGATCGTAAGAACGTATATGTAGTTAGTAAGACTCTTATCAATTGCACTCGCATAAGAATTTTTTGATAATGGAGATCTTTATCCTTGTTTTTTACCCAAGGATATAAACCGTGTTCTTCAATTTGTTGATATTGTTTATTT F2: 3 TCCATG 2 Unidirectional alignment (log-probability: -31.8) AAAAAACTATTACCTCTtGAAATAGGAACAAAAAATGGGTgtacCtTATATTTGGCACAAGAAGTTAAACAACTATAACAAATAAA AAAAAACTATTACCTCTAGAAATAGGAACAAAAAATGGGTT---CCTATATTTGGCACAAGAAGTTAAACAACTATAACAAATAAA Template switch alignment (log-probability: -22) AAAAAACTATTACCTCTtGAAATAGGAACAAAAAATGGGT|GTACCT|TATATTTGGCACAAGAAGTTAAACAACTATAACAAATAAA AAAAAACTATTACCTCTAGAAATAGGAACAAAAAATGGGT|GTACCT|TATATTTGGCACAAGAAGTTAAACAACTATAACAAATAAA ========== Event 3985 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: CATTCTGTGCAGACACCACTCAGAGGAACTGTGGTTAGAGAAAAGCTTGATAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG-------------- Chimp: Gorilla: CATTCTGTGCAGACACCACTCC--AGGCCTGGGATC--------------AAGCTTTTCTCTAACCACAGTTCCTctgagcagccaggatggatggg ↓ 1 3 4 2 Human: CATTCTGTGCAGACACCACTCAGAGGAACTGTGGTTAGAGAAAAGCTTGATAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG-------------- Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chrX:155112130-155112159 Template switch process: F1: L GTCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTC 1 F3: 4 AGCTTTTCTCTAACCACAGTTCCTCTGAGCAG R RF: GTCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTCCAGGCCTGGGATCAAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG RR: CAGGAAGACAAAGACAGGACGTAAGACACGTCTGTGGTGAGGTCCGGACCCTAGTTCGAAAAGAGATTGGTGTCAAGGAGACTCGTC F2: 3 TAGTTCGAAAAGAGATTGGTGTCAAGGAGA 2 Unidirectional alignment (log-probability: -70) TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCAC-------------TCAgaggaactgtggttagagaaaagcttgatAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG-------- TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTCCAGGCCTGGGATCA-----------------------------AGCTTTTCTCTAACCACAGTTCCTCTGAGCAGCCAGGATG Template switch alignment (log-probability: -19.4) TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTC|AGAGGAACTGTGGTTAGAGAAAAGCTTGAT|AGCTTTTCTCTAACCACAGTTCCTCTGAGCAG TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTC|AGAGGAACTGTGGTTAGAGAAAAGCTTGAT|AGCTTTTCTCTAACCACAGTTCCTCTGAGCAG ========== Event 3986 ========== Phylogenetic placement: species tree consistent Significant comparisons: 1 Detected in comparisons: 13 Multiple sequence alignment: Human: AGTA-GAGTACCACC-TATTTG-AAGCT-GGTAGACAGCTTCAAAATGTGGTAGACACATTTTCttaca-gaatc-c ↑ 3 4 2 1 Chimp: AGTA-GAGTACCACC-TATTTG-AAGCT-GG--------------------TAGACACATTTTCTTACA-GAATC-C Gorilla: GGTA-GAGTACCACC-TATTTC-AAGCT-GG--------------------TAGACACATTTTCTTAGA-GAATC-C Human: AGTA-GAGTACCACC-TATTTG-AAGCT-GGTAGACAGCTTCAAAATGTGGTAGACACATTTTCttaca-gaatc-c Cluster: [ ] Orangutan: AGTAGGAGTACCACCTTATTTGAAAGCTGAG--------------------TAGATGCATTTTCTTAGAGGAATCCT Chimp > Human ------------- chrX:85145650-85145656 Template switch process: F1: L GCCACATCCTTTTAAGTAGAGTACCACCTATTTGAAGCTGGTAGACA 1 F3: 4 AATGTGGTAGACACATTTTCTTACAGAATCCTAGACAGTCATAGCTA R RF: GCCACATCCTTTTAAGTAGAGTACCACCTATTTGAAGCTGGTAGACACATTTTCTTACAGAATCCTAGACAGTCATAGCTA RR: CGGTGTAGGAAAATTCATCTCATGGTGGATAAACTTCGACCATCTGTGTAAAAGAATGTCTTAGGATCTGTCAGTATCGAT F2: 3 AACTTCG 2 Unidirectional alignment (log-probability: -39.7) CCTTTTAAGTAGAGTACCACCTATTTGAAGCTGGTAGACagcttcaaaatgtggtagacACATTTTCTTACAGAATCCTAGACAGTC CCTTTTAAGTAGAGTACCACCTATTTGAAGCTGGTAGAC--------------------ACATTTTCTTACAGAATCCTAGACAGTC Template switch alignment (log-probability: -28.4) CCTTTTAAGTAGAGTACCACCTATTTGAAGCTGGTAGACA|GCTTCAA|AAtgTGGTAGACACATTTTCTTACAGAATCCTAGACAGTC CCTTTTAAGTAGAGTACCACCTATTTGAAGCTGGTAGACA|GCTTCAA|AAGCTGGTAGACACATTTTCTTACAGAATCCTAGACAGTC ========== Event 3987 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: CCAGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGGATGCATCTAATTGGCAATTAGAAAATCagggcaa ↑ 3 2 4 1 Chimp: CTAGCTAAATCAGTTAGAATGCATAACTGATTTTCTA--------------ATTGGCAATTAGAAAATCagggcaa Gorilla: CCAGCTAAATCAGTTAGAATGCATAACTGATTTTCTA--------------ATTGGCAATTAGAAAATCagggcaa ↓ 3 2 4 1 Human: CCAGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGGATGCATCTAATTGGCAATTAGAAAATCagggcaa Cluster: [ ] Orangutan: CCAGCTAAATCAGTTGGAATGCATAACTGATTTTCTA--------------ATTGGCAATTAGAAAATCagggcaa Chimp > Human ------------- chrX:87817551-87817555 Template switch process: F1: L TGCTCCAGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGG 1 F3: 4 TCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACATGGG R RF: TGCTCTAGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACATGGG RR: ACGAGATCGATTTAGTCAATCTTACGTATTGACTAAAAGATTAACCGTTAATCTTTTAGTCCCGTTGTAAAATCTGTACCC F2: 3 ACGTA 2 Unidirectional alignment (log-probability: -37) AGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGgatgcatctaattgGCAATTAGAAAATCAGGGCAACATTTTAGACA AGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTG--------------GCAATTAGAAAATCAGGGCAACATTTTAGACA Template switch alignment (log-probability: -22.1) AGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGG|ATGCA|TCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACA AGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGG|ATGCA|TCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACA Gorilla > Human --------------- chrX:87817551-87817555 Template switch process: F1: L TGCTCCAGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGG 1 F3: 4 TCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACATGGG R RF: TGCTCCAGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACATGGG RR: ACGAGGTCGATTTAGTCAATCTTACGTATTGACTAAAAGATTAACCGTTAATCTTTTAGTCCCGTTGTAAAATCTGTACCC F2: 3 ACGTA 2 Unidirectional alignment (log-probability: -31) AGCTAAATCAGTTAGAATGCATAACTGATTTTCtaattggatgcatcTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACA AGCTAAATCAGTTAGAATGCATAACTGATTTTC--------------TAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACA Template switch alignment (log-probability: -16.6) AGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGG|ATGCA|TCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACA AGCTAAATCAGTTAGAATGCATAACTGATTTTCTAATTGG|ATGCA|TCTAATTGGCAATTAGAAAATCAGGGCAACATTTTAGACA ========== Event 3988 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: GGAAATTAATTCAATATTATTGCATTAGGTGCAATTTAACTGGTGAAAAATTATC ↑ 3 2 1 4 Chimp: GGAAATTAATTCAATATTATTGCATTAGGCTGTCTTTAACTGGTGAAAAATTATC Gorilla: Human: GGAAATTAATTCAATATTATTGCATTAGGTGCAATTTAACTGGTGAAAAATTATC Cluster: [ ] Orangutan: GGAAATTAATTCAATATTATTGCATTAGGCTGTCTTTAATTGGTGAAAAATTATC Chimp > Human ------------- chrX:89375493-89375497 Template switch process: F1: L AGCACATCCATAGGAAATTAATTCAATATTATTGCATTAGG 1 F3: 4 TTTAACTGGTGAAAAATTATCTGGCTGTGACCAATGGAAA R RF: AGCACATCCATAGGAAATTAATTCAATATTATTGCATTAGGCTGTCTTTAACTGGTGAAAAATTATCTGGCTGTGACCAATGGAAA RR: TCGTGTAGGTATCCTTTAATTAAGTTATAATAACGTAATCCGACAGAAATTGACCACTTTTTAATAGACCGACACTGGTTACCTTT F2: 3 AACGT 2 Unidirectional alignment (log-probability: -28.6) GCACATCCATAGGAAATTAATTCAATATTATTGCATTAGGtgcaa-----TTTAACTGGTGAAAAATTATCTGGCTGTGACCAATGGAAA GCACATCCATAGGAAATTAATTCAATATTATTGCATTAGG-----CTGTCTTTAACTGGTGAAAAATTATCTGGCTGTGACCAATGGAAA Template switch alignment (log-probability: -15.9) GCACATCCATAGGAAATTAATTCAATATTATTGCATTAGG|TGCAA|TTTAACTGGTGAAAAATTATCTGGCTGTGACCAATGGAAA GCACATCCATAGGAAATTAATTCAATATTATTGCATTAGG|TGCAA|TTTAACTGGTGAAAAATTATCTGGCTGTGACCAATGGAAA ========== Event 3989 ========== Phylogenetic placement: species tree consistent Significant comparisons: 13 Detected in comparisons: 13 Multiple sequence alignment: Human: TTAACACATTTTTGACCTAGG----TTTT--------ATAGCAGT----ACTATCAGGAGAGTAACTGG----CAACAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTC ↑ 1 3 4 2 Chimp: TTAACACATTTTTGACCTAGG--AGCTCT----GTTGCTGGAAGT--ATAGTCTCCAGCCAGTTACTCT--CCTGATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTC Gorilla: TTAACACATTTTTGACCTAGGAG--CTCTGTTG----CTGGAAGTAT--AGTCTCCAGCCAGTTACTCTCC--TGATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTC ↓ 1 3 4 2 Human: TTAACACATTTTTGACCTAGG----TTTT--------ATAGCAGT----ACTATCAGGAGAGTAACTGG----CAACAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTC Cluster: [ ] Orangutan: TTAACATATTCTTGACCTAGGAG--CTCTGTTG----CTGGAAGTAT--AGTCTCCAGCCAGTTACTCTCC--TGATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTC Chimp > Human ------------- chrX:88370148-88370180 Template switch process: F1: L CTTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG 1 F3: 4 AACAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTGTGC R RF: CTTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGGAGCTCTGTTGCTGGAAGTATAGTCTCCAGCCAGTTACTCTCCTGATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTGTGC RR: GAATAACTGTAATGTTCGAAAATTGTGTAAAAACTGGATCCTCGAGACAACGACCTTCATATCAGAGGTCGGTCAATGAGAGGACTATCATGACGATATTTTGAGTAAGAACACACCAAAAGACACG F2: 3 CGGTCAATGAGAGGACTATCATGACGATATTTT 2 Unidirectional alignment (log-probability: -73.8) TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG---------------------------------------------TtttatagcagtactatcaggagagtaactggcaacAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGGAGCTCTGTTGCTGGAAGTATAGTCTCCAGCCAGTTACTCTCCTGAT-----------------------------------AGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG Template switch alignment (log-probability: -31.4) TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG|TTTTATAGCAGTACTATCAGGAGAGTAACTGGC|aAcAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG|TTTTATAGCAGTACTATCAGGAGAGTAACTGGC|GATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG Gorilla > Human --------------- chrX:88370148-88370180 Template switch process: F1: L CTTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG 1 F3: 4 AACAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTGTGC R RF: CTTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGGAGCTCTGTTGCTGGAAGTATAGTCTCCAGCCAGTTACTCTCCTGATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTGTGC RR: GAATAACTGTAATGTTCGAAAATTGTGTAAAAACTGGATCCTCGAGACAACGACCTTCATATCAGAGGTCGGTCAATGAGAGGACTATCATGACGATATTTTGAGTAAGAACACACCAAAAGACACG F2: 3 CGGTCAATGAGAGGACTATCATGACGATATTTT 2 Unidirectional alignment (log-probability: -73.3) TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG---------------------------------------------TtttatagcagtactatcaggagagtaactggcaacAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGGAGCTCTGTTGCTGGAAGTATAGTCTCCAGCCAGTTACTCTCCTGAT-----------------------------------AGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG Template switch alignment (log-probability: -31) TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG|TTTTATAGCAGTACTATCAGGAGAGTAACTGGC|aAcAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG TTATTGACATTACAAGCTTTTAACACATTTTTGACCTAGG|TTTTATAGCAGTACTATCAGGAGAGTAACTGGC|GATAGTACTGCTATAAAACTCATTCTTGTGTGGTTTTCTG ========== Event 3990 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 25 Multiple sequence alignment: Human: TGGTGGACACTTTTATAGGTACTCTGTGTCATTTTTGATACTGTAGGTATCTTATTTCATTTATCTTTATTCTTAATGTACGAATTCATAATATTTGATTCAGAACAAATTTATCACT----AATTAA--CAGAGTGTCAATTATGCTAACATCTCAT Chimp: TGGTGGACACTTTTATAGGTACTCTGTGTCATTTTTGATACTGTAGGTATCTTATTTCATTTATCTTTATTCTTAATGTACGAATTCATAATATTTGATTCAGAACAAATTTATCACT--------AA--CAGAGTATCAATTATGCTAACATCTCAT ↑ 3 2 1 4 Gorilla: TGGTGGACACTTTTATAGGTACTCTGTGTCATTTTTGATACTGTAGGTATCTTATTTCATTTATCTTTATTCTTAATGTACAAATTCATAATATTTGATTCAGAACAAATTTATCACT--------AATTAACAGTGTCAATTATGCTAACATCTCAT Human: TGGTGGACACTTTTATAGGTACTCTGTGTCATTTTTGATACTGTAGGTATCTTATTTCATTTATCTTTATTCTTAATGTACGAATTCATAATATTTGATTCAGAACAAATTTATCACT----AATTAA--CAGAGTGTCAATTATGCTAACATCTCAT Cluster: [ ] Orangutan: TGGTGGACACTTTTATAGGTACTCTGTGTCATTTTTGATACTGTAGGTATCTTATTTCATTTATCTTTATTCTTAATGTACAAATTCATAATATTCGATTCAGAACAAATTTATCACTAATT----AA--CAGAGTGTCAATTATGCTAACATCTCAT Gorilla > Chimp --------------- chrKV421409:28972-28978 Template switch process: F1: L ACGAATTCATAATATTTGATTCAGAACAAATTTATCACTAA 1 F3: 4 TCAATTATGCTAACATCTCATTTACTGATTTTAATTTAAA R RF: TACTCTGTGTCATTTTTGATACTGTAGGTATCTTATTTCATTTATCTTTATTCTTAATGTACAAATTCATAATATTTGATTCAGAACAAATTTATCACTAATTAACAGTGTCAATTATGCTAACATCTCATTTACTGATTTTAATTTGAA RR: ATGAGACACAGTAAAAACTATGACATCCATAGAATAAAGTAAATAGAAATAAGAATTACATGTTTAAGTATTATAAACTAAGTCTTGTTTAAATAGTGATTAATTGTCACAGTTAATACGATTGTAGAGTAAATGACTAAAATTAAACTT F2: 3 ATGAGAC 2 Unidirectional alignment (log-probability: -38.7) CgAATTCATAATATTTGATTCAGAACAAATTTATCACTAA--cAgAGTaTCAATTATGCTAACATCTCATTTACTGATTTTAATTTaAA CAAATTCATAATATTTGATTCAGAACAAATTTATCACTAATTAACAGTGTCAATTATGCTAACATCTCATTTACTGATTTTAATTTGAA Template switch alignment (log-probability: -27.7) CgAATTCATAATATTTGATTCAGAACAAATTTATCACTAA|CAGAGTA|TCAATTATGCTAACATCTCATTTACTGATTTTAATTTaAA CAAATTCATAATATTTGATTCAGAACAAATTTATCACTAA|CAGAGTA|TCAATTATGCTAACATCTCATTTACTGATTTTAATTTGAA ========== Event 3991 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 2 Detected in comparisons: 2 Multiple sequence alignment: Human: TTGATCATGCTTCTTAATTTG------AACGCTTAAGTACTCTGTCAAAACCTAATTGTCAGCT ↓ 1 4 3 2 Chimp: TTGATCATGCCTCTTAATTTGACAGAGTACTCTTAAGTACTCTGTCAAAACCTAATTGTCAGCT Gorilla: Human: TTGATCATGCTTCTTAATTTG------AACGCTTAAGTACTCTGTCAAAACCTAATTGTCAGCT Cluster: [ ] Orangutan: Human > Chimp ------------- chrKV421406:1741-1749 Template switch process: F1: L AAGTGATGAATCATCATGAATTGATCATGCCTCTTAATTTGA 1 F3: 4 CTTAAGTACTCTGTCAAAACCTAATTGTCAGCTTCGTAAT R RF: AAGTGATGAATCATCATGAATTGATCATGCTTCTTAATTTGAACGCTTAAGTACTCTGTCAAAACCTAATTGTCAGCTTCGTAAT RR: TTCACTACTTAGTAGTACTTAACTAGTACGAAGAATTAAACTTGCGAATTCATGAGACAGTTTTGGATTAACAGTCGAAGCATTA F2: 3 TCATGAGAC 2 Unidirectional alignment (log-probability: -31.6) GTGATGAATCATCATGAATTGATCATGCcTCTTAATTTGAcagagtACtCTTAAGTACTCTGTCAAAACCTAATTGTCAGCTTCGTAAT GTGATGAATCATCATGAATTGATCATGCTTCTTAATTTGA------ACGCTTAAGTACTCTGTCAAAACCTAATTGTCAGCTTCGTAAT Template switch alignment (log-probability: -22.4) GTGATGAATCATCATGAATTGATCATGCcTCTTAATTTGA|CAGAGTACT|CTTAAGTACTCTGTCAAAACCTAATTGTCAGCTTCGTAAT GTGATGAATCATCATGAATTGATCATGCTTCTTAATTTGA|CAGAGTACT|CTTAAGTACTCTGTCAAAACCTAATTGTCAGCTTCGTAAT ========== Event 3992 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT Chimp: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT ↓ 1 4 3 2 Gorilla: TAATAGTAACTATTCCCTGTATTGAATCCCTAGAAAGAGATTCAAAGAAGCCAGTGGGCTGAGT ↑ 1 4 3 2 Human: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT Cluster: [ ] Orangutan: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT Human > Gorilla --------------- chrX:63997666-63997672 Template switch process: F1: L ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT 1 F3: 4 CTAGAAAGAGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA R RF: ATACAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA RR: TATGTTAAAATCTCGATCTGATTATCATTGATAAGGGACATATAGATCTTTCCCTAAGTTTCTTCGGTCACCCGACTCATGATACGTTTTTTT F2: 3 CCTAAGT 2 Unidirectional alignment (log-probability: -39) AaAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATtgaATccCTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT ACAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT---AT--CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT Template switch alignment (log-probability: -27.9) AaAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT ACAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT Chimp > Gorilla --------------- chrX:63997666-63997672 Template switch process: F1: L ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT 1 F3: 4 CTAGAAAGAGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA R RF: ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA RR: TATTTTAAAATCTCGATCTGATTATCATTGATAAGGGACATATAGATCTTTCCCTAAGTTTCTTCGGTCACCCGACTCATGATACGTTTTTTT F2: 3 CCTAAGT 2 Unidirectional alignment (log-probability: -33.5) AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATtgaATccCTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT---AT--CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT Template switch alignment (log-probability: -22.4) AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT ========== Event 3993 ========== Phylogenetic placement: species tree consistent Significant comparisons: 35 Detected in comparisons: 35 Multiple sequence alignment: Human: TACAATAAATATCCACATTAGAATGTCTGAAGAATGGGCCCAGGAGTATACAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCAGCTAATAAAACCTGCTCAGATCACATCTTTGATACTTT-- Chimp: TACAATAAATATCCACATTAGAATGTCTGAAGAATGGGCCCAGGAGTATACAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCAGCTAATAAAACCTGCTCAGATCACATCTTTGATACTTT-- ↑ 4 1 3 2 Gorilla: TACAATAAATATCCACATTAG-----------AATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCAGCTAATAAAACCTGCTCAGATCACATCTTTGATACTTT-- ↓ 4 1 3 2 Human: TACAATAAATATCCACATTAGAATGTCTGAAGAATGGGCCCAGGAGTATACAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCAGCTAATAAAACCTGCTCAGATCACATCTTTGATACTTT-- Cluster: [ ] Orangutan: TACAATAAATACCCACATTAGAATGTCTGAAGAATGGGCCCAGGAGTATACAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCGGCTAATAAAACGTGCTCAGATCACATCTTTGATACTCTAA Gorilla > Human --------------- chrX:93281871-93281875 Template switch process: F1: L GCAAATATGGCAAAGGCTTATACAATAAATATCCACATTAGAATG 1 F3: 4 AGAATGGGCCCAGGAGTATACAGTTTGTAAAAGTACCTTAAT R RF: GCAAATATGGCAAAGGCTTATACAATAAATATCCACATTAGAATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCAGCTAATAAAACCTGCTCAGA RR: CGTTTATACCGTTTCCGAATATGTTATTTATAGGTGTAATCTTACCCGGGTCCTCATATCTCAAACATTTTCATGGAATTAAACTAAGATTGACCGTGGAGGTCGATTATTTTGGACGAGTCT F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -32.2) TATGGCAAAGGCTTATACAATAAATATCCACATTagaatgtctgaAGAATGGGCCCAGGAGTATAcAGTTTGTAAAAGTACCTTA TATGGCAAAGGCTTATACAATAAATATCCACATT-----------AGAATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTA Template switch alignment (log-probability: -22) TATGGCAAAGGCTTATACAATAAATATCCACATTAGAATG|TCTGA|AGAATGGGCCCAGGAGTATAcAGTTTGTAAAAGTACCTTA TATGGCAAAGGCTTATACAATAAATATCCACATTAGAATG|TCTGA|AGAATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTA Gorilla > Chimp --------------- chrKV421408:130584-130588 Template switch process: F1: L GCAAATATGGCAAAGGCTTATACAATAAATATCCACATTAGAATG 1 F3: 4 AGAATGGGCCCAGGAGTATACAGTTTGTAAAAGTACCTTAAT R RF: GCAAATATGGCAAAGGCTTATACAATAAATATCCACATTAGAATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTAATTTGATTCTAACTGGCACCTCCAGCTAATAAAACCTGCTCAGA RR: CGTTTATACCGTTTCCGAATATGTTATTTATAGGTGTAATCTTACCCGGGTCCTCATATCTCAAACATTTTCATGGAATTAAACTAAGATTGACCGTGGAGGTCGATTATTTTGGACGAGTCT F2: 3 AGTCT 2 Unidirectional alignment (log-probability: -32.2) TATGGCAAAGGCTTATACAATAAATATCCACATTagaatgtctgaAGAATGGGCCCAGGAGTATAcAGTTTGTAAAAGTACCTTA TATGGCAAAGGCTTATACAATAAATATCCACATT-----------AGAATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTA Template switch alignment (log-probability: -22) TATGGCAAAGGCTTATACAATAAATATCCACATTAGAATG|TCTGA|AGAATGGGCCCAGGAGTATAcAGTTTGTAAAAGTACCTTA TATGGCAAAGGCTTATACAATAAATATCCACATTAGAATG|TCTGA|AGAATGGGCCCAGGAGTATAGAGTTTGTAAAAGTACCTTA ========== Event 3994 ========== Phylogenetic placement: species tree consistent Significant comparisons: 3 Detected in comparisons: 35 Multiple sequence alignment: Human: ACCGTTTATTTGGTGTGGGAAGAA----ATCTATGTTTTATTAGATTTCTATTATGAGCTTAttt---- Chimp: ACCGTTTATTTGGTGTGGGAAAAA----ATCTATGTTTTATTAGATTTCTATTATGAGCTTAttt---t Gorilla: ACCGTTTATTTGGTGTGGGAAAAA--------ATGTTTTATTAGATTTCTATTATGAGCTTAttt-tt- ↓ 1 4 3 2 Human: ACCGTTTATTTGGTGTGGGAAGAA----ATCTATGTTTTATTAGATTTCTATTATGAGCTTAttt---- Cluster: [ ] Orangutan: ACCGTTTATTTGGTGTGGGAAAAAATCT----ATGTTTTATTAGATTTCTATTATGAGCttttttt--- Gorilla > Human --------------- chrX:9490855-9490862 Template switch process: F1: L ATTAGTAGCTTAATAAATGGACCGTTTATTTGGTGTGGGAA 1 F3: 4 TGTTTTATTAGATTTCTATTATGAGCTTATTTTTTTT R RF: ATTAGTAGCTTAATAAATGGACCGTTTATTTGGTGTGGGAAAAAATGTTTTATTAGATTTCTATTATGAGCTTATTTTTTTT RR: TAATCATCGAATTATTTACCTGGCAAATAAACCACACCCTTTTTTACAAAATAATCTAAAGATAATACTCGAATAAAAAAAA F2: 3 ATCTAAAG 2 Unidirectional alignment (log-probability: -29) TTAGTAGCTTAATAAATGGACCGTTTATTTGGTGTGGGAAgAAatctATGTTTTATTAGATTTCTATTATGAGCTTATTTTTTTT-- TTAGTAGCTTAATAAATGGACCGTTTATTTGGTGTGGGAAAAA----ATGTTTTATTAGATTTCTATTATGAGCTTATTTTTTTTTT Template switch alignment (log-probability: -16.7) TTAGTAGCTTAATAAATGGACCGTTTATTTGGTGTGGGAA|GAAATCTA|TGTTTTATTAGATTTCTATTATGAGCTTATTTTTTTT TTAGTAGCTTAATAAATGGACCGTTTATTTGGTGTGGGAA|GAAATCTA|TGTTTTATTAGATTTCTATTATGAGCTTATTTTTTTT ========== Event 3995 ========== Phylogenetic placement: species tree consistent Significant comparisons: 2 Detected in comparisons: 25 Multiple sequence alignment: Human: ttatatatgtataaatACAAGGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGT------------------------------------------------------------------------------------------------------TCCTAATGTCAAACCCTACTTTTATTTGAACATCTCCTTTATTTATA ↓ 4 1 3 2 Chimp: ttatatatgtataaatACAAGGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGT--------------------------------------------------------------------TCAAATAAAAGTAGGGTTTGACATTAGGAGATATACCTAATGTCAAACCCTACTTTTATTTGAACATCTCCTTTATTTATA Gorilla: ttatatatgtataaatacaaggaga---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgc----------------------------------tcaaataaaagtagggtttgacattaggtatatc----------------------------------tcctaatgTCAAACCCTACTTTTATTTGAGCATCTCCTTTATTTATA Human: ttatatatgtataaatACAAGGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGT------------------------------------------------------------------------------------------------------TCCTAATGTCAAACCCTACTTTTATTTGAACATCTCCTTTATTTATA Cluster: [ ] Orangutan: gcttatatgtata-ATCTGAGGAGAACTTATTTGTTTGTGTTACATGGTAGGAAAGATACAGCAATAATGAGATCACTGAAATGACTGGAAATATGGCTATTTTATACTGCCTTACGTTTTATCAGAGTTTTTGCTGATGTTGTTACCTTGACAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGACATTAGGTATATC--------------------------------------------------------------------TCCTAATGTCGAACCCTACTTTTATTTGAACATCTCCTTTATTTATA Human > Chimp ------------- chrX:94952790-94952812 Template switch process: F1: L ACGTGCAGGTTTGTTATATATGTATAAATACAAGGAGATGTTC 1 F3: 4 AGGAGATATACCTAATGTCAAACCCTACTTTTATTTGAACATCTCCTTTA R RF: ACGTGCAGGTTTGTTATATATGTATAAATACAAGGAGATGTTCCTAATGTCAAACCCTACTTTTATTTGAACATCTCCTTTA RR: TGCACGTCCAAACAATATATACATATTTATGTTCCTCTACAAGGATTACAGTTTGGGATGAAAATAAACTTGTAGAGGAAAT F2: 3 TTACAGTTTGGGATGAAAATAAA 2 Unidirectional alignment (log-probability: -59.8) TGCAGGTTTGTTATATATGTATAAATACAAGGAGATGTTcaaataaaagtagggtttgacattaggagatataCCTAATGTCAAACCCTACTTTTATTTGAAC TGCAGGTTTGTTATATATGTATAAATACAAGGAGATGTT----------------------------------CCTAATGTCAAACCCTACTTTTATTTGAAC Template switch alignment (log-probability: -30.3) TGCAGGTTTGTTATATATGTATAAATACAAGGAGATGTTC|AAATAAAAGTAGGGTTTGACATT|AGGAGATaTaCCTAATGTCAAACCCTACTTTTATTTGAAC TGCAGGTTTGTTATATATGTATAAATACAAGGAGATGTTC|AAATAAAAGTAGGGTTTGACATT|AGGAGATGTTCCTAATGTCAAACCCTACTTTTATTTGAAC ========== Event 3996 ========== Phylogenetic placement: ambiguous, species tree or ILS consistent Significant comparisons: 12 Detected in comparisons: 1256 Multiple sequence alignment: Human: CACGCAGACCCCGGGGGGTGAGGCAGGGATGTCTAATGCAGAAAGCTCTGGCTTCTGTTTTTCAGAGAAAAA ↓ 13 2 4 ↑ 31 4 2 Chimp: CACGCAGACCCCGGGGGGTGA------GCTTTCTGCATTAGACATCCCTGCCTTCTGTTTTTCAGAGAAAAA Gorilla: CGCGCAGACCCCGGGGGGTGAGGCAGGGATGTCTAATGCAGAAAGTTCTGGCTTCTGTTTTTCAGAGAAAAA Human: CACGCAGACCCCGGGGGGTGAGGCAGGGATGTCTAATGCAGAAAGCTCTGGCTTCTGTTTTTCAGAGAAAAA Cluster: [ ] Orangutan: CACGCAGACCCCGGGGGGTGAGGCAGGGATGTCTAATGCAGAAAGCTCTGGCTTCTGTTTTTCAGAGAAAAA Chimp > Human ------------- chrX:9700257-9700281 Template switch process: F1: L GACAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG 1 F3: 4 CTGGCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC R RF: GACAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAGCTTTCTGCATTAGACATCCCTGCCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC RR: CTGTCCAAGTGTCGGGATCTGTGCGTCTGGGGCCCCCCACTCGAAAGACGTAATCTGTAGGGACGGAAGACAAAAAGTCTCTTTTTATACGGGCTCCATTTGTAG F2: 3 TCGAAAGACGTAATCTGTAGGGACG 2 Unidirectional alignment (log-probability: -61.1) CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG---------------------GCagggatgtctaatgcagaaagctctggCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAA CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAGCTTTCTGCATTAGACATCCCTGC---------------------------CTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAA Template switch alignment (log-probability: -24.4) CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG|GCAGGGATGTCTAATGCAGAAAGCT|CTGgCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAA CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG|GCAGGGATGTCTAATGCAGAAAGCT|CTGCCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAA Human > Chimp ------------- chrX:9529012-9529034 Template switch process: F1: L GACAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG 1 F3: 4 CTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC R RF: GACAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAGGCAGGGATGTCTAATGCAGAAAGCTCTGGCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC RR: CTGTCCAAGTGTCGGGATCTGTGCGTCTGGGGCCCCCCACTCCGTCCCTACAGATTACGTCTTTCGAGACCGAAGACAAAAAGTCTCTTTTTATACGGGCTCCATTTGTAG F2: 3 CGTCCCTACAGATTACGTCTTTC 2 Unidirectional alignment (log-probability: -52.7) CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAGctttctgcattagacatccctGC---------------------------CTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG---------------------GCAGGGATGTCTAATGCAGAAAGCTCTGGCTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC Template switch alignment (log-probability: -18.1) CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG|CTTTCTGCATTAGACATCCCTGC|CTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC CAGGTTCACAGCCCTAGACACGCAGACCCCGGGGGGTGAG|CTTTCTGCATTAGACATCCCTGC|CTTCTGTTTTTCAGAGAAAAATATGCCCGAGGTAAACATC ========== Event 3997 ========== Phylogenetic placement: species tree consistent Significant comparisons: 5 Detected in comparisons: 35 Multiple sequence alignment: Human: GAAAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTAAAC-------------------AAGGTCATATGACCTGCACAAGGTCATGAGAAAAGCTTGACTGAATG Chimp: GAAAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTAAAC-------------------AAGGTCATATGACCTGCACAAGGTCATGAGAAAAGCTTGACTGAATG ↑ 4 3 2 Gorilla: GAAAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTAAAC--------------------------------------AAGGTCATGAGAAAAGTTTGACTGAATG Human: GAAAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTAAAC-------------------AAGGTCATATGACCTGCACAAGGTCATGAGAAAAGCTTGACTGAATG Cluster: [ ] Orangutan: GAAAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTGAACGAGGTCATATGACCTGCAC-------------------GAGGTCATGAGAAAAGCTTGACTGAATG Gorilla > Chimp --------------- chrX:95730645-95730650 Template switch process: F1: L AAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTAAACAAGGTCAT 1 F3: 4 TGC-------------------ACAAGGTCATGAGAAAAGCTTGACTGAATGAAAATTAGGGAA R RF: AAACTTTAAAAAGCAGATGCTCATAGATATGTGAGTTAAACAAGGTCATGAGAAAAGTTTGACTGAATGAAAATTAGGGAA RR: TTTGAAATTTTTCGTCTACGAGTATCTATACACTCAATTTGTTCCAGTACTCTTTTCAAACTGACTTACTTTTAATCCCTT F2: 3 CCAGTA 2 Unidirectional alignment (log-probability: -43.7) AAAGCAGATGCTCATAGATATGTGAGTTAAacaaggtcatatgacctgcACAAGGTCATGAGAAAAGcTTGACTGAATGAAAATTA AAAGCAGATGCTCATAGATATGTGAGTTAA-------------------ACAAGGTCATGAGAAAAGTTTGACTGAATGAAAATTA Template switch alignment (log-probability: -33) AAAGCAGATGCTCATAGATATGTGAGTTAAACAAGGTCAT|ATGACC|TGC-------------------ACAAGGTCATGAGAAAAGcTTGACTGAATGAAAATTA AAAGCAGATGCTCATAGATATGTGAGTTAAACAAGGTCAT|ATGACC|TGCTCATAGATATGTGAGTTAAACAAGGTCATGAGAAAAGTTTGACTGAATGAAAATTA ========== Event 3998 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 1 Detected in comparisons: 1 Multiple sequence alignment: Human: CAATTCCAGCCAGATGCAATATTTTTTCAGAATAA------------CAATTCTCCAGTTATTCTGAAAAAATAATACAATCATTAGCTAAG ↑ 1 4 3 2 Chimp: CAATTCCAGCCAGATGCAATAC----TAAGAATACCGGTGATAAAAGAAATTCTCCAGTTATTCTGAAAAAAGAATACAATCATTAGCTAAG Gorilla: Human: CAATTCCAGCCAGATGCAATATTTTTTCAGAATAA------------CAATTCTCCAGTTATTCTGAAAAAATAATACAATCATTAGCTAAG Cluster: [ ] Orangutan: Chimp > Human ------------- chrY:44317233-44317247 Template switch process: F1: L CAGTTAATAAACCTTTGATGCAATTCCAGCCAGATGCAATA 1 F3: 4 AATTCTCCAGTTATTCTGAAAAAATAATACAATCATTAGC R RF: CAGTTAATAAACCTTTGATGCAATTCCAGCCAGATGCAATACTAAGAATACCGGTGATAAAAGAAATTCTCCAGTTATTCTGAAAAAAGAATACAATCATTAGC RR: GTCAATTATTTGGAAACTACGTTAAGGTCGGTCTACGTTATGATTCTTATGGCCACTATTTTCTTTAAGAGGTCAATAAGACTTTTTTCTTATGTTAGTAATCG F2: 3 CAATAAGACTTTTTT 2 Unidirectional alignment (log-probability: -48.4) AGTTAATAAACCTTTGATGCAATTCCAGCCAGATGCAATattttttcagaataAC----------------------AATTCTCCAGTTATTCTGAAAAAAtAATACAATCATTAGC AGTTAATAAACCTTTGATGCAATTCCAGCCAGATGCAAT--------------ACTAAGAATACCGGTGATAAAAGAAATTCTCCAGTTATTCTGAAAAAAGAATACAATCATTAGC Template switch alignment (log-probability: -23.1) AGTTAATAAACCTTTGATGCAATTCCAGCCAGATGCAATA|TTTTTTCAGAATAAC|AATTCTCCAGTTATTCTGAAAAAAtAATACAATCATTAGC AGTTAATAAACCTTTGATGCAATTCCAGCCAGATGCAATA|TTTTTTCAGAATAAC|AATTCTCCAGTTATTCTGAAAAAAGAATACAATCATTAGC ========== Event 3999 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 12 Detected in comparisons: 12 Multiple sequence alignment: Human: GAGTCATCATACAGATTAGATAGTTTGGCCAAAGGATTTGGCCAAATTTTCTTAAAATATATTCTT ↓ 1 3 4 2 ↑ 1 3 4 2 Chimp: GAGTCATCATACAGATTAGAT---ATGGCCAAATCCTTTGGCCAAATTTTCTTAAAATATATTCTT Gorilla: Human: GAGTCATCATACAGATTAGATAGTTTGGCCAAAGGATTTGGCCAAATTTTCTTAAAATATATTCTT Cluster: [ ] Orangutan: Chimp > Human ------------- chrY:42262084-42262096 Template switch process: F1: L TAGGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATAG 1 F3: 4 TTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA R RF: TAGGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATATGGCCAAATCCTTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA RR: ATCCCTGTGTGTCCACCCCTCTCAGTAGTATGTCTAATCTATACCGGTTTAGGAAACCGGTTTAAAAGAATTTTATATAAGAATTGAAGAAAT F2: 3 AGGAAACCGGTTT 2 Unidirectional alignment (log-probability: -33.3) GGACACACAGGTGGGGAGAGTCATCATACAGATTAGATAgttTGGCCAAAggaTTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA GGACACACAGGTGGGGAGAGTCATCATACAGATTAGATA---TGGCCAAATCCTTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA Template switch alignment (log-probability: -22.9) GGACACACAGGTGGGGAGAGTCATCATACAGATTAGATAg|TTTGGCCAAAGGA|TTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA GGACACACAGGTGGGGAGAGTCATCATACAGATTAGATAT|TTTGGCCAAAGGA|TTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA Human > Chimp ------------- chrY:22820390-22820400 Template switch process: F1: L TAGGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATA 1 F3: 4 TTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA R RF: TAGGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATAGTTTGGCCAAAGGATTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA RR: ATCCCTGTGTGTCCACCCCTCTCAGTAGTATGTCTAATCTATCAAACCGGTTTCCTAAACCGGTTTAAAAGAATTTTATATAAGAATTGAAGAAAT F2: 3 CCTAAACCGGT 2 Unidirectional alignment (log-probability: -29.2) GGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATA---TGGCCAAAtccTTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA GGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATAGTTTGGCCAAAGGATTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA Template switch alignment (log-probability: -16.7) GGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATA|TGGCCAAATCC|TTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA GGGACACACAGGTGGGGAGAGTCATCATACAGATTAGATA|TGGCCAAATCC|TTTGGCCAAATTTTCTTAAAATATATTCTTAACTTCTTTA ========== Event 4000 ========== Phylogenetic placement: species tree consistent Significant comparisons: 46 Detected in comparisons: 46 Multiple sequence alignment: Human: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT Chimp: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT ↓ 1 4 3 2 Gorilla: TAATAGTAACTATTCCCTGTATTGAATCCCTAGAAAGAGATTCAAAGAAGCCAGTGGGCTGAGT ↑ 1 4 3 2 Human: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT Cluster: [ ] Orangutan: TAATAGTAACTATTCCCTGTA-----TATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGT Human > Gorilla --------------- chrX:63997666-63997672 Template switch process: F1: L ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT 1 F3: 4 CTAGAAAGAGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA R RF: ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA RR: TATTTTAAAATCTCGATCTGATTATCATTGATAAGGGACATATAGATCTTTCCCTAAGTTTCTTCGGTCACCCGACTCATGATACGTTTTTTT F2: 3 CCTAAGT 2 Unidirectional alignment (log-probability: -33.5) AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATtgaATccCTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT---AT--CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT Template switch alignment (log-probability: -22.4) AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT Chimp > Gorilla --------------- chrX:63997666-63997672 Template switch process: F1: L ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT 1 F3: 4 CTAGAAAGAGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA R RF: ATAAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATATCTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTATGCAAAAAAA RR: TATTTTAAAATCTCGATCTGATTATCATTGATAAGGGACATATAGATCTTTCCCTAAGTTTCTTCGGTCACCCGACTCATGATACGTTTTTTT F2: 3 CCTAAGT 2 Unidirectional alignment (log-probability: -33.5) AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTATtgaATccCTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT---AT--CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT Template switch alignment (log-probability: -22.4) AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGaGATTCAAAGAAGCCAGTGGGCTGAGTACTAT AAAATTTTAGAGCTAGACTAATAGTAACTATTCCCTGTAT|TGAATCC|CTAGAAAGGGATTCAAAGAAGCCAGTGGGCTGAGTACTAT ========== Event 4001 ========== Phylogenetic placement: ILS consistent Significant comparisons: 16 Detected in comparisons: 16 Multiple sequence alignment: Human: TAGGTCTCCGTGACTTCAGGG--TGCAGCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG ↑ 1 4 3 2 Chimp: TAGGTCTCCGTGACTTCAGGGCGTGATTCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGATGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG ↓ 1 4 3 2 Gorilla: TAGGTCTCCGTGACTTCAGGG--TGCAGCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTTATTTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG Human: TAGGTCTCCGTGACTTCAGGG--TGCAGCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG Cluster: [ ] Orangutan: TAGGTCTCCGTGACTTCAGGG--TACAGCCAGGTTGGACCAGATAGACTGGGGTCCCCCGTGTGGCCAGGTGACCTGGGGACTCTGGGTCTCCAAGGACGAGAGGTTCTTCTGCACACAGGCCACGATGCCCAGG Chimp > Human ------------- chrY:56609431-56609435 Template switch process: F1: L GGGACATGTTTTGGGGTCTCTAGGTCTCCGTGACTTCAGGG 1 F3: 4 CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA R RF: GGGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATTCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGATGAGAGGTTCTTCTGCA RR: CCCTGTACAAAACCCCAGAAATCCAGAGGCACTGAAGTCCCGCACTAAGGTCCAACCTGGTCTTTCTGACCCCAGGGGGCACACCGGTCCACTAAACCCCTGAGACCCAGAGGTTCCTACTCTCCAAGAAGACGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -33.2) GGACATGTTTTGGGGTCTcTAGGTCTCCGTGACTTCAGGG------TgcagCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATT----CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA Template switch alignment (log-probability: -21.9) GGACATGTTTTGGGGTCTcTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA Chimp > Gorilla --------------- chrX:155860686-155860690 Template switch process: F1: L GGGACATGTTTTGGGGTCCCTAGGTCTCCGTGACTTCAGGG 1 F3: 4 CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA R RF: GGGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATTCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCAGGTGATTTGGGGACTCTGGGTCTCCAAGGATGAGAGGTTCTTCTGCA RR: CCCTGTACAAAACCCCAGAAATCCAGAGGCACTGAAGTCCCGCACTAAGGTCCAACCTGGTCTTTCTGACCCCAGGGGGCACACCGGTCCACTAAACCCCTGAGACCCAGAGGTTCCTACTCTCCAAGAAGACGT F2: 3 GACGT 2 Unidirectional alignment (log-probability: -37.7) GGACATGTTTTGGGGTCccTAGGTCTCCGTGACTTCAGGG------TgcagCCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGGCGTGATT----CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA Template switch alignment (log-probability: -27.4) GGACATGTTTTGGGGTCccTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA GGACATGTTTTGGGGTCTTTAGGTCTCCGTGACTTCAGGG|TGCAG|CCAGGTTGGACCAGAAAGACTGGGGTCCCCCGTGTGGCCA ========== Event 4002 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: GCGAATTTTTTCTCCTTCTCACTGTCCCCAGGGACAGTGTCCCAGGGAAGGGACAGCCCT Chimp: Gorilla: GCGAATTTTTTCTCCTTCTCAGTGTCCCCAG----CATTTCCCAGGGAAGGGACAGCCCT ↓ 3 2 1 4 Human: GCGAATTTTTTCTCCTTCTCACTGTCCCCAGGGACAGTGTCCCAGGGAAGGGACAGCCCT Cluster: [ ] Orangutan: GTGAATTTTTTCTCCTTCTCACTGTCCCCAG----CATTTCCCAGGGAGGGGACAGCCCT Gorilla > Human --------------- chrY:804732-804739 Template switch process: F1: L TTTCACAACTGCGAATTTTTTCTCCTTCTCACTGTCCCCAG 1 F3: 4 TCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT R RF: TTTCACAACTGCGAATTTTTTCTCCTTCTCAGTGTCCCCAGCATTTCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT RR: AAAGTGTTGACGCTTAAAAAAGAGGAAGAGTCACAGGGGTCGTAAAGGGTCCCTTCCCTGTCGGGAAGGGTTAAGCTAGAGGGAA F2: 3 GTGACAGG 2 Unidirectional alignment (log-probability: -37.5) TTCACAACTGCGAATTTTTTCTCCTTCTCAcTGTCCCCAGggaCAgTgTCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT TTCACAACTGCGAATTTTTTCTCCTTCTCAGTGTCCCCAG---CA-TTTCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT Template switch alignment (log-probability: -27.8) TTCACAACTGCGAATTTTTTCTCCTTCTCAcTGTCCCCAG|GGACAgTG|TCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT TTCACAACTGCGAATTTTTTCTCCTTCTCAGTGTCCCCAG|GGACACTG|TCCCAGGGAAGGGACAGCCCTTCCCAATTCGATCTCCCTT ========== Event 4003 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 3 Detected in comparisons: 3 Multiple sequence alignment: Human: CATTCTGTGCAGACACCACTCAGAGGAACTGTGGTTAGAGAAAAGCTTGATAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG-------------- Chimp: Gorilla: CATTCTGTGCAGACACCACTCC--AGGCCTGGGATC--------------AAGCTTTTCTCTAACCACAGTTCCTctgagcagccaggatggatggg ↓ 1 3 4 2 Human: CATTCTGTGCAGACACCACTCAGAGGAACTGTGGTTAGAGAAAAGCTTGATAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG-------------- Cluster: [ ] Orangutan: ------------------------------------------------------------------------------------------------- Gorilla > Human --------------- chrY:56298650-56298679 Template switch process: F1: L GTCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTC 1 F3: 4 AGCTTTTCTCTAACCACAGTTCCTCTGAGCAG R RF: GTCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTCCAGGCCTGGGATCAAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG RR: CAGGAAGACAAAGACAGGACGTAAGACACGTCTGTGGTGAGGTCCGGACCCTAGTTCGAAAAGAGATTGGTGTCAAGGAGACTCGTC F2: 3 TAGTTCGAAAAGAGATTGGTGTCAAGGAGA 2 Unidirectional alignment (log-probability: -70) TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCAC-------------TCAgaggaactgtggttagagaaaagcttgatAGCTTTTCTCTAACCACAGTTCCTCTGAGCAG-------- TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTCCAGGCCTGGGATCA-----------------------------AGCTTTTCTCTAACCACAGTTCCTCTGAGCAGCCAGGATG Template switch alignment (log-probability: -19.4) TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTC|AGAGGAACTGTGGTTAGAGAAAAGCTTGAT|AGCTTTTCTCTAACCACAGTTCCTCTGAGCAG TCCTTCTGTTTCTGTCCTGCATTCTGTGCAGACACCACTC|AGAGGAACTGTGGTTAGAGAAAAGCTTGAT|AGCTTTTCTCTAACCACAGTTCCTCTGAGCAG ========== Event 4004 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: Chimp: TATGATATTTATTCCCCTTTCACAA------CAGGAACTTCatatatatatatatt ↓ 3 1 2 4 Gorilla: TATGATATTTATTCCCCTTTCACAACCTGTTGTGAAACTTCatatatatat----- Human: Cluster: [ ] Orangutan: TATGATATTTATTCCCCTTTCACAA------GAGGAACTTCATAT----------- Chimp > Gorilla --------------- chr10:118653674-118653682 Template switch process: F1: L CTATTTTAGTCATGAATATGATATTTATTCCCCTTTCACAAC 1 F3: 4 AACTTCATATA-------------TATATATATATTCATT R RF: CTATTTTAGTCATGAATATGATATTTATTCCCCTTTCACAACAGGAACTTCATATATATATATATTCATTATATATATATTCATT RR: GATAAAATCAGTACTTATACTATAAATAAGGGGAAAGTGTTGTCCTTGAAGTATATATATATATAAGTAATATATATATAAGTAA F2: 3 AGTGTTGTC 2 Unidirectional alignment (log-probability: -40.8) ATTTTAGTCATGAATATGATATTTATTCCCCTTTCACAACctgttgtGaAACTTCATATA-------------TATATATATATTCATT ATTTTAGTCATGAATATGATATTTATTCCCCTTTCACAACA------GGAACTTCATATATATATATATTCATTATATATATATTCATT Template switch alignment (log-probability: -27) ATTTTAGTCATGAATATGATATTTATTCCCCTTTCACAAC|CTGTTGTGA|AACTTCATATA-------------TATATATATATTCATT ATTTTAGTCATGAATATGATATTTATTCCCCTTTCACAAC|CTGTTGTGA|AACTTCATATATATATATATTCATTATATATATATTCATT ========== Event 4005 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: Chimp: TTGGCCAAAATAACTCTTGCTGGTGAAGAAAGCTGGGAGAAACGTGAG--GTCTGAATGGTTACTCGCCACCGTCTGGCGTAGGTGACTCAGCCAGGCA ↓ 3 2 1 4 Gorilla: TTGGCCAAAACAACTCTTGCTGGTGAAGAAAGCTGGGAGAAACAGCTTTCTTCACCAGGGTTACTCGCCACTGTCTGGAGTAGGTGACTCAGCCAGGCA Human: Cluster: [ ] Orangutan: TTGGCCAAAATAACTCTTGCTGGTGAAGAAAGCTGGGAGGAACATGAG--GCCTGAAGGGTTACTCGCCACCGTCTGGCGTAGGCGACTCTGCCAGGCA Chimp > Gorilla --------------- chr18:69468642-69468656 Template switch process: F1: L AGCTGGGAGAAAC 1 F3: 4 GGTTACTCGCCACTGTCTGGAGTAGGTGACTCAGCCAGGCAGGACCTCACACAGAAGAAAC R RF: CTGGTGAAGAAAGCTGGGAGAAACGTGAGGTCTGAATGGTTACTCGCCACCGTCTGGCGTAGGTGACTCAGCCAGGCAGGACCTCACACAGAAGAAAC RR: GACCACTTCTTTCGACCCTCTTTGCACTCCAGACTTACCAATGAGCGGTGGCAGACCGCATCCACTGAGTCGGTCCGTCCTGGAGTGTGTCTTCTTTG F2: 3 GACCACTTCTTTCGA 2 Unidirectional alignment (log-probability: -52.3) AGCTGGGAGAAACagctttcttcaccaG------------GGTTACTCGCCACtGTCTGGaGTAGGTGACTCAGCCAGGC AGCTGGGAGAAAC--------------GTGAGGTCTGAATGGTTACTCGCCACCGTCTGGCGTAGGTGACTCAGCCAGGC Template switch alignment (log-probability: -28.5) AGCTGGGAGAAAC|AGCTTTCTTCACCAG|GGTTACTCGCCACtGTCTGGaGTAGGTGACTCAGCCAGGC AGCTGGGAGAAAC|AGCTTTCTTCACCAG|GGTTACTCGCCACCGTCTGGCGTAGGTGACTCAGCCAGGC ========== Event 4006 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: ACCCTGGCACTGGGCTCTTGC----CGATCTTCTGGCACCTCAGGGCCGTAGTCTTGGGCACAGAGGCC ↑ 31 4 Gorilla: ACCCTGGCACTGGGCTCTTGCCAGAAGAT-------CACCCCAGGGCCCTAGTCTTGGGCACAGAGGCC Human: Cluster: [ ] Orangutan: ACCCTGGCACTGGGCTCTTGCCAGAAGAT-------CA-CCCAGGGCCCTAGTCTTGGGCACAGAGGCC Gorilla > Chimp --------------- chr19:19412302-19412311 Template switch process: F1: L ACGTTTCAAATCCTGCTGAGACCCTGGCACTGGGCTCTTGCC 1 F3: 4 CACCTCAGGGCCGTAGTCTTGGGCACAGAGGCCTCCAGGACCTGGAGAAATTG R RF: ACATTTCAAATCCTGCTGAGACCCTGGCACTGGGCTCTTGCCAGAAGATCACCCCAGGGCCCTAGTCTTGGGCACAGAGGCCTCCAGGACCTGGAGAAATTG RR: TGTAAAGTTTAGGACGACTCTGGGACCGTGACCCGAGAACGGTCTTCTAGTGGGGTCCCGGGATCAGAACCCGTGTCTCCGGAGGTCCTGGACCTCTTTAAC F2: 3 GGTCTTCTAG 2 Unidirectional alignment (log-probability: -47.7) gTTTCAAATCCTGCTGAGACCCTGGCACTGGGCTCTTGCC----GATcttctggCACCtCAGGGCCgTAGTCTTGGGCACAGAGGCCTCCAGGA ATTTCAAATCCTGCTGAGACCCTGGCACTGGGCTCTTGCCAGAAGAT-------CACCCCAGGGCCCTAGTCTTGGGCACAGAGGCCTCCAGGA Template switch alignment (log-probability: -33.9) gTTTCAAATCCTGCTGAGACCCTGGCACTGGGCTCTTGCC|GATCTTCTGG|CACCtCAGGGCCgTAGTCTTGGGCACAGAGGCCTCCAGGA ATTTCAAATCCTGCTGAGACCCTGGCACTGGGCTCTTGCC|GATCTTCTGG|CACCCCAGGGCCCTAGTCTTGGGCACAGAGGCCTCCAGGA ========== Event 4007 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: Chimp: GGTGCTGGGCCTGTCCCTTCC-------CAGGGCCCAGCAGCTG-AGCTGGAGGACAAAGCCCAGGTGGA ↓ 1 3 4 2 Gorilla: GGTGCTGGGCCTGTCCCTTCC--------------CAGCAGCTCAGGCTGGAGGACGAAGCCCAGGTGGA Human: Cluster: [ ] Orangutan: GGTGCTGGGCCTGTCCCTTCCCAGGGCC-------CAGCAGCTG-AGCTGGAGGATGAAGCCAGGGTGGA Chimp > Gorilla --------------- chr21:3407562-3407569 Template switch process: F1: L CAGCTCAGCCCGGCTGCACGGGTGCTGGGCCTGTCCCTTCCCAG 1 F3: 4 GCTGGAGGACGAAGCCCAGGTGGACGCTCCACACCATGGC R RF: CAGCTCAGCCCGGCTGAACGGGTGCTGGGCCTGTCCCTTCCCAGGGCCCAGCAGCTGAGCTGGAGGACAAAGCCCAGGTGGACGCTCCACACCATGGG RR: GTCGAGTCGGGCCGACTTGCCCACGACCCGGACAGGGAAGGGTCCCGGGTCGTCGACTCGACCTCCTGTTTCGGGTCCACCTGCGAGGTGTGGTACCC F2: 3 GACTCGAC 2 Unidirectional alignment (log-probability: -44.6) TCAGCCCGGCTGcACGGGTGCTGGGCCTGTCCCTT-------CCCAGCAGCTcAgGCTGGAGGACgAAGCCCAGGTGGACGCTCCACACCATGGc TCAGCCCGGCTGAACGGGTGCTGGGCCTGTCCCTTCCCAGGGCCCAGCAGCTGA-GCTGGAGGACAAAGCCCAGGTGGACGCTCCACACCATGGG Template switch alignment (log-probability: -33.4) TCAGCCCGGCTGcACGGGTGCTGGGCCTGTCCCTTCCCAG|CAGCTCAG|GCTGGAGGACgAAGCCCAGGTGGACGCTCCACACCATGGc TCAGCCCGGCTGAACGGGTGCTGGGCCTGTCCCTTCCCAG|CAGCTCAG|GCTGGAGGACAAAGCCCAGGTGGACGCTCCACACCATGGG ========== Event 4008 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: Chimp: ATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATT---TTGTG-AGCCAGGAAAACATTTTTCACAA ↓ 3 2 1 4 Gorilla: ATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTTACCTATGATACCAGGAAAACATTTTTCACAA Human: Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr21:15641814-15641823 Template switch process: F1: L GGATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTT 1 F3: 4 CCAGGAAAACATTTTTCACAAGCAATCAGTTTGTACTAAA R RF: GGATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTTTGTGAGCCAGGAAAACATTTTTCACAAACAATCAGTTTGTACTAAA RR: CCTAATTTCACTTCGATCTCAATAGTATGCATTTCCTTTAAAACACTCGGTCCTTTTGTAAAAAGTGTTTGTTAGTCAAACATGATTT F2: 3 ATAGTATCCA 2 Unidirectional alignment (log-probability: -40.8) ATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTT------acctatgataCCAGGAAAACATTTTTCACAAgCAATCAGTTTGTACTAAA ATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTTTGTGAG----------CCAGGAAAACATTTTTCACAAACAATCAGTTTGTACTAAA Template switch alignment (log-probability: -28.1) ATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTT|ACcTATGATA|CCAGGAAAACATTTTTCACAAgCAATCAGTTTGTACTAAA ATTAAAGTGAAGCTAGAGTTATCATACGTAAAGGAAATTT|ACGTATGATA|CCAGGAAAACATTTTTCACAAACAATCAGTTTGTACTAAA ========== Event 4009 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: TAACATATTTTTAATAAAGATACATGATAATATTTTATTATC-----ATGTATAAAAGGGCAAGTATAGTGCTGTGGCAG ↑ 3 2 1 4 Gorilla: TAACATATTTTTAATAAAGATACATGATAATATTTTATTCACACGAACTGTACAAAAGGACAAGTATAGTGCTGTGGCAG Human: Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr21:16659608-16659616 Template switch process: F1: L TTTAACATATTTTTAATAAAGATACATGATAATATTTTATT 1 F3: 4 AAAAGGGCAAGTATAGTGCTGTGGCAGAAGTTATTAACATAGAAACA R RF: TTTAACATATTTTTAATAAAGATACATGATAATATTTTATTCACACGAACTGTACAAAAGGACAAGTATAGTGCTGTGGCAGAAATTATTAACATAGAAACA RR: AAATTGTATAAAAATTATTTCTATGTACTATTATAAAATAAGTGTGCTTGACATGTTTTCCTGTTCATATCACGACACCGTCTTTAATAATTGTATCTTTGT F2: 3 TATGTACTA 2 Unidirectional alignment (log-probability: -39) TTAACATATTTTTAATAAAGATACATGATAATATTTTATTatCA-----TGTAtAAAAGGgCAAGTATAGTGCTGTGGCAGAAgTTATTAACAT TTAACATATTTTTAATAAAGATACATGATAATATTTTATTCACACGAACTGTACAAAAGGACAAGTATAGTGCTGTGGCAGAAATTATTAACAT Template switch alignment (log-probability: -28.1) TTAACATATTTTTAATAAAGATACATGATAATATTTTATT|ATCATGTAT|AAAAGGgCAAGTATAGTGCTGTGGCAGAAgTTATTAACAT TTAACATATTTTTAATAAAGATACATGATAATATTTTATT|ATCATGTAT|AAAAGGACAAGTATAGTGCTGTGGCAGAAATTATTAACAT ========== Event 4010 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: Chimp: TTCGGGGAAGGAGGGCGCGGCGCTGGGCCAGGCCGGAGGGGCGGCCAGGGCTGATAGAAAGGGGCTGTGGAGAAGGGGCCCGGGGAGGAGCCAGGACGGGTCTGGACCCAGCTCCACGCCGTGCGCCCCTCACGTACCCCGGCGGGGCACGGTCGGCC--------------------CTCGGGAGCTTCCCTCAAGCCGTGCCCT ↓ 3 2 4 1 Gorilla: TTCGGGGAAGGAGGGCGCGGCGCTGGGCCAGGCCGGAgggggggCCAGGGCTGATAGAAAGGGGCTGTGGAGAAGGGGCCCGGGGAGGAGCCAGGACGGGTCTGGACCCAGCTCCACGCCGTGCGCCCCTCACGTACACCGGCGGGGCACGGTCGGCCCTCGGGAGGCCCATCGCGCCCTCGGGAGCTTCCCTCAAGCCGTGCCCT Human: Cluster: [ ] Orangutan: Chimp > Gorilla --------------- chr22:778262-778270 Template switch process: F1: L GCCGTGCGCCCCTCACGTACACCGGCGGGGCACGGTCGGCCCTCGGGAG 1 F3: 4 GCCCTCGGGAGCTTCCCTCAAGCCGTGCCCTTCATGCCGCCGA R RF: GCGCTGGGCCAGGCCGGAGGGGCGGCCAGGGCTGATAGAAAGGGGCTGTGGAGAAGGGGCCCGGGGAGGAGCCAGGACGGGTCTGGACCCAGCTCCACGCCGTGCGCCCCTCACGTACCCCGGCGGGGCACGGTCGGCCCTCGGGAGCTTCCCTCAAGCCGTGCCCTTCATGCCGCCGA RR: CGCGACCCGGTCCGGCCTCCCCGCCGGTCCCGACTATCTTTCCCCGACACCTCTTCCCCGGGCCCCTCCTCGGTCCTGCCCAGACCTGGGTCGAGGTGCGGCACGCGGGGAGTGCATGGGGCCGCCCCGTGCCAGCCGGGAGCCCTCGAAGGGAGTTCGGCACGGGAAGTACGGCGGCT F2: 3 CGCTACCCG 2 Unidirectional alignment (log-probability: -45.2) CCCTCACGTACaCCGGCGGGGCACGGTCGgccctcgggaggcccatcgcGCCCTCGGGAGCTTCCCTCAAGCCGTGCCCTTCATGCCGC CCCTCACGTACCCCGGCGGGGCACGGTCG--------------------GCCCTCGGGAGCTTCCCTCAAGCCGTGCCCTTCATGCCGC Template switch alignment (log-probability: -28.2) CCCTCACGTACaCCGGCGGGGCACGGTCGGCCCTCGGGAG|GCCCAtCGC|GCCCTCGGGAGCTTCCCTCAAGCCGTGCCCTTCATGCCGC CCCTCACGTACCCCGGCGGGGCACGGTCGGCCCTCGGGAG|GCCCAGCGC|GCCCTCGGGAGCTTCCCTCAAGCCGTGCCCTTCATGCCGC ========== Event 4011 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: AATTAAATTGAACACTTGGTTATGACAAGAATTTTCTTGTCATACTTATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAA ↑ 4 2 1 Gorilla: AATTAAATTGAACACTTGGTTA--------------------------TGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAA Human: Cluster: [ ] Orangutan: AATTAAATTGAACACTTGGTTA--------------------------TGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAA Gorilla > Chimp --------------- chr2A:58789825-58789831 Template switch process: F1: L TGCCTACATGCTTTCTATAAATTAAATTGAACACTTGGTTATGACAAGAATTTTCTT 1 F3: 4 TTATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAAAACT R RF: TGCCTACATGCTTTCTATAAATTAAATTGAACACTTGGTTATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAAAACT RR: ACGGATGTACGAAAGATATTTAATTTAACTTGTGAACCAATACTGTTCTTAAAAGAATAGACTTCTTTCTCTTCTTTTTGA F2: 3 CATACTG 2 Unidirectional alignment (log-probability: -48.3) TAAATTAAATTGAACACTTGGTtatgacaagaattttcttgtcatactTATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAAA TAAATTAAATTGAACACTTGGT--------------------------TATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAAA Template switch alignment (log-probability: -22.6) TAAATTAAATTGAACACTTGGTTATGACAAGAATTTTCTT|GTCATAc|TTATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAAA TAAATTAAATTGAACACTTGGTTATGACAAGAATTTTCTT|GTCATAA|TTATGACAAGAATTTTCTTATCTGAAGAAAGAGAAGAAAA ========== Event 4012 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 6 Detected in comparisons: 6 Multiple sequence alignment: Human: Chimp: CTTCTTCCTTGGGGTTGGGTG----T-GTCTTTTGGATACAGGGcagtgtggtatgatggttaaaggcac ↓ 1 4 3 2 Gorilla: CTTCTTCCTTGGGGTTGGGTGACACTGCCCTTTTGGATACACGGcagtgtggtatgatggttaaaggcac Human: Cluster: [ ] Orangutan: CTTCTTCCTTGAGGTTGGGTG----T-GTCTTTTGGATACAGGGcagtgtggtatgatggttaaaggcac Chimp > Gorilla --------------- chr2A:12186482-12186489 Template switch process: F1: L TTTTTTCTGAAGCTTCTCCCCTTCTTCCTTGGGGTTGGGTG 1 F3: 4 CTTTTGGATACACGGCAGTGTGGTATGATGGTTAAAGGCA R RF: TTTTTTCTGAAGCTTCTCCCCTTCTTCCTTGGGGTTGGGTGTGTCTTTTGGATACAGGGCAGTGTGGTATGATGGTTAAAGGCA RR: AAAAAAGACTTCGAAGAGGGGAAGAAGGAACCCCAACCCACACAGAAAACCTATGTCCCGTCACACCATACTACCAATTTCCGT F2: 3 CCGTCACA 2 Unidirectional alignment (log-probability: -37.8) TTTTTCTGAAGCTTCTCCCCTTCTTCCTTGGGGTTGGGTG---acactgccCTTTTGGATACAcGGCAGTGTGGTATGATGGTTAAAGGCA TTTTTCTGAAGCTTCTCCCCTTCTTCCTTGGGGTTGGGTGTGT--------CTTTTGGATACAGGGCAGTGTGGTATGATGGTTAAAGGCA Template switch alignment (log-probability: -22.3) TTTTTCTGAAGCTTCTCCCCTTCTTCCTTGGGGTTGGGTG|ACACTGCC|CTTTTGGATACAcGGCAGTGTGGTATGATGGTTAAAGGCA TTTTTCTGAAGCTTCTCCCCTTCTTCCTTGGGGTTGGGTG|ACACTGCC|CTTTTGGATACAGGGCAGTGTGGTATGATGGTTAAAGGCA ========== Event 4013 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: GGTATATTCATGCTTGGCTAT-TTAAGTACTTACTTAAGTGTTTGTTCAGGAGATA ↑ 1 3 4 2 Gorilla: GGTATATTCACGCTTGGCTATTTTAAGTA----CTTAAGTGTTTGTTCAGGAGATA Human: Cluster: [ ] Orangutan: GGTATATTCATGCTTGGCTATTTTAAGTA----CTTAAGCGTTGGTTCAGGAGATA Gorilla > Chimp --------------- chr4:133847145-133847151 Template switch process: F1: L TACTTAAAATGGCCCCTGTTGGTATATTCATGCTTGGCTATTT 1 F3: 4 TACTTAAGTGTTTGTTCAGGAGATACTAATTGAAAGATTGAT R RF: TGCTTAAAATGGCCCCTGTTGGTATATTCACGCTTGGCTATTTTAAGTACTTAAGTGTTTGTTCAGGAGATACTAACTGAAAGATTGAT RR: ACGAATTTTACCGGGGACAACCATATAAGTGCGAACCGATAAAATTCATGAATTCACAAACAAGTCCTCTATGATTGACTTTCTAACTA F2: 3 TCATGAA 2 Unidirectional alignment (log-probability: -42.9) TTAAAATGGCCCCTGTTGGTATATTCAtGCTTGGCTATTTaagTActTACTTAAGTGTTTGTTCAGGAGATACTAAtTGAAAGATTG TTAAAATGGCCCCTGTTGGTATATTCACGCTTGGCTATTT---TAAGTACTTAAGTGTTTGTTCAGGAGATACTAACTGAAAGATTG Template switch alignment (log-probability: -33.3) TTAAAATGGCCCCTGTTGGTATATTCAtGCTTGGCTATTT|AAGTACT|TACTTAAGTGTTTGTTCAGGAGATACTAAtTGAAAGATTG TTAAAATGGCCCCTGTTGGTATATTCACGCTTGGCTATTT|AAGTACT|TACTTAAGTGTTTGTTCAGGAGATACTAACTGAAAGATTG ========== Event 4014 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: tCAGTTGTACTGATAAATTAGCTACTGCCAGGTTAAGAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACAAAATCTATTCATTCTTTAATGTAGCTTCTTAACCTGGCAGTAGCtttttttGCTGTGCTTAAATTT ↑ 3 2 1 4 Gorilla: tCAGTTTTACTGATAAATTAGCTACTGCCAGGTTAAGAAGCTACATTAAAGAATGAATAGATTTTGCAGTTAC-----------------AAATGTAGCTTCTTAACTTGGCAGTAGCT-TTTTTGCTGTGCTTAAATTT Human: Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr4:126602027-126602069 Template switch process: F1: L TTAAGAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACAAA 1 F3: 4 TTTTTTGCTGTG R RF: AGCTACTGCCAGGTTAAGAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACAAATGTAGCTTCTTAACTTGGCAGTAGCTTTTTTGCTGTG RR: TCGATGACGGTCCAATTCTTCGATGTAATTTCTTACTTATCTAAAACGTCAATGTTTACATCGAAGAATTGAACCGTCATCGAAAAAACGACAC F2: 3 TCGATGACGGTCCAATTCTTCGATGTAATTTCTTACTTATCTA 2 Unidirectional alignment (log-probability: -52) GAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACAaaatctattcattctttAATGTAGCTTCTTAACcTGGCAGTAGCtTTTTTTGCTGTG GAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACA-----------------AATGTAGCTTCTTAACTTGGCAGTAGC-TTTTTTGCTGTG Template switch alignment (log-probability: -20.6) GAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACAAA|ATCTATTCATTCTTTAATGTAGCTTCTTAACCTGGCAGTAGCT|TTTTTTGCTGTG GAAGCTACATTAAAGAATGAATAGATTTTGCAGTTACAAA|ATCTATTCATTCTTTAATGTAGCTTCTTAACCTGGCAGTAGCT|TTTTTTGCTGTG ========== Event 4015 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: GGAAAAGGGCAAAGCGCAGTCAGGGGT-----------CTGCCCTGAGTCTGCAACTTGCCCAGGCCACAAAG ↑ 3 2 4 1 Gorilla: GGAAAAGGGCAAAGCGCAGTCAGGGGT----------------------CTGCAACTTGCCCAGGCCACAAAG Human: Cluster: [ ] Orangutan: GGAAAAAGGCAAAGCGCAGTCAGGGGTCTCCCCTGAGT-----------CTGCAACTTGCCCAGGCCACAAAG Gorilla > Chimp --------------- chr7:4638505-4638509 Template switch process: F1: L CAATCAGGGTACAGGGAAAAGGGCAAAGCGCAGTCAGGGGTCTGC 1 F3: 4 GTCTGCAACTTGCCCAGGCCACAAAGCTCAGAGTCGAGTCCT R RF: CAATCAGGGTACAGGGAAAAGGGCAAAGCGCAGTCAGGGGTCTGCAACTTGCCCAGGCCACAAAGCTCAGAGTCGAGTCCT RR: GTTAGTCCCATGTCCCTTTTCCCGTTTCGCGTCAGTCCCCAGACGTTGAACGGGTCCGGTGTTTCGAGTCTCAGCTCAGGA F2: 3 AGTCC 2 Unidirectional alignment (log-probability: -26.7) AGGGTACAGGGAAAAGGGCAAAGCGCAGTCAGGGgtctgccctgaGTCTGCAACTTGCCCAGGCCACAAAGCTCAGAGTCGAGTC AGGGTACAGGGAAAAGGGCAAAGCGCAGTCAGGG-----------GTCTGCAACTTGCCCAGGCCACAAAGCTCAGAGTCGAGTC Template switch alignment (log-probability: -16.5) AGGGTACAGGGAAAAGGGCAAAGCGCAGTCAGGGGTCTGC|CCTGA|GTCTGCAACTTGCCCAGGCCACAAAGCTCAGAGTCGAGTC AGGGTACAGGGAAAAGGGCAAAGCGCAGTCAGGGGTCTGC|CCTGA|GTCTGCAACTTGCCCAGGCCACAAAGCTCAGAGTCGAGTC ========== Event 4016 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 5 Detected in comparisons: 5 Multiple sequence alignment: Human: Chimp: TGTGTGTATGTTTGTACCTGTTTTCTTCTGAAAA------CATTGGAA-----CAAATCATTTTAATAAGGTG ↑ 3 1 2 4 Gorilla: TGTGAGTATGTTTGTACCTGTTTTCAGAAGAAAACAGCAATATTGGAACAAAACAAATCATTTTAATAAGGTG Human: Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr7:64990103-64990112 Template switch process: F1: L AGAGTAAGTGTGCTTGTGTGTGTATGTTTGTACCTGTTTTC 1 F3: 4 ATTGG-----AACAAATCATTTTAATAAGGTGACTAATTTATTAGAAAACTA R RF: AGAGTAAGTGTGCTTGTGTGAGTATGTTTGTACCTGTTTTCAGAAGAAAACAGCAATATTGGAACAAAACAAATCATTTTAATAAGGTGACTAATTTATTAGAAAACTA RR: TCTCATTCACACGAACACACTCATACAAACATGGACAAAAGTCTTCTTTTGTCGTTATAACCTTGTTTTGTTTAGTAAAATTATTCCACTGATTAAATAATCTTTTGAT F2: 3 CAAAAGTCTT 2 Unidirectional alignment (log-probability: -49) GAGTAAGTGTGCTTGTGTGtGTATGTTTGTACCTGTTTTCttctGAAAAC------ATTGG-----AACAAATCATTTTAATAAGGTGACTAATTTATTAG GAGTAAGTGTGCTTGTGTGAGTATGTTTGTACCTGTTTTCAGAAGAAAACAGCAATATTGGAACAAAACAAATCATTTTAATAAGGTGACTAATTTATTAG Template switch alignment (log-probability: -32.7) GAGTAAGTGTGCTTGTGTGtGTATGTTTGTACCTGTTTTC|TTCTGAAAAC|ATTGG-----AACAAATCATTTTAATAAGGTGACTAATTTATTAG GAGTAAGTGTGCTTGTGTGAGTATGTTTGTACCTGTTTTC|TTCTGAAAAC|ATTGGAACAAAACAAATCATTTTAATAAGGTGACTAATTTATTAG ========== Event 4017 ========== Phylogenetic placement: ambiguous, missing/gapped/masked alignment block Significant comparisons: 56 Detected in comparisons: 56 Multiple sequence alignment: Human: Chimp: ACTCCAGGGGGGAACTCGCAGAACTCGCTGTGCAGAGCACTGCCGGAGGCTGCGAGTTCCCCCGAGGAGCACAGACCC ↓ 1 3 2 4 ↑ 31 4 2 Gorilla: ACTCCAGGTGGGAACTCGCAGCCTCC----GGCAGTGCTCTG-----CACAGCGAGTTCCCCGGAGGAGCACAGACCC Human: Cluster: [ ] Orangutan: Gorilla > Chimp --------------- chr9:116704871-116704900 Template switch process: F1: L TGGGCAGATGCAGACGCCGCACTCCAGGGGGGAACTCGCAG 1 F3: 4 GCGAGTTCCCCCGAGGAGCACAGACCCACCCACACCCCAC R RF: TGGGCAGATGCAGACGCCGCACTCCAGGTGGGAACTCGCAGCCTCCGGCAGTGCTCTGCACAGCGAGTTCCCCGGAGGAGCACAGACCCACCCACACCCCAC RR: ACCCGTCTACGTCTGCGGCGTGAGGTCCACCCTTGAGCGTCGGAGGCCGTCACGAGACGTGTCGCTCAAGGGGCCTCCTCGTGTCTGGGTGGGTGTGGGGTG F2: 3 TCGGAGGCCGTCACGAGACGTGTCGCTCAA 2 Unidirectional alignment (log-probability: -74.4) GGGCAGATGCAGACGCCGCACTCCAGGgGGGAACTCGCAG--------------------AactcgctgtgcagagcactgccggaggctGCGAGTTCCCCcGAGGAGCACAGACCCACCCACACCCCAC GGGCAGATGCAGACGCCGCACTCCAGGTGGGAACTCGCAGCCTCCGGCAGTGCTCTGCACA-----------------------------GCGAGTTCCCCGGAGGAGCACAGACCCACCCACACCCCAC Template switch alignment (log-probability: -30.6) GGGCAGATGCAGACGCCGCACTCCAGGgGGGAACTCGCAG|AACTCGCTGTGCAGAGCACTGCCGGAGGCT|GCGAGTTCCCCcGAGGAGCACAGACCCACCCACACCCCAC GGGCAGATGCAGACGCCGCACTCCAGGTGGGAACTCGCAG|AACTCGCTGTGCAGAGCACTGCCGGAGGCT|GCGAGTTCCCCGGAGGAGCACAGACCCACCCACACCCCAC Chimp > Gorilla --------------- chr9:121588085-121588105 Template switch process: F1: L TGGGCAGATGCAGACGCCGCACTCCAGGTGGGAACTCGCAG 1 F3: 4 GCGAGTTCCCCGGAGGAGCACAGACCCACCCACACCCCAC R RF: TGGGCAGATGCAGACGCCGCACTCCAGGGGGGAACTCGCAGAACTCGCTGTGCAGAGCACTGCCGGAGGCTGCGAGTTCCCCCGAGGAGCACAGACCCACCCACACCCCAC RR: ACCCGTCTACGTCTGCGGCGTGAGGTCCCCCCTTGAGCGTCTTGAGCGACACGTCTCGTGACGGCCTCCGACGCTCAAGGGGGCTCCTCGTGTCTGGGTGGGTGTGGGGTG F2: 3 ACACGTCTCGTGACGGCCTCC 2 Unidirectional alignment (log-probability: -61.9) GGGCAGATGCAGACGCCGCACTCCAGGtGGGAACTCGCAGcctccggcagtgctctgcacA-----------------------------GCGAGTTCCCCgGAGGAGCACAGACCCACCCACACCCCAC GGGCAGATGCAGACGCCGCACTCCAGGGGGGAACTCGCAG--------------------AACTCGCTGTGCAGAGCACTGCCGGAGGCTGCGAGTTCCCCCGAGGAGCACAGACCCACCCACACCCCAC Template switch alignment (log-probability: -29.4) GGGCAGATGCAGACGCCGCACTCCAGGtGGGAACTCGCAG|CCTCCGGCAGTGCTCTGCACA|GCGAGTTCCCCgGAGGAGCACAGACCCACCCACACCCCAC GGGCAGATGCAGACGCCGCACTCCAGGGGGGAACTCGCAG|CCTCCGGCAGTGCTCTGCACA|GCGAGTTCCCCCGAGGAGCACAGACCCACCCACACCCCAC